# hmmscan :: search sequence(s) against a profile database
# HMMER 3.2.1 (June 2018); http://hmmer.org/
# Copyright (C) 2018 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query sequence file:             /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Methanohalobium_evestigatum_Z_7303_uid49857/all.faa
# target HMM database:             /oak/stanford/groups/akundaje/marinovg/genomes/PFam/PFam32.0/Pfam-A.hmm
# output directed to file:         /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Methanohalobium_evestigatum_Z_7303_uid49857/all.PFam32-A
# per-seq hits tabular output:     /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Methanohalobium_evestigatum_Z_7303_uid49857/all.PFam32-A.tblout
# number of worker threads:        20
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       gi|298673979|ref|YP_003725729.1|  [L=412]
Description: orc1/cdc6 family replication initiation protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-22   79.7   0.3    3.2e-22   78.3   0.3    1.8  1  Cdc6_C           CDC6, C terminal winged helix domain
    8.2e-11   42.3   0.1    3.3e-10   40.4   0.0    1.9  2  AAA_22           AAA domain
    2.9e-10   40.8   0.6    1.1e-08   35.6   0.1    2.6  2  AAA_16           AAA ATPase domain
    3.1e-08   34.1   0.4    9.1e-08   32.6   0.4    1.8  1  AAA              ATPase family associated with various cellul
    2.5e-07   30.3   0.2    1.9e-06   27.4   0.0    2.0  2  TniB             Bacterial TniB protein
    5.3e-07   29.8   0.6    1.5e-06   28.3   0.6    1.8  1  ATPase_2         ATPase domain predominantly from Archaea
    1.9e-06   27.9   0.0      4e-06   26.8   0.0    1.5  1  NACHT            NACHT domain
    0.00066   19.0   0.0    0.00096   18.5   0.0    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
     0.0011   18.2   2.2       0.68    9.1   0.7    2.3  2  KAP_NTPase       KAP family P-loop domain
     0.0033   16.6   0.2      0.029   13.6   0.0    2.1  2  DUF815           Protein of unknown function (DUF815)
     0.0039   17.0   5.4       0.56    9.9   0.2    3.0  3  DEAD             DEAD/DEAH box helicase
     0.0043   16.8   0.0       0.35   10.6   0.0    2.6  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
  ------ inclusion threshold ------
      0.011   15.5   0.1      0.026   14.2   0.0    1.6  2  Sigma54_activat  Sigma-54 interaction domain
      0.012   15.4   1.4       0.12   12.2   1.4    2.1  1  Bac_DnaA         Bacterial dnaA  protein
      0.014   15.9   0.2      0.056   14.0   0.0    2.0  2  AAA_18           AAA domain
      0.027   14.6   0.2       0.16   12.1   0.1    2.3  2  AAA_2            AAA domain (Cdc48 subfamily)
      0.037   13.7   0.1      0.069   12.9   0.1    1.5  1  AAA_24           AAA domain
      0.058   12.4   0.2       0.15   11.0   0.0    1.7  2  T2SSE            Type II/IV secretion system protein
      0.062   12.8   0.0       0.11   12.0   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
      0.077   13.0   0.2       0.29   11.1   0.2    2.0  1  ResIII           Type III restriction enzyme, res subunit
       0.13   12.6   0.1       0.34   11.3   0.1    1.7  1  AAA_assoc_2      AAA C-terminal domain
       0.14   12.6   0.0       0.37   11.2   0.0    1.7  1  RNA_helicase     RNA helicase
       0.15   11.6   0.0        0.4   10.2   0.0    1.7  1  AAA_25           AAA domain
       0.16   12.0   0.0       0.34   10.9   0.0    1.5  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro


Domain annotation for each model (and alignments):
>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.3   0.3   4.2e-25   3.2e-22       1      83 [.     308     388 ..     308     389 .. 0.96

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 4.2e-25
                                       HHHHHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSS CS
                            Cdc6_C   1 LcalvlllrksgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLnvd 77 
                                       L++++ll + +g   vttgevy+vY++l +  ++d ltqr+v dl+seL+mlgil++ ++skGr +grt++i L+v+
  gi|298673979|ref|YP_003725729.1| 308 LYSVILLRK-NGYVNVTTGEVYNVYRQLSQNIDMDILTQRRVTDLISELDMLGILNAVVVSKGR-YGRTKEIDLSVP 382
                                       899999988.*****************************************************9.************ PP

                                       CHHHHH CS
                            Cdc6_C  78 pddvle 83 
                                        +  le
  gi|298673979|ref|YP_003725729.1| 383 VESTLE 388
                                       998776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.0   4.5e-13   3.3e-10       4     128 ..      58     183 ..      55     190 .. 0.85
   2 ?   -1.2   0.0       3.1   2.3e+03      25      61 ..     275     313 ..     272     345 .. 0.73

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 4.5e-13
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseelle 80 
                                       t + ++++G +GtGKT   r +  +l++ ++  +   +v+++++    ++  l  +l+r++g++    +  ++++++
  gi|298673979|ref|YP_003725729.1|  58 TPSNILIYGKTGTGKTAATRHVGFELEKKSENLNTFCSVLYINCEIIDTQYRLVANLARQFGEDIPMTGWPTDQVFT 134
                                       56789********************976555555888889*************************99899999999* PP

                            AAA_22  81 aleqalraravielliiDEaqhlr..seealeeLrsllnl.srkgvqliLv 128
                                       ++ + +++++ + ++i+DE+++l+   +++l +L+++ ++ + ++v+  ++
  gi|298673979|ref|YP_003725729.1| 135 KFKETIDSKQQVLIIILDEVDKLIkkGDDVLYNLSRINEDlKNSKVS--II 183
                                       **********99**********99755*******8876644444444..44 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.1
                            AAA_22  25 lleqldeeakaee.erpevvfvtlpsst.sskdllrell 61 
                                       ++e+ + ++++e+ e++++v+v  + +t s   l++ +l
  gi|298673979|ref|YP_003725729.1| 275 VVEERHVRNAQEKiENDRIVEVVRTLPTqSKLALYSVIL 313
                                       556666666666688999998888888867777777776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.1   1.5e-11   1.1e-08       2     164 ..      36     174 ..      36     183 .. 0.65
   2 ?   -2.7   0.0       8.9   6.7e+03      91      91 ..     264     264 ..     212     308 .. 0.50

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 1.5e-11
                            AAA_16   2 lvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekd.....g.giflrgkcdqlesaipysa 71 
                                       l+ R+++++ L+++l ++ +g++ +++l++G  G+GK++  r++  +lek+       + +l+ +c+          
  gi|298673979|ref|YP_003725729.1|  36 LPHRDRQINSLATILVSALRGDTpSNILIYGKTGTGKTAATRHVGFELEKKsenlnTfCSVLYINCEII-------- 104
                                       578********9999999999988*********************999999444421122233333333........ PP

                            AAA_16  72 laqalareellrqlldeaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqwad 148
                                                      +   +++++++ e ++ +                ++++++ + + ++++ l+++lD+++++ 
  gi|298673979|ref|YP_003725729.1| 105 -----------DTQYRL-VANLARQFGEDIPMTG-----------WPTDQVFTKFKETIDSKQQVLIIILDEVDKLI 158
                                       ...........222211.1222333333333322...........24445555555444444556999999999999 PP

                            AAA_16 149 easlqllaaLlrlles 164
                                           ++l++L r  e+
  gi|298673979|ref|YP_003725729.1| 159 KKGDDVLYNLSRINED 174
                                       9999999999888666 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 8.9
                            AAA_16  91 s 91 
                                       s
  gi|298673979|ref|YP_003725729.1| 264 S 264
                                       2 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.4   1.2e-10   9.1e-08       1     112 [.      62     189 ..      62     208 .. 0.76

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 1.2e-10
                                       EEEESSTTSSHHHHHHHHHHHHT..HE.......EEEEETTTCSSS................STTHHHHHHHHHHHH CS
                               AAA   1 vllyGppGtGKTllakavakelg..ve.......fleisgsellsk................yvgesekkirelfke 52 
                                       +l+yG  GtGKT++ + v  el+  +e       +l i++  +  +                + g   +++   fke
  gi|298673979|ref|YP_003725729.1|  62 ILIYGKTGTGKTAATRHVGFELEkkSEnlntfcsVLYINCEIIDTQyrlvanlarqfgedipMTGWPTDQVFTKFKE 138
                                       699******************95232233333336666665555448888999999999888666666666666666 PP

                                       .HHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSG CS
                               AAA  53 .akekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrp 112
                                        + +k++  i+++DE+d+l+k+         ++v+  L +  +++k+  skv +ig++n+ 
  gi|298673979|ref|YP_003725729.1| 139 tIDSKQQVLIIILDEVDKLIKKG--------DDVLYNLSRINEDLKN--SKVSIIGVSNDL 189
                                       234444459***********999........999***********99..69********84 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   2.5e-09   1.9e-06      21     156 ..      44     178 ..      31     194 .. 0.78
   2 ?    0.3   0.1      0.54     4e+02      63      93 ..     285     315 ..     273     344 .. 0.59

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 2.5e-09
                              TniB  21 erLee.LleypkrkrmpnlllvGdsnnGKtmivekFarlhppekdedaekvpvlvvqappkpdekrlyaaiLealga 96 
                                       ++L+  L+++ + + ++n+l++G++ +GKt+  ++   + ++++++ ++ + vl++++    ++ rl a++ +++g+
  gi|298673979|ref|YP_003725729.1|  44 NSLATiLVSALRGDTPSNILIYGKTGTGKTAATRHVGFELEKKSENLNTFCSVLYINCEIIDTQYRLVANLARQFGE 120
                                       45544155667777889***************9999988888888889999************************** PP

                              TniB  97 plkara.rvskleqqvlrllr.elkvrvLiiDEihnllagsarkqreflnalksLgnelkip 156
                                       ++  +   +++   +  ++++ + +v ++i+DE+++l+    +k   +l  l +++++lk +
  gi|298673979|ref|YP_003725729.1| 121 DIPMTGwPTDQVFTKFKETIDsKQQVLIIILDEVDKLI----KKGDDVLYNLSRINEDLKNS 178
                                       998775366677777777775268899999******99....56666777777777776544 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.54
                              TniB  63 kdedaekvpvlvvqappkpdekrlyaaiLea 93 
                                       +++ ++ + v vv++ p+ ++ +ly+ iL +
  gi|298673979|ref|YP_003725729.1| 285 QEKIENDRIVEVVRTLPTQSKLALYSVILLR 315
                                       2333445567788999999999****99944 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.6     2e-09   1.5e-06       4     156 ..      39     179 ..      37     232 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 2e-09
                          ATPase_2   4 Rekelkeleei....lerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekk 76 
                                       R++ +++l +i    l+ ++ + ++iYG  g GKta  +++  +le+k+++   + ++  ++ + +d+     + + 
  gi|298673979|ref|YP_003725729.1|  39 RDRQINSLATIlvsaLRGDTPSNILIYGKTGTGKTAATRHVGFELEKKSENLNTFCSVLYINCEIIDTQ---YRLVA 112
                                       56666665554111167789999******************9999777773333333334444444444...34456 PP

                          ATPase_2  77 klekalgiavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnlieslt 153
                                       +l++++g+++p +             ++ +++++e i  k++ +iii+De+ kli    ++  +++++L ++ e+l 
  gi|298673979|ref|YP_003725729.1| 113 NLARQFGEDIPMTGW---------PTDQVFTKFKETIDSKQQVLIIILDEVDKLI----KKGDDVLYNLSRINEDLK 176
                                       799999999999777.........558999**********999************....7889999**999998865 PP

                          ATPase_2 154 kek 156
                                       ++k
  gi|298673979|ref|YP_003725729.1| 177 NSK 179
                                       443 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   5.4e-09     4e-06       3      96 ..      62     160 ..      60     183 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 5.4e-09
                                       EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-....-HCHHHCCCCTS--SSS-C...CHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna.rsladllfsqlpepaapvse...vwav 75 
                                       +++ G+ G GKT+  +++ +++ ++  + ++f+ v+++++  + ++ +    la++  ++ p  + p ++   ++++
  gi|298673979|ref|YP_003725729.1|  62 ILIYGKTGTGKTAATRHVGFELEKKSENLNTFCSVLYINCEIIDTQYRLvANLARQFGEDIPMTGWPTDQvftKFKE 138
                                       799*************************999**************98878888888888888887777776666667 PP

                                       HCCSCCCEE.EEEE-STT-SS- CS
                             NACHT  76 llelperlL.lilDglDelvtd 96 
                                        +  ++++L +ilD +D+l ++
  gi|298673979|ref|YP_003725729.1| 139 TIDSKQQVLiIILDEVDKLIKK 160
                                       7777777775889****99765 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.3e-06   0.00096       3     127 ..      61     182 ..      59     188 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.3e-06
                           DUF2075   3 vvlVtGvaGtGKtvvllnllael..eddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnlsef 77 
                                        +l+ G++GtGKt    ++ +el  ++++++    +l+ N + +++ ++ +a+ +  ++++e++        ++ ++
  gi|298673979|ref|YP_003725729.1|  61 NILIYGKTGTGKTAATRHVGFELekKSENLNTFCSVLYINCEIIDTQYRLVANLA--RQFGEDIPMTGWPTDQVFTK 135
                                       689********************5555556666778899*999999999888877..77777777665555554433 PP

                           DUF2075  78 .kkaeekkeepkedvvivDEAhrlltksdqaekqseenqlkelmkrakvvv 127
                                        k  e  ++++++ ++i DE  +l +k+d     ++   ++e +k++kv++
  gi|298673979|ref|YP_003725729.1| 136 fK--ETIDSKQQVLIIILDEVDKLIKKGDD--VLYNLSRINEDLKNSKVSI 182
                                       23..44456678999***********8877..5556667777777777666 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0016       1.2       1      35 [.      39      74 ..      39      96 .. 0.84
   2 !    9.1   0.7   0.00092      0.68     158     186 ..     130     158 ..     103     183 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0016
                        KAP_NTPase  1 ydlyasaladilseptl..atpivvgLygkWGsGKss 35
                                      +d  +++la+il++  l   tp+ + +ygk G+GK++
  gi|298673979|ref|YP_003725729.1| 39 RDRQINSLATILVSA-LrgDTPSNILIYGKTGTGKTA 74
                                      57789********55.6689****************7 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00092
                        KAP_NTPase 158 eelladmektLdalqkrlVvviDdLDrce 186
                                       +++++++++t+d +q+ l++++D+ D + 
  gi|298673979|ref|YP_003725729.1| 130 DQVFTKFKETIDSKQQVLIIILDEVDKLI 158
                                       5689**********************875 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   3.8e-05     0.029      33      80 ..      39      86 ..      25     118 .. 0.83
   2 ?    0.5   0.3      0.37   2.7e+02      84     120 ..     157     193 ..     144     201 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.8e-05
                            DUF815 33 idkqkealventeqfleglpannvLLwGarGtGKSslvkallneyaee 80
                                       d+q ++l +     l+g + +n+L++G+ GtGK +  + +  e++++
  gi|298673979|ref|YP_003725729.1| 39 RDRQINSLATILVSALRGDTPSNILIYGKTGTGKTAATRHVGFELEKK 86
                                      6888999999999999********************999987777665 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.37
                            DUF815  84 lievekedlkelpklvellrerperfilfvDDLsFee 120
                                       li+   + l +l+++ e l++++  +i +  DL F+e
  gi|298673979|ref|YP_003725729.1| 157 LIKKGDDVLYNLSRINEDLKNSKVSIIGVSNDLKFTE 193
                                       66666788999************************86 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.2    0.0023       1.7       4      31 ..      42      76 ..      39      99 .. 0.76
   2 !    9.9   0.2   0.00075      0.56     119     166 ..     143     186 ..      84     193 .. 0.79
   3 ?   -0.4   0.0       1.1   8.3e+02      89     114 ..     329     354 ..     293     378 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0023
                                      HHHHHHHHH.......TTCEEEEEESTTSSHHHHH CS
                                      xxxxxxxxx.......xxxxxxxxxxxxxxxxxxx RF
                              DEAD  4 Qaeaiplil.......gggdvlvaaeTGsGKTlaf 31
                                      Q +++ +il       +  ++l+ ++TG+GKT+a 
  gi|298673979|ref|YP_003725729.1| 42 QINSLATILvsalrgdTPSNILIYGKTGTGKTAAT 76
                                      55666666655554333379************996 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00075
                                       CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 119 lsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvivlS 166
                                        +qv +++lDE+d+l ++  +d++   l+++++  ++ k    +i +S
  gi|298673979|ref|YP_003725729.1| 143 KQQVLIIILDEVDKLIKK--GDDVLYNLSRINEDLKNSK--VSIIGVS 186
                                       589999***********9..6666666788865555555..3477666 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.1
                                       HHHHHHHTTCSEEEEEHHHHHHHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  89 dqlskldngvdivvgtpgrlddllst 114
                                       + +++l++++d+ + t  r+ dl+s+
  gi|298673979|ref|YP_003725729.1| 329 NVYRQLSQNIDMDILTQRRVTDLISE 354
                                       34455556677777777777776642 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00047      0.35       1      60 [.      27      86 ..      27      99 .. 0.80
   2 ?    3.4   0.0     0.075        56      53     106 ..     114     167 ..     106     182 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00047
                            RuvB_N  1 lrPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvk 60
                                      lrP+   e++  ++ + +   +i  +  r+++   +l+yG  G Gkt+ ++ +  el+ k
  gi|298673979|ref|YP_003725729.1| 27 LRPSYTPEFLPHRDRQINSLATILVSALRGDTPSNILIYGKTGTGKTAATRHVGFELEKK 86
                                      789999999877665544444555566899******************999998888765 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.075
                            RuvB_N  53 iakelgvklkitsgPvlekagdlaalltnleekdvlfideihrlsraveevlys 106
                                       +a+++g ++ +t  P+ +  + +   + + ++  ++ +de+ +l ++ ++vly+
  gi|298673979|ref|YP_003725729.1| 114 LARQFGEDIPMTGWPTDQVFTKFKETIDSKQQVLIIILDEVDKLIKKGDDVLYN 167
                                       56667777777777777777777777777788888999***************6 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.5e-05     0.026      20      53 ..      57      90 ..      38     119 .. 0.68
   2 ?   -3.3   0.0       8.2   6.1e+03      96     108 ..     148     160 ..     131     168 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.5e-05
                                      TSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-E CS
                   Sigma54_activat 20 ktdlsvlitGesGtGKellaraiheaskrkekpf 53
                                      +t++++li G++GtGK+   r++  + ++k++++
  gi|298673979|ref|YP_003725729.1| 57 DTPSNILIYGKTGTGKTAATRHVGFELEKKSENL 90
                                      5679**************9999854444433332 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 8.2
                                       EEEEETGGGS-HH CS
                   Sigma54_activat  96 tlfLDeigelple 108
                                       ++ LDe+ +l  +
  gi|298673979|ref|YP_003725729.1| 148 IIILDEVDKLIKK 160
                                       4677777777655 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.4   0.00016      0.12      22     186 ..      47     234 ..      28     263 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                                       HHHHHHHSTTT.S--EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-....EEEEEHH......HHHHHHHHHHHT... CS
                          Bac_DnaA  22 aalkvaeapgkkynPlfiygevGlGktHLlkaignevlenapelr....vvYltae......eFlnelvkalrd... 85 
                                       a+  v+   g +   ++iyg++G Gkt   + +g e+++++++l     v+Y++ e      +    lv  l     
  gi|298673979|ref|YP_003725729.1|  47 ATILVSALRGDTPSNILIYGKTGTGKTAATRHVGFELEKKSENLNtfcsVLYINCEiidtqyR----LVANLARqfg 119
                                       5555666666666679*********************99998874334499*99983322222....3333322122 PP

                                       ...........T-HHHHHHHHT...T-SEEEEE-GGGGTT-HH.HHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS- CS
                          Bac_DnaA  86 ...........kkaeefkeklr...kvDvLliDDiqflagkek.tqeelfhtfnalleegkqvvlssDrsPkeleel 147
                                                  +  ++fke++    +v ++++D++  l +k + +  +l  + + l ++ k  ++      k  e l
  gi|298673979|ref|YP_003725729.1| 120 edipmtgwptdQVFTKFKETIDskqQVLIIILDEVDKLIKKGDdVLYNLSRINEDLKNS-KVSIIGVSNDLKFTEFL 195
                                       23333344333556788888754223445556999888888631444444444444444.44444444555666678 PP

                                       -HHHHHHHHSSEEEE-----HHHHHHHHHHHHHHTT--.- CS
                          Bac_DnaA 148 edrlrsrfeaGlvvdieppdletrlailkkkieaekle.v 186
                                       + r++s +     +   p d e   +il++++e++  e v
  gi|298673979|ref|YP_003725729.1| 196 DPRVKSSLGEE-EIVFPPYDAEQISDILHQRAEMAYKEgV 234
                                       88888888765.4456788888888888888887665553 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   7.5e-05     0.056       1      82 [.      62     154 ..      62     172 .. 0.69
   2 ?   -1.5   0.0       4.7   3.5e+03      17      44 ..     266     288 ..     243     317 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.5e-05
                            AAA_18   1 IlltGtpGvGKttlakeL....skrlgfgvnlrdvakenglllevdpe..........aldeskrldedkldkllda 63 
                                       Il+ G+ G+GKt  ++++    +k+   ++nl+  ++  ++  e  +           ++ e   +  + +d+++++
  gi|298673979|ref|YP_003725729.1|  62 ILIYGKTGTGKTAATRHVgfelEKK---SENLNTFCSVLYINCEIIDTqyrlvanlarQFGEDIPMTGWPTDQVFTK 135
                                       99************99996666444...4555555555554444444444444444566888888888888999999 PP

                            AAA_18  64 leenssaleegknlvidgh 82 
                                       ++e +++ ++   +++d +
  gi|298673979|ref|YP_003725729.1| 136 FKETIDSKQQVLIIILDEV 154
                                       9998885555555566655 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.7
                            AAA_18  17 eLskrlgfgvnlrdvakenglllevdpe 44 
                                       eL++r+     +++v+ e++ +  +++ 
  gi|298673979|ref|YP_003725729.1| 266 ELAERE-----SKQVVEERHVRNAQEKI 288
                                       333332.....34444444433333333 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00022      0.16       4      95 ..      60     164 ..      57     189 .. 0.72
   2 ?   -3.0   0.0       9.2   6.8e+03     101     113 ..     274     286 ..     238     297 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00022
                                       --EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHH.HHHTTT-HHHHTTS......... CS
                             AAA_2   4 isilllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrl.igappgyvgaeegG......... 70 
                                       ++il+ g+tg+Gkt +++ +   l+ kk+++l ++    ++      ++++      ++   ++ e+          
  gi|298673979|ref|YP_003725729.1|  60 SNILIYGKTGTGKTAATRHVGFELE-KKSENLNTFCSVLYIN----CEIIDTQyRLVANLARQFGEDIpmtgwptdq 131
                                       7999***********9999999998.7888888888888887....4444432022233333333333666688888 PP

                                       ................EEEEETGGG-------------HHH CS
                             AAA_2  71 ................ivllDEidKihpkessgadvSregV 95 
                                                       i+ lDE+dK  +k        +++V
  gi|298673979|ref|YP_003725729.1| 132 vftkfketidskqqvlIIILDEVDKLIKK--------GDDV 164
                                       9999999999999999*********9994........3333 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 9.2
                                       HHHH--EE----- CS
                             AAA_2 101 qileggtltdkqg 113
                                       q++e+ +++++q+
  gi|298673979|ref|YP_003725729.1| 274 QVVEERHVRNAQE 286
                                       4444444444444 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   9.2e-05     0.069       3      80 ..      60     160 ..      58     179 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.2e-05
                            AAA_24   3 lkiliyGpsgiGKTtlakel....gpkplfidtekGlksldadkfpdie...................swedfldev 56 
                                        +iliyG+ g+GKT   ++     ++k   ++t+ ++  ++   +++                       +++  ++
  gi|298673979|ref|YP_003725729.1|  60 SNILIYGKTGTGKTAATRHVgfelEKKSENLNTFCSVLYINCEIIDTQYrlvanlarqfgedipmtgwPTDQVFTKF 136
                                       589*************9999888877777777777777777777664435555555666666666655445555555 PP

                            AAA_24  57 velaaeladyktlviDtideleel 80 
                                       +e  + +++  ++++D +d+l + 
  gi|298673979|ref|YP_003725729.1| 137 KETIDSKQQVLIIILDEVDKLIKK 160
                                       555777777888888888888765 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00021      0.15     122     162 ..      50      92 ..      22     107 .. 0.80
   2 ?   -1.7   0.1       1.6   1.2e+03      48      90 ..     261     305 ..     212     349 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00021
                             T2SSE 122 lrkavr..erglilvsGgTgsGKttllyallkeinksderivt 162
                                       l +a+r  +  +il+ G Tg+GKt  +  +  e++k++e++ t
  gi|298673979|ref|YP_003725729.1|  50 LVSALRgdTPSNILIYGKTGTGKTAATRHVGFELEKKSENLNT 92 
                                       444444114579**************99999999999888865 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.6
                             T2SSE  48 erlisriaalakldiseerplqdarlp.ekgvrlr.vvllPvvag 90 
                                        r+  ++a   ++++ eer + +a+ + e+   ++ v +lP+  +
  gi|298673979|ref|YP_003725729.1| 261 LRVSGELAERESKQVVEERHVRNAQEKiENDRIVEvVRTLPTQSK 305
                                       455566666666666666666666655323333331335666555 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00015      0.11      34      62 ..      60      88 ..      43     118 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
                             AAA_7 34 kpvllvGptGtGKtviikdllkkldkeky 62
                                       ++l++G+tGtGKt+ ++++  +l+k++ 
  gi|298673979|ref|YP_003725729.1| 60 SNILIYGKTGTGKTAATRHVGFELEKKSE 88
                                      689**************998877774443 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00039      0.29       5      55 ..      39      90 ..      35     183 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00039
                                      -HHHHHHHHHHT.......TTSEEEEEESTTSTHHHHHHHHHHHH-S..... CS
                            ResIII  5 reyQeeaienll.eklkskrdkrglikmaTGtGKTlvaaklierllkkgkee 55
                                      r+ Q++ +  +l ++l  +   ++li   TGtGKT    ++  +l kk ++ 
  gi|298673979|ref|YP_003725729.1| 39 RDRQINSLATILvSALRGDTPSNILIYGKTGTGKTAATRHVGFELEKKSENL 90
                                      7778888888775666668888**************9999999988886654 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00045      0.34      16      55 ..     247     285 ..     235     299 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00045
                                       XXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXX CS
                       AAA_assoc_2  16 aeladGDaRkaLnlLElaaeaaeakegkieitledleeal 55 
                                       a+  +GDaR+aL lL +  e ae+ e+k+++++ ++++a 
  gi|298673979|ref|YP_003725729.1| 247 AAQEHGDARRALDLLRVSGELAER-ESKQVVEERHVRNAQ 285
                                       56668***********99999986.777777777777654 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0005      0.37       1      28 [.      62      89 ..      62     106 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0005
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklkl 28
                                      i++yG++g+GK+ +++++  +l+kk+++
  gi|298673979|ref|YP_003725729.1| 62 ILIYGKTGTGKTAATRHVGFELEKKSEN 89
                                      789**************99999988843 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00054       0.4      36      97 ..      62     117 ..      51     165 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00054
                            AAA_25  36 allaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal 97 
                                       +l++G +gtGKt+++ ++++++ + ++ l     +   Vly+++E     ++ Rl a ++ +
  gi|298673979|ref|YP_003725729.1|  62 ILIYGKTGTGKTAATRHVGFELEKKSENLN----TFCSVLYINCEIID--TQYRLVANLARQ 117
                                       799*******************97776555....5699*******877..666666655443 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00045      0.34       5      44 ..      41      84 ..      38      97 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00045
                                      HHHHHHHHHHHHCH.TEE...EEEEESTTSSHHHHHHHHHHHTT CS
                              TsaE  5 eetealgkklakal.gdv...ilLeGdLGaGKTtlvrglakalg 44
                                      +++++l++ l +al gd+   il++G+ G+GKT+ +r++  +l+
  gi|298673979|ref|YP_003725729.1| 41 RQINSLATILVSALrGDTpsnILIYGKTGTGKTAATRHVGFELE 84
                                      567778888888778443455****************9987775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       849  (0.0473534); expected 358.6 (0.02)
Passed bias filter:                      601  (0.0335211); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.60u 1.09s 00:00:01.69 Elapsed: 00:00:02.29
# Mc/sec: 544.79
//
Query:       gi|298673980|ref|YP_003725730.1|  [L=345]
Description: hypothetical protein Metev_0002 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.4e-50  169.8  13.2    1.1e-49  169.6  13.2    1.0  1  LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region


Domain annotation for each model (and alignments):
>> LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.6  13.2   6.3e-54   1.1e-49       4     301 .]      14     326 ..      11     326 .. 0.93

  Alignments for each domain:
  == domain 1  score: 169.6 bits;  conditional E-value: 6.3e-54
                   LPG_synthase_TM   4 glals.alllalllrgvdlaalaaalrsldpwwlllalllallsvllralrWrlllrslgarislrrllrayliglf 79 
                                       +l++s ++++++l+ +vd++ ++++++++   +llla++l+ +s++++++r +l+ ++lg++ +l r++ +++ ++f
  gi|298673980|ref|YP_003725730.1|  14 SLLISfISIIVVLVFTVDPT-TFEIIKEVKTEYLLLAVALHSFSYVIWGARTQLMSNALGHKTKLIRCIEIVTSSTF 89 
                                       55666644444444457876.569***************************************************** PP

                   LPG_synthase_TM  80 vnnvtPgalgGevvrayllkrkegvslskalasvvverlldllalvllgllallllggllaegaa...vllllalal 153
                                       v  +tP+++gGe++r++ll + e++++++a a+v+ er++d + ++ + ++al+++    ++++    +++++ +++
  gi|298673980|ref|YP_003725730.1|  90 VAALTPSSVGGEPLRVHLLYK-ENLPVGRASAVVLGERIMDAILMLTFAPFALYIFRDI-MQDSKidtIFAIGQIFM 164
                                       *********************.*****************************99777765.5556669999999**** PP

                   LPG_synthase_TM 154 lllavlalllllllrrrlarlarvlkrlarllarfarklasakr...............klvlasprrlllafllsl 215
                                       ++++vl++++++   +++  ++ ++ ++++ll +  ++++++ +               +++   +r ll   ++++
  gi|298673980|ref|YP_003725730.1| 165 AVILVLLIYTIWKPEKTKSGMHYIVDKITGLLGKKSEGKHHKLIeqidheleqfheslvTFLKDGRRGLLYGAGCTA 241
                                       ********************************999999999888**************9777777778********* PP

                   LPG_synthase_TM 216 liwllealtlylllralgvdvslallllillaltlvgalpplPgGlGvrEaalalllallGvsaaealaaallyrli 292
                                       l w++e+ +l ++l +l+ ++ l+l+ +++++l+l++++p++Pg +G++E ++++l++ + v+++ ++++++++r++
  gi|298673980|ref|YP_003725730.1| 242 LFWIVEFTMLPVILLGLNQEPQLLLVYAAQVLLILLIVIPATPGSSGIAELGATTLFSVF-VPSSILGIIVVAWRAL 317
                                       ************************************************************.**************** PP

                   LPG_synthase_TM 293 tlylllllG 301
                                       t+y+ l++G
  gi|298673980|ref|YP_003725730.1| 318 TFYMNLVVG 326
                                       ******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       855  (0.0476881); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.50s 00:00:01.00 Elapsed: 00:00:00.62
# Mc/sec: 1666.99
//
Query:       gi|298673981|ref|YP_003725731.1|  [L=374]
Description: glycosyl transferase family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-17   64.2   0.0    4.6e-17   62.3   0.0    1.8  1  Glyco_trans_1_3  Glycosyl transferase family 1
    2.4e-13   50.4   0.0    3.8e-13   49.7   0.0    1.2  1  Glyco_tran_28_C  Glycosyltransferase family 28 C-terminal dom
    2.2e-09   36.7   0.0    7.9e-09   34.8   0.0    1.7  2  UDPGT            UDP-glucoronosyl and UDP-glucosyl transferas
     0.0013   18.7   0.0     0.0029   17.6   0.0    1.5  1  Glyco_transf_4   Glycosyltransferase Family 4
  ------ inclusion threshold ------
       0.01   16.3   0.0      0.016   15.6   0.0    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glyco_trans_1_3  Glycosyl transferase family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.3   0.0   1.3e-20   4.6e-17       1     311 [.       1     331 [.       1     340 [. 0.76

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 1.3e-20
                   Glyco_trans_1_3   1 arilYgvsGeGaGhasRsrvvlehLar.ghevkvvvsgraldvLekef.dvneivg.lsivyeenrvrklktllknl 74 
                                       ++il  v GeG Gh+sR   + + L+  +hev + ++g +++++e +  +  ei++ +++v +  ++   + + + l
  gi|298673981|ref|YP_003725731.1|   1 MKILILVCGEGLGHTSRCVSLGRELTSaNHEVLFGAYGYSKEFIEGSGyQTREIPSeIRLVGRSGSLDLKASIGATL 77 
                                       79***********************777****************9996699999875899999999*9999999999 PP

                   Glyco_trans_1_3  75 qvaaklaknvkalvelvedfrpdlvvtDFealtallakrhkLPvisvdnqqvvnrtdyelell........akkdal 143
                                       +          +++ l ++f+pd vv+D   l +l+ak +kLPv  + nq  +++   +  +          +   +
  gi|298673981|ref|YP_003725731.1|  78 KEGD--LLGAPRIFRLFNEFNPDAVVSDSYYLGVLAAKAKKLPVYFIINQSNMEEFFKNKGVPykligeivKRFYST 152
                                       6432..233445788889**************************999999988876554433211112221222233 PP

                   Glyco_trans_1_3 144 lakavvkaklPkadly.lvttF...fqapvrkkerttlvPpilRkei..laakptegehlLvYltsegnea..lpev 212
                                       + k v k ++P  ++   +  +   f +p    e+++   p+++++   + akp ++ h+L  +   g  +  + +v
  gi|298673981|ref|YP_003725731.1| 153 VFKKVDKIVIPDFPMPyTICQYnlsF-QPEIA-ENVFYSGPLIKRKYheVEAKPLDKPHILSAVGGFGYREpiFRKV 227
                                       47888899999987752555442223.56664.899999999987651245788999****9998766553338899 PP

                   Glyco_trans_1_3 213 Lkklg.vefvvYglrrd..teeekegnltykafseegFleD...LataraviagagftLmtealyLkkPlLavPvar 283
                                       ++ ++  + + Y l      + ek++nl       + + e     ++  avia +g+t + eal  + P+L+ P  +
  gi|298673981|ref|YP_003725731.1| 228 IETAKkDSSINYTLMMGptIDPEKYSNLPENVGVMDFYSEPfpyFKSVDAVIAPGGHTTIMEALSFGVPVLSFPDMN 304
                                       9888834556687665444688999998765554444444322278999**************************** PP

                   Glyco_trans_1_3 284 qFeqvlnalyLerlgyGaavdakdldke 311
                                         eq  na+ ++ +gyG+ ++ +  ++e
  gi|298673981|ref|YP_003725731.1| 305 HSEQENNARVIDEMGYGRCLNYS-TSSE 331
                                       *****************987643.3444 PP

>> Glyco_tran_28_C  Glycosyltransferase family 28 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.0   1.1e-16   3.8e-13      48     153 ..     250     352 ..     225     361 .. 0.86

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 1.1e-16
                                       TT-TTTTCEEEEEESSSSHHHHHHHH-EEEECS-CHHHHHHHHTT--EEEE--TT....S-HHHHHHHHHHHHHHSS CS
                   Glyco_tran_28_C  48 ikveeltlkvevfefidkmaeaikaadLvIsRAGagtiaEllalgkplIlvplpeaaenhqdnNakelekagaalvl 124
                                        k+++l ++v v++f  +   + k+ d vI  +G++ti+E+l++g+p + +p   ++  +q+nNa+ + + g++++l
  gi|298673981|ref|YP_003725731.1| 250 EKYSNLPENVGVMDFYSEPFPYFKSVDAVIAPGGHTTIMEALSFGVPVLSFPDMNHS--EQENNARVIDEMGYGRCL 324
                                       44777778999*******************************************977..****************** PP

                                       EEEE-STTCHHHHHHHHCCS---S---SS CS
                   Glyco_tran_28_C 125 eqkeltpekLeeallelaaeklrlaeksk 153
                                        +++   e+L   ++e+ ++++  ++++k
  gi|298673981|ref|YP_003725731.1| 325 NYSTS-SEELLHCIKEITDNSKFKENTQK 352
                                       *****.999999*******9996443333 PP

>> UDPGT  UDP-glucoronosyl and UDP-glucosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.17     6e+02     109     160 ..      87     137 ..      70     163 .. 0.78
   2 !   34.8   0.0   2.2e-12   7.9e-09     341     424 ..     275     359 ..     271     367 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.17
                             UDPGT 109 kllkklqeskfdvvladpvlpcgellAellkiptvyllrdvpgqaaekvsGk 160
                                       ++++ ++e + d+v++d+    g l A+  k+p+ ++++++  +   k++G 
  gi|298673981|ref|YP_003725731.1|  87 RIFRLFNEFNPDAVVSDSYYL-GVLAAKAKKLPVYFIINQSNMEEFFKNKGV 137
                                       566777888889999999888.999999999999999999999998888864 PP

  == domain 2  score: 34.8 bits;  conditional E-value: 2.2e-12
                             UDPGT 341 tkAFvtHaGangvyEaisnGvPmvglP..lFgdqrdNikrmeakgaavtlnvkemtsedllnAlkevindksykeni 415
                                       + A ++ +G  +++Ea+s GvP+   P    ++q++N++ +   g +  ln ++ +se+ll  +ke+ ++  +ken 
  gi|298673981|ref|YP_003725731.1| 275 VDAVIAPGGHTTIMEALSFGVPVLSFPdmNHSEQENNARVIDEMGYGRCLNYST-SSEELLHCIKEITDNSKFKENT 350
                                       7899***********************433689************999999986.899******************* PP

                             UDPGT 416 mrLsslhkD 424
                                        +L  + kD
  gi|298673981|ref|YP_003725731.1| 351 QKLKDISKD 359
                                       ******998 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   8.1e-07    0.0029       6     139 ..      16     162 ..      13     176 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 8.1e-07
                    Glyco_transf_4   6 rhvleLaraLarrGheVtvvtpgddgpleeev.elvvrvprvplpllkrllrslafl.............rrlrrll 68 
                                         ++ L r+L  ++heV + + g+++++ e   +  +++p+  ++  +   ++l ++             +r+ rl+
  gi|298673981|ref|YP_003725731.1|  16 SRCVSLGRELTSANHEVLFGAYGYSKEFIEGSgYQTREIPSEIRLVGRSGSLDLKASigatlkegdllgaPRIFRLF 92 
                                       66889**********************99999944444444444444444443333312222222222227999999 PP

                    Glyco_transf_4  69 krekpDvvHahspaalgaallalrrrlgiplVltvHglye...krllkarlkplsrllralerrllrradrvia 139
                                        +++pD v + s++ +++a+ a    +++p+ + +  +      +  +   k+   ++++++  +++++d+++ 
  gi|298673981|ref|YP_003725731.1|  93 NEFNPDAVVSDSYYLGVLAAKA----KKLPVYFIINQSNMeefFKNKGVPYKLIGEIVKRFYSTVFKKVDKIVI 162
                                       999*****88888887555433....456666665555542243333334445555666666666999998886 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.0   4.4e-06     0.016      36     107 ..     242     307 ..     209     343 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.4e-06
                                       EES---....HHHHHHHTT-T.TEEEE---THHHHHHHH-SEEEE-----SHHHHHHHHTT-EEEE-.TGGGTTT CS
                   Glyco_trans_1_4  36 ivGdgp..rpeeleelaagleerveftGfvedlaellaaadvfvaPsegfglkllEamaaglpvVat.dvggiae 107
                                       ++G  p  +pe++    ++l e+v ++ f ++  ++++++d ++aP      +++Ea+++g+pv ++ d+   +e
  gi|298673981|ref|YP_003725731.1| 242 MMG--PtiDPEKY----SNLPENVGVMDFYSEPFPYFKSVDAVIAPG--GHTTIMEALSFGVPVLSFpDM-NHSE 307
                                       445..32333333....367799*******9***************7..479*************99434.3344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.63s 00:00:01.19 Elapsed: 00:00:00.59
# Mc/sec: 1906.90
//
Query:       gi|298673982|ref|YP_003725732.1|  [L=184]
Description: peptidase S26B, signal peptidase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      8e-06   25.7   0.0    1.3e-05   25.0   0.0    1.4  1  Peptidase_S24  Peptidase S24-like


Domain annotation for each model (and alignments):
>> Peptidase_S24  Peptidase S24-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   7.5e-10   1.3e-05       2      40 ..      51     106 ..      50     120 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 7.5e-10
                                       XXSSTTCCTXXTTXEEEEECTS...............---TTSEEEEEETTCE..- CS
                     Peptidase_S24   2 vpGdSMeptlldGdlilVdkfs...............epkrGdivvfrlpgee..e 40 
                                       v+++SMep ++ Gd+i+V+  +                 + Gd++  +  g e  +
  gi|298673982|ref|YP_003725732.1|  51 VESGSMEPNIHVGDIIFVEDIDrtqiqthtssnnytsFGNEGDVILYQPYGREgvT 106
                                       89*****************7776778888888888888888888877766666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.33s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 1169.72
//
Query:       gi|298673983|ref|YP_003725733.1|  [L=525]
Description: DNA-directed DNA polymerase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.9e-15   54.6   0.0    1.5e-14   53.9   0.0    1.4  1  DNA_pol_E_B      DNA polymerase alpha/epsilon subunit B
    3.8e-11   43.9   1.1    6.4e-11   43.1   1.1    1.4  1  Metallophos      Calcineurin-like phosphoesterase
    7.2e-10   39.3   0.2    2.9e-09   37.4   0.2    2.0  1  Metallophos_2    Calcineurin-like phosphoesterase superfamily
    6.6e-06   26.0   0.7    1.5e-05   24.8   0.1    2.0  2  tRNA_anti-codon  OB-fold nucleic acid binding domain


Domain annotation for each model (and alignments):
>> DNA_pol_E_B  DNA polymerase alpha/epsilon subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.0   3.3e-18   1.5e-14      68     204 ..     341     470 ..     268     474 .. 0.84

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 3.3e-18
                                       HHTHHHHTTS-TTSEEEEE--TTBTT-S-SBSB----TTTTT--TTT...EEE--BSEEEEETTEEEEE--S-HHHH CS
                       DNA_pol_E_B  68 alllsilesllekttvvlvPgpnDpanstvlPqqPlprlllsrikrvfkelklvtNPsrielnsvevvltsddivkd 144
                                       ++  + ++++ e++tv++ Pg  D++ + + Pq+ + + l s   +   ++++v NP +++l++v+v+++ +  ++d
  gi|298673983|ref|YP_003725733.1| 341 RKAAEYFKQIPEHITVIIGPGNHDAVRQ-AEPQPCFGEELKSYFPK---NVTFVGNPAMVDLDGVKVLMYHGRSIDD 413
                                       55677899********************.99999886665555555...59************************** PP

                                       ---EEESHHHHHS-HHHHHHHHHHHHTBS---SS--B-GGGGGGGB-GGG---SEEE--- CS
                       DNA_pol_E_B 145 lkreslkesntdverlrklvktildqrhlaPlaptlrpvswdkddalvleplPdvlvlpd 204
                                       + +++ + s    ++   ++  +++ rhl+P++   +++  +k d +v++++Pd+l ++ 
  gi|298673983|ref|YP_003725733.1| 414 FVASVPHVSY---QKPTTAMVEMMKFRHLSPIYGGRVSIAPEKHDHFVINQIPDILHCGH 470
                                       ***9999999...79999999***********************************9986 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   1.1   1.4e-14   6.4e-11       2     203 ..     266     473 ..     265     474 .. 0.76

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 1.4e-14
                                       EEEEEESBTB...TTCCTHHHHHHHHHHHH........HHHTTESEEEEESTSSSSS................HHHH CS
                       Metallophos   2 rilvigDlHl...algggqlddllkllddl........lreekpdlvllaGDlvdrg................dlek 51 
                                       + ++i+D+H+      +  + +++++l+          ++ +++ +v++ GDlvd+                 +  +
  gi|298673983|ref|YP_003725733.1| 266 KAVFISDVHVgssTFLEDEWLRFIDFLNGYiddkkmqdIS-NDIRYVVVSGDLVDGIgiypgqdkelsipdvyE--Q 339
                                       5689*****9777444466666666665554444444223.69999999*******88********98886442..3 PP

                                       HHHHHHHHHHHH..TSEEEEEC-TTSCHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEE CS
                       Metallophos  52 ellellaalvky..pipvylllGNHegfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspe 126
                                        + +  +++ +   +i v++ +GNH+      +++  + ++ +  + +++++++n+  ++l +   kvl +hG s++
  gi|298673983|ref|YP_003725733.1| 340 -YRKAAEYFKQIpeHITVIIGPGNHD-AVRQAEPQPCFGEELKSYFPKNVTFVGNPAMVDLDGV--KVLMYHGRSID 412
                                       .44443333333557999********.55566666666677799999999**********9999..********888 PP

                                       ETHHHHHHHHHHHSCHHHHCCHHHHHHHHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHHHHHTTESEEEEESSSS CS
                       Metallophos 127 llvsldklgslnleleapepgdewlkdlekrekadwvivlgHsplyrgsgylfgdealedllkkygvdlvisGHtHv 203
                                       +  ++ ++ +++++++++    e++k              + sp+y g+  + ++e  + +  +  +d+  +GH+H+
  gi|298673983|ref|YP_003725733.1| 413 D--FVASVPHVSYQKPTTAM-VEMMKF------------RHLSPIY-GGRVSIAPEKHDHFVINQIPDILHCGHVHT 473
                                       8..99999999999998887.666666............5567777.9999999999998877777999999***96 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.2   6.4e-13   2.9e-09       3     149 ..     267     493 ..     266     504 .. 0.73

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 6.4e-13
                     Metallophos_2   3 laiiSDlH.........snldaleav...............lealkevgvdaiihaGD................lee 39 
                                        ++iSD+H         +       +               ++++++  + +++++GD                +  
  gi|298673983|ref|YP_003725733.1| 267 AVFISDVHvgsstfledE-------WlrfidflngyiddkkMQDISND-IRYVVVSGDlvdgigiypgqdkelsI-- 333
                                       678*******65555550.......44555555555555559999999.*********66666655555544441.. PP

                     Metallophos_2  40 eep.......evleellela.......pvlaVrGNnD......eev.veedvlreaaelgtdlpeeaelelagekvl 95 
                                         p       ++ e     +        v++ +GN+D      ++  + e++   + +  t + + a ++l+g+kvl
  gi|298673983|ref|YP_003725733.1| 334 --PdvyeqyrKAAEY----FkqipehiTVIIGPGNHDavrqaePQPcFGEELKSYFPKNVTFVGNPAMVDLDGVKVL 404
                                       ..1333222223333....144457446666689***998765333788888888888889999************* PP

                     Metallophos_2  96 liHgdpl................................gvkdalaellke...aeegsdvvvcGHtHvpevekegg 137
                                       ++Hg                                   g++ ++a+   +     +  d++ cGH H+ +ve  ++
  gi|298673983|ref|YP_003725733.1| 405 MYHGRSIddfvasvphvsyqkpttamvemmkfrhlspiyGGRVSIAPEKHDhfvINQIPDILHCGHVHTVGVEPYKN 481
                                       ****977*************9999999999999999999555555544444333346666***************** PP

                     Metallophos_2 138 vlvvnPGsvgep 149
                                       vl++n G  + +
  gi|298673983|ref|YP_003725733.1| 482 VLLINSGTWQSQ 493
                                       *******87765 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.1   3.4e-09   1.5e-05       1      62 [.     178     240 ..     178     250 .. 0.94
   2 ?   -3.7   0.0       2.7   1.2e+04       9      21 ..     260     270 ..     259     271 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 3.4e-09
                                       EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET..HHHHHHHTTS-TTSEEEEEEEEEECT CS
                   tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfr..eeatklaenlkeGdvvrvtGrvkrrp 62 
                                       V+v G++++++ + ++++  i+++D+tg++ v +    +e +++a+++  + vv+vtG ++ ++
  gi|298673983|ref|YP_003725733.1| 178 VSVIGMISDVR-TTTNGHKLIEIEDNTGSLSVLVRTadKELFEQANSFVLDEVVGVTGMLTNDK 240
                                       89********9.9999******************************************998765 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.7
                                       EEEEEEETTEEEE CS
                   tRNA_anti-codon   9 sisdrsggkvifi 21 
                                       ++  +s+gk++fi
  gi|298673983|ref|YP_003725733.1| 260 NK--GSHGKAVFI 270
                                       56..89*****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (525 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.47s 00:00:01.06 Elapsed: 00:00:00.61
# Mc/sec: 2600.66
//
Query:       gi|298673984|ref|YP_003725734.1|  [L=311]
Description: wyosine base formation domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.6e-21   76.3   0.1    1.1e-20   74.7   0.1    1.7  1  Radical_SAM   Radical SAM superfamily
    7.3e-20   71.1   0.0    1.2e-19   70.3   0.0    1.4  1  Wyosine_form  Wyosine base formation
  ------ inclusion threshold ------
      0.036   14.3   0.0       0.05   13.9   0.0    1.4  1  Hydrolase     haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.7   0.1   1.8e-24   1.1e-20       2     166 ..      63     238 ..      62     239 .. 0.85

  Alignments for each domain:
  == domain 1  score: 74.7 bits;  conditional E-value: 1.8e-24
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEE.......................SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................xx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilg.......................gg 55 
                                       ++t  Cn++C++C+rp+     ++++   +++ +e++ +   +   + +i+g                       +g
  gi|298673984|ref|YP_003725734.1|  63 TPTLLCNQKCIHCWRPT---EIEVPAPEEWDSPVEIMGSS-IYA-QRKLISGfggsaprerwmeankpehaaislSG 134
                                       78889***********9...56666666666666666666.344.444444446679999999999999999999** PP

                                       TGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT..CTSHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                       Radical_SAM  56 epllypdfvellerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn..rghtfeev 130
                                       ep+lyp + el+++  k+   gi+++v+tngt+p  e++ r+++   ++++l+l+a+d+ ++l+ +n   ++ +e +
  gi|298673984|ref|YP_003725734.1| 135 EPTLYPYLPELIDEFTKE---GITTFVVTNGTRP--EMITRIRP---TQLYLSLDAPDKNTYLEVCNpeSPELWENI 203
                                       *****************8...************5..88888888...9*******************999999**** PP

                                       HHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 131 lealeklreagikrvvdrivglpGendeeleellel 166
                                       +++l +l +++++ +v+ri++++G+n+   e ++el
  gi|298673984|ref|YP_003725734.1| 204 KKSLSNLYSKDVR-TVVRITLIKGVNMYNPEGFAEL 238
                                       *************.************9776666665 PP

>> Wyosine_form  Wyosine base formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.3   0.0   2.1e-23   1.2e-19       2      63 .]     242     302 ..     241     302 .. 0.98

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 2.1e-23
                                       HT-SEEEEEE------------------HHHHHHHHHHHHTSSS.EEEEEEETTTTEEEEEE CS
                      Wyosine_form   2 aepdFvEvKaytyvGssrsrLtmknvPwheevadfakrlegsaedYellaehrhSrvvllar 63 
                                       a+pdFvE+Kay+++G sr rL+++ +P+h+ev+ fa ++++++  Ye+++  + Srvvll+r
  gi|298673984|ref|YP_003725734.1| 242 AKPDFVEIKAYMHLGFSRGRLSRESMPSHDEVYAFASKIADYLD-YEVADNVEISRVVLLSR 302
                                       89******************************************.**************986 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   8.3e-06      0.05     103     150 ..     112     170 ..      12     215 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.3e-06
                                       H..........TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEH.HHHHH CS
                                       x..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                         Hydrolase 103 l..........qaralavftiadplkvkpeaaeavasLkaagievvlltgdnp.etaer 150
                                                  ++ ++a + ++ + +++p + e++ ++ + gi ++++t++ + e+  r
  gi|298673984|ref|YP_003725734.1| 112 GsaprerwmeaNKPEHAAISLSGEPTLYPYLPELIDEFTKEGITTFVVTNGTRpEMITR 170
                                       0444444444677999*********************************7766144445 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1901.86
//
Query:       gi|298673985|ref|YP_003725735.1|  [L=413]
Description: peptide chain release factor 1 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.1e-42  143.1   0.0    1.5e-41  141.8   0.0    1.7  2  eRF1_2          eRF1 domain 2
    9.2e-35  119.5   0.2    8.1e-34  116.5   0.1    2.2  2  eRF1_3          eRF1 domain 3
    1.1e-12   48.4   0.0    1.7e-12   47.8   0.0    1.2  1  baeRF_family10  Bacterial archaeo-eukaryotic release factor f
    1.6e-12   47.6   0.0    3.3e-12   46.5   0.0    1.6  1  eRF1_1          eRF1 domain 1
    3.1e-12   46.9   0.0    5.2e-12   46.2   0.0    1.4  1  acVLRF1         Actinobacteria/chloroflexi VLRF1 release fact
     0.0096   15.7   0.1        5.4    6.9   0.0    3.9  4  Rad50_zn_hook   Rad50 zinc hook motif
  ------ inclusion threshold ------
      0.023   14.7   0.0      0.049   13.7   0.0    1.6  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.025   14.7   0.1       0.05   13.8   0.1    1.4  1  PknG_rubred     Protein kinase G rubredoxin domain
      0.026   15.1   0.1      0.063   13.9   0.1    1.7  1  baeRF_family12  Bacterial archaeo-eukaryotic release factor f
      0.085   12.8   0.7        1.1    9.2   0.0    2.6  3  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
       0.11   12.7   0.2       0.24   11.6   0.2    1.5  1  IBR             IBR domain, a half RING-finger domain
       0.12   11.9   0.3        6.5    6.4   0.1    2.6  2  TF_Zn_Ribbon    TFIIB zinc-binding
       0.14   12.3   4.5        0.6   10.3   1.8    2.6  2  Zn-ribbon_8     Zinc ribbon domain
       0.18   11.5   2.0       0.23   11.2   0.1    2.0  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
       0.27   11.2   0.6         30    4.6   0.1    2.5  2  zinc_ribbon_4   zinc-ribbon domain
       0.53   10.3   1.9        6.8    6.7   0.1    2.3  3  Prok-RING_1     Prokaryotic RING finger family 1
          2    8.2   5.1         13    5.6   0.6    2.3  2  Rubredoxin_2    Rubredoxin metal binding domain
        6.2    6.4   5.5         36    4.0   0.2    2.4  2  zf-ribbon_3     zinc-ribbon domain


Domain annotation for each model (and alignments):
>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.8   0.0   1.5e-44   1.5e-41       2     133 .]     141     272 ..     140     272 .. 0.99
   2 ?   -2.9   0.0       8.1   8.1e+03      65      94 ..     312     341 ..     308     343 .. 0.78

  Alignments for each domain:
  == domain 1  score: 141.8 bits;  conditional E-value: 1.5e-44
                                       EEEEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTTES CS
                            eRF1_2   2 vglivldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafllvdkdklk 78 
                                       +gl+vld++eAtigll g+r+e+ ++++++vP+K+k+Ggqsa+rfe lr  +++ f k+++eaa++ fl+vd+++ +
  gi|298673985|ref|YP_003725735.1| 141 YGLVVLDRREATIGLLVGKRIETHRHLTSTVPGKQKKGGQSADRFEQLRLIAIHDFNKRIGEAASDVFLNVDQENFE 217
                                       8**************************************************************************** PP

                                       EEEEEESSTHHHHHHHHHHHHHHHHTCCEEEEE-S-TSCHHHHHHHHCCHHHHCC CS
                            eRF1_2  79 giilagpgfvkeefldkdlldaelkkkviklvdvsyggesglnevlekaaevlkd 133
                                       g++++gp+++keef ++++l++e +kk++ ++dvsy++esgl+e++++a ++l+d
  gi|298673985|ref|YP_003725735.1| 218 GVLIGGPSPTKEEFKEGEFLHHEIQKKILGMFDVSYTDESGLSELVNAATDKLAD 272
                                       ****************************************************987 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 8.1
                                       HHHHHHHCHTTTESEEEEEESSTHHHHHHH CS
                            eRF1_2  65 ankafllvdkdklkgiilagpgfvkeefld 94 
                                       +n+ +++ d +  + ii +++  +k+ f +
  gi|298673985|ref|YP_003725735.1| 312 VNTLLISEDMKSERDIIRCSSCGYKTSFTR 341
                                       666667778888888999999999999976 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.93   9.3e+02       7      42 ..      39      74 ..      36     120 .. 0.76
   2 !  116.5   0.1   8.1e-37   8.1e-34       1     112 [.     275     410 ..     275     411 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.93
                                      HHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEE CS
                            eRF1_3  7 lleefleelakdtgkavYGveevlkalemgAvetLL 42
                                       ++e++++l+ + g+a   + +v + +  gA++ L+
  gi|298673985|ref|YP_003725735.1| 39 PISEVTSQLKDEYGQASNIKSKVTRTNVQGAIDSLV 74
                                      578888899999999999999999999999999986 PP

  == domain 2  score: 116.5 bits;  conditional E-value: 8.1e-37
                                       HHHHHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS................... CS
                            eRF1_3   1 liqekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekv................... 58 
                                       l++ekkl+ +f++el  ++gka+YG+e v+k le+gAv+tLL+se+++++rd+++++                    
  gi|298673985|ref|YP_003725735.1| 275 LMKEKKLMRQFFNELIAESGKAAYGEETVRKNLEIGAVNTLLISEDMKSERDIIRCSScgyktsftrkpsgqvtdyg 351
                                       589**************************************************888878****************** PP

                                       ..-HHH-HHHHHH...HHHHHHHHHHHTT-EEEEE-TTSHHHHHHHHHTTTEEEEESS- CS
                            eRF1_3  59 ..ketgeelelve...lieelvenveesgakveiisseseeGeqlvkafgGiaaiLRyk 112
                                         +++g   e v+   ++e+l ++++++gakve+is+e+eeG ql++afgGi+aiLRy+
  gi|298673985|ref|YP_003725735.1| 352 tcPKCGGSFEFVDsidIVEDLSTMADQTGAKVEFISTEFEEGSQLLNAFGGIVAILRYN 410
                                       ******9999999999******************************************7 PP

>> baeRF_family10  Bacterial archaeo-eukaryotic release factor family 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.0   1.7e-15   1.7e-12       2     126 ..     127     255 ..     127     270 .. 0.89

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 1.7e-15
                    baeRF_family10   2 ylapLlealdeyerygvvlvdreraRlfevylgeleeveevegevpgrtktggwksqdrfqrreeeqaerhlkevAe 78 
                                       +l+p+ + l+e + yg+v++dr++a +    + ++e+++++++ vpg++k+gg+ s drf++ +   ++ + k+++e
  gi|298673985|ref|YP_003725735.1| 127 FLEPMEDMLKESKTYGLVVLDRREATIGLLVGKRIETHRHLTSTVPGKQKKGGQ-SADRFEQLRLIAIHDFNKRIGE 202
                                       699***************************************************.********************** PP

                    baeRF_family10  79 llakll...eergverlvlgGdeeetaall..drlpkalrarvvgtlplpvda 126
                                       ++ +++   +++++e +++gG+   +++++  + l+ ++++++ g ++++ ++
  gi|298673985|ref|YP_003725735.1| 203 AASDVFlnvDQENFEGVLIGGPSPTKEEFKegEFLHHEIQKKILGMFDVSYTD 255
                                       *****83324566*********9999999833589999999999999988754 PP

>> eRF1_1  eRF1 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.0   3.3e-15   3.3e-12       6     128 ..      18     134 ..      13     135 .. 0.94

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 3.3e-15
                                       E..CTBTTSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......--CEEEEEEEEEEEEEEECTT... CS
                            eRF1_1   6 r..dlekdgsgsvtLipeddedlwhlynliapgdsvrastvrkvqresstgsreservklkLtikvekvdfdkd... 77 
                                       +  + +++g+++++L+ ++d+ +++++  +++++++++++++kv+r         ++v+ ++ + v ++++ ++   
  gi|298673985|ref|YP_003725735.1|  18 ElrNKKGRGTELISLYLPPDKPISEVTSQLKDEYGQASNIKSKVTR---------TNVQGAIDSLVSRLKYLEEvpe 85 
                                       4458899*************************************99.........8***************999999 PP

                                       SSEEEEEEEEEEGGGG--TTSEEEEEE-TTSEEEEEECE.ESHHHHHHHHHH CS
                            eRF1_1  78 agvlrisGkvieenehvklgafhtldlelkrpftiikee.wdsfalerLkea 128
                                       +g++ ++G v  + +   ++++ t  +e+++++ +++++ ++sf le+++++
  gi|298673985|ref|YP_003725735.1|  86 NGIVFFTGAVDVGAN---KTNMETTVIEPPEQLVTYRYHcDSSFFLEPMEDM 134
                                       *************99...9******************999*******99987 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.0   5.2e-15   5.2e-12       4     121 ..     143     263 ..     140     272 .. 0.83

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 5.2e-15
                           acVLRF1   4 gvllvrrggfavgvveggelvaskvgtrdvqgrtaaGGwSqqRfaRrrenqadalleavaeaaarllaeesae.... 76 
                                       +v+l+rr + ++g++ g++++++++ t+ v g+ ++GG+S  Rf++ r   + +  +++ eaa +++ + ++e    
  gi|298673985|ref|YP_003725735.1| 143 LVVLDRREA-TIGLLVGKRIETHRHLTSTVPGKQKKGGQSADRFEQLRLIAIHDFNKRIGEAASDVFLNVDQEnfeg 218
                                       699******.*********************************************************8888888889 PP

                           acVLRF1  77 vvlgGdrslvaevledarlaplatlareelldvpdprravLedav 121
                                       v++gG+  + +e++e + l++  + +   ++dv   +++ L + v
  gi|298673985|ref|YP_003725735.1| 219 VLIGGPSPTKEEFKEGEFLHHEIQKKILGMFDVSYTDESGLSELV 263
                                       **************9966443222222244555555555555555 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.5      0.17   1.7e+02       7      20 ..      11      24 ..       9      25 .. 0.89
   2 ?    0.6   0.0      0.53   5.3e+02      29      44 ..      34      50 ..      33      54 .. 0.90
   3 ?   -2.8   0.0         6     6e+03       5      17 ..     193     205 ..     192     206 .. 0.82
   4 !    6.9   0.0    0.0055       5.4      19      47 ..     351     378 ..     342     382 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.17
                                      HHHHHHHHHTT-SE CS
                     Rad50_zn_hook  7 elnkkieelkeakg 20
                                      e++kk+eel ++kg
  gi|298673985|ref|YP_003725735.1| 11 EFKKKLEELRNKKG 24
                                      89*******99986 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.53
                                      E-HHH.HHHHHHHHHHH CS
                     Rad50_zn_hook 29 ldeeh.rseLikelqsk 44
                                      l++++  se++++l+++
  gi|298673985|ref|YP_003725735.1| 34 LPPDKpISEVTSQLKDE 50
                                      789999*********98 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 6
                                       HHHHHHHHHHHTT CS
                     Rad50_zn_hook   5 teelnkkieelke 17 
                                       + ++nk+i e ++
  gi|298673985|ref|YP_003725735.1| 193 IHDFNKRIGEAAS 205
                                       789****999876 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.0055
                                       SEE-TTT--EE-HHHHHHHHHHHHHHHHH CS
                     Rad50_zn_hook  19 kgcCPlCgReldeehrseLikelqskler 47 
                                       +  CP Cg +++  +  +++++l+++ ++
  gi|298673985|ref|YP_003725735.1| 351 G-TCPKCGGSFEFVDSIDIVEDLSTMADQ 378
                                       4.9********999988888888888776 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.9e-05     0.049      64      95 ..     321     359 ..     276     370 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.9e-05
                                       EEEE--EEEETTTS-EEECHHH.HH......S-TTTSSS CS
                              HypA  64 ieevpvkvrCreCgkefeleek.al......rCpkCgsa 95 
                                       +++++  +rC++Cg++++ ++k +       +CpkCg++
  gi|298673985|ref|YP_003725735.1| 321 MKSERDIIRCSSCGYKTSFTRKpSGqvtdygTCPKCGGS 359
                                       67778899*********96653211457889*****984 PP

>> PknG_rubred  Protein kinase G rubredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1     5e-05      0.05      95     129 ..     330     365 ..     308     371 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5e-05
                                       -TTT--B-S---S.S----SEEE-TTT--EEE-S-S CS
                       PknG_rubred  95 CwrCGrpvGRsek.erkgaseGtCpkCgspysFlPq 129
                                       C+ CG +   ++k  ++ +  GtCpkCg +++F+ +
  gi|298673985|ref|YP_003725735.1| 330 CSSCGYKTSFTRKpSGQVTDYGTCPKCGGSFEFVDS 365
                                       999**9988776515678889************965 PP

>> baeRF_family12  Bacterial archaeo-eukaryotic release factor family 12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   6.4e-05     0.063      39     130 ..     163     257 ..     158     265 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.4e-05
                    baeRF_family12  39 sdregssdrpGrsssggagrsameetdfkeq.eeerFakeladeLkk...rakegkferlvlvappetlgelrkh.. 109
                                       + r ++s+ pG+++ gg++   +++++   + + ++F k++ ++  +    + +++fe + + +p +t +e+++   
  gi|298673985|ref|YP_003725735.1| 163 THRHLTSTVPGKQKKGGQS---ADRFEQLRLiAIHDFNKRIGEAASDvflNVDQENFEGVLIGGPSPTKEEFKEGef 236
                                       5678889999998888887...4577777777999999988888777333577899*****************7555 PP

                    baeRF_family12 110 lhkevkkrlvgeiaknltkhp 130
                                       lh e++k++ g ++  +t+++
  gi|298673985|ref|YP_003725735.1| 237 LHHEIQKKILGMFDVSYTDES 257
                                       ******************987 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       7.6   7.6e+03      17      26 ..     114     124 ..     111     124 .. 0.80
   2 ?    9.2   0.0    0.0011       1.1      10      30 ..     315     336 ..     313     341 .. 0.71
   3 ?    0.5   0.1      0.57   5.6e+02       4       8 ..     353     357 ..     349     362 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 7.6
                                       SCCCE.EEESS CS
                    RNA_POL_M_15KD  17 kegkn.feCrq 26 
                                       +++++ + C++
  gi|298673985|ref|YP_003725735.1| 114 QLVTYrYHCDS 124
                                       68889999985 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0011
                                       BEEEEECSCCCE.EEESSSS-E CS
                    RNA_POL_M_15KD  10 lLlpkedkegkn.feCrqCgYe 30 
                                       lL++ + k+ +    C++CgY+
  gi|298673985|ref|YP_003725735.1| 315 LLISEDMKSERDiIRCSSCGYK 336
                                       5555555555559********8 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.57
                                       ESTTT CS
                    RNA_POL_M_15KD   4 CpkCg 8  
                                       CpkCg
  gi|298673985|ref|YP_003725735.1| 353 CPKCG 357
                                       89997 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00024      0.24       9      48 ..     318     360 ..     311     362 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00024
                               IBR   9 kkslesdpnlkwCprpdCeaiiekseg.....cksvtCskCgfef 48 
                                        + ++s+++++ C    C++  + + +     +++ tC+kCg +f
  gi|298673985|ref|YP_003725735.1| 318 SEDMKSERDIIRCS--SCGYKTSFTRKpsgqvTDYGTCPKCGGSF 360
                                       455889999****9..9**877555554336666688*****998 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.087        87      20      28 ..     328     336 ..     319     341 .. 0.82
   2 ?    6.4   0.1    0.0065       6.5       2      12 ..     352     363 ..     351     374 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.087
                                       EEESSSSBE CS
                      TF_Zn_Ribbon  20 lvCtdCGlV 28 
                                       ++C++CG+ 
  gi|298673985|ref|YP_003725735.1| 328 IRCSSCGYK 336
                                       58*****86 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0065
                                       EETTTTCEE.CH CS
                      TF_Zn_Ribbon   2 kCPnCgstn.lv 12 
                                       +CP+Cg+++ +v
  gi|298673985|ref|YP_003725735.1| 352 TCPKCGGSFeFV 363
                                       7*****998664 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.29   2.9e+02       3      10 ..     117     124 ..     116     140 .. 0.78
   2 ?   10.3   1.8   0.00061       0.6       7      35 ..     329     359 ..     327     363 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.29
                       Zn-ribbon_8   3 iYeYrCee 10 
                                       +Y Y+C++
  gi|298673985|ref|YP_003725735.1| 117 TYRYHCDS 124
                                       7*****97 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00061
                       Zn-ribbon_8   7 rCeeCghefevlqsis.daplta.CPeCgse 35 
                                       rC +Cg +    ++ s +  +   CP+Cg+ 
  gi|298673985|ref|YP_003725735.1| 329 RCSSCGYKTSFTRKPSgQVTDYGtCPKCGGS 359
                                       8*****999988888878888888*****85 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00023      0.23      14      26 ..     324     336 ..     320     339 .. 0.88
   2 ?   -1.8   0.2       2.6   2.6e+03      20      24 ..     353     357 ..     352     362 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                                       SSS----SSS--- CS
                    DNA_RNApol_7kD  14 kgdpiRCkeCGhR 26 
                                       ++d+iRC  CG++
  gi|298673985|ref|YP_003725735.1| 324 ERDIIRCSSCGYK 336
                                       679********98 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.6
                                       -SSS- CS
                    DNA_RNApol_7kD  20 CkeCG 24 
                                       C +CG
  gi|298673985|ref|YP_003725735.1| 353 CPKCG 357
                                       77777 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1      0.04        40      25      33 ..     327     335 ..     318     337 .. 0.72
   2 ?    4.6   0.1      0.03        30       4      14 ..     352     362 ..     352     366 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.04
                     zinc_ribbon_4  25 kvrCskCgh 33 
                                        +rCs Cg 
  gi|298673985|ref|YP_003725735.1| 327 IIRCSSCGY 335
                                       578888875 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.03
                     zinc_ribbon_4   4 tCpsCkakyei 14 
                                       tCp+C+  +e+
  gi|298673985|ref|YP_003725735.1| 352 TCPKCGGSFEF 362
                                       57777777766 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0068       6.8      12      27 ..     319     334 ..     316     342 .. 0.86
   2 ?    2.4   0.2      0.15   1.5e+02      19      29 ..     349     359 ..     340     362 .. 0.79
   3 ?    2.3   0.3      0.16   1.6e+02      22      29 ..     352     359 ..     347     369 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0068
                       Prok-RING_1  12 kelkeedDiVvCpeCg 27 
                                       + +k+e Di+ C  Cg
  gi|298673985|ref|YP_003725735.1| 319 EDMKSERDIIRCSSCG 334
                                       67999**********9 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.15
                       Prok-RING_1  19 DiVvCpeCgtp 29 
                                       D  +Cp+Cg +
  gi|298673985|ref|YP_003725735.1| 349 DYGTCPKCGGS 359
                                       55579999976 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.16
                       Prok-RING_1  22 vCpeCgtp 29 
                                       +Cp+Cg +
  gi|298673985|ref|YP_003725735.1| 352 TCPKCGGS 359
                                       57777755 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.6     0.013        13       2      10 ..     329     337 ..     329     339 .. 0.89
   2 ?    4.3   0.3     0.034        33      14      21 ..     350     357 ..     345     359 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.013
                      Rubredoxin_2   2 vCsqCGfes 10 
                                       +Cs+CG+++
  gi|298673985|ref|YP_003725735.1| 329 RCSSCGYKT 337
                                       8******87 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.034
                      Rubredoxin_2  14 fGrCpsCg 21 
                                       +G Cp Cg
  gi|298673985|ref|YP_003725735.1| 350 YGTCPKCG 357
                                       8******9 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.2     0.036        36       3       9 ..     328     334 ..     327     338 .. 0.73
   2 ?    3.8   1.3     0.041        41      19      23 ..     353     357 ..     351     360 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.036
                       zf-ribbon_3   3 vrCPnCG 9  
                                       +rC++CG
  gi|298673985|ref|YP_003725735.1| 328 IRCSSCG 334
                                       5788887 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.041
                       zf-ribbon_3  19 CpyCG 23 
                                       Cp+CG
  gi|298673985|ref|YP_003725735.1| 353 CPKCG 357
                                       66666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      708  (0.0394891); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.63u 0.38s 00:00:01.01 Elapsed: 00:00:00.55
# Mc/sec: 2280.91
//
Query:       gi|298673986|ref|YP_003725736.1|  [L=563]
Description: arginyl-tRNA synthetase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-42  145.1   3.9    3.5e-42  144.6   3.9    1.2  1  tRNA-synt_1d     tRNA synthetases class I (R)
    2.2e-34  118.2   0.0    4.8e-34  117.1   0.0    1.6  1  DALR_1           DALR anticodon binding domain
    5.8e-13   49.2   0.0    1.5e-12   48.0   0.0    1.8  1  Arg_tRNA_synt_N  Arginyl tRNA synthetase N terminal domain
    7.9e-07   28.3   0.1       0.01   14.8   0.0    2.4  2  tRNA-synt_1f     tRNA synthetases class I (K)
    6.1e-05   21.9   5.2      0.056   12.2   0.1    4.1  5  tRNA-synt_1g     tRNA synthetases class I (M)
    0.00011   21.7   0.3    0.00028   20.3   0.2    1.8  2  tRNA-synt_1e     tRNA synthetases class I (C) catalytic domai
     0.0041   15.4   0.1     0.0084   14.4   0.0    1.6  2  tRNA-synt_1      tRNA synthetases class I (I, L, M and V)
  ------ inclusion threshold ------
      0.018   15.3   0.4      0.051   13.8   0.1    1.9  2  DUF4375          Domain of unknown function (DUF4375)


Domain annotation for each model (and alignments):
>> tRNA-synt_1d  tRNA synthetases class I (R)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.6   3.9   1.6e-45   3.5e-42      19     349 .]     109     431 ..      92     431 .. 0.88

  Alignments for each domain:
  == domain 1  score: 144.6 bits;  conditional E-value: 1.6e-45
                                       T-EEEEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEEEEE--B-SSTCHHHHHHHHHHHTTTTTTS----- CS
                      tRNA-synt_1d  19 kkkvvvdfssPniakemhvGhLrstiiGdavsrlleflGydvirlnhvGDWGtqfGlLiaylekkqdekllqeqelq 95 
                                          ++++++s n   ++hvGh+r  +iGd++sr+l  +Gy+v    +v D G+q  ++  +l++ + ++    +   
  gi|298673986|ref|YP_003725736.1| 109 SGDIILEHTSANPNGPLHVGHIRNSVIGDTLSRVLKHAGYNVRTQYYVNDIGRQIAIVSWGLKNFGFDESK--KSDH 183
                                       5579************************************************************9766633..3334 PP

                                       SCCCHHHHHHHHCCCSHCCCHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHCT---EC.--CC..CCCCC CS
                      tRNA-synt_1d  96 dLeafykeakkdydeeeifaerarnyvvkLqsgdedirklwkllvditrtelqklydrldvtlie.rGes..lykes 169
                                        + ++y +++++++++    +   + ++ +++gded+ k++   v ++ +  +++ + l+v+  e   es  + + s
  gi|298673986|ref|YP_003725736.1| 184 AIADLYIKSNQELEKDTSKVQDIDSLMQMVENGDEDTIKIFDESVRYSLEGTKQTLKTLNVSHDEfVYESefIRNGS 260
                                       56677**********************************************************998555554999** PP

                                       HHHHHHHHHCTT-EEECTTCEEEEECCCTSSCCEECC-TTS-B-HHHHHHHHHHHHHHTT--SEEEEEEECCCHHHH CS
                      tRNA-synt_1d 170 lneivkelkkkglvkesdGalvvfldefgkrlgvvvqksDGgylytttDiaaakerkeelkadkvlyvidsrqslhl 246
                                       + +iv+elk  g  + ++Galvv+l+ +g +  +v+q+sDG+ lytt+D+a   ++    + d+v+ ++ +  +l  
  gi|298673986|ref|YP_003725736.1| 261 VSKIVNELKSTGHTEMDNGALVVDLSGYGFEKQLVIQRSDGTSLYTTRDLAYHEQK--SAESDRVIDILGADHKLVS 335
                                       **************************************************987665..5678*********999999 PP

                                       HHHHHHHHCTT.SSTTTSEEEEEEE--EE-TTSSBSBCSSSTC-BHHHHHHHHHHHHHHHHCCCCCCTS-CCCCHCH CS
                      tRNA-synt_1d 247 qqiflilkkig.yvpeskdlehanfGmvlgkdkkkfktrkGetvkLadlLdealeralqlikeknkdkvlqadelek 322
                                       +q+ + ++ ++  +pe++      f  v    + +++trkG+ +  +d++d    +a + +  + +d  ++ad +++
  gi|298673986|ref|YP_003725736.1| 336 SQLKATMNLLDkKEPEVVI-----FEFV-SLPEGSMSTRKGKFITADDVFDKVKSQAYKEVDKRRPD--MPADFKKE 404
                                       9998887777644455444.....4444.335679********************************..******** PP

                                       HHHHHHHHHHHCCCCTS-TTS-EE--H CS
                      tRNA-synt_1d 323 vaeavgvgaikyaDlsknrindyifdw 349
                                       + + vg+ga++y  +s    +  +fdw
  gi|298673986|ref|YP_003725736.1| 405 ISDQVGMGAVRYDIISVSPEKSTVFDW 431
                                       ************999999888889988 PP

>> DALR_1  DALR anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.1   0.0   2.1e-37   4.8e-34       1     119 []     445     563 .]     445     563 .] 0.98

  Alignments for each domain:
  == domain 1  score: 117.1 bits;  conditional E-value: 2.1e-37
                                       HHHHHHHHHHHHHHTTCTTCCCCHCCHCCS-SHHHHHHHHHHHTHHHHHHHHHHHT-THHHHHHHHHHHHHHHHHHH CS
                            DALR_1   1 vqyahaRiksilrkaeeegekleeealalleeeeekeLlkalaqfpevleeaaeelephklaeylyeLaatfhkfYn 77 
                                       +qy+haR+++il+kae+  + +++ + ++l e++e +L+k++a+f +++ ++a+el+ph++a+y+ eLa++f++fY+
  gi|298673986|ref|YP_003725736.1| 445 IQYSHARACNILKKAETFWNPEDAVNPSVLVEDDEVALIKKMAKFDQMIDQSAKELKPHTVATYARELADDFNQFYR 521
                                       7****************9999999998889*********************************************** PP

                                       HCTSTTSCTHHH.HHHHHHHHHHHHHHHHHHHHTT----S-- CS
                            DALR_1  78 kervlkeeeeelaaaRLaLvkavrqvLangLdlLGieapekm 119
                                        ++v+ +e++e ++aRL Lv+++r +Lan+L +LGi+ape m
  gi|298673986|ref|YP_003725736.1| 522 YVPVNSAEDDEVRNARLGLVDCARIMLANTLYILGISAPESM 563
                                       ****************************************99 PP

>> Arg_tRNA_synt_N  Arginyl tRNA synthetase N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   0.0   6.5e-16   1.5e-12       3      84 ..       3      83 ..       1      84 [. 0.80

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 6.5e-16
                                      HHHHHHHHHHHHH.SS-HHHHGGG-E-.SSGGG-SEEEEGGGG--TT-..-HHHHHHHHHH..T---TTTEEEEEEETT CS
                   Arg_tRNA_synt_N  3 lkeaiaealkkaa.gadleeeeiviekpknpkfGDyatnvamqlakklkknPreiAeeiae..klekseiiekvevagp 78
                                      lk++++  l++a+   + e++ + +e+   +++ D+a+nva++la+k+++nP++iAe+i +   + ++ +i k+ev+gp
  gi|298673986|ref|YP_003725736.1|  3 LKKQVESILNDAVvSLGYEIDSLYVEA---SQHSDVASNVAFRLASKYRQNPKDIAEKIGNtaVIGDKSYIGKMEVTGP 78
                                      566666666666553357777778875...9****************************98435555566********* PP

                                      .EEEEE CS
                   Arg_tRNA_synt_N 79 GFiNff 84
                                       ++Nf 
  gi|298673986|ref|YP_003725736.1| 79 -YLNFW 83
                                      .***95 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0     6e-05      0.13      12      71 ..      97     159 ..      86     162 .. 0.76
   2 !   14.8   0.0   4.6e-06      0.01     239     302 ..     326     385 ..     321     408 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6e-05
                      tRNA-synt_1f  12 ieerkkkka..ekdevvv.esGispSGliHiGnlrevltadlvaralrkrgeevrlilisDdm 71 
                                        +e+++ ++  +++++++  + + p G++H+G +r+ + +d + r l++ g +vr+ ++++d+
  gi|298673986|ref|YP_003725736.1|  97 RKEKENFASnfSSGDIILeHTSANPNGPLHVGHIRNSVIGDTLSRVLKHAGYNVRTQYYVNDI 159
                                       444444333344444444168999*******************************99998886 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 4.6e-06
                      tRNA-synt_1f 239 paGkDhaaaGgSvdvsskiaeilggeaPekvvYelillkggekmssSkGnvltledwlevaepe 302
                                         G Dh     S ++ ++ +++l+ ++Pe v++e+++l +g  ms  kG+++t +d+++ ++ +
  gi|298673986|ref|YP_003725736.1| 326 ILGADHKL--VS-SQLKATMNLLDKKEPEVVIFEFVSLPEG-SMSTRKGKFITADDVFDKVKSQ 385
                                       56888887..23.33445569*******************9.9*************99877766 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.1   2.5e-05     0.056      10      40 ..     121     151 ..     116     164 .. 0.92
   2 !    5.5   0.1    0.0026       5.8      25     114 ..     186     275 ..     181     288 .. 0.77
   3 ?    3.2   0.0     0.014        30     313     348 ..     350     385 ..     325     390 .. 0.86
   4 ?   -2.9   0.0      0.98   2.2e+03     339     370 ..     403     433 ..     401     438 .. 0.81
   5 ?   -1.5   0.0      0.36     8e+02     140     182 ..     443     486 ..     436     517 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.5e-05
                                       -SS---HHHHHHHHHHHHHHHHHHHTT-EEE CS
                      tRNA-synt_1g  10 angklHlGhllevisaDifaRykrlrgeevl 40 
                                       +ng+lH+Gh+++ +++D ++R  +  g++v 
  gi|298673986|ref|YP_003725736.1| 121 PNGPLHVGHIRNSVIGDTLSRVLKHAGYNVR 151
                                       69*************************9985 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0026
                                       HHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT---SEEEETTSHHHHHHHH CS
                      tRNA-synt_1g  25 aDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikelfkklnisfdkygrttseehkelvq 101
                                       aD +++ ++   +++  v   D+  + +e   e+     +e v+   e +k+++k+ln+s+d++   ++   +  v+
  gi|298673986|ref|YP_003725736.1| 186 ADLYIKSNQELEKDTSKVQDIDSLMQMVENGDEDTIKIFDESVRYSLEGTKQTLKTLNVSHDEFVYESEFIRNGSVS 262
                                       6777777777777777777777666555555555555556666667788999************************* PP

                                       HHHHHHHHTT-EE CS
                      tRNA-synt_1g 102 eifkklkekgliy 114
                                       +i+++lk+ g+ +
  gi|298673986|ref|YP_003725736.1| 263 KIVNELKSTGHTE 275
                                       *********9976 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.014
                                       S-EEEE--EEE--------------HHHHHHHH-HH CS
                      tRNA-synt_1g 313 kkvvaheyltvegkKlSkSrgvvvkakealerldad 348
                                        +vv  e++ + ++ +S+ +g +++a+++ ++++++
  gi|298673986|ref|YP_003725736.1| 350 PEVVIFEFVSLPEGSMSTRKGKFITADDVFDKVKSQ 385
                                       468889***********************9998876 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 0.98
                                       HHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHH CS
                      tRNA-synt_1g 339 kealerldadllRYylaaeapekkDldfswed 370
                                       ke+ +++ + ++RY +++ +pek+ + f w++
  gi|298673986|ref|YP_003725736.1| 403 KEISDQVGMGAVRYDIISVSPEKS-TVFDWKK 433
                                       6888999999*******9999876.5677776 PP

  == domain 5  score: -1.5 bits;  conditional E-value: 0.36
                                       ......-TTS-EE.-TTSSB-E................EEE.EE CS
                      tRNA-synt_1g 140 Pkckseeargdqc.eecgkkleptelinpksaisgskpevkete 182
                                       P++++++ar+ ++ ++  +  +p++ +np   + +++  + ++ 
  gi|298673986|ref|YP_003725736.1| 443 PYIQYSHARACNIlKKAETFWNPEDAVNPSVLVEDDEVALIKKM 486
                                       89999999999996777777899999999999887765443333 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.2   1.3e-07   0.00028      23      94 ..     125     246 ..     118     324 .. 0.67
   2 ?   -3.6   0.0       2.5   5.6e+03     250     275 ..     361     386 ..     356     400 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.3e-07
                                       -BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-............................ CS
                      tRNA-synt_1e  23 shlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeks............................ 71 
                                        h+Gh R+ v+ D l r+l+++gY+v+    v Di  +i   +   +++                            
  gi|298673986|ref|YP_003725736.1| 125 LHVGHIRNSVIGDTLSRVLKHAGYNVRTQYYVNDIGRQIAIVSWGLKNFgfdeskksdhaiadlyiksnqelekdts 201
                                       7**************************9999****999877666666654455566666666666666666666666 PP

                                       ......................HHHHHHHHHHHHHHHHHHTT--- CS
                      tRNA-synt_1e  72 ......................vkelaekfieefkkdleaLnvlk 94 
                                                             ++e + +  e  k+ l++Lnv +
  gi|298673986|ref|YP_003725736.1| 202 kvqdidslmqmvengdedtikiFDESVRYSLEGTKQTLKTLNVSH 246
                                       666666666666666666555555555555555555555555555 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.5
                                       TTBE--TTTT---BHHHHHTTS-HHH CS
                      tRNA-synt_1e 250 egekmsksLknfitikdvlkkfdprq 275
                                        +  ms   + fit  dv+ k+++++
  gi|298673986|ref|YP_003725736.1| 361 PEGSMSTRKGKFITADDVFDKVKSQA 386
                                       55567777777777777777766554 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   3.8e-06    0.0084       4      66 ..      81     153 ..      78     203 .. 0.77
   2 ?   -3.0   0.0      0.68   1.5e+03     560     592 ..     362     420 ..     339     427 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.8e-06
                       tRNA-synt_1   4 ekWeeedvfkke.lekekekkef.........ilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyv 66 
                                       ++W + d+ + + l+ +kek++f         il     + +G lH+Gh+ ++++ d++ r+ +  G++v+ +
  gi|298673986|ref|YP_003725736.1|  81 NFWAKRDYLDDTvLKIRKEKENFasnfssgdiILEHTSANPNGPLHVGHIRNSVIGDTLSRVLKHAGYNVRTQ 153
                                       66777777554313444445554222233332566778899****************************9876 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.68
                       tRNA-synt_1 560 eGrKmSKslgNvidpldvik...........................kygadalRltlil 592
                                       eG  mS ++g  i  +dv +                           ++g  a+R+ +i+
  gi|298673986|ref|YP_003725736.1| 362 EG-SMSTRKGKFITADDVFDkvksqaykevdkrrpdmpadfkkeisdQVGMGAVRYDIIS 420
                                       55.388899999999999887777777777777777777777777777788888877774 PP

>> DUF4375  Domain of unknown function (DUF4375)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   2.3e-05     0.051      27      96 ..     152     226 ..     144     244 .. 0.85
   2 ?   -3.1   0.0       4.1   9.3e+03      55      80 ..     491     516 ..     479     527 .. 0.47

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.3e-05
                                       HHHHHCT-HHHHCCHHHHHHCTT--HHHHHHHHHHHHHHHHHHHHHHHHHTT-....HHHHHHH..-GGGHHHHH CS
                           DUF4375  27 vqlfqnssgefinealkalrliGaeelakllekakklykkgkeelereerdee....lealyeee.eeefdelDd 96 
                                       +q++ n  g+ i  +  +l+++G +e +k    +++ly k+++ele+++++ +    l+++ e+  e++++ +D+
  gi|298673986|ref|YP_003725736.1| 152 TQYYVNDIGRQIAIVSWGLKNFGFDESKKSDHAIADLYIKSNQELEKDTSKVQdidsLMQMVENGdEDTIKIFDE 226
                                       59***************************9999999***********9988766666999999876555655555 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.1
                                       HHHHHHHHHHHHHHHHHHHHHHTT-H CS
                           DUF4375  55 kllekakklykkgkeelereerdeel 80 
                                       +++++ +k +k +++++  +e  +++
  gi|298673986|ref|YP_003725736.1| 491 QMIDQSAKELKPHTVATYARELADDF 516
                                       33333333223333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (563 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 3337.79
//
Query:       gi|298673987|ref|YP_003725737.1|  [L=154]
Description: FKBP-type peptidylprolyl isomerase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.2e-23   80.7   0.2    9.7e-23   80.3   0.2    1.2  1  FKBP_C    FKBP-type peptidyl-prolyl cis-trans isomerase


Domain annotation for each model (and alignments):
>> FKBP_C  FKBP-type peptidyl-prolyl cis-trans isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.3   0.2   5.4e-27   9.7e-23       6      92 ..       4     137 ..       2     139 .. 0.75

  Alignments for each domain:
  == domain 1  score: 80.3 bits;  conditional E-value: 5.4e-27
                                       -TTCEEEEEEEEEETTSSEEEEHCCHTSEEEEETTSSSSCHHHHHHHTTSBTT-EEEEEEEGGGTTTT......... CS
                            FKBP_C   6 kegdtVtvhykgkledgkvfdssrsrakplefkvGsgqvikGfeealegmkvGekrtltippelaYge......... 73 
                                       k+gd+V+v+y+g+ledg+vfds+ + ++plef++Gsgq+i+Gfee ++gm+ Ge++++  +p++aYge         
  gi|298673987|ref|YP_003725737.1|   4 KQGDKVKVEYEGTLEDGSVFDSTENHGEPLEFEIGSGQIIEGFEESIKGMEEGEEKQFQLQPSEAYGEprddltrdv 80 
                                       89*********************99*******************************************988888777 PP

                                       ............................TTBCTTTB.TT...................SEEEEEEE CS
                            FKBP_C  74 ............................kglaggvippn...................atLvFeve 92 
                                                                             +                   + L F+v+
  gi|298673987|ref|YP_003725737.1|  81 pkeqvpddqeitpgmmllvtlpdesqipA---------EvlevteekvtldlnhplagKVLNFKVK 137
                                       77766666555555555555444444440.........1333333333333333444477777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 1051.09
//
Query:       gi|298673988|ref|YP_003725738.1|  [L=383]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.6e-27   94.4   1.9    1.3e-26   93.2   1.9    1.6  1  OrfB_IS605      Probable transposase
    1.8e-23   82.3   0.3    3.6e-23   81.3   0.3    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    8.6e-20   70.0   2.6    1.9e-19   68.9   2.6    1.6  1  HTH_OrfB_IS605  Helix-turn-helix domain
  ------ inclusion threshold ------
      0.012   15.7   0.3       0.03   14.5   0.3    1.6  1  zf-piccolo      Piccolo Zn-finger
      0.032   14.1   3.5       0.29   10.9   1.7    2.4  2  Phage_GP20      Phage minor structural protein GP20
       0.52   10.5   6.0       0.21   11.8   1.3    2.3  2  MapZ_EC1        MapZ extracellular domain 1


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.2   1.9   4.4e-30   1.3e-26      10     117 ..     180     284 ..     167     286 .. 0.91

  Alignments for each domain:
  == domain 1  score: 93.2 bits;  conditional E-value: 4.4e-30
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsr 86 
                                       +++  + +++g+D+Gi+++a++++++   ++ ++r lk+  ++l+  +++l++k+k+s+ny+k + ++a++h+k+++
  gi|298673988|ref|YP_003725738.1| 180 KQTFYEVNTVGVDVGIKDFAVTSDGE---KIDNPRYLKNSIERLKVLQKRLSRKKKGSNNYRKLKHQIAKYHEKIAN 253
                                       45555789******************...************************************************ PP

                        OrfB_IS605  87 rrkhllhklathliktlkevgvetLnvgnmk 117
                                       +r +++hkl+++li ++++v++e Lnv+++ 
  gi|298673988|ref|YP_003725738.1| 254 QREDFQHKLSSRLISENQAVALECLNVKGLL 284
                                       ****************************986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.3   0.3   1.2e-26   3.6e-23       1      68 [.     298     367 ..     298     368 .. 0.98

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 1.2e-26
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpay.TSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       ++++ ++leyka++yG++++++ ++  +Sk C++Cg+ +++ +l++r+++Cp+C++ +drD+nA++Ni k
  gi|298673988|ref|YP_003725738.1| 298 WSSFVQKLEYKAEWYGKNIIKIGRFDpSSKICHVCGYYHQDlELKDREWECPDCKTIHDRDINASVNIKK 367
                                       99******************************************************************87 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.9   2.6   6.2e-23   1.9e-19       1      47 []       9      54 ..       9      54 .. 0.98

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 6.2e-23
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeegk 47
                                      M lkaykyr yP++ Q+e++a+++G++Rf+YN+aL+ ++++ye+ gk
  gi|298673988|ref|YP_003725738.1|  9 M-LKAYKYRMYPNQIQQELIAKHIGACRFIYNWALENKIKYYEQDGK 54
                                      8.******************************************997 PP

>> zf-piccolo  Piccolo Zn-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.3     1e-05      0.03      28      55 ..     326     353 ..     322     356 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1e-05
                        zf-piccolo  28 kqvCnlCGFnptphltekkeWlclnCQt 55 
                                       +++C +CG+  ++   + +eW c  C t
  gi|298673988|ref|YP_003725738.1| 326 SKICHVCGYYHQDLELKDREWECPDCKT 353
                                       79***********999**********86 PP

>> Phage_GP20  Phage minor structural protein GP20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.047   1.4e+02     114     137 ..      52      78 ..      27      87 .. 0.74
   2 ?   10.9   1.7   9.7e-05      0.29      32      90 ..     218     276 ..     205     286 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.047
                        Phage_GP20 114 dgelkg...LdeqikkLkesdkyLFee 137
                                       dg+ +    L++qi  Lk+++++L e 
  gi|298673988|ref|YP_003725738.1|  52 DGKAISrfeLNKQIRVLKQDHEWLNEI 78 
                                       555554344899999999999998763 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 9.7e-05
                        Phage_GP20  32 eqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeyeakiadlkldnaielaLk 90 
                                       e+lk  +k L+  kk +++  +L+ qi+++ +k++++ ++ + k++ + +++    aL+
  gi|298673988|ref|YP_003725738.1| 218 ERLKVLQKRLSRKKKGSNNYRKLKHQIAKYHEKIANQREDFQHKLSSRLISENQAVALE 276
                                       6788889999999********************************99888776666666 PP

>> MapZ_EC1  MapZ extracellular domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.2      0.22   6.5e+02      63      84 ..      60      81 ..      40      89 .. 0.76
   2 ?   11.8   1.3   7.1e-05      0.21      37      78 ..     213     254 ..     173     277 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.22
                          MapZ_EC1 63 klkkkldslkkqisaieavNsq 84
                                      +l+k++  lk+  + ++++Nsq
  gi|298673988|ref|YP_003725738.1| 60 ELNKQIRVLKQDHEWLNEINSQ 81
                                      6899999999999999999987 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 7.1e-05
                          MapZ_EC1  37 lknsefaklseLekkLeklk.gskeYkklkkkldslkkqisai 78 
                                       lkns ++ l+ L+k L   k gs++Y+klk+++++  ++i+ +
  gi|298673988|ref|YP_003725738.1| 213 LKNS-IERLKVLQKRLSRKKkGSNNYRKLKHQIAKYHEKIANQ 254
                                       4443.688999*****98777*****************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1509  (0.0841653); expected 358.6 (0.02)
Passed bias filter:                      679  (0.0378716); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.36s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 2439.85
//
Query:       gi|298673989|ref|YP_003725739.1|  [L=223]
Description: oxidoreductase molybdopterin-binding protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-39  135.2   0.0    2.4e-39  134.7   0.0    1.2  1  Oxidored_molyb  Oxidoreductase molybdopterin binding domain


Domain annotation for each model (and alignments):
>> Oxidored_molyb  Oxidoreductase molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.7   0.0   1.3e-43   2.4e-39       4     172 .]      64     207 ..      61     207 .. 0.97

  Alignments for each domain:
  == domain 1  score: 134.7 bits;  conditional E-value: 1.3e-43
                                       ---.GCCC-EEEEESTCSSEEEEEHHHHHHC-EEEEEEEEE-TTTTHHHHCHH--SS----TTSEEEEEEEEEEHHH CS
                    Oxidored_molyb   4 vpkvdpekwrlevdglvekplslslddLkalpavevtatlqCagnrrkelnkkkvkglqwgagavsnaeWtGvrlrd 80 
                                       +p++++e++rl+++g+ve+p +++++++k++p+v+ +++l+C++              +w    +++a+WtG++l++
  gi|298673989|ref|YP_003725739.1|  64 TPNINIESYRLQINGMVENPENFTYEQIKSYPNVSKVIDLNCVE--------------GW----SFTAKWTGIPLKT 122
                                       688999**************************************..............89....9************ PP

                                       HHHHTTB-ETT..EEEEEEEEE-TCCTEEEEEEEHHHHCTTT-EEEEEETTEE--CCCTTT-EEE-TTB-GGGSBTT CS
                    Oxidored_molyb  81 vLekagvkkpearhvvfegadeeleeskygasiplekaleddvlLAyemngepLppdhGyPlRlvvpglvgarsvKw 157
                                       + ++ gvk ++a+ vvf++ad      +y++s++l+++++++++LAy++n+  Lp+d+G+Pl lv +  +g++++Kw
  gi|298673989|ref|YP_003725739.1| 123 LFNETGVK-DNATNVVFYSAD------GYSTSLKLDYLMDNNIILAYKINDVILPRDRGFPLQLVAESKYGYKWAKW 192
                                       *******7.9**********9......5***********999*********************************** PP

                                       EEEEEEESS---SHH CS
                    Oxidored_molyb 158 lkrievsdeesegyw 172
                                       +++ie++++  egyw
  gi|298673989|ref|YP_003725739.1| 193 ITEIEITNQSYEGYW 207
                                       **************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1459.03
//
Query:       gi|298673990|ref|YP_003725740.1|  [L=341]
Description: MtaA/CmuA family methyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-82  276.9   0.0    2.6e-82  276.7   0.0    1.0  1  URO-D     Uroporphyrinogen decarboxylase (URO-D)
  ------ inclusion threshold ------
       0.16   11.3   0.0       0.26   10.6   0.0    1.2  1  HPS3_C    Hermansky-Pudlak syndrome 3, C-terminal


Domain annotation for each model (and alignments):
>> URO-D  Uroporphyrinogen decarboxylase (URO-D)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  276.7   0.0   2.9e-86   2.6e-82       1     346 []       5     338 ..       5     338 .. 0.97

  Alignments for each domain:
  == domain 1  score: 276.7 bits;  conditional E-value: 2.9e-86
                                       ----HHHHHHTT---SS--B--TT-SSTTSHHHHHHHTSSSHHHHHH-HHHHHHHHHHHHHHH--S-EE-S--TTGG CS
                             URO-D   1 tknerllralrgekvdrvPvwlmRqaGrylpeyraeragvsflelcknpelaaevtlqpvrrfglDaailfsdilve 77 
                                       t++er++r l+g++vd++Pv      +++ p   +e +g + +e+ ++ e++a +++++ + +g++++ +++d+++ 
  gi|298673990|ref|YP_003725740.1|   5 TPKERMVRLLKGKTVDKTPVGS---FTSMSPVDLMELSGSQRPEADRDSEKMATLAISASKFAGFETVRYPFDMVTL 78 
                                       689*******************...**************************************************** PP

                                       GGGGT-EEEEETTTE.EEEE--S-....GGGS----GGG..G..HHHHHHHHHHHHH.--SS-EEEEEE-HHHHHHH CS
                             URO-D  78 aealGlevefeegeg.Pvvekpvrtaedveklevpddvee.grlpyvleaikllkkelggevpligfvgaPftlasy 152
                                        ea+G+e+++++++  P+v++ +  +e +++le p+d+ e gr+p++l+a +++k+e+++e+p+i +v +P+ las 
  gi|298673990|ref|YP_003725740.1|  79 GEAMGCEIDIGTKKRtPSVTSGLS-EEAIRELELPEDFLEnGRIPTILDASRIIKEEVKDELPVIMGVEGPIDLASN 154
                                       ************8777*****865.99**********97789*********************************** PP

                                       HHCTT-SS-HHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEE..TTGGGS-HHHHHHHTHHHHHHH CS
                             URO-D 153 lveGgskgfekllkllykdpeevhklldkltdvvieylkaqieagAdaiqifD..swagllspedfeefvlpylkri 227
                                       +      +++ ++k+l+kd+e v+klld++td++iey++a++++gAd ++i++  ++++ll+p+df+ +  p +++i
  gi|298673990|ref|YP_003725740.1| 155 IA-----DIKTFMKWLLKDREIVEKLLDVCTDACIEYANACLKHGADTVCIAEavASPDLLPPSDFDNLLKPRYQKI 226
                                       **.....********************************************************************** PP

                                       HHHHHH.H--S-EEEEESSHH.HHHHHHTTS--SEEE--TTS.-HHHHHHSS.....EEE--B-G.GGGG.S-HHHH CS
                             URO-D 228 vdevkaegpkvpvilfikgagaeiledlaelgadvlsldwtv.dlkeaarevg.dkvalqGnldPialLl.gspeei 301
                                       ++++++       +l+++g++++i++ + e+g++++s++++v d k a+++ + ++ +++Gn++++++L+ g+pe++
  gi|298673990|ref|YP_003725740.1| 227 AENLEG-----HRVLHVCGKSDKIIPSMVECGFNGISIEENVrDFKTAVETAHkNNNIVIGNVSTSQTLYnGTPEQV 298
                                       *****9.....68********9********************666666666667999******************** PP

                                       HHHHHHHHT.T---SSSEEB-BSS---TTS-HHHHHHHHHHHHT- CS
                             URO-D 302 ekevkeilekgaggkkgyilnlGhgippetppenvkalveavkey 346
                                         e  ++l++g++     +l++G+gi+pe+p++n+ka+v+a++ey
  gi|298673990|ref|YP_003725740.1| 299 ISESFDCLKNGVD-----VLAPGCGIAPESPLANLKAMVQARNEY 338
                                       *********99**.....***********************9987 PP

>> HPS3_C  Hermansky-Pudlak syndrome 3, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0     3e-05      0.26     256     281 ..     170     195 ..     162     202 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 3e-05
                            HPS3_C 256 ssidkLLdrcPeaiiayanhelkeek 281
                                       + ++kLLd c +a i yan  lk+  
  gi|298673990|ref|YP_003725740.1| 170 EIVEKLLDVCTDACIEYANACLKHGA 195
                                       679*****************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1971.09
//
Query:       gi|298673991|ref|YP_003725741.1|  [L=337]
Description: MtaA/CmuA family methyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-84  282.5   0.0    5.4e-84  282.3   0.0    1.0  1  URO-D     Uroporphyrinogen decarboxylase (URO-D)


Domain annotation for each model (and alignments):
>> URO-D  Uroporphyrinogen decarboxylase (URO-D)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  282.3   0.0     3e-88   5.4e-84       2     346 .]       3     334 ..       2     334 .. 0.97

  Alignments for each domain:
  == domain 1  score: 282.3 bits;  conditional E-value: 3e-88
                                       ---HHHHHHTT---SS--B--TT-SSTTSHHHHHHHTSSSHHHHHH-HHHHHHHHHHHHHHH--S-EE-S--TTGGG CS
                             URO-D   2 knerllralrgekvdrvPvwlmRqaGrylpeyraeragvsflelcknpelaaevtlqpvrrfglDaailfsdilvea 78 
                                       +++rll++l+g+kvd vP      ++++++ + +++++  ++e++++pe++++++++ ++ +gl+a+ ++++++v a
  gi|298673991|ref|YP_003725741.1|   3 PRDRLLNCLKGKKVDIVPALS---VTQTATVELMRMTDSEWPEAHSDPEKMVKLAVSGHEIAGLEAVRYPFCLTVLA 76 
                                       689******************...999************************************************** PP

                                       GGGT-EEEEETTTE.EEEE--S-.....GGGS----GGG..G..HHHHHHHHHHHHH.--SS-EEEEEE-HHHHHHH CS
                             URO-D  79 ealGlevefeegeg.Pvvekpvr.taedveklevpddvee.grlpyvleaikllkkelggevpligfvgaPftlasy 152
                                       ea+G+ev++++ +  P++ +++  + +d+ ++  pdd+e+ gr+p +le  +l++++l+++vp+i+++ +P tl ++
  gi|298673991|ref|YP_003725741.1|  77 EAMGCEVNMGAMDIqPSIVSNPYsNNSDIPQI--PDDLEKrGRIPVMLEVAELIRDKLDENVPIIAGLVGPATLTAH 151
                                       ***********777799998888799999998..55665669*********************************** PP

                                       HHCTT-SS-HHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEE..TTGGGS-HHHHHHHTHHHHHHH CS
                             URO-D 153 lveGgskgfekllkllykdpeevhklldkltdvvieylkaqieagAdaiqifD..swagllspedfeefvlpylkri 227
                                       l+     g++++l  l+k+pe v+++l++ td++i+++++++e+gAd++++ D  + ++l++p++fe f+ p ++r 
  gi|298673991|ref|YP_003725741.1| 152 LM-----GTSNFLIGLIKKPEYVRQFLEVSTDICIRHANNLLEHGADVVCVPDgtAGPDLIDPAMFENFIKPEYQRF 223
                                       **.....**********************************************99999******************* PP

                                       HHHHHH.H--S-EEEEESSHH.HHHHHHTTS--SEEE--TTS.-HHHHHHSS....EEE--B-G.GGGG.S-HHHHH CS
                             URO-D 228 vdevkaegpkvpvilfikgagaeiledlaelgadvlsldwtv.dlkeaarevgdkvalqGnldPialLl.gspeeie 302
                                       ++ vk+       + +++g++++ile l e+g++++s+++++ dl+ a++ +gdk  l+Gn++++ ++l  s ++++
  gi|298673991|ref|YP_003725741.1| 224 CRDVKG-----FKVSHMCGDINAILEPLSECGFEGISVEEKIiDLQTAKEILGDKSKLIGNVSTSGTMLmRSYDDVK 295
                                       ******.....89***************************998**99999999************************ PP

                                       HHHHHHHT.T---SSSEEB-BSS---TTS-HHHHHHHHHHHHT- CS
                             URO-D 303 kevkeilekgaggkkgyilnlGhgippetppenvkalveavkey 346
                                       +e+k++le+g++     +l++G+gi+p+tp++n+kalv+a++ey
  gi|298673991|ref|YP_003725741.1| 296 NEAKNCLEEGVD-----VLAPGCGIAPNTPLKNIKALVDARNEY 334
                                       ************.....***********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 2173.64
//
Query:       gi|298673992|ref|YP_003725742.1|  [L=341]
Description: 5-methyltetrahydropteroyltriglutamate/homocysteine S-methyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.17   11.1   0.1        1.1    8.5   0.0    2.4  2  Meth_synt_2  Cobalamin-independent synthase, Catalytic domain


Domain annotation for each model (and alignments):
>> Meth_synt_2  Cobalamin-independent synthase, Catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0     0.099   1.8e+03       6      54 ..       9      54 ..       7      74 .. 0.62
   2 ?    8.5   0.0     6e-05       1.1     274     319 ..     288     333 ..     138     337 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.099
                                      -SB---SS-----------------HHHHHHHHHHHHHHHHHHTT--SC CS
                       Meth_synt_2  6 iGSfPqtaevrearaevkkgelseeeyekaireeiekvvrrqeelgvDv 54
                                      iGS+P  + v    +e+ + ++s  e  +++ ++i++  +++ +++v v
  gi|298673992|ref|YP_003725742.1|  9 IGSYPLPEGV---TKEWLAHAFSTREEDEQLFSVINNTFQKKIDAEVQV 54
                                      8999976554...456777777777777777777777655544444444 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 6e-05
                                       -THHHHHHHHHCHHCTS-STSB-BB-SS-STTS-HHHHHHHHHHHH CS
                       Meth_synt_2 274 psmeeiaalikkaldvapkerlwvnPdCGLktrkreearaalknmv 319
                                       ++ e + +++++a         +v PdCGL   +++e  ++l n v
  gi|298673992|ref|YP_003725742.1| 288 ETPETVSKRLENAYSKFGDRVKYVGPDCGLGSWPTQEMASRLLNNV 333
                                       56677777777777776555569*************9999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2177.70
//
Query:       gi|298673993|ref|YP_003725743.1|  [L=343]
Description: hypothetical protein Metev_0015 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.5e-14   52.8  13.9    4.5e-14   52.8   5.9    2.3  2  SpoIIM      Stage II sporulation protein M
  ------ inclusion threshold ------
      0.048   13.6   0.4      0.096   12.6   0.4    1.4  1  Phage_30_8  Phage GP30.8 protein


Domain annotation for each model (and alignments):
>> SpoIIM  Stage II sporulation protein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.7   1.0    0.0031        27      50     112 ..      28      95 ..      12     136 .. 0.50
   2 !   52.8   5.9     5e-18   4.5e-14      48     156 .]     190     325 ..     174     325 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0031
                            SpoIIM  50 llfllGllllgiptilvllinGfvlG......avaalvaef....gglllflllilPhgilelpaiiiagaag 112
                                       ++++ G+ +  +++ l l++n+f+ G      a+   +++     +++  ++ +i P   + ++  i a++a+
  gi|298673993|ref|YP_003725743.1|  28 FAMAIGF-ACLLGFSLYLIMNSFT-GpetvnkAI---TTTSstatKKVEVSAKYISPVWSIFIFNTIAAFTAA 95 
                                       3344443.3333444444444443.223212211...111122233344444444443333333333333332 PP

  == domain 2  score: 52.8 bits;  conditional E-value: 5e-18
                            SpoIIM  48 alllfllGllllgiptilvllinGfvlG.....avaalvaefgglllflllilPhgilelpaiiiagaaglrl..gk 117
                                       ++++f+ G+ l+g+++ +++ +nG++ G     + + ++    ++ +f+++ilPhgilelpa+++ +++g r+    
  gi|298673993|ref|YP_003725743.1| 190 VIIIFVNGI-LIGLLFSYFI-FNGIIDGyevmgLKGIMFGGVYSFSYFISSILPHGILELPALLLTASMGHRFakI- 263
                                       689999997.8888888776.8999977764322233333336699***************************550. PP

                            SpoIIM 118 al.....................rsrrkalke........akrellklllllvp.llliAaliEafvtp 156
                                                                     ++        +k + l++ll ++  +l++Aa iE  +tp
  gi|298673993|ref|YP_003725743.1| 264 -QsctvknkslfrgdsiasiyqsL------EQvnsttktyLKSKPLWILLTSITvVLFAAAYIEINITP 325
                                       .25555666667777776665552......2233333344444445555555557*************8 PP

>> Phage_30_8  Phage GP30.8 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.4   1.1e-05     0.096      54      96 ..     129     170 ..     103     180 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.1e-05
                        Phage_30_8  54 ievenfftgeiyrlnsvvvgkirsktyedeelgesedvvwyet 96 
                                        ++  ff+ +iy+l + +    + + y  +   +++d +wy++
  gi|298673993|ref|YP_003725743.1| 129 EQLFRFFSNKIYKLTTKINKSYKQNGYRPNS-EYTQDSIWYYS 170
                                       355679****************999998775.5679*****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       834  (0.0465168); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 2454.32
//
Query:       gi|298673994|ref|YP_003725744.1|  [L=249]
Description: putative circadian clock protein KaiC [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-49  167.3   0.0    4.8e-49  166.8   0.0    1.2  1  ATPase    KaiC
    1.3e-06   28.1   0.0     0.0065   16.1   0.0    2.1  2  AAA_25    AAA domain
    5.5e-06   25.9   0.0    1.5e-05   24.5   0.0    1.6  1  DnaB_C    DnaB-like helicase C terminal domain
    0.00049   19.4   0.4      0.041   13.1   0.2    2.1  2  Rad51     Rad51
    0.00098   17.9   0.0     0.0023   16.6   0.0    1.6  1  GvpD      GvpD gas vesicle protein
     0.0014   17.9   0.0     0.0021   17.4   0.0    1.2  1  DUF2075   Uncharacterized conserved protein (DUF2075)
      0.002   17.9   0.1      0.071   12.8   0.1    2.5  1  AAA_24    AAA domain
     0.0027   18.0   0.0      0.011   16.0   0.0    1.8  1  AAA_22    AAA domain
  ------ inclusion threshold ------
      0.012   15.6   0.0       0.04   13.9   0.0    1.9  1  AAA_14    AAA domain
       0.04   14.1   0.0       0.13   12.4   0.0    1.8  2  AAA_33    AAA domain
      0.048   13.1   0.1        0.1   12.0   0.0    1.5  2  RecA      recA bacterial DNA recombination protein
      0.056   12.5   0.1      0.095   11.7   0.1    1.3  1  T2SSE     Type II/IV secretion system protein
      0.057   13.8   0.1      0.066   13.6   0.1    1.4  1  AAA_16    AAA ATPase domain
       0.09   13.1   0.0       0.18   12.2   0.0    1.5  1  AAA_19    AAA domain
      0.096   12.5   0.0       0.16   11.8   0.0    1.3  1  AAA_11    AAA domain
        0.2   11.3   0.0       0.33   10.7   0.0    1.3  1  AAA_30    AAA domain


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.8   0.0   4.2e-52   4.8e-49       1     229 [.       5     247 ..       5     249 .] 0.94

  Alignments for each domain:
  == domain 1  score: 166.8 bits;  conditional E-value: 4.2e-52
                            ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekl 77 
                                       ++tgI g+De+++gG+ ++rv+l++G pG+GKt+f+ qFl +ga++ ge g+++t++e++++++ ++++    +  l
  gi|298673994|ref|YP_003725744.1|   5 IQTGISGFDELVQGGLLSERVYLVSGPPGSGKTTFGIQFLTHGAAN-GEIGLYITLNESPQNVIDDMSNYKLGIPSL 80 
                                       68********************************************.****************************** PP

                            ATPase  78 eeegklaiidasesaeesaee..................kdkedleelieelaeaikeikakrvviDsitgl.ayee 135
                                        ++ kl + d+   +e   ++                  ++  +++ + ++++ ++ e+++kr+viDs++++  +++
  gi|298673994|ref|YP_003725744.1|  81 IKKRKLLFADLGPRMEYGYSDemnevispnydvgyapveSEAPSPNLVFKQITAYVMEYNVKRLVIDSVSAIrFTSK 157
                                       ***********99888666656889***********9976777788899***********************99999 PP

                            ATPase 136 keavaReilrqlvrvlkklgvTailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhsk 212
                                       + ++  +++ +++r lk+lg+T++l se+ +     + y  e+f++ gvi L++ +++++++R l+i+kmRgt+h+ 
  gi|298673994|ref|YP_003725744.1| 158 DRSLEEKEMSRFIRSLKNLGCTTVLLSEMVD----PTSYSTEQFSSHGVIFLHNFLYQKTMTRALQIIKMRGTRHDC 230
                                       99999***********************755....4789999*********************************** PP

                            ATPase 213 kehpfeIteegikvlee 229
                                       ++  +e te+g k+ ++
  gi|298673994|ref|YP_003725744.1| 231 NMRGIEFTEKGLKINDQ 247
                                       *************9876 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   5.8e-06    0.0065      23      59 ..      13      50 ..       2      66 .. 0.83
   2 !   10.1   0.0    0.0004      0.45     126     186 ..     125     183 ..     111     184 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.8e-06
                            AAA_25 23 rwlvkgllpagelallaGapgtGKttlaldlalava.t 59
                                      + lv+g l  + + l+ G+pg+GKtt+ ++   + a  
  gi|298673994|ref|YP_003725744.1| 13 DELVQGGLLSERVYLVSGPPGSGKTTFGIQFLTHGAaN 50
                                      568997777899******************99998844 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0004
                            AAA_25 126 ltadvdaleaaieevegvrlvviDplsralggdensnsd...vgalvealeriarrtgaavllv 186
                                        + +++++ a + e ++v+ +viD++s++   +++++ +   +++++  l+++    g++++l+
  gi|298673994|ref|YP_003725744.1| 125 PNLVFKQITAYVME-YNVKRLVIDSVSAIRFTSKDRSLEekeMSRFIRSLKNL----GCTTVLL 183
                                       56678999******.77**********98888666554411156666666665....9998875 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   1.4e-08   1.5e-05       2     169 ..       5     177 ..       4     191 .. 0.64

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.4e-08
                                       BXSSTHHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHH....HHHT CS
                                       xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxx RF
                            DnaB_C   2 lstgfkdLDklts.GlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRlls....seae 73 
                                       ++tg + +D+l++ Gl +  ++++ + p+ Gkt++ +++ ++ a++ +++  +  l+ s +++++ +        + 
  gi|298673994|ref|YP_003725744.1|   5 IQTGISGFDELVQgGLLSERVYLVSGPPGSGKTTFGIQFLTHGAANGEIGLYI-TLNESPQNVIDDMSNyklgIPSL 80 
                                       7899999**98862799999**********************99888877655.55555555655555500005555 PP

                                       XXHHHHHHTTSXH.......HHHHHHHHHHHHHHHSEEEEEEXSSXCHHHHHHHHHHHHHHTTEEEEEEEEGGGTBT CS
                                       xxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  74 idskklrtgklke.......edweklteaieelseaklfiddtpaltvseirskarrlkkekglgliviDyLqlmeg 143
                                       i+++kl  ++l         ++++++ +   ++  a++    + a +++ + +++  + +e +++ +viD +  ++ 
  gi|298673994|ref|YP_003725744.1|  81 IKKRKLLFADLGPrmeygysDEMNEVISPNYDVGYAPVE---SEAPSPNLVFKQITAYVMEYNVKRLVIDSVSAIRF 154
                                       666666444444212222224444444444445555543...3444555556666667777899************7 PP

                                       SCS.SSCCCHHHHHHHHHHHHHHHHCT CS
                                       xxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C 144 see.kenreqevseisrsLkalakeln 169
                                       +++ ++ +e+e+s+  rsLk+l     
  gi|298673994|ref|YP_003725744.1| 155 TSKdRSLEEKEMSRFIRSLKNL----G 177
                                       5422445566666666666665....4 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.2   3.7e-05     0.041      16      56 ..       2      42 ..       1      48 [. 0.93
   2 ?    4.6   0.0     0.014        16     120     227 ..     128     227 ..      99     235 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.7e-05
                                      S-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHH CS
                             Rad51 16 llqlttGskklDelLgGGietgsiteifGefrsGktqlcht 56
                                      + ++ tG + +Del++GG+ +  +  + G  +sGkt +  +
  gi|298673994|ref|YP_003725744.1|  2 VTRIQTGISGFDELVQGGLLSERVYLVSGPPGSGKTTFGIQ 42
                                      5789********************************99876 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.014
                                       HHHHTHHHHHHS-EEEEEEETTTGGGCH-------THHHHHHHHHHHHHHHHHHHHH--EEEEEEE-------.--- CS
                             Rad51 120 llqqaaallaedkfallivDsvtalyRtdfsgrgelakRqqklgkllrtLrkladefevavvitnqvvaqvdgqaal 196
                                       + +q++a ++e +++ l++Dsv a  R  f+ ++  +  ++++++++r+L++l      + v+  ++v+   ++++ 
  gi|298673994|ref|YP_003725744.1| 128 VFKQITAYVMEYNVKRLVIDSVSAI-R--FTSKDR-SLEEKEMSRFIRSLKNLG----CTTVLLSEMVDPTSYSTEQ 196
                                       4568889999999999*****9885.4..444443.445678899999999985....4556666677778888888 PP

                                       ---------HHHHHHHH-SEEEEEEE-STTE CS
                             Rad51 197 fsadpkkPigGlvlahasttRlalrkgkgee 227
                                       fs+   +     +  +++t  l+++k +g++
  gi|298673994|ref|YP_003725744.1| 197 FSSHGVIFLHNFLYQKTMTRALQIIKMRGTR 227
                                       8888888777777777777778888888765 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0     2e-06    0.0023      13      56 ..      26      71 ..      22     243 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2e-06
                              GvpD 13 llikGaPGtGktlftlrgldvlrresdv.lyvs.trvddetvseay 56
                                       l+ G PG+Gkt+f +++l+    ++++ ly++   + ++ + ++ 
  gi|298673994|ref|YP_003725744.1| 26 YLVSGPPGSGKTTFGIQFLTHGAANGEIgLYITlNESPQNVIDDMS 71
                                      689*****************98888887688872456677777763 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.8e-06    0.0021       2      52 ..      24      72 ..      23      92 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.8e-06
                           DUF2075  2 avvlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlreala 52
                                      +v+lV+G +G+GKt  ++++l+     ++++   y++ N++ ++v+    +
  gi|298673994|ref|YP_003725744.1| 24 RVYLVSGPPGSGKTTFGIQFLTHG--AANGEIGLYITLNESPQNVIDDMSN 72
                                      799*******************99..99**************999876555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1   6.3e-05     0.071       3      60 ..      24     135 ..      22     199 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.3e-05
                            AAA_24   3 lkiliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdieswedfldevvel............. 59 
                                       + +l+ Gp+g+GKTt+  ++       g+  l+i ++++ +++ +d  ++  +++ ++++ + l             
  gi|298673994|ref|YP_003725744.1|  24 RVYLVSGPPGSGKTTFGIQFlthgaanGEIGLYITLNESPQNVIDDMSNYKLGIPSLIKKRKLLfadlgprmeygys 100
                                       568999**********9999888888777788888877766665555443334444444444444445555555555 PP

                            AAA_24  60 ..................................a 60 
                                                                         +
  gi|298673994|ref|YP_003725744.1| 101 demnevispnydvgyapveseapspnlvfkqitaY 135
                                       55555555566666666444444444444444442 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   9.6e-06     0.011       5     118 ..      23     176 ..      21     187 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9.6e-06
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee..............................erpevvfvtlpsst 51 
                                       +++ +v G++G+GKTt   ++l    +                                    ++++++        
  gi|298673994|ref|YP_003725744.1|  23 ERVYLVSGPPGSGKTTFGIQFLTHGAAN----GeiglyitlnespqnviddmsnyklgipsliKKRKLL-------- 87 
                                       67899**********9866666554222....1234467777544444422222222222222222222........ PP

                            AAA_22  52 sskdllrellralglelka......................erlsseell.ealeqalraravielliiDEaqhlr. 104
                                            + +l   ++    +                      +++ s  l+ ++++ ++ ++ v + l+iD +  +r 
  gi|298673994|ref|YP_003725744.1|  88 -----FADLGPRME----YgysdemnevispnydvgyapveSEAPSPNLVfKQITAYVMEYNV-KRLVIDSVSAIRf 154
                                       .....333333333....245557777777777777878996666666666999999999999.******9999988 PP

                            AAA_22 105 ..s......eealeeLrsllnl 118
                                         +      +e+ +++rsl nl
  gi|298673994|ref|YP_003725744.1| 155 tsKdrsleeKEMSRFIRSLKNL 176
                                       7515567778898999999884 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.6e-05      0.04       2      77 ..      23     126 ..      22     184 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.6e-05
                            AAA_14   2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe....kllelileklke.......ekkty 67 
                                       +++++++G+  +GKTt+  q++ +  ++ e  lyi+l++ ++  ++d +     +++li+++  +       ++++y
  gi|298673994|ref|YP_003725744.1|  23 ERVYLVSGPPGSGKTTFGIQFLTHGAANGEIGLYITLNESPQNVIDDMSnyklGIPSLIKKR--KllfadlgPRMEY 97 
                                       6899******************8888899999*****9988865554431223333444443..0222345556666 PP

                            AAA_14  68 lflDEiqev...................p 77 
                                        + DE+ ev                   +
  gi|298673994|ref|YP_003725744.1|  98 GYSDEMNEVispnydvgyapveseapspN 126
                                       66666666655555555555555555543 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00011      0.13       2      20 ..      26      44 ..      25     113 .. 0.85
   2 ?   -0.8   0.0       1.4   1.5e+03      85     100 ..     166     181 ..     140     231 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                            AAA_33  2 vllvGlpGsGKstlaerll 20
                                       l+ G+pGsGK+t+  + l
  gi|298673994|ref|YP_003725744.1| 26 YLVSGPPGSGKTTFGIQFL 44
                                      6789*********987766 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.4
                            AAA_33  85 rarflklarrlgvpvr 100
                                       ++rf++ +++lg+   
  gi|298673994|ref|YP_003725744.1| 166 MSRFIRSLKNLGCTTV 181
                                       4444444444443322 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   9.2e-05       0.1      32      90 ..       3      60 ..       1      83 [. 0.80
   2 ?   -2.6   0.0       2.7     3e+03     131     143 ..     140     152 ..     132     169 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.2e-05
                                      -EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS CS
                              RecA 32 etissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafidae 90
                                        i +G  ++d  +  GGl   r+  + Gp  sGktt+ ++ +++   +g +  +i  +
  gi|298673994|ref|YP_003725744.1|  3 TRIQTGISGFDELV-QGGLLSERVYLVSGPPGSGKTTFGIQFLTHGAANGEIGLYITLN 60
                                      56778888888755.59*****************************9999999999765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.7
                                       --SEEEEE-TTT- CS
                              RecA 131 aidlivvdsvaal 143
                                        +  +v+dsv+a+
  gi|298673994|ref|YP_003725744.1| 140 NVKRLVIDSVSAI 152
                                       5667899999997 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   8.5e-05     0.095     119     147 ..      13      41 ..       5      55 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.5e-05
                             T2SSE 119 aevlrkavrerglilvsGgTgsGKttlly 147
                                       +e+++  + ++ + lvsG+ gsGKtt+  
  gi|298673994|ref|YP_003725744.1|  13 DELVQGGLLSERVYLVSGPPGSGKTTFGI 41 
                                       56666667778899************865 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   5.9e-05     0.066      25      47 ..      24      46 ..      12     185 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.9e-05
                            AAA_16 25 elvllsGesGvGKsslvrellra 47
                                      ++ l+sG++G+GK++   ++l++
  gi|298673994|ref|YP_003725744.1| 24 RVYLVSGPPGSGKTTFGIQFLTH 46
                                      889***********987666664 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00016      0.18       8      31 ..      21      44 ..      14      74 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                            AAA_19  8 lkekvllvtaGpGtGKTrvlkhiv 31
                                      l+e+v lv ++pG+GKT+   + +
  gi|298673994|ref|YP_003725744.1| 21 LSERVYLVSGPPGSGKTTFGIQFL 44
                                      67899************9755555 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00014      0.16      16      39 ..      22      45 ..      13      86 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                            AAA_11 16 eseitliqGPPGtgKTktivells 39
                                      ++ + l++GPPG+gKT++ +++l 
  gi|298673994|ref|YP_003725744.1| 22 SERVYLVSGPPGSGKTTFGIQFLT 45
                                      55579***********98777665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00029      0.33      15      34 ..      21      39 ..      13      57 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00029
                            AAA_30 15 tsgdrvavltGpAGtGKtta 34
                                       s+ rv ++ Gp+G+GKtt 
  gi|298673994|ref|YP_003725744.1| 21 LSE-RVYLVSGPPGSGKTTF 39
                                      455.59************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1596.87
//
Query:       gi|298673995|ref|YP_003725745.1|  [L=173]
Description: hypothetical protein Metev_0017 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1316  (0.0734006); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 1.41s 00:00:01.88 Elapsed: 00:00:00.80
# Mc/sec: 656.43
//
Query:       gi|298673996|ref|YP_003725746.1|  [L=347]
Description: elongation factor Tu domain 2 protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-07   31.6   0.0    4.8e-07   30.1   0.0    1.8  1  GTP_EFTU_D2  Elongation factor Tu domain 2
    0.00026   20.6   0.0      0.001   18.7   0.0    1.8  2  GTP_EFTU     Elongation factor Tu GTP binding domain


Domain annotation for each model (and alignments):
>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   5.3e-11   4.8e-07       2      73 ..     183     248 ..     182     249 .. 0.92

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 5.3e-11
                                       EEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                       GTP_EFTU_D2   2 tvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                        valg+v +Gt++  d++++ +++  k     +i+s++++ ed + a ag ++G+ ++ + +++ i +G ++
  gi|298673996|ref|YP_003725746.1| 183 CVALGSVSQGTIHSKDKMYLYPLE--KP---LEIRSIQMHDEDTKSAGAGSRVGLALKHVQTKE-IDRGFII 248
                                       59******************6653..44...*********************************.****987 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       0.1   9.2e+02       5      26 ..       3      24 ..       1      32 [. 0.83
   2 !   18.7   0.0   1.1e-07     0.001      61     190 ..      31     151 ..      23     155 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.1
                                      EEEEEESTTSSHHHHHHHHHHH CS
                          GTP_EFTU  5 nigiighvDhGKtTLtdrLlyk 26
                                       ++iig   +G t+L  +L +k
  gi|298673996|ref|YP_003725746.1|  3 SVAIIGSEQSGRTSLASHLGKK 24
                                      689*************999765 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 1.1e-07
                                       EEEETTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTE.EEEEEESCGST. CS
                          GTP_EFTU  61 isleketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvp.iivfiNKmDrl. 135
                                       +++e ++  + ++ iD+ G  + +k  i++l+  D+a++ v   eG ++   e +  +  ++ +  i++++K D + 
  gi|298673996|ref|YP_003725746.1|  31 TKFEYSKGGRILTAIDANGYPESVKPLITALSLSDIALICVPP-EGLNATIGECIIALDIMKYQhGIFVLTKSDTTy 106
                                       444444778999**************************99975.6*******************99**********8 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHH CS
                          GTP_EFTU 136 kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealve 190
                                          ++e++e++k+           +g++  ++  ++ +S  + eg+++l ++++e
  gi|298673996|ref|YP_003725746.1| 107 PYAIEELKEQIKKVT---------AGTSL-ENWDCISTSTTSFEGMNELRDMIFE 151
                                       445555555555333.........22222.2456888888888888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.40s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1997.96
//
Query:       gi|298673997|ref|YP_003725747.1|  [L=389]
Description: ATP dependent DNA ligase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.6e-45  152.7   0.3    9.6e-45  151.6   0.3    1.6  1  Lig_C           Ligase Pab1020 C-terminal region
    5.1e-19   69.1   0.2    8.7e-19   68.4   0.2    1.4  1  RNA_ligase      RNA ligase
    3.2e-10   40.0   0.1    2.9e-08   33.6   0.1    2.3  1  DNA_ligase_A_M  ATP dependent DNA ligase domain


Domain annotation for each model (and alignments):
>> Lig_C  Ligase Pab1020 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.6   0.3   1.6e-48   9.6e-45       3     125 .]     263     385 ..     261     385 .. 0.99

  Alignments for each domain:
  == domain 1  score: 151.6 bits;  conditional E-value: 1.6e-48
                                       CCSCCGS-STSCHHHHHHHHHHHHHH--SHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---EEEEEEE-SSHHHHHH CS
                             Lig_C   3 fsylfelgrdFlfsRviReafqavefeeseeelrerakeLGesiLepmvetikkvkeeekvkeefrvrfkdeeniee 79 
                                       f++++++grd+++sRviRe+fq+ve+ eseee++er+ +LG+siLepm +t++kv+++e+v++++++r+k++e+i e
  gi|298673997|ref|YP_003725747.1| 263 FKFYNDFGRDYFYSRVIREGFQSVELGESEEEFQERCLQLGRSILEPMSRTMRKVAQGEEVHDDVQIRVKEPETIYE 339
                                       9**************************************************************************** PP

                                       HHHHHHCTT--EEEEEEE..TTEEEEE..EE-HHHHHHHHHHHTT- CS
                             Lig_C  80 llehLrrlgvkaeveekekedgelvvkfkkiaqsttdkikslLeGg 125
                                       +++hL+r+g++a++  +++ ++e++v+++k++qst+dk+k++++G+
  gi|298673997|ref|YP_003725747.1| 340 FEKHLKRMGIDAKFGAPQQVGDEYLVSIRKLNQSTNDKTKAIWNGS 385
                                       ********************************************95 PP

>> RNA_ligase  RNA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.4   0.2   1.5e-22   8.7e-19       2     160 ..      95     249 ..      94     250 .. 0.72

  Alignments for each domain:
  == domain 1  score: 68.4 bits;  conditional E-value: 1.5e-22
                                       EEEEEEE-SSEEEEEEEETT.EEEEETTCEB.CTTTHHHHHHTHHHHHHHHHHHHH....ECCEEEEEEEES...SS CS
                        RNA_ligase   2 evvvtEKlDGtnfriylvke.vgvasRsqil.pfgeekfkefkrwaaalrkklkekla..neelilyGElig..hsi 72 
                                       +v v+EK++G+n+r+   ++ v++++Rs+i+ p          +  +  ++ + + +   ++e++lyGE++g  +++
  gi|298673997|ref|YP_003725747.1|  95 TVSVEEKMNGYNVRVASINGdVTAFTRSGIVcP----------YTTERAKYLIGQEFFekHPEFVLYGEMVGpdNPY 161
                                       688*************99667**********54..........12222222222222246678*********75333 PP

                                       ......TTSS.EEEEEEEEEEECTTBECE--HHHHHHHHHCCT..B..EEEEE.SS.HHHHHCCC..HHHHTC--EE CS
                        RNA_ligase  73 ....kygglpkefyvFdifdirdkeeqrylspdevealakglg..tvpvlyegkfl.aaeellell.lskgnkrEGl 141
                                            y+    e + F ifdir k++++ l+  e+++l ++++  +v +++e+k++ a +++++++ +  ++ rEG+
  gi|298673997|ref|YP_003725747.1| 162 vpknIYNI---ESLDFFIFDIRYKNTGEPLPVYERRKLMNDYNlnQVQLFGEYKIEeAPKNITKIIkEIGKQEREGV 235
                                       43333333...44445555555777**********9999999999**********98888888884335777***** PP

                                       EEEESSSSBETTEBSEEEE CS
                        RNA_ligase 142 VikpeselyknkgraifKv 160
                                       Vik+++++      + +K+
  gi|298673997|ref|YP_003725747.1| 236 VIKDPQMR-----INAIKY 249
                                       ***99986.....555555 PP

>> DNA_ligase_A_M  ATP dependent DNA ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.1   4.8e-12   2.9e-08       9     190 ..      85     243 ..      77     253 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 4.8e-12
                                       CHHHHHHHTTTSEEEEEEEESSEEEEEEEETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEEEEEEEEEEET CS
                    DNA_ligase_A_M   9 siekalkkleekafivEiKyDGeRaqvhkegdkvklfSRrlkditaakpelvkalkeafkkdeksvilDGElvavdk 85 
                                       ++++ +k+  ++++ vE+K++G+ ++v   +++v+ f+R++   +++ ++    + + f+++  +++l GE+v  d+
  gi|298673997|ref|YP_003725747.1|  85 AVKSHFKN--SGTVSVEEKMNGYNVRVASINGDVTAFTRSGIVCPYTTERAKYLIGQEFFEKHPEFVLYGEMVGPDN 159
                                       55666666..57888*****************************99999998889999999999**********544 PP

                                       TTTCBEHHHHHCHHHHCHCCTHHHHHHSEEEEEEEEEEEETTEEHTTSCHHHHHHHHHHHB--BTTTEEE--EEEE. CS
                    DNA_ligase_A_M  86 etgeilpfqklasrkkkkkkveeklkeaelclfvFDiLyldgesltdeplkeRrklLeeilkesedrvelaeslev. 161
                                            +p++         +++       +l +f+FDi y +  +   +p+ eRrkl++++     ++v+l  ++++ 
  gi|298673997|ref|YP_003725747.1| 160 P---YVPKNI--------YNI------ESLDFFIFDIRYKNTGE--PLPVYERRKLMNDYN---LNQVQLFGEYKIe 214
                                       4...444443........322......3569*********9866..78***********99...7888888777772 PP

                                       SSHHHHHHHHHHHHHTTECEEEEEETT-C CS
                    DNA_ligase_A_M 162 kdveeleelleeaiseglEGlvvKnpdsk 190
                                       +  ++++++++e  +++ EG+v+K+p+ +
  gi|298673997|ref|YP_003725747.1| 215 EAPKNITKIIKEIGKQEREGVVIKDPQMR 243
                                       56799********************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.35s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 2258.18
//
Query:       gi|298673998|ref|YP_003725748.1|  [L=258]
Description: hypothetical protein Metev_0020 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-40  135.3  15.0    1.1e-12   48.1   0.2    4.1  4  CBS       CBS domain
  ------ inclusion threshold ------
       0.27   11.4   3.7         36    4.6   0.1    3.3  3  DUF370    Domain of unknown function (DUF370)


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.4   7.2e-12   6.4e-08       1      51 [.       3      51 ..       3      56 .. 0.91
   2 !   22.3   0.1   1.5e-08   0.00014       6      53 ..      75     120 ..      70     121 .. 0.78
   3 !   48.1   0.2   1.3e-16   1.1e-12       1      53 [.     128     179 ..     128     182 .. 0.95
   4 !   40.6   0.8     3e-14   2.7e-10       1      55 [.     202     256 ..     202     258 .] 0.95

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 7.2e-12
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDl 51
                                      V++im +++ t++ ++t + al+ m++k+ +rl+V+  d+k+ G++t+r l
  gi|298673998|ref|YP_003725748.1|  3 VKEIMVEPP-TIDKSDTTSHALDVMEKKNTRRLLVT-HDDKIMGVLTMRSL 51
                                      899**9999.***************9999****888.7888*******987 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 1.5e-08
                                       BSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS   6 trdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                       ++d+  v pdt++++a+ lm++k  + + VV +++ + G vt + ll+
  gi|298673998|ref|YP_003725748.1|  75 SDDYSKVLPDTDIKDAITLMKNK--GKVIVVTDNDDIYGWVTPEELLK 120
                                       55667899************555..56657745555********9996 PP

  == domain 3  score: 48.1 bits;  conditional E-value: 1.3e-16
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                       +g+im +d++ ++p++ +  +  +m e++++r+PVV ed+k+vGivt++D+++
  gi|298673998|ref|YP_003725748.1| 128 AGEIMQKDPLKANPSDRVIHIRHQMLENNIGRVPVV-EDEKIVGIVTEKDIAK 179
                                       689*********************************.7888**********97 PP

  == domain 4  score: 40.6 bits;  conditional E-value: 3e-14
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       ++dimtr   tv+ +t+ ++++++m+e +++++PV++ +++lvGi+t+r +++ +
  gi|298673998|ref|YP_003725748.1| 202 IEDIMTRGAKTVYTNTPTSDVVNMMIEDNIGGVPVLNLEDELVGIITRRNIIESM 256
                                       579*********************************99999***********976 PP

>> DUF370  Domain of unknown function (DUF370)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.004        36      30      60 ..      13      43 ..      11      52 .. 0.88
   2 ?    2.0   0.0     0.025   2.2e+02      26      46 ..      87     107 ..      82     118 .. 0.70
   3 ?    3.9   0.3    0.0065        58       3      22 ..     156     179 ..     155     204 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.004
                            DUF370 30 iqeakeegklidategrktksviitdsghvi 60
                                      i+++  + + +d+ e+++t+  ++t +++++
  gi|298673998|ref|YP_003725748.1| 13 IDKSDTTSHALDVMEKKNTRRLLVTHDDKIM 43
                                      67777888999**************999985 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.025
                            DUF370  26 ikrliqeakeegklidategr 46 
                                       ik+ i   k++gk+i +t ++
  gi|298673998|ref|YP_003725748.1|  87 IKDAITLMKNKGKVIVVTDND 107
                                       666666677777777666553 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.0065
                            DUF370   3 niGfgnvVnadriiaivsp....e 22 
                                       niG   vV  ++i+ iv+     +
  gi|298673998|ref|YP_003725748.1| 156 NIGRVPVVEDEKIVGIVTEkdiaK 179
                                       899999***********9754331 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.35s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1554.47
//
Query:       gi|298673999|ref|YP_003725749.1|  [L=286]
Description: hypothetical protein Metev_0021 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-49  164.7  17.1    6.4e-13   48.9   0.7    4.1  4  CBS              CBS domain
  ------ inclusion threshold ------
      0.022   14.7   0.0         10    6.1   0.0    3.1  3  Acetyltransf_10  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.7   7.1e-17   6.4e-13       1      53 [.       3      55 ..       3      58 .. 0.95
   2 !   44.6   0.5   1.6e-15   1.5e-11       3      56 ..      76     127 ..      69     128 .. 0.91
   3 !   38.4   0.1   1.4e-13   1.3e-09       2      52 ..     137     187 ..     134     191 .. 0.93
   4 !   43.2   0.4   4.3e-15   3.9e-11       1      56 [.     227     281 ..     226     282 .. 0.92

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 7.1e-17
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53
                                      V+dim+++v +++p++t++ a +lm +++++ l VVd++++ vGivt++Dl r
  gi|298673999|ref|YP_003725749.1|  3 VKDIMSSPVYVLKPNDTVAHARNLMLRHKINTLIVVDDEEEMVGIVTMSDLSR 55
                                      89*******************************9999999**********966 PP

  == domain 2  score: 44.6 bits;  conditional E-value: 1.6e-15
                                       HHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   3 dimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                        +mt+ ++t++ ++++++a  +m e+++s+lPV+   +k+ Gi+t++D++++++
  gi|298673999|ref|YP_003725749.1|  76 RVMTESPLTIYSSASISQATSMMLENHISSLPVM--KNKVAGIITRTDIVKYIV 127
                                       57********************************..556*************97 PP

  == domain 3  score: 38.4 bits;  conditional E-value: 1.4e-13
                                       HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHH CS
                               CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDll 52 
                                       ++ mt+++++v+   t+  ++++m +++++ l+VV++ +k vG+++ rDl+
  gi|298673999|ref|YP_003725749.1| 137 SEWMTKNPIFVHRHHTINHVIDEMDKSNIHKLLVVNDVEKTVGMISTRDLA 187
                                       677*********************8888*********************97 PP

  == domain 4  score: 43.2 bits;  conditional E-value: 4.3e-15
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       ++dim++++++++ +++l  a ++m++++v +lPV  e++ +vGi++++D+lra+ 
  gi|298673999|ref|YP_003725749.1| 227 AEDIMSTQLHVIDSSDSLNNATKIMIDENVLGLPVR-ENEDIVGIISRSDILRAIQ 281
                                       469**************************88****7.5666*************96 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0012        10      22      50 ..      23      52 ..      13      58 .. 0.82
   2 ?    4.4   0.0    0.0037        33      20      50 ..     154     185 ..     138     191 .. 0.79
   3 ?   -0.6   0.0      0.13   1.2e+03      20      47 ..     246     272 ..     226     278 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0012
                   Acetyltransf_10 22 lreri.eegealllvaeeggkivGvielrd 50
                                       r+ + +++ ++l+v+++++++vG+++++d
  gi|298673999|ref|YP_003725749.1| 23 ARNLMlRHKINTLIVVDDEEEMVGIVTMSD 52
                                      45556579999***************9976 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0037
                   Acetyltransf_10  20 ealreri.eegealllvaeeggkivGvielrd 50 
                                       +++ +++ +++ ++llv+++ +k vG+i++rd
  gi|298673999|ref|YP_003725749.1| 154 NHVIDEMdKSNIHKLLVVNDVEKTVGMISTRD 185
                                       34455664689999**************9876 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.13
                   Acetyltransf_10  20 ealrerieegealllvaeeggkivGvie 47 
                                       +a + +  ++++l l + e++ ivG+i+
  gi|298673999|ref|YP_003725749.1| 246 NATKIM-IDENVLGLPVRENEDIVGIIS 272
                                       333344.48888888889999****995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1777.59
//
Query:       gi|298674000|ref|YP_003725750.1|  [L=353]
Description: putative signal transduction protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-55  184.4   7.1    1.6e-13   50.9   0.0    4.2  4  CBS       CBS domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.1   1.6e-14   2.9e-10       4      55 ..      83     135 ..      78     137 .. 0.86
   2 !   46.3   0.2   2.4e-16   4.4e-12       1      56 [.     160     215 ..     160     216 .. 0.95
   3 !   48.6   0.0   4.7e-17   8.4e-13       1      55 [.     223     276 ..     223     278 .. 0.95
   4 !   50.9   0.0   8.8e-18   1.6e-13       2      56 ..     299     352 ..     298     353 .] 0.94

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 1.6e-14
                                       HSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTT..BEEEEEEHHHHHHHH CS
                               CBS   4 imtrdvvtvppdttleealelmrekgvsrlPVVdedg..klvGivtlrDllral 55 
                                       i  rdv+tvpp+tt+  a+++m +kg++r+P++ + g  +l Givt  D+++++
  gi|298674000|ref|YP_003725750.1|  83 IAKRDVITVPPTTTIMGAIKTMMNKGFRRIPIT-DAGtnRLEGIVTSVDIINFM 135
                                       4567**********999999977**********.466569***********987 PP

  == domain 2  score: 46.3 bits;  conditional E-value: 2.4e-16
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       +++im  d+v+++ ++++ +a+++m  k++++lP+Vded++++ i t+rD l+++ 
  gi|298674000|ref|YP_003725750.1| 160 IREIMENDIVYLHNTDSIDDAIDTMNTKNIGGLPIVDEDNRVHAICTERDFLQFID 215
                                       589**********************7788************************996 PP

  == domain 3  score: 48.6 bits;  conditional E-value: 4.7e-17
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       Vg++m+++v+ v+ ++t+e+a+++m ++g++rlPVV +d  l+Givt + ++++l
  gi|298674000|ref|YP_003725750.1| 223 VGEYMNKNVMRVKSNATIEDAAKIMMNEGFRRLPVV-KDSILLGIVTATNIMNYL 276
                                       89**********************87999*******.8999***********998 PP

  == domain 4  score: 50.9 bits;  conditional E-value: 8.8e-18
                                       HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       +++ t+dvv  + dt+l+ea++lm e++v++lP++ ++g+++Gi+t+rD l+a++
  gi|298674000|ref|YP_003725750.1| 299 SSMITKDVVWTTSDTDLGEAARLMQENNVGSLPII-DNGQFIGIITERDFLKAIV 352
                                       67889*******************9999*******.6****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.60s 00:00:01.19 Elapsed: 00:00:00.59
# Mc/sec: 1794.77
//
Query:       gi|298674001|ref|YP_003725751.1|  [L=255]
Description: hypothetical protein Metev_0023 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-46  156.4   8.3    1.2e-11   44.8   0.3    4.0  4  CBS       CBS domain
  ------ inclusion threshold ------
       0.19   11.3   0.1       0.33   10.5   0.1    1.4  1  Tom6      Mitochondrial import receptor subunit Tom6, fungal


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.4   1.2e-14   1.1e-10       1      53 [.       4      58 ..       4      60 .. 0.88
   2 !   29.0   0.0   1.2e-10   1.1e-06       8      55 ..      74     123 ..      68     125 .. 0.90
   3 !   43.5   0.0   3.5e-15   3.1e-11       1      53 [.     133     185 ..     133     187 .. 0.95
   4 !   44.8   0.3   1.4e-15   1.2e-11       1      55 [.     200     253 ..     200     255 .] 0.94

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 1.2e-14
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE..ETTTBEEEEEEHHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVV..dedgklvGivtlrDllr 53
                                      V+dimt+d+v v++++ +  a +lmr++ ++++PVV   +++++ G++t+ D+l+
  gi|298674001|ref|YP_003725751.1|  4 VEDIMTKDPVKVTENDYITHARQLMRDYFLRSVPVVdnHDSNHVTGLLTDQDILN 58
                                      89***********************77668******663344699********96 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 1.2e-10
                                       SCEEEETTSBHHHHHHHHHHHTSSEEEEE..ETTTBEEEEEEHHHHHHHH CS
                               CBS   8 dvvtvppdttleealelmrekgvsrlPVV..dedgklvGivtlrDllral 55 
                                        ++t+ pdt++ +a +l+ +++++r PV+    +++l Gi++ rDll+++
  gi|298674001|ref|YP_003725751.1|  74 AFPTILPDTDILKASKLLLDAKLHRSPVMisTTEKRLAGIISNRDLLEKI 123
                                       578**************99*********66988889***********987 PP

  == domain 3  score: 43.5 bits;  conditional E-value: 3.5e-15
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                       +g+im+++v+t++ d++++ + + m + +++++PVV+  ++++G+vt+rD+++
  gi|298674001|ref|YP_003725751.1| 133 IGEIMNTKVITCYTDDNVARIWNNMLDWDYTGIPVVNQKNEPIGVVTRRDIIK 185
                                       689*********************99888*******99999**********97 PP

  == domain 4  score: 44.8 bits;  conditional E-value: 1.4e-15
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       V+ im+++  t++p+t++ ea++++++++v+rl VV+ ++k+vGiv + Dll+a 
  gi|298674001|ref|YP_003725751.1| 200 VEKIMSTPTYTITPNTPITEAIDKIIHYDVGRLTVVN-NNKVVGIVDRNDLLEAC 253
                                       788*********************99*99*******5.889***********985 PP

>> Tom6  Mitochondrial import receptor subunit Tom6, fungal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   3.7e-05      0.33       2      22 ..     194     214 ..     193     217 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 3.7e-05
                              Tom6   2 kkkkSkfeqfketPaftvlln 22 
                                       ++k S++e++ +tP +t+  n
  gi|298674001|ref|YP_003725751.1| 194 PEKSSRVEKIMSTPTYTITPN 214
                                       5799*************9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1559.77
//
Query:       gi|298674002|ref|YP_003725752.1|  [L=211]
Description: putative signal transduction protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.8e-28   96.7   6.4    5.9e-14   52.2   0.3    2.2  2  CBS       CBS domain
  ------ inclusion threshold ------
      0.025   13.8   0.6       0.69    9.0   0.1    2.1  2  DUF5508   Family of unknown function (DUF5508)


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4   1.3   2.2e-16     2e-12       1      56 [.      24      78 ..      24      79 .. 0.93
   2 !   52.2   0.3   6.6e-18   5.9e-14       1      53 [.      89     140 ..      89     144 .. 0.92

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 2.2e-16
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56
                                      V++im+r v t++ d+++ +++++m +++v+++ +V +++ +vG++t+rDl++++l
  gi|298674002|ref|YP_003725752.1| 24 VHEIMNRSVYTIDIDASVVDVAKEMSKNNVGSIIIVQNND-PVGVITERDLVKKIL 78
                                      89***********************8888****8897677.***********9985 PP

  == domain 2  score: 52.2 bits;  conditional E-value: 6.6e-18
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                       +g++m+++++t +p+t++ +a+elm++++++rl V+  d+k+vG +t+rD+l 
  gi|298674002|ref|YP_003725752.1|  89 AGEVMSSPLITTKPSTSVIDAAELMVKSNIRRLIVM-QDNKIVGFITDRDILT 140
                                       689******************************666.5788**********96 PP

>> DUF5508  Family of unknown function (DUF5508)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   7.7e-05      0.69     169     220 ..      29      80 ..      19      87 .. 0.89
   2 ?    3.2   0.0    0.0045        41     179     213 ..     104     138 ..      98     182 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 7.7e-05
                           DUF5508 169 nwgtslfdvdtpcifnapaynksnekslkpvsenglsgvltdrnnkiklitg 220
                                       n     +d+d+ ++  a    k n  s+  v +n   gv+t+r+   k++tg
  gi|298674002|ref|YP_003725752.1|  29 NRSVYTIDIDASVVDVAKEMSKNNVGSIIIVQNNDPVGVITERDLVKKILTG 80 
                                       66667789************************************99999998 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.0045
                           DUF5508 179 tpcifnapaynksnekslkpvsenglsgvltdrnn 213
                                       t +i  a    ksn + l  + +n + g +tdr+ 
  gi|298674002|ref|YP_003725752.1| 104 TSVIDAAELMVKSNIRRLIVMQDNKIVGFITDRDI 138
                                       56677788899*********************974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1213  (0.0676558); expected 358.6 (0.02)
Passed bias filter:                      686  (0.038262); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1266.30
//
Query:       gi|298674003|ref|YP_003725753.1|  [L=179]
Description: hypothetical protein Metev_0025 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.015   15.3   1.8      0.026   14.5   1.8    1.3  1  Alpha-2-MRAP_N  Alpha-2-macroglobulin RAP, N-terminal domain


Domain annotation for each model (and alignments):
>> Alpha-2-MRAP_N  Alpha-2-macroglobulin RAP, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.8   1.5e-06     0.026      15      69 ..      41     100 ..      32     108 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.5e-06
                    Alpha-2-MRAP_N  15 akKysreaNekk.....esdlreldkeFriaklnlvWeKAkrrltevklksLysdLkihd 69 
                                       ++Ky+++  e++     ++    ++ke    k+  + eK k++l++  l +L sdLki +
  gi|298674003|ref|YP_003725753.1|  41 NEKYNKKETESQnqrleREGYIATKKENGQLKIDSITEKGKKKLSKDLLDELNSDLKIDE 100
                                       4555555555551212333444556999999***************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1393  (0.0776954); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1224.74
//
Query:       gi|298674004|ref|YP_003725754.1|  [L=152]
Description: hypothetical protein Metev_0026 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0011   19.2   5.9     0.0013   19.0   5.9    1.2  1  ATG16         Autophagy protein 16 (ATG16)
      0.002   17.6  10.3     0.0024   17.3  10.3    1.2  1  DUF3552       Domain of unknown function (DUF3552)
     0.0044   16.4   6.7     0.0053   16.2   6.7    1.2  1  FAM76         FAM76 protein
  ------ inclusion threshold ------
      0.066   13.5   0.4       0.11   12.8   0.4    1.4  1  NTP_transf_2  Nucleotidyltransferase domain


Domain annotation for each model (and alignments):
>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   5.9     3e-07    0.0013      60     141 ..      43     124 ..       3     134 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 3e-07
                             ATG16  60 ekeasasqsnskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraale 136
                                       ++++++s+++++++ ++   e+++++l+++ + lyk  g    +l+++ ++l +++++lk++e ++ ++ ++++++e
  gi|298674004|ref|YP_003725754.1|  43 KNQETSSDEEKNSDVDVLVYEERIQELKQDKERLYKLLGNKDLQLQNKDNQLTEKDNQLKNKEYQISSMFHKINTVE 119
                                       2222233335667889999*********************************************************9 PP

                             ATG16 137 tklkd 141
                                       +k ++
  gi|298674004|ref|YP_003725754.1| 120 QKQNN 124
                                       99665 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3  10.3   5.3e-07    0.0024      74     163 ..      63     149 ..      43     152 .] 0.84

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.3e-07
                           DUF3552  74 kerrnelqrlekRllqkeetLdrkeeslekkeesleekekelkqkeqsleekeeeleelveeqrqeLerisgLtkee 150
                                       +er +el++  +Rl    + L +k+ +l++k+++l+ek+++lk+ke +++++ ++++++ ++q+++      L++++
  gi|298674004|ref|YP_003725754.1|  63 EERIQELKQDKERLY---KLLGNKDLQLQNKDNQLTEKDNQLKNKEYQISSMFHKINTVEQKQNNKPHLTDHLKTDD 136
                                       466677777777776...47999*****************************************9988888899998 PP

                           DUF3552 151 Akeilleeveeel 163
                                           ll++++++ 
  gi|298674004|ref|YP_003725754.1| 137 GNPGLLKRLKSKF 149
                                       8888888888765 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   6.7   1.2e-06    0.0053     196     276 ..      43     124 ..       2     138 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-06
                             FAM76 196 laeekesnetskksldsnssdhlv...avtqLkeeiaslkkqleqkdqellekdkkitelkaellekekelre...k 266
                                       +++e++s+e+     + +  d lv    +++Lk++ ++l k l +kd +l +kd ++te   +l +ke ++ +   k
  gi|298674004|ref|YP_003725754.1|  43 KNQETSSDEE-----KNSDVDVLVyeeRIQELKQDKERLYKLLGNKDLQLQNKDNQLTEKDNQLKNKEYQISSmfhK 114
                                       2222222222.....22223334423258999***************************999988888766551115 PP

                             FAM76 267 lkelekeake 276
                                       ++++e++ ++
  gi|298674004|ref|YP_003725754.1| 115 INTVEQKQNN 124
                                       5555555444 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.4   2.5e-05      0.11      29      59 ..      52      94 ..      48     131 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.5e-05
                                      CTTSSEEEEEEESTTCHHH............HHHEHHHHHHHH CS
                      NTP_transf_2 29 lkgSDiDllvvlpeevsre............kkeegleklaei 59
                                       k+SD+D+lv+ ++  +              k    ++k+ + 
  gi|298674004|ref|YP_003725754.1| 52 EKNSDVDVLVYEERIQELKqdkerlykllgnKDLQLQNKDNQL 94
                                      589***********95543545544444444222222333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2266  (0.126387); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 969.98
//
Query:       gi|298674005|ref|YP_003725755.1|  [L=378]
Description: nucleic acid-binding OB-fold tRNA/helicase-type protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-25   88.9   8.4    1.9e-08   34.1   0.3    3.7  4  tRNA_anti-codon  OB-fold nucleic acid binding domain
    8.2e-13   48.1   6.7     0.0028   17.6   0.7    3.3  3  REPA_OB_2        Replication protein A OB domain
    2.3e-12   47.1   2.1    0.00016   21.4   0.2    3.2  3  CDC24_OB3        Cell division control protein 24, OB domain 
     0.0015   18.7   2.9       0.34   11.2   0.4    3.6  3  DUF3127          Domain of unknown function (DUF3127)
  ------ inclusion threshold ------
       0.02   14.7   0.4         12    5.6   0.0    3.2  3  Rep_fac-A_C      Replication factor-A C terminal domain
      0.033   14.5   0.5       0.55   10.6   0.0    2.7  3  DUF961           Bacterial protein of unknown function (DUF96
      0.039   14.0   0.1         21    5.2   0.0    3.1  3  DUF4082          Domain of unknown function (DUF4082)
      0.079   13.0   1.0        1.6    8.7   0.0    2.6  2  CspB_prodomain   Csp protease B prodomain
      0.083   12.5   0.0       0.14   11.8   0.0    1.4  1  DUF2240          Uncharacterized protein conserved in archaea


Domain annotation for each model (and alignments):
>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.3   9.8e-12   1.9e-08       1      71 [.      72     150 ..      72     155 .. 0.87
   2 ?   -1.3   0.0       1.1   2.2e+03      23      32 ..     174     183 ..     171     192 .. 0.88
   3 !   32.5   0.4   3.1e-11   6.2e-08       3      72 ..     183     261 ..     181     265 .. 0.89
   4 !   25.6   0.0   4.6e-09   9.1e-06       2      70 ..     293     369 ..     292     371 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 9.8e-12
                                       EEEEEEEEEEE........EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTT..S-TTSEEEEEEEEEECTTSSEE CS
                   tRNA_anti-codon   1 VtvaGrvtsis........drsggkvifidlrDgtgriqvvlfreeatklaen..lkeGdvvrvtGrvkrrpggele 67 
                                       V++ ++v+s+         d+ +gkv ++++ D+tg+i+++l++ ++ +l e+  +++++ ++++G+ k+ ++g le
  gi|298674005|ref|YP_003725755.1|  72 VKFIAKVVSVFgtkdfnknDGTEGKVGNLIVADETGSIRLTLWD-DKASLIESgeFEVDQSLQISGYAKEGYKG-LE 146
                                       56667777777777888889************************.888877776699*****************.** PP

                                       EEEE CS
                   tRNA_anti-codon  68 lkve 71 
                                       +++ 
  gi|298674005|ref|YP_003725755.1| 147 VHIG 150
                                       *986 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.1
                                       EEETTEEEEE CS
                   tRNA_anti-codon  23 lrDgtgriqv 32 
                                       ++Dgtg i++
  gi|298674005|ref|YP_003725755.1| 174 IEDGTGDINI 183
                                       79****9987 PP

  == domain 3  score: 32.5 bits;  conditional E-value: 3.1e-11
                                       EEEEEEEEE........EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEEC.TTSSEEEE CS
                   tRNA_anti-codon   3 vaGrvtsis........drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrr.pggelelk 69 
                                       + G+v +i         d+s g+v+++++ D+tg+i+v+l++ ++ +l ++++ +d v++  G  ++  +++e+e++
  gi|298674005|ref|YP_003725755.1| 183 ILGKVLNIWdvktfqrkDGSQGRVSNLQIGDDTGKIKVTLWD-DKADLVKEVDYNDNVEIInGFARTNnYNQEVEIQ 258
                                       668888888888888999************************.*************************666699999 PP

                                       EEE CS
                   tRNA_anti-codon  70 vee 72 
                                       + +
  gi|298674005|ref|YP_003725755.1| 259 IGN 261
                                       865 PP

  == domain 4  score: 25.6 bits;  conditional E-value: 4.6e-09
                                       EEEEEEEEEE........EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTSSEEEE CS
                   tRNA_anti-codon   2 tvaGrvtsis........drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpggelelk 69 
                                       +v+G v+           d+s++ v++i l D+tgri++ l+  e+ +l ++l+ ++ ++v   + k  ++ ++el+
  gi|298674005|ref|YP_003725755.1| 293 SVEGAVSGLGdikeftkkDGSTNTVANIYLSDDTGRIRIALWG-EKANLIDQLDFDSKIQVIdATSKPGYQDDVELS 368
                                       6677777777777777889************************.*****************9999999988889987 PP

                                       E CS
                   tRNA_anti-codon  70 v 70 
                                       +
  gi|298674005|ref|YP_003725755.1| 369 A 369
                                       6 PP

>> REPA_OB_2  Replication protein A OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   7.4e-06     0.015       3      71 ..      62     128 ..      60     155 .. 0.84
   2 !   17.6   0.7   1.4e-06    0.0028      12      70 ..     180     238 ..     169     260 .. 0.78
   3 !   17.3   0.1   1.7e-06    0.0033      13      65 ..     292     342 ..     281     359 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.4e-06
                         REPA_OB_2   3 elenvekdsivDvigvvksveevseitskstekelkkreltlvDesgasvevtlWgkeaekfesseepv 71 
                                       ++++++ ++ v  i+ v sv  ++++++ +++ e k  +l + De+g s+++tlW+++a+ +es+e +v
  gi|298674005|ref|YP_003725755.1|  62 KISDISPNNNVKFIAKVVSVFGTKDFNKNDGT-EGKVGNLIVADETG-SIRLTLWDDKASLIESGEFEV 128
                                       67889999999****9*****99999888777.99**********98.7*********99999777665 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 1.4e-06
                         REPA_OB_2  12 ivDvigvvksveevseitskstekelkkreltlvDesgasvevtlWgkeaekfe..sseep 70 
                                        + ++g v ++ +v+++++k+++ + +  +l++ D++g +++vtlW+++a+ ++    +++
  gi|298674005|ref|YP_003725755.1| 180 DINILGKVLNIWDVKTFQRKDGS-QGRVSNLQIGDDTG-KIKVTLWDDKADLVKevDYNDN 238
                                       48899****************99.9999*********9.59*******9988774434444 PP

  == domain 3  score: 17.3 bits;  conditional E-value: 1.7e-06
                         REPA_OB_2  13 vDvigvvksveevseitskstekelkkreltlvDesgasvevtlWgkeaekfe 65 
                                         v g v+ +++++e+t+k+++ + +  ++ l D++g+ ++++lWg++a+ ++
  gi|298674005|ref|YP_003725755.1| 292 YSVEGAVSGLGDIKEFTKKDGS-TNTVANIYLSDDTGR-IRIALWGEKANLID 342
                                       557799999***********99.88889********96.9*******998776 PP

>> CDC24_OB3  Cell division control protein 24, OB domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0     3e-06    0.0059       8      87 ..      71     175 ..      67     182 .. 0.74
   2 !   21.4   0.2   8.2e-08   0.00016       5      59 ..     177     233 ..     174     282 .. 0.72
   3 !    8.4   0.0   0.00082       1.6      12      57 ..     301     343 ..     290     354 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3e-06
                         CDC24_OB3   8 nvtLlGrvvai.....freknsek.kkmdryslrieDttGaidatlweeagklhfk..................... 57 
                                       nv  +++vv +     f   n+++ ++ ++ +l ++D+tG+i++tlw+  + l+++                     
  gi|298674005|ref|YP_003725755.1|  71 NVKFIAKVVSVfgtkdF---NKNDgTEGKVGNLIVADETGSIRLTLWDDKASLIESgefevdqslqisgyakegykg 144
                                       7889999****775444...333334566669******************999999988788877777777777777 PP

                         CDC24_OB3  58 .rlrvGhlvllsgLatsetkqskklevswve 87 
                                        ++ +G++  +++     ++  +++++ ++e
  gi|298674005|ref|YP_003725755.1| 145 lEVHIGQYGTIDEADERIDTSANSQKIEYIE 175
                                       7777777777776666666655566666666 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 8.2e-08
                         CDC24_OB3   5 kmlnvtLlGrvvai.....freknsekkkmdryslrieDttGaidatlweeagklhfkrl 59 
                                        + ++ +lG+v +i     f+ k+++  + ++++l+i D+tG+i++tlw+  + l++  +
  gi|298674005|ref|YP_003725755.1| 177 GTGDINILGKVLNIwdvktFQRKDGS--QGRVSNLQIGDDTGKIKVTLWDDKADLVKE-V 233
                                       566899********997766555554..45666******************9998887.3 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.00082
                         CDC24_OB3  12 lGrvvaifreknsekkkmdryslrieDttGaidatlweeagklhfk 57 
                                       lG + +   +k+++++++   ++ + D+tG i+++lw e ++l+++
  gi|298674005|ref|YP_003725755.1| 301 LGDIKEF-TKKDGSTNTV--ANIYLSDDTGRIRIALWGEKANLIDQ 343
                                       4444444.4555555444..59*****************9998876 PP

>> DUF3127  Domain of unknown function (DUF3127)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.25     5e+02       5      62 ..      77     134 ..      74     139 .. 0.66
   2 !   11.2   0.4   0.00017      0.34       2      63 ..     183     242 ..     182     262 .. 0.80
   3 ?    4.4   0.0     0.022        44      37      62 ..     327     352 ..     293     363 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.25
                           DUF3127   5 kiikilptqegssknG.efkkrefvleteeqYpkkiclevvgdkideld..klqvgdevkv 62 
                                       k+++++ t++++++ G e k  ++++  e     +i l++++dk+++++  +++v++++++
  gi|298674005|ref|YP_003725755.1|  77 KVVSVFGTKDFNKNDGtEGKVGNLIVADE---TGSIRLTLWDDKASLIEsgEFEVDQSLQI 134
                                       56666666666666666666666666555...35789999999999886224666666665 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00017
                           DUF3127   2 itGkiikilptqegssknGefkkrefvlete.eqYpkkiclevvgdkideldklqvgdevkvs 63 
                                       i Gk+ +i ++++++ k G   ++  v + + ++   ki++++++dk+d+++++  +d+v++ 
  gi|298674005|ref|YP_003725755.1| 183 ILGKVLNIWDVKTFQRKDG---SQGRVSNLQiGDDTGKIKVTLWDDKADLVKEVDYNDNVEII 242
                                       6799999999999999977...3455555554566789**********************984 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.022
                           DUF3127  37 kkiclevvgdkideldklqvgdevkv 62 
                                        +i + ++g+k++++d+l  + +++v
  gi|298674005|ref|YP_003725755.1| 327 GRIRIALWGEKANLIDQLDFDSKIQV 352
                                       57899******************998 PP

>> Rep_fac-A_C  Replication factor-A C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.015        30      58      79 ..     100     121 ..      97     133 .. 0.88
   2 ?    5.6   0.0    0.0062        12      57      80 ..     208     231 ..     200     277 .. 0.81
   3 ?    0.6   0.0      0.21   4.2e+02      55      79 ..     317     341 ..     309     356 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.015
                                       EEEE-SS-EEEEEEEHHHHHHH CS
                       Rep_fac-A_C  58 ikvsDstgqlwvtlFneaaekl 79 
                                       + v+D+tg++++tl++++a  +
  gi|298674005|ref|YP_003725755.1| 100 LIVADETGSIRLTLWDDKASLI 121
                                       5699**************9765 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0062
                                       EEEEE-SS-EEEEEEEHHHHHHHH CS
                       Rep_fac-A_C  57 sikvsDstgqlwvtlFneaaekll 80 
                                       ++++ D tg++ vtl++++a  + 
  gi|298674005|ref|YP_003725755.1| 208 NLQIGDDTGKIKVTLWDDKADLVK 231
                                       789****************98665 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.21
                                       EEEEEEE-SS-EEEEEEEHHHHHHH CS
                       Rep_fac-A_C  55 ilsikvsDstgqlwvtlFneaaekl 79 
                                       + +i +sD tg++++ l+ e+a+ +
  gi|298674005|ref|YP_003725755.1| 317 VANIYLSDDTGRIRIALWGEKANLI 341
                                       567889**************99865 PP

>> DUF961  Bacterial protein of unknown function (DUF961)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.32   6.5e+02      60      89 ..      61      90 ..      58     105 .. 0.77
   2 ?   10.6   0.0   0.00027      0.55      36      86 ..     202     254 ..     175     264 .. 0.77
   3 ?   -2.4   0.0       3.2   6.4e+03      42      76 ..     319     355 ..     305     358 .. 0.57

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.32
                            DUF961 60 agvkefeyedeVkLvnpkieavgnsingra 89
                                      ++ ++++++++Vk ++ ++++ g++ ++++
  gi|298674005|ref|YP_003725755.1| 61 VKISDISPNNNVKFIAKVVSVFGTKDFNKN 90
                                      57788999***********99999965544 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00027
                            DUF961  36 vkartyklyssaqgedieVtipaeag..vkefeyedeVkLvnpkieavgnsin 86 
                                        ++r  +l+     ++i+Vt+  +    vke +y+d+V+++n  +++ +++++
  gi|298674005|ref|YP_003725755.1| 202 SQGRVSNLQIGDDTGKIKVTLWDDKAdlVKEVDYNDNVEIINGFARTNNYNQE 254
                                       44777778877888899999976443238*****************9999865 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 3.2
                            DUF961  42 klyssaqgedieVtip.aeagv.kefeyedeVkLvnp 76 
                                       ++y s   + i + +  ++a++  ++++++++++++ 
  gi|298674005|ref|YP_003725755.1| 319 NIYLSDDTGRIRIALWgEKANLiDQLDFDSKIQVIDA 355
                                       5555555555555554133443146788888887765 PP

>> DUF4082  Domain of unknown function (DUF4082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.033        65      38      62 ..     103     127 ..      88     137 .. 0.87
   2 ?    5.2   0.0      0.01        21      38      81 ..     212     258 ..     199     275 .. 0.71
   3 ?    1.3   0.0      0.16   3.2e+02      25      62 ..     310     347 ..     305     370 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.033
                           DUF4082  38 agntgthtgslWsatgtlLasatft 62 
                                       a++tg+++ +lW+ + +l+ s+ f+
  gi|298674005|ref|YP_003725755.1| 103 ADETGSIRLTLWDDKASLIESGEFE 127
                                       689*****************99997 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.01
                           DUF4082  38 agntgthtgslWsatgtlLasatftne..tasG.wqtvtlsspvavt 81 
                                        ++tg+++++lW+ + +l++++  +++     G  +t ++++ v+++
  gi|298674005|ref|YP_003725755.1| 212 GDDTGKIKVTLWDDKADLVKEVDYNDNveIINGfARTNNYNQEVEIQ 258
                                       468****************9997776522233433555555555555 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.16
                           DUF4082  25 vdGsitgvrfykgagntgthtgslWsatgtlLasatft 62 
                                       +dGs + v     +++tg +++ lW ++ +l+ +  f 
  gi|298674005|ref|YP_003725755.1| 310 KDGSTNTVANIYLSDDTGRIRIALWGEKANLIDQLDFD 347
                                       556666665444479**********9999988877665 PP

>> CspB_prodomain  Csp protease B prodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00083       1.6      61      86 ..     150     175 ..     131     177 .. 0.91
   2 ?    2.1   0.2     0.098   1.9e+02      39      83 ..     233     282 ..     217     287 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00083
                    CspB_prodomain  61 ngYAivtipeskieelaalpeieYiE 86 
                                       ++Y+ +    ++i++ a++++ieYiE
  gi|298674005|ref|YP_003725755.1| 150 GQYGTIDEADERIDTSANSQKIEYIE 175
                                       78999999*****************9 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.098
                    CspB_prodomain  39 vkysgdleele.....eelgieveeLlngYAivtipeskieelaalpeie 83 
                                       v y++++e ++     ++++ eve  +++Y++++  +++++   +++ ie
  gi|298674005|ref|YP_003725755.1| 233 VDYNDNVEIINgfartNNYNQEVEIQIGNYGLIKKTNTNVDYNEHFTPIE 282
                                       78999999999999999999999999******998888888766666665 PP

>> DUF2240  Uncharacterized protein conserved in archaea (DUF2240)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   7.2e-05      0.14      84     135 ..       4      53 ..       1      61 [. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.2e-05
                           DUF2240  84 kstferildaiaastgiekkevvaeinelqeelkglvdveaaalvvakkegv 135
                                        + +++i d +     i++++  +++ e+ e+++gl d ++aal+va++ gv
  gi|298674005|ref|YP_003725755.1|   4 TEEIDKIYDKLED--SISREDFLSKVDEKVEQMSGLCDRKTAALLVANDLGV 53 
                                       5677888888877..89********************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2578.19
//
Query:       gi|298674006|ref|YP_003725756.1|  [L=208]
Description: phosphotransferase KptA/Tpt1 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    8.4e-26   91.1   0.0    1.1e-25   90.8   0.0    1.1  1  PTS_2-RNA  RNA 2'-phosphotransferase, Tpt1 / KptA family
  ------ inclusion threshold ------
      0.071   12.9   0.0       0.21   11.5   0.0    1.9  1  OST-HTH    OST-HTH/LOTUS domain
      0.087   12.9   0.0        0.1   12.7   0.0    1.1  1  GvpH       GvpH


Domain annotation for each model (and alignments):
>> PTS_2-RNA  RNA 2'-phosphotransferase, Tpt1 / KptA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.8   0.0   1.8e-29   1.1e-25       3     179 ..      32     194 ..      30     195 .. 0.90

  Alignments for each domain:
  == domain 1  score: 90.8 bits;  conditional E-value: 1.8e-29
                         PTS_2-RNA   3 evqlskaLsyiLRhgaekegLkiredGyvkvedlLelpklkslkvtleeikevVesndKqRFelveleelliranqg 79 
                                       e++l+k +s  LRh ++ +gL+++++G+v++++  +  k k + +t e++ ++Ves+ K+R+e   +++ ++ra  g
  gi|298674006|ref|YP_003725756.1|  32 EERLGKFVSGALRHFPNATGLEMDKKGWVNLDQFCNILKQKYKWATKESLISLVESDIKNRYE---IDGGYLRACYG 105
                                       6799*****************************99977777666*******************...8889******* PP

                         PTS_2-RNA  80 hsikkvesselllepiesaeelpevvvHgTylkawesilasggLkrmsrnhihlatglpgekevisgmrksaevliy 156
                                       hs+ +  +   +l++ e   +lp  +++g + ++ + il ++g+k+++++++hl+t+  g+++    + +++ ++i 
  gi|298674006|ref|YP_003725756.1| 106 HSV-D--V---ELDHCEC--DLPY-LYYGVSQEEADMIL-ENGIKPVHQRYVHLSTSY-GKANDAAQVHTDNPIIIK 171
                                       **5.2..2...3777543..4676.**************.99**************97.56778888999******* PP

                         PTS_2-RNA 157 idvekaladgikfyvsengviLt 179
                                       idv+ a ++g++f+ ++++++L+
  gi|298674006|ref|YP_003725756.1| 172 IDVDVARENGMSFMSATDEIVLA 194
                                       *******************9996 PP

>> OST-HTH  OST-HTH/LOTUS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.5e-05      0.21      15      36 ..      53      74 ..      35      97 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.5e-05
                                      HHTTTTSBEHHHHHHHHHHHHS CS
                           OST-HTH 15 rsdpdgwvslsrlgslykkkyg 36
                                        d++gwv+l+++++ +k+ky+
  gi|298674006|ref|YP_003725756.1| 53 EMDKKGWVNLDQFCNILKQKYK 74
                                      33999***************97 PP

>> GvpH  GvpH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.7e-05       0.1      37     137 ..      92     192 ..      63     205 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.7e-05
                              GvpH  37 ssridrGraridydydvsiGlG..dadssstdeenaddasdaeqrsgqqrttedsihvetrasddsdelvvvadlpG 111
                                          id G  r  y ++v + l   + d +    + +++ +d    +g + + +  +h+ t  ++ +d   v +d p 
  gi|298674006|ref|YP_003725756.1|  92 RYEIDGGYLRACYGHSVDVELDhcECDLPYLYYGVSQEEADMILENGIKPVHQRYVHLSTSYGKANDAAQVHTDNPI 168
                                       5579***********999999866778899999*********999******************************** PP

                              GvpH 112 vtdedvdvaletdeqaltlrvdddvv 137
                                       +   dvdva e  ++   ++  d++v
  gi|298674006|ref|YP_003725756.1| 169 IIKIDVDVARE--NGMSFMSATDEIV 192
                                       *********99..5555566666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1396.71
//
Query:       gi|298674007|ref|YP_003725757.1|  [L=334]
Description: RNA 3'-phosphate cyclase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.6e-78  263.0   0.0    1.8e-78  262.8   0.0    1.0  1  RTC         RNA 3'-terminal phosphate cyclase
    5.9e-14   52.4   0.0      1e-13   51.7   0.0    1.4  1  RTC_insert  RNA 3'-terminal phosphate cyclase (RTC), insert d


Domain annotation for each model (and alignments):
>> RTC  RNA 3'-terminal phosphate cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  262.8   0.0     2e-82   1.8e-78       1     222 []       8     322 ..       8     322 .. 0.99

  Alignments for each domain:
  == domain 1  score: 262.8 bits;  conditional E-value: 2e-82
                                       STTTSTHHHHHHHHHHHHH---EEEESTTTTSSS-S--HHHHHHHHHHHHHHT-EEE--STT-SEEEEE------SE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RTC   1 lgegGgqiLRtalaLsaltgkpvrIenIRanRkkPGLraqhltavrllakitnaevegaeigsteleFkPgeikage 77 
                                       +gegGgqi+Rta+aLsa tgk+v+I+nIR+ R++PGL++qh+++++ +a+i+na+++g+ +gs ++ F Pgeik+g 
  gi|298674007|ref|YP_003725757.1|   8 YGEGGGQIVRTAIALSATTGKSVKIYNIRKFRSNPGLKKQHIKTLETAARICNAQIDGEYLGSLRISFFPGEIKGGY 84 
                                       69*************************************************************************** PP

                                       EEEEEESSEBHHHHHHHHHHHHTTSSS-EEEEEEEBSBBTTS--HHHHHHTHHHHHHHHT.-EEEEEEEE--BTTTB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RTC  78 yevdigtAGsitlllqtllplllfakkpseltlkGgTnvsaapsvdylktvllpllkrfgvlelelelkkrGfypkG 154
                                       ++vdi+tAGsitlllq+++pl++ ++++++l+++GgT+v ++p++dylk++++ +l+++g ++++++  +rG+ypkG
  gi|298674007|ref|YP_003725757.1|  85 FDVDIKTAGSITLLLQCIMPLVIKSNEDIQLKITGGTDVAWSPTIDYLKHITVTALSKMG-YTCDIKNIRRGYYPKG 160
                                       ************************************************************.8*************** PP

                                       -EEEEEEEE-.-S---EB........................................................... CS
                                       xxxxxxxxxxxxxxxxxx........................................................... RF
                               RTC 155 gGevelevepskklkpie........................................................... 172
                                       +G v ++++  kkl++++                                                           
  gi|298674007|ref|YP_003725757.1| 161 QGVVYANLKS-KKLHKFNfcnqkttvskiygishcsnlpehiaqrqaesasyhlnyknfdcniatevtnnpskgtgi 236
                                       ********97.479999999********************************************************* PP

                                       .....................................BSS-HHHHHHHHHHHHHHT.-EEEEESS--HHHHHHHHHH CS
                                       .....................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RTC 173 .....................................acvDehlqdqlilfmaLakgksrirvaeltlhtetairvi 212
                                                                            a vD +l+dqli++m L +g ++++v+++t+ht+t+i+v+
  gi|298674007|ref|YP_003725757.1| 237 tlwknlcggsalgkrgfpaeevgkkaadkvsvelesgADVDINLADQLIPYMGLVPG-CSYTVKDITQHTKTNIWVT 312
                                       ********************************************************9.67***************** PP

                                       HHHSS-EEEE CS
                                       xxxxxxxxxx RF
                               RTC 213 eqflgvkfkv 222
                                       e+fl+v+f++
  gi|298674007|ref|YP_003725757.1| 313 EKFLDVEFNI 322
                                       ********97 PP

>> RTC_insert  RNA 3'-terminal phosphate cyclase (RTC), insert domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   0.0   1.1e-17     1e-13       5     101 ..     184     269 ..     180     271 .. 0.90

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 1.1e-17
                                       --SEEEEEEEEESS-THHHHHHHHHHHHHHTTTSSEEEEEEE.EE-CGGC-SS-EEEEEEEEE-T.TS-EEEEEEEE CS
                        RTC_insert   5 rvkrirGvafaarvspsvanrmveaargvLnkllpdvyiytdvvkegkesgkspGfgisLvaetttegvllgaealg 81 
                                       +v++i G++++++++ ++a+r++e+a   Ln    d++i+t+v     +++ s+G+gi+L+          g++alg
  gi|298674007|ref|YP_003725757.1| 184 TVSKIYGISHCSNLPEHIAQRQAESASYHLNYKNFDCNIATEV-----TNNPSKGTGITLWKNL------CGGSALG 249
                                       699****************************9999***99994.....567789*******777......689**** PP

                                       -TT--HHHHHHHHHHHHHHH CS
                        RTC_insert  82 ekgvppedvGeeaaeeLlee 101
                                       ++g p+e+vG++aa+++  e
  gi|298674007|ref|YP_003725757.1| 250 KRGFPAEEVGKKAADKVSVE 269
                                       **************987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.67s 00:00:01.24 Elapsed: 00:00:00.72
# Mc/sec: 1395.71
//
Query:       gi|298674008|ref|YP_003725758.1|  [L=467]
Description: FAD-dependent pyridine nucleotide-disulfide oxidoreductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-47  162.6   1.5    1.5e-47  162.2   1.5    1.1  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
    8.7e-23   80.7   5.6    7.3e-17   61.7   0.5    3.4  3  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
    2.4e-15   56.6   2.8    1.1e-10   41.3   0.6    2.3  2  Pyr_redox_3      Pyridine nucleotide-disulphide oxidoreductas
    9.1e-15   54.9   0.0    2.6e-14   53.4   0.0    1.7  1  Pyr_redox_dim    Pyridine nucleotide-disulphide oxidoreductas
      2e-11   44.1   4.1    0.00048   19.8   0.1    4.2  4  DAO              FAD dependent oxidoreductase
    1.6e-10   40.7   0.8      5e-07   29.2   0.0    3.0  3  K_oxygenase      L-lysine 6-monooxygenase (NADPH-requiring)
    5.3e-08   32.4   5.0      6e-05   22.3   0.1    3.4  3  FAD_binding_2    FAD binding domain
    5.3e-06   25.4   8.6      0.045   12.5   0.0    4.1  4  HI0933_like      HI0933-like protein
    0.00037   20.7   1.6      0.013   15.7   0.2    2.4  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0013   18.8   1.7        1.4    8.9   0.2    2.6  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
     0.0013   17.9   1.2        0.2   10.7   0.1    2.9  3  Lycopene_cycl    Lycopene cyclase protein
     0.0013   19.1   0.2        0.1   13.1   0.0    2.4  2  NAD_binding_7    Putative NAD(P)-binding
     0.0021   18.2   2.3     0.0088   16.3   0.1    2.4  2  NAD_binding_8    NAD(P)-binding Rossmann-like domain
     0.0032   17.4   7.7      0.024   14.5   1.6    3.5  3  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
     0.0038   16.6   0.3        1.9    7.8   0.0    2.3  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
      0.004   17.8   4.8      0.086   13.5   0.1    2.7  2  PglD_N           PglD N-terminal domain
     0.0061   16.0   1.1       0.34   10.2   0.3    2.5  2  ThiF             ThiF family
     0.0067   15.7   3.6        7.5    5.7   0.0    3.3  4  FAD_binding_3    FAD binding domain
     0.0073   16.0   0.4        2.2    7.9   0.0    2.4  2  ApbA             Ketopantoate reductase PanE/ApbA
  ------ inclusion threshold ------
      0.011   16.0   0.3       0.89    9.8   0.0    2.7  2  TrkA_N           TrkA-N domain
      0.044   13.5   0.1        0.1   12.3   0.1    1.6  1  DUF1699          Protein of unknown function (DUF1699)
      0.051   13.6   0.4        4.1    7.4   0.0    2.6  2  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
      0.076   12.1   8.5       0.14   11.3   0.9    3.2  3  GIDA             Glucose inhibited division protein A
       0.18   12.4   3.4       0.73   10.5   0.0    3.0  3  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
       0.85    8.9  10.7         10    5.3   0.3    3.5  4  FAD_oxidored     FAD dependent oxidoreductase


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.2   1.5   2.1e-50   1.5e-47       2     294 .]      14     323 ..      13     323 .. 0.89

  Alignments for each domain:
  == domain 1  score: 162.2 bits;  conditional E-value: 2.1e-50
                                       SEEEE--SHHHHHHHHHHHHH.TS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.HHHHCHHHH.CCCCHCCTC CS
                                       xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx.xxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqa.gakvtlvelegtclnggcllskallgvaedaeias.evvkklnqg.ielllgeev 75 
                                       d+v+iGgG+ G+a+a++++++ ++++ +++++ ++ + +c ++ +l+g   d + +  ++++ ++   i+++l+++v
  gi|298674008|ref|YP_003725758.1|  14 DLVIIGGGAVGMAVATHVQRHgNYNIKVLSKDSHTAYSQCGMPFVLAGDIPDFNKLIvKNLQFFKDMgIDVRLNTQV 90 
                                       89******************769*******************99888877777765574445555444********* PP

                                       EEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BC.TCTTC...TTBEECCSECHHHHHHCCSS-T.SEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx..xxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                       Pyr_redox_2  76 vkidpgkkkvklekkkegdeekiaydklvlAtGssprdl.gipGv..aenvgklvrtldsaealklkllp.krivvv 148
                                        +id ++++v+ +        ++ ydklv+AtGssp ++ +++    ++nv++l rtl +  +++ +l + k++vv+
  gi|298674008|ref|YP_003725758.1|  91 NSIDLENHTVHTQI------DTVRYDKLVIATGSSPSIPePLKEFikMDNVFTL-RTLSDGIKIQNNLEKsKNLVVI 160
                                       ************43......37*****************999977766888777.******9999999889****** PP

                                       S-SHHHHHHHHHHHHHT-EEEEEESSSSSS.TTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE....EEE.EE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxx.xx RF
                       Pyr_redox_2 149 GgGyiGvElAaalaklgkevtlveardrll.raldkelsaaleealekeGvevklgtsvkeidgnge....kle.vv 219
                                       G+G iGvE+A a  k g  +tl+ + +++l  +ld+++s++l+++l  +G+++ +g++++ i+g ++     ++  +
  gi|298674008|ref|YP_003725758.1| 161 GAGGIGVEIAVAGVKRGISTTLINRSKNVLsHNLDSDMSQILQNHLDSKGINLLTGHTPVSINGSDTaesvTIKeNI 237
                                       ******************************************************************97744333666 PP

                                       ETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBE....S.STTEEE-GGGC.......TECCSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x.xxxxxxxxxxx.......xxxxxx RF
                       Pyr_redox_2 220 ledgeeidadlvvvavGvrpstelleeklglelderggivvdeflrt....n.vpgiyaiGDva.......ggkggp 284
                                       +++ + i +d++v+++Gv p+ +l+ +++g+ + e gg++v+ +l++    +  ++++a G +a       g+  + 
  gi|298674008|ref|YP_003725758.1| 238 TGKIKNISVDTIVISTGVNPEVSLA-KNAGISVGESGGLLVNNKLQVkydnKyLDDVFAGGECAqvydfvtGNPFVS 313
                                       666677******************9.*******************98777535899********9999999999999 PP

                                       --HHHHHHHH CS
                                       xxxxxxxxxx RF
                       Pyr_redox_2 285 elaqaAvqqG 294
                                       +la +A +++
  gi|298674008|ref|YP_003725758.1| 314 QLASTARRMA 323
                                       9999999886 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.1    0.0012      0.87       2      23 ..      15      36 ..      14      50 .. 0.84
   2 !    9.6   0.0    0.0019       1.4      50      72 ..      77      99 ..      63     107 .. 0.78
   3 !   61.7   0.5     1e-19   7.3e-17       2      79 ..     157     234 ..     156     239 .. 0.96

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0012
                                      EEEECSSHHHHHHHHHHHHTTS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgk 23
                                      +v++GgG +g+ +A+  +++g+
  gi|298674008|ref|YP_003725758.1| 15 LVIIGGGAVGMAVATHVQRHGN 36
                                      79*************9999985 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0019
                                      HHHTTEEEECSEEEEEEEEETTS CS
                         Pyr_redox 50 lekngievllntkveeiegsedg 72
                                      ++++gi+v+lnt+v++i+ ++ +
  gi|298674008|ref|YP_003725758.1| 77 FKDMGIDVRLNTQVNSIDLENHT 99
                                      6899*************987765 PP

  == domain 3  score: 61.7 bits;  conditional E-value: 1e-19
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEE CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkll.rllDeeaskilqeklekngievllntkveeiegsedgvesvk 77 
                                       +vv+G+G ig+E A a  + g ++t++ rs+++l  +lD ++s+ilq++l  +gi++l+++++++i+gs+   esv+
  gi|298674008|ref|YP_003725758.1| 157 LVVIGAGGIGVEIAVAGVKRGISTTLINRSKNVLsHNLDSDMSQILQNHLDSKGINLLTGHTPVSINGSDT-AESVT 232
                                       8*********************************************************************9.69999 PP

                                       EE CS
                         Pyr_redox  78 lk 79 
                                       +k
  gi|298674008|ref|YP_003725758.1| 233 IK 234
                                       97 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   1.4e-05      0.01       1      33 [.      16      48 ..      16      53 .. 0.92
   2 !   41.3   0.6   1.5e-13   1.1e-10      93     291 ..      79     279 ..      61     288 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.4e-05
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgnig 33
                                      +IiG+G+ G+a+a++++++g  ++ +l k++++
  gi|298674008|ref|YP_003725758.1| 16 VIIGGGAVGMAVATHVQRHGNYNIKVLSKDSHT 48
                                      7**************************999876 PP

  == domain 2  score: 41.3 bits;  conditional E-value: 1.5e-13
                       Pyr_redox_3  93 sfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGef.dk..PnklnipGeek..lvkhyskvkefhkya. 163
                                          ++++l+++V+s++ e+   +v+t+ +t++ +k++iAtG   ++  P k  i+  +   l + +  +k  ++++ 
  gi|298674008|ref|YP_003725758.1|  79 DMGIDVRLNTQVNSIDLEN--HTVHTQIDTVRYDKLVIATGSSpSIpePLKEFIKMDNVftLRTLSDGIKIQNNLEk 153
                                       56799**********9986..79******************832331144444555542224444545554444443 PP

                       Pyr_redox_3 164 gqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeike 240
                                        +++vViG++  +v++A+  v++g + t++ r++++ ++       l  d+ + l++ ++++ i++l+ ++  +i+ 
  gi|298674008|ref|YP_003725758.1| 154 SKNLVVIGAGGIGVEIAVAGVKRGISTTLINRSKNVLSH------NLDSDMSQILQNHLDSKGINLLTGHTPVSING 224
                                       6899*****************************865555......57777777777777666688888888888875 PP

                       Pyr_redox_3 241 kee..eykvktedgkkvev..kddvvlatGykpdlsflkkslfeldedgrpvlte 291
                                       +++  ++++k++ + k+++   d +v+ tG +p++s+ k+++++  e+g  ++++
  gi|298674008|ref|YP_003725758.1| 225 SDTaeSVTIKENITGKIKNisVDTIVISTGVNPEVSLAKNAGISVGESGGLLVNN 279
                                       5540045555443333333424555666***************999998877776 PP

>> Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.0   3.6e-17   2.6e-14       5     106 ..     347     447 ..     345     449 .. 0.94

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 3.6e-17
                                       EESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTH.TEEEEEEEEETTTTBEEEEEEEC.TTHHHHHHHH CS
                     Pyr_redox_dim   5 vftdpevasvGlteeeAkaagieikvgkfpfkangralayae.tkgfvKlvadaktgkvlGahivG.pgageliqel 79 
                                       v  d++v+ vGlte+ A +++  i++++ + +  +ra +y+  +k+++Kl++ +  + + Ga+i+G +g++e+i++l
  gi|298674008|ref|YP_003725758.1| 347 VIGDYQVGNVGLTEKTAYKNK--INTVTGSSTGFTRAGYYPGgEKIYIKLLFSN--RCLSGAQIIGrKGVKERIDGL 419
                                       5679*****************..99999999*********************88..99********999******** PP

                                       HHHHHTTSBHH.HHHTSBSSSSSTGGGG CS
                     Pyr_redox_dim  80 avaikagltve.dladtihihPtlseal 106
                                       ++ai+++++++ +l ++ ++ P++se +
  gi|298674008|ref|YP_003725758.1| 420 SLAIRKKASIDdMLKMETCYTPPVSELV 447
                                       ***********66************865 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   6.7e-07   0.00048       1      32 [.      14      48 ..      14      55 .. 0.89
   2 !   12.0   0.0   0.00016      0.11     146     203 ..      67     119 ..      58     137 .. 0.78
   3 !    8.1   0.8    0.0025       1.8       2      29 ..     157     186 ..     156     193 .. 0.91
   4 ?    1.8   0.0      0.21   1.5e+02     153     205 ..     203     258 ..     196     282 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 6.7e-07
                                      EEEEECTSHHHHHHHHHHHHTT...EEEEESSSST CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg...Vtllekgdia 32
                                      d+viiGGG +G+++A + +r+g   + +l k++  
  gi|298674008|ref|YP_003725758.1| 14 DLVIIGGGAVGMAVATHVQRHGnynIKVLSKDSHT 48
                                      89****************99999*****9999655 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00016
                                       HHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGG CS
                               DAO 146 akltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGaw 203
                                        kl+   ++ +++ G++++++t+v +++ e    ++v  +t+  ++ ++d++V+a+G  
  gi|298674008|ref|YP_003725758.1|  67 NKLIVKNLQFFKDMGIDVRLNTQVNSIDLE---NHTV--HTQiDTV-RYDKLVIATGSS 119
                                       577788889999***************776...6788..6665554.5699******54 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0025
                                       EEEECTSHHHHHHHHHHHHTT..EEEEESS CS
                               DAO   2 vviiGGGiiGlstAyeLarrg..Vtllekg 29 
                                       +v+iG+G iG+ +A +  +rg  +tl+ ++
  gi|298674008|ref|YP_003725758.1| 157 LVVIGAGGIGVEIAVAGVKRGisTTLINRS 186
                                       69***********************99886 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.21
                                       HHHHHHTT-EEEESECEEEEEEEE.TCEEEEE.EECTEEE..EEEEEEEE--GGGHH CS
                               DAO 153 araaealGveilegtevtgleeed.gkvwgve.rttpgen..daadavVnaaGawsd 205
                                       ++ + ++G+++l+g++ ++++  d    ++++ + t g +   ++d++V+++G+   
  gi|298674008|ref|YP_003725758.1| 203 QNHLDSKGINLLTGHTPVSINGSDtAESVTIKeNIT-GKIknISVDTIVISTGVNPE 258
                                       556778899999998888884433322233324333.3332337899******8754 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.014        10       3      38 ..      13      47 ..      11      59 .. 0.83
   2 !   29.2   0.0     7e-10     5e-07     118     227 ..      89     188 ..      69     210 .. 0.76
   3 ?    2.5   0.0     0.092        66     293     340 ..     209     255 ..     199     257 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.014
                       K_oxygenase  3 lDligiGiGpsnLsLailleevkkelkalflerqpe 38
                                       Dl++iG G+  +++a +++ +  + ++ +l + ++
  gi|298674008|ref|YP_003725758.1| 13 QDLVIIGGGAVGMAVATHVQRHG-NYNIKVLSKDSH 47
                                      59999999999999999999999.888888877666 PP

  == domain 2  score: 29.2 bits;  conditional E-value: 7e-10
                       K_oxygenase 118 eveevepdeeeeeelltveskdaegeeeelearnlvlgvGtepkiPevleklegkervvHsseylerkee...llak 191
                                       +v           +  ++e+++ + + ++++  +lv+++G++p+iPe l+++ + ++v+   ++   ++    l+++
  gi|298674008|ref|YP_003725758.1|  89 QV-----------NSIDLENHTVHTQIDTVRYDKLVIATGSSPSIPEPLKEFIKMDNVFTLRTLSDGIKIqnnLEKS 154
                                       33...........3444555555568899999*********************99**99987776655334448999 PP

                       K_oxygenase 192 kriaVvGsGqSaaeifedllrrqkkvelklvtrsea 227
                                       k+++V+G+G  + ei+   ++r    + +l+ rs++
  gi|298674008|ref|YP_003725758.1| 155 KNLVVIGAGGIGVEIAVAGVKRGI--STTLINRSKN 188
                                       ***************998887754..5566666665 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.092
                       K_oxygenase 293 erlrllpnrevesaeaegkgeveltlrneesgeeetlevdavvlATGY 340
                                       + ++ll+ ++  s++ + + +  +t++++ +g+ ++++vd++v++TG 
  gi|298674008|ref|YP_003725758.1| 209 KGINLLTGHTPVSINGSDT-AESVTIKENITGKIKNISVDTIVISTGV 255
                                       5566666666666666653.6789999999****************95 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.1   8.4e-08     6e-05       1      49 [.      14      59 ..      14      68 .. 0.93
   2 ?    4.6   0.2     0.019        14       2      36 ..     157     191 ..     156     200 .. 0.89
   3 !    6.0   0.0    0.0074       5.3     372     405 ..     271     302 ..     237     310 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 8.4e-08
                                      SEEEE--SHHHHHHHHHHHHTTT.-EEEEESSSGGGSGGGG--S-EE-TT CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGl.kvavvekeqefggatawsqGgidavl 49
                                      D+++iG+G+ G+a A+  +++G  ++ v++k +    +ta+sq g+ +vl
  gi|298674008|ref|YP_003725758.1| 14 DLVIIGGGAVGMAVATHVQRHGNyNIKVLSKDS----HTAYSQCGMPFVL 59
                                      89*********************9******999....8********9987 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.019
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36 
                                       ++ViG+G+ G   A++  ++G ++++++  +++ +
  gi|298674008|ref|YP_003725758.1| 157 LVVIGAGGIGVEIAVAGVKRGISTTLINRSKNVLS 191
                                       69*************************99887655 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0074
                                       ES-EEEBETTSBESTTEEESSBTEEE-STCEESS CS
                     FAD_binding_2 372 tmgGvetdengrvldadgqpipGLYAaGevaagg 405
                                         gG+ ++ +++v + d++ +++ +A Ge+a   
  gi|298674008|ref|YP_003725758.1| 271 ESGGLLVNNKLQV-KYDNKYLDDVFAGGECA-QV 302
                                       579**********.****************9.44 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.1   0.00069      0.49       2      29 ..      14      42 ..      13      50 .. 0.77
   2 !   12.5   0.0   6.2e-05     0.045     118     168 ..      76     123 ..      67     124 .. 0.81
   3 ?    4.6   1.1     0.015        11       2      36 ..     156     190 ..     155     196 .. 0.92
   4 ?    1.3   0.1      0.15   1.1e+02     110     164 ..     197     255 ..     191     277 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00069
                                      SEEEE--SHHHHHHHHHHHHTT-.-EEEE CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgk.rVlll 29
                                      d+++iGgGa G+  A +++++g+ ++ +l
  gi|298674008|ref|YP_003725758.1| 14 DLVIIGGGAVGMAVATHVQRHGNyNIKVL 42
                                      89***************977764145555 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 6.2e-05
                                       HHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----S.S-G CS
                       HI0933_like 118 elkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGl.SiP 168
                                         k+ g+++rl+t+v+s++    ++++v+t + ++++ dklv+AtG+  SiP
  gi|298674008|ref|YP_003725758.1|  76 FFKDMGIDVRLNTQVNSIDL---ENHTVHT-QIDTVRYDKLVIATGSSpSIP 123
                                       56899*************44...4467999.99*************742555 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.015
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36 
                                       +++viG+G  G+  A++  krg +++l+++ k+++
  gi|298674008|ref|YP_003725758.1| 156 NLVVIGAGGIGVEIAVAGVKRGISTTLINRSKNVL 190
                                       689**************************999876 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHHHHT-EEE-S--EEEEECET.TE.EEEEE....TTEEEEESEEEE---- CS
                       HI0933_like 110 divdallkelkeagvklrletevksvekee.dgkfrvktk...seeeleadklvlAtGG 164
                                       d+ ++l+++l+++g++l + ++  s++ ++  +++++k +   + ++++ d++v++tG 
  gi|298674008|ref|YP_003725758.1| 197 DMSQILQNHLDSKGINLLTGHTPVSINGSDtAESVTIKENitgKIKNISVDTIVISTGV 255
                                       5668999**********99998888854330344444442434678999999***9995 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   1.9e-05     0.013       2      36 ..      16      48 ..      15      54 .. 0.91
   2 ?    3.8   0.1     0.088        63       2      36 ..     158     189 ..     157     213 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.9e-05
                                      EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHH CS
                   Sacchrp_dh_NADP  2 liiGaGsvGqavaellarhfdvdaeitvadrskek 36
                                      +iiG+G+vG ava  ++rh+++  +i v +++ + 
  gi|298674008|ref|YP_003725758.1| 16 VIIGGGAVGMAVATHVQRHGNY--NIKVLSKDSHT 48
                                      8*********************..9****998765 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.088
                                       EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHH CS
                   Sacchrp_dh_NADP   2 liiGaGsvGqavaellarhfdvdaeitvadrskek 36 
                                       ++iGaG++G  +a   ++++ +    t++ rsk+ 
  gi|298674008|ref|YP_003725758.1| 158 VVIGAGGIGVEIAVAGVKRG-I--STTLINRSKNV 189
                                       8********99987777765.3..46666666665 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.1    0.0027       1.9       8      45 ..       8      45 ..       2      54 .. 0.85
   2 !    8.9   0.2     0.002       1.4      11      47 ..     153     188 ..     145     215 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0027
                                      S..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESS CS
                      Shikimate_DH  8 eslkekkvlliGaGemaelvakhLlakgvkkvvvaNRt 45
                                      ++ k++  ++iG G ++  va+h  ++g  ++ v+  +
  gi|298674008|ref|YP_003725758.1|  8 NNTKKQDLVIIGGGAVGMAVATHVQRHGNYNIKVLSKD 45
                                      4788999********************99999998765 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.002
                                       TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHH CS
                      Shikimate_DH  11 kekkvlliGaGemaelvakhLlakgvkkvvvaNRtle 47 
                                       k+k+ ++iGaG ++ ++a + +++g+   + +NR+ +
  gi|298674008|ref|YP_003725758.1| 153 KSKNLVVIGAGGIGVEIAVAGVKRGIS-TTLINRSKN 188
                                       678999*******************99.888999865 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1   0.00028       0.2       1      28 [.      14      42 ..      14      50 .. 0.78
   2 ?    4.5   0.2      0.02        15       2      38 ..     157     191 ..     156     197 .. 0.89
   3 ?   -1.2   0.0       1.1     8e+02     258     297 ..     293     333 ..     285     346 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00028
                     Lycopene_cycl  1 DvvviGaGpAglslAarl.teakpglkvv 28
                                      D+v+iG+G+ g+++A ++  + ++++kv+
  gi|298674008|ref|YP_003725758.1| 14 DLVIIGGGAVGMAVATHVqRHGNYNIKVL 42
                                      9*****************33345556554 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.02
                     Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieaspsllf 38 
                                       +vviGaG  g+ +A      k g++ +li+ s+++l 
  gi|298674008|ref|YP_003725758.1| 157 LVVIGAGGIGVEIAVAG--VKRGISTTLINRSKNVLS 191
                                       89************988..99********99998865 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.1
                     Lycopene_cycl 258 vlaiGaaaglvhPaTGYsvarsla.eapllasaiaaalres 297
                                       v+a G  a +    TG  ++  la  a+++as+ia+ l e+
  gi|298674008|ref|YP_003725758.1| 293 VFAGGECAQVYDFVTGNPFVSQLAsTARRMASVIAENLLEK 333
                                       66667777777778898888777526899******998754 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   0.00014       0.1       5      73 ..      10     121 ..       8     139 .. 0.75
   2 ?    3.6   0.1      0.12        87       7      41 ..     154     192 ..     151     269 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00014
                     NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleag.akvtvvapevkeele................................... 45 
                                        k++  +++GgG v++  + ++ + g  +++v++++++ + +                                   
  gi|298674008|ref|YP_003725758.1|  10 TKKQDLVIIGGGAVGMAVATHVQRHGnYNIKVLSKDSHTAYSqcgmpfvlagdipdfnklivknlqffkdmgidvrl 86 
                                       578899******************99789*******75554467788888888888888888888888888777777 PP

                     NAD_binding_7  46 ....elvklaeeelekdlegad...lviaatddre 73 
                                           + ++l++ +++ +++ +    lvia+ + ++
  gi|298674008|ref|YP_003725758.1|  87 ntqvNSIDLENHTVHTQIDTVRydkLVIATGSSPS 121
                                       77666666777777666665444467777666655 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.12
                     NAD_binding_7   7 gkkvlvvGgGevAarkvrklleagakvtvvapev....k 41 
                                        k+ +v+G+G ++ + +   ++ g   t++        +
  gi|298674008|ref|YP_003725758.1| 154 SKNLVVIGAGGIGVEIAVAGVKRGISTTLINRSKnvlsH 192
                                       6899**********9999999999999999777432321 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   1.2e-05    0.0088       1      31 [.      17      48 ..      17      51 .. 0.93
   2 ?    1.1   0.2      0.64   4.6e+02       1      27 [.     159     185 ..     159     196 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.2e-05
                                      EE--SHHHHHHHHHHHCC.TEEEEEE-SSSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLaka.gfdvlllekrdrl 31
                                      I+G+G+ G++ A + +++ ++++ +l k +++
  gi|298674008|ref|YP_003725758.1| 17 IIGGGAVGMAVATHVQRHgNYNIKVLSKDSHT 48
                                      9*****************9999****999886 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.64
                                       EE--SHHHHHHHHHHHCCTEEEEEE-S CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllek 27 
                                       ++GaG  G  +A +  k+g++ +l+ +
  gi|298674008|ref|YP_003725758.1| 159 VIGAGGIGVEIAVAGVKRGISTTLINR 185
                                       8*******************9999876 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.2     0.067        48       3      31 ..      16      45 ..      14      54 .. 0.79
   2 ?   -1.1   0.0       2.1   1.5e+03      94     125 ..      98     129 ..      81     137 .. 0.78
   3 !   14.5   1.6   3.3e-05     0.024       2      41 ..     157     196 ..     156     256 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.067
                                      EEE--SCCHHHHHHHHHHT.T-EEEEE-S- CS
                           3HCDH_N  3 aviGaGtmGagiaavfasa.gleVvlvdis 31
                                       +iG G +G  +a+ + ++ +++++++  +
  gi|298674008|ref|YP_003725758.1| 16 VIIGGGAVGMAVATHVQRHgNYNIKVLSKD 45
                                      69***************9955677776655 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.1
                                       HHHHHHHHCCS-TTSEEEE--SSS-HHHHCCC CS
                           3HCDH_N  94 rkvfaelekiakpdailasnTSslsiselaea 125
                                       + v ++++++  ++ ++a+ +S   ++ l e 
  gi|298674008|ref|YP_003725758.1|  98 HTVHTQIDTVRYDKLVIATGSSPSIPEPLKEF 129
                                       56788999999999999999887666666655 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 3.3e-05
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHH CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalek 41 
                                       + viGaG +G +ia + +++g++++l+++s++ l + l++
  gi|298674008|ref|YP_003725758.1| 157 LVVIGAGGIGVEIAVAGVKRGISTTLINRSKNVLSHNLDS 196
                                       57******************************99887765 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.1    0.0061       4.4      31      59 ..       7      35 ..       3      55 .. 0.77
   2 !    7.8   0.0    0.0027       1.9      35      71 ..     153     189 ..     126     209 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0061
                                      BS-GTTSEEEEES-SHHHHHHHHHHHHTT CS
                      2-Hacid_dh_C 31 gkelsgktvGiiGlGrIGqavakrlkafg 59
                                       ++ +++ + iiG G++G ava  ++  g
  gi|298674008|ref|YP_003725758.1|  7 ENNTKKQDLVIIGGGAVGMAVATHVQRHG 35
                                      56778999**************9998654 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0027
                                       TTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHH CS
                      2-Hacid_dh_C  35 sgktvGiiGlGrIGqavakrlkafgmkviaydrskkk 71 
                                       + k + +iG+G IG ++a    + g+  + ++rsk+ 
  gi|298674008|ref|YP_003725758.1| 153 KSKNLVVIGAGGIGVEIAVAGVKRGISTTLINRSKNV 189
                                       67899***************99999999999999874 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.1   0.00012     0.086       1      61 [.      14      76 ..      14      82 .. 0.74
   2 ?    4.9   1.3     0.059        42       1      15 [.     156     170 ..     156     184 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00012
                            PglD_N  1 kivIiGaGGhgkvvadiieangeyeiigflDdnkkt.evegypvl.gkaiellkslseeeyev 61
                                      ++vIiG G  g  va  +++ g+y+i+++  d+++  ++ g+p +  ++i + ++l  +++++
  gi|298674008|ref|YP_003725758.1| 14 DLVIIGGGAVGMAVATHVQRHGNYNIKVLSKDSHTAySQCGMPFVlAGDIPDFNKLIVKNLQF 76
                                      58**************************99999864245576543144555555555556555 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.059
                            PglD_N   1 kivIiGaGGhgkvva 15 
                                       ++v+iGaGG g ++a
  gi|298674008|ref|YP_003725758.1| 156 NLVVIGAGGIGVEIA 170
                                       79*********9987 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.048        34      17      51 ..      11      45 ..       2      47 .. 0.84
   2 !   10.2   0.3   0.00048      0.34      11      40 ..     146     176 ..     137     183 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.048
                                      HTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEESS CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 17 rdskvllvGaGglGsellknLalsGvgkltlvDnD 51
                                      +++  +++G G++G  +++   + G  ++++   D
  gi|298674008|ref|YP_003725758.1| 11 KKQDLVIIGGGAVGMAVATHVQRHGNYNIKVLSKD 45
                                      667889***************99999999887555 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00048
                                       HHHHHHHTSE.EEEE--SHHHHHHHHHHHHH CS
                                       xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                              ThiF  11 dgqekLrdsk.vllvGaGglGsellknLals 40 
                                       + q+ L++sk  +++GaGg+G e++++ ++ 
  gi|298674008|ref|YP_003725758.1| 146 KIQNNLEKSKnLVVIGAGGIGVEIAVAGVKR 176
                                       668888886515678*********9875555 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.011       7.5       3      37 ..      14      49 ..      12      57 .. 0.77
   2 ?   -3.4   0.0         6   4.3e+03     118     143 ..      80     105 ..      67     118 .. 0.66
   3 ?    5.5   0.5     0.012       8.3       5      35 ..     158     188 ..     154     193 .. 0.90
   4 ?    3.5   0.0     0.049        35     106     202 ..     197     296 ..     194     336 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.011
                                      EEEEE--SHHHHHHHHHHHHTTHHEE.EEESSSSSC CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvv.lvekrsttv 37
                                      d +I+G+G +G+  a+  +++G  ++ ++ k s t+
  gi|298674008|ref|YP_003725758.1| 14 DLVIIGGGAVGMAVATHVQRHGNYNIkVLSKDSHTA 49
                                      678******************976542555555554 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 6
                                       HTEEETCSEEEECCEECCCCCCCEEE CS
                     FAD_binding_3 118 rglqvrfktevesleqdeegvtaevr 143
                                        g++vr +t+v+s+  ++ +v++++ 
  gi|298674008|ref|YP_003725758.1|  80 MGIDVRLNTQVNSIDLENHTVHTQID 105
                                       45666666666666666666665554 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.012
                                       EEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                     FAD_binding_3   5 lIVGaGpaGlmlallLseaGvrvvlvekrst 35 
                                       +++GaG  G+  a    ++G++++l+++ ++
  gi|298674008|ref|YP_003725758.1| 158 VVIGAGGIGVEIAVAGVKRGISTTLINRSKN 188
                                       69*************************9875 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.049
                                       HHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--GTT-HH..HHHHTGGEEEEE CS
                     FAD_binding_3 106 eleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaDGgrStv..rktlgiefegee 180
                                       ++ +iL +h+ ++g+++  ++  +s++  ++ ++ +++++ tg++++++ + +v   G++  v  +k++gi++ +++
  gi|298674008|ref|YP_003725758.1| 197 DMSQILQNHLDSKGINLLTGHTPVSINGSDTAESVTIKENITGKIKNISVDTIVISTGVNPEVslAKNAGISVGESG 273
                                       57789************************************************999999877644688888888888 PP

                                       EEEEEEEEEEEEEC.-SCCCTTC CS
                     FAD_binding_3 181 tvyeagvldvlfda.dlsdivep 202
                                       ++   + l+v  d   l+d+ ++
  gi|298674008|ref|YP_003725758.1| 274 GLLVNNKLQVKYDNkYLDDVFAG 296
                                       88778888887777666666555 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0     0.003       2.2       2      40 ..      16      54 ..      15     116 .. 0.80
   2 ?    6.1   0.1     0.011         8       2      35 ..     158     192 ..     157     221 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.003
                                      EEES-SHHHHHHHHHHHHHTHC.EEEE-SCHHHHHHHHHC CS
                              ApbA  2 ailGaGaiGsllaakLakagad.vtlilrsrrlealkknG 40
                                      +i+G Ga+G  +a + +++g+  + ++ ++    a ++ G
  gi|298674008|ref|YP_003725758.1| 16 VIIGGGAVGMAVATHVQRHGNYnIKVLSKDS-HTAYSQCG 54
                                      79****************7665154444444.44456655 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.011
                                       EEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHH CS
                              ApbA   2 ailGaGaiGsllaakLakagadvtlilrsr.rlea 35 
                                       +++GaG+iG  +a+   k g   tli+rs+  l +
  gi|298674008|ref|YP_003725758.1| 158 VVIGAGGIGVEIAVAGVKRGISTTLINRSKnVLSH 192
                                       69*************999**********9955544 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0    0.0012      0.89       2      33 ..      16      48 ..      15      69 .. 0.80
   2 ?    3.5   0.1      0.11        82       2      36 ..     158     192 ..     157     210 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0012
                                      EEES-SHHHHHHHHHHHH.TTEEEEEEESSHHH CS
                            TrkA_N  2 iiiGlGrvGrslaeeLse.ggkdvvvidkdeer 33
                                      +iiG G vG+++a  +++ g+ ++ v  kd  +
  gi|298674008|ref|YP_003725758.1| 16 VIIGGGAVGMAVATHVQRhGNYNIKVLSKDSHT 48
                                      8*****************766569999998754 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.11
                                       EEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHH CS
                            TrkA_N   2 iiiGlGrvGrslaeeLseggkdvvvidkdeervee 36 
                                       ++iG+G +G ++a    ++g++ ++i ++++++ +
  gi|298674008|ref|YP_003725758.1| 158 VVIGAGGIGVEIAVAGVKRGISTTLINRSKNVLSH 192
                                       8************9999988779999998877655 PP

>> DUF1699  Protein of unknown function (DUF1699)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00014       0.1      54     103 ..     196     247 ..     182     260 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                           DUF1699  54 ktlsksakmfleiqgielleg..dvwghrkdineyyevseevierikelkse 103
                                         +s+  +  l+ +gi+ll g  +v+   +d  e  +++e+++ +ik++  +
  gi|298674008|ref|YP_003725758.1| 196 SDMSQILQNHLDSKGINLLTGhtPVSINGSDTAESVTIKENITGKIKNISVD 247
                                       679****************974469999*******************98766 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0057       4.1       3      28 ..      16      42 ..      14      52 .. 0.79
   2 ?    3.8   0.1     0.072        52       3      33 ..     158     196 ..     156     246 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0057
                                      EEE--SHHHHHHHHHHHTTT.--EEEE CS
                    NAD_Gly3P_dh_N  3 avlGaGswGtalAkvlaeng.hevrlw 28
                                       ++G+G+ G a+A++++++g  ++++ 
  gi|298674008|ref|YP_003725758.1| 16 VIIGGGAVGMAVATHVQRHGnYNIKVL 42
                                      69****************995455554 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.072
                                       EEE--SHHHHHHHHHHHTTT--EEEE-S-H........H CS
                    NAD_Gly3P_dh_N   3 avlGaGswGtalAkvlaenghevrlwvree........e 33 
                                        v+GaG  G  +A +  ++g +++l+ r++         
  gi|298674008|ref|YP_003725758.1| 158 VVIGAGGIGVEIAVAGVKRGISTTLINRSKnvlshnldS 196
                                       699**********99999999999999988544443333 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2     0.049        35       1      23 [.      14      36 ..      14      54 .. 0.86
   2 ?    0.4   0.0      0.38   2.7e+02     110     150 ..      73     118 ..      66     150 .. 0.62
   3 ?   11.3   0.9   0.00019      0.14       2      29 ..     157     191 ..     156     215 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.049
                                      CEEEE-SSHHHHHHHHHHHHTT- CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGa 23
                                      d+++iGgG  G++ A ++ r G 
  gi|298674008|ref|YP_003725758.1| 14 DLVIIGGGAVGMAVATHVQRHGN 36
                                      689***************99984 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.38
                                       TEEEEES-EEEEEECTTEEEEEEETTS-EEEEC......EEEE--TT CS
                              GIDA 110 nleiieeeveeliveekkvkgvvtedgetikak......avviatGt 150
                                       nl+ ++++  ++ + +++v+ + +e++++ ++       + viatG+
  gi|298674008|ref|YP_003725758.1|  73 NLQFFKDMGIDVRL-NTQVNSIDLENHTVHTQIdtvrydKLVIATGS 118
                                       55556666666655.55555554444443322223333399*****9 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00019
                                       EEEE-SSHHHHHHHHHHHHTT--EEEE.......E CS
                              GIDA   2 viViGgGhAGceAAlaaarlGakvlLi.......t 29 
                                       ++ViG+G  G+e A+a  ++G++++Li        
  gi|298674008|ref|YP_003725758.1| 157 LVVIGAGGIGVEIAVAGVKRGISTTLInrsknvlS 191
                                       69*************************55554443 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0     0.001      0.73       2      37 ..      15      47 ..      14      53 .. 0.83
   2 ?    1.5   0.1      0.62   4.5e+02       2      31 ..     157     183 ..     156     212 .. 0.78
   3 ?   -1.9   0.1       7.3   5.2e+03      77      96 ..     237     255 ..     225     256 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.001
                                      EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCC CS
                     F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpe 37
                                      + iiG+G +g a+a  ++++g  +++i v  s++ +
  gi|298674008|ref|YP_003725758.1| 15 LVIIGGGAVGMAVATHVQRHG--NYNIKVL-SKDSH 47
                                      579******************..8999865.66655 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.62
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEE CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivva 31 
                                       + +iGaG +g  +a   +++g    + +++
  gi|298674008|ref|YP_003725758.1| 157 LVVIGAGGIGVEIAVAGVKRG---ISTTLI 183
                                       579***********9999999...444444 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 7.3
                                       HHHHCGHHHHTTSEEEEESS CS
                     F420_oxidored  77 vlselakdalkgklvisvla 96 
                                       +  ++ k+ + +++vis+ +
  gi|298674008|ref|YP_003725758.1| 237 ITGKI-KNISVDTIVISTGV 255
                                       55566.88899999999865 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.3     0.015        10       1      23 [.      14      36 ..      14      42 .. 0.94
   2 ?   -2.6   0.0       3.8   2.7e+03      97     120 ..      75     101 ..      64     112 .. 0.65
   3 ?    3.7   1.8     0.045        32       2      32 ..     157     187 ..     156     189 .. 0.93
   4 ?    4.1   0.0     0.035        25      89     132 ..     198     242 ..     194     284 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.015
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGa 23
                                      D+v++GGg+ G+a A    r+G 
  gi|298674008|ref|YP_003725758.1| 14 DLVIIGGGAVGMAVATHVQRHGN 36
                                      99****************99995 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.8
                      FAD_oxidored  97 l..aeagvtvllntrlvevekegkr.i 120
                                          ++ g++v lnt++ +++ e+++  
  gi|298674008|ref|YP_003725758.1|  75 QffKDMGIDVRLNTQVNSIDLENHTvH 101
                                       345788999999999999999873322 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.045
                      FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveerg 32 
                                       +vV+G+g  Gv  A+a  ++G ++ L+++++
  gi|298674008|ref|YP_003725758.1| 157 LVVIGAGGIGVEIAVAGVKRGISTTLINRSK 187
                                       79*************************9875 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.035
                      FAD_oxidored  89 akavleemlaeagvtvllntrlvevekegkriesvtveske.g.rk 132
                                       + ++l++ l+ +g+++l+++++v+++ ++ + esvt++++  g  k
  gi|298674008|ref|YP_003725758.1| 198 MSQILQNHLDSKGINLLTGHTPVSINGSD-TAESVTIKENItGkIK 242
                                       67899**********************98.99****9876555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.51
# Mc/sec: 2768.92
//
Query:       gi|298674009|ref|YP_003725759.1|  [L=161]
Description: hypothetical protein Metev_0031 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 978.60
//
Query:       gi|298674010|ref|YP_003725760.1|  [L=452]
Description: TOPRIM domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.8e-12   45.2   0.9    5.7e-11   42.7   0.1    2.5  3  Toprim_4  Toprim domain
    1.2e-05   25.6   0.0    2.9e-05   24.4   0.0    1.7  1  Toprim_2  Toprim-like
  ------ inclusion threshold ------
      0.071   13.3   0.0        0.3   11.3   0.0    2.1  1  Toprim    Toprim domain


Domain annotation for each model (and alignments):
>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.39   2.4e+03      25      50 ..      94     122 ..      92     131 .. 0.71
   2 !   42.7   0.1   9.5e-15   5.7e-11       1      76 [.     182     266 ..     182     280 .. 0.88
   3 ?   -2.7   0.0       1.4   8.5e+03      18      31 ..     423     436 ..     419     450 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.39
                          Toprim_4  25 avlggalspldgirpeklkt.enlve..a 50 
                                       +vl  al++ d ++p + k+  +++e  +
  gi|298674010|ref|YP_003725760.1|  94 SVLAAALETIDRVGPCSAKIeVSKIEdiR 122
                                       68999999999999999998444444553 PP

  == domain 2  score: 42.7 bits;  conditional E-value: 9.5e-15
                          Toprim_4   1 seiiiVEgyaDvlalekagiknvvavlggalspldgirpeklkt.enlve....aekkvkevilaldgDa.....eG 67 
                                       +e+i+VEg+aDvl+l ++gikn++ v g+++ p++ ++++k++  +++++    +  ++ke++++ + D+     eG
  gi|298674010|ref|YP_003725760.1| 182 DEVILVEGRADVLNLLRYGIKNTICVGGTNI-PPEIAELTKKRNvTAFTDgdrgGVLIIKELLQVANIDYiarapEG 257
                                       589****************************.99999999999989999999999999***********99999999 PP

                          Toprim_4  68 eataerlae 76 
                                       + + + + +
  gi|298674010|ref|YP_003725760.1| 258 KSVEDLVHR 266
                                       888877666 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.4
                          Toprim_4  18 agiknvvavlggal 31 
                                        gikn+v v  g++
  gi|298674010|ref|YP_003725760.1| 423 KGIKNLVGVKLGNV 436
                                       48888888866555 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   4.9e-09   2.9e-05       1      86 [.     185     260 ..     185     264 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 4.9e-09
                          Toprim_2   1 vvfEgaiDalSlaqlgikektnvvalgGtalteaalkllerypekkvvlalDnDkaGrkaakrlaellreagvreki 77 
                                       +++Eg  D+l l+++gik   n + +gGt+++++ ++l +++   +v   +D D+ G   +k+l ++++     + i
  gi|298674010|ref|YP_003725760.1| 185 ILVEGRADVLNLLRYGIK---NTICVGGTNIPPEIAELTKKR---NVTAFTDGDRGGVLIIKELLQVAN----IDYI 251
                                       69***************9...********8888888777777...79*************999999985....2446 PP

                          Toprim_2  78 relpegkDw 86 
                                       ++ pegk +
  gi|298674010|ref|YP_003725760.1| 252 ARAPEGKSV 260
                                       667777655 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0     5e-05       0.3       1      91 [.     183     251 ..     183     261 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5e-05
                                       EEEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHSTTEEEEEECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHH CS
                            Toprim   1 elvivEgpsdaktiakalgsgfqavtaslGhildletefkpvyeeiedkkkvlkalkelakradeiilatDpDreGe 77 
                                       e+++vEg +d+ ++ ++   g ++++ + G+ +  e                    +el  +  ++   tD+Dr G 
  gi|298674010|ref|YP_003725760.1| 183 EVILVEGRADVLNLLRY---GIKNTICVGGTNIPPEI-------------------AELT-KKRNVTAFTDGDRGGV 236
                                       5899*************...99999999999998775...................5555.6779999********* PP

                                       HHHHHHHHHHT.HHH CS
                            Toprim  78 aiawellevlk.ell 91 
                                        i +ell+v+  +++
  gi|298674010|ref|YP_003725760.1| 237 LIIKELLQVANiDYI 251
                                       *******99885544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.43s 00:00:01.04 Elapsed: 00:00:00.53
# Mc/sec: 2580.91
//
Query:       gi|298674011|ref|YP_003725761.1|  [L=94]
Description: hypothetical protein Metev_0033 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      3e-35  120.3   0.3    3.4e-35  120.2   0.3    1.0  1  UPF0058    Uncharacterised protein family UPF0058
  ------ inclusion threshold ------
      0.043   13.8   0.2        0.1   12.6   0.0    1.8  2  Ogr_Delta  Ogr/Delta-like zinc finger


Domain annotation for each model (and alignments):
>> UPF0058  Uncharacterised protein family UPF0058
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.2   0.3   3.8e-39   3.4e-35       1      86 [.       1      85 [.       1      86 [. 0.98

  Alignments for each domain:
  == domain 1  score: 120.2 bits;  conditional E-value: 3.8e-39
                                      --HHHHHHHHHHHHHHHHHHTSTT--TTTTHHHHHH---TT-TTS-HHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHH CS
                           UPF0058  1 MhKdeLieLHqllvevkkeleeeevekeefkeYeeLdisPhhihrsKaehkaAifvLgnaiakalsekeessaervskr 79
                                      MhKdeLi+LH+l++++k+++e+++ve + f+eY++L+isP+h+hrsKaehk+AifvLgn iak++se+e+   +r+s+r
  gi|298674011|ref|YP_003725761.1|  1 MHKDELIQLHTLMAQLKRYFECQGVECD-FSEYKSLSISPVHVHRSKAEHKHAIFVLGNDIAKIISEDENMGGGRTSER 78
                                      *************************988.************************************************** PP

                                      HHHHHHH CS
                           UPF0058 80 lkelaek 86
                                      ++ela +
  gi|298674011|ref|YP_003725761.1| 79 MQELAAR 85
                                      ****987 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.1e-05       0.1      16      36 ..       8      30 ..       1      40 [. 0.75
   2 ?   -1.8   0.1      0.35   3.1e+03      12      21 ..      74      83 ..      73      86 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.1e-05
                         Ogr_Delta 16 nlskdvre..ryyqCsnfeCgat 36
                                      +l+++ ++  ry++C+ +eC ++
  gi|298674011|ref|YP_003725761.1|  8 QLHTLMAQlkRYFECQGVECDFS 30
                                      6666677667**********876 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.35
                         Ogr_Delta 12 rtsrnlskdv 21
                                      rts+++ ++ 
  gi|298674011|ref|YP_003725761.1| 74 RTSERMQELA 83
                                      8899888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 700.80
//
Query:       gi|298674012|ref|YP_003725762.1|  [L=174]
Description: ribosomal-protein-alanine acetyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-17   62.9   0.2      4e-17   62.5   0.2    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
      1e-14   54.5   0.1    1.2e-14   54.3   0.1    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    2.5e-12   47.1   1.0    4.4e-12   46.3   1.0    1.4  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    1.7e-06   28.7   0.2    5.1e-06   27.2   0.2    1.8  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
      3e-06   27.1   0.1    4.9e-06   26.4   0.1    1.3  1  FR47             FR47-like protein
    4.2e-05   23.7   0.3    0.00013   22.1   0.2    1.8  2  Acetyltransf_4   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.011   15.2   0.1      0.039   13.4   0.1    1.8  1  Acetyltransf_15  Putative acetyl-transferase
       0.02   15.0   0.0      0.037   14.2   0.0    1.4  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
      0.053   13.6   0.0       0.54   10.3   0.0    2.1  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
      0.065   12.9   0.0       0.25   11.0   0.0    1.9  1  Acetyltransf_8   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.2   2.2e-20     4e-17       3     117 .]      13     120 ..       5     120 .. 0.82

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 2.2e-20
                                       HHHHHHHHHTHHHHHHHHHHH.HHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHH CS
                    Acetyltransf_1   3 dlvellvesffppnedaseee.feesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlG 78 
                                       d+ e+++e+f +  + +++++ f+e+   + +g++va  +++++G++ +++i++   +++ i  laV++ yr kG+G
  gi|298674012|ref|YP_003725762.1|  13 DILEIEMETFSE--HNPFVYInFYEI---NSDGFIVATVGDKVAGYVVGYQIYE---NEGRIFTLAVKKGYRDKGIG 81 
                                       455555554322..222333334555...6679999******************...9******************* PP

                                       HHHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  79 saLlealeerareegikkivlaveedndaairlYeklGF 117
                                       s+Ll+a++  + + g+k+  l+v+ +n++a++lY  +GF
  gi|298674012|ref|YP_003725762.1|  82 SELLRAILNLFCRTGLKYARLEVRRSNVRAQKLYNSMGF 120
                                       *********77777**999***************88**9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   0.1   6.9e-18   1.2e-14      32     124 ..      40     140 ..       9     143 .. 0.88

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 6.9e-18
                   Acetyltransf_10  32 lllvaeeggkivGvi...el.rdgshisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYe 102
                                        ++va++g+k++G++   ++ +++++i  l+V++ yr +Gig++Ll a+++ + + g+k  +l+v+ s+  a+++Y 
  gi|298674012|ref|YP_003725762.1|  40 GFIVATVGDKVAGYVvgyQIyENEGRIFTLAVKKGYRDKGIGSELLRAILNLFCRTGLKYaRLEVRRSNvRAQKLYN 116
                                       4899**********99999989999***************************558999999**************** PP

                   Acetyltransf_10 103 klGFkav..geeqeenGirfvpMe 124
                                       ++GF+++  +++ + +G   + M+
  gi|298674012|ref|YP_003725762.1| 117 SMGFVQCwvEKKYYSDGEDGIIMK 140
                                       ******988888888887777776 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   1.0   2.4e-15   4.4e-12       3      75 ..      39     121 ..      29     122 .. 0.75

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 2.4e-15
                                       EEEEEEEETTEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHHHHTT.....SEEEEE.EEEE..THHHHHHH CS
                    Acetyltransf_7   3 gevfVaeddgkivGfialslld...aeitrlaVdpeyrgkGiGraLleaae.....kgiile.qlel..naekaikf 68 
                                       + ++Va  ++k+ G+++ + +    + i  laV++ yr kGiG++Ll+a+      +g++ + +le+  ++ +a+k+
  gi|298674012|ref|YP_003725762.1|  39 DGFIVATVGDKVAGYVVGYQIYeneGRIFTLAVKKGYRDKGIGSELLRAILnlfcrTGLK-YaRLEVrrSNVRAQKL 114
                                       4588999999****9999888765555555******************822345555533.233333433349**** PP

                                       HHHTTEE CS
                    Acetyltransf_7  69 YeklGFe 75 
                                       Y ++GF+
  gi|298674012|ref|YP_003725762.1| 115 YNSMGFV 121
                                       ******8 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.2   2.8e-09   5.1e-06      52     137 ..      37     120 ..       1     121 [. 0.72

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2.8e-09
                    Acetyltransf_3  52 egygwaivlkdtgviGsv.glrdleeedeeaelgymlapsfwgkGyateavralleyafeelglerlvavidkeNea 127
                                       ++ g+++ + +++v G+v g++ +e+e     + + +++ ++ kG+++e +ra+l+++ ++  l++ + ++  +N +
  gi|298674012|ref|YP_003725762.1|  37 NSDGFIVATVGDKVAGYVvGYQIYENEG--RIFTLAVKKGYRDKGIGSELLRAILNLFCRTG-LKYARLEVRRSNVR 110
                                       3335777665665899996666666653..4556677777******************6555.************** PP

                    Acetyltransf_3 128 SirvleklGf 137
                                        ++++ ++Gf
  gi|298674012|ref|YP_003725762.1| 111 AQKLYNSMGF 120
                                       *********9 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.1   2.7e-09   4.9e-06      15      82 ..      57     125 ..      47     130 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 2.7e-09
                                       EEEE-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-.S-EEEEEETT-HHHHHHHHHHT-EEEEE CS
                              FR47  15 wilrkdggelgalqvlpehrrrGlgsrlvkalakeiaerg.ktvllvvvasNtpsirlyeklGfekiee 82 
                                         + ++ g ++ l v++  r +G gs l +a+ +   + g k + l v+ sN ++++ly+++Gf + + 
  gi|298674012|ref|YP_003725762.1|  57 YQIYENEGRIFTLAVKKGYRDKGIGSELLRAILNLFCRTGlKYARLEVRRSNVRAQKLYNSMGFVQCWV 125
                                       55667889******************************883567899*****************98764 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.65   1.2e+03       2      18 ..       4      20 ..       3      38 .. 0.71
   2 !   22.1   0.2   7.3e-08   0.00013      52     145 ..      41     131 ..      17     139 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.65
                    Acetyltransf_4  2 raateeDakeilaiyae 18
                                      r  ++eD++ il+i  e
  gi|298674012|ref|YP_003725762.1|  4 RYFEPEDFEDILEIEME 20
                                      77889999999999743 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 7.3e-08
                    Acetyltransf_4  52 flvae.sdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiq 127
                                       f va   d+++Gy  + q+    +++++ ++++ +++  +++g+g+el+ a+ + + + ++++   e+  +n  +++
  gi|298674012|ref|YP_003725762.1|  41 FIVATvGDKVAGYVVGYQI----YENEGRIFTLAVKKGYRDKGIGSELLRAILNLFCRTGLKYARLEVRRSNVRAQK 113
                                       4444444555555555544....445665655555588*************************************** PP

                    Acetyltransf_4 128 fhkalGFelvgifkkcik 145
                                       +++++GF     +kk++ 
  gi|298674012|ref|YP_003725762.1| 114 LYNSMGFVQCWVEKKYYS 131
                                       *******88777777765 PP

>> Acetyltransf_15  Putative acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   2.1e-05     0.039      64     138 ..      38     122 ..      17     136 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.1e-05
                   Acetyltransf_15  64 s.................silieknvleiYtlyvsekyrgkGlakklLeeslkelkknYkvdnelllaLHlnpkDks 123
                                       s                  + i +n   i+tl v++ yr kG+  +lL  +    ++ +  +  ++  L +  +   
  gi|298674012|ref|YP_003725762.1|  38 SdgfivatvgdkvagyvvGYQIYENEGRIFTLAVKKGYRDKGIGSELLRAI----LNLFCRTGLKYARLEVRRSNV- 109
                                       4555555555555555554455555558********************999....566666667777776665443. PP

                   Acetyltransf_15 124 MnisfalYyslgFrk 138
                                          +  lY s+gF++
  gi|298674012|ref|YP_003725762.1| 110 --RAQKLYNSMGFVQ 122
                                       ..4556777777766 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.1e-05     0.037      13      59 ..      52      98 ..      34     100 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.1e-05
                   Acetyltransf_CG 13 afl.eYevrkegvldfthTeVpeelrGkGiAkkLvkaalddareeglk 59
                                      +++  Y+   e++  +    V++ +r kGi+++L +a+l+   ++glk
  gi|298674012|ref|YP_003725762.1| 52 GYVvGYQ-IYENEGRIFTLAVKKGYRDKGIGSELLRAILNLFCRTGLK 98
                                      4433676.444566777789*******************988888776 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0    0.0003      0.54       2     100 ..       3      90 ..       2     121 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0003
                                       EEEE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEEEETTEEEEE.EEEE CS
                    Acetyltransf_9   2 irelteedldevlellkyaFqdeespleeireyfrklleesrvlgaedngelvgqlallplelnvpGktlka.agvt 77 
                                       +r+ ++ed++++le+  + F ++++ +    +   + ++++ +++a  +++++g +  ++        +++  + + 
  gi|298674012|ref|YP_003725762.1|   3 LRYFEPEDFEDILEIEMETFSEHNPFV----YINFYEINSDGFIVATVGDKVAGYVVGYQ--------IYENeGRIF 67 
                                       688899999999999999999999986....44556777788888888888888776654........233225567 PP

                                       EEEE-CCGTTS-HHHHHHHHHHH CS
                    Acetyltransf_9  78 gVavapehrgrgvlskLlarale 100
                                         av+  +r +g+ s+Ll++ l+
  gi|298674012|ref|YP_003725762.1|  68 TLAVKKGYRDKGIGSELLRAILN 90 
                                       78899999999999998888775 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00014      0.25      88     138 ..      72     121 ..      21     124 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
                                       SHHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-E CS
                    Acetyltransf_8  88 eaeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfe 138
                                       ++ +r kg++++llra++++  +  + +   +E + +N ra +l++++Gf+
  gi|298674012|ref|YP_003725762.1|  72 KKGYRDKGIGSELLRAILNLFCRT-GLKYARLEVRRSNVRAQKLYNSMGFV 121
                                       567899************977666.9999999******************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1344.51
//
Query:       gi|298674013|ref|YP_003725763.1|  [L=613]
Description: tRNA-guanine transglycosylase, various specificities [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-62  209.9   0.3      5e-62  208.3   0.2    1.8  2  DUF5591   Domain of unknown function (DUF5591)
    2.1e-19   69.9   0.0    2.7e-17   63.0   0.0    2.4  3  TGT       Queuine tRNA-ribosyltransferase
    1.1e-16   60.7   0.0    2.4e-16   59.6   0.0    1.6  1  TGT_C2    Patch-forming domain C2 of tRNA-guanine transglycos
    1.2e-12   47.6   0.2      3e-12   46.3   0.2    1.7  1  PUA       PUA domain


Domain annotation for each model (and alignments):
>> DUF5591  Domain of unknown function (DUF5591)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       0.6   2.7e+03      85     117 ..      51      83 ..      47     108 .. 0.60
   2 !  208.3   0.2   1.1e-65     5e-62       1     154 []     310     461 ..     310     461 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.6
                                       --HHHHHHHHHHHHHHHHHHT-SEEEE---THH CS
                           DUF5591  85 wseeeiefvaellakylektkyekviahleeey 117
                                       w++ +  f +++l++  +k ++++ i+  +++y
  gi|298674013|ref|YP_003725763.1|  51 WKQGKHIFENQYLNQLRQKVSENNLIILPHQNY 83 
                                       555555666666666666666655444444443 PP

  == domain 2  score: 208.3 bits;  conditional E-value: 1.1e-65
                                       X-HHHHHHHHH---S..SSEEEEEE--SSSSGGGSHHHHHHHHHS---...SEEEEE-SS-.EEEGGGTT------- CS
                           DUF5591   1 vkrfrervlerYeppeekkvlvLlPcsakkPyseskshrkfaeaikkrkakvheviltsPlGvvPreleevYPaaqY 77 
                                       ++rf+erv++rY+pp+ k++l+LlPcsa+kPys+s+sh+kf+++++++++ vhe++ltsPlG+vPrele++YPaa+Y
  gi|298674013|ref|YP_003725763.1| 310 ITRFAERVQNRYTPPK-KDILLLLPCSARKPYSTSNSHQKFIDTLGQYRKYVHELVLTSPLGIVPRELELTYPAAHY 385
                                       78*************7.************************************************************ PP

                                       ---------HHHHHHHHHHHHHHHHHHT-SEEEE---THHHHHHHHHHTT-SSEEEE--.SS-TTSHHHHHHHHHHH CS
                           DUF5591  78 diavtgewseeeiefvaellakylektkyekviahleeeyreiveevaeelgleiiytvvedkptskeslknLkeaL 154
                                       diavtg+w+++e+e+v+++l +yl+k+ky+ v+ah+e++y+++++ +a++lg++i+yt+ e ++tskesl+ Lk+++
  gi|298674013|ref|YP_003725763.1| 386 DIAVTGHWDADEVEWVTDCLVNYLSKNKYSCVVAHVEGAYQKVCDLAARKLGIDIVYTC-ESDVTSKESLEVLKDTI 461
                                       ***********************************************************.999**********9985 PP

>> TGT  Queuine tRNA-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.1   0.0    0.0047        21       2      59 ..      13      70 ..      10      78 .. 0.78
   2 !   63.0   0.0     6e-21   2.7e-17     191     347 ..     121     267 ..     114     269 .. 0.90
   3 ?   -3.3   0.0      0.84   3.8e+03     153     185 ..     399     436 ..     398     468 .. 0.50

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0047
                                      TEEEEEEEETTEEEEESEEEEBETTSSBTTB-HHHHH.HT.TES-EEEEHHHHHHTTTH CS
                               TGT  2 gaRlGklelphgtietPafmpvgtqgtvkgltpdelkeel.gaqiilsntyhlelrpge 59
                                      +aRlGkl l+++ ++tP+++++   g  ++l   +  + + + + i++n+y  +lr++ 
  gi|298674013|ref|YP_003725763.1| 13 KARLGKLILSRN-LKTPCIINIEDIGDTEKLPIIDAGSVWkQGKHIFENQYLNQLRQKV 70
                                      59*******995.********99888888888887754443578889999976666654 PP

  == domain 2  score: 63.0 bits;  conditional E-value: 6e-21
                                       SEEEE-SSSSSS.HHHHHHHHHHHHGGGS-TTS-EEETTB-SHHHHHHHHHTT--EEEESHHHHHHHTTEEEETTEE CS
                               TGT 191 dgyaigGlsvge.ekeellevveavtellpedkprylmGvgtPedlleavalGvDmfdcvyptrtarngraltsege 266
                                       d y  +G  + e + +++++ ++ ++e++p d  +y+  +  Pe+l+ ++ lG+D+fd + +t  a n+ +lts+g+
  gi|298674013|ref|YP_003725763.1| 121 DLYIMEGGGGLEnNARQFFNALKGLKEEIPHDTAVYVPNIALPENLAMLIYLGADVFDYTRATISAYNDIYLTSSGK 197
                                       456666655555489************************************************************** PP

                                       EETTSGGGTT--SBSSSS--SHHHHH-BHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHH CS
                               TGT 267 lnlknakyaedfspldegCsCytCknytraylhhllktkemlgaiLltiHNlhyylelfkriReaIkegtfeefvee 343
                                       + l     +    p    C C +C++ t   l+ + ++++    i+l++HN  ++  +++ +Re+I++g + e+ve 
  gi|298674013|ref|YP_003725763.1| 198 FYLY----NITELP----CRCDACTSVTVDDLKLMDAENR---GIILEEHNKNMLDSELSLVREKIRKGYLREYVEG 263
                                       *996....334448....*****************99999...9*******************************98 PP

                                       HHHH CS
                               TGT 344 fark 347
                                        +r+
  gi|298674013|ref|YP_003725763.1| 264 QCRT 267
                                       7765 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 0.84
                                       HHHHHHHHHH......SEEEEEE--TT-HHHHHHHHHHH CS
                               TGT 153 rwldrcleah......qalfgivqGglyedlreesaeel 185
                                       +w+ +cl ++      + +++ v+G++ +++   +a++l
  gi|298674013|ref|YP_003725763.1| 399 EWVTDCLVNYlsknkySCVVAHVEGAY-QKVCDLAARKL 436
                                       577777644445555333666666643.33444444444 PP

>> TGT_C2  Patch-forming domain C2 of tRNA-guanine transglycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.6   0.0   5.2e-20   2.4e-16       3      67 ..     480     542 ..     478     545 .. 0.94

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 5.2e-20
                            TGT_C2   3 lraiadYqFGagagdaLfpedvtitrsatgrirqvlvdgerlatlraqdgrltLsleGarrlhes 67 
                                       +raiadYqFG+gag+ L+p+d+ i+  a    +qv++++e++atl+++ g+l+L+  Ga++l  +
  gi|298674013|ref|YP_003725763.1| 480 MRAIADYQFGKGAGNILVPDDAVIK--APYPKHQVYLNKEQIATLVPHHGTLSLTARGAELLIPH 542
                                       79***********************..*********************************99766 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.2   6.8e-16     3e-12      17      73 ..     556     610 ..     546     611 .. 0.94

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 6.8e-16
                                       -EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEEE CS
                               PUA  17 asLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveierv 73 
                                        s+lapG+ e++ ++++gd+V i  e  ++++vG+a++s+ e++k ++g+++ +++v
  gi|298674013|ref|YP_003725763.1| 556 GSILAPGIQEADVSIRPGDEVLISGE--NAIGVGRALMSGREMEKSTRGIAITLRHV 610
                                       49*********************999..**************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (613 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.50s 00:00:01.12 Elapsed: 00:00:01.07
# Mc/sec: 1728.02
//
Query:       gi|298674014|ref|YP_003725764.1|  [L=457]
Description: FAD linked oxidase domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.4e-58  196.9   0.0      6e-58  196.4   0.0    1.2  1  FAD-oxidase_C  FAD linked oxidases, C-terminal domain
      7e-45  152.2   0.1    1.2e-44  151.4   0.1    1.4  1  FAD_binding_4  FAD binding domain


Domain annotation for each model (and alignments):
>> FAD-oxidase_C  FAD linked oxidases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.4   0.0   6.6e-62     6e-58       1     250 []     212     455 ..     212     455 .. 0.98

  Alignments for each domain:
  == domain 1  score: 196.4 bits;  conditional E-value: 6.6e-62
                                       --SEEEEEEEEESSHHHHHHHHHHHHHHT---SEEEEE-HHHHHHHHHTS-SSTTS-TTT-EEEEEEEEE-HHHHHH CS
                     FAD-oxidase_C   1 lpearavalvafpsfeaavkavreiaqagiipaalelmdkkaldlveatkgakkglpdeeealllvefegddeeeae 77 
                                       lp+ar+v+l++f++ e a + v+++ ++gi p+a+e++dk+a+++ +a+++      ++ +a+l++e++g++  ++e
  gi|298674014|ref|YP_003725764.1| 212 LPKARTVILASFENPELAGEGVVKTLSSGIVPSACEILDKTAIEALNAFDPN--LNLPDVGAILMFEVDGTE-GAVE 285
                                       599*************************************************..999***************.9*** PP

                                       HHHHHHHHHTTT-EEEEE..........ETGGGGGGGGHHHHHHHHHCTTEEEEEEEEEEEHHHHHHHHHHHHHHHH CS
                     FAD-oxidase_C  78 eelealveaileatgaadvlvaqdeaeaealwkaRkaalpylrdallkagvavlseDtsvPvsrladlvrdikalld 154
                                       ee++ l+e+++++ ++     a++++e e+lw+aR+ + + ++++  ++  +++ eD+ vP++++++++++++++ +
  gi|298674014|ref|YP_003725764.1| 286 EEAK-LIESACSSLATNV-KSASTKQESEELWRARRLVGAAISRLDPNRTRVYVGEDVGVPIKEIPRMLKKVREISE 360
                                       ****.********99996.*********************99999999999999*********************** PP

                                       HHHEEEEEEEEEETTEEEEEEEEEEE..--TT--THHHHHHHHHHHHTT-----------------------THHHH CS
                     FAD-oxidase_C 155 kyglevvlfgHagdgnlhlyilfdladeaeeeraeklvdevvdlavelgGsisgEHGvGldkkaylerekgeeglal 231
                                       ++++ ++++gH+gdgnlh  +++d+ d+ ++++++k+ d++ + a+elgG++s+EHG+G ++++y+e e g+ +l++
  gi|298674014|ref|YP_003725764.1| 361 EFNIPIMTYGHIGDGNLHTGMAIDVLDDSQWDSLNKAGDKIHRTAIELGGTVSAEHGIGGARSEYMELELGP-ALDV 436
                                       ************************************************************************.9*** PP

                                       HHHHHHHH-TT--BSTT-- CS
                     FAD-oxidase_C 232 mrriKaalDPkgiLNPgkv 250
                                       m +iK+alDP++iLNPgk+
  gi|298674014|ref|YP_003725764.1| 437 MLNIKNALDPNNILNPGKL 455
                                       *****************96 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.4   0.1   1.4e-48   1.2e-44       1     138 [.      37     175 ..      37     176 .. 0.98

  Alignments for each domain:
  == domain 1  score: 151.4 bits;  conditional E-value: 1.4e-48
                                       EEEEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTC.SCCEEEEEETTS--EEEEETTTTEEEEETTSBHHH CS
                     FAD_binding_4   1 paavvrpeseeevaaalrlaneaglpvlvrGgGssllgqav.atggvvldlsrlnrileideeegtatveaGvtlgd 76 
                                       p++vvrp s+++v++++++an++++pv+ rG+G++l+g+av  +gg+vldls +nril++d e+ ++ ve+Gv+ ++
  gi|298674014|ref|YP_003725764.1|  37 PDYVVRPDSTDQVSKIVQFANKHKIPVTSRGAGTGLAGGAVpISGGIVLDLSSMNRILDVDIENLQVAVEPGVVHAK 113
                                       89***********************************999989********99************************ PP

                                       HHHHHHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSEEEEE CS
                     FAD_binding_4  77 lvealaakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGevvrl 138
                                       l+e l+++g++++++pgs   +t+GG+ia+n++G++s kyG+++ + l levv+adG+v+++
  gi|298674014|ref|YP_003725764.1| 114 LNEKLKPYGFFFPPDPGSSAMCTIGGLIANNGSGMRSVKYGTSSRYALDLEVVMADGTVINT 175
                                       ***********************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 3099.86
//
Query:       gi|298674015|ref|YP_003725765.1|  [L=360]
Description: CoB--CoM heterodisulfide reductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-29  101.3   9.3    1.6e-14   53.9   0.3    2.6  2  CCG            Cysteine-rich domain
      4e-11   43.2   4.1      4e-11   43.2   4.1    2.4  3  Fer4_8         4Fe-4S dicluster domain
    1.9e-09   37.9   3.6    1.9e-09   37.9   3.6    3.1  4  Fer4_17        4Fe-4S dicluster domain
    2.3e-07   31.3   5.9    2.3e-07   31.3   5.9    2.6  2  Fer4_7         4Fe-4S dicluster domain
    7.4e-07   29.2  19.7    8.1e-06   25.9  10.3    3.4  4  Fer4_10        4Fe-4S dicluster domain
    3.4e-05   23.5  20.5     0.0018   18.0   1.5    2.9  2  Fer4           4Fe-4S binding domain
    5.8e-05   23.2  15.0    0.00013   22.0  11.0    3.2  3  Fer4_9         4Fe-4S dicluster domain
    0.00075   19.4  13.8     0.0011   18.9   3.7    3.5  4  Fer4_2         4Fe-4S binding domain
    0.00094   19.3  13.1      0.033   14.3   0.6    3.7  4  Fer4_21        4Fe-4S dicluster domain
     0.0018   19.1  17.0      0.013   16.4   0.7    3.5  3  Fer4_16        4Fe-4S double cluster binding domain
     0.0035   17.7   1.3     0.0035   17.7   1.3    3.8  4  Fer4_4         4Fe-4S binding domain
     0.0082   16.3   3.2        2.7    8.2   0.3    2.7  2  Fer4_18        4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.028   15.4   5.0      0.028   15.4   5.0    3.5  2  Fer4_3         4Fe-4S binding domain
      0.044   13.6   0.6       0.48   10.3   0.1    2.9  3  Rad50_zn_hook  Rad50 zinc hook motif
      0.069   13.7   9.7       0.78   10.3   0.9    2.9  2  Fer4_13        4Fe-4S single cluster domain of Ferredoxin I
        1.6    8.9  22.9      0.068   13.3   1.8    3.5  4  Fer4_6         4Fe-4S binding domain
        2.5    7.9  12.4        1.8    8.4   0.8    3.6  3  zinc_ribbon_5  zinc-ribbon domain


Domain annotation for each model (and alignments):
>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.8   0.1   1.6e-17   1.7e-14       1      85 []     142     221 ..     142     221 .. 0.97
   2 !   53.9   0.3   1.5e-17   1.6e-14       1      84 [.     253     337 ..     253     338 .. 0.88

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 1.6e-17
                               CCG   1 vayfdgChllraaypevrkalkkllealgveleelekesCCGagggrsgkeelaealakrnvetaeetgadaivtac 77 
                                       +++f+gC l  ++ypev k +  +l++  v+l ++  e CCG++  r+g+e  a +++++n+e++++ ga  ++t c
  gi|298674015|ref|YP_003725765.1| 142 YVFFVGC-LESYRYPEVAKTTFDILKKFDVTLLPN--EHCCGSPLLRTGFE--ADDVTEENIEQIRKIGAHTVITGC 213
                                       68*****.*************************99..**************..8*********************** PP

                               CCG  78 pgCllqlk 85 
                                       +gC++++k
  gi|298674015|ref|YP_003725765.1| 214 AGCYTTFK 221
                                       ****9985 PP

  == domain 2  score: 53.9 bits;  conditional E-value: 1.5e-17
                               CCG   1 vayfdgChllraa..ypevrkalkkllealgveleelekesCCGagggr.sgkeelaealakrnvetaeetgadaiv 74 
                                       v+y+d+Ch++r++  y+++rk++k++ + + +++++  ++ CCG ggg+ sg+ el+ ++a+ ++ ++ e g+d++v
  gi|298674015|ref|YP_003725765.1| 253 VTYHDPCHIGRKHgiYEAPRKVIKAICNLKEMKTVRE-NARCCGGGGGVlSGYPELSHSIAETRMTEVPE-GVDYVV 327
                                       89************************88887777765.99999998887255566***************.9***** PP

                               CCG  75 tacpgCllql 84 
                                       t cp C  +l
  gi|298674015|ref|YP_003725765.1| 328 TSCPLCRRNL 337
                                       ******8776 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   4.1   3.8e-14     4e-11       3      64 ..      16      81 ..      14      82 .. 0.82
   2 ?   -2.4   0.0       6.4   6.7e+03      45      54 ..     207     216 ..     182     218 .. 0.58
   3 ?   -2.0   0.0       4.9   5.2e+03      14      19 ..     329     334 ..     302     340 .. 0.70

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 3.8e-14
                            Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaae.......dvqeeqvlee.....eealwsCttcgaCtevCpvg 64
                                       kC++Cg C+s Cpv+ + + ++  arg+                   +      ++l++Cttcg C+++Cp g
  gi|298674015|ref|YP_003725765.1| 16 LKCVRCGTCRSVCPVFDELGWESSGARGRILVahalsqgM--------DvdsdvLNSLNTCTTCGLCEQNCPSG 81
                                      69******************99999999988744544442........445556799***************86 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.4
                            Fer4_8  45 eealwsCttc 54 
                                       ++ +  C +c
  gi|298674015|ref|YP_003725765.1| 207 HTVITGCAGC 216
                                       6667777777 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 4.9
                            Fer4_8  14 aCpvlr 19 
                                       +Cp++r
  gi|298674015|ref|YP_003725765.1| 329 SCPLCR 334
                                       344444 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   3.6   1.8e-12   1.9e-09       1      59 [.      17      81 ..      17      83 .. 0.78
   2 ?   -1.1   0.0       2.7   2.8e+03      37      49 ..     204     216 ..     184     218 .. 0.65
   3 ?   -1.6   0.1         4   4.2e+03      12      47 ..     259     294 ..     257     298 .. 0.51
   4 ?   -1.5   0.0       3.7   3.9e+03      11      19 ..     329     337 ..     322     347 .. 0.69

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 1.8e-12
                           Fer4_17  1 rCiqCgyClpeCpsyeaydnepkkllraakl....glleeaeke....ekaslCieCgeCerkCPqg 59
                                      +C +Cg C+ +Cp + + ++e    + ++ +    ++  ++  +    +  ++C++Cg+Ce+ CP+g
  gi|298674015|ref|YP_003725765.1| 17 KCVRCGTCRSVCPVFDELGWESSGARGRILVahalSQGMDV--DsdvlNSLNTCTTCGLCEQNCPSG 81
                                      6****************999988777777665422333333..2346789***************97 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.7
                           Fer4_17  37 aekeekaslCieC 49 
                                       + + +++  C++C
  gi|298674015|ref|YP_003725765.1| 204 IGAHTVITGCAGC 216
                                       3334677788877 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 4
                           Fer4_17  12 Cpsyeaydne..pkkllraaklglleeaekeekaslCi 47 
                                       C  +++++ +  p+k+++a+ +  l+e+++ ++  +C+
  gi|298674015|ref|YP_003725765.1| 259 CHIGRKHGIYeaPRKVIKAICN--LKEMKTVRENARCC 294
                                       6666665543125566666433..33444445555555 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 3.7
                           Fer4_17  11 eCpsyeayd 19 
                                       +Cp ++++ 
  gi|298674015|ref|YP_003725765.1| 329 SCPLCRRNL 337
                                       577777655 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   5.9   2.2e-10   2.3e-07       1      52 []      17      82 ..      17      82 .. 0.72
   2 ?   -1.5   0.0       3.8     4e+03      34      42 ..     209     217 ..     185     219 .. 0.63

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 2.2e-10
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgt..............ekveidpekClgCgaCvavCPtga 52
                                      +C+ Cg C ++Cpv     +e++ ++g+               +v  + ++C++Cg C++ CP+ga
  gi|298674015|ref|YP_003725765.1| 17 KCVRCGTCRSVCPVFDELGWESSGARGRilvahalsqgmdvdSDVLNSLNTCTTCGLCEQNCPSGA 82
                                      7************77777777778886655555555332332333444578*************98 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.8
                            Fer4_7  34 dpekClgCg 42 
                                       + + C gC+
  gi|298674015|ref|YP_003725765.1| 209 VITGCAGCY 217
                                       455677775 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9  10.3   7.6e-09   8.1e-06       8      56 .]      17      79 ..      13      79 .. 0.91
   2 !   16.5   1.9   6.6e-06    0.0069       5      24 ..      64      91 ..      59     116 .. 0.69
   3 ?   -2.0   0.1       3.8     4e+03      43      48 ..     211     216 ..     193     219 .. 0.64
   4 ?   -0.8   0.0       1.7   1.7e+03      40      49 ..     325     334 ..     310     345 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 7.6e-09
                           Fer4_10  8 tCirCgkCvkaCPadl..............tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      +C+rCg+C+++CP+                 ++  ++  + ++ v   +  Ct+cg C + CP
  gi|298674015|ref|YP_003725765.1| 17 KCVRCGTCRSVCPVFDelgwessgargrilVAHALSQGMDVDSDVLNSLNTCTTCGLCEQNCP 79
                                      7*************55************99888888888888888889**************9 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 6.6e-06
                           Fer4_10  5 dddtCirCgkCvkaCPadl........t 24
                                        +tC+ Cg C + CP+ +        t
  gi|298674015|ref|YP_003725765.1| 64 SLNTCTTCGLCEQNCPSGAkppdviedT 91
                                      5789*************55444444330 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 3.8
                           Fer4_10  43 ekCtgc 48 
                                         C gc
  gi|298674015|ref|YP_003725765.1| 211 TGCAGC 216
                                       334443 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 1.7
                           Fer4_10  40 kkvekCtgcg 49 
                                        +v +C+ c 
  gi|298674015|ref|YP_003725765.1| 325 YVVTSCPLCR 334
                                       5666777664 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   4.1   3.2e-06    0.0034       7      20 ..      17      30 ..      16      31 .. 0.96
   2 !   18.0   1.5   1.7e-06    0.0018       7      22 ..      67      82 ..      64      83 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.2e-06
                                      TSSS-THHHHHSTT CS
                              Fer4  7 kCigCGaCvevCPv 20
                                      kC++CG+C +vCPv
  gi|298674015|ref|YP_003725765.1| 17 KCVRCGTCRSVCPV 30
                                      8************8 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 1.7e-06
                                      TSSS-THHHHHSTTTE CS
                              Fer4  7 kCigCGaCvevCPvgA 22
                                       C+ CG+C++ CP gA
  gi|298674015|ref|YP_003725765.1| 67 TCTTCGLCEQNCPSGA 82
                                      7*************99 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   2.7   0.00015      0.16      34      47 ..      16      29 ..       2      33 .. 0.72
   2 !   22.0  11.0   1.3e-07   0.00013       1      50 [.      17      82 ..      17      83 .. 0.67
   3 ?   -1.2   0.0       2.3   2.4e+03      34      39 ..     211     216 ..     187     219 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                            Fer4_9 34 eaCigCgaCveaCp 47
                                       +C+ Cg+C  +Cp
  gi|298674015|ref|YP_003725765.1| 16 LKCVRCGTCRSVCP 29
                                      57999999999998 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 1.3e-07
                            Fer4_9  1 kCtgCgaCveaC.............pagvvvedaaerkarlraase...............eaCigCgaCveaCpkga 50
                                      kC++Cg+C ++C                + v +            +               + C++Cg C++ Cp+ga
  gi|298674015|ref|YP_003725765.1| 17 KCVRCGTCRSVCpvfdelgwessgaRGRILVAH------------AlsqgmdvdsdvlnslNTCTTCGLCEQNCPSGA 82
                                      7***********766554444333322222222............223455666777889999************985 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 2.3
                            Fer4_9  34 eaCigC 39 
                                       + C gC
  gi|298674015|ref|YP_003725765.1| 211 TGCAGC 216
                                       445555 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   3.7     1e-06    0.0011       9      21 ..      17      29 ..      12      30 .. 0.93
   2 !   13.8   2.5   4.6e-05     0.049       8      21 ..      66      79 ..      58      80 .. 0.88
   3 ?   -2.8   0.6       8.5   8.9e+03      10      14 ..     213     217 ..     211     218 .. 0.61
   4 ?   -2.7   0.4         8   8.4e+03      18      21 ..     328     331 ..     326     335 .. 0.58

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1e-06
                            Fer4_2  9 rCigCgaCvsaCP 21
                                      +C++Cg+C+s+CP
  gi|298674015|ref|YP_003725765.1| 17 KCVRCGTCRSVCP 29
                                      8************ PP

  == domain 2  score: 13.8 bits;  conditional E-value: 4.6e-05
                            Fer4_2  8 drCigCgaCvsaCP 21
                                      ++C+ Cg C ++CP
  gi|298674015|ref|YP_003725765.1| 66 NTCTTCGLCEQNCP 79
                                      69************ PP

  == domain 3  score: -2.8 bits;  conditional E-value: 8.5
                            Fer4_2  10 CigCg 14 
                                       C gC 
  gi|298674015|ref|YP_003725765.1| 213 CAGCY 217
                                       66664 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 8
                            Fer4_2  18 saCP 21 
                                       ++CP
  gi|298674015|ref|YP_003725765.1| 328 TSCP 331
                                       4455 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.6   3.1e-05     0.033      40      55 ..      17      32 ..       5      35 .. 0.87
   2 !   11.3   0.8   0.00027      0.28      39      52 ..      66      79 ..      50      89 .. 0.82
   3 ?   -0.6   0.1       1.4   1.5e+03      36      44 ..     208     216 ..     190     220 .. 0.58
   4 ?   -2.8   0.0       7.1   7.5e+03      42      47 ..     328     333 ..     309     335 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.1e-05
                           Fer4_21 40 eCvGCnlCssvCPved 55
                                      +Cv C  C svCPv d
  gi|298674015|ref|YP_003725765.1| 17 KCVRCGTCRSVCPVFD 32
                                      7************965 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00027
                           Fer4_21 39 deCvGCnlCssvCP 52
                                      ++C+ C lC + CP
  gi|298674015|ref|YP_003725765.1| 66 NTCTTCGLCEQNCP 79
                                      67999999999999 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.4
                           Fer4_21  36 vvedeCvGC 44 
                                       +v   C GC
  gi|298674015|ref|YP_003725765.1| 208 TVITGCAGC 216
                                       444455555 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 7.1
                           Fer4_21  42 vGCnlC 47 
                                       + C lC
  gi|298674015|ref|YP_003725765.1| 328 TSCPLC 333
                                       567777 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   4.2    0.0026       2.7       1      14 [.      17      30 ..      17      32 .. 0.90
   2 !   16.4   0.7   1.3e-05     0.013       1      26 [.      67      89 ..      67     124 .. 0.61
   3 ?    0.9   0.3      0.87   9.1e+02      40      61 ..     196     217 ..     175     219 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0026
                           Fer4_16  1 rCgtCgkCaevCPt 14
                                      +C++Cg C +vCP+
  gi|298674015|ref|YP_003725765.1| 17 KCVRCGTCRSVCPV 30
                                      599*********96 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 1.3e-05
                           Fer4_16  1 rCgtCgkCaevCPtnaikekkekeie 26
                                      +C+tCg C + CP++a   +   +ie
  gi|298674015|ref|YP_003725765.1| 67 TCTTCGLCEQNCPSGAKPPD---VIE 89
                                      5**************96555...222 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.87
                           Fer4_16  40 dlaedeekckkqeaitgCdiCq 61 
                                       + +e+++k   ++ itgC+ C 
  gi|298674015|ref|YP_003725765.1| 196 ENIEQIRKIGAHTVITGCAGCY 217
                                       3444555555667789**9995 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   1.3   3.3e-06    0.0035       3      15 ..      17      29 ..      15      40 .. 0.93
   2 !   11.6   2.6   0.00031      0.33       2      17 .]      66      81 ..      65      83 .. 0.91
   3 ?   -1.0   0.3       3.3   3.5e+03       6      11 ..     212     217 ..     211     219 .. 0.68
   4 ?   -1.2   0.3       3.8     4e+03       6      11 ..     329     334 ..     328     335 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.3e-06
                            Fer4_4  3 rCigCgsCvaaCP 15
                                      +C++Cg C+++CP
  gi|298674015|ref|YP_003725765.1| 17 KCVRCGTCRSVCP 29
                                      7************ PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00031
                            Fer4_4  2 erCigCgsCvaaCPqg 17
                                      ++C+ Cg C+  CP+g
  gi|298674015|ref|YP_003725765.1| 66 NTCTTCGLCEQNCPSG 81
                                      79************75 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 3.3
                            Fer4_4   6 gCgsCv 11 
                                       gC  C+
  gi|298674015|ref|YP_003725765.1| 212 GCAGCY 217
                                       777776 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 3.8
                            Fer4_4   6 gCgsCv 11 
                                        C+ C+
  gi|298674015|ref|YP_003725765.1| 329 SCPLCR 334
                                       588887 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.3    0.0025       2.7      57      73 ..      14      30 ..       2      35 .. 0.79
   2 !    7.8   0.2    0.0033       3.5      50      74 ..      57      81 ..      38      91 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0025
                           Fer4_18 57 gagdcidcescvkvcPt 73
                                      +  +c+ c++c +vcP+
  gi|298674015|ref|YP_003725765.1| 14 SILKCVRCGTCRSVCPV 30
                                      5668************7 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0033
                           Fer4_18 50 keerkekgagdcidcescvkvcPtg 74
                                      +++   ++ + c++c+ c + cP g
  gi|298674015|ref|YP_003725765.1| 57 VDSDVLNSLNTCTTCGLCEQNCPSG 81
                                      45555678899************87 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   4.9    0.0027       2.8       1      13 [.      18      30 ..      18      32 .. 0.95
   2 ?   15.4   5.0   2.6e-05     0.028       1      15 []      68      82 ..      68      82 .. 0.98

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0027
                            Fer4_3  1 CtgCgaCvevCPv 13
                                      C+ Cg+C  vCPv
  gi|298674015|ref|YP_003725765.1| 18 CVRCGTCRSVCPV 30
                                      99**********7 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 2.6e-05
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      Ct Cg+C++ CP+gA
  gi|298674015|ref|YP_003725765.1| 68 CTTCGLCEQNCPSGA 82
                                      **************9 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       3.3   3.5e+03      25      47 ..     179     203 ..     174     207 .. 0.58
   2 ?   -1.3   0.0       1.9     2e+03      29      45 ..     228     244 ..     227     249 .. 0.80
   3 ?   10.3   0.1   0.00046      0.48      21      34 ..     329     342 ..     327     344 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.3
                                       T--EE-HHH..HHHHHHHHHHHHHH CS
                     Rad50_zn_hook  25 CgReldeeh..rseLikelqskler 47 
                                       Cg++l +    + ++++e  +++++
  gi|298674015|ref|YP_003725765.1| 179 CGSPLLRTGfeADDVTEENIEQIRK 203
                                       6666655444455555555555555 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.9
                                       E-HHHHHHHHHHHHHHH CS
                     Rad50_zn_hook  29 ldeehrseLikelqskl 45 
                                       ++ +h se++ ++ ++l
  gi|298674015|ref|YP_003725765.1| 228 FNVKHVSEFLADHIDEL 244
                                       777899****9999997 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00046
                                       E-TTT--EE-HHHH CS
                     Rad50_zn_hook  21 cCPlCgReldeehr 34 
                                       +CPlC R+l++ ++
  gi|298674015|ref|YP_003725765.1| 329 SCPLCRRNLSQGNK 342
                                       7********98775 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.9   0.00074      0.78       5      17 ..      17      29 ..      16      35 .. 0.88
   2 ?    6.6   2.3     0.011        11       4      18 ..      66      80 ..      64      81 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00074
                           Fer4_13  5 tCiacgaCvelaP 17
                                      +C+ cg+C++++P
  gi|298674015|ref|YP_003725765.1| 17 KCVRCGTCRSVCP 29
                                      7************ PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.011
                           Fer4_13  4 dtCiacgaCvelaPd 18
                                      +tC+ cg+C + +P 
  gi|298674015|ref|YP_003725765.1| 66 NTCTTCGLCEQNCPS 80
                                      69************5 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   2.6    0.0014       1.5       8      21 ..      17      30 ..      16      34 .. 0.93
   2 ?   13.3   1.8   6.4e-05     0.068       7      23 ..      66      82 ..      64      82 .. 0.93
   3 ?   -1.6   0.4       3.2   3.4e+03      11      17 ..     212     218 ..     211     219 .. 0.65
   4 ?   -1.6   0.2       3.2   3.3e+03       8      14 ..     329     335 ..     327     335 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0014
                            Fer4_6  8 kCigCgdCvrvCPe 21
                                      kC+ Cg C +vCP 
  gi|298674015|ref|YP_003725765.1| 17 KCVRCGTCRSVCPV 30
                                      8************4 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 6.4e-05
                            Fer4_6  7 dkCigCgdCvrvCPega 23
                                      + C+ Cg C+ +CP ga
  gi|298674015|ref|YP_003725765.1| 66 NTCTTCGLCEQNCPSGA 82
                                      78************997 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 3.2
                            Fer4_6  11 gCgdCvr 17 
                                       gC  C++
  gi|298674015|ref|YP_003725765.1| 212 GCAGCYT 218
                                       6777765 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 3.2
                            Fer4_6   8 kCigCgd 14 
                                       +C  C++
  gi|298674015|ref|YP_003725765.1| 329 SCPLCRR 335
                                       6999985 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.8    0.0017       1.8      19      34 ..      12      27 ..       8      31 .. 0.78
   2 ?    5.3   0.0     0.016        17       2      13 ..     210     221 ..     209     229 .. 0.90
   3 ?    0.8   0.2      0.41   4.3e+02       2       9 ..     327     334 ..     326     336 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0017
                     zinc_ribbon_5 19 lKksgkkVrCakCaev 34
                                      l+   k VrC+ C++v
  gi|298674015|ref|YP_003725765.1| 12 LRSILKCVRCGTCRSV 27
                                      5555678********9 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.016
                     zinc_ribbon_5   2 iirCpdCdtkFk 13 
                                       i+ C  C t+Fk
  gi|298674015|ref|YP_003725765.1| 210 ITGCAGCYTTFK 221
                                       899********9 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.41
                     zinc_ribbon_5   2 iirCpdCd 9  
                                       +++Cp C+
  gi|298674015|ref|YP_003725765.1| 327 VTSCPLCR 334
                                       69*****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 2499.66
//
Query:       gi|298674016|ref|YP_003725766.1|  [L=611]
Description: radical SAM domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   9.8e-132  438.7   0.2   1.7e-131  437.9   0.0    1.5  2  Radical_SAM_N  Radical SAM N-terminal
    2.2e-26   93.0   0.1    3.8e-26   92.2   0.1    1.4  1  DUF3362        Domain of unknown function (DUF3362)
    9.7e-17   61.8   0.1    8.3e-16   58.8   0.1    2.2  2  Radical_SAM    Radical SAM superfamily
    7.4e-05   22.8   0.0       0.46   10.5   0.0    3.2  4  B12-binding    B12 binding domain


Domain annotation for each model (and alignments):
>> Radical_SAM_N  Radical SAM N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  437.9   0.0  3.8e-135  1.7e-131       1     298 []      14     315 ..      14     315 .. 0.97
   2 ?   -3.3   0.1      0.91   4.1e+03      97     118 ..     557     578 ..     547     583 .. 0.84

  Alignments for each domain:
  == domain 1  score: 437.9 bits;  conditional E-value: 3.8e-135
                     Radical_SAM_N   1 flpvsrkemeergwdelDvilvsgDaYvDhpsfgaaligrlLeaeGfrvgiiaqPdwksaedfkklGkPrlffgvsa 77 
                                       flpvs ++ ++rgw+elDvi+v+gDaYvDhp fga++igr+Le+eGfrvgiiaqPdw++ +dfkklGkPrlff+v+a
  gi|298674016|ref|YP_003725766.1|  14 FLPVSLEDANKRGWEELDVIIVTGDAYVDHPGFGATIIGRVLEDEGFRVGIIAQPDWNNIDDFKKLGKPRLFFAVTA 90 
                                       9**************************************************************************** PP

                     Radical_SAM_N  78 GnlDsmvnkytaekklrsdDaytpggkagkRPdravivYsnlireaykdvpvvlGgiEaSLRriahYDywsdkvrrs 154
                                       Gn Dsmv++yt++ k rs+Day+pgg++++RP+ra++vY+n+++e+y+dvp+vlGgiEaSLRr+a+YDy s+kvr+s
  gi|298674016|ref|YP_003725766.1|  91 GNTDSMVSNYTSSLKPRSSDAYSPGGEKNRRPNRATLVYTNRLKEVYPDVPIVLGGIEASLRRFAQYDYLSNKVRKS 167
                                       ***************************************************************************** PP

                     Radical_SAM_N 155 illdskadllvyGmgeraiveiakrlakgeeveelkdirgtavllkkea.kake....kevielpsyeevkedkkly 226
                                       il+d+ ad+lvyGmge +  eiak+l++g++v+e+++i+gt+++l  ++ k+++    ++++e+ sy+ev+++kk+y
  gi|298674016|ref|YP_003725766.1| 168 ILADAPADILVYGMGELQNKEIAKQLDNGKSVNEIQNIDGTVWKLAVKKwKKQKgdylNDYVEIASYDEVSTNKKSY 244
                                       *******************************************88864433333445679***************** PP

                     Radical_SAM_N 227 aeafrlleeetnplnakalvqkhgdravvlnppalplsteelDevyelpyarkahpsykkkkipalemikfS 298
                                       a+af++++ee++ +n+ka+vq h ++++v+n+p++pl+++elD+vyelp++r+ahpsy k+ ipal+++kfS
  gi|298674016|ref|YP_003725766.1| 245 ANAFKTIYEEQDYINGKAIVQPHPKTIIVQNKPMRPLTQQELDHVYELPFTREAHPSY-KEPIPALDTVKFS 315
                                       **********************************************************.59**********8 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.91
                     Radical_SAM_N  97 DaytpggkagkRPdravivYsn 118
                                         y p++ ++kR +ra + Y n
  gi|298674016|ref|YP_003725766.1| 557 KVYIPDSPKEKRIQRALMHYRN 578
                                       6799*************99976 PP

>> DUF3362  Domain of unknown function (DUF3362)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.2   0.1   8.5e-30   3.8e-26       1      87 [.     529     610 ..     529     611 .] 0.97

  Alignments for each domain:
  == domain 1  score: 92.2 bits;  conditional E-value: 8.5e-30
                           DUF3362   1 dqVqtFyPsPmatattmYhtgknpltkvkreeesvdvvrgekerrlhkAllrYhdpknwpllreALkkmGredLiGn 77 
                                       +qVq+F P+Pm+++t+m++tg +p t       +v+++ ++ke+r+++Al++Y++pkn++l+ e Lkk+ r dL+Gn
  gi|298674016|ref|YP_003725766.1| 529 EQVQDFTPTPMTVSTCMFYTGIDPFT-----GKKVYIPDSPKEKRIQRALMHYRNPKNHKLVYEGLKKANRMDLVGN 600
                                       7*************************.....99******************************************** PP

                           DUF3362  78 gkkhLiptfq 87 
                                         k+Li  ++
  gi|298674016|ref|YP_003725766.1| 601 AWKCLISRRK 610
                                       ******8765 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.18     8e+02      47     115 ..      30      94 ..      17     122 .. 0.75
   2 !   58.8   0.1   1.9e-19   8.3e-16       2     167 .]     317     521 ..     316     521 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.18
                                       SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  47 vkevilgggepllypdfvellerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaadde 115
                                        +++i++g+   ++p f   +  ++ ++ +g+r+ +++ + +     ++ +++lg  r+ + + a++ +
  gi|298674016|ref|YP_003725766.1|  30 LDVIIVTGDAYVDHPGFGATIIGRVLED-EGFRVGIIAQPDWN---NIDDFKKLGKPRLFFAVTAGNTD 94 
                                       6777777777777777777777777764.77777777766665...99999999999999999999887 PP

  == domain 2  score: 58.8 bits;  conditional E-value: 1.9e-19
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGS................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx................. RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggeplly................. 60 
                                       +  rgC ++CsfCa++++  +++   s+s+e+i++e+  + ++++ +++v  +gg p+++                 
  gi|298674016|ref|YP_003725766.1| 317 TSHRGCFGNCSFCAITQH--QGRIITSRSIESIVREATGFTERPDfKGTVSGVGG-PSANmygmeckkwhksgvckn 390
                                       6779*************8..********************988886666666666.********************* PP

                                       ................TTHHHHHHHHHHTCCCTEEEEEEECSSCHG.....HHHHHHHHHTT.-SEEEEEEBSSSHH CS
                                       ................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxx.xxxxxxxxxxxxxx RF
                       Radical_SAM  61 ................pdfvellerlaklavpgiritvetngtlpd.....eeklerllelg.vdrvslgleaadde 115
                                                       ++ ++ l+rl+++  pg++ +++  g+++d     e ++e+l   +   ++ +  e+++de
  gi|298674016|ref|YP_003725766.1| 391 kfclypepcpsldtkhKKSIDMLRRLRQI--PGVSKVLIGYGIRHDlalqdENYMEELCAHHvGGQLKVAPEHFSDE 465
                                       *************8888888888888888..9****************************99*************** PP

                                       HHHHHHT..CTSHHHHHHHHHHHHHHTTSET...EEEEEEEBTTTSHHHHHHHHHHH CS
                                       xxxxxxx..xxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 116 kvlklmn..rghtfeevlealeklreagikr...vvdrivglpGendeeleellell 167
                                        v + m+  +++ fee+   +  ++e+ +k+   v++ i g+pG   e ++el+e++
  gi|298674016|ref|YP_003725766.1| 466 -VTDVMRkpGKQVFEEFASKFNEINEKLGKEqylVSFLISGHPGSKIENMVELAEYI 521
                                       .*****8888888888888888888886666999******************99976 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0    0.0001      0.46       4      36 ..      35      66 ..      32     110 .. 0.79
   2 !    8.4   0.0   0.00047       2.1      71      94 ..     129     152 ..     123     161 .. 0.84
   3 ?   -2.8   0.0       1.4   6.2e+03      86     120 ..     451     481 ..     450     482 .. 0.78
   4 ?   -2.8   0.0       1.4   6.3e+03      55      76 ..     501     522 ..     483     526 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0001
                       B12-binding  4 llatvggdlhplGlavlaaalrdagfeVqllga 36
                                      + + ++ d++ +G+ ++ ++l+d+gf+V ++ a
  gi|298674016|ref|YP_003725766.1| 35 VTGDAYVDHPGFGATIIGRVLEDEGFRVGII-A 66
                                      6667889*********************988.3 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00047
                       B12-binding  71 lvellkrirprvkvvvGGahpsld 94 
                                       ++++lk++ p+v++v+GG+ +sl 
  gi|298674016|ref|YP_003725766.1| 129 YTNRLKEVYPDVPIVLGGIEASLR 152
                                       56789**************98875 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.4
                       B12-binding  86 vGGahpsldpeetleaklgiddvvvgegedaleal 120
                                       vGG    ++pe +     ++ dv++  g++ +e++
  gi|298674016|ref|YP_003725766.1| 451 VGGQL-KVAPEHFS---DEVTDVMRKPGKQVFEEF 481
                                       78865.88888844...567899999999999987 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 1.4
                       B12-binding  55 vglSalltsqleavkelvellk 76 
                                        ++S +++s++e++ el+e ++
  gi|298674016|ref|YP_003725766.1| 501 FLISGHPGSKIENMVELAEYIR 522
                                       5788889999999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (611 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 4166.13
//
Query:       gi|298674017|ref|YP_003725767.1|  [L=215]
Description: hypothetical protein Metev_0039 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-30  106.6   0.2    1.9e-30  106.4   0.2    1.0  1  Lactamase_B     Metallo-beta-lactamase superfamily
      2e-06   27.5   0.2    2.8e-06   27.0   0.2    1.4  1  Lactamase_B_2   Beta-lactamase superfamily domain
    0.00031   20.3   0.9    0.00064   19.2   0.1    1.8  2  Lactamase_B_6   Metallo-beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.022   15.0   0.1      0.063   13.6   0.1    1.8  2  T3RM_EcoP15I_C  Type III R-M EcoP15I C-terminal domain
      0.053   13.7   0.1       0.31   11.2   0.0    2.1  2  IF-2            Translation-initiation factor 2


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.4   0.2   5.3e-34   1.9e-30       4     197 .]      11     188 ..       8     188 .. 0.94

  Alignments for each domain:
  == domain 1  score: 106.4 bits;  conditional E-value: 5.3e-34
                                       CSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHH CS
                       Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeap 80 
                                         +n+yli   ++ +LiDtG++++a  + l    ++++++ +d++ilTH H+DH G++ +++e+ ++++++++++ +
  gi|298674017|ref|YP_003725767.1|  11 YDSNIYLI---NKKFLIDTGMDAAALIKEL---ENHIDLNTLDTIILTHCHFDHSGAASEVAEKSGAKIAIHEDDVE 81 
                                       569*****...7****************98...******************************************** PP

                                       CCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTS.SHH CS
                       Lactamase_B  81 alfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDall.age 156
                                        l+++ a  a  ++   ++++ + ++++ ++++ +  ++++ l ++++pgh+ g+++++ +  k lf+GD+++ +g+
  gi|298674017|ref|YP_003725767.1|  82 CLKDNSASAADLFG---YKAPGIEPDIIYKDGDKVQIADDEYLQIIHTPGHTKGCICLYEPQSKSLFSGDTVFpSGS 155
                                       *******7766666...599*****************************************************5666 PP

                                       CCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 157 tgridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                        gr+dl        d+++a+k+ +s++kl + +++vl+pgH
  gi|298674017|ref|YP_003725767.1| 156 VGRTDL--------DGGSADKLEQSIEKLTEFDVKVLYPGH 188
                                       666666........*************************** PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.2   7.8e-10   2.8e-06       2      74 ..      21      87 ..      20     159 .. 0.73

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 7.8e-10
                                      EEEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTC CS
                     Lactamase_B_2  2 riLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanf 74
                                       +LiD+g d ++  + +        +l+ +d ++lth+H+DH   +  ++e ++   ++  +++  + l++n+
  gi|298674017|ref|YP_003725767.1| 21 KFLIDTGMDAAALIKELE----NHIDLNTLDTIILTHCHFDHSGAASEVAEKSGA--KIAIHEDDVECLKDNS 87
                                      58*******777733332....456899***************888899996664..4445565555555554 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   1.8e-07   0.00064       7      57 ..      20      67 ..      15      77 .. 0.81
   2 ?   -0.9   0.1      0.26   9.3e+02     103     120 ..     197     214 ..     168     215 .] 0.74

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.8e-07
                     Lactamase_B_6  7 vkiLlDvGwdeskvslesalkelekvi..ptvdliLLshatlehlGayallya 57
                                       k+L+D G+d         +kele++i  +t+d i+L+h   +h Ga + +  
  gi|298674017|ref|YP_003725767.1| 20 KKFLIDTGMDAA-----ALIKELENHIdlNTLDTIILTHCHFDHSGAASEVAE 67
                                      689*******86.....479******7558****************9655544 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.26
                     Lactamase_B_6 103 ledideafdkiktlkYsQ 120
                                        e i+++ +  k+lkY Q
  gi|298674017|ref|YP_003725767.1| 197 NEQIKQSHQASKQLKYLQ 214
                                       377888889999999998 PP

>> T3RM_EcoP15I_C  Type III R-M EcoP15I C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.8e-05     0.063      27      78 ..       3      58 ..       1      68 [. 0.78
   2 ?   -3.5   0.0       3.8   1.4e+04      22      36 ..      88     102 ..      84     107 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.8e-05
                    T3RM_EcoP15I_C 27 legYtayliekkLYliekgl...esealkaLiekldedkefni.ekivlfgysfes 78
                                      +++ +a  +++++Yli+k++   +  + +aLi++l+++ ++n  ++i+l   +f+ 
  gi|298674017|ref|YP_003725767.1|  3 VQKINASPYDSNIYLINKKFlidTGMDAAALIKELENHIDLNTlDTIILTHCHFDH 58
                                      567889999**********94444568899*******9999852678877777774 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.8
                    T3RM_EcoP15I_C  22 veevdlegYtaylie 36 
                                       +++ dl gY+a  ie
  gi|298674017|ref|YP_003725767.1|  88 ASAADLFGYKAPGIE 102
                                       566789999997766 PP

>> IF-2  Translation-initiation factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.36   1.3e+03      74      94 ..      56      76 ..      37      96 .. 0.70
   2 ?   11.2   0.0   8.5e-05      0.31      25      61 ..     164     198 ..     157     207 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.36
                                      SSCTHHHHHCCCCCTSEEEEE CS
                              IF-2 74 vkvskkakklaekegvkirly 94
                                       + s +a+++aek+g ki  +
  gi|298674017|ref|YP_003725767.1| 56 FDHSGAASEVAEKSGAKIAIH 76
                                      456667777777777666544 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 8.5e-05
                                       HHHHHHHHHHHCTT.SSTEEEECEEEESSB-HHHHHH CS
                              IF-2  25 GsleAlkeaLekleseevkvkvihsgvGaitesDvel 61 
                                       Gs++ l++++ekl  +e  vkv++ g G+++ ++v+ 
  gi|298674017|ref|YP_003725767.1| 164 GSADKLEQSIEKL--TEFDVKVLYPGHGNVSVDNVNE 198
                                       8************..79**************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1374.72
//
Query:       gi|298674018|ref|YP_003725768.1|  [L=253]
Description: TatD family hydrolase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.9e-66  224.1   0.2    2.1e-66  223.9   0.2    1.0  1  TatD_DNase  TatD related DNase


Domain annotation for each model (and alignments):
>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.9   0.2   1.2e-70   2.1e-66       1     254 [.       6     251 ..       6     252 .. 0.96

  Alignments for each domain:
  == domain 1  score: 223.9 bits;  conditional E-value: 1.2e-70
                                       EEEEE-TTSCCCTTTHHHHHHHHHHTTEEEEEEE-SSGGGHHHHHHHHTT.TTTEEEEE---GGGGGCC.CCHHHHH CS
                        TatD_DNase   1 iDaHcHldskefeedreeileraeeagvaavvvvgtsskdskavlelakkypnkvyavlGiHPnevdeasedlleel 77 
                                       iD+HcHld+k+f++dree++era+ +gv+ +++ g++ k+++  l+l+ kypn ++a+lG+ P  + + ++d+++++
  gi|298674018|ref|YP_003725768.1|   6 IDSHCHLDFKKFNKDREEAIERANLNGVTELINSGIDYKTNESSLKLSDKYPN-IHATLGLSPMVASNSEDDVVDDI 81 
                                       8***************************************************9.*********99998888888888 PP

                                       HHHHHCCCTSEEEEEEEEEET-.CCCCCGHHHHHHHHHHHHHHHHHTTEEEEEEEES-HHHHHHHHHHCGGCCSEEE CS
                        TatD_DNase  78 kelanvkhskvvaiGeiGLDyy.sreestkeaqeevFeeqlrlAkelklplviHlrkaeedlleilkeaaeakakvv 153
                                        +  + + + +v+iGe G+D+y  ++es+k+ q ++F++ ++lA  +++ lviH r+ae++ll++++ ++     vv
  gi|298674018|ref|YP_003725768.1|  82 LSHIEQNLETAVGIGEAGMDFYhCKNESEKDDQLQAFKNVVELADSFDKTLVIHGRDAEDKLLNLVQHLD----NVV 154
                                       7777889999***********658999*****************************************95....59* PP

                                       ETT--S-HHHHHHHHHTTEEEEE-GGGGTTTTHHHHHHHHHS-GGGEEE---TTSSEECCCTTSE--GGGHHHHHHH CS
                        TatD_DNase 154 lHsfsgsaeeakkflklgyyislsglltfknakelrelvkavpldrlLiETDaPyltpkpyrgkrnepanvayvvek 230
                                       +H++sgs+e++kk++ +gyyis++ l++f  +k++++lv+++p d++L+ETD+Pyl+p  yrgkrnepa++ ++v+k
  gi|298674018|ref|YP_003725768.1| 155 FHCYSGSIETMKKITGMGYYISIATLVCF--SKHHQSLVRELPIDKMLLETDSPYLSP--YRGKRNEPAFIVNSVDK 227
                                       *****************************..7799***********************..***************** PP

                                       HHHHHTS-HHHHHHHHHHHHHHHH CS
                        TatD_DNase 231 laelkaltleelaeitaeNakrlf 254
                                       +a++ + +   +a +ta+N+ r+f
  gi|298674018|ref|YP_003725768.1| 228 IANILNTDASYIASKTAKNTHRVF 251
                                       ***********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 2047.56
//
Query:       gi|298674019|ref|YP_003725769.1|  [L=510]
Description: isopropylmalate/citramalate/homocitrate synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-87  293.3   3.7    3.6e-87  292.3   3.7    1.5  1  HMGL-like        HMGL-like
    1.3e-31  109.3   3.9    2.8e-31  108.2   3.9    1.6  1  LeuA_dimer       LeuA allosteric (dimerisation) domain
    0.00025   21.5   0.2     0.0056   17.1   0.0    2.8  3  Radical_SAM      Radical SAM superfamily
  ------ inclusion threshold ------
       0.27   11.7   3.3        2.4    8.6   0.1    3.6  4  Phage_holin_6_1  Bacteriophage holin of superfamily 6 (Holin_


Domain annotation for each model (and alignments):
>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  292.3   3.7     8e-91   3.6e-87       2     264 .]      17     274 ..      16     274 .. 0.99

  Alignments for each domain:
  == domain 1  score: 292.3 bits;  conditional E-value: 8e-91
                                       -EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHH CS
                         HMGL-like   2 vkivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdi 78 
                                       + i+dttLRDGeq+++ +l++e+kl+ia++Ld++gvd++E+gf++++++d+e+v+aia+a+ + ++++l+r + +di
  gi|298674019|ref|YP_003725769.1|  17 ISIFDTTLRDGEQTPGISLNTEQKLNIAQQLDKLGVDVLEAGFAVSTKGDRESVQAIANAGLSLDVCGLARVKREDI 93 
                                       78*************************************************************************** PP

                                       HHHHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHHH CS
                         HMGL-like  79 kaavealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkdvelsledasrtdleflaevveaa 155
                                       +a ve    +g++++h+f++ts++++ + ++k+reev+++a++av++++++ +++ +s++da+rtd ++l+++++ +
  gi|298674019|ref|YP_003725769.1|  94 DACVE----TGVDMIHTFVSTSDVQRIHTINKSREEVLEMAVDAVEYIKDHDIKCLFSAMDATRTDFDYLIDIYKSV 166
                                       *****....******************************************************************** PP

                                       HHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS--SSBB CS
                         HMGL-like 156 eeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGlGeraG 232
                                       e aG+++in++DtvGv++P+++++lis + ++v+  +++ vHcHnd+GlAvan+l+AveaGa++  +t+nGlGeraG
  gi|298674019|ref|YP_003725769.1| 167 EGAGCDIINVPDTVGVMSPSSMYNLISDINNNVN--IPIDVHCHNDFGLAVANSLMAVEAGASQTQVTINGLGERAG 241
                                       **********************************..***************************************** PP

                                       B-BHHHHHHHHHHTT.-B----HHHHHHHHHHH CS
                         HMGL-like 233 naaleelvaalealg.vdtgldlqklrsiaalv 264
                                       na+l e ++ l+    ++t+++++ ++++a++v
  gi|298674019|ref|YP_003725769.1| 242 NADLAETAMSLNSIYgAKTNINTKYIMETAKMV 274
                                       ***********97655**************997 PP

>> LeuA_dimer  LeuA allosteric (dimerisation) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.2   3.9   6.2e-35   2.8e-31       2     132 ..     372     505 ..     371     506 .. 0.95

  Alignments for each domain:
  == domain 1  score: 108.2 bits;  conditional E-value: 6.2e-35
                                       XXXXXXXXXXXXXXXXXX..--EEEEEEEEEEETTCEEEEEEEEEE.TTEEEEEEEE-SSHHHHHHHHHHHHHHH.. CS
                        LeuA_dimer   2 vtdedlealvkdelleae..erlkleklqvssgedelstatvklevkdgeekeasaeGnGpvdAllnAlrkalgv.. 74 
                                       +td+dl++++++++++++  + +kl++l+v++g+ +++ta+vk+ +  ++e+ as +G+GpvdA+++A+++++g+  
  gi|298674019|ref|YP_003725769.1| 372 ITDADLYTIASTVMGKPSgeDAIKLKELSVMTGNISTPTAVVKAVI-RDSETIASNTGVGPVDAAIKAVEEIIGEya 447
                                       9***************766699************************.88888***********************88 PP

                                       T-EEEEEEEE--TT-TT--EEEEEEEE--GGGEEEEEEEESSHHHHHHHHHHHHHHHH CS
                        LeuA_dimer  75 dikLldYsvhaitegtdaqaevrVelevddgkkvsgvGvdsdiveASlkAlisalnrl 132
                                        i++ d++++ai++g+da+aev++ +e ++gk++s++++++div AS+ Ali +ln +
  gi|298674019|ref|YP_003725769.1| 448 TINIHDFRIEAISGGSDALAEVTIGVEDEKGKIISARSASADIVIASVDALITSLNIM 505
                                       88*************************999*************************976 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.3e-06    0.0056      74     149 ..      48     147 ..      12     164 .. 0.76
   2 ?   -1.8   0.0      0.78   3.5e+03      47      96 ..     229     276 ..     216     287 .. 0.73
   3 ?    0.9   0.0      0.12   5.3e+02      78     134 ..     339     362 ..     307     422 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.3e-06
                                       C.....CCTEEEEEEECSSCHG....................HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CT CS
                                       x.....xxxxxxxxxxxxxxxx....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                       Radical_SAM  74 a.....vpgiritvetngtlpd....................eeklerllelgvdrvslgleaaddekvlklmn.rg 124
                                       +     v +  ++v+t g + +                    +e +++ +e gvd ++  + + d  +++ +++ r 
  gi|298674019|ref|YP_003725769.1|  48 DklgvdVLEAGFAVSTKGDRESvqaianaglsldvcglarvkREDIDACVETGVDMIHTFVSTSDVQRIHTINKsRE 124
                                       444555445555555555555555555555556666666689*********************************** PP

                                       SHHHHHHHHHHHHHHTTSETEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 125 htfeevlealeklreagikrvvdri 149
                                       + +e  ++a+e++++++ik  + + 
  gi|298674019|ref|YP_003725769.1| 125 EVLEMAVDAVEYIKDHDIK--CLFS 147
                                       ******************9..5554 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.78
                                       SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  47 vkevilgggepllypdfvellerlaklavpgiritvetngtlpdeekler 96 
                                       + + i g ge   ++d++e +  l  +   g ++ + t +++ + +++er
  gi|298674019|ref|YP_003725769.1| 229 TQVTINGLGERAGNADLAETAMSLNSI--YGAKTNINTKYIMETAKMVER 276
                                       556666778999999999999999999..699999999998876544444 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.12
                                       EEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  78 iritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevleal 134
                                       i+ ++et g+ p++e+l ++ +                                 ++
  gi|298674019|ref|YP_003725769.1| 339 IKKSLETAGIYPTDEQLNEIID---------------------------------NI 362
                                       5555555555555555555544.................................33 PP

>> Phage_holin_6_1  Bacteriophage holin of superfamily 6 (Holin_LLH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.51   2.3e+03      47      97 ..      51     102 ..      33     106 .. 0.67
   2 ?   -0.4   0.0      0.34   1.5e+03      39      61 ..     125     144 ..     112     151 .. 0.77
   3 ?    8.6   0.1   0.00054       2.4      69      93 ..     336     360 ..     332     362 .. 0.89
   4 ?   -0.3   0.0      0.31   1.4e+03      43      70 ..     431     460 ..     406     480 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.51
                   Phage_holin_6_1  47 aVkaveqvakedakgeeKkeeAleklkellkekgi.sitddeleglIEaaVk 97 
                                        V + e     ++kg+    +A+ ++   l+  g+  +  +++++ +E  V 
  gi|298674019|ref|YP_003725769.1|  51 GVDVLEAGFAVSTKGDRESVQAIANAGLSLDVCGLaRVKREDIDACVETGVD 102
                                       5555555444456777777788888888888889988999999999998886 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.34
                   Phage_holin_6_1  39 kiaeiaknaVkaveqvakedakg 61 
                                       +++   + aV ave +++ d+k+
  gi|298674019|ref|YP_003725769.1| 125 EVL---EMAVDAVEYIKDHDIKC 144
                                       444...55999999998888876 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.00054
                   Phage_holin_6_1  69 leklkellkekgisitddeleglIE 93 
                                       ++++k+ l+ +gi +td++l+ +I 
  gi|298674019|ref|YP_003725769.1| 336 KHAIKKSLETAGIYPTDEQLNEIID 360
                                       7899*****************9996 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.31
                   Phage_holin_6_1  43 iaknaVkaveqvake..dakgeeKkeeAle 70 
                                        +++a kave+++ e   +++ + + eA+ 
  gi|298674019|ref|YP_003725769.1| 431 PVDAAIKAVEEIIGEyaTINIHDFRIEAIS 460
                                       478999999999888444445555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (510 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3622.86
//
Query:       gi|298674020|ref|YP_003725770.1|  [L=344]
Description: phosphate-binding protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.7e-34  117.7   1.6    1.2e-33  117.0   1.6    1.2  1  PBP_like_2  PBP superfamily domain
    4.8e-26   91.1   0.0    7.6e-26   90.4   0.0    1.3  1  PBP_like    PBP superfamily domain
     0.0078   16.2   4.6      0.012   15.5   4.3    1.6  1  SBP_bac_1   Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
       0.13   12.0   0.0       0.47   10.2   0.0    1.9  2  SBP_bac_11  Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> PBP_like_2  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.0   1.6   2.7e-37   1.2e-33       6     279 ..      57     302 ..      51     305 .. 0.86

  Alignments for each domain:
  == domain 1  score: 117.0 bits;  conditional E-value: 2.7e-37
                        PBP_like_2   6 atsvgeifgaGsttpapalrkladafekaapgakvnyastGSgagikalrngdvdfagsdrplteseiaagwaanga 82 
                                       ++ +g++ + Gs+t++p+ +++a+ f+k++pg++  ++s+G+g+g k++ +g++d+  ++rp++ se  ++++ ng 
  gi|298674020|ref|YP_003725770.1|  57 QQLSGQVIVDGSSTVYPVSQAMAEEFKKQHPGVTTSVTSSGTGGGFKKFVQGETDINDASRPIKPSES-QKCKENG- 131
                                       45567899**********************************************************99.9******. PP

                        PBP_like_2  83 ggliqvpvaigaialvvnkdnpln..lsreaLakIfsgkI..tnWndvlglpadgpIkvvhrsdgsgttflfstala 155
                                       ++ ++++va+++i +vvn++ +     s+++La+I   +   ++W+dv++  +d+++ ++ ++  sgt+++f++++ 
  gi|298674020|ref|YP_003725770.1| 132 IEYVEFKVATDGISVVVNQNADWIdsVSKDTLAEIWGPENppQKWSDVKSEWPDKNVELYGPTSASGTFDFFTEHIV 208
                                       ******************664333589********6633255*********************************** PP

                        PBP_like_2 156 eqgpwtasgigasg..segvasavsn.ngaigyvsvaywlavkgysladvtngagkfvlptaataasalkvakiasn 229
                                        +++++ ++ +++   +  +++ v++ ++a+gy+ +ay +++                    ++ ++a+ +      
  gi|298674020|ref|YP_003725770.1| 209 GEEDASRTDYQTTEndNFIIKG-VRGsENAMGYLGYAYYQQN--------------------ENSVKAIGI------ 258
                                       **99888777755553223333.4666**********99877....................222566666...... PP

                        PBP_like_2 230 plawslqpveeniadgayPlsrftyiivyqpyayhgnnaalakaFldyll 279
                                         ++ ++p+e +i +g+yPlsr+++++v+ ++ +    ++++++F+++ +
  gi|298674020|ref|YP_003725770.1| 259 --NG-VKPTEQTISSGEYPLSRPLFFYVNIDHLKE---NEALREFVKFYI 302
                                       ..34.9************************99988...********9975 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.4   0.0   1.7e-29   7.6e-26       1     192 [.      79     301 ..      79     302 .. 0.85

  Alignments for each domain:
  == domain 1  score: 90.4 bits;  conditional E-value: 1.7e-29
                                       HHHHHHH-TTCEEEEEES-HHHHHHHHHTTS-SEEEESS---CCCHHCCCCCEEEEEEEEEEEE-CC-HCHCCCCHC CS
                          PBP_like   1 aeelaeknpgvrvavanvGsggGlkalrageadiagshlldketeeynapalrkaldgievvlvnlarreqglvvak 77 
                                       aee+++++pgv+ +v+ +G+ggG+k++ +ge+di  +++++k +e+ +++  +   +gie+v+ ++a++ +++vv++
  gi|298674020|ref|YP_003725770.1|  79 AEEFKKQHPGVTTSVTSSGTGGGFKKFVQGETDINDASRPIKPSESQKCK--E---NGIEYVEFKVATDGISVVVNQ 150
                                       79************************************************..7...79******************* PP

                                       CHHH..S...............--BGGGC....-S-B-EEEEE-TTSHHHHHHHHHHC-CEECTE-SSTTSEEESSH CS
                          PBP_like  78 gnpk..k...............itnwkdl....adaplrlvnRetGSGtrdlfdellkkegiskssikgyaqearsh 133
                                       + ++                   ++w+d+    +d+++ l+++   SGt+d+f+e++ +   + +s+++y+++++++
  gi|298674020|ref|YP_003725770.1| 151 NADWidSvskdtlaeiwgpenpPQKWSDVksewPDKNVELYGPTSASGTFDFFTEHIVG--EEDASRTDYQTTENDN 225
                                       ****651556777788888888*******999999**********************66..59999****9999998 PP

                                       HHH.................HCCHCCETTCCEC.CCGG-HCCCCCCECTTCE-EEEEEEEECTCCCS.HHHHHHHHH CS
                          PBP_like 134 lav.................aaaVaagradvgv.gieavaeelkgldfvplaeerydlvvrkealdd.pevqaflef 191
                                         +                  +  ++   ++g+ g++++ +++ + +  pl++ +++++v+ + l++ +++++f++f
  gi|298674020|ref|YP_003725770.1| 226 FIIkgvrgsenamgylgyayYQQNENSVKAIGInGVKPTEQTI-SSGEYPLSR-PLFFYVNIDHLKEnEALREFVKF 300
                                       8776667777777777743333333333566677889999888.777779**8.99999999988764889999999 PP

                                       H CS
                          PBP_like 192 l 192
                                       +
  gi|298674020|ref|YP_003725770.1| 301 Y 301
                                       7 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   4.3   2.7e-06     0.012      10     208 ..      75     249 ..      66     334 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.7e-06
                                       HHHHHHHHHHHHHTTEEEEEEEECHHHHHH...HHHHHHHTTS...SSCSEEEECGGHHH....HHHHTTSBECCHH CS
                         SBP_bac_1  10 lqalvakafekehpgikVeiesvgsgslaq...kltlaiaaGd...gpaDviavdndwia....rlakaglllpldp 76 
                                        qa++ ++f+k+hpg++  ++s+g+g++     ++ ++i   +   +p +  ++     +    ++++ +++++  +
  gi|298674020|ref|YP_003725770.1|  75 SQAMA-EEFKKQHPGVTTSVTSSGTGGGFKkfvQGETDINDASrpiKPSESQKC-----KengiEYVEFKVATDGIS 145
                                       46666.99**********************899999999999944444444444.....333333333388899999 PP

                                       HHHHTTECTTCCTEEEEHHHHTHHHHCEEEESEEEEEEEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTCTH CS
                         SBP_bac_1  77 yvkaylapgvkdaadklsssvlpkildskvlyvPlyaargliYNkdlfekagldppwtWdelveaakklkekgkkpi 153
                                       +v++++a++     d+ s+++l+ i++ +                        +pp  W+++           ++p 
  gi|298674020|ref|YP_003725770.1| 146 VVVNQNADW----IDSVSKDTLAEIWGPE------------------------NPPQKWSDVKSEWPDKNVELYGP- 193
                                       999998777....7899999999999842........................56999998886555444444444. PP

                                       CCHCCEEHHHHHHHHHHHHHHHHTGGGEECCCT......HHCSHHHHSHHHHHHHHHHHHH CS
                         SBP_bac_1 154 ggarggsasgtayyfalalakslggkvfdkdgg......gldnpegvtaatylvklyavan 208
                                             sasgt + f++++ +  ++   d           +  ++ ++a +yl ++y+++n
  gi|298674020|ref|YP_003725770.1| 194 -----TSASGTFDFFTEHIVGEEDASRTDYQTTendnfiIKGVRGSENAMGYLGYAYYQQN 249
                                       .....77889988888888888885555555556665554344444447777777777776 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0001      0.47       5      42 ..      67     105 ..      63     199 .. 0.77
   2 ?   -0.7   0.0      0.21   9.4e+02     194     229 ..     280     315 ..     227     316 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0001
                                       E-SSTHHHHHHHHHHH.HHHH---EEEEESSHHHHHHHH CS
                        SBP_bac_11   5 aagslaaalrelaaaF.eahtgvkvevsaggsgklarqi 42 
                                        +++++++ +++a++F ++h+gv+  v++ g g   ++ 
  gi|298674020|ref|YP_003725770.1|  67 GSSTVYPVSQAMAEEFkKQHPGVTTSVTSSGTGGGFKKF 105
                                       57888899999*****777*********99998766665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.21
                                       EEEEEEE-TT--HHHHHHHHHTTSHHHHHHHHHTT- CS
                        SBP_bac_11 194 ypaavlkkaakreaAraFlafLrspeaqailrkyGf 229
                                       + ++ +++ +++ea r+F++f   +   +i+ + G+
  gi|298674020|ref|YP_003725770.1| 280 FFYVNIDHLKENEALREFVKFYIEKSDSEIINQVGY 315
                                       335566777899999999999888887777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.24s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2212.63
//
Query:       gi|298674021|ref|YP_003725771.1|  [L=302]
Description: phosphate ABC transporter permease [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.8e-19   68.8  10.0    4.8e-19   68.8  10.0    2.1  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
        1.7    8.6   5.9       0.28   11.1   0.6    2.4  2  DUF5408       Family of unknown function (DUF5408)
        2.2    8.6   6.8        7.2    7.0   0.0    3.2  3  Sigma_reg_N   Sigma factor regulator N-terminal


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   3.7     0.013        81     109     172 ..      37      92 ..      33      96 .. 0.67
   2 !   68.8  10.0     8e-23   4.8e-19       5     184 ..      97     299 ..      93     300 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.013
                      BPD_transp_1 109 piitglilafggllggavlleflgswpGlgtllleailgydyseisnggvlalviavlllnlva 172
                                        ii++l+  +++++++ +++efl+     gt +  +   ++ys++   +++++++++ ++++++
  gi|298674021|ref|YP_003725771.1|  37 LIIATLLGDAINFFTEVSIVEFLT-----GTNWSPSM--KPYSFGV-LPLVTGTLMITVISAAV 92 
                                       799999******************.....43333333..3333334.55666666666665554 PP

  == domain 2  score: 68.8 bits;  conditional E-value: 8e-23
                      BPD_transp_1   5 Gilaa....lnrnkkldkllrpliivllslPsfvlaillvlvf......vilsilghlilpviillllsaapyvrli 71 
                                       G+ +      +  kk++k++ p+ +vl ++P++v +++ + ++      ++  i  + +l++ i++ ++++p++  +
  gi|298674021|ref|YP_003725771.1|  97 GVATSvylsEYADKKVRKVVKPVLEVLAGIPTVVYGFFALTFItpvlqtIFPEISLYNALSAGIVVGIMILPMISSL 173
                                       5555555558999*********************777766555677777788888999999**************** PP

                      BPD_transp_1  72 rraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgy 148
                                        ++a++s+p+dl+   +alGas++ +   +v+P++++ i++++il + +++g+++++ + ++   l ++ l+++ + 
  gi|298674021|ref|YP_003725771.1| 174 SEDAMSSVPDDLRDGGYALGASKFNVTTGIVVPASISGILSSFILGISRAIGETMAVTIAAGR--LANMSLDPLKSI 248
                                       *************************************************************55..888888888888 PP

                      BPD_transp_1 149 dyseis...............nggvlalviavlllnlvadilqrlldprvr 184
                                        +  ++               + +++a+++++++++l+++ + ++l  r +
  gi|298674021|ref|YP_003725771.1| 249 ETMTAAmvevaegdiaagtaaYDSLFAIGLLLFVITLAMNMVSQYLKSRYK 299
                                       77777788*********9999999999999999999999999999998865 PP

>> DUF5408  Family of unknown function (DUF5408)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.6   4.7e-05      0.28       8      35 ..      15      43 ..       6      48 .. 0.75
   2 ?   -1.8   0.5      0.48   2.9e+03      15      32 ..     276     293 ..     273     294 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.7e-05
                           DUF5408  8 iAkRAvkiALv.CvvitlllallslyvLl 35
                                        +RA+k AL+ C ++ ll+++l +  Ll
  gi|298674021|ref|YP_003725771.1| 15 LKERAIKSALFsCAFVSLLVTILIIATLL 43
                                      357*******9788999999998887666 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.48
                           DUF5408  15 iALvCvvitlllallsly 32 
                                       i L+  vitl + ++s y
  gi|298674021|ref|YP_003725771.1| 276 IGLLLFVITLAMNMVSQY 293
                                       678888999999998877 PP

>> Sigma_reg_N  Sigma factor regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.8     0.019   1.1e+02       6      30 ..      18      42 ..      13      53 .. 0.84
   2 ?    7.0   0.0    0.0012       7.2      15      54 ..      82     121 ..      81     124 .. 0.89
   3 ?   -0.4   0.1      0.24   1.4e+03      18      37 ..     274     294 ..     272     302 .] 0.40

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.019
                       Sigma_reg_N  6 kakrksilrivlislivlllifvil 30
                                      +a++ ++++ +++sl+v++li++ l
  gi|298674021|ref|YP_003725771.1| 18 RAIKSALFSCAFVSLLVTILIIATL 42
                                      78899999999******99999876 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0012
                       Sigma_reg_N  15 ivlislivlllifvilvvtllylaekegnklrevlelave 54 
                                       + +i++i++ + +++ v t  yl+e  ++k r+v++ ++e
  gi|298674021|ref|YP_003725771.1|  82 TLMITVISAAVAIPLGVATSVYLSEYADKKVRKVVKPVLE 121
                                       689********************99999999999887766 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.24
                       Sigma_reg_N  18 islivlllifvil.vvtllyl 37 
                                       +++++ll+++ +   +  +yl
  gi|298674021|ref|YP_003725771.1| 274 FAIGLLLFVITLAmNMVSQYL 294
                                       344444444444423333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       799  (0.0445647); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 1956.11
//
Query:       gi|298674022|ref|YP_003725772.1|  [L=283]
Description: phosphate ABC transporter permease [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-21   76.1  16.3    2.7e-21   76.1  16.3    2.1  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
        4.3    7.5   9.3        2.5    8.3   0.1    3.4  3  DUF5368       Family of unknown function (DUF5368)


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   2.3     0.046   4.1e+02     110     172 ..      21      80 ..      13      84 .. 0.44
   2 !   76.1  16.3     3e-25   2.7e-21       1     181 [.      85     278 ..      81     282 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.046
                      BPD_transp_1 110 iitglilafggllggavlleflgswpGlgtllleailgydyseis.nggvlalviavlllnlva 172
                                       i+t +++a+ ++l  +vl   +g      +l + +++ + ++e + + ++l++ i+++ll++v+
  gi|298674022|ref|YP_003725772.1|  21 IATCVGVASLAILVYSVLEDSIG----WFDLAFIFNSPSRFPEEAgIYPALIGSIYLMLLVAVF 80 
                                       22222222222222222222222....3344444444444444447666666666666666665 PP

  == domain 2  score: 76.1 bits;  conditional E-value: 3e-25
                      BPD_transp_1   1 gillGilaa.lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraal 76 
                                       g++++i++  ++  +++++++   i  l ++Ps+v ++l +++fv     g + ++++++l+l ++p+v++  ++a+
  gi|298674022|ref|YP_003725772.1|  85 GVGTAIYLEeYAGQSRIKNIIELNISNLAAVPSIVYGLLGLALFVRALNMGRSLIAGALTLTLLILPIVIVSSQEAI 161
                                       455566666999999*****************************99999**************************** PP

                      BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydysei 153
                                       +++p++l+ a++  Ga++wq++rk+v+P alp i+tg il++ +++g+++ l ++g   + +++   +  ++ + ++
  gi|298674022|ref|YP_003725772.1| 162 KAVPDSLRDASYGIGATKWQTIRKIVIPEALPGIMTGTILSLSRAIGETAPLIMIG---AATSMYSAPDGIFSLFSA 235
                                       ********************************************************...677888888877777777 PP

                      BPD_transp_1 154 s...............nggvlalviavlllnlvadilqrlldp 181
                                       +                 gv+ ++i++ll++l+++  +++l +
  gi|298674022|ref|YP_003725772.1| 236 MplqiyawvgqpqyafQEGVASAGILLLLIVLLTMNSVAILIR 278
                                       7888999999999999888888888888888888877777755 PP

>> DUF5368  Family of unknown function (DUF5368)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1   0.00028       2.5      74     106 ..       5      37 ..       3      41 .. 0.88
   2 ?    0.9   0.2     0.055   4.9e+02      50     105 ..      75     131 ..      71     137 .. 0.78
   3 ?    2.0   0.4     0.025   2.3e+02      23      43 ..     260     280 ..     255     282 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00028
                           DUF5368  74 sglsDiggpvDlllllliaaaglvgstilvYtv 106
                                       s+  D+ g   l+ll+++  +g+  ++ilvY+v
  gi|298674022|ref|YP_003725772.1|   5 SNKGDLKGQTFLFLLVIATCVGVASLAILVYSV 37 
                                       555688888899*******************98 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.055
                           DUF5368  50 lvraelvglvGgvlalllvaavtqsglsDi.ggpvDlllllliaaaglvgstilvYt 105
                                       l++a  + ++G   a++l     qs+++ i    +  l+ +  ++ gl+g+++ v +
  gi|298674022|ref|YP_003725772.1|  75 LLVAVFSFPLGVGTAIYLEEYAGQSRIKNIiELNISNLAAVPSIVYGLLGLALFVRA 131
                                       566777788898899999999999999886245788888888888899988887755 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.025
                           DUF5368  23 illalavlvtvafvlvlirer 43 
                                       ill+l+vl+t+  v++lir+r
  gi|298674022|ref|YP_003725772.1| 260 ILLLLIVLLTMNSVAILIRNR 280
                                       689999999*********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1944.34
//
Query:       gi|298674023|ref|YP_003725773.1|  [L=271]
Description: phosphate ABC transporter ATPase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.3e-33  113.8   0.0    1.2e-32  113.3   0.0    1.2  1  ABC_tran      ABC transporter
    1.2e-14   54.8   0.0      2e-07   31.1   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    5.1e-10   39.2   0.1    4.5e-09   36.1   0.1    2.0  1  SMC_N         RecF/RecN/SMC N terminal domain
    1.4e-05   25.3   0.0    3.4e-05   24.1   0.0    1.6  1  AAA_22        AAA domain
    2.3e-05   24.3   0.0     0.0012   18.6   0.0    2.2  2  AAA_15        AAA ATPase domain
    0.00018   21.5   0.0     0.0004   20.3   0.0    1.6  1  RsgA_GTPase   RsgA GTPase
    0.00032   20.7   0.0    0.00059   19.8   0.0    1.5  1  Rad17         Rad17 P-loop domain
    0.00041   20.0   0.0    0.00089   19.0   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
    0.00048   20.7   0.2      0.001   19.6   0.0    1.7  1  AAA_23        AAA domain
     0.0021   18.3   0.1       0.13   12.5   0.0    2.3  2  AAA_28        AAA domain
     0.0023   17.7   0.1       0.03   14.0   0.0    2.2  2  AAA_24        AAA domain
     0.0039   16.4   0.0     0.0062   15.8   0.0    1.2  1  NB-ARC        NB-ARC domain
     0.0044   15.9   0.0        1.1    8.0   0.0    2.2  2  ABC_ATPase    Predicted ATPase of the ABC class
     0.0059   17.2   0.0      0.015   15.8   0.0    1.7  1  AAA_18        AAA domain
     0.0059   17.0   0.0     0.0098   16.3   0.0    1.6  1  AAA_16        AAA ATPase domain
     0.0093   15.6   0.1       0.11   12.0   0.0    2.1  2  AAA_25        AAA domain
     0.0095   15.7   0.0       0.15   11.8   0.0    2.1  2  AAA_30        AAA domain
  ------ inclusion threshold ------
       0.01   15.5   0.0      0.015   15.0   0.0    1.2  1  ATP-synt_ab   ATP synthase alpha/beta family, nucleotide-bind
      0.014   15.5   0.0      0.022   14.9   0.0    1.6  1  AAA_33        AAA domain
      0.017   14.5   0.0       0.25   10.7   0.0    2.1  2  ATPase        KaiC
      0.019   14.7   0.0      0.034   13.9   0.0    1.4  1  PRK           Phosphoribulokinase / Uridine kinase family
      0.027   13.3   0.0       0.16   10.7   0.0    1.9  2  Adeno_IVa2    Adenovirus IVa2 protein
      0.056   13.4   0.3       0.32   10.9   0.0    2.1  2  ATPase_2      ATPase domain predominantly from Archaea
       0.07   13.5   0.0       0.25   11.7   0.0    1.9  2  RNA_helicase  RNA helicase
      0.076   12.9   0.0       0.18   11.7   0.0    1.5  1  NACHT         NACHT domain
       0.12   12.8   0.0        2.9    8.3   0.0    2.4  2  AAA           ATPase family associated with various cellular 
       0.12   12.5   0.0       0.39   10.7   0.0    1.9  2  AAA_14        AAA domain
       0.12   12.5   0.1       0.31   11.1   0.0    1.7  2  MMR_HSR1      50S ribosome-binding GTPase
       0.12   12.7   0.1       0.19   12.1   0.1    1.3  1  DUF3619       Protein of unknown function (DUF3619)


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.3   0.0   1.9e-35   1.2e-32       1     136 [.      40     195 ..      40     196 .. 0.96

  Alignments for each domain:
  == domain 1  score: 113.3 bits;  conditional E-value: 1.9e-35
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS--S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp.....teGeilldgkdlke..qeleslrkeigvlpqepql 70 
                                       l++++l++ e +++ai+G++G+GKSt+l++l ++ +       eG+i +dg ++ e  ++   lrke+g+++q+p+ 
  gi|298674023|ref|YP_003725773.1|  40 LNEITLEIPEKQVTAIIGPSGCGKSTFLRTLNRMNDRipnvrIEGSIVYDGINIYEgdIDVATLRKEVGMVFQKPNP 116
                                       789*******************************99999999**************999****************** PP

                                       -TTSBHHHH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEE CS
                                       xxxxxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  71 fpeltvren..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllD 133
                                       fp++ ++en              + +e +e+ l++  l +  +++++ s+  LSgGq+qr+++aral+ +pk+ll+D
  gi|298674023|ref|YP_003725773.1| 117 FPKS-IYENvaygprvhgvndktKLNEVVEESLKNAALWDEVKDRLDASAVDLSGGQQQRLCIARALAVEPKVLLMD 192
                                       ****.99***********9888777788************************************************* PP

                                       STT CS
                                       xxx RF
                          ABC_tran 134 Ept 136
                                       Ep 
  gi|298674023|ref|YP_003725773.1| 193 EPA 195
                                       **7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   2.1e-07   0.00013       1      61 [.      52     112 ..      52     126 .. 0.82
   2 !   31.1   0.0   3.3e-10     2e-07     203     298 ..     141     225 ..     119     228 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2.1e-07
                            AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefe 61 
                                       ++++iGp g+GKS++L++l  + + +++v+ ++++  +g +i + +    +  +e  ++f+
  gi|298674023|ref|YP_003725773.1|  52 VTAIIGPSGCGKSTFLRTLNRMNDRIPNVRIEGSIVYDGINIYEGDIDVATLRKEVGMVFQ 112
                                       69********************999888888888888888888877777777777766666 PP

  == domain 2  score: 31.1 bits;  conditional E-value: 3.3e-10
                            AAA_21 203 gegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll 279
                                       +e++e++ ++          + e +d+ + +a +lS G+++ l+++ al+  +   ++ll DEp + L+P +++++ 
  gi|298674023|ref|YP_003725773.1| 141 NEVVEESLKN-------AALWDEVKDRLDASAVDLSGGQQQRLCIARALAVEP---KVLLMDEPASALDPVAMSKIE 207
                                       3333333333.......4445569999***************99999999988...9******************** PP

                            AAA_21 280 ellkelsrngaQviltTHS 298
                                       +l+ el++ +  v+++TH+
  gi|298674023|ref|YP_003725773.1| 208 DLIYELKK-NYTVVIVTHN 225
                                       ***99999.9********8 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.1   7.3e-12   4.5e-09      22     204 ..      48     231 ..      27     242 .. 0.67

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 7.3e-12
                                       TTSSEEEEEESTTSSHHHHHHHHHHHCTT..TTTTTTCHCCCCCC--..BTTCSSTTEEEEEEEEEETTEESSSSSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  22 fsksftaivGpNGSGKsnlldAilFvLGer.sakklrseklsdlihk..skekasvkkaeveitfdnedkklkieke 95 
                                        +k++tai+Gp G+GKs +l  +   + +r  +  +  + + d i+    +   ++ + ev ++f++++   k   e
  gi|298674023|ref|YP_003725773.1|  48 PEKQVTAIIGPSGCGKSTFLRTLN-RMNDRiPNVRIEGSIVYDGINIyeGDIDVATLRKEVGMVFQKPNPFPKSIYE 123
                                       3689*******************4.4443313334444444554443334445556667888888888887555555 PP

                                       CEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT..........CS-HHHHHHHHHHHHHHHHCCS--SEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  96 evsisrrvkrkgeseykingkevtkkevsellesagiske..........lLSgGektLvalaLlfAiqkvkpaply 162
                                       +v    rv   ++       k+  ++ v+e l++a +  e           LSgG+++ + +a  +A++   p+ + 
  gi|298674023|ref|YP_003725773.1| 124 NVAYGPRVHGVND-------KTKLNEVVEESLKNAALWDEvkdrldasavDLSGGQQQRLCIARALAVE---PK-VL 189
                                       5555444443333.......3333333333333333333333333333448*******99999998875...55.56 PP

                                       EECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 163 llDeidaaLDeknvkkvaellkeksknaQfivislreemlek 204
                                       l+De ++aLD   ++k+ +l+ e +kn  +++++++ +  ++
  gi|298674023|ref|YP_003725773.1| 190 LMDEPASALDPVAMSKIEDLIYELKKNYTVVIVTHNMQEAAR 231
                                       9*********************************98776554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   5.6e-08   3.4e-05       5     103 ..      50     198 ..      48     230 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 5.6e-08
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsst.sskdllrellralglelka......... 70 
                                       +++++++G+sG+GK+t lr+l + +d+ ++ + e++ v+  +++ ++  + ++l++e+   ++ ++           
  gi|298674023|ref|YP_003725773.1|  50 KQVTAIIGPSGCGKSTFLRTLNRMNDRIPNVRIEGSIVYdGINIYEGDiDVATLRKEVGMVFQKPNPFpksiyenva 126
                                       7899*********************9877777788888888888888888888888888888888777788888888 PP

                            AAA_22  71 ...................erlsseellealeqalrarav...................ielliiDEaqh.l 103
                                                          e l++ +l++ + + l+a av                   +++l+ DE    l
  gi|298674023|ref|YP_003725773.1| 127 ygprvhgvndktklnevveESLKNAALWDEVKDRLDASAVdlsggqqqrlciaralavePKVLLMDEPASaL 198
                                       777777777888888888777777777777777777776666666666666666666666666666655545 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0     2e-06    0.0012      15      49 ..      41      76 ..      38     113 .. 0.79
   2 ?    3.5   0.0     0.077        47     323     365 ..     185     225 ..     119     227 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2e-06
                            AAA_15 15 kdveidlsee.ltvliGkNnsGKSsilealdlFlnn 49
                                       ++++++ e+ +t +iG+ ++GKS++l+ l+ + ++
  gi|298674023|ref|YP_003725773.1| 41 NEITLEIPEKqVTAIIGPSGCGKSTFLRTLNRMNDR 76
                                      56667776667*******************999885 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.077
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                       ++++ll++EP   L p a + + +l++el ++    v+i TH+
  gi|298674023|ref|YP_003725773.1| 185 EPKVLLMDEPASALDPVAMSKIEDLIYELKKNYT--VVIVTHN 225
                                       45799************************99996..******8 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   6.5e-07    0.0004      81     122 ..      31      73 ..       7      85 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 6.5e-07
                                       E--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  81 lvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                        +   ++++l+e++ ++ + ++++++G+SG GKSt++ +l+  
  gi|298674023|ref|YP_003725773.1|  31 NLWYGESHALNEITLEIPEkQVTAIIGPSGCGKSTFLRTLNRM 73 
                                       444556678888888887779****************999864 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   9.5e-07   0.00059      34      67 ..      39      72 ..      26      82 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 9.5e-07
                             Rad17 34 wlkadvLesrkkriLLisGPsGCgkstvvkvLsk 67
                                      +l+  +Le  +k++  i GPsGCgkst ++ L +
  gi|298674023|ref|YP_003725773.1| 39 ALNEITLEIPEKQVTAIIGPSGCGKSTFLRTLNR 72
                                      67777899999*******************9986 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.4e-06   0.00089      13      39 ..      41      67 ..      30      72 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.4e-06
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTll 39
                                      ++ t+ei +k++t ++GpsG GKST+l
  gi|298674023|ref|YP_003725773.1| 41 NEITLEIPEKQVTAIIGPSGCGKSTFL 67
                                      55678888888**************98 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.7e-06     0.001      14      39 ..      42      70 ..      15      73 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.7e-06
                            AAA_23 14 eidF...skgltlItGpNGaGKTTildAi 39
                                      ei +   +k +t+I+Gp G+GK+T+l+ +
  gi|298674023|ref|YP_003725773.1| 42 EITLeipEKQVTAIIGPSGCGKSTFLRTL 70
                                      344466899****************9865 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   0.00021      0.13       3      22 ..      54      73 ..      52      85 .. 0.84
   2 ?    3.7   0.0      0.11        67      98     135 ..     224     261 ..     140     269 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00021
                            AAA_28  3 vitGgestGKTtlleaLaar 22
                                      +i+G++++GK+t l+ L+++
  gi|298674023|ref|YP_003725773.1| 54 AIIGPSGCGKSTFLRTLNRM 73
                                      79***************976 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.11
                            AAA_28  98 aeleaaarekrydlvfllppapeidddgeRredleere 135
                                        ++++aar + y+++f+l +  e+++++   e +++r+
  gi|298674023|ref|YP_003725773.1| 224 HNMQEAARVSDYTAFFHLGELIEYSKTKKLFENPDKRM 261
                                       34667999999*******99999966665567777665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   4.9e-05      0.03       2      24 ..      50      71 ..      49      94 .. 0.85
   2 ?    1.2   0.1      0.41   2.6e+02     111     142 ..     203     236 ..     201     256 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.9e-05
                            AAA_24  2 klkiliyGpsgiGKTtlakelgp 24
                                      k+  +i+Gpsg GK+t++++l +
  gi|298674023|ref|YP_003725773.1| 50 KQVTAIIGPSGCGKSTFLRTL-N 71
                                      67789**************99.3 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.41
                            AAA_24 111 frrllkklqelrk..nvifiahektrkdedpege 142
                                       ++++ + ++el+k  +v+++ h  ++     + +
  gi|298674023|ref|YP_003725773.1| 203 MSKIEDLIYELKKnyTVVIVTHNMQEAARVSDYT 236
                                       5666778999999999****99999877665555 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0     1e-05    0.0062      16     171 ..      48     257 ..      38     266 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1e-05
                                       TTSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCC.CBTEEEEE.................................. CS
                            NB-ARC  16 delqslvvalvGmgGvGKttlakqilnksdeveg.rFdsvawv.................................. 57 
                                        e q  v a+ G  G+GK+t ++  ++  d + + r ++ +                                    
  gi|298674023|ref|YP_003725773.1|  48 PEKQ--VTAIIGPSGCGKSTFLRTLNRMNDRIPNvRIEGSIVYdginiyegdidvatlrkevgmvfqkpnpfpksiy 122
                                       4445..99*******************9999988788865555688889**************************** PP

                                       ....................EEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTSHHHHHHHHCCCTTEEEEEEEE-S CS
                            NB-ARC  58 ....................vvsktdkseeiletilkeLslseddleekeeveslkrklvrlLltkrfllvlDDVwe 114
                                                           vv ++ k   +++++  +L  s  dl+  +++      + r+L     +l++D    
  gi|298674023|ref|YP_003725773.1| 123 envaygprvhgvndktklneVVEESLKNAALWDEVKDRLDASAVDLSGGQQQR---LCIARALAVEPKVLLMDEPAS 196
                                       ***************************************99999998888666...889999*99999999998655 PP

                                       HHH...H.....HHHHCHTTSEEEEEESBCCCCCCS-S-.EEEEEESS--HHHHHHHHHHC CS
                            NB-ARC 115 eed...wdkigvvlparenrlrvllTTRdeevanavsat.sekievelLekdeawellenk 171
                                         d   + ki   + + ++   v++ T +++ a +vs+    ++  el+e  +  +l+en 
  gi|298674023|ref|YP_003725773.1| 197 ALDpvaMSKIEDLIYELKKNYTVVIVTHNMQEAARVSDYtAFFHLGELIEYSKTKKLFENP 257
                                       5444457777766666666677777777777777777775777778888888888888875 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0018       1.1     241     266 ..      46      72 ..      41      78 .. 0.88
   2 !    5.8   0.0    0.0081         5     317     353 ..     162     198 ..     156     233 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0018
                                       EE-SS.EEEEEE-TTSSHHHHHHHHHH CS
                        ABC_ATPase 241 gipkG.vtlIvGggfhGKsTLLeAlek 266
                                        ip++ vt+I+G+   GKsT L+ l++
  gi|298674023|ref|YP_003725773.1|  46 EIPEKqVTAIIGPSGCGKSTFLRTLNR 72 
                                       588877*****************9986 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0081
                                       TEEESS--HHHHHHHHHHHHHHTT-SEEEEEGGGS-H CS
                        ABC_ATPase 317 kfstedASGStsqAanimealeagakllLiDEDtsAt 353
                                       ++s  d SG   q   i++al ++ k+lL+DE  sA 
  gi|298674023|ref|YP_003725773.1| 162 DASAVDLSGGQQQRLCIARALAVEPKVLLMDEPASAL 198
                                       6778899*************************99995 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.5e-05     0.015       3      44 ..      55      99 ..      54     114 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.5e-05
                            AAA_18  3 ltGtpGvGKttlakeLskrl.gf..gvnlrdvakenglllevdpe 44
                                      + G++G+GK+t+ + L++++  +  +++ +++++++   +e d +
  gi|298674023|ref|YP_003725773.1| 55 IIGPSGCGKSTFLRTLNRMNdRIpnVRIEGSIVYDGINIYEGDID 99
                                      89****************985558877777777776666666655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.6e-05    0.0098      23      51 ..      49      76 ..      37     234 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.6e-05
                            AAA_16 23 rpelvllsGesGvGKsslvrellralekd 51
                                      + +++ ++G+sG+GKs+ +r+l r ++++
  gi|298674023|ref|YP_003725773.1| 49 EKQVTAIIGPSGCGKSTFLRTLNR-MNDR 76
                                      557889***************994.5555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   0.00018      0.11      30      50 ..      47      67 ..      41      71 .. 0.92
   2 ?    1.1   0.1      0.42   2.6e+02      84     148 ..     155     222 ..     154     234 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00018
                            AAA_25 30 lpagelallaGapgtGKttla 50
                                      +p++ +++++G++g+GK+t++
  gi|298674023|ref|YP_003725773.1| 47 IPEKQVTAIIGPSGCGKSTFL 67
                                      799****************97 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.42
                            AAA_25  84 delrrRlravgeal..rddarllvldlagveslpLfakdrggtl...ltadvdaleaaieevegvrlvvi 148
                                       de++ Rl a   +l   +++rl +  +  ve+  L++++  ++l   + +++++l+ ++++ + + +v++
  gi|298674023|ref|YP_003725773.1| 155 DEVKDRLDASAVDLsgGQQQRLCIARALAVEPKVLLMDEPASALdpvAMSKIEDLIYELKK-N-YTVVIV 222
                                       5678888888888877777888777776664444444444444422245555555555555.2.555553 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00024      0.15      17      43 ..      49      75 ..      38      85 .. 0.84
   2 ?    1.7   0.0      0.29   1.8e+02      81     129 ..     170     229 ..     121     252 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00024
                            AAA_30 17 gdrvavltGpAGtGKttalkalreawe 43
                                      +++v+++ Gp G GK+t l++l+++ +
  gi|298674023|ref|YP_003725773.1| 49 EKQVTAIIGPSGCGKSTFLRTLNRMND 75
                                      4679*****************998765 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.29
                            AAA_30  81 k........grarlepgtllivDEagmv....dtkqlaallkaaekagakvilvGDerQla 129
                                       +        +ra   + ++l+ DE + +    +++++++l+ +++k + +v++v  + Q a
  gi|298674023|ref|YP_003725773.1| 170 GgqqqrlciARALAVEPKVLLMDEPASAldpvAMSKIEDLIYELKK-NYTVVIVTHNMQEA 229
                                       0444455553333333477777775554455566666677777766.66666666666654 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   2.4e-05     0.015      15      99 ..      51     244 ..      42     254 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.4e-05
                                       -EEEEEESTTSSHHHHHHHHHHHSSTS......S.EEEEEE.................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx......x.xxxxxx.................................... RF
                       ATP-synt_ab  15 qrtlipgafgvGktvisqslskqsnsd......d.aiiyvg.................................... 48 
                                       q t+i+g +g+Gk++ +++l + + ++      +  i+y g                                    
  gi|298674023|ref|YP_003725773.1|  51 QVTAIIGPSGCGKSTFLRTLNRMN-DRipnvriEgSIVYDGiniyegdidvatlrkevgmvfqkpnpfpksiyenva 126
                                       7899****************9995.4468888844666666888888****************************** PP

                                       ................................................................ESEEHHHHHHHHH CS
                                       ................................................................xxxxxxxxxxxxx RF
                       ATP-synt_ab  49 ................................................................iGergnevaevle 61 
                                                                                                       + e ++ +  v +
  gi|298674023|ref|YP_003725773.1| 127 ygprvhgvndktklnevveeslknaalwdevkdrldasavdlsggqqqrlciaralavepkvllMDEPASALDPVAM 203
                                       *********************************************************99999999999999999999 PP

                                       HCHH...SSGGGGEEEEEEETTS-HHHHHHHHHHHHHHHHH CS
                                       xxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  62 efpe...gtimkrtvlvantsnepvaareasiytgitlAEy 99 
                                       +  e    ++ k+ ++v+ t n++ aar+    +   l+E 
  gi|298674023|ref|YP_003725773.1| 204 SKIEdliYELKKNYTVVIVTHNMQEAARVSDYTAFFHLGEL 244
                                       999877777999****************8766655666665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   3.6e-05     0.022       2      30 ..      53      84 ..      52     195 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.6e-05
                            AAA_33  2 vllvGlpGsGKstlaerllkklg...avllss 30
                                      + ++G++G+GKst+++ l + ++    v+++ 
  gi|298674023|ref|YP_003725773.1| 53 TAIIGPSGCGKSTFLRTLNRMNDripNVRIEG 84
                                      6789************9988776666666655 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0    0.0004      0.25      15      35 ..      46      66 ..      38      70 .. 0.87
   2 ?    1.4   0.0      0.27   1.7e+02     142     168 ..     204     230 ..     193     245 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0004
                            ATPase 15 GipegrvvlitGepGtGKtif 35
                                       ipe++v+ i G +G+GK++f
  gi|298674023|ref|YP_003725773.1| 46 EIPEKQVTAIIGPSGCGKSTF 66
                                      59*****************99 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.27
                            ATPase 142 eilrqlvrvlkklgvTailvsekssse 168
                                       + +  l+++lkk++++ i + ++++ +
  gi|298674023|ref|YP_003725773.1| 204 SKIEDLIYELKKNYTVVIVTHNMQEAA 230
                                       6788999****9999999988876643 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.5e-05     0.034       2      35 ..      53      84 ..      52     113 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.5e-05
                               PRK  2 IgvagsSGaGkttvarklekifgrekvkaaeieg 35
                                       ++ g+SG+Gk+t+ r+l+ +     ++ + ieg
  gi|298674023|ref|YP_003725773.1| 53 TAIIGPSGCGKSTFLRTLNRMND--RIPNVRIEG 84
                                      5899*************987655..555556655 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00027      0.16      88     112 ..      51      73 ..       6      82 .. 0.62
   2 ?    0.1   0.0      0.43   2.6e+02     233     249 ..     214     230 ..     187     238 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00027
                        Adeno_IVa2  88 viGviyGPtGsGksqllrnlisskl 112
                                        +  i GP G+Gks +lr+l  +++
  gi|298674023|ref|YP_003725773.1|  51 QVTAIIGPSGCGKSTFLRTL--NRM 73 
                                       466788************99..444 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.43
                        Adeno_IVa2 233 ctgfsvlvvlhnlnPrs 249
                                          ++v++v hn++  +
  gi|298674023|ref|YP_003725773.1| 214 KKNYTVVIVTHNMQEAA 230
                                       3589*********8655 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00052      0.32      16      40 ..      46      70 ..      37      97 .. 0.83
   2 ?    0.4   0.1      0.79   4.9e+02      98     131 ..     198     230 ..     124     256 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00052
                          ATPase_2 16 erepneiyfiYGpegsGKtaLlkei 40
                                      e  ++++  i Gp g+GK+++l+ +
  gi|298674023|ref|YP_003725773.1| 46 EIPEKQVTAIIGPSGCGKSTFLRTL 70
                                      444578999*************975 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.79
                          ATPase_2  98 ksklvfkaielllekikkkgkkiiiiiDelqkli 131
                                           + ++ie+l+ ++kk+ + ++i+   +q++ 
  gi|298674023|ref|YP_003725773.1| 198 LDPVAMSKIEDLIYELKKNYT-VVIVTHNMQEAA 230
                                       445566667777777776644.666665665555 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00041      0.25       3      20 ..      55      72 ..      53      90 .. 0.81
   2 ?   -1.9   0.0       6.9   4.3e+03      51      90 ..     187     227 ..     184     239 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00041
                      RNA_helicase  3 lyGpsgeGKStlakeLak 20
                                      + Gpsg+GKSt+ ++L +
  gi|298674023|ref|YP_003725773.1| 55 IIGPSGCGKSTFLRTLNR 72
                                      78***********99543 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 6.9
                      RNA_helicase  51 evvvidDfgqvkdee.npsdlaelirlvsstpyplnmasle 90 
                                       +v+++d+ ++  d     +++  + +l +++++ + + +++
  gi|298674023|ref|YP_003725773.1| 187 KVLLMDEPASALDPVaMSKIEDLIYELKKNYTVVIVTHNMQ 227
                                       56666665555565544447777777777777666655555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00029      0.18       2      20 ..      52      70 ..      51      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00029
                                      CEEEEC-TTTCHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqkl 20
                                      + ++ G++G+GK+t+l+ l
  gi|298674023|ref|YP_003725773.1| 52 VTAIIGPSGCGKSTFLRTL 70
                                      6789************987 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0047       2.9       3      30 ..      55      83 ..      53     113 .. 0.78
   2 ?    2.2   0.0      0.37   2.3e+02      47      69 ..     175     196 ..     137     231 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0047
                                      EESSTTSSHHHHHHHHHHHHT.HEEEEEE CS
                               AAA  3 lyGppGtGKTllakavakelg.vefleis 30
                                      ++Gp G+GK+++ + + +  + ++ ++i+
  gi|298674023|ref|YP_003725773.1| 55 IIGPSGCGKSTFLRTLNRMNDrIPNVRIE 83
                                      68**********99886654234445555 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.37
                                       HHHHHHHHHTS.TSEEEEEETGGG CS
                               AAA  47 relfkeakeka.kpsilfiDEida 69 
                                       r ++  a++ a +p++l++DE  +
  gi|298674023|ref|YP_003725773.1| 175 RLCI--ARALAvEPKVLLMDEPAS 196
                                       3333..455556799999999554 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00063      0.39       2      26 ..      50      74 ..      49      95 .. 0.82
   2 ?   -1.4   0.0       3.7   2.3e+03      64      73 ..     185     194 ..     128     231 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00063
                            AAA_14  2 rkilvitGaRrvGKTtllkqlikel 26
                                      +++ +i G+  +GK+t+l++l + +
  gi|298674023|ref|YP_003725773.1| 50 KQVTAIIGPSGCGKSTFLRTLNRMN 74
                                      57899*************9996655 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.7
                            AAA_14  64 kktylflDEi 73 
                                       + ++l++DE 
  gi|298674023|ref|YP_003725773.1| 185 EPKVLLMDEP 194
                                       3445555554 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00051      0.31       3      21 ..      54      72 ..      52     106 .. 0.87
   2 ?   -1.9   0.0       5.7   3.5e+03      82      84 ..     190     192 ..     137     231 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00051
                                      EEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1  3 aivGrpNvGKStLinaltg 21
                                      ai+G +  GKSt++++l +
  gi|298674023|ref|YP_003725773.1| 54 AIIGPSGCGKSTFLRTLNR 72
                                      8**************9965 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.7
                                       EEE CS
                          MMR_HSR1  82 vvd 84 
                                       ++d
  gi|298674023|ref|YP_003725773.1| 190 LMD 192
                                       333 PP

>> DUF3619  Protein of unknown function (DUF3619)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1    0.0003      0.19       7      40 ..     155     188 ..     149     237 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0003
                           DUF3619   7 rkvaaaLdegaadlpediaeRLaaAReqAlarkk 40 
                                        +v+ +Ld++a dl+   ++RL  AR  A++ k 
  gi|298674023|ref|YP_003725773.1| 155 DEVKDRLDASAVDLSGGQQQRLCIARALAVEPKV 188
                                       57999*************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 1797.00
//
Query:       gi|298674024|ref|YP_003725774.1|  [L=119]
Description: alpha-NAC-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-19   68.8   2.4    4.2e-19   68.3   2.4    1.3  1  NAC       NAC domain
  ------ inclusion threshold ------
      0.081   12.8   0.1       0.15   11.9   0.1    1.4  1  UBA_4     UBA-like domain
      0.089   12.7   0.1      0.089   12.7   0.1    1.8  2  UBA       UBA/TS-N domain


Domain annotation for each model (and alignments):
>> NAC  NAC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.3   2.4     7e-23   4.2e-19       1      56 [.      12      70 ..      12      71 .. 0.97

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 7e-23
                               NAC  1 ekKlrkalkklgl..keipgieeVtirksdgkvlvfdnPkVq..kspgsntyvvfGeaee 56
                                      + K+++++k++g+  +ei+++e+V+irksd k +vf++++V+  +++g +ty+++G++ee
  gi|298674024|ref|YP_003725774.1| 12 PSKMKQMMKQMGIstEEINDVEQVIIRKSD-KDIVFNDASVTvmTAQGVDTYQIVGTPEE 70
                                      57****************************.***************************98 PP

>> UBA_4  UBA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   2.5e-05      0.15      11      34 ..      89     112 ..      86     113 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.5e-05
                             UBA_4  11 TGadeekArqlLeannWdLerAis 34 
                                       +G++e+ Ar+ L+ + +dL  Ai+
  gi|298674024|ref|YP_003725774.1|  89 AGTSEDAAREALKNTKGDLAEAIT 112
                                       599*******************96 PP

>> UBA  UBA/TS-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.6   1.3         3   1.8e+04       7      13 ..      17      23 ..      17      23 .. 0.83
   2 ?   12.7   0.1   1.5e-05     0.089      16      35 ..      93     112 ..      92     114 .. 0.89

  Alignments for each domain:
  == domain 1  score: -4.6 bits;  conditional E-value: 3
                                      HHHHHTT CS
                               UBA  7 qrLveMG 13
                                      q +++MG
  gi|298674024|ref|YP_003725774.1| 17 QMMKQMG 23
                                      6789999 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 1.5e-05
                                       HHHHHHHHHHTTTSHHHHHH CS
                               UBA  16 reevveALratgnNeErAve 35 
                                       +++++eAL +t++++  A+ 
  gi|298674024|ref|YP_003725774.1|  93 EDAAREALKNTKGDLAEAIT 112
                                       89*************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1256  (0.0700541); expected 358.6 (0.02)
Passed bias filter:                      673  (0.037537); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 822.79
//
Query:       gi|298674025|ref|YP_003725775.1|  [L=105]
Description: iron-sulfur cluster assembly accessory protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.7e-14   52.0   0.0    7.7e-14   51.8   0.0    1.0  1  Fe-S_biosyn  Iron-sulphur cluster biosynthesis


Domain annotation for each model (and alignments):
>> Fe-S_biosyn  Iron-sulphur cluster biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.0   4.3e-18   7.7e-14       3     103 ..       2      95 ..       1     102 [. 0.95

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 4.3e-18
                                       EEE-HHHHHHHHHHHHCTTEC...EEEEEECCTSCCGGS.TT.EEEEEEEEESSTSTTTEEEEEETTEEEEEEGGGH CS
                       Fe-S_biosyn   3 itlteaAaeklkkllaedkke...lrLdvddgggpyskggCsiggkyslvlvdeedeeydevlesnggkvyvksysl 76 
                                       +++t++Aa +lk+ll++++ke   lr+++   g       Cs g +y l l +e  +e+d++ esng+kv+++s+ +
  gi|298674025|ref|YP_003725775.1|   2 VNITDEAASELKSLLESEEKEdhaLRIFIAGMG-------CS-GIQYGLALDNEI-KEEDVTEESNGLKVVMSSDIE 69 
                                       79***************99999*********99.......**.************.********************* PP

                                       HHS.TTEEEEEEEETTEEEEEEETCCE CS
                       Fe-S_biosyn  77 vfldeglvldfvedlgtlgLksdngil 103
                                       + l  + ++d+ve++++ g+  dn++ 
  gi|298674025|ref|YP_003725775.1|  70 EGL-SDATIDYVETEEGKGFVIDNPNP 95 
                                       ***.89******************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 670.22
//
Query:       gi|298674026|ref|YP_003725776.1|  [L=347]
Description: hypothetical protein Metev_0048 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       873  (0.0486921); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2523.20
//
Query:       gi|298674027|ref|YP_003725777.1|  [L=131]
Description: response regulator receiver protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.5e-28   96.6   0.0    1.1e-27   96.4   0.0    1.1  1  Response_reg  Response regulator receiver domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.4   0.0   6.2e-32   1.1e-27       1     108 [.       6     114 ..       6     118 .. 0.96

  Alignments for each domain:
  == domain 1  score: 96.4 bits;  conditional E-value: 6.2e-32
                                       EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCT..TTSEEE CS
                      Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireed..pelpvi 75 
                                       +l+v+Dd+l+rel++++l+ +gy ++  aedg eale+l+   vdlillDi++p+m+Gle++ +++++    ++pv+
  gi|298674027|ref|YP_003725777.1|   6 ILLVEDDRLNRELISDFLNPHGY-NIINAEDGFEALEKLEDYYVDLILLDIQLPQMNGLEFIYKLKNNFlfTDIPVV 81 
                                       89*********************.9999****************************************999****** PP

                                       EEESSTSHHHHHHHHHCTESEEEESSG-HHHHH CS
                      Response_reg  76 iltahseeedavealkagaddflsKpfdpeeLl 108
                                       +ltah+   d+++ ++ag d+++ Kp++ +   
  gi|298674027|ref|YP_003725777.1|  82 ALTAHAMLGDKKKFIDAGCDGYIPKPINVDVFE 114
                                       ***************************988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 967.72
//
Query:       gi|298674028|ref|YP_003725778.1|  [L=120]
Description: phosphoribosyl-AMP cyclohydrolase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-33  113.2   2.5    4.7e-33  112.9   2.5    1.2  1  PRA-CH    Phosphoribosyl-AMP cyclohydrolase


Domain annotation for each model (and alignments):
>> PRA-CH  Phosphoribosyl-AMP cyclohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.9   2.5   2.6e-37   4.7e-33       1      74 []      28     101 ..      28     101 .. 0.99

  Alignments for each domain:
  == domain 1  score: 112.9 bits;  conditional E-value: 2.6e-37
                                       EEEEE-HHHHHHHHHHSB-EEEETTTTEEEETTTTTS--EEEEEEEE-TTSSEEEEEEEESS-SSTTSBSSS-- CS
                            PRA-CH   1 mlaymnkealektletgkavyySrsrkklWkKGetSgnvqkvkeirlDcDqDalllkveqkgaaCHtgkesCFy 74 
                                       m+aym+k+alekt+etg+++y+Srsr+klWkKGe+Sg++q ++e+++DcD Da+llk++q ga+CH g +sCFy
  gi|298674028|ref|YP_003725778.1|  28 MCAYMDKTALEKTVETGYVHYWSRSRNKLWKKGESSGHLQLLHEMYVDCDMDAVLLKIKQMGASCHEGFYSCFY 101
                                       99***********************************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 734.89
//
Query:       gi|298674029|ref|YP_003725779.1|  [L=613]
Description: PilT protein domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-10   40.4   0.0    2.9e-10   39.6   0.0    1.3  1  T2SSE            Type II/IV secretion system protein
    4.8e-06   26.3   0.6    1.8e-05   24.5   0.6    2.0  1  KH_1             KH domain
    9.2e-06   26.2   0.0    2.4e-05   24.8   0.0    1.8  1  PIN              PIN domain
     0.0061   15.8   0.2      0.033   13.4   0.0    2.1  2  TIP49            TIP49 P-loop domain
      0.009   15.8   1.6       0.03   14.1   1.6    1.9  1  KH_2             KH domain
     0.0099   15.8   0.0      0.031   14.2   0.0    1.9  1  NTPase_1         NTPase
  ------ inclusion threshold ------
      0.012   15.4   0.0      0.024   14.4   0.0    1.5  1  IstB_IS21        IstB-like ATP binding protein
      0.013   15.3   0.0      0.037   13.8   0.0    1.7  1  AAA_29           P-loop containing region of AAA domain
       0.02   15.3   0.0      0.044   14.2   0.0    1.6  1  AAA_16           AAA ATPase domain
      0.022   15.3   0.0       0.05   14.1   0.0    1.6  1  AAA_18           AAA domain
      0.024   13.9   0.0      0.054   12.8   0.0    1.5  1  Zeta_toxin       Zeta toxin
      0.024   14.6   0.0      0.047   13.6   0.0    1.5  1  NACHT            NACHT domain
      0.024   14.1   0.0       0.05   13.1   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
      0.035   13.8   0.1        0.1   12.3   0.0    1.8  1  AAA_24           AAA domain
      0.043   14.2   0.0       0.14   12.6   0.0    1.9  1  AAA              ATPase family associated with various cellul
      0.043   14.0   0.0      0.094   12.9   0.0    1.6  1  AAA_33           AAA domain
      0.044   13.3   0.0      0.094   12.3   0.0    1.5  1  AAA_25           AAA domain
      0.054   13.8   0.0        1.8    8.9   0.0    2.5  2  AAA_22           AAA domain
      0.059   13.7   0.0       0.13   12.6   0.0    1.6  1  PIN_4            PIN domain
      0.074   13.0   0.0       0.26   11.3   0.0    1.9  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.075   12.8   0.0       0.17   11.6   0.0    1.5  1  AAA_11           AAA domain
       0.13   12.0   0.0        8.4    6.1   0.0    2.3  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.13   11.7   0.0       0.27   10.6   0.0    1.5  1  KTI12            Chromatin associated protein KTI12
       0.31   11.2   2.8       0.21   11.7   0.3    2.1  1  KH_5             NusA-like KH domain


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.0   3.9e-13   2.9e-10      74     244 ..     219     379 ..     172     398 .. 0.79

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 3.9e-13
                             T2SSE  74 p..ekgvrlrvvllPvvag.ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttlly 147
                                           +++r+ ++ +P + + e  ++R   ++++tld+++ + +lk        + +  +  il++G+ g GK+t++ 
  gi|298674029|ref|YP_003725779.1| 219 VlqIRNMRIAISNPPFSDDiEITAVR--PVAAVTLDEYRLSDQLK--------QRIVDQRGILIAGPPGAGKSTFAA 285
                                       34478999999999999998999999..45567899998776655........44445668**************** PP

                             T2SSE 148 allkeinksderivtvEDpvEiql.eganqvqlnakkakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTG 223
                                        +  +++++d  + t+E p+ +q+ +++ q +  ++    ++adl   +L  rPD  +  E+R +  ++i   +   
  gi|298674029|ref|YP_003725779.1| 286 GIAVYLKEKDFVVKTMESPRDLQVpKEITQYSPLDE-DMANTADL---LLLVRPDYTVYDEVRKTRDFQIFADMRFA 358
                                       *********999***********9544444444333.34445555...5889******************8888777 PP

                             T2SSE 224 HlgslsTlHansaagalerLe 244
                                         g ++ +H+  a++a++rL 
  gi|298674029|ref|YP_003725779.1| 359 GVGMVGVVHSYRAVDAIQRLI 379
                                       77779**************95 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.6   2.4e-08   1.8e-05      11      40 ..     501     531 ..     491     547 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2.4e-08
                                       HHHHHTGGGHHHHHHHHHHT-EEEEES.STT CS
                              KH_1  11 vgriIGkgGsnIkeIreetgakIkvpk.sed 40 
                                       +++iIGkgGs+I eI+++ g +I+v + +e+
  gi|298674029|ref|YP_003725779.1| 501 IPKIIGKGGSMIAEIERQLGIHIDVQRiEEE 531
                                       89***************88*****9975554 PP

>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   3.2e-08   2.4e-05       1     120 [.      11     125 ..      11     127 .. 0.73

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 3.2e-08
                                       EEE-HHHHHHHH.TTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHS....SCHCHHHHHHHHHHHHHHHTSEEEE CS
                               PIN   1 ivlDTsvliall.rgeekaeaarklleeleelvtsalvlaEllyvlar....rkskrekaaelvelllllsalkilp 72 
                                       iv DTsv+i+   ++++k+ ++++     + ++++++v++El + ++r    ++++ e+   l+el+ l+++ +i  
  gi|298674029|ref|YP_003725779.1|  11 IVPDTSVIIDGRiSEKVKSGKYKR-----SMIYIPEAVVSELEAQANRglevGYKGLEE---LRELRRLADSGEIDL 79 
                                       688******887777777766666.....88*****************64433333333...333333355555555 PP

                                       BCHHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                               PIN  73 idaeiaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrva 120
                                         ++ +    +i+l +  + +Dali ++A   ++  + t D+  ++va
  gi|298674029|ref|YP_003725779.1|  80 KYTGTRPSLDQIKLVK-GGEIDALIRSVAADMDAMFV-TGDKVQSEVA 125
                                       5555666666666655.899**************888.****999987 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   4.4e-05     0.033      44      77 ..     261     294 ..     255     303 .. 0.83
   2 ?   -0.9   0.1      0.99   7.4e+02     274     299 ..     387     412 ..     361     432 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.4e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  44 kekklaGravLlaGpsgtGktalaiaiskelged 77 
                                       k++ +  r++L+aGp+g+Gk+  a +i+  l e+
  gi|298674029|ref|YP_003725779.1| 261 KQRIVDQRGILIAGPPGAGKSTFAAGIAVYLKEK 294
                                       66667789********************988754 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.99
                                       XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 274 kaeivpGvlfiDevhmlDiecfsyln 299
                                       + +iv  v+fiD+  +  + +  +  
  gi|298674029|ref|YP_003725779.1| 387 IPQIVDTVIFIDKGEVSKVQVLEFTV 412
                                       56899999999988777777666654 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   1.6   4.1e-05      0.03      18      58 ..     482     523 ..     469     531 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.1e-05
                                       EEEEC.CSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHH CS
                              KH_2  18 veIer.tanrviiviresqpgivIGkgGsnikkigkelrkdi 58 
                                       +e+e  + +++i+ + e     +IGkgGs+i +i+ +l+  i
  gi|298674029|ref|YP_003725779.1| 482 FEVEMvSDEKAIVRVMEYDIPKIIGKGGSMIAEIERQLGIHI 523
                                       4555534588999999999999**************998666 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   4.1e-05     0.031       2      31 ..     270     299 ..     269     308 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.1e-05
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvg 31 
                                       ++i GppG GK+T+   ++  lk++++ v+
  gi|298674029|ref|YP_003725779.1| 270 ILIAGPPGAGKSTFAAGIAVYLKEKDFVVK 299
                                       789**********************99887 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.2e-05     0.024      44      80 ..     264     300 ..     231     353 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.2e-05
                         IstB_IS21  44 iekkenivllGpsGvGKshlaialgveavraglsvlf 80 
                                       i ++ +i++ Gp+G+GKs +a+ ++v   ++++ v  
  gi|298674029|ref|YP_003725779.1| 264 IVDQRGILIAGPPGAGKSTFAAGIAVYLKEKDFVVKT 300
                                       556789*******************999888887765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.9e-05     0.037      19      39 ..     265     284 ..     251     295 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.9e-05
                            AAA_29  19 idlkgatlltGpsGsGKSTll 39 
                                       +d++g +l++Gp G+GKST+ 
  gi|298674029|ref|YP_003725779.1| 265 VDQRG-ILIAGPPGAGKSTFA 284
                                       56678.*************86 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   5.9e-05     0.044      18      63 ..     263     307 ..     252     401 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.9e-05
                            AAA_16  18 rvrsgrpelvllsGesGvGKsslvrellralekdggif.lrgkcdql 63 
                                       r+ ++  + +l+ G++G GKs+ +  ++ +l+++++++ + +  ++l
  gi|298674029|ref|YP_003725779.1| 263 RIVDQ--RGILIAGPPGAGKSTFAAGIAVYLKEKDFVVkTMESPRDL 307
                                       44444..78****************9999999998777544444444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   6.8e-05      0.05       1      18 [.     270     287 ..     270     352 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.8e-05
                            AAA_18   1 IlltGtpGvGKttlakeL 18 
                                       Il++G+pG+GK+t+a  +
  gi|298674029|ref|YP_003725779.1| 270 ILIAGPPGAGKSTFAAGI 287
                                       99***********87654 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   7.3e-05     0.054      19      46 ..     270     297 ..     257     304 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.3e-05
                        Zeta_toxin  19 illgGqpGAGKselaellkdelerqgnv 46 
                                       il++G pGAGKs+ a+ ++ +l++++ v
  gi|298674029|ref|YP_003725779.1| 270 ILIAGPPGAGKSTFAAGIAVYLKEKDFV 297
                                       89*******************9755444 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   6.3e-05     0.047       3      28 ..     270     295 ..     268     303 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.3e-05
                                       EEEEC-TTTCHHHHHHHHHHHHCTS- CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaegk 28 
                                       +++ G++G GK+t+++++a+ ++e++
  gi|298674029|ref|YP_003725779.1| 270 ILIAGPPGAGKSTFAAGIAVYLKEKD 295
                                       899*****************999875 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.7e-05      0.05      15      67 ..     249     301 ..     239     307 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.7e-05
                             AAA_7  15 ptvdtvrysyllelllknkkpvllvGptGtGKtviikdllkkldkekylslti 67 
                                        t d  r+s  l++ +  ++ +l+ Gp G GK++ +  +   l++++++++t+
  gi|298674029|ref|YP_003725779.1| 249 VTLDEYRLSDQLKQRIVDQRGILIAGPPGAGKSTFAAGIAVYLKEKDFVVKTM 301
                                       589999********************************999999999998887 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00013       0.1       5      25 ..     270     294 ..     266     326 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                            AAA_24   5 iliyGpsgiGKTtlakel....gpk 25 
                                       ili Gp+g+GK+t+a+ +    ++k
  gi|298674029|ref|YP_003725779.1| 270 ILIAGPPGAGKSTFAAGIavylKEK 294
                                       89*************9886666444 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00019      0.14       1      25 [.     270     294 ..     270     317 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00019
                                       EEEESSTTSSHHHHHHHHHHHHTHE CS
                               AAA   1 vllyGppGtGKTllakavakelgve 25 
                                       +l+ GppG GK+++a  +a  l+ +
  gi|298674029|ref|YP_003725779.1| 270 ILIAGPPGAGKSTFAAGIAVYLKEK 294
                                       699****************998743 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00013     0.094       2      21 ..     270     289 ..     270     331 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00013
                            AAA_33   2 vllvGlpGsGKstlaerllk 21 
                                       +l+ G+pG+GKst+a +++ 
  gi|298674029|ref|YP_003725779.1| 270 ILIAGPPGAGKSTFAAGIAV 289
                                       5789***********99863 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00013     0.094      28      55 ..     262     289 ..     251     303 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                            AAA_25  28 gllpagelallaGapgtGKttlaldlal 55 
                                         ++ +  +l+aG+pg+GK+t+a  +a+
  gi|298674029|ref|YP_003725779.1| 262 QRIVDQRGILIAGPPGAGKSTFAAGIAV 289
                                       5566677789*************99987 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.31   2.3e+02     106     135 ..      62      90 ..      43      91 .. 0.79
   2 ?    8.9   0.0    0.0024       1.8       5      23 ..     267     285 ..     262     308 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.31
                            AAA_22 106 eealeeLrsllnlsrkgvqliLvGtp.elrk 135
                                        e l+eLr+l++  +  + l + Gt+ +l++
  gi|298674029|ref|YP_003725779.1|  62 LEELRELRRLAD--SGEIDLKYTGTRpSLDQ 90 
                                       78999*******..**********9978876 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0024
                            AAA_22   5 agilvvtGesGtGKTtllr 23 
                                       ++ +++ G++G+GK+t ++
  gi|298674029|ref|YP_003725779.1| 267 QRGILIAGPPGAGKSTFAA 285
                                       67799***********886 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00017      0.13       1     100 [.      11     112 ..      11     135 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00017
                             PIN_4   1 fVlDTnvlLhdpealksf....keehdvviPitVleELdklKkgsserelarlarqanrlldellekesgrlkvqts 73 
                                       +V DT+v+++   + +++     +   ++iP  V++EL+++ ++    e++++  + +r l+ l  + + +lk   +
  gi|298674029|ref|YP_003725779.1|  11 IVPDTSVIIDGR-ISEKVksgkYKRSMIYIPEAVVSELEAQANRGL--EVGYKGLEELRELRRLADSGEIDLKYTGT 84 
                                       699*****9877.44555677667777************9999997..99999889999998888888888888888 PP

                             PIN_4  74 aeelpee.eseseknDnrIlavalelke 100
                                       + +l++    ++ + D  I +va  ++ 
  gi|298674029|ref|YP_003725779.1|  85 RPSLDQIkLVKGGEIDALIRSVAADMDA 112
                                       7777765444467888888888876655 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00035      0.26      10      46 ..     256     294 ..     250     305 .. 0.73
   2 ?   -2.7   0.0       7.5   5.6e+03      67      77 ..     521     531 ..     514     543 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00035
                                       HHHHHHHCH..TEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                              TsaE  10 lgkklakal..gdvilLeGdLGaGKTtlvrglakalgve 46 
                                       l  +l++ +  ++ il+ G+ GaGK+t++ g+a  l+ +
  gi|298674029|ref|YP_003725779.1| 256 LSDQLKQRIvdQRGILIAGPPGAGKSTFAAGIAVYLKEK 294
                                       55566665544566******************9988654 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.5
                                       EEEE-TT-SST CS
                              TsaE  67 yHfDlYRlede 77 
                                       +H+D+ R+e+e
  gi|298674029|ref|YP_003725779.1| 521 IHIDVQRIEEE 531
                                       799*9999754 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00023      0.17      12      44 ..     263     294 ..     255     333 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                            AAA_11  12 salseseitliqGPPGtgKTktivellsqllsr 44 
                                       +++ +++  li GPPG gK+++ +++  +l ++
  gi|298674029|ref|YP_003725779.1| 263 RIVDQRG-ILIAGPPGAGKSTFAAGIAVYLKEK 294
                                       5566777.7******************999533 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.011       8.4      65     148 ..      85     172 ..      51     212 .. 0.77
   2 ?    3.6   0.0     0.065        48       1      14 [.     270     283 ..     270     304 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.011
                   Viral_helicase1  65 ililDEylllhaGyilllaalskakl..vilfGDplQipfhsrnasfllahlpsslshrvgrrttyllpsdvaeils 139
                                       +  lD + l++ G+i++l++   a++   +++GD  Q++    ++  ++ +l+++  ++++  + +++ +d+  +  
  gi|298674029|ref|YP_003725779.1|  85 RPSLDQIKLVKGGEIDALIRSVAADMdaMFVTGDKVQSEVA-IAKGLKVEQLFPQSFEFKPLLIESFFTEDTMSVHL 160
                                       556899999999*****999887766115678*****7655.69999********99***************99999 PP

                   Viral_helicase1 140 ak...vgtevev 148
                                       ++    + +  +
  gi|298674029|ref|YP_003725779.1| 161 KNkvpPMAKRGS 172
                                       996553333333 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.065
                   Viral_helicase1   1 ivvhGvpGcGKStl 14 
                                       i+++G pG+GKSt 
  gi|298674029|ref|YP_003725779.1| 270 ILIAGPPGAGKSTF 283
                                       6899********96 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00037      0.27       4      34 ..     270     300 ..     269     319 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00037
                                       EEEE--TTSSHHHHHHHHHHHHHHTT--EEE CS
                             KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvv 34 
                                       +++ G P +GKst+a+ +a +l+e++  v  
  gi|298674029|ref|YP_003725779.1| 270 ILIAGPPGAGKSTFAAGIAVYLKEKDFVVKT 300
                                       799********************98766654 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   0.00029      0.21       2      44 ..     489     525 ..     488     534 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00029
                              KH_5   2 GertkvaVkshnpnvdpvGaivgkkGsrikavsseLkgekidv 44 
                                       +e+++v V++ +     + +i+gk+Gs i +++++L g  idv
  gi|298674029|ref|YP_003725779.1| 489 DEKAIVRVMEYD-----IPKIIGKGGSMIAEIERQL-GIHIDV 525
                                       788999999999.....*******************.999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (613 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.49
# Mc/sec: 3767.70
//
Query:       gi|298674030|ref|YP_003725780.1|  [L=433]
Description: nucleotide sugar dehydrogenase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-67  225.7   0.2    5.6e-67  224.9   0.2    1.4  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
    3.5e-37  126.5   0.0    7.4e-37  125.5   0.0    1.6  1  UDPG_MGDP_dh    UDP-glucose/GDP-mannose dehydrogenase family,
    5.9e-30  103.8   0.0    5.9e-28   97.4   0.0    2.4  2  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,
    4.2e-06   26.8   0.0    1.2e-05   25.4   0.0    1.9  1  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
    5.3e-06   26.4   0.0    9.8e-06   25.6   0.0    1.4  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
    3.2e-05   24.4   0.0     0.0063   17.1   0.0    2.8  2  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    0.00027   20.6   0.0    0.00067   19.3   0.0    1.8  1  ApbA            Ketopantoate reductase PanE/ApbA
    0.00036   19.9   0.4      0.002   17.5   0.3    2.2  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
    0.00054   20.5   0.1     0.0019   18.7   0.1    2.0  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    0.00097   18.4   0.0     0.0031   16.8   0.0    1.8  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
     0.0024   18.1   0.1     0.0055   17.0   0.1    1.6  1  TrkA_N          TrkA-N domain
     0.0037   16.5   0.1     0.0057   15.9   0.1    1.2  1  FAD_binding_3   FAD binding domain
  ------ inclusion threshold ------
      0.012   15.8   0.0      0.099   12.8   0.0    2.3  2  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
      0.015   14.6   0.1       0.14   11.5   0.0    2.2  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
      0.018   15.9   0.0      0.048   14.5   0.0    1.7  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
      0.029   14.6   2.0      0.037   14.2   0.2    2.2  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
      0.042   12.7   0.0      0.063   12.2   0.0    1.2  1  CitF            Citrate lyase, alpha subunit (CitF)
       0.12   12.4   0.0        0.3   11.1   0.0    1.7  1  ADH_zinc_N      Zinc-binding dehydrogenase
       0.23   11.4   0.1        0.4   10.5   0.1    1.4  1  Rossmann-like   Rossmann-like domain
       0.26   10.8   0.3        0.5    9.9   0.3    1.4  1  DAO             FAD dependent oxidoreductase


Domain annotation for each model (and alignments):
>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.9   0.2   6.3e-70   5.6e-67       1     186 [.       1     188 [.       1     189 [. 0.97

  Alignments for each domain:
  == domain 1  score: 224.9 bits;  conditional E-value: 6.3e-70
                                       SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHHHCHTTTEEEES-HHHHHHC- CS
                    UDPG_MGDP_dh_N   1 mkisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLeelvkkavesgrlsfttdvekaveea 77 
                                       mk+sv+G+GYvG vtaa+lae+gh+vi++Didee+v+k+nsg +pi e+gL+el+++++  g+l++t+d+e+av+++
  gi|298674030|ref|YP_003725780.1|   1 MKVSVVGSGYVGTVTAACLAELGHQVICIDIDEERVNKINSGVSPIWEQGLDELIQNHA-GGNLKATSDYESAVNDS 76 
                                       89******************************************************999.9**************** PP

                                       SEEEE-----B-TTTTCB-THHHHHHHHHHHHHHHC...EEEEEE-S---TTHHHHCHHHHHHHHCSS-.TTCEEEE CS
                    UDPG_MGDP_dh_N  78 dvifiaVgTPskkkgkaaDlkyvesaarsiaealkk...gkvvvvkSTvpvgtaeelvkkileeaskkk.gvdfdvv 150
                                       d+ fi+VgTPs++ + ++Dl+ v+sa++s++ a+ +   ++vvv+kSTv++ t+e++v +ile+as k+ g+df+v 
  gi|298674030|ref|YP_003725780.1|  77 DISFICVGTPSDD-YGNIDLSIVKSASESLGYAIGSkddYHVVVLKSTVVPETTENFVTPILEQASGKQaGKDFGVS 152
                                       *************.9999***************9887889**************************9999******* PP

                                       E------TTSHHHHHHS-S-EEEEESSCHHHHHHHH CS
                    UDPG_MGDP_dh_N 151 snPEflregsavkdllnpdrvviGveekkaeaalee 186
                                       +nPEflreg+av+d++npdr+viG+ +k++++++++
  gi|298674030|ref|YP_003725780.1| 153 MNPEFLREGKAVYDFMNPDRIVIGALDKHSGDVVSH 188
                                       ****************************99988765 PP

>> UDPG_MGDP_dh  UDP-glucose/GDP-mannose dehydrogenase family, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.5   0.0   8.2e-40   7.4e-37       1      93 [.     205     297 ..     205     298 .. 0.99

  Alignments for each domain:
  == domain 1  score: 125.5 bits;  conditional E-value: 8.2e-40
                      UDPG_MGDP_dh   1 etAEliKlaaNaflatkIsfiNelanlcealgidveeVieavgldprigpkflkpglGvGGsclpkDvkaLvalaee 77 
                                       +tAE+iK+a+N+flatkIsf+Ne++n+c++l+id+ eV+++vg+d ri+p fl+ g+G+GGsc+pkDv+aL+ +++e
  gi|298674030|ref|YP_003725780.1| 205 RTAEMIKYANNSFLATKISFSNEIGNICKKLDIDTYEVMKVVGMDFRISPYFLNSGAGFGGSCFPKDVRALTGKSKE 281
                                       69*************************************************************************** PP

                      UDPG_MGDP_dh  78 lgleaelleavrevNe 93 
                                        g+e+ ll++v++vNe
  gi|298674030|ref|YP_003725780.1| 282 IGYEPILLDSVIRVNE 297
                                       ***************8 PP

>> UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.081        73      51      88 ..      60      99 ..      16     104 .. 0.76
   2 !   97.4   0.0   6.6e-31   5.9e-28       1     103 [.     320     417 ..     320     418 .. 0.95

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.081
                                      BTCCEEES-CHHHHTT-SE..EEE-S--GGGGGS-HHHHH CS
                    UDPG_MGDP_dh_C 51 ekgvevvdsleealkgada..iviltehdefkeldlaklk 88
                                        +++ +++ e+a++++d+  i++ t+ d++ ++dl+ +k
  gi|298674030|ref|YP_003725780.1| 60 GGNLKATSDYESAVNDSDIsfICVGTPSDDYGNIDLSIVK 99
                                      568999999*****99987336667788999999987655 PP

  == domain 2  score: 97.4 bits;  conditional E-value: 6.6e-31
                                       EEE-SSSSTT-S--TT-HHHHHHHHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S--G CS
                    UDPG_MGDP_dh_C   1 ailGlafKkdtdDlReSpaldiieeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaiviltehd 77 
                                       ++lGlafK++tdD+ReS+++ +i++Ll +ga++k+yDP+++ + ++      +v+++ds+eeal +++a++++t+++
  gi|298674030|ref|YP_003725780.1| 320 TVLGLAFKNGTDDIRESRSVPVIADLLYNGAKIKAYDPQANGNMKKV---FSSVNYCDSAEEALYNSEACLVMTDWN 393
                                       59*******************************************99...789************************ PP

                                       GGGGS-HHHHHHCCSS-EEEESSS-C CS
                    UDPG_MGDP_dh_C  78 efkeldlaklkelmkpavvfDgrnvl 103
                                       efk+ld      lmk++vv+Dgr+++
  gi|298674030|ref|YP_003725780.1| 394 EFKNLDS--EFGLMKNKVVVDGRRII 417
                                       ****864..56799*********986 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   1.3e-08   1.2e-05       1      78 [.       2      84 ..       2     154 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.3e-08
                                      -EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHH.....SSBTTTBTT----TTEEEES-HHHHHTT--EEE CS
                    NAD_Gly3P_dh_N  1 kiavlGaGswGtalAkvlaenghevrlwvreeelieeinee.....henvkyLpgiklpenlvattdlaealkgadiiv 74
                                      k++v+G+G  Gt  A+ lae gh+v  +  +ee +++in+      ++  + L + +   nl+at+d ++a++++di +
  gi|298674030|ref|YP_003725780.1|  2 KVSVVGSGYVGTVTAACLAELGHQVICIDIDEERVNKINSGvspiwEQGLDELIQNHAGGNLKATSDYESAVNDSDISF 80
                                      79*************************************9622222344455555667789***************988 PP

                                      E--- CS
                    NAD_Gly3P_dh_N 75 lvvP 78
                                      + v 
  gi|298674030|ref|YP_003725780.1| 81 ICVG 84
                                      8774 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   1.1e-08   9.8e-06       1      81 [.       2      78 ..       2      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.1e-08
                                      EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHH.C CS
                           3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeav.d 78
                                      kv v+G+G +G+  aa +a+ g++V  +di+ee+++k ++ ++  +e+      l+e   ++a  ++++t+d+e+av d
  gi|298674030|ref|YP_003725780.1|  2 KVSVVGSGYVGTVTAACLAELGHQVICIDIDEERVNKINSGVSPIWEQG-----LDELIQNHAGGNLKATSDYESAVnD 75
                                      699***********************************99999977765.....3445557778889999999998877 PP

                                      -SE CS
                           3HCDH_N 79 adl 81
                                       d+
  gi|298674030|ref|YP_003725780.1| 76 SDI 78
                                      775 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0     7e-06    0.0063       1      70 [.       2      84 ..       2      89 .. 0.95
   2 ?    4.1   0.0     0.077        69      48      93 ..     370     412 ..     343     413 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 7e-06
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC..................-EEECECHHHHHHH CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg..................vkvtavdneeaaee 61
                                      k+ ++G+G +g   a  l++ g   h+++ + + ++e+++++ + ++                   k+t+ d+e a+++
  gi|298674030|ref|YP_003725780.1|  2 KVSVVGSGYVGTVTAACLAELG---HQVICI-DIDEERVNKINSGVSpiweqgldeliqnhaggnLKATS-DYESAVND 75
                                      6889******************...****88.********************************999999.******** PP

                                      -SEEEE-S- CS
                     F420_oxidored 62 advvvlavk 70
                                      +d+ +++v 
  gi|298674030|ref|YP_003725780.1| 76 SDISFICVG 84
                                      *******95 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.077
                                       -EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHCGHHHHTTSEEEE CS
                     F420_oxidored  48 vkvtavdneeaaeeadvvvlavkpedveevlselakdalkgklvis 93 
                                       v+ +  ++eea+ +++  ++   ++ ++++ se    + k+k+v++
  gi|298674030|ref|YP_003725780.1| 370 VNYCD-SAEEALYNSEACLVMTDWNEFKNLDSEF--GLMKNKVVVD 412
                                       66677.99**************************..*********8 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   7.5e-07   0.00067       2      43 ..       4      46 ..       3      98 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 7.5e-07
                                      EEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEE CS
                              ApbA  2 ailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrl 43
                                       ++G+G +G++ aa+La+ g++v++i+ ++ r++++++  + +
  gi|298674030|ref|YP_003725780.1|  4 SVVGSGYVGTVTAACLAELGHQVICIDIDEeRVNKINSGVSPI 46
                                      69****************************9999998765555 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.3   2.2e-06     0.002      30      69 ..       2      41 ..       1      87 [. 0.84
   2 ?   -2.8   0.0       3.6   3.3e+03      59      94 ..     202     237 ..     198     237 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.2e-06
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqles 69
                                      kv v+G G +G+  +a  ++lg +V  +D++++r ++++s
  gi|298674030|ref|YP_003725780.1|  2 KVSVVGSGYVGTVTAACLAELGHQVICIDIDEERVNKINS 41
                                      89*********************************99998 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.6
                                       SSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH-SE CS
                       AlaDh_PNT_C  59 vrparleqleslgakfvevlksqeellaeavkeadv 94 
                                       ++p+++e ++  +++f+ ++ s ++++ + +k+ d+
  gi|298674030|ref|YP_003725780.1| 202 TNPRTAEMIKYANNSFLATKISFSNEIGNICKKLDI 237
                                       688889999999999999999999999999999986 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   2.1e-06    0.0019       1      51 [.       2      52 ..       2      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.1e-06
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHH CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqekle 51
                                      kv vvG+Gy+g   A+ laelg++V +++  ++  ++++  +s i+++ l 
  gi|298674030|ref|YP_003725780.1|  2 KVSVVGSGYVGTVTAACLAELGHQVICIDIDEERVNKINSGVSPIWEQGLD 52
                                      678*************************99998888888888877776665 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   3.4e-06    0.0031     144     190 ..       2      48 ..       1      86 [. 0.81
   2 ?   -2.0   0.0       1.8   1.6e+03     110     136 ..     353     379 ..     346     388 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.4e-06
                                       EEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 144 rivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaale 190
                                       ++ vvG+Gy+G+++Aa la+lg++v  ++  ++ +++ ++ +s + e
  gi|298674030|ref|YP_003725780.1|   2 KVSVVGSGYVGTVTAACLAELGHQVICIDIDEERVNKINSGVSPIWE 48 
                                       5789*********************9998877666666666665554 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.8
                                       EE-BCTCTTC.TTBEECCSECHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 110 sprdlgipGvaenvgklvrtldsaeal 136
                                       ++ d++  G +++v+ +v ++dsae+ 
  gi|298674030|ref|YP_003725780.1| 353 KAYDPQANGNMKKVFSSVNYCDSAEEA 379
                                       57789999999************9975 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   6.1e-06    0.0055       3      40 ..       5      41 ..       3      61 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.1e-06
                                      EES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHT CS
                            TrkA_N  3 iiGlGrvGrslaeeLse.ggkdvvvidkdeerveelree 40
                                      ++G G vG+  a  L e g+ +v+ id deerv+++   
  gi|298674030|ref|YP_003725780.1|  5 VVGSGYVGTVTAACLAElGH-QVICIDIDEERVNKIN-S 41
                                      9****************888.7************975.4 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   6.4e-06    0.0057       3      39 ..       2      38 ..       1      45 [. 0.90

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.4e-06
                                      EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCS CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvl 39
                                      +V +VG+G +G ++a  L+e G +v++++  +++v++
  gi|298674030|ref|YP_003725780.1|  2 KVSVVGSGYVGTVTAACLAELGHQVICIDIDEERVNK 38
                                      799**************************98888775 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00011     0.099       1      74 [.       2      94 ..       2     162 .. 0.78
   2 ?    0.2   0.0      0.82   7.4e+02      16      62 ..     343     389 ..     339     400 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                                      EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT...................EEE-SSHHHHHHHCSEEE CS
                     NAD_binding_2  1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg...................akaaesieelvasldvvi 60
                                      k+ ++G G  G+  a  l++ g++v++++ ++e+v+++ +                     +ka+++ e++v++ d+ +
  gi|298674030|ref|YP_003725780.1|  2 KVSVVGSGYVGTVTAACLAELGHQVICIDIDEERVNKINSGVspiweqgldeliqnhaggnLKATSDYESAVNDSDISF 80
                                      5899*********************************998878999999***********9999*************** PP

                                      E-SSSHHHHHHHHH CS
                     NAD_binding_2 61 tmvkagkavdevie 74
                                      ++v   ++    i+
  gi|298674030|ref|YP_003725780.1| 81 ICVGTPSDDYGNID 94
                                      ***98776444444 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.82
                                       HHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE- CS
                     NAD_binding_2  16 lnllkagykvavynrtkekveelvaegakaaesieelvasldvvitm 62 
                                         ll +g k+ +y+ +++   + v + ++ ++s+ee++ + ++ ++m
  gi|298674030|ref|YP_003725780.1| 343 ADLLYNGAKIKAYDPQANGNMKKVFSSVNYCDSAEEALYNSEACLVM 389
                                       667889999999997766555555677999*****999999887777 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00015      0.14      38      73 ..       2      37 ..       1      58 [. 0.80
   2 ?    0.4   0.0      0.41   3.7e+02      58      99 ..     348     390 ..     340     411 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00015
                                      EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkee 73
                                      +v ++G G +G+ +a +l+++g +vi++d  +++ +
  gi|298674030|ref|YP_003725780.1|  2 KVSVVGSGYVGTVTAACLAELGHQVICIDIDEERVN 37
                                      799**************************9977655 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.41
                                       TT-EEEEESSSHHHHHCHHHHTC.EECSHHHHHHH-SEEEE-S CS
                      2-Hacid_dh_C  58 fgmkviaydrskkkeeeeeelgv.elvsleellaesDivslhl 99 
                                        g+k+ ayd++ + + ++    v +++s ee+l +s+   +++
  gi|298674030|ref|YP_003725780.1| 348 NGAKIKAYDPQANGNMKKVFSSVnYCDSAEEALYNSEACLVMT 390
                                       58999******99887555556635669999999998766554 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   5.4e-05     0.048       1      74 [.       1      89 [.       1     103 [. 0.74

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.4e-05
                                      EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHH................HHHTTHE..EESSHHHHHTCT CS
                      GFO_IDH_MocA  1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeav................aesfgve..aysdleelladp 61
                                      ++v ++G+G++g+  ++ l e   +++v+  +d+d+er  ++                 ++ g +  a sd+e  ++d+
  gi|298674030|ref|YP_003725780.1|  1 MKVSVVGSGYVGTVTAACLAEL--GHQVI-CIDIDEERVNKInsgvspiweqgldeliQNHAGGNlkATSDYESAVNDS 76
                                      5899***********9555555..45555.56888888888877777766666666664444443558888******** PP

                                      TESEEEE-S-GGG CS
                      GFO_IDH_MocA 62 eidavivatpngt 74
                                      +i +++v+tp++ 
  gi|298674030|ref|YP_003725780.1| 77 DISFICVGTPSDD 89
                                      **********964 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   4.2e-05     0.037       1      27 [.       5      31 ..       5      35 .. 0.94
   2 ?   -2.8   0.1       8.6   7.7e+03       3      11 ..     260     268 ..     260     279 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.2e-05
                                      EE--SHHHHHHHHHHHCCTEEEEEE-S CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllek 27
                                      +vG+G  G v+A+ La+ g++v +++ 
  gi|298674030|ref|YP_003725780.1|  5 VVGSGYVGTVTAACLAELGHQVICIDI 31
                                      8*********************99996 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 8.6
                                       --SHHHHHH CS
                     NAD_binding_8   3 GaGlsGlva 11 
                                       GaG++G+++
  gi|298674030|ref|YP_003725780.1| 260 GAGFGGSCF 268
                                       899999875 PP

>> CitF  Citrate lyase, alpha subunit (CitF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.1e-05     0.063     116     168 ..      74     126 ..      24     142 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.1e-05
                              CitF 116 lkidvaflGvps.adefGnanGlkGkakcGslGyalvdaeyadkvvllteelve 168
                                          d++f+ v + +d++Gn++    k++  slGya+  ++   +vv+l   +v+
  gi|298674030|ref|YP_003725780.1|  74 NDSDISFICVGTpSDDYGNIDLSIVKSASESLGYAI-GSKDDYHVVVLKSTVVP 126
                                       3457888755432699******************96.56666778888877775 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00033       0.3       2      69 ..      11      86 ..      11     115 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00033
                                      HHHHHHHHHHHTT-EEEEEESSHHHHHHHHHT.......TESEEEET..TTC.HHHHHHHHHTTTSSEEEEEESSCSH CS
                        ADH_zinc_N  2 vGlaavqlAkalGaeviavdsseeklelakkl.......Gadeviny..kea.dlverikeltggegvdvvfecvGsg 69
                                      vG+ + ++++ lG +vi++d++ee++ +  +        G de+i +      +  ++ +++   ++ d++f cvG++
  gi|298674030|ref|YP_003725780.1| 11 VGTVTAACLAELGHQVICIDIDEERVNKINSGvspiweqGLDELIQNhaGGNlKATSDYESAV--NDSDISFICVGTP 86
                                      8999999999****************9999955899999999999995522224555555555..6999999999965 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00045       0.4      12      40 ..       2      30 ..       1      40 [. 0.91

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00045
                     Rossmann-like 12 svGiisaGrvGtalgaaleraghvvvgis 40
                                      +v ++++G vGt+ +a l+  gh+v+ i 
  gi|298674030|ref|YP_003725780.1|  2 KVSVVGSGYVGTVTAACLAELGHQVICID 30
                                      799**********************9885 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.3   0.00056       0.5       2      27 ..       3      30 ..       2      44 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00056
                                      EEEECTSHHHHHHHHHHHHTT..EEEEE CS
                               DAO  2 vviiGGGiiGlstAyeLarrg..Vtlle 27
                                      v ++G+G++G  tA  La+ g  V+ ++
  gi|298674030|ref|YP_003725780.1|  3 VSVVGSGYVGTVTAACLAELGhqVICID 30
                                      67****************9998987776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.63u 0.39s 00:00:01.02 Elapsed: 00:00:00.52
# Mc/sec: 2516.05
//
Query:       gi|298674031|ref|YP_003725781.1|  [L=60]
Description: hypothetical protein Metev_0053 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.011   16.2   0.5      0.014   15.8   0.5    1.2  1  DUF1660   Prophage protein (DUF1660)


Domain annotation for each model (and alignments):
>> DUF1660  Prophage protein (DUF1660)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   0.5   7.9e-07     0.014       3      33 ..      17      54 ..      15      60 .] 0.72

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.9e-07
                           DUF1660  3 LlCKLfgHKwd.......enpaadseelyCeRCeivke 33
                                      +lC L  HKw+       +  +   +e  CeRC   k+
  gi|298674031|ref|YP_003725781.1| 17 ILCYLGLHKWKraggsshFSSNVREKEYRCERCGRTKT 54
                                      69*********999998844444444559****55554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 390.00
//
Query:       gi|298674032|ref|YP_003725782.1|  [L=202]
Description: imidazole glycerol phosphate synthase glutamine amidotransferase subunit [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.3e-22   78.8   0.0    5.3e-22   78.5   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    7.6e-09   35.7   0.0     0.0001   22.2   0.0    2.0  2  SNO            SNO glutamine amidotransferase family
      3e-07   30.4   0.0    5.3e-07   29.6   0.0    1.4  1  Peptidase_C26  Peptidase C26
    1.2e-06   28.2   0.1    9.1e-06   25.4   0.0    1.9  2  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
     0.0031   17.3   0.0     0.0049   16.7   0.0    1.3  1  DJ-1_PfpI      DJ-1/PfpI family
     0.0077   16.3   0.0      0.013   15.6   0.0    1.3  1  LPD18          Large polyvalent protein-associated domain 18


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.5   0.0   1.8e-25   5.3e-22       2     186 ..       6     198 ..       5     201 .. 0.86

  Alignments for each domain:
  == domain 1  score: 78.5 bits;  conditional E-value: 1.8e-25
                                       EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.....TTTHHHHHHHHCTSTS- CS
                            GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.....vegkieaikearenkiP 73 
                                       +iD++ ++ +++ +al ++g+k  +  +    eei     ++dg++++ G+g+        +   ++i e+ + ++P
  gi|298674032|ref|YP_003725782.1|   6 IIDYGLGNLRSIRKALEKVGAKPVISSNP---EEI----LDADGVILP-GVGAFIdamknLQPLTDVIYEYVDTGKP 74 
                                       79**********************99998...566....478999886.666666666788888899999999**** PP

                                       EEEETHHHHHHHHHTTT............EEE.....EEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEE CS
                            GATase  74 iLGICLGmQllaiefgr............kvv.....kekekehhggtmrlgddetallyglknevierhrHryevn 133
                                       +LGICLG Q+l+ ++ +            +v      + k  +h+g+++   ++++ ll+g ++  ++++ H++ v+
  gi|298674032|ref|YP_003725782.1|  75 LLGICLGQQILMSKSDEggltegidlvpgHVRripssELK-VPHMGWNSITINKSHPLLKGISDGDYVYFVHSFYVD 150
                                       ************9998877787776666533377784555.************9*********************** PP

                                       SGCHHHTTEEEEEEEETTEEEEEEEEETT.TEEEESSBTTSTTSTTHHHHHHHH CS
                            GATase 134 pkelepaglevtakseddeelmeiiekkn.pfvgvQFHPEststpegpellfnf 186
                                             ++++ +  ++ + ++++++ +++ ++vg+QFHPE++ +++  ++++nf
  gi|298674032|ref|YP_003725782.1| 151 T-----DEFHTLSSCDYGLSFAAVVVNEKgNVVGTQFHPEKSGKTG-LKIVENF 198
                                       7.....999******9999999999999966*********988876.8888887 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   3.4e-08    0.0001       6     102 ..      12     107 ..      11     112 .. 0.84
   2 !   11.7   0.0   5.8e-05      0.17     147     186 ..     157     202 .]     132     202 .] 0.75

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 3.4e-08
                                       SSHHHHHHHHHHTTSEEEEE-SGGGGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHH.HHH CS
                               SNO   6 GaveehveaikkclaenktvkrkedlaevdaliiPGGestamskliertglyedllefvknsekvvlGtCaGl.ill 81 
                                       G+++   +a++k++a+     ++e++ + d++i+PG   + +  + +   l + ++e+v  + k++lG C G  il+
  gi|298674032|ref|YP_003725782.1|  12 GNLRSIRKALEKVGAKPVISSNPEEILDADGVILPGVG-AFIDAMKNLQPLTDVIYEYVDTG-KPLLGICLGQqILM 86 
                                       5666777899*************************964.45666666677889******999.********964888 PP

                                       CCEETTBSS-SS--CCEEEET CS
                               SNO  82 skelenelvktlellkvkvkr 102
                                       sk  e+ l + ++l+  +v+r
  gi|298674032|ref|YP_003725782.1|  87 SKSDEGGLTEGIDLVPGHVRR 107
                                       998888888888888777776 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 5.8e-05
                                       EEECT.T....EEEEEEETTEEEESS-GGGST.THCHHHHHHHHHH CS
                               SNO 147 lyeld.g....eivvakqkkilatsfhPelae.ddirvhdyfveev 186
                                       l+  d g     +vv +++++++t fhPe +   + ++ + fv+++
  gi|298674032|ref|YP_003725782.1| 157 LSSCDyGlsfaAVVVNEKGNVVGTQFHPEKSGkTGLKIVENFVNMC 202
                                       5555552323256777788**********98516899999999986 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   1.8e-10   5.3e-07      97     216 .]      64     185 ..      59     185 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 1.8e-10
                     Peptidase_C26  97 LiraalergvPilgiCrGlqllnv.alGGtlyqdieeqsgltdhreheq....saashavkvekgsllaellgseei 168
                                       +i++ ++ g+P+lgiC+G q+l      G l + i+ ++g+++    ++         +++++k+  l + ++ +  
  gi|298674032|ref|YP_003725782.1|  64 VIYEYVDTGKPLLGICLGQQILMSkSDEGGLTEGIDLVPGHVRRIPSSElkvpHMGWNSITINKSHPLLKGIS-DGD 139
                                       688999**************8765155799*******9999987777745556777889******99999998.788 PP

                     Peptidase_C26 169 evnslHhqaikelaeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                        v  +H++ +++  +e++  + ++ g+  a  + ++k  v+g Q+HPE
  gi|298674032|ref|YP_003725782.1| 140 YVYFVHSFYVDT--DEFHTLSSCDYGLSFAAVVVNEKGNVVGTQFHPE 185
                                       99********96..89***********999999999***********9 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0     3e-09   9.1e-06      18     111 ..      20     101 ..       6     109 .. 0.79
   2 ?    0.6   0.0      0.12   3.7e+02     174     188 ..     170     183 ..     150     187 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 3e-09
                          GATase_3  18 pLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeeied 94 
                                       +Le+ +++ v+ ++ ++e l  dad vilpG    i++++ l+   l + i e++ +g+p+lgiC G q+L ++  d
  gi|298674032|ref|YP_003725782.1|  20 ALEKVGAKPVISSN-PEEIL--DADGVILPGVGAFIDAMKNLQP--LTDVIYEYVDTGKPLLGICLGQQILMSK-SD 90 
                                       67777777777777.66666..59********999988777766..*************************998.44 PP

                          GATase_3  95 pegvegeageveglglL 111
                                       + g        eg++l+
  gi|298674032|ref|YP_003725782.1|  91 EGGL------TEGIDLV 101
                                       4443......5555555 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.12
                          GATase_3 174 vkksedgnvlGtYlH 188
                                       v  +e+gnv+Gt +H
  gi|298674032|ref|YP_003725782.1| 170 V-VNEKGNVVGTQFH 183
                                       3.3689*******99 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.6e-06    0.0049      61     110 ..      39      88 ..      19      94 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.6e-06
                                       G-SEEEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHT CS
                         DJ-1_PfpI  61 eyDalvlpGGragperlrenekvvelvkefaekgklvaaICagpqlLaaa 110
                                       + D ++lpG  a  + +++ + +++++ e ++ gk++  IC g+q+L+++
  gi|298674032|ref|YP_003725782.1|  39 DADGVILPGVGAFIDAMKNLQPLTDVIYEYVDTGKPLLGICLGQQILMSK 88 
                                       67*******9999**********************************986 PP

>> LPD18  Large polyvalent protein-associated domain 18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   4.3e-06     0.013      24      58 ..     144     178 ..     121     183 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.3e-06
                             LPD18  24 idekeidgkefflmeheeygddaagiivdeegklv 58 
                                       + +  +d  ef  + +  yg + a ++v+e+g++v
  gi|298674032|ref|YP_003725782.1| 144 VHSFYVDTDEFHTLSSCDYGLSFAAVVVNEKGNVV 178
                                       55678999*************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1278.83
//
Query:       gi|298674033|ref|YP_003725783.1|  [L=442]
Description: AIR synthase-like protein domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-17   62.7   1.6    7.1e-17   62.0   1.6    1.4  1  AIRS_C    AIR synthase related protein, C-terminal domain
    2.2e-08   34.7   1.4    6.9e-08   33.0   1.4    1.8  1  AIRS      AIR synthase related protein, N-terminal domain


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.0   1.6   7.9e-21   7.1e-17       1     155 [.     231     383 ..     231     384 .. 0.85

  Alignments for each domain:
  == domain 1  score: 62.0 bits;  conditional E-value: 7.9e-21
                                       STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHH..HTTECEEEE--TTHHHHH CS
                            AIRS_C   1 kpGdvliltgslGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaal..kglvkaahDvTgGGLlga 75 
                                       k+Gdv+++t++ G g ++t +   ++ +e        ++d+    + +++++al+++  + +++a++DvT+GG+ g+
  gi|298674033|ref|YP_003725783.1| 231 KAGDVILMTEGAGGGTVSTTALY-HGMHE--------VVDETINIKFLEACEALIESglTSDIHAMTDVTNGGVRGD 298
                                       69*********999999977765.55555........56677777******************************** PP

                                       HHHHHHTTTEEEEEECG......THHHHHHHHHHHHHHHC.......STTTEEEEEEEHGGHHHHHHHHHHTTCCCE CS
                            AIRS_C  76 laemapasgvgaeidld......kvpifdelesplemlls.......ensGrllvavppeeadavlaileeeglpea 139
                                       ++e+ + +g+++++d++      +          +eml s        +   ll++ p+e a+ +++++++ g+ + 
  gi|298674033|ref|YP_003725783.1| 299 AQEISRTAGLKLVFDESrmsklvNS-------PVMEMLESlgidylgVSLDSLLIISPEEYAEDIINTVKSSGV-DI 367
                                       *****************55444433.......44566666666666688888**********************.8* PP

                                       EEEEEEEESSSEEEEE CS
                            AIRS_C 140 avIGevtakeelsviv 155
                                        ++G v+++ ++++i+
  gi|298674033|ref|YP_003725783.1| 368 DIVGNVEEGSGSELII 383
                                       *********9999886 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   1.4   7.7e-12   6.9e-08       1      90 [.     106     217 ..     106     220 .. 0.71

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 7.7e-12
                                       SSSEEEEEEEEEE.EECC...TCCCC........HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHHHH CS
                              AIRS   1 dDaavvvttdshnrpvlv...epvhf........iGakavavnlsDlaamGArPlalllslalp......wleevvr 60 
                                       dD + +v t+ +++++++   +++h         +G  ++ ++l+D+++mGArP+all  + +       ++ + ++
  gi|298674033|ref|YP_003725783.1| 106 DDSG-AVVTE-NGSKYVIvtvDGMHSrlsdfsylAGFHVARAALRDIYVMGARPVALLSDIHVAddgdvaKIFDHIA 180
                                       5666.44444.333333312234443666777788********************9999999889**9998888899 PP

                                       HHHHHHHHTT-EEEEEEEEEESS.......EEEEEEE CS
                              AIRS  61 glaeaaeelgvplvgGdtsfsne.......ptisvta 90 
                                       g+    e ++vplv+G t +  +       +t  v+a
  gi|298674033|ref|YP_003725783.1| 181 GITTVSELIDVPLVTGSTLRIGGdmvigdrMTGGVGA 217
                                       ****************998654444444445555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2849.32
//
Query:       gi|298674034|ref|YP_003725784.1|  [L=434]
Description: hypothetical protein Metev_0056 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-14   54.6   0.5    1.1e-14   54.6   0.5    2.8  3  NfeD          NfeD-like C-terminal, partner-binding
    1.8e-07   31.3   0.6      3e-07   30.5   0.6    1.3  1  CLP_protease  Clp protease
  ------ inclusion threshold ------
        6.3    6.7   8.6        4.1    7.3   0.5    2.9  3  TMEM154       TMEM154 protein family


Domain annotation for each model (and alignments):
>> NfeD  NfeD-like C-terminal, partner-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.25   1.5e+03      63      77 ..      26      40 ..       9      44 .. 0.72
   2 ?   -3.4   0.1       2.2   1.3e+04       4      19 ..     241     256 ..     240     280 .. 0.55
   3 !   54.6   0.5   1.8e-18   1.1e-14       3      84 .]     352     432 ..     350     432 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.25
                                      SB-TT-EEEEEEE-S CS
                              NfeD 63 eiekgerVrVveveG 77
                                       i++ e+V Vve++ 
  gi|298674034|ref|YP_003725784.1| 26 AIAQEEKVLVVEISD 40
                                      377788888888765 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.2
                                       XXXXXXXXXXXXXS-- CS
                              NfeD   4 vvsvlllvllrplllk 19 
                                       ++s+ll++ l+ ++  
  gi|298674034|ref|YP_003725784.1| 241 IASLLLIIGLYSIVIG 256
                                       6677777777766655 PP

  == domain 3  score: 54.6 bits;  conditional E-value: 1.8e-18
                                       XXXXXXXXXXXXXXS---SSS--S.S---GGTTSEEEEEE-B..S.-EEEEETTEEEEEE-.SSB-TT-EEEEEEE- CS
                              NfeD   3 avvsvlllvllrplllkklkkkekktnaealiGkegvvledi..g.tGrvkvdGeeWsarsegeiekgerVrVveve 76 
                                       ++++v +l+++++++  +++k       ++++G ++++ e+i  g +G vk++Ge+W+a+s++ei+kg +V++++ e
  gi|298674034|ref|YP_003725784.1| 352 IIMGVFMLFIVYKIIEVRHRK----PIIGEIVGNTAITNEKIkrGeEGYVKYKGEYWKAKSDEEIDKGVKVEIIDKE 424
                                       678889999999988776644....55679************98568****************************** PP

                                       SSSEEEEE CS
                              NfeD  77 GltliVep 84 
                                       G tl+V++
  gi|298674034|ref|YP_003725784.1| 425 GPTLVVKR 432
                                       ******96 PP

>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.6   5.1e-11     3e-07      19     175 ..      36     190 ..      26     193 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 5.1e-11
                                       EEEES-BSHHHHHHHHHHHHHHHHH-SSS-EEEEEEE--B-HHHHHHHHHHHHHSSS-EEEEEE..EE.EETHHHHH CS
                      CLP_protease  19 iflgseiddevankiiaqLllLeaedpdkdillyinspGGsvtaglaIydtmqyikpdvsticl..Gl.aaSmgsll 92 
                                       + ++++i++++ + +++ + ++e e+ d  i+l +n+pGG++++++ I + ++  + +v+ ++   G+ a S+g+++
  gi|298674034|ref|YP_003725784.1|  36 VEISDSITSASDDLVTNAISVAEDENYD-AIVLTLNTPGGKLSETFNIIESIESTNVPVIGYVYpeGTkAWSAGTII 111
                                       6678889999999999999999877776.9*****************************988877775488****** PP

                                       HHTS-TTGEEEETTEEEEES-TEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHCSTEEEEHHHH CS
                      CLP_protease  93 laagekgkRfalpnarimihqPlggaqgqasdieieaeellkikerlneilakhtgqslekiekdldrdtflsaeeA 169
                                       l++ +    ++ p + i   qP++ ++g ++ i+   + ++ i e   e  a++ ++++   e+ ++++  ++ae A
  gi|298674034|ref|YP_003725784.1| 112 LISTDIA--AMAPFSVIGSAQPVQLTGGGSQPIND-SKTINAIVEYTRE-KARQNNRNVTAAEEFITKNLNINAETA 184
                                       ******9..799****************8888875.5666666555433.345556666666778888899999999 PP

                                       HHHTSS CS
                      CLP_protease 170 veyGLi 175
                                       +ey  i
  gi|298674034|ref|YP_003725784.1| 185 LEYNVI 190
                                       999766 PP

>> TMEM154  TMEM154 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.2       1.4   8.2e+03      69      82 ..      10      23 ..       8      32 .. 0.63
   2 ?    4.2   0.2    0.0063        38      11      75 ..     184     249 ..     153     259 .. 0.68
   3 ?    7.3   0.5   0.00069       4.1      53      86 ..     338     371 ..     328     391 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.4
                           TMEM154 69 lillllvviiliqk 82
                                      li+++l   i+++ 
  gi|298674034|ref|YP_003725784.1| 10 LIIISLFFFIVMMS 23
                                      56666666666554 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0063
                           TMEM154  11 aletatleeesadatsaasteseslkqeeakeslssaelsnesdqlelvlmiii..Plvllillllv 75 
                                       ale + +e +s   +   s  +  ++ + ++ + s a+++  + + ++ +m ii  Pl++ +ll++ 
  gi|298674034|ref|YP_003725784.1| 184 ALEYNVIEYTSPSIGDLLSQVDGDVA-KGKQLNVSGAQIDRYEPSINIAIMSIIsdPLIASLLLIIG 249
                                       55555555444444444444444444.4455567778888888888888888887799998887763 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.00069
                           TMEM154  53 sdqlelvlmiiiPlvllillllvviiliqkkkrk 86 
                                       + q+e+++ i+ P++++ + +l ++  i   +++
  gi|298674034|ref|YP_003725784.1| 338 EIQQEIIIAIVTPSIIMGVFMLFIVYKIIEVRHR 371
                                       6699************988777666555333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       803  (0.0447878); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.75s 00:00:01.36 Elapsed: 00:00:00.63
# Mc/sec: 2082.76
//
Query:       gi|298674035|ref|YP_003725785.1|  [L=298]
Description: hypothetical protein Metev_0057 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-33  116.7   3.9    1.6e-33  116.2   3.9    1.2  1  Band_7    SPFH domain / Band 7 family
    0.00029   20.6   0.1    0.00053   19.8   0.1    1.4  1  Band_7_1  SPFH domain-Band 7 family
  ------ inclusion threshold ------
       0.03   13.8   0.0      0.046   13.2   0.0    1.3  1  SOP4      Suppressor of PMA 1-7 protein


Domain annotation for each model (and alignments):
>> Band_7  SPFH domain / Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.2   3.9   2.7e-37   1.6e-33       2     176 ..      24     192 ..      23     194 .. 0.97

  Alignments for each domain:
  == domain 1  score: 116.2 bits;  conditional E-value: 2.7e-37
                            Band_7   2 iieegevgvvvrfGklsrvlepGlhfilPfgrsvtvvsvrvqtldvsvsltvptkDglpvtidvtviyrvpddapkl 78 
                                       i++e e+ vv+r G+  + ++pGl +i+P++++v++v++rv+t+dv++ + v+t D++ +++d++v+yrv + +  +
  gi|298674035|ref|YP_003725785.1|  24 IVKEYERVVVFRLGRFLGEKGPGLFIIIPIVDTVVKVDLRVVTIDVPK-QAVITLDNVTIDVDAVVYYRV-TSPGDA 98 
                                       799*********************************************.*********************.****** PP

                            Band_7  79 vaaveresanldnlirrvlesalrevisemtleellsnreelaeelknelneqlrkyGvevldvritdidpppevaq 155
                                       v+av    +n++     + + +lr ++++ +++++ls+r+e++++++n l +  + +G+ v++v+i+d+++p+   +
  gi|298674035|ref|YP_003725785.1|  99 VTAV----ENYKYATAMLSQTTLRDILGQVEFDDVLSKRDEINQKIQNVLDSLTDPWGIKVTNVTIRDVVLPESMYR 171
                                       ****....999999999999********************************************************* PP

                            Band_7 156 alaakqaaeaeaqaeiaraea 176
                                       a+a+ ++ae+e++a++  a +
  gi|298674035|ref|YP_003725785.1| 172 AIARQAEAEREKRARTILADG 192
                                       **************9988866 PP

>> Band_7_1  SPFH domain-Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   8.8e-08   0.00053     153     209 ..     123     179 ..      99     181 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 8.8e-08
                          Band_7_1 153 kipvldlaakseelaeklkealkeelaeyGlelekleienislpeevekaldkrasm 209
                                       ++   d+ +k +e+ +k++++l++  +  G+++++++i+++ lpe++ +a+ ++a++
  gi|298674035|ref|YP_003725785.1| 123 QVEFDDVLSKRDEINQKIQNVLDSLTDPWGIKVTNVTIRDVVLPESMYRAIARQAEA 179
                                       455678899*******************************************99876 PP

>> SOP4  Suppressor of PMA 1-7 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   7.8e-06     0.046      27      85 ..      99     158 ..      77     177 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.8e-06
                              SOP4  27 lyqignyssekpysastklkdieGnFeFedlPln.kgvnettyfvlvsssldfnLkPnRi 85 
                                       +  ++ny+  ++  ++t+l+di G+ eF+d+  + +++n++ + vl s    + +k   +
  gi|298674035|ref|YP_003725785.1|  99 VTAVENYKYATAMLSQTTLRDILGQVEFDDVLSKrDEINQKIQNVLDSLTDPWGIKVTNV 158
                                       67799*************************86551679***9999999877777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       958  (0.053433); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1856.88
//
Query:       gi|298674036|ref|YP_003725786.1|  [L=711]
Description: phosphoesterase RecJ domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-09   38.1   9.9    1.5e-09   38.1   9.9    2.4  2  DnaJ_CXXCXGXG    DnaJ central domain
    5.2e-08   32.8   0.1    2.3e-07   30.7   0.1    2.2  3  tRNA_anti-codon  OB-fold nucleic acid binding domain
    1.8e-06   28.1   0.2    3.9e-06   27.0   0.2    1.5  1  DHH              DHH family
    2.2e-06   27.9   1.9    2.2e-06   27.9   1.9    2.1  2  S1               S1 RNA binding domain
  ------ inclusion threshold ------
       0.04   14.1   0.0       0.11   12.8   0.0    1.8  1  tRNA_anti_2      OB-fold nucleic acid binding domain
      0.072   13.2   0.1       0.17   12.0   0.1    1.6  1  S1_2             S1 domain
      0.084   13.2   0.1         15    6.0   0.0    3.2  4  DUF4854          Domain of unknown function (DUF4854)
        0.2   10.8   0.0       0.35   10.0   0.0    1.3  1  Arb1             Argonaute siRNA chaperone (ARC) complex subu
       0.46   10.5  19.9       0.64   10.0   5.7    3.1  2  Anti-TRAP        Tryptophan RNA-binding attenuator protein in


Domain annotation for each model (and alignments):
>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   9.9   7.4e-13   1.5e-09       1      67 []       5      75 ..       5      75 .. 0.75
   2 ?   -0.2   1.1      0.65   1.3e+03       1      21 [.      80     101 ..      79     113 .. 0.69

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 7.4e-13
                     DnaJ_CXXCXGXG  1 CkkCkGsgakkgkkktCktCkGsGvvree......qkt.lgpfvqqsqstCpeCeGtGkvikekdkCkkCkGkg 67
                                      C +C+G+g +  ++++C++CkG+G++++       + + +  f  +  s Cp+CeG+G++  +++ C++CkG+g
  gi|298674036|ref|YP_003725786.1|  5 CIECEGRGYQIISVEKCPECKGTGKTKSVdlmkltE-QdVDDFL-SDGSYCPKCEGSGQIE-TTKYCETCKGRG 75
                                      99******9878899*********754443333322.2244455.45789*********65.6669******86 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.65
                     DnaJ_CXXCXGXG   1 CkkCkGsgakk.gkkktCktCk 21 
                                       Ck C  s  ++ ++++ C+ C 
  gi|298674036|ref|YP_003725786.1|  80 CKVCGTSIDEPvDDEEICRVCA 101
                                       7777777766634466677775 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       3.1   6.2e+03      41      64 ..     152     175 ..     149     185 .. 0.70
   2 !   30.7   0.1   1.2e-10   2.3e-07       1      74 [.     211     281 ..     211     283 .. 0.96
   3 ?   -3.3   0.0       4.7   9.3e+03      12      30 ..     380     398 ..     372     411 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.1
                                       HHHTTS-TTSEEEEEEEEEECTTS CS
                   tRNA_anti-codon  41 klaenlkeGdvvrvtGrvkrrpgg 64 
                                       +l+e+l++Gd v v+ +  +++g+
  gi|298674036|ref|YP_003725786.1| 152 NLKEELDIGDPVIVYVKEIKSNGN 175
                                       788999999999987665555555 PP

  == domain 2  score: 30.7 bits;  conditional E-value: 1.2e-10
                                       EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEEEE CS
                   tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrrpggelelkveeie 74 
                                       V+++G+v+++  +++++   +++ D+ g i+  +f ++ ++ + +++ ++vv +tG++++r ++ ++l +++++
  gi|298674036|ref|YP_003725786.1| 211 VRIEGEVIQV--KQTAGPTIFTISDEAGLITGAAFEKAGERAYPHIDSNMVVTATGEITSRGDE-VQLEIKSMK 281
                                       89********..*************************************************998.999999886 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 4.7
                                       EEEETTEEEEEEEETTEEE CS
                   tRNA_anti-codon  12 drsggkvifidlrDgtgri 30 
                                       +rs +k+ f++l D t  +
  gi|298674036|ref|YP_003725786.1| 380 RRSPSKAPFYELADVTKDL 398
                                       3888999999999998766 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.2   1.9e-09   3.9e-06       2      73 ..     341     467 ..     340     498 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1.9e-09
                                       EEEE-ECSSSHHHHHHHHHHHH....................................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxx....................................................... RF
                               DHH   2 ilivghknpDtDsigSaialan....................................................... 23 
                                       i+i   ++ D+D+++Sa+al++                                                       
  gi|298674036|ref|YP_003725786.1| 341 IVI--RHHADADGMTSAVALERavlplisevsgsdaeyylyrrspskapfyeladvtkdlsfaledmerhgqkfpli 415
                                       445..7899*************8888888888888888888888888888888777777777777777777777777 PP

                                       CECS--TCGGCGCCH..HCCCSEEEEEEE-S---SS---SS--EEEE-SSS- CS
                                       xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH  24 llvDhneksqavege..akeeaedviiiDHHrlgeefetlapilflnepvgs 73 
                                       llvD+++++++  +   a+  + d+i++DHH++ e ++++ +  +   ++g 
  gi|298674036|ref|YP_003725786.1| 416 LLVDNGSTDEDTPAMrqARVYGIDMIVVDHHNPDEVVDQYLQSHINPAHAGG 467
                                       7******999887654588899***********9866666555555445554 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   1.9   1.1e-09   2.2e-06       2      71 ..     118     177 ..     117     179 .. 0.92
   2 ?   -3.1   0.2       5.1     1e+04       8      16 ..     213     221 ..     207     224 .. 0.69

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.1e-09
                                       STTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEE CS
                                S1   2 pekgevveGeVtsvtkgGafVelgngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrrii 71 
                                       +e+g+ + G+V  +  +G+fV+l ++++g++++++l+ +         l +Gd+v v+v +++ + + ++
  gi|298674036|ref|YP_003725786.1| 118 VEVGQLYHGIVDGIAAFGVFVNLNAHIRGLIHIKNLKEE---------LDIGDPVIVYVKEIKSNGN-VD 177
                                       799**********************************65.........*************998876.65 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.1
                                       EEEEEEEEE CS
                                S1   8 veGeVtsvt 16 
                                       +eGeV++v 
  gi|298674036|ref|YP_003725786.1| 213 IEGEVIQVK 221
                                       577777765 PP

>> tRNA_anti_2  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.3e-05      0.11      20      93 ..     209     279 ..     193     281 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.3e-05
                       tRNA_anti_2  20 kavwvrGeisnlkrkasghvYftLkDekakisavifrsraaklkftledGmkVlvkgrlsvYeprGsyqlived 93 
                                       + v ++Ge+ ++k ++ g + ft++De   i  + f+++ ++    +++ m V ++g+++   +  ++ql +++
  gi|298674036|ref|YP_003725786.1| 209 RVVRIEGEVIQVK-QTAGPTIFTISDEAGLITGAAFEKAGERAYPHIDSNMVVTATGEITS--RGDEVQLEIKS 279
                                       5699********5.469********************888877777888999999888874..22255666665 PP

>> S1_2  S1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   8.5e-05      0.17       2      48 ..     121     167 ..     120     167 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.5e-05
                              S1_2   2 GkintlkvlretdfgyfLqkdesgevlLpkkevpeeleiGdeveVFv 48 
                                       G+     v+ +  fg+f++ +     l + k+++eel iGd v V v
  gi|298674036|ref|YP_003725786.1| 121 GQLYHGIVDGIAAFGVFVNLNAHIRGLIHIKNLKEELDIGDPVIVYV 167
                                       6677778888999******9999********************9976 PP

>> DUF4854  Domain of unknown function (DUF4854)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       2.3   4.6e+03      75      98 ..     151     175 ..     150     176 .. 0.74
   2 ?    3.3   0.0      0.05        99      26      72 ..     262     308 ..     254     321 .. 0.86
   3 ?    6.0   0.0    0.0076        15      61      98 ..     315     352 ..     311     355 .. 0.91
   4 ?   -3.8   0.0       8.3   1.6e+04      51      88 ..     522     560 ..     517     563 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.3
                           DUF4854  75 kqlkkevkv.enpivvvrvltsdGk 98 
                                       k+lk+e+++ + +iv v+ ++s+G+
  gi|298674036|ref|YP_003725786.1| 151 KNLKEELDIgDPVIVYVKEIKSNGN 175
                                       68999****4445667888888886 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.05
                           DUF4854  26 islevtaegntLvyeytlskslddaaldalkealaesldsqastfes 72 
                                        + e+t++g+++ +e +  k l+ ++ +a+ e++++++d+ a+ +es
  gi|298674036|ref|YP_003725786.1| 262 ATGEITSRGDEVQLEIKSMKRLSGEKESAVWERIEKAIDERAEPYES 308
                                       46799******999999999899999999999999999999998886 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0076
                           DUF4854  61 esldsqastfeslakqlkkevkvenpivvvrvltsdGk 98 
                                       e+ld+ +   +++ak++ k+v  ++piv+    ++dG 
  gi|298674036|ref|YP_003725786.1| 315 EILDKLKPGMKKVAKEIRKAVIKSKPIVIRHHADADGM 352
                                       6789999999***********************99996 PP

  == domain 4  score: -3.8 bits;  conditional E-value: 8.3
                           DUF4854  51 aldalke.alaesldsqastfeslakqlkkevkvenpiv 88 
                                       +ld+lk+ ala  +++ +  f+s    +++ ++ ++p+v
  gi|298674036|ref|YP_003725786.1| 522 SLDQLKDiALALDFEAFWLKFSSGKGIVNDILNFGDPMV 560
                                       667777734667788888888887777777777777776 PP

>> Arb1  Argonaute siRNA chaperone (ARC) complex subunit Arb1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00017      0.35     325     360 ..     292     325 ..     252     333 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00017
                              Arb1 325 wen.psaaeedlakeeekeveflleedilellfvGmk 360
                                       we+ ++a +e     e  e efl+e++il++l +Gmk
  gi|298674036|ref|YP_003725786.1| 292 WERiEKAIDERA---EPYESEFLIESEILDKLKPGMK 325
                                       666333333333...3349*****************9 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   3.9    0.0024       4.8      11      41 ..       3      29 ..       1      40 [. 0.72
   2 ?   10.0   5.7   0.00032      0.64      12      41 ..      52      76 ..      47      84 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0024
                                      EE-TTTTTTSEETTE......E-TTTTTSSE CS
                         Anti-TRAP 11 tkCdaCngsGkiepeeprasleCPkCsGkgl 41
                                      ++C +C+g G           +CP+C+G g 
  gi|298674036|ref|YP_003725786.1|  3 EECIECEGRGYQIIS----VEKCPECKGTGK 29
                                      679999999964433....348999999875 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00032
                                      E-TTTTTTSEETTE......E-TTTTTSSE CS
                         Anti-TRAP 12 kCdaCngsGkiepeeprasleCPkCsGkgl 41
                                       C++C+gsG+ie++       C  C+G+g+
  gi|298674036|ref|YP_003725786.1| 52 YCPKCEGSGQIETT-----KYCETCKGRGI 76
                                      5************9.....78******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (711 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.71u 0.26s 00:00:00.97 Elapsed: 00:00:00.46
# Mc/sec: 4661.69
//
Query:       gi|298674037|ref|YP_003725787.1|  [L=203]
Description: phosphoribosyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.9e-20   70.8   0.7    1.4e-19   70.2   0.7    1.3  1  Pribosyltran    Phosphoribosyl transferase domain
    2.1e-05   24.1   0.1    2.7e-05   23.7   0.1    1.2  1  UPRTase         Uracil phosphoribosyltransferase
    9.7e-05   21.9   0.4     0.0043   16.6   0.3    2.1  2  PRTase_2        Phosphoribosyl transferase
    0.00095   19.3   0.8      0.059   13.4   0.3    2.5  2  Pribosyl_synth  Phosphoribosyl synthetase-associated domain
     0.0041   17.0   0.4      0.054   13.4   0.1    2.3  2  HTH_11          HTH domain
  ------ inclusion threshold ------
      0.014   15.5   0.0       0.03   14.4   0.0    1.5  1  HTH_7           Helix-turn-helix domain of resolvase
      0.017   14.7   0.0      0.034   13.7   0.0    1.5  1  GerE            Bacterial regulatory proteins, luxR family
      0.058   12.9   0.0       0.14   11.7   0.0    1.6  1  Sigma70_r4      Sigma-70, region 4
       0.11   12.4   0.1       0.95    9.5   0.0    2.5  3  HTH_Crp_2       Crp-like helix-turn-helix domain
       0.16   11.8   0.0       0.32   10.8   0.0    1.5  1  HTH_23          Homeodomain-like domain


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.2   0.7   7.8e-23   1.4e-19      25     143 ..      85     199 ..      58     203 .] 0.88

  Alignments for each domain:
  == domain 1  score: 70.2 bits;  conditional E-value: 7.8e-23
                                       E--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE-SEESSSH CS
                      Pribosyltran  25 eyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkVliVDDildtGg 101
                                       e + ++d++vgi   Gvp+a+++ad L+ +la+   + ++++++ +  ++s    r+ +++ gk +++VDD++++G 
  gi|298674037|ref|YP_003725787.1|  85 ETDSEIDTIVGIGLSGVPLASHIADDLDKELAIFHGTTKQNEDKRVPGTVS----RNFGEVTGKNCVVVDDVITSGA 157
                                       35889***************************9999999999999988776....6********************* PP

                                       HHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHHHHH-TTS... CS
                      Pribosyltran 102 TllaalelLkekgpeevriavlvdkpateeevdknakrvfsl 143
                                       T++++++ L++ g+  v + v++dk+ +e+ +d  +k+++ +
  gi|298674037|ref|YP_003725787.1| 158 TITEVINQLRDFGANPVVVTVIIDKKGSEKISDVPVKSMVRI 199
                                       ********************************9999999876 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.1   1.5e-08   2.7e-05      71     172 ..      93     191 ..      70     203 .] 0.79

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.5e-08
                           UPRTase  71 lVpilRaGegmeealrellpea.rvghlglqreeetlepveyynkLPkkiaertvlllDpviaTGgsaaaaiqlLke 146
                                       +V i  +G ++++ + + l +  +++h   +++e++  p  +  ++ + ++ ++ +++D vi +G+++ ++i++L++
  gi|298674037|ref|YP_003725787.1|  93 IVGIGLSGVPLASHIADDLDKElAIFHGTTKQNEDKRVPGTVSRNFGE-VTGKNCVVVDDVITSGATITEVINQLRD 168
                                       555555888999888776655549999999999999999999988877.57788999******************** PP

                           UPRTase 147 rgvgeekIlvlsvlaseegvkrlaee 172
                                        g+   + +v++v+  ++g +++++ 
  gi|298674037|ref|YP_003725787.1| 169 FGA---NPVVVTVIIDKKGSEKISDV 191
                                       776...45899999999999988764 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.025        44      33      91 ..      69     127 ..      60     135 .. 0.76
   2 !   16.6   0.3   2.4e-06    0.0043     122     165 ..     144     186 ..     132     202 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.025
                          PRTase_2  33 reagaaLaellaeakkeelpepvlvigfAEtAtaLghgvadaleeealylhtTRekvag 91 
                                       r + +aLa++ +e++ e+ +e  +++g+    + L+  +ad l++e  ++h T ++ ++
  gi|298674037|ref|YP_003725787.1|  69 RYISNALADMTMESACETDSEIDTIVGIGLSGVPLASHIADDLDKELAIFHGTTKQNED 127
                                       55677888888866666666777889999999***********8888888877666544 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 2.4e-06
                          PRTase_2 122 kelvLvDDEistGktalnliralqeklprkryvvvslvdwrsee 165
                                       k+ v+vDD i++G t++++i++l++   ++ +vv+ ++d + +e
  gi|298674037|ref|YP_003725787.1| 144 KNCVVVDDVITSGATITEVINQLRDF-GANPVVVTVIIDKKGSE 186
                                       6789******************9875.56678888888887777 PP

>> Pribosyl_synth  Phosphoribosyl synthetase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.025        45      18      47 ..     104     133 ..      92     137 .. 0.85
   2 !   13.4   0.3   3.3e-05     0.059      78     118 ..     138     178 ..     131     201 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.025
                                       HHHHHHHTT-EEEEE--------------- CS
                    Pribosyl_synth  18 atsyaerlrlglavihGeqkeaeadevdgr 47 
                                       a+  a+ l   la+ hG +k++e ++v g 
  gi|298674037|ref|YP_003725787.1| 104 ASHIADDLDKELAIFHGTTKQNEDKRVPGT 133
                                       66789999*************998887765 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 3.3e-05
                                       ES--TTSEEEEEEEEE-S-HHHHHHHHHHHHTT--EEEEEE CS
                    Pribosyl_synth  78 vGdvgGriaiivddliddvesfvaaaevlkerGaykiyvla 118
                                        G+v+G+  ++vdd+i    ++ +  + l++ Ga  ++v +
  gi|298674037|ref|YP_003725787.1| 138 FGEVTGKNCVVVDDVITSGATITEVINQLRDFGANPVVVTV 178
                                       599*******************************9988765 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.1     3e-05     0.054       9      32 ..      14      35 ..       7      36 .. 0.80
   2 ?    1.1   0.0      0.21   3.8e+02      28      44 ..     155     178 ..     153     185 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3e-05
                            HTH_11  9 LleargpisgeeLAeeLnvSrrtv 32
                                      L +++g ++g ++A+eLnvSr t+
  gi|298674037|ref|YP_003725787.1| 14 L-QSKGLVTG-QIADELNVSRETI 35
                                      5.67775555.6***********9 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.21
                            HTH_11  28 SrrtvrrdIkaLeelg.......v 44 
                                       S +t+   I +L++ g       v
  gi|298674037|ref|YP_003725787.1| 155 SGATITEVINQLRDFGanpvvvtV 178
                                       778999*********985555433 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.7e-05      0.03      11      38 ..       8      35 ..       2      35 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.7e-05
                                      HGGGGSSTTTT--STTTSSSS---SSSS CS
                             HTH_7 11 inrvvkLleeGisiskIAkevnisRsTv 38
                                      i+ + +L ++G    +IA+e+n+sR+T+
  gi|298674037|ref|YP_003725787.1|  8 IEKAEELQSKGLVTGQIADELNVSRETI 35
                                      666778888898999************7 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.9e-05     0.034      15      40 ..      16      41 ..      13      44 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.9e-05
                                      CTTS-HHHHHHHHTS-HHHHHHHHHH CS
                              GerE 15 aeGksnkeIAeelniSekTVkvhksn 40
                                       +G+ + +IA+eln+S +T++  +++
  gi|298674037|ref|YP_003725787.1| 16 SKGLVTGQIADELNVSRETITWLLTR 41
                                      68999***************876665 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   7.7e-05      0.14      25      44 ..      23      42 ..      17      44 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.7e-05
                                      HHHHHHTS-HHHHHHHHHHH CS
                        Sigma70_r4 25 EIgerlgiSrerVrqiekrA 44
                                      +I+++l++Sre++  +++rA
  gi|298674037|ref|YP_003725787.1| 23 QIADELNVSRETITWLLTRA 42
                                      8************8888887 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00053      0.95      26      47 ..      23      44 ..      12      46 .. 0.90
   2 ?   -2.6   0.0       3.1   5.6e+03      37      51 ..     133     147 ..     131     160 .. 0.75
   3 ?   -0.9   0.0      0.95   1.7e+03      35      48 ..     156     169 ..     152     172 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00053
                                      HHHHHTTSSHHHHHHHHHHHHH CS
                         HTH_Crp_2 26 elAsmlGltretvsrilseLkr 47
                                      ++A+ l+++ret++ +l++ k+
  gi|298674037|ref|YP_003725787.1| 23 QIADELNVSRETITWLLTRAKK 44
                                      8*************99998776 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.1
                                       HHHHHHHHHHHTTSE CS
                         HTH_Crp_2  37 tvsrilseLkregli 51 
                                       tvsr ++e   ++++
  gi|298674037|ref|YP_003725787.1| 133 TVSRNFGEVTGKNCV 147
                                       899988887766665 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.95
                                       HHHHHHHHHHHHHT CS
                         HTH_Crp_2  35 retvsrilseLkre 48 
                                         t++ ++++L++ 
  gi|298674037|ref|YP_003725787.1| 156 GATITEVINQLRDF 169
                                       56888899999875 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00018      0.32      22      35 ..      23      36 ..      12      43 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00018
                            HTH_23 22 eIAreLgvsrrTvy 35
                                      +IA+eL+vsr T+ 
  gi|298674037|ref|YP_003725787.1| 23 QIADELNVSRETIT 36
                                      9***********94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1276.68
//
Query:       gi|298674038|ref|YP_003725788.1|  [L=163]
Description: hypothetical protein Metev_0060 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-11   44.7   0.1    2.4e-11   44.0   0.1    1.4  1  PIN_6           PIN domain of ribonuclease
     0.0019   18.5   0.2     0.0022   18.3   0.2    1.2  1  PIN_4           PIN domain
  ------ inclusion threshold ------
      0.011   15.7   0.3      0.029   14.4   0.1    1.8  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai


Domain annotation for each model (and alignments):
>> PIN_6  PIN domain of ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.1   3.9e-15   2.4e-11       2      88 ..       5      90 ..       4      91 .. 0.91

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 3.9e-15
                             PIN_6  2 VlDagaliknslsslqnlaeklyttpeVvaEirdkkarerlellpl.elevrePspesvkkvtefakktGDlsvLSktD 79
                                      ++D++ +i + ++++    ++++t+ +V +E++ ++a  r +++ + ++ v+ P+p++ + v e a+ t Dl+ LSk+D
  gi|298674038|ref|YP_003725788.1|  5 IADSAVFIMDGFKNI--NYSSFITVASVTEELKSDEAVMRYDIAREnGIIVEVPEPDKRNSVIETARYTRDLNELSKAD 81
                                      789999998855555..46789*********************9977******************************** PP

                             PIN_6 80 ievlALtye 88
                                      i++lA ++e
  gi|298674038|ref|YP_003725788.1| 82 IDILAKALE 90
                                      *****9876 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.2   3.7e-07    0.0022      29     128 ..      29     118 ..       4     121 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.7e-07
                             PIN_4  29 tVleELdklKkgsserelarlarqanrlldellekesgrlkvqts..aeelpeeeseseknDnrIlavalelkeekp 103
                                        V eEL   K+++    +++ + + n ++ e+ e  + + +++t+  + +l+e     +k+D  Ila ale++ ++ 
  gi|298674038|ref|YP_003725788.1|  29 SVTEEL---KSDEA--VMRYDIARENGIIVEVPEPDKRNSVIETAryTRDLNE----LSKADIDILAKALEYRDKE- 95 
                                       455555...66666..7788888888888888887777777777732333333....469**************97. PP

                             PIN_4 104 drkvvLvskDinlrikAkalgieae 128
                                         +++L+++D  +++ A+ l i+ e
  gi|298674038|ref|YP_003725788.1|  96 --NITLLTDDYAVQNVAELLKINIE 118
                                       ..9**************99998765 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.4   8.6e+03      13      19 ..      36      42 ..      31      42 .. 0.71
   2 ?   14.4   0.1   4.9e-06     0.029       1      12 [.     147     158 ..     147     161 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.4
                    DNA_ligase_ZBD 13 egeaiyR 19
                                       +ea+ R
  gi|298674038|ref|YP_003725788.1| 36 SDEAVMR 42
                                      4799987 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 4.9e-06
                    DNA_ligase_ZBD   1 hCPvCGsavvRe 12 
                                       +CP+CGs++ R+
  gi|298674038|ref|YP_003725788.1| 147 TCPICGSKLKRK 158
                                       7********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1078  (0.0601261); expected 358.6 (0.02)
Passed bias filter:                      634  (0.0353617); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1065.76
//
Query:       gi|298674039|ref|YP_003725789.1|  [L=495]
Description: carotenoid oxygenase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.8e-104  350.6   0.1     2e-104  350.4   0.1    1.0  1  RPE65     Retinal pigment epithelial membrane protein


Domain annotation for each model (and alignments):
>> RPE65  Retinal pigment epithelial membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  350.4   0.1  1.1e-108    2e-104       6     462 ..      32     492 ..      27     493 .. 0.85

  Alignments for each domain:
  == domain 1  score: 350.4 bits;  conditional E-value: 1.1e-108
                                       S-EEEC--E..EEE---TT--EEEEEEEEE.ESCETTCCSSSGGGSEEEEEEEEECTTEEEEEEEE---HHHHHHHH CS
                             RPE65   6 eevpeplevkvieGeiPawlkGtllRnGpgkpevgedgkvshwFDGdGmlhrfefkdgkvtyrnRfvrtdaylaerk 82 
                                        e++   e+++ eG+iP++lkGtl+ nGpg +  g + + + +FDGdGm+++f+f++g v y+n+fvrtd++++e++
  gi|298674039|ref|YP_003725789.1|  32 GEYSY--EAEI-EGTIPNDLKGTLYLNGPGLFDRG-NLRKRYIFDGDGMIQSFHFHEGGVYYQNKFVRTDKFVDEQE 104
                                       45544..5666.8*****************88888.9999***************99******************** PP

                                       HTS--S..BSTT............TTSB-----SEEEEETTEEEEEETTCEEEEEETTTTEEEEE--CCC......T CS
                             RPE65  83 agkslf..dglp............akkkknnantnvvyhggrllalteagkpyeidpetLetlgkvdldg......e 139
                                       +gk+l+                   +k ++ a ++v++ +g+l+a+ +++++ye+dp+tLet+gk++l g       
  gi|298674039|ref|YP_003725789.1| 105 KGKLLYasW--TtlapggpisnifGRKLESQAGVTVIERNGKLYAFDDGSYIYELDPDTLETKGKTQL-GlnkskiP 178
                                       ***999550..344455556666699****************************************99.33445542 PP

                                       TS-B-SS-EEETTCEEEEEEEECCTCECEEEEEEE-.T...T-.EEEEEEEECS.S..------EEE-SSEEEEEE- CS
                             RPE65 140 seaftAHpkvdpetgelynfglslgkppsvtysvfdvaaaidk.srevkiklpgeklkpayiHdfalTenyvvlvel 215
                                         +f AH k+d +t+e+++++  l  + +++++++d +   d+  + +k+k+p+     +yiHdf++++n+++l  +
  gi|298674039|ref|YP_003725789.1| 179 -VNFMAHSKIDGQTEEWILVSG-L--KDKLNITTVDKN---DNlVKFQKVKIPK----NSYIHDFFVSDNHIILNFQ 244
                                       .367************999884.2..355899999955...4444555666666....9****************** PP

                                       -EE...CHC.HCCCTCGGCEEE-TTS-EEEEEEETTTT--GG...EEEEE--SEEEEEEEEEEET.TCEEEEEEEEE CS
                             RPE65 216 plk...lnlkkgkksggdalewdpekptrfgvipRrgekegvakfrwfeteaffvfHtaNayeeeedgevvvdlcry 289
                                       p++   +++ +g +s+ ++l w+p+++  ++v++R++ + +v+ + +f +e+ +++Ht+Nayee  ++++v+d + y
  gi|298674039|ref|YP_003725789.1| 245 PAEpyvFKFMSGLSSFLESLYWRPKQGNILLVLNRNE-EGEVEPY-QFSVESSWMWHTLNAYEE--GNKIVADFVGY 317
                                       **998888888*************************5.2234667.99999************9..77788****** PP

                                       .SS..--STTS-CT.T----.-...GGTGGG-EEEEEEEEETTTTTCEECE.EEEEESS-EEEEE--GGGTTS--SE CS
                             RPE65 290 edae.vldnlylenlrsrkgeakkeekaeesqsrlrryrldlktgsateekeeaalsdrslEfPrinpaysgrkyry 365
                                       + +e ++++        ++g++   + +++ ++++rry +dl++++++++    +l++ + E P++n+ +s+rk++y
  gi|298674039|ref|YP_003725789.1| 318 RYPEqIFGDDPTF-YAIMEGRE---K-KSDYPGEIRRYIIDLDKETVQQQ----VLDGANYEYPVVNQYHSCRKHKY 385
                                       9996587776322.22222222...2.236789*********98888888....*********************** PP

                                       EEEEE-SSTTSS-..-.-EEEEEET.....-TTTE.........EE--EEEEESTT.....TSSTT-EEEEEEEEET CS
                             RPE65 366 vYgasasggsdkaskf.dglvkvDl.....etkgrea....eghypgEpiFVPrag.....ateEDdGvllsvvlde 427
                                        Y++ a++++    +f +++v++D+     e          +g y+ Ep+FVP++g     + +++ G++l+ v+d+
  gi|298674039|ref|YP_003725789.1| 386 GYFVRAHKPE---DVFwSSVVRMDMdtglpE-----FydfgKGYYCTEPVFVPKPGynyssDINDEPGWILTEVYDS 454
                                       ******9996...4677********554440.....25666667****************999999*********99 PP

                                       .TTEEEEEEEETTBCCC..SEEEEESS---S--BEEEE CS
                             RPE65 428 .eersellvldAktlte..vArvelpqrvpygfHGtfv 462
                                         ++s+l +l A++l++  vA+v+l+++vp++fHG++ 
  gi|298674039|ref|YP_003725789.1| 455 yLKKSFLAILQADNLESgpVAKVHLKHHVPLSFHGFWK 492
                                       *************************************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 2894.54
//
Query:       gi|298674040|ref|YP_003725790.1|  [L=263]
Description: NAD+ synthetase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.4e-85  283.7   0.0      1e-84  283.4   0.0    1.0  1  NAD_synthase   NAD synthase
    2.1e-07   30.1   0.0      3e-06   26.3   0.0    2.0  2  tRNA_Me_trans  tRNA methyl transferase
  ------ inclusion threshold ------
      0.015   15.0   0.0      0.018   14.8   0.0    1.1  1  Asn_synthase   Asparagine synthase
       0.04   13.7   0.1      0.072   12.9   0.1    1.3  1  CHIPS          Chemotaxis-inhibiting protein CHIPS
       0.13   11.8   0.0       0.28   10.6   0.0    1.5  2  QueC           Queuosine biosynthesis protein QueC
       0.14   11.7   0.0       0.23   11.0   0.0    1.3  1  ThiI           Thiamine biosynthesis protein (ThiI)


Domain annotation for each model (and alignments):
>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  283.4   0.0   3.5e-88     1e-84       5     242 .]      10     250 ..       7     250 .. 0.98

  Alignments for each domain:
  == domain 1  score: 283.4 bits;  conditional E-value: 3.5e-88
                                       HHHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--.SSSTTHHHHHHHHHHHHHHTSEEEE-- CS
                      NAD_synthase   5 lvdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllP.ssvsseedvedalalaenlgievktid 80 
                                       +v+f++++vk+a+++gvv+GlSGG+DS+++a lav+alg+envl++ lP + v+s +d +d+  +a++lgi++k+id
  gi|298674040|ref|YP_003725790.1|  10 IVNFIRSKVKEADSTGVVIGLSGGIDSAVTANLAVEALGSENVLGIHLPeEGVTSTKDSKDSEIIANSLGINFKNID 86 
                                       799**********************************************999************************* PP

                                       -HHHHHHHHHHHHHHH..-HHHHHHHHHHHHHHHHHHHHHHHTEEEB---BHHHHTTT-S-TTTTT--SBETTTTS- CS
                      NAD_synthase  81 ikpivrafeqelkeak..edlakgNlkaRiRmailyaianklnllvlgTgnksElvvGyfTkyGDgaadlapiaell 155
                                       i+ i++ f +e+ +++  +  + gNlk+RiRm++ly++an++ ++v+gTgnksE+++GyfTkyGDg++dl+pi++l+
  gi|298674040|ref|YP_003725790.1|  87 ISRILNCFISEIPDESgeKPPVVGNLKSRIRMCLLYYYANSFYKMVVGTGNKSEIMLGYFTKYGDGGVDLEPIGDLY 163
                                       ************99998778899****************************************************** PP

                                       HHHHHHHHHHTT--HHHHCS--B--SSTT-BHHHHHSS-HHHHHHHHTHSSSS...HHHHHTTT--HHHHHHHHHHH CS
                      NAD_synthase 156 KtevkeLakelnvPervlkkpPsAdLkpgqtDeeeLgikYdelDeiLklvekkkspeeiikekelpaevvekieklv 232
                                       Ktev+eLak l +Pe++++k+PsA+L+ gqtDe+eLg++Y+++D iL+lv ++++pe++ +  +l  +++  + +++
  gi|298674040|ref|YP_003725790.1| 164 KTEVFELAKLLSIPEHIINKKPSAGLWSGQTDENELGLPYEIIDRILNLVFHGEKPENLQEIFDLTPDQIDLLLSRM 240
                                       ***************************************************************************** PP

                                       HHTGGGGSSS CS
                      NAD_synthase 233 kksehKrklp 242
                                       k++ hKrk+p
  gi|298674040|ref|YP_003725790.1| 241 KSNIHKRKVP 250
                                       ********98 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0     1e-09     3e-06       3      72 ..      26      89 ..      24     136 .. 0.86
   2 ?    1.8   0.0     0.028        83     167     195 ..     158     188 ..     155     190 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1e-09
                     tRNA_Me_trans  3 vvvalSgGVDSsvaaallkeqg..yevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfek 72
                                      vv++lSgG+DS+v+a l  e+    +v g++l           + ++++d kd e +a+ lgi+++ +d+++
  gi|298674040|ref|YP_003725790.1| 26 VVIGLSGGIDSAVTANLAVEALgsENVLGIHLPEE--------GVTSTKDSKDSEIIANSLGINFKNIDISR 89
                                      99**************9999864578888888532........57899*******************99865 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.028
                     tRNA_Me_trans 167 PlgeltKeevrkiAkeagla..vaekkdSqg 195
                                       P+g+l K+ev ++Ak  +++  + +kk S g
  gi|298674040|ref|YP_003725790.1| 158 PIGDLYKTEVFELAKLLSIPehIINKKPSAG 188
                                       9**************9999777889998887 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   5.9e-06     0.018      22     123 ..      28     133 ..      18     199 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.9e-06
                      Asn_synthase  22 alLSGGlDSSliaalaarqsksplktFsigf.ee..kgsdeakyakevaehlgtehtelvlteeellda.lpdviy. 93 
                                       + LSGG+DS++ a la + +  + +   i++ ee   + +++k  + +a+ lg++  ++ +++  +l++ + +++  
  gi|298674040|ref|YP_003725790.1|  28 IGLSGGIDSAVTANLAVEALG-SENVLGIHLpEEgvTSTKDSKDSEIIANSLGINFKNIDISR--ILNCfISEIPDe 101
                                       569***************997.67788888843367999****************65555554..666556666653 PP

                      Asn_synthase  94 hlee.pfad..rsaiplyllsrlakrkgvkvvL 123
                                         e+ p+++  +s i ++ll+ +a ++++k+v 
  gi|298674040|ref|YP_003725790.1| 102 SGEKpPVVGnlKSRIRMCLLYYYA-NSFYKMVV 133
                                       445585555236888999999999.88888875 PP

>> CHIPS  Chemotaxis-inhibiting protein CHIPS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   2.4e-05     0.072       5      71 ..     106     170 ..     102     187 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.4e-05
                             CHIPS   5 pttlgklderlrnylkkgtknsaqfekmviltenkgyytvylntplaedrknvellgkmyktyffkk 71 
                                       p  +g+l  r+r  l     ns  f kmv+ t nk    +   t   +   ++e +g +ykt +f  
  gi|298674040|ref|YP_003725790.1| 106 PPVVGNLKSRIRMCLLYYYANS--FYKMVVGTGNKSEIMLGYFTKYGDGGVDLEPIGDLYKTEVFEL 170
                                       7788999999999999888776..99**********9999999999****************99974 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   9.4e-05      0.28       2      64 ..      26      90 ..      25     106 .. 0.75
   2 ?   -2.8   0.0       1.2   3.6e+03     157     176 ..     158     177 ..     156     181 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 9.4e-05
                                      EEEE--SSHHHHHHHHHHHHH-..SEEEEEEEESS-T.TSHHHHHHHHHHHHT--.-EEEEE-GGG CS
                              QueC  2 avvllSGGlDSttvlalakkeg..kevealtfdYgqr.hkkeleaakkiakelgveehkildldll 64
                                      +v+ lSGG+DS++ + la ++   ++v  +++  +    +k+ +  + ia++lg+ + k +d++ +
  gi|298674040|ref|YP_003725790.1| 26 VVIGLSGGIDSAVTANLAVEALgsENVLGIHLPEEGVtSTKDSKDSEIIANSLGI-NFKNIDISRI 90
                                      5788***********9999987335566666644333377888888888999999.8888888754 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.2
                                       TTTT--HHHHHHHHHHTTHH CS
                              QueC 157 PlidlsKaeivklgkelgvp 176
                                       P+ dl K+e+++l+k l +p
  gi|298674040|ref|YP_003725790.1| 158 PIGDLYKTEVFELAKLLSIP 177
                                       899999******99988765 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   7.8e-05      0.23       6      56 ..      26      78 ..      22      98 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.8e-05
                              ThiI  6 vlaLlSgGiDSpVaaylllkR.Gc.rvvlvhlknepgtseeaiekveklaell 56
                                      v+  lSgGiDS V+a l+++  G  +v  +hl +e +ts +  +  e +a+ l
  gi|298674040|ref|YP_003725790.1| 26 VVIGLSGGIDSAVTANLAVEAlGSeNVLGIHLPEEGVTSTKDSKDSEIIANSL 78
                                      67779***********9997546525777999999999999988888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1698.03
//
Query:       gi|298674041|ref|YP_003725791.1|  [L=427]
Description: hypothetical protein Metev_0063 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.5e-41  138.8   0.2    1.6e-40  137.8   0.1    1.6  2  DUF1743          Domain of unknown function (DUF1743)
    0.00029   21.0   0.0    0.00065   19.8   0.0    1.5  1  tRNA_anti_2      OB-fold nucleic acid binding domain
    0.00054   19.9   0.0      0.001   19.0   0.0    1.4  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
      0.029   14.3   1.8      0.086   12.8   1.8    1.7  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.042   13.5   0.1        0.1   12.2   0.1    1.6  1  tRNA_anti-like   tRNA_anti-like
      0.052   13.5   1.7      0.091   12.7   1.7    1.3  1  C1_1             Phorbol esters/diacylglycerol binding domain
      0.061   13.1   0.2       0.15   11.8   0.2    1.6  1  YdjO             Cold-inducible protein YdjO
      0.066   13.8   0.4       0.48   11.0   0.0    2.3  2  MatP             MatP N-terminal domain
       0.21   11.5   1.7       0.53   10.3   1.7    1.7  1  DUF4428          Domain of unknown function (DUF4428)
       0.43   10.5   2.1          1    9.3   2.1    1.6  1  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
       0.54   10.3   3.4          1    9.4   3.4    1.5  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain


Domain annotation for each model (and alignments):
>> DUF1743  Domain of unknown function (DUF1743)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       5.9   9.6e+03      82      89 ..      63      70 ..      42      89 .. 0.54
   2 !  137.8   0.1     1e-43   1.6e-40       2     116 .]     141     255 ..     140     255 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 5.9
                                      S-HHHHHH CS
                           DUF1743 82 edpeallk 89
                                      ++p+++++
  gi|298674041|ref|YP_003725791.1| 63 KYPDKVIE 70
                                      33333332 PP

  == domain 2  score: 137.8 bits;  conditional E-value: 1e-43
                                       THHHHHHHHHH-..-TT.S-EEEEEEEE-GGGTT.---EEHHHHHHHHHHHTTCECTSEBTTTTCECCS-STTSSEE CS
                           DUF1743   2 rgiiGAtaalganiale.dstyEllaYreperwg.erevdeesvieadektypetfdnvDlshklvvlvPhtpdpvl 76 
                                       rg+iGA+aa ga ++ e dstyE+l+Yr++e+wg +r vde+s+++ d + yp+t+d+vD+++ ++v+vP++pdpvl
  gi|298674041|ref|YP_003725791.1| 141 RGLIGALAATGAMLDSEwDSTYEYLTYRKKEKWGlSRVVDENSIYKSDLDFYPDTWDTVDWENYVIVCVPKSPDPVL 217
                                       9***********9998899********************************************************** PP

                                       EEEEES-HHHHHHHHHCSEE..S-EECEEEEEESTTS-TT CS
                           DUF1743  77 fGirgedpeallkaakeilskeeeseemavfrtnqgtdah 116
                                       +Girg+d +++++a ++i+s  e +e++av++tnqgtd+h
  gi|298674041|ref|YP_003725791.1| 218 YGIRGKDDHTVKSATEDIKS--ETVERSAVYKTNQGTDMH 255
                                       ********************..*****************9 PP

>> tRNA_anti_2  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0     4e-07   0.00065       9      79 ..     261     332 ..     256     335 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4e-07
                       tRNA_anti_2   9 aikelleaelkkavwvrGeisnlk.rkasghvYftLkD.ekakisavifr..sraaklkftledGmkVlvkgrls 79 
                                       +ike+ +  + +++ v+G + n   + + gh+ ftL D +  +i+++  +  ++++ l  +l+ G+++ v g+++
  gi|298674041|ref|YP_003725791.1| 261 SIKEVTD--M-QSYIVQGTVKNHPyTIEGGHTIFTLGDnSGNTIDCAAYEptKNFRYLVRKLKTGDNITVYGSVK 332
                                       5777764..5.559*********6334488********65578****99977777888899***********986 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   6.3e-07     0.001       2      60 ..     272     333 ..     271     344 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 6.3e-07
                                       EEEEEEEEEEEEEETTEEEEEEEETT.EEEEEEEET..HHHHHHHTTS-TTSEEEEEEEEEE CS
                   tRNA_anti-codon   2 tvaGrvtsisdrsggkvifidlrDgt.griqvvlfr..eeatklaenlkeGdvvrvtGrvkr 60 
                                        v+G v++   + +g++  ++l D++  +i + +    +++++l  +lk Gd + v+G vk 
  gi|298674041|ref|YP_003725791.1| 272 IVQGTVKNHPYTIEGGHTIFTLGDNSgNTIDCAAYEptKNFRYLVRKLKTGDNITVYGSVKN 333
                                       58999999999999************669*******************************96 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.8   5.3e-05     0.086      30      56 ..     356     382 ..     347     385 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.3e-05
                    OrfB_Zn_ribbon  30 tCseCgsknkealsgrtfkCpnCgfea 56 
                                       tC+ C +++k a +++ fkC++C+++a
  gi|298674041|ref|YP_003725791.1| 356 TCPICNKRMKSAGKNQGFKCRKCKTKA 382
                                       8**********************9875 PP

>> tRNA_anti-like  tRNA_anti-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   6.3e-05       0.1      90     149 ..     272     333 ..     269     343 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.3e-05
                                       EEEEEEEEEEE.-STT-EEEEEE-TT-S-S--EEEEEEG.GHHHHHH--TTSEEEEEEE--- CS
                    tRNA_anti-like  90 eVeGvvsdikk.ieassvvvlardddgltnVrclledea.teasaakiskGqkvtivGqvng 149
                                       +V+G+v++ +  ie+  ++ ++ d+ g+t   +  e  +     + k++ G+++t+ G v+ 
  gi|298674041|ref|YP_003725791.1| 272 IVQGTVKNHPYtIEGGHTIFTLGDNSGNTIDCAAYEPTKnFRYLVRKLKTGDNITVYGSVKN 333
                                       7********777************7777766666666663344589************9975 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.7   5.6e-05     0.091      13      36 ..     356     380 ..     350     383 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.6e-05
                                       B-TTT-SB--S.SSS-EEEETTT-- CS
                              C1_1  13 fCkhCgeflwg.kekqglkCswCkl 36 
                                       +C  C++ ++  +  qg+kC+ Ck 
  gi|298674041|ref|YP_003725791.1| 356 TCPICNKRMKSaGKNQGFKCRKCKT 380
                                       7********999***********96 PP

>> YdjO  Cold-inducible protein YdjO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   9.2e-05      0.15      38      53 ..     353     368 ..     350     370 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.2e-05
                              YdjO  38 eePtCplCkseMvkev 53 
                                        +PtCp+C+++M++  
  gi|298674041|ref|YP_003725791.1| 353 RNPTCPICNKRMKSAG 368
                                       58**********9875 PP

>> MatP  MatP N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       1.2     2e+03       8      34 ..     154     182 ..     152     191 .. 0.72
   2 ?   11.0   0.0    0.0003      0.48       9      42 ..     307     340 ..     303     351 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.2
                                       HHHHH..HHHHHHHHHHTT---BS-SSHH CS
                              MatP   8 leagW..kwkYLvkkhregeeitryieks 34 
                                       l+++W   ++YL  +++e   ++r +++ 
  gi|298674041|ref|YP_003725791.1| 154 LDSEWdsTYEYLTYRKKEKWGLSRVVDEN 182
                                       56677335899999999998888877654 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0003
                                       HHHHHHHHHHHHHHTT---BS-SSHHHHHHHHHH CS
                              MatP   9 eagWkwkYLvkkhregeeitryieksaaeeavqq 42 
                                       e + +++YLv+k + g++it y    ++  ++++
  gi|298674041|ref|YP_003725791.1| 307 EPTKNFRYLVRKLKTGDNITVYGSVKNQTLNIEK 340
                                       556689****************877666666655 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.7   0.00032      0.53       1      31 [.     356     384 ..     356     396 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00032
                           DUF4428   1 iCaiCgkKigllkrlkleDgyvCkdClkKl.s 31 
                                       +C+iC+k  +  +    + g+ C +C  K+ s
  gi|298674041|ref|YP_003725791.1| 356 TCPICNKRMKSAG---KNQGFKCRKCKTKAgS 384
                                       5***********9...9************942 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   2.1   0.00064         1       4      29 ..     357     380 ..     357     384 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00064
                                       ESTTTSBEEEEECSCCCEEEESSSS- CS
                    RNA_POL_M_15KD   4 CpkCgNlLlpkedkegknfeCrqCgY 29 
                                       Cp C+  + ++++  g  f Cr+C+ 
  gi|298674041|ref|YP_003725791.1| 357 CPICNKRMKSAGKNQG--FKCRKCKT 380
                                       9**********99999..99****85 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   3.4   0.00064         1      18      45 ..     354     380 ..     349     381 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00064
                     Zn_Tnp_IS1595  18 gfvCPhCgsr..kayriktrglfqCkeCrk 45 
                                       +++CP C +r  +a +    + f+C++C++
  gi|298674041|ref|YP_003725791.1| 354 NPTCPICNKRmkSAGKN---QGFKCRKCKT 380
                                       499*****997333333...46******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1008  (0.0562218); expected 358.6 (0.02)
Passed bias filter:                      690  (0.0384851); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 2488.09
//
Query:       gi|298674042|ref|YP_003725792.1|  [L=328]
Description: transcriptional regulator, XRE family [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-10   39.0   1.5    9.9e-09   35.1   0.1    3.2  4  HTH_3     Helix-turn-helix
    4.4e-06   26.6   0.7    1.4e-05   25.0   0.0    2.3  3  HTH_19    Helix-turn-helix domain
    8.6e-05   22.8   0.0    0.00015   22.0   0.0    1.4  1  HTH_31    Helix-turn-helix domain
     0.0013   18.6   0.1     0.0052   16.7   0.1    2.0  1  HTH_11    HTH domain
     0.0062   16.3   0.0      0.012   15.4   0.0    1.5  1  HTH_23    Homeodomain-like domain
  ------ inclusion threshold ------
      0.022   14.7   0.0      0.058   13.3   0.0    1.6  1  HTH_36    Helix-turn-helix domain
      0.024   14.4   0.1      0.077   12.8   0.1    1.9  2  MerR      MerR family regulatory protein
      0.025   14.4   0.1      0.068   13.0   0.0    1.8  2  HTH_25    Helix-turn-helix domain
      0.027   14.2   0.3      0.051   13.3   0.3    1.5  1  HTH_38    Helix-turn-helix domain
      0.086   12.9   0.1        0.3   11.2   0.1    1.9  1  HTH_7     Helix-turn-helix domain of resolvase
       0.12   12.5   0.0       0.27   11.3   0.0    1.6  1  MerR_1    MerR HTH family regulatory protein


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.3   3.8e+03      39      49 ..      60      70 ..      58      73 .. 0.76
   2 !   35.1   0.1   6.1e-12   9.9e-09       1      52 [.     132     183 ..     132     185 .. 0.96
   3 ?    0.6   0.0      0.38   6.1e+02      30      51 ..     202     225 ..     202     227 .. 0.88
   4 ?   -2.1   0.0       2.5   4.1e+03      26      48 ..     249     270 ..     247     272 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.3
                                      HHHHHHHHHHT CS
                             HTH_3 39 etlkklakaLg 49
                                      + +k lak+L+
  gi|298674042|ref|YP_003725792.1| 60 QEMKSLAKYLD 70
                                      67899999998 PP

  == domain 2  score: 35.1 bits;  conditional E-value: 6.1e-12
                                       HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEH CS
                             HTH_3   1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvsl 52 
                                       l+e+R    +s+  +A  lGvsr+tis++E G    s+++++ l++ ++v l
  gi|298674042|ref|YP_003725792.1| 132 LREARMSVSMSIGTIASQLGVSRRTISKYEEGGMDASIDIALQLEELFDVAL 183
                                       89***********************************************987 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.38
                                       HTT..SSCSBHHHHHHHHHHHTSE CS
                             HTH_3  30 EnG..ernPsletlkklakaLgvs 51 
                                       En+  e++P  ++++ l  +Lg++
  gi|298674042|ref|YP_003725792.1| 202 ENNeyETKPPEDNILNLISTLGYD 225
                                       6777799**************987 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 2.5
                                       HHHHHTTSSCSBHHHHHHHHHHH CS
                             HTH_3  26 isriEnGernPsletlkklakaL 48 
                                       is++ n   + + e +  ++++ 
  gi|298674042|ref|YP_003725792.1| 249 ISKYCNS-MIKRAELMSSISNVT 270
                                       8999998.557777777777765 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   8.6e-09   1.4e-05       1      54 [.     129     181 ..     129     196 .. 0.90
   2 ?   -3.2   0.1       5.3   8.7e+03      33      55 ..     202     225 ..     202     226 .. 0.65
   3 ?   -3.2   0.0       5.3   8.7e+03      39      48 ..     303     312 ..     292     315 .. 0.56

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 8.6e-09
                            HTH_19   1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgi 54 
                                       G+ L+eaR    +++  +a++lg+sr+ is++E g + ++s++  l++ e++++
  gi|298674042|ref|YP_003725792.1| 129 GDVLREARMSVSMSIGTIASQLGVSRRTISKYEEGGM-DASIDIALQLEELFDV 181
                                       6779*******************************88.8998888888777765 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.3
                            HTH_19  33 Eng..kkdvpsaelllkiaealgid 55 
                                       En+  ++ +p+ +++l +  +lg+d
  gi|298674042|ref|YP_003725792.1| 202 ENNeyET-KPPEDNILNLISTLGYD 225
                                       6775555.67777777777777766 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 5.3
                            HTH_19  39 vpsaelllki 48 
                                        +++e+ll++
  gi|298674042|ref|YP_003725792.1| 303 LLDPEDLLQL 312
                                       4445555554 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   9.4e-08   0.00015       3      56 ..     129     181 ..     129     186 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 9.4e-08
                            HTH_31   3 GalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgl 56 
                                       G+ Lr++R    +s    A +lgvs+ t+s++E G  +  s +   +l +++++
  gi|298674042|ref|YP_003725792.1| 129 GDVLREARMSVSMSIGTIASQLGVSRRTISKYEEGGMD-ASIDIALQLEELFDV 181
                                       899********************************986.777766666666655 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   3.2e-06    0.0052      16      35 ..     141     160 ..     131     160 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.2e-06
                            HTH_11  16 isgeeLAeeLnvSrrtvrrd 35 
                                       +s+ ++A +L+vSrrt+ ++
  gi|298674042|ref|YP_003725792.1| 141 MSIGTIASQLGVSRRTISKY 160
                                       7999*************986 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   7.5e-06     0.012      18      43 ..     141     162 ..     131     169 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.5e-06
                            HTH_23  18 lsvreIAreLgvsrrTvyrwlkryre 43 
                                       +s+ +IA +LgvsrrT+++    y+e
  gi|298674042|ref|YP_003725792.1| 141 MSIGTIASQLGVSRRTISK----YEE 162
                                       78889************95....444 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.6e-05     0.058      27      45 ..     142     160 ..     137     161 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.6e-05
                            HTH_36  27 sqetlakrlglsknTvsra 45 
                                       s  t+a++lg+s++T+s++
  gi|298674042|ref|YP_003725792.1| 142 SIGTIASQLGVSRRTISKY 160
                                       678**************97 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0         3   4.9e+03       5      14 ..      21      30 ..      20      30 .. 0.88
   2 ?   12.8   0.1   4.7e-05     0.077       1      21 [.     142     162 ..     142     165 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3
                                      HHHHHTTTHH CS
                              MerR  5 vAeltGvspr 14
                                      v++++++ pr
  gi|298674042|ref|YP_003725792.1| 21 VSKRCNIRPR 30
                                      89****9997 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 4.7e-05
                                       EHHHHHHHHTTTHHHHHHHHH CS
                              MerR   1 tIgevAeltGvsprtLRyYEr 21 
                                       +Ig +A  +Gvs rt+  YE+
  gi|298674042|ref|YP_003725792.1| 142 SIGTIASQLGVSRRTISKYEE 162
                                       7*******************8 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.2e-05     0.068       2      35 ..     132     165 ..     131     168 .. 0.92
   2 ?   -3.8   0.1       7.3   1.2e+04      24      32 ..     307     315 ..     306     317 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.2e-05
                                       HHHHHHTTT--HHHHHHHSS--HHHHHHHHCT-- CS
                            HTH_25   2 LraaRearglsleevaketkIrkdylealEeddf 35 
                                       Lr+aR++ ++s+  +a ++ ++ +++ + Ee+ +
  gi|298674042|ref|YP_003725792.1| 132 LREARMSVSMSIGTIASQLGVSRRTISKYEEGGM 165
                                       9*************************99999855 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 7.3
                                       HHHHHHHHC CS
                            HTH_25  24 kdylealEe 32 
                                       +d+l+ +Ee
  gi|298674042|ref|YP_003725792.1| 307 EDLLQLIEE 315
                                       789999998 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   3.1e-05     0.051      21      39 ..     141     159 ..     131     160 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.1e-05
                            HTH_38  21 lslreIArrLgrspsTIsR 39 
                                       +s+ +IA +Lg+s+ TIs+
  gi|298674042|ref|YP_003725792.1| 141 MSIGTIASQLGVSRRTISK 159
                                       7888*************96 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00018       0.3      22      41 ..     141     160 ..     136     163 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
                                       --STTTSSSS---SSSS--S CS
                             HTH_7  22 isiskIAkevnisRsTvYRy 41 
                                       +si +IA ++++sR T+ +y
  gi|298674042|ref|YP_003725792.1| 141 MSIGTIASQLGVSRRTISKY 160
                                       89**************9777 PP

>> MerR_1  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00017      0.27       1      24 [.     141     164 ..     141     170 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                                       EEHHHHHHHHTS-HHHHHHHHHHT CS
                            MerR_1   1 ysigevakilgvtthtlrywekeg 24 
                                       +sig  a +lgv+ +t+  +e+ g
  gi|298674042|ref|YP_003725792.1| 141 MSIGTIASQLGVSRRTISKYEEGG 164
                                       89*******************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2003.02
//
Query:       gi|298674043|ref|YP_003725793.1|  [L=192]
Description: phosphoribosylglycinamide formyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-58  197.0   0.0    2.4e-58  196.9   0.0    1.0  1  Formyl_trans_N  Formyl transferase


Domain annotation for each model (and alignments):
>> Formyl_trans_N  Formyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.9   0.0   1.3e-62   2.4e-58       2     181 .]       4     184 ..       3     184 .. 0.99

  Alignments for each domain:
  == domain 1  score: 196.9 bits;  conditional E-value: 1.3e-62
                                       EEEEEESESSHHHHHHHHHHHHTTSE.CEEEEEEESCTTEHCHHHHHHCCHCCCECHHCCSCCCCCCCHHHHHHHHC CS
                    Formyl_trans_N   2 kivvlisgtgsnlqalldalkkgsle.advvlvvsnkdkaaglekaeaasiptkvfeekkleprsqfeeelaeelke 77 
                                       +i+vl+sg g+nlq +++++++g ++ a++ +v+s+  +a  le+a++ +i +  ++ ++++ +s++e+el+++l+e
  gi|298674043|ref|YP_003725793.1|   4 NIAVLASGRGTNLQSIINNVENGYIHdANIKAVISDVRDAHALERAKKYGISAVFIDPSEFSDKSEYEKELIKKLEE 80 
                                       8***********************999************************************************** PP

                                       TT-SEEEEES--S---HHHHHSSTTSEEEEESSSTTTTBSS-HHHHHHHTTSSEEEEEEEE--SSSSTS-EEEEEEE CS
                    Formyl_trans_N  78 lkadlivlagymkllpkelvqavrlkilniHpSLLPrfkGaaaiqraleaGdketGvtihfvdeelDtGailaqkkv 154
                                       ++ dl++lag+m++l++++v+ ++++ilniHpSLLP+fkG++a+++al  G+k++G+t+h+v+e++D G+i++q+ v
  gi|298674043|ref|YP_003725793.1|  81 FNTDLVLLAGFMRILGNKFVRFYKHRILNIHPSLLPAFKGLRAQKQALDYGVKVSGCTVHYVTEDMDSGPIILQECV 157
                                       ***************************************************************************** PP

                                       E--TT--HHHHHHHHHHHHHHHHHHHH CS
                    Formyl_trans_N 155 eiiaedtkeeleqrvadaehkalveal 181
                                       ++ ++dt+e+le+r+ ++eh++++ea+
  gi|298674043|ref|YP_003725793.1| 158 PVYEDDTEETLENRILQEEHEIYPEAV 184
                                       ************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1253.41
//
Query:       gi|298674044|ref|YP_003725794.1|  [L=411]
Description: glycine hydroxymethyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.1e-171  570.8   1.2   1.3e-171  570.6   1.2    1.0  1  SHMT             Serine hydroxymethyltransferase
  ------ inclusion threshold ------
      0.018   14.3   0.1      0.026   13.8   0.1    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family


Domain annotation for each model (and alignments):
>> SHMT  Serine hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  570.6   1.2  1.5e-175  1.3e-171       1     398 [.       4     379 ..       4     380 .. 0.99

  Alignments for each domain:
  == domain 1  score: 570.6 bits;  conditional E-value: 1.5e-175
                                       HHHHTHHHHHHHHHHHHHHHHSEE-STT-----HHHHHHHTSGGGG----EETTEESSST-HHHHHHHHHHHHHHHH CS
                              SHMT   1 leesdpevaeiikkekerqkeeieliasenftskavlealGsvltnkyaeGyPGkryyGGcefvdeveelaqdrake 77 
                                       ++e dpe+ae+++ e +rq  +++liasen+ts+av+ea+Gs++tnkyaeGy GkryyGGce+vd++e+la+drak+
  gi|298674044|ref|YP_003725794.1|   4 ISEIDPEIAEAMELEAKRQDYKLNLIASENYTSRAVMEAQGSIMTNKYAEGYSGKRYYGGCEYVDIAENLAIDRAKQ 80 
                                       5789************************************************************************* PP

                                       HCT-STTTEEEE---SSHHHHHHHHHHHHT-TT-EEEEESCTTTSTGGGT-BTSS-B-SHHHHHSEEEEE-B-TTTS CS
                              SHMT  78 lfkldpakwgvnvqplsGsqanlavytallepgdrilgldladGGhlthGakveskkisassklfesveykvdketg 154
                                       +f+++    +vnvqp+sGs+an+avy ++le gd+i+++dl++GGhl+hG++v++     ++k++++v+y+v+ket+
  gi|298674044|ref|YP_003725794.1|  81 IFGAE----HVNVQPHSGSNANMAVYFSVLEYGDTIMAMDLSQGGHLSHGSPVNF-----TGKFYNVVPYGVNKETE 148
                                       *****....**********************************************.....***************** PP

                                       SB-HHHHHHHHHHH--SEEEEE-SST-S---HHHHHHHHHHTT-EEEEE-GGGHHHHHTTSS--GCCTSSEEEEESS CS
                              SHMT 155 lidydelekkakefkPklivaGtsaysrlidyarlreiadevgayllvdmahiaGlvaagvipsPfeyadvvtttth 231
                                       +idydel   ake kPk+ivaG+saysr id++r+reiadevgayll+d+ahiaGlvaagv+ +P++yad+vtttth
  gi|298674044|ref|YP_003725794.1| 149 TIDYDELMDIAKENKPKMIVAGASAYSREIDFKRFREIADEVGAYLLADIAHIAGLVAAGVHQNPVPYADFVTTTTH 225
                                       ***************************************************************************** PP

                                       STT-S-S-EEEEEC-SEEEEETTTEEEEHHHHHHHHHHHTTTT-SS--HHHHHHHHHHHHHCTSHHHHHHHHHHHHH CS
                              SHMT 232 ktlrGprgglillrkgvksvdktgkevleelekkinsavfPglqGGPlnhviaakavalkealepefkvyqkqvlkn 308
                                       ktlrGprgg+i+++              e+++k i+++vfPg+qGGPl+hvia+kava+kea +p+fk+  +q +kn
  gi|298674044|ref|YP_003725794.1| 226 KTLRGPRGGMIMCS--------------EDYAKAIDKTVFPGIQGGPLMHVIAGKAVAFKEAQTPQFKKDLEQTVKN 288
                                       *************9..............89*********************************************** PP

                                       HHHHHHHHHHTT-EEGGGS-SSSEEEEEGGGGTS-HHHHHHHHHHTTEE-EEE--TTS.STTTT-SEEEEESHHHHH CS
                              SHMT 309 akalaealkekgyklvsgGtdnhlvlvdlrekgldGkraekvlekvnitankntvPgd.ksalvtsGlrlGtpalts 384
                                       akal ++l+++g+++vsg tdnh++lv+l++ +++Gk+ae+v +k+ i  nknt+P + + +++tsG+r+Gtp +t+
  gi|298674044|ref|YP_003725794.1| 289 AKALCKNLEDRGFTIVSGDTDNHMMLVNLNDFDITGKDAETVFSKAGIVLNKNTIPSEtRGPFITSGVRVGTPPITT 365
                                       **********************************************************99***************** PP

                                       TT--HHHHHHHHHH CS
                              SHMT 385 rgfkeedlekvakf 398
                                       rg+ke+++e va+f
  gi|298674044|ref|YP_003725794.1| 366 RGMKESEMEDVADF 379
                                       ************98 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1     3e-06     0.026      86     186 ..     137     239 ..     125     313 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3e-06
                                       EEEEE-B-TTTSSB-GGGCGGG--TTE.EEEEE.B-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETTEECCC CS
                   DegT_DnrJ_EryC1  86 kpvfvDvdpdtynidpaaieaaitert.kaIlp.VhlyGqvadmdalkaiaakhglkvieDaAhAlGatykgkkvGa 160
                                       ++v+  v+++t +id +++     e+  k I++ + +y++  d+++ ++ia++ g +++ D Ah  G   +g +   
  gi|298674044|ref|YP_003725794.1| 137 NVVPYGVNKETETIDYDELMDIAKENKpKMIVAgASAYSREIDFKRFREIADEVGAYLLADIAHIAGLVAAGVHQNP 213
                                       5788889999999999999888777766777754899******************************9888855555 PP

                                       SSSEEEEE-BTTSSS-SSS-EEEEES CS
                   DegT_DnrJ_EryC1 161 lgdaavfSFyptKnlttGeGGavvtn 186
                                       +  a  +     K+l    GG+++  
  gi|298674044|ref|YP_003725794.1| 214 VPYADFVTTTTHKTLRGPRGGMIMCS 239
                                       55555555566777777778877764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       876  (0.0488594); expected 358.6 (0.02)
Passed bias filter:                      715  (0.0398795); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.52
# Mc/sec: 2377.94
//
Query:       gi|298674045|ref|YP_003725795.1|  [L=288]
Description: methylenetetrahydrofolate dehydrogenase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.1e-65  217.7   4.6    6.9e-65  217.2   4.6    1.2  1  THF_DHG_CYH_C   Tetrahydrofolate dehydrogenase/cyclohydrolase
    5.2e-37  126.7   0.8    7.7e-37  126.1   0.8    1.3  1  THF_DHG_CYH     Tetrahydrofolate dehydrogenase/cyclohydrolase
  ------ inclusion threshold ------
      0.092   12.8   3.1        4.7    7.2   3.1    2.4  1  AdoHcyase_NAD   S-adenosyl-L-homocysteine hydrolase, NAD bind
       0.12   12.8   0.5        2.6    8.5   0.1    2.3  2  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai


Domain annotation for each model (and alignments):
>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.2   4.6   1.5e-68   6.9e-65       1     158 [.     130     286 ..     130     288 .] 0.99

  Alignments for each domain:
  == domain 1  score: 217.2 bits;  conditional E-value: 1.5e-68
                                       SHHHHHHHHTT--SS--HHHHHHHHHHHHCT---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCHHHHH CS
                     THF_DHG_CYH_C   1 hplnlgrlvkgeeallpctpkgvvellketgielegkkvvvvGrsnivgkplallLleknatVtvchsktkdlaeit 77 
                                       hp+n+g+l+ g+e ++pctpkg+++ l+e+++ +eg +vvvvG+sn+vgkp+a++Ll++natV+vch  t++l+++t
  gi|298674045|ref|YP_003725795.1| 130 HPQNMGNLLIGNEEFVPCTPKGIMTALEEYDVGIEGSDVVVVGHSNVVGKPMATMLLNRNATVSVCHVYTSNLNRYT 206
                                       899************************************************************************** PP

                                       CCSSEEEE-SS-TT-B-GGGS-TT-EEEE---EEC-TTEEE-SB-HHHHCTTSSEE--TTTSCHHHHHHHHHHHHHH CS
                     THF_DHG_CYH_C  78 readivvvavGkpelikaemvkegavviDvGinrvekgklvGDvdfeevkevasaitPvpgGVGpmTvamllkntle 154
                                        +adi++va+G+++lik++mvkeg vviD Gi++  ++k++GDvdf++vk++as+itPvpgGVGp+T+a+l++++l+
  gi|298674045|ref|YP_003725795.1| 207 VNADILIVATGVKHLIKSDMVKEGVVVIDAGISKE-GDKVYGDVDFDNVKQKASLITPVPGGVGPLTIATLMQHVLK 282
                                       **********************************9.***************************************** PP

                                       HHHC CS
                     THF_DHG_CYH_C 155 aakr 158
                                       +a++
  gi|298674045|ref|YP_003725795.1| 283 SAQN 286
                                       *987 PP

>> THF_DHG_CYH  Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.1   0.8   1.7e-40   7.7e-37       1     116 []      11     127 ..      11     127 .. 0.99

  Alignments for each domain:
  == domain 1  score: 126.1 bits;  conditional E-value: 1.7e-40
                                       E--HHHHHHHHHHHHHHHHHHHHHH.T---EEEEEEES--HHHHHHHHHHHHHHHHTT-EEEEEEE-TT--HHHHHH CS
                       THF_DHG_CYH   1 lldGkalakeireelkeeveklkek.gvkpkLavilvgddpasevYvrnkkkaceevGieseliklpedvseeellk 76 
                                       ++dG++l+k+i++e++++v++lk++ +++p+L +i+vgddpas++Yv+ k+kac++vGi  e + l+ed++++el++
  gi|298674045|ref|YP_003725795.1|  11 IIDGRSLSKKIESEVSSKVQNLKDRyNITPSLSTIVVGDDPASKMYVKLKHKACDRVGIIAEDHFLSEDTTQDELIE 87 
                                       79*********************98799************************************************* PP

                                       HHHHHHH-TT--EEEE-SS-STTS-HHHHHCCS-GGGBTT CS
                       THF_DHG_CYH  77 lieelneddsvdGilvqlPlpkhidekaileaispeKDVD 116
                                       l+++ln++d+++GilvqlPlp+hi+e++++  i+p KD D
  gi|298674045|ref|YP_003725795.1|  88 LVHSLNSRDDIHGILVQLPLPEHINEQKVMMEIDPLKDAD 127
                                       **************************************88 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   3.1    0.0011       4.7      18      98 ..     160     228 ..     147     258 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0011
                                       -S--TTSEEEEE--SH.HHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTTT-SEEEE-SSSSSSB- CS
                     AdoHcyase_NAD  18 dvllaGkvavvaGyGd.vGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvkkadivvtttGnkdiit 93 
                                       dv + G  +vv+G+ + vGk  a+ l +  a v v  v                +l+  + +adi++ +tG k +i+
  gi|298674045|ref|YP_003725795.1| 160 DVGIEGSDVVVVGHSNvVGKPMATMLLNRNATVSVCHVYT-------------SNLNRYTVNADILIVATGVKHLIK 223
                                       7888888888888887358888888888888888877643.............345555667899999999999999 PP

                                       HHHHC CS
                     AdoHcyase_NAD  94 lehlk 98 
                                       ++++k
  gi|298674045|ref|YP_003725795.1| 224 SDMVK 228
                                       88754 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1   0.00057       2.6       2      35 ..     168     202 ..     167     210 .. 0.91
   2 ?    2.2   0.1     0.052   2.3e+02      67      96 ..     209     236 ..     202     244 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00057
                                       EEEETTTSHHHHHHHHHHHC.TSSEEEEEEEESTT CS
                    Semialdhyde_dh   2 vaivGatGyvGqellrlLee.hpevelvvllsssr 35 
                                       v +vG +  vG+ ++++L + +  v+++++++s+ 
  gi|298674045|ref|YP_003725795.1| 168 VVVVGHSNVVGKPMATMLLNrNATVSVCHVYTSNL 202
                                       89************9999999*********99875 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.052
                                       -SEEEE-SCHHHHHHHHHHHHHTTSEEEES CS
                    Semialdhyde_dh  67 vdivflalpagvskelapklaeagvkviDl 96 
                                       +di++ a+  gv + +  +++++gv+viD+
  gi|298674045|ref|YP_003725795.1| 209 ADILIVAT--GVKHLIKSDMVKEGVVVIDA 236
                                       56666666..588889999**********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.35s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1703.68
//
Query:       gi|298674046|ref|YP_003725796.1|  [L=414]
Description: dihydropteroate synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-53  182.1   0.1    2.2e-53  181.5   0.1    1.3  1  Pterin_bind  Pterin binding enzyme


Domain annotation for each model (and alignments):
>> Pterin_bind  Pterin binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.5   0.1   1.2e-57   2.2e-53       1     244 []      28     263 ..      28     263 .. 0.93

  Alignments for each domain:
  == domain 1  score: 181.5 bits;  conditional E-value: 1.2e-57
                                       EEEEETTTTTCHCCHHCTHHHHHHHHHHHHHHTT-SEEEEESS-TSTT--CCHHHHHHHHHHHHHHHHHHHCTSEEE CS
                       Pterin_bind   1 mgilNvtpdsfsdggkfedldkalaqarkmveeGAdilDiggestrPgaervdeeeelervvpvlealrdeadvpis 77 
                                       mg++N++++sf++++ + d d+++++a++mv++GA+++D+gg st P ae + +++e er++p le+l++++d  is
  gi|298674046|ref|YP_003725796.1|  28 MGVINLSQESFYKNSVI-DKDSIINTAQDMVDKGATMIDVGGRSTWPLAEKITKKQETERLLPALEELKGNVDAVIS 103
                                       9************9999.9********************************************************** PP

                                       EE-S-HHHHHHHHHTTSEEEEETTTTSSSTTHHHHHHHHT-EEEEESECSSTTTHCCCCCCCSSHHHHHHHHHHHHH CS
                       Pterin_bind  78 iDttkaevaeaAlkagadivNdvsgeerdpkmlelvaeagaavvvmhmrgtpktmqeeegqyedvveeveaflearv 154
                                       +Dt+ a++ae+ lk+g+d+vNdvsg+++d +m+ l+a+++++ vvm++ +tp +     +     ++ v   l++ +
  gi|298674046|ref|YP_003725796.1| 104 VDTMFADIAEESLKRGVDVVNDVSGLTADSRMVDLIADYDCPAVVMASYQTPGDP----F----GMDAVMDSLSSII 172
                                       *************************************************555432....2....3445666677788 PP

                                       HHHHHTT--GGGEEEETTTTS...STTHHHHHHHHHTHHHHHHTTSSEBEEEGTTGHHHHHHHCTTCHGHHHHHHHH CS
                       Pterin_bind 155 eaaeeaGvaperillDpgigf...gkteehnlellrrldelrealevpvllGvSrksflgrllelgkaeeRdagtaa 228
                                       ++ae+  ++p++++lDp +g     k++  ++e  +++++l +++e p+l +vSrks++ +++  + aeeR  g++a
  gi|298674046|ref|YP_003725796.1| 173 KKAESKDIDPNKLILDPAFGKwvpEKDPIYDFETADQFERL-KIFEKPLLAAVSRKSMIKAVT-GKPAEERLYGSLA 247
                                       8******************9988899999999999999999.9999***************97.34599******** PP

                                       HHHHHHHTT-SEEEES CS
                       Pterin_bind 229 flalaaaaGadivrVh 244
                                       +++l + +Gadi+r+h
  gi|298674046|ref|YP_003725796.1| 248 ATSLVVHKGADIIRTH 263
                                       ***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2550.03
//
Query:       gi|298674047|ref|YP_003725797.1|  [L=207]
Description: hypothetical protein Metev_0069 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-35  120.2   1.7    2.2e-35  120.2   1.7    1.9  2  MTHFR_C   Methylene-tetrahydrofolate reductase C terminal


Domain annotation for each model (and alignments):
>> MTHFR_C  Methylene-tetrahydrofolate reductase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.5      0.13   2.4e+03      22      26 ..      27      31 ..       9      71 .. 0.62
   2 !  120.2   1.7   1.2e-39   2.2e-35       1      93 [.     108     200 ..     108     202 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.13
                           MTHFR_C 22 CkaCg 26
                                      C+ C 
  gi|298674047|ref|YP_003725797.1| 27 CDVCA 31
                                      44443 PP

  == domain 2  score: 120.2 bits;  conditional E-value: 1.2e-39
                           MTHFR_C   1 ypalntlflgveeevkvleekCkaCgdCvlaetggiCpvsrCakkllnGpCggskngkCevkpekeCaweliyerlk 77 
                                       ypa+nt +lg   + +v++ +C++Cg+C++a++ggiCp+++C+k llnGpCggs +gkCev+++++C+weliy+rl+
  gi|298674047|ref|YP_003725797.1| 108 YPANNTDSLGGIYQGNVFHAQCAMCGNCTIADFGGICPTAQCPKGLLNGPCGGSMSGKCEVNSDMDCVWELIYQRLE 184
                                       799************************************************************************** PP

                           MTHFR_C  78 klgklekleeivppkd 93 
                                       klg+l+ le++++pkd
  gi|298674047|ref|YP_003725797.1| 185 KLGRLDLLEKVIEPKD 200
                                       **************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 1215.75
//
Query:       gi|298674048|ref|YP_003725798.1|  [L=291]
Description: methylenetetrahydrofolate reductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-37  129.6   0.1    1.5e-37  129.5   0.1    1.0  1  MTHFR           Methylenetetrahydrofolate reductase
     0.0031   17.5   0.0     0.0058   16.7   0.0    1.4  1  Hydrolase_like  HAD-hyrolase-like


Domain annotation for each model (and alignments):
>> MTHFR  Methylenetetrahydrofolate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.5   0.1   1.7e-41   1.5e-37       3     286 ..       5     286 ..       3     287 .. 0.85

  Alignments for each domain:
  == domain 1  score: 129.5 bits;  conditional E-value: 1.7e-41
                                       HHHHT.SS-EEEEEE---SSHHHHHHHHHHHHHHGGGG-SEEEE---CCCTTHHHHHHHHHHHHHHH-S-EEEEEES CS
                             MTHFR   3 eqaleegkalisfEffpPkteegernLleridrleevkplfvdvTwgaggstaeltssiakviqqelgleailhlTc 79 
                                        q+l++g+++++ E +pPk+++  + L    d l+ +  + +++T++ ++ + +++  +  +i +++g ++i+++Tc
  gi|298674048|ref|YP_003725798.1|   5 GQKLKSGEFVVTSEITPPKGSDISSVLKI-SDTLKGWV-DAINITDNNRA-VMRMSPLALGKILADTGHNVIMQMTC 78 
                                       578899***************99887754.45555555.79*********.99************************ PP

                                       TTS-HHHHHHHHHHHHHCT--EEEEE--S--TT-GG.C---S--..--SHHHHHHHHHHHHCGGSEE.EEEE-TT-- CS
                             MTHFR  80 tdaskeeldkalekakelGirnilALrGDppkdedk.weekeee..fkyaldLvrlireeygdlfdi.gvaaYPevh 152
                                       +d+++  ++++l  a++lGi +i  ++GD   ++d+  ++++++  + ++l++v+ + +  g  f+  ++ + P+  
  gi|298674048|ref|YP_003725798.1|  79 RDRNRLAIQSDLLGANALGIDSICIMTGDHTTKGDHpGAKPVYDldSVQLLSMVKKLTQ--GYDFSGnQLEGTPHFT 153
                                       ************************************99999999556677788888874..4345542789999776 PP

                                       T.....T-S-HHHHHHHHHHHHHCT--EEEEEE-S-HHHHHHHHHHHHHCT-SS-EEEEE---SSHHHHHHHHHHH. CS
                             MTHFR 153 p.....eaksleadlkylkeKvdaGAdfiitQlffdvdkflkfveqvreagidipiipgimpiksykslkrlakls. 223
                                       +      + s + ++++lk+K + G dfi+tQ ++dvd+f +f+e+v++ ++  pii+gi+p+ks+++++++++   
  gi|298674048|ref|YP_003725798.1| 154 VgvvsnIDISQKMQMMKLKKKAEMGVDFIQTQAVYDVDQFKEFTESVKHLSV--PIIAGIIPLKSANMARFMNNNIp 228
                                       66564444557778999*******************************9887..******************98766 PP

                                       T----HHHHCCCTCHCT-HHHHHHHHHHHHHHHHHHHHHCT--EEEEE-TT--HHHHHHHHHC CS
                             MTHFR 224 kvkiPqelldrleeikdddeavkkigielavemvkkllaegvkglHlytlnkekaileileql 286
                                       ++ki + +++rle  +++d+  + ++i++++    + +++g   +H++ + k+  + ++le++
  gi|298674048|ref|YP_003725798.1| 229 GIKIGDDIISRLE--EAKDPVYEGLAISAETINEIRDICNG---VHIMPIGKSLNTVTLLEMA 286
                                       *************..77899999999887653333334455...9999999998888888776 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   6.5e-07    0.0058      32      72 ..      87     126 ..      85     129 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.5e-07
                                       TTHHHHHHHCT-EEEEESSSSS-TTTHHHHHHHHT---SEE CS
                    Hydrolase_like  32 atDiagAnnaGwksvLVltGvtrpedleepehkptyvaddl 72 
                                        +D++gAn+ G++s+ + tG ++ +   +p +kp y +d++
  gi|298674048|ref|YP_003725798.1|  87 QSDLLGANALGIDSICIMTGDHTTKG-DHPGAKPVYDLDSV 126
                                       79******************988744.56788888877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1855.95
//
Query:       gi|298674049|ref|YP_003725799.1|  [L=419]
Description: thiamine biosynthesis protein ThiC [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   4.7e-145  483.5   0.2   5.3e-145  483.4   0.2    1.0  1  ThiC_Rad_SAM  Radical SAM ThiC family


Domain annotation for each model (and alignments):
>> ThiC_Rad_SAM  Radical SAM ThiC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  483.4   0.2    3e-149  5.3e-145       1     417 [.       4     408 ..       4     409 .. 0.98

  Alignments for each domain:
  == domain 1  score: 483.4 bits;  conditional E-value: 3e-149
                      ThiC_Rad_SAM   1 tqleaarkgiiteemeevaekenvepefvreevaeGrivipanknhkekpvaiGkglrtkvnaniGtsadasdieeE 77 
                                       tq++ ar+gi+t+em++vae+en+++ ++ + va+G++vi+++ +++  pvaiGkg++tk+n+n+Gts++ +d  +E
  gi|298674049|ref|YP_003725799.1|   4 TQIDCARDGILTPEMKYVAEAENLDETTILSYVANGKLVIMTRDKNP--PVAIGKGVTTKINVNLGTSSANVDPGSE 78 
                                       89***************************************988765..9*************************** PP

                      ThiC_Rad_SAM  78 veKlkvalkagadtvmdLstggdideirekileespvpvgtvpiYqaleekekkveelteeellevieeqaedGvdf 154
                                       +eK+k+a ++gadt+ dLs+gg+i+ ir++++e++++p++tvpiYq ++  e+ ++++t++++++++e+++++Gv+ 
  gi|298674049|ref|YP_003725799.1|  79 IEKVKIADRYGADTITDLSMGGNISYIRSRVFENTTIPITTVPIYQSIV--EHGMNNVTSKDIFSTLEKHVDEGVSS 153
                                       ************************************************7..67999********************* PP

                      ThiC_Rad_SAM 155 ltiHagvtlellellkkekRltgivSrgGsllaawmlanekenplyeefdelleilkeydvtlSlgdglRpGsiaDa 231
                                       + +H+ v +++l +lk ++R++g+vS+gGs+++ +ml+ne +np+ ++fd +leil++ dv+lSlg+++R+G+i+D 
  gi|298674049|ref|YP_003725799.1| 154 VVLHC-VDNNTLGKLKGSERVMGMVSKGGSFTSVFMLTNECKNPFIQNFDAVLEILRKNDVVLSLGNTMRSGCIHDL 229
                                       *****.9********************************************************************** PP

                      ThiC_Rad_SAM 232 tdeaqlaelivlgelvkrareagvqvmveG.PGHvpldeieanvklqkklckeaPfyvlGplvtDiapgYDhitsai 307
                                       +d+aq++e++++ +l++ra+e+gvqv+veG  GHv+ ++i  +v+  k+l++  P++v Gpl++D+a gYDhi++++
  gi|298674049|ref|YP_003725799.1| 230 SDDAQMSEIETNIHLANRANEKGVQVIVEGtGGHVQANDIPDTVRYYKSLSE-YPLFVAGPLPIDVALGYDHIAGSV 305
                                       ******************************778****************986.9*********************** PP

                      ThiC_Rad_SAM 308 GaalaaaaGadllCyvtpaEHlglPdeedvkeGviaakiaahaadlakglkkarerdkalskaRkeldwekqfelal 384
                                       Ga++a+ aGad+lCy+tp+ Hl+lP+ e+v+eG++a+kia h++d++k   ++++rd  ls +R+++dw+ q+e+a+
  gi|298674049|ref|YP_003725799.1| 306 GASMASGAGADYLCYITPSGHLALPTPEQVREGLVAFKIAGHIGDTIKY--GMSDRDLMLSVKRRKFDWDGQIEMAI 380
                                       ************************************************8..999*********************** PP

                      ThiC_Rad_SAM 385 dpekareireeklpeeeeaCsmCgekCavkive 417
                                       dp+k +e+   +       C+mCge+Ca+ki++
  gi|298674049|ref|YP_003725799.1| 381 DPDKPKEMCPMEG-----PCTMCGEYCAIKIMQ 408
                                       ********99766.....5************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 2567.74
//
Query:       gi|298674050|ref|YP_003725800.1|  [L=266]
Description: F420-dependent oxidoreductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-59  199.8   0.2    5.2e-59  199.5   0.2    1.1  1  F420_ligase     F420-0:Gamma-glutamyl ligase
  ------ inclusion threshold ------
      0.042   13.7   0.2      0.091   12.6   0.2    1.5  1  L_biotic_typeA  Type-A lantibiotic


Domain annotation for each model (and alignments):
>> F420_ligase  F420-0:Gamma-glutamyl ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.5   0.2   5.8e-63   5.2e-59       1     244 []      12     229 ..      12     229 .. 0.99

  Alignments for each domain:
  == domain 1  score: 199.5 bits;  conditional E-value: 5.8e-63
                                       -..-----TT--HHHHHHCCS-.....--TT-EEEEEHHHHHHHTT-EEEGGGS---HHHHHHHHHH.TS-H..... CS
                       F420_ligase   1 giktplikegddlaeivvesvkkagleledgDivvvtekvvakaegnyvsledikpsekAeeiaeklkvidpilSrn 77 
                                       giktp+ik+gdd+ + v   +++ag++ +d+Di++++e++va+ae ++++l+d+k+se A+e+a+k+ +idp     
  gi|298674050|ref|YP_003725800.1|  12 GIKTPIIKSGDDILKAVGAGFENAGISPQDNDILILAESAVATAEHRMIKLSDVKTSEMAKEYAQKY-EIDP----- 82 
                                       89*****************************************************************.****..... PP

                                       .............HHHHHHHHTEEEEEE-...S-EEEE.......TTS-EEEGGG-B-TTS-TTEEE---S-HHHHH CS
                       F420_ligase  78 rfsliLkalakatrkvevvlsepsdevgn...qlidekytdevlvklGllgsnagidesnveegllkllPedpdksa 151
                                                    r++e++l+e+++++g     +++ +         G l  nagid sn+++g+++llPe+++ksa
  gi|298674050|ref|YP_003725800.1|  83 -------------REMELILQECDEIIGGvpgAVLTIT--------RGNLSPNAGIDSSNAPDGYVILLPENAQKSA 138
                                       .............***************9888888888........5****************************** PP

                                       HHHHHHHHHHHS---EEEE..EEEEEETTEECEEEEEEEEESB-SEEE-TT-B-TTS-B-S--EEEHHHHHHHHHHH CS
                       F420_ligase 152 eeikkklkertgkdveVliygkDpegriweladpvvaigtsglealrdlrgkkdldgkelgttpravtdelgsladL 228
                                       e+i++ +++++ ++++V+i   D+++++++l+++++a+gtsg+ +++d rg +dl+gk+l++t++a +d+l s+a++
  gi|298674050|ref|YP_003725800.1| 139 ESIREGINKQFFCNLGVII--GDSRTQPMRLGCVGIALGTSGIVPVEDARGCQDLYGKSLNITHKATADNLVSAAQI 213
                                       *******************..******************************************************** PP

                                       HC-SSSS---EEEEES CS
                       F420_ligase 229 vsGsadegtPvvlvrg 244
                                       ++G+a e+tP++lvrg
  gi|298674050|ref|YP_003725800.1| 214 IMGEAGECTPAILVRG 229
                                       ***************8 PP

>> L_biotic_typeA  Type-A lantibiotic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2     1e-05     0.091      14      36 ..      86     107 ..      84     109 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1e-05
                    L_biotic_typeA  14 evseeELdqilGGkgsgvikTiS 36 
                                       e+ ++E d+i+GG   g++ Ti+
  gi|298674050|ref|YP_003725800.1|  86 ELILQECDEIIGG-VPGAVLTIT 107
                                       66789********.********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1779.96
//
Query:       gi|298674051|ref|YP_003725801.1|  [L=89]
Description: thioredoxin domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-24   85.9   0.0    1.7e-24   85.8   0.0    1.0  1  Thioredoxin    Thioredoxin
    1.1e-09   38.5   0.0      2e-05   24.8   0.0    2.1  2  Thioredoxin_8  Thioredoxin-like
    1.4e-09   38.4   0.2    5.8e-09   36.4   0.2    1.7  1  Thioredoxin_2  Thioredoxin-like domain
    2.8e-06   27.5   0.0    4.3e-06   26.8   0.0    1.4  1  Glutaredoxin   Glutaredoxin
    7.6e-06   25.7   0.1     0.0045   16.7   0.0    2.1  2  Redoxin        Redoxin
      4e-05   23.6   0.1    4.6e-05   23.4   0.1    1.1  1  Thioredoxin_3  Thioredoxin domain
    0.00021   21.4   0.1    0.00047   20.3   0.1    1.7  1  Thioredoxin_7  Thioredoxin-like
    0.00024   21.0   0.0      0.067   13.1   0.0    2.1  2  AhpC-TSA       AhpC/TSA family
    0.00073   19.2   0.0    0.00086   19.0   0.0    1.1  1  KaiB           KaiB domain
    0.00073   19.4   0.0    0.00092   19.1   0.0    1.1  1  TraF           F plasmid transfer operon protein
     0.0011   18.8   0.0     0.0013   18.5   0.0    1.1  1  Thioredoxin_9  Thioredoxin
     0.0072   16.7   0.0     0.0079   16.6   0.0    1.1  1  DUF836         Glutaredoxin-like domain (DUF836)
  ------ inclusion threshold ------
      0.017   14.9   0.2       0.09   12.5   0.0    1.8  2  DSBA           DSBA-like thioredoxin domain
       0.03   14.0   0.2          3    7.5   0.0    2.0  2  Thioredoxin_5  Thioredoxin
        0.1   12.6   0.0       0.12   12.5   0.0    1.1  1  TrbC_Ftype     Type-F conjugative transfer system pilin assem


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.8   0.0   1.4e-27   1.7e-24      19     102 ..       3      86 ..       1      87 [. 0.97

  Alignments for each domain:
  == domain 1  score: 85.8 bits;  conditional E-value: 1.4e-27
                                       SEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEEEEEEESS-HHH CS
                       Thioredoxin  19 klvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngkevkkyegareke 95 
                                       k++l++F A+wCg+Ck+ +P +++l+e++ d+v + +vdvden ++a++y+v ++Pt+++ k+g+evk+++g ++++
  gi|298674051|ref|YP_003725801.1|   3 KPILLDFSATWCGPCKMQKPIIDDLKEKYGDQVDIKEVDVDENGEMARNYNVMAVPTIVIEKDGEEVKRFTGLKQAD 79 
                                       789************************************************************************** PP

                                       HHHHHHH CS
                       Thioredoxin  96 klaaflk 102
                                        l a l+
  gi|298674051|ref|YP_003725801.1|  80 VLSAELD 86 
                                       *999887 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   1.7e-08     2e-05       1      46 [.       2      45 ..       2      48 .. 0.91
   2 !   14.3   0.0   3.2e-05     0.038      67      94 ..      41      67 ..      39      68 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.7e-08
                                      .SEEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS- CS
                     Thioredoxin_8  1 gkvvlLyfgaswcppckaftpklkelyeklkkkkkveivyvsldkk 46
                                      gk +lL f+a+wc pck   p +++l+ek+   ++v i  v +d++
  gi|298674051|ref|YP_003725801.1|  2 GKPILLDFSATWCGPCKMQKPIIDDLKEKYG--DQVDIKEVDVDEN 45
                                      699***************************9..9999988888886 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 3.2e-05
                                      -TT-HHHHTT-S--TT-SEEEEE-TT-B CS
                     Thioredoxin_8 67 ddkkrnklkkkynvkaiPtlvvldknge 94
                                      d +++ +++++ynv+a+Pt +v+ k+ge
  gi|298674051|ref|YP_003725801.1| 41 DVDENGEMARNYNVMAVPT-IVIEKDGE 67
                                      456789*************.88888886 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.2   4.9e-12   5.8e-09       5     108 ..       2      84 ..       1      85 [. 0.84

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 4.9e-12
                     Thioredoxin_2   5 gkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgt 81 
                                       gkp+l++f++++C+ Ck  k  +++l   +++     +++++++k v+++ + e              ar y+v ++
  gi|298674051|ref|YP_003725801.1|   2 GKPILLDFSATWCGPCKMQKPIIDDL---KEK-----YGDQVDIKEVDVDENGEM-------------ARNYNVMAV 57 
                                       8*****************88888887...777.....999977777777777765.............7******** PP

                     Thioredoxin_2  82 PtivfldgkeivarlpGyvpaeeleal 108
                                       Ptiv+    e+v r +G+ +a+ l+a 
  gi|298674051|ref|YP_003725801.1|  58 PTIVIEKDGEEVKRFTGLKQADVLSAE 84 
                                       **9965544599******999988876 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   3.6e-09   4.3e-06       4      57 ..       9      64 ..       7      76 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 3.6e-09
                                      EESTSSHHHHHHHHHHHHTT......GGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEETT CS
                      Glutaredoxin  4 ftkptCpyCkkakrlLkelg......vkfeeidvdkdeeireelkelsgvrtvPqvfidg 57
                                      f+ ++C+ Ck+ k + ++l+      v+++e+dvd++     e+ ++ +v++vP+++i  
  gi|298674051|ref|YP_003725801.1|  9 FSATWCGPCKMQKPIIDDLKekygdqVDIKEVDVDEN----GEMARNYNVMAVPTIVIEK 64
                                      7889************999977778888888888888....5555555*********954 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   3.8e-06    0.0045      28      60 ..       2      33 ..       1      38 [. 0.93
   2 !    7.4   0.0    0.0027       3.2      91     137 ..      42      78 ..      40      89 .] 0.77

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.8e-06
                                      TSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHC CS
                           Redoxin 28 gkkvvvnfvpgafcPtCsaehpyleklaellke 60
                                      gk++++ f ++ +c++C+ + p +++l+e++++
  gi|298674051|ref|YP_003725801.1|  2 GKPILLDFSAT-WCGPCKMQKPIIDDLKEKYGD 33
                                      899********.******************986 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0027
                                       E-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEESSSCH CS
                           Redoxin  91 sDgsaaftkalGlrleedaseglrtpryavidedgkvvylevepepe 137
                                       +D+++++++++++           +  ++vi +dg  v+++++    
  gi|298674051|ref|YP_003725801.1|  42 VDENGEMARNYNVM----------AVPTIVIEKDGEEVKRFTGLKQA 78 
                                       599999*****944..........445799**********9987664 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.1   3.9e-08   4.6e-05      10      63 ..      14      74 ..       5      86 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3.9e-08
                                      STTCHHHHHHHHHHCHCCT..CECEEECCTTHHHH.HHCT-SSSSEEECT....TCEEEES CS
                     Thioredoxin_3 10 CakCpklekavkeaaaekg..ikaevekvtdfeei.ekygVmsvPalvid....gkvvvsG 63
                                      C  C+  + ++  + ++ g  ++++ ++v ++ e+  +y+Vm+vP++vi+    ++ +++G
  gi|298674051|ref|YP_003725801.1| 14 CGPCKMQKPIIDDLKEKYGdqVDIKEVDVDENGEMaRNYNVMAVPTIVIEkdgeEVKRFTG 74
                                      8888877777777777777235555566699******************987644445666 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   3.9e-07   0.00047      17      36 ..       2      21 ..       1      63 [. 0.66

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.9e-07
                                      T--EEEEE--TT-HHHHHHH CS
                     Thioredoxin_7 17 gkpvlvffgaswcftCqale 36
                                      gkp+l++f+a+wc++C+ ++
  gi|298674051|ref|YP_003725801.1|  2 GKPILLDFSATWCGPCKMQK 21
                                      7***************9765 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   5.6e-05     0.067      25      57 ..       2      33 ..       1      42 [. 0.88
   2 !    6.3   0.0     0.007       8.4      88     119 ..      42      66 ..      39      71 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.6e-05
                                      TSEEEEEEESTST-CCHHHHHHHHHHCHHHCCC CS
                          AhpC-TSA 25 gkpvvlffypkdwcpvCttelpalaklyeefke 57
                                      gkp++l f ++ wc +C+ + p + +l e++ +
  gi|298674051|ref|YP_003725801.1|  2 GKPILLDFSAT-WCGPCKMQKPIIDDLKEKYGD 33
                                      89*********.********9999999988865 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.007
                                       E-TTSHHHHHTT-EETTTTECSCEEEEE-TTS CS
                          AhpC-TSA  88 sDeegkvakaygvlkeekglalratfvidkeg 119
                                        De+g++a++y+v+      a++ t+vi k+g
  gi|298674051|ref|YP_003725801.1|  42 VDENGEMARNYNVM------AVP-TIVIEKDG 66 
                                       69************......555.45666665 PP

>> KaiB  KaiB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   7.2e-07   0.00086      20      68 ..      26      74 ..      18      85 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 7.2e-07
                                      HHCCCHCTTTEEEEEEETTTSHCHHCCTCEESCCCCC.CCCSCCHCCCCC CS
                              KaiB 20 kleeedlgfqyeLqvvdvleqPelaeedrlvatPaLi.klsPePkqrlaG 68
                                      +l+ e+ g q++++ vdv e+ e a+++ ++a+P+ +   + e ++r+ G
  gi|298674051|ref|YP_003725801.1| 26 DLK-EKYGDQVDIKEVDVDENGEMARNYNVMAVPTIViEKDGEEVKRFTG 74
                                      554.4599***************************851455555555555 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   7.7e-07   0.00092     133     198 ..       6      62 ..       3      73 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 7.7e-07
                              TraF 133 LlfFyrgkcpyceaqapilqafadkyg..levraVsvdgrplpelpnarvdkgqaarlgvkrtPalvl 198
                                       Ll F +  c+ c++q pi++++++kyg   +++ V+vd++    ++          +++v  +P++v+
  gi|298674051|ref|YP_003725801.1|   6 LLDFSATWCGPCKMQKPIIDDLKEKYGdqVDIKEVDVDENGE--MAR---------NYNVMAVPTIVI 62 
                                       55688889******************7225567799999877..666.........899999999987 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.1e-06    0.0013      48     114 ..       9      72 ..       4      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.1e-06
                                       E--TT-HHHHHHHHHHHHHH.HH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE-TT--EEEEE CS
                     Thioredoxin_9  48 ltedwCgDaavnvPvlakia.elnpnievkillrdenlelmdqyltngaraiPtliildeegeelgvw 114
                                       + + wCg + +  P+++ ++ ++ +++++k +  den e+ ++y      a+Pt++i +++gee+  +
  gi|298674051|ref|YP_003725801.1|   9 FSATWCGPCKMQKPIIDDLKeKYGDQVDIKEVDVDENGEMARNYN---VMAVPTIVI-EKDGEEVKRF 72 
                                       5689***************9457799******************5...599**9775.5777777665 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   6.6e-06    0.0079       6      60 ..      10      67 ..       5      88 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.6e-06
                                      E-TT-HHHHHHHHHHHHHCCCTT..EEEEEEETTT-CCCHCCCCTT.TTEEEECTTCG CS
                            DUF836  6 skpgChlCeqakekLkelkleeg..leleviDIakdeeleakYgle.ipvlalegvkk 60
                                      s   C+ C+  k ++ +lk++ g  ++++++D++++ e+ + Y+++ +p +++e+  +
  gi|298674051|ref|YP_003725801.1| 10 SATWCGPCKMQKPIIDDLKEKYGdqVDIKEVDVDENGEMARNYNVMaVPTIVIEKDGE 67
                                      5667999**9999999888877778*******************85489999888333 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.098   1.2e+02       5      35 ..       9      38 ..       6      43 .. 0.76
   2 ?   12.5   0.0   7.5e-05      0.09     151     192 ..      40      85 ..      24      86 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.098
                                      EEBTTBHHHHHHHHHHHHHHHHCCTEEEEEE CS
                              DSBA  5 ffDvlCPyCylgkerleklaarspdvkvvlr 35
                                      f+   C+ C++ k+ ++ l +++ + +v ++
  gi|298674051|ref|YP_003725801.1|  9 FSATWCGPCKMQKPIIDDLKEKY-GDQVDIK 38
                                      55567*****************9.4444444 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 7.5e-05
                                       HHHHHHHHHHHHTT-SSSSEEEE..TTC..EEEESSSSHHHHHHHH CS
                              DSBA 151 eavrentaaaqslgvtGvPtvvv..dgk..rmvfGadrldtladal 192
                                        +v+en ++a+ ++v  vPt+v+  dg+  + ++G ++ d l  +l
  gi|298674051|ref|YP_003725801.1|  40 VDVDENGEMARNYNVMAVPTIVIekDGEevKRFTGLKQADVLSAEL 85 
                                       4689999****************87776778999999999998776 PP

>> Thioredoxin_5  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.013        15       7      34 ..      13      40 ..       9      45 .. 0.90
   2 ?    7.5   0.0    0.0025         3     148     183 ..      47      80 ..      41      83 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.013
                     Thioredoxin_5  7 lcseCweiEpelkklkveygekiklrfi 34
                                      +c  C   +p++  lk++yg++++++ +
  gi|298674051|ref|YP_003725801.1| 13 WCGPCKMQKPIIDDLKEKYGDQVDIKEV 40
                                      7999*********************976 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0025
                     Thioredoxin_5 148 klakemgvtevPtlvffneneeeeglkveglksyev 183
                                       ++a++++v  vPt+v+    + ee   ++glk+ +v
  gi|298674051|ref|YP_003725801.1|  47 EMARNYNVMAVPTIVIEK--DGEEVKRFTGLKQADV 80 
                                       69*************976..5555566666666665 PP

>> TrbC_Ftype  Type-F conjugative transfer system pilin assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.9e-05      0.12      51      86 ..      36      71 ..      16      86 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.9e-05
                        TrbC_Ftype 51 emekasvqidPllFrqfkitaVPalvlaeedkasee 86
                                      + ++++v+ + ++ r++++ aVP++v++++ ++ + 
  gi|298674051|ref|YP_003725801.1| 36 DIKEVDVDENGEMARNYNVMAVPTIVIEKDGEEVKR 71
                                      445566666778999**************9887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.40u 0.32s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 575.19
//
Query:       gi|298674052|ref|YP_003725802.1|  [L=342]
Description: hypothetical protein Metev_0074 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-06   27.3   0.5    8.7e-06   25.4   0.1    1.9  2  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.053   13.4   0.1        0.2   11.5   0.0    2.0  2  Lactamase_B_3  Beta-lactamase superfamily domain
       0.08   12.1   0.0       0.13   11.4   0.0    1.2  1  URO-D          Uroporphyrinogen decarboxylase (URO-D)
       0.54   10.2   5.6        4.6    7.2   5.6    2.1  1  Lactamase_B    Metallo-beta-lactamase superfamily


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.1   1.9e-09   8.7e-06      28     171 ..      53     168 ..      35     187 .. 0.84
   2 ?   -0.6   0.0      0.17   7.8e+02      38      64 ..     283     308 ..     280     314 .. 0.69

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.9e-09
                                       ..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECSTTEE CS
                     Lactamase_B_2  28 lppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfelgdggle 104
                                         + da l+thaH DH     +l   r      +++++++  lea+    + ++        +++ge++++g  +++
  gi|298674052|ref|YP_003725802.1|  53 YTQPDAYLITHAHGDHHGKSAMLSN-R-----SLCSDKTALALEARYGKKFNGKS-------VKIGETIDVG--DVS 114
                                       56889************66666666.2.....47************876666666.......*********9..578 PP

                                       EEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTH CS
                     Lactamase_B_2 105 itatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipeeigerlggadllllditayedde 171
                                       i + p +h+ g         t+ ++  + g r++ +gD++  +      l ++d+l+ ++++ ++  
  gi|298674052|ref|YP_003725802.1| 115 IYTYPTEHTVGS--------TAFYWENDVGTRILVTGDVKDAS-----SLPDCDVLITEANYGDPAD 168
                                       ***********9........99999999***********9444.....6889999999999877765 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.17
                                       S--HHHHGGGGCCCC.C--EEEEEEEEH CS
                     Lactamase_B_2  38 haHyDHlaglltlre.lrpkklplyapk 64 
                                        +H D++ gl ++ + + p +++++ ++
  gi|298674052|ref|YP_003725802.1| 283 SDHLDAF-GLVDMVKsINP-EITIVYHP 308
                                       5899999.88888884544.67866444 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.5e-05       0.2      32     116 ..      51     147 ..      23     164 .. 0.65
   2 ?   -1.8   0.0      0.55   2.5e+03     105     124 ..     301     320 ..     281     330 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.5e-05
                     Lactamase_B_3  32 ppaeeaDlvlisqaledHahletlkql..................aenvkvleegeslevggleiravatshdavgg 90 
                                       ++  ++D+ li++a+ dH    ++ +                   + n k ++ ge+++vg+++i + +t+h+    
  gi|298674052|ref|YP_003725802.1|  51 EKYTQPDAYLITHAHGDHHGKSAMLSNrslcsdktalalearygkKFNGKSVKIGETIDVGDVSIYTYPTEHT---- 123
                                       344899***********88777766633556555555555555544444555557777777777777777773.... PP

                     Lactamase_B_3  91 sergenngflleqd.gltiyhlGhlah 116
                                           + ++f +e d g +i+  G++  
  gi|298674052|ref|YP_003725802.1| 124 ---VGSTAFYWENDvGTRILVTGDVKD 147
                                       ...335566666644666666666654 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.55
                     Lactamase_B_3 105 gltiyhlGhlahelsseelk 124
                                       ++ti++ + ++ + +++++ 
  gi|298674052|ref|YP_003725802.1| 301 EITIVYHPKGHRPSKFSDYL 320
                                       56777777777776666655 PP

>> URO-D  Uroporphyrinogen decarboxylase (URO-D)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0     3e-05      0.13     227     271 ..     291     336 ..     290     340 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3e-05
                                       HHHHHHH.H--S-EEEEESSHH.H.HHHHHTTS--SEEE--TTS-H CS
                             URO-D 227 ivdevkaegpkvpvilfikgagae.iledlaelgadvlsldwtvdl 271
                                       +vd vk+ +p++ +++++kg   + + ++l+++g+d +s+d+ +++
  gi|298674052|ref|YP_003725802.1| 291 LVDMVKSINPEITIVYHPKGHRPSkFSDYLNSIGIDSISIDNINNV 336
                                       57899****************8777999999**********98765 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   5.6     0.001       4.6      44     152 ..      55     146 ..      39     186 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.001
                                       GEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTE CS
                       Lactamase_B  44 dvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasrkglllagvsadkpdvdeeeldgnaggr 120
                                       ++da ++TH+H DH G  + l ++  +      + ++ + +                      +    ++++++ g+
  gi|298674052|ref|YP_003725802.1|  55 QPDAYLITHAHGDHHGKSAMLSNRSLCSDKTALALEARYGKKFN-------------------GKSVKIGETIDVGD 112
                                       789999**********9999999887776655444444444444...................36666666666666 PP

                                       EEEEHECT..TSTSCCEEEEEETTCCEEEECTTT CS
                       Lactamase_B 121 ralyvtgg..pghghghgvveygggkvlftGDal 152
                                       ++ y++++   + +   +   + g ++l+tGD+ 
  gi|298674052|ref|YP_003725802.1| 113 VSIYTYPTehTVGSTAFYWENDVGTRILVTGDVK 146
                                       6666665520444444444445889999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 2041.96
//
Query:       gi|298674053|ref|YP_003725803.1|  [L=130]
Description: hypothetical protein Metev_0075 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0036   17.4   0.3     0.0055   16.8   0.3    1.2  1  FUSC_2    Fusaric acid resistance protein-like
  ------ inclusion threshold ------
       0.32   11.3   7.4       0.44   10.8   7.4    1.2  1  DUF5379   Family of unknown function (DUF5379)


Domain annotation for each model (and alignments):
>> FUSC_2  Fusaric acid resistance protein-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.3   6.2e-07    0.0055      29      78 ..      44      91 ..      38     104 .. 0.58

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.2e-07
                            FUSC_2 29 lgasltravqRilGtvlGavlallllyllpgn.lalallvfllvfliaffl 78
                                      +++  ++av+ ilG ++G+v+ ++l +   ++ +a+++++++++ +   ++
  gi|298674053|ref|YP_003725803.1| 44 VEGIIKTAVASILGIIAGVVAEYILGTGEGTTwYAIIVIIAIVTYY---IQ 91
                                      4555666666777777776666666664444434444444444444...44 PP

>> DUF5379  Family of unknown function (DUF5379)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   7.4     5e-05      0.44      10      88 ..      52     130 .]      44     130 .] 0.67

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5e-05
                           DUF5379  10 lhaiggiifgylanyvytlglgllsglatllflfiglvilghlsakv.lgeesltqkqwlgsgvlpfflvaivvwil 85 
                                       + +i gii g +a+y+   g g       +++ +++  i   +  ++ +  + +  k+w+    l   + a+v w+l
  gi|298674053|ref|YP_003725803.1|  52 VASILGIIAGVVAEYILGTGEGTTWYAIIVIIAIVTYYIQRVIYPQInISTKEFGLKDWFYVEFLVVDF-ALVTWVL 127
                                       57899***********99999976554444455555555555555443456677778888766554443.7899999 PP

                           DUF5379  86 kyn 88 
                                         n
  gi|298674053|ref|YP_003725803.1| 128 MLN 130
                                       766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1512  (0.0843326); expected 358.6 (0.02)
Passed bias filter:                      802  (0.044732); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 771.35
//
Query:       gi|298674054|ref|YP_003725804.1|  [L=592]
Description: ABC transporter-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-42  144.8   0.0    1.7e-20   73.9   0.0    2.6  2  ABC_tran      ABC transporter
    2.7e-17   62.9   6.8    1.3e-10   41.1   0.3    3.5  3  SMC_N         RecF/RecN/SMC N terminal domain
    8.4e-12   44.7   4.1    1.7e-11   43.8   4.1    1.5  1  RLI           Possible Fer4-like domain in RNase L inhibitor,
    1.7e-09   37.9   6.6       0.04   13.7   0.1    4.2  4  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.3e-07   31.1   5.1    1.3e-07   31.1   5.1    2.4  2  Fer4          4Fe-4S binding domain
    3.5e-07   30.3   0.1      0.027   14.4   0.0    2.9  3  Rad17         Rad17 P-loop domain
    5.3e-07   29.7   0.1      0.014   15.3   0.0    2.4  2  RsgA_GTPase   RsgA GTPase
    1.3e-06   29.1   0.7      0.001   19.6   0.0    2.5  2  AAA_23        AAA domain
    1.6e-06   28.6   0.3      0.041   14.3   0.0    3.3  2  AAA_16        AAA ATPase domain
      3e-05   24.4   0.0        0.5   10.8   0.0    2.6  2  RNA_helicase  RNA helicase
      6e-05   22.7   1.8      0.055   13.2   0.0    2.4  2  AAA_29        P-loop containing region of AAA domain
    6.8e-05   22.8  12.4    7.3e-05   22.7   3.4    2.4  2  Fer4_6        4Fe-4S binding domain
    7.2e-05   23.2   0.0       0.49   10.8   0.0    2.6  2  AAA           ATPase family associated with various cellular 
    0.00015   21.6   1.5        1.2    8.7   0.0    3.4  3  AAA_15        AAA ATPase domain
    0.00026   21.0   6.5    0.00047   20.2   6.5    1.4  1  Fer4_21       4Fe-4S dicluster domain
     0.0004   20.5   8.4    0.00075   19.6   8.4    1.4  1  Fer4_9        4Fe-4S dicluster domain
     0.0005   20.0   1.6     0.0005   20.0   1.6    2.4  2  Fer4_2        4Fe-4S binding domain
    0.00057   20.4   1.4    0.00057   20.4   1.4    2.4  3  Fer4_7        4Fe-4S dicluster domain
    0.00058   19.6   0.0       0.57    9.9   0.0    2.3  2  AAA_24        AAA domain
    0.00084   19.3   0.0      0.083   12.8   0.0    2.4  2  NACHT         NACHT domain
     0.0015   18.8   0.0       0.71   10.2   0.0    2.6  2  AAA_22        AAA domain
     0.0028   17.7  10.3     0.0066   16.5   1.4    2.4  2  Fer4_10       4Fe-4S dicluster domain
     0.0032   17.5   1.6        7.4    6.6   0.0    3.6  3  AAA_14        AAA domain
     0.0069   16.5   1.1        6.2    6.9   0.4    3.0  2  MMR_HSR1      50S ribosome-binding GTPase
     0.0075   16.4   0.1        1.3    9.2   0.0    3.1  2  AAA_33        AAA domain
     0.0092   16.5   0.1        3.8    8.1   0.0    3.3  3  AAA_18        AAA domain
  ------ inclusion threshold ------
      0.014   16.3   0.7      0.014   16.3   0.7    2.5  2  Fer4_16       4Fe-4S double cluster binding domain
      0.015   15.4   1.9          4    7.5   0.0    3.4  3  DUF87         Helicase HerA, central domain
      0.024   13.8   0.0          2    7.5   0.0    2.3  2  NB-ARC        NB-ARC domain
       0.04   13.2   0.0        4.4    6.5   0.0    2.2  2  Septin        Septin
      0.052   13.5   0.1         16    5.5   0.0    2.8  2  AAA_5         AAA domain (dynein-related subfamily)
      0.077   12.8   0.0        3.3    7.5   0.0    2.6  2  MukB          MukB N-terminal
      0.085   11.8   2.6        3.6    6.5   0.1    2.2  2  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
       0.12   12.1   0.0        8.1    6.1   0.0    2.3  2  VirE          Virulence-associated protein E
       0.15   11.9   0.1         14    5.5   0.0    2.6  2  dNK           Deoxynucleoside kinase
       0.15   11.8   0.1         29    4.4   0.0    2.8  2  CLP1_P        mRNA cleavage and polyadenylation factor CLP1 P
       0.15   11.8   0.1        6.8    6.4   0.0    2.4  2  ATP_bind_1    Conserved hypothetical ATP binding protein
       0.17   12.2   0.0        8.6    6.6   0.0    2.6  2  AAA_28        AAA domain
        0.2   10.5   0.6          1    8.2   0.2    2.0  2  Spore_IV_A    Stage IV sporulation protein A (spore_IV_A)
       0.22   11.2   0.7         17    5.1   0.0    2.8  3  AAA_30        AAA domain
       0.23   11.8   1.6        0.8   10.1   0.1    2.4  2  DUF4277       Domain of unknown function (DUF4277)
       0.27   10.8   1.8        6.9    6.2   0.0    3.2  4  AAA_25        AAA domain
       0.27   11.8  14.0      0.055   14.0   3.3    2.4  2  Fer4_4        4Fe-4S binding domain
       0.34   10.8   4.0        7.3    6.5   0.0    3.0  2  NTPase_1      NTPase
        7.3    7.2  11.5         88    3.8  11.5    2.3  1  Fer4_17       4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.1   0.0   2.8e-21   1.1e-18       9     134 ..      95     236 ..      93     238 .. 0.75
   2 !   73.9   0.0   4.4e-23   1.7e-20       7     137 .]     360     481 ..     355     481 .. 0.86

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 2.8e-21
                                       ETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE...........EETTCEGGGB-HHHCCHCEEEE-SS--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   9 kegekvaivGenGaGKStLlkllagllkpteGei...........lldgkdlkeqeleslrkeigvlpqepqlfpel 74 
                                       ++g++++i+G+nG GKSt++++l+g l p+ Ge            ++ g+++++  ++ ++ ++  ++q+pq  +++
  gi|298674054|ref|YP_003725804.1|  95 QAGRVTGILGPNGIGKSTVVNILSGTLVPNLGEYkeesswdrvieRYSGTQIQDYFRKLVNGKVN-VSQKPQYIDKI 170
                                       5899*****************************97777777777777777777755555555544.34444444444 PP

                                       BHHHH........HHHTC..HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEES CS
                                       xxxxx........xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  75 tvren........esdee..iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDE 134
                                         + n        ++d++  +++++++l+l+e+ d+++    ++LSgG+ qrva+a++++k+++++++DE
  gi|298674054|ref|YP_003725804.1| 171 PKAFNgntrelleKADDRgvLNQLIERLDLDEIIDRNI----NELSGGELQRVAIAACMVKDAEFYFFDE 236
                                       32222556777653333355788888888888777777....***************************9 PP

  == domain 2  score: 73.9 bits;  conditional E-value: 4.4e-23
                                       EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET.TCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGeilld.gkdlkeqeleslrkeigvlpqepqlfpeltvrenesd 82 
                                       +lk+ge++++vG+nG GKSt++k+lag+ +p+ Ge+ +d + ++k    + ++  i    q+ +l + +   + + +
  gi|298674054|ref|YP_003725804.1| 360 SLKQGEVLGVVGPNGIGKSTFVKVLAGEIEPDDGELDFDiNISFKP---QYVKGDINLRVQD-FLRSIT--SRFDTS 430
                                       799*********************************9997777777...8999999999999.333333..222455 PP

                                       TCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  83 eeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                           ++++ l+++el d+ +     +LSgG+ qrva+a++l +++++++lDEp+a
  gi|298674054|ref|YP_003725804.1| 431 YYQGEIARPLQIEELYDKML----PNLSGGELQRVAIAACLSRDADMYILDEPSA 481
                                       55667888899999999999....*****************************75 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.3   3.3e-13   1.3e-10      24     210 ..      97     280 ..      91     286 .. 0.70
   2 ?    6.0   0.4     0.018       7.2      26      42 ..     366     382 ..     358     385 .. 0.84
   3 !   17.4   0.0   5.9e-06    0.0023     136     203 ..     452     517 ..     398     531 .. 0.75

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 3.3e-13
                                       SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSS.SSCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                             SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkie.keevsi 99 
                                        ++t i+GpNG GKs +++ ++ +L  +  +   +++ +++i +  ++ +++    +++    + k++++ k+++  
  gi|298674054|ref|YP_003725804.1|  97 GRVTGILGPNGIGKSTVVNILSGTLVPNLGEYKEESSWDRVIER-YSGTQIQDYFRKLV----NGKVNVSqKPQYID 168
                                       57999****************99999777755556678888987.44444443333333....33333330444444 PP

                                       EEEEETTSEEEEEETTEE..E-HHHHHHHHHCTT-...STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS CS
                                       xxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 100 srrvkrkgeseykingke..vtkkevsellesagi...skelLSgGektLvalaLlfAiqkvkpaplyllDeidaaL 171
                                       +  +  +g+++  +++ +     +++ e l   +i   ++++LSgGe + va+a      +vk a +y++Dei   L
  gi|298674054|ref|YP_003725804.1| 169 KIPKAFNGNTRELLEKADdrGVLNQLIERLDLDEIidrNINELSGGELQRVAIAAC----MVKDAEFYFFDEISPYL 241
                                       444445555555554433003346666666655553445679*****999998755....99*************** PP

                                       -HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 172 DeknvkkvaellkeksknaQfivislreemlekadklvg 210
                                       D  ++ +va+l++e  ++  ++v+ ++  +l     +v 
  gi|298674054|ref|YP_003725804.1| 242 DIYQRINVAQLIQELAQEKAVLVVEHDLAILDMLADVVH 280
                                       ************************998877766655555 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.018
                                       EEEEEESTTSSHHHHHH CS
                                       xxxxxxxxxxxxxxxxx RF
                             SMC_N  26 ftaivGpNGSGKsnlld 42 
                                       +  +vGpNG GKs ++ 
  gi|298674054|ref|YP_003725804.1| 366 VLGVVGPNGIGKSTFVK 382
                                       5579*********9986 PP

  == domain 3  score: 17.4 bits;  conditional E-value: 5.9e-06
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislreemle 203
                                       +LSgGe + va+a  +     + a +y+lDe  a+LD ++++   + +k+  +n     +v+ ++  m+ 
  gi|298674054|ref|YP_003725804.1| 452 NLSGGELQRVAIAACL----SRDADMYILDEPSAHLDVEQRSLATKAIKRFAENnkKTAMVVDHDIYMID 517
                                       79*****999998776....47899************************765552255667766666655 PP

>> RLI  Possible Fer4-like domain in RNase L inhibitor, RLI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   4.1   4.2e-14   1.7e-11       1      35 []       1      32 [.       1      32 [. 0.97

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 4.2e-14
                                      --EEEES---------TTHHHHHTTSEEEESS--S CS
                               RLI  1 mrlAivdadqCdPKKCtgkkcarfcpvrlvrtgkk 35
                                      mr+A+ ++d+C+P+KC+  +c ++cp   vrtg++
  gi|298674054|ref|YP_003725804.1|  1 MRIAVLNYDRCQPRKCSK-ECHKYCPR--VRTGDE 32
                                      9*****************.********..****85 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.8   0.00031      0.12       1      21 [.      99     119 ..      99     155 .. 0.77
   2 ?    5.4   0.1     0.033        13     166     291 ..     172     261 ..     142     273 .. 0.75
   3 !   13.7   0.1    0.0001      0.04       3      42 ..     368     401 ..     366     447 .. 0.78
   4 ?    6.9   0.0     0.012       4.9     237     287 ..     453     500 ..     449     517 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00031
                            AAA_21   1 lnvliGpNgsGKSnLLdaldl 21 
                                       ++++ GpNg GKS++  +l++
  gi|298674054|ref|YP_003725804.1|  99 VTGILGPNGIGKSTVVNILSG 119
                                       699**************9975 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.033
                            AAA_21 166 igllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtk 242
                                       ++++ + ++++ +a+ ++ l +l+ +l+l+ei ++++                                +elS G +
  gi|298674054|ref|YP_003725804.1| 172 KAFNGNTRELLEKADDRGVLNQLIERLDLDEIIDRNI--------------------------------NELSGGEL 216
                                       5666777777777777777777777777777777666................................799***** PP

                            AAA_21 243 rllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQ 291
                                       +  a+++ +  ++    ++++DE+   L+      +++l+ el++    
  gi|298674054|ref|YP_003725804.1| 217 QRVAIAACMVKDA---EFYFFDEISPYLDIYQRINVAQLIQELAQ-EKA 261
                                       9977777777766...9********99999999999999977776.334 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 0.0001
                            AAA_21   3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggi 42 
                                       +++GpNg GKS++ + l      ++++e++  el+   +i
  gi|298674054|ref|YP_003725804.1| 368 GVVGPNGIGKSTFVKVL------AGEIEPDDGELDFDINI 401
                                       79***************......66666666666444444 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.012
                            AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr 287
                                       lS G ++  a+++ l r++   + +++DEp ++L+ +  +   + +k+ ++
  gi|298674054|ref|YP_003725804.1| 453 LSGGELQRVAIAACLSRDA---DMYILDEPSAHLDVEQRSLATKAIKRFAE 500
                                       6666666645555555555...9************9544333355544444 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.2       2.9   1.2e+03      13      19 ..      19      25 ..      18      26 .. 0.86
   2 !   31.1   5.1   3.3e-10   1.3e-07       1      23 [.      42      64 ..      42      65 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2.9
                                      HHHHHST CS
                              Fer4 13 aCvevCP 19
                                      +C + CP
  gi|298674054|ref|YP_003725804.1| 19 ECHKYCP 25
                                      6****** PP

  == domain 2  score: 31.1 bits;  conditional E-value: 3.3e-10
                                      EEEETTTSSS-THHHHHSTTTEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAI 23
                                      ++i ee+C+gCG+Cv+ CP+ AI
  gi|298674054|ref|YP_003725804.1| 42 PIISEELCVGCGICVDKCPYKAI 64
                                      5899******************9 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   6.8e-05     0.027      47      78 ..      99     130 ..      91     153 .. 0.86
   2 ?    0.3   0.0       1.4   5.6e+02      98     152 ..     130     181 ..     125     185 .. 0.65
   3 !   12.1   0.0   0.00035      0.14      46      72 ..     365     391 ..     353     429 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.8e-05
                             Rad17  47 iLLisGPsGCgkstvvkvLskelgiklrewln 78 
                                       +  i GP G gkstvv++Ls  l+++l e+  
  gi|298674054|ref|YP_003725804.1|  99 VTGILGPNGIGKSTVVNILSGTLVPNLGEYKE 130
                                       66689********************9988765 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.4
                             Rad17  98 kesrflsqiesfkeleLkdakylklqklGddlrtdkklilvedlPnkfyrdsdal 152
                                        es++   ie ++  +++d    kl   G +++  +k  +++ +P  f+++++ l
  gi|298674054|ref|YP_003725804.1| 130 EESSWDRVIERYSGTQIQDYFR-KLV-NG-KVNVSQKPQYIDKIPKAFNGNTREL 181
                                       5666666667777666665444.333.23.35556677799*********99876 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.00035
                             Rad17  46 riLLisGPsGCgkstvvkvLskelgik 72 
                                       ++L + GP G gkst vkvL+ e  ++
  gi|298674054|ref|YP_003725804.1| 365 EVLGVVGPNGIGKSTFVKVLAGEIEPD 391
                                       58999****************987665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   3.5e-05     0.014      98     134 ..      96     132 ..      89     136 .. 0.87
   2 !   11.9   0.0    0.0004      0.16      99     124 ..     364     389 ..     339     400 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.5e-05
                                       TTSEEEEECSTTSSHHHHHHHHCTT-----S------ CS
                       RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpelelktgevsekl 134
                                       +++++ ++G+ G+GKSt++n l ++l  + ge +e++
  gi|298674054|ref|YP_003725804.1|  96 AGRVTGILGPNGIGKSTVVNILSGTLVPNLGEYKEES 132
                                       568999******************9999888888765 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.0004
                                       TSEEEEECSTTSSHHHHHHHHCTT-- CS
                       RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpele 124
                                       +++  +vG+ G+GKSt++++l++e e
  gi|298674054|ref|YP_003725804.1| 364 GEVLGVVGPNGIGKSTFVKVLAGEIE 389
                                       478889****************9876 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   2.5e-06     0.001      21     139 ..      99     212 ..      94     266 .. 0.67
   2 ?    7.2   0.1     0.016       6.4      24      37 ..     369     382 ..     346     386 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.5e-06
                            AAA_23  21 ltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayveltfenkdgrytrsiererels 97 
                                       +t I GpNG GK+T+++ +   L       +  +++++ ++ +e  s+++ + y++  +   +g+  ++++++ + +
  gi|298674054|ref|YP_003725804.1|  99 VTGILGPNGIGKSTVVNILSGTLVPNL---GEYKEESSWDRVIERYSGTQIQDYFRKLV---NGK--VNVSQKPQYI 167
                                       799********************9755...55556667788888888888888855444...243..5687777777 PP

                            AAA_23  98 kkkgkttkkaklelleideleqfisellg...skkiilnlilflg 139
                                       +k  k  +++++elle+++ +  +++l++    ++ii ++i  l 
  gi|298674054|ref|YP_003725804.1| 168 DKIPKAFNGNTRELLEKADDRGVLNQLIErldLDEIIDRNINELS 212
                                       777788888888888886666666654441114444445544444 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.016
                            AAA_23  24 ItGpNGaGKTTild 37 
                                       ++GpNG GK+T++ 
  gi|298674054|ref|YP_003725804.1| 369 VVGPNGIGKSTFVK 382
                                       79*********976 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.3    0.0028       1.1      25      51 ..      98     124 ..      88     286 .. 0.75
   2 !   14.3   0.0    0.0001     0.041      23      76 ..     363     423 ..     353     512 .. 0.48

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0028
                            AAA_16  25 elvllsGesGvGKsslvrellralekd 51 
                                       +++ + G+ G+GKs++v+ l   l  +
  gi|298674054|ref|YP_003725804.1|  98 RVTGILGPNGIGKSTVVNILSGTLVPN 124
                                       667799***********9887666665 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 0.0001
                            AAA_16  23 rpelvllsGesGvGKsslvrellralekd.............ggiflrgkcdqlesaipysalaqal 76 
                                       ++e++ ++G+ G+GKs+ v+ l+ ++e d                  + k d +   ++ + +++ +
  gi|298674054|ref|YP_003725804.1| 363 QGEVLGVVGPNGIGKSTFVKVLAGEIEPDdgeldfdinisfkP---QYVKGDIN---LRVQDFLRSI 423
                                       347889**********************966555544332220...22222222...2122233333 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0    0.0013      0.53       3      33 ..     102     132 ..     101     162 .. 0.68
   2 !   10.8   0.0    0.0012       0.5       3      23 ..     369     389 ..     367     408 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0013
                      RNA_helicase   3 lyGpsgeGKStlakeLakallkklklkkkds 33 
                                       + Gp+g+GKSt+++ L+ +l  +l++ k++s
  gi|298674054|ref|YP_003725804.1| 102 ILGPNGIGKSTVVNILSGTLVPNLGEYKEES 132
                                       67*************9999997773333332 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0012
                      RNA_helicase   3 lyGpsgeGKStlakeLakall 23 
                                       ++Gp+g+GKSt++k La +++
  gi|298674054|ref|YP_003725804.1| 369 VVGPNGIGKSTFVKVLAGEIE 389
                                       78*************998886 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   0.00014     0.055      22      49 ..      96     124 ..      90     131 .. 0.84
   2 !    8.3   0.4    0.0049         2      24      39 ..     366     381 ..     357     386 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00014
                            AAA_29  22 kg.atlltGpsGsGKSTllDAiqalLvpa 49 
                                       +g +t + Gp+G GKST++  ++  Lvp+
  gi|298674054|ref|YP_003725804.1|  96 AGrVTGILGPNGIGKSTVVNILSGTLVPN 124
                                       566899*************9888888886 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0049
                            AAA_29  24 atlltGpsGsGKSTll 39 
                                       +  ++Gp+G GKST++
  gi|298674054|ref|YP_003725804.1| 366 VLGVVGPNGIGKSTFV 381
                                       56689*********97 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   1.6     0.068        27       5      20 ..       7      25 ..       3      30 .. 0.83
   2 !   22.7   3.4   1.8e-07   7.3e-05       2      24 .]      42      64 ..      41      64 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.068
                            Fer4_6  5 dpdkCi..gC.gdCvrvCP 20
                                      ++d+C    C  +C + CP
  gi|298674054|ref|YP_003725804.1|  7 NYDRCQprKCsKECHKYCP 25
                                      789**9888*666*****9 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 1.8e-07
                            Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                      + i +++C+gCg Cv+ CP++ai
  gi|298674054|ref|YP_003725804.1| 42 PIISEELCVGCGICVDKCPYKAI 64
                                      67899****************98 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0    0.0028       1.1       4      95 ..     103     200 ..     101     228 .. 0.76
   2 !   10.8   0.0    0.0012      0.49       3      23 ..     369     389 ..     367     436 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0028
                                       ESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS.STTHHHHHHHHHHHHHHHTS...TSEEEEEETGGGHHHHH.. CS
                               AAA   4 yGppGtGKTllakavakelgvefleisgsellsk.yvgesekkirelfkeakeka...kpsilfiDEidalaksr.. 74 
                                        Gp G+GK+++++ +  +l  ++ e +  + ++  +   s  +i+++f+++ + +   +++   iD i + ++ +  
  gi|298674054|ref|YP_003725804.1| 103 LGPNGIGKSTVVNILSGTLVPNLGEYKEESSWDRvIERYSGTQIQDYFRKLVNGKvnvSQKPQYIDKIPKAFNGNtr 179
                                       7*****************98777777777777441445577788888888755556664456689999999888843 PP

                                       TTCCCHHHHHHHHHHHHHHHH CS
                               AAA  75 sgseseeeervvnqLlteldg 95 
                                       +  e+ +++ v+nqL++ ld 
  gi|298674054|ref|YP_003725804.1| 180 ELLEKADDRGVLNQLIERLDL 200
                                       444888899999999998885 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0012
                                       EESSTTSSHHHHHHHHHHHHT CS
                               AAA   3 lyGppGtGKTllakavakelg 23 
                                       ++Gp G+GK++++k +a e++
  gi|298674054|ref|YP_003725804.1| 369 VVGPNGIGKSTFVKVLAGEIE 389
                                       79****************974 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.2     0.019       7.4      25      43 ..      99     117 ..      94     119 .. 0.89
   2 !    8.7   0.0    0.0031       1.2      28      43 ..     369     384 ..     356     441 .. 0.84
   3 ?    2.9   0.0      0.18        71     323     368 ..     470     515 ..     462     516 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.019
                            AAA_15  25 ltvliGkNnsGKSsileal 43 
                                       +t + G+N++GKS+++++l
  gi|298674054|ref|YP_003725804.1|  99 VTGILGPNGIGKSTVVNIL 117
                                       67799***********998 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0031
                            AAA_15  28 liGkNnsGKSsileal 43 
                                       ++G+N++GKS+++++l
  gi|298674054|ref|YP_003725804.1| 369 VVGPNGIGKSTFVKVL 384
                                       8*************98 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.18
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSphi 368
                                       + + ++++EP ahL  ++ +   k++k+ a++nk+  ++  H  ++
  gi|298674054|ref|YP_003725804.1| 470 DADMYILDEPSAHLDVEQRSLATKAIKRFAENNKKTAMVVDHDIYM 515
                                       56789****************************9877777676666 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   6.5   1.2e-06   0.00047      10      57 ..      15      64 ..       4      66 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.2e-06
                           Fer4_21 10 gCgk.CliaCed..tshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57
                                      +C k C++ C+   t+ + i + +k +  + e+ CvGC +C++ CP  ++i
  gi|298674054|ref|YP_003725804.1| 15 KCSKeCHKYCPRvrTGDETIYFGEKGKPIISEELCVGCGICVDKCPY-KAI 64
                                      57544999**9533788999998888877789**************6.555 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   8.4   1.9e-06   0.00075       5      51 .]      11      64 ..       9      64 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.9e-06
                            Fer4_9  5 Cg..aCveaCpagvvvedaaerkarlraase.....eaCigCgaCveaCpkgai 51
                                      C+  +C + C +   + + + +++   ++++     e C+gCg Cv++Cp +ai
  gi|298674054|ref|YP_003725804.1| 11 CQprKCSKECHKYCPRVRTGDETIYFGEKGKpiiseELCVGCGICVDKCPYKAI 64
                                      6422599999999999999999999888888999999**************987 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   2.1       1.5   6.1e+02       3      21 ..       4      25 ..       2      26 .. 0.74
   2 !   20.0   1.6   1.3e-06    0.0005       3      22 .]      42      61 ..      40      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 1.5
                            Fer4_2  3 vvvdtdrC.ig.Cg.aCvsaCP 21
                                      +v + drC  + C+  C + CP
  gi|298674054|ref|YP_003725804.1|  4 AVLNYDRCqPRkCSkECHKYCP 25
                                      6788999954569658999999 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 1.3e-06
                            Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                                      + + ++ C+gCg+Cv+ CP+
  gi|298674054|ref|YP_003725804.1| 42 PIISEELCVGCGICVDKCPY 61
                                      77889**************5 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   3.2       5.9   2.4e+03      33      49 ..       6      25 ..       2      27 .. 0.68
   2 !   13.3  12.0   0.00023     0.092       4      52 .]      15      63 ..       9      63 .. 0.85
   3 !   20.4   1.4   1.4e-06   0.00057       2      19 ..      49      66 ..      48      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 5.9
                            Fer4_7 33 idpekCl..gCga.CvavCP 49
                                      +++++C+   C + C + CP
  gi|298674054|ref|YP_003725804.1|  6 LNYDRCQprKCSKeCHKYCP 25
                                      56778864467766888888 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00023
                            Fer4_7  4 gC.gaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      +C + C ++Cp ++++ de  +  ++ k+ i++e C+gCg Cv+ CP++a
  gi|298674054|ref|YP_003725804.1| 15 KCsKECHKYCP-RVRTGDETIYFGEKGKPIISEELCVGCGICVDKCPYKA 63
                                      56358999999.7888888877778899*******************986 PP

  == domain 3  score: 20.4 bits;  conditional E-value: 1.4e-06
                            Fer4_7  2 CigCgaCvaaCpvkaiel 19
                                      C+gCg Cv+ Cp+kai++
  gi|298674054|ref|YP_003725804.1| 49 CVGCGICVDKCPYKAIMI 66
                                      ****************96 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0068       2.7       5      28 ..     100     122 ..      96     137 .. 0.84
   2 !    9.9   0.0    0.0014      0.57       5      23 ..     367     389 ..     363     477 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0068
                            AAA_24   5 iliyGpsgiGKTtlakelgpkplf 28 
                                         i Gp+giGK+t+++ l   +l+
  gi|298674054|ref|YP_003725804.1| 100 TGILGPNGIGKSTVVNIL-SGTLV 122
                                       6799**********9988.66655 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0014
                            AAA_24   5 iliyGpsgiGKTtlakel....g 23 
                                       + ++Gp+giGK+t++k l    +
  gi|298674054|ref|YP_003725804.1| 367 LGVVGPNGIGKSTFVKVLageiE 389
                                       6799***********98855444 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.2      0.12        49       2      18 ..      99     115 ..      98     122 .. 0.81
   2 !   12.8   0.0   0.00021     0.083       3      60 ..     367     422 ..     365     426 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.12
                                       CEEEEC-TTTCHHHHHH CS
                             NACHT   2 lvilqGeaGsGKTtLlq 18 
                                       +  + G++G+GK+t + 
  gi|298674054|ref|YP_003725804.1|  99 VTGILGPNGIGKSTVVN 115
                                       56699*********886 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00021
                                       EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCC CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfs 60 
                                       + + G++G+GK+t+++ la ++  ++ + + f+  + ++ + ++ + n  +++d+l+s
  gi|298674054|ref|YP_003725804.1| 367 LGVVGPNGIGKSTFVKVLAGEIEPDDGELD-FDINISFKPQYVKGDINL-RVQDFLRS 422
                                       5689******************99998887.999999999999988888.88888875 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.033        13       8      29 ..     100     121 ..      95     204 .. 0.74
   2 !   10.2   0.0    0.0018      0.71       6      91 ..     365     458 ..     360     509 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.033
                            AAA_22   8 lvvtGesGtGKTtllrrlleql 29 
                                       + + G+ G+GK+t+++ l  +l
  gi|298674054|ref|YP_003725804.1| 100 TGILGPNGIGKSTVVNILSGTL 121
                                       5689**********99887776 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0018
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee..........erpevvfvtlpsstsskdllrellralglelka.. 70 
                                        +l v+G+ G+GK+t ++ l+ + +     ++           +p++v+ +++     +d+lr + + ++ +     
  gi|298674054|ref|YP_003725804.1| 365 EVLGVVGPNGIGKSTFVKVLAGEIEP----DDgeldfdinisFKPQYVKGDINLR--VQDFLRSITSRFDTSYYQge 435
                                       56779***************999742....2244666666666666664444333..46777777777776666677 PP

                            AAA_22  71 ..erlsseellealeqalrarav 91 
                                         ++l+ eel++++  +l+    
  gi|298674054|ref|YP_003725804.1| 436 iaRPLQIEELYDKMLPNLSGGEL 458
                                       77888888888877777766655 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9  11.8   0.00046      0.18       2      56 .]       4      60 ..       3      60 .. 0.77
   2 !   16.5   1.4   1.7e-05    0.0066       2      23 ..      42      63 ..      41      90 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00046
                           Fer4_10  2 vvidddtC..irCg.kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      +v++ d+C   +C  +C k CP   t+++++++ ++++++    e C gcg Cv++CP
  gi|298674054|ref|YP_003725804.1|  4 AVLNYDRCqpRKCSkECHKYCPRVRTGDETIYFGEKGKPII-SEELCVGCGICVDKCP 60
                                      5789999976699889*******556666666655555553.4678***********9 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.7e-05
                           Fer4_10  2 vvidddtCirCgkCvkaCPadl 23
                                      ++i ++ C++Cg Cv+ CP+++
  gi|298674054|ref|YP_003725804.1| 42 PIISEELCVGCGICVDKCPYKA 63
                                      68999**************954 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.069        27       3      27 ..      98     122 ..      96     173 .. 0.71
   2 ?    3.0   0.2      0.25        99      33      84 ..     195     248 ..     177     265 .. 0.68
   3 ?    6.6   0.0     0.019       7.4       2      25 ..     364     387 ..     363     429 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.069
                            AAA_14   3 kilvitGaRrvGKTtllkqlikell 27 
                                       ++  i G+  +GK+t+++ l  +l 
  gi|298674054|ref|YP_003725804.1|  98 RVTGILGPNGIGKSTVVNILSGTLV 122
                                       7889************987765555 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.25
                            AAA_14  33 ilyinldderdkkladpe..kllelileklkeekktylflDEiqevpewekalk 84 
                                       i  ++ld+  d+++++ +  +l ++  +  + ++ ++ f+DEi+ + ++++ ++
  gi|298674054|ref|YP_003725804.1| 195 IERLDLDEIIDRNINELSggELQRVAIAACMVKDAEFYFFDEISPYLDIYQRIN 248
                                       5566777777776665555556655555533357899******99866665554 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.019
                            AAA_14   2 rkilvitGaRrvGKTtllkqlike 25 
                                       +++l ++G+  +GK+t++k l+ e
  gi|298674054|ref|YP_003725804.1| 364 GEVLGVVGPNGIGKSTFVKVLAGE 387
                                       57899*************998865 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.4     0.016       6.2       3      22 ..     101     120 ..      99     166 .. 0.86
   2 ?    6.7   0.0     0.019       7.5       3      22 ..     368     387 ..     366     398 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.016
                                       EEEESTTSSHHHHHHHHHTS CS
                          MMR_HSR1   3 aivGrpNvGKStLinaltge 22 
                                       +i+G    GKSt++n l+g+
  gi|298674054|ref|YP_003725804.1| 101 GILGPNGIGKSTVVNILSGT 120
                                       799**************986 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.019
                                       EEEESTTSSHHHHHHHHHTS CS
                          MMR_HSR1   3 aivGrpNvGKStLinaltge 22 
                                       ++vG    GKSt+++ l ge
  gi|298674054|ref|YP_003725804.1| 368 GVVGPNGIGKSTFVKVLAGE 387
                                       89**************9986 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0      0.17        67       5      18 ..     103     116 ..      99     191 .. 0.80
   2 !    9.2   0.0    0.0032       1.3       4      21 ..     369     386 ..     366     396 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.17
                            AAA_33   5 vGlpGsGKstlaer 18 
                                        G++G GKst++  
  gi|298674054|ref|YP_003725804.1| 103 LGPNGIGKSTVVNI 116
                                       6*********9875 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0032
                            AAA_33   4 lvGlpGsGKstlaerllk 21 
                                       +vG++G GKst+++ l+ 
  gi|298674054|ref|YP_003725804.1| 369 VVGPNGIGKSTFVKVLAG 386
                                       89***********98875 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0095       3.8       3      34 ..     102     152 ..     101     212 .. 0.68
   2 ?    3.8   0.0       0.2        79       3      20 ..     369     386 ..     367     422 .. 0.86
   3 ?    0.2   0.0       2.6     1e+03      30      86 ..     466     533 ..     441     584 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0095
                            AAA_18   3 ltGtpGvGKttlakeLskrl.gf..................gvnlrdvake 34 
                                       + G+ G GK+t+ + Ls  l  +                  g++++d++++
  gi|298674054|ref|YP_003725804.1| 102 ILGPNGIGKSTVVNILSGTLvPNlgeykeesswdrvierysGTQIQDYFRK 152
                                       89**************88873334444555555555555555555555554 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.2
                            AAA_18   3 ltGtpGvGKttlakeLsk 20 
                                       + G+ G GK+t+ k L+ 
  gi|298674054|ref|YP_003725804.1| 369 VVGPNGIGKSTFVKVLAG 386
                                       89************9975 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 2.6
                            AAA_18  30 dvakenglllevdpealdeskrldedkldklldaleenss.............aleegknlvidghlael 86 
                                       ++ ++ ++++ ++p      +++++    k+++ + en++             ++ ++  +v++g +a +
  gi|298674054|ref|YP_003725804.1| 466 CLSRDADMYILDEPS--AHLDVEQRSLATKAIKRFAENNKktamvvdhdiymiDMLSERLIVFEGKPAVY 533
                                       555666777777777..66777777777777888888777776555555555444444444444444444 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   2.2       9.5   3.8e+03       4      14 ..      15      26 ..      10      34 .. 0.79
   2 ?   16.3   0.7   3.6e-05     0.014       2      17 ..      49      64 ..      48      84 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 9.5
                           Fer4_16  4 tCgk.CaevCPt 14
                                      +C k C + CP 
  gi|298674054|ref|YP_003725804.1| 15 KCSKeCHKYCPR 26
                                      677778888885 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 3.6e-05
                           Fer4_16  2 CgtCgkCaevCPtnai 17
                                      C++Cg C++ CP +ai
  gi|298674054|ref|YP_003725804.1| 49 CVGCGICVDKCPYKAI 64
                                      ***************8 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.2     0.075        30      26      48 ..     100     122 ..      96     127 .. 0.86
   2 ?    7.5   0.0      0.01         4      26      47 ..     367     388 ..     365     394 .. 0.89
   3 ?   -0.4   0.0       2.6     1e+03     113     182 ..     483     563 ..     461     584 .. 0.56

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.075
                             DUF87  26 lAilgsTGsGKSntvavLleell 48 
                                       ++ilg  G GKS+ v +L   l+
  gi|298674054|ref|YP_003725804.1| 100 TGILGPNGIGKSTVVNILSGTLV 122
                                       69*************99976665 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.01
                             DUF87  26 lAilgsTGsGKSntvavLleel 47 
                                       l+++g  G GKS++v+vL  e+
  gi|298674054|ref|YP_003725804.1| 367 LGVVGPNGIGKSTFVKVLAGEI 388
                                       689999************8776 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 2.6
                             DUF87 113 aaavqrsvleealdqakakeekeklssdepveklleelk...........kekeelrklknqaiarlldkledllrk 178
                                       +  +qrs+  +a+++  ++++k+ + +d+ ++ +    +           +++++++++ ++ +++ l+ l+  +r+
  gi|298674054|ref|YP_003725804.1| 483 LDVEQRSLATKAIKRFAENNKKTAMVVDHDIYMIDMLSErlivfegkpavYGVAKRPSSMQEGMNKFLSNLDITFRR 559
                                       44557777777777777777777777777776444443366666666666444444444444444444444444444 PP

                             DUF87 179 ggsf 182
                                         + 
  gi|298674054|ref|YP_003725804.1| 560 DDDT 563
                                       3333 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.068        27      22      87 ..      99     164 ..      92     186 .. 0.67
   2 ?    7.5   0.0     0.005         2      21      68 ..     365     412 ..     358     471 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.068
                                       EEEEEESTTSSHHHHHHHHCCSHCCCCCCBT.EEEEEEEESXXHHHHHHHXXHHHHHCCCTTSSSS- CS
                            NB-ARC  22 vvalvGmgGvGKttlakqilnksdevegrFd.svawvvvsktdkseeiletilkeLslseddleeke 87 
                                       v ++ G  G+GK+t+++     +    g++     w  v + ++  +i++   ++L + + + ++k+
  gi|298674054|ref|YP_003725804.1|  99 VTGILGPNGIGKSTVVNILSGTLVPNLGEYKeESSWDRVIERYSGTQIQD-YFRKLVNGKVNVSQKP 164
                                       6789**********987555554444456654667777777777777766.4555555555555555 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.005
                                       EEEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEEEEESXXHHHHH CS
                            NB-ARC  21 lvvalvGmgGvGKttlakqilnksdevegrFdsvawvvvsktdkseei 68 
                                        v+++vG  G+GK+t +k    + +  +g+ d  + ++   ++ + +i
  gi|298674054|ref|YP_003725804.1| 365 EVLGVVGPNGIGKSTFVKVLAGEIEPDDGELDFDINISFKPQYVKGDI 412
                                       599************998877776666665555555544444444444 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.049        20       9      37 ..     102     130 ..     100     184 .. 0.71
   2 ?    6.5   0.0     0.011       4.4       9      25 ..     369     385 ..     365     405 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.049
                                       EEEBTTSSCCCCCCTTSSSS--------- CS
                            Septin   9 vvGesglGkttlintlfetdlieeeklee 37 
                                       + G +g+Gk+t++n l  t + +  +++e
  gi|298674054|ref|YP_003725804.1| 102 ILGPNGIGKSTVVNILSGTLVPNLGEYKE 130
                                       5799**********998887766654443 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.011
                                       EEEBTTSSCCCCCCTTS CS
                            Septin   9 vvGesglGkttlintlf 25 
                                       vvG +g+Gk+t+++ l 
  gi|298674054|ref|YP_003725804.1| 369 VVGPNGIGKSTFVKVLA 385
                                       9************9986 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.059        24       4      23 ..     102     121 ..     101     132 .. 0.85
   2 ?    5.5   0.0     0.039        16       4      23 ..     369     388 ..     367     478 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.059
                                       EE--SSSSHHHHHHHGGGGB CS
                             AAA_5   4 LvGppGtgKselaerlaaal 23 
                                       ++Gp G+gKs+++  l+  l
  gi|298674054|ref|YP_003725804.1| 102 ILGPNGIGKSTVVNILSGTL 121
                                       58***********9998766 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.039
                                       EE--SSSSHHHHHHHGGGGB CS
                             AAA_5   4 LvGppGtgKselaerlaaal 23 
                                       +vGp G+gKs++++ la  +
  gi|298674054|ref|YP_003725804.1| 369 VVGPNGIGKSTFVKVLAGEI 388
                                       59************998765 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0082       3.3      27      55 ..      98     126 ..      94     132 .. 0.91
   2 ?    2.2   0.0      0.34   1.4e+02      30      59 ..     368     397 ..     362     402 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0082
                                       HHHHHHS--SHHHHHHHHHHHHHHS--TT CS
                              MukB  27 lvttlsGgnGaGksttmaafvtaliPdls 55 
                                        vt + G nG Gkst++  +  +l+P+l 
  gi|298674054|ref|YP_003725804.1|  98 RVTGILGPNGIGKSTVVNILSGTLVPNLG 126
                                       59999*********************985 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.34
                                       HHHS--SHHHHHHHHHHHHHHS--TTT--- CS
                              MukB  30 tlsGgnGaGksttmaafvtaliPdlsllhf 59 
                                        + G nG Gkst +  +   + Pd   l f
  gi|298674054|ref|YP_003725804.1| 368 GVVGPNGIGKSTFVKVLAGEIEPDDGELDF 397
                                       57799********99999999999999988 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.3     0.021       8.5      26      53 ..      96     121 ..      88     127 .. 0.82
   2 ?    6.5   0.1    0.0091       3.6      29      52 ..     364     387 ..     353     394 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.021
                                       -S-SEEEEEEE-TTSSHHHHHHHHHHHH CS
                              MeaB  26 aGraqvvGltGvPGaGkstlvealglel 53 
                                       aGr  v G+ G  G Gkst+v+ l  +l
  gi|298674054|ref|YP_003725804.1|  96 AGR--VTGILGPNGIGKSTVVNILSGTL 121
                                       454..679*************9998766 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0091
                                       SEEEEEEE-TTSSHHHHHHHHHHH CS
                              MeaB  29 aqvvGltGvPGaGkstlvealgle 52 
                                        +v+G+ G  G Gkst+v+ l+ e
  gi|298674054|ref|YP_003725804.1| 364 GEVLGVVGPNGIGKSTFVKVLAGE 387
                                       579***************998765 PP

>> VirE  Virulence-associated protein E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.13        54      52      76 ..      97     121 ..      88     167 .. 0.79
   2 ?    6.1   0.0      0.02       8.1      50      75 ..     362     387 ..     357     394 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.13
                              VirE  52 DfvlvLvGkqgsgKstfleklgeew 76 
                                         v+ + G+ g+gKst++++l++  
  gi|298674054|ref|YP_003725804.1|  97 GRVTGILGPNGIGKSTVVNILSGTL 121
                                       5678889**************7765 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.02
                              VirE  50 KfDfvlvLvGkqgsgKstfleklgee 75 
                                       K  +vl +vG+ g+gKstf++ l++e
  gi|298674054|ref|YP_003725804.1| 362 KQGEVLGVVGPNGIGKSTFVKVLAGE 387
                                       7788999***************9654 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.034        14       4      29 ..     103     127 ..     101     155 .. 0.76
   2 ?    3.5   0.0      0.14        55       3      21 ..     369     387 ..     367     391 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.034
                                       EESTTSSHHHHHHHHHCCSTCEEEE- CS
                               dNK   4 eGnIgaGKstlvklLskklgvkvfeE 29 
                                        G+ g GKst+v++Ls +l v+ + E
  gi|298674054|ref|YP_003725804.1| 103 LGPNGIGKSTVVNILSGTL-VPNLGE 127
                                       58889***********988.555555 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.14
                                       EEESTTSSHHHHHHHHHCC CS
                               dNK   3 veGnIgaGKstlvklLskk 21 
                                       v G+ g GKst+vk+L+ +
  gi|298674054|ref|YP_003725804.1| 369 VVGPNGIGKSTFVKVLAGE 387
                                       66899***********876 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.078        31       1      19 [.     104     122 ..     104     128 .. 0.90
   2 ?    4.4   0.0     0.074        29       1      17 [.     371     387 ..     371     396 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.078
                            CLP1_P   1 GpkdsGKSTlarlLlNyal 19 
                                       Gp+  GKST++ +L  +++
  gi|298674054|ref|YP_003725804.1| 104 GPNGIGKSTVVNILSGTLV 122
                                       8999***********9998 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.074
                            CLP1_P   1 GpkdsGKSTlarlLlNy 17 
                                       Gp+  GKST++++L+ +
  gi|298674054|ref|YP_003725804.1| 371 GPNGIGKSTFVKVLAGE 387
                                       8999**********976 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.22        88       1      17 [.     102     118 ..     102     124 .. 0.87
   2 ?    6.4   0.0     0.017       6.8       1      17 [.     369     385 ..     369     394 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.22
                        ATP_bind_1   1 vvGpaGsGKttfvgals 17 
                                       ++Gp G GK+t v+ ls
  gi|298674054|ref|YP_003725804.1| 102 ILGPNGIGKSTVVNILS 118
                                       68***********9887 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.017
                        ATP_bind_1   1 vvGpaGsGKttfvgals 17 
                                       vvGp G GK+tfv+ l+
  gi|298674054|ref|YP_003725804.1| 369 VVGPNGIGKSTFVKVLA 385
                                       89***********9875 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.021       8.6       4      30 ..     102     128 ..     100     159 .. 0.81
   2 ?    2.4   0.0      0.42   1.7e+02       4      20 ..     369     385 ..     368     394 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.021
                            AAA_28   4 itGgestGKTtlleaLaargypvvpEa 30 
                                       i+G+ + GK+t+++ L+ + +p + E+
  gi|298674054|ref|YP_003725804.1| 102 ILGPNGIGKSTVVNILSGTLVPNLGEY 128
                                       89**************97766665555 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.42
                            AAA_28   4 itGgestGKTtlleaLa 20 
                                       ++G+ + GK+t ++ La
  gi|298674054|ref|YP_003725804.1| 369 VVGPNGIGKSTFVKVLA 385
                                       58***********9998 PP

>> Spore_IV_A  Stage IV sporulation protein A (spore_IV_A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.78   3.1e+02      21      61 ..     101     139 ..      97     174 .. 0.73
   2 ?    8.2   0.2    0.0026         1      15      36 ..     363     383 ..     350     388 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.78
                        Spore_IV_A  21 gvvGpvRtGKStfikrfmellvlpniedeeekerakDelPq 61 
                                       g+ Gp   GKSt ++ ++  +++pn+ + ++ e   D +  
  gi|298674054|ref|YP_003725804.1| 101 GILGPNGIGKSTVVN-ILSGTLVPNLGE-YKEESSWDRVIE 139
                                       89999999****886.566666788865.444555555555 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0026
                        Spore_IV_A  15 ngdiyigvvGpvRtGKStfikr 36 
                                       +g++ +gvvGp   GKStf+k 
  gi|298674054|ref|YP_003725804.1| 363 QGEV-LGVVGPNGIGKSTFVKV 383
                                       6666.8**************96 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1      0.17        67      18      38 ..      97     117 ..      93     126 .. 0.85
   2 ?    5.1   0.0     0.042        17      19      43 ..     365     389 ..     360     398 .. 0.81
   3 ?   -2.5   0.0       8.6   3.4e+03      89     103 ..     471     486 ..     453     512 .. 0.54

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.17
                            AAA_30  18 drvavltGpAGtGKttalkal 38 
                                        rv+ + Gp G GK+t+++ l
  gi|298674054|ref|YP_003725804.1|  97 GRVTGILGPNGIGKSTVVNIL 117
                                       46999************9876 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.042
                            AAA_30  19 rvavltGpAGtGKttalkalreawe 43 
                                        v  ++Gp G GK+t +k+l+  +e
  gi|298674054|ref|YP_003725804.1| 365 EVLGVVGPNGIGKSTFVKVLAGEIE 389
                                       48889*************9986655 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 8.6
                            AAA_30  89 gtllivDEagmv.dtk 103
                                       ++++i DE +   d +
  gi|298674054|ref|YP_003725804.1| 471 ADMYILDEPSAHlDVE 486
                                       3778888876543222 PP

>> DUF4277  Domain of unknown function (DUF4277)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1     0.002       0.8       5      47 ..     184     226 ..     180     230 .. 0.89
   2 ?   -1.1   0.1       5.9   2.3e+03      15      51 ..     243     279 ..     241     283 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.002
                           DUF4277   5 sldhlglvaglidelglaelidelipkksqekvsagevvkali 47 
                                       + d+ g++++li++l+l+e+id+ i++ s  +++   +  +++
  gi|298674054|ref|YP_003725804.1| 184 KADDRGVLNQLIERLDLDEIIDRNINELSGGELQRVAIAACMV 226
                                       56888**********************9999999888888887 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 5.9
                           DUF4277  15 lidelglaelidelipkksqekvsagevvkalilngL 51 
                                       +++++++a+li+el ++k    v++  ++  ++ ++ 
  gi|298674054|ref|YP_003725804.1| 243 IYQRINVAQLIQELAQEKAVLVVEHDLAILDMLADVV 279
                                       57899999***99999999999999988888887765 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.49     2e+02      32      50 ..      96     114 ..      93     127 .. 0.86
   2 ?   -1.2   0.1       3.1   1.3e+03     103     155 ..     232     279 ..     209     282 .. 0.60
   3 ?    6.2   0.0     0.017       6.9      28      55 ..     359     386 ..     357     406 .. 0.87
   4 ?   -1.9   0.0       5.3   2.1e+03     143     184 ..     471     507 ..     454     520 .. 0.47

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.49
                            AAA_25  32 agelallaGapgtGKttla 50 
                                       ag ++ + G+ g GK+t++
  gi|298674054|ref|YP_003725804.1|  96 AGRVTGILGPNGIGKSTVV 114
                                       67888999*********97 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.1
                            AAA_25 103 llvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsral 155
                                        ++  +     l++++ ++  +l+++  ++ +  + e +  +l ++D+l+ ++
  gi|298674054|ref|YP_003725804.1| 232 YFFDEIS--PYLDIYQRINVAQLIQELAQEKAVLVVE-H--DLAILDMLADVV 279
                                       3344332..3477777788888887777666666666.4..788888888765 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.017
                            AAA_25  28 gllpagelallaGapgtGKttlaldlal 55 
                                       g l  ge+  ++G+ g GK+t++  la 
  gi|298674054|ref|YP_003725804.1| 359 GSLKQGEVLGVVGPNGIGKSTFVKVLAG 386
                                       5678899999************988875 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 5.3
                            AAA_25 143 vrlvviDplsralggdensnsdvgalvealeriarrtgaavl 184
                                       +++ ++D  s+ l+   +  s +    +a++r+a++ + + +
  gi|298674054|ref|YP_003725804.1| 471 ADMYILDEPSAHLDV--EQRSLA---TKAIKRFAENNKKTAM 507
                                       444444443332222..222222...2333333333333334 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   3.0      0.44   1.8e+02       2      15 ..       9      25 ..       8      33 .. 0.81
   2 ?   14.0   3.3   0.00014     0.055       2      16 ..      47      61 ..      46      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.44
                            Fer4_4  2 erCi..gCgs.CvaaCP 15
                                      +rC+   C + C+ +CP
  gi|298674054|ref|YP_003725804.1|  9 DRCQprKCSKeCHKYCP 25
                                      88865589867****** PP

  == domain 2  score: 14.0 bits;  conditional E-value: 0.00014
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      e C+gCg Cv+ CP+
  gi|298674054|ref|YP_003725804.1| 47 ELCVGCGICVDKCPY 61
                                      67************8 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.073        29       4      23 ..     102     121 ..      99     129 .. 0.85
   2 ?    6.5   0.0     0.018       7.3       3      24 ..     368     389 ..     366     395 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.073
                                       EE--TTSSHHHHHHHHHHHH CS
                          NTPase_1   4 iTGppGvGKtTlvkkvlell 23 
                                       i Gp G+GK+T+v+ ++ +l
  gi|298674054|ref|YP_003725804.1| 102 ILGPNGIGKSTVVNILSGTL 121
                                       669**********9887766 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.018
                                       EEE--TTSSHHHHHHHHHHHH. CS
                          NTPase_1   3 fiTGppGvGKtTlvkkvlellk 24 
                                        + Gp G+GK+T+vk ++ +++
  gi|298674054|ref|YP_003725804.1| 368 GVVGPNGIGKSTFVKVLAGEIE 389
                                       578***********99887775 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8  11.5      0.22        88      43      59 ..      46      62 ..      10      64 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.22
                           Fer4_17 43 aslCieCgeCerkCPqg 59
                                       +lC++Cg C+ kCP++
  gi|298674054|ref|YP_003725804.1| 46 EELCVGCGICVDKCPYK 62
                                      4789**********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (592 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); expected 17.9 (0.001)
Passed Fwd filter:                        47  (0.00262145); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              45  [number of targets reported over threshold]
# CPU time: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.49
# Mc/sec: 3653.78
//
Query:       gi|298674055|ref|YP_003725805.1|  [L=85]
Description: TM2 domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      0.003   16.8   0.2     0.0037   16.5   0.2    1.0  1  Polysacc_synt_3  Polysaccharide biosynthesis protein
  ------ inclusion threshold ------
      0.028   14.5   2.7      0.029   14.5   2.3    1.2  1  DUF4870          Domain of unknown function (DUF4870)
      0.045   13.9   0.4      0.047   13.8   0.4    1.1  1  DUF2614          Zinc-ribbon containing domain
      0.049   13.0   0.2      0.056   12.9   0.2    1.1  1  DUF639           Plant protein of unknown function (DUF639)
      0.083   13.0   0.1      0.087   12.9   0.1    1.2  1  DUF3742          Protein of unknown function (DUF3742)
        0.9    9.8   6.5        2.7    8.2   6.5    1.5  1  EI24             Etoposide-induced protein 2.4 (EI24)


Domain annotation for each model (and alignments):
>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2   1.2e-06    0.0037      77     139 ..       5      67 ..       3      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.2e-06
                   Polysacc_synt_3  77 nqpelvtvlrvlalvlilsglssvqeallrrelkFkklfkitlvssvvgvivaivlAllglgv 139
                                       n+++l++ l  l+l+li+ gl ++ + ++++   F  +++i +v+++++v + ++  ++++++
  gi|298674055|ref|YP_003725805.1|   5 NEERLKNPLAALGLSLIFPGLGQIYNQQVKKGQMFFVIAIILIVTMFAAVGFVLYPIFWIYNM 67 
                                       6889******************************************99988887777776665 PP

>> DUF4870  Domain of unknown function (DUF4870)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   2.3   9.8e-06     0.029      54      99 ..      38      81 ..      27      84 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 9.8e-06
                           DUF4870 54 lliysiilivlsllvligflllllllllllnlvlviiaaikanege 99
                                      ++++++i+++++++  +gf  +l ++++++n++     a+k+n+ge
  gi|298674055|ref|YP_003725805.1| 38 MFFVIAIILIVTMFAAVGF--VLYPIFWIYNMYDAYTDAVKMNRGE 81
                                      4555555555569999999..***********************98 PP

>> DUF2614  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.4   1.6e-05     0.047       7      58 ..      11      64 ..       5      83 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.6e-05
                           DUF2614  7 nkirtfalllvfiglivmyigllfkeselllvlflllGlllvlastvvy..fwi 58
                                      n + ++ l+l+f gl  +y   + k + ++++ ++l+ +++  + +v+y  fwi
  gi|298674055|ref|YP_003725805.1| 11 NPLAALGLSLIFPGLGQIYNQQVKKGQMFFVIAIILIVTMFAAVGFVLYpiFWI 64
                                      5567789************99877766655555555555666667788755666 PP

>> DUF639  Plant protein of unknown function (DUF639)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   1.9e-05     0.056     157     203 ..      31      77 ..      18      83 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.9e-05
                            DUF639 157 skapqaaskvalamlvlatvlavvPfkyllafvlvelftresegrke 203
                                        +  +    +++a++ + t++a v f +  +f +++++  + ++ k+
  gi|298674055|ref|YP_003725805.1|  31 QQVKKGQMFFVIAIILIVTMFAAVGFVLYPIFWIYNMYDAYTDAVKM 77 
                                       455555556799*********************99999988887666 PP

>> DUF3742  Protein of unknown function (DUF3742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   2.9e-05     0.087      33      67 ..      30      64 ..       5      78 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.9e-05
                           DUF3742 33 swlvakGvpaavatavlwvvklavlGvllyvafWl 67
                                      +  v+kG    v+  +l+v+  a++G  ly +fW+
  gi|298674055|ref|YP_003725805.1| 30 NQQVKKGQMFFVIAIILIVTMFAAVGFVLYPIFWI 64
                                      66689999999999********************7 PP

>> EI24  Etoposide-induced protein 2.4 (EI24)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   6.5    0.0009       2.7      89     125 ..      29      66 ..      13      80 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0009
                                       H.HHHHHHHHHHHHHHHHHHHHHTTHHH....HHHHHH CS
                              EI24  89 a.eslkslllllllllvllplliPvvglilsplllswl 125
                                         +++k+  ++++++++l+++++  vg++l p+++ + 
  gi|298674055|ref|YP_003725805.1|  29 YnQQVKKGQMFFVIAIILIVTMFAAVGFVLYPIFWIYN 66 
                                       258999***************8899**********994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1048  (0.0584528); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 531.91
//
Query:       gi|298674056|ref|YP_003725806.1|  [L=464]
Description: MATE efflux family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-51  174.4  38.8    6.1e-27   94.3  17.1    3.1  4  MatE             MatE
    5.2e-11   42.8  23.0    2.3e-09   37.5  10.7    5.1  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
  ------ inclusion threshold ------
        7.9    6.2  10.3       0.46   10.2   2.4    2.5  3  TIC20            Chloroplast import apparatus Tic20-like


Domain annotation for each model (and alignments):
>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.3  17.1     1e-30   6.1e-27       1     161 []      23     187 ..      23     187 .. 0.98
   2 ?    0.1   0.3     0.094   5.6e+02      40      62 ..     188     211 ..     186     212 .. 0.75
   3 !   94.1  13.8   1.1e-30   6.7e-27      10     158 ..     257     407 ..     250     410 .. 0.93
   4 ?   -4.1   0.3       1.8   1.1e+04      33      90 ..     422     434 ..     416     439 .. 0.40

  Alignments for each domain:
  == domain 1  score: 94.3 bits;  conditional E-value: 1e-30
                              MatE   1 Pialenllesllslidtllvgrl....gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealr 73 
                                       P++  ++++ l++++dt++vg+     +++ ++++++a+++ +++  ++l ++++ +++++++lG++n +ra+++l 
  gi|298674056|ref|YP_003725806.1|  23 PAIAGMVIQALYNIVDTIFVGKAlgeaSAQGIGGLTVAFPVQMIMAGLGLIIGIGGASIISRNLGSNNIDRAEKTLG 99 
                                       99*******************9998788999********************************************** PP

                              MatE  74 qglilllllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyisli 150
                                         ++l +++s++i+++v l++++i++ f++++++l++a +ylri+ +g +++++ +++++++r+ g++ ++++ ++i
  gi|298674056|ref|YP_003725806.1| 100 NVIFLIFVFSALITVAVSLYINPIMKAFGATDTILPYAVDYLRIITYGCIFFIFAMATNNVVRAEGNANMAMFTMVI 176
                                       ***************************************************************************** PP

                              MatE 151 slllniplnyl 161
                                       + + ni+l+++
  gi|298674056|ref|YP_003725806.1| 177 AGVTNIILDPI 187
                                       99******986 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.094
                              MatE  40 llfvfllgl.stalttlvgqalGa 62 
                                       ++f f++g+ ++a +t+++q +G+
  gi|298674056|ref|YP_003725806.1| 188 FIFGFGWGVkGAASATIISQLIGS 211
                                       5666888874567789*****996 PP

  == domain 3  score: 94.1 bits;  conditional E-value: 1.1e-30
                              MatE  10 sllslidtllvgrl.gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglilllllsli 85 
                                       sl+  +++ +++ + g++++A+ +i +++++++f++++g+  +l+++vg ++Ga+nf+r+ e++r ++i++++++ i
  gi|298674056|ref|YP_003725806.1| 257 SLMVVVLNNVLAIYgGDVSIAVFGIINRLFMFIFMPMIGIVQGLQPIVGFNYGARNFERVMESVRLSIIVTTVMASI 333
                                       455556666677778************************************************************** PP

                              MatE  86 iallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislisl.llnipl 158
                                        +++ ++f+eq++ +f++d+++++ +k  +ri++l++p+ ++ ++ ++ ++++gk+k+++++s+++  l+ ipl
  gi|298674056|ref|YP_003725806.1| 334 GFAIFYAFPEQLFGVFSNDPNLINSGKSAIRIMVLVVPLASFEFIGATLYQAIGKAKPSFVLSVSRQiLFLIPL 407
                                       ******************************************************************98887877 PP

  == domain 4  score: -4.1 bits;  conditional E-value: 1.8
                              MatE  33 ialsilsllfvfllglstalttlvgqalGaknfkrakealrqglilllllsliiallv 90 
                                       ia++i+ +l                                             ++++
  gi|298674056|ref|YP_003725806.1| 422 IAFPIAGFL---------------------------------------------SFML 434
                                       333333333.............................................2222 PP

>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.3   8.0         3   1.8e+04      57     127 ..      22     101 ..      10     126 .. 0.50
   2 !   37.5  10.7   3.8e-13   2.3e-09       1      78 [.     140     219 ..     140     236 .. 0.90
   3 ?   -3.2   5.3       1.3   7.9e+03      91     113 ..     316     342 ..     256     352 .. 0.52
   4 !   19.2   4.3   1.6e-07   0.00097       2      83 ..     363     445 ..     362     451 .. 0.89

  Alignments for each domain:
  == domain 1  score: -4.3 bits;  conditional E-value: 3
                   Polysacc_synt_C  57 Gaaiatvlallvvavlnlyalrrllgikl.ellrrllkpllaalvmgivvylllllllglllla............. 119
                                        +aia ++ ++++ ++  +++ + lg    + +  l + + + ++m+++ +++     ++++ +             
  gi|298674056|ref|YP_003725806.1|  22 APAIAGMVIQALYNIVDTIFVGKALGEASaQGIGGLTVAFPVQMIMAGLGLIIGIGGASIISRNlgsnnidraektl 98 
                                       56777777777777777777777777777633444433333333333332222222222222223334455555533 PP

                   Polysacc_synt_C 120 .alalllav 127
                                        +      v
  gi|298674056|ref|YP_003725806.1|  99 gN------V 101
                                       31......2 PP

  == domain 2  score: 37.5 bits;  conditional E-value: 3.8e-13
                   Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllli..plfgivGaaiatvlallvvavlnly 75 
                                       +L+i+++++if+ +++ ++++  + g +  a+  +vi+ + ++il  ++i    +g+ Gaa at++++l+++++++y
  gi|298674056|ref|YP_003725806.1| 140 YLRIITYGCIFFIFAMATNNVVRAEGNANMAMFTMVIAGVTNIILDPIFIfgFGWGVKGAASATIISQLIGSLFLVY 216
                                       699***********************************************777789*******************99 PP

                   Polysacc_synt_C  76 alr 78 
                                       +l 
  gi|298674056|ref|YP_003725806.1| 217 YLF 219
                                       874 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 1.3
                   Polysacc_synt_C  91 ll....kpllaalvmgivvylllllll 113
                                       ++      ++++ vm+ + +++++ ++
  gi|298674056|ref|YP_003725806.1| 316 VMesvrLSIIVTTVMASIGFAIFYAFP 342
                                       222222455555555555555555555 PP

  == domain 4  score: 19.2 bits;  conditional E-value: 1.6e-07
                   Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigal.vklilnllliplfgivGaaiatvlallvvavlnlyal 77 
                                       ++i++l+++++s+  +++++ q++g++k  ++ +v   + + + l ++l  +f + G+ ia  +a +++++l ++++
  gi|298674056|ref|YP_003725806.1| 363 IRIMVLVVPLASFEFIGATLYQAIGKAKPSFVLSVSRQIlFLIPLVIILPGFFDLKGVWIAFPIAGFLSFMLSIFMM 439
                                       79****************************99999876615666666677799************************ PP

                   Polysacc_synt_C  78 rrllgi 83 
                                       +r++++
  gi|298674056|ref|YP_003725806.1| 440 NREFKV 445
                                       **9876 PP

>> TIC20  Chloroplast import apparatus Tic20-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   2.4   7.6e-05      0.46      37     122 ..      97     182 ..      92     191 .. 0.90
   2 ?   -0.4   0.1      0.14   8.2e+02      45      96 ..     216     265 ..     207     270 .. 0.73
   3 ?   -1.6   0.3      0.33     2e+03      73      90 ..     274     291 ..     247     332 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 7.6e-05
                             TIC20  37 tlscvpYllplfnglqyskvgyyleplleqfellqlliypilgainllksyfslvvffvlylvvVrnkelprylRFh 113
                                       tl  v +l+ +f +l   +v+ y++p+++ f +  +++ + ++ ++++     + +f ++   vVr +   ++  F 
  gi|298674056|ref|YP_003725806.1|  97 TLGNVIFLIFVFSALITVAVSLYINPIMKAFGATDTILPYAVDYLRIITYGCIFFIFAMATNNVVRAEGNANMAMFT 173
                                       788999*****************************999999****9999999999*************999999999 PP

                             TIC20 114 vmlailLdv 122
                                       +++a + ++
  gi|298674056|ref|YP_003725806.1| 174 MVIAGVTNI 182
                                       998866555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.14
                             TIC20  45 lplfnglqyskvgyyleplleqfellqlliypilgainllksyfslvvffvl 96 
                                       + lf g ++ k+  +++ l+ q++++++ i + l   ++  s  ++vv++  
  gi|298674056|ref|YP_003725806.1| 216 YYLFSGKSILKL--HIKNLIPQYDIIKENITIGLSPFARQSSSSLMVVVLNN 265
                                       456666677666..9999*******999998877777777777777766655 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.33
                             TIC20  73 liypilgainllksyfsl 90 
                                       +  +++g+in+l  ++++
  gi|298674056|ref|YP_003725806.1| 274 VSIAVFGIINRLFMFIFM 291
                                       444444444444432222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 3061.27
//
Query:       gi|298674057|ref|YP_003725807.1|  [L=100]
Description: hypothetical protein Metev_0079 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1068  (0.0595683); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 722.18
//
Query:       gi|298674058|ref|YP_003725808.1|  [L=585]
Description: hypothetical protein Metev_0080 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-10   41.3   1.9    6.4e-06   26.4   0.0    3.7  3  DUF11            Domain of unknown function DUF11
    4.7e-07   29.0  15.6    5.8e-05   22.1   0.2    3.3  4  BatD             Oxygen tolerance
     0.0001   22.4   4.1      0.047   13.8   0.1    3.6  3  Cupredoxin_1     Cupredoxin-like domain
     0.0016   18.7   1.1        5.9    7.1   0.0    3.8  3  bMG10            Bacterial Alpha-2-macroglobulin MG10 domain
     0.0019   18.4  15.0       0.59   10.4   0.5    3.8  3  CARDB            CARDB
  ------ inclusion threshold ------
      0.022   15.0   7.8        1.9    8.8   0.2    4.4  5  DUF3127          Domain of unknown function (DUF3127)
      0.023   15.0   0.1        3.8    7.8   0.0    3.6  3  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
       0.09   12.6   0.0       0.09   12.6   0.0    3.8  5  Motile_Sperm     MSP (Major sperm protein) domain
       0.11   12.7   7.2       0.41   10.9   0.2    3.6  4  SdrD_B           SdrD B-like domain
       0.13   12.4  17.1        0.7   10.1   0.5    5.0  4  Top6b_C          Type 2 DNA topoisomerase 6 subunit B C-termi


Domain annotation for each model (and alignments):
>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.015        26       9      36 ..     222     249 ..     217     300 .. 0.89
   2 !    7.0   0.1    0.0039         7       9      51 ..     335     376 ..     309     409 .. 0.73
   3 !   26.4   0.0   3.6e-09   6.4e-06       1      83 [.     436     509 ..     436     517 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.015
                             DUF11   9 evrpGdtvtytltvtNtgpasangvvvt 36 
                                         +p  t++y + v N g+ + ++v+++
  gi|298674058|ref|YP_003725808.1| 222 SYNPNKTIEYKVLVENIGNIPVQEVKLE 249
                                       57999*******************9986 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0039
                             DUF11   9 evrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsas 51 
                                       + +  dtv++ l+  N g ++   + vtD  P +++++ + + 
  gi|298674058|ref|YP_003725808.1| 335 RENKNDTVQVSLIIHNMGKSKK-LLDVTDEIPDSFTLIGNDSL 376
                                       557789*************999.9********99998866555 PP

  == domain 3  score: 26.4 bits;  conditional E-value: 3.6e-09
                             DUF11   1 ltKtvdksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvr 77 
                                       ++K+ ++  ++   +v++t+   Ntg++ a ++  tD  P+gl++vs+  +       +s g++ + + + +++t++
  gi|298674058|ref|YP_003725808.1| 436 VDKSLSSDSINISNNVEVTINIENTGNRIA-NISFTDSIPEGLNLVSGDLQ-------WS-GKVGPKADKEITYTIT 503
                                       68999999**********************.*******************9.......44.8999999999999988 PP

                             DUF11  78 vtrtaa 83 
                                        + +++
  gi|298674058|ref|YP_003725808.1| 504 TNESGR 509
                                       887775 PP

>> BatD  Oxygen tolerance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.6      0.35   6.3e+02     102     177 ..      62     130 ..      45     183 .. 0.60
   2 ?   -2.1   0.0      0.72   1.3e+03      61      97 ..     213     249 ..     198     270 .. 0.67
   3 !   22.1   0.2   3.2e-08   5.8e-05      23     107 ..     338     422 ..     331     432 .. 0.80
   4 !   16.4   1.2   1.7e-06    0.0031      10     114 ..     434     537 ..     427     562 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.35
                              BatD 102 tyksnpitikVlkseasqsssaisdedlflraevskksvYvqeqvlvtlklytrvnvnledgkl..pdlegflveel 176
                                       +  +np + +Vl       ++++ +e+lf+++++++++ Y+     +++k++  ++ n++ ++l    ++ ++v++ 
  gi|298674058|ref|YP_003725808.1|  62 NPGTNPPSANVLI-----YQNNVYKEKLFFDTKANSENTYEDD---LKIKIHDINRNNVS-VELyrHVYKKAWVKDT 129
                                       4444444444432.....3445556678888888888888764...45555544222333.2223455566666666 PP

                              BatD 177 g 177
                                       +
  gi|298674058|ref|YP_003725808.1| 130 E 130
                                       6 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.72
                              BatD  61 stqiinGkssssssktwtytLapkkeGtltIpaatie 97 
                                       s+ i n+k s + +kt++y +  ++ G++ + ++++e
  gi|298674058|ref|YP_003725808.1| 213 SIDILNNKDSYNPNKTIEYKVLVENIGNIPVQEVKLE 249
                                       4556666666666666666666666666666665554 PP

  == domain 3  score: 22.1 bits;  conditional E-value: 3.2e-08
                              BatD  23 vgetfrLtftvngas...gepdfsapslekdfevlsg.sqssstqiinGkssssssktwtytLapkkeGtltIpaat 95 
                                       +++t+++++++ +     +  d++ +++++ f+++++ s ++s+ ++n +s++  +   ty ++p+k+G++t+++a 
  gi|298674058|ref|YP_003725808.1| 338 KNDTVQVSLIIHNMGkskKLLDVT-DEIPDSFTLIGNdSLEKSV-VVNSDSTK--K--VTYQIKPTKPGRYTLKPAV 408
                                       799999999999987644455666.58999*******6666666.99999998..6..889**************** PP

                              BatD  96 iev..dgktyksnp 107
                                       +e+  +g++y++++
  gi|298674058|ref|YP_003725808.1| 409 LEWvdEGNKYTTES 422
                                       *9987788888775 PP

  == domain 4  score: 16.4 bits;  conditional E-value: 1.7e-06
                              BatD  10 aeftasvdknevevgetfrLtftvngas.gepdfsap.slekdfevlsgsqssstqiinGkssssssktwtytLapk 84 
                                       +++  s++++ +++ +++++t+ ++++  +  ++s+  s++++++++sg    ++    Gk+  +  k +tyt+  +
  gi|298674058|ref|YP_003725808.1| 434 VQVDKSLSSDSINISNNVEVTINIENTGnRIANISFTdSIPEGLNLVSGDL--QW---SGKVGPKADKEITYTITTN 505
                                       567778999999999*********999875555555548999*****9973..34...3555555556699****** PP

                              BatD  85 keGtltIpaatiev..dgktyksnpitikVlk 114
                                       ++G++ +p++++ +  ++ +  sn+  + V k
  gi|298674058|ref|YP_003725808.1| 506 ESGRYVLPELEVDInnNQTKAISNSAILYVDK 537
                                       ************99333445557777777744 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       3.8   6.8e+03      28      36 ..     219     227 ..     206     276 .. 0.62
   2 !    7.9   0.1    0.0018       3.2      44      90 ..     343     404 ..     335     410 .. 0.76
   3 !   13.8   0.1   2.6e-05     0.047      28      88 ..     436     510 ..     407     514 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.8
                      Cupredoxin_1  28 kdggfePsk 36 
                                       ++++++P+k
  gi|298674058|ref|YP_003725808.1| 219 NKDSYNPNK 227
                                       444444443 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0018
                      Cupredoxin_1  44 kvklkiknkdktpeefesed.............lgeekvlapgkttti..tiaplkpGeYef 90 
                                       +v+l i+n +k+ + + ++d             l+++ v+++++t+++  +i+p kpG+Y++
  gi|298674058|ref|YP_003725808.1| 343 QVSLIIHNMGKSKKLLDVTDeipdsftligndsLEKSVVVNSDSTKKVtyQIKPTKPGRYTL 404
                                       5778888888886666665556667777777889999999988776652279********85 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 2.6e-05
                      Cupredoxin_1  28 kdggfePskievkagekvklkiknkdktpeefesed............lgeekvlapgkttti..tiaplkpGeY 88 
                                        d++ + ++i++  + +v+++i+n++++ ++++++d            l+ + ++ p++ ++i  ti++ + G+Y
  gi|298674058|ref|YP_003725808.1| 436 VDKSLSSDSINISNNVEVTINIENTGNRIANISFTDsipeglnlvsgdLQWSGKVGPKADKEItyTITTNESGRY 510
                                       37899***********************77777777666666666666888888877655554226778888887 PP

>> bMG10  Bacterial Alpha-2-macroglobulin MG10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.5   2.6e+03      23      39 ..     134     151 ..      80     214 .. 0.66
   2 !    6.9   0.0    0.0037       6.6     100     124 ..     386     410 ..     373     412 .. 0.89
   3 !    7.1   0.0    0.0033       5.9      17      71 ..     442     494 ..     419     517 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.5
                             bMG10  23 lkvGdkvr.vrltvttpr 39 
                                       +++Gd+++  + tv++++
  gi|298674058|ref|YP_003725808.1| 134 FHKGDELKnGNYTVQVKE 151
                                       444444431233333333 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0037
                             bMG10 100 gtytfeylvravtpGtfsvppakae 124
                                        t +++y+++ + pG++++ pa +e
  gi|298674058|ref|YP_003725808.1| 386 STKKVTYQIKPTKPGRYTLKPAVLE 410
                                       57789****************9876 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0033
                             bMG10  17 sksdaklkvGdkvrvrltvt.tprdleyvaledplPAGlepvnpslgtesesaeey 71 
                                       s   ++++  + v+v+++++ t +++ ++   d++P Gl++v  +l+ + + + ++
  gi|298674058|ref|YP_003725808.1| 442 S---DSINISNNVEVTINIEnTGNRIANISFTDSIPEGLNLVSGDLQWSGKVGPKA 494
                                       2...26899999********888899***************998887655555444 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.5   0.00033      0.59       2      45 ..     210     253 ..     209     284 .. 0.88
   2 !    6.4   0.4    0.0058        10      14      82 ..     335     406 ..     325     425 .. 0.80
   3 !    8.6   2.5    0.0012       2.2       8      88 ..     438     521 ..     434     526 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00033
                                       --EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEET CS
                             CARDB   2 pDLtvtntlnpseafvgeentitvtvkNqGtaasgatkvalyld 45 
                                       pD+ ++   n ++ +++++++ +v v+N G++  +++k++   +
  gi|298674058|ref|YP_003725808.1| 210 PDFSIDILNNKDSYNPNKTIEYKVLVENIGNIPVQEVKLESSSN 253
                                       9******************************9999998876655 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0058
                                       EEETTSEEEEEEEEEE-SSS-.EEEEEEEEEETTEEEEEEEE...SEE-CTEEEEEEEEEE-S-S-CEEEEEE CS
                             CARDB  14 eafvgeentitvtvkNqGtaa.sgatkvalyldgelvgtvtv...psLaagesttvsftwtteategevtltv 82 
                                         ++++++++++ ++N G+ +   +++ ++  + +l g+ ++     ++++++++v+++++++ ++g +tl+ 
  gi|298674058|ref|YP_003725808.1| 335 RENKNDTVQVSLIIHNMGKSKkLLDVTDEIPDSFTLIGNDSLeksVVVNSDSTKKVTYQIKPT-KPGRYTLKP 406
                                       5567888999999*****998788999999888888877777665568999999999999998.*****9974 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0012
                                       EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEE...SEE-CTEEEEEEEEEE-S-S-CEEE.E CS
                             CARDB   8 ntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtv...psLaagesttvsftwtteategevt.l 80 
                                       ++l+ ++ +  +++++t++++N+G+  +  + ++ + +g +  + ++    ++ +++ +++++t+tt+ ++g +   
  gi|298674058|ref|YP_003725808.1| 438 KSLSSDSINISNNVEVTINIENTGNRIANISFTDSIPEGLNLVSGDLqwsGKVGPKADKEITYTITTN-ESGRYVlP 513
                                       566777888899*************99877777777777666444444578999*************9.99999967 PP

                                       EEEESTT- CS
                             CARDB  81 tvvvDpdn 88 
                                       ++ vD +n
  gi|298674058|ref|YP_003725808.1| 514 ELEVDINN 521
                                       88888877 PP

>> DUF3127  Domain of unknown function (DUF3127)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       4.6   8.2e+03      36      36 ..      97      97 ..      71     128 .. 0.49
   2 ?    8.8   0.2    0.0011       1.9      16      42 ..     148     172 ..     139     192 .. 0.80
   3 ?    4.2   0.0     0.029        52      56      78 ..     286     308 ..     279     314 .. 0.89
   4 ?   -2.5   0.0       3.4   6.2e+03      39      66 ..     322     348 ..     310     350 .. 0.72
   5 ?    3.6   0.0     0.044        79      39      67 ..     429     458 ..     387     467 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.6
                           DUF3127 36 p 36
                                      +
  gi|298674058|ref|YP_003725808.1| 97 E 97
                                      1 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0011
                           DUF3127  16 ssknGefkkrefvleteeqYpkkicle 42 
                                       + k  efkk+e+vle+++ Y+k+i  +
  gi|298674058|ref|YP_003725808.1| 148 QVK--EFKKKEVVLEVSNPYKKNIFTD 172
                                       444..8****************99765 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.029
                           DUF3127  56 vgdevkvsfnlegrewngkyfns 78 
                                       +g+++  sf ++gr + g+ +++
  gi|298674058|ref|YP_003725808.1| 286 IGENMATSFVVSGRDYRGNTYTD 308
                                       7999**************99997 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 3.4
                           DUF3127  39 iclevvgdkideldklqvgdevkvsfnl 66 
                                       i  e++++ ++++   + +d+v+vs+ +
  gi|298674058|ref|YP_003725808.1| 322 IEKEISKEDVTLYR-ENKNDTVQVSLII 348
                                       44566777777777.7889999999765 PP

  == domain 5  score: 3.6 bits;  conditional E-value: 0.044
                           DUF3127  39 iclevvg.dkideldklqvgdevkvsfnle 67 
                                       ++ + v+ dk  + d++++ ++v+v++n+e
  gi|298674058|ref|YP_003725808.1| 429 VHSSWVQvDKSLSSDSINISNNVEVTINIE 458
                                       44456677999999**************98 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0       0.2   3.5e+02      34      56 ..     129     151 ..     110     169 .. 0.71
   2 ?    0.1   0.0      0.54   9.7e+02      28      52 ..     390     404 ..     372     427 .. 0.67
   3 ?    7.8   0.0    0.0021       3.8      25      46 ..     495     516 ..     490     525 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.2
                   CarboxypepD_reg  34 tdadGafrlrglppgtysvtvsa 56 
                                       t+++G  + + l+ g+y+v+v  
  gi|298674058|ref|YP_003725808.1| 129 TERKGFHKGDELKNGNYTVQVKE 151
                                       777888888999********954 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.54
                   CarboxypepD_reg  28 tvastttdadGafrlrglppgtysv 52 
                                       ++          ++++  +pg+y++
  gi|298674058|ref|YP_003725808.1| 390 VT----------YQIKPTKPGRYTL 404
                                       34..........5555555555554 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0021
                   CarboxypepD_reg  25 dtgtvastttdadGafrlrglp 46 
                                       d++ +++ tt+++G++ l+ l+
  gi|298674058|ref|YP_003725808.1| 495 DKEITYTITTNESGRYVLPELE 516
                                       67789*************9987 PP

>> Motile_Sperm  MSP (Major sperm protein) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       4.7   8.5e+03      28      46 ..      78      96 ..      77     109 .. 0.70
   2 ?   -1.0   0.2      0.85   1.5e+03      11      34 ..     147     169 ..     141     170 .. 0.76
   3 ?   -1.0   0.6      0.89   1.6e+03      17      84 ..     226     296 ..     215     313 .. 0.70
   4 ?   12.6   0.0     5e-05      0.09      15      51 ..     371     407 ..     363     419 .. 0.89
   5 ?   -3.4   0.0       4.9   8.9e+03      31      47 ..     495     511 ..     492     514 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 4.7
                                      E-SSSSEEEEEEES-TTTE CS
                      Motile_Sperm 28 NtskkrvaFkvkttapkky 46
                                      N++k+++ F  k ++ + y
  gi|298674058|ref|YP_003725808.1| 78 NVYKEKLFFDTKANSENTY 96
                                      6666666666666666655 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.85
                                       EEESSTSSHEEEEEEEEE-SSSSE CS
                      Motile_Sperm  11 vfaaelnkqgtsklklkNtskkrv 34 
                                       v+ +e+ k+++  l++ N++kk++
  gi|298674058|ref|YP_003725808.1| 147 VQVKEF-KKKEVVLEVSNPYKKNI 169
                                       555556.5568999******9987 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.89
                                       SSHEEEEEEEEE-SSSSEE.EEEEES-TTTEEEESSE..EEETTTCEEEEEEEEESSSSSTTSTCCEEEEE CS
                      Motile_Sperm  17 nkqgtsklklkNtskkrva.FkvkttapkkyrvrPnv..Giikpgesveitvtlkpldeepsekkkdkfvi 84 
                                       nk+ ++k+ + N+ + +v  +k  +++++  + +P++   +i+ ++s  + v+  p+++  +e+    fv+
  gi|298674058|ref|YP_003725808.1| 226 NKTIEYKVLVENIGNIPVQeVKLESSSNNGKIAQPVMvrNVIDQNKSKIFPVMIDPPNNPIGENMATSFVV 296
                                       44566666677776665533777777777777777653368999999999999888777666655666665 PP

  == domain 4  score: 12.6 bits;  conditional E-value: 5e-05
                                       STSSHEEEEEEEEE-SSSSEEEEEEES-TTTEEEESS CS
                      Motile_Sperm  15 elnkqgtsklklkNtskkrvaFkvkttapkkyrvrPn 51 
                                        +n++ ++++ +   s+k+v +++k t+p +y+ +P+
  gi|298674058|ref|YP_003725808.1| 371 IGNDSLEKSVVVNSDSTKKVTYQIKPTKPGRYTLKPA 407
                                       567778899999***********************97 PP

  == domain 5  score: -3.4 bits;  conditional E-value: 4.9
                                       SSSEEEEEEES-TTTEE CS
                      Motile_Sperm  31 kkrvaFkvkttapkkyr 47 
                                       +k + + + t+   +y+
  gi|298674058|ref|YP_003725808.1| 495 DKEITYTITTNESGRYV 511
                                       67889999999888886 PP

>> SdrD_B  SdrD B-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   0.00023      0.41      25      66 ..     110     151 ..      94     178 .. 0.88
   2 ?   -3.1   0.1       4.9   8.8e+03      90     108 ..     323     342 ..     295     346 .. 0.54
   3 ?    0.2   0.1      0.49   8.7e+02      49      93 ..     391     430 ..     374     464 .. 0.53
   4 ?    3.1   0.0     0.059   1.1e+02      35      55 ..     495     515 ..     483     526 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00023
                            SdrD_B  25 sgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVefta 66 
                                       ++v V+L+++  +++    T+ +G  k ++l++G+Y+V++++
  gi|298674058|ref|YP_003725808.1| 110 NNVSVELYRHVYKKAWVKDTERKGFHKGDELKNGNYTVQVKE 151
                                       5799*****999999999*********************976 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.9
                            SdrD_B  90 atg.ltktvtlasgesneti 108
                                        ++   ++vtl  +++n t+
  gi|298674058|ref|YP_003725808.1| 323 EKEiSKEDVTLYRENKNDTV 342
                                       33323445555555555554 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.49
                            SdrD_B  49 kYkFtnltpGeYkVeftapagytvtakkaGsddaldSdadpatgl 93 
                                       +Y+ +  +pG+Y+++ +      ++  ++G+  +++S  ++ +  
  gi|298674058|ref|YP_003725808.1| 391 TYQIKPTKPGRYTLKPAV-----LEWVDEGNKYTTESSEKEIDVH 430
                                       455555555555544322.....1122334444444433333333 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.059
                            SdrD_B  35 kgevvatttTdasGkYkFtnl 55 
                                       ++e++ t tT++sG+Y   +l
  gi|298674058|ref|YP_003725808.1| 495 DKEITYTITTNESGRYVLPEL 515
                                       4555689*********86665 PP

>> Top6b_C  Type 2 DNA topoisomerase 6 subunit B C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.4       2.2   3.9e+03      63      63 ..     130     130 ..      78     169 .. 0.55
   2 ?   -2.3   0.1       2.7   4.8e+03      29      45 ..     254     271 ..     227     284 .. 0.58
   3 ?    9.7   0.7    0.0005      0.89      18      57 ..     331     368 ..     320     415 .. 0.69
   4 ?   10.1   0.5   0.00039       0.7      28      98 ..     448     507 ..     433     519 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.2
                                       - CS
                           Top6b_C  63 e 63 
                                       e
  gi|298674058|ref|YP_003725808.1| 130 E 130
                                       2 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.7
                                       S-.EEEEEEE-------- CS
                           Top6b_C  29 dg.vevslkvkNfsdkke 45 
                                       +g ++  ++v+N  d+++
  gi|298674058|ref|YP_003725808.1| 254 NGkIAQPVMVRNVIDQNK 271
                                       333444455555555444 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0005
                                       EEEEEEE--SSS-EEEEEEE---------EEE--EES--- CS
                           Top6b_C  18 vlvereveengdgvevslkvkNfsdkkeefelheilpaei 57 
                                       v+  re +  +d v+vsl ++N +++k+ +++++ +p + 
  gi|298674058|ref|YP_003725808.1| 331 VTLYRENK--NDTVQVSLIIHNMGKSKKLLDVTDEIPDSF 368
                                       45555444..457******************999777554 PP

  == domain 4  score: 10.1 bits;  conditional E-value: 0.00039
                                       SS-EEEEEEE---------EEE--EES-----------EEE-SSSEEE-EEE---TT-EEEE----SS-GG CS
                           Top6b_C  28 gdgvevslkvkNfsdkkeefelheilpaeieeaspeakvvemdneydlkWelsvsageskvleYsvdseae 98 
                                       +++vev+++++N +++ ++++ ++ +p   + +s            dl+W+ +v+++  k+++Y+++++++
  gi|298674058|ref|YP_003725808.1| 448 SNNVEVTINIENTGNRIANISFTDSIPEGLNLVS-----------GDLQWSGKVGPKADKEITYTITTNES 507
                                       46799*****************999998887776...........37999**************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (585 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1004  (0.0559987); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.68u 0.29s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 3679.83
//
Query:       gi|298674059|ref|YP_003725809.1|  [L=271]
Description: mechanosensitive ion channel protein MscS [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-48  163.3   1.1    7.2e-48  162.9   1.1    1.2  1  MS_channel       Mechanosensitive ion channel
    0.00019   21.3   0.2    0.00019   21.3   0.2    2.3  2  TM_helix         Conserved TM helix
  ------ inclusion threshold ------
       0.74    9.1   4.0        1.3    8.4   4.0    1.4  1  TssN             Type VI secretion system, TssN
        4.6    6.3  12.0        6.6    5.7  12.0    1.2  1  ABC2_membrane_3  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.9   1.1   1.6e-51   7.2e-48       3     206 .]      61     258 ..      59     258 .. 0.97

  Alignments for each domain:
  == domain 1  score: 162.9 bits;  conditional E-value: 1.6e-51
                                       HHHHHHHHHHHHHHHHTTT--SCCHHHHH.HHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEE CS
                        MS_channel   3 ilkiliivvgilivlsllgvnvsallavl.GalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVed 78 
                                        l+il++v++il++   lg+ v++++ +l +++gl lg++++d++ nl aGi + + +p++ +D+v+i+++ G+Ve 
  gi|298674059|ref|YP_003725809.1|  61 FLSILLYVLVILAFAGALGFAVGSVFLGLsAVIGLILGFGMQDTLTNLTAGIWIATLRPIDKDDYVTINGMFGKVEA 137
                                       5789*****************887655542789******************************************** PP

                                       E-SSEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS- CS
                        MS_channel  79 iglrttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdke 155
                                       +g+ +t i t+d++ +tiPn+ ++ s+++N +r ++ rr++v++gv y++d   l+k++++  +++k++++vl+d++
  gi|298674059|ref|YP_003725809.1| 138 VGMMATEILTPDNQFITIPNQLVWGSAVINDTR-MPIRRARVDVGVSYDTD---LDKAIQVAFDVMKNNSMVLDDPA 210
                                       *********************************.*****************...*********************** PP

                                       EEEEEEEE-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT--- CS
                        MS_channel 156 llvvldefgdsslnfevrvfvktvvpeeylsvqseinlrikkileeegiei 206
                                       + v+  e+gdss+n+++r+++++   e+ + v+ +i+ +i+k+ ++egiei
  gi|298674059|ref|YP_003725809.1| 211 PAVITSELGDSSVNLQLRAWANN---EDVWTVKWDITSEIFKAYRKEGIEI 258
                                       ***********************...***********************97 PP

>> TM_helix  Conserved TM helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.2   4.2e-08   0.00019      13      46 ..      16      49 ..       6      51 .. 0.91
   2 ?   -3.5   2.9       2.3     1e+04      27      27 ..      75      75 ..      54     107 .. 0.62

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 4.2e-08
                                      THSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                          TM_helix 13 flPnLvgAilILlvGwiiAkfvsrlvtkllaktg 46
                                      f+  Lv Ai++Ll G+i A+++  l +k l+kt+
  gi|298674059|ref|YP_003725809.1| 16 FVSDLVFAIAVLLAGFIFARILISLFNKGLKKTH 49
                                      7889****************************98 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.3
                                      H CS
                          TM_helix 27 G 27
                                      +
  gi|298674059|ref|YP_003725809.1| 75 A 75
                                      2 PP

>> TssN  Type VI secretion system, TssN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   4.0   0.00028       1.3      63     121 ..      20      77 ..       4     110 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00028
                              TssN  63 illqilylllGilhlylllkkffkelkekkilfeilltlivillglvlfvlvfnllsel 121
                                       +++ i++ll G++++++l+  f+k lk+++ l  +++ +++ +l+++l+vlv   + + 
  gi|298674059|ref|YP_003725809.1|  20 LVFAIAVLLAGFIFARILISLFNKGLKKTH-LPGLVIEFLSRFLSILLYVLVILAFAGA 77 
                                       5778999*********************99.5555556666666666666665555444 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7  12.0    0.0015       6.6     218     279 ..      23      98 ..      12     123 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0015
                   ABC2_membrane_3 218 llqlllilllafgl.............gipfg..nlglllllfllfglayialgyllsslfknsetaqilifivill 279
                                       ++ +ll+  ++f++              +p    ++++ +l +ll+ l+++a++ +l++++ +   + ++++ +il 
  gi|298674059|ref|YP_003725809.1|  23 AIAVLLAG-FIFARilislfnkglkktHLPGLviEFLSRFLSILLYVLVILAFAGALGFAVGSVFLGLSAVIGLILG 98 
                                       22222222.22222333345558887744444556677778888888888888888888888887777766666552 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1712.15
//
Query:       gi|298674060|ref|YP_003725810.1|  [L=378]
Description: 3-isopropylmalate dehydrogenase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-93  312.4   0.0    4.4e-93  312.2   0.0    1.0  1  Iso_dh    Isocitrate/isopropylmalate dehydrogenase


Domain annotation for each model (and alignments):
>> Iso_dh  Isocitrate/isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  312.2   0.0   2.5e-97   4.4e-93       1     348 []       5     370 ..       5     370 .. 0.97

  Alignments for each domain:
  == domain 1  score: 312.2 bits;  conditional E-value: 2.5e-97
                                       EEEEEEESTTHHHHHHHHHHHHHHHHHHHT-EEEEEE---THHHHHHHSSSS-HHHHHHHHHSSEEEEEE---CS.S CS
                            Iso_dh   1 kiallegdgiGpevveaalkvlkaakekaglelefeevdvGgaaidetgeplpeetleaikeadvvllgavgtpk.e 76 
                                       k+++++gdg+Gpe++++  kv++aa ek+g ++++ e+  G+  + etge l+e+tl+ + +++ + lg++g p  +
  gi|298674060|ref|YP_003725810.1|   5 KVPVIPGDGVGPEIIAEGRKVIDAAGEKHGFDVDWIEFPNGADHYLETGELLSEDTLKELSNYKSIYLGSIGDPRvA 81 
                                       699************************************************************************76 PP

                                       SSSSHHHHHHHHHHHTTEEEEEEEEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEET.......... CS
                            Iso_dh  77 kevrpengLlaLrkeldlfanlrpvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkg.......... 143
                                        +v  +  Ll+ r  +d + nlrpvk++   +v +plk+++++++d+ +vRe+t++ Y+g+   +k+          
  gi|298674060|ref|YP_003725810.1|  82 PGVLEKGILLKARFYFDQYINLRPVKLL--DGVWTPLKNKNPKDIDFTVVRENTEDFYIGIGGRAKKgiseeelevt 156
                                       66666667999*****************..89*****************************99988889******** PP

                                       ............TG.GGGEEEEEEEEEHHHHHHHHHHHHHHHHHT.TTSEEEEEESTTTTHHHH.HHHHHHHHHHCC CS
                            Iso_dh 144 ............sifteevavdtklyseeeieriaraafelAlkr.gkkkvtlvdKanvlksse.lwrkiveevaee 206
                                                   ++ +ee a+++ ++s+e+++r++++af+lA+kr ++k+v +vdKanvl+    +wr++++++ e 
  gi|298674060|ref|YP_003725810.1| 157 rsmystkfgldiETDSEEIAYQIGMISKEGTRRVIKYAFDLAMKRnKDKHVASVDKANVLSDIYgFWREQFNDISE- 232
                                       **********9755789****************************77899**********98877***********. PP

                                       TTTTSEEEEEEHHHHHHHHHHSGGGGSEEEE-HHHHHHHHHHHHHHTTSGCC-EEEEEETSS-EEEEESS---CCCT CS
                            Iso_dh 207 eypdielehqlvDsaamqlvkspkqfdVivtkNlfGDilSDeaaalvGslGllpSaslgekkvaifEavHGsapdia 283
                                       +yp+i  +  +vD+++m   k+p+ +dV+vt+N+fGDi+ D+ a++ G+lGl+p+ +++++++ +fE++HGsap++ 
  gi|298674060|ref|YP_003725810.1| 233 NYPEIDTDFNYVDAITMWFAKNPEWYDVVVTPNMFGDIITDLGAMIQGGLGLAPGGNINPEGTSMFEPIHGSAPKYK 309
                                       ***************************************************************************** PP

                                       TSS-S-THHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHHH.TSCCHHHCTTSTCCCHHHHHHHHH CS
                            Iso_dh 284 gkdkaNpiavilSaalmLryslgleeaAdkiekAvekvlea.givTkDlageaakevstsefgdav 348
                                       g+dk+Npia+i + +++    lg++ea+++i +A+ek++++ +i+T+D++g++    +tse+gd++
  gi|298674060|ref|YP_003725810.1| 310 GQDKVNPIATIWAGSMLVDQ-LGETEASNDILSAIEKSIAEnKIKTYDMGGSS----KTSEVGDNI 370
                                       *******************9.******************9989**********....******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2556.91
//
Query:       gi|298674061|ref|YP_003725811.1|  [L=160]
Description: 3-isopropylmalate dehydratase small subunit [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-17   64.7   0.2    2.1e-17   63.7   0.1    1.6  2  Aconitase_C    Aconitase C-terminal domain
     0.0015   18.2   0.2      0.018   14.7   0.2    2.2  1  Aconitase_2_N  Aconitate hydratase 2 N-terminus


Domain annotation for each model (and alignments):
>> Aconitase_C  Aconitase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.7   0.1   2.3e-21   2.1e-17      66     127 ..      44     102 ..      27     106 .. 0.85
   2 ?   -3.4   0.0       1.3   1.2e+04      45      50 ..     126     131 ..     110     143 .. 0.52

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 2.3e-21
                                       HHHHHHTT--EEEE--SSBTBS---THHHHHHHHTTEEEEEES-B-HHHHHHHHHTT-EEEE CS
                       Aconitase_C  66 aerykkegaklvviagknfGeGSSRehAAkalrllGikaviaeSFerIfennliknglLple 127
                                       ae+ k  + +++v++  nfG+GSSRehA++al+   i  via+SF+rIf +n+i+ g+  le
  gi|298674061|ref|YP_003725811.1|  44 AENVK--ENDIIVAG-SNFGCGSSREHAPLALKGTKIGCVIAKSFARIFFRNAINIGVPLLE 102
                                       45555..77788777.*****************************************86555 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.3
                                       TSBBSE CS
                       Aconitase_C  45 ekrank 50 
                                       +k  n+
  gi|298674061|ref|YP_003725811.1| 126 NKTKNE 131
                                       222222 PP

>> Aconitase_2_N  Aconitate hydratase 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.2     2e-06     0.018      93     167 ..      77     152 ..       4     157 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2e-06
                                       --EEEEEEE-HHHHHHHHHTT-EEEE-.--TT--TT-EEEEETTTTEEEETT--EEEE---S-TCHHHHHHHTSHH CS
                     Aconitase_2_N  93 ggvvlGgkiaPiFfntvedsGalpiea.dvskletGdvieikpkegkikkeegevvsefklkpetlldevraggri 167
                                        g v+  + a iFf  + + G   +e+ + +k+e+ d ie++  +g i++++++   + +  p+ + + v agg i
  gi|298674061|ref|YP_003725811.1|  77 IGCVIAKSFARIFFRNAINIGVPLLECsETDKIEEEDEIEVELSTGVIENKTKNEKYQATPLPDFVREIVDAGGLI 152
                                       4677888899****999999987777636889******************99998888888999999******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1141.99
//
Query:       gi|298674062|ref|YP_003725812.1|  [L=398]
Description: major facilitator superfamily protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.5e-57  193.6  82.5    1.6e-47  162.2  47.1    2.0  2  MFS_1       Major Facilitator Superfamily
      7e-11   41.6  42.1    1.3e-07   30.8  18.1    3.7  4  Sugar_tr    Sugar (and other) transporter
    5.1e-05   22.3  35.2      0.019   13.8  13.4    3.5  2  MFS_1_like  MFS_1 like family


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.2  47.1   2.6e-51   1.6e-47       1     349 [.      17     354 ..      17     355 .. 0.88
   2 !   45.2  27.5     1e-15     6e-12       2     171 ..     217     388 ..     216     397 .. 0.85

  Alignments for each domain:
  == domain 1  score: 162.2 bits;  conditional E-value: 2.6e-51
                             MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgll 77 
                                       l++++f+++l++  l+p+lp  ++edl+is+s +g++++++ +++a++++p+G +sdrfGr+ +++ g+++f+ g+ 
  gi|298674062|ref|YP_003725812.1|  17 LSIGTFCVFLGILSLIPLLP-DISEDLNISKSHLGWVAGTFLIFMALLQVPFGLISDRFGRKVLIFSGIFIFGTGVG 92 
                                       5799****************.******************************************************66 PP

                             MFS_1  78 lllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravf 154
                                       +l+fas++ +ll++r+++G ga+++f ++ +++ d+f+ +ergra+++l++++++G+i g+ +gg++   +gWr vf
  gi|298674062|ref|YP_003725812.1|  93 ILSFASNFITLLFARAVSGTGAAIFFQTSFTMVGDMFKYQERGRAMSVLAVATGFGTISGYSVGGIFGGIYGWREVF 169
                                       666977766******************************************************************** PP

                             MFS_1 155 yilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvp.awkallkdpvlwillialllfffgfsglltll 230
                                       ++la++++++  l   l+++e + + ++++++        ++++  + +++k+  ++i lia+l+  ++  g+++ +
  gi|298674062|ref|YP_003725812.1| 170 MALAGIAFFVSFL--SLFMRETRVEITERKTTS-------NVLQfSFDMFRKRTIVFITLIAMLCD-MAAIGASYVV 236
                                       **********666..888888888888887777.......33332356677777444444444444.46666***** PP

                             MFS_1 231 plylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvl 307
                                       p++  ++ g++   ++gl++   a+v+  +a ++g++sd +gr+++l+++ +l+ +a+++l  ++++  ++++++ +
  gi|298674062|ref|YP_003725812.1| 237 PFF-AKDAGIT-TAITGLIFIPHAAVSSLGASFSGWVSDIVGRKKPLVIIAILGGCALFLLSQIPPI--SLIIAFNF 309
                                       **9.*******.899999999999999999*********************************9999..66666678 PP

                             MFS_1 308 vliGfglgfvfpsllalasdla...ppeeagtasglfntagslgg 349
                                       +++G+++g v+++  +l++d +     +  +t +g fn+++ lg+
  gi|298674062|ref|YP_003725812.1| 310 AFVGLCFGPVVTLTSTLLVDEVvkvDSSIIATTMGTFNMVRWLGS 354
                                       99***99999888888888888555558889*********99997 PP

  == domain 2  score: 45.2 bits;  conditional E-value: 1e-15
                             MFS_1   2 llaaflsalarsilgpalpl.alaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgll 77 
                                       +++++ + ++++++g+++   + a+d gi+ +  gl++   a+++++++ + G++sd +Gr++ l++ ++l + +l+
  gi|298674062|ref|YP_003725812.1| 217 FITLIAMLCDMAAIGASYVVpFFAKDAGITTAITGLIFIPHAAVSSLGASFSGWVSDIVGRKKPLVIIAILGGCALF 293
                                       677777777777777777777******************************************77777777777735 PP

                             MFS_1  78 lll.fasslw.lllvlrvlqGlgagalfpagaaliadwfpkeer...graigllsagfslGailgpllggllasslg 149
                                       ll+ + +++  ++++  ++ Gl+ g ++++  +l++d + k +    +  +g +++   lG++ gp+ +g++++ +g
  gi|298674062|ref|YP_003725812.1| 294 LLSqI-PPISlIIAFNFAFVGLCFGPVVTLTSTLLVDEVVKVDSsiiATTMGTFNMVRWLGSAAGPVMAGIFLEFYG 369
                                       55545.888877777788*******************9999865222688999999********************* PP

                             MFS_1 150 Wravfyilaivsllafvlflll 171
                                        r +f++l +  +++++l    
  gi|298674062|ref|YP_003725812.1| 370 TRIAFILLSVTVFVSVLL---A 388
                                       **************9885...3 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8  18.1   2.3e-11   1.3e-07      44     194 ..      45     189 ..       7     207 .. 0.92
   2 ?   -0.5   0.7     0.072   4.3e+02     310     354 ..     206     250 ..     198     255 .. 0.66
   3 !    9.5   6.7   6.7e-05       0.4      44     129 ..     246     330 ..     214     335 .. 0.72
   4 !   11.4   4.3   1.7e-05       0.1      19     102 ..     316     397 ..     299     398 .] 0.77

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 2.3e-11
                                       ...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHH CS
                          Sugar_tr  44 ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlas 120
                                       s++ +g++++ fl+  ++ ++ +gl++drfGRk  +  ++++f  g  +  +a    ++  l+++R ++G g+ ++ 
  gi|298674062|ref|YP_003725812.1|  45 SKSHLGWVAGTFLIFMALLQVPFGLISDRFGRKVLIFSGIFIFGTGVGILSFAS---NFITLLFARAVSGTGAAIFF 118
                                       78899******************************************9999999...9******************* PP

                                       HHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS--- CS
                          Sugar_tr 121 vlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllflPES 194
                                        ++ + ++ + + + Rg+ +s+  +a+ fG + ++ +g ++  + +   wr  +   + +a ++++l lf++E+
  gi|298674062|ref|YP_003725812.1| 119 QTSFTMVGDMFKYQERGRAMSVLAVATGFGTISGYSVGGIFGGIYG---WREVFMALAGIAFFVSFLSLFMRET 189
                                       *********************************************9...************************9 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.072
                                       HHHHS-SHHHHHHHHHHHHHHHHHHH...HHHHTTSS...CHHHHH CS
                          Sugar_tr 310 lvdrfGRRtllllGaagmaicfvilg.ivalllvakskaasivaiv 354
                                         d f +Rt++++ ++ m++ ++ +g   + ++ ak+ a    ai+
  gi|298674062|ref|YP_003725812.1| 206 SFDMFRKRTIVFITLIAMLCDMAAIGaSYVVPFFAKD-AGITTAIT 250
                                       5677888999999999999999999975555555553.22223333 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 6.7e-05
                                       ...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHH.HHHHHHH.H CS
                          Sugar_tr  44 ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRv.lvGigvG.l 118
                                       ++  +gli+    +++ +G+ f+g+++d++GRkk l+i+a+l   + +l   ++    + ++i+  + +vG++ G +
  gi|298674062|ref|YP_003725812.1| 246 TTAITGLIFIPHAAVSSLGASFSGWVSDIVGRKKPLVIIAILGGCALFLLSQIP---PISLIIAFNFaFVGLCFGpV 319
                                       345568899999999**********************99888766666666666...57777776542688888833 PP

                                       HHHHHHHHHHT CS
                          Sugar_tr 119 asvlvPmyisE 129
                                       ++ +++++++E
  gi|298674062|ref|YP_003725812.1| 320 VTLTSTLLVDE 330
                                       44445555555 PP

  == domain 4  score: 11.4 bits;  conditional E-value: 1.7e-05
                                       GGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH- CS
                          Sugar_tr  19 igafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaa 95 
                                        g+++tl++++    + k +ss  +  +++g +  +  +G+++G ++ag++ +++G + +++  +v ++++ +l + 
  gi|298674062|ref|YP_003725812.1| 316 FGPVVTLTSTLLVDEVVKVDSSIIA--TTMGTFNMVRWLGSAAGPVMAGIFLEFYGTRIAFILLSVTVFVSVLLAVG 390
                                       4566666666655555555554543..68899999999*************************************99 PP

                                       TTTTSS- CS
                          Sugar_tr  96 akgknsv 102
                                       +k+k+++
  gi|298674062|ref|YP_003725812.1| 391 IKEKREY 397
                                       9988776 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8  13.4   3.2e-06     0.019     261     384 ..      52     170 ..      39     171 .. 0.89
   2 !   12.9  14.8   6.1e-06     0.036     183     384 ..     169     375 ..     165     376 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.2e-06
                        MFS_1_like 261 llGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaavey 337
                                       ++G+++++ +++++p+      + +++G  +l++ +++++     ++++ +n+  +l++ + +g   ++++ +  + 
  gi|298674062|ref|YP_003725812.1|  52 VAGTFLIFMALLQVPFG----LISDRFGRKVLIFSGIFIFGTGVGILSFASNFITLLFARAVSGTGAAIFFQTSFTM 124
                                       56777888888888874....46789*************************************************** PP

                        MFS_1_like 338 vskiapksleatgqgllsglyfglGralGsliGGllwdlksaiflFr 384
                                       v +++  + +++ +++l+ +  g+G+ +G  +GG++ ++++ + +F+
  gi|298674062|ref|YP_003725812.1| 125 VGDMFKYQERGRAMSVLAVA-TGFGTISGYSVGGIFGGIYGWREVFM 170
                                       ****************9877.9************9989998888886 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 6.1e-06
                        MFS_1_like 183 lyvlaallvisllvvlilneteke..sklkvtkslqvllnilknpeviifllvalilgmswgiienFlflYL.kelg 256
                                       ++ la++   +++++l + et+ e  +     ++lq  + +++++ ++++ l+a+++ m  +i  +++  ++ k+ g
  gi|298674062|ref|YP_003725812.1| 169 FMALAGIAFFVSFLSLFMRETRVEitERKTTSNVLQFSFDMFRKRTIVFITLIAMLCDM-AAIGASYVVPFFaKDAG 244
                                       44455554444444456655554411444445566888888888888777777777777.5799999999999**** PP

                        MFS_1_like 257 asntllGsl.valgvvaeiplfffaeklleklGhvk.lliiallayilrfllyaii..enawlvlpievLhgisfgl 329
                                        ++ + G + ++  +v+++    f+ ++ +++G  k l+iia+l   + ++l++ i  +++ +++ + ++ g++fg 
  gi|298674062|ref|YP_003725812.1| 245 ITTAITGLIfIPHAAVSSLGA-SFSGWVSDIVGRKKpLVIIAILGGCA-LFLLSQIppISLIIAFNF-AFVGLCFGP 318
                                       *******76155666666665.7899*******987366666666555.555666625555444444.367899986 PP

                        MFS_1_like 330 lwa.aaveyvski..apksleatgqgllsglyfglGralGsliGGllwdlksaiflFr 384
                                       +   + +  v ++  +  s++at++g ++++ + lG+a G +++G++ + ++++++F 
  gi|298674062|ref|YP_003725812.1| 319 VVTlTSTLLVDEVvkVDSSIIATTMGTFNMVRW-LGSAAGPVMAGIFLEFYGTRIAFI 375
                                       6430333344443226789************88.*********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       910  (0.0507558); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.49
# Mc/sec: 2429.22
//
Query:       gi|298674063|ref|YP_003725813.1|  [L=472]
Description: hypothetical protein Metev_0085 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-15   56.7   0.0    1.7e-06   27.4   0.0    3.1  3  FAD_binding_2   FAD binding domain
    2.4e-14   53.2   0.2      1e-07   31.5   0.0    3.2  3  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      9e-13   48.1   1.6    8.8e-05   21.7   0.0    3.2  3  GIDA            Glucose inhibited division protein A
    1.3e-09   37.3   0.1    1.6e-06   27.1   0.0    2.4  2  HI0933_like     HI0933-like protein
    1.9e-06   27.3   0.1    3.8e-05   23.0   0.0    2.4  2  Thi4            Thi4 family
    2.3e-06   28.1   0.1      0.073   13.6   0.0    2.6  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    7.9e-06   25.7   0.0     0.0055   16.3   0.0    2.3  2  DAO             FAD dependent oxidoreductase
    8.6e-06   25.9   0.0    7.3e-05   22.9   0.0    2.4  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    2.4e-05   23.6   0.0    0.00024   20.3   0.0    2.0  2  Lycopene_cycl   Lycopene cyclase protein
    2.7e-05   23.6   0.0    4.3e-05   22.9   0.0    1.3  1  FAD_binding_3   FAD binding domain
    9.1e-05   22.0   0.0      0.014   14.8   0.0    2.2  2  FAD_oxidored    FAD dependent oxidoreductase
    0.00014   21.2   0.1      0.001   18.4   0.0    2.3  3  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
       0.06   12.6   0.0        2.3    7.4   0.0    2.7  3  Amino_oxidase   Flavin containing amine oxidoreductase
       0.12   11.2   0.1       0.26   10.1   0.0    1.5  2  Trp_halogenase  Tryptophan halogenase
       0.13   10.8   0.3          6    5.3   0.0    2.4  2  GDI             GDP dissociation inhibitor


Domain annotation for each model (and alignments):
>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   1.5e-09   1.7e-06       1      33 [.      15      47 ..      15      55 .. 0.94
   2 !   22.1   0.0   5.9e-08   7.1e-05     139     215 ..     158     225 ..     111     300 .. 0.83
   3 ?    3.8   0.0     0.021        25     376     402 ..     425     445 ..     415     458 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.5e-09
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqe 33
                                      Dvi+iGsG AG+ AA e+++++lkv+vve +q 
  gi|298674063|ref|YP_003725813.1| 15 DVIIIGSGPAGMFAANELSDQNLKVLVVEMGQD 47
                                      9****************************9885 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 5.9e-08
                                       HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG..........G CS
                     FAD_binding_2 139 tghallarlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgrallkellgaaa 215
                                       + +al+ r+ +++++ gv f+ +t++++++ve+++++G+v+      ++  i+++ + la g +g+++++     ++
  gi|298674063|ref|YP_003725813.1| 158 NTPALISRFKKGLDDKGVSFLLNTKVQDILVENNECRGIVLD-----NDKIIKSRYTMLAPGRVGGEWVNN----IV 225
                                       7899**************************************.....444566778888888888855433....34 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.021
                                       EEBETTSBESTTEEESSBTEEE-STCE CS
                     FAD_binding_2 376 vetdengrvldadgqpipGLYAaGeva 402
                                       v++++n++        i++LYAaG  +
  gi|298674063|ref|YP_003725813.1| 425 VQINQNMES------SIKNLYAAGDGT 445
                                       667777777......*********866 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   8.3e-11     1e-07       1      45 [.      14      58 ..      14      66 .. 0.93
   2 !    6.9   0.0    0.0026       3.1     179     237 ..     156     215 ..     133     247 .. 0.82
   3 !   11.1   0.0   0.00014      0.17     256     293 ..     423     457 ..     403     459 .. 0.79

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 8.3e-11
                                      CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllska 45
                                      +dv++iG+GpAG+ aa +l+ +++kv++ve ++ + n++c++ ++
  gi|298674063|ref|YP_003725813.1| 14 YDVIIIGSGPAGMFAANELSDQNLKVLVVEMGQDIENRQCSMDSV 58
                                      69***************************************9765 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0026
                                       TTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEE.EEETTSCEEEESEEEE-S-E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 179 raldkelsaaleealekeGvevklgtsvkeidgngekle.vvledgeeidadlvvvavGv 237
                                       +   ++l  + ++ l ++Gv + l+t+v++i  ++++ +  vl++ + i+ ++ ++a G+
  gi|298674063|ref|YP_003725813.1| 156 SDNTPALISRFKKGLDDKGVSFLLNTKVQDILVENNECRgIVLDNDKIIKSRYTMLAPGR 215
                                       55566777888999*****************99999888988888888999888888776 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00014
                                       TEEE--TTSBESSTTEEE-GGGCTECCSS--HHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 256 ggivvdeflrtnvpgiyaiGDvaggkggpelaqaAvqq 293
                                        +++++++++++++++ya+GD +   g  + +++A ++
  gi|298674063|ref|YP_003725813.1| 423 MQVQINQNMESSIKNLYAAGDGT---GLSRDIVNAAAT 457
                                       5899*****************99...777777777765 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.3   1.4e-05     0.017       1      41 [.      15      54 ..      15      78 .. 0.84
   2 !    9.8   0.0   0.00031      0.37     113     150 ..     178     215 ..     164     232 .. 0.86
   3 !   21.7   0.0   7.4e-08   8.8e-05     301     383 ..     376     464 ..     265     470 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.4e-05
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SSS CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldtiaelsCn 41
                                      dvi+iG G AG+ AA +++  ++kvl + +  ++i +  C+
  gi|298674063|ref|YP_003725813.1| 15 DVIIIGSGPAGMFAANELSDQNLKVLVV-EMGQDIENRQCS 54
                                      8************************988.556666666664 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00031
                                       EEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                              GIDA 113 iieeeveeliveekkvkgvvtedgetikakavviatGt 150
                                       +++ +v++++ve+++++g+v++++++ik++ + +a G 
  gi|298674063|ref|YP_003725813.1| 178 LLNTKVQDILVENNECRGIVLDNDKIIKSRYTMLAPGR 215
                                       67899******************************997 PP

  == domain 3  score: 21.7 bits;  conditional E-value: 7.4e-08
                                       EEET----S-HHHHHHHHTTSTT-TT--EEE--EEEEEEEE-GGGB-T.TSBBS.......SSBTEEE-CGGGTB.- CS
                              GIDA 301 ylvgfstslpeevqkevlrsipGLenaeivrpGyaieydyvdprqlln.tLetk.......kvkgLflAGqinGt.e 368
                                       ++  +s  +p+   + v+  i+GLe ++ + pG+a + + + +++++   ++++       ++k+L++AG+ +G   
  gi|298674063|ref|YP_003725813.1| 376 TPGDISMAMPH---RIVMDIIEGLETLNQIIPGVASDSTLLYAPEIKFyAMQVQinqnmesSIKNLYAAGDGTGLsR 449
                                       55666777777...4578899******************9999998866666642222222589***********66 PP

                                       SHHHHHHHHHHHHHH CS
                              GIDA 369 GYeEaaaqGllAGin 383
                                         + aaa+G++A++ 
  gi|298674063|ref|YP_003725813.1| 450 DIVNAAATGVMAARG 464
                                       699*********975 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   1.3e-09   1.6e-06       1      35 [.      14      48 ..      14      52 .. 0.93
   2 !    7.8   0.0   0.00094       1.1     107     163 ..     158     214 ..     132     227 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1.3e-09
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakkl 35
                                      +dvi+iG G+AG++aA ++++++ +Vl++e ++ +
  gi|298674063|ref|YP_003725813.1| 14 YDVIIIGSGPAGMFAANELSDQNLKVLVVEMGQDI 48
                                      59****************************98865 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00094
                                       -CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE--- CS
                       HI0933_like 107 kaedivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtG 163
                                       +   +++ ++k l+++gv++ l+t+v+++  e+++   + +++++ +++++++lA G
  gi|298674063|ref|YP_003725813.1| 158 NTPALISRFKKGLDDKGVSFLLNTKVQDILVENNECRGIVLDNDKIIKSRYTMLAPG 214
                                       56678899999************************999999*************977 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   3.2e-08   3.8e-05      12      49 ..       8      44 ..       3      48 .. 0.90
   2 ?    1.4   0.0      0.13   1.6e+02     106     142 ..     168     203 ..     141     215 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 3.2e-08
                                      HHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4 12 llkyaesDvvivGaGssGLtaayylakkpdlkvailer 49
                                      ++  +e Dv+i+G+G++G+ aa  l+ + +lkv+++e 
  gi|298674063|ref|YP_003725813.1|  8 IDPDVEYDVIIIGSGPAGMFAANELSDQ-NLKVLVVEM 44
                                      5666899*********************.******995 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.13
                                       HHHTSTTEEEEESEEEEEEEEETBTEEEEEEEEEHHH CS
                              Thi4 106 kvlqlanvkllnavaveDlivregegvaGvvinwtlv 142
                                       k l+  +v  l  + v D++v + ++ +G+v++   +
  gi|298674063|ref|YP_003725813.1| 168 KGLDDKGVSFLLNTKVQDILVEN-NECRGIVLDNDKI 203
                                       6677889999999********99.99*****987665 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   6.1e-05     0.073       2      35 ..      16      49 ..      15      62 .. 0.89
   2 !   11.9   0.0   0.00021      0.25      39      78 ..     159     198 ..     130     202 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.1e-05
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      v+++G+G  g+ +A++l++ + kV vve++  + 
  gi|298674063|ref|YP_003725813.1| 16 VIIIGSGPAGMFAANELSDQNLKVLVVEMGQDIE 49
                                      89***************************98876 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00021
                                       SHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEE CS
                         Pyr_redox  39 Deeaskilqeklekngievllntkveeiegsedgvesvkl 78 
                                        +++ +++++ l ++g+ +llntkv+ i  ++++ ++++l
  gi|298674063|ref|YP_003725813.1| 159 TPALISRFKKGLDDKGVSFLLNTKVQDILVENNECRGIVL 198
                                       55667789999******************99998888887 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   4.6e-06    0.0055       1      33 [.      15      49 ..      15      64 .. 0.86
   2 !    7.2   0.0    0.0028       3.3     144     201 ..     158     214 ..      90     309 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.6e-06
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                      dv+iiG+G +G+++A eL+ ++  V+++e+g ++ 
  gi|298674063|ref|YP_003725813.1| 15 DVIIIGSGPAGMFAANELSDQNlkVLVVEMGQDIE 49
                                      9*****************988889******98776 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0028
                                       EHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--G CS
                               DAO 144 dpakltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaG 201
                                       ++ +l+  + + + ++Gv +l++t+v+++  e++   g+    +  ++++ ++  +a G
  gi|298674063|ref|YP_003725813.1| 158 NTPALISRFKKGLDDKGVSFLLNTKVQDILVENNECRGIV-LDNdKIIKS-RYTMLAPG 214
                                       5667777788888999************955555567774.333244344.77888876 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   6.1e-08   7.3e-05       1      31 [.      18      48 ..      18      51 .. 0.97
   2 ?   -0.6   0.0       1.4   1.6e+03      28      50 ..      87     113 ..      75     124 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 6.1e-08
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrl 31
                                      I+G+G +G+ aA +L++++++vl++e+++++
  gi|298674063|ref|YP_003725813.1| 18 IIGSGPAGMFAANELSDQNLKVLVVEMGQDI 48
                                      9**************************9886 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.4
                                       SSSSSGGG-EECETT....CEECTS-- CS
                     NAD_binding_8  28 rdrlGGraasyevpg....vrvdygah 50 
                                       r+++GG++a  + ++      vdy   
  gi|298674063|ref|YP_003725813.1|  87 RPDIGGNLAKLTGDQdsawKLVDYVDD 113
                                       788888888766644345555666555 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0     2e-07   0.00024       1      36 [.      15      48 ..      15      64 .. 0.91
   2 ?    1.0   0.0      0.15   1.8e+02      95     140 ..     168     214 ..     150     255 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2e-07
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsl 36
                                      Dv++iG+GpAg+  A++l  + ++lkv+++e ++++
  gi|298674063|ref|YP_003725813.1| 15 DVIIIGSGPAGMFAANEL--SDQNLKVLVVEMGQDI 48
                                      9*****************..99***********998 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.15
                     Lycopene_cycl  95 erlvengvkl.leakvesveeeeageslvvleggrkirarlvvdarg 140
                                       + l ++gv++ l+ kv+ +  e++  + +vl++++ i++r  + a g
  gi|298674063|ref|YP_003725813.1| 168 KGLDDKGVSFlLNTKVQDILVENNECRGIVLDNDKIIKSRYTMLAPG 214
                                       55556677652799*****999998999************9998877 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   3.6e-08   4.3e-05       1      32 [.      13      44 ..      13      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 3.6e-08
                                      EEEEEEE--SHHHHHHHHHHHHTTHHEEEEES CS
                     FAD_binding_3  1 etdVlIVGaGpaGlmlallLseaGvrvvlvek 32
                                      e+dV+I+G+GpaG+ +a++Ls +  +v++ve 
  gi|298674063|ref|YP_003725813.1| 13 EYDVIIIGSGPAGMFAANELSDQNLKVLVVEM 44
                                      589*************************9995 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.2e-05     0.014       1      30 [.      15      44 ..      15      48 .. 0.95
   2 !    5.2   0.0    0.0096        12      92     129 ..     165     202 ..      91     213 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.2e-05
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLvee 30
                                      Dv+++G+gpaG+ AA     +  kvl+ve 
  gi|298674063|ref|YP_003725813.1| 15 DVIIIGSGPAGMFAANELSDQNLKVLVVEM 44
                                      9***************************96 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0096
                      FAD_oxidored  92 vleemlaeagvtvllntrlvevekegkriesvtveske 129
                                        +++ l+++gv  llnt+++++ +e+++++++++ +++
  gi|298674063|ref|YP_003725813.1| 165 RFKKGLDDKGVSFLLNTKVQDILVENNECRGIVLDNDK 202
                                       577778999****************99*******8754 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   8.7e-07     0.001       1      31 [.      17      46 ..      17      52 .. 0.92
   2 ?   -1.1   0.0      0.76   9.1e+02     212     265 ..     160     213 ..     142     229 .. 0.74
   3 ?   -2.0   0.0       1.4   1.7e+03     291     305 .]     428     442 ..     407     442 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 8.7e-07
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgn 31
                                      iIiG GPaG+ aa el + +l ++l++E g+
  gi|298674063|ref|YP_003725813.1| 17 IIIGSGPAGMFAANELSDQNL-KVLVVEMGQ 46
                                      8********************.7*****995 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.76
                       Pyr_redox_3 212 pdienrleelvkeekikvlfnaevkeikekeeeykvktedgkkvevkddvvlat 265
                                       p   +r++++++ + + +l n++v++i  +++e +    d++k+ ++   +la 
  gi|298674063|ref|YP_003725813.1| 160 PALISRFKKGLDDKGVSFLLNTKVQDILVENNECRGIVLDNDKIIKSRYTMLAP 213
                                       666677888877766888888888888888888776666666666666666654 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.4
                       Pyr_redox_3 291 eeteetnvpglflaG 305
                                       ++++e+ +++l+ aG
  gi|298674063|ref|YP_003725813.1| 428 NQNMESSIKNLYAAG 442
                                       5789999*****998 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0019       2.3       2      23 ..      24      45 ..      23      48 .. 0.92
   2 ?    0.3   0.0      0.27   3.3e+02     212     242 ..     162     194 ..     113     211 .. 0.77
   3 ?    0.7   0.0      0.21   2.5e+02     411     452 .]     428     466 ..     418     466 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0019
                                      HHHHHHHHHHHTTEEEEEEESS CS
                     Amino_oxidase  2 aGLaaArqLlsaGfdVtvlEar 23
                                      aG+ aA++L++++++V+v+E  
  gi|298674063|ref|YP_003725813.1| 24 AGMFAANELSDQNLKVLVVEMG 45
                                      9*******************76 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.27
                                       HHHHHHH..TTTTEEEETSEEEEEEEEETTCEE CS
                     Amino_oxidase 212 lpealae..elrgldirlntrVkeikregdgvt 242
                                       l+ ++ +  + +g++++lnt+V +i  e+++++
  gi|298674063|ref|YP_003725813.1| 162 LISRFKKglDDKGVSFLLNTKVQDILVENNECR 194
                                       4444455778899************99777744 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.21
                                       HHHHCHHCSTTEEE.SGGGCTTTTTS.HHHHHHHHHHHHHHHH CS
                     Amino_oxidase 411 dplakpegdprlffAGehtsreypgt.vegAilSGlraAaril 452
                                        + +++  +++l+ AG+ t     ++ +  A  +G  aA+ il
  gi|298674063|ref|YP_003725813.1| 428 NQNMES-SIKNLYAAGDGTG---LSRdIVNAAATGVMAARGIL 466
                                       455566.79**********9...7999************9886 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00022      0.26       1      33 [.      15      44 ..      15      50 .. 0.91
   2 ?   -3.6   0.0       3.2   3.8e+03     149     167 ..     262     280 ..     258     289 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00022
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE- CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlves 33
                                      +++i+G G+aG  aA+ l+ +    l+v++ve 
  gi|298674063|ref|YP_003725813.1| 15 DVIIIGSGPAGMFAANELSDQN---LKVLVVEM 44
                                      699****************999...89999985 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3.2
                                       EEE-HHHHHHHHHHHHHHC CS
                    Trp_halogenase 149 yhldaalyakfLrrvaear 167
                                       +h+  ++y++f r++ +++
  gi|298674063|ref|YP_003725813.1| 262 FHIQTQRYDDFVRTFCTNE 280
                                       8999999999999987665 PP

>> GDI  GDP dissociation inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.005         6       2      37 ..      11      46 ..      10      63 .. 0.85
   2 ?    2.8   0.1     0.029        34     245     355 ..     174     295 ..     168     325 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.005
                                      XXEECEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                               GDI  2 deeydvivlGtGlkecilsGllsvdgkkvlhldrnd 37
                                      d eydvi++G+G      +  ls ++ kvl+++  +
  gi|298674063|ref|YP_003725813.1| 11 DVEYDVIIIGSGPAGMFAANELSDQNLKVLVVEMGQ 46
                                      569***************************998655 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.029
                                       T-EEETS--ECEEEE-TTS-EEEEEE.TTEEEEECEEEE-GGG-C..............CCEEE.....EEEEEEEE CS
                               GDI 245 GGtymlnkpvdevvldedgkvvGvks.eeevakakkvicdpsylp..............ekvrk.....vgkvirai 301
                                       G +++ln++v+++++ e++   G+   +++++k++  +  p  +                   k     +g  + + 
  gi|298674063|ref|YP_003725813.1| 174 GVSFLLNTKVQDILV-ENNECRGIVLdNDKIIKSRYTMLAPGRVGgewvnnivskhsisA---KyggidIGVRVEVP 246
                                       668999999999999.66677776542777888888777776554322222221111111...11111112223344 PP

                                       EEESS--TTSTT-SSEEEEE-GGGCTSSS-EEEEEEEGGGTSS-TT-EEEEEEE CS
                               GDI 302 cilshpipntddadsvqiiipqkqlgrksdiyvalvssahnvaakgkylaivst 355
                                       +i+ +p++n +      i     q++r  d   +++++ h+ + k++y  +++t
  gi|298674063|ref|YP_003725813.1| 247 AIIMDPVTNINRDPKFHI-----QTQRYDDFVRTFCTNEHGFVVKEEYEDFIAT 295
                                       566666666666555554.....5666666666666777777777666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 2923.22
//
Query:       gi|298674064|ref|YP_003725814.1|  [L=355]
Description: IMP biosynthesis enzyme PurP domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.5e-56  188.7   0.0    1.1e-55  188.2   0.0    1.2  1  DUF1297      Domain of unknown function (DUF1297)
    1.2e-45  154.4   0.0    2.2e-45  153.6   0.0    1.4  1  DUF1246      Protein of unknown function (DUF1246)
    6.4e-05   23.1   0.0    0.00031   20.8   0.0    2.0  1  ATP-grasp_3  ATP-grasp domain
  ------ inclusion threshold ------
      0.016   14.8   0.0      0.034   13.7   0.0    1.5  1  RimK         RimK-like ATP-grasp domain
      0.028   13.9   0.0       0.05   13.1   0.0    1.3  1  CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP bindin


Domain annotation for each model (and alignments):
>> DUF1297  Domain of unknown function (DUF1297)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.2   0.0   2.9e-59   1.1e-55      21     187 ..     181     354 ..     170     355 .] 0.94

  Alignments for each domain:
  == domain 1  score: 188.2 bits;  conditional E-value: 2.9e-59
                                       CCEEEEE---SEEEEEEEEEETTT........TEEEEEEEEEEEEEECCCHCCS-HHHHHC.CT----EEEEEEEEE CS
                           DUF1297  21 kkasieeyvvGanfnlnyfysplk........eevellgidrRyesnldglvrlpakeqle.levepeyvvvGnipv 88 
                                       ++ +++e++vG+++++++fyspl+        +++e+l++drR+esn d++ rl ++++le + ++p+yvv+Gn+p+
  gi|298674064|ref|YP_003725814.1| 181 ENYVVQEFIVGTRYYFHFFYSPLReegyklskGTLEMLSMDRRVESNADEIFRLGSSKELEdAGINPTYVVTGNVPL 257
                                       6889********************99**9*999*********************98777652777************ PP

                                       EE-GGGHHHHHHHHHHHHHHHHHHSTT---EEEEEEEEE-TTS-EEEEEEESSB-GGGGGGTT--CCHHHTTSS--- CS
                           DUF1297  89 vlREsllekvfelgekfveaakklvppGiiGpFcLqsvvtkdlelvvfdvsaRivggtnvymegspyskllfgepls 165
                                       v REsll++vf+lgek+ve++ +l+  G+iGpFcL++vvt++le+ vf++saRiv+gtn+y +gspys    ++ ls
  gi|298674064|ref|YP_003725814.1| 258 VARESLLPHVFSLGEKVVEESLSLFG-GMIGPFCLETVVTDKLEIKVFEISARIVAGTNLYPSGSPYSDF-IESDLS 332
                                       **********************9997.*****************************************86.5899** PP

                                       HHHHHHHHHHHHHHCT-GGGCE CS
                           DUF1297 166 mGrrialEikeaiekdrleeiv 187
                                       +Grria Eik a + d+le+i+
  gi|298674064|ref|YP_003725814.1| 333 TGRRIAQEIKLAKSMDKLEKIL 354
                                       ********************97 PP

>> DUF1246  Protein of unknown function (DUF1246)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.6   0.0   6.1e-49   2.2e-45       1     122 []      21     142 ..      21     142 .. 0.97

  Alignments for each domain:
  == domain 1  score: 153.6 bits;  conditional E-value: 6.1e-49
                                       EEEESSTTHHHHHHHHHHTT--EEEEC-CCCHHHHHTTTT-..SEEEE.S.S..TTSS--HHHHHHTTCEE--BTTH CS
                           DUF1246   1 iatlaSHsalqilkgAkkegfrtlavcekgreklYekfkvi..devivldkfkdilkeevqeklreenailvPhgsf 75 
                                       iat++SHs+lqi++gA+kegf+t+ +c  +  k+Y++f+ +  de+i++d++kdi + +  +k +e+nailvPhgsf
  gi|298674064|ref|YP_003725814.1|  21 IATVCSHSSLQIFDGARKEGFKTIGICVGNPPKYYDAFPKAkpDEFIIVDSYKDIPNMT--DKFIEKNAILVPHGSF 95 
                                       89************************************77777************9765..**************** PP

                                       HHHC-HHHHHC-SS-EES-TTHHHHHCSHHHHHHHHHHTT-BB--BE CS
                           DUF1246  76 veYvgiekieelkvpifGnrkllrwEerrekkrkyLekAgiriPkki 122
                                       veYvg++++ +lk+p+fGnr++l wE++r+k+r++Le+Agi++P++i
  gi|298674064|ref|YP_003725814.1|  96 VEYVGADNFANLKIPTFGNRDVLDWESNRTKEREWLERAGIHMPRVI 142
                                       ********************************************975 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   8.8e-08   0.00031       2      82 ..     122     201 ..     121     313 .. 0.66

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 8.8e-08
                                       TSHHHHHHHHTTT.S---....-EESS--SSSEEEEESS-------B--SS--TTE.........EEEE---SEEEE CS
                       ATP-grasp_3   2 sdKlktykkLkeagvkvPtkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve..lvqefieGkplS 76 
                                       s+  k  ++L++ag+++P   +  +++  + ++ vK   + gg + +++++ ee ++ ++ +e  +vqefi G+ + 
  gi|298674064|ref|YP_003725814.1| 122 SNRTKEREWLERAGIHMP---RVINPQDINGPVMVKYQGAKGGRGFFIAKNYEEFKENVDPNEnyVVQEFIVGTRYY 195
                                       57778889**********...99999999***********************9998887766667********9987 PP

                                       EEEEE. CS
                       ATP-grasp_3  77 vsllsd 82 
                                         +  +
  gi|298674064|ref|YP_003725814.1| 196 FHFFYS 201
                                       666655 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   9.6e-06     0.034      33      82 ..     141     189 ..     128     193 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.6e-06
                                       HHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHHGGG--EEEEE- CS
                              RimK  33 liekiklrfPvvvKsvegsqGikvvlakkeqklkqvlealkeailvqeyi 82 
                                       +i+  +++ Pv+vK   ++ G + ++ak++++ k+ ++  +e+ +vqe+i
  gi|298674064|ref|YP_003725814.1| 141 VINPQDINGPVMVKYQGAKGGRGFFIAKNYEEFKENVDP-NENYVVQEFI 189
                                       666677899**************************9886.788899***9 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.4e-05      0.05      35      68 ..     145     178 ..     140     193 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
                                       HHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHH CS
                       CPSase_L_D2  35 keigyPviikaafglGGkGmrvarneeelaelvk 68 
                                       ++i  Pv++k   + GG+G  +a+n ee++e v 
  gi|298674064|ref|YP_003725814.1| 145 QDINGPVMVKYQGAKGGRGFFIAKNYEEFKENVD 178
                                       57788************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2289.80
//
Query:       gi|298674065|ref|YP_003725815.1|  [L=277]
Description: tRNA pseudouridine synthase A [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-28   99.0   0.0      5e-23   81.6   0.0    2.2  2  PseudoU_synth_1  tRNA pseudouridine synthase


Domain annotation for each model (and alignments):
>> PseudoU_synth_1  tRNA pseudouridine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.2e-06     0.021       5      89 ..      11      89 ..       8     102 .. 0.72
   2 !   81.6   0.0   2.8e-27     5e-23       1     107 [.     130     230 ..     130     231 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-06
                   PseudoU_synth_1  5 lvGthdfgsfckqkqekkntvrtileaaieevsgeekellvvtvkgsgFldhqVRamvgvl.favgqgklspedvkell 82
                                      ++Gt + g   +q q++  t+   l  ++++++  +++   +++ +sg++d +V+ +++v+ f+  + +     v++++
  gi|298674065|ref|YP_003725815.1| 11 YIGTEYHG---SQVQPELPTIEGELFKSLKNLEIIDDPK-SANFVSSGRTDTGVHSLGQVVtFDTDNPR---LAVPRVI 82
                                      88999999...5666676777777777777666665444.89*******************77766655...4567777 PP

                   PseudoU_synth_1 83 nakkrkk 89
                                      n++++++
  gi|298674065|ref|YP_003725815.1| 83 NSQLPES 89
                                      7777776 PP

  == domain 2  score: 81.6 bits;  conditional E-value: 2.8e-27
                   PseudoU_synth_1   1 AakelvGthdfgsfckqkqekkntvrtileaaieevsgeekellvvtvkgsgFldhqVRamvgvlfavgqgklsped 77 
                                       A+k+l+Gthdf++fc    ++k+tvrt+ +++i+     +++l+ +++++++Fl+++VR +v +l+ vg g +++e+
  gi|298674065|ref|YP_003725815.1| 130 ASKYLIGTHDFANFC-TPVKGKSTVRTVQRINIR----VKGTLTLIDIQADSFLWKMVRKIVTALMMVGYGTRDTEW 201
                                       89************8.77778*************....666699********************************* PP

                   PseudoU_synth_1  78 vkellnakkrkkiavetapavglvlfhvrY 107
                                       ++++ln +  ++  +e ap  gl+l +v+Y
  gi|298674065|ref|YP_003725815.1| 202 LEQMLNPEYYEE-GIEPAPSYGLILKDVDY 230
                                       *********999.9**************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.52s 00:00:01.04 Elapsed: 00:00:00.58
# Mc/sec: 1442.95
//
Query:       gi|298674066|ref|YP_003725816.1|  [L=349]
Description: putative RNA methylase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-24   85.4   0.0    2.4e-23   82.9   0.0    2.0  1  UPF0020          Putative RNA methylase family UPF0020
    3.4e-15   56.4   1.5    3.8e-15   56.3   0.7    1.4  2  THUMP            THUMP domain
    2.6e-06   26.9   0.0    8.7e-05   21.9   0.0    2.5  2  N6_Mtase         N-6 DNA Methylase
    3.1e-05   24.5   0.1    0.00091   19.8   0.0    2.9  2  Methyltransf_11  Methyltransferase domain
    4.7e-05   23.2   0.0       0.24   11.1   0.0    2.4  2  N6_N4_Mtase      DNA methylase
    0.00013   22.6   0.0    0.00091   19.9   0.0    2.3  2  Methyltransf_25  Methyltransferase domain
    0.00039   20.3   0.1     0.0015   18.4   0.0    1.8  2  Methyltransf_31  Methyltransferase domain
    0.00052   19.6   0.1       0.44   10.0   0.0    2.4  2  AviRa            RRNA methyltransferase AviRa
  ------ inclusion threshold ------
      0.026   14.3   0.0       0.07   12.9   0.0    1.7  2  N6-adenineMlase  Probable N6-adenine methyltransferase
      0.062   12.9   0.0       0.13   11.9   0.0    1.5  1  Cons_hypoth95    Conserved hypothetical protein 95


Domain annotation for each model (and alignments):
>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.9   0.0   1.3e-26   2.4e-23       1     196 [.     174     342 ..     174     343 .. 0.88

  Alignments for each domain:
  == domain 1  score: 82.9 bits;  conditional E-value: 1.3e-26
                                       -SSS-SS---SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH- CS
                           UPF0020   1 RgyRefngpapLketLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearael 77 
                                       +++R+f++p+ L ++ A+  v+l+++k ge+l+DP+CG+ +il+E +l+g n++                       
  gi|298674066|ref|YP_003725816.1| 174 PHKRPFFYPGVLMPRTARTVVNLSKVKSGETLFDPFCGTAGILMETGLVGINCI----------------------- 227
                                       689***************************************************....................... PP

                                       -EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE--------.--HHHHHHHHHHHHHHHH CS
                           UPF0020  78 klygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerl.gskkalekLYseflrelk 153
                                          g++ + ++++ga  N+   +++ +  +   da+ L+  ++++d+ivt+pPYG++   ++++++ LY    +e+ 
  gi|298674066|ref|YP_003725816.1| 228 ---GLEVQYKIMAGACMNLDDLNLDYSLLM--GDACRLPFVDESMDAIVTDPPYGKSAlIKAESMNYLYAMSFKEMY 299
                                       ...******************999887766..56999997778************9861566677************ PP

                                       HH-TT..-EEEEEESSHHHHHCC---..ESEEEEEEETTEEEEEE CS
                           UPF0020 154 rvlrgggrlvlltsenkalekaleer..alrkvkeknvklglllk 196
                                       rvl++ g+ ++++++n    ++++++   l k + ++v+ +l+++
  gi|298674066|ref|YP_003725816.1| 300 RVLKK-GKYAVIVTGNPVR-ELVKDAgfVLHKEHHQRVHRSLTRV 342
                                       *****.7777777777655.5555554789999999999999875 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   0.7   2.1e-18   3.8e-15       3     131 ..      19     149 ..      18     160 .. 0.87
   2 ?   -3.6   0.0       6.2   1.1e+04       2      89 ..     297     310 ..     283     322 .. 0.59

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 2.1e-18
                                       HHHHHHHTT.H-SEEEEETTEEEEECTEEEEEETHHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHHHH CS
                             THUMP   3 ieellkegkvnverveagkgrivvelkgekpeedeellkealekargiqrvipvcevceadledileaakeivkkkf 79 
                                       i++ l  ++ +++++   ++++vv++ +e+ +e  ++l++   +++  ++++ v  +c +d++di++ +++++  k+
  gi|298674066|ref|YP_003725816.1|  19 IFACLDVEELEYSEYAHFDQCLVVDI-SENNKEVINKLDSVSNRLAMSHSILKVAGICDTDFDDIIKTTENLNINKH 94 
                                       66666667777776666655555555.6888999999999999999******************************* PP

                                       HHCT-EEEEEEEESSSTSSSHHHHHHHHHHHHHHCCTT...-EE-SSS-SEEEEE CS
                             THUMP  80 eeeketFaVrvkrrgkhfeftsreinrevGkaivektg...lkVdlenPdivvrv 131
                                       + +++t+aVrv+++++  +++  +++++vG+ i +k++    +V+l nPdi +r+
  gi|298674066|ref|YP_003725816.1|  95 ITPEQTYAVRVNKVKHYTSINGEQLEKKVGGCIYRKGNeksYRVNLRNPDIEFRL 149
                                       *************99988*********************************9987 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 6.2
                                       HHHHHHHHTT.H-SEEEEETTEEEEECTEEEEEETHHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHHH CS
                             THUMP   2 eieellkegkvnverveagkgrivvelkgekpeedeellkealekargiqrvipvcevceadledileaakeivkkk 78 
                                       e++                                                                        + 
  gi|298674066|ref|YP_003725816.1| 297 EMY------------------------------------------------------------------------RV 301
                                       333........................................................................33 PP

                                       HHHCT-EEEEE CS
                             THUMP  79 feeeketFaVr 89 
                                       ++++  ++aV 
  gi|298674066|ref|YP_003725816.1| 302 LKKG--KYAVI 310
                                       3333..44444 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1     0.046        82     286     308 ..      77      99 ..      38     102 .. 0.85
   2 !   21.9   0.0   4.8e-08   8.7e-05      35     140 ..     190     281 ..     178     315 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.046
                          N6_Mtase 286 veleeiaendynlnvgryvetee 308
                                        ++++i+++ +nln+++++ +e+
  gi|298674066|ref|YP_003725816.1|  77 TDFDDIIKTTENLNINKHITPEQ 99 
                                       4789**************99887 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 4.8e-08
                          N6_Mtase  35 sklivellepksgesvyDpacGsggllvqaekvlkeedgktkelsiyGqeknettyrLakmNlllhgieykkvkirl 111
                                        +++v+l + ksge+ +Dp cG++g+l+++  v          ++  G+e++ + ++ a mNl   + + +  +  +
  gi|298674066|ref|YP_003725816.1| 190 ARTVVNLSKVKSGETLFDPFCGTAGILMETGLV---------GINCIGLEVQYKIMAGACMNLD--DLNLD-YSLLM 254
                                       57899999********************98773.........79999*******9999999975..55555.5599* PP

                          N6_Mtase 112 gdtlekpkfekdkkfdvvvaNppfnqkew 140
                                       gd+   p  +  +++d++v+ pp++++  
  gi|298674066|ref|YP_003725816.1| 255 GDACRLPFVD--ESMDAIVTDPPYGKSAL 281
                                       ****999887..9************9854 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.48   8.6e+02      18      38 ..      36      56 ..      10      81 .. 0.57
   2 !   19.8   0.0   5.1e-07   0.00091       5      96 .]     210     310 ..     207     310 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.48
                                      TSEEEEEES-HHHHHHHHHHC CS
                   Methyltransf_11 18 garvvgvDlskemlklakeka 38
                                      + +++ vD+s++  ++ ++  
  gi|298674066|ref|YP_003725816.1| 36 FDQCLVVDISENNKEVINKLD 56
                                      245556666666665554443 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 5.1e-07
                                       -TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES........-CCC CS
                   Methyltransf_11   5 cGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvsse........vlhh 73 
                                       cGt  ++ +    g +++g+++  + ++ a ++  + +l  +++ +da +lpf d+s+D++v             + 
  gi|298674066|ref|YP_003725816.1| 210 CGTAGILMETGLVGINCIGLEVQYKIMAGACMNLDDLNLDYSLLMGDACRLPFVDESMDAIVTDPpygksaliKAES 286
                                       6655555555556699999999999999999999999987888*******************988777775443333 PP

                                       -.CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  74 v.edpekalkeiaRvLkpgGllvi 96 
                                       +    +  +ke++RvLk+g + vi
  gi|298674066|ref|YP_003725816.1| 287 MnYLYAMSFKEMYRVLKKGKYAVI 310
                                       34467889**********988775 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00013      0.24     173     226 ..     182     236 ..      37     241 .. 0.77
   2 !   10.0   0.0   0.00028       0.5       2      57 ..     268     313 ..     267     328 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
                                       SS---HHHHHHHHHHHS-T.T-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHH CS
                       N6_N4_Mtase 173 paqkPvallerlIklstkk.gdivlDpFaGSGtTavaakelgrkfiGieieeeyv 226
                                       p +    +++ +++ls  k g++ +DpF+G+  ++++    g ++iG e++ +++
  gi|298674066|ref|YP_003725816.1| 182 PGVLMPRTARTVVNLSKVKsGETLFDPFCGTAGILMETGLVGINCIGLEVQYKIM 236
                                       55555566777776665444*****************************998877 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00028
                                       EEEEE--SSSSSCS.....GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE- CS
                       N6_N4_Mtase   2 dlivtdpPYntgkdyendeqyeeedsyeeyleflekvlkevrrvLkddgsifinid 57 
                                       d ivtdpPY+ +           + +  +yl  +   +ke++rvLk+++ ++i  +
  gi|298674066|ref|YP_003725816.1| 268 DAIVTDPPYGKSAL--------IKAESMNYLYAM--SFKEMYRVLKKGKYAVIVTG 313
                                       78*******99887........344444555544..69*************99865 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.4   2.4e+03      22      36 ..      37      51 ..      19      84 .. 0.66
   2 !   19.9   0.0   5.1e-07   0.00091       6      96 ..     210     305 ..     206     305 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.4
                                      SEEEEEESSHHHHHH CS
                   Methyltransf_25 22 akvtgvDiseemlea 36
                                       + + vDise+  e 
  gi|298674066|ref|YP_003725816.1| 37 DQCLVVDISENNKEV 51
                                      455566666655444 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 5.1e-07
                                       -TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEE......ESTGGG CS
                   Methyltransf_25   6 cGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvs......sgalhh 76 
                                       cGt  ++++     g  + +g++++ + ++ a  ++++ +l+ +++ gda +lpf d+s+D++v       s    +
  gi|298674066|ref|YP_003725816.1| 210 CGTAGILMETGLV-G-INCIGLEVQYKIMAGACMNLDDLNLDYSLLMGDACRLPFVDESMDAIVTdppygkS---AL 281
                                       9999888888755.5.9*********************99*************************8875531...23 PP

                                       SSHHHH....HHHHHHHHHHEEEE CS
                   Methyltransf_25  77 lsdedl....ekalkeiarvLkpg 96 
                                       ++ e +    +  +ke++rvLk+g
  gi|298674066|ref|YP_003725816.1| 282 IKAESMnylyAMSFKEMYRVLKKG 305
                                       33332211225679*******997 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       0.7   1.2e+03      89      89 ..      57      57 ..      19     131 .. 0.45
   2 !   18.4   0.0   8.2e-07    0.0015       2     119 ..     200     320 ..     199     342 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.7
                   Methyltransf_31 89 d 89
                                      +
  gi|298674066|ref|YP_003725816.1| 57 S 57
                                      2 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 8.2e-07
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDli 78 
                                       ++g ++ D+ CGt  ++ e   ++  +++ +G++ + +    A  n+++l+ld +++  gd+  l+  + de+ D i
  gi|298674066|ref|YP_003725816.1| 200 KSGETLFDPFCGTAGILMETG-LV--GINCIGLEVQYKIMAGACMNLDDLNLD-YSLLMGDACRLP--FVDESMDAI 270
                                       5788999******66666665.54..699***********************8.************..9******** PP

                   Methyltransf_31  79 lsn.....evl......naladpdkile....eiervlkpggilliedprllaelp 119
                                       +++     ++l      n+l+           e+ rvlk+g + +i + +  +el 
  gi|298674066|ref|YP_003725816.1| 271 VTDppygkSALikaesmNYLY------AmsfkEMYRVLKKGKYAVIVTGNPVRELV 320
                                       ***777664443333213332......24455**************9999444443 PP

>> AviRa  RRNA methyltransferase AviRa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0016       2.8      46      75 ..     194     223 ..     185     250 .. 0.73
   2 !   10.0   0.0   0.00025      0.44     163     213 ..     263     314 ..     237     331 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0016
                             AviRa  46 lekkeegapltlyDpCCGgayLltvlgllh 75 
                                       ++ ++ +++ tl+Dp CG+a +l   gl+ 
  gi|298674066|ref|YP_003725816.1| 194 VNLSKVKSGETLFDPFCGTAGILMETGLVG 223
                                       3344555689**********9999999875 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00025
                             AviRa 163 aekevdivitDlPYGelvswqgeseepvkql.leslaavldpeesvvaviad 213
                                       + +++d ++tD PYG+ +  + es + + ++ ++++++vl++ +  v+v+ +
  gi|298674066|ref|YP_003725816.1| 263 VDESMDAIVTDPPYGKSALIKAESMNYLYAMsFKEMYRVLKKGKYAVIVTGN 314
                                       456699*****************9888888779*******988777766655 PP

>> N6-adenineMlase  Probable N6-adenine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.1   3.8e+03     106     120 ..      54      84 ..      25     119 .. 0.53
   2 ?   12.9   0.0   3.9e-05      0.07      84     134 ..     262     324 ..     245     348 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.1
                   N6-adenineMlase 106 klaktaklllk................klil 120
                                       kl  + + l+                  +i 
  gi|298674066|ref|YP_003725816.1|  54 KLDSVSNRLAMshsilkvagicdtdfdDIIK 84 
                                       3333333332233333333333333333333 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 3.9e-05
                   N6-adenineMlase  84 elkgkfdviviDPPF..........lseeclkklaktaklllk..klilctgevmeelekllg 134
                                       ++++++d iv+DPP+          ++   + +++++ + l+k    +++tg+ ++el k +g
  gi|298674066|ref|YP_003725816.1| 262 FVDESMDAIVTDPPYgksalikaesMNYLYAMSFKEMYRVLKKgkYAVIVTGNPVRELVKDAG 324
                                       56899**********777766444444444444666666665586478888888888555554 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.1e-05      0.13      42     131 ..     202     284 ..     190     337 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.1e-05
                                       C-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEE CS
                     Cons_hypoth95  42 garvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivf 118
                                       g+++ D f+G++++ +E    g  +++ +e + + ++    nl+ l+l+   + l + ++ +l+     +e++d + 
  gi|298674066|ref|YP_003725816.1| 202 GETLFDPFCGTAGILMETGLVG-INCIGLEVQYKIMAGACMNLDDLNLDY--SLL-MGDACRLPFV---DESMDAIV 271
                                       5677899999999999998888.468889999999999999999999874..555.5555555555...6789**** PP

                                       E--SSSTTCH.HH CS
                     Cons_hypoth95 119 lDPPyakelliee 131
                                        DPPy k++li++
  gi|298674066|ref|YP_003725816.1| 272 TDPPYGKSALIKA 284
                                       ********98653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2083.75
//
Query:       gi|298674067|ref|YP_003725817.1|  [L=95]
Description: hypothetical protein Metev_0089 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-26   91.8   1.2    3.5e-26   91.3   1.2    1.2  1  DUF1805   Domain of unknown function (DUF1805)
    0.00094   19.2   0.0     0.0012   18.9   0.0    1.1  1  IMS       impB/mucB/samB family


Domain annotation for each model (and alignments):
>> DUF1805  Domain of unknown function (DUF1805)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.3   1.2   3.9e-30   3.5e-26       1      63 []      36      94 ..      36      94 .. 1.00

  Alignments for each domain:
  == domain 1  score: 91.3 bits;  conditional E-value: 3.9e-30
                                      E-TT--HHHHHHTT--EEE-....-S--SHHHHHHSB-SEE-HHHHHTT--TT-BHHHHGGGG CS
                           DUF1805  1 mCGaLdvealeklgdlaarvivagsGVrtledllaapvesvteaAeelGikeGmtgkeaLekl 63
                                      mCG+Ld++a++klgd+aa+v    +GV+++ed+l+a++ ++++ A+e+Gi  GmtgkeaLek+
  gi|298674067|ref|YP_003725817.1| 36 MCGYLDINAANKLGDAAAKV----KGVNSFEDVLNAKIIEASQPAKEMGIDTGMTGKEALEKM 94
                                      9*******************....**************************************9 PP

>> IMS  impB/mucB/samB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.3e-07    0.0012      17      59 ..      19      93 ..      12      94 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.3e-07
                                      T-TTS-EEEEET....................................TEEEEE-HHHHTTT--TTSBHHHHHTT CS
                               IMS 17 eLkgkPvvvaqgsek................................rgiviavsyeArayGvkrgmrikeakkl 59
                                      ++++ P++v + ++                                 ++ +i +s++A+++G+ +gm+ kea+++
  gi|298674067|ref|YP_003725817.1| 19 NMHNAPIIVIKADKGfvmcgyldinaanklgdaaakvkgvnsfedvlNAKIIEASQPAKEMGIDTGMTGKEALEK 93
                                      5778888888886668999999999999999999999999999999999***********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 590.25
//
Query:       gi|298674068|ref|YP_003725818.1|  [L=237]
Description: hypothetical protein Metev_0090 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0003   20.0   6.5       0.03   13.4   1.1    4.0  3  SQHop_cyclase_C  Squalene-hopene cyclase C-terminal domain
     0.0026   16.8   4.4       0.25   10.3   0.7    3.1  4  TED_complement   A-macroglobulin TED domain
  ------ inclusion threshold ------
      0.079   13.2   0.2       0.15   12.3   0.2    1.5  1  HECA             Headcase protein family homologue


Domain annotation for each model (and alignments):
>> SQHop_cyclase_C  Squalene-hopene cyclase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0     0.046   2.7e+02     207     220 ..       5      18 ..       3      42 .. 0.68
   2 !   13.4   1.1   5.1e-06      0.03      54     116 ..     116     179 ..      60     186 .. 0.86
   3 !    5.4   0.1    0.0014       8.2     196     230 ..     185     216 ..     174     233 .. 0.52

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.046
                                       HHHHHHHHHHHTT- CS
                   SQHop_cyclase_C 207 pvirkavdWlksvq 220
                                       p+i+k+++Wlk+++
  gi|298674068|ref|YP_003725818.1|   5 PYIKKSLEWLKKQK 18 
                                       45555555554432 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 5.1e-06
                                       -BB-SSSS-TT--BHHHHHHHHHHHTT-.--STHHHHHHHHHHHHHHHHHTB-TTSSB-SSSSS CS
                   SQHop_cyclase_C  54 gGwafefaneyyPdvddtavvvlalkrv.rlkeekkkeeaiaraveWilglqsknGGwaafdkd 116
                                         w  e  ++ +  v  t++v++al +  +l +++++++ i+  +eWil+   k GGw+   + 
  gi|298674068|ref|YP_003725818.1| 116 CDWLIENYDTNWEHVGTTSLVITALVKQeKLLSSNHYQNFIQNRAEWILSQSDKGGGWSYISTS 179
                                       56888888888899999*****9997663667889999999999******999999**876655 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.0014
                                       HHHHTT--TTSHHHHHHHHHHHTT--TTSSBB--G CS
                   SQHop_cyclase_C 196 alaavgedleepvirkavdWlksvqnedGGWGesa 230
                                       al        ++ ++  ++Wl +  ne+G WG ++
  gi|298674068|ref|YP_003725818.1| 185 ALM---LAGYRNQLKPHIQWLLDNFNENGYWGYNN 216
                                       222...22223344445555555555555555443 PP

>> TED_complement  A-macroglobulin TED domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       0.7   4.2e+03     118     128 ..       7      17 ..       5      27 .. 0.64
   2 !    6.1   0.0   0.00079       4.7     138     169 ..      79     109 ..      74     117 .. 0.86
   3 !   10.3   0.7   4.1e-05      0.25     260     311 ..     129     187 ..     111     191 .. 0.82
   4 ?   -1.0   0.0      0.12     7e+02     117     136 ..     194     213 ..     190     226 .. 0.68

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 0.7
                                       HHHHHHHHHTT CS
                    TED_complement 118 iseslewLlse 128
                                       i++slewL ++
  gi|298674068|ref|YP_003725818.1|   7 IKKSLEWLKKQ 17 
                                       55666666444 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.00079
                                       SS-SS-TTCSSSTHCHHHHHHHHHHHHHHHHT CS
                    TED_complement 138 egsllnrkmkggvekevtLtAyvliaLleake 169
                                       +++lln+k   + +k+v+ tAy+liaL  + +
  gi|298674068|ref|YP_003725818.1|  79 KEWLLNQKTDDSWNKDVYDTAYALIALSDM-D 109
                                       57899999*******************998.3 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 4.1e-05
                                       HHHHHHHHHHHHHH.......TTSCHHHHHHHHHHHHTHTSTSSSSSHHHHHHHHHHHH CS
                    TED_complement 260 evettaYaLLalls.......ekdleladkivkWLtkqrnsaGGFsStqDtvvaLqaLs 311
                                       +v tt+ ++ al++       ++  ++ ++ ++W+ +q  + GG+s      +a+qaL 
  gi|298674068|ref|YP_003725818.1| 129 HVGTTSLVITALVKqekllssNHYQNFIQNRAEWILSQSDKGGGWSYISTSNLAIQALM 187
                                       588999999999996666554444566777899*************999999****995 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHTTB-TTS-B- CS
                    TED_complement 117 eiseslewLlseQkedGsFk 136
                                       +++  ++wLl + +e+G++ 
  gi|298674068|ref|YP_003725818.1| 194 QLKPHIQWLLDNFNENGYWG 213
                                       56667778887777777765 PP

>> HECA  Headcase protein family homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   2.5e-05      0.15      26      86 ..      29     102 ..       7     106 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.5e-05
                              HECA  26 kvvcs...nekckagkymhrecfeaweeevlkylkslgrars..........wsekqrkqnlWtkkgydlafka 86 
                                        v c+    e+  a+k +h++  ++w++++  + +++++  +          w  +q++ + W k +yd a+ +
  gi|298674068|ref|YP_003725818.1|  29 TVACDlwgIENHYAAKLIHKKHNSSWNNSIRDTSRACSALANigiifpdakeWLLNQKTDDSWNKDVYDTAYAL 102
                                       456652224667789999***********99999996665555666666666*******************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1468.73
//
Query:       gi|298674069|ref|YP_003725819.1|  [L=58]
Description: preprotein translocase subunit SecG [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-14   54.0   0.1    1.5e-14   53.7   0.1    1.1  1  Sec61_beta  Sec61beta family


Domain annotation for each model (and alignments):
>> Sec61_beta  Sec61beta family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.7   0.1   8.4e-19   1.5e-14       1      40 [.      14      53 ..      14      54 .. 0.97

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 8.4e-19
                                      XXXXXXXXXX----SS-B-THHHHHHHHHHHHHHHHHTSS CS
                        Sec61_beta  1 SsaGLlryyeedapgikidPkvVlvlsvafiasVilLhil 40
                                      SsaGL+ryye d+++i++dPk ++++++a+++ +++L++ 
  gi|298674069|ref|YP_003725819.1| 14 SSAGLMRYYEADKRAIHLDPKPIVIFGLAVGVGILALNAS 53
                                      9*************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 368.05
//
Query:       gi|298674070|ref|YP_003725820.1|  [L=334]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.1e-25   86.4   0.4    3.3e-24   84.6   0.0    2.2  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    0.00011   22.4   0.7    0.00024   21.3   0.7    1.5  1  OrfB_IS605      Probable transposase
  ------ inclusion threshold ------
      0.016   15.2   4.3       0.11   12.5   0.6    3.0  3  HypA            Hydrogenase/urease nickel incorporation, meta
      0.017   14.7   0.8      0.035   13.7   0.8    1.5  1  Zn_ribbon_17    Zinc-ribbon, C4HC2 type
      0.035   14.2   5.0       0.15   12.2   1.1    2.5  2  UPF0547         Uncharacterised protein family UPF0547
       0.35   10.9   2.9        0.4   10.7   1.5    1.9  2  DZR             Double zinc ribbon
        1.2    8.7   3.4        9.2    5.8   3.4    2.3  1  Mu-like_Com     Mu-like prophage protein Com
        1.4    8.7   8.3        1.6    8.6   5.5    2.6  3  zinc_ribbon_2   zinc-ribbon domain
          2    8.5   5.2       0.76    9.8   0.6    2.2  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
        3.2    7.8   5.1        2.9    7.9   0.2    3.1  3  zinc_ribbon_4   zinc-ribbon domain


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       3.6   6.4e+03      33      48 ..     214     230 ..     209     234 .. 0.53
   2 !   84.6   0.0   1.9e-27   3.3e-24       1      68 [.     244     309 ..     244     310 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.6
                    OrfB_Zn_ribbon  33 eCgsknke.alsgrtfk 48 
                                       +Cg ++++ +  ++  k
  gi|298674070|ref|YP_003725820.1| 214 NCGIRMENlEGIRDSAK 230
                                       56666665433333344 PP

  == domain 2  score: 84.6 bits;  conditional E-value: 1.9e-27
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       f++l+ +leyka+  G+k+e v+p+yTS++Cs+Cg+ + +  +g+ fkCp+Cg++ ++D nAa+Ni+ 
  gi|298674070|ref|YP_003725820.1| 244 FYQLQFMLEYKARLLGVKIEFVEPEYTSQDCSRCGYLGIR--NGEAFKCPHCGHVDHADANAAFNIAM 309
                                       899*************************************..************************96 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.7   1.3e-07   0.00024       3     107 ..     118     214 ..     113     223 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.3e-07
                        OrfB_IS605   3 pvevevelpkpkgnkaagiDlGin.nLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrkla 78 
                                        v+v++  ++ ++++ +g+Dl+   ++a++++ ++  + + g++++    ++++ +++lq k k         +k++
  gi|298674070|ref|YP_003725820.1| 118 SVTVPE-REQIEPENYLGVDLNTTgHIAVMSNPKTGKIWKLGKKAQHIHLKYKNDRRKLQVKGKY--------KKVK 185
                                       344443.88999**********87367777777766677889******************98433........5799 PP

                        OrfB_IS605  79 rlhrkrsrrrkhllhklathliktlkevg 107
                                        + ++ sr++++l hk+++++++t  +++
  gi|298674070|ref|YP_003725820.1| 186 QVNDRESRIVRDLNHKISSKIVETAAANN 214
                                       9**********************988775 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.065   1.2e+02       9      34 ..      46      72 ..      40      78 .. 0.75
   2 ?   -3.1   0.0       4.4   7.9e+03      25      42 ..     113     130 ..     103     132 .. 0.74
   3 ?   12.5   0.6   6.4e-05      0.11      58      96 ..     258     297 ..     191     307 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.065
                                      HHHHHHHHHH.CCTT..EEEEEEEEEE CS
                              HypA  9 sivevveeea.keaaarkvtkvkvevG 34
                                      +i +++ ++  ++++a+kvt+vk+++ 
  gi|298674070|ref|YP_003725820.1| 46 AISNQILKKYaNDKSAKKVTNVKLTIP 72
                                      5666666666366899*******9985 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.4
                                       EEEEEEEEEETTCT--HH CS
                              HypA  25 kvtkvkvevGelsgvepe 42 
                                       k   v v+v e +++epe
  gi|298674070|ref|YP_003725820.1| 113 KYVYVSVTVPEREQIEPE 130
                                       555688999999999987 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 6.4e-05
                                       TT-EEE.EEEE--EEEETTTS-EEECHHHHHS-TTTSSS- CS
                              HypA  58 egaeLe.ieevpvkvrCreCgkefeleekalrCpkCgsad 96 
                                        g ++e +e +  +  C++Cg+ +  + +a++Cp+Cg+ d
  gi|298674070|ref|YP_003725820.1| 258 LGVKIEfVEPEYTSQDCSRCGYLGIRNGEAFKCPHCGHVD 297
                                       4455553455556778*****9888776799******875 PP

>> Zn_ribbon_17  Zinc-ribbon, C4HC2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.8   1.9e-05     0.035       6      34 ..     273     303 ..     269     317 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.9e-05
                      Zn_ribbon_17   6 sCayCe.lav.kgrvvlcgvCeHvlHasCar 34 
                                        C+ C  l + +g  + c+ C+Hv Ha+  +
  gi|298674070|ref|YP_003725820.1| 273 DCSRCGyLGIrNGEAFKCPHCGHVDHADANA 303
                                       566665244415899************9765 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2     0.051        91      15      22 ..     272     279 ..     271     280 .. 0.88
   2 ?   12.2   1.1   8.3e-05      0.15      16      25 ..     289     298 ..     286     299 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.051
                           UPF0547  15 qfCphCGy 22 
                                       q C+ CGy
  gi|298674070|ref|YP_003725820.1| 272 QDCSRCGY 279
                                       78*****9 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 8.3e-05
                           UPF0547  16 fCphCGyvFq 25 
                                       +CphCG+v+ 
  gi|298674070|ref|YP_003725820.1| 289 KCPHCGHVDH 298
                                       8******985 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.5   0.00022       0.4      27      49 .]     267     294 ..     212     294 .. 0.80
   2 ?   -3.7   0.0       7.3   1.3e+04      17      20 ..     314     317 ..     309     321 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00022
                               DZR  27 a...edrCpsCgek.vdpearf.CpeCG 49 
                                           ++ C++Cg+  + ++++f Cp+CG
  gi|298674070|ref|YP_003725820.1| 267 PeytSQDCSRCGYLgIRNGEAFkCPHCG 294
                                       0444899*******99999999*****9 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 7.3
                               DZR  17 eCgt 20 
                                       +Cg+
  gi|298674070|ref|YP_003725820.1| 314 QCGA 317
                                       3443 PP

>> Mu-like_Com  Mu-like prophage protein Com
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   3.4    0.0051       9.2      25      39 ..     288     302 ..     273     314 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0051
                       Mu-like_Com  25 iKCPRCGtLnHlkae 39 
                                        KCP CG + H  a+
  gi|298674070|ref|YP_003725820.1| 288 FKCPHCGHVDHADAN 302
                                       47*********8775 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.2     0.068   1.2e+02      16      21 ..     274     279 ..     270     281 .. 0.73
   2 ?    8.6   5.5   0.00087       1.6       2      21 ..     274     295 ..     274     296 .. 0.93
   3 ?   -3.0   0.0       3.9   7.1e+03      19      21 ..     315     317 ..     314     318 .. 0.52

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.068
                     zinc_ribbon_2  16 CpyCGt 21 
                                       C++CG+
  gi|298674070|ref|YP_003725820.1| 274 CSRCGY 279
                                       777775 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00087
                     zinc_ribbon_2   2 CpnCGael.qdnakF.CpyCGt 21 
                                       C++CG+    +++ F Cp+CG+
  gi|298674070|ref|YP_003725820.1| 274 CSRCGYLGiRNGEAFkCPHCGH 295
                                       9999999879***********8 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 3.9
                     zinc_ribbon_2  19 CGt 21 
                                       CG+
  gi|298674070|ref|YP_003725820.1| 315 CGA 317
                                       554 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   5.5     0.015        26      21      45 ..     274     295 ..     269     296 .. 0.61
   2 ?    9.8   0.6   0.00043      0.76      15      27 ..     284     296 ..     280     305 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.015
                     Zn_Tnp_IS1595  21 CPhCgsrkayriktrglfqCkeCrk 45 
                                       C +Cg   +  i++ + f+C +C++
  gi|298674070|ref|YP_003725820.1| 274 CSRCG---YLGIRNGEAFKCPHCGH 295
                                       66666...55555555566666655 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00043
                     Zn_Tnp_IS1595  15 WpngfvCPhCgsr 27 
                                        ++ f CPhCg+ 
  gi|298674070|ref|YP_003725820.1| 284 NGEAFKCPHCGHV 296
                                       45669******87 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       2.7   4.8e+03      30      35 ..     230     235 ..     228     236 .. 0.55
   2 ?    0.5   0.0      0.33   5.9e+02      28      33 ..     274     279 ..     265     280 .. 0.83
   3 ?    7.9   0.2    0.0016       2.9      22      34 ..     284     296 ..     283     296 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.7
                     zinc_ribbon_4  30 kCghvF 35 
                                       kC+++F
  gi|298674070|ref|YP_003725820.1| 230 KCKKSF 235
                                       555555 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.33
                     zinc_ribbon_4  28 CskCgh 33 
                                       Cs+Cg 
  gi|298674070|ref|YP_003725820.1| 274 CSRCGY 279
                                       999985 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0016
                     zinc_ribbon_4  22 kgvkvrCskCghv 34 
                                       +g   +C++Cghv
  gi|298674070|ref|YP_003725820.1| 284 NGEAFKCPHCGHV 296
                                       56778*******7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1376  (0.0767472); expected 358.6 (0.02)
Passed bias filter:                      675  (0.0376485); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2407.77
//
Query:       gi|298674071|ref|YP_003725821.1|  [L=339]
Description: aIF-2BI family translation initiation factor [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-88  296.8   0.1    1.7e-88  296.5   0.1    1.1  1  IF-2B       Initiation factor 2 subunit family
  ------ inclusion threshold ------
      0.017   15.0   0.0       0.13   12.2   0.0    2.2  2  Peroxin-22  Peroxisomal biogenesis protein family


Domain annotation for each model (and alignments):
>> IF-2B  Initiation factor 2 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  296.5   0.1   1.9e-92   1.7e-88       2     282 .]      45     330 ..      44     330 .. 0.98

  Alignments for each domain:
  == domain 1  score: 296.5 bits;  conditional E-value: 1.9e-92
                                       S-SHHHHHHHHHHHHHHHHHHCCCSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHHH CS
                             IF-2B   2 vrGspaiaiaalevllevikdaktskvaeLkeelrkaidlLkkarPtavslgnairrllkeiselksssdvkeakks 78 
                                       +rG+pa++ a+ ++++ ++  +kt+++++L+++l++a++++k++rPtav+l + ++r+ k   + ++  d + +k+ 
  gi|298674071|ref|YP_003725821.1|  45 IRGAPALGAAGGYGIALAAVLSKTDNMDNLTKDLQSAAETIKATRPTAVNLAWGVERVIK---ATSDAYDFEGMKNI 118
                                       89**********************************************************...78899********* PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SH........HHHHHHHHHHTTEEEEEEEEEXTTTTHH CS
                             IF-2B  79 liekikelikeieeadekigdiaaelikdgdtilTicnskt........vlevlraaakekkkfkVivvEsrPrlqG 147
                                       +ie++k++++e++++++kig+++++l++dgdt+lT+cn++         +l+v+r+a++++k++kV+++E+rP +qG
  gi|298674071|ref|YP_003725821.1| 119 AIEEAKQIADEDVAINKKIGEHGSKLLEDGDTVLTHCNAGKlacvdwgtALGVIRSAIESGKNIKVVACETRPLNQG 195
                                       ***************************************************************************** PP

                                       .HTHHHHHHHTTXEEEEEEGGGHHHHHHC.TESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGGB CS
                             IF-2B 148 .rltakeLvqagipvtlitdsavayvmse.evdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslkf 222
                                        rlt +eL+q++ipvtli ds++++v+++  +dkvivGAdri+e+  ++nkiGT++ +vlAke++ip++v+a++++f
  gi|298674071|ref|YP_003725821.1| 196 sRLTTWELMQDNIPVTLISDSMAGHVIRHeAIDKVIVGADRITEDA-VFNKIGTYTHSVLAKEHEIPFYVAAPTSTF 271
                                       *****************************9***************9.****************************** PP

                                       ESTSSSGGGSSXXBEXTHHHHEETTEESSTTTEEEEEBSEEEEEGGGXSEEEETTEEEXC CS
                             IF-2B 223 servqldedifieerdpeellnitgeriaeeelkvvnpafDvtPpelItliITevGvlpp 282
                                       + +  ++  + ie r+++el ++ +++ia+e+++v+npafD tP e+I++iITe Gv+ p
  gi|298674071|ref|YP_003725821.1| 272 DFK-GWEGSVKIEQRNADELRYFGNVQIAPENVNVYNPAFDATPMENISAIITENGVFHP 330
                                       ***.78888899*********************************************987 PP

>> Peroxin-22  Peroxisomal biogenesis protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.5e-05      0.13      58      79 ..      23      44 ..       5      87 .. 0.83
   2 ?    0.2   0.0     0.077   6.9e+02      52      67 ..     174     196 ..     165     253 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.5e-05
                        Peroxin-22 58 neyKiilcdssdglsavvkqLk 79
                                       eyK+i+c+++++l + +k+L+
  gi|298674071|ref|YP_003725821.1| 23 SEYKVIECKTIESLCESIKSLR 44
                                      46******************98 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.077
                        Peroxin-22  52 eevsskneyKiilcd.......s 67 
                                       + ++s+++ K++ c+       s
  gi|298674071|ref|YP_003725821.1| 174 SAIESGKNIKVVACEtrplnqgS 196
                                       56789999999999955555551 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 2004.03
//
Query:       gi|298674072|ref|YP_003725822.1|  [L=250]
Description: type 11 methyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-11   42.4   0.0    4.9e-09   36.2   0.0    2.1  2  GCD14            tRNA methyltransferase complex GCD14 subunit
    1.2e-10   41.4   0.0    1.7e-10   40.9   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    1.2e-08   34.4   0.0    1.8e-08   33.8   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
    3.3e-08   34.1   0.0    8.7e-08   32.8   0.0    1.7  1  Methyltransf_25  Methyltransferase domain
      3e-07   30.4   0.0      4e-07   30.0   0.0    1.1  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    3.5e-07   30.8   0.0    8.2e-07   29.6   0.0    1.7  1  Methyltransf_11  Methyltransferase domain
    2.5e-06   27.1   0.2    3.4e-06   26.7   0.2    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    5.3e-06   26.4   0.1    8.7e-06   25.7   0.1    1.2  1  Methyltransf_18  Methyltransferase domain
    6.9e-06   25.7   0.1    1.2e-05   24.9   0.1    1.4  1  MTS              Methyltransferase small domain
    4.7e-05   22.8   0.0    6.5e-05   22.4   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    0.00014   21.6   0.1     0.0017   18.0   0.0    2.1  2  Cons_hypoth95    Conserved hypothetical protein 95
    0.00051   19.9   0.0     0.0011   18.8   0.0    1.6  1  Methyltransf_23  Methyltransferase domain
    0.00055   19.3   0.0    0.00089   18.6   0.0    1.3  1  GidB             rRNA small subunit methyltransferase G
      0.001   19.8   0.1     0.0029   18.3   0.1    1.8  1  Methyltransf_12  Methyltransferase domain
     0.0088   17.0   0.0       0.02   15.9   0.0    1.6  1  Methyltransf_24  Methyltransferase domain
  ------ inclusion threshold ------
      0.011   15.3   0.3       0.12   11.9   0.3    2.1  1  DOT1             Histone methylation protein DOT1
      0.013   15.1   0.0      0.035   13.7   0.0    1.6  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
      0.019   14.5   0.1      0.032   13.8   0.1    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
      0.021   14.8   0.0      0.028   14.4   0.0    1.3  1  Methyltransf_32  Methyltransferase domain
       0.03   13.6   0.0      0.044   13.1   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
      0.046   13.5   0.1      0.093   12.5   0.1    1.5  1  Met_10           Met-10+ like-protein
       0.06   13.0   0.0      0.082   12.6   0.0    1.2  1  N6_N4_Mtase      DNA methylase
       0.14   11.9   0.0       0.19   11.5   0.0    1.3  1  Methyltransf_16  Lysine methyltransferase


Domain annotation for each model (and alignments):
>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.0   6.2e-12   4.9e-09      25     177 ..      80     225 ..      63     231 .. 0.89
   2 ?    5.0   0.0     0.022        17     225     246 ..     228     249 ..     222     250 .] 0.83

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 6.2e-12
                             GCD14  25 ytaDisliimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrDv 101
                                          Di +ii++  +++  vv++ GtG+g l+ ++  +va   ++ t+e  e+  + +r++ ++ + s+++ ++h + 
  gi|298674072|ref|YP_003725822.1|  80 MPRDIGIIITNTGINKNDVVLDVGTGTGILAMYLG-SVA--KRVVTYESNEEFFKVSRKNINSLG-SDNIELRHGNF 152
                                       457***************************99986.555..589****************98766.7799****999 PP

                             GCD14 102 ckeGfdeevsgkvDavfLDlPaPweaiphaakalkkeggrlCsfsPCieqvqrtceaLrelgfteietlevllrty 177
                                         e   e+++++ D + LD     + +p  ++ l + gg l ++sP  eq ++  ea  +++f+e++t+e   r+ 
  gi|298674072|ref|YP_003725822.1| 153 VDEI--EHINEQFDVITLDTVDAGKIVPYTVNLL-RPGGYLAAYSPFFEQTKQIREAADNTNFIEVSTVECIERNI 225
                                       8774..69**************************.99*********************************998865 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.022
                             GCD14 225 tevllkPvselkghtgyLtfat 246
                                       te  ++P s  +ghtg++t a+
  gi|298674072|ref|YP_003725822.1| 228 TERGTRPASSRVGHTGFITIAR 249
                                       566689*************997 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.0   2.2e-13   1.7e-10       2     127 ..      94     208 ..      93     238 .. 0.77

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 2.2e-13
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgp.kaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfD 76 
                                       +k+ +vlD+G+GtG l+  l     +  ++vv  + +ee  +++r+n  +lg+dn+e+++g++ + +e  ++ e+fD
  gi|298674072|ref|YP_003725822.1|  94 NKNDVVLDVGTGTGILAMYLG----SvAKRVVTYESNEEFFKVSRKNINSLGSDNIELRHGNFVDeIEH-IN-EQFD 164
                                       7999*********87766666....41456***********************************8885.56.89** PP

                   Methyltransf_31  77 lilsnevlnaladpdkileeiervlkpggilliedprllaelpakveeesk 127
                                       +i+ +     + d  ki     ++l+pgg+l++ +p    e+ ++++e  +
  gi|298674072|ref|YP_003725822.1| 165 VITLD-----TVDAGKIVPYTVNLLRPGGYLAAYSPF--FEQTKQIREAAD 208
                                       **995.....888889999889999999999988887..444444444444 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.0   2.2e-11   1.8e-08      22      86 ..      87     153 ..      81     166 .. 0.92

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 2.2e-11
                                       HHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S-CC CS
                            RrnaAD  22 IldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls..kdeklkvvhqDfl 86 
                                       I+ ++ +++++ vl++g+G+Gil   L   ak vv +E+ e+++k+ +k+++   + ++++ h +f 
  gi|298674072|ref|YP_003725822.1|  87 IITNTGINKNDVVLDVGTGTGILAMYLGSVAKRVVTYESNEEFFKVSRKNINslGSDNIELRHGNFV 153
                                       88899999*****************************************999888899999888876 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0   1.1e-10   8.7e-08       1      97 []      99     188 ..      99     188 .. 0.86

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 1.1e-10
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBC.CGBSSSTTTEEEEEEESTGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgda.edlpfedgsfDlvvssgalh 75 
                                       vLd+G+GtG l+++l      ++v+  + +ee+ +  r+++++ g  n+e+++g++ ++++  +++fD++++  +  
  gi|298674072|ref|YP_003725822.1|  99 VLDVGTGTGILAMYLGSVA--KRVVTYESNEEFFKVSRKNINSLGSdNIELRHGNFvDEIEHINEQFDVITLD-T-- 170
                                       9**************9885..9*******************998889*********777***********993.3.. PP

                                       GSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  76 hlsdedlekalkeiarvLkpgG 97 
                                        +   d+ k++    ++L+pgG
  gi|298674072|ref|YP_003725822.1| 171 -V---DAGKIVPYTVNLLRPGG 188
                                       .2...45566667777777776 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   5.1e-10     4e-07      69     171 ..      91     192 ..      72     223 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 5.1e-10
                                       TT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGG.G-SEE CS
                              PCMT  69 lelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyee.kaPYd 144
                                         ++k + vL+vG+G+G+l+  l  + +   rvv+ e  +e+ + +++n++ l+++n+ +++g      e+ +  +d
  gi|298674072|ref|YP_003725822.1|  91 TGINKNDVVLDVGTGTGILAMYLGSVAK---RVVTYESNEEFFKVSRKNINSLGSDNIELRHGNFVDEIEHiNEQFD 164
                                       45899999*********98877777665...578*****************************99888887245799 PP

                                       EEEE.SSBBSS--HHHHHTEEEEEEEEE CS
                              PCMT 145 aihv.gaaapeiPealidQLkeGGrlvv 171
                                       +i + ++ a +i    ++ L +GG l +
  gi|298674072|ref|YP_003725822.1| 165 VITLdTVDAGKIVPYTVNLLRPGGYLAA 192
                                       9987345555555556889999998864 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0     1e-09   8.2e-07       1      95 [.     100     191 ..     100     192 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 1e-09
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCC.TSS-TT-EEEEEEES-CCC-C CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl.kvefvvadaek.lpfednsfDlvvssevlhhve 75 
                                       LdvG+GtG+la +l + ++rvv+ + ++e+ k+++++++  g  ++e++++++ + +   +++fD++++     +v 
  gi|298674072|ref|YP_003725822.1| 100 LDVGTGTGILAMYLGSVAKRVVTYESNEEFFKVSRKNINSLGSdNIELRHGNFVDeIEHINEQFDVITLD----TV- 171
                                       8**************999************************9*********997589999******755....56. PP

                                       CHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  76 dpekalkeiaRvLkpgGllv 95 
                                       d  k++   + +L+pgG+l+
  gi|298674072|ref|YP_003725822.1| 172 DAGKIVPYTVNLLRPGGYLA 191
                                       78999999999999999986 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.2   4.4e-09   3.4e-06     159     280 ..      93     215 ..      84     226 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 4.4e-09
                              PrmA 159 vkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkvea.klev.alseellk..eekadviv 231
                                       +++++ vlDvGtG+GiLa+    + ak+vv +  +e   kv+++N++  + ++ +l+  +  +e+ +  +e++dvi 
  gi|298674072|ref|YP_003725822.1|  93 INKNDVVLDVGTGTGILAMYLGSV-AKRVVTYESNEEFFKVSRKNINSLGSDNiELRHgNFVDEI-EhiNEQFDVIT 167
                                       678899***********9865554.89******************98776655333322223333.24789****98 PP

                              PrmA 232 aNILaevlielaedikklvkeggllilSGilkekaeevaealeq.gfele 280
                                          +     ++++ + +l+++gg+l++     e++++++ea+ + +f  +
  gi|298674072|ref|YP_003725822.1| 168 LDTVDA--GKIVPYTVNLLRPGGYLAAYSPFFEQTKQIREAADNtNFIEV 215
                                       776643..5889999*********99988899999999998865455433 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.1   1.1e-08   8.7e-06      12      87 ..      93     167 ..      88     173 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.1e-08
                   Methyltransf_18  12 vekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklk.eee.vdtv 86 
                                       ++k+++v+D+Gt  g+l++yl   + ak+v+  + ne+ ++ +++ni++ g  d+ie+r ++ +++++  +e +d++
  gi|298674072|ref|YP_003725822.1|  93 INKNDVVLDVGTGTGILAMYLG--SVAKRVVTYESNEEFFKVSRKNINSLGS-DNIELRHGNFVDEIEhINEqFDVI 166
                                       78999****************8..7999*********************986.89**********999634448877 PP

                   Methyltransf_18  87 v 87 
                                       +
  gi|298674072|ref|YP_003725822.1| 167 T 167
                                       6 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.1   1.6e-08   1.2e-05      31     101 ..      95     166 ..      83     169 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.6e-08
                                       TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTST..TS-EEEE CS
                               MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeve..ekkfdli 101
                                       +++ vlD+G+G+G+l++ l +  ++  v+ ++ + +  +++++n+++ + + +e+++ + ++e+e  +++fd+i
  gi|298674072|ref|YP_003725822.1|  95 KNDVVLDVGTGTGILAMYLGSVAKR--VVTYESNEEFFKVSRKNINSLGSDnIELRHGNFVDEIEhiNEQFDVI 166
                                       56779****************9888..9**********************99**********999778999998 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   8.4e-08   6.5e-05      43     149 ..      91     190 ..      81     209 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 8.4e-08
                                       --S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--.TTT-TTS-T-EE CS
                   Ubie_methyltran  43 vavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqan.aeeLpfeddsfD 118
                                       ++  +   vlDv +Gtg la+ l + ++   +vv  + ne+ +kv++k ++  g  nie+ ++n   e++  ++ fD
  gi|298674072|ref|YP_003725822.1|  91 TGINKNDVVLDVGTGTGILAMYLGSVAK---RVVTYESNEEFFKVSRKNINSLGSDNIELRHGNfVDEIEHINEQFD 164
                                       455667789************9987765...69999****************************4579********* PP

                                       EEEEES-GGG-S-HHHHHHHHHHHEEEEEEE CS
                   Ubie_methyltran 119 vvtvsfGlrnvtDklkaLkeayrvlkpGGrl 149
                                       v+t+     ++ D  k +      l+pGG l
  gi|298674072|ref|YP_003725822.1| 165 VITL-----DTVDAGKIVPYTVNLLRPGGYL 190
                                       ***8.....4667777777777777777766 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.2e-06    0.0017      42     120 ..      96     169 ..      85     217 .. 0.80
   2 ?    1.6   0.0      0.25   1.9e+02      10      37 ..     222     248 ..     215     250 .] 0.81

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.2e-06
                                       C-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEE CS
                     Cons_hypoth95  42 garvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivf 118
                                       +  vLD+  G+G l++  l   ak++v  e+++e +k+ ++n+++l+ ++ ++    + ++++++    +e+fd++ 
  gi|298674072|ref|YP_003725822.1|  96 NDVVLDVGTGTGILAMY-LGSVAKRVVTYESNEEFFKVSRKNINSLGSDN-IELRHGNFVDEIEHI---NEQFDVIT 167
                                       56799*******99996.56689************************776.777777777777666...789****9 PP

                                       E- CS
                     Cons_hypoth95 119 lD 120
                                       lD
  gi|298674072|ref|YP_003725822.1| 168 LD 169
                                       99 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.25
                                       TXEEEXTTXXXXXSSSHHHHHHHHHHHC CS
                     Cons_hypoth95  10 grkLkvlegkstRPttdrvrealFnila 37 
                                       +r+++++e ++tRP ++rv ++ F ++a
  gi|298674072|ref|YP_003725822.1| 222 ERNISFTE-RGTRPASSRVGHTGFITIA 248
                                       67777777.69********999997775 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.4e-06    0.0011      21      88 ..      94     168 ..      81     222 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.4e-06
                   Methyltransf_23  21 raggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae........kakkaqkdqfdeqeaaepqgkfdlIvl 88 
                                       +++  vLd+G+GtGil+ +l    + v+ ++ ++e  +  +          +  ++ +f  +e++  +++fd+I+l
  gi|298674072|ref|YP_003725822.1|  94 NKNDVVLDVGTGTGILAMYLGSVAKRVVTYESNEEFFKVSRkninslgsDNIELRHGNF-VDEIEHINEQFDVITL 168
                                       78899***************777777777777654333222555556654444444444.6667777777777765 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.1e-06   0.00089      48     153 ..      95     199 ..      80     227 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.1e-06
                                       CC-.EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCC..TTTTT-EEEEEEC CS
                              GidB  48 krdkviDvGsGaGlPGipLaiarpelkltLleslekkiaFLeevkeelklenveivearaee..kqeeekydvvtsR 122
                                       k+d v+DvG+G G+ ++ L  +   ++++  es+e   +  ++ ++ l+ +n+e  + +  +   + +e++dv+t  
  gi|298674072|ref|YP_003725822.1|  95 KNDVVLDVGTGTGILAMYLGSV--AKRVVTYESNEEFFKVSRKNINSLGSDNIELRHGNFVDeiEHINEQFDVITLD 169
                                       3335*********855555444..445778899999999999************99877544456699********* PP

                                       -SSSHHHHHHHHCCCEEEEEEEEEEESS--H CS
                              GidB 123 AlaslnelteillkllkegglilalKGksae 153
                                        + +  +++ ++ +ll++gg++ a+    ++
  gi|298674072|ref|YP_003725822.1| 170 TVDAG-KIVPYTVNLLRPGGYLAAYSPFFEQ 199
                                       99765.7899**************9854333 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   3.7e-06    0.0029       1      72 [.     100     168 ..     100     190 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.7e-06
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg..ssfDlvva 72 
                                       L++G+GtG l+++l      ++++ ++ ++++++  ++ +++ +    +n+el++ +  d+ +   ++fD++++
  gi|298674072|ref|YP_003725822.1| 100 LDVGTGTGILAMYLGSV--AKRVVTYESNEEFFKVSRKNINSLGS---DNIELRHGNFVDEIEHinEQFDVITL 168
                                       8****************..**************777777777775...5566666666655555669*****86 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.6e-05      0.02       3     100 ..     102     189 ..     100     192 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.6e-05
                   Methyltransf_24   3 iGvysGvstlwllralrrngagrlvavdhdpgaeeaaalare...aglddrvrlikadseealaslaagsiDllfiD 76 
                                       +G+  G  +++l++ ++     r+v+ + ++   e+ ++ r+   +  +d+++l+++++ +++++ + +++D++ +D
  gi|298674072|ref|YP_003725822.1| 102 VGTGTGILAMYLGSVAK-----RVVTYESNE---EFFKVSRKninSLGSDNIELRHGNFVDEIEHIN-EQFDVITLD 169
                                       67777777777776665.....566788888...76666666665577889****************.9******** PP

                   Methyltransf_24  77 gghaaeavledleallprlapggv 100
                                             ++ + ++   ++l+pgg+
  gi|298674072|ref|YP_003725822.1| 170 TV----DAGKIVPYTVNLLRPGGY 189
                                       76....455555666666677766 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   0.00016      0.12      29     197 ..      82     231 ..      74     234 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00016
                                       HHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHHHHHHHHHHHHHHHTTB----EEE CS
                              DOT1  29 eflsevldkvnlkkedvFvDLGSGvGnvvlqaalevgcklsvGvEimdnaselaekqkeelkkrlklfGkklakief 105
                                         +  +++++ ++k+dv +D G G G + ++    ++    v  E         e+  ++ +k ++ +G +  +ie+
  gi|298674072|ref|YP_003725822.1|  82 RDIGIIITNTGINKNDVVLDVGTGTGILAMYLGSVAKR--VVTYESN-------EEFFKVSRKNINSLGSD--NIEL 147
                                       55667899999************999877766554433..3444443.......45555666777777865..6788 PP

                                       ESS-STT-HHHHHHGGG-SEEEE--TT--HHHHHHHHHHHTT--TT-EEEESS-SS-TT----SSSTT-GGGGEEEE CS
                              DOT1 106 irksFvenekveeiieeadvilvNNfaFdaelnkqlkellqdlkegtkiislkslvpskykinsrnledivnilkve 182
                                        +++Fv+  ++e+i e+ dvi    +  ++ +  +    +  l+ g+ + +  ++ +++++i  r++ d +n ++v+
  gi|298674072|ref|YP_003725822.1| 148 RHGNFVD--EIEHINEQFDVITLDTVDAGKIVPYT----VNLLRPGGYLAAYSPFFEQTKQI--REAADNTNFIEVS 216
                                       899**97..58899999****99887766655555....55689*************99995..67788899999** PP

                                       EEE--TT-BTTBSS- CS
                              DOT1 183 elkllegsVSWTskk 197
                                        +++ e ++S+T ++
  gi|298674072|ref|YP_003725822.1| 217 TVECIERNISFTERG 231
                                       **********99886 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.5e-05     0.035       8      91 ..      95     174 ..      92     182 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.5e-05
                                       TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..EEEEE CS
                   Methyltr_RsmB-F   8 eeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDriL 84 
                                       +++ +lD+ ++ G    ++  +   +++vv  + n+e  k   +n++ Lg  n+ + ++      + + + +fD i 
  gi|298674072|ref|YP_003725822.1|  95 KNDVVLDVGTGTGILAMYLGSV---AKRVVTYESNEEFFKVSRKNINSLGSDNIELRHGNFVDEIEHINE-QFDVIT 167
                                       68999***99999999999999...899********************************9988888885.9***** PP

                                       EEE--CC CS
                   Methyltr_RsmB-F  85 lDaPCsg 91 
                                       lD   +g
  gi|298674072|ref|YP_003725822.1| 168 LDTVDAG 174
                                       *986555 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1     4e-05     0.032       3      68 ..      98     162 ..      96     175 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4e-05
                   Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklkle 68 
                                       v+lD+ +G+G  ++ +  v ++v++ e+n+e  +++ +N ++ g sd+i l +g++ + +++++++
  gi|298674072|ref|YP_003725822.1|  98 VVLDVGTGTGILAMYLGSVAKRVVTYESNEEFFKVSRKNINSLG-SDNIELRHGNFVDEIEHINEQ 162
                                       79*****************************************6.899**********99987654 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.6e-05     0.028      24      90 ..      94     153 ..      84     223 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.6e-05
                   Methyltransf_32  24 sgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfaelsie 90 
                                       +++  v+DvG G g L+  l +       +vv  +++ee  + ++k  + lg+   ++++  +++  
  gi|298674072|ref|YP_003725822.1|  94 NKNDVVLDVGTGTGILAMYLGS----VAKRVVTYESNEEFFKVSRKNINSLGS---DNIELRHGNFV 153
                                       567889****************....689******************999993...44555555444 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.7e-05     0.044      53     186 ..      86     214 ..      69     219 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.7e-05
                                       HHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----S CS
                              CMAS  53 lileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvd 129
                                       +i+   ++++ + +Ld+G+G G l+++  +    +vv     +e  k+++k++++l+ +++ e++  ++ d  e+++
  gi|298674072|ref|YP_003725822.1|  86 IIITNTGINKNDVVLDVGTGTGILAMYLGSV-AKRVVTYESNEEFFKVSRKNINSLG-SDNIELRHGNFVDEIEHIN 160
                                       566777889999**********999986555.55899888889999***********.6778888888877555555 PP

                                       EEEEES-GGGTSGGGHHHHHHHHHHHS-TT-EEEEEEEEE--HHHHHCTTCCCHHHH CS
                              CMAS 130 rvvsvgafehvgkenydtffkklkkllkedGllllhtitslhkkelaerglklkfid 186
                                       +   v  ++ v   +   +   + +ll+++G l+  + +  ++k++ e+  +++fi+
  gi|298674072|ref|YP_003725822.1| 161 EQFDVITLDTVDAGKIVPY---TVNLLRPGGYLAAYSPFFEQTKQIREAADNTNFIE 214
                                       5444555555655555555...46788888888888888888888888877778875 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00012     0.093      98     145 ..      93     138 ..      87     165 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                                       --TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHH CS
                            Met_10  98 veegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkenik 145
                                       +++++vV+dv  G G +a+ ++    akrv++ + n e +k  ++ni+
  gi|298674072|ref|YP_003725822.1|  93 INKNDVVLDVGTGTGILAMYLGS--VAKRVVTYESNEEFFKVSRKNIN 138
                                       789*******************7..89999***************997 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00011     0.082     186     229 ..      90     133 ..      55     135 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                                       HHHS-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHHHHH CS
                       N6_N4_Mtase 186 klstkkgdivlDpFaGSGtTavaakelgrkfiGieieeeyvela 229
                                       +   +k+d+vlD   G+G  a++  +  ++ + +e +ee+++ +
  gi|298674072|ref|YP_003725822.1|  90 NTGINKNDVVLDVGTGTGILAMYLGSVAKRVVTYESNEEFFKVS 133
                                       567899*********************************99876 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00024      0.19      47     136 ..      96     177 ..      82     218 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00024
                   Methyltransf_16  47 klsvlELGsGtGlvGlavaellpeakviltDleellellkknielnknalkskvkvevLdWgeeleedllekeevDl 123
                                       +  vl++G GtG+  + + +   +  v+    ee  ++ +kni+    + +++++ +  +  +e+ e++  +e++D+
  gi|298674072|ref|YP_003725822.1|  96 NDVVLDVGTGTGILAMYLGSV-AKRVVTYESNEEFFKVSRKNINS---LGSDNIELRHGNFVDEI-EHI--NEQFDV 165
                                       5679**************999.788899999999*********99...56999999999999988.444..455775 PP

                   Methyltransf_16 124 ilaaDcvYledsl 136
                                       i   D v   + +
  gi|298674072|ref|YP_003725822.1| 166 I-TLDTVDAGKIV 177
                                       5.44555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1884.37
//
Query:       gi|298674073|ref|YP_003725823.1|  [L=222]
Description: DNA repair and recombination protein RadB [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-36  124.7   0.0    4.3e-36  124.5   0.0    1.0  1  Rad51         Rad51
      3e-12   46.6   0.0    3.6e-12   46.3   0.0    1.1  1  RecA          recA bacterial DNA recombination protein
    5.2e-11   42.3   0.5    3.4e-10   39.7   0.5    1.9  1  ATPase        KaiC
    5.9e-08   32.5   0.0    1.2e-07   31.5   0.0    1.5  1  AAA_25        AAA domain
    3.7e-07   30.1   0.0    5.6e-07   29.5   0.0    1.3  1  AAA_24        AAA domain
    7.9e-07   28.9   0.0    8.7e-07   28.8   0.0    1.1  1  Zot           Zonular occludens toxin (Zot)
    3.4e-05   23.3   0.0     0.0021   17.5   0.0    2.4  2  DnaB_C        DnaB-like helicase C terminal domain
    0.00031   20.5   0.0    0.00058   19.6   0.0    1.4  1  IstB_IS21     IstB-like ATP binding protein
    0.00078   19.4   0.0     0.0021   18.0   0.0    1.6  2  AAA_31        AAA domain
     0.0013   18.1   0.0     0.0014   17.9   0.0    1.1  1  DUF2075       Uncharacterized conserved protein (DUF2075)
     0.0016   19.0   0.0     0.0031   18.1   0.0    1.5  1  AAA_18        AAA domain
     0.0027   17.2   0.0     0.0042   16.6   0.0    1.4  1  KTI12         Chromatin associated protein KTI12
     0.0032   17.1   0.0      0.004   16.8   0.0    1.2  1  SRP54         SRP54-type protein, GTPase domain
     0.0063   16.5   0.2     0.0099   15.8   0.2    1.3  1  ATPase_2      ATPase domain predominantly from Archaea
  ------ inclusion threshold ------
      0.011   15.0   0.0      0.014   14.6   0.0    1.2  1  KAP_NTPase    KAP family P-loop domain
      0.013   15.5   0.0      0.018   15.1   0.0    1.2  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
      0.032   14.0   0.0      0.056   13.2   0.0    1.4  1  CLP1_P        mRNA cleavage and polyadenylation factor CLP1 P
       0.04   14.2   0.0       0.08   13.2   0.0    1.6  1  AAA_22        AAA domain
       0.04   13.4   0.0      0.052   13.1   0.0    1.2  1  RVT_1         Reverse transcriptase (RNA-dependent DNA polyme
      0.045   14.2   0.1      0.085   13.3   0.1    1.5  1  AAA           ATPase family associated with various cellular 
      0.093   11.3   0.0       0.15   10.7   0.0    1.3  1  GvpD          GvpD gas vesicle protein
       0.12   11.8   0.0       0.21   11.0   0.0    1.4  1  PhoH          PhoH-like protein
       0.12   12.9   1.0       0.28   11.7   1.0    1.7  1  ABC_tran      ABC transporter
       0.14   12.6   0.0       0.23   11.8   0.0    1.6  1  RNA_helicase  RNA helicase


Domain annotation for each model (and alignments):
>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.5   0.0   5.7e-39   4.3e-36      17     252 ..       3     221 ..       1     222 [] 0.92

  Alignments for each domain:
  == domain 1  score: 124.5 bits;  conditional E-value: 5.7e-39
                                       -EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGGHHHHH CS
                             Rad51  17 lqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrperlveiae 93 
                                       ++l  G+k lD+lLgGG+etg ++ ++Ge +sGkt lc +l+v +        +e+k++y+dte+ + p+r  +ia 
  gi|298674073|ref|YP_003725823.1|   3 VRLPSGCKPLDNLLGGGFETGIVSQVYGEPGSGKTNLCIQLSVECV------KQEKKVIYVDTEA-LSPDRFKQIA- 71 
                                       57889*********************************99999885......469*********6.9*********. PP

                                       HTT--HHHHGGGEEEEE--STTHHHHHHHHTHHHHHHS-EEEEEEETTTGGGCH-------THHHHHHHHHHHHHHH CS
                             Rad51  94 rykldkeevlenvayaRaytiehqeellqqaaallaedkfallivDsvtalyRtdfsgrgelakRqqklgkllrtLr 170
                                         + +++e+ +n+ +   ++ e+q++ ++  +++++e++++l+ivDs+ta yR + ++ +   +  ++l++ +  L+
  gi|298674073|ref|YP_003725823.1|  72 --GDNSKEIAQNIIIYEPFNFEEQYSAIKD-TEKISEENIGLIIVDSATAFYRFELENEDSSIQTRRELSNQIGYLH 145
                                       ..5699*********************987.5789************************998888899********* PP

                                       HHHHHH--EEEEEEE-------.------------HHHHHHHH-SEEEEEEE-STTEEEEEEES-SSS-S-E.EEEE CS
                             Rad51 171 kladefevavvitnqvvaqvdgqaalfsadpkkPigGlvlahasttRlalrkgkgeeRivkvvdsPnlpele.avfa 246
                                        la +++++vvitnq+  +  +        + kPigG  + h s+t l++ +  +++R + +++  + pe e + f+
  gi|298674073|ref|YP_003725823.1| 146 GLARKHSLSVVITNQIYTDAST-------GEVKPIGGSGIEHLSKTILQFERTGNNKRRAILQKHRSRPEGEtCEFM 215
                                       ****************987655.......6789*******************9999999999999999998746899 PP

                                       EETTEE CS
                             Rad51 247 igeeGi 252
                                       ig +G+
  gi|298674073|ref|YP_003725823.1| 216 IGPDGL 221
                                       999886 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.0   4.8e-15   3.6e-12      34     192 ..       5     164 ..       2     202 .. 0.81

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 4.8e-15
                                       E--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS----HHHHHHTT--.....G CS
                              RecA  34 issGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafidaehaldpkyakklGvd.....i 105
                                       ++sG   ld+ lG GG+  G + ++yG   sGkt l++++ +e+ k+ + + ++d+e al p+  k++  d      
  gi|298674073|ref|YP_003725823.1|   5 LPSGCKPLDNLLG-GGFETGIVSQVYGEPGSGKTNLCIQLSVECVKQEKKVIYVDTE-ALSPDRFKQIAGDnskeiA 79 
                                       68999********.*****************************************99.7888777776554233333 PP

                                       GG-EEE--SSH.HHHHHHHHH.HHTTT--SEEEEE-TTT---STT-----------HHHHHHHHHHHHHHHHHTTT- CS
                              RecA 106 dellvsqpdtG.eqaleiada.lvrsgaidlivvdsvaalvpkaeieGemgdskvglqarlmsqalrkltgaisksn 180
                                       +++++ +p +  eq   i d+  +    i li+vds +a+  + e+e e  ds++    r +s+ +  l g  +k  
  gi|298674073|ref|YP_003725823.1|  80 QNIIIYEPFNFeEQYSAIKDTeKISEENIGLIIVDSATAFY-RFELENE--DSSIQT-RRELSNQIGYLHGLARKHS 152
                                       689999**77615666777762577889********99975.7788765..665544.4778999************ PP

                                       -EEEEEEE---- CS
                              RecA 181 tvvifinqirek 192
                                         v+  nqi + 
  gi|298674073|ref|YP_003725823.1| 153 LSVVITNQIYTD 164
                                       ********9765 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.5   4.5e-13   3.4e-10       2     207 ..       6     205 ..       5     222 .] 0.66

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 4.5e-13
                            ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekle 78 
                                       ++g + lD++l gG+  g v  ++GepG+GKt ++ q  ++ +++ ++++++v +e  + d  +++   G + +++ 
  gi|298674073|ref|YP_003725823.1|   6 PSGCKPLDNLLGGGFETGIVSQVYGEPGSGKTNLCIQLSVECVKQ-EKKVIYVDTEALSPDRFKQI--AGDNSKEIA 79 
                                       8999*************************************9988.*******9999776544433..477777777 PP

                            ATPase  79 eegklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitgl..ayeekeav...aReilrqlvrv 150
                                       ++  ++i + ++ +e++++ kd+           e i+e ++  +++Ds t++   + e+e+    +R++l + +  
  gi|298674073|ref|YP_003725823.1|  80 QN--IIIYEPFNFEEQYSAIKDT-----------EKISEENIGLIIVDSATAFyrFELENEDSsiqTRRELSNQIGY 143
                                       77..9999999987764443333...........3445556666666666665432222222212255555543333 PP

                            ATPase 151 l....kklgvTailvsekss.....seeaaggygveefivdgvivLdlkeieeelvRtleivkmRg 207
                                       l    +k  +  ++++++ +     + + +gg g+e+ +++ +++ +++ ++   +R  +  k R+
  gi|298674073|ref|YP_003725823.1| 144 LhglaRKHSLSVVITNQIYTdastgEVKPIGGSGIEH-LSKTILQFERTGNN---KRRAILQKHRS 205
                                       3111367778888888887777777778899999999.77776666543333...33334455555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   1.7e-10   1.2e-07      20     165 ..      10     131 ..       4     159 .. 0.75

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 1.7e-10
                            AAA_25  20 pprrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgea 96 
                                       +p++ l++g    g ++ ++G pg+GKt l+++l++++++ +           kV+yv++E      + R++++  +
  gi|298674073|ref|YP_003725823.1|  10 KPLDNLLGGGFETGIVSQVYGEPGSGKTNLCIQLSVECVKQE----------KKVIYVDTEALS---PDRFKQIAGD 73 
                                       578888998889***************************755..........49*******999...******9999 PP

                            AAA_25  97 l.rddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralgg.densnsdv 165
                                       + ++ a+           + ++++ + +++  +++++ e+  ee  +++l+++D+ +++++   en++s +
  gi|298674073|ref|YP_003725823.1|  74 NsKEIAQN----------IIIYEPFNFEEQ-YSAIKDTEKISEE--NIGLIIVDSATAFYRFeLENEDSSI 131
                                       83222222..........333333222222.3677776655555..6***************867766665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   7.6e-10   5.6e-07       4      82 ..      25     124 ..      22     148 .. 0.80

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 7.6e-10
                            AAA_24   4 kiliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdie.................swedfldev 56 
                                         ++yG++g+GKT l+ +l       ++k++++dte+    l +d+f++i                  ++e+ ++++
  gi|298674073|ref|YP_003725823.1|  25 VSQVYGEPGSGKTNLCIQLsvecvkqEKKVIYVDTEA----LSPDRFKQIAgdnskeiaqniiiyepfNFEEQYSAI 97 
                                       5689********************************9....667777777666555666777777666666666666 PP

                            AAA_24  57 vel.aaeladyktlviDtideleelcl 82 
                                       +   +  ++++  +++D+++ ++++ l
  gi|298674073|ref|YP_003725823.1|  98 KDTeKISEENIGLIIVDSATAFYRFEL 124
                                       6666566788************99765 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   1.2e-09   8.7e-07       4     125 ..      27     160 ..      24     206 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1.2e-09
                               Zot   4 lvtGapGsgKtsgavkkdllpalkegRkiitnidGlrlerieqvlgekvs..tarliridnpegaetlkefakwati 78 
                                        v+G+pGsgKt   ++  +   ++e ++i+ + + l  +r++q+ g++ +  ++++i  +  +++e+ +++++  +i
  gi|298674073|ref|YP_003725823.1|  27 QVYGEPGSGKTNLCIQLSVECVKQEKKVIYVDTEALSPDRFKQIAGDNSKeiAQNIIIYEPFNFEEQYSAIKDTEKI 103
                                       589**************99999999*********************9999999999998866777777777777776 PP

                               Zot  79 d..kgallviDEcqeifpvrakegrkd.........pevi.naftehRhlgwDivlltq 125
                                          + +l+++D +  ++  + +++  d          + i      +R++   +v++ q
  gi|298674073|ref|YP_003725823.1| 104 SeeNIGLIIVDSATAFYRFELENE--DssiqtrrelSNQIgYLHGLARKHSLSVVITNQ 160
                                       654669************999973..334666666633332444556666666666655 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.8e-06    0.0021       2     104 ..       5     108 ..       4     118 .. 0.75
   2 !    6.5   0.2     0.006       4.5     124     181 ..     102     164 ..      58     212 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.8e-06
                                       BXSSTHHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHHHHH.TXXH CS
                                       xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                            DnaB_C   2 lstgfkdLDklts.GlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRllssea.eids 76 
                                       l++g k LD+l++ G++ g +  + + p+ Gkt l++++  ++++ ++++v+++  e  + + ++++   ++ ei +
  gi|298674073|ref|YP_003725823.1|   5 LPSGCKPLDNLLGgGFETGIVSQVYGEPGSGKTNLCIQLSVECVK-QEKKVIYVDTEALSPDRFKQIAGDNSkEIAQ 80 
                                       6899999**9986379***99*******************98875.6679999999998888888888765537777 PP

                                       HHHHHTTSX.HHHHHHHHHHHHHHHHSEE CS
                                       xxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  77 kklrtgklk.eedweklteaieelseakl 104
                                       + +    ++ ee+++   + +e++se ++
  gi|298674073|ref|YP_003725823.1|  81 NIIIYEPFNfEEQYS-AIKDTEKISEENI 108
                                       777666666343444.4444566776653 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.006
                                       HHHHTTEEEEEEEEGGGTB....TSCS..SS.CCCHHHHHHHHHHHHHHHHCTSXEEEEEEXSGG CS
                                       xxxxxxxxxxxxxxxxxxx....xxxx..xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C 124 lkkekglgliviDyLqlme....gsee..ke.nreqevseisrsLkalakelnvpvialsqLsra 181
                                         +e+++gli++D          +  +  ++ + ++e+s+    L  la+  ++ v++  q+  +
  gi|298674073|ref|YP_003725823.1| 102 KISEENIGLIIVDSATAFYrfelE--NedSSiQTRRELSNQIGYLHGLARKHSLSVVITNQIYTD 164
                                       224599*******88776633221..223223566789998899**************9998655 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   7.7e-07   0.00058      52      87 ..      28      63 ..      21      84 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 7.7e-07
                         IstB_IS21 52 llGpsGvGKshlaialgveavraglsvlfvrvedLv 87
                                      + G +G GK+ l i l+ve v+++++v++v +e+L 
  gi|298674073|ref|YP_003725823.1| 28 VYGEPGSGKTNLCIQLSVECVKQEKKVIYVDTEALS 63
                                      68******************************9985 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.9e-06    0.0021      12      98 ..      33     125 ..      23     147 .. 0.58
   2 ?   -1.4   0.0       2.5   1.9e+03     151     173 ..     172     194 ..     150     197 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.9e-06
                            AAA_31  12 GvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgi..ekneiektlyevl.....ieeknikeaiiktkvenl 81 
                                       G GKT  +++l++   k++kkv+ vD  + +   ++     +++ei ++++         + + ik++ +  + en+
  gi|298674073|ref|YP_003725823.1|  33 GSGKTNLCIQLSVECVKQEKKVIYVDTEALSPDRFKQIAgdNSKEIAQNIIIYEpfnfeEQYSAIKDTEK-ISEENI 108
                                       99************************99876665532221134444444433323232112223333332.334555 PP

                            AAA_31  82 dlipssidLaeaeielv 98 
                                        li  +   a +  el 
  gi|298674073|ref|YP_003725823.1| 109 GLIIVDSATAFYRFELE 125
                                       55554444444444444 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.5
                            AAA_31 151 ayaleGleqllktieevkkklnp 173
                                       +   +G+e+l kti +++++ n+
  gi|298674073|ref|YP_003725823.1| 172 PIGGSGIEHLSKTILQFERTGNN 194
                                       45668999999999999988665 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.9e-06    0.0014       6     102 ..      28     121 ..      24     183 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.9e-06
                           DUF2075   6 VtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakkeekkkkkea.feklssfinnlsefkkae 81 
                                       V G++G+GKt + ++l +e+    +++++v+ +  ++l     +++a++++k+  ++  + ++ +f +++s   k +
  gi|298674073|ref|YP_003725823.1|  28 VYGEPGSGKTNLCIQLSVEC---VKQEKKVIYVDTEALSPDRFKQIAGDNSKEIAQNIiIYEPFNFEEQYS-AIKDT 100
                                       99******************...556666666677777778888999999555555541567778888888.45556 PP

                           DUF2075  82 ekkeepkedvvivDEAhrllt 102
                                       ek +e+++ ++ivD A     
  gi|298674073|ref|YP_003725823.1| 101 EKISEENIGLIIVDSATAFYR 121
                                       666788899999998865555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   4.2e-06    0.0031       3      89 ..      28     123 ..      27     136 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 4.2e-06
                            AAA_18   3 ltGtpGvGKttlakeLskrlgf..gvnlrdvakenglllevdpealdeskrldedkldklldaleenss........ 69 
                                       + G pG+GKt l+  Ls ++ +    +++ v +e  + + + + a d+sk++ ++   +   ++ee++s        
  gi|298674073|ref|YP_003725823.1|  28 VYGEPGSGKTNLCIQLSVEC-VkqEKKVIYVDTEALSPDRFKQIAGDNSKEIAQNIIIYEPFNFEEQYSaikdteki 103
                                       6799************8886.24333344333443333333333778888888888888888888888888888777 PP

                            AAA_18  70 aleegknlvidghlaelese 89 
                                       ++e+ + +++d+  a +++e
  gi|298674073|ref|YP_003725823.1| 104 SEENIGLIIVDSATAFYRFE 123
                                       66777777888877776655 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   5.6e-06    0.0042       6      50 ..      28      72 ..      26     137 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.6e-06
                                      EE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH.TTSSS--G CS
                             KTI12  6 ltGlPssGKstrakeLakaleeekrsvvviddeslgiekdsykds 50
                                      + G P sGK+ +  +L+ +  +++++v+++d+e+l  ++ +    
  gi|298674073|ref|YP_003725823.1| 28 VYGEPGSGKTNLCIQLSVECVKQEKKVIYVDTEALSPDRFKQIAG 72
                                      579*******************************99666654433 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   5.3e-06     0.004       6      92 ..      28     116 ..      24     158 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.3e-06
                                       EEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHH.....HHHHHTTEEEEESSTTSCHHHHHHHHHH CS
                             SRP54   6 lvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLk.....tlaeklgvpvikkkeeadpaavakeave 77 
                                       + G  G+GKT  + +L+  + k++kkv+ v +    +  ++Q++     ++a+++   +++   + ++   a +  e
  gi|298674073|ref|YP_003725823.1|  28 VYGEPGSGKTNLCIQLSVECVKQEKKVIYVDTEALSPDRFKQIAgdnskEIAQNII--IYE-PFNFEEQYSAIKDTE 101
                                       67899**********************99977666666666665100004444444..444.444456667778889 PP

                                       HHHHTTSSEEEEEE- CS
                             SRP54  78 kakeekidvvlvDTa 92 
                                       k  ee+i +++vD+a
  gi|298674073|ref|YP_003725823.1| 102 KISEENIGLIIVDSA 116
                                       99999********98 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2   1.3e-05    0.0099      21      82 ..      24      82 ..      18     132 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.3e-05
                          ATPase_2 21 eiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal 82
                                       +  +YG  gsGKt L  ++  +  +++k+viy++  +  s +++++     +++k++++ +
  gi|298674073|ref|YP_003725823.1| 24 IVSQVYGEPGSGKTNLCIQLSVECVKQEKKVIYVD-TEALSPDRFKQI--AGDNSKEIAQNI 82
                                      56679***********9999999988899999986.566666666666..334444445544 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.9e-05     0.014      18      78 ..      21      79 ..      11     113 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.9e-05
                        KAP_NTPase 18 atpivvgLygkWGsGKssllnkledelkefakpvrflfaefnawsfkggddavaellaaLa 78
                                      +t+iv  +yg+ GsGK+ l+  l  e  ++  +++++ ++ +a+s++   ++  +  +++a
  gi|298674073|ref|YP_003725823.1| 21 ETGIVSQVYGEPGSGKTNLCIQLSVECVKQ--EKKVIYVDTEALSPDRFKQIAGDNSKEIA 79
                                      6899999********************999..99***********9987777666666665 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   2.4e-05     0.018       9      84 ..      33     203 ..      26     214 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.4e-05
                                       TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................... RF
                              CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................... 54 
                                       G+GKT l++ L +   +++++V+ vD+   ++  +   +  +d  +                               
  gi|298674073|ref|YP_003725823.1|  33 GSGKTNLCIQLSVECVKQEKKVIYVDTEALSPDRFK--QIAGDNSKeiaqniiiyepfnfeeqysaikdtekiseen 107
                                       9*************************9999998873..333333335556899999999999999999999998888 PP

                                       .....................................................................CCHCCCHH CS
                                       .....................................................................xxxxxxxx RF
                              CbiA  55 .....................................................................dlkrllel 62 
                                                                                                            +++ l+++
  gi|298674073|ref|YP_003725823.1| 108 igliivdsatafyrfelenedssiqtrrelsnqigylhglarkhslsvvitnqiytdastgevkpiggsGIEHLSKT 184
                                       88888888888888888888888888888888888888888877777777777777777777777766666666666 PP

                                       HHHHCHCHHHH..EEEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  63 lealgkkkalllkiagvvlnrv 84 
                                       + ++ ++ +   +  + +l ++
  gi|298674073|ref|YP_003725823.1| 185 ILQFERTGN---NKRRAILQKH 203
                                       655554433...4555555555 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   7.5e-05     0.056       1      30 [.      30      59 ..      30      64 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.5e-05
                            CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDl 30
                                      G+  sGK+ l+  L  +++++++k++yvD+
  gi|298674073|ref|YP_003725823.1| 30 GEPGSGKTNLCIQLSVECVKQEKKVIYVDT 59
                                      7789*************************7 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00011      0.08      10     104 ..      28     120 ..      23     161 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                            AAA_22  10 vtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka.....erlsseellea 81 
                                       v+Ge+G+GKT l+ +l  + +++      +++v++v+  +++ ++ + ++++ +   e        e+ + ee ++a
  gi|298674073|ref|YP_003725823.1|  28 VYGEPGSGKTNLCIQLSVECVKQ------EKKVIYVDTEALS-PDRF-KQIAGDNSKEIAQniiiyEPFNFEEQYSA 96 
                                       89***********9999998776......8999999999888.3333.33333333222223555777788888888 PP

                            AAA_22  82 leqalrarav.ielliiDEaqhlr 104
                                       + +  +     i+l+i+D a  + 
  gi|298674073|ref|YP_003725823.1|  97 IKDTEKISEEnIGLIIVDSATAFY 120
                                       877777776677888888777764 PP

>> RVT_1  Reverse transcriptase (RNA-dependent DNA polymerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.9e-05     0.052      32     128 ..      77     167 ..      53     177 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.9e-05
                                       ......-------HHHH.............HCCHTS--EEEEEEBCCGCCCSBB-GGGGGGG-EEET.......... CS
                             RVT_1  32 dvlekllsenqpgfrpgrstldavedllkalkkkkkaklllklDlkkaFdsvpleellrkltafkvptklinliksf 108
                                       +++++++ ++ ++f+++ s       ++++ k   ++  l+ +D   aF + +le +++ +++ +  +++i +++ +
  gi|298674073|ref|YP_003725823.1|  77 EIAQNIIIYEPFNFEEQYSA------IKDTEKISEENIGLIIVDSATAFYRFELENEDSSIQTRRELSNQIGYLHGL 147
                                       44467777777777777666......445555667799*************************************** PP

                                       ...............TEEEE CS
                             RVT_1 109 lstrsfsvrvngeeskgrye 128
                                        ++ s sv ++++  +   +
  gi|298674073|ref|YP_003725823.1| 148 ARKHSLSVVITNQIYTDAST 167
                                       *****999998874455555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   0.00011     0.085       3      74 ..      28     123 ..      27     165 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                                       EESSTTSSHHHHHHHHHHHH...THEEEEEETTTCSSS.......................STTHHHHHHHHHHHHH CS
                               AAA   3 lyGppGtGKTllakavakel...gvefleisgsellsk.......................yvgesekkirelfkea 53 
                                       +yG pG GKT l+ ++  e+   + +++ ++   l  +                        ++e+ + i+++ k  
  gi|298674073|ref|YP_003725823.1|  28 VYGEPGSGKTNLCIQLSVECvkqEKKVIYVDTEALSPDrfkqiagdnskeiaqniiiyepfNFEEQYSAIKDTEKI- 103
                                       79**************999865435566666555553345555555555555566665555555555555555443. PP

                                       HHTSTSEEEEEETGGGHHHHH CS
                               AAA  54 kekakpsilfiDEidalaksr 74 
                                       +e++    +++D + a+ + +
  gi|298674073|ref|YP_003725823.1| 104 SEEN-IGLIIVDSATAFYRFE 123
                                       3333.5777777777776666 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0    0.0002      0.15      14      46 ..      27      60 ..      10      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0002
                              GvpD 14 likGaPGtGktlftlr.gldvlrresdvlyvstr 46
                                       + G+PG+Gkt + ++  ++ +++e++v+yv t 
  gi|298674073|ref|YP_003725823.1| 27 QVYGEPGSGKTNLCIQlSVECVKQEKKVIYVDTE 60
                                      478************945899**********985 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00028      0.21      23      52 ..      27      54 ..      19      82 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00028
                                      EEE--TTSSTTHHHHHHHHHHHHTTS-SEE CS
                              PhoH 23 faiGpaGtGKtylavalavealkkkkvkri 52
                                       + G+ G+GKt l ++l ve +k++k  ++
  gi|298674073|ref|YP_003725823.1| 27 QVYGEPGSGKTNLCIQLSVECVKQEK--KV 54
                                      578*******************9974..44 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.0   0.00038      0.28       8      65 ..      20     112 ..      15     202 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00038
                                       EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE.......................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................................... RF
                          ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGei.......................................... 42 
                                       ++ g + ++ Ge G+GK+ L+  l+ +  ++e ++                                          
  gi|298674073|ref|YP_003725823.1|  20 FETGIVSQVYGEPGSGKTNLCIQLSVECVKQEKKViyvdtealspdrfkqiagdnskeiaqniiiyepfnfeeqysa 96 
                                       5677788999***************9999999999655555555555554444444443333333333322222222 PP

                                       .EETTCEGGGB-HHHCCHCEEEE- CS
                                       .xxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  43 .lldgkdlkeqeleslrkeigvlp 65 
                                        +        +++++++++ig + 
  gi|298674073|ref|YP_003725823.1|  97 iK--------DTEKISEENIGLII 112
                                       20........23333333333333 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00031      0.23       3      35 ..      28      56 ..      26     105 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00031
                      RNA_helicase  3 lyGpsgeGKStlakeLakallkklklkkkdsvy 35
                                      +yG++g GK++l+ +L+ +  k+     k+ +y
  gi|298674073|ref|YP_003725823.1| 28 VYGEPGSGKTNLCIQLSVECVKQE----KKVIY 56
                                      8**************988887433....34444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 1462.52
//
Query:       gi|298674074|ref|YP_003725824.1|  [L=83]
Description: glutaredoxin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.8e-09   35.8   0.0    8.8e-09   35.5   0.0    1.2  1  Glutaredoxin   Glutaredoxin
    0.00019   21.7   0.1    0.00025   21.4   0.1    1.3  1  DUF836         Glutaredoxin-like domain (DUF836)
  ------ inclusion threshold ------
      0.029   14.4   0.2      0.044   13.8   0.2    1.4  1  Thioredoxin_3  Thioredoxin domain
       0.04   14.3   0.0      0.054   13.9   0.0    1.3  1  GST_N_3        Glutathione S-transferase, N-terminal domain
       0.06   13.0   0.0      0.064   12.9   0.0    1.1  1  DUF5095        Domain of unknown function (DUF5095)
      0.072   13.5   0.0      0.074   13.5   0.0    1.2  1  Thioredoxin_2  Thioredoxin-like domain
       0.12   12.6   0.0       0.12   12.6   0.0    1.2  1  MSV199         MSV199 domain


Domain annotation for each model (and alignments):
>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.0   3.4e-12   8.8e-09       1      59 [.       4      62 ..       4      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 3.4e-12
                                      EEEEESTSSHHHHHHHHHHHHTTGGEEEEEGCCSHHHHHHHHHHH..TSSSSSEEEETTEE CS
                      Glutaredoxin  1 vvlftkptCpyCkkakrlLkelgvkfeeidvdkdeeireelkels..gvrtvPqvfidgkh 59
                                      ++++t+ tCp C + k+lLk+++++f+e d +  +e+  el+ +   + +t P + id+k+
  gi|298674074|ref|YP_003725824.1|  4 IIIYTTETCPKCEQLKKLLKSNNISFKEADMST-PEALTELRVNGvfD-VTAPILQIDDKF 62
                                      79****************************999.69999998887866.999999999987 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.1   9.9e-08   0.00025       2      57 ..       4      60 ..       3      81 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 9.9e-08
                                      EEEEE-TT-HHHHHHHHHHHHHCCCTTEEEEEEETTT-CCCHC.....CCCTTTTEEEECT CS
                            DUF836  2 ltLyskpgChlCeqakekLkelkleegleleviDIakdeelea.....kYgleipvlaleg 57
                                      +++y+++ C+ Ceq+k++Lk     ++++ ++ D  + e l +      ++++ p l +++
  gi|298674074|ref|YP_003725824.1|  4 IIIYTTETCPKCEQLKKLLKS----NNISFKEADMSTPEALTElrvngVFDVTAPILQIDD 60
                                      9*******************4....445666777777666655555667777777777766 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   1.7e-05     0.044       3      58 ..       4      61 ..       2      75 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.7e-05
                                      EEE.ESSSSTTCHHHHHHHHHHCHCCTCEC...EEECCTTHHHHHHCT-SSS..SEEECTTC CS
                     Thioredoxin_3  3 ikv.lgpgCakCpklekavkeaaaekgika...evekvtdfeeiekygVmsv..Palvidgk 58
                                      i +  + +C+kC++l+k++k    +++i++   ++   + + e+  +gV  v  P l id+k
  gi|298674074|ref|YP_003725824.1|  4 IIIyTTETCPKCEQLKKLLK----SNNISFkeaDMSTPEALTELRVNGVFDVtaPILQIDDK 61
                                      56644677*****9877765....45555522244444555555555554434466666666 PP

>> GST_N_3  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.1e-05     0.054       2      58 ..       7      64 ..       6      83 .] 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.1e-05
                                      ES-TTSHHHHHHHHHHHHHT--EEEE---TTTTHHHHHHH-.TT--SSEEETTS-EEE CS
                           GST_N_3  2 ygfpaSpyarrvrlaLnekglpvevvevtpgehdeellakn.plgkvPvLeddgealt 58
                                      y ++++p +   + +L+  ++++++++++  e   el+       ++P+L++d++ lt
  gi|298674074|ref|YP_003725824.1|  7 YTTETCPKCEQLKKLLKSNNISFKEADMSTPEALTELRVNGvFDVTAPILQIDDKFLT 64
                                      899************************988887666655557899*****98877543 PP

>> DUF5095  Domain of unknown function (DUF5095)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.5e-05     0.064     136     166 ..       2      33 ..       1      55 [. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.5e-05
                           DUF5095 136 dellifstelk.vskklkklLesneiefveen 166
                                       +e++i+ te++ + ++lkklL+sn+i f e +
  gi|298674074|ref|YP_003725824.1|   2 SEIIIYTTETCpKCEQLKKLLKSNNISFKEAD 33 
                                       689***7766537799************6655 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.9e-05     0.074       9      35 ..       4      29 ..       2      64 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.9e-05
                     Thioredoxin_2  9 lvvftdpdCpyCkklkkelkelddvtv 35
                                      ++++t+++Cp C++lkk lk++ ++ +
  gi|298674074|ref|YP_003725824.1|  4 IIIYTTETCPKCEQLKKLLKSN-NISF 29
                                      68999************88887.5444 PP

>> MSV199  MSV199 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.7e-05      0.12      40      75 ..       4      39 ..       1      64 [. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.7e-05
                            MSV199 40 flgyeGeykkqkkkfkklLkrnnieykelkykdeei 75
                                      ++ y+ e   + +++kklLk+nni++ke + + +e 
  gi|298674074|ref|YP_003725824.1|  4 IIIYTTETCPKCEQLKKLLKSNNISFKEADMSTPEA 39
                                      56677777778899**************99887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 533.14
//
Query:       gi|298674075|ref|YP_003725825.1|  [L=776]
Description: anaerobic ribonucleoside-triphosphate reductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.4e-156  521.8   0.0   2.9e-156  521.5   0.0    1.1  1  NRDD      Anaerobic ribonucleoside-triphosphate reductase


Domain annotation for each model (and alignments):
>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  521.5   0.0  1.6e-160  2.9e-156       1     561 []     146     770 ..     146     770 .. 0.93

  Alignments for each domain:
  == domain 1  score: 521.5 bits;  conditional E-value: 1.6e-160
                                       .XHTTHHHHHHHHHHHHHHHHHHHH-H..HHHHHHHHHHHTTSEEETTGGGTTT.S--EEE--SHHHHHH-CTT-SS CS
                              NRDD   1 enanvdskslsglrlklasevskeyalkkllpkevaeaheegdiHiHDldylallttyClgidlkdlleeGlktgng 77 
                                       +nan+ +++++++++k a+++ske +   +lp+++a+ h +gd+HiHDl+y+ +  ++C+++dl++++ +Gl+  +g
  gi|298674075|ref|YP_003725825.1| 146 DNANL-QDNAETSHKKKADKISKEQYTL-MLPPKLADLHLNGDLHIHDLEYFGT-RPFCQDHDLRYFFYYGLMP-DG 218
                                       69***.*****************99995.************************9.77***************65.66 PP

                                       S......-B---SHHHHHHHHHHHHHHHHTSSSS-EEETTHHHHHHHHHHHHHHTTSS-GHHHHHHHHHHHHHHHTT CS
                              NRDD  78 v......srppkhietalalavnilqtlqneqaGgqaissfdtylapfvrkdyekklkkltkkeikqamqefvynln 148
                                       +      + p+k++e+a+ +av++l+++q+++aGgq++++f+t+lap++++        ++++eikq mq+fvy+++
  gi|298674075|ref|YP_003725825.1| 219 SgtkasvAGPAKNAEVAVLHAVKALGSAQTNFAGGQGFYNFLTFLAPYMEN--------KDYNEIKQLMQMFVYEMT 287
                                       6689999******************************************55........6***************** PP

                                       S-S..SSSS---EEEEEE.-HH......................................HHHHHTTTTS-HCH--- CS
                              NRDD 149 tlpsrrGaQvpFtninlgldtp.......................tegrfee..kliikallevmleGdgnkgtpft 200
                                       +++++rG+Q +F++++l  ++p                       t+g+fe+  +l +kal+evml Gd++ g+pf+
  gi|298674075|ref|YP_003725825.1| 288 QMMVARGGQLVFSSVQLSPGVPelwvdkpvvshgtvhdgyyaehrTYGEFERevRLTFKALMEVMLDGDYW-GKPFN 363
                                       ***********************************************************************.***** PP

                                       -SEEEEEEEEETETTH...............HHHHHHHHHHTTT--EEE.......EEES--GGGTT-------... CS
                              NRDD 201 FPilifklkedfnleeed..........pnydlfklalevtakrgfpyffnlledlepedekevasmgCRlrld... 264
                                       FP++ ++++ +f +ee++          +++dl++l +e++ak g+pyf n+l+++++  +  +++++C ++++   
  gi|298674075|ref|YP_003725825.1| 364 FPKPEISIEPQF-MEEDEefnkqhpelpTYEDLYDLSFELAAKFGTPYFDNQLPPYRGAGKGISCYQCCAYQFSade 439
                                       ***********9.6665579*******99************************99999999*************543 PP

                                       -...............S---EEEEEEEEEEHHHHHH..HH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.-H CS
                              NRDD 265 ege.............rlggrgslgvvtiNlprlaleakgdeekffelLdellelakealeerrkilekllakg.lp 327
                                       + +             ++ ++g ++v t+N+pr a++a+gd +++++ L++l++   e+++++++++  +++++ +p
  gi|298674075|ref|YP_003725825.1| 440 D-NdadfedklyfkegKHFSMGAWQVLTLNCPRSAYRANGDYDALISDLKRLMNRSVEVFLAKKQWMDYIIDNNrMP 515
                                       1.134555667766555555********************************************************* PP

                                       HH.HTTSS-G.E.............EEEEEEE-HHHHHHHTTEEEE..-HHHHHHHHHHHHHHHHHHHHHHHHHSS- CS
                              NRDD 328 flmgkgylks.rkkkdeveevlkngtltiGfiGlaEalkaltgkkigeseeakefalkvlkhmrekadelkeetgln 403
                                       f+ +++  +  +++k ++    ++ ++tiG+iG++E+++++tg++++es+ea ++a++v+++++ +a++l++++g++
  gi|298674075|ref|YP_003725825.1| 516 FA-SQRPKDPiTGEKGSILVDTDSLVYTIGIIGINEMVQYYTGNQLHESKEAFRLAVRVMTELEMYAKDLSNKYGMQ 591
                                       *6.4444432235677888888999**************************************************** PP

                                       EEEEE---TTHHHHHHHHH....HH..................................HHG-SSSS-TTSSB-HHH CS
                              NRDD 404 fsleatPaEslsgrfakldk..kkf........geipgvdke................pyYtNsfhvpvdekislfe 454
                                       ++l +tPaE++++rfa  d   k f        +       +                +yYtN +h+p +++is+++
  gi|298674075|ref|YP_003725825.1| 592 IALARTPAETTGQRFAVADLlqKDFaskaeqviK-------GdvesakqklskdhdlpVYYTNGTHIPPSADISIID 661
                                       ****************999876899544444330.......3566666678999*********************** PP

                                       HHHHHHHHTGGGTT-S-EEEEBSS--SSHHHHHHHHH.HHHHTT--EEEEE--EEEETT.--..EESSSB-TTT--B CS
                              NRDD 455 kikleaefqklttGGailyieldeekknpealeklvk.iakktgigYfsinpkidvCnecgy..kgeiekCpkCgse 528
                                       +i++e+ f ++++GG+i++i+++e++++p+ l+++   iak+t++gYf+++++++vC++  +  +g++++Cp+Cgs+
  gi|298674075|ref|YP_003725825.1| 662 RINYEHTFFPIVDGGNIMHIWMGEAHPDPKGLKQFALnIAKNTQTGYFAFTKDMTVCMDDFHvaDGLKDNCPNCGSD 738
                                       ************************************99************************999**********88 PP

                                       E.EEEEEESSSSEEEHHHHHHHHHHHSGG---B CS
                              NRDD 529 eevevirRitGYlrpvsswnkgkkaElkdRvkh 561
                                       + ve ++R+tGY++ v  wn++kk+El+dR+++
  gi|298674075|ref|YP_003725825.1| 739 N-VEFLSRVTGYIQAVGGWNEAKKQELEDRKRY 770
                                       8.*****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (776 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.73u 0.33s 00:00:01.06 Elapsed: 00:00:00.51
# Mc/sec: 4604.49
//
Query:       gi|298674076|ref|YP_003725826.1|  [L=251]
Description: anaerobic ribonucleoside-triphosphate reductase activating protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.7e-18   66.9   0.0    3.8e-18   66.4   0.0    1.1  1  Radical_SAM  Radical SAM superfamily
    2.2e-09   37.7   0.0    3.8e-09   36.9   0.0    1.4  1  Fer4_12      4Fe-4S single cluster domain
      3e-08   33.8   0.0    4.9e-08   33.1   0.0    1.3  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.4   0.0   6.3e-22   3.8e-18       2     153 ..      24     173 ..      23     178 .. 0.84

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 6.3e-22
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgi 78 
                                       + +rgC++rC++C+++e       + ++++ ei+ ++ + k    v++v+++ggep+++pd  + l   ak   +++
  gi|298674076|ref|YP_003725826.1|  24 ISFRGCPFRCPYCHNYE---LLTGSNFVDISEIESQINKSKIF--VDNVVFTGGEPFMQPDALKHLVGFAKQ--NNL 93 
                                       679*************9...9****************999633..***************************..8** PP

                                       EEEEEECSSCHGHHHHHHHHHTT.-SEEEEEEBSSSHH.....HHHHHHTCTSHH.......HHHHHHHHHHHHTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx.....xxxxxxxxxxxx.......xxxxxxxxxxxxxxx RF
                       Radical_SAM  79 ritvetngtlpdeeklerllelg.vdrvslgleaadde.....kvlklmnrghtf.......eevlealeklreagi 142
                                        + + tng+ p  e ++++   g vd + ++l+a+ d      k    +  g++         +v e+l++l e+g+
  gi|298674076|ref|YP_003725826.1|  94 LVGINTNGFYP--ERIKEIICEGkVDKFFVDLKAPLDNvdlyrK----I-SGYNSsdypepvNRVAESLKILYENGV 163
                                       **********6..66666666667**************864442....2.333333445555999999999999999 PP

                                       ETEEEEEEEBT CS
                                       xxxxxxxxxxx RF
                       Radical_SAM 143 krvvdrivglp 153
                                       +    r+++++
  gi|298674076|ref|YP_003725826.1| 164 E-FELRTTVVR 173
                                       9.888877765 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.0   6.3e-13   3.8e-09       6     101 ..      20     109 ..      15     140 .. 0.78

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 6.3e-13
                           Fer4_12   6 vrlslfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesi..egltllGGEPllpenaeallelvkevk 80 
                                       v +++ + gC+++C++C+n e+   ++  ++      ei  +++k++i  + ++++GGEP++  + +al  lv   k
  gi|298674076|ref|YP_003725826.1|  20 VSIVISFRGCPFRCPYCHNYELLTGSNFVDI-----SEIESQINKSKIfvDNVVFTGGEPFM--QPDALKHLVGFAK 89 
                                       5678889************999876544444.....345555555555559***********..999*****99999 PP

                           Fer4_12  81 eekpekdiwlytgytleelsk 101
                                       ++++  + + ++g+  e +++
  gi|298674076|ref|YP_003725826.1|  90 QNNL-LVGINTNGFYPERIKE 109
                                       9998.6889999998887764 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0   8.3e-12   4.9e-08       2      96 ..      23     108 ..      22     126 .. 0.76

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 8.3e-12
                           Fer4_14   2 fvrlsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeey 78 
                                       ++ + gC++ C+ C n e    +  +  +  ++e+++   +ks+i  +++v+tGGeP+  ++ ++l +lv   k++ 
  gi|298674076|ref|YP_003725826.1|  23 VISFRGCPFRCPYCHNYEL--LTGSNFVDISEIESQI---NKSKIFVDNVVFTGGEPF--MQPDALKHLVGFAKQNN 92 
                                       67899***********993..3333333334444555...566666788*********..66899999999999998 PP

                           Fer4_14  79 pekkiwletngtleiele 96 
                                         + + ++tng +   ++
  gi|298674076|ref|YP_003725826.1|  93 --LLVGINTNGFYPERIK 108
                                       ..9999999998765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1521.25
//
Query:       gi|298674077|ref|YP_003725827.1|  [L=143]
Description: hypothetical protein Metev_0099 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00077   19.9   0.0     0.0011   19.5   0.0    1.2  1  CoA_binding_2  CoA binding domain


Domain annotation for each model (and alignments):
>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   5.9e-08    0.0011      49     113 ..      57     121 ..      24     123 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 5.9e-08
                                       -T....T--EEEE-S-HHHHGGGHHHHHHH--SEEEE-TT---HHHHHHHHHTT-EEE.ES-HHH CS
                     CoA_binding_2  49 laedpepvdlvdvftppeatpeivkealalgakavwlqpgsedeeaaelaeeagirvvgdrCilv 113
                                       +++ p  ++ +++ t     ++ ++ ++++g+k+vw+   +  +e+ e+ ++ +++++ d+C+++
  gi|298674077|ref|YP_003725827.1|  57 ISDIPDGMENAVIGTTKYNPADFINTLQDKGVKRVWVHWRTSTPELDEASRKSEMEFITDKCPMM 121
                                       333245566899999999999*****************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 945.94
//
Query:       gi|298674078|ref|YP_003725828.1|  [L=229]
Description: hypothetical protein Metev_0100 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 1673.54
//
Query:       gi|298674079|ref|YP_003725829.1|  [L=497]
Description: cobyric acid synthase CobQ [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-51  174.8   0.1    2.5e-51  174.1   0.1    1.4  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
      1e-20   74.1   0.0    1.6e-20   73.4   0.0    1.3  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
    2.4e-18   66.7   0.0    2.4e-17   63.4   0.0    2.2  1  AAA_26         AAA domain
     0.0001   22.1   0.0    0.00021   21.1   0.0    1.5  1  GATase         Glutamine amidotransferase class-I
      0.002   18.0   0.0     0.0047   16.8   0.0    1.5  1  SNO            SNO glutamine amidotransferase family
  ------ inclusion threshold ------
      0.053   13.2   0.0        0.1   12.2   0.0    1.4  1  Peptidase_S51  Peptidase family S51
        0.2   11.4   0.0       0.34   10.6   0.0    1.3  1  DUF3799        PDDEXK-like domain of unknown function (DUF379


Domain annotation for each model (and alignments):
>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.1   0.1   9.8e-55   2.5e-51       1     195 [.     259     441 ..     259     442 .. 0.92

  Alignments for each domain:
  == domain 1  score: 174.1 bits;  conditional E-value: 9.8e-55
                          GATase_3   1 kiavirlpaisnytdldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggp 77 
                                       +ia+irlp+isn+td++pLe+ +  +v++v+  +++lg+ +d+vi+pG+k+ti+d   lresg+ ++ik+++  ++p
  gi|298674079|ref|YP_003725829.1| 259 EIAIIRLPRISNFTDFEPLEKLA--KVNYVD-LEDNLGN-PDAVIIPGTKNTISDFVDLRESGMYDQIKKLHG-KIP 330
                                       69*****************9977..788999.8899*87.******************************886.9** PP

                          GATase_3  78 vlgiCGGlqmLGeeiedpegvegeag.eveglglLdietefek.ekltgqvegevel......aaegeevkGyEiHs 146
                                       ++giCGG+qmLG++i+d+ gvege++ e+eglglLdiet f   +k+t q+++++          +ge+++GyEiH+
  gi|298674079|ref|YP_003725829.1| 331 IIGICGGYQMLGTKIHDS-GVEGEQKaEYEGLGLLDIETIFDAyKKTTVQTTKTITCggpllePIKGEKISGYEIHM 406
                                       *****************6.78887666****************99999999999777****998899********** PP

                          GATase_3 147 GrtilkekakpllkvkvggnngekdGavkksedgnvlGtYlHglfdnrn 195
                                       G t++++     + +       ++dG++  + +g v+GtYlHglf+n+n
  gi|298674079|ref|YP_003725829.1| 407 GDTTSQN-----FVF-------DDDGCM--DDTGLVFGTYLHGLFENEN 441
                                       *998755.....667.......89****..77**************997 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.4   0.0   6.4e-24   1.6e-20       1     116 [.      12     234 ..      12     245 .. 0.97

  Alignments for each domain:
  == domain 1  score: 73.4 bits;  conditional E-value: 6.4e-24
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.HTTEB-HHHH...................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx...................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai.leglendiep...................... 54 
                                       ++i +t + vGK+ ++++L+  ++r ++rV++++a++++ n+ i  +g+e+ i++                      
  gi|298674079|ref|YP_003725829.1|  12 LLILGTASHVGKSAIVTALCNVFSR-NYRVAPFKAQNMSLNSWItKDGKEIGIAQaiqakaagveptadmnpillkp 87 
                                       5799*********************.****************9999******************************* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|298674079|ref|YP_003725829.1|  88 kgdrqsqviilgepyadktageyydsiedtheilkgsldrlsdeyeiivmegaggaaeinlyerdvvnigtaratna 164
                                       ***************************************************************************** PP

                                       ......CCHCCCHHHHHHCHCHHHH.......EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--C CS
                                       ......xxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ......dlkrllellealgkkkall.....lkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprde 116
                                             d++r ++++++l+++ +ll      ++ g+++n+++g+   + l+ +leel++r+g+pvlgv+p+++
  gi|298674079|ref|YP_003725829.1| 165 piilvgDIER-GGVFASLYGTIELLpedvrKRVSGFIINKFRGD--PEILNPGLEELEKRTGIPVLGVLPFSS 234
                                       **********.************99*******************..************************987 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4   0.0   9.5e-21   2.4e-17       1     191 [.      10     233 ..      10     238 .. 0.79

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 9.5e-21
                            AAA_26   1 rtifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiqtgie.....................ededselikellg 56 
                                       +++++ gt  +vGK+++ ++L++ + +++++v+ fK  +  ++                       e ++++  +l 
  gi|298674079|ref|YP_003725829.1|  10 KSLLILGTASHVGKSAIVTALCNVF-SRNYRVAPFKAQNMSLNswitkdgkeigiaqaiqakaaGVEPTADMNPILL 85 
                                       689*******************999.9*********98887778888765544444444443322223334444443 PP

                            AAA_26  57 ldqtyelpeplalsaplspelaarqegedidlekiv....kelekdadivvVEGagglgvpitee..llnadiaknl 127
                                        ++     + ++l +p++++ a++  +   d  +i     ++l+++++i+v EGagg  +  ++e   +n+  a++ 
  gi|298674079|ref|YP_003725829.1|  86 KPKGDRQSQVIILGEPYADKTAGEYYDSIEDTHEILkgslDRLSDEYEIIVMEGAGGAAEINLYErdVVNIGTARAT 162
                                       3333334666777788888888888887777777779999*******************87665545799******* PP

                            AAA_26 128 gapvilVarggl.gtinqllltieal.rqknvrvlGvilNkvrnp.e....nvetlekksgipvlGvvPyl 191
                                       +ap+ilV+ +++ g ++ l+ tie+l  +  +rv G i+Nk+r + e     +e+lek +gipvlGv+P +
  gi|298674079|ref|YP_003725829.1| 163 NAPIILVGDIERgGVFASLYGTIELLpEDVRKRVSGFIINKFRGDpEilnpGLEELEKRTGIPVLGVLPFS 233
                                       **********994589**********4456889*********8886366679*****************86 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   8.3e-08   0.00021      33      89 ..     287     346 ..     267     409 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 8.3e-08
                                       HHHHHHTHHSTSEEEEEEESSCTT......TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTT CS
                            GATase  33 aeeilellknpdgilvsgGpgspg......vegkieaikearenkiPiLGICLGmQllaiefg 89 
                                       ++e   +l npd+++++g  ++ +        g+ + ik++ + kiPi+GIC G Q+l+ ++ 
  gi|298674079|ref|YP_003725829.1| 287 DLED--NLGNPDAVIIPGTKNTISdfvdlrESGMYDQIKKLHG-KIPIIGICGGYQMLGTKIH 346
                                       3444..489*********99999999999889***********.*************987765 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.8e-06    0.0047      24     117 ..     285     385 ..     275     422 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.8e-06
                                       EE-SGGGGCC-SEEEE-SS-HHHHHHH.HHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEETTB........SS- CS
                               SNO  24 tvkrkedlaevdaliiPGGestamskl.iertglyedllefvknsekvvlGtCaGlillskelene........lvk 91 
                                        v  +++l + da+iiPG   t    + + + g+y+++++ ++ ++ +++G C G  +l  +++ +        + +
  gi|298674079|ref|YP_003725829.1| 285 YVDLEDNLGNPDAVIIPGTKNTISDFVdLRESGMYDQIKK-LH-GKIPIIGICGGYQMLGTKIHDSgvegeqkaEYE 359
                                       567788999*********9988555542345677777654.44.558************999877655555555566 PP

                                       SS--CCEEEETTTT-SCCGEEEEEEE CS
                               SNO  92 tlellkvkvkrnafGrqvdsfekeld 117
                                        l+ll+++   +a+ +     +k+++
  gi|298674079|ref|YP_003725829.1| 360 GLGLLDIETIFDAYKKTTVQTTKTIT 385
                                       79999999999999887776676665 PP

>> Peptidase_S51  Peptidase family S51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     4e-05       0.1      75     159 ..     287     368 ..     275     385 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4e-05
                                       HHHHHHHHSSEEEE--S.-HHHHHHHHHHTTHHHHHHHHHHTT-EEEEETHHHHTTSSB-GGGTTTS-GGG-S---B CS
                     Peptidase_S51  75 eieeklleadviyvgGG.ntfrLlkllketgldkllreavqqglvyiGvSAGaivagesiettsysdspikapesfe 150
                                       ++e+ l + d++++ G  nt++    l+e g+ + +++     +++iG+  G  + g++i+ + ++++    + ++e
  gi|298674079|ref|YP_003725829.1| 287 DLEDNLGNPDAVIIPGTkNTISDFVDLRESGMYDQIKKLH-GKIPIIGICGGYQMLGTKIHDSGVEGEQ---KAEYE 359
                                       689999999*****9966999999***********98765.99******************99955555...5789* PP

                                       ----SSSEE CS
                     Peptidase_S51 151 aLgLvkfqi 159
                                       +LgL++  +
  gi|298674079|ref|YP_003725829.1| 360 GLGLLDIET 368
                                       *****9764 PP

>> DUF3799  PDDEXK-like domain of unknown function (DUF3799)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00013      0.34      27      80 ..     423     477 ..     411     490 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00013
                                       --HHHHHHHHHHHHHHT-H..HHHHH...H-GGGB-T.....TSSB-HH.HHHHHHHH CS
                           DUF3799  27 etkallvGsyvHsyfEsklfeeeFkk...enkealakektakkgelkae.fkaaekmi 80 
                                       + + l +G+y H +fE +++ + F+    e k + +k   ++k + ++e ++ + +m+
  gi|298674079|ref|YP_003725829.1| 423 DDTGLVFGTYLHGLFENENIRNSFVRylcEKKGLEFK---PQKIISQQEaYNMLGDMV 477
                                       67899********************977655555555...555666666677766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (497 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.51
# Mc/sec: 2948.09
//
Query:       gi|298674080|ref|YP_003725830.1|  [L=188]
Description: precorrin-6y C5,15-methyltransferase subunit CbiT [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-11   43.1   0.3    4.4e-11   42.8   0.3    1.2  1  Methyltransf_31  Methyltransferase domain
    1.7e-10   41.0   0.5    2.3e-10   40.6   0.5    1.2  1  Methyltransf_18  Methyltransferase domain
    1.8e-09   37.3   0.3    2.5e-09   36.9   0.3    1.2  1  MTS              Methyltransferase small domain
    2.3e-08   34.6   0.1    4.2e-08   33.8   0.1    1.5  1  Methyltransf_25  Methyltransferase domain
    2.7e-07   30.3   0.6    4.8e-07   29.4   0.2    1.6  2  PrmA             Ribosomal protein L11 methyltransferase (Prm
    1.2e-06   28.1   1.0    4.2e-06   26.3   0.0    1.9  2  Methyltransf_4   Putative methyltransferase
    1.8e-06   28.6   0.2    2.5e-06   28.2   0.2    1.4  1  Methyltransf_12  Methyltransferase domain
    8.7e-06   25.5   0.1    1.2e-05   25.1   0.1    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
    1.4e-05   25.0   0.1      2e-05   24.4   0.1    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    1.8e-05   24.5   0.5    0.00041   20.1   0.5    2.2  1  UPF0020          Putative RNA methylase family UPF0020
    3.5e-05   23.4   0.1    5.7e-05   22.7   0.1    1.5  1  DOT1             Histone methylation protein DOT1
    4.4e-05   24.0   0.1      9e-05   23.1   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
    6.3e-05   22.6   0.2    8.2e-05   22.2   0.2    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    0.00011   21.8   0.1    0.00015   21.4   0.1    1.1  1  Methyltransf_5   MraW methylase family
    0.00017   21.0   0.1    0.00019   20.8   0.1    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
     0.0002   20.8   0.8    0.00028   20.3   0.3    1.4  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    0.00071   19.6   0.1    0.00087   19.3   0.1    1.2  1  Methyltransf_32  Methyltransferase domain
    0.00094   19.3   0.2     0.0014   18.8   0.2    1.3  1  FtsJ             FtsJ-like methyltransferase
    0.00096   19.0   0.0     0.0011   18.8   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
     0.0044   18.0   0.0     0.0077   17.2   0.0    1.4  1  Methyltransf_24  Methyltransferase domain
     0.0044   16.8   0.2     0.0056   16.4   0.2    1.2  1  Met_10           Met-10+ like-protein
     0.0044   16.4   0.1     0.0057   16.0   0.1    1.1  1  GidB             rRNA small subunit methyltransferase G
     0.0056   16.0   0.0     0.0094   15.3   0.0    1.3  1  Methyltransf_2   O-methyltransferase domain
     0.0093   15.6   0.0      0.014   15.0   0.0    1.3  1  GATase_3         CobB/CobQ-like glutamine amidotransferase do
  ------ inclusion threshold ------
      0.011   15.4   0.1      0.018   14.7   0.1    1.4  1  GCD14            tRNA methyltransferase complex GCD14 subunit
       0.02   13.9   0.2       0.98    8.4   0.0    2.0  2  RrnaAD           Ribosomal RNA adenine dimethylase
      0.021   14.5   0.0      0.031   13.9   0.0    1.3  1  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
      0.029   14.0   0.1      0.062   12.9   0.0    1.5  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
      0.037   13.8   0.0      0.061   13.1   0.0    1.3  1  Methyltransf_16  Lysine methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   0.3   7.1e-14   4.4e-11       2      96 ..      27     117 ..      26     173 .. 0.73

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 7.1e-14
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDl 77 
                                       ++g +++DlGCGtG+ ++e+  +++++ +++ iD   eai  A +n +  +l+ v++ +g+  + l ++   + +D 
  gi|298674080|ref|YP_003725830.1|  27 HDGDTFVDLGCGTGAVSIEAS-KMRQGLKIYAIDSRSEAIDTAAQNFETYQLQDVNLIHGESSKvLTEN---ADIDS 99 
                                       678899***************.******************************************88755...55666 PP

                   Methyltransf_31  78 ilsnevlnaladpdkilee 96 
                                       i + +++  +++ +++le 
  gi|298674080|ref|YP_003725830.1| 100 IDC-AFIGGTKNINQVLEI 117
                                       555.344455555555554 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.5   3.7e-13   2.3e-10      14     141 ..      28     154 ..      23     178 .. 0.92

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 3.7e-13
                   Methyltransf_18  14 kgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeee.vdtvvia 89 
                                       +g++++D G+  g ++i++ k ++  k++a+D +++++++a +n e+++l+ +++++ ++  ++l+e+  +d + +a
  gi|298674080|ref|YP_003725830.1|  28 DGDTFVDLGCGTGAVSIEASKMRQGLKIYAIDSRSEAIDTAAQNFETYQLQ-DVNLIHGESSKVLTENAdIDSIDCA 103
                                       6889**********************************************6.5*************88669999999 PP

                   Methyltransf_18  90 GmGg.elileILeeakeklkkikklilqpnseaeelRkylvengfkiedEelv 141
                                        +Gg ++i ++Le    + k +++l++++ + +  ++ +   ++ +i dE l 
  gi|298674080|ref|YP_003725830.1| 104 FIGGtKNINQVLEIL--VDKGVNNLVINAVRMETVVKAMQKMRNMDIFDEVLH 154
                                       998835788999987..778999************************999875 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.3     4e-12   2.5e-09      24     128 ..      21     125 ..      18     158 .. 0.76

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 4e-12
                                       HHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS-EE CS
                               MTS  24 letlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeveekkfd 99 
                                       l++l+ +  ++ +DlGcG+G++++++ k+ + +++ ++d   +A++ a +n+e+ +l+ v++++ +  + ++ ++ d
  gi|298674080|ref|YP_003725830.1|  21 LSKLDLHDGDTFVDLGCGTGAVSIEASKMRQGLKIYAIDSRSEAIDTAAQNFETYQLQdVNLIHGESSKVLT-ENAD 96 
                                       567777788899*********************************************999988888777666.4444 PP

                                       EEEE---STTTCHCHHHHHHHHHHHHHHH CS
                               MTS 100 livsNPPfhagkatelavaeeliaeAkea 128
                                       +      f  g++  ++v e l+ +  + 
  gi|298674080|ref|YP_003725830.1|  97 IDSIDCAFIGGTKNINQVLEILVDKGVNN 125
                                       33333346666665555555555555555 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.1   6.7e-11   4.2e-08       2      71 ..      33     103 ..      32     133 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 6.7e-11
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEE CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvss 71 
                                       +dlGcGtG ++++++k  +  k++++D  +e++++a++++e  +l +v++++g+ +++  e++ +D + ++
  gi|298674080|ref|YP_003725830.1|  33 VDLGCGTGAVSIEASKMRQGLKIYAIDSRSEAIDTAAQNFETYQLqDVNLIHGESSKVLTENADIDSIDCA 103
                                       7**************99745********************999999*********9988777777766553 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.2   7.8e-10   4.8e-07     159     229 ..      26      97 ..      16     122 .. 0.80
   2 ?   -1.2   0.0       1.7   1.1e+03      13      38 ..     110     135 ..      98     157 .. 0.60

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 7.8e-10
                              PrmA 159 vkegeevlDvGtGSGiLaiaaakLgak.kvvavDiDevAvkvakeNaelNkvea.klevalseellkeekadv 229
                                       ++ g++++D+G+G+G  +i a+k+    k++a+D  + A++ a++N+e  ++++ +l ++ +++ + +e+ad+
  gi|298674080|ref|YP_003725830.1|  26 LHDGDTFVDLGCGTGAVSIEASKMRQGlKIYAIDSRSEAIDTAAQNFETYQLQDvNL-IHGESSKVLTENADI 97 
                                       4567899***************9976449**********************999655.654333332355554 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.7
                              PrmA  13 aeeavsniLeelgakgvaiedsklle 38 
                                       + ++v +iL + g + ++i+  ++ +
  gi|298674080|ref|YP_003725830.1| 110 NINQVLEILVDKGVNNLVINAVRMET 135
                                       56667777777777777776655222 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   6.8e-09   4.2e-06       4      67 ..      31      94 ..      28     106 .. 0.92
   2 ?    0.2   0.4      0.71   4.4e+02      36      69 ..     109     141 ..     102     150 .. 0.70

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 6.8e-09
                                      EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHHHHC CS
                    Methyltransf_4  4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkvllel 67
                                      +++++GcG G + ++ +k++   ++ +i+ r++ ++++ ++ e ++l+ +++++g+  kvl+e 
  gi|298674080|ref|YP_003725830.1| 31 TFVDLGCGTGAVSIEASKMRQGLKIYAIDSRSEAIDTAAQNFETYQLQDVNLIHGESSKVLTEN 94
                                      79**********************************************************9875 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.71
                                       HHHHHHHHHHHHCTTSSEEEEES-CCCHHHHCS- CS
                    Methyltransf_4  36 kvvakvlkkiealelkNlrilrgdalkvllelle 69 
                                       k +++vl+   +++++Nl i     ++++ ++++
  gi|298674080|ref|YP_003725830.1| 109 KNINQVLEILVDKGVNNLVINAVR-METVVKAMQ 141
                                       678899999999999999775554.455544444 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.2     4e-09   2.5e-06       1      71 [.      33     104 ..      33     161 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 4e-09
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvv 71 
                                       +++GcGtG+++ +  +  ++++++++D  ++ai+ a++ +  ++ +++n ++ e   +l +    +s D  +
  gi|298674080|ref|YP_003725830.1|  33 VDLGCGTGAVSIEASKMRQGLKIYAIDSRSEAIDTAAQNFETYQLQDVNLIHGESSKVLTENADiDSIDCAF 104
                                       59*************************************************999999876655466666655 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.1   1.9e-08   1.2e-05      41     139 ..      28     121 ..      15     154 .. 0.70

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.9e-08
                                       CC-EEEETT-TTSHHHHHHH.HTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEE CS
                     Cons_hypoth95  41 egarvLDlfaGsGalglEAl.SRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdi 116
                                       +g +++Dl +G+Ga+++EA   R+  k++++++ +ea+ +  +n e+ +l++ ++ +  ++++ l ++ +   ++d 
  gi|298674080|ref|YP_003725830.1|  28 DGDTFVDLGCGTGAVSIEASkMRQGLKIYAIDSRSEAIDTAAQNFETYQLQD-VNLIHGESSKVLTEN-ADIDSIDC 102
                                       56789**************746***************************997.666666666666555.34445555 PP

                                       EEE--SSSTTCH..HHHHHHHHHT CS
                     Cons_hypoth95 117 vflDPPyakell.ieevlelleek 139
                                        f+      +   i++vle l +k
  gi|298674080|ref|YP_003725830.1| 103 AFIG-----GTKnINQVLEILVDK 121
                                       5553.....322357777776643 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.1   3.3e-08     2e-05      58     159 ..      13     115 ..       5     162 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 3.3e-08
                                       -HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GG CS
                              PCMT  58 aphmvalalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGr 134
                                       +p ++++ l  l+l++g+  +++G+G+G  +   a  +++  ++ +i+   e +++a +n ++ +l++v +++g+  
  gi|298674080|ref|YP_003725830.1|  13 KPEVISVSLSKLDLHDGDTFVDLGCGTGAVSI-EASKMRQGLKIYAIDSRSEAIDTAAQNFETYQLQDVNLIHGESS 88 
                                       57888899999*****************8765.5555678889********************************** PP

                                       GTTGGG-SEEEEEES..SBBSS--HHH CS
                              PCMT 135 kGyeekaPYdaihvg..aaapeiPeal 159
                                       k   e+a  d i  +   ++++i + l
  gi|298674080|ref|YP_003725830.1|  89 KVLTENADIDSIDCAfiGGTKNINQVL 115
                                       *********999654114556665554 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.5   6.6e-07   0.00041      25     125 ..      25     100 ..       7     103 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6.6e-07
                                       T--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHHHHHHHTT- CS
                           UPF0020  25 gwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvvqgareNaekagv 101
                                       ++++g++++D  CG+G++ IEa  + +                           +y++D+ ++++++a +N e +++
  gi|298674080|ref|YP_003725830.1|  25 DLHDGDTFVDLGCGTGAVSIEASKMRQGLK------------------------IYAIDSRSEAIDTAAQNFETYQL 77 
                                       7899********************999888........................89999999999999999999999 PP

                                       GGGEEEEE--GGG--STTS---EE CS
                           UPF0020 102 gdliefsqadaakLrlkegevdvi 125
                                       +d   +     + L+ +++++d+i
  gi|298674080|ref|YP_003725830.1|  78 QDVNLIHGESSKVLT-ENADIDSI 100
                                       987777766666666.55566665 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1   9.2e-08   5.7e-05      24      88 ..      10      74 ..       2     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 9.2e-08
                                      --B-HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHHHHHHHH CS
                              DOT1 24 GEllpeflsevldkvnlkkedvFvDLGSGvGnvvlqaalevgcklsvGvEimdnaselaekqkee 88
                                      G ++pe++s  l+k++l++ d+FvDLG G G v + a+   +  + + ++   +a + a ++ e+
  gi|298674080|ref|YP_003725830.1| 10 GPTKPEVISVSLSKLDLHDGDTFVDLGCGTGAVSIEASKMRQGLKIYAIDSRSEAIDTAAQNFET 74
                                      778999******************************99877766677777777777766665554 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   1.5e-07     9e-05       1      65 [.      33     100 ..      33     120 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.5e-07
                                       EEET-TTSHHHHHHH..HTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEE CS
                   Methyltransf_11   1 LdvGcGtGrlaeala..krgarvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlv 65 
                                       +d+GcGtG+++ +    ++g +++++D   e++++a ++ ++ +l  v++++++ +k+  e++ +D +
  gi|298674080|ref|YP_003725830.1|  33 VDLGCGTGAVSIEASkmRQGLKIYAIDSRSEAIDTAAQNFETYQLqDVNLIHGESSKVLTENADIDSI 100
                                       59************988888**********************99998999999999865454444443 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.2   1.3e-07   8.2e-05       3      77 ..      31     105 ..      29     160 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.3e-07
                   Methyltransf_15   3 vilDlfsGaGGnviqfalv..fekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvfl 77 
                                       + +Dl +G+G  +i+  ++  + k++ai++  e +  a++N e Y+  + + l++g+  ++l +      ++d+ f+
  gi|298674080|ref|YP_003725830.1|  31 TFVDLGCGTGAVSIEASKMrqGLKIYAIDSRSEAIDTAAQNFETYQ-LQDVNLIHGESSKVLTENADI-DSIDCAFI 105
                                       579**********9988776688**********************5.567*******99977653222.23577764 PP

>> Methyltransf_5  MraW methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.1   2.5e-07   0.00015      12     103 ..      20     124 ..      13     132 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.5e-07
                                       HHHHT---TT-EEEES--TTSHHHHHHHTT--TTEEEEEES-HHHHHHHTT.....-.--EEEEES-GGGHHHHHHH CS
                    Methyltransf_5  12 vvellepkedgvyiDaTlGaggHsealLeqlselrligidrDksalarakerLkefe.krltlvkgnfkelkealae 87 
                                       +++ l+ +++ +++D   G+g  s +  +  + l++++id  ++a+++a +++++++ ++++l++g+++++ ++ a+
  gi|298674080|ref|YP_003725830.1|  20 SLSKLDLHDGDTFVDLGCGTGAVSIEASKMRQGLKIYAIDSRSEAIDTAAQNFETYQlQDVNLIHGESSKVLTENAD 96 
                                       6788999999****************99999999**********************9566********666555555 PP

                                       TT.TT...........-EEEEEEE-S-- CS
                    Methyltransf_5  88 an.vt...........kvdgillDLGvS 103
                                        + ++           +v  il+D Gv 
  gi|298674080|ref|YP_003725830.1|  97 IDsIDcafiggtkninQVLEILVDKGVN 124
                                       4434466777777777888888888886 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1     3e-07   0.00019      52     126 ..      18      93 ..      13     147 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3e-07
                                       HHHHTTTT--TT-EEEEES-TTSHHHHHHHH.HH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG--- CS
                              CMAS  52 dlileklelkpGmtlLdiGcGWGslvrrave.rydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde 126
                                        + l kl+l++G+t +d+GcG G++ ++a + r + k+ ++   +e   +a ++++  +l++ + ++    + l e
  gi|298674080|ref|YP_003725830.1|  18 SVSLSKLDLHDGDTFVDLGCGTGAVSIEASKmRQGLKIYAIDSRSEAIDTAAQNFETYQLQDVNLIHGESSKVLTE 93 
                                       56799********************999875367999999999999999999999999888877666555555555 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.3   4.5e-07   0.00028      46     134 ..      27     116 ..      19     124 .. 0.83
   2 ?   -2.7   0.0       4.7   2.9e+03      63      86 ..     131     154 ..     123     159 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.5e-07
                                       --TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEE CS
                   Ubie_methyltran  46 krgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtv 122
                                       + g +++D+ +Gtg ++++ s+ +++  k+  +D  ++ ++++ +  +    ++++++++++ ++  e+   D++  
  gi|298674080|ref|YP_003725830.1|  27 HDGDTFVDLGCGTGAVSIEASK-MRQGLKIYAIDSRSEAIDTAAQNFETYQLQDVNLIHGESSKVLTENADIDSIDC 102
                                       5799*************99775.68889*********************************9998777766666655 PP

                                       ES..-GGG-S-HHH CS
                   Ubie_methyltran 123 sf..GlrnvtDklk 134
                                       +f  G +n+   l+
  gi|298674080|ref|YP_003725830.1| 103 AFigGTKNINQVLE 116
                                       55447788776655 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.7
                                       HHHHHHHHHHHEEEEEES-HHHHH CS
                   Ubie_methyltran  63 fklsdsvgekgkvvvlDinenmLk 86 
                                       +++   v++  k+  +Di +++L+
  gi|298674080|ref|YP_003725830.1| 131 VRMETVVKAMQKMRNMDIFDEVLH 154
                                       566666777777777777777765 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   1.4e-06   0.00087      24      90 ..      27      88 ..      15     149 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.4e-06
                   Methyltransf_32 24 sgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfaelsie 90
                                      ++  t vD+G+G g  s   +   ++++lk+++id+++e +++a +  e ++  + ++++ ++++++
  gi|298674080|ref|YP_003725830.1| 27 HDGDTFVDLGCGTGAVSIEASK--MRQGLKIYAIDSRSEAIDTAAQNFETYQ--L-QDVNLIHGESS 88
                                      566899********98888777..667***************9999888877..5.55555555544 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.2   2.2e-06    0.0014      17     120 ..      25     126 ..      19     163 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.2e-06
                                       T-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS...HHH.TTEEEE...CS-CCCSSHHHHHCHCHHHS CS
                              FtsJ  17 klfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm...apl.pgvtti...qgditdpetiekikealser 86 
                                       + ++ g+t+vDlg+++G+ s  +++   ++ k++a+D ++    +   ++ +t+     +  + e  + +      +
  gi|298674080|ref|YP_003725830.1|  25 D-LHDGDTFVDLGCGTGAVSIEASKM-RQGLKIYAIDSRSEaidT-AaQNFETYqlqDVNLIHGESSKVLT-----E 93 
                                       5.68999***************9999.567********8775652.2355555543355555555554333.....3 PP

                                       SEEEEEE--S-SS-CHHHHHHHHHCCCCHHHHCC CS
                              FtsJ  87 kvdlvvsDgapdvsgvhdldeylqsqLllaalel 120
                                        +d+   D a ++ g++++ ++l++   +   +l
  gi|298674080|ref|YP_003725830.1|  94 NADIDSIDCA-FIGGTKNINQVLEILVDKGVNNL 126
                                       6888888988.88898888888885333333333 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.8e-06    0.0011      24      62 ..      30      78 ..      17     147 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.8e-06
                   Methyltransf_23 24 grvLdiGcGtGillevl..rengfsvtgvDlspeaveiae........k 62
                                         +d+GcGtG ++ ++   ++g +++++D ++ea++ a+        +
  gi|298674080|ref|YP_003725830.1| 30 DTFVDLGCGTGAVSIEAskMRQGLKIYAIDSRSEAIDTAAqnfetyqlQ 78
                                      5678*************6556899************9886644333331 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.2e-05    0.0077       1      87 [.      33     117 ..      33     122 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.2e-05
                   Methyltransf_24   1 vEiGvysGvstlwllralrrngagrlvavdhdpg.aeeaaalareaglddrvrlikadseealasla.agsiDllfi 75 
                                       v +G  +G  ++ + +   r g  +++a+d   +   +aa+++++ +  + v+li+++s+++l++ a  +siD++fi
  gi|298674080|ref|YP_003725830.1|  33 VDLG--CGTGAVSIEASKMRQGL-KIYAIDSRSEaIDTAAQNFET-YQLQDVNLIHGESSKVLTENAdIDSIDCAFI 105
                                       5689..88888888766666666.9******88433345555655.77777************98776789****** PP

                   Methyltransf_24  76 Dgghaaeavled 87 
                                        g  + ++vle 
  gi|298674080|ref|YP_003725830.1| 106 GGTKNINQVLEI 117
                                       999888888765 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.2   9.1e-06    0.0056      98     171 ..      26     125 ..      18     159 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 9.1e-06
                                       --TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---.TT-EE... CS
                            Met_10  98 veegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevir.eqlad... 170
                                        ++g++ vd+  G G  +i ++k+ ++ +++aid   e++    +n +  ++++v + i +++ +v++ +  +d   
  gi|298674080|ref|YP_003725830.1|  26 LHDGDTFVDLGCGTGAVSIEASKMRQGLKIYAIDSRSEAIDTAAQNFETYQLQDV-NLIHGESSKVLTeNADIDsid 101
                                       689**********************************************999875.689999999985333344555 PP

                                       .......................E CS
                            Met_10 171 .......................r 171
                                                               
  gi|298674080|ref|YP_003725830.1| 102 cafiggtkninqvleilvdkgvnN 125
                                       555555555555555555544441 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   9.2e-06    0.0057      39     163 ..      21     144 ..      15     161 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9.2e-06
                                       HHHGGCS-CCC-.EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCC.TTTTT CS
                              GidB  39 lsvlellkekrdkviDvGsGaGlPGipLaiarpelkltLleslekkiaFLeevkeelklenveivearaee.kqeee 114
                                       ls l l + +  +++D+G G G  +i  + +r+ lk++ ++s++  i   ++  e+ +l++v+ ++ +  +   e+ 
  gi|298674080|ref|YP_003725830.1|  21 LSKLDLHDGD--TFVDLGCGTGAVSIEASKMRQGLKIYAIDSRSEAIDTAAQNFETYQLQDVNLIHGESSKvLTENA 95 
                                       4444444444..5********************************************************99877778 PP

                                       -EEEEEEC-SSSHHHHHHHHCCCEEEEEEEEEEESS--HHHHHCCHCCC CS
                              GidB 115 kydvvtsRAlaslnelteillkllkegglilalKGksaedeleekekal 163
                                       ++d + +  ++  ++++++l+ l+++g   l++ + + e+ +++ +k  
  gi|298674080|ref|YP_003725830.1|  96 DIDSIDCAFIGGTKNINQVLEILVDKGVNNLVINAVRMETVVKAMQKMR 144
                                       8888888888888888888888888888888887777666666555544 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.5e-05    0.0094      54     129 ..      20      96 ..      11     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.5e-05
                                       HHHSS-GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-.HHHHHHHHHHS-----TTEEEEES-TTTS-----S CS
                    Methyltransf_2  54 vleafdleglkslvDvGGGtGalakaivsayPtikvivfDl.peVveaAkehlsageeervefvgGdffkdslPeaD 129
                                        l + dl+   ++vD+G GtGa+  +++++  ++k+   D  +e + +A + +++ + ++v+ + G+  k    +aD
  gi|298674080|ref|YP_003725830.1|  20 SLSKLDLHDGDTFVDLGCGTGAVSIEASKMRQGLKIYAIDSrSEAIDTAAQNFETYQLQDVNLIHGESSKVLTENAD 96 
                                       57889999999*****************************63789********************997755555666 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.3e-05     0.014      10      78 ..      72     137 ..      65     140 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.3e-05
                          GATase_3  10 isnyt..dldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpv 78 
                                       +++y+  d+++++ e+    ++++ ++ ++++ +d  +++G+k+  q l++l ++g+++ + +a++ ++ v
  gi|298674080|ref|YP_003725830.1|  72 FETYQlqDVNLIHGES---SKVLT-ENADIDS-IDCAFIGGTKNINQVLEILVDKGVNNLVINAVRMETVV 137
                                       5566666666665544...44455.7888966.******************************99988877 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1     3e-05     0.018      29     119 ..      17     105 ..      14     161 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3e-05
                             GCD14  29 isliimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsq..lvtvthrDvck 103
                                       is+   kL+l+ G   v+ G G+g++s   ++      ++++++   + +++a ++f+  +l++  l++ +   v +
  gi|298674080|ref|YP_003725830.1|  17 ISVSLSKLDLHDGDTFVDLGCGTGAVSIEASKMR-QGLKIYAIDSRSEAIDTAAQNFETYQLQDvnLIHGESSKVLT 92 
                                       7888899*****************9998877654.4459***********************763255555555555 PP

                             GCD14 104 eGfdeevsgkvDavfL 119
                                       e   +++ +++D+ f+
  gi|298674080|ref|YP_003725830.1|  93 EN--ADI-DSIDCAFI 105
                                       53..355.55666665 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0016      0.98      16      72 ..      14      72 ..      12     101 .. 0.74
   2 ?    3.8   0.1     0.041        25     210     262 ..     100     151 ..      97     153 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0016
                                      HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-..SEEEEE-S-HHHHHHHHCHT CS
                            RrnaAD 16 kkvineIldklnleekltvleigpGkGilTeeLakra..kqvvvlElderLakllqkkl 72
                                      + vi   l+kl+l + +t +++g G+G+ + e  k+    +  ++ ++++ +    +++
  gi|298674080|ref|YP_003725830.1| 14 PEVISVSLSKLDLHDGDTFVDLGCGTGAVSIEASKMRqgLKIYAIDSRSEAIDTAAQNF 72
                                      67888899*********************999888875555566666665555555555 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.041
                                       HHHHHCTTTSBCCCHCCCTSTCHHHHHCTT.T--TTTCCCCSGHHHHHHHHHH CS
                            RrnaAD 210 vrkllnrkrktlstslksllpggelqalsstgindnalvkklsaeqtldifke 262
                                       + ++++   k+++++l+ l+ +g  +++++  + +++ vk  ++   +dif+e
  gi|298674080|ref|YP_003725830.1| 100 IDCAFIGGTKNINQVLEILVDKGVNNLVIN-AVRMETVVKAMQKMRNMDIFDE 151
                                       56899999*********9999999888877.8***********9999999987 PP

>> MethyltransfD12  D12 class N6 adenine-specific DNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.1e-05     0.031      18      58 ..      26      68 ..      15      95 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.1e-05
                                      ..--SEEEETT-TTSCCHHCS.....SSCEEEEES-HHHHHHH CS
                   MethyltransfD12 18 kdkgktfvepFaGggaVffeakk..qgkkvlinDinedlinly 58
                                       ++g+tfv++ +G+gaV++ea k  qg k+++ D  ++ i  +
  gi|298674080|ref|YP_003725830.1| 26 LHDGDTFVDLGCGTGAVSIEASKmrQGLKIYAIDSRSEAIDTA 68
                                      34899****************9999999999999988887665 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0    0.0001     0.062       4      73 ..      24      92 ..      21     105 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0001
                                      H---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHH CS
                   Methyltr_RsmB-F  4 LapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidk 73
                                      L++++++t++Dl ++ G+     +++ ++  +++A+d  +e ++  a+n +   ++++ +++++ +k+ +
  gi|298674080|ref|YP_003725830.1| 24 LDLHDGDTFVDLGCGTGAVSIEASKM-RQGLKIYAIDSRSEAIDTAAQNFETYQLQDVNLIHGESSKVLT 92
                                      899*************9988777777.88899******************************99988744 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   9.8e-05     0.061      48      92 ..      30      75 ..      16     101 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.8e-05
                   Methyltransf_16 48 lsvlELGsGtGlvGlavaellpeakviltDl.eellellkknieln 92
                                       + ++LG GtG v + + ++ +++k++  D  +e+++   +n e  
  gi|298674080|ref|YP_003725830.1| 30 DTFVDLGCGTGAVSIEASKMRQGLKIYAIDSrSEAIDTAAQNFETY 75
                                      56799**********************998625699**99999984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1244.41
//
Query:       gi|298674081|ref|YP_003725831.1|  [L=210]
Description: uroporphyrin-III C/tetrapyrrole (Corrin/Porphyrin) methyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-33  115.3   0.0    6.9e-33  114.4   0.0    1.4  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.4   0.0   3.8e-37   6.9e-33       1     204 [.       1     181 [.       1     187 [. 0.87

  Alignments for each domain:
  == domain 1  score: 114.4 bits;  conditional E-value: 3.8e-37
                      TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealr 77 
                                       +l++VG+GpGdpellT++A+++lk++  v+ ++++a e++++++++e  le+pm k+ ++l+ +++++ae++ae++r
  gi|298674081|ref|YP_003725831.1|   1 MLIGVGLGPGDPELLTLKAVNTLKKSSKVYVPGRLAAELVEPYADPE-ILEFPMLKDYDVLNDVWKQNAEIVAEDAR 76 
                                       79*******************************77********9887.99*************************** PP

                      TP_methylase  78 agkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllpglakeeerel 154
                                       ++  V +  +GDP++++t+s+l + l + ++++e+++iPG+ss++a a+r+++p++ ++ev + +          ++
  gi|298674081|ref|YP_003725831.1|  77 DDL-VSFGLIGDPNFFSTFSHLERVLNRLYPEVETDTIPGISSITAFASRTRTPVYSSFEVNDGS----------DI 142
                                       *97.********************************************************99988..........44 PP

                      TP_methylase 155 eallangdtlvllkaprklaelaelLkealyddttpvavveragtederv 204
                                              d+ v+lka + + e++ +++++  + + + a+++r+ +++e v
  gi|298674081|ref|YP_003725831.1| 143 -------DSKVVLKAKK-PREIMGEMRKE--GFN-DFAFAQRLFMDNEVV 181
                                       .......5556664444.66666666555..322.566666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1360.54
//
Query:       gi|298674082|ref|YP_003725832.1|  [L=243]
Description: precorrin-4 C(11)-methyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-46  158.2   0.0    3.1e-46  158.0   0.0    1.0  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
  ------ inclusion threshold ------
      0.019   15.4   0.1      0.037   14.4   0.1    1.5  1  Radical_SAM   Radical SAM superfamily
      0.046   12.4   0.0      0.055   12.1   0.0    1.2  1  Transferase   Transferase family
       0.17   11.6   0.3        2.7    7.6   0.0    2.2  2  tRNA_m1G_MT   tRNA (Guanine-1)-methyltransferase


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.0   0.0     7e-50   3.1e-46       1     212 [.       5     204 ..       5     205 .. 0.95

  Alignments for each domain:
  == domain 1  score: 158.0 bits;  conditional E-value: 7e-50
                      TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealr 77 
                                       k+y+VG GpGd++l+Tv++ ++l++ad v++++s++   +ld+          +g+  ++ + + +ei ++++++++
  gi|298674082|ref|YP_003725832.1|   5 KVYFVGSGPGDAKLITVKGKELLENADTVIYAGSLVNPEILDYS---------NGEMMDSYGMTLDEITSKIVDDVK 72 
                                       79*******************************99888887764.........55667789999************* PP

                      TP_methylase  78 agkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl..lpglakeeer 152
                                       ++k Vv+l+sGDP++yg+  e +++l++  ++i+ve++PGvss+ a a++l++ +t +g++ s++  +p+ ++ +e+
  gi|298674082|ref|YP_003725832.1|  73 SDKMVVRLHSGDPSLYGSILEQMDELKK--HDIDVEIVPGVSSVFASASSLKTQMTLNGVSDSLIitRPAGKTLDED 147
                                       ****************************..*********************************************** PP

                      TP_methylase 153 eleallangdtlvllkaprklaelaelLkealyddttpvavveragtedervvrgtleel 212
                                       ++++l+++ +t++++ +++k+++++e      y+ +tpvav+ +a+++de+v++gt++++
  gi|298674082|ref|YP_003725832.1| 148 KINELSKHHETMAIFLGTQKIDQIMEKV--D-YPSDTPVAVIYHASWDDEKVIKGTVSDI 204
                                       ****************************..5.47788*******************9976 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   8.2e-06     0.037      25     108 ..      54     164 ..      41     229 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.2e-06
                                       HHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC...............CCTEEEEEEECS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...............xxxxxxxxxxxx RF
                       Radical_SAM  25 rgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla...............vpgiritvetng 86 
                                       +++ ++++ei  ++    ++ ++ +v l++g+p+ly  + e +++l+k +                + +++ ++ ng
  gi|298674082|ref|YP_003725832.1|  54 DSYGMTLDEITSKIVDD-VKSDKMVVRLHSGDPSLYGSILEQMDELKKHDidveivpgvssvfasASSLKTQMTLNG 129
                                       56779999999999999.7888***************************9999998888888888777777777777 PP

                                       SCHG............HHHHHHHHHTT.-SEEEEE CS
                                       xxxx............xxxxxxxxxxx.xxxxxxx RF
                       Radical_SAM  87 tlpd............eeklerllelg.vdrvslg 108
                                       + ++            e+k+ +l + + +  + lg
  gi|298674082|ref|YP_003725832.1| 130 VSDSliitrpagktldEDKINELSKHHeTMAIFLG 164
                                       77668888888888887777777776553333333 PP

>> Transferase  Transferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.2e-05     0.055     364     400 ..     160     196 ..      86     218 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.2e-05
                       Transferase 364 eevtvsswlklplyevdFGwgkPvyvvpvvsskkdnk 400
                                       + ++ +     ++ +vd++++ Pv+v ++ s+ ++++
  gi|298674082|ref|YP_003725832.1| 160 AIFLGTQKIDQIMEKVDYPSDTPVAVIYHASWDDEKV 196
                                       444445566899********************99887 PP

>> tRNA_m1G_MT  tRNA (Guanine-1)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0006       2.7      36      99 ..     110     176 ..      88     186 .. 0.74
   2 ?    1.9   0.1     0.035   1.5e+02      94     114 ..     204     227 ..     196     232 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0006
                                       TSSHHHHHHHHHHHCCGHHCGG-TTEEEESSCGGHHHHCCCHHHCGG...GEEEEETTTSSBECCGG CS
                       tRNA_m1G_MT  36 gagmvlkaepelealesvntekwkvilltptGkkftqelaeeLseke...klvylcgdyegvdervd 99 
                                       g+++v ++  +l+   ++n    ++i++ p Gk +++++ +eLs++     + + + + ++++e+vd
  gi|298674082|ref|YP_003725832.1| 110 GVSSVFASASSLKTQMTLNGVSDSLIITRPAGKTLDEDKINELSKHHetmAIFLGTQKIDQIMEKVD 176
                                       5555556666666666666667899********************9855445555777788888876 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.035
                                       BECCGGTTSSE...EEEEESSSST CS
                       tRNA_m1G_MT  94 vdervdddkvd...eysIGdfVlk 114
                                       + ++v+d  v+    ++IG+ V+ 
  gi|298674082|ref|YP_003725832.1| 204 ISQKVKDAGVKrsaMIIIGGVVDP 227
                                       567777777777889*******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1794.45
//
Query:       gi|298674083|ref|YP_003725833.1|  [L=264]
Description: precorrin-3B C(17)-methyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-37  128.7   0.0    3.5e-37  128.4   0.0    1.1  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.4   0.0   1.9e-41   3.5e-37       1     211 [.      14     220 ..      14     222 .. 0.88

  Alignments for each domain:
  == domain 1  score: 128.4 bits;  conditional E-value: 1.9e-41
                      TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealr 77 
                                       kly+VG+GpG+ e+lT+ A+++++++d v+g +  +l+ ++ ll+        ++  +++++++ + +++a+  +l+
  gi|298674083|ref|YP_003725833.1|  14 KLYVVGIGPGSVEYLTIHARDVIQNSDYVIGNG-TYLDQIESLLNG-------QEIIRSSMGKEVDRASRAV--ELA 80 
                                       79*******************************.9*****999975.......4555666655555444444..334 PP

                      TP_methylase  78 agkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl..lpglakeeer 152
                                       +   V ++++GD ++yg+++ ++e ++++++++eve++PGv++++a a+ lg p+++++ v s++  l++++++e+r
  gi|298674083|ref|YP_003725833.1|  81 QSSVVSMVSGGDANIYGMAGLVLEVAENAKQDVEVEIVPGVTAITASASILGSPIVNDFAVISLSdlLTPWDMIEKR 157
                                       444599999***************************************************************99999 PP

                      TP_methylase 153 eleallangdtlvllkapr.k.....laelaelLkealyddttpvavveragte.dervvrgtlee 211
                                       + +a++   d+++ l++p+ +     +a+++e++k++ +d   pv +v++a ++ ++  +++tl  
  gi|298674083|ref|YP_003725833.1| 158 LDSAAST--DFVISLYNPKsRkrnsnFARAIEIIKQY-RDGSVPVGLVKNALRDeKQDYIVTTLDN 220
                                       9999877..**********7468999********999.88899**********9558899999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1688.93
//
Query:       gi|298674084|ref|YP_003725834.1|  [L=243]
Description: precorrin-8X methylmutase CbiC/CobH [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-62  210.9   1.2    1.6e-62  210.7   1.2    1.1  1  CbiC      Precorrin-8X methylmutase
  ------ inclusion threshold ------
      0.036   14.7   0.1      0.087   13.5   0.1    1.6  1  PglD_N    PglD N-terminal domain


Domain annotation for each model (and alignments):
>> CbiC  Precorrin-8X methylmutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.7   1.2   1.7e-66   1.6e-62       2     195 ..      48     234 ..      47     235 .. 0.97

  Alignments for each domain:
  == domain 1  score: 210.7 bits;  conditional E-value: 1.7e-66
                                       HHHHHHHHHHCHC-TT.S-CHHHHHHHHHHHHHT-CCHHHHEEE-TTHHHHHHHHHHCT-EEEESSHHHHCCS-HHH CS
                              CbiC   2 IeaeSfaiideelgeeelseeeeevvrRvihatadfelaellrfspdaveaglealkagapivtDvemvkaGitkkr 78 
                                       I+ +S +i ++ +g+e   + e+++ +R++ +t+d+++ae+++f++d +++g++a+k+g pi++D++mvkaGit k 
  gi|298674084|ref|YP_003725834.1|  48 IYMTSRNIARKIVGDE---TPEDRIRQRCVISTGDPSVAEIMKFKNDPINSGVDAIKKGSPIFVDIRMVKAGITTKG 121
                                       999**********987...99****************************************************9998 PP

                                       HHTTC-EEEECTC-HHHHHHHHHHTS-HHHHHHHHHHHCTTTCEEEESS-HHHHHHHHHHHHHS..HTSEEEE---- CS
                              CbiC  79 leklgnevlclladpevaelakekgitrsaaamekaaeelegaivviGnAPtALlellelieegkvkpalvigvPvG 155
                                       ++   ++v+c+l+ +e ae+a++ gitr+aa++ k+++e egai++iGnAP+A +++++lie+g v+palv+g+PvG
  gi|298674084|ref|YP_003725834.1| 122 HN---CDVICVLDRDENAEIAHKYGITRTAAGFLKCKDEIEGAIIAIGNAPSAAITVCRLIEHG-VRPALVVGTPVG 194
                                       75...59*******************************************************99.6*********** PP

                                       SCCHHHHHHHHHCSSS-EEEESSS---HHHHHHHHHHHHH CS
                              CbiC 156 FvgaaesKealaesevpyitveGrkGGsavAaaivnaLle 195
                                       Fv+ aesKe++++++vp+it+eG++GG+++A+a+vn+L++
  gi|298674084|ref|YP_003725834.1| 195 FVNSAESKEMVRNMDVPSITCEGTRGGTPIAVACVNELVS 234
                                       **************************************86 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   9.7e-06     0.087      19      68 ..     119     168 ..     111     170 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.7e-06
                            PglD_N  19 eangeyeiigflDdnkk.tevegypvlgkaiellkslseeeyevviAIGnn 68 
                                        + ++ ++i++lD +++ +  ++y +  +a  +lk    e   ++iAIGn+
  gi|298674084|ref|YP_003725834.1| 119 TKGHNCDVICVLDRDENaEIAHKYGITRTAAGFLKCK-DEIEGAIIAIGNA 168
                                       45556899*****9887255678*****999999988.445569*****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1537.19
//
Query:       gi|298674085|ref|YP_003725835.1|  [L=222]
Description: cytochrome c biogenesis protein transmembrane region [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-32  111.9  24.8    1.4e-31  110.1  24.8    1.7  1  DsbD      Cytochrome C biogenesis protein transmembrane regio
    2.8e-11   43.7  16.9    3.5e-11   43.4  16.9    1.1  1  DsbD_2    Cytochrome C biogenesis protein transmembrane regio


Domain annotation for each model (and alignments):
>> DsbD  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.1  24.8   1.5e-35   1.4e-31       1     212 [.      15     212 ..      15     213 .. 0.88

  Alignments for each domain:
  == domain 1  score: 110.1 bits;  conditional E-value: 1.5e-35
                              DsbD   1 aflaGllsflsPCilpliPaylsyisgvsvedvktekkkvkvllkallFvlGlslvfvslglsaaflgqllkdvkev 77 
                                       af aG++s +sPC+lpl+Pa l+y s       +++  k     + +  +lGls+ f+++g+ +++  + ++ ++++
  gi|298674085|ref|YP_003725835.1|  15 AFVAGIASIISPCVLPLLPAILAYSS-------NNG--K----YRPIAIILGLSISFTLMGIITSAFSAGFQAYRDY 78 
                                       699*********************99.......333..2....356899**************************** PP

                              DsbD  78 irrvaglivillGlhflgvfkievleklklllki.kkkaelsvlgalllGltFalgwsPCigPvlasvlalaaskes 153
                                       i  va +++i lGl +l   +++++++  l ++  k+ ++   lg l+lG++ +++w PC+gP+l+++l+++a   +
  gi|298674085|ref|YP_003725835.1|  79 IYLVAEIVIIGLGLVMLL--EFNIFNNALLDKFSsKRLNNNGLLGGLVLGISLGIIWIPCVGPILGAILTMVAVGSN 153
                                       **********9**99884..43344433333222033445558********************************** PP

                              DsbD 154 lakgallllvyvlGlaipfllvglllellkkklkslkkyskaveiaggvllvllGvlll 212
                                       + +g  ll++y++G+a+p+l+++  ++    kl +++ky  +v++a+g++l+++G+ ++
  gi|298674085|ref|YP_003725835.1| 154 IIQGGFLLFIYSMGFAVPMLIIAYSANITTSKLGKISKYGIYVKKAAGIVLISIGLWMI 212
                                       *******************************************************9886 PP

>> DsbD_2  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4  16.9   3.9e-15   3.5e-11       1     199 []      14     210 ..      14     210 .. 0.82

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 3.9e-15
                            DsbD_2   1 aafllgLlgsl.hClgmCggivlalslskpkralalllynlGRilsYallGalvgllgsvlqlageleglrallgvl 76 
                                       aaf++g+++ + +C++   + +la+s+++   + + ++  lG  +s++l+G++  ++++++q+    +++  ++ ++
  gi|298674085|ref|YP_003725835.1|  14 AAFVAGIASIIsPCVLPLLPAILAYSSNNG--KYRPIAIILGLSISFTLMGIITSAFSAGFQAYR--DYIYLVAEIV 86 
                                       69***********************99996..557889999********************7766..4666777777 PP

                            DsbD_2  77 lgllllllglklllkkkllklerlgkllsrllkklakklkslasalllGllnG..llpC..glvysalllalasgsa 149
                                       ++ l+l+++l++          + ++ll ++ +k +++ ++l + l+lG+  G  ++pC  +++ ++l+++++ +++
  gi|298674085|ref|YP_003725835.1|  87 IIGLGLVMLLEF--------NIFNNALLDKFSSKRLNN-NGLLGGLVLGISLGiiWIPCvgPILGAILTMVAVGSNI 154
                                       777777766655........356777888888888886.899**********96667**94445556677778889* PP

                            DsbD_2 150 leGalvmlaFgLGTlpalllfglllgllskklr......kkllrlagvllillgll 199
                                       ++G+++++++++G  +++l++++ +++ ++kl         + ++ag++li +gl+
  gi|298674085|ref|YP_003725835.1| 155 IQGGFLLFIYSMGFAVPMLIIAYSANITTSKLGkiskygIYVKKAAGIVLISIGLW 210
                                       ***************************97755545455356677********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1453.25
//
Query:       gi|298674086|ref|YP_003725836.1|  [L=164]
Description: thioredoxin domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-14   54.3   0.1    1.4e-14   53.9   0.1    1.3  1  Thioredoxin    Thioredoxin
      8e-07   29.3   0.1    1.4e-05   25.3   0.0    2.1  2  Thioredoxin_8  Thioredoxin-like
    1.3e-05   25.1   0.0    1.8e-05   24.7   0.0    1.2  1  TraF           F plasmid transfer operon protein
    0.00052   19.8   0.2    0.00081   19.2   0.2    1.4  1  DIM1           Mitosis protein DIM1
      0.003   17.5   0.0     0.0039   17.1   0.0    1.2  1  Thioredoxin_6  Thioredoxin-like domain
     0.0032   17.4   0.0     0.0048   16.8   0.0    1.2  1  AhpC-TSA       AhpC/TSA family
     0.0038   16.9   0.0     0.0049   16.6   0.0    1.2  1  Redoxin        Redoxin
      0.004   17.2   0.1       0.01   15.8   0.1    1.7  2  Thioredoxin_3  Thioredoxin domain
     0.0069   16.8   0.1      0.014   15.9   0.1    1.6  1  Thioredoxin_2  Thioredoxin-like domain
     0.0093   15.7   0.6      0.014   15.2   0.4    1.3  1  Thioredoxin_9  Thioredoxin
  ------ inclusion threshold ------
      0.045   13.9   0.1      0.089   13.0   0.1    1.5  1  Thioredoxin_7  Thioredoxin-like
      0.068   13.5   1.3       0.64   10.4   0.1    2.5  2  DUF4969        Domain of unknown function (DUF4969)
      0.069   12.5   0.0      0.089   12.1   0.0    1.2  1  DUF929         Domain of unknown function (DUF929)
      0.085   12.9   0.4       0.22   11.6   0.1    1.8  2  DUF4884        Domain of unknown function (DUF4884)
       0.16   11.6   0.2       0.34   10.5   0.2    1.6  2  DUF953         Eukaryotic protein of unknown function (DUF953


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.1   1.2e-17   1.4e-14      11      81 ..      49     117 ..      41     156 .. 0.87

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 1.2e-17
                                       HHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEET CS
                       Thioredoxin  11 eeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkn 81 
                                       +++v  e+k vl+eF A+wC  C +  P +e++a+e+kdk  ++ v+vd  +d+ak++++++iP  +++ +
  gi|298674086|ref|YP_003725836.1|  49 NNTV--ENKSVLIEFGAEWCSACDRQRPIIEDIANEYKDKAEVMYVNVDMTPDIAKRFNIRSIPDSVVVVD 117
                                       3344..56********************************************************9777655 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   1.2e-08   1.4e-05       1      46 [.      54      97 ..      54     104 .. 0.91
   2 ?    2.3   0.0      0.18   2.1e+02      74      89 ..     100     115 ..      97     122 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.2e-08
                                      .SEEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS- CS
                     Thioredoxin_8  1 gkvvlLyfgaswcppckaftpklkelyeklkkkkkveivyvsldkk 46
                                      +k vl+ fga+wc+ c++ +p + ++ +++k  +k e+ yv++d +
  gi|298674086|ref|YP_003725836.1| 54 NKSVLIEFGAEWCSACDRQRPIIEDIANEYK--DKAEVMYVNVDMT 97
                                      689***************************9..9999999999854 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.18
                                       HTT-S--TT-SEEEEE CS
                     Thioredoxin_8  74 lkkkynvkaiPtlvvl 89 
                                       ++k++n+ +iP  vv+
  gi|298674086|ref|YP_003725836.1| 100 IAKRFNIRSIPDSVVV 115
                                       6899*******76665 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   1.5e-08   1.8e-05     121     199 ..      46     115 ..      31     125 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.5e-08
                              TraF 121 eaalkklakeygLlfFyrgkcpyceaqapilqafadky..glevraVsvdgrplpelpnarvdkgqaarlgvkrtPa 195
                                       +++ ++++++  L+ F ++ c++c+ q pi++++a++y  + ev++V+vd +p+  +++         r++++++P 
  gi|298674086|ref|YP_003725836.1|  46 QQINNTVENKSVLIEFGAEWCSACDRQRPIIEDIANEYkdKAEVMYVNVDMTPD--IAK---------RFNIRSIPD 111
                                       445556778899**************************77799*********99..777.........999999997 PP

                              TraF 196 lvlv 199
                                        v+v
  gi|298674086|ref|YP_003725836.1| 112 SVVV 115
                                       7666 PP

>> DIM1  Mitosis protein DIM1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.2   6.8e-07   0.00081      12      78 ..      46     113 ..      40     158 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 6.8e-07
                                       HHHHHH-SSSEEEEEEE-TT-HHHHHHHHHHHHHHHHTTTTEEEEEEETTT--TTSCCCTT-.SSSEE CS
                              DIM1  12 dqailseeerlvviRFGrdedaeClklDelLakiaeklknfaviylvdidevpdfnkmyele.dpvti 78 
                                       +q  ++ e++ v+i FG ++ ++C ++  +++ ia++ k  a++  v++d  pd  k ++++  p ++
  gi|298674086|ref|YP_003725836.1|  46 QQINNTVENKSVLIEFGAEWCSACDRQRPIIEDIANEYKDKAEVMYVNVDMTPDIAKRFNIRsIPDSV 113
                                       44445567899*************************************************98655554 PP

>> Thioredoxin_6  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.3e-06    0.0039     114     172 ..      73     132 ..      49     139 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.3e-06
                                       HHHHHHHHHHTTTT-EEEEEETTGGHHHHHHTT--GGG-SEEEEEESSS.S-EEEET.TSS CS
                     Thioredoxin_6 114 kkaiekvakefkdkinfaladaksfkrpleylglsssdlPvivivdsas.hkykypp.kde 172
                                       + +ie +a+e+kdk  + +++++ ++++ ++++++s    v+v vd  s ++y y+  +++
  gi|298674086|ref|YP_003725836.1|  73 RPIIEDIANEYKDKAEVMYVNVDMTPDIAKRFNIRSIPDSVVV-VDINSgGEYVYMTeNGD 132
                                       5579*******************************88887777.88888356888765555 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0     4e-06    0.0048      21      75 ..      50     102 ..      38     120 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4e-06
                                       HHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHH CS
                          AhpC-TSA  21 sdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkk 75 
                                       +++++k v++ f ++ wc  C ++ p +++ ++e+k  ++ev+ v+vd   +++k
  gi|298674086|ref|YP_003725836.1|  50 NTVENKSVLIEFGAE-WCSACDRQRPIIEDIANEYK-DKAEVMYVNVDMTPDIAK 102
                                       566889999999999.********************.579*******98877665 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   4.1e-06    0.0049      26      82 ..      52     107 ..      40     143 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.1e-06
                                       HTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH.HHHHHHH CS
                           Redoxin  26 fkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf.vkefwgk 82 
                                       +++k+v++ f +  +c  C ++ p +e++a+++k+k  +v +v++d  +  +k+f  +
  gi|298674086|ref|YP_003725836.1|  52 VENKSVLIEFGAE-WCSACDRQRPIIEDIANEYKDK-AEVMYVNVDMTPDiAKRFNIR 107
                                       5788888888888.******************9999.677799988776656666555 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   8.7e-06      0.01       5      55 ..      59     114 ..      55     127 .. 0.79
   2 ?   -2.4   0.0       4.2   5.1e+03      57      75 ..     138     155 ..     133     156 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.7e-06
                                       E.ESSS.STTCHHHHHHHHHHCHCCTCEC..EEECCTTHHHH.HHCT-SSSSEEEC CS
                     Thioredoxin_3   5 v.lgpg.CakCpklekavkeaaaekgika..evekvtdfeei.ekygVmsvPalvi 55 
                                       + +g   C  C++ + +++ +a+e + ka   +++v  +++i ++++++s+P  v+
  gi|298674086|ref|YP_003725836.1|  59 IeFGAEwCSACDRQRPIIEDIANEYKDKAevMYVNVDMTPDIaKRFNIRSIPDSVV 114
                                       5567777******************76661155667899*************8754 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.2
                                       TCEEEESS---CCHHHHHH CS
                     Thioredoxin_3  57 gkvvvsGkvpseeeirkll 75 
                                       +k ++ G v +++ + k l
  gi|298674086|ref|YP_003725836.1| 138 EKARFLG-VTQKQRLVKTL 155
                                       7889999.99998888776 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.1e-05     0.014       4      89 ..      53     118 ..      50     146 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.1e-05
                     Thioredoxin_2   4 ngkpvlvvftdpdCpyCkklkkelkel.ddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvr 79 
                                       ++k vl+ f +++C  C++ +  ++++ ++         +k+++e  +v+++ +++ +             +++++r
  gi|298674086|ref|YP_003725836.1|  53 ENKSVLIEFGAEWCSACDRQRPIIEDIaNE---------YKDKAEVMYVNVDMTPDIA-------------KRFNIR 107
                                       6899***************99999988333.........5666899999999999875.............888888 PP

                     Thioredoxin_2  80 gtPt.ivfldg 89 
                                       + P+ +v+ d 
  gi|298674086|ref|YP_003725836.1| 108 SIPDsVVVVDI 118
                                       88886666665 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.4   1.1e-05     0.014      35     104 ..      47     115 ..      27     131 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.1e-05
                                       HHHT--S-EEEEE.E--TT-HHHHHHHHHHHHHH.HH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE CS
                     Thioredoxin_9  35 kiksiekklkilv.ltedwCgDaavnvPvlakia.elnpnievkillrdenlelmdqyltngaraiPtliil 104
                                       +i++  ++ ++l+ + ++wC  + +  P+++ ia e++++ ev ++  d  +++ +++     r+iP  +++
  gi|298674086|ref|YP_003725836.1|  47 QINNTVENKSVLIeFGAEWCSACDRQRPIIEDIAnEYKDKAEVMYVNVDMTPDIAKRFNI---RSIPDSVVV 115
                                       4444444444555499*****************978999*******************65...999955443 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   7.4e-05     0.089      16      35 ..      53      72 ..      51     111 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.4e-05
                                      HT--EEEEE--TT-HHHHHH CS
                     Thioredoxin_7 16 rgkpvlvffgaswcftCqal 35
                                      ++k vl+ fga+wc+ C ++
  gi|298674086|ref|YP_003725836.1| 53 ENKSVLIEFGAEWCSACDRQ 72
                                      689**************986 PP

>> DUF4969  Domain of unknown function (DUF4969)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00054      0.64       5      59 ..       3      60 ..       1      68 [. 0.72
   2 ?    1.7   0.0      0.29   3.4e+02      48      60 ..     125     137 ..     108     148 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00054
                           DUF4969  5 gllLvsvLvlFillavaCsdse...dneesveiilkeielsvddpiklvdengeatve 59
                                       l+L  +L +Fil ++ C +s+   +n++ +  +     ++  + i  + en    +e
  gi|298674086|ref|YP_003725836.1|  3 KLVLFTILSIFILSTIGCIESDtgaENNNNGYTSGGSDRVTSIQQINNTVENKSVLIE 60
                                      589999************8875333455556666666667767778888888777766 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.29
                           DUF4969  48 klvdengeatvev 60 
                                       + ++eng++t++ 
  gi|298674086|ref|YP_003725836.1| 125 VYMTENGDTTIQR 137
                                       5689******975 PP

>> DUF929  Domain of unknown function (DUF929)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.5e-05     0.089      11      76 ..       8      72 ..       2      98 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.5e-05
                            DUF929 11 liivvivvvslsaivsnalvelskqvyaseplstkfvkvsnqdlasngkvevyfvswegCPvgaae 76
                                       i+ ++++ ++  i s    e ++++y+s  +   ++ +++ + + ++k+ +++ ++e+C  +  +
  gi|298674086|ref|YP_003725836.1|  8 TILSIFILSTIGCIESDTGAENNNNGYTSGGSD-RVTSIQQINNTVENKSVLIEFGAEWCSACDRQ 72
                                      344455555555555556677888999999999.9*************************999655 PP

>> DUF4884  Domain of unknown function (DUF4884)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       6.3   7.6e+03      36      40 ..      42      46 ..      33      47 .. 0.69
   2 ?   11.6   0.1   0.00019      0.22      25      37 ..     122     134 ..     114     140 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6.3
                           DUF4884 36 vTsik 40
                                      vTsi+
  gi|298674086|ref|YP_003725836.1| 42 VTSIQ 46
                                      89997 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00019
                           DUF4884  25 gsYvYFTtrGDvT 37 
                                       g+YvY T +GD T
  gi|298674086|ref|YP_003725836.1| 122 GEYVYMTENGDTT 134
                                       99*********88 PP

>> DUF953  Eukaryotic protein of unknown function (DUF953)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   0.00029      0.34      32      66 ..      60      94 ..      43     116 .. 0.83
   2 ?   -2.4   0.0         3   3.6e+03      52      75 ..     106     129 ..     100     137 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00029
                                      TTS-BSSHHHHHHHHHHHHHHHH-SS-EEEEEEE- CS
                            DUF953 32 teGesWCPdCvkaepvieealkeapedvklvrvdv 66
                                      + G  WC  C +  p+ie+  +e    +++++v+v
  gi|298674086|ref|YP_003725836.1| 60 EFGAEWCSACDRQRPIIEDIANEYKDKAEVMYVNV 94
                                      56999***************999887666666555 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3
                                       HHH-SS-EEEEEEE---HHHHT-T CS
                            DUF953  52 lkeapedvklvrvdvGdrevWkdp 75 
                                       ++++p  v++v ++ G   v+ ++
  gi|298674086|ref|YP_003725836.1| 106 IRSIPDSVVVVDINSGGEYVYMTE 129
                                       567777788888777766666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      631  (0.0351944); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1016.62
//
Query:       gi|298674087|ref|YP_003725837.1|  [L=234]
Description: 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine 1-reductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-53  179.6   0.0      7e-53  179.4   0.0    1.0  1  RibD_C    RibD C-terminal domain


Domain annotation for each model (and alignments):
>> RibD_C  RibD C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.4   0.0   3.9e-57     7e-53       1     199 [.      12     226 ..      12     227 .. 0.96

  Alignments for each domain:
  == domain 1  score: 179.4 bits;  conditional E-value: 3.9e-57
                                       -EEEEEEEEETTSBSSCTTSSGCTSS-HHHHHHHHHHHHTSSEEEEEHHHHHHHT--SS--SSCHSCHH.HTT.GSS CS
                            RibD_C   1 pyvilklavSlDGklaaaggeskwitgeearadvhelraeadailvGrgtvladnpsltvrwvkkreae.adaearq 76 
                                       p++ l++avS+DGk++++++++ +i+g+ + ++v+el +e+d+++vG+gtvlad+pslt +  + ++ + +++  ++
  gi|298674087|ref|YP_003725837.1|  12 PFIFLNAAVSADGKISTKERKQVKISGDNDFERVDELKKESDGVMVGIGTVLADDPSLTIKSENRKKYRkNNGLDEN 88 
                                       79***************************************************************9888566666** PP

                                       -EEEEEETTS-S-TTSHHHHSS.S-EEEEESSCSCHHHHHHCC......E....SE-HHHHHHHHHHTT--EEEEEE CS
                            RibD_C  77 pvrvVvdstlrvpldakvltdd.aptlvatteeadkekveklk......v....rvdlkelleeLkergirsllveG 142
                                       p r+Vvds  r+p da++++++  + ++a+++ a+++k+++lk      v    +vdlk l+e+Lk++gi++l+veG
  gi|298674087|ref|YP_003725837.1|  89 PARIVVDSNGRTPIDADIFKKGeGKRVIAVSKCAPEKKIKTLKekadiiVagndKVDLKILVEKLKDMGIEKLMVEG 165
                                       *******************************************9888643899************************ PP

                                       THHHHHHHHHTTT-SEEEEEEESCE--T.TSBCSSSSST-SS...EEEEEEEEEEETTEEE CS
                            RibD_C 143 GatLagsllraglvDelrlyiaPkllGg.agktlfdgegfka...lklklvksealgegvv 199
                                       G++L++sll  +lvDe++ +i  +++Gg  +++l++g gf++   lklklv +e++++g++
  gi|298674087|ref|YP_003725837.1| 166 GSNLNWSLLSLKLVDEIHAFIGNIIIGGsTAPSLVGGSGFPEtdmLKLKLVDFEQMDDGLL 226
                                       ********************************************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1755.25
//
Query:       gi|298674088|ref|YP_003725838.1|  [L=284]
Description: hypothetical protein Metev_0111 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-41  140.4  13.3    2.2e-12   47.2   1.4    4.3  4  CBS       CBS domain
  ------ inclusion threshold ------
      0.014   15.8   0.0        4.7    7.7   0.0    2.4  2  HTHP      Hexameric tyrosine-coordinated heme protein (HTHP)


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.2   8.5e-14   7.6e-10       1      54 [.       7      59 ..       7      62 .. 0.94
   2 !   47.2   1.4   2.4e-16   2.2e-12       4      53 ..      68     116 ..      63     120 .. 0.90
   3 !   19.3   0.1   1.3e-07    0.0012       9      54 ..     135     180 ..     124     182 .. 0.86
   4 !   41.1   0.1     2e-14   1.8e-10       2      56 ..     228     282 ..     226     283 .. 0.96

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 8.5e-14
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54
                                      ++dim +dv +++   + ee+le++++k vs++PV+ +++k+vGiv++  ll++
  gi|298674088|ref|YP_003725838.1|  7 IRDIMIKDVAYATIPGSREEVLEILKDKQVSGVPVI-KENKVVGIVSRNNLLKY 59
                                      58***********************9999*******.7888***********98 PP

  == domain 2  score: 47.2 bits;  conditional E-value: 2.4e-16
                                       HSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS   4 imtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                       +mtrd+vt++pd ++  a++l+ +++v+rlPVVd+d  lvG+vt  D++ 
  gi|298674088|ref|YP_003725838.1|  68 LMTRDPVTISPDVDITVAARLLLDHDVRRLPVVDGDQ-LVGLVTIADVVG 116
                                       5********************99**********8666.*********986 PP

  == domain 3  score: 19.3 bits;  conditional E-value: 1.3e-07
                                       CEEEETTSBHHHHHHHHHHHTSSEE.EEEETTTBEEEEEEHHHHHHH CS
                               CBS   9 vvtvppdttleealelmrekgvsrl.PVVdedgklvGivtlrDllra 54 
                                       +v v  +t+l  ++++m+ ++v  + PV+d++  +vG++++rD+++a
  gi|298674088|ref|YP_003725838.1| 135 LVPVWDETPLPVVAKIMEFSNV-NVsPVLDKSLGFVGLISDRDIISA 180
                                       5789999**********53559.666***88889***********97 PP

  == domain 4  score: 41.1 bits;  conditional E-value: 2e-14
                                       HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       ++im +d++t++p + ++e++  m++++++++PV++++g l+G++ +rDll+all
  gi|298674088|ref|YP_003725838.1| 228 SEIMVTDLITATPMSGVSECALSMKRHDIDQIPVINGNGDLLGLLRDRDLLKALL 282
                                       58**********************9999*************************97 PP

>> HTHP  Hexameric tyrosine-coordinated heme protein (HTHP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0    0.0022        20      15      50 ..      63      97 ..      56     113 .. 0.84
   2 ?    7.7   0.0   0.00053       4.7       3      29 ..     232     259 ..     230     267 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0022
                                      HHHHHHHHHHHHHHH---HHHHHHHHHHHTT-HHHH CS
                              HTHP 15 feLAvklaRkavkttQpdaevrkklReeYaeDaasL 50
                                       +LA+ ++R  v t+ pd ++  + R   ++D + L
  gi|298674088|ref|YP_003725838.1| 63 EQLALLMTRDPV-TISPDVDITVAARLLLDHDVRRL 97
                                      69*********9.589**********9999998887 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00053
                                       ---S--SSHHHHH.HHHHHHHHHHHHHH CS
                              HTHP   3 lpsLiteTPeeGf.eLAvklaRkavktt 29 
                                       ++ Lit+TP  G  e A+++ R+ + ++
  gi|298674088|ref|YP_003725838.1| 232 VTDLITATPMSGVsECALSMKRHDIDQI 259
                                       678*********7479*******99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1814.69
//
Query:       gi|298674089|ref|YP_003725839.1|  [L=151]
Description: UspA domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-37  128.6   0.0    2.7e-37  128.4   0.0    1.0  1  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.4   0.0   1.5e-41   2.7e-37       2     141 .]       6     145 ..       5     145 .. 0.96

  Alignments for each domain:
  == domain 1  score: 128.4 bits;  conditional E-value: 1.5e-41
                                       -SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                               Usp   2 ykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeag 78 
                                       yk+Il+a+Dgse+ +kA+e++++lak ++a+++ ++v+d+ a+++ ++    +    l ++e +++ d+  ++ae++
  gi|298674089|ref|YP_003725839.1|   6 YKKILIATDGSEQNQKAIEYGVDLAKISNAKVYPVYVVDTAAFSSIPMDSGWEMMYDLIKKEGREATDQVVKLAEEA 82 
                                       9*********************************************999988888888888888888889******* PP

                                       TCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  79 gvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       g + e +v+eg+p++ei+++a+++d+d iV+G+ g+sgl+++llGSv+e+v+r++p pVlvVr
  gi|298674089|ref|YP_003725839.1|  83 GLESEPTVLEGHPSHEIIDFAKNNDIDVIVMGTLGKSGLDKFLLGSVAEKVIRNSPAPVLVVR 145
                                       **************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 967.72
//
Query:       gi|298674090|ref|YP_003725840.1|  [L=368]
Description: amidohydrolase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-31  109.0   0.0    2.5e-30  106.0   0.0    1.9  1  Amidohydro_1     Amidohydrolase family
    7.2e-10   38.7   0.0    1.2e-09   38.0   0.0    1.4  1  A_deaminase      Adenosine/AMP deaminase
    6.3e-09   35.8   0.0    1.3e-07   31.5   0.0    2.5  2  Amidohydro_3     Amidohydrolase family
  ------ inclusion threshold ------
      0.047   14.1   0.0      0.087   13.2   0.0    1.4  1  RuvX             Holliday junction resolvase
      0.055   13.5   0.2        1.7    8.7   0.0    2.7  3  Phage_int_SAM_6  Phage integrase SAM-like domain


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.0   0.0     7e-34   2.5e-30       1     329 [.      44     354 ..      44     363 .. 0.87

  Alignments for each domain:
  == domain 1  score: 106.0 bits;  conditional E-value: 7e-34
                                       EEEE-EEEEEEECETTECSSSGHHHHH.........................STTHHHHHHHHHHHHHHHHTTEEEE CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrgatledwl.........................vppetaaealesgiktalksGtttv 52 
                                       i+ P ++++H+H+ +s++++++l + +                         ++ + + e ++s ik +++ Gt+ +
  gi|298674090|ref|YP_003725840.1|  44 IIAPCFVNSHTHIGDSVFKDPPLGKYRgyrlerdldllvkppdglkhqilrrTSYNKLVESMKSSIKDMINTGTGAF 120
                                       6889************99999777777777777778889************************************** PP

                                       EEEEHSSTHHHHHHHHHHHTSSSEEEEEEESSEGGS.GCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCC CS
                      Amidohydro_1  53 admgattstgiealleaaeelplglrilggkvsldr.gsaetskasreklkagaaetikgkadgvvkvalapheapa 128
                                       ad+++  +tgi+al+ea++++  ++  ++ + + d+ g +++ + ++ ++++ a              +l+ ++   
  gi|298674090|ref|YP_003725840.1| 121 ADFRESGVTGIQALKEAIDDT--DIDNIILGRPTDTeGPESNTISEIDRILKNA-------------EGLGISGVND 182
                                       ********************8..6655555557777899999999999999999.............9********* PP

                                       SHHHHHHHHHHHHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHH CS
                      Amidohydro_1 129 fsdeelkealkeakkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteael 205
                                           +l+++++  +k    +aiHa+e     +d+++a           +              ++h +h    +++ 
  gi|298674090|ref|YP_003725840.1| 183 MDMKLLEKISDYTRKNRGLFAIHAGEK--QRSDISEALS---LK---PDL-------------MVHLTHANRQDLKE 238
                                       ************************663..3335566666...22...344.............88999999999999 PP

                                       HHHHHHHHCEEHHHHHHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHH CS
                      Amidohydro_1 206 lkerlkeagvahcpfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllyedeegglsl 282
                                       +     ++ v+ cp+sn   + g+++++++l+e ++v++gtD + + ns+n++ e+  +           +  g++ 
  gi|298674090|ref|YP_003725840.1| 239 VSDE--NIPVVVCPRSNFTTGVGMPPVADMLEEEINVAVGTD-NVMLNSVNMFAEMETLS----------KLFGIED 302
                                       9999..************************************.**************999..........5778*** PP

                                       HHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECC......CTCGGGTTTC CS
                      Amidohydro_1 283 kealrmaTingAkalglddkvGsievGkdADlvvvdl......dilaafvglk 329
                                        ++++m+T++gA algl+ k Gsi++G  A l v+++      +i++++ g+ 
  gi|298674090|ref|YP_003725840.1| 303 RQVFKMCTLKGATALGLE-KNGSIQEGNFASLMVLNGksnnlsNINNPISGIV 354
                                       *****************5.****************664332222255554444 PP

>> A_deaminase  Adenosine/AMP deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.0   3.4e-13   1.2e-09     179     303 ..     188     304 ..     131     314 .. 0.86

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 3.4e-13
                                       HHHHHCCCCHTT-EEEEEESSSS-CHHHHHHHHCS--SCECE-GGGGGSHHHHHHHHHCT-EEEE-HHHHCCCSST- CS
                       A_deaminase 179 flklraeagkstllltpHaGEagglehvveAllllkaerigHGvrlrkdpvLqyllalaqiplevcPlSNvalgafl 255
                                         k+ ++ +k+  l+++HaGE      ++eAl l k + + H +++   ++ ++  ++++ip+ vcP SN  +    
  gi|298674090|ref|YP_003725840.1| 188 LEKISDYTRKNRGLFAIHAGEKQR-SDISEALSL-KPDLMVHLTHANR-QD-LKEVSDENIPVVVCPRSNFTT---- 256
                                       5677889999999********976.569****99.9999999666544.44.57899****************.... PP

                                       TTTT-CHHHHHHTT-EEEE--BSCCCCT-SHHHHHHHHHHHHT--HHH CS
                       A_deaminase 256 eyaenPlkeflerglnvslntDDPlqfgttLieeYaiaaqvfklseed 303
                                        +   P+ + le+++nv+++tD+ ++ ++++ +e++ +++ f+ ++++
  gi|298674090|ref|YP_003725840.1| 257 GVGMPPVADMLEEEINVAVGTDNVMLNSVNMFAEMETLSKLFGIEDRQ 304
                                       67889*************************************998876 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1     0.053   1.9e+02       9      21 ..      44      56 ..      41      64 .. 0.86
   2 !   31.5   0.0   3.7e-11   1.3e-07     316     448 ..     230     342 ..     211     359 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.053
                      Amidohydro_3  9 lvlPGFvDsHtHl 21
                                      + +P Fv sHtH+
  gi|298674090|ref|YP_003725840.1| 44 IIAPCFVNSHTHI 56
                                      679*********5 PP

  == domain 2  score: 31.5 bits;  conditional E-value: 3.7e-11
                      Amidohydro_3 316 gvtesqiervaalqvaagvqpvfnfedelldsrlgperargstpvkellnagvkvalgsD.apvgpfdpwprigaav 391
                                         + +++++v + ++   v+p++nf             + g +pv+ +l+  ++va g+D   +++++ + +++++ 
  gi|298674090|ref|YP_003725840.1| 230 HANRQDLKEVSDENIPVVVCPRSNF-----------TTGVGMPPVADMLEEEINVAVGTDnVMLNSVNMFAEMETLS 295
                                       5556666666666666666777777...........4456679*****************76666666666666555 PP

                      Amidohydro_3 392 mrktrrggevlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvld...ad 448
                                               ++++++     +++++++T ++A+algle++ G++++G  A+l+vl+   ++
  gi|298674090|ref|YP_003725840.1| 296 --------KLFGIE----DRQVFKMCTLKGATALGLEKN-GSIQEGNFASLMVLNgksNN 342
                                       ........344444....579*****************9.**************966544 PP

>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.4e-05     0.087      33      80 ..     124     171 ..     107     183 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.4e-05
                                       ---HHHHHHHHHHHHHHTT--EEEEE------SSS---SSTTHHHHHH CS
                              RuvX  33 rkskekdleelkelvkeeeveeiVvGlPlnldgsegesakkvrkfaee 80 
                                       r+s+ + +++lke +++ ++++i++G P++++g e+++  +++++ ++
  gi|298674090|ref|YP_003725840.1| 124 RESGVTGIQALKEAIDDTDIDNIILGRPTDTEGPESNTISEIDRILKN 171
                                       455567899****************************99999988765 PP

>> Phage_int_SAM_6  Phage integrase SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.073   2.6e+02      28      70 ..      90     133 ..      87     141 .. 0.79
   2 ?    8.7   0.0   0.00047       1.7      47      83 ..     159     196 ..     153     234 .. 0.82
   3 ?   -1.8   0.0      0.83     3e+03      78      98 ..     224     244 ..     214     249 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.073
                   Phage_int_SAM_6  28 kqvkdkealakviqelkkgvks.ieelekivkeaRniGliGint 70 
                                       +q+  +++ +k ++++k+++k+ i+  + +  + R+ G++Gi+ 
  gi|298674090|ref|YP_003725840.1|  90 HQILRRTSYNKLVESMKSSIKDmINTGTGAFADFRESGVTGIQA 133
                                       7788888889999999999665156667899999*******986 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00047
                   Phage_int_SAM_6  47 vksieelekivkeaRniGliGinty.anPllklyeyli 83 
                                        ++i+e+++i+k+a   G+ G+n   ++ l+k+ +y  
  gi|298674090|ref|YP_003725840.1| 159 SNTISEIDRILKNAEGLGISGVNDMdMKLLEKISDYTR 196
                                       5789*******************762455667777765 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.83
                   Phage_int_SAM_6  78 lyeyliklelaslkeideell 98 
                                       l+ +l++++ ++lke+++e++
  gi|298674090|ref|YP_003725840.1| 224 LMVHLTHANRQDLKEVSDENI 244
                                       567889999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2580.03
//
Query:       gi|298674091|ref|YP_003725841.1|  [L=91]
Description: hypothetical protein Metev_0114 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 596.35
//
Query:       gi|298674092|ref|YP_003725842.1|  [L=109]
Description: hypothetical protein Metev_0115 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-22   78.6   0.3    3.4e-22   78.3   0.3    1.1  1  DUF167    Uncharacterised ACR, YggU family COG1872


Domain annotation for each model (and alignments):
>> DUF167  Uncharacterised ACR, YggU family COG1872
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.3   0.3   1.9e-26   3.4e-22       2      76 ..      14      87 ..      13      88 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 1.9e-26
                                      EEEEEES---SSS----...--TTTT-------TTIIIIIHHHHHHHHHHHHHS...SEEEE-S-GGGSEEEEEE CS
                            DUF167  2 vilavrvkPgakkdaigleedaegrealkvrvaappvdGkANkalikfLakalgvpksdveivsGeksreKvvri 76
                                      v++++ v+P++k+ +++ ++++++r++++v+++++++ GkAN++li+ +++ +gv+ks+++i+sGeks++K v +
  gi|298674092|ref|YP_003725842.1| 14 VVIDISVTPNSKTINVP-DNYNQWRNRIEVKLTQKAESGKANNQLIENFSEFFGVNKSSIKITSGEKSSQKSVSV 87
                                      78***************.8899***************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 762.82
//
Query:       gi|298674093|ref|YP_003725843.1|  [L=401]
Description: ketose-bisphosphate aldolase class-II [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-33  116.9   0.0    1.4e-33  116.6   0.0    1.1  1  F_bP_aldolase   Fructose-bisphosphate aldolase class-II
    2.2e-10   39.8   0.0    3.6e-10   39.1   0.0    1.3  1  Tagatose_6_P_K  Tagatose 6 phosphate kinase
     0.0013   17.5   0.2     0.0059   15.3   0.0    2.0  2  UxaE            tagaturonate epimerase
  ------ inclusion threshold ------
       0.25   11.8   2.3          2    9.0   1.0    2.4  2  YflT            Heat induced stress protein YflT


Domain annotation for each model (and alignments):
>> F_bP_aldolase  Fructose-bisphosphate aldolase class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.6   0.0   3.1e-37   1.4e-33       4     256 ..      34     328 ..      31     368 .. 0.80

  Alignments for each domain:
  == domain 1  score: 116.6 bits;  conditional E-value: 3.1e-37
                                       HHHHHHHHHHT--EEEEE--SHHHHHHHHHHHHHHTS-EEEEE-HHHHHHHH-HHHHHH..HHHHHHHHHHT...-E CS
                     F_bP_aldolase   4 kellkkAkeegyavgafnvtnletvkavleaaeeaksPvIlqlsegaaakyaggaeala..elvraaaeaykkasvp 78 
                                       k +++  +++++ v+a n      ++++l+aa++a++P+Il+l++++  + + g++ l   ++ +++++a+k +   
  gi|298674093|ref|YP_003725843.1|  34 KYIFNILQNQKTIVMAANPRIGLVTRGILRAAKDADAPIILELARSEC-NLENGYTGLYpsDFSEQCYQAAKDVGYD 109
                                       668888999**************************************9.5556555544337888888888877788 PP

                                       E.EEEE--.--G..........HHHHHHHHHHS-SEEEE--TTS..........-HHHHHHHHHHHHHHHHH....T CS
                     F_bP_aldolase  79 v.alhlDH.gak..........leglkkaieagfsSvMiDgSel..........pleeNialtkevveraha....l 129
                                       + alh DH g k           e +k+ i+ag++S  iD+S+l          +l++Ni+ t e+++++++    +
  gi|298674093|ref|YP_003725843.1| 110 IwALHADHiGIKkgdrediektKELVKAQIDAGYTSFAIDASHLfnfqggdlreELKDNIDATTEIAKFIEEqmddR 186
                                       67******76668999**88888888888999**********8888888888889************9877654447 PP

                                       T-EEEEE-----------TT-TTTS--HHHHHHHHHHHH.....-EEEE--SS---SS.--SS........--THHH CS
                     F_bP_aldolase 130 gvsvEaElGriggeedgvvaeeklyTdpeeaeefveetg.....vdalAvaiGnvHGv.ykpk....pk..Ldferl 194
                                       +  +E+E+G+ig e++    + +++T+peea++f+++++      ++lA+a G++HG  y+++     +  +d+   
  gi|298674093|ref|YP_003725843.1| 187 EYGLEVEVGEIGREDE----HGRVLTNPEEAVTFIKALNengvyPQVLAIANGSAHGNtYDSQgrliEQvsIDIPQT 259
                                       7**********96554....357*******************999************97777766653356777777 PP

                                       HHHHHHH......--SEE-SGTTS-HHHHHHHHHTT.EEEEEE-HHHHHHHHHHHHHGGE-HHH-HHHH CS
                     F_bP_aldolase 195 keiqkav......vplVlHGgsgvpdeeirkaiklG.vvKiNidtdlrlaytkavkkekenkkydprkl 256
                                        ++++a+      v ++ HG +g+p+e i++++ +G ++K N+ t +++ +++a+k  +++  +d  ++
  gi|298674093|ref|YP_003725843.1| 260 IKVAQALkennlkVRIAQHGITGTPRELIHDHFPHGeIIKGNVGTFYMNLVWDAFKLFEPELYNDIWNW 328
                                       7777777898888889*************************************9966543322222222 PP

>> Tagatose_6_P_K  Tagatose 6 phosphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.0   7.9e-14   3.6e-10      25     140 ..      56     169 ..      40     215 .. 0.81

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 7.9e-14
                                       HHHHHHHHHHHHS-S-EEEEEETTTS-TT-TTTT--HHHHHHHHHHHHHHTT--GGGEEEEEEEESSGGGTTS-HHH CS
                    Tagatose_6_P_K  25 lvieaaleqakekesavLiEatsNqvnqfGGYtGmtpadFrefvleiaeevglpkerlilGGDHLGPnawkklpaee 101
                                       lv +  l++ak+ ++++++E     +n + GYtG+ p+dF e +++ a++vg++     l  DH+G     k+  +e
  gi|298674093|ref|YP_003725843.1|  56 LVTRGILRAAKDADAPIILELARSECNLENGYTGLYPSDFSEQCYQAAKDVGYDIW--ALHADHIGI----KKGDRE 126
                                       677888999******************************************99875..5789****6....466778 PP

                                       HHHHHHHHHHHHHTTT--EEEE---B--SSS....-SB--HHH CS
                    Tagatose_6_P_K 102 AmakaeelvaayvaagfkKiHlDasmscadd....paplsdev 140
                                        ++k++elv+a + ag++   +Das   + +     ++l+d++
  gi|298674093|ref|YP_003725843.1| 127 DIEKTKELVKAQIDAGYTSFAIDASHLFNFQggdlREELKDNI 169
                                       899**********************866544112344444444 PP

>> UxaE  tagaturonate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.3e-06    0.0059      77     245 ..      42     222 ..      22     231 .. 0.73
   2 ?   -0.5   0.0     0.085   3.8e+02     372     391 ..     317     336 ..     299     381 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.3e-06
                              UxaE  77 kkkkasfGlGDRlGlatpghiravkksdvfPvlaqqSiR....ElnltnRtfkdvldaavwavfqeGykkgfgaDaD 149
                                       ++k++ +    R+Gl+t g +ra k+ d  P++   +      E   t+   +d  ++   a  + Gy + ++  aD
  gi|298674093|ref|YP_003725843.1|  42 NQKTIVMAANPRIGLVTRGILRAAKDADA-PIILELARSecnlENGYTGLYPSDFSEQCYQAAKDVGY-DIWALHAD 116
                                       55556667777999999999999999986.54433333300014555777778888887778888888.57999999 PP

                              UxaE 150 Hl...........KteedveealeagftmitlDlsekikneveklsekelkekyeeleeelrekleekylgkkfkik 215
                                       H+           Kt+e v+  ++ag+t + +D+s   +       ++elk+++++ ++e+ + +ee+  ++++ ++
  gi|298674093|ref|YP_003725843.1| 117 HIgikkgdredieKTKELVKAQIDAGYTSFAIDASHLFNF-QGGDLREELKDNIDA-TTEIAKFIEEQMDDREYGLE 191
                                       9866655555555677778899************976666.444556899999999.6999*************999 PP

                              UxaE 216 eeelelseke.llkavliYekaikfvekvye 245
                                        e  e+ +++   +++   e+a++f++ ++e
  gi|298674093|ref|YP_003725843.1| 192 VEVGEIGREDeHGRVLTNPEEAVTFIKALNE 222
                                       6666666555055566667899999998876 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.085
                              UxaE 372 kdpelyreiykfalekleea 391
                                        +pely +i++ + e+++++
  gi|298674093|ref|YP_003725843.1| 317 FEPELYNDIWNWTVENYKQK 336
                                       57888888888888888875 PP

>> YflT  Heat induced stress protein YflT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.0   0.00044         2      24      94 ..     115     185 ..     112     188 .. 0.87
   2 ?    1.3   0.0      0.11     5e+02       3      29 ..     206     232 ..     205     283 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00044
                              YflT  24 eddiyvvakdkdrlerlaentdaetettseeglwdsiknlfrskgdelrekle.slGltedeaeeyeeelde 94 
                                        d+i +   d++++e+ +e  +a+ +  +++++  ++ +lf+ +g +lre+l+ +++ t + a+  ee++d+
  gi|298674093|ref|YP_003725843.1| 115 ADHIGIKKGDREDIEKTKELVKAQIDA-GYTSFAIDASHLFNFQGGDLREELKdNIDATTEIAKFIEEQMDD 185
                                       689999999999999999999999886.67*******************97762689999999998998886 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.11
                              YflT   3 vyeneeellsaieelkaeGyneddiyv 29 
                                       v +n ee++  i+ l+++G+  + + +
  gi|298674093|ref|YP_003725843.1| 206 VLTNPEEAVTFIKALNENGVYPQVLAI 232
                                       67899**************97776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2557.03
//
Query:       gi|298674094|ref|YP_003725844.1|  [L=160]
Description: hypothetical protein Metev_0117 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-39  134.1   0.0    3.9e-39  133.5   0.0    1.2  1  TrmO      tRNA-methyltransferase O


Domain annotation for each model (and alignments):
>> TrmO  tRNA-methyltransferase O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.5   0.0   2.2e-43   3.9e-39       2     117 ..      19     128 ..      18     129 .. 0.94

  Alignments for each domain:
  == domain 1  score: 133.5 bits;  conditional E-value: 2.2e-43
                                       S-SSGGG--.-EEEEEE-HHH..HGGGTTGGG-SEEEEEEE-TTS...-.SS--E-TT-.SS-E.EGGGS--S-SSS CS
                              TrmO   2 iPrqpglaeeaeaeielepeynseealegleefshlwllfvfhenaekklkakvrpprlggnervGvfatRsphRpn 78 
                                        P+qp+ a+ +++ ie+ pey  e++le+le+fsh++l+++fh +  ++  ++ ++p++++ +++G+fatR+p+Rpn
  gi|298674094|ref|YP_003725844.1|  19 SPIQPAGAKGIKGYIEIYPEY--EKGLEDLEGFSHIYLIYHFHLS--ND-YSLSVKPFMDS-KKHGLFATRAPKRPN 89 
                                       59*******************..********************77..34.67888999997.666************ PP

                                       -EEEEEEEEEEEETTEEEEES----TT-EEEEEEE--HH CS
                              TrmO  79 piglsvvklekvegnvlevsgvDlldgtpvlDiKPYvpy 117
                                       pig+svv++ +v++n++++++vD++dgtp+lDiKPYvp+
  gi|298674094|ref|YP_003725844.1|  90 PIGISVVRVVDVDENIVHIKDVDIVDGTPLLDIKPYVPD 128
                                       *************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1027.63
//
Query:       gi|298674095|ref|YP_003725845.1|  [L=193]
Description: formylmethanofuran dehydrogenase subunit E [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.2e-44  148.7   0.1    1.2e-43  148.3   0.1    1.1  1  FmdE            FmdE, Molybdenum formylmethanofuran dehydroge
    2.6e-06   27.3   0.9    4.5e-06   26.5   0.9    1.4  1  zf-dskA_traR    Prokaryotic dksA/traR C4-type zinc finger
  ------ inclusion threshold ------
      0.056   13.2   0.7       0.11   12.2   0.7    1.5  1  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
      0.088   12.8   0.0       0.23   11.5   0.0    1.7  1  ADK_lid         Adenylate kinase, active site lid
        2.7    8.0   6.8        1.4    8.9   3.7    2.2  2  DUF4428         Domain of unknown function (DUF4428)


Domain annotation for each model (and alignments):
>> FmdE  FmdE, Molybdenum formylmethanofuran dehydrogenase operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.3   0.1   3.3e-47   1.2e-43       1     131 [.       9     143 ..       9     144 .. 0.97

  Alignments for each domain:
  == domain 1  score: 148.3 bits;  conditional E-value: 3.3e-47
                                       HHSS--CHHHHHHHHHHHHHHCC....-TTSSSEEEEES-STCHHHHHHHHCS--TTTTSEEE--SS-SEEEEEETT CS
                              FmdE   1 fHGHlCpglvlGyrmakaalkelgpkeeegdeelvaivetdsCldDAiqvltgctlGkgnlivmdygkkaltfkkrk 77 
                                       fHGH Cpgl++Gyr+a++al++++   +++deelvaive++sC++DAiq+ltgct+Gkgn++++dygk+++tf+kr+
  gi|298674095|ref|YP_003725845.1|   9 FHGHQCPGLAIGYRVAQIALDKFKN--RSEDEELVAIVENNSCAVDAIQALTGCTFGKGNFVFKDYGKHVYTFIKRG 83 
                                       9**********************95..3448********************************************** PP

                                       T-EEEEEEE-.......CCTHHHHHHHCCT--GGGS-HHHHHHHHHHHHHHHHHS.HHHHE CS
                              FmdE  78 tgkavrlklk.......eelpelreklakgkakeekeeeeleeeleeaikkilnapeeelf 131
                                       + k++r++lk       e++ e+++k+ +++a+ee e +e+++ +e+   +il+ape+e+f
  gi|298674095|ref|YP_003725845.1|  84 DEKGIRISLKpqndpasERHLEIFKKIQNNRATEE-EIREFRKIHEQKTVNILEAPENEIF 143
                                       ********************************999.9999********************9 PP

>> zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.9   1.2e-09   4.5e-06       2      33 ..     158     191 ..     157     192 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.2e-09
                      zf-dskA_traR   2 iygs..CeeCGEpIpeaRlralPgarlCveCqek 33 
                                       i+++  C+eCGE ++  R + +  + +C++C ek
  gi|298674095|ref|YP_003725845.1| 158 IFETiiCDECGEGVMSSRTKTINEKYVCIPCYEK 191
                                       677778**************************98 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.7   3.1e-05      0.11      14      53 ..     153     191 ..     147     192 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.1e-05
                    zinc_ribbon_10  14 etsaknryalICskChshnGlap.keeleevkyrCpkCgal 53 
                                       ++ a+ +  +IC +C +  G+++ + +  + ky+C  C ++
  gi|298674095|ref|YP_003725845.1| 153 PQKAQIFETIICDECGE--GVMSsRTKTINEKYVCIPCYEK 191
                                       47788999*******97..777534444445*******876 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   6.5e-05      0.23       8      30 ..     140     170 ..     138     173 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.5e-05
                                       --EEETT..T.B--S.....STTB-TTT--. CS
                           ADK_lid   8 GrsYhvv..f.npPk.....veglCDkCGep 30 
                                       ++++hv+    + P+     +  +CD+CGe 
  gi|298674095|ref|YP_003725845.1| 140 NEIFHVEnvSdKAPQkaqifETIICDECGEG 170
                                       68999886525567669999999******95 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       1.6   5.7e+03      41      50 ..     113     122 ..     105     122 .. 0.64
   2 ?    8.9   3.7   0.00039       1.4       2      31 ..     164     193 .]     162     193 .] 0.71

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.6
                           DUF4428  41 kiltledIke 50 
                                       + +t e+I+e
  gi|298674095|ref|YP_003725845.1| 113 NRATEEEIRE 122
                                       6678888886 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00039
                           DUF4428   2 CaiCgkKigllkr.lkleDg.yvCkdClkKls 31 
                                       C+ Cg+  g++++ +k+ ++ yvC  C++Kl+
  gi|298674095|ref|YP_003725845.1| 164 CDECGE--GVMSSrTKTINEkYVCIPCYEKLC 193
                                       777777..5565555555555*********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1091  (0.0608511); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1286.16
//
Query:       gi|298674096|ref|YP_003725846.1|  [L=163]
Description: TOPRIM domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-05   25.3   0.0    4.3e-05   23.9   0.0    1.8  1  Toprim_4     Toprim domain
    3.3e-05   24.0   0.2    0.00038   20.6   0.2    2.2  1  Toprim       Toprim domain
  ------ inclusion threshold ------
      0.032   14.7   0.0      0.057   13.9   0.0    1.5  1  Toprim_2     Toprim-like
      0.068   13.4   0.9        5.6    7.3   0.1    2.5  2  TBP-binding  TATA box-binding protein binding
       0.11   12.9   0.0       0.16   12.4   0.0    1.3  1  Toprim_3     Toprim domain


Domain annotation for each model (and alignments):
>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   1.2e-08   4.3e-05       2      77 ..      36     102 ..      35     114 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.2e-08
                          Toprim_4   2 eiiiVEgyaDvlalekagiknvvavlg..galspldgirpeklktenlveaekkvkevilaldgDaeGeataerlae 76 
                                        i +VEg  D  +lek gi + + ++   + l+ +++++     +        + k v++++d D +Ge  a +l+e
  gi|298674096|ref|YP_003725846.1|  36 DILVVEGKRDICSLEKLGIDGDIETVSnkSLLDFSENVA-----Y--------TGKSVVILTDWDRRGEILASKLSE 99 
                                       599****************98888876545554444444.....3........359********************9 PP

                          Toprim_4  77 ..l 77 
                                         +
  gi|298674096|ref|YP_003725846.1| 100 ylQ 102
                                       542 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.2     1e-07   0.00038       3     100 ..      38     112 ..      36     115 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1e-07
                                       EEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHSTTEEEEEECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHH CS
                            Toprim   3 vivEgpsdaktiakalgsgfqavtaslGhildletefkpvyeeiedkkkvlkalkelakradeiilatDpDreGeai 79 
                                        +vEg++d  +++k+ g ++ + t s   +ld  +                      a   + ++++tD Dr Ge +
  gi|298674096|ref|YP_003725846.1|  38 LVVEGKRDICSLEKL-GIDGDIETVSNKSLLDFSE--------------------NVAYTGKSVVILTDWDRRGEIL 93 
                                       567777777777777.5455555555555555555....................7789999*************** PP

                                       HHHHHHHHTHHHTTTEEEEEE CS
                            Toprim  80 awellevlkellenkigrvef 100
                                       a +l e+l+ l+ +  + +e+
  gi|298674096|ref|YP_003725846.1|  94 ASKLSEYLQTLDTD--YDIEI 112
                                       ********988877..77766 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.6e-05     0.057       2      72 ..      39     105 ..      38     129 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.6e-05
                          Toprim_2   2 vfEgaiDalSlaqlgikektnvvalgGtalteaalkllerypekkvvlalDnDkaGrkaakrlaellreag 72 
                                       v+Eg  D  Sl +lgi+ + + v+  +  l     + ++ y  k vv+ +D D+ G+  a++l+e l+   
  gi|298674096|ref|YP_003725846.1|  39 VVEGKRDICSLEKLGIDGDIETVSNKSL-L--DFSENVA-YTGKSVVILTDWDRRGEILASKLSEYLQTLD 105
                                       89**************877777777777.2..2222222.33567*******************9998555 PP

>> TBP-binding  TATA box-binding protein binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1    0.0016       5.6      29      54 ..      35      59 ..      31      65 .. 0.80
   2 ?    4.3   0.1     0.013        48      27      46 ..     104     121 ..     101     132 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0016
                       TBP-binding 29 dDdvLDeeskknLssLskLGLgsllk 54
                                      +D +L  e k+ + sL kLG++  ++
  gi|298674096|ref|YP_003725846.1| 35 GD-ILVVEGKRDICSLEKLGIDGDIE 59
                                      44.9999**************97665 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.013
                       TBP-binding  27 LedDdvLDeeskknLssLsk 46 
                                       L++D   D e +++L+sL k
  gi|298674096|ref|YP_003725846.1| 104 LDTD--YDIEIREQLKSLVK 121
                                       6666..9**********965 PP

>> Toprim_3  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.4e-05      0.16       2      71 ..      37     105 ..      36     130 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.4e-05
                          Toprim_3   2 liivEGietaLsileartgaaviAllsaanlk.aiawpergkrvviaaDnDaandGreaaeklaerleaag 71 
                                       +++vEG  ++ s+++   + ++  + +++ l+ + +++ +gk vvi+ D D    G+  a kl e l+  +
  gi|298674096|ref|YP_003725846.1|  37 ILVVEGKRDICSLEKLGIDGDIETVSNKSLLDfSENVAYTGKSVVILTDWDRR--GEILASKLSEYLQTLD 105
                                       678999999999988888888888899999996666667**************..**********999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1233  (0.0687713); expected 358.6 (0.02)
Passed bias filter:                      728  (0.0406046); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1079.59
//
Query:       gi|298674097|ref|YP_003725847.1|  [L=124]
Description: hypothetical protein Metev_0120 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-43  147.6   0.4    1.5e-43  147.4   0.4    1.0  1  DUF356    Protein of unknown function (DUF356)


Domain annotation for each model (and alignments):
>> DUF356  Protein of unknown function (DUF356)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.4   0.4   8.1e-48   1.5e-43       1     106 []       4     109 ..       4     109 .. 0.99

  Alignments for each domain:
  == domain 1  score: 147.4 bits;  conditional E-value: 8.1e-48
                            DUF356   1 liliRadnkeKvlnalaDlerygklkiegkPriiepevadkilekvlkeelkkkvkvaalveveedatkaisklrki 77 
                                       +++iR+dn++Kv++al+Dle+ygk+++++kP++iep++ad++l++vl+++lk ++k+aalve++++a+++is+l+ki
  gi|298674097|ref|YP_003725847.1|   4 FAVIRGDNTDKVKIALHDLEQYGKFQFQAKPKQIEPDYADHLLVSVLRVPLKARCKSAALVELDDNAGAVISRLKKI 80 
                                       79*************************************************************************** PP

                            DUF356  78 HPPaHvvvvseeydeyeellekleklkel 106
                                       HPPaH+v+vs+++++y+el++k+++++ +
  gi|298674097|ref|YP_003725847.1|  81 HPPAHIVIVSPRHEAYNELINKSKNYPVF 109
                                       *************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.32s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 767.66
//
Query:       gi|298674098|ref|YP_003725848.1|  [L=271]
Description: pyrroline-5-carboxylate reductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.5e-40  135.2   0.1    1.3e-39  134.5   0.1    1.3  1  P5CR_dimer       Pyrroline-5-carboxylate reductase dimerisati
    3.5e-21   75.6   0.6    8.2e-21   74.4   0.6    1.6  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    3.2e-08   33.9   0.6    1.2e-07   32.0   0.6    2.0  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    8.4e-05   21.7   0.4    0.00027   20.0   0.4    1.8  1  PDH              Prephenate dehydrogenase
    9.5e-05   22.8   0.1    0.00019   21.9   0.1    1.5  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
    0.00011   22.2   2.0    0.00027   21.0   2.0    1.7  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
     0.0022   18.1   0.2     0.0045   17.1   0.2    1.5  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
     0.0028   17.0   0.1     0.0043   16.4   0.1    1.3  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
     0.0047   15.9   0.2     0.0072   15.3   0.2    1.2  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil
  ------ inclusion threshold ------
      0.024   14.5   1.2        3.3    7.6   0.3    2.6  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
      0.043   13.9   1.1      0.098   12.7   1.1    1.6  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      0.059   14.2   0.0       0.12   13.2   0.0    1.5  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
        0.1   13.1   0.0       0.73   10.3   0.0    2.1  2  UDPG_MGDP_dh_C   UDP-glucose/GDP-mannose dehydrogenase family


Domain annotation for each model (and alignments):
>> P5CR_dimer  Pyrroline-5-carboxylate reductase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.5   0.1   9.8e-43   1.3e-39       1     103 []     165     269 ..     165     269 .. 0.97

  Alignments for each domain:
  == domain 1  score: 134.5 bits;  conditional E-value: 9.8e-43
                                       CCHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHCHS..HHHHHHHH--TTSHHHH CS
                        P5CR_dimer   1 EkqldavtalsGsgpAyvflliealadagvklGlsreeArelaaqtvaGaaklllese..paelrdkvtspgGtTia 75 
                                       E ++da+t++sGsgpAy+f +iea+ad++v +Gl+r++A+ +aaqtv+Gaakl+le++  pael+d+vtspgGtTi+
  gi|298674098|ref|YP_003725848.1| 165 EYLMDAFTGVSGSGPAYIFPVIEAMADGAVYEGLDRKNALTFAAQTVLGAAKLVLETDshPAELKDMVTSPGGTTIR 241
                                       678*************************************************99966668***************** PP

                                       HHHHHHHTTHHHHHHHHHHHHHHHHHHH CS
                        P5CR_dimer  76 glkeleegglraavieaveaaakrskel 103
                                       g +elee+g+r+a+++av ++ krs+el
  gi|298674098|ref|YP_003725848.1| 242 GFHELEEHGIRSAFMDAVIESSKRSREL 269
                                       **************************97 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.4   0.6   5.9e-24   8.2e-21       2      97 .]       8     102 ..       7     102 .. 0.98

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 5.9e-24
                                       EEEETTSHHHHHHHHHHHHTTS.-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHH CS
                     F420_oxidored   2 igiiGaGnmgealasgllaaga.qpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveev 77 
                                       ig+iG+G+mg++l++g+l+++  + ++++ a++  ++++e l++elg++v+  dn++++ ++d+++lavkp+++ +v
  gi|298674098|ref|YP_003725848.1|   8 IGLIGTGKMGSSLIRGILKSNIvDSSNVY-ASDIYNQSLENLQNELGINVSN-DNKQTVMNSDIIILAVKPQVIRKV 82 
                                       9****************************.99********************.************************ PP

                                       HHHCGHHHHTTSEEEEESSS CS
                     F420_oxidored  78 lselakdalkgklvisvlag 97 
                                       ++  +++  ++klvis++ag
  gi|298674098|ref|YP_003725848.1|  83 IAGFKDEMTEDKLVISIAAG 102
                                       ******************97 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.6     9e-11   1.2e-07       1      91 [.       7     101 ..       7     167 .. 0.82

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 9e-11
                                       EEEEE--SHHHHHHHHHHHHTT-....EEEEE-SSHHHHHHHHHT.TEEE-SSHHHHHHHCSEEEE-SSSHHHHHHH CS
                     NAD_binding_2   1 kigfiGlGvMGsnmalnllkagy....kvavynrtkekveelvae.gakaaesieelvasldvvitmvkagkavdev 72 
                                       +ig+iG+G+MGs++++ +lk+++    +v++ +  ++++e+l +e g+++ ++ ++ v + d++i+ vk  + +++v
  gi|298674098|ref|YP_003725848.1|   7 NIGLIGTGKMGSSLIRGILKSNIvdssNVYASDIYNQSLENLQNElGINVSNDNKQTVMNSDIIILAVKP-QVIRKV 82 
                                       69****************8765333339**************99967*********************85.89**** PP

                                       HHSHCCC--TT-EEEE-S- CS
                     NAD_binding_2  73 iegllealkkgdilidgst 91 
                                       i g ++++ +++++i  + 
  gi|298674098|ref|YP_003725848.1|  83 IAGFKDEMTEDKLVISIAA 101
                                       **************98765 PP

>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.4   1.9e-07   0.00027      14     151 ..      35     159 ..      25     232 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.9e-07
                                       EEEE-S.SHHHHHHHHHTTSSSEEES-GGGGCCGSEEEE-S-GGGHHHHHHHHHHHS-TT-EEEE--S--CHHHHHH CS
                               PDH  14 vigydi.deekaeaalelglvdeatddieavkeadivvlavPvevilevlkelaphlkedalitDvgsvKekvvrel 89 
                                       v+  di +++  +   elg+   +++  + v + di++lav ++vi++v++  +  + ed l++ ++     ++ e+
  gi|298674098|ref|YP_003725848.1|  35 VYASDIyNQSLENLQNELGINVSNDN-KQTVMNSDIIILAVKPQVIRKVIAGFKDEMTEDKLVISIAA--GVPISEI 108
                                       55556523333445568999999988.599*********************************98875..6789999 PP

                                       HHHCC..GCEEEEEES---S-SSGGG--TTTTTT-EEEEEE-TTS-HHHHHHHHHHHHHCT- CS
                               PDH  90 eellkegksfvgghPmaGteksGvdaareelfenavviLtPtektdkealekvkelleevga 151
                                       e+ l++g +++   P +                +   +++P  +t +e +e + e+++ vg 
  gi|298674098|ref|YP_003725848.1| 109 EDELNSGSKLIRVMPNIAA-----------TVGESSSAICPGGNTTNEDVENALEIFKTVGT 159
                                       9999999999999885544...........22334456788888888888888888887774 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.1   1.3e-07   0.00019       1      99 [.       7     102 ..       7     133 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.3e-07
                                       EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHH CS
                    Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpag 77 
                                       +++++G tG +G+ l+r + ++  v+ + +++s+    + l+++ +    +  ++v++ +++ + + di++la+  +
  gi|298674098|ref|YP_003725848.1|   7 NIGLIG-TGKMGSSLIRGILKSNIVDSSNVYASDI-YNQSLENLQN----ELGINVSNDNKQTVMNSDIIILAVKPQ 77 
                                       69****.***************************9.8888888844....77888888789999************* PP

                                       HHHHHHHHH...HHTTSEEEESSST CS
                    Semialdhyde_dh  78 vskelapkl...aeagvkviDlssd 99 
                                       v +++ + +   + ++  vi+ ++ 
  gi|298674098|ref|YP_003725848.1|  78 VIRKVIAGFkdeMTEDKLVISIAAG 102
                                       *******994444445588888775 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   2.0   1.9e-07   0.00027      45     107 ..      42     109 ..       7     151 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.9e-07
                                       TTTBTT----TTEEEES-HHHHHTT--EEEE---HHHHHHHHHHHCCC--TT-EEEE---SE.....E CS
                    NAD_Gly3P_dh_N  45 vkyLpgiklpenlvattdlaealkgadiivlvvPsqalrevlkklkgllkkkailvsliKGi.....e 107
                                       ++ L++++ +  + +++d ++++ ++dii+l+v  q++r+v++  k+ +++++ ++s++ G+     e
  gi|298674098|ref|YP_003725848.1|  42 NQSLENLQNELGINVSNDNKQTVMNSDIIILAVKPQVIRKVIAGFKDEMTEDKLVISIAAGVpiseiE 109
                                       456778888888999**********************************************9765441 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.2   3.3e-06    0.0045       2      83 ..       7      82 ..       6     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.3e-06
                                      EEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS.--S-BEBSSHHHHHHH-SEEEE-S-HHH CS
                            DapB_N  2 kvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglg.klgvavtddleevlekadvliDFTtpea 79
                                      +++++G  G+mG+++++ + +++ +  + ++ ++     ++++    +l+ +lg++v++d ++++ ++d++i   +p++
  gi|298674098|ref|YP_003725848.1|  7 NIGLIGT-GKMGSSLIRGILKSNIVDSSNVYASDI---YNQSLE---NLQnELGINVSNDNKQTVMNSDIIILAVKPQV 78
                                      6899997.*************88888777777754...444443...33338********************9998888 PP

                                      HHHH CS
                            DapB_N 80 vlen 83
                                      + ++
  gi|298674098|ref|YP_003725848.1| 79 IRKV 82
                                      7765 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   3.1e-06    0.0043      34     100 ..       3      75 ..       1     106 [. 0.83

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.1e-06
                                       GTTSEEEEES-SHHHHHHHHHHHHTT-....EEEEESSSHHHHH.CHHHHTCEEC.SHHHHHHH-SEEEE-S- CS
                      2-Hacid_dh_C  34 lsgktvGiiGlGrIGqavakrlkafgm....kviaydrskkkee.eeeelgvelv.sleellaesDivslhlp 100
                                       l++k +G+iG+G++G+++++ + + ++    +v+a d ++++ e  ++elg+++  + ++ + +sDi++l++ 
  gi|298674098|ref|YP_003725848.1|   3 LKNKNIGLIGTGKMGSSLIRGILKSNIvdssNVYASDIYNQSLEnLQNELGINVSnDNKQTVMNSDIIILAVK 75 
                                       799**************999665444334479*******9987766778888666599999********9986 PP

>> OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   5.2e-06    0.0072     131     277 ..       7     153 ..       4     165 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.2e-06
                                       EEEEE--SHHHHHHHHHHCCCS--SEEEEE-SSHHHHHHHHHHCCS.CTT-EEECSCHHHHTTSSEEEE----SS.. CS
                   OCD_Mu_crystall 131 vlaiiGaGvqaetqlealkavldikevriydrdeeaaekfaenlqefefevsackseeeavegadivvtvTaaka.. 205
                                        +++iG G +  + ++ + +   ++   +y+ d    ++ +enlq+ e+ +++++++++ v + di++ +   +   
  gi|298674098|ref|YP_003725848.1|   7 NIGLIGTGKMGSSLIRGILKSNIVDSSNVYASDI--YNQSLENLQN-ELGINVSNDNKQTVMNSDIIILAVKPQVir 80 
                                       57899****9999999999999999999999875..5778999997.*******************99877666567 PP

                                       ...-SB-GGGS-TT-EEEE-S--STT--SB-HHHHHCCEEEESHHHHHHHCCCCHCHHHTTSSTCGGEEEEHHHH CS
                   OCD_Mu_crystall 206 ...pilkaewvkpGahinavgadapgkteLdddilkradifvdseaqareeGeiqvaiekgvlaedakvaelgev 277
                                            +k+e+ +   ++  ++a+ p   e++d++   ++++   ++ a   Ge   ai  g+   ++ v++  e+
  gi|298674098|ref|YP_003725848.1|  81 kviAGFKDEMTED-KLVISIAAGVP-ISEIEDELNSGSKLIRVMPNIAATVGESSSAICPGGNTTNEDVENALEI 153
                                       7777788888766.78889999988.5799999999999999999999999999999997776666665555444 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0045       6.2       1      51 [.       7      61 ..       7      66 .. 0.74
   2 ?    7.6   0.3    0.0024       3.3      67     176 ..      54     163 ..      49     166 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0045
                                      EEEEE--SCCHHHHHHHHHHTT-....EEEEE-S-HHHHHHHHHHHHHHHHCCTT CS
                           3HCDH_N  1 kvaviGaGtmGagiaavfasagl....eVvlvdiseealekalekieksleklve 51
                                      +++ iG+G mG+++   ++++++    +V   di +++le+ ++++  ++++  +
  gi|298674098|ref|YP_003725848.1|  7 NIGLIGTGKMGSSLIRGILKSNIvdssNVYASDIYNQSLENLQNELGINVSNDNK 61
                                      5899*******98777776665433338999999999999998888776666554 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0024
                                       EEEES-HHHHH.C-SEEEE-S-SSHHHHHHHHHHHHCCS-TTSEEEE--SSS-HHHHCCCSSSGGGEEEEEE-SSTT CS
                           3HCDH_N  67 isfttdleeav.dadlviEavvEnlelKrkvfaelekiakpdailasnTSslsiselaealkrperviglHFfnPpp 142
                                       i++++d ++ v + d++i av    ++ rkv+a  +  + +d +++s + +++ise+ ++l++ +++i + +   ++
  gi|298674098|ref|YP_003725848.1|  54 INVSNDNKQTVmNSDIIILAVK--PQVIRKVIAGFKDEMTEDKLVISIAAGVPISEIEDELNSGSKLIRVMPNIAAT 128
                                       6788888888889999999995..677899***********************************999887766666 PP

                                       T--.EEEEEE-TT--HHHHHHHHHHHHHTT-EEEE CS
                           3HCDH_N 143 lmk.LvEvvrgekTseetvatvvelakkigktpvv 176
                                       + +    +++g +T +e v+++ e++k +g   vv
  gi|298674098|ref|YP_003725848.1| 129 VGEsSSAICPGGNTTNEDVENALEIFKTVGTARVV 163
                                       65414568888888888888888888888877665 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.1   7.1e-05     0.098      10      86 ..       3      77 ..       1     115 [. 0.66

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.1e-05
                                      .TT-EEEEES-SHHHHHHHHHHHCCT-CE.EEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSS CS
                      Shikimate_DH 10 lkekkvlliGaGemaelvakhLlakgvkk.vvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisatase 86
                                      lk+k++ liG+G+m++ +++ +l++++ +   v   ++   ++l e+l ++e+ +   ++ k+ + ++d++i a++ +
  gi|298674098|ref|YP_003725848.1|  3 LKNKNIGLIGTGKMGSSLIRGILKSNIVDsSNVYASDI-YNQSL-ENL-QNELGINVSNDNKQTVMNSDIIILAVKPQ 77
                                      799**************999988776543033333322.22223.333.33355667788899999999999998654 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   8.9e-05      0.12       2      73 ..       7      77 ..       6      99 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.9e-05
                                      EEEEETTSHHHHHHHHHHHHTTTTE.EEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GG CS
                      GFO_IDH_MocA  2 rvaiiGaGkigskhlrplnesqrle.evvalldpdaeraeavaesfgveaysdleelladpeidavivatpng 73
                                      ++++iG+Gk+gs  +r + +s+      v + d+ +++ e++ +++g+++ +d ++ +   + d++i a+ ++
  gi|298674098|ref|YP_003725848.1|  7 NIGLIGTGKMGSSLIRGILKSNIVDsSNVYASDIYNQSLENLQNELGINVSNDNKQTVM--NSDIIILAVKPQ 77
                                      89*************9999995433567778899999************7666555555..478999998884 PP

>> UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00053      0.73      45      97 ..      45      97 ..      19     102 .. 0.80
   2 ?   -0.1   0.0       0.9   1.2e+03      20      47 ..     240     267 ..     229     270 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00053
                                      CCHHGGBTCCEEES-CHHHHTT-SEEEE-S--GGGGGS-HHHHHHCC.SS-EEE CS
                    UDPG_MGDP_dh_C 45 veaeleekgvevvdsleealkgadaiviltehdefkeldlaklkelm.kpavvf 97
                                       e+ ++e g++v ++ ++++ ++d+i+++++ + ++++ +a +k+ m ++++v+
  gi|298674098|ref|YP_003725848.1| 45 LENLQNELGINVSNDNKQTVMNSDIIILAVKPQVIRKV-IAGFKDEMtEDKLVI 97
                                      333333679****************************6.999999999888887 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.9
                                       HHHHHHHHHCTSEEEEE-SSTHHCCCCH CS
                    UDPG_MGDP_dh_C  20 ldiieeLleegaevkiyDPkvkeeavea 47 
                                       ++  +eL+e+g++   +D +++++++++
  gi|298674098|ref|YP_003725848.1| 240 IRGFHELEEHGIRSAFMDAVIESSKRSR 267
                                       555789*************999998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1719.43
//
Query:       gi|298674099|ref|YP_003725849.1|  [L=169]
Description: transcriptional regulator, XRE family [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-08   33.2   1.4    6.6e-08   32.5   1.4    1.4  1  HTH_3     Helix-turn-helix
    3.6e-06   26.9   1.4    7.3e-06   25.9   1.4    1.5  1  HTH_19    Helix-turn-helix domain
    1.9e-05   24.9   0.0    3.2e-05   24.2   0.0    1.3  1  HTH_31    Helix-turn-helix domain
     0.0005   19.9   1.4    0.00084   19.2   1.4    1.4  1  HTH_25    Helix-turn-helix domain
    0.00088   19.2   2.9       0.16   11.9   0.1    2.4  2  zf-FCS    MYM-type Zinc finger with FCS sequence motif
  ------ inclusion threshold ------
      0.078   12.9   0.3        0.1   12.5   0.3    1.2  1  DUF4509   Domain of unknown function (DUF4509)
      0.078   12.9   0.1       0.16   12.0   0.1    1.4  1  HTH_37    Helix-turn-helix domain
       0.39   10.8   6.1          2    8.4   0.5    2.7  2  DUF2089   Protein of unknown function (DUF2089)
       0.56   10.6   4.5        0.3   11.5   0.7    2.0  2  Eaf7      Chromatin modification-related protein EAF7
       0.93    9.1   4.0        3.8    7.2   0.1    2.6  3  RecR      RecR protein


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   1.4   3.7e-11   6.6e-08       1      54 [.      89     142 ..      89     143 .. 0.97

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 3.7e-11
                                       HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHHH CS
                             HTH_3   1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvslde 54 
                                       ++  R+ l +++eeLA+k+  + s i +iE+Ge  P  ++ kkl+ +L+++l+e
  gi|298674099|ref|YP_003725849.1|  89 IRDTRERLEWTLEELAAKIKEKESLIKKIERGEITPEDSVRKKLEHTLNIKLTE 142
                                       7999**********************************************9987 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   1.4   4.1e-09   7.3e-06       3      57 ..      88     141 ..      87     148 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 4.1e-09
                            HTH_19   3 rLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidle 57 
                                        ++  Re l +t+eela +++   s i +iE g++ +p+ ++ +k+ ++l+i l+
  gi|298674099|ref|YP_003725849.1|  88 IIRDTRERLEWTLEELAAKIKEKESLIKKIERGEI-TPEDSVRKKLEHTLNIKLT 141
                                       6999*******************************.******9********9976 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   1.8e-08   3.2e-05       7      56 ..      90     138 ..      87     146 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.8e-08
                            HTH_31   7 ralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgl 56 
                                       r+ Rer  +++ee+A+ +   es + ++E+G+++ p  +v  +l + l+ 
  gi|298674099|ref|YP_003725849.1|  90 RDTRERLEWTLEELAAKIKEKESLIKKIERGEIT-PEDSVRKKLEHTLNI 138
                                       899******************************6.*99999999888876 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   1.4   4.7e-07   0.00084       2      35 ..      89     122 ..      88     127 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.7e-07
                                       HHHHHHTTT--HHHHHHHSS--HHHHHHHHCT-- CS
                            HTH_25   2 LraaRearglsleevaketkIrkdylealEeddf 35 
                                        r  Re++ ++lee+a+++k ++++++++E++++
  gi|298674099|ref|YP_003725849.1|  89 IRDTRERLEWTLEELAAKIKEKESLIKKIERGEI 122
                                       5899***************************986 PP

>> zf-FCS  MYM-type Zinc finger with FCS sequence motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   8.8e-05      0.16       3      18 ..       5      20 ..       3      28 .. 0.79
   2 !    7.4   0.3    0.0023       4.2       6      26 ..      32      49 ..      31      57 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.8e-05
                            zf-FCS  3 kkrCwfCkkyikgkpe 18
                                      +  C++C+++ikgkp+
  gi|298674099|ref|YP_003725849.1|  5 QVQCEICGTEIKGKPT 20
                                      578************8 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0023
                            zf-FCS  6 CwfCkkyikgkpeftyvlend 26
                                      C++C +y + +++    ++ +
  gi|298674099|ref|YP_003725849.1| 32 CSICAQYGTSVET---RTQTK 49
                                      ************8...66665 PP

>> DUF4509  Domain of unknown function (DUF4509)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3   5.7e-05       0.1      89     174 ..      46     136 ..      18     149 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.7e-05
                           DUF4509  89 vkleDslsvssislkalesnkpkskaaeleas....veevdkvkhlqwLngklrlqlkslsslqkeqcallhkih.. 159
                                       ++++ ++++ ++s ++++++kp+ k+ ++e      ve  d  + +     +l+  l +l +  ke++ l++ki+  
  gi|298674099|ref|YP_003725849.1|  46 TQTKQQTNTGKKSATKKPEKKPATKKTRFEGPaydlVEDYD--QIIRDTRERLEWTLEELAAKIKEKESLIKKIErg 120
                                       33333333333356666666777777777655533344444..55667889************************88 PP

                           DUF4509 160 sytqgakidqnlkh.l 174
                                       + t + +++++l+h l
  gi|298674099|ref|YP_003725849.1| 121 EITPEDSVRKKLEHtL 136
                                       8999999999999944 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   8.7e-05      0.16      23      57 ..      89     123 ..      81     124 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.7e-05
                                       HHHHHHHCT--HHHHHHHHT--HHHHHHHHTT--T CS
                            HTH_37  23 iaeliekrelsqseaaqllgiaqPkvsrllrgkls 57 
                                       i++++e++e++ +e+a++ + +++ + +++rg+++
  gi|298674099|ref|YP_003725849.1|  89 IRDTRERLEWTLEELAAKIKEKESLIKKIERGEIT 123
                                       899****************************9985 PP

>> DUF2089  Protein of unknown function (DUF2089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2     0.014        24       8      25 ..       1      18 [.       1      30 [. 0.88
   2 ?    8.4   0.5    0.0011         2      67     111 ..      93     129 ..      81     133 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.014
                           DUF2089  8 lvvtrlkcescettiege 25
                                      ++ t+++ce c+t+i+g+
  gi|298674099|ref|YP_003725849.1|  1 MQTTQVQCEICGTEIKGK 18
                                      57799***********97 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0011
                           DUF2089  67 rnrldeileaLgyeeeeeeeeeeeerkeileklekgeisveeAle 111
                                       r+rl+  le+L  + +        e++++++k+e+gei+ e+ ++
  gi|298674099|ref|YP_003725849.1|  93 RERLEWTLEELAAKIK--------EKESLIKKIERGEITPEDSVR 129
                                       4555555555555544........5789************99876 PP

>> Eaf7  Chromatin modification-related protein EAF7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.2      0.41   7.3e+02      80     103 ..      51      78 ..      36      85 .. 0.52
   2 ?   11.5   0.7   0.00017       0.3      42      84 ..     115     157 ..      89     168 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.41
                              Eaf7  80 eeeekekee.....kakeleekkdFeLPe 103
                                       ++++ +k +     ++k +++k+ Fe P 
  gi|298674099|ref|YP_003725849.1|  51 QTNTGKK-SatkkpEKKPATKKTRFEGPA 78 
                                       2222111.122333566667777777665 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00017
                              Eaf7  42 ekpksgkhtsiediwekLktlYdLkaldelenekeeeeeeeek 84 
                                       +k ++g++t  +++++kL++  ++k  +++e+  + e++++++
  gi|298674099|ref|YP_003725849.1| 115 KKIERGEITPEDSVRKKLEHTLNIKLTEKVEDVDTGEDNKSKN 157
                                       34578899999**********************6665555544 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.2     0.054        98      30      34 ..       7      11 ..       2      14 .. 0.58
   2 ?    7.2   0.1    0.0021       3.8      26      35 ..      27      36 ..      22      38 .. 0.83
   3 ?   -3.1   0.0       3.3   5.9e+03       9      17 ..     100     108 ..      95     109 .. 0.57

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.054
                                      S-CCC CS
                              RecR 30 lCaIC 34
                                       C+IC
  gi|298674099|ref|YP_003725849.1|  7 QCEIC 11
                                      46666 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0021
                                      ESSSS-CCCC CS
                              RecR 26 teedlCaICs 35
                                      +e ++C+IC+
  gi|298674099|ref|YP_003725849.1| 27 SELEVCSICA 36
                                      7999*****8 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 3.3
                                       HHHHHHH-E CS
                              RecR   9 Lqeakekvr 17 
                                       L+e+  k++
  gi|298674099|ref|YP_003725849.1| 100 LEELAAKIK 108
                                       455555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1703  (0.0949858); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1138.18
//
Query:       gi|298674100|ref|YP_003725850.1|  [L=446]
Description: 26S proteasome subunit P45 family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-44  150.1   0.2    2.1e-43  147.9   0.0    2.1  2  AAA              ATPase family associated with various cellul
    1.3e-13   50.5   0.3    4.2e-13   48.9   0.3    1.9  1  AAA_lid_3        AAA+ lid domain
    5.1e-10   39.2   0.1    1.1e-09   38.0   0.1    1.6  1  Prot_ATP_ID_OB   Proteasomal ATPase OB C-terminal domain
    5.8e-09   36.1   0.2      1e-07   32.0   0.0    2.8  2  AAA_5            AAA domain (dynein-related subfamily)
      1e-07   32.2   2.7    3.4e-07   30.5   0.0    2.8  2  AAA_2            AAA domain (Cdc48 subfamily)
    2.3e-05   23.7   0.0    5.7e-05   22.4   0.0    1.6  1  DUF815           Protein of unknown function (DUF815)
    2.9e-05   24.5   1.2     0.0019   18.6   0.1    2.7  3  AAA_16           AAA ATPase domain
    5.2e-05   23.8   3.3      8e-05   23.2   0.0    2.8  2  AAA_18           AAA domain
    0.00025   21.4   0.2      0.011   16.0   0.0    2.5  2  AAA_22           AAA domain
    0.00026   20.8   0.0     0.0008   19.2   0.0    1.8  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0003   20.4   0.1     0.0011   18.6   0.1    2.0  1  Prot_ATP_OB_N    Proteasomal ATPase OB N-terminal domain
    0.00039   19.7   0.8    0.00062   19.1   0.1    1.7  2  TIP49            TIP49 P-loop domain
    0.00061   20.1   0.0     0.0016   18.7   0.0    1.8  1  AAA_28           AAA domain
     0.0016   18.2   0.0     0.0062   16.3   0.0    2.0  2  IstB_IS21        IstB-like ATP binding protein
     0.0024   17.2   3.1      0.022   14.1   0.0    3.1  3  ATPase           KaiC
     0.0025   17.1   0.6     0.0067   15.7   0.0    1.9  2  Zeta_toxin       Zeta toxin
     0.0055   16.1   0.1      0.012   15.0   0.1    1.5  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0059   16.8   0.0      0.015   15.4   0.0    1.8  1  AAA_33           AAA domain
     0.0063   16.4   0.0      0.014   15.3   0.0    1.7  1  AAA_3            ATPase family associated with various cellul
     0.0074   16.0   0.0       0.16   11.7   0.0    2.4  2  Sigma54_activat  Sigma-54 interaction domain
     0.0081   15.7   4.5      0.015   14.9   4.5    1.5  1  Leu_zip          Leucine zipper
     0.0097   15.7   3.1       0.67    9.7   0.0    2.3  2  AAA_11           AAA domain
  ------ inclusion threshold ------
      0.017   14.6   0.0      0.044   13.3   0.0    1.6  1  AAA_7            P-loop containing dynein motor region
      0.033   14.2   2.2      0.057   13.5   0.0    2.3  2  AAA_14           AAA domain
      0.042   13.7   0.5       0.61   10.0   0.0    2.9  2  NTPase_1         NTPase
      0.045   12.6   6.7      0.093   11.6   6.1    1.8  2  Spc7             Spc7 kinetochore protein
      0.065   13.0   0.8       0.24   11.1   0.0    2.4  2  AAA_24           AAA domain
      0.081   13.3   0.6       0.25   11.7   0.0    2.2  1  RNA_helicase     RNA helicase
      0.088   12.8   0.0       0.18   11.8   0.0    1.5  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.09   12.5   0.3       0.27   10.9   0.3    1.9  1  AAA_30           AAA domain
       0.12   12.2   0.2        1.3    8.9   0.1    2.2  2  NACHT            NACHT domain
       0.14   11.8   3.7       0.34   10.5   0.3    2.8  3  AAA_25           AAA domain
       0.16   12.3   0.3       0.51   10.7   0.3    1.8  1  AAA_19           AAA domain
       0.23   10.8   5.0        5.3    6.3   0.0    3.7  4  DnaB_C           DnaB-like helicase C terminal domain
       0.63   10.6   2.5        1.6    9.3   0.0    2.6  2  ABC_tran         ABC transporter
        1.2    8.9   5.6        5.4    6.7   2.6    3.0  3  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
        2.2    6.1   7.7          3    5.6   7.7    1.1  1  V_ATPase_I       V-type ATPase 116kDa subunit family


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0         4   1.9e+03      76     108 ..      85     114 ..      49     127 .. 0.77
   2 !  147.9   0.0   4.2e-46   2.1e-43       1     131 [.     225     357 ..     225     358 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 4
                                       TCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEE CS
                               AAA  76 gseseeeervvnqLlteldgvkkkeskviviga 108
                                       ++++ + er v +L +e+d++k++    ++ig+
  gi|298674100|ref|YP_003725850.1|  85 ENQKLKYEREVRKLQAEIDRLKSS---PLIIGT 114
                                       455666678888899999998884...355554 PP

  == domain 2  score: 147.9 bits;  conditional E-value: 4.2e-46
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH... CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr... 74 
                                       +ll GppGtGKTllakava+ ++++f+++ gsel++ky+ge++k +re+f+ a++ka psi+fiDE+da+a +r   
  gi|298674100|ref|YP_003725850.1| 225 ILLAGPPGTGKTLLAKAVAHRTDASFIRVVGSELVQKYIGEGAKLVREVFEMARKKA-PSIVFIDELDAIAAKRlnd 300
                                       69******************************************************9.*****************98 PP

                                       TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  75 sgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       ++++++e +r++ qLl+e+dg++++ ++v +i+atnr d ldpa+lr gRfdr+i ++
  gi|298674100|ref|YP_003725850.1| 301 TNGADREVQRTLMQLLAEMDGFDER-GDVRIIAATNRSDVLDPAILRpGRFDRVITVP 357
                                       77899999****************7.66***************************987 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.3   8.8e-16   4.2e-13       1      44 [.     380     423 ..     380     424 .. 0.97

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 8.8e-16
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedfe 44 
                                       ++d+k+LA +TeG SGADl+a+  eA++lA+r +  +++++df 
  gi|298674100|ref|YP_003725850.1| 380 NIDFKKLANLTEGASGADLSAIAMEAGMLAVRNDKGSVETDDFL 423
                                       79****************************************96 PP

>> Prot_ATP_ID_OB  Proteasomal ATPase OB C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.1   2.4e-12   1.1e-09       1      56 [.     112     166 ..     112     167 .. 0.97

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 2.4e-12
                                       EEEEEEE-TTSSEEEEE-TTS-EEEEEE-GGGSSST--TTEEEEEETTTTEEEEEE CS
                    Prot_ATP_ID_OB   1 VatVsEvlddteraiVktssdeevvvslagavpremLrpgDlVavdkdtgfifEkL 56 
                                       ++tV +vld  +++ V +s++ +++vs+++ + +e++ pg++Va++++t+++++++
  gi|298674100|ref|YP_003725850.1| 112 IGTVMDVLDN-GKLMVRSSTGPQFMVSMSKYLEDEEIEPGTTVALNQQTFAVVDVV 166
                                       89********.****************************************99875 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1         1   4.9e+02      93     100 ..     123     130 ..      63     179 .. 0.66
   2 !   32.0   0.0   2.1e-10     1e-07       2     135 ..     225     345 ..     224     347 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1
                                       EEE..-SS CS
                             AAA_5  93 rllleegg 100
                                       +l++ +++
  gi|298674100|ref|YP_003725850.1| 123 KLMVRSST 130
                                       44443333 PP

  == domain 2  score: 32.0 bits;  conditional E-value: 2.1e-10
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGGG- CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEvera 77 
                                       +lL GppGtgK+ la+ +a+++ +++  v +++      l++++   +++++lv  ++  a +  ++i+++DE++ +
  gi|298674100|ref|YP_003725850.1| 225 ILLAGPPGTGKTLLAKAVAHRTDASFIRVVGSE------LVQKYI--GEGAKLVREVFEMARKkAPSIVFIDELDAI 293
                                       89***************************9986......99*999..6778888887775555689*********99 PP

                                       -HHHHHHHHHHHHSSEEE..-SSSEEE---........-EEEEEESS--.-TT-TTHHHH CS
                             AAA_5  78 esevlnsLlslleerrllleeggelvkaknddller..frviatanpldrslnelspalr 135
                                         + ln  +    e ++ l+++  +++     + er  +r+ia++n+ d     l+pa++
  gi|298674100|ref|YP_003725850.1| 294 AAKRLNDTNGADREVQRTLMQLLAEMDG----FDERgdVRIIAATNRSD----VLDPAIL 345
                                       9999999999988888888887777755....455667*********99....7777765 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.3       1.3   6.4e+02      30      70 ..     155     191 ..     115     201 .. 0.68
   2 !   30.5   0.0   7.1e-10   3.4e-07       6     105 ..     225     318 ..     222     335 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.3
                                       ....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS CS
                             AAA_2  30 kkekkliradaselleeeevehlvsrligappgyvgaeegG 70 
                                        ++++++++d  + +e    e +vs  ++ +   v +++ G
  gi|298674100|ref|YP_003725850.1| 155 LNQQTFAVVDVVQSTE----EPMVSAMEVIESQQVDYDQIG 191
                                       3467778888888888....777777777777777777765 PP

  == domain 2  score: 30.5 bits;  conditional E-value: 7.1e-10
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       ill+gp g+Gkt+laka+a   ++    ++ir+  sel +    + + +  +  ++    a ++   iv++DE+d i
  gi|298674100|ref|YP_003725850.1| 225 ILLAGPPGTGKTLLAKAVAHRTDA----SFIRVVGSELVQ----KYIGEGAKLVREVFEMARKKApsIVFIDELDAI 293
                                       899*****************9996....************....55555555555555555555456********** PP

                                       ------------HHHHHHHHHHHH- CS
                             AAA_2  81 hpkessgadvSregVqrdLLqileg 105
                                       ++k+ +  +    +Vqr L+q+l +
  gi|298674100|ref|YP_003725850.1| 294 AAKRLNDTNGADREVQRTLMQLLAE 318
                                       **977777888889********965 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.2e-07   5.7e-05      18     116 ..     178     290 ..     163     300 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.2e-07
                            DUF815  18 pveevdevklddLvgidkqkealvente.......qfle.glpa.nnvLLwGarGtGKSslvkallneyaeegLrli 85 
                                        v e ++v+ d++ g+d+q ++++e +e        f++ g +a + +LL G  GtGK  l ka+ +++ ++ +r++
  gi|298674100|ref|YP_003725850.1| 178 EVIESQQVDYDQIGGLDEQIKEIIESVEypltkpeSFARiGISApKGILLAGPPGTGKTLLAKAVAHRTDASFIRVV 254
                                       35567899***************998862222222565545555368*****************************9 PP

                            DUF815  86 ..evekedlkelpklvellrerper...filfvDDL 116
                                         e+ ++ + e  klv+++ e++++    i+f+D L
  gi|298674100|ref|YP_003725850.1| 255 gsELVQKYIGEGAKLVREVFEMARKkapSIVFIDEL 290
                                       88899999**9999999987555442227*****98 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0         9   4.4e+03     117     125 ..      92     100 ..      31     113 .. 0.43
   2 !   18.6   0.1   3.9e-06    0.0019      18      51 ..     216     249 ..     212     263 .. 0.79
   3 ?    3.7   0.0      0.15        71     123     154 ..     270     311 ..     264     331 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 9
                            AAA_16 117 srllellkr 125
                                       +r  ++l++
  gi|298674100|ref|YP_003725850.1|  92 EREVRKLQA 100
                                       333333333 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 3.9e-06
                            AAA_16  18 rvrsgrpelvllsGesGvGKsslvrellralekd 51 
                                       r+  + p  +ll G++G+GK+ l+++++++  ++
  gi|298674100|ref|YP_003725850.1| 216 RIGISAPKGILLAGPPGTGKTLLAKAVAHRTDAS 249
                                       566678899******************9865555 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.15
                            AAA_16 123 lkrllallsrderplvlvlDdlq...........wadeaslql 154
                                       +++ ++ +++ + p ++++D+l+            ad + +  
  gi|298674100|ref|YP_003725850.1| 270 VREVFEMARK-KAPSIVFIDELDaiaakrlndtnGADREVQRT 311
                                       4455566777.778*********66666555555333333333 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   1.6e-07     8e-05       1      79 [.     225     331 ..     225     346 .. 0.87
   2 ?   -1.2   0.0       5.7   2.8e+03      20      58 ..     388     431 ..     375     439 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.6e-07
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf....................gvnlrdvakenglllevdpe.......aldes 49 
                                       Ill+G+pG+GKt lak+++ r+ ++                    ++++ ++a+++ +++ + +e        l+++
  gi|298674100|ref|YP_003725850.1| 225 ILLAGPPGTGKTLLAKAVAHRTdASfirvvgselvqkyigegaklVREVFEMARKKAPSIVFIDEldaiaakRLNDT 301
                                       99****************99986558999999999999********************************9988888 PP

                            AAA_18  50 krldedkldklldaleenssaleegknlvi 79 
                                       + +d++++  l+++l e +   e g++ +i
  gi|298674100|ref|YP_003725850.1| 302 NGADREVQRTLMQLLAEMDGFDERGDVRII 331
                                       888888888888888888776666666555 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 5.7
                            AAA_18  20 krlgf.....gvnlrdvakenglllevdpe...aldeskrldedkld 58 
                                       +   +     g  l+ +a e g+l  ++++   ++d+++++++++++
  gi|298674100|ref|YP_003725850.1| 388 N---LtegasGADLSAIAMEAGMLAVRNDKgsvETDDFLKAVDKVMN 431
                                       3...2444578999999999999999999988888888887777765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.2e-05     0.011       8      41 ..     225     249 ..     220     261 .. 0.83
   2 ?    3.0   0.0      0.24   1.1e+02      77     111 ..     268     300 ..     248     333 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.2e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpe 41 
                                       +++ G++GtGKT+l++ ++++          +++
  gi|298674100|ref|YP_003725850.1| 225 ILLAGPPGTGKTLLAKAVAHRT---------DAS 249
                                       7899***************998.........444 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.24
                            AAA_22  77 ellealeqalraravielliiDEaqhlrseealee 111
                                        l++ + + +r++a  +++ iDE + +  ++ l++
  gi|298674100|ref|YP_003725850.1| 268 KLVREVFEMARKKAP-SIVFIDELDAI-AAKRLND 300
                                       556666666677777.9*********9.5554444 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.7e-06    0.0008      34      96 ..     223     293 ..     213     300 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.7e-06
                            RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvkl.kitsgPvleka.gdlaalltnl......eekdvlfideihrl 96 
                                         +ll+GpPG Gkt lak +a+  ++++ ++  +  ++k  g+ a l+ ++      ++  ++fide+  +
  gi|298674100|ref|YP_003725850.1| 223 KGILLAGPPGTGKTLLAKAVAHRTDASFiRVVGSELVQKYiGEGAKLVREVfemarkKAPSIVFIDELDAI 293
                                       569*********************99861555555666533454545443311122133469999998765 PP

>> Prot_ATP_OB_N  Proteasomal ATPase OB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   2.2e-06    0.0011      18      54 ..     128     164 ..     111     171 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.2e-06
                     Prot_ATP_OB_N  18 lvggrrmrVavsPlvdaeeLrpGqeVlLnEalvvVea 54 
                                       ++ g ++ V++s  ++ ee++pG++V Ln++  +V +
  gi|298674100|ref|YP_003725850.1| 128 SSTGPQFMVSMSKYLEDEEIEPGTTVALNQQTFAVVD 164
                                       5679999**********************98655543 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       5.4   2.6e+03     161     194 ..     137     170 ..      87     204 .. 0.69
   2 !   19.1   0.1   1.3e-06   0.00062      49      93 ..     221     263 ..     215     290 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 5.4
                                       HHHHHHHHHT--TT-EEEEETTT--EEE-SSS-S CS
                             TIP49 161 kiaeellkekvkegDviviekesGkvkklGrsea 194
                                       ++ + l+ e+++ g  + +++++ +v  + +s++
  gi|298674100|ref|YP_003725850.1| 137 SMSKYLEDEEIEPGTTVALNQQTFAVVDVVQSTE 170
                                       5666666677777777777666666666555544 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 1.3e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  49 aGravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslev 93 
                                       a +++LlaGp+gtGkt la a+++    d  f+ ++gse+ +  +
  gi|298674100|ref|YP_003725850.1| 221 APKGILLAGPPGTGKTLLAKAVAHRT--DASFIRVVGSELVQKYI 263
                                       5699*******************975..689*******9976554 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   3.3e-06    0.0016       2      52 ..     225     279 ..     224     366 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 3.3e-06
                            AAA_28   2 ivitGgestGKTtlleaLaar....gypvv.pEaareileeklakgedalpwvedl 52 
                                       i + G+++tGKT l++a a r     ++vv  E + +++ e+++  ++  +++ ++
  gi|298674100|ref|YP_003725850.1| 225 ILLAGPPGTGKTLLAKAVAHRtdasFIRVVgSELVQKYIGEGAKLVREVFEMA-RK 279
                                       7899***************7777778999999999999999886666655554.22 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.3e-05    0.0062      46      71 ..     221     246 ..     214     290 .. 0.88
   2 ?   -2.6   0.0       7.9   3.8e+03      52      75 ..     390     413 ..     360     426 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.3e-05
                         IstB_IS21  46 kkenivllGpsGvGKshlaialgvea 71 
                                       + ++i+l Gp+G+GK+ la a+++++
  gi|298674100|ref|YP_003725850.1| 221 APKGILLAGPPGTGKTLLAKAVAHRT 246
                                       56789*****************9875 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 7.9
                         IstB_IS21  52 llGpsGvGKshlaialgveavrag 75 
                                         G sG+  s +a+  g+ avr++
  gi|298674100|ref|YP_003725850.1| 390 TEGASGADLSAIAMEAGMLAVRND 413
                                       348888888888888888888876 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.69   3.3e+02      94     142 ..      81     128 ..      51     141 .. 0.69
   2 !   14.1   0.0   4.6e-05     0.022       5      37 ..     190     240 ..     187     250 .. 0.85
   3 ?    0.9   0.1      0.48   2.3e+02     105     154 ..     267     319 ..     248     322 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.69
                            ATPase  94 esaeekdkedleelieelaeaikeikakrvviDsitglayeekeavaRe 142
                                       ++  e++k + e  +++l+  i+++k + ++i ++  +  ++ + ++R+
  gi|298674100|ref|YP_003725850.1|  81 KRYVENQKLKYEREVRKLQAEIDRLKSSPLIIGTVMDV-LDNGKLMVRS 128
                                       22233777888888899999999999999999888887.6666666665 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 4.6e-05
                            ATPase   5 IeglDeilk..................gGipegrvvlitGepGtGKtifal 37 
                                       I glDe +k                   Gi   + +l++G pGtGKt++a+
  gi|298674100|ref|YP_003725850.1| 190 IGGLDEQIKeiiesveypltkpesfarIGISAPKGILLAGPPGTGKTLLAK 240
                                       677888886688888888888888888899*******************97 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.48
                            ATPase 105 eelieelaeaikeikakrvviDsitgl.ayeekeav..aReilrqlvrvlkkl 154
                                        +l++e+ e+ +++  + v iD ++++ a++ ++     Re  r+l++ l+++
  gi|298674100|ref|YP_003725850.1| 267 AKLVREVFEMARKKAPSIVFIDELDAIaAKRLNDTNgaDREVQRTLMQLLAEM 319
                                       5788888999999999********99964433332221455556666666554 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       3.9   1.9e+03     144     177 ..      70     109 ..      62     124 .. 0.59
   2 !   15.7   0.0   1.4e-05    0.0067      14      51 ..     220     255 ..     212     280 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.9
                        Zeta_toxin 144 yeeevae....gRlvpkee..hdeafeglresvealeeek 177
                                         e+ ++     R+v+ ++   ++ +++l+ ++++l+++ 
  gi|298674100|ref|YP_003725850.1|  70 LNEQYNQieseKRYVENQKlkYEREVRKLQAEIDRLKSSP 109
                                       4444222333357776654114567777888888877776 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.4e-05
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrldp 51 
                                       + Pk ill+G pG GK+ la++++ ++  + +++r+ +
  gi|298674100|ref|YP_003725850.1| 220 SAPKGILLAGPPGTGKTLLAKAVAHRT--DASFIRVVG 255
                                       579*********************998..788888765 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   2.5e-05     0.012      20      42 ..     220     242 ..     210     248 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.5e-05
                      Mg_chelatase  20 aGgHnlllvGppGsGKtmlakrl 42 
                                       +    +ll+GppG+GKt+lak++
  gi|298674100|ref|YP_003725850.1| 220 SAPKGILLAGPPGTGKTLLAKAV 242
                                       555679**************987 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   3.2e-05     0.015       2      39 ..     225     264 ..     225     337 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.2e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfg 39 
                                       +ll G+pG+GK+ la+ ++ +++  ++++   +l +++ g
  gi|298674100|ref|YP_003725850.1| 225 ILLAGPPGTGKTLLAKAVAHRTDasFIRVVGSELVQKYIG 264
                                       6899**************9888877777666665554444 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.9e-05     0.014       2      31 ..     225     254 ..     224     320 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.9e-05
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriq 31 
                                       +ll g PG++ktll+ka+a+  d++f r+ 
  gi|298674100|ref|YP_003725850.1| 225 ILLAGPPGTGKTLLAKAVAHRTDASFIRVV 254
                                       799************************984 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00033      0.16      20      55 ..     220     252 ..     202     265 .. 0.78
   2 ?    1.6   0.0       0.4   1.9e+02     132     144 ..     325     337 ..     279     356 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00033
                                       TSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEE CS
                   Sigma54_activat  20 ktdlsvlitGesGtGKellaraiheaskrkekpfva 55 
                                       + +  +l+ G  GtGK+lla+a+ +   r++++f++
  gi|298674100|ref|YP_003725850.1| 220 SAPKGILLAGPPGTGKTLLAKAVAH---RTDASFIR 252
                                       556789***************9854...44455555 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.4
                                       E--EEEEEEESS- CS
                   Sigma54_activat 132 kvdvriiaatned 144
                                       + dvriiaatn++
  gi|298674100|ref|YP_003725850.1| 325 RGDVRIIAATNRS 337
                                       569*******985 PP

>> Leu_zip  Leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   4.5     3e-05     0.015      97     182 ..      20     107 ..       1     139 [. 0.82

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3e-05
                           Leu_zip  97 efEekefkssnkkeseelkkkkLePlneg..GgaeLLkkeierLkeenekLkerlkelEkqatsaleeksklekalk 171
                                       +++e++ k + +k+ ++++++  e l+++    ++ L   +++L+  n++L+e+ +++E++   + ++k k e++++
  gi|298674100|ref|YP_003725850.1|  20 NMNENNYKYNINKDRFDENENSYEYLADNegDFSKYLLDRMKQLEHRNSRLNEQYNQIESEKRYVENQKLKYEREVR 96 
                                       5677777777788888888999999976641567899999************************************* PP

                           Leu_zip 172 elqkelgekkd 182
                                       +lq+e++  k+
  gi|298674100|ref|YP_003725850.1|  97 KLQAEIDRLKS 107
                                       **999887765 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   3.0     0.077        37     113     202 ..      17     114 ..       1     122 [. 0.50
   2 !    9.7   0.0    0.0014      0.67      18      41 ..     223     246 ..     210     310 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.077
                            AAA_11 113 vekrlekee.kaqlakeiskeleklakelrafeeeeek.........eklkkskekskskleqerrklkkerkelsk 179
                                       +e+++++++ k +++k+  +e+e+  + l ++e +++k         e ++   +++ ++ e e+r +++++ ++++
  gi|298674100|ref|YP_003725850.1|  17 TEENMNENNyKYNINKDRFDENENSYEYLADNEGDFSKylldrmkqlEHRNSRLNEQYNQIESEKRYVENQKLKYER 93 
                                       22222222234555555555555555555555555555777776665444444445555555555555555555555 PP

                            AAA_11 180 eleeaeesleeevldeaeivltT 202
                                       e+++ ++++  + l+++ +++ T
  gi|298674100|ref|YP_003725850.1|  94 EVRKLQAEI--DRLKSSPLIIGT 114
                                       555555554..445666666555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0014
                            AAA_11  18 eitliqGPPGtgKTktivellsql 41 
                                       +  l+ GPPGtgKT    ++ ++ 
  gi|298674100|ref|YP_003725850.1| 223 KGILLAGPPGTGKTLLAKAVAHRT 246
                                       55699*********7666666655 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     9e-05     0.044      28      70 ..     217     251 ..     208     300 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9e-05
                             AAA_7  28 lllknkkpvllvGptGtGKtviikdllkkldkekylsltinfs 70 
                                         +++ k +ll Gp GtGKt+++k + ++ d         +f 
  gi|298674100|ref|YP_003725850.1| 217 IGISAPKGILLAGPPGTGKTLLAKAVAHRTD--------ASFI 251
                                       55778899*****************999988........3333 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   2.3       7.3   3.6e+03      68      87 ..      55      74 ..       8     148 .. 0.62
   2 ?   13.5   0.0   0.00012     0.057       5      76 ..     225     293 ..     221     340 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 7.3
                            AAA_14 68 lflDEiqevpewekalkslv 87
                                       +lD ++++++  + l++ +
  gi|298674100|ref|YP_003725850.1| 55 YLLDRMKQLEHRNSRLNEQY 74
                                      34444444444444444433 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00012
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                       +++ G+  +GKT l+k ++++      s++ +   +  +k + + +kl ++++e+++++  +++f+DE   +
  gi|298674100|ref|YP_003725850.1| 225 ILLAGPPGTGKTLLAKAVAHRTD---ASFIRVVGSELVQKYIGEGAKLVREVFEMARKKAPSIVFIDELDAI 293
                                       7899***********99997766...888888888877777777678999999986667999******9877 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1       1.4   6.7e+02      78     123 ..     166     209 ..     152     215 .. 0.67
   2 ?   10.0   0.0    0.0013      0.61       2      49 ..     225     273 ..     224     305 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHHHHHHHHH-EEEE---STTGGG-HHHHHHHHHHHT CS
                          NTPase_1  78 vesfeelalealrkalseadviviDEiGkmElkskkfkeaveevLk 123
                                       v+s ee +++a++    e++ +  D iG +  ++k+++e+ve  L+
  gi|298674100|ref|YP_003725850.1| 166 VQSTEEPMVSAMEV--IESQQVDYDQIGGLDEQIKEIIESVEYPLT 209
                                       34556666666653..244444568888888888888888887665 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0013
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEEE.EEEEE-------EEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgGf.yteevreggrrigFki 49 
                                       +++ GppG+GKt l k v++  + s ++v G  +++++  +g +   ++
  gi|298674100|ref|YP_003725850.1| 225 ILLAGPPGTGKTLLAKAVAHRTDASFIRVVGSeLVQKYIGEGAKLVREV 273
                                       789****************999999888888523455555555555555 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   6.1   0.00019     0.093     198     280 ..      25     107 ..       3     121 .. 0.87
   2 ?   -2.6   0.0       4.1     2e+03      71      95 ..     260     284 ..     256     285 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00019
                              Spc7 198 keeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkee 274
                                       + + +  +++++e+++ +e + ++  +  + l +  +++e+ +++ +e  ++i++++r++e++k   e ev++l++e
  gi|298674100|ref|YP_003725850.1|  25 NYKYNINKDRFDENENSYEYLADNEGDFSKYLLDRMKQLEHRNSRLNEQYNQIESEKRYVENQKLKYEREVRKLQAE 101
                                       445556688999999999999999999999999999***************************************** PP

                              Spc7 275 vkalee 280
                                        ++l++
  gi|298674100|ref|YP_003725850.1| 102 IDRLKS 107
                                       **9986 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.1
                              Spc7  71 kkyisegrkiireieeetleenPpL 95 
                                       +kyi eg k++re+ e + ++ P +
  gi|298674100|ref|YP_003725850.1| 260 QKYIGEGAKLVREVFEMARKKAPSI 284
                                       799**********999999999976 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       2.8   1.3e+03      49      94 ..      35      79 ..       9     116 .. 0.58
   2 ?   11.1   0.0    0.0005      0.24       4      22 ..     224     242 ..     221     312 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.8
                            AAA_24 49 wedfldevvelaaeladyktlviDtideleelclaevirqnekaes 94
                                      +++  + +++la+++ d++ + +D   +le   ++   + n++ es
  gi|298674100|ref|YP_003725850.1| 35 FDENENSYEYLADNEGDFSKYLLDRMKQLEHRNSRLNEQYNQI-ES 79
                                      3344445555577777788888887777755444433444444.33 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0005
                            AAA_24   4 kiliyGpsgiGKTtlakel 22 
                                        il+ Gp+g+GKT lak  
  gi|298674100|ref|YP_003725850.1| 224 GILLAGPPGTGKTLLAKAV 242
                                       699*************987 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00052      0.25       1      62 [.     225     277 ..     225     307 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00052
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqvk 62 
                                       i+l Gp+g+GK++lak +a         +++d  ++r + ++ +++Y g+ + ++ ++ ++ 
  gi|298674100|ref|YP_003725850.1| 225 ILLAGPPGTGKTLLAKAVA---------HRTDASFIRVVGSELVQKYIGEGAKLVREVFEMA 277
                                       6899*************44.........4445555666777777777766666666655555 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00037      0.18      19      49 ..     222     252 ..     193     273 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00037
                                       TEEEEEEESTTSSHHHHHHHHHHHTT----- CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglakalgveevk 49 
                                        + ilL G+ G+GKT l++++a+  + + ++
  gi|298674100|ref|YP_003725850.1| 222 PKGILLAGPPGTGKTLLAKAVAHRTDASFIR 252
                                       3459******************998877333 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.3   0.00056      0.27      22      51 ..     226     255 ..     217     331 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00056
                            AAA_30  22 vltGpAGtGKttalkalreaweaaggrvig 51 
                                       +l Gp+GtGKt + ka+++  +a+  rv+g
  gi|298674100|ref|YP_003725850.1| 226 LLAGPPGTGKTLLAKAVAHRTDASFIRVVG 255
                                       789**************9988888777766 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1    0.0026       1.3       3      22 ..     225     244 ..     223     251 .. 0.89
   2 ?    0.7   0.0      0.87   4.2e+02      63     113 ..     264     316 ..     247     322 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0026
                                       EEEEC-TTTCHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklal 22 
                                       ++l G++G GKT L++ +a+
  gi|298674100|ref|YP_003725850.1| 225 ILLAGPPGTGKTLLAKAVAH 244
                                       7899************9987 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.87
                                       TS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH............HHHHH CS
                             NACHT  63 pepaapvsevwavllelperlLlilDglDelvtdlgq...kekqpvrtlLseli 113
                                        e a+ v+ev+++  + + ++++i D lD ++++  +      ++v++ L +l+
  gi|298674100|ref|YP_003725850.1| 264 GEGAKLVREVFEMARKKAPSIVFI-DELDAIAAKRLNdtnGADREVQRTLMQLL 316
                                       455678899999999999999985.88888877544445533444555555555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       4.2     2e+03     116     141 ..      60      85 ..      42     120 .. 0.65
   2 ?   10.5   0.3   0.00069      0.34      36      55 ..     225     244 ..     204     249 .. 0.88
   3 ?    0.6   0.1      0.71   3.5e+02     132     166 ..     272     305 ..     264     332 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4.2
                            AAA_25 116 Lfakdrggtlltadvdaleaaieeve 141
                                       + ++++++++l+++++++e + ++ve
  gi|298674100|ref|YP_003725850.1|  60 MKQLEHRNSRLNEQYNQIESEKRYVE 85 
                                       33455666666666666655544443 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00069
                            AAA_25  36 allaGapgtGKttlaldlal 55 
                                       +llaG+pgtGKt la  +a+
  gi|298674100|ref|YP_003725850.1| 225 ILLAGPPGTGKTLLAKAVAH 244
                                       79************987776 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.71
                            AAA_25 132 aleaaieevegvrlvviDplsralggdensnsdvg 166
                                       ++ + +++ + +  v iD l+++ +   n+ + ++
  gi|298674100|ref|YP_003725850.1| 272 EVFEMARK-KAPSIVFIDELDAIAAKRLNDTNGAD 305
                                       44444555.55999*******98888555444442 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3    0.0011      0.51      11      38 ..     223     249 ..     215     334 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0011
                            AAA_19  11 kvllvtaGpGtGKTrvlkhivallvelg 38 
                                       k +l+ ++pGtGKT + k +va+  ++ 
  gi|298674100|ref|YP_003725850.1| 223 KGILLAGPPGTGKTLLAK-AVAHRTDAS 249
                                       56889999*****97655.555555544 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.2       0.1        49      66     107 ..      69     113 ..      57     130 .. 0.75
   2 ?    6.3   0.0     0.011       5.3      22      44 ..     225     247 ..     216     265 .. 0.82
   3 ?   -0.5   0.0       1.3   6.4e+02     123     167 ..     275     318 ..     259     322 .. 0.66
   4 ?   -0.2   0.0       1.1   5.2e+02       5      30 ..     382     407 ..     380     409 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.1
                                       HHHHHHHTXXHHH..HHHTTSX.HHHHHHHHHHHHHHHHSEEEEE CS
                                       xxxxxxxxxxxxx..xxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  66 Rllsseaeidskk..lrtgklk.eedweklteaieelseaklfid 107
                                       Rl  +  +i+s+k  +++ klk e++++kl+++i++l++++l+i 
  gi|298674100|ref|YP_003725850.1|  69 RLNEQYNQIESEKryVENQKLKyEREVRKLQAEIDRLKSSPLIIG 113
                                       444555566655411577788888999999999999999999986 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.011
                                       EEEEEXTTSSHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  22 iiiAarpsmGktalalniaenaa 44 
                                       i++A+ p++Gkt la  +a+++ 
  gi|298674100|ref|YP_003725850.1| 225 ILLAGPPGTGKTLLAKAVAHRTD 247
                                       89****************98754 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.3
                                       HHHHHTTEEEEEEEEGGGTBTSCSSSCCCHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C 123 rlkkekglgliviDyLqlmegseekenreqevseisrsLkalake 167
                                       +++++k  ++++iD L+ + +++  ++ +    e+ r+L +l  e
  gi|298674100|ref|YP_003725850.1| 275 EMARKKAPSIVFIDELDAIAAKR-LNDTNGADREVQRTLMQLLAE 318
                                       5677788899*******999653.222333344556666666555 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 1.1
                                       STHHHHHHCTSBXTTXEEEEEEXTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C   5 gfkdLDkltsGlqkgdliiiAarpsm 30 
                                       +fk+L +lt+G   +dl  iA  ++m
  gi|298674100|ref|YP_003725850.1| 382 DFKKLANLTEGASGADLSAIAMEAGM 407
                                       79******************988776 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   1.8       4.1     2e+03      63      91 ..      70     101 ..       7     208 .. 0.68
   2 ?    9.3   0.0    0.0032       1.6       8      37 ..     219     248 ..     215     321 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 4.1
                                       EE-SS--S-TTSBHHHH...HHHTCHHHHHHH CS
                                       xxxxxxxxxxxxxxxxx...xxxxxxxxxxxx RF
                          ABC_tran  63 vlpqepqlfpeltvren...esdeeiekalsk 91 
                                         +q +q+ +e++  en   ++++e+ k+ ++
  gi|298674100|ref|YP_003725850.1|  70 LNEQYNQIESEKRYVENqklKYEREVRKLQAE 101
                                       33344555555554444455333333333333 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0032
                                       EETTSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkp 37 
                                       +++ + + + G+ G+GK+ L+k++a+ ++ 
  gi|298674100|ref|YP_003725850.1| 219 ISAPKGILLAGPPGTGKTLLAKAVAHRTDA 248
                                       5566678899**************998764 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   2.6     0.011       5.4      59     114 ..      13      72 ..       4     106 .. 0.86
   2 ?   -0.0   0.0       1.3   6.2e+02       3      20 ..     226     243 ..     225     275 .. 0.82
   3 ?    0.5   0.0      0.87   4.2e+02     257     268 ..     281     292 ..     276     341 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.011
                            AAA_21  59 efeieeflsqgvryryglrlersqv....eeklssvetllesgllldkrsleeedvfnpe 114
                                       ++ei+e ++++++y+y+++ +r++     +e l ++e + +++ll++ + le ++   +e
  gi|298674100|ref|YP_003725850.1|  13 KYEITEENMNENNYKYNINKDRFDEnensYEYLADNEGDFSKYLLDRMKQLEHRNSRLNE 72 
                                       589999**************************************9998877766665555 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.3
                            AAA_21   3 vliGpNgsGKSnLLdald 20 
                                       +l Gp g+GK+ L +a  
  gi|298674100|ref|YP_003725850.1| 226 LLAGPPGTGKTLLAKAVA 243
                                       688999*******99984 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.87
                            AAA_21 257 kgsllliDEpEn 268
                                        +s+++iDE+++
  gi|298674100|ref|YP_003725850.1| 281 APSIVFIDELDA 292
                                       348888888874 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   7.7    0.0062         3      15     166 ..      18     167 ..      10     187 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0062
                        V_ATPase_I  15 nedvnafqrkfvkevrrcdemerklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnen 91 
                                       +e++n+ + k+  +  r+de e+++++l ++  +++k    ++++ e+++++ +++ +++e+e + +e++  + +++
  gi|298674100|ref|YP_003725850.1|  18 EENMNENNYKYNINKDRFDENENSYEYLADNEGDFSKYLLDRMKQLEHRNSRLNEQYNQIESEKRYVENQKLKYERE 94 
                                       5667778888888999******************9*********99******************************* PP

                        V_ATPase_I  92 leklkkelnelvelkavlekakefleee.eeeeeeeeseeeeeekeeeeeeeseeeeeeelleeeeelsfvaGvik 166
                                        +kl++e  +l+    ++ ++ ++l++   + ++++  + + + ++  e+ee+e  ++ +l+++   +  v+ v++
  gi|298674100|ref|YP_003725850.1|  95 VRKLQAEIDRLKSSPLIIGTVMDVLDNGkLMVRSSTGPQFMVSMSKYLEDEEIEPGTTVALNQQ---TFAVVDVVQ 167
                                       ************9999999999999877333333333333333355555555555544433332...233445554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1486  (0.0828825); expected 358.6 (0.02)
Passed bias filter:                      678  (0.0378158); expected 358.6 (0.02)
Passed Vit filter:                       146  (0.00814323); expected 17.9 (0.001)
Passed Fwd filter:                        40  (0.00223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              37  [number of targets reported over threshold]
# CPU time: 0.77u 0.31s 00:00:01.08 Elapsed: 00:00:00.50
# Mc/sec: 2701.64
//
Query:       gi|298674101|ref|YP_003725851.1|  [L=105]
Description: hypothetical protein Metev_0124 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-32  110.8   1.5      4e-32  110.3   1.5    1.2  1  DUF2551   Protein of unknown function (DUF2551)


Domain annotation for each model (and alignments):
>> DUF2551  Protein of unknown function (DUF2551)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.3   1.5   2.2e-36     4e-32       1      83 []      12      94 ..      12      94 .. 0.98

  Alignments for each domain:
  == domain 1  score: 110.3 bits;  conditional E-value: 2.2e-36
                           DUF2551  1 LkkylerDksGiRrevLklfleakkltveeiyeklkekfdvsykgvasmvGliasrlGIlkvkkeskgeknvYsLkeey 79
                                      L+k++e+D++G+R+++L++fl+++klt++++y+ +++k+++s+++vasmvG+i+s+lGI++++k+++++++vY+Lk++y
  gi|298674101|ref|YP_003725851.1| 12 LQKFIEKDEDGVRSNILCVFLNKNKLTIDDLYSIITTKYNISRNSVASMVGYIQSKLGIIQSYKKDYKSPTVYYLKDKY 90
                                      89***************************************************************************** PP

                           DUF2551 80 adlv 83
                                      a ++
  gi|298674101|ref|YP_003725851.1| 91 AFII 94
                                      9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 667.70
//
Query:       gi|298674102|ref|YP_003725852.1|  [L=83]
Description: hypothetical protein Metev_0125 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.9e-07   30.0  19.9    8.9e-06   26.0  10.5    2.1  2  DnaJ_CXXCXGXG  DnaJ central domain
     0.0063   16.7  12.4       0.77   10.0   0.7    4.0  4  DUF5351        Family of unknown function (DUF5351)
  ------ inclusion threshold ------
      0.017   15.1  13.6      0.037   14.0   2.3    2.7  3  Anti-TRAP      Tryptophan RNA-binding attenuator protein inhi


Domain annotation for each model (and alignments):
>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0  10.5   1.5e-09   8.9e-06       1      67 []      15      74 ..       7      74 .. 0.81
   2 !   15.2   1.9   3.6e-06     0.021       1      25 [.      50      75 ..      50      82 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.5e-09
                     DnaJ_CXXCXGXG  1 CkkCkGsgakkgk.kktCktCkGsGvvreeqktlgpfvqqsqstCpeCeGtGk.vikekdkCkkCkGkg 67
                                      C  C+G+g ++++ ++ C+ C+G G+v +          q  ++C  C+G+    i+++++C++C+G+g
  gi|298674102|ref|YP_003725852.1| 15 CGWCRGTGNDRSThERPCRICEGLGSVLV---------AQPANSCAWCNGNSVdRIDTDKPCRSCDGTG 74
                                      899*****877554778********5433.........345679******98647877789******86 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 3.6e-06
                     DnaJ_CXXCXGXG  1 CkkCkGsgakk.gkkktCktCkGsGv 25
                                      C  C+G+  ++ ++ k C++C+G+G 
  gi|298674102|ref|YP_003725852.1| 50 CAWCNGNSVDRiDTDKPCRSCDGTGW 75
                                      999****9987566888*******93 PP

>> DUF5351  Family of unknown function (DUF5351)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.7   0.00013      0.77      18      28 ..      13      23 ..      12      24 .. 0.91
   2 ?    3.6   0.0     0.013        79      20      27 ..      32      39 ..      31      43 .. 0.74
   3 ?    3.5   0.1     0.013        80       1       7 [.      50      56 ..      48      59 .. 0.68
   4 !    5.7   0.3    0.0027        16      20      27 ..      67      74 ..      65      76 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00013
                           DUF5351 18 ETCesCeGtgk 28
                                      ETC  C Gtg+
  gi|298674102|ref|YP_003725852.1| 13 ETCGWCRGTGN 23
                                      9********97 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.013
                           DUF5351 20 CesCeGtg 27
                                      C  CeG g
  gi|298674102|ref|YP_003725852.1| 32 CRICEGLG 39
                                      77777766 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.013
                           DUF5351  1 CpYCeGk 7 
                                      C +C+G+
  gi|298674102|ref|YP_003725852.1| 50 CAWCNGN 56
                                      6666665 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.0027
                           DUF5351 20 CesCeGtg 27
                                      C sC Gtg
  gi|298674102|ref|YP_003725852.1| 67 CRSCDGTG 74
                                      999***99 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   2.3   6.1e-06     0.037      11      46 ..      13      45 ..       4      48 .. 0.88
   2 ?    9.2   1.6   0.00019       1.1      10      41 ..      29      58 ..      26      64 .. 0.85
   3 ?    7.4   0.2   0.00069       4.1      10      24 ..      64      78 ..      58      82 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.1e-06
                                      EE-TTTTTTSEETTE......E-TTTTTSSEEE-HH CS
                         Anti-TRAP 11 tkCdaCngsGkiepeeprasleCPkCsGkglipTaq 46
                                      ++C  C g+G+  ++      +C  C+G g ++ aq
  gi|298674102|ref|YP_003725852.1| 13 ETCGWCRGTGNDRSTH---ERPCRICEGLGSVLVAQ 45
                                      79*************4...459********999887 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00019
                                      EEE-TTTTTTSEETTE......E-TTTTTSSE CS
                         Anti-TRAP 10 EtkCdaCngsGkiepeeprasleCPkCsGkgl 41
                                      E +C  C+g G +  ++p     C  C+G+ +
  gi|298674102|ref|YP_003725852.1| 29 ERPCRICEGLGSVLVAQPA--NSCAWCNGNSV 58
                                      89***********999555..56999999865 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.00069
                                      EEE-TTTTTTSEETT CS
                         Anti-TRAP 10 EtkCdaCngsGkiep 24
                                      +++C  C+g+G + +
  gi|298674102|ref|YP_003725852.1| 64 DKPCRSCDGTGWAHS 78
                                      578888888887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      143  (0.0079759); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 629.95
//
Query:       gi|298674103|ref|YP_003725853.1|  [L=33]
Description: hypothetical protein Metev_0126 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (33 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       865  (0.0482459); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 219.89
//
Query:       gi|298674104|ref|YP_003725854.1|  [L=204]
Description: hypothetical protein Metev_0127 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-64  215.9   0.0    3.2e-64  215.7   0.0    1.0  1  DUF99           Protein of unknown function DUF99
     0.0057   16.4   0.0     0.0082   15.8   0.0    1.3  1  Endonuclease_5  Endonuclease V


Domain annotation for each model (and alignments):
>> DUF99  Protein of unknown function DUF99
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.7   0.0   3.5e-68   3.2e-64       2     182 ..      16     195 ..      15     196 .. 0.97

  Alignments for each domain:
  == domain 1  score: 215.7 bits;  conditional E-value: 3.5e-68
                                       GSEEEEEEEEE.....-SS-EEEEEEEEETT.EEEEEEEEEE-TT-S-HHHHHHHHHCC-.TTTTEEEEEESSSEET CS
                             DUF99   2 eirvlGiddsfferkkkdgksvlvGvvmradrvvdgvafgrvtvdGtDateaiielvkrl.eredirvvlldGitia 77 
                                       eirvlGidds +     ++++++vG+v+r+++++dgv+ +++t+dG+D t++ii++vk + ++ ++rv++ldGit++
  gi|298674104|ref|YP_003725854.1|  16 EIRVLGIDDSALL----SDRIMIVGAVFRGGDWLDGVLRSEITRDGMDGTDTIIQMVKPSkHFVQLRVIMLDGITFG 88 
                                       79*********66....79********************************************************** PP

                                       TTEE--HHHHHHHH---EEEEESS---HHHHHHCCT.TSTTHHHHHHHHHHC.---EEETT........EEEEEESS CS
                             DUF99  78 gFNvvDlerlheetglPviavtreepdlgklekaLrkhfpdeeeRlelieklgerieevek....tgeelyvravGi 150
                                       gFN +D+ +l eetglPv+a++r+ pd++k+e+aL+ ++p++e+R+++i+k+ ++i+ev++    +g++ly+++ G+
  gi|298674104|ref|YP_003725854.1|  89 GFNPIDIVKLNEETGLPVVAIMRKYPDFEKIESALK-YLPEPEKRMDIIKKA-GKIAEVTTyadqRGSPLYIQWSGL 163
                                       ***********************************9.***************.888888888999999********* PP

                                       -HHHHHHHHHHC-SSSSS-HHHHHHHHHHHHH CS
                             DUF99 151 eleeaaklvrkltlegriPEPlRvAhliAsal 182
                                       e+e+a+++v+++ ++++iPEPlRvAhliA+++
  gi|298674104|ref|YP_003725854.1| 164 EEEDARRIVQQTSTRSNIPEPLRVAHLIATGI 195
                                       *****************************997 PP

>> Endonuclease_5  Endonuclease V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   9.1e-07    0.0082     135     197 .]     128     190 ..     102     190 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 9.1e-07
                                       STTEEEEEEET.TEEEEEEEESSTTS--EEEEEECSS-HHHHHHHHHHCS-T-SS-HHHHHHHH CS
                    Endonuclease_5 135 ekgsvvplvse.gevigaalrtkknvkpiyvSvGhrisletalelvlallkkyrlPepirqAdl 197
                                       e ++ ++++++ g++  +     ++  p+y+     ++ e+a ++v++++++ ++Pep+r A+l
  gi|298674104|ref|YP_003725854.1| 128 EPEKRMDIIKKaGKIAEVTTYADQRGSPLYIQW-SGLEEEDARRIVQQTSTRSNIPEPLRVAHL 190
                                       445556666442777777777778889***976.56899***********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1387.27
//
Query:       gi|298674105|ref|YP_003725855.1|  [L=449]
Description: phosphoglucomutase/phosphomannomutase alpha/beta/alpha domain I [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-42  142.9   1.0    6.9e-42  142.4   0.2    1.7  2  PGM_PMM_I        Phosphoglucomutase/phosphomannomutase, alpha
      1e-27   96.7   0.0    2.4e-27   95.6   0.0    1.6  1  PGM_PMM_II       Phosphoglucomutase/phosphomannomutase, alpha
    6.4e-26   90.8   0.0    1.2e-25   89.9   0.0    1.5  1  PGM_PMM_III      Phosphoglucomutase/phosphomannomutase, alpha
    4.3e-14   52.5   0.0    1.4e-13   50.8   0.0    1.9  1  PGM_PMM_IV       Phosphoglucomutase/phosphomannomutase, C-ter
  ------ inclusion threshold ------
      0.016   14.5   0.0      0.029   13.7   0.0    1.4  1  GidB             rRNA small subunit methyltransferase G
      0.066   11.8   0.2       0.25    9.8   0.0    1.9  2  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m


Domain annotation for each model (and alignments):
>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.4   0.2   2.3e-45   6.9e-42       3     134 ..       3     130 ..       1     134 [. 0.96
   2 ?   -3.9   0.0       3.5     1e+04     102     117 ..     164     179 ..     151     182 .. 0.59

  Alignments for each domain:
  == domain 1  score: 142.4 bits;  conditional E-value: 2.3e-45
                                       GBBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB-H CS
                         PGM_PMM_I   3 kfgtsGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllpt 79 
                                       +fgt+G+Rg+++ +e+tpel+  +++++++yl +   +++v++GrDtRvs+++++ a+++g +++G++vi+++++pt
  gi|298674105|ref|YP_003725855.1|   3 LFGTNGVRGIAN-EEITPELAVDIAKSLGTYLGN---NATVAIGRDTRVSGNMIKYAAISGSLSSGLSVIDVDMVPT 75 
                                       7***********.77******************9...7*************************************** PP

                                       HHHHHHHHHCCECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHHHHCCT CS
                         PGM_PMM_I  80 PavsfairklkadagimitaSHnppeyngiKvylsnGgpispeveekIeaiieke 134
                                       P ++++i++ + dagi+itaSHnp eyngiK+++ +G ++s+e e+++e+i+ ++
  gi|298674105|ref|YP_003725855.1|  76 PSIQYYIKNTRTDAGIIITASHNPREYNGIKLIDGDGTEFSREGEKEVENIYYSK 130
                                       **************************************************98765 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 3.5
                                       S-TTCCCEEEEETTTC CS
                         PGM_PMM_I 102 nppeyngiKvylsnGg 117
                                       +  +++++Kv+   G+
  gi|298674105|ref|YP_003725855.1| 164 EKIQKQNFKVVVDTGC 179
                                       4445666666666665 PP

>> PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.6   0.0   7.9e-31   2.4e-27       2     103 .]     152     252 ..     151     252 .. 0.99

  Alignments for each domain:
  == domain 1  score: 95.6 bits;  conditional E-value: 7.9e-31
                                       HHHHHGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHHG CS
                        PGM_PMM_II   2 aYiealkekvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealkllielv 78 
                                        Yi+++ + vd e+i+k+++kvv+d++ Gag+ +l+ ll++lg++v+++na+ d++fp ++p+p++ ++l++l+e++
  gi|298674105|ref|YP_003725855.1| 152 YYIKGIINSVDAEKIQKQNFKVVVDTGCGAGSLTLPFLLRKLGCEVITINAQIDGTFPWRNPEPTP-DVLEELSEII 227
                                       6*****************************************************************.********** PP

                                       GGGG-SEEEEE-TTS-BEEEEETTE CS
                        PGM_PMM_II  79 kkegadlglafDgDaDRlgvvderG 103
                                       + +gad+g+a DgDaDR ++ de+G
  gi|298674105|ref|YP_003725855.1| 228 RLSGADMGVAQDGDADRAVFTDENG 252
                                       ***********************98 PP

>> PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.9   0.0     4e-29   1.2e-25       4     113 ..     259     364 ..     256     365 .. 0.93

  Alignments for each domain:
  == domain 1  score: 89.9 bits;  conditional E-value: 4e-29
                                       HHHHHHHHHHHCHCSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETTCEEEETTTB CS
                       PGM_PMM_III   4 qllallakylleeklkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeSghiifldea 80 
                                        ll l+ak++l++  k+g  +v++v++s+ + +vak++g++l+ t+vG+ +v+++m e +av+GgE +g++if++++
  gi|298674105|ref|YP_003725855.1| 259 VLLSLVAKNILNQ--KKGP-IVTPVSSSQRMADVAKEAGVELIWTAVGSINVARKMMEMNAVFGGEGNGGLIFPEHQ 332
                                       5789999999995..6676.********************************************************* PP

                                       SS--HHHHHHHHHHHHHHHTS-HHHHHHHHHHH CS
                       PGM_PMM_III  81 ttkDGilaallvleilaetgkslselleellkk 113
                                       +++DG+++++++lei+a  g++ls+l+e++++ 
  gi|298674105|ref|YP_003725855.1| 333 YCRDGAMSCAKLLEIMAS-GTPLSKLAEDVPEY 364
                                       ****************97.89******887664 PP

>> PGM_PMM_IV  Phosphoglucomutase/phosphomannomutase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.0   4.8e-17   1.4e-13      12      67 ..     387     439 ..     368     443 .. 0.78

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 4.8e-17
                                       ..EECCCCCTTH......HCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEESSHHHHHHHHH CS
                        PGM_PMM_IV  12 vvaalaallkva......sikeglkilledGrrlavRpSGTepllrvyvEaksdeelarlae 67 
                                       v +               ++++g+k+ +edG++l vRpSGTep +rvy+E+k+ +++++l e
  gi|298674105|ref|YP_003725855.1| 387 VHE--------DnvgikiDTIDGVKVWFEDGWVL-VRPSGTEPIIRVYAESKTMSRAEKLME 439
                                       333........03333347***************.*****************9999998865 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   9.8e-06     0.029      14      65 ..     136     187 ..     128     203 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.8e-06
                                       HHHHHS---S--SHHHHHHHCHHHHHHHGGCS-CCC-.EEEETSTTTTTHHH CS
                              GidB  14 kwNkkinLtsikepeellerhlldslsvlellkekrdkviDvGsGaGlPGip 65 
                                        w ++ nL   +++++ + + +++s+ + ++ k++ + v+D G GaG   +p
  gi|298674105|ref|YP_003725855.1| 136 GWENTGNLQTDHNVNDYYIKGIINSVDAEKIQKQNFKVVVDTGCGAGSLTLP 187
                                       588999***********************999999966*********65555 PP

>> Methyltransf_29  Putative S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   8.4e-05      0.25      95     134 ..     146     187 ..     121     201 .. 0.76
   2 ?   -1.0   0.1      0.17     5e+02     364     378 ..     306     320 ..     288     323 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 8.4e-05
                   Methyltransf_29  95 kkga.dkYidklaeliplia.aggkvrtvlDvGCgvasfgay 134
                                        +++ d Yi+ + +++++++ ++++ ++v+D+GCg  s++  
  gi|298674105|ref|YP_003725855.1| 146 DHNVnDYYIKGIINSVDAEKiQKQNFKVVVDTGCGAGSLTLP 187
                                       44541568999999999885156789**********998754 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.17
                   Methyltransf_29 364 skvRnvlDmnavlGg 378
                                       +  R +++mnav+Gg
  gi|298674105|ref|YP_003725855.1| 306 NVARKMMEMNAVFGG 320
                                       45699*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 3053.90
//
Query:       gi|298674106|ref|YP_003725856.1|  [L=129]
Description: N-acetyltransferase GCN5 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-11   42.9   0.0    6.1e-11   42.6   0.0    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    4.2e-10   39.9   0.0    5.2e-10   39.6   0.0    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    4.5e-10   39.6   0.1      6e-10   39.2   0.1    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    4.2e-06   26.9   0.0    0.00036   20.6   0.0    2.1  2  Acetyltransf_9   Acetyltransferase (GNAT) domain
    0.00016   21.6   0.0    0.00025   20.9   0.0    1.4  1  FR47             FR47-like protein
     0.0011   19.0   0.0     0.0024   17.9   0.0    1.5  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
  ------ inclusion threshold ------
      0.029   14.3   0.0       0.04   13.8   0.0    1.3  1  NT5C             5' nucleotidase, deoxy (Pyrimidine), cytosol
      0.065   12.7   0.0      0.077   12.4   0.0    1.3  1  Acetyltransf_15  Putative acetyl-transferase
       0.11   12.1   0.0       0.13   11.8   0.0    1.0  1  Choline_kinase   Choline/ethanolamine kinase
       0.11   12.5   0.1       0.36   10.8   0.0    1.8  2  Acetyltransf_13  ESCO1/2 acetyl-transferase


Domain annotation for each model (and alignments):
>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.0   3.4e-14   6.1e-11       5      74 ..      37     110 ..      23     112 .. 0.70

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 3.4e-14
                                       EEEEEET..TEEEEEEEEEEES..TCTEEEEE-GGGTTSSHHHHHHHH...TT..SEEEEE.EEEETHHHHHHHHHH CS
                    Acetyltransf_7   5 vfVaedd..gkivGfialslld..aeitrlaVdpeyrgkGiGraLlea...ae..kgiile.qlelnaekaikfYek 71 
                                       ++Vae     ki+G +a ++++   ei+ +aV+p+yr kGiG++L+++   ++  +      + ++++  a +f+ k
  gi|298674106|ref|YP_003725856.1|  37 FIVAETIdrTKIIGIAA-EVNQnhPEIHTVAVHPNYRAKGIGSKLVRYilnRQpeQ----ReRIYVHT-VAPEFFNK 107
                                       55665447789999554.55556888888******************844311321....11223333.5788**** PP

                                       TTE CS
                    Acetyltransf_7  72 lGF 74 
                                       lGF
  gi|298674106|ref|YP_003725856.1| 108 LGF 110
                                       *** PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.0   2.9e-13   5.2e-10      35     117 .]      37     110 ..      16     110 .. 0.77

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 2.9e-13
                                       EEEEEETTE..EEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHH CS
                    Acetyltransf_1  35 llvaeedge..liGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaai 109
                                       ++vae +++  +iG +    +++      +i+ +aV+p+yr kG+Gs+L+++++ r  e+  ++i++++ +      
  gi|298674106|ref|YP_003725856.1|  37 FIVAETIDRtkIIGIAAEVNQNH-----PEIHTVAVHPNYRAKGIGSKLVRYILNRQPEQ-RERIYVHTVA-----P 102
                                       45566664445999995555555.....9*************************965555.3678995544.....5 PP

                                       HHHHHTTE CS
                    Acetyltransf_1 110 rlYeklGF 117
                                       +++ klGF
  gi|298674106|ref|YP_003725856.1| 103 EFFNKLGF 110
                                       79999998 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.1   3.3e-13     6e-10      38     119 ..      44     123 ..      32     126 .. 0.82

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 3.3e-13
                   Acetyltransf_10  38 eggkivGvi.el.rdgshisllfVdpeyrgqGigkaLleaveeeaekdgikleltvnaspyavpfYeklGFkavgee 112
                                       + +ki+G++ e+ +++ +i+ ++V+p+yr +Gig++L+ +++++  ++  + ++ v  ++ a +f+ klGF + +e+
  gi|298674106|ref|YP_003725856.1|  44 DRTKIIGIAaEVnQNHPEIHTVAVHPNYRAKGIGSKLVRYILNRQPEQ-RE-RIYV--HTVAPEFFNKLGFLRADEV 116
                                       45799**9978877777***************************6444.34.5555..5799**********99999 PP

                   Acetyltransf_10 113 qeenGir 119
                                        ++  i+
  gi|298674106|ref|YP_003725856.1| 117 YYRGYIT 123
                                       8887665 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.018        31       1      47 [.       6      51 ..       6      58 .. 0.84
   2 !   20.6   0.0     2e-07   0.00036      76     125 ..      62     110 ..      57     113 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.018
                                      .EEEE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTTSEEEEE CS
                    Acetyltransf_9  1 eirelteedldevlellkyaFqdeespleeireyfrklleesrvlga 47
                                      +ire+t  dl  v  ll+++F + ++ +   ++ + +++++ +++g+
  gi|298674106|ref|YP_003725856.1|  6 RIREATNVDLLSVRLLLSTCFLEMDDVA-IDDFIVAETIDRTKIIGI 51
                                      69********************999987.235777888888888776 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 2e-07
                                       EEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--SSHHHHHTTT- CS
                    Acetyltransf_9  76 vtgVavapehrgrgvlskLlaraleemreegqplsllfPssipiYrrfGy 125
                                       +  Vav+p++r +g+ skL+++ l++  e+++++ + + + ++++ ++G+
  gi|298674106|ref|YP_003725856.1|  62 IHTVAVHPNYRAKGIGSKLVRYILNRQPEQRERIYVHTVA-PEFFNKLGF 110
                                       668**************************99999998877.999999998 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.4e-07   0.00025      18      84 ..      56     117 ..      43     119 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.4e-07
                                       E-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEEEEEE CS
                              FR47  18 rkdggelgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGfekieete 84 
                                       +++  e+  + v+p+ r +G gs+lv+ + ++  e+ + + +++v     + ++++klGf  ++e +
  gi|298674106|ref|YP_003725856.1|  56 NQNHPEIHTVAVHPNYRAKGIGSKLVRYILNRQPEQRERIYVHTV-----APEFFNKLGFLRADEVY 117
                                       4556799****************************9999999987.....578*******8886655 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.4e-06    0.0024      23      61 ..      58      96 ..      41     100 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.4e-06
                   Acetyltransf_CG 23 gvldfthTeVpeelrGkGiAkkLvkaalddareeglkvv 61
                                      ++ +++ + V++ +r kGi++kLv+++l+   e++ ++ 
  gi|298674106|ref|YP_003725856.1| 58 NHPEIHTVAVHPNYRAKGIGSKLVRYILNRQPEQRERIY 96
                                      456777889********************9998888875 PP

>> NT5C  5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.2e-05      0.04      10      67 ..      50     109 ..      41     119 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.2e-05
                              NT5C  10 gvladlygkmlevankrfeatllpeevsswdleef..vkPeqreslyrfltepglFadle 67 
                                       g+ a++ +++ e+     + + +   + s+    +   +Peqre++y +   p++F+ l 
  gi|298674106|ref|YP_003725856.1|  50 GIAAEVNQNHPEIHTVAVHPNYRAKGIGSKLVRYIlnRQPEQRERIYVHTVAPEFFNKLG 109
                                       667778888888888888888888888876666666678*****************9985 PP

>> Acetyltransf_15  Putative acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.3e-05     0.077      68      99 ..      55      86 ..      20     113 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.3e-05
                   Acetyltransf_15 68 ieknvleiYtlyvsekyrgkGlakklLeeslk 99
                                      +++n  ei t+ v+++yr kG+  kl+  +l+
  gi|298674106|ref|YP_003725856.1| 55 VNQNHPEIHTVAVHPNYRAKGIGSKLVRYILN 86
                                      5667789******************9988866 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   7.2e-05      0.13      20     105 ..       6      88 ..       3     108 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.2e-05
                                       HHHHHHHHHHHHHTTSSS-EEEEETTEEEEE--TCEE--TTGGGCHHHHHHHHHHHHHHTTCHH.TTSSSS-HHHHH CS
                    Choline_kinase  20 retElvvfallserglgpklygifenGrieefiesrtlstedlrepeiskkiAkklaelHsleleseskespslwkt 96 
                                       r +E+ ++ lls r l    +   ++  i  fi ++t++ +++    i +++ ++  e+H++++ +++ + + + ++
  gi|298674106|ref|YP_003725856.1|   6 RIREATNVDLLSVRLLLSTCFLEMDDVAIDDFIVAETIDRTKIIG--IAAEVNQNHPEIHTVAV-HPNYRAKGIGSK 79 
                                       67999999******9999999999*******************99..*****************.899999999999 PP

                                       HHHHHHCCS CS
                    Choline_kinase  97 mqkwllnke 105
                                       + +++ln +
  gi|298674106|ref|YP_003725856.1|  80 LVRYILNRQ 88 
                                       999944433 PP

>> Acetyltransf_13  ESCO1/2 acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.7     3e+03      27      43 ..      31      47 ..      23      48 .. 0.72
   2 ?   10.8   0.0    0.0002      0.36       7      32 ..      62      87 ..      61     101 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.7
                   Acetyltransf_13 27 daarenfiyglelekee 43
                                      d+a+++fi+  ++++++
  gi|298674106|ref|YP_003725856.1| 31 DVAIDDFIVAETIDRTK 47
                                      77888888877777665 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0002
                   Acetyltransf_13  7 isriWvssshRrkgiAtkLldaaren 32
                                      i+ + v++++R kgi +kL+  + ++
  gi|298674106|ref|YP_003725856.1| 62 IHTVAVHPNYRAKGIGSKLVRYILNR 87
                                      677889**************988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 785.26
//
Query:       gi|298674107|ref|YP_003725857.1|  [L=251]
Description: hypothetical protein Metev_0130 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-75  253.0   0.0    2.5e-75  252.8   0.0    1.0  1  DUF166    Domain of unknown function
     0.0033   17.5   1.2     0.0064   16.6   1.2    1.4  1  zf-B_box  B-box zinc finger
  ------ inclusion threshold ------
      0.041   14.0   0.0      0.076   13.2   0.0    1.4  1  FYVE      FYVE zinc finger


Domain annotation for each model (and alignments):
>> DUF166  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  252.8   0.0   4.2e-79   2.5e-75       2     218 ..       5     246 ..       4     248 .. 0.97

  Alignments for each domain:
  == domain 1  score: 252.8 bits;  conditional E-value: 4.2e-79
                            DUF166   2 vltsgeyGervvenilnepdfersl..................ivavvevpeeldefiedpeelLpe.lkeaDivia 59 
                                       vl+ g++Ge+v++n+ n+++f++s+                  iv ++e++e+l+e+i+dp+e++pe l+e D+++a
  gi|298674107|ref|YP_003725857.1|   5 VLYTGAFGEKVIGNLINNTNFCTSCgellcdhcrsvrkgishlIVQTYEFQEDLPELIDDPAEYIPEnLSETDLILA 81 
                                       89*************************************************************************** PP

                            DUF166  60 ytlhpDlllelaekakekkvkalivpaeapk...aglrkelkekleelgievavpkpfCsleeegkpkideFlee.f 132
                                       ++lhpDll +l+e+a+++k  a+i p+e+p+   +gl +++k++le++g+e+++pkpfCsle++gk+ id+F++  f
  gi|298674107|ref|YP_003725857.1|  82 IDLHPDLLTVLPEIARRTKSSAVISPVERPQlapPGLVEQVKHELENAGVEAEFPKPFCSLEKTGKKIIDQFVDLgF 158
                                       ***************************************************************************** PP

                            DUF166 133 GkPelevevkdgki..kkVeVlrsapCGstwyvakklkGkeveeaeekageahqsYpClAsmerdfelketklhkAg 207
                                       G+P l++e++ ++   + V+Vlr+apCGstw+vak+l+G++v++++e  ++ah+sYpC+Asme+d el++t+lh+Ag
  gi|298674107|ref|YP_003725857.1| 159 GRPLLKIELNTDNDtfRFVRVLRDAPCGSTWFVAKQLTGTDVDNYKETVSKAHHSYPCTASMEKDVELGDTILHQAG 235
                                       *********9554446************************************************************* PP

                            DUF166 208 yihkeavekAl 218
                                        i++++ve+++
  gi|298674107|ref|YP_003725857.1| 236 FIIRKSVEEGM 246
                                       *******9976 PP

>> zf-B_box  B-box zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   1.2   1.1e-06    0.0064      15      30 ..      23      39 ..      21      49 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.1e-06
                          zf-B_box 15 tlfCedCqqplCeeC.s 30
                                      t fC++C+++lC+ C s
  gi|298674107|ref|YP_003725857.1| 23 TNFCTSCGELLCDHCrS 39
                                      68*************53 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.3e-05     0.076      21      44 ..      19      42 ..      11      83 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.3e-05
                                      SSS--EE-TTT--EE-STTS-EEE CS
                              FYVE 21 llrrrhhCrlCGkvvCekCssklv 44
                                      l++    C  CG+++C++C s + 
  gi|298674107|ref|YP_003725857.1| 19 LINNTNFCTSCGELLCDHCRSVRK 42
                                      5677789************97654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1678.78
//
Query:       gi|298674108|ref|YP_003725858.1|  [L=125]
Description: hypothetical protein Metev_0131 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.014   15.7   0.0      0.016   15.5   0.0    1.1  1  DUF1400   Alpha/beta hydrolase of unknown function (DUF1400)


Domain annotation for each model (and alignments):
>> DUF1400  Alpha/beta hydrolase of unknown function (DUF1400)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   9.1e-07     0.016      27      87 ..       5      66 ..       3      82 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 9.1e-07
                           DUF1400 27 tgevsseLatylk.llskeqreelreaLqaeiklspvllsqllnspigeklLerlgeviqte 87
                                      t+++++ L+ +++  +++ q+ elr++L  ++  + ++++++l+s ige ++e+  ++ + +
  gi|298674108|ref|YP_003725858.1|  5 TNNIDKGLEIIAAlDVNQLQPIELRDILYYTVAKNYEVVDEILSSAIGEGIVEKRDDIYHLN 66
                                      667777777776644899999*******************************9988887755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 790.58
//
Query:       gi|298674109|ref|YP_003725859.1|  [L=139]
Description: nucleoside 2-deoxyribosyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.9e-27   93.7   0.0      1e-26   93.5   0.0    1.1  1  Nuc_deoxyrib_tr  Nucleoside 2-deoxyribosyltransferase
    1.8e-19   70.0   0.0    2.7e-19   69.5   0.0    1.2  1  Nuc_deoxyri_tr2  Nucleoside 2-deoxyribosyltransferase like
  ------ inclusion threshold ------
      0.039   13.5   0.0      0.058   13.0   0.0    1.3  1  LDcluster4       SLOG cluster4 family
      0.077   13.5   0.0       0.12   12.9   0.0    1.2  1  DUF4406          Domain of unknown function (DUF4406)


Domain annotation for each model (and alignments):
>> Nuc_deoxyrib_tr  Nucleoside 2-deoxyribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.5   0.0   2.3e-30     1e-26       1     106 [.       7     109 ..       7     128 .. 0.93

  Alignments for each domain:
  == domain 1  score: 93.5 bits;  conditional E-value: 2.3e-30
                                       EEEESGGGCSCCCHHHHHHHHHHHHTTTTEEE-CCTT-TT.....--SSHHHHHHHHHHHHHC-SEEEEE--SSSSS CS
                   Nuc_deoxyrib_tr   1 iYLAgplvFrpdakalaarlkallaengldglaPldneaelel.paeetaraiyeadialirqaDavianldpfrgp 76 
                                       +Y+Agpl F++ + + +++l++++a++g+ ++ P++++++  + + e +++ i++++++ i+ +D+++a+ld+++  
  gi|298674109|ref|YP_003725859.1|   7 VYIAGPL-FSEGELDFNKKLRDAVAKKGFPVYLPQEHTEDTVDmRHEHKQNYIFQNNVEIIDDSDIILAVLDGAD-- 80 
                                       8******.***************************999887778999999***********************99.. PP

                                       S--HHHHHHHHHHHHCT-EEEEE-S-GCGH CS
                   Nuc_deoxyrib_tr  77 eaDsGtafEvGyavalgkpvlayttdarel 106
                                         DsGta+E+Gya+a gk +++++td+r++
  gi|298674109|ref|YP_003725859.1|  81 -VDSGTAWEIGYAYAKGKMIFGLRTDFRTM 109
                                       .***************************96 PP

>> Nuc_deoxyri_tr2  Nucleoside 2-deoxyribosyltransferase like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.5   0.0     6e-23   2.7e-19       2     108 .]       5     106 ..       4     106 .. 0.95

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 6e-23
                                       EEEEEEE---SSSST-HHHHHHHHHHTSSS-EEEEE----SS-----HHHHH.....HHHHHHHHHHHH-SEEEEEE CS
                   Nuc_deoxyri_tr2   2 ksvFLaGsteseaetdWredlteaLsaipklgvtvfnPqredwdseleedrskkrfreqvewelealekAdvvvfvf 78 
                                       k+v++aG+++se+e d++++l +a+++   +g+ v+ Pq+++ d+   + r++++++ +++ + e ++++d++++v+
  gi|298674109|ref|YP_003725859.1|   5 KKVYIAGPLFSEGELDFNKKLRDAVAK---KGFPVYLPQEHTEDT--VDMRHEHKQNYIFQNNVEIIDDSDIILAVL 76 
                                       79***********************66...8***********776..599999************************ PP

                                       -TT---HHHHHHHHHHTTSS-EEEEE-TT- CS
                   Nuc_deoxyri_tr2  79 dgedsatrslvElglaaakgkkvvlvpkgf 108
                                       dg+d++  + +E+g+a+akgk++++++++f
  gi|298674109|ref|YP_003725859.1|  77 DGADVDSGTAWEIGYAYAKGKMIFGLRTDF 106
                                       ****999999****************9997 PP

>> LDcluster4  SLOG cluster4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.3e-05     0.058      90     130 ..      62     107 ..      40     129 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.3e-05
                        LDcluster4  90 nlilvlssdvviai....ggrsGTlsEialaleegkpvivlkgt.d 130
                                       n+ ++  sd+++a+    +  sGT+ Ei +a+ +gk +  l+++  
  gi|298674109|ref|YP_003725859.1|  62 NVEIIDDSDIILAVldgaDVDSGTAWEIGYAYAKGKMIFGLRTDfR 107
                                       6677888999998744445789*******************95552 PP

>> DUF4406  Domain of unknown function (DUF4406)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.6e-05      0.12       1      88 [.       7      99 ..       7     101 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.6e-05
                           DUF4406  1 vYiaGpitGlpeynkeafe.eaaeklkeaGytvlnpavl......lpaglsweaymriclalllkcdai.vmLpgweeS 71
                                      vYiaGp+       +  f+ +  + ++++G+ v+ p+++      ++++ + +   + +++ +++ d i ++L+g    
  gi|298674109|ref|YP_003725859.1|  7 VYIAGPLFSEG---ELDFNkKLRDAVAKKGFPVYLPQEHtedtvdMRHEHKQNYIFQNNVEIIDDSDIIlAVLDGADVD 82
                                      7*****95422...334541345667889*******9995566444455555555688999999***98469******* PP

                           DUF4406 72 kGAtlElelakklglai 88
                                       G+  E+ +a + g+ i
  gi|298674109|ref|YP_003725859.1| 83 SGTAWEIGYAYAKGKMI 99
                                      *********99998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 1041.08
//
Query:       gi|298674110|ref|YP_003725860.1|  [L=483]
Description: FAD-dependent pyridine nucleotide-disulfide oxidoreductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-45  155.7   0.0    2.7e-45  154.9   0.0    1.4  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.5e-21   76.7   0.2    3.1e-21   75.7   0.2    1.6  1  Pyr_redox_dim   Pyridine nucleotide-disulphide oxidoreductase
    7.7e-15   55.2   0.0      2e-14   53.9   0.0    1.7  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    4.2e-10   39.4   0.0    7.4e-10   38.6   0.0    1.4  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    2.9e-07   29.9   0.1    0.00072   18.8   0.0    2.8  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
     0.0053   16.7   0.0      0.023   14.6   0.0    2.0  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
  ------ inclusion threshold ------
      0.054   13.1   0.1        0.3   10.7   0.0    2.3  3  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
      0.061   12.6   0.0       0.12   11.6   0.0    1.5  1  Thi4            Thi4 family


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.9   0.0   1.2e-48   2.7e-45       1     286 [.       4     317 ..       4     324 .. 0.88

  Alignments for each domain:
  == domain 1  score: 154.9 bits;  conditional E-value: 1.2e-48
                                       CSEEEE--SHHHHHHHHHHHH..HTS-EEEEE...TTHCHHHCSHHHHCHHHHHHHHHHHHH............... CS
                                       xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx............... RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaq..agakvtlve...legtclnggcllskallgvaedaeias............... 57 
                                       +d+++iG G  G+++   +     ++k+++++    +g cl++gc++sk l   ae  + ++               
  gi|298674110|ref|YP_003725860.1|   4 YDLIIIGTGS-GMNFVNAIIDsnPEIKIAVIDkdaPGGICLTRGCIPSKLLIYPAELIRDIEsaerfginvdiqnid 79 
                                       689******7.78888888884349******9999**************9999998888777899************ PP

                                       .............HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.T CS
                                       .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 .............evvkklnqgielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvae 121
                                                      ++ ++qg   l +++ v+++p++++++   + +  +e+i  d ++++tGs+p +++++ + +
  gi|298674110|ref|YP_003725860.1|  80 fknimdnmrdkisSDINMIRQG---LSESKNVDYYPESAEFVEPYTMKVGNETIYSDMIFICTGSKPVIPPVKSL-N 152
                                       *999998876443223333333...3334569999***9***9999998899*********************99.3 PP

                                       TBEECCSECHHHHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 122 nvgklvrtldsaealklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGv 198
                                       +v     +l+s+  l+ ++lp +i+v+GgGyi+ E+  +++ +g++vtl+ ++++++++ ++e+sa +++++     
  gi|298674110|ref|YP_003725860.1| 153 EV----GYLTSDTVLEMDNLPGSIAVIGGGYIAAEYGHFFSAMGSNVTLIGRNPQFVPEEEPEISALATNKMSG-YM 224
                                       33....368***************************************************************99.5* PP

                                       EEEESCEEEEEEETTEEEEEEETTSCE.....EEESEEEE-S-EEES-HHCS.HCCT-EEEETTEEE--TTSBESST CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 199 evklgtsvkeidgngeklevvledgee.....idadlvvvavGvrpstelle.eklglelderggivvdeflrtnvp 269
                                       +++++++++e++++++k +v+ +d  +     i +d ++va+G+ p+t++l  ek g+e+de+g+i+vd++l+t+ p
  gi|298674110|ref|YP_003725860.1| 225 NLYTNHEAVEVQNEDNKKKVIFKDRGSgehkeITVDDILVATGRGPNTDILRpEKGGIETDEKGWIKVDDHLETSKP 301
                                       ************99997778888888888899********************************************* PP

                                       TEEE-GGGCTECCSS-- CS
                                       xxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 270 giyaiGDvaggkggpel 286
                                       +++a+GD   gk+ +++
  gi|298674110|ref|YP_003725860.1| 302 NVWALGDAN-GKYLLKH 317
                                       *******77.5554444 PP

>> Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.7   0.2   1.4e-24   3.1e-21       1     109 [.     343     454 ..     343     455 .. 0.92

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 1.4e-24
                                       BEEEEESSSEEEEEES-HHHHHHHHSG..EEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHH CS
                     Pyr_redox_dim   1 iptvvftdpevasvGlteeeAkaagie..ikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgagel 75 
                                       +p +vf++pe+asvGl e+eA + ++e  i +g  +++++++ +a++ ++ fvK++++ +++k+lGahi+Gp a+ l
  gi|298674110|ref|YP_003725860.1| 343 VPHAVFSHPEIASVGLKEKEAVEIYGEdnIIIGFYSYEETAKGQAMKVQDDFVKIIMEYSSEKILGAHIIGPYASIL 419
                                       799************************99999999999**************************************9 PP

                                       HHHHHHHHHT.TSBHHHHHTSBSSSSSTGGGGHCH CS
                     Pyr_redox_dim  76 iqelavaika.gltvedladtihihPtlsealkea 109
                                       i+++  ++   + +++ ++d + ihP+lse++++a
  gi|298674110|ref|YP_003725860.1| 420 IHQIIPLMYTpDQSAAPIMDSMTIHPSLSEVVTNA 454
                                       99987666651566669*************99876 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.0   8.9e-18     2e-14       1      80 [.     171     248 ..     171     252 .. 0.95

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 8.9e-18
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEE CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgvesvk 77 
                                       +++v+GgGyi+ E++ +++++g++Vt++ r++++ + +++e+s++ ++k++   +++++n++++e++ ++++ ++v 
  gi|298674110|ref|YP_003725860.1| 171 SIAVIGGGYIAAEYGHFFSAMGSNVTLIGRNPQFVPEEEPEISALATNKMSGY-MNLYTNHEAVEVQNEDNK-KKVI 245
                                       689*************************************************9.*************88885.8899 PP

                                       EET CS
                         Pyr_redox  78 lkd 80 
                                       +kd
  gi|298674110|ref|YP_003725860.1| 246 FKD 248
                                       985 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.0   3.3e-13   7.4e-10     114     304 ..     121     306 ..     114     307 .. 0.79

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 3.3e-13
                       Pyr_redox_3 114 fevetsketyeAkkviiAtGefdkPnklnipGeeklvkhysk.vkefhkyagqkvvViGgknSavDaAlelvrkgae 189
                                       ++ +  +et+ ++ ++i tG   kP  + ++  ++    +s  v e+ +     ++ViGg+  a+++   + ++g++
  gi|298674110|ref|YP_003725860.1| 121 YTMKVGNETIYSDMIFICTGS--KPVIPPVKSLNEVGYLTSDtVLEM-DNLPGSIAVIGGGYIAAEYGHFFSAMGSN 194
                                       566667889999999*****8..9***99999997555444404455.4446789********************** PP

                       Pyr_redox_3 190 Vtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeykvkted....gkkvevkddvv 262
                                       Vt++ r+ +   ee   + ++++   n++  +     +++++n+e+ e+++++++ kv ++d    ++k  + dd++
  gi|298674110|ref|YP_003725860.1| 195 VTLIGRNPQFVPEE---EPEISALATNKMSGY-----MNLYTNHEAVEVQNEDNKKKVIFKDrgsgEHKEITVDDIL 263
                                       *******9655553...555788888888765.....6799*********999999999876222122333358889 PP

                       Pyr_redox_3 263 latGykpdlsflkk..slfeldedgrpvlteeteetnvpglfla 304
                                       +atG  p++++l+    ++e+de+g+++++++  et  p+++  
  gi|298674110|ref|YP_003725860.1| 264 VATGRGPNTDILRPekGGIETDEKGWIKVDDHL-ETSKPNVWAL 306
                                       99**********99889************9875.5667777665 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       0.3   6.7e+02       3      35 ..       4      35 ..       3      38 .. 0.66
   2 !   18.8   0.0   3.2e-07   0.00072     133     234 ..     121     210 ..     103     218 .. 0.77
   3 !    7.5   0.1    0.0009         2     294     339 ..     223     267 ..     213     269 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.3
                       K_oxygenase  3 lDligiGiGpsnLsLailleevkkelkalfler 35
                                      +Dli+iG G     + + +++++ e+k+ ++++
  gi|298674110|ref|YP_003725860.1|  4 YDLIIIGTGSGMNFVNAIIDSNP-EIKIAVIDK 35
                                      89*****9964333444444444.778777776 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 3.2e-07
                       K_oxygenase 133 ltveskdaegeeeelearnlvlgvGtepkiPevleklegkervvHsseylerkeellakkriaVvGsGqSaaeifed 209
                                       +t+++      +e++++  + + +G++p iP+v   l+ +   + s+++le     + + +iaV+G+G  aae  + 
  gi|298674110|ref|YP_003725860.1| 121 YTMKV-----GNETIYSDMIFICTGSKPVIPPVKS-LN-EVGYLTSDTVLEMD---NLPGSIAVIGGGYIAAEYGHF 187
                                       44444.....367899999************9755.66.47788888888776...7899*************7776 PP

                       K_oxygenase 210 llrrqkkvelklvtrsealepldds 234
                                         +  +  +++l+ r++++ p ++ 
  gi|298674110|ref|YP_003725860.1| 188 FSAMGS--NVTLIGRNPQFVPEEEP 210
                                       666555..89999999999998875 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0009
                       K_oxygenase 294 rlrllpnrevesaeaegkgeveltlrneesgeeetlevdavvlATG 339
                                        ++l++n+e  ++++e + + ++ ++++ sge+++++vd +++ATG
  gi|298674110|ref|YP_003725860.1| 223 YMNLYTNHEAVEVQNEDN-KKKVIFKDRGSGEHKEITVDDILVATG 267
                                       478999999999999985.99************************9 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0     1e-05     0.023       2      55 ..     172     224 ..     171     247 .. 0.82
   2 ?   -1.6   0.0      0.98   2.2e+03     129     165 ..     403     439 ..     399     443 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1e-05
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgkl 55 
                                       +aviG G + a+  + f + g +V+l+ ++++++ + + +i++ l+  + +g +
  gi|298674110|ref|YP_003725860.1| 172 IAVIGGGYIAAEYGHFFSAMGSNVTLIGRNPQFVPEEEPEISA-LATNKMSGYM 224
                                       9*********************************999999997.4444445554 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.98
                                       GGGEEEEEE-SSTTT--EEEEEE-TT--HHHHHHHHH CS
                           3HCDH_N 129 perviglHFfnPpplmkLvEvvrgekTseetvatvve 165
                                        e+++g+H + P   + +  +++   T ++  a +++
  gi|298674110|ref|YP_003725860.1| 403 SEKILGAHIIGPYASILIHQIIPLMYTPDQSAAPIMD 439
                                       6899********9999999999999999988877766 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.5   3.5e+03      67      85 ..     122     140 ..      93     144 .. 0.81
   2 ?   10.7   0.0   0.00013       0.3       3      39 ..     172     208 ..     170     245 .. 0.80
   3 ?   -1.8   0.0      0.88     2e+03     148     181 ..     346     382 ..     326     388 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.5
                                       ES-HHHHHHC-SEEEE--- CS
                    UDPG_MGDP_dh_N  67 ttdvekaveeadvifiaVg 85 
                                       t++v ++   +d+ifi+ g
  gi|298674110|ref|YP_003725860.1| 122 TMKVGNETIYSDMIFICTG 140
                                       6677777788899999976 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00013
                                       EEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHH CS
                    UDPG_MGDP_dh_N   3 isviGlGYvGlvtaavlaeighevigvDideekvdkl 39 
                                       i+viG GY+ +  +  ++++g +v+++  + + v + 
  gi|298674110|ref|YP_003725860.1| 172 IAVIGGGYIAAEYGHFFSAMGSNVTLIGRNPQFVPEE 208
                                       9**************************9998877665 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.88
                                       EEEE------TTSHHH...HHHS-S-EEEEESSCHHH CS
                    UDPG_MGDP_dh_N 148 dvvsnPEflregsavk...dllnpdrvviGveekkae 181
                                        v s PE    g   k   ++  +d ++iG  + ++ 
  gi|298674110|ref|YP_003725860.1| 346 AVFSHPEIASVGLKEKeavEIYGEDNIIIGFYSYEET 382
                                       5777777766554444000566689999998776655 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.4e-05      0.12      17      69 ..       3      54 ..       1      73 [. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.4e-05
                                      EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBSEEEE CS
                              Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfsaivv 69
                                      + D++i+G+Gs       ++  +p++k+a++++  +pGG     G + s++++
  gi|298674110|ref|YP_003725860.1|  3 NYDLIIIGTGSGMNFVNAIIDSNPEIKIAVIDKD-APGGICLTRGCIPSKLLI 54
                                      67********8777778888899********987.788877777766666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (483 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 3101.77
//
Query:       gi|298674111|ref|YP_003725861.1|  [L=309]
Description: permease [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-62  209.9  18.5    4.9e-62  209.7  18.5    1.0  1  ArsP_1    Predicted permease


Domain annotation for each model (and alignments):
>> ArsP_1  Predicted permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.7  18.5   2.7e-66   4.9e-62       3     294 .]      21     307 ..      19     307 .. 0.95

  Alignments for each domain:
  == domain 1  score: 209.7 bits;  conditional E-value: 2.7e-66
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ArsP_1   3 aealtlfasilleallaLvlgflisgaiqvfvkeekiielLgprnrlisllvaallGfllpvCscsavPlarrllkk 79 
                                       aeal++ +++ l+++++L+l ++ +g++++++  ek++ +L  ++ + ++ +aallG+++p+Cscs +Pl+ +++ +
  gi|298674111|ref|YP_003725861.1|  21 AEALHFWIYDSLKIITILLLVIFGIGFLRTYLAPEKLRDYLKGKHSIFGYGIAALLGIVSPFCSCSTIPLFLGFVSA 97 
                                       799**************************************99********************************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ArsP_1  80 GaplgaavaFlvaaPainiiaiiltlillgwqllvarivlalivaiviglvleylfkeeelekaarevaeagleklt 156
                                       G+p+g+ ++Fl+++P++n++ai+++l  lgw+++ ++++++++v    g++l  l  ++ +ek ++  +       +
  gi|298674111|ref|YP_003725861.1|  98 GVPFGMIITFLFVSPMVNEAAIVVLLGTLGWKITGLYVLGGVVVGSFGGFLLNNLGFDKYVEKFDFGAQTY----CE 170
                                       ******************************************************************98663....44 PP

                                       xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ArsP_1 157 lkpklealkafaknevkew.lelgkyLiiGvaiagviqaflpesvllsllggnsvsssllamligvvlyvcslgevp 232
                                          +++++  +a+ e k++  ++ +y++iGv ++++i++f+p+++++s+    +  +++ a+++g+++y + +g +p
  gi|298674111|ref|YP_003725861.1| 171 EDVSIRERCNIAYTEAKNIvKQIIPYVLIGVGLGALIHGFVPQEIITSY--LTGSLAVPGAVIVGIPIYTNIMGVIP 245
                                       44555566669********99****************************..556689999***************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ArsP_1 233 fiaalfesglalGsalAfLlagpllslpellillkvlkkklvavllglvvvsvvlaglvinf 294
                                       +i++l+++gl++G+ lAf++  ++ls+pe+ +l+kv+kk+l+++++g+v++ ++l+g+v+nf
  gi|298674111|ref|YP_003725861.1| 246 VIESLVGKGLPVGTSLAFMMSVAALSFPEFVMLKKVMKKQLIIAYAGIVGLGITLMGIVFNF 307
                                       ***********************************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2059.81
//
Query:       gi|298674112|ref|YP_003725862.1|  [L=645]
Description: hydantoinase/oxoprolinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-32  111.9   0.7    2.1e-31  109.3   0.0    2.3  2  Hydantoinase_A  Hydantoinase/oxoprolinase
    1.2e-31  109.8   4.4    3.1e-28   98.7   1.4    3.6  2  Hydant_A_N      Hydantoinase/oxoprolinase N-terminal region
    2.4e-05   23.1   0.8       0.13   10.8   0.1    2.3  2  MutL            MutL protein
     0.0035   16.9   0.3       0.55    9.7   0.1    2.3  2  BcrAD_BadFG     BadF/BadG/BcrA/BcrD ATPase family
     0.0055   17.1   1.2       0.63   10.5   0.1    2.9  3  FtsA            Cell division protein FtsA


Domain annotation for each model (and alignments):
>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1     0.096   3.5e+02      82      98 ..       5      21 ..       2      34 .. 0.85
   2 !  109.3   0.0   5.9e-35   2.1e-31       1     146 [.     179     321 ..     179     381 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.096
                    Hydantoinase_A 82 ItfDmGGTstDvslikd 98
                                      +++D GGT tDv  +++
  gi|298674112|ref|YP_003725862.1|  5 LGIDAGGTYTDVVIMRN 21
                                      578*********98875 PP

  == domain 2  score: 109.3 bits;  conditional E-value: 5.9e-35
                    Hydantoinase_A   1 rtetavvnAylspilreylesvekslekrgakarlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaatsklag 77 
                                       r+ ta++nA l pi  ++++sv+ ++e rg+ a++ ++++dG++v ++ea +kp+e+i SGP a+++gaa+   l++
  gi|298674112|ref|YP_003725862.1| 179 RGITAYLNAQLLPITTKFIDSVKYEIERRGIDAKMRMLKCDGSIVGINEALEKPIELIFSGPSASLMGAAY---LTN 252
                                       789********************************************************************...888 PP

                    Hydantoinase_A  78 ekkvItfDmGGTstDvslikdgevevsletei.agvkvrlpaldirtvgagGgsilvvdeggklrvgpes 146
                                        +++ ++D+GGTstDvsl+++g +e +    + +g +++++al+++t ++gG+s ++v++ +++r+gp+ 
  gi|298674112|ref|YP_003725862.1| 253 LDSCAVVDIGGTSTDVSLMENGLPELVDTGAVvGGWQTKVRALRMETSAMGGDSHVWVKN-QTIRIGPRR 321
                                       899*********************977665554***********************6655.99****984 PP

>> Hydant_A_N  Hydantoinase/oxoprolinase N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.7   1.4   8.5e-32   3.1e-28       2     177 ..       5     159 ..       4     160 .. 0.90
   2 !    6.9   0.1    0.0013       4.7       3      18 ..     258     273 ..     257     302 .. 0.82

  Alignments for each domain:
  == domain 1  score: 98.7 bits;  conditional E-value: 8.5e-32
                        Hydant_A_N   2 igIDvGGTfTDavaldekeee.vavlKllstpdavaegirealeevleesiprtskidvvrmGTTvatNallerkge 77 
                                       +gID+GGT+TD+v++++++++ v  +K l+t  + +eg+++a++ +  +     + ++ v ++TT+atN++le++g 
  gi|298674112|ref|YP_003725862.1|   5 LGIDAGGTYTDVVIMRNHDGViVDFYKSLTTYPDLVEGVKNAIDGLDCSY---LKGVNIVSVSTTLATNTVLENTGY 78 
                                       79**************9996515689*******************96554...67********************** PP

                        Hydant_A_N  78 rvaLittkgfrdlleigrqnrpdlfelrikkplvlyeevvevderveadgevlkpldeeevrealkalkaagvesia 154
                                       +v+L+   +++    ++                   e  + v+++++ +g++ ++ldee+v+  +k++k++ v+++a
  gi|298674112|ref|YP_003725862.1|  79 PVGLVLVGDYEVPEDLD------------------VEHYIVVSGGHTTRGDEASKLDEEKVEDFIKNVKDK-VSAFA 136
                                       *****999887655444..................345679****************************99.***** PP

                        Hydant_A_N 155 vvllhSylnpehElrvaeiarei 177
                                       v++++S++np+hElrv++ ++e+
  gi|298674112|ref|YP_003725862.1| 137 VSSYFSVRNPDHELRVKQKIKEL 159
                                       ******************99985 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0013
                        Hydant_A_N   3 gIDvGGTfTDavalde 18 
                                        +D+GGT TD+ ++++
  gi|298674112|ref|YP_003725862.1| 258 VVDIGGTSTDVSLMEN 273
                                       59*********99984 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.1   3.6e-05      0.13       2      53 ..       5      52 ..       4      70 .. 0.86
   2 !   10.5   0.1   4.6e-05      0.16     224     270 ..     236     277 ..     222     290 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.6e-05
                              MutL  2 lviDiGSttTkvtlvdlekvderllgqaeapTtveeedvleGleealeelee 53
                                      l iD G t+T v+++++++  + ++   +++Tt    d++eG+++a++ l  
  gi|298674112|ref|YP_003725862.1|  5 LGIDAGGTYTDVVIMRNHD--GVIVDFYKSLTTYP--DLVEGVKNAIDGLDC 52
                                      569**************76..*************5..**********98875 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 4.6e-05
                              MutL 224 impTPaAvlkavellaeeeekglgdllvvDvGGaTTdvhsvaegspe 270
                                       i   P+A l ++  l +     l+ + vvD+GG++Tdv  + +g pe
  gi|298674112|ref|YP_003725862.1| 236 IFSGPSASLMGAAYLTN-----LDSCAVVDIGGTSTDVSLMENGLPE 277
                                       56678888888888888.....66899************99888776 PP

>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.1   0.00015      0.55       1      25 [.       5      29 ..       5     140 .. 0.75
   2 !    5.3   0.0    0.0034        12       3      33 ..     259     296 ..     246     391 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00015
                                      EEEEE-SSEEEEEEEETTTEEEEEE CS
                       BcrAD_BadFG  1 vGiDgGsTttkavlmdekgevlgrg 25
                                      +GiD G+T t +v+m++   v+   
  gi|298674112|ref|YP_003725862.1|  5 LGIDAGGTYTDVVIMRNHDGVIVDF 29
                                      8**************9887766544 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0034
                                       EEE-SSEEEEEEEE.......TTTEEEEEEEE--TTS- CS
                       BcrAD_BadFG   3 iDgGsTttkavlmd.......ekgevlgrgitnsanle 33 
                                       +D+G+T+t + lm+       + g v+g ++t+ + l+
  gi|298674112|ref|YP_003725862.1| 259 VDIGGTSTDVSLMEnglpelvDTGAVVGGWQTKVRALR 296
                                       899*******9999999999999999999988876555 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.014        51       2      19 ..       6      23 ..       5      60 .. 0.80
   2 ?   -2.7   0.0       2.2     8e+03      63      63 ..     203     203 ..     107     256 .. 0.57
   3 !   10.5   0.1   0.00018      0.63       1      21 [.     257     277 ..     257     300 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.014
                                      EEEE-SSSEEEEEEETTE CS
                                      xxxxxxxxxxxxxxxxxx RF
                              FtsA  2 lvDiGagktdvavaedga 19
                                      ++D G++ tdv++++++ 
  gi|298674112|ref|YP_003725862.1|  6 GIDAGGTYTDVVIMRNHD 23
                                      79*************953 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.2
                                       E CS
                                       x RF
                              FtsA  63 e 63 
                                       e
  gi|298674112|ref|YP_003725862.1| 203 E 203
                                       1 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00018
                                       EEEEE-SSSEEEEEEETTEEE CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                              FtsA   1 alvDiGagktdvavaedgalv 21 
                                       a+vDiG+++tdv+++e+g + 
  gi|298674112|ref|YP_003725862.1| 257 AVVDIGGTSTDVSLMENGLPE 277
                                       79***************8655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (645 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.71u 0.34s 00:00:01.05 Elapsed: 00:00:00.51
# Mc/sec: 3841.08
//
Query:       gi|298674113|ref|YP_003725863.1|  [L=378]
Description: DegT/DnrJ/EryC1/StrS aminotransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-92  311.0   0.0    1.4e-92  310.8   0.0    1.0  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
      4e-08   32.8   0.0    6.3e-08   32.2   0.0    1.3  1  Aminotran_1_2    Aminotransferase class I and II
    4.2e-06   26.0   0.1    8.5e-06   24.9   0.0    1.4  2  Aminotran_5      Aminotransferase class-V
    0.00013   20.7   0.0     0.0002   20.0   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    0.00024   20.5   0.0    0.00056   19.3   0.0    1.6  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.011   14.3   0.0      0.016   13.8   0.0    1.2  1  SHMT             Serine hydroxymethyltransferase
      0.087   12.6   0.0          1    9.1   0.0    2.3  2  DUF2913          Protein of unknown function (DUF2913)


Domain annotation for each model (and alignments):
>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  310.8   0.0   5.5e-96   1.4e-92       6     360 ..      23     369 ..      19     370 .. 0.96

  Alignments for each domain:
  == domain 1  score: 310.8 bits;  conditional E-value: 5.5e-96
                                       HHHHHHHHHTSS-SSSSHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHH CS
                   DegT_DnrJ_EryC1   6 eleaveevlksgwltsgpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavle 82 
                                       +  ++ e+l+ g++t+ ++vee+E+ +a+ylgv+ha+avss ta+++l+++ +g++   eVI p + F ++a +vl+
  gi|298674113|ref|YP_003725863.1|  23 IAPDISEILEEGKTTNAKHVEELENTVAEYLGVEHAVAVSSSTAGMMLTIKSMGLN--GEVILPGFDFHSSADTVLW 97 
                                       5667899*************************************************..9****************** PP

                                       TT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETTEECC CS
                   DegT_DnrJ_EryC1  83 lgakpvfvDvdpdtynidpaaieaaitertkaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykgkkvG 159
                                       +g+k  fvD+dp+t++idp+++e+ ite+t+aI  +h++G+++d+++l++ia++ +lk+  DaAhAlG++y+++++G
  gi|298674113|ref|YP_003725863.1|  98 NGLKLKFVDIDPETWTIDPDKVEENITENTSAICGAHIFGNPCDIEKLQQIAEDNNLKLYFDAAHALGSKYHNEYIG 174
                                       ***************************************************************************** PP

                                       CSSSEEEEE-BTTSSS-SSS-EEEEESTHHHHHHHHHHHBTTCECCTCSSCECCSS---B-B-BHHHHHHHHHHHCT CS
                   DegT_DnrJ_EryC1 160 algdaavfSFyptKnlttGeGGavvtndeelaekarvlrnhGlkrkaekryvgevelGynyrlteiqAAiglaqLer 236
                                       ++g+a++fS+ p+    +GeGG+v+tnd++l++ + + rn+G +    ++  +++ + +n+r++e++A + +  L++
  gi|298674113|ref|YP_003725863.1| 175 NFGNAEIFSLNPSTSNFVGEGGIVTTNDDDLKDYLLAGRNYGDE----NELSSRF-PAFNARMSEFNAVLANYSLQN 246
                                       ******************************************77....7999999.********************* PP

                                       HHHHHHHHHHHHHHHHHHHHTCCCCEESCGGTTSSSEEESCEEEEEHCCHH.HCHHHHHHHHHHCCEE-B-SGSCHG CS
                   DegT_DnrJ_EryC1 237 ldelvarRreiaelykeeLaelegtaelttpketkkhawhlyavlveeeae.vkrdelvealkeegigtrvhypnpl 312
                                       +++ + +R+ +++ y++ L +++g+   +  +e++++a+  +a+ ++ ++  ++rdel  +l+e +i+t+  y+ p+
  gi|298674113|ref|YP_003725863.1| 247 IEKNIRSRNGVVTKYRNVLGNIPGI-SFQKITEHSRSAYNDFAISINPDEFgMTRDELSDKLSEVNIETKKNYYPPV 322
                                       ***********************97.45555555569*********999988*******************9999** PP

                                       GGSCCHHHHHHCCCHC-HHHHHHHHHEEEEEGGTTGSHHHHHHHHHHH CS
                   DegT_DnrJ_EryC1 313 hrqpvyaerkeeasgdlpnaerlaervlsLplypelteedvdrVveal 360
                                       hrq++y e +++ ++dlp++++l+e vlsLp++++++++ + +V++++
  gi|298674113|ref|YP_003725863.1| 323 HRQQAYSEHAQS-ETDLPVTDELSEHVLSLPIWSQMSSNLAGKVCTNI 369
                                       *********866.679***********************999999877 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0   2.4e-11   6.3e-08      36     194 ..      32     166 ..      13     208 .. 0.87

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 2.4e-11
                                       STTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHH CS
                     Aminotran_1_2  36 tlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrl 112
                                       +  ++++ ++  ele+++a++lg         e av v+s +  +  +++ +  ln +  +++p   + s  + + +
  gi|298674113|ref|YP_003725863.1|  32 EEGKTTNAKHVEELENTVAEYLG--------VEHAVAVSSSTAGMMLTIKSMG-LNGE--VILPGFDFHSSADTVLW 97 
                                       556677888899***********........999*******************.8877..99*************** PP

                                       TTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEET CS
                     Aminotran_1_2 113 sggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDea 189
                                       +g+++  + ++ +e++++d +++ee ++e       t  i+ + ++   G  ++ e+l+++   a+ +nl l++D a
  gi|298674113|ref|YP_003725863.1|  98 NGLKLKFVDID-PETWTIDPDKVEENITE------NTSAICGAHIF---GNPCDIEKLQQI---AEDNNLKLYFDAA 161
                                       *********66.*****************......77888877776...788899******...************* PP

                                       TTTCB CS
                     Aminotran_1_2 190 Yagfv 194
                                       +a + 
  gi|298674113|ref|YP_003725863.1| 162 HALGS 166
                                       *9765 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   3.3e-09   8.5e-06      42     183 ..      39     167 ..      22     170 .. 0.87
   2 ?   -3.4   0.0       1.3   3.4e+03     127     156 ..     242     269 ..     237     284 .. 0.68

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 3.3e-09
                                       HHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEE CS
                       Aminotran_5  42 tkaveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkv 118
                                       +k vee +++vae +++e     + +s++t ++ l ++s+        e+++   + h+      +     g+k+k+
  gi|298674113|ref|YP_003725863.1|  39 AKHVEELENTVAEYLGVEH---AVAVSSSTAGMMLTIKSM----GLNGEVILPGFDFHSSA----DTVLWNGLKLKF 104
                                       5789**************7...889999999999999999....56899999999999988....333467899999 PP

                                       EEBE.TTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS CS
                       Aminotran_5 119 ipld.eegeldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghi 183
                                       + +d e++++d+d++e++++e+t++++ +h   + G+  ++e++ ++a +++  +  Daa a+g++
  gi|298674113|ref|YP_003725863.1| 105 VDIDpETWTIDPDKVEENITENTSAICGAH---IFGNPCDIEKLQQIAEDNNLKLYFDAAHALGSK 167
                                       99993469****************999888...69**************************99875 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.3
                                       BEGGGHHHH--TTEEEEEEESBETTTTEB- CS
                       Aminotran_5 127 ldldelekllnektklvaithvsnvtGtiq 156
                                       + l+++ek+++ +  +v  t   nv+G+i 
  gi|298674113|ref|YP_003725863.1| 242 YSLQNIEKNIRSRNGVV--TKYRNVLGNIP 269
                                       56777888887777766..56677777764 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   7.8e-08    0.0002      54     175 ..      42     161 ..      34     169 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 7.8e-08
                                       HHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEES.TTSHHH CS
                   Cys_Met_Meta_PP  54 rsvleeriaaLeggeaalavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvd.tsdlee 129
                                       ++ le+++a+  g+e+a+avss +a ++++i ++  +G+ i+   d ++++  +l + lk   ++++    t d+++
  gi|298674113|ref|YP_003725863.1|  42 VEELENTVAEYLGVEHAVAVSSSTAGMMLTIKSMGLNGEVILPGFDFHSSADTVLWNGLKLKFVDIDPETwTIDPDK 118
                                       578*************************************************99998888777777654415699** PP

                                       HHHHCCTTEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGT CS
                   Cys_Met_Meta_PP 130 lekaikentklvylEtptnpllkvvDiekiaklakkagvlvvvDnt 175
                                       +e+ i+ent+++     + ++ + +Diek+ ++a ++++ +  D++
  gi|298674113|ref|YP_003725863.1| 119 VEENITENTSAICG---AHIFGNPCDIEKLQQIAEDNNLKLYFDAA 161
                                       ***********964...44555558*********999999998876 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   2.2e-07   0.00056      30     219 ..      38     209 ..      31     257 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.2e-07
                                       --HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTT CS
                   Beta_elim_lyase  30 edktvnrLedavaelfgkeaalfvpqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlknkea 106
                                       ++k v++Le++vae++g e+a+ v + ta+  + +k +   ge ++ + + h   d+       +g kl+ ++++ +
  gi|298674113|ref|YP_003725863.1|  38 NAKHVEELENTVAEYLGVEHAVAVSSSTAGMMLTIKSMGLNGEVILPGFDFHSSADTV----LWNGLKLKFVDIDPE 110
                                       57899**********************************9999999999988888885....456777766665544 PP

                                       .TBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-C CS
                   Beta_elim_lyase 107 .GkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeiv 182
                                         ++d++k+e+ i+e      ++++i+   ++    G++  +e+   +++ia++++++l +D+A  +      +e +
  gi|298674113|ref|YP_003725863.1| 111 tWTIDPDKVEENITE------NTSAICG--AHIF--GNPCDIEK---LQQIAEDNNLKLYFDAAHALGSK-YHNEYI 173
                                       39************9......6888885..4555..88887665...567899**********9766543.333333 PP

                                       HHHHTTSSEEEEESSSTT--SS-EEEEE-HH....HH CS
                   Beta_elim_lyase 183 kemfsyvDsvtmslkKdllanvGgvlafrddeledyl 219
                                          f  + ++++  +   ++  Gg++ ++dd+l+dyl
  gi|298674113|ref|YP_003725863.1| 174 -GNFGNAEIFSLNPSTSNFVGEGGIVTTNDDDLKDYL 209
                                       .345667788888888888888888888888887776 PP

>> SHMT  Serine hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   6.4e-06     0.016     147     210 ..     105     166 ..      60     206 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.4e-06
                                       E-B-TTTSSB-HHHHHHHHHHH--SEEEEE-SST-S---HHHHHHHHHHTT-EEEEE-GGGHHH CS
                              SHMT 147 ykvdketglidydelekkakefkPklivaGtsaysrlidyarlreiadevgayllvdmahiaGl 210
                                         +d+et +id d++e++ +e      ++G+  + + +d ++l++ia++ +  l  d ah  G 
  gi|298674113|ref|YP_003725863.1| 105 VDIDPETWTIDPDKVEENITENTS--AICGAHIFGNPCDIEKLQQIAEDNNLKLYFDAAHALGS 166
                                       46899************9998765..68********************************8875 PP

>> DUF2913  Protein of unknown function (DUF2913)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.13   3.4e+02      53     110 ..      22      76 ..      18     180 .. 0.44
   2 ?    9.1   0.0   0.00039         1      56     119 ..     203     264 ..     200     276 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.13
                           DUF2913  53 lvakdLkrwqkqgrskGknaqLkalleriseqykevaeeekeldskleallaeleeke 110
                                       ++a d+ +++++g+   +na+  + le+  + y  v+    ++ s+ + ++ ++++++
  gi|298674113|ref|YP_003725863.1|  22 TIAPDISEILEEGK--TTNAKHVEELENTVAEYLGVEHA-VAVSSSTAGMMLTIKSMG 76 
                                       56677777777777..55555555555555555444432.233344444444444333 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00039
                           DUF2913  56 kdLkrwqkqgrskGknaqLkalleriseqykevaeeekeldskleallaeleekewvvitdeev 119
                                       +dLk+ + +gr  G + +L +++   ++ ++e+++   +   +l+++ ++++++++vv++  +v
  gi|298674113|ref|YP_003725863.1| 203 DDLKDYLLAGRNYGDENELSSRFPAFNARMSEFNAVLANY--SLQNIEKNIRSRNGVVTKYRNV 264
                                       79********************************988776..9************999987666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 2411.90
//
Query:       gi|298674114|ref|YP_003725864.1|  [L=410]
Description: glucoamylase and related glycosyl hydrolase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0046   15.8   0.3      0.022   13.6   0.6    2.1  2  Glyco_hydro_15  Glycosyl hydrolases family 15


Domain annotation for each model (and alignments):
>> Glyco_hydro_15  Glycosyl hydrolases family 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.04   7.2e+02       4      51 ..       7      50 ..       5      62 .. 0.74
   2 !   13.6   0.6   1.2e-06     0.022     114     235 ..      83     235 ..      70     402 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.04
                                      HHHHHHCBCSTTSSBTTS-TT-B-S-S-BSSSB--SEEHHHHHHHHHH CS
                    Glyco_hydro_15  4 ldlylrnvktlilleqnpvtGlliASpstsdpDYrytWvRDsvyvila 51
                                      ++ly ++vk l+    +   G++ ASp  +   Y +   RD ++ il 
  gi|298674114|ref|YP_003725864.1|  7 HKLYENSVKILKKNQHEN--GGFYASPPGT--RYPFIYPRDHSIAILG 50
                                      678889999766555555..9999999833..4679999999998875 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 1.2e-06
                                       --S-...-S--BTTHHHHHHHHHHHH.HCTT.........HCHCCCCHHHHTHHHHHHHHHHHTTS-......EE-T CS
                    Glyco_hydro_15 114 vvGdde.wghlQlDatslyllalaqm.tasg.........lqiistldevafvqnlvdYieaayktp......dfgl 173
                                       ++G+d+ ++ lQ+D+t+l+l++l ++  a+g           ++ ++++   ++n v++i  + ++          +
  gi|298674114|ref|YP_003725864.1|  83 IDGNDAsYKDLQIDGTGLVLYTLGKYfEATGgsffeemadRDFVLKYWST--IRNAVEFILMNKNEEvdlihtINSI 157
                                       5666653889****************744446777776546666667777..********98877654333335677 PP

                                       TS...--ECEEHH..HHHHHHHHHHHHHHHHHHCT-HH.HHCCHHHHHHHHHHHHHSTTT..G..GG.......... CS
                    Glyco_hydro_15 174 WE...enqgeselnassvgmakAlleaideadlfgakg.daqlvektkdeilnklqgkygckr..gf.......... 234
                                        E   +++g + +     +  +++l a+++ +++ga++ + + +++ ++++ n +  +++  r  +f          
  gi|298674114|ref|YP_003725864.1| 158 HEypaYEHGFEIY--ANSACCAGILSAVEMGKAIGADDnELDRWKNEAEKVKNAILTRMYSPRrrSFikcirvkdkn 232
                                       7787777777777..66667788999999999999765467789999999999995555544433334444444444 PP

                                       ..E CS
                    Glyco_hydro_15 235 ..w 235
                                          
  gi|298674114|ref|YP_003725864.1| 233 skP 235
                                       440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2678.41
//
Query:       gi|298674115|ref|YP_003725865.1|  [L=178]
Description: hypothetical protein Metev_0138 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.36s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1102.45
//
Query:       gi|298674116|ref|YP_003725866.1|  [L=269]
Description: mannosyl-3-phosphoglycerate phosphatase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.8e-17   62.0   0.2    1.2e-16   61.3   0.2    1.4  1  Hydrolase_3  haloacid dehalogenase-like hydrolase
    1.6e-06   27.8   0.0     0.0014   18.2   0.0    2.2  2  S6PP         Sucrose-6F-phosphate phosphohydrolase
      2e-05   24.6   0.0      4e-05   23.7   0.0    1.4  1  Hydrolase_6  Haloacid dehalogenase-like hydrolase
    0.00011   22.7   2.5       0.14   12.5   0.0    3.2  3  HAD          haloacid dehalogenase-like hydrolase
     0.0011   19.1   1.2      0.047   13.8   0.0    3.1  3  HAD_2        Haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.013   15.8   0.2        1.7    8.9   0.2    2.9  1  Hydrolase    haloacid dehalogenase-like hydrolase
       0.17   12.1   0.8       0.29   11.3   0.1    1.7  2  DUF2812      Protein of unknown function (DUF2812)


Domain annotation for each model (and alignments):
>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.3   0.2   4.6e-20   1.2e-16       1     228 [.       5     232 ..       5     235 .. 0.75

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 4.6e-20
                                       EEEEIIIIIS-TTS---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEE.ECTTTEEE.E CS
                       Hydrolase_3   1 ialDlDGTLlnsdkkisektkeaikklkekgikvviATGRslravlpvleelgldlpvialNGali.ddekgkil.y 75 
                                       + +DlDGTL+++d    e +k a++ l++++i ++i+T     +++ ++++l+   p+i+ NG+ i   +    + y
  gi|298674116|ref|YP_003725866.1|   5 VYTDLDGTLIDHDTYSYEPAKPALELLEKHNIPLIICTSKTRAEIEVYVKKLNSPHPFISENGGAIfIPKGYFDVdY 81 
                                       579***********999*************************************************84555555547 PP

                                       E--B-HHHHHHHHHHHHHTT.CEEEEEESSEEEESTT...THHHHHHHHHCHCTCEEEESHHHHHCHCSESEEEEES CS
                       Hydrolase_3  76 kstiskedvkeiikllkenn.veillytedkvyvlnk..eksekkkkeeektkkkkeeidseeeledeeiakililk 149
                                       + ti+ +++ +ii+l  e+  ++ +l++ ++ +  +     + ++++  ++t  + e+ +  + +e +e++k+   +
  gi|298674116|ref|YP_003725866.1|  82 DYTITYKNY-NIIELGTEYPkLRQVLEDIKSSVDVEIlgFGDLDDENVSKDTGLDIESARLAKMREYDEAFKV-KGE 156
                                       888887776.699999999977777777666666666333334444444444444444445555555555555.777 PP

                                       -HHHHHHHHHHHHHHCTTTEEEEEESTTEEEEEETT-SHHHHHHHHH..HHCT--GGGEEEEESSGGGHHHHHHSSE CS
                       Hydrolase_3 150 dkekldelekelksklnklltitssskgyleimpkgvsKgtalkkla..kelnisleeviafGDgeNDieMLeaagl 224
                                       +k+  d++++ +ks+    l++t+ +++   i  +  +Kg+a++ l    e ++ + +++  GD+ ND++ML+ +++
  gi|298674116|ref|YP_003725866.1| 157 EKNVADRIIEIIKSHG---LNYTRGGRYWHLIGDN--DKGKAVEILSdiYEKQFGNLQTVGLGDSLNDYPMLKSVDI 228
                                       8888999999999995...3666666655555544..666666666622667888999*****************99 PP

                                       EEEE CS
                       Hydrolase_3 225 gvAm 228
                                        + +
  gi|298674116|ref|YP_003725866.1| 229 PYLV 232
                                       8766 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   5.4e-07    0.0014       3      86 ..       3      83 ..       1     108 [. 0.79
   2 !    7.8   0.0   0.00083       2.1     164     198 ..     188     224 ..     144     232 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 5.4e-07
                                      EEEEE-TBTTTB.S-HHHHHHHHHHHH.GGGGGEEEEEE-SS-HHHHHHHHHHHT----SEEEETTTTEEEE..TTEE- CS
                              S6PP  3 lllvsdLDntlvdgdnealarlnelleaeerkdvllvfaTGRsldsakellkeknllkPdvlitsvGteiyygeelvpd 81
                                       ++ +dLD+tl+d+d  + +  +  le  e++++ l+++T ++ ++ +  +k+ n ++P   i++ G  i   ++   d
  gi|298674116|ref|YP_003725866.1|  3 YVVYTDLDGTLIDHDTYSYEPAKPALELLEKHNIPLIICTSKTRAEIEVYVKKLNSPHP--FISENGGAIFI-PKGYFD 78
                                      5789**************************************99999988887765555..67777777766.444445 PP

                                      HHHHH CS
                              S6PP 82 kawee 86
                                       ++  
  gi|298674116|ref|YP_003725866.1| 79 VDYDY 83
                                      55555 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00083
                                       -SHHHHHHHHHHHHT--..GGGEEEEE-SGGGHHHHT CS
                              S6PP 164 askgeAlryLakklele..leqilvcGdsgnDeelli 198
                                        +kg+A++ L++ +e +    q++  Gds nD  +l+
  gi|298674116|ref|YP_003725866.1| 188 NDKGKAVEILSDIYEKQfgNLQTVGLGDSLNDYPMLK 224
                                       69**********9998877889999********9996 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   1.5e-08     4e-05       2      53 ..       6      58 ..       5      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.5e-08
                                      EEESTTTSEETTE.E-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHHHH CS
                       Hydrolase_6  2 lfDidGvLwrgdk.aipgaaealnalraagkpvvllTNnsskseeeyakklek 53
                                       +D+dG+L++ d+  ++ a+ al+ l+++++p++++T +++   e y+kkl++
  gi|298674116|ref|YP_003725866.1|  6 YTDLDGTLIDHDTySYEPAKPALELLEKHNIPLIICTSKTRAEIEVYVKKLNS 58
                                      68*******865527**********************************9975 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   1.1     0.025        64       3      15 ..       7      19 ..       5      22 .. 0.86
   2 ?    4.3   0.0     0.018        47      89     129 ..      26      64 ..      19      81 .. 0.79
   3 !   12.5   0.0   5.5e-05      0.14     125     188 .]     165     224 ..     146     224 .. 0.65

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.025
                               HAD  3 fDfDgTLldgdsl 15
                                       D+DgTL+d d++
  gi|298674116|ref|YP_003725866.1|  7 TDLDGTLIDHDTY 19
                                      6********9987 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.018
                               HAD  89 galellaahraaGdrvvvvSgglrplvepllaelg.adevla 129
                                        alell+   + +++++++++  r  +e   ++l+ ++ +++
  gi|298674116|ref|YP_003725866.1|  26 PALELLE---KHNIPLIICTSKTRAEIEVYVKKLNsPHPFIS 64 
                                       5677777...99************999999999986666665 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 5.5e-05
                               HAD 125 devlatelevdd..rltge..lglegkpvrgegkvaalrewlaaegegidleevvayGDspsDlpllr 188
                                       +e++ +    ++  +  g+  + l+g++ +g  k+ ++ + ++++  g     +v  GDs +D+p+l+
  gi|298674116|ref|YP_003725866.1| 165 IEIIKS----HGlnYTRGGryWHLIGDNDKG--KAVEILSDIYEKQFGNL--QTVGLGDSLNDYPMLK 224
                                       344444....446344444445555555555..77777775666555553..39************97 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.1    0.0069        18       4      19 ..       8      23 ..       5      28 .. 0.87
   2 !   13.8   0.0   1.8e-05     0.047      78     121 ..      18      61 ..      15      64 .. 0.89
   3 ?   -1.2   0.0      0.71   1.8e+03      37     172 ..     128     143 ..      98     175 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0069
                             HAD_2  4 DlDgTlldteeliiqa 19
                                      DlDgTl+d  +++++ 
  gi|298674116|ref|YP_003725866.1|  8 DLDGTLIDHDTYSYEP 23
                                      9**********99985 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.8e-05
                             HAD_2  78 vkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesy 121
                                       +  y+ +k +Le L+++++ l i Tsk+r+++e  +++l+  + 
  gi|298674116|ref|YP_003725866.1|  18 TYSYEPAKPALELLEKHNIPLIICTSKTRAEIEVYVKKLNSPHP 61 
                                       77899999******************************997665 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.71
                             HAD_2  37 lrkliglslrellrklgeseeeeekieellrkyneekkkkevkpydgvkelLeeLkeagyklgivTsksreaveekl 113
                                       ++k  gl+                                                                     
  gi|298674116|ref|YP_003725866.1| 128 VSKDTGLDI-------------------------------------------------------------------- 136
                                       444444444.................................................................... PP

                             HAD_2 114 eqlgiesyFdvivtsedvekkKPdpeviekaleklklkkeeviyvGDsptDieaakkag 172
                                                                                           e+a+ a 
  gi|298674116|ref|YP_003725866.1| 137 ----------------------------------------------------ESARLAK 143
                                       ....................................................3333333 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.2   0.00065       1.7     171     209 ..     193     226 ..       3     227 .. 0.41

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00065
                                       STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 171 vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaA 209
                                         + + +++++    L     +++  GD++nD ++l+ +
  gi|298674116|ref|YP_003725866.1| 193 AVEILSDIYEKQFGNL-----QTVGLGDSLNDYPMLKSV 226
                                       3333333333333333.....477788888888888876 PP

>> DUF2812  Protein of unknown function (DUF2812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       4.9   1.3e+04      36      46 ..      80      90 ..      79     102 .. 0.71
   2 ?   11.3   0.1   0.00011      0.29      38      94 ..     148     203 ..     141     209 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 4.9
                           DUF2812 36 eyryrvdyike 46
                                      +y y+++y++ 
  gi|298674116|ref|YP_003725866.1| 80 DYDYTITYKNY 90
                                      68888888776 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00011
                           DUF2812  38 ryrvdyikekskeeseeylelleesGweyvakskewlifrkeedgkpfelytDeesk 94 
                                         ++++++e +k+ +++ +e++++ G +y  + + w+ + ++++gk+ e+ +D  +k
  gi|298674116|ref|YP_003725866.1| 148 DEAFKVKGE-EKNVADRIIEIIKSHGLNYTRGGRYWHLIGDNDKGKAVEILSDIYEK 203
                                       455566666.7889999************************************8776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 1754.34
//
Query:       gi|298674117|ref|YP_003725867.1|  [L=302]
Description: mechanosensitive ion channel protein MscS [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.2e-40  138.4   2.2    3.7e-40  137.7   2.2    1.3  1  MS_channel  Mechanosensitive ion channel
  ------ inclusion threshold ------
       0.43   10.6   2.7       0.28   11.2   0.5    1.7  2  DUF3043     Protein of unknown function (DUF3043)


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.7   2.2   4.2e-44   3.7e-40       4     206 .]      68     277 ..      62     277 .. 0.92

  Alignments for each domain:
  == domain 1  score: 137.7 bits;  conditional E-value: 4.2e-44
                                       HHHHHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE- CS
                        MS_channel   4 lkiliivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVedig 80 
                                       +++   +++i++   +l     al+a++G++g+++g+a+++++sn++aG+ l + +pf++GD+v+i++  GtV+di+
  gi|298674117|ref|YP_003725867.1|  68 VYFA-GIIVIILSVPFLRNISLALFAGAGFAGIVVGMAAQSTLSNVIAGVSLATFRPFRVGDRVNINNEYGTVTDIT 143
                                       3333.344444444444445679****************************************************** PP

                                       SSEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-T..... CS
                        MS_channel  81 lrttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlk..... 152
                                       l  t ++t+d+r ++iPn  +++++i+N++ e+ t+   +++g+ y+sd   ++++ +++ e+++++p+v +     
  gi|298674117|ref|YP_003725867.1| 144 LGHTVVNTWDNRRLMIPNHIISDQSIINWTIEDSTVLWPIDMGISYDSD---IDHAKSIMIEEARKHPNVMRyedii 217
                                       *************************************************...************************* PP

                                       ........TS-EEEEEEEE-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT--- CS
                        MS_channel 153 ........dkellvvldefgdsslnfevrvfvktvvpeeylsvqseinlrikkileeegiei 206
                                               d+  +v+++e gd ++n+++ v++ t   +  + +  e+++ ikk +++egiei
  gi|298674117|ref|YP_003725867.1| 218 nyhpmsskDEGIEVYVTECGDFAVNLRLFVWIVT--RGIAYTTGCELREAIKKRFDAEGIEI 277
                                       **********************************..7999********************97 PP

>> DUF3043  Protein of unknown function (DUF3043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.5   3.1e-05      0.28     107     155 ..      13      63 ..       2      67 .. 0.85
   2 ?   -1.7   0.1      0.28   2.5e+03      84     119 ..      71     104 ..      61     112 .. 0.41

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.1e-05
                           DUF3043 107 vsllllvllllvvidgillgrkvkkkvrekFp..etesekglglYavsRal 155
                                        +l+ lv++l+v+i +++++  v +++++ F+  +++     ++Y ++R +
  gi|298674117|ref|YP_003725867.1|  13 KNLANLVFVLAVIIASFIIAKIVDRALKTYFGivSKKMVIDETVYGLVRRI 63 
                                       4678899*************************8666666677999999977 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.28
                           DUF3043  84 plalvvlvlllvslvkvpevqavvsllllvllllvv 119
                                         ++v+++   v + ++ +++ ++  ++  +++ ++
  gi|298674117|ref|YP_003725867.1|  71 AGIIVIILS--VPFLRNISLALFAGAGFAGIVVGMA 104
                                       112222211..2344444444444444444555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       897  (0.0500307); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2027.66
//
Query:       gi|298674118|ref|YP_003725868.1|  [L=382]
Description: integrase family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-24   87.3   0.8      2e-24   86.3   0.1    1.8  3  Phage_integrase  Phage integrase family
    3.1e-07   29.9   3.1    7.8e-07   28.6   3.1    1.7  1  zinc_ribbon_2    zinc-ribbon domain
    3.3e-07   30.5   0.0    8.5e-07   29.2   0.0    1.7  1  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
    2.7e-06   27.7   0.0    9.4e-05   22.8   0.0    2.6  2  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
      5e-05   23.2   0.5    0.00012   22.0   0.5    1.5  1  DZR              Double zinc ribbon
    0.00035   19.9   1.7    0.00069   18.9   1.7    1.5  1  zf-ribbon_3      zinc-ribbon domain
     0.0053   16.0   2.7     0.0091   15.3   2.7    1.4  1  zf-RanBP         Zn-finger in Ran binding protein and others
     0.0054   17.4   0.7      0.013   16.2   0.7    1.7  1  zinc_ribbon_15   zinc-ribbon family
     0.0065   16.1   0.5       0.29   10.8   0.1    2.4  2  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
  ------ inclusion threshold ------
      0.011   15.6   0.7          3    7.8   0.0    2.6  2  Nudix_N_2        Nudix N-terminal
       0.17   11.9   0.2        1.1    9.3   0.1    2.4  2  DUF4248          Domain of unknown function (DUF4248)
       0.24   11.0   1.2       0.59    9.8   1.2    1.7  1  RecR             RecR protein
        1.7    8.9   4.2         33    4.7   3.8    2.5  2  NOB1_Zn_bind     Nin one binding (NOB1) Zn-ribbon like


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       6.1   8.5e+03      45      71 ..     101     125 ..     101     125 .. 0.82
   2 !   86.3   0.1   1.4e-27     2e-24       3     170 ..     129     292 ..     127     294 .. 0.91
   3 ?   -2.9   0.0       3.8   5.2e+03      88     148 ..     308     370 ..     297     377 .. 0.55

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 6.1
                                       GGGEECTTTEEEEEEEECSSSSEEEEE CS
                   Phage_integrase  45 vkdldlengvilvheregKgskeravp 71 
                                       +kd++l+  + ++  + gK+s ++ +p
  gi|298674118|ref|YP_003725868.1| 101 IKDMELDVPTDII--KTGKNSNQHKLP 125
                                       5788899999999..899999998776 PP

  == domain 2  score: 86.3 bits;  conditional E-value: 1.4e-27
                                       HHHHHHHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECTHHHHHH CS
                   Phage_integrase   3 ltedeverllaaleeslkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgskeravplseealel 79 
                                       +te+e++ +++ + +   +rdk+l+ +lye+++R+++l +Lr+kd+d++++  +     gK++  r+  +    +++
  gi|298674118|ref|YP_003725868.1| 129 ITEHEAKMMIDSTSS---LRDKALMSVLYESAARVGDLSELRIKDIDFNKRDGTYLRLDGKTGARRIKLIA--STPY 200
                                       577788888887777...********************************998887889999999999886..5678 PP

                                       HHHHHHHHCHCCTTTSBSSBET.TSSB--HHHHHHHHHHHHHHCT-SSC--TTHHHHHHHHHHHHHCTSHHHHHHHH CS
                   Phage_integrase  80 lkellskaleeaeksellfask.rgkplsrqtvrkafkraveeagiekpltpHtlRhsfataLleagvdlrvvqkll 155
                                       ++ +l+++ e+++++  + +sk +++pl+ q vr+++k a+e+a+i+k+++pH +Rhs +t L+++   ++ +++++
  gi|298674118|ref|YP_003725868.1| 201 ITSWLNNHPEKENQNAPVWLSKiKNQPLKYQGVRRVLKIAAEKAQIQKDIHPHLFRHSRSTFLANHL-TPSQLESYM 276
                                       99******8888888888888889*****************************************98.56789**** PP

                                       T-SSCCHH.HHHHCCC CS
                   Phage_integrase 156 GHssistt.qiYthva 170
                                       G+++ s    iY+h++
  gi|298674118|ref|YP_003725868.1| 277 GWEHGSRMpAIYVHLS 292
                                       ******999*****75 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 3.8
                                       CHCCTTTSBSSBET..TSSB--HHHHHHHHHHHHHHCT-SSC--TTHHHHHHHHHHHHHCTSH CS
                   Phage_integrase  88 leeaeksellfask..rgkplsrqtvrkafkraveeagiekpltpHtlRhsfataLleagvdl 148
                                        ee+ek++  f ++  ++  ++++t  k+ +  + + +i++++   + R ++  +L+e  ++ 
  gi|298674118|ref|YP_003725868.1| 308 DEEDEKDDSEFTNRycPRCGKMNETTAKFCNVCGAALDITNAIEIDEKRNEVINKLMEMIANN 370
                                       556666666666666644445555555555555555566655555555555555555555555 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   3.1   5.7e-10   7.8e-07       1      23 []     322     344 ..     322     344 .. 0.95

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 5.7e-10
                     zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCGtpl 23 
                                       +Cp+CG+ ++ +akFC  CG+ l
  gi|298674118|ref|YP_003725868.1| 322 YCPRCGKMNETTAKFCNVCGAAL 344
                                       8*******************976 PP

>> Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   6.1e-10   8.5e-07       4      77 ..      33     101 ..      30     103 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 6.1e-10
                                       HHHHHHHTT-S-HHHHHHHHHHHHHHHHHHHH.TS--TTT--HHHHHHHHHS----------HHHHHHHHHHHH CS
                   Phage_int_SAM_1   4 fleyLikerglspnTlraYrrdLrrflkflaergkesleqlttedvraflaeleeeglsatslarrlsalrsFf 77 
                                       +++ L+ +++ sp+T+++Y++ L+ ++k+ ++     +e+ + +d+ + l + e++g++ ++ ++++  l++F 
  gi|298674118|ref|YP_003725868.1|  33 YKNILF-AKSSSPHTVLNYLNNLNQISKMCEK----PIENFDKDDIISLLGKIEQSGYKPSTKNLYRVNLKKFI 101
                                       655566.6788*********************....************************************96 PP

>> Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   6.8e-08   9.4e-05      10      76 ..      38     102 ..      29     104 .. 0.89
   2 !   10.2   0.0   0.00059      0.81       8      40 ..      79     111 ..      75     133 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 6.8e-08
                   Phage_int_SAM_4  10 rlaglserTiksYlsaikrflrflkkkapeeltkedieaYlnyLanerklsastqknalnalsffyk 76 
                                        ++  s+ T+ +Yl++++++ + ++ k++e ++k+di++ l +   +  +++st + ++ +l+ f k
  gi|298674118|ref|YP_003725868.1|  38 FAKSSSPHTVLNYLNNLNQISKMCE-KPIENFDKDDIISLLGKIE-QSGYKPSTKNLYRVNLKKFIK 102
                                       5677899******************.*****************87.999************998866 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00059
                   Phage_int_SAM_4   8 alrlaglserTiksYlsaikrflrflkkkapee 40 
                                       +++++g++++T + Y  ++k f++ ++ + p +
  gi|298674118|ref|YP_003725868.1|  79 KIEQSGYKPSTKNLYRVNLKKFIKDMELDVPTD 111
                                       7899********************998665554 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.5   8.6e-08   0.00012       1      23 [.     323     345 ..     322     362 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 8.6e-08
                               DZR   1 CpqCgeelppdarfCseCgtklk 23 
                                       Cp+Cg+ ++  a+fC+ Cg++l+
  gi|298674118|ref|YP_003725868.1| 323 CPRCGKMNETTAKFCNVCGAALD 345
                                       9*******************997 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   1.7     5e-07   0.00069       3      24 ..     321     342 ..     320     344 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5e-07
                       zf-ribbon_3   3 vrCPnCGa.plssddnvCpyCGt 24 
                                       ++CP+CG+ + ++ +++C  CG+
  gi|298674118|ref|YP_003725868.1| 321 RYCPRCGKmN-ETTAKFCNVCGA 342
                                       79********.***********7 PP

>> zf-RanBP  Zn-finger in Ran binding protein and others
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   2.7   6.6e-06    0.0091       7      26 ..     323     342 ..     322     343 .. 0.96

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.6e-06
                                       -SSS--EEESSSSB-TTT-- CS
                          zf-RanBP   7 CskClvqNfawstkCvaCqa 26 
                                       C+ C+ +N+ ++  C+ C+a
  gi|298674118|ref|YP_003725868.1| 323 CPRCGKMNETTAKFCNVCGA 342
                                       ******************99 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.7   9.6e-06     0.013      55      86 .]     306     341 ..     286     341 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.6e-06
                    zinc_ribbon_15  55 keiekkesse....kkeCknCgkeveeefkyCpkCg 86 
                                       ke e+ e+ +    +++C++Cgk  e   k+C  Cg
  gi|298674118|ref|YP_003725868.1| 306 KEDEEDEKDDseftNRYCPRCGKMNETTAKFCNVCG 341
                                       33333333335577*********************9 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.1   0.00021      0.29       2      10 ..     319     327 ..     319     331 .. 0.89
   2 ?    3.1   0.0     0.056        77       2      13 ..     333     344 ..     332     348 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00021
                     zf-NADH-PPase   2 thrFCgrCG 10 
                                       t+r+C+rCG
  gi|298674118|ref|YP_003725868.1| 319 TNRYCPRCG 327
                                       79******* PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.056
                     zf-NADH-PPase   2 thrFCgrCGapt 13 
                                       t +FC  CGa+ 
  gi|298674118|ref|YP_003725868.1| 333 TAKFCNVCGAAL 344
                                       5689*****985 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.2      0.01        14       1       8 [.     321     328 ..     321     333 .. 0.83
   2 ?    7.8   0.0    0.0022         3       1      11 [.     335     345 ..     335     357 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.01
                                       -B-TTT-- CS
                         Nudix_N_2   1 kFCsqCGt 8  
                                       ++C+ CG+
  gi|298674118|ref|YP_003725868.1| 321 RYCPRCGK 328
                                       8******7 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0022
                                       -B-TTT--B-E CS
                         Nudix_N_2   1 kFCsqCGtpve 11 
                                       kFC+ CG+++ 
  gi|298674118|ref|YP_003725868.1| 335 KFCNVCGAALD 345
                                       9*******976 PP

>> DUF4248  Domain of unknown function (DUF4248)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.7   3.7e+03      37      53 ..      76      92 ..      74     100 .. 0.81
   2 ?    9.3   0.1   0.00082       1.1      24      43 ..     360     379 ..     355     381 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.7
                           DUF4248 37 LkeeLtatgykkktrlf 53
                                      L  ++++ gyk++t+ +
  gi|298674118|ref|YP_003725868.1| 76 LLGKIEQSGYKPSTKNL 92
                                      67788999***999876 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00082
                           DUF4248  24 vrrLrrwIkrnpeLkeeLta 43 
                                       +++L++ I +npeL e L++
  gi|298674118|ref|YP_003725868.1| 360 INKLMEMIANNPELAEMLKE 379
                                       79****************97 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.2   0.00042      0.59      17      34 ..     321     340 ..     319     343 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00042
                                       EE-TTT--EESSS..S-CCC CS
                              RecR  17 rhCsrCgnlteed..lCaIC 34 
                                       r+C+rCg + e++   C++C
  gi|298674118|ref|YP_003725868.1| 321 RYCPRCGKMNETTakFCNVC 340
                                       8********7776447**** PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.6     0.029        40      21      31 ..     318     328 ..     313     332 .. 0.82
   2 ?    4.7   3.8     0.024        33      11      32 ..     323     343 ..     321     372 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.029
                      NOB1_Zn_bind  21 mtkkFCpkCGn 31 
                                        t ++Cp+CG+
  gi|298674118|ref|YP_003725868.1| 318 FTNRYCPRCGK 328
                                       6889******8 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.024
                      NOB1_Zn_bind  11 ChaCfkvtkdmtkkFCpkCGnk 32 
                                       C  C k+ +++t kFC+ CG +
  gi|298674118|ref|YP_003725868.1| 323 CPRCGKM-NETTAKFCNVCGAA 343
                                       7778875.678889******86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1144  (0.0638072); expected 358.6 (0.02)
Passed bias filter:                      703  (0.0392102); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2750.23
//
Query:       gi|298674119|ref|YP_003725869.1|  [L=78]
Description: hypothetical protein Metev_0142 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.072   12.5   0.8      0.077   12.4   0.8    1.1  1  Cytokin-bind  Cytokinin dehydrogenase 1, FAD and cytokinin bi


Domain annotation for each model (and alignments):
>> Cytokin-bind  Cytokinin dehydrogenase 1, FAD and cytokinin binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.8   4.3e-06     0.077     221     260 ..      26      65 ..       2      72 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.3e-06
                                       HHHHHHHHHHHHTT--EEESS---SSHHHHHHHHGHHHHH CS
                      Cytokin-bind 221 eqneeilefcekagikvkqYlphyesqeeWkkhfGakWer 260
                                       + +++ l++ e+++i++ qY    ++  e++++fG++Wer
  gi|298674119|ref|YP_003725869.1|  26 DGHKRSLNILESDQISIAQYCEDNQEWIEFMEKFGNDWER 65 
                                       2345556666688*************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1225  (0.0683251); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 494.17
//
Query:       gi|298674120|ref|YP_003725870.1|  [L=184]
Description: hypothetical protein Metev_0143 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.039   14.1   0.7      0.046   13.9   0.7    1.2  1  Maf1      Maf1 regulator


Domain annotation for each model (and alignments):
>> Maf1  Maf1 regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.7   2.6e-06     0.046      45     113 ..      64     136 ..      23     168 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.6e-06
                              Maf1  45 seslssssPfg......plsdkssrktlayLiatLnasfpdYDFsslrsseFkkekslksvinnidstLsslvee 113
                                       +  l+   P g       +   + +k l+ L   L +++ + ++  l +s+F  e  + +vi+++d++L ++ e+
  gi|298674120|ref|YP_003725870.1|  64 QYLLEGPLPAGisdsgrAVVGYKLKKNLTTLRFLLTYVYDESNYYMLMNSDFYHE-MIPQVIEHLDKKLVEM-ED 136
                                       2223333333355555577788899*****************************9.9*************93.32 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1139.90
//
Query:       gi|298674121|ref|YP_003725871.1|  [L=71]
Description: hypothetical protein Metev_0144 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.21s 00:00:00.55 Elapsed: 00:00:00.37
# Mc/sec: 574.82
//
Query:       gi|298674122|ref|YP_003725872.1|  [L=1277]
Description: hypothetical protein Metev_0145 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-20   73.0   0.6    4.9e-20   72.0   0.0    1.8  2  AAA_12           AAA domain
    7.5e-20   71.8   0.0    2.1e-10   40.8   0.0    2.3  2  AAA_11           AAA domain
    1.2e-12   47.9   0.0    2.2e-12   47.1   0.0    1.3  1  AAA_30           AAA domain
    3.2e-11   43.8   0.0    6.7e-11   42.7   0.0    1.6  1  AAA_19           AAA domain
      1e-05   25.1   0.0     0.0074   15.8   0.0    2.5  2  PhoH             PhoH-like protein
    0.00013   21.9   0.0    0.00078   19.3   0.0    2.4  2  Helicase_RecD    Helicase
    0.00023   20.8   0.1     0.0017   18.0   0.0    2.3  2  UvrD-helicase    UvrD/REP helicase N-terminal domain
    0.00034   20.4   0.0    0.00073   19.4   0.0    1.5  1  DEAD             DEAD/DEAH box helicase
    0.00038   20.2   0.0    0.00088   19.1   0.0    1.7  1  UvrD_C_2         UvrD-like helicase C-terminal domain
     0.0011   18.8   0.4       0.95    9.1   0.0    4.1  4  Viral_helicase1  Viral (Superfamily 1) RNA helicase
     0.0036   16.9   0.0      0.015   14.9   0.0    2.0  1  AAA_25           AAA domain
     0.0064   16.9   0.0      0.034   14.6   0.0    2.2  2  AAA              ATPase family associated with various cellul
  ------ inclusion threshold ------
      0.021   14.1   0.1        1.2    8.2   0.0    2.7  2  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.023   15.0   0.0      0.084   13.1   0.0    2.0  1  AAA_22           AAA domain
      0.026   14.5   0.0      0.079   13.0   0.0    1.8  1  ResIII           Type III restriction enzyme, res subunit
      0.032   14.0   0.2       0.16   11.7   0.0    2.2  2  AAA_24           AAA domain
      0.039   13.9   0.0       0.31   10.9   0.0    2.5  2  NACHT            NACHT domain
      0.074   12.6   0.1       0.16   11.5   0.1    1.5  1  AAA_7            P-loop containing dynein motor region
       0.14   11.3   0.7        1.9    7.6   0.3    2.6  2  PIF1             PIF1-like helicase


Domain annotation for each model (and alignments):
>> AAA_12  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.3       5.3     5e+03      34     105 ..     364     442 ..     361     450 .. 0.52
   2 !   72.0   0.0   5.2e-23   4.9e-20       5     194 ..     985    1203 ..     981    1205 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 5.3
                            AAA_12  34 psklfYkgkLkdaesvkkrele....aqealeeplep.lvfidvekseeekekke..ksyiNeeEaelvvklvekll 103
                                         k++Y+++ +++  +++++ e    +++ l + + +  +++d ++++e +e+k+  + ++ + E +l  +l+++++
  gi|298674122|ref|YP_003725872.1| 364 KGKQVYENTSNEKIYIASYPDEcteiQKKFLIDLYDElKTLHDYNREREWTEQKSlqTYVFDSYELQLFYDLLNEFT 440
                                       55566665555444444444443442122222222222455666666666666555566667777777777777776 PP

                            AAA_12 104 kk 105
                                       k+
  gi|298674122|ref|YP_003725872.1| 441 KE 442
                                       65 PP

  == domain 2  score: 72.0 bits;  conditional E-value: 5.2e-23
                            AAA_12    5 lferllkke...kekvvlLdtqYRmhpeIsrfpsklfYkgk.Lkdaesvkkrele.........aqealeeplep 66  
                                        +f  l ++    +  ++ L +++Rm++++srf+ +++Y+ + + + +++  ++le           + +e+ le 
  gi|298674122|ref|YP_003725872.1|  985 IFSYLRRRDnenNPYTQQLLENWRMNKTLSRFSAETLYGLDyIPATDNIGLQKLElgtplqangLPDSYEKLLES 1059
                                        555554444443677888999******************652666667777777778888777655666666666 PP

                            AAA_12   67 lvfidvekseeekekkeksyiNeeEaelvvklvekllkkgsee...............erkkigvitpYraqvel 126 
                                        +v  +        e+ + s+ Ne Eae+v++l   l ++  +e               +++ + +++p+++q+++
  gi|298674122|ref|YP_003725872.1| 1060 IVDSEYPLTVCILENVQASVENEIEAEIVARLSVLLRNNLLSEdwryypnneegdrkfWKDGLFIVSPHHSQIKT 1134
                                        666666666555566669*********************99999**************99*************** PP

                            AAA_12  127 lkkklkekeeeksekeievntvdgfQGrekdviilslVRsn...ekkeigflkderrlNValTRAksklii 194 
                                        ++++l++ ++ +++    v+tvd++QG+e +++i+s   s    + +e  f+ + +rlNV++TRAksk+++
  gi|298674122|ref|YP_003725872.1| 1135 IHNHLDSLRSWSHY--PFVDTVDKMQGQETQAVIVSYGVSDvetALNEAEFIYSLNRLNVSVTRAKSKCVL 1203
                                        ******87777655..9********************9997555667789******************986 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.0   2.3e-13   2.1e-10       2     119 ..     792     903 ..     791     922 .. 0.88
   2 !   29.4   0.0     7e-10   6.6e-07     198     258 ..     907     967 ..     899     969 .. 0.76

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 2.3e-13
                            AAA_11   2 lndsqreaiksalseseitliqGPPGtgKTktivellsqllsrrkseeeksakpriLvCapSNaAvDellerllrgl 78 
                                       + +sq +a++++++++  tl++GPPGtgKT ++++ + ++l++    +++ +  +i ++a+++aA+ +ll+++ +  
  gi|298674122|ref|YP_003725872.1| 792 FTSSQMKAFEHMVKNRL-TLVWGPPGTGKTYFLAKSVLNILKT---WKNNGYRFHIAITASTHAAIENLLLKIQE-- 862
                                       5789***********96.************8888877777554...46899999*********************.. PP

                            AAA_11  79 ldsegekykpkivRvgneeeriseavksvsleekvekrlek 119
                                       +++++   ++ + ++ ++++++s++  +v+ e++v++ l+ 
  gi|298674122|ref|YP_003725872.1| 863 ISKDYDFDNLPVYKLKSAKTAPSKESLQVCQEYEVDDLLNF 903
                                       9999999999999999999999************9998765 PP

  == domain 2  score: 29.4 bits;  conditional E-value: 7e-10
                            AAA_11 198 ivltTlsgagsklleklakkfdvviIDEAaqavEpstliPl..rlgakkvvLvGDpkQLpatv 258
                                       +v  T+++   k+ +k+   +d++i+DEA+q   +++   +      k++vL+GD  QLp+++
  gi|298674122|ref|YP_003725872.1| 907 VVGGTVNSL-DKVGRKIP-TIDMLIVDEASQVKPAEIALGMsiIDYGKRLVLAGDDLQLPPII 967
                                       566666666.55556665.9***********9888887777444444**************97 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.0   2.3e-15   2.2e-12       3     131 ..     793     966 ..     791     969 .. 0.76

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 2.3e-15
                            AAA_30   3 naeQaaavealltsgdrvavltGpAGtGKttalka....lreaweaag..grviglAptgkaAkvLa.......... 63 
                                       +++Q +a+e++++++  ++++ Gp+GtGKt+ l++    + ++w+++g  +++++ A+t++a ++L           
  gi|298674122|ref|YP_003725872.1| 793 TSSQMKAFEHMVKNR--LTLVWGPPGTGKTYFLAKsvlnILKTWKNNGyrFHIAITASTHAAIENLLlkiqeiskdy 867
                                       578********9888..9*************9986322256888888866678899*********886787777555 PP

                            AAA_30  64 ...................eelgieastiakllkrlk............................grarlepgtlli 93 
                                                          e+l              +                            g  ++ + ++li
  gi|298674122|ref|YP_003725872.1| 868 dfdnlpvyklksaktapskESL--------------QvcqeyevddllnfqhlvvggtvnsldkvG-RKIPTIDMLI 929
                                       5555544444444333333333..............1444555666666666999*****999743.456666**** PP

                            AAA_30  94 vDEagmvdtkqlaallkaaekagakvilvGDerQlasV 131
                                       vDEa+ v  +++a  +++++  g +++l+GD+ Ql+++
  gi|298674122|ref|YP_003725872.1| 930 VDEASQVKPAEIALGMSIIDY-GKRLVLAGDDLQLPPI 966
                                       ************988888866.**************98 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.0   7.1e-14   6.7e-11       1     143 [.     796     965 ..     796     968 .. 0.75

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 7.1e-14
                            AAA_19   1 qreave.alkekvllvtaGpGtGKTrvlkhivallvelggvkp..eeillvaftgrAakelrerlaalgae...... 68 
                                       q +a e  +k+++ lv ++pGtGKT+ l + v  ++++ + +    +i++ a t+ A ++l  +++++ ++      
  gi|298674122|ref|YP_003725872.1| 796 QMKAFEhMVKNRLTLVWGPPGTGKTYFLAKSVLNILKTWKNNGyrFHIAITASTHAAIENLLLKIQEISKDydfdnl 872
                                       678888799*****************9987765555544443333899999**********9999888888999999 PP

                            AAA_19  69 .......atTiHrlal............ldfddlltealelle........eaeeekklqeeellivDEfqdvdelq 118
                                              a+T  +               l+f++l                 + +  +k+   ++livDE+++v++ +
  gi|298674122|ref|YP_003725872.1| 873 pvyklksAKTAPSKESlqvcqeyevddlLNFQHL--------VvggtvnslD-KVGRKIPTIDMLIVDEASQVKPAE 940
                                       9888888777664433455666333333333333........1446666642.4556776677************** PP

                            AAA_19 119 yrLlkallgekkklllvGDpdQliy 143
                                        +L   + + +k+l+l GD+ Ql++
  gi|298674122|ref|YP_003725872.1| 941 IALGMSIIDYGKRLVLAGDDLQLPP 965
                                       ********999************97 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   7.8e-06    0.0074       6      45 ..     793     832 ..     790     876 .. 0.86
   2 !    6.5   0.0    0.0055       5.2     122     157 ..     927     962 ..     919     983 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.8e-06
                                       SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHH CS
                              PhoH   6 tkeQkeylealkkndivfaiGpaGtGKtylavalavealk 45 
                                       t++Q +++e + kn ++ + Gp GtGKty+     +++lk
  gi|298674122|ref|YP_003725872.1| 793 TSSQMKAFEHMVKNRLTLVWGPPGTGKTYFLAKSVLNILK 832
                                       789**************************87666666555 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0055
                                       EEEE-SGGG--HHHHHHHHTTB-TT-EEEEEE---- CS
                              PhoH 122 fvilDEAQnttkeqmkmfltRlGenskvvvtGdvtq 157
                                       ++i+DEA  ++++++   ++ ++ + ++v++Gd  q
  gi|298674122|ref|YP_003725872.1| 927 MLIVDEASQVKPAEIALGMSIIDYGKRLVLAGDDLQ 962
                                       68*******************************877 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0         4   3.8e+03     143     174 ..      43      73 ..      38      74 .. 0.81
   2 !   19.3   0.0   8.3e-07   0.00078       3     104 ..     812     938 ..     810     958 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4
                     Helicase_RecD 143 kekkrelreleleepiRyaegdplEkwlndlL 174
                                       +++ + + ++ l+++i ++e+  +Ek++++++
  gi|298674122|ref|YP_003725872.1|  43 QDQ-NPIMRVLLKAGIEWEEEVITEKLVDNVI 73 
                                       444.4788999***************999875 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 8.3e-07
                     Helicase_RecD   3 tAdRGRGKSaalGlalaaliaegk.....snilvtapskenvktlfeflakglealglke..........eekkkka 64 
                                        + +G+GK+  l++ + +++++ k      +i +ta +++++++l+  +++  ++ ++++          +  +k++
  gi|298674122|ref|YP_003725872.1| 812 WGPPGTGKTYFLAKSVLNILKTWKnngyrFHIAITASTHAAIENLLLKIQEISKDYDFDNlpvyklksakTAPSKES 888
                                       5789***********999998877778899********************999999999988776655431112222 PP

                     Helicase_RecD  65 ekaelrvr...........kqrieyiapdellklkeqa..................dllvvDEAAaipl 104
                                        +++   +                                                d+l+vDEA++++ 
  gi|298674122|ref|YP_003725872.1| 889 LQVCQ--EyevddllnfqhL-----------------VvggtvnsldkvgrkiptiDMLIVDEASQVKP 938
                                       22222..1335453333220.................1333333333345555666*********9864 PP

>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.66   6.2e+02     114     228 ..     373     613 ..     304     698 .. 0.59
   2 !   18.0   0.0   1.8e-06    0.0017       3      86 ..     794     881 ..     792     907 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.66
                                       SHTTTEEECHHHHHHCCHHHHHHHHHSC.HSHTTTTHHHHHHHHHHHHHHCCCCCH..................... CS
                     UvrD-helicase 114 ldpnfrildeedeedlkqqellkellek.saddslnldkkkleklikelsksrnik..................... 168
                                        +++++i+++ de + +q++ l +l ++ ++  ++n + + +e++    s++ ++                      
  gi|298674122|ref|YP_003725872.1| 373 SNEKIYIASYPDECTEIQKKFLIDLYDElKTLHDYNREREWTEQK----SLQTYVFdsyelqlfydllneftkesem 445
                                       445555555555445555555555554321111222222222211....1111111233334444444444444444 PP

                                       ............................................................................. CS
                     UvrD-helicase 169 ............................................................................. 168
                                                                                                                    
  gi|298674122|ref|YP_003725872.1| 446 apialrllfyfqntnlagqvehppteikhpiviltneidqlvslpvpfslrlpeiskvlqspdfnydfepsdlfwfe 522
                                       45555555555555555555555555555555555555555555555555555555555555555555555555555 PP

                                       .........................HHHCCCHHHHHCHHHHHHHHHHHTTCCTTHHCHSS......TSCSHHHHHHH CS
                     UvrD-helicase 169 .........................keelslskskaeelrelvskakekqlspkelkkaf......ekasdlqkkia 214
                                                                k els       ++ e +  + +++l++ ++k ++      e+++  q  ++
  gi|298674122|ref|YP_003725872.1| 523 qsnvmksdtitmvwdgtrpeavdwiKNELSKRLLATSSVLEGLRYIAKDKLITWSQKFKIpdsyyfENKELSQLSFI 599
                                       55555555555555555555555555555555555555555555555666666665555556665555555555566 PP

                                       HHHHHHHHHHHHHT CS
                     UvrD-helicase 215 eflkeyqeqkkeen 228
                                       + ++ y++ +++++
  gi|298674122|ref|YP_003725872.1| 600 TRYESYMTAMDIRE 613
                                       66666666666555 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 1.8e-06
                                       HHHHHHHHS..-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGG..EEEEESSHHHHHHHHHHHHHHHHHCCHH CS
                     UvrD-helicase   3 peqreaias..lggpilveAsAGsGKTfvlaerilrlikeeeiepdr..ilvvTFTnkAaeElkeRieealkkaeqe 75 
                                        +q +a ++   +  +lv   +G+GKT+ la+ +l+ +k+ + +  r  i +   T +A e l  +i+e+ k   + 
  gi|298674122|ref|YP_003725872.1| 794 SSQMKAFEHmvKNRLTLVWGPPGTGKTYFLAKSVLNILKTWKNNGYRfhIAITASTHAAIENLLLKIQEISKDYDFD 870
                                       6788888886556668999********************9986666666999999**************76666554 PP

                                       CTT-HHHHHHH CS
                     UvrD-helicase  76 ssdderlrlal 86 
                                       ++   +l+ a+
  gi|298674122|ref|YP_003725872.1| 871 NLPVYKLKSAK 881
                                       44444555544 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   7.7e-07   0.00073       1     133 [.     793     936 ..     793     942 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 7.7e-07
                                       -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS..TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet..kgktgpkalivePtreLaeqtlnnlkkfkkyid 75 
                                       t+ Q +a++++++++  lv ++ G+GKT   +  vl+i+ +t  ++  +  + i + t++ +e+ l +++++ k +d
  gi|298674122|ref|YP_003725872.1| 793 TSSQMKAFEHMVKNRLTLVWGPPGTGKTYFLAKSVLNIL-KTwkNNGYRFHIAITASTHAAIENLLLKIQEISKDYD 868
                                       5679********************************888.6666678888999*********************877 PP

                                       ......SEEEEEET.......TSSHHHHHHHHHTTCSEEEE.EHHHHHHHHHCTSSHCTTEEEEEEETHHHH CS
                                       ......xxxxxxxx.......xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  76 ......lrvlliig.......gvaardqlskldngvdivvg.tpgrlddllstgklnlsqvrflVlDEadrl 133
                                             +++++  +       +v ++ ++++l n  ++vvg t   ld++   +  ++  + +l++DEa ++
  gi|298674122|ref|YP_003725872.1| 869 fdnlpvYKLKSAKTapskeslQVCQEYEVDDLLNFQHLVVGgTVNSLDKVG--R--KIPTIDMLIVDEASQV 936
                                       556443222211111111122233333333333446666651445555432..3..4999********9765 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   9.3e-07   0.00088       3      51 ..    1150    1203 ..    1148    1204 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 9.3e-07
                          UvrD_C_2    3 yaltihkaQGsefpaVivfdpdlaaarmgel.......rrrlLYtavTRAreklil 51  
                                        +++t+ k QG+e +aViv   +  +  + +l       + + L + vTRA+ k++l
  gi|298674122|ref|YP_003725872.1| 1150 FVDTVDKMQGQETQAVIV--SYGVSDVETALneaefiySLNRLNVSVTRAKSKCVL 1203
                                        689***************..6666555555577899*****************998 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.73   6.8e+02     106     163 ..     213     270 ..     208     322 .. 0.72
   2 ?    0.0   0.0      0.62   5.8e+02       2      21 ..     810     829 ..     809     839 .. 0.81
   3 !    9.1   0.0     0.001      0.95      62     103 ..     924     966 ..     900    1008 .. 0.86
   4 ?    2.9   0.0     0.081        77     184     233 ..    1150    1204 ..    1092    1205 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.73
                   Viral_helicase1 106 nasfllahlpssl...shrvgrrttyllpsdvaeilsakvgteveversgelkvetepkgq 163
                                       +++fl++hlp+ l    +  +++ ++++    ++  ++++ +++e+ + +++    +++g+
  gi|298674122|ref|YP_003725872.1| 213 VEDFLRNHLPVILespIDKLSWHLYHRCELCEFYRHCKSEAEKNESVSMIPY---LSSNGK 270
                                       6789999999999888566777778888888888888885556665555555...444444 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.62
                   Viral_helicase1   2 vvhGvpGcGKStlirkllrt 21 
                                       +v G pG GK+  + k + +
  gi|298674122|ref|YP_003725872.1| 810 LVWGPPGTGKTYFLAKSVLN 829
                                       78899*******99887755 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.001
                   Viral_helicase1  62 kgkililDEylllhaGyill.laalskaklvilfGDplQipfh 103
                                       + + li+DE+ ++++++i l    ++  k ++l GD lQ p +
  gi|298674122|ref|YP_003725872.1| 924 TIDMLIVDEASQVKPAEIALgMSIIDYGKRLVLAGDDLQLPPI 966
                                       4689*****************99999999**********9976 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.081
                   Viral_helicase1  184 evttvhevqGltfdkVtl...vllketdlelis..esrenllvAlTRhrkslvil 233 
                                         v tv   qG++ + V++   v + et l++++   s + l v  TR+++++v++
  gi|298674122|ref|YP_003725872.1| 1150 FVDTVDKMQGQETQAVIVsygVSDVETALNEAEfiYSLNRLNVSVTRAKSKCVLF 1204
                                        6889************99444455555555555886799999********99875 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.6e-05     0.015      29     154 ..     802     936 ..     794     941 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.6e-05
                            AAA_25  29 llpagelallaGapgtGKttlaldlalavatGkpwlg.pvapeqgkVlyvsaEdsedelrrRlravgeal....... 97 
                                       +++++ l+l++G+pgtGKt ++   +l +++ ++  g ++       +  s+  + ++l  +++++ +++       
  gi|298674122|ref|YP_003725872.1| 802 HMVKNRLTLVWGPPGTGKTYFLAKSVLNILKTWKNNGyRF----HIAITASTHAAIENLLLKIQEISKDYdfdnlpv 874
                                       678999***********************98887777422....223334444445566667777777775555555 PP

                            AAA_25  98 .........rddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsra 154
                                                + ++ l+v++  +v++l    + +++ ++ + v+ l+++ ++++ ++++++D  s++
  gi|298674122|ref|YP_003725872.1| 875 yklksaktaPSKESLQVCQEYEVDDL----LNFQHLVVGGTVNSLDKVGRKIPTIDMLIVDEASQV 936
                                       55555555555566666654444332....234555677777778888888877888888877766 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       4.4   4.1e+03      58      71 ..     474     487 ..     458     489 .. 0.76
   2 !   14.6   0.0   3.6e-05     0.034       2      23 ..     810     832 ..     809     869 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4.4
                                       TSEEEEEETGGGHH CS
                               AAA  58 kpsilfiDEidala 71 
                                       +p +++  Eid+l+
  gi|298674122|ref|YP_003725872.1| 474 HPIVILTNEIDQLV 487
                                       4799999****997 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 3.6e-05
                                       EEESSTTSSHHH.HHHHHHHHHT CS
                               AAA   2 llyGppGtGKTl.lakavakelg 23 
                                       l++GppGtGKT+ lak+v + l+
  gi|298674122|ref|YP_003725872.1| 810 LVWGPPGTGKTYfLAKSVLNILK 832
                                       89*********7489***99985 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0013       1.2       2      26 ..     807     846 ..     806     938 .. 0.54
   2 ?    2.8   0.0      0.06        57     335     362 ..    1179    1206 ..    1153    1207 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0013
                           DUF2075   2 avvlVtGvaGtGKtvvllnllael...............e 26 
                                       ++ lV G +GtGKt+ l + + ++               +
  gi|298674122|ref|YP_003725872.1| 807 RLTLVWGPPGTGKTYFLAKSVLNIlktwknngyrfhiaiT 846
                                       5789**************9999997654433333333221 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.06
                           DUF2075  335 eekaqkllkNayrVLLtRGrkGlyiyae 362 
                                        +e +  + +N+++V  tR+ + ++++ +
  gi|298674122|ref|YP_003725872.1| 1179 NEAEFIYSLNRLNVSVTRAKSKCVLFLP 1206
                                        556677899****************975 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   8.9e-05     0.084       5     102 ..     806     935 ..     802     960 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.9e-05
                            AAA_22   5 agilvvtGesGtGKTt.llrrlleqldeeakaee...........erpevvfvtlpsstsskdllrellralglelk 69 
                                        ++++v+G++GtGKT+ l++ +l+ l+ +++  +           +               ++ll ++ ++ ++   
  gi|298674122|ref|YP_003725872.1| 806 NRLTLVWGPPGTGKTYfLAKSVLNILKTWKNNGYrfhiaitasthA-------------AIENLLLKIQEISKDYDF 869
                                       5789***********7255666666766644433443333333331.............333333333333332222 PP

                            AAA_22  70 a............................erlsseell.ealeqalrarav....ielliiDEaqh 102
                                       +                              l+ ++l+     + l++ ++    i +li+DEa  
  gi|298674122|ref|YP_003725872.1| 870 DnlpvyklksaktapskeslqvcqeyevdDLLNFQHLVvGGTVNSLDKVGRkiptIDMLIVDEASQ 935
                                       244444444444444444555555555554556666664444444444444777777777777765 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.4e-05     0.079      12      94 ..     800     883 ..     782     936 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.4e-05
                                       HHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.........-EEEEESSHHHHHHHHHHGGGGTGG.... CS
                            ResIII  12 ienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkee....kflflvprkslleqtleefkkflseayke 84 
                                        e ++      +++  l++ + GtGKT+ +ak + ++lk  k++    ++ + + + + +e +l ++++++++++ +
  gi|298674122|ref|YP_003725872.1| 800 FEHMV------KNRLTLVWGPPGTGKTYFLAKSVLNILKTWKNNgyrfHIAITASTHAAIENLLLKIQEISKDYDFD 870
                                       44443......566789**************9999998876666777799999999999999999999999888766 PP

                                       ...GEEEESSS-B CS
                            ResIII  85 ...igkkvsgdkk 94 
                                          + k +s ++ 
  gi|298674122|ref|YP_003725872.1| 871 nlpVYKLKSAKTA 883
                                       6653333333333 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       1.5   1.5e+03      51      75 ..     396     428 ..     375     441 .. 0.75
   2 ?   11.7   0.0   0.00017      0.16       5      33 ..     809     837 ..     805     940 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.5
                            AAA_24  51 dfldevvel........aaeladyktlviDtid 75 
                                       d++de+++l         +e++ ++t+v+D+++
  gi|298674122|ref|YP_003725872.1| 396 DLYDELKTLhdynrereWTEQKSLQTYVFDSYE 428
                                       34444444477777777789999*******985 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00017
                            AAA_24   5 iliyGpsgiGKTtlakelgpkplfidtek 33 
                                        l++Gp+g+GKT+++++   ++l    ++
  gi|298674122|ref|YP_003725872.1| 809 TLVWGPPGTGKTYFLAKSVLNILKTWKNN 837
                                       689***********998744444444444 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.3   2.2e+03      84      99 ..     387     407 ..     340     423 .. 0.74
   2 ?   10.9   0.0   0.00033      0.31       1      50 [.     807     855 ..     807     868 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.3
                                       E.....EEEE-STT-SS-TCH CS
                             NACHT  84 L.....lilDglDelvtdlgq 99 
                                             +++D +Del+t  + 
  gi|298674122|ref|YP_003725872.1| 387 TeiqkkFLIDLYDELKTLHDY 407
                                       34445599*******996555 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00033
                                       SCEEEEC-TTTCHHHHHHH.HHHHHCTS-SCCCC-SEEEEEETTTTTTS-. CS
                             NACHT   1 rlvilqGeaGsGKTtLlqk.lalawaegklpqgafklvFflslrelsrsgn 50 
                                       rl ++ G++G GKT++l+k +   ++++k ++  +++ + ++ ++   ++n
  gi|298674122|ref|YP_003725872.1| 807 RLTLVWGPPGTGKTYFLAKsVLNILKTWKNNG--YRFHIAITASTHAAIEN 855
                                       678999********987652667788888777..56766666666655555 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00017      0.16      29      77 ..     802     849 ..     793     865 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                             AAA_7  29 llknkkpvllvGptGtGKtviikd.llkkldkekylsltinfsaqtsanq 77 
                                       ++ +++ +l+ Gp GtGKt  + + +l+ l+  +++ +   f+   +a++
  gi|298674122|ref|YP_003725872.1| 802 HMVKNRLTLVWGPPGTGKTYFLAKsVLNILK--TWKNNGYRFHIAITAST 849
                                       455677899***********99997888888..77777777776666643 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.0       6.9   6.5e+03     164     234 ..      47     115 ..      42     119 .. 0.53
   2 ?    7.6   0.3     0.002       1.9      21     158 ..     805     968 ..     792     984 .. 0.57

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 6.9
                                       --BGC...CSCHHHH.--EEEE-S-STTTT...........HHHHHHHHHHHCT---CCCCHH......... CS
                              PIF1 164 eivaasikeSklWke.vkvlkLtknmRllsesldetekkelkeFskwllkigdGkineedeeealieiPedl 234
                                        i++  +k+   W+e v + kL  n+ + + +     +++ ++F + l+ i+d k  ++  +  +i++Pe++
  gi|298674122|ref|YP_003725872.1|  47 PIMRVLLKAGIEWEEeVITEKLVDNVIVPDGE--GALNERAHTFDETLKIIKDIKSGHNIYQ-PTIHVPEQF 115
                                       56666667777777766677777777776653..3333444444444444444333333322.356666665 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.002
                                       CTS-EEEEESTTSSCHHHH.HHHHHHCHC.....TCCCEEEEESSHHHHHCC.TSEECHHHHT-TTSSS-HHHHHHH CS
                              PIF1  21 kgklfFvtGsgGtgKtflw.kallkklrs.....egkivlavAssGvAalllegGrtahsrfkiplekdeestckik 91 
                                       k +l  v G  GtgKt+++ k +l++l++      +  ++ +As+  A  +l   ++       + ++    ++k +
  gi|298674122|ref|YP_003725872.1| 805 KNRLTLVWGPPGTGKTYFLaKSVLNILKTwknngYRFHIAITASTHAAIENL-LLKIQEISKDYDFDNLPVYKLKSA 880
                                       5677788999999999755267777777743322234578888887765554.234444444455555555555555 PP

                                       TSCCCHHHHHC-SEEEEECGGGSBH....HHHHHHHHHHHHHCT-..................-SCCC......C-E CS
                              PIF1  92 rgsklaellkktsliiwDEapmver....ecfealdrtlrdilkeke...............idkpFG......Gkt 143
                                       +    +e l+ ++   +D+    ++       ++ld++ r+i   +                +    G      Gk 
  gi|298674122|ref|YP_003725872.1| 881 KTAPSKESLQVCQEYEVDDLLNFQHlvvgGTVNSLDKVGRKIPTIDMlivdeasqvkpaeiaL----GmsiidyGKR 953
                                       555555555555555555543333301003345566665555443334444445555744440....3334444899 PP

                                       EEEE--TTS-----S CS
                              PIF1 144 vvlgGDfrQilPvie 158
                                       +vl+GD  Q++P+i+
  gi|298674122|ref|YP_003725872.1| 954 LVLAGDDLQLPPIIN 968
                                       999999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.97u 0.33s 00:00:01.30 Elapsed: 00:00:00.55
# Mc/sec: 7053.31
//
Query:       gi|298674123|ref|YP_003725873.1|  [L=286]
Description: hypothetical protein Metev_0146 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      0.007   17.1   4.5      0.016   16.0   4.5    1.6  1  Tnp_zf-ribbon_2  DDE_Tnp_1-like zinc-ribbon
  ------ inclusion threshold ------
       0.16   12.3   2.4       0.85   10.0   0.6    2.3  2  TSNAXIP1_N       Translin-associated factor X-interacting N-t


Domain annotation for each model (and alignments):
>> Tnp_zf-ribbon_2  DDE_Tnp_1-like zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   4.5   1.8e-06     0.016       3      24 ..       4      25 ..       2      27 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.8e-06
                   Tnp_zf-ribbon_2  3 CkvClkkkikkeTriiCqeCdv 24
                                      C+ C +kk+  e+++iC  C++
  gi|298674123|ref|YP_003725873.1|  4 CIKCGYKKRGSESNYICEDCQK 25
                                      ********************86 PP

>> TSNAXIP1_N  Translin-associated factor X-interacting N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.6   9.5e-05      0.85      22      62 ..      22      62 ..       5     112 .. 0.72
   2 ?    2.5   0.3     0.021   1.9e+02      15      80 ..      89     151 ..      80     161 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 9.5e-05
                        TSNAXIP1_N 22 rlqvyrevFedlieefkaYkdlLseIKkEYelyiahllesq 62
                                       +q ++e+F++l +e++   + L+ I  E +++++ l ++ 
  gi|298674123|ref|YP_003725873.1| 22 DCQKFSEIFDKLWNEVNYIFNNLEIINPETDKVLKFLSDTA 62
                                      5799**************9999**************99975 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.021
                        TSNAXIP1_N  15 edgpqekrlqvyrevFedlieefkaYkdlLseIKkEYelyiahllesqreaqylkaklktlsessd 80 
                                       ed+ +e  ++ y +  ++l+e  k + + L  +K EY  y  +l+ + ++ +   a+ +  ses d
  gi|298674123|ref|YP_003725873.1|  89 EDTINEVEVNKYTNTTKNLLEALKVFEE-LGIVKIEYSGYERILKIQNKAFK--VANAWRSSESLD 151
                                       5666677777788888888888899887.799999*9999888876655443..345555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       932  (0.0519828); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1953.04
//
Query:       gi|298674124|ref|YP_003725874.1|  [L=260]
Description: AAA ATPase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.6e-21   74.9   0.0    1.3e-20   74.1   0.0    1.3  1  AAA           ATPase family associated with various cellular 
    1.5e-05   25.0   0.0    3.2e-05   23.9   0.0    1.7  1  AAA_5         AAA domain (dynein-related subfamily)
    0.00018   22.0   0.0    0.00085   19.7   0.0    2.0  1  AAA_16        AAA ATPase domain
    0.00022   20.4   0.0     0.0016   17.7   0.0    2.0  1  DUF815        Protein of unknown function (DUF815)
    0.00025   21.1   0.0    0.00042   20.4   0.0    1.3  1  AAA_14        AAA domain
    0.00035   20.6   0.3      0.074   12.9   0.3    2.2  1  ATPase_2      ATPase domain predominantly from Archaea
    0.00085   19.7   0.0     0.0017   18.7   0.0    1.4  1  AAA_19        AAA domain
     0.0013   18.7   0.0     0.0022   17.9   0.0    1.4  1  NTPase_1      NTPase
     0.0014   19.2   0.0     0.0025   18.3   0.0    1.5  1  AAA_18        AAA domain
     0.0015   18.4   0.1     0.0034   17.2   0.1    1.7  1  AAA_11        AAA domain
     0.0039   16.2   0.0     0.0084   15.1   0.0    1.5  1  AAA_6         Hydrolytic ATP binding site of dynein motor reg
     0.0054   17.0   0.0      0.018   15.3   0.0    1.9  1  AAA_22        AAA domain
     0.0067   16.0   0.0      0.011   15.2   0.0    1.5  1  AAA_7         P-loop containing dynein motor region
  ------ inclusion threshold ------
      0.012   15.7   0.0       0.11   12.6   0.0    2.3  1  AAA_2         AAA domain (Cdc48 subfamily)
      0.017   14.9   0.0      0.033   14.0   0.0    1.5  1  RuvB_N        Holliday junction DNA helicase RuvB P-loop doma
      0.024   14.4   0.0      0.036   13.8   0.0    1.2  1  AAA_30        AAA domain
       0.03   14.7   0.0       0.12   12.8   0.0    2.0  2  RNA_helicase  RNA helicase
      0.053   13.9   0.1       0.56   10.6   0.0    2.5  3  AAA_17        AAA domain
      0.055   14.0   0.0      0.099   13.2   0.0    1.6  1  ABC_tran      ABC transporter
      0.062   13.5   0.0       0.12   12.5   0.0    1.6  1  AAA_33        AAA domain
       0.11   12.5   0.0       0.17   11.9   0.0    1.4  1  ResIII        Type III restriction enzyme, res subunit
       0.14   12.3   0.0        0.2   11.9   0.0    1.3  1  AAA_28        AAA domain
       0.19   11.7   0.1       0.93    9.4   0.1    2.0  1  NACHT         NACHT domain
        0.2   10.9   0.0       0.36   10.1   0.0    1.4  1  Zeta_toxin    Zeta toxin


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.1   0.0   1.8e-23   1.3e-20       2     124 ..      57     192 ..      56     196 .. 0.88

  Alignments for each domain:
  == domain 1  score: 74.1 bits;  conditional E-value: 1.8e-23
                                       EEESSTTSSHHHHHHHHHHHHT.........HEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS......TSEEEE CS
                               AAA   2 llyGppGtGKTllakavakelg.........vefleisgsellskyvgesekkirelfkeakeka......kpsilf 63 
                                       +l GppGtGKT ++++vake++         ++f  ++g+++    +g++ek+++++f+++   +      ++ il+
  gi|298674124|ref|YP_003725874.1|  57 ILLGPPGTGKTEVIRQVAKEIDknlqvhniiTYFALVDGANIAAPKWGDAEKNLKDVFQKINYLNqgegnsNKIILL 133
                                       799*****************853333444546699********999***************777777788777**** PP

                                       EETGGGHHHHH.TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTS CS
                               AAA  64 iDEidalaksr.sgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRf 124
                                       +D+i++l+ +r  + ++e + ++ + L++eld+ +   s+vi+++++n+p+ +d+a+l  R+
  gi|298674124|ref|YP_003725874.1| 134 FDDIESLVLKRgADLAKEWHYSINSILFHELDKINP--SNVIMCATSNKPELVDDAIL-TRL 192
                                       ***********66669999***************99..58******************.775 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   4.3e-08   3.2e-05       2      75 ..      56     138 ..      55     191 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 4.3e-08
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--..................--------...G- CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik.........ngttslvdsplvraar...eg 66 
                                       ++L+GppGtgK+e+++++a+ + ++++    +  +t+  l+ + +i+         n + ++++  + ++++   ++
  gi|298674124|ref|YP_003725874.1|  56 FILLGPPGTGKTEVIRQVAKEIDKNLQ---VHNIITYFALVDGANIAapkwgdaekNLKDVFQKINYLNQGEgnsNK 129
                                       89********************99985...56668888888888888777544444444444444444444488777 PP

                                       SEEEEESGG CS
                             AAA_5  67 eilvlDEve 75 
                                        il++D++e
  gi|298674124|ref|YP_003725874.1| 130 IILLFDDIE 138
                                       777788887 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.1e-06   0.00085      25      52 ..      54      84 ..      45     152 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.1e-06
                            AAA_16 25 elvllsGesGvGKsslvrellralekd...g 52
                                      +  +l G++G+GK+ ++r++++++ k+   +
  gi|298674124|ref|YP_003725874.1| 54 RGFILLGPPGTGKTEVIRQVAKEIDKNlqvH 84
                                      6789********************9994331 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   2.1e-06    0.0016      26     157 ..      20     186 ..       2     194 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.1e-06
                            DUF815  26 klddLvgidkqkealventeqflegl.pannv.....LLwGarGtGKSslvkallneyaeeg........Lrlie.. 86 
                                        ++ L  ++  ke++ +  + f +g+ + n+v     +L G  GtGK  +++ + +e+ ++          +l++  
  gi|298674124|ref|YP_003725874.1|  20 GIELLSQLKPTKEKIRKTCSYFFKGKyEGNDVpfrgfILLGPPGTGKTEVIRQVAKEIDKNLqvhniityFALVDga 96 
                                       46778999999*********999996345665555559********************9988889999997777522 PP

                            DUF815  87 .vek....edlkelpklvellr......erperfilfvDD...LsFeeeeeeyk....sLksvLeGslea.kpenvl 144
                                        ++     +  k+l++++++++       +++++il+ DD   L  +++ + +k    s+ s+L   l++ +p+nv+
  gi|298674124|ref|YP_003725874.1|  97 nIAApkwgDAEKNLKDVFQKINylnqgeGNSNKIILLFDDiesLVLKRGADLAKewhySINSILFHELDKiNPSNVI 173
                                       244322223446788888888766666567789*******444456666555541112678888888876489**** PP

                            DUF815 145 iyaTsNrRhLlpe 157
                                       + aTsN+ +L+ +
  gi|298674124|ref|YP_003725874.1| 174 MCATSNKPELVDD 186
                                       *******999976 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   5.6e-07   0.00042       6     125 ..      57     195 ..      53     199 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 5.6e-07
                            AAA_14   6 vitGaRrvGKTtllkqlikell...vkkesilyinldderd.......kkladpe.kllelilek.lke.....ekk 65 
                                       ++ G+  +GKT +++q++ke       ++ i y++l d  +       +     e +l +++++  + +     ++k
  gi|298674124|ref|YP_003725874.1|  57 ILLGPPGTGKTEVIRQVAKEIDknlQVHNIITYFALVDGANiaapkwgD----AEkNLKDVFQKInYLNqgegnSNK 129
                                       899**************98877886556778899999988844443331....222334444443322246677899 PP

                            AAA_14  66 tylflDEiqev.........pewekalkslvdeg.knldvivtGSnskllskeiatslagrvaeielypl 125
                                        +l++D i  +         +ew   ++s++ ++ +     +  Sn  +     + +l++ +   +lyp+
  gi|298674124|ref|YP_003725874.1| 130 IILLFDDIESLvlkrgadlaKEWHYSINSILFHElD----KINPSNVIMCATSNKPELVDDAILTRLYPI 195
                                       99*********9****************99987722....355666666666666667777666666665 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.3    0.0001     0.074      27     151 ..      60     158 ..      52     181 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0001
                          ATPase_2  27 GpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekalgiavpkaeleeilkeksklvf 103
                                       Gp g GKt ++++++++ ++         +l+ ++i ++              + ++ia pk       +++ k+vf
  gi|298674124|ref|YP_003725874.1|  60 GPPGTGKTEVIRQVAKEIDK---------NLQVHNIITYFAL----------VDGANIAAPKWGD---AEKNLKDVF 114
                                       55555555555555555522.........3333443333333..........1112333333222...135678888 PP

                          ATPase_2 104 kaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnlies 151
                                       ++i++l ++ + +  kii+++D++  l+   l++ ++l ke  + i s
  gi|298674124|ref|YP_003725874.1| 115 QKINYL-NQGEGNSNKIILLFDDIESLV---LKRGADLAKEWHYSINS 158
                                       888765.445566677999999999999...77777777776554433 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.3e-06    0.0017      13      43 ..      56      85 ..      49     117 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.3e-06
                            AAA_19 13 llvtaGpGtGKTrvlkhivallvelggvkpe 43
                                      ++++++pGtGKT+v++++ +++ ++ +v+ +
  gi|298674124|ref|YP_003725874.1| 56 FILLGPPGTGKTEVIRQVAKEIDKNLQVH-N 85
                                      789*******************9999885.3 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0     3e-06    0.0022       3      45 ..      57      98 ..      55     146 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3e-06
                                      EEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE------- CS
                          NTPase_1  3 fiTGppGvGKtTlvkkvlellkssgvkvgGfyteevreggrri 45
                                      ++ GppG+GKt ++++v++++ +++++v+ ++t     +g  i
  gi|298674124|ref|YP_003725874.1| 57 ILLGPPGTGKTEVIRQVAKEI-DKNLQVHNIITYFALVDGANI 98
                                      788******************.899********9988777766 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   3.4e-06    0.0025       2      25 ..      57      95 ..      57     180 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.4e-06
                            AAA_18  2 lltGtpGvGKttlakeLskrl.gf..............g 25
                                      +l G+pG+GKt++ + ++k+  ++              g
  gi|298674124|ref|YP_003725874.1| 57 ILLGPPGTGKTEVIRQVAKEIdKNlqvhniityfalvdG 95
                                      689****************97766785444443333330 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   4.5e-06    0.0034      21      65 ..      57     180 ..      45     249 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.5e-06
                            AAA_11  21 liqGPPGtgKTktivellsqll....................................................... 42 
                                       ++ GPPGtgKT +i ++ +++                                                        
  gi|298674124|ref|YP_003725874.1|  57 ILLGPPGTGKTEVIRQVAKEIDknlqvhniityfalvdganiaapkwgdaeknlkdvfqkinylnqgegnsnkiill 133
                                       678*****************987777777777777777777777777776666666666666665555555555555 PP

                            AAA_11  43 .........sr............rk...seeeksakpriLvCapSNa 65 
                                                +r            ++    e +k ++ ++ +Ca SN+
  gi|298674124|ref|YP_003725874.1| 134 fddieslvlKRgadlakewhysiNSilfHELDKINPSNVIMCATSNK 180
                                       55444444411334444444444113335566777777777777776 PP

>> AAA_6  Hydrolytic ATP binding site of dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.1e-05    0.0084      37      65 ..      58      86 ..      52      98 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.1e-05
                             AAA_6 37 paGpagtGKtEtvkdLakalakqvvvfnc 65
                                      + Gp gtGKtE ++++ak++ k + v n+
  gi|298674124|ref|YP_003725874.1| 58 LLGPPGTGKTEVIRQVAKEIDKNLQVHNI 86
                                      67********************9999986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.4e-05     0.018       9      37 ..      57      85 ..      54     172 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.4e-05
                            AAA_22  9 vvtGesGtGKTtllrrlleqldeeakaee 37
                                      ++ G++GtGKT ++r+++++ d+  +  +
  gi|298674124|ref|YP_003725874.1| 57 ILLGPPGTGKTEVIRQVAKEIDKNLQVHN 85
                                      688****************9875443333 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.5e-05     0.011      36      69 ..      56      89 ..      29     139 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.5e-05
                             AAA_7 36 vllvGptGtGKtviikdllkkldkekylsltinf 69
                                      ++l Gp GtGKt +i+++ k++dk+  + ++i+ 
  gi|298674124|ref|YP_003725874.1| 56 FILLGPPGTGKTEVIRQVAKEIDKNLQVHNIITY 89
                                      6899*******************66666666655 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00014      0.11       6      89 ..      56     147 ..      52     195 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS............ CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG............ 70 
                                       ++llgp g+Gkte+ +++a+ ++    k+l + +  ++        lv+   +a+p    ae++             
  gi|298674124|ref|YP_003725874.1|  56 FILLGPPGTGKTEVIRQVAKEID----KNLQVHNIITYFA------LVDGANIAAPKWGDAEKNLkdvfqkinylnq 122
                                       899**********9999999888....4566666666655......4444444444433333333444444444444 PP

                                       ........EEEEETGGG---------- CS
                             AAA_2  71 ........ivllDEidKihpkessgad 89 
                                               i+l+D+i+      + gad
  gi|298674124|ref|YP_003725874.1| 123 gegnsnkiILLFDDIESLVL--KRGAD 147
                                       44455788888999987666..44444 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.4e-05     0.033      35      63 ..      55      83 ..      29      94 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.4e-05
                            RuvB_N 35 hvllyGpPGlGkttlakiiakelgvklki 63
                                        +l GpPG Gkt + + +ake++ +l++
  gi|298674124|ref|YP_003725874.1| 55 GFILLGPPGTGKTEVIRQVAKEIDKNLQV 83
                                      56899*******************99986 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.8e-05     0.036      22      45 ..      57      80 ..      53     111 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.8e-05
                            AAA_30 22 vltGpAGtGKttalkalreaweaa 45
                                      +l Gp+GtGKt +++++++ ++++
  gi|298674124|ref|YP_003725874.1| 57 ILLGPPGTGKTEVIRQVAKEIDKN 80
                                      789**************7766554 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00016      0.12       2      29 ..      57      84 ..      56      98 .. 0.85
   2 ?   -1.9   0.0         6   4.5e+03       8      25 ..     123     140 ..     117     175 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00016
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklk 29
                                      +l Gp+g+GK+ +++++ak++ k+l+ +
  gi|298674124|ref|YP_003725874.1| 57 ILLGPPGTGKTEVIRQVAKEIDKNLQVH 84
                                      689******************9888544 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 6
                      RNA_helicase   8 geGKStlakeLakallkk 25 
                                       geG S+ +  L +++++ 
  gi|298674124|ref|YP_003725874.1| 123 GEGNSNKIILLFDDIESL 140
                                       666666666666666533 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00075      0.56       1      20 [.      59      78 ..      59      87 .. 0.87
   2 ?   -0.9   0.0       2.7     2e+03      99     119 ..     124     144 ..      91     152 .. 0.63
   3 ?   -0.6   0.0       2.2   1.7e+03      59     114 ..     203     257 ..     163     260 .] 0.61

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00075
                                      EE-TTSSHHHHHHHHHHHHT CS
                            AAA_17  1 lGgPGsGKgtqceklvekyg 20
                                      lG+PG GK++++++++++++
  gi|298674124|ref|YP_003725874.1| 59 LGPPGTGKTEVIRQVAKEID 78
                                      7***************9984 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.7
                                       HH..SEEEEEE--HHHHHHHH CS
                            AAA_17  99 elkpdaiilleadpeeilerr 119
                                       e + ++iill +d e ++ +r
  gi|298674124|ref|YP_003725874.1| 124 EGNSNKIILLFDDIESLVLKR 144
                                       334678888888888777666 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 2.2
                                       HHHHHHHHHHHHSSEEEEEE-SEEEET.TEEEESSHHHHHHHH..SEEEEEE--HHH CS
                            AAA_17  59 keaaekiaeeakkkgvlvdghprikeq.agfldglpkevleelkpdaiilleadpee 114
                                       ++++ k+++  +++gv  d +  +k + ++ l++l+  +++++  ++++++e+ + e
  gi|298674124|ref|YP_003725874.1| 203 DQLIVKVENILNNSGVTGDDFELVKSNiQKRLETLENPTIRDA--QHFTIVECIENE 257
                                       4455555555556666666666555552444677777777777..777777776665 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00013     0.099      15      80 ..      57     147 ..      53     237 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00013
                                       EEEESTTSSHHHHHHHHTTSS--..SEEEE.....EETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH..... CS
                                       xxxxxxxxxxxxxxxxxxxxxxx..xxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..... RF
                          ABC_tran  15 aivGenGaGKStLlkllagllkp..teGei.....lldgkdlkeqeleslrkeigvlpqepqlfpeltvren..... 79 
                                        ++G+ G+GK+ +++ +a++ ++  +  +i     l+dg+++   ++  ++k+++ ++q+ +  ++ +  +n     
  gi|298674124|ref|YP_003725874.1|  57 ILLGPPGTGKTEVIRQVAKEIDKnlQVHNIityfaLVDGANIAAPKWGDAEKNLKDVFQKINYLNQGEGNSNkiill 133
                                       599*****************997664444479999999******999999999999999966555554444446666 PP

                                       .............H CS
                                       .............x RF
                          ABC_tran  80 .............e 80 
                                                    +
  gi|298674124|ref|YP_003725874.1| 134 fddieslvlkrgaD 147
                                       66665555555550 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00016      0.12       3      22 ..      57      76 ..      56     122 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                            AAA_33  3 llvGlpGsGKstlaerllkk 22
                                      +l G+pG+GK+ ++++++k+
  gi|298674124|ref|YP_003725874.1| 57 ILLGPPGTGKTEVIRQVAKE 76
                                      789**************987 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00023      0.17      25     113 ..      54     139 ..      18     177 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00023
                                       SEEEEEESTTSTHHHHHHHHHHHH-S........-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--.. CS
                            ResIII  25 krglikmaTGtGKTlvaaklierllkkgkee...kflflvprkslleqtleefkkflseaykeigkkvsgdkkkake 98 
                                       + +++  + GtGKT v+ ++++++ k+ +       + lv++ ++      + +k l++ +++i+   +g+++++  
  gi|298674124|ref|YP_003725874.1|  54 RGFILLGPPGTGKTEVIRQVAKEIDKNLQVHniiTYFALVDGANIAAPKWGDAEKNLKDVFQKINYLNQGEGNSN-- 128
                                       356688899*****************9999855555678999988887777777777777766665555555555.. PP

                                       .....-SEEEEEHHH CS
                            ResIII  99 kdstnkkilvttiqs 113
                                           ++ +l+  i+s
  gi|298674124|ref|YP_003725874.1| 129 ----KIILLFDDIES 139
                                       ....44444444444 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00027       0.2       3      23 ..      57      80 ..      55     115 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00027
                            AAA_28  3 vitGgestGKTtlleaLaar...g 23
                                      +++G+++tGKT ++++ a++   +
  gi|298674124|ref|YP_003725874.1| 57 ILLGPPGTGKTEVIRQVAKEidkN 80
                                      799*************99754444 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1    0.0012      0.93       3      31 ..      56      84 ..      54     188 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0012
                                      EEEEC-TTTCHHHHHHHHHHHHCTS-SCC CS
                             NACHT  3 vilqGeaGsGKTtLlqklalawaegklpq 31
                                       il G++G GKT  ++++a ++ ++ + +
  gi|298674124|ref|YP_003725874.1| 56 FILLGPPGTGKTEVIRQVAKEIDKNLQVH 84
                                      5899****************998876555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00048      0.36      20      44 ..      57      81 ..      54      88 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00048
                        Zeta_toxin 20 llgGqpGAGKselaellkdelerqg 44
                                      +l G pG GK+e+++ +++e++++ 
  gi|298674124|ref|YP_003725874.1| 57 ILLGPPGTGKTEVIRQVAKEIDKNL 81
                                      67799***************97654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 1658.67
//
Query:       gi|298674125|ref|YP_003725875.1|  [L=253]
Description: hypothetical protein Metev_0148 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0076   16.3   0.0        6.4    6.9   0.0    2.6  2  Trans_reg_C     Transcriptional regulatory protein, C termina
  ------ inclusion threshold ------
      0.017   14.6   0.2       0.62    9.5   0.0    2.3  2  HEPN_AbiU2      AbiU2
      0.046   13.5   0.0        1.2    8.8   0.0    2.8  3  DNA_pol3_delta  DNA polymerase III, delta subunit
       0.14   11.7   0.2         13    5.2   0.1    2.1  2  Ebp2            Eukaryotic rRNA processing protein EBP2
       0.75    9.6   2.9        4.9    7.0   0.1    2.2  2  BRCT_assoc      Serine-rich domain associated with BRCT


Domain annotation for each model (and alignments):
>> Trans_reg_C  Transcriptional regulatory protein, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0018       6.4       4      27 ..      57      80 ..      54      96 .. 0.86
   2 !    6.6   0.0    0.0023       8.4       3      27 ..     183     207 ..     181     225 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0018
                                      EE-SHHHHHHHHHHHHTTTSEEEH CS
                       Trans_reg_C  4 veltpkefklLelLlenpgrvvsr 27
                                      +el+pk ++lL++++ n+gr +  
  gi|298674125|ref|YP_003725875.1| 57 LELKPKTYSLLRTMIGNRGRTFGA 80
                                      79******************9876 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0023
                                       EEE-SHHHHHHHHHHHHTTTSEEEH CS
                       Trans_reg_C   3 eveltpkefklLelLlenpgrvvsr 27 
                                       +++ltpk f+lL++ + n+gr +  
  gi|298674125|ref|YP_003725875.1| 183 NYTLTPKTFSLLRYTIGNKGRSFGA 207
                                       589****************998765 PP

>> HEPN_AbiU2  AbiU2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00017      0.62     155     186 ..      36      65 ..      23      76 .. 0.79
   2 ?    2.8   0.1     0.021        74     154     185 ..     207     239 ..     196     249 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00017
                        HEPN_AbiU2 155 ityddieeliddaleivnklllllfgtsfdyd 186
                                        ty++ +elid +++i+n ++l l     +y+
  gi|298674125|ref|YP_003725875.1|  36 GTYPEYNELIDLIKSILNNVNLELK--PKTYS 65 
                                       69********************994..55555 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.021
                        HEPN_AbiU2 154 d.ityddieeliddaleivnklllllfgtsfdy 185
                                       + +ty+   +  ++++ei+nk++  +++t   +
  gi|298674125|ref|YP_003725875.1| 207 AaHTYKYSVNNSKELEEIINKINEWFNNTGINW 239
                                       25888888899999*********9999875544 PP

>> DNA_pol3_delta  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00035       1.2     124     160 ..      37      73 ..      28      77 .. 0.88
   2 ?    0.1   0.0      0.16   5.9e+02     127     160 ..     167     200 ..     154     203 .. 0.85
   3 ?   -0.5   0.0      0.26   9.4e+02      76      92 ..     214     230 ..     209     238 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00035
                                       ----TTTHHHHHHHHHHHTT-EE-HHHHHHHHHHHTT CS
                    DNA_pol3_delta 124 ktlkeeelkkwiqkraqelglkiekealelLlelven 160
                                       + ++ +el++ i++++++ +l++++++ +lL  +++n
  gi|298674125|ref|YP_003725875.1|  37 TYPEYNELIDLIKSILNNVNLELKPKTYSLLRTMIGN 73 
                                       568999*************************999988 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.16
                                       -TTTHHHHHHHHHHHTT-EE-HHHHHHHHHHHTT CS
                    DNA_pol3_delta 127 keeelkkwiqkraqelglkiekealelLlelven 160
                                       k   l +++ ++++ ++  +++++++lL + ++n
  gi|298674125|ref|YP_003725875.1| 167 KVRGLSDYVYNKTSPKNYTLTPKTFSLLRYTIGN 200
                                       6678899999******************999887 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.26
                                       -TTHHHHHHHHTTT--S CS
                    DNA_pol3_delta  76 nekllkeLeeylsnlpe 92 
                                       + ++ keLee++++++e
  gi|298674125|ref|YP_003725875.1| 214 SVNNSKELEEIINKINE 230
                                       56778888888887764 PP

>> Ebp2  Eukaryotic rRNA processing protein EBP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.006        22      24      66 ..      82     128 ..      72     133 .. 0.80
   2 ?    5.2   0.1    0.0037        13      24      58 ..     209     247 ..     199     252 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.006
                              Ebp2  24 kkkkltinnkeaLkekleeikl....kklpwvetldltskpaeiedv 66 
                                       ++ k++ n++++Lk++l+ ++     ++l w+   d+++ +++ +++
  gi|298674125|ref|YP_003725875.1|  82 HTYKYNLNDNSELKQILNLVNEwfqnQNLYWIRDFDVVYCKNAQKRI 128
                                       4568899***********999889999**********9974444344 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0037
                              Ebp2  24 kkkkltinnkeaLkekleeikl....kklpwvetldlts 58 
                                       ++ k+++nn+++L+e++++i+     + ++w + ld+ +
  gi|298674125|ref|YP_003725875.1| 209 HTYKYSVNNSKELEEIINKINEwfnnTGINWWDDLDIET 247
                                       457889**************9989888889999988865 PP

>> BRCT_assoc  Serine-rich domain associated with BRCT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.4     0.027        97      30      46 ..      93     109 ..      81     115 .. 0.84
   2 ?    7.0   0.1    0.0014       4.9      29      44 ..     219     234 ..     207     237 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.027
                        BRCT_assoc  30 tlnssIqKVNeWfsrsd 46 
                                        l++ +  VNeWf   +
  gi|298674125|ref|YP_003725875.1|  93 ELKQILNLVNEWFQNQN 109
                                       68899999*****8765 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0014
                        BRCT_assoc  29 itlnssIqKVNeWfsr 44 
                                       + l++ I K+NeWf  
  gi|298674125|ref|YP_003725875.1| 219 KELEEIINKINEWFNN 234
                                       679999********76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       959  (0.0534888); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1822.90
//
Query:       gi|298674126|ref|YP_003725876.1|  [L=634]
Description: SMC domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00026   20.7  59.3     0.0061   16.2  16.1    3.7  4  Filament        Intermediate filament protein
    0.00028   21.4  19.2    0.00028   21.4  19.2    3.2  1  Fez1            Fez1
    0.00033   20.7  21.2    0.00033   20.7  21.2    5.4  4  BRE1            BRE1 E3 ubiquitin ligase
     0.0013   17.4  21.7     0.0013   17.4  21.7    2.1  2  Macoilin        Macoilin family
     0.0016   18.6  19.0     0.0016   18.6  19.0    4.0  4  TMF_TATA_bd     TATA element modulatory factor 1 TATA binding
     0.0039   15.9  59.5     0.0055   15.4  17.8    2.9  3  AAA_13          AAA domain
     0.0083   16.2  50.5       0.04   13.9   9.6    4.2  4  Laminin_II      Laminin Domain II
  ------ inclusion threshold ------
      0.021   15.1  51.7       0.13   12.4  21.2    3.1  3  ATG16           Autophagy protein 16 (ATG16)
      0.084   12.9  41.1        1.3    9.1   5.7    5.0  5  DUF1664         Protein of unknown function (DUF1664)
       0.12   11.3  64.2       0.13   11.2  25.0    3.5  3  Spc7            Spc7 kinetochore protein
       0.13   12.9  49.9        1.1   10.0  16.6    4.8  5  HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interac
       0.15   11.8  47.9      0.055   13.3  17.2    2.7  2  ERM             Ezrin/radixin/moesin family
       0.18   12.4  21.4      0.068   13.8   1.6    5.4  5  SlyX            SlyX
       0.36   10.4  59.7        1.4    8.5  25.6    2.5  2  DUF4795         Domain of unknown function (DUF4795)
       0.45   10.5  65.9       0.11   12.5  27.8    3.4  3  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
       0.47   10.5  68.8      0.044   13.9  22.3    3.3  3  UPF0242         Uncharacterised protein family (UPF0242) N-te
        0.6   10.4  27.6        2.7    8.3   2.9    4.8  4  DUF948          Bacterial protein of unknown function (DUF948
        1.2    9.6  81.6      0.026   15.0  31.1    4.4  2  AAA_23          AAA domain
        2.4    8.4  58.8        1.2    9.4  25.5    3.3  2  zf-C4H2         Zinc finger-containing protein
        2.5    7.9  59.4      0.076   12.8  11.6    5.1  6  DUF724          Protein of unknown function (DUF724)
        2.8    8.0  14.2      0.021   14.9   2.5    2.6  2  DUF1644         Protein of unknown function (DUF1644)
        3.1    8.4  68.4        5.8    7.4  22.1    4.6  4  APG6_N          Apg6 coiled-coil region
        3.8    6.8  25.1       0.26   10.6   7.3    3.0  3  Aminopep        Putative aminopeptidase
        5.9    6.6  15.5       0.12   12.1   0.8    4.1  4  DUF3287         Protein of unknown function (DUF3287)
        6.4    5.9  49.6        1.8    7.7  15.0    3.6  4  TMPIT           TMPIT-like protein
        9.7    6.5  60.8        4.5    7.6  20.9    4.3  3  DUF5082         Domain of unknown function (DUF5082)


Domain annotation for each model (and alignments):
>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   9.1    0.0084       5.8     193     273 ..     151     232 ..     147     239 .. 0.82
   2 ?    4.5   3.3     0.033        23     165     228 ..     214     275 ..     208     278 .. 0.59
   3 !   16.2  16.1   8.9e-06    0.0061      19     139 ..     250     373 ..     236     376 .. 0.86
   4 !    7.9  19.8    0.0029         2      55     200 ..     373     525 ..     371     532 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0084
                                       XXXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHH CS
                          Filament 193 ykskleelqeaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerle.aeleklqeklsele 268
                                       +   +eel + a++  +++ s k+ +++ + + ++l +ele++kkqk+ + +  +e+ ++++ ++++++ e+ +++ 
  gi|298674126|ref|YP_003725876.1| 151 FADNYEELYNLAQSYINDITSKKTSLNKRKSKAKELASELEKVKKQKEEIDQDREEISKKVNdNDIREIVEERKSIF 227
                                       778899**************************************************988765145555555555555 PP

                                       HHHHH CS
                          Filament 269 eelae 273
                                       e++++
  gi|298674126|ref|YP_003725876.1| 228 EKIQN 232
                                       55555 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.033
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHH CS
                          Filament 165 ldLteilkeiraqyeelaeknreeaeewykskleelqeaaeknsealrsakeeitelrrqiqsl 228
                                        d+ ei++e ++ +e++ ++ ++++++ y+ ++++ +++++k++e +++ +e++++l+++i+ l
  gi|298674126|ref|YP_003725876.1| 214 NDIREIVEERKSIFEKI-QNFHRDLNDIYN-RINNKKTKIQKKEEIVNELNENLSNLNKEIEGL 275
                                       45666666666666553.445556666664.566666666666666666666666666666655 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 8.9e-06
                                       XXXXXXXXXXXXXXXXXXXXXXX.XXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament  19 kVraLEqenkeLeakieeleekk.saevsklkelyekeleelrkqldeltkerarlqleldnlreeledlrkkyeke 94 
                                       k+++ E+  +eL+ ++++l+++     vs+ k+ + ++++e  +++++l++++a +++ ++  + +  +l++ +++e
  gi|298674126|ref|YP_003725876.1| 250 KIQKKEEIVNELNENLSNLNKEIeGLDVSNYKKKFDQKVNENTSKIESLKEDKAEVNASINLFQSAKLKLKNENKSE 326
                                       6777777788888888888777438899************************************9999999877777 PP

                                       ..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament  95 ..lnkreevEaelkalrkdldeatlarvdLekkvesLkeelaflkkv 139
                                           + e+ + +++ + k l+ ++ ++ ++e++++sL+ee+a++k+ 
  gi|298674126|ref|YP_003725876.1| 327 ttCILCEQGNLNINVIDKTLESLNDKKRNIESEIQSLNEEIAIMKNK 373
                                       334577888999*********************************86 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.0029
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXX CS
                          Filament  55 eleelrkqldeltkerarlqleldnlreeledlrkkyekelnkreevEaelkalrkdldea.tlarvdLekkvesLk 130
                                       +l++l ++ ++ ++e  rl+ el++++ +l++lr+ ++++  +++e E++lk+l  + + +  la+ d+ kk+++L 
  gi|298674126|ref|YP_003725876.1| 373 KLNNLESEKNKKEQEIFRLEHELEDTKSDLKTLRNEVKNDDDLKNEKEQTLKELENEYERLkELAKGDIVKKIDEL- 448
                                       6778888888888999999999999999999999999999999999999999999666664257777776666544. PP

                                       XXXXXXXXXXXXXXXXXXXXXX........XXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament 131 eelaflkkvheeEvkelqkqvs........eqvlvevdaarkl..dLteilkeiraqyeelaeknreeaeewykskl 197
                                          +   +  +eE+  ++++++           +v++d+a  +  d    l+e+++  +e+ ++ r+ea + +++k+
  gi|298674126|ref|YP_003725876.1| 449 ---EAKSSELQEEIGSINEKIRsttgeeviYGENVDTDTALAIynDWLYYLEELKEFANEMYSSHRNEARKKFNEKI 522
                                       ...34444445555555555541111000344455555544331146677888888888888888888888888888 PP

                                       XXX CS
                          Filament 198 eel 200
                                       + l
  gi|298674126|ref|YP_003725876.1| 523 SVL 525
                                       766 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4  19.2   4.1e-07   0.00028      11     115 ..     366     500 ..     357     555 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 4.1e-07
                              Fez1  11 EislLKqQLkdsqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseae.llr 86 
                                       Ei+++K+ L +  +e ++k +ei+ l  +l +++++l++  +e+k+ ++  +ek++ l+++ene +r k+ a+  + 
  gi|298674126|ref|YP_003725876.1| 366 EIAIMKNKLNNLESEKNKKEQEIFRLEHELEDTKSDLKTLRNEVKNDDDLKNEKEQTLKELENEYERLKELAKgDIV 442
                                       9******************************************************************9776542467 PP

                              Fez1  87 ekvekleeelkelreelselsleeeeaa.............................l 115
                                       +k+++le++ +el+ee+ + +++ ++++                             +
  gi|298674126|ref|YP_003725876.1| 443 KKIDELEAKSSELQEEIGSINEKIRSTTgeeviygenvdtdtalaiyndwlyyleelK 500
                                       7799999999999998888766555544444455555444444444444443333330 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4  11.2       7.3     5e+03      12      69 ..     155     212 ..     150     225 .. 0.67
   2 ?   -0.9  14.4       2.6   1.8e+03       2      90 ..     187     273 ..     186     277 .. 0.87
   3 !   20.7  21.2   4.7e-07   0.00033       3      91 ..     344     432 ..     342     438 .. 0.87
   4 ?    3.9   4.3     0.084        58       3      47 ..     421     466 ..     419     472 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 7.3
                              BRE1  12 feelseqlskkvkeltileekklrleaekakadqkyfaamrskdalenelkkLnklls 69 
                                       +eel +++++ ++++t+ +  +++ +++ ++   +   ++++k+ ++++   ++k+++
  gi|298674126|ref|YP_003725876.1| 155 YEELYNLAQSYINDITSKKTSLNKRKSKAKELASELEKVKKQKEEIDQDREEISKKVN 212
                                       6666666666666666666666666666666666777777777777777777666655 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.6
                              BRE1   2 qkELvklekafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdalenelkkLnkllsKsselieqL 78 
                                        +EL+k++k++ee ++  ++  k+     + +  +  e +   +k+ +  r+ +++ n +++ +++++K+ e++++L
  gi|298674126|ref|YP_003725876.1| 187 ASELEKVKKQKEEIDQDREEISKK--VNDNDIREIVEERKSIFEKIQNFHRDLNDIYNRINNKKTKIQKKEEIVNEL 261
                                       679999999888888877777666..4457899999***************************************** PP

                              BRE1  79 kelekefvrklk 90 
                                       +e  ++++++++
  gi|298674126|ref|YP_003725876.1| 262 NENLSNLNKEIE 273
                                       **8888888876 PP

  == domain 3  score: 20.7 bits;  conditional E-value: 4.7e-07
                              BRE1   3 kELvklekafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdalenelkkLnkllsKsselieqLk 79 
                                       k L++l+  +++ +++++++ +e++i+++k++ le+ek+k +q++f ++++ ++ + +lk+L++ ++   +l ++ +
  gi|298674126|ref|YP_003725876.1| 344 KTLESLNDKKRNIESEIQSLNEEIAIMKNKLNNLESEKNKKEQEIFRLEHELEDTKSDLKTLRNEVKNDDDLKNEKE 420
                                       6799*************************************************************999888877777 PP

                              BRE1  80 elekefvrklke 91 
                                       ++ ke+ ++ + 
  gi|298674126|ref|YP_003725876.1| 421 QTLKELENEYER 432
                                       755555554443 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.084
                              BRE1   3 kELvklekafeelseqls.kkvkeltileekklrleaekakadqky 47 
                                       + L++le+++e l+e+++ + vk++  le k + l+ e+    +k+
  gi|298674126|ref|YP_003725876.1| 421 QTLKELENEYERLKELAKgDIVKKIDELEAKSSELQEEIGSINEKI 466
                                       789**************945799**************997766665 PP

>> Macoilin  Macoilin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3  19.9      0.29     2e+02     209     358 ..     176     328 ..     152     341 .. 0.65
   2 !   17.4  21.7   1.9e-06    0.0013     424     550 ..     344     470 ..     336     488 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.29
                          Macoilin 209 ldkeereaeeqlaaakelvevdpvalsknnhslnkkdsslklpeleyrekkksakss..rsdskkkhehnesvdskl 283
                                       l+k +++a+e la+  e v+ +   ++++ ++ +kk + +++ e+ ++ k+  +k +  + d +  +++ +++++k+
  gi|298674126|ref|YP_003725876.1| 176 LNKRKSKAKE-LASELEKVKKQKEEIDQDREEISKKVNDNDIREIVEERKSIFEKIQnfHRDLNDIYNRINNKKTKI 251
                                       3444444555.333333334557788888999999989999998877666554443301344445555558899999 PP

                          Macoilin 284 qekeymenkskskrls..ksessgsesellveesvkskssssssssnknskkasagsagssnssskkhsessksvts 358
                                       q+ke + n+++++ ++  k+ +  + s+ +++ + k ++++s+ +s k+ k + + s++  +s+  k+++++ks t+
  gi|298674126|ref|YP_003725876.1| 252 QKKEEIVNELNENLSNlnKEIEGLDVSNYKKKFDQKVNENTSKIESLKEDKAEVNASINLFQSAKLKLKNENKSETT 328
                                       99999999988765441044344445555555555555555566666888888899999999999999999999876 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 1.9e-06
                          Macoilin 424 skissltseerslkselqqlkkendllqtklhelvsakqkdkqtlqqlekrLkeekearaslekqLaeekkrkkeee 500
                                       + ++sl  ++r++ se+q+l++e   +++kl++l s+k k  q++ +le+ L++ k+  ++l + ++++   k e+e
  gi|298674126|ref|YP_003725876.1| 344 KTLESLNDKKRNIESEIQSLNEEIAIMKNKLNNLESEKNKKEQEIFRLEHELEDTKSDLKTLRNEVKNDDDLKNEKE 420
                                       67899***************************************************999999999999999999999 PP

                          Macoilin 501 etaaravalaaasr.secteslkskkreleaeikkLekelklkeeqirele 550
                                       +t ++        +   +++ + +k+ elea  + L++e+   +e+ir+  
  gi|298674126|ref|YP_003725876.1| 421 QTLKELENEYERLKeLAKGD-IVKKIDELEAKSSELQEEIGSINEKIRSTT 470
                                       99998555544444233444.455789999999999999977777777654 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8  15.6     0.011       7.6      12     105 ..     174     269 ..     166     277 .. 0.85
   2 ?   -1.1   1.0       3.1   2.1e+03      48      68 ..     287     307 ..     275     353 .. 0.56
   3 !   18.6  19.0   2.3e-06    0.0016      16      98 ..     355     437 ..     350     443 .. 0.94
   4 ?    0.4   0.1       1.1   7.3e+02      59      81 ..     445     467 ..     439     482 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.011
                       TMF_TATA_bd  12 qlverlsseirrlEgElaslkeelerleaerdeareeivk..lmkeneelkelkkeleelekeleelqeryetlLel 86 
                                       + +++ +s+ ++l +El+++k++ e++ + r+e+++ + +  + + +ee k+  +++++  + l+++ +r ++  + 
  gi|298674126|ref|YP_003725876.1| 174 TSLNKRKSKAKELASELEKVKKQKEEIDQDREEISKKVNDndIREIVEERKSIFEKIQNFHRDLNDIYNRINNKKTK 250
                                       55667778888999999999999999999999999999752155778999999999999999*************** PP

                       TMF_TATA_bd  87 lGeksEeveELraDvaDlK 105
                                       +++k+E v+EL + ++ l 
  gi|298674126|ref|YP_003725876.1| 251 IQKKEEIVNELNENLSNLN 269
                                       *************999885 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3.1
                       TMF_TATA_bd  48 eivklmkeneelkelkkelee 68 
                                        + + +++ e+lke k+e++ 
  gi|298674126|ref|YP_003725876.1| 287 KVNENTSKIESLKEDKAEVNA 307
                                       333333333333333333322 PP

  == domain 3  score: 18.6 bits;  conditional E-value: 2.3e-06
                       TMF_TATA_bd  16 rlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetlLellGeksE 92 
                                       +++sei++l  E+a +k++l++le+e+++ ++ei +l +e e++k+  k+l++  k+ ++l+++ e++L+ l    E
  gi|298674126|ref|YP_003725876.1| 355 NIESEIQSLNEEIAIMKNKLNNLESEKNKKEQEIFRLEHELEDTKSDLKTLRNEVKNDDDLKNEKEQTLKELENEYE 431
                                       5789*****************************************9999999999999******************* PP

                       TMF_TATA_bd  93 eveELr 98 
                                       + +EL 
  gi|298674126|ref|YP_003725876.1| 432 RLKELA 437
                                       ****95 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 1.1
                       TMF_TATA_bd  59 lkelkkeleelekeleelqerye 81 
                                        +el+++++el++e+ +++e+  
  gi|298674126|ref|YP_003725876.1| 445 IDELEAKSSELQEEIGSINEKIR 467
                                       34455555555555555555544 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2      0.67   4.6e+02      16      32 ..      24      40 ..      16      49 .. 0.87
   2 !    9.5  28.8    0.0005      0.35     277     440 ..     151     324 ..     145     331 .. 0.61
   3 !   15.4  17.8     8e-06    0.0055     356     472 ..     345     472 ..     337     488 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.67
                            AAA_13 16 kriNliYGwNGaGKTtL 32
                                      ++ N i G+N  GKT+L
  gi|298674126|ref|YP_003725876.1| 24 GKANKILGSNAVGKTSL 40
                                      689*************9 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0005
                            AAA_13 277 FddefeekqerLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkgl.qraleaKrkepf 352
                                       F d++ee ++  ++ i+++ skk +l ++  ++ + ase ++ +++kee+++  e+++++ + +  r++ + rk +f
  gi|298674126|ref|YP_003725876.1| 151 FADNYEELYNLAQSYINDITSKKTSLNKRKSKAKELASELEKVKKQKEEIDQDREEISKKVNDNdIREIVEERKSIF 227
                                       5556666666666666666666666666666666669999999999**************99862467888888999 PP

                            AAA_13 353 ksve.....lesvkakiesikklvaeineliakhNekvanleeeke.....eakkklelhlveeleseldeykkkyk 419
                                       ++++     l+++ ++i++ k ++++ +e++++ Ne  +nl++e e     + kkk+ +  v+e +s+++ +k++++
  gi|298674126|ref|YP_003725876.1| 228 EKIQnfhrdLNDIYNRINNKKTKIQKKEEIVNELNENLSNLNKEIEgldvsNYKKKFDQ-KVNENTSKIESLKEDKA 303
                                       95543222244444555555666666666666666666666665541111133444444.34555566666666666 PP

                            AAA_13 420 klekaieklekelkeeeaelk 440
                                       +++++i+  + ++ + ++e k
  gi|298674126|ref|YP_003725876.1| 304 EVNASINLFQSAKLKLKNENK 324
                                       666666666655555554443 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 8e-06
                            AAA_13 356 elesvkakiesikklvaeineliakhNekvanleeekeeakkklel..hlveeleseldeykkkykk...lekaiek 427
                                       +les+++k  +i+++++++ne ia   +k +nle+ek++ ++++ +  h++e+ +s+l+++ +++k+   l+++ e+
  gi|298674126|ref|YP_003725876.1| 345 TLESLNDKKRNIESEIQSLNEEIAIMKNKLNNLESEKNKKEQEIFRleHELEDTKSDLKTLRNEVKNdddLKNEKEQ 421
                                       6899999999*********************************9762356899999999999777661114555555 PP

                            AAA_13 428 lekelkeeeaelkkleee.....ikeLekqlrdekpaaeeinkeLkaf.Gl 472
                                       + kel++e+++lk+l++      i eLe++ ++ ++ +  in+++++  G 
  gi|298674126|ref|YP_003725876.1| 422 TLKELENEYERLKELAKGdivkkIDELEAKSSELQEEIGSINEKIRSTtGE 472
                                       55555555555555443366666**********************998774 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   6.9     0.088        61      40     100 ..     155     221 ..     130     225 .. 0.60
   2 !   13.9   9.6   5.8e-05      0.04       7      86 ..     225     306 ..     217     320 .. 0.89
   3 ?    3.4   3.7       0.1        70      25      68 ..     338     381 ..     315     389 .. 0.70
   4 !    9.6  12.5    0.0013      0.88       9     100 ..     378     467 ..     371     470 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.088
                                       XXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH.......HHHHHH..HHHHHHH CS
                        Laminin_II  40 veetnekvkdankairdArrsvkkLeklapqLldklkelkqleeasss....lsdnis..eikelIa 100
                                        ee  ++++++ + i + ++s  k + +a +L + l+++k+++e+       +s++++   i+e+++
  gi|298674126|ref|YP_003725876.1| 155 YEELYNLAQSYINDITSKKTSLNKRKSKAKELASELEKVKKQKEEIDQdreeISKKVNdnDIREIVE 221
                                       4555555555555555555555555555555555555555555554334445777774224666665 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 5.8e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXX--TTTTTGGGHHHHHHH CS
                        Laminin_II   7 eanetakevleqlaplsqnlentkeklseinrsveetnekvkdankair..dArrsvkkLeklapqLldklkelkql 81 
                                       ++ e++++  ++l+++ ++++n k k+++ ++ v+e ne+++++nk i+  d+++  kk ++++++  +k+++lk+ 
  gi|298674126|ref|YP_003725876.1| 225 SIFEKIQNFHRDLNDIYNRINNKKTKIQKKEEIVNELNENLSNLNKEIEglDVSNYKKKFDQKVNENTSKIESLKED 301
                                       6778999999************************************995449***********************98 PP

                                       HHH.. CS
                        Laminin_II  82 eeass 86 
                                       + + +
  gi|298674126|ref|YP_003725876.1| 302 KAEVN 306
                                       87744 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.1
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TT CS
                        Laminin_II  25 nlentkeklseinrsveetnekvkdankairdArrsvkkLekla 68 
                                       n++ + + l+++n++ ++++ +++++n+ i+  +++  +Le + 
  gi|298674126|ref|YP_003725876.1| 338 NINVIDKTLESLNDKKRNIESEIQSLNEEIAIMKNKLNNLESEK 381
                                       55556666666666666677777777777777777777766554 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.0013
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTT.TTGGGHHHHHHHHHH CS
                        Laminin_II   9 netakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklap.qLldklkelkqleea 84 
                                       ++  ++ ++ +  l+ +le tk++l++++++v++ +++ +++ +++++ +++   L++la  ++++k+ el+ ++++
  gi|298674126|ref|YP_003725876.1| 378 ESEKNKKEQEIFRLEHELEDTKSDLKTLRNEVKNDDDLKNEKEQTLKELENEYERLKELAKgDIVKKIDELEAKSSE 454
                                       555556677778899******************9999999*******************9769****9999999999 PP

                                       ...HHHHHHHHHHHHH CS
                        Laminin_II  85 ssslsdniseikelIa 100
                                          l ++i  i e I 
  gi|298674126|ref|YP_003725876.1| 455 ---LQEEIGSINEKIR 467
                                       ...99***99999886 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4  21.2   0.00019      0.13      16     183 ..     158     325 ..     145     325 .. 0.78
   2 ?    7.2  20.7    0.0078       5.4      73     164 ..     343     434 ..     333     455 .. 0.88
   3 ?    1.6   0.4      0.41   2.8e+02      97     129 ..     438     470 ..     431     481 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00019
                             ATG16  16 afaeliqaynrLldrtsaleaenaklekaaasakssksskksakekeasasq..snskqsakiqsleqklaqlreel 90 
                                       +++   ++ n++  +  +l+++++k++ + as+ + k+  k++ke+ ++ ++  s+++++++i +  ++++++ e  
  gi|298674126|ref|YP_003725876.1| 158 LYNLAQSYINDITSKKTSLNKRKSKAK-ELASELE-KV--KKQKEEIDQDREeiSKKVNDNDIREIVEERKSIFEKI 230
                                       443333344667777777777777773.3333333.22..223333333333567899******************* PP

                             ATG16  91 aelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletk..lkdreeelrekeklvqdlqDElsaLql 165
                                       ++ ++  ++  +r++++++++qk+ee  +e +e+l +l++e++ l      k+ +++++e +  ++ l+++ +  + 
  gi|298674126|ref|YP_003725876.1| 231 QNFHRDLNDIYNRINNKKTKIQKKEEIVNELNENLSNLNKEIEGLDVSnyKKKFDQKVNENTSKIESLKEDKAEVNA 307
                                       *******************************************987542268899********************** PP

                             ATG16 166 qlnqaEeklrklekENke 183
                                         n   +++ kl++ENk+
  gi|298674126|ref|YP_003725876.1| 308 SINLFQSAKLKLKNENKS 325
                                       ****************95 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0078
                             ATG16  73 sakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrek 149
                                       +++++sl++k   + +e + l  + + ++++l++l++e  k+e+++ + e +l++ +++ ++l+ ++k+ ++  +ek
  gi|298674126|ref|YP_003725876.1| 343 DKTLESLNDKKRNIESEIQSLNEEIAIMKNKLNNLESEKNKKEQEIFRLEHELEDTKSDLKTLRNEVKNDDDLKNEK 419
                                       567899999999999999999999999************************************************** PP

                             ATG16 150 eklvqdlqDElsaLq 164
                                       e+++++l  E++ L+
  gi|298674126|ref|YP_003725876.1| 420 EQTLKELENEYERLK 434
                                       **********99885 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.41
                             ATG16  97 rgelaqrllelneelqkleeklkedeerlaele 129
                                       +g+  +++ el+++ ++l+e++ + +e++++ +
  gi|298674126|ref|YP_003725876.1| 438 KGDIVKKIDELEAKSSELQEEIGSINEKIRSTT 470
                                       566667788888888888888888888887766 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   6.4    0.0023       1.6      38     120 ..     157     240 ..     130     247 .. 0.72
   2 ?    0.3  14.1      0.97   6.7e+02      42     101 ..     203     263 ..     183     302 .. 0.47
   3 ?    4.2   2.5      0.06        41      64     111 ..     261     310 ..     255     330 .. 0.50
   4 ?    9.1   5.7    0.0019       1.3      48     111 ..     347     410 ..     336     414 .. 0.65
   5 ?    7.4   1.4    0.0061       4.2      40      91 ..     416     468 ..     412     482 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0023
                           DUF1664  38 slsdavesvskqleqvseslaatk...rhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeave 111
                                        l +  +s  +++++ ++sl++ k   ++L+s++++v k+ +e  +  +ei+++v++  +d++ei e+ +s+ e ++
  gi|298674126|ref|YP_003725876.1| 157 ELYNLAQSYINDITSKKTSLNKRKskaKELASELEKVKKQKEEIDQDREEISKKVND--NDIREIVEERKSIFEKIQ 231
                                       566666666677777777777666434689999999999999999999999999985..678888888888888888 PP

                           DUF1664 112 gleskleri 120
                                       ++   l++i
  gi|298674126|ref|YP_003725876.1| 232 NFHRDLNDI 240
                                       877777766 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.97
                           DUF1664  42 avesvskqleq.vseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseige 101
                                         e++sk++++    ++ + ++ + ++i++  + l++  + +++ k ++++ +e ++e++e
  gi|298674126|ref|YP_003725876.1| 203 DREEISKKVNDnDIREIVEERKSIFEKIQNFHRDLNDIYNRINNKKTKIQKKEEIVNELNE 263
                                       2222232222101233333333333333333333333333333333333333333333333 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.06
                           DUF1664  64 Lssridrvdkkld..eqkeiskeikeevtevredlseigedvesvkeave 111
                                       L++++ +++k+++  ++++ +k+ +++v+e  +++++++ed  +v++ ++
  gi|298674126|ref|YP_003725876.1| 261 LNENLSNLNKEIEglDVSNYKKKFDQKVNENTSKIESLKEDKAEVNASIN 310
                                       44444444444442223444455555555555555555555555544443 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.0019
                           DUF1664  48 kqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeave 111
                                       ++l++ + ++++  + L+++i+ + +kl++ +  +++ ++e+ +++++l+++++d++++++ v+
  gi|298674126|ref|YP_003725876.1| 347 ESLNDKKRNIESEIQSLNEEIAIMKNKLNNLESEKNKKEQEIFRLEHELEDTKSDLKTLRNEVK 410
                                       2333334556666666666777777777777777777788888888888888888888877776 PP

  == domain 5  score: 7.4 bits;  conditional E-value: 0.0061
                           DUF1664  40 sdavesvskqleqvseslaa.tkrhLssridrvdkkldeqkeiskeikeevte 91 
                                       ++  e+  k+le+ +e l++ +k ++ ++id++++k  e +e + +i+e++ +
  gi|298674126|ref|YP_003725876.1| 416 KNEKEQTLKELENEYERLKElAKGDIVKKIDELEAKSSELQEEIGSINEKIRS 468
                                       45555666777777777765467777777777777777777777777777765 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1  11.1     0.026        18     194     239 ..     169     214 ..     150     235 .. 0.43
   2 ?    6.1  15.2    0.0064       4.4     156     265 ..     228     324 ..     214     334 .. 0.43
   3 ?   11.2  25.0   0.00018      0.13     162     283 ..     339     460 ..     333     481 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.026
                              Spc7 194 esidkeeLeelreelaelkaeieekkkelaelqeqleeleekieel 239
                                        +++k++L++ +++ +el +e+e+ kk+ +e  +++ee+++k+++ 
  gi|298674126|ref|YP_003725876.1| 169 ITSKKTSLNKRKSKAKELASELEKVKKQKEEIDQDREEISKKVNDN 214
                                       2234444444444444444444444444444444444444444433 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0064
                              Spc7 156 elLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieek..kkelaelqeqle 230
                                       e++++    l++++++++++k++++++ e                ++el e+l++l++eie +  ++  ++  ++++
  gi|298674126|ref|YP_003725876.1| 228 EKIQNFHRDLNDIYNRINNKKTKIQKKEEI---------------VNELNENLSNLNKEIEGLdvSNYKKKFDQKVN 289
                                       223333333333333333333333333333...............34444444444444432211233444555556 PP

                              Spc7 231 eleekieelkeqkseleeeiaeaervleeckgwse 265
                                       e ++kie+lke k+e+++ i+  ++ + + k+ ++
  gi|298674126|ref|YP_003725876.1| 290 ENTSKIESLKEDKAEVNASINLFQSAKLKLKNENK 324
                                       66666666666666666666555544444444444 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00018
                              Spc7 162 eeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekiee 238
                                        + +d+ l++l+ +k ++e+e+++l+e+ +    i k++L++l +e ++ ++ei +++ el++ +++l++l++++++
  gi|298674126|ref|YP_003725876.1| 339 INVIDKTLESLNDKKRNIESEIQSLNEEIA----IMKNKLNNLESEKNKKEQEIFRLEHELEDTKSDLKTLRNEVKN 411
                                       578999999999999999999999999665....6778999999999999999999999999999999999999987 PP

                              Spc7 239 lkeqkseleeeiaea....ervleeckgwsesevsrlkeevkaleeltg 283
                                        ++ k+e e+ ++e     er++e  kg   + +++l+++ ++l+e+ g
  gi|298674126|ref|YP_003725876.1| 412 DDDLKNEKEQTLKELeneyERLKELAKGDIVKKIDELEAKSSELQEEIG 460
                                       6666665555555550001444555555555666677777777777665 PP

>> HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4  12.2    0.0048       3.3       8      99 .]     183     275 ..     168     275 .. 0.77
   2 ?    6.2   2.7     0.023        16      37      83 ..     278     327 ..     276     333 .. 0.75
   3 ?    2.0   0.6      0.48   3.3e+02      66      95 ..     337     366 ..     322     370 .. 0.85
   4 ?   10.0  16.6    0.0015       1.1      16      99 .]     347     433 ..     340     433 .. 0.80
   5 ?   -0.8   0.0       3.5   2.4e+03      23      44 ..     446     467 ..     439     483 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0048
                    HIP1_clath_bdg   8 nAevtkqlsvarqaqeeverekkeleeelerlkeeaerkleeqk...eelekLkreleakraelarlkssLesseqs 81 
                                         e++  l   ++++ee+++ ++e+++++++   + ++ +ee+k   e++++++r+l++  +++++ k+ ++++e+ 
  gi|298674126|ref|YP_003725876.1| 183 AKELASELEKVKKQKEEIDQDREEISKKVNDN--DIREIVEERKsifEKIQNFHRDLNDIYNRINNKKTKIQKKEEI 257
                                       44666677777888888888888888888763..33344445551225677889*********************** PP

                    HIP1_clath_bdg  82 geqlssqlaaLqaEkesL 99 
                                        ++l+++l++L++E e L
  gi|298674126|ref|YP_003725876.1| 258 VNELNENLSNLNKEIEGL 275
                                       **************8876 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.023
                    HIP1_clath_bdg  37 erlkeeaerkleeqkeelekLkreleakraelarlkss...Lesseqsge 83 
                                        + k++ ++k++e ++++e+Lk++ ++ +a ++ ++s+   L+++++s++
  gi|298674126|ref|YP_003725876.1| 278 SNYKKKFDQKVNENTSKIESLKEDKAEVNASINLFQSAklkLKNENKSET 327
                                       67889999**************9988888877666653211666666665 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.48
                    HIP1_clath_bdg  66 aelarlkssLesseqsgeqlssqlaaLqaE 95 
                                        +++ + ++Les + ++ +++s++++L++E
  gi|298674126|ref|YP_003725876.1| 337 LNINVIDKTLESLNDKKRNIESEIQSLNEE 366
                                       567888999999999999999999999988 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.0015
                    HIP1_clath_bdg  16 svarqaqeeverekkeleeelerlkeeaerkle...eqkeelekLkreleakraelarlkssLesseqsgeqlssql 89 
                                        +   ++ ++e e + l+ee+  +k++ ++ ++   ++++e+ +L++ele+++ +l++l++ +++    +++ +++l
  gi|298674126|ref|YP_003725876.1| 347 ESLNDKKRNIESEIQSLNEEIAIMKNKLNNLESeknKKEQEIFRLEHELEDTKSDLKTLRNEVKNDDDLKNEKEQTL 423
                                       55556667777788888888777777666555433366778889********************************* PP

                    HIP1_clath_bdg  90 aaLqaEkesL 99 
                                       ++L++E e+L
  gi|298674126|ref|YP_003725876.1| 424 KELENEYERL 433
                                       ******9987 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 3.5
                    HIP1_clath_bdg  23 eeverekkeleeelerlkeeae 44 
                                       +e+e++ +el+ee+ +++e+ +
  gi|298674126|ref|YP_003725876.1| 446 DELEAKSSELQEEIGSINEKIR 467
                                       4555555555555555555444 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9  20.6     0.029        20      89     219 ..     167     293 ..     152     302 .. 0.71
   2 ?   13.3  17.2   7.9e-05     0.055      33     183 ..     344     521 ..     332     530 .. 0.53

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.029
                               ERM  89 leaarleeeserkeeeaerLkeeleeareaeeeakekllealstpskseseenveeseteeeeenseeesaeletde 165
                                         ++  +   ++++++a++L +ele++++++ee  +   e++++ ++++ +e vee ++  e      + ++++ d 
  gi|298674126|ref|YP_003725876.1| 167 NDITSKKTSLNKRKSKAKELASELEKVKKQKEEIDQDREEISKKVNDNDIREIVEERKSIFE------KIQNFHRD- 236
                                       44555566677899999999999999999999999999999999854434334443333333......33455555. PP

                               ERM 166 veklsleieeeRvtyleksk...rlqeqLkeLkseleqlkdeekqtelDklheenvr 219
                                        +++ ++i++++++  +k++   +l+e L++L++e+e l + + + ++D+  +en++
  gi|298674126|ref|YP_003725876.1| 237 LNDIYNRINNKKTKIQKKEEivnELNENLSNLNKEIEGLDVSNYKKKFDQKVNENTS 293
                                       445667777777666666643336788999*************999***99999975 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 7.9e-05
                               ERM  33 etaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerklreaeleaarleeeserkeeeaerLk 109
                                       +t e L+ k+r  e e + L+++ a ++++ ++l+ +++k+e+e  +le++l++ ++ +++l++e+++ +     Lk
  gi|298674126|ref|YP_003725876.1| 344 KTLESLNDKKRNIESEIQSLNEEIAIMKNKLNNLESEKNKKEQEIFRLEHELEDTKSDLKTLRNEVKNDD----DLK 416
                                       5677777777777777777777777777777777777777777777777777777777777777777633....344 PP

                               ERM 110 eeleeareaeeeakekllealstpskseseenveeseteeeeensee.............................. 156
                                       +e e++ +++e++ e+l+e+++    ++  e +++s++ +ee  s +                              
  gi|298674126|ref|YP_003725876.1| 417 NEKEQTLKELENEYERLKELAKGDIVKKIDELEAKSSELQEEIGSINekirsttgeeviygenvdtdtalaiyndwl 493
                                       44444444444444444444444322211111222222222211111233444455555555555555555655555 PP

                               ERM 157 .esaeletdeveklsleieeeRvtylek 183
                                        +  el+  ++e  s +++e R +  ek
  gi|298674126|ref|YP_003725876.1| 494 yYLEELKEFANEMYSSHRNEARKKFNEK 521
                                       5223333333333566666666666555 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.2       5.3   3.7e+03      40      51 ..     190     201 ..     169     214 .. 0.52
   2 ?    5.6   0.1     0.036        25       9      36 ..     248     275 ..     240     308 .. 0.85
   3 ?   13.8   1.6   9.8e-05     0.068      15      58 ..     342     385 ..     337     388 .. 0.89
   4 ?    3.1   0.9      0.21   1.5e+02      30      59 ..     385     414 ..     382     429 .. 0.70
   5 ?    2.3   0.1      0.38   2.7e+02       4      26 ..     444     466 ..     441     474 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 5.3
                                       HHHHHHT-XXXX CS
                              SlyX  40 lrllaerlkele 51 
                                       l++++++ +e++
  gi|298674126|ref|YP_003725876.1| 190 LEKVKKQKEEID 201
                                       222222222222 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.036
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SlyX   9 EiklafqedtieeLndvvaeqqqqidrl 36 
                                        +k+   e+ ++eLn+ + + +++i+ l
  gi|298674126|ref|YP_003725876.1| 248 KTKIQKKEEIVNELNENLSNLNKEIEGL 275
                                       5889999******************977 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 9.8e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXX CS
                              SlyX  15 qedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessgase 58 
                                        ++t+e+Lnd   + + +i+ l ++++ ++++l++le++++++e
  gi|298674126|ref|YP_003725876.1| 342 IDKTLESLNDKKRNIESEIQSLNEEIAIMKNKLNNLESEKNKKE 385
                                       689***********************************987654 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.21
                                       HHHHHHHHHHHHHHHHT-XXXXXXXXXXXX CS
                              SlyX  30 qqqidrlqrqlrllaerlkeleessgasea 59 
                                       +q+i rl+++l+  +  lk+l+++ +++++
  gi|298674126|ref|YP_003725876.1| 385 EQEIFRLEHELEDTKSDLKTLRNEVKNDDD 414
                                       677778888888888888777777665444 PP

  == domain 5  score: 2.3 bits;  conditional E-value: 0.38
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                              SlyX   4 rleeLEiklafqedtieeLndvv 26 
                                       +++eLE k + +++ i + n+ +
  gi|298674126|ref|YP_003725876.1| 444 KIDELEAKSSELQEEIGSINEKI 466
                                       57777777777777776666654 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5  25.6     0.002       1.4      13     151 ..     146     297 ..     124     318 .. 0.72
   2 ?    6.8  26.6    0.0067       4.6      14     121 ..     337     461 ..     308     535 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.002
                           DUF4795  13 q......eaieklqeelekleekvkelekrledkekklealkkqieelekvkadkeeveeelaekadkeaLatkvsr 83 
                                              +++e+l++  ++  +  ++ +++l+++++k + l +++e+ +k+k++ ++  ee++ k++ ++++  v++
  gi|298674126|ref|YP_003725876.1| 146 InqlsfaDNYEELYNLAQSYINDITSKKTSLNKRKSKAKELASELEKVKKQKEEIDQDREEISKKVNDNDIREIVEE 222
                                       0444466677777777777778888899999********************************************99 PP

                           DUF4795  84 dq.fDeakkeLekmleellekle.......eqeealkkaldtLqeelkekldrlelepLkeqleerlkelqkelqe 151
                                        + + e+++ +++ l++++++++       ++ee ++++ ++L+ +l++ ++ l++++ k++++++++e   ++++
  gi|298674126|ref|YP_003725876.1| 223 RKsIFEKIQNFHRDLNDIYNRINnkktkiqKKEEIVNELNENLS-NLNKEIEGLDVSNYKKKFDQKVNENTSKIES 297
                                       98944556666666666666655333333377777777777777.8888888999999999999666655544442 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0067
                           DUF4795  14 eaieklqeelekleekvkelekrledkekklealkkqieelekvkadkee....v.eeelaekadkeaLatkvsrdq 85 
                                        +i  +++ le+l++k++++e++++ + +++  +k+++++le++k +ke+    + +e ++ k+d ++L++ v +d+
  gi|298674126|ref|YP_003725876.1| 337 LNINVIDKTLESLNDKKRNIESEIQSLNEEIAIMKNKLNNLESEKNKKEQeifrLeHELEDTKSDLKTLRNEVKNDD 413
                                       68999****************************************99998444432566799***********9999 PP

                           DUF4795  86 ............fDeakkeLekml.eellekleeqeealkkaldtLqee 121
                                                   +++  ++L++ +  ++++k++e e++  ++ +++  +
  gi|298674126|ref|YP_003725876.1| 414 dlknekeqtlkeLENEYERLKELAkGDIVKKIDELEAKSSELQEEIG-S 461
                                       99999555555544444444444454444444433333333333322.2 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   9.0      0.36   2.5e+02      60      98 ..     175     213 ..     156     225 .. 0.64
   2 ?    5.7  15.4      0.02        14      26     129 ..     230     328 ..     214     338 .. 0.80
   3 ?   12.5  27.8   0.00017      0.11      12     131 ..     346     466 ..     340     473 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.36
                    CENP-F_leu_zip  60 eieelaeelreleldLvalrsekeeLekelqkkqervse 98 
                                        +++ +++ +el ++L++++++kee++++ ++  ++v++
  gi|298674126|ref|YP_003725876.1| 175 SLNKRKSKAKELASELEKVKKQKEEIDQDREEISKKVND 213
                                       333334556667777777777777777777776666665 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.02
                    CENP-F_leu_zip  26 venLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalr..sekeeLekelqkkqervseLe 100
                                       +       ++  ++++++     ++k ++++ +e ++el+e+l++l+ +++ l   + k++ +++++++ +++++L+
  gi|298674126|ref|YP_003725876.1| 230 I-------QNFHRDLNDIYNRINNKKTKIQKKEEIVNELNENLSNLNKEIEGLDvsNYKKKFDQKVNENTSKIESLK 299
                                       3.......44445555566668899999999999999999999999999986543399******************* PP

                    CENP-F_leu_zip 101 slnsslenlleekEqekvqmkeeskaave 129
                                       + + +++  ++     k ++k+e k++  
  gi|298674126|ref|YP_003725876.1| 300 EDKAEVNASINLFQSAKLKLKNENKSETT 328
                                       **********9999999999999998765 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 0.00017
                    CENP-F_leu_zip  12 LKeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLva...lrsekeeL 85 
                                       L   + k+ +++  +++L+ e+ ++++++++++ e+ ++ +e+  l++e+e  ++ l+ l+ ++++   l++eke+ 
  gi|298674126|ref|YP_003725876.1| 346 LESLNDKKRNIESEIQSLNEEIAIMKNKLNNLESEKNKKEQEIFRLEHELEDTKSDLKTLRNEVKNdddLKNEKEQT 422
                                       5566778999999***************************************************8655599****** PP

                    CENP-F_leu_zip  86 ekelqkkqervseLeslnsslenlleekEqekvqmkeeskaaveeL 131
                                        kel+++ er +eL   + ++ + + e+E++  +++ee  +  e++
  gi|298674126|ref|YP_003725876.1| 423 LKELENEYERLKELA--KGDIVKKIDELEAKSSELQEEIGSINEKI 466
                                       *************95..67999*************99987766655 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9  22.3   6.4e-05     0.044      75     189 ..     160     275 ..     130     276 .. 0.85
   2 ?    5.0  21.1     0.034        24      68     189 ..     286     405 ..     276     407 .. 0.77
   3 ?    3.6  10.2     0.093        64      77     169 ..     409     518 ..     402     536 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.4e-05
                           UPF0242  75 aklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleai.aedfeelkleleeqLaekqel 150
                                       ++ ++  ++++ k+ +l++++++ +eL+ el++ +++ e+  ++ +++++k ++   +++ e ++ + e++++ +  
  gi|298674126|ref|YP_003725876.1| 160 NLAQSYINDITSKKTSLNKRKSKAKELASELEKVKKQKEEIDQDREEISKKVNDNdIREIVEERKSIFEKIQNFHRD 236
                                       3334444899999**************************************998524799999************** PP

                           UPF0242 151 lqeyqetieeqrsvlekrqdqieqLeskVrDlnyEiktL 189
                                       l++  + i++++  ++k+++ +++L+   + ln Ei  L
  gi|298674126|ref|YP_003725876.1| 237 LNDIYNRINNKKTKIQKKEEIVNELNENLSNLNKEIEGL 275
                                       ***********************************9765 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.034
                           UPF0242  68 skleekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqL 144
                                       +k++e+ +k+ +l+e+ ++ + +++  q+ + +Lk+e ++ ++ +   ++ n +++    ++ e  ++ k+++e+++
  gi|298674126|ref|YP_003725876.1| 286 QKVNENTSKIESLKEDKAEVNASINLFQSAKLKLKNENKSETTCIL-CEQGNLNIN-VIDKTLESLNDKKRNIESEI 360
                                       3455666777777777777777787777777777776555555444.455555555.4567788999********** PP

                           UPF0242 145 aekqellqeyqetieeqrsvlekrqdqieqLeskVrDlnyEiktL 189
                                       +  +e +  ++++++++ s+ +k++++i +Le   +D +  +ktL
  gi|298674126|ref|YP_003725876.1| 361 QSLNEEIAIMKNKLNNLESEKNKKEQEIFRLEHELEDTKSDLKTL 405
                                       ********************************************9 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.093
                           UPF0242  77 lteldeglkt.keealeelqeeeeeLkee........ldakeeelerlkeenqqLqekleaiae.........dfee 135
                                       +++ d +lk+ ke++l+el++e e+Lke         +d+ e ++ +l+ee  +++ek   +           d + 
  gi|298674126|ref|YP_003725876.1| 409 VKNDD-DLKNeKEQTLKELENEYERLKELakgdivkkIDELEAKSSELQEEIGSINEKIRSTTGeeviygenvDTDT 484
                                       44444.55541566999999999999998888888888888888888888888888888777666777887777777 PP

                           UPF0242 136 lkleleeqLaekqellqeyqetieeqrsvlekrq 169
                                        +  +++ L + +el +  +e+ ++ r++  k+ 
  gi|298674126|ref|YP_003725876.1| 485 ALAIYNDWLYYLEELKEFANEMYSSHRNEARKKF 518
                                       7888888888888888888888888887766664 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   7.6     0.013       8.8      33      88 ..     214     269 ..     169     276 .. 0.62
   2 ?    2.7   1.6      0.22   1.5e+02      30      82 ..     253     307 ..     241     314 .. 0.50
   3 ?    8.3   2.9    0.0039       2.7      23      87 ..     341     405 ..     335     407 .. 0.88
   4 ?    2.0   0.8      0.36   2.5e+02      26      61 ..     421     457 ..     387     480 .. 0.51

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.013
                            DUF948  33 atieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                       + i+e+ ++ ++i +++++  +  n++ + +n+k  k+++  e v++l e++s+ln
  gi|298674126|ref|YP_003725876.1| 214 NDIREIVEERKSIFEKIQNFHRDLNDIYNRINNKKTKIQKKEEIVNELNENLSNLN 269
                                       33555556666666666666666666666666666666666666666666666665 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.22
                            DUF948  30 eaaatieelekqvdpilkevedl.lakvne.lledvneklekvdplteavadlge 82 
                                       + ++ ++el++++ ++ ke+e+l +++ ++   + vne + k+++l e  a++ +
  gi|298674126|ref|YP_003725876.1| 253 KKEEIVNELNENLSNLNKEIEGLdVSNYKKkFDQKVNENTSKIESLKEDKAEVNA 307
                                       3344445555555555555554422222222444555566666665555555555 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0039
                            DUF948  23 klkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                        + ktl+++++  +++e++++++ +e++ + +k n+l ++ n+k +++ +l ++++d+   +++l
  gi|298674126|ref|YP_003725876.1| 341 VIDKTLESLNDKKRNIESEIQSLNEEIAIMKNKLNNLESEKNKKEQEIFRLEHELEDTKSDLKTL 405
                                       578*************************************9999999988888888877776665 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.36
                            DUF948  26 ktldeaaatieelekqvd.pilkevedllakvnelle 61 
                                       +tl+e+++  e l++ ++  i+k++++l ak+ el+e
  gi|298674126|ref|YP_003725876.1| 421 QTLKELENEYERLKELAKgDIVKKIDELEAKSSELQE 457
                                       3333333333333333221233333333333333333 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0  31.1   3.8e-05     0.026       2     200 .]       5     273 ..       4     303 .. 0.67
   2 ?   -0.5  27.0       2.1   1.4e+03      96     197 ..     279     407 ..     275     410 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.8e-05
                            AAA_23   2 Lkienfrsfrdqe.idF.skgltlItGpNGaGKTTildAiklaLygetprlsrks.....grgfeksdveiese... 68 
                                       L ++ ++ +r+++ + F s + + I G N  GKT+++  +  +L   ++++  k      + g++ ++ +++ +   
  gi|298674126|ref|YP_003725876.1|   5 LDLKDVGGLRGENnFSFeSGKANKILGSNAVGKTSLIKGMVSVLSIPPSGTFLKYgddaeRLGIKGDELSVHEGfvn 81 
                                       67899999987766***6669***********************987666555443344422444444444433667 PP

                            AAA_23  69 .gkvkayveltfenkdgry.......................................................... 86 
                                         +++a+v+l++ ++ ++y                                                          
  gi|298674126|ref|YP_003725876.1|  82 iYSDSAQVKLSYDSIEDTYtvepdgtviespdgnekflltgvvmdnsrvvqqlkygenshfgwfinqlsfadnyeel 158
                                       6788999****99999999999************************************************9999999 PP

                            AAA_23  87 ...trsiererelskkkgkttkkaklelleideleqfisellgskkiilnlilflgqerfeefelkdkkerleelek 160
                                           +s  ++++ +k++ +++k +++el ++ e+ ++ +e+++++ ++++  +   + r+  +e+k+ +e+++++ +
  gi|298674126|ref|YP_003725876.1| 159 ynlAQSYINDITSKKTSLNKRKSKAKELASELEKVKKQKEEIDQDREEISKKVNDNDIREIVEERKSIFEKIQNFHR 235
                                       99944444455555555555555555555554444444444555555555555555555555555555555555555 PP

                            AAA_23 161 eleeledekkllekleqekekekeleeleeeleeilkele 200
                                       +l+++ ++++  ++++  ++ke+  +el+e+l +++ke+e
  gi|298674126|ref|YP_003725876.1| 236 DLNDIYNRINNKKTKI--QKKEEIVNELNENLSNLNKEIE 273
                                       5555555554444433..3344444555555555555544 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2.1
                            AAA_23  96 lskkkgkttkkaklellei.deleqfisellgskki..........ilnlilflgqer.......feefelkdkker 154
                                       ++kkk +++ +++++++e  +e + +++ +++ +++          + + ++++ q++       +  ++l+dkk  
  gi|298674126|ref|YP_003725876.1| 279 NYKKKFDQKVNENTSKIESlKEDKAEVNASINLFQSaklklknenkSETTCILCEQGNlninvidKTLESLNDKKRN 355
                                       56677777777777777666667777777444444444444444437799999999998888887555666777776 PP

                            AAA_23 155 leelekeleeled.ekkllekleqekekek........eleeleeeleeilk 197
                                       +e+ +++l+e+ + +k++l++le ek+k++        ele+ +++l+++ +
  gi|298674126|ref|YP_003725876.1| 356 IESEIQSLNEEIAiMKNKLNNLESEKNKKEqeifrlehELEDTKSDLKTLRN 407
                                       6666666655554466677777666665555556666666666666666655 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4  25.5    0.0017       1.2       3     127 ..     177     301 ..     166     328 .. 0.80
   2 ?   -0.8  28.6       2.4   1.6e+03      21     123 ..     327     430 ..     304     565 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0017
                           zf-C4H2   3 keirektleleklknklakevealekeekcleey..kkelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekek 77 
                                       ++ ++k +el +  +k++k+ e++++ ++ +++    + + ++ +E+++  e+++  h+D+n++ + i++ +++ +k
  gi|298674126|ref|YP_003725876.1| 177 NKRKSKAKELASELEKVKKQKEEIDQDREEISKKvnDNDIREIVEERKSIFEKIQNFHRDLNDIYNRINNKKTKIQK 253
                                       567888888888889999988888888888876412567899*********************************** PP

                           zf-C4H2  78 slekakklyeeykklkeevnelrselglekledleeeeeellkeeifekq 127
                                       ++e +++l e++++l +e++ l  ++  +k +++ +e+++ +++    + 
  gi|298674126|ref|YP_003725876.1| 254 KEEIVNELNENLSNLNKEIEGLDVSNYKKKFDQKVNENTSKIESLK--ED 301
                                       *************************999999999888888765433..32 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.4
                           zf-C4H2  21 kevealekeekcleeykkelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekekslekakklyeeykklkeevn 97 
                                       + + ++e+ +  ++ + k+le L+  k++   e++ +++ i  + + +++ e+ek+k+++++ +l +e++  k+++ 
  gi|298674126|ref|YP_003725876.1| 327 TTCILCEQGNLNINVIDKTLESLNDKKRNIESEIQSLNEEIAIMKNKLNNLESEKNKKEQEIFRLEHELEDTKSDLK 403
                                       333457888899999************************************************************** PP

                           zf-C4H2  98 elrse.lglekledleeeeeellkeei 123
                                       +lr+e  + + l++ +e+  + l++e+
  gi|298674126|ref|YP_003725876.1| 404 TLRNEvKNDDDLKNEKEQTLKELENEY 430
                                       ****94444555554444444444444 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9  18.0       1.8   1.2e+03      91     183 ..     163     253 ..     159     275 .. 0.65
   2 ?    2.4  12.3      0.18   1.2e+02      91     175 ..     224     310 ..     214     322 .. 0.85
   3 ?    3.7   5.0     0.069        47     107     156 ..     277     326 ..     258     339 .. 0.78
   4 ?   12.8  11.6   0.00011     0.076     113     182 ..     341     410 ..     317     412 .. 0.86
   5 ?    3.9   4.9      0.06        41     132     184 ..     416     469 ..     407     473 .. 0.72
   6 ?   -0.6   0.0       1.4   9.9e+02      97     132 ..     485     522 ..     480     545 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.8
                            DUF724  91 qsrlnkLlslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlksea 167
                                       qs +n++ s k++ +k +++ k+l +++e+ +++k++++++ +e++kk+ +   ++    e++++  ++i + + + 
  gi|298674126|ref|YP_003725876.1| 163 QSYINDITSKKTSLNKRKSKAKELASELEKVKKQKEEIDQDREEISKKVNDNDIREI--VEERKSIFEKIQNFHRDL 237
                                       788999999999999999999999999999999999999999988888886666553..344444445555555555 PP

                            DUF724 168 ekleeeledveqeFea 183
                                       +++ +++++ +++ ++
  gi|298674126|ref|YP_003725876.1| 238 NDIYNRINNKKTKIQK 253
                                       5554444444444433 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.18
                            DUF724  91 qsrlnkLlslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallk..ekkeaadkeiarlks 165
                                       +s  +k+ +++ + + + +++++ + ki+++e+  ++l+e++++l+k+i  l   +  +k  +k +++ ++i +lk 
  gi|298674126|ref|YP_003725876.1| 224 KSIFEKIQNFHRDLNDIYNRINNKKTKIQKKEEIVNELNENLSNLNKEIEGLDVSNYKKKfdQKVNENTSKIESLKE 300
                                       56667888888888899999999999999999999999999999999999999999888898888889999999*99 PP

                            DUF724 166 eaekleeele 175
                                       ++++++ +++
  gi|298674126|ref|YP_003725876.1| 301 DKAEVNASIN 310
                                       9999999886 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.069
                            DUF724 107 lleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaa 156
                                       + + +kk+++k+ e++s+ ++l+e+ +e++  i  ++  +  lk++++++
  gi|298674126|ref|YP_003725876.1| 277 VSNYKKKFDQKVNENTSKIESLKEDKAEVNASINLFQSAKLKLKNENKSE 326
                                       56778999999999999999999999999999999988887777655554 PP

  == domain 4  score: 12.8 bits;  conditional E-value: 0.00011
                            DUF724 113 klekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledveqeFe 182
                                        ++k +e  +++kr++e+ei+ l+++i+ ++++l  l ++k+++++ei+rl++e e+ + +l+  ++e++
  gi|298674126|ref|YP_003725876.1| 341 VIDKTLESLNDKKRNIESEIQSLNEEIAIMKNKLNNLESEKNKKEQEIFRLEHELEDTKSDLKTLRNEVK 410
                                       456777777889999*********************************************9999998876 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.06
                            DUF724 132 idelekkilelerqlallk.ekkeaadkeiarlkseaekleeeledveqeFeav 184
                                        +e+e++ +ele++ ++lk   k +  k+i +l+++ ++l+ee+ +++++ +++
  gi|298674126|ref|YP_003725876.1| 416 KNEKEQTLKELENEYERLKeLAKGDIVKKIDELEAKSSELQEEIGSINEKIRST 469
                                       357888888888888888854667777888888888888888888777777666 PP

  == domain 6  score: -0.6 bits;  conditional E-value: 1.4
                            DUF724  97 Llslkdeqtklleerkklekkieee..esekrkleeei 132
                                        l++ +++  +lee+k++ +++     +++++k++e+i
  gi|298674126|ref|YP_003725876.1| 485 ALAIYNDWLYYLEELKEFANEMYSShrNEARKKFNEKI 522
                                       67888888899999999887775430033333444443 PP

>> DUF1644  Protein of unknown function (DUF1644)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   2.5       1.6   1.1e+03      61     165 ..     171     276 ..     147     279 .. 0.51
   2 ?   14.9   2.5   3.1e-05     0.021      39     120 ..     278     360 ..     274     385 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.6
                           DUF1644  61 ssass.ekeseeveeeseleekeesaelkCPlCrGevkgwkvveearkylnekkrsCseesCsfvGnykelrkharr 136
                                       s+++s +k++++++e ++  ek ++++ +    r e+++ +  +++r++++e+k s  e+  +f  + +++ + + +
  gi|298674126|ref|YP_003725876.1| 171 SKKTSlNKRKSKAKELASELEKVKKQKEEIDQDREEISKKVNDNDIREIVEERK-SIFEKIQNFHRDLNDIYNRINN 246
                                       222220222222222222233445555566666777777777777777776654.4555566677777777666655 PP

                           DUF1644 137 ehp.tarpsevdpsrereWrrlerereleD 165
                                       + +  ++ +e+  + +++ ++l++e e  D
  gi|298674126|ref|YP_003725876.1| 247 KKTkIQKKEEIVNELNENLSNLNKEIEGLD 276
                                       444034555666666666666666666555 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 3.1e-05
                           DUF1644  39 snCldrfkkakaksksse.eessssassekeseeveeeseleekeesaelkCPlCrGevkgwkvveearkylnekkr 114
                                       sn  ++f +  ++++s+  + ++++a+ +++ +  ++++ + ++e+++e +C lC     + +v++++ + ln kkr
  gi|298674126|ref|YP_003725876.1| 278 SNYKKKFDQKVNENTSKIeSLKEDKAEVNASINLFQSAKLKLKNENKSETTCILCEQGNLNINVIDKTLESLNDKKR 354
                                       566666665555444444044444444444444455555556689999*******99999***************** PP

                           DUF1644 115 sCsees 120
                                         ++e 
  gi|298674126|ref|YP_003725876.1| 355 NIESEI 360
                                       988875 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7  11.4     0.015        10      26      96 ..     153     216 ..     147     242 .. 0.76
   2 ?    2.6  12.7      0.27   1.8e+02      29     121 ..     231     325 ..     215     337 .. 0.74
   3 ?    7.4  22.1    0.0085       5.8      34     127 ..     348     431 ..     333     433 .. 0.63
   4 ?    4.4  12.4     0.073        51      33      97 ..     407     472 ..     400     476 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.015
                            APG6_N  26 daYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealee 96 
                                       d+Yee  +  +++        +++ + + +l k +++ +el +eL++++k++ee+++++++++++ ++ + 
  gi|298674126|ref|YP_003725876.1| 153 DNYEELYNLAQSY---I----NDITSKKTSLNKRKSKAKELASELEKVKKQKEEIDQDREEISKKVNDNDI 216
                                       5666666666666...2....3778889999999**************************99998766554 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.27
                            APG6_N  29 eeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkele..kereeleaelaaleeelealeeeeerfwr 103
                                       ++f + l++  +  +++++++++ ee + +l++  ++l +e++ l+  + +++ ++++++ +++ e l+e++++   
  gi|298674126|ref|YP_003725876.1| 231 QNFHRDLNDIYNRINNKKTKIQKKEEIVNELNENLSNLNKEIEGLDvsNYKKKFDQKVNENTSKIESLKEDKAEVNA 307
                                       34444444443333445677888888888899999999999887652267899999999999999999999999999 PP

                            APG6_N 104 eynelqlelleleeelds 121
                                       + n +q  +l+l++e +s
  gi|298674126|ref|YP_003725876.1| 308 SINLFQSAKLKLKNENKS 325
                                       999999999999999887 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0085
                            APG6_N  34 klkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelql 110
                                                   +++ +++e e++ l++e + + ++L++le+e+ + e+e+  le ele+ + + +   +e ++ + 
  gi|298674126|ref|YP_003725876.1| 348 S----------LNDKKRNIESEIQSLNEEIAIMKNKLNNLESEKNKKEQEIFRLEHELEDTKSDLKTLRNEVKNDDD 414
                                       2..........234556666666666666666666666666666666666666666666666666666666666666 PP

                            APG6_N 111 elleleeeldsleaqye 127
                                        ++e+e+ l+ le++ye
  gi|298674126|ref|YP_003725876.1| 415 LKNEKEQTLKELENEYE 431
                                       66666666666666665 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.073
                            APG6_N  33 kklkkekkeeekqdeeleeleeeleklek.eeeelleeLkelekereeleaelaaleeelealeee 97 
                                       +++k++++ ++++++ l+ele+e+e+l++ ++ + +++++ele++ +el++e+ ++ e+ +    e
  gi|298674126|ref|YP_003725876.1| 407 NEVKNDDDLKNEKEQTLKELENEYERLKElAKGDIVKKIDELEAKSSELQEEIGSINEKIRSTTGE 472
                                       44555555555588899999999999987245689999***************9999988766555 PP

>> Aminopep  Putative aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.6      0.77   5.3e+02     220     272 ..     160     212 ..     150     220 .. 0.63
   2 ?   10.6   7.3   0.00038      0.26     195     294 ..     211     313 ..     191     322 .. 0.78
   3 ?    4.2   5.6     0.033        22     198     257 ..     379     438 ..     364     516 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.77
                          Aminopep 220 rLealYasdlsaeek.raakaeileelraeyaelkaeelkglagydewvakpln 272
                                       +L++ Y +d+++++   +++++  +el +e +++k+++ +  +  +e  + ++n
  gi|298674126|ref|YP_003725876.1| 160 NLAQSYINDITSKKTsLNKRKSKAKELASELEKVKKQKEEIDQDREEISK-KVN 212
                                       67788888766555404555667888999999998865555444444333.355 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00038
                          Aminopep 195 aareeaaaekarreqfralvkatrerLealYasdlsaeekraakaeileelraeyaelkaeelkg..lagydewvak 269
                                        +++++++  ++r++  + +++ +++L+++Y++  ++++k ++k+ei++el ++ ++l++ e++g  +++y++ +++
  gi|298674126|ref|YP_003725876.1| 211 VNDNDIREIVEERKSIFEKIQNFHRDLNDIYNRINNKKTKIQKKEEIVNELNENLSNLNK-EIEGldVSNYKKKFDQ 286
                                       4467788888999999999***************************************99.6666567899999999 PP

                          Aminopep 270 plnN..akllavaaYdelvpafealfe 294
                                       ++n    k++ +++ +++v+a  +lf+
  gi|298674126|ref|YP_003725876.1| 287 KVNEntSKIESLKEDKAEVNASINLFQ 313
                                       876411345555555555555555555 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.033
                          Aminopep 198 eeaaaekarreqfralvkatrerLealYasdlsaeekraakaeileelraeyaelkaeel 257
                                       +e ++++++  ++++ +++t+++L++l ++  ++++ +++k+++l+el +ey++lk+   
  gi|298674126|ref|YP_003725876.1| 379 SEKNKKEQEIFRLEHELEDTKSDLKTLRNEVKNDDDLKNEKEQTLKELENEYERLKELAK 438
                                       33334444444556678999***********************************98433 PP

>> DUF3287  Protein of unknown function (DUF3287)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       3.5   2.4e+03      10      36 ..      43      69 ..      37      75 .. 0.75
   2 ?   -0.1   0.7         1   6.9e+02      56      91 ..     189     224 ..     172     227 .. 0.77
   3 ?    1.5   0.6      0.34   2.3e+02      57      84 ..     227     254 ..     220     274 .. 0.71
   4 ?   12.1   0.8   0.00018      0.12      65     102 ..     347     384 ..     338     397 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.5
                           DUF3287 10 phesnlllldlplflssprdFerasvk 36
                                         s l++   + fl +++d er ++k
  gi|298674126|ref|YP_003725876.1| 43 GMVSVLSIPPSGTFLKYGDDAERLGIK 69
                                      5444455555899********999987 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1
                           DUF3287  56 fidkvvekHrrlcderqklgkkrqtleaRiarveRk 91 
                                        ++kv+++     ++r+++ kk++    R +  eRk
  gi|298674126|ref|YP_003725876.1| 189 ELEKVKKQKEEIDQDREEISKKVNDNDIREIVEERK 224
                                       468999999999999999999999877776666665 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.34
                           DUF3287  57 idkvvekHrrlcderqklgkkrqtleaR 84 
                                       ++k+ + Hr l+d  +++  k  +++++
  gi|298674126|ref|YP_003725876.1| 227 FEKIQNFHRDLNDIYNRINNKKTKIQKK 254
                                       7889999999999999998887777543 PP

  == domain 4  score: 12.1 bits;  conditional E-value: 0.00018
                           DUF3287  65 rrlcderqklgkkrqtleaRiarveRklreleseprdW 102
                                        +l+d+++++   +q+l+  ia ++ kl +lese  + 
  gi|298674126|ref|YP_003725876.1| 347 ESLNDKKRNIESEIQSLNEEIAIMKNKLNNLESEKNKK 384
                                       589******************************98764 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   6.8     0.094        65      23      82 ..     153     211 ..     146     215 .. 0.59
   2 ?    7.5  11.8     0.003       2.1       2      84 ..     214     314 ..     213     348 .. 0.77
   3 ?    7.7  15.0    0.0027       1.8       5      83 ..     354     438 ..     350     468 .. 0.88
   4 ?    3.5   0.6     0.051        35       2      48 ..     421     468 ..     420     484 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.094
                             TMPIT  23 qkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvl 82 
                                        + eel +l ++  ++i+++k  l++ ks+ k+l +++ e+ +++ ee++++ +e++k +
  gi|298674126|ref|YP_003725876.1| 153 DNYEELYNLAQSYINDITSKKTSLNKRKSKAKELASEL-EKVKKQKEEIDQDREEISKKV 211
                                       55666677777777777777777777777777776665.344555555555555554444 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.003
                             TMPIT   2 eeweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk...............ee 63 
                                       ++++e+ +e k++ e+ ++++++l+++ + +++ +++i+k+++ ++el+++l++l+k+++               +e
  gi|298674126|ref|YP_003725876.1| 214 NDIREIVEERKSIFEKIQNFHRDLNDIYNRINNKKTKIQKKEEIVNELNENLSNLNKEIEgldvsnykkkfdqkvNE 290
                                       5789999***************************************************8877788888888877777 PP

                             TMPIT  64 eeeeveelkeelkerkkvlk...e 84 
                                       + +++e+lke+ +e +++++   +
  gi|298674126|ref|YP_003725876.1| 291 NTSKIESLKEDKAEVNASINlfqS 314
                                       777788888777777776664423 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0027
                             TMPIT   5 eelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk......eeeeeeveelkeel 75 
                                       +++e+e+++l+e+   +k+kl++l++ ++k  +ei + +++l++ ks+lk+l+++vk      +e+e++++el++e 
  gi|298674126|ref|YP_003725876.1| 354 RNIESEIQSLNEEIAIMKNKLNNLESEKNKKEQEIFRLEHELEDTKSDLKTLRNEVKndddlkNEKEQTLKELENEY 430
                                       6899**************************************************98778888889999999999999 PP

                             TMPIT  76 kerkkvlk 83 
                                       ++ k+  k
  gi|298674126|ref|YP_003725876.1| 431 ERLKELAK 438
                                       99887766 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.051
                             TMPIT   2 eeweelekefkeleetak.eykqkleelsklqskcskeikkqkkrlke 48 
                                       + ++ele+e+++l+e ak  + +k++el++  s++++ei + ++++++
  gi|298674126|ref|YP_003725876.1| 421 QTLKELENEYERLKELAKgDIVKKIDELEAKSSELQEEIGSINEKIRS 468
                                       567889999999998874368888899998888888888888777765 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1  20.8     0.019        13      13     120 ..     160     274 ..     153     277 .. 0.86
   2 ?    5.3  15.4     0.033        23      15     118 ..     284     388 ..     275     392 .. 0.82
   3 ?    7.6  20.9    0.0065       4.5       3     121 ..     351     469 ..     347     470 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.019
                           DUF5082  13 aelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnssesWkGk.eennydgirs...nlessyqtyvdk 85 
                                         ++s i+++ +k + L + k+k ++  ++l++ kk+ e+++ + e+  +k ++n+  +i++   ++ +++q+++++
  gi|298674126|ref|YP_003725876.1| 160 NLAQSYINDITSKKTSLNKRKSKAKELASELEKVKKQKEEIDQDREEISKKvNDNDIREIVEerkSIFEKIQNFHRD 236
                                       55789999*******************************************9********99999************ PP

                           DUF5082  86 ldelidaieeEIerLenq...iseaqgvldtlqsqlns 120
                                       l ++  +i+++ ++++++   ++e+  +l++l+++++ 
  gi|298674126|ref|YP_003725876.1| 237 LNDIYNRINNKKTKIQKKeeiVNELNENLSNLNKEIEG 274
                                       ********987555544322267888888888877765 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.033
                           DUF5082  15 lrseiaaleekIerLkeaktklsdekeslkqkkkklekplnsse..sWkGkeennydgirsnlessyqtyvdkldel 89 
                                         ++++ + +kIe Lke k ++ +  + ++++k kl++   s+    ++ ++ n  ++   ++ +s +  ++++++ 
  gi|298674126|ref|YP_003725876.1| 284 FDQKVNENTSKIESLKEDKAEVNASINLFQSAKLKLKNENKSETtcILC-EQGNLNINVIDKTLESLNDKKRNIESE 359
                                       567899999************************9999887777753343.445555566669999999999999999 PP

                           DUF5082  90 idaieeEIerLenqiseaqgvldtlqsql 118
                                       i++++eEI  ++n+++++++  +++++++
  gi|298674126|ref|YP_003725876.1| 360 IQSLNEEIAIMKNKLNNLESEKNKKEQEI 388
                                       ****************9999888888777 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0065
                           DUF5082   3 tkisklqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnsse....sWkGk..eennydgirs 73 
                                        k+++        +sei++l+e I+  k     l++ek++ +q++  le+ l +++    +++++  ++++ +++ +
  gi|298674126|ref|YP_003725876.1| 351 DKKRNI-------ESEIQSLNEEIAIMKNKLNNLESEKNKKEQEIFRLEHELEDTKsdlkTLRNEvkNDDDLKNEKE 420
                                       344555.......5555555555555555555555555555555555555555555444477777336666777777 PP

                           DUF5082  74 nlessyqtyvdkldel.idaieeEIerLenqiseaqgvldtlqsqlnsl 121
                                       ++ ++ ++ +++l+el +  i ++I +Le + se+q  ++++++++ s+
  gi|298674126|ref|YP_003725876.1| 421 QTLKELENEYERLKELaKGDIVKKIDELEAKSSELQEEIGSINEKIRST 469
                                       99999999999999972569***********************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (634 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3857  (0.215126); expected 358.6 (0.02)
Passed bias filter:                      710  (0.0396006); expected 358.6 (0.02)
Passed Vit filter:                       241  (0.0134419); expected 17.9 (0.001)
Passed Fwd filter:                       141  (0.00786435); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 2.28u 0.37s 00:00:02.65 Elapsed: 00:00:00.60
# Mc/sec: 3172.67
//
Query:       gi|298674127|ref|YP_003725877.1|  [L=267]
Description: hypothetical protein Metev_0150 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1729.11
//
Query:       gi|298674128|ref|YP_003725878.1|  [L=377]
Description: phosphoadenosine phosphosulfate reductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.4e-39  135.2   0.4    3.9e-38  131.2   0.0    2.5  2  PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
    2.5e-05   24.2   9.7      0.016   15.2   0.3    3.0  2  Fer4_6       4Fe-4S binding domain
     0.0001   22.8  19.9    0.00058   20.4   8.1    2.4  2  Fer4_7       4Fe-4S dicluster domain
    0.00042   20.4  20.4     0.0034   17.5   9.2    2.5  3  Fer4_9       4Fe-4S dicluster domain
     0.0011   18.7   4.1     0.0011   18.7   4.1    3.0  2  Fer4         4Fe-4S binding domain
     0.0011   18.9  12.4       0.21   11.8   6.0    2.8  2  Fer4_2       4Fe-4S binding domain
     0.0064   16.9   5.8      0.011   16.2   0.4    2.6  2  Fer4_8       4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.013   16.4   0.4      0.013   16.4   0.4    3.1  3  Fer4_16      4Fe-4S double cluster binding domain
       0.02   15.4   0.4       0.02   15.4   0.4    2.9  3  Fer4_17      4Fe-4S dicluster domain
      0.021   15.3   3.8      0.021   15.3   3.8    2.9  2  Fer4_4       4Fe-4S binding domain
      0.039   14.1  13.5       0.12   12.5   4.3    2.6  2  Fer4_21      4Fe-4S dicluster domain
        4.4    8.5  15.7       0.79   10.8   6.8    2.8  2  Fer4_3       4Fe-4S binding domain
        5.2    7.3  22.6       0.31   11.2   6.4    2.5  2  Fer4_10      4Fe-4S dicluster domain
          6    7.7  10.5        7.2    7.4   0.3    2.8  2  Fer4_15      4Fe-4S single cluster domain
        8.6    7.0  12.7         17    6.0   3.9    3.1  3  Fer4_13      4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.2   0.0   3.3e-41   3.9e-38       2     172 ..      23     189 ..      22     191 .. 0.94
   2 ?    1.0   0.6      0.31   3.7e+02      40      81 ..     199     242 ..     192     325 .. 0.56

  Alignments for each domain:
  == domain 1  score: 131.2 bits;  conditional E-value: 3.3e-41
                                       EEEE--SSCTCHHHHHHHHHHCTTHEEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-THH CS
                       PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpvpvvfvdtghefpetiefvdeleeryglrlkvyepeeevaekinaekhgssly 78 
                                       l+vs+sgGkdslV+l+L++++  + +vvf dt  ef+e ++f++ +e+ yg+++ v+++++++ + + + + +s+  
  gi|298674128|ref|YP_003725878.1|  23 LAVSFSGGKDSLVVLDLCTRVGIE-KVVFSDTTIEFKENLNFIKTVEKVYGIKIDVVSSNNDFFDVVDRVGFPSRRL 98 
                                       789*********************.7*************************************************** PP

                                       HCHHHHHHTHHHHHHHHHCTTECEEE----CCCTTTTTTSSSEEECTTT-SCEEE-CCCT--HHHHHHHHHHCT--B CS
                       PAPS_reduct  79 eeaaeriaKveplkkaLekldedalltGaRrdesksraklpiveidedfekslrvfPllnWteedvwqyilrenipy 155
                                       ++ ++++ K  pl k   + + d  +tG+Rr e k+ra    v  ++  +   +++P+lnW+e dvw+yi ++n+p+
  gi|298674128|ref|YP_003725878.1|  99 RW-CCDVFKFGPLAKYAIDKNLDGYVTGLRRAEAKTRADYFDVDNNQMVP-ISQINPILNWEEDDVWEYINEHNLPI 173
                                       **.**********9987777889***************876666666655.8899********************** PP

                                       -CCCCTT-SS--BCTTB CS
                       PAPS_reduct 156 npLydqgfrsiGcvpct 172
                                       npLy+  f++iGc+ c+
  gi|298674128|ref|YP_003725878.1| 174 NPLYE-YFDRIGCWCCP 189
                                       ****7.6*******997 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.31
                                       HHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-THHHC....H CS
                       PAPS_reduct  40 tiefvdeleeryglrlkvyepeeevaekinaekhgsslyee....a 81 
                                       + +++ el e+++ +l  +  ++++++k++  k  +++++     +
  gi|298674128|ref|YP_003725878.1| 199 LEKYFPELMEKLEAKLDQFADQIGIKDKEQFIK--EKKWTGwataQ 242
                                       566667777777777777777776666666555..35555433232 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   4.0    0.0003      0.35       8      20 ..     315     327 ..     315     331 .. 0.86
   2 !   15.2   0.3   1.4e-05     0.016       2      16 ..     338     352 ..     337     354 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0003
                            Fer4_6   8 kCigCgdCvrvCP 20 
                                       +C+gCg+C++ CP
  gi|298674128|ref|YP_003725878.1| 315 NCVGCGACTALCP 327
                                       6************ PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.4e-05
                            Fer4_6   2 veidpdkCigCgdCv 16 
                                       +++d+++C+ C++C 
  gi|298674128|ref|YP_003725878.1| 338 ITVDENLCTKCEKCL 352
                                       79************6 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   3.9   1.1e-05     0.013      24      52 .]     302     330 ..     292     330 .. 0.64
   2 !   20.4   8.1   4.9e-07   0.00058       2      46 ..     316     353 ..     315     361 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.1e-05
                            Fer4_7  24 nekgtekveidpekClgCgaCvavCPtga 52 
                                       +++++ ++  + ++C+gCgaC a CP ga
  gi|298674128|ref|YP_003725878.1| 302 KKQRVNTLIEKCMNCVGCGACTALCPLGA 330
                                       23333444445678889999999999886 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 4.9e-07
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCva 46 
                                       C+gCgaC+a Cp +a+++++         +++d++ C+ C++C +
  gi|298674128|ref|YP_003725878.1| 316 CVGCGACTALCPLGALYVEN-------GLITVDENLCTKCEKCLS 353
                                       *****************954.......479*************75 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       5.4   6.5e+03      36      39 ..     185     188 ..     166     195 .. 0.72
   2 !   16.4   3.3   6.2e-06    0.0074      20      50 ..     300     330 ..     292     331 .. 0.68
   3 !   17.5   9.2   2.8e-06    0.0034       1      43 [.     315     352 ..     315     354 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 5.4
                            Fer4_9  36 CigC 39 
                                       C+ C
  gi|298674128|ref|YP_003725878.1| 185 CWCC 188
                                       5544 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 6.2e-06
                            Fer4_9  20 daaerkarlraaseeaCigCgaCveaCpkga 50 
                                       +++++ ++  +++  +C+gCgaC++ Cp ga
  gi|298674128|ref|YP_003725878.1| 300 KNKKQRVNTLIEKCMNCVGCGACTALCPLGA 330
                                       4444444444444479************886 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 2.8e-06
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCv 43 
                                       +C+gCgaC++ Cp g+   +++  ++  +      C++C++C+
  gi|298674128|ref|YP_003725878.1| 315 NCVGCGACTALCPLGALYVENGLITVDEN-----LCTKCEKCL 352
                                       6****************999999999874.....6*******7 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   4.1   9.2e-07    0.0011       7      24 .]     315     332 ..     314     332 .. 0.92
   2 !   10.8   0.9   0.00028      0.33       1      14 [.     338     351 ..     338     353 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 9.2e-07
                                       TSSS-THHHHHSTTTEEE CS
                              Fer4   7 kCigCGaCvevCPvgAIt 24 
                                        C+gCGaC   CP gA++
  gi|298674128|ref|YP_003725878.1| 315 NCVGCGACTALCPLGALY 332
                                       5***************85 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00028
                                       EEEETTTSSS-THH CS
                              Fer4   1 vvideekCigCGaC 14 
                                       +++de++C++C +C
  gi|298674128|ref|YP_003725878.1| 338 ITVDENLCTKCEKC 351
                                       689*********** PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   6.0   0.00017      0.21       9      21 ..     315     327 ..     308     328 .. 0.87
   2 !   10.1   0.4   0.00057      0.69       3      18 ..     338     353 ..     336     354 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00017
                            Fer4_2   9 rCigCgaCvsaCP 21 
                                       +C+gCgaC+  CP
  gi|298674128|ref|YP_003725878.1| 315 NCVGCGACTALCP 327
                                       7999****888*9 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00057
                            Fer4_2   3 vvvdtdrCigCgaCvs 18 
                                       + vd++ C+ C++C+s
  gi|298674128|ref|YP_003725878.1| 338 ITVDENLCTKCEKCLS 353
                                       679***********86 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.4   9.2e-06     0.011       2      17 ..     313     328 ..     282     338 .. 0.76
   2 ?    2.5   0.8      0.17     2e+02       5      12 ..     345     352 ..     339     371 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.2e-06
                            Fer4_8   2 lekCieCgaCqsaCpv 17 
                                       +++C++CgaC++ Cp+
  gi|298674128|ref|YP_003725878.1| 313 CMNCVGCGACTALCPL 328
                                       5666666666666664 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.17
                            Fer4_8   5 CieCgaCq 12 
                                       C++C+ C 
  gi|298674128|ref|YP_003725878.1| 345 CTKCEKCL 352
                                       55555554 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.6       9.6   1.1e+04      40      40 ..     216     216 ..     185     255 .. 0.55
   2 ?   16.4   0.4   1.1e-05     0.013      36      66 ..     301     328 ..     282     336 .. 0.69
   3 ?    1.5   2.1      0.51   6.1e+02       2      10 ..     345     353 ..     344     354 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 9.6
                           Fer4_16  40 d 40 
                                       +
  gi|298674128|ref|YP_003725878.1| 216 Q 216
                                       1 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 1.1e-05
                           Fer4_16  36 aekkdlaedeekckkqeaitgCdiCqdvCPa 66 
                                       ++k+++++ +ekc+   ++ gC++C++ CP 
  gi|298674128|ref|YP_003725878.1| 301 NKKQRVNTLIEKCM---NCVGCGACTALCPL 328
                                       45555666666666...67777777777774 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.51
                           Fer4_16   2 CgtCgkCae 10 
                                       C++C+kC++
  gi|298674128|ref|YP_003725878.1| 345 CTKCEKCLS 353
                                       *******86 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       9.5   1.1e+04      20      20 ..     196     196 ..     184     235 .. 0.49
   2 ?   15.4   0.4   1.7e-05      0.02      40      58 ..     307     328 ..     280     331 .. 0.74
   3 ?    3.4   1.1     0.098   1.2e+02      44      53 ..     343     352 ..     339     367 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 9.5
                           Fer4_17  20 n 20 
                                       +
  gi|298674128|ref|YP_003725878.1| 196 W 196
                                       2 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.7e-05
                           Fer4_17  40 e...ekaslCieCgeCerkCPq 58 
                                       +   ek+ +C++Cg C++ CP 
  gi|298674128|ref|YP_003725878.1| 307 NtliEKCMNCVGCGACTALCPL 328
                                       245679999***********96 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.098
                           Fer4_17  44 slCieCgeCe 53 
                                       +lC++C++C 
  gi|298674128|ref|YP_003725878.1| 343 NLCTKCEKCL 352
                                       5788888886 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   3.8   1.8e-05     0.021       3      16 ..     315     328 ..     310     332 .. 0.91
   2 ?    3.2   1.2      0.13   1.5e+02       2      12 ..     343     353 ..     342     354 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.8e-05
                            Fer4_4   3 rCigCgsCvaaCPq 16 
                                       +C+gCg+C+a CP 
  gi|298674128|ref|YP_003725878.1| 315 NCVGCGACTALCPL 328
                                       69***********6 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.13
                            Fer4_4   2 erCigCgsCva 12 
                                       + C+ C +C +
  gi|298674128|ref|YP_003725878.1| 343 NLCTKCEKCLS 353
                                       56*******65 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   4.3   9.9e-05      0.12      32      55 ..     305     329 ..     293     333 .. 0.64
   2 ?    5.4   1.9     0.017        20       3      16 ..     340     353 ..     338     363 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.9e-05
                           Fer4_21  32 tvlkvved..eCvGCnlCssvCPved 55 
                                       +v +++e+  +CvGC  C++ CP+ +
  gi|298674128|ref|YP_003725878.1| 305 RVNTLIEKcmNCVGCGACTALCPL-G 329
                                       233334433389***********7.4 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.017
                           Fer4_21   3 idedkCigCgkCli 16 
                                       +de+ C +C+kCl 
  gi|298674128|ref|YP_003725878.1| 340 VDENLCTKCEKCLS 353
                                       78888888888864 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   6.8   0.00066      0.79       1      15 []     316     330 ..     316     330 .. 0.97
   2 ?    1.9   1.5      0.47   5.6e+02       1       8 [.     345     352 ..     345     354 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00066
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+gCgaC   CP gA
  gi|298674128|ref|YP_003725878.1| 316 CVGCGACTALCPLGA 330
                                       ************998 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.47
                            Fer4_3   1 CtgCgaCv 8  
                                       Ct C+ C+
  gi|298674128|ref|YP_003725878.1| 345 CTKCEKCL 352
                                       *******7 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   6.4   0.00026      0.31      36      56 .]     307     327 ..     292     327 .. 0.71
   2 ?    5.5   3.1     0.015        18       2      17 ..     338     353 ..     337     367 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00026
                           Fer4_10  36 eavrkkvekCtgcgaCveaCP 56 
                                       ++  +k+ +C gcgaC++ CP
  gi|298674128|ref|YP_003725878.1| 307 NTLIEKCMNCVGCGACTALCP 327
                                       3344568888889*******9 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.015
                           Fer4_10   2 vvidddtCirCgkCvk 17 
                                       + +d++ C++C+kC +
  gi|298674128|ref|YP_003725878.1| 338 ITVDENLCTKCEKCLS 353
                                       568999********75 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   4.5      0.18   2.2e+02       7      19 ..     315     327 ..     313     332 .. 0.93
   2 ?    7.4   0.3     0.006       7.2       1      16 [.     338     353 ..     338     359 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.18
                           Fer4_15   7 aCigcglCvaeap 19 
                                       +C gcg+C a++p
  gi|298674128|ref|YP_003725878.1| 315 NCVGCGACTALCP 327
                                       7**********98 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.006
                           Fer4_15   1 VvvDrdaCigcglCva 16 
                                       ++vD+++C+ c+ C+ 
  gi|298674128|ref|YP_003725878.1| 338 ITVDENLCTKCEKCLS 353
                                       79************86 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0         6   7.2e+03      16      26 ..     101     111 ..      99     121 .. 0.73
   2 ?    6.0   3.9     0.014        17       5      17 ..     315     327 ..     312     333 .. 0.95
   3 ?    5.0   1.0     0.029        35       1      15 [.     340     354 ..     340     355 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 6
                           Fer4_13  16 aPdvFeeddeg 26 
                                       + dvF+  +  
  gi|298674128|ref|YP_003725878.1| 101 CCDVFKFGPLA 111
                                       999**998863 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.014
                           Fer4_13   5 tCiacgaCvelaP 17 
                                       +C++cgaC +l+P
  gi|298674128|ref|YP_003725878.1| 315 NCVGCGACTALCP 327
                                       7***********9 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.029
                           Fer4_13   1 VDrdtCiacgaCvel 15 
                                       VD++ C+ c++C ++
  gi|298674128|ref|YP_003725878.1| 340 VDENLCTKCEKCLST 354
                                       89**********875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       939  (0.0523733); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 2248.53
//
Query:       gi|298674129|ref|YP_003725879.1|  [L=280]
Description: hypothetical protein Metev_0152 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1780.56
//
Query:       gi|298674130|ref|YP_003725880.1|  [L=43]
Description: hypothetical protein Metev_0153 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1098  (0.0612416); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 297.48
//
Query:       gi|298674131|ref|YP_003725881.1|  [L=525]
Description: hypothetical protein Metev_0154 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (525 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       999  (0.0557198); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 3309.16
//
Query:       gi|298674132|ref|YP_003725882.1|  [L=611]
Description: hypothetical protein Metev_0155 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
        0.2   11.8   0.1        0.2   11.8   0.1    2.3  3  tRNA_lig_kinase  tRNA ligase kinase domain
        3.7    7.1   5.8        3.2    7.3   0.1    2.7  3  JAMP             JNK1/MAPK8-associated membrane protein


Domain annotation for each model (and alignments):
>> tRNA_lig_kinase  tRNA ligase kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.62   5.6e+03      65     102 ..      72     108 ..      44     115 .. 0.68
   2 ?   -3.2   0.1      0.89     8e+03      56      80 ..     297     322 ..     290     332 .. 0.67
   3 ?   11.8   0.1   2.2e-05       0.2      38     135 ..     388     482 ..     365     499 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.62
                                       -SHHHHHHHHHHHHHHHHHH--TT-EEEEEEEE-S-TT CS
                   tRNA_lig_kinase  65 hqkreRkqlfeeidelkeeylsydvnvkvvalsFvded 102
                                       ++k+ +k   e+ ++ + + + +   +++v +sF+++d
  gi|298674132|ref|YP_003725882.1|  72 SKKKGKKITTEQYSRARLDLI-NARIINYVKMSFKKHD 108
                                       455555555556666666555.4445788889998877 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.89
                                       -EEEEE.S---SHHHHHHHHHHHHHH CS
                   tRNA_lig_kinase  56 kvvlvD.rnnhqkreRkqlfeeidel 80 
                                       ++vl   +n ++kr++k+l ++ + +
  gi|298674132|ref|YP_003725882.1| 297 NLVLSQlKNTSEKRKKKNLSNWYSYM 322
                                       44554427778888888888887655 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 2.2e-05
                                       -SS-HHHHHHHTTSSTT--EEEEES---SHHHHHHHHHHHHHHHHHH--TT-EEEEEEEE-S-TT-HHHHHHHHHHH CS
                   tRNA_lig_kinase  38 dkkklvkealellkkdeskvvlvDrnnhqkreRkqlfeeidelkeeylsydvnvkvvalsFvdeddleevreltkdR 114
                                       +  +  +++++++k+++s+v+++Drn +++   ++ +   +   ++y+  + +  ++ ++F d+  ++ ++   ++ 
  gi|298674132|ref|YP_003725882.1| 388 KADEQHNKTIDIFKEHGSEVIYADRNHAKAVLDSENLIIHSMATTSYM-GNKRESYIIINFEDHPLKDMIHSTFYNM 463
                                       4455678899****************9887665544333333344455.778889999***9998778888888999 PP

                                       HH-------------.-HHHH CS
                   tRNA_lig_kinase 115 vlkRGdnhqsikvesedekkv 135
                                       +   G+  qs  +++   kk+
  gi|298674132|ref|YP_003725882.1| 464 IYYLGQGKQSSFIHE--WKKI 482
                                       999999999866655..4555 PP

>> JAMP  JNK1/MAPK8-associated membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1   0.00036       3.2     171     204 ..     209     242 ..     176     271 .. 0.82
   2 ?    1.7   0.2     0.019   1.7e+02     111     126 ..     311     326 ..     302     336 .. 0.86
   3 ?   -1.5   0.1      0.17   1.5e+03     161     203 ..     426     466 ..     421     467 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00036
                              JAMP 171 kkkkkaaksiYaalyflPilvvihavlaGliyys 204
                                       k+   +++++Y+  +++ ++  + a++aGliyys
  gi|298674132|ref|YP_003725882.1| 209 KECVNKNMTLYCPAISMGMMKRVSAIIAGLIYYS 242
                                       344445689************************8 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.019
                              JAMP 111 evkklsdwYtllyNPs 126
                                       ++k+ls+wY+ +y P 
  gi|298674132|ref|YP_003725882.1| 311 KKKNLSNWYSYMYEPV 326
                                       6789**********96 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.17
                              JAMP 161 irpllvkklekkkkkaaksiYaalyf..lPilvvihavlaGliyy 203
                                       i++++++ ++ +k+      Y+ + f  +P+  +ih+++  +iyy
  gi|298674132|ref|YP_003725882.1| 426 IHSMATTSYMGNKR----ESYIIINFedHPLKDMIHSTFYNMIYY 466
                                       44444444333333....345554443389999***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (611 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 3756.19
//
Query:       gi|298674133|ref|YP_003725883.1|  [L=79]
Description: hypothetical protein Metev_0156 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.024   15.5   0.0      0.036   14.9   0.0    1.3  1  EF-hand_11  EF-hand domain


Domain annotation for each model (and alignments):
>> EF-hand_11  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0     2e-06     0.036      64      85 ..      12      33 ..       8      45 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2e-06
                                      TS-B-TTS-EEHHHHHHHHCS- CS
                        EF-hand_11 64 elpvnakgrlkyqdflsklsie 85
                                      e+ vn k +lky+d++ klsi 
  gi|298674133|ref|YP_003725883.1| 12 EVIVNLKTKLKYPDYIQKLSIR 33
                                      789*****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       992  (0.0553294); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 509.60
//
Query:       gi|298674134|ref|YP_003725884.1|  [L=382]
Description: restriction endonuclease [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-20   71.3   0.5    1.6e-19   70.0   0.5    1.7  1  Mrr_cat   Restriction endonuclease


Domain annotation for each model (and alignments):
>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.0   0.5   9.1e-24   1.6e-19       2     114 ..     265     377 ..     264     378 .. 0.92

  Alignments for each domain:
  == domain 1  score: 70.0 bits;  conditional E-value: 9.1e-24
                                       TTT-TTCHHHHHHHHHHHHSSSEEE---B-TTSSB--EEEETTEEEEEEEEEEE--T.....S-B-HHHHHHHHHHC CS
                           Mrr_cat   2 dkmspkeFeklvaellealGykeveltgrsgDggiDliakkdplgserilvqaKryk.....nkvgvkeVqeligal 73 
                                       ++++ +e+ek+v +l+ea+ y+ v+ t+  +D+g D+ia+k  lg+eri++q+K +k     n+++  +Vq++  a 
  gi|298674134|ref|YP_003725884.1| 265 QDLKSHELEKVVYNLYEAMYYH-VDFTE-YQDQGGDIIATK--LGKERIIIQVKSHKnnkdgNRISNFAVQQVKTAQ 337
                                       68899****************9.99996.789999****98..99***********7656667899999******** PP

                                       TTS..SEEEEEESS-B-HHHHHHHHTT--EEEE-HHHHHHH CS
                           Mrr_cat  74 kkrgadkgifvttsdftkaAreeaeelnkieLldgdeLael 114
                                       + + a+k ++v +++f++aA e a++ n++eL+d d L+ l
  gi|298674134|ref|YP_003725884.1| 338 NVYFATKCVVVANNYFSPAAVELARA-NNVELIDIDSLQAL 377
                                       *9************************.***********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       934  (0.0520944); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2375.03
//
Query:       gi|298674135|ref|YP_003725885.1|  [L=197]
Description: transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-32  111.3   0.1      4e-32  111.0   0.1    1.1  1  DDE_3     DDE superfamily endonuclease
  ------ inclusion threshold ------
      0.053   13.0   0.2      0.097   12.1   0.1    1.5  2  AviRa     RRNA methyltransferase AviRa
        0.1   12.2   0.0       0.17   11.5   0.0    1.5  1  SMC_ScpB  Segregation and condensation complex subunit ScpB


Domain annotation for each model (and alignments):
>> DDE_3  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.0   0.1   6.7e-36     4e-32       2     142 ..      18     164 ..      17     167 .. 0.97

  Alignments for each domain:
  == domain 1  score: 111.0 bits;  conditional E-value: 6.7e-36
                             DDE_3   2 vvfiDEsgfqlgt.vrrrawakkGkrer.leeygrrgrvnligaldekgglafvtfeetlnaedfaeflerlletal 76 
                                       vv++DEs+ ql + +r +  a  Gk e+ ++ey+r+ ++n+++a ++ +g+++v+++++ +++d+++f+e+++ ++ 
  gi|298674135|ref|YP_003725885.1|  18 VVCMDESPKQLISeTRNKIQASAGKPEKyDYEYRRKCSCNIFMACEPLTGERIVQITKRKTKKDWVQFIEKIATKYN 94 
                                       9************9************999************************************************ PP

                             DDE_3  77 qakkivlilDnasiHkseslrelveee.....adrlellylPpySPelNpiEivwsklkrellkrrsfksl 142
                                       +ak+i li+Dn ++H+  s++e+++ e     +dr+el+++P++ ++lN+ Ei  ++l++++l+ r++ ++
  gi|298674135|ref|YP_003725885.1|  95 SAKRITLIMDNYNTHTPGSFYEAFHPEkakqlLDRFELVFTPKHGSWLNMAEIELNVLNKQCLN-RRIGDI 164
                                       ****************************************************************.887765 PP

>> AviRa  RRNA methyltransferase AviRa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0      0.67     4e+03     224     224 ..      87      87 ..      64     119 .. 0.53
   2 ?   12.1   0.1   1.6e-05     0.097      89     141 ..     139     191 ..     121     197 .] 0.90

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.67
                             AviRa 224 r 224
                                       +
  gi|298674135|ref|YP_003725885.1|  87 E 87 
                                       1 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 1.6e-05
                             AviRa  89 eevlelakkNLsLLtkeglakreeelrelaeeyekeshaealesaerleella 141
                                        + l++a+  L++L k+ l++r+ +++ + ++ e+  h+e  ++a+ + +ll+
  gi|298674135|ref|YP_003725885.1| 139 GSWLNMAEIELNVLNKQCLNRRIGDIQVSLTKSEHGNHIEMRNTAKSIGNLLH 191
                                       67899****************************************99999884 PP

>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.9e-05      0.17       7      46 ..      58      98 ..      52     131 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.9e-05
                          SMC_ScpB  7 LfvageplsleeLakilels.keeveealeeLkeeyeeedr 46
                                      +f+a epl+ e++ +i++ + k++  + +e+++++y++++r
  gi|298674135|ref|YP_003725885.1| 58 IFMACEPLTGERIVQITKRKtKKDWVQFIEKIATKYNSAKR 98
                                      899**************86679**************77666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       829  (0.0462379); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1347.50
//
Query:       gi|298674136|ref|YP_003725886.1|  [L=158]
Description: transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.6e-11   42.3   0.0    4.8e-10   39.9   0.0    1.9  2  HTH_32    Homeodomain-like domain
    6.4e-10   38.9   0.0    1.1e-09   38.1   0.0    1.4  1  HTH_29    Winged helix-turn helix
    4.2e-05   23.2   0.0    0.00018   21.2   0.0    2.0  2  HTH_23    Homeodomain-like domain
  ------ inclusion threshold ------
      0.034   14.0   0.3      0.072   13.0   0.3    1.5  1  Clathrin  Region in Clathrin and VPS


Domain annotation for each model (and alignments):
>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.26   1.2e+03      28      42 ..      11      25 ..       5      47 .. 0.79
   2 !   39.9   0.0   1.1e-13   4.8e-10       2      73 .]      69     148 ..      68     148 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.26
                            HTH_32 28 klsdevrariiallr 42
                                      +ls+e+r+++ a++ 
  gi|298674136|ref|YP_003725886.1| 11 TLSKEERKELEAIVS 25
                                      589999999999984 PP

  == domain 2  score: 39.9 bits;  conditional E-value: 1.1e-13
                            HTH_32   2 vsrwlkRyneeGle.gLkdrprrg.rprklsdevrariiallreep.....rWsprqlaarlaere.gvkvShstvy 70 
                                       + r+ kR+ e+Gl+ +L  ++  +   +k++ + +a+iial +++p     + s+r+la++++e e  +++S++++ 
  gi|298674136|ref|YP_003725886.1|  69 IDRVKKRFVEDGLDmALNGKEYERtYEKKIDGDMEAHIIALSCSDPsqghsQCSLRLLADKVVELEyIDSISYESIK 145
                                       67999*************88554223358***************999**99***********88885777******* PP

                            HTH_32  71 riL 73 
                                       r+L
  gi|298674136|ref|YP_003725886.1| 146 RVL 148
                                       *98 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.0   2.5e-13   1.1e-09       1      63 []      36     104 ..      36     104 .. 0.92

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 2.5e-13
                            HTH_29   1 RaqallllaeGvs.....tvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsgrprn.rlseeqea 63 
                                       +a++ll+++eG++     t   +  +l++ +r+++r++krf+e+Gl+ +l++++  r ++ ++++++ea
  gi|298674136|ref|YP_003725886.1|  36 NALILLNCDEGEYqkqkhTNEVVSSVLNIGMRKIDRVKKRFVEDGLDMALNGKEYERTYEkKIDGDMEA 104
                                       589************************************************87755555559****997 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0     4e-08   0.00018       6      48 ..      35      83 ..      31      85 .. 0.89
   2 ?   -1.9   0.0      0.74   3.3e+03      29      40 ..     139     150 ..     138     152 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 4e-08
                            HTH_23  6 eRlrillllae......GlsvreIAreLgvsrrTvyrwlkryreeGleg 48
                                      + ++ill ++e      +++ + ++  L++  r ++r++kr++e+Gl+ 
  gi|298674136|ref|YP_003725886.1| 35 QNALILLNCDEgeyqkqKHTNEVVSSVLNIGMRKIDRVKKRFVEDGLDM 83
                                      67899999997777788*****************************986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.74
                            HTH_23  29 vsrrTvyrwlkr 40 
                                       +s+  + r+lk+
  gi|298674136|ref|YP_003725886.1| 139 ISYESIKRVLKK 150
                                       788999999987 PP

>> Clathrin  Region in Clathrin and VPS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   1.6e-05     0.072      30      60 ..      20      50 ..      12      56 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.6e-05
                                      HCCHHHCHTS--HHHHHHHHHHHHHTT-HHH CS
                          Clathrin 30 Lekvlkedskenpalqtallelyakyddpqe 60
                                      Le+++++++++++++q+al+ l+++++++q+
  gi|298674136|ref|YP_003725886.1| 20 LEAIVSKGKHKSQKYQNALILLNCDEGEYQK 50
                                      9*************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1082  (0.0603492); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1283.10
//
Query:       gi|298674137|ref|YP_003725887.1|  [L=246]
Description: hypothetical protein Metev_0160 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1819.03
//
Query:       gi|298674138|ref|YP_003725888.1|  [L=138]
Description: hypothetical protein Metev_0161 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.016   14.7   0.3      0.026   14.0   0.3    1.4  1  Pneumovirus_M2  Pneumovirus matrix protein 2 (M2)
      0.036   14.1   2.1      0.054   13.6   1.7    1.6  1  DUF2040         Coiled-coil domain-containing protein 55 (DUF
       0.04   12.6   0.2      0.061   12.0   0.2    1.3  1  Tagatose_6_P_K  Tagatose 6 phosphate kinase
      0.074   13.9   2.9       0.12   13.2   0.4    2.4  2  ERp29           Endoplasmic reticulum protein ERp29, C-termin


Domain annotation for each model (and alignments):
>> Pneumovirus_M2  Pneumovirus matrix protein 2 (M2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   5.9e-06     0.026      92     139 ..       3      52 ..       1      64 [. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.9e-06
                    Pneumovirus_M2  92 ddskkvalynlvlsyiessrktnkslinl..lkklpkeklkklikntlii 139
                                       ++ +++  yn+vl y e +rk  +++i++  l +  ++ l  l+ + l  
  gi|298674138|ref|YP_003725888.1|   3 PEENNLSYYNMVLEYQEKERKRLHDIIENkkLTRNTADSLHELVDEFLTK 52 
                                       56678899*******************87336689999999999876654 PP

>> DUF2040  Coiled-coil domain-containing protein 55 (DUF2040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.7   1.2e-05     0.054      44     105 ..       8      66 ..       1      80 [. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                           DUF2040  44 kpkYienLlkaaekRkrereraeerklqkereaegdefadkekFVTsaYkkkleelkkleee 105
                                        + Y   L  + ++Rkr ++++e++kl ++ +   +e  d  +F T+ Y+    ++++++ +
  gi|298674138|ref|YP_003725888.1|   8 LSYYNMVLEYQEKERKRLHDIIENKKLTRNTADSLHELVD--EFLTKNYRGI-SQNERWKLH 66 
                                       45566667778999***************99988887776..7******975.444555544 PP

>> Tagatose_6_P_K  Tagatose 6 phosphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   1.4e-05     0.061     323     390 ..      46     115 ..      18     129 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.4e-05
                                       -THHHHTT--SSHHHHHHHHHH-TT-GGGGTTTSHHHHHHHHHHHHHSTT-.---.HHHHHHH-GGGHHH CS
                    Tagatose_6_P_K 323 epkkWkkyYkgdeeelrlarkysysDRiRYYwpkpevkaavekLlanleek.eip.ltllsqylpeqyek 390
                                        ++  +k Y+g ++++r++ +ys+ +Ri Y    + v++  e+ +++++e+ ei  +t+l q + +q++ 
  gi|298674138|ref|YP_003725888.1|  46 VDEFLTKNYRGISQNERWKLHYSLKERISYKKVFSPVSKIEESEFDDITEQlEICfNTFLDQSVEKQKKD 115
                                       34556789**********************8888888888887777776651222245555555555444 PP

>> ERp29  Endoplasmic reticulum protein ERp29, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.4   2.8e-05      0.12      60      87 ..      16      43 ..       4      47 .. 0.90
   2 ?    1.0   0.1      0.19   8.4e+02      54      54 ..      82      82 ..      40     121 .. 0.51

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.8e-05
                             ERp29 60 eyvekElkRLekllkkgklaaekkdelk 87
                                      ey ekE+kRL+ +++++kl+ + +d+l+
  gi|298674138|ref|YP_003725888.1| 16 EYQEKERKRLHDIIENKKLTRNTADSLH 43
                                      899*******************999986 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.19
                             ERp29 54 i 54
                                      +
  gi|298674138|ref|YP_003725888.1| 82 V 82
                                      1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1133  (0.0631937); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 897.75
//
Query:       gi|298674139|ref|YP_003725889.1|  [L=482]
Description: DNA methylase-type I restriction-modification system [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1011  (0.0563891); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 3121.22
//
Query:       gi|298674140|ref|YP_003725890.1|  [L=686]
Description: N-6 DNA methylase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-34  118.1   0.0    8.9e-34  117.2   0.0    1.4  1  N6_Mtase  N-6 DNA Methylase
    2.5e-29  101.5   0.2    1.2e-28   99.3   0.0    2.1  2  HSDR_N_2  Type I restriction enzyme R protein N terminus (HSD
  ------ inclusion threshold ------
      0.016   14.9   0.0       0.38   10.4   0.0    2.4  2  UPF0020   Putative RNA methylase family UPF0020


Domain annotation for each model (and alignments):
>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.2   0.0   1.5e-37   8.9e-34       7     243 ..     341     618 ..     338     644 .. 0.85

  Alignments for each domain:
  == domain 1  score: 117.2 bits;  conditional E-value: 1.5e-37
                          N6_Mtase   7 GdvYEyllrkfaeeegksgGeffTPrevsklivellepksgesvyDpacGsggllvqaekvlkee.........dgk 74 
                                        +++Eyl++k a   + ++G++fTPr+v+ + v++l+pk+ge ++Dpa+Gs g+ v++  +l+ +         +++
  gi|298674140|ref|YP_003725890.1| 341 DEAFEYLVNKSA---KGEKGQYFTPRHVIDMCVKMLNPKRGEYMIDPAAGSCGFPVHTIFHLTGHlfenteisdEDQ 414
                                       6899****9984...4567*******************************************999*******96666 PP

                          N6_Mtase  75 tkelsiyGqeknettyrLak.mNlllhgieykkvkirlgdtlekpkfe............................. 121
                                       +  l+++G + +e+t+r+a+ +Nl+  + e++   + + ++l  ++++                             
  gi|298674140|ref|YP_003725890.1| 415 EDILKVFGIDFDEKTVRVARtLNLIAGDGETN---VLHLNSLDYERWNeyvnnhnwsqtygsgynrleklresrnsn 488
                                       66789**************8469998888888...6777777777777777888888******************99 PP

                          N6_Mtase 122 kdkkfdvvvaNppfnqkewkektlekde..rfrea..vapksnadlafllhiieslkpkGraavvlangvLfrggke 194
                                       kd  fdv +aNppf  +  ke+++++     f++      k  +d+ f+   +  lk +Gr+a+vl++g L +++ +
  gi|298674140|ref|YP_003725890.1| 489 KDFDFDVLMANPPFAGD-IKESRIIHKYelGFKNNgkAYSKIGRDILFIERNLDFLKSGGRMAIVLPQGRLNNSS-D 563
                                       9999***********99.77777766552345555667777889***************************8766.5 PP

                          N6_Mtase 195 gkIrkalvekdlveavialpeklFyn.tsiptcilvlkkekae.....rkgkvlf 243
                                       ++Ir+ + e+  + av++l ++ F +  + +t+il+++k  +e     ++  ++f
  gi|298674140|ref|YP_003725890.1| 564 ERIREFISEHARILAVVSLDQNTFKPhAGTKTSILFVQKWDNElcpvvEDYPIFF 618
                                       68***********************9899**********8877666644444444 PP

>> HSDR_N_2  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.27   1.6e+03       9      56 ..       6      50 ..       4      58 .. 0.75
   2 !   99.3   0.0     2e-32   1.2e-28       1     110 []      59     166 ..      59     166 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.27
                          HSDR_N_2  9 likyLveelgypkeliavekelqlgskkkraDivvykkdkkpllivec 56
                                      +i++++++ +y  +l++ e+   +++ k+r+ + v++ ++kp++ + +
  gi|298674140|ref|YP_003725890.1|  6 IIQTILNDSNYSLSLFEEEE---VNDLKGRIYTKVVNGNEKPYITCII 50
                                      78899999999999998885...6788888888888888888886655 PP

  == domain 2  score: 99.3 bits;  conditional E-value: 2e-32
                          HSDR_N_2   1 pEEwvRqklikyLveelgypkeliavekelqlgskkkraDivvykkd..kkpllivecKapsvkiseevleqlksYl 75 
                                       pEE+vRq ++k+L+++++ypk+++a e+++++g+++k  Div++++d  ++p++ive+K+p++k     ++ql sY+
  gi|298674140|ref|YP_003725890.1|  59 PEEIVRQLYAKRLMDKYEYPKNRFAFEYPVSFGRETKNSDIVIFDRDspETPYIIVELKKPKLKDG---KDQLRSYC 132
                                       8**********************************************9889************885...6******* PP

                          HSDR_N_2  76 ealkaeylvvtNglehivykvdkkkkkfeelkdiP 110
                                       +a++a+ +++tNg+++  y+ +k++++f  + diP
  gi|298674140|ref|YP_003725890.1| 133 NATGAPIGIWTNGEQISHYH-RKEPNYFIDITDIP 166
                                       ********************.7************9 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   6.4e-05      0.38      21      94 ..     370     435 ..     367     448 .. 0.79
   2 ?    1.6   0.0     0.032   1.9e+02     120     172 ..     491     542 ..     469     553 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 6.4e-05
                                       HHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHHH CS
                           UPF0020  21 vrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvvqgare 94 
                                       v++ + k+ge ++DP  Gs ++++      +           +e  +   e++++ lk++g+D+d++ v+ ar+
  gi|298674140|ref|YP_003725890.1| 370 VKMLNPKRGEYMIDPAAGSCGFPVHTIFHLTGHL--------FENTEISDEDQEDILKVFGIDFDEKTVRVART 435
                                       6778899****************97655444444........3344444556669999**************97 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.032
                                       S---EEEE----------HHHHHHHHHHHHHHHHHH-TT..-EEEEEESSHHH CS
                           UPF0020 120 gevdvivtnpPYGerlgskkalekLYseflrelkrvlrgggrlvlltsenkal 172
                                        ++dv+ +npP+   +++ + ++k    f +  k  +++ gr +l ++ n ++
  gi|298674140|ref|YP_003725890.1| 491 FDFDVLMANPPFAGDIKESRIIHKYELGFKNNGK-AYSKIGRDILFIERNLDF 542
                                       379*********9999998877664333333333.355556666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (686 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.50
# Mc/sec: 4164.46
//
Query:       gi|298674141|ref|YP_003725891.1|  [L=68]
Description: hypothetical protein Metev_0164 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 431.30
//
Query:       gi|298674142|ref|YP_003725892.1|  [L=315]
Description: transposase IS4 family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.8e-20   72.5   2.3    7.2e-20   71.5   2.3    1.5  1  DDE_Tnp_1  Transposase DDE domain
    7.3e-05   22.7   0.3    0.00019   21.4   0.3    1.7  1  DUF772     Transposase domain (DUF772)
  ------ inclusion threshold ------
      0.045   13.6   2.3      0.047   13.5   0.1    2.2  3  Fam20C     Golgi casein kinase, C-terminal, Fam20


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.5   2.3   1.2e-23   7.2e-20       4     214 .]     121     291 ..     118     291 .. 0.92

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 1.2e-23
                         DDE_Tnp_1   4 revlivDattvrvpgtkedarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrpr.kgkl 79 
                                       +ev++vD+t ++  g+ ++ +     +k++  +k  iavdt + +i++v+++ + vhd+k++ +ll++++++ k+  
  gi|298674142|ref|YP_003725892.1| 121 IEVTAVDSTGFTS-GHCSYYYSLRTDKKRHSFLKTSIAVDTSNLVIIGVKVSGRPVHDTKHAVTLLKQCHRIrKSEF 196
                                       789*********6.555577777789999*****************************************99***** PP

                         DDE_Tnp_1  80 vlaDaGYasaelldtle.ekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyyvt 155
                                       +++D++Y+s+++++ ++ e g   ii++               ++r rk+++++ ++   + ++             
  gi|298674142|ref|YP_003725892.1| 197 YVMDKAYDSEDIHKLVRdELGSIAIIPV---------------KDRKRKRIKGRYRRLMIEDFDV------------ 246
                                       *****************88888888887...............7888999999999988888888............ PP

                         DDE_Tnp_1 156 ntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                                    +l r+R+  E++ + lkrk+g +  r+r ++  + +++l+  ++nl
  gi|298674142|ref|YP_003725892.1| 247 -------------ALHRKRSMSETSNSVLKRKYG-EEIRARIYRNQVKEIILKVVVYNL 291
                                       .............9*****************999.99*********************8 PP

>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.3   3.2e-08   0.00019       6      72 ..      45     109 ..      41     110 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 3.2e-08
                            DUF772   6 ppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee..lerlfee 72 
                                         + +l l+ll+++ +   r+++e ++    ++  lgl    +++p+++tl +f +r+++  l rl+ +
  gi|298674142|ref|YP_003725892.1|  45 TQHQLLALVLLKEYLNEDYRDIVELVELMDKVQTKLGL----KQIPHFTTLHKFVTRIRTilLNRLLHQ 109
                                       55789********************************9....99****************999999877 PP

>> Fam20C  Golgi casein kinase, C-terminal, Fam20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1      0.59   3.5e+03      82      94 ..      62      74 ..      29     104 .. 0.51
   2 ?   13.5   0.1   7.8e-06     0.047     105     185 ..     146     224 ..     131     242 .. 0.78
   3 ?   -2.0   0.0      0.43   2.6e+03     169     197 ..     266     294 ..     248     302 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.59
                            Fam20C 82 pyeegkrlldlid 94
                                       y++  +l++l+d
  gi|298674142|ref|YP_003725892.1| 62 DYRDIVELVELMD 74
                                      2333333333333 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 7.8e-06
                            Fam20C 105 mDrhhyetfekfgnetfllhlDngrgfGrpshdelsilaPlyqCClirkstlerlkllasgeyrLsdvlreslakds 181
                                       + rh +  ++    +t  l +   +  Grp hd  + ++ l+qC +irks +  + +  ++ + + +++r+ l + +
  gi|298674142|ref|YP_003725892.1| 146 KKRHSFLKTSIA-VDTSNLVIIGVKVSGRPVHDTKHAVTLLKQCHRIRKSEFYVMDKAYDS-EDIHKLVRDELGSIA 220
                                       344444444333.35666666678999**************************99998877.799999999998888 PP

                            Fam20C 182 lapv 185
                                       + pv
  gi|298674142|ref|YP_003725892.1| 221 IIPV 224
                                       8887 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.43
                            Fam20C 169 LsdvlreslakdslapvlteehlealdrR 197
                                        ++ +r+ + ++++++++ +  +  ldr 
  gi|298674142|ref|YP_003725892.1| 266 YGEEIRARIYRNQVKEIILKVVVYNLDRF 294
                                       45566677777777777777777777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1932.31
//
Query:       gi|298674143|ref|YP_003725893.1|  [L=75]
Description: hypothetical protein Metev_0166 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 535.92
//
Query:       gi|298674144|ref|YP_003725894.1|  [L=34]
Description: hypothetical protein Metev_0167 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (34 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.45
# Mc/sec: 225.07
//
Query:       gi|298674145|ref|YP_003725895.1|  [L=287]
Description: glutamine amidotransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-75  253.8   0.0    1.6e-75  253.5   0.0    1.0  1  GATase_4  Glutamine amidotransferases class-II
     0.0025   18.0   0.0     0.0041   17.3   0.0    1.3  1  GATase_6  Glutamine amidotransferase domain
  ------ inclusion threshold ------
       0.13   11.9   1.1       0.26   11.0   0.1    2.0  2  DUF5053   Domain of unknown function (DUF5053)


Domain annotation for each model (and alignments):
>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  253.5   0.0   2.6e-79   1.6e-75       1     262 [.       1     275 [.       1     283 [. 0.92

  Alignments for each domain:
  == domain 1  score: 253.5 bits;  conditional E-value: 2.6e-79
                          GATase_4   1 mceLLgmssnvptdisfsftgfaarggltdahadGwGiafye........gkaarvfkdpepsaesplaelvreyp. 68 
                                       mceLLg+s+n  +++s+sftgf+++g +     dGwGia+y+        +k+a+++k+p  s++s+l+ ++ +y+ 
  gi|298674145|ref|YP_003725895.1|   1 MCELLGLSFNISIKPSISFTGFRSKGEQ---NPDGWGIAYYPvannknksEKSAQIIKEPINSKKSNLSSFLTDYQk 74 
                                       9***********************8888...9*******************************************99 PP

                          GATase_4  69 iksknvvaHiRkatqGevklenthpFvRelwgrewifAHnGdlkeykpkl.egrfePvGsTDsElafCelleelasr 144
                                       ++sk++++H+Rk ++ +   +nthpF+Rel g e+ifAHnG+ ++ k+   +grf P+G TDsE +fC++l  ++++
  gi|298674145|ref|YP_003725895.1|  75 LESKLIISHVRKSSKKNFGHKNTHPFSRELNGCEYIFAHNGTFNNNKDDFnKGRFIPMGVTDSENIFCHILGCIEEN 151
                                       *******************************************776666559************************9 PP

                          GATase_4 145 f..ekaepsaeeleralaelakeiaelGvfnlllsdgralfahastr.....LvyilRkaPfgeaelkdedlevdfe 214
                                          + ++ + +e ++ l++ ++e++e+G++n ++sd+++lf + +++     L+y+ Rk+P+++a+l+de+l+++++
  gi|298674145|ref|YP_003725895.1| 152 GitQWDSGNGKENFEWLSNKLNEVNENGKLNCIFSDSEYLFCYQDNNghhnnLYYLHRKPPYDKANLSDEELKIKLD 228
                                       832334667788999******************************5555555************************* PP

                          GATase_4 215 evttkedrvavvatepLtrdetWkklepGellvfrdGalvataseste 262
                                       e++ ++++  vvat+ Lt +e W+++epGel+vf+dG+++ +++ + +
  gi|298674145|ref|YP_003725895.1| 229 EEKYDDQTGYVVATKRLT-NEYWESFEPGELIVFKDGEIIYSNKRDFD 275
                                       ******************.99******************998655444 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   6.9e-07    0.0041      11      83 ..      76     150 ..      62     181 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 6.9e-07
                          GATase_6  11 edevalaHvRlaivglaeeega.qPfpsedgr..lllvhNGeiynykelreelpalkglafrsrsDtevlla.ll.. 81 
                                       e+++++ HvR +++ +   +++ +Pf++e  +  ++++hNG+  n k   +++ +  +    + +D+e ++  +l  
  gi|298674145|ref|YP_003725895.1|  76 ESKLIISHVRKSSKKNF-GHKNtHPFSRELNGceYIFAHNGTFNNNK---DDFNK-GRFIPMGVTDSENIFChILgc 147
                                       67899*****9999885.88888***44433355********99996...66666.333345577887776634455 PP

                          GATase_6  82 .ee 83 
                                        ee
  gi|298674145|ref|YP_003725895.1| 148 iEE 150
                                       544 PP

>> DUF5053  Domain of unknown function (DUF5053)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1      0.62   3.7e+03      18      32 ..      94     108 ..      83     121 .. 0.68
   2 ?   11.0   0.1   4.3e-05      0.26      22      44 ..     166     189 ..     161     191 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.62
                           DUF5053  18 gKsksWlyqrlnGid 32 
                                       +K +  ++  lnG++
  gi|298674145|ref|YP_003725895.1|  94 HKNTHPFSRELNGCE 108
                                       466666777888875 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 4.3e-05
                           DUF5053  22 sWlyqrlnGidvngk.vatFteee 44 
                                        Wl+++ln ++ ngk  + F+++e
  gi|298674145|ref|YP_003725895.1| 166 EWLSNKLNEVNENGKlNCIFSDSE 189
                                       6**************345577776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1877.63
//
Query:       gi|298674146|ref|YP_003725896.1|  [L=360]
Description: glutamine amidotransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-78  262.1   0.0    5.1e-78  261.7   0.0    1.1  1  GATase_4  Glutamine amidotransferases class-II
    1.2e-07   32.0   0.0      2e-07   31.2   0.0    1.3  1  GATase_6  Glutamine amidotransferase domain
  ------ inclusion threshold ------
      0.031   13.9   0.1      0.068   12.8   0.1    1.5  1  DUF5053   Domain of unknown function (DUF5053)


Domain annotation for each model (and alignments):
>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.7   0.0   8.5e-82   5.1e-78       1     259 [.       1     277 [.       1     290 [. 0.94

  Alignments for each domain:
  == domain 1  score: 261.7 bits;  conditional E-value: 8.5e-82
                          GATase_4   1 mceLLgmssnvptdisfsftgfaarggltdahadGwGiafye...................gkaarvfkdpepsaes 58 
                                       mceLLg+s+n  +++s+sftgf+++g +     dGwGia+y+                   +k+a+++k+p  + +s
  gi|298674146|ref|YP_003725896.1|   1 MCELLGLSFNISIKPSISFTGFRSKGEQ---NPDGWGIAYYPvaytknkssgkyvpnkyksEKSAQIIKEPIKPENS 74 
                                       9***********************8888...9********************************************* PP

                          GATase_4  59 plaelvreyp.iksknvvaHiRkatqGevklenthpFvRelwgrewifAHnGdlkeykpklegrfePvGsTDsElaf 134
                                       +l++++ + + i+sk++++H+Rk t+G+ +  nthpF+Rel g+e++fAHnG++++ + +++g+f+P+GsTDsE +f
  gi|298674146|ref|YP_003725896.1|  75 KLSRFLINHQkIESKLIISHLRKSTKGKKNHTNTHPFSRELYGKEYVFAHNGTIQNKRLSSTGKFTPIGSTDSENIF 151
                                       ****8766555*********************************************99999**************** PP

                          GATase_4 135 CelleelasrfekaepsaeeleralaelakeiaelGvfnlllsdgralfahas....trLvyilRkaPfgeaelkde 207
                                       C+ll+ ++++    ++   e ++ l++ ++ei+e+G++n ++sd+++lf + +    ++L+yi Rk+P g+++l+d+
  gi|298674146|ref|YP_003725896.1| 152 CYLLNCIEEHG--IAQWDFESFEWLSNKLNEINENGKLNCIFSDSEYLFCYQDnnlfNKLCYINRKPPNGTIRLSDN 226
                                       ********999..4567778999******************************666666****************** PP

                          GATase_4 208 dlevdfeevttkedrvavvatepLtrdetWkklepGellvfrdGalvatase 259
                                       dle+d++e+++++++  v+at++Lt de+W ++epGellvf++G+l+ +++ 
  gi|298674146|ref|YP_003725896.1| 227 DLEIDLDEEKDDNQTGYVIATKKLT-DENWIDFEPGELLVFKNGSLIYSNKC 277
                                       *************************.89****************99887554 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   3.4e-11     2e-07      10      85 ..      86     162 ..      77     187 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 3.4e-11
                          GATase_6  10 vedevalaHvRlaivglaeeega.qPf..psedgrlllvhNGeiynykelreelpalkglafrsrsDtevlla.ll. 81 
                                       +e+++++ H R +++g + ++++ +Pf    + ++++++hNG+i+n +     l++    +  + +D+e ++  ll 
  gi|298674146|ref|YP_003725896.1|  86 IESKLIISHLRKSTKGKK-NHTNtHPFsrELYGKEYVFAHNGTIQNKR-----LSSTGKFTPIGSTDSENIFCyLLn 156
                                       68899************9.77777***76677889************6.....99988888999*****99984556 PP

                          GATase_6  82 ..eelG 85 
                                         ee+G
  gi|298674146|ref|YP_003725896.1| 157 ciEEHG 162
                                       665444 PP

>> DUF5053  Domain of unknown function (DUF5053)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   1.1e-05     0.068      20      44 ..     170     195 ..     154     198 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.1e-05
                           DUF5053  20 sksWlyqrlnGidvngk.vatFteee 44 
                                       s  Wl+++ln i+ ngk  + F+++e
  gi|298674146|ref|YP_003725896.1| 170 SFEWLSNKLNEINENGKlNCIFSDSE 195
                                       678**************345577776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2643.36
//
Query:       gi|298674147|ref|YP_003725897.1|  [L=97]
Description: hypothetical protein Metev_0170 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.13   12.0   1.0       0.18   11.4   1.0    1.3  1  zf-SNAP50_C  snRNA-activating protein of 50kDa MW C terminal
       0.14   12.3   3.9       0.25   11.5   3.9    1.4  1  Zn-ribbon_8  Zinc ribbon domain


Domain annotation for each model (and alignments):
>> zf-SNAP50_C  snRNA-activating protein of 50kDa MW C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.0     2e-05      0.18     148     179 ..       2      32 ..       1      48 [. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2e-05
                       zf-SNAP50_C 148 kCkvCekfsakwvvlndkllpedpsyfCdkCf 179
                                       +C++C +++ +++v  +k ++ +p+ +C+ C 
  gi|298674147|ref|YP_003725897.1|   2 ECEICGHEKETVIVP-SKEADAKPINCCKGCA 32 
                                       7*****988777766.9**************6 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   3.9   2.8e-05      0.25       7      33 ..       2      32 ..       1      36 [. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.8e-05
                       Zn-ribbon_8  7 rCeeCghefe.vlqsis..daplta.CPeCg 33
                                      +Ce Cghe e v+++++  da+++  C+ C 
  gi|298674147|ref|YP_003725897.1|  2 ECEICGHEKEtVIVPSKeaDAKPINcCKGCA 32
                                      7*********988888865555777799995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 607.46
//
Query:       gi|298674148|ref|YP_003725898.1|  [L=482]
Description: N-6 DNA methylase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.8e-54  182.7   0.0    1.4e-53  182.3   0.0    1.1  1  N6_Mtase      N-6 DNA Methylase
    6.1e-07   30.1   3.9    6.3e-07   30.1   0.4    2.7  2  HsdM_N        HsdM N-terminal domain
  ------ inclusion threshold ------
        0.1   12.3   0.0        0.2   11.3   0.0    1.4  1  UPF0020       Putative RNA methylase family UPF0020
       0.12   12.3   2.3       0.15   11.9   0.3    2.1  2  Sec8_exocyst  Sec8 exocyst complex component specific domain


Domain annotation for each model (and alignments):
>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.3   0.0     3e-57   1.4e-53      28     310 ..     150     440 ..     145     442 .. 0.90

  Alignments for each domain:
  == domain 1  score: 182.3 bits;  conditional E-value: 3e-57
                          N6_Mtase  28 ffTPrevsklivellepksgesvyDpacGsggllvqaekvlkeedgktkelsiyGqeknettyrLakmNlllhgiey 104
                                       +fTPr++  l+v+ll+  ++ +vy p c  g +lv + +++ke +g+  e  +yGq  n++ +  + +Nl+  +  +
  gi|298674148|ref|YP_003725898.1| 150 VFTPRKLAYLVVKLLNIDKDMTVYEPFCTLGTFLVRSGNYIKECTGEFDEPYLYGQSPNKEYRLTTMLNLYFNDFFK 226
                                       8*******************************************************999987777778****99988 PP

                          N6_Mtase 105 kkvkirlgdtlekpkfe.....kdkkfdvvvaNppfnqkewkektlekde..rfreavapksnadlafllhiieslk 174
                                       +  +++ g+ + +p+f        +kfd v+   p  ++ w  +  + d+  rf+++v+p+++ d+a++ h+++slk
  gi|298674148|ref|YP_003725898.1| 227 A--QVKSGNLIFNPQFLtedgdGVRKFDRVLGSYPIIKD-WGYEFAKYDPyrRFSYGVPPQKKGDYAYIEHMVASLK 300
                                       8..5666666666666555555699**********9777.97777777776699999******************** PP

                          N6_Mtase 175 pkGraavvlangvLfr.ggkegkIrkalve.kdlveavialpeklFyntsiptcilvlkkekae.rkgkvlfidase 248
                                       ++G ++v+++n++L+r + ke+kI++ +++ +dl+e+vi+lp+k+ ++t    ++l+++k+k e r+++vlfidas+
  gi|298674148|ref|YP_003725898.1| 301 KDGMMGVLVPNNSLSRtNEKETKIKQLMLKrDDLIESVISLPPKVLRSTATSYSLLIINKNKREeRRNQVLFIDASR 377
                                       ****************666899***998873689****************************9889*********** PP

                          N6_Mtase 249 efkkkd..rkknklteediekildtykekskevdkfskvveleeiaendynlnvgryveteeee 310
                                       e++  +    +n ++ ++i++i+ ty+++ k++d+fs vv +e+i++ ++ l+v++y+ +e +e
  gi|298674148|ref|YP_003725898.1| 378 EYRPRKteVTRNVIKYKHIDNIVSTYQSF-KDEDNFSSVVPIEKIEKHNFSLDVSSYILPEPIE 440
                                       *986654478999****************.***************************9988776 PP

>> HsdM_N  HsdM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.4   1.4e-10   6.3e-07      22     136 ..      38     127 ..      26     128 .. 0.83
   2 ?   -0.9   0.2      0.51   2.3e+03      68      93 ..     444     469 ..     357     477 .. 0.64

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 1.4e-10
                                       HHHHHHHHHHHHHHHHHHHHHHCC.......--..--------....S-CCCSHHHHHHS--HHHHHHHHHHCHHHH CS
                            HsdM_N  22 keyilgLlFlKrlddveeereeklleeykenaleeleeklkskeafyipeelrWkelakkkdddelgenlnkafpal 98 
                                       ++++l L+ lK l++++e   + +                      ++p+ + W++++   ++  +g+ ln+af++l
  gi|298674148|ref|YP_003725898.1|  38 INHVLSLMLLKKLSEQYEHGVKHI----------------------VLPASAYWTNIKSS-YN-DIGNLLNNAFEEL 90 
                                       566777777777777776665555......................69***********7.44.6************ PP

                                       CT--STHHHHHHHS.......S-----SSHHHHHHHHHH CS
                            HsdM_N  99 eelnkslkgvfmkd.dfnafalgeitkkspalLskviek 136
                                       e +n++ kgvf+   df + +lg+    +++ ++++i+ 
  gi|298674148|ref|YP_003725898.1|  91 EMKNPEIKGVFD-SlDFESNELGN-VHHKNEIWKSIIDS 127
                                       ***********7.56999998877.69999999999985 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.51
                                       .S-C..CCSHHHHHHS--HHHHHHHHHH CS
                            HsdM_N  68 yipe..elrWkelakkkdddelgenlnk 93 
                                        +p+    r++e+ +  d++el +n+ +
  gi|298674148|ref|YP_003725898.1| 444 INPNdaLSRLREIQN--DKNELINNIHD 469
                                       233222445555555..33355555555 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   4.5e-05       0.2      15      54 ..     155     194 ..     153     232 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.5e-05
                                       HHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT-- CS
                           UPF0020  15 tLAaalvrlagwkpgepllDPmCGsGtilIEaallgania 54 
                                       +LA+  v+l +++++ + ++P+C  Gt+l+  +   +++ 
  gi|298674148|ref|YP_003725898.1| 155 KLAYLVVKLLNIDKDMTVYEPFCTLGTFLVRSGNYIKECT 194
                                       89***************************98877666665 PP

>> Sec8_exocyst  Sec8 exocyst complex component specific domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   3.4e-05      0.15      45     131 ..      47     133 ..      41     139 .. 0.94
   2 ?   -1.7   0.1      0.53   2.4e+03     106     139 ..     311     345 ..     297     346 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.4e-05
                      Sec8_exocyst  45 fkqlkkqieeaLqevvnehhqaFnssiasYskilssiqesqekvselKesleeakkklstkkkeLkelnarsakyke 121
                                       +k+l++q e+ ++++v   +  +++  +sY+ i + ++++ e+++    +++    +l  +++eL ++++++   k 
  gi|298674148|ref|YP_003725898.1|  47 LKKLSEQYEHGVKHIVLPASAYWTNIKSSYNDIGNLLNNAFEELEMKNPEIKGVFDSLDFESNELGNVHHKNEIWKS 123
                                       689999************9999999999****************99999**************************** PP

                      Sec8_exocyst 122 vieiLdaiee 131
                                       +i+ L++ie 
  gi|298674148|ref|YP_003725898.1| 124 IIDSLSSIEL 133
                                       *******985 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.53
                      Sec8_exocyst 106 kkeLkelnarsakyke.vieiLdaieelkkvpdki 139
                                       +++L+ +n++  k k+ +++  d ie + ++p k+
  gi|298674148|ref|YP_003725898.1| 311 NNSLSRTNEKETKIKQlMLKRDDLIESVISLPPKV 345
                                       67888888888888774677778888888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 2974.65
//
Query:       gi|298674149|ref|YP_003725899.1|  [L=204]
Description: restriction modification system DNA specificity domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.3e-06   27.4   5.9    4.6e-06   26.9   5.9    1.1  1  Methylase_S  Type I restriction modification DNA specificity 
  ------ inclusion threshold ------
       0.17   11.5   0.1       0.35   10.4   0.0    1.5  2  HXXSHH       Protein of unknown function (DUF1552)


Domain annotation for each model (and alignments):
>> Methylase_S  Type I restriction modification DNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   5.9   5.2e-10   4.6e-06       5     161 ..       8     185 ..       6     189 .. 0.71

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 5.2e-10
                                       EEEEHHHHEEE....EE-----TTGGTTT--EEEE-HHHCCT........EE-HHHHCCTT---B-..TT-EEEE-S CS
                       Methylase_S   5 evvkLgdvfei....kkgktpkkkelkengkypyiragilnn........kvvkdglgykkkyilp..kgdilissr 67 
                                       e++kL+ + e     ++  + + ++ ++ +k+ ++ ++i+n         ++ +  ++++++++ +  kgd++i +r
  gi|298674149|ref|YP_003725899.1|   8 ETIKLKNLLESnkliRGIAKTREDNSNDTEKINVFMVNIKNLedgivdlkSTEECNVKKSDFEKPKpkKGDVIIPIR 84 
                                       566777777775553333333333555566666666665566669999965555555555544443459******** PP

                                       .....SSTT-EEEESS-BEE-TTEEEEEESTTT--HHHHHHHHHHCHH..HHHHHCCSSTTT---HHHHCC-EEEE- CS
                       Methylase_S  68 .....atiGkvayrdkkyylnqsvivlipknkkkineflylylllklk..klkslsvgstqpkltkenlkkikIplP 137
                                              +    + +k y+ + ++  l+++n k + + l  y+   +   +l+++s+g+ ++++  ++lk++ Ip+P
  gi|298674149|ref|YP_003725899.1|  85 gsdfkSAVAPSGIENKGYVISLNLVALRVNN-KILPRVLSEYFNSPQGqiSLERISKGTKIKSIPIKELKELDIPVP 160
                                       66665555556666668***********963.44469999999855444578888********************** PP

                                       -HHHHHHHHHHHHHHHH.HHHHHHH CS
                       Methylase_S 138 pleeQkkIakiLsqldn.tielekk 161
                                       +l+ Q k  k+L+++ + ++ l ++
  gi|298674149|ref|YP_003725899.1| 161 NLDDQNKFDKYLEAIQDyKLRLREE 185
                                       ************9999877777664 PP

>> HXXSHH  Protein of unknown function (DUF1552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.27   2.4e+03     184     218 ..      33      67 ..      28      90 .. 0.66
   2 ?   10.4   0.0   3.9e-05      0.35     185     214 ..     163     192 ..     120     201 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.27
                            HXXSHH 184 aadrqKLdeylesvreiekrlekaekwaptakaea 218
                                       ++d +K+  ++  ++++e+ +   ++ ++   +++
  gi|298674149|ref|YP_003725899.1|  33 SNDTEKINVFMVNIKNLEDGIVDLKSTEECNVKKS 67 
                                       67889999999999999999933333333222222 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 3.9e-05
                            HXXSHH 185 adrqKLdeylesvreiekrlekaekwapta 214
                                       +d++K+d+yle++++ + rl ++++ +++ 
  gi|298674149|ref|YP_003725899.1| 163 DDQNKFDKYLEAIQDYKLRLREEKEFTEKM 192
                                       59******************5555544443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       965  (0.0538234); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1388.28
//
Query:       gi|298674150|ref|YP_003725900.1|  [L=212]
Description: protein serine/threonine phosphatase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-12   46.1   0.0    7.7e-12   45.3   0.0    1.4  1  PP2C_2    Protein phosphatase 2C
    3.1e-11   43.4   0.2    4.8e-06   26.4   0.1    2.1  2  PP2C      Protein phosphatase 2C
    5.5e-07   29.7   0.2    1.4e-06   28.4   0.2    1.7  1  SpoIIE    Stage II sporulation protein E (SpoIIE)
  ------ inclusion threshold ------
      0.029   14.2   0.2        1.1    9.1   0.1    2.8  2  DUF4295   Domain of unknown function (DUF4295)
      0.043   12.4   0.0      0.055   12.1   0.0    1.1  1  Actin     Actin


Domain annotation for each model (and alignments):
>> PP2C_2  Protein phosphatase 2C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.0   2.2e-15   7.7e-12      27     191 ..       2     179 ..       1     195 [. 0.73

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 2.2e-15
                            PP2C_2  27 laVaDGaGSakrSerGariaveavvealaelleseeee..eeallraleaailadvlkeeaeaqdaelkdyatTlla 101
                                       laVaDG+G  + +e+++++av+ +++ + ++   e+e+    ++l+ +++++++ +    ++++  e   + tTl+ 
  gi|298674150|ref|YP_003725900.1|   2 LAVADGVGGNNAGEVASNLAVHEITNMMYSYPVGEMETedVINFLKVAHQKVREVI----NKESVGEKVGMDTTLVS 74 
                                       69******************************877777334456666777777544....333344677899***** PP

                            PP2C_2 102 avvtpdeivalqiGDGaivvrdrdgevqllgepds..................geyanq.ttfltsedaeeelrirr 159
                                        v+++d +v+++ GD+ ++v+d+ g+v+l +++++                  +   n+ t ++t     +++ + +
  gi|298674150|ref|YP_003725900.1|  75 SVIKDDIAVIANTGDSKAFVIDKGGNVKLKTKEHTypqylfdegiinkddvknHPLNNMlTCSIT-----GNFTVDT 146
                                       *****************************999888777777755555533333333333333444.....4445554 PP

                            PP2C_2 160 lk..ledgdalllmTDGlanslrdeerfaellee 191
                                        k  l +gd+++l++DG+ + +  +e+ ++++++
  gi|298674150|ref|YP_003725900.1| 147 YKvdLISGDSIILTSDGIHDYIY-KEDIISSIKD 179
                                       44336779**********98887.5555554444 PP

>> PP2C  Protein phosphatase 2C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.1   1.3e-09   4.8e-06      37     141 ..       2     109 ..       1     112 [. 0.78
   2 !   15.3   0.0   3.3e-06     0.012     207     250 ..     156     198 ..     145     205 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 1.3e-09
                                       EEEEEEESSSHHHHHHHHHHH.HHHHHHHHCHTTH....HHHHHHHHHHHHHHHHHHHHHHHHCHCCT-EEEEE..E CS
                              PP2C  37 favfdghggseaakyarehle.eilksqksfeele....kleqalrksfladtdeelksskantepsksGstav..v 106
                                       +av dg+gg  a ++a++    ei     s + +e    ++ + l+ ++++  +e++++++     +k+G + +  +
  gi|298674150|ref|YP_003725900.1|   2 LAVADGVGGNNAGEVASNLAVhEITNMMYSYPVGEmeteDVINFLKVAHQK-VREVINKES---VGEKVGMDTTlvS 74 
                                       79**************99866366666777777778899999999*****9.889999833...4678886544104 PP

                                       EEEETTEEEEEEESS-EEEEEETTEEEEECS---S CS
                              PP2C 107 alirgtklyvAnvGDSravLcrkgnakkeltedHk 141
                                       ++i ++   +An+GDS+a +++kg++ k  t+ H+
  gi|298674150|ref|YP_003725900.1|  75 SVIKDDIAVIANTGDSKAFVIDKGGNVKLKTKEHT 109
                                       44444449******************988888886 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 3.3e-06
                                       EEEEE-HHHHTTSHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHH CS
                              PP2C 207 fliLacdGlwdvlsdqeavdlvrdelekkkspeevaeelvdeai 250
                                        +iL +dG+ d++ ++++++ ++d++  +++p+ev  e+ ++a 
  gi|298674150|ref|YP_003725900.1| 156 SIILTSDGIHDYIYKEDIISSIKDNIF-GNNPREVVAEISEKAF 198
                                       58************************9.5799999999988875 PP

>> SpoIIE  Stage II sporulation protein E (SpoIIE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.2   3.9e-10   1.4e-06       7     139 ..       2     170 ..       1     209 [. 0.81

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 3.9e-10
                                       EEEEECSS....SSHHHHHHHHHHHHHHHHHHHTTTSHHHHHHHHHHHCHCTTSTT...........TTCEEEEEEE CS
                            SpoIIE   7 lvvgDvvG....hGleAalimgllrsalrelataglepaevlkrlnralardleee..........erfaTavlavy 69 
                                       l+v+D+vG      +++ l + ++ +++ ++   ++e ++v++ l  a  ++++e            + +T+v  v 
  gi|298674150|ref|YP_003725900.1|   2 LAVADGVGgnnaGEVASNLAVHEITNMMYSYPVGEMETEDVINFLKVAH-QKVREVinkesvgekvGMDTTLVSSV- 76 
                                       7899999998877899999999**********99999888877777777.55555556679999876777777777. PP

                                       ETTTTEEEEEEESSSSEEEEETTSTEEEEE--SS--TTTSSS........................T-EEEEEEE-- CS
                            SpoIIE  70 dpstgkleyanaGhpppllvrpdggtklllastglplGilpe........................adyetaelele 122
                                        +++  + +an G++  +++++ g++kl+++++  p  +++e                        ++++t++++l 
  gi|298674150|ref|YP_003725900.1|  77 -IKDDIAVIANTGDSKAFVIDKGGNVKLKTKEHTYPQYLFDEgiinkddvknhplnnmltcsitgnFTVDTYKVDLI 152
                                       .5666679**************99************44444445666****************************** PP

                                       TTEEEEEESCCCCSSS.H CS
                            SpoIIE 123 pgdtlllyTDGvtEar.d 139
                                        gd ++l +DG+ +   +
  gi|298674150|ref|YP_003725900.1| 153 SGDSIILTSDGIHDYIyK 170
                                       ************987741 PP

>> DUF4295  Domain of unknown function (DUF4295)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1   0.00032       1.1      32      46 ..     113     127 ..     104     128 .. 0.92
   2 ?    1.8   0.0      0.06   2.2e+02      32      40 ..     167     175 ..     162     180 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00032
                           DUF4295  32 YtFkEeiVpkdqVkd 46 
                                       Y F+E i++kd+Vk+
  gi|298674150|ref|YP_003725900.1| 113 YLFDEGIINKDDVKN 127
                                       *************96 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.06
                           DUF4295  32 YtFkEeiVp 40 
                                       Y++kE+i+ 
  gi|298674150|ref|YP_003725900.1| 167 YIYKEDIIS 175
                                       *******96 PP

>> Actin  Actin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.5e-05     0.055     215     306 ..      23     137 ..      10     161 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.5e-05
                             Actin 215 eelekltesy..ktleeeevleeiKesvcevsedpegdeekss......................sspeksYeLPDg 267
                                       +e++++ +sy   ++e+e v++ +K ++ +v+e +++ e++ +                      +   k +++  g
  gi|298674150|ref|YP_003725900.1|  23 HEITNMMYSYpvGEMETEDVINFLKVAHQKVREVINK-ESVGEkvgmdttlvssvikddiavianTGDSKAFVIDKG 98 
                                       4555666666335788999999999999999999985.333334556666666788888888887999999****** PP

                             Actin 268 seiklgeeRfkvpEiLFdpsligsesaleeekskllgis 306
                                        ++kl+++ ++ p  LFd+ +i+++  ++++ +++l+ s
  gi|298674150|ref|YP_003725900.1|  99 GNVKLKTKEHTYPQYLFDEGIINKDDVKNHPLNNMLTCS 137
                                       *************************99888877777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1382.28
//
Query:       gi|298674151|ref|YP_003725901.1|  [L=62]
Description: hypothetical protein Metev_0174 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0031   17.3   0.0     0.0055   16.5   0.0    1.4  1  DUF4025   Protein of unknown function (DUF4025)


Domain annotation for each model (and alignments):
>> DUF4025  Protein of unknown function (DUF4025)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   3.1e-07    0.0055      21      42 ..       6      27 ..       2      30 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.1e-07
                           DUF4025 21 ssdelskGlAvtHEQVSDvyaE 42
                                      + +e++k lA+ +EQ++D+ +E
  gi|298674151|ref|YP_003725901.1|  6 KFKETDKILAEWEEQFEDDFME 27
                                      556889***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 419.95
//
Query:       gi|298674152|ref|YP_003725902.1|  [L=57]
Description: hypothetical protein Metev_0175 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 381.59
//
Query:       gi|298674153|ref|YP_003725903.1|  [L=31]
Description: hypothetical protein Metev_0176 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (31 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      133  (0.00741815); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 219.41
//
Query:       gi|298674154|ref|YP_003725904.1|  [L=733]
Description: DEAD/DEAH box helicase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-25   89.6   0.1    1.5e-24   86.7   0.0    2.4  3  DEAD             DEAD/DEAH box helicase
    2.9e-12   46.9   0.0      7e-12   45.7   0.0    1.7  1  ResIII           Type III restriction enzyme, res subunit
    4.5e-10   39.9   0.0    1.4e-08   35.1   0.0    2.9  2  Helicase_C       Helicase conserved C-terminal domain
    2.1e-07   31.4   0.3    1.8e-06   28.5   0.1    2.7  2  HHH_5            Helix-hairpin-helix domain
    2.9e-05   23.8   0.0    0.00017   21.3   0.0    2.3  2  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
    0.00031   20.0   0.0    0.00048   19.4   0.0    1.2  1  Sec63            Sec63 Brl domain
  ------ inclusion threshold ------
      0.017   15.4   0.0      0.055   13.7   0.0    1.9  1  Cdd1             Pathogenicity locus
      0.057   13.2   0.0       0.15   11.8   0.0    1.7  1  UPF0254          Uncharacterised protein family (UPF0254)


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.7   0.0   6.7e-28   1.5e-24       2     170 ..      26     182 ..      25     187 .. 0.87
   2 ?   -1.3   0.0      0.69   1.6e+03      58     131 ..     391     467 ..     389     480 .. 0.72
   3 ?   -2.7   0.0       1.9   4.2e+03      79     111 ..     506     537 ..     488     553 .. 0.63

  Alignments for each domain:
  == domain 1  score: 86.7 bits;  conditional E-value: 6.7e-28
                                       HHHHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSE CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   2 diQaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlr 77 
                                       + Qaea++  l +++++l+a++T+sGKTl+  +++l+++     ++g k+l+++P+r+La + ++++k+f + i+  
  gi|298674154|ref|YP_003725904.1|  26 PPQAEAVEKGLlDNKNLLAAIPTASGKTLISELAMLKSI-----SNGGKCLYIVPLRALASEKFERFKQFSS-IG-- 94 
                                       67999999988799**********************999.....6799************************.55.. PP

                                       EEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  78 vlliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitc 154
                                       v+  i+  + ++  + l  + di+v+t ++ d+ll++++  +++++++V+DE++ l + +++++++  +++l +   
  gi|298674154|ref|YP_003725904.1|  95 VNIGISTGDFDSTDEWL-GSNDIIVATSEKADSLLRNETSWMKDITTIVVDEIHLLDSADRGPTLEITIAKLLRL-- 168
                                       55456666777777788.779**************777777**************************99999433.. PP

                                       TSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxx RF
                              DEAD 155 dgklqrqvivlSATlp 170
                                         + ++q+i lSAT+ 
  gi|298674154|ref|YP_003725904.1| 169 --NPNSQIIGLSATIG 182
                                       ..33456*******96 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.69
                                       HHHHHHHHHHHHHTTT.STSEEEEEET..TSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHH CS
                                       xxxxxxxxxxxxxxxx.xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  58 eLaeqtlnnlkkfkky.idlrvlliig..gvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEad 131
                                        L+  t+n+++ +++  id + + i++  g++      +l+  v+ + +t + ++d++ +  + ++q ++  +D +d
  gi|298674154|ref|YP_003725904.1| 391 VLISHTYNEFTDLLDRyIDAEPEDILSklGTENALRTHVLSTIVNGFATTRQGMVDFMGSSFFAYQQQKWSLIDVVD 467
                                       58899999999999954997777666645666667777774448889999999999886666777777776666555 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.9
                                       EEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  79 lliiggvaardqlskldngvdivvgtpgrlddl 111
                                         ii + ++ d+++++   ++i+ +tp++ +  
  gi|298674154|ref|YP_003725904.1| 506 AIIIDKLKKADKVTDM-TMLHIICSTPDMRQLY 537
                                       4555655666666666.6688888888665544 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.0   3.1e-15     7e-12       3     169 ..      23     181 ..      21     183 .. 0.90

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 3.1e-15
                                       EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTG CS
                            ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkfls 79 
                                       +l++ Q+ea+e+ l      ++k++l +++T +GKTl++  ++ +  ++g+  k+l +vp ++l +   e+fk+f+s
  gi|298674154|ref|YP_003725904.1|  23 KLYPPQAEAVEKGL-----LDNKNLLAAIPTASGKTLISELAMLKSISNGG--KCLYIVPLRALASEKFERFKQFSS 92 
                                       68899999999998.....5799****************777777777788..9*********************** PP

                                       G....GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T.......T CS
                            ResIII  80 eaykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk.......s 149
                                         +  + ++ +gd ++   +   +++i+v+t +++d+ +      +e+   + +  i++DE H l +++       +
  gi|298674154|ref|YP_003725904.1|  93 IGV--NIGISTGDFDST-DEWLGSNDIIVATSEKADSLL-----RNETSWMKDITTIVVDEIHLLDSADrgptleiT 161
                                       *99..789999999999.88999****************.....77788888899***********98466677789 PP

                                       THHHHHT---SEEEEEESS- CS
                            ResIII 150 wreilekfkeavllglTATp 169
                                       + ++l+ ++++ ++gl+AT+
  gi|298674154|ref|YP_003725904.1| 162 IAKLLRLNPNSQIIGLSATI 181
                                       9999***************7 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.24   5.4e+02       8      74 ..      59     121 ..      52     132 .. 0.64
   2 !   35.1   0.0   6.2e-12   1.4e-08      32     109 ..     295     381 ..     229     383 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.24
                                       HHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESG CS
                        Helicase_C   8 ellkleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatd 74 
                                       ++lk+ ++ggk+l +v+ +  +++ ++ +   k+++++ ++  +++ + + + e    g+ d+++at+
  gi|298674154|ref|YP_003725904.1|  59 AMLKSISNGGKCLYIVPLRALASEkFERF---KQFSSIGVNIGISTGDFDSTDEWL--GSNDIIVATS 121
                                       33488899999999999999665224444...245555555555555555555555..5666666665 PP

  == domain 2  score: 35.1 bits;  conditional E-value: 6.2e-12
                                       HHHHHHHT...TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEE....ESSSSSSH.... CS
                        Helicase_C  32 vklllekk...gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVi....nfdlprnv.... 97 
                                       +k l       +  +a +h+ l++ +r+ + ++f++++++v+ +t  ++ G+++p  ++++    ++d+ +++    
  gi|298674154|ref|YP_003725904.1| 295 TKEL---AsciKRGTAFHHAGLNSAQRKIVEDNFRNNKIKVISSTPTLAAGLNLPARRVIVrnykRYDPNFGMqpip 368
                                       2333...1344788999**************************************8888887777555554424444 PP

                                       .HHHHHHHTTSSS CS
                        Helicase_C  98 .tsyiqriGRtgR 109
                                         +y+q++GR+gR
  gi|298674154|ref|YP_003725904.1| 369 vLDYKQMAGRAGR 381
                                       5************ PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.1   2.5e+03      13      40 ..     577     611 ..     575     613 .. 0.72
   2 !   28.5   0.1     8e-10   1.8e-06       3      55 ..     650     700 ..     646     702 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.1
                                       HHHHHHHTTT--..SHHHHHHS......-HHHHHTS CS
                             HHH_5  13 ktAlallsaGie..svedlaaa......dveeLaki 40 
                                       ktAl + +  i+  +++d+ a+      d+++L++i
  gi|298674154|ref|YP_003725904.1| 577 KTALLINEW-IDekTLDDITAEfgvgegDINALSDI 611
                                       788888888.77668999977555555688888877 PP

  == domain 2  score: 28.5 bits;  conditional E-value: 8e-10
                                       HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHH CS
                             HHH_5   3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilel 55 
                                       +L s+s iG+++A++l++aGi sv d+++   + L+    +G ktA +++++l
  gi|298674154|ref|YP_003725904.1| 650 QLVSISNIGRVRARKLYEAGIQSVSDIKNTKLHILSNY--LGRKTAYKVLEQL 700
                                       5779*********************************9..***********98 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       5.8   1.3e+04      23      30 ..     589     596 ..     585     601 .. 0.80
   2 !   21.3   0.0   7.7e-08   0.00017       2      30 ..     650     678 ..     650     687 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 5.8
                   DNA_pol_lambd_f  23 rtledlra 30 
                                       +tl+d+ a
  gi|298674154|ref|YP_003725904.1| 589 KTLDDITA 596
                                       69999976 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 7.7e-08
                   DNA_pol_lambd_f   2 lFtkvyGVGpktAkkwyakGirtledlra 30 
                                       ++ ++  +G+++A+k+y++Gi ++ d+++
  gi|298674154|ref|YP_003725904.1| 650 QLVSISNIGRVRARKLYEAGIQSVSDIKN 678
                                       57899***********************9 PP

>> Sec63  Sec63 Brl domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   2.1e-07   0.00048       2      94 ..     489     593 ..     488     600 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.1e-07
                                       CHHHHHHHHHT--HHHHHHHHHHS-TT-..-HHHHHHHHHTSGGGGGS---TTHHHHHHHHHHT.......SSS--S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxx RF
                             Sec63   2 telGriaShYyisyetiklfneslkpnt..tlkdlLeilssasEFeeipvReeEkkelkkLlek.......vpikvk 69 
                                       t lG++ S  yi   + +++ ++lk+    t+  +L+i++s  +  ++ +R +E + +++   +       vp ++k
  gi|298674154|ref|YP_003725904.1| 489 TRLGQVISTLYIDPLSGAIIIDKLKKADkvTDMTMLHIICSTPDMRQLYLRSKEYEKINEYVMThsdefveVPNPFK 565
                                       89**********************9544359999********************88877766444789988666664 PP

                                       ...SSTTSHHHHHHHHHHHHHTT---SS CS
                                       ...xxxxxxxxxxxxxxxxxxxxxxxxx RF
                             Sec63  70 ...ediespeaKvniLlqayisrlkleg 94 
                                           ++   e+K+ +L++ +i + +l++
  gi|298674154|ref|YP_003725904.1| 566 sieYEWFLGEVKTALLINEWIDEKTLDD 593
                                       4447777899999999999998888775 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.5e-05     0.055       3      50 ..     646     693 ..     644     697 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.5e-05
                              Cdd1   3 kalkelqdiPniGkalaedlvelGirsveelkgedpeelyeklekltg 50 
                                       k l +l +i niG+  a++l+e Gi+sv+++k+ + + l + l ++t+
  gi|298674154|ref|YP_003725904.1| 646 KDLIQLVSISNIGRVRARKLYEAGIQSVSDIKNTKLHILSNYLGRKTA 693
                                       56778999************************9988777776666655 PP

>> UPF0254  Uncharacterised protein family (UPF0254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.6e-05      0.15      88     161 ..     578     653 ..     573     655 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.6e-05
                                       HHHHHHHHHHHHHT-SEEEEEE-SEES-EEEEE-SS-EEEE--S--....EETTTT..TTHHHHHHHHHHHHHHHHH CS
                           UPF0254  88 vallmakavkkitnadigigttAGiGrGaiaivtdkkellttsdve....adlrksdaeeilkRqksgiekalklle 160
                                        all+ + + ++t  di+  +  G+G+G i  ++d +e l++s v+    +dl   +a+e+ kR ++g++k l +l+
  gi|298674154|ref|YP_003725904.1| 578 TALLINEWIDEKTLDDIT--AEFGVGEGDINALSDISEWLMHSAVNlanlTDLDADKAQELEKRIHHGVNKDLIQLV 652
                                       567777777777777765..678*********************9884445666778899**********9988776 PP

                                       H CS
                           UPF0254 161 e 161
                                       +
  gi|298674154|ref|YP_003725904.1| 653 S 653
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (733 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.70u 0.30s 00:00:01.00 Elapsed: 00:00:00.48
# Mc/sec: 4577.75
//
Query:       gi|298674155|ref|YP_003725905.1|  [L=426]
Description: histidinol dehydrogenase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   5.4e-167  555.9   3.6   6.4e-167  555.7   3.6    1.0  1  Histidinol_dh  Histidinol dehydrogenase
  ------ inclusion threshold ------
       0.16   12.3   0.8        1.7    9.1   0.1    2.5  2  Toprim_3       Toprim domain


Domain annotation for each model (and alignments):
>> Histidinol_dh  Histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  555.7   3.6  7.1e-171  6.4e-167       8     409 .]      24     424 ..      19     424 .. 0.99

  Alignments for each domain:
  == domain 1  score: 555.7 bits;  conditional E-value: 7.1e-171
                                       -HHHHHHHHHHHHHHHHHCHHHHHHHHHHCCSSSSGGCCEE-HHHHHHHHHCS-HHHHHHHHHHHHHHHHHHHCC-- CS
                     Histidinol_dh   8 seeveetvkeiledvreeGdealleytekFDkvkkleslrvseeeieealekldeelkealeeaaenirkfheaqke 84 
                                        ++ve++v+ il++++++Gdeal++yt++FD++ + e+++vs++ei+ea+ ++de++ + le+aa nirk+he+q++
  gi|298674155|ref|YP_003725905.1|  24 LANVEDKVSVILDEIHNHGDEALKKYTKQFDNA-EIENIEVSRQEIDEAFYNVDEAFIKHLETAAYNIRKYHESQLP 99 
                                       5789***************************66.4799*************************************** PP

                                       --EEEEEECTTEEEEEEEEE-SEEEEE---STT--CHHHHHHHHHHHHHT-SEEEEEE-SS.GG.--HHHHHHHHHC CS
                     Histidinol_dh  85 seeevketepgvvlgqkvrpiervGlYvPgGkaaypStvlmnavpAkvAgvkeivvvtPpq.dgkvnpavlaaakla 160
                                       ++++++et pg+ lgqkv+p++++G YvPgG+a+ypSt+lm+++pAkvAgv+++ v+tPp+ dg+v+p +la a++a
  gi|298674155|ref|YP_003725905.1| 100 AQKWMSETLPGIELGQKVTPLKNIGAYVPGGSASYPSTALMTVIPAKVAGVENVSVCTPPRyDGTVHPITLASARIA 176
                                       99*************************************************************************** PP

                                       T-SEEEE--HHHHHHHHHH--SSS---SEEE---SHHHHHHHHHHCTTBEES----S-EEEEEE-TTS-HHHHHHHH CS
                     Histidinol_dh 161 gvdeiykvGGaqAiaalAyGtesipkvdkivGPGniyVaaAKrlvsgevgiDmiaGPsEvlviaDetadpefvAaDL 237
                                       g+d+iy++GG+qAi+alAyGt+s++kvdkivGPGn++V++AK++v+++v+iD++aGPsEvl+iaDe+ad+++ A+D+
  gi|298674155|ref|YP_003725905.1| 177 GADHIYRLGGVQAIGALAYGTSSVKKVDKIVGPGNVFVTTAKMQVRNRVEIDFPAGPSEVLIIADESADAKMAASDI 253
                                       ***************************************************************************** PP

                                       HHHHTT-TT-EEEEEES-HHHHHHHHHHHHHHHCC-TTHHHHHHHHCCH-EEEE-SSHHHHHHHHHHH--SEEEEES CS
                     Histidinol_dh 238 lsqaEHdedaqavlvttseelaeaveeevekqleelprkeiaekslekqsaiilvedleeaielaneyApEHlelqv 314
                                       ++q EHd++a ++l+tts++lae+v++ev  q++++pr++i++ksl++  +i+++++++++ie+++e+ApEHle++v
  gi|298674155|ref|YP_003725905.1| 254 VAQLEHDPNAVSILITTSKSLAEKVNQEVLYQAKSTPRNDIVKKSLKN-VVILIADTVDSCIEFSDEFAPEHLEIMV 329
                                       ************************************************.99************************** PP

                                       TTHHHHGGG--S-SEEEESTT--HHHHHHTSSS------TTGGGT---S-GGGGEEEEEEEEE-HHHHHHHHHHHHH CS
                     Histidinol_dh 315 edpeellekiknaGaiflGeyspeslgDYaaGtnhvLPTsgtArfssglsvedFlkkisvqelskealkelaeavet 391
                                        d e +l++i+naG+if+G+ysp+++gDYa+GtnhvLPTsg+A+++sgl+v++F+k +s+q++ske+l+++++++++
  gi|298674155|ref|YP_003725905.1| 330 YDDEYVLNRIENAGSIFVGNYSPVAAGDYASGTNHVLPTSGYAKIYSGLNVNHFIKYSSIQKISKEGLENIKDTIIS 406
                                       ***************************************************************************** PP

                                       HHHHTT-HHHHHHHHHHH CS
                     Histidinol_dh 392 lAeaEgLeaHaeavkvRl 409
                                       ++e EgL aH+++vk+R+
  gi|298674155|ref|YP_003725905.1| 407 ISEEEGLYAHSDSVKTRF 424
                                       ****************96 PP

>> Toprim_3  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1     0.071   6.3e+02      43      78 ..      30      64 ..      23      77 .. 0.80
   2 ?    9.1   0.1   0.00019       1.7      24      79 ..     216     269 ..     210     281 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.071
                          Toprim_3 43 rvviaaD.nDaandGreaaeklaerleaagieavlle 78
                                      +v + +D   ++  G ea +k +++++ a ie + ++
  gi|298674155|ref|YP_003725905.1| 30 KVSVILDeIHNH--GDEALKKYTKQFDNAEIENIEVS 64
                                      566667755566..**************999988776 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00019
                          Toprim_3  24 iAllsaanlkaiawpergkrvviaaDnDaandGreaaeklaerleaagieavllep 79 
                                       +A ++++n  +i++p +  +v i aD+ a    + aa +++++le +  ++++l  
  gi|298674155|ref|YP_003725905.1| 216 TAKMQVRNRVEIDFPAGPSEVLIIADESAD--AKMAASDIVAQLEHDPNAVSILIT 269
                                       67788888889***************9998..999*****9999998777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       960  (0.0535445); expected 358.6 (0.02)
Passed bias filter:                      645  (0.0359752); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 2755.39
//
Query:       gi|298674156|ref|YP_003725906.1|  [L=136]
Description: hypothetical protein Metev_0179 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-62  207.1   1.6    6.6e-62  207.0   1.6    1.0  1  DUF1699   Protein of unknown function (DUF1699)


Domain annotation for each model (and alignments):
>> DUF1699  Protein of unknown function (DUF1699)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.0   1.6   3.7e-66   6.6e-62       1     129 [.       1     129 [.       1     130 [. 0.99

  Alignments for each domain:
  == domain 1  score: 207.0 bits;  conditional E-value: 3.7e-66
                           DUF1699   1 mkirvvsskeeietlnenekivHlafrpsntdilslvkkcpklkaiqvpeSykktlsksakmfleiqgiellegdvw 77 
                                       mkirvvss++ei ++++ne+++H+afrpsn+di+slvk+cp++++iq+p+Sy+ tlsks++mfl++q+i+l+egdvw
  gi|298674156|ref|YP_003725906.1|   1 MKIRVVSSRDEIPKIDSNENVIHFAFRPSNKDIFSLVKRCPNVEVIQIPSSYRSTLSKSIEMFLDMQNIKLIEGDVW 77 
                                       9**************************************************************************** PP

                           DUF1699  78 ghrkdineyyevseevierikelkseglseeeiaeklsketklspdlikfll 129
                                       ghrkdineyy+++ +v+++ikelkseg+s+e+ia+kls+e k++++++k++l
  gi|298674156|ref|YP_003725906.1|  78 GHRKDINEYYSIPPAVVDKIKELKSEGKSNEDIADKLSREGKMNKEMLKYVL 129
                                       **************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 978.94
//
Query:       gi|298674157|ref|YP_003725907.1|  [L=409]
Description: hypothetical protein Metev_0180 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.088   12.8   2.5        4.2    7.4   0.3    2.5  2  Rad10     Binding domain of DNA repair protein Ercc1 (rad10/S


Domain annotation for each model (and alignments):
>> Rad10  Binding domain of DNA repair protein Ercc1 (rad10/Swi10)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1    0.0015        26      47     110 ..      14      79 ..       8      83 .. 0.64
   2 ?    7.4   0.3   0.00023       4.2      16      62 ..     312     359 ..     303     393 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0015
                             Rad10  47 hklhpeYieerlkklk..kkyklrvlLvlvDved..seevlkeLnkicilndltlllawsaeeaaryl 110
                                       ++++ + ++er+++l+  +   + + +++ ++++   + ++ +Lnk ++l+++t+  a sae++a+y 
  gi|298674157|ref|YP_003725907.1|  14 YSINGQNVTERINRLSlvRPGVVIIPMLYDEIKSdsLQLIVDQLNKSSYLKQITI--ALSAENSAQYR 79 
                                       66777889999999995322333333333334443356677899**999999887..55677788875 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00023
                             Rad10  16 slknvpweykdivpDyvigsttcvlflslkyhklhpe.Yieerlkklk 62 
                                       +l++++++yk+  +D + + +  ++f  lky++ ++e Y+++  k ++
  gi|298674157|ref|YP_003725907.1| 312 FLHSISVRYKRFSQDLIRQYHADAIFNDLKYNRHQEEiYVDTFAKIIQ 359
                                       5778899*************************9998527766555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2653.41
//
Query:       gi|298674158|ref|YP_003725908.1|  [L=434]
Description: pyridoxal-phosphate dependent TrpB-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-42  144.2   0.0    6.4e-42  144.0   0.0    1.0  1  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.0   0.0   3.6e-46   6.4e-42       5     294 .]      77     414 ..      73     414 .. 0.86

  Alignments for each domain:
  == domain 1  score: 144.0 bits;  conditional E-value: 3.6e-46
                                       SSS--EEEECCTCCCCCCE..EEEEEGGGSTTSBTTHHHHHHHHHH.HHTTTTTSEEEEEBSSHHHHHHHHHHHHHT CS
                              PALP   5 igpTPlvrlprlskelgvp..lflKlEslnptgSfKdRgaeyllar.lkegtgaktvveassGNhgralAaaaallG 78 
                                        +p+Pl+r++rl++ l +p  +++K+E+  p gS+K ++    +++  keg   ++ +e+++G++g al++a++ + 
  gi|298674158|ref|YP_003725908.1|  77 WRPSPLHRAHRLEELLDTPakIYYKNEGVSPAGSHKPNTSIAQVYYnMKEG-NERVTTETGAGQWGSALSLACNYFD 152
                                       699*******************************************88888.9999999999*************** PP

                                       -EEEEEEETTS-...HHHHHHHHHTT-EEEEE..................CCHHHHHHHHHHHHHHHSTTCEE--TT CS
                              PALP  79 lkvtivvpadas...pekvallrllGaevvev..................ggdydeavaaaaelaaegegaylvsqf 134
                                       l++ +++ +++    p ++ l+ l+Ga+v+ +                   g+   a + a e a+e+++  ++  +
  gi|298674158|ref|YP_003725908.1| 153 LECKVYMVRSSFeqkPFRKSLINLWGATVIPSpsketkfgqqfleqypdtTGSLGIAISEAIEDASENDNTKYALGS 229
                                       ********999977789***************888888777777555444444555555566777777888888888 PP

                                       TSHHHHHHHHTHHHHHHHHTT...TTEEEEEEE-SSSHHHHHHHHHHHH....HSTT-EEEEEEECTTCGGTTCC.. CS
                              PALP 135 dnptviegygtiglEileqlg...gkpdavvvpvGgGgliaGiaaglke....rrpdvrvigvepegsdalarsl.. 202
                                          +v++ ++ iglE  +ql    + pd v+ ++GgG+++aGi++++ +    ++ d+++igvep+ +++l+++   
  gi|298674158|ref|YP_003725908.1| 230 VLNHVMLHQTVIGLESQKQLEkvdEYPDIVIGCCGGGSNLAGISFPYIKdkinKKHDPEIIGVEPSACPTLTEGSfk 306
                                       8899************8676666699***********************77655555*****************944 PP

                                       .S..S.SS..B...................SSS.CCSTCSCGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHS CS
                              PALP 203 .ragrrvtvpvs..................dtiadglavgspselafelldrlvdeivtvsdeealeamrllarreg 260
                                        + g+      +                  +    gl+ +  s+   +l+d+ + ++    + e+++ ++++ar+eg
  gi|298674158|ref|YP_003725908.1| 307 yDSGDT-----AmmtpllkmytlghdfvppSIHSGGLRYHGCSPIISRLYDDGLMKGRNYHQVEIFDSAVKFARTEG 378
                                       444444.....2555569*******777766666677777************************************* PP

                                       B-B-H.HHHHHHHHH.HHHHHHCCTTCEEEEEEE-B CS
                              PALP 261 ivvep.ssaaalaal.klreagelkegdrvvviltg 294
                                       iv+ p ss+a  +a+ ++ +++e +e++++++ l+g
  gi|298674158|ref|YP_003725908.1| 379 IVPAPeSSHAIKCAMdEATKCRETGEEKTILFNLSG 414
                                       *****5555555555*******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2715.22
//
Query:       gi|298674159|ref|YP_003725909.1|  [L=442]
Description: phosphomethylpyrimidine kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-84  282.9   0.4    2.9e-84  282.3   0.4    1.3  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
    1.3e-67  226.6   0.1    2.4e-67  225.7   0.1    1.4  1  ThiP_synth    Thiamine-phosphate synthase
      4e-10   39.5   0.1    1.2e-09   37.9   0.0    1.7  2  PfkB          pfkB family carbohydrate kinase
    0.00023   20.6   0.1    0.00062   19.2   0.1    1.7  1  HK            Hydroxyethylthiazole kinase family
     0.0071   15.9   0.6      0.012   15.1   0.6    1.4  1  Carb_kinase   Carbohydrate kinase
  ------ inclusion threshold ------
      0.019   15.2   0.0       0.04   14.1   0.0    1.5  1  LAM_C         Lysine-2,3-aminomutase


Domain annotation for each model (and alignments):
>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  282.3   0.4   9.8e-88   2.9e-84       1     246 []      14     255 ..      14     255 .. 0.98

  Alignments for each domain:
  == domain 1  score: 282.3 bits;  conditional E-value: 9.8e-88
                                       ETTSSSHHHHHHHHHHHTTEEEEEEEEEEEEEETTCEEEEEE--HHHHHHHHHHHHHTS--SEEEE-S--SHHHHHH CS
                      Phos_pyr_kin   1 DssGGAGiqADlktfsalgvygmsvitaltaqntkgvkevhplpaelveaqleavledvkvdavKiGmlasaeiiev 77 
                                       Ds+GGAGi+AD+ktf+algvyg+++it++taqnt+gv + ++lp+++v++q++av++d++v   K+Gml+s+ei+++
  gi|298674159|ref|YP_003725909.1|  14 DSGGGAGIEADIKTFAALGVYGTCAITSVTAQNTEGVISSYDLPKNIVSEQIDAVCKDMNVGWTKTGMLGSNEIVKT 90 
                                       9**************************************************************************** PP

                                       HHHHHHHTTSSEEEE---SSCTSSSBSSHHHHHHHHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHT CS
                      Phos_pyr_kin  78 vaeklkkykvpvVlDPVmvaksgselleeeavealkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllkl 154
                                       va+ +kk+++ +VlDPVm+a+ g +ll+e+a+ +l++eLlpl++++tPN++Ea +L+g  ik+++d+++aa+k+++ 
  gi|298674159|ref|YP_003725909.1|  91 VADSIKKHNLSIVLDPVMAAQAGGTLLKEDAMPLLTDELLPLCKIVTPNTEEAYKLSGIYIKDLNDARDAARKIAEK 167
                                       ***************************************************************************** PP

                                       T-SEEEEEEGGS-SSSEEEEEEEE..TSSEEEEEEEE----S--BTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHH CS
                      Phos_pyr_kin 155 gakaVlikGghlegeeavvtdvly..dgeeveeleaerietknthGtGCtlssaiaaelakgesleeAvkkAkeyvt 229
                                       g+ +V+i+Gghl   ea   d++y  ++++++ + ++ +e   thG+GCt+ssai ++l kg sle+A k Ak++v+
  gi|298674159|ref|YP_003725909.1| 168 GKCHVIITGGHL---EAC--DLVYdyEKDDFTVIYGSFVE-GGTHGSGCTYSSAIVSYLNKGFSLEDAAKYAKQFVE 238
                                       ***********9...455..89988788999999999999.************************************ PP

                                       HHHHCG-BSTSSS-B-- CS
                      Phos_pyr_kin 230 eaikealelgkgagpvn 246
                                       +aike+l++g+g++pvn
  gi|298674159|ref|YP_003725909.1| 239 NAIKESLHIGNGVNPVN 255
                                       ***************97 PP

>> ThiP_synth  Thiamine-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.7   0.1   7.9e-71   2.4e-67       4     164 ..     275     435 ..     274     436 .. 0.98

  Alignments for each domain:
  == domain 1  score: 225.7 bits;  conditional E-value: 7.9e-71
                                       HHHHHHHCC--.GCC--TT-B-EEEE-ST--SGGGEEEETT-EEE-TSSEEE-S-EEETS-CHHHHHHHHHHCC-TT CS
                        ThiP_synth   4 ralelleeeeefakliPevgsNiayalpdAksieDvaavpGRIvrvkgrvkvvgepefgasshvarvllaamkfdpe 80 
                                       +al+ll+++++f++liPevgsNia+a+p+A++i+Dvaav+GRIv  k+ +k+vg++ fgasshvar++laamkf+pe
  gi|298674159|ref|YP_003725909.1| 275 DALDLLQNNQAFTNLIPEVGSNIAMAIPNASEISDVAAVEGRIVHLKKYPKPVGSIDFGASSHVARIVLAAMKFNPE 351
                                       699************************************************************************** PP

                                       --EEEEEE--HHHHHHHCCTTSEEEE--CCCS-CCCT-HHHHHHHHHHHCC.S-ECEEEE--BCTB--EEEEEESSH CS
                        ThiP_synth  81 vraainirydekilealeelglkvvefdreeepeevgstmewgvaeaieel.evpdviydeGgvGkEpmiyvlgkda 156
                                       +++aini+y+++il++++e g+++++f+r +epee  stm+wgv  ai+++ +vpd+iyd+Gg+GkEpm+++lgk+a
  gi|298674159|ref|YP_003725909.1| 352 IKSAINIKYTPRILDICNEIGYDISSFNRADEPEE-TSTMDWGVTFAISTYgTVPDAIYDKGGIGKEPMVRLLGKSA 427
                                       ***********************************.7**************99************************ PP

                                       HHHHHHHH CS
                        ThiP_synth 157 eevvekvl 164
                                       ++vv+k++
  gi|298674159|ref|YP_003725909.1| 428 VDVVNKAI 435
                                       ******97 PP

>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.0   4.1e-13   1.2e-09     149     283 ..      89     234 ..      83     247 .. 0.78
   2 ?   -1.8   0.0       0.5   1.5e+03     165     200 ..     279     313 ..     240     323 .. 0.69

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 4.1e-13
                                       HHHHHHHHHTTE...EEEEECESSSHH......HHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHH CS
                              PfkB 149 eelaeaaknggt...fdpnlldplgaq......fkeallellaladllkpneeElealtgekledieealaalhklk 216
                                       +++a+  k+++     dp++ + +g        +    +ell+l+ +++pn eE+ +l+g  ++d ++a +a+ k+ 
  gi|298674159|ref|YP_003725909.1|  89 KTVADSIKKHNLsivLDPVMAAQAGGTllkedaMPLLTDELLPLCKIVTPNTEEAYKLSGIYIKDLNDARDAARKIA 165
                                       555555555553355555555555544755554444557899*********************************** PP

                                       HTTSSEEEEEEGGGEE.EEEE....TTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHH CS
                              PfkB 217 akgaktvvvtlGkeGa.lvve....kdgelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfan 283
                                       +kg+ +v++t G   a  +v      d +++  + +      t G G ++ +++++ l +g sle+a+++a 
  gi|298674159|ref|YP_003725909.1| 166 EKGKCHVIITGGHLEAcDLVYdyekDDFTVIYGS-F--VEGGTHGSGCTYSSAIVSYLNKGFSLEDAAKYAK 234
                                       ************9665355556986666666666.4..2378***************************996 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.5
                                       ECESSSHHHHHHHHHHHCTESEEEEEHHHHHHHHTS CS
                              PfkB 165 lldplgaqfkeallellaladllkpneeElealtge 200
                                       ll    a f   + e+ + +  ++pn++E++ ++  
  gi|298674159|ref|YP_003725909.1| 279 LLQNNQA-FTNLIPEVGSNIAMAIPNASEISDVAAV 313
                                       3333443.7788888888899999999999877655 PP

>> HK  Hydroxyethylthiazole kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   2.1e-07   0.00062      58     198 ..      80     220 ..      63     244 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.1e-07
                                       TT--HHHHHHHHHHHHHHHHTT--EEEE-TTB...TTBHHHHHHHHHHHHHS--...SEEEEEHHHHHHHHTSSCCS CS
                                HK  58 GtleekaiealkaAvksakevnrPvvlDPVgv...gAtelRrelalellkevkl...avikGNasEilslaglelkv 128
                                       G l +   e++k+ ++s k++n  +vlDPV +   g t   +e a  ll+++ l   +++  N+ E  +l+g+  k 
  gi|298674159|ref|YP_003725909.1|  80 GMLGS--NEIVKTVADSIKKHNLSIVLDPVMAaqaGGTL-LKEDAMPLLTDELLplcKIVTPNTEEAYKLSGIYIK- 152
                                       44444..6889999999************9541113344.444555566555431115667777777777777654. PP

                                       CSSSSSS-SHHHHHHHHHHHHHHTSEEEEES....SSEEEEESSE.EEEEE-S-GGGGGSTTHHHHHHHHHHHHH CS
                                HK 129 kGvDskeaataavaavqkvAqklrvvvvvtG....evDvvsdgkk.vyklknGtellgkitasGCllgsvvaafl 198
                                          D ++a      a++k+A+k ++ v++tG    ++D+v d +k  +++  G+ + g   +sGC+++s++ + l
  gi|298674159|ref|YP_003725909.1| 153 ---DLNDA----RDAARKIAEKGKCHVIITGghleACDLVYDYEKdDFTVIYGSFVEGGTHGSGCTYSSAIVSYL 220
                                       ...44444....457999************9666668*****988799**********************99876 PP

>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.6   3.9e-06     0.012      77     164 ..      82     178 ..       7     245 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.9e-06
                                       -SSSHCHHHHCHHHCCCCS-EEEE......GGGGGSGGGG......TTTTSSEEEE--HHHHHHHCTTTCHHCCSHH CS
                       Carb_kinase  77 LgrdekikklleevlekdeplviD......AdgLnllaqkne...lserkaeviLTPhkkEfkrLlkaivkkeddrl 144
                                       Lg++e +k + + + +++ ++v+D      A+g  l+++              i TP+  E  +L++  +k  +d  
  gi|298674159|ref|YP_003725909.1|  82 LGSNEIVKTVADSIKKHNLSIVLDpvmaaqAGGTLLKEDAMPlltDELLPLCKIVTPNTEEAYKLSGIYIKDLNDAR 158
                                       7888888887777777777777775555444444444443324332233344699****************999*** PP

                                       HHHHHHHHHHTTEEEEESTT CS
                       Carb_kinase 145 elarelaqklnavvllkgek 164
                                       ++ar++a+k ++ v++ g +
  gi|298674159|ref|YP_003725909.1| 159 DAARKIAEKGKCHVIITGGH 178
                                       ************99999976 PP

>> LAM_C  Lysine-2,3-aminomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.3e-05      0.04      42      90 ..      42      89 ..      36     103 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.3e-05
                             LAM_C 42 vvlrnfeGvitsypePenyvkgkaddyfkevypdtekkkeevGisalle 90
                                      v  +n eGvi+sy  P+n v+++ d++ k+++   +k +   G +++++
  gi|298674159|ref|YP_003725909.1| 42 VTAQNTEGVISSYDLPKNIVSEQIDAVCKDMNVGWTK-TGMLGSNEIVK 89
                                      6678*********************999999865544.33455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3355.36
//
Query:       gi|298674160|ref|YP_003725910.1|  [L=72]
Description: Sm ribonucleoprotein-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-23   80.5   0.4    5.6e-23   80.4   0.4    1.0  1  LSM       LSM domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.4   0.4   3.1e-27   5.6e-23       3      67 .]       9      72 .]       7      72 .] 0.97

  Alignments for each domain:
  == domain 1  score: 80.4 bits;  conditional E-value: 3.1e-27
                                      HHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEEE CS
                               LSM  3 lkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivlisl 67
                                      l++ +n  v+v+l++ re+rG L+g+D +mNlvL+++ee ++++  +rklg v+iRG+n+v++s+
  gi|298674160|ref|YP_003725910.1|  9 LNNALNTPVIVRLRGSREFRGELQGYDVHMNLVLDNAEELNDGE-IVRKLGSVVIRGDNVVYVSP 72
                                      899**************************************999.******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 448.11
//
Query:       gi|298674161|ref|YP_003725911.1|  [L=53]
Description: 50S ribosomal protein L37e [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-22   79.2  12.6      2e-22   79.1  12.6    1.0  1  Ribosomal_L37e  Ribosomal protein L37e
  ------ inclusion threshold ------
      0.046   13.5   2.7        3.4    7.5   0.2    2.3  2  Rubredoxin_2    Rubredoxin metal binding domain
      0.063   13.4   3.9        1.3    9.2   3.5    2.0  2  Zn-ribbon_8     Zinc ribbon domain
      0.076   13.0   1.2      0.083   12.9   1.2    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.53    9.8   8.5        5.6    6.6   8.4    2.0  1  zn-ribbon_14    Zinc-ribbon
       0.95    9.3   7.1        0.8    9.6   0.8    2.2  2  zf-C2H2_3       zinc-finger of acetyl-transferase ESCO


Domain annotation for each model (and alignments):
>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.1  12.6   6.7e-26     2e-22       1      51 [.       2      52 ..       2      53 .] 0.95

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 6.7e-26
                    Ribosomal_L37e  1 tkGtssfGkrqkkktHilCrrCgkrsyhvqkktCascGy.psaklrkynWsa 51
                                      +kGt+sfGkr +k+tH++CrrCg+ s++v+ k+C scG+ +++++r+ynW++
  gi|298674161|ref|YP_003725911.1|  2 SKGTESFGKR-QKRTHTKCRRCGSMSFNVRDKECKSCGFgKTKRMRSYNWNK 52
                                      69********.555************************************87 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.2    0.0028       8.5       3      10 ..      19      26 ..      18      29 .. 0.68
   2 ?    7.5   0.2    0.0011       3.4       2      12 ..      33      43 ..      33      45 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0028
                      Rubredoxin_2  3 CsqCGfes 10
                                      C++CG+ s
  gi|298674161|ref|YP_003725911.1| 19 CRRCGSMS 26
                                      77777765 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0011
                      Rubredoxin_2  2 vCsqCGfesak 12
                                      +C++CGf   k
  gi|298674161|ref|YP_003725911.1| 33 ECKSCGFGKTK 43
                                      6*****98665 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.3    0.0009       2.7      16      34 ..       9      24 ..       3      30 .. 0.69
   2 ?    9.2   3.5   0.00044       1.3       7      39 ..      18      45 ..      18      46 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0009
                       Zn-ribbon_8 16 evlqsisdapltaCPeCgs 34
                                       ++q+   +  t+C +Cgs
  gi|298674161|ref|YP_003725911.1|  9 GKRQK---RTHTKCRRCGS 24
                                      44454...45888****99 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00044
                       Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCgs.evrrv 39
                                      +C++Cg+    ++      +++C++Cg  +++r+
  gi|298674161|ref|YP_003725911.1| 18 KCRRCGSMSFNVR------DKECKSCGFgKTKRM 45
                                      7999993333333......677*****9999986 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.2   2.8e-05     0.083      66      97 ..      12      42 ..       4      49 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.8e-05
                                      EE--EEEETTTS-EEECHHHHHS-TTTSSS-E CS
                              HypA 66 evpvkvrCreCgkefeleekalrCpkCgsadv 97
                                      +++ +++Cr+Cg+      ++ +C++Cg  ++
  gi|298674161|ref|YP_003725911.1| 12 QKRTHTKCRRCGSMSFNV-RDKECKSCGFGKT 42
                                      5677899*****544433.3468****97665 PP

>> zn-ribbon_14  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   8.4    0.0019       5.6       2      18 ..      18      37 ..      17      39 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0019
                      zn-ribbon_14  2 kCerCGylSSq...kiCkAC 18
                                      kC+rCG +S +   k Ck C
  gi|298674161|ref|YP_003725911.1| 18 KCRRCGSMSFNvrdKECKSC 37
                                      8********66444778888 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.8   0.00027       0.8       6      26 ..       8      30 ..       7      33 .. 0.76
   2 ?    5.0   0.7    0.0074        22      14      21 ..      32      39 ..      24      40 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00027
                         zf-C2H2_3  6 lgqksfga.sqCkeCg.MvYnpg 26
                                      +g++++++ ++C  Cg M++n  
  gi|298674161|ref|YP_003725911.1|  8 FGKRQKRThTKCRRCGsMSFNVR 30
                                      89999999677****96777765 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0074
                         zf-C2H2_3 14 sqCkeCgM 21
                                      ++Ck Cg 
  gi|298674161|ref|YP_003725911.1| 32 KECKSCGF 39
                                      45****95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 351.56
//
Query:       gi|298674162|ref|YP_003725912.1|  [L=471]
Description: amidophosphoribosyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.9e-23   80.7   0.0    1.5e-22   79.8   0.0    1.5  1  GATase_7      Glutamine amidotransferase domain
      2e-22   79.9   0.0    6.1e-22   78.3   0.0    1.8  2  GATase_6      Glutamine amidotransferase domain
    4.1e-08   32.5   0.0    3.4e-07   29.4   0.0    2.0  2  GATase_4      Glutamine amidotransferases class-II
    0.00076   19.0   0.1     0.0014   18.2   0.1    1.4  1  Pribosyltran  Phosphoribosyl transferase domain


Domain annotation for each model (and alignments):
>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.8   0.0   3.4e-26   1.5e-22      11     121 ..      92     208 ..      80     210 .. 0.93

  Alignments for each domain:
  == domain 1  score: 79.8 bits;  conditional E-value: 3.4e-26
                          GATase_7  11 agaQPmvs.sedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea........ewgeealerlnGmf 78 
                                       ++ QP+v   ++g+++i++nG ++N  elr+eLe++g  f t+sDtev+++ll +        + ++++++rl G++
  gi|298674162|ref|YP_003725912.1|  92 ENCQPLVVnFKGGTVAIAHNGNLVNACELRDELESEGRIFITDSDTEVIAHLLVKqllkhnifDSIRQVMQRLVGSY 168
                                       578***99779*****************************************9999********************* PP

                          GATase_7  79 AfaiwdeeekrlllaRDrlGikPLyygedkgdallfaSelkal 121
                                       ++ i+ + +  l+++RD+lGikPL +ge +g ++++aSe  a+
  gi|298674162|ref|YP_003725912.1| 169 SLTILIDGQ--LIAVRDPLGIKPLCIGEVEG-GYAVASESVAI 208
                                       *****9888..******************86.*******9987 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.3   0.0   1.4e-25   6.1e-22      11     134 .]      73     204 ..      62     204 .. 0.88
   2 ?   -3.4   0.0       2.2     1e+04      40      58 ..     222     239 ..     220     245 .. 0.72

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 1.4e-25
                          GATase_6  11 edevalaHvRlaivglaeeega.qPf..psedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall... 81 
                                       +++v+++HvR +++g++   ++ qP+    + g+++++hNG   n+ elr+el++ +g+ f ++sDtev+++ll   
  gi|298674162|ref|YP_003725912.1|  73 TGNVGIGHVRYSTSGNS-GIENcQPLvvNFKGGTVAIAHNGNLVNACELRDELES-EGRIFITDSDTEVIAHLLvkq 147
                                       4569************9.88888***98889999*********************.****************88775 PP

                          GATase_6  82 .eelG.......eevlerlrGmfafaiwdkrentlilardrlgvkplyyavdesglafase 134
                                                    +v++rl+G ++  i     ++li +rd lg+kpl++++ e+g a+ase
  gi|298674162|ref|YP_003725912.1| 148 lL--KhnifdsiRQVMQRLVGSYSLTIL--IDGQLIAVRDPLGIKPLCIGEVEGGYAVASE 204
                                       51..255667999999*****8888655..6899**************************8 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.2
                          GATase_6  40 grlllvhNGeiynykelre 58 
                                       g++l+   Gei+ y+ l +
  gi|298674162|ref|YP_003725912.1| 222 GEVLFFNDGEIESYQ-LDN 239
                                       567888889**9996.544 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   7.7e-11   3.4e-07      70     146 ..      73     153 ..      41     180 .. 0.79
   2 ?    0.5   0.0     0.052   2.3e+02     238     258 ..     217     237 ..     201     247 .. 0.75

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 7.7e-11
                          GATase_4  70 ksknvvaHiRkatqGevklenthpFvRelwgrewifAHnGdlke...ykpkl.egrfePvGsTDsElafCelleela 142
                                         ++ + H+R  t G+   en++p v +++g +  +AHnG+l +   ++++l ++    + + D+E++   l+++l 
  gi|298674162|ref|YP_003725912.1|  73 TGNVGIGHVRYSTSGNSGIENCQPLVVNFKGGTVAIAHNGNLVNaceLRDELeSEGRIFITDSDTEVIAHLLVKQLL 149
                                       5567799***********************************66344666665344456888899999999999998 PP

                          GATase_4 143 srfe 146
                                       +++ 
  gi|298674162|ref|YP_003725912.1| 150 KHNI 153
                                       8773 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.052
                          GATase_4 238 kklepGellvfrdGalvatas 258
                                       +++ pGe+l+f+dG++   + 
  gi|298674162|ref|YP_003725912.1| 217 RDVYPGEVLFFNDGEIESYQL 237
                                       6889***********988743 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   3.1e-07    0.0014      29     119 ..     283     380 ..     261     382 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.1e-07
                                       GGEEEEEEETTTHHHHHHHHHHSTT-EE.-EEEEEE-TTT--EE..............EE----TTSEEEEE-SEES CS
                      Pribosyltran  29 kpdvvvgiargGvpfakiladeLevpla.yvrkvkyrpdgseeaargssdes......rlledpagkkVliVDDild 98 
                                       + dvv +++  G++ a  +++e ++++   + k +y + +     + + d+       + + +++g++ +++DD + 
  gi|298674162|ref|YP_003725912.1| 283 ESDVVSPVPDSGITSAIGYSKESGIKYSeGLMKNRYIGRTFILPGQEMRDIAvrlkmnTISDNIDGERLILIDDSIV 359
                                       55566666666666666666666666554555555555555555544444448888888999*************** PP

                                       SSHHHHHHHHHHHCC-BSEEE CS
                      Pribosyltran  99 tGgTllaalelLkekgpeevr 119
                                        G+T +++++ +++ g++ev+
  gi|298674162|ref|YP_003725912.1| 360 RGTTSKRIVNMIRDSGAKEVH 380
                                       *******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3283.25
//
Query:       gi|298674163|ref|YP_003725913.1|  [L=380]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-26   91.9   1.9    7.6e-26   90.7   1.9    1.5  1  OrfB_IS605      Probable transposase
    5.3e-24   83.9   0.4    1.1e-23   82.9   0.4    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    4.2e-20   71.0   1.4    9.2e-20   69.9   1.4    1.6  1  HTH_OrfB_IS605  Helix-turn-helix domain
      0.008   16.3   0.3       0.02   15.1   0.3    1.6  1  zf-piccolo      Piccolo Zn-finger
  ------ inclusion threshold ------
      0.039   13.8   4.7       0.24   11.2   1.9    2.4  2  Phage_GP20      Phage minor structural protein GP20
       0.06   13.2   0.7        1.1    9.1   0.1    2.3  2  LemA            LemA family
       0.39   10.9   1.6          2    8.6   1.6    2.1  1  zf-UDP          Zinc-binding RING-finger


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.7   1.9     3e-29   7.6e-26      10     117 ..     180     284 ..     167     286 .. 0.91

  Alignments for each domain:
  == domain 1  score: 90.7 bits;  conditional E-value: 3e-29
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsr 86 
                                       +++  + +++g+D+Gi+++a++++++   ++ ++r lk+  ++l+  +++l++k+k+s+n++k + ++a++h+k+++
  gi|298674163|ref|YP_003725913.1| 180 KQTFYEVNTIGVDVGIKDFAVTSDGE---KIDNPRYLKNSIERLKVLQKRLSRKKKGSNNHRKLKHQIAKYHEKIAN 253
                                       44555689******************...************************************************ PP

                        OrfB_IS605  87 rrkhllhklathliktlkevgvetLnvgnmk 117
                                       +r +++hkl+++li ++++v++e Lnv+++ 
  gi|298674163|ref|YP_003725913.1| 254 QREDFQHKLSSRLISENQAVALECLNVKGLL 284
                                       ****************************986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.9   0.4   4.3e-27   1.1e-23       1      68 [.     298     367 ..     298     368 .. 0.98

  Alignments for each domain:
  == domain 1  score: 82.9 bits;  conditional E-value: 4.3e-27
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpay.TSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       ++++ ++leyka++yG++++++ ++  +Sk C++Cg+ +++ +l++r+++Cp+C++e+drD+nA++Ni k
  gi|298674163|ref|YP_003725913.1| 298 WSSFVQKLEYKAEWYGKNIIKIGRFDpSSKICHVCGYYHQDlELKDREWECPDCKTEHDRDINASVNIKK 367
                                       99******************************************************************87 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9   1.4   3.6e-23   9.2e-20       1      47 []       9      54 ..       9      54 .. 0.98

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 3.6e-23
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeegk 47
                                      M lkaykyr yP++ Q+e++a+++G++Rf+YN+aL+ +++ ye+ gk
  gi|298674163|ref|YP_003725913.1|  9 M-LKAYKYRMYPNQIQQELIAKHIGACRFIYNWALENKIKSYEQDGK 54
                                      8.******************************************997 PP

>> zf-piccolo  Piccolo Zn-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.3   7.6e-06      0.02      28      56 ..     326     354 ..     322     356 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7.6e-06
                        zf-piccolo  28 kqvCnlCGFnptphltekkeWlclnCQtq 56 
                                       +++C +CG+  ++   + +eW c  C t+
  gi|298674163|ref|YP_003725913.1| 326 SKICHVCGYYHQDLELKDREWECPDCKTE 354
                                       79***********999**********985 PP

>> Phage_GP20  Phage minor structural protein GP20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.041   1.1e+02     113     136 ..      51      77 ..      24      88 .. 0.71
   2 ?   11.2   1.9   9.3e-05      0.24      32      90 ..     218     276 ..     205     286 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.041
                        Phage_GP20 113 edgelkg...LdeqikkLkesdkyLFe 136
                                       +dg+ +    L++qi  Lk+++++L e
  gi|298674163|ref|YP_003725913.1|  51 QDGKAISrfeLNKQIRVLKQDHEWLNE 77 
                                       455555334488888888888888876 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 9.3e-05
                        Phage_GP20  32 eqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeyeakiadlkldnaielaLk 90 
                                       e+lk  +k L+  kk +++  +L+ qi+++ +k++++ ++ + k++ + +++    aL+
  gi|298674163|ref|YP_003725913.1| 218 ERLKVLQKRLSRKKKGSNNHRKLKHQIAKYHEKIANQREDFQHKLSSRLISENQAVALE 276
                                       6788889999999********************************99888776666666 PP

>> LemA  LemA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1     0.062   1.6e+02      30      82 ..      60     112 ..      42     117 .. 0.82
   2 ?    9.1   0.1   0.00042       1.1      56     107 ..     209     261 ..     181     268 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.062
                              LemA  30 EketleevteaRakaaeaesveekaeaenqlssalsrllavaEnYPdLkanen 82 
                                       E +   +v +  ++  ++ + ++ + a  +l++a+ +++     +P++k+++n
  gi|298674163|ref|YP_003725913.1|  60 ELNKQIRVLKQDHEWLNEINSQSLQGATLNLENAFTKFFREKSGFPKFKSKKN 112
                                       55555566666667788889999999************************987 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00042
                              LemA  56 aenqlssalsrllavaEnY.PdLkanenfleLqeelegtEnriavaRrrYnea 107
                                       + + l+++++rl +++ +   + k ++n ++L++++++  ++ia++R++++++
  gi|298674163|ref|YP_003725913.1| 209 NPRYLKNSIERLKVLQKRLsRKKKGSNNHRKLKHQIAKYHEKIANQREDFQHK 261
                                       5556777777777777664145578999*********************9876 PP

>> zf-UDP  Zinc-binding RING-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   1.6   0.00076         2      36      62 ..     327     357 ..     322     366 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00076
                            zf-UDP  36 pvcrpc....yeyerkdgnqsCPqCktrykr 62 
                                        +c+ c     + e kd +  CP Ckt+  r
  gi|298674163|ref|YP_003725913.1| 327 KICHVCgyyhQDLELKDREWECPDCKTEHDR 357
                                       56666622112457789999*******9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1518  (0.0846673); expected 358.6 (0.02)
Passed bias filter:                      638  (0.0355848); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2590.72
//
Query:       gi|298674164|ref|YP_003725914.1|  [L=258]
Description: thiazole biosynthesis enzyme [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      9e-77  257.5   1.6    1.1e-76  257.2   1.6    1.0  1  Thi4           Thi4 family
    1.4e-10   41.1   0.3    1.9e-10   40.7   0.3    1.2  1  FAD_oxidored   FAD dependent oxidoreductase
    2.3e-07   30.4   0.2    2.6e-07   30.1   0.2    1.1  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    4.8e-06   25.9   3.2    0.00015   21.0   0.9    2.1  2  FAD_binding_2  FAD binding domain
    5.7e-06   26.5   0.1    1.3e-05   25.3   0.1    1.7  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    6.5e-05   21.8   1.4    0.00011   21.1   1.4    1.3  1  HI0933_like    HI0933-like protein
     0.0043   16.3   0.0     0.0072   15.6   0.0    1.3  1  FAD_binding_3  FAD binding domain
     0.0054   15.9   0.3      0.011   14.8   0.3    1.5  1  GIDA           Glucose inhibited division protein A
  ------ inclusion threshold ------
       0.01   14.9   1.4      0.076   12.1   0.2    2.0  2  Lycopene_cycl  Lycopene cyclase protein
      0.039   13.5   1.8       0.23   11.0   0.2    2.0  2  DAO            FAD dependent oxidoreductase
       0.08   12.9   0.3       0.17   11.9   0.3    1.5  1  NAD_binding_9  FAD-NAD(P)-binding


Domain annotation for each model (and alignments):
>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  257.2   1.6   6.6e-80   1.1e-76       1     235 []       9     239 ..       9     239 .. 0.97

  Alignments for each domain:
  == domain 1  score: 257.2 bits;  conditional E-value: 6.6e-80
                                       HHHHHHHHHHHHHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBSEEEEETTTHHHH CS
                              Thi4   1 sraiveryfedllkyaesDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfsaivvrkpakelL 77 
                                       ++aiv   ++ +++y e Dv++vG+G++ + aa  la++ + kva++e+++++GGG+w+GG++f +ivv+++a+++L
  gi|298674164|ref|YP_003725914.1|   9 TKAIVDDFSKTFIDYTEVDVALVGGGPANMIAATRLAQE-GYKVALFEKKLALGGGMWGGGMMFPRIVVQDEARKIL 84 
                                       79*************************************.************************************* PP

                                       HHTT---EEESS..EEEESEHHHHHHHHHHHHHTSTTEEEEESEEEEEEEEETBTEEEEEEEEEHHHHTC..TTTSS CS
                              Thi4  78 delgikyedegd..yvvvkdaalftstllskvlqlanvkllnavaveDlivregegvaGvvinwtlvela..hdtqs 150
                                       +e++i++ ++++  +++++++++ +s+l+ k++  ++v+++n v  eD+++re+++v+G+vinwt+v++a  h    
  gi|298674164|ref|YP_003725914.1|  85 EEFDINHYEYDNekGYYIANSIESVSRLINKTVT-SGVQVFNLVNFEDVMIREDDRVTGIVINWTAVSIAnlH---- 156
                                       *****9765543228*******************.**********************************9777.... PP

                                       .-B-EEEEEEEEEE--GSSSTTTTHHHHHHHHCTTTS-----ECB-HHHHHHHHHHHECEEETTEEE-THHHHHHHT CS
                              Thi4 151 cvDPlvirakvvvdatGhdgeivavvvkkikleakiekvkgeksldaekaedaivkktrevvpnlyvaGmevaevdg 227
                                        vDPl+irakvv+d tGh++ + ++v++ki +++  e v ge++++a+ +e+++ ++trev+p+l+v+Gm++++v g
  gi|298674164|ref|YP_003725914.1| 157 -VDPLTIRAKVVIDGTGHEAVVCNTVQRKIPNAK-FEGVVGERPMWADAGEKSLKETTREVYPGLIVTGMAANAVAG 231
                                       .*****************************9988.899*************************************** PP

                                       -EB--SB- CS
                              Thi4 228 anRmGpif 235
                                       a+RmGp+f
  gi|298674164|ref|YP_003725914.1| 232 APRMGPVF 239
                                       *******9 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.3   1.2e-13   1.9e-10       1     145 [.      27     173 ..      27     179 .. 0.72

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 1.2e-13
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaeeqvvtgiareflerlrqrggarlkk 77 
                                       Dv  vGGgpa ++AA   a++G kv+L e++  lGG + +g+++ +        vv+  ar++le+  + +++++ +
  gi|298674164|ref|YP_003725914.1|  27 DVALVGGGPANMIAATRLAQEGYKVALFEKKLALGGGMWGGGMMFPRI------VVQDEARKILEEF-DINHYEYDN 96 
                                       9***********************************999998655554......4444455555555.223343332 PP

                      FAD_oxidored  78 rskw.ntfepevakavleemlaeagvtvllntrlvevek.eg.......kriesvtveske.grktirAkvfiDATg 144
                                       +++   +   e + +++++ ++  gv+v+    +++v   e+        + ++v +++      tirAkv+iD+Tg
  gi|298674164|ref|YP_003725914.1|  97 EKGYyIANSIESVSRLINKTVTS-GVQVFNLVNFEDVMIrEDdrvtgivINWTAVSIANLHvDPLTIRAKVVIDGTG 172
                                       23322367788888888888877.8888888888888773342333333236777788888679************9 PP

                      FAD_oxidored 145 d 145
                                        
  gi|298674164|ref|YP_003725914.1| 173 H 173
                                       5 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.2   1.6e-10   2.6e-07       2     114 ..      27     178 ..      26     223 .. 0.75

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 1.6e-10
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEE....TTHCHHHCSHHHHCHHHHHHHHHHHHH................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx................. RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve....legtclnggcllskallgvaedaeias................. 57 
                                       dv+ +GgGpA + aa++laq g+kv+l+e    l+g + +gg++ + ++++ ++++ i++                 
  gi|298674164|ref|YP_003725914.1|  27 DVALVGGGPANMIAATRLAQEGYKVALFEkklaLGGGMWGGGMMFPRIVVQDEARK-ILEefdinhyeydnekgyyi 102
                                       89**************************9999866666555555544444443333.444466666*********99 PP

                                       ...................HHHHCHHHH.CCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BC CS
                                       ...................xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 ...................evvkklnqg.ielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdl 114
                                                          +v++ +n + ++ + +  v++i  ++  v + ++   d  +i ++ ++  tG ++  +
  gi|298674164|ref|YP_003725914.1| 103 ansiesvsrlinktvtsgvQVFNLVNFEdVMIREDDRVTGIVINWTAVSIANLH-VDPLTIRAKVVIDGTGHEAVVC 178
                                       999988888887777777755555555556666667788888888777777766.6777888888888888666555 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.9   9.1e-08   0.00015       1      45 [.      27      70 ..      27      83 .. 0.86
   2 !    5.4   0.1    0.0048       7.8     140     200 ..     105     172 ..      68     196 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 9.1e-08
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-E CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgi 45
                                      Dv  +G+G A + AA+++a++G kva+ ek+ + gg   w +G++
  gi|298674164|ref|YP_003725914.1| 27 DVALVGGGPANMIAATRLAQEGYKVALFEKKLALGGG-MWGGGMM 70
                                      899***************************9997764.4555555 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0048
                                       HHHHHHHHHHHHHTCTEEEEESEEEEEEEE.CTTEEEEEEEEET......TTTCEE....EEEESEEEE--- CS
                     FAD_binding_2 140 ghallarlvesarkagvdfqerteadeLiv.edgrvtGavvenp......esgrev....rirakavvlatg 200
                                         + + rl+++    gv++++  + +++++ ed+rvtG+v++             +    +irak v++ tg
  gi|298674164|ref|YP_003725914.1| 105 SIESVSRLINKTVTSGVQVFNLVNFEDVMIrEDDRVTGIVINWTavsianL----HvdplTIRAKVVIDGTG 172
                                       5566889999999999*********998774788******98555544222....13334666666665555 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.1   8.2e-09   1.3e-05       2      34 ..      31      63 ..      30      84 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 8.2e-09
                                      E--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGG CS
                     NAD_binding_8  2 vGaGlsGlvaAylLakagfdvlllekrdrlGGr 34
                                      vG+G + + aA +La++g++v l+ek   lGG 
  gi|298674164|ref|YP_003725914.1| 31 VGGGPANMIAATRLAQEGYKVALFEKKLALGGG 63
                                      9*****************************995 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   1.4   6.7e-08   0.00011       2      36 ..      27      61 ..      26      71 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 6.7e-08
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                      dv+ +GgG+A + aA ++a++g +V+l+ek+ +lg
  gi|298674164|ref|YP_003725914.1| 27 DVALVGGGPANMIAATRLAQEGYKVALFEKKLALG 61
                                      899***************************98887 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   4.4e-06    0.0072       1      32 [.      25      56 ..      25      59 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.4e-06
                                      EEEEEEE--SHHHHHHHHHHHHTTHHEEEEES CS
                     FAD_binding_3  1 etdVlIVGaGpaGlmlallLseaGvrvvlvek 32
                                      e+dV+ VG+Gpa +++a+ L++ G +v l ek
  gi|298674164|ref|YP_003725914.1| 25 EVDVALVGGGPANMIAATRLAQEGYKVALFEK 56
                                      689*************************9998 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.3   6.8e-06     0.011       1      32 [.      27      58 ..      27      65 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.8e-06
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES-G CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkl 32
                                      dv  +GgG A + AA  +a+ G+kv+L+ +kl
  gi|298674164|ref|YP_003725914.1| 27 DVALVGGGPANMIAATRLAQEGYKVALFEKKL 58
                                      7999************************8776 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   4.6e-05     0.076       1      31 [.      27      55 ..      27      64 .. 0.90
   2 ?    1.9   0.1     0.056        91     104     144 ..     135     175 ..     121     196 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.6e-05
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlie 31
                                      Dv+++G+GpA++  A rl  a+ g kv l e
  gi|298674164|ref|YP_003725914.1| 27 DVALVGGGPANMIAATRL--AQEGYKVALFE 55
                                      9*****************..88888888876 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.056
                     Lycopene_cycl 104 lleakvesveeeeageslvvleggr.kirarlvvdarglasl 144
                                       + + +v+ ++ +  + s + l+ +  +ira++v+d++g  ++
  gi|298674164|ref|YP_003725914.1| 135 REDDRVTGIVINWTAVSIANLHVDPlTIRAKVVIDGTG-HEA 175
                                       555666666666666666777766669***********.443 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   0.00014      0.23       1      36 [.      27      63 ..      27     108 .. 0.78
   2 ?    1.8   0.1     0.091   1.5e+02     147     204 ..     107     175 ..      97     207 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSG CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiagsga 36
                                      dv+ +GGG + + +A  La++g  V+l+ek+  +g g 
  gi|298674164|ref|YP_003725914.1| 27 DVALVGGGPANMIAATRLAQEGykVALFEKKLALG-GG 63
                                      8999***************************7777.33 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.091
                                       HHHHHHHHHHHHTT-EEEESECEEEE.EEEETCEEEEE.EECT.EEEE......EEEE..EEE--GGGH CS
                               DAO 147 kltaalaraaealGveilegtevtgl.eeedgkvwgve.rttp.gend......aada..vVnaaGaws 204
                                       + +  l ++  + Gv++++  + +++  +ed++v+g+  + t+  +        +++a  v+  +G+ +
  gi|298674164|ref|YP_003725914.1| 107 ESVSRLINKTVTSGVQVFNLVNFEDVmIREDDRVTGIViNWTAvSIANlhvdplTIRAkvVIDGTGHEA 175
                                       566778889999999999999999974556689999977333333321335556334444887777765 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3    0.0001      0.17       1      42 [.      29      65 ..      29      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0001
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsep.gagrvw 42
                                      a+vG+Gp+ + +++rL+++       ++ lf+++ + g g++w
  gi|298674164|ref|YP_003725914.1| 29 ALVGGGPANMIAATRLAQE-----GYKVALFEKKLAlG-GGMW 65
                                      79****************9.....59*******87747.9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 1614.41
//
Query:       gi|298674165|ref|YP_003725915.1|  [L=360]
Description: AAA ATPase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.7e-38  129.9   0.0    1.3e-37  129.2   0.0    1.4  1  AAA              ATPase family associated with various cellul
    4.3e-09   36.7   0.4    2.8e-08   34.1   0.0    2.1  2  AAA_2            AAA domain (Cdc48 subfamily)
    1.3e-07   31.0   0.0    1.8e-05   24.0   0.0    2.1  1  DUF815           Protein of unknown function (DUF815)
    3.3e-07   29.8   0.0    8.8e-07   28.4   0.0    1.7  1  TIP49            TIP49 P-loop domain
    1.1e-05   25.1   0.0    2.2e-05   24.1   0.0    1.6  1  AAA_lid_3        AAA+ lid domain
    3.9e-05   23.5   0.0    0.00025   20.8   0.0    2.1  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    8.6e-05   22.7   0.0    0.00018   21.7   0.0    1.6  1  AAA_33           AAA domain
    8.8e-05   22.8   0.5     0.0042   17.3   0.1    2.5  2  AAA_22           AAA domain
     0.0002   21.7   0.0     0.0016   18.7   0.0    2.2  2  AAA_28           AAA domain
    0.00029   21.3   0.1      0.019   15.3   0.0    2.4  2  AAA_16           AAA ATPase domain
    0.00037   20.5   0.1     0.0018   18.3   0.0    2.3  2  AAA_5            AAA domain (dynein-related subfamily)
    0.00085   18.9   0.1      0.016   14.8   0.0    2.3  2  AAA_7            P-loop containing dynein motor region
     0.0026   17.6   0.1      0.005   16.7   0.1    1.5  1  Bac_DnaA         Bacterial dnaA  protein
      0.003   17.0   0.1     0.0064   15.9   0.1    1.5  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0035   17.1   0.0     0.0049   16.6   0.0    1.3  1  IstB_IS21        IstB-like ATP binding protein
     0.0058   17.0   0.1      0.018   15.4   0.0    2.0  1  RNA_helicase     RNA helicase
     0.0062   16.3   0.3      0.014   15.1   0.2    1.7  1  AAA_24           AAA domain
     0.0063   16.5   0.0      0.012   15.6   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
     0.0086   15.5   0.0      0.038   13.4   0.0    2.0  2  TniB             Bacterial TniB protein
  ------ inclusion threshold ------
      0.015   15.8   0.0      0.042   14.4   0.0    1.9  1  AAA_18           AAA domain
      0.052   13.6   0.0       0.16   12.1   0.0    1.7  2  Torsin           Torsin
      0.058   12.8   0.0       0.12   11.8   0.0    1.4  1  IPT              Isopentenyl transferase
      0.058   13.7   0.0        9.3    6.7   0.0    2.5  2  HYR              HYR domain
      0.062   13.2   0.0       0.11   12.4   0.0    1.4  1  NACHT            NACHT domain
      0.072   12.8   0.0       0.15   11.8   0.0    1.6  1  Sigma54_activat  Sigma-54 interaction domain
       0.28   10.7   0.4       0.89    9.1   0.1    1.8  2  AAA_25           AAA domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.2   0.0   1.9e-40   1.3e-37       1     130 [.     144     271 ..     144     273 .. 0.97

  Alignments for each domain:
  == domain 1  score: 129.2 bits;  conditional E-value: 1.9e-40
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TT CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sg 76 
                                       +l+yGp GtGKT+lak +a++++v++++i+++el+ +yvge++k+i+++ ++a+++a p+i+fiDE+da+a +r  +
  gi|298674165|ref|YP_003725915.1| 144 ILFYGPSGTGKTMLAKGLANKTDVPIITIKATELIGEYVGEGAKQIHQVYDRAENMA-PCIIFIDELDAVALDRrYQ 219
                                       69******************************************************9.****************999 PP

                                       CCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEEET CS
                               AAA  77 seseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrkiei 130
                                       + +++  ++vn+Llte+dg  ++++ v+ igatnr d+ld+a+  +Rf+++ie+
  gi|298674165|ref|YP_003725915.1| 220 ELRGDVAEIVNALLTEMDGIIERKG-VCTIGATNRKDTLDSAVS-NRFEEEIEF 271
                                       999******************9877.******************.******997 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0     4e-11   2.8e-08       5     104 ..     143     237 ..     141     244 .. 0.89
   2 ?    0.0   0.1       1.2     8e+02      77     113 ..     299     333 ..     298     352 .. 0.79

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 4e-11
                                       -EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG CS
                             AAA_2   5 silllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidK 79 
                                       +il+ gp+g+Gkt+lak la+  +v    ++i++ a+el+     e + +  ++ ++ y +ae+    i+++DE+d 
  gi|298674165|ref|YP_003725915.1| 143 NILFYGPSGTGKTMLAKGLANKTDV----PIITIKATELIG----EYVGEGAKQIHQVYDRAENMApcIIFIDELDA 211
                                       89**********************8....************....9999999999**********9*********** PP

                                       ----...---------HHHHHHHHHHHH CS
                             AAA_2  80 ihpk...essgadvSregVqrdLLqile 104
                                       ++     ++ + dv   +++++LL  ++
  gi|298674165|ref|YP_003725915.1| 212 VALDrryQELRGDVA--EIVNALLTEMD 237
                                       *98776777777776..78888887666 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.2
                                       GGG-------------HHHHHHHHHH.HH--EE----- CS
                             AAA_2  77 idKihpkessgadvSregVqrdLLqi.leggtltdkqg 113
                                       i Ki++    ++  S+ ++++  L++ l ++ + dk++
  gi|298674165|ref|YP_003725915.1| 299 ISKIAK---LTQGFSGRDIVEKVLKVsLHQTIIDDKEE 333
                                       778888...99999999999999999556666665555 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   2.7e-08   1.8e-05      18     222 ..     101     301 ..      91     314 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.7e-08
                            DUF815  18 pveevdevklddLvgidkqkea......lventeqfleglpannvLLwGarGtGKSslvkallneyaeeg..Lrlie 86 
                                       + e +  +++dd++g d+ +++      ++en  +f + +  +n+L++G  GtGK  l k l n++      ++  e
  gi|298674165|ref|YP_003725915.1| 101 TSELNTDINFDDVIGQDNARKKcklvekFLENPDKFGKWA-PRNILFYGPSGTGKTMLAKGLANKTDVPIitIKATE 176
                                       5555677888999999887765111111456666665544.489*******************99988765567778 PP

                            DUF815  87 vekedlkelpklvellrerper...filfvDDLsFeeeeeeyksLksvLeGsleakpenvliyaTsNrRhLlpekls 160
                                       +  e + e  k ++++ +r+e+   +i+f+D L   + +++y++L+    G +++  + +l         ++++k  
  gi|298674165|ref|YP_003725915.1| 177 LIGEYVGEGAKQIHQVYDRAENmapCIIFIDELDAVALDRRYQELR----GDVAEIVNALLT----EMDGIIERKGV 245
                                       87888777777777776555432228*****************998....666554443332....23345555444 PP

                            DUF815 161 dneeleeeeihaseaveeklsLsdRFGlwlgFykldqeeYleiveklakklglelekeelee 222
                                            + ++ +++++++  +  s+RF   + F  +d++e l+i+e+ +k++ l++++ ++++
  gi|298674165|ref|YP_003725915.1| 246 C----TIGATNRKDTLDSAV--SNRFEEEIEFVLPDENERLKIIETNIKTFPLPIKNVNISK 301
                                       3....345777788887754..5888888888888888888888888888877777655554 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   1.3e-09   8.8e-07      22      89 ..     109     178 ..      91     196 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1.3e-09
                                       XXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  22 eeeglvGqkkareaagvivelike....kklaGravLlaGpsgtGktalaiaiskelgedvpfvalsgsevy 89 
                                       + + ++Gq +ar+ + ++ +++++    +k a r +L+ GpsgtGkt la +++++  +dvp ++++++e+ 
  gi|298674165|ref|YP_003725915.1| 109 NFDDVIGQDNARKKCKLVEKFLENpdkfGKWAPRNILFYGPSGTGKTMLAKGLANK--TDVPIITIKATELI 178
                                       44589****************9764333688999********************97..57*******99985 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   3.2e-08   2.2e-05       1      21 [.     296     316 ..     296     341 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 3.2e-08
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaa 21 
                                       +v+++++A++T+G+SG D+++
  gi|298674165|ref|YP_003725915.1| 296 NVNISKIAKLTQGFSGRDIVE 316
                                       7******************76 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   3.6e-07   0.00025       6     153 ..     110     265 ..     107     271 .. 0.61

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.6e-07
                            RuvB_N   6 leeyigqekvkeklki...fieaakk.reealdhvllyGpPGlGkttlakiiakelgvklkitsgPvl......eka 72 
                                       +++ igq++ ++k k+   f+e   k  + a   +l+yGp G Gkt lak +a++ +v + +  +  l      e a
  gi|298674165|ref|YP_003725915.1| 110 FDDVIGQDNARKKCKLvekFLENPDKfGKWAPRNILFYGPSGTGKTMLAKGLANKTDVPIITIKATELigeyvgEGA 186
                                       78999***99999887222455544414557889***********************98755443332131112344 PP

                            RuvB_N  73 gdlaalltnleekd..vlfideihrlsraveevlysamedfrldivigkGpsarsikldlpkftlvgattragllss 147
                                       +++  +  + e+    ++fide+  ++    +  y+ +     +i ++   +     ++ +    +gat r+ +l s
  gi|298674165|ref|YP_003725915.1| 187 KQIHQVYDRAENMApcIIFIDELDAVA---LDRRYQELRGDVAEI-VNALLTEMDGIIERKGVCTIGATNRKDTLDS 259
                                       455555554444324488888876433...333444444433333.3333444444566666667777777777777 PP

                            RuvB_N 148 Plrdrf 153
                                        + +rf
  gi|298674165|ref|YP_003725915.1| 260 AVSNRF 265
                                       777777 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   2.6e-07   0.00018       2      65 ..     144     235 ..     144     280 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.6e-07
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt..........................dytr 50 
                                       +l+ G++G+GK+ la++l++k++   +++   +l+  ++g++ +++                           +y++
  gi|298674165|ref|YP_003725915.1| 144 ILFYGPSGTGKTMLAKGLANKTDvpIITIKATELIGEYVGEGAKQIHqvydraenmapciifideldavaldrRYQE 220
                                       6899***************999999999***********99888887677777777777777777777766666666 PP

                            AAA_33  51 vldrlyqilnelark 65 
                                       ++ ++ +i+n+l+++
  gi|298674165|ref|YP_003725915.1| 221 LRGDVAEIVNALLTE 235
                                       666666666666554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   6.1e-06    0.0042       7      48 ..     143     175 ..     140     180 .. 0.83
   2 ?    2.9   0.0      0.18   1.2e+02      80     106 ..     190     226 ..     183     248 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 6.1e-06
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlp 48 
                                        ++ +G+sGtGKT+l++ l+++          ++++++++++
  gi|298674165|ref|YP_003725915.1| 143 NILFYGPSGTGKTMLAKGLANKT---------DVPIITIKAT 175
                                       6899*****************98.........6666666655 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.18
                            AAA_22  80 ealeqalraravielliiDEaqhlr...s........e 106
                                       +++++ +++ a   ++ iDE + +    +        +
  gi|298674165|ref|YP_003725915.1| 190 HQVYDRAENMAP-CIIFIDELDAVAldrRyqelrgdvA 226
                                       445555555555.9********9854431323333343 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0         1   7.2e+02      25      58 ..      40      73 ..      31      78 .. 0.73
   2 !   18.7   0.0   2.4e-06    0.0016       1      50 [.     143     194 ..     143     224 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1
                            AAA_28 25 pvvpEaareileeklakgedalpwvedllafaer 58
                                      +v++ +are +ee+la++++ l + +   +fa++
  gi|298674165|ref|YP_003725915.1| 40 EVFECYAREQWEEHLARKGEYLFDRRMYPDFAYK 73
                                      5677789999999999988877765555566655 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 2.4e-06
                            AAA_28   1 kivitGgestGKTtlleaLaar.gypvvpEaareileeklakgedalpwv.e 50 
                                       +i + G+++tGKT l++ La++ ++p+++  a+e++ e   +g +++++v +
  gi|298674165|ref|YP_003725915.1| 143 NILFYGPSGTGKTMLAKGLANKtDVPIITIKATELIGEYVGEGAKQIHQVyD 194
                                       5899****************87789988666666666666555555555533 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.8e-05     0.019      24      46 ..     141     163 ..     126     178 .. 0.84
   2 ?    3.5   0.0      0.12        81     124     146 ..     190     213 ..     173     248 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.8e-05
                            AAA_16  24 pelvllsGesGvGKsslvrellr 46 
                                       p+++l++G+sG+GK+ l++ l++
  gi|298674165|ref|YP_003725915.1| 141 PRNILFYGPSGTGKTMLAKGLAN 163
                                       699**************988775 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.12
                            AAA_16 124 krllallsrderplvlvlDdlq..w 146
                                        +  +++++   p ++++D+l+   
  gi|298674165|ref|YP_003725915.1| 190 HQVYDRAEN-MAPCIIFIDELDavA 213
                                       455577888.667*********652 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       4.1   2.8e+03      24      45 ..      96     117 ..      63     128 .. 0.74
   2 !   18.3   0.0   2.6e-06    0.0018       1      76 [.     143     211 ..     143     265 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.1
                                       S--EEEEE--TT--HHHHH--B CS
                             AAA_5  24 nreveyvqltrdtteedlkgrr 45 
                                       n++ve+  l+ d++ +d++g+ 
  gi|298674165|ref|YP_003725915.1|  96 NNNVETSELNTDINFDDVIGQD 117
                                       6677777777777777777765 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 2.6e-06
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEver 76 
                                       ++l  Gp+GtgK++la+ la  +  ++ ++  t      +l+g++   +++++   +++ ra +  ++i+++DE++ 
  gi|298674165|ref|YP_003725915.1| 143 NILFYGPSGTGKTMLAKGLANKTDVPIITIKAT------ELIGEYV--GEGAKQIHQVYDRAENmAPCIIFIDELDA 211
                                       57999******************9999988665......5888888..45555555555555447889999999885 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   2.3e-05     0.016      34      58 ..     142     166 ..     140     179 .. 0.86
   2 ?    1.4   0.0      0.29     2e+02     100     115 ..     200     215 ..     183     220 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.3e-05
                             AAA_7  34 kpvllvGptGtGKtviikdllkkld 58 
                                       +++l++Gp+GtGKt+++k l +k d
  gi|298674165|ref|YP_003725915.1| 142 RNILFYGPSGTGKTMLAKGLANKTD 166
                                       689****************999887 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.29
                             AAA_7 100 kklvvFvDDlnmpake 115
                                         +++F+D+l+  a +
  gi|298674165|ref|YP_003725915.1| 200 APCIIFIDELDAVALD 215
                                       569*******998887 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   7.3e-06     0.005       1     211 [.     104     320 ..     104     328 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 7.3e-06
                                       --SS-SGGG----TTT.HHHHHHHHHHHHSTTT...S--..EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEH CS
                          Bac_DnaA   1 LnkrytFetFviGasn.rlAlaaalkvaeapgk..kynP..lfiygevGlGktHLlkaignevlenapelrvvYlta 72 
                                       Ln++  F+  viG+ n r   + + k  e+p+k  k+ P  +++yg++G Gkt L k ++n++     +  ++ ++a
  gi|298674165|ref|YP_003725915.1| 104 LNTDINFDD-VIGQDNaRKKCKLVEKFLENPDKfgKWAPrnILFYGPSGTGKTMLAKGLANKT-----DVPIITIKA 174
                                       567777887.4555552566778889999999888888866899***********99998875.....566666777 PP

                                       HHHHHHHHHHHHTT-HHHH.HHHHTT-SEEEEE-GGGGTT-HHHHH...HHHHHHHHHHTTT-EEE....EEESS-T CS
                          Bac_DnaA  73 eeFlnelvkalrdkkaeef.keklrkvDvLliDDiqflagkektqe...elfhtfnalleegkqvv....lssDrsP 141
                                        e + e v    ++  + + + +  +  ++ iD++  +a   + qe   ++  ++nall e   ++    +++  + 
  gi|298674165|ref|YP_003725915.1| 175 TELIGEYVGEGAKQIHQVYdRAENMAPCIIFIDELDAVALDRRYQElrgDVAEIVNALLTEMDGIIerkgVCTIGAT 251
                                       77777777554433333331333445567889998888877777764336899999999998888756656777788 PP

                                       TT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHHHHHHTT----TTHHHHHHHH--S.-HHHHHHHHHH CS
                          Bac_DnaA 142 keleeledrlrsrfeaGlvvdieppdletrlailkkkieaeklevpeevlefiaervtd.nvRelegalnr 211
                                       ++ ++l++ + +rfe    ++   pd++ rl+i++ +i++  l +++  ++ ia+  +  + R++   + +
  gi|298674165|ref|YP_003725915.1| 252 NRKDTLDSAVSNRFEEE--IEFVLPDENERLKIIETNIKTFPLPIKNVNISKIAKLTQGfSGRDIVEKVLK 320
                                       88899999999999986..5666799999*******99988888888777777775543255665555555 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   9.2e-06    0.0064      23      43 ..     142     162 ..     109     168 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.2e-06
                      Mg_chelatase  23 HnlllvGppGsGKtmlakrlp 43 
                                        n+l++Gp+G+GKtmlak l+
  gi|298674165|ref|YP_003725915.1| 142 RNILFYGPSGTGKTMLAKGLA 162
                                       59***************9875 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   7.1e-06    0.0049      48      89 ..     142     180 ..      96     240 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 7.1e-06
                         IstB_IS21  48 enivllGpsGvGKshlaialgveavraglsvlfvrvedLvee 89 
                                        ni++ GpsG+GK+ la  l+ +   +++ ++ +++++L+ e
  gi|298674165|ref|YP_003725915.1| 142 RNILFYGPSGTGKTMLAKGLANK---TDVPIITIKATELIGE 180
                                       69*****************9876...4566666666666555 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.6e-05     0.018       1      26 [.     144     169 ..     144     231 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.6e-05
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                       i++yGpsg+GK++lak La++    +
  gi|298674165|ref|YP_003725915.1| 144 ILFYGPSGTGKTMLAKGLANKTDVPI 169
                                       789***************99877555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.2   2.1e-05     0.014       3      23 ..     142     162 ..     140     213 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.1e-05
                            AAA_24   3 lkiliyGpsgiGKTtlakelg 23 
                                       ++il yGpsg+GKT+lak l 
  gi|298674165|ref|YP_003725915.1| 142 RNILFYGPSGTGKTMLAKGLA 162
                                       689***************983 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.7e-05     0.012      15      59 ..     137     181 ..     117     207 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.7e-05
                                       HHCHTEEEEEEESTTSSHHHHHHHHHHHTT------TTTTSEEEE CS
                              TsaE  15 akalgdvilLeGdLGaGKTtlvrglakalgveevkSPTFtlveeY 59 
                                       +k + + il++G+ G+GKT+l++gla++ +v  ++     l+ eY
  gi|298674165|ref|YP_003725915.1| 137 GKWAPRNILFYGPSGTGKTMLAKGLANKTDVPIITIKATELIGEY 181
                                       3323446********************999875555555566666 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   5.6e-05     0.038       5      57 ..     108     163 ..     105     177 .. 0.83
   2 ?   -0.8   0.0       1.2   8.5e+02     109     132 ..     190     213 ..     182     268 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.6e-05
                              TniB   5 iradrwigyprakeilerLeeLleypk...rkrmpnlllvGdsnnGKtmivekFar 57 
                                       i+ d+ ig ++a++  +  e+ le+p+   +  ++n+l++G+s +GKtm+++  a+
  gi|298674165|ref|YP_003725915.1| 108 INFDDVIGQDNARKKCKLVEKFLENPDkfgKWAPRNILFYGPSGTGKTMLAKGLAN 163
                                       56678899999999999999999999844445679***************997765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.2
                              TniB 109 qqvlrllrelkvrvLiiDEihnll 132
                                       +qv+   +++ + ++ iDE++ + 
  gi|298674165|ref|YP_003725915.1| 190 HQVYDRAENMAPCIIFIDELDAVA 213
                                       567777788888899999988765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0     6e-05     0.042       1      28 [.     144     182 ..     144     270 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf...........gvnl 28 
                                       Il  G++G+GKt lak L++++ +           g+ +
  gi|298674165|ref|YP_003725915.1| 144 ILFYGPSGTGKTMLAKGLANKTDVpiitikateliGEYV 182
                                       8999****************9865666666655553333 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00023      0.16      12      76 ..      97     164 ..      88     167 .. 0.82
   2 ?   -2.4   0.0       7.1   4.9e+03      41      60 ..     306     325 ..     296     334 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00023
                                       .---HHHHHHHHH.HH--S-HHHHHHHHHHHHHHHT-S.S-SS..-EEEEEEE-TTSSHHHHHHHHHHH CS
                            Torsin  12 isanleeLekdle.kklfGqhlvkklvvksvkaylene.kpkk..pLvlsfhGwtGtGknfvaeiiaen 76 
                                        +++++eL++d++ + ++Gq  ++k   k v+ +len+ k  k  p  + f+G +GtGk  +a+ +a++
  gi|298674165|ref|YP_003725915.1|  97 NNVETSELNTDINfDDVIGQDNARKK-CKLVEKFLENPdKFGKwaPRNILFYGPSGTGKTMLAKGLANK 164
                                       36788999999985689****99987.5899******95555544899****************99987 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 7.1
                                       HHHHHT-SS-SS-EEEEEEE CS
                            Torsin  41 vkaylenekpkkpLvlsfhG 60 
                                        +++  ++ ++k L +s+h 
  gi|298674165|ref|YP_003725915.1| 306 TQGFSGRDIVEKVLKVSLHQ 325
                                       45666666677777777774 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00017      0.12       5      32 ..     145     172 ..     142     179 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00017
                               IPT   5 lifGatttGKtaeaiklaketgapvivl 32 
                                       l +G+ +tGKt  a  la++t +p+i++
  gi|298674165|ref|YP_003725915.1| 145 LFYGPSGTGKTMLAKGLANKTDVPIITI 172
                                       78***********************986 PP

>> HYR  HYR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.013       9.3      16      54 ..      97     136 ..      86     138 .. 0.89
   2 ?    4.4   0.0     0.068        47      47      76 ..     175     203 ..     161     207 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.013
                               HYR  16 rtvelgkstvevffteptakdnsg.qaalvsrtaqpGdsF 54 
                                         ve  ++++ + f+++  +dn+  + +lv++++++ d+F
  gi|298674165|ref|YP_003725915.1|  97 NNVETSELNTDINFDDVIGQDNARkKCKLVEKFLENPDKF 136
                                       579999999**************9999********99999 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.068
                               HYR  47 taqpGdsFpvGsttVtyvaeDesgneasCk 76 
                                       t   G+   +G +++  +++D+++n a+C 
  gi|298674165|ref|YP_003725915.1| 175 TELIGEYVGEGAKQIH-QVYDRAENMAPCI 203
                                       5555777778888886.789*********6 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00016      0.11       2      23 ..     143     164 ..     142     168 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00016
                                       CEEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   2 lvilqGeaGsGKTtLlqklala 23 
                                        ++  G++G GKT+L+++la +
  gi|298674165|ref|YP_003725915.1| 143 NILFYGPSGTGKTMLAKGLANK 164
                                       57899*************9976 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00022      0.15      22      46 ..     141     165 ..     116     220 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00022
                                       SS-EEEECSTTSSHHHHHHHHHHHS CS
                   Sigma54_activat  22 dlsvlitGesGtGKellaraiheas 46 
                                       + ++l  G sGtGK++la+ + +++
  gi|298674165|ref|YP_003725915.1| 141 PRNILFYGPSGTGKTMLAKGLANKT 165
                                       4799**************9887654 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1    0.0013      0.89      36      54 ..     144     162 ..     137     165 .. 0.87
   2 ?   -1.3   0.0         2   1.4e+03     130     170 ..     189     230 ..     181     250 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0013
                            AAA_25  36 allaGapgtGKttlaldla 54 
                                       +l++G++gtGKt+la  la
  gi|298674165|ref|YP_003725915.1| 144 ILFYGPSGTGKTMLAKGLA 162
                                       689***********98877 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2
                            AAA_25 130 vdaleaaieevegvrlvviDplsralgg..densnsdvgalve 170
                                       ++++ +++e ++ +  + iD l+++       +   dv+++v+
  gi|298674165|ref|YP_003725915.1| 189 IHQVYDRAENMA-PCIIFIDELDAVALDrrYQELRGDVAEIVN 230
                                       555556666644.777777777774333243333334333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.49
# Mc/sec: 2192.35
//
Query:       gi|298674166|ref|YP_003725916.1|  [L=90]
Description: hypothetical protein Metev_0190 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.01   15.9   0.0      0.014   15.5   0.0    1.3  1  SH3_12    Xrn1 SH3-like domain
      0.037   14.4   0.0      0.046   14.1   0.0    1.1  1  LTD       Lamin Tail Domain


Domain annotation for each model (and alignments):
>> SH3_12  Xrn1 SH3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   1.5e-06     0.014       8      30 ..      12      50 ..       8      81 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.5e-06
                            SH3_12  8 rVvyvrdngksVPlGlrGtVVg....................r 30
                                      rVv+v d  +  PlG +G+VV                     +
  gi|298674166|ref|YP_003725916.1| 12 RVVNVVD--N--PLGFKGIVVEdidtegriyfgrtkpkdctlQ 50
                                      9******..9..*********9777766666666555555550 PP

>> LTD  Lamin Tail Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   5.1e-06     0.046      28     107 ..      13      87 ..      11      89 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.1e-06
                               LTD  28 lyNtsskavdLsgwkledasge..ytfpngt...gtlaageyvvvwsgsgttsasngskasssavwnn..ggdavaL 97 
                                       ++N  +++   +g  +ed  +e  + f   +    tl+ g+++ v+ +             ++ v+ +  + ++v+L
  gi|298674166|ref|YP_003725916.1|  13 VVNVVDNPLGFKGIVVEDIDTEgrIYFGRTKpkdCTLQQGDTAYVYVNP------------VNMVFEDdeRTMEVTL 77 
                                       56777888888999999999888844544446667*************6............455555555889**** PP

                               LTD  98 ydasgevvds 107
                                       yd +++  d+
  gi|298674166|ref|YP_003725916.1|  78 YDENNNKLDW 87 
                                       *****99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 614.95
//
Query:       gi|298674167|ref|YP_003725917.1|  [L=304]
Description: ribonuclease Z [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.7e-20   72.3   0.0    5.1e-09   35.9   0.0    2.1  2  Lactamase_B_2  Beta-lactamase superfamily domain
    2.6e-09   37.4   0.0    1.1e-08   35.3   0.0    2.1  1  Lactamase_B    Metallo-beta-lactamase superfamily
    1.8e-05   24.3   0.0    3.2e-05   23.5   0.0    1.3  1  Lactamase_B_4  tRNase Z endonuclease


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.0   2.3e-12   1.4e-08       4     128 ..      33     145 ..      31     164 .. 0.81
   2 !   35.9   0.0   8.6e-13   5.1e-09     132     201 .]     198     267 ..     176     267 .. 0.91

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 2.3e-12
                                       EES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC...C--EE..EEEEEEHHHHH...HCCT CS
                     Lactamase_B_2   4 LiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlre...lrpkk..lplyapkgvla...vlea 72 
                                        +D+g +  qq++ra+        + ++  +++th H+DH+ g++ l +   ++++   l +y+p+++     +l+a
  gi|298674167|ref|YP_003725917.1|  33 MFDCGEGAQQQMMRAR------TGMMSLSSIFITHFHADHVLGIPGLLQtmsFQGRTepLYIYGPEKIDVfiqILTA 103
                                       79*****888888875......6789***********************9886665556888999765433315555 PP

                                       TCGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEE CS
                     Lactamase_B_2  73 nfvylaleeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGl 128
                                          y++l+ e  ++++el++g+ +e +  g +i+a   +h+ +          +G+
  gi|298674167|ref|YP_003725917.1| 104 L-GYCQLGYE--IKTVELKPGDIIEKN--GYHIKALKTEHGVKS---------IGY 145
                                       5.79999999..9*********99998..789***999999887.........444 PP

  == domain 2  score: 35.9 bits;  conditional E-value: 8.6e-13
                                       CTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHH.HHT---STSHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 132 gggkrvyyigDtgyipeeigerlggadllllditayeddemir.hmgHltpeeaveaaadlgakrlvliHi 201
                                       ++g++v+y+gDt  +++   + l+ ad+l++d+ + ++++  + +  H+t +ea+e+a+++g+ +lvl+Hi
  gi|298674167|ref|YP_003725917.1| 198 RPGRTVVYSGDTRPCEDVFNASLE-ADVLIHDGSLDDSQSEWAaESMHSTASEAAELAKKAGVIKLVLTHI 267
                                       689*************99998888.********98888765558**************************8 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.0   1.9e-12   1.1e-08       7      83 ..      21      92 ..      16     211 .. 0.89

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 1.9e-12
                                      EEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCH CS
                       Lactamase_B  7 nsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalf 83
                                       s+li  d +++++D+G ++++++++     ++ +   ++ +++TH+H+DH+ g +gl ++  +  + ++++ + ++
  gi|298674167|ref|YP_003725917.1| 21 PSILIKKDSELLMFDCGEGAQQQMMR-----ARTGMMSLSSIFITHFHADHVLGIPGLLQTMSFQGRTEPLYIYGPE 92
                                      689**********************8.....8***************************998888888887777665 PP

>> Lactamase_B_4  tRNase Z endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   5.3e-09   3.2e-05      11      56 ..      19      63 ..      12      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 5.3e-09
                     Lactamase_B_4 11 sgPlllLqldskrYlfGkvgEgtQRavneqkvrlsklesiFLtgkv 56
                                      + P++l++ ds+  +f ++gEg Q+ ++  ++ +  l+siF+t+ +
  gi|298674167|ref|YP_003725917.1| 19 NPPSILIKKDSELLMF-DCGEGAQQQMMRARTGMMSLSSIFITHFH 63
                                      569*************.**************************977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1860.02
//
Query:       gi|298674168|ref|YP_003725918.1|  [L=103]
Description: hypothetical protein Metev_0192 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 626.78
//
Query:       gi|298674169|ref|YP_003725919.1|  [L=125]
Description: 30S ribosomal protein S8e [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-35  122.3   4.9    1.8e-35  122.1   4.9    1.0  1  Ribosomal_S8e  Ribosomal protein S8e


Domain annotation for each model (and alignments):
>> Ribosomal_S8e  Ribosomal protein S8e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.1   4.9     1e-39   1.8e-35       4     137 .]       2     124 ..       1     124 [. 0.99

  Alignments for each domain:
  == domain 1  score: 122.1 bits;  conditional E-value: 1e-39
                                       BXXCCCSEESSTEEXXXSSXXXCCSBXXXXXXXEESSHEEEEEEETTCEEEEEEESESEEEEEETTTTEEEEEEEEE CS
                     Ribosomal_S8e   4 srdskhkrkltGgkakllrkkrkielgrkekatklgaervkvvrvrgGkrkkralrlkkanvthpeekvtkklkIlg 80 
                                       ++++++kr+ +G+k  ++r krk+e gr++++t +++++ k++  rg +rk+r+lr+++anvt+p  ++t+k +I +
  gi|298674169|ref|YP_003725919.1|   2 KWQGRSKRTPSGAKITPVRGKRKHEIGRESTETYVSETKRKNIASRGCNRKYRLLRCNEANVTNPADGTTQKSTIEN 78 
                                       689************************************************************************** PP

                                       EECSSSTCHHHHTTC--TTEEEEEESHHHHHHHHTTEEEEEEESEHHHHSSEEEEEE CS
                     Ribosomal_S8e  81 VkknpsnneyvrlgvltKgaiievdvseLgevtqsgkvvAqvtsrPgqdGcvnavlL 137
                                       V++np+n +y+r++++tKg++i++ +++           A+vtsrPgqdG+vnavl+
  gi|298674169|ref|YP_003725919.1|  79 VVENPANVHYMRRNIITKGSVIKTGLGN-----------AKVTSRPGQDGVVNAVLI 124
                                       ****************************...........****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 792.71
//
Query:       gi|298674170|ref|YP_003725920.1|  [L=163]
Description: AsnC family transcriptional regulator [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.4e-15   54.3   0.8    1.3e-14   53.9   0.2    1.6  2  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    7.5e-12   44.6   0.1    2.1e-11   43.2   0.1    1.8  2  HTH_24          Winged helix-turn-helix DNA-binding
      4e-06   26.6   0.0    1.3e-05   25.0   0.0    1.9  2  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    2.6e-05   24.0   0.5    4.7e-05   23.2   0.5    1.4  1  TFIIE_alpha     TFIIE alpha subunit
    0.00014   21.8   0.0    0.00033   20.6   0.0    1.6  1  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0002   21.2   0.1    0.00069   19.5   0.0    1.8  2  MarR            MarR family
    0.00043   20.1   0.0     0.0013   18.6   0.0    1.8  2  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0013   18.5   0.0     0.0033   17.2   0.0    1.6  2  HTH_IclR        IclR helix-turn-helix domain
     0.0028   17.5   0.0     0.0053   16.6   0.0    1.4  1  MarR_2          MarR family
     0.0052   16.5   0.1      0.021   14.5   0.1    1.8  2  DUF4423         Domain of unknown function (DUF4423)
     0.0062   16.4   0.0     0.0071   16.3   0.0    1.2  1  Utp13           Utp13 specific WD40 associated domain
     0.0066   16.6   0.0       0.18   12.1   0.0    2.3  2  Rio2_N          Rio2, N-terminal
  ------ inclusion threshold ------
      0.059   12.9   0.0        0.1   12.2   0.0    1.4  1  PnpCD_PnpD_N    Hydroquinone 1,2-dioxygenase large subunit N-
      0.071   13.5   0.0       0.38   11.1   0.0    2.1  2  Rrf2            Transcriptional regulator
       0.08   13.1   0.0       0.15   12.2   0.0    1.4  1  DprA_WH         DprA winged helix domain
      0.084   12.4   0.0       0.15   11.6   0.0    1.4  1  HTH_47          winged helix-turn-helix
      0.087   12.9   0.0       0.15   12.2   0.0    1.5  1  DUF2250         Uncharacterized protein conserved in archaea 
       0.19   11.8   0.0       0.38   10.8   0.0    1.4  1  HTH_20          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       8.4   8.4e+03      51      71 ..      35      54 ..      32      54 .. 0.65
   2 !   53.9   0.2   1.3e-17   1.3e-14       3      75 .]      72     142 ..      68     142 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 8.4
                                      HHHHHHTTTTSTTEEEEEEEE CS
                    AsnC_trans_reg 51 erflreklaslpgvartetsi 71
                                      ++++++ l + + +++++t i
  gi|298674170|ref|YP_003725920.1| 35 NDIISK-LEKDKIIRKYKTII 54
                                      556666.77777777777765 PP

  == domain 2  score: 53.9 bits;  conditional E-value: 1.3e-17
                                       EEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEEE CS
                    AsnC_trans_reg   3 vslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivlet 75 
                                       v le+++   +++++e+l ++peV+++  ++Gd+d+ + v+ r++++   f+ ek+a+l+ + +t+t++vl+t
  gi|298674170|ref|YP_003725920.1|  72 VVLERKQ--GYQAIAERLYKFPEVRSVRLISGDHDISITVRGRSMKEVAFFVAEKIATLEQIHSTSTHFVLKT 142
                                       5566666..9*************************************************************96 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.1   2.1e-14   2.1e-11       1      48 []       1      48 [.       1      48 [. 0.98
   2 ?   -3.2   0.0       6.6   6.5e+03      21      27 ..      81      87 ..      80      88 .. 0.80

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 2.1e-14
                            HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +d+ ++ ILe+L++n+r +  ++A ++gl+++ vn  + +Le++ +I+
  gi|298674170|ref|YP_003725920.1|  1 MDKHTWHILEILEENARATPEDIASQTGLPVTEVNDIISKLEKDKIIR 48
                                      7999******************************************97 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6.6
                            HTH_24 21 reLAerl 27
                                      + +Aerl
  gi|298674170|ref|YP_003725920.1| 81 QAIAERL 87
                                      7899998 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   1.3e-08   1.3e-05       6      42 .]       6      42 ..       1      42 [. 0.87
   2 ?   -2.1   0.0       3.6   3.6e+03      20      27 ..      80      87 ..      78      87 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.3e-08
                     HTH_AsnC-type  6 rkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                        ILe+L+e+aR++ +++A ++Gl  ++v   + +Le
  gi|298674170|ref|YP_003725920.1|  6 WHILEILEENARATPEDIASQTGLPVTEVNDIISKLE 42
                                      68**************************987776665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.6
                     HTH_AsnC-type 20 yaeLAerv 27
                                      y+++Aer+
  gi|298674170|ref|YP_003725920.1| 80 YQAIAERL 87
                                      78999986 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.5   4.7e-08   4.7e-05      15      83 ..       5      74 ..       1      93 [. 0.84

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 4.7e-08
                                      HHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSE.EEEEEEETTTEEEEEEEEEECCCHCC CS
                       TFIIE_alpha 15 avlvldvLlekgevteedlakelkidlnelrklLnrLyearlv.kykrrrdeekswykyywrinyeklvd 83
                                         +l++L e++  t ed+a ++++  +e+  ++ +L +++++ kyk   d e+  + y + i   k+v 
  gi|298674170|ref|YP_003725920.1|  5 TWHILEILEENARATPEDIASQTGLPVTEVNDIISKLEKDKIIrKYKTIIDWEQAGEDYVYAIIELKVVL 74
                                      5689**************************************97799999*9999999999987777654 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   3.3e-07   0.00033      21      62 ..      17      56 ..       6      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.3e-07
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEEES-H CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisrgrririldl 62
                                      + t e++As  Gl    v+ i+s+L+++++i++ +  +i d+
  gi|298674170|ref|YP_003725920.1| 17 RATPEDIASQTGLPVTEVNDIISKLEKDKIIRKYK--TIIDW 56
                                      6789****************************765..55555 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0     7e-07   0.00069       6      51 ..       6      51 ..       3      52 .. 0.96
   2 ?   -1.7   0.0       2.8   2.8e+03      22      47 ..     124     149 ..     121     149 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 7e-07
                                      HHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR  6 fviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                      ++iL+il+e+  ++  ++a++ g+  + v  ++ +Lek+  i+++k
  gi|298674170|ref|YP_003725920.1|  6 WHILEILEENARATPEDIASQTGLPVTEVNDIISKLEKDKIIRKYK 51
                                      9*****************************************9987 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.8
                                       HHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              MarR  22 eLakklgvskstvtrvldrLekkGli 47 
                                       ++a   +++++++  vl++  ++G+i
  gi|298674170|ref|YP_003725920.1| 124 KIATLEQIHSTSTHFVLKTYKEDGFI 149
                                       67777777777776666666666665 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.3e-06    0.0013      18      56 ..      12      51 ..       7      71 .. 0.78
   2 ?   -2.0   0.0       3.3   3.3e+03      29      58 ..     126     155 ..     121     160 .. 0.64

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.3e-06
                                      H.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB 18 l.klgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                      l ++ +at ++ia+++g+p + v++++++Le+  ++++ k
  gi|298674170|ref|YP_003725920.1| 12 LeENARATPEDIASQTGLPVTEVNDIISKLEKDKIIRKYK 51
                                      448999*************************988887765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.3
                                       CCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB  29 aeelgvprskvYevLrsLedkGlVerekgr 58 
                                       a    +  ++   vL+  ++ G++  e+++
  gi|298674170|ref|YP_003725920.1| 126 ATLEQIHSTSTHFVLKTYKEDGFIFDEPEK 155
                                       555555556666677777788888877766 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.3e-06    0.0033       7      49 ..       7      48 ..       4      50 .. 0.92
   2 ?   -2.6   0.0         5     5e+03      30      47 ..     131     148 ..     125     149 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.3e-06
                                      HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      +iL++l+e +++ t  ++A +tglp + v  +++ L++ ++++
  gi|298674170|ref|YP_003725920.1|  7 HILEILEENARA-TPEDIASQTGLPVTEVNDIISKLEKDKIIR 48
                                      69*********8.*****************9999999988877 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5
                                       S-HHHHHHHHHHHHHTTS CS
                          HTH_IclR  30 lpkStvhRlLqtLvelGy 47 
                                       ++ +++h  L+t  e G+
  gi|298674170|ref|YP_003725920.1| 131 IHSTSTHFVLKTYKEDGF 148
                                       567788888887666665 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   5.3e-06    0.0053       7      53 ..       5      49 ..       1      52 [. 0.92

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.3e-06
                                      HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                       +++L  L  + +   t+ ++a  +gl+   v+ i+ +L++   +++
  gi|298674170|ref|YP_003725920.1|  5 TWHILEILEENAR--ATPEDIASQTGLPVTEVNDIISKLEKDKIIRK 49
                                      5899999999998..9**************************99986 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   2.1e-05     0.021      26      73 ..       8      52 ..       3      66 .. 0.80
   2 ?   -0.2   0.0      0.74   7.3e+02      21      47 ..      62      88 ..      56      97 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.1e-05
                           DUF4423 26 irellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkded 73
                                      i+e+l+ + ++a+pe +a +++  +++ ev+++++ L+k ++++k + 
  gi|298674170|ref|YP_003725920.1|  8 ILEILEEN-ARATPEDIASQTG--LPVTEVNDIISKLEKDKIIRKYKT 52
                                      44544444.459**********..*******************99876 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.74
                           DUF4423 21 Wyypvirellplkdfkadpeelakrlr 47
                                       y  +i el  + + k+ ++++a+rl 
  gi|298674170|ref|YP_003725920.1| 62 DYVYAIIELKVVLERKQGYQAIAERLY 88
                                      678899999555555599999999997 PP

>> Utp13  Utp13 specific WD40 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   7.1e-06    0.0071      28      97 ..       7      78 ..       3     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.1e-06
                                      HHHHHHHHHHS-SS--STSSSSS..HHHHHHHHC--HHHHHHHHHHHHHHHTSTTTHHHHHHHHHHHHHHS- CS
                             Utp13 28 rllkllkevleseeeeeesitgs..kevdevlkslskeqleklLkyirdWntnartsevAqrvLnailksls 97
                                      ++l++l+e +++++e+  s+tg+  +ev++++++l+k+++ +  k i dW         A   L+++l++ +
  gi|298674170|ref|YP_003725920.1|  7 HILEILEENARATPEDIASQTGLpvTEVNDIISKLEKDKIIRKYKTIIDWEQAGEDYVYAIIELKVVLERKQ 78
                                      68999***999999999999999667***************************9999999999999998654 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00018      0.18       5      57 ..       2      51 ..       1      56 [. 0.82
   2 ?    2.1   0.0      0.23   2.3e+02      19      56 ..     114     151 ..     108     157 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00018
                            Rio2_N  5 skedfrvLtavEmgmrnhevVptelieeisrlkeeevkkrlsrllkaklisr.k 57
                                      +k+ +++L+ +E   r       e i++ ++l  +ev++ +s+l k k+i++ k
  gi|298674170|ref|YP_003725920.1|  2 DKHTWHILEILEENARA----TPEDIASQTGLPVTEVNDIISKLEKDKIIRKyK 51
                                      67788888888877775....35779999*********************9944 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.23
                            Rio2_N  19 mrnhevVptelieeisrlkeeevkkrlsrllkaklisr 56 
                                       m++  +   e+i+++ ++++++++ +l++  + ++i  
  gi|298674170|ref|YP_003725920.1| 114 MKEVAFFVAEKIATLEQIHSTSTHFVLKTYKEDGFIFD 151
                                       78888888899999999999*******99999999876 PP

>> PnpCD_PnpD_N  Hydroquinone 1,2-dioxygenase large subunit N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0    0.0001       0.1      95     143 ..      35      82 ..      23      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0001
                      PnpCD_PnpD_N  95 vdyieqfetpkimatfkailrdwtnagfdpfaapeetgsafgrkhgdni 143
                                        d i ++e  ki+  +k+i+ dw +ag d + a  e    + rk+g + 
  gi|298674170|ref|YP_003725920.1|  35 NDIISKLEKDKIIRKYKTII-DWEQAGEDYVYAIIELKVVLERKQGYQA 82 
                                       48999*************97.9*********************999654 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00039      0.38      17      56 ..       9      48 ..       4      51 .. 0.83
   2 ?   -1.2   0.0       2.6   2.6e+03      29      51 ..     123     145 ..     113     149 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00039
                                      HHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 17 LakeeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      L+  ee+  ++ e+ia++++++ + +  i++kL+k ++++
  gi|298674170|ref|YP_003725920.1|  9 LEILEENARATPEDIASQTGLPVTEVNDIISKLEKDKIIR 48
                                      444555556899*************************997 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.6
                                       HHHHHHHTS-HHHHHHHHHHHHH CS
                              Rrf2  29 eeiaerqnispsylekilakLrk 51 
                                       e+ia+  +i+ +    +l++ ++
  gi|298674170|ref|YP_003725920.1| 123 EKIATLEQIHSTSTHFVLKTYKE 145
                                       56666666665555555555555 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00015      0.15      17      50 ..       8      42 ..       5      48 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                           DprA_WH 17 vLaaLgp.ePvhvDqLvrrtglpaaevsaaLleLE 50
                                      +L+ L+  +  + ++++ +tglp+ ev+ + + LE
  gi|298674170|ref|YP_003725920.1|  8 ILEILEEnARATPEDIASQTGLPVTEVNDIISKLE 42
                                      77778662455899*******************99 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00015      0.15      51      77 ..      22      48 ..      21      49 .. 0.96

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                                      HHHHHHT--HHHHHHHHHHHHHTT-EE CS
                            HTH_47 51 diAeriglpfdrvaaiaraLaeaglla 77
                                      diA+++glp+ +v +i+ +L++ ++++
  gi|298674170|ref|YP_003725920.1| 22 DIASQTGLPVTEVNDIISKLEKDKIIR 48
                                      8************************97 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00015      0.15       8      56 ..       3      51 ..       1      61 [. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                           DUF2250  8 elalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerve 56
                                      +   ++l++l++     +  ia ++ +p++ev++++ kLe+  ++ +++
  gi|298674170|ref|YP_003725920.1|  3 KHTWHILEILEENARATPEDIASQTGLPVTEVNDIISKLEKDKIIRKYK 51
                                      5677899999999999999*********************998888876 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00038      0.38      15      56 ..       8      49 ..       3      52 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00038
                                      HHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20 15 ilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      il  L +++ +t++++a + +l+ +++++ + +Le+  +++ 
  gi|298674170|ref|YP_003725920.1|  8 ILEILEENARATPEDIASQTGLPVTEVNDIISKLEKDKIIRK 49
                                      999999*****************************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1066.85
//
Query:       gi|298674171|ref|YP_003725921.1|  [L=391]
Description: class I/II aminotransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      6e-68  229.7   0.0    6.8e-68  229.5   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    2.7e-13   50.0   0.2    4.1e-13   49.4   0.2    1.1  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    1.9e-08   33.7   0.1    2.9e-08   33.1   0.1    1.2  1  Aminotran_5      Aminotransferase class-V
    1.4e-06   27.1   0.4    2.3e-06   26.4   0.4    1.3  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    1.4e-05   24.5   0.0    2.3e-05   23.9   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
     0.0034   16.2   0.1     0.0059   15.4   0.1    1.3  1  OKR_DC_1         Orn/Lys/Arg decarboxylase, major domain
  ------ inclusion threshold ------
       0.18   11.3   0.0        0.3   10.5   0.0    1.3  1  DUF3396          Protein of unknown function (DUF3396)


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  229.5   0.0   2.6e-71   6.8e-68       2     363 .]      35     384 ..      34     384 .. 0.96

  Alignments for each domain:
  == domain 1  score: 229.5 bits;  conditional E-value: 2.6e-71
                                       EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGag 78 
                                       dvi Lg++e+++     t+ ++++  ++  +  ++ ++y+ + gl el+e++ +++++++++++++e++v+v++G +
  gi|298674171|ref|YP_003725921.1|  35 DVISLGVGEPDYI----TPWHIRESCIH--SIEQGETSYTSNYGLLELREQISELFSKKYNVEYNPESEVLVTTGVS 105
                                       79***********....*******9997..999999***************************************** PP

                                       HHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEE CS
                     Aminotran_1_2  79 aliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilve 155
                                       ++++++i+++ +npgde++v +p+y  y + +  +gg  v+++++ +++f+++ e+l++ ++e       tk ++++
  gi|298674171|ref|YP_003725921.1| 106 EALDIAIRAI-VNPGDEVIVVQPSYVAYVPSIIFAGGVPVTVSTKMSNNFKITPEELKNVITE------NTKAVVLN 175
                                       **********.9***************************************************......99****** PP

                                       SS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHH.HGGSTTSTT.EEEEEESSSTTSSGGG-E CS
                     Aminotran_1_2 156 sphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavat.ranveeepn.llivgslsKafGlaGeRv 230
                                        p+NPtG+ +++++le+++d++  + l++++De+Y  + ++ +    t  + +e   n +++++++sK+++++G+R+
  gi|298674171|ref|YP_003725921.1| 176 YPNNPTGATMDKADLEAIADVVVDNDLMVISDEVYDCLTYEGE---HTcFSSLEGMRNrTILLNGFSKSYAMTGFRI 249
                                       ****************************************976...33355566666689***************** PP

                                       EEEEEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCS CS
                     Aminotran_1_2 231 Gyilgnaavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsg 305
                                       +y+lg++++++ +  +++      + ++q  +++al++ ++   el++m +++ +rr  ++d+L+++gl++++++++
  gi|298674171|ref|YP_003725921.1| 250 AYALGDSEIINSMMLIHQYTMLcaPIVAQLGAMEALRNGND---ELDKMIREYDRRRNLIVDGLNRIGLECFEPKGA 323
                                       ****************998777789999999*******996...9******************************** PP

                                       SEEEEEETHH..CHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHHH CS
                     Aminotran_1_2 306 mflltdlsae..takelskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelveal 363
                                       ++ +  +     t +e+++ Ll+ ++v+ +pg  f+   +g+lR ++ + +++e++e++e++
  gi|298674171|ref|YP_003725921.1| 324 FYAFPSIQSTgmTSSEFAENLLDDQKVVTIPGDVFGEagQGFLRCSY-AASKDEIQEALERI 384
                                       ***********************************************.9999********98 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.4   0.2   1.6e-16   4.1e-13      35     144 ..      92     207 ..      67     210 .. 0.84

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 1.6e-16
                                       HHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-.TTTSSB-GGGCGGG--T CS
                   DegT_DnrJ_EryC1  35 ylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvd.pdtynidpaaieaaite 110
                                       y  +  ++ ++  ++Al +a+ra+ v+pgdeVIv++ ++va + +++ +g +pv v  +  + + i+p++++++ite
  gi|298674171|ref|YP_003725921.1|  92 YNPESEVLVTTGVSEALDIAIRAI-VNPGDEVIVVQPSYVAYVPSIIFAGGVPVTVSTKmSNNFKITPEELKNVITE 167
                                       445667777888899********8.99*****************************9983579************** PP

                                       TEEEEE...EB-GGGB--...-HHHHHHHHHHCT-EEEEE CS
                   DegT_DnrJ_EryC1 111 rtkaIl...pVhlyGqva...dmdalkaiaakhglkvieD 144
                                       +tka++   p +  G+ +   d++a+ ++  + +l+vi+D
  gi|298674171|ref|YP_003725921.1| 168 NTKAVVlnyPNNPTGATMdkaDLEAIADVVVDNDLMVISD 207
                                       *****95554556665542228888888888999***999 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.1   1.1e-11   2.9e-08      52     175 ..      84     207 ..      57     215 .. 0.77

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 1.1e-11
                                       HHHHHT-ST..GGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEE.EBETTS CS
                       Aminotran_5  52 vaelinaes..eeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvi.pldeeg 125
                                       + + +n+e   e+e+++t G +ea+ ++++++   ++pgde++v++  + a + p      + g+ v+v  ++ ++ 
  gi|298674171|ref|YP_003725921.1|  84 FSKKYNVEYnpESEVLVTTGVSEALDIAIRAI---VNPGDEVIVVQPSYVAYV-PSIIF--AGGVPVTVStKMSNNF 154
                                       44444544311589******************...9***************99.44444..4799999874788999 PP

                                       CBEGGGHHHH--TTEEEEEEESBETTTTEB-...-HHHHHHHHHHTT-EEEEE CS
                       Aminotran_5 126 eldldelekllnektklvaithvsnvtGtiq...pveeigklakkkgalvlvD 175
                                       +++++el++ ++e+tk+v ++  +n tG      ++e+i++++ +++ +v+ D
  gi|298674171|ref|YP_003725921.1| 155 KITPEELKNVITENTKAVVLNYPNNPTGATMdkaDLEAIADVVVDNDLMVISD 207
                                       ****************************9761114566666666666666666 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.4   9.2e-10   2.3e-06      69     175 ..      96     209 ..      76     212 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 9.2e-10
                                       EEEEESSHHH.HHHHHHHTTS-TTEEEEEESTSSHH...HHHHHHHTHHHTTCEEEEEST..TSHHHHHHHCCTTEE CS
                   Cys_Met_Meta_PP  69 aalavssGma.AiaaailallkaGdeivvsddlYgg...tqrllkkvlkklgievkfvdt..sdleelekaikentk 139
                                       + ++v++G++ A++ ai+a+++ Gde++v +  Y     +  +   v   + +++k+ +     +eel+++i+entk
  gi|298674171|ref|YP_003725921.1|  96 SEVLVTTGVSeALDIAIRAIVNPGDEVIVVQPSYVAyvpSIIFAGGVP--VTVSTKMSNNfkITPEELKNVITENTK 170
                                       55677777765999************9999887765100333333333..445555555422779************ PP

                                       EEEEESS-TTT...T----HHHHHHHHHHTT-EEEEEGT CS
                   Cys_Met_Meta_PP 140 lvylEtptnpl...lkvvDiekiaklakkagvlvvvDnt 175
                                       +v l  p np+   ++ +D+e+ia+++ +++++v+ D +
  gi|298674171|ref|YP_003725921.1| 171 AVVLNYPNNPTgatMDKADLEAIADVVVDNDLMVISDEV 209
                                       ****99999963337778999*****9999999998875 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   8.9e-09   2.3e-05      19     167 ..      58     207 ..      50     208 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 8.9e-09
                                       HCS----CCCT--HHHHHHHHHHHHHTT-SEEEE........ES-H.HHHHHHHHHHH--TTEEEEEETT-HHHHSS CS
                   Beta_elim_lyase  19 aaamlGdesYgedktvnrLedavaelfgkeaalf........vpqG.taAnsillkillqrgeevivtepahihfde 86 
                                         +++G+ sY  + +  +L +++ elf k++ +         v++G   A  i++++++++g+eviv +p+ +    
  gi|298674171|ref|YP_003725921.1|  58 HSIEQGETSYTSNYGLLELREQISELFSKKYNVEynpesevlVTTGvSEALDIAIRAIVNPGDEVIVVQPSYVAY-- 132
                                       56899**************************9955889999977773579999*****************97765.. PP

                                       TTHHHHCC--EEEEE-EBTT..TBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT CS
                   Beta_elim_lyase  87 tgaiaelagvklrdlknkea..GkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkyg 161
                                          i + +gv ++++ +k     k+++e+l+++i+e      ++k+++l   nn   G  +  + l+++a+++ +++
  gi|298674171|ref|YP_003725921.1| 133 VPSIIFAGGV-PVTVSTKMSnnFKITPEELKNVITE------NTKAVVLNYPNNP-TGATMDKADLEAIADVVVDND 201
                                       4567777777.999998877335678899***9999......799*********5.9******************** PP

                                       -EEEEE CS
                   Beta_elim_lyase 162 iplhlD 167
                                       + ++ D
  gi|298674171|ref|YP_003725921.1| 202 LMVISD 207
                                       999887 PP

>> OKR_DC_1  Orn/Lys/Arg decarboxylase, major domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   2.3e-06    0.0059      79     165 ..      92     178 ..      79     223 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.3e-06
                                       CT-SEEEEESSHHHHHHHHHHHHH--TTEEEEEESS--HHHHHHHHHS-EEEEEE--E.B-TTS-BE---GGGGSHH CS
                          OKR_DC_1  79 fgadksyfvvnGTsssnkvvlnavltpgdlvlvdRNcHKSiehalvlsgatPvylepe.rnalgiiggidlkefeee 154
                                       ++ +   +v+ G s +  + + a+++pgd v+v      +    ++++g +Pv ++++  n++ i+ +  +  + +e
  gi|298674171|ref|YP_003725921.1|  92 YNPESEVLVTTGVSEALDIAIRAIVNPGDEVIVVQPSYVAYVPSIIFAGGVPVTVSTKmSNNFKITPEELK-NVITE 167
                                       677778899************************************************98999988654333.34444 PP

                                       HHHHHHHHSTT CS
                          OKR_DC_1 155 tlkekikevpd 165
                                         k  + ++p+
  gi|298674171|ref|YP_003725921.1| 168 NTKAVVLNYPN 178
                                       44555555555 PP

>> DUF3396  Protein of unknown function (DUF3396)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00012       0.3      95     142 ..     257     302 ..     235     310 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00012
                           DUF3396  95 krravtrikgvnWltlLgeellekLGGveaLrqalkseeeivlslygd 142
                                       + +  +++  ++ +t+L+++++++LG +eaLr+ + + ++++ + ++ 
  gi|298674171|ref|YP_003725921.1| 257 EII--NSMMLIHQYTMLCAPIVAQLGAMEALRNGNDELDKMIREYDRR 302
                                       544..566667779******************9985555544444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2579.97
//
Query:       gi|298674172|ref|YP_003725922.1|  [L=124]
Description: transcriptional regulator TrmB [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-17   63.4   0.2    2.1e-17   62.8   0.2    1.3  1  TrmB         Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.012   15.4   0.2      0.015   15.2   0.2    1.2  1  TFIIE_alpha  TFIIE alpha subunit
      0.031   14.2   0.0       0.33   11.0   0.0    2.0  2  HTH_Crp_2    Crp-like helix-turn-helix domain
      0.034   14.0   0.0       0.05   13.4   0.0    1.3  1  HTH_IclR     IclR helix-turn-helix domain
      0.063   13.2   0.0      0.094   12.7   0.0    1.2  1  MarR         MarR family
      0.078   12.9   0.0       0.13   12.2   0.0    1.3  1  HTH_11       HTH domain
      0.079   13.0   0.1       0.11   12.6   0.1    1.3  1  HTH_20       Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.8   0.2   8.1e-21   2.1e-17       3      68 .]      22      93 ..      20      93 .. 0.97

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 8.1e-21
                                      HCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST......TTEEEE--HH CS
                              TrmB  3 klGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr......pklYravdpe 68
                                       lGL+e + ++Y+ Ll +gp+ta+++ + l+++rs+ Y++L++L+++GlV+re ++      ++ Y+a++pe
  gi|298674172|ref|YP_003725922.1| 22 ILGLKELDLQAYKLLLVNGPMTAEKLGKLLDRERSTSYRSLQNLISCGLVYRESRSidvggyYYEYVAISPE 93
                                      69***************************************************999*****999******97 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.2   5.8e-06     0.015      18      98 ..      32     112 ..      16     120 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.8e-06
                                       HHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEE.TTTEEEEEEEEEECCCHCCCHHHHHHHHH CS
                       TFIIE_alpha  18 vldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrd.eekswykyywrinyeklvdvvkrkleevv 93 
                                       + + Ll +g +t e l k+l  ++    + L +L + +lv y+ +r  +  + y  y  i +e + +++++ ++   
  gi|298674172|ref|YP_003725922.1|  32 AYKLLLVNGPMTAEKLGKLLDRERSTSYRSLQNLISCGLV-YRESRSiDVGGYYYEYVAISPESVKKMMQDNIDDWY 107
                                       5578999********************************9.8888884666666667789*************9999 PP

                                       HHHHH CS
                       TFIIE_alpha  94 kkLee 98 
                                       kk+  
  gi|298674172|ref|YP_003725922.1| 108 KKVSS 112
                                       98765 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00013      0.33       4      57 ..      19      78 ..      18      80 .. 0.74
   2 ?    0.9   0.0      0.18   4.5e+02      29      44 ..      86     101 ..      86     104 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00013
                                      HHHHHHHHCT.TTC....EEEEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEE.E CS
                         HTH_Crp_2  4 ArfLlrlaer.agg....eielpltqeelAsmlGltretvsrilseLkreglisrgrr.i 57
                                      A+ +l l e   ++     ++ p+t e l+ +l   r+t  r l+ L   gl+ r+ r i
  gi|298674172|ref|YP_003725922.1| 19 AKCILGLKELdLQAykllLVNGPMTAEKLGKLLDRERSTSYRSLQNLISCGLVYRESRsI 78
                                      6667777332122233566778******************************99753335 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.18
                                       HHTTSSHHHHHHHHHH CS
                         HTH_Crp_2  29 smlGltretvsrilse 44 
                                       +++ +++e+v +++++
  gi|298674172|ref|YP_003725922.1|  86 EYVAISPESVKKMMQD 101
                                       58899*******9985 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.9e-05      0.05      17      51 ..      40      74 ..      38      75 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.9e-05
                                      SS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR 17 qeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                      +++t   l + ++  +St +R Lq L+ +G+v ++
  gi|298674172|ref|YP_003725922.1| 40 GPMTAEKLGKLLDRERSTSYRSLQNLISCGLVYRE 74
                                      78999999999999******************986 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.7e-05     0.094      14      51 ..      38      75 ..      34      79 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.7e-05
                                      HSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR 14 eqgplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                       +gp++  +L+k l  ++st  r l  L+  Gl++R+ 
  gi|298674172|ref|YP_003725922.1| 38 VNGPMTAEKLGKLLDRERSTSYRSLQNLISCGLVYRES 75
                                      689*********************************86 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     5e-05      0.13       5      43 ..      32      69 ..      29      83 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5e-05
                            HTH_11  5 ilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                       ++lL   +gp+++e+L + L++ r+t +r ++ L + g
  gi|298674172|ref|YP_003725922.1| 32 AYKLL-LVNGPMTAEKLGKLLDRERSTSYRSLQNLISCG 69
                                      55666.66778************************9998 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   4.4e-05      0.11      19      54 ..      36      71 ..      25      77 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.4e-05
                                      HSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTE CS
                            HTH_20 19 LaraegltaselaerldlskntlsyHLrvLeeagLv 54
                                      L  ++++ta+ l ++ld  ++t ++ L+ L + gLv
  gi|298674172|ref|YP_003725922.1| 36 LLVNGPMTAEKLGKLLDRERSTSYRSLQNLISCGLV 71
                                      45899*************************999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      642  (0.0358079); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 899.55
//
Query:       gi|298674173|ref|YP_003725923.1|  [L=227]
Description: hypothetical protein Metev_0197 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-23   81.2   0.2    9.6e-23   80.7   0.2    1.2  1  DUF5591   Domain of unknown function (DUF5591)
  ------ inclusion threshold ------
      0.055   13.2   0.0      0.087   12.6   0.0    1.3  1  DUF508    Domain of unknown function (DUF508)


Domain annotation for each model (and alignments):
>> DUF5591  Domain of unknown function (DUF5591)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.7   0.2   1.1e-26   9.6e-23       3     142 ..      28     173 ..      26     180 .. 0.86

  Alignments for each domain:
  == domain 1  score: 80.7 bits;  conditional E-value: 1.1e-26
                                       HHHHHHHHH---S..SSEEEEEE--SSSSGGGSHHHHHHHHHS---.....SEEEEE-SS-.EEEGGGTT------- CS
                           DUF5591   3 rfrervlerYeppeekkvlvLlPcsakkPyseskshrkfaeaikkrka..kvheviltsPlGvvPreleevYPaaqY 77 
                                       r ++ +l+ Yeppe ++v++ +Pc +kkPy+es sh++f + i    +  +vh+v+ +   Gv Prel++ YP+++Y
  gi|298674173|ref|YP_003725923.1|  28 RANDWILDEYEPPE-RDVCIFVPCAKKKPYHESPSHQTFDKVIFGLLNpeQVHVVVFGT-CGVTPRELDNQYPFMHY 102
                                       556778999****7.***************************99988666999999885.7**************** PP

                                       ----....-----HHHHHHHHHHHHHHHHHHT-..SEEEE---THHHHHHHHHHTT-SSEEEE--.SS-TT CS
                           DUF5591  78 diav....tgewseeeiefvaellakylektky..ekviahleeeyreiveevaeelgleiiytvvedkpt 142
                                          +     ++ +++ i++ +e la+ylekt+y  ++ ia++ +++r+++e++ e +++++ +  +ed+  
  gi|298674173|ref|YP_003725923.1| 103 QFMLgkcdVPKIKRDFIKMESERLARYLEKTRYkyKHRIAYCIGDFRKAMEKAVEMVDIDVKIVPKEDTIQ 173
                                       98753223468999****************98844669**********************99988666554 PP

>> DUF508  Domain of unknown function (DUF508)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   9.7e-06     0.087      91     128 ..     123     162 ..     108     172 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.7e-06
                            DUF508  91 qqlcarqlkda..klnPrlsyCiGelnyknskPvlsedlk 128
                                        +  ar l ++  k++ r++yCiG++     k v   d++
  gi|298674173|ref|YP_003725923.1| 123 SERLARYLEKTryKYKHRIAYCIGDFRKAMEKAVEMVDID 162
                                       5678999999978899***********9999999888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1454.88
//
Query:       gi|298674174|ref|YP_003725924.1|  [L=246]
Description: putative circadian clock protein KaiC [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.5e-50  169.4   2.4    9.4e-50  169.1   2.4    1.0  1  ATPase    KaiC
    1.4e-07   30.5   0.2    1.8e-07   30.2   0.2    1.1  1  GvpD      GvpD gas vesicle protein
    1.9e-05   24.3   0.0    2.6e-05   23.9   0.0    1.1  1  AAA_25    AAA domain
     0.0015   17.9   0.2     0.0083   15.4   0.1    1.9  2  Rad51     Rad51
     0.0024   17.3   0.1     0.0069   15.8   0.0    1.7  2  DnaB_C    DnaB-like helicase C terminal domain
     0.0035   16.6   0.3     0.0047   16.2   0.3    1.4  1  DUF2075   Uncharacterized conserved protein (DUF2075)
     0.0092   16.4   1.3       0.03   14.7   1.3    1.8  1  AAA       ATPase family associated with various cellular acti
  ------ inclusion threshold ------
      0.052   13.8   0.1       0.12   12.6   0.1    1.6  1  AAA_22    AAA domain
      0.065   13.0   0.1       0.16   11.6   0.1    1.7  1  AAA_24    AAA domain


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.1   2.4   4.7e-53   9.4e-50       1     228 [.      15     241 ..      15     243 .. 0.90

  Alignments for each domain:
  == domain 1  score: 169.1 bits;  conditional E-value: 4.7e-53
                            ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenak.slGwdlek 76 
                                       v+t I+glD++l+gG+  ++v  ++G++GtGKtif+ qFl++ga+k ge+g+++ + e++++l +++k s+Gwdl++
  gi|298674174|ref|YP_003725924.1|  15 VSTEIPGLDDMLHGGFFTETVNVVSGNSGTGKTIFGSQFLYEGAKK-GEKGMLIITSEESKSLVREMKtSFGWDLKE 90 
                                       689*******************************************.***99876666666666666659******* PP

                            ATPase  77 leeegklaiidasesaeesaee...kdkedleelieelaeaikeikakrvviDsitgl.ayeekeavaReilrqlvr 149
                                       +e++g + ++d++  + + +++     +e ++++++ +++ i++ k +rv +Dsi++l   +e++ ++R+ ++ +++
  gi|298674174|ref|YP_003725924.1|  91 MEQQGYISFVDITDPSLRLQKSveiAPSELIKSFKKLVESKIEKEKPERVFVDSIEALfLAIESNYKLRTMVDDVFS 167
                                       ************99987766545555555556666666666777788***********99***************** PP

                            ATPase 150 vlkklgvTailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegikv 226
                                       v++  gvT++ +       + ++ ++v e+ +d vi+L++ +  ++l+R++ ++kmRg+k+ +++ +++I+++g  v
  gi|298674174|ref|YP_003725924.1| 168 VFRSHGVTSVVTVG-----TLFELNDVVEYGADSVIKLERFKTGNTLQRSIYVMKMRGSKTINEIRVLNISDNGMGV 239
                                       *************9.....7999***************************************************998 PP

                            ATPase 227 le 228
                                       l+
  gi|298674174|ref|YP_003725924.1| 240 LA 241
                                       76 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.2     9e-11   1.8e-07      14     203 ..      37     230 ..      26     243 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 9e-11
                              GvpD  14 likGaPGtGktlftlrgld..vlrresdvlyvstrvddetvseay...fsgeaeldktall...dllkdpleldldv 82 
                                       ++ G+ GtGkt+f  ++l   + + e+ +l +++   ++ v e+      +  e+++  ++   d+   +l l+  v
  gi|298674174|ref|YP_003725924.1|  37 VVSGNSGTGKTIFGSQFLYegAKKGEKGMLIITSEESKSLVREMKtsfGWDLKEMEQQGYIsfvDITDPSLRLQKSV 113
                                       89****************7224455778999*************955422455566555553337777778887777 PP

                              GvpD  83 dvPiekldlesllefvdeiaaiatkliialdswelvyeylaerydsPediktvkndlvvlaresgvrlvlvlet..a 157
                                       ++   +l ++s+ + v++  +  +   + +ds    +e+l    +s  +++t+ +d+  + r +gv  v+ + t  +
  gi|298674174|ref|YP_003725924.1| 114 EIAPSEL-IKSFKKLVESKIEKEKPERVFVDS----IEALFLAIESNYKLRTMVDDVFSVFRSHGVTSVVTVGTlfE 185
                                       6654333.7999999*95555555557889**....88888888888899****************98887776336 PP

                              GvpD 158 ansrleyivdGvvtl.nvkeddrgrlrrdlrleklrGvrignrlqPf 203
                                        n+ +ey +d v+ l + k      l+r++ + k+rG +  n ++ +
  gi|298674174|ref|YP_003725924.1| 186 LNDVVEYGADSVIKLeRFKTG--NTLQRSIYVMKMRGSKTINEIRVL 230
                                       7999***********656655..689***********9877766555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   1.3e-08   2.6e-05       9     184 ..       9     177 ..       2     181 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.3e-08
                            AAA_25   9 avsvadlaapppprrwlvkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsed 84 
                                       +++ +++ +++p +++ ++g    ++++++ G +gtGKt + ++  ++ a +G++            l++  E+s  
  gi|298674174|ref|YP_003725924.1|   9 TSQPERVSTEIPGLDDMLHGGFFTETVNVVSGNSGTGKTIFGSQFLYEGAkKGEK----------GMLIITSEESK- 74 
                                       456778999**********88889**************************66662..........57999999999. PP

                            AAA_25  85 elrrRlravg....ealrddarllvldlagveslpLfak..drggtlltadvdaleaaieevegvrlvviDplsral 155
                                        l r ++  +    +++++++   ++d+ +  sl+L ++  ++ ++l++++ + +e +ie+ e+++ v +D++ +++
  gi|298674174|ref|YP_003725924.1|  75 SLVREMKTSFgwdlKEMEQQGYISFVDITD-PSLRLQKSveIAPSELIKSFKKLVESKIEK-EKPERVFVDSIEALF 149
                                       777777776655556779999999999977.689988764356667788887777888888.99*********9976 PP

                            AAA_25 156 ggdensnsdvgalvealeriarrtgaavl 184
                                        + e sn + + +v+++ ++ r +g++ +
  gi|298674174|ref|YP_003725924.1| 150 LAIE-SNYKLRTMVDDVFSVFRSHGVTSV 177
                                       6533.356666666666666667777655 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   4.1e-06    0.0083      18      56 ..      14      52 ..       2      57 .. 0.86
   2 ?    0.0   0.0      0.21   4.1e+02      79     145 ..     103     149 ..      85     182 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.1e-06
                                      EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHH CS
                             Rad51 18 qlttGskklDelLgGGietgsiteifGefrsGktqlcht 56
                                      +++t    lD++L+GG+ t ++  + G++++Gkt +  +
  gi|298674174|ref|YP_003725924.1| 14 RVSTEIPGLDDMLHGGFFTETVNVVSGNSGTGKTIFGSQ 52
                                      57888889**************************88766 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.21
                                       SSS---GGGGHHHH.....HHTT--HHHHGGGEEEEE--STTHHHHHHHHTHHHHHHS-EEEEEEETTTGGG CS
                             Rad51  79 tegtfrperlveia.....erykldkeevlenvayaRaytiehqeellqqaaallaedkfallivDsvtaly 145
                                       t+ ++r ++ veia     + +k   e+ +e+ + +R++                          Ds+ al+
  gi|298674174|ref|YP_003725924.1| 103 TDPSLRLQKSVEIApseliKSFKKLVESKIEKEKPERVFV-------------------------DSIEALF 149
                                       5566666666666665555555555555555555556553.........................3333333 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   3.4e-06    0.0069       3      65 ..      16      78 ..      15     148 .. 0.80
   2 ?   -2.6   0.0       1.4   2.8e+03     201     237 ..     190     221 ..     186     230 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.4e-06
                                      XSSTHHHHHHC.TSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHH CS
                                      xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  3 stgfkdLDklt.sGlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvq 65
                                      st+   LD+++ +G+   ++ ++ + +++Gkt +  ++  + a+k +++++++  e s++ lv+
  gi|298674174|ref|YP_003725924.1| 16 STEIPGLDDMLhGGFFTETVNVVSGNSGTGKTIFGSQFLYEGAKKGEKGMLIITSEESKS-LVR 78
                                      6777889977626899***************************99999999988887654.444 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.4
                                       CCCCXSEEEEEEECCHHHHHHCHHCEEEEEEEEETTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C 201 ieqdADvvlflyrdeyykedseekgkaeiiiaKhRnG 237
                                       +e  AD v+ l r ++ ++      +  i+++K R  
  gi|298674174|ref|YP_003725924.1| 190 VEYGADSVIKLERFKTGNTL-----QRSIYVMKMRGS 221
                                       56678888888775444322.....245666666654 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.3   2.4e-06    0.0047       3      46 ..      35      75 ..      33     143 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.4e-06
                           DUF2075  3 vvlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlv 46
                                      v +V+G++GtGKt+ ++++l+e    +++++  +++ + ++ + 
  gi|298674174|ref|YP_003725924.1| 35 VNVVSGNSGTGKTIFGSQFLYEG--AKKGEKGMLIITS-EESKS 75
                                      779*******************8..3333333333333.33333 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   1.3   1.5e-05      0.03       3      91 ..      38     167 ..      36     189 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.5e-05
                                       EESSTTSSHHHHHHHHHHH.............HTHE...........................EEEEETTTCS.SSS CS
                               AAA   3 lyGppGtGKTllakavake.............lgve...........................fleisgsell.sky 38 
                                       ++G+ GtGKT++ ++   e             +  e                           f+ i  ++l+ +k 
  gi|298674174|ref|YP_003725924.1|  38 VSGNSGTGKTIFGSQFLYEgakkgekgmliitS--EeskslvremktsfgwdlkemeqqgyisFVDITDPSLRlQKS 112
                                       789************999965555555544430..0444555555555666666666666666************** PP

                                       TTHHHHHHHHHHHHHHHTS....TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHH CS
                               AAA  39 vgesekkirelfkeakeka....kpsilfiDEidalaksrsgseseeeervvnqLlt 91 
                                       v+ +++++ + fk++ e++    kp  +f+D i+al+ +   +++ + +++v+  ++
  gi|298674174|ref|YP_003725924.1| 113 VEIAPSELIKSFKKLVESKiekeKPERVFVDSIEALFLAI--ESNYKLRTMVDDVFS 167
                                       *************987777788889***********9998..445555555555555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   6.3e-05      0.12       6     135 ..      34     188 ..      31     190 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.3e-05
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka............ 70 
                                       ++ vv G sGtGKT    ++l++          +++   + +  s++sk+l re+   +g +lk+            
  gi|298674174|ref|YP_003725924.1|  34 TVNVVSGNSGTGKTIFGSQFLYEGA--------KKGEKGMLIITSEESKSLVREMKTSFGWDLKEmeqqgyisfvdi 102
                                       66799****************9973........23323333333334567777777777777777777777777777 PP

                            AAA_22  71 ..............erlsseellealeqalraravielliiDEaqhlr.seealeeLrsllnl......srkgvqli 126
                                                     +    + + +++e  +++ +  e + +D ++ l+   e   +Lr+++++      s+  ++++
  gi|298674174|ref|YP_003725924.1| 103 tdpslrlqksveiaPSELIKSFKKLVESKIEKEKP-ERVFVDSIEALFlAIESNYKLRTMVDDvfsvfrSHGVTSVV 178
                                       77778877777775555555555777777777777.99999999999887888888888888888888788888888 PP

                            AAA_22 127 LvGtp.elrk 135
                                        vGt  el++
  gi|298674174|ref|YP_003725924.1| 179 TVGTLfELND 188
                                       8888777765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   8.2e-05      0.16       6      77 ..      37     148 ..      32     161 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.2e-05
                            AAA_24   6 liyGpsgiGKTtlakel........gpkplfi.....................dtek.Glksldadkfpdie..... 47 
                                       ++ G sg+GKT + +++        ++  l+i                      +e+ G+ s  ++     +     
  gi|298674174|ref|YP_003725924.1|  37 VVSGNSGTGKTIFGSQFlyegakkgEKGMLIItseeskslvremktsfgwdlkEMEQqGYISFVDI-----Tdpslr 108
                                       789*****************9999878888884444444444444444443332222222222222.....133333 PP

                            AAA_24  48 ..........swedfldevvel..........aaeladyktlviDtidel 77 
                                                            l          + e+++ + +++D+i+ l
  gi|298674174|ref|YP_003725924.1| 109 lqksveiapsE----------LiksfkklvesKIEKEKPERVFVDSIEAL 148
                                       55555554443..........03334444554677777789999999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1804.69
//
Query:       gi|298674175|ref|YP_003725925.1|  [L=208]
Description: 4-diphosphocytidyl-2C-methyl-D-erythritol synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-15   55.8   0.0    9.3e-15   55.3   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
    2.9e-08   33.7   0.0    4.2e-08   33.2   0.0    1.3  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
    4.9e-06   26.6   0.0    7.2e-06   26.1   0.0    1.2  1  CTP_transf_3     Cytidylyltransferase
    7.9e-05   22.3   0.0    0.00012   21.8   0.0    1.3  1  NTP_transferase  Nucleotidyl transferase
  ------ inclusion threshold ------
      0.016   14.4   0.5      0.032   13.4   0.2    1.6  2  CofC             Guanylyl transferase CofC like
       0.14   12.0   0.0       0.22   11.4   0.0    1.3  1  DUF2064          Uncharacterized protein conserved in bacteri


Domain annotation for each model (and alignments):
>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.3   0.0   3.1e-18   9.3e-15       1     118 [.       3     125 ..       3     140 .. 0.84

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 3.1e-18
                                       EEEEEESS-TTTT.TTHHHHCCCCCCHHHHHHHHHCTT..-CEEEEECSH....CHHHHHHTTCTS-EEE-TTSS-S CS
                      NTP_transf_3   1 aviLAGGrSsRmg.gdKallplggkpllervldalraa.gvdevvvvggd....eevlaalarlgvrvvededpgkg 71 
                                       +v++AGGr++R+g g+K+ ++l g pl+ +v+dal++a ++d+++v++ +     e++   ++++ rv + e +g  
  gi|298674175|ref|YP_003725925.1|   3 VVVMAGGRGTRLGmGEKPCVQLLGSPLISYVIDALEKAdNIDNIYVAVSQatpnTEIY-VSNQYQNRVNVIETAGGD 78 
                                       69***********66***********************77*******86643223444.345566555555666899 PP

                                       HHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSE CS
                      NTP_transf_3  72 plaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadv 118
                                        ++ +  a+++a+ +++v++++ D++l+tpel++++++++++ g+ +
  gi|298674175|ref|YP_003725925.1|  79 YVGDMIYAVENAGIKEPVMIIMSDLALITPELIDKIVDEYRECGKPA 125
                                       99999999999999***********************9998766655 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0   1.4e-11   4.2e-08       2     120 ..       2     121 ..       1     151 [. 0.78

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 1.4e-11
                                       EEEEECTTSSCTT-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGG..CCEEEE..E-- CS
                              IspD   2 vvvipAAGsGkRmkaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllld..ksiqlv..aGG 74 
                                        vv+ A G+G+R++ g  K  ++l g +l++  +dal +  ++d+i v+vs+   ++   ++ +  ++++++  aGG
  gi|298674175|ref|YP_003725925.1|   2 DVVVMAGGRGTRLGMGE-KPCVQLLGSPLISYVIDALEKADNIDNIYVAVSQATPNTEIYVSNQyqNRVNVIetAGG 77 
                                       589************95.999******************************99844444444447767888744699 PP

                                       SSHHHHHHHHHHTTSSTTSEEEE--TT-TT--HHHHHHHHHHHHTT CS
                              IspD  75 deRaesVlnglkalegeakfVLvHDaARpllkaadiaellaaaeqs 120
                                       d   + +++  +a  g ++ V++  +  +l++++ i++++ + ++ 
  gi|298674175|ref|YP_003725925.1|  78 DYVGDMIYAVENA--GIKEPVMIIMSDLALITPELIDKIVDEYREC 121
                                       9999998877777..4445566666666689********9998762 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   2.4e-09   7.2e-06      14     120 ..      17     123 ..       4     148 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 2.4e-09
                                       TTGGGSEETTEEHHHHHHHHHHHTTTTSEEEEEES-HHHHH..HH.HHTTSEEEE--TTCSSHHHHHHHHHHHHTTT CS
                      CTP_transf_3  14 pgKnlldlggkpliayvleaalkskafekvivaTDseeikn..va.kefgasvlvtrsslesdterflevvkaflms 87 
                                        +K+  +l+g pli yv++a+ k+ ++++++va ++        +  ++   v+v+++   +    +  +v++  ++
  gi|298674175|ref|YP_003725925.1|  17 GEKPCVQLLGSPLISYVIDALEKADNIDNIYVAVSQATPNTeiYVsNQYQNRVNVIETAGGDYVGDMIYAVENAGIK 93 
                                       58***************************999876654333013303333666666655555555555555555555 PP

                                       .TTSEEEEE-TT-TT--HHHHHHHHHHHHHSTT CS
                      CTP_transf_3  88 eneeiivnlqGdnPllqeevikkaietlkenqe 120
                                          e ++ + +d +l+ +e+i+k++++++e ++
  gi|298674175|ref|YP_003725925.1|  94 ---EPVMIIMSDLALITPELIDKIVDEYRECGK 123
                                       ...78888999****************999766 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0     4e-08   0.00012       3     117 ..       4     108 ..       2     134 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 4e-08
                                       EEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHH.TT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEE CS
                   NTP_transferase   3 vILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlan.sgieeiivvltqehsflveeqlkegskfgvevlia 78 
                                       v++aGG+GtRL        k+ v  lg+ +li +++ +l +  +i++ i+v  ++  +  e +++++++ +  v+++
  gi|298674175|ref|YP_003725925.1|   4 VVMAGGRGTRLG----MGEKPCVQLLGS-PLISYVIDALEKaDNIDN-IYVAVSQATPNTEIYVSNQYQNR--VNVI 72 
                                       9**********5....799*********.***********9455666.99999999999********9988..6666 PP

                                       EESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEEST CS
                   NTP_transferase  79 lepegkgtAdAvalaaelledeksdelvlvLggDhlikd 117
                                           g+   d ++ +++   +e    +++++++  li+ 
  gi|298674175|ref|YP_003725925.1|  73 ETAGGDYVGDMIYAVENAGIKEP---VMIIMSDLALITP 108
                                       66666666666666666666555...3666666666665 PP

>> CofC  Guanylyl transferase CofC like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   1.1e-05     0.032      37     112 ..      33     117 ..      23     122 .. 0.63
   2 ?   -2.3   0.0      0.69   2.1e+03     163     180 ..     176     193 ..     167     195 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.1e-05
                              CofC  37 vidalkr...ld.v.lvvse...deevleyaldelgvevvkekekd....lntavekafeeieekeviiipsdiPli 101
                                       vidal++   +d + + vs+   + e+  +++ + +v+v++    d    +  ave+a     +++v+ii+sd+ li
  gi|298674175|ref|YP_003725925.1|  33 VIDALEKadnIDnIyVAVSQatpNTEIYVSNQYQNRVNVIETAGGDyvgdMIYAVENA---GIKEPVMIIMSDLALI 106
                                       5555544222665313455422235677777778889999877555000044445554...34789*********** PP

                              CofC 102 kkedvkdllel 112
                                       + e ++++++ 
  gi|298674175|ref|YP_003725925.1| 107 TPELIDKIVDE 117
                                       ******99986 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.69
                              CofC 163 iydsfylsvdinteedlg 180
                                       i d   l+++int++dl 
  gi|298674175|ref|YP_003725925.1| 176 IMDHPELALNINTADDLE 193
                                       666677889999999985 PP

>> DUF2064  Uncharacterized protein conserved in bacteria (DUF2064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   7.3e-05      0.22      14      84 ..      47     116 ..      33     123 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.3e-05
                                       EEEE----TTHH.HHHHHH-TTSEEEE--SSSHHHHHHHHHHHHHHTT-S.EEEEE-SS-TT--HHHHHHHHH CS
                           DUF2064  14 vlaldgaldkal.aeqlalakglevlpQqggdlgeRlarafdrafeagee.pvlliGsDcpqltaalleqAfe 84 
                                       ++a+++a++++    + + +++++v++  ggd    + +a+++a   g + pv++i sD+  +t++l+++ ++
  gi|298674175|ref|YP_003725925.1|  47 YVAVSQATPNTEiYVSNQYQNRVNVIETAGGDYVGDMIYAVENA---GIKePVMIIMSDLALITPELIDKIVD 116
                                       55555554443303344889999*********************...6666*****************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1569.11
//
Query:       gi|298674176|ref|YP_003725926.1|  [L=272]
Description: cobalamin 5'-phosphate synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-40  139.5  15.5      2e-40  139.2  15.5    1.1  1  CobS             Cobalamin-5-phosphate synthase


Domain annotation for each model (and alignments):
>> CobS  Cobalamin-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.2  15.5   1.1e-44     2e-40       2     204 .]      12     252 ..      11     252 .. 0.81

  Alignments for each domain:
  == domain 1  score: 139.2 bits;  conditional E-value: 1.1e-44
                              CobS   2 lsflTrlPvp.......elaralaffPlvGlllGlll.llallllllllll.aallavaalvlltgglHlDGlaDta 69 
                                       ++fl+++P+        el + +++fP+vG+++Gl++  +a+l+ ++++++ +a++++++++++tg++HlDGlaD++
  gi|298674176|ref|YP_003725926.1|  12 FGFLSTIPFGltmegldELVKRIYLFPFVGIVIGLIIgTFAYLFGFVFPPViSAVAIIITVYYFTGFNHLDGLADFG 88 
                                       79*******8766655555779***************99999999998866366666667778************** PP

                              CobS  70 DglgsgrdrerrleImkDsrvGafGvlalvlvlllkvaalaala...................lllapvlsRlaall 127
                                       Dgl ++++re+++++mkD ++G +G++++vl l+  +a++++l+                   l++a++ ++ ++l+
  gi|298674176|ref|YP_003725926.1|  89 DGLTAHGSREKKINAMKDVSLGIGGAAFCVLGLVSLYAVITTLLdeslvqninlstsllifssLVVAEISAKQSMLT 165
                                       ***9999******************************99755555566677778888889999999*********** PP

                              CobS 128 aiallpyaeeglgalfaeaqkk.....lvllal........avlllll.alllaallvalllrrlarrklggvtGDv 190
                                       ++a++++ +eglg++++++++           l        +vl ++  + ++aa++ al++ ++++r++ggvtGD 
  gi|298674176|ref|YP_003725926.1| 166 IAAFGKSIHEGLGSMVIDNTTFpkfiiG----LagggffcwLVLGIFGiVGFIAAMISALIILNITNRHFGGVTGDG 238
                                       ******9999*******86544553220....13445544333333332355777778889999************* PP

                              CobS 191 lGavieltellvll 204
                                       lG ++e++++++ll
  gi|298674176|ref|YP_003725926.1| 239 LGTSNEVGRIITLL 252
                                       **********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1761.26
//
Query:       gi|298674177|ref|YP_003725927.1|  [L=185]
Description: alpha-ribazole phosphatase CobZ [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-08   35.2   0.0    1.3e-08   34.9   0.0    1.2  1  PgpA      Phosphatidylglycerophosphatase A


Domain annotation for each model (and alignments):
>> PgpA  Phosphatidylglycerophosphatase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.0   7.5e-13   1.3e-08      42     141 ..      74     169 ..      31     171 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 7.5e-13
                                       H..HHHHHHHHHHHHHHHHHHT.-S-.......HHT-TT--HHHHTTHHHHH........TTHHHHHHHHHHHHS-- CS
                              PgpA  42 l..llilllflvGiwackktek.elg.......ekDpgeiviDEvvgqwiallllpatllalllafilFrlfDivKp 108
                                       +  +++++l++ Gi ++k+ ++  l        ekD + i+ DEv+g++i        ++    +++ +  fD+ Kp
  gi|298674177|ref|YP_003725927.1|  74 FsdPNLCILVYSGILLEKEGKEgSLPnlskssyEKDLSFIIADEVLGMSISK------YISGDKGMFEYVRFDKEKP 144
                                       256778889999999999999865658999999*******************......3344789************ PP

                                       THHHHTSSS.-S---TTHHHHHHHHHHHHHHHH CS
                              PgpA 109 gpigwldrklkgglgvmlDDllAgiaaalvlal 141
                                       g++++l          ++DD++Agi++++   +
  gi|298674177|ref|YP_003725927.1| 145 GILSKLGP--------FMDDVVAGIVGGVSANM 169
                                       ******77........9*********9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 1261.83
//
Query:       gi|298674178|ref|YP_003725928.1|  [L=330]
Description: cobalamin biosynthesis protein CobD [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.1e-86  290.6   0.0    1.3e-86  290.2   0.0    1.1  1  CobD_Cbib  CobD/Cbib protein
    0.00011   21.7   0.0     0.0002   20.8   0.0    1.4  1  AmpE       Regulatory signalling modulator protein AmpE


Domain annotation for each model (and alignments):
>> CobD_Cbib  CobD/Cbib protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  290.2   0.0   1.5e-90   1.3e-86       1     271 [.      16     300 ..      16     310 .. 0.88

  Alignments for each domain:
  == domain 1  score: 290.2 bits;  conditional E-value: 1.5e-90
                         CobD_Cbib   1 lllAlllDlllgdprrllhPvvligklisalekrlrkakkerlaGvllalllvllallvallllllalaall....g 73 
                                       l++A ++Dll+g+p++ +hPvv+igk+i++++k     k+++l+G++la++++++a +++++++l+++a+++    +
  gi|298674178|ref|YP_003725928.1|  16 LIIATVFDLLVGEPPASIHPVVWIGKFIAFMDKSSP-DKSRKLYGIFLAAICIVFASAIGYIITLFTAASYIpetvA 91 
                                       689******************************664.36899*********************99884443346567 PP

                         CobD_Cbib  74 lvlealllkltlalrsLleevrkvakal.kgdleaaReavsmiVgRdtseldeeeiarAavEsvaENlsDgvvaPlf 149
                                       ++++a++lk+t+a+rsL++ +++++++l ++ l++ R++++ +V+Rd+sel+ +++++A++Es++EN++Dg+++P+f
  gi|298674178|ref|YP_003725928.1|  92 ILISAYFLKSTFAIRSLITPGQDIYNDLiQNRLDDVRSKLKIFVSRDPSELNSSQMSSAVIESTSENFTDGILSPIF 168
                                       89**************************889********************************************** PP

                         CobD_Cbib 150 yflll...glpgalaykavnTlDsmvGYkneryedfGwaaArlDDllnyiPARltalllala............... 208
                                       y+ +l   gl++++aykavnTlDsm+GYkn+ y+++G+++A+lDD+ln+iPAR++++++al+               
  gi|298674178|ref|YP_003725928.1| 169 YYSILgpfGLVAVYAYKAVNTLDSMIGYKNDAYKELGYVSAKLDDILNWIPARISVVFIALSafvvnifvekklsii 245
                                       ****95556677999**********************************************6455555555555455 PP

                         CobD_Cbib 209 aalriarrdarkhpSpNsgwpeaalAgalgvrLggpnvY.lgkleekptlgdkkrpleaedier 271
                                        +l++a+ ++  ++SpNsg+p+aa+ gal+v+L++p++Y lg+             +e++di+r
  gi|298674178|ref|YP_003725928.1| 246 DSLKCAYYEGGLTSSPNSGYPMAAVSGALRVKLEKPDTYtLGDSFPG---------PEPSDIKR 300
                                       55*************************************87743222.........23455555 PP

>> AmpE  Regulatory signalling modulator protein AmpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   2.3e-08    0.0002     145     211 ..     164     230 ..     158     253 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.3e-08
                              AmpE 145 laplfwfvvagpygpvalvgyavlrayqtwlarrktpleraqsgvdallhvldwipvrlagvayall 211
                                       l+p+f++ + gp+g va+ +y  + + ++++  ++  ++        l  +l+wip+r+  v  al 
  gi|298674178|ref|YP_003725928.1| 164 LSPIFYYSILGPFGLVAVYAYKAVNTLDSMIGYKNDAYKELGYVSAKLDDILNWIPARISVVFIALS 230
                                       89*****************************9999998888777777889*********99888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       952  (0.0530983); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2237.97
//
Query:       gi|298674179|ref|YP_003725929.1|  [L=495]
Description: class I/II aminotransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.9e-47  159.8   0.0    1.2e-46  159.5   0.0    1.1  1  Aminotran_1_2    Aminotransferase class I and II
    1.1e-24   86.2   7.2    2.6e-24   84.9   7.2    1.6  1  zf-like          Cysteine-rich small domain
  ------ inclusion threshold ------
      0.024   13.6   0.0       0.19   10.6   0.0    2.3  2  Aminotran_5      Aminotransferase class-V
       0.17   11.2   0.0       0.27   10.5   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.5   0.0   2.8e-50   1.2e-46      32     363 .]      67     376 ..      38     376 .. 0.90

  Alignments for each domain:
  == domain 1  score: 159.5 bits;  conditional E-value: 2.8e-50
                                       HHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHH CS
                     Aminotran_1_2  32 laggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasykn 108
                                       + +++l++y++++ + e++ a a f+g     + +re +++ g+G+++li +++ +  +++gd++++p+pt+++y+ 
  gi|298674179|ref|YP_003725929.1|  67 NNTEKLTRYPDNR-YLEFRDAAAGFIG-----NQDRE-NIIPGNGSCELIRLVAECV-VEKGDQVIIPQPTFDEYEL 135
                                       667899*******.*************.....999**.*******************.9****************** PP

                                       HHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEE CS
                     Aminotran_1_2 109 ilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllf 185
                                        +r+ g+  v+++++        + ++ + l +        k+++v++p+NPtG ++++  l++l+d + +   llf
  gi|298674179|ref|YP_003725929.1| 136 QCRIFGARPVYINYS-------EIPQISDELLN------SSKILFVCNPNNPTGELLSRSILKDLADRCAETSTLLF 199
                                       *************77.......89999998888......679*********************************** PP

                                       EEETTTTCBSSSSHTHHHHGGSTTSTT.EEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTS...SHHHHH CS
                     Aminotran_1_2 186 vDeaYagfvfgsldavatranveeepn.llivgslsKafGlaGeRvGyilgnaavvsqlrklsrpfls...ssllqa 258
                                       vDea+ ++   +++    +a++ ++ n +++++sl K+f+++G+RvG+ ++++++++ l ++  +++    s ++  
  gi|298674179|ref|YP_003725929.1| 200 VDEAFIELSDPEQS----VAELVKDNNfVFVMRSLTKSFAIPGIRVGFGVASQKLANVLDNARLSWNMgfvSDVVGT 272
                                       *********99664....7777777788*************************888777777766666444666666 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.TEEEECCSCSSEEEEEETHH.CHHHHHHHHHHTCTEEEE CS
                     Aminotran_1_2 259 avaaalsdallkqseleemrqrlqkrrkelrdeLael.glkvlasqsgmflltdlsae.takelskkLleevgvyvt 333
                                        ++++   +    s++ ++r+ + ++rk+l d++ ++ g++ l+s  +++l+ + +   + kels+ L+ + g++v+
  gi|298674179|ref|YP_003725929.1| 273 KLLKMKGGVYS--SYFRDSRKMIDRERKYLIDRISRIhGFTPLDSSVNYILVDVSESVmDSKELSQRLAAR-GILVR 346
                                       66666666553..4********************999********9999999666666999**********.***** PP

                                       EGGGGTS..TTEEEEECTTS-HHHHHHHHHHH CS
                     Aminotran_1_2 334 pgtsftv..pgrlRitvAglteeeleelveal 363
                                        ++sf     +++R+ v   ++e+ ++l++ +
  gi|298674179|ref|YP_003725929.1| 347 DCSSFCSlgDEFIRVAV--RNSEDTDKLAKNI 376
                                       *****999*********..9999999999865 PP

>> zf-like  Cysteine-rich small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.9   7.2   5.9e-28   2.6e-24       7      79 ..     407     480 ..     403     483 .. 0.89

  Alignments for each domain:
  == domain 1  score: 84.9 bits;  conditional E-value: 5.9e-28
                           zf-like   7 nkeCeyyPCHktedenClfCyCPlYaledeel.Gefveteng.kvkdCskCllvHkkevadellkklkeileelk 79 
                                       +++CeyyPCH+  +++C+fC+CP+Y++ede++ G++++++ g kv++Cs+C ++H++++++++l+ l++    +k
  gi|298674179|ref|YP_003725929.1| 407 RSTCEYYPCHY-PGQDCTFCFCPFYPCEDERTgGQYIKSTGGgKVWSCSDCHIIHREKIVEQVLDVLMDENGDTK 480
                                       578********.99***************98858888888889*********************99888766665 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   4.3e-05      0.19      29      95 ..      64     127 ..      54     204 .. 0.88
   2 ?   -0.6   0.0      0.11     5e+02     276     337 ..     289     347 ..     283     364 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 4.3e-05
                                       SSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEET CS
                       Aminotran_5  29 nvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvte 95 
                                        v +++ +l+    + + e r+  a +i+ +++e+ii   G+ e i lva ++   +++gd++++ +
  gi|298674179|ref|YP_003725929.1|  64 LVSNNTEKLTRYPDNRYLEFRDAAAGFIGNQDRENIIPGNGSCELIRLVAECV---VEKGDQVIIPQ 127
                                       466678888888899999***********************************...********965 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTCSHHHHHHHHHHTTEEEEE CS
                       Aminotran_5 276 iekhekelaeyllerlkslpgvrlygpdkaerrasivsfnfkgvhaedvatlLdeegIavrs 337
                                       ++k  ++ ++yl +r++ + g++ +++     +  +v ++   ++++++ + L+ +gI vr 
  gi|298674179|ref|YP_003725929.1| 289 SRKMIDRERKYLIDRISRIHGFTPLDS---SVNYILVDVSESVMDSKELSQRLAARGILVRD 347
                                       567778889999999999999998664...7889999999999***************9995 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   6.1e-05      0.27      18      91 ..      71     148 ..      59     155 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 6.1e-05
                                       -SSS..SHHHHHHHHHHHHHHT..-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE CS
                   DegT_DnrJ_EryC1  18 wlts..gpeveeFEkafaaylg..vkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfv 90 
                                       +lt+  +++  eF  a a ++g  ++  i   +G+  l  +   + v++gd+VI+p+ tF       +  ga+pv++
  gi|298674179|ref|YP_003725929.1|  71 KLTRypDNRYLEFRDAAAGFIGnqDRENIIPGNGSCELIRLVAECVVEKGDQVIIPQPTFDEYELQCRIFGARPVYI 147
                                       45555677788999999999995445677777777766555555*******************************98 PP

                                       - CS
                   DegT_DnrJ_EryC1  91 D 91 
                                       +
  gi|298674179|ref|YP_003725929.1| 148 N 148
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.63u 0.26s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 3251.13
//
Query:       gi|298674180|ref|YP_003725930.1|  [L=408]
Description: histidyl-tRNA synthetase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-64  217.8   0.0    2.5e-64  217.5   0.0    1.1  1  tRNA-synt_His    Histidyl-tRNA synthetase
    2.4e-16   60.2   0.0    9.1e-16   58.3   0.0    1.8  2  tRNA-synt_2b     tRNA synthetase class II core domain (G, H, 
    2.8e-11   43.4   0.1    5.3e-11   42.5   0.1    1.4  1  HGTP_anticodon   Anticodon binding domain
    8.8e-05   21.7   2.2       0.31   10.1   0.0    3.1  2  tRNA-synt_2      tRNA synthetases class II (D, K and N)
     0.0021   17.6   0.0      0.023   14.2   0.0    2.4  2  tRNA-synt_2d     tRNA synthetases class II core domain (F)
  ------ inclusion threshold ------
      0.076   12.4   0.0       0.43   10.0   0.0    2.1  2  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 


Domain annotation for each model (and alignments):
>> tRNA-synt_His  Histidyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.5   0.0   8.2e-68   2.5e-64       1     309 [.       8     309 ..       8     310 .. 0.95

  Alignments for each domain:
  == domain 1  score: 217.5 bits;  conditional E-value: 8.2e-68
                                       T---EETCHHHHHHHHHHHHHHHHHHTT-EEEE--SEEEHHHHCTTSTCCHH.HS-EEE-TTSSEEEE-SSSHHHHH CS
                     tRNA-synt_His   1 glrdllpeeaekieelrrrlldlfeswGYelVspPllEyldslltgagedld.qtfklvDqsgrllglRaDiTpqva 76 
                                       g+rd+lp e ++++ +++++ d++ +wGY++V++P++E l+ ++ ++g d   +++ ++D+ gr ++lR+++T+ v 
  gi|298674180|ref|YP_003725930.1|   8 GTRDFLPGETARRRYVENTIRDVVIKWGYSEVMTPTFETLELFTLKSGDDIIgELYNFTDKGGREIALRPELTAPVM 84 
                                       78************************************************655************************ PP

                                       HHHHHHHH.TSS-EEEEEEEEEEESS-SSTT--CCEEEEEEEEESS-SHHHHHHHHHHHHHHHHHHCTSSSEEEEEE CS
                     tRNA-synt_His  77 Riaahrln.rerplRlcYaGsvlrtrpdglgrsreplQvGaEliGaegleadlEvlslllealeaaagvkelrldlg 152
                                       R++ + l+ ++ pl+l Y+++++r ++ + gr re+ Q+G E+iG++++ead+Ev+ l++++l+ ++gv +  l +g
  gi|298674180|ref|YP_003725930.1|  85 RMYVNKLQsEPHPLKLFYFENCFRYERPQKGRFREFWQFGTEVIGSDKPEADAEVIALAVNILD-SVGV-NGALHVG 159
                                       *******99******************************************************7.****.67899** PP

                                       ETCHHHHHHHHTT--HHHHHHHHHHHHCT-HHHHHHHHHCCTTHHHCCHCC....HCCHCCCHHHHCHCCHCTHHHH CS
                     tRNA-synt_His 153 hvglvralleaaglsesleeallaalarkdlaelkelaaeaglkealrellkal.elygdaevleealealaaapal 228
                                       + +++r +l+  gl+++++ ++++++++ d ++l++ ++e ++++++r+ l  l +l+ ++++le+a+e + + p+ 
  gi|298674180|ref|YP_003725930.1| 160 DLRIIRHILS--GLDNEQQTKVMRYVDKNDDKGLDDYLEEIEVPAETRRNLFELiSLQ-GNDALEKAREITGDIPE- 232
                                       *********9..57799******************************99999998996.569*****997777777. PP

                                       HHHHHHHHHHHHHHHHHHHH-TTEEE-TT--TTTTT--SEEEEEEETT-SS..-SEEEEEECTTTGGG.T---EEEE CS
                     tRNA-synt_His 229 qaaldeleelaallealakpevrvtlDlaelrgyeYytGlvFaayaegvgq..aiarGGrYdelgaaf.grarpAtG 302
                                          ld++eel +ll+ ++   +++t+D++  rg++YytG+vF++yaeg g+  ++ +GG Y +l++ f g + p+tG
  gi|298674180|ref|YP_003725930.1| 233 ---LDNFEELLKLLDVYG---LDYTIDFGIARGLDYYTGMVFEIYAEGLGAqnQVCGGGSY-QLIKLFgGGEVPSTG 302
                                       ...9***********986...**************************988555********.9*****9999***** PP

                                       EEEEHHH CS
                     tRNA-synt_His 303 fsldlea 309
                                       f +  ++
  gi|298674180|ref|YP_003725930.1| 303 FGIGFDR 309
                                       *987776 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   0.0     3e-19   9.1e-16       1     131 [.      63     281 ..      63     316 .. 0.89
   2 ?   -1.9   0.0      0.97   2.9e+03      10      31 ..     385     406 ..     378     407 .. 0.86

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 3e-19
                                       EEEEETTSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b   1 YkledrndreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeasld 77 
                                       Y + d+ +re +L+P+ ++++++++ ++ l+s+  Plkl+++  ++R+E++ ++G  R reF q + +v+++++  +
  gi|298674180|ref|YP_003725930.1|  63 YNFTDKGGREIALRPELTAPVMRMYVNK-LQSEPHPLKLFYFENCFRYERP-QKG--RFREFWQFGTEVIGSDK--P 133
                                       8999************************.**********************.***..***************99..9 PP

                                       HHHHHHHHHHHHHHHHTT.SC.......EEEEEEGTTSC...................................... CS
                                       xxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxx...................................... RF
                      tRNA-synt_2b  78 dslrdlikaisriferlglef.......raiielmsaks...................................... 109
                                       + ++++i ++ +i+ ++g++        r       ++                                       
  gi|298674180|ref|YP_003725930.1| 134 EADAEVIALAVNILDSVGVNGalhvgdlR-------IIRhilsgldneqqtkvmryvdknddkglddyleeievpae 203
                                       ******************99954444442.......33333445556778899999999999999999999999999 PP

                                       ........................................................BTTSEEEEEEEEETTTSEEEE CS
                                       ........................................................xxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b 110 ........................................................adykdkkefeavsesltkgie 130
                                                                                               +dy+   +fe++ e l+++ +
  gi|298674180|ref|YP_003725930.1| 204 trrnlfelislqgndalekareitgdipeldnfeellklldvygldytidfgiargLDYYTGMVFEIYAEGLGAQNQ 280
                                       99999999999999999999999999999999999999999999999999999999999999999999999999887 PP

                                       E CS
                                       x RF
                      tRNA-synt_2b 131 i 131
                                       +
  gi|298674180|ref|YP_003725930.1| 281 V 281
                                       6 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.97
                                       EEEE-SSSHHHHHHHHHHHEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  10 eyiLkPtneetfvelirdevlr 31 
                                       +++Lk +++   +++  de+l+
  gi|298674180|ref|YP_003725930.1| 385 KLTLKNMHTGEQCSMTVDEILN 406
                                       689**************99887 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.1   1.8e-14   5.3e-11      14      89 ..     332     406 ..     323     407 .. 0.89

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 1.8e-14
                                       HHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEEEEETTHHHH CS
                    HGTP_anticodon  14 leeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqervsldelve 89 
                                          +a ++a++Lr+  + +++d  +++++ +++ a+++   +av+vGe+e+e+g++t+++++t+eq ++++de+++
  gi|298674180|ref|YP_003725930.1| 332 TRFEAIDIANRLREV-YPTHVDIMERNFKSQLSFANMVEADYAVIVGEREIESGKLTLKNMHTGEQCSMTVDEILN 406
                                       34468999*****99.899******************************************************975 PP

>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   1.0   0.00044       1.3      28     122 ..      23     127 ..      16     154 .. 0.66
   2 !   10.1   0.0    0.0001      0.31     271     296 ..     287     312 ..     277     325 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00044
                                       HHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT..TEEE..............-E-S.-SHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx..............xxxx.xxxxxxxxxxx RF
                       tRNA-synt_2  28 vtkavrkyleengfieietPiLsksdteegarlFkvksrek.ekeff..............aLtq.spqlylelliv 88 
                                       v + +r++  + g+ e+ tP++ +       +lF++ks     +e++               Lt   + +y   l +
  gi|298674180|ref|YP_003725930.1|  23 VENTIRDVVIKWGYSEVMTPTFETL------ELFTLKSGDDiIGELYnftdkggreialrpELTApVMRMYVNKLQS 93 
                                       5566677777777777777766666......6666655554422333333555555544443332134556555554 PP

                                       CT.HSEEEEEEEEE--S--BTTB-S-CEEEEEEEE CS
                                       xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  89 ag.idrvfqiaraFRaEdsrtdrhlaEFtqieaem 122
                                            + f + ++FR E+ ++ r   EF+q+  e+
  gi|298674180|ref|YP_003725930.1|  94 EPhPLKLFYFENCFRYERPQKGRFR-EFWQFGTEV 127
                                       4324589*************99999.****98886 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0001
                                       HHHHHHHHCT--SEEEEEEEHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 271 swylealeyGapphgGlglGldRlvm 296
                                       +++++++  G +p  G+g+G+dR++ 
  gi|298674180|ref|YP_003725930.1| 287 YQLIKLFGGGEVPSTGFGIGFDRIME 312
                                       5789999****************875 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   7.7e-06     0.023      23     133 ..      24     129 ..       8     139 .. 0.69
   2 ?   -0.4   0.0      0.21   6.3e+02     208     222 ..     297     311 ..     285     325 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.7e-06
                                       HHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-ECESEEE-SSTHHHHHHHH.... CS
                      tRNA-synt_2d  23 leeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpekaveekllLRthttavqirtl.... 95 
                                        + i+++ ++ g++ev  p         + L++   ++  d+   +y  +++    ++  LR   ta  +r+     
  gi|298674180|ref|YP_003725930.1|  24 ENTIRDVVIKWGYSEVMTPTF-------ETLELFTLKSGDDIIGELYNFTDKG--GREIALRPELTAPVMRMYvnkl 91 
                                       555666666666666655543.......3333333333344444444434444..6789999999988877766766 PP

                                       TTS-SSEEEEEEEEEEBSST-SSSB-SEEEEEEEEEEE CS
                      tRNA-synt_2d  96 ekkkppikiisigrvfRrdavDathlaeFhqveglvvd 133
                                       +++ +p+k++ ++++fR +   + +  eF q    v++
  gi|298674180|ref|YP_003725930.1|  92 QSEPHPLKLFYFENCFRYERPQKGRFREFWQFGTEVIG 129
                                       9999****************999999999998666655 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.21
                                       TSEEEEEEEEHHHHH CS
                      tRNA-synt_2d 208 evsgfafGlGveRla 222
                                       ev+  +fG+G++R+ 
  gi|298674180|ref|YP_003725930.1| 297 EVPSTGFGIGFDRIM 311
                                       678899*******86 PP

>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00015      0.43      13     147 ..      15     140 ..       9     161 .. 0.77
   2 ?   -1.2   0.0      0.38   1.1e+03      31      69 ..     304     345 ..     298     369 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00015
                   tRNA_synthFbeta  13 gelnkeqklrrklrdllagaGlnEvitysfvsekeldklleddderkavelanPlsedqs..vlRtsLlpglLevla 87 
                                       ge  +++ +++++rd++++ G++Ev+t +f   + +      + ++   el n  ++     +lR+ L++ ++    
  gi|298674180|ref|YP_003725930.1|  15 GETARRRYVENTIRDVVIKWGYSEVMTPTFETLELFTLK---SGDDIIGELYNFTDKGGReiALRPELTAPVMRMYV 88 
                                       5566788899********************988887666...77777778888776653322789999999999998 PP

                   tRNA_synthFbeta  88 rNlargnedvrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlk 147
                                       + l+ + + ++lF + ++f+ +  ++ +++e ++++  + g++         +++  +++ 
  gi|298674180|ref|YP_003725930.1|  89 NKLQSEPHPLKLFYFENCFRYErPQKGRFREFWQFGTEVIGSD---------KPEADAEVI 140
                                       8888888889999999999999888889999999999999988.........344444444 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.38
                   tRNA_synthFbeta  31 gaGlnEvitysfvsekeldkll...eddderkavelanPlse 69 
                                       g+G+  ++  + + ++e +kl     d+++ +a+ +an l e
  gi|298674180|ref|YP_003725930.1| 304 GIGFDRIMEVASIEPEETKKLVvvsTDSTRFEAIDIANRLRE 345
                                       677777777777778888777777666677778888776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2515.09
//
Query:       gi|298674181|ref|YP_003725931.1|  [L=152]
Description: 30S ribosomal protein S15 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-27   94.2   0.9      1e-26   92.7   0.5    1.9  2  Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
      4e-15   55.8   0.5    6.3e-15   55.2   0.5    1.3  1  Ribosomal_S15    Ribosomal protein S15


Domain annotation for each model (and alignments):
>> Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.7   0.5   1.1e-30     1e-26       1      60 []       1      60 [.       1      60 [. 1.00
   2 ?   -1.3   0.0      0.26   2.3e+03      29      42 ..     114     127 ..     108     131 .. 0.83

  Alignments for each domain:
  == domain 1  score: 92.7 bits;  conditional E-value: 1.1e-30
                                      X--SSSSSS--------S-SS--TTS---HHHHHHHHHHHHHTT--HHHHHHHHHHCCT- CS
                   Ribosomal_S13_N  1 MarmhsrgkGkSgSarPyrreapsWlklskeeveelivklakkGltpSqIGviLRDqyGv 60
                                      Ma+mh+r+kG+SgS+rP+r+e+p+W+ l+ +e+e+++++l+k+G+++S+IG+iLRD +Gv
  gi|298674181|ref|YP_003725931.1|  1 MAKMHTRRKGQSGSTRPMRNEVPEWSPLDVNEIEQKVIELWKNGYSSSEIGMILRDIHGV 60
                                      ***********************************************************8 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.26
                                       -HHHHHHHHHHHHH CS
                   Ribosomal_S13_N  29 skeeveelivklak 42 
                                       s +++e +i +lak
  gi|298674181|ref|YP_003725931.1| 114 SLQNIEAKIRRLAK 127
                                       66899999999998 PP

>> Ribosomal_S15  Ribosomal protein S15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   0.5     7e-19   6.3e-15      16      79 ..      82     147 ..      70     149 .. 0.92

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 7e-19
                                       SSHHHHHHHHHHHHHHHHHHHHCTTT-HHHHHHHHHHHHHHHHHHHHHHHH-H..HHHHHHHHHCT CS
                     Ribosomal_S15  16 GspevqiallterInnltehlkenkkDkhsrrgLlklvskRrkllkYLkrkdv..erYkklieklg 79 
                                         +++++++l+ ++ ++++hl+ n++D h++r+L+++++k+r+l kY+++++v   ++k+  e+++
  gi|298674181|ref|YP_003725931.1|  82 FHVPEDLYNLVVKAIRIRKHLDINPHDIHNKRSLQNIEAKIRRLAKYYRSNNVlpSDWKYKPETAE 147
                                       46899********************************************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1094.05
//
Query:       gi|298674182|ref|YP_003725932.1|  [L=450]
Description: phosphoesterase RecJ domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-15   56.0   1.4    1.5e-14   54.6   0.5    2.2  2  DHHA1     DHHA1 domain
    7.4e-06   26.1   0.6    1.9e-05   24.8   0.6    1.7  1  DHH       DHH family


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.66   5.9e+03      60      60 ..      46      46 ..       8      87 .. 0.53
   2 !   54.6   0.5   1.7e-18   1.5e-14      44     138 .]     341     436 ..     307     436 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.66
                                      H CS
                             DHHA1 60 a 60
                                      +
  gi|298674182|ref|YP_003725932.1| 46 C 46
                                      3 PP

  == domain 2  score: 54.6 bits;  conditional E-value: 1.7e-18
                                       EEECHCCHHHHHHHHHHHHHHTHG.BTTCEEEEEEEECTEEEEEEEESSH....SS-HHHHHHHHHHHTTCCEEEET CS
                             DHHA1  44 vaevgeewdagalgiaadklkskl.kkpvivfvakeegdkvkvsarskkd....gvdagelakeaaaklgggGGGHd 115
                                       + +      ++ +gi+a+ +   + ++ + v++++e +d vkvsar++      gvd++ +++eaa+   g+GGGH+
  gi|298674182|ref|YP_003725932.1| 341 YLNA---ESMDSIGIVAGVIIRYMyPD-MPVIATNEVEDVVKVSARATHHliekGVDLNYAMREAAKLTVGSGGGHN 413
                                       3333...23667777777777733144.44444444445*********88*************************** PP

                                       CEEEEEEEHCHHHHHHHHHHHHH CS
                             DHHA1 116 lAaGagipaekleealealeeai 138
                                        AaGa i+++++e +++ ++++i
  gi|298674182|ref|YP_003725932.1| 414 IAAGAAIEKGQVENFINIVDDII 436
                                       *****************999876 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.6   2.2e-09   1.9e-05       4      80 ..      30     145 ..      27     162 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 2.2e-09
                                       EE-ECSSSHHHHHH.HHHHHH..................................CECS--TCGGCGCCHHCCCSEE CS
                                       xxxxxxxxxxxxxx.xxxxxx..................................xxxxxxxxxxxxxxxxxxxxxx RF
                               DHH   4 ivghknpDtDsigS.aialan..................................llvDhneksqavegeakeeaed 45 
                                       +  + + DtD+i+S ai  ++                                  + +D+++ + + +    +  ed
  gi|298674182|ref|YP_003725932.1|  30 V--VSHNDTDGITSaAIICQAllrekiryhativsrldesviedvnntisegdlvIFCDMGSGQPDLIS---NVSED 101
                                       5..7789*******6666666888888888888888888877777777777777779999999999887...999** PP

                                       EEEEE-S---S..........S---SS--EEEE-SSS-HHHHHHH CS
                                       xxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH  46 viiiDHHrlge..........efetlapilflnepvgstaeivae 80 
                                       +++iDHH+++            f+++   ++l +  gst  ++ e
  gi|298674182|ref|YP_003725932.1| 102 TVVIDHHNPEGestakavlnpHFSEIDGSTYL-SASGSTYMVARE 145
                                       *********87777777777644444333443.444555544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2869.91
//
Query:       gi|298674183|ref|YP_003725933.1|  [L=78]
Description: hypothetical protein Metev_0207 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.21s 00:00:00.54 Elapsed: 00:00:00.34
# Mc/sec: 680.65
//
Query:       gi|298674184|ref|YP_003725934.1|  [L=503]
Description: serine--tRNA ligase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      9e-61  204.4   0.1    1.4e-60  203.8   0.1    1.3  1  tRNA_bind_4   tRNA-binding domain
    2.6e-05   24.3   0.0    5.8e-05   23.1   0.0    1.6  1  tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, 


Domain annotation for each model (and alignments):
>> tRNA_bind_4  tRNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.8   0.1   1.5e-64   1.4e-60       1     159 [.       3     158 ..       3     160 .. 0.97

  Alignments for each domain:
  == domain 1  score: 203.8 bits;  conditional E-value: 1.5e-64
                                       EEEEEEEEEEESS-SCCCHHHHHHHHHHHCCTGGGTTSSTTT.S.SSEEEEEEE-SSEEEEEEEEESSS-HHHHHHH CS
                       tRNA_bind_4   1 lkfelkgklklskdieeaeeeieefieeanktiLkkGvpegkeeegakitewkiegnelkleieSgryvRahdallr 77 
                                       lkf++kg++k+s+d+++a+e+i efi+ean+tiLkkG+peg+   ga++++w+++g++++++ieSgryvRahdallr
  gi|298674184|ref|YP_003725934.1|   3 LKFNIKGSFKTSDDASPATEAIDEFINEANETILKKGAPEGE---GANVVDWNVDGSKINITIESGRYVRAHDALLR 76 
                                       69***************************************7...******************************** PP

                                       HHHHHHHHCCCCCS--EEEEEEEEEEEEEE-S.S--HH---TTECEEEEETTEEEEEEES--HHHHHTTHHHHHHHH CS
                       tRNA_bind_4  78 lkkplaeklGkkyriGvRgikveeyeieiese.kelkaekipeveeveveegkitlelkdvdeselkkrvvdRiikl 153
                                       ++kpla+klGk+yriG+Rgi++++++i+i+se ++l + kip+v++++++++ i+l+l dv+esel++rv+dRi++l
  gi|298674184|ref|YP_003725934.1|  77 MRKPLAKKLGKDYRIGIRGIEIDSFNISIPSEnQDLGELKIPYVTDIDYNDSVIKLSL-DVGESELQNRVPDRILTL 152
                                       *******************************95667**********************.****************** PP

                                       HHHHHC CS
                       tRNA_bind_4 154 veekie 159
                                       +e+ki 
  gi|298674184|ref|YP_003725934.1| 153 MEDKIA 158
                                       ***996 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   6.4e-09   5.8e-05      26      95 ..     315     385 ..     304     478 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 6.4e-09
                                       HHHEEEBGGSSEEEEEE.EEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHHHHHHHHHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  26 rdevlrskrLPlklyqi.qtkyRdEksdsrGLlRvreFhqkdgyvfhaeaslddslrdlikaisriferlg 95 
                                       + e++  ++ Plk+++  +t +R+E   ++G+ Rv eFh  + +  ++ +++ ++ + l  ++ +if +++
  gi|298674184|ref|YP_003725934.1| 315 QGETIPTNEFPLKVFDHsGTSHRYESGGIHGIERVDEFHRIEIVWLGTHDQVVSESKALQDKYRHIFDDIL 385
                                       4455666679***9975279******99***************************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.24s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 3181.02
//
Query:       gi|298674185|ref|YP_003725935.1|  [L=196]
Description: 30S ribosomal protein S3Ae [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-63  214.0   6.9    1.7e-63  213.9   6.9    1.0  1  Ribosomal_S3Ae  Ribosomal S3Ae family
  ------ inclusion threshold ------
       0.15   11.9   0.6       0.15   11.9   0.6    2.1  2  Myosin_N        Myosin N-terminal SH3-like domain


Domain annotation for each model (and alignments):
>> Ribosomal_S3Ae  Ribosomal S3Ae family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.9   6.9   1.9e-67   1.7e-63       3     202 .]       5     193 ..       3     193 .. 0.97

  Alignments for each domain:
  == domain 1  score: 213.9 bits;  conditional E-value: 1.9e-67
                                       ----S-TCCSEEEEEEEB-TTSSSSEEEEEEEE--BSSSESHHSHTT-EEEEESHHHHTCS.HTSSSEEEEEEEEEE CS
                    Ribosomal_S3Ae   3 kkkvvDkfkkKeWydvkaPslfgkreiGktlvnrtqgtkiaseklkgrvvevslaDLtnde.keqafrklklkieev 78 
                                        +k+ Dk+k+K+Wy+++ P++++++ iG t++        +++ l grvve++++ Ltnd  ke   +kl+l+i++v
  gi|298674185|ref|YP_003725935.1|   5 VQKKLDKWKSKNWYNIEPPEFLSSSYIGVTPA-------ENTKDLLGRVVETTVGQLTNDItKE--KTKLRLQIDNV 72 
                                       6899****************************.......*********************9666..*********** PP

                                       ESSEEEEEEEEEEE-HHHHHHH--SSB-EEEEEEEEEESSSEEEEEEEEEEE-STTB---HHHHHHHHHHHHHHHHH CS
                    Ribosomal_S3Ae  79 qgknaltnFkgmeltrDklrslvrkwsslIeaivdvktkDgyllrvfvvafTkkrnsYakssqkkaIrkkmveilte 155
                                        g++a+t+F g+e+t+D+lrs+v++++s+I+ +v v+t+Dg ++rv++++fT kr   a+ssq+kaIrk+m++++++
  gi|298674185|ref|YP_003725935.1|  73 VGDSAKTRFIGHEITTDYLRSIVKRQTSRIDNNVVVTTNDGNKVRVKPICFTVKR---AHSSQIKAIRKVMKDVVKA 146
                                       *******************************************************...******************* PP

                                       HHHHS-HHHHHHHHTTTHHHHHHHHHHTTTS-EEEEEEEEEEEEE-S CS
                    Ribosomal_S3Ae 156 easeldlkelvkklipeslgkeiekeakkIyplrnveirKvkvlkkP 202
                                       +ase+d+ +++++ i+ +l+++i++++kk+yp+r+ eirK++v  +P
  gi|298674185|ref|YP_003725935.1| 147 RASEVDYGQFIDEAISGKLAANIYRNTKKVYPIRRAEIRKTEVQAEP 193
                                       ****************77*************************8877 PP

>> Myosin_N  Myosin N-terminal SH3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.2       0.2   1.8e+03      15      27 ..      43      55 ..      42      64 .. 0.75
   2 ?   11.9   0.6   1.7e-05      0.15      20      39 ..     100     119 ..      93     120 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.2
                                      EEEEEEEESSEEE CS
                          Myosin_N 15 kGeIkeeeGdkvt 27
                                       G+++e++ +++t
  gi|298674185|ref|YP_003725935.1| 43 LGRVVETTVGQLT 55
                                      6899999888877 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 1.7e-05
                                       EEESSEEEEEETTSEEEEEE CS
                          Myosin_N  20 eeeGdkvtVetedGktvtVk 39 
                                       ++ +++v+V t+dG++v+Vk
  gi|298674185|ref|YP_003725935.1| 100 SRIDNNVVVTTNDGNKVRVK 119
                                       555789*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       966  (0.0538792); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1310.01
//
Query:       gi|298674186|ref|YP_003725936.1|  [L=67]
Description: hypothetical protein Metev_0210 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00015   21.6   1.9    0.00021   21.2   1.9    1.2  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
    0.00043   19.9   1.7       0.56   10.0   0.2    2.3  2  A2L_zn_ribbon    A2L zinc ribbon domain
    0.00046   20.5   0.3    0.00056   20.2   0.3    1.2  1  Lar_restr_allev  Restriction alleviation protein Lar
    0.00081   19.0   0.5    0.00081   19.0   0.5    2.0  2  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
      0.002   18.2   0.3        1.8    8.7   0.0    2.3  2  Zn-ribbon_8      Zinc ribbon domain
     0.0063   16.2   0.2      0.009   15.7   0.2    1.5  1  TackOD1          Thaumarchaeal output domain 1
  ------ inclusion threshold ------
      0.011   15.2   2.6      0.041   13.4   2.6    2.0  1  TF_Zn_Ribbon     TFIIB zinc-binding
      0.014   15.1   3.5       0.33   10.8   3.8    2.1  2  PADR1            PADR1 (NUC008) domain
      0.016   15.2   0.1      0.022   14.8   0.1    1.2  1  DZR              Double zinc ribbon
      0.017   15.0   0.8      0.029   14.3   0.8    1.3  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.021   14.7   0.8      0.056   13.3   0.8    1.8  1  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
      0.025   14.7   0.0      0.026   14.7   0.0    1.3  1  FYVE             FYVE zinc finger
      0.037   13.8   4.7       0.19   11.5   0.2    2.3  2  Rubredoxin_2     Rubredoxin metal binding domain
      0.093   12.7   1.7       0.15   12.1   1.7    1.3  1  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
      0.095   12.4   1.5        2.2    8.0   0.1    2.2  2  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
       0.11   12.4   1.0        3.4    7.6   0.1    2.2  2  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
       0.19   11.3   1.4         10    5.8   0.1    2.4  2  RecR             RecR protein
       0.42   10.5   3.5        9.5    6.2   0.2    2.2  2  TFIIS_C          Transcription factor S-II (TFIIS)
       0.44   10.5   0.3       0.44   10.5   0.3    2.2  2  Cys_rich_CPXG    Cysteine-rich CPXCG
        4.4    6.9   8.8        5.6    6.5   0.5    2.2  2  zf-ribbon_3      zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   1.9   2.3e-07   0.00021      20      45 ..       9      37 ..       4      38 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.3e-07
                     Zn_Tnp_IS1595 20 vCPhCgsr....kayriktrglfqCkeCrk 45
                                      vCP Cgs+    +a  +++ +l++Ck C++
  gi|298674186|ref|YP_003725936.1|  9 VCPVCGSShwyyEAGGYTG-KLYHCKNCGY 37
                                      8*******76666666776.********97 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.2   0.00062      0.56      21      31 ..       7      17 ..       3      19 .. 0.87
   2 !    9.4   0.1   0.00095      0.85      22      30 ..      30      38 ..      27      48 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00062
                     A2L_zn_ribbon 21 ylvCieCgasf 31
                                      ++vC+ Cg+s+
  gi|298674186|ref|YP_003725936.1|  7 IEVCPVCGSSH 17
                                      79*******98 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00095
                     A2L_zn_ribbon 22 lvCieCgas 30
                                      + C++Cg++
  gi|298674186|ref|YP_003725936.1| 30 YHCKNCGYI 38
                                      456666666 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.3   6.3e-07   0.00056       4      37 ..       8      45 ..       5      63 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 6.3e-07
                   Lar_restr_allev  4 kpCPfCggravlersqrvvaeigqcvyCadCga.......s 37
                                      + CP Cg+   + ++++ + +     +C++Cg+       +
  gi|298674186|ref|YP_003725936.1|  8 EVCPVCGSSHWYYEAGGYTGK---LYHCKNCGYigpliveA 45
                                      67*************999998...9********44444221 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.5     9e-07   0.00081       2      22 ..       5      25 ..       4      26 .. 0.86
   2 ?    0.2   1.0      0.69   6.2e+02      24      28 ..      32      36 ..      29      36 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 9e-07
                           zf-RRN7  2 ekgppCgvCgcrsftlddGfy 22
                                      e+ ++C+vCg+  ++ ++G y
  gi|298674186|ref|YP_003725936.1|  5 EYIEVCPVCGSSHWYYEAGGY 25
                                      6789************88876 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.69
                           zf-RRN7 24 CrrCh 28
                                      C++C+
  gi|298674186|ref|YP_003725936.1| 32 CKNCG 36
                                      88887 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0     0.002       1.8      23      34 ..       3      15 ..       1      18 [. 0.68
   2 !    7.9   0.0    0.0037       3.3       6      13 ..      30      37 ..      29      52 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.002
                       Zn-ribbon_8 23 daplta.CPeCgs 34
                                      +++ ++ CP Cgs
  gi|298674186|ref|YP_003725936.1|  3 EEEYIEvCPVCGS 15
                                      4444555*****9 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0037
                       Zn-ribbon_8  6 YrCeeCgh 13
                                      Y+C++Cg 
  gi|298674186|ref|YP_003725936.1| 30 YHCKNCGY 37
                                      9******6 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2     1e-05     0.009      85     115 ..       5      41 ..       2      65 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1e-05
                           TackOD1  85 nvrevCpkCkSidie......eqelihhftCgnvgpe 115
                                       +++evCp C+S++        + +l h+ +Cg++gp 
  gi|298674186|ref|YP_003725936.1|   5 EYIEVCPVCGSSHWYyeaggyTGKLYHCKNCGYIGPL 41 
                                       699*********9862222225689*********985 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   2.6   4.5e-05     0.041       2      27 ..       9      37 ..       8      47 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.5e-05
                                      EETTTTCEECHEE...TSTTCE.EESSSSB CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveD...pergel.vCtdCGl 27
                                      +CP+Cgs++ +++   +  g l  C++CG+
  gi|298674186|ref|YP_003725936.1|  9 VCPVCGSSHWYYEaggYT-GKLyHCKNCGY 37
                                      8********777746455.55549*****7 PP

>> PADR1  PADR1 (NUC008) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   3.8   0.00036      0.33      13      41 ..       7      33 ..       6      39 .. 0.76
   2 ?    4.3   0.6     0.038        34      11      20 ..      27      36 ..      25      47 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00036
                             PADR1 13 lekCpeCkegqlvfdssgYkCtGnmsewt 41
                                      +e Cp C++++++++ +gY+  G++   +
  gi|298674186|ref|YP_003725936.1|  7 IEVCPVCGSSHWYYEAGGYT--GKLYHCK 33
                                      678*************9884..5555544 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.038
                             PADR1 11 GalekCpeCk 20
                                      G+l +C++C+
  gi|298674186|ref|YP_003725936.1| 27 GKLYHCKNCG 36
                                      9999*****8 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   2.4e-05     0.022      13      37 ..       8      38 ..       3      46 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.4e-05
                               DZR 13 rfCseCgtklkavaa......edrCpsCgek 37
                                      ++C+ Cg++   ++a       ++C +Cg+ 
  gi|298674186|ref|YP_003725936.1|  8 EVCPVCGSSHWYYEAggytgkLYHCKNCGYI 38
                                      58*******9988889*************86 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.8   3.2e-05     0.029      30      54 ..       9      37 ..       8      39 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.2e-05
                    OrfB_Zn_ribbon 30 tCseCgsknke....alsgrtfkCpnCgf 54
                                       C++Cgs + +      +g++++C+nCg+
  gi|298674186|ref|YP_003725936.1|  9 VCPVCGSSHWYyeagGYTGKLYHCKNCGY 37
                                      6********99999999***********7 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.8   6.3e-05     0.056       4      32 ..      10      40 ..       7      42 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.3e-05
                                      ESTTTS.BEEEEECSCCCE.EEESSSS-EEE CS
                    RNA_POL_M_15KD  4 CpkCgN.lLlpkedkegkn.feCrqCgYeep 32
                                      Cp Cg+ + ++  +  +   + C +CgY+ p
  gi|298674186|ref|YP_003725936.1| 10 CPVCGSsHWYYEAGGYTGKlYHCKNCGYIGP 40
                                      99999547777766666566********977 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.9e-05     0.026       5      34 ..       3      38 ..       1      64 [. 0.81

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.9e-05
                                      ...--SB-TTT--B--S......SS--EE-TTT--E CS
                              FYVE  5 ddsevkkCeiCakkFsl......lrrrhhCrlCGkv 34
                                      +++ ++ C+ C ++  +      + + +hC++CG +
  gi|298674186|ref|YP_003725936.1|  3 EEEYIEVCPVCGSSHWYyeaggyTGKLYHCKNCGYI 38
                                      5678899******99643445548999*******86 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.8     0.047        42      17      22 ..      10      15 ..       9      18 .. 0.78
   2 ?   11.5   0.2   0.00021      0.19       1       9 [.      30      38 ..      30      42 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.047
                      Rubredoxin_2 17 CpsCgs 22
                                      Cp Cgs
  gi|298674186|ref|YP_003725936.1| 10 CPVCGS 15
                                      899987 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00021
                      Rubredoxin_2  1 YvCsqCGfe 9 
                                      Y+C++CG+ 
  gi|298674186|ref|YP_003725936.1| 30 YHCKNCGYI 38
                                      9******96 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.7   0.00016      0.15       5      27 ..      10      37 ..       9      37 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
                    PhnA_Zn_Ribbon  5 CplCaSeytY.....edgallvCpeCah 27
                                      Cp C+S++ Y       g l+ C +C++
  gi|298674186|ref|YP_003725936.1| 10 CPVCGSSHWYyeaggYTGKLYHCKNCGY 37
                                      ************99999*********96 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1    0.0025       2.2      19      31 ..       5      17 ..       1      18 [. 0.73
   2 ?    3.8   0.2      0.05        45      23      30 ..      31      38 ..      30      39 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0025
                     zf-NADH-PPase 19 gwarvCpaCgleh 31
                                      ++  vCp Cg  h
  gi|298674186|ref|YP_003725936.1|  5 EYIEVCPVCGSSH 17
                                      5666899999877 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.05
                     zf-NADH-PPase 23 vCpaCgle 30
                                      +C +Cg++
  gi|298674186|ref|YP_003725936.1| 31 HCKNCGYI 38
                                      8*****86 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1    0.0038       3.4      13      23 ..       9      19 ..       6      21 .. 0.70
   2 ?    3.7   0.0     0.066        59      13      18 ..      31      36 ..      28      38 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0038
                           DUF35_N 13 rCpdCGtvqfP 23
                                       Cp CG+ +++
  gi|298674186|ref|YP_003725936.1|  9 VCPVCGSSHWY 19
                                      47777777765 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.066
                           DUF35_N 13 rCpdCG 18
                                      +C++CG
  gi|298674186|ref|YP_003725936.1| 31 HCKNCG 36
                                      899999 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.026        23      29      35 ..       8      14 ..       1      17 [. 0.59
   2 ?    5.8   0.1     0.012        10      16      25 ..      29      38 ..      26      40 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.026
                                      SS-CCCC CS
                              RecR 29 dlCaICs 35
                                      ++C++C 
  gi|298674186|ref|YP_003725936.1|  8 EVCPVCG 14
                                      3677775 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.012
                                      -EE-TTT--E CS
                              RecR 16 vrhCsrCgnl 25
                                      + hC++Cg +
  gi|298674186|ref|YP_003725936.1| 29 LYHCKNCGYI 38
                                      679****976 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.2     0.011       9.5       3      13 ..      10      20 ..       8      22 .. 0.88
   2 ?    5.5   0.4     0.018        16      28      36 ..      29      37 ..      26      38 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.011
                           TFIIS_C  3 CpkCgsreayf 13
                                      Cp Cgs   y+
  gi|298674186|ref|YP_003725936.1| 10 CPVCGSSHWYY 20
                                      ******99987 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.018
                           TFIIS_C 28 fykCtkCgh 36
                                       y C++Cg+
  gi|298674186|ref|YP_003725936.1| 29 LYHCKNCGY 37
                                      599****96 PP

>> Cys_rich_CPXG  Cysteine-rich CPXCG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.3   0.00049      0.44      20      32 ..       3      15 ..       1      22 [. 0.87
   2 ?    1.2   0.5       0.4   3.6e+02       1      16 [.      30      45 ..      30      58 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00049
                     Cys_rich_CPXG 20 dqeYieDCqvCCr 32
                                      ++eYie C+vC +
  gi|298674186|ref|YP_003725936.1|  3 EEEYIEVCPVCGS 15
                                      789********86 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.4
                     Cys_rich_CPXG  1 iqCPyCgeeievlvDl 16
                                      ++C +Cg    + v++
  gi|298674186|ref|YP_003725936.1| 30 YHCKNCGYIGPLIVEA 45
                                      6788898665555554 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.5    0.0062       5.6       5      10 ..      10      15 ..       8      17 .. 0.75
   2 ?    4.2   2.5     0.034        30      18      24 ..      31      37 ..      30      37 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0062
                       zf-ribbon_3  5 CPnCGa 10
                                      CP CG+
  gi|298674186|ref|YP_003725936.1| 10 CPVCGS 15
                                      999987 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.034
                       zf-ribbon_3 18 vCpyCGt 24
                                      +C++CG+
  gi|298674186|ref|YP_003725936.1| 31 HCKNCGY 37
                                      7999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       908  (0.0506442); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 525.48
//
Query:       gi|298674187|ref|YP_003725937.1|  [L=315]
Description: hypothetical protein Metev_0211 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-32  111.9   0.1    3.7e-32  111.2   0.1    1.4  1  DUF523    Protein of unknown function (DUF523)
    3.4e-25   88.6   1.2      6e-25   87.8   1.2    1.4  1  DUF1722   Protein of unknown function (DUF1722)


Domain annotation for each model (and alignments):
>> DUF523  Protein of unknown function (DUF523)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.2   0.1   4.1e-36   3.7e-32       1     137 []       9     150 ..       9     150 .. 0.91

  Alignments for each domain:
  == domain 1  score: 111.2 bits;  conditional E-value: 4.1e-36
                            DUF523   1 ilvSaCLlgekvrydgkakksevleeelkelvkeelvpvCPEvaggLptPRepael.....akr.vlkkegedvtea 71 
                                       i++S+C+ +e +ry+g+  k+ ++e+  k ++  +++pvCPE+a+g+++PRep+++     +kr +++++g+d+te+
  gi|298674187|ref|YP_003725937.1|   9 IVISKCIEFEVCRYNGQIIKCPFIEK-TKPYM--NFIPVCPECAIGMGVPREPIDIiiegnKKRlIQTSTGKDFTEK 82 
                                       89*******************99998.999**..**************************9778899********** PP

                            DUF523  72 lekgaeealeelkeeeikgailkekSPSCGveki..Y..dgtfskklvegeGvfaallkeegievpseee 137
                                       ++++  +++++l+  +i+g++lk+kSPSCG++++  Y  + +++  +++ +G+f + + + +++++ e+e
  gi|298674187|ref|YP_003725937.1|  83 MHRFNYSYFKSLN--NIDGFLLKSKSPSCGIGNVkaYadSKKLKLITTTENGFFGDEVVNYYPSLAREDE 150
                                       **********999..6******************9995323444444889**********9999998875 PP

>> DUF1722  Protein of unknown function (DUF1722)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.8   1.2   6.7e-29     6e-25       2     117 .]     190     305 ..     190     305 .. 0.99

  Alignments for each domain:
  == domain 1  score: 87.8 bits;  conditional E-value: 6.7e-29
                           DUF1722   2 yllmahsqkeyrelgrlvanakkepleelaeeYeellmealskpatrkkhinvlqhilgyfkkklsaeekqelleli 78 
                                       +l+ a++++e + +++++++ +++++ +++eeY+++l++++ +p++++ +i+ +  i+ +f++ +s++ek  ++e i
  gi|298674187|ref|YP_003725937.1| 190 LLFKAYNPDEKKIMDNIISKIESNNPVNVVEEYRNHLYKLFVHPPKPNDYIEFMIEIFNQFSNLISNQEKLLFMENI 266
                                       6899************************************************************************* PP

                           DUF1722  79 ekYregkvplsvpltlLkhyarkydneylleqtylnpyP 117
                                       ++Y+egk++ls+  +lLk+++++ +n+  ++q+++npyP
  gi|298674187|ref|YP_003725937.1| 267 QRYKEGKITLSTNRKLLKSLIQRAGNTSYADQSFFNPYP 305
                                       **************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       821  (0.0457917); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2252.94
//
Query:       gi|298674188|ref|YP_003725938.1|  [L=569]
Description: glutamyl-tRNA synthetase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-62  211.1   0.0    2.2e-62  210.8   0.0    1.1  1  tRNA-synt_1c    tRNA synthetases class I (E and Q), catalytic
    1.6e-28   99.8   0.0    2.8e-28   99.0   0.0    1.4  1  tRNA-synt_1c_C  tRNA synthetases class I (E and Q), anti-codo
  ------ inclusion threshold ------
       0.13   12.7   0.2       0.27   11.7   0.2    1.5  1  FOXO-TAD        Transactivation domain of FOXO protein family


Domain annotation for each model (and alignments):
>> tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.8   0.0   3.6e-66   2.2e-62       1     310 [.     103     409 ..     103     413 .. 0.95

  Alignments for each domain:
  == domain 1  score: 210.8 bits;  conditional E-value: 3.6e-66
                                       S-EEEE---SSSS-BHHHHHHHHHHHHHHHHTT-EEEEEE--SSCC..C--HHHHHHHHHHHHHTT---SSEEEEGG CS
                      tRNA-synt_1c   1 kVrtRfaPePtGyLHiGhakaallnylfAknnnGkfilRieDTdpe..rekeeaeesiledlkwlgikwdekptyqs 75 
                                       +V+ RfaP+P+G + +G+ + +++n  + k++nG+fi+R++DTdp+  r   ea +  +ed kwlg ++ +k++y+s
  gi|298674188|ref|YP_003725938.1| 103 EVVMRFAPNPNGPPTLGSTRGIVVNSEYVKKYNGTFIIRFDDTDPQtkRPMMEAYDWYIEDCKWLGAEP-DKVVYAS 178
                                       699*****************************************9622566789999************.77***** PP

                                       GGHHHHHHHHHHHHHTTSEEEE-STHHHHHHHHCCSSHSS-TTTTS-HHHHHHHHHHHHHTTHSTTTS-EEEESSBT CS
                      tRNA-synt_1c  76 drfdelkkyaeeLikkGkAYvcectkeeleeereeqeklgskerdrydeenlklfeeemkkgkaegekavvRlkide 152
                                       dr   +++yae+Li+ G AYvc+c+ +e ++++ +  k+++++r+++ e+nl  + ++m +g++ +++av+R+k d 
  gi|298674188|ref|YP_003725938.1| 179 DRIPVYYEYAEKLIEMGNAYVCFCKGDEFKKYKDN--KKACPHRNQSPEDNLYYW-NNMLNGEYGEKEAVLRIKTDI 252
                                       *********************************99..99999*************.89******************9 PP

                                       TSS.GGGSSTEEEEEEESGGGSBTTTBTSTSEEE-HHHHHHHHHHHTT-SEEEEEGGGGCCHHHHHHHHHHTT-S.- CS
                      tRNA-synt_1c 153 ess.vefrDlvrgriklepqeihdlvivksdiyPtYdfavvidDaleeithvlrteefldntpkyiwllealglevp 228
                                       +++  ++rD  + ri  ++ +  + v  k+ + P  df  +i D   e+ h++r+++ +d+++++  ++e++g++ p
  gi|298674188|ref|YP_003725938.1| 253 QHKdPALRDFGAFRIIKTS-HPRPEVDGKYVVWPLLDFEGAIEDLECEVNHIIRGKDLRDSERRQRYIYEYFGWKYP 328
                                       9999***********9888.66788999************************************************* PP

                                       EEEEEE--EEETTSB-SHHHHHHHHHTTSSSSTT-TTSCBHHHHHHCTB-HHHHHHHHHHHCCCSSS.EEEEHHHHH CS
                      tRNA-synt_1c 229 pfiheylrlnlekkklSKRklsllvdekqvkewddlreallnflrrlGwtpekerelftreeliksfdlnresksle 305
                                       +  h   +   e  k S   ++ ++++ ++ +wdd+ ++++++lrr+G++pe++r+++   ++ + + ++++ +sl 
  gi|298674188|ref|YP_003725938.1| 329 KTTHWGRVKIHEFGKFSTSSIAKSIENGEYLGWDDPALPTIRALRRRGIQPEAIRKFMIDMGVGETD-ISISLESLY 404
                                       ****999999999**************************************************9998.888888887 PP

                                       HHHHH CS
                      tRNA-synt_1c 306 afdrk 310
                                       a +rk
  gi|298674188|ref|YP_003725938.1| 405 AENRK 409
                                       77766 PP

>> tRNA-synt_1c_C  tRNA synthetases class I (E and Q), anti-codon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.0   0.0   4.6e-32   2.8e-28       1     174 []     415     556 ..     415     556 .. 0.95

  Alignments for each domain:
  == domain 1  score: 99.0 bits;  conditional E-value: 4.6e-32
                    tRNA-synt_1c_C   1 ApRymaVldpvkvtienlpegkeeelevplhpknpelgtrkvpfskeiyiereDakrlkpgeevrLkelynikveev 77 
                                       A+Ry++V++pv+++i++++   + +++++lhpk +++g+r++++++++y+ +eD++++  g+++rLk+lyni+v++ 
  gi|298674188|ref|YP_003725938.1| 415 ANRYFFVWNPVELEITGVE---PRNVKLSLHPK-EKRGYRELEIGSKLYVCQEDIDSINVGDKLRLKDLYNIEVTSL 487
                                       89**************776...89*********.9***************************************999 PP

                    tRNA-synt_1c_C  78 ekdesgevtelkleydgesleearkkkg.iihWvsaeeaveaevrlYdrLfkeeededfllnpdslkvleeglaepa 153
                                       +         lk++y ++s+e  +k +  iihW++  + v++                +++ pd++    eg++e  
  gi|298674188|ref|YP_003725938.1| 488 N--------PLKARYLDDSVERIKKANLpIIHWIPV-NGVSV----------------KVIAPDGQ---YEGFGEHG 536
                                       3........5789*******99899999*******7.89999................9******9...69****** PP

                    tRNA-synt_1c_C 154 lanlkkgdivQfeRiGyfrvd 174
                                       +a+ +++++vQfeR+G++r+d
  gi|298674188|ref|YP_003725938.1| 537 IAD-EVDSVVQFERFGFCRID 556
                                       ***.***************98 PP

>> FOXO-TAD  Transactivation domain of FOXO protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   4.5e-05      0.27       8      33 ..     287     313 ..     286     314 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.5e-05
                          FOXO-TAD   8 LDldmfqesLeCDvdsIir.ndLmdgd 33 
                                       LD + ++e+LeC+v  Iir +dL d++
  gi|298674188|ref|YP_003725938.1| 287 LDFEGAIEDLECEVNHIIRgKDLRDSE 313
                                       899999************966888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (569 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 4229.27
//
Query:       gi|298674189|ref|YP_003725939.1|  [L=101]
Description: hypothetical protein Metev_0213 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0055   16.5   0.2      0.011   15.5   0.2    1.5  1  HTH_5          Bacterial regulatory protein, arsR family
     0.0059   16.5   0.0       0.01   15.7   0.0    1.3  1  TrmB           Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.017   14.5   0.1      0.024   14.0   0.1    1.2  1  RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
       0.03   14.6   0.0      0.042   14.2   0.0    1.2  1  Rrf2           Transcriptional regulator
      0.055   13.4   1.0        0.1   12.5   0.1    2.0  2  HTH_12         Ribonuclease R winged-helix domain
      0.057   12.8   0.0       0.11   11.9   0.0    1.6  1  RepL           Firmicute plasmid replication protein (RepL)


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   3.8e-06     0.011       5      46 ..      17      59 ..      13      59 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.8e-06
                                      HHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  5 lkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      l +Lk + e g+  +  laee++++  +v++ L++L++++L++
  gi|298674189|ref|YP_003725939.1| 17 LLVLKKVIEkGPIGILRLAEETEMPTHKVRYSLRILEQENLIK 59
                                      56677777777777888************************95 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   3.5e-06      0.01       3      53 ..       9      59 ..       7      64 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.5e-06
                                      HCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                              TrmB  3 klGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVe 53
                                      +l L+e    v ++++++gp  +  +aee++ p  kv  +Lr Le+  l++
  gi|298674189|ref|YP_003725939.1|  9 ELELTERHLLVLKKVIEKGPIGILRLAEETEMPTHKVRYSLRILEQENLIK 59
                                      789*******************************************99987 PP

>> RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   7.9e-06     0.024      78     133 ..       6      59 ..       2      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.9e-06
                                       HHHHHTSXHHHHHHHHHHHHHXSSXEEHHHHHHTTGXXHHHHHHHHHHHHHTTXXE CS
                     RNA_pol_Rpc34  78 AkkktslsedeslVysiIeesGneGIwsrtiksklnLhksvvkkcLksLeskkyik 133
                                        +k  +l+e   lV++ + e G  GI +  + + + ++ + v+ +L++Le++++ik
  gi|298674189|ref|YP_003725939.1|   6 VNKELELTERHLLVLKKVIEKGPIGILR--LAEETEMPTHKVRYSLRILEQENLIK 59 
                                       567778889999*************985..89***********************9 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.4e-05     0.042       3      62 ..       6      66 ..       5      78 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.4e-05
                                      --HHHHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE.EETTT- CS
                              Rrf2  3 lsskteyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvk.svrGkg 62
                                      +++++e+  + ll+L+k  e++p+ +  +ae+++++ + ++  l+ L++++l+k s+ G+ 
  gi|298674189|ref|YP_003725939.1|  6 VNKELELTERHLLVLKKVIEKGPIGILRLAEETEMPTHKVRYSLRILEQENLIKpSIHGAT 66
                                      57788888899******************************************86667765 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   3.5e-05       0.1      27      49 ..      37      59 ..      17      69 .. 0.76
   2 ?   -2.7   0.0         2   5.9e+03      27      36 ..      82      91 ..      74      96 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.5e-05
                            HTH_12 27 gydigeravRyrLrkleergltr 49
                                      + ++ +  vRy Lr+le+++l++
  gi|298674189|ref|YP_003725939.1| 37 ETEMPTHKVRYSLRILEQENLIK 59
                                      445667789************98 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2
                            HTH_12 27 gydigeravR 36
                                         i+e++ R
  gi|298674189|ref|YP_003725939.1| 82 TKSIQEKTAR 91
                                      4445555544 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.6e-05      0.11      80     112 ..      33      65 ..      29     100 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.6e-05
                              RepL  80 elaeetgislktvsetlkileeanilkkkanGv 112
                                       +laeet++ ++ v+  l+ile+ n++k    G+
  gi|298674189|ref|YP_003725939.1|  33 RLAEETEMPTHKVRYSLRILEQENLIKPSIHGA 65 
                                       59************************9877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1034  (0.0576719); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 662.57
//
Query:       gi|298674190|ref|YP_003725940.1|  [L=247]
Description: ureidoglycolate lyase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-66  223.9   0.0    2.2e-66  223.6   0.0    1.1  1  FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
  ------ inclusion threshold ------
      0.091   12.6   0.0       0.18   11.7   0.0    1.4  1  KH_2           KH domain


Domain annotation for each model (and alignments):
>> FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.6   0.0   2.5e-70   2.2e-66       1     218 []      49     246 ..      49     246 .. 0.97

  Alignments for each domain:
  == domain 1  score: 223.6 bits;  conditional E-value: 2.5e-70
                                       .EEEEEEE--SHHHHHTTT.-SS-EEEEEEGGGE.EETTE..EE-TTSSSS-EE......EEEEEEEESS-B--T-- CS
                     FAA_hydrolase   1 kivcdglnyaehvreagkaaeeppdrhiplepvfflkrasslvgpgdpirrPagsekldyEvELavvigkplrevls 77 
                                       ki+c+glny++h++e+g    + p      +p +flk++ss++g  d+i+ P+ s++++yE+EL+vvigk++++v +
  gi|298674190|ref|YP_003725940.1|  49 KIICVGLNYQDHANELG---LDIPN-----KPLIFLKPSSSIIGNCDKIVHPKTSNHIEYEAELGVVIGKKCKHV-K 116
                                       69**************8...67777.....666******************************************.9 PP

                                       HHHHHTTEEEEEEEEEEE-SBGGG---.HHHHHHTGGGEEEEEE-B--B-.STT---SS-EEEEEETTEEEEEEEGG CS
                     FAA_hydrolase  78 veeAedaiaGytllnDvsaRdlqaeekaplgwflgksfdtftpiGpwivtpdeledpedlelrlrvngeevqdsntk 154
                                       ++   ++iaGyt +nDv+aRdlq+++    +w+++ksfdtf+p+Gp+i t+d++ + ++ ++++rvng + q+snt+
  gi|298674190|ref|YP_003725940.1| 117 ADSTNNVIAGYTCFNDVTARDLQKQDG---QWTRAKSFDTFAPVGPFIATADDI-NLHNANIKCRVNGITCQNSNTS 189
                                       9**************************...************************.689******************* PP

                                       GTTTSHHHHHHHHHHHH-B-TT-EEEEEES.......S--EE--TT-EEEEEETTTEEEEEEE. CS
                     FAA_hydrolase 155 dmifspaeliahlsagltLepGdliltGTpsgvgaeeeslkflkdgDeveveieglGelrnrVa 218
                                       ++if+++ li+ +s ++tL+pGd+i+tGTp+gvg        ++ gD ve+eieg+G+l n+V+
  gi|298674190|ref|YP_003725940.1| 190 NLIFGVPHLIEFISDIMTLQPGDIIATGTPPGVG-------KIHSGDIVEIEIEGIGTLSNEVV 246
                                       ********************************99.......4*******************995 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0     2e-05      0.18      24      48 ..      92     116 ..      79     120 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2e-05
                                       SCEEEEEEEESCHHHHHTGGGHHHH CS
                              KH_2  24 anrviiviresqpgivIGkgGsnik 48 
                                       ++  + +++e++ g+vIGk+ + +k
  gi|298674190|ref|YP_003725940.1|  92 PKTSNHIEYEAELGVVIGKKCKHVK 116
                                       5778899*************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1537.75
//
Query:       gi|298674191|ref|YP_003725941.1|  [L=213]
Description: ribosyldihydronicotinamide dehydrogenase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.4e-56  188.7   0.0    1.1e-55  188.4   0.0    1.0  1  Flavodoxin_2  Flavodoxin-like fold
    1.4e-11   44.3   0.0    4.1e-11   42.9   0.0    1.7  1  FMN_red       NADPH-dependent FMN reductase


Domain annotation for each model (and alignments):
>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.4   0.0   1.2e-59   1.1e-55       1     197 [.       1     209 [.       1     210 [. 0.91

  Alignments for each domain:
  == domain 1  score: 188.4 bits;  conditional E-value: 1.2e-59
                                       -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCC.T-----CCCCHC............C.HHHHTT CS
                      Flavodoxin_2   1 mkiLiinahprpeksfssalaqafvealekagphevtvrdLyad.flpvlttrdlaa............k.layeek 63 
                                       m++L+++ah++p ksf+s++ ++++ea+e+ g + v+v dLya+ f+pvl+++d+++            + +a+++ 
  gi|298674191|ref|YP_003725941.1|   1 MNVLYVYAHQEP-KSFNSSMKDTALEAFEERG-DSVKVSDLYAMnFDPVLDENDFKNrkytdifnpfleQlHANKTD 75 
                                       9***********.8******************.9******************************9988536555555 PP

                                       ..CHHHHHHHHHHHHCSSEEEEEEE-BTTB--HHHHHHHHHHS-TTTSC.EETTCS.SCCCCTTTTSEEEEEEEESS CS
                      Flavodoxin_2  64 ..padveseqiekllaadaivlqfPlwwfgvPailKgwiDrvltagfaf.yteegg.egrgggLkgkkalvivttGg 136
                                         ++d+++e  +k+ +ad +++qfP+++ g+Pai+KgwiDrv+++gfaf     ++ ++++g+Lkgkk ++++t+G+
  gi|298674191|ref|YP_003725941.1|  76 gfAPDIKAEM-DKINWADMLIFQFPIYFTGFPAIMKGWIDRVFSPGFAFnP--LTQsAYETGLLKGKKSMLVTTAGA 149
                                       655*******.**************************************44..444457899*************** PP

                                       -GGGSSTTSSS-S-HHHHHHH.HHHHHHHTT-EEEEEEEEESCTCCCHHHHHHHHHHHHHHH CS
                      Flavodoxin_2 137 peesyqerglegaamdellpp.lrgilgfiGikdvepvlvegvagaedeealaealerleel 197
                                       +++ y++ g +g ++ ell+   + +l+f+G++++++++v+g+++ + e++ +++ler++el
  gi|298674191|ref|YP_003725941.1| 150 DKDWYSKGGMHG-DIHELLKSiTHCTLEFTGLEVLPTHVVYGASNLS-EDDAKKELERYREL 209
                                       ******988887.********999******************87766.77789999999884 PP

>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.0   4.6e-15   4.1e-11       1     120 [.       1     149 [.       1     154 [. 0.86

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 4.6e-15
                                       -EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS..--..---HCHGHT...................C CS
                           FMN_red   1 mkilvisGSlrkgsntrklaewaaealkeagaevelidladl.ilpcalcdkdlese...................g 57 
                                       m++l +++   ++s++  + + a+ea++e+g  v++ dl  +   p  ++d+ + ++                    
  gi|298674191|ref|YP_003725941.1|   1 MNVLYVYAHQEPKSFNSSMKDTALEAFEERGDSVKVSDLYAMnFDP--VLDENDFKNrkytdifnpfleqlhanktD 75 
                                       89****************************9999999999987777..44444433346666777777777778889 PP

                                       GGSHHHHHHHHHHHH-SCEEEEEEECTTCE-HHHHHHHHCHT-............SSCHCCTT-EEEEEEE-SS CS
                           FMN_red  58 qtsddvaellekiaaadaliivtPeYngsysgllKnalDrlsr...........trgkkelrgKpvalvavggg 120
                                       +  +d+++  +ki++ad+li+  P+Y+ ++++++K  +Dr+              ++   l+gK  +lv+++g 
  gi|298674191|ref|YP_003725941.1|  76 GFAPDIKAEMDKINWADMLIFQFPIYFTGFPAIMKGWIDRVFSpgfafnpltqsAYETGLLKGKKSMLVTTAGA 149
                                       999999***********************************879999999999999999999999999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1372.12
//
Query:       gi|298674192|ref|YP_003725942.1|  [L=38]
Description: zinc finger C2H2-type domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-07   30.0   2.7    6.3e-07   29.7   2.7    1.1  1  zf-C2H2_4        C2H2-type zinc finger
    2.3e-06   27.8   3.2    2.8e-06   27.5   3.2    1.1  1  zf-C2H2          Zinc finger, C2H2 type
    1.8e-05   25.0   0.3      3e-05   24.3   0.3    1.4  1  zf-met           Zinc-finger of C2H2 type
      2e-05   24.4   2.3    2.6e-05   24.1   2.3    1.2  1  zf-C2H2_6        C2H2-type zinc finger
      3e-05   24.2   1.2    5.4e-05   23.4   1.2    1.4  1  zf-C2H2_jaz      Zinc-finger double-stranded RNA-binding
    0.00052   20.3   8.5      0.081   13.4   1.4    2.1  2  zf-H2C2_2        Zinc-finger double domain
    0.00085   19.6   2.7    0.00097   19.4   2.7    1.0  1  zf-C2H2_2        C2H2 type zinc-finger (2 copies)
     0.0081   16.9   0.8     0.0093   16.7   0.8    1.1  1  MRNIP            MRN-interacting protein
  ------ inclusion threshold ------
      0.013   14.7   2.5      0.013   14.7   2.5    1.0  1  Actin_micro      Putative actin-like family
      0.023   14.5   0.4      0.029   14.3   0.4    1.2  1  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
      0.045   14.1   0.5      0.045   14.1   0.5    1.1  1  Lar_restr_allev  Restriction alleviation protein Lar
        1.3    8.9   7.4        2.7    7.9   7.4    1.7  1  zf-C2H2_3        zinc-finger of acetyl-transferase ESCO


Domain annotation for each model (and alignments):
>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   2.7   4.2e-10   6.3e-07       1      24 []      12      35 ..      12      35 .. 0.99

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 4.2e-10
                         zf-C2H2_4  1 fkCpiCgksFsskkaLlrHlkthH 24
                                      f+C++C  +F++++++ rH+k+hH
  gi|298674192|ref|YP_003725942.1| 12 FECKVCEMTFPTRQDYERHMKKHH 35
                                      89********************** PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   3.2   1.9e-09   2.8e-06       1      23 []      12      34 ..      12      35 .. 0.95

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.9e-09
                                      EEETTTTEEESSHHHHHHHHHCC CS
                           zf-C2H2  1 ykCpdCgksFkrksnLkrHirtH 23
                                      ++C++C ++F+++ +++rH+++H
  gi|298674192|ref|YP_003725942.1| 12 FECKVCEMTFPTRQDYERHMKKH 34
                                      89********************6 PP

>> zf-met  Zinc-finger of C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.3     2e-08     3e-05       1      21 [.      12      32 ..      12      34 .. 0.95

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 2e-08
                            zf-met  1 fyCelCnvtfnsesqlksHlq 21
                                      f+C++C +tf  +++++ H++
  gi|298674192|ref|YP_003725942.1| 12 FECKVCEMTFPTRQDYERHMK 32
                                      89*****************97 PP

>> zf-C2H2_6  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   2.3   1.7e-08   2.6e-05       2      26 ..      12      36 ..      11      37 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.7e-08
                         zf-C2H2_6  2 heCsvCsksFpslqaLggHkksHrk 26
                                      +eC+vC  +Fp+ q+ + H+k H++
  gi|298674192|ref|YP_003725942.1| 12 FECKVCEMTFPTRQDYERHMKKHHE 36
                                      9*******************99986 PP

>> zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   1.2   3.6e-08   5.4e-05       1      22 [.      11      32 ..      11      34 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3.6e-08
                                      ECBBTTTTBBBSSHHHHHCCTT CS
                       zf-C2H2_jaz  1 qfYCvlCdKyFksenaldnHlk 22
                                      +f+C++C+ +F + ++++ H+k
  gi|298674192|ref|YP_003725942.1| 11 KFECKVCEMTFPTRQDYERHMK 32
                                      69*******************9 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   1.4   5.4e-05     0.081      10      24 ..       7      21 ..       3      23 .. 0.85
   2 !   11.8   0.9   0.00017      0.26       1      10 [.      26      35 ..      26      38 .] 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.4e-05
                         zf-H2C2_2 10 tgekpyeCplCdkaF 24
                                      ++e+++eC++C  +F
  gi|298674192|ref|YP_003725942.1|  7 KKENKFECKVCEMTF 21
                                      68999*******999 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00017
                         zf-H2C2_2  1 nLrrHirkHt 10
                                      +++rH++kH+
  gi|298674192|ref|YP_003725942.1| 26 DYERHMKKHH 35
                                      589******9 PP

>> zf-C2H2_2  C2H2 type zinc-finger (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   2.7   6.5e-07   0.00097      45      73 ..       6      34 ..       3      37 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 6.5e-07
                         zf-C2H2_2 45 ekieekleClyCekefkslealreHmkkk 73
                                      ek e+k+eC +Ce +f ++++++ Hmkk+
  gi|298674192|ref|YP_003725942.1|  6 EKKENKFECKVCEMTFPTRQDYERHMKKH 34
                                      566789********************875 PP

>> MRNIP  MRN-interacting protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.8   6.2e-06    0.0093      14      39 ..       5      30 ..       3      36 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.2e-06
                             MRNIP 14 qvkKskkwkCkvCnekqslkkvygsg 39
                                       +kK++k++CkvC+     ++ y + 
  gi|298674192|ref|YP_003725942.1|  5 SEKKENKFECKVCEMTFPTRQDYERH 30
                                      579***********998888888765 PP

>> Actin_micro  Putative actin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   2.5   8.8e-06     0.013     220     249 ..       6      36 ..       3      38 .] 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 8.8e-06
                       Actin_micro 220 lkekkefsCkvCdvkfev.ekiseHllkkHi 249
                                        k++++f+CkvC++ f + ++ + H++k+H 
  gi|298674192|ref|YP_003725942.1|   6 EKKENKFECKVCEMTFPTrQDYERHMKKHHE 36 
                                       58899***********9999*******9995 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.4   1.9e-05     0.029      15      35 ..       6      25 ..       2      26 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.9e-05
                                      ECSCCCEEEESSSS-EEESSC CS
                    RNA_POL_M_15KD 15 edkegknfeCrqCgYeepadq 35
                                      e+ke+k feC  C   +p+ q
  gi|298674192|ref|YP_003725942.1|  6 EKKENK-FECKVCEMTFPTRQ 25
                                      445554.*********99865 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.5     3e-05     0.045      25      53 ..       8      33 ..       1      37 [. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3e-05
                   Lar_restr_allev 25 igqcvyCadCgastpwfkiaedeaeaeke 53
                                      ++  ++C+ C++   +f++++d+++++k+
  gi|298674192|ref|YP_003725942.1|  8 KENKFECKVCEM---TFPTRQDYERHMKK 33
                                      233799******...9**********998 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   7.4    0.0018       2.7       9      25 ..       7      23 ..       1      37 [. 0.59

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0018
                         zf-C2H2_3  9 ksfgasq..CkeCgMvYnp 25
                                      k+ +  +  Ck+C+M++  
  gi|298674192|ref|YP_003725942.1|  7 KKEN--KfeCKVCEMTFPT 23
                                      3334..355******9854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       864  (0.0481901); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 261.76
//
Query:       gi|298674193|ref|YP_003725943.1|  [L=659]
Description: glycoside hydrolase 15-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-23   82.7   0.5    2.7e-15   56.1   0.2    3.0  3  Glyco_hydro_15  Glycosyl hydrolases family 15


Domain annotation for each model (and alignments):
>> Glyco_hydro_15  Glycosyl hydrolases family 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   3.8e-06     0.068       7      56 ..     279     331 ..     274     346 .. 0.79
   2 !   56.1   0.2   1.5e-19   2.7e-15     123     358 ..     380     592 ..     373     605 .. 0.84
   3 !   11.5   0.0     5e-06     0.091     409     446 ..     606     644 ..     592     646 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.8e-06
                                       HHHCBCSTTSSBTTS-TT-B-S-S-BSSS.....B--SEEHHHHHHHHHHHH... CS
                    Glyco_hydro_15   7 ylrnvktlilleqnpvtGlliASpstsdp.....DYrytWvRDsvyvilavwglg 56 
                                       y r++   + +++    G++iA+++ ++       Y y W RD ++v+ +++++g
  gi|298674193|ref|YP_003725943.1| 279 YKRSLLIIKTQYDT--HGAIIAANDSDNLqfnrdTYSYMWSRDGALVAITLINAG 331
                                       55555544444443..6********66669***89****************9988 PP

  == domain 2  score: 56.1 bits;  conditional E-value: 1.5e-19
                                       -BTTHHHHHHHHHHHHHCTT..HCHCCCCHHHHTHHHHHHHHHHHTTS-......EE-TTS--ECEEHH..HHHHHH CS
                    Glyco_hydro_15 123 lQlDatslyllalaqmtasg..lqiistldevafvqnlvdYieaayktp......dfglWEenqgeselnassvgma 191
                                       +Q D t+l+++al+++++s   l +i++l e   +++ v++    y+ p      +++lWEe+ g+  +  +s+ + 
  gi|298674193|ref|YP_003725943.1| 380 IQEDETALVIYALWKYYESTgdLDFIKQLYEP-LIKKAVFFMDD-YRYPnslpreSYDLWEERRGIYTF--TSATVY 452
                                       79**************8877786666666655.5******9975.44444578889*************..****** PP

                                       HHHHHHHHHHHHCT-HHHHCCHHHHHHHHHHHHHSTTT..GGGEETTCCECECSCH.....HHHTTS--S-BCHHHH CS
                    Glyco_hydro_15 192 kAlleaideadlfgakgdaqlvektkdeilnklqgkygckrgfwplfntylildgsfaedkeqvqeyrealdaslll 268
                                       ++l  a ++  lf +++ ++++++    + n +      k  f+ ++ ++++  +  ++ +  ++e +   d+s++ 
  gi|298674193|ref|YP_003725943.1| 453 AGLASAEKISYLFNDTEICNICRSRYFPLRNAI-----LKELFDRDKEIFIRGLKY-QKSNPDQKEIDHTIDSSIYA 523
                                       ***********************9888888888.....777799999999999988.555556699999******** PP

                                       HHHHCS-TTS-TT-TT-TTTSHHHHHHHHHHHHHHHHHSGGGTT-STTS--SBTT--CGS.SSBSCT--BHHHHHHH CS
                    Glyco_hydro_15 269 lpelyfvpaddvdeeyqnpqsprllaqslyildsllsegflavgeldplvrRysedvkpd.klglsGrpyylctlwt 344
                                       + e +  +add          +++ +++++i+++l            + v Ry++d + +   +++G+p+ +ctlw 
  gi|298674193|ref|YP_003725943.1| 524 IFEFGLLSADD----------EKVKNTMKNIESKLWVNKS-------GGVARYENDHYHKvSDKSTGNPWIICTLW- 582
                                       ***********..........*************988754.......3499999999985245899**********. PP

                                       HHHHHHHHHHHHHH CS
                    Glyco_hydro_15 345 vetlldelyekagk 358
                                           l++ y k+++
  gi|298674193|ref|YP_003725943.1| 583 ----LAKWYIKKSE 592
                                       ....6666666554 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 5e-06
                                       HHHH.S-TTS---SEE-TTT--EESSTT-HHHHHHHHHH CS
                    Glyco_hydro_15 409 avee.dnslgvLteevdvylgeliraqpllfsealllri 446
                                        v++ + ++g++ e+v+  + e+i+  pl++s+a+++ +
  gi|298674193|ref|YP_003725943.1| 606 WVADcSFETGIMPEQVNPLTRESISVAPLTWSHAEFVDT 644
                                       455658899**************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (659 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 4760.02
//
Query:       gi|298674194|ref|YP_003725944.1|  [L=145]
Description: hypothetical protein Metev_0218 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-31  107.1   0.3    6.5e-31  106.7   0.3    1.1  1  SnoaL     SnoaL-like polyketide cyclase
    2.6e-15   56.9   0.1    3.3e-15   56.6   0.1    1.2  1  SnoaL_2   SnoaL-like domain
  ------ inclusion threshold ------
      0.033   14.6   0.0      0.045   14.2   0.0    1.3  1  DUF4440   Domain of unknown function (DUF4440)


Domain annotation for each model (and alignments):
>> SnoaL  SnoaL-like polyketide cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.7   0.3   1.1e-34   6.5e-31      13     125 ..      28     138 ..      19     139 .. 0.94

  Alignments for each domain:
  == domain 1  score: 106.7 bits;  conditional E-value: 1.1e-34
                                       TT-HHHHHGTEEEEEEETCCTTTCECHHHHHHHHHHHHHHHCTTCEEEEEEEEEETTEEEEEEEEEEEESSEBTTBE CS
                             SnoaL  13 sgdldaldelvaedvvdhnpeeeparGlegfrafveelfkafPDlkvevedlvaegdkvaarltftGthtgeflGip 89 
                                        ++++ ++e++a d+v h    +++  ++++ +f+++l  a+ Dl+++ +d++aegdkv++r+t++Gth+g f+Gi+
  gi|298674194|ref|YP_003725944.1|  28 AWKPSVIKEVCASDYVIHFG--RETLTRDDLIEFMSMLHSALMDLRFTADDIIAEGDKVVTRWTASGTHQGVFQGIQ 102
                                       57889*************55..89999************************************************** PP

                                       -TT-EEEEEEEEEEEEETTEEEEEEEEECHHHHHHH CS
                             SnoaL  90 ptGkkvkfeeitllrvedGkIveewdviDllgllrQ 125
                                       ptG++v f++it+ r+e+G Ive w+ +D+l   +Q
  gi|298674194|ref|YP_003725944.1| 103 PTGNHVVFTGITISRIENGIIVEDWEEVDQLNFTQQ 138
                                       *******************************99999 PP

>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   0.1   5.5e-19   3.3e-15      13     101 ..      31     125 ..      18     126 .. 0.93

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 5.5e-19
                                       HHHHHHTEEEEEEEEETTSEEESHHHHHHHHHHHHHHEEEEEEEEEEEEEETTEEEEEEEEEEE.......EETTSS CS
                           SnoaL_2  13 ldalaalfapdvvwedpggelrGreairaffralfaafpdlrfeihdvvadgdrvavewtvtgt.......ipatgr 82 
                                       ++ + +++a d+v +    e+  r+++ +f+  l+ a+ dlrf+ +d++a+gd+v+++wt++gt       i +tg+
  gi|298674194|ref|YP_003725944.1|  31 PSVIKEVCASDYVIHFGR-ETLTRDDLIEFMSMLHSALMDLRFTADDIIAEGDKVVTRWTASGThqgvfqgIQPTGN 106
                                       5778999********964.6789****************************************************** PP

                                       EEEEEEEEEEEEETTEEEE CS
                           SnoaL_2  83 gvtvrgvdvfrvrdGkive 101
                                       +v ++g+++ r+++G ive
  gi|298674194|ref|YP_003725944.1| 107 HVVFTGITISRIENGIIVE 125
                                       *****************98 PP

>> DUF4440  Domain of unknown function (DUF4440)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   7.5e-06     0.045      19      83 ..      33      96 ..      19     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.5e-06
                                      HHHHCEEEEEEEE-TTS-EEEHHHHHHHHHCCHCEEEEEEEEEEEEEEETTEEEEEEEEEEEECC CS
                           DUF4440 19 alaallapdavlvgpsgtvldkeellealeagfaagrslelteeevrvlgdlAvvtgrytfegrg 83
                                       +++++a d  +++ + ++l++++l+e +   ++a  +l++t  ++   gd +v++++ + +++g
  gi|298674194|ref|YP_003725944.1| 33 VIKEVCASDY-VIHFGRETLTRDDLIEFMSMLHSALMDLRFTADDIIAEGDKVVTRWTASGTHQG 96
                                      5667777777.556567799************************************999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1001.77
//
Query:       gi|298674195|ref|YP_003725945.1|  [L=259]
Description: dihydroorotate dehydrogenase, electron transfer subunit, iron-sulfur cluster-binding domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-12   46.0   5.8    6.4e-12   45.1   5.8    1.5  1  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr
     0.0015   19.2   0.0     0.0067   17.1   0.0    2.0  1  NAD_binding_1    Oxidoreductase NAD-binding domain


Domain annotation for each model (and alignments):
>> DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   5.8   7.1e-16   6.4e-12       2      41 ..     207     240 ..     206     241 .. 0.93

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 7.1e-16
                                       ---SSSSSSS-TTEEEETTCTT.CEEETTTT-CEEECCCB CS
                   DHODB_Fe-S_bind   2 erMaCGvGaClgCvvktkggdggeykrvCkdGPvFdadev 41 
                                       ++ +CG+G+C++C+++ kg       rvCkdGPvF++ e+
  gi|298674195|ref|YP_003725945.1| 207 RYFKCGIGVCGACCIDPKG------LRVCKDGPVFKGTEL 240
                                       799**************86......8***********997 PP

>> NAD_binding_1  Oxidoreductase NAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   7.5e-07    0.0067       1     106 [.      97     186 ..      97     188 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 7.5e-07
                                       EEEEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGSTTHHHHHHHHHHCTTEEEEEEEESSCTTTSSSEESSH CS
                     NAD_binding_1   1 miagGtGiaPvrsvlraileeakdktkvvlvyGnrteedllyreeleelakklpgrlkvvavvsreeagweggkgrv 77 
                                       ++agG G aP+  + +  +++      v+ + G+r++ +l++ e++ ++     g l ++++    ++g +g  g+v
  gi|298674195|ref|YP_003725945.1|  97 LVAGGLGAAPLAPLAEYSFKN---GVDVTTILGARSSTELIFGERFSSA-----GDL-YITT----DDGTSGTCGFV 160
                                       79******************8...678*******************999.....433.3333....55566789*** PP

                                       HHHHHHHHHHHSSTTEEEEEECSHHHHHH CS
                     NAD_binding_1  78 qdalleellslkkeethvyvCGppgMika 106
                                       +d l  +l    ++ + +y CGp+ M ++
  gi|298674195|ref|YP_003725945.1| 161 TDIL-TNLNL--SDYDRIYTCGPEVMLRC 186
                                       *998.55555..799***********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1626.33
//
Query:       gi|298674196|ref|YP_003725946.1|  [L=302]
Description: dihydroorotate dehydrogenase family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.8e-63  213.5   1.3    4.5e-63  213.2   1.3    1.0  1  DHO_dh        Dihydroorotate dehydrogenase
      9e-08   31.6   0.9    1.3e-06   27.7   0.9    2.2  1  Dus           Dihydrouridine synthase (Dus)
    0.00032   20.2   1.5    0.00059   19.3   1.5    1.5  1  NMO           Nitronate monooxygenase
    0.00033   20.2   0.2    0.00085   18.8   0.0    1.7  2  His_biosynth  Histidine biosynthesis protein
     0.0086   15.1   1.1      0.012   14.6   1.1    1.3  1  IMPDH         IMP dehydrogenase / GMP reductase domain
  ------ inclusion threshold ------
      0.011   15.0   3.9      0.017   14.3   0.4    2.5  3  DUF561        Protein of unknown function (DUF561)
      0.071   12.4   0.2      0.071   12.4   0.2    2.1  2  ThiG          Thiazole biosynthesis protein ThiG
        0.1   12.0   2.3         22    4.4   0.1    3.3  4  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
       0.15   11.3   1.1          1    8.5   0.9    2.5  2  NanE          Putative N-acetylmannosamine-6-phosphate epimer


Domain annotation for each model (and alignments):
>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.2   1.3   2.3e-66   4.5e-63      12     295 .]      12     283 ..       2     283 .. 0.94

  Alignments for each domain:
  == domain 1  score: 213.2 bits;  conditional E-value: 2.3e-66
                                       SSSEEE-TTSSTTSSSHHHHHCTT.SSEEEEEEE-SS-B--S-S--EEEETTCTEEEE---S-BS-HHHHHHHHHHH CS
                            DHO_dh  12 knpiglAaGfdkegeeilkllklg.fgaieigsvtpkpqeGnpkPrvfrlkedrsvlNslGlnneGldavlekllkr 87 
                                       knp++lA+G+++ + + l+ ++ + +ga+ ++s++p p++G+ +P++++l+++  +lN++Gl+n+   + ++++++ 
  gi|298674196|ref|YP_003725946.1|  12 KNPVILASGIMGTTGASLTRMAYNgAGAVVTKSIGPVPKKGHSNPTMIELENG--FLNAMGLPNPSYTEFVQEIENA 86 
                                       8************999999998888****************************..*******************999 PP

                                       HHHHHCC.CEEEEEEE-TTSS.HHHHHHHHHHHHG.GGESEEEEES-SCTCC.TSCCCGCHHHHHHHHHHHHHHHHS CS
                            DHO_dh  88 rkeqeekkelginlskakktenavddyvevvrkig.pfadilelNvSsPntp.glrdlqekeelkaillkvvkevsk 162
                                       +++      ++i++s+   +    + +v+v+++++  + d +elNvS+P++  ++++++ ++ l +++++ v +v +
  gi|298674196|ref|YP_003725946.1|  87 KNNT----STPIIASIFAGD---TEGFVKVAEELSsANPDGFELNVSCPHAEgYGATIGCDSCLVEEITASVCDVID 156
                                       8773....479999997666...7***********8999*************889********************** PP

                                       SEEEEEE-SSSSHHHHHHHHHHHH.HHTECEEEE...BSEE--CTTCCGCCCCTTSSEEEEEGGGHHHHHHHHHHHH CS
                            DHO_dh 163 vpvlvKlaPdltdeekkdiadvll.elkldgiivtNttvqrlaidlkseknvkanktGGlsGkalkdialkvirely 238
                                       vpv+vKl+P++t+++ + +a++   ++ +  i+    tv+++ id+++  ++  n+ GGlsG+a+++ia+k +++ly
  gi|298674196|ref|YP_003725946.1| 157 VPVWVKLTPNVTNIVDIGKAAERGgADAVVSIN----TVRGMSIDINTGYPILGNRYGGLSGRAIRPIAVKCVYDLY 229
                                       **************9999998888777777777....899************************************* PP

                                       HHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHHHHHHH CS
                            DHO_dh 239 krlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikkeleelL 295
                                       + l+  ip++gvGG++  +Da+e+i+aGAs+vqv++a+  + + ++k i  ++e+ L
  gi|298674196|ref|YP_003725946.1| 230 ASLD--IPVVGVGGVSCWQDAVEMIMAGASAVQVGSAV-SQSMDVFKSISSGIEDYL 283
                                       ****..*******************************9.99**********999865 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.9   6.7e-10   1.3e-06      48     220 ..      86     269 ..      75     287 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 6.7e-10
                                       GGGGGTSCEEEEEE-S-HHHHHHHHHHHHHTT-SCEEEEESSTTEEETTEEEGGGGGGSHHHHHHHHHHHHCCSSS- CS
                               Dus  48 seeeeetplavQlggsdpallaeaAklvadlgadeIdlNvGCPskkvtrggaGaaLlrkpdlvaqivkavvkaveiP 124
                                        +++++tp++  +++ d +  ++ A+     + d+ +lNv CP      +g+Ga+   ++ lv++i + v + +++P
  gi|298674196|ref|YP_003725946.1|  86 AKNNTSTPIIASIFAGDTEGFVKVAEELSSANPDGFELNVSCPHA----EGYGATIGCDSCLVEEITASVCDVIDVP 158
                                       344555899*****************99999************86....6788888889****************** PP

                                       EEEEEESESSTTTC.HHHHHHHHHHCT-SEE....EEESS...............ECCCTT-C.G--CHHHHHHHHH CS
                               Dus 125 vtvkirigiddeeenalelakiveaaGaqal....tvHgR...............traqnyeg.tadweaIkevkqa 181
                                       v vk    +     n+++++k++e+ Ga+a+    tv g                    ++ + ++  + ++++  +
  gi|298674196|ref|YP_003725946.1| 159 VWVKLTPNVT----NIVDIGKAAERGGADAVvsinTVRGMsidintgypilgnryGGLSGRAIrPIAVKCVYDLYAS 231
                                       ***9876665....99*************99444445555*********9996554444555589999********* PP

                                       -SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCST CS
                               Dus 182 vsipviaNGdIkdaedaqaileetGadgvmigrgalgnP 220
                                       + ipv++ G++  ++da +++   Ga +v +g +  +  
  gi|298674196|ref|YP_003725946.1| 232 LDIPVVGVGGVSCWQDAVEMIMA-GASAVQVGSAVSQSM 269
                                       ********************999.*******98877665 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   1.5     3e-07   0.00059      52     224 ..      81     264 ..      64     270 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 3e-07
                               NMO  52 keirkvkaltdkPfgvnlflpkkdaadraekykkeleeaalelnieegvr..................fyrkvevvl 110
                                       +ei+++k+ t+ P+ + +f+   +     +++++  + ++ + + +++ +                      v  v 
  gi|298674196|ref|YP_003725946.1|  81 QEIENAKNNTSTPIIASIFAGDTEGFV--KVAEELSSANPDGFELNVSCPhaegygatigcdsclveeITASVCDVI 155
                                       666666666666666666654443332..244444444555555555555556666666665664443333444444 PP

                               NMO 111 dekvevvsfgfglpteevvarlkeagvvliptissvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpq 187
                                       d++v v  + +  +  +  ++ +++g+ ++++i +v  + + ++ G  +l   G   GG  G +++     ++ v  
  gi|298674196|ref|YP_003725946.1| 156 DVPVWVKLTPNVTNIVDIGKAAERGGADAVVSINTVRGMSIDINTGYPIL---GNRYGGLSG-RAIR-PIAVKCVYD 227
                                       44555555555555566666777788888888888888888888887766...999999999.4443.345777777 PP

                               NMO 188 vldavdiPviAaGGiidrrgvaaaLalGAsgvqigtr 224
                                           +diPv+  GG+   ++   ++ +GAs+vq+g++
  gi|298674196|ref|YP_003725946.1| 228 LYASLDIPVVGVGGVSCWQDAVEMIMAGASAVQVGSA 264
                                       888899*****************************98 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.6   3.1e+03     112     133 ..     173     193 ..     153     201 .. 0.60
   2 !   18.8   0.0   4.3e-07   0.00085      58     118 ..     218     278 ..     212     284 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.6
                                       HHHHHHHHCGGGEEEEEEEEEC CS
                      His_biosynth 112 ikelaekfgsqkivvaiDarrg 133
                                       i ++ae+ g+   vv+i + rg
  gi|298674196|ref|YP_003725946.1| 173 IGKAAERGGA-DAVVSINTVRG 193
                                       4455555444.56666666555 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 4.3e-07
                                       HHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHH CS
                      His_biosynth  58 reanldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpelikelaek 118
                                       r++  ++v  +  +++ipv   GG++  +d+ e++ aga+ v +g+a+ ++ +++k++++ 
  gi|298674196|ref|YP_003725946.1| 218 RPIAVKCVYDLYASLDIPVVGVGGVSCWQDAVEMIMAGASAVQVGSAVSQSMDVFKSISSG 278
                                       66778899999999******9***********************************99875 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   1.1   6.2e-06     0.012     195     241 ..     221     267 ..     137     274 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.2e-06
                                       HHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCCTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 195 AvaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGsllag 241
                                       Av  v++  ++ ++pv+  GG++  +d v  + aGa+av +Gs ++ 
  gi|298674196|ref|YP_003725946.1| 221 AVKCVYDLYASLDIPVVGVGGVSCWQDAVEMIMAGASAVQVGSAVSQ 267
                                       88889999999********************************9875 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.12   2.4e+02     187     217 ..      13      45 ..       4      60 .. 0.76
   2 ?   -2.5   0.0       1.1   2.3e+03      25      41 ..     166     182 ..     164     190 .. 0.84
   3 ?   14.3   0.4   8.8e-06     0.017     174     226 ..     221     274 ..     213     289 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.12
                            DUF561 187 lPvicasGlsdvt.vpl.alslgasGiGigsav 217
                                        Pvi asG+   t ++l  ++++ +G  + +++
  gi|298674196|ref|YP_003725946.1|  13 NPVILASGIMGTTgASLtRMAYNGAGAVVTKSI 45 
                                       59*******988733441477777777777666 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.1
                            DUF561  25 nveqvlkiaraaekaka 41 
                                       nv++++ i +aae++ a
  gi|298674196|ref|YP_003725946.1| 166 NVTNIVDIGKAAERGGA 182
                                       7899999****999887 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 8.8e-06
                            DUF561 174 tlastyeiskkvslPvicasGlsdvtvpla.lslgasGiGigsavsklndeeem 226
                                       ++ ++y +  ++++Pv+   G+s     +  + +gas + +gsavs+  d  + 
  gi|298674196|ref|YP_003725946.1| 221 AVKCVYDLYASLDIPVVGVGGVSCWQDAVEmIMAGASAVQVGSAVSQSMDVFKS 274
                                       5789*******************98877752578************98887553 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2      0.32   6.3e+02     151     202 ..     133     186 ..     123     197 .. 0.64
   2 ?   12.4   0.2   3.6e-05     0.071     169     214 ..     227     272 ..     210     285 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.32
                                       BSSSTTS----S-HHHHHHHHHH-SS-BEEES..---SHHHHHHHHHT.T-SEEE CS
                              ThiG 151 laapiGsglGllnkealkiiieeakvPvivDA..Gigspsdaaqamel.Gadavl 202
                                       ++a iG    l+++     +++ ++vPv v     + +  d+ +a e  Gadav+
  gi|298674196|ref|YP_003725946.1| 133 YGATIGCDSCLVEE-ITASVCDVIDVPVWVKLtpNVTNIVDIGKAAERgGADAVV 186
                                       67888888777654.4566788889998875311455566666666642456654 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 3.6e-05
                                       HHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHH CS
                              ThiG 169 iiieeakvPvivDAGigspsdaaqamelGadavllntavaeakdpv 214
                                        + +++++Pv+   G+   +da++ +  Ga+av + +av+++ d  
  gi|298674196|ref|YP_003725946.1| 227 DLYASLDIPVVGVGGVSCWQDAVEMIMAGASAVQVGSAVSQSMDVF 272
                                       467789***********************************99976 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1       3.4   6.9e+03     142     165 ..      16      40 ..      13      43 .. 0.50
   2 ?    1.2   0.0      0.11   2.2e+02      84     121 ..      84     122 ..      76     125 .. 0.70
   3 ?    4.1   0.0     0.013        27      19      59 ..     157     197 ..     144     202 .. 0.86
   4 ?    4.4   0.1     0.011        22     128     168 ..     222     262 ..     216     265 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3.4
                                       EEEESS--S.HHHHHHHCTT.SSEE CS
                      G3P_antiterm 142 iiaGGLiet.kedveealkaGaiav 165
                                       i+a+G++ t    ++++  +Ga av
  gi|298674196|ref|YP_003725946.1|  16 ILASGIMGTtGASLTRMAYNGAGAV 40 
                                       4555554330345555555555555 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.11
                                       HHHHHT.T--EEEEEE--SHHHHHHHHHHHHHHT-SEEE CS
                      G3P_antiterm  84 kkakkl.glltiqrlfliDssalekalkqiekskpdave 121
                                       ++ak++ +   i  +f  D++ + k+ + +++++pd  e
  gi|298674196|ref|YP_003725946.1|  84 ENAKNNtSTPIIASIFAGDTEGFVKVAEELSSANPDGFE 122
                                       445443134567788888888888888888888888766 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.013
                                       SSEEEE--EETTTHHHHHHHHHHTT-EEEEEGGGEET--SS CS
                      G3P_antiterm  19 vevvfllegdilnlkeiveklkkagkkvfvhiDlieGlskd 59 
                                       v v + l+ +++n+ +i + +++ g  ++v i+ ++G+s d
  gi|298674196|ref|YP_003725946.1| 157 VPVWVKLTPNVTNIVDIGKAAERGGADAVVSINTVRGMSID 197
                                       5666778899****************************976 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.011
                                       HHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE- CS
                      G3P_antiterm 128 pkvikeikkelkipiiaGGLietkedveealkaGaiavsts 168
                                        k++ ++  +l+ip++  G ++  +d  e++ aGa+av ++
  gi|298674196|ref|YP_003725946.1| 222 VKCVYDLYASLDIPVVGVGGVSCWQDAVEMIMAGASAVQVG 262
                                       56677788899******999******************875 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.59   1.2e+03      19      37 ..      78      96 ..      74     106 .. 0.78
   2 ?    8.5   0.9    0.0005         1     135     185 ..     223     274 ..     143     281 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.59
                                      ESHHHHHHHHTT--S-EEE CS
                              NanE 19 egvedikaikavvdlPiiG 37
                                      e v++i++ k+ ++ Pii 
  gi|298674196|ref|YP_003725946.1| 78 EFVQEIENAKNNTSTPIIA 96
                                      5578888888888888885 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0005
                                       HHHHHHH.HTT--EEEES---SHHHHHHHHTT--SEEEE-HHHH-HHHHHHH CS
                              NanE 135 alvkals.eaglkviaeGrintPekakkaieiGvdavvvGsaitrleeiakk 185
                                       + v +l  + ++ v+  G +   + a ++i  G+ av vGsa+ +  ++ k 
  gi|298674196|ref|YP_003725946.1| 223 KCVYDLYaSLDIPVVGVGGVSCWQDAVEMIMAGASAVQVGSAVSQSMDVFKS 274
                                       44555541447889999999999********************999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2013.65
//
Query:       gi|298674197|ref|YP_003725947.1|  [L=308]
Description: porphobilinogen deaminase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-71  239.3   0.0    3.5e-71  238.9   0.0    1.1  1  Porphobil_deam   Porphobilinogen deaminase, dipyromethane cof
    9.2e-11   42.0   0.1    2.1e-10   40.8   0.1    1.6  1  Porphobil_deamC  Porphobilinogen deaminase, C-terminal domain


Domain annotation for each model (and alignments):
>> Porphobil_deam  Porphobilinogen deaminase, dipyromethane cofactor binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.9   0.0     4e-75   3.5e-71       1     200 [.       3     204 ..       3     207 .. 0.95

  Alignments for each domain:
  == domain 1  score: 238.9 bits;  conditional E-value: 4e-75
                    Porphobil_deam   1 irigtRkSkLAlaqaelvaeaLke.eeeveivtiktkGDkildkpLakiggkglFtkeleeaLlegeidlaVhSlKD 76 
                                       + igtR+S LAl+q++ v ++Lke   ++ +++ikt+GD  +d+pL+++gg g+F++e++e++l+ge+d+aVhS+KD
  gi|298674197|ref|YP_003725947.1|   3 LIIGTRGSSLALTQTRRVSQMLKEeGVNTFLKIIKTSGDSFTDRPLHELGGVGAFVREIDERMLSGELDIAVHSMKD 79 
                                       57********************6533346999********************************************* PP

                    Porphobil_deam  77 lptelpeglelaavlkredprDvlvvks..sleelpegavvgTsSlRRkaqlkklrpdlevkdlRGnvdtRlrklde 151
                                       lpte pe+l + avlkr++p D+l++++  +l+elpegav+gT+SlRRk+q+ ++rpd++v++lRGn+dtRl+kl++
  gi|298674197|ref|YP_003725947.1|  80 LPTERPEELPTSAVLKRDSPFDALLTRDgsTLDELPEGAVIGTTSLRRKSQVLRYRPDFDVQSLRGNIDTRLKKLES 156
                                       *************************855679********************************************** PP

                    Porphobil_deam 152 geydaiiLAaAGLkRlgleerisevlspeellpavgQGalavevrkede 200
                                       g yd+iiLA+AGL+R+g++  +++ l++++++p++ QGa+av ++++de
  gi|298674197|ref|YP_003725947.1| 157 GIYDGIILAEAGLRRMGWDIPVHQ-LDTDHFCPSANQGAIAVVAKSGDE 204
                                       *****************9999998.********************9997 PP

>> Porphobil_deamC  Porphobilinogen deaminase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.1   2.3e-14   2.1e-10       3      69 ..     220     288 ..     218     291 .. 0.80

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 2.3e-14
                                       HHHHHHHHHHHTT--TTSSEEEEEEEETTE.EEEEEEEE-TTS..S.-EEEEEEEE.-GGGHHHHHHHH CS
                   Porphobil_deamC   3 evlaERallkeLeGGCsvPiGvyaeveaneelkLkglvlsldglks.aveeaeakg.eleeaeelGkkl 69 
                                       e   ER l+ + +GGC vPiG+yae +++e++ ++  vl+ldg+   av+++ + +  +eea elG +l
  gi|298674197|ref|YP_003725947.1| 220 ETEIERILIGNVGGGCIVPIGAYAEFVNDEKIHIRSEVLALDGSHYvAVDDVISADnYKEEANELGEEL 288
                                       5678***********************9999************87312333333335679999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1813.32
//
Query:       gi|298674198|ref|YP_003725948.1|  [L=425]
Description: glutamate-1-semialdehyde-2,1-aminomutase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-73  247.4   0.0    2.5e-73  247.1   0.0    1.0  1  Aminotran_3    Aminotransferase class-III
  ------ inclusion threshold ------
      0.021   14.0   0.0      0.027   13.6   0.0    1.3  1  Aminotran_1_2  Aminotransferase class I and II


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  247.1   0.0   2.8e-77   2.5e-73      10     376 ..      34     394 ..      26     421 .. 0.92

  Alignments for each domain:
  == domain 1  score: 247.1 bits;  conditional E-value: 2.8e-77
                                       CEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-. CS
                       Aminotran_3  10 llvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkg 86 
                                       ++  + a+G++++dvdg++y+D+  ++ +++lGhahP++ +a++eq+++ ++     +  e+ +klaek++++ p  
  gi|298674198|ref|YP_003725948.1|  34 PFYTESAQGSRIKDVDGNEYIDFCMGYGPNLLGHAHPEIKQAIAEQLDNGWLYG---TPLENEVKLAEKVTDAYPS- 106
                                       4667889*******************************************9988...788899************9. PP

                                       .SEEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TT CS
                       Aminotran_3  87 ldkvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkyp 163
                                       +d++ ++ sGseA+++A+++ar       +t k+ki++++g+fHG     l  +gs  +  tl +p++ +v+    +
  gi|298674198|ref|YP_003725948.1| 107 MDMLRFVSSGSEATMSAIRTARG------YTGKNKILKIEGGFHGTHDSVLVKAGS--GATTLGKPNSKGVPEEVTK 175
                                       ***********************......9*************************9..99999*********99999 PP

                                       BGGGTB-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTT.. CS
                       Aminotran_3 164 deevlkeneeeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGf.. 238
                                        + ++++n+      +e +++l++k  d+ aAvi+Ep+ g+ G + +++++l+++r++++++dv+li+DEv tGf  
  gi|298674198|ref|YP_003725948.1| 176 HTLQAPFND------IESMTELIEKNRDDMAAVIMEPVMGNIGPILPKENYLKEVRKVTEENDVVLIFDEVITGFrl 246
                                       99*******......89999999****************************************************88 PP

                                       TTTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTS...B--TTTT-HHHHHHHHHHHHHHHHTT CS
                       Aminotran_3 239 GrTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgs...hgsTfgGnplacavalavleiieeek 312
                                       +  G   A e+++v+pD++tl+K ++gG+p+ ++ +++e+m+++ap++   +++Tf+Gnp   ++ +a+++++e+e+
  gi|298674198|ref|YP_003725948.1| 247 AMGG---AQEYYNVTPDMTTLGKIVGGGMPVGVFGGKREIMDMVAPNGnvyQAGTFSGNPATLSAGIATMDVLENEN 320
                                       8888...***************************************99999************************** PP

                                       HHHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC...........HHHHHHHHHCTEE-EE CS
                       Aminotran_3 313 llenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevke...........keilkkakekGvlils 376
                                       + +  +++g+++++ L+++ ++     ev g   m+ + ++ +a ++             +++k++++ G+ + +
  gi|298674198|ref|YP_003725948.1| 321 VHDTLNKKGDEIRSCLSDIISDAGLDYEVSGISSMFKV-FFGKAPTNYqetlkcdksgyFDFFKRMLNDGIFLPP 394
                                       ********************999888899999999999.555554454578889998888899999999988655 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.1e-06     0.027     130     246 ..     183     290 ..     172     417 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.1e-06
                                       E-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHH.HHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHG CS
                     Aminotran_1_2 130 ldlealeealkeapegnkktkvilvesphNPtGtvatlee.leklldlakkynlllfvDeaYagfvfgsldavatra 205
                                       +d+e++ e+++++  + +    ++ e +  + G ++++e  l+++ ++++++ ++l++De+  gf +   +a++ + 
  gi|298674198|ref|YP_003725948.1| 183 NDIESMTELIEKNRDDMA---AVIMEPVMGNIGPILPKENyLKEVRKVTEENDVVLIFDEVITGFRLAMGGAQE-YY 255
                                       8***********777777...************999998747999999*************9999888334444.55 PP

                                       GSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHH CS
                     Aminotran_1_2 206 nveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrkl 246
                                       nv ++     +++l+K  G  G  vG + g+ ++ + ++  
  gi|298674198|ref|YP_003725948.1| 256 NVTPD-----MTTLGKIVG-GGMPVGVFGGKREIMDMVAPN 290
                                       55554.....447777665.244446666666655555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 3045.44
//
Query:       gi|298674199|ref|YP_003725949.1|  [L=325]
Description: porphobilinogen synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   1.2e-145  484.6   0.2   1.3e-145  484.5   0.2    1.0  1  ALAD        Delta-aminolevulinic acid dehydratase
  ------ inclusion threshold ------
       0.15   11.8   0.0       0.38   10.4   0.0    1.7  1  MukB_hinge  MukB hinge domain


Domain annotation for each model (and alignments):
>> ALAD  Delta-aminolevulinic acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  484.5   0.2  1.5e-149  1.3e-145       2     316 ..       5     322 ..       4     323 .. 0.98

  Alignments for each domain:
  == domain 1  score: 484.5 bits;  conditional E-value: 1.5e-149
                                       --GGGGGSSHHHHHHC-S----GGGEEEEEEEESS-SS-EE-TTSTT-EEEEGGGHHHHHHHHHHTT--EEEEEEE- CS
                              ALAD   2 krlrrlrksealrelvretrlsasdlilplfvkegeeekeeiksmpgvyrlsvdelvkeveelvklgikavllFgvp 78 
                                        r+rrlr+ + l++lvret+++a+dli+p+fv+e+ e+++e++smpg+y+l+vd +++e++e+ +lgi+++++Fgvp
  gi|298674199|ref|YP_003725949.1|   5 VRMRRLRQGK-LQNLVRETTITADDLICPVFVDENIETPQEVPSMPGTYKLPVDYAADEAKEISDLGIPSIMIFGVP 80 
                                       699***9987.9***************************************************************** PP

                                       SS-BSS-GGGGSTTSHHHHHHHHHHHH-..TTSEEEEEE-STTTBSS-SSSEE..ESS.EEHHHHHHHHHHHHHHHH CS
                              ALAD  79 eekdeegsealnedglvqrairaikeev..pelvvitDvclceytshGhcgil..eekevdndetlellakvavsqa 151
                                       ++kde+gs+a+ ++++vqra+r+i++++  +++++itDvclceyt+hGhcg++  +++e++nd tl ll k+avs+a
  gi|298674199|ref|YP_003725949.1|  81 ARKDESGSSAWGNNEVVQRAVRNIRNDIssRDMAIITDVCLCEYTTHGHCGVVdyDKEEILNDPTLPLLGKTAVSHA 157
                                       **************************996678*********************443666****************** PP

                                       HCT-SEEEE-S--TTHHHHHHHHHHHTT-TT-EEB---EEB--CGGHHHHHHHT---S.S--TTTSB-TT-HHHHHH CS
                              ALAD 152 eaGadivapSdmmDgrvaaireaLdeagfeevailsYsaKyaSafYgPFrdaaesapsfgdrktYqmdpansrealr 228
                                       eaGad+vapS+mmDg+v++ir++Ld+++fe+++i+sY+aKy SafYgPFrdaaes  sfgdr++Yqm+p+ns+ea+r
  gi|298674199|ref|YP_003725949.1| 158 EAGADMVAPSGMMDGMVESIRSELDNNNFENIPIMSYAAKYFSAFYGPFRDAAESGYSFGDRSSYQMNPSNSNEAIR 234
                                       ***************************************************************************** PP

                                       HHHHHHHTT-SBEEEES-TTGHHHHHHHHTT-SS-EEEEE-HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHTT-SE CS
                              ALAD 229 eveldleeGADivmvKPalaylDiirevkeefdlpvaayqvSGEYamikaaaengwldekkvvlEsllsikRAGadl 305
                                       eveld++eGADivmvKPal+ylDi+ ++k+e+++p+aay+vSGEYamikaaa+ngw+de+k+++Es++sikRAGad+
  gi|298674199|ref|YP_003725949.1| 235 EVELDIDEGADIVMVKPALPYLDILYRIKDELEMPTAAYNVSGEYAMIKAAAQNGWMDENKIIYESITSIKRAGADM 311
                                       ***************************************************************************** PP

                                       EEETTHHHHHH CS
                              ALAD 306 iltYfakevak 316
                                       iltYfak++ak
  gi|298674199|ref|YP_003725949.1| 312 ILTYFAKDMAK 322
                                       ********997 PP

>> MukB_hinge  MukB hinge domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   4.2e-05      0.38      31      68 ..     170     209 ..     157     211 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 4.2e-05
                        MukB_hinge  31 LlelaerlggvLLseiyddisled..apyfealyGplrkA 68 
                                       +  ++e +  +L  + +++i++    a+yf+a yGp r A
  gi|298674199|ref|YP_003725949.1| 170 MDGMVESIRSELDNNNFENIPIMSyaAKYFSAFYGPFRDA 209
                                       667788889999999*******744499**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2262.74
//
Query:       gi|298674200|ref|YP_003725950.1|  [L=416]
Description: glutamyl-tRNA reductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-41  142.2   0.5    2.4e-41  141.0   0.5    1.6  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    1.4e-37  128.7   0.1    3.4e-37  127.4   0.1    1.7  1  GlutR_N          Glutamyl-tRNAGlu reductase, N-terminal domai
    1.3e-21   76.8   1.1    3.2e-21   75.6   1.1    1.7  1  GlutR_dimer      Glutamyl-tRNAGlu reductase, dimerisation dom
    2.2e-10   41.0   0.1    6.7e-10   39.4   0.1    1.9  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    8.8e-08   32.5   0.0      2e-07   31.3   0.0    1.6  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    9.1e-07   28.4   0.3    2.1e-06   27.2   0.1    1.7  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
    2.3e-05   24.7   0.1    8.9e-05   22.9   0.1    2.0  2  NAD_binding_7    Putative NAD(P)-binding
    2.6e-05   24.1   0.1    5.2e-05   23.1   0.1    1.5  1  DFP              DNA / pantothenate metabolism flavoprotein
    3.6e-05   23.4   0.1     0.0025   17.4   0.0    2.3  2  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
    5.7e-05   23.9   0.1    0.00016   22.4   0.0    1.8  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
     0.0002   21.5   0.1    0.00054   20.1   0.1    1.8  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
    0.00076   18.8   0.9        0.1   11.9   0.3    3.1  3  THF_DHG_CYH_C    Tetrahydrofolate dehydrogenase/cyclohydrolas
     0.0012   18.4   0.1     0.0028   17.2   0.1    1.6  1  Glu_dehyd_C      Glucose dehydrogenase C-terminus
     0.0028   17.6   0.1     0.0055   16.6   0.1    1.5  1  NAD_binding_10   NAD(P)H-binding
     0.0031   17.2   0.0     0.0067   16.1   0.0    1.7  1  ApbA             Ketopantoate reductase PanE/ApbA
     0.0065   17.0   4.5       0.15   12.6   0.9    3.2  3  V-ATPase_G       Vacuolar (H+)-ATPase G subunit
     0.0087   15.4   0.4      0.019   14.2   0.4    1.7  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
     0.0098   16.1   1.2      0.047   13.9   0.6    2.5  2  TrkA_N           TrkA-N domain
  ------ inclusion threshold ------
      0.015   14.3   0.1      0.026   13.5   0.1    1.3  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil
      0.024   14.5   0.1      0.085   12.7   0.1    2.0  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
      0.026   14.8   0.6       0.12   12.6   0.1    2.4  3  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.028   14.0   0.1      0.064   12.8   0.1    1.6  1  NmrA             NmrA-like family
      0.055   13.4   0.1       0.41   10.6   0.1    2.3  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
      0.057   12.1   1.0       0.12   11.1   0.6    1.8  2  Oxidored_nitro   Nitrogenase component 1 type Oxidoreductase
       0.12   12.5   0.1       0.44   10.7   0.1    2.1  1  SAM_Exu          Exuperantia SAM-like domain


Domain annotation for each model (and alignments):
>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.0   0.5   3.3e-44   2.4e-41       1     138 []     163     297 ..     163     297 .. 0.98

  Alignments for each domain:
  == domain 1  score: 141.0 bits;  conditional E-value: 3.3e-44
                                       HHHHHHHS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-S CS
                      Shikimate_DH   1 elakkkleslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaead 77 
                                       +la ++l+ l++k++l+iG+Gem++lva++L++k ++ v  aNRt+e ak+laee++g+   a+ +++++e++++ad
  gi|298674200|ref|YP_003725950.1| 163 DLADEILGGLTGKNILVIGTGEMGTLVARALAHKDMDVVYLANRTFETAKQLAEEIGGD---AVLFDNIDECIRNAD 236
                                       5899*****************************************************99...*************** PP

                                       EEEE-SSSSS-SB-HHHHHCCHHH.S..EEEEE--SS-SB-TTGGGSTTCCCEEHHHHHHH CS
                      Shikimate_DH  78 vvisataseepilekeeveealkkrkkplllvDiavPRdvepevaeledvrlytvDdLkev 138
                                       vvi+ata+++++l+k+ +e+a+++r+k+lll+Dia PRd+epe++e+e+v+l+++D L+++
  gi|298674200|ref|YP_003725950.1| 237 VVICATAAPHFVLRKSTIEKAMDDRNKELLLIDIATPRDIEPEISEIEHVKLHNIDSLRRI 297
                                       **********************************************************986 PP

>> GlutR_N  Glutamyl-tRNAGlu reductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.4   0.1   4.8e-40   3.4e-37       3     146 .]      10     148 ..       8     148 .. 0.86

  Alignments for each domain:
  == domain 1  score: 127.4 bits;  conditional E-value: 4.8e-40
                           GlutR_N   3 inhktapvelreklafseeelkellkel.ee.kvkeaviLsTCNRtEiylsaeeeeeaseellellaevsleelkek 77 
                                       i+h++a++e +ek++    +++ +lk+l ++  v e+++L+TCNR+E+y+++ +   as+ l+++ +++     ++ 
  gi|298674200|ref|YP_003725950.1|  10 ITHTKASIEEMEKAWHG--DIEYVLKSLySHeYVYECAVLKTCNRVEVYVVSPK---ASSVLFHFAKDM--GASSHI 79 
                                       89************997..5666777775443677**************75544...566667777666..334468 PP

                           GlutR_N  78 lyvlegeeavrHlfrVasGLdSlvlGEdqIlgQvkeayelakeagtlgkvLerlfqkaikvakrvrtet 146
                                       ++++++e++++Hl+r+asGL+S+++GEdqIlgQ+k+ y++ak+ gt+g+ L++ f+kai+v+k++rtet
  gi|298674200|ref|YP_003725950.1|  80 VEFYDHEDSLKHLLRLASGLESMIVGEDQILGQIKDLYTTAKNVGTIGPALDTAFSKAIQVGKKARTET 148
                                       99******************************************************************8 PP

>> GlutR_dimer  Glutamyl-tRNAGlu reductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.6   1.1   4.4e-24   3.2e-21       1      97 []     311     412 ..     311     412 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 4.4e-24
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-S......--------TTHHHHHHHHHHHHH CS
                       GlutR_dimer   1 kAeaiIeeeveefeawlkslevvptIkalrekaeeireeeleralkkla....ldgedreelekltrslvnkllhep 73 
                                       k+ a+Ieee+e +++++k+++++ +I++l+ +++++re+e +ra+++l+    + + + e+l++lt+s+vnk+l ep
  gi|298674200|ref|YP_003725950.1| 311 KVDALIEEEFELLNTQYKRQKADGLISQLYGQVHNVREREKQRAINRLSsyhtIGDIESEVLDDLTHSIVNKILAEP 387
                                       5789***********************************************9888888999**************** PP

                                       HHHHHSS.-TTTTHHHHHHHHH... CS
                       GlutR_dimer  74 tarLkea.edeeeellealrrlFnl 97 
                                       t+ L++a e++e+el+++++rlFnl
  gi|298674200|ref|YP_003725950.1| 388 TKMLRKAaENDEDELMDTASRLFNL 412
                                       *******777777**********97 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.1   9.3e-13   6.7e-10       2      96 ..     177     272 ..     176     273 .. 0.88

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 9.3e-13
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECH.HHHHHH-SEEEE-S-HHHH... CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdn.eeaaeeadvvvlavkpedv... 74 
                                       i +iG+G+mg  +a+ l++++    ++v  ++r+ e+a++laee+g ++   dn  e++++advv+ a    ++   
  gi|298674200|ref|YP_003725950.1| 177 ILVIGTGEMGTLVARALAHKD---MDVVYLANRTFETAKQLAEEIGGDAVLFDNiDECIRNADVVICATAAPHFvlr 250
                                       679******************...7777788***************99998888356888*******9988877555 PP

                                       HHHHHHCGHHHHTTSEEEEESS CS
                     F420_oxidored  75 eevlselakdalkgklvisvla 96 
                                       +++++++++d  k+ l+i+++ 
  gi|298674200|ref|YP_003725950.1| 251 KSTIEKAMDDRNKELLLIDIAT 272
                                       7999999************986 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.0   2.8e-10     2e-07       2      91 ..     177     272 ..     176     293 .. 0.86

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 2.8e-10
                                       EEEE--SHHHHHHHHHHHHTT-EE.EEE-SSHHHHHHHHHTT...EEE-SSHHHHHHHCSEEEE-SSSHHHH..HHH CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykv.avynrtkekveelvaeg...akaaesieelvasldvvitmvkagkav..dev 72 
                                       i +iG+G+MG+  a+ l++++++v ++ nrt e +++l++e    a+++++i e+++++dvvi+   a + v  +++
  gi|298674200|ref|YP_003725950.1| 177 ILVIGTGEMGTLVARALAHKDMDVvYLANRTFETAKQLAEEIggdAVLFDNIDECIRNADVVICATAAPHFVlrKST 253
                                       779***************99998625789**********995578******************99999988855789 PP

                                       HHSHCCC--TT-EEEE-S- CS
                     NAD_binding_2  73 iegllealkkgdilidgst 91 
                                       ie+ ++  +k+ +lid +t
  gi|298674200|ref|YP_003725950.1| 254 IEKAMDDRNKELLLIDIAT 272
                                       9999999999999999987 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.1   2.9e-09   2.1e-06      33     100 ..     171     243 ..     144     271 .. 0.79
   2 ?   -3.0   0.0       5.6     4e+03       6      24 ..     292     310 ..     290     320 .. 0.73

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2.9e-09
                                       -GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.....CHHHHTCEECSHHHHHHH-SEEEE-S- CS
                      2-Hacid_dh_C  33 elsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee.....eeeelgvelvsleellaesDivslhlp 100
                                        l+gk + +iG+G++G+ va+ l+  +m+v++   +  +++     e     v +++++e ++++D+v++++ 
  gi|298674200|ref|YP_003725950.1| 171 GLTGKNILVIGTGEMGTLVARALAHKDMDVVYLANRTFETAkqlaeEIGGDAVLFDNIDECIRNADVVICATA 243
                                       689*************************9999876655444344322223334678************99765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.6
                                       HHHTTHHHHHHHHHTTCCH CS
                      2-Hacid_dh_C   6 allrrlaeadeevregewk 24 
                                       + lrr++e + e+r+ge k
  gi|298674200|ref|YP_003725950.1| 292 DSLRRINEKNMEMRRGEAK 310
                                       5689999999999999873 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       5.4   3.9e+03      32      45 ..      54      64 ..      46     139 .. 0.68
   2 !   22.9   0.1   1.2e-07   8.9e-05       5      73 ..     172     246 ..     168     275 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 5.4
                     NAD_binding_7 32 kvtvvapevkeele 45
                                      +v vv+p+    ++
  gi|298674200|ref|YP_003725950.1| 54 EVYVVSPKA---SS 64
                                      677788873...33 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 1.2e-07
                     NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvk......laeeelekdlegadlviaatddre 73 
                                       l+gk++lv+G Ge+++  +r l+ ++ +v+ +a++++e +++l +      +  +++++ + +ad+vi+at  ++
  gi|298674200|ref|YP_003725950.1| 172 LTGKNILVIGTGEMGTLVARALAHKDMDVVYLANRTFETAKQLAEeiggdaVLFDNIDECIRNADVVICATAAPH 246
                                       799********************************877777776632222222344678899********98765 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1   7.3e-08   5.2e-05      28     130 ..     182     282 ..     177     319 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 7.3e-08
                                       --HHHHHHHHHHHHTT-EEEEEE-S-SS---TT-EEEE--SHHHHHHHHHHHHTT-SEEEE---S--EEES------ CS
                               DFP  28 SGkmGyalAeaaaarGaeVtlvsgpvsletpegvevvkvesaeemleaveealkeadivimaAAvaDyrpkeaaeeK 104
                                       +G+mG  +A+a+a++ ++V + +  +  et  ++   ++   + + ++++e++++ad+vi+a A   +  ++++ eK
  gi|298674200|ref|YP_003725950.1| 182 TGEMGTLVARALAHKDMDVVYLANRT-FETA-KQLAEEIGGDAVLFDNIDECIRNADVVICATAAPHFVLRKSTIEK 256
                                       8**********************995.4444.44467899*******************************999999 PP

                                       -------..----EEE---HHHHHHH CS
                               DFP 105 ikkeeeeeeltleleknpdilaelae 130
                                          ++++e l +++   +di  e++e
  gi|298674200|ref|YP_003725950.1| 257 AMDDRNKELLLIDIATPRDIEPEISE 282
                                       99888888888999999999888754 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.057        41      92     121 ..      35      64 ..      12      96 .. 0.83
   2 !   17.4   0.0   3.5e-06    0.0025       2      68 ..     172     242 ..     171     268 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.057
                                       EESSSHHHHTTSS---TTSEEEEEEESS-S CS
                              IlvN  92 afahGfnihfglikppkdvdvvlvAPkgpG 121
                                        ++h +      +k+ ++v+v++v Pk+  
  gi|298674200|ref|YP_003725950.1|  35 LYSHEYVYECAVLKTCNRVEVYVVSPKASS 64 
                                       69999999999****************864 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 3.5e-06
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEE.EE-TT-HHHHHHHHTT-EEE...EHHHHHHT-SEEEE-S CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvv.glregsksvkkAkeegfevl...tvaeavkkadvvmili 68 
                                       l+gk+i viG G  G   a+ l    +dvv+ ++r+ ++  + A+e g + +   +++e +++advv++ +
  gi|298674200|ref|YP_003725950.1| 172 LTGKNILVIGTGEMGTLVARALAHKDMDVVYlANRTFETAKQLAEEIGGDAVlfdNIDECIRNADVVICAT 242
                                       789*************************986255666667788888765543233899********99764 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   2.3e-07   0.00016       2      72 ..     176     244 ..     175     267 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2.3e-07
                                       EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE..EESSHHHHHTCTTESEEEE-S-G CS
                      GFO_IDH_MocA   2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgve..aysdleelladpeidavivatpn 72 
                                       ++++iG+G +g+  +r+l ++  + +vv l ++  e a+++ae+ g +   +++++e  +  ++d+vi at +
  gi|298674200|ref|YP_003725950.1| 176 NILVIGTGEMGTLVARALAHK--DMDVVYLANRTFETAKQLAEEIGGDavLFDNIDECIR--NADVVICATAA 244
                                       89*************999888..99***********************999*********..88988877765 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   7.6e-07   0.00054       2      76 ..     176     243 ..     175     261 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 7.6e-07
                                       EEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH-SEEEE-S- CS
                            DapB_N   2 kvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlekadvliDFTt 76 
                                       +++v+G  G mG+ v++a+ + +d+ +v   +r+      + a +l++    +  ++d+++e++++adv+i  T+
  gi|298674200|ref|YP_003725950.1| 176 NILVIGT-GEMGTLVARALAH-KDMDVVYLANRTF-----ETAKQLAEEIGGDAVLFDNIDECIRNADVVICATA 243
                                       699***8.**********999.9*****9999986.....3334444444569999***************8885 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       4.4   3.1e+03      35      50 ..      97     112 ..      90     125 .. 0.79
   2 !   11.9   0.3   0.00014       0.1      24      96 ..     162     251 ..     144     259 .. 0.70
   3 ?   -1.9   0.0       2.5   1.8e+03     109     129 ..     355     375 ..     354     380 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.4
                                       TT-EEEEE---TTTHH CS
                     THF_DHG_CYH_C  35 egkkvvvvGrsnivgk 50 
                                       +g + ++vG+ +i+g+
  gi|298674200|ref|YP_003725950.1|  97 SGLESMIVGEDQILGQ 112
                                       6788999999999997 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00014
                                       HHHHHHCT---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTS..................CCHHHHHCCSSE CS
                     THF_DHG_CYH_C  24 vellketgielegkkvvvvGrsnivgkplallLleknatVtvchskt..................kdlaeitreadi 82 
                                       v+l +e    l+gk+++v+G ++ +g  +a  L++k++ V ++ ++t                  ++++e +r+ad+
  gi|298674200|ref|YP_003725950.1| 162 VDLADEILGGLTGKNILVIGTGE-MGTLVARALAHKDMDVVYLANRTfetakqlaeeiggdavlfDNIDECIRNADV 237
                                       56666666677888888888876.477777777777665555555555545444455555555556889999***** PP

                                       EEE-SS-TT-B-GG CS
                     THF_DHG_CYH_C  83 vvvavGkpelikae 96 
                                       v+ a+  p+++ ++
  gi|298674200|ref|YP_003725950.1| 238 VICATAAPHFVLRK 251
                                       *********99654 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.5
                                       -EEC-TTEEE-SB-HHHHCTT CS
                     THF_DHG_CYH_C 109 inrvekgklvGDvdfeevkev 129
                                       inr+++++++GD++ e ++++
  gi|298674200|ref|YP_003725950.1| 355 INRLSSYHTIGDIESEVLDDL 375
                                       899999*******98877665 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   3.9e-06    0.0028      31     116 ..     174     250 ..     154     291 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.9e-06
                       Glu_dehyd_C  31 pesalvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlveelGatYvdsretpvdeipeaseemdlvvEa 107
                                        +  lv+G+G +G L + +l++  ++++ vy  +r+   + + +l ee+G+  v       d+i e  ++ d+v+ a
  gi|298674200|ref|YP_003725950.1| 174 GKNILVIGTGEMGTLVARALAH--KDMDVVYLANRTF--ETAKQLAEEIGGDAVL-----FDNIDECIRNADVVICA 241
                                       5678************999986..6899787777644..455679*****98884.....56777779********* PP

                       Glu_dehyd_C 108 TGsakhafe 116
                                       T +++ ++ 
  gi|298674200|ref|YP_003725950.1| 242 TAAPHFVLR 250
                                       *99988764 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   7.6e-06    0.0055       2      73 ..     181     247 ..     181     288 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 7.6e-06
                                       TTSHHHHHHHHHHHHC-T-EEEEEETTH.HHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC CS
                    NAD_binding_10   2 AtGkvGrllvkellargghevtalvRnp.eklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk 73 
                                       +tG  G l+++ l+++ +++v+ l+ ++ e +++      +e + gd+   + + e +++ad+V++a+++ + 
  gi|298674200|ref|YP_003725950.1| 181 GTGEMGTLVARALAHK-DMDVVYLANRTfETAKQ-----LAEEIGGDAVLFDNIDECIRNADVVICATAAPHF 247
                                       79********999999.79999998655155554.....567899999999*****************88654 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   9.4e-06    0.0067       1      38 [.     177     213 ..     177     267 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 9.4e-06
                                       EEEES-SHHHHHHHHHHHHHTHCEEEE-SCHHHHHHHH CS
                              ApbA   1 iailGaGaiGsllaakLakagadvtlilrsrrlealkk 38 
                                       i+++G+G +G+l+a  La++  dv+ ++++  +e+ k+
  gi|298674200|ref|YP_003725950.1| 177 ILVIGTGEMGTLVARALAHKDMDVVYLANRT-FETAKQ 213
                                       89*********************88888877.554444 PP

>> V-ATPase_G  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.15   1.1e+02      65     100 ..       3      38 ..       1      44 [. 0.87
   2 !   12.6   0.9   0.00021      0.15      40     104 ..     281     346 ..     277     347 .. 0.91
   3 ?   -0.3   0.0       2.2   1.6e+03      17      42 ..     377     402 ..     374     407 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHSSHHHHHHHHHHHHHHHHHHHHHHHH CS
                        V-ATPase_G  65 eelekkieketeekikelkesvkknkeavvkellkl 100
                                       +++++ + ++t+  i+e++++ +   e v+k l+++
  gi|298674200|ref|YP_003725950.1|   3 QQISSMVITHTKASIEEMEKAWHGDIEYVLKSLYSH 38 
                                       5677788899***********************986 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00021
                                       HHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHSSHHHHHHHHHHHHHH.HHHHHHHHHHHTSX CS
                        V-ATPase_G  40 kEieeyrakkekefkekeaeklgseeelekkieketeekikelkesvkknk.eavvkellklvldv 104
                                       +Eie+ + ++   +++ +++++  +   +kk+++  ee+++ l++++k++k +  +++l+  v +v
  gi|298674200|ref|YP_003725950.1| 281 SEIEHVKLHNIDSLRRINEKNMEMRRGEAKKVDALIEEEFELLNTQYKRQKaDGLISQLYGQVHNV 346
                                       599********************************************9988256999999988876 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 2.2
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        V-ATPase_G  17 aeivkeArkrkakrlkqAkeeAekEi 42 
                                       + iv++   + +k+l++A e+ e+E+
  gi|298674200|ref|YP_003725950.1| 377 HSIVNKILAEPTKMLRKAAENDEDEL 402
                                       679999999999******99988886 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.4   2.7e-05     0.019      21     102 ..     170     245 ..     142     274 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.7e-05
                                       CEETCB---EEEEESTSHHHHHHHHHHHHTT.-EEEEEESSHHHHHHHHH.TTTCECEEHCHHHHHHHHHHHH-SEE CS
                       AlaDh_PNT_C  21 GgvpgvepakvlviGgGvaGlqAiatakglg.akVtvlDvrparleqles.lgakfvevlksqeellaeavkeadvv 95 
                                       Gg++     ++lviG G  G+  +++ +  +  +V++ +   ++++ql + +g+      +   ++++e +++advv
  gi|298674200|ref|YP_003725950.1| 170 GGLT---GKNILVIGTGEMGTLVARALAHKDmDVVYLANRTFETAKQLAEeIGGD-----AVLFDNIDECIRNADVV 238
                                       4444...6789*********87776655555055666677778888887778888.....556689*********** PP

                                       EE---BT CS
                       AlaDh_PNT_C  96 igtvlip 102
                                       i++ + p
  gi|298674200|ref|YP_003725950.1| 239 ICATAAP 245
                                       **97665 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       3.9   2.8e+03      26     103 ..       9      90 ..       3     103 .. 0.60
   2 !   13.9   0.6   6.6e-05     0.047       1      71 [.     177     243 ..     177     268 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.9
                                       EEESSHHHHHHHHHTT...SE.EEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHHHHHHHHHHTSSSEEEEEESS CS
                            TrkA_N  26 vidkdeerveelreeg...le.vvvgdatdeevLeeagiekadaviaatgddeanilavllakelnpkkkiiaraqd 98 
                                       vi + ++ +ee+++     +e v++  +++e v e a +++++ v + + + +a+ ++ + ak++    +i+   ++
  gi|298674200|ref|YP_003725950.1|   9 VITHTKASIEEMEKAWhgdIEyVLKSLYSHEYVYECAVLKTCNRVEVYVVSPKASSVLFHFAKDMGASSHIVEFYDH 85 
                                       55555555555544333344434445556666666667777777766666777777777777777776666655555 PP

                                       GGGHH CS
                            TrkA_N  99 pehae 103
                                       ++  +
  gi|298674200|ref|YP_003725950.1|  86 EDSLK 90 
                                       55544 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 6.6e-05
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSH.HHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SS CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkde.erveelreeglevvvgdatdeevLeeagiekadaviaatg 71 
                                       i++iG G++G+ +a+ L ++ +dvv   ++  e++++l+    e + gda   + ++e  i +ad+vi+at 
  gi|298674200|ref|YP_003725950.1| 177 ILVIGTGEMGTLVARALAHKDMDVVYLANRTfETAKQLA----EEIGGDAVLFDNIDE-CIRNADVVICATA 243
                                       79*****************77678888775435555554....556677766666655.5899999999886 PP

>> OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   3.6e-05     0.026     132     214 ..     177     255 ..     163     258 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.6e-05
                                       EEEE--SHHHHHHHHHHCCCS--SEEEEE-SSHHHHHHHHHHCCS.CTT-EEECSCHHHHTTSSEEEE----SS-SB CS
                   OCD_Mu_crystall 132 laiiGaGvqaetqlealkavldikevriydrdeeaaekfaenlqefefevsackseeeavegadivvtvTaakapil 208
                                       + +iG G +  + ++al    d++ v + +r+ e+a+++ae++ +   + +  ++  e + +ad+v+ +Taa + +l
  gi|298674200|ref|YP_003725950.1| 177 ILVIGTGEMGTLVARALA-HKDMDVVYLANRTFETAKQLAEEIGG---DAVLFDNIDECIRNADVVICATAAPHFVL 249
                                       569*************96.579*******************9997...88899********************9999 PP

                                       -GGGS- CS
                   OCD_Mu_crystall 209 kaewvk 214
                                        ++ ++
  gi|298674200|ref|YP_003725950.1| 250 RKSTIE 255
                                       988776 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00012     0.085       2      32 ..     177     207 ..     176     241 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S-H CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdise 32 
                                       + viG+G mG+ +a ++a+++++Vv +  ++
  gi|298674200|ref|YP_003725950.1| 177 ILVIGTGEMGTLVARALAHKDMDVVYLANRT 207
                                       77*********************98775533 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       5.3   3.8e+03      83      99 ..      44      60 ..      37      95 .. 0.53
   2 ?   12.6   0.1   0.00017      0.12       1      51 [.     177     225 ..     177     249 .. 0.84
   3 ?   -2.3   0.0       6.8   4.9e+03      63     101 ..     312     327 ..     287     353 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5.3
                                      HHHHHHHHHHT-EEEES CS
                   Sacchrp_dh_NADP 83 ldvlkaCietgvhyvdt 99
                                       +vlk+C +  v +v +
  gi|298674200|ref|YP_003725950.1| 44 CAVLKTCNRVEVYVVSP 60
                                      55556665555555442 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00017
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEE CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfea 51 
                                       +l+iG G +G  va+ la ++     + +a r+ e +++la+++ g  + +
  gi|298674200|ref|YP_003725950.1| 177 ILVIGTGEMGTLVARALAHKDMD--VVYLANRTFETAKQLAEEIGGDAVLF 225
                                       89**************9987544..8**************99986665544 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 6.8
                                       HHHHHTTSSEEEE-SSGGGHHHHHHHHHHHT-EEEESS- CS
                   Sacchrp_dh_NADP  63 LaallkegdlvvnlsppissldvlkaCietgvhyvdtsi 101
                                       ++                       a ie     ++t++
  gi|298674200|ref|YP_003725950.1| 312 VD-----------------------ALIEEEFELLNTQY 327
                                       33.......................34444444455555 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   8.9e-05     0.064       1      74 [.     177     244 ..     177     259 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.9e-05
                                       EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE---G CS
                              NmrA   1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtgf 74 
                                       IlviG TG++G  v+ral++++ +v  l  + + e+ak+l+e+    + gd+   ++++e ++++dvv+++t++
  gi|298674200|ref|YP_003725950.1| 177 ILVIG-TGEMGTLVARALAHKDMDVVYLA-NRTFETAKQLAEE----IGGDAVLFDNIDECIRNADVVICATAA 244
                                       78886.9******************8775.7788999999765....899999999***************984 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00057      0.41       2      41 ..     177     217 ..     176     270 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00057
                                       EEEE--SHHHHHHHHHHHTTT--EEEE-S-H.HHHHHHHHH CS
                    NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaenghevrlwvree.elieeinee 41 
                                       i v+G+G  Gt +A++la++  +v+  +++  e+++++ ee
  gi|298674200|ref|YP_003725950.1| 177 ILVIGTGEMGTLVARALAHKDMDVVYLANRTfETAKQLAEE 217
                                       88*******************99999998887555555544 PP

>> Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.2   8.5e+02     281     354 ..      60     139 ..      46     148 .. 0.61
   2 ?   11.1   0.6   0.00017      0.12     241     354 ..     139     257 ..     128     349 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.2
                                       SHHHHHHHHHHHHHT-EEEEEEESSS-HHHH..HHHHHHS.TT.......SEEEES..CHHHHHHHHHHHT-SEEEE CS
                    Oxidored_nitro 281 pdrvvalarllkelGmevvaagtetahrdde..erlkaeleeg......epevidd.adleeleelikelkpdlllg 348
                                       p+ +  l ++ k++G+    + ++++++ ++   rl             e++++ + +dl+++++ + + +p l  +
  gi|298674200|ref|YP_003725950.1|  60 PKASSVLFHFAKDMGASSHIVEFYDHEDSLKhlLRLASG---LesmivgEDQILGQiKDLYTTAKNVGTIGPALDTA 133
                                       455666778999999999999888887777733222222...22235554455555566666666666666666555 PP

                                       -CCHHH CS
                    Oxidored_nitro 349 gskery 354
                                        sk+ +
  gi|298674200|ref|YP_003725950.1| 134 FSKAIQ 139
                                       555555 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00017
                                       HHHTCHHHHHHHHHHHHHHHHHHHH.HHHHHT...T-EEEEECSSHHHHHHHHHHHHHT-EEEEEEESSS-HHHHHH CS
                    Oxidored_nitro 241 kllgkevaperiaeerarlldalad.yheyla...gkrvaiygdpdrvvalarllkelGmevvaagtetahrddeer 313
                                       ++ +k++++ ri++ +  +  a +d + e l+   gk+++++g +++   +ar+l+   m+vv+++ +t + + +  
  gi|298674200|ref|YP_003725950.1| 139 QVGKKARTETRINKGSVSIGSAAVDlADEILGgltGKNILVIGTGEMGTLVARALAHKDMDVVYLANRTFETAKQ-- 213
                                       555566677777776666666666644444443339*****************************9999966644.. PP

                                       HHHHS.TT.SEEEES.CH...HHHHHHHHHHT-SEEEE-CC.HHH CS
                    Oxidored_nitro 314 lkaeleegepeviddadl...eeleelikelkpdlllggsk.ery 354
                                       l +e+++   + +d+ d+        +  + +p+++l +s  e++
  gi|298674200|ref|YP_003725950.1| 214 LAEEIGGD-AVLFDNIDEcirNADVVICATAAPHFVLRKSTiEKA 257
                                       44444443.133333332111222223344455555555553333 PP

>> SAM_Exu  Exuperantia SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00062      0.44      30      73 .]     318     361 ..     301     361 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00062
                           SAM_Exu  30 idyesLkeiweekkkeGlekllkekitslkeedkeeLlelLdsh 73 
                                        ++e L++ ++ +k +Gl ++l  +++++ e +k+  ++ L s+
  gi|298674200|ref|YP_003725950.1| 318 EEFELLNTQYKRQKADGLISQLYGQVHNVREREKQRAINRLSSY 361
                                       46788****************************98777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       979  (0.0546043); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2665.53
//
Query:       gi|298674201|ref|YP_003725951.1|  [L=227]
Description: siroheme synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-20   74.1   0.6    1.6e-18   67.1   0.1    2.1  2  NAD_binding_7    Putative NAD(P)-binding
    7.8e-05   22.0   0.1    0.00016   21.1   0.1    1.6  1  Sirohm_synth_M   Sirohaem biosynthesis protein central
    0.00091   19.5   0.0      0.015   15.6   0.0    2.1  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
        0.1   11.6   0.9       0.15   11.1   0.6    1.5  1  MCR_C            Methyl-coenzyme M reductase operon protein C
       0.11   13.5   3.1       0.13   13.3   0.1    2.6  3  RNase_J_C        Ribonuclease J C-terminal domain


Domain annotation for each model (and alignments):
>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.1   0.1   4.3e-22   1.6e-18       1     104 []      10     125 ..      10     125 .. 0.82
   2 !    5.7   0.1    0.0057        20      43      95 ..     167     220 ..     140     226 .. 0.71

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 4.3e-22
                     NAD_binding_7   1 lfldlkgkkvlvvGgGevAarkvrklleagakvtvvapevkeele........elvk.....laeeelekdlegadl 64 
                                       l++dl+gkk++++G+G+v++rk+  + ++ a+ t+++  +++ ++        +l++     l+++++++ + +a++
  gi|298674201|ref|YP_003725951.1|  10 LMIDLSGKKIIIFGAGSVGERKALFFSAY-ADTTIISTSFTSSIKelensrkiKLITsninsLNDSQIKDLIYDAFM 85 
                                       79*************************99.*********96666656677666333333223566777888999*** PP

                     NAD_binding_7  65 viaatddrelneriaeaa..karrilvnvadkpelcdfifpa 104
                                       vi at++r+ln+ri e a   +++ilvn +d  + +d+i+p+
  gi|298674201|ref|YP_003725951.1|  86 VIPATNNRQLNQRITEVAnkTDKNILVNQVD--DIGDVIVPS 125
                                       ****************9964459********..567888886 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0057
                     NAD_binding_7  43 eleelvklaeeelekdlegadlviaatddrelneriaeaa.karrilvnvadkp 95 
                                       + +++ ++ +e ++++ ++ ++++ +++d+++ +++ +   ka++i +n++d++
  gi|298674201|ref|YP_003725951.1| 167 IQNDIRTYLKEVISDQRKRKQILWNIIEDDSVWSALSDSYeKAYNIALNIVDEQ 220
                                       2224444455556777888999*************99988799*********87 PP

>> Sirohm_synth_M  Sirohaem biosynthesis protein central
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   4.4e-08   0.00016       1      27 [.     129     155 ..     129     156 .. 0.96

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 4.4e-08
                    Sirohm_synth_M   1 rGpLQIaiSTnGksPrLAaliRreier 27 
                                       rG+L I iST G+sP+ ++  R+ ie+
  gi|298674201|ref|YP_003725951.1| 129 RGDLTIGISTLGSSPAISKFTRENIEQ 155
                                       8************************97 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   4.2e-06     0.015       1      95 [.      19     109 ..      19     188 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.2e-06
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-S CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnls 77 
                                       ++i+GaGsvG+  a   ++  d     t+++ s ++  +++++ +++++++  ++  n+++ ++ l+ ++ +v+ ++
  gi|298674201|ref|YP_003725951.1|  19 IIIFGAGSVGERKALFFSAYADT----TIISTSFTSSIKELENSRKIKLITSNINSLNDSQ-IKDLIYDAFMVIPAT 90 
                                       79*****************9998....67777777767999999*****************.************999 PP

                                       SGG.GHHHHHHHHHHHT-E CS
                   Sacchrp_dh_NADP  78 ppi.ssldvlkaCietgvh 95 
                                        +  ++  + + + +t  +
  gi|298674201|ref|YP_003725951.1|  91 NNRqLNQRITEVANKTDKN 109
                                       9987888888888877766 PP

>> MCR_C  Methyl-coenzyme M reductase operon protein C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.6   4.3e-05      0.15     187     254 ..      50     117 ..      18     123 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.3e-05
                             MCR_C 187 hrlrkeeeiealdelveeveevldkkreelakDpllvsparvkkeieeqveeieevlsPapitlqldg 254
                                         +++ e+ ++++ ++ +++++ d++ ++l  D+ +v pa+  +++++++ e+ + +    ++ q+d 
  gi|298674201|ref|YP_003725951.1|  50 SSIKELENSRKIKLITSNINSLNDSQIKDLIYDAFMVIPATNNRQLNQRITEVANKTDKNILVNQVDD 117
                                       567899999*********************************************99999988888875 PP

>> RNase_J_C  Ribonuclease J C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.55     2e+03      17      40 ..      78     101 ..      49     117 .. 0.67
   2 ?   13.3   0.1   3.7e-05      0.13      22      63 ..     145     186 ..     124     194 .. 0.91
   3 ?   -2.5   0.0       3.1   1.1e+04      20      39 ..     207     226 ..     203     227 .] 0.76

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.55
                         RNase_J_C  17 eLieeakkvvretieealeekesd 40 
                                       +Li +a  v+ +t +++l++++++
  gi|298674201|ref|YP_003725951.1|  78 DLIYDAFMVIPATNNRQLNQRITE 101
                                       455555555555555555554433 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 3.7e-05
                         RNase_J_C  22 akkvvretieealeekesdwnelkrkirealkkflykktkrr 63 
                                       ++k +re ie++++ + s+++e++++ir+ lk+++ ++ kr+
  gi|298674201|ref|YP_003725951.1| 145 ISKFTRENIEQTITPEYSEMAEIQNDIRTYLKEVISDQRKRK 186
                                       67789999******9************************997 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 3.1
                         RNase_J_C  20 eeakkvvretieealeekes 39 
                                       e+a +++ ++++e+l+++++
  gi|298674201|ref|YP_003725951.1| 207 EKAYNIALNIVDEQLRSEKI 226
                                       77888888999988887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1051  (0.0586201); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1458.90
//
Query:       gi|298674202|ref|YP_003725952.1|  [L=167]
Description: putative AsnC family transcriptional regulator [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.5e-33  112.7   0.1    1.6e-32  111.4   0.0    1.7  2  AsnC_trans_reg2  AsnC-like ligand binding domain
    0.00015   21.6   0.0    0.00026   20.9   0.0    1.4  1  HTH_Crp_2        Crp-like helix-turn-helix domain
    0.00028   20.8   0.0    0.00063   19.7   0.0    1.7  1  HTH_36           Helix-turn-helix domain
     0.0042   16.5   0.0     0.0096   15.3   0.0    1.6  1  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil
  ------ inclusion threshold ------
      0.016   15.1   0.0      0.029   14.3   0.0    1.4  1  MarR             MarR family
      0.016   14.7   0.0      0.072   12.7   0.0    2.0  2  HTH_24           Winged helix-turn-helix DNA-binding
      0.034   14.2   0.0      0.077   13.0   0.0    1.5  1  HTH_29           Winged helix-turn helix
      0.044   13.7   0.0      0.076   12.9   0.0    1.4  1  MarR_2           MarR family
      0.077   12.9   0.0       0.42   10.5   0.0    2.1  2  TrmB             Sugar-specific transcriptional regulator Trm
      0.085   12.7   0.0       0.28   11.1   0.0    1.9  2  HTH_AsnC-type    AsnC-type helix-turn-helix domain
       0.13   12.4   0.0        2.4    8.3   0.0    2.1  2  HEPN             HEPN domain
       0.15   12.2   0.0       0.69   10.1   0.0    1.9  2  HisG_C           HisG, C-terminal domain


Domain annotation for each model (and alignments):
>> AsnC_trans_reg2  AsnC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.8   4.2e+03      52      66 ..      48      62 ..      42      66 .. 0.79
   2 !  111.4   0.0   1.1e-35   1.6e-32       2      82 .]      77     161 ..      76     161 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.8
                   AsnC_trans_reg2 52 seeeveevlaeiaaa 66
                                      se+ev ++++e++++
  gi|298674202|ref|YP_003725952.1| 48 SEDEVINIIKEMENK 62
                                      788888999988865 PP

  == domain 2  score: 111.4 bits;  conditional E-value: 1.1e-35
                   AsnC_trans_reg2   2 lGfkanalvawkvpeerveevaevvaelpevtHcYeR....ewpynlyfmvharseeeveevlaeiaaatgledyev 74 
                                       +G++ana+++w+vp+e+veev++++a ++evtHcYeR    +wpynl++mvh  s++++e v++ei++atg++dy++
  gi|298674202|ref|YP_003725952.1|  77 IGITANAMCIWNVPDEKVEEVGAIMAGFSEVTHCYERprypDWPYNLFTMVHSYSKRDCEYVAEEISKATGITDYKL 153
                                       8************************************88888*********************************** PP

                   AsnC_trans_reg2  75 LpstrefK 82 
                                       L+s++efK
  gi|298674202|ref|YP_003725952.1| 154 LFSEHEFK 161
                                       *******9 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.8e-07   0.00026      25      54 ..      39      69 ..      19      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.8e-07
                                      HHHHHHTTSSHHHHHHHHHHHHHTTSEEE.T CS
                         HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglisr.g 54
                                      +++As+lG++   v  i++e++++g+i+r g
  gi|298674202|ref|YP_003725952.1| 39 AQIASYLGISEDEVINIIKEMENKGIIRRfG 69
                                      59*************************9534 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   4.2e-07   0.00063      13      55 .]      22      65 ..       5      65 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 4.2e-07
                            HTH_36 13 slasfanknggcfp..sqetlakrlglsknTvsraikeLeqlGyi 55
                                       + ++  ++g+ f    ++ +a+ lg+s++ v+++ike e +G+i
  gi|298674202|ref|YP_003725952.1| 22 KIIKLT-QDGIPFThsPFAQIASYLGISEDEVINIIKEMENKGII 65
                                      555555.67776665449*************************98 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   6.5e-06    0.0096      25      49 ..      34      57 ..      34      58 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.5e-06
                      HTH_Tnp_ISL3 25 lesrsvkavArqlgvSwtTVwrild 49
                                      ++s +++++A  lg+S++ V++i++
  gi|298674202|ref|YP_003725952.1| 34 THS-PFAQIASYLGISEDEVINIIK 57
                                      578.*******************98 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.9e-05     0.029      21      49 ..      39      67 ..      27      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.9e-05
                                      HHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR 21 seLakklgvskstvtrvldrLekkGlieR 49
                                      +++a+ lg+s   v ++++++e kG i+R
  gi|298674202|ref|YP_003725952.1| 39 AQIASYLGISEDEVINIIKEMENKGIIRR 67
                                      59**************************9 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.8e-05     0.072      20      48 .]      38      66 ..      34      66 .. 0.92
   2 ?   -1.2   0.0         1   1.6e+03      22      30 ..     141     149 ..     139     150 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.8e-05
                            HTH_24 20 qreLAerlglSpstvnrrlkrLeeeGlIk 48
                                       +++A  lg+S   v   +k++e++G+I+
  gi|298674202|ref|YP_003725952.1| 38 FAQIASYLGISEDEVINIIKEMENKGIIR 66
                                      6789999*********************7 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1
                            HTH_24  22 eLAerlglS 30 
                                       e+++++g++
  gi|298674202|ref|YP_003725952.1| 141 EISKATGIT 149
                                       99*****97 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.2e-05     0.077      16      41 ..      39      64 ..      35      78 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.2e-05
                            HTH_29 16 sqiAkllglsrrtvyrwlkrfeegGl 41
                                      +qiA  lg+s++ v +++k +e++G+
  gi|298674202|ref|YP_003725952.1| 39 AQIASYLGISEDEVINIIKEMENKGI 64
                                      69***********************7 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.1e-05     0.076      24      53 ..      38      67 ..      32      76 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.1e-05
                                      HHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2 24 vgelarrlglsksavsrilkrLvaaGLver 53
                                       +++a +lg+s   v +i+k+++ +G ++r
  gi|298674202|ref|YP_003725952.1| 38 FAQIASYLGISEDEVINIIKEMENKGIIRR 67
                                      689*************************98 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00028      0.42      27      54 ..      40      67 ..      35      72 .. 0.93
   2 ?   -1.2   0.0       1.3     2e+03      24      34 ..     138     148 ..     133     152 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00028
                                      HHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                              TrmB 27 eiaeelgvprskvYevLrsLedkGlVer 54
                                      +ia+ lg+++  v ++++++e+kG+++r
  gi|298674202|ref|YP_003725952.1| 40 QIASYLGISEDEVINIIKEMENKGIIRR 67
                                      79***********************987 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.3
                                       HHCHHCCCTTS CS
                              TrmB  24 tadeiaeelgv 34 
                                        a+ei++++g+
  gi|298674202|ref|YP_003725952.1| 138 VAEEISKATGI 148
                                       58999999998 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00019      0.28       7      42 .]      22      60 ..      17      60 .. 0.81
   2 ?   -1.9   0.0       2.1   3.1e+03      21      30 ..     140     149 ..     133     150 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00019
                     HTH_AsnC-type  7 kILeaLqed...aRisyaeLAervGlSestvlrRvrrLe 42
                                      kI+++ q        ++a++A  +G+Se++v++ ++ +e
  gi|298674202|ref|YP_003725952.1| 22 KIIKLTQDGipfTHSPFAQIASYLGISEDEVINIIKEME 60
                                      677777766777788****************98777776 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.1
                     HTH_AsnC-type  21 aeLAervGlS 30 
                                       +e+++++G++
  gi|298674202|ref|YP_003725952.1| 140 EEISKATGIT 149
                                       7999999986 PP

>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.24   3.6e+02      47      88 ..      27      67 ..      20      83 .. 0.62
   2 ?    8.3   0.0    0.0016       2.4      70     106 ..      97     140 ..      84     149 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.24
                                      T--..SSCCHHHHHHC.CHHHT...-HHHHHHHHHHHCCCHHCC CS
                              HEPN 47 gge.ppkthdlreLle.elkkelkeseelreeleeLekayiesr 88
                                      +++ +p th+  + +  +l   +++++e++++++e+e+  i  r
  gi|298674202|ref|YP_003725952.1| 27 TQDgIPFTHSPFAQIAsYL---GISEDEVINIIKEMENKGIIRR 67
                                      4444555555443333233...2336777777777777666655 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0016
                                       -HHHHHHHHHHHCCCHHCCCTSS--S.......--HHHHHHHHH CS
                              HEPN  70 seelreeleeLekayiesrYpdakee.......yteedaeealk 106
                                          +   ++e+++ y   rYpd  ++       y+++d+e + +
  gi|298674202|ref|YP_003725952.1|  97 VGAIMAGFSEVTHCYERPRYPDWPYNlftmvhsYSKRDCEYVAE 140
                                       4555666799************9999************998765 PP

>> HisG_C  HisG, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.4   2.2e+03      46      62 ..      47      63 ..      44      64 .. 0.82
   2 ?   10.1   0.0   0.00046      0.69       5      28 ..      83     106 ..      80     113 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.4
                                      EECCCHHHHHHHHHCTT CS
                            HisG_C 46 veekevaevideLkaaG 62
                                      ++e+ev ++i+e+++ G
  gi|298674202|ref|YP_003725952.1| 47 ISEDEVINIIKEMENKG 63
                                      67899999999988765 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00046
                                       EEEEEEEEGGGHHHHHHH---SSS CS
                            HisG_C   5 vllmynvpkesleevlkilPGlrs 28 
                                        ++  nvp e++eev +i++G ++
  gi|298674202|ref|YP_003725952.1|  83 AMCIWNVPDEKVEEVGAIMAGFSE 106
                                       6999****************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       781  (0.0435607); expected 358.6 (0.02)
Passed bias filter:                      685  (0.0382063); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1100.68
//
Query:       gi|298674203|ref|YP_003725953.1|  [L=151]
Description: putative AsnC family transcriptional regulator [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-23   82.8   0.0    2.8e-23   81.9   0.0    1.5  1  AsnC_trans_reg2  AsnC-like ligand binding domain
    3.4e-10   39.6   0.0      6e-10   38.8   0.0    1.4  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    8.9e-05   22.0   2.3    0.00053   19.5   0.9    2.6  2  HTH_24           Winged helix-turn-helix DNA-binding
     0.0068   15.9   0.7      0.011   15.3   0.1    1.7  2  Sigma70_r4       Sigma-70, region 4
  ------ inclusion threshold ------
      0.012   15.4   0.1      0.058   13.2   0.1    2.2  1  IF2_N            Translation initiation factor IF-2, N-termin
      0.041   13.8   0.1       0.13   12.2   0.0    1.9  2  HTH_11           HTH domain
      0.053   13.5   0.0      0.097   12.6   0.0    1.5  1  AsnC_trans_reg   Lrp/AsnC ligand binding domain
      0.062   13.2   0.1       0.16   11.9   0.0    1.7  2  TrmB             Sugar-specific transcriptional regulator Trm
      0.064   13.2   0.0       0.14   12.1   0.0    1.7  2  HTH_Crp_2        Crp-like helix-turn-helix domain
      0.097   12.7   0.2       0.34   11.0   0.0    1.8  2  Sulfolobus_pRN   Sulfolobus plasmid regulatory protein


Domain annotation for each model (and alignments):
>> AsnC_trans_reg2  AsnC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.9   0.0   1.6e-26   2.8e-23       1      82 []      64     143 ..      64     143 .. 0.98

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 1.6e-26
                   AsnC_trans_reg2   1 klGfkanalvawkvpeerveevaevvaelpevtHcYeRewpynlyfmvharseeeveevlaeiaaatgledyevLps 77 
                                       k G   ++lva+k+p+++v ++a +++++pev+H+Y+R+ +ynl+f+v+a s+++++e+l+ei+++tg+  + +Lp+
  gi|298674203|ref|YP_003725953.1|  64 KTGGI-STLVAVKAPDSQVSDIADYINQYPEVSHNYLRPDKYNLWFTVSASSKQRLDEILEEIRNETGCP-LINLPT 138
                                       56888.9***************************************************************.****** PP

                   AsnC_trans_reg2  78 trefK 82 
                                       +r fK
  gi|298674203|ref|YP_003725953.1| 139 KRLFK 143
                                       ****9 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.0   3.3e-13     6e-10       1      41 [.       4      47 ..       4      48 .. 0.96

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 3.3e-13
                     HTH_AsnC-type  1 LDeiDrkILeaLqed...aRisyaeLAervGlSestvlrRvrrL 41
                                      LDe+D+kIL+++q d      +y++LAer+G+Se++v++R++ L
  gi|298674203|ref|YP_003725953.1|  4 LDETDKKILNEIQLDfplDTHPYEKLAERLGISEEEVIKRLEDL 47
                                      8***************************************9876 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.9     3e-07   0.00053       1      41 [.       4      47 ..       4      54 .. 0.91
   2 ?   -1.9   0.0       1.4   2.5e+03       7      16 ..     120     129 ..     120     133 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3e-07
                            HTH_24  1 ldetdrkILelLqk...nprisqreLAerlglSpstvnrrlkrL 41
                                      ldetd+kIL+++q        ++  LAerlg+S   v +rl+ L
  gi|298674203|ref|YP_003725953.1|  4 LDETDKKILNEIQLdfpLDTHPYEKLAERLGISEEEVIKRLEDL 47
                                      7*************666599**************9999999987 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.4
                            HTH_24   7 kILelLqknp 16 
                                       +ILe+++ + 
  gi|298674203|ref|YP_003725953.1| 120 EILEEIRNET 129
                                       5999999865 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   5.9e-06     0.011       4      37 ..       3      40 ..       1      47 [. 0.86
   2 ?   -2.9   0.1       2.9   5.2e+03      38      49 ..     115     126 ..     115     127 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.9e-06
                                      HS-HHHHHHHHHHH....TTT--HHHHHHHHTS-HHHH CS
                        Sigma70_r4  4 sLpererevlelrf....geglTleEIgerlgiSrerV 37
                                      +L+e ++++l        ++ +++e ++erlgiS+e V
  gi|298674203|ref|YP_003725953.1|  3 QLDETDKKILNEIQldfpLDTHPYEKLAERLGISEEEV 40
                                      688999999888888889999**************988 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.9
                                       HHHHHHHHHHHH CS
                        Sigma70_r4  38 rqiekrAlrkLR 49 
                                       +q++ + l+ +R
  gi|298674203|ref|YP_003725953.1| 115 KQRLDEILEEIR 126
                                       688888888777 PP

>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   3.3e-05     0.058       8      27 ..      28      46 ..      27      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.3e-05
                             IF2_N  8 eLAkeLgvkskevikkLfke 27
                                       LA++Lg++ +evik+L ++
  gi|298674203|ref|YP_003725953.1| 28 KLAERLGISEEEVIKRL-ED 46
                                      69***************.54 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.3e-05      0.13      19      50 ..      27      63 ..      21      68 .. 0.79
   2 ?   -2.4   0.0       2.8   4.9e+03       1      13 [.     117     129 ..     117     131 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.3e-05
                            HTH_11 19 eeLAeeLnvSrrtvrrdIkaLeelg.....vpIesep 50
                                      e+LAe+L++S+  v +++++L  +g      pI+ ++
  gi|298674203|ref|YP_003725953.1| 27 EKLAERLGISEEEVIKRLEDLYYKGavrriGPIINTR 63
                                      89*******************8888665555555555 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.8
                            HTH_11   1 RllqilelLlear 13 
                                       Rl  ile +++++
  gi|298674203|ref|YP_003725953.1| 117 RLDEILEEIRNET 129
                                       7788999987765 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.4e-05     0.097       6      60 ..      77     127 ..      65     131 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.4e-05
                                       -GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTT CS
                    AsnC_trans_reg   6 epghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklas 60 
                                           + q+ ++++ + ++peV + y     y++ + v + + + l+++l+e +++
  gi|298674203|ref|YP_003725953.1|  77 P---DSQVSDIADYINQYPEVSHNYLRPDKYNLWFTVSASSKQRLDEILEE-IRN 127
                                       3...35699***************************************999.776 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   9.1e-05      0.16      26      55 ..      27      56 ..      22      62 .. 0.93
   2 ?   -2.9   0.0       3.8   6.8e+03      19      31 ..      75      87 ..      70      89 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.1e-05
                                      CHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                              TrmB 26 deiaeelgvprskvYevLrsLedkGlVere 55
                                      +++ae+lg+++  v + L+ L  kG V+r+
  gi|298674203|ref|YP_003725953.1| 27 EKLAERLGISEEEVIKRLEDLYYKGAVRRI 56
                                      689************************997 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.8
                                      HHCCCHHCHHCCC CS
                              TrmB 19 klgpatadeiaee 31
                                      k   +++++ia  
  gi|298674203|ref|YP_003725953.1| 75 KAPDSQVSDIADY 87
                                      5566777888765 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     8e-05      0.14      24      57 ..      26      59 ..       2      65 .. 0.83
   2 ?   -3.3   0.0       5.2   9.3e+03      26      32 ..      83      89 ..      81      93 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8e-05
                                      HHHHHHHTTSSHHHHHHHHHHHHHTTSEEE.TEEE CS
                         HTH_Crp_2 24 qeelAsmlGltretvsrilseLkreglisr.grri 57
                                       e lA++lG++ e v + l +L  +g ++r g  i
  gi|298674203|ref|YP_003725953.1| 26 YEKLAERLGISEEEVIKRLEDLYYKGAVRRiGP-I 59
                                      689***********************9995364.4 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 5.2
                                      HHHHHTT CS
                         HTH_Crp_2 26 elAsmlG 32
                                      ++A++++
  gi|298674203|ref|YP_003725953.1| 83 DIADYIN 89
                                      8999987 PP

>> Sulfolobus_pRN  Sulfolobus plasmid regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00019      0.34      21      50 ..      26      55 ..       8      70 .. 0.85
   2 ?   -0.9   0.0      0.94   1.7e+03      20      32 ..     121     133 ..     114     147 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00019
                    Sulfolobus_pRN 21 leeleektGiekeellvyltrlykrGlisr 50
                                       e+l e+ Gi  ee++  l  ly +G + r
  gi|298674203|ref|YP_003725953.1| 26 YEKLAERLGISEEEVIKRLEDLYYKGAVRR 55
                                      69************************9988 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.94
                    Sulfolobus_pRN  20 tleeleektGiek 32 
                                        lee+++ tG + 
  gi|298674203|ref|YP_003725953.1| 121 ILEEIRNETGCPL 133
                                       5889999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      693  (0.0386525); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 946.53
//
Query:       gi|298674204|ref|YP_003725954.1|  [L=353]
Description: radical SAM domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-19   70.9   0.1    5.2e-19   69.2   0.0    1.9  2  Radical_SAM  Radical SAM superfamily
    5.6e-10   39.6   0.0    1.1e-09   38.6   0.0    1.5  1  Fer4_12      4Fe-4S single cluster domain
    8.8e-09   35.8   2.4    2.2e-08   34.5   2.4    1.7  1  SPASM        Iron-sulfur cluster-binding domain
    1.6e-06   28.2   0.0    3.5e-06   27.1   0.0    1.5  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.2   0.0   1.2e-22   5.2e-19       2     165 ..      11     166 ..      10     168 .. 0.88
   2 ?   -1.8   0.1       0.8   3.6e+03       4      19 ..     252     267 ..     250     300 .. 0.71

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 1.2e-22
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgi 78 
                                       ++t+ Cnl C +C  ++t  +  +  +ls+ e ++ ++e+ a+ g+  +il+ggepl+++d+ e++    ++   g+
  gi|298674204|ref|YP_003725954.1|  11 EFTKSCNLSCAHCRGSST--SKMDKDELSTGESKRFIDEI-ANFGKPILILSGGEPLVRSDIFEIASYGTHK---GL 81 
                                       6899*************8..********************.8******************996666666665...** PP

                                       EEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  79 ritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglpG 154
                                       r+++ tngt+++  ++++l++ g+ rvs++++ a+ + +++ ++  ++ fe  l+++e+l++ gi  + +++++ + 
  gi|298674204|ref|YP_003725954.1|  82 RVVMATNGTMVTSNIADKLKRSGIQRVSISIDGATAR-THDEFRgMPGAFEGALNGIEILKNTGIG-IQINTTITK- 155
                                       *************************************.77777778899****************9.555555544. PP

                                       TSHHHHHHHHH CS
                                       xxxxxxxxxxx RF
                       Radical_SAM 155 endeeleelle 165
                                        n +e+ +++e
  gi|298674204|ref|YP_003725954.1| 156 RNIKEIPDIFE 166
                                       66666666655 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.8
                                       ESEESS--TTTSCCTT CS
                                       xxxxxxxxxxxxxxxx RF
                       Radical_SAM   4 trgCnlrCsfCarpet 19 
                                       trgC ++  fC ++++
  gi|298674204|ref|YP_003725954.1| 252 TRGCLGGTGFCFVSSK 267
                                       7899999999998875 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.0   2.5e-13   1.1e-09      10     120 ..      11     117 ..       2     125 .. 0.86

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 2.5e-13
                           Fer4_12  10 lfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpek 86 
                                        f++ CnlsC+ C   +t ++++ +  t e  ++ i+++++  ++ l+l+GGEPl+   ++++ e++ +   +++  
  gi|298674204|ref|YP_003725954.1|  11 EFTKSCNLSCAHCRGSSTSKMDKDELSTGES-KRFIDEIANFGKPILILSGGEPLV---RSDIFEIASYGTHKGL-R 82 
                                       58999****************9999998775.7999********************...99**************.6 PP

                           Fer4_12  87 diwlytgytleelskk.ekeellkeidvlvdGkfe 120
                                       ++++++g++     ++  k++ ++ + + +dG  +
  gi|298674204|ref|YP_003725954.1|  83 VVMATNGTMVTSNIADkLKRSGIQRVSISIDGATA 117
                                       9******9987666554778889999999999765 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   2.4   4.9e-12   2.2e-08       1      64 [.     255     314 ..     255     324 .. 0.74

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 4.9e-12
                             SPASM   1 CfapsrslfInsdGdVvpCcvdkktyveelklGnireesleeIwnse.eyqefr..kskkfplielC 64 
                                       C  ++  +f++s+G+V+pC     +   +   Gnir+e++eeIwn +  ++++r  ++  +  + +C
  gi|298674204|ref|YP_003725954.1| 255 CLGGTGFCFVSSKGEVYPC----GYL--PALAGNIRDEKFEEIWNYSkVFNDLRdvTKL-KGKCGIC 314
                                       77788899***********....233..699*************98879999**75322.2223333 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   7.8e-10   3.5e-06       6      96 ..      14      96 ..      11     115 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 7.8e-10
                           Fer4_14  6 sgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiw 84
                                       +CnlsC  C  ++t k++  + +t e   + +  ++  ++ +  l l+GGePL     ++++++ ++  +++  +++ 
  gi|298674204|ref|YP_003725954.1| 14 KSCNLSCAHCRGSSTSKMDKDELSTGESK-RFI--DEIANFGKPILILSGGEPLV---RSDIFEIASYGTHKG--LRVV 84
                                      79*********999999999988887776.777..4555565566*********5...599******999999..**** PP

                           Fer4_14 85 letngtleiele 96
                                      + tngt+  +  
  gi|298674204|ref|YP_003725954.1| 85 MATNGTMVTSNI 96
                                      ******985544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2106.26
//
Query:       gi|298674205|ref|YP_003725955.1|  [L=130]
Description: hypothetical protein Metev_0229 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.8e-16   58.9   0.0    5.2e-16   58.8   0.0    1.0  1  CcmE       CcmE
  ------ inclusion threshold ------
      0.035   14.1   0.0       0.06   13.3   0.0    1.4  1  PTCB-BRCT  twin BRCT domain


Domain annotation for each model (and alignments):
>> CcmE  CcmE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   0.0   5.8e-20   5.2e-16       5     126 ..       5     125 ..       1     127 [. 0.89

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 5.8e-20
                                       XXXXXXXXXXXXXXXXXXXXXXXXXSSSXXBXTTTTTS--S-.TTSEEEEEEEE-TTT-EE-TTSSEEEEEEE-... CS
                              CcmE   5 rlklivllllvlaavvvlvlsalqenlvyfltpsevlekkae.egrrlrvgGlVkegsvkrdpesleveFvvtd... 77 
                                       + +l+++++++++a+v+l    +++    +l +se+ +++++ +g ++   G +k+g+++++pes   +F ++d   
  gi|298674205|ref|YP_003725955.1|   5 KKILTAMVFIAIVAIVGLWNVDFSDG---YLMVSELKSNPKDyVGGKVNTMGSIKNGTLNKTPES--TSFILKDaes 76 
                                       56777888888888888888888887...9*********8888****************998876..79*****766 PP

                                       T.-EEEEEEES---TT--TTSEEEEEEEE-TTSEEEECCEEESS-XXXX CS
                              CcmE  78 lekelkVeYegilPdlFregqgvvveGrleedgvfeAeevlaKhdekYm 126
                                       ++ ++ +eY+g lP ++ eg+ +   G++ +d+ ++A+++++ +++kY+
  gi|298674205|ref|YP_003725955.1|  77 KTYQIYIEYTGDLPANLAEGKRISLSGTMINDKKIKANKIVMGCPSKYN 125
                                       5679********************************************7 PP

>> PTCB-BRCT  twin BRCT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.7e-06      0.06       3      51 ..      32      82 ..      31      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.7e-06
                                      EEEECB-TTCHHHHHHHHHHTT-EEESSE..ETT-SEEEECSS-CHHHHHH CS
                         PTCB-BRCT  3 icvtgysgddrkslqklieamGaeyskdl..tksvTHLicksgeGekyekA 51
                                      ++v+ ++++ ++++   ++ mG   +++l  t + T +i k++e+++y+ +
  gi|298674205|ref|YP_003725955.1| 32 LMVSELKSNPKDYVGGKVNTMGSIKNGTLnkTPESTSFILKDAESKTYQIY 82
                                      5899999999*******************444479*************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 834.30
//
Query:       gi|298674206|ref|YP_003725956.1|  [L=288]
Description: polyprenyl synthetase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-48  165.5   0.4    1.4e-48  165.2   0.4    1.1  1  polyprenyl_synt  Polyprenyl synthetase


Domain annotation for each model (and alignments):
>> polyprenyl_synt  Polyprenyl synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.2   0.4   7.7e-53   1.4e-48       3     230 ..      28     239 ..      26     260 .. 0.86

  Alignments for each domain:
  == domain 1  score: 165.2 bits;  conditional E-value: 7.7e-53
                                       HHHHHHHHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCTC CS
                   polyprenyl_synt   3 lleealeylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlvG 79 
                                       +++++++++++ gGKr+Rp++++l+  +++ ++   +++ ++a +vel+h+asL+hDD++Dd ++RRG p+ah+++G
  gi|298674206|ref|YP_003725956.1|  28 QIKNVVSHVCNYGGKRIRPIILMLSTDICGGDS---KTSINAALAVELMHSASLIHDDLIDDGIIRRGVPSAHKKFG 101
                                       68999*************************444...889************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHTHHHCH CS
                   polyprenyl_synt  80 nklAindgdfllarafellaklfekslellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKTaylfa 156
                                       +++A++ gdfl +++ el++++  ++ +++  f ++ + ++ G+ +dl      d + f + +y + +++KTa+lfa
  gi|298674206|ref|YP_003725956.1| 102 HSAAMLCGDFLISKSIELMSSY--GH-NAITEFGQAGMSMAHGETIDLG----GDDAGFVEVNYFDCIYKKTASLFA 171
                                       **********************..77.99*******************3....334447799*************** PP

                                       HHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHSS-TSHHHHTT---HHHHHHHHCT-HH CS
                   polyprenyl_synt 157 lpvalaallagasdeelealkdiglelGlaFQiqDDylDlfgdpevlgKpagtDiqegkctlpilkalelaspe 230
                                       +++ ++a+++ga+de++ +++ +g+++G+a+Qi+DD+l +  +     K        + +tlp +++ +++++e
  gi|298674206|ref|YP_003725956.1| 172 ACASIGAYISGADDEMVHRCRLYGEYMGTAYQIVDDLLEYLHE--IDDKS----SVRKSVTLPQIYTKQMTHEE 239
                                       ************99**************************944..44455....55666777777777755444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 1920.82
//
Query:       gi|298674207|ref|YP_003725957.1|  [L=394]
Description: radical SAM domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-13   52.0   0.0    1.4e-13   51.5   0.0    1.2  1  Radical_SAM  Radical SAM superfamily
    8.5e-10   39.0   0.1    2.4e-09   37.6   0.1    1.8  1  SPASM        Iron-sulfur cluster-binding domain
     0.0036   17.6   0.0     0.0067   16.7   0.0    1.4  1  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   0.0   2.4e-17   1.4e-13       4     166 ..      95     247 ..      92     248 .. 0.92

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 2.4e-17
                                       ESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   4 trgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiri 80 
                                       t  C+++C++C         +   +ls++ei + v +   + g   + + gge +l++d+++ +e+  k+  + i +
  gi|298674207|ref|YP_003725957.1|  95 TMKCPNNCIHCGAAD----VVANPELSLDEINNAVTQS-IDLGSYLISFDGGETMLRKDLEDMVENVDKE--RAIAT 164
                                       667***********5....8******************.8**99999999*******************9..57777 PP

                                       EEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  81 tvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGend 157
                                       ++++ ++l  e  ++ l+++g+  v ++ +++ ++++ k  +r + +++ + a++++++a++   +d+ v++   n 
  gi|298674207|ref|YP_003725957.1| 165 VFTSGYGLT-EQRAQSLKNAGLYAVRVSFDSPFEDEHDKVRGRDGAYQDAISAVKNAKSANLL--TDMFVVVSPDNI 238
                                       777777776.*************************8888888******************999..888888888*** PP

                                       HHHHHHHHH CS
                                       xxxxxxxxx RF
                       Radical_SAM 158 eeleellel 166
                                       + l+e+++l
  gi|298674207|ref|YP_003725957.1| 239 DNLKEFYDL 247
                                       99***9987 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.1     4e-13   2.4e-09       1      47 [.     313     353 ..     313     379 .. 0.78

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 4e-13
                             SPASM   1 CfapsrslfInsdGdVvpCcvdkktyveelklGnireesleeIwnse 47 
                                       Cfa++r + ++s GdV pC +      ++l++Gnire+ l++Iw+  
  gi|298674207|ref|YP_003725957.1| 313 CFAGRRWIHVTSAGDVLPCAY------TPLSFGNIREDNLKDIWKRM 353
                                       9******************33......37***************544 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.1e-06    0.0067      17     131 ..      96     204 ..      90     212 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.1e-06
                           Fer4_12  17 lsCk.gCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiwlyt 92 
                                       ++C+ +C+ + + ++ ++ e + + +++++++  +     +++ GGE +l   +++l ++v++v +e      + ++
  gi|298674207|ref|YP_003725957.1|  96 MKCPnNCIHCGAADVVANPELSLDEINNAVTQSIDLGSYLISFDGGETML---RKDLEDMVENVDKERA-IATVFTS 168
                                       55642466677888899999998888888888889999************...9***********9999.789999* PP

                           Fer4_12  93 gytleelskkekeellkeidv.lvdGkfeesledeslrfr 131
                                       gy l e +++   + lk+    +v + f+   ede+ ++r
  gi|298674207|ref|YP_003725957.1| 169 GYGLTEQRAQ---S-LKNAGLyAVRVSFDSPFEDEHDKVR 204
                                       ****999876...3.3333322666666655555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2528.88
//
Query:       gi|298674208|ref|YP_003725958.1|  [L=109]
Description: ATP synthase H subunit [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-07   31.1  19.9    2.8e-07   30.9  19.9    1.0  1  V-ATPase_G_2    Vacuolar (H+)-ATPase G subunit
    1.3e-05   25.7  21.4    1.6e-05   25.4  21.4    1.1  1  V-ATPase_G      Vacuolar (H+)-ATPase G subunit
    0.00016   21.7  26.4    0.00081   19.5  15.4    2.0  2  ATP-synt_B      ATP synthase B/B' CF(0)
  ------ inclusion threshold ------
       0.21   11.3  11.6       0.25   11.0  11.6    1.2  1  Pns11_12        Non-structural protein 11 and 12
       0.72   10.5  11.8        2.1    9.0   4.9    2.1  2  DUF883          Bacterial protein of unknown function (DUF883
        1.3    9.1   9.7        1.6    8.8   9.7    1.0  1  DDHD            DDHD domain
        1.4    8.3  27.4       0.64    9.4  10.6    3.0  3  DUF3552         Domain of unknown function (DUF3552)
        1.9    8.5   8.6        2.1    8.4   8.6    1.0  1  DUF45           Protein of unknown function DUF45
        2.1    9.1   8.4        2.9    8.6   8.4    1.2  1  DUF2203         Uncharacterized conserved protein (DUF2203)
        2.9    6.4  19.9          3    6.4  19.9    1.0  1  AAA_13          AAA domain
        3.3    6.7   9.0         15    4.5   8.7    1.8  1  DUF2252         Uncharacterized protein conserved in bacteria
        4.6    7.5  15.2         12    6.2   0.8    2.1  2  SMBP            Small metal-binding protein
        6.2    7.2  16.6        7.2    7.0   0.6    2.9  3  FAM25           FAM25 family
        7.8    6.5  10.0          7    6.7   0.2    2.8  2  DUF2335         Predicted membrane protein (DUF2335)


Domain annotation for each model (and alignments):
>> V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9  19.9   2.2e-10   2.8e-07       1     101 [.       1     101 [.       1     103 [. 0.95

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 2.2e-10
                                       XXXXHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      V-ATPase_G_2   1 dessrllkeLaerEaeLdqrlEaArkeaereveaAeaeAarilreAeakakalqaeyeqelaeevarireeararae 77 
                                       +++  +l +++e E+  ++ +E+  ke ++++++A+aeA+ i+++A+++a++ +++  + ++e+++++++++ + ++
  gi|298674208|ref|YP_003725958.1|   1 MAKDDVLLKIKEAEQSAEKTVEESVKEKNERISNAKAEADEIIKQAKKDAEESANNSYKSEEEKIRNENAKIIEDGK 77 
                                       566789999*******************************************9999999999*************** PP

                                       HHHHHHHHHHHCSHHHHHHHHHHH CS
                      V-ATPase_G_2  78 aeaqavrkraearlqqAvelilka 101
                                       +ea++++++a +  ++Av+  +k+
  gi|298674208|ref|YP_003725958.1|  78 NEAESIKQKARENEDKAVDYLIKE 101
                                       ******************999887 PP

>> V-ATPase_G  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4  21.4   1.3e-08   1.6e-05      11      99 ..      12     100 ..       4     104 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.3e-08
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHSSHHHHHHHHHHH CS
                        V-ATPase_G  11 qAEkeAaeivkeArkrkakrlkqAkeeAekEieeyrakkekefkekeaeklgseeelekkieketeekikelkesvk 87 
                                       +AE++A++ v+e  k+k++r+ +Ak+eA + i++ ++  e+  +++ +++  +  + ++ki ++ +++ +++k++++
  gi|298674208|ref|YP_003725958.1|  12 EAEQSAEKTVEESVKEKNERISNAKAEADEIIKQAKKDAEESANNSYKSEEEKIRNENAKIIEDGKNEAESIKQKAR 88 
                                       7****************************************9999999999999999999***************** PP

                                       HHHHHHHHHHHH CS
                        V-ATPase_G  88 knkeavvkellk 99 
                                       +n+++ v+ l+k
  gi|298674208|ref|YP_003725958.1|  89 ENEDKAVDYLIK 100
                                       *********997 PP

>> ATP-synt_B  ATP synthase B/B' CF(0)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5  15.4   6.3e-07   0.00081      35      94 ..       6      66 ..       3      67 .. 0.87
   2 !    8.2   7.6    0.0019       2.4      52     102 ..      54     104 ..      52     109 .] 0.84

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 6.3e-07
                        ATP-synt_B 35 IadeiaeAeerrkea.aallaeaeqqlkeAraeAaeiiknAkkeaeklkeeieaeaeaeae 94
                                      +  +i+eAe++++++ ++  +e+ ++  +A+aeA+eiik+Akk+ae+++++  ++ e++++
  gi|298674208|ref|YP_003725958.1|  6 VLLKIKEAEQSAEKTvEESVKEKNERISNAKAEADEIIKQAKKDAEESANNSYKSEEEKIR 66
                                      56689****99876538999******************************99998888775 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0019
                        ATP-synt_B  52 llaeaeqqlkeAraeAaeiiknAkkeaeklkeeieaeaeaeaerlkesAaa 102
                                       + ++++ + ++ r e a+ii+++k+eae +k++++++  ++++ l+++ + 
  gi|298674208|ref|YP_003725958.1|  54 ANNSYKSEEEKIRNENAKIIEDGKNEAESIKQKARENEDKAVDYLIKEFER 104
                                       667899999999**********************99999999888876555 PP

>> Pns11_12  Non-structural protein 11 and 12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0  11.6   0.00019      0.25     116     197 ..      10      87 ..       1      93 [. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00019
                          Pns11_12 116 rkkakaskdkkvekasrdrkdksrskGkgsfkknGkdrreedkrdeysednsykseeelsededapltkkdmlkmms 192
                                        k a+ s +k ve + +++ ++  s  k          ++ +k  e s +nsykseee   +e+a + +    +  s
  gi|298674208|ref|YP_003725958.1|  10 IKEAEQSAEKTVEESVKEK-NERISNAKAE---ADEIIKQAKKDAEESANNSYKSEEEKIRNENAKIIEDGKNEAES 82 
                                       4789999999999999554.4445555555...34445566777899******************888776666666 PP

                          Pns11_12 193 mfqsg 197
                                       + q++
  gi|298674208|ref|YP_003725958.1|  83 IKQKA 87 
                                       66655 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   4.9    0.0016       2.1       6      51 ..       9      54 ..       4      62 .. 0.85
   2 ?    5.4   2.1     0.022        29      23      63 ..      56      96 ..      48     101 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0016
                            DUF883  6 eleslladleellkeaadeageeaeelRerleerlerarerlrdae 51
                                       ++++ +++e+ ++e+ +e +e +++++++++e +++a++ +++ +
  gi|298674208|ref|YP_003725958.1|  9 KIKEAEQSAEKTVEESVKEKNERISNAKAEADEIIKQAKKDAEESA 54
                                      57889999999999999999************99999999988765 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.022
                            DUF883 23 deageeaeelRerleerlerarerlrdaeeavaerakeaae 63
                                      ++ ++e e++R++  + +e+ +++++  +++++e+ ++a++
  gi|298674208|ref|YP_003725958.1| 56 NSYKSEEEKIRNENAKIIEDGKNEAESIKQKARENEDKAVD 96
                                      44455556666666666666666666666666666555554 PP

>> DDHD  DDHD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   9.7    0.0012       1.6      96     191 ..       9     101 ..       2     108 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0012
                              DDHD  96 sigaalkqkvsglvsslsallnrslelaeeesaslaessksherasesskasqeskaaesstasssaksskaeekve 172
                                       +i++a ++ ++++ +s++  ++r  + + e  +  ++++k+ e+++++s +s+e+k +++++ + ++++++++  ++
  gi|298674208|ref|YP_003725958.1|   9 KIKEAEQSAEKTVEESVKEKNERISNAKAEADEIIKQAKKDAEESANNSYKSEEEKIRNENA-KIIEDGKNEA--ES 82 
                                       45555555556666666666666666666666666666666666666666666655444443.4444444444..34 PP

                              DDHD 173 lekvralnwwgRiDYaLqe 191
                                       +++  + n+ + +DY ++e
  gi|298674208|ref|YP_003725958.1|  83 IKQKARENEDKAVDYLIKE 101
                                       44434677777****9995 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   1.7     0.024        30      28      47 ..       9      28 ..       1      31 [. 0.65
   2 ?    9.4  10.6    0.0005      0.64      25      62 ..      28      65 ..      24      70 .. 0.79
   3 ?    3.5   7.0     0.031        40      26      71 ..      59     104 ..      53     108 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.024
                           DUF3552 28 kiaeAeeeAkkiieeAkkeA 47
                                      ki+eAe++A+k +ee  ke 
  gi|298674208|ref|YP_003725958.1|  9 KIKEAEQSAEKTVEESVKEK 28
                                      67777777777777776664 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0005
                           DUF3552 25 aekkiaeAeeeAkkiieeAkkeAeakkkealleakeei 62
                                      ++++i++A++eA++ii++Akk+Ae+   +      e+i
  gi|298674208|ref|YP_003725958.1| 28 KNERISNAKAEADEIIKQAKKDAEESANNSYKSEEEKI 65
                                      6789********************98776655544444 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.031
                           DUF3552  26 ekkiaeAeeeAkkiieeAkkeAeakkkealleakeeihklreelek 71 
                                       +++ ++ ++e +kiie+ k+eAe++k++a  +    +  l +e+e+
  gi|298674208|ref|YP_003725958.1|  59 KSEEEKIRNENAKIIEDGKNEAESIKQKARENEDKAVDYLIKEFER 104
                                       5555667788999************998866555555555566665 PP

>> DUF45  Protein of unknown function DUF45
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   8.6    0.0016       2.1      14     113 ..       9     103 ..       2     109 .] 0.72

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0016
                             DUF45  14 evsaPkgvseeeiedfvkkkakwiekklakleerakeaekelesgesfpllGkkyrlkvekgkeasvklkreelela 90 
                                       +++  ++  e+++e+ vk+k + i +  a+ +e  k+a+k+ e+ +++ +  ++ +++ e  k      +++ +++a
  gi|298674208|ref|YP_003725958.1|   9 KIKEAEQSAEKTVEESVKEKNERISNAKAEADEIIKQAKKDAEESANNSYKSEEEKIRNENAK-----IIEDGKNEA 80 
                                       5666678899****************************************9999999999988.....333333333 PP

                             DUF45  91 vkkeeeeeklrkaleewlrkeak 113
                                       ++ ++++++ +++  ++l ke +
  gi|298674208|ref|YP_003725958.1|  81 ESIKQKARENEDKAVDYLIKEFE 103
                                       33333333334444444444444 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   8.4    0.0023       2.9       8      93 ..      17     104 ..       9     107 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0023
                           DUF2203   8 AnalLp.llkelleelralrkeleeleeeleeakaeaekseaaeleaeleele.aeieelveeieelGvevkdleag 82 
                                       A++++   +ke+ e++ ++++e+ e+ ++ ++  +e+++++++++e+++++ + + ie+  +e e+++ + ++ e  
  gi|298674208|ref|YP_003725958.1|  17 AEKTVEeSVKEKNERISNAKAEADEIIKQAKKDAEESANNSYKSEEEKIRNENaKIIEDGKNEAESIKQKARENEDK 93 
                                       6666652599999**************99999999988888777777766555055788899999999999999999 PP

                           DUF2203  83 lvDFpakldge 93 
                                        vD+  k  ++
  gi|298674208|ref|YP_003725958.1|  94 AVDYLIKEFER 104
                                       99998776665 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4  19.9    0.0023         3     359     455 ..       5     108 ..       1     109 [] 0.72

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0023
                            AAA_13 359 svkakiesi.kklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekai.eklekelk 433
                                       +v  ki+++ +++ ++++e++++ Ne+++n ++e+ e+ k+ +++  e++++ ++  ++k+++ +++i e+ ++e++
  gi|298674208|ref|YP_003725958.1|   5 DVLLKIKEAeQSAEKTVEESVKEKNERISNAKAEADEIIKQAKKDAEESANNSYKSEEEKIRNENAKIiEDGKNEAE 81 
                                       5555664440455578999****************************999999999999999988775244555555 PP

                            AAA_13 434 eeeaelkkleee.....ikeLekqlrd 455
                                        +++++++ e++     ike e+ +++
  gi|298674208|ref|YP_003725958.1|  82 SIKQKARENEDKavdylIKEFERAITN 108
                                       555544444444666667777777765 PP

>> DUF2252  Uncharacterized protein conserved in bacteria (DUF2252)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   8.7     0.011        15     123     205 ..      14      90 ..       7     107 .. 0.49

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.011
                           DUF2252 123 erealdewyeridvelleeatseeakgvvrkalekarkrtreklldklteleegkrrikddppkllrlseaereaie 199
                                       e++a+++++e+      ++ + ++ak + ++++++a+k+++e++ +++ + e   ++i++++ k+++  ++e+e+i+
  gi|298674208|ref|YP_003725958.1|  14 EQSAEKTVEES---VKEKNERISNAKAEADEIIKQAKKDAEESANNSYKSEE---EKIRNENAKIIEDGKNEAESIK 84 
                                       23333333333...33444455555556666666666665555555555544...4555555555555555554444 PP

                           DUF2252 200 aalesy 205
                                       +  ++ 
  gi|298674208|ref|YP_003725958.1|  85 QKAREN 90 
                                       433333 PP

>> SMBP  Small metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   8.2     0.012        16      51      99 ..       8      56 ..       2      67 .. 0.76
   2 ?    6.2   0.8    0.0091        12      55      89 ..      75     109 .]      62     109 .] 0.78

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.012
                                      HHHHHHHHHHHHH...-------HHHHHHHHHHHHHHHHHCT-HHHHHH CS
                              SMBP 51 eHaeealkhakaaaekakeeekehldegikhLeeAIkhgkaghadvAtk 99
                                         +ea + a+++ e++ +e++e+++++  + +e Ik++k++  + A +
  gi|298674208|ref|YP_003725958.1|  8 LKIKEAEQSAEKTVEESVKEKNERISNAKAEADEIIKQAKKDAEESANN 56
                                      5567777888888888888888888888888888888888888777765 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0091
                                       HHHHHHHHH...-------HHHHHHHHHHHHHHHH CS
                              SMBP  55 ealkhakaaaekakeeekehldegikhLeeAIkhg 89 
                                       + +++a++ ++ka+e+e++ +d  ik+ e AI+ +
  gi|298674208|ref|YP_003725958.1|  75 DGKNEAESIKQKARENEDKAVDYLIKEFERAITNA 109
                                       44555666667799999***************875 PP

>> FAM25  FAM25 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   4.1     0.019        24      28      59 ..      10      41 ..       4      44 .. 0.78
   2 ?    3.2   9.2     0.088   1.1e+02       1      48 [.      17      67 ..      17      78 .. 0.79
   3 ?    7.0   0.6    0.0057       7.2      25      53 ..      80     109 .]      68     109 .] 0.80

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.019
                             FAM25 28 lKkAqesgekvvKevtekvtntvtnavtHAaE 59
                                      +K+A++s ek v e  ++  + ++na + A E
  gi|298674208|ref|YP_003725958.1| 10 IKEAEQSAEKTVEESVKEKNERISNAKAEADE 41
                                      78999999999888877777888887776655 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.088
                             FAM25  1 Avhaveevvkev...veHaKeaGEKAiadalKkAqesgekvvKevtekvtn 48
                                      A++ vee vke    +  aK   +  i +a K A+es +   K   ek+ n
  gi|298674208|ref|YP_003725958.1| 17 AEKTVEESVKEKnerISNAKAEADEIIKQAKKDAEESANNSYKSEEEKIRN 67
                                      6789*****9871125556777778899999*******9999998888766 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0057
                             FAM25  25 adalK.kAqesgekvvKevtekvtntvtna 53 
                                       a+ +K kA+e ++k+v    ++   ++tna
  gi|298674208|ref|YP_003725958.1|  80 AESIKqKARENEDKAVDYLIKEFERAITNA 109
                                       6667658********988888888888886 PP

>> DUF2335  Predicted membrane protein (DUF2335)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   4.3      0.12   1.5e+02      17      46 ..      17      46 ..      14      71 .. 0.85
   2 ?    6.7   0.2    0.0054         7      24      48 ..      80     104 ..      69     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.12
                           DUF2335 17 AeRIiamaekEqehRheleeklldaqires 46
                                      Ae  +++ +kE + R+++ + + d  i++ 
  gi|298674208|ref|YP_003725958.1| 17 AEKTVEESVKEKNERISNAKAEADEIIKQA 46
                                      788888999999999999999999888865 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0054
                           DUF2335  24 aekEqehRheleeklldaqiresrr 48 
                                       ae+  + ++e+e+k++d++i+e +r
  gi|298674208|ref|YP_003725958.1|  80 AESIKQKARENEDKAVDYLIKEFER 104
                                       56666889************98666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3438  (0.191756); expected 358.6 (0.02)
Passed bias filter:                      809  (0.0451224); expected 358.6 (0.02)
Passed Vit filter:                       167  (0.00931452); expected 17.9 (0.001)
Passed Fwd filter:                        40  (0.00223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.67u 0.35s 00:00:01.02 Elapsed: 00:00:00.49
# Mc/sec: 663.33
//
Query:       gi|298674209|ref|YP_003725959.1|  [L=676]
Description: V-type ATPase 116 kDa subunit [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-27   95.5  11.4    2.1e-19   69.0   0.0    4.0  4  V_ATPase_I    V-type ATPase 116kDa subunit family
     0.0081   16.1   9.0       0.55   10.2   1.7    2.7  2  Prefoldin_2   Prefoldin subunit
  ------ inclusion threshold ------
      0.016   15.5   7.0       0.67   10.2   2.1    3.2  3  ABC_tran_CTD  ABC transporter C-terminal domain
       0.02   15.1   1.9       0.02   15.1   1.9    2.3  2  Osmo_CC       Osmosensory transporter coiled coil
      0.046   13.6   2.4        1.8    8.5   0.2    2.5  2  Prefoldin     Prefoldin subunit
      0.051   13.6   0.2       0.21   11.5   0.0    2.2  1  TOM13         Outer membrane protein TOM13
       0.08   13.2   3.8        1.6    9.0   0.3    2.6  2  Spc24         Spc24 subunit of Ndc80
       0.14   12.6   3.5        6.8    7.2   0.3    2.7  2  TBCC_N        Tubulin-specific chaperone C N-terminal domain
       0.22   12.0   3.3        6.8    7.2   0.7    3.0  3  NPV_P10       Nucleopolyhedrovirus P10 protein
       0.26   11.3   3.6        8.1    6.5   1.2    2.7  2  DUF1664       Protein of unknown function (DUF1664)
       0.36   10.9   4.1        0.3   11.2   0.2    2.7  2  Vps51         Vps51/Vps67
       0.47   10.1  12.6       0.22   11.2   1.8    2.4  2  YkyA          Putative cell-wall binding lipoprotein
        0.6    9.9   7.1        1.1    9.1   0.3    2.3  2  Phage_GP20    Phage minor structural protein GP20
       0.69    9.8   2.7        6.5    6.6   0.2    2.5  2  Sec34         Sec34-like family
        1.6    8.1   8.4       0.38   10.1   0.1    2.7  3  GAS           Growth-arrest specific micro-tubule binding
        2.2    7.9   6.4          6    6.5   0.2    2.3  2  Lebercilin    Ciliary protein causing Leber congenital amauro
        2.4    8.4  10.9         18    5.6   0.6    3.3  2  DUF5082       Domain of unknown function (DUF5082)
        2.7    6.8   7.8        2.5    6.9   1.7    2.1  2  Spc7          Spc7 kinetochore protein
        5.2    7.4   9.8       0.55   10.6   0.5    3.1  3  BLOC1_2       Biogenesis of lysosome-related organelles compl
        9.2    6.2  10.2        2.5    8.0   2.9    2.4  2  Cauli_AT      Aphid transmission protein


Domain annotation for each model (and alignments):
>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.5      0.15   1.3e+02      60     107 ..      75     122 ..      51     130 .. 0.64
   2 !   69.0   0.0   2.4e-22   2.1e-19     221     462 ..     189     424 ..     173     434 .. 0.75
   3 ?    0.1   0.3      0.16   1.4e+02     517     547 ..     494     524 ..     491     533 .. 0.89
   4 !   29.6   0.1     2e-10   1.8e-07     717     811 ..     579     668 ..     576     669 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.15
                        V_ATPase_I  60 eesleapeekeldeleeelekleeelkelnenleklkkelnelvelka 107
                                       +es +++ +k  ++l+++l++l+++++e +e+ ++l+++l+++++lk+
  gi|298674209|ref|YP_003725959.1|  75 DESVSEDADKVWSNLDDRLNELDSKITEKTEERSELESKLKDIENLKK 122
                                       455556666666777777777777777777777777777777766655 PP

  == domain 2  score: 69.0 bits;  conditional E-value: 2.4e-22
                        V_ATPase_I 221 ekikkicesfgaklyelpeseeereeklkeveeriedlekvleqteealkevleeiakeleewklkvkkeka.iyht 296
                                        +++ki + ++ k  ++pe++   ++ l++ e + + +e+ +e+ +e+++++ e++++ + +    ++ e +   + 
  gi|298674209|ref|YP_003725959.1| 189 GQVSKILSDYSFKELRIPEKSGVPKDILSKFEGDKQSIEEKIESIDEEIESIKEQYSNFILASDELLSMEAEkAEAP 265
                                       56788888888888888888887777777777777777777777777777777777666655555444443303344 PP

                        V_ATPase_I 297 LnlfnldvtkkvliaegWvpkeeleeiqkalkeateess......ssvpsilneietketpPTyfrtnkfteafQei 367
                                       L +    +++++++ +gWvp +e +++ ++l++at+ +       s+ +   +e++++e pPT  +  k+t+   ++
  gi|298674209|ref|YP_003725959.1| 266 LKMA---TSENTFVINGWVPDDEYDTVVQSLDKATNGHAyvsiveSEESDEHEEYSEEEIPPTEYNNSKLTKPLETV 339
                                       5555...7889**********************996655555544444444444455678***************** PP

                        V_ATPase_I 368 vdaYGiarYrEvNpalftiitFPFlFavMFGDiGHGlllllfalllvlkekklkkkkkdeilemlfsgRYiillmGl 444
                                       +d Y+ +rY+E+ p+ +  i  P  +++M GD+G +l++l++a+ +  k  +++  + + +++       +++   +
  gi|298674209|ref|YP_003725959.1| 340 MDLYSRPRYKELDPTSLIFIALPLFYGMMLGDVGYALVILAAAFGI-KKYVNME--SLKPVMN-------VLIYCQI 406
                                       ***********************************99988777653.3333332..3334444.......5666789 PP

                        V_ATPase_I 445 fsiYtGliYNdifsksln 462
                                       fs+  G++Y ++f++sl 
  gi|298674209|ref|YP_003725959.1| 407 FSFIFGILYGEVFGISLG 424
                                       **************9985 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.16
                        V_ATPase_I 517 vilGviqMlfgvllslvNalyfkkkldiile 547
                                        +lG+iq  +g++l +vN   ++  +d ile
  gi|298674209|ref|YP_003725959.1| 494 AVLGIIQINIGYVLGMVNVYRNHGLMDAILE 524
                                       589****************999988887765 PP

  == domain 4  score: 29.6 bits;  conditional E-value: 2e-10
                        V_ATPase_I 717 iSnTASYLRLWALSLAHaqLseVlwemvlkkallksksvlgvillvilfavfavltvavLllmeglsafLHaLRLhW 793
                                       +Sn  SY R+ A+ L+   ++ ++ e  + + l+      + ill+il ++ +++  a   ++ ++   L aLRL+ 
  gi|298674209|ref|YP_003725959.1| 579 LSNVLSYARIAAVGLSSIYIAYIVNEIAFVM-LSP----DTSILLAILSILVFIFGHALNTVLGVIAPGLQALRLQY 650
                                       6888899999888887777777777777766.333....333444444444444445555556677888999***** PP

                        V_ATPase_I 794 VEfqsKFykgdGykFepf 811
                                       VEf +KFy+g G k++pf
  gi|298674209|ref|YP_003725959.1| 651 VEFFTKFYEGGGKKYNPF 668
                                       *****************9 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   1.7   0.00061      0.55       8      44 ..      87     123 ..      73     130 .. 0.55
   2 !    9.2   0.9    0.0013       1.1       8      44 ..     224     260 ..     214     268 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00061
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT CS
                       Prefoldin_2   8 qqlqqqlqqlaqqikqletqlkelelvleelellded 44 
                                       ++l ++l +l+++i+++ ++ +ele+ l+ +e+l++d
  gi|298674209|ref|YP_003725959.1|  87 SNLDDRLNELDSKITEKTEERSELESKLKDIENLKKD 123
                                       3444555555555555555555555555555555554 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0013
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT CS
                       Prefoldin_2   8 qqlqqqlqqlaqqikqletqlkelelvleelellded 44 
                                       q ++++++ ++++i+++++q ++  l+++el +++ +
  gi|298674209|ref|YP_003725959.1| 224 QSIEEKIESIDEEIESIKEQYSNFILASDELLSMEAE 260
                                       6777888888888888888888888888888887766 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.2     0.015        14       9      36 ..      92     119 ..      78     144 .. 0.74
   2 ?   -1.5   0.0       3.5   3.2e+03      14      29 ..     151     166 ..     146     169 .. 0.81
   3 ?   10.2   2.1   0.00075      0.67      12      52 ..     225     263 ..     198     274 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.015
                      ABC_tran_CTD   9 eleeleaeIeaLEeeiaeleaeladpel 36 
                                       +l el+++I +  ee +ele +l d e 
  gi|298674209|ref|YP_003725959.1|  92 RLNELDSKITEKTEERSELESKLKDIEN 119
                                       5667777777777777777777777664 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.5
                      ABC_tran_CTD  14 eaeIeaLEeeiaelea 29 
                                        + I++LE++i+ +++
  gi|298674209|ref|YP_003725959.1| 151 KENIDSLETDISGITN 166
                                       5789999999988765 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00075
                      ABC_tran_CTD  12 eleaeIeaLEeeiaeleaeladpelysdpeklaelsaelee 52 
                                        +e++Ie+++eei+++ ++ ++  l sd+  l    ae++e
  gi|298674209|ref|YP_003725959.1| 225 SIEEKIESIDEEIESIKEQYSNFILASDE--LLSMEAEKAE 263
                                       59*******************88777665..4444444444 PP

>> Osmo_CC  Osmosensory transporter coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.2       5.5     5e+03      20      38 ..      92     110 ..      86     122 .. 0.61
   2 ?   15.1   1.9   2.3e-05      0.02      15      36 ..     224     245 ..     219     249 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 5.5
                                       HHHHHHHHHHHHHHHHHHH CS
                           Osmo_CC  20 kvedideeIaaLeekRqrL 38 
                                       +++++d  I++  e R +L
  gi|298674209|ref|YP_003725959.1|  92 RLNELDSKITEKTEERSEL 110
                                       5556666666555555544 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2.3e-05
                                       THHHHHHHHHHHHHHHHHHHHH CS
                           Osmo_CC  15 dnIEqkvedideeIaaLeekRq 36 
                                       ++IE+k+e ideeI+ ++e+  
  gi|298674209|ref|YP_003725959.1| 224 QSIEEKIESIDEEIESIKEQYS 245
                                       78**************999855 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.2     0.002       1.8       2      34 ..      97     129 ..      77     138 .. 0.71
   2 ?    4.2   0.1     0.042        37       2      29 ..     227     254 ..     220     285 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.002
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                         Prefoldin   2 keeleslqaelaqlkeaieelektletlktlkk 34 
                                       +++++++++e+++l+++++++e++++ l+ l++
  gi|298674209|ref|YP_003725959.1|  97 DSKITEKTEERSELESKLKDIENLKKDLQPLSN 129
                                       456666777777777777777777777766665 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.042
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin   2 keeleslqaelaqlkeaieelektletl 29 
                                       +e++es+ +e++++ke+ +++  + + l
  gi|298674209|ref|YP_003725959.1| 227 EEKIESIDEEIESIKEQYSNFILASDEL 254
                                       4455555555555555555555555555 PP

>> TOM13  Outer membrane protein TOM13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00024      0.21      13      59 ..     324     370 ..     307     383 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00024
                             TOM13  13 eeeelesssesssssplilykpptllsllrsaainlvLPFinGlmLG 59 
                                        +e  +s+ ++  ++++ ly+ p+  +l   + i + LP + G+mLG
  gi|298674209|ref|YP_003725959.1| 324 PTEYNNSKLTKPLETVMDLYSRPRYKELDPTSLIFIALPLFYGMMLG 370
                                       222223333333444788****************************9 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.3    0.0018       1.6       9      62 ..      89     139 ..      79     171 .. 0.68
   2 ?    4.6   0.3     0.042        37       3      46 ..     220     263 ..     218     294 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0018
                             Spc24   9 iakelsdleselesleselaelkeeleeleeeseekeserve.detl.lklklYrs 62 
                                       +   l++l+s++++ ++e +el+++l+++e+ +++      +  +++ l l lYr 
  gi|298674209|ref|YP_003725959.1|  89 LDDRLNELDSKITEKTEERSELESKLKDIENLKKD-----LQpLSNIpLDLDLYRG 139
                                       34455555555555555555555555555555555.....3335555788888885 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.042
                             Spc24   3 dnekfriakelsdleselesleselaelkeeleeleeeseekes 46 
                                       + +k++i ++++++++e+es++++ ++     +el +++ ek++
  gi|298674209|ref|YP_003725959.1| 220 EGDKQSIEEKIESIDEEIESIKEQYSNFILASDELLSMEAEKAE 263
                                       66899999**************9999999988888888877333 PP

>> TBCC_N  Tubulin-specific chaperone C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.3    0.0076       6.8      26      77 ..      77     126 ..      71     130 .. 0.85
   2 ?    5.4   0.3     0.026        24      33      64 ..     214     246 ..     193     264 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0076
                            TBCC_N  26 veeekvdsFlkaFteekaaieellesveesadksklkqkldeitaeiqeLqk 77 
                                       + +e +d+ +++++++ +++++++++ +  +++s+l++kl++i++  ++Lq 
  gi|298674209|ref|YP_003725959.1|  77 SVSEDADKVWSNLDDRLNELDSKITEKT--EERSELESKLKDIENLKKDLQP 126
                                       568999********************99..8999999999999988888875 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.026
                            TBCC_N  33 sFlkaFteekaaieellesve.esadksklkqk 64 
                                        +l++F+  k++iee++es++ e ++ +++ ++
  gi|298674209|ref|YP_003725959.1| 214 DILSKFEGDKQSIEEKIESIDeEIESIKEQYSN 246
                                       6899****************9433333333344 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.7    0.0075       6.8      13      48 ..      93     128 ..      76     136 .. 0.72
   2 ?   -2.1   0.0       6.2   5.5e+03      49      63 ..     152     166 ..     141     175 .. 0.67
   3 ?    3.5   0.0      0.11        99       5      37 ..     215     247 ..     212     262 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0075
                           NPV_P10  13 ikavddkVdalqqqvddvqenlpdvtelnekLdaqs 48 
                                        +++d+k++   ++  +++++l+d+++l++ L+ +s
  gi|298674209|ref|YP_003725959.1|  93 LNELDSKITEKTEERSELESKLKDIENLKKDLQPLS 128
                                       456666666666666888888888888888777666 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 6.2
                           NPV_P10  49 aqLaeletkvenIqd 63 
                                       +++++let ++ I++
  gi|298674209|ref|YP_003725959.1| 152 ENIDSLETDISGITN 166
                                       455566666666655 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.11
                           NPV_P10   5 iLlvIradikavddkVdalqqqvddvqenlpdv 37 
                                       iL     d + +++k++++++++++++e+  ++
  gi|298674209|ref|YP_003725959.1| 215 ILSKFEGDKQSIEEKIESIDEEIESIKEQYSNF 247
                                       566666677889999999999999999988875 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   1.2     0.009       8.1      51     102 ..      76     123 ..      63     166 .. 0.82
   2 ?    4.1   0.0      0.05        45      96     122 ..     216     242 ..     204     250 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.009
                           DUF1664  51 eqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseiged 102
                                       e+vse+  ++  +L +r++++d+k+ e +e  +e+++++++++    ++++d
  gi|298674209|ref|YP_003725959.1|  76 ESVSEDADKVWSNLDDRLNELDSKITEKTEERSELESKLKDIE----NLKKD 123
                                       5788888888899999999999999999999888888876554....33333 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.05
                           DUF1664  96 lseigedvesvkeavegleskleriee 122
                                       ls+++ d +s++e +e++++++e+i+e
  gi|298674209|ref|YP_003725959.1| 216 LSKFEGDKQSIEEKIESIDEEIESIKE 242
                                       566666777777777777777776654 PP

>> Vps51  Vps51/Vps67
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.5       1.8   1.6e+03      41      41 ..     106     106 ..      79     127 .. 0.52
   2 ?   11.2   0.2   0.00034       0.3      28      66 ..     223     260 ..     190     273 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.8
                             Vps51  41 e 41 
                                       e
  gi|298674209|ref|YP_003725959.1| 106 E 106
                                       2 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00034
                             Vps51  28 easllseiraldselkalVydnYskLisasdtIrkmkse 66 
                                       ++s++ +i+  d+e+ + + + Ys +i asd++ +m+ e
  gi|298674209|ref|YP_003725959.1| 223 KQSIEEKIESIDEEI-ESIKEQYSNFILASDELLSMEAE 260
                                       456669999999999.569*****************987 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.8   0.00025      0.22      28     107 ..      54     128 ..      32     132 .. 0.78
   2 ?    3.7   3.5     0.047        42      60     100 ..     223     263 ..     212     273 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00025
                              YkyA  28 telekkeqelyeeiielgmdefdkikklsdealenveeReellekekesieeakeefekikeeieeiedeelkkeae 104
                                       ++  kk  ++ +  + lg +  + +++ +d++ +n+++R ++l++    i e  ee +++++++++ie  +lkk+++
  gi|298674209|ref|YP_003725959.1|  54 EDISKKLVKIRSLSNYLGVKGDESVSEDADKVWSNLDDRLNELDS---KITEKTEERSELESKLKDIE--NLKKDLQ 125
                                       455566666666677788999999********************9...89999999999********5..5788888 PP

                              YkyA 105 eli 107
                                        l 
  gi|298674209|ref|YP_003725959.1| 126 PLS 128
                                       765 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.047
                              YkyA  60 lenveeReellekekesieeakeefekikeeieeiedeelk 100
                                        +++ee+ e +++e esi+e + +f  +++e+ ++e e+++
  gi|298674209|ref|YP_003725959.1| 223 KQSIEEKIESIDEEIESIKEQYSNFILASDELLSMEAEKAE 263
                                       56778888888888888888888887777777777666544 PP

>> Phage_GP20  Phage minor structural protein GP20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   1.9      0.07        63      22      59 ..      88     125 ..      71     130 .. 0.67
   2 ?    9.1   0.3    0.0012       1.1      13      49 ..     209     245 ..     150     273 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.07
                        Phage_GP20  22 eveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqie 59 
                                       ++++  ++l ++++++ ++ ++L+ k kd e+L+k+++
  gi|298674209|ref|YP_003725959.1|  88 NLDDRLNELDSKITEKTEERSELESKLKDIENLKKDLQ 125
                                       44555566777777777777777777777777777765 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0012
                        Phage_GP20  13 kditkakldeveeerdtlkeqlkdrdkqLedLkkkak 49 
                                       + ++k+ l++ e ++++++e+++  d+++e +k+++ 
  gi|298674209|ref|YP_003725959.1| 209 SGVPKDILSKFEGDKQSIEEKIESIDEEIESIKEQYS 245
                                       4566777777777777777777777777777777654 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.2      0.12     1e+02      21      77 ..      88     143 ..      76     146 .. 0.76
   2 ?    6.6   0.2    0.0073       6.5      17      56 ..     221     260 ..     212     275 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.12
                             Sec34  21 ealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFeeldpi 77 
                                       ++ + L+el +k ++ +e+ s+l+++ +++ + +k+l+ l+ +i+ +L+ ++ +++i
  gi|298674209|ref|YP_003725959.1|  88 NLDDRLNELDSKITEKTEERSELESKLKDIENLKKDLQPLS-NIPLDLDLYRGYENI 143
                                       56677888888888888888888888888888888887775.588888887777776 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0073
                             Sec34  17 eqtdealeqLeeleekfksvsektsslheaceqlleeqkr 56 
                                        + ++++e++e++ e+ +s++e+ s++  a+++ll+ + +
  gi|298674209|ref|YP_003725959.1| 221 GDKQSIEEKIESIDEEIESIKEQYSNFILASDELLSMEAE 260
                                       566889999***********************99987655 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00042      0.38      43      92 ..      80     129 ..      57     168 .. 0.82
   2 ?    2.3   0.3       0.1        93      54      80 ..     221     247 ..     207     272 .. 0.53
   3 ?   -1.6   0.3       1.6   1.4e+03      35      65 ..     308     338 ..     307     341 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00042
                               GAS  43 ernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlka 92 
                                       e ++k  s++  + ++l  ++++ +ee+ eL+ +lk+ e+ k++l+ l +
  gi|298674209|ref|YP_003725959.1|  80 EDADKVWSNLDDRLNELDSKITEKTEERSELESKLKDIENLKKDLQPLSN 129
                                       566778888999999999**********************9999997765 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.1
                               GAS  54 qenkrlkepLkkaeeeveeLrkqlkny 80 
                                        ++++++e+++  +ee+e  ++q  n+
  gi|298674209|ref|YP_003725959.1| 221 GDKQSIEEKIESIDEEIESIKEQYSNF 247
                                       333333333333333333333333333 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.6
                               GAS  35 ieelkkkeernekelseisqenkrlkepLkk 65 
                                        ee ++ ee  e e+  ++ +n++l++pL++
  gi|298674209|ref|YP_003725959.1| 308 SEESDEHEEYSEEEIPPTEYNNSKLTKPLET 338
                                       5788899999999999999**********97 PP

>> Lebercilin  Ciliary protein causing Leber congenital amaurosis disease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   1.5      0.05        45      80     109 ..      90     119 ..      76     128 .. 0.48
   2 ?    6.5   0.2    0.0067         6      47      78 ..     215     246 ..     211     273 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.05
                        Lebercilin  80 qekerelekklkekeaellrlkdklkklkk 109
                                        ++ +el++k+ ek +e  +l++klk+ ++
  gi|298674209|ref|YP_003725959.1|  90 DDRLNELDSKITEKTEERSELESKLKDIEN 119
                                       233333333333333333333333333333 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0067
                        Lebercilin  47 aLskyedteaeLpqllarhneEvrvlrerlRk 78 
                                        Lsk+e++++++ + +++ +eE++ ++e++ +
  gi|298674209|ref|YP_003725959.1| 215 ILSKFEGDKQSIEEKIESIDEEIESIKEQYSN 246
                                       69***************************987 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.6      0.02        18      76     116 ..      79     119 ..      59     129 .. 0.59
   2 ?    2.6   3.9      0.17   1.5e+02      74     105 ..     214     245 ..     142     248 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.02
                           DUF5082  76 essyqtyvdkldelidaieeEIerLenqiseaqgvldtlqs 116
                                        ++ +++ ++ld+   +++++I++  +++se++++l+ +++
  gi|298674209|ref|YP_003725959.1|  79 SEDADKVWSNLDDRLNELDSKITEKTEERSELESKLKDIEN 119
                                       44555555555555555555555555555555555554444 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.17
                           DUF5082  74 nlessyqtyvdkldelidaieeEIerLenqis 105
                                       ++ s+ +  ++ ++e i +i+eEIe +++q s
  gi|298674209|ref|YP_003725959.1| 214 DILSKFEGDKQSIEEKIESIDEEIESIKEQYS 245
                                       66666777778888889999999999988876 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   1.7    0.0027       2.5     202     238 ..      87     123 ..      51     129 .. 0.58
   2 ?    3.3   0.5     0.035        32     147     178 ..     215     246 ..     202     274 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0027
                              Spc7 202 eelreelaelkaeieekkkelaelqeqleeleekiee 238
                                        +l ++l+el+++i ek +e +el+++l+++e+  ++
  gi|298674209|ref|YP_003725959.1|  87 SNLDDRLNELDSKITEKTEERSELESKLKDIENLKKD 123
                                       3455566666666666666666666666555544333 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.035
                              Spc7 147 nlegleedkelLekqeeeldellpeleeekae 178
                                       +l+++e dk+ +e++ e +de  ++++e++++
  gi|298674209|ref|YP_003725959.1| 215 ILSKFEGDKQSIEEKIESIDEEIESIKEQYSN 246
                                       45555555555555555555555555555553 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       6.6   5.9e+03      17      38 ..      18      39 ..      12      45 .. 0.77
   2 ?   10.6   0.5   0.00062      0.55      37      87 ..      87     137 ..      76     139 .. 0.88
   3 ?    1.9   0.3      0.32   2.9e+02      38      60 ..     225     247 ..     217     260 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 6.6
                           BLOC1_2 17 atvedyklLeklNeaasekykk 38
                                      + ++ +++L++lN   +e y++
  gi|298674209|ref|YP_003725959.1| 18 IMKDTVETLHNLNVYHIEDYNE 39
                                      5667788888888888887765 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00062
                           BLOC1_2  37 kklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDey 87 
                                        +l+d++++l +k+ +  e+  el+++l+ i++++k+++ L ++   LD y
  gi|298674209|ref|YP_003725959.1|  87 SNLDDRLNELDSKITEKTEERSELESKLKDIENLKKDLQPLSNIPLDLDLY 137
                                       67999*********************************9999887777765 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.32
                           BLOC1_2  38 klkdvaaslekkleklnekyeel 60 
                                       +++++++s+ +++e ++e+y ++
  gi|298674209|ref|YP_003725959.1| 225 SIEEKIESIDEEIESIKEQYSNF 247
                                       57788888888888888888776 PP

>> Cauli_AT  Aphid transmission protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   2.9    0.0028       2.5      54     124 ..      56     125 ..      53     166 .. 0.73
   2 ?    2.0   1.0      0.19   1.7e+02     119     159 ..     204     245 ..     143     249 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0028
                          Cauli_AT  54 varslLklskllsylGLekDesealsksksPfgsvfkklkkifkeggedkekktklletLkeaqnrikkle 124
                                       ++++l+k+  l  ylG++ Des +   +k+  +++ ++l++   +  e++e++++l + Lk+++n  k+l+
  gi|298674209|ref|YP_003725959.1|  56 ISKKLVKIRSLSNYLGVKGDESVSEDADKVW-SNLDDRLNELDSKITEKTEERSELESKLKDIENLKKDLQ 125
                                       5789999**************9866666654.455555555555555555555555556666665555544 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.19
                          Cauli_AT 119 rikkleeetkklaekivtekl.lkeevkdlderlseirdslk 159
                                       ri + +   k + +k + +k+ ++e++  +de++++i+++  
  gi|298674209|ref|YP_003725959.1| 204 RIPEKSGVPKDILSKFEGDKQsIEEKIESIDEEIESIKEQYS 245
                                       444455556778888776655378899999999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (676 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1600  (0.0892409); expected 358.6 (0.02)
Passed bias filter:                      962  (0.0536561); expected 358.6 (0.02)
Passed Vit filter:                       155  (0.00864521); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.89u 0.31s 00:00:01.20 Elapsed: 00:00:00.53
# Mc/sec: 3817.98
//
Query:       gi|298674210|ref|YP_003725960.1|  [L=78]
Description: H+transporting two-sector ATPase subunit C [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-16   60.6  11.5    1.6e-16   60.4  11.5    1.1  1  ATP-synt_C  ATP synthase subunit C


Domain annotation for each model (and alignments):
>> ATP-synt_C  ATP synthase subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4  11.5   8.7e-21   1.6e-16       1      59 [.      17      75 ..      17      76 .. 0.98

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 8.7e-21
                                      HHHHHHH.GGGHHHHHHHHHHHHHHHHHHHHSGHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_C  1 lgaglavGlsalgsGigiGkagsagiravarnpklftksliilafaeaialygLivali 59
                                      +gag+avGl+++++Gi+   +gsa+++a+a+n +lf+k li+ +++e+i ++gL+vali
  gi|298674210|ref|YP_003725960.1| 17 IGAGIAVGLAGIATGIAEKDIGSAAVGAMAENESLFGKGLILTVIPETIVIFGLVVALI 75
                                      7*********************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.32u 0.26s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 606.33
//
Query:       gi|298674211|ref|YP_003725961.1|  [L=183]
Description: H+transporting two-sector ATPase E subunit [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.8e-23   80.6  20.5    3.7e-21   75.5  20.5    2.0  1  vATP-synt_E     ATP synthase (E/31 kDa) subunit
    3.8e-06   27.0  13.6      7e-06   26.2  13.6    1.4  1  ATP-synt_B      ATP synthase B/B' CF(0)
    0.00082   19.7  12.2    0.00082   19.7  12.2    1.8  2  V-ATPase_G_2    Vacuolar (H+)-ATPase G subunit
  ------ inclusion threshold ------
      0.015   15.4  10.2      0.015   15.4  10.2    2.1  2  DivIVA          DivIVA protein
      0.015   13.7   4.3      0.018   13.4   4.3    1.0  1  DUF390          Protein of unknown function (DUF390)
       0.12   11.8  19.4       0.22   10.9  19.4    1.4  1  DUF3552         Domain of unknown function (DUF3552)
       0.15   11.9   1.2       0.28   11.1   1.2    1.4  1  LpxI_N          LpxI N-terminal domain
       0.32   10.7   1.7        1.6    8.4   0.1    2.4  2  HrcA_DNA-bdg    Winged helix-turn-helix transcription repress
       0.76    9.6  11.3        1.1    9.1  11.3    1.2  1  eIF3_subunit    Translation initiation factor eIF3 subunit


Domain annotation for each model (and alignments):
>> vATP-synt_E  ATP synthase (E/31 kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.5  20.5   1.8e-24   3.7e-21       1     199 []       9     182 ..       9     182 .. 0.93

  Alignments for each domain:
  == domain 1  score: 75.5 bits;  conditional E-value: 1.8e-24
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       vATP-synt_E   1 fIrqeAeekAeeIkakaeeefeiekaklveeeeekieeayekkeKqaelqkkiaiSnalnkarlkvLkareevleev 77 
                                       +I++ A+++A + k++a+ e++++ + ++e++++ +  ++++ e ++e+ ++++iS+a ++ ++  L+ar+e+l+ev
  gi|298674211|ref|YP_003725961.1|   9 DIMDVAHAEAAQKKEEADTEAAQIIEDAKEKAKKIKGDRLAETEAKIERLRRQEISSANLEVKRVKLNARKEILDEV 85 
                                       59999************************************************************************ PP

                                       HHHHHHHHHHHTTSHHCCCCHHHHHHCCCCCCC-SSCEEEEECCCCHHCCCCTHCCCCCCHHCCSSSS--SEEEEES CS
                       vATP-synt_E  78 feeaekkLaeveedkdeYkellkkLivqalvkleepevivrarkeDaelveealdkaaeeykaktkkktvevagdee 154
                                        ++a   +++++  k   +ellk+Li+    k e+    v+++ke +e+v+++    +            ++++ + 
  gi|298674211|ref|YP_003725961.1|  86 YNKAVDSVSNLSPSK--NEELLKSLID----KYEQHGTRVYSNKESEEIVKKL---SS------------LEYAGN- 140
                                       ************999..7788888877....6899999**************5...22............233445. PP

                                       SEBTTSSSEEEECCSSSCEEECCCHHHCHHHHHHHHHHCCCCCHC CS
                       vATP-synt_E 155 dfledvlGGvvleaadgkikvnnTlearLelvleqllpeirkaLF 199
                                          +d++GG+v+e++dg +++n T + +L+ v++q l++i+  LF
  gi|298674211|ref|YP_003725961.1| 141 ---IDCIGGIVIENSDGSVRLNYTYDTILKSVYDQSLKQISDILF 182
                                       ...7**************************************999 PP

>> ATP-synt_B  ATP synthase B/B' CF(0)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2  13.6   3.5e-09     7e-06      50     127 ..      12      93 ..       8      96 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 3.5e-09
                        ATP-synt_B  50 aallaeaeqqlkeAraeAaeiiknAkkeaeklkeeieaeaeaeaerlkes....AaaeIeqekdralaeLreqvval 122
                                       + + aea q+++eA  eAa+ii++Ak++a+k+k ++ ae+ea++erl+ +    A+ e+++ k  a++e+ ++v + 
  gi|298674211|ref|YP_003725961.1|  12 DVAHAEAAQKKEEADTEAAQIIEDAKEKAKKIKGDRLAETEAKIERLRRQeissANLEVKRVKLNARKEILDEVYNK 88 
                                       56889****************************************99765122266666666666666666666666 PP

                        ATP-synt_B 123 avqia 127
                                       av+ +
  gi|298674211|ref|YP_003725961.1|  89 AVDSV 93 
                                       66665 PP

>> V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7  12.2   4.1e-07   0.00082      22      94 ..      12      84 ..       4      95 .. 0.89
   2 ?   -1.2   0.0       1.4   2.8e+03      48      66 ..     103     121 ..      99     136 .. 0.54

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 4.1e-07
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHH CS
                      V-ATPase_G_2 22 EaArkeaereveaAeaeAarilreAeakakalqaeyeqelaeevarireeararaeaeaqavrkraearlqqA 94
                                      + A+ ea+++ e+A+ eAa+i+++A++kak+++ +  +e++++++r+r +  + a+ e+++v+ +a + + + 
  gi|298674211|ref|YP_003725961.1| 12 DVAHAEAAQKKEEADTEAAQIIEDAKEKAKKIKGDRLAETEAKIERLRRQEISSANLEVKRVKLNARKEILDE 84
                                      67999**********************************************************9998876544 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHHHHHHHHH CS
                      V-ATPase_G_2  48 akakalqaeyeqelaeeva 66 
                                       + +k+l ++yeq+ ++  +
  gi|298674211|ref|YP_003725961.1| 103 ELLKSLIDKYEQHGTRVYS 121
                                       5566666666666554433 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4  10.2   7.4e-06     0.015      62     123 ..       4      62 ..       2      67 .. 0.90
   2 ?   -0.2   0.1       0.5     1e+03      24      46 ..     102     124 ..      79     139 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.4e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                            DivIVA  62 eetLkktlvvaqetaeevkanakkeaeliikeAekkaekiveeaeeeakkiaeeieelkrqa 123
                                       e+ +++ + va+  a + k++a +ea +ii++A++ka+ki     +++++ +++ie+l+rq+
  gi|298674211|ref|YP_003725961.1|   4 ETVVNDIMDVAHAEAAQKKEEADTEAAQIIEDAKEKAKKI---KGDRLAETEAKIERLRRQE 62 
                                       56677778899*****************************...5899************996 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.5
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                            DivIVA  24 deFLdqvakdyeallkeneelke 46 
                                       +e L++++++ye+   ++ + ke
  gi|298674211|ref|YP_003725961.1| 102 EELLKSLIDKYEQHGTRVYSNKE 124
                                       45566666666665544433333 PP

>> DUF390  Protein of unknown function (DUF390)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   4.3     9e-06     0.018     227     322 ..      12     107 ..       7     129 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9e-06
                            DUF390 227 etaaaee.rrreadrreaadrlreaeeaareavrvrqaeeaareeaarlrraeeavre.eaararqaeaqasseavh 301
                                       + a ae+ +++e    eaa+ + +a+e a++    r ae  a+ e  rlrr e +  + e  r +  + +   + v+
  gi|298674211|ref|YP_003725961.1|  12 DVAHAEAaQKKEEADTEAAQIIEDAKEKAKKIKGDRLAETEAKIE--RLRRQEISSANlEVKRVKLNARKEILDEVY 86 
                                       5566664244555568*****************************..******988888*****999999999999* PP

                            DUF390 302 dktagaslgpdpsgdeaatts 322
                                       +k++ +    +ps +e+   s
  gi|298674211|ref|YP_003725961.1|  87 NKAVDSVSNLSPSKNEELLKS 107
                                       999999888888888876655 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9  19.4   0.00011      0.22      22     136 ..      15     123 ..       5     138 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                           DUF3552  22 kkiaekkiaeAeeeAkkiieeAkkeAeakkkealleakeeihklreelekelkerrnelqrlekRllqkeetLdrke 98 
                                       +  a++k +eA +eA++iie+Ak +A+++k   l e+  +i +lr+   +e+ + + e++r+  +l+ ++e Ld+  
  gi|298674211|ref|YP_003725961.1|  15 HAEAAQKKEEADTEAAQIIEDAKEKAKKIKGDRLAETEAKIERLRR---QEISSANLEVKRV--KLNARKEILDEVY 86 
                                       56788999*************************************9...5999999999987..8999*****9988 PP

                           DUF3552  99 eslekkeesleekekelkqkeqsleekeeeleelveeq 136
                                       ++  +  ++l+  ++e +  ++ +++ e++ +++++++
  gi|298674211|ref|YP_003725961.1|  87 NKAVDSVSNLSPSKNE-ELLKSLIDKYEQHGTRVYSNK 123
                                       8777777777766665.455555666666666555444 PP

>> LpxI_N  LpxI N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.2   0.00014      0.28      25     124 ..      26     124 ..      12     130 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
                            LpxI_N  25 evvvvalegeadeelekivdevaevsvgqlgklikaLkregvtevvmaGkvekpkll..dlrpDlralkllak...l 96 
                                       ++ ++ + + a+e+ +ki       ++++ +  i+ L+r++++ + +  +v++ kl   +   D    k + +   l
  gi|298674211|ref|YP_003725961.1|  26 DTEAAQIIEDAKEKAKKI----KGDRLAETEAKIERLRRQEISSANL--EVKRVKLNarKEILDEVYNKAVDSvsnL 96 
                                       555555555555555554....3457888888999999999999999..6777777753333465555555554448 PP

                            LpxI_N  97 kdrgddalLravveelekeGikvlgate 124
                                          + ++lL+++++  e++G +v + +e
  gi|298674211|ref|YP_003725961.1|  97 SPSKNEELLKSLIDKYEQHGTRVYSNKE 124
                                       899********************98776 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.2      0.19   3.7e+02      13      32 ..      32      51 ..      28      66 .. 0.80
   2 ?    8.4   0.1    0.0008       1.6       6      33 ..     101     128 ..      95     136 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.19
                      HrcA_DNA-bdg 13 LielyrkkkravKgeeiAev 32
                                      +ie  ++k + +Kg  +Ae+
  gi|298674211|ref|YP_003725961.1| 32 IIEDAKEKAKKIKGDRLAET 51
                                      5777789999*****99986 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0008
                      HrcA_DNA-bdg   6 qkeilqaLielyrkkkravKgeeiAevl 33 
                                        +e+l++Li+ y+++++ v +++  e +
  gi|298674211|ref|YP_003725961.1| 101 NEELLKSLIDKYEQHGTRVYSNKESEEI 128
                                       4689***********9999776544443 PP

>> eIF3_subunit  Translation initiation factor eIF3 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1  11.3   0.00055       1.1      35     124 ..       9      96 ..       4     138 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00055
                      eIF3_subunit  35 dswdaeeeeee.ekekakkaaeakak...aakakkkkskkqkiaekeerrkaeeeeaeeeeeleeedeaarkerlrk 107
                                       d  d +  e + +ke+a ++a+   +    ak k+kk k  ++ae e   ++ e+  ++e ++++++ +  k+ +rk
  gi|298674211|ref|YP_003725961.1|   9 DIMDVAHAEAAqKKEEADTEAA---QiieDAKEKAKKIKGDRLAETE---AKIERLRRQEISSANLEVKRVKLNARK 79 
                                       4455555555413333333332...235699999************9...555556677888888888889999999 PP

                      eIF3_subunit 108 aeeesDlknaadlFGgv 124
                                       + ++  ++ a d   ++
  gi|298674211|ref|YP_003725961.1|  80 EILDEVYNKAVDSVSNL 96 
                                       99888888888877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2094  (0.116794); expected 358.6 (0.02)
Passed bias filter:                      699  (0.0389871); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1327.60
//
Query:       gi|298674212|ref|YP_003725962.1|  [L=356]
Description: ATP synthase A1 subunit C [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-75  253.2   9.1    5.4e-75  253.0   9.1    1.0  1  vATP-synt_AC39  ATP synthase (C/AC39) subunit
     0.0072   15.7   3.0      0.015   14.7   3.0    1.5  1  UvrD_C          UvrD-like helicase C-terminal domain


Domain annotation for each model (and alignments):
>> vATP-synt_AC39  ATP synthase (C/AC39) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  253.0   9.1     6e-79   5.4e-75       2     335 ..      25     352 ..      24     353 .. 0.95

  Alignments for each domain:
  == domain 1  score: 253.0 bits;  conditional E-value: 6e-79
                                       HHHHHHHGGGS--HHHHHHHTTS.-HHHHHHHHHTSGGGGG--.....SSSHHHHHHHHHHHHHHHTTTGGGGS-H. CS
                    vATP-synt_AC39   2 eArvramrsglLteedyenLlqcesledvkryLketdYgnfladelseplsrsdiekalreklarefnklreqapgp 78 
                                       +Arvram+s+lL++++y++ l++  ++++ r ++e +Y++++   + ++++ + ie+al+++la +f k++++a+g+
  gi|298674212|ref|YP_003725962.1|  25 TARVRAMKSKLLPADTYSKFLNM-GIDEITRTIEELEYKQDIDVLARQYSGADLIEHALNRNLAVTFTKVLNMAEGE 100
                                       7*******************655.*****************5555599***************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHH.T--GGGS-..--.SSSS-HHHHHHHHHSSSHHHHHHHHHT-HHHHHHHHH CS
                    vATP-synt_AC39  79 srefldyllyrydidNvklllrgklsgdldleeleeklhplgelsaldldklieaksveelyeallgtpyakyleea 155
                                       ++ +l+ +l+ryd++ +k++lrgk   +++++++ee ++ +g++s + l++l++++s+++++++l++t+y+++l++ 
  gi|298674212|ref|YP_003725962.1| 101 PNYLLSKYLKRYDVWSLKTILRGKHY-NASPNKIEENIISAGKYSFDFLSDLANKDSYTDVISTLENTEYYPILKQ- 175
                                       88************************.7999********************************************9. PP

                                       HCC...--SHHHHHHHHHHHHHHHHHHHHHTSS-HH...HHHHHHHHHHHHHHHHHHHTTTSS......T...--SS CS
                    vATP-synt_AC39 156 ldeleetgdleiienaLdkayledllkfckklggetaeilreilgfeiDlrniniilrskkygelskedrkkllipg 232
                                       +d      +l++ien+L k y++dl+ +++kl+++++ i++e++g+eiD++n+++++r+k +g   +e+++kl+i+g
  gi|298674212|ref|YP_003725962.1| 176 YD---G-TNLSDIENELEKEYYKDLFISVSKLKSKNSRIFSEFVGTEIDIKNLRTLFRLKMSG-IEPEETRKLMIEG 247
                                       44...4.566***************************************************88.5677799****** PP

                                       -.S--HHHHHHHHTT-G.....GG..GGSSTSSTTGGGTT--S.HHHHHHHHHHHHHHHHHT.TTSSSTSTHHHHHH CS
                    vATP-synt_AC39 233 g.slypeglealaeaedveellaal.kyteygelleealeeagslksledaldealvkllkk.afrqqfsvgvfyaY 306
                                       g +++ +++e+l+   +++e+l+a+ ky+++ ++ + + +e +sl +le++l ++ vk++++ ++ +++s+ +++ Y
  gi|298674212|ref|YP_003725962.1| 248 GhRVKMKDIESLLPL-SFDEFLSAVdKYSYWYNFSDVVSSEMESLIDLETQLLKQNVKFASSiSHVYPLSIVPIMDY 323
                                       ***************.9********8888888888877777888********************************* PP

                                       HHHHHHHHHHHHHHHHHHHHT--SHHHHG CS
                    vATP-synt_AC39 307 lklkeqEirnlrwIaegiaqglpkekIre 335
                                       ++ k+ E++nlr+I++g+++gl+ke Ir+
  gi|298674212|ref|YP_003725962.1| 324 ILNKKIEVDNLRIIIRGKSAGLDKEVIRK 352
                                       ***************************98 PP

>> UvrD_C  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   3.0   1.7e-06     0.015      57     257 ..      51     240 ..      41     301 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.7e-06
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C  57 kiaatikallekneklediavLvRsnkdadkiskaLkkegipfnvvdeekfFkreeikdilaylkllankqdkialk 133
                                        i +ti++l      ++di vL R+ + ad+i++aL+++   ++    +k ++  e     ++l   + ++d  +lk
  gi|298674212|ref|YP_003725962.1|  51 EITRTIEELE----YKQDIDVLARQYSGADLIEHALNRNLAVTF----TKVLNMAEGE-PNYLLSKYLKRYDVWSLK 118
                                       4556666666....999********************9987777....6777777754.457777888899****** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxx RF
                            UvrD_C 134 rilkrlvlgigkatveriseelkklglsltDfikedtleygeeFieliraleeknlelllkkiektaeer..qalvs 208
                                        il+++  + +++++e+    + ++g    Df+++     ++ ++  i+ le+ +   +lk+ + t+     ++l +
  gi|298674212|ref|YP_003725962.1| 119 TILRGKHYNASPNKIEEN---IISAGKYSFDFLSDLA--NKDSYTDVISTLENTEYYPILKQYDGTNLSDieNELEK 190
                                       ************999876...5677777778887655..56889999999999998666666444443332244444 PP

                                       x.xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 209 k.yadlfkelaeklaelkekseskrkkee.klenlreLysllkelekkeee 257
                                       + y+dlf  + +kl++ ++   s+   +e  ++nlr+L++l  + ++ ee+
  gi|298674212|ref|YP_003725962.1| 191 EyYKDLFISV-SKLKSKNSRIFSEFVGTEiDIKNLRTLFRLKMSGIEPEET 240
                                       4045555444.3444444444444445556999999999886666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2277.08
//
Query:       gi|298674213|ref|YP_003725963.1|  [L=99]
Description: vacuolar H+transporting two-sector ATPase subunit F [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.9e-16   58.6   0.0    6.7e-16   58.4   0.0    1.0  1  ATP-synt_F       ATP synthase (F/14-kDa) subunit
     0.0031   17.8   0.0       0.65   10.4   0.0    2.1  2  YcgL             YcgL domain
     0.0056   16.6   0.1      0.042   13.8   0.1    2.0  2  ParE-like_toxin  ParE-like toxin of type II bacterial toxin-a
  ------ inclusion threshold ------
      0.033   14.5   0.3       0.38   11.1   0.3    2.2  1  BON              BON domain
       0.15   12.2   0.1        7.8    6.7   0.0    2.3  2  DUF3475          Domain of unknown function (DUF3475)


Domain annotation for each model (and alignments):
>> ATP-synt_F  ATP synthase (F/14-kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.4   0.0   1.9e-19   6.7e-16       2      88 ..       4      90 ..       3      93 .. 0.86

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 1.9e-19
                                      EEEESHHHHHHHHHTTCEEEECSSHHHHHHHHHHHHHHTTEEEEEEEHHHHCCCH.HHHHHCTCSSSSEEEEESCSCCG CS
                        ATP-synt_F  2 avIGdedtvtgfrlaGvgevevtdeeeieealkelleredigiilitekiaeeir.elideykeealPaileIPskegp 79
                                       v+G+ ++vtgfrlaG++++ + ++e++e+a+ke+++++++gi++++++ +++++ +l d+++e++ P+++++ + +++
  gi|298674213|ref|YP_003725963.1|  4 SVVGNGEFVTGFRLAGIRKIHEVSDENLESAVKEVIKDPEVGILVMHDDDFNKLPqNLRDKLNESVEPTVVTLGGTGQS 82
                                      59****************************************************95666777888********776664 PP

                                      GSHHCHHHH CS
                        ATP-synt_F 80 ydeekdsvr 88
                                       +  +++++
  gi|298674213|ref|YP_003725963.1| 83 SNL-REKIK 90
                                      432.55555 PP

>> YcgL  YcgL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0    0.0045        16      31      64 ..       4      37 ..       3      39 .. 0.90
   2 !   10.4   0.0   0.00018      0.65      13      43 ..      45      75 ..      35      95 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0045
                              YcgL 31 esfGkpefvmeleLskerkLaradaekVlaaLee 64
                                      +  G+ efv  + L+  rk+++++ e++ +a++e
  gi|298674213|ref|YP_003725963.1|  4 SVVGNGEFVTGFRLAGIRKIHEVSDENLESAVKE 37
                                      56899********************999998876 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00018
                              YcgL 13 YLYvekkddfsevPeeLlesfGkpefvmele 43
                                       + v + ddf+++P++L++++ +      ++
  gi|298674213|ref|YP_003725963.1| 45 GILVMHDDDFNKLPQNLRDKLNESVEPTVVT 75
                                      5678899*************99876655554 PP

>> ParE-like_toxin  ParE-like toxin of type II bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   1.2e-05     0.042      11      36 ..      20      45 ..      15      51 .. 0.93
   2 ?    0.6   0.0      0.15   5.4e+02       6      26 ..      53      73 ..      47      79 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.2e-05
                   ParE-like_toxin 11 lkklkeklkadldkavkeiiedPelG 36
                                      ++k++e   ++l++avke+i+dPe+G
  gi|298674213|ref|YP_003725963.1| 20 IRKIHEVSDENLESAVKEVIKDPEVG 45
                                      579*********************99 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.15
                   ParE-like_toxin  6 rfkkalkklkeklkadldkav 26
                                       f+k  + l++kl+++++ +v
  gi|298674213|ref|YP_003725963.1| 53 DFNKLPQNLRDKLNESVEPTV 73
                                      555555556666555555544 PP

>> BON  BON domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.3   0.00011      0.38      22      51 ..      63      92 ..      27      95 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00011
                                      CCCEEEEETTCEEEECEEECHHHHHHHHHH CS
                               BON 22 adinVevenGvVtLsGtVdseaekekAvei 51
                                      +++n +ve  vVtL Gt +s + +ek+ + 
  gi|298674213|ref|YP_003725963.1| 63 DKLNESVEPTVVTLGGTGQSSNLREKIKQS 92
                                      67888999999***************9875 PP

>> DUF3475  Domain of unknown function (DUF3475)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0022       7.8      18      48 ..      24      54 ..      16      55 .. 0.93
   2 ?    3.4   0.0     0.022        80      25      38 ..      82      95 ..      78      97 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0022
                           DUF3475 18 qsLsdkevarLreeilrseGVrkLvSkDedf 48
                                      + +sd++++   +e+++   V  Lv  D+df
  gi|298674213|ref|YP_003725963.1| 24 HEVSDENLESAVKEVIKDPEVGILVMHDDDF 54
                                      578**************************98 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.022
                           DUF3475 25 varLreeilrseGV 38
                                       ++Lre+i +s GV
  gi|298674213|ref|YP_003725963.1| 82 SSNLREKIKQSVGV 95
                                      689**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      653  (0.0364214); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 583.55
//
Query:       gi|298674214|ref|YP_003725964.1|  [L=578]
Description: ATP synthase subunit A [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-94  315.1   0.0    3.1e-94  314.6   0.0    1.2  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
    3.3e-43  146.4   0.1    6.2e-43  145.5   0.1    1.5  1  ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extens
    1.8e-15   57.2   1.1    1.8e-15   57.2   1.1    2.2  3  ATP-synt_ab_N    ATP synthase alpha/beta family, beta-barrel 
  ------ inclusion threshold ------
       0.02   15.1   0.1          5    7.4   0.0    2.6  2  Peptidase_M23    Peptidase family M23
       0.02   15.1   0.0      0.043   14.1   0.0    1.5  1  AAA_22           AAA domain


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  314.6   0.0   8.8e-98   3.1e-94       1     213 []     209     430 ..     209     430 .. 0.97

  Alignments for each domain:
  == domain 1  score: 314.6 bits;  conditional E-value: 8.8e-98
                                       SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEESEEHHHHHHHHHHCHH......SS.GGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xx.xxx RF
                       ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvgiGergnevaevleefpe......gt.imk 70 
                                       G+r+lD +fp+++G++ +ipg fg Gktv +q+l+k+s++d +++yvg+Gergne+a+vl+efpe      g+ +m+
  gi|298674214|ref|YP_003725964.1| 209 GQRILDGMFPVAKGGTAAIPGPFGSGKTVTQQQLAKWSDTD-IVVYVGCGERGNEMADVLDEFPEledpkaGRpLME 284
                                       9************************************9888.***********************988775337*** PP

                                       GEEEEEEETTS-HHHHHHHHHHHHHHHHHHHHTTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  71 rtvlvantsnepvaareasiytgitlAEyfrdqgknvlliadslsrwaeAlreislrlgempadqgypaylgaklas 147
                                       rtvl+antsn+pvaareas+ytgit++Ey+rd+g++v l+ads+srwaeA+reis rl+emp+++gypayl+a+l++
  gi|298674214|ref|YP_003725964.1| 285 RTVLIANTSNMPVAAREASVYTGITISEYYRDMGYDVALMADSTSRWAEAMREISSRLEEMPGEEGYPAYLAARLSE 361
                                       ***************************************************************************** PP

                                       HHTTSEEETSS...EEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                       xxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 148 lyERagkapdr...tGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                       +yERag ++++    Gs+t++ avsp+ggDfs+pvt++tl+i+++f+ Ld kl qr+hfPain+l+S+S
  gi|298674214|ref|YP_003725964.1| 362 FYERAGYVKSNsgyDGSITVIGAVSPPGGDFSEPVTQNTLRIVKVFWALDAKLSQRRHFPAINWLTSYS 430
                                       ********5555669*****************************************************9 PP

>> ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.5   0.1   1.7e-46   6.2e-43       1     121 []      84     200 ..      84     200 .. 0.96

  Alignments for each domain:
  == domain 1  score: 145.5 bits;  conditional E-value: 1.7e-46
                                       EETTS-BHHHHHHHHTSBE-TT----SS-SSS-EEEEESS-TT-EEETT-EEEEEECTTCEEEEEE--TT-E.EEEE CS
                   ATP-synt_ab_Xtn   1 yDGiqrpLekiaeksgsfierGvkvpaldrekkwefkpkvkvgdkvsggdilGtvqeteliehkimvppkve.gkvk 76 
                                       yDGiqrpL+ +++k+g+fi+rG++++ +drek+wefkp v +gdkv++gdi+G+vqet  +eh+imvpp+++ g+v+
  gi|298674214|ref|YP_003725964.1|  84 YDGIQRPLQVLQDKMGDFIARGATANGIDREKQWEFKPIVDKGDKVEPGDIIGVVQETPNLEHQIMVPPNMQgGTVS 160
                                       9********************************************************************99615699 PP

                                       EE--EEEE-TTSECEEECETT.ECEEEESSEEEETTS---ESEEE CS
                   ATP-synt_ab_Xtn  77 eiaeegeytvedtiaeveteegkekeltllqkwPvrkprpvkekl 121
                                        i  +g++tv++t++++++++    el++lqkwPvr+prp+k+kl
  gi|298674214|ref|YP_003725964.1| 161 DIY-SGKFTVDETVCVLSNGK----ELSMLQKWPVRTPRPTKRKL 200
                                       999.**************666....8****************996 PP

>> ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   1.1   5.1e-19   1.8e-15       1      69 []       7      68 ..       7      68 .. 0.98
   2 ?   -3.1   0.1       3.4   1.2e+04      31      46 ..     460     475 ..     455     476 .. 0.75
   3 ?   -3.0   0.0       3.1   1.1e+04      19      31 ..     535     547 ..     532     556 .. 0.63

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 5.1e-19
                                      EEEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEEES CS
                     ATP-synt_ab_N  1 ivqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsrGteVkrTG 69
                                      i++v+Gpvv++  gi   p++y++++v+  +  ++l+g+++ +++dk  ++v+++t+G+++G++V++TG
  gi|298674214|ref|YP_003725964.1|  7 IYRVSGPVVIA-TGIR--PKMYDVVKVG--H--EGLMGEVIKIEGDKSTIQVYEDTSGIKPGEPVENTG 68
                                      789********.9***..**********..9..9**********************************9 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.4
                                       TCSTEEEEEEEEEETT CS
                     ATP-synt_ab_N  31 efgtlllgvalnlged 46 
                                       e+++ l++ ++ +g d
  gi|298674214|ref|YP_003725964.1| 460 EEESELQEIVQLVGSD 475
                                       4589999999998876 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 3.1
                                       TCTTEEEEECCET CS
                     ATP-synt_ab_N  19 pgiynalevelve 31 
                                       + i++++++e ++
  gi|298674214|ref|YP_003725964.1| 535 YSINDIMAMESKD 547
                                       6778888877555 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0      0.01        36      24      64 ..      27      65 ..      22      68 .. 0.87
   2 ?    7.4   0.0    0.0014         5      57      76 ..     123     142 ..     115     152 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.01
                                      EEEEEEETTTEEEEEEEECTCEEEEEEEESEESS-TTEEE- CS
                     Peptidase_M23 24 VvfagkkegyGnvviidhgdgystlyahlskisvkegqkVk 64
                                      Vv++g ++ +G+v+ i+ ++ ++++y   s   +k+g+ V+
  gi|298674214|ref|YP_003725964.1| 27 VVKVGHEGLMGEVIKIEGDKSTIQVYEDTSG--IKPGEPVE 65
                                      8999998677****************99998..88888776 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0014
                                       S-TTEEE-TTCEEEEEBSTS CS
                     Peptidase_M23  57 vkegqkVkaGqvIGtvgstg 76 
                                       v++g+kV+ G++IG v +t 
  gi|298674214|ref|YP_003725964.1| 123 VDKGDKVEPGDIIGVVQETP 142
                                       89*************99875 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.2e-05     0.043       6      59 ..     223     269 ..     220     295 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.2e-05
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllre 59 
                                       g  ++ G+ G+GKT++ ++l+++ d         + vv+v + + + + +d+l e
  gi|298674214|ref|YP_003725964.1| 223 GTAAIPGPFGSGKTVTQQQLAKWSD--------TDIVVYVGCGERGnEMADVLDE 269
                                       66799******************98........8888899998888555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (578 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 3651.78
//
Query:       gi|298674215|ref|YP_003725965.1|  [L=475]
Description: ATP synthase subunit B [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.6e-67  225.5   0.0    7.3e-67  225.1   0.0    1.1  1  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
    1.2e-11   44.9   1.8    1.2e-11   44.9   1.8    1.9  2  ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel do
    1.8e-05   24.8   1.4      3e-05   24.1   0.6    1.8  2  HAS-barrel     HAS barrel domain


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.1   0.0   1.2e-70   7.3e-67       1     213 []     130     348 ..     130     348 .. 0.98

  Alignments for each domain:
  == domain 1  score: 225.1 bits;  conditional E-value: 1.2e-70
                                       SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS....S.EEEEEEESEEHHHHHHHHHHCHHSSGGGGE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsd....d.aiiyvgiGergnevaevleefpegtimkrt 72 
                                       Gi+++D   ++v+Gq++ i++++g+++++i+ ++++qs+      + a++++++G  ++e + ++++f+++++++r 
  gi|298674215|ref|YP_003725965.1| 130 GISTIDGTNTLVRGQKLPIFSGSGLPHNEIALQIARQSTVLgseeEfAVVFAAMGITHEESQTFMDDFEKTGALERA 206
                                       899**********************************8655887768****************************** PP

                                       EEEEEETTS-HHHHHHHHHHHHHHHHHHHH.TTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  73 vlvantsnepvaareasiytgitlAEyfrd.qgknvlliadslsrwaeAlreislrlgempadqgypaylgaklasl 148
                                       v+++n++++p+++r++++++++t+AEy+++ ++++vl+i+++++++aeAlr+++++ +e+p++qgyp+y++++lasl
  gi|298674215|ref|YP_003725965.1| 207 VVFLNHADDPAVERMITPRMALTAAEYLAYeHDMHVLVILTDMTNYAEALRQMGAAREEVPGRQGYPGYMYTDLASL 283
                                       *****************************9899******************************************** PP

                                       HTTSEEETSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 149 yERagkapdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                       yERag ++ r+Gsvt++++++++g+D+++p+++   +it+g+iv++++l++++++P+invl S+S
  gi|298674215|ref|YP_003725965.1| 284 YERAGVIKGRKGSVTQIPILTMPGDDITHPIPDLSGYITEGQIVVSRELHRKGIYPPINVLPSLS 348
                                       ***************************************************************98 PP

>> ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   1.8     2e-15   1.2e-11       1      69 []       8      73 ..       8      73 .. 0.96
   2 ?   -3.7   0.0         3   1.8e+04      53      64 ..     134     145 ..     130     145 .. 0.77

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 2e-15
                                      EEEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEEES CS
                     ATP-synt_ab_N  1 ivqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsrGteVkrTG 69
                                      i+q++Gp++  e+ + + +g+++ +++e  + g+  +g++l  ++d+V+v+v+++t Gl   + V++TG
  gi|298674215|ref|YP_003725965.1|  8 ITQISGPLIFLEKTEPVGYGELVQINTE--D-GSTKRGQVLDTSGDTVVVQVFEGTGGLNDSAGVVFTG 73
                                      89**************888888888888..8.************************************9 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3
                                       SS-STTBBTTSE CS
                     ATP-synt_ab_N  53 mgstdGlsrGte 64 
                                       +++t  l+rG++
  gi|298674215|ref|YP_003725965.1| 134 IDGTNTLVRGQK 145
                                       688999999985 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.6     5e-09     3e-05       1      84 [.       1      69 [.       1      89 [. 0.85
   2 ?   -3.8   0.0       2.5   1.5e+04       5      21 ..     129     145 ..     129     149 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 5e-09
                        HAS-barrel  1 iGevigests.sslifrvegskdvkvGeyVeielpdgeivlGmvtdirrgnselsndlalvlsleeleeangddevala 78
                                      + +++ + t+ s++++++e +++v++Ge+V+i+++dg+   G+v+d +                        d +v+++
  gi|298674215|ref|YP_003725965.1|  1 MTKEYKTITQiSGPLIFLEKTEPVGYGELVQINTEDGSTKRGQVLDTSG-----------------------DTVVVQV 56
                                      56889999999**************************************.......................9999999 PP

                        HAS-barrel 79 tedt.......gv 84
                                      +e+t       gv
  gi|298674215|ref|YP_003725965.1| 57 FEGTgglndsaGV 69
                                      9988777776633 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2.5
                        HAS-barrel   5 igestssslifrvegsk 21 
                                       +g st++++ + v+g+k
  gi|298674215|ref|YP_003725965.1| 129 TGISTIDGTNTLVRGQK 145
                                       68899999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 3100.99
//
Query:       gi|298674216|ref|YP_003725966.1|  [L=206]
Description: V-type ATPase subunit D [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.2e-57  193.1   6.9    4.8e-57  193.0   6.9    1.0  1  ATP-synt_D  ATP synthase subunit D
  ------ inclusion threshold ------
      0.027   14.2   2.2        3.9    7.1   0.1    2.1  2  Laminin_I   Laminin Domain I
      0.049   12.5   0.1      0.066   12.0   0.1    1.2  1  Nup188_C    Nuclear pore protein NUP188 C-terminal domain
       0.16   11.6   0.0       0.22   11.1   0.0    1.2  1  SMRP1       Spermatid-specific manchette-related protein 1
       0.37   11.1   3.6        5.2    7.4   0.1    2.8  3  DUF5082     Domain of unknown function (DUF5082)


Domain annotation for each model (and alignments):
>> ATP-synt_D  ATP synthase subunit D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.0   6.9   1.3e-60   4.8e-57       1     196 []      12     205 ..      12     205 .. 0.95

  Alignments for each domain:
  == domain 1  score: 193.0 bits;  conditional E-value: 1.3e-60
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTSTTSTSHHHHHHHSSS.SS-. CS
                        ATP-synt_D   1 eLirlkkrlklaqrghslLkkKrdaLilefreilkelkelreeleeelkeayfslaeafaaggeediesavlesvkl 77 
                                       eL+++kk++kl + gh+lLkkKrd Lilef++il+++k+ r el++++k+a++++  a++++g  +++s++ + ++ 
  gi|298674216|ref|YP_003725966.1|  12 ELLEIKKKIKLSEDGHKLLKKKRDGLILEFFDILNQAKDVRSELDDAYKDANSKIGIAKSVEGTITVNSTAFSLKD- 87 
                                       799*******************************************************99999*********6665. PP

                                       .TSS-SEEEEEEBTTSEEEEEEE-...S.SSTSSSSSSSSTCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_D  78 akvvkvelktenvaGVkvpvfeleee.ksdstelygllrtgaqldeavealrellellvelasletslelLdeeikk 153
                                           k+ l+++n++GV vp++e ++  k  +++ yg+l+t++++dea +a++ l+e+++++a++et++++L +ei+k
  gi|298674216|ref|YP_003725966.1|  88 --YPKIHLQSNNIMGVVVPKIESSSVrKPINQRGYGILGTSSYIDEATDAYETLVEKIIQAAEMETTMKRLLAEIEK 162
                                       ..689****************8876675555678******************************************* PP

                                       HHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_D 154 tnrRvNaLekvvIPrleetikyIkseLdEqereeffrlkkvkk 196
                                       t+rRvNaLe +vIP+l+e+  +Ik +LdE+ere +frlkk+kk
  gi|298674216|ref|YP_003725966.1| 163 TKRRVNALEFKVIPELKEARDFIKLRLDEMEREGTFRLKKIKK 205
                                       *****************************************97 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1    0.0011       3.9      21      91 ..       6      76 ..       3      81 .. 0.91
   2 ?    7.0   0.3    0.0012       4.3     194     245 ..     134     185 ..     126     194 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0011
                         Laminin_I 21 ledltkeLqeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaeki 91
                                      ++ +++eL e  +k++  ++  ++l+k+  +L  e+    ++a+ v+ +  + +++++  ++ ak+ +  i
  gi|298674216|ref|YP_003725966.1|  6 VKPTRSELLEIKKKIKLSEDGHKLLKKKRDGLILEFFDILNQAKDVRSELDDAYKDANSKIGIAKSVEGTI 76
                                      67799********************************************9999999999999999877665 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0012
                         Laminin_I 194 elleeAaaktrdanrlnlanqanlreiekkkeevseeknqleetlktardsL 245
                                       ++ e  ++k  +a ++    ++ l eiek k +v+  + ++   lk+ard++
  gi|298674216|ref|YP_003725966.1| 134 DAYETLVEKIIQAAEMETTMKRLLAEIEKTKRRVNALEFKVIPELKEARDFI 185
                                       45555567888999************************************98 PP

>> Nup188_C  Nuclear pore protein NUP188 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   1.8e-05     0.066     314     369 ..     128     184 ..      91     185 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.8e-05
                                       HHHHHHT-HHHHHHHB---SHHHHHHHHS---..SS-S-SSHHHHHHHHHHHHHHHH CS
                          Nup188_C 314 dvefwlssrklLrerlvplgerelelarkkae.desskaenrLeekvvaeleavrdv 369
                                        +++     ++L e+++   e e++++r  ae +++++  n Le kv+ el+++rd 
  gi|298674216|ref|YP_003725966.1| 128 YIDEATDAYETLVEKIIQAAEMETTMKRLLAEiEKTKRRVNALEFKVIPELKEARDF 184
                                       57777788899*****************98887899999**************9985 PP

>> SMRP1  Spermatid-specific manchette-related protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   6.1e-05      0.22     105     164 ..     118     177 ..     104     188 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.1e-05
                             SMRP1 105 dryatwrtapynssywnkyttclprlpkeagmetvvrgmpleyppkperlnayerevvvn 164
                                         y+   t+ y     + y t + ++ + a met ++ +  e+     r+na e +v+ +
  gi|298674216|ref|YP_003725966.1| 118 RGYGILGTSSYIDEATDAYETLVEKIIQAAEMETTMKRLLAEIEKTKRRVNALEFKVIPE 177
                                       56888899999999****************************************999855 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.48   1.7e+03      59      94 ..      28      63 ..       6      70 .. 0.60
   2 ?    3.9   0.2     0.017        60      70      98 ..     124     152 ..     104     153 .. 0.86
   3 ?    7.4   0.1    0.0015       5.2       6      37 ..     154     186 ..     150     197 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.48
                           DUF5082 59 sWkGkeennydgirsnlessyqtyvdkldelidaie 94
                                       + +k+++  + +  ++  + + + ++ld++ +  +
  gi|298674216|ref|YP_003725966.1| 28 KLLKKKRDGLILEFFDILNQAKDVRSELDDAYKDAN 63
                                      455555555555555666666666666666655544 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.017
                           DUF5082  70 girsnlessyqtyvdkldelidaieeEIe 98 
                                       g  s++++++++y++ ++++i+a e+E++
  gi|298674216|ref|YP_003725966.1| 124 GTSSYIDEATDAYETLVEKIIQAAEMETT 152
                                       556799********************986 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0015
                           DUF5082   6 sklqaqiaelrseiaaleek.IerLkeaktkls 37 
                                       ++l a+i++++ +++ale k I +Lkea+++++
  gi|298674216|ref|YP_003725966.1| 154 KRLLAEIEKTKRRVNALEFKvIPELKEARDFIK 186
                                       68999*************88689*******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1385  (0.0772491); expected 358.6 (0.02)
Passed bias filter:                      751  (0.0418874); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1481.43
//
Query:       gi|298674217|ref|YP_003725967.1|  [L=68]
Description: deoxyribonuclease/rho motif-like TRAM protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-15   56.7   0.2    1.9e-15   56.6   0.2    1.0  1  TRAM      TRAM domain


Domain annotation for each model (and alignments):
>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   0.2   1.1e-19   1.9e-15       2      61 ..      11      66 ..      10      67 .. 0.96

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 1.1e-19
                                      XXXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEE CS
                              TRAM  2 syvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGel 61
                                      ++ G+ ++V++e  + s+g+gi+r++ g+v+fvp+++   Gd+V++k+tkv  +++++el
  gi|298674217|ref|YP_003725967.1| 11 VQSGEMYDVEIENIA-SKGDGIARVN-GFVIFVPDTSV--GDEVTIKVTKVMQKFAFAEL 66
                                      688***********9.**********.********999..******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.40
# Mc/sec: 510.37
//
Query:       gi|298674218|ref|YP_003725968.1|  [L=431]
Description: DEAD/DEAH box helicase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-54  183.5   0.2    7.8e-54  182.1   0.1    1.7  2  DEAD           DEAD/DEAH box helicase
    1.3e-34  118.8   0.1    2.1e-30  105.3   0.0    2.5  2  Helicase_C     Helicase conserved C-terminal domain
    2.8e-07   30.7   0.0    5.8e-07   29.7   0.0    1.5  1  ResIII         Type III restriction enzyme, res subunit
    0.00062   19.2   0.0     0.0035   16.7   0.1    2.1  2  CMS1           U3-containing 90S pre-ribosomal complex subuni
     0.0025   17.6   0.1     0.0054   16.5   0.1    1.6  1  AAA_30         AAA domain
     0.0063   16.4   0.0      0.015   15.1   0.0    1.7  1  Helicase_RecD  Helicase
  ------ inclusion threshold ------
      0.036   14.0   0.1       0.11   12.5   0.1    1.9  1  Flavi_DEAD     Flavivirus DEAD domain
      0.039   13.2   0.0      0.062   12.5   0.0    1.3  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
      0.057   13.7   0.7        3.3    8.1   0.0    3.5  3  3H             3H domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.1   0.1   3.9e-57   7.8e-54       1     172 [.      28     190 ..      28     194 .. 0.96
   2 ?   -2.0   0.0       1.3   2.6e+03      60     102 ..     255     297 ..     217     302 .. 0.50

  Alignments for each domain:
  == domain 1  score: 182.1 bits;  conditional E-value: 3.9e-57
                                       -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlr 77 
                                       t+iQa++ip i++g+dv+++a+TG+GKT+af ip+l++v   +++++ ++++++PtreLa+q++++l+k+  y +++
  gi|298674218|ref|YP_003725968.1|  28 TPIQARSIPYIMQGRDVIGQAQTGTGKTAAFGIPALEKVD--RNSKKVQTIVLCPTRELANQVADELNKLARYKKIK 102
                                       89*************************************5..6999******************************* PP

                                       EEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  78 vlliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitc 154
                                       vl i+gg++ ++q+++l++g++iv+gtpgr++d++++++l+l++v++ VlDEad++ld+gf+++i+ il++l     
  gi|298674218|ref|YP_003725968.1| 103 VLPIYGGQPIERQIKALNKGAQIVIGTPGRILDHMERHTLSLDNVKMTVLDEADEMLDMGFREDIELILSKL----- 174
                                       *****************999****************************************************..... PP

                                       TSTTTSEEEEEESSBSHH CS
                                       xxxxxxxxxxxxxxxxxx RF
                              DEAD 155 dgklqrqvivlSATlpkd 172
                                         + +rq+ ++SAT+p  
  gi|298674218|ref|YP_003725968.1| 175 --PDKRQTTLFSATMPGP 190
                                       ..56688********954 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHHHTT.CSEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                              DEAD  60 aeqtlnnlkkfkkyidlrvlliiggvaardqlskldng.vdivv 102
                                       + + +++lk+++  +d  ++  ++++++++ +s+++ng ++ +v
  gi|298674218|ref|YP_003725968.1| 255 VDNLVETLKTRGYLAD-GLHGDMKQKQRDKVMSNFKNGeIETLV 297
                                       3334444444444333.222223334444444444444555555 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00021      0.43      11      61 ..      67     121 ..      60     129 .. 0.79
   2 !  105.3   0.0   1.1e-33   2.1e-30       2     111 .]     229     337 ..     228     337 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00021
                                       HHTTTTSEEEEEESSHHHHHH....HHHHHHHTTSTEEEESTTSTHHHHHHHHHH CS
                        Helicase_C  11 kleeeggkilifvntidrlek....vklllekkgikvavlhgelpqnereeileq 61 
                                       ++++++ ++++ ++t++ +++    ++ l + k+ikv++++g  p + ++++l++
  gi|298674218|ref|YP_003725968.1|  67 DRNSKKVQTIVLCPTRELANQvadeLNKLARYKKIKVLPIYGGQPIERQIKALNK 121
                                       56778899*********66555445666667779*************99999987 PP

  == domain 2  score: 105.3 bits;  conditional E-value: 1.1e-33
                                       HHHHHHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGT CS
                        Helicase_C   2 kleallellkleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvae 77 
                                       k+eal++l     + + +l+f+nt++ +++ v+ l +++g+ +  lhg+++q++r++++++f++ge+  L+atdva+
  gi|298674218|ref|YP_003725968.1| 229 KPEALCRLT-DFYNIKSSLVFCNTKKGVDNlVETL-KTRGYLADGLHGDMKQKQRDKVMSNFKNGEIETLVATDVAA 303
                                       778888885.77788999**********9755555.6779************************************* PP

                                       SSSTSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                        Helicase_C  78 rGidipkvnlVinfdlprnvtsyiqriGRtgRag 111
                                       rGid++++++V+n+d+p++ +sy++riGRtgRag
  gi|298674218|ref|YP_003725968.1| 304 RGIDVENIEVVFNYDVPQDEESYVHRIGRTGRAG 337
                                       ********************************97 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   2.9e-10   5.8e-07      26     169 ..      43     187 ..      10     189 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 2.9e-10
                                       EEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--..... CS
                            ResIII  26 rglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkka.kekd 100
                                        ++ ++ TGtGKT    + + e++ ++ k+ ++++l+p+++l +q  +e++k++  ++ ++  ++ g+  ++  +  
  gi|298674218|ref|YP_003725968.1|  43 DVIGQAQTGTGKTAAFgIPALEKVDRNSKKVQTIVLCPTRELANQVADELNKLARYKKIKVLPIYGGQPIERqIKAL 119
                                       5566889*********99*********9999*********************9998766633344444333323445 PP

                                       ...-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS....TTTHHHHHT---SEEEE.EESS- CS
                            ResIII 101 stnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak...kswreilekfkeavllg.lTATp 169
                                       ++ ++i++ t  ++  ++     e+++l+ d+ ++ + DEa  + ++   + ++ il k++++ +   ++AT+
  gi|298674218|ref|YP_003725968.1| 120 NKGAQIVIGTPGRILDHM-----ERHTLSLDNVKMTVLDEADEMLDMgfrEDIELILSKLPDKRQTTlFSATM 187
                                       7788**************.....99****************99999855556667777775544332167775 PP

>> CMS1  U3-containing 90S pre-ribosomal complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   1.7e-06    0.0035     167     209 ..     113     154 ..      63     160 .. 0.77
   2 ?   -1.0   0.0      0.44   8.8e+02     121     143 ..     287     309 ..     266     314 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.7e-06
                              CMS1 167 eesvtylkksrigiavGtpgRildLleeeslsvdeLkrivlDa 209
                                       e +++ l+k    i +GtpgRild +e  +ls+d++k  vlD 
  gi|298674218|ref|YP_003725968.1| 113 ERQIKALNKG-AQIVIGTPGRILDHMERHTLSLDNVKMTVLDE 154
                                       5566666554.46889*************************96 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.44
                              CMS1 121 aksngsPelLvltlaalRaaDla 143
                                          ng  e+Lv t  a R +D+ 
  gi|298674218|ref|YP_003725968.1| 287 NFKNGEIETLVATDVAARGIDVE 309
                                       55689999999999999999996 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   2.7e-06    0.0054       6      97 ..      31     155 ..      27     238 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.7e-06
                            AAA_30   6 QaaavealltsgdrvavltGpAGtGKttalk..alreaweaa.ggrviglAptgkaAkvLaeelg.........i.. 68 
                                       Qa+ +  +++++d  ++ ++  GtGKt a +  al+++ +++ + + i+l pt + A+++a+el+         +  
  gi|298674218|ref|YP_003725968.1|  31 QARSIPYIMQGRD--VIGQAQTGTGKTAAFGipALEKVDRNSkKVQTIVLCPTRELANQVADELNklarykkikVlp 105
                                       7777888888887..999*********996533789999999889****************8777322222221122 PP

                            AAA_30  69 ..eastiakllkrlk...................grarlepgtllivDEa 97 
                                          ++ i++ +k+l+                   ++ +l++ ++ + DEa
  gi|298674218|ref|YP_003725968.1| 106 iyGGQPIERQIKALNkgaqivigtpgrildhmerHTLSLDNVKMTVLDEA 155
                                       22333333333333366667777777666666665566666677777776 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   7.7e-06     0.015       4     100 ..      48     156 ..      45     189 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7.7e-06
                     Helicase_RecD   4 AdRGRGKSaalGlalaaliaegk..snilvtapskenvktlfeflakglealglke............eekkkkaek 66 
                                       A+ G+GK+aa G+ + + + +++  ++ +v  p++e ++++ + l+k  +  ++k              +  +k+ +
  gi|298674218|ref|YP_003725968.1|  48 AQTGTGKTAAFGIPALEKVDRNSkkVQTIVLCPTRELANQVADELNKLARYKKIKVlpiyggqpierqIKALNKGAQ 124
                                       899**********8888888777678899****************99998888777999998777654334444555 PP

                     Helicase_RecD  67 aelrvrkqrieyiapdellklkeqadllvvDEAA 100
                                       + + + ++ +++++ ++l     + ++ v DEA 
  gi|298674218|ref|YP_003725968.1| 125 IVIGTPGRILDHMERHTLSLD--NVKMTVLDEAD 156
                                       555555889999988888885..46999999995 PP

>> Flavi_DEAD  Flavivirus DEAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   5.5e-05      0.11      11      60 ..      48      98 ..      40     191 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.5e-05
                                      --TTS-TTTTH.HHHHHH.HHHHTT--EEEEESSHHHHHHHHHHTTTS-EEE CS
                        Flavi_DEAD 11 lhPGaGktrkv.lpelvk.eaierrlrtlvLaPtrvvlaemeealkglevry 60
                                      +  G+Gkt  + +p l k +  +++++t+vL Ptr  ++ +++ l++l  ry
  gi|298674218|ref|YP_003725968.1| 48 AQTGTGKTAAFgIPALEKvDRNSKKVQTIVLCPTRELANQVADELNKLA-RY 98
                                      56799999987466665523456789**************999998763.55 PP

>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.1e-05     0.062      85     154 ..     272     339 ..     224     363 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.1e-05
                     ERCC3_RAD25_C  85 iyGetseaerlkilqkfkknpkvntiflskvgDtsiDlPeanvliqisshfgsrrqeaqrlGriLrakkk 154
                                       ++G++++++r k++++fk+  +++t++   v+   iD+ + +v+   +  +        r+Gr  ra k+
  gi|298674218|ref|YP_003725968.1| 272 LHGDMKQKQRDKVMSNFKNG-EIETLVATDVAARGIDVENIEVVFNYDVPQDE-ESYVHRIGRTGRAGKQ 339
                                       68***************976.89****************99999865544332.2345666666666554 PP

>> 3H  3H domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.18   3.7e+02      29      68 ..     147     186 ..     114     213 .. 0.84
   2 ?    8.1   0.0    0.0017       3.3      51      97 .]     219     268 ..     200     268 .. 0.79
   3 ?   -0.4   0.1      0.71   1.4e+03      43      85 ..     370     413 ..     353     418 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.18
                                       EEETTTEEEEEEEEE-SHHHHHHHHHHHHH--S--STTGG CS
                                3H  29 vehpvygeltaklnissredvkkfieklkkskaslLselt 68 
                                       v++ v  e  ++l++  red++  ++kl +++++ L + t
  gi|298674218|ref|YP_003725968.1| 147 VKMTVLDEADEMLDMGFREDIELILSKLPDKRQTTLFSAT 186
                                       4556777778899999999999999999999999988877 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0017
                                       HHHHHHHH.--S--STTGG..GGEEEEEEEESSHHHHHHHHHHHHHTT-B CS
                                3H  51 kfieklkk.skaslLselt..sgvHlHtieapseetldkieeeLkekgfl 97 
                                       +   ++k+ sk + L++lt   ++++  + +++++ +d+ +e Lk +g+l
  gi|298674218|ref|YP_003725968.1| 219 QTYFEVKErSKPEALCRLTdfYNIKSSLVFCNTKKGVDNLVETLKTRGYL 268
                                       44444555379999*****44489999*********************98 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.71
                                       E-SHHHHHHHHHHHHH-.-S--STTGGGGEEEEEEEESSHHHHH CS
                                3H  43 issredvkkfieklkks.kaslLseltsgvHlHtieapseetld 85 
                                       i s++dv++f  ++ ++  ++ + +   g  +H++e   ee++ 
  gi|298674218|ref|YP_003725968.1| 370 IPSQSDVEDFRANMLSQkVKETIDSGHLGKYVHWVENLLEEDYT 413
                                       77899999999888775245557777777777777776666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 2496.94
//
Query:       gi|298674219|ref|YP_003725969.1|  [L=59]
Description: transcriptional regulator, XRE family [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-11   43.6   0.0    2.5e-11   43.5   0.0    1.1  1  HTH_3     Helix-turn-helix
     0.0038   17.2   0.1     0.0042   17.1   0.1    1.1  1  HTH_19    Helix-turn-helix domain
  ------ inclusion threshold ------
      0.016   15.6   0.0      0.016   15.5   0.0    1.0  1  HTH_31    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   0.0   4.2e-15   2.5e-11       7      47 ..      11      51 ..       5      51 .. 0.94

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 4.2e-15
                                      HTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHH CS
                             HTH_3  7 qlglsqeeLAeklGvsrstisriEnGernPsletlkklaka 47
                                      +++++qe+ A+++Gv+r+ti++iE+++  Ps++ ++kla++
  gi|298674219|ref|YP_003725969.1| 11 KKDITQEYRAKEMGVTRQTINAIERDKYDPSIQLAFKLARF 51
                                      899************************************96 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1     7e-07    0.0042      10      50 ..      11      50 ..       3      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 7e-07
                            HTH_19 10 elgltqeelaerlgisrskisaiEngkkdvpsaelllkiae 50
                                      ++ +tqe  a++ g++r  i+aiE +k+ +ps+ l  k+a+
  gi|298674219|ref|YP_003725969.1| 11 KKDITQEYRAKEMGVTRQTINAIERDKY-DPSIQLAFKLAR 50
                                      677999999*****************99.***999988886 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   2.8e-06     0.016      15      52 ..      14      50 ..       5      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.8e-06
                            HTH_31 15 LsqeevAerlgvsestlsrlEqGrrgrpspavlealar 52
                                      ++qe  A+  gv++ t++ +E+ + + ps +   +lar
  gi|298674219|ref|YP_003725969.1| 14 ITQEYRAKEMGVTRQTINAIERDKYD-PSIQLAFKLAR 50
                                      6888889******************7.*****999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 384.01
//
Query:       gi|298674220|ref|YP_003725970.1|  [L=350]
Description: outer membrane lipoprotein-sorting protein-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.9e-11   42.6   1.9    6.9e-11   42.6   1.9    3.0  3  DUF4367    Domain of unknown function (DUF4367)
    3.4e-07   30.2   0.6    1.1e-06   28.5   0.6    1.8  1  LolA_like  Outer membrane lipoprotein-sorting protein
    0.00038   19.9   0.4     0.0013   18.1   0.4    1.9  1  DUF2092    Predicted periplasmic protein (DUF2092)
     0.0098   15.6   0.4      0.021   14.5   0.4    1.6  1  LolA       Outer membrane lipoprotein carrier protein LolA
  ------ inclusion threshold ------
      0.026   14.6   0.0      0.052   13.6   0.0    1.5  1  DUF5061    17 kDa common-antigen outer membrane protein


Domain annotation for each model (and alignments):
>> DUF4367  Domain of unknown function (DUF4367)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   4.7      0.16   5.7e+02      17      79 ..      29      94 ..      21     125 .. 0.74
   2 ?   -1.8   0.1       1.2   4.3e+03      33      50 ..     177     194 ..     158     225 .. 0.63
   3 !   42.6   1.9   1.9e-14   6.9e-11       3     110 .]     237     346 ..     235     346 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.16
                           DUF4367 17 nisedsesalleYkd.engelisfsiskqskees.qklsidteda.evekieingikatyyekedg 79
                                       +s +++s+l+   + e++e  +++i++ ++ ++  k+ i++++   +  +  ng+++  y++e +
  gi|298674220|ref|YP_003725970.1| 29 FESANDYSYLIILNSsEYEEVNNVTIEMFYESSGkGKMIIEKSYEdLMYVVVNNGNNILTYDSEHD 94
                                      467788888888888677777777799999999888999999999445555556777888887766 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.2
                           DUF4367  33 ngelisfsiskqskeesq 50 
                                       ++e+i++s   ++ ++++
  gi|298674220|ref|YP_003725970.1| 177 KNEKIVISAAFKNFRFNT 194
                                       455555553333333333 PP

  == domain 3  score: 42.6 bits;  conditional E-value: 1.9e-14
                           DUF4367   3 eptylPeGykfkktnisedsesalleYkdengelisfs.iskqskeesqklsidtedaevekieingikatyyeked 78 
                                       +p+y+P+ ++f  ++     +s++++Y  en+   s+  +  + +e+sqk  ++      e+++i+  k+ y+e+ +
  gi|298674220|ref|YP_003725970.1| 237 KPSYVPDEFEFDHVQYTPSTSSVVIYY--ENDVMRSVLaVVQMPYESSQKPEVA----GQENTTIGTTKGNYFESTN 307
                                       79*******999999999999999999..7777777776666666666666665....8899*************** PP

                           DUF4367  79 geyvlvwedegvvytls........gniskeelikiaesi 110
                                         + l w+++++ yt++        ++i+k e+ikiaes+
  gi|298674220|ref|YP_003725970.1| 308 S-KHLKWSENNIEYTIMlnpplerdNEIDKREMIKIAESL 346
                                       9.9***************99998888************96 PP

>> LolA_like  Outer membrane lipoprotein-sorting protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.6   3.1e-10   1.1e-06      22     124 ..      76     180 ..      66     222 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 3.1e-10
                                       EE..SSSTTEEEEEETTTTCEEEE-GGGTTSECCTTC.EHHHHC--SCCCEEEEEEEEEEETTEEEEEEEEEESS.. CS
                         LolA_like  22 tl..kekdddlWlYlPalkrvrrisssdksqsfmGsdfsyeDlssrevedythellgeeevggkdcyvleltpkd.a 95 
                                       ++   +++++   Y+ + + v r + +  s+ f+   ++y  l++r +e+ +  l g+e+++g+++y+le +  +  
  gi|298674220|ref|YP_003725970.1|  76 MYvvVNNGNNILTYDSEHDVVTRNP-DPISNVFQENPLTYYSLMERIIENNKPVLQGTETINGNKTYILEFVFESsI 151
                                       4444478888899999999999988.888999***************************************998855 PP

                                       TTSSECEEEEEEETTT--EEEEEEEETTS CS
                         LolA_like  96 advsYskivlwvdketylplkvefydksg 124
                                       +d   + ++lw++ +++ p+k+e+y+ ++
  gi|298674220|ref|YP_003725970.1| 152 SDFPVDSTKLWINSDNWSPVKYELYKNEK 180
                                       6888899******************9754 PP

>> DUF2092  Predicted periplasmic protein (DUF2092)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.4   3.7e-07    0.0013     126     210 ..     126     213 ..      64     214 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.7e-07
                           DUF2092 126 sakyvgtskvngqecehl.......afrnkdvdwqlWIsqgdkpLprkivityktdpgapqytaefsdWnldpeipe 195
                                       + ++ gt+++ng++++ l         +       lWI++++   p k+   yk++  +  ++a f+++ +++ i++
  gi|298674220|ref|YP_003725970.1| 126 KPVLQGTETINGNKTYILefvfessISDFPVDSTKLWINSDNW-SPVKYEL-YKNE--KIVISAAFKNFRFNTGISD 198
                                       445679999999999999443333222223345689**77666.7888875.4444..4789*************** PP

                           DUF2092 196 dtFrftpPkgArkie 210
                                       + F+++pPk+A+ ie
  gi|298674220|ref|YP_003725970.1| 199 KKFEYQPPKNAKVIE 213
                                       ************886 PP

>> LolA  Outer membrane lipoprotein carrier protein LolA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.4   5.9e-06     0.021      48     164 ..      78     203 ..      63     204 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.9e-06
                                       EEEEETTEEEEEETTTTEEEEEE..HHHHTTT-GGGGGG......S-HHHHTTTEEEEEEEETTEEEEEEEESSS-S CS
                              LolA  48 livsdgktvwlydpdleqvties..lkqalsktplvlLl......edkaklskdynvsvkkeqdldtltlkpkakda 116
                                       ++v +g+++  yd++ + vt+++  ++++ +++pl + +      e+++ + + ++    ++  +  ++++   +d+
  gi|298674220|ref|YP_003725970.1|  78 VVVNNGNNILTYDSEHDVVTRNPdpISNVFQENPLTYYSlmeriiENNKPVLQGTETINGNKTYILEFVFESSISDF 154
                                       799******************997789999999997633334444788888888777789999999*********** PP

                                       SECEEEEEE.ETTE.EEEEEEEETT--EEEEEEEEEEES----GGGG-- CS
                              LolA 117 nlsritigfdkkgl.lkqlkvvdaqGqrttitfsnvkenakladdlFkf 164
                                        +++ +++++ ++  + + +++ +++  ++  f+n++ n  ++d++F++
  gi|298674220|ref|YP_003725970.1| 155 PVDSTKLWINSDNWsPVKYELYKNEKIVISAAFKNFRFNTGISDKKFEY 203
                                       ***********************************************87 PP

>> DUF5061  17 kDa common-antigen outer membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.4e-05     0.052       7      70 ..       4      62 ..       1      79 [. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.4e-05
                           DUF5061  7 lllLaaCalkqeaasqeeegevvekpleeflsqepagasavLddsefGksvrvlveekftsAsG 70
                                      +ll+++C+     +++  e+evv++++e+f s ++   +++L+ se+ +  +v +e  + s sG
  gi|298674220|ref|YP_003725970.1|  4 VLLITGCTE----QPEPSEKEVVNNTIEKFESANDYSYLIILNSSEYEEVNNVTIEMFYES-SG 62
                                      688999999....57889999**************************99888998877765.44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2191.15
//
Query:       gi|298674221|ref|YP_003725971.1|  [L=75]
Description: hypothetical protein Metev_0245 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-13   51.0   1.6      1e-13   51.0   1.6    1.8  2  PLDc_N           Phospholipase_D-nuclease N-terminal
    0.00021   21.4   1.2    0.00027   21.1   1.2    1.2  1  YbjM             Putative inner membrane protein of Enterobac
     0.0013   18.4   3.8     0.0015   18.3   3.8    1.0  1  DUF4203          Domain of unknown function (DUF4203)
     0.0022   17.7   0.6     0.0024   17.6   0.6    1.0  1  HlyIII           Haemolysin-III related
  ------ inclusion threshold ------
       0.01   15.9   3.5       0.72   10.0   0.7    2.0  2  DUF4870          Domain of unknown function (DUF4870)
      0.019   15.7   1.7      0.024   15.4   1.7    1.1  1  Ribosomal_S12    Ribosomal protein S12
      0.039   14.2   4.1      0.093   13.0   4.1    1.6  1  DUF2516          Protein of unknown function (DUF2516)
       0.29   11.3   4.8        6.9    6.9   1.9    2.0  2  DUF5368          Family of unknown function (DUF5368)
       0.33   11.3   0.1       0.33   11.3   0.1    1.9  2  Wzz              Chain length determinant protein
       0.51   10.2   4.2         21    5.0   0.0    2.1  2  LapA_dom         Lipopolysaccharide assembly protein A domain
       0.98    9.1   4.7        5.8    6.6   6.1    1.5  2  Tetraspanin      Tetraspanin family
        1.2    9.4   7.2        2.1    8.6   0.1    2.0  2  COX2_TM          Cytochrome C oxidase subunit II, transmembra
        2.1    8.5   3.7        1.6    8.9   0.2    2.0  2  YebO             YebO-like protein
        2.5    8.3   7.2        2.1    8.6   0.3    2.0  2  Glycophorin_A    Glycophorin A
        2.7    7.8   5.3         14    5.6   0.3    2.0  2  DUF4307          Domain of unknown function (DUF4307)
        7.2    5.2   6.2         10    4.7   6.2    1.3  1  DUF2207          Predicted membrane protein (DUF2207)
        8.2    6.9   8.2        2.4    8.6   1.5    2.2  2  FeoB_associated  FeoB-associated Cys-rich membrane protein


Domain annotation for each model (and alignments):
>> PLDc_N  Phospholipase_D-nuclease N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.6       1.7   1.8e+03       7      10 ..      12      15 ..       5      21 .. 0.52
   2 !   51.0   1.6   9.5e-17     1e-13       1      42 []      23      66 ..      23      66 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.7
                            PLDc_N  7 lidi 10
                                      li i
  gi|298674221|ref|YP_003725971.1| 12 LIFI 15
                                      2222 PP

  == domain 2  score: 51.0 bits;  conditional E-value: 9.5e-17
                            PLDc_N  1 ilwiialidiirdrnpss...klaWllvilflPvlGailYllfGr 42
                                      ++wi++lid+ + ++ps    k++W+++i+f  v+Ga++Y++++r
  gi|298674221|ref|YP_003725971.1| 23 VFWIWMLIDCAT-KEPSQgndKVVWIIIIVFTQVIGALIYYFVRR 66
                                      79**********.88888899**********************98 PP

>> YbjM  Putative inner membrane protein of Enterobacteriaceae
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   1.2   2.5e-07   0.00027      60     113 ..      12      65 ..       2      67 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.5e-07
                              YbjM  60 llvpllGallaapvcllvlklvlaseeslwqelayllSavFWcalGallvlllr 113
                                       l+  l+G l+++ +++++++  + + ++   ++ +++  vF  ++Gal++ ++r
  gi|298674221|ref|YP_003725971.1|  12 LIFILIGILATVFWIWMLIDCATKEPSQGNDKVVWIIIIVFTQVIGALIYYFVR 65 
                                       67789****************99999999***********************97 PP

>> DUF4203  Domain of unknown function (DUF4203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   3.8   1.4e-06    0.0015      16      74 ..       5      63 ..       1      67 [. 0.90

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.4e-06
                           DUF4203 16 fGyrlfkltlflsgfllgsllvlvlilkvvvlpsslvqgaslvaalvvGllgGllallf 74
                                      +G+ ++ l ++l+g l++++ +++li   +++ps+ +  + +++++v   ++G+l+ +f
  gi|298674221|ref|YP_003725971.1|  5 MGFPFYMLIFILIGILATVFWIWMLIDCATKEPSQGNDKVVWIIIIVFTQVIGALIYYF 63
                                      8999*****************************99999999999999999999987554 PP

>> HlyIII  Haemolysin-III related
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.6   2.3e-06    0.0024     137     196 ..       8      69 ..       3      74 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.3e-06
                            HlyIII 137 plravlfillgllgvipllhlllvltqlgeaa.elalvllvlggvlylvGavfYa.lrvPEr 196
                                       p+++++fil+g+l+ ++ + +l+ +++++ ++ + ++v+++  +++ ++Ga++Y  +r P r
  gi|298674221|ref|YP_003725971.1|   8 PFYMLIFILIGILATVFWIWMLIDCATKEPSQgNDKVVWIIIIVFTQVIGALIYYfVRRPKR 69 
                                       78999********99999988888898998889******************97651566666 PP

>> DUF4870  Domain of unknown function (DUF4870)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.7   0.00068      0.72      69     100 ..       4      37 ..       1      40 [. 0.78
   2 ?    7.1   0.1    0.0053       5.6      14      36 ..      46      68 ..      42      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00068
                           DUF4870  69 ligf..lllllllllllnlvlviiaaikanegee 100
                                        +gf  ++l+++l+++l+ v+ i+  i +  +e+
  gi|298674221|ref|YP_003725971.1|   4 AMGFpfYMLIFILIGILATVFWIWMLIDCATKEP 37 
                                       567753449999999*********9999987776 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0053
                           DUF4870 14 sklliplgniilPlviwllkkdk 36
                                      + ++i ++++i++l+ +++++ k
  gi|298674221|ref|YP_003725971.1| 46 WIIIIVFTQVIGALIYYFVRRPK 68
                                      678999************99876 PP

>> Ribosomal_S12  Ribosomal protein S12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   1.7   2.3e-05     0.024       2      55 ..       9      62 ..       8      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.3e-05
                     Ribosomal_S12  2 ffvrslllyGlcvrflllllvlyvsprlpssGnrrilvaifllfnivllllvff 55
                                      f++  ++l G+   ++ + +++  + + ps Gn +++ +i+++f+ v+  l+++
  gi|298674221|ref|YP_003725971.1|  9 FYMLIFILIGILATVFWIWMLIDCATKEPSQGNDKVVWIIIIVFTQVIGALIYY 62
                                      7888999****99999999999**********************9998776664 PP

>> DUF2516  Protein of unknown function (DUF2516)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   4.1   8.9e-05     0.093       4      58 ..      10      59 ..       7      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.9e-05
                           DUF2516  4 qalvllllalvvlvlslvAlvdalrrradaFeaagkrtKpfWlailgvallvlll 58
                                       +l+++l++++++v+ ++ l+d++++ + +      + K +W++i++ + +++ l
  gi|298674221|ref|YP_003725971.1| 10 YMLIFILIGILATVFWIWMLIDCATKEPSQ-----GNDKVVWIIIIVFTQVIGAL 59
                                      5789*********************98764.....56699*********999988 PP

>> DUF5368  Family of unknown function (DUF5368)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   1.9    0.0065       6.9       4      27 ..       7      30 ..       5      36 .. 0.86
   2 ?    5.6   0.1     0.016        17      20      41 ..      44      65 ..      40      71 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0065
                           DUF5368  4 ldlevllavleellgalfwillal 27
                                      + + +l+ +l  +l+++fwi +++
  gi|298674221|ref|YP_003725971.1|  7 FPFYMLIFILIGILATVFWIWMLI 30
                                      6799***************98876 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.016
                           DUF5368 20 lfwillalavlvtvafvlvlir 41
                                      + wi++++   v+ a+++ ++r
  gi|298674221|ref|YP_003725971.1| 44 VVWIIIIVFTQVIGALIYYFVR 65
                                      4566666666666666665555 PP

>> Wzz  Chain length determinant protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   1.3       1.5   1.6e+03      25      34 ..      13      22 ..       9      33 .. 0.52
   2 ?   11.3   0.1   0.00031      0.33      15      42 ..      43      70 ..      41      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.5
                                      XXXXXXXXXX CS
                               Wzz 25 lfallaviya 34
                                      +f+l++++ +
  gi|298674221|ref|YP_003725971.1| 13 IFILIGILAT 22
                                      3333333332 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00031
                                      XXXXXXXXXXXXXXXXXXXXXXXXX-EE CS
                               Wzz 15 rkklIilvtllfallaviyaflatpkYt 42
                                      + ++Ii++++  +++a+iy f+ +pk +
  gi|298674221|ref|YP_003725971.1| 43 KVVWIIIIVFTQVIGALIYYFVRRPKRK 70
                                      56899999999999********999855 PP

>> LapA_dom  Lipopolysaccharide assembly protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   4.4     0.065        69      18      40 ..       8      28 ..       1      35 [. 0.57
   2 ?    5.0   0.0      0.02        21      20      36 ..      47      63 ..      41      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.065
                          LapA_dom 18 pLsllllvafgiGallgwllslw 40
                                      p +  +l++++iG+l+++++ ++
  gi|298674221|ref|YP_003725971.1|  8 PFY--MLIFILIGILATVFWIWM 28
                                      444..555555555555555443 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.02
                          LapA_dom 20 sllllvafgiGallgwl 36
                                      +++++++ +iGal+ ++
  gi|298674221|ref|YP_003725971.1| 47 IIIIVFTQVIGALIYYF 63
                                      68999999****99876 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   6.1    0.0055       5.8       7      59 ..       9      59 ..       4      64 .. 0.62
   2 ?    3.0   0.4     0.067        70      85     108 ..      47      70 ..      44      75 .] 0.64

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0055
                                      XXXXXXXXXXXXXXXXXXXXXX..XXX.....................XXXXXXX CS
                                      xxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin  7 ffnllfwligivllavGvwlrl..khaeaalacllsesaedpailaillivvGvl 59
                                      f+ l+f+ligi++ ++ +w+++       +++  + +  +   i+ ++  v+G+l
  gi|298674221|ref|YP_003725971.1|  9 FYMLIFILIGILATVFWIWMLIdcA----TKEPSQGNDKVVWIIIIVFTQVIGAL 59
                                      66788***************66431....12222233344444444555566665 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.067
                                       XXXXXXXXXXXXXXXXX--HHH.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin  85 lllvlfllelaagilgfvfsdkar 108
                                       +++++f   ++a i+ fv + k++
  gi|298674221|ref|YP_003725971.1|  47 IIIIVFTQVIGALIYYFVRRPKRK 70 
                                       456666666777777777777654 PP

>> COX2_TM  Cytochrome C oxidase subunit II, transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   2.1     0.034        36      27      45 ..      12      30 ..       3      40 .. 0.74
   2 ?    8.6   0.1    0.0019       2.1      24      53 ..      41      70 ..      33      75 .] 0.82

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.034
                           COX2_TM 27 illiltlililVlyilvli 45
                                      +++il+ il +V++i +li
  gi|298674221|ref|YP_003725971.1| 12 LIFILIGILATVFWIWMLI 30
                                      5678999999999876544 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0019
                           COX2_TM 24 hdyilliltlililVlyilvlilvefrrrk 53
                                      +d+++ i++++++ V+++l++  v+  +rk
  gi|298674221|ref|YP_003725971.1| 41 NDKVVWIIIIVFTQVIGALIYYFVRRPKRK 70
                                      789999*************99998855555 PP

>> YebO  YebO-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.4      0.54   5.7e+02       4      16 ..      17      29 ..       9      39 .. 0.55
   2 ?    8.9   0.2    0.0015       1.6       2      24 ..      49      71 ..      48      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.54
                              YebO  4 vivvlvgllvwFF 16
                                      + ++  ++++w +
  gi|298674221|ref|YP_003725971.1| 17 IGILATVFWIWML 29
                                      2222334555555 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0015
                              YebO  2 vlvivvlvgllvwFFvnRasvrA 24
                                      ++v++ ++g l+++Fv R   +A
  gi|298674221|ref|YP_003725971.1| 49 IIVFTQVIGALIYYFVRRPKRKA 71
                                      789999***********976665 PP

>> Glycophorin_A  Glycophorin A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   1.9     0.094        99      55      79 ..       7      31 ..       4      39 .. 0.74
   2 ?    8.6   0.3     0.002       2.1      59      92 ..      43      74 ..      38      75 .] 0.87

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.094
                                      SS-TTHHHHHHHHHHHHHHHHHHHH CS
                     Glycophorin_A 55 FselvitliifgvmAgvigtillis 79
                                      F+   ++ i++g++A v  + +li 
  gi|298674221|ref|YP_003725971.1|  7 FPFYMLIFILIGILATVFWIWMLID 31
                                      6667778888888888888777774 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.002
                                      THHHHHHHHHHHHHHHHHHHHHHHHTHSXXXXXX CS
                     Glycophorin_A 59 vitliifgvmAgvigtillisYlirRliKKssvd 92
                                       ++ ii+ v   vig   li Y +rR ++K+++d
  gi|298674221|ref|YP_003725971.1| 43 KVVWIIIIVFTQVIGA--LIYYFVRRPKRKAEFD 74
                                      56789999*******7..799*******999887 PP

>> DUF4307  Domain of unknown function (DUF4307)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.3     0.013        14       5      31 ..      10      36 ..       8      42 .. 0.77
   2 ?    5.3   0.6     0.016        17       2      27 ..      42      67 ..      41      74 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.013
                           DUF4307  5 lvillvvlvvvalalvawigysqgsad 31
                                       ++++++++++a+++++w++++ ++++
  gi|298674221|ref|YP_003725971.1| 10 YMLIFILIGILATVFWIWMLIDCATKE 36
                                      567889999999999999999885544 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.016
                           DUF4307  2 rrllvillvvlvvvalalvawigysq 27
                                      +++++i+++v++ v++al+ +++ + 
  gi|298674221|ref|YP_003725971.1| 42 DKVVWIIIIVFTQVIGALIYYFVRRP 67
                                      67889999999999999998888766 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   6.2    0.0097        10     394     438 ..      11      70 ..       2      75 .] 0.50

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0097
                           DUF2207 394 glilillallllvll...............lvfllilllillliaiivlllfsrllgrrt 438
                                       +li+il+++l+ v++               +   +++++i++ ++i++l+++  + ++r+
  gi|298674221|ref|YP_003725971.1|  11 MLIFILIGILATVFWiwmlidcatkepsqgNDKVVWIIIIVFTQVIGALIYYFVRRPKRK 70 
                                       222222233333333455566778899*99555555555555555555555422334444 PP

>> FeoB_associated  FeoB-associated Cys-rich membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.7       0.2   2.2e+02       4      16 ..      14      26 ..       3      35 .. 0.72
   2 ?    8.6   1.5    0.0023       2.4       4      25 ..      47      69 ..      44      72 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.2
                   FeoB_associated  4 IVgliiaaavafv 16
                                       +++ i+a v+++
  gi|298674221|ref|YP_003725971.1| 14 FILIGILATVFWI 26
                                      4555555666665 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0023
                   FeoB_associated  4 IVgliiaaavafvirrlikk.kk 25
                                      I++++   +++++i++++++ k+
  gi|298674221|ref|YP_003725971.1| 47 IIIIVFTQVIGALIYYFVRRpKR 69
                                      56666667888888888888533 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1168  (0.0651459); expected 358.6 (0.02)
Passed bias filter:                      625  (0.0348597); expected 358.6 (0.02)
Passed Vit filter:                       121  (0.00674884); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 469.78
//
Query:       gi|298674222|ref|YP_003725972.1|  [L=165]
Description: hypothetical protein Metev_0246 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      0.004   16.9   0.2      0.004   16.9   0.2    1.1  1  Cation_efflux  Cation efflux family
  ------ inclusion threshold ------
      0.053   13.3   4.2        2.1    8.3   0.2    2.3  2  DUF3955        Protein of unknown function (DUF3955)


Domain annotation for each model (and alignments):
>> Cation_efflux  Cation efflux family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.2   4.5e-07     0.004      77     128 ..      21      74 ..      18     144 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.5e-07
                     Cation_efflux  77 lllglavfllleaiqkli..kegereihaglalvvalvslvvnlalllilrrag 128
                                       ++lg+avf++++aiq+++   e + +  ++l lv++l+ ++v l +l+++ +  
  gi|298674222|ref|YP_003725972.1|  21 IILGIAVFAWYNAIQQFVyvVEIGSNPVSDLGLVILLIVFGVILPVLFYINKLE 74 
                                       799***************995666666666666666666666666666666555 PP

>> DUF3955  Protein of unknown function (DUF3955)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.5   0.00088       7.9       6      24 ..      18      36 ..      16      40 .. 0.88
   2 ?    8.3   0.2   0.00023       2.1       4      33 ..      53      84 ..      50      98 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00088
                           DUF3955  6 llllllgiilliisnisgs 24
                                      +++++lgi++++ +n +++
  gi|298674222|ref|YP_003725972.1| 18 MFFIILGIAVFAWYNAIQQ 36
                                      79*************9987 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00023
                           DUF3955  4 igllllllgiilliisni..sgsyvdedGiLh 33
                                      +++ll+++g+il++++ i    + v edGi++
  gi|298674222|ref|YP_003725972.1| 53 LVILLIVFGVILPVLFYInkLETRVYEDGIYV 84
                                      789*********99986522678899999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       894  (0.0498633); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1005.20
//
Query:       gi|298674223|ref|YP_003725973.1|  [L=130]
Description: hypothetical protein Metev_0247 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.042   14.5   0.3      0.083   13.6   0.3    1.5  1  DUF3139   Protein of unknown function (DUF3139)
       0.14   12.3   0.1       0.36   11.0   0.1    1.6  1  TxDE      Toxoflavin-degrading enzyme


Domain annotation for each model (and alignments):
>> DUF3139  Protein of unknown function (DUF3139)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3   9.3e-06     0.083       2      76 ..      21     119 ..      20     121 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.3e-06
                           DUF3139   2 kkiiiililliillvivkvfl..glvgskpikkylankkldkyl.....................qekgykeddIks 55 
                                       k i+i+l+ l+  l+++++f+   +v+      y++     ++l                      ++  +++dI +
  gi|298674223|ref|YP_003725973.1|  21 KGIYILLLALVGTLAVLAPFMydAYVKTTDD--YYVS----AHLsditpddytgisdedldkhpkLKEAFDKKDIVE 91 
                                       6788889999988999999995444444443..5555....333444477777777777777777788999999999 PP

                           DUF3139  56 ikpkydskkgsyya.......kVvFKDe 76 
                                          + +sk++++ a       ++ +KDe
  gi|298674223|ref|YP_003725973.1|  92 LTESEYSKMDEFLAegddgitYIKYKDE 119
                                       9999999999887756666666666666 PP

>> TxDE  Toxoflavin-degrading enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1     4e-05      0.36      31      50 ..       8      27 ..       5      29 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4e-05
                              TxDE 31 iepdaLNFlGekedgayiLL 50
                                      ++++  N +Ge+++g+yiLL
  gi|298674223|ref|YP_003725973.1|  8 FDTEGVNSMGEDNKGIYILL 27
                                      67788999***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 832.37
//
Query:       gi|298674224|ref|YP_003725974.1|  [L=52]
Description: hypothetical protein Metev_0248 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 330.53
//
Query:       gi|298674225|ref|YP_003725975.1|  [L=89]
Description: translation elongation factor aEF-1 beta [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.6e-21   74.3   0.5    7.3e-21   74.2   0.5    1.0  1  EF1_GNE        EF-1 guanine nucleotide exchange domain
  ------ inclusion threshold ------
      0.044   14.8   0.9       0.32   12.0   0.1    2.1  2  AMP-binding_C  AMP-binding enzyme C-terminal domain
      0.082   13.4   1.0        8.1    7.0   0.0    2.2  2  HMA            Heavy-metal-associated domain
        2.3    8.5   7.0        3.7    7.8   7.0    1.3  1  GFD1           GFD1 mRNA transport factor


Domain annotation for each model (and alignments):
>> EF1_GNE  EF-1 guanine nucleotide exchange domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.2   0.5   1.6e-24   7.3e-21       3      87 ..       7      85 ..       5      87 .. 0.92

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 1.6e-24
                                      EEEEEESSS---HHHHHHHHHH.HS-T.SEE--.--EEE-SSS-EEEEEEEEESSS-GGGGHHHHHHTTS-S.....SE CS
                           EF1_GNE  3 vlevkPeddetdleelekkvksikleg.lvwgeasklepiafGlkkLqiscvieddkvstdeleekieeiegeledlVq 80
                                       ++v+Pe+++tdleel+kk+++ +l++  +++    +epiafGlk+L + + + d++++t+e+ee++ ++ g     V 
  gi|298674225|ref|YP_003725975.1|  7 KIKVMPESVDTDLEELKKKIEE-ALPEeTELHG-TSEEPIAFGLKALMLDISVSDKEGGTEEVEEAFMNVPG-----VD 78
                                      79********************.77776****5.9*************************************.....99 PP

                                      EEEEEEE CS
                           EF1_GNE 81 sveivsf 87
                                      +v++v +
  gi|298674225|ref|YP_003725975.1| 79 NVQVVGL 85
                                      9998865 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1      0.14   6.3e+02      42      56 ..      18      32 ..       2      37 .. 0.66
   2 ?   12.0   0.1   7.2e-05      0.32       1      19 [.      66      84 ..      66      87 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.14
                                      HHHHHHHHHHHHT-T CS
                     AMP-binding_C 42 leeeLkahvrkelgp 56
                                        eeLk++++++l++
  gi|298674225|ref|YP_003725975.1| 18 DLEELKKKIEEALPE 32
                                      458999999888875 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 7.2e-05
                                      HHHHHHHSSTTEEEEEEE- CS
                     AMP-binding_C  1 evEsalvshpaVaeaaVvG 19
                                      evE+a +++p+V+++ VvG
  gi|298674225|ref|YP_003725975.1| 66 EVEEAFMNVPGVDNVQVVG 84
                                      8*****************9 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.3    0.0071        32      40      59 ..      10      29 ..       4      32 .. 0.74
   2 ?    7.0   0.0    0.0018       8.1      15      31 ..      66      82 ..      64      87 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0071
                               HMA 40 Vegdaestklrkiieaieka 59
                                      V+ +  +t+l++++++ie+a
  gi|298674225|ref|YP_003725975.1| 10 VMPESVDTDLEELKKKIEEA 29
                                      55556667889999999985 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0018
                               HMA 15 kvekvLselpgVesvkv 31
                                       ve+++ ++pgV++v v
  gi|298674225|ref|YP_003725975.1| 66 EVEEAFMNVPGVDNVQV 82
                                      69*************98 PP

>> GFD1  GFD1 mRNA transport factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   7.0   0.00083       3.7       2      11 ..      19      28 ..      19      28 .. 0.94

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00083
                              GFD1  2 lelLKKKIEE 11
                                      le+LKKKIEE
  gi|298674225|ref|YP_003725975.1| 19 LEELKKKIEE 28
                                      69*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       793  (0.04423); expected 358.6 (0.02)
Passed bias filter:                      664  (0.037035); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 617.22
//
Query:       gi|298674226|ref|YP_003725976.1|  [L=56]
Description: hypothetical protein Metev_0252 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-06   27.1   4.2      3e-06   27.1   4.2    2.4  2  DUF1610         Domain of unknown function (DUF1610)
    0.00025   21.0  13.2      0.016   15.2  13.2    2.3  1  DZR             Double zinc ribbon
     0.0033   16.2   2.5     0.0036   16.1   2.5    1.1  1  tRNA-synt_1g    tRNA synthetases class I (M)
     0.0061   16.2  15.5        1.5    8.7   0.1    3.9  3  zinc_ribbon_2   zinc-ribbon domain
      0.007   16.8   9.4      0.067   13.7   5.4    2.0  2  zf-CHY          CHY zinc finger
  ------ inclusion threshold ------
      0.019   14.5   0.2      0.019   14.5   0.2    2.5  2  RecR            RecR protein
      0.026   14.5   0.7      0.026   14.5   0.7    2.2  2  zf-C2HC5        Putative zinc finger motif, C2HC5-type
      0.065   13.1   5.2      0.065   13.1   5.2    2.9  1  zf-HIT          HIT zinc finger
       0.24   11.4  10.2        1.5    8.8   6.0    2.2  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.24   11.4   0.1       0.24   11.4   0.1    3.0  2  YhfH            YhfH-like protein
       0.35   10.9   9.6        2.7    8.1   9.7    1.9  1  zinc-ribbons_6  zinc-ribbons
       0.47   10.6  11.2         45    4.3  11.2    2.3  1  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
       0.57   10.2  10.7        2.6    8.1   2.7    2.0  2  HypA            Hydrogenase/urease nickel incorporation, meta
       0.58   10.0  14.4        1.4    8.8   9.6    2.1  2  zf-HYPF         HypF finger
       0.59   10.3  13.0        8.1    6.6  13.0    2.2  1  DUF1272         Protein of unknown function (DUF1272)
        1.2    8.8  17.3        1.2    8.8   0.1    3.1  3  zf-tcix         Putative treble-clef, zinc-finger, Zn-binding
        1.7    8.6  15.4        1.3    9.0   3.9    3.1  2  Nudix_N_2       Nudix N-terminal
        1.9    8.3  15.5        1.2    9.0   0.3    3.9  3  Rubredoxin_2    Rubredoxin metal binding domain
        2.1    8.5   9.5        4.3    7.4   9.5    1.6  1  Zn_Tnp_IS91     Transposase zinc-binding domain
        2.3    8.4   9.6        7.9    6.7   4.3    2.1  2  Spt4            Spt4/RpoE2 zinc finger
          3    8.1  11.4        5.8    7.2   3.4    2.5  2  zf-AN1          AN1-like Zinc finger
        3.3    7.9  15.5         12    6.1   0.1    3.2  3  Zn-ribbon_8     Zinc ribbon domain
        3.5    7.7   8.5         30    4.8   0.2    3.2  3  DUF2752         Protein of unknown function (DUF2752)
        3.9    5.2   5.4        4.3    5.1   5.4    1.0  1  PolC_DP2        DNA polymerase II large subunit DP2
          6    6.8  13.4        3.5    7.6   1.2    2.2  2  zf-C3HC4        Zinc finger, C3HC4 type (RING finger)
          6    6.4  15.9       0.82    9.2   0.7    3.5  4  zf-ribbon_3     zinc-ribbon domain
        6.6    6.9  13.6        5.9    7.1   0.5    3.4  3  UPF0547         Uncharacterised protein family UPF0547
        6.8    6.1  14.8         15    5.0   0.1    3.0  2  zf-TFIIB        Transcription factor zinc-finger
        7.6    5.9   8.7        9.5    5.6   8.7    1.1  1  NMD3            NMD3 family


Domain annotation for each model (and alignments):
>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   4.2   4.8e-09     3e-06       1      22 [.       9      29 ..       9      29 .. 0.99
   2 !    8.8   2.4    0.0026       1.6      18      23 ..      47      52 ..      43      52 .. 0.89

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 4.8e-09
                           DUF1610  1 CtSCGaelaprEravvFpCPNC 22
                                      Ct+CG+ la+r+  v FpCP C
  gi|298674226|ref|YP_003725976.1|  9 CTTCGVHLAERG-FVRFPCPSC 29
                                      ************.*******99 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0026
                           DUF1610 18 pCPNCG 23
                                       CPNCG
  gi|298674226|ref|YP_003725976.1| 47 TCPNCG 52
                                      6****9 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2  13.2   2.6e-05     0.016      10      49 .]       4      52 ..       2      54 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.6e-05
                               DZR 10 pdarfCseCgtklkavaa............edrCpsCgekvdpearfCpeCG 49
                                      p+ ++C +Cg +l +                 rC +C ++ +p   +Cp+CG
  gi|298674226|ref|YP_003725976.1|  4 PEVKYCTTCGVHLAER-GfvrfpcpscsteLGRCINCRQQSNPY--TCPNCG 52
                                      5678888888888633.258888888888889*******99888..8****9 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   2.5   5.7e-06    0.0036     119     160 ..       5      47 ..       1      55 [. 0.89

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.7e-06
                                       EEEEETTTTEEE-GG.G-EE........-TTS-EE-TTSSB-E CS
                      tRNA-synt_1g 119 eqlycpkderflpdr.yvegtCPkckseeargdqceecgkkle 160
                                       e+ yc++++  l++r +v+  CP c +e  r  +c ++++ ++
  gi|298674226|ref|YP_003725976.1|   5 EVKYCTTCGVHLAERgFVRFPCPSCSTELGRCINCRQQSNPYT 47 
                                       788***********966******************99998876 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.1    0.0024       1.5      11      22 ..       4      15 ..       2      16 .. 0.81
   2 ?    5.4   0.2     0.025        15       2       8 ..      26      32 ..      22      34 .. 0.59
   3 ?    5.3   6.5     0.028        17      15      22 ..      46      54 ..      35      55 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0024
                     zinc_ribbon_2 11 dnakFCpyCGtp 22
                                      +++k+C+ CG +
  gi|298674226|ref|YP_003725976.1|  4 PEVKYCTTCGVH 15
                                      7899*****965 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.025
                     zinc_ribbon_2  2 CpnCGae 8 
                                      Cp+C +e
  gi|298674226|ref|YP_003725976.1| 26 CPSCSTE 32
                                      5555554 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.028
                     zinc_ribbon_2 15 F.CpyCGtp 22
                                      + Cp+CG++
  gi|298674226|ref|YP_003725976.1| 46 YtCPNCGFE 54
                                      458888876 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.7    0.0028       1.8      51      73 ..       3      30 ..       1      32 [. 0.74
   2 !   13.7   5.4   0.00011     0.067      43      73 ..      25      52 ..      21      54 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0028
                            zf-CHY 51 qekavlCkkCkk.....efaeyfCpiCk 73
                                      +++++ C++C+       f ++ Cp C+
  gi|298674226|ref|YP_003725976.1|  3 KPEVKYCTTCGVhlaerGFVRFPCPSCS 30
                                      578899****9955554455668****7 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00011
                            zf-CHY 43 lcllCeteqekavlCkkCkkefaeyfCpiCk 73
                                       c  C+te      C +C+++ + y+Cp+C 
  gi|298674226|ref|YP_003725976.1| 25 PCPSCSTE---LGRCINCRQQSNPYTCPNCG 52
                                      57778775...889****************7 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2     3e-05     0.019      12      36 ..       2      31 ..       1      33 [. 0.87
   2 ?    0.1   5.4      0.96   5.9e+02      15      34 ..      32      51 ..      30      52 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3e-05
                                      HHHH-EE-TTT-.-EESSS....S-CCCCS CS
                              RecR 12 akekvrhCsrCg.nlteed....lCaICsd 36
                                      ak +v++C  Cg +l+e+     +C+ Cs 
  gi|298674226|ref|YP_003725976.1|  2 AKPEVKYCTTCGvHLAERGfvrfPCPSCST 31
                                      6789********667999899999****96 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.96
                                      H-EE-TTT--EESSSS-CCC CS
                              RecR 15 kvrhCsrCgnlteedlCaIC 34
                                      ++++C +C+  +    C+ C
  gi|298674226|ref|YP_003725976.1| 32 ELGRCINCRQQSNPYTCPNC 51
                                      56789999998888888888 PP

>> zf-C2HC5  Putative zinc finger motif, C2HC5-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.7   4.1e-05     0.026      19      44 ..       8      33 ..       3      35 .. 0.89
   2 ?    2.2   2.6      0.29   1.8e+02      26      41 ..      37      52 ..      34      54 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.1e-05
                          zf-C2HC5 19 nClnCGkiiCakeglskpCsfCgspl 44
                                       C++CG  + ++  +  pC++C+++l
  gi|298674226|ref|YP_003725976.1|  8 YCTTCGVHLAERGFVRFPCPSCSTEL 33
                                      7*****9999999999*******997 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.29
                          zf-C2HC5 26 iiCakeglskpCsfCg 41
                                      i C ++    +C+ Cg
  gi|298674226|ref|YP_003725976.1| 37 INCRQQSNPYTCPNCG 52
                                      5677777778999997 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   5.2   0.00011     0.065       3      20 ..      34      52 ..      32      54 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                                      -B-TTT-S.B-SEE-TTT- CS
                            zf-HIT  3 klCgvCgf.pakYkCpkCn 20
                                      + C+ C +    Y+Cp+C+
  gi|298674226|ref|YP_003725976.1| 34 GRCINCRQqSNPYTCPNCG 52
                                      57******9999******8 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   4.8      0.02        12      29      58 ..       7      35 ..       5      39 .. 0.88
   2 ?    8.8   6.0    0.0025       1.5      31      55 ..      26      54 ..      25      55 .. 0.94

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.02
                    OrfB_Zn_ribbon 29 ktCseCgsknkealsgrtfkCpnCgfeadr 58
                                      k C  Cg  + e +   +f Cp+C +e+ r
  gi|298674226|ref|YP_003725976.1|  7 KYCTTCGVHLAE-RGFVRFPCPSCSTELGR 35
                                      78**********.99999******999877 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0025
                    OrfB_Zn_ribbon 31 CseCgsknke....alsgrtfkCpnCgfe 55
                                      C+ C  ++ +    +++++ ++CpnCgfe
  gi|298674226|ref|YP_003725976.1| 26 CPSCSTELGRcincRQQSNPYTCPNCGFE 54
                                      999999999999999************97 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1    0.0004      0.24      13      25 ..       6      18 ..       3      20 .. 0.88
   2 ?    3.1   0.7      0.15        91      15      20 ..      47      52 ..      42      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0004
                              YhfH 13 kKkCteCGkeieE 25
                                       K Ct+CG ++ E
  gi|298674226|ref|YP_003725976.1|  6 VKYCTTCGVHLAE 18
                                      69*******9988 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.15
                              YhfH 15 kCteCG 20
                                      +C++CG
  gi|298674226|ref|YP_003725976.1| 47 TCPNCG 52
                                      7****9 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   9.7    0.0043       2.7       3      55 ..       9      51 ..       7      54 .. 0.47

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0043
                                      -SSS-S--EE-S.SEEE-TTT--EEEEEEE-SSS-S---EEEETTEEE..E--TTT CS
                    zinc-ribbons_6  3 CpeCqqelekrg.eqyhCeaCqedlkkealCpeCeqelevlkaCgavd..yfCnkc 55
                                      C +C  +l +rg  ++              Cp C+ el ++  C   +  y C +c
  gi|298674226|ref|YP_003725976.1|  9 CTTCGVHLAERGfVRFP-------------CPSCSTELGRCINCRQQSnpYTCPNC 51
                                      55555555433333444.............55555555555555433222555555 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3  11.2     0.072        45       2      24 ..      26      53 ..       6      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.072
                          zf-Mss51  2 CPvpkhkqt.....apkhvdfeCpdCGi 24
                                      CP ++++ +      +++  ++Cp+CG+
  gi|298674226|ref|YP_003725976.1| 26 CPSCSTELGrcincRQQSNPYTCPNCGF 53
                                      999988888999888888999*****96 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   2.7    0.0042       2.6      70      95 ..       6      32 ..       2      36 .. 0.79
   2 ?    5.5   3.5     0.026        16      72      93 ..      35      52 ..      31      55 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0042
                                      EEEETTTS-EEECHHH.HHS-TTTSSS CS
                              HypA 70 kvrCreCgkefeleek.alrCpkCgsa 95
                                      + +C++Cg +  ++   ++ Cp+C+++
  gi|298674226|ref|YP_003725976.1|  6 VKYCTTCGVHLAERGFvRFPCPSCSTE 32
                                      568*****88887765689*****875 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.026
                                      EETTTS-EEECHHHHHS-TTTS CS
                              HypA 72 rCreCgkefeleekalrCpkCg 93
                                      rC +C+++ +     ++Cp+Cg
  gi|298674226|ref|YP_003725976.1| 35 RCINCRQQSNP----YTCPNCG 52
                                      899***88874....48****9 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.2     0.082        51      24      31 ..       9      16 ..       7      17 .. 0.85
   2 ?    8.8   9.6    0.0022       1.4       2      28 ..      26      52 ..      26      53 .. 0.99

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.082
                                      -TTTS--E CS
                           zf-HYPF 24 CtnCGPrl 31
                                      Ct CG +l
  gi|298674226|ref|YP_003725976.1|  9 CTTCGVHL 16
                                      *****776 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0022
                                      -HHHHHHHC-TTSTTTT-TT---TTTS CS
                           zf-HYPF  2 CedClrEykdpldRRfhaqfisCtnCG 28
                                      C++C  E+    + R +  + +C+nCG
  gi|298674226|ref|YP_003725976.1| 26 CPSCSTELGRCINCRQQSNPYTCPNCG 52
                                      **************************9 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6  13.0     0.013       8.1       8      48 ..       9      52 ..       6      54 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.013
                           DUF1272  8 CecCdkdlppdse...earicsyEctFCaeCaeevlenvCPncg 48
                                      C +C  +l +          cs E   C +C ++    +CPncg
  gi|298674226|ref|YP_003725976.1|  9 CTTCGVHLAERGFvrfPCPSCSTELGRCINCRQQSNPYTCPNCG 52
                                      778888887765311145579**************99******9 PP

>> zf-tcix  Putative treble-clef, zinc-finger, Zn-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1     0.002       1.2      10      25 ..       6      21 ..       4      23 .. 0.86
   2 ?    4.0   4.7     0.064        39      12      29 ..      25      41 ..      19      47 .. 0.86
   3 ?    4.7   1.2     0.037        23      13      18 ..      48      53 ..      46      56 .] 0.82

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.002
                           zf-tcix 10 vrkCpkCGtyNGtRgl 25
                                      v+ C++CG+    Rg+
  gi|298674226|ref|YP_003725976.1|  6 VKYCTTCGVHLAERGF 21
                                      899*****98888875 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.064
                           zf-tcix 12 kCpkCGtyNGtRglsCkN 29
                                       Cp+C t+ G R++ C+ 
  gi|298674226|ref|YP_003725976.1| 25 PCPSCSTELG-RCINCRQ 41
                                      5********9.9999985 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.037
                           zf-tcix 13 CpkCGt 18
                                      Cp+CG 
  gi|298674226|ref|YP_003725976.1| 48 CPNCGF 53
                                      *****6 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   3.9    0.0021       1.3       1      30 [.       7      31 ..       7      32 .. 0.86
   2 ?    2.0   9.3      0.33   2.1e+02       3      30 ..      26      53 ..      23      53 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0021
                                      -B-TTT--B-EEE--TT-SS-EEEETTTTE CS
                         Nudix_N_2  1 kFCsqCGtpvelripdgDnreRlvCpaCgt 30
                                      k+C+ CG  ++ r        R+ Cp+C+t
  gi|298674226|ref|YP_003725976.1|  7 KYCTTCGVHLAERG-----FVRFPCPSCST 31
                                      8*******988776.....58999999976 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.33
                                      -TTT--B-EEE--TT-SS-EEEETTTTE CS
                         Nudix_N_2  3 CsqCGtpvelripdgDnreRlvCpaCgt 30
                                      C++C t++ + i    +   ++Cp+Cg+
  gi|298674226|ref|YP_003725976.1| 26 CPSCSTELGRCINCRQQSNPYTCPNCGF 53
                                      9************9999999******96 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.55   3.4e+02       3       7 ..       9      13 ..       8      16 .. 0.76
   2 ?    0.8   5.3      0.69   4.3e+02      14      21 ..      33      40 ..      26      42 .. 0.76
   3 ?    9.0   0.3    0.0019       1.2       1      10 [.      46      55 ..      46      56 .] 0.86

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.55
                      Rubredoxin_2  3 CsqCG 7 
                                      C  CG
  gi|298674226|ref|YP_003725976.1|  9 CTTCG 13
                                      77887 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.69
                      Rubredoxin_2 14 fGrCpsCg 21
                                      +GrC +C+
  gi|298674226|ref|YP_003725976.1| 33 LGRCINCR 40
                                      68888887 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0019
                      Rubredoxin_2  1 YvCsqCGfes 10
                                      Y C +CGfe 
  gi|298674226|ref|YP_003725976.1| 46 YTCPNCGFEG 55
                                      99*****986 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   9.5     0.007       4.3      24      64 ..       6      52 ..       2      55 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.007
                       Zn_Tnp_IS91 24 vekilrCrt..aalGfaryeCeeCghekivyfsCksrh....CpsCq 64
                                      v+  + C+   a+ Gf r+ C++C+ e   +  C++++    Cp+C+
  gi|298674226|ref|YP_003725976.1|  6 VKYCTTCGVhlAERGFVRFPCPSCSTELGRCINCRQQSnpytCPNCG 52
                                      55666777633578********************9875455699998 PP

>> Spt4  Spt4/RpoE2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   4.3     0.013       7.9       2      25 ..       7      30 ..       6      41 .. 0.88
   2 ?    3.1   2.7      0.17     1e+02       4      24 ..      36      51 ..      33      55 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.013
                              Spt4  2 rACllCklvktedqFeeegCpnCe 25
                                      + C+ C++   e+ F +  Cp C+
  gi|298674226|ref|YP_003725976.1|  7 KYCTTCGVHLAERGFVRFPCPSCS 30
                                      67*********************3 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.17
                              Spt4  4 CllCklvktedqFeeegCpnC 24
                                      C++C+      q +  +CpnC
  gi|298674226|ref|YP_003725976.1| 36 CINCRQ-----QSNPYTCPNC 51
                                      555553.....334567**** PP

>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   1.0     0.031        19       1      21 [.       9      31 ..       9      33 .. 0.76
   2 ?    7.2   3.4    0.0094       5.8       5      20 ..      38      52 ..      35      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.031
                            zf-AN1  1 CsfksCkkkd....flpfkCryCgk 21
                                      C+  +C+ ++    f+ f C++C+ 
  gi|298674226|ref|YP_003725976.1|  9 CT--TCGVHLaergFVRFPCPSCST 31
                                      55..6888877776777******85 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0094
                            zf-AN1  5 sCkkkdflpfkCryCg 20
                                      +C+++ + p++C++Cg
  gi|298674226|ref|YP_003725976.1| 38 NCRQQSN-PYTCPNCG 52
                                      7999998.*******8 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1      0.02        12      24      38 ..       3      19 ..       1      21 [. 0.68
   2 ?    4.5   4.7      0.06        37       8      38 ..       9      35 ..       8      37 .. 0.67
   3 ?    2.1  10.8      0.35   2.2e+02       6      33 ..      24      52 ..      23      54 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.02
                       Zn-ribbon_8 24 aplta.CPeCgs.evrr 38
                                      +p+++ C +Cg   ++r
  gi|298674226|ref|YP_003725976.1|  3 KPEVKyCTTCGVhLAER 19
                                      456666****9855555 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.06
                       Zn-ribbon_8  8 CeeCghefevlqsisdapltaCPeCgsevrr 38
                                      C+ Cg ++ + + + + p   CP+C  e+ r
  gi|298674226|ref|YP_003725976.1|  9 CTTCG-VHLAERGFVRFP---CPSCSTELGR 35
                                      99999.555555455545...****888877 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.35
                       Zn-ribbon_8  6 YrCeeCghefevlqsisdaplta.CPeCg 33
                                      + C +C +e  +     + +++  CP+Cg
  gi|298674226|ref|YP_003725976.1| 24 FPCPSCSTELGRCINCRQQSNPYtCPNCG 52
                                      669999999998888886666777****8 PP

>> DUF2752  Protein of unknown function (DUF2752)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1      0.16        96      10      16 ..       8      14 ..       6      17 .. 0.89
   2 ?    4.8   0.2     0.049        30       7      14 ..      22      29 ..      19      31 .. 0.82
   3 ?    3.8   0.7     0.094        58      10      15 ..      47      52 ..      45      54 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.16
                           DUF2752 10 pCPGCGl 16
                                      +C +CG+
  gi|298674226|ref|YP_003725976.1|  8 YCTTCGV 14
                                      9*****6 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.049
                           DUF2752  7 tGipCPGC 14
                                        +pCP C
  gi|298674226|ref|YP_003725976.1| 22 VRFPCPSC 29
                                      679***** PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.094
                           DUF2752 10 pCPGCG 15
                                       CP CG
  gi|298674226|ref|YP_003725976.1| 47 TCPNCG 52
                                      7***** PP

>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   5.4    0.0069       4.3     620     662 ..       8      52 ..       2      55 .. 0.55

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0069
                          PolC_DP2 620 kCkkCgket.....learCeeCgekteeklvCkkceeeveeekcekce 662
                                       +C++Cg +      +++ C++C ++      C +c+++++  +c++c+
  gi|298674226|ref|YP_003725976.1|   8 YCTTCGVHLaergfVRFPCPSCSTELGR---CINCRQQSNPYTCPNCG 52 
                                       6667765531111133456666555544...77777777777777775 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   1.2    0.0056       3.5      21      41 .]       8      29 ..       7      29 .. 0.80
   2 ?    4.5   5.0     0.052        32      25      41 .]      36      51 ..      34      51 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0056
                                      B-CHHHHHHHHC.TSSB--TTT CS
                          zf-C3HC4 21 fCskCirkilks.rkkvkCPlC 41
                                      +C++C +++ +     ++CP C
  gi|298674226|ref|YP_003725976.1|  8 YCTTCGVHLAERgFVRFPCPSC 29
                                      8**********5444566**** PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.052
                                      HHHHHHHCTSSB--TTT CS
                          zf-C3HC4 25 CirkilksrkkvkCPlC 41
                                      Ci   ++ ++ ++CP+C
  gi|298674226|ref|YP_003725976.1| 36 CINCRQQ-SNPYTCPNC 51
                                      6655555.999****** PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.042        26      15      23 ..       5      13 ..       2      19 .. 0.62
   2 ?    3.4   0.4     0.086        53       5       8 ..      26      29 ..      24      33 .. 0.72
   3 ?   -2.5   0.6       6.4   3.9e+03       5       8 ..      36      39 ..      35      40 .. 0.50
   4 ?    9.2   0.7    0.0013      0.82       4      23 ..      47      52 ..      46      54 .. 0.56

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.042
                       zf-ribbon_3 15 ddnvCpyCG 23
                                      +++ C+ CG
  gi|298674226|ref|YP_003725976.1|  5 EVKYCTTCG 13
                                      555566666 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.086
                       zf-ribbon_3  5 CPnC 8 
                                      CP+C
  gi|298674226|ref|YP_003725976.1| 26 CPSC 29
                                      7776 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 6.4
                       zf-ribbon_3  5 CPnC 8 
                                      C nC
  gi|298674226|ref|YP_003725976.1| 36 CINC 39
                                      4344 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.0013
                       zf-ribbon_3  4 rCPnCGaplssddnvCpyCG 23
                                      +              Cp+CG
  gi|298674226|ref|YP_003725976.1| 47 T--------------CPNCG 52
                                      4..............55555 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1         1   6.3e+02      15      21 ..       7      13 ..       5      15 .. 0.82
   2 ?    5.8   2.2     0.023        14       3      10 ..      26      33 ..      25      41 .. 0.91
   3 ?    7.1   0.5    0.0095       5.9      17      23 ..      48      54 ..      44      54 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1
                           UPF0547 15 qfCphCG 21
                                      + C  CG
  gi|298674226|ref|YP_003725976.1|  7 KYCTTCG 13
                                      6799999 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.023
                           UPF0547  3 CPeCeakv 10
                                      CP C++++
  gi|298674226|ref|YP_003725976.1| 26 CPSCSTEL 33
                                      *****997 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0095
                           UPF0547 17 CphCGyv 23
                                      Cp CG++
  gi|298674226|ref|YP_003725976.1| 48 CPNCGFE 54
                                      9999996 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.025        15      18      26 ..       5      13 ..       3      20 .. 0.80
   2 ?    1.7  11.1      0.26   1.6e+02       2      26 ..      26      52 ..      25      52 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.025
                          zf-TFIIB 18 eidyCpqCr 26
                                      e++yC+ C+
  gi|298674226|ref|YP_003725976.1|  5 EVKYCTTCG 13
                                      678888886 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.26
                          zf-TFIIB  2 CPkCqdele..eserggveidyCpqCr 26
                                      CP+C++el   +  r+    ++Cp+C+
  gi|298674226|ref|YP_003725976.1| 26 CPSCSTELGrcINCRQQSNPYTCPNCG 52
                                      *********55444599999******7 PP

>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   8.7     0.015       9.5       1      42 [.       9      52 ..       9      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.015
                              NMD3  1 CcrCGkeieeling....lCedCllkevditegiekievevCkeCg 42
                                      C  CG+   e  +g     C++C ++  + +++ ++ +   C++Cg
  gi|298674226|ref|YP_003725976.1|  9 CTTCGVHLAE--RGfvrfPCPSCSTELGRCINCRQQSNPYTCPNCG 52
                                      99*****953..4556779**************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        41  (0.0022868); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 358.64
//
Query:       gi|298674227|ref|YP_003725977.1|  [L=200]
Description: aspartate/glutamate/uridylate kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-09   38.0   0.0    9.7e-07   28.6   0.0    2.1  2  AA_kinase   Amino acid kinase family
  ------ inclusion threshold ------
      0.016   13.8   0.0       0.02   13.5   0.0    1.1  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0   0.00025       2.2      19      63 ..       7      53 ..       2      77 .. 0.79
   2 !   28.6   0.0   1.1e-10   9.7e-07     131     217 ..      79     151 ..      67     175 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00025
                                      HHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHH..TCCCCCHHHC CS
                         AA_kinase 19 slrrlaeqiaalkesgnklvvVhGggsftdgllal..ksglssgela 63
                                       +++++e i + +e+ + +v+V Ggg f+d   ++  k+++s + ++
  gi|298674227|ref|YP_003725977.1|  7 IVNHVIEYINTTSEEMKSVVIVPGGGIFADCVRDIskKYHISNDASH 53
                                      57889999999999999********9998887777655776666655 PP

  == domain 2  score: 28.6 bits;  conditional E-value: 1.1e-10
                                       HHHHHHTT-EEEEESEEEEETTTE...EEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEH CS
                         AA_kinase 131 ieelleagvvpvltgfigldeege...lgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisv 204
                                       + el +   ++vl +++ l ++ e    ++++sDti a++A++l+A + + +tdVdG++           l++ei++
  gi|298674227|ref|YP_003725977.1|  79 LSELYSG--IMVLKPYQYLKNNDElphGWNVTSDTIGAWIAKKLDA-SFVKITDVDGIFKEQ-------SLVSEINA 145
                                       4455444..89999999777777778888*****************.9***********554.......89999999 PP

                                       HHCHHCSSS.TTT CS
                         AA_kinase 205 deaeesaselatg 217
                                       +++++        
  gi|298674227|ref|YP_003725977.1| 146 SDIDK-------S 151
                                       99998.......3 PP

>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.3e-06      0.02     361     457 ..      16     118 ..       2     130 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.3e-06
                                       HHHHHHHHHHEEEETTTCHHHHHHHHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHH.. CS
                        Cpn60_TCP1 361 nvvknaiedekvvpGGGatelelakklkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraah.. 435
                                       n ++  +++  +vpGGG +    a  +++++k+++  +  +  +   ++e+ ++ ++   Gl++i++l++l+++   
  gi|298674227|ref|YP_003725977.1|  16 NTTSEEMKSVVIVPGGGIF----ADCVRDISKKYHISNDASHWIAIASMEQYAYYIIDKTGLESIDTLSELYSGImv 88 
                                       566666778889*****76....5566666667666666666777789*************************9999 PP

                                       ........HTTXTTEEEETTTTCEEECCCC CS
                        Cpn60_TCP1 436 ........nkgekelgidvesgeiidlvea 457
                                               n++e  +g++v+s++i   +++
  gi|298674227|ref|YP_003725977.1|  89 lkpyqylkNNDELPHGWNVTSDTIGAWIAK 118
                                       *******999999*******9998766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1341.57
//
Query:       gi|298674228|ref|YP_003725978.1|  [L=323]
Description: H4MPT-linked C1 transfer pathway protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-29  102.1   0.1    2.8e-28   99.0   0.0    1.9  2  Hydantoinase_A  Hydantoinase/oxoprolinase
    4.9e-05   22.1   0.0     0.0048   15.6   0.0    2.2  2  MutL            MutL protein
    0.00054   19.3   1.5       0.11   11.7   0.2    2.6  3  StbA            StbA protein
  ------ inclusion threshold ------
      0.026   14.9   0.2      0.067   13.6   0.2    1.6  1  SHS2_FTSA       SHS2 domain inserted in FTSA
        0.1   12.3   3.9          2    8.1   0.1    3.1  3  Hydant_A_N      Hydantoinase/oxoprolinase N-terminal region


Domain annotation for each model (and alignments):
>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.061   2.2e+02      79     100 ..       3      23 ..       1      33 [. 0.82
   2 !   99.0   0.0   7.9e-32   2.8e-28       4     272 ..      55     302 ..      53     320 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.061
                    Hydantoinase_A  79 kkvItfDmGGTstDvslikdge 100
                                       ++ I++D+GG  t+vs  + g+
  gi|298674228|ref|YP_003725978.1|   3 NSTIGIDIGGANTKVSSND-GN 23 
                                       568************9866.55 PP

  == domain 2  score: 99.0 bits;  conditional E-value: 7.9e-32
                    Hydantoinase_A   4 tavvnAylspilreylesvekslekrgak..arlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaatsklage 78 
                                       ++v++++l++++ ++ ++++ +++ ++ +  +++ +++ dG +++ ++  +   +++++++aa++  + +   + g+
  gi|298674228|ref|YP_003725978.1|  55 AVVMTGELADCFDNKHNGIKFIMDSVDNAfnCEVNFVNVDGQFINDSNNIN---HLAAANWAASARIIGN---EIGN 125
                                       78*******************99998766669*************997766...5**************9...7777 PP

                    Hydantoinase_A  79 kkvItfDmGGTstDvslikdgevevsleteiagvkvrlpaldirtvgagGgsil.vvdeggklrvgpesagadpgpa 154
                                         +I++DmG+T+tD+++i+dg++        ++  +++++l  +++ + G +++ +    +k+++   s++ +++  
  gi|298674228|ref|YP_003725978.1| 126 --CIFVDMGSTTTDIIPIIDGKH--------KAQYTDFKRLLHDELLYTGLLRTnIATVVDKMDLNEGSCRPSSEL- 191
                                       ..*********************........67789******************999*******************. PP

                    Hydantoinase_A 155 cyrkGgteltvTDanlvLGrlqpedfls.gpdgdqkldvelarraf.eelakelnlk...veevAegilsvavenma 226
                                              ++t++Da+l+LG +  + +++  +d ++  +++++rr +   +++  + +   +e++A+ + +++ + + 
  gi|298674228|ref|YP_003725978.1| 192 -------FATTADAYLMLGDISSDMYTCePADNAGVEKNDALRRLArVVCSDLNEISnddIEKIAQSVKEKQISLIR 261
                                       .......*********************86777777777777777744444433332445***************** PP

                    Hydantoinase_A 227 navrklsvergldpkeltlvvfGGaGaqhaaalaeelgvkkvivpp 272
                                       +a+ ++s+++ ld      +v +G G+ +++ + e+lg+++  v+ 
  gi|298674228|ref|YP_003725978.1| 262 EAISSVSKQYNLD-----KIVTAGIGEYIIKNAVEQLGFECLSVTD 302
                                       ******6666555.....58999******99999999988766542 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.4   0.0    0.0032        12     249     267 ..       5      22 ..       2      41 .. 0.76
   2 !   15.6   0.0   1.3e-06    0.0048     244     277 ..     121     154 ..     103     196 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0032
                              MutL 249 llvvDvGGaTTdvhsvaeg 267
                                       ++++D+GGa T v s  +g
  gi|298674228|ref|YP_003725978.1|   5 TIGIDIGGANTKVSSN-DG 22 
                                       689**********998.44 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.3e-06
                              MutL 244 kglgdllvvDvGGaTTdvhsvaegspekekvllk 277
                                       +++g+++ vD+G++TTd++ +++g+++ + + +k
  gi|298674228|ref|YP_003725978.1| 121 NEIGNCIFVDMGSTTTDIIPIIDGKHKAQYTDFK 154
                                       369*******************999998877655 PP

>> StbA  StbA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0     0.094   3.4e+02     164     211 ..       4      51 ..       2      82 .. 0.78
   2 !    5.8   0.0    0.0019       6.7      90     180 ..      49     141 ..      40     185 .. 0.77
   3 !   11.7   0.2   3.2e-05      0.11     241     292 ..     242     293 ..     230     302 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.094
                              StbA 164 slLiiDlGGttLDvakvrgklegiskvkgdskiGvslitdavkealet 211
                                       s + iD+GG+   v++  g+++++  v   +++    i +++ +++e 
  gi|298674228|ref|YP_003725978.1|   4 STIGIDIGGANTKVSSNDGNFTELHYVPLWKNTVLPNILQEIARKIEP 51 
                                       566699999999999999999998888887777777777777776664 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0019
                              StbA  90 lkpqdvdvvvtLPlseyydannqpneenierkkanvmrevelqggesftikkvkvlPeslPagfealkel..deles 164
                                       ++p  v vv+t  l++ +d++++  +  ++   + +  ev++ + +   i + + +     a + a +++  +e+ +
  gi|298674228|ref|YP_003725978.1|  49 IEPYRVAVVMTGELADCFDNKHNGIKFIMDSVDNAFNCEVNFVNVDGQFINDSNNINHLAAANWAASARIigNEIGN 125
                                       78889999999999999998877666666666666888999888888889999999888888888888843478889 PP

                              StbA 165 lLiiDlGGttLDvakv 180
                                        + +D+G tt D+  +
  gi|298674228|ref|YP_003725978.1| 126 CIFVDMGSTTTDIIPI 141
                                       9***********9655 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 3.2e-05
                              StbA 241 edkresvlevinekvkkLkerviravsefsgythvmvvGGGaeliaeaikka 292
                                       +d++e++ + ++ek+ +L ++ i++vs+  +  +++  G G ++i++a+ + 
  gi|298674228|ref|YP_003725978.1| 242 NDDIEKIAQSVKEKQISLIREAISSVSKQYNLDKIVTAGIGEYIIKNAVEQL 293
                                       57899********************************************985 PP

>> SHS2_FTSA  SHS2 domain inserted in FTSA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   1.9e-05     0.067      15      56 ..     234     275 ..     227     282 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.9e-05
                                       -TTS-E--HHHHHHHHHHH....CHTTEEEEEEEEEEEEETT CS
                         SHS2_FTSA  15 isgedeiteedvervleaakavaipedreilhvipqeyivDg 56 
                                        s+ +ei+++d+e++ ++ k+ +i+  re +  + ++y +D+
  gi|298674228|ref|YP_003725978.1| 234 CSDLNEISNDDIEKIAQSVKEKQISLIREAISSVSKQYNLDK 275
                                       45555************************************7 PP

>> Hydant_A_N  Hydantoinase/oxoprolinase N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1      0.01        37       2      20 ..       6      24 ..       5      93 .. 0.79
   2 ?    8.1   0.1   0.00056         2       2      20 ..     127     145 ..     126     180 .. 0.78
   3 ?   -0.3   0.0      0.21   7.5e+02      29      49 ..     250     270 ..     226     296 .. 0.61

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.01
                        Hydant_A_N  2 igIDvGGTfTDavaldeke 20
                                      igID+GG +T +   d++ 
  gi|298674228|ref|YP_003725978.1|  6 IGIDIGGANTKVSSNDGNF 24
                                      9*********887777654 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00056
                        Hydant_A_N   2 igIDvGGTfTDavaldeke 20 
                                       i++D+G+T TD++ + +++
  gi|298674228|ref|YP_003725978.1| 127 IFVDMGSTTTDIIPIIDGK 145
                                       89**********9877553 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.21
                        Hydant_A_N  29 lstpdavaegirealeevlee 49 
                                       +s+++++++ irea+++v+++
  gi|298674228|ref|YP_003725978.1| 250 QSVKEKQISLIREAISSVSKQ 270
                                       333455555555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       953  (0.0531541); expected 358.6 (0.02)
Passed bias filter:                      735  (0.040995); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 2240.13
//
Query:       gi|298674229|ref|YP_003725979.1|  [L=305]
Description: hypothetical protein Metev_0255 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-38  131.7   0.1    3.4e-38  131.2   0.1    1.2  1  ATP-grasp_3      ATP-grasp domain
      2e-06   27.5   0.1    3.1e-06   26.9   0.1    1.2  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    2.3e-05   24.6   0.0      4e-05   23.8   0.0    1.3  1  preATP-grasp_3   pre ATP-grasp 3 domain
    2.5e-05   24.1   0.0    4.7e-05   23.1   0.0    1.4  1  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
    9.7e-05   21.8   0.0     0.0095   15.2   0.0    2.2  2  ATPgrasp_ST      Sugar-transfer associated ATP-grasp
     0.0011   18.7   0.2      0.031   13.9   0.0    2.2  2  RimK             RimK-like ATP-grasp domain
  ------ inclusion threshold ------
       0.02   14.0   0.2        2.5    7.2   0.0    2.1  2  TTL              Tubulin-tyrosine ligase family


Domain annotation for each model (and alignments):
>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.2   0.1   1.3e-41   3.4e-38       1     161 []     109     263 ..     109     263 .. 0.92

  Alignments for each domain:
  == domain 1  score: 131.2 bits;  conditional E-value: 1.3e-41
                                       HTSHHHHHHHHTTT.S---....-EESS--SSSEEEEESS-------B--SS--TTE.......EEEE---SEEEEE CS
                       ATP-grasp_3   1 asdKlktykkLkeagvkvPtkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieevelvqefieGkplSv 77 
                                       + dK+k+ ++L+++++++P    ++  e ++  +v+Kpr+G+++e ++v   k  +    e++ ++ e+i+G+++Sv
  gi|298674229|ref|YP_003725979.1| 109 CVDKIKCSEFLSKSNIPIP----KTTREIKNGWWVIKPRYGSASENTFVTSIKGYK---PENNYIATEYIDGEHVSV 178
                                       67*****************....6666777889***********888887777333...47777************* PP

                                       EEEE.SSSEEEEEEEEEEEET.......TEEEEEEES----HHHHHHHHHHHHHTTSTT--EEEEEEEEESS.SEEE CS
                       ATP-grasp_3  78 sllsdgekvlvlavnrqliekaeke...fvyaGnvtpietelkeevvelaeevvekleglaGyvGvDlvlkdeepyv 151
                                       sl+s g + l+l+vn+qli+  + +   ++y+Gn+tp+ t++k++++++a ++ + l +++GyvG+D++l+++ py+
  gi|298674229|ref|YP_003725979.1| 179 SLIS-GDNQLPLTVNKQLIDIPQINdseIKYNGNLTPYSTSKKQKLYNIAVSASRLL-DCRGYVGIDFILNNDTPYI 253
                                       ****.889************98877888*****************************.******************* PP

                                       EEEESS--GG CS
                       ATP-grasp_3 152 iEvNPRltts 161
                                       ++vNPR+tts
  gi|298674229|ref|YP_003725979.1| 254 VDVNPRPTTS 263
                                       ********97 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.1   1.2e-09   3.1e-06      76     183 ..     166     267 ..     153     277 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 1.2e-09
                                       EEEE--ESEEEEEEEEETSS.CEEEEEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT- CS
                   Dala_Dala_lig_C  76 lvEeaiegreievavlgnek.levsevgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldl 151
                                       +  e+i+g+ + v+++  ++ l  ++ ++ +   ++ d e ky ++       +  ++++++k+ ++a+ a ++ld+
  gi|298674229|ref|YP_003725979.1| 166 IATEYIDGEHVSVSLISGDNqLPLTVNKQLIDIPQINDSEIKYNGNL------TPYSTSKKQKLYNIAVSASRLLDC 236
                                       55678899999999887554144444444555558888888885443......3456788899************** PP

                                       -SEEEEEEEEETTTEEEEEEEESS---STTSH CS
                   Dala_Dala_lig_C 152 rGlaRvDfflteegeivlnEvNtlPGfTeiSl 183
                                       rG + +Df+l+ ++++++ +vN+ P    +S+
  gi|298674229|ref|YP_003725979.1| 237 RGYVGIDFILN-NDTPYIVDVNPRPTTSLVSI 267
                                       **********9.899**********7666665 PP

>> preATP-grasp_3  pre ATP-grasp 3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   1.5e-08     4e-05      22      77 .]      53     106 ..      42     106 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.5e-08
                    preATP-grasp_3  22 lvvdseedvd.etfrrlaaeaDaVlvIAPEtdgiLarltrlveaagkrlLGssskAi 77 
                                       ++v s+ +++  + + la+++Da lvIAP  d++L  ltr++e +  ++LG++++A+
  gi|298674229|ref|YP_003725979.1|  53 FPVESDSSNFeYIIEMLAKKCDAGLVIAP--DELLPVLTRIIENN-TINLGCPPEAV 106
                                       667777777724556679***********..9***********99.9*********8 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   1.8e-08   4.7e-05       4      94 ..     164     268 ..     162     297 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.8e-08
                      ATPgrasp_Ter   4 allvmeyLegpEySvDvlaek.......gevlaavpRrKekgglq........elekdeelielaerlaeefgldgl 65 
                                       +++ +ey++g+ +Sv  ++++       ++ l+ +p   + ++++        +++k+++l ++a +  + + + g+
  gi|298674229|ref|YP_003725979.1| 164 NYIATEYIDGEHVSVSLISGDnqlpltvNKQLIDIPQIND-SEIKyngnltpySTSKKQKLYNIAVSASRLLDCRGY 239
                                       67889**************975788888778888888877.44444455559999********************** PP

                      ATPgrasp_Ter  66 vnvQvrededgpkLLEiNpRasGGlgysa 94 
                                       v++ +  ++d+p++ ++NpR+   l+  +
  gi|298674229|ref|YP_003725979.1| 240 VGIDFILNNDTPYIVDVNPRPTTSLVSIC 268
                                       *********************98887655 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.5   0.0     0.007        18      19      47 ..     109     143 ..      95     174 .. 0.77
   2 !   15.2   0.0   3.7e-06    0.0095     226     275 ..     221     269 ..     209     281 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.007
                       ATPgrasp_ST  19 vddKlkfkelalraglkvpkllgvikeq......a 47 
                                         dK+k++e++++  +++pk+   ik++      +
  gi|298674229|ref|YP_003725979.1| 109 CVDKIKCSEFLSKSNIPIPKTTREIKNGwwvikpR 143
                                       559*****************999998875555550 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 3.7e-06
                       ATPgrasp_ST 226 eevlelaakaaeklpglgylGwDivldeekgplllElNarpglaivqian 275
                                       +++ ++a++a+  l + gy+G+D+ l ++  p+++ +N rp  ++v i n
  gi|298674229|ref|YP_003725979.1| 221 QKLYNIAVSASRLLDCRGYVGIDFILNNDT-PYIVDVNPRPTTSLVSICN 269
                                       788999******999**************9.*********9998877644 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.03        78       3      22 ..     111     130 ..     109     135 .. 0.91
   2 !   13.9   0.0   1.2e-05     0.031     128     173 ..     220     266 ..     190     282 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.03
                                       -HHHHHHHHHHTT-----EE CS
                              RimK   3 dKlkslklLakakikvpnta 22 
                                       dK+k+ + L k +i++p+t+
  gi|298674229|ref|YP_003725979.1| 111 DKIKCSEFLSKSNIPIPKTT 130
                                       9****************985 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.2e-05
                                       -HHHHHHHHHHHHHCT-S.EEEEEEEEETTEEEEEEEESS--SHHHH CS
                              RimK 128 seeekelAikaakamelv.vaGvDllrakrgllvlEvnsspglekie 173
                                       ++++ ++A+ a+++++   ++G+D + +++ +++++vn  p +  ++
  gi|298674229|ref|YP_003725979.1| 220 KQKLYNIAVSASRLLDCRgYVGIDFILNNDTPYIVDVNPRPTTSLVS 266
                                       466789********997549****9999***********99887653 PP

>> TTL  Tubulin-tyrosine ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0    0.0039        10      59     110 ..     128     172 ..      87     173 .. 0.79
   2 ?    7.2   0.0   0.00096       2.5     234     276 ..     234     274 ..     213     294 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0039
                                       TTTS--S-B----SS---XX------BSSTHHHHHHHH..SSS-EEEEB--S CS
                               TTL  59 eeaekeesntwIvKpsasarGkgirvfnkledikkivsqsqkeplvvqkYie 110
                                       +  ++ +  +w++Kp +++ +++++v++ ++  k       ++++++ +Yi+
  gi|298674229|ref|YP_003725979.1| 128 KTTREIKNGWWVIKPRYGSASENTFVTS-IKGYK------PENNYIATEYID 172
                                       455555668****************986.44455......689999999996 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00096
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXX CS
                               TTL 234 kncfelyGvDilidenlkpwLlEvNasPdlksttkldaelkee 276
                                         c+   G+D+++++++ p++++vN  P+++   +    +kee
  gi|298674229|ref|YP_003725979.1| 234 LDCRGYVGIDFILNNDT-PYIVDVNPRPTTS-LVSICNVMKEE 274
                                       5799999******9985.**********653.33333334444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1803.10
//
Query:       gi|298674230|ref|YP_003725980.1|  [L=141]
Description: hypothetical protein Metev_0256 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0026   16.9   8.8     0.0031   16.6   8.8    1.0  1  Acyl_transf_3   Acyltransferase family
  ------ inclusion threshold ------
       0.63    9.3  14.7       0.16   11.2   4.7    2.0  2  Peptidase_U4    Sporulation factor SpoIIGA


Domain annotation for each model (and alignments):
>> Acyl_transf_3  Acyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   8.8   3.5e-07    0.0031     160     273 ..      13     130 ..      10     138 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.5e-07
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Acyl_transf_3 160 shlllllilllllslvfirhelfgpatsvgllplpsvla....llfflfGalladaddrdrnlsrglkislllslll 232
                                       ++l +l i +++ +++++++ + ++ +s g  p+p + +    ++ f++G +++  +  d+  s+    ++++s + 
  gi|298674230|ref|YP_003725980.1|  13 PFLKALTISTTMAVFIIGIALGLKYMFSEGTIPMPLWTLllifAIIFIIGSVFFEQRGADQMGSLIGGSIVAVSTTF 89 
                                       7788999********************************99999999999999999999999988777777777777 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Acyl_transf_3 233 lalillalfgqtdggglvasvliqsaslllvslgimlllll 273
                                       +++++++  ++++ gg  a+    + s+l++++ + +ll+ 
  gi|298674230|ref|YP_003725980.1|  90 ASVSFFGGMVYAFSGGIEALGVEPIISALAICMIASMLLIK 130
                                       77777777777777666666666666666666655555544 PP

>> Peptidase_U4  Sporulation factor SpoIIGA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   4.7   1.8e-05      0.16      83     136 ..      12      68 ..       5      76 .. 0.82
   2 ?    3.9   2.4    0.0031        28      91     134 ..      87     133 ..      76     140 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.8e-05
                      Peptidase_U4  83 keflkalllfylvsfllgGilfalsylllkskn...llvlllgalvaylllkllvki 136
                                       + flkal +  ++++++ Gi+++l y++ + +    l++lll++ +++++ ++++++
  gi|298674230|ref|YP_003725980.1|  12 NPFLKALTISTTMAVFIIGIALGLKYMFSEGTIpmpLWTLLLIFAIIFIIGSVFFEQ 68 
                                       479***********************7743333777999999999999999977765 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0031
                      Peptidase_U4  91 lfylvsfllgGilfalsyll..lkskn....llvlllgalvaylllkllv 134
                                       + ++   ++gG+++a+s  +  l   +    ++ l++++++ +ll+kll 
  gi|298674230|ref|YP_003725980.1|  87 TTFASVSFFGGMVYAFSGGIeaL---GvepiISALAICMIASMLLIKLLS 133
                                       44444556888999888833432...244456777777777777777443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       873  (0.0486921); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 858.15
//
Query:       gi|298674231|ref|YP_003725981.1|  [L=204]
Description: GrpE protein HSP-70 cofactor [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-55  186.2   7.9      5e-55  185.7   7.9    1.3  1  GrpE             GrpE
    0.00045   20.5   3.0     0.0013   19.0   3.0    1.9  1  CLZ              C-terminal leucine zipper domain of cyclic n
     0.0066   16.6   6.9     0.0079   16.4   5.4    1.9  2  Lge1             Transcriptional regulatory protein LGE1
  ------ inclusion threshold ------
      0.018   15.4   1.6      0.018   15.4   1.6    1.9  1  TSC22            TSC-22/dip/bun family
      0.021   14.8   6.8      0.047   13.7   6.8    1.7  1  Bap31_Bap29_C    Bap31/Bap29 cytoplasmic coiled-coil domain
      0.022   14.1   3.3      0.022   14.1   3.3    1.2  1  DUF4407          Domain of unknown function (DUF4407)
      0.065   13.4   4.0       0.19   11.9   1.0    2.7  2  KIP1             KIP1-like protein
       0.13   11.4   4.2       0.16   11.0   4.2    1.2  1  Atg14            Vacuolar sorting 38 and autophagy-related su
       0.17   11.6   1.2       0.28   10.9   1.2    1.3  1  Hema_stalk       Influenza C hemagglutinin stalk
       0.22   10.7  10.4        1.4    8.1  10.9    1.9  2  Tho2             Transcription factor/nuclear export subunit 
       0.27   11.7  12.0      0.034   14.6   7.0    2.1  2  Enkurin          Calmodulin-binding
       0.54   10.1  10.0       0.18   11.6   5.9    2.2  2  DivIC            Septum formation initiator
        2.7    8.0  13.4        1.1    9.3  10.4    1.6  1  UPF0242          Uncharacterised protein family (UPF0242) N-t
          8    7.2   7.9       0.37   11.5   1.4    2.2  2  DUF573           Protein of unknown function, DUF573
        8.9    7.0  11.2        3.5    8.3   7.8    2.4  2  YabA             Initiation control protein YabA
          9    6.2  14.0       0.57   10.1   7.9    2.1  2  Ax_dynein_light  Axonemal dynein light chain


Domain annotation for each model (and alignments):
>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.7   7.9   4.4e-58     5e-55       4     166 .]      24     186 ..       3     186 .. 0.96

  Alignments for each domain:
  == domain 1  score: 185.7 bits;  conditional E-value: 4.4e-58
                                       ...CTTTHHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              GrpE   4 eeeeeeeedeeeeleeeleelekevkelkekllrllaefenlrkrtekekeeakkfaiekfakdLLpvlDnleralk 80 
                                       e+++ +ee e  + +ee+e+l++++++l++k+ rl+ae++n+rkr+ +ekee++k++ie+++ dLL+vlDn+eral+
  gi|298674231|ref|YP_003725981.1|  24 ESQNLNEESEMSSKDEEIERLNQQIEDLNQKYRRLAAEYDNFRKRASREKEELRKYGIENVVIDLLEVLDNFERALE 100
                                       67788899999999999************************************************************ PP

                                       C..HHH-HHHHHHHHHHHHHHHHHHHHHTT-EE---TTSB--TTTEEEEEEECSSC...TBEEEEEE--EEETTEEE CS
                              GrpE  81 sakeneeekslleGvemtlkqllkiLekhgvekiepkgepFDpnlheavstveddekeegtvvevvqkGYklkdrvl 157
                                       sa+++++++s++eG+em+++q+ ++L+k+g+ek+ ++ge+FDp  hea+s+ve++e +e+tvv+v++ GY l+++v+
  gi|298674231|ref|YP_003725981.1| 101 SARNTNDTNSIIEGIEMVYNQFYSTLNKYGLEKLICEGEEFDPYKHEALSHVEKSENPEDTVVDVCKPGYALNSKVI 177
                                       ***************************************************************************** PP

                                       E-EEEEEEE CS
                              GrpE 158 RpAmVkVsk 166
                                       RpAmV+Vsk
  gi|298674231|ref|YP_003725981.1| 178 RPAMVTVSK 186
                                       *******97 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   3.0   1.2e-06    0.0013      19      60 ..      27      68 ..      20      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.2e-06
                               CLZ 19 aakagaeqkeleekverLessLeaLqtrlarLlaeyessqrk 60
                                      + ++++e  + +e +erL++++e L+++++rL aey++  ++
  gi|298674231|ref|YP_003725981.1| 27 NLNEESEMSSKDEEIERLNQQIEDLNQKYRRLAAEYDNFRKR 68
                                      45677899999*************************998765 PP

>> Lge1  Transcriptional regulatory protein LGE1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   5.4     7e-06    0.0079       9      56 ..      25      72 ..      12      95 .. 0.86
   2 ?   -1.6   0.0       2.8   3.2e+03      12      34 ..     102     124 ..      83     128 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7e-06
                              Lge1  9 lndestlkkiesklkeiesldkqleelklkvlkleleldlleeqierd 56
                                      +++ ++ ++++sk +eie l++q+e+l++k   l +e+d++ + + r+
  gi|298674231|ref|YP_003725981.1| 25 SQNLNEESEMSSKDEEIERLNQQIEDLNQKYRRLAAEYDNFRKRASRE 72
                                      44456678*********************************9999886 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.8
                              Lge1  12 estlkkiesklkeiesldkqlee 34 
                                       ++  + ++s+ + ie ++ q   
  gi|298674231|ref|YP_003725981.1| 102 ARNTNDTNSIIEGIEMVYNQFYS 124
                                       44556778888888888877655 PP

>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   1.6   1.6e-05     0.018      14      47 ..      39      72 ..      34      79 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.6e-05
                             TSC22 14 EeVevLkekIkeLeernseleeENslLkalaspe 47
                                      Ee+e L ++I +L ++ ++l  E   +++ as e
  gi|298674231|ref|YP_003725981.1| 39 EEIERLNQQIEDLNQKYRRLAAEYDNFRKRASRE 72
                                      9****************************99987 PP

>> Bap31_Bap29_C  Bap31/Bap29 cytoplasmic coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   6.8   4.2e-05     0.047       3      48 ..      25      73 ..      23      78 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.2e-05
                     Bap31_Bap29_C  3 iekLkk..eLkkkkkDlealKkQaeglakEYDrLadehskl.desedKK 48
                                       ++L++  e  +k+ ++e l +Q+e l++ Y rLa e+    + +++ K
  gi|298674231|ref|YP_003725981.1| 25 SQNLNEesEMSSKDEEIERLNQQIEDLNQKYRRLAAEYDNFrKRASREK 73
                                      56777766888999************************98874444444 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   3.3   1.9e-05     0.022     111     207 ..      14     107 ..       5     201 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.9e-05
                           DUF4407 111 elaeeqqeeakelkeqlaaa...ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpa 184
                                       e+ae+++e a++++ + +++    ++e+++l++qi++l+++++ + a++d+ r+ a +e +        ++ G + +
  gi|298674231|ref|YP_003725981.1|  14 EVAENNAEGAESQNLNEESEmssKDEEIERLNQQIEDLNQKYRRLAAEYDNFRKRASREKEE------LRKYGIENV 84 
                                       33344443333333222222444667777777777777777777777777777777777664......235666677 PP

                           DUF4407 185 akekkaqldaaqaelaelkakld 207
                                            + ld  +++l++++++ d
  gi|298674231|ref|YP_003725981.1|  85 VIDLLEVLDNFERALESARNTND 107
                                       77777777777777777777744 PP

>> KIP1  KIP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.0   0.00017      0.19      39      74 .]      28      63 ..      17      63 .. 0.77
   2 ?    1.4   0.1      0.31   3.5e+02      30      73 ..      88     129 ..      72     130 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00017
                              KIP1 39 dsfakraemyykkrpeLielveefyrsyrsLaeryD 74
                                       +++ + + + ++ + L + +e+++++yr La  yD
  gi|298674231|ref|YP_003725981.1| 28 LNEESEMSSKDEEIERLNQQIEDLNQKYRRLAAEYD 63
                                      4444445555666688999****************9 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.31
                              KIP1  30 mlklieedadsfakraemyykkrpeLielveefyrsyrsLaery 73 
                                       +l+++  d+ + a +   + +  + +ie +e +y+++ s  ++y
  gi|298674231|ref|YP_003725981.1|  88 LLEVL--DNFERALESARNTNDTNSIIEGIEMVYNQFYSTLNKY 129
                                       45555..2333333344455566788888999988888777776 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   4.2   0.00014      0.16      44     107 ..      19      79 ..       2     121 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
                             Atg14  44 kiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklakl 107
                                         e a++   ++ ++e++  +k + +e+l ++i+dl+++ ++l +  ++ +k+    k++l+k+
  gi|298674231|ref|YP_003725981.1|  19 NAEGAES---QNLNEESEMSSKDEEIERLNQQIEDLNQKYRRLAAEYDNFRKRASREKEELRKY 79 
                                       3333333...445788899999999999999999999999999999999999999999999987 PP

>> Hema_stalk  Influenza C hemagglutinin stalk
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.2   0.00025      0.28      56     118 ..      34      95 ..      10     122 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00025
                        Hema_stalk  56 rsstniaieklndrishdeqairdltleienarseallgelgiirallvgnisiglqeslwel 118
                                        ss +  ie+ln++i   +q  r l+ e +n r  a   e   +r   + n+ i l e l ++
  gi|298674231|ref|YP_003725981.1|  34 MSSKDEEIERLNQQIEDLNQKYRRLAAEYDNFRKRAS-REKEELRKYGIENVVIDLLEVLDNF 95 
                                       5888999**************************9997.5677889999999999999988433 PP

>> Tho2  Transcription factor/nuclear export subunit protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1  10.9    0.0012       1.4      24      96 ..       5      78 ..       2     129 .. 0.84
   2 ?    0.2   0.0       0.3   3.4e+02       4      41 ..     118     155 ..     115     203 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0012
                              Tho2 24 keqYekeieklkseieelakdrsde.raaakkkkkekkrlkeliekLeeEkkeqiehvekvkkrLkeekkswfk 96
                                      +++Ye+e +++ ++ +e a++++ + ++++++k++e++rl+++ie L++   +  +++ +++kr ++ek+++ k
  gi|298674231|ref|YP_003725981.1|  5 SDKYEAENSEVAENNAEGAESQNLNeESEMSSKDEEIERLNQQIEDLNQKYRRLAAEYDNFRKRASREKEELRK 78
                                      578999999999998888888888889*****************************************998766 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.3
                              Tho2   4 lspefyvtFWslslyDiyvpkeqYekeieklkseieel 41 
                                       +  +fy+t +++ l+ + +  e+++ +  +  s++e+ 
  gi|298674231|ref|YP_003725981.1| 118 VYNQFYSTLNKYGLEKLICEGEEFDPYKHEALSHVEKS 155
                                       56789999999999999999998888877777777666 PP

>> Enkurin  Calmodulin-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   7.0   3.1e-05     0.034      12      81 ..       6      75 ..       1      89 [. 0.77
   2 ?   -1.4   0.2       2.9   3.2e+03      13      26 ..     187     200 ..     172     204 .] 0.53

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.1e-05
                           Enkurin 12 keleeeeeeeekeeaekkeappgmrllseeerqellegLkkkweelnkeyqslpllidtlskrqrKeklE 81
                                      ++ e+e+ e+++++ae +e ++  +  + + ++e +e L+++ e+ln++y++l+  +d+ +kr+ +ek E
  gi|298674231|ref|YP_003725981.1|  6 DKYEAENSEVAENNAEGAESQNLNEESEMSSKDEEIERLNQQIEDLNQKYRRLAAEYDNFRKRASREKEE 75
                                      445666666666666666655555555555688999******************************9977 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.9
                           Enkurin  13 eleeeeeeeekeea 26 
                                       + e+e e+e++ ++
  gi|298674231|ref|YP_003725981.1| 187 KSESETEDENEDNN 200
                                       23333333333333 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2      0.98   1.1e+03      21      41 ..      10      30 ..       2      34 .. 0.51
   2 ?   11.6   5.9   0.00016      0.18      18      55 ..      33      70 ..      29      81 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.98
                                      HHHHHHHHHHHHHHHHHHHHH CS
                             DivIC 21 qlkqeiaalqaelaklkaene 41
                                      + ++e+a+ +ae a+ ++ ne
  gi|298674231|ref|YP_003725981.1| 10 AENSEVAENNAEGAESQNLNE 30
                                      344455555555444444444 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00016
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXX CS
                             DivIC 18 aykqlkqeiaalqaelaklkaeneeLeaevkdLksded 55
                                       ++++++ei++l+++++ l+++ ++L+ae ++ ++  +
  gi|298674231|ref|YP_003725981.1| 33 EMSSKDEEIERLNQQIEDLNQKYRRLAAEYDNFRKRAS 70
                                      688999************************99987444 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3  10.4   0.00099       1.1      64     119 ..      22      76 ..       7     107 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00099
                           UPF0242  64 klekskleekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeen 119
                                       + e+++l ++e+ ++++de+++  ++++e+l+++ ++L+ e+d+  +   r kee 
  gi|298674231|ref|YP_003725981.1|  22 GAESQNL-NEESEMSSKDEEIERLNQQIEDLNQKYRRLAAEYDNFRKRASREKEEL 76 
                                       3333333.445667777788888888888888888888888666555554444443 PP

>> DUF573  Protein of unknown function, DUF573
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.4   0.00033      0.37      46      86 ..      45      85 ..      13      92 .. 0.69
   2 ?   -1.6   0.0       3.9   4.4e+03      14      40 ..      89     116 ..      85     132 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00033
                            DUF573 46 dvsksqlseKlrrLkkkyrnavskikkgkdpsfkkphdrkl 86
                                      + + ++l +K+rrL   y+n +++++++k++  k   ++ +
  gi|298674231|ref|YP_003725981.1| 45 NQQIEDLNQKYRRLAAEYDNFRKRASREKEELRKYGIENVV 85
                                      44458899999999999999999988888776666555555 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.9
                            DUF573  14 Lqglldfksktgtspk.sdldafyeavk 40 
                                       L+ l +f++  ++  + +d+++++e ++
  gi|298674231|ref|YP_003725981.1|  89 LEVLDNFERALESARNtNDTNSIIEGIE 116
                                       5555555443333222356666665444 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.6      0.86   9.7e+02      35      64 ..       2      31 ..       1      39 [. 0.54
   2 ?    8.3   7.8    0.0031       3.5      14      58 ..      31      75 ..      23     203 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.86
                                      HHHHHHHHHHHHHHHHHHXXXXXXXXXXXX CS
                              YabA 35 leenaeLeleneklrerleeeekkekekkk 64
                                       ee ++ e+en+++ e+ +e  ++++ +++
  gi|298674231|ref|YP_003725981.1|  2 AEESDKYEAENSEVAENNAEGAESQNLNEE 31
                                      577777788888887777443333333333 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0031
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXX CS
                              YabA 14 eeqleelleeleelkeelaelleenaeLeleneklrerleeeekk 58
                                      e+++++  ee+e+l++++++l ++ ++L +e +++r+r ++e+++
  gi|298674231|ref|YP_003725981.1| 31 ESEMSSKDEEIERLNQQIEDLNQKYRRLAAEYDNFRKRASREKEE 75
                                      567888899*****************************9544433 PP

>> Ax_dynein_light  Axonemal dynein light chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   7.9   0.00051      0.57     113     166 ..      26      79 ..      10     101 .. 0.90
   2 ?   -0.3   0.4      0.78   8.7e+02     140     140 ..     174     174 ..      91     204 .] 0.54

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00051
                   Ax_dynein_light 113 kalqaeqgkselekkikeLeeekeelekqvaelkaklealekrekerrqeeekk 166
                                       ++l++e ++s  +++i++L+++ e+l+++   l a++++ +kr++++++e +k 
  gi|298674231|ref|YP_003725981.1|  26 QNLNEESEMSSKDEEIERLNQQIEDLNQKYRRLAAEYDNFRKRASREKEELRKY 79 
                                       57899999*************************************999998876 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.78
                   Ax_dynein_light 140 k 140
                                       +
  gi|298674231|ref|YP_003725981.1| 174 S 174
                                       2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2685  (0.149757); expected 358.6 (0.02)
Passed bias filter:                      959  (0.0534888); expected 358.6 (0.02)
Passed Vit filter:                       156  (0.00870099); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.49
# Mc/sec: 1252.95
//
Query:       gi|298674232|ref|YP_003725982.1|  [L=616]
Description: chaperone protein DnaK [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.5e-246  819.3  23.0   1.2e-244  813.0  23.0    2.0  1  HSP70           Hsp70 protein
    2.7e-20   72.4   2.3    2.7e-20   72.4   2.3    2.1  2  MreB_Mbl        MreB/Mbl protein
  ------ inclusion threshold ------
      0.037   13.8   0.1      0.096   12.4   0.1    1.6  1  FGGY_C          FGGY family of carbohydrate kinases, C-termin
      0.049   13.3   0.0      0.049   13.3   0.0    3.2  4  Raco_middle     RACo middle region
      0.086   13.0  21.0        1.1    9.5  15.1    2.5  2  DUF3347         Protein of unknown function (DUF3347)
       0.11   13.0  19.0       0.64   10.5   0.8    4.4  4  FtsA            Cell division protein FtsA
       0.15   11.0   4.3        0.3   10.1   4.3    1.4  1  Emaravirus_P4   P4 movement protein of Emaravirus, and the 30
        2.6    8.3  22.5       0.59   10.4  18.6    1.9  2  Vfa1            AAA-ATPase Vps4-associated protein 1


Domain annotation for each model (and alignments):
>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  813.0  23.0  5.4e-248  1.2e-244       1     599 []       4     577 ..       4     577 .. 0.99

  Alignments for each domain:
  == domain 1  score: 813.0 bits;  conditional E-value: 5.4e-248
                                       EEEEEEXSSEEEEEEEETTEEEEEXXTTSXSSEESEEEEXTT.SEEETHHHHHCTTTTGGGEEEXGGGTTTXBTTSH CS
                             HSP70   1 viGiDLGttnsvvavmeggkievianeegnrttPsvvaFtkk.erlvGeaAkrqavtnpkntvfsvKrliGrkfsdp 76 
                                       +iGiDLGttns++a+megg+++vi n+eg+r+tPsvv+F+kk e lvG++Akrq + np+ntv+s+Kr++G+  +d 
  gi|298674232|ref|YP_003725982.1|   4 IIGIDLGTTNSCMAIMEGGEPNVIPNAEGSRITPSVVGFSKKgELLVGQVAKRQLIANPDNTVYSIKRHMGE--QD- 77 
                                       69**********************************************************************..66. PP

                                       HHHHHHTTXSSEEEEETTSBEEEEEEETTEEEEHHHHHHHHHHHHHHHHHHHHTSBEEEEEEEEXTTXXHHHHHHHH CS
                             HSP70  77 evqkeikelpykvvkkengkavveveaagekftpeqisamvLkklketaeaylgkkvtdavitvPaYfndaqRqatk 153
                                                 ykv+ +            ++++tp++isa++L+k+k+++e+ylg++++davitvPaYfndaqRqatk
  gi|298674232|ref|YP_003725982.1|  78 ----------YKVTLQ------------DKEYTPQEISAKILRKMKDDTEDYLGEELQDAVITVPAYFNDAQRQATK 132
                                       ..........777776............89*********************************************** PP

                                       HHHHHTTXEEEEEEEHHHHHHHHHHTCCSSSCEEEEEEEEXSSXEEEEEEEEETTEEEEEEEEEETTXSHHHHHHHH CS
                             HSP70 154 dAgkiAGLnvlRivNepTAaalaYGldkkdkernvlvyDlGggtfdvSilelekGvfevkaTagDthlGGedfDeal 230
                                       dAg+iAG+nv Ri+NepTAaalaYG+dk++ e+++lvyDlGggtfdvSil++++Gv+ev++T gD+hlGG+dfD++l
  gi|298674232|ref|YP_003725982.1| 133 DAGRIAGFNVKRIINEPTAAALAYGIDKEE-EQKILVYDLGGGTFDVSILDIGDGVYEVVSTTGDSHLGGDDFDQRL 208
                                       *****************************9.********************************************** PP

                                       HHHHHHHHHHHHSXXGGGSHHHHHHHHHHHHHHHHHTTTSSCSEEEEEEEEEETTT..EEEEEEEEHHHHHHHHHHH CS
                             HSP70 231 vehlveefkkkegidlskdkkalqrlkeaaekaKkeLSsskqteinleietvdedg..kdlseklsRakfeelvedl 305
                                       v+hlv++fk++eg+dls+d+ alqrl++aaekaK+eLSs++ t++nl+++t+d++g  k+l++++sR++f++l+edl
  gi|298674232|ref|YP_003725982.1| 209 VNHLVKKFKEEEGLDLSQDRSALQRLTDAAEKAKIELSSVTTTNVNLPFITADANGqpKHLDIDVSRSQFQQLTEDL 285
                                       *******************************************************999******************* PP

                                       HHHTHHHHHHHHHHCTEEGGGCSEEEEESGGGGSHHHHHHHHHHTTCHHBSSSHTTTHHHHHHHHHHHHHCTCGCSH CS
                             HSP70 306 lertlepvekalkdaklkkeeidevvlvGGstRiPkvqelvkelfgkepsktvnpDeavaiGAAvqagvlsgeeevk 382
                                       +e+t++ +++alkda+l++++i++v+lvGGstR+P+v++++++++gkep k++npDeava+GAA+q+gvlsg  e++
  gi|298674232|ref|YP_003725982.1| 286 VEETVDLMQQALKDANLTANDINKVLLVGGSTRMPAVTDAINKVVGKEPYKNINPDEAVAVGAAIQGGVLSG--ETE 360
                                       ************************************************************************..*** PP

                                       CCEEEEBESS-EEEEETTTEEEEEESTTCBSSEEEEEEEEESSTTSSSEEEEEEESSSSBGGGSEEEEEEEEECESS CS
                             HSP70 383 dllllDvtpLslgietlggvmtkliernttiptkksqvfstaadnqtaveievlqgerelvkdnkllgsfeldgipp 459
                                       +llllDvtpL+lgiet+ggvmt liernttiptkk+qvfsta+dnqtav+++vlqger ++kdn++lg+f+l+gip+
  gi|298674232|ref|YP_003725982.1| 361 ELLLLDVTPLTLGIETEGGVMTPLIERNTTIPTKKTQVFSTAEDNQTAVDVHVLQGERPMAKDNQSLGRFRLEGIPA 437
                                       ***************************************************************************** PP

                                       CSTTCSEEEEEEEEETTSCEEEEEEETTTCCEEEEEEECCSSSBHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH CS
                             HSP70 460 aprGvpqieVtfdidanGiltvsakdketgkeeeitieaseglseeeiekmvkdaeesaeedkkkkeaieakneaee 536
                                       aprGvpqieVtfdidanGil+vsakd +t+ke++itie+   lse+ei++mvk+aee+aeedkk+ke++e++n+a++
  gi|298674232|ref|YP_003725982.1| 438 APRGVPQIEVTFDIDANGILNVSAKDLGTNKEQSITIEKPGALSEDEINQMVKEAEEHAEEDKKRKEEVETRNRADT 514
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHGGGSTHHHHHHHHHHHHHHHCHTTSSCHHHHHHHHHHHHHHHHHHHHHHHH CS
                             HSP70 537 lvyslekkleeeaekvseaekekvesaieeLkeeleeeekeeieakteelkkvvekiaeklye 599
                                       lv+s++k+lee+++ ++e+ek+k+e+a++eL+e+l+++++e+i++kte+l+++++++ +k+y+
  gi|298674232|ref|YP_003725982.1| 515 LVNSADKTLEEAKDVITEDEKSKIENAKSELQEALKGDDIEDIKSKTETLQNAIYEVSQKMYQ 577
                                       *************************************************************96 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.4   2.3   1.2e-23   2.7e-20       3     316 ..       4     349 ..       2     355 .. 0.72
   2 ?   -2.9   1.0         1   2.3e+03     213     262 ..     497     546 ..     479     582 .. 0.58

  Alignments for each domain:
  == domain 1  score: 72.4 bits;  conditional E-value: 1.2e-23
                                       EEEEEE-SSEEEEEETTTE..EEE.E.E.....ES-EEEETTT--EEEESHHHHTTTTS-GTTE.E.EE-SEETT.. CS
                          MreB_Mbl   3 dlgiDLGtantlvyvkgkg..ivl.n.e.....psvvAikkktkkvlavGeeAkkmlgktpgni.k.avrPlkdG.. 66 
                                        +giDLGt+n  + + + g   v+ n e     psvv ++kk +  l vG+ Ak+ l   p+n    + r + +   
  gi|298674232|ref|YP_003725982.1|   4 IIGIDLGTTNSCMAIMEGGepNVIpNaEgsritPSVVGFSKKGE--LLVGQVAKRQLIANPDNTvYsIKRHMGEQdy 78 
                                       59********9875554442344423323333488888877644..6689999876666666541314566643222 PP

                                       ..EESSHHHHHHHH.HHHHHHHHT..SS-S..S--EEEEEE-SS--HHHHHHHHHHHHHTT-SEEEEEEHHHHHHHH CS
                          MreB_Mbl  67 ..viadlevaeell.kyfikkvkk..kksl..skprvvicvPsgiteverrAvkeaakkaGarevllieeplaAAiG 136
                                         +++d e++ + +  ++++k+k+  ++ l  + +  vi+vP   ++ +r+A k+a + aG +   +i+ep aAA+ 
  gi|298674232|ref|YP_003725982.1|  79 kvTLQDKEYTPQEIsAKILRKMKDdtEDYLgeELQDAVITVPAYFNDAQRQATKDAGRIAGFNVKRIINEPTAAALA 155
                                       2266787777544414566666664333333367889**************************************** PP

                                       TT--TTSSS-EEEEEE-SS-EEEEEEETTEEEEEE.....EES-SHHHHHHHHHHHHHHHHSEE--........... CS
                          MreB_Mbl 137 aglpveepsgnmvvdiGggttevavislggivtsk.....svrvaGdeldeaiikyirkkynlliG........... 197
                                        g++ ee +  +v d+Gggt +v+++ +g+ v+         +++Gd++d+ +++++ kk++   G           
  gi|298674232|ref|YP_003725982.1| 156 YGIDKEEEQKILVYDLGGGTFDVSILDIGDGVYEVvsttgDSHLGGDDFDQRLVNHLVKKFKEEEGldlsqdrsalq 232
                                       *****************************9765431111146799************99998554422212221111 PP

                                       ..HHHHHHHHHHH-BSS--HHHHEEEEEEEETTTTCEEE..EEEEHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHH CS
                          MreB_Mbl 198 ..ertaekikieigsavkeeeeekmeikGrdlvtglpke..vevsseevrealkepvsaiveavkevLektppeLaa 270
                                         +  aek kie++s+++++ +  +     d ++g pk+  + vs ++ ++  ++ v++ v+ ++++L+++  +L+a
  gi|298674232|ref|YP_003725982.1| 233 rlTDAAEKAKIELSSVTTTNVNLPFI--TAD-ANGQPKHldIDVSRSQFQQLTEDLVEETVDLMQQALKDA--NLTA 304
                                       11235777888887777766665433..223.578898722456789999******************975..6877 PP

                                       HHHHH-EEEESGGGGSBTHHHHHHHHHSS-EEE-SSTTTHHHHHHH CS
                          MreB_Mbl 271 divdrgivltGGgallkgldkllseetglpvkvaedpltcvakGtg 316
                                       + +++ ++l+GG++ +  + + +++ +g + +   +p ++va G++
  gi|298674232|ref|YP_003725982.1| 305 NDINK-VLLVGGSTRMPAVTDAINKVVGKEPYKNINPDEAVAVGAA 349
                                       66665.7888********************************9986 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1
                                       --HHHHEEEEEEEETTTTCEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHH CS
                          MreB_Mbl 213 keeeeekmeikGrdlvtglpkevevsseevrealkepvsaiveavkevLe 262
                                       +e++++k e++ r+ +  l  ++  + ee +++++e  ++ +e++k+ L+
  gi|298674232|ref|YP_003725982.1| 497 EEDKKRKEEVETRNRADTLVNSADKTLEEAKDVITEDEKSKIENAKSELQ 546
                                       44444566666666666666666666666666665555444444444443 PP

>> FGGY_C  FGGY family of carbohydrate kinases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   4.3e-05     0.096     145     196 ..     296     354 ..     276     355 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.3e-05
                            FGGY_C 145 d......sgkpldrlavdGGgskndllmqllAdilg.vpVerpktaeatalGaAilAav 196
                                              +  ++++++++GG ++ +++   +  ++g  p +   ++ea+a+GaAi ++v
  gi|298674232|ref|YP_003725982.1| 296 AlkdanlTANDINKVLLVGGSTRMPAVTDAINKVVGkEPYKNINPDEAVAVGAAIQGGV 354
                                       23334556778*************************989899999**********9986 PP

>> Raco_middle  RACo middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.52   1.2e+03       4      18 ..       6      20 ..       5      30 .. 0.81
   2 ?   13.3   0.0   2.2e-05     0.049      52     115 ..     275     338 ..     270     354 .. 0.88
   3 ?   -4.0   0.1       4.8   1.1e+04      64      82 ..     483     501 ..     479     507 .. 0.71
   4 ?   -1.5   0.4      0.78   1.7e+03      52      80 ..     558     586 ..     527     593 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.52
                       Raco_middle  4 avDiGtTtvvaaLvd 18
                                       +D+GtT+ ++a+++
  gi|298674232|ref|YP_003725982.1|  6 GIDLGTTNSCMAIME 20
                                      69*****98888775 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 2.2e-05
                       Raco_middle  52 eegleklqkavveeinelieelleeagiekeeiyevvvagNttMlhlllgldpkslakapyvpv 115
                                       +++ ++l++ +vee  +l++++l++a++++++i++v ++g +t +  +++   k ++k+py+ +
  gi|298674232|ref|YP_003725982.1| 275 RSQFQQLTEDLVEETVDLMQQALKDANLTANDINKVLLVGGSTRMPAVTDAINKVVGKEPYKNI 338
                                       46789**********************************9999999999999999******875 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 4.8
                       Raco_middle  64 eeinelieelleeagieke 82 
                                       +ein++++e+ e+a+ +k+
  gi|298674232|ref|YP_003725982.1| 483 DEINQMVKEAEEHAEEDKK 501
                                       5789999888877766655 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 0.78
                       Raco_middle  52 eegleklqkavveeinelieelleeagie 80 
                                       +++ e+lq+a+ e  +++ +++ e+a+ +
  gi|298674232|ref|YP_003725982.1| 558 KSKTETLQNAIYEVSQKMYQQAQEQAQQQ 586
                                       45667777777777777777777776655 PP

>> DUF3347  Protein of unknown function (DUF3347)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.3     0.004       8.9      78     135 ..     230     287 ..     211     299 .. 0.79
   2 ?    9.5  15.1   0.00047       1.1      16     116 ..     490     601 ..     473     609 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.004
                           DUF3347  78 kleeklkavdtsklkekekkelkeiseelkekaekiaeskdieeqReaFkklsedlik 135
                                       +l++ ++a +++k++ ++ ++++ +   ++++a+   ++ di+  R++F++l+edl++
  gi|298674232|ref|YP_003725982.1| 230 ALQRLTDAAEKAKIELSSVTTTNVNLPFITADANGQPKHLDIDVSRSQFQQLTEDLVE 287
                                       4555555566667777777888888899999999999999**************9875 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00047
                           DUF3347  16 neeeekeeeeeeeeeeekekkkekse..........eeee........kdeklkevlesYlklkdALvaddakeakk 74 
                                       +e+ee++ee+++++ee +++     +          +  +        ++++ +++ ++  +l++AL  dd +++k+
  gi|298674232|ref|YP_003725982.1| 490 KEAEEHAEEDKKRKEEVETR-----NradtlvnsadK--TleeakdviTEDEKSKIENAKSELQEALKGDDIEDIKS 559
                                       22222222222222222221.....122223444430..1444455678888888********************** PP

                           DUF3347  75 aakkleeklkavdtsklkekekkelkeiseelkekaekiaes 116
                                       ++++l++++ +v+++ +++ ++++ +++++e +e+a   +e+
  gi|298674232|ref|YP_003725982.1| 560 KTETLQNAIYEVSQKMYQQAQEQAQQQAETEGAESAGGSSEE 601
                                       ************999999999999999888888877666655 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1   0.00093       2.1       1      34 [.       5      36 ..       5     139 .. 0.87
   2 ?   10.5   0.8   0.00029      0.64       4     101 ..     170     345 ..     167     349 .. 0.63
   3 ?   -1.1   7.2       1.1   2.5e+03      34      89 ..     482     552 ..     456     586 .. 0.68
   4 ?   -2.1   0.1       2.3   5.2e+03      38      58 ..     573     593 ..     557     605 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00093
                                      EEEEE-SSSEEEEEEETTEEEEEEEES-.-HHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                              FtsA  1 alvDiGagktdvavaedgalvhlrvigv.ggngit 34
                                      +++D+G++ +++a++e+g     +vi+  +g+ it
  gi|298674232|ref|YP_003725982.1|  5 IGIDLGTTNSCMAIMEGG---EPNVIPNaEGSRIT 36
                                      58***************9...66777766666666 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00029
                                       EE-SSSEEEEEEETTEEEEEEEES-......-HHHHHHH...................HHHHHT--HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxx...................xxxxxxxxxxxxxxxxxxx RF
                              FtsA   4 DiGagktdvavaedgalvhlrvigv......ggngitkd...................iakalrtaveeAerikiky 55 
                                       D+G+g+ dv++++ g  v+ +v+ +      gg+ +++                       al+   ++Ae+ ki+ 
  gi|298674232|ref|YP_003725982.1| 170 DLGGGTFDVSILDIGDGVY-EVVSTtgdshlGGDDFDQRlvnhlvkkfkeeegldlsqDRSALQRLTDAAEKAKIEL 245
                                       9*************97665.444444446667777777755555555555555554443345566666677777666 PP

                                       --S--...................EEEEEHHHHH........................................... CS
                                       xxxxx...................xxxxxxxxxx........................................... RF
                              FtsA  56 Gsala...................ekeigrkels........................................... 70 
                                        s+                     +                                                    
  gi|298674232|ref|YP_003725982.1| 246 SSVTTtnvnlpfitadangqpkhlD--------Idvsrsqfqqltedlveetvdlmqqalkdanltandinkvllvg 314
                                       6655566666666666666655552........04445555566666666777777777778888888888888889 PP

                                       GGGGSTTHHHHHHHHH..T-..HH.HT-GGGHHH CS
                                       xxxxxxxxxxxxxxxx..xxxxxx.xxxxxxxxx RF
                              FtsA  71 ggsalpnleelaeral..spklee.vsdpeyasa 101
                                       g++ +p +++++++++  +p       +p  a+a
  gi|298674232|ref|YP_003725982.1| 315 GSTRMPAVTDAINKVVgkEP---YkNINPDEAVA 345
                                       99999999999999964433...22445555555 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.1
                                       HHHHHHHHT--HHHHHHHHHHH--S--EEEEEHHHHH..........................GGGGSTTHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........................xxxxxxxxxxxxxx RF
                              FtsA  34 tkdiakalrtaveeAerikikyGsalaekeigrkels..........................ggsalpnleelaer 84 
                                        ++i +++++a e Ae+ k++   +           +                          ++s+++n +  +++
  gi|298674232|ref|YP_003725982.1| 482 EDEINQMVKEAEEHAEEDKKRKEEV-----------EtrnradtlvnsadktleeakdvitedEKSKIENAKSELQE 547
                                       344999999******9999543333...........23334445555677777777788889999999999999999 PP

                                       HHT-. CS
                                       xxxxx RF
                              FtsA  85 alspk 89 
                                       al+ +
  gi|298674232|ref|YP_003725982.1| 548 ALKGD 552
                                       88443 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 2.3
                                       HHHHT--HHHHHHHHHHH--S CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                              FtsA  38 akalrtaveeAerikikyGsa 58 
                                       +k++++a e+A++ + + G+ 
  gi|298674232|ref|YP_003725982.1| 573 QKMYQQAQEQAQQQAETEGAE 593
                                       456677778887777666664 PP

>> Emaravirus_P4  P4 movement protein of Emaravirus, and the 30K superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   4.3   0.00013       0.3     261     324 ..     501     567 ..     476     589 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00013
                     Emaravirus_P4 261 vkaklkedtssstlllidsekrveaiklkliqde...iseakaklsealagidlaiieaakaklvav 324
                                        ++   e  + ++ l+  ++k  e  k    +de   i +ak++l eal g d++ i++   +l   
  gi|298674232|ref|YP_003725982.1| 501 KRKEEVETRNRADTLVNSADKTLEEAKDVITEDEkskIENAKSELQEALKGDDIEDIKSKTETLQNA 567
                                       2333334445666777777888877776655554222779*****************9977666543 PP

>> Vfa1  AAA-ATPase Vps4-associated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       2.6   5.9e+03      38      66 ..      67      95 ..      57     134 .. 0.56
   2 ?   10.4  18.6   0.00026      0.59      67     162 ..     478     588 ..     460     600 .. 0.46

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.6
                              Vfa1 38 YvCesHLkDkqFatpivdeeeeeaakkkk 66
                                      Y  + H+ ++ +   ++d+e++ ++ + k
  gi|298674232|ref|YP_003725982.1| 67 YSIKRHMGEQDYKVTLQDKEYTPQEISAK 95
                                      44455555555555555554444222222 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00026
                              Vfa1  67 e..leeeiekvkkeyeekqkkkkekekkkkekd.......kkdkdkkkekekdkkkekekeeekkkelkkaeeelee 134
                                          +e+ei+++ ke ee+ +++k+++++ ++++       + dk+ ++ k+  +++ek+k e++k+el++a +  + 
  gi|298674232|ref|YP_003725982.1| 478 GalSEDEINQMVKEAEEHAEEDKKRKEEVETRNradtlvnSADKTLEEAKDVITEDEKSKIENAKSELQEALKGDDI 554
                                       13477788888888888777777655555222233355332222222222223333333333333333333333322 PP

                              Vfa1 135 ......keeprvkkykLhkefyqsRlerkrqaea 162
                                             +e  +++ y+ ++++yq+ +e+ +q+ +
  gi|298674232|ref|YP_003725982.1| 555 edikskTETLQNAIYEVSQKMYQQAQEQAQQQAE 588
                                       2222222333333366666666666655443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (616 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2719  (0.151654); expected 358.6 (0.02)
Passed bias filter:                      735  (0.040995); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.70u 0.28s 00:00:00.98 Elapsed: 00:00:00.42
# Mc/sec: 4355.32
//
Query:       gi|298674233|ref|YP_003725983.1|  [L=377]
Description: chaperone protein DnaJ [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.6e-42  142.7   0.0    1.1e-41  142.4   0.0    1.1  1  DnaJ_C           DnaJ C terminal domain
    1.4e-30  105.1   5.3      2e-30  104.7   4.0    2.0  2  DnaJ             DnaJ domain
    7.6e-13   48.6  17.2    1.5e-12   47.7  17.2    1.5  1  DnaJ_CXXCXGXG    DnaJ central domain
    0.00027   20.9  18.1      0.027   14.4   5.8    2.4  2  Anti-TRAP        Tryptophan RNA-binding attenuator protein in
  ------ inclusion threshold ------
      0.047   14.1   5.6        1.3    9.4   0.7    2.6  2  Lar_restr_allev  Restriction alleviation protein Lar
       0.09   12.9   0.1       0.16   12.0   0.1    1.3  1  Octopine_DH      NAD/NADP octopine/nopaline dehydrogenase, al
       0.16   12.3   1.8       0.35   11.2   1.8    1.5  1  Cytochrom_CIII   Class III cytochrome C family
        0.3   11.6   3.1       0.73   10.3   3.1    1.7  1  Cytochrom_c3_2   Cytochrome c3
        3.5    7.6   5.8         15    5.5   0.3    2.2  2  zf-C3HC4_3       Zinc finger, C3HC4 type (RING finger)
        4.2    7.4  11.5        1.6    8.8   1.9    2.3  2  HypA             Hydrogenase/urease nickel incorporation, met


Domain annotation for each model (and alignments):
>> DnaJ_C  DnaJ C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.4   0.0   6.1e-45   1.1e-41       2     148 .]     119     334 ..     118     334 .. 0.96

  Alignments for each domain:
  == domain 1  score: 142.4 bits;  conditional E-value: 6.1e-45
                                       EEEEEE-HHHHHH-.EEE.EEEE...................................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx................................................... RF
                            DnaJ_C   2 eveleisleelykGktkkikikrnvi................................................... 27 
                                       +++l+i+le++++G +++i++ r ++                                                   
  gi|298674233|ref|YP_003725983.1| 119 RYDLSITLEDAAFGLNTEIDVPRAEKcgecegtgakdgkvkncptchgrgqitqtrstplgrfmttsicstcygqgq 195
                                       799********************999*************************************************** PP

                                       ..................T.EEEEEE-TT--TT-EEEETT-SSSS....S---EEEEEEE---SS-EEETTEEEEEE CS
                                       ..............xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaJ_C  28 ..............kkekk.tlevkipaGikdgqkirlegeGdeeg..gepGDlivtikvkphpvFkrkgndlyvev 87 
                                                     + +++ ++ vk+p+G  dg +++++geG+++   ++pGDl+++++vkph++F+r g+d+ +e+
  gi|298674233|ref|YP_003725983.1| 196 vaetpcpscsgtgkV-KRTaKVPVKVPPGSYDGLRLKVSGEGEQGSpgAPPGDLYIVLHVKPHDTFERVGDDIACEI 271
                                       *************54.55559**********************54458***************************** PP

                                       EEEHHHHHHTEEEEEE-SS-EEEEEE...--TT-EEEETT-S-EET...TEE--EEEEEEEE-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaJ_C  88 eislaeallGgklevptldgkvklki...tqpgevlrikgkGmpklkkpgkrGdlyvevkvefP 148
                                       +i++++a+lG++++vptl g+v++k+   tq+++++r+k+kGmp+l+ ++++Gd++v+v v++P
  gi|298674233|ref|YP_003725983.1| 272 PITITQAALGTTITVPTLYGNVNMKVpseTQTNTIFRLKDKGMPHLN-GRGHGDQHVKVIVKTP 334
                                       **********************************************7.**************99 PP

>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.7   4.0   1.1e-33     2e-30       1      63 []       6      67 ..       6      67 .. 0.99
   2 ?   -2.4   0.0       3.1   5.5e+03       1      13 [.     247     259 ..     247     263 .. 0.80

  Alignments for each domain:
  == domain 1  score: 104.7 bits;  conditional E-value: 1.1e-33
                                      HHHHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHTSHHHHHHHH CS
                              DnaJ  1 dyYeiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLsdpekRkqYD 63
                                      dyYeiLgvskdas+deIkkaYrkla+kyHPDk+ +dp+aeekFkei+eAy vLsdp+kR+qYD
  gi|298674233|ref|YP_003725983.1|  6 DYYEILGVSKDASQDEIKKAYRKLAMKYHPDKS-DDPDAEEKFKEISEAYGVLSDPDKRAQYD 67
                                      8********************************.****************************9 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.1
                                       HHHHHHTSSTTG- CS
                              DnaJ   1 dyYeiLgvskdas 13 
                                       d+Y +L v+++ +
  gi|298674233|ref|YP_003725983.1| 247 DLYIVLHVKPHDT 259
                                       7899****99866 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7  17.2   8.3e-16   1.5e-12       1      67 []     145     208 ..     145     208 .. 0.90

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 8.3e-16
                     DnaJ_CXXCXGXG   1 CkkCkGsgakkgkkktCktCkGsGvvreeqkt.lgpfvqqsqstCpeCeGtGkvikekdkCkkCkGkg 67 
                                       C +C+G+gak+gk+k+C+tC+G+G+++++++t lg f+  ++s C++C G+G+v   +++C++C+G+g
  gi|298674233|ref|YP_003725983.1| 145 CGECEGTGAKDGKVKNCPTCHGRGQITQTRSTpLGRFM--TTSICSTCYGQGQVA--ETPCPSCSGTG 208
                                       9***********************98887776788877..5789*********99..779******86 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   5.8   1.5e-05     0.027      11      43 ..     143     171 ..     135     183 .. 0.86
   2 !   12.0   4.3   8.6e-05      0.15      12      42 ..     186     210 ..     182     215 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.5e-05
                                       EE-TTTTTTSEETTE......E-TTTTTSSEEE CS
                         Anti-TRAP  11 tkCdaCngsGkiepeeprasleCPkCsGkglip 43 
                                       +kC +C+g+G  +++      +CP C G+g i 
  gi|298674233|ref|YP_003725983.1| 143 EKCGECEGTGAKDGK----VKNCPTCHGRGQIT 171
                                       69**********999....88********9885 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 8.6e-05
                                       E-TTTTTTSEETTE......E-TTTTTSSEE CS
                         Anti-TRAP  12 kCdaCngsGkiepeeprasleCPkCsGkgli 42 
                                        C +C g G+++ +      +CP CsG g +
  gi|298674233|ref|YP_003725983.1| 186 ICSTCYGQGQVAET------PCPSCSGTGKV 210
                                       59***********9......*******9854 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.7   0.00074       1.3       2      36 ..     157     192 ..     156     199 .. 0.78
   2 ?    6.5   0.4    0.0059        11       5      22 ..     200     217 ..     196     222 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00074
                   Lar_restr_allev   2 eLkpCPfCggravlersqrvvaeigq.cvyCadCga 36 
                                       ++k CP C gr+ + ++ +++ ++ + + +C  C+ 
  gi|298674233|ref|YP_003725983.1| 157 KVKNCPTCHGRGQITQTRSTPLGRFMtTSICSTCYG 192
                                       579**********99998887644448999999987 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0059
                   Lar_restr_allev   5 pCPfCggravlersqrvv 22 
                                       pCP C g ++++r+ +v+
  gi|298674233|ref|YP_003725983.1| 200 PCPSCSGTGKVKRTAKVP 217
                                       9***********998876 PP

>> Octopine_DH  NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   9.2e-05      0.16      68     118 ..      21      83 ..       7      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.2e-05
                       Octopine_DH  68 evlplaerlldaYgdeikdksslaevirt.neaykgikaPmsl.d..........hRyltEDi 118
                                       e++++   l+ +Y+ +++d  + +e++++ +eay  +  P++  +          +Ry  EDi
  gi|298674233|ref|YP_003725983.1|  21 EIKKAYRKLAMKYHPDKSDDPDAEEKFKEiSEAYGVLSDPDKRaQydkfghsgidSRYTEEDI 83 
                                       567777889999**99**************************8569****************9 PP

>> Cytochrom_CIII  Class III cytochrome C family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.8    0.0002      0.35      31      87 ..     142     195 ..     127     215 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0002
                                       SHTHHHTSTTCTTSCSTS-CTCTS-SSS.TTTSTTCHHHHHHCSSTTTCHHHHHHHHH CS
                    Cytochrom_CIII  31 vkeCeeCHhkeeekeeiekcstcHaeek.ekkekkslekavHkkkaaksCvgCHkkkk 87 
                                       +++C eC  + ++++++++c tcH   + ++++++ l + + +    + C  C  + +
  gi|298674233|ref|YP_003725983.1| 142 AEKCGECEGTGAKDGKVKNCPTCHGRGQiTQTRSTPLGRFMTT----SICSTCYGQGQ 195
                                       459*********************9987655565666666655....34666665544 PP

>> Cytochrom_c3_2  Cytochrome c3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   3.1   0.00041      0.73       8      78 ..     144     204 ..     139     209 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00041
                                       TGGGTSSSST-SSTTHHHHHHHHHHH--HHHCHTTSST.TSSBTTSSCTSSS-GGGTS-TTTSBT-GGGGT CS
                    Cytochrom_c3_2   8 kCadCHtkekpkkdkaveeekClsCHgkleelakktkeakeanphkshekeleCteCHkeHkksekvCaeC 78 
                                       kC +C ++  +    + + ++C +CHg+ + ++++++      p  +++++  C++C  + +  e+ C +C
  gi|298674233|ref|YP_003725983.1| 144 KCGECEGTGAK----DGKVKNCPTCHGRGQITQTRST------PLGRFMTTSICSTCYGQGQVAETPCPSC 204
                                       78888887775....567899******9988766644......7888999999999999999999999998 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.9      0.02        36      26      44 ..     145     165 ..     144     173 .. 0.86
   2 ?    5.5   0.3    0.0083        15      25      44 ..     186     205 ..     178     209 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.02
                                       -HHHHHHHHH..TT-B-TTT- CS
                        zf-C3HC4_3  26 CeeCaekllk..rkkkCpiCr 44 
                                       C eC  +  k  + k+Cp C+
  gi|298674233|ref|YP_003725983.1| 145 CGECEGTGAKdgKVKNCPTCH 165
                                       89999999888999******7 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0083
                                       E-HHHHHHHHHTT-B-TTT- CS
                        zf-C3HC4_3  25 lCeeCaekllkrkkkCpiCr 44 
                                       +C++C  + +  ++ Cp C 
  gi|298674233|ref|YP_003725983.1| 186 ICSTCYGQGQVAETPCPSCS 205
                                       8********88********6 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.9   0.00087       1.6      66     101 ..     138     172 ..     123     183 .. 0.77
   2 ?    3.9   2.1     0.029        52      71      96 ..     185     208 ..     178     219 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00087
                                       EE--EEEETTTS-EEECHHHHHS-TTTSSS-EEEEE CS
                              HypA  66 evpvkvrCreCgkefeleekalrCpkCgsadveivs 101
                                       +vp   +C eC+ ++ ++ k  +Cp+C++++ +i++
  gi|298674233|ref|YP_003725983.1| 138 DVPRAEKCGECEGTGAKDGKVKNCPTCHGRG-QITQ 172
                                       4667779*****99998877778****9964.4554 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.029
                                       EEETTTS-EEECHHHHHS-TTTSSS- CS
                              HypA  71 vrCreCgkefeleekalrCpkCgsad 96 
                                         C++C  +++++e  + Cp+C++++
  gi|298674233|ref|YP_003725983.1| 185 SICSTCYGQGQVAE--TPCPSCSGTG 208
                                       57*****9999884..48****9864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2731.01
//
Query:       gi|298674234|ref|YP_003725984.1|  [L=444]
Description: TrkA-N domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-49  165.5   3.5    5.9e-24   84.6   0.1    2.3  2  TrkA_N           TrkA-N domain
    2.8e-32  110.3   0.5    2.1e-15   56.3   0.0    2.8  2  TrkA_C           TrkA-C domain
    2.3e-12   47.2   3.6    1.5e-08   34.8   0.6    2.3  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    5.1e-10   39.7   3.2    0.00049   20.5   0.3    2.6  2  NAD_binding_7    Putative NAD(P)-binding
    1.1e-09   37.9   4.1    0.00024   20.5   0.2    2.4  2  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
      1e-08   35.6   2.1     0.0039   17.8   0.2    3.4  3  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    1.7e-08   34.8   3.5    2.2e-05   24.7   0.6    2.7  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    9.4e-08   32.1   0.7      0.012   15.5   0.1    2.3  2  NAD_binding_10   NAD(P)H-binding
    1.6e-07   31.4   0.1     0.0075   16.2   0.0    2.5  2  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
    2.3e-06   27.6   0.6      0.066   13.1   0.1    2.6  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
    3.4e-06   27.5   3.3      0.013   16.1   0.4    3.2  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
    4.1e-06   26.2   1.1     0.0037   16.5   0.1    2.3  2  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
      6e-06   25.7   0.0       0.02   14.1   0.0    2.2  2  FAD_binding_3    FAD binding domain
    0.00011   22.5   1.0       0.46   10.6   0.0    3.2  3  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    0.00017   21.3   0.1     0.0018   17.9   0.0    2.2  2  ApbA             Ketopantoate reductase PanE/ApbA
    0.00024   20.8   0.2      0.015   14.9   0.0    2.3  2  DAO              FAD dependent oxidoreductase
    0.00037   19.3   0.6      0.043   12.5   0.2    2.2  2  HI0933_like      HI0933-like protein
    0.00039   20.9   0.1      0.038   14.5   0.0    2.5  2  XdhC_C           XdhC Rossmann domain
     0.0012   18.2   1.0       0.34   10.2   0.2    2.4  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
     0.0013   18.3   5.8       0.16   11.5   0.2    3.3  3  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
     0.0029   17.2   3.8       0.81    9.2   0.4    2.3  2  NmrA             NmrA-like family
  ------ inclusion threshold ------
      0.012   14.8   4.0        0.7    9.1   0.6    2.4  2  Pyr_redox_3      Pyridine nucleotide-disulphide oxidoreductas
      0.015   15.3   0.1        4.2    7.4   0.0    2.7  2  Castor_Poll_mid  Castor and Pollux, part of voltage-gated ion
      0.015   15.9   5.2       0.21   12.3   0.4    2.8  2  PglD_N           PglD N-terminal domain
      0.016   15.3   5.4      0.026   14.6   0.6    2.7  3  AdoHcyase_NAD    S-adenosyl-L-homocysteine hydrolase, NAD bin
      0.022   14.0   2.3          1    8.5   0.1    3.0  3  Thi4             Thi4 family
       0.05   13.0   2.3       0.22   10.9   1.4    2.3  2  Spermine_synth   Spermine/spermidine synthase domain
       0.06   13.5   1.0        2.3    8.4   0.2    2.8  2  DUF2325          Uncharacterized protein conserved in bacteri
      0.064   12.3   0.1        1.8    7.5   0.0    2.1  2  Lycopene_cycl    Lycopene cyclase protein
       0.11   12.7   0.1        3.2    8.1   0.1    2.5  2  NAD_binding_8    NAD(P)-binding Rossmann-like domain
       0.58   10.8   3.3        7.3    7.3   0.0    3.7  4  ThiS             ThiS family


Domain annotation for each model (and alignments):
>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.6   0.9   8.7e-26   5.1e-23       1     116 []       3     123 ..       3     123 .. 0.91
   2 !   84.6   0.1     1e-26   5.9e-24       1     116 []     230     346 ..     230     346 .. 0.94

  Alignments for each domain:
  == domain 1  score: 81.6 bits;  conditional E-value: 8.7e-26
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeani 77 
                                       i+iiG+G+vG+++a+ L e++ dv++id+d+e++e++ e  l+v++g++++  +L +  + +ad+++a+tg+de+ni
  gi|298674234|ref|YP_003725984.1|   3 IVIIGAGEVGYHIANSLYENN-DVIIIDRDDEACERADELDLQVIQGNGANVRLLTQV-LTNADLLVAVTGSDEVNI 77 
                                       89*****************99.7********************************997.99**************** PP

                                       HHHHHHHHHTSS...SEEEEEESSGGG..HHHHHH..HTTSEEEEH CS
                            TrkA_N  78 lavllakelnpk...kkiiaraqdpeh..aellkk..lgadvvisp 116
                                       + +++ak   +    +k++ar+++p++  + ++++  +g+d++i p
  gi|298674234|ref|YP_003725984.1|  78 VSCMAAKLVSKSkkpLKTMARVSNPDYidKPVARRtqIGIDTMICP 123
                                       ******98777777778**********6655566667999999976 PP

  == domain 2  score: 84.6 bits;  conditional E-value: 1e-26
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTT..SEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeg..levvvgdatdeevLeeagiekadaviaatgddea 75 
                                       ++iiG G+vG +la+  +++g+++ +i++d++r+e +++    + v++gd+td ++L+e +++++d+v  ++++de+
  gi|298674234|ref|YP_003725984.1| 230 VMIIGGGKVGFHLAQIAQKSGIKIKIIEHDKKRCEYIADVLpeVLVINGDGTDVNLLKEEEVSNMDTVFSVMDSDEK 306
                                       69*****************8878****************9955669******************************* PP

                                       HHHHHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEEEH CS
                            TrkA_N  76 nilavllakelnpkkkiiaraqdpehaellkklgadvvisp 116
                                       n+l +llak++    k+iar++++ +  l++ +g+d + sp
  gi|298674234|ref|YP_003725984.1| 307 NLLSALLAKQFGV-GKVIARVERSGYSPLFEMVGVDLAASP 346
                                       *********8555.79********************99887 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6   0.1   1.1e-16   6.1e-14       1      70 []     153     221 ..     153     221 .. 0.96
   2 !   56.3   0.0   3.7e-18   2.1e-15       2      69 ..     377     443 ..     376     444 .] 0.96

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 1.1e-16
                                       CEEEEEE--GGGTTSBHHHHTHHHHS-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHHHHH CS
                            TrkA_C   1 lvevtvpagsplvGktlkelnlrargvlvvairRggeliipsgdtvLeeGDvllvvgspsdlaelrellg 70 
                                       ++e++ + +  +vGk +k l+l + ++++ a+ Rgge+iip gd+ +++GD+++++g+ ++++ +r ++g
  gi|298674234|ref|YP_003725984.1| 153 MIEFVAKDNTEIVGKQVKNLQLSE-SCIISALFRGGEVIIPHGDDAINSGDHVVIIGKTDEMKSIRGIFG 221
                                       6899********************.**************************************9998876 PP

  == domain 2  score: 56.3 bits;  conditional E-value: 3.7e-18
                                       EEEEEE--GGGTTSBHHHHTHHHHS-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHHHH CS
                            TrkA_C   2 vevtvpagsplvGktlkelnlrargvlvvairRggeliipsgdtvLeeGDvllvvgspsdlaelrell 69 
                                       +e+   ++s++ Gk+lk+++++  g++v  + +g+e++ip+gd v+e GD++l+++ ps++ ++++l+
  gi|298674234|ref|YP_003725984.1| 377 IEYIAYKNSKITGKPLKDIKFPS-GAIVSMVIHGNEPFIPRGDHVIEDGDRVLIFSLPSAVTDVEKLF 443
                                       6888899****************.******************************************98 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.6   2.6e-11   1.5e-08      14     126 ..       2     114 ..       1     120 [. 0.86
   2 !   12.9   0.1   0.00015     0.086      11      87 ..     226     305 ..     217     316 .. 0.77

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 2.6e-11
                                       EEEEES-SHHHHHHHHHHHCCT-CEEEEEESS...HHHHHHHHHHH.T.ET-EEEEGCGHHHHHHT-SEEEE-SSSS CS
                      Shikimate_DH  14 kvlliGaGemaelvakhLlakgvkkvvvaNRt...lerakelaeel.kgeeiealkleelkellaeadvvisatase 86 
                                       k+++iGaGe++  +a+ L+++  ++v+++ R+    era+el  ++ +g   +  ++  l+++l +ad++++ t+s 
  gi|298674234|ref|YP_003725984.1|   2 KIVIIGAGEVGYHIANSLYEN--NDVIIIDRDdeaCERADELDLQViQG---NGANVRLLTQVLTNADLLVAVTGSD 73 
                                       89*****************65..689*****833357999998888444...58888889999************** PP

                                       S-SB-HHHHHCCHHH.S..E.EEEE--SS-SB-TTGGGSTT CS
                      Shikimate_DH  87 epilekeeveealkkrkkpl.llvDiavPRdvepevaeled 126
                                       e+ + + +  ++++k+kkpl  +  +++P  +++ va  ++
  gi|298674234|ref|YP_003725984.1|  74 EVNIVSCMAAKLVSKSKKPLkTMARVSNPDYIDKPVARRTQ 114
                                       **9999999999999999988********999999887665 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00015
                                       TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHH....HHHHT-SEEEE-S CS
                      Shikimate_DH  11 kekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelk....ellaeadvvisat 83 
                                       + +kv++iG G+++  +a+   ++g+k + ++  + +r + +a+ l ++ +   + ++++    e ++++d v+s  
  gi|298674234|ref|YP_003725984.1| 226 NVNKVMIIGGGKVGFHLAQIAQKSGIK-IKIIEHDKKRCEYIADVLPEVLVINGDGTDVNllkeEEVSNMDTVFSVM 301
                                       5689***************99999999.****************998886554443433211124677788888777 PP

                                       SSSS CS
                      Shikimate_DH  84 asee 87 
                                        s e
  gi|298674234|ref|YP_003725984.1| 302 DSDE 305
                                       6655 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.3   8.5e-07   0.00049       9      82 ..       2      83 ..       1     100 [. 0.74
   2 !   19.3   0.2   2.1e-06    0.0012       8      77 ..     228     309 ..     225     328 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 8.5e-07
                     NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapevkeele.......elvk...laeeelekdlegadlviaatddrelner 77
                                      k++++G+Gev+++ +++l e+  +v++++ +  e++e       + ++   ++ + l + l++adl++a+t  +e+n  
  gi|298674234|ref|YP_003725984.1|  2 KIVIIGAGEVGYHIANSLYEN-NDVIIIDRD-DEACEradeldlQVIQgngANVRLLTQVLTNADLLVAVTGSDEVNIV 78
                                      789*****************9.9********.6777744333222222111222334677***************9966 PP

                     NAD_binding_7 78 iaeaa 82
                                       + aa
  gi|298674234|ref|YP_003725984.1| 79 SCMAA 83
                                      55555 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 2.1e-06
                     NAD_binding_7   8 kkvlvvGgGevAarkvrklleagakvtvvapevkeele.......elvklaeee...l....ekdlegadlviaatd 70 
                                        kv+++GgG+v+ + ++   ++g k++++  + k+ +e       e + ++  +   +    e++++++d+v+ ++d
  gi|298674234|ref|YP_003725984.1| 228 NKVMIIGGGKVGFHLAQIAQKSGIKIKIIEHD-KKRCEyiadvlpEVLVING-DgtdVnllkEEEVSNMDTVFSVMD 302
                                       589*****************************.6777744444442222222.123323456788**********99 PP

                     NAD_binding_7  71 drelner 77 
                                        +e n  
  gi|298674234|ref|YP_003725984.1| 303 SDEKNLL 309
                                       9988755 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.6   1.6e-06   0.00093      30     112 ..       2      88 ..       1     100 [. 0.83
   2 !   20.5   0.2   4.2e-07   0.00024      26      76 ..     225     275 ..     206     322 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.6e-06
                                       EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH-SEEEE-.....--B CS
                       AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaeavkeadvvigt.....vli 101
                                       k+++iG+G +G + ia++   + +V ++D + ++ e+ ++l  ++++   ++ +ll++ + +ad+++       v i
  gi|298674234|ref|YP_003725984.1|   2 KIVIIGAGEVGYH-IANSLYENNDVIIIDRDDEACERADELDLQVIQGNGANVRLLTQVLTNADLLVAVtgsdeVNI 77 
                                       89*********98.566677799******************************************986323344777 PP

                                       TTSS---SC-H CS
                       AlaDh_PNT_C 102 pGkkaPkLvte 112
                                           a+kLv++
  gi|298674234|ref|YP_003725984.1|  78 VSCMAAKLVSK 88 
                                       77778888765 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 4.2e-07
                                       B---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECE CS
                       AlaDh_PNT_C  26 vepakvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfve 76 
                                        +  kv++iGgG +G + +++a++ g k+++++ +++r e++ ++  +++ 
  gi|298674234|ref|YP_003725984.1| 225 QNVNKVMIIGGGKVGFHLAQIAQKSGIKIKIIEHDKKRCEYIADVLPEVLV 275
                                       55679*************************************997666333 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   3.5e-05      0.02       1      52 [.       2      47 ..       2      67 .. 0.81
   2 ?   -1.4   0.0       6.4   3.7e+03      19      42 ..     198     219 ..     186     228 .. 0.59
   3 !   17.8   0.2   6.7e-06    0.0039       1      48 [.     229     281 ..     229     323 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.5e-05
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEEC CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvta 52
                                      ki iiGaG++g  +a+ l +++    +++++ +r+ e  e  a+el  +v++
  gi|298674234|ref|YP_003725984.1|  2 KIVIIGAGEVGYHIANSLYENN----DVIII-DRDDEACE-RADELDLQVIQ 47
                                      799******************7....99988.99988654.45666655555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 6.4
                                       HHTTS-GGCEEEEEESSCCCHHHH CS
                     F420_oxidored  19 laagaqpheivvansrnpekaeel 42 
                                       +++g  +h ++++ + + ++++ +
  gi|298674234|ref|YP_003725984.1| 198 INSG--DHVVIIGKTDEMKSIRGI 219
                                       4555..455555555555555555 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 6.7e-06
                                       EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.........- CS
                     F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.........v 48 
                                       k+ iiG+G++g+ la+ ++++g    +i ++ + ++++ e++a+ l           
  gi|298674234|ref|YP_003725984.1| 229 KVMIIGGGKVGFHLAQIAQKSG---IKIKII-EHDKKRCEYIADVLPevlvingdgT 281
                                       688*******************...****88.*********9998776555444442 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.6   3.9e-08   2.2e-05       1      78 [.       3      71 ..       3      86 .. 0.91
   2 !   10.2   0.1    0.0012      0.68       1      44 [.     230     270 ..     230     323 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 3.9e-08
                                      EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SS CS
                   Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnlsp 78
                                      ++iiGaG vG  +a  l +++dv    +++dr++e +e++     + +++ i+ + +n++  L+++l+ +dl+v +++
  gi|298674234|ref|YP_003725984.1|  3 IVIIGAGEVGYHIANSLYENNDV----IIIDRDDEACERA----DELDLQVIQGNGANVRL-LTQVLTNADLLVAVTG 71
                                      89******************986....**********999....6799************9.***********98765 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0012
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka 44 
                                       v+iiG+G+vG  +a+  +++  +  +i +++ +k+++e +a+ +
  gi|298674234|ref|YP_003725984.1| 230 VMIIGGGKVGFHLAQIAQKS-GI--KIKIIEHDKKRCEYIADVL 270
                                       78********8888776666.58..8************999866 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   2.1e-05     0.012       3      81 ..       8      85 ..       7     113 .. 0.84
   2 !   15.1   0.0   2.7e-05     0.016       3      90 ..     235     331 ..     234     368 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.1e-05
                                      TSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC..HHHHHH CS
                    NAD_binding_10  3 tGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk..deegak 79
                                       G vG ++++ l +++  +v ++ R+ e  ++  +e  l+v++g+  +v  l+++l++ad  v+ +g+++    + +a+
  gi|298674234|ref|YP_003725984.1|  8 AGEVGYHIANSLYENN--DVIIIDRDDEACERA-DELDLQVIQGNGANVRLLTQVLTNADLLVAVTGSDEVniVSCMAA 83
                                      79************95..8999*****999975.689***********************9999888776533333344 PP

                                      HH CS
                    NAD_binding_10 80 ni 81
                                      ++
  gi|298674234|ref|YP_003725984.1| 84 KL 85
                                      44 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2.7e-05
                                       TSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCT.TTCEEEE--TT-CCHHH.HHHTT-SEEEES---TCC.... CS
                    NAD_binding_10   3 tGkvGrllvkellargghevtalvRnpeklaeleae.eglevvegdvtdvedla.ealkgadaVvsalggggk.... 73 
                                        GkvG +l++ + ++ g++++++  ++++ + +++  +++ v+ gd tdv+ l+ e +++ d+V+s + +++k    
  gi|298674234|ref|YP_003725984.1| 235 GGKVGFHLAQIAQKS-GIKIKIIEHDKKRCEYIADVlPEVLVINGDGTDVNLLKeEEVSNMDTVFSVMDSDEKnlls 310
                                       69************9.5**************9997789************99862689**********877765655 PP

                                       ....HHHH..HHHHHHHHHHCT- CS
                    NAD_binding_10  74 ....deeg..aknivdaakeagv 90 
                                           +  +  + ++++ ++++g 
  gi|298674234|ref|YP_003725984.1| 311 allaK--QfgVGKVIARVERSGY 331
                                       55433..1457777777777775 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.3e-05    0.0075       1      76 [.       2      78 ..       2     136 .. 0.75
   2 !   12.9   0.0   0.00014     0.083       1      40 [.     229     268 ..     229     295 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.3e-05
                                      -EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSSBTTT..BTT----TTEEEES-HHHHHTT--EEEE- CS
                    NAD_Gly3P_dh_N  1 kiavlGaGswGtalAkvlaenghevrlwvreeelieeineehenvky..Lpgiklpenlvattdlaealkgadiivlv 76
                                      ki ++GaG  G  +A++l en+ +v ++ r++e +e+ +e    v      +++l +++  ++dl  a++g+d + +v
  gi|298674234|ref|YP_003725984.1|  2 KIVIIGAGEVGYHIANSLYENN-DVIIIDRDDEACERADELDLQVIQgnGANVRLLTQVLTNADLLVAVTGSDEVNIV 78
                                      799******************9.99******97766655544433320033467777888888888888888865333 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00014
                                       -EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHH CS
                    NAD_Gly3P_dh_N   1 kiavlGaGswGtalAkvlaenghevrlwvreeelieeine 40 
                                       k+ ++G+G+ G  lA++ ++ g +++++ ++++ +e i +
  gi|298674234|ref|YP_003725984.1| 229 KVMIIGGGKVGFHLAQIAQKSGIKIKIIEHDKKRCEYIAD 268
                                       799*****************************99998865 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.1   0.00016      0.09       1      40 [.       2      40 ..       2      98 .. 0.88
   2 !   13.1   0.1   0.00011     0.066       1      40 [.     229     268 ..     229     302 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00016
                                      EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHH CS
                           3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdiseealekale 40
                                      k+ +iGaG +G  ia+ +  ++ +V ++d+++ea e+a e
  gi|298674234|ref|YP_003725984.1|  2 KIVIIGAGEVGYHIANSLY-ENNDVIIIDRDDEACERADE 40
                                      689************9876.567*************9976 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00011
                                       EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHH CS
                           3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealekale 40 
                                       kv +iG G +G  +a+++ ++g+++++++ ++++ e  ++
  gi|298674234|ref|YP_003725984.1| 229 KVMIIGGGKVGFHLAQIAQKSGIKIKIIEHDKKRCEYIAD 268
                                       699****************************999887665 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.1   0.00091      0.53       1      38 [.       2      38 ..       2      75 .. 0.82
   2 !   16.1   0.4   2.2e-05     0.013       1      35 [.     229     263 ..     229     300 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00091
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrll 38
                                      k+v++G+G +g   A+ l e + +V +++r d+ +   
  gi|298674234|ref|YP_003725984.1|  2 KIVIIGAGEVGYHIANSLYENN-DVIIIDRDDEACERA 38
                                      79****************9866.9********999333 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 2.2e-05
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkll 35 
                                       kv+++GgG +g  lA+++++ g k++++e  +k +
  gi|298674234|ref|YP_003725984.1| 229 KVMIIGGGKVGFHLAQIAQKSGIKIKIIEHDKKRC 263
                                       799**************************988766 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.1    0.0019       1.1       2     183 ..       2      36 ..       1      99 [. 0.62
   2 !   16.5   0.1   6.4e-06    0.0037       2      58 ..     229     289 ..     211     330 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0019
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHHCCCCHCCTCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeiasevvkklnqgielllgeevvki 78 
                                       ++v+iG+G  G++ a  l + + +                                                     
  gi|298674234|ref|YP_003725984.1|   2 KIVIIGAGEVGYHIANSLYE-NND----------------------------------------------------- 24 
                                       45555555555555555555.444..................................................... PP

                                       EESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSEEEEES-SHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  79 dpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllpkrivvvGgGyiGv 155
                                                                                                                    
  gi|298674234|ref|YP_003725984.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       HHHHHHHHHT-EEEEEESSSSSSTTS-H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 156 ElAaalaklgkevtlveardrllraldk 183
                                                   v ++++ d+ +    +
  gi|298674234|ref|YP_003725984.1|  25 ------------VIIIDRDDEAC----E 36 
                                       ............55555555555....3 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 6.4e-06
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEE.TTHCHHHCSHHHHCHHHHHHHHHHHHH...H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx...x RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve.legtclnggcllskallgvaedaeias...e 58 
                                       +v++iGgG  G+++a+ ++++g+k+ ++e +++ c +   +l+++l+  ++ +++ +   e
  gi|298674234|ref|YP_003725984.1| 229 KVMIIGGGKVGFHLAQIAQKSGIKIKIIEhDKKRCEYIADVLPEVLVINGDGTDVNLlkeE 289
                                       7999999999999999999999999999988888888888887766655555544444442 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0     0.001      0.58       3      36 ..       2      34 ..       1      54 [. 0.91
   2 !   14.1   0.0   3.5e-05      0.02       3      36 ..     229     262 ..     228     267 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.001
                                      EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSS CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrstt 36
                                      +++I+GaG +G   a+ L e   +v+++++ +++
  gi|298674234|ref|YP_003725984.1|  2 KIVIIGAGEVGYHIANSLYEN-NDVIIIDRDDEA 34
                                      689******************.9*******9876 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 3.5e-05
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSS CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrstt 36 
                                       +V+I+G+G +G+ la++ ++ G++  ++e  +++
  gi|298674234|ref|YP_003725984.1| 229 KVMIIGGGKVGFHLAQIAQKSGIKIKIIEHDKKR 262
                                       69***************************98775 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0    0.0008      0.46       1      50 [.       2      50 ..       2     110 .. 0.71
   2 ?    0.2   0.0       1.3   7.5e+02     120     155 ..     195     229 ..     191     232 .. 0.82
   3 !    8.6   0.1    0.0033       1.9       2      63 ..     230     301 ..     229     327 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0008
                                      EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHH CS
                     NAD_binding_2  1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesie 50
                                      ki +iG G+ G ++a+ l ++  +v++++r+ e++e++ +  +++++   
  gi|298674234|ref|YP_003725984.1|  2 KIVIIGAGEVGYHIANSLYEN-NDVIIIDRDDEACERADELDLQVIQGNG 50
                                      5889***********999876.6899*********999887755444433 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.3
                                       HHHHHHT-EEEEEEE-HHHHHHHHHHHHHHEEEEEE CS
                     NAD_binding_2 120 eegAekGtLsimvGGseeafervkpvleaigakvth 155
                                       +   ++G   +++ G+ +++++++ ++ +ig++v +
  gi|298674234|ref|YP_003725984.1| 195 DDAINSGD-HVVIIGKTDEMKSIRGIFGEIGQNVNK 229
                                       55667777.788889999**************9875 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0033
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT..........EEE-SSHHHHHHHCSEEEE-S CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg..........akaaesieelvasldvvitmv 63 
                                       + +iG G+ G ++a+  +k+g+k+ +++++k+++e +++             ++    ee v+++d+v+ ++
  gi|298674234|ref|YP_003725984.1| 230 VMIIGGGKVGFHLAQIAQKSGIKIKIIEHDKKRCEYIADVLpevlvingdgTDVNLLKEEEVSNMDTVFSVM 301
                                       678*****************************9998887645556655554333333345566666666554 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   3.2e-06    0.0018       1      54 [.       3      57 ..       3      94 .. 0.80
   2 ?    1.0   0.0      0.53   3.1e+02       1      37 [.     230     267 ..     230     307 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.2e-06
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETT.CEEEEEE CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseg.geeilrp 54
                                      i+i+GaG +G  +a +L++ ++dv++i+r++  +e+  + +l++ + +  +++l++
  gi|298674234|ref|YP_003725984.1|  3 IVIIGAGEVGYHIANSLYE-NNDVIIIDRDDeACERADELDLQVIQGNgANVRLLT 57
                                      89***************66.99*********9999988888887776644444444 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.53
                                       EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHH CS
                              ApbA   1 iailGaGaiGsllaakLakagadvtlilrsr.rlealk 37 
                                       + i+G G +G  la   +k g ++ +i +++ r+e + 
  gi|298674234|ref|YP_003725984.1| 230 VMIIGGGKVGFHLAQIAQKSGIKIKIIEHDKkRCEYIA 267
                                       57999999998887766669999999999999988765 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.6e-05     0.015       1      34 [.       2      36 ..       2      58 .. 0.92
   2 ?    3.8   0.0     0.064        37       2      29 ..     230     259 ..     229     263 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.6e-05
                                      EEEEECTSHHHHHHHHHHHHTT.EEEEESSSSTTS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg.Vtllekgdiags 34
                                      ++viiG+G +G  +A  L + + V++++++d+a++
  gi|298674234|ref|YP_003725984.1|  2 KIVIIGAGEVGYHIANSLYENNdVIIIDRDDEACE 36
                                      59****************99889*******99875 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.064
                                       EEEECTSHHHHHHHHHHHHTT..EEEEESS CS
                               DAO   2 vviiGGGiiGlstAyeLarrg..Vtllekg 29 
                                       v iiGGG +G   A  +++ g  + ++e +
  gi|298674234|ref|YP_003725984.1| 230 VMIIGGGKVGFHLAQIAQKSGikIKIIEHD 259
                                       89************9998889999999966 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.015       8.6       2      35 ..       2      34 ..       1      38 [. 0.87
   2 !   12.5   0.2   7.4e-05     0.043       2      35 ..     229     262 ..     228     269 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.015
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakkl 35
                                      ++++iG+G  G   A s+  ++++V+++++ +++
  gi|298674234|ref|YP_003725984.1|  2 KIVIIGAGEVGYHIANSL-YENNDVIIIDRDDEA 34
                                      79*************999.77889*****98765 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 7.4e-05
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakkl 35 
                                       +v++iGgG  G+  A  a+k g ++ ++e+ kk 
  gi|298674234|ref|YP_003725984.1| 229 KVMIIGGGKVGFHLAQIAQKSGIKIKIIEHDKKR 262
                                       79****************************9985 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0      0.11        64       2      65 ..       4      60 ..       3     105 .. 0.60
   2 !   14.5   0.0   6.5e-05     0.038       1      64 [.     230     312 ..     230     329 .. 0.63

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.11
                                      EEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT-SE.......-EEEE--S-HHHHHHHHHHHS CS
                            XdhC_C  2 vifGaghvaqalarlaaalgfrvtvvdpreefatkerfpeade.......tavvvlthdhklDaealeaal 65
                                      vi+Gag+v+ ++a+ + +   +v+++d ++e+   er+ e d        +             ++l ++l
  gi|298674234|ref|YP_003725984.1|  4 VIIGAGEVGYHIANSLYEN-NDVIIIDRDDEAC--ERADELDLqviqgngA-----------NVRLLTQVL 60
                                      89***********999885.5888999888633..2322111122334431...........333333333 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 6.5e-05
                                       EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG..................-GGG-TT-SE............-EE CS
                            XdhC_C   1 lvifGaghvaqalarlaaalgfrvtvvdpreefa..................tkerfpeade............tav 47 
                                       ++i+G+g+v+ +la++a++ g+++ +++++++                    +                     t++
  gi|298674234|ref|YP_003725984.1| 230 VMIIGGGKVGFHLAQIAQKSGIKIKIIEHDKKRCeyiadvlpevlvingdgtD--------VnllkeeevsnmdTVF 298
                                       68***************************996444555555555555554441........0333333344343444 PP

                                       EE--S-HHHHHHHHHHH CS
                            XdhC_C  48 vvlthdhklDaealeaa 64 
                                        v+  d   ++++l+a+
  gi|298674234|ref|YP_003725984.1| 299 SVMDSD---EKNLLSAL 312
                                       444444...34444444 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0      0.01       5.8      38      77 ..       2      40 ..       1      77 [. 0.68
   2 !   10.2   0.2   0.00059      0.34      37      71 ..     228     262 ..     211     274 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.01
                                      EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHH CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeee 77
                                      ++ iiG+G++G ++a+ l + + +vi++dr  ++ e+++e
  gi|298674234|ref|YP_003725984.1|  2 KIVIIGAGEVGYHIANSLYE-NNDVIIIDRDDEACERADE 40
                                      789*************9986.4578888887765553333 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00059
                                       SEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHH CS
                      2-Hacid_dh_C  37 ktvGiiGlGrIGqavakrlkafgmkviaydrskkk 71 
                                        +v iiG G++G ++a+++++ g+k+ ++++ kk+
  gi|298674234|ref|YP_003725984.1| 228 NKVMIIGGGKVGFHLAQIAQKSGIKIKIIEHDKKR 262
                                       5899****************999988777666554 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.2   0.00028      0.16       1      45 [.       1      44 [.       1      54 [. 0.85
   2 ?    0.9   0.0      0.52     3e+02     100     160 ..      68     130 ..      57     141 .. 0.69
   3 !    7.0   0.2    0.0066       3.8       2      39 ..     229     266 ..     228     292 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00028
                                      SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-S CS
                    UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkip 45
                                      mki++iG+G vG   a  l e  ++vi++D d+e+ +   + +++
  gi|298674234|ref|YP_003725984.1|  1 MKIVIIGAGEVGYHIANSLYE-NNDVIIIDRDDEACERADELDLQ 44
                                      89**************99976.589********998877666555 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.52
                                       HHHHHHHHHHHHHCEEEEEE-S---TTHHHHCHHHHHHHHCSS-..TTCEEEEE------TTS CS
                    UDPG_MGDP_dh_N 100 vesaarsiaealkkgkvvvvkSTvpvgtaeelvkkileeaskkk..gvdfdvvsnPEflregs 160
                                         + +++++ +      +v kS  p +t+  + ++   +++ ++  ++ +d + +PE    ++
  gi|298674234|ref|YP_003725984.1|  68 AVTGSDEVNIVSCMAAKLVSKSKKPLKTMARVSNPDYIDKPVARrtQIGIDTMICPELAMASE 130
                                       555555555555566678999999999999988875544444333588899999999776554 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0066
                                       EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHH CS
                    UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigvDideekvdkl 39 
                                       k+ +iG G vG   a +  + g+++ ++  d+++ + +
  gi|298674234|ref|YP_003725984.1| 229 KVMIIGGGKVGFHLAQIAQKSGIKIKIIEHDKKRCEYI 266
                                       899****************************9998766 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.4    0.0014      0.81       2      81 ..       4      77 ..       3      87 .. 0.78
   2 !    8.9   0.2    0.0017      0.96       2      77 ..     231     306 ..     230     326 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0014
                                      EESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE---GGS-HHH CS
                              NmrA  2 lviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtgfyskeie 80
                                      ++i ++G+ G ++++ l  ++++v ++ Rd   e+ +   e   ++++g+  +  +l ++l ++d+  +vtg  s+e++
  gi|298674234|ref|YP_003725984.1|  4 VII-GAGEVGYHIANSLY-ENNDVIIIDRDD--EACERADELDLQVIQGNGANVRLLTQVLTNADLLVAVTG--SDEVN 76
                                      455.569***99987665.567888887775..555666666789***************************..77776 PP

                                      H CS
                              NmrA 81 d 81
                                      +
  gi|298674234|ref|YP_003725984.1| 77 I 77
                                      6 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0017
                                       EESSTTSHHHHHHHHHHHHHT-EEEEEES-S-S.HHHHHHHHSTTEEE.ES-TT-HHHHH.HHHTT-SEEEE---GG CS
                              NmrA   2 lviGaTGrqGksvvrallkaghkvralvRdtks.elakslkeaGvelv.kgdlddkeslv.ealkgvdvvfsvtgfy 75 
                                       ++iG  G+ G ++++++ k+g k++++ +d k+ e ++ +   + +lv +gd  d ++l+ e +++ d+vfsv+ + 
  gi|298674234|ref|YP_003725984.1| 231 MIIG-GGKVGFHLAQIAQKSGIKIKIIEHDKKRcEYIADV--LPEVLViNGDGTDVNLLKeEEVSNMDTVFSVMDSD 304
                                       4555.5*********************9998551333333..4555556********997257***********954 PP

                                       S- CS
                              NmrA  76 sk 77 
                                       +k
  gi|298674234|ref|YP_003725984.1| 305 EK 306
                                       33 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2    0.0062       3.6     166     207 ..       2      42 ..       1      91 [. 0.82
   2 ?    9.1   0.6    0.0012       0.7       2      30 ..     232     259 ..     231     267 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0062
                       Pyr_redox_3 166 kvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdps 207
                                       k+v+iG+++ +  +A  l+++ ++V +++r++e  ++ ++ +
  gi|298674234|ref|YP_003725984.1|   2 KIVIIGAGEVGYHIANSLYEN-NDVIIIDRDDEACERADELD 42 
                                       789999999999999999998.78888998888776665555 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0012
                       Pyr_redox_3   2 IiGaGPaGlaaaielkkagledylilEkg 30 
                                       IiG+G  G   a  ++k+g+ ++ i+E +
  gi|298674234|ref|YP_003725984.1| 232 IIGGGKVGFHLAQIAQKSGI-KIKIIEHD 259
                                       9*******************.799***86 PP

>> Castor_Poll_mid  Castor and Pollux, part of voltage-gated ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0073       4.2      34      94 ..     158     214 ..     151     223 .. 0.69
   2 ?    4.9   0.0     0.044        25      65      88 ..     408     431 ..     378     441 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0073
                   Castor_Poll_mid  34 lkelpelegkkyedvllafqeavviGikvassgkiylnPeddevlqegdkllviaedddtk 94 
                                        k+ +e+ gk+ ++++l  +e+ +i    ++ g++ + P+ d  ++ gd++++i++ d+ k
  gi|298674234|ref|YP_003725984.1| 158 AKDNTEIVGKQVKNLQL--SESCIISA-LFRGGEV-IIPHGDDAINSGDHVVIIGKTDEMK 214
                                       55666666666666544..34444433.3665555.66999**************999876 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.044
                   Castor_Poll_mid  65 sgkiylnPeddevlqegdkllvia 88 
                                       +g+  + P+ d+v+++gd++l+ +
  gi|298674234|ref|YP_003725984.1| 408 HGNEPFIPRGDHVIEDGDRVLIFS 431
                                       4777899**************976 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.4   0.00036      0.21       1      55 [.       2      57 ..       2      72 .. 0.65
   2 ?    4.9   0.5     0.074        43       1      57 [.     229     289 ..     229     300 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00036
                            PglD_N  1 kivIiGaGGhgkvvadiieangeyeiigflDdnkk.tevegypvlgkaiellksls 55
                                      kivIiGaG  g  +a+ +  n++  ii   D++ +   + +++v+++  ++ + l+
  gi|298674234|ref|YP_003725984.1|  2 KIVIIGAGEVGYHIANSLYENNDVIIIDRDDEACErADELDLQVIQGNGANVRLLT 57
                                      8***************9999995444444444333233446888877666655554 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.074
                            PglD_N   1 kivIiGaGGhgkvvadiieangeyeiigflDdnkk.teveg....ypvlgkaiellkslsee 57 
                                       k++IiG G  g   a+i++++g  +i+++  d+k  + + +    + v+ ++ ++ + l+ee
  gi|298674234|ref|YP_003725984.1| 229 KVMIIGGGKVGFHLAQIAQKSG-IKIKIIEHDKKRcEYIADvlpeVLVINGDGTDVNLLKEE 289
                                       799*******************.777777777664332222333366666666666666554 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.6   4.5e-05     0.026      26      97 ..       3      81 ..       1      90 [. 0.82
   2 ?   -2.4   0.0       7.7   4.5e+03      18      35 ..     196     213 ..     190     232 .. 0.58
   3 ?    2.0   0.2      0.34     2e+02      25      55 ..     229     259 ..     223     267 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.5e-05
                                      EEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHH......HHHHC.TT-EE--HHHCTTT-SEEEE-SSSSSSB-HHHH CS
                     AdoHcyase_NAD 26 avvaGyGdvGkGcaaslkglGarvivtevdPica......lqaam.eGfevvtleevvkkadivvtttGnkdiitlehl 97
                                      +v++G G+vG   a+sl +    +i+   d  c       lq +  +G +v+ l +v+++ad++v++tG++++  +  +
  gi|298674234|ref|YP_003725984.1|  3 IVIIGAGEVGYHIANSLYENNDVIIIDRDDEACEradeldLQVIQgNGANVRLLTQVLTNADLLVAVTGSDEVNIVSCM 81
                                      799*****************9999999989888433443367653389**********************998665555 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 7.7
                                       -S--TTSEEEEE--SHHH CS
                     AdoHcyase_NAD  18 dvllaGkvavvaGyGdvG 35 
                                       d + +G  +v++G  d  
  gi|298674234|ref|YP_003725984.1| 196 DAINSGDHVVIIGKTDEM 213
                                       555556666666555443 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.34
                                       EEEEE--SHHHHHHHHHHHHCT-EEEEE-S- CS
                     AdoHcyase_NAD  25 vavvaGyGdvGkGcaaslkglGarvivtevd 55 
                                       +++++G G vG   a+  ++ G ++ + e d
  gi|298674234|ref|YP_003725984.1| 229 KVMIIGGGKVGFHLAQIAQKSGIKIKIIEHD 259
                                       5789999********************9987 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.061        36      19      47 ..       2      28 ..       1      32 [. 0.82
   2 ?   -0.3   0.1      0.88   5.1e+02     158     221 ..      62     126 ..      48     134 .. 0.71
   3 ?    8.5   0.1    0.0018         1      18      50 ..     228     259 ..     217     322 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.061
                                      EEEEE--SHHHHHHHHHHHHCTTS-EEEE CS
                              Thi4 19 DvvivGaGssGLtaayylakkpdlkvail 47
                                       +vi+GaG  G   a  l ++ d  v+i+
  gi|298674234|ref|YP_003725984.1|  2 KIVIIGAGEVGYHIANSLYENND--VIII 28
                                      69***************999954..5555 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.88
                                       EEEEEEE--GSS.STTTTHHHHHHHHCTTTS-----.ECB-HHHHHHHHHHHECEEETTEEE-THH CS
                              Thi4 158 rakvvvdatGhd.geivavvvkkikleakiekvkge.ksldaekaedaivkktrevvpnlyvaGme 221
                                       +a ++v  tG d  +iv+ ++ k+++++ ++ +k + +    +  ++ + ++t+  ++ ++   ++
  gi|298674234|ref|YP_003725984.1|  62 NADLLVAVTGSDeVNIVSCMAAKLVSKS-KKPLKTMaRVSNPDYIDKPVARRTQIGIDTMICPELA 126
                                       6778899999763689999999998887.4555555144455667777777777777777766555 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0018
                                       EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESS CS
                              Thi4  18 sDvvivGaGssGLtaayylakkpdlkvailers 50 
                                         v+i+G+G  G   a++ a+k ++k+ i+e+ 
  gi|298674234|ref|YP_003725984.1| 228 NKVMIIGGGKVGFHLAQI-AQKSGIKIKIIEHD 259
                                       5799***********985.5555********75 PP

>> Spermine_synth  Spermine/spermidine synthase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.95   5.5e+02      86     112 ..      16      42 ..       4      69 .. 0.78
   2 ?   10.9   1.4   0.00038      0.22      11      75 ..     219     283 ..     210     306 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.95
                                       HCTCSS-EEEEEEECCSTTCSSCGCSS CS
                    Spermine_synth  86 lkayekkfdvvivdsldpvgpaenlFs 112
                                        + + ++ dv+i d  d+ +  +++ +
  gi|298674234|ref|YP_003725984.1|  16 ANSLYENNDVIIIDRDDEACERADELD 42 
                                       444455789999999999988777555 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00038
                                       HHHCCSSST-EEEEESSTT.SHHHHHHTTSTT-SEEEEEES-HHHHHHHHHHSHHHHTTCGGCTTE CS
                    Spermine_synth  11 vplmlhknpkevLiiGGgD.GgvlrevvkhntvekitlvdiDqkvidfskkflpslaisafndarv 75 
                                       + ++  +n  +v+iiGGg  G  l ++ + +   ki +++ D+k +++   +lp++ + + +++ v
  gi|298674234|ref|YP_003725984.1| 219 IFGEIGQNVNKVMIIGGGKvGFHLAQIAQKS-GIKIKIIEHDKKRCEYIADVLPEVLVINGDGTDV 283
                                       5556667899********8799999999988.789*****************99987654555555 PP

>> DUF2325  Uncharacterized protein conserved in bacteria (DUF2325)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.23   1.4e+02      25      75 ..      42      92 ..      31     101 .. 0.70
   2 ?    8.4   0.2    0.0039       2.3       1      34 [.     229     261 ..     229     279 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.23
                           DUF2325 25 klkvfdgrkekkkkkleskigkaDlvvlftdtvsHkavkkvk.keakkkgkp 75
                                      +l+v++g+   + + l + + +aDl+v +t+  + ++v ++  k++ k++kp
  gi|298674234|ref|YP_003725984.1| 42 DLQVIQGNGA-NVRLLTQVLTNADLLVAVTGSDEVNIVSCMAaKLVSKSKKP 92
                                      6777777777.77799************998877777766541344555555 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0039
                           DUF2325   1 svlivGGddrmeeqyrklleklggklkvfdgrke 34 
                                       +v+i+GG + +  ++ ++++k+g+k+k+++++k+
  gi|298674234|ref|YP_003725984.1| 229 KVMIIGGGK-VGFHLAQIAQKSGIKIKIIEHDKK 261
                                       5999***77.999****************99998 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.097        56       2      28 ..       3      26 ..       2      37 .. 0.78
   2 ?    7.5   0.0    0.0031       1.8       2      32 ..     230     258 ..     229     264 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.097
                     Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvv 28
                                      +v+iGaG  g  +A+ l e++    v+
  gi|298674234|ref|YP_003725984.1|  3 IVIIGAGEVGYHIANSLYENN---DVI 26
                                      89*************994443...444 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0031
                     Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvliea 32 
                                       v++iG+G  g  lA+    +k g+k+ +ie 
  gi|298674234|ref|YP_003725984.1| 230 VMIIGGGKVGFHLAQIA--QKSGIKIKIIEH 258
                                       89************999..*********986 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.45   2.6e+02       1      32 [.       5      35 ..       5      59 .. 0.84
   2 ?    8.1   0.1    0.0055       3.2       1      28 [.     232     259 ..     232     263 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.45
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlG 32
                                      I+GaG  G  +A  L ++  dv ++++ d  +
  gi|298674234|ref|YP_003725984.1|  5 IIGAGEVGYHIANSLYEN-NDVIIIDRDDEAC 35
                                      9**********9999885.8999999988766 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0055
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SS CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekr 28 
                                       I+G+G  G  +A+ ++k g+++ ++e+ 
  gi|298674234|ref|YP_003725984.1| 232 IIGGGKVGFHLAQIAQKSGIKIKIIEHD 259
                                       9************************975 PP

>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1         9   5.2e+03      44      59 ..      26      42 ..      15      70 .. 0.60
   2 ?    1.2   0.0      0.99   5.7e+02      52      71 ..     190     207 ..     185     208 .. 0.84
   3 ?   -1.2   0.1       5.8   3.3e+03      28      67 ..     256     296 ..     242     297 .. 0.71
   4 ?    7.3   0.0     0.013       7.3      27      71 ..     376     430 ..     364     434 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 9
                                      EEEEETTEEEGC.CTTT CS
                              ThiS 44 vavavNgeivpr.lwld 59
                                      +++ +++e ++r ++ld
  gi|298674234|ref|YP_003725984.1| 26 IIIDRDDEACERaDELD 42
                                      44444444444433333 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.99
                                       EEGCCTTTSB--TTCEEEEE CS
                              ThiS  52 ivprlwldtelkdgDevail 71 
                                       i+p+   d ++++gD v+i+
  gi|298674234|ref|YP_003725984.1| 190 IIPH--GDDAINSGDHVVII 207
                                       5666..8999********98 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 5.8
                                       HHHHHHHTCHHG..TTTTEEEEETTEEEGCCTTTSB--TTCE CS
                              ThiS  28 leaLgerypela..lerrvavavNgeivprlwldtelkdgDe 67 
                                       +e+ ++r + +a  l++++++  +g++v+   +++e+++ D+
  gi|298674234|ref|YP_003725984.1| 256 IEHDKKRCEYIAdvLPEVLVINGDGTDVNL-LKEEEVSNMDT 296
                                       555555555555888888999999999998.45777777766 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.013
                                       HHHHHHHHTCHHG............TTTTEEEEETTEEEGCCTTTSB--TTCEEEEE CS
                              ThiS  27 lleaLgerypela............lerrvavavNgeivprlwldtelkdgDevail 71 
                                       ++e ++++ ++++            ++  +++  N+ ++pr   d+++ dgD+v i+
  gi|298674234|ref|YP_003725984.1| 376 IIEYIAYKNSKITgkplkdikfpsgAIVSMVIHGNEPFIPR--GDHVIEDGDRVLIF 430
                                       5555555555555566666666655556677778999****..9**********999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2912.67
//
Query:       gi|298674235|ref|YP_003725985.1|  [L=479]
Description: cation transporter [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-61  208.9  18.1    5.3e-60  203.3  18.1    2.0  1  TrkH      Cation transport protein


Domain annotation for each model (and alignments):
>> TrkH  Cation transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.3  18.1     3e-64   5.3e-60       5     490 ..      38     471 ..      35     478 .. 0.92

  Alignments for each domain:
  == domain 1  score: 203.3 bits;  conditional E-value: 3e-64
                              TrkH   5 ifkggiitialgavllfldkeskyplalkddfqivkaaeialsvdgtlklllesaslafldalfeavsgltttglsv 81 
                                       ++ ++ +ti++g+v lfl++  + +   +++f iv   ++     g+++ +l    ++ l+a fe++sg+tttg +v
  gi|298674235|ref|YP_003725985.1|  38 FTVAITMTILVGTVFLFLFRSTEDEWHHREGFAIVALGWLFAAIFGSIPYML--DGVTPLNAFFESMSGFTTTGSTV 112
                                       6678899******************************************994..55788****************** PP

                              TrkH  82 ivveeslprsgltlraqlqqiGglgvvvlaylslptlgrgsaflylseaqkeelggkelrslselikilvvyyvgle 158
                                       +v+ e  p+ +l++r +++++Gg+g++vl  ++lp lg  + ++ ++e++++  ++k  ++++e++kil+++y+++ 
  gi|298674235|ref|YP_003725985.1| 113 FVNIEAHPKGILFWRNMTEWLGGMGIIVLFIAILPKLGVAGRQMFRAEVPGPQ-EDKLKPRIRETSKILWMVYLVVS 188
                                       *************************************************9996.667789***************** PP

                              TrkH 159 ilafvllvvliytakaysevvdstgvsplwwaffhsmSafnnlGfsltpnSlasfnknivillvaiifiilGnigFp 235
                                       i+ +++l           +++      ++++a+ h++++++ +Gfs ++ S++ f + ++++ ++++fi++++ +F 
  gi|298674235|ref|YP_003725985.1| 189 IAEAIAL---------KLAGL------SVYDAVTHTFTTVSCGGFSPYARSIEAFGS-PLVETIIMVFIFISGANFA 249
                                       *******.........68998......9*****************************.******************* PP

                              TrkH 236 illrviiaikkkilrdlkqikeslsflldlprrcftLllasgfvwllllelavlnvtdnilfilldegslvvksipk 312
                                       ++++++ a  k+ ++             d ++++       +fv+  ++ l+       +l  + d +  +++s+  
  gi|298674235|ref|YP_003725985.1| 250 LHYKTLYASRKSLIK-------------DDEFKFY------SFVIFSAIALL-------TLILWRDINIPIIESLR- 299
                                       *******99888755.............7777777......33333333333.......33367888877777776. PP

                              TrkH 313 gsrvlkalFqsvstrta.GFsvvdlsnlhpaikvllvlmmyigglpgStaggIrrtnvyeefslgkyeieqekepka 388
                                             a+Fq+ +  t+ G+++ d+ +++ + +++l++ m+ gg++gStagg + ++ + + + +++ei +  + +a
  gi|298674235|ref|YP_003725985.1| 300 -----YAAFQVLTIITTtGYATTDFIAWPHSAQMILLILMFAGGCAGSTAGGPKMVRWLLMLKYSRREIFKVIHRRA 371
                                       .....899******9999*********************************************************** PP

                              TrkH 389 vskksidgkhlerqllvdlwslflvlliilileglklsdvqepdfsffdiLfevvSaygtvGLSlGa.knaslsaql 464
                                       v ++++ +k + ++++ ++ s++ ++++i+ +++  l   +   ++++ ++ ++++++g++G++lGa   +  +  +
  gi|298674235|ref|YP_003725985.1| 372 VTRIKFNKKSVPEDIMQSVISFIAIYFLIFAASSVLLGLLG---MDLVSSITASIATLGNIGPGLGAvGPMDNFDVV 445
                                       ********************************965555555...**********************88********* PP

                              TrkH 465 ttisklvlialmirGrlrglpvlldr 490
                                       + ++k+ li +m++Grl++++v +  
  gi|298674235|ref|YP_003725985.1| 446 PALGKVALIGNMWMGRLEIFTVFVML 471
                                       *********************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       830  (0.0462937); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 2937.42
//
Query:       gi|298674236|ref|YP_003725986.1|  [L=410]
Description: geranylgeranyl reductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.5e-14   52.2   0.7    1.8e-10   40.6   0.2    2.9  2  FAD_binding_3   FAD binding domain
      2e-10   40.4   0.8    9.3e-07   28.3   0.5    2.2  2  FAD_binding_2   FAD binding domain
    2.9e-09   36.8   1.6    1.3e-08   34.6   1.6    1.9  1  FAD_oxidored    FAD dependent oxidoreductase
    3.6e-08   32.5   0.3    1.4e-07   30.6   0.0    1.9  2  HI0933_like     HI0933-like protein
    3.5e-07   30.3   0.0    9.2e-07   29.0   0.0    1.7  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    2.2e-06   27.2   0.6    2.2e-06   27.2   0.6    2.1  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    7.5e-06   25.2   0.0     0.0077   15.3   0.1    2.2  2  Lycopene_cycl   Lycopene cyclase protein
    1.4e-05   24.4   1.1    2.7e-05   23.4   1.1    1.6  1  GIDA            Glucose inhibited division protein A
    6.1e-05   22.8   0.3      0.011   15.4   0.2    2.2  2  DAO             FAD dependent oxidoreductase
    7.8e-05   22.0   0.1    0.00016   21.0   0.1    1.4  1  Thi4            Thi4 family
    0.00012   21.1   0.3       0.13   11.1   0.1    2.5  2  Trp_halogenase  Tryptophan halogenase
     0.0069   15.7   0.4      0.011   15.0   0.4    1.3  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.081   12.2   0.1       0.19   11.0   0.1    1.6  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
       0.15   11.9   0.2       0.36   10.7   0.2    1.6  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
       0.22   10.5   1.0        0.7    8.9   1.0    1.8  1  SE              Squalene epoxidase
        1.6    9.3   6.1       0.81   10.3   0.2    2.9  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.2   1.6e-13   1.8e-10       2     175 ..       5     169 ..       4     180 .. 0.83
   2 !    7.5   0.0    0.0018         2     281     319 ..     269     306 ..     233     338 .. 0.73

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 1.6e-13
                                       EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHHHHHTT-HHHHHHHSE..ECCCCEEEE CS
                     FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmellrqlGledrilaega..pnelmgeal 76 
                                       +dV++VGaGp G ++a+  ++ G +v+l+ekr++  +  r         e + + Gl++ i+ + +    ++ g   
  gi|298674236|ref|YP_003725986.1|   5 YDVIVVGAGPGGSIAAKTAAKNGLDVLLIEKRQEIGDPVR-------CAEGIGKEGLKHHIEPDPKwiCADVKGSRI 74 
                                       79******************************98766554.......56888999*****99988311345555555 PP

                                       EEECCCCCEEEEEHH.CHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEE CS
                     FAD_binding_3  77 ynelsdtpkaradle.lesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeet 152
                                       y +    ++  ++++ ++s++e  +v+  + ++r Lv++a++ g++v  kt+ ++l  ++  v+        gee++
  gi|298674236|ref|YP_003725986.1|  75 YSP----NETVVEMSeELSGGEVGYVLERKIFDRELVNQAASYGVDVMVKTRATGLISENGYVRGIKAIY-LGEEYN 146
                                       555....77777777355888889999*******************************999999876655.6999** PP

                                       EEEEEEEE--GTT-HHHHHHTGG CS
                     FAD_binding_3 153 vrakYlvGaDGgrStvrktlgie 175
                                       + ++ ++GaDG+ S++ +  gi+
  gi|298674236|ref|YP_003725986.1| 147 FYSNIVIGADGVESKIGRWGGID 169
                                       **************998877765 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0018
                                       SEETTEEE-GGGTEEE-STTSHHHHHHHHHHHHHHHHHH CS
                     FAD_binding_3 281 yrkgrvflaGDAaHihpPtgGqGlNtaiqDavnLawkLa 319
                                          + ++l+GDAa    P +G Gl  a +Da ++a   a
  gi|298674236|ref|YP_003725986.1| 269 TIADGLMLVGDAARQSDPITGGGLVNA-MDAGEIAGNVA 306
                                       557899*****************9555.46666555554 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.5   8.3e-10   9.3e-07       1      43 [.       6      48 ..       6      52 .. 0.92
   2 !   10.2   0.0   0.00025      0.28     147     196 ..     106     153 ..     100     165 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 8.3e-10
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqG 43
                                      DviV+G+G +G  AA +aa++Gl+v+++ek qe g    +++G
  gi|298674236|ref|YP_003725986.1|  6 DVIVVGAGPGGSIAAKTAAKNGLDVLLIEKRQEIGDPVRCAEG 48
                                      9*******************************98877777766 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00025
                                       HHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEE CS
                     FAD_binding_2 147 lvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavv 196
                                       lv++a ++gvd++ +t+a+ Li e+g v+G+ +     g+e  + ++ v+
  gi|298674236|ref|YP_003725986.1| 106 LVNQAASYGVDVMVKTRATGLISENGYVRGIKAI--YLGEEYNFYSNIVI 153
                                       899***************************9887..66666666555555 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   1.6   1.2e-11   1.3e-08       1      36 [.       6      41 ..       6     172 .. 0.58

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 1.2e-11
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGG 36
                                      Dv+VvG+gp+G +AA +Aa++G  vlL+e+r+ +G 
  gi|298674236|ref|YP_003725986.1|  6 DVIVVGAGPGGSIAAKTAAKNGLDVLLIEKRQEIGD 41
                                      9*********************************94 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   1.3e-10   1.4e-07       1      52 [.       5      57 ..       5      76 .. 0.85
   2 ?   -0.8   0.0      0.42   4.7e+02     317     344 ..     340     367 ..     296     374 .. 0.64

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 1.3e-10
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHC.GGGT-EEEET CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklgrKilis.GgGrcNvTnl 52
                                      +dviv+G+G+ G  aA +aak+g +Vll+ek +++g  ++ + G G+  + ++
  gi|298674236|ref|YP_003725986.1|  5 YDVIVVGAGPGGSIAAKTAAKNGLDVLLIEKRQEIGDPVRCAeGIGKEGLKHH 57
                                      59**********************************99998757777766664 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.42
                                       T-TTBGGG--HHHHHHHHHHHHSEEE-- CS
                       HI0933_like 317 eedkklaqlskkelkklaealkaltvkv 344
                                         ++k  ++++++l+++a++l++++++ 
  gi|298674236|ref|YP_003725986.1| 340 IVKNKFVEFTDEQLNTFAHSLQNVNFNT 367
                                       2456678888888888888888888875 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   8.2e-10   9.2e-07       1      32 [.       9      40 ..       9      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 8.2e-10
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlG 32
                                      +vGaG +G+ aA ++ak+g+dvll+ekr+ +G
  gi|298674236|ref|YP_003725986.1|  9 VVGAGPGGSIAAKTAAKNGLDVLLIEKRQEIG 40
                                      8******************************9 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.6   1.9e-09   2.2e-06       1      37 [.       5      40 ..       5     161 .. 0.70
   2 ?   -2.3   0.1       1.9   2.1e+03     257     279 ..     259     284 ..     250     311 .. 0.71

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 1.9e-09
                                      CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtcln 37
                                      +dv+v+G+Gp+G  aa+t+a++g++v+l+e+ ++  +
  gi|298674236|ref|YP_003725986.1|  5 YDVIVVGAGPGGSIAAKTAAKNGLDVLLIEK-RQEIG 40
                                      69***************************53.33333 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.9
                                       EEE--TTS.BESSTTEEE-GGGC..T CS
                                       xxxxxxxx.xxxxxxxxxxxxxx..x RF
                       Pyr_redox_2 257 givvdefl.rtnvpgiyaiGDva..g 279
                                       g+ v  +  +t  +g+ ++GD a  +
  gi|298674236|ref|YP_003725986.1| 259 GVPVSGTIdQTIADGLMLVGDAArqS 284
                                       44455555477899999999999431 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   6.9e-06    0.0077       1      36 [.       6      39 ..       6     166 .. 0.87
   2 !    8.1   0.0    0.0011       1.2     232     308 ..     249     331 ..     238     357 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.9e-06
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsl 36
                                      Dv+v+GaGp g s+Aa+  +ak gl v+lie  +++
  gi|298674236|ref|YP_003725986.1|  6 DVIVVGAGPGG-SIAAKT-AAKNGLDVLLIEKRQEI 39
                                      9********88.566665.6**********987766 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0011
                     Lycopene_cycl 232 vkevveeEqgviPvtlggslprleqk.vlaiGaaaglvhPaTGYsvarslaeapllasaia.aalres.......sl 299
                                       + ++ e + g +Pv   g + ++ +   + +G aa    P TG  +++++ + + +a  +a +a   +       ++
  gi|298674236|ref|YP_003725986.1| 249 EGKILELDVGGVPV--SGTIDQTIADgLMLVGDAARQSDPITGGGLVNAMDAGE-IAGNVAyEAISANdvstkmlQR 322
                                       567888889999**..88998888876999********************9988.5555551444444444444444 PP

                     Lycopene_cycl 300 sarawatlw 308
                                       +++ w++  
  gi|298674236|ref|YP_003725986.1| 323 YESRWRKTI 331
                                       444444444 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   1.1   2.4e-08   2.7e-05       1      45 [.       6      50 ..       6     166 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2.4e-08
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT-.-SSSSEEE CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldtiae.lsCnpsig 45
                                      dviV+G+G  G+ AA +aa+ G++vlLi +k ++i+  + C + ig
  gi|298674236|ref|YP_003725986.1|  6 DVIVVGAGPGGSIAAKTAAKNGLDVLLI-EKRQEIGDpVRCAEGIG 50
                                      8***************************.66667765134555554 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.2   9.6e-06     0.011       1      33 [.       6      40 ..       6      45 .. 0.96
   2 !    5.6   0.0    0.0088       9.9     148     214 ..     102     169 ..      58     299 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9.6e-06
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                      dv+++G+G  G+ +A  +a+ g  V+l+ek+ ++g
  gi|298674236|ref|YP_003725986.1|  6 DVIVVGAGPGGSIAAKTAAKNGldVLLIEKRQEIG 40
                                      9******************************8887 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0088
                                       HHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE...EECTEEE.E..EEEEEEE--GGGHH..HHHTTCTTT CS
                               DAO 148 ltaalaraaealGveilegtevtgleeedgkvwgve...rttpgen.d..aadavVnaaGawsd..llgllkeld 214
                                       + + l ++a++ Gv++  +t++tgl  e+g v g++       ge+    + + v+ a G+ s+   +   + +d
  gi|298674236|ref|YP_003725986.1| 102 FDRELVNQAASYGVDVMVKTRATGLISENGYVRGIKaiyL---GEEyNfyS-NIVIGADGVESKigRW---GGID 169
                                       5567999*****************8677777788855542...44322223.5588888888874444...3333 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1   1.4e-07   0.00016      18      54 ..       5      40 ..       2      48 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.4e-07
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS-- CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspG 54
                                       Dv++vGaG+ G  aa++ ak+ +l v+++e++  +G
  gi|298674236|ref|YP_003725986.1|  5 YDVIVVGAGPGGSIAAKTAAKN-GLDVLLIEKRQEIG 40
                                      6*********************.********998777 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.1   0.00011      0.13       1      35 [.       6      37 ..       6      44 .. 0.89
   2 !    8.0   0.0   0.00098       1.1     140     213 ..      86     162 ..      64     341 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00011
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SS CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlvesee 35
                                      ++++vG+G+ G++aA + ak +   l+v+l+e+ +
  gi|298674236|ref|YP_003725986.1|  6 DVIVVGAGPGGSIAAKTAAKNG---LDVLLIEKRQ 37
                                      699*************999999...9******864 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00098
                                       TS-B-S--EEEE-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETT...S-EEE-SEEEE-SGGG-II CS
                    Trp_halogenase 140 dglsalsyAyhldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrled...greveadlfiDcsGfrgll 213
                                       + ls+ + +y l+++ +++ L + a + Gv+++  + ++  + e+g+v +++      + ++  +++i + G ++++
  gi|298674236|ref|YP_003725986.1|  86 EELSGGEVGYVLERKIFDRELVNQAASYGVDVMVKTRATGLISENGYVRGIKAIYlgeEYNFYSNIVIGADGVESKI 162
                                       357888899**************************************988765433216666778888888888765 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.4   9.7e-06     0.011       1      33 [.       8      40 ..       8      45 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9.7e-06
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg.nig 33
                                      i++GaGP G  aa ++ k+gl d+l +Ek  +ig
  gi|298674236|ref|YP_003725986.1|  8 IVVGAGPGGSIAAKTAAKNGL-DVLLIEKRqEIG 40
                                      89*******************.8*****985666 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00017      0.19      30      63 ..       6      39 ..       2      60 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00017
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHH CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrpar 63
                                       v+v+G+G  G  A++ta++ g +V ++++r++ 
  gi|298674236|ref|YP_003725986.1|  6 DVIVVGAGPGGSIAAKTAAKNGLDVLLIEKRQEI 39
                                      69***************************99875 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   0.00032      0.36       2      34 ..       7      39 ..       6      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00032
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseea 34
                                      v v+GaG  G+  a+ +a++gl+V l++ ++e+
  gi|298674236|ref|YP_003725986.1|  7 VIVVGAGPGGSIAAKTAAKNGLDVLLIEKRQEI 39
                                      78**************************99875 PP

>> SE  Squalene epoxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.0   0.00062       0.7     129     155 ..     271     297 ..     263     400 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00062
                                SE 129 kkGlillGDalnmRHPltggGmtvaln 155
                                         Gl+l+GDa     P+tggG++ a+ 
  gi|298674236|ref|YP_003725986.1| 271 ADGLMLVGDAARQSDPITGGGLVNAMD 297
                                       58*******************987765 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2   0.00073      0.81       2      35 ..       7      40 ..       6      56 .. 0.93
   2 ?    0.9   0.0       0.6   6.7e+02      44      77 ..     104     137 ..      78     138 .. 0.58
   3 ?   -1.7   0.3         4   4.4e+03       4      19 ..     287     302 ..     287     317 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00073
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      v+vvG+G  g  +A+++a+ g +V ++e + ++ 
  gi|298674236|ref|YP_003725986.1|  7 VIVVGAGPGGSIAAKTAAKNGLDVLLIEKRQEIG 40
                                      89****************************9997 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.6
                                       HHHHHHHHHTTEEEECSEEEEEEEEETTS.EEEEE CS
                         Pyr_redox  44 kilqeklekngievllntkveeiegsedg.vesvk 77 
                                       ++l ++    g++v+ +t+++ +  se+g v+++k
  gi|298674236|ref|YP_003725986.1| 104 RELVNQAASYGVDVMVKTRATGLI-SENGyVRGIK 137
                                       233444444499999999999888.4445577765 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 4
                                       EECSSHHHHHHHHHHH CS
                         Pyr_redox   4 vvGgGyiglElAgala 19 
                                       + GgG+++ + Ag++a
  gi|298674236|ref|YP_003725986.1| 287 ITGGGLVNAMDAGEIA 302
                                       5799999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 2500.69
//
Query:       gi|298674237|ref|YP_003725987.1|  [L=57]
Description: 4Fe-4S ferredoxin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.9e-16   57.0  17.5    2.2e-08   33.6   5.5    2.1  2  Fer4             4Fe-4S binding domain
    4.2e-13   49.7  35.8    1.8e-07   31.6  13.6    2.0  3  Fer4_7           4Fe-4S dicluster domain
    2.6e-11   43.1  13.5    2.1e-06   27.6   4.1    2.1  2  Fer4_6           4Fe-4S binding domain
    5.2e-10   40.1  10.1    5.9e-05   23.9   0.7    2.1  2  Fer4_16          4Fe-4S double cluster binding domain
    3.2e-09   36.8  10.4    8.7e-09   35.4  10.4    1.6  1  Fer4_21          4Fe-4S dicluster domain
    3.9e-09   36.5  24.2    6.2e-06   26.2  13.6    2.0  2  Fer4_10          4Fe-4S dicluster domain
    6.4e-09   35.8  21.7    8.1e-07   29.1  12.2    1.9  2  Fer4_9           4Fe-4S dicluster domain
    7.5e-08   32.0  12.9    0.00034   20.5   2.3    2.1  2  Fer4_2           4Fe-4S binding domain
    2.7e-06   27.9  21.1    0.00054   20.7   6.1    2.2  2  Fer4_3           4Fe-4S binding domain
    1.2e-05   25.4  12.8    0.00062   20.1   3.1    2.3  2  Fer4_4           4Fe-4S binding domain
    3.1e-05   24.3  13.0      0.005   17.3   2.5    2.1  2  Fer4_8           4Fe-4S dicluster domain
    6.3e-05   23.4   8.7      0.026   15.0   1.9    2.3  2  Fer4_13          4Fe-4S single cluster domain of Ferredoxin I
    0.00076   20.0  12.7      0.013   16.0   2.0    2.1  3  Fer4_17          4Fe-4S dicluster domain
     0.0035   18.0  14.1       0.18   12.5   1.0    3.0  3  Fer4_15          4Fe-4S single cluster domain
     0.0062   16.7  10.9      0.073   13.3   1.8    2.0  2  Fer4_18          4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.075   13.9   2.8      0.075   13.9   2.8    2.0  3  Fer4_22          4Fe-4S dicluster domain
       0.73   10.0   8.6        2.2    8.4   0.2    3.1  4  Fer4_19          Divergent 4Fe-4S mono-cluster
        1.7    8.4  17.2      0.064   12.9   5.4    2.1  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
        2.3    8.1   8.1        3.9    7.3   1.2    2.2  2  zf-C2H2_11       zinc-finger C2H2-type


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   4.1   4.1e-10   3.9e-07       2      24 .]       4      26 ..       3      26 .. 0.91
   2 !   33.6   5.5   2.4e-11   2.2e-08       6      24 .]      36      54 ..      35      54 .. 0.95

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 4.1e-10
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                       ++  kC +CGaCv vCP gA++
  gi|298674237|ref|YP_003725987.1|  4 NVNRYKCGYCGACVGVCPEGALE 26
                                      68999****************85 PP

  == domain 2  score: 33.6 bits;  conditional E-value: 2.4e-11
                                      TTSSS-THHHHHSTTTEEE CS
                              Fer4  6 ekCigCGaCvevCPvgAIt 24
                                      +kC+gCG+C+++CPvgAI+
  gi|298674237|ref|YP_003725987.1| 36 NKCTGCGLCAKICPVGAIE 54
                                      69****************6 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   3.3   2.9e-06    0.0028      31      52 .]       3      24 ..       1      24 [. 0.85
   2 !   31.6  13.6   1.9e-10   1.8e-07       1      52 []       9      52 ..       9      52 .. 0.89
   3 !   21.7   3.2   2.5e-07   0.00024       1      19 [.      37      55 ..      37      57 .] 0.84

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.9e-06
                            Fer4_7 31 veidpekClgCgaCvavCPtga 52
                                      ++++  kC +CgaCv vCP ga
  gi|298674237|ref|YP_003725987.1|  3 INVNRYKCGYCGACVGVCPEGA 24
                                      5677889************997 PP

  == domain 2  score: 31.6 bits;  conditional E-value: 1.9e-10
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      +C  CgaCv +Cp +a+el e              +kC+gCg C++ CP+ga
  gi|298674237|ref|YP_003725987.1|  9 KCGYCGACVGVCPEGALELVET--------FIEADNKCTGCGLCAKICPVGA 52
                                      7******************886........3335689*************98 PP

  == domain 3  score: 21.7 bits;  conditional E-value: 2.5e-07
                            Fer4_7  1 rCigCgaCvaaCpvkaiel 19
                                      +C+gCg C++ Cpv+aie+
  gi|298674237|ref|YP_003725987.1| 37 KCTGCGLCAKICPVGAIEV 55
                                      6999999999999999875 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   1.9   2.1e-07    0.0002       2      24 .]       3      25 ..       2      25 .. 0.91
   2 !   27.6   4.1   2.2e-09   2.1e-06       6      24 .]      35      53 ..      33      53 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.1e-07
                            Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                      + +++ kC  Cg+Cv vCPega+
  gi|298674237|ref|YP_003725987.1|  3 INVNRYKCGYCGACVGVCPEGAL 25
                                      5689999999***********97 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 2.2e-09
                            Fer4_6  6 pdkCigCgdCvrvCPegai 24
                                      ++kC+gCg C+++CP gai
  gi|298674237|ref|YP_003725987.1| 35 DNKCTGCGLCAKICPVGAI 53
                                      59****************8 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.7   6.2e-08   5.9e-05       1      20 [.       9      28 ..       9      37 .. 0.82
   2 !   21.3   3.1   4.1e-07   0.00038       1      18 [.      37      54 ..      37      57 .] 0.92

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 6.2e-08
                           Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                      +Cg Cg+C+ vCP++a++  
  gi|298674237|ref|YP_003725987.1|  9 KCGYCGACVGVCPEGALELV 28
                                      6****************987 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 4.1e-07
                           Fer4_16  1 rCgtCgkCaevCPtnaik 18
                                      +C++Cg Ca++CP++ai+
  gi|298674237|ref|YP_003725987.1| 37 KCTGCGLCAKICPVGAIE 54
                                      6****************8 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4  10.4   9.2e-12   8.7e-09       3      58 ..       5      54 ..       3      55 .. 0.87

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 9.2e-12
                           Fer4_21  3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58
                                      +++ kC  Cg C+ +C++++ + +e+     +   +++C+GC lC+++CPv ++ie
  gi|298674237|ref|YP_003725987.1|  5 VNRYKCGYCGACVGVCPEGALELVET-----FIEADNKCTGCGLCAKICPV-GAIE 54
                                      78899*************99988875.....345689*************9.9997 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2  13.6   6.5e-09   6.2e-06       3      56 .]       4      49 ..       2      49 .. 0.83
   2 !   21.1   2.9   2.7e-07   0.00025       5      22 ..      34      51 ..      29      57 .] 0.82

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 6.5e-09
                           Fer4_10  3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                       +++ +C  Cg+Cv +CP         g+ +  e+  ++  kCtgcg C+++CP
  gi|298674237|ref|YP_003725987.1|  4 NVNRYKCGYCGACVGVCPE--------GALELVETFIEADNKCTGCGLCAKICP 49
                                      567889*************........666666666666677***********9 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 2.7e-07
                           Fer4_10  5 dddtCirCgkCvkaCPad 22
                                       d++C++Cg C k CP+ 
  gi|298674237|ref|YP_003725987.1| 34 ADNKCTGCGLCAKICPVG 51
                                      5799************94 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   1.9   4.1e-06    0.0038      33      50 ..       8      24 ..       1      25 [. 0.78
   2 !   29.1  12.2   8.5e-10   8.1e-07       1      51 []       9      53 ..       9      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.1e-06
                            Fer4_9 33 eeaCigCgaCveaCpkga 50
                                      + +C  CgaCv +Cp+ga
  gi|298674237|ref|YP_003725987.1|  8 Y-KCGYCGACVGVCPEGA 24
                                      3.7*99*********997 PP

  == domain 2  score: 29.1 bits;  conditional E-value: 8.5e-10
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      kC  CgaCv +Cp g+ +  +   +a +      +C+gCg C+++Cp gai
  gi|298674237|ref|YP_003725987.1|  9 KCGYCGACVGVCPEGALELVETFIEADN------KCTGCGLCAKICPVGAI 53
                                      7999************998887777776......6*************997 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   3.1   3.9e-06    0.0037       5      22 .]       5      22 ..       3      22 .. 0.90
   2 !   20.5   2.3   3.6e-07   0.00034       8      21 ..      36      49 ..      30      50 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.9e-06
                            Fer4_2  5 vdtdrCigCgaCvsaCPa 22
                                      v++ +C  CgaCv +CP+
  gi|298674237|ref|YP_003725987.1|  5 VNRYKCGYCGACVGVCPE 22
                                      57889************5 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 3.6e-07
                            Fer4_2  8 drCigCgaCvsaCP 21
                                      ++C+gCg C + CP
  gi|298674237|ref|YP_003725987.1| 36 NKCTGCGLCAKICP 49
                                      59************ PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   7.1   0.00013      0.12       3      15 .]      12      24 ..       9      24 .. 0.87
   2 !   20.7   6.1   5.7e-07   0.00054       1      15 []      38      52 ..      38      52 .. 0.99

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00013
                            Fer4_3  3 gCgaCvevCPvgA 15
                                       CgaCv vCP+gA
  gi|298674237|ref|YP_003725987.1| 12 YCGACVGVCPEGA 24
                                      499*********9 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 5.7e-07
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      CtgCg+C + CPvgA
  gi|298674237|ref|YP_003725987.1| 38 CTGCGLCAKICPVGA 52
                                      **************9 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   2.3   0.00059      0.56       7      16 ..      13      22 ..       8      28 .. 0.90
   2 !   20.1   3.1   6.6e-07   0.00062       2      17 .]      36      51 ..      35      51 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00059
                            Fer4_4  7 CgsCvaaCPq 16
                                      Cg+Cv +CP 
  gi|298674237|ref|YP_003725987.1| 13 CGACVGVCPE 22
                                      *********6 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 6.6e-07
                            Fer4_4  2 erCigCgsCvaaCPqg 17
                                      ++C+gCg C  +CP+g
  gi|298674237|ref|YP_003725987.1| 36 NKCTGCGLCAKICPVG 51
                                      79************86 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   3.1   0.00014      0.13      49      64 ..       8      23 ..       4      24 .. 0.76
   2 !   17.3   2.5   5.3e-06     0.005       3      17 ..      36      50 ..      25      53 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00014
                            Fer4_8 49 wsCttcgaCtevCpvg 64
                                      ++C  cgaC+ vCp+g
  gi|298674237|ref|YP_003725987.1|  8 YKCGYCGACVGVCPEG 23
                                      6788888888888875 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 5.3e-06
                            Fer4_8  3 ekCieCgaCqsaCpv 17
                                      +kC++Cg+C + Cpv
  gi|298674237|ref|YP_003725987.1| 36 NKCTGCGLCAKICPV 50
                                      356666666666655 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.7   0.00015      0.14       1      18 [.       5      22 ..       5      23 .. 0.95
   2 !   15.0   1.9   2.8e-05     0.026       2      17 ..      35      49 ..      32      55 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00015
                           Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                      V+r +C  cgaCv ++P+
  gi|298674237|ref|YP_003725987.1|  5 VNRYKCGYCGACVGVCPE 22
                                      8999*************8 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.8e-05
                           Fer4_13  2 DrdtCiacgaCvelaP 17
                                      D ++C++cg+C++++P
  gi|298674237|ref|YP_003725987.1| 35 D-NKCTGCGLCAKICP 49
                                      5.89***********9 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   2.6   0.00081      0.77      45      58 ..       9      22 ..       4      25 .. 0.62
   2 !   10.9   2.2   0.00053       0.5       1      15 [.       9      23 ..       9      35 .. 0.74
   3 !   16.0   2.0   1.4e-05     0.013      44      58 ..      36      50 ..      23      53 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00081
                           Fer4_17 45 lCieCgeCerkCPq 58
                                      +C  Cg C+ +CP+
  gi|298674237|ref|YP_003725987.1|  9 KCGYCGACVGVCPE 22
                                      45555555555555 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00053
                           Fer4_17  1 rCiqCgyClpeCpsy 15
                                      +C  Cg+C+ +Cp +
  gi|298674237|ref|YP_003725987.1|  9 KCGYCGACVGVCPEG 23
                                      477777777777765 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 1.4e-05
                           Fer4_17 44 slCieCgeCerkCPq 58
                                      ++C++Cg+C++ CP 
  gi|298674237|ref|YP_003725987.1| 36 NKCTGCGLCAKICPV 50
                                      567777777777764 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   1.0   0.00019      0.18       1      20 [.       3      22 ..       3      35 .. 0.89
   2 !    8.2   5.7    0.0045       4.3       6      19 ..      36      49 ..      30      50 .. 0.88
   3 ?    7.0   0.1     0.011        10      56      66 .]      45      55 ..      45      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00019
                           Fer4_15  1 VvvDrdaCigcglCvaeape 20
                                      + v+r +C  cg+Cv ++pe
  gi|298674237|ref|YP_003725987.1|  3 INVNRYKCGYCGACVGVCPE 22
                                      6799**************97 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0045
                           Fer4_15  6 daCigcglCvaeap 19
                                      ++C+gcglC++ +p
  gi|298674237|ref|YP_003725987.1| 36 NKCTGCGLCAKICP 49
                                      68*********998 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.011
                           Fer4_15 56 araCPvdAIrv 66
                                      a+ CPv+AI+v
  gi|298674237|ref|YP_003725987.1| 45 AKICPVGAIEV 55
                                      678******97 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   1.9    0.0012       1.1      59      74 ..       8      23 ..       2      27 .. 0.85
   2 !   13.3   1.8   7.8e-05     0.073      56      74 ..      33      51 ..      24      56 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0012
                           Fer4_18 59 gdcidcescvkvcPtg 74
                                       +c  c++cv vcP g
  gi|298674237|ref|YP_003725987.1|  8 YKCGYCGACVGVCPEG 23
                                      57999*********86 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 7.8e-05
                           Fer4_18 56 kgagdcidcescvkvcPtg 74
                                      +++++c+ c+ c k+cP+g
  gi|298674237|ref|YP_003725987.1| 33 EADNKCTGCGLCAKICPVG 51
                                      67899************97 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   4.1     0.027        26      78      94 ..       6      22 ..       1      25 [. 0.66
   2 ?    5.4   3.5     0.037        34       1      14 [.       9      22 ..       9      35 .. 0.83
   3 ?   13.9   2.8     8e-05     0.075      78      95 ..      34      51 ..      23      52 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.027
                           Fer4_22 78 gesgCvGCgRCieacpv 94
                                      ++++C  Cg C+ +cp+
  gi|298674237|ref|YP_003725987.1|  6 NRYKCGYCGACVGVCPE 22
                                      56666667777666665 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.037
                           Fer4_22  1 rClsCgaCtlvCpt 14
                                      +C  CgaC  vCp 
  gi|298674237|ref|YP_003725987.1|  9 KCGYCGACVGVCPE 22
                                      68889999999985 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 8e-05
                           Fer4_22 78 gesgCvGCgRCieacpvk 95
                                        ++C+GCg C + cpv+
  gi|298674237|ref|YP_003725987.1| 34 ADNKCTGCGLCAKICPVG 51
                                      4678***********985 PP

>> Fer4_19  Divergent 4Fe-4S mono-cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.3      0.45   4.3e+02       7      22 ..       2      17 ..       1      19 [. 0.87
   2 ?    8.4   0.2    0.0023       2.2      50      63 ..      16      29 ..      11      30 .. 0.87
   3 ?    0.4   0.5      0.77   7.2e+02      12      23 ..      35      46 ..      31      47 .. 0.82
   4 ?    5.6   0.1     0.017        16      51      63 ..      45      57 .]      42      57 .] 0.86

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.45
                           Fer4_19  7 tiednrelCihsgnCv 22
                                       i  nr  C   g Cv
  gi|298674237|ref|YP_003725987.1|  2 SINVNRYKCGYCGACV 17
                                      688999****99*998 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0023
                           Fer4_19 50 vverCPSGALsyve 63
                                       v  CP GAL++ve
  gi|298674237|ref|YP_003725987.1| 16 CVGVCPEGALELVE 29
                                      6889*******997 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.77
                           Fer4_19 12 relCihsgnCvk 23
                                       + C++ g C k
  gi|298674237|ref|YP_003725987.1| 35 DNKCTGCGLCAK 46
                                      578*******87 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.017
                           Fer4_19 51 verCPSGALsyve 63
                                      ++ CP GA+++v+
  gi|298674237|ref|YP_003725987.1| 45 AKICPVGAIEVVR 57
                                      578******9985 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   5.4   6.8e-05     0.064       6      27 ..       7      28 ..       3      28 .. 0.92
   2 ?    1.5   3.9      0.25   2.4e+02       8      24 ..      37      53 ..      35      56 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.8e-05
                                      EEE-TTT--EEEECC--SS-EE CS
                   Desulfoferrod_N  6 vYkCevCGniVeVleaGgGeLV 27
                                       YkC  CG  V V  +G+ eLV
  gi|298674237|ref|YP_003725987.1|  7 RYKCGYCGACVGVCPEGALELV 28
                                      6*****************9998 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.25
                                      E-TTT--EEEECC--SS CS
                   Desulfoferrod_N  8 kCevCGniVeVleaGgG 24
                                      kC+ CG   ++  +G+ 
  gi|298674237|ref|YP_003725987.1| 37 KCTGCGLCAKICPVGAI 53
                                      9*****99998888875 PP

>> zf-C2H2_11  zinc-finger C2H2-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.9     0.023        22       5      13 ..       8      16 ..       4      17 .. 0.84
   2 ?    7.3   1.2    0.0041       3.9       6      13 ..      37      44 ..      33      45 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.023
                        zf-C2H2_11  5 cqCleCGlc 13
                                      ++C  CG c
  gi|298674237|ref|YP_003725987.1|  8 YKCGYCGAC 16
                                      79*****99 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0041
                        zf-C2H2_11  6 qCleCGlc 13
                                      +C+ CGlc
  gi|298674237|ref|YP_003725987.1| 37 KCTGCGLC 44
                                      8******* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 458.64
//
Query:       gi|298674238|ref|YP_003725988.1|  [L=207]
Description: 2-phospho-L-lactate guanylyltransferase CofC [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.4e-52  176.8   3.1      4e-52  176.5   3.1    1.0  1  CofC          Guanylyl transferase CofC like
    1.6e-05   25.3   0.0      2e-05   25.0   0.0    1.1  1  NTP_transf_3  MobA-like NTP transferase domain
  ------ inclusion threshold ------
      0.045   13.6   0.0      0.072   12.9   0.0    1.3  1  DUF2064       Uncharacterized protein conserved in bacteria (


Domain annotation for each model (and alignments):
>> CofC  Guanylyl transferase CofC like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.5   3.1   6.7e-56     4e-52       1     200 [.       1     196 [.       1     205 [. 0.92

  Alignments for each domain:
  == domain 1  score: 176.5 bits;  conditional E-value: 6.7e-56
                              CofC   1 mkviiPvsainsaktrlseilseeerkellkamlldvidalkrldvlvvsedeevleyaldelgvevvkekekdlnt 77 
                                       m+++iP+++ + ak+rls++l+ +er+e++  ml+dv+++l+  ++  +       ++  d+l+v+v+  + ++ln+
  gi|298674238|ref|YP_003725988.1|   1 MRAVIPYKKTK-AKSRLSSVLTLKEREEFVESMLKDVVNTLSDAQIKNIDVLTTTSNSIPDNLDVKVITSE-HGLNE 75 
                                       899*****988.******************************9999999999999999999********99.9**** PP

                              CofC  78 avekafeeieekeviiipsdiPlikkedvkdllelekradvviaPargGGtnllllr.ksalevkyedfsflkhlee 153
                                       a++  + +i +++v+ii++d+Pl+k +++ d+++++k  dvvi P++gGGtn+l+l+ ++ + vky + sfl h + 
  gi|298674238|ref|YP_003725988.1|  76 AINSYLKNI-QEPVLIIMADLPLVKSNHITDIINTKK--DVVIVPGKGGGTNILYLKkPEKFTVKYYGSSFLTHCNI 149
                                       ***997755.679**********************99..*****************9889***************** PP

                              CofC 154 arkrglkvkiydsfylsvdinteedlgeillhGegtkakeyl.rklgf 200
                                       a+k    v+iydsf+ s di++++dl eillhG+g   ++y+ +k+ +
  gi|298674238|ref|YP_003725988.1| 150 AKKNLNAVEIYDSFLASTDIDEPHDLVEILLHGQGLS-RKYIeKKFEI 196
                                       ***9999***************************975.5565144444 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   3.3e-09     2e-05      24     127 ..      30     122 ..      17     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 3.3e-09
                                       CCHHHHHHHHHCTT.-CEEEEECSH.CHHHHHHTTCTS-EEE-TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT- CS
                      NTP_transf_3  24 kpllervldalraagvdevvvvggd.eevlaalarlgvrvvededpgkgplaslaaalraaadadavlvlacDmPll 99 
                                       +++l+ v+++l++a+++++ v +   +++    + l+v+v++ e    g  +++ + l+++  +++vl++++D+Pl+
  gi|298674238|ref|YP_003725988.1|  30 ESMLKDVVNTLSDAQIKNIDVLTTTsNSIP---DNLDVKVITSE---HGLNEAINSYLKNI--QEPVLIIMADLPLV 98 
                                       489****************99987724555...5789******8...7***********98..7************* PP

                                       -HHHHHHHHHCHHHHTSSEEEEESSSEE CS
                      NTP_transf_3 100 tpelverllaaaaasgadvvvptyeger 127
                                       +++++  +++     ++ v+vp   g  
  gi|298674238|ref|YP_003725988.1|  99 KSNHITDIINTK---KDVVIVPGKGG-G 122
                                       *********973...34445554444.3 PP

>> DUF2064  Uncharacterized protein conserved in bacteria (DUF2064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.2e-05     0.072      49     108 ..      73     130 ..      68     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.2e-05
                                       HHHHHHHHHHTT-SEEEEE-SS-TT--HHHHHHHHHHTTT-SEEEEEBTTSSEEEEEEEG CS
                           DUF2064  49 larafdrafeageepvlliGsDcpqltaalleqAfeaLeeadaVlgpaeDGGYyllGlkk 108
                                       l++a+++ +++  epvl+i +D+p ++++++ + +++  ++d+V+ p + GG  +l lkk
  gi|298674238|ref|YP_003725988.1|  73 LNEAINSYLKNIQEPVLIIMADLPLVKSNHITDIINT--KKDVVIVPGKGGGTNILYLKK 130
                                       66677777555666********************995..89***********98888884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       916  (0.0510904); expected 358.6 (0.02)
Passed bias filter:                      630  (0.0351386); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1427.74
//
Query:       gi|298674239|ref|YP_003725989.1|  [L=363]
Description: 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.6e-15   56.1   0.1    8.1e-15   55.6   0.1    1.3  1  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
      0.039   14.1   0.4       0.09   12.9   0.4    1.6  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   0.1     9e-19   8.1e-15       1     164 [.      61     230 ..      61     233 .. 0.90

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 9e-19
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavp 76 
                                       +++t+ C + C fCa++    + + g++ s+ ei e+vk        ++ +i+gg   +++ df++ +++ +k++ p
  gi|298674239|ref|YP_003725989.1|  61 INFTNQCEGTCGFCAFRN---SSESGYIYSINEITEKVKDE-TGLYlTEICIQGGLLQDVDIDFYKNILESVKKEAP 133
                                       689**************8...7******************9.67777***************************99* PP

                                       TEEEEEEECSSCHG.........HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTS CS
                                       xxxxxxxxxxxxxx.........xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  77 giritvetngtlpd.........eeklerllelg.vdrvslgleaaddekvlklmn.rghtfeevlealeklreagi 142
                                       +i+i+  ++              ++ l++l++ g        +e+++d+ v+++++ ++ t +e++++++++++ gi
  gi|298674239|ref|YP_003725989.1| 134 DIHIHAFSPMEIYHlskinnlsvKKTLQELKNSGlDSMPGTAAEILSDR-VREIICpDKLTTDEWINVVKLAHKTGI 209
                                       ******9999998899******************555556666777776.*************************** PP

                                       ETEEEEEEEBTTTSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 143 krvvdrivglpGendeeleell 164
                                       + ++++++ ++ e+ ee+ +++
  gi|298674239|ref|YP_003725989.1| 210 P-TTSTMMYGHIETLEERIDHI 230
                                       *.78888888889999887765 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.4     1e-05      0.09       5     108 ..      64     160 ..      61     168 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1e-05
                           Fer4_14   5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellk.lvkrlkeeype 80 
                                       +++C+  C +C  ++  +se+g +++ +++ + +kd +  +    ++ + GG  L+   + +++k +++ +k+e p+
  gi|298674239|ref|YP_003725989.1|  64 TNQCEGTCGFCAFRN--SSESGYIYSINEITEKVKDETGLYL--TEICIQGG--LLQDVDIDFYKnILESVKKEAPD 134
                                       699*********999..8899999999999999966666666..88******..5555666665438999999**99 PP

                           Fer4_14  81 kkiwletngtleielektpdlkekleal 108
                                       ++i+  +   +  +l k+++l +++++l
  gi|298674239|ref|YP_003725989.1| 135 IHIHAFSPMEIY-HLSKINNL-SVKKTL 160
                                       999998877666.33333333.444455 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2560.79
//
Query:       gi|298674240|ref|YP_003725990.1|  [L=330]
Description: 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.1e-15   55.6   0.0    1.7e-14   54.5   0.0    1.6  1  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   0.0   9.6e-19   1.7e-14       1     166 [.      15     187 ..      15     188 .. 0.85

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 9.6e-19
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpg 77 
                                       ++vt+ C++rC +C ++++  + + ++ +sv+ei+ ++k++ +e g+ e +++ ge     +++++++ ++    + 
  gi|298674240|ref|YP_003725990.1|  15 IPVTNICRNRCGYCGFRRD-PDDPQAQLMSVDEIIPILKKG-YESGCTEALFTFGESAEEVPEYRYWLYEMGYS-ST 88 
                                       689***************8.*********************.79999999999888888866666666666664.55 PP

                                       EEEEEEECSSCHG.............HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  78 iritvetngtlpd.............eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreag 141
                                       ++ ++e ++t +d             +++l  l++l+   + l le++++ + ++   +g+ +e+++e+++++ ++ 
  gi|298674240|ref|YP_003725990.1|  89 VEYVMELCETAIDngllphtnagvldKKQLTMLKPLN-ASMGLMLETISKLDAHENS-PGKIPEKRIETIKLAGQLK 163
                                       55555555555555555555555555***********.************9999999.******************* PP

                                       SETEEEEEEEBTTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 142 ikrvvdrivglpGendeeleellel 166
                                       i+  +++i+++ Ge+   + e l++
  gi|298674240|ref|YP_003725990.1| 164 IP-FTTGILVGIGETANNRIESLNE 187
                                       **.*************999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2412.06
//
Query:       gi|298674241|ref|YP_003725991.1|  [L=426]
Description: FAD dependent oxidoreductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.3e-21   75.0   0.0    9.5e-21   74.6   0.0    1.1  1  Amino_oxidase  Flavin containing amine oxidoreductase
    1.4e-12   47.7   0.1    3.2e-12   46.5   0.1    1.7  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    9.4e-09   34.9   0.1     0.0017   17.7   0.0    3.2  3  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    6.4e-07   28.8   0.0    0.00037   19.7   0.0    2.8  3  FAD_binding_2  FAD binding domain
      1e-05   25.3   0.3    0.00017   21.3   0.3    2.1  1  DAO            FAD dependent oxidoreductase
    4.1e-05   24.1   1.9       0.12   13.0   0.1    3.0  3  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    0.00097   17.9   0.0       0.09   11.5   0.0    2.3  2  HI0933_like    HI0933-like protein
     0.0065   15.9   0.0      0.037   13.4   0.0    1.9  2  FAD_oxidored   FAD dependent oxidoreductase
     0.0087   14.9   0.0      0.015   14.2   0.0    1.4  1  MCRA           MCRA family
  ------ inclusion threshold ------
      0.066   12.5   0.1       0.15   11.2   0.1    1.6  2  FAD_binding_3  FAD binding domain
      0.078   12.0   0.6       0.41    9.7   0.0    2.1  2  GIDA           Glucose inhibited division protein A
        0.1   11.8   0.3       0.77    9.0   0.1    2.2  2  Thi4           Thi4 family


Domain annotation for each model (and alignments):
>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.6   0.0   6.3e-24   9.5e-21       2     432 ..      11     404 ..      10     413 .. 0.82

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 6.3e-24
                                       HHHHHHHHHHHTTEEEEEEESSSSSBTTS-EEEETTEEEESS--EEET..TTHHHHHHHHHTTCCCCEEEESCCGCE CS
                     Amino_oxidase   2 aGLaaArqLlsaGfdVtvlEardrvGGRirtvrsdGylielGamwftg..agnpllellkelgledslslpdpgapk 76 
                                        GL  A +L+  G+dV v+Ea + +GGR   +  +G+++ +Ga  + +  +  pl ++lk+l+ + + ++++p+ + 
  gi|298674241|ref|YP_003725991.1|  11 GGLLSAAYLAKSGHDVEVFEALPFTGGRFTNIDYKGFKLSTGALHMVPhgDSGPLSQMLKKLNADVNIVTSNPSSVI 87 
                                       7******************************************9999999999**************9999999666 PP

                                       EEEETTEECCTTEECHHHHHHHHHHHHHHHH..CHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCHHHHHHHHH CS
                     Amino_oxidase  77 rvlskggrefpgdlspvpaewealleqgals..aellsleeklrlgleallqktldeldldskslaesleelgrrep 151
                                       r+        + + ++  ++++++++    +  + ++sl  +++ ++ a++     ++++++++++++  +++++e 
  gi|298674241|ref|YP_003725991.1|  88 RMPA------NDNDTDYKNGFRDMAF----HdfKVPFSLINRIKIAFLAFT---TKYFPPKKGTFDDW-IKHHINEK 150
                                       6666......5666666666777777....334468999***********9...99999999999999.45555555 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHCHTSTTTTCBHHHHTCCCCHHHHHTSCCCEETTHTHHHHHHHHH..TTTTEEEE CS
                     Amino_oxidase 152 gdvevwdrliepelfaklefasglfagdpselsaklalpllwelegfggslllprgGlsqlpealae..elrgldir 226
                                        +    +r+ +        f++     + s+ sak  +   ++l  ++g+  +p+gG + + +al e  ++ g++i 
  gi|298674241|ref|YP_003725991.1| 151 WA----TRIANS-------FCGWSISLKSSDVSAKEVFEIISNLYRYSGP-GVPTGGCKGITNALVEiiQENGGKIY 215
                                       55....677775.......8888888888*********************.889*********************** PP

                                       TSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S-HHHHH....SSEEES..CCSH..HHHHHHHHSEEEEEEEEEE CS
                     Amino_oxidase 227 lntrVkeikregdgvtvtledgevveaDaVvvTvplgvlk....ailfsP..plpd..ekaeairnlgfgsvnkvil 295
                                       ++++V+ei ++++  +  + dg+++  D +++  ++g++         +   +  +  +  + ++n+++   +k+ l
  gi|298674241|ref|YP_003725991.1| 216 TGKEVTEIITSNNHAKGVVADGDKYYSDLIIS--DIGHIEtnrlC---KNvtETEEyvQYKNQLQNIKSSAGIKISL 287
                                       **************9999***********996..77777753441...3333232245888899************* PP

                                       EESSGGSGCSTSECECECCCEEETTTEEEEECC.ECCCSTTTEEEEEEEEECHHHHHHHTTS-HHHHHHHHHHHHHH CS
                     Amino_oxidase 296 efdrkfwednalgqgvlvseltttlgeafissd.fpsrappgkglvllvyvggdaaneleslsdeelvqavlrdLrk 371
                                       + d++   +     gv ++  ++  + +   ++     ap+gk+lv+++    +++++    + ee ++  l+d+r 
  gi|298674241|ref|YP_003725991.1| 288 ACDEPLIGHG----GVVLTPYSKRIDGMNEVTNvDKTLAPEGKHLVMTHQCL-RWDRLD---DIEEEIELGLQDIRD 356
                                       ******5542....345555555555555555559999*******8888777.666666...88************* PP

                                       HHTGTSSTCSEEEEEECCTETTTSSSEEE.BTTHHHHHHHHHHCHHCSTTEEE.SGGGCTT CS
                     Amino_oxidase 372 lfgeevpepkatlvtrWhtdplargsysyvsvgpghedydplakpegdprlffAGehtsre 432
                                       +f  + ++++   v  +h d ++        v+ +    d ++k+ ++++l++ G+    +
  gi|298674241|ref|YP_003725991.1| 357 IFL-NKDYEVL-MVQSYH-DGWP--------VNRSASSQDLSNKT-PISNLYVVGDGAK-G 404
                                       *99.6666665.666687.****........77788888999999.9********9855.3 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.1   2.1e-15   3.2e-12       1      68 []       5      72 ..       5      72 .. 0.97

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 2.1e-15
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECETTCEECTS---EEETTHHHHCHHHHCCC CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyevpgvrvdygahifhgsgyypnvrrllrel 68
                                      +vG+Gl+Gl+ A++Lak g+dv+++e+ + +GGr + ++++g+++ +ga  + + g++  ++++l++l
  gi|298674241|ref|YP_003725991.1|  5 VVGSGLGGLLSAAYLAKSGHDVEVFEALPFTGGRFTNIDYKGFKLSTGALHMVPHGDSGPLSQMLKKL 72
                                      8************************************************99999999*******9986 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.1e-06    0.0017       2      72 ..       2      81 ..       1     101 [. 0.76
   2 !   11.5   0.0   8.3e-05      0.12     183     244 ..     197     258 ..     136     321 .. 0.80
   3 ?    2.1   0.0     0.062        93     260     284 ..     384     408 ..     367     410 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.1e-06
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEE.......TTHCHHHCSHHHHCHHHHHHHHHHHHH..HHHHCHHHHCCCCH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlve.......legtclnggcllskallgvaedaeias..evvkklnqgielll 71
                                      + +v+G+G +Gl  a +la++g++v ++e       + +++ + g  ls+ +l++  +++     + +kkln+++  ++
  gi|298674241|ref|YP_003725991.1|  2 KTIVVGSGLGGLLSAAYLAKSGHDVEVFEalpftggRFTNIDYKGFKLSTGALHMVPHGDSGPlsQMLKKLNADVNIVT 80
                                      789*************************888885566666667777777777777777765557766666777666655 PP

                                      C CS
                                      x RF
                       Pyr_redox_2 72 g 72
                                       
  gi|298674241|ref|YP_003725991.1| 81 S 81
                                      5 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 8.3e-05
                                       HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 183 kelsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpstell 244
                                       k +++al e ++++G ++++g++v+ei+  +++++ v  dg+++  dl++  +G    ++l 
  gi|298674241|ref|YP_003725991.1| 197 KGITNALVEIIQENGGKIYTGKEVTEIITSNNHAKGVVADGDKYYSDLIISDIGHIETNRLC 258
                                       78999999********************9999888999****************98877775 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.062
                                       --TTSBESSTTEEE-GGGCTECCSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 260 vdeflrtnvpgiyaiGDvaggkggp 284
                                        d + +t + ++y++GD a+g+gg+
  gi|298674241|ref|YP_003725991.1| 384 QDLSNKTPISNLYVVGDGAKGEGGI 408
                                       56677999**********9776665 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   2.5e-07   0.00037       3      36 ..       4      37 ..       2      50 .. 0.93
   2 !    5.5   0.0    0.0049       7.3     138     186 ..     194     242 ..     174     297 .. 0.74
   3 ?   -0.8   0.0       0.4     6e+02     378     402 ..     377     402 ..     341     413 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.5e-07
                                      EEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                     FAD_binding_2  3 iViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                                      iV+GsGl+GL +A+ +a+ G++v v e  + +gg
  gi|298674241|ref|YP_003725991.1|  4 IVVGSGLGGLLSAAYLAKSGHDVEVFEALPFTGG 37
                                      9***************************999988 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0049
                                       .HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTC CS
                     FAD_binding_2 138 vtghallarlvesarkagvdfqerteadeLivedgrvtGavvenpesgr 186
                                       +  +++  +lve ++++g ++++  e++e+i+ ++++ G+v+  ++  +
  gi|298674241|ref|YP_003725991.1| 194 GGCKGITNALVEIIQENGGKIYTGKEVTEIITSNNHAKGVVADGDKYYS 242
                                       566889999********************************98763333 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.4
                                       BETTSBE.STTEEESSBTEEE-STCE CS
                     FAD_binding_2 378 tdengrv.ldadgqpipGLYAaGeva 402
                                       ++ ++   + ++++pi++LY +G  a
  gi|298674241|ref|YP_003725991.1| 377 VNRSASSqDLSNKTPISNLYVVGDGA 402
                                       55555554567899********9877 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.3   1.2e-07   0.00017       2     190 ..       3     239 ..       2     371 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.2e-07
                                       EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHH.H.HHHHHHHHH CS
                               DAO   2 vviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslea.l.eelreleee 74 
                                        +++G+G  Gl  A +La+ g  V ++e+ ++ g    gr + + + g+     a  +++    + l ++l++l+++
  gi|298674241|ref|YP_003725991.1|   3 TIVVGSGLGGLLSAAYLAKSGhdVEVFEALPFTG----GRFTNIDYKGFKLSTGALHMVPHGDSGpLsQMLKKLNAD 75 
                                       69*****************999*******97777....888877777775333334566777776434566999999 PP

                                       HSSTTSEEEEEEEEEESS....................................................HHHHHHH CS
                               DAO  75 lgididyrrtGllslaad....................................................eeeleal 99 
                                        +i +   ++ ++ + a+                                                    ++  e++
  gi|298674241|ref|YP_003725991.1|  76 VNI-VTSNPSSVIRMPANdndtdykngfrdmafhdfkvpfslinrikiaflafttkyfppkkgtfddwikHHINEKW 151
                                       887.6677788888876534444555555555555555555555555555555555555555555555543334444 PP

                                       HHHHHHH..HHTTT..TEEEEEHHHHHHHSTTSTTTSEEEEETTEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEE CS
                               DAO 100 dkllall..leagl..daelldaeevrelepalpgllgalfypdtgqvdpakltaalaraaealGveilegtevtgl 172
                                       + ++a+   + + +  +++ ++a+ev e+ ++l ++  + ++p++g+      t+al + ++++G++i++g evt++
  gi|298674241|ref|YP_003725991.1| 152 ATRIANSfcG-WSIslKSSDVSAKEVFEIISNLYRY-SGPGVPTGGC---KGITNALVEIIQENGGKIYTGKEVTEI 223
                                       4666665662.4442144457887788888754243.66899**998...**************************9 PP

                                       EEEETCEEEEEEECTEEE CS
                               DAO 173 eeedgkvwgverttpgen 190
                                          ++ ++gv  +++g +
  gi|298674241|ref|YP_003725991.1| 224 ITSNNHAKGV--VADGDK 239
                                       6666677888..333554 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.1     8e-05      0.12       2      32 ..       3      33 ..       2      43 .. 0.91
   2 ?   -1.3   0.0       2.2   3.3e+03      16      33 ..      67      84 ..      65      95 .. 0.80
   3 !    9.0   0.3    0.0014       2.1      42      78 ..     199     235 ..     197     239 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8e-05
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversd 32
                                       +vvG+G+ gl  A++la+ g++V v+e+ +
  gi|298674241|ref|YP_003725991.1|  3 TIVVGSGLGGLLSAAYLAKSGHDVEVFEALP 33
                                      79*************************9875 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.2
                                      HHHHHTTSEEEEEESSSS CS
                         Pyr_redox 16 galaelgkkVtvversdk 33
                                      ++l++l+++V +v  ++ 
  gi|298674241|ref|YP_003725991.1| 67 QMLKKLNADVNIVTSNPS 84
                                      789999999999987765 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0014
                                       HHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEE CS
                         Pyr_redox  42 askilqeklekngievllntkveeiegsedgvesvkl 78 
                                       + ++l e +++ng +++++++v+ei +s++  ++v+ 
  gi|298674241|ref|YP_003725991.1| 199 ITNALVEIIQENGGKIYTGKEVTEIITSNNHAKGVVA 235
                                       67889999******************99999888876 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0     6e-05      0.09       2      34 ..       2      34 ..       1      41 [. 0.89
   2 ?    4.1   0.0     0.011        16     109     159 ..     197     246 ..     192     253 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6e-05
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakk 34
                                      ++iv+G G  Gl+ A+ +ak g++V ++e+ + 
  gi|298674241|ref|YP_003725991.1|  2 KTIVVGSGLGGLLSAAYLAKSGHDVEVFEALPF 34
                                      68***************************8765 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEE CS
                       HI0933_like 109 edivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklv 159
                                       + i +al++ ++e+g k+++ +ev+++ ++++++  v + +++++ +d ++
  gi|298674241|ref|YP_003725991.1| 197 KGITNALVEIIQENGGKIYTGKEVTEIITSNNHAKGVVA-DGDKYYSDLII 246
                                       66899**********************999999888888.77777666554 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   2.5e-05     0.037       3      40 ..       4      41 ..       3      43 .. 0.97
   2 ?   -0.3   0.0      0.34   5.1e+02      89     125 ..     199     235 ..     146     245 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.5e-05
                      FAD_oxidored  3 vVvGGgpaGvaAAiaAaraGakvlLveergvlGGllts 40
                                      +VvG+g++G+  A   a++G  v + e  ++ GG +t+
  gi|298674241|ref|YP_003725991.1|  4 IVVGSGLGGLLSAAYLAKSGHDVEVFEALPFTGGRFTN 41
                                      7*********************************9996 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.34
                      FAD_oxidored  89 akavleemlaeagvtvllntrlvevekegkriesvtv 125
                                        +++l e+++e+g +++++++++e++++++  ++v++
  gi|298674241|ref|YP_003725991.1| 199 ITNALVEIIQENGGKIYTGKEVTEIITSNNHAKGVVA 235
                                       4567778889*****************9989999987 PP

>> MCRA  MCRA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   9.7e-06     0.015       4      66 ..       3      60 ..       1     128 [. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.7e-06
                                      EEEE--SHHHHHHHHHHHHTT---GGGEEEE-SS-----------------CCC----B.-TT- CS
                              MCRA  4 aylvGsGiasLaaAvyLirdakvpgenihileelkvaggsldgagdpekGyvlrggrel.eehy 66
                                        +vGsG+++L +A+yL +     g+++ ++e+l+ +gg +++++   kG+ l +g     +h+
  gi|298674241|ref|YP_003725991.1|  3 TIVVGSGLGGLLSAAYLAKS----GHDVEVFEALPFTGGRFTNIDY--KGFKLSTGALHmVPHG 60
                                      678**************986....679*************999765..6899888875436554 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1    0.0001      0.15       3      31 ..       2      30 ..       1      35 [. 0.89
   2 ?   -3.1   0.0       2.4   3.6e+03     108     144 ..     200     236 ..     196     239 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0001
                                      EEEEE--SHHHHHHHHHHHHTTHHEEEEE CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlve 31
                                      ++++VG+G+ Gl++a  L++ G +v + e
  gi|298674241|ref|YP_003725991.1|  2 KTIVVGSGLGGLLSAAYLAKSGHDVEVFE 30
                                      679*******************9998776 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.4
                                       HHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEE CS
                     FAD_binding_3 108 eriLvehaeerglqvrfktevesleqdeegvtaevrd 144
                                       +++Lve  +e g +++ ++ev+ +   +++ + +v d
  gi|298674241|ref|YP_003725991.1| 200 TNALVEIIQENGGKIYTGKEVTEIITSNNHAKGVVAD 236
                                       6789999999999999999998887777777666655 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00027      0.41       2      28 ..       3      29 ..       2      59 .. 0.87
   2 ?    0.3   0.1       0.2     3e+02     116     140 ..     218     242 ..     201     272 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00027
                                      EEEE-SSHHHHHHHHHHHHTT--EEEE CS
                              GIDA  2 viViGgGhAGceAAlaaarlGakvlLi 28
                                       iV+G G+ G+  A+ +a++G++v  +
  gi|298674241|ref|YP_003725991.1|  3 TIVVGSGLGGLLSAAYLAKSGHDVEVF 29
                                      69**********************987 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.2
                                       S-EEEEEECTTEEEEEEETTS-EEE CS
                              GIDA 116 eeveeliveekkvkgvvtedgetik 140
                                       +ev+e+i+++++ kgvv + +++++
  gi|298674241|ref|YP_003725991.1| 218 KEVTEIITSNNHAKGVVADGDKYYS 242
                                       6899999999999999988777665 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   0.00051      0.77      20      56 ..       3      37 ..       1      41 [. 0.83
   2 ?    0.3   0.0      0.23   3.4e+02     104     138 ..     203     236 ..     195     281 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00051
                                      EEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TT CS
                              Thi4 20 vvivGaGssGLtaayylakkpdlkvailersvspGGG 56
                                       ++vG+G  GL +a ylak+ +  v ++e+ + + GG
  gi|298674241|ref|YP_003725991.1|  3 TIVVGSGLGGLLSAAYLAKS-GHDVEVFEA-LPFTGG 37
                                      69******************.999999997.444444 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.23
                                       HHHHHTSTTEEEEESEEEEEEEEETBTEEEEEEEE CS
                              Thi4 104 lskvlqlanvkllnavaveDlivregegvaGvvin 138
                                       l++++q  + k++++  v ++i+ + +  +Gvv +
  gi|298674241|ref|YP_003725991.1| 203 LVEIIQENGGKIYTGKEVTEIITSN-NHAKGVVAD 236
                                       4566777777777777777777777.677777754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 2660.32
//
Query:       gi|298674242|ref|YP_003725992.1|  [L=52]
Description: 4Fe-4S ferredoxin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-12   46.4  13.9    2.8e-07   30.1   4.2    2.1  2  Fer4      4Fe-4S binding domain
    1.7e-08   34.4  13.1    2.4e-08   34.0  13.1    1.2  1  Fer4_21   4Fe-4S dicluster domain
    1.1e-07   32.4  13.5    2.2e-05   25.0  14.2    2.0  1  Fer4_7    4Fe-4S dicluster domain
    2.9e-07   30.5  13.9    0.00016   21.9   3.1    2.1  2  Fer4_4    4Fe-4S binding domain
    1.6e-06   27.8  12.4     0.0012   18.8   2.1    2.1  2  Fer4_2    4Fe-4S binding domain
    5.9e-06   26.3  15.4     0.0025   18.0   4.7    2.0  2  Fer4_9    4Fe-4S dicluster domain
    1.1e-05   26.3  13.1      0.013   16.4   3.0    2.0  2  Fer4_16   4Fe-4S double cluster binding domain
    1.6e-05   24.8  15.4    0.00063   19.7   5.3    2.1  2  Fer4_6    4Fe-4S binding domain
     0.0011   19.5  15.3      0.035   14.6   3.4    2.0  2  Fer4_17   4Fe-4S dicluster domain
     0.0017   18.8  15.5        4.9    7.7  15.5    2.0  1  Fer4_8    4Fe-4S dicluster domain
     0.0021   18.1  16.3      0.015   15.4  16.9    1.8  2  Fer4_10   4Fe-4S dicluster domain
     0.0079   17.1  16.3       0.37   11.9   5.8    2.2  2  Fer4_3    4Fe-4S binding domain
     0.0086   16.9  10.8      0.063   14.1   2.8    2.1  2  Fer4_22   4Fe-4S dicluster domain
  ------ inclusion threshold ------
        0.1   13.2  15.7       0.34   11.5   3.9    2.3  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
        1.3    9.3  12.4       0.73   10.0   1.7    2.0  2  Fer4_18   4Fe-4S dicluster domain
        2.5    8.9  14.4       0.24   12.2   3.5    2.6  2  Fer4_15   4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   4.2   2.5e-10   2.8e-07       4      24 .]       3      23 ..       1      23 [. 0.92
   2 !   22.4   2.1   6.5e-08   7.3e-05       6      24 .]      32      50 ..      28      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 2.5e-10
                                      ETTTSSS-THHHHHSTTTEEE CS
                              Fer4  4 deekCigCGaCvevCPvgAIt 24
                                      + +kC+gCG+C+ +C ++AI+
  gi|298674242|ref|YP_003725992.1|  3 INDKCVGCGQCAAICKNDAIQ 23
                                      579****************95 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 6.5e-08
                                      TTSSS-THHHHHSTTTEEE CS
                              Fer4  6 ekCigCGaCvevCPvgAIt 24
                                        C++C++C   CP +AI+
  gi|298674242|ref|YP_003725992.1| 32 QNCTNCKICSYYCPLNAIE 50
                                      68****************6 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0  13.1   2.2e-11   2.4e-08       5      58 ..       4      50 ..       2      51 .. 0.90

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 2.2e-11
                           Fer4_21  5 edkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58
                                      +dkC+gCg+C+  C++   +ai++ +k++   ++++C+ C++Cs  CP+ ++ie
  gi|298674242|ref|YP_003725992.1|  4 NDKCVGCGQCAAICKN---DAIQVWGKAK---ITQNCTNCKICSYYCPL-NAIE 50
                                      49*************5...9**9998887...789*************8.9987 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0  14.2   1.9e-08   2.2e-05       1      52 []       6      48 ..       6      48 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.9e-08
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      +C+gCg+C+a C+++ai+++ ++            ++C++C+ C   CP +a
  gi|298674242|ref|YP_003725992.1|  6 KCVGCGQCAAICKNDAIQVWGKA---------KITQNCTNCKICSYYCPLNA 48
                                      7******************9873.........34579************886 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   3.1   1.5e-07   0.00016       2      15 ..       5      18 ..       4      23 .. 0.92
   2 !   14.5   3.2   3.3e-05     0.037       2      16 ..      32      46 ..      31      47 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.5e-07
                            Fer4_4  2 erCigCgsCvaaCP 15
                                      ++C+gCg+C a+C+
  gi|298674242|ref|YP_003725992.1|  5 DKCVGCGQCAAICK 18
                                      89***********8 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3.3e-05
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      ++C++C+ C ++CP 
  gi|298674242|ref|YP_003725992.1| 32 QNCTNCKICSYYCPL 46
                                      79************6 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   2.8     2e-05     0.022       8      20 ..       5      17 ..       1      19 [. 0.87
   2 !   18.8   2.1   1.1e-06    0.0012       7      21 ..      31      45 ..      27      46 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2e-05
                            Fer4_2  8 drCigCgaCvsaC 20
                                      d+C+gCg C   C
  gi|298674242|ref|YP_003725992.1|  5 DKCVGCGQCAAIC 17
                                      89*******9999 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 1.1e-06
                            Fer4_2  7 tdrCigCgaCvsaCP 21
                                      t++C++C++C   CP
  gi|298674242|ref|YP_003725992.1| 31 TQNCTNCKICSYYCP 45
                                      789***********9 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   4.7   2.2e-06    0.0025      34      51 .]       5      22 ..       1      22 [. 0.86
   2 !   14.1   3.1   3.5e-05     0.039       1      18 [.      33      50 ..      33      52 .] 0.86

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.2e-06
                            Fer4_9 34 eaCigCgaCveaCpkgai 51
                                      ++C+gCg+C+++C+++ai
  gi|298674242|ref|YP_003725992.1|  5 DKCVGCGQCAAICKNDAI 22
                                      37*************987 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 3.5e-05
                            Fer4_9  1 kCtgCgaCveaCpagvvv 18
                                      +Ct+C+ C + Cp ++++
  gi|298674242|ref|YP_003725992.1| 33 NCTNCKICSYYCPLNAIE 50
                                      5***********998875 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   3.0   1.2e-05     0.013       1      21 [.       6      26 ..       6      33 .. 0.82
   2 !   16.1   2.6   1.4e-05     0.016       1      18 [.      33      50 ..      33      52 .] 0.91

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.2e-05
                           Fer4_16  1 rCgtCgkCaevCPtnaikekk 21
                                      +C++Cg+Ca +C  +ai+   
  gi|298674242|ref|YP_003725992.1|  6 KCVGCGQCAAICKNDAIQVWG 26
                                      6****************9764 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.4e-05
                           Fer4_16  1 rCgtCgkCaevCPtnaik 18
                                      +C++C+ C   CP nai+
  gi|298674242|ref|YP_003725992.1| 33 NCTNCKICSYYCPLNAIE 50
                                      6***************98 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   5.3   5.6e-07   0.00063       6      24 .]       4      22 ..       3      22 .. 0.90
   2 !   11.0   2.5   0.00033      0.37       7      23 ..      32      48 ..      29      49 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 5.6e-07
                            Fer4_6  6 pdkCigCgdCvrvCPegai 24
                                       dkC+gCg C+++C  +ai
  gi|298674242|ref|YP_003725992.1|  4 NDKCVGCGQCAAICKNDAI 22
                                      59************98887 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00033
                            Fer4_6  7 dkCigCgdCvrvCPega 23
                                      ++C+ C  C   CP +a
  gi|298674242|ref|YP_003725992.1| 32 QNCTNCKICSYYCPLNA 48
                                      79************665 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   3.9   0.00024      0.27      44      59 ..       5      20 ..       1      22 [. 0.84
   2 !   14.6   3.4   3.1e-05     0.035      41      58 ..      29      46 ..      18      48 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00024
                           Fer4_17 44 slCieCgeCerkCPqg 59
                                      ++C++Cg+C++ C ++
  gi|298674242|ref|YP_003725992.1|  5 DKCVGCGQCAAICKND 20
                                      79***********876 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 3.1e-05
                           Fer4_17 41 ekaslCieCgeCerkCPq 58
                                      +  ++C++C+ C+++CP 
  gi|298674242|ref|YP_003725992.1| 29 KITQNCTNCKICSYYCPL 46
                                      45689************6 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7  15.5    0.0044       4.9       3      64 ..       5      47 ..       3      48 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0044
                            Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                      +kC++Cg C + C             +++a++ v+ + +     + ++Ct+c+ C+  Cp +
  gi|298674242|ref|YP_003725992.1|  5 DKCVGCGQCAAIC-------------KNDAIQ-VWGKAK-----ITQNCTNCKICSYYCPLN 47
                                      6899999999999.............344444.444444.....5789************76 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4  16.9   1.4e-05     0.015       6      56 .]       4      45 ..       1      45 [. 0.90
   2 !   11.0   4.0   0.00031      0.35       6      21 ..      31      46 ..      27      51 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.4e-05
                           Fer4_10  6 ddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                       d+C++Cg+C + C         k+ a +   + k  ++Ct+c  C   CP
  gi|298674242|ref|YP_003725992.1|  4 NDKCVGCGQCAAIC---------KNDAIQVWGKAKITQNCTNCKICSYYCP 45
                                      59************.........6888888999999**************9 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00031
                           Fer4_10  6 ddtCirCgkCvkaCPa 21
                                      ++ C++C+ C   CP 
  gi|298674242|ref|YP_003725992.1| 31 TQNCTNCKICSYYCPL 46
                                      4679999999999987 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   5.8   0.00033      0.37       1      15 []       7      21 ..       7      21 .. 0.94
   2 !   11.2   2.8   0.00051      0.57       1      15 []      34      48 ..      34      48 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00033
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+gCg+C   C ++A
  gi|298674242|ref|YP_003725992.1|  7 CVGCGQCAAICKNDA 21
                                      ***********9887 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00051
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      Ct+C  C   CP +A
  gi|298674242|ref|YP_003725992.1| 34 CTNCKICSYYCPLNA 48
                                      ****99******987 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   2.8   5.7e-05     0.063      80      94 ..       5      19 ..       2      21 .. 0.86
   2 !    8.2   1.1     0.004       4.5       1      13 [.      33      45 ..      22      49 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.7e-05
                           Fer4_22 80 sgCvGCgRCieacpv 94
                                       +CvGCg C + c++
  gi|298674242|ref|YP_003725992.1|  5 DKCVGCGQCAAICKN 19
                                      68***********86 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.004
                           Fer4_22  1 rClsCgaCtlvCp 13
                                      +C +C  C++ Cp
  gi|298674242|ref|YP_003725992.1| 33 NCTNCKICSYYCP 45
                                      4788888888887 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   3.9    0.0003      0.34       1      17 [.       3      18 ..       3      19 .. 0.89
   2 ?    7.7   3.7    0.0045       5.1       4      17 ..      32      45 ..      30      47 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0003
                           Fer4_13  1 VDrdtCiacgaCvelaP 17
                                      ++ d+C++cg+C++++ 
  gi|298674242|ref|YP_003725992.1|  3 IN-DKCVGCGQCAAICK 18
                                      56.9***********95 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0045
                           Fer4_13  4 dtCiacgaCvelaP 17
                                      ++C++c++C   +P
  gi|298674242|ref|YP_003725992.1| 32 QNCTNCKICSYYCP 45
                                      78***********9 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   3.3     0.018        21      59      72 ..       5      18 ..       1      26 [. 0.70
   2 ?   10.0   1.7   0.00065      0.73      55      74 ..      28      47 ..      21      51 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.018
                           Fer4_18 59 gdcidcescvkvcP 72
                                       +c+ c++c ++c 
  gi|298674242|ref|YP_003725992.1|  5 DKCVGCGQCAAICK 18
                                      56777777777775 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00065
                           Fer4_18 55 ekgagdcidcescvkvcPtg 74
                                      +k + +c++c+ c   cP +
  gi|298674242|ref|YP_003725992.1| 28 AKITQNCTNCKICSYYCPLN 47
                                      567889************75 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   3.5   0.00021      0.24       6      20 ..       5      19 ..       4      33 .. 0.82
   2 ?    2.5   3.0      0.23   2.6e+02       7      19 ..      33      45 ..      31      51 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00021
                           Fer4_15  6 daCigcglCvaeape 20
                                      d+C gcg+C+a +++
  gi|298674242|ref|YP_003725992.1|  5 DKCVGCGQCAAICKN 19
                                      89**********964 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.23
                           Fer4_15  7 aCigcglCvaeap 19
                                      +C+ c  C   +p
  gi|298674242|ref|YP_003725992.1| 33 NCTNCKICSYYCP 45
                                      7999999988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       852  (0.0475208); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 379.42
//
Query:       gi|298674243|ref|YP_003725993.1|  [L=139]
Description: hypothetical protein Metev_0269 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-36  124.8   1.0    1.2e-36  124.6   1.0    1.1  1  DUF22     Domain of unknown function DUF22


Domain annotation for each model (and alignments):
>> DUF22  Domain of unknown function DUF22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.6   1.0   6.9e-41   1.2e-36       2     106 .]       6     110 ..       5     110 .. 0.99

  Alignments for each domain:
  == domain 1  score: 124.6 bits;  conditional E-value: 6.9e-41
                             DUF22   2 vkivyrkdgeivrekvevepfgytrstvakwelliAdedvevkkGevkkikikeielpentivvplsimrhalgtvl 78 
                                       +++v+rk+ge++++kv+++++++t++t+akwe++iA+ed+++++Ge+kki++k+i+++++++++p+ +++ha+++vl
  gi|298674243|ref|YP_003725993.1|   6 IQVVSRKNGELNSTKVKASSYEFTMATRAKWEMIIANEDMSIRSGEFKKIDVKDINVEPDMVAMPCIFSQHAVASVL 82 
                                       79*************************************************************************** PP

                             DUF22  79 dvvekgkpkkveeereiteavflpvedG 106
                                       ++++k+++ +v++er+i++a+++++e+G
  gi|298674243|ref|YP_003725993.1|  83 KIGAKEGNVPVDKERVIDSAYVIGQETG 110
                                       **************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 882.85
//
Query:       gi|298674244|ref|YP_003725994.1|  [L=167]
Description: hypothetical protein Metev_0270 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.096   13.4   1.0       0.22   12.2   1.0    1.8  1  MUG113           Meiotically up-regulated gene 113
       0.11   12.8   2.6      0.092   13.0   1.0    1.7  2  GEMIN8           Gemini of Cajal bodies-associated protein 8
       0.25   11.3   6.5        1.5    8.8   1.9    2.7  2  DUF4428          Domain of unknown function (DUF4428)
        1.5    9.3  13.3       0.15   12.4   3.8    2.9  3  Arc_trans_TRASH  Archaeal TRASH domain
        6.7    6.3  14.9         15    5.2   5.9    3.3  2  TF_Zn_Ribbon     TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> MUG113  Meiotically up-regulated gene 113
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.0   6.2e-05      0.22      43      76 ..     116     160 ..      55     161 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.2e-05
                            MUG113  43 llhleLkdkrlrdekcdc...........EwFevpaeslkavirk 76 
                                         h  +k++ +  ++c+            EwF +++++ +a+i+k
  gi|298674244|ref|YP_003725994.1| 116 FYHYYFKEYYVCPNCCASlfekyttnsigEWFVITCSNCEALIKK 160
                                       5699*********9*999**********************99997 PP

>> GEMIN8  Gemini of Cajal bodies-associated protein 8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.63   2.3e+03      20      46 ..      40      66 ..      30      88 .. 0.59
   2 ?   13.0   1.0   2.6e-05     0.092       3      46 ..      91     134 ..      89     160 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.63
                            GEMIN8 20 awmrrhqkayrkalesyysspwyleea 46
                                      +++++  kay++ l+ +y ++ y++  
  gi|298674244|ref|YP_003725994.1| 40 TIYNNTPKAYDNFLNYLYRTTRYISDY 66
                                      566666677777777777765444433 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 2.6e-05
                            GEMIN8   3 yshpvyarYwqHyeqamawmrrhqkayrkalesyysspwyleea 46 
                                         hp+ +rY++H + +++w+++  + y+ + ++yy +p ++++ 
  gi|298674244|ref|YP_003725994.1|  91 TTHPSKQRYFEHMHVVLEWLKNNPEFYHYYFKEYYVCPNCCASL 134
                                       57999******************************998776654 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.9   0.00041       1.5       1      30 [.       3      29 ..       3      45 .. 0.77
   2 ?    4.1   0.2     0.012        44      18      29 ..     122     133 ..     117     145 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00041
                           DUF4428  1 iCaiCgkKigllkrlkleDgyvCkdClkKl 30
                                      +C+iCg++        +e  ++C++C   l
  gi|298674244|ref|YP_003725994.1|  3 NCIICGQEQDSKQ---YEGYNICTACVDIL 29
                                      6*******99988...66668*****8655 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.012
                           DUF4428  18 eDgyvCkdClkK 29 
                                       ++ yvC++C   
  gi|298674244|ref|YP_003725994.1| 122 KEYYVCPNCCAS 133
                                       5669*****765 PP

>> Arc_trans_TRASH  Archaeal TRASH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.2         3   1.1e+04      23      29 ..      19      25 ..      13      29 .. 0.70
   2 ?   12.4   3.8   4.2e-05      0.15       8      35 ..     110     137 ..     108     139 .. 0.90
   3 ?    2.9   0.1      0.04   1.4e+02      23      35 ..     148     160 ..     145     162 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3
                   Arc_trans_TRASH 23 yvCCktC 29
                                      y  C  C
  gi|298674244|ref|YP_003725994.1| 19 YNICTAC 25
                                      4557777 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 4.2e-05
                   Arc_trans_TRASH   8 ivgePivyklknkvYyvCCktCkselkk 35 
                                       ++++P  y++  k YyvC + C s + k
  gi|298674244|ref|YP_003725994.1| 110 LKNNPEFYHYYFKEYYVCPNCCASLFEK 137
                                       5789******************998877 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.04
                   Arc_trans_TRASH  23 yvCCktCkselkk 35 
                                       ++ C++C+  +kk
  gi|298674244|ref|YP_003725994.1| 148 VITCSNCEALIKK 160
                                       567*****98887 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   1.6     0.011        38       3      31 ..       4      31 ..       3      36 .. 0.79
   2 ?    5.2   5.9    0.0042        15       1      30 [.     125     159 ..     125     165 .. 0.64

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.011
                                      ETTTTCEECHEETSTTCEEESSSSBEEEE CS
                      TF_Zn_Ribbon  3 CPnCgstnlveDpergelvCtdCGlVled 31
                                      C +Cg +++   +e g  +Ct+C  +led
  gi|298674244|ref|YP_003725994.1|  4 CIICGQEQDSKQYE-GYNICTACVDILED 31
                                      77888877666676.899*****888877 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0042
                                       EEETTTTCEEC..HEETSTTC...EEESSSSBEEE CS
                      TF_Zn_Ribbon   1 ykCPnCgstnl..veDperge...lvCtdCGlVle 30 
                                       y+CPnC+ + +  ++ ++ ge   ++C++C++++ 
  gi|298674244|ref|YP_003725994.1| 125 YVCPNCCASLFekYTTNSIGEwfvITCSNCEALIK 159
                                       89*****9755552233333343348888887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1416  (0.0789782); expected 358.6 (0.02)
Passed bias filter:                      632  (0.0352502); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.35s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 932.84
//
Query:       gi|298674245|ref|YP_003725995.1|  [L=131]
Description: NADH-ubiquinone/plastoquinone oxidoreductase subunit 3 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-35  121.4   0.8    1.4e-35  121.4   0.8    1.4  2  Oxidored_q4  NADH-ubiquinone/plastoquinone oxidoreductase, ch
  ------ inclusion threshold ------
      0.011   14.8   3.5      0.014   14.5   3.5    1.0  1  DUF973       Protein of unknown function (DUF973)


Domain annotation for each model (and alignments):
>> Oxidored_q4  NADH-ubiquinone/plastoquinone oxidoreductase, chain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       0.8   7.2e+03      75      83 ..      15      23 ..       7      27 .. 0.52
   2 !  121.4   0.8   1.5e-39   1.4e-35       3      99 .]      30     128 ..      28     128 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.8
                                      HHHHHHHHH CS
                       Oxidored_q4 75 iemllFlli 83
                                      + +++Fl++
  gi|298674245|ref|YP_003725995.1| 15 VPVAIFLIV 23
                                      334444433 PP

  == domain 2  score: 121.4 bits;  conditional E-value: 1.5e-39
                                       HHHHHHCHSS-----HHHHS-SSSS--SS---.--HHCHHHHHHHHHHHHHHHHHHHHHHHHSST..HHHH..HHHH CS
                       Oxidored_q4   3 lllllsallgpkkpnkeklspYEcGfepvgearlrfsvkfylvallFliFDvevvflfpwavslkelglfg..liem 77 
                                       +++l+ +ll+p++++k+k ++YE+G +p+g+ar++f+v++y++a+ F++FDve++fl+pwa++++ +g+++  ++++
  gi|298674245|ref|YP_003725995.1|  30 ITMLIVKLLSPRSKSKQKFTTYESGSDPTGDARIQFNVEYYIYAIAFVLFDVEILFLYPWATVYRGHGITSiaTTAI 106
                                       57889999********************************************************9996554338999 PP

                                       HHHHHHHHHHHHHHHHH-S-XX CS
                       Oxidored_q4  78 llFllillvglvYewkkgaLeW 99 
                                       l F++i+++g++YewkkgaL+W
  gi|298674245|ref|YP_003725995.1| 107 LAFIVIMVIGFIYEWKKGALQW 128
                                       ********************** PP

>> DUF973  Protein of unknown function (DUF973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   3.5   1.5e-06     0.014      49     155 ..       8     119 ..       3     122 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.5e-06
                            DUF973  49 asilssvlllliaaii.liiiasvllilgll....kirsgfsiLsstgrdvgiGitgltliligaiiiiigvilaiv 120
                                       +si++s + ++i+ i+ + +  + +li+ ll    k ++ f + +s + ++g   +  ++    ++i+++ + + i+
  gi|298674245|ref|YP_003725995.1|   8 SSIINSYVPVAIFLIVgVVMPPITMLIVKLLsprsKSKQKFTTYESGSDPTGDARIQFNVEYYIYAIAFVLFDVEIL 84 
                                       456666666666666653333333333333322348999*********************99999999999999999 PP

                            DUF973 121 sllslilslillgviilligiilaliGqillglsf 155
                                       +l +  ++    g++ +++ +ila+i  +++g+ +
  gi|298674245|ref|YP_003725995.1|  85 FLYPWATVYRGHGITSIATTAILAFIVIMVIGFIY 119
                                       99999999999999999999999999988888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1037  (0.0578393); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 762.86
//
Query:       gi|298674246|ref|YP_003725996.1|  [L=189]
Description: NADH-quinone oxidoreductase subunit B [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.4e-24   84.5   0.1    7.7e-24   84.0   0.1    1.3  1  Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit


Domain annotation for each model (and alignments):
>> Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.0   0.1   4.3e-28   7.7e-24      32     130 ..      87     171 ..      62     172 .. 0.83

  Alignments for each domain:
  == domain 1  score: 84.0 bits;  conditional E-value: 4.3e-28
                                       S--HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEEEESHHHHH-TGGGSTT-TEE-HHHHHHHC.S CS
                       Oxidored_q6  32 adskeeeieakekeadvlvveGavtrkpkealellkelaekakaviavGtCAafGGipaaannpsvgeevgellevv 108
                                       ++++         +adv++++G vt+k  +al++++e+++++k+via+G+CA++GG +  ++++s+   v++++e  
  gi|298674246|ref|YP_003725996.1|  87 NSPR---------QADVMIISGYVTKKYFPALKKVYEQMPSPKWVIAMGDCAISGGPF--YESYST---VQNIDEIF 149
                                       4444.........9********************************************..664444...579***** PP

                                       -E.EEE-SSS--HHHHHHHHHH CS
                       Oxidored_q6 109 pvdinipGCPphpeailetlla 130
                                       p+d++ipGCPp+pea+++++++
  gi|298674246|ref|YP_003725996.1| 150 PIDVYIPGCPPRPEALIQGFVE 171
                                       ******************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1206.30
//
Query:       gi|298674247|ref|YP_003725997.1|  [L=158]
Description: NADH (or F420H2) dehydrogenase subunit C [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-36  125.7   0.1    2.1e-36  125.2   0.1    1.2  1  Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd s
  ------ inclusion threshold ------
      0.052   13.5   0.2       0.07   13.1   0.2    1.1  1  RNase_H_2       RNase_H superfamily


Domain annotation for each model (and alignments):
>> Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.2   0.1   2.4e-40   2.1e-36       2     117 ..      32     147 ..      31     152 .. 0.95

  Alignments for each domain:
  == domain 1  score: 125.2 bits;  conditional E-value: 2.4e-40
                                       E--HHHHHHHHHHHHH...TT--EEEEEEEEETT.SSSEEEEEEEE--S-.-EEEEEE....-S-BEE--TTT-STH CS
                    Complex1_30kDa   2 vvepedllevakflkdeeelgfdvlsdltavDek.eerfevvyhllsleknerirvkvevdeeepevpSvtdlfpga 77 
                                       +v++++++ev+++lk++  l f++l + ++vD+  +++fevvyh++s+e+ + + +k+++++++p+++S++d++ +a
  gi|298674247|ref|YP_003725997.1|  32 YVDKDHVKEVCEYLKND--LDFNHLCCESGVDYIlRNEFEVVYHIASYEHPVILALKARLNRDDPVIESIVDVYWNA 106
                                       79**************6..99***********9999************************99*************** PP

                                       HHHHHHHHHHSHHBCTTSSTSS-SSSSTT.SSS-TTSTTS- CS
                    Complex1_30kDa  78 dwyEREayDmfGivfeghpdlrrillped.feghPLRkdfp 117
                                       +wyERE+y++fGi f+ hp+l+ ++lped    +PLRkd++
  gi|298674247|ref|YP_003725997.1| 107 NWYERETYELFGIMFKYHPNLKPLVLPEDlLGDWPLRKDYE 147
                                       *****************************54667*****96 PP

>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   7.8e-06      0.07      23     102 ..      31     114 ..      26     124 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.8e-06
                         RNase_H_2  23 ldvdekeiekltqllaeepeeekailelflellekkkalvtfngksFDvpflkrlfkkyklde.eefrhiDLl...k 95 
                                       ++vd++++++++++l+++ +  +   e  ++ + +++  v+++ +s++ p++  l  + + d       +D++   +
  gi|298674247|ref|YP_003725997.1|  31 AYVDKDHVKEVCEYLKNDLDFNHLCCESGVDYILRNEFEVVYHIASYEHPVILALKARLNRDDpVIESIVDVYwnaN 107
                                       5799***********************99***********************9988777777622347778883333 PP

                         RNase_H_2  96 elrkkkl 102
                                       +++++++
  gi|298674247|ref|YP_003725997.1| 108 WYERETY 114
                                       5566655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 962.53
//
Query:       gi|298674248|ref|YP_003725998.1|  [L=377]
Description: NADH dehydrogenase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-89  298.7   0.1    1.4e-87  293.3   0.1    2.1  1  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s
    3.6e-06   26.1   0.0    5.8e-06   25.5   0.0    1.3  1  NiFeSe_Hases    Nickel-dependent hydrogenase


Domain annotation for each model (and alignments):
>> Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  293.3   0.1   1.5e-91   1.4e-87       2     271 .]     126     377 .]     126     377 .] 0.95

  Alignments for each domain:
  == domain 1  score: 293.3 bits;  conditional E-value: 1.5e-91
                                       TT-HHHHHHHHHHHHHHHHHHHHHHSSSSS-TTBESSBBSS---TTHHHHHHHHHHHHHHH.HHHHHHHHHSSSSHH CS
                    Complex1_49kDa   2 lGaltvflyafreRekildlleevtGaRltasyiriGGvarDlpegllekikeflkelekk.ldeleklltknrifk 77 
                                       +G  ++f+y+++eRe++l+ll+++tGaR+t++++++GGv++Dlp+g+ +k+++++++l+++ lde+e+ll++++i+k
  gi|298674248|ref|YP_003725998.1| 126 IGYQSMFMYTIKERENVLSLLDSITGARITHTFLKFGGVREDLPPGFKDKFTRTMEQLKSTvLDEYERLLKSDTIYK 202
                                       6999****************************************************99875279************* PP

                                       HHHSSSS-BSHHHHHHHTT-SSSSGGGT-TTTHHHHSS-SSGGGS-------SSBSHHHHHHHHHHHHHHHHHHHHH CS
                    Complex1_49kDa  78 kRtkgvgvlskeealelgltGpvlRasGvkyDlRkaepYeaYdeldfdvpvgeegDvydRylvrveEmrqSlkIieq 154
                                       +Rt+gvgvls e a e+g++GpvlRa+Gv++D+Rk+epY +Yd+ldf+v++++egD+y+R++vr++E+r+S+ Iieq
  gi|298674248|ref|YP_003725998.1| 203 DRTVGVGVLSPEVAKEVGVAGPVLRATGVPFDIRKDEPYLVYDDLDFKVCTQKEGDSYARIMVRLNEIRESIYIIEQ 279
                                       ***************************************************************************** PP

                                       HHHT--.S-SB---TTTS---GGGGGT-HHHHHHHHHHHHS-----SEEEEEEEEETTEEEEEEEEEESSSS-SEEE CS
                    Complex1_49kDa 155 aleklpegpvlaedkkvalpkkeevkksmealihhfklvtegfkvpkgevyaavEapkGelgvylvsdgsskpyrlk 231
                                       al+++p+gp+  e++ +         k+              ++vp+gev+++vE+p+Ge+g+y+vsdgs+kpyr+k
  gi|298674248|ref|YP_003725998.1| 280 ALDQIPDGPIFPENTPY--------GKRT-----------PTMRVPEGEVFNRVENPRGEMGIYMVSDGSDKPYRVK 337
                                       *********87765443........2222...........3457********************************* PP

                                       EE-HHHHTTTTHHHHTTTS-SGGGTHHHHTT---HHHHH- CS
                    Complex1_49kDa 232 irapsfvnlqaleellkgellaDvvailgsldivlgevDR 271
                                       +r p++ +lqal+ +l+g ++aDv +i gs+d +++evDR
  gi|298674248|ref|YP_003725998.1| 338 VRGPAYPTLQALPPVLRGVYVADVNTIAGSMDGCTSEVDR 377
                                       ***************************************9 PP

>> NiFeSe_Hases  Nickel-dependent hydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   6.5e-10   5.8e-06       1      70 [.      50     119 ..      50     139 .. 0.96

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 6.5e-10
                                       --HHHHTTTS-GGGHHHHHHTT-SSSTTHHHHHHHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHHHH CS
                      NiFeSe_Hases   1 RGlElilkgrdprdawalvqRiCGVCttvHalasvravedAlgikipknarlirnliaaalllhdhivhF 70 
                                       +G+E+il+ ++  +   +v+R+C   + +   a   +ve+  gi++p+ a++ir + +    +++h++ F
  gi|298674248|ref|YP_003725998.1|  50 KGIEKILESKTYLQGIPIVDRMCYLGALSNEEAFCGCVEQLAGIEVPERAQYIRVITEELSRIQSHLLGF 119
                                       59*****************************************************************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2478.94
//
Query:       gi|298674249|ref|YP_003725999.1|  [L=353]
Description: respiratory-chain NADH dehydrogenase subunit 1 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   6.7e-106  353.9  24.4   8.1e-106  353.7  24.4    1.0  1  NADHdh    NADH dehydrogenase
  ------ inclusion threshold ------
       0.11   12.9   1.9          5    7.6   0.1    3.3  3  PEN-2     Presenilin enhancer-2 subunit of gamma secretase


Domain annotation for each model (and alignments):
>> NADHdh  NADH dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  353.7  24.4    9e-110  8.1e-106       6     298 ..      30     344 ..      26     345 .. 0.97

  Alignments for each domain:
  == domain 1  score: 353.7 bits;  conditional E-value: 9e-110
                                       HHHHHHHHHHHHHHHHHHHHHHHTTS--S-SSTTTTTTHHHHHHHHHCCS-----TTS-HHHHHHHHHHHHHHHHCT CS
                            NADHdh   6 llvvlllvvalltlleRkvlAriqdRlGPnrvGplGllqplaDalKlllKediipkkadkllfllapvlalilalla 82 
                                       l+ ++++ ++ +++leRk++A +q R+GP rvGp G++q++aDa+Kl++Kedi+p+kad+++f  ap++++++++l+
  gi|298674249|ref|YP_003725999.1|  30 LIGFIFVSAMAAVWLERKISADVQFRIGPCRVGPIGIFQLIADAIKLFTKEDIVPRKADSIMFRSAPIFLMVSVFLM 106
                                       5667888888******************************************************************* PP

                                       TTTS-SSS..........SSS--TTHHHHHHHHHHHCHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            NADHdh  83 faviPfge..........vladlnvglllilalsslgvygillaGwasnskYallGalRsaaqmisyEvalglslla 149
                                       +++iP+g+          v++d+++++l++ a+ss++++g+++ +++sn+kYallGa+R+ a m+ yE+++g+s++a
  gi|298674249|ref|YP_003725999.1| 107 LVAIPIGAivingvayplVVTDMDISILYVEAVSSISIIGVFMVAYSSNNKYALLGAFRNFARMVGYEIPFGISIIA 183
                                       *******5556678899************************************************************ PP

                                       HHHHH-SS-HHHHHHCCCTT-CCCCHHHHHHHHHHHHHHCCTCTTBTTTTSTTSSSSCCCTT-HCHHHHHHHHHHHH CS
                            NADHdh 150 vvllagslslseiveaqeeiwfillqllafiifliallaetnraPFDlpeaesELvaGfhtEYsgmkfalfflaeya 226
                                       v++++gsl++ eive+q+ iw+++lq+++f++f++al+  ++r PFD +eae+E+vaG+ tEYsgm+f+l f+aey+
  gi|298674249|ref|YP_003725999.1| 184 VAITTGSLNIIEIVENQT-IWNVILQPIGFFVFFVALMGDLGRLPFDQTEAEQEVVAGWITEYSGMRFGLGFFAEYI 259
                                       *****************6.9********************************************************* PP

                                       HHHHHHHHHHHHCT.SS-HCCS.............HHHHHHHHHHHHHHHHHHHHHC----TCHHHHHHHCCTCHHH CS
                            NADHdh 227 nmvlvsalavllFlgGwllpfs.............gllwfllKvllllflfiwiratlpRlRydqlmklgwkvllpl 290
                                       +mvl s+l+vllFlgGw+lp               ++l+fl K +++l ++i++r+++pR+R+dq+++lgwk ++pl
  gi|298674249|ref|YP_003725999.1| 260 HMVLGSFLVVLLFLGGWNLPGLglltsipvigfimPTLVFLGKSAIVLAFIILLRWAVPRFRIDQVVDLGWKRIIPL 336
                                       *******************988999999***99999999************************************** PP

                                       HHHHHHHH CS
                            NADHdh 291 alanlllt 298
                                       +++nl+++
  gi|298674249|ref|YP_003725999.1| 337 SIVNLIWA 344
                                       *****985 PP

>> PEN-2  Presenilin enhancer-2 subunit of gamma secretase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1   0.00056         5      44      69 ..      19      44 ..      12      52 .. 0.89
   2 ?    2.6   0.0      0.02   1.8e+02      46      66 ..     200     220 ..     187     226 .. 0.85
   3 ?   -2.0   0.0      0.57   5.1e+03      65      89 ..     238     262 ..     235     265 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00056
                             PEN-2 44 qkeirkyvilSaiGalvwlvvllaWa 69
                                      ++ ir y+ lS+iG+++ +++ ++W 
  gi|298674249|ref|YP_003725999.1| 19 NPWIRGYLGLSLIGFIFVSAMAAVWL 44
                                      5779*****************99996 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.02
                             PEN-2  46 eirkyvilSaiGalvwlvvll 66 
                                       +  + vil  iG++v++v+l+
  gi|298674249|ref|YP_003725999.1| 200 QTIWNVILQPIGFFVFFVALM 220
                                       5567899999********997 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.57
                             PEN-2  65 llaWalvfqikraewgevgdklsvv 89 
                                       ++ W++ ++  r   g +++++ +v
  gi|298674249|ref|YP_003725999.1| 238 VAGWITEYSGMRFGLGFFAEYIHMV 262
                                       6789999999999999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2290.59
//
Query:       gi|298674250|ref|YP_003726000.1|  [L=143]
Description: 4Fe-4S ferredoxin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-15   55.4  16.1    3.7e-09   36.0   4.0    2.6  3  Fer4      4Fe-4S binding domain
    3.7e-12   46.6   7.8    6.8e-12   45.8   7.8    1.5  1  Fer4_7    4Fe-4S dicluster domain
    3.9e-11   42.9  19.4      7e-09   35.7   8.5    1.6  2  Fer4_9    4Fe-4S dicluster domain
    3.6e-10   40.6   4.0    0.00018   22.4   1.2    2.4  2  Fer4_16   4Fe-4S double cluster binding domain
    3.9e-10   39.7   6.4    3.9e-10   39.7   6.4    1.8  2  Fer4_10   4Fe-4S dicluster domain
    5.7e-08   32.8  10.5    6.4e-08   32.6   9.5    1.6  1  Fer4_21   4Fe-4S dicluster domain
    2.2e-07   30.5   8.5    4.7e-05   23.2   1.6    2.5  2  Fer4_2    4Fe-4S binding domain
    4.9e-07   30.1   8.0    2.4e-06   27.9   8.4    1.8  1  Fer4_8    4Fe-4S dicluster domain
    1.9e-05   24.8   9.1     0.0032   17.8   1.6    2.5  2  Fer4_4    4Fe-4S binding domain
    3.9e-05   23.5   4.0    3.9e-05   23.5   4.0    2.7  3  Fer4_6    4Fe-4S binding domain
    0.00015   22.3  11.6     0.0025   18.3  11.1    2.4  3  Fer4_17   4Fe-4S dicluster domain
    0.00027   21.7   8.8      0.052   14.4   2.2    2.2  2  Fer4_22   4Fe-4S dicluster domain
     0.0011   19.6   9.9     0.0086   16.8   0.6    2.7  2  Fer4_15   4Fe-4S single cluster domain
     0.0014   19.1  11.9     0.0022   18.5   2.5    2.5  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
     0.0035   18.2  19.4      0.054   14.4   3.3    2.7  3  Fer4_3    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.056   13.6   9.5        7.5    6.8   9.5    2.3  1  Fer4_18   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1         6   6.7e+03      17      20 ..      21      24 ..      20      25 .. 0.73
   2 !   36.0   4.0   3.3e-12   3.7e-09       3      24 .]      40      61 ..      39      61 .. 0.94
   3 !   27.3   1.6   1.9e-09   2.1e-06       1      23 [.      78     100 ..      78     101 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 6
                                      HSTT CS
                              Fer4 17 vCPv 20
                                      +CP 
  gi|298674250|ref|YP_003726000.1| 21 MCPE 24
                                      6996 PP

  == domain 2  score: 36.0 bits;  conditional E-value: 3.3e-12
                                      EETTTSSS-THHHHHSTTTEEE CS
                              Fer4  3 ideekCigCGaCvevCPvgAIt 24
                                       d++kCigCG+C++ CP++AI+
  gi|298674250|ref|YP_003726000.1| 40 LDKSKCIGCGICANTCPNNAIK 61
                                      799******************6 PP

  == domain 3  score: 27.3 bits;  conditional E-value: 1.9e-09
                                       EEEETTTSSS-THHHHHSTTTEE CS
                              Fer4   1 vvideekCigCGaCvevCPvgAI 23 
                                       ++id   C++CG+C++ CP +A+
  gi|298674250|ref|YP_003726000.1|  78 PEIDIGHCMFCGLCIDQCPQDAL 100
                                       579999****************8 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   7.8   6.1e-15   6.8e-12       1      52 []      44      99 ..      44      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 6.1e-15
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgt..ekv..eidpekClgCgaCvavCPtga 52
                                      +CigCg C+++Cp++ai++  + + k+   +++  eid   C++Cg C++ CP +a
  gi|298674250|ref|YP_003726000.1| 44 KCIGCGICANTCPNNAIKIVRSRVSKTSdkQRWfpEIDIGHCMFCGLCIDQCPQDA 99
                                      7*****************9977555533224546699****************987 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   3.1   8.2e-07   0.00092      33      51 .]      37      60 ..      19      60 .. 0.63
   2 !   35.7   8.5   6.2e-12     7e-09       1      50 [.      44      99 ..      44     100 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 8.2e-07
                            Fer4_9 33 e.....eaCigCgaCveaCpkgai 51
                                            ++CigCg C++ Cp++ai
  gi|298674250|ref|YP_003726000.1| 37 LqvldkSKCIGCGICANTCPNNAI 60
                                      12233369*************987 PP

  == domain 2  score: 35.7 bits;  conditional E-value: 6.2e-12
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase......eaCigCgaCveaCpkga 50
                                      kC+gCg C + Cp+++++  +++     +++++        C++Cg C++ Cp++a
  gi|298674250|ref|YP_003726000.1| 44 KCIGCGICANTCPNNAIKIVRSRVSKTSDKQRWfpeidiGHCMFCGLCIDQCPQDA 99
                                      7****************999998888888888899****99*************97 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   1.2   1.6e-07   0.00018       1      23 [.      44      66 ..      44      80 .. 0.78
   2 !   18.9   0.1     2e-06    0.0023       1      24 [.      84     104 ..      84     140 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.6e-07
                           Fer4_16  1 rCgtCgkCaevCPtnaikekkek 23
                                      +C++Cg Ca++CP naik  +++
  gi|298674250|ref|YP_003726000.1| 44 KCIGCGICANTCPNNAIKIVRSR 66
                                      5****************977444 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 2e-06
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkeke 24 
                                       +C  Cg C++ CP++a+++    +
  gi|298674250|ref|YP_003726000.1|  84 HCMFCGLCIDQCPQDALSSS---K 104
                                       79***************998...3 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       4.1   4.6e+03      18      26 ..      21      27 ..      19      36 .. 0.61
   2 !   39.7   6.4   3.5e-13   3.9e-10       3      56 .]      39      96 ..      37     104 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.1
                           Fer4_10 18 aCPadltsv 26
                                      +CP   +++
  gi|298674250|ref|YP_003726000.1| 21 MCPE--EKS 27
                                      6998..444 PP

  == domain 2  score: 39.7 bits;  conditional E-value: 3.5e-13
                           Fer4_10  3 vidddtCirCgkCvkaCPadl....tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      v+d+++Ci+Cg C + CP ++    +s + k  +++    ++++++C++cg C+++CP
  gi|298674250|ref|YP_003726000.1| 39 VLDKSKCIGCGICANTCPNNAikivRSRVSKTSDKQRWFPEIDIGHCMFCGLCIDQCP 96
                                      7899***************99*9988888888999999999****************9 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   9.5   5.7e-11   6.4e-08       3      57 ..      40     100 ..      38     102 .. 0.78

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 5.7e-11
                           Fer4_21   3 idedkCigCgkCliaCedtshqai......eidaktvlkvv.edeCvGCnlCssvCPvedci 57 
                                       +d++kCigCg C+ +C++++++ +      + d+++ ++ +   +C+ C lC++ CP +d++
  gi|298674250|ref|YP_003726000.1|  40 LDKSKCIGCGICANTCPNNAIKIVrsrvskTSDKQRWFPEIdIGHCMFCGLCIDQCP-QDAL 100
                                       799***************99999977665334444555554268*************.5765 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   1.6   4.2e-08   4.7e-05       4      22 .]      39      57 ..      36      57 .. 0.90
   2 !   11.2   0.8   0.00028      0.32       3      22 .]      78      97 ..      76      97 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 4.2e-08
                            Fer4_2  4 vvdtdrCigCgaCvsaCPa 22
                                      v d  +CigCg+C + CP+
  gi|298674250|ref|YP_003726000.1| 39 VLDKSKCIGCGICANTCPN 57
                                      67999*************5 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00028
                            Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                                      +++d  +C+ Cg C++ CP+
  gi|298674250|ref|YP_003726000.1| 78 PEIDIGHCMFCGLCIDQCPQ 97
                                      7788889************6 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   8.4   2.2e-09   2.4e-06       3      64 ..      43      98 ..      41      99 .. 0.70

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 2.2e-09
                            Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                      +kCi+Cg C ++Cp      + ++  r ++++   ++q+   e  +++C+ cg C ++Cp++
  gi|298674250|ref|YP_003726000.1| 43 SKCIGCGICANTCPN-----NAIKIVRSRVSK-TSDKQRWFPEIDIGHCMFCGLCIDQCPQD 98
                                      79***********93.....333344444444.333333333678***************85 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   1.6   2.9e-06    0.0032       2      16 ..      43      57 ..      42      69 .. 0.90
   2 !   10.8   1.1    0.0005      0.56       4      16 ..      85      97 ..      73      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.9e-06
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      ++CigCg C ++CP 
  gi|298674250|ref|YP_003726000.1| 43 SKCIGCGICANTCPN 57
                                      79************5 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0005
                            Fer4_4  4 CigCgsCvaaCPq 16
                                      C  Cg C++ CPq
  gi|298674250|ref|YP_003726000.1| 85 CMFCGLCIDQCPQ 97
                                      66699*******8 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       5.9   6.7e+03      19      21 ..      22      24 ..      18      25 .. 0.68
   2 !   23.5   4.0   3.5e-08   3.9e-05       5      24 .]      41      60 ..      40      60 .. 0.96
   3 !    7.7   1.6    0.0035       3.9       4      24 .]      80     100 ..      77     100 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.9
                            Fer4_6 19 CPe 21
                                      CPe
  gi|298674250|ref|YP_003726000.1| 22 CPE 24
                                      997 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 3.5e-08
                            Fer4_6  5 dpdkCigCgdCvrvCPegai 24
                                      d++kCigCg C++ CP +ai
  gi|298674250|ref|YP_003726000.1| 41 DKSKCIGCGICANTCPNNAI 60
                                      89**************9998 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0035
                            Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                                       id   C  Cg C++ CP +a+
  gi|298674250|ref|YP_003726000.1|  80 IDIGHCMFCGLCIDQCPQDAL 100
                                       55555666*********8875 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   3.3   9.4e-05      0.11      44      59 ..      43      58 ..      23      60 .. 0.82
   2 !   18.3  11.1   2.2e-06    0.0025       1      59 [.      44      98 ..      44     100 .. 0.70
   3 !   11.3   2.0   0.00035      0.39       2      16 ..      85      99 ..      84     141 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.4e-05
                           Fer4_17 44 slCieCgeCerkCPqg 59
                                      s+Ci+Cg C+  CP++
  gi|298674250|ref|YP_003726000.1| 43 SKCIGCGICANTCPNN 58
                                      5788888888888875 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 2.2e-06
                           Fer4_17  1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqg 59
                                      +Ci+Cg C++ Cp +++    + ++ +    +++++   e  ++ C+ Cg+C  +CPq+
  gi|298674250|ref|YP_003726000.1| 44 KCIGCGICANTCPNNAIK-IVRSRVSKT---SDKQRWFPEIDIGHCMFCGLCIDQCPQD 98
                                      6************88773.223333332...222222223599**************97 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00035
                           Fer4_17  2 CiqCgyClpeCpsye 16
                                      C+ Cg C+++Cp+ +
  gi|298674250|ref|YP_003726000.1| 85 CMFCGLCIDQCPQDA 99
                                      888888888888743 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   2.2   4.7e-05     0.052      76      95 ..      39      58 ..      24      60 .. 0.82
   2 !   11.8   0.5   0.00029      0.33      65      95 ..      68      98 ..      57      99 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.7e-05
                           Fer4_22 76 kfgesgCvGCgRCieacpvk 95
                                        ++s+C+GCg C ++cp++
  gi|298674250|ref|YP_003726000.1| 39 VLDKSKCIGCGICANTCPNN 58
                                      45899************975 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00029
                           Fer4_22 65 rllhklsefkekfgesgCvGCgRCieacpvk 95
                                        +   + +  +++  +C+ Cg Ci++cp++
  gi|298674250|ref|YP_003726000.1| 68 SKTSDKQRWFPEIDIGHCMFCGLCIDQCPQD 98
                                      334445678888999*************985 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.6   7.7e-06    0.0086       2      20 ..      39      57 ..      39      63 .. 0.92
   2 ?    6.6   2.9     0.012        13       3      20 ..      80      97 ..      79     138 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.7e-06
                           Fer4_15  2 vvDrdaCigcglCvaeape 20
                                      v+D+++Cigcg C+  +p+
  gi|298674250|ref|YP_003726000.1| 39 VLDKSKCIGCGICANTCPN 57
                                      68***************97 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.012
                           Fer4_15  3 vDrdaCigcglCvaeape 20
                                      +D   C+ cglC++ +p+
  gi|298674250|ref|YP_003726000.1| 80 IDIGHCMFCGLCIDQCPQ 97
                                      78889***********84 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   2.5   1.9e-06    0.0022       2      18 ..      41      57 ..      40      58 .. 0.94
   2 ?    5.4   2.0     0.025        28       1      18 [.      80      97 ..      80      98 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.9e-06
                           Fer4_13  2 DrdtCiacgaCvelaPd 18
                                      D+++Ci+cg+C++++P+
  gi|298674250|ref|YP_003726000.1| 41 DKSKCIGCGICANTCPN 57
                                      99**************7 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.025
                           Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                      +D   C+ cg+C + +P+
  gi|298674250|ref|YP_003726000.1| 80 IDIGHCMFCGLCIDQCPQ 97
                                      56678************5 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       9.9   1.1e+04      11      12 ..      22      23 ..      20      25 .. 0.65
   2 !   11.6   5.5   0.00039      0.44       1      15 []      45      59 ..      45      59 .. 0.98
   3 !   14.4   3.3   4.8e-05     0.054       1      15 []      85      99 ..      85      99 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 9.9
                            Fer4_3 11 CP 12
                                      CP
  gi|298674250|ref|YP_003726000.1| 22 CP 23
                                      66 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00039
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+gCg C + CP++A
  gi|298674250|ref|YP_003726000.1| 45 CIGCGICANTCPNNA 59
                                      *************98 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 4.8e-05
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+ Cg+C + CP +A
  gi|298674250|ref|YP_003726000.1| 85 CMFCGLCIDQCPQDA 99
                                      99**********998 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   9.5    0.0067       7.5      56     112 ..      40     114 ..      21     116 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0067
                           Fer4_18  56 kgagdcidcescvkvcPtg.idi.rkGl......ql........eciscllcidacdk..vmeklgkpkglirys 112
                                        ++++ci c+ c + cP + i i r  +      q         +c+ c+lcid c +  +  +  +  g+++++
  gi|298674250|ref|YP_003726000.1|  40 LDKSKCIGCGICANTCPNNaIKIvRSRVsktsdkQRwfpeidigHCMFCGLCIDQCPQdaLSSSKIYTSGVVKWN 114
                                       56789***********97436653322111111121222223346999*******95421444445566788876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 914.03
//
Query:       gi|298674251|ref|YP_003726001.1|  [L=105]
Description: NADH-ubiquinone/plastoquinone oxidoreductase subunit 6 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-21   75.7   9.5    2.9e-21   75.7   9.5    1.6  2  Oxidored_q3   NADH-ubiquinone/plastoquinone oxidoreductase ch
  ------ inclusion threshold ------
      0.084   13.0  15.8      0.042   14.0  13.5    1.6  2  DUF4040       Domain of unknown function (DUF4040)
        1.2    8.3   7.7        1.4    8.1   7.7    1.0  1  Peptidase_U4  Sporulation factor SpoIIGA


Domain annotation for each model (and alignments):
>> Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase chain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.2      0.14   8.6e+02      81      89 ..      26      33 ..       9      38 .. 0.46
   2 !   75.7   9.5   4.8e-25   2.9e-21       2      64 ..      36      98 ..      35     104 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.14
                                      HHHHHHHHH CS
                       Oxidored_q3 81 ligllllal 89
                                      ++   l+++
  gi|298674251|ref|YP_003726001.1| 26 ALL-SLIII 33
                                      111.11111 PP

  == domain 2  score: 75.7 bits;  conditional E-value: 4.8e-25
                                      HHHHHH-SBHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHIIIIIHHHHHHHHHHHSSTTS CS
                       Oxidored_q3  2 allvitsknpvysalfLilsfvgvaglfillgaeFlallqilvYvGAilvlflFvimllesae 64
                                      +ll+i+s+ +v++a++Li+s+++vagl+ill+a+Fl+++q+lvYvGA+ vl+lF +ml+++++
  gi|298674251|ref|YP_003726001.1| 36 SLLTIVSRDVVRAAISLIVSLFSVAGLYILLNAQFLGVVQVLVYVGAVGVLILFGVMLTKTES 98
                                      799*******************************************************75433 PP

>> DUF4040  Domain of unknown function (DUF4040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1     0.097   5.8e+02       8      33 ..       7      32 ..       1      36 [. 0.64
   2 ?   14.0  13.5     7e-06     0.042       1      64 [.      30      93 ..      30      96 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.097
                           DUF4040  8 laavlardrlaavillgvvGllvall 33
                                      +++ ++ d l+ +  +g++ ll+ ++
  gi|298674251|ref|YP_003726001.1|  7 YLTSFTFDDLTTIARFGAFALLSLII 32
                                      56666777778888888887765544 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 7e-06
                           DUF4040  1 lllvlaalaavlardrlaavillgvvGllvallfvllgAPDvAlTqaavveglttvllllalrr 64
                                      l+++l++l+++++rd+++a+i+l+v  + va l++ll+A  +   q++v  g ++vl+l+ +  
  gi|298674251|ref|YP_003726001.1| 30 LIIILFSLLTIVSRDVVRAAISLIVSLFSVAGLYILLNAQFLGVVQVLVYVGAVGVLILFGVML 93
                                      5899******************************************************998765 PP

>> Peptidase_U4  Sporulation factor SpoIIGA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   7.7   0.00024       1.4      59     130 ..      19      90 ..       3     100 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00024
                      Peptidase_U4  59 llsillkilvsllmvliafgpkslkeflkalllfylvsfllgGilfalsylllksknllvlllgalvaylll 130
                                       ++ + + +l+sl+++l++  +   +++++a + +++  f ++G++++l  ++l+  ++lv + +++v++l+ 
  gi|298674251|ref|YP_003726001.1|  19 IARFGAFALLSLIIILFSLLTIVSRDVVRAAISLIVSLFSVAGLYILLNAQFLGVVQVLVYVGAVGVLILFG 90 
                                       4445555677778877766666679*************************9987666555554444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       882  (0.049194); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 645.68
//
Query:       gi|298674252|ref|YP_003726002.1|  [L=86]
Description: NADH-ubiquinone/plastoquinone oxidoreductase subunit 6 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.6e-12   45.9   2.1    5.4e-12   45.6   2.1    1.1  1  Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase cha
  ------ inclusion threshold ------
      0.063   12.5   0.1      0.086   12.1   0.1    1.3  1  Ion_trans    Ion transport protein
       0.12   12.5   2.4       0.56   10.4   0.4    2.0  2  CBP_BcsF     Cellulose biosynthesis protein BcsF
       0.34   11.2   4.9        1.3    9.4   1.0    2.1  2  TadE         TadE-like protein


Domain annotation for each model (and alignments):
>> Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase chain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   2.1   1.2e-15   5.4e-12      76     143 ..       8      78 ..       2      79 .. 0.73

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 1.2e-15
                                       HHHHHHHHHHHHHHHTT--.........--------TT-HHHHHHHHTTTTHHHHHHHHHHHHHHHHHHHH CS
                       Oxidored_q3  76 alaalligllllallllllles...sssavdaqvadvsnieaigsllftkyllpfelasllLLvaligaiv 143
                                       +++all++ll+l ++ + +  +   + ++  ++ +d+snie+ig ++ftky++pfe+++++LL aliga +
  gi|298674252|ref|YP_003726002.1|   8 VIVALLVVLLFLGMIGVSVIGTgwdTVEELPQTPEDQSNIERIGVSVFTKYVVPFEIMAIVLLSALIGAFY 78 
                                       44445555555555544444436654444477889999*******************************86 PP

>> Ion_trans  Ion transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   1.9e-05     0.086     126     183 ..       1      54 [.       1      81 [. 0.67

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.9e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCCCCCCSCCSTSSSTTTSSSSSSHHHHH CS
                         Ion_trans 126 svkdllnvlllllvvlfifaligvqlfkgklreknecaktwenpnngntnFdnfftal 183
                                       ++ +++nv+++llvvl++ ++igv + ++ +   +e  +t     ++++n ++++ ++
  gi|298674252|ref|YP_003726002.1|   1 MLGKIINVIVALLVVLLFLGMIGVSVIGTGWDTVEELPQTP----EDQSNIERIGVSV 54 
                                       5789***********************99999444433333....3344444433333 PP

>> CBP_BcsF  Cellulose biosynthesis protein BcsF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.4   0.00012      0.56       5      34 ..       4      33 ..       1      39 [. 0.85
   2 ?    2.2   0.1     0.045     2e+02       5      16 ..      63      74 ..      62      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00012
                          CBP_BcsF  5 DivqiiilcaLiflpLgyllarllrrlsdt 34
                                       i+ +i+ +++++l+Lg++ + ++   +dt
  gi|298674252|ref|YP_003726002.1|  4 KIINVIVALLVVLLFLGMIGVSVIGTGWDT 33
                                      699***************998888777776 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.045
                          CBP_BcsF  5 DivqiiilcaLi 16
                                      +i+ i++l+aLi
  gi|298674252|ref|YP_003726002.1| 63 EIMAIVLLSALI 74
                                      5889*******9 PP

>> TadE  TadE-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   1.0   0.00028       1.3       8      27 ..       8      27 ..       8      36 .. 0.82
   2 ?    3.6   0.2     0.018        81      11      26 ..      66      81 ..      64      85 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00028
                              TadE  8 ALvlPlllllllgiiefgry 27
                                      ++v+ l++ll+lg+i ++ +
  gi|298674252|ref|YP_003726002.1|  8 VIVALLVVLLFLGMIGVSVI 27
                                      68999**********87765 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.018
                              TadE 11 lPlllllllgiiefgr 26
                                      + +ll  l g +++gr
  gi|298674252|ref|YP_003726002.1| 66 AIVLLSALIGAFYMGR 81
                                      445666999*****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       809  (0.0451224); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 539.12
//
Query:       gi|298674253|ref|YP_003726003.1|  [L=104]
Description: NADH-ubiquinone oxidoreductase subunit 4L [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.1e-23   81.4   5.6    3.4e-23   81.3   5.6    1.0  1  Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase cha
  ------ inclusion threshold ------
      0.011   15.7   0.1      0.015   15.3   0.1    1.1  1  BMC          BMC domain
        0.1   12.5   0.0       0.12   12.3   0.0    1.2  1  VIT_2        Vault protein inter-alpha-trypsin domain


Domain annotation for each model (and alignments):
>> Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.3   5.6   5.6e-27   3.4e-23       1     103 [.      10      99 ..      10     104 .] 0.97

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 5.6e-27
                                       HHHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC.............TTSCGGHHHHHHHHHH CS
                       Oxidored_q2   1 flllliallfliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvitnpatefadplpqalvLtaivig 77 
                                       f+l+l+a++f iGl+gv++++n ++ l+++el++n++n++lv+++++              +d+ +q++vL+ i+++
  gi|298674253|ref|YP_003726003.1|  10 FYLILSAVVFSIGLLGVMTKQNGVRLLMCVELMLNSANINLVAFSSYN-------------NDITGQVFVLFTIALA 73 
                                       699********************************************9.............**************** PP

                                       HHHHHHHHHHHHHHHHHSSS-BCCG- CS
                       Oxidored_q2  78 aaetavgLallvrlyreygtddvqel 103
                                       aae+a+g ++++++yr ++ +d++++
  gi|298674253|ref|YP_003726003.1|  74 AAEAAIGFGIFMAVYRMKNRIDLNDF 99 
                                       *********************99876 PP

>> BMC  BMC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.1   2.5e-06     0.015       2      58 ..      24      83 ..      24      95 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.5e-06
                                      EEEEEEESHHHHHHHHHHHHHHSSEEEEEEEECTTT...CEEEEEEESHHHHHHHHHHHH CS
                               BMC  2 lGlietrglaaaieaaDaalKaAnVelvgvekvggg...kvtviitGdvaaVkaAveagv 58
                                      lG+++ ++++  ++++  +l +An++lv +++ ++    +v+v++t  +aa +aA+  g+
  gi|298674253|ref|YP_003726003.1| 24 LGVMTKQNGVRLLMCVELMLNSANINLVAFSSYNNDitgQVFVLFTIALAAAEAAIGFGI 83
                                      7999999999********************9999944779***************97775 PP

>> VIT_2  Vault protein inter-alpha-trypsin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.9e-05      0.12      17      62 ..      37      82 ..      21      94 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.9e-05
                             VIT_2 17 skvsacvlgaslgvtasltYyNdqeqpvegvFvyPldekttvvgfe 62
                                      ++v+  +++a   + a  +Y Nd +++v ++F+  l+ ++ ++gf 
  gi|298674253|ref|YP_003726003.1| 37 MCVELMLNSANINLVAFSSYNNDITGQVFVLFTIALAAAEAAIGFG 82
                                      577888999999********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       746  (0.0416086); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 754.22
//
Query:       gi|298674254|ref|YP_003726004.1|  [L=666]
Description: proton-translocating NADH-quinone oxidoreductase subunit L [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-75  252.7  25.7    4.3e-75  252.7  25.7    2.1  2  Proton_antipo_M  Proton-conducting membrane transporter
    2.9e-18   65.7   0.4    2.9e-18   65.7   0.4    4.2  4  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 
  ------ inclusion threshold ------
      0.012   15.2   2.8      0.029   14.0   2.8    1.6  1  Proton_antipo_C  NADH-dehyrogenase subunit F, TMs, (complex I
       0.12   11.7   0.2       0.67    9.3   0.2    2.3  1  SLATT_5          SMODS and SLOG-associating 2TM effector doma


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  252.7  25.7   9.5e-79   4.3e-75       1     279 [.     130     435 ..     130     454 .. 0.92
   2 ?   -2.5   0.3       0.5   2.2e+03      43      55 ..     489     501 ..     477     557 .. 0.61

  Alignments for each domain:
  == domain 1  score: 252.7 bits;  conditional E-value: 9.5e-79
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllyn.....ltg......tlefe 66 
                                       ++++l+l++++Elv+l++ylLig+w+ kp++++A+ k+fl+t++g++++L gi++l++     ++g       l+f+
  gi|298674254|ref|YP_003726004.1| 130 SDNILQLFVFWELVGLSSYLLIGFWYGKPSAASAAKKAFLTTRIGDVMFLAGIIILFSdlfaiFNGfpdnayMLQFT 206
                                       789***************************************************9986443334559999999**** PP

                   Proton_antipo_M  67 elskal.........elglnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsall.Aatlvkagvllli 133
                                       e+++ +          +g++ + l+l++ll++ g++ Ks+q+plh+Wlpda +e+Pt vsal+ Aat+v+agv+l++
  gi|298674254|ref|YP_003726004.1| 207 EMFNHIpeiagmsaqIFGFEVSHLTLITLLFFGGAVGKSGQFPLHVWLPDA-MEGPTTVSALIhAATMVTAGVYLVA 282
                                       ****99******99989999*******************************.************************* PP

                   Proton_antipo_M 134 rlllllavssneisqlllilaiismllgslvalaqtdiKrllAySsishlGymlialavatqygvea...aiihllt 207
                                       r++++++ s+++  ++++ l+  ++l+++++a++ +d+Kr+lAyS+is+lGym+++l+++ ++g+ea   +i+hl+ 
  gi|298674254|ref|YP_003726004.1| 283 RTFPMFI-SAPDTLIVIAYLGGFTALFAATMAIVMNDLKRVLAYSTISQLGYMMLGLGMGAVIGMEAvglSIFHLIN 358
                                       **99999.***************************************************8777777622269***** PP

                   Proton_antipo_M 208 halfkallFllagsviyerektrdirayggLakkmPilalvllvlllsla..GlPpt....agFlskfliLeaavav 278
                                       ha+fkallFl agsvi++   t+d+r++gg  k+mPi+a+++l++ lsla  G+P+t    +gFlsk++i+eaa+  
  gi|298674254|ref|YP_003726004.1| 359 HAFFKALLFLSAGSVIHAV-GTHDMRELGGVGKVMPITAITMLIAGLSLAgfGIPGTiigtSGFLSKDAIIEAAFLF 434
                                       ***************9987.9****************************9889**999999************9965 PP

                   Proton_antipo_M 279 s 279
                                       +
  gi|298674254|ref|YP_003726004.1| 435 G 435
                                       3 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.5
                   Proton_antipo_M  43 llgsliLLlgill 55 
                                        l+ ++L++g++ 
  gi|298674254|ref|YP_003726004.1| 489 ILAAFSLFFGMFT 501
                                       4555566666653 PP

>> Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.7   0.4   6.4e-22   2.9e-18      11      55 ..      71     115 ..      65     117 .. 0.95
   2 ?   -0.1   0.0      0.23     1e+03      14      28 ..     223     237 ..     209     241 .. 0.80
   3 ?   -3.0   0.1       1.9   8.4e+03      30      37 ..     262     269 ..     262     270 .. 0.91
   4 ?    1.5   0.1     0.069   3.1e+02      20      47 ..     540     568 ..     526     587 .. 0.76

  Alignments for each domain:
  == domain 1  score: 65.7 bits;  conditional E-value: 6.4e-22
                   Proton_antipo_N  11 sieigfllDklsalmllvvtfvsllvhlYSigYMaddegyqRFfa 55 
                                        +++g+l+D+l a+ml++v+fvsll+h+YS+gYM++d++++R+fa
  gi|298674254|ref|YP_003726004.1|  71 AFNLGILIDPLAAVMLTMVSFVSLLIHIYSVGYMEHDKSKPRYFA 115
                                       589*****************************************8 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.23
                   Proton_antipo_N  14 igfllDklsalmllv 28 
                                       +gf ++ l+++ ll+
  gi|298674254|ref|YP_003726004.1| 223 FGFEVSHLTLITLLF 237
                                       79*********9987 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.9
                   Proton_antipo_N  30 tfvsllvh 37 
                                       t+vs+l+h
  gi|298674254|ref|YP_003726004.1| 262 TTVSALIH 269
                                       89*****9 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.069
                   Proton_antipo_N  20 klsalmllvvtfvsllvhlYSigYMa.dd 47 
                                       +l +l l ++  v+ l + Y i+Y++  d
  gi|298674254|ref|YP_003726004.1| 540 PLIILWLPLILAVAGLLITYLIYYLRvLD 568
                                       67889999****************97334 PP

>> Proton_antipo_C  NADH-dehyrogenase subunit F, TMs, (complex I) C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   2.8   6.4e-06     0.029      89     177 ..     472     562 ..     454     602 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.4e-06
                   Proton_antipo_C  89 tlsyPhEsdntmlfpllvLvlftlfvGliGip.fnqe.gidldilskwLtpsinllhknsnesvdwyefltnaifSv 163
                                       t    hEs+++m++p+++L+ f+lf G+  +  f++  g +++ ++  L+     l +    +    e l+   + +
  gi|298674254|ref|YP_003726004.1| 472 TDYDGHESPSSMTVPMVILAAFSLFFGMFTTGtFSRFlGDTFNFINMNLNELAASLGNYELLHEAGHEPLIILWLPL 548
                                       445579*********************87654333210112222222222222222222221122222333334556 PP

                   Proton_antipo_C 164 sialfGifiAsllY 177
                                        +a+ G++i +l+Y
  gi|298674254|ref|YP_003726004.1| 549 ILAVAGLLITYLIY 562
                                       67777777777776 PP

>> SLATT_5  SMODS and SLOG-associating 2TM effector domain family 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.2   0.00015      0.67      35      79 ..      84     130 ..      79     136 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00015
                           SLATT_5  35 fslsllSvylivlslls.nkssestinenll.dflsiilSilvlvis 79 
                                        +l+++S+++++++++s  + ++++++ +++ + + +++S+l l++s
  gi|298674254|ref|YP_003726004.1|  84 VMLTMVSFVSLLIHIYSvGYMEHDKSKPRYFaETALFTCSMLGLILS 130
                                       689**************9555555555555505667789**999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (666 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       872  (0.0486363); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.49
# Mc/sec: 4058.70
//
Query:       gi|298674255|ref|YP_003726005.1|  [L=495]
Description: proton-translocating NADH-quinone oxidoreductase subunit M [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.3e-64  216.2  29.9    5.3e-64  216.2  29.9    2.1  2  Proton_antipo_M  Proton-conducting membrane transporter
     0.0086   16.2   6.3     0.0086   16.2   6.3    5.4  5  Oxidored_q5_N    NADH-ubiquinone oxidoreductase chain 4, amin
  ------ inclusion threshold ------
       0.36   11.2   3.3       0.47   10.8   0.2    2.8  3  ERGIC_N          Endoplasmic Reticulum-Golgi Intermediate Com


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   1.8      0.16   9.7e+02      15      73 ..      10      72 ..       6      98 .. 0.55
   2 !  216.2  29.9   8.8e-68   5.3e-64       1     293 []     127     424 ..     127     424 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.16
                   Proton_antipo_M 15 llplylLiglwkkkpksleAslklflltllgsliLLlgilllynltg.tlefeelskal.....e 73
                                      l+pl++ +  +++k  + e +  ++l++++ sl+L l + + +  +  +l+f e+sk +     +
  gi|298674255|ref|YP_003726005.1| 10 LIPLIFAVITFFTK--TKEQARTTALTGSVISLVLALYMYMNFDSSIaSLQFVEISKWVpslgiT 72
                                      55655554444444..3333444555555555555555544444332589999998886554441 PP

  == domain 2  score: 216.2 bits;  conditional E-value: 8.8e-68
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgillly....nltg..tlefeelska 71 
                                       a d +l+y+++El+l+ply+++  w+   ++  A++k+f++t ++sl++Llgi++ly    ++tg  t +++el+++
  gi|298674255|ref|YP_003726005.1| 127 ALDFFLFYVFWELTLIPLYFMVSQWGGP-NKEFAAIKFFIYTHVASLVMLLGIFALYftawSQTGspTFNIQELLTQ 202
                                       57899********************766.9999*********************999444345669999******** PP

                   Proton_antipo_M  72 lelglnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla...vssne 145
                                       ++   + l   +++++ll+g++vK++ +p+h Wlpday e+P+++ +l+  +l+k+g+++l+r++l++       n 
  gi|298674255|ref|YP_003726005.1| 203 FQSFEAPLVKDAIFIALLFGFIVKIPTFPFHSWLPDAYTESPIAGNVLF--ILLKIGGYGLFRIMLPILpftGTPNL 277
                                       99999999999**************************************..*************9999965445566 PP

                   Proton_antipo_M 146 isqlllilaiismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsv 222
                                       + +++++l+++s+++g++valaq+d Kr++A+ s+sh+G+++++ a   + +v++a+++ ++h+l+ + +F+ + +v
  gi|298674255|ref|YP_003726005.1| 278 MISIMALLGTASIIYGAFVALAQRDFKRMIAFASVSHMGFVVLGSAGLVSLSVSGAMFQQFSHGLILSVMFMSV-GV 353
                                       77788899************************************99889999**********************.77 PP

                   Proton_antipo_M 223 iyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvlavvasvlt 293
                                       i+ +  tr i+++ggL+kkmP lal+++v++++  GlP+++gF+++fl+L++++   +  ++++++++v+t
  gi|298674255|ref|YP_003726005.1| 354 IQTNAGTRIINQLGGLSKKMPKLALIMVVVFMASLGLPGLTGFVAEFLVLTSSYVNLPGYVLAVMIGIVIT 424
                                       78888**********************************************99877777766667888876 PP

>> Oxidored_q5_N  NADH-ubiquinone oxidoreductase chain 4, amino terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   6.3   1.4e-06    0.0086       4     103 ..       9     117 ..       6     124 .. 0.61
   2 ?    0.3   1.1      0.12   7.2e+02      19      40 ..     155     176 ..     131     211 .. 0.54
   3 ?   -3.1   2.9       1.4   8.4e+03      14      70 ..     269     329 ..     260     350 .. 0.48
   4 ?   -2.8   1.9       1.1   6.5e+03      19      19 ..     411     411 ..     369     466 .. 0.56
   5 ?   -1.0   0.4      0.31   1.9e+03      30      47 ..     454     471 ..     436     492 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.4e-06
                     Oxidored_q5_N   4 illptlmliplvllskkkllwststlvslllallsll.l............lnlsssfslsnlsyllglDslSapLi 67 
                                       il+p+++ +++ ++++k+   +t ++ s++ ++l l  +            +  s+      ++y +g+D +S+pLi
  gi|298674255|ref|YP_003726005.1|   9 ILIPLIFAVITFFTKTKEQARTTALTGSVISLVLALYmYmnfdssiaslqfVEISKWVPSLGITYSVGVDGVSMPLI 85 
                                       777888777777776666655555555555444444433111222111000222333333467899*********** PP

                     Oxidored_q5_N  68 lLSlWllpLmilASqkhlkkepknrqrlFllllilL 103
                                       lL + ++p  i+ S++  k+    + + F  l++ +
  gi|298674255|ref|YP_003726005.1|  86 LLNAIVIPFLIIYSWNEEKS----YPNRFFGLILAM 117
                                       **************999888....444444444444 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.12
                     Oxidored_q5_N  19 kkkllwststlvslllallsll 40 
                                       +k++  + +++++ + +l++ll
  gi|298674255|ref|YP_003726005.1| 155 NKEFAAIKFFIYTHVASLVMLL 176
                                       2223333333344444444444 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 1.4
                     Oxidored_q5_N  14 lvllskkkllwststlv.slllallsll.l..lnlsssfslsnlsyllglDslSapLilLS 70 
                                       l ++ +++l++s++ l+ ++ ++   ++ l    ++ +  + ++s++  +   Sa L+ LS
  gi|298674255|ref|YP_003726005.1| 269 LPFTGTPNLMISIMALLgTASIIYGAFVaLaqRDFKRMIAFASVSHMGFVVLGSAGLVSLS 329
                                       4444444444333332202222222222110022233333344444444444455555555 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 1.1
                     Oxidored_q5_N  19 k 19 
                                       +
  gi|298674255|ref|YP_003726005.1| 411 P 411
                                       0 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 0.31
                     Oxidored_q5_N  30 vslllallsllllnlsss 47 
                                       +sl +a++sll++++  +
  gi|298674255|ref|YP_003726005.1| 454 QSLSMAVISLLVIYFGLN 471
                                       455566666665444433 PP

>> ERGIC_N  Endoplasmic Reticulum-Golgi Intermediate Compartment (ERGIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   7.9e-05      0.47       5      41 ..      19      55 ..      15      78 .. 0.85
   2 ?   -3.3   0.1         2   1.2e+04      23      41 ..     169     187 ..     165     195 .. 0.62
   3 ?   -1.5   0.0      0.55   3.3e+03      12      31 ..     448     468 ..     443     470 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7.9e-05
                                      XXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                           ERGIC_N  5 DafpKvpedltqktlsGgiislvcillilfLllselt 41
                                       +f+K++e+ +++ l+G++islv +l + + + s ++
  gi|298674255|ref|YP_003726005.1| 19 TFFTKTKEQARTTALTGSVISLVLALYMYMNFDSSIA 55
                                      58********99*************999887766655 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2
                                       XXXXXXXXXXXXXXXXXXX CS
                           ERGIC_N  23 iislvcillilfLllselt 41 
                                       + slv++l i+ L ++ ++
  gi|298674255|ref|YP_003726005.1| 169 VASLVMLLGIFALYFTAWS 187
                                       4566666666666665554 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.55
                                       XXX.X.XXXXXXXXXXXXXXX CS
                           ERGIC_N  12 edltq.ktlsGgiislvcill 31 
                                       +dlt+ ++ls ++isl++i +
  gi|298674255|ref|YP_003726005.1| 448 KDLTNyQSLSMAVISLLVIYF 468
                                       688888999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       994  (0.0554409); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 3092.14
//
Query:       gi|298674256|ref|YP_003726006.1|  [L=482]
Description: proton-translocating NADH-quinone oxidoreductase subunit N [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.9e-73  244.9  32.9    9.9e-73  244.9  32.9    2.1  2  Proton_antipo_M  Proton-conducting membrane transporter
  ------ inclusion threshold ------
      0.013   15.2   1.9      0.024   14.3   1.9    1.5  1  GET2             GET complex subunit GET2
      0.013   15.6   0.3      0.013   15.6   0.3    4.6  7  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   2.9      0.28   1.7e+03      60      95 ..      62      86 ..       9     117 .. 0.48
   2 !  244.9  32.9   1.7e-76   9.9e-73       1     292 [.     119     419 ..     119     420 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.28
                   Proton_antipo_M 60 tgtlefeelskalelglnslelllllllllvgllvK 95
                                      +gt           l+++ l +++ +++l+v+llv 
  gi|298674256|ref|YP_003726006.1| 62 SGT-----------LTVDALSQFFKIVFLIVALLVS 86
                                      122...........2233333333333333333333 PP

  == domain 2  score: 244.9 bits;  conditional E-value: 1.7e-76
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelgln 77 
                                       +ndLl l++++El ++++y L+g+ +++ ksle+++k+f++++l+s ++L+gi+ +y+l+gt++++e++++  + ++
  gi|298674256|ref|YP_003726006.1| 119 SNDLLVLFVSFELASISTYALAGFERRNLKSLESAMKYFIIGALSSALMLFGISFVYGLAGTTNIPEIAQNSAMLVS 195
                                       79*********************************************************************9***** PP

                   Proton_antipo_M  78 slelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla.vssneisqlllil 153
                                       s+   + ++ll++g+ +K+a+vp+h+W pd y+++P +vs llAa   k+g  + ++++++     + e++  ++il
  gi|298674256|ref|YP_003726006.1| 196 SPLGIVSIVLLVAGFGFKIALVPFHMWAPDTYEGSPSVVSSLLAAGSKKMGFVAAFKVFMIALvALKTEWTMAFAIL 272
                                       *******************************************999******999988888777899********** PP

                   Proton_antipo_M 154 aiismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFll...agsviyere 227
                                       ++i+m lg+++al+q+++Kr+lAySs+++ Gy+ +a++v++ ++v++ ++++l+h+++ka+ Fl+   +g +i +++
  gi|298674256|ref|YP_003726006.1| 273 SVITMTLGNVIALSQNSVKRMLAYSSVAQAGYISMAFVVMSPMAVTGGLFYILSHGFMKAGAFLVtavVGYMILSEN 349
                                       ***************************************************************97221344444444 PP

                   Proton_antipo_M 228 ....ktrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvla.vvasvl 292
                                           +++ +++ +gLak+mPi a  +++++++laG+P+tag++skf ++++ ++++l++l+++ ++ s++
  gi|298674256|ref|YP_003726006.1| 350 reaeNVDHLENFKGLAKRMPISAFSMMIFVFALAGIPLTAGYMSKFVLFSSTIEAGLVWLAVIaILNSAI 419
                                       6677999******************************************************997877776 PP

>> GET2  GET complex subunit GET2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   1.9   4.1e-06     0.024     180     249 ..      71     146 ..      62     209 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.1e-06
                              GET2 180 vkklkarfllvrllllllnfvYhvfrssks..........alvralteasvrnFftvFltfEvvllsiyylllkkie 246
                                        + +k++fl+v+ll+ ++ + Y+   ++++          a+v +++ as++    +F++fE++++s+y l+    e
  gi|298674256|ref|YP_003726006.1|  71 SQFFKIVFLIVALLVSVASIKYTE--NNEHveefftlvllAVVGMMMVASSNDLLVLFVSFELASISTYALAG--FE 143
                                       5789*************9999987..3333456677777788888888889*******************997..33 PP

                              GET2 247 ken 249
                                       ++n
  gi|298674256|ref|YP_003726006.1| 144 RRN 146
                                       333 PP

>> Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.3   2.2e-06     0.013      15      56 ..      64     105 ..      54     107 .. 0.92
   2 ?   -2.6   0.2      0.99   5.9e+03      22      32 ..     164     174 ..     153     177 .. 0.76
   3 ?   -2.0   1.1      0.64   3.8e+03      10      33 ..     261     284 ..     254     286 .. 0.78
   4 ?   -3.3   0.2       1.7     1e+04      25      36 ..     334     345 ..     324     346 .. 0.71
   5 ?   -3.0   0.1       1.3   7.8e+03      35      40 ..     376     381 ..     370     394 .. 0.50
   6 ?   -2.2   0.6      0.74   4.4e+03      23      39 ..     406     422 ..     404     431 .. 0.86
   7 ?   -3.3   0.2       1.7     1e+04      26      37 ..     450     461 ..     445     463 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.2e-06
                   Proton_antipo_N  15 gfllDklsalmllvvtfvsllvhlYSigYMaddegyqRFfay 56 
                                       ++ +D ls  + +v  +v+llv + Si+Y ++ e+   Ff++
  gi|298674256|ref|YP_003726006.1|  64 TLTVDALSQFFKIVFLIVALLVSVASIKYTENNEHVEEFFTL 105
                                       688*************************************86 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.99
                   Proton_antipo_N  22 salmllvvtfv 32 
                                       salml+ ++fv
  gi|298674256|ref|YP_003726006.1| 164 SALMLFGISFV 174
                                       67888877777 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.64
                   Proton_antipo_N  10 lsieigfllDklsalmllvvtfvs 33 
                                       l+ e+++ +  ls++ +++  +++
  gi|298674256|ref|YP_003726006.1| 261 LKTEWTMAFAILSVITMTLGNVIA 284
                                       678888888899999998877776 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 1.7
                   Proton_antipo_N  25 mllvvtfvsllv 36 
                                         lv  +v+ ++
  gi|298674256|ref|YP_003726006.1| 334 AFLVTAVVGYMI 345
                                       456667777776 PP

  == domain 5  score: -3.0 bits;  conditional E-value: 1.3
                   Proton_antipo_N  35 lvhlYS 40 
                                       ++ +++
  gi|298674256|ref|YP_003726006.1| 376 MIFVFA 381
                                       444443 PP

  == domain 6  score: -2.2 bits;  conditional E-value: 0.74
                   Proton_antipo_N  23 almllvvtfvsllvhlY 39 
                                       ++ l+v+ ++ + + lY
  gi|298674256|ref|YP_003726006.1| 406 LVWLAVIAILNSAISLY 422
                                       57899999999999998 PP

  == domain 7  score: -3.3 bits;  conditional E-value: 1.7
                   Proton_antipo_N  26 llvvtfvsllvh 37 
                                       +lv  +v++l++
  gi|298674256|ref|YP_003726006.1| 450 TLVAAVVGVLIL 461
                                       577788888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1166  (0.0650343); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 3145.39
//
Query:       gi|298674257|ref|YP_003726007.1|  [L=117]
Description: F420H2 dehydrogenase subunit FpoO [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.1e-51  172.9   6.6    2.4e-51  172.7   6.6    1.0  1  FpoO        F420H2 dehydrogenase subunit FpoO
  ------ inclusion threshold ------
      0.061   13.4  10.0       0.15   12.2   1.2    3.0  3  Fer4_10     4Fe-4S dicluster domain
       0.11   12.5   9.8      0.093   12.7   1.0    3.5  3  DUF4428     Domain of unknown function (DUF4428)
       0.47   10.4  11.1        7.6    6.5   3.4    3.8  3  zf-C4_ClpX  ClpX C4-type zinc finger
        2.7    8.3   9.8         12    6.3   0.5    2.7  2  zf-AD       Zinc-finger associated domain (zf-AD)


Domain annotation for each model (and alignments):
>> FpoO  F420H2 dehydrogenase subunit FpoO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.7   6.6   6.7e-55   2.4e-51       1     110 []       1     110 [.       1     110 [. 0.99

  Alignments for each domain:
  == domain 1  score: 172.7 bits;  conditional E-value: 6.7e-55
                              FpoO   1 madcdlcgvsiPtviPvrvfkPrlelsyPeGvwkGlcekclkaakktydelskeeasgtaGkcdlcgkktrlydvev 77 
                                       madc+lcg+s+Pt++Pvrv++Prl ++yPeGv+kGlc++c+kaa++ty++l+++  s+++Gkc+lcgk trly+vev
  gi|298674257|ref|YP_003726007.1|   1 MADCELCGESLPTLCPVRVYAPRLIITYPEGVCKGLCPTCVKAAEDTYSKLDQSILSVSSGKCNLCGKPTRLYPVEV 77 
                                       9**************************************************************************** PP

                              FpoO  78 qvPsfskgsekktaklckrcleaveeayekkke 110
                                       q+Psf++g+ek +++lc++clea++e++ek++e
  gi|298674257|ref|YP_003726007.1|  78 QIPSFKQGVEKVDMNLCRTCLEACHETHEKYHE 110
                                       ******************************986 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.2      0.16   5.7e+02       9      21 ..       4      17 ..       1      27 [. 0.57
   2 ?   12.2   1.2   4.2e-05      0.15      14      50 ..      32      68 ..      30      72 .. 0.94
   3 ?    5.6   0.1     0.005        18      12      19 ..      94     101 ..      75     115 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.16
                           Fer4_10  9 CirCgkCvk.aCPa 21
                                      C  Cg+     CP+
  gi|298674257|ref|YP_003726007.1|  4 CELCGESLPtLCPV 17
                                      44444332223666 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 4.2e-05
                           Fer4_10 14 kCvkaCPadltsvgakgeaseeeavrkkvekCtgcga 50
                                       C+  CP+++++ + ++ + +++  ++ ++kC  cg+
  gi|298674257|ref|YP_003726007.1| 32 VCKGLCPTCVKAAEDTYSKLDQSILSVSSGKCNLCGK 68
                                      69*********************************96 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.005
                           Fer4_10  12 CgkCvkaC 19 
                                       C++C +aC
  gi|298674257|ref|YP_003726007.1|  94 CRTCLEAC 101
                                       66677777 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.2     0.062   2.2e+02       1      11 [.       3      13 ..       3      20 .. 0.83
   2 ?    2.1   0.2     0.053   1.9e+02      22      36 ..      36      52 ..      26      60 .. 0.72
   3 ?   12.7   1.0   2.6e-05     0.093       1      28 [.      62      99 ..      62     111 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.062
                           DUF4428  1 iCaiCgkKigl 11
                                      +C +Cg+ ++ 
  gi|298674257|ref|YP_003726007.1|  3 DCELCGESLPT 13
                                      6*****98765 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.053
                           DUF4428 22 vCkdClkKl..seflsd 36
                                      +C++C k +  + ++ d
  gi|298674257|ref|YP_003726007.1| 36 LCPTCVKAAedTYSKLD 52
                                      8****997754444444 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 2.6e-05
                           DUF4428  1 iCaiCgkKigll.........kr.lkleDgyvCkdClk 28
                                      +C++Cgk + l+         k+ +   D ++C +Cl+
  gi|298674257|ref|YP_003726007.1| 62 KCNLCGKPTRLYpvevqipsfKQgVEKVDMNLCRTCLE 99
                                      7**********8888888887668************97 PP

>> zf-C4_ClpX  ClpX C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.42   1.5e+03       3       9 ..       4      10 ..       3      11 .. 0.83
   2 ?    4.8   0.1    0.0071        25      15      35 ..      24      46 ..      21      49 .. 0.79
   3 ?    6.5   3.4    0.0021       7.6       2      36 ..      62     104 ..      61     107 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.42
                        zf-C4_ClpX  3 CSFCgks 9 
                                      C  Cg s
  gi|298674257|ref|YP_003726007.1|  4 CELCGES 10
                                      9999975 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0071
                        zf-C4_ClpX 15 klIagpngvy..ICdeCvelcne 35
                                      ++I+ p+gv+   C  Cv+ + +
  gi|298674257|ref|YP_003726007.1| 24 LIITYPEGVCkgLCPTCVKAAED 46
                                      5678888876668******9987 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0021
                        zf-C4_ClpX   2 rCSFCgksesevkklIagpng........vyICdeCvelcnei 36 
                                       +C  Cgk+       ++ p+         ++ C  C e c+e 
  gi|298674257|ref|YP_003726007.1|  62 KCNLCGKPTRLYPVEVQIPSFkqgvekvdMNLCRTCLEACHET 104
                                       68888888876555555553355688888999********996 PP

>> zf-AD  Zinc-finger associated domain (zf-AD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.5    0.0032        12      40      61 ..      28      49 ..       7      60 .. 0.82
   2 ?    4.6   7.0     0.011        38       2      67 ..      37     113 ..      36     117 .] 0.54

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0032
                             zf-AD 40 pddslpekiCesCleklqefye 61
                                       ++++++ +C +C+++ ++ y+
  gi|298674257|ref|YP_003726007.1| 28 YPEGVCKGLCPTCVKAAEDTYS 49
                                      67788899*********99996 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.011
                             zf-AD   2 CRlClseeseellsifdts...nss..islaeileeltglele......pddslpekiCesCleklqefye.Frekc 66 
                                       C +C ++ ++  +++ d+s    ss   +l+ +  +l ++e++        +++ +++C++Cle+ +e +e ++ek+
  gi|298674257|ref|YP_003726007.1|  37 CPTCVKAAEDTYSKL-DQSilsVSSgkCNLCGKPTRLYPVEVQipsfkqGVEKVDMNLCRTCLEACHETHEkYHEKF 112
                                       777883333333322.3332221114567777777777777778784444444455799999988887774244555 PP

                             zf-AD  67 v 67 
                                       +
  gi|298674257|ref|YP_003726007.1| 113 E 113
                                       4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 785.84
//
Query:       gi|298674258|ref|YP_003726008.1|  [L=315]
Description: nucleoside recognition domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.1e-07   29.1  19.7    0.00052   20.3   4.7    3.0  3  Gate      Nucleoside recognition


Domain annotation for each model (and alignments):
>> Gate  Nucleoside recognition
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   4.7   2.9e-08   0.00052       4      94 ..      18      99 ..      15     147 .. 0.73
   2 ?   -0.7   1.1     0.091   1.6e+03      34      62 ..     113     142 ..      85     172 .. 0.70
   3 !   13.5   7.0   3.8e-06     0.068       2      96 ..     183     266 ..     182     286 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.9e-08
                              Gate  4 agpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqgfdtp 82
                                      ++ ii+++++  ++l +++l+++++++ +p+f+     l+  ++ s+l+ ++   v++ t+++ +         g  ++
  gi|298674258|ref|YP_003726008.1| 18 VLVIIFIGIFGSGVLIEKGLMQKLSRFARPIFKYTY--LPETCASSFLVALG-SSVAANTMIVKR------QDDGCLNR 87
                                      789*******************************77..9**********999.999999999888......44444444 PP

                              Gate 83 ksalafllfvll 94
                                      +++l + l++++
  gi|298674258|ref|YP_003726008.1| 88 REVLLCSLMNST 99
                                      444433333333 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.091
                              Gate  34 vfap.lg.qeldwkatvslltgfaakevvvg 62 
                                       ++ p lg    +  a+v ++t ++ k +vv 
  gi|298674258|ref|YP_003726008.1| 113 IMLPaLGaVVGSFYAFVFIITAII-KIIVVV 142
                                       444444554455555566666665.444433 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 3.8e-06
                              Gate   2 lkagpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqg 78 
                                       lk+  i l++++l+  l+++++++ ++ l  p+   +g  l+ +++v+l++ +a+  +++++lg +        ++g
  gi|298674258|ref|YP_003726008.1| 183 LKIAVIYLVMTTLVFALRDQGAFEVFSVL--PLAEIFG--LPSESIVPLTSYIASPILGASILGPMI-------HSG 248
                                       78999**********************99..*******..***********************9996.......9** PP

                              Gate  79 fdtpksalafllfvllyt 96 
                                         t  +a+++l+++++ +
  gi|298674258|ref|YP_003726008.1| 249 SITYLQAMIVLMVGSMFM 266
                                       ******886666665543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       934  (0.0520944); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2214.50
//
Query:       gi|298674259|ref|YP_003726009.1|  [L=370]
Description: hypothetical protein Metev_0285 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.4e-179  596.1   0.0   2.7e-179  596.0   0.0    1.0  1  FBPase_3  Fructose-1,6-bisphosphatase


Domain annotation for each model (and alignments):
>> FBPase_3  Fructose-1,6-bisphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  596.0   0.0  1.5e-183  2.7e-179       2     361 .]       3     367 ..       2     367 .. 0.99

  Alignments for each domain:
  == domain 1  score: 596.0 bits;  conditional E-value: 1.5e-183
                          FBPase_3   2 vtlsvikaDvGslaGhtkvheellekveevleeakkkgllidfyvtkvGDDielimthtkgvdneevhklawdafke 78 
                                       +t+s+ikaDvGs+aGh+ v eel e++ +vleeak k  + d++vt++GDD+eli+th+kg+d+eev+++aw+af +
  gi|298674259|ref|YP_003726009.1|   3 TTFSAIKADVGSVAGHHVVPEELEESAISVLEEAKGK-DIFDYFVTHCGDDLELIITHDKGEDSEEVYEIAWNAFLK 78 
                                       79********************************998.899************************************ PP

                          FBPase_3  79 atevakelklygaGqDlLkdafsGnvkGlGPgvaelefeeRksepvvvfaaDktepgafnlplykifadpfntaGlv 155
                                       ate akel+lygaGqDlL+dafsGn+kG+GPg+ae+ef+eRks+pv++f++Dktepgafnlp+ykifadpfntaGlv
  gi|298674259|ref|YP_003726009.1|  79 ATEKAKELGLYGAGQDLLSDAFSGNIKGMGPGIAEMEFKERKSNPVFTFMMDKTEPGAFNLPMYKIFADPFNTAGLV 155
                                       ***************************************************************************** PP

                          FBPase_3 156 idpklheGfkfevlDvieekkillsapeelydllallgakeryvikrvysk......kdeeiaavvsterlsliaGk 226
                                       +dp++h+Gf fev+D++e+kki++ +p++lyd+lal+gak+ryvikrvy k      +++e+aav+ste+ls+iaG+
  gi|298674259|ref|YP_003726009.1| 156 LDPNMHSGFVFEVWDIKESKKINFYCPNDLYDMLALIGAKSRYVIKRVYPKednpkaTSQEPAAVISTEKLSHIAGE 232
                                       **************************************************98877777788**************** PP

                          FBPase_3 227 YvGkDDPvaivRaqsglPavgevlepfalphlvaGwmrGshngplmPvslkdakptrfdgpprvvalgfqlkegklv 303
                                       YvGkDDPva+vR qsglPa+ge+lepf++p+lv+Gwm+GshngplmPv+++da+ptrfdgppr ++lgfq+k+g+l+
  gi|298674259|ref|YP_003726009.1| 233 YVGKDDPVAVVRGQSGLPAAGEILEPFTHPELVSGWMKGSHNGPLMPVPVEDATPTRFDGPPRAICLGFQVKDGMLI 309
                                       ***************************************************************************** PP

                          FBPase_3 304 gpvDlfddpafdeaRekaaeiadelRrqGpfephrlpeeeleYttlpevleklkerfe 361
                                       gpvD f+dpafd++Reka++++d++R++Gpfephrlpeee+eYttlp+v+ek+++rfe
  gi|298674259|ref|YP_003726009.1| 310 GPVDSFADPAFDKTREKAHQVSDYMRAHGPFEPHRLPEEEMEYTTLPDVMEKINHRFE 367
                                       ********************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2580.81
//
Query:       gi|298674260|ref|YP_003726010.1|  [L=60]
Description: hypothetical protein Metev_0286 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.7e-12   45.4   1.3    1.9e-11   44.3   1.3    1.5  1  Trm112p          Trm112p-like protein
     0.0043   16.5   0.7     0.0064   16.0   0.7    1.4  1  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0046   16.7   0.0     0.0067   16.2   0.0    1.3  1  Cys_rich_KTR     Cysteine-rich KTR
  ------ inclusion threshold ------
      0.012   15.8   0.6      0.022   14.9   0.6    1.6  1  zf-RRPl_C4       Putative ribonucleoprotein zinc-finger pf C4
      0.016   15.0   0.2      0.016   15.0   0.2    1.0  1  CK_II_beta       Casein kinase II regulatory subunit
       0.02   15.3   0.2      0.024   15.0   0.2    1.1  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.021   14.9   0.0      0.023   14.8   0.0    1.1  1  Elf1             Transcription elongation factor Elf1 like
      0.052   13.4   0.0      0.053   13.4   0.0    1.0  1  FdhE             Protein involved in formate dehydrogenase fo
      0.075   12.9   0.0        1.3    8.9   0.0    2.1  2  HscB_4_cys       Co-chaperone HscB tetracysteine metal bindin
      0.085   12.2   1.7       0.21   11.0   1.7    1.6  1  zf-TFIIB         Transcription factor zinc-finger
       0.21   11.9   2.0        1.6    9.0   2.0    1.9  1  Prim_Zn_Ribbon   Zinc-binding domain of primase-helicase


Domain annotation for each model (and alignments):
>> Trm112p  Trm112p-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   1.3   1.2e-14   1.9e-11       1      68 []       2      49 ..       2      49 .. 0.84

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 1.2e-14
                                      BTGGCCC-B-TTTHHC--HHHHHHHHHTT---S-SS----SCHHTTEECCCCEEEETTTTEEEEEETT CS
                           Trm112p  1 kllllniLaCpackgpLdwealvevaalglnelpkekpedyellleldieegeLvCpncgraYpIkdG 68
                                      k++l++iLaCp+ckg L ++ + e                     e++i++g+L+C+ c+  Yp++dG
  gi|298674260|ref|YP_003726010.1|  2 KKELMDILACPICKGDLVLNIIEED--------------------EVEIKSGTLYCSQCREYYPVEDG 49
                                      789************9933333333....................389*******************9 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.7   3.9e-06    0.0064       2      25 ..      10      40 ..       9      49 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.9e-06
                                      EETTTTCEE.C......HEETSTTCEEESSS CS
                      TF_Zn_Ribbon  2 kCPnCgstn.l......veDpergelvCtdC 25
                                       CP+C+++  l      +++ ++g+l+C+ C
  gi|298674260|ref|YP_003726010.1| 10 ACPICKGDLvLniieedEVEIKSGTLYCSQC 40
                                      5******9855***888888*********** PP

>> Cys_rich_KTR  Cysteine-rich KTR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   4.1e-06    0.0067       4      35 ..       9      42 ..       6      47 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.1e-06
                      Cys_rich_KTR  4 vlcPvCgnkTRlkired..TvLknfpLfCPKCkq 35
                                      + cP+C++   l i e+   ++k   L+C  C++
  gi|298674260|ref|YP_003726010.1|  9 LACPICKGDLVLNIIEEdeVEIKSGTLYCSQCRE 42
                                      68*********99987622568999*******97 PP

>> zf-RRPl_C4  Putative ribonucleoprotein zinc-finger pf C4 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.6   1.3e-05     0.022      10      33 ..      26      49 ..       8      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.3e-05
                        zf-RRPl_C4 10 kklknlnetvyCeaCeiyfkvkne 33
                                       +++  + t+yC++C+ y+ v+++
  gi|298674260|ref|YP_003726010.1| 26 DEVEIKSGTLYCSQCREYYPVEDG 49
                                      56788899***********99886 PP

>> CK_II_beta  Casein kinase II regulatory subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.2   9.7e-06     0.016     100     137 ..      11      46 ..       1      52 [. 0.86

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9.7e-06
                        CK_II_beta 100 CprvlCekqkvLPvGlsdkpgektvklyCpkCedvYsp 137
                                       Cp  +C++  vL +   d+++ k+  lyC +C++ Y  
  gi|298674260|ref|YP_003726010.1|  11 CP--ICKGDLVLNIIEEDEVEIKSGTLYCSQCREYYPV 46 
                                       44..7*****************************9965 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.2   1.5e-05     0.024       2      36 ..       7      42 ..       6      51 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.5e-05
                   Lar_restr_allev  2 eLkpCPfCggravlersqrvvaeigq.cvyCadCga 36
                                      +++ CP C+g+ vl   +    ei   + yC +C  
  gi|298674260|ref|YP_003726010.1|  7 DILACPICKGDLVLNIIEEDEVEIKSgTLYCSQCRE 42
                                      6889*********98877777777777*******75 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.4e-05     0.023      17      58 ..       4      47 ..       1      56 [. 0.73

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.4e-05
                              Elf1 17 klptkFdCpfCnheksvevkldkkek...iaevsCkvCgesfetk 58
                                      +l     Cp C+ + ++++  + +      +++ C++C+e++ ++
  gi|298674260|ref|YP_003726010.1|  4 ELMDILACPICKGDLVLNIIEEDE-VeikSGTLYCSQCREYYPVE 47
                                      4777889*******5555543333.24779**********99765 PP

>> FdhE  Protein involved in formate dehydrogenase formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.3e-05     0.053     169     203 ..       9      43 ..       1      47 [. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.3e-05
                                       SS-TTT---EEEEEEE-------EEEEEETTT--E CS
                              FdhE 169 glCPvCgsaPvasvvriggeaeglRylhCslCete 203
                                         CP+C +  v  +++ ++ + +   l Cs C   
  gi|298674260|ref|YP_003726010.1|   9 LACPICKGDLVLNIIEEDEVEIKSGTLYCSQCREY 43 
                                       57******************************865 PP

>> HscB_4_cys  Co-chaperone HscB tetracysteine metal binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0       0.1   1.6e+02      16      23 ..       7      14 ..       1      16 [. 0.82
   2 ?    8.9   0.0    0.0008       1.3      17      24 ..      34      41 ..      29      42 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.1
                                      ---B-TTT CS
                        HscB_4_cys 16 defFCpqC 23
                                      d++ Cp C
  gi|298674260|ref|YP_003726010.1|  7 DILACPIC 14
                                      8899***9 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0008
                                      --B-TTT- CS
                        HscB_4_cys 17 efFCpqCR 24
                                       ++C+qCR
  gi|298674260|ref|YP_003726010.1| 34 TLYCSQCR 41
                                      689****9 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.7   0.00013      0.21       2      26 ..      11      41 ..      10      41 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00013
                          zf-TFIIB  2 CPkCqdele..eserggveid....yCpqCr 26
                                      CP C+ +l+  ++e ++vei+    yC qCr
  gi|298674260|ref|YP_003726010.1| 11 CPICKGDLVlnIIEEDEVEIKsgtlYCSQCR 41
                                      ****98877779999****987777999998 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   2.0     0.001       1.6       5      33 ..      10      41 ..       9      50 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.001
                                      --TTTT-TTTEE.ETT.......S-EEETTTTB CS
                    Prim_Zn_Ribbon  5 pCPvCGGrDrFr.fddkdgr...GtwfCrqCgg 33
                                      +CP+C+G      +++ +     Gt  C+qC +
  gi|298674260|ref|YP_003726010.1| 10 ACPICKGDLVLNiIEEDEVEiksGTLYCSQC-R 41
                                      69999999988855555555899********.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 385.53
//
Query:       gi|298674261|ref|YP_003726011.1|  [L=217]
Description: hypothetical protein Metev_0287 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
        6.6    7.6   7.4        2.1    9.2   0.4    2.3  2  HKR_ArcB_TM  Histidine kinase receptor ArcB trans-membrane do


Domain annotation for each model (and alignments):
>> HKR_ArcB_TM  Histidine kinase receptor ArcB trans-membrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.4   0.00012       2.1      29      61 ..     149     181 ..     145     188 .. 0.84
   2 ?    1.3   1.7     0.033   5.9e+02      41      61 ..     192     212 ..     185     215 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00012
                       HKR_ArcB_TM  29 slllsgeveiedllrsilfgllsaPwvlYFlsv 61 
                                        + ++++++++  +  ++ g+l+a +++YFls+
  gi|298674261|ref|YP_003726011.1| 149 AYSIKSSLDVSPRIALLIAGVLIASFMIYFLST 181
                                       56677888888889999**************96 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.033
                       HKR_ArcB_TM  41 llrsilfgllsaPwvlYFlsv 61 
                                       ++ ++++++l + +++Y + +
  gi|298674261|ref|YP_003726011.1| 192 FYPAVILAILFTALIMYLFLK 212
                                       667899999999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1581.96
//
Query:       gi|298674262|ref|YP_003726012.1|  [L=529]
Description: CTP synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   2.5e-124  413.9   0.2   3.3e-124  413.5   0.2    1.1  1  CTP_synth_N    CTP synthase N-terminus
    5.8e-55  186.0   0.0      1e-54  185.2   0.0    1.4  1  GATase         Glutamine amidotransferase class-I
    2.7e-05   24.2   0.0    6.2e-05   23.1   0.0    1.9  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
    0.00027   20.8   0.1     0.0014   18.4   0.1    2.3  2  Peptidase_C26  Peptidase C26
  ------ inclusion threshold ------
      0.029   13.4   0.4       0.15   11.1   0.2    1.9  2  MeaB           Methylmalonyl Co-A mutase-associated GTPase Me


Domain annotation for each model (and alignments):
>> CTP_synth_N  CTP synthase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  413.5   0.2  9.1e-128  3.3e-124       1     265 []       2     265 ..       2     265 .. 0.99

  Alignments for each domain:
  == domain 1  score: 413.5 bits;  conditional E-value: 9.1e-128
                                       EEEEEEE--STTTTHHHHHHHHHHHHHCTT--EEEEEEE-SSSSSSTT--CCCC--EEE-TT--EEETHHHHHHHHH CS
                       CTP_synth_N   1 kyilvtGGvvSglGkGiiaaslgallksrglkvtlikiDPYlnvdagtlsplehGEvfvlddGaetDlDlGnYeRfl 77 
                                       kyi+vtGGv+SglGkGi++as+g+ lk++g++vt+ikiDPY+n+dagt+sp++hGEv+vl+dG+e+DlDlGnYeRfl
  gi|298674262|ref|YP_003726012.1|   2 KYIVVTGGVMSGLGKGITTASIGRNLKNKGYRVTAIKIDPYINIDAGTMSPYQHGEVYVLKDGGEVDLDLGNYERFL 78 
                                       8**************************************************************************** PP

                                       T----GGGEEEHHHHHHHHHHHHHTTTTTT----CCCHHHHHHHHHHHHHH.HCT-SEEEEEE-S-TTSGGGHHHHH CS
                       CTP_synth_N  78 dikltkennittGkiyksviekerrGdylGktvqviphvtdeikeriekvakkveadvviveigGtvgdieslpfle 154
                                       d++lt+++nittGk y+svi+kerrG+ylGktvq+iphvt+eik++i++va+ + ad++++e+gGt+gdies+pfle
  gi|298674262|ref|YP_003726012.1|  79 DTELTHDHNITTGKFYNSVISKERRGEYLGKTVQIIPHVTNEIKDWIRDVASDSGADICLIEVGGTIGDIESMPFLE 155
                                       ***************************************************9999********************** PP

                                       HHHHHHHHH-TTTEEEEEEEE--B-TTTSSB-HHHHHHHHHHHHHHT---SEEEEEESS---HHHHHHHHHHCT--G CS
                       CTP_synth_N 155 airqlklelgkenvllihvtlvpvlkaagelktkptqhsvkelrslGiqpdiivcrsekeleeevkekialfcnvek 231
                                       a+rq++ e  +en++++hvtlvp  +a+ge+ktkptqhs +++r+lG++p+++v+r+e++l e++ +ki+lf++v++
  gi|298674262|ref|YP_003726012.1| 156 ALRQMHREEPEENTIFVHVTLVPL-DAQGEQKTKPTQHSTRDMRELGLTPNVVVARCEEPLLESTISKISLFSDVPE 231
                                       ***********************5.58************************************************** PP

                                       GGEEEEE--S-GGGHHHHHHHCTHHHHHHHHTT- CS
                       CTP_synth_N 232 eavisvkdvesiyevpllleeqglaelileklkl 265
                                       eavis++dve+iyevpl+le++gl+++++++l+l
  gi|298674262|ref|YP_003726012.1| 232 EAVISANDVEDIYEVPLMLEKEGLTNYLMKMLDL 265
                                       ******************************9976 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.2   0.0   2.8e-58     1e-54       2     190 .]     299     524 ..     298     524 .. 0.94

  Alignments for each domain:
  == domain 1  score: 185.2 bits;  conditional E-value: 2.8e-58
                                       EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHH....THHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-E CS
                            GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeile....llknpdgilvsgGpgspgvegkieaikearenkiPi 74 
                                       l D+y s+ e+l+ha++e g++ +  +ida+  + ++    +l+++dgilv+gG+g++g+egki+ai++are++iP+
  gi|298674262|ref|YP_003726012.1| 299 LGDSYISIREALKHAAIESGCNFKSTWIDAELINRDSdaleNLSEYDGILVPGGFGERGIEGKIKAIQYAREHDIPY 375
                                       66***************************98777755666459********************************** PP

                                       EEETHHHHHHHHHTTTEEE.......................EEECEEEEEEEEEEEETTT........CGGTTTTS CS
                            GATase  75 LGICLGmQllaiefgrkvv.......................kekekehhggtmrlgddet........allyglkn 120
                                       LG CLGmQl +ief+r+v                        ++k+  ++g+tmrlg +++        +++y   +
  gi|298674262|ref|YP_003726012.1| 376 LGLCLGMQLSVIEFARNVAglenanstefdpstphpvidilpEQKDLVNMGATMRLGTYKAclkqgtlaQQIYSA-D 451
                                       ****************9999999999999999999999****9****************99*******8888888.* PP

                                       EEEEEEEEEEEEESG...CHHHTTEEEEEEEETTEEEEEEEEETT.T.EEEESSBTTSTTSTTHHHHHHHHHHHH CS
                            GATase 121 evierhrHryevnpk...elepaglevtakseddeelmeiiekkn.p.fvgvQFHPEststpegpellfnflika 190
                                       e+ erhrHryevnp+   ++e++g++++a + ++ ++mei e ++ + f+  QFHPE+ts+p++p+++f+ +i+a
  gi|298674262|ref|YP_003726012.1| 452 EIVERHRHRYEVNPEyieKIEKHGMIFSAMN-NG-KRMEIAEIPEkKfFFTSQFHPEFTSRPGHPSPPFKAFIEA 524
                                       *****************************99.77.7*********889***********************9985 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   1.7e-08   6.2e-05       6      55 ..      10     264 ..       4     497 .. 0.62

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.7e-08
                                       SSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................ RF
                              CbiA   6 tkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................ 54 
                                         +G GK  ++a+++r l+++g+rV +++ Dp  n +a   g+    +                             
  gi|298674262|ref|YP_003726012.1|  10 VMSGLGKGITTASIGRNLKNKGYRVTAIKIDPYINIDA---GTMSPYQHgevyvlkdggevdldlgnyerfldtelt 83 
                                       479******************************99988...333333334666666677777777777777777777 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|298674262|ref|YP_003726012.1|  84 hdhnittgkfynsviskerrgeylgktvqiiphvtneikdwirdvasdsgadiclievggtigdiesmpflealrqm 160
                                       77777777777777777777777777777777777777777777777777777777777777766666666666666 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|298674262|ref|YP_003726012.1| 161 hreepeentifvhvtlvpldaqgeqktkptqhstrdmrelgltpnvvvarceepllestiskislfsdvpeeavisa 237
                                       66666666666666666666666666666666666666666666666666666666665555555555555555555 PP

                                       ..........................C CS
                                       ..........................x RF
                              CbiA  55 ..........................d 55 
                                                                 d
  gi|298674262|ref|YP_003726012.1| 238 ndvediyevplmlekegltnylmkmlD 264
                                       555555555555555555555555550 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.4   5.1e+03      50      67 ..     335     352 ..     331     353 .. 0.79
   2 !   18.4   0.1   3.9e-07    0.0014      96     216 .]     363     506 ..     358     506 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.4
                     Peptidase_C26  50 edvkaildkldgllltGg 67 
                                       +d+ + l++ dg+l++Gg
  gi|298674262|ref|YP_003726012.1| 335 SDALENLSEYDGILVPGG 352
                                       5566678999*******8 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 3.9e-07
                     Peptidase_C26  96 aLiraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhrehe..............q....saashavkve 154
                                       + i+ a e+++P lg C+G+ql  + +  +++   +++s++ d   ++                      + +  ++
  gi|298674262|ref|YP_003726012.1| 363 KAIQYAREHDIPYLGLCLGMQLSVIEFARNVAGLENANSTEFDPSTPHpvidilpeqkdlvnMgatmRLGTYKACLK 439
                                       56788999**************9998887776544443344433333357777776554443033334445555566 PP

                     Peptidase_C26 155 kgsllaellgseeievnslHhqaike......laeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                       +g+l +++++++ei     H+  ++         +++  +A+ +   +E  e++e+k f++  Q+HPE
  gi|298674262|ref|YP_003726012.1| 440 QGTLAQQIYSADEIVERHRHRYEVNPeyiekiEKHGMIFSAMNNGKRMEIAEIPEKK-FFFTSQFHPE 506
                                       999999999999999999***99887777775566788888899999********55.*********9 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   4.1e-05      0.15      34      74 ..       6      48 ..       2      51 .. 0.84
   2 ?   -0.6   0.0      0.14   5.2e+02     186     216 ..     256     287 ..     239     296 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.1e-05
                                      EEE..-TTSSHHHHHHHHHHHHHCTT--EEEEEE--------- CS
                              MeaB 34 ltG..vPGaGkstlvealglelrrrGkrvavlavDPsspftGG 74
                                      +tG  + G Gk  ++  +g +l+++G+rv+ + +DP  ++  G
  gi|298674262|ref|YP_003726012.1|  6 VTGgvMSGLGKGITTASIGRNLKNKGYRVTAIKIDPYINIDAG 48
                                      55544689****************************8777666 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHCSTT.BTTB--EEEEEBCCCTB CS
                              MeaB 186 arelraaleleeek.ekeWrpkvlktsavege 216
                                       +++l+++l+l++ + +++W+  v k+ + +ge
  gi|298674262|ref|YP_003726012.1| 256 TNYLMKMLDLKKITeDTSWNEMVSKMKSITGE 287
                                       578999999999885789*******9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (529 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 3490.02
//
Query:       gi|298674263|ref|YP_003726013.1|  [L=438]
Description: tRNA pseudouridine synthase D [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   3.7e-166  553.1   0.0   4.2e-166  552.9   0.0    1.0  1  TruD      tRNA pseudouridine synthase D (TruD)


Domain annotation for each model (and alignments):
>> TruD  tRNA pseudouridine synthase D (TruD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  552.9   0.0  2.3e-170  4.2e-166       2     416 .]      10     429 ..       9     429 .. 0.99

  Alignments for each domain:
  == domain 1  score: 552.9 bits;  conditional E-value: 2.3e-170
                              TruD   2 lgielyvtdtegigGrlrespeDFiVeEieefsgeeeadegeylvlrvekrnwdtldlvrelaralgisrkrvgfaG 78 
                                       +gi+ly+t+t+gigG+lr++ +DFiV+Ei   +++ee d+g+ylvl+++k+nw+t++l+r+l+r+lgis+kr+gfaG
  gi|298674263|ref|YP_003726013.1|  10 IGIDLYTTSTNGIGGTLRQEIDDFIVKEI---TNREEGDTGKYLVLELKKSNWETHHLIRDLTRKLGISQKRIGFAG 83 
                                       89***************************...666899*************************************** PP

                              TruD  79 tKDkrAvTtQlisirkvepeelealeikdvelevvgrarrklrlGdLaGNkFeirvrdv.aeeeeaakraeeileel 154
                                       tKDkrAvTtQ isi++++ e+++++++kd e++ +gr++++++lGdL+GN+F i+vr++ ++ +e+ +++e i++++
  gi|298674263|ref|YP_003726013.1|  84 TKDKRAVTTQKISIYDLSLEDINNVTLKDSEMNYIGRSDKSIELGDLIGNEFYITVRNTdHSIDELYNQLEIITKDI 160
                                       **********************************************************999999************* PP

                              TruD 155 eekggvPNyfGvQRFGsrrpvthlvGkaivkgdleeAvelyvgkpfeeesedtreareavaetgdleealeelpksl 231
                                       ++++g+PN+fGvQRFGs+rpvth+vG+ +v+gd e+A+ +y++ +f+ee+edt++ar++v et+d+ e+l+++p +l
  gi|298674263|ref|YP_003726013.1| 161 KQMEGIPNFFGVQRFGSTRPVTHIVGESLVRGDPEDAALKYIAFAFPEEPEDTKSARKYVYETRDYIEGLKLYPLRL 237
                                       ***************************************************************************** PP

                              TruD 232 ryErallkrLaekpkdykkAlealpknLqrlFvhAyqSylFNrvlseRlerglpldepveGDvvifaeer.lpdtdr 307
                                       ryEr+++++L+++p+dy++A+++lp+n+qr+FvhAyqSylFN++l++R+++glpl+++veGD+v+f++++ lpdt+r
  gi|298674263|ref|YP_003726013.1| 238 RYERSMMDYLIKNPDDYSGAFNVLPRNIQRIFVHAYQSYLFNKILCQRIKEGLPLNRAVEGDIVCFRNKAgLPDTSR 314
                                       *******************************************************************9999****** PP

                              TruD 308 lqlvteknveevkrliergrafvtaplvGtetelaegevgeierevleeegleledFklpklpelsskGtrRaillr 384
                                       +q vt++n++ +++li+r+rafvtapl+G++te+++g++geie+++++e+gl+ledFk+p++pel+skG rR+ill+
  gi|298674263|ref|YP_003726013.1| 315 IQEVTSTNIDGMNNLIKRKRAFVTAPLIGYQTEFSSGKPGEIEKKIFDETGLTLEDFKVPSTPELASKGVRREILLH 391
                                       ***************************************************************************** PP

                              TruD 385 ve......dlelsaeedeltleFsLpkGsYATvvlrEi 416
                                       +e      ++el+  +++++leF+LpkGsYAT++lrE+
  gi|298674263|ref|YP_003726013.1| 392 TEpsfkadEDELNPGKSKAVLEFTLPKGSYATTLLREY 429
                                       *****99988999************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 3189.65
//
Query:       gi|298674264|ref|YP_003726014.1|  [L=115]
Description: aminoacyl-tRNa hydrolase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.1e-40  135.8   0.2      9e-40  135.6   0.2    1.0  1  PTH2          Peptidyl-tRNA hydrolase PTH2
  ------ inclusion threshold ------
      0.023   14.7   0.0      0.041   13.9   0.0    1.4  1  HTH_19        Helix-turn-helix domain
       0.03   13.5   0.0       0.03   13.5   0.0    1.0  1  Phage_portal  Phage portal protein
      0.047   13.1   0.0      0.056   12.8   0.0    1.1  1  DUF4568       Domain of unknown function (DUF4568)
       0.13   12.6   0.1       0.19   12.1   0.1    1.2  1  DUF4288       Domain of unknown function (DUF4288)


Domain annotation for each model (and alignments):
>> PTH2  Peptidyl-tRNA hydrolase PTH2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.6   0.2   2.5e-43     9e-40       1     116 [.       4     114 ..       4     115 .] 0.97

  Alignments for each domain:
  == domain 1  score: 135.6 bits;  conditional E-value: 2.5e-43
                                       EEEEEEEESSSSS-HHHHHHHHHHHHHHHHHHHHHH.CHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHHHTT-S CS
                              PTH2   1 lkmvlvvrkDLkmskGkiaaqcahAavalvkkllkesnekellkeWeeegqkkivlkveseeeLlelaakakalglp 77 
                                       +k+++++r+DLk+skGk+a+q+ahAav+ v+k++k+     ++++W++ gqkk+vlkv+s ++L el++ a+++++p
  gi|298674264|ref|YP_003726014.1|   4 YKQCIIIREDLKLSKGKLATQAAHAAVSSVEKASKS-----TIENWKNGGQKKVVLKVPSLQDLYELKEIAEKKEIP 75 
                                       79*****************************99996.....5899******************************** PP

                                       EEEEEETSSSSSSTTCEEEEEEEEEEHHHHHHHHTTSEB CS
                              PTH2  78 aalirDagrtqiepgtkTvlaigPapksivdkvtgkLkl 116
                                       +ali+Dag+tqi++gt+T+l+igPa+ +++d++tg+Lkl
  gi|298674264|ref|YP_003726014.1|  76 TALISDAGHTQIPAGTVTALGIGPAKVEELDSFTGNLKL 114
                                       **************************************9 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.1e-05     0.041       7      54 ..      10      68 ..      10      83 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.1e-05
                            HTH_19  7 aReelgltqeelaerlgis.........rskisaiEng..kkdvpsaelllkiaealgi 54
                                      +Re l+l++ +la ++ +          +s i ++ ng  kk v++ + l++++e+ +i
  gi|298674264|ref|YP_003726014.1| 10 IREDLKLSKGKLATQAAHAavssvekasKSTIENWKNGgqKKVVLKVPSLQDLYELKEI 68
                                      7*************66666666888889***********65545555555444444333 PP

>> Phage_portal  Phage portal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   8.3e-06      0.03     104     177 ..       3      80 ..       1     112 [. 0.70

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.3e-06
                      Phage_portal 104 paddvlhirglpld.lkGlspleaareaielalaaeeyaakffkngarpsgilkikapgk...lseeqrek.lkeef 175
                                       ++++++ ir  +l   kG+   +aa  a+   ++a+++    +kng++ +++lk+++ ++   l+e + +k +  ++
  gi|298674264|ref|YP_003726014.1|   3 DYKQCIIIR-EDLKlSKGKLATQAAHAAVSSVEKASKSTIENWKNGGQKKVVLKVPSLQDlyeLKEIAEKKeIPTAL 78 
                                       678889999.444468899999*******************************666666644445544444455555 PP

                      Phage_portal 176 ee 177
                                        +
  gi|298674264|ref|YP_003726014.1|  79 IS 80 
                                       54 PP

>> DUF4568  Domain of unknown function (DUF4568)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.6e-05     0.056     122     177 ..      18      73 ..       7      81 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.6e-05
                           DUF4568 122 kkvvkrqqsfksikeapldlrswynrwricgeghlllkwqqlqalhqeeplaeekp 177
                                       k  +  q +   +      ++s  + w+  g+++ +lk   lq l+  +++ae+k+
  gi|298674264|ref|YP_003726014.1|  18 KGKLATQAAHAAVSSVEKASKSTIENWKNGGQKKVVLKVPSLQDLYELKEIAEKKE 73 
                                       44556677778888888999*******************************99875 PP

>> DUF4288  Domain of unknown function (DUF4288)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   5.4e-05      0.19      34      83 ..      26      74 ..      21      75 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.4e-05
                           DUF4288 34 eeeAyekaeklgkeeeepyknadgetvtwellavldvfelydelddgsEv 83
                                        +A+  +ek  k   e  kn  +++v +++ ++ d++el +e++++ E+
  gi|298674264|ref|YP_003726014.1| 26 AHAAVSSVEKASKSTIENWKNGGQKKVVLKVPSLQDLYEL-KEIAEKKEI 74
                                      57899*****9999**************************.999888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 688.02
//
Query:       gi|298674265|ref|YP_003726015.1|  [L=304]
Description: alpha-L-glutamate ligase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.5e-31  107.2   0.0    1.1e-30  106.6   0.0    1.3  1  RimK            RimK-like ATP-grasp domain
    1.9e-16   60.0   0.1    3.1e-16   59.3   0.1    1.3  1  GSH-S_ATP       Prokaryotic glutathione synthetase, ATP-grasp
    6.5e-11   42.5   0.0    1.2e-10   41.6   0.0    1.4  1  Rimk_N          RimK PreATP-grasp domain
    1.3e-09   37.7   0.0      2e-08   33.8   0.0    2.3  1  ATPgrasp_YheCD  YheC/D like ATP-grasp
    7.5e-05   22.1   0.2     0.0099   15.2   0.0    2.7  2  ATPgrasp_ST     Sugar-transfer associated ATP-grasp
    0.00023   21.3   0.1     0.0014   18.7   0.1    2.1  1  ATP-grasp_3     ATP-grasp domain
  ------ inclusion threshold ------
      0.028   14.7   0.0       0.06   13.6   0.0    1.5  1  Asparaginase_C  Glutaminase/Asparaginase C-terminal domain


Domain annotation for each model (and alignments):
>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.6   0.0   4.3e-34   1.1e-30       1     188 []     101     298 ..     101     298 .. 0.90

  Alignments for each domain:
  == domain 1  score: 106.6 bits;  conditional E-value: 4.3e-34
                                       HH-HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHH........HHHH CS
                              RimK   1 ardKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqkl........kqvl 69 
                                       a +K+ s  l+aka+++vp t+++++ e a k+++ ++     ++K v+g  Gi+++  k++  +        kq+ 
  gi|298674265|ref|YP_003726015.1| 101 AANKYYSTYLMAKANLPVPCTRVVQSVESALKTLDDFR---DAIIKPVFGFKGIGIIRIKNYSIIepdnttnpKQIE 174
                                       679*********************************96...89**************99988655111111114555 PP

                                       HHGGG--......EEEEE--SS-SEEEEEEEETTEEEEEEEEE--SSS----TTTT-EEEE----HHHHHHHHHHHH CS
                              RimK  70 ealkeai......lvqeyieeaenediRvlvvddevvaalrrvskeGdFRsnlhrGgvaeklqlseeekelAikaak 140
                                       e +k++i       +qeyi +  ++diR  vvd++v++a+ r++ +G +  nl +Gg  ++ +l++ +ke+ ikaak
  gi|298674265|ref|YP_003726015.1| 175 EMVKNEIdnkgmlYIQEYIPNM-GRDIRAYVVDGKVIGAIYRTAPDGKWLNNLSQGGSCQRCSLTPSQKEISIKAAK 250
                                       557777788888789****865.79**************************************************** PP

                                       HCT-SEEEEEEEEETTEEEEEEEESS--SHHHHHHHT--HHHHHHHHH CS
                              RimK 141 amelvvaGvDllrakrgllvlEvnsspglekiektlgidiakklieai 188
                                       +++ v+aGvDl++ ++  ++lEvn  p   +i k lgi+ a  ++++i
  gi|298674265|ref|YP_003726015.1| 251 TIGTVFAGVDLIEGNNKTMLLEVNGTPSGAGIYKSLGINPADYIMDYI 298
                                       ******************************************999987 PP

>> GSH-S_ATP  Prokaryotic glutathione synthetase, ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.3   0.1   1.2e-19   3.1e-16      12     162 ..     118     276 ..     108     285 .. 0.84

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 1.2e-19
                                       S--EEEES-HHHHHHHHHHHSSEEEEESS--TTTT-EEE-T.......T-TTHHHHHHHHTTTTTS-EE..EEE--G CS
                         GSH-S_ATP  12 ipktlvskdkeeirafleeqgdvilKPldgkgGegvfrvkk.......sdpnlksilellteegkepvi..aqrylp 79 
                                       +p t v +++e+  + l++ +d+i+KP+ g  G g++r+k+       + +n k+i e++ +e  ++ +  +q+y+p
  gi|298674265|ref|YP_003726015.1| 118 VPCTRVVQSVESALKTLDDFRDAIIKPVFGFKGIGIIRIKNysiiepdNTTNPKQIEEMVKNEIDNKGMlyIQEYIP 194
                                       68899999999999999*********************9863333332467889999999998666544238***** PP

                                       GGGG-EEEEEEETTEE-SEEEEEE--SS-S---GGGTSCEEEEE--HHHHHHHHHHHHHHHHTT--EEEEEEETT.. CS
                         GSH-S_ATP  80 eikeGDkRillvdGepigyalaRvpaegevRsnlaaggraeatelterdreiaeelapkLkekGllfvGlDvigd.. 154
                                       ++ + D R  +vdG+ ig a+ R + +g   +nl+ gg+ +  +lt +++ei+ + a++    G +f+G+D+i++  
  gi|298674265|ref|YP_003726015.1| 195 NMGR-DIRAYVVDGKVIG-AIYRTAPDGKWLNNLSQGGSCQRCSLTPSQKEISIKAAKT---IGTVFAGVDLIEGnn 266
                                       *998.*************.*********************************9988765...59*********8633 PP

                                       ..EEEEEE-S CS
                         GSH-S_ATP 155 ..kltEinvt 162
                                         +l E+n t
  gi|298674265|ref|YP_003726015.1| 267 ktMLLEVNGT 276
                                       3369999966 PP

>> Rimk_N  RimK PreATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.0   4.6e-14   1.2e-10       2      94 .]       3      98 ..       2      98 .. 0.93

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 4.6e-14
                            Rimk_N  2 kiaiLsrnpelystrrLveaaekrghevevldplrcylkieaekpevyykgekleefdavipR.igasi...tfygtav 76
                                      ki+i+ ++++ ++ r L +aa++r+ +  +++ ++++++i + + +  ++++ l+e+dav++R +ga +   + ++ +v
  gi|298674265|ref|YP_003726015.1|  3 KIGIIVTDNNDWTARALYNAAKERNFNPVFINLENIEVSIGS-TIRYSLRENSLSELDAVVVRdVGAGSiesVSFRFDV 80
                                      899**************************************9.78889999************998765345889**** PP

                            Rimk_N 77 lrqFemmgvfvlneseAi 94
                                      lrq+ ++g+ ++n++e+i
  gi|298674265|ref|YP_003726015.1| 81 LRQLYELGILIVNTPESI 98
                                      ***************998 PP

>> ATPgrasp_YheCD  YheC/D like ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.0   7.7e-12     2e-08      29     166 ..     118     235 ..     109     287 .. 0.88

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 7.7e-12
                    ATPgrasp_YheCD  29 LPetellesledleemlekyksvylKpanGskGkgilriekeekellllsrekkkkkkkrlaslselesllkkllkk 105
                                       +P t+ ++s e+  + l+ +++ ++Kp+ G kG gi+ri++            +  +  ++++ +++e+++k+ + +
  gi|298674265|ref|YP_003726015.1| 118 VPCTRVVQSVESALKTLDDFRDAIIKPVFGFKGIGIIRIKN-----------YSIIEPDNTTNPKQIEEMVKNEIDN 183
                                       799**************************************...........444456667899********99999 PP

                    ATPgrasp_YheCD 106 kr.ylvQqgidlatidgrpfDfRvlvqKngkgkWevtgiaaRiagkgsittnlsrGGtalpl 166
                                       k    +Q++i+ +       D+R+ v  +g    +v+g++ R+a++g+   nls+GG+  + 
  gi|298674265|ref|YP_003726015.1| 184 KGmLYIQEYIPNMG-----RDIRAYVV-DG----KVIGAIYRTAPDGKWLNNLSQGGSCQRC 235
                                       995669****9887.....7******9.33....69*********************98665 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   3.9e-06    0.0099      10     104 ..      92     181 ..      88     241 .. 0.81
   2 !    4.0   0.0    0.0099        25     231     267 ..     244     278 ..     238     290 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.9e-06
                       ATPgrasp_ST  10 yNpraefplvddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilviteredqd 86 
                                       +N  + +++ ++K   + l+ +a l+vp + +v +    ++++ + + ++ ++ +iKp+ g+ G Gi+ i++ +  +
  gi|298674265|ref|YP_003726015.1|  92 VNTPESIQNAANKYYSTYLMAKANLPVPCTRVVQS----VESALKTLDDF-RDAIIKPVFGFKGIGIIRIKNYSIIE 163
                                       6888999999*******************666555....55555555555.5678*************998876666 PP

                       ATPgrasp_ST  87 ylkssgksalldelerhv 104
                                         + ++ ++  + +++++
  gi|298674265|ref|YP_003726015.1| 164 PDNTTNPKQIEEMVKNEI 181
                                       666666666666666554 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0099
                       ATPgrasp_ST 231 laakaaeklpglgylGwDivldeekgplllElNarpg 267
                                       +  kaa+ + g    G+D+   ++k  +llE+N +p+
  gi|298674265|ref|YP_003726015.1| 244 ISIKAAK-TIGTVFAGVDLIEGNNK-TMLLEVNGTPS 278
                                       5556666.66666778887555555.88888888854 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   5.3e-07    0.0014       1     156 [.     101     275 ..     101     280 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 5.3e-07
                                       HTSHHHHHHHHTTT.S---..........-EESS--SSSEEEEESS-------B--SS--TTE.............. CS
                       ATP-grasp_3   1 asdKlktykkLkeagvkvP......tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve....... 64 
                                       a++K+ ++  + +a+++vP      +  +a +        ++Kp+ G  g ++  +++    e    + +       
  gi|298674265|ref|YP_003726015.1| 101 AANKYYSTYLMAKANLPVPctrvvqSVESALKTLDDFRDAIIKPVFGFKGIGIIRIKNYSIIEPDNTT-Npkqieem 176
                                       689**9999999999****76555222233334444999***************99998544433222.13556788 PP

                                       ...........EEEE---..SEEEEEEEEE.SSSEEEEEEEEEEEET....TEEEEEEES----HHHHHHHHHHHHH CS
                       ATP-grasp_3  65 ...........lvqefie..GkplSvsllsdgekvlvlavnrqliekaekefvyaGnvtpietelkeevvelaeevv 128
                                                   +qe+i+  G+++ + ++      ++ a+ r   + +++++  +G++ +   +l+ +  e+  ++ 
  gi|298674265|ref|YP_003726015.1| 177 vkneidnkgmlYIQEYIPnmGRDIRAYVVD---GKVIGAIYRTAPDGKWLNNLSQGGSCQRC-SLTPSQKEISIKAA 249
                                       8999******999****8335555555554...34677888899999999988888887644.55555555555555 PP

                                       TTSTT--EEEEEEEEESS.SEEEEEEES CS
                       ATP-grasp_3 129 ekleglaGyvGvDlvlkdeepyviEvNP 156
                                       + + g++ ++GvDl+  +++ +++EvN 
  gi|298674265|ref|YP_003726015.1| 250 KTI-GTV-FAGVDLIEGNNKTMLLEVNG 275
                                       555.333.99*****************6 PP

>> Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.4e-05      0.06      22      69 ..      56     105 ..      42     129 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.4e-05
                                       TT--EEEEEEBTTTB--H..HHHHHHHHHHTTT-EEEEEESSSBS----- CS
                    Asparaginase_C  22 kgakGvvlegtGvGnlps..allealkeakargivvvatsqcpsgsvsns 69 
                                       +++++vv+  +G+G+++s     ++l+++ + gi++v+t   ++   ++ 
  gi|298674265|ref|YP_003726015.1|  56 SELDAVVVRDVGAGSIESvsFRFDVLRQLYELGILIVNTPESIQNAANKY 105
                                       468**************985456899999999******998888776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 1932.02
//
Query:       gi|298674266|ref|YP_003726016.1|  [L=103]
Description: hypothetical protein Metev_0292 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00048   20.5   4.5    0.00048   20.5   4.5    2.1  2  DUF3566   Transmembrane domain of unknown function (DUF3566)
  ------ inclusion threshold ------
      0.094   12.2  12.2        0.1   12.2  12.2    1.1  1  DUF1700   Protein of unknown function (DUF1700)
        0.7    9.6  15.0          1    9.1  15.0    1.2  1  Yip1      Yip1 domain
        1.3    9.5  18.8       0.36   11.3   4.3    2.5  3  HRG       Haem-transporter, endosomal/lysosomal, haem-respons
          4    7.5  12.1       0.61   10.1   2.6    2.4  2  DUF4514   Domain of unknown function (DUF4514)
        5.9    6.8  16.3        1.9    8.4   4.2    2.4  2  MtrG      Tetrahydromethanopterin S-methyltransferase, subuni
          7    6.8   7.7        8.2    6.6   0.3    2.2  2  DUF4229   Protein of unknown function (DUF4229)
        8.5    6.5  13.6       0.65   10.1   2.4    2.7  2  DUF2953   Protein of unknown function (DUF2953)


Domain annotation for each model (and alignments):
>> DUF3566  Transmembrane domain of unknown function (DUF3566)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   1.4     0.034        77      10     101 ..       8      36 ..       2      50 .. 0.48
   2 !   20.5   4.5   2.2e-07   0.00048      77     117 ..      56      98 ..      43      99 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.034
                           DUF3566  10 rvdpwSvlklsfllsvalfivlvvavavlylvldalgvfdkvnslvkdlvgeessldleevlslgrvlslaalvgvv 86 
                                       r+  +S  k+                                                               +g++
  gi|298674266|ref|YP_003726016.1|   8 RIGELSLGKI---------------------------------------------------------------LGII 21 
                                       4555555443...............................................................3333 PP

                           DUF3566  87 nvvlltalatlaall 101
                                        +v+  +++++++++
  gi|298674266|ref|YP_003726016.1|  22 YAVIGLIIGVIVSFV 36 
                                       333333333333332 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 2.2e-07
                           DUF3566  77 lslaalvg..vvnvvlltalatlaallYNlvadlvGGlevtLa 117
                                       +++aa++   v+  ++  +l+ ++a++YNl+a ++GGle+ L+
  gi|298674266|ref|YP_003726016.1|  56 FGAAAIITmpVFYGIMGFVLGLIIAVIYNLIAGFIGGLEIDLE 98 
                                       5566665522455677889*********************995 PP

>> DUF1700  Protein of unknown function (DUF1700)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2  12.2   4.4e-05       0.1      92     164 ..      13      90 ..       1      97 [. 0.67

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.4e-05
                           DUF1700  92 nlilvlipliviislvlsllvvalallvspl.....vllvksllkgfeelslnvfvsigllglGllllivayylvki 163
                                       +l  +l ++ ++i l++ ++v  ++l+++ +     +   + l+++   +++ vf +i+ + lGl+++++ + ++ +
  gi|298674266|ref|YP_003726016.1|  13 SLGKILGIIYAVIGLIIGVIVSFVTLIAGNIgmgnaIGGPAYLFGAAAIITMPVFYGIMGFVLGLIIAVIYNLIAGF 89 
                                       44446666666666666666655555544441111033446799999999999*****************9988766 PP

                           DUF1700 164 l 164
                                       +
  gi|298674266|ref|YP_003726016.1|  90 I 90 
                                       5 PP

>> Yip1  Yip1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1  15.0   0.00045         1      29      93 ..      22      92 ..       9      94 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00045
                              Yip1 29 lalltlllgllas........lnlgqtlasgeevqgltlssllgaiiggylglllgllllalllhliakllgg 93
                                       a+++l+ g+++s          +g+ ++++  ++ ++  +++++++++ +++++  l++a++++lia + gg
  gi|298674266|ref|YP_003726016.1| 22 YAVIGLIIGVIVSfvtliagnIGMGNAIGGP--AYLFGAAAIITMPVFYGIMGFVLGLIIAVIYNLIAGFIGG 92
                                      4444444444444442233334445555555..89999999999999999999**************998887 PP

>> HRG  Haem-transporter, endosomal/lysosomal, haem-responsive gene
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   4.8     0.012        27       5      25 ..      20      40 ..      18      44 .. 0.90
   2 ?   -1.1   0.0       1.2   2.7e+03      11      25 ..      50      64 ..      43      67 .. 0.68
   3 ?   11.3   4.3   0.00016      0.36       5      28 ..      66      89 ..      62      92 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.012
                               HRG  5 iaygifgsilglsaflvylvl 25
                                      i y+++g+i+g+++ +v l++
  gi|298674266|ref|YP_003726016.1| 20 IIYAVIGLIIGVIVSFVTLIA 40
                                      89*************999988 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.2
                               HRG 11 gsilglsaflvylvl 25
                                      g+   l+++++ +++
  gi|298674266|ref|YP_003726016.1| 50 GGPAYLFGAAAIITM 64
                                      555667777777776 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00016
                               HRG  5 iaygifgsilglsaflvylvlaiv 28
                                      ++ygi g++lgl+++++y+ +a++
  gi|298674266|ref|YP_003726016.1| 66 VFYGIMGFVLGLIIAVIYNLIAGF 89
                                      68******************9986 PP

>> DUF4514  Domain of unknown function (DUF4514)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.6   0.00027      0.61      19      37 ..      19      37 ..      12      47 .. 0.82
   2 ?    2.9   2.1      0.05   1.1e+02      15      35 ..      61      81 ..      48      92 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00027
                           DUF4514 19 diKYaiiGtalGvaisAgF 37
                                       i Ya+iG ++Gv++s + 
  gi|298674266|ref|YP_003726016.1| 19 GIIYAVIGLIIGVIVSFVT 37
                                      578************9654 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.05
                           DUF4514 15 gaeidiKYaiiGtalGvaisA 35
                                         + + Y i+G  lG +i+ 
  gi|298674266|ref|YP_003726016.1| 61 IITMPVFYGIMGFVLGLIIAV 81
                                      55566779*********9985 PP

>> MtrG  Tetrahydromethanopterin S-methyltransferase, subunit G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   4.2   0.00085       1.9      33      61 ..       5      33 ..       1      39 [. 0.71
   2 ?    4.3   4.3     0.016        37      49      63 ..      71      85 ..      61      86 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00085
                              MtrG 33 iaqriGk.kvGRdiGilYGlviGliillvy 61
                                      i++riG  ++G+ +Gi+Y +viGlii ++ 
  gi|298674266|ref|YP_003726016.1|  5 IIKRIGElSLGKILGIIY-AVIGLIIGVIV 33
                                      7889997579********.45566665554 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.016
                              MtrG 49 YGlviGliillvyil 63
                                       G+v+Glii ++y l
  gi|298674266|ref|YP_003726016.1| 71 MGFVLGLIIAVIYNL 85
                                      3899*********87 PP

>> DUF4229  Protein of unknown function (DUF4229)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.3    0.0036       8.2      30      50 ..      18      38 ..       4      41 .. 0.80
   2 ?    3.7   2.1      0.03        67      18      44 ..      55      82 ..      48      90 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0036
                           DUF4229 30 pllvaallAlvvalplSmvll 50
                                        ++ a+++l++  ++S+v l
  gi|298674266|ref|YP_003726016.1| 18 LGIIYAVIGLIIGVIVSFVTL 38
                                      5678899***********987 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.03
                           DUF4229 18 illvarliglp.vpllvaallAlvvalp 44
                                      ++++a +i++p +  ++ ++l+l++a +
  gi|298674266|ref|YP_003726016.1| 55 LFGAAAIITMPvFYGIMGFVLGLIIAVI 82
                                      6777888888898888888999999875 PP

>> DUF2953  Protein of unknown function (DUF2953)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.4   0.00029      0.65      12      35 ..      15      38 ..      15      43 .. 0.87
   2 ?    2.8   2.1     0.055   1.2e+02      14      32 ..      67      85 ..      60      93 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00029
                           DUF2953 12 gilyGliwaikgllygllsnlfni 35
                                      g ++G+i+a++gl++g++ +++++
  gi|298674266|ref|YP_003726016.1| 15 GKILGIIYAVIGLIIGVIVSFVTL 38
                                      789**************9888765 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.055
                           DUF2953 14 lyGliwaikgllygllsnl 32
                                      +yG+   + gl++++++nl
  gi|298674266|ref|YP_003726016.1| 67 FYGIMGFVLGLIIAVIYNL 85
                                      6888888999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1105  (0.061632); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 653.99
//
Query:       gi|298674267|ref|YP_003726017.1|  [L=84]
Description: hypothetical protein Metev_0293 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 542.99
//
Query:       gi|298674268|ref|YP_003726018.1|  [L=226]
Description: hypothetical protein Metev_0295 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-46  158.6   1.9    1.7e-46  158.0   1.9    1.3  1  DUF5616   Domain of unknown function (DUF5616)
    9.3e-23   79.7   0.1    1.9e-22   78.7   0.1    1.5  1  DUF434    Protein of unknown function (DUF434)


Domain annotation for each model (and alignments):
>> DUF5616  Domain of unknown function (DUF5616)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.0   1.9   1.9e-50   1.7e-46       1     140 []      73     214 ..      73     214 .. 0.97

  Alignments for each domain:
  == domain 1  score: 158.0 bits;  conditional E-value: 1.9e-50
                           DUF5616   1 leelkgkelliDGfNvlitlesalsgevlllcdDgviRDlagvrgkyklveeteealelilellkelkvkkvifllD 77 
                                       ++++++ +l+iDG+Nv it+es+l++ +l+++dDg++RD++g+++k+k+++ t +a++ i+++l ++++++vi+l+D
  gi|298674268|ref|YP_003726018.1|  73 CNQINNMNLIIDGYNVFITVESLLKNYILWKSDDGFFRDTRGIFNKFKITDVTYKAIDEIITFLLKYQINSVIILFD 149
                                       6899************************************************************************* PP

                           DUF5616  78 kpvSnSgelaklireileeaglegevelvknvDkeLkesee..ivatsDsvildkvksvldlaae 140
                                       k++S+Sgela+++ e+l++++++g ++++++vD++Lk+ ++  i+atsD++++d+ k+v+d++++
  gi|298674268|ref|YP_003726018.1| 150 KQISKSGELARFVSEKLKNYSIKGYARTSRHVDFDLKNNSSdyIIATSDGAVIDNSKQVIDIPEC 214
                                       *************************************766666*******************986 PP

>> DUF434  Protein of unknown function (DUF434)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.7   0.1   2.2e-26   1.9e-22       1      55 [.      14      68 ..      14      68 .. 0.98

  Alignments for each domain:
  == domain 1  score: 78.7 bits;  conditional E-value: 2.2e-26
                            DUF434  1 kLkeAaeDlryLLnRGYpkksalelVgnhYqLskrqRlaLaRcvssdeeiearks 55
                                      kL+e+a D+ryL nRGYp++s++++VgnhY+L++++R++L+R+v+s++ ++ rk+
  gi|298674268|ref|YP_003726018.1| 14 KLSEPAVDVRYLFNRGYPRTSTIQFVGNHYRLNEEERHILTRVVVSSNRSKLRKQ 68
                                      799**************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       737  (0.0411066); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1396.59
//
Query:       gi|298674269|ref|YP_003726019.1|  [L=325]
Description: alanine dehydrogenase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.6e-105  352.6   0.1   1.8e-105  352.4   0.1    1.0  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil
     0.0025   18.4   0.0      0.007   16.9   0.0    1.7  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.022   15.2   0.0      0.061   13.8   0.0    1.7  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma


Domain annotation for each model (and alignments):
>> OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  352.4   0.1    3e-109  1.8e-105       6     317 ..       6     316 ..       1     317 [. 0.96

  Alignments for each domain:
  == domain 1  score: 352.4 bits;  conditional E-value: 3e-109
                                       E-HHHHHCCH-HCCCHHHHHHHHHHHHCC-CE----EEEEECCGTEEEEEEEEEETTTTEEEEEEEEEETTTCCCTS CS
                   OCD_Mu_crystall   6 ltaveveeelllddlakaveeafrrlasgkvkkpprvalevkdsrgelevmpaylagrellgvKlvnshpenkksgl 82 
                                       l +++v++ l ++  +++ve+af++  + +v++p +++l +++++g+l+ mp+yl+  +  gvK+vn+hp+n+ + l
  gi|298674269|ref|YP_003726019.1|   6 LNQSDVKNVLDMKSTIDVVEKAFEQHGLKRVQMPSKLYLYFNKYNGDLRTMPTYLEDMDISGVKIVNVHPDNPSRDL 82 
                                       5789*********************9999************************************************ PP

                                       SSEEEEEEEE-TTT--EEEEEE-HHHHHHHHHHHHHHHHHHHS-TT--EEEEE--SHHHHHHHHHHCCCS--SEEEE CS
                   OCD_Mu_crystall  83 ptvtalvvLndpetGvplalmdatlltalRTaAvsavaakyLarkdasvlaiiGaGvqaetqlealkavldikevri 159
                                       ptv+a+v+Ln++etG+p+ +md+t+lt++RT+A ++vaakyLar+d++ ++iiG G qa++ql+al+++++i++v+i
  gi|298674269|ref|YP_003726019.1|  83 PTVMATVILNSTETGAPISIMDGTYLTDMRTGAGGGVAAKYLARPDSKIIGIIGTGNQARSQLLALSHIFNIEQVKI 159
                                       ***************************************************************************** PP

                                       E-SSHHHHHHHHHHCCS.CTT-EEECSCHHHHTTSSEEEE----SS-SB-GGGS-TT-EEEE-S--STT--SB-HHH CS
                   OCD_Mu_crystall 160 ydrdeeaaekfaenlqefefevsackseeeavegadivvtvTaakapilkaewvkpGahinavgadapgkteLdddi 236
                                          + +  + f ++++   +     k   + v ++di+vt+T+ + pi+k ew+++G+hina+gada gk+eL+ +i
  gi|298674269|ref|YP_003726019.1| 160 TSKSSKHCDEFEKRMKP-VVGGDFTKTDIKDVCDCDILVTTTPVRDPIVKFEWINEGTHINAIGADARGKQELESEI 235
                                       ****************6.3333445556667899******************************************* PP

                                       HHCCEEEESHHHHHHHCCCCHCHHHTTSSTCGGEEEEHHHHHCTSS-..-STTSEEEEE----HHHHHHHHHHHHHH CS
                   OCD_Mu_crystall 237 lkradifvdseaqareeGeiqvaiekgvlaedakvaelgeviaGkkpGRtsdeeitlfdsvGlaveDvaaaklvyer 313
                                       lk ++++vd+ +qa ++Gei+v++++++++  ++  elge+i+G+++GR+s +eit+fds+Gla++D+++a +vy +
  gi|298674269|ref|YP_003726019.1| 236 LKSSKVIVDDTEQASHSGEINVPLSNNIISTTDIYGELGEIITGHLTGRESRKEITIFDSTGLAIQDISTADFVYRK 312
                                       ****************************************************************************9 PP

                                       HCCC CS
                   OCD_Mu_crystall 314 aeek 317
                                       a e+
  gi|298674269|ref|YP_003726019.1| 313 AVEN 316
                                       9875 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.2e-06     0.007       2      71 ..     132     202 ..     131     206 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.2e-06
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC....-EEECECHHHHHHH-SEEEE-S-H CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg....vkvtavdneeaaeeadvvvlavkp 71 
                                       igiiG+Gn++++ ++ l++  ++ +++ ++ s++ +  +e++++++     + t++d +++++ +d++v + + 
  gi|298674269|ref|YP_003726019.1| 132 IGIIGTGNQARSQLLALSHI-FNIEQVKIT-SKSSKHCDEFEKRMKpvvgGDFTKTDIKDVCD-CDILVTTTPV 202
                                       9***********99988777.699****55.*************9988887888889999997.9999988876 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     1e-05     0.061       2      75 ..     132     201 ..     131     204 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1e-05
                                       EEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SC CS
                    Semialdhyde_dh   2 vaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalp 75 
                                       ++i+G tG+  +  l  L++ +++e v ++s+s+++  +++++   ++ +    ++++d++++ ++di+++ +p
  gi|298674269|ref|YP_003726019.1| 132 IGIIG-TGNQARSQLLALSHIFNIEQVKITSKSSKHCDEFEKR---MKPVVGGDFTKTDIKDVCDCDILVTTTP 201
                                       79***.****************************555555555...6689999999999***********9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2088.77
//
Query:       gi|298674270|ref|YP_003726020.1|  [L=67]
Description: hypothetical protein Metev_0297 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00039   20.0   1.7    0.00058   19.4   1.7    1.3  1  zf-tcix         Putative treble-clef, zinc-finger, Zn-binding
      0.006   16.4   0.9     0.0061   16.4   0.9    1.1  1  MCM_OB          MCM OB domain
  ------ inclusion threshold ------
       0.01   15.2   1.0      0.017   14.5   1.0    1.5  1  zf-ribbon_3     zinc-ribbon domain
      0.017   15.4   0.4      0.019   15.4   0.4    1.1  1  Rhodanese_C     Rhodanase C-terminal
      0.024   14.5   0.8      0.047   13.6   0.8    1.5  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.067   13.1   1.8       0.08   12.9   1.8    1.1  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain


Domain annotation for each model (and alignments):
>> zf-tcix  Putative treble-clef, zinc-finger, Zn-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   1.7   1.9e-07   0.00058       6      34 ..      17      47 ..      13      53 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.9e-07
                           zf-tcix  6 tlRGvrkCpkCGtyN..GtRglsCkNkaCdq 34
                                      t++   +CpkCGty   G   + C N++C +
  gi|298674270|ref|YP_003726020.1| 17 TKKTMQRCPKCGTYQkvGDEPQKCVNEKCRA 47
                                      6667789******9555************75 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.9     2e-06    0.0061      27      62 ..      14      48 ..       4      66 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2e-06
                                      EEEEEEEEEEETTT-.-EEES----SB-..TTT-HH CS
                            MCM_OB 27 kpklkkavfeckkcgktveveleePrkCeekeCesk 62
                                      k+  kk++ +c+kcg+ ++v   eP+kC +++C+++
  gi|298674270|ref|YP_003726020.1| 14 KSITKKTMQRCPKCGTYQKV-GDEPQKCVNEKCRAE 48
                                      5667888999*****86664.578*********943 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.0   5.7e-06     0.017       2      16 ..      21      35 ..      20      42 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.7e-06
                       zf-ribbon_3  2 tvrCPnCGa.plssdd 16
                                      ++rCP+CG+ + + +d
  gi|298674270|ref|YP_003726020.1| 21 MQRCPKCGTyQ-KVGD 35
                                      89*******99.5444 PP

>> Rhodanese_C  Rhodanase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.4   6.2e-06     0.019      13      46 ..      16      50 ..       5      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.2e-06
                       Rhodanese_C 13 lksevvgkCieCgkpvdelr.krnCanedCnelvl 46
                                      ++++++ +C  Cg+  +     ++C ne+C+  ++
  gi|298674270|ref|YP_003726020.1| 16 ITKKTMQRCPKCGTYQKVGDePQKCVNEKCRAEII 50
                                      467799*******987754579*********9987 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.8   1.6e-05     0.047      11      21 ..      21      31 ..      20      31 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.6e-05
                           DUF35_N 11 gqrCpdCGtvq 21
                                       qrCp+CGt+q
  gi|298674270|ref|YP_003726020.1| 21 MQRCPKCGTYQ 31
                                      6********97 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.8   2.7e-05      0.08      27      58 ..      20      51 ..      12      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.7e-05
                    OrfB_Zn_ribbon 27 TSktCseCgsknkealsgrtfkCpnCgfeadr 58
                                      T ++C++Cg  +k  +++++ + ++C +e+ r
  gi|298674270|ref|YP_003726020.1| 20 TMQRCPKCGTYQKVGDEPQKCVNEKCRAEIIR 51
                                      779***********999999******998655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 421.54
//
Query:       gi|298674271|ref|YP_003726021.1|  [L=184]
Description: PEBP family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-34  117.9   0.0    4.6e-34  117.6   0.0    1.1  1  PBP       Phosphatidylethanolamine-binding protein


Domain annotation for each model (and alignments):
>> PBP  Phosphatidylethanolamine-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.6   0.0   2.6e-38   4.6e-34       2     132 .]      55     182 ..      54     182 .. 0.92

  Alignments for each domain:
  == domain 1  score: 117.6 bits;  conditional E-value: 2.6e-38
                                       --GGG..CSBGGS-EEEEES--TTSSEEEEEEEETTSCCTCTTEEEEEEEEEETTSSEE-TTC...EE-B-TTSSCC CS
                               PBP   2 lpkky..egentsPplswsdvpegtksyalvviDpDapkvsetflHwvvtnipasvtslpega...vqgknslgees 73 
                                       +p++y  +gen++Ppl++s++p+++ks++l+v+D Dap ++  f+Hw+v+ni+++ + +++ +   ++g+ns+ge  
  gi|298674271|ref|YP_003726021.1|  55 IPVAYtcDGENINPPLQFSGIPDDAKSLVLIVEDSDAP-DGV-FTHWIVWNINPESNIMEN-SvpgIEGENSFGE-- 126
                                       78888889******************************.555.*********966655554.559**********.. PP

                                       CCS---B--STTS..EEEEEEEEEESSSG--BGSS-SHHHHHHHHCTTEEEEEEEEEEE CS
                               PBP  74 esgYlgpcPpkgdgkHrYvfllyaldvealdlkagftraelgaaiaghvlakatlagnY 132
                                         +Y+gpcPp  + +HrY+f +yald+e  +l+ g++r++l++a++gh+lak +l g Y
  gi|298674271|ref|YP_003726021.1| 127 -VSYGGPCPPSDT-THRYIFGVYALDTEL-NLDGGANRQNLENAMDGHILAKGELIGLY 182
                                       .************.6*************5.89***********************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 1323.39
//
Query:       gi|298674272|ref|YP_003726022.1|  [L=281]
Description: mechanosensitive ion channel protein MscS [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-52  177.3   9.3    2.7e-52  177.3   9.3    1.6  2  MS_channel       Mechanosensitive ion channel
  ------ inclusion threshold ------
        6.1    7.3   7.3        2.8    8.4   0.8    3.3  4  Phage_holin_6_1  Bacteriophage holin of superfamily 6 (Holin_


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -5.7   4.4         2   1.8e+04       2      20 ..      19      37 ..      17      41 .. 0.58
   2 !  177.3   9.3     3e-56   2.7e-52       3     206 .]      60     257 ..      58     257 .. 0.96

  Alignments for each domain:
  == domain 1  score: -5.7 bits;  conditional E-value: 2
                                      .HHHHHHHHHHHHHHHHTT CS
                        MS_channel  2 kilkiliivvgilivlsll 20
                                      ki++++i++++ l +++ +
  gi|298674272|ref|YP_003726022.1| 19 KIFSVVIFILIALFISKII 37
                                      4556666666666665555 PP

  == domain 2  score: 177.3 bits;  conditional E-value: 3e-56
                                       HHHHHHH.HHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEE CS
                        MS_channel   3 ilkilii.vvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVed 78 
                                       ++++ ii v++ + +l  +g+++s+ll++ G++g+++g+a+++++ nl++Gi+l++e+p+kiG+ v+i + +G+Ved
  gi|298674272|ref|YP_003726022.1|  60 LIYYSIItVTIGIFILPIVGIQPSSLLVAGGIVGIVIGFASQSIVGNLISGIFLIVERPIKIGNQVNIDNNIGIVED 136
                                       555655505566899************************************************************** PP

                                       E-SSEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS- CS
                        MS_channel  79 iglrttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdke 155
                                       i+l +t irtfdg ++ iPn++++t+ni+N+   + +rr+++ +g++ys d   +e++++++k+ ++++p  lk +e
  gi|298674272|ref|YP_003726022.1| 137 INLISTIIRTFDGLYIRIPNEKVFTNNITNYVA-NVARRFEYIVGIRYSDD---AEQAIDIIKDLIEKEPLALKHPE 209
                                       *********************************.*****************...*********************** PP

                                       EEEEEEEE-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT--- CS
                        MS_channel 156 llvvldefgdsslnfevrvfvktvvpeeylsvqseinlrikkileeegiei 206
                                        lv++d++g++++n+ vr++++     e++s+++++  +ik  le +giei
  gi|298674272|ref|YP_003726022.1| 210 SLVFVDNLGNNAVNLSVRIWAPA---TEWFSLRTSFLWKIKTTLEDNGIEI 257
                                       ***********************...9**********************97 PP

>> Phage_holin_6_1  Bacteriophage holin of superfamily 6 (Holin_LLH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.8   0.00032       2.8       3      30 ..      15      41 ..      14      55 .. 0.83
   2 ?   -0.2   0.2      0.15   1.3e+03      10      26 ..      89     105 ..      83     131 .. 0.79
   3 ?   -1.0   0.0      0.27   2.4e+03      33      50 ..     207     224 ..     189     258 .. 0.77
   4 ?   -1.1   0.0      0.29   2.6e+03      28      57 ..     244     273 ..     217     279 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00032
                   Phage_holin_6_1  3 eilvsvlviiitivlgllvkkikkllkl 30
                                      eil+++++++i i+++l+ +ki+ ++ l
  gi|298674272|ref|YP_003726022.1| 15 EILIKIFSVVIFILIALFISKIITVY-L 41
                                      799*******************9988.3 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.15
                   Phage_holin_6_1  10 viiitivlgllvkkikk 26 
                                         i++iv+g++++ i+ 
  gi|298674272|ref|YP_003726022.1|  89 GGIVGIVIGFASQSIVG 105
                                       56999999999998875 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.27
                   Phage_holin_6_1  33 qgekakkiaeiaknaVka 50 
                                         e ++ ++++ +naV++
  gi|298674272|ref|YP_003726022.1| 207 HPESLVFVDNLGNNAVNL 224
                                       556778888888888886 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 0.29
                   Phage_holin_6_1  28 lklkkqgekakkiaeiaknaVkaveqvake 57 
                                        k+k++ e +    +  + +V +++q+  e
  gi|298674272|ref|YP_003726022.1| 244 WKIKTTLEDNGIEIAFPQRTVWFANQTQGE 273
                                       466666665554444468888888887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       977  (0.0544927); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1912.27
//
Query:       gi|298674273|ref|YP_003726023.1|  [L=242]
Description: hypothetical protein Metev_0300 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-45  153.2   0.5    5.7e-45  152.5   0.5    1.4  1  DUF432    Protein of unknown function (DUF432)


Domain annotation for each model (and alignments):
>> DUF432  Protein of unknown function (DUF432)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.5   0.5   3.2e-49   5.7e-45       1     123 []      61     184 ..      61     184 .. 0.98

  Alignments for each domain:
  == domain 1  score: 152.5 bits;  conditional E-value: 3.2e-49
                            DUF432   1 Pvnlpkeitkyllveleeplvvepkseveiyvkvpveigvfik.skkeveliDvfslskkkYaLYGspesGviaryv 76 
                                       Pvnlpk+it++ll+e++++++++p+s ++iy+++p+eigvfi+ +k+++e++D+f+l+kkkY++YG+p++G+i++y+
  gi|298674273|ref|YP_003726023.1|  61 PVNLPKKITSLLLIEFTKSIFISPSSIKKIYLTFPIEIGVFISdNKDNYEVLDFFTLAKKKYSIYGTPSNGTICKYW 137
                                       9****************************************5559******************************** PP

                            DUF432  77 ksevyseppeldpleeavveleikNetdevvevskivfdalglklyy 123
                                        s+++ ++pe++pl+e+++el+i+N+t +++evsk+v++a+g+klyy
  gi|298674273|ref|YP_003726023.1| 138 SSDTHLSIPETNPLYEGILELQITNSTVRWMEVSKTVLNAYGMKLYY 184
                                       **********************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1631.92
//
Query:       gi|298674274|ref|YP_003726024.1|  [L=146]
Description: UspA domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-37  128.3   0.0    3.2e-37  128.2   0.0    1.0  1  Usp              Universal stress protein family
  ------ inclusion threshold ------
      0.035   14.8   0.0      0.052   14.3   0.0    1.4  1  DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomer
       0.14   12.1   0.0       0.32   11.0   0.0    1.6  1  DNA_photolyase   DNA photolyase


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.2   0.0   5.4e-41   3.2e-37       2     141 .]       5     145 ..       4     145 .. 0.97

  Alignments for each domain:
  == domain 1  score: 128.2 bits;  conditional E-value: 5.4e-41
                                       -SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH.HHHHHHC CS
                               Usp   2 ykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada.akaaaea 77 
                                       y +Il+a+Dgse+sk+A++ +++la ++ga++++++vi+p + ++   +++ +e ++++ + + ++a++  k++ ++
  gi|298674274|ref|YP_003726024.1|   5 YNNILIATDGSENSKNAIQSGINLASKTGAKVYAVYVIHPVSVTTGRKGPDWVEAAREMMRDEGEKATNyIKKMGDE 81 
                                       89**********************************************99999999999999999999999****** PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       +  +ve v++egdp++ei+++a+++d+dliV+G+rg+sg++r+++GSv+++v++h++  Vl+V+
  gi|298674274|ref|YP_003726024.1|  82 ENLEVESVILEGDPGDEIVKFADKNDVDLIVMGTRGLSGIQRFMVGSVADKVVKHSNTEVLIVP 145
                                       ***************************************************************7 PP

>> DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   8.8e-06     0.052      71     127 ..      86     144 ..      51     146 .] 0.78

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.8e-06
                                       SSSEEEESH..HHHHHHHCHTT-SEEEE--SSGGGHHHHHHHHHTTSEEEE--SHHHHH CS
                   DXP_reductoisom  71 lktevlvGe..ealkelaeeeeadvvvaaivGaaGLkptlaaikagkriaLANKEsLVv 127
                                       ++  +l G+  + +++ a ++++d++v +  G+ G++  +    a+k +  +N E L+v
  gi|298674274|ref|YP_003726024.1|  86 VESVILEGDpgDEIVKFADKNDVDLIVMGTRGLSGIQRFMVGSVADKVVKHSNTEVLIV 144
                                       34445666533568999****************************************97 PP

>> DNA_photolyase  DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   5.3e-05      0.32      18      95 ..      27     114 ..      21     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.3e-05
                                       HHHHCTTSEEEEEEEE-HH..HHTCG.S-CHHHHHHHHHHHHHHHHHH....HHTT......--EEEEESSHHHHHH CS
                    DNA_photolyase  18 aaAaasgepvipvfvldpe..kahkl.rvgaarvdfllesLadLdeeL....relg......irLvvrrgdpadvlp 81 
                                       + A ++g++v++v+v+ p       + r+g+  v+   e ++d  e+     +++g      ++ v+++gdp d+++
  gi|298674274|ref|YP_003726024.1|  27 NLASKTGAKVYAVYVIHPVsvT---TgRKGPDWVEAAREMMRDEGEKAtnyiKKMGdeenleVESVILEGDPGDEIV 100
                                       56899999**********9431...2356776666666666666555555554444444444899************ PP

                                       HHHHHCTECEEEEE CS
                    DNA_photolyase  82 elakelgasavvan 95 
                                       ++a +++++ +v+ 
  gi|298674274|ref|YP_003726024.1| 101 KFADKNDVDLIVMG 114
                                       ********999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 944.85
//
Query:       gi|298674275|ref|YP_003726025.1|  [L=146]
Description: UspA domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-36  125.5   0.0    2.4e-36  125.4   0.0    1.0  1  Usp              Universal stress protein family
     0.0016   19.1   0.7     0.0021   18.8   0.6    1.3  1  DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomer


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.4   0.0   2.6e-40   2.4e-36       2     141 .]       6     146 .]       5     146 .] 0.99

  Alignments for each domain:
  == domain 1  score: 125.4 bits;  conditional E-value: 2.6e-40
                                       -SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH.HHHHHHC CS
                               Usp   2 ykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada.akaaaea 77 
                                       +k+Il+a+Dgs++sk+A+  ++e ak ++a++++++vi+p + +a+  +++ ae  +++l+e+ ++a++  ++aa++
  gi|298674275|ref|YP_003726025.1|   6 FKKILIATDGSDNSKNAVNSGIEIAKINNADVYAVYVIPPVSAPAAQRGRSWAESIRQDLTEDGKKATKdVEDAAKE 82 
                                       89*************************************************************************** PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                        gv+ve++++eg+p+eei+ +ae++d dliV+Gs g+sg++++l+GSv+e+v+ +a++ Vl+V+
  gi|298674275|ref|YP_003726025.1|  83 TGVNVETILLEGNPSEEIINFAEKNDMDLIVLGSLGKSGIEKFLIGSVAEKVVMNANKQVLIVP 146
                                       ***************************************************************7 PP

>> DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.6   2.3e-07    0.0021      56     127 ..      70     145 ..      33     146 .] 0.85

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.3e-07
                                       HHHHHHHHHHHHHTTS..SSEEEESH..HHHHHHHCHTT-SEEEE--SSGGGHHHHHHHHHTTSEEEE--SHHHHH CS
                   DXP_reductoisom  56 eeaaeelkealkekel..ktevlvGe..ealkelaeeeeadvvvaaivGaaGLkptlaaikagkriaLANKEsLVv 127
                                       ++a++++++a ke+++  +t +l G+  e +++ ae++++d++v +  G  G++  l    a+k ++ ANK  L+v
  gi|298674275|ref|YP_003726025.1|  70 KKATKDVEDAAKETGVnvETILLEGNpsEEIINFAEKNDMDLIVLGSLGKSGIEKFLIGSVAEKVVMNANKQVLIV 145
                                       566778888888876622555666743388999****************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1095.66
//
Query:       gi|298674276|ref|YP_003726026.1|  [L=250]
Description: uroporphyrin-III C-methyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-55  188.0   0.0    2.3e-55  187.8   0.0    1.0  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.8   0.0   1.3e-59   2.3e-55       1     212 [.       7     219 ..       7     220 .. 0.92

  Alignments for each domain:
  == domain 1  score: 187.8 bits;  conditional E-value: 1.3e-59
                      TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealr 77 
                                       k++lVG GpGdpellT++A r++k+adv ++d+    +il+  ++e  +   + gk++ ++   ++ei++ l+ ++r
  gi|298674276|ref|YP_003726026.1|   7 KVFLVGSGPGDPELLTLKADRLIKSADVMVCDQLPGKKILE-SIPES-VEKIDAGKSAGDHKLSQNEINQVLVNKAR 81 
                                       789******************************44555554.45543.5666777778888889************* PP

                      TP_methylase  78 agkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl.....lpglake 149
                                       +gk+Vv+l++GDP+++g+g+e++e+l +  +gi++ev+PG++s+ a++a++giplt+++ +++v+     ++++++e
  gi|298674276|ref|YP_003726026.1|  82 EGKTVVRLKGGDPYIFGRGGEEAEELIK--EGINFEVVPGITSAIAVPAYAGIPLTHRDHASMVTfitghEDPTKDE 156
                                       ****************************..9***************************************888899* PP

                      TP_methylase 150 eereleallangdtlvllkaprklaelaelLkealyddttpvavveragtedervvrgtleel 212
                                       +  ++e l++  +t+v+l+++++l++ a++L+++ +++ tpva++e+++  d+rv++g++e +
  gi|298674276|ref|YP_003726026.1| 157 SSLDWESLANFEGTIVILMGVKRLKQNAQQLIKHGKNPKTPVAIIENGTHSDQRVTVGSIESI 219
                                       **********************************777788*******************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1535.82
//
Query:       gi|298674277|ref|YP_003726027.1|  [L=275]
Description: uroporphyrinogen III synthase HEM4 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.7e-38  130.3   0.0    8.4e-38  130.0   0.0    1.0  1  HEM4      Uroporphyrinogen-III synthase HemD


Domain annotation for each model (and alignments):
>> HEM4  Uroporphyrinogen-III synthase HemD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.0   0.0   4.7e-42   8.4e-38       7     231 ..      31     264 ..      27     265 .. 0.92

  Alignments for each domain:
  == domain 1  score: 130.0 bits;  conditional E-value: 4.7e-42
                                       HHHTTEEEEE---EECCECCHHHHHHHHHT.....--SEEEE--HHHHHHHHHHHH..HTT---HHHHHCSEEESSH CS
                              HEM4   7 learGaeplelPlieiepaedraelraalddleagkydwliftSanavealfealk..reeedvkalaslkvaavGp 81 
                                        +++G+e + +P+iei+  +++a  ++++ ++  gk d++iftSan++++ +++     ++e + al+++ v a+Gp
  gi|298674277|ref|YP_003726027.1|  31 AQEYGFETFSAPMIEIVD-KKDACFDDFVYRVLNGKSDYVIFTSANGIDFTLNKISdeIKQEFLVALNNTNVLAIGP 106
                                       579***************.666666666655556****************8888888988999999*********** PP

                                       HHHHHHHHTT---SEE-..SSSHHHHGGGS-.---EEEEEE-SS.S--HHHHHHHHHTTEEEEEE-SEEE.EE-HHH CS
                              HEM4  82 aTaraLeelglrvdlvpseegtaegLaeelaeslagkrvlllrgeiarddlaegLeergaevdevevYet.vpaeee 157
                                        T++aLe+ g++   +p  ++++eg++++l   + gk++ + r+ ++++ l +gL ++ga+v e  vY+   p++ +
  gi|298674277|ref|YP_003726027.1| 107 NTQKALEDTGIECIDLPD-SYSSEGVVDYLSLYVEGKTIDIARSSHGSKYLISGLINNGATVFETQVYTLnTPDNIT 182
                                       *****************9.************99999**********************************5555558 PP

                                       HHHHHHHHHTT--SEEEESSHHHHHHHHHH-S-HH........HHHCTSEEEEESHHHHHHHHHTT---SEEETS-- CS
                              HEM4 158 peelkealkagevdavvftSpstvrnllellkdeg........delkevkvaaiGptTaealkklglkvdvvaeept 226
                                       +++l +   ag++++ +ftS+  v n++  + d +         + ++++vaaiG  Ta +lk++g+kvd+v+e++ 
  gi|298674277|ref|YP_003726027.1| 183 QKNLIRCALAGNISVFAFTSSMIVHNFFTKANDVEaedriieiLNSNDTTVAAIGTPTASTLKNYGVKVDIVPEKYL 259
                                       888888888***********************9999*****998999*****************************9 PP

                                       HHHHH CS
                              HEM4 227 aeglv 231
                                        e ++
  gi|298674277|ref|YP_003726027.1| 260 FENML 264
                                       98887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1981.87
//
Query:       gi|298674278|ref|YP_003726028.1|  [L=399]
Description: radical SAM domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.7e-24   85.6   0.0    2.5e-23   83.3   0.0    1.9  2  Radical_SAM  Radical SAM superfamily
    8.4e-14   52.0   0.0    1.7e-13   51.0   0.0    1.5  1  Fer4_12      4Fe-4S single cluster domain
    1.6e-09   37.9   0.0    4.8e-09   36.4   0.0    1.9  2  Fer4_14      4Fe-4S single cluster domain
    1.7e-05   25.2   0.1    5.3e-05   23.7   0.1    1.8  1  SPASM        Iron-sulfur cluster-binding domain
     0.0064   16.6   0.0        6.8    6.8   0.0    2.8  3  GHL6         Hypothetical glycosyl hydrolase 6


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.3   0.0     7e-27   2.5e-23       2     167 .]      45     201 ..      44     201 .. 0.93
   2 ?   -0.1   0.0      0.29     1e+03      29      53 ..     235     258 ..     226     299 .. 0.66

  Alignments for each domain:
  == domain 1  score: 83.3 bits;  conditional E-value: 7e-27
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgi 78 
                                       +vtr Cnl+C +C+  +  ++ +++ +l++ e +e+++ l ae g  +++++ggepl++ d+ el++ ++ +   gi
  gi|298674278|ref|YP_003726028.1|  45 NVTRRCNLKCAHCYAQS--QDIDYSDELTTNEGKELIDDL-AEFGSPVILFSGGEPLMRHDLFELVRYARSK---GI 115
                                       79**************9..5********************.8999*****************9888888887...** PP

                                       EEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  79 ritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGe 155
                                       r +++tngtl+d +++ +l+  g+ +v ++l+ + d    +  + ++ f + le+l+++ + gik v  r ++ + e
  gi|298674278|ref|YP_003726028.1| 116 RAVISTNGTLIDSDMATTLKGIGLSYVGISLDGVKDT-NDRFRGVRGAFNAALEGLQNCQKEGIK-VGLRFTMNK-E 189
                                       ************************************8.77777788*******************.787777777.9 PP

                                       SHHHHHHHHHHH CS
                                       xxxxxxxxxxxx RF
                       Radical_SAM 156 ndeeleellell 167
                                       n +++ +l++l+
  gi|298674278|ref|YP_003726028.1| 190 NVADIPALFDLI 201
                                       999999888875 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.29
                                       HHHHHHHHHHHHHHHHTTSEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  29 lsveeileevkelkaekgvkevilg 53 
                                       ++++ i++  k+l ++kg+ + +l+
  gi|298674278|ref|YP_003726028.1| 235 KTLDLIMDRTKQL-HDKGKQVEVLT 258
                                       4455555555555.45543333333 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.0   4.7e-17   1.7e-13       8     117 ..      41     148 ..      35     164 .. 0.85

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 4.7e-17
                           Fer4_12   8 lslf..vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkee 82 
                                       ++++  + +Cnl+C+ C+  + ++ ++++e t++  +e+i+dl++   + + ++GGEPl+   + +l elv++ +++
  gi|298674278|ref|YP_003726028.1|  41 VVVWnvTRRCNLKCAHCY-AQSQDIDYSDELTTNEGKELIDDLAEFGSPVILFSGGEPLM---RHDLFELVRYARSK 113
                                       566666889*********.789**********************999*************...99************ PP

                           Fer4_12  83 kpekdiwlytgytleelskkekeel.lkeidvlvdG 117
                                       ++   +++++g+ ++  +++  + + l+++ + +dG
  gi|298674278|ref|YP_003726028.1| 114 GI-RAVISTNGTLIDSDMATTLKGIgLSYVGISLDG 148
                                       **.58*******999888763333336666666666 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.0   1.3e-12   4.8e-09       4     113 ..      46     144 ..      43     149 .. 0.78
   2 ?   -3.3   0.0       2.6   9.3e+03      89     105 ..     235     251 ..     227     264 .. 0.46

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 1.3e-12
                           Fer4_14   4 rlsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeype 80 
                                        + +Cnl+C  C+ ++ ++ ++  + t ++ ++ ++dl +  +    + ++GGePL+    ++l++lv++ + ++  
  gi|298674278|ref|YP_003726028.1|  46 VTRRCNLKCAHCYAQS-QDIDYSDELTTNEGKELIDDLAEFGS--PVILFSGGEPLMR---HDLFELVRYARSKG-- 114
                                       5789*********999.88888888888888899977766666..669********66...9*************.. PP

                           Fer4_14  81 kkiwletngtleielektpdlkeklealskidl 113
                                       ++  + tngtl  + +++     k   ls++ +
  gi|298674278|ref|YP_003726028.1| 115 IRAVISTNGTLI-DSDMAT--TLKGIGLSYVGI 144
                                       9999*****997.666433..334455555555 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.6
                           Fer4_14  89 gtleielektpdlkekl 105
                                        tl++ +++t++l++k 
  gi|298674278|ref|YP_003726028.1| 235 KTLDLIMDRTKQLHDKG 251
                                       33333333333333333 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.1   1.5e-08   5.3e-05       9      67 ..     301     359 ..     295     360 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.5e-08
                             SPASM   9 fInsdGdVvpCcvdkktyveelklGnireesleeIw..nseeyqe.frksk......kfplielCrnC 67 
                                       ++++dG V+p     + +++ ++lGn++e ++++Iw  +s+ + + +++ +      +    + C++C
  gi|298674278|ref|YP_003726028.1| 301 CVSWDGSVHPD----QFWRH-YTLGNVKERKFSDIWtdTSDDLMAgLKN-RkpliisN---ADRCASC 359
                                       799*******9....67755.***************5544444444442.12342223...3347776 PP

>> GHL6  Hypothetical glycosyl hydrolase 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0019       6.8      42      76 ..      98     131 ..      86     134 .. 0.84
   2 !    6.4   0.0    0.0026       9.3      46      70 ..     164     188 ..     142     193 .. 0.76
   3 ?   -2.3   0.0       1.2   4.4e+03      37      65 ..     229     257 ..     223     270 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0019
                              GHL6  42 klkrdllkelvkachregikvvvrvdfskaderiy 76 
                                        +++dl  elv+ ++++gi++v+ ++ + +d++++
  gi|298674278|ref|YP_003726028.1|  98 LMRHDL-FELVRYARSKGIRAVISTNGTLIDSDMA 131
                                       456777.9*****************9999988876 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0026
                              GHL6  46 dllkelvkachregikvvvrvdfsk 70 
                                       +  +e  + c++egikv  r+++ k
  gi|298674278|ref|YP_003726028.1| 164 NAALEGLQNCQKEGIKVGLRFTMNK 188
                                       66789999*************9986 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.2
                              GHL6  37 vtehpklkrdllkelvkachregikvvvr 65 
                                        +e  + + dl+ +  k +h++g +v v 
  gi|298674278|ref|YP_003726028.1| 229 SPEETRKTLDLIMDRTKQLHDKGKQVEVL 257
                                       56677778899999999999999777554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2732.73
//
Query:       gi|298674279|ref|YP_003726029.1|  [L=119]
Description: desulfoferrodoxin ferrous iron-binding region [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.3e-24   84.4   0.4    7.8e-24   84.1   0.4    1.1  1  Desulfoferrodox  Desulfoferrodoxin


Domain annotation for each model (and alignments):
>> Desulfoferrodox  Desulfoferrodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.1   0.4   4.4e-28   7.8e-24       3      95 ..      15     115 ..      13     116 .. 0.87

  Alignments for each domain:
  == domain 1  score: 84.1 bits;  conditional E-value: 4.4e-28
                                       HTTTHTTSEEEEEESEEEETTEEEEEEEESS.SS--BSSSS-EEEEEEEEEETTSS.....EEEE-TBS.ESEEEEE CS
                   Desulfoferrodox   3 dekeekHvPvieadevvkagelfevkvkvgk.ipHpneeeHyIewielyleeegek.....rvelsaed.epevtft 72 
                                       ++ +ekH+P ie+ + + +++   ++v vgk +pHpn+ eH+I+w+el   +++ +     ++++++ + ep+++f+
  gi|298674279|ref|YP_003726029.1|  15 SKLKEKHIPSIEIMKGQGKQGGDFIEVAVGKeTPHPNKVEHHIAWVELHGVRNNGQvvnlgKMDFAPVYvEPNAKFE 91 
                                       5789***********999999999*************************9999999455555555555588****** PP

                                       EEESSS.EEEEEEEEETTTEEEEE CS
                   Desulfoferrodox  73 vklkke.kklvalsyCnlHGlWes 95 
                                       v++ ++ k ++a++yCn+HGlWe+
  gi|298674279|ref|YP_003726029.1|  92 VNSIDDfKSFYAVEYCNIHGLWEN 115
                                       *98877689**************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 763.58
//
Query:       gi|298674280|ref|YP_003726030.1|  [L=186]
Description: ferroxidase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.3e-44  148.8   4.6    1.1e-43  148.5   4.6    1.1  1  Ferritin   Ferritin-like domain
     0.0007   19.6   0.2     0.0015   18.6   0.2    1.5  1  ANAPC5     Anaphase-promoting complex subunit 5
  ------ inclusion threshold ------
      0.051   13.5   0.1       0.65    9.9   0.0    2.3  2  TnpB_IS66  IS66 Orf2 like protein


Domain annotation for each model (and alignments):
>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.5   4.6   1.9e-47   1.1e-43       2     142 .]       8     144 ..       7     144 .. 0.99

  Alignments for each domain:
  == domain 1  score: 148.5 bits;  conditional E-value: 1.9e-47
                                       HHHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHHC-SSSS. CS
                          Ferritin   2 kaLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraeleeieapke. 77 
                                       +aLn ql++e+++ay+y++m++y   +gl+g+a++f+ q++ee++ha+k++++i++ G+     +++l ei++p+  
  gi|298674280|ref|YP_003726030.1|   8 EALNVQLNKEMYSAYLYMSMSAYSTYIGLNGFANWFMVQYQEEMTHAMKFYDYINDHGA-----QVKLMEIPQPPTa 79 
                                       79*********************************************************.....************9 PP

                                       CSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin  78 fgsveevleaalehekkvteslrelielaeeegDpatadfledfleeqeeheweleallekleri 142
                                       f+s+++++e+ l+hek vt+s++el++la ee+D+at+ fl++++ eq e+e++ ++++ kl+++
  gi|298674280|ref|YP_003726030.1|  80 FDSALDMFEKTLKHEKFVTKSINELVDLAVEEKDHATYTFLQWYVSEQIEEEANDNEIISKLKLM 144
                                       99***********************************************************9986 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.2   2.5e-07    0.0015       6      84 ..      39     121 ..      35     130 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.5e-07
                            ANAPC5   6 lnalrakdYqqaldsLhryFDyvlsqnessq.......kksyqyalLnlaslhadfghneeAvkaleeairlArenk 75 
                                       ++++   +Yq+ + + ++ +Dy++ + ++ +          +++a   l +++ ++ h++  +k+++e + lA e+k
  gi|298674280|ref|YP_003726030.1|  39 FANWFMVQYQEEMTHAMKFYDYINDHGAQVKlmeipqpPTAFDSA---LDMFEKTLKHEKFVTKSINELVDLAVEEK 112
                                       67899999**********************877776665566665...689************************** PP

                            ANAPC5  76 DkscLalal 84 
                                       D+++ ++  
  gi|298674280|ref|YP_003726030.1| 113 DHATYTFLQ 121
                                       **9987754 PP

>> TnpB_IS66  IS66 Orf2 like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0     0.063   3.8e+02      35      73 ..      56     100 ..      21     116 .. 0.60
   2 ?    9.9   0.0   0.00011      0.65      45      73 ..     139     167 ..     134     182 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.063
                         TnpB_IS66  35 alFvFrnrrrdrlKiLlwdg......nGfvllykrLekgrFkwpk 73 
                                       + + ++n ++ ++K++   +      + + ++ k L++++F  ++
  gi|298674280|ref|YP_003726030.1|  56 KFYDYINDHGAQVKLMEIPQpptafdSALDMFEKTLKHEKFVTKS 100
                                       466666666666666543321111113445667777777777664 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00011
                         TnpB_IS66  45 drlKiLlwdgnGfvllykrLekgrFkwpk 73 
                                       ++lK++  dg+G+ +l k L++  F    
  gi|298674280|ref|YP_003726030.1| 139 SKLKLMGEDGSGMYMLDKELSQRVFVPEY 167
                                       689*******************9998664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       833  (0.046461); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1128.54
//
Query:       gi|298674281|ref|YP_003726031.1|  [L=871]
Description: valyl-tRNA synthetase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   2.1e-131  439.2   3.5   3.2e-130  435.2   3.5    2.0  1  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    3.8e-39  134.1   0.4    7.5e-39  133.1   0.4    1.5  1  Anticodon_1    Anticodon-binding domain of tRNA
    1.4e-22   80.0   0.5    8.2e-13   47.8   0.0    3.5  3  tRNA-synt_1g   tRNA synthetases class I (M)
    4.3e-07   29.6   0.0    1.8e-06   27.6   0.0    1.9  2  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
    5.1e-05   22.8   0.0       0.31   10.3   0.0    2.6  2  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
  ------ inclusion threshold ------
      0.031   13.6   0.1       0.78    9.0   0.0    2.8  3  tRNA-synt_1b   tRNA synthetases class I (W and Y)
        1.5    9.1   3.3        6.9    7.0   0.0    3.4  4  PMBR           Pseudomurein-binding repeat


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  435.2   3.5  1.3e-133  3.2e-130       2     599 ..      16     555 ..      15     558 .. 0.93

  Alignments for each domain:
  == domain 1  score: 435.2 bits;  conditional E-value: 1.3e-133
                       tRNA-synt_1   2 lyekWeeedv.fkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaie 77 
                                       +++ W+ +++ f+ e   +++++++i+  +PPy tG+ HiG+al+    d++ rykrm+G++v +  GwD++Gl++e
  gi|298674281|ref|YP_003726031.1|  16 WQSSWDMSKYhFDWE---DQSRPQYIIDTPPPYPTGNFHIGNALNWCYIDFIARYKRMRGYNVMFPQGWDCHGLPTE 89 
                                       788999998844444...888******************************************************** PP

                       tRNA-synt_1  78 akvekklgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkg 154
                                        kve+  g++++    +++r+efr+ +++  ++ +e++r+++ rlG s+D+++e +T+++e+   +++ fv+++d  
  gi|298674281|ref|YP_003726031.1|  90 VKVEELHGITKN----EVSRAEFRKMCKDLTSQNIEKMRETMMRLGFSIDWNNEFVTMEPEYFVKTQKSFVQMYDIN 162
                                       *****9998886....9************************************************************ PP

                       tRNA-synt_1 155 liyrgkklvnwstklktalselEveykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyvitke 231
                                        iy++ ++vnw+++++ta++ +Evey   + +l ++ f+        l+iaTT+Pe l++ +avavnpe        
  gi|298674281|ref|YP_003726031.1| 163 RIYQSDYPVNWCPRCETAIALAEVEYDSRDTSLNYLYFD-------DLEIATTRPELLPACVAVAVNPE-------- 224
                                       *************************97777766666664.......478********************........ PP

                       tRNA-synt_1 232 klilaeallkslvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVkiaPahdedDyevgkk 308
                                                              der++e +  eve p+ ++k+p++ad+ vd+ +GtGvV i    d++D + + k
  gi|298674281|ref|YP_003726031.1| 225 -----------------------DERYREHINDEVEVPIFGQKVPVLADEAVDTSFGTGVVMICTFGDKQDVRWCVK 278
                                       .......................9***************************************************** PP

                       tRNA-synt_1 309 ynlevinildedgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvk 385
                                       y+l+v  +++++g++t+ a++++g+++ ++++++++el++kg l ++e+ e +v++c+r k+pi+  + +qWfv+v+
  gi|298674281|ref|YP_003726031.1| 279 YDLPVRKAINKNGRMTDVAGKYSGMTISECKDAITQELSDKGHLYQQETLEQNVGLCWRCKTPIEILSEPQWFVSVN 355
                                       ***************************************************************************98 PP

                       tRNA-synt_1 386 eladaalkavekvqfvpkskekryaswleniq.dWciSRqrwWGhriplfvsketeevvvreelkelvagreeeeae 461
                                       +  d++ ++ ++v++ p+  ++r ++w   ++ dWciSRqr+  ++ip+++ ++ +e++v   ++e+          
  gi|298674281|ref|YP_003726031.1| 356 D--DEIHNTADEVNWHPEYMKTRLKNWTDVMEwDWCISRQRVFATPIPVWYCNKCGETMV--AKEEWLP-------- 420
                                       4..66777777****************987756************************999..3333333........ PP

                       tRNA-synt_1 462 kkalekeakdklkkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlills 538
                                          +++e  +  +++  ++e ++dvlD+W +S+++   + g+ +e  +el+   p+++  +G Di+r W    il +
  gi|298674281|ref|YP_003726031.1| 421 LDPIQTEPPEPCNCGSTDFEPENDVLDTWMDSSLTALHVSGWLSE--HELR--LPTQIRPQGHDILRTWAFYTILRT 493
                                       22223344555678999************************9888..7888..9*********************** PP

                       tRNA-synt_1 539 laltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltli.lsdvgrdi 599
                                        a++g +P++ +lv+g+v+ e+G+KmSKs gN+i+p++v+ +ygada R + +   + g+d+
  gi|298674281|ref|YP_003726031.1| 494 KAIKGIKPWEFILVNGMVLGEDGHKMSKSQGNIISPDEVVGQYGADAFRQWGAvGGTPGSDV 555
                                       *************************************************9977666666665 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.1   0.4   2.9e-42   7.5e-39       1     151 [.     605     750 ..     605     752 .. 0.91

  Alignments for each domain:
  == domain 1  score: 133.1 bits;  conditional E-value: 2.9e-42
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrll 77 
                                       d+w+ls+lnkl+++vt +++++ f++a++++ +f w+ l+d+ylelvk+rly++++e+++aaq++l+++++tl+ +l
  gi|298674281|ref|YP_003726031.1| 605 DKWLLSKLNKLIESVTTSMDKLLFDEAYKSMRTFAWEVLADNYLELVKSRLYGKDPESRKAAQTTLYYAIDTLIHVL 681
                                       9*****************************************************9977766**************** PP

                       Anticodon_1  78 aPfmPfitEelwqreeeelgkkesimlaewpekaeel.ekeleeeevellkeivkairklrselkikpsselkvv 151
                                       aP++Pf++Ee++ r      k+ s++ ++wpe +e l +++  e++ e++k+i + ir+++s+++++ +++l++v
  gi|298674281|ref|YP_003726031.1| 682 APITPFFAEEMYSR-----FKEGSVHEQSWPEVNELLiDNDV-ESKGEVIKDIASNIRRYKSDNGMALNAPLEKV 750
                                       ************43.....45689*******96656676666.88*************************96554 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.0   3.2e-16   8.2e-13       2     129 ..      38     180 ..      37     195 .. 0.66
   2 !    3.6   0.6     0.009        23     143     238 ..     309     401 ..     296     412 .. 0.77
   3 !   24.0   0.0   5.6e-09   1.4e-05     307     373 ..     497     564 ..     462     567 .. 0.82

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 3.2e-16
                                       EEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHH.TTS-HHHHHHHHHHHHHHH CS
                      tRNA-synt_1g   2 lvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAek.egvtpeelvekvheeikel 77 
                                       ++ t+ pY++g+ H+G++l+    D +aRykr+rg++v+f  g D hG p+e+k e+ +g+t +e+ +   +++ ++
  gi|298674281|ref|YP_003726031.1|  38 IIDTPPPYPTGNFHIGNALNWCYIDFIARYKRMRGYNVMFPQGWDCHGLPTEVKVEElHGITKNEVSRAEFRKMCKD 114
                                       789999************************************************98746787766554444444444 PP

                                       HHH..............TT---SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEE CS
                      tRNA-synt_1g  78 fkk..............lnisfdkygrttseehkelvqeifkklkekgliyekeieqlycpkderf 129
                                       +++              ++i +++   t + e    +q+ f ++++ + iy++++ + +cp++e+ 
  gi|298674281|ref|YP_003726031.1| 115 LTSqniekmretmmrlgFSIDWNNEFVTMEPEYFVKTQKSFVQMYDINRIYQSDYPVNWCPRCETA 180
                                       444000000000111123333333334555555555566666666666666666666666666655 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.009
                                       ...-TTS-EE-TTSSB-E..................EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HH CS
                      tRNA-synt_1g 143 kseeargdqceecgkkleptelinpk..saisgskpevketehlffklskfekklkewieeeekeleenvkkivkew 217
                                       k  +a  ++  + g+ ++ ++l++ +  +  +++  e+ ++ ++f ++++  +++++    e +  +e +k+ +k+w
  gi|298674281|ref|YP_003726031.1| 309 K--DAITQELSDKGHLYQQETLEQNVglCWRCKTPIEILSEPQWFVSVND--DEIHNTA-DEVNWHPEYMKTRLKNW 380
                                       3..67777888889999988888765337788888899989999988775..5666655.444457788999999** PP

                                       HHT----EE-ESS-SSS-EET CS
                      tRNA-synt_1g 218 lkegLkdlaisrdldwGipvP 238
                                        +    d++isr+  ++ p+P
  gi|298674281|ref|YP_003726031.1| 381 TDVMEWDWCISRQRVFATPIP 401
                                       999889*************99 PP

  == domain 3  score: 24.0 bits;  conditional E-value: 5.6e-09
                                       TT----S-EEEE--EE.E--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHHHH CS
                      tRNA-synt_1g 307 aelklpkkvvaheylt.vegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedfve 373
                                       +++k  + + +++++   +g+K+SkS+g+++ ++e++ ++ ad++R + a+ +   +D+ f+w+d+v 
  gi|298674281|ref|YP_003726031.1| 497 KGIKPWEFILVNGMVLgEDGHKMSKSQGNIISPDEVVGQYGADAFRQWGAVGGTPGSDVMFRWKDVVS 564
                                       556666677888876515689********************************************986 PP

>> tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.83   2.1e+03      22      46 ..     202     226 ..     189     238 .. 0.82
   2 !   27.6   0.0   7.1e-10   1.8e-06      89     149 ..     236     296 ..     230     317 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.83
                     tRNA-synt_1_2  22 klevfttrpdtlfGvtfvalapehp 46 
                                       +le+ ttrp+ l     va+ pe +
  gi|298674281|ref|YP_003726031.1| 202 DLEIATTRPELLPACVAVAVNPEDE 226
                                       78999*******9999999999876 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 7.1e-10
                     tRNA-synt_1_2  89 aihPitgekipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikqvikpedeekkl 149
                                       +  Pi g+k+p+   + v +++gtg+vm +   d++D ++  ky+lp+++ i+++++ +++
  gi|298674281|ref|YP_003726031.1| 236 VEVPIFGQKVPVLADEAVDTSFGTGVVMICTFGDKQDVRWCVKYDLPVRKAINKNGRMTDV 296
                                       667*************************************************987765444 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   0.00019      0.48      22      52 ..      49      79 ..      45     161 .. 0.83
   2 !   10.3   0.0   0.00012      0.31     228     277 ..     492     542 ..     464     547 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00019
                                      --BHHHHHHHHHHHHHHHHHHHTT-EEEEEE CS
                      tRNA-synt_1e 22 ashlGhaRslvafDilrrilqalgYdvqfvq 52
                                      + h+G+a +   +D ++r+ +++gY+v+f q
  gi|298674281|ref|YP_003726031.1| 49 NFHIGNALNWCYIDFIARYKRMRGYNVMFPQ 79
                                      57**************************977 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00012
                                       HHHHHSSS--EEEEEEE--EE.ETTBE--TTTT---BHHHHHTTS-HHHHH CS
                      tRNA-synt_1e 228 qseaafdkqlvkyflhnghlk.iegekmsksLknfitikdvlkkfdprqlR 277
                                       +++a  + +  ++ l ng++   +g+kmsks +n+i+  +v+ ++ + ++R
  gi|298674281|ref|YP_003726031.1| 492 RTKAIKGIKPWEFILVNGMVLgEDGHKMSKSQGNIISPDEVVGQYGADAFR 542
                                       56777777777888999997625799******************9998887 PP

>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.57   1.5e+03      14      24 ..      46      56 ..      45      80 .. 0.84
   2 ?    9.0   0.0    0.0003      0.78     183     209 ..     503     527 ..     488     533 .. 0.75
   3 ?    0.5   0.1      0.12   3.1e+02     179     215 ..     799     834 ..     788     848 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.57
                                      TSSS-BGGGHH CS
                      tRNA-synt_1b 14 PTgklHlGylv 24
                                      PTg++H+G+ +
  gi|298674281|ref|YP_003726031.1| 46 PTGNFHIGNAL 56
                                      9*******654 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0003
                                       -EEEEET-BBSTTSSSBTTCETTCGC- CS
                      tRNA-synt_1b 183 pegltvplltgldGekKmSKSagnsaI 209
                                        ++l++ ++ g dG  KmSKS+gn  I
  gi|298674281|ref|YP_003726031.1| 503 EFILVNGMVLGEDGH-KMSKSQGN-II 527
                                       4566666999*****.********.43 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.12
                                       TTSS-EEEEET-BBSTTSSSBTTCETTCGC-BTTCCH CS
                      tRNA-synt_1b 179 vfkkpegltvplltgldGekKmSKSagnsaIfLddek 215
                                       +f+   g +v+ l++ d+e K+SK a++++I  + + 
  gi|298674281|ref|YP_003726031.1| 799 KFRDKAGSIVKTLKSEDPE-KISKQADEGKIVVSVDG 834
                                       4888899999*********.****9999787665544 PP

>> PMBR  Pseudomurein-binding repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.47   1.2e+03      17      27 ..      60      70 ..      60      70 .. 0.86
   2 ?   -1.1   0.0         1   2.6e+03       5      16 ..     103     114 ..     100     117 .. 0.84
   3 ?   -2.8   0.1       3.5   9.1e+03      21      27 ..     287     293 ..     285     293 .. 0.91
   4 ?    7.0   0.0    0.0027       6.9       9      26 ..     724     741 ..     723     746 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.47
                              PMBR 17 vlafiesngrl 27
                                      +++fi +++r+
  gi|298674281|ref|YP_003726031.1| 60 YIDFIARYKRM 70
                                      68999999998 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1
                              PMBR   5 isyeeyldmasr 16 
                                       +s+ e+++m+++
  gi|298674281|ref|YP_003726031.1| 103 VSRAEFRKMCKD 114
                                       89*******986 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 3.5
                              PMBR  21 iesngrl 27 
                                       i++ngr+
  gi|298674281|ref|YP_003726031.1| 287 INKNGRM 293
                                       79****8 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.0027
                              PMBR   9 eyldmasrvlafiesngr 26 
                                        ++d+as++ +++  ng 
  gi|298674281|ref|YP_003726031.1| 724 VIKDIASNIRRYKSDNGM 741
                                       589*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (871 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.75u 0.29s 00:00:01.04 Elapsed: 00:00:00.50
# Mc/sec: 5204.23
//
Query:       gi|298674282|ref|YP_003726032.1|  [L=414]
Description: pyrrolysyl-tRNA synthetase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.6e-13   48.9   0.0    1.1e-11   44.7   0.0    2.3  1  tRNA-synt_2d     tRNA synthetases class II core domain (F)
    2.2e-08   33.6   2.7    8.1e-08   31.7   0.0    3.0  4  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    4.1e-06   26.4   0.0    8.5e-06   25.3   0.0    1.5  1  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    0.00065   19.7   0.1     0.0049   16.9   0.0    2.5  2  tRNA-synt_2b     tRNA synthetase class II core domain (G, H, 
  ------ inclusion threshold ------
          1    9.9   3.9        0.6   10.7   1.0    2.1  2  Zn_ribbon_recom  Recombinase zinc beta ribbon domain


Domain annotation for each model (and alignments):
>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.0   3.1e-15   1.1e-11       9     233 ..     193     399 ..     188     407 .. 0.86

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 3.1e-15
                                       SCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-ECESEEE-S CS
                      tRNA-synt_2d   9 krieagklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpekaveekllLRt 85 
                                       +++e+ + + ++k+ + i+++f++ gf e++ p +  ++   + + ++ dh     ++ Fyl       ++k  LR 
  gi|298674282|ref|YP_003726032.1| 193 QMYENDREEQIAKLERTISQFFVDKGFIEIKAPII-IDIDSVKKMGIDTDHK--LSKQIFYL-------DNKHCLRP 259
                                       556777888999**********************9.8999999999999995..57899***.......67899*** PP

                                       STHHHHHHHH....TTS-SSEEEEEEEEEEBSST-SSSB-SEEEEEEEEEEETT--HHHHHHHHHHHHHHHCTSTEE CS
                      tRNA-synt_2d  86 httavqirtl....ekkkppikiisigrvfRrdavDathlaeFhqveglvvdenvsladlkgvleellkklfgaevk 158
                                          +   + l    +    piki+ ig ++R++++ ++hl eF+  ++  ++++ + ++l+  +++llk+l + + k
  gi|298674282|ref|YP_003726032.1| 260 MLAPGLYQWLknfdKILPDPIKIFEIGPCYRKESEGSQHLEEFTMFNFCQMGSGANRENLLNHIDDLLKHL-NIDYK 335
                                       **********655444558****************************************************.88855 PP

                                       EEEEECEETTEEEEEEEEEEECCSSSSEEEEEEEEEE-HHHHHHTT-.TTSEEEEEEEEHHHHHHHHHT-SSGHH CS
                      tRNA-synt_2d 159 vrfrpsyfpftePsaevdvylvekkkkwlEllgaGmvrpevleavgideevsgfafGlGveRlamlkygieDiRe 233
                                       + ++ +   + e    +d+++     + lEl  a +    +  + gi  +++ ++ GlG+eRl  +k+g+++i++
  gi|298674282|ref|YP_003726032.1| 336 I-IDDNCHVYGE---TIDIVH-----GDLELSSAVVGPVPIDMNWGI--DKTWIGAGLGLERLLKVKHGYKNIKR 399
                                       4.4555566655...578888.....889998875555556667899..899999******************97 PP

>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.7      0.56     2e+03     150     197 ..      76     123 ..      60     159 .. 0.68
   2 ?   -2.2   0.0      0.47   1.7e+03     104     136 ..     165     197 ..     164     207 .. 0.82
   3 !   31.7   0.0   2.3e-11   8.1e-08      28     142 ..     206     331 ..     180     351 .. 0.74
   4 ?   -0.0   0.0       0.1   3.6e+02     286     307 ..     379     400 ..     375     402 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.56
                                       CCCCCHTTTTTSEE-SSS-EEEEHHHHHHHHHTS-SS--HHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 150 akdiefvirrnskdlkkpfkrltykeaieklneigkdldkaderalvk 197
                                        + i++  +++++   ++   ++y+e+ +k +++    +k++ +++v+
  gi|298674282|ref|YP_003726032.1|  76 DEVINRFLQKHTDRTDTKVTAFSYSESKKKKSKQLGHKKKKQSKVQVN 123
                                       344555555555666667777777777777666655556666666665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.47
                                       S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 104 EdsrtdrhlaEFtqieaemsfieeedimqvlee 136
                                       E++  +++++ F +ie e+     +d  q+ e+
  gi|298674282|ref|YP_003726032.1| 165 EKIPFSNEPSKFKEIESELVNKRRNDFKQMYEN 197
                                       677778999999999999988888888888775 PP

  == domain 3  score: 31.7 bits;  conditional E-value: 2.3e-11
                                       HHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT...TEEE.........-E-S-SHHHHHHH..HHCTH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxx.........xxxxxxxxxxxxx..xxxxx RF
                       tRNA-synt_2  28 vtkavrkyleengfieietPiLsksdteegarlFkvksrek..ekeff.........aLtqspqlylell..ivagi 91 
                                       + + + +++ ++gfiei+ Pi+++ d     ++  + + +k  ++ f+         +L+    ++l+    i    
  gi|298674282|ref|YP_003726032.1| 206 LERTISQFFVDKGFIEIKAPIIIDID---SVKKMGIDTDHKlsKQIFYldnkhclrpMLAPGLYQWLKNFdkILPDP 279
                                       5567899*****************95...444444444444324456688888777745444444444332233345 PP

                                       SEEEEEEEEE--S--BTTB-S-CEEEEEEEE..ET-SCHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  92 drvfqiaraFRaEdsrtdrhlaEFtqieaem..sfieeedimqvleelikslv 142
                                        ++f+i++++R+E+   ++hl+EFt++++    s ++ e++++ +++l+k+l 
  gi|298674282|ref|YP_003726032.1| 280 IKIFEIGPCYRKESE-GSQHLEEFTMFNFCQmgSGANRENLLNHIDDLLKHLN 331
                                       89***********65.589999******854467777888********99985 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 0.1
                                       EEEEEHHHHHHHHCT-SSGGGC CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 286 GlglGldRlvmlllgsesIrdv 307
                                       G glGl+Rl+ +  g ++I+ +
  gi|298674282|ref|YP_003726032.1| 379 GAGLGLERLLKVKHGYKNIKRA 400
                                       99****************9975 PP

>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   2.4e-09   8.5e-06      15     164 ..     200     336 ..     191     357 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 2.4e-09
                   tRNA_synthFbeta  15 lnkeqklrrklrdllagaGlnEvitysfvsekeldklleddderkavelanPlsedqsvlRtsLlpglLevlarNla 91 
                                       +++  kl+r+++++ ++ G+ E+     ++ + ++k+   d++ k+ + +  l + + +lR+ L pgl + l+ N++
  gi|298674282|ref|YP_003726032.1| 200 EEQIAKLERTISQFFVDKGFIEIKAPIIIDIDSVKKMG-IDTDHKLSKQIFYL-DNKHCLRPMLAPGLYQWLK-NFD 273
                                       567889*******************************5.34444444444444.5678************996.787 PP

                   tRNA_synthFbeta  92 rgned.vrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlkgivealleslgiekvef 164
                                       + ++d +++FEig +++k+ ++++  ee +++ +  +g+            ++ ++l   ++ ll++l+i ++++
  gi|298674282|ref|YP_003726032.1| 274 KILPDpIKIFEIGPCYRKEsEGSQHLEEFTMFNFCQMGSG-----------ANRENLLNHIDDLLKHLNI-DYKI 336
                                       777666*************888888999999999999999...........8899999999999999999.6655 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.56     2e+03      73      98 ..     196     221 ..     186     254 .. 0.70
   2 !   16.9   0.0   1.4e-06    0.0049       9     105 ..     253     340 ..     248     391 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.56
                                       GGGHHHHHHHHHHHHHHHHHHTT.SC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  73 easlddslrdlikaisriferlglef 98 
                                       e++ ++++++l+++is++f + g+ +
  gi|298674282|ref|YP_003726032.1| 196 ENDREEQIAKLERTISQFFVDKGFIE 221
                                       56678889999999999998887643 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1.4e-06
                                       EEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b   9 reyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeaslddslrdlik 85 
                                       ++ +L+P+  +++++  ++   +    P+k+++i+++yR+E +   G   + eF++ +   +++ a      ++l++
  gi|298674282|ref|YP_003726032.1| 253 NKHCLRPMLAPGLYQWLKNF-DKILPDPIKIFEIGPCYRKESE---GSQHLEEFTMFNFCQMGSGA----NRENLLN 321
                                       57899999999999988866.4433349*************99...43446788776655555543....5667777 PP

                                       HHHHHHHHTT.SCEEEEEEG CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  86 aisriferlglefraiielm 105
                                        i++++++l +  ++ii ++
  gi|298674282|ref|YP_003726032.1| 322 HIDDLLKHLNID-YKIIDDN 340
                                       777777777776.5566664 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.0   0.00017       0.6      10      52 ..      41      82 ..      40      86 .. 0.75
   2 ?   -1.8   0.1       1.3   4.6e+03      39      51 ..     130     142 ..      98     145 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00017
                   Zn_ribbon_recom 10 eCGspmtrrkrkgkr..hyYrCstyrrkgkkCsnhsireekleea 52
                                      +CG + t+r+++++r  +  r ++y  k+  C+n  +++e++ ++
  gi|298674282|ref|YP_003726032.1| 41 DCGEKITVRNSRNSRtaRILRLKKY--KK-PCKNCKVSDEVINRF 82
                                      8********9997774444677776..33.588888999998875 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.3
                   Zn_ribbon_recom  39 Csnhsireeklee 51 
                                        sn+s++e+k+++
  gi|298674282|ref|YP_003726032.1| 130 QSNTSVSEDKTDN 142
                                       5677888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2291  (0.127782); expected 358.6 (0.02)
Passed bias filter:                      633  (0.0353059); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.68u 0.28s 00:00:00.96 Elapsed: 00:00:00.47
# Mc/sec: 2620.75
//
Query:       gi|298674283|ref|YP_003726033.1|  [L=340]
Description: MtaA/CmuA family methyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-81  273.3   0.0    3.2e-81  273.2   0.0    1.0  1  URO-D     Uroporphyrinogen decarboxylase (URO-D)


Domain annotation for each model (and alignments):
>> URO-D  Uroporphyrinogen decarboxylase (URO-D)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  273.2   0.0   1.8e-85   3.2e-81       1     346 []       6     338 ..       6     338 .. 0.97

  Alignments for each domain:
  == domain 1  score: 273.2 bits;  conditional E-value: 1.8e-85
                                       ----HHHHHHTT---SS--B--TT-SSTTSHHHHHHHTSSSHHHHHH-HHHHHHHHHHHHHHH--S-EE-S--TTGG CS
                             URO-D   1 tknerllralrgekvdrvPvwlmRqaGrylpeyraeragvsflelcknpelaaevtlqpvrrfglDaailfsdilve 77 
                                       t++er+ +al+ge vdr+P ++   a+++ + +++e +g+ ++++++++++++ ++ +++  +g++++ +++di+ e
  gi|298674283|ref|YP_003726033.1|   6 TPKERFAKALKGESVDRMPAIC---ATQTGTVEQMEASGAYWPDAHYDADKMTTLAEAAHTAVGFEMVRVPFDITAE 79 
                                       689*******************...**************************************************** PP

                                       GGGGT-EEEEETTTE.EEEE--S-.....GGGS----GGG.G..HHHHHHHHHHHHH.--SS-EEEEEE-HHHHHHH CS
                             URO-D  78 aealGlevefeegeg.Pvvekpvr.taedveklevpddveegrlpyvleaikllkkelggevpligfvgaPftlasy 152
                                       ae +G+e++ +++++ P+v  +v+ t++d++ le +d  + +r+++++e+ik l +++g+e+p++g +++Pf+la +
  gi|298674283|ref|YP_003726033.1|  80 AEFFGCELKEGTQKQqPSVVGHVVkTEDDIKSLEGYDLSQ-KRIGTICESIKQLADKYGDELPIFGSMIGPFSLAQH 155
                                       ************8877**9999999***********9865.9*********************************** PP

                                       HHCTT-SS-HHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEE..TTGGGS-HHHHHHHTHHHHHHH CS
                             URO-D 153 lveGgskgfekllkllykdpeevhklldkltdvvieylkaqieagAdaiqifD..swagllspedfeefvlpylkri 227
                                       l      g + + + ++ + e  +klld++t+++++y+k+q+e+gAd ++i D  ++ +ll p+ f++fvlpy+k++
  gi|298674283|ref|YP_003726033.1| 156 LN-----GDDWFTNVMI-NEEFGKKLLDFTTEFCVAYAKKQVENGADTVVIIDptASYELLGPDFFRKFVLPYHKQV 226
                                       **.....8888888888.77889****************************************************** PP

                                       HHHHHH.H--S-EEEEESSHH.HHHHHHTTS--SEEE--TTS-HHHHHHSS....EEE--B-G.GGGG.S-HHHHHH CS
                             URO-D 228 vdevkaegpkvpvilfikgagaeiledlaelgadvlsldwtvdlkeaarevgdkvalqGnldPialLl.gspeeiek 303
                                       vd+ k+   +v  i++i+g++++ l+ + e+g d++s+d++vd++ a+++v +++ ++GnldP+++L  g+p++i++
  gi|298674283|ref|YP_003726033.1| 227 VDACKDM--GVGTIVHICGDTTKGLPIMDESGTDAISVDQKVDVATAKENV-QNAKIVGNLDPVETLWnGNPDVIKE 300
                                       ******8..57*********************************8888888.999********************** PP

                                       HHHHHHT.T---SSSEEB-BSS---TTS-HHHHHHHHHHHHT- CS
                             URO-D 304 evkeilekgaggkkgyilnlGhgippetppenvkalveavkey 346
                                       + +e l+kg++      l++G+gi   t+ en++++ve++k++
  gi|298674283|ref|YP_003726033.1| 301 KSQESLDKGVD-----FLAPGCGIVSATSNENLQTMVECAKSW 338
                                       ***********.....************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2350.14
//
Query:       gi|298674284|ref|YP_003726034.1|  [L=525]
Description: D-3-phosphoglycerate dehydrogenase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-63  212.3   0.1    1.7e-62  209.9   0.0    2.3  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
      3e-42  143.4   1.6    6.7e-42  142.3   0.8    2.0  2  2-Hacid_dh      D-isomer specific 2-hydroxyacid dehydrogenase
    4.8e-05   23.0   0.3    0.00037   20.2   0.0    2.6  2  ACT             ACT domain
    0.00015   21.9   2.1      0.001   19.3   0.1    2.9  3  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    0.00017   21.2   0.2     0.0054   16.3   0.0    2.4  2  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
     0.0015   19.1   0.5       0.15   12.7   0.0    3.5  4  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.017   15.5   0.1       0.15   12.5   0.0    2.4  2  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,


Domain annotation for each model (and alignments):
>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.9   0.0   6.8e-66   1.7e-62       1     178 []     104     278 ..     104     278 .. 0.98
   2 ?   -1.7   0.0      0.62   1.6e+03       9      51 ..     392     438 ..     386     448 .. 0.67

  Alignments for each domain:
  == domain 1  score: 209.9 bits;  conditional E-value: 6.8e-66
                                       HHHHHHHHTTHHHHHHHHHTTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHH CS
                      2-Hacid_dh_C   1 lalllallrrlaeadeevregewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeee 77 
                                       +++++a++r++++a++++++++w ++k+++g e++gk +G+iGlGrIG+ va+r +a+ mkv++yd++ ++e+ ++e
  gi|298674284|ref|YP_003726034.1| 104 ISMMMAMCRNIPQAHASLKSRKW-ERKKFMGVEVNGKYLGVIGLGRIGSYVAQRGQALHMKVLGYDPYVSQEQ-ADE 178
                                       589********************.9********************************************9888.999 PP

                                       HTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES-- CS
                      2-Hacid_dh_C  78 lgvelvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvf 154
                                       +gvel+s+e++++++D++++h+plt+ t++lina+++a+mk+g+ ++N+aRGg+++e+aL+eaL+sgk+agaa+Dvf
  gi|298674284|ref|YP_003726034.1| 179 MGVELTSVEDICKRADFITVHTPLTKGTENLINADKFALMKDGVRVLNCARGGIINEDALAEALRSGKVAGAAIDVF 255
                                       ***************************************************************************** PP

                                       SSSSSGTCHHHHHSTTEEE-SS-T CS
                      2-Hacid_dh_C 155 eeeplpedspllelpnviltPHia 178
                                        eep+ e+ pll+++nvi tPH++
  gi|298674284|ref|YP_003726034.1| 256 VEEPPFES-PLLDFDNVITTPHLG 278
                                       ****9955.*************97 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.62
                                       TTHHHHHHHHHTTCC....HTTCCGSBS-GTTSEEEEES-SHHHHHH CS
                      2-Hacid_dh_C   9 rrlaeadeevregew....ksekallgkelsgktvGiiGlGrIGqav 51 
                                       r+++ ++++ ++ +      + + ++g++ +  t  + G G+IG+ +
  gi|298674284|ref|YP_003726034.1| 392 RKIKVIESKSETTNKfpstITLELTRGSDTKSITGTVSGNGKIGRII 438
                                       5555555555444333444455566778888889999999***9865 PP

>> 2-Hacid_dh  D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.3   0.8   2.6e-45   6.7e-42       1     134 []       3     310 ..       3     310 .. 0.99
   2 ?   -1.5   0.0      0.71   1.8e+03      46      66 ..     379     398 ..     341     407 .. 0.66

  Alignments for each domain:
  == domain 1  score: 142.3 bits;  conditional E-value: 2.6e-45
                                       EEEEST.CHHHHHHHHHTTEEEEEESCSSHHHCHHHHTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB-H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh   1 vlileplreeelellkeegvevevkdellteellekakdadalivrsntkvtaevlealpkLkviaragvGvDnvDl 77 
                                       vl++++l ee+++ lke +++v+v + l+++el+ek+kd+dal+vrs t+vt++v++a+++Lk+i+ragvGvDn+D+
  gi|298674284|ref|YP_003726034.1|   3 VLVSDSLAEEGINKLKE-QFTVDVITGLSEDELVEKIKDYDALVVRSGTNVTEKVINAADNLKIIGRAGVGVDNIDV 78 
                                       79999************.66********************************************************* PP

                                       HHHHHTT-EEEE-TTTTHHHHHHHH.................................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.................................................... RF
                        2-Hacid_dh  78 daakerGilVtnvpgystesvAElt.................................................... 102
                                       daa+++Gi+V+n+p+ + +s+AE+t                                                    
  gi|298674284|ref|YP_003726034.1|  79 DAATNKGIIVVNTPEGNMISAAEHTismmmamcrnipqahaslksrkwerkkfmgvevngkylgviglgrigsyvaq 155
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                        2-Hacid_dh 103 ............................................................................. 102
                                                                                                                    
  gi|298674284|ref|YP_003726034.1| 156 rgqalhmkvlgydpyvsqeqademgveltsvedickradfitvhtpltkgtenlinadkfalmkdgvrvlncarggi 232
                                       ***************************************************************************** PP

                                       ..............................................T-BHHHHHHHHHHHHHHHHHHHTTCCGTTBC CS
                                       ..............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh 103 ..............................................aaTeeaqeniaeeaaenlvaflkgespanav 133
                                                                                     a+Teeaq n+ae aa++++++l+g++++na+
  gi|298674284|ref|YP_003726034.1| 233 inedalaealrsgkvagaaidvfveeppfesplldfdnvittphlgASTEEAQVNVAEAAADEVISALTGGPVNNAI 309
                                       ***************************************************************************99 PP

                                       S CS
                                       x RF
                        2-Hacid_dh 134 n 134
                                       n
  gi|298674284|ref|YP_003726034.1| 310 N 310
                                       8 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.71
                                       -TTS-BSHHHHHHHTT--EEE CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh  46 rsntkvtaevlealpkLkvia 66 
                                        +n  v+a+ l++  k+kvi 
  gi|298674284|ref|YP_003726034.1| 379 GVNF-VNANSLAKSRKIKVIE 398
                                       3343.7777778877887775 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.56   1.4e+03      41      64 ..      17      40 ..       8      42 .. 0.78
   2 !   20.2   0.0   1.5e-07   0.00037      21      66 ..     472     515 ..     469     516 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.56
                                      CEEEEEEEEEEHHHHHHHHHHHHT CS
                               ACT 41 agivfvvivvdeedleevlealkk 64
                                       ++ f+v+v+   + +e++e++k+
  gi|298674284|ref|YP_003726034.1| 17 LKEQFTVDVITGLSEDELVEKIKD 40
                                      578899999999999999999987 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 1.5e-07
                                       HHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTTC CS
                               ACT  21 ladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkle 66 
                                       l++++iNi  ++++ ++   ++ +++v+ vd e++e++l++ k++e
  gi|298674284|ref|YP_003726034.1| 472 LGKNDINISGMQVGQVGL--GEKTIMVLNVDSEVPESILNEMKSIE 515
                                       899***************..9**********************987 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.2      0.91   2.3e+03      87      87 ..      71      71 ..      11     110 .. 0.55
   2 !   19.3   0.1     4e-07     0.001       2     101 ..     141     239 ..     140     252 .. 0.82
   3 ?    0.4   0.0      0.26   6.7e+02      37      86 ..     387     438 ..     380     453 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.91
                                      E CS
                     NAD_binding_2 87 i 87
                                      +
  gi|298674284|ref|YP_003726034.1| 71 V 71
                                      1 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 4e-07
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS.HC CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg.ll 77 
                                       +g+iGlG +Gs  a++ ++  +kv +y+      +e ++e  + ++s+e++++++d++ +  + +k ++++i+   +
  gi|298674284|ref|YP_003726034.1| 141 LGVIGLGRIGSYVAQRGQALHMKVLGYDPY--VSQEQADEMGVELTSVEDICKRADFITVHTPLTKGTENLINAdKF 215
                                       69**************************44..6667777777899*************************9998777 PP

                                       CC--TT-EEEE-S---HHHHHHHH CS
                     NAD_binding_2  78 ealkkgdilidgstsspedtrela 101
                                       + +k g  +++++   + +   la
  gi|298674284|ref|YP_003726034.1| 216 ALMKDGVRVLNCARGGIINEDALA 239
                                       777777777776655555555555 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.26
                                       HHHHTT.EEE-SSHHHHHHHC.SEEEE-SSSHHHHHHHHHSHCCC--TT-EE CS
                     NAD_binding_2  37 elvaeg.akaaesieelvasl.dvvitmvkagkavdeviegllealkkgdil 86 
                                       +l++++ +k++es +e +++   ++ + ++ g+++++++  +  + k g+i+
  gi|298674284|ref|YP_003726034.1| 387 SLAKSRkIKVIESKSETTNKFpSTITLELTRGSDTKSITGTVSGNGKIGRII 438
                                       444443499999999***999999999**********999998888888776 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.039        99      77     113 ..      30      66 ..      23     116 .. 0.88
   2 !   16.3   0.0   2.1e-06    0.0054       3      96 ..     137     230 ..     135     242 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.039
                                       HHHHTGGG--TT-EEEESSSHHHHTTSS---TTSEEE CS
                              IlvN  77 yeeeiepnlkegkalafahGfnihfglikppkdvdvv 113
                                        e+e+ +++k+ +al+  +G n+  + i++ ++++++
  gi|298674284|ref|YP_003726034.1|  30 SEDELVEKIKDYDALVVRSGTNVTEKVINAADNLKII 66 
                                       577888999999****************999998876 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 2.1e-06
                                       HTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHH.HHHHHH CS
                              IlvN   3 kgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDel.qkevye 78 
                                       +gk + viG G  G   a+    + l++ v  ++   s ++A e g+e ++v++++k+ad++++ +P +   +++++
  gi|298674284|ref|YP_003726034.1| 137 NGKYLGVIGLGRIGSYVAQR--GQALHMKVLGYDPYVSQEQADEMGVELTSVEDICKRADFITVHTPLTKgTENLIN 211
                                       789999*********99985..5566665555666669*****************************6541566777 PP

                                       HHTGGG--TT-.EEEESSS CS
                              IlvN  79 eeiepnlkegk.alafahG 96 
                                       ++    +k+g  +l +a G
  gi|298674284|ref|YP_003726034.1| 212 ADKFALMKDGVrVLNCARG 230
                                       7666677776436666666 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1     0.098   2.5e+02      27      80 ..       2      59 ..       1      66 [. 0.66
   2 ?   -2.0   0.0       2.2   5.7e+03      48      77 ..      71      99 ..      43     105 .. 0.60
   3 !   12.7   0.0   5.8e-05      0.15       2      71 ..     141     202 ..     140     214 .. 0.87
   4 ?   -2.4   0.0       2.9   7.4e+03      23      41 ..     387     406 ..     375     423 .. 0.58

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.098
                                      CEEEEEESSCCCHHHHHHHHC-EEECE.CHHHHHH...H-SEEEE-S-HHHHHHHHHH CS
                     F420_oxidored 27 eivvansrnpekaeelaeelgvkvtav.dneeaae...eadvvvlavkpedveevlse 80
                                      +++v  s  +e +++l+e++ v+v+++ +  e++e   + d +v+   ++++e+v+++
  gi|298674284|ref|YP_003726034.1|  2 KVLVSDSLAEEGINKLKEQFTVDVITGlSEDELVEkikDYDALVVRSGTNVTEKVINA 59
                                      5778888999***********8877641333444322266666666666666666665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.2
                                      -EEECECHHHHHHH-SEEEE-S-HHHHHHH CS
                     F420_oxidored 48 vkvtavdneeaaeeadvvvlavkpedveev 77
                                      v+v      +aa++  ++v+  +  ++ ++
  gi|298674284|ref|YP_003726034.1| 71 VGVDN-IDVDAATNKGIIVVNTPEGNMISA 99
                                      55555.446677777777777766666555 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 5.8e-05
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-H CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkp 71 
                                       +g+iG G++g+ +a++ +a      +++ +   +p   +e a+e+gv++t+   e+ +++ad++ +  + 
  gi|298674284|ref|YP_003726034.1| 141 LGVIGLGRIGSYVAQRGQALH---MKVL-G--YDPYVSQEQADEMGVELTS--VEDICKRADFITVHTPL 202
                                       69*************988887...7777.5..899999********99999..**********9887665 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 2.9
                                       S..-GGCEEEEEESSCCCHHH CS
                     F420_oxidored  23 a..qpheivvansrnpekaee 41 
                                          + ++i v+ +++ e+ ++
  gi|298674284|ref|YP_003726034.1| 387 SlaKSRKIKVI-ESKSETTNK 406
                                       22333555555.444444444 PP

>> UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       0.5   1.3e+03      58      73 ..      32      47 ..       8     108 .. 0.65
   2 ?   12.5   0.0     6e-05      0.15      28      76 ..     159     202 ..     151     225 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.5
                                      S-CHHHHTT-SEEEE- CS
                    UDPG_MGDP_dh_C 58 dsleealkgadaivil 73
                                      d+l e +k++da+v+ 
  gi|298674284|ref|YP_003726034.1| 32 DELVEKIKDYDALVVR 47
                                      3444555555555553 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 6e-05
                                       HCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S-- CS
                    UDPG_MGDP_dh_C  28 eegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaivilteh 76 
                                       + +++v  yDP+v++e++ +     gve++ s+e+ +k ad i ++t+ 
  gi|298674284|ref|YP_003726034.1| 159 ALHMKVLGYDPYVSQEQADE----MGVELT-SVEDICKRADFITVHTPL 202
                                       55679999*********987....578887.79************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (525 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.44
# Mc/sec: 3548.43
//
Query:       gi|298674285|ref|YP_003726035.1|  [L=161]
Description: hypothetical protein Metev_0312 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1186.80
//
Query:       gi|298674286|ref|YP_003726036.1|  [L=161]
Description: hypothetical protein Metev_0313 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.7e-42  142.0   0.4    1.1e-41  141.8   0.4    1.0  1  DUF2240   Uncharacterized protein conserved in archaea (DUF22


Domain annotation for each model (and alignments):
>> DUF2240  Uncharacterized protein conserved in archaea (DUF2240)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.8   0.4   6.2e-46   1.1e-41       1     143 [.      10     152 ..      10     153 .. 0.98

  Alignments for each domain:
  == domain 1  score: 141.8 bits;  conditional E-value: 6.2e-46
                           DUF2240   1 elkiavaapfkkkrkdklsesdfvfalsldrkwlspdqakklldraeeegLlekkdgdlvpnfdvaeveiPlgFkpd 77 
                                       el  +va+ +kkk  ++ls ++f+fals+d kw+spd+a+++ d+a e+ ++ ++dg++ +n ++ +v+iP++Fkp+
  gi|298674286|ref|YP_003726036.1|  10 ELTKVVASVYKKKSSSELSLKEFEFALSFDFKWMSPDEASRVSDMAIESNIVYEQDGYINLNINLDNVSIPHDFKPS 86 
                                       57789************************************************************************ PP

                           DUF2240  78 eellkekstferildaiaastgiekkevvaeinelqeelkglvdveaaalvvakkegvdvddliee 143
                                       +el+keks++e+i++ i+ + +++k++v++ ine+qee ++l+ +e+ a++vak+ g+d++ + ++
  gi|298674286|ref|YP_003726036.1|  87 DELFKEKSIIEQIMEYITVTMNMDKQKVASLINEKQEEYSQLLYPEISAILVAKELGCDITPFYQK 152
                                       ************************************************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1256  (0.0700541); expected 358.6 (0.02)
Passed bias filter:                      634  (0.0353617); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1190.06
//
Query:       gi|298674287|ref|YP_003726037.1|  [L=126]
Description: 50S ribosomal protein L15 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-11   43.6   0.0    2.4e-11   43.4   0.0    1.1  1  Ribosomal_L18   Ribosomal protein 60S L18 and 50S L18e
    1.1e-07   32.5   1.6    3.5e-07   31.0   1.6    1.8  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27
  ------ inclusion threshold ------
      0.069   13.0   0.0      0.087   12.6   0.0    1.2  1  AAA_26          AAA domain


Domain annotation for each model (and alignments):
>> Ribosomal_L18  Ribosomal protein 60S L18 and 50S L18e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.0     4e-15   2.4e-11      10     139 ..       3     126 .]       1     126 [] 0.93

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 4e-15
                     Ribosomal_L18  10 kkskrkapksenvylklLvklyrfLarRtdskFnkvvlkrLfmsrinrpplslsrlvkkvkkkeeekkiavvvgtvt 86 
                                       kks+++  k +n+ +  L+ l +  ++  ++   k + krL +  + ++ + ls++ ++++    e++i+ v g+v+
  gi|298674287|ref|YP_003726037.1|   3 KKSQKRVAKKTNPRIVELIGLLKETSHTENAPIWKDLAKRLEKPNRTHAEINLSKIDRNTD----ENEIVLVPGKVL 75 
                                       78899999999999999999999999999***************************99988....579********* PP

                     Ribosomal_L18  87 dDvrllevPklsvaALrftetararilkaGGeiltlDqLalraPtGkntvLlr 139
                                           l +   ++vaAL++++ta+++i+  GG+ilt++++  ++P G+   +l+
  gi|298674287|ref|YP_003726037.1|  76 GAGDLGH--GVTVAALKISNTAKDKIESVGGKILTIEDILEENPSGSGIKILQ 126
                                       9998876..69***********************************9987775 PP

>> Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   1.6   5.8e-11   3.5e-07      60     127 ..      42     107 ..       6     108 .. 0.76

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 5.8e-11
                                       TTTTGTTS------EEEGGGTTTTSSS....SE..EEE--S---.--EEEESEE-HHHHHHHHHTT-EEE CS
                    Ribosomal_L27A  60 lideerleladeaeeidleelaeaglikkkdgv..KvlgkgeltkklkvkaskfSkkAkekIeaaGGkve 127
                                        +++ +     +++ei+l+++ ++   ++   v  Kvlg g+l + ++v a k+S++Ak kIe++GGk+ 
  gi|298674287|ref|YP_003726037.1|  42 RLEKPN----RTHAEINLSKIDRNTDENEIVLVpgKVLGAGDLGHGVTVAALKISNTAKDKIESVGGKIL 107
                                       333322....3556888888844444444334445*********************************96 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.5e-05     0.087      40     106 ..       6      72 ..       3      99 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.5e-05
                            AAA_26  40 tgieededselikellgldqtyelpeplalsaplspel.aarqegedidlekivkelekdadivvVEG 106
                                       +++++++ + +i el+gl ++++++e+  + + l+++l + +++  +i l+ki ++++++++iv+V G
  gi|298674287|ref|YP_003726037.1|   6 QKRVAKKTNPRIVELIGLLKETSHTENAPIWKDLAKRLeKPNRTHAEINLSKI-DRNTDENEIVLVPG 72 
                                       66677888889999******99999999999999888835566689999****.***********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 799.93
//
Query:       gi|298674288|ref|YP_003726038.1|  [L=139]
Description: 50S ribosomal protein L13 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-10   41.5   0.6    1.9e-08   34.6   0.6    2.1  1  Ribosomal_L13  Ribosomal protein L13


Domain annotation for each model (and alignments):
>> Ribosomal_L13  Ribosomal protein L13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.6     1e-12   1.9e-08       4     115 ..       3     100 ..       2     109 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 1e-12
                                       EEEETTSBHHHHHHHHHHHHHTTTSTT--TTS--S-EEEEEEGGCBB-SSTHHTT-EEEEE-SSTTSEEEEEHHHHH CS
                     Ribosomal_L13   4 viDAegqvlgrlaskiakvLrGkhkptytphvdcGdyvvvinaekvaltgkkleqkvyyrhtgypgglkevtakell 80 
                                       +iDA++ ++grlas++ak L             +G+ + ++nae+ +++g+k+++ + y++++ +g++++      +
  gi|298674288|ref|YP_003726038.1|   3 IIDANDLIIGRLASTVAKEL------------LAGEEIAIVNAENAVISGSKVRTLTDYNEKREIGSIEHG---PHF 64 
                                       68888888888888888766............57999*******************999999999988775...567 PP

                                       CCSHHHHHHHHHHCCS-.SSHHHHHHGCTEEEESSS CS
                     Ribosomal_L13  81 ekkpeeilekaVkgmLp.knklgrrrlkrLkvyage 115
                                        k+p++i++++V+gmLp k + g++ ++rLkv  g 
  gi|298674288|ref|YP_003726038.1|  65 PKRPDRIITRTVRGMLPyKREKGKKAMSRLKVHVGV 100
                                       899**************55669999*******9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 877.58
//
Query:       gi|298674289|ref|YP_003726039.1|  [L=134]
Description: 30S ribosomal protein S9 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.1e-32  110.3   0.9    9.1e-32  110.1   0.9    1.0  1  Ribosomal_S9  Ribosomal protein S9/S16


Domain annotation for each model (and alignments):
>> Ribosomal_S9  Ribosomal protein S9/S16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.1   0.9   5.1e-36   9.1e-32       1     121 []      10     134 .]      10     134 .] 0.92

  Alignments for each domain:
  == domain 1  score: 110.1 bits;  conditional E-value: 5.1e-36
                                       EECTTEEEEEEEEESSSEEEETTEECCHHSTTSCHHHHHCHHHHHTTTSSS.EEEEEEEESS-HHHHHHHHHHHHHH CS
                      Ribosomal_S9   1 GrrKesvArvwikegkgkilvngksleeYfkeeaarekvleplkltgllgk.fdvfvkvkgGGlsgqaeAirlgiar 76 
                                       G+ K ++Ar++i +g+gk++vn++++e Y + +  r k++e+lkl+g + + +d+ v+v+gGGl+gqa+A+r++iar
  gi|298674289|ref|YP_003726039.1|  10 GKNKAAIARATISKGTGKVRVNKVPIEIYEP-KFGRLKMQEALKLAGDVVSeMDIDVNVRGGGLMGQANAVRTAIAR 85 
                                       899*************************888.899***********987755************************* PP

                                       HHHHHHHHHHHHHC......TCCCTS-B--------TTSSCTTB----S-- CS
                      Ribosomal_S9  77 aLvalekeekkeLk......kaglltrDpRvvErkKtgkkkARkkyqwskR 121
                                       ++v +++   ++++      +++l+++++R++E kK+g ++AR+kyq+s+R
  gi|298674289|ref|YP_003726039.1|  86 GIVDWTN--DTNIRdtymayDRNLIVNNSRQKESKKFGGPGARAKYQKSYR 134
                                       *****88..355554445678****************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 897.07
//
Query:       gi|298674290|ref|YP_003726040.1|  [L=62]
Description: RNA polymerase N/8 Kd subunit [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-31  108.2   0.3    1.9e-31  108.1   0.3    1.0  1  RNA_pol_N       RNA polymerases N / 8 kDa subunit
  ------ inclusion threshold ------
      0.024   14.9   0.1      0.032   14.5   0.1    1.2  1  Chordopox_RPO7  Chordopoxvirus DNA-directed RNA polymerase 7 


Domain annotation for each model (and alignments):
>> RNA_pol_N  RNA polymerases N / 8 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.1   0.3   2.1e-35   1.9e-31       2      59 .]       1      58 [.       1      58 [. 0.98

  Alignments for each domain:
  == domain 1  score: 108.1 bits;  conditional E-value: 2.1e-35
                                      ---SS-TTT--B-STHHHHHHHHHHTT--HHHHHHHHT--SHHHHHHHHTB--THHHH CS
                         RNA_pol_N  2 iiPVrCFtCGkvigekweeylellekgeepkdaLdaLglkryCCrrmllthvdliekl 59
                                      +iP+rCFtCGkvi+++w+ey++++e+ge+++ +Ld+Lg+kryCCrrm+lthv+l+++l
  gi|298674290|ref|YP_003726040.1|  1 MIPIRCFTCGKVIANQWHEYKNRVEEGENSGAVLDDLGIKRYCCRRMFLTHVELVDTL 58
                                      8******************************************************975 PP

>> Chordopox_RPO7  Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   3.5e-06     0.032       4      49 ..       3      53 ..       1      59 [. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.5e-06
                    Chordopox_RPO7  4 plvCstCGrDlsee..ryrLlvkkkkLk.dvlat..vkrkCCrlkLstqie 49
                                      p+ C tCG+ ++++   y+  v++ + +  vl+   +kr CCr    t +e
  gi|298674290|ref|YP_003726040.1|  3 PIRCFTCGKVIANQwhEYKNRVEEGENSgAVLDDlgIKRYCCRRMFLTHVE 53
                                      788********986336999998866552788863369*****98888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 429.01
//
Query:       gi|298674291|ref|YP_003726041.1|  [L=65]
Description: RNA polymerase Rpb6 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-14   52.6   0.1    3.9e-14   52.3   0.1    1.1  1  RNA_pol_Rpb6  RNA polymerase Rpb6
  ------ inclusion threshold ------
      0.065   13.6   0.1      0.072   13.4   0.1    1.1  1  DUF190        Uncharacterized ACR, COG1993


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb6  RNA polymerase Rpb6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.3   0.1   4.3e-18   3.9e-14       5      48 ..       8      56 ..       6      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 4.3e-18
                                      SS--HHHHHHHHHHHHHHH....HT.........SS-SSSSTTCHHHHTT-S- CS
                      RNA_pol_Rpb6  5 kvltrYelvriaakRArQieegesl.........etqkpvviAlrEiaegkip 48
                                      ++ trYe +ri+++RA+Qi    s+         e+ +p+++A++E+  g ip
  gi|298674291|ref|YP_003726041.1|  8 QTFTRYERARIIGARALQI----SMdapilienvENLDPLQVAIEELKHGVIP 56
                                      677****************....99999999887677***************9 PP

>> DUF190  Uncharacterized ACR, COG1993
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1     8e-06     0.072      46      83 ..      15      52 ..       9      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8e-06
                                      ----------------EEEEEEEE-HHHHHHHHHHHHT CS
                            DUF190 46 ssrihtakllelsedlPvvieivdteekieaflpelke 83
                                      + ri  a+ l++s d P++ie v++ + ++  ++elk+
  gi|298674291|ref|YP_003726041.1| 15 RARIIGARALQISMDAPILIENVENLDPLQVAIEELKH 52
                                      6678899************************9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 446.73
//
Query:       gi|298674292|ref|YP_003726042.1|  [L=236]
Description: 30S ribosomal protein S2 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-23   82.7   0.3    1.9e-12   46.9   0.1    2.3  2  Ribosomal_S2  Ribosomal protein S2
  ------ inclusion threshold ------
       0.14   11.2   0.2        0.2   10.7   0.2    1.1  1  DUF3131       Protein of unknown function (DUF3131)


Domain annotation for each model (and alignments):
>> Ribosomal_S2  Ribosomal protein S2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0     2e-12   1.8e-08       2      96 ..      55     146 ..      54     151 .. 0.91
   2 !   46.9   0.1   2.1e-16   1.9e-12     148     213 ..     153     218 ..     147     220 .. 0.95

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 2e-12
                      Ribosomal_S2   2 LeagvhfGhqtrrwnpkmkpyIyger.ngihiidlektlaalrraykvvkevaakggkilfvgtkkqakeavkeaak 77 
                                       L++gvh+G q++  +++m ++Iy +r +g +++d++ t + ++ a++++++   + ++il  + ++  ++  +  ak
  gi|298674292|ref|YP_003726042.1|  55 LASGVHIGTQQK--TKDMINFIYRVRtDGLYVLDIQSTEERIKLAASFLSKY--NPSTILVTSARQYGQHPATMFAK 127
                                       799*****6666..899******999569********************985..77899999999999999999*** PP

                      Ribosomal_S2  78 rangyyvnerWlgGtLTNf 96 
                                         ++  +  r+++GtLTN 
  gi|298674292|ref|YP_003726042.1| 128 AIGAKSMVGRFIPGTLTNP 146
                                       ******************5 PP

  == domain 2  score: 46.9 bits;  conditional E-value: 2.1e-16
                      Ribosomal_S2 148 lPdlvvvldpkkekiavkEakklgipviaivDtnvdpdlvdypIpaNddsirsiklilgvladaie 213
                                        P++ +v+dp+ +  ++kE  ++g+pv+a++Dtn +++ vd +Ip N++  ++++l++ +la+ ++
  gi|298674292|ref|YP_003726042.1| 153 EPEVTLVTDPTGDAQVIKESVNVGVPVVAFCDTNNQTSSVDLVIPTNNKGRKALSLVYWLLAKEVA 218
                                       59999********************************************************99886 PP

>> DUF3131  Protein of unknown function (DUF3131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   2.2e-05       0.2     185     247 ..      13      78 ..       5      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.2e-05
                           DUF3131 185 kalskepy.ktvevegvevpvdrrdlkktea..nnyvvsepylleglElGfdaelkelaerlleaq 247
                                       k l++e++ +t++v+  + p  +++++++e+  ++ +  + yl  g+ +G ++++k++++ +++++
  gi|298674292|ref|YP_003726042.1|  13 KNLETEETeETATVSQSATPQPSEESTESEEesTSLIPIDEYLASGVHIGTQQKTKDMINFIYRVR 78 
                                       55555665589999999999988888877333589999************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1071  (0.0597356); expected 358.6 (0.02)
Passed bias filter:                      709  (0.0395449); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 1408.66
//
Query:       gi|298674293|ref|YP_003726043.1|  [L=265]
Description: hypothetical protein Metev_0320 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-78  264.2   0.0    1.2e-78  264.0   0.0    1.0  1  Memo      Memo-like protein
     0.0051   15.9   0.0     0.0058   15.7   0.0    1.3  1  LigB      Catalytic LigB subunit of aromatic ring-opening dio


Domain annotation for each model (and alignments):
>> Memo  Memo-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  264.0   0.0   1.3e-82   1.2e-78       2     270 ..       4     262 ..       3     263 .. 0.97

  Alignments for each domain:
  == domain 1  score: 264.0 bits;  conditional E-value: 1.3e-82
                              Memo   2 aavAGsfYpedeeelkkqleeflekntgkkeiarviisPHagyvysgevaakayaelesskvervvilGpsHtilgs 78 
                                       ++vAG+fY  d+  l+k +  ++ +    ++     ++PHagy++sg+vaa+a+a+l ++  ++ +ilGp+Ht+lgs
  gi|298674293|ref|YP_003726043.1|   4 PTVAGQFYALDPSGLEKEISRCFGDIDISQQNIHGAVIPHAGYMFSGPVAAYAFAQLPEA--DTYIILGPNHTGLGS 78 
                                       89********************9987777766888889*******************998..9************** PP

                              Memo  79 kvsvlaaseleTPlGdlkvDeelveeLvkkeeiadldetaalaEHSlEvqlpfLkellkekkfkivPilvsaqseet 155
                                        v++++ ++++TPlG+++ D+el + L    +i d+de+a+++EHS+Evq+pfL++++ +  fk++Pi+++ q+eet
  gi|298674293|ref|YP_003726043.1|  79 AVAISQ-DTWSTPLGNVETDKELGKSLAG--SILDVDEMAHMYEHSIEVQIPFLQYRFSH-GFKVLPICMGLQDEET 151
                                       ******.********************99..5****************************.6*************** PP

                              Memo 156 akevgealakvikdes..nlviiSsDlsHygrrFgspqeiaesieDrevikaleelneeelkeylektnnticGekp 230
                                       a evg+ ++++i +++  + vi+SsDl+H++     p+++a+ + D+++i+ +e+++ +e++  +++  +t cG++p
  gi|298674293|ref|YP_003726043.1| 152 ALEVGNQISSAITESNkkIFVIASSDLTHFE-----PENVANDT-DKYLIESIENMDVHEFYRRISERSATACGYGP 222
                                       ***************9989999*********.....*******9.******************************** PP

                              Memo 231 iavilkalkklgakkakllkYaqssdvtsdtdsvVsyasl 270
                                       i+++l ++k lg + +kllkY +s dvt+d +svV+ya++
  gi|298674293|ref|YP_003726043.1| 223 ISAMLTVAKSLGGRTGKLLKYGTSADVTGDSSSVVGYAAV 262
                                       **************************************87 PP

>> LigB  Catalytic LigB subunit of aromatic ring-opening dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   6.4e-07    0.0058     144     215 ..     142     202 ..      88     258 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.4e-07
                              LigB 144 vaypllsferlykLGeAlrkaveeldknvlilgsGglsHqlegdeaakadaqtlllneefdeelldllkegr 215
                                       + ++l + e   ++G+ + +a+ e++k++ +++s +l+H  +++ a+             d+ l++ +++++
  gi|298674293|ref|YP_003726043.1| 142 ICMGLQDEETALEVGNQISSAITESNKKIFVIASSDLTHFEPENVAN-----------DTDKYLIESIENMD 202
                                       34567899999****************************65555444...........22444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1640.76
//
Query:       gi|298674294|ref|YP_003726044.1|  [L=304]
Description: mevalonate kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.4e-17   61.2   0.2    1.7e-16   60.2   0.2    1.5  1  GHMP_kinases_N   GHMP kinases N terminal domain
    9.5e-15   54.7   2.2    6.8e-14   52.0   0.3    2.5  2  GHMP_kinases_C   GHMP kinases C terminal
     0.0022   17.5   0.1     0.0046   16.5   0.1    1.5  1  GalKase_gal_bdg  Galactokinase galactose-binding signature


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.2   0.2   2.8e-20   1.7e-16       1      66 []      79     146 ..      79     146 .. 0.93

  Alignments for each domain:
  == domain 1  score: 60.2 bits;  conditional E-value: 2.8e-20
                                       EEEEEESSHTTSSSCHHHHHHHHHHHHHHHHT..TEHHHH.HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                    GHMP_kinases_N   1 divikseiPvgaGLGSSAAlavalvaAllall..glslee.aklaleaerlaqggngsggDvaasvyGg 66 
                                       +i+i+se+Pvg+GLGSSAAl+v+++ Al++l+  glsle  a+l+++ e  +q gn s+ D ++s++Gg
  gi|298674294|ref|YP_003726044.1|  79 KININSELPVGSGLGSSAALTVSTIQALNHLFhcGLSLEQiADLGYNVEWDVQ-GNASPTDTYVSTMGG 146
                                       699***************************99556667668************.**************8 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1     0.058   3.5e+02       8      43 ..      40      73 ..      28     102 .. 0.69
   2 !   52.0   0.3   1.1e-17   6.8e-14       5      81 ..     210     283 ..     207     286 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.058
                    GHMP_kinases_C  8 gdlellgellnlsqrs.elkavvgilppeleelleal 43
                                      +d+ +++  l +s  + e+   ++ ++ ++e+++e++
  gi|298674294|ref|YP_003726044.1| 40 NDHIEINSVLGRSGLNfEK---HPYVSAAIERMKEFA 73
                                      6666666666666665444...777777777777765 PP

  == domain 2  score: 52.0 bits;  conditional E-value: 1.1e-17
                    GHMP_kinases_C   5 lergdlellgellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvaralre 81 
                                       +++gd+e++g+l+n +q   l++ +g+ + el +l+ ++++ Ga+gakl+GaGgG++ +al+ d ++  +v +a+++
  gi|298674294|ref|YP_003726044.1| 210 VCNGDYESIGKLMNINQG--LLDSIGVGSLELSQLIYSARSKGAYGAKLTGAGGGGCMIALA-DASKTVDVSDAIKS 283
                                       789***************..9****************************************9.88777777777765 PP

>> GalKase_gal_bdg  Galactokinase galactose-binding signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   7.7e-07    0.0046      14      46 ..       4      36 ..       2      38 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.7e-07
                                      EEEEEEEEEE--S-TTTT-EEEEEEEEEEEEEE CS
                   GalKase_gal_bdg 14 asAPGRvnLiGEHtDYngGfVlpmAieqdiyia 46
                                       sAPG + L GEH    g   + +Aie+++++ 
  gi|298674294|ref|YP_003726044.1|  4 SSAPGKIYLFGEHAVVYGENAICCAIELRTHVQ 36
                                      69****************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1951.14
//
Query:       gi|298674295|ref|YP_003726045.1|  [L=263]
Description: aspartate/glutamate/uridylate kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.3e-35  120.4   1.5    1.1e-34  120.2   1.5    1.0  1  AA_kinase  Amino acid kinase family
  ------ inclusion threshold ------
      0.061   13.2   0.1       0.57   10.1   0.0    2.2  2  pXO2-34    Family of unknown function


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.2   1.5   1.2e-38   1.1e-34       2     241 .]      11     238 ..      10     238 .. 0.96

  Alignments for each domain:
  == domain 1  score: 120.2 bits;  conditional E-value: 1.2e-38
                                       EEEEEE-TTCCCCTCC.......HHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..H CS
                         AA_kinase   2 rvVvKlGGssltdkee.......aslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstle 71 
                                       ++++K+GGs++tdk++       + ++r+ ++i+++   + klv+VhG+gsf++ ++++ +++++++ a        
  gi|298674295|ref|YP_003726045.1|  11 ITILKIGGSVITDKNAdenfakhDEIDRISKEISEF---DGKLVIVHGAGSFGHPQAKK-YQITDKFDA-------- 75 
                                       79**********999999******************...889*****************.********9........ PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEE CS
                         AA_kinase  72 eagevatrdalaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfig 148
                                        +g ++t+ ++  l++   ++l+++ ++av++++   +++++gr       +     +++  +l++++vpvl+g+++
  gi|298674295|ref|YP_003726045.1|  76 -KGSIITHKSVNLLNQLFIDSLIDNNVNAVSVHPMNNTISKNGR-------IQDMFLDNLYYMLDNKIVPVLHGDVV 144
                                       .8**********************************99999888.......99999********************* PP

                                       EETTTEEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH....CSSS.TTTHHHH CS
                         AA_kinase 149 ldeegelgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee....saselatgGmkv 221
                                       +d + +  ++s+D+i  +lA  +gA ++ i +  +GV+d ++k     +l++  ++  +++    s+++++tgGm  
  gi|298674295|ref|YP_003726045.1| 145 MDKNTGTSIISGDQIVPYLATQMGAIRIGIGSIKEGVLDENGKTL---KLITHDNFANVKNnigsSEGTDVTGGMLG 218
                                       ******99********************************99888...8888888888888**************** PP

                                       CHHHHHHHHHCTT-EEEEEE CS
                         AA_kinase 222 khpaalaaarrggipvvItn 241
                                       k+ + l++ +  g   +I+n
  gi|298674295|ref|YP_003726045.1| 219 KVTELLKLNELTGSTSYIFN 238
                                       **********9999999987 PP

>> pXO2-34  Family of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   6.3e-05      0.57       8      40 ..      35      67 ..      31      79 .. 0.87
   2 ?    0.1   0.0     0.081   7.3e+02       9      29 ..     182     202 ..     175     204 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 6.3e-05
                           pXO2-34  8 eilnrahtvrlfdgsiwinlgnGkfinqetrqv 40
                                      ei + +++++ fdg+  i+ g G f +++ ++ 
  gi|298674295|ref|YP_003726045.1| 35 EIDRISKEISEFDGKLVIVHGAGSFGHPQAKKY 67
                                      57777999********************99986 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.081
                           pXO2-34   9 ilnrahtvrlfdgsiwinlgn 29 
                                       + +  +t +l+   +++n++n
  gi|298674295|ref|YP_003726045.1| 182 LDENGKTLKLITHDNFANVKN 202
                                       556678999**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1653.80
//
Query:       gi|298674296|ref|YP_003726046.1|  [L=358]
Description: isopentenyl-diphosphate delta-isomerase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-27   96.6   0.1    7.2e-26   91.0   0.1    2.1  1  FMN_dh        FMN-dependent dehydrogenase
    1.8e-05   23.9   6.7      0.057   12.4   0.2    3.4  3  IMPDH         IMP dehydrogenase / GMP reductase domain
     0.0014   17.9   3.0      0.089   12.0   0.0    3.4  3  DHO_dh        Dihydroorotate dehydrogenase
     0.0081   15.3   0.0      0.018   14.2   0.0    1.6  1  Glu_synthase  Conserved region in glutamate synthase
  ------ inclusion threshold ------
      0.055   12.8   2.9       0.16   11.3   2.6    2.0  1  NMO           Nitronate monooxygenase


Domain annotation for each model (and alignments):
>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.0   0.1     2e-29   7.2e-26       6     342 ..       4     331 ..       2     336 .. 0.85

  Alignments for each domain:
  == domain 1  score: 91.0 bits;  conditional E-value: 2e-29
                                       -HHHHHHHH--STTSHHHHHHHHGGGGEEE---SSSS-S..S-B--EEETTEEESSSEEE--B..STGGGTSTTHHH CS
                            FMN_dh   6 pkkafayvaggagdevtlrenraaferirlrprvlrdvs..kvdlsttllGqklslPvliaPv..glaklahpdgel 78 
                                       +++++++++ +a++ v  r++ + f++i+l +r+l +v+  ++dlst++lG+++s+P++ia++  g + ++    ++
  gi|298674296|ref|YP_003726046.1|   4 SRRKIEHLNFCAHSPVESRKKGSGFDDITLIHRALPEVNmdEIDLSTRFLGKDFSAPFMIASItgGHEDTI--PVNR 78 
                                       567889999999***********************98862267********************64444444..5899 PP

                                       HHHHHHHHHTS-EEEETT-SS-HHHHHHHHTT-EEEEEE-CSSHHHHHHHHHHHHHCTESEEEEESSTSS---BHHH CS
                            FMN_dh  79 alaraaakagipfvlstvastsleevaaaaegplwfqlyvpkdrelteellkraeaagykalvltvDtpvlgkRerd 155
                                       ala+a +++g+ ++++++ ++++e+ a++       ++ v++d++ ++ +  ++ aa++k   ++v        ++d
  gi|298674296|ref|YP_003726046.1|  79 ALAKAVEEMGVGIGVGSQ-RAAIEDPAQE------ESFRVVRDEAPNAFIYGNVGAAQIKEYGVEVVEKLVDMIDAD 148
                                       *****************9.999***9995......46899*****************99999988744443323322 PP

                                       HHCT--BSTT-T.G.TTGGGSTSGSCCTTH..THHHHHHCCCHB-TC--HHHHHHHHHHHSSEEEEEEE...-SHHH CS
                            FMN_dh 156 lrngfslppklklrnllqelakpewaaealkkasaaaefvgkqldpsltwddikwlreqtklplvvKGv...ltaed 229
                                            ++  +l+   +lqe+++pe+  +a                   t + i+++++ +++p++ K+    +++ed
  gi|298674296|ref|YP_003726046.1| 149 -----AMAVHLN---FLQEAVQPEGDRDAS-----------------GTLEAISEITS-LNIPVIAKETgagISHED 199
                                       .....3334544...99*******999988.................46788999987.789*****998899**** PP

                                       HHHHHHTTESEEEE--GGG.........TSSTT---HHHCHHHH...........HHHH..SS-EEEESS--SHHHH CS
                            FMN_dh 230 akraveaGvdgivvSNHGG.........RqldgapatidvLpei...........veavggrievlvDgGirrGsDv 286
                                       a ++ +aGv++i v   GG         R  d      + L ei             +++ ++++++ gGir+G D+
  gi|298674296|ref|YP_003726046.1| 200 AVLLKNAGVSAIDVGGVGGtswsgvefyRAKDRNDLRSQLLGEIfwdhgiptasdLIECDVSLPLIATGGIRSGLDI 276
                                       ****************************88888888888888887666655533322334489************** PP

                                       HHHHHTT-SEEEESHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-SBHHHHH CS
                            FMN_dh 287 lkAlalGAdavllGRpflyglaagGeeGvervleilraelertmallGvksvaeld 342
                                       +k + +GAd+   + pf+   a++ e+ v ++l+ +  +l+ +m l+G+k+v++l+
  gi|298674296|ref|YP_003726046.1| 277 AKSVTMGADVASAALPFVE-PALKNEQEVINTLSNFIYQLKVSMFLCGCKTVSDLR 331
                                       *****************55.599*******************************96 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.6   2.2    0.0037        13       3     173 ..      27     214 ..      25     222 .. 0.55
   2 !   12.4   0.2   1.6e-05     0.057     206     232 ..     260     286 ..     247     290 .. 0.87
   3 !    7.1   0.0   0.00065       2.3     290     328 ..     295     333 ..     293     342 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0037
                                       -GGGEEEE---B.-S-GGGSB--EESSTTEEESSSEEE-SS.....TTT.-SHHHHHHHHHTT.SEEEE-SSS-HHH CS
                                       xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxx.xxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                             IMPDH   3 tfddvllvpaks.evlpkevdlktkltkkiklniPlvsaam.....dtv.tesemAialareG.gigvihknlsiee 71 
                                        fdd+ l+ ++  ev+ +e+dl+t++  k + + P++ a++     dt+  ++ +A a+ ++G gigv  +   ie+
  gi|298674296|ref|YP_003726046.1|  27 GFDDITLIHRALpEVNMDEIDLSTRFLGK-DFSAPFMIASItggheDTIpVNRALAKAVEEMGvGIGVGSQRAAIED 102
                                       69**999988766999*********9866.67777766655333337773467799999999989999999999998 PP

                                       HHHH..HHHHHTSTTSXBXTTSXB-EEEEE-SSTTHHHHHHHHHHT.T-SEEEEE..-S......TS..SSHHHHHH CS
                                       xxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx..xx......xx..xxxxxxxx RF
                             IMPDH  72 qaee..vkkvkrspnaakdekgrllvgaavgvkedalervkalvea.gvdvlvvd..sa......hg..hsekvlea 135
                                        a+e   + v+   ++a ++     vgaa  +ke   e v++lv+  ++d+++v           +g    +++lea
  gi|298674296|ref|YP_003726046.1| 103 PAQEesFRVVR---DEAPNAFIYGNVGAAQ-IKEYGVEVVEKLVDMiDADAMAVHlnFLqeavqpEGdrDASGTLEA 175
                                       77651133443...3444444445555553.2223333333333321333333321122111111221122344445 PP

                                       HHHHHHHTTTSEEEE...EEE-SHHHHHHHHHTT-SEEEE- CS
                                       xxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 136 vkeikkkveevevia...GnvataegakaLieagadavkvG 173
                                       ++ei +    + via   G   ++e a  L +ag+ a+ vG
  gi|298674296|ref|YP_003726046.1| 176 ISEITSLN--IPVIAketGAGISHEDAVLLKNAGVSAIDVG 214
                                       55554332..5555322266666777777777777777775 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 1.6e-05
                                       CT-EEEEES---SHHHHHHHHHTT-SE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 206 agvpviaDGGikysgdivkAlaaGada 232
                                          p+ia GGi++  di+k++++Gad+
  gi|298674296|ref|YP_003726046.1| 260 VSLPLIATGGIRSGLDIAKSVTMGADV 286
                                       5689*********************97 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.00065
                                       EEEEE--B-HHHHHHHHHHHHHHHHHHHT-SSHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 290 egrvpykgsvkevveqlvgglrsgmgylGaktieelkek 328
                                       e +++ + +v +++++++ +l+ +m  +G+kt+++l++ 
  gi|298674296|ref|YP_003726046.1| 295 EPALKNEQEVINTLSNFIYQLKVSMFLCGCKTVSDLRDV 333
                                       5566777889999***********************975 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.024        85       2      21 ..      48      69 ..      47     144 .. 0.79
   2 ?    1.8   0.3      0.03   1.1e+02     233     273 ..     172     214 ..     167     226 .. 0.83
   3 !   12.0   0.0   2.5e-05     0.089     243     269 ..     260     286 ..     246     310 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.024
                                      G-EEETTEEESSSEEE-T..TS CS
                            DHO_dh  2 latkvlglkfknpiglAa..Gf 21
                                      l+t++lg++f  p+++A+  G 
  gi|298674296|ref|YP_003726046.1| 48 LSTRFLGKDFSAPFMIASitGG 69
                                      789999**********983344 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.03
                                       HHHHHHHHTTT.S-EEE..ESS--SHHHHHHHHHHTECEEEES CS
                            DHO_dh 233 virelykrlkkeipiIg..vGGiesgeDalekieaGAslvqvy 273
                                       ++ ++++ ++ +ip+I+  +G   s eDa+   +aG s++ v+
  gi|298674296|ref|YP_003726046.1| 172 TLEAISEITSLNIPVIAkeTGAGISHEDAVLLKNAGVSAIDVG 214
                                       566778888899****8656866799*************9998 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 2.5e-05
                                       T.S-EEEESS--SHHHHHHHHHHTECE CS
                            DHO_dh 243 keipiIgvGGiesgeDalekieaGAsl 269
                                        ++p+I++GGi sg D    ++ GA +
  gi|298674296|ref|YP_003726046.1| 260 VSLPLIATGGIRSGLDIAKSVTMGADV 286
                                       469*********************976 PP

>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   5.1e-06     0.018     275     301 ..     262     288 ..     245     294 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.1e-06
                                       -EEEEESS--SHHHHHHHHHHT-SEEE CS
                      Glu_synthase 275 vsliadGglktgadvvkalalGAdavg 301
                                       + lia+Gg+++g d++k++ +GAd  +
  gi|298674296|ref|YP_003726046.1| 262 LPLIATGGIRSGLDIAKSVTMGADVAS 288
                                       5699********************755 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   2.6   4.5e-05      0.16     191     219 ..     259     287 ..      97     296 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.5e-05
                               NMO 191 avdiPviAaGGiidrrgvaaaLalGAsgv 219
                                        v++P+iA+GGi  + ++a   ++GA  +
  gi|298674296|ref|YP_003726046.1| 259 DVSLPLIATGGIRSGLDIAKSVTMGADVA 287
                                       355***********************866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2165.95
//
Query:       gi|298674297|ref|YP_003726047.1|  [L=447]
Description: RNA-metabolising metallo-beta-lactamase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-08   34.3   1.0    2.9e-08   33.5   0.1    1.8  2  Lactamase_B_2  Beta-lactamase superfamily domain
    4.3e-08   33.0   1.0    2.1e-07   30.8   0.1    2.5  3  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    1.3e-07   31.9   1.2    5.7e-07   29.7   1.3    1.8  1  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
       0.16   12.1   0.0       0.39   10.9   0.0    1.6  1  Nkap_C         NF-kappa-B-activating protein C-terminal domai


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.1   6.5e-12   2.9e-08      30     144 ..      74     176 ..      65     189 .. 0.90
   2 ?   -2.6   0.1       0.7   3.2e+03     175     200 ..     385     410 ..     362     410 .. 0.77

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 6.5e-12
                                       SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEE CS
                     Lactamase_B_2  30 pidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfelgdggleit 106
                                        + a++ th+H DH+  ++ l+++++  +p++ ++ + + +++++  +++    + ++++l++g+  +++ ++++i+
  gi|298674297|ref|YP_003726047.1|  74 TVRAIVCTHGHLDHIGAIPKLAHRYA--APIISTPYTTSLIKQQIESEVKFGV-KNKIVTLNAGGIYQVT-EDISIE 146
                                       589********************665..89**************999888888.9**************8.69**** PP

                                       EEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S CS
                     Lactamase_B_2 107 atparhksgrrldrnagdtlGlriegggkrvyyigDtg 144
                                       ++ a+h+           ++  +i +++ +++y+ D +
  gi|298674297|ref|YP_003726047.1| 147 FIRAQHSIID--------CVFAVIHTPDGAILYACDYK 176
                                       ******9998........99999999999999999876 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.7
                                       HHT---STSHHHHCTTSSSSEEEEES CS
                     Lactamase_B_2 175 hmgHltpeeaveaaadlgakrlvliH 200
                                         gH+  e+ +e+++ ++++ +++ H
  gi|298674297|ref|YP_003726047.1| 385 VSGHACKEDHWELLRIINPEHVIPAH 410
                                       45777779999999999999999998 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.62   2.8e+03      32      49 ..      76      93 ..      70     106 .. 0.79
   2 ?   -2.2   0.0      0.91   4.1e+03      22      41 ..     305     324 ..     304     331 .. 0.79
   3 !   30.8   0.1   4.6e-11   2.1e-07      10      53 ..     382     424 ..     375     432 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.62
                             RMMBL 32 rnvilvHGeeeatsalar 49
                                      r ++  HG+ +++ a  +
  gi|298674297|ref|YP_003726047.1| 76 RAIVCTHGHLDHIGAIPK 93
                                      458999999998887655 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.91
                             RMMBL  22 llelirklkprnvilvHGee 41 
                                       l+++++k k +++ +v G++
  gi|298674297|ref|YP_003726047.1| 305 LKKIVNKGKDKYLPIVTGHQ 324
                                       78999999999987777765 PP

  == domain 3  score: 30.8 bits;  conditional E-value: 4.6e-11
                             RMMBL  10 eidfSgHadknellelirklkprnvilvHGeeeatsalarllke 53 
                                       ++++SgHa k+++ el+r ++p++vi+ HG  ++ s++ + + e
  gi|298674297|ref|YP_003726047.1| 382 DVHVSGHACKEDHWELLRIINPEHVIPAHGTINMHSSYIEMA-E 424
                                       789***************************999998887766.4 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   1.3   1.3e-10   5.7e-07      42      74 ..      72     104 ..      13     114 .. 0.72

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 1.3e-10
                                       GGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETC CS
                       Lactamase_B  42 pkdvdavilTHlHlDHiGglgglveatdvpvga 74 
                                          v+a++ TH+HlDHiG+ ++l++++ +p++ 
  gi|298674297|ref|YP_003726047.1|  72 NGTVRAIVCTHGHLDHIGAIPKLAHRYAAPIIS 104
                                       5689************************99986 PP

>> Nkap_C  NF-kappa-B-activating protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   8.6e-05      0.39      18      51 ..     399     432 ..     386     441 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.6e-05
                            Nkap_C  18 qyvqegkRiPrRGevGltseeiekfekaGyvmsG 51 
                                       + ++ ++ iP  G + ++s+ ie  e+aGyv+  
  gi|298674297|ref|YP_003726047.1| 399 RIINPEHVIPAHGTINMHSSYIEMAEDAGYVLGN 432
                                       56788899***********************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2763.91
//
Query:       gi|298674298|ref|YP_003726048.1|  [L=886]
Description: pyruvate, phosphate dikinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-90  303.5   0.0    2.6e-90  302.5   0.0    1.5  2  PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
      4e-64  217.0   0.9    5.6e-47  160.6   0.0    3.2  2  PPDK_N           Pyruvate phosphate dikinase, PEP/pyruvate bi
    2.6e-28   97.5   0.7      7e-28   96.2   0.7    1.8  1  PEP-utilizers    PEP-utilising enzyme, mobile domain
     0.0039   15.5   2.1     0.0059   14.9   2.1    1.1  1  FPP              Filament-like plant protein, long coiled-coi
  ------ inclusion threshold ------
       0.07   13.4   1.0         16    5.8   0.1    3.0  2  WXG100           Proteins of 100 residues with WXG
       0.81    9.9   3.1        2.4    8.4   0.1    2.9  2  PEP-utilisers_N  PEP-utilising enzyme, N-terminal
        5.1    7.4   8.2        7.3    6.9   0.1    3.9  3  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
        5.7    7.4   5.7         32    5.0   0.1    3.5  3  Syntaxin_2       Syntaxin-like protein


Domain annotation for each model (and alignments):
>> PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.1       2.8   6.3e+03     112     146 ..     326     359 ..     325     376 .. 0.68
   2 !  302.5   0.0   1.2e-93   2.6e-90       4     292 ..     520     878 ..     517     880 .. 0.96

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 2.8
                                       HHHHCCSHHHHHHHHHHHHHHCCCCEEEEEESSXX CS
                   PEP-utilizers_C 112 irlglsepelfetqlrAllrasaagkleimlPmva 146
                                       i +++++ +l+  q r  +r +a + l++ + mv 
  gi|298674298|ref|YP_003726048.1| 326 IEFTIEKGKLYMLQTRNAKRTAA-AALKVAVDMVY 359
                                       56788899999999999888765.45666666664 PP

  == domain 2  score: 302.5 bits;  conditional E-value: 1.2e-93
                                       STSCCCCCCCHCCCXBCEEEEEESSCHHHHHHHHCTXSSEEEEEHHHHCTTSCCHHHHHH................. CS
                   PEP-utilizers_C   4 sgklktllavtkdgkkikvlaNidtpedaekalengaeGiGLlRtEflfmareelpteee................. 63 
                                       sg+l+t+l+++++++ ++v  N+dtpeda+ a+++gaeGiGL+RtE++f+  e++p ++e                 
  gi|298674298|ref|YP_003726048.1| 520 SGELETMLQWADEIRSLNVRTNADTPEDAKLARDFGAEGIGLCRTEHMFFGEERIPVVREmimadnkedrekalqkl 596
                                       678999*********************************************************************** PP

                                       ...HHHHHHHHHHHTTTSEEEEEXXXSSCCGGSGGC.............................HHHH.XSXGGGS CS
                   PEP-utilizers_C  64 ...qaeaykkvleamngrpvvvRtlDiggdkelpel.............................keepeevNPmlG 108
                                          q++++  +++am+g p+++R+lD++ +++lp+                              +++++e+NPmlG
  gi|298674298|ref|YP_003726048.1| 597 qpmQKDDFLDIFRAMDGYPITIRLLDPPLHEFLPNYedliekikkleseggkqeeikrvndllrnVDTLKETNPMLG 673
                                       ***********************************99****************************9*********** PP

                                       SXTHHHHCCSHHHHHHHHHHHHHHCCCC.......EEEEEESSXXSHHHHHHHHHHHHHHHHHHHHCTCTXXTTXEE CS
                   PEP-utilizers_C 109 fRgirlglsepelfetqlrAllrasaag.......kleimlPmvasveeleeakkiieevkeelekegvkkkkkvkv 178
                                       +Rg+rlg+++pe++e+q++A+++a+ +          eim+P+v++ +el+  kk +  ++e + +e  +++ ++ +
  gi|298674298|ref|YP_003726048.1| 674 HRGCRLGITYPEIYEMQIKAIIEAACELssegtnvIPEIMIPLVSNEKELDFVKKTVTDTAESVMNE-KGTNIDYLC 749
                                       ************************9955567777789****************************99.99******* PP

                                       EEEEXSHHHHHTHHHHCTTSSEEEEXHHHHHHHHHTXXCCCHC...HHHH......SXTTTCHHCCCHHHHHHHHHH CS
                   PEP-utilizers_C 179 GiMiEvpsaalladklakevdFfSiGtNDLtQytlavdRdnee...vakl......ydplepavlrlikevikaaee 246
                                       G+MiE p+aal+adk+ak ++FfS+GtNDLtQ t++++Rd++    + ++       dp+ ++++++++e++k+   
  gi|298674298|ref|YP_003726048.1| 750 GTMIELPRAALTADKIAKGAEFFSFGTNDLTQTTFGYSRDDAGkflPLYIdkgileSDPFAVLDQEGVGELMKIGID 826
                                       ******************************************98875555778999********************* PP

                                       CC......XEEEEESCCCCSCCCHHHHHHCTXSEEEEXGGGHHHHHHHHHCT CS
                   PEP-utilizers_C 247 kg......lkvgiCGelagdpsavellvglGldelSmsaasvpaaraalaqv 292
                                       kg      +k+giCGe++gdp+++++  ++Gl+++S+s+++vp+ar a aq+
  gi|298674298|ref|YP_003726048.1| 827 KGrssrpdIKMGICGEHGGDPESISFSYEAGLNYVSCSPYRVPIARLASAQA 878
                                       **99***9**************************************998886 PP

>> PPDK_N  Pyruvate phosphate dikinase, PEP/pyruvate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.6   0.0   2.5e-50   5.6e-47       2     226 ..      23     301 ..      22     307 .. 0.96
   2 !   46.5   0.5   1.3e-15   2.8e-12     271     325 ..     307     359 ..     302     362 .. 0.92

  Alignments for each domain:
  == domain 1  score: 160.6 bits;  conditional E-value: 2.5e-50
                            PPDK_N   2 elvGGKganLaellneagipvPpgfaitadafrefleengleekideelkeldvddvdelrkaskeirelilsaelP 78 
                                        l+GGKganLae+ +++g+pvPpgf+i+++a+  ++++n    +  e +                            
  gi|298674298|ref|YP_003726048.1|  23 HLLGGKGANLAEM-ANLGVPVPPGFTISTEACVLYMKNN----DYPEGMW--------------------------- 67 
                                       689**********.77*********************99....3333333........................... PP

                            PPDK_N  79 eeleeaikeayeelgkkfgde..elpvaVRSSataEDlpkasfaGqqdtyLnvggeeevle................ 137
                                       +e++++i ++++++gkkfgd   +l+ +VRS+      +  s++G++dt+Ln+g ++e+++                
  gi|298674298|ref|YP_003726048.1|  68 DEIDKNIDKLEKSTGKKFGDPenPLLSSVRSG------APISMPGMMDTVLNLGLNDETVRglakrtdnewfaydsy 138
                                       3899****************9888999*****......99************************************* PP

                            PPDK_N 138 ........................................................................aikav 142
                                                                                                               ai+av
  gi|298674298|ref|YP_003726048.1| 139 rrfimmfsdvvlgidtnefenliqqkkdelgvtedteldtntmkdlveefksvykektgsdfpqeikqqlkmAINAV 215
                                       ***************************************************************************** PP

                            PPDK_N 143 faSlfnerAilYrkekgldheevalavvvqkmvnsdlg...asGVafsldpetG...fkdevlinasyGlGeaVVaG 213
                                       f+S++nerA  Yr+ ++++ +e+++av+vq+mv++++g    +GVaf+++p+tG   f +e+l na   +Ge+VVaG
  gi|298674298|ref|YP_003726048.1| 216 FNSWNNERAKKYRQLNDIS-DELGTAVNVQAMVFGNMGetsGTGVAFTRNPATGekeFYGEYLTNA---QGEDVVAG 288
                                       *******************.*******************999************************...******** PP

                            PPDK_N 214 rvtpdefvvekst 226
                                       ++tp ++   k++
  gi|298674298|ref|YP_003726048.1| 289 IRTPKSIQALKEN 301
                                       *****99887766 PP

  == domain 2  score: 46.5 bits;  conditional E-value: 1.3e-15
                            PPDK_N 271 eeLaeiakkiekhygtpmdiEfaideeegklyllQaRpetrtsekkekkaaetle 325
                                       ++L++i++k+e+hy++++diEf+i+  +gkly+lQ+R+ +rt +++ k a ++  
  gi|298674298|ref|YP_003726048.1| 307 KQLDDITQKLEQHYKDMQDIEFTIE--KGKLYMLQTRNAKRTAAAALKVAVDMVY 359
                                       89***********************..****************999988888765 PP

>> PEP-utilizers  PEP-utilising enzyme, mobile domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.2   0.7   3.1e-31     7e-28       3      73 .]     423     505 ..     421     505 .. 0.98

  Alignments for each domain:
  == domain 1  score: 96.2 bits;  conditional E-value: 3.1e-31
                                       -S-EEEEES---HHHHTTS-GEEEEEES--TTHHHHHHHHHHTT--EEE--SSHH.............HH--TEEEE CS
                     PEP-utilizers   3 eegvILvaeetspsdiagldkaaGivterGGmtSHaAivArelgiPaVvgvgeati............elkegdlit 67 
                                       +e+vILv++etsp+di g+++a+G++t rGGmtSHaA+vAr++g+P+V+g+++++i            +++eg+ i+
  gi|298674298|ref|YP_003726048.1| 423 NEDVILVRTETSPEDIGGMHAAKGVLTVRGGMTSHAAVVARGMGKPCVCGCDGISIdmnkgvftakgySINEGECIS 499
                                       578************************************************************************** PP

                                       EETTTT CS
                     PEP-utilizers  68 vDgstG 73 
                                       +Dgs+G
  gi|298674298|ref|YP_003726048.1| 500 IDGSEG 505
                                       ****99 PP

>> FPP  Filament-like plant protein, long coiled-coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   2.1   2.7e-06    0.0059     560     767 ..     159     366 ..     140     378 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.7e-06
                               FPP 560 elveslskealklqdkssksselsevleqFsavvndllsgkadledfvleLssvldeiselkfslldvssmeeeikk 636
                                       +l+++ + e   ++d++ +++++++ +e+F +v++     +++ +df +e+ + l+ +++  f+  +++  ++  + 
  gi|298674298|ref|YP_003726048.1| 159 NLIQQKKDELGVTEDTELDTNTMKDLVEEFKSVYK-----EKTGSDFPQEIKQQLKMAINAVFNSWNNERAKKYRQL 230
                                       44555555555566777788888888888877664.....567789******************9999999999999 PP

                               FPP 637 sddidkvalsenkvaqk....gessnecaeisklssekeipselplvsgsneskkeenkllkeeleelksekenlev 709
                                       +d  d++    n  a +    ge+s++ + + +     e+  ++   +++++++     ++ + ++ lk +  ++  
  gi|298674298|ref|YP_003726048.1| 231 NDISDELGTAVNVQAMVfgnmGETSGTGVAFTRNPATGEKEFYGEYLTNAQGEDVVAGIRTPKSIQALKENMPDVYK 307
                                       999999887777664446678899777777777777777777889999989999999999***************** PP

                               FPP 710 elksatenleslkaqlqesEqllaelkseLeslkeskslaetqlkcm.kesyesletra 767
                                       +l + t++le+    +q++E ++++ k+ + +++++k+ a   lk    ++ye+l  ++
  gi|298674298|ref|YP_003726048.1| 308 QLDDITQKLEQHYKDMQDIEFTIEKGKLYMLQTRNAKRTAAAALKVAvDMVYENLINKK 366
                                       ****************************************9999975156677775554 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.014        32      47      78 ..     210     241 ..     178     245 .. 0.86
   2 ?    5.8   0.1    0.0072        16      53      85 ..     295     327 ..     292     327 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.014
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  47 dafqaefeewkqaaqklvdaLeeisealkqaa 78 
                                        a +a+f+ w+++ +k +++L++is++l +a 
  gi|298674298|ref|YP_003726048.1| 210 MAINAVFNSWNNERAKKYRQLNDISDELGTAV 241
                                       57788889999999999999999999888775 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0072
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  53 feewkqaaqklvdaLeeisealkqaanafedaD 85 
                                       ++ +k+++ +++++L++i+++l+q  + ++d +
  gi|298674298|ref|YP_003726048.1| 295 IQALKENMPDVYKQLDDITQKLEQHYKDMQDIE 327
                                       577899999***************999999876 PP

>> PEP-utilisers_N  PEP-utilising enzyme, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.6      0.34   7.7e+02      84     114 ..     341     371 ..     276     373 .. 0.79
   2 ?    8.4   0.1    0.0011       2.4       2      16 ..     397     418 ..     396     444 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.34
                                       HHHT--HHHHHHHHHHHHHHHHHHTT-HHHH CS
                   PEP-utilisers_N  84 regglnaeaAveevveefaaqfealddeylr 114
                                       r+++ +a+aA++ +v+ + + + + +++++r
  gi|298674298|ref|YP_003726048.1| 341 RNAKRTAAAALKVAVDMVYENLINKKEAVMR 371
                                       4567789999999999888888777777766 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0011
                                       -EEEE-SEEEEEEE.......- CS
                   PEP-utilisers_N   2 GiaaspGiaiGkav.......e 16 
                                       G+aaspG a+Gk+v       e
  gi|298674298|ref|YP_003726048.1| 397 GLAASPGAAVGKVVfsaehaeE 418
                                       99************86543331 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.2     0.076   1.7e+02      52      89 ..     154     194 ..     149     219 .. 0.81
   2 ?    6.9   0.1    0.0033       7.3      61     102 ..     287     328 ..     277     331 .. 0.81
   3 ?   -0.6   0.5      0.67   1.5e+03      58      88 ..     638     667 ..     633     670 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.076
                                       HHHHHHHCCCCCCTT...S-TCCCCCCCHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  52 rNelskeIgkakkkk...edaeeliaevkelkeelkaleae 89 
                                        Ne  + I+++k++    ed+e   + +k+l ee+k + +e
  gi|298674298|ref|YP_003726048.1| 154 TNEFENLIQQKKDELgvtEDTELDTNTMKDLVEEFKSVYKE 194
                                       5999999*****99899999999999999999999876554 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0033
                                       CCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                      Seryl_tRNA_N  61 kakkkkedaeeliaevkelkeelkaleaelkeleaeleklll 102
                                         ++  + +++l++ + ++ ++l++++++l++  ++++++  
  gi|298674298|ref|YP_003726048.1| 287 AGIRTPKSIQALKENMPDVYKQLDDITQKLEQHYKDMQDIEF 328
                                       555666799***************************999865 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.67
                                       HCCCCCCTTS-TCCCCCCCHHHHHHHHHHHH CS
                      Seryl_tRNA_N  58 eIgkakkkkedaeeliaevkelkeelkalea 88 
                                       +I+k+  ++  ++e i++v++l  ++++l++
  gi|298674298|ref|YP_003726048.1| 638 KIKKLESEG-GKQEEIKRVNDLLRNVDTLKE 667
                                       677777777.788889999999888888877 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.3         1   2.3e+03      17      48 ..     163     194 ..     153     235 .. 0.67
   2 ?    5.0   0.1     0.014        32      21      66 ..     288     333 ..     279     355 .. 0.82
   3 ?    2.9   0.0     0.064   1.4e+02      29      63 ..     633     669 ..     626     675 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1
                        Syntaxin_2  17 klvkqLgtkkdteelreklhelieeinelikk 48 
                                       ++ + Lg   dte   + +++l+ee + + k+
  gi|298674298|ref|YP_003726048.1| 163 QKKDELGVTEDTELDTNTMKDLVEEFKSVYKE 194
                                       33333555555444444446666665555544 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.014
                        Syntaxin_2  21 qLgtkkdteelreklhelieeinelikktnellkklsqldnsssds 66 
                                        + t+k  + l+e++ ++ +++ ++ +k +++ k+++ ++ + ++ 
  gi|298674298|ref|YP_003726048.1| 288 GIRTPKSIQALKENMPDVYKQLDDITQKLEQHYKDMQDIEFTIEKG 333
                                       5889*********************************998776554 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.064
                        Syntaxin_2  29 eelreklhelieei..nelikktnellkklsqldnss 63 
                                       e+l ek+++l +e   +e ik++n+ll+++++l++++
  gi|298674298|ref|YP_003726048.1| 633 EDLIEKIKKLESEGgkQEEIKRVNDLLRNVDTLKETN 669
                                       56778888888887335679***********999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (886 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1003  (0.0559429); expected 358.6 (0.02)
Passed bias filter:                      675  (0.0376485); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.83u 0.34s 00:00:01.17 Elapsed: 00:00:00.51
# Mc/sec: 5250.13
//
Query:       gi|298674299|ref|YP_003726049.1|  [L=86]
Description: H/ACA RNA-protein complex component Gar1 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.2e-09   35.4   0.1    8.9e-09   35.3   0.1    1.1  1  Gar1      Gar1/Naf1 RNA binding region


Domain annotation for each model (and alignments):
>> Gar1  Gar1/Naf1 RNA binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.1     5e-13   8.9e-09      21      99 ..       2      85 ..       1      86 [] 0.80

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 5e-13
                                      EEEEEEEEEETT.EEEEEE---S--B-....-BTT-EEEETT--EEEE--EEES-SSS-EEEEE--GGHHHHHHHT..T CS
                              Gar1 21 leiGtvssiven.evviksttsgekkv....ldfnsilflenktqiGkVdEifGpvnepyysVklnsseeikaksf..k 92
                                      +++Gtvs+  ++ +++++ ++ ++++     +++ns++ ++  ++iG + +i+Gpv++py+ + ++   +++++++   
  gi|298674299|ref|YP_003726049.1|  2 KKLGTVSHLSKSrNLIVRMDKLKPSDAfkkaPKINSVVLNKSVKPIGEINDIIGPVSHPYVIINVS--RKVTDSELlnY 78
                                      689*****99886888888876554435556**********************************9..66665544225 PP

                                      TTSEEEE CS
                              Gar1 93 vgdkvyi 99
                                      v+++vyi
  gi|298674299|ref|YP_003726049.1| 79 VNERVYI 85
                                      6777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      201  (0.0112109); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 555.90
//
Query:       gi|298674300|ref|YP_003726050.1|  [L=341]
Description: transcription factor tFIIB cyclin-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-44  149.3   1.4    2.2e-21   75.7   0.3    2.3  2  TFIIB           Transcription factor TFIIB repeat
    2.1e-17   62.4   1.5    2.1e-17   62.4   1.5    1.9  2  TF_Zn_Ribbon    TFIIB zinc-binding
    9.7e-06   25.4   1.3    2.4e-05   24.2   1.3    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    6.8e-05   22.3   0.8      0.026   14.0   0.2    3.0  2  Sigma70_r4      Sigma-70, region 4
    0.00021   21.3   3.9     0.0053   16.8   2.3    2.7  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain
  ------ inclusion threshold ------
      0.015   15.1   0.8      0.051   13.4   0.2    2.3  2  HTH_AsnC-type   AsnC-type helix-turn-helix domain
      0.039   14.0   0.8      0.039   14.0   0.8    1.9  2  Elf1            Transcription elongation factor Elf1 like
      0.044   14.3   0.1        3.4    8.3   0.0    2.5  2  RPA_interact_C  Replication protein A interacting C-terminal
      0.079   13.0   0.0         14    5.8   0.0    2.4  2  Cyclin_C        Cyclin, C-terminal domain
      0.087   13.0   0.2        1.4    9.2   0.0    2.7  2  zf-RING_7       C4-type zinc ribbon domain
      0.092   12.4   0.4       0.36   10.5   0.0    2.1  2  zf-tcix         Putative treble-clef, zinc-finger, Zn-binding
      0.093   12.9   0.7      0.093   12.9   0.7    3.1  3  Zn-ribbon_8     Zinc ribbon domain
       0.13   11.8   3.3        1.3    8.5   3.3    2.3  1  zf-ribbon_3     zinc-ribbon domain
       0.13   12.3   1.5        1.3    9.0   1.1    2.4  2  HypA            Hydrogenase/urease nickel incorporation, meta
       0.24   11.1   2.3         11    5.8   2.5    2.5  2  A2L_zn_ribbon   A2L zinc ribbon domain
       0.25   11.7   4.1        7.8    6.9   0.1    3.3  3  HTH_31          Helix-turn-helix domain
       0.25   11.5   2.3        2.5    8.3   1.0    2.3  2  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
        0.4   11.0   4.6       0.17   12.1   1.9    1.7  1  IBR             IBR domain, a half RING-finger domain
        1.9    8.5   4.1        2.1    8.4   0.5    2.9  2  Nudix_N_2       Nudix N-terminal


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.7   0.3   2.4e-24   2.2e-21       2      71 .]     161     230 ..     160     230 .. 0.98
   2 !   72.7   0.0     2e-23   1.9e-20       1      71 []     254     324 ..     254     324 .. 0.99

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 2.4e-24
                                       HHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   2 krfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                        r+a+al+Lp +V++ A  ++++a++++++ Grs +g+aAA+ly Acr++ v rt+ ei +v++Vs k+i
  gi|298674300|ref|YP_003726050.1| 161 DRMASALGLPRTVRETAAVVYRKAVDKNLIRGRSIEGVAAAALYAACRQCSVPRTLDEIGEVSRVSRKEI 230
                                       69*****************************************************************997 PP

  == domain 2  score: 72.7 bits;  conditional E-value: 2e-23
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       ++rf++ l+L+ +V+++ +e++++a+e+++++Gr p+g+aAA++yiA+ +++++rtq+e+++v+ V+e+ti
  gi|298674300|ref|YP_003726050.1| 254 VPRFCSGLKLKGEVQSKGVEILRQASEKELTSGRGPTGVAAAAIYIASILCGERRTQREVADVAGVTEVTI 324
                                       689******************************************************************98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.4   1.5   2.2e-20   2.1e-17       2      43 .]      44      85 ..      43      85 .. 0.98
   2 ?   -3.6   0.1       8.6   8.1e+03       3      10 ..     207     214 ..     206     218 .. 0.70

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 2.2e-20
                                      EETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                                      kCP+Cgs nl+ D+er+elvC+dCGlV++ + +degpewr+f
  gi|298674300|ref|YP_003726050.1| 44 KCPECGSINLEQDYERAELVCSDCGLVVDAELVDEGPEWRAF 85
                                      9***************************************98 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 8.6
                                       ETTTTCEE CS
                      TF_Zn_Ribbon   3 CPnCgstn 10 
                                       C  C+ ++
  gi|298674300|ref|YP_003726050.1| 207 CRQCSVPR 214
                                       89998875 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   1.3   2.6e-08   2.4e-05       7      60 ..      21      75 ..      16      76 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2.6e-08
                    OrfB_Zn_ribbon  7 qleykakeyGikveevnpayTS.ktCseCgsknke.alsgrtfkCpnCgfeadrDv 60
                                      +++   ke+ ++ e+ ++  +S ++C+eCgs+n e + ++ +++C++Cg++ d+ +
  gi|298674300|ref|YP_003726050.1| 21 MIKA-RKEKEKEKEKSSETESSvTKCPECGSINLEqDYERAELVCSDCGLVVDAEL 75
                                      4444.35677888888899977257********99999***************976 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.013        12      20      36 ..     213     229 ..     208     241 .. 0.90
   2 !   14.0   0.2   2.8e-05     0.026      18      43 ..     305     330 ..     296     335 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.013
                                       T--HHHHHHHHTS-HHH CS
                        Sigma70_r4  20 glTleEIgerlgiSrer 36 
                                       ++Tl EIge+  +Sr  
  gi|298674300|ref|YP_003726050.1| 213 PRTLDEIGEVSRVSRKE 229
                                       79*********999965 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 2.8e-05
                                       TTT--HHHHHHHHTS-HHHHHHHHHH CS
                        Sigma70_r4  18 geglTleEIgerlgiSrerVrqiekr 43 
                                       ge +T+ E++++ g+++ ++r + k+
  gi|298674300|ref|YP_003726050.1| 305 GERRTQREVADVAGVTEVTIRNRYKE 330
                                       7899******************9986 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   2.3   5.6e-06    0.0053       2      26 .]      43      67 ..      43      67 .. 0.96
   2 ?    3.2   0.0     0.099        94       9      20 ..     178     189 ..     177     189 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.6e-06
                            zf-ACC  2 tKCpsCgemlykkeLernlyVCPkC 26
                                      tKCp+Cg++ + ++ er   VC  C
  gi|298674300|ref|YP_003726050.1| 43 TKCPECGSINLEQDYERAELVCSDC 67
                                      8****************99999988 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.099
                            zf-ACC   9 emlykkeLernl 20 
                                       +++y+k +++nl
  gi|298674300|ref|YP_003726050.1| 178 AVVYRKAVDKNL 189
                                       79*********7 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       3.6   3.4e+03      19      36 ..     215     232 ..     212     235 .. 0.63
   2 ?   13.4   0.2   5.4e-05     0.051      17      41 ..     307     331 ..     305     332 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3.6
                     HTH_AsnC-type  19 syaeLAervGlSestvlr 36 
                                       +  e++e   +S+ ++ r
  gi|298674300|ref|YP_003726050.1| 215 TLDEIGEVSRVSRKEIGR 232
                                       556777766666666655 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 5.4e-05
                     HTH_AsnC-type  17 RisyaeLAervGlSestvlrRvrrL 41 
                                       R++ +e+A+  G++e t+++R++ L
  gi|298674300|ref|YP_003726050.1| 307 RRTQREVADVAGVTEVTIRNRYKEL 331
                                       99********************988 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.8   4.1e-05     0.039       3      56 ..      25      72 ..      23      79 .. 0.82
   2 ?   -2.4   0.1       5.6   5.2e+03      46      53 ..     205     212 ..     200     219 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.1e-05
                              Elf1  3 RkkkakkrkkkkkkklptkFdCpfCnheksvevkldkkekiaevsCkvCgesfe 56
                                      Rk+k+k +k+k++++ +++ +Cp C++      +l++  ++ae+ C+ Cg+ ++
  gi|298674300|ref|YP_003726050.1| 25 RKEKEK-EKEKSSETESSVTKCPECGSI-----NLEQDYERAELVCSDCGLVVD 72
                                      676775.5777777789999******87.....999*************98665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.6
                              Elf1  46 vsCkvCge 53 
                                       + C++C+ 
  gi|298674300|ref|YP_003726050.1| 205 AACRQCSV 212
                                       67888875 PP

>> RPA_interact_C  Replication protein A interacting C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0036       3.4       2      27 ..      45      73 ..      44     121 .. 0.83
   2 ?    3.5   0.0      0.11     1e+02      65      78 ..     199     212 ..     184     215 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0036
                    RPA_interact_C  2 CPvCkkrklkets..evifCe.Cglrlet 27
                                      CP C + +l+++     ++C+ Cgl ++ 
  gi|298674300|ref|YP_003726050.1| 45 CPECGSINLEQDYerAELVCSdCGLVVDA 73
                                      **********9653477***99**98876 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.11
                    RPA_interact_C  65 gveaLlaeCeeCdf 78 
                                         +aL+a C++C++
  gi|298674300|ref|YP_003726050.1| 199 AAAALYAACRQCSV 212
                                       5689********97 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.039        37      47      87 ..     198     238 ..     195     248 .. 0.86
   2 ?    5.8   0.0     0.015        14      47      88 ..     292     333 ..     288     337 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.039
                                       HHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHH CS
                          Cyclin_C  47 iAaaalllarstlnspewtetlehytgyskedlkpcvelil 87 
                                       +Aaaal++a+++ + p   +++ +++++s +++   ++ i 
  gi|298674300|ref|YP_003726050.1| 198 VAAAALYAACRQCSVPRTLDEIGEVSRVSRKEIGRTYRFIS 238
                                       7***********99999999999999999988888777775 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.015
                                       HHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHH CS
                          Cyclin_C  47 iAaaalllarstlnspewtetlehytgyskedlkpcvelile 88 
                                       +Aaaa+++a+   ++   ++++  + g+++  +++ ++ + e
  gi|298674300|ref|YP_003726050.1| 292 VAAAAIYIASILCGERRTQREVADVAGVTEVTIRNRYKELSE 333
                                       8***********9********************999998876 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0015       1.4      22      32 ..      37      51 ..      15      51 .. 0.73
   2 ?    0.8   0.0      0.61   5.8e+02       1      15 [.      63      77 ..      63      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0015
                                      B....-EE-TTT--E CS
                         zf-RING_7 22 e....vvtCpeCGRI 32
                                      e    v +CpeCG I
  gi|298674300|ref|YP_003726050.1| 37 EtessVTKCPECGSI 51
                                      0445599******88 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.61
                                      EETTT--B--CCHHH CS
                         zf-RING_7  1 tCgGChmelppqvls 15
                                      +C+ C+++++ +++ 
  gi|298674300|ref|YP_003726050.1| 63 VCSDCGLVVDAELVD 77
                                      6999*****999875 PP

>> zf-tcix  Putative treble-clef, zinc-finger, Zn-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00039      0.36       9      20 ..      41      52 ..      35      54 .. 0.84
   2 ?   -1.9   0.1       2.8   2.6e+03      13      17 ..      64      68 ..      63      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00039
                           zf-tcix  9 GvrkCpkCGtyN 20
                                       v kCp+CG +N
  gi|298674300|ref|YP_003726050.1| 41 SVTKCPECGSIN 52
                                      588*******99 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.8
                           zf-tcix 13 CpkCG 17
                                      C+ CG
  gi|298674300|ref|YP_003726050.1| 64 CSDCG 68
                                      ****9 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.7   9.8e-05     0.093      16      38 ..      31      55 ..      25      57 .. 0.71
   2 ?    2.1   0.1      0.22   2.1e+02       5      16 ..      61      72 ..      56      81 .. 0.69
   3 ?   -1.8   0.1       3.8   3.6e+03      28      32 ..     205     210 ..     196     215 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.8e-05
                       Zn-ribbon_8 16 evlqsis.dapltaCPeCgs.evrr 38
                                      e+  s+  +++ t+CPeCgs ++++
  gi|298674300|ref|YP_003726050.1| 31 EKEKSSEtESSVTKCPECGSiNLEQ 55
                                      55565665566667******99986 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.22
                       Zn-ribbon_8  5 eYrCeeCghefe 16
                                      e  C +Cg + +
  gi|298674300|ref|YP_003726050.1| 61 ELVCSDCGLVVD 72
                                      345888876655 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 3.8
                       Zn-ribbon_8  28 a.CPeC 32 
                                       a C +C
  gi|298674300|ref|YP_003726050.1| 205 AaCRQC 210
                                       447777 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   3.3    0.0014       1.3       3      24 ..      43      69 ..      41      71 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0014
                       zf-ribbon_3  3 vrCPnCGa.plssd....dnvCpyCGt 24
                                      ++CP+CG+ +l+ d      vC  CG 
  gi|298674300|ref|YP_003726050.1| 43 TKCPECGSiNLEQDyeraELVCSDCGL 69
                                      78******8898774444567777775 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.1    0.0014       1.3      58      94 ..      30      69 ..      11      81 .. 0.68
   2 ?    0.6   0.0      0.59   5.6e+02      47      78 ..     180     212 ..     148     243 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0014
                                      TT-EEEEEEE--EEEETTTS-EEECHH..H..HHS-TTTSS CS
                              HypA 58 egaeLeieevpvkvrCreCgkefelee..k..alrCpkCgs 94
                                      +++e + e+++ +++C eCg+  +le+  +  +l C +Cg 
  gi|298674300|ref|YP_003726050.1| 30 KEKEKSSETESSVTKCPECGSI-NLEQdyEraELVCSDCGL 69
                                      4455667888999999999954.433323246779999985 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.59
                                       HHHHHHCC.TTTT-EEE.EEEE--EEEETTTS- CS
                              HypA  47 afellaegtvlegaeLe.ieevpvkvrCreCgk 78 
                                       +++ + ++++++g ++e +    + + Cr+C+ 
  gi|298674300|ref|YP_003726050.1| 180 VYRKAVDKNLIRGRSIEgVAAAALYAACRQCSV 212
                                       555555555566655554556667777888864 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.2     0.057        54      24      30 ..      45      51 ..      38      53 .. 0.82
   2 ?    5.8   2.5     0.012        11       6      30 ..      45      70 ..      44      71 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.057
                     A2L_zn_ribbon 24 CieCgas 30
                                      C+eCg++
  gi|298674300|ref|YP_003726050.1| 45 CPECGSI 51
                                      *****97 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.012
                     A2L_zn_ribbon  6 CsvCggngiln.seqgylvCieCgas 30
                                      C  Cg+ ++ +  e+++lvC +Cg++
  gi|298674300|ref|YP_003726050.1| 45 CPECGSINLEQdYERAELVCSDCGLV 70
                                      555555555555688999*****986 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.049        46      44      62 ..     157     175 ..     135     178 .. 0.82
   2 ?   -0.6   0.1       1.9   1.8e+03      16      33 ..     215     232 ..     191     236 .. 0.76
   3 ?    6.9   0.1    0.0083       7.8      14      32 ..     307     325 ..     273     326 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.049
                            HTH_31  44 pavlealaralgldpaera 62 
                                       ++ l+++a algl++  r+
  gi|298674300|ref|YP_003726050.1| 157 LSELDRMASALGLPRTVRE 175
                                       5799**********88776 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.9
                            HTH_31  16 sqeevAerlgvsestlsr 33 
                                       +++e +e ++vs+  ++r
  gi|298674300|ref|YP_003726050.1| 215 TLDEIGEVSRVSRKEIGR 232
                                       667777777788777766 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0083
                            HTH_31  14 GLsqeevAerlgvsestls 32 
                                       + +q+evA+ +gv+e t++
  gi|298674300|ref|YP_003726050.1| 307 RRTQREVADVAGVTEVTIR 325
                                       78************99986 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   1.0    0.0027       2.5      17      40 .]      44      68 ..      42      68 .. 0.89
   2 ?    1.9   0.0      0.26   2.5e+02      16      25 ..     205     214 ..     201     223 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0027
                     Auto_anti-p27 17 tCpvCgvPLmrdr.kggkvyCvaCd 40
                                       Cp+Cg++ +++  ++ +++C  C+
  gi|298674300|ref|YP_003726050.1| 44 KCPECGSINLEQDyERAELVCSDCG 68
                                      6********99988899*****996 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.26
                     Auto_anti-p27  16 etCpvCgvPL 25 
                                       + C +C+vP 
  gi|298674300|ref|YP_003726050.1| 205 AACRQCSVPR 214
                                       46*******7 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.9   0.00018      0.17       5      45 ..      29      68 ..      24      70 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00018
                               IBR  5 klklkkslesdpnlkwCprpdCeaiiekseg.cksvtCskCg 45
                                      ++ ++ks e+++++++Cp  +C++i  +++   +++ Cs+Cg
  gi|298674300|ref|YP_003726050.1| 29 EKEKEKSSETESSVTKCP--ECGSINLEQDYeRAELVCSDCG 68
                                      4555666788999*****..***98866666666788****7 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.5    0.0022       2.1       3      31 ..      45      70 ..      45      72 .. 0.84
   2 ?   -1.6   0.2       2.9   2.8e+03       3       7 ..     207     211 ..     206     216 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0022
                                      -TTT--B-EEE--TT-SS-EEEETTTTEE CS
                         Nudix_N_2  3 CsqCGtpvelripdgDnreRlvCpaCgti 31
                                      C++CG+     ++++ +r  lvC++Cg +
  gi|298674300|ref|YP_003726050.1| 45 CPECGSI---NLEQDYERAELVCSDCGLV 70
                                      9999986...6666679999*******87 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.9
                                       -TTT- CS
                         Nudix_N_2   3 CsqCG 7  
                                       C+qC 
  gi|298674300|ref|YP_003726050.1| 207 CRQCS 211
                                       77875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1447  (0.0807072); expected 358.6 (0.02)
Passed bias filter:                      814  (0.0454013); expected 358.6 (0.02)
Passed Vit filter:                       116  (0.00646996); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2417.76
//
Query:       gi|298674301|ref|YP_003726051.1|  [L=205]
Description: lysine exporter protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-33  114.1  14.4    6.7e-33  113.8  14.4    1.1  1  LysE             LysE type translocator
  ------ inclusion threshold ------
       0.11   12.0   0.0        1.6    8.3   0.1    2.1  2  MaoC_dehydratas  MaoC like domain
       0.13   12.3   0.1       0.13   12.3   0.1    3.4  4  DUF3185          Protein of unknown function (DUF3185)
       0.87    9.6   5.9        4.4    7.3   1.1    2.2  2  CRPA             Chlamydia 15 kDa cysteine-rich outer membran
        3.5    6.9   7.4        1.4    8.2   0.9    2.2  2  TMEM43           Transmembrane protein 43


Domain annotation for each model (and alignments):
>> LysE  LysE type translocator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.8  14.4   1.9e-36   6.7e-33       2     191 ..      17     202 ..      16     203 .. 0.98

  Alignments for each domain:
  == domain 1  score: 113.8 bits;  conditional E-value: 1.9e-36
                              LysE   2 slllspGpqnllvlkqgikrgfkggilvalgvligdavlillgllGlalLlkaapivlsilrllGgayLlwlgvlal 78 
                                       ++++ pGp ++++++++ k+g+ +g  v+lg+++ + v  ll+++G++ +++    ++si++++Gg+ L+ +g+ ++
  gi|298674301|ref|YP_003726051.1|  17 TGAVVPGPMLFATIETSFKKGWSAGPEVVLGHALIESVITLLIIFGISSFIN--DDIFSIISVVGGIALVVFGIFTV 91 
                                       5799************************************************..9********************** PP

                              LysE  79 rdakekkveaeksveaslvkpflkglllslsNPkailfwlsvisallakaeqygdagrlilaaglvvasliwfslla 155
                                       ++ ++ + + ++s e  l +p+ +g+++s sNP++ ++w+  +sal+ ++++ g ++ +++ ag+++a+l w+s ++
  gi|298674301|ref|YP_003726051.1|  92 KSPVNDQYSCSNSYE-MLTSPIVSGVVTSASNPYFWMWWFTAGSALVLRGYEIGLIAAVFFIAGHWIADLGWYSAVS 167
                                       ********9999998.********************************99*************************** PP

                              LysE 156 flaarlsrrlsskkvlriinvvvgvlligfavklll 191
                                       ++++r  + +ss  +  ++++++gv+li+f++ +++
  gi|298674301|ref|YP_003726051.1| 168 LSFSRGKKLISSGMHN-WMMKICGVFLILFGLWFVI 202
                                       *************877.**************99986 PP

>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.069   2.5e+02      83     109 ..      14      40 ..      10      53 .. 0.77
   2 ?    8.3   0.1   0.00045       1.6      47      90 ..     107     150 ..     102     151 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.069
                                       EEE-S--BTTCEEEEEEEEEEEEEEEE CS
                   MaoC_dehydratas  83 vrFtkpVlpgdtlkvelevvgkrdvrk 109
                                       v Ft+ V pg  l +++e + k+ +  
  gi|298674301|ref|YP_003726051.1|  14 VGFTGAVVPGPMLFATIETSFKKGWSA 40 
                                       679999999999999999887777765 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00045
                                       TTSSSB--HHHHHHHHHHHHHHHHSTTEGGGEEEEEEEE-S--B CS
                   MaoC_dehydratas  47 gfggpIahGmltlaivaklveeelgdnvvarvgeikvrFtkpVl 90 
                                        +  pI++G +t+a     ++++++ + +  ++++++  ++ V+
  gi|298674301|ref|YP_003726051.1| 107 MLTSPIVSGVVTSASNPYFWMWWFTAGSALVLRGYEIGLIAAVF 150
                                       6789**********************988888888777766665 PP

>> DUF3185  Protein of unknown function (DUF3185)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       2.4   8.8e+03      14      19 ..      58      63 ..      55      66 .. 0.52
   2 ?   12.3   0.1   3.6e-05      0.13       2      27 ..      71      96 ..      71     110 .. 0.87
   3 ?   -2.4   0.0       1.4     5e+03      45      52 ..     130     137 ..     111     142 .. 0.55
   4 ?    1.1   1.9      0.11   3.9e+02      40      56 ..     182     198 ..     144     201 .. 0.64

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.4
                           DUF3185 14 LlvfGy 19
                                      L++fG+
  gi|298674301|ref|YP_003726051.1| 58 LIIFGI 63
                                      344443 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 3.6e-05
                           DUF3185  2 iiGiiLlvaGivLlvfGynasdSlgs 27
                                      i++ii +v+Gi+L+vfG+   +S ++
  gi|298674301|ref|YP_003726051.1| 71 IFSIISVVGGIALVVFGIFTVKSPVN 96
                                      6899999**********988877665 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.4
                           DUF3185  45 ligGgvaa 52 
                                       + +G +++
  gi|298674301|ref|YP_003726051.1| 130 FTAGSALV 137
                                       44444443 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.11
                           DUF3185  40 ktlllligGgvaaivGl 56 
                                         +++ i G+ ++++Gl
  gi|298674301|ref|YP_003726051.1| 182 HNWMMKICGVFLILFGL 198
                                       45666677777777776 PP

>> CRPA  Chlamydia 15 kDa cysteine-rich outer membrane protein (CRPA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   1.1    0.0012       4.4      69     119 ..      44      94 ..      41     120 .. 0.81
   2 ?    4.7   0.3     0.008        29      42      81 ..     160     199 ..     155     203 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0012
                              CRPA  69 vvlGilLviaglallfilqaqlganafylliPaviGlvkllvtslsmekaC 119
                                       vvlG  L+   ++ll i+  +++ n   + i +v+G + l+v  ++  k+ 
  gi|298674301|ref|YP_003726051.1|  44 VVLGHALIESVITLLIIFGISSFINDDIFSIISVVGGIALVVFGIFTVKSP 94 
                                       799999999999999999999999999999999999999988766654444 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.008
                              CRPA  42 lgwakikiidpireskllqsrafkitlvvlGilLviagla 81 
                                       lgw  +  +   r  kl++s   +  + + G++L++ gl 
  gi|298674301|ref|YP_003726051.1| 160 LGWYSAVSLSFSRGKKLISSGMHNWMMKICGVFLILFGLW 199
                                       7999999999999**********************99874 PP

>> TMEM43  Transmembrane protein 43
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.8     0.024        88     187     222 ..      74     109 ..      46     132 .. 0.75
   2 ?    8.2   0.9   0.00039       1.4     178     205 ..     175     202 ..     163     204 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.024
                            TMEM43 187 wllRllGfllmflglllllsplsvlvslipllgelv 222
                                        +  ++G+ l+++g++++ sp++  +s+    + l+
  gi|298674301|ref|YP_003726051.1|  74 IISVVGGIALVVFGIFTVKSPVNDQYSCSNSYEMLT 109
                                       455578999999999999999988888776644444 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00039
                            TMEM43 178 eksenklltwllRllGfllmflglllll 205
                                       +  ++ +++w+++++G++l+++gl++++
  gi|298674301|ref|YP_003726051.1| 175 KLISSGMHNWMMKICGVFLILFGLWFVI 202
                                       5667789*****************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       854  (0.0476323); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1302.33
//
Query:       gi|298674302|ref|YP_003726052.1|  [L=341]
Description: hypothetical protein Metev_0330 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-62  209.3   1.0    6.2e-62  208.9   1.0    1.1  1  Met_10           Met-10+ like-protein
    7.3e-17   61.0   0.0    1.7e-16   59.8   0.0    1.6  1  Trm5_N           tRNA methyltransferase 5 N-terminal domain
    4.2e-08   32.9   0.1    9.8e-08   31.7   0.0    1.6  2  MTS              Methyltransferase small domain
    1.6e-07   31.0   0.4    3.4e-07   30.0   0.4    1.4  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    2.6e-07   31.2   0.0    7.7e-07   29.7   0.0    1.8  2  Methyltransf_25  Methyltransferase domain
    6.2e-07   29.3   0.0      9e-07   28.8   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    3.4e-06   26.5   0.1    4.4e-06   26.1   0.1    1.2  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
    3.4e-05   23.5   0.0    6.5e-05   22.6   0.0    1.5  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    9.1e-05   22.2   0.1    0.00023   20.8   0.0    1.8  1  Cons_hypoth95    Conserved hypothetical protein 95
     0.0001   22.0   0.0     0.0029   17.3   0.0    2.7  3  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
     0.0017   19.0   0.0     0.0042   17.7   0.0    1.7  1  Methyltransf_11  Methyltransferase domain
       0.01   14.9   0.0      0.015   14.3   0.0    1.2  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
  ------ inclusion threshold ------
      0.013   14.9   0.1      0.068   12.6   0.1    2.2  3  Methyltransf_4   Putative methyltransferase
      0.022   14.7   0.0      0.041   13.8   0.0    1.4  1  Methyltransf_18  Methyltransferase domain
      0.027   13.8   0.0      0.044   13.1   0.0    1.3  1  GidB             rRNA small subunit methyltransferase G
      0.033   14.9   0.0      0.071   13.9   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
       0.11   12.3   0.0       0.19   11.6   0.0    1.4  1  PRMT5            PRMT5 arginine-N-methyltransferase


Domain annotation for each model (and alignments):
>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.9   1.0   5.9e-65   6.2e-62       2     199 .]      91     288 ..      90     288 .. 0.98

  Alignments for each domain:
  == domain 1  score: 208.9 bits;  conditional E-value: 5.9e-65
                                       EEEEETTEEEEEB-TTSSHHHHHHHHHHHHHS.S-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEE CS
                            Met_10   2 kfeiiGdvvilnlreelkeykkvigevildkt.kvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklD 77 
                                       ++ei+Gd++i++ ++e +   ++i+++i+  + ++ktv+  +  + ge+R+++++v+aG+d+tetihkE+gcr+ +D
  gi|298674302|ref|YP_003726052.1|  91 HYEIVGDIAIVDEDDESEA--RKIADAIIRLHpNIKTVVGTTAPIGGEYRVRNVKVIAGEDRTETIHKEHGCRYVVD 165
                                       59*********99998887..99****************************************************** PP

                                       TTTS---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEE CS
                            Met_10  78 vskvyfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvk 154
                                       +++ yf ++l++Erer+ +l++  ++Vvd+fAG+Gp++i iak  + k+v+aid+nP++v++l++ni+lN v++vv 
  gi|298674302|ref|YP_003726052.1| 166 IAEAYFTPRLSTERERVLSLISSRDLVVDMFAGVGPYSILIAKKVDVKKVIAIDKNPTAVRFLRRNIELNSVNNVV- 241
                                       ****************************************************************************. PP

                                       EEES-GGG---..TT-EEEEEE--TTTGGGGHHHHHHHEEEEEEEEE CS
                            Met_10 155 pileDgrevir..eqladrvvmnlpksaieFldkvlaalkdggvihy 199
                                       +i++D+ +  +  e +ad+v+mnlp+sa+eFl++++++ k gg+ihy
  gi|298674302|ref|YP_003726052.1| 242 AIEGDAGDKEQelEGIADHVIMNLPHSAEEFLNAAVNITKPGGIIHY 288
                                       *****988887779********************************9 PP

>> Trm5_N  tRNA methyltransferase 5 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   0.0   1.6e-19   1.7e-16       1      46 [.       9      54 ..       9      55 .. 0.96

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 1.6e-19
                                      EEEEEGGGHHHHHHHHHHTT-B-TTS--EEETTEEEEEB-S--HHH CS
                            Trm5_N  1 cikVpkkegEkvRkkLlekglLdrnyKIksdddylyIPvkeepegy 46
                                      +ikV+kk+gE++R++L+ekglLd + KI s++++l++P+ ++p + 
  gi|298674302|ref|YP_003726052.1|  9 GIKVSKKKGEPTRRVLIEKGLLDASAKIFSSNGFLFLPILKQPVNS 54
                                      7****************************************99875 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   9.2e-11   9.8e-08      32     110 ..     189     270 ..     160     287 .. 0.77
   2 ?   -3.6   0.0       6.5   6.8e+03      68     100 ..     302     334 ..     298     336 .. 0.71

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 9.2e-11
                                       CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTST..TS-EEEEEE-- CS
                               MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeve..ekkfdlivsNP 105
                                       ++ v+D+ +G+G+ ++ +ak+ +  +v ++d++  A+++ ++n+e n ++ v +++ d+ ++ +  e+  d++++N 
  gi|298674302|ref|YP_003726052.1| 189 RDLVVDMFAGVGPYSILIAKKVDVKKVIAIDKNPTAVRFLRRNIELNSVNnVVAIEGDAGDKEQelEGIADHVIMNL 265
                                       3459*********************************************99666666655444324599*******9 PP

                                       -STTT CS
                               MTS 106 Pfhag 110
                                       P  a+
  gi|298674302|ref|YP_003726052.1| 266 PHSAE 270
                                       96554 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 6.5
                                       HHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEE CS
                               MTS  68 lesakenleanklevevvasdvleeveekkfdl 100
                                       le+ ++ ++ ++ ++evv++ v+   ++++f++
  gi|298674302|ref|YP_003726052.1| 302 LELIRNAANYKGRQIEVVNKRVVRSYAPHEFNI 334
                                       666666666777778888888888888787776 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.4   3.2e-10   3.4e-07     159     256 ..     186     286 ..     180     292 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 3.2e-10
                              PrmA 159 vkegeevlDvGtGSGiLai.aaakLgakkvvavDiDevAvkvakeNaelNkveakleva.lseellk..eekadviv 231
                                       + +++ v+D+ +G G  +i  a+k++ kkv+a+D ++ Av+  ++N+elN+v++ + +   +++  +  e+ ad ++
  gi|298674302|ref|YP_003726052.1| 186 ISSRDLVVDMFAGVGPYSIlIAKKVDVKKVIAIDKNPTAVRFLRRNIELNSVNNVVAIEgDAGDKEQelEGIADHVI 262
                                       56677899**9****999934789******************************8877522222222357899**** PP

                              PrmA 232 aNILaevlielaedikklvkeggll 256
                                        N L +   e+++ + ++ k+gg++
  gi|298674302|ref|YP_003726052.1| 263 MN-LPHSAEEFLNAAVNITKPGGII 286
                                       **.7888999999999999999987 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   7.3e-10   7.7e-07       1      97 []     192     284 ..     192     284 .. 0.90
   2 ?   -2.6   0.0       8.7   9.1e+03      31      54 ..     299     322 ..     296     333 .. 0.64

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 7.3e-10
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBS.SSTTTEEEEEEESTGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlp.fedgsfDlvvssgalh 75 
                                       v+d+ +G G +++ +ak++  +kv+++D ++++++  r+++e +++ nv  ++gda d + + +g  D v+++  l 
  gi|298674302|ref|YP_003726052.1| 192 VVDMFAGVGPYSILIAKKVDVKKVIAIDKNPTAVRFLRRNIELNSVnNVVAIEGDAGDKEqELEGIADHVIMN--LP 266
                                       899***************988********************999999*********77551677899*****5..56 PP

                                       GSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  76 hlsdedlekalkeiarvLkpgG 97 
                                       h     +e++l+ + +++kpgG
  gi|298674302|ref|YP_003726052.1| 267 H----SAEEFLNAAVNITKPGG 284
                                       6....4579************9 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 8.7
                                       HHHHHHHHHHHHHTTTTEEEEESB CS
                   Methyltransf_25  31 eemleaareraeeeglnvefvqgd 54 
                                       ++ le +r+ a+ +g ++e+v++ 
  gi|298674302|ref|YP_003726052.1| 299 DSSLELIRNAANYKGRQIEVVNKR 322
                                       455666666666666677777665 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   8.5e-10     9e-07       7     119 ..     192     298 ..     186     331 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 8.5e-10
                   Methyltransf_31   7 vlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnev 83 
                                       v+D  +G G +++ +a +  + ++v+ iD +++a+++ r n + + ++nv   +gd+ ++e+ le    D ++    
  gi|298674302|ref|YP_003726052.1| 192 VVDMFAGVGPYSILIA-KKVDVKKVIAIDKNPTAVRFLRRNIELNSVNNVVAIEGDAGDKEQELE-GIADHVIM--- 263
                                       89**************.6678899***********************************994444.44555444... PP

                   Methyltransf_31  84 lnaladpdkileeiervlkpggilliedprllaelp 119
                                        n+  + +++l+ + +  kpggi+   d+  +++l 
  gi|298674302|ref|YP_003726052.1| 264 -NLPHSAEEFLNAAVNITKPGGIIHYYDITPEDDLF 298
                                       .55566778888888889999998887777666665 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.1   4.2e-09   4.4e-06      52     149 ..     191     286 ..     107     295 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 4.2e-09
                                       EEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT--GGEEEE-S-HHHHHC--SS-EEEEEE-- CS
                               TRM  52 kvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklneveeivvineddAnvllaekkkrfdviDlDP 128
                                        v+d +++ G  +i  a+    vk+v+a D ++ Av  +++N++ln+v+++v i+  dA    +e +   d++ +  
  gi|298674302|ref|YP_003726052.1| 191 LVVDMFAGVGPYSILIAKK-VDVKKVIAIDKNPTAVRFLRRNIELNSVNNVVAIEG-DAGDKEQELEGIADHVIMNL 265
                                       58999*************9.57999*************************777776.99999999898888888887 PP

                                       SS--GGGHHHHHHHEEEEEEE CS
                               TRM 129 fGspapfldsavqsvkekglL 149
                                         s+ +fl++av+  k +g++
  gi|298674302|ref|YP_003726052.1| 266 PHSAEEFLNAAVNITKPGGII 286
                                       7899********999999986 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   6.2e-08   6.5e-05       3      80 ..     191     266 ..     189     295 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 6.2e-08
                   Methyltransf_15   3 vilDlfsGaGGnviqfalv..fekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvfl 77 
                                       +++D+f+G G  +i +a++   +kviai++n+  +    +N e+  v +++  + gd  +  ++  le i  d v++
  gi|298674302|ref|YP_003726052.1| 191 LVVDMFAGVGPYSILIAKKvdVKKVIAIDKNPTAVRFLRRNIELNSV-NNVVAIEGDAGDKEQE--LEGI-ADHVIM 263
                                       79***************997789*********************966.5678899998874333..3333.444444 PP

                   Methyltransf_15  78 SpP 80 
                                         P
  gi|298674302|ref|YP_003726052.1| 264 NLP 266
                                       444 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   2.2e-07   0.00023      42     138 ..     189     282 ..     133     315 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.2e-07
                                       C-EEEETT-TTSHHHHH.HHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEE CS
                     Cons_hypoth95  42 garvLDlfaGsGalglE.AlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdiv 117
                                       +  v+D+faG G  ++  A   ++kk+++++k+++av+ l++n+e   +++ + ++  da ++ ++l   ++  d v
  gi|298674302|ref|YP_003726052.1| 189 RDLVVDMFAGVGPYSILiAKKVDVKKVIAIDKNPTAVRFLRRNIELNSVNN-VVAIEGDAGDKEQEL---EGIADHV 261
                                       55699********99861555689*********************999886.777777777777666...5567999 PP

                                       EE--SSSTTCH.HHHHHHHHH CS
                     Cons_hypoth95 118 flDPPyakellieevlellee 138
                                        ++ P  +e++++++++  + 
  gi|298674302|ref|YP_003726052.1| 262 IMNLPHSAEEFLNAAVNITKP 282
                                       999999999999888877665 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.53   5.6e+02      97     134 ..       6      43 ..       2      47 .. 0.90
   2 !   17.3   0.0   2.7e-06    0.0029       9      96 ..     189     274 ..     182     281 .. 0.90
   3 ?    5.4   0.0     0.012        13     109     136 ..     261     288 ..     258     296 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.53
                                       T-TCHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEEEE CS
                   Methyltr_RsmB-F  97 rdpdvklrrkekdiaqlaklqkellsaaidllkkgGvl 134
                                       +++ +k+++k+ + ++ +  +k ll+a ++   ++G+l
  gi|298674302|ref|YP_003726052.1|   6 KRKGIKVSKKKGEPTRRVLIEKGLLDASAKIFSSNGFL 43 
                                       7789999***99999999************99999998 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 2.7e-06
                                       T-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..EEEEEE CS
                   Methyltr_RsmB-F   9 eetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDriLl 85 
                                        + ++D+ a+ G    +ia+   + ++v+A+d+n + ++ + +n++  +v+n+  +e+Da   ++ l g   D++++
  gi|298674302|ref|YP_003726052.1| 189 RDLVVDMFAGVGPYSILIAKK-VDVKKVIAIDKNPTAVRFLRRNIELNSVNNVVAIEGDAGDKEQELEG-IADHVIM 263
                                       57899*******999999997.68899************************************999998.99***** PP

                                       EE--CCGGGTT CS
                   Methyltr_RsmB-F  86 DaPCsgtgvir 96 
                                         P s+   ++
  gi|298674302|ref|YP_003726052.1| 264 NLPHSAEEFLN 274
                                       ****9987665 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHHHHHHHCCCEEEEEEEEE CS
                   Methyltr_RsmB-F 109 diaqlaklqkellsaaidllkkgGvlvY 136
                                        i++l +  +e l+aa++ +k+gG++ Y
  gi|298674302|ref|YP_003726052.1| 261 VIMNLPHSAEEFLNAAVNITKPGGIIHY 288
                                       5889999******************999 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0     4e-06    0.0042       5      94 ..     197     286 ..     193     288 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4e-06
                                       -TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC-.CCH CS
                   Methyltransf_11   5 cGtGrlaealakrg..arvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhhv.edp 77 
                                       +G G ++  +ak++  ++v+++D ++++++  +++++ + + +v  +++da +   +++    + + +v++++ +  
  gi|298674302|ref|YP_003726052.1| 197 AGVGPYSILIAKKVdvKKVIAIDKNPTAVRFLRRNIELNSVnNVVAIEGDAGD---KEQELEGI-ADHVIMNLpHSA 269
                                       5788888888888888***********************9999999******9...55555554.445566666889 PP

                                       HHHHHHHHHHEEEEEEE CS
                   Methyltransf_11  78 ekalkeiaRvLkpgGll 94 
                                       e++l+ ++ + kpgG++
  gi|298674302|ref|YP_003726052.1| 270 EEFLNAAVNITKPGGII 286
                                       9**************97 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   1.4e-05     0.015     203     255 ..     189     244 ..     177     260 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.4e-05
                   tRNA_U5-meth_tr 203 gdl.lelycGnGnfslalarn..fekvlateiakssveaaqyniaankidnvqiir 255
                                       +dl ++++ G G +s+ +a++  ++kv+a +   ++v + + ni+ n+++nv  i 
  gi|298674302|ref|YP_003726052.1| 189 RDLvVDMFAGVGPYSILIAKKvdVKKVIAIDKNPTAVRFLRRNIELNSVNNVVAIE 244
                                       4552699***********9973358**************************98775 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       8.2   8.6e+03      46      59 ..     135     148 ..     125     155 .. 0.74
   2 ?   12.6   0.1   6.5e-05     0.068       3      61 ..     190     248 ..     188     264 .. 0.91
   3 ?   -1.9   0.0       1.9     2e+03      97     135 ..     270     310 ..     269     324 .. 0.68

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 8.2
                                       HHCTTSSEEEEES- CS
                    Methyltransf_4  46 ealelkNlrilrgd 59 
                                       ++++++N++++ g+
  gi|298674302|ref|YP_003726052.1| 135 GEYRVRNVKVIAGE 148
                                       56789999988776 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 6.5e-05
                                       EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CC CS
                    Methyltransf_4   3 pvvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdal 61 
                                        +v+++  G G   + +Akk   k++++i+++ + v+ + ++ie + ++N+  ++gda 
  gi|298674302|ref|YP_003726052.1| 190 DLVVDMFAGVGPYSILIAKKVDVKKVIAIDKNPTAVRFLRRNIELNSVNNVVAIEGDAG 248
                                       57899999*************************************************94 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHEEEEEEEEE..EESHHHHHHHHHHHHHCSTT CS
                    Methyltransf_4  97 pellkelarvLkkgGvlel..aTDveeyaeemlkvleeepl 135
                                       +e+l+++ ++ k+gG+++   +T   +++  +l+ +++  +
  gi|298674302|ref|YP_003726052.1| 270 EEFLNAAVNITKPGGIIHYydITPEDDLFDSSLELIRNAAN 310
                                       67899999999999999862234455555555555555555 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.8e-05     0.041       6      78 ..     180     252 ..     173     264 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.8e-05
                   Methyltransf_18   6 kaiaslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGlekl 78 
                                       +++ sl+++ + v+D  +  g  +i ++k+  +kkvia+D n+ +++  ++nie +++++ + +    G ++ 
  gi|298674302|ref|YP_003726052.1| 180 ERVLSLISSRDLVVDMFAGVGPYSILIAKKVDVKKVIAIDKNPTAVRFLRRNIELNSVNNVVAIEGDAGDKEQ 252
                                       578999*************************************************999887766555554444 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.2e-05     0.044      43     147 ..     184     289 ..     172     305 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.2e-05
                                       GCS-CCC-.EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCC..TTTTT-EE CS
                              GidB  43 ellkekrdkviDvGsGaGlPGipLaiarpelkltLleslekkiaFLeevkeelklenveivearaee..kqeeekyd 117
                                       +l+++ +  v+D  +G G  +i +a     +k++ ++++   ++FL+  +e   ++nv ++e +a +  ++ e   d
  gi|298674302|ref|YP_003726052.1| 184 SLISSRD-LVVDMFAGVGPYSILIAKKVDVKKVIAIDKNPTAVRFLRRNIELNSVNNVVAIEGDAGDkeQELEGIAD 259
                                       5555555.59****************9999************************************94333344467 PP

                                       EEEEC-SSSHHHHHHHHCCCEEEEEEEEEE CS
                              GidB 118 vvtsRAlaslnelteillkllkegglilal 147
                                        v++    s +e+ + + ++ k+gg i  +
  gi|298674302|ref|YP_003726052.1| 260 HVIMNLPHSAEEFLNAAVNITKPGGIIHYY 289
                                       777777777788888888888888877655 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   6.7e-05     0.071       5      98 ..     197     285 ..     193     286 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.7e-05
                   Methyltransf_12   5 cGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkd 81 
                                       +G+G ++  +++k   ++++++D +p a+   ++ +  ++ nn+  +e +a d +++ +g   D v+++   ++   
  gi|298674302|ref|YP_003726052.1| 197 AGVGPYSILIAKKVDVKKVIAIDKNPTAVRFLRRNIELNSVNNVVAIEGDAGDKEQELEG-IADHVIMNLPHSA--- 269
                                       899**********9999************8888888888888888888888887666665.9999999866555... PP

                   Methyltransf_12  82 irevldnirklLkpgGr 98 
                                        +e+l+ + +  kpgG+
  gi|298674302|ref|YP_003726052.1| 270 -EEFLNAAVNITKPGGI 285
                                       .8999999999999997 PP

>> PRMT5  PRMT5 arginine-N-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00018      0.19      90     128 ..     209     246 ..     176     265 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                                       CCCEEEEEEEES-HHHHHHHHHHHHHHTTCCGCEEEES- CS
                             PRMT5  90 kvtkvkivavEKnpnavvtLqkkvneekWeekveviksd 128
                                       kv   k++a++Knp+av  L+++++ ++ ++ v  i+ d
  gi|298674302|ref|YP_003726052.1| 209 KVDVKKVIAIDKNPTAVRFLRRNIELNSVNNVV-AIEGD 246
                                       3345689*****************999995555.45555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2167.52
//
Query:       gi|298674303|ref|YP_003726053.1|  [L=479]
Description: phage/plasmid primase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.7e-13   48.8   0.3    1.7e-12   47.8   0.3    1.6  1  D5_N      D5 N terminal like
    0.00022   21.7   0.4    0.00055   20.4   0.4    1.7  1  Pox_D5    Poxvirus D5 protein-like


Domain annotation for each model (and alignments):
>> D5_N  D5 N terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.3   1.9e-16   1.7e-12      68     151 .]      93     176 ..      12     176 .. 0.84

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 1.9e-16
                              D5_N  68 ssrskkkvdnvlreaaelprldleideldadplllafaNGvldlktgelrdhepedyltkitpvdydpda..dcptf 142
                                       s+  k +v+ v   +++ + + ++  ++++d+ +l+++NG l+lktg+l + +pe y+tk++p+dy++d   +c++f
  gi|298674303|ref|YP_003726053.1|  93 SNLIKEEVERVKHVIQSKL-RCIDKSQINTDKFYLPVNNGLLELKTGKLKNFSPEIYFTKKIPIDYKKDTnvPCEFF 168
                                       5555555555555555553.7789999***************************************99875577777 PP

                              D5_N 143 kewlddilp 151
                                         +l+di++
  gi|298674303|ref|YP_003726053.1| 169 -NFLKDIFE 176
                                       .9****995 PP

>> Pox_D5  Poxvirus D5 protein-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.4   6.1e-08   0.00055       4      71 ..     390     457 ..     387     472 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 6.1e-08
                            Pox_D5   4 DpvldFveelfeeekstrvpsdvlYeaYkafcekngykpvlskrtFqkrlkkilee.gfekkkkkkgqq 71 
                                       +++  +v++ +  + + + psd++Y  Y +f ++ g++p  +k++F+ ++  +  + g++  k++k ++
  gi|298674303|ref|YP_003726053.1| 390 NHIDLYVGQRIAHNTGSFCPSDMVYSDYISFASELGITP-YGKSKFYSEFIDACIKfGYKLYKTQKTYN 457
                                       55666888888889999**********************.**********9977666766555553333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 2881.42
//
Query:       gi|298674304|ref|YP_003726054.1|  [L=341]
Description: hypothetical protein Metev_0332 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0034   17.8   0.0      0.014   15.8   0.0    2.0  1  Transglut_core   Transglutaminase-like superfamily
  ------ inclusion threshold ------
      0.062   13.7   0.0       0.11   12.8   0.0    1.3  1  DUF4198          Domain of unknown function (DUF4198)
       0.17   12.2   0.0       0.29   11.4   0.0    1.4  1  CarboxypepD_reg  Carboxypeptidase regulatory-like domain


Domain annotation for each model (and alignments):
>> Transglut_core  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.3e-06     0.014       6     112 .]      53     168 ..      48     168 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.3e-06
                    Transglut_core   6 eltagakdplekakaiyewvr......knveys...........aprrtpgsrdaeavletgkGncedfaslfvall 65 
                                       e+ +  ++ +ek+k i +w +       nv  +             +++  ++++ + l  gk+ c++ a +f  ++
  gi|298674304|ref|YP_003726054.1|  53 EILSHSDNNTEKVKNIIKWEQhriidnPNV--EyftisnilslfFINPYRLPDNPGWYLYIGKASCQELAFVFENMA 127
                                       555555566666666666655444433112..122333444444334445555688889999*************** PP

                    Transglut_core  66 RalGipaRvvtgylsgeeekeqsvasedaHawvevylegygWvplDp 112
                                       +   +  R ++     +     ++  +++H w ev l g++W  +D+
  gi|298674304|ref|YP_003726054.1| 128 KRTNLTYRRIYADKLIK-----PNGESNNHRWSEVKL-GGKWTIADA 168
                                       **********9999987.....6999***********.****99986 PP

>> DUF4198  Domain of unknown function (DUF4198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.9e-05      0.11     150     201 ..     214     267 ..     201     270 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.9e-05
                           DUF4198 150 geelevqvlldGkPlagaeveveyggt..ryrdapdeikvktdadGvvtftlpk 201
                                        + l+++ + +GkP+++a +++    +   y+   + i ++t+++G++++ l  
  gi|298674304|ref|YP_003726054.1| 214 TGHLKIEATKNGKPVENANISIYMMHEnsYYQVVGHSIDYSTNSNGIFELDLAT 267
                                       456899999********99997655555234444444555********998865 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   4.9e-05      0.29       9      81 ..     223     308 ..     216     309 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.9e-05
                   CarboxypepD_reg   9 asgapiagatVtvtnadtg.......tvastttdadGafrlrglppgtysvtv..sapGyatatr....eevtltag 72 
                                       ++g+p+++a+++++   ++        +    t+++G f l+  + g+ +  +  s++      +    ++++l+++
  gi|298674304|ref|YP_003726054.1| 223 KNGKPVENANISIYMMHENsyyqvvgHSIDYSTNSNGIFELDLATYGNTNYIIklSSTELNGIYQyegkKSLSLNNN 299
                                       48***********9866653444333577789*********855556555554224443333333444455666666 PP

                   CarboxypepD_reg  73 qtttlditL 81 
                                       +++ l+++L
  gi|298674304|ref|YP_003726054.1| 300 ENKILNVKL 308
                                       666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 1992.78
//
Query:       gi|298674305|ref|YP_003726055.1|  [L=191]
Description: integrase family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-29  103.3   0.6    1.4e-29  103.1   0.6    1.0  1  Phage_integrase  Phage integrase family
  ------ inclusion threshold ------
       0.11   12.3   0.0       0.14   12.0   0.0    1.2  1  PSI_PsaF         Photosystem I reaction centre subunit III


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.1   0.6   1.5e-33   1.4e-29       2     170 ..       7     172 ..       6     174 .. 0.93

  Alignments for each domain:
  == domain 1  score: 103.1 bits;  conditional E-value: 1.5e-33
                                       HHHHHHHHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSE.EEEECTHHHH CS
                   Phage_integrase   2 vltedeverllaaleeslkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgske.ravplseeal 77 
                                       +l+e+e++++l+++    + +  + + l+y  +lR+sE+l+ rv dld+en++i +   +gK  +e    p + ++l
  gi|298674305|ref|YP_003726055.1|   7 WLRENELKKILNNTTI--SEKYEIWILLMYTPALRVSEALNVRVRDLDFENECIEIYGGKGKDDTEmQKAPCNISVL 81 
                                       89***********999..8888999*******************************55555555557778999**** PP

                                       HHHHHHHHHHCHCCTTTSBSSBETTSSB--HHHHHHHHHHHHHHCT-SSC--TTHHHHHHHHHHHHHCTSHHHHHHH CS
                   Phage_integrase  78 ellkellskaleeaeksellfaskrgkplsrqtvrkafkraveeagiekpltpHtlRhsfataLleagvdlrvvqkl 154
                                       + lk++ +++     ++e+++ s+++k+ sr  v+ ++++++ +agi+k++ +HtlR+s a +Ll +g++l  v ++
  gi|298674305|ref|YP_003726055.1|  82 KRLKRYAEHS--DLRPKEYIMFSQKKKKASRFHVYNVLNKLCSQAGIDKKIGTHTLRRSRAEHLLDRGLSLTYVSRF 156
                                       ********99..7788999999999**************************************************** PP

                                       HT-SSCCHHHHHHCCC CS
                   Phage_integrase 155 lGHssisttqiYthva 170
                                       l H++++tt+ Y +v+
  gi|298674305|ref|YP_003726055.1| 157 LRHKNLATTMAYLDVS 172
                                       ************9986 PP

>> PSI_PsaF  Photosystem I reaction centre subunit III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.5e-05      0.14      45     116 ..      81     157 ..      64     183 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.5e-05
                          PSI_PsaF  45 ekrlkkyeads..aPalalk.akiektkkrfekyskagllCGedGlPhliadg..ryehagefliPgllflyiaGwi 116
                                        krlk+y+++s   P  ++  ++ +k   rf+ y   + lC + G+   i     r ++a  +l  gl + y++ ++
  gi|298674305|ref|YP_003726055.1|  81 LKRLKRYAEHSdlRPKEYIMfSQKKKKASRFHVYNVLNKLCSQAGIDKKIGTHtlRRSRAEHLLDRGLSLTYVSRFL 157
                                       47999998876336888776244556668******************999877567778888899999999999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       747  (0.0416643); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1426.52
//
Query:       gi|298674306|ref|YP_003726056.1|  [L=151]
Description: hypothetical protein Metev_0334 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-08   33.9   0.9    1.5e-07   31.5   0.9    1.9  1  EVE       EVE domain


Domain annotation for each model (and alignments):
>> EVE  EVE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.9   8.3e-12   1.5e-07       1     143 [.       2     145 ..       2     147 .. 0.74

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 8.3e-12
                                       -EEEEEEBHHTSHHHHHCHHHCEEE-EE-GHHHHHHHCC--TT-EEEEEETSSSS-EEEEEEEEECEEEE-GGGG-T CS
                               EVE   1 ayWllksepdefsiddlkrkkeegWdgvrnyqarnllramkkGDlvlfYhsgeklqaivgiaeVvseaypdetqfdp 77 
                                       +yW l ++ d  +++    k+++ W g+  + +  l++ +++GD++++Y s++k  ++v+ ++ +     d +++  
  gi|298674306|ref|YP_003726056.1|   2 RYWCLSTSID--NWKVC--KENNLW-GMDYRYYPTLAKFVNPGDKAVIYTSKNK--RFVATVKFTGSYFYDDSDI-- 69 
                                       6*********..99999..99****.998877777777***********99999..9********7777777777.. PP

                                       TSTT--TTTBTTS--EEEEEEEE........................EEEEEEEEHHHHTTHGTCTTSHHHHCCT-S CS
                               EVE  78 kskyydpkskkekpwlrvdvkpv........................kklkrplslkelkaepelegmkllrkgrls 130
                                        ++y          ++r++ +++                          l +++s+   k+  + ++  +    + s
  gi|298674306|ref|YP_003726056.1|  70 GWNYLF--------PYRINFEILhenekspqinytvsndgneanwfgDNLIDEISFIADKS--RTWNQYF----QVS 132
                                       333332........33333333322222333333344556666677788888888888888..5688888....*** PP

                                       EEEE-HHHHHHHH CS
                               EVE 131 vrpvteedwelil 143
                                       ++++teed+++i 
  gi|298674306|ref|YP_003726056.1| 133 IIRITEEDFNTIQ 145
                                       **********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 965.95
//
Query:       gi|298674307|ref|YP_003726057.1|  [L=475]
Description: HNH endonuclease [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-11   44.3   4.2    1.6e-11   44.2   2.5    2.0  2  HNH       HNH endonuclease
    0.00015   21.6   0.4    0.00048   19.9   0.4    1.9  1  HNH_5     HNH endonuclease
  ------ inclusion threshold ------
      0.015   15.3   0.0       0.15   12.1   0.0    2.3  2  DUF4385   Domain of unknown function (DUF4385)
      0.029   14.5   0.9       0.46   10.6   0.3    3.0  2  HNH_2     HNH endonuclease


Domain annotation for each model (and alignments):
>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.3     1e+04      27      35 ..     225     233 ..     221     233 .. 0.78
   2 !   44.2   2.5   3.6e-15   1.6e-11       1      45 [.     405     454 ..     405     455 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.3
                               HNH  27 addieNlql 35 
                                       + di+N+q+
  gi|298674307|ref|YP_003726057.1| 225 PADIDNIQA 233
                                       6799**985 PP

  == domain 2  score: 44.2 bits;  conditional E-value: 3.6e-15
                               HNH   1 CeyCgrkfhks.....ealevdHiipisqggaddieNlqllCksCHnkkh 45 
                                       C+ Cg++  ++     ++le +Hii +s+ g d+i+N+++lC +CH+k h
  gi|298674307|ref|YP_003726057.1| 405 CQLCGNNAPFYdrggnPYLETHHIIRVSKDGDDTIDNVVALCANCHRKMH 454
                                       ***********************************************977 PP

>> HNH_5  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.4   1.1e-07   0.00048       1      43 [.     405     453 ..     405     461 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.1e-07
                             HNH_5   1 CiyCgkeiaekel......seeHIiPeslGGkltisnlvtlCkkCNqkk 43 
                                       C++Cg++ +  +       +  HIi  s+ G  ti+n+v+lC  C+ k+
  gi|298674307|ref|YP_003726057.1| 405 CQLCGNNAPFYDRggnpylETHHIIRVSKDGDDTIDNVVALCANCHRKM 453
                                       7777777544332223333999************************987 PP

>> DUF4385  Domain of unknown function (DUF4385)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.3e-05      0.15      57     111 ..      77     132 ..      62     147 .. 0.83
   2 ?   -0.0   0.0      0.19   8.3e+02      58      80 ..     232     255 ..     225     285 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.3e-05
                           DUF4385  57 yelfleyleeddfvGaDmaRkflqmGytRarRYanhkgG.kkykkekeeeeleeee 111
                                       ++ fl+ ++++d v + +  k++++G  ++  Y  h+ G +ky ++ +e+el++ +
  gi|298674307|ref|YP_003726057.1|  77 VNRFLNQVKKGDIVLMPIGNKYVNIGKIKTGEYEYHPDGfRKYLYDINEKELNRLK 132
                                       578999******************************98879**9866666655543 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.19
                           DUF4385  58 elfley.leeddfvGaDmaRkflq 80 
                                       ++f+e+ +e++   G+D++ kf++
  gi|298674307|ref|YP_003726057.1| 232 QAFKEWmVENGHQFGVDLSTKFIN 255
                                       56666624677889********96 PP

>> HNH_2  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.29   1.3e+03      44      54 ..     161     171 ..     138     174 .. 0.86
   2 ?   10.6   0.3    0.0001      0.46       1      62 [.     405     451 ..     405     454 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.29
                             HNH_2  44 gstidspsNgl 54 
                                       +s+idspsN++
  gi|298674307|ref|YP_003726057.1| 161 NSSIDSPSNVF 171
                                       789******85 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0001
                             HNH_2   1 Cvitgiddp......s.lleaAHIiPwslssffndlilnrfeigrillekgstidspsNgllLspdiHk 62 
                                       C+++g ++p      + +le +HIi            ++ +             d  +N+  L++++H+
  gi|298674307|ref|YP_003726057.1| 405 CQLCGNNAPfydrggNpYLETHHIIR----------VSKDG------------DDTIDNVVALCANCHR 451
                                       999**777788889977*********..........55555............6889999999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1083  (0.0604049); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.35s 00:00:01.01 Elapsed: 00:00:00.52
# Mc/sec: 2755.86
//
Query:       gi|298674308|ref|YP_003726058.1|  [L=305]
Description: hypothetical protein Metev_0336 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1420  (0.0792013); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2317.87
//
Query:       gi|298674309|ref|YP_003726059.1|  [L=569]
Description: restriction endonuclease AlwI [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-57  194.5  23.0    2.8e-57  194.5  23.0    1.7  2  RE_AlwI          AlwI restriction endonuclease
  ------ inclusion threshold ------
      0.033   14.7   0.5         12    6.4   0.0    3.2  3  Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransfer


Domain annotation for each model (and alignments):
>> RE_AlwI  AlwI restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.5  23.0   3.1e-61   2.8e-57      11     440 ..      83     516 ..      77     517 .. 0.81
   2 ?   -3.0   0.5      0.26   2.4e+03     273     300 ..     530     557 ..     520     566 .. 0.47

  Alignments for each domain:
  == domain 1  score: 194.5 bits;  conditional E-value: 3.1e-61
                           RE_AlwI  11 slekfrltpvGrkLleeeniedeseiflkqllkyqipsdlersyke.kdvkpfivvlkvlleleketkeeelsyeef 86 
                                       +l++++lt+ G +Ll ++    + eif++q++k+q+ps+++ +    + v p+  +l++++el      ++l+++e+
  gi|298674309|ref|YP_003726059.1|  83 NLKPIELTNAGARLLSNKR---INEIFIRQMMKFQLPSPYHTDNSGrFYVRPYLEILRLIYEL------DGLTKHEL 150
                                       45799***********999...99****************8765444999*************......9******* PP

                           RE_AlwI  87 alfiplltdkesieeivnqilkyrkkklkkediiakkkllkekvqe.....................nqnetkkiet 142
                                       a f   ++     e i  +i ++r +k+kk     kk++++e++                       n  + + i+t
  gi|298674309|ref|YP_003726059.1| 151 AIFGLQIIHIDYYELIKTEIQNFRLEKSKKF-YTRKKEYIQESYIRaiekiyadeinqknfktretdNNDYRQFINT 226
                                       ***998888888888889*********9976.556666666666666888999999888888888888888888999 PP

                           RE_AlwI 143 kvktleDYaDlnlRyLklTelfifkskgklvilakekkeeIekLleeaaik.....nkddylelmskinkaelple. 213
                                       k +++ DYaD ++RyLk+Tel+ f  +  ++ + ++kk  ++ Ll++   +     n+++++    + n+  l ++ 
  gi|298674309|ref|YP_003726059.1| 227 KRRNIIDYADAAIRYLKATELVSFDVNSLKLTITHDKKDDVKFLLDNVPREpvyinNENEFKNHLFDANNIILYTDn 303
                                       999********************99999999999**************99988887788888888788777777774 PP

                           RE_AlwI 214 ..nisnnlleqlnrivsnlskql..nikklneneaskl..slvkdelkdrlnelik.ikyadeekaheikellnlLe 283
                                         ++ +++ e  + ++++l k +  ++++l+++e+++l  +l +d+  d ln+ i+  k +d+      +  +n  +
  gi|298674309|ref|YP_003726059.1| 304 keETTKKIFELYKYLYKKLPKGFikKVRNLHIEELKDLkdKLEQDKIDDVLNKQINsLKVTDD-----FNDIINVYD 375
                                       444555555566666666666554455666666666665555555555555543332455555.....222223323 PP

                           RE_AlwI 284 efikredkeeeklvideaeePaklEyilglillaidslkniilEarklkvdddllpithApGnkpDiifeyddfslv 360
                                                   +  + a  P+++E+ ++++l+++d+  ni     ++k+d d+ p++ Ap ++pDi + y++f+l+
  gi|298674309|ref|YP_003726059.1| 376 ----------SIIQGEVADPPLIFEWNTWRALVILDDG-NING---NFKIDTDGSPLFSAPPKYPDISCYYNEFNLI 438
                                       ..........3333455889****************95.5555...9****************************** PP

                           RE_AlwI 361 iEvTLskgsnQekaEgepvsrHlaefrikyknnknvyslFiapkieqntittFrirviygleekkeklkIiPltieq 437
                                       +EvTLs g++Q  +E epv rHl++f  k++  k+ ++lFia+++ + t+  F     ++  +   k kIiP++++ 
  gi|298674309|ref|YP_003726059.1| 439 VEVTLSYGEKQYDMESEPVPRHLGDF-SKSS-DKESFCLFIAKNVSEGTLAYFYGLNNIEISYYGGKSKIIPMDLNS 513
                                       **************************.6666.8******************9998888888899************* PP

                           RE_AlwI 438 fke 440
                                       fk 
  gi|298674309|ref|YP_003726059.1| 514 FKA 516
                                       *96 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.26
                           RE_AlwI 273 heikellnlLeefikredkeeeklvide 300
                                       ++++ +l+ L+e     ++e+e+  +++
  gi|298674309|ref|YP_003726059.1| 530 NQLHSYLKYLIEQTNSTENEIEWYKTIK 557
                                       3344444444444444444444444433 PP

>> Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransferase RsmF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0014        12       4      72 ..     222     288 ..     220     294 .. 0.78
   2 ?    4.7   0.0    0.0047        42       1      38 [.     322     362 ..     322     376 .. 0.74
   3 ?   -2.0   0.0      0.59   5.3e+03      17      60 ..     511     554 ..     504     556 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0014
                                       HHHHHHHHHHGGGHHHHHHHHH-----EEE--TTS..TTHHHHHHH-SS--B-TT-TTEEES---...T CS
                   Methyltr_RsmF_N   4 eFiekmkellgeeaeaflaaleeprkkglRvNtlKisveeleklseefelepvpwceeGfyleeeerpg 72 
                                       +Fi++ ++ + + a+a +++l+++  +++ vN lK++ ++ +k   +f l++vp   e +y+++e+++ 
  gi|298674309|ref|YP_003726059.1| 222 QFINTKRRNIIDYADAAIRYLKATELVSFDVNSLKLTITHDKKDDVKFLLDNVPR--EPVYINNENEFK 288
                                       79999999999999*********************88776555544788999884..556666665555 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0047
                                       --HHHHHHHHHHHGGGHHHHHHHHH----.-EE..E--TTS CS
                   Methyltr_RsmF_N   1 LPeeFiekmkellgeeaeaflaaleeprk.kgl..RvNtlK 38 
                                       LP+ Fi+k+++l  ee++++ + le+++    l   +N lK
  gi|298674309|ref|YP_003726059.1| 322 LPKGFIKKVRNLHIEELKDLKDKLEQDKIdDVLnkQINSLK 362
                                       8********************99966543033333566666 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.59
                                       HHHHHHHH.H-----EEE--TTS..TTHHHHHHH-SS--B-TT-T CS
                   Methyltr_RsmF_N  17 aeaflaal.eeprkkglRvNtlKisveeleklseefelepvpwce 60 
                                       +++f a l +++ k  +  N+l    + l + ++  + ++++w +
  gi|298674309|ref|YP_003726059.1| 511 LNSFKAFLhHANEKDNIESNQLHSYLKYLIEQTN-STENEIEWYK 554
                                       5555555555566677888888854444444443.6788888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (569 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1202  (0.0670422); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.47
# Mc/sec: 3621.31
//
Query:       gi|298674310|ref|YP_003726060.1|  [L=260]
Description: DNA methylase N-4/N-6 domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.6e-24   84.9   3.5    1.6e-21   77.1   3.5    2.1  1  N6_N4_Mtase      DNA methylase
    0.00013   21.7   0.3       0.46   10.1   0.0    3.1  3  UPF0020          Putative RNA methylase family UPF0020
    0.00033   20.4   3.0     0.0049   16.6   0.0    2.5  2  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
     0.0069   16.2   0.2       0.29   10.9   0.0    2.2  2  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
      0.013   16.2   0.0        3.6    8.4   0.0    3.0  3  Methyltransf_25  Methyltransferase domain
      0.014   14.7   0.2       0.21   10.8   0.1    2.0  2  N6_Mtase         N-6 DNA Methylase
      0.029   15.0   0.0         56    4.5   0.0    3.1  3  Methyltransf_11  Methyltransferase domain
      0.049   14.4   0.1        9.5    7.0   0.0    3.0  3  Methyltransf_12  Methyltransferase domain
       0.13   11.6   0.0       0.23   10.9   0.0    1.3  1  UPRTase          Uracil phosphoribosyltransferase


Domain annotation for each model (and alignments):
>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.1   3.5   8.1e-25   1.6e-21       1     229 [.      35     231 ..      35     233 .. 0.89

  Alignments for each domain:
  == domain 1  score: 77.1 bits;  conditional E-value: 8.1e-25
                                       EEEEEE--SSSSSCS.................GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE-CCCHHTHH CS
                       N6_N4_Mtase   1 vdlivtdpPYntgkdy............endeqyeeedsyeeyleflekvlkevrrvLkddgsifiniddseikkel 65 
                                       vd+ivtdp Y   +++            +n+++ + ++++++  +  + +l+++++vLkd+  i+i +d     + l
  gi|298674310|ref|YP_003726060.1|  35 VDIIVTDPAYSGMNQKmkfgngrivgeyKNENNNKWFQEFHDTEDNYRYFLSQCYKVLKDNSHIYIMFDSYSLLS-L 110
                                       799*********99999********999888888888999999999***********************999998.* PP

                                       HHHHHHHTT-EEEEEEEEEEESS.STTTSTCCS-B--EEEEEEEESSTT-..---GGGSSBSS-HHHHHHHHHHCHH CS
                       N6_N4_Mtase  66 kaladeifggffllnvivwkkpn.smpesnkdrltsthEyilvfsknkkyllkfnldaikvpyeekdklekrgayts 141
                                         l++e    f+++n ivw+k n +m++    +++++hE++++ +k+ k+           + +  d ++ ++    
  gi|298674310|ref|YP_003726060.1| 111 GNLLREY---FNVKNIIVWDKVNmGMGH----YFRRRHEFVIFATKGNKK---------LISRSIPDVWRFKR---- 167
                                       *******...55**********777777....9*****************.........56666666666666.... PP

                                       HCC-B--BSEEE-SCCCTTSTTS-CHH----SS---HHHHHHHHHHHS.-TT-EEEETT-TTTHHHHHHHHTT-EEE CS
                       N6_N4_Mtase 142 kkkgkkiediWdlseiqsnekkskgdtkkkHpaqkPvallerlIklst.kkgdivlDpFaGSGtTavaakelgrkfi 217
                                                i+                +k++p+qkPv+l e ++  s  +++ +v DpF GSG+ a+aa++ + +fi
  gi|298674310|ref|YP_003726060.1| 168 ---------IY----------------NKCYPTQKPVELFEAMLAGSVdNENLTVCDPFVGSGSSAIAALKKNCNFI 219
                                       .........66................2579*************6665166999*********************** PP

                                       EEESSHHHHHHH CS
                       N6_N4_Mtase 218 Gieieeeyvela 229
                                       G +++e++++++
  gi|298674310|ref|YP_003726060.1| 220 GNDTDEKALKTS 231
                                       ******998865 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00023      0.46      98     131 ..       9      44 ..       4      52 .. 0.86
   2 ?   -0.4   0.0      0.39   7.8e+02     143     172 ..      79     108 ..      72     125 .. 0.85
   3 !    7.6   0.0    0.0013       2.7      18      46 ..     183     211 ..     178     246 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00023
                                       HTT-GGGEEEEE--GGG--..STTS---EEEE---- CS
                           UPF0020  98 kagvgdliefsqadaakLr..lkegevdvivtnpPY 131
                                       ++  +++++++q da ++   l+e++vd+ivt+p Y
  gi|298674310|ref|YP_003726060.1|   9 YTSQEGKVKLYQDDALDFIkgLPENSVDIIVTDPAY 44 
                                       5667899999*****9998899999*********98 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.39
                                       HHHHHHHHHHHHH-TT..-EEEEEESSHHH CS
                           UPF0020 143 kLYseflrelkrvlrgggrlvlltsenkal 172
                                       + Y+ fl++  +vl+ ++ + +++ +++ l
  gi|298674310|ref|YP_003726060.1|  79 DNYRYFLSQCYKVLKDNSHIYIMFDSYSLL 108
                                       55999*****************99987654 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0013
                                       HHHHHHTT--TTS-EEETT-TTSHHHHHH CS
                           UPF0020  18 aalvrlagwkpgepllDPmCGsGtilIEa 46 
                                        a++  +  +++ +  DP+ GsG+ +I a
  gi|298674310|ref|YP_003726060.1| 183 EAMLAGSVDNENLTVCDPFVGSGSSAIAA 211
                                       5777777778888999********99944 PP

>> MethyltransfD12  D12 class N6 adenine-specific DNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   1.4     0.034        68     173     246 ..      30     105 ..       4     131 .. 0.61
   2 !   16.6   0.0   2.5e-06    0.0049      20      56 ..     193     229 ..     183     252 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.034
                                       T--TTE.EEEE--S-T.S...TS--GGGG.CS-HHHHHHHHHHHHHH..HHTT-EEEEEEES...EESHHHHHHCTT CS
                   MethyltransfD12 173 kakieddivYlDPPYnprqytanytlyetlafsdedevrlaevlksls.skfgvkvllsnsf...kdtklfrelyks 245
                                        ++++ di+  DP Y + ++++++      + +++++    + ++++  ++  +++ ls  +   kd++ +  +++s
  gi|298674310|ref|YP_003726060.1|  30 LPENSVDIIVTDPAYSGMNQKMKFGNGRIVGEYKNEN--NNKWFQEFHdTEDNYRYFLSQCYkvlKDNSHIYIMFDS 104
                                       4578899999999999999999887544444444333..44444444332222222222222334555555555555 PP

                                       . CS
                   MethyltransfD12 246 Y 246
                                       Y
  gi|298674310|ref|YP_003726060.1| 105 Y 105
                                       4 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 2.5e-06
                                       --SEEEETT-TTSCCHHCS...SSCEEEEES-HHHHH CS
                   MethyltransfD12  20 kgktfvepFaGggaVffeakkqgkkvlinDinedlin 56 
                                        + t+++pF+G+g+ +++a+k++ + + nD+ e+   
  gi|298674310|ref|YP_003726060.1| 193 ENLTVCDPFVGSGSSAIAALKKNCNFIGNDTDEKALK 229
                                       56689*************************9987655 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.03        60      55     107 ..      15      98 ..       2     131 .. 0.59
   2 !   10.9   0.0   0.00015      0.29       2      49 ..     192     236 ..     191     243 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.03
                   Methyltransf_31  55 nveFeqgdiee.leklledekfDlilsn...........................evlnaladpdkile........ 95 
                                        v++ q d+ + ++  l ++++D+i+++                                                 
  gi|298674310|ref|YP_003726060.1|  15 KVKLYQDDALDfIKG-LPENSVDIIVTDpaysgmnqkmkfgngrivgeyknennnK------------Wfqefhdte 78 
                                       678888888885554.5669999999994444444443333333333333333321............022222222 PP

                   Methyltransf_31  96 ........eiervlkpggil 107
                                               +  +vlk+++++
  gi|298674310|ref|YP_003726060.1|  79 dnyryflsQCYKVLKDNSHI 98 
                                       22223333566666665554 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00015
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaq 49 
                                       +++l+v+D+  G+G  ++++ ++   +++++G D +e+a++ + e+ +
  gi|298674310|ref|YP_003726060.1| 192 NENLTVCDPFVGSGSSAIAALKK---NCNFIGNDTDEKALKTSSERID 236
                                       6899****999999988888854...899************9999865 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.068   1.4e+02      44      70 ..      12      40 ..       2      53 .. 0.78
   2 ?    0.4   0.0      0.54   1.1e+03      74      95 ..      74      94 ..      68      95 .. 0.76
   3 ?    8.4   0.0    0.0018       3.6       2      43 ..     198     237 ..     197     257 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.068
                                      TTTTEEEEESBCCGBS..SSTTTEEEEEE CS
                   Methyltransf_25 44 eglnvefvqgdaedlp..fedgsfDlvvs 70
                                      ++ +v+++q da d+   ++++s+D++v 
  gi|298674310|ref|YP_003726060.1| 12 QEGKVKLYQDDALDFIkgLPENSVDIIVT 40
                                      44599*******99753479*******97 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.54
                                      GGGSSHHHHHHHHHHHHHHEEE CS
                   Methyltransf_25 74 lhhlsdedlekalkeiarvLkp 95
                                      +h  ++++++ +l+++++vLk+
  gi|298674310|ref|YP_003726060.1| 74 FHD-TEDNYRYFLSQCYKVLKD 94
                                      444.4567899*********97 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0018
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHH CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraee 43 
                                        d   G+G  ++a++k+   ++++g D +e++l++  er+++
  gi|298674310|ref|YP_003726060.1| 198 CDPFVGSGSSAIAALKKN--CNFIGNDTDEKALKTSSERIDS 237
                                       5667899*9999999994..***************9999864 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00011      0.21     109     190 ..      18     109 ..       9     124 .. 0.83
   2 ?    1.8   0.0     0.058   1.2e+02      42      66 ..     190     213 ..     173     231 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
                          N6_Mtase 109 irlgdtlekpkfekdkkfdvvvaNppfnqkew..........kektlekderfreavapksnadlafllhiieslkp 175
                                         ++d+l   k   ++++d++v+ p ++  +            e ++e+++++ + +++++ +   fl  + ++lk+
  gi|298674310|ref|YP_003726060.1|  18 LYQDDALDFIKGLPENSVDIIVTDPAYSGMNQkmkfgngrivGEYKNENNNKWFQEFHDTEDNYRYFLSQCYKVLKD 94 
                                       55566665555556899**********9987788899999998999999999*******9999999*********** PP

                          N6_Mtase 176 kGraavvlangvLfr 190
                                       + ++ ++ ++ +L +
  gi|298674310|ref|YP_003726060.1|  95 NSHIYIMFDSYSLLS 109
                                       *99999888777765 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.058
                          N6_Mtase  42 lepksgesvyDpacGsggllvqaek 66 
                                       ++ +++ +v Dp +Gsg+  + a k
  gi|298674310|ref|YP_003726060.1| 190 VD-NENLTVCDPFVGSGSSAIAALK 213
                                       24.44456*********98887766 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.055   1.1e+02      43      68 ..      13      41 ..       2      55 .. 0.75
   2 ?    3.2   0.0     0.068   1.4e+02      70      96 .]      74     100 ..      68     100 .. 0.78
   3 ?    4.5   0.0     0.028        56       6      39 ..     203     236 ..     199     252 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.055
                                      -.EEEETTEECCCT..SS-TT-EEEEEEE CS
                   Methyltransf_11 43 l.kvefvvadaekl..pfednsfDlvvss 68
                                      + kv++ + da ++   +++ns+D++v  
  gi|298674310|ref|YP_003726060.1| 13 EgKVKLYQDDALDFikGLPENSVDIIVTD 41
                                      23688899999994457*********975 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.068
                                       -CCC-CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  70 vlhhvedpekalkeiaRvLkpgGllvi 96 
                                       + ++ ++ + +l+++++vLk + +++i
  gi|298674310|ref|YP_003726060.1|  74 FHDTEDNYRYFLSQCYKVLKDNSHIYI 100
                                       34444788899**********998875 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.028
                                       TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCC CS
                   Methyltransf_11   6 GtGrlaealakrgarvvgvDlskemlklakekas 39 
                                       G+G+ a a  k+ ++ +g D+++++lk+++e++ 
  gi|298674310|ref|YP_003726060.1| 203 GSGSSAIAALKKNCNFIGNDTDEKALKTSSERID 236
                                       67777777777778*************9998875 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.91   1.8e+03      48      72 ..      16      40 ..       5      58 .. 0.76
   2 ?    3.3   0.0     0.072   1.4e+02      80      98 ..      79      97 ..      70      98 .. 0.79
   3 ?    7.0   0.0    0.0047       9.5       6      50 ..     203     245 ..     202     257 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.91
                   Methyltransf_12 48 nnnvelealdlldldggssfDlvva 72
                                      ++ ++ +ald ++  +++s+D++v 
  gi|298674310|ref|YP_003726060.1| 16 VKLYQDDALDFIKGLPENSVDIIVT 40
                                      4555666677777777799999985 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.072
                   Methyltransf_12 80 kdirevldnirklLkpgGr 98
                                      ++ r +l++++k+Lk++ +
  gi|298674310|ref|YP_003726060.1| 79 DNYRYFLSQCYKVLKDNSH 97
                                      566789**********976 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0047
                   Methyltransf_12   6 GtGsllralleklpdieytgvDispsaiedakeklakrennnnnn 50 
                                       G+Gs + a l+k  +++++g D +++a++  +e++ +  +  n+ 
  gi|298674310|ref|YP_003726060.1| 203 GSGSSAIAALKK--NCNFIGNDTDEKALKTSSERIDSFLKTENDI 245
                                       556666666666..**************99888888776665554 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00011      0.23      87     142 ..     157     213 ..     149     217 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                           UPRTase  87 ellpea.rvghlglqreeetlepveyynk.LPkkiaertvlllDpviaTGgsaaaaiq 142
                                       + +p++ r+  +  +  + t++pve ++  L  ++++++  ++Dp + +G+sa+aa++
  gi|298674310|ref|YP_003726060.1| 157 RSIPDVwRFKRIYNKCYP-TQKPVELFEAmLAGSVDNENLTVCDPFVGSGSSAIAALK 213
                                       556666666677655666.7889998887255566********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       809  (0.0451224); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1677.17
//
Query:       gi|298674311|ref|YP_003726061.1|  [L=776]
Description: hypothetical protein Metev_0339 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-09   36.5   3.7    3.9e-09   35.8   3.7    1.3  1  DUF2254   Predicted membrane protein (DUF2254)


Domain annotation for each model (and alignments):
>> DUF2254  Predicted membrane protein (DUF2254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   3.7   2.2e-13   3.9e-09       4     208 ..      89     295 ..      87     299 .. 0.73

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 2.2e-13
                           DUF2254   4 lwfipllivllavllalllllldealslsldleel.kegaeaaralLstiagsmltvagfvfSitvvalqlassqfs 79 
                                       lw++ + i++l +l+ + l++l       +  +e+ + +a++a+ ++s ++ s  +++++v+++ +v +q+ +s++s
  gi|298674311|ref|YP_003726061.1|  89 LWLRQITILTLLILFIIYLPTLLTP----F--DEFlPIKANSAKYMISSLVQSEAAIIALVITLSLVGIQYSASSYS 159
                                       6888888888888888888888444....2..22224499************************************* PP

                           DUF2254  80 PRllrnfmrdrvtqvvLGtfigtfvYsllvlrairteee....vpqlsvlvalllaivsvllLiyFihhlarsiqvs 152
                                        +++  f + + + + + +++g++vY l +l  i ++ +    + +  v+  +++ +++ ++L+++i+++ ++ + s
  gi|298674311|ref|YP_003726061.1| 160 TKIIDIFSKKPDMWILIVIYLGSIVYGLYILKGIPET-NinssI-EENVIRLFFINLIAFIYLLFYINSTLKLFKSS 234
                                       **********************************955.345542.2455555688899999**************** PP

                           DUF2254 153 nviarveeelr.kai...........learedeeeeeeeeakdeeeseeeeatpiraersGylqaidv 208
                                       n+i + ++++  k+i           +       e++  ++  +  + +   + i++ + G+l  id+
  gi|298674311|ref|YP_003726061.1| 235 NLILWFGDKITpKSIndnlistnlnfN-------EDNPYQKVIDITKSSIRNQNINTVKLGVLSIIDY 295
                                       ***999887652444555544322111.......1122222222233344455555666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (776 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1423  (0.0793686); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.46
# Mc/sec: 5078.93
//
Query:       gi|298674312|ref|YP_003726062.1|  [L=391]
Description: integrase family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-25   89.5   0.1    4.4e-25   88.4   0.1    1.6  2  Phage_integrase  Phage integrase family
    1.8e-06   28.1   0.2    4.9e-06   26.8   0.1    1.8  2  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
    1.4e-05   24.3   3.9    2.6e-05   23.4   3.9    1.4  1  zf-ribbon_3      zinc-ribbon domain
    9.9e-05   21.9   3.6    0.00018   21.1   3.6    1.5  1  zinc_ribbon_2    zinc-ribbon domain
    0.00014   21.8   1.1    0.00025   21.0   1.1    1.3  1  DZR              Double zinc ribbon
     0.0013   19.2   0.9      0.007   16.8   0.8    2.2  2  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
  ------ inclusion threshold ------
      0.092   12.3   2.9       0.21   11.2   0.1    2.7  3  zf_C2H2_13       Zinc finger domain
       0.11   12.7   0.0       0.34   11.1   0.0    1.8  1  PEP-utilisers_N  PEP-utilising enzyme, N-terminal
       0.16   12.0   1.2       0.54   10.3   1.2    1.9  1  DUF2116          Uncharacterized protein containing a Zn-ribb
       0.24   12.1   1.7       0.48   11.2   1.7    1.4  1  zinc_ribbon_15   zinc-ribbon family


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.8     5e+03       4      18 ..      69      88 ..      66     107 .. 0.60
   2 !   88.4   0.1   2.5e-28   4.4e-25       2     171 ..     131     298 ..     130     299 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.8
                                      HHHHHHHHHHCCGC.....H CS
                   Phage_integrase  4 tedeverllaalee.....s 18
                                      +e++ve+l+  le+     s
  gi|298674312|ref|YP_003726062.1| 69 DEKDVEQLVGSLERsskkyS 88
                                      67788888888887533320 PP

  == domain 2  score: 88.4 bits;  conditional E-value: 2.5e-28
                                       HHHHHHHHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECTHHHHH CS
                   Phage_integrase   2 vltedeverllaaleeslkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgskeravplseeale 78 
                                       +lt+d+++++++a+ +   +rd++++ +lye+++RisEl+++++ d+++++  +l+h    K+   r+v +    ++
  gi|298674312|ref|YP_003726062.1| 131 MLTPDDIKKMVDAAGN---ARDRAIIYTLYESAARISELANMKMRDVKFDEDGALIHLDG-KT-GPRTVRVA-YSVP 201
                                       59**************...*************************************4444.43.34565554.5678 PP

                                       HHHHHHHHHCHCCTTTSBSSBET....TSSB--HHHHHHHHHHHHHHCT-SSC--TTHHHHHHHHHHHHHCTSHHHH CS
                   Phage_integrase  79 llkellskaleeaeksellfask....rgkplsrqtvrkafkraveeagiekpltpHtlRhsfataLleagvdlrvv 151
                                       +l ++++ + ++++k+ ++ ++     +g+p++ +++++ +kr++++a+i+k+++ H +Rhs at+L +  + +  +
  gi|298674312|ref|YP_003726062.1| 202 ALGTWIEMHPNKNDKDAYVWINIgsrsKGQPMKYSSFQRLIKRTAKKANIDKNVHHHLFRHSRATELSQI-IEQPLL 277
                                       888999988778899999999888899***************************************9875.7***** PP

                                       HHHHT-SSCC.HHHHHHCCCH CS
                   Phage_integrase 152 qkllGHssis.ttqiYthvak 171
                                       +k++G+ + s +t++Y h+++
  gi|298674312|ref|YP_003726062.1| 278 EKFMGWVHGSgMTSVYLHLSD 298
                                       ******9977588*****976 PP

>> Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.1   2.7e-09   4.9e-06       3      82 ..      32     106 ..      30     108 .. 0.90
   2 ?   -3.1   0.0       5.5   9.8e+03      42      58 ..     130     146 ..     122     161 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 2.7e-09
                                       HHHHHHHHTT-S-HHHHHHHHHHHHHHHHHHHH.TS--TTT--HHHHHHHHHS----------HHHHHHHHHHHHHH CS
                   Phage_int_SAM_1   3 qfleyLikerglspnTlraYrrdLrrflkflaergkesleqlttedvraflaeleeeglsatslarrlsalrsFfqf 79 
                                       +f+++L+ + gl+   ++ Y  + +++++++ +    +l+ ++++dv + +  le++ ++ ++ + + +++++Ff++
  gi|298674312|ref|YP_003726062.1|  32 EFENRLF-AEGLETSRVLKYMSQMNMISRWFGK----NLADVDEKDVEQLVGSLERSSKKYSTKRDYKITIKKFFKW 103
                                       6777777.6778888899***************....*******************9988888888*********** PP

                                       HHH CS
                   Phage_int_SAM_1  80 lvr 82 
                                       l+r
  gi|298674312|ref|YP_003726062.1| 104 LYR 106
                                       *98 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.5
                                       TT--HHHHHHHHHS--- CS
                   Phage_int_SAM_1  42 eqlttedvraflaelee 58 
                                       + lt++d+ +++++  +
  gi|298674312|ref|YP_003726062.1| 130 DMLTPDDIKKMVDAAGN 146
                                       66888899888887665 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   3.9   1.5e-08   2.6e-05       4      26 .]     325     347 ..     324     347 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.5e-08
                       zf-ribbon_3   4 rCPnCGaplssddnvCpyCGtkl 26 
                                       +CP C++p+s+  + C++CG++l
  gi|298674312|ref|YP_003726062.1| 325 FCPFCDKPISPTSQLCTNCGKPL 347
                                       8******99***********997 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   3.6     1e-07   0.00018       1      23 []     325     347 ..     325     347 .. 0.98

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1e-07
                     zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCGtpl 23 
                                       fCp C ++++++++ C++CG pl
  gi|298674312|ref|YP_003726062.1| 325 FCPFCDKPISPTSQLCTNCGKPL 347
                                       9********************97 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   1.1   1.4e-07   0.00025       1      26 [.     326     351 ..     302     367 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.4e-07
                               DZR   1 CpqCgeelppdarfCseCgtklkava 26 
                                       Cp C ++++p ++ C +Cg++l+a++
  gi|298674312|ref|YP_003726062.1| 326 CPFCDKPISPTSQLCTNCGKPLNAET 351
                                       88888888888888888888887665 PP

>> Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.8   3.9e-06     0.007       5      80 ..      33     106 ..      29     111 .. 0.88
   2 !   10.4   0.6   0.00038      0.69       8      34 ..      79     105 ..      74     138 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.9e-06
                   Phage_int_SAM_4   5 frealrlaglserTiksYlsaikrflrflkkkapeeltkedieaYlnyLanerklsastqknalnalsffykkvle 80 
                                       f + l ++gl  + +  Y+s+ + + r++  k+ ++++++d+e+   +L ++ k ++st + ++  ++ f+k++ +
  gi|298674312|ref|YP_003726062.1|  33 FENRLFAEGLETSRVLKYMSQMNMISRWFG-KNLADVDEKDVEQLVGSLERSSK-KYSTKRDYKITIKKFFKWLYR 106
                                       66666777777778889*************.*******************8888.******************865 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00038
                   Phage_int_SAM_4   8 alrlaglserTiksYlsaikrflrflk 34 
                                        l+ + ++++T + Y+ +ik f ++l 
  gi|298674312|ref|YP_003726062.1|  79 SLERSSKKYSTKRDYKITIKKFFKWLY 105
                                       688999*******************95 PP

>> zf_C2H2_13  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.8     5e+03       4      12 ..     269     277 ..     268     280 .. 0.79
   2 ?    0.0   0.1      0.36   6.5e+02      20      28 ..     326     334 ..     318     338 .. 0.84
   3 ?   11.2   0.1   0.00012      0.21      19      34 ..     339     354 ..     337     357 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.8
                        zf_C2H2_13   4 trliedpLd 12 
                                       +++ie pL 
  gi|298674312|ref|YP_003726062.1| 269 SQIIEQPLL 277
                                       589**9985 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.36
                        zf_C2H2_13  20 CnkCGkPis 28 
                                       C  C kPis
  gi|298674312|ref|YP_003726062.1| 326 CPFCDKPIS 334
                                       999*****8 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00012
                        zf_C2H2_13  19 vCnkCGkPisleaivd 34 
                                       +C +CGkP+  e+ +d
  gi|298674312|ref|YP_003726062.1| 339 LCTNCGKPLNAETAID 354
                                       7*********999887 PP

>> PEP-utilisers_N  PEP-utilising enzyme, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00019      0.34      54      85 ..     352     385 ..     338     389 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00019
                                       H..T-HHHHHHHHHHHHHHT-HHHHHHHHHHHHH CS
                   PEP-utilisers_N  54 a..lgeeeaaifeahlmlleDpelleeveerIre 85 
                                       a  l e+++++ ++ ++l++Dpel + v+e+I e
  gi|298674312|ref|YP_003726062.1| 352 AidLDEKRKQVADVMQLLISDPELNQLVQEKISE 385
                                       2566677899**********************86 PP

>> DUF2116  Uncharacterized protein containing a Zn-ribbon (DUF2116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.2    0.0003      0.54       5      42 ..     325     369 ..     322     371 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0003
                           DUF2116   5 HCivCGkaIpldesfCsekCqe........eyekkrkkvarsqqil 42 
                                        C+ C k+I ++ ++C  +C +         +++krk+va  +q+l
  gi|298674312|ref|YP_003726062.1| 325 FCPFCDKPISPTSQLCT-NCGKplnaetaiDLDEKRKQVADVMQLL 369
                                       6***************7.5766122222223556777777777776 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.7   0.00027      0.48      57      86 .]     315     344 ..     298     344 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00027
                    zinc_ribbon_15  57 iekkessekkeCknCgkeveeefkyCpkCg 86 
                                        +k+ + + + C+ C+k +++ ++ C++Cg
  gi|298674312|ref|YP_003726062.1| 315 KSKEPALKPQFCPFCDKPISPTSQLCTNCG 344
                                       33334445899******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1066  (0.0594567); expected 358.6 (0.02)
Passed bias filter:                      699  (0.0389871); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2658.03
//
Query:       gi|298674313|ref|YP_003726063.1|  [L=91]
Description: hypothetical protein Metev_0342 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 593.73
//
Query:       gi|298674314|ref|YP_003726064.1|  [L=359]
Description: hypothetical protein Metev_0343 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.028   14.5   1.2       0.12   12.5   1.2    2.1  1  Plasmod_dom_1  Plasmodium protein of unknown function (Plasmo


Domain annotation for each model (and alignments):
>> Plasmod_dom_1  Plasmodium protein of unknown function (Plasmod_dom_1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.2   6.6e-06      0.12      11      33 ..      14      36 ..       8      43 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.6e-06
                     Plasmod_dom_1 11 difDnifidklidnnvqnkssei 33
                                      + fDnifi+ +i+nn   k+s++
  gi|298674314|ref|YP_003726064.1| 14 NSFDNIFIEETINNNNLRKQSQV 36
                                      78************998888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2586.96
//
Query:       gi|298674315|ref|YP_003726065.1|  [L=46]
Description: hypothetical protein Metev_0344 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.015   14.7   0.1      0.016   14.6   0.1    1.0  1  Diphthamide_syn  Putative diphthamide synthesis protein
      0.039   14.1   0.4      0.042   14.0   0.4    1.0  1  DUF3654          Protein of unknown function (DUF3654)
      0.095   12.7   0.1      0.095   12.7   0.1    1.2  1  ArsC             ArsC family


Domain annotation for each model (and alignments):
>> Diphthamide_syn  Putative diphthamide synthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   2.7e-06     0.016     235     271 ..       6      40 ..       1      42 [. 0.85

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.7e-06
                   Diphthamide_syn 235 keagkksylvlvgelnpakLanfaeidafVlvaCprl 271
                                       +  +kk ++  + el+ +kL +f++i+  V++aC +l
  gi|298674315|ref|YP_003726065.1|   6 N--KKKETIRELAELDSEKLTKFSDIEKAVILACREL 40 
                                       3..5677788899*********************987 PP

>> DUF3654  Protein of unknown function (DUF3654)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.4     7e-06     0.042      16      56 ..       1      43 [.       1      45 [. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7e-06
                           DUF3654 16 eeevlqkikeygesLc..tkekqeeiveaqkivcdaCkeiwer 56
                                      +ee+l+k ke  ++L   + ek+ +   ++k v+ aC+e+ ++
  gi|298674315|ref|YP_003726065.1|  1 MEEMLNKKKETIRELAelDSEKLTKFSDIEKAVILACRELVNK 43
                                      589************733689******************9876 PP

>> ArsC  ArsC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   1.6e-05     0.095       6      27 ..       3      25 ..       2      42 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.6e-05
                                      GCB-TTSHHHHHCT.CCCTTSBH CS
                                      xxxxxxxxxxxxxx.xxxxxxxx RF
                              ArsC  6 ellskrgttyreLn.ldkedlse 27
                                      e+l+k+++t+reL  ld e+l++
  gi|298674315|ref|YP_003726065.1|  3 EMLNKKKETIRELAeLDSEKLTK 25
                                      79************99***9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       918  (0.051202); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.34s 00:00:00.85 Elapsed: 00:00:00.55
# Mc/sec: 252.11
//
Query:       gi|298674316|ref|YP_003726066.1|  [L=87]
Description: putative transposase IS891/IS1136/IS1341 family [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.3e-13   47.6   0.0    1.3e-12   47.0   0.0    1.2  1  HTH_OrfB_IS605  Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.0   7.2e-17   1.3e-12       6      44 ..      12      50 ..       9      52 .. 0.91

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 7.2e-17
                    HTH_OrfB_IS605  6 ykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayee 44
                                       +  +yPTpeQe+kl  t++c+R ++N+ L+ + + y +
  gi|298674316|ref|YP_003726066.1| 12 LRLKIYPTPEQERKLDDTLECCRSIWNHLLSLQVDLYDR 50
                                      6789*****************************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.52
# Mc/sec: 505.32
//
Query:       gi|298674317|ref|YP_003726067.1|  [L=353]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-28   98.3   0.5    6.6e-28   97.4   0.2    1.6  2  OrfB_IS605      Probable transposase
    1.4e-26   92.2   1.1    2.9e-26   91.2   1.1    1.5  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0053   16.4   1.0        3.3    7.6   0.0    2.7  2  zinc_ribbon_2   zinc-ribbon domain
  ------ inclusion threshold ------
      0.028   14.4   1.9      0.061   13.3   1.9    1.6  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
      0.064   13.3   0.5       0.15   12.1   0.5    1.6  1  DZR             Double zinc ribbon
      0.071   11.6   0.1       0.11   11.0   0.1    1.1  1  DUF4503         Domain of unknown function (DUF4503)
      0.074   12.9   4.7       0.15   12.0   4.7    1.4  1  Remorin_C       Remorin, C-terminal region
       0.29   10.7   2.5        1.7    8.3   2.5    2.2  2  TF_Zn_Ribbon    TFIIB zinc-binding
       0.97    8.9   4.9          7    6.2   0.0    2.7  3  zf-ribbon_3     zinc-ribbon domain
        8.9    6.7  11.2         21    5.5  11.2    1.6  1  SLX9            Ribosome biogenesis protein SLX9


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.4   0.2   3.7e-31   6.6e-28       3     117 ..     111     222 ..     109     225 .. 0.97
   2 ?   -2.7   0.0       3.7   6.6e+03      22      50 ..     233     258 ..     232     279 .. 0.61

  Alignments for each domain:
  == domain 1  score: 97.4 bits;  conditional E-value: 3.7e-31
                        OrfB_IS605   3 pvevevelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklar 79 
                                        ve+++++++ ++++a+giDlG++ ++t+++ d   f+  +r+l++++k+lake+++l++   +skny+k+++k+ r
  gi|298674317|ref|YP_003726067.1| 111 TVELPENPTPSTPTNAVGIDLGLKSFITTSDDD---FVEPPRFLRKAEKRLAKEQRKLSKMEFRSKNYQKQKQKVNR 184
                                       6999999**************************...***************************************** PP

                        OrfB_IS605  80 lhrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       +hrk++  r+h+ h l++ l+++++ v+ e+L+++n+ 
  gi|298674317|ref|YP_003726067.1| 185 IHRKVASARNHFSHCLSKLLVEKYDLVVFEDLKIKNLI 222
                                       ***********************************986 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.7
                        OrfB_IS605  22 DlGinnLatvvtedgtwflykgrrlksdy 50 
                                       D+G n+L+  vt +       g+ +++ +
  gi|298674317|ref|YP_003726067.1| 233 DVGWNKLVQHVTYK---AAERGKIVDKVN 258
                                       66667776666666...444444444444 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.2   1.1   1.6e-29   2.9e-26       1      69 []     236     306 ..     236     306 .. 0.98

  Alignments for each domain:
  == domain 1  score: 91.2 bits;  conditional E-value: 1.6e-29
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke..alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       ++kl + + yka e+G+ v +vnp+yTS+ Cs+Cg+k+ke  +l++rtf+C+nCg+e+drD+nAaiNil +
  gi|298674317|ref|YP_003726067.1| 236 WNKLVQHVTYKAAERGKIVDKVNPNYTSQVCSHCGRKKKEklKLEDRTFYCSNCGLEIDRDLNAAINILTK 306
                                       99******************************************************************975 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.3    0.0037       6.7       2       8 ..     266     272 ..     257     276 .. 0.76
   2 !    7.6   0.0    0.0018       3.3       1      10 [.     285     294 ..     279     299 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0037
                     zinc_ribbon_2   2 CpnCGae 8  
                                       C++CG++
  gi|298674317|ref|YP_003726067.1| 266 CSHCGRK 272
                                       7777776 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0018
                     zinc_ribbon_2   1 fCpnCGaelq 10 
                                       +C+nCG e++
  gi|298674317|ref|YP_003726067.1| 285 YCSNCGLEID 294
                                       7888888875 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.9   3.4e-05     0.061      19      44 ..     264     290 ..     258     292 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.4e-05
                     Zn_Tnp_IS1595  19 fvCPhCgsr..kayriktrglfqCkeCr 44 
                                       +vC hCg +  +  ++++ + f C+ C+
  gi|298674317|ref|YP_003726067.1| 264 QVCSHCGRKkkEKLKLED-RTFYCSNCG 290
                                       79*****99889999998.********7 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.5   8.2e-05      0.15       1      22 [.     266     293 ..     256     302 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.2e-05
                               DZR   1 CpqCgee......lppdarfCseCgtkl 22 
                                       C++Cg++      l+++  +Cs+Cg ++
  gi|298674317|ref|YP_003726067.1| 266 CSHCGRKkkeklkLEDRTFYCSNCGLEI 293
                                       6666666666666666666666666554 PP

>> DUF4503  Domain of unknown function (DUF4503)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   5.9e-05      0.11     277     311 ..     260     294 ..     247     309 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.9e-05
                           DUF4503 277 afsWPvCdrCgsekleqspedrgafsCgsCssvvt 311
                                        +   vC++Cg +k e+ + ++++f+C++C   ++
  gi|298674317|ref|YP_003726067.1| 260 NYTSQVCSHCGRKKKEKLKLEDRTFYCSNCGLEID 294
                                       577789************************87766 PP

>> Remorin_C  Remorin, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   4.7   8.1e-05      0.15      39      79 ..     153     195 ..     151     201 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.1e-05
                         Remorin_C  39 kaeaelrkleeklEkk..rakaleklknklariekkAeekRas 79 
                                       kae++l+k ++kl k+  r+k+ +k k+k++ri++k + +R +
  gi|298674317|ref|YP_003726067.1| 153 KAEKRLAKEQRKLSKMefRSKNYQKQKQKVNRIHRKVASARNH 195
                                       9*************998899*******************9986 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1      0.14   2.5e+02      20      27 ..     264     271 ..     256     277 .. 0.74
   2 ?    8.3   2.5   0.00093       1.7       2      32 ..     265     296 ..     264     299 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.14
                                       EEESSSSB CS
                      TF_Zn_Ribbon  20 lvCtdCGl 27 
                                        vC+ CG 
  gi|298674317|ref|YP_003726067.1| 264 QVCSHCGR 271
                                       48999995 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00093
                                       EETTTTCEE.CHEETSTTCEEESSSSBEEEEC CS
                      TF_Zn_Ribbon   2 kCPnCgstn.lveDpergelvCtdCGlVledn 32 
                                       +C  Cg ++   +  e  +++C++CGl ++ +
  gi|298674317|ref|YP_003726067.1| 265 VCSHCGRKKkEKLKLEDRTFYCSNCGLEIDRD 296
                                       6888888664444455568********99865 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.2       4.5   8.1e+03       8      14 ..      24      29 ..      24      30 .. 0.69
   2 ?    4.3   0.2     0.015        27      17      23 ..     264     270 ..     262     273 .. 0.76
   3 ?    6.2   0.0    0.0039         7       2       9 ..     283     290 ..     282     298 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4.5
                       zf-ribbon_3  8 CGaplss 14
                                      CG++ ss
  gi|298674317|ref|YP_003726067.1| 24 CGNN-SS 29
                                      8987.65 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.015
                       zf-ribbon_3  17 nvCpyCG 23 
                                       +vC +CG
  gi|298674317|ref|YP_003726067.1| 264 QVCSHCG 270
                                       6788888 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0039
                       zf-ribbon_3   2 tvrCPnCG 9  
                                       t +C+nCG
  gi|298674317|ref|YP_003726067.1| 283 TFYCSNCG 290
                                       67999999 PP

>> SLX9  Ribosome biogenesis protein SLX9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  11.2     0.012        21       5      60 ..     152     219 ..     149     286 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.012
                              SLX9   5 sKkdKrkiKheaflsKieksisksaskkkkkrkrrpskklvtdlesLadaLpdle..............e 60 
                                        K +Kr++K ++ lsK+e   ++++ +k+k++ +r   k+++  + +   L +l               +
  gi|298674317|ref|YP_003726067.1| 152 RKAEKRLAKEQRKLSKMEF--RSKNYQKQKQKVNRIHRKVASARNHFSHCLSKLLvekydlvvfedlkiK 219
                                       699****************..9999999999999999999998888888888766555555555555550 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1491  (0.0831614); expected 358.6 (0.02)
Passed bias filter:                      702  (0.0391544); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 2148.16
//
Query:       gi|298674318|ref|YP_003726068.1|  [L=130]
Description: glyoxalase/bleomycin resistance protein/dioxygenase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-18   66.3   0.0    3.3e-18   66.1   0.0    1.0  1  Glyoxalase       Glyoxalase/Bleomycin resistance protein/Diox
    1.6e-11   44.5   0.0      2e-11   44.1   0.0    1.1  1  Glyoxalase_4     Glyoxalase/Bleomycin resistance protein/Diox
    0.00098   19.0   0.3      0.015   15.3   0.3    2.1  1  Glyoxalase_2     Glyoxalase-like domain
     0.0018   18.4   0.0     0.0024   18.0   0.0    1.2  1  Glyoxalase_3     Glyoxalase-like domain
  ------ inclusion threshold ------
       0.06   12.6   0.0      0.071   12.3   0.0    1.0  1  Arabinose_Isome  L-arabinose isomerase
      0.069   13.2   0.0         12    6.2   0.0    2.6  2  TPR_7            Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.1   0.0   1.1e-21   3.3e-18       1     128 []       4     123 ..       4     123 .. 0.95

  Alignments for each domain:
  == domain 1  score: 66.1 bits;  conditional E-value: 1.1e-21
                                       EEEEEEEEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCTSEEE CS
                        Glyoxalase   1 gidhvallvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkieetvhhv 77 
                                       +idhv ++ +d ek+l+FY++vL+fkl  + +   + + + ia+++ g++++el+  e  + + + ++       + 
  gi|298674318|ref|YP_003726068.1|   4 RIDHVEIIPTDFEKALNFYQDVLNFKLWQRQE-VDMPPLQQIAYLTLGDTMLELLQVEGNKESIVNYWG-----IGY 74 
                                       69*************************99999.7888****************************9955.....568 PP

                                       EEEEEEHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSEEEEE CS
                        Glyoxalase  78 afialdvedvgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGillei 128
                                         +al+v+d ++a+++l+ + vkv+ +p + + +++    ++DpdGi +e+
  gi|298674318|ref|YP_003726068.1|  75 RMMALEVDDMDEAVEYLENQNVKVTWGPIDLGGTKRAE--IQDPDGISIEL 123
                                       9***************************9999999997..9*******996 PP

>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.0   6.8e-15     2e-11       1     101 [.       6     106 ..       6     112 .. 0.88

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 6.8e-15
                                       EEEEEE-S-HHHHHHHHHH.TT-EESS--E..EETTTTEEEEEEEETTEEEEEEEESSTT-THHH.TS-EEEEEEEE CS
                      Glyoxalase_4   1 dQigivVeDleaavarfsallGvgpwqryr.depqevdlafallgsgsvqieLieplegpeflae.hgeglhhlayw 75 
                                       d+++i+ +D+e+a+++++++l+++ wqr++ d+p   ++a ++lg++  ++eL +   ++e++ +  g g    a++
  gi|298674318|ref|YP_003726068.1|   6 DHVEIIPTDFEKALNFYQDVLNFKLWQRQEvDMPPLQQIAYLTLGDT--MLELLQVEGNKESIVNyWGIGYRMMALE 80 
                                       6*************************997735666677888999995..9********99887777*********** PP

                                       ES-HHHHHHHHCTTTEEEEEEEE-GG CS
                      Glyoxalase_4  76 vddldaavarleeqGfevvqkgvrag 101
                                       vdd+d+av+ le+q ++v+   +  g
  gi|298674318|ref|YP_003726068.1|  81 VDDMDEAVEYLENQNVKVTWGPIDLG 106
                                       ******************99776665 PP

>> Glyoxalase_2  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.3   4.9e-06     0.015       7     114 ..      11     124 ..       5     127 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.9e-06
                                       EES-HHHHHHHHHHTT---EEEE-S......SEEEETTS-EEEEHHHHHH--...-----S..--SS-EEEEEES-H CS
                      Glyoxalase_2   7 vvkdieeskkFYedvlelkikldfG......envsfetgfalkedlkelinl...desiae..qsnnfeLyFevedv 72 
                                       +  d+e++ +FY+dvl+ k+ +         + + +   ++l + + el+++   +esi +        +  ev+d+
  gi|298674318|ref|YP_003726068.1|  11 IPTDFEKALNFYQDVLNFKLWQRQEvdmpplQQIAY---LTLGDTMLELLQVegnKESIVNywGIGYRMMALEVDDM 84 
                                       56799***********99986543300101133333...3555666666655211334433334444567789**** PP

                                       HHHHHHH..GGGS-EEEEEEE-TTS-EEEEEE-TT--EEEEE CS
                      Glyoxalase_2  73 daflqklkeaeniellhelkekpWgqrvirfyDpDkhiiEig 114
                                       d++++ l e++n+++   ++    g + + + DpD+  iE+ 
  gi|298674318|ref|YP_003726068.1|  85 DEAVEYL-ENQNVKVTWGPIDLG-GTKRAEIQDPDGISIELR 124
                                       *******.6777******99876.666689******999986 PP

>> Glyoxalase_3  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0     8e-07    0.0024       1     113 [.       5     109 ..       5     127 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 8e-07
                      Glyoxalase_3   1 lDHvvlavpdleeaaarfarrlGftvtpggehp.glgtaNalvmfgdgYlEllavdpeapaperprlfgldrlakge 76 
                                       +DHv ++  d e+a + +++ l+f++ ++ e   +   + a + +gd+ lEll+v+ ++++    + +       g 
  gi|298674318|ref|YP_003726068.1|   5 IDHVEIIPTDFEKALNFYQDVLNFKLWQRQEVDmPPLQQIAYLTLGDTMLELLQVEGNKES--IVNYW-------GI 72 
                                       7*************************9988766222455556666999*******999998..33333.......78 PP

                      Glyoxalase_3  77 glhtlalrtddidataarlraaGvdeagrrvrpdggd 113
                                       g  ++al++dd+d++++ l+++ v+++ +++++ g++
  gi|298674318|ref|YP_003726068.1|  73 GYRMMALEVDDMDEAVEYLENQNVKVTWGPIDLGGTK 109
                                       99*********************99777777766643 PP

>> Arabinose_Isome  L-arabinose isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.4e-05     0.071     157     224 ..      28      97 ..       9     102 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.4e-05
                                       HHHHHHHHHHHHHHTT-EEEEES---TT-STT---HHHHHH..HH--EEEEE-HHHHHHHHHTS-HHHHH CS
                   Arabinose_Isome 157 iaawaraaaavaeskklkvarfgdnmrevavteGdkveaei..klGvsvntygvgdlvevveavsdeevd 224
                                       ++ w+r  + +  ++++  + +gd+m e+  +eG+k ++     +G+++ +++v+d+ e+ve +++++v+
  gi|298674318|ref|YP_003726068.1|  28 FKLWQRQEVDMPPLQQIAYLTLGDTMLELLQVEGNKESIVNywGIGYRMMALEVDDMDEAVEYLENQNVK 97 
                                       67899999***************************98876511678999999*************99997 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.014        42      14      27 ..      14      27 ..      13      35 .. 0.82
   2 ?    6.2   0.0    0.0041        12      12      24 ..      81      93 ..      77     113 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.014
                             TPR_7 14 dyeeAielyeqsLa 27
                                      d+e+A+ +y+ +L 
  gi|298674318|ref|YP_003726068.1| 14 DFEKALNFYQDVLN 27
                                      8********98775 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0041
                             TPR_7 12 lGdyeeAielyeq 24
                                      + d++eA+e++e 
  gi|298674318|ref|YP_003726068.1| 81 VDDMDEAVEYLEN 93
                                      679********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 825.49
//
Query:       gi|298674319|ref|YP_003726069.1|  [L=142]
Description: putative cytoplasmic protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.14   12.5   0.1       0.17   12.3   0.1    1.2  1  FA_hydroxylase  Fatty acid hydroxylase superfamily


Domain annotation for each model (and alignments):
>> FA_hydroxylase  Fatty acid hydroxylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   9.3e-06      0.17      87     126 ..      81     119 ..      33     127 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.3e-06
                    FA_hydroxylase  87 HsglhvslgwllerllatpraHrlHHskneegnfgvllsl 126
                                       ++    +++ + + +l ++ +H+ H s+  ++n+g ++++
  gi|298674319|ref|YP_003726069.1|  81 FML-VSRYKLVFPEWLGSKDFHDSHKSNLLRKNYGYYSRF 119
                                       333.35566666899********************99877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 963.43
//
Query:       gi|298674320|ref|YP_003726070.1|  [L=99]
Description: heterotrimeric replication protein A subunit [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.38
# Mc/sec: 786.44
//
Query:       gi|298674321|ref|YP_003726071.1|  [L=195]
Description: hypothetical protein Metev_0350 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.027   14.9   0.1       0.87   10.0   0.0    2.1  2  Syntaxin_2  Syntaxin-like protein


Domain annotation for each model (and alignments):
>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   4.8e-05      0.87      27      60 ..       2      35 ..       1      57 [. 0.91
   2 ?    2.9   0.0    0.0079   1.4e+02      10      39 ..     158     187 ..     154     192 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 4.8e-05
                        Syntaxin_2 27 dteelreklhelieeinelikktnellkklsqld 60
                                      d++ l++++++ ++++n+ ++++  llk++++l 
  gi|298674321|ref|YP_003726071.1|  2 DNQSLKQQIEDACNNLNQFFNNIAVLLKDCDRLM 35
                                      89***************************99886 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.0079
                        Syntaxin_2  10 snvstleklvkqLgtkkdteelreklheli 39 
                                       +nv++++++   Lg+ k+t++++ k+ e  
  gi|298674321|ref|YP_003726071.1| 158 KNVKEIKSFAYPLGNIKNTTDIKGKIIERL 187
                                       6999*******************9997765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1592.87
//
Query:       gi|298674322|ref|YP_003726072.1|  [L=302]
Description: hypothetical protein Metev_0351 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2005.66
//
Query:       gi|298674323|ref|YP_003726073.1|  [L=630]
Description: hypothetical protein Metev_0352 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.8e-17   62.0   2.5    3.9e-08   33.2   0.0    3.3  4  UvrD-helicase    UvrD/REP helicase N-terminal domain
    1.5e-14   54.6   0.0    1.9e-13   51.0   0.0    2.5  3  AAA_19           AAA domain
      5e-08   32.6   0.0    1.2e-07   31.5   0.0    1.6  1  UvrD_C_2         UvrD-like helicase C-terminal domain
    2.4e-07   31.2   0.2    6.2e-07   29.9   0.2    1.7  1  NERD             Nuclease-related domain
    2.5e-07   30.7   0.1       0.15   11.7   0.0    3.6  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    2.8e-06   27.4   0.6    8.3e-05   22.7   0.1    2.5  2  ResIII           Type III restriction enzyme, res subunit
    1.3e-05   25.0   1.0    8.3e-05   22.3   0.1    2.6  2  AAA_12           AAA domain
      3e-05   23.6   0.2      3e-05   23.6   0.2    2.7  3  UvrD_C           UvrD-like helicase C-terminal domain
    4.6e-05   22.8   0.0    0.00016   21.1   0.0    1.9  2  DUF2075          Uncharacterized conserved protein (DUF2075)
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.042   13.6   0.0    1.9  2  DEAD             DEAD/DEAH box helicase
      0.036   13.2   0.1      0.085   12.0   0.0    1.6  2  DAP3             Mitochondrial ribosomal death-associated pro
       0.05   13.9   0.0       0.38   11.0   0.0    2.4  2  AAA_22           AAA domain
      0.053   13.2   0.0      0.085   12.6   0.0    1.4  1  AAA_30           AAA domain
      0.063   12.7   0.0       0.17   11.3   0.0    1.8  1  PhoH             PhoH-like protein
      0.067   12.5   0.0       0.12   11.7   0.0    1.4  1  ATPase           KaiC


Domain annotation for each model (and alignments):
>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.1   2.5e+03     259     265 ..      52      58 ..      46     144 .. 0.69
   2 !   27.0   0.0   2.4e-09   2.9e-06       3     105 ..     220     311 ..     218     317 .. 0.81
   3 !   33.2   0.0   3.3e-11   3.9e-08     248     297 ..     332     388 ..     320     389 .. 0.93
   4 ?   -1.5   0.1       1.2   1.4e+03     146     160 ..     501     515 ..     419     604 .. 0.57

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.1
                                       EEEESSG CS
                     UvrD-helicase 259 eiliDEy 265
                                       +iliDEy
  gi|298674323|ref|YP_003726073.1|  52 FILIDEY 58 
                                       5666666 PP

  == domain 2  score: 27.0 bits;  conditional E-value: 2.4e-09
                                       HHHHHHHHS.-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHHCCHHCTT CS
                     UvrD-helicase   3 peqreaias.lggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRieealkkaeqessd 78 
                                       ++q++  +  + g+ +v+  +GsGKT +l++r ++l +e+     +il++T+ +     lk++++++lk+       
  gi|298674323|ref|YP_003726073.1| 220 TDQEKFSKRiPYGHYMVSGVPGSGKTVILVARAVHLAREN--PEWNILILTYNRS----LKSKLKNILKSMH----- 285
                                       5666666666778999********************9999..8899******975....6666666666543..... PP

                                       -HHHHHHHHHCTTSEEEEHHHHHHHHH CS
                     UvrD-helicase  79 derlrlalqnlseanisTlHsfcqkil 105
                                        + l +   n ++++is +H+ + k+ 
  gi|298674323|ref|YP_003726073.1| 286 -KDLDNMGVNYENIEISSFHKTAMKVA 311
                                       .35778999************999875 PP

  == domain 3  score: 33.2 bits;  conditional E-value: 3.3e-11
                                       HHHHHHHHHSSEEEESSGGG-BHHHHHHHHHHHTTTTT.......EEEEE-GGG--G CS
                     UvrD-helicase 248 elaealrerykeiliDEyQDTnkiQyrilkllasghee.......lfmvGDpkQsIY 297
                                       ++ +++++ y+ +liDEyQD  +i  ++  +l+++he+       lf+ GD  QsIY
  gi|298674323|ref|YP_003726073.1| 332 KAINNVESMYDAVLIDEYQDFHNIWLKLCLKLCRKHEYkgeytenLFLAGDRLQSIY 388
                                       678999******************************99******************* PP

  == domain 4  score: -1.5 bits;  conditional E-value: 1.2
                                       TTTHHHHHHHHHHHH CS
                     UvrD-helicase 146 slnldkkkleklike 160
                                       +l+ d +k+ +++k+
  gi|298674323|ref|YP_003726073.1| 501 YLDEDLQKMAEVSKN 515
                                       222233333322222 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       4.2     5e+03     100     115 ..      48      62 ..      31      67 .. 0.76
   2 !   51.0   0.0   1.6e-16   1.9e-13       7     143 ..     228     388 ..     222     390 .. 0.83
   3 ?   -0.1   0.0      0.87     1e+03      57      92 ..     511     546 ..     466     604 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.2
                            AAA_19 100 lqeeellivDEfqdvd 115
                                       l e + +++DE+  ++
  gi|298674323|ref|YP_003726073.1|  48 L-EPDFILIDEYKGIS 62 
                                       5.67799****98876 PP

  == domain 2  score: 51.0 bits;  conditional E-value: 1.6e-16
                            AAA_19   7 alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae............atT 71 
                                        ++ ++ +v + pG+GKT +l+++  +l +++ +   +il++++++   ++l++ l+++ ++            ++ 
  gi|298674323|ref|YP_003726073.1| 228 RIPYGHYMVSGVPGSGKTVILVARAVHLARENPE--WNILILTYNRSLKSKLKNILKSMHKDldnmgvnyenieISS 302
                                       56678899***********************955..8*******************999999*************** PP

                            AAA_19  72 iHrlal..............ldfddlltealelleeaeeekklqeee.llivDEfqdvdelqyrLlkallgekkk.. 131
                                       +H+ a+                       + ell +++ + ++++ + ++++DE+qd      +L  +l+ ++++  
  gi|298674323|ref|YP_003726073.1| 303 FHKTAMkvanettipkptpdN-------YWDELLPYKAIN-NVESMYdAVLIDEYQDFHNIWLKLCLKLCRKHEYkg 371
                                       ****99888887765443322.......334444454444.4446666******************99995554479 PP

                            AAA_19 132 .....lllvGDpdQliy 143
                                            l+l GD+ Q+iy
  gi|298674323|ref|YP_003726073.1| 372 eytenLFLAGDRLQSIY 388
                                       9999************9 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.87
                            AAA_19  57 elrerlaalgaeatTiHrlalldfddlltealelle 92 
                                       e++++++  ++ +tT+H+   ++ +  +  ++  le
  gi|298674323|ref|YP_003726073.1| 511 EVSKNISDNLMTITTYHSSKGVECKVCVLAEVDKLE 546
                                       344444444455999998765444444433333333 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   9.8e-11   1.2e-07       3      51 ..     522     572 ..     520     572 .. 0.88

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 9.8e-11
                          UvrD_C_2   3 yaltihkaQGsefpaVivfdpdlaaarmgel..rrrlLYtavTRAreklil 51 
                                       +++t h ++G e ++ +++++d  +   ++   + +lLY+++TRA+ek+++
  gi|298674323|ref|YP_003726073.1| 522 TITTYHSSKGVECKVCVLAEVDKLENSKMDNtkYTKLLYVGMTRASEKVMI 572
                                       689*******************77776444479***************976 PP

>> NERD  Nuclease-related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.2   5.2e-10   6.2e-07       4     107 ..      17     132 ..      14     133 .. 0.70

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 5.2e-10
                              NERD   4 egEravakeLkelked.eylvlhdvrlrpg.tg.eiDhlvispk.gifviEvKnwsG.wifgd..kegrwtqkikkg 73 
                                       +gEr+va+ +k+  +d +++ +  ++++p  ++ e D+++i ++ gi +iEvK ws  +i  +  +  + + + +++
  gi|298674323|ref|YP_003726073.1|  17 YGERKVANKIKQIYSDvDWKAY--LYVQPSiSNlEPDFILIDEYkGISIIEVKDWSLdKIDISklNPAEVFVS-GHR 90 
                                       79*********66445566633..5555555448**********9***********76777776544445555.455 PP

                              NERD  74 fknpleqakrhakalkksl........lekgkgvpvesvvvf 107
                                        +np+ +a+ + +++k++l        ++   +++v+s +vf
  gi|298674323|ref|YP_003726073.1|  91 RENPFSKANTYFNTVKNRLqkepelidEDYSLKYQVYSNLVF 132
                                       56*************999965554443323333366666666 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00013      0.15       2      39 ..     235     270 ..     234     295 .. 0.71
   2 !    6.7   0.0    0.0044       5.2      60     153 ..     339     438 ..     299     464 .. 0.68
   3 !    8.1   0.0    0.0016         2     172     232 ..     511     572 ..     482     574 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                   Viral_helicase1   2 vvhGvpGcGKStlirkllrtsliltvnrptaelltegk 39 
                                       +v+GvpG+GK+ +++  + +    ++n++ ++l+    
  gi|298674323|ref|YP_003726073.1| 235 MVSGVPGSGKTVILVARAVH--LARENPEWNILILTYN 270
                                       79************999988..6666776666655554 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0044
                   Viral_helicase1  60 stkgkililDEylllhaGyilllaal........skaklvilfGDplQipfhsrnasfllahlpsslshrvg.rrtt 127
                                       s  ++ +++DEy+  h   ++l+++l        +  ++++l GD+lQ+ +++  +   +++l  ++  r++  +t 
  gi|298674323|ref|YP_003726073.1| 339 S-MYDAVLIDEYQDFHNIWLKLCLKLcrkheykgEYTENLFLAGDRLQSIYNPSTH--NWKSLGIHIRGRSKlLKTS 412
                                       3.48899999999999877777766522112211234689********99997555..5555555554444413455 PP

                   Viral_helicase1 128 yllpsdvaeilsakvgteveversge 153
                                       y+ +s  +++  +  ++++++ +++e
  gi|298674323|ref|YP_003726073.1| 413 YRSGSTHINLALEYLMKNSNTRSEVE 438
                                       77777777777777444444444444 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0016
                   Viral_helicase1 172 ftqalkealgvrevttvhevqGltfdkVtlvllketdlelis..esrenllvAlTRhrkslvi 232
                                       ++ ++ ++   + +tt+h+  G ++++++l   ++ +++ +   +    l+v++TR+ ++++i
  gi|298674323|ref|YP_003726073.1| 511 EVSKNISDNLMT-ITTYHSSKGVECKVCVLAEVDKLENSKMDntKYTKLLYVGMTRASEKVMI 572
                                       444444444455.9************99998665544444445566899**********9987 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1   6.9e-08   8.3e-05      21     140 ..     214     348 ..     191     362 .. 0.70
   2 ?    2.6   0.1       0.1   1.2e+02      50     121 ..     478     552 ..     468     580 .. 0.63

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 6.9e-08
                                       ........TTS........EEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG... CS
                            ResIII  21 s......krdk........rglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayk 83 
                                       +      +++k        ++++    G+GKT+++++ + +l+++++e ++l+l  ++sl +++++ +k++ ++ ++
  gi|298674323|ref|YP_003726073.1| 214 IiktldtDQEKfskripygHYMVSGVPGSGKTVILVARAVHLARENPEWNILILTYNRSLKSKLKNILKSMHKDLDN 290
                                       0444443333344556677999*************99999999999999****************999999988753 PP

                                       .GEEEESSS-B--.......-SEEEEEHHHHHHTH..............HHHTTT-SEEEEET CS
                            ResIII  84 eigkkvsgdkkkakekdstnkkilvttiqsldadseee......eeeseellrdrfdviiiDE 140
                                         g ++++ + ++     +++ + v+++ ++ ++ + +       ++   + ++ +d ++iDE
  gi|298674323|ref|YP_003726073.1| 291 -MGVNYENIEISS----FHKTAMKVANETTIPKPTPDNywdellPYKAINNVESMYDAVLIDE 348
                                       .444444444444....7778888888888888885545544443333344444444777777 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.1
                                       S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--..........-SE.EEEEHHHHHHTH... CS
                            ResIII  50 kkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkka...kekdstnkki.lvttiqsldadseee 121
                                       ++++ e +l+l p k+l +++++ + + l++ + e++k++s++  ++   ++++  ++k+ +++++++l ++++ +
  gi|298674323|ref|YP_003726073.1| 478 SQYNPEDILVLLPFKNLRDKLYRYLDEDLQKMA-EVSKNISDNLMTIttyHSSKGVECKVcVLAEVDKLENSKMDN 552
                                       3444559**************966655555543.355555555555544422333334441456677777766544 PP

>> AAA_12  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.51   6.1e+02      94     139 ..     245     289 ..     182     306 .. 0.64
   2 !   22.3   0.1   6.9e-08   8.3e-05      93     194 ..     465     572 ..     408     576 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.51
                            AAA_12  94 lvvklvekllkkgseeerkkigvitpYraqvellkkklkekeeeks 139
                                       +v+ + ++++ + ++  + +i ++t  r+ ++ lk+ lk+ +++ +
  gi|298674323|ref|YP_003726073.1| 245 TVILVARAVHLARENP-EWNILILTYNRSLKSKLKNILKSMHKDLD 289
                                       4444445555555555.68999999999999999999987555543 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 6.9e-08
                            AAA_12  93 elvvklvekllkkgseeerkkigvitpYraqvellkkklkekeeekseke.......ievntvdgfQGrekdviils 162
                                       + + +++++l+ + + +  ++i v+ p+++  + l + l+e+ ++  e +       +++ t  +  G e++v +l 
  gi|298674323|ref|YP_003726073.1| 465 REINDYLKSLIYESQYN-PEDILVLLPFKNLRDKLYRYLDEDLQKMAEVSknisdnlMTITTYHSSKGVECKVCVLA 540
                                       56777888888887777.8*********************988876555588999********************** PP

                            AAA_12 163 lVRsnekkeigflkderrlNValTRAksklii 194
                                        V + e++++   k  + l V +TRA +k++i
  gi|298674323|ref|YP_003726073.1| 541 EVDKLENSKMDNTKYTKLLYVGMTRASEKVMI 572
                                       *****************************998 PP

>> UvrD_C  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.7      0.48   5.8e+02     257     294 ..     270     305 ..      62     307 .. 0.81
   2 ?    1.7   0.1      0.11   1.3e+02       3      93 ..     409     503 ..     407     512 .. 0.60
   3 !   23.6   0.2   2.5e-08     3e-05     270     345 ..     504     573 ..     465     576 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.48
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                            UvrD_C 257 eeeveeklneileiatLseseleeskkk.ekipiiTiHq 294
                                       + + + kl++il+     +++l+++  + e+i+i++ H+
  gi|298674323|ref|YP_003726073.1| 270 NRSLKSKLKNILKSM---HKDLDNMGVNyENIEISSFHK 305
                                       344556677887777...666667777778888888887 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.11
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                            UvrD_C   3 LekNyRStksLlkaankflenilnrralekek........ktvekgekivvleaeteeeEaekiaatikall.ekne 70 
                                       L++ yRS ++ +++a ++l ++ n r++  ek          + ++e+ v       +   + i + +k+l  e + 
  gi|298674323|ref|YP_003726073.1| 409 LKTSYRSGSTHINLALEYLMKNSNTRSE-VEKfyegkdgiCCNYDTENNVDFL----NGDFREINDYLKSLIyESQY 480
                                       7889***********9999777776222.223311223332222222212222....23334444444444455568 PP

                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C  71 klediavLvRsnkdadkiskaLk 93 
                                       + edi vL   ++  dk+ + L 
  gi|298674323|ref|YP_003726073.1| 481 NPEDILVLLPFKNLRDKLYRYLD 503
                                       88999999999988888888776 PP

  == domain 3  score: 23.6 bits;  conditional E-value: 2.5e-08
                                       xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 270 iatLseseleeskkk.ekipiiTiHqAKGlEFdvVflagleegtfPsyrskkekrleEEkRlfYVaiTRAkkrLfis 345
                                       +  L+++ + + ++  +  +i+T H++KG E  v +la++++ +  ++ ++k        +l+YV++TRA ++++i 
  gi|298674323|ref|YP_003726073.1| 504 ED-LQKMAEVSKNISdNLMTITTYHSSKGVECKVCVLAEVDKLENSKMDNTKY------TKLLYVGMTRASEKVMIQ 573
                                       44.55655555555568999*******************98877776666665......89***********99986 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.3e-07   0.00016       4      75 ..     234     308 ..     232     378 .. 0.75
   2 ?   -1.7   0.0       1.1   1.3e+03      42     122 ..     493     566 ..     479     573 .. 0.56

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.3e-07
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakke...ekkkkkeafeklssfinnls 75 
                                       ++V+Gv+G+GKtv+l++ ++ l +++ e +  +l+ N++l  +l++ l++      ++  + +  + ssf +++ 
  gi|298674323|ref|YP_003726073.1| 234 YMVSGVPGSGKTVILVARAVHLARENPEWNILILTYNRSLKSKLKNILKSMHkdlDNMGVNYENIEISSFHKTAM 308
                                       68********************88888888888999********9999877744433444444444444444433 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.1
                           DUF2075  42 plvlvlrealakke.ekkkkkeafeklssfinnlsefkkaeekkeepkedvvivDEAhrlltksdqaekqseenqlk 117
                                       +l+++l++ l+++  +  + ++++++    i++       +++ +  +++v +  E  +l +++   ++++++  + 
  gi|298674323|ref|YP_003726073.1| 493 NLRDKLYRYLDEDLqKMAEVSKNISDNLMTITT-------YHSSKGVECKVCVLAEVDKLENSKMD-NTKYTKLLYV 561
                                       667777777777772223333333333333333.......44777778888888888888884444.4444444444 PP

                           DUF2075 118 elmkr 122
                                        + ++
  gi|298674323|ref|YP_003726073.1| 562 GMTRA 566
                                       44444 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.5e-05     0.042       8     133 ..     226     352 ..     219     372 .. 0.76
   2 ?   -1.6   0.0       1.7     2e+03      51      83 ..     486     517 ..     470     559 .. 0.46

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.5e-05
                                       HHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST.SEEE.EEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxx RF
                              DEAD   8 iplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyid.lrvl.lii 82 
                                        + i   g+ +v++  GsGKT + +  +++     +++++  +li++  r+L  +  n lk++ k +d + v+   i
  gi|298674323|ref|YP_003726073.1| 226 SKRIPY-GHYMVSGVPGSGKTVILVARAVHLA---RENPEWNILILTYNRSLKSKLKNILKSMHKDLDnMGVNyENI 298
                                       555553.47899999********999999655...589999************************877644443346 PP

                                       TTSSHHHHHHHHHTTCSEEEEEHHHHHH.HHHCTSSH..CTTEEEEEEETHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx..xxxxxxxxxxxxxxx RF
                              DEAD  83 ggvaardqlskldngvdivvgtpgrldd.llstgkln..lsqvrflVlDEadrl 133
                                       + ++ ++   k+ n++ i   tp+   d ll  + +n   s    + +DE + +
  gi|298674323|ref|YP_003726073.1| 299 EISSFHKTAMKVANETTIPKPTPDNYWDeLLPYKAINnvESMYDAVLIDEYQDF 352
                                       667788888888899999999999988856654554432333466888887665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.7
                                       EEEESSHHHHHHHHHHHHHHTTTSTSEEEEEET CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  51 livePtreLaeqtlnnlkkfkkyidlrvlliig 83 
                                       l++ P + L  + ++ l + ++++  +v+  i+
  gi|298674323|ref|YP_003726073.1| 486 LVLLPFKNLRDKLYRYLDEDLQKMA-EVSKNIS 517
                                       5555555555555554444444322.2222222 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.1e-05     0.085      11      66 ..     215     276 ..     204     289 .. 0.68
   2 ?   -3.3   0.0       3.2   3.8e+03     135     176 ..     510     556 ..     496     558 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.1e-05
                                       HHHHTTS....-SSS---EEEEE-SSSSSTTTTH.HHHHHHGGGS.--EEEEES-GGGGTSS CS
                              DAP3  11 ikklkka....dkkkkvkrlvltGekgsGKSvlL.lqalayAlek.gwvvlhvpeaedlvng 66 
                                       ik+l+ +    +k  +   ++++G +gsGK+v L + a++ A e+ +w +l + + ++l  +
  gi|298674323|ref|YP_003726073.1| 215 IKTLDTDqekfSKRIPYGHYMVSGVPGSGKTVILvARAVHLARENpEWNILILTYNRSLKSK 276
                                       555554431123334556899**********976379*******998988877776666555 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.2
                                       SSSHHHHHHHHHHHHHHHTT....SS--EEEEEE-G.GGGSS-BS-- CS
                              DAP3 135 aksawdvfqallkeLkaqsk....grvpvlvtvDgl.nallkntkyk 176
                                       a++++++ + l++  + +s+     +v vl  vD l n+ ++ntky+
  gi|298674323|ref|YP_003726073.1| 510 AEVSKNISDNLMTITTYHSSkgveCKVCVLAEVDKLeNSKMDNTKYT 556
                                       44455555566655555555666667778888888834567778886 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00032      0.38       6     114 ..     232     362 ..     229     382 .. 0.65
   2 ?   -1.0   0.0       1.6     2e+03      92     129 ..     534     562 ..     469     570 .. 0.49

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00032
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka............ 70 
                                       g+ +v G +G+GKT+ l   +  l  ++++e+ +  +++++ + ++++k++l+ + ++l++ + +            
  gi|298674323|ref|YP_003726073.1| 232 GHYMVSGVPGSGKTVILVARAVHLA-RENPEW-NILILTYNRSLKSKLKNILKSMHKDLDNMGVNyenieissfhkt 306
                                       7899**********86543333331.222222.44444555555555555555555555544444888888888888 PP

                            AAA_22  71 ..............erlsseell.ealeqalraravielliiDEaqhlrseealeeLrs 114
                                                     + +  +ell  +  +++++ ++  +++iDE q + ++  l+ + +
  gi|298674323|ref|YP_003726073.1| 307 amkvanettipkptPDNYWDELLpYKAINNVESMYD--AVLIDEYQDF-HNIWLKLCLK 362
                                       888888888877766667777776666666666666..8999999988.6555555544 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.6
                            AAA_22  92 ielliiDEaqhlrseealeeLrsllnlsrkgvqliLvG 129
                                        ++ ++ E+++l         +++ n  +k ++l++vG
  gi|298674323|ref|YP_003726073.1| 534 CKVCVLAEVDKLE-------NSKMDN--TKYTKLLYVG 562
                                       3666666666663.......123333..4555555555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   7.1e-05     0.085       2     127 ..     218     385 ..     217     449 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.1e-05
                            AAA_30   2 lnaeQaaavealltsgdrvavltGpAGtGKttalkal.reaweaa.ggrviglAptgkaAkvLa............. 63 
                                       l+++Q++  +++  ++    ++ G++G+GKt +l a  +++++++ + ++++l+ +     +L+             
  gi|298674323|ref|YP_003726073.1| 218 LDTDQEKFSKRIPYGH---YMVSGVPGSGKTVILVARaVHLARENpEWNILILTYNRSLKSKLKnilksmhkdldnm 291
                                       5667777777665555...589**********997762555555556999999999999999995555555555332 PP

                            AAA_30  64 ....eelgieastiakllkrlk..........................grarlepg.tllivDEagmvdtkqlaall 109
                                           e+  ie s+ +k     +                          + +++e+  + +++DE     +  l+  l
  gi|298674323|ref|YP_003726073.1| 292 gvnyEN--IEISSFHK-----TamkvanettipkptpdnywdellpykAINNVESMyDAVLIDEYQDFHNIWLKLCL 361
                                       222211..12222222.....12223344445567777778788888755566777788888887766655555555 PP

                            AAA_30 110 kaaeka......gakvilvGDerQ 127
                                       k ++k+         + l+GD+ Q
  gi|298674323|ref|YP_003726073.1| 362 KLCRKHeykgeyTENLFLAGDRLQ 385
                                       555554333333455666666654 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00015      0.17       2      55 ..     215     268 ..     214     291 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                                       ----SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHT.TS-SEEEEE CS
                              PhoH   2 ikpktkeQkeylealkkndivfaiGpaGtGKtylavalavealkk.kkvkriilt 55 
                                       ik+ ++ Q+++ + +      ++ G  G+GKt + va av++ ++  + + +ilt
  gi|298674323|ref|YP_003726073.1| 215 IKTLDTDQEKFSKRIPY-GHYMVSGVPGSGKTVILVARAVHLAREnPEWNILILT 268
                                       77888999999999973.345567999**************99883455555555 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0    0.0001      0.12      11      79 ..     224     300 ..     212     348 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0001
                            ATPase  11 ilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepa.........edlrenakslGwdlekle 78 
                                        ++  ip g+ + ++G+pG+GKt++    +++ a++  e  +++ +  ++         ++++++  ++G++ e++e
  gi|298674323|ref|YP_003726073.1| 224 KFSKRIPYGH-YMVSGVPGSGKTVILVARAVHLARENPEWNILILTYNRSlksklknilKSMHKDLDNMGVNYENIE 299
                                       4567788776.679**********99999999999988877777666665586666666666666667777776666 PP

                            ATPase  79 e 79 
                                        
  gi|298674323|ref|YP_003726073.1| 300 I 300
                                       4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (630 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       971  (0.0541581); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.71u 0.30s 00:00:01.01 Elapsed: 00:00:00.49
# Mc/sec: 3845.78
//
Query:       gi|298674324|ref|YP_003726074.1|  [L=286]
Description: hypothetical protein Metev_0353 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00013   22.0   0.0     0.0003   20.8   0.0    1.5  1  Zn_dep_PLPC     Zinc dependent phospholipase C
  ------ inclusion threshold ------
      0.019   14.9   0.0      0.039   13.9   0.0    1.5  1  Pribosyltran_N  N-terminal domain of ribose phosphate pyropho


Domain annotation for each model (and alignments):
>> Zn_dep_PLPC  Zinc dependent phospholipase C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   3.3e-08    0.0003      24     117 ..      22     103 ..       5     114 .. 0.64

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.3e-08
                                       HTHHHHHHHHHGGGG..-TT...-GGG--BTTTTB-HHHHS-HHHHHHHHHHHHHHHHHC.....T-HHHHHHHHHH CS
                       Zn_dep_PLPC  24 lnkaalllGsvaPDleylfn...asshsykthtkagllgedhhweetgkfllllikklrelyksegslklaafllGv 97 
                                       ++ + +l G+v+PD   + +   ++    ++h            +et+  + +   + r+  +  +     af +G 
  gi|298674324|ref|YP_003726074.1|  22 DHVNSILEGCVYPDKVGFKDeglMGVPISFPHH-----------KETNQRIYQILVNMRK--MVLKGDGVSAFEIGC 85 
                                       7889999********443334653333444444...........3444444444444445..2335899******** PP

                                       HHHHHHHHTS..H.....HTT- CS
                       Zn_dep_PLPC  98 lsHyvaDvft..Hgstlgenei 117
                                       l H+++D +t  H    ++ ++
  gi|298674324|ref|YP_003726074.1|  86 LAHLIQDRVTfpH----AHPNF 103
                                       ************9....44444 PP

>> Pribosyltran_N  N-terminal domain of ribose phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.4e-06     0.039      12      58 ..      86     149 ..      79     169 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.4e-06
                    Pribosyltran_N  12 LaekiakrlgvelgkakvsrfadgEikveieesvrgkdvfiiqsls.................k 58 
                                       La+ i++r+ ++ ++++   f++g +k++i+++ r++dv ++   +                 k
  gi|298674324|ref|YP_003726074.1|  86 LAHLIQDRVTFPHAHPNFDDFQNGVAKCRIKSKWREEDVPVLDARVldeldniltlnnpddpeK 149
                                       899************************************9998776555555555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1767.22
//
Query:       gi|298674325|ref|YP_003726075.1|  [L=1085]
Description: UvrD/REP helicase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-63  213.6   5.9    4.8e-63  213.6   5.9    2.6  2  UvrD-helicase    UvrD/REP helicase N-terminal domain
    3.1e-50  171.5   0.0    4.6e-49  167.7   0.0    2.7  2  UvrD_C           UvrD-like helicase C-terminal domain
    4.2e-34  118.0   0.0    1.3e-33  116.4   0.0    1.9  2  AAA_19           AAA domain
    5.5e-25   88.7   0.1    1.2e-24   87.7   0.1    1.6  1  PDDEXK_1         PD-(D/E)XK nuclease superfamily
      8e-11   41.6   0.0    0.00026   20.7   0.0    2.6  2  UvrD_C_2         UvrD-like helicase C-terminal domain
    4.4e-08   32.8   0.0    8.8e-08   31.8   0.0    1.4  1  DUF2800          Protein of unknown function (DUF2800)
    4.5e-08   33.0   0.0    1.2e-05   25.1   0.0    2.4  2  AAA_30           AAA domain
    1.3e-06   28.3   2.8       0.73    9.5   0.2    4.8  5  Viral_helicase1  Viral (Superfamily 1) RNA helicase
     0.0028   17.3   2.0        1.3    8.6   0.0    3.6  3  AAA_12           AAA domain
      0.008   16.0   0.3      0.062   13.1   0.0    2.4  2  Dna2             DNA replication factor Dna2


Domain annotation for each model (and alignments):
>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.6   5.9   2.7e-66   4.8e-63       1     315 []       9     320 ..       9     320 .. 0.88
   2 ?   -0.0   0.9      0.28     5e+02     110     229 ..     723     857 ..     659     922 .. 0.71

  Alignments for each domain:
  == domain 1  score: 213.6 bits;  conditional E-value: 2.7e-66
                                       SSHHHHHHHHS-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHHCCHHCT CS
                     UvrD-helicase   1 lnpeqreaiaslggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRieealkkaeqess 77 
                                       l+p+qr+a+++++gp+lv+A+AG+GKT++++ +i+++i+  ++ p++il++TF + Aa+ ++++++e+++ +     
  gi|298674325|ref|YP_003726075.1|   9 LKPKQRQAVEHSEGPLLVLAGAGTGKTTTITTKIAYMIEYLGVPPEEILALTFSRDAAKNMQQKVQELVGRR----- 80 
                                       5799******************************************************************98..... PP

                                       T-HHHHHHHHHCTTSEEEEHHHHHHHHHHHHHGGTTSHTTTEEECHHHHH.........HCCHHHHHHHHHSCHSHT CS
                     UvrD-helicase  78 dderlrlalqnlseanisTlHsfcqkilkkeanrigldpnfrildeedee.........dlkqqellkelleksadd 145
                                                   +++n+sT+Hsfc ++l+++ ++ g+ +nf+i+++ d           d k+ ++    +   + +
  gi|298674325|ref|YP_003726075.1|  81 ------------RDVNVSTFHSFCAELLREHPDECGVSENFTIYEDMDMAiylhrelgiDSKKAAHYSSSIS--KAK 143
                                       ............59**********************************778888887766666666666664..555 PP

                                       TTTHHHHHHHHHHHHHHCCCCCH......HHHCCCHHHHHCHHHHHHHHHHHTTCCTTHHCHSS......TSCSHHH CS
                     UvrD-helicase 146 slnldkkkleklikelsksrnik......keelslskskaeelrelvskakekqlspkelkkaf......ekasdlq 210
                                       +lnl+ k++e  i    k+   +       e ++l++  + +l+ +  k k++q   ke+kk        + +  ++
  gi|298674325|ref|YP_003726075.1| 144 DLNLSMKDFEDYID-GKKEI--LykfsseGEWEQLYHDYKVNLNTFHLKDKSEQKALKEEKKSWqefinvYDEYRKY 217
                                       58888888885532.22222..134555556667777778888888888888888888888766899**999999** PP

                                       HHHHHHHHHHHHHHHHHTCEEHHHHHHHHHHHHHHCHHHHHHHHHHSSEEEESSGGG-BHHHHHHHHHHHTTTTTEE CS
                     UvrD-helicase 211 kkiaeflkeyqeqkkeenalDfsdllhallelleeneelaealrerykeiliDEyQDTnkiQyrilkllasgheelf 287
                                       +++++++k y+++k+  nalD+ dl + +l++l+     +e+l+  y++i +DE+QDTn  Q++++k+l++++++++
  gi|298674325|ref|YP_003726075.1| 218 QDFIDAWKSYEDKKSSINALDYGDLNYIALQYLDT--YGTEELNDTYRYIVVDEFQDTNYLQFELIKRLTAREQNVT 292
                                       *********************************98..5679************************************ PP

                                       EEE-GGG--GGGGTB-THHHHHHHHHST CS
                     UvrD-helicase 288 mvGDpkQsIYgFRgAdielflkkkkdfk 315
                                       +v+Dp+QsIY+FRgA  +++ ++kk+++
  gi|298674325|ref|YP_003726075.1| 293 IVADPNQSIYAFRGAYTDNIEEFKKQYD 320
                                       *************************996 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.28
                                       GGTTSHTTTEEECHHHHH..HCCHHHHHHHHHSCHSHTTTTHHHHHHHHHHHHHHCCCCCH...HHHCCCHHHHHCH CS
                     UvrD-helicase 110 nrigldpnfrildeedee..dlkqqellkelleksaddslnldkkkleklikelsksrnik...keelslskskaee 181
                                       ++ig+d+ f+  d  d +  + ++++  kel+    dd+ + +k+  ++l  + + s ni    k  l+ ++ + +e
  gi|298674325|ref|YP_003726075.1| 723 YDIGFDESFEDCDTLDDVtfYRDTENKAKELVM---DDDIEREKQRRRELLMDSMGSGNITeplKHLLVYQELVNKE 796
                                       455677777777777765666666666666665...77777777777777777666666667775666666666666 PP

                                       HHHHHHHHHHTTCCTTHHCHSS.............TSCSHHHHHHHHHHHHHHHHHHHHTC CS
                     UvrD-helicase 182 lrelvskakekqlspkelkkaf.............ekasdlqkkiaeflkeyqeqkkeena 229
                                        r +++++k++  + + l +a+             + + d+ ++ +  +k+y+e  k++++
  gi|298674325|ref|YP_003726075.1| 797 DRDYLEEIKSNWSKINPLPEASeildscksskcspKFKPDNLSFSYSSIKTYEECPKKYEL 857
                                       6666666666555555444444445555565555555555666666666666666555555 PP

>> UvrD_C  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.6      0.35   6.2e+02     212     253 ..     174     229 ..     103     295 .. 0.64
   2 !  167.7   0.0   2.6e-52   4.6e-49       6     347 ..     332     708 ..     327     710 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.35
                                       xxxxxxxxxxxxxxxxxxxxx.......xxxx.........xxxxxxxxxxxxxxxxx RF
                            UvrD_C 212 dlfkelaeklaelkekseskr.......kkee.........klenlreLysllkelek 253
                                       +l++ ++ +l++++ k +s++       k  +         + ++ ++++++ k++e+
  gi|298674325|ref|YP_003726075.1| 174 QLYHDYKVNLNTFHLKDKSEQkalkeekK--SwqefinvydEYRKYQDFIDAWKSYED 229
                                       34444444444333222222222332211..122222333344444444444444444 PP

  == domain 2  score: 167.7 bits;  conditional E-value: 2.6e-52
                                       xxxxxxxxxxxxxxxxxxxxxx.xxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C   6 NyRStksLlkaankflenilnr.rale...kekktvekgekivvleaeteeeEaekiaatikallekneklediavL 78 
                                        yRSt+++l+++ ++++n++++ r +e    ++ + ++g+++v+ e+ +++eEa+kia+ +   +e+ + lediavL
  gi|298674325|ref|YP_003726075.1| 332 SYRSTNKILRVSHELIQNNYSDdRKSEcilLKNHEDNEGDNVVIQETLDDKEEARKIAEMVDWCAEEGTPLEDIAVL 408
                                       5********************9777777644449999999************************************* PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                            UvrD_C  79 vRsnkdadkiskaLkkegipfnvvdeekfFkreeikdilaylkllankqdkialkrilkrl.vlgigkatverisee 154
                                       +R++++ + ++++L++ g+p+ v ++++f+k +eik++layl +l+n +  +   r +++   l+  +++++r    
  gi|298674325|ref|YP_003726075.1| 409 YRTHSQGRVVKDTLQRRGFPVSVKENTDFLKLPEIKTALAYLYVLNNFTHPT--PRGTESWwRLFHYNNSLDRS--- 480
                                       **********************************************974433..33333320334444444444... PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 155 lkklglsltDfikedtleygeeFieliraleeknlelllkk.iektaeerqalvskyadlfkelaeklaelkekses 230
                                           +++++++ik++ +++++  ++   +l+e  ++   ++ +e  +  +q++ + +++    ++  l e+ + +  
  gi|298674325|ref|YP_003726075.1| 481 ---DSIKIAEYIKNNRTTFQDVIYH---HLDELGIS---DRgLEIINSVKQSIAKLFEKTIYDISDLLLEIYDYTGL 548
                                       ...667889*********9998884...44444444...44455555555555555555555555555555555554 PP

                                       xx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx RF
                            UvrD_C 231 kr........kkeeklenlreLysllkelekkeeeeeveeklneileiatLseseleeskkk..ekipiiTiHqAKG 297
                                        r         ++e l nlr+Ly+ ++ +e+ +   + +  +  +lei    ++++ + ++   + ++++TiH+AKG
  gi|298674325|ref|YP_003726075.1| 549 VRqfsgsdtiRNREALLNLRKLYENAETFEQMHDR-DLSG-FIAYLEILDEMDGNPSAANITddNAVNLMTIHSAKG 623
                                       44555555554445899999999999998883333.2222.44444444333444444444468************* PP

                                       xxxxxxxxxxxxxxxxx.................................xxxxxx......xxxxxxxxxxxxxxx RF
                            UvrD_C 298 lEFdvVflagleegtfP.................................syrskk......ekrleEEkRlfYVai 335
                                       lEFd+Vf++++++++fP                                 +           + ++eEE+Rl YVa 
  gi|298674325|ref|YP_003726075.1| 624 LEFDTVFVINMADNRFPlkrggkeplipyelmeqyrdifesdfssekelnK----AidarkkQLKIEEERRLCYVAF 696
                                       *****************************9999999999987776655551....15555555689*********** PP

                                       xxxxxxxxxxxx RF
                            UvrD_C 336 TRAkkrLfisys 347
                                       TRAk+ L++++s
  gi|298674325|ref|YP_003726075.1| 697 TRAKNHLVLTFS 708
                                       *********987 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.4   0.0     7e-37   1.3e-33       1     146 []      13     305 ..      13     305 .. 0.97
   2 ?   -4.2   0.0        10   1.8e+04      66      83 ..     612     629 ..     603     657 .. 0.73

  Alignments for each domain:
  == domain 1  score: 116.4 bits;  conditional E-value: 7e-37
                            AAA_19   1 qreavealkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae.....atTi 72 
                                       qr+av +++e++llv+aG+GtGKT+++++++a+++e  gv+peeil+++f + Aak++++++++l ++      +T+
  gi|298674325|ref|YP_003726075.1|  13 QRQAV-EHSEGPLLVLAGAGTGKTTTITTKIAYMIEYLGVPPEEILALTFSRDAAKNMQQKVQELVGRrrdvnVSTF 88 
                                       89***.********************************************************99988899999**** PP

                            AAA_19  73 Hrlal........................................................................ 77 
                                       H++                                                                          
  gi|298674325|ref|YP_003726075.1|  89 HSFCAellrehpdecgvsenftiyedmdmaiylhrelgidskkaahysssiskakdlnlsmkdfedyidgkkeilyk 165
                                       *99779*********************************************************************** PP

                            AAA_19  78 .......................................................................ldfddl 83 
                                                                                                              ld+ dl
  gi|298674325|ref|YP_003726075.1| 166 fssegeweqlyhdykvnlntfhlkdkseqkalkeekkswqefinvydeyrkyqdfidawksyedkkssinaLDYGDL 242
                                       **********************************************************************9999999 PP

                            AAA_19  84 ltealelleeaeeekklqeee.llivDEfqdvdelqyrLlkallgekkklllvGDpdQliyvfr 146
                                       +  al++l+ +  +++l++++ +++vDEfqd++ lq++L+k+l+ +++++++v Dp+Q+iy+fr
  gi|298674325|ref|YP_003726075.1| 243 NYIALQYLD-TYGTEELNDTYrYIVVDEFQDTNYLQFELIKRLTAREQNVTIVADPNQSIYAFR 305
                                       999999988.467889999999**********************99999*************97 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 10
                            AAA_19  66 gaeatTiHrlalldfddl 83 
                                        ++ +TiH+   l+fd+ 
  gi|298674325|ref|YP_003726075.1| 612 AVNLMTIHSAKGLEFDTV 629
                                       566799998877777765 PP

>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.7   0.1   6.5e-28   1.2e-24       1     255 []     839    1085 .]     839    1085 .] 0.65

  Alignments for each domain:
  == domain 1  score: 87.7 bits;  conditional E-value: 6.5e-28
                          PDDEXK_1    1 rlSvsrletfleCplrfflryllglre..eeeleap.dlGtlvHaaleefyewkkldke.dleelleeaveelwp 71  
                                        ++S+s+++t++eCp ++ l+ ll++++  +e+l ++  +G++vH++le  ++    +k    ++l  ++v el++
  gi|298674325|ref|YP_003726075.1|  839 SFSYSSIKTYEECPKKYELQELLRMPDrsSEKLGEAaNIGSFVHKVLEIGVK----RKVeTKDQLY-NIVYELAE 908 
                                        58***********************555577777766**********98777....3332444555.66667776 PP

                          PDDEXK_1   72 ellleeeilessarlrylaeklkevleklverlaeeleakrg.frpvalelefg....gekvrLkGriDrvddke 141 
                                        +               +   +lk++ + + ++++e  + k++    +a+e +f+    g  + +kG+iDrvd  +
  gi|298674325|ref|YP_003726075.1|  909 K----P---------DWKMIDLKKTYTLF-DTFWE--RHKDKiHYNFAVEKRFSvpigG--FYFKGFIDRVDFLS 965 
                                        6....2.........34444443333333.55555..2222235667777655555546..99*********555 PP

                          PDDEXK_1  142 g...elriiDyKtgsappkskelaelkeglQlllYllalaegeelkeege.pagalylrleepkvk.......de 205 
                                        g   ++++iDyK g++ p++++     +  QlllY++       ++e +  ++ +  l+ e+p+          e
  gi|298674325|ref|YP_003726075.1|  966 GcdtDVEVIDYKAGKTDPPTED-----RARQLLLYAYGFNYL--YPEYTVrRVTLEMLGKEKPRSFelngagvYE 1033
                                        55689**********8877777.....334************..5544223555555665554444788666655 PP

                          PDDEXK_1  206 evvkkm..alteeeleallqeleelaeeilagefparpskk.CeyCpyksvCr 255 
                                        +++ +m  +l+ + ++++ + ++ +a  +++g  +  ++ + Ce+C ++ +C+
  gi|298674325|ref|YP_003726075.1| 1034 SIIDRMtkPLDNNAIQNMVETAKWIAHDYENGFEKTGDH-RiCENCGFRLYCQ 1085
                                        555555333333333555555555466666554444444.46**********7 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   1.5e-07   0.00026       4      23 ..     615     634 ..     613     643 .. 0.84
   2 !   18.1   0.1   9.9e-07    0.0018      32      51 ..     686     705 ..     675     706 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.5e-07
                          UvrD_C_2   4 altihkaQGsefpaVivfdp 23 
                                        +tih a+G+ef++V+v+++
  gi|298674325|ref|YP_003726075.1| 615 LMTIHSAKGLEFDTVFVINM 634
                                       59***************653 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 9.9e-07
                          UvrD_C_2  32 elrrrlLYtavTRAreklil 51 
                                       e+ rrl Y+a+TRA+ +l+l
  gi|298674325|ref|YP_003726075.1| 686 EEERRLCYVAFTRAKNHLVL 705
                                       458***************98 PP

>> DUF2800  Protein of unknown function (DUF2800)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0   4.9e-11   8.8e-08       4     169 ..     840    1012 ..     838    1023 .. 0.77

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 4.9e-11
                           DUF2800    4 lSaSsahrWlkCppSarlee..eipdesS....eyAeeGtlaHelaelklrkaldakekkgvkselkkkeeevte 72  
                                        +S Ss + + +Cp   +l+e  ++pd+sS    e+A+ G++ H++ e+ ++++++ k++      + +  e+ + 
  gi|298674325|ref|YP_003726075.1|  840 FSYSSIKTYEECPKKYELQEllRMPDRSSeklgEAANIGSFVHKVLEIGVKRKVETKDQLYNI--VYELAEKPDW 912 
                                        689***************98556899997333369*****************99666555433..3334455556 PP

                           DUF2800   73 emeeavdey..vdfvlekieeakkdalvlvEqr..vdfskyvpe.gfGtaDvviiaddvLeviDlKyGkgvkVsa 142 
                                         m++  ++y  +d+ +e++++   +    vE+r  v+++ +  +    + D++  +d+ +eviD+K Gk  +   
  gi|298674325|ref|YP_003726075.1|  913 KMIDLKKTYtlFDTFWERHKDK-IHYNFAVEKRfsVPIGGFYFKgFIDRVDFLSGCDTDVEVIDYKAGKTDPPTE 986 
                                        6777777773358899998875.588899***844667776666266899************************* PP

                           DUF2800  143 ekNpQlalYAlGAleefdllydiktVr 169 
                                        ++  Ql lYA G    +   y +++V+
  gi|298674325|ref|YP_003726075.1|  987 DRARQLLLYAYGFNYLYP-EYTVRRVT 1012
                                        **********99544433.45555555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   6.7e-09   1.2e-05       1      79 [.       8      94 ..       8     119 .. 0.77
   2 !    5.4   0.0    0.0072        13      82     140 ..     254     312 ..     218     357 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 6.7e-09
                            AAA_30  1 elnaeQaaavealltsgdrvavltGpAGtGKttalkal.reaweaag...grviglAptgkaAkvLaeelg........ 67
                                      +l+++Q++ave+   +g    ++ ++AGtGKtt++++  + ++e  g   +++++l+ +  aAk+++++++        
  gi|298674325|ref|YP_003726075.1|  8 TLKPKQRQAVEHS--EG--PLLVLAGAGTGKTTTITTKiAYMIEYLGvppEEILALTFSRDAAKNMQQKVQelvgrrrd 82
                                      58999*****964..33..4788899*******99876266677669999*****************865543334333 PP

                            AAA_30 68 ieastiakllkr 79
                                      ++ st +++  +
  gi|298674325|ref|YP_003726075.1| 83 VNVSTFHSFCAE 94
                                      688888887755 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0072
                            AAA_30  82 grarlepg.tllivDEagmvdtkqlaallkaaekagakvilvGDerQlasVeaGgvlrdl 140
                                       g+++l++  + ++vDE   ++  q+ +l+k++++++  v +v D++Q     +G+  + +
  gi|298674325|ref|YP_003726075.1| 254 GTEELNDTyRYIVVDEFQDTNYLQF-ELIKRLTAREQNVTIVADPNQSIYAFRGAYTDNI 312
                                       44567777799*****999888887.588888888***********97655556655555 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.05        90       2      20 ..      25      43 ..      24      86 .. 0.74
   2 !    9.5   0.2   0.00041      0.73      47     106 ..     247     306 ..     225     389 .. 0.75
   3 ?    3.4   0.0      0.03        54     179     202 ..     610     632 ..     566     643 .. 0.84
   4 !    8.4   0.1   0.00089       1.6     209     232 ..     682     705 ..     674     707 .. 0.78
   5 ?   -2.1   0.0       1.4   2.6e+03     195     210 ..     736     751 ..     734     757 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.05
                   Viral_helicase1  2 vvhGvpGcGKStlirkllr 20
                                      +v + +G GK+t i + + 
  gi|298674325|ref|YP_003726075.1| 25 LVLAGAGTGKTTTITTKIA 43
                                      78899********998764 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00041
                   Viral_helicase1  47 vrtvdsflmalvkstkgkililDEylllhaGyill.laalskak..lvilfGDplQipfhsrn 106
                                         ++d++    +++ +++++++DE++  +  y+++ l+++ +a+  +v +++Dp+Q+ +  r 
  gi|298674325|ref|YP_003726075.1| 247 LQYLDTYGTEELND-TYRYIVVDEFQDTN--YLQFeLIKRLTAReqNVTIVADPNQSIYAFRG 306
                                       56778888888887.7*********9999..888888888776522799*******9888543 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.03
                   Viral_helicase1 179 algvrevttvhevqGltfdkVtlv 202
                                       +  v+  +t h++ Gl+fd+V ++
  gi|298674325|ref|YP_003726075.1| 610 DNAVN-LMTIHSAKGLEFDTVFVI 632
                                       34445.9**************887 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.00089
                   Viral_helicase1 209 lelisesrenllvAlTRhrkslvi 232
                                       ++ i+e+r  ++vA+TR+++ lv+
  gi|298674325|ref|YP_003726075.1| 682 QLKIEEERRLCYVAFTRAKNHLVL 705
                                       3445667*************9986 PP

  == domain 5  score: -2.1 bits;  conditional E-value: 1.4
                   Viral_helicase1 195 tfdkVtlvllketdle 210
                                       t d+Vt+++++e++ +
  gi|298674325|ref|YP_003726075.1| 736 TLDDVTFYRDTENKAK 751
                                       899*******987654 PP

>> AAA_12  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.2       2.4   4.3e+03     116     116 ..     210     210 ..     133     295 .. 0.57
   2 !    5.5   0.1    0.0063        11      60     135 ..     353     426 ..     311     449 .. 0.59
   3 !    8.6   0.0   0.00074       1.3     143     194 ..     613     705 ..     565     709 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.4
                            AAA_12 116 v 116
                                       v
  gi|298674325|ref|YP_003726075.1| 210 V 210
                                       2 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0063
                            AAA_12  60 leepleplvfidvekseeekekkeksyiNeeEaelvvklvekllkkgseeerkkigvitpYraqvellkkklkeke 135
                                        + ++e++++ + e++e  +   ++++  +eEa+ ++++v+   ++g+    ++i+v+   ++q +++k++l+++ 
  gi|298674325|ref|YP_003726075.1| 353 DDRKSECILLKNHEDNEGDNVVIQETLDDKEEARKIAEMVDWCAEEGTPL--EDIAVLYRTHSQGRVVKDTLQRRG 426
                                       22222334444444444444444477778888888888888888888887..888888888888888888888754 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.00074
                            AAA_12 143 ievntvdgfQGrekdviilslVRsn....ekk.....................................eigflkde 178
                                       ++  t+ +  G e d +++     n    +++                                     ++ + +++
  gi|298674325|ref|YP_003726075.1| 613 VNLMTIHSAKGLEFDTVFVINMADNrfplKRGgkeplipyelmeqyrdifesdfssekelnkaidarkkQLKIEEER 689
                                       66677777777777776666555554444222455566666666666666666666666666666666455555555 PP

                            AAA_12 179 rrlNValTRAksklii 194
                                       r   Va+TRAk++l++
  gi|298674325|ref|YP_003726075.1| 690 RLCYVAFTRAKNHLVL 705
                                       5556**********86 PP

>> Dna2  DNA replication factor Dna2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.7      0.94   1.7e+03     114     176 ..     172     234 ..     161     239 .. 0.80
   2 !   13.1   0.0   3.4e-05     0.062      51     124 ..     835     913 ..     833     936 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.94
                              Dna2 114 ldklleknleelyalglteeeakeeikekleeiekwakkyvkksnkakakvekkkekkeklsi 176
                                        ++l ++++ +l + +l+ ++ ++ +ke+ ++ +++++ y + ++ ++ + + k+ + +k si
  gi|298674325|ref|YP_003726075.1| 172 WEQLYHDYKVNLNTFHLKDKSEQKALKEEKKSWQEFINVYDEYRKYQDFIDAWKSYEDKKSSI 234
                                       578888999999999999999999999999999999999988888777776666666656555 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 3.4e-05
                              Dna2  51 PdlL.vsaTsvanslsClRravLqerlkvsge....sskamliGtilHelfqkalleeeldkekleelldklleknl 122
                                       Pd L  s +s+++  +C+++  Lqe l++++       +a+ iG+ +H++++  ++++  +k++l +++ +l ek  
  gi|298674325|ref|YP_003726075.1| 835 PDNLsFSYSSIKTYEECPKKYELQELLRMPDRssekLGEAANIGSFVHKVLEIGVKRKVETKDQLYNIVYELAEKPD 911
                                       55554588999****************777662222567899***********999999889999888888877655 PP

                              Dna2 123 ee 124
                                        +
  gi|298674325|ref|YP_003726075.1| 912 WK 913
                                       55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1085 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       861  (0.0480228); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.77u 0.27s 00:00:01.04 Elapsed: 00:00:00.52
# Mc/sec: 6232.75
//
Query:       gi|298674326|ref|YP_003726076.1|  [L=98]
Description: nuclease [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-08   33.9   0.4    4.9e-08   33.4   0.4    1.2  1  SNase     Staphylococcal nuclease homologue


Domain annotation for each model (and alignments):
>> SNase  Staphylococcal nuclease homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.4   2.7e-12   4.9e-08       1      75 [.      26      94 ..      26      97 .. 0.94

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 2.7e-12
                                      EEEETTEE-STSSBTTTTTSTTHHHHHHHHHHHHHHCSSEEEEE-SSBSTTSEEEEEEEETTEEHHHHHHHTTSS CS
                             SNase  1 kvrLvgidaPetakpkktvqpfgkeAkeflkklvlqkkvvvleldkkkDkygrllayvylnkknineeLvkeGlA 75
                                      ++rL +++aPe+       q+ g++Ak +++  + ++k +v++++  +Dkygr l ++  ++ +in+ L k+G+ 
  gi|298674326|ref|YP_003726076.1| 26 RFRLQNVRAPESG------QKGGQKAKRVAAGITGRSKNQVTVEEVGRDKYGRKLVKMKNKDGSINKRLRKKGYT 94
                                      68***********......999************99999999999999*************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.35s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 570.36
//
Query:       gi|298674327|ref|YP_003726077.1|  [L=199]
Description: ArsR family transcriptional regulator [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.3e-07   29.4   0.1    1.1e-06   28.4   0.0    1.6  2  HTH_5         Bacterial regulatory protein, arsR family
    1.6e-06   27.6   0.1    2.5e-06   26.9   0.1    1.3  1  HTH_24        Winged helix-turn-helix DNA-binding
    6.7e-05   22.9   0.0     0.0005   20.1   0.0    2.0  2  HTH_20        Helix-turn-helix domain
    0.00014   21.6   0.0    0.00023   20.9   0.0    1.3  1  HTH_IclR      IclR helix-turn-helix domain
    0.00027   20.8   0.1    0.00052   19.9   0.1    1.5  1  HTH_11        HTH domain
    0.00066   19.5   0.0     0.0017   18.2   0.0    1.7  1  TrmB          Sugar-specific transcriptional regulator TrmB
     0.0012   18.8   0.0     0.0016   18.3   0.0    1.3  1  Cas_APE2256   CRISPR-associated protein (Cas_APE2256)
     0.0014   17.5   0.4     0.0018   17.1   0.4    1.1  1  Cas_Cas02710  CRISPR-associated protein (Cas_Cas02710)
     0.0021   18.0   0.3     0.0052   16.8   0.3    1.6  1  HTH_45        Winged helix-turn-helix
     0.0025   17.7   0.0     0.0045   16.9   0.0    1.3  1  MarR_2        MarR family
  ------ inclusion threshold ------
      0.033   14.7   0.0      0.086   13.3   0.0    1.7  1  HTH_27        Winged helix DNA-binding domain
      0.042   13.7   0.0      0.089   12.6   0.0    1.5  1  HTH_10        HTH DNA binding domain
      0.045   13.8   0.5      0.068   13.2   0.3    1.4  1  AAA_14        AAA domain
      0.051   13.9   0.0        0.1   13.0   0.0    1.4  1  Rrf2          Transcriptional regulator
      0.068   12.8   0.0       0.17   11.5   0.0    1.7  1  HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor
      0.076   13.1   0.0       0.13   12.5   0.0    1.3  1  HTH_28        Helix-turn-helix domain
      0.079   12.9   0.1       0.14   12.1   0.1    1.4  1  MarR          MarR family
        0.1   12.2   1.6       0.44   10.1   0.0    2.4  3  ArsR          ArsR transcriptional regulator


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       8.3   8.3e+03      23      32 ..      19      28 ..      17      28 .. 0.79
   2 !   28.4   0.0   1.1e-09   1.1e-06       3      46 ..     140     183 ..     138     184 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 8.3
                                      HHHTS-HHHH CS
                             HTH_5 23 eelglsqstv 32
                                      ++++ s+s+v
  gi|298674327|ref|YP_003726077.1| 19 CITKFSPSKV 28
                                      6899999987 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 1.1e-09
                                       HHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5   3 tRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46 
                                       t+  IL + ++g  +v+++a +l++s++ +  HL+ L+ +G+++
  gi|298674327|ref|YP_003726077.1| 140 TKKSILEQIQSGTSSVGDIAQKLDISKGMTYNHLRELKSLGYIT 183
                                       67789*************************************96 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.1   2.5e-09   2.5e-06       3      48 .]     139     183 ..     137     183 .. 0.96

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 2.5e-09
                            HTH_24   3 etdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                        t++ ILe +q  +  s  ++A++l++S++ +  +l++L++ G+I+
  gi|298674327|ref|YP_003726077.1| 139 TTKKSILEQIQS-GTSSVGDIAQKLDISKGMTYNHLRELKSLGYIT 183
                                       68999*******.********************************6 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.73   7.3e+02      40      57 ..      62      81 ..      39      84 .. 0.77
   2 !   20.1   0.0   5.1e-07    0.0005      15      57 ..     144     185 ..     138     188 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.73
                                      H.HHHHHHHHHH.CTTEEEE CS
                            HTH_20 40 t.lsyHLrvLee.agLvevv 57
                                      t l++H++v ++ a+L++ +
  gi|298674327|ref|YP_003726077.1| 62 TsLYDHVQVASDvADLIDEE 81
                                      44999999999999999865 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 5.1e-07
                                       HHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20  15 ilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57 
                                       il  + + +  +++++a+ ld+sk   ++HLr+L + g+++ +
  gi|298674327|ref|YP_003726077.1| 144 ILEQI-QSGTSSVGDIAQKLDISKGMTYNHLRELKSLGYITDE 185
                                       67777.777889***************************9876 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   2.3e-07   0.00023       8      49 ..     144     183 ..     143     186 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.3e-07
                                       HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR   8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49 
                                       iL+++ +++    + ++A++++++k  ++++L+ L  lGy++
  gi|298674327|ref|YP_003726077.1| 144 ILEQIQSGTSS--VGDIAQKLDISKGMTYNHLRELKSLGYIT 183
                                       99999999995..***************************97 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   5.2e-07   0.00052       3      44 ..     142     181 ..     140     195 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 5.2e-07
                            HTH_11   3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44 
                                       ++ile++ +   + s  ++A++L++S+   ++++++L++lg+
  gi|298674327|ref|YP_003726077.1| 142 KSILEQIQSG--TSSVGDIAQKLDISKGMTYNHLRELKSLGY 181
                                       6899999333..46***************************4 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.7e-06    0.0017      19      57 ..     149     187 ..     142     191 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.7e-06
                                       HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                              TrmB  19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57 
                                       ++g +++ +ia++l++++   Y+ Lr+L++ G+++ e+g
  gi|298674327|ref|YP_003726077.1| 149 QSGTSSVGDIAQKLDISKGMTYNHLRELKSLGYITDEDG 187
                                       578999****************************99876 PP

>> Cas_APE2256  CRISPR-associated protein (Cas_APE2256)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.6e-06    0.0016      77     136 .]      71     133 ..      34     133 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.6e-06
                       Cas_APE2256  77 veklarevknkkregekvlinaTgGfKpeiavltlvall...ladevyYihEsfsevvelPkl 136
                                       +  +a+ ++++ ++g++++ n++g+ K ++  ++  a++   + ++v+Y+ E+ +e++ +P+l
  gi|298674327|ref|YP_003726077.1|  71 ASDVADLIDEEHDKGNQIITNVSGSRKTQAFGALYGAYArkdMVKRVVYVTEEDHEIIDFPIL 133
                                       457889999*******************9988887777754556799**************85 PP

>> Cas_Cas02710  CRISPR-associated protein (Cas_Cas02710)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.4   1.8e-06    0.0018       1     104 [.      14     124 ..      14     128 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.8e-06
                                       HHHHHHHHHH--SEEEEEE-TGGGGGHHHHHHHH-S-...EEEEE--TT-HHHHHHHHHHHHHHS.....TTS-EEE CS
                      Cas_Cas02710   1 eplalsIaelrPerVvflasekSekkleevkealgkklkqevlldedandllelykkikevleka....leeeeviv 73 
                                       ep++l I+++ P +V++l  e+ ++k  e +e ++k + + ++++  + +l    + + +v++       + +++i 
  gi|298674327|ref|YP_003726077.1|  14 EPVILCITKFSPSKVILLTEEDAADKKVESIETIEKTFGSMIEIKRKYTSLYDHVQVASDVADLIdeehDKGNQIIT 90 
                                       799******************99999999999*******************99999999999999877455578999 PP

                                       E-SSS-HHHHHHHHHHHHHH...TEEEEEEE--B CS
                      Cas_Cas02710  74 DlTgGtkeMtaglalagill...rvklsyVggea 104
                                       +++g  k+ + g+   + ++    ++++yV+ e+
  gi|298674327|ref|YP_003726077.1|  91 NVSGSRKTQAFGALYGAYARkdmVKRVVYVTEED 124
                                       9999999999999888777754468999**9975 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.3   5.2e-06    0.0052      10      63 ..     143     195 ..     140     197 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.2e-06
                            HTH_45  10 dILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGl 63 
                                       +ILe+i++g ++   i  k ++s  ++ + L  L + g+i++++  Y++T+ G+
  gi|298674327|ref|YP_003726077.1| 143 SILEQIQSGTSSVGDIAQKLDISKGMTYNHLRELKSLGYITDED-GYKITDSGK 195
                                       6***************************************8765.6*****996 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   4.5e-06    0.0045      16      55 ..     150     186 ..     136     188 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.5e-06
                                       CTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2  16 rrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55 
                                        +     +vg++a++l++sk+ + ++l++L + G+++ ++
  gi|298674327|ref|YP_003726077.1| 150 SGT---SSVGDIAQKLDISKGMTYNHLRELKSLGYITDED 186
                                       444...49****************************9775 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   8.6e-05     0.086       8      68 .]     144     194 ..     139     194 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.6e-05
                            HTH_27   8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68 
                                       +L++i+   ++++  d++++l++++  + + l++L   G++   +de       +++Td+G
  gi|298674327|ref|YP_003726077.1| 144 ILEQIQ--SGTSSVGDIAQKLDISKGMTYNHLRELKSLGYI---TDE-----DGYKITDSG 194
                                       788888..999999***************************...565.....346666665 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   8.9e-05     0.089      25      46 ..     154     175 ..     152     178 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.9e-05
                            HTH_10  25 tlkeLAkelGIskstlsehLrk 46 
                                       ++ ++A++l+Isk  +++hLr+
  gi|298674327|ref|YP_003726077.1| 154 SVGDIAQKLDISKGMTYNHLRE 175
                                       678******************7 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   6.8e-05     0.068      29     103 ..      24      98 ..       5     118 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.8e-05
                            AAA_14  29 kkesilyinldderdkkladpekllelileklkeekktylflDEiqevpewekalkslvdegknldvivtGSnsk 103
                                       ++++++ ++ +d  dkk +  e++++ + ++++ ++k+  + D +q ++++ + + + +d+g+++   v+GS + 
  gi|298674327|ref|YP_003726077.1|  24 SPSKVILLTEEDAADKKVESIETIEKTFGSMIEIKRKYTSLYDHVQVASDVADLIDEEHDKGNQIITNVSGSRKT 98 
                                       578899999999999999988889999999876679999***********************8888889999765 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0    0.0001       0.1      23      60 ..     150     187 ..     138     189 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.0001
                                       CC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                              Rrf2  23 eepvsseeiaerqnispsylekilakLrkaglvksvrG 60 
                                       +++ s+ +ia++ +is+ +    l++L+  g+++ + G
  gi|298674327|ref|YP_003726077.1| 150 SGTSSVGDIAQKLDISKGMTYNHLRELKSLGYITDEDG 187
                                       345899***************************98887 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00018      0.17      27      58 ..     156     187 ..     136     191 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00018
                      HrcA_DNA-bdg  27 eeiAevlkrneGtvRNqlqsLkalgLvegvpG 58 
                                        +iA++l+  +G   N l  Lk+lg +    G
  gi|298674327|ref|YP_003726077.1| 156 GDIAQKLDISKGMTYNHLRELKSLGYITDEDG 187
                                       48***********************9987665 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00013      0.13       2      40 ..     141     180 ..     140     184 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                            HTH_28   2 RleiikllaaGh.svreaArelgisrrtvyrWikryeegG 40 
                                       ++ i++++++G  sv ++A++l is  + y  ++ + + G
  gi|298674327|ref|YP_003726077.1| 141 KKSILEQIQSGTsSVGDIAQKLDISKGMTYNHLRELKSLG 180
                                       77899*************************9999877655 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00014      0.14      14      48 ..     149     183 ..     137     185 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                                       HSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR  14 eqgplsvseLakklgvskstvtrvldrLekkGlie 48 
                                       ++g  sv ++a kl +sk+++ + l++L   G+i+
  gi|298674327|ref|YP_003726077.1| 149 QSGTSSVGDIAQKLDISKGMTYNHLRELKSLGYIT 183
                                       57888999********************9999996 PP

>> ArsR  ArsR transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       0.8     8e+02      99     131 ..      29      61 ..      26      65 .. 0.67
   2 ?   -0.4   0.1      0.76   7.6e+02      73      84 ..      60      71 ..      53     102 .. 0.58
   3 ?   10.1   0.0   0.00044      0.44     105     137 ..     136     168 ..     113     181 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.8
                              ArsR  99 afmsdeeleelvekiekeveegntsisdlsrkl 131
                                       +++++e+  +   + ++++e++  s+ +++rk+
  gi|298674327|ref|YP_003726077.1|  29 ILLTEEDAADKKVESIETIEKTFGSMIEIKRKY 61 
                                       445555555555555677888888888888876 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.76
                              ArsR 73 eYhtsYskvqan 84
                                      +Y + Y++vq+ 
  gi|298674327|ref|YP_003726077.1| 60 KYTSLYDHVQVA 71
                                      555555555543 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00044
                              ArsR 105 eleelvekiekeveegntsisdlsrklglsplf 137
                                       +++++ ++i +++++g+ s++d+++kl++s+ +
  gi|298674327|ref|YP_003726077.1| 136 NISTTKKSILEQIQSGTSSVGDIAQKLDISKGM 168
                                       56788999********************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1265.16
//
Query:       gi|298674328|ref|YP_003726078.1|  [L=38]
Description: hypothetical protein Metev_0358 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 243.24
//
Query:       gi|298674329|ref|YP_003726079.1|  [L=233]
Description: hypothetical protein Metev_0359 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-34  117.6   0.0    7.2e-34  117.3   0.0    1.0  1  AIM24     Mitochondrial biogenesis AIM24


Domain annotation for each model (and alignments):
>> AIM24  Mitochondrial biogenesis AIM24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.3   0.0     4e-38   7.2e-34       9     200 ..      29     221 ..      24     222 .. 0.93

  Alignments for each domain:
  == domain 1  score: 117.3 bits;  conditional E-value: 4e-38
                                       -EEEEEE-TT-EEEE-CCGEEEEETTEEEEE......--------------EEEEEEES.SS-EEEEE--SSSE.EE CS
                             AIM24   9 sllsvtLspgeelyaerGalvamsgkvemet......gllkalkrlltgeslfllkftakissgtvllapklpg.ti 78 
                                       ++l  +L+ +++++a++G+++a+ g++++e       g++k lk  ltge + l+k ++   +g++++a + ++ +i
  gi|298674329|ref|YP_003726079.1|  29 RILIANLE-DDKIWAKTGSMIAYHGDIKFERegitehGIGKLLKSKLTGEEMELMKAQG---TGQAYFAEDGKKiSI 101
                                       56777786.56***********************************************5...5********998888 PP

                                       EEEEGGTT.EEEEEGGGEEEEETT-EEEEEEEE--SSGGGTS-EEEEEEESSSEEEEEEECSEEEEEEE.EEEEEEE CS
                             AIM24  79 vtlelgggdwlivqkdafLAatgnveldikfqkglkglfggeglflqkltGrGlvalsgyGaiyeielkageelvvd 155
                                       ++l+   g++++v+++ +LA+++++++d+++ k+++g ++g glf+ k++G+G+va++ + ++++ ++ +++++  d
  gi|298674329|ref|YP_003726079.1| 102 IDLK---GESITVNSNDLLAFEDGLDWDVHSMKSIAGAVSG-GLFNVKIEGEGMVAITTHYDPLTFKVSKDKPIYTD 174
                                       8888...569**********************999888866.9********************************** PP

                                       GGGEEEEETTEEEEEEEE...TT---STTTTS-EEEEEEEEEEEEEES CS
                             AIM24 156 pghlvafsgslkfdierv...gglkrrligGeglflkltGpgtvllqs 200
                                       p+  va+sg+l+ di++    +++++r  +Ge++++k++G+g v++q+
  gi|298674329|ref|YP_003726079.1| 175 PDTTVAWSGNLNPDINTDvsfKTFIGRE-SGESIQMKFEGEGFVVVQP 221
                                       *****************98888999999.******************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1478.60
//
Query:       gi|298674330|ref|YP_003726080.1|  [L=480]
Description: hypothetical protein Metev_0360 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00011   22.0   3.9    0.00017   21.4   1.7    2.3  2  DUF4139   Domain of unknown function (DUF4139)
     0.0031   17.6   0.9     0.0082   16.3   0.0    2.2  2  DUF150_C  RimP C-terminal SH3 domain
  ------ inclusion threshold ------
      0.035   13.9   0.3        5.8    6.7   0.0    2.5  2  RMI2      RecQ-mediated genome instability protein 2
        3.1    8.5   6.7        1.3    9.7   0.6    3.3  5  YtkA      YtkA-like


Domain annotation for each model (and alignments):
>> DUF4139  Domain of unknown function (DUF4139)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       0.8   3.6e+03      88      88 ..     112     112 ..      58     174 .. 0.47
   2 !   21.4   1.7   3.7e-08   0.00017       2     201 ..     180     445 ..     179     448 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.8
                                       x RF
                           DUF4139  88 k 88 
                                       +
  gi|298674330|ref|YP_003726080.1| 112 E 112
                                       2 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 3.7e-08
                                       xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx... RF
                           DUF4139   2 kvsyvvseagWsPlYdlrldtake.evqltykAkvyQktgeDWknvnLtLstakpnrg.gsppelspwylrvvn... 73 
                                       k++y ++ ++W+P+Y+l l++  + e +++    +++ +g  ++  ++ L +++ ++g    pe+++   + ++   
  gi|298674330|ref|YP_003726080.1| 180 KLKYRMEGVTWNPSYELMLNDGPQsESEFEGDIVIQNPSGKTFDG-QVNLISGDVRSGrVILPEYGDSMGSGAEafk 255
                                       799******************87758*****************97.6888999999985667888777776666999 PP

                                       ...............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxx................. RF
                           DUF4139  74 ...............................evteggtsvtfeipkkvsipsdgeetkvt................. 102
                                                                      +  + + ++  +   k s  sd ++t+ +                 
  gi|298674330|ref|YP_003726080.1| 256 stavgdlqtigrvnlynlgmytidsysqksiNYMNDNVDTDVNHVYKSSAHSDHSRTVSKqltfdnnmkdlpegris 332
                                       **998887777777777777777777777663333344444444444444444444444488888888888899999 PP

                                       ......................xxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4139 103 ......................Gvdpkikverkllkkkksetgli...gsqrrveyaytitvkNtksepvtlkvedq 154
                                                             G+d  ++++  +  + +++t+++    +q+ ++ +++it++N+ +e+ +++ve+q
  gi|298674330|ref|YP_003726080.1| 333 iyrnhngsevmvgsdfiertaeGND--VEIDLGKSYDIEGSTKVLdaqMNQNNITREINITITNHADETREVTVEHQ 407
                                       9999999999999999999977666..455555556666667888777789999*********************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4139 155 vPvSrdeeikveledaepskaevdkdtgilewklklapgekkkiefs 201
                                       +   + e i     ++ep+++ vdk      wk+++ ++++k+i+f+
  gi|298674330|ref|YP_003726080.1| 408 W--INGEIIDT---NIEPAETLVDKA----IWKIEVDANSEKNINFK 445
                                       7..67777777...789998888888....8********99999986 PP

>> DUF150_C  RimP C-terminal SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.8e-06    0.0082       1      46 [.     100     141 ..     100     154 .. 0.87
   2 ?   -2.9   0.1       1.7   7.8e+03      41      61 ..     430     447 ..     398     448 .. 0.60

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.8e-06
                          DUF150_C   1 LktaedFarflGelVkvklklpvegrkkftGkivevdeetitlevd 46 
                                       L ta  F+ ++Ge+++v+++      +++tGk+v+ ++ +i+ + d
  gi|298674330|ref|YP_003726080.1| 100 LNTANGFEENIGEEITVVFS----SDQNITGKLVRTEGMNIVMDTD 141
                                       667888**************....****************998765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.7
                          DUF150_C  41 itlevdgkkrkkettipladi 61 
                                         +evd +   +e +i+++ i
  gi|298674330|ref|YP_003726080.1| 430 WKIEVDAN---SEKNINFKSI 447
                                       45677766...3334777665 PP

>> RMI2  RecQ-mediated genome instability protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0    0.0055        25      45      79 ..      44      75 ..      42      83 .. 0.79
   2 ?    6.7   0.0    0.0013       5.8       3      61 ..     372     426 ..     370     448 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0055
                              RMI2 45 QGtvvevdaskesllldDgtgvfvveglnelpktk 79
                                      QG vve +    s+ l+Dgt  +++++ ++l   k
  gi|298674330|ref|YP_003726080.1| 44 QGAVVEKQM---SVDLEDGTQWITINTTSSLDFDK 75
                                      9****5444...578**********9999987665 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0013
                              RMI2   3 lKlllsqLretseedgsssaatlrllraavgreglevsrvWlQGtvvevdaskesllld 61 
                                       +K+l +q++  +++  ++ +  ++++++a  +++++v+  W+ G +++ + + ++ l+d
  gi|298674330|ref|YP_003726080.1| 372 TKVLDAQMN--QNNITREIN--ITITNHADETREVTVEHQWINGEIIDTNIEPAETLVD 426
                                       688888888..343444444..44477777799**************988887766665 PP

>> YtkA  YtkA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.36   1.6e+03       3      42 ..      92     131 ..      90     146 .. 0.59
   2 ?    9.7   0.6   0.00029       1.3      42      79 ..     152     187 ..     108     191 .. 0.68
   3 ?   -2.5   0.0       1.8   8.2e+03      10      38 ..     316     345 ..     309     359 .. 0.64
   4 ?   -3.0   0.0       2.7   1.2e+04      30      30 ..     381     381 ..     352     407 .. 0.49
   5 ?   -1.2   0.1      0.71   3.2e+03      21      58 ..     427     464 ..     414     474 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.36
                              YtkA   3 esddlevelvspeep..kagen.tivvtvtqggkpVedadvkv 42 
                                       +++  e++l++++ +  + ge+ t+v+    +++ ++++ v+ 
  gi|298674330|ref|YP_003726080.1|  92 NVEVTEIKLNTANGFeeNIGEEiTVVFS---SDQNITGKLVRT 131
                                       6777889999998886555555344443...334444444443 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00029
                              YtkA  42 vefwmpameGmeemttkvelkesedGvYeaevnfsmeG 79 
                                       ++++ +++ G ++ ++k++ k +  G Ye+++++ meG
  gi|298674330|ref|YP_003726080.1| 152 INRMITEN-GNSP-DVKAKIKAQTEGDYEFKLKYRMEG 187
                                       45555553.4444.6777777778*************9 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.8
                              YtkA  10 elvspeepkagen.tivvtvtqggkpVeda 38 
                                       +l+ ++++k+  + +i++ ++++g++V   
  gi|298674330|ref|YP_003726080.1| 316 QLTFDNNMKDLPEgRISIYRNHNGSEVMVG 345
                                       555556665544447888888888888654 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 2.7
                              YtkA  30 q 30 
                                       q
  gi|298674330|ref|YP_003726080.1| 381 Q 381
                                       2 PP

  == domain 5  score: -1.2 bits;  conditional E-value: 0.71
                              YtkA  21 entivvt.vtqggkpVedadvkvefwmpameGmeemttk 58 
                                       ++ ++++ +  ++k ++ ++++ +f+    eG e+++t 
  gi|298674330|ref|YP_003726080.1| 427 KAIWKIEvDANSEKNINFKSIEQKFDSR-VEGTETSSTA 464
                                       4567887344778888888888888887.4777766544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       803  (0.0447878); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.22s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3444.51
//
Query:       gi|298674331|ref|YP_003726081.1|  [L=61]
Description: hypothetical protein Metev_0361 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.026   14.5   0.0       0.03   14.3   0.0    1.3  1  UCR_6-4kD  Ubiquinol-cytochrome C reductase complex, 6.4kD pr


Domain annotation for each model (and alignments):
>> UCR_6-4kD  Ubiquinol-cytochrome C reductase complex, 6.4kD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.7e-06      0.03      41      53 ..      39      51 ..      19      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.7e-06
                                      HHTTSSS-----X CS
                         UCR_6-4kD 41 iLdYvPyingKFk 53
                                      +Ld +PyingK+ 
  gi|298674331|ref|YP_003726081.1| 39 LLDHIPYINGKYA 51
                                      69*********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 389.66
//
Query:       gi|298674332|ref|YP_003726082.1|  [L=274]
Description: hypothetical protein Metev_0362 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.013   14.8   5.2      0.018   14.4   5.2    1.2  1  Peptidase_U4     Sporulation factor SpoIIGA
      0.029   13.7   2.7      0.053   12.8   0.7    2.0  2  Heliorhodopsin   Heliorhodopsin
      0.039   13.3   2.4      0.061   12.6   2.4    1.3  1  Mannosyl_trans2  Mannosyltransferase (PIG-V)
       0.25   12.1   0.1       0.25   12.1   0.1    2.3  2  Cadherin_C_2     Cadherin cytoplasmic C-terminal
          2    7.7   9.0        2.7    7.3   5.2    2.1  2  DUF1616          Protein of unknown function (DUF1616)
        2.9    7.8  10.9       0.46   10.4   5.5    2.0  2  DUF981           Protein of unknown function (DUF981)
        3.8    7.2   5.8       0.94    9.2   1.5    2.1  2  Neurensin        Neurensin
        5.2    7.6  16.2       0.15   12.5   2.2    3.2  3  DUF202           Domain of unknown function (DUF202)
        6.4    7.0  15.6        1.1    9.4   0.8    3.0  4  DUF3784          Domain of unknown function (DUF3784)


Domain annotation for each model (and alignments):
>> Peptidase_U4  Sporulation factor SpoIIGA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   5.2     9e-06     0.018      33     149 ..       5     121 ..       2     158 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9e-06
                      Peptidase_U4  33 lrlllaAllGalyvvlvlflpklesillsillki..lvsllmvliafgpkslkeflkalllfylvsfllgGilfals 107
                                       +r++la++ G   + +v+ + + e +++s+++    l+++ ++++a  +++  + +++++++++   +++ +l++++
  gi|298674332|ref|YP_003726082.1|   5 IRTILAGIGGVTGIGAVISFLQTE-LFSSPVTTSiaLIAVGILILAITHRTEDKAIRNIGVIICSFSIIASVLYGVI 80 
                                       677787777766554444443333.3333333322445555555567777777999999999888888888888888 PP

                      Peptidase_U4 108 yll...lksknllvlllgalvaylllkllvkiikkkkkkekeiye 149
                                       +l+   l    +++l l++l++ +l+ + +++ ++k+ ++k++  
  gi|298674332|ref|YP_003726082.1|  81 SLTsgtL----TVTLSLAILTTGFLTAAYISQTERKILTQKKLSV 121
                                       8443331....3333344444444444444444444444444433 PP

>> Heliorhodopsin  Heliorhodopsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.2     0.012        24       7      76 ..      11      82 ..       5      87 .. 0.73
   2 ?   12.8   0.7   2.6e-05     0.053       8      97 ..      66     160 ..      59     167 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.012
                    Heliorhodopsin  7 imgvlhlvqavlllvlandfslpvttsylegdpeta..alapeteelfevelgvlvalFlllsalahlliat 76
                                       +g +  + av+ ++ ++ fs pvtts++  + +    a++++te  +  ++gv++ +F +++++ + +i+ 
  gi|298674332|ref|YP_003726082.1| 11 GIGGVTGIGAVISFLQTELFSSPVTTSIALIAVGILilAITHRTEDKAIRNIGVIICSFSIIASVLYGVISL 82
                                      555566666666677777999999999987776655115556677777778************999988875 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2.6e-05
                    Heliorhodopsin   8 mgvlhlvqavlllvlan.......dfslpvttsylegdpetaalapeteelfevelgvlvalFlllsalahlliatv 77 
                                       ++ + ++ +vl  v++        ++sl + t+   + + +   ++e + l++ +l+vl ++Fl+l a+  ++ a+v
  gi|298674332|ref|YP_003726082.1|  66 ICSFSIIASVLYGVISLtsgtltvTLSLAILTT--GFLTAAYISQTERKILTQKKLSVLSVIFLCLFAFTAVVDAVV 140
                                       555555555544444333232200333333322..33344455556688889999********************** PP

                    Heliorhodopsin  78 lfkrYeenLkkginkfRWve 97 
                                           Y+ +L+++i ++  ++
  gi|298674332|ref|YP_003726082.1| 141 SEPEYNLELEETITEVESTD 160
                                       **********9998776555 PP

>> Mannosyl_trans2  Mannosyltransferase (PIG-V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.4     3e-05     0.061      98     179 ..      73     155 ..      60     179 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3e-05
                   Mannosyl_trans2  98 laplvgllslravlvlsvfslsill.fllaavilsdvsvlvlkareasfkasllfclspaavflasiYseaLfalla 173
                                        + l+g++sl +  + +  sl+il   +l+a ++s+  + +l +++ s  + ++ cl + +  + ++ se+ + l  
  gi|298674332|ref|YP_003726082.1|  73 ASVLYGVISLTSGTLTVTLSLAILTtGFLTAAYISQTERKILTQKKLSVLSVIFLCLFAFTAVVDAVVSEPEYNLEL 149
                                       45689*****************876269******************************************9998755 PP

                   Mannosyl_trans2 174 fsgvys 179
                                         ++ +
  gi|298674332|ref|YP_003726082.1| 150 EETITE 155
                                       555555 PP

>> Cadherin_C_2  Cadherin cytoplasmic C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   1.2       2.7   5.4e+03       3      21 ..      86     104 ..      76     109 .. 0.79
   2 ?   12.1   0.1   0.00013      0.25      10      74 ..     119     193 ..     118     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.7
                      Cadherin_C_2   3 tlYLviaLasvSflFLltv 21 
                                       tl  +++La+ +  FL++ 
  gi|298674332|ref|YP_003726082.1|  86 TLTVTLSLAILTTGFLTAA 104
                                       4555778999999998875 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00013
                      Cadherin_C_2  10 LasvSflFLltvivlvavrlrkerksaalqkkkslvskpalkvpphvsgngtls...........qsysYevcltp 74 
                                       L++ S++FL+ + + ++v    ++++ +l+  ++++++ ++++ ++ + +gtl+           + +sY+ clt 
  gi|298674332|ref|YP_003726082.1| 119 LSVLSVIFLCLFAFTAVVDAVVSEPEYNLELEETITEVESTDYRSN-YIVGTLTvsnpsflpldtERQSYRACLTG 193
                                       7899***************988888888888446777777999999.777777777888889***9********97 PP

>> DUF1616  Protein of unknown function (DUF1616)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   5.2    0.0013       2.7      68     159 ..      16     105 ..       9     112 .. 0.76
   2 ?    3.7   1.2     0.017        33      57     128 ..      86     159 ..      77     172 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0013
                           DUF1616  68 pliglvlnvtpwgirlepilvslslftlllalvAivrRsrlpeeerfsvplralieslkeeleeksesrldkalnvl 144
                                         ig v+++ + ++   p+++s++l+ + + ++Ai  R++ ++ +   v + + ++ + + l+    s ++  l+v 
  gi|298674332|ref|YP_003726082.1|  16 TGIGAVISFLQTELFSSPVTTSIALIAVGILILAITHRTEDKAIRNIGVIICS-FSIIASVLYG-VISLTSGTLTVT 90 
                                       5699**********************************998888888875443.4445555555.344567888888 PP

                           DUF1616 145 Lvvsivlavaalgya 159
                                       L ++i++ +  ++ +
  gi|298674332|ref|YP_003726082.1|  91 LSLAILTTGFLTAAY 105
                                       888888777644433 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.017
                           DUF1616  57 aLSfglSiaivp...liglvlnvtpwgirlepilvslslftlllalvAivrRsrlpeeerfsvplralieslkee 128
                                       +L + lS+ai+    l +  ++ t+ +i ++  l +ls++ l+l +  +v   ++ +e +++++l+++i+++++ 
  gi|298674332|ref|YP_003726082.1|  86 TLTVTLSLAILTtgfLTAAYISQTERKILTQKKLSVLSVIFLCLFAFTAVVD-AVVSEPEYNLELEETITEVEST 159
                                       6899999999986667888899999999999888888876665544444433.4555555677777777776665 PP

>> DUF981  Protein of unknown function (DUF981)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   5.5   0.00023      0.46      96     176 ..       2      80 ..       1      90 [. 0.72
   2 ?    0.2   0.4      0.31   6.1e+02      11      27 ..      93     108 ..      81     140 .. 0.43

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00023
                            DUF981  96 klkalgilalflGlilivygvailklgLtaePlaalllyilvGLagllsplvllkldksrsvllvlaavlliiagll 172
                                       ++++ +ila + G+  i   +++l+ +L+++P+++++  i+vG+  l+ +++ ++ dk+ + + v+   + iia +l
  gi|298674332|ref|YP_003726082.1|   2 DINIRTILAGIGGVTGIGAVISFLQTELFSSPVTTSIALIAVGI--LILAITHRTEDKAIRNIGVIICSFSIIASVL 76 
                                       677889*******************************9999998..4555555556664444555555555555444 PP

                            DUF981 173 alli 176
                                         +i
  gi|298674332|ref|YP_003726082.1|  77 YGVI 80 
                                       4444 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.31
                            DUF981  11 litlgagllllayyvlk 27 
                                       l +l++g+l++ay+  +
  gi|298674332|ref|YP_003726082.1|  93 LAILTTGFLTAAYIS-Q 108
                                       333333333333322.2 PP

>> Neurensin  Neurensin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       0.5     1e+03      46      65 ..      35      54 ..      23      64 .. 0.75
   2 ?    9.2   1.5   0.00047      0.94      37      69 ..      74     106 ..      51     140 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.5
                         Neurensin 46 vvgtlvlllGvtallvGylv 65
                                      + ++ ++++G+ +l++   +
  gi|298674332|ref|YP_003726082.1| 35 TTSIALIAVGILILAITHRT 54
                                      55677778888888776655 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00047
                         Neurensin  37 esllwkvslvvgtlvlllGvtallvGylvprrl 69 
                                       ++l   +sl++gtl ++l +++l++G+l+ + +
  gi|298674332|ref|YP_003726082.1|  74 SVLYGVISLTSGTLTVTLSLAILTTGFLTAAYI 106
                                       3334445*********************98754 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.2      0.35     7e+02      45      65 ..       7      27 ..       5      29 .. 0.87
   2 ?   12.5   2.2   7.4e-05      0.15      16      57 ..      36      76 ..      34      85 .. 0.67
   3 ?    2.0   1.6      0.14   2.8e+02      17      57 ..      92     136 ..      85     141 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.35
                            DUF202 45 lilivlgiltllvglvrylrr 65
                                      +il+++g +t + +++++l++
  gi|298674332|ref|YP_003726082.1|  7 TILAGIGGVTGIGAVISFLQT 27
                                      589999999999999999987 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 7.4e-05
                            DUF202 16 tslalialglallrffltgepsalgkilglilivlgiltllv 57
                                      ts+alia+g+++l++ ++ e +a+ + +g+i+  ++i++ ++
  gi|298674332|ref|YP_003726082.1| 36 TSIALIAVGILILAITHRTEDKAI-RNIGVIICSFSIIASVL 76
                                      9*************9664444443.66666666666655433 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.14
                            DUF202  17 slalialglallrffltgepsalg....kilglilivlgiltllv 57 
                                       sla++++g++ ++  ++ e++ l+    ++l++i++ l ++t++v
  gi|298674332|ref|YP_003726082.1|  92 SLAILTTGFLTAAYISQTERKILTqkklSVLSVIFLCLFAFTAVV 136
                                       788888888888766655555553333467777777777777766 PP

>> DUF3784  Domain of unknown function (DUF3784)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   2.6     0.028        55      47      92 ..       6      51 ..       3      55 .. 0.75
   2 ?    2.8   4.8      0.07   1.4e+02      50      89 ..      38      81 ..      31      86 .. 0.71
   3 ?    3.4   1.7     0.046        91      40      89 ..      56     105 ..      52     107 .. 0.58
   4 ?    9.4   0.8   0.00057       1.1       5      62 ..      86     139 ..      79     154 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.028
                           DUF3784 47 givllligilflllgllsaiesealliialiviiiiviylivyank 92
                                      + +l  ig ++ + +++s++++e ++  ++  i +i+++++++a +
  gi|298674332|ref|YP_003726082.1|  6 RTILAGIGGVTGIGAVISFLQTELFSSPVTTSIALIAVGILILAIT 51
                                      6677889999999999989999999998888666666666666544 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.07
                           DUF3784 50 llligilflllgll....saiesealliialiviiiiviylivy 89
                                      + li++ +l+l++     +++ ++  +ii+ + ii++v+y ++ 
  gi|298674332|ref|YP_003726082.1| 38 IALIAVGILILAIThrteDKAIRNIGVIICSFSIIASVLYGVIS 81
                                      55666667777777667777777777777888888888888776 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.046
                           DUF3784  40 kklsrfmgivllligilflllgllsaiesealliialiviiiiviylivy 89 
                                       +k  r++g++++  +i+  +l+ ++ ++s +l++   ++i+ + +++ +y
  gi|298674332|ref|YP_003726082.1|  56 DKAIRNIGVIICSFSIIASVLYGVISLTSGTLTVTLSLAILTTGFLTAAY 105
                                       55566777777777744333333346666666666666666666666555 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.00057
                           DUF3784   5 llflilGilflkgkganLiaGYntmskeekekydekklsrfmgivllligilflllgl 62 
                                       +l + l++ +l     +L a+Y   s+ e++   +kkls  + i+l+l +   ++ ++
  gi|298674332|ref|YP_003726082.1|  86 TLTVTLSLAIL--TTGFLTAAYI--SQTERKILTQKKLSVLSVIFLCLFAFTAVVDAV 139
                                       45555666666..6667778884..8**********************9955554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       909  (0.0507); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1743.50
//
Query:       gi|298674333|ref|YP_003726083.1|  [L=161]
Description: hypothetical protein Metev_0363 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1099.26
//
Query:       gi|298674334|ref|YP_003726084.1|  [L=94]
Description: hypothetical protein Metev_0364 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-13   50.1   0.9    1.9e-13   50.1   0.9    2.3  3  PLDc_N         Phospholipase_D-nuclease N-terminal
     0.0028   17.8   1.7     0.0037   17.4   1.7    1.2  1  YbjM           Putative inner membrane protein of Enterobacte
     0.0031   17.2   2.5     0.0038   16.9   2.5    1.0  1  DUF4203        Domain of unknown function (DUF4203)
  ------ inclusion threshold ------
       0.14   12.6   2.2       0.17   12.3   2.2    1.1  1  DUF805         Protein of unknown function (DUF805)
       0.51    8.5   3.1       0.55    8.4   3.1    1.0  1  YfhO           Bacterial membrane protein YfhO
       0.79    9.7   7.1          1    9.3   7.0    1.4  1  Caveolin       Caveolin
       0.94    9.7   5.5       0.17   12.1   1.4    1.7  2  DPM3           Dolichol-phosphate mannosyltransferase subunit
        1.6    8.7   5.9        1.4    8.9   3.4    1.8  2  RseC_MucC      Positive regulator of sigma(E), RseC/MucC
          2    8.7   8.5       0.22   11.9   3.9    1.8  2  DUF2516        Protein of unknown function (DUF2516)
        5.5    6.6  10.8         58    3.3  11.0    1.9  1  DUF4131        Domain of unknown function (DUF4131)
        8.7    6.5  12.4        2.5    8.3   7.8    2.0  2  DUF4229        Protein of unknown function (DUF4229)


Domain annotation for each model (and alignments):
>> PLDc_N  Phospholipase_D-nuclease N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   2.3       4.5   7.3e+03      31      35 ..      13      17 ..       8      25 .. 0.48
   2 ?   -3.0   1.3       4.5   7.3e+03       7      28 ..      35      37 ..      31      41 .. 0.40
   3 !   50.1   0.9   1.1e-16   1.9e-13       1      42 []      42      85 ..      42      85 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4.5
                            PLDc_N 31 vlGai 35
                                      +lG++
  gi|298674334|ref|YP_003726084.1| 13 ILGIL 17
                                      33333 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.5
                            PLDc_N  7 lidiirdrnpssklaWllvilf 28
                                      +i                   f
  gi|298674334|ref|YP_003726084.1| 35 II-------------------F 37
                                      22...................1 PP

  == domain 3  score: 50.1 bits;  conditional E-value: 1.1e-16
                            PLDc_N  1 ilwiialidiirdrnpss...klaWllvilflPvlGailYllfGr 42
                                      ++w+++l+d+ + r+ps    kl+W+++i+f  ++Ga+lY++++r
  gi|298674334|ref|YP_003726084.1| 42 AFWLWVLVDCAT-REPSQdndKLVWVIIIVFTHFIGALLYYFIRR 85
                                      69**********.88888888**********************98 PP

>> YbjM  Putative inner membrane protein of Enterobacteriaceae
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   1.7   2.3e-06    0.0037      58     113 ..      29      84 ..       4      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.3e-06
                              YbjM  58 krllvpllGallaapvcllvlklvlaseeslwqelayllSavFWcalGallvlllr 113
                                        ++l++++ all a + +++++  + + ++   +l +++  vF   +Gall+ ++r
  gi|298674334|ref|YP_003726084.1|  29 INVLIAIIFALLFAFWLWVLVDCATREPSQDNDKLVWVIIIVFTHFIGALLYYFIR 84 
                                       467799999**************9999999999*********************97 PP

>> DUF4203  Domain of unknown function (DUF4203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   2.5   2.3e-06    0.0038      56     131 ..       7      85 ..       3      88 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.3e-06
                           DUF4203  56 slvaalvvGllgGllallfwelglfllgalgGlllallilsll..egglitslpskaiflvivvlgllgavlslkl. 129
                                        +++ +++G+l+ +  +++ +   +l+ ++  ll+a+++ +l+  +++  ++ ++k ++++i+v++ ++++l+ ++ 
  gi|298674334|ref|YP_003726084.1|   7 KFLIPIILGILISVYGIILGYPINVLIAIIFALLFAFWLWVLVdcATREPSQDNDKLVWVIIIVFTHFIGALLYYFi 83 
                                       56778889999998876666666667777888899999988886666667777888888777777777776655553 PP

                           DUF4203 130 qk 131
                                       ++
  gi|298674334|ref|YP_003726084.1|  84 RR 85 
                                       54 PP

>> DUF805  Protein of unknown function (DUF805)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.2   0.00011      0.17      18      93 ..       9      85 ..       3      94 .] 0.60

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                            DUF805 18 lfllllvivlallaavlaa...aavasalsvvlallllvpslavtvRRlHDtgrsgwllllllvplialllllvllllp 93
                                      l+ ++l i++++  ++l     + +a ++++++a++l+v+  + t     D ++  w++++++  +i+  ll   ++++
  gi|298674334|ref|YP_003726084.1|  9 LIPIILGILISVYGIILGYpinVLIAIIFALLFAFWLWVLVDCATREPSQDNDKLVWVIIIVFTHFIG-ALLY-YFIRR 85
                                      3333333443333333333655667777777777777777777777889*********9999999887.3333.33333 PP

>> YfhO  Bacterial membrane protein YfhO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   3.1   0.00034      0.55     363     437 ..       3      74 ..       1      91 [. 0.60

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00034
                              YfhO 363 qlkklkllaailllvlllliilllknkksynfltssqlllgllllllalllllllll......kkkkkklvllllll 433
                                       +l + k+l+ i+l +l+ ++ ++l ++ +  ++   +++++ll+ + +++l+           ++ + klv++++++
  gi|298674334|ref|YP_003726084.1|   3 KL-TYKFLIPIILGILISVYGIILGYPIN-VLI---AIIFALLFAFWLWVLV----DcatrepSQDNDKLVWVIIIV 70 
                                       45.78999999999999999999998777.122...3444444444444444....244569955555555555555 PP

                              YfhO 434 vlvl 437
                                       ++ +
  gi|298674334|ref|YP_003726084.1|  71 FTHF 74 
                                       5322 PP

>> Caveolin  Caveolin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   7.0   0.00064         1      61      92 ..      21      52 ..       4      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00064
                          Caveolin 61 ltallaiPlalilgilfallsalhiwlvvPlv 92
                                        ++l+ P+ ++++i+fall a+  w++v ++
  gi|298674334|ref|YP_003726084.1| 21 YGIILGYPINVLIAIIFALLFAFWLWVLVDCA 52
                                      56799**********************99886 PP

>> DPM3  Dolichol-phosphate mannosyltransferase subunit 3 (DPM3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       1.3   2.1e+03      39      54 ..       8      23 ..       2      31 .. 0.68
   2 ?   12.1   1.4    0.0001      0.17       8      53 ..      34      79 ..      30      84 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.3
                              DPM3 39 pvlPlwalvlfGaysl 54
                                      +++P+++ +l+ +y +
  gi|298674334|ref|YP_003726084.1|  8 FLIPIILGILISVYGI 23
                                      5667777666666654 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.0001
                              DPM3  8 lalallllalwlalllrlvslplskvqdevvpvlPlwalvlfGays 53
                                       ++++ll+a+wl++l++  +++ s+  d++v+v+ +++   +Ga +
  gi|298674334|ref|YP_003726084.1| 34 AIIFALLFAFWLWVLVDCATREPSQDNDKLVWVIIIVFTHFIGALL 79
                                      578999*************88889999****999998888888765 PP

>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   3.4   0.00084       1.4      69     120 ..       6      58 ..       1      69 [. 0.78
   2 ?    1.1   0.0      0.22   3.6e+02      96     113 ..      69      85 ..      57      93 .. 0.49

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00084
                         RseC_MucC  69 lvYllPllllilgallgsall.gssellaalgallglvlgflivrllskrlkk 120
                                       + +l+P++l il  + g +l+   + l+a+++all+++  +++v + +++ ++
  gi|298674334|ref|YP_003726084.1|   6 YKFLIPIILGILISVYGIILGyPINVLIAIIFALLFAFWLWVLVDCATREPSQ 58 
                                       5699*****99999999999876788889999999998888888887776444 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.22
                         RseC_MucC  96 aalgallglvlgflivrl 113
                                        +++ ++g++l+++i r+
  gi|298674334|ref|YP_003726084.1|  69 IVFTHFIGALLYYFI-RR 85 
                                       233334444444433.33 PP

>> DUF2516  Protein of unknown function (DUF2516)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       4.9   8.1e+03      11      76 ..      14      19 ..       5      25 .. 0.43
   2 ?   11.9   3.9   0.00013      0.22       5      58 ..      30      78 ..      26      85 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4.9
                           DUF2516 11 lalvvlvlslvAlvdalrrradaFeaagkrtKpfWlailgvallvlllglfgalsllgliavvaal 76
                                      l++++                                                             
  gi|298674334|ref|YP_003726084.1| 14 LGILI------------------------------------------------------------S 19
                                      22222............................................................2 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00013
                           DUF2516  5 alvllllalvvlvlslvAlvdalrrradaFeaagkrtKpfWlailgvallvlll 58
                                      ++++++++ +++++ l+ lvd+++r +      + + K +W++i++ + +++ l
  gi|298674334|ref|YP_003726084.1| 30 NVLIAIIFALLFAFWLWVLVDCATREPS-----QDNDKLVWVIIIVFTHFIGAL 78
                                      688999999***************9876.....455688********9999987 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3  11.0     0.035        58       4      59 ..       5      57 ..       2      88 .. 0.54

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.035
                           DUF4131  4 plalvllalllllllllllllrrrprrrvllllllllllallgfalrapqpnandl 59
                                      ++++++ ++l++l+ + +++l     +   l++++++ll+++++++ ++ +++++ 
  gi|298674334|ref|YP_003726084.1|  5 TYKFLIPIILGILISVYGIIL---GYPINVLIAIIFALLFAFWLWVLVDCATREPS 57
                                      666777777777777776663...33333333333444444444333333333222 PP

>> DUF4229  Protein of unknown function (DUF4229)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   7.8    0.0015       2.5       9      45 ..       9      45 ..       5      55 .. 0.87
   2 ?    0.9   0.5       0.3   4.9e+02      30      49 ..      64      83 ..      45      90 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0015
                           DUF4229  9 aLfvvltavillvarliglpvpllvaallAlvvalpl 45
                                      ++ ++l ++i + + ++g p+++l+a+++Al+ a+ l
  gi|298674334|ref|YP_003726084.1|  9 LIPIILGILISVYGIILGYPINVLIAIIFALLFAFWL 45
                                      666788888889999999****************987 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.3
                           DUF4229 30 pllvaallAlvvalplSmvl 49
                                       +++++++   + ++l +++
  gi|298674334|ref|YP_003726084.1| 64 VWVIIIVFTHFIGALLYYFI 83
                                      45555566666666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1198  (0.0668191); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); expected 358.6 (0.02)
Passed Vit filter:                       126  (0.00702772); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 722.30
//
Query:       gi|298674335|ref|YP_003726085.1|  [L=410]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      6e-24   84.6   0.2    1.8e-23   83.0   0.0    1.9  2  OrfB_IS605      Probable transposase
    1.6e-09   37.5   1.0    4.6e-09   36.1   0.2    2.2  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    0.00051   19.8   0.4     0.0014   18.5   0.4    1.7  1  DUF919          Nucleopolyhedrovirus protein of unknown funct
  ------ inclusion threshold ------
      0.056   13.2   0.1        0.1   12.3   0.1    1.4  1  Ydc2-catalyt    Mitochondrial resolvase Ydc2 / RNA splicing M
      0.075   13.4   0.0       0.18   12.2   0.0    1.6  1  RuvX            Holliday junction resolvase


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.2       1.6   5.7e+03      75      87 ..      20      32 ..       7      64 .. 0.61
   2 !   83.0   0.0   5.1e-27   1.8e-23      10     119 ..     185     292 ..     176     293 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.6
                        OrfB_IS605 75 rklarlhrkrsrr 87
                                      ++l++l+++++++
  gi|298674335|ref|YP_003726085.1| 20 KRLTKLSKNLYNF 32
                                      4444444444443 PP

  == domain 2  score: 83.0 bits;  conditional E-value: 5.1e-27
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsr 86 
                                        ++ + n++++iDlG+ n+at+vt++gt+f+ +gr +ks +++++ke+ +lqs ++k++       k+ r ++kr  
  gi|298674335|ref|YP_003726085.1| 185 IAELDYNSHLSIDLGVDNFATCVTTSGTAFILDGRGIKSYNRWWNKEKSRLQSVYDKQN--VDDGIKMDRFSNKRFW 259
                                       66677899**************************************************9..9*************** PP

                        OrfB_IS605  87 rrkhllhklathliktlkevgvetLnvgnmkdi 119
                                       ++++++++ ++h++k++ e+ ++++++g+mk+i
  gi|298674335|ref|YP_003726085.1| 260 KINDFMNQCVNHIVKHCLENRIGNIVIGEMKEI 292
                                       *******************************87 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.1   4.1e+03       9      21 ..     167     179 ..     162     181 .. 0.88
   2 !   36.1   0.2   1.3e-12   4.6e-09       1      69 []     311     385 ..     311     385 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.1
                    OrfB_Zn_ribbon   9 eykakeyGikvee 21 
                                       +yk +++ i++++
  gi|298674335|ref|YP_003726085.1| 167 KYKGRWFEIEYVY 179
                                       79*******9987 PP

  == domain 2  score: 36.1 bits;  conditional E-value: 1.3e-12
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke......alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f+++k++l  k++ +Gi+++evn+ayTSk  +   +  ++      ++++r    ++ g  +++D+n+a+Nil++
  gi|298674335|ref|YP_003726085.1| 311 FARFKQKLVSKCEYHGINYHEVNEAYTSKVDALALEPIRKhnkylgKRHKRGIFQSSTGRLINADINGALNILRK 385
                                       899**************************98777766666667899999***99999***************986 PP

>> DUF919  Nucleopolyhedrovirus protein of unknown function (DUF919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.4   3.8e-07    0.0014      15      58 ..       4      45 ..       2      47 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3.8e-07
                            DUF919 15 qaKrkltiksqHfErlkkitKnpkElqdlekklnklRqeFLnfg 58
                                       +K  l+ + q +E lk++tK +k l +   +l ++Rq+F+n+g
  gi|298674335|ref|YP_003726085.1|  4 TQKNHLRTDKQTYETLKRLTKLSKNLYNF--TLYTIRQYFFNYG 45
                                      58999******************888765..8***********9 PP

>> Ydc2-catalyt  Mitochondrial resolvase Ydc2 / RNA splicing MRS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   2.9e-05       0.1       2      88 ..     194     320 ..     194     325 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.9e-05
                                       EEEEE-STTEEEEEEEE.......................-TTS-EEEEEEE.EE-TT................... CS
                      Ydc2-catalyt   2 lSIDmGikNlAfaklkv................ekkskkakekelptlnawk.klnlsellstsaeesk........ 53 
                                       lSID+G+ N+A +++++                +       +ke+ +l+  + k n++ +  +++++s+        
  gi|298674335|ref|YP_003726085.1| 194 LSIDLGVDNFATCVTTSgtafildgrgiksynrW------WNKEKSRLQSVYdKQNVD-DGIKMDRFSNkrfwkind 263
                                       8***************988888888886644431......222222222222222222.111121111133444444 PP

                                       ..............................SS-TT--------SHHHHHHHHHHHHH CS
                      Ydc2-catalyt  54 ......................seeeeeskskektkekekesfspdalaelAykLvs 88 
                                                               e +e k++++  +k++++f+   +a+  +kLvs
  gi|298674335|ref|YP_003726085.1| 264 fmnqcvnhivkhclenrignivIGEMKEIKQEQNIGKKNNQNFQTIPFARFKQKLVS 320
                                       555555555566665555655533345555555555666666666666666666655 PP

>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.9e-05      0.18      37     106 ..     266     345 ..     253     367 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.9e-05
                                       HHHHHHHHHHHHHTT--EEEEE--........----SSS---SSTTHHHHHHHHHT....T-EEEEE--S----XXX CS
                              RuvX  37 ekdleelkelvkeeeveeiVvGlP........lnldgsegesakkvrkfaeeLakrl..kklpvelvDErlttveae 103
                                       ++ ++++ + + e+++ +iV+G          +  +++++ ++  +++f ++L +++  ++++ + v+E +t++  +
  gi|298674335|ref|YP_003726085.1| 266 NQCVNHIVKHCLENRIGNIVIGEMkeikqeqnIGKKNNQNFQTIPFARFKQKLVSKCeyHGINYHEVNEAYTSKVDA 342
                                       68899*****************9977777755556667777778889999999999877899***********8755 PP

                                       XXX CS
                              RuvX 104 ril 106
                                        +l
  gi|298674335|ref|YP_003726085.1| 343 LAL 345
                                       444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       972  (0.0542138); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2679.74
//
Query:       gi|298674336|ref|YP_003726086.1|  [L=144]
Description: hypothetical protein Metev_0366 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.29   11.1   6.4       0.09   12.8   3.3    1.7  2  MARVEL         Membrane-associating domain
          1    9.4   3.5        1.4    9.1   0.1    2.3  2  Col_cuticle_N  Nematode cuticle collagen N-terminal domain
        1.4    9.2   8.5       0.17   12.2   2.2    2.2  2  DUF4064        Protein of unknown function (DUF4064)
        4.8    7.4  10.6       0.27   11.5   1.2    2.8  3  DUF3784        Domain of unknown function (DUF3784)
        7.3    6.2   7.1        6.7    6.4   2.5    2.6  2  DUF1673        Protein of unknown function (DUF1673)


Domain annotation for each model (and alignments):
>> MARVEL  Membrane-associating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   3.3   2.5e-05      0.09      23      95 ..      16     103 ..       7     108 .. 0.73
   2 ?   -2.0   0.1      0.92   3.3e+03      17      28 ..     120     131 ..     116     141 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.5e-05
                            MARVEL  23 liaslia.................kldqllgspssalnfavfvavfsflyalfllvlylfknsaftsilwplidliv 82 
                                       +++++++                 ++      + + +++ ++++ f f+++l+l+vl ++ + a+  ++   +++++
  gi|298674336|ref|YP_003726086.1|  16 IMGTFLKwhefmeyyraygpsgigEVS--QRVSGTVAGYDLTAGKFIFALSLILVVLVFLPKPALYHKRLLSAEFFL 90 
                                       444444444566666666666555332..2233466788889999999999999999777799************** PP

                            MARVEL  83 dalaallwlvafi 95 
                                       + ++a l+++++ 
  gi|298674336|ref|YP_003726086.1|  91 TSVIAGLFFIGGL 103
                                       **********986 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.92
                            MARVEL  17 aiiilgliasli 28 
                                       a++  g++++l+
  gi|298674336|ref|YP_003726086.1| 120 AVLLAGCVITLV 131
                                       344444444443 PP

>> Col_cuticle_N  Nematode cuticle collagen N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   1.0      0.24   8.5e+02       6      19 ..      61      74 ..      59      75 .. 0.76
   2 ?    9.1   0.1   0.00039       1.4       8      32 ..     120     144 .]     117     144 .] 0.91

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.24
                     Col_cuticle_N  6 lStvailsslitlp 19
                                      +++  il++l++lp
  gi|298674336|ref|YP_003726086.1| 61 FALSLILVVLVFLP 74
                                      67778888888887 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00039
                     Col_cuticle_N   8 tvailsslitlpsiyndiqsfqsev 32 
                                       +v + +++itl +i  d++sf s++
  gi|298674336|ref|YP_003726086.1| 120 AVLLAGCVITLVYIKKDLNSFNSDI 144
                                       678899****************986 PP

>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   2.2   4.6e-05      0.17      17     102 ..       8      98 ..       6      99 .. 0.74
   2 ?   -0.9   3.1      0.56     2e+03      80      80 ..     107     107 ..      85     139 .. 0.46

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.6e-05
                           DUF4064  17 illglllllflfllssgefsqeltee.....qalsgedasavleflstllivlgvialiaivlgivgalllkknkkv 88 
                                       +l+gl+l+++  +l++ ef++ + +      +++s+ ++ +v+++  t + +++ ++li+ vl ++    l +++ +
  gi|298674336|ref|YP_003726086.1|   8 VLAGLFLIIMGTFLKWHEFMEYYRAYgpsgiGEVSQRVSGTVAGYDLTAGKFIFALSLILVVLVFLPKPALYHKRLL 84 
                                       5788999999999*******999888977777777777777777777777777777777777766655555555668 PP

                           DUF4064  89 sGilfiiaailslf 102
                                       s+ +f+ + i++lf
  gi|298674336|ref|YP_003726086.1|  85 SAEFFLTSVIAGLF 98 
                                       88888888888877 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.56
                           DUF4064  80 l 80 
                                       +
  gi|298674336|ref|YP_003726086.1| 107 F 107
                                       2 PP

>> DUF3784  Domain of unknown function (DUF3784)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.25   8.9e+02       4      14 ..      11      21 ..       7      32 .. 0.53
   2 ?    1.9   2.7      0.07   2.5e+02      46      84 ..      56      96 ..      48     100 .. 0.70
   3 ?   11.5   1.2   7.4e-05      0.27      41      92 ..      82     135 ..      75     136 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.25
                           DUF3784  4 allflilGilf 14
                                      +l+++i+G ++
  gi|298674336|ref|YP_003726086.1| 11 GLFLIIMGTFL 21
                                      34444444433 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.07
                           DUF3784 46 mgivllligilflllgll..saiesealliialiviiiivi 84
                                      +g++++ +++++++l +l  +a+ ++ ll + +++  +i+ 
  gi|298674336|ref|YP_003726086.1| 56 AGKFIFALSLILVVLVFLpkPALYHKRLLSAEFFLTSVIAG 96
                                      79999999999999999999777777777776664443333 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 7.4e-05
                           DUF3784  41 klsrfmgivllligilflllgllsaieseallii..aliviiiiviylivyank 92 
                                       +l  +   ++ +i+ lf++ gl++ ++ ++ +    +l+v+++++++++vy++k
  gi|298674336|ref|YP_003726086.1|  82 RLLSAEFFLTSVIAGLFFIGGLIPVFTPTQNIGPgiGLAVLLAGCVITLVYIKK 135
                                       455555556677888********6666655555434778************997 PP

>> DUF1673  Protein of unknown function (DUF1673)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   2.5    0.0019       6.7      83     117 ..       7      41 ..       2     108 .. 0.71
   2 ?    0.2   0.7      0.14     5e+02      77      96 ..     115     134 ..      97     140 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0019
                           DUF1673  83 alliglllsllliiltwkkqmqiyddikralvekt 117
                                        +l+gl+l+++   l+w + m++y    ++ + + 
  gi|298674336|ref|YP_003726086.1|   7 RVLAGLFLIIMGTFLKWHEFMEYYRAYGPSGIGEV 41 
                                       689*********************96655555444 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.14
                           DUF1673  77 lGinlialliglllslllii 96 
                                        Gi l++ll+g+++ l+ i+
  gi|298674336|ref|YP_003726086.1| 115 PGIGLAVLLAGCVITLVYIK 134
                                       4889999*****99998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.33s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 901.80
//
Query:       gi|298674337|ref|YP_003726087.1|  [L=94]
Description: hypothetical protein Metev_0369 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.037   14.1   1.7       0.05   13.7   1.7    1.2  1  DUF3923   Protein of unknown function (DUF3923)


Domain annotation for each model (and alignments):
>> DUF3923  Protein of unknown function (DUF3923)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.7   2.8e-06      0.05       6      52 ..      37      81 ..      32      87 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.8e-06
                           DUF3923  6 ilnifwillfvilalfIfiRkvDgaGvvqTpelklitllvlviafvl 52
                                      il+ + +l+f i+alf+ ++ v    v++++++++++ ++l++a+++
  gi|298674337|ref|YP_003726087.1| 37 ILSAASMLVFSIIALFLATYMVEY--VANSANYQVVGNYILLSASII 81
                                      6778999***************85..9*****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1068  (0.0595683); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 595.65
//
Query:       gi|298674338|ref|YP_003726088.1|  [L=55]
Description: hypothetical protein Metev_0370 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.046   14.1   0.8      0.048   14.0   0.8    1.1  1  ERGIC_N   Endoplasmic Reticulum-Golgi Intermediate Compartmen
       0.13   12.3   0.2       0.16   12.1   0.2    1.3  1  DapB_N    Dihydrodipicolinate reductase, N-terminus


Domain annotation for each model (and alignments):
>> ERGIC_N  Endoplasmic Reticulum-Golgi Intermediate Compartment (ERGIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.8   5.3e-06     0.048       4      45 ..       3      41 ..       1      52 [. 0.69

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.3e-06
                                      XXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXX.X CS
                           ERGIC_N  4 fDafpKvpedltqktlsGgiislvcillilfLllselteylt 45
                                      f++++Kv ed+   +++  iis+ +il +l+++l  + ++++
  gi|298674338|ref|YP_003726088.1|  3 FNIYSKVLEDF---SKKNTIISITIILALLIVILDIIVDFTD 41
                                      89*********...5555566666666666666655555555 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   1.8e-05      0.16      56      82 ..      21      47 ..       3      52 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.8e-05
                                      BEBSSHHHHHHH-SEEEE-S-HHHHHH CS
                            DapB_N 56 avtddleevlekadvliDFTtpeavle 82
                                       +t  l+ ++   d+++DFT pea+l 
  gi|298674338|ref|YP_003726088.1| 21 SITIILALLIVILDIIVDFTDPEASLT 47
                                      4444455555568**********9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       908  (0.0506442); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 348.66
//
Query:       gi|298674339|ref|YP_003726089.1|  [L=499]
Description: integral membrane sensor signal transduction histidine kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.1e-23   81.1   0.4    4.6e-22   78.6   0.0    2.1  2  HATPase_c        Histidine kinase-, DNA gyrase B-, and HSP90-
    2.4e-06   27.5   0.0    5.9e-06   26.2   0.0    1.7  1  HisKA            His Kinase A (phospho-acceptor) domain
    7.9e-05   22.6   0.0    0.00022   21.2   0.0    1.8  1  HATPase_c_2      Histidine kinase-like ATPase domain
  ------ inclusion threshold ------
      0.039   13.1   0.5        0.1   11.7   0.4    1.5  2  Iso_dh           Isocitrate/isopropylmalate dehydrogenase
        1.4    8.9  11.4        2.7    8.0   0.2    3.5  3  DUF4083          Domain of unknown function (DUF4083)
        3.1    7.6   6.4        0.7    9.7   0.8    2.5  2  Methyltransf_31  Methyltransferase domain


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.2       0.6   1.8e+03      10      33 ..     329     352 ..     328     373 .. 0.67
   2 !   78.6   0.0   1.5e-25   4.6e-22       6     110 ..     393     496 ..     390     498 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.6
                                       HHHHHHHHHHHHSTTTEEEEEEEE CS
                         HATPase_c  10 isnlvdNavkfatkageieveika 33 
                                       i++l++Na +fa+ +++  +e + 
  gi|298674339|ref|YP_003726089.1| 329 IIELLENASEFAKLENTENIEFEN 352
                                       789********7766665665552 PP

  == domain 2  score: 78.6 bits;  conditional E-value: 1.5e-25
                                       HHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHHH CS
                         HATPase_c   6 LrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsivk 82 
                                       ++q+i nl++Na+k+++++++i++ ++ + +  +i v D G G+p ed ++lf++fs+  ++k g +gtG+Gl+ivk
  gi|298674339|ref|YP_003726089.1| 393 IEQAIANLLSNAIKYSPENSTIKIYLTDKGNFWRINVADFGEGVPDEDKPHLFDRFSR--KDKKGIKGTGFGLAIVK 467
                                       689************99**********55599**************************..778888*********** PP

                                       HHHHHTTTEEEEEEET.TTEEEEEEEEES CS
                         HATPase_c  83 klvelmgGeiwvesep.grGttftftlpl 110
                                        +v+l+gG + v+++p g+G+ f+ftl +
  gi|298674339|ref|YP_003726089.1| 468 MVVDLHGGYVGVDDNPeGKGSVFWFTLVK 496
                                       ************88888********9975 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0     2e-09   5.9e-06       2      66 ..     281     344 ..     280     345 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 2e-09
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                             HisKA   2 lgrflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsriea 66 
                                       +  f+  + H+L +P s i+g+a++L ++ + + +  ++l++i+s+ + + +l+e+  +++++e+
  gi|298674339|ref|YP_003726089.1| 281 KDTFTDIIRHDLLNPASIISGYAKLLINK-ESDTSKIQMLKKIQSSNDKIIELLENASEFAKLEN 344
                                       5678899*******************553.36677888************************997 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   7.3e-08   0.00022      31     111 ..     392     472 ..     349     493 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 7.3e-08
                       HATPase_c_2  31 eirlaveEactNavehayleapegpvevrlesdeealtvevaDsGpg.fdpe..tlpdpteeepkeslkegGrGlal 104
                                        i+ a++ +++Na+++  ++    ++++ l+++++  ++ vaD G+g  d    +l d+   ++k   k  G+Gla+
  gi|298674339|ref|YP_003726089.1| 392 MIEQAIANLLSNAIKYSPEN---STIKIYLTDKGNFWRINVADFGEGvPDEDkpHLFDRFSRKDKKGIKGTGFGLAI 465
                                       57888888999999998874...67******************9999444431134455555558889999****** PP

                       HATPase_c_2 105 ikglvDe 111
                                       +k++vD 
  gi|298674339|ref|YP_003726089.1| 466 VKMVVDL 472
                                       *****95 PP

>> Iso_dh  Isocitrate/isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       0.5   1.5e+03     279     302 ..     284     307 ..     280     328 .. 0.80
   2 ?   11.7   0.4   3.4e-05       0.1      83     190 ..     317     425 ..     306     441 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.5
                                       -CCCTTSS-S-THHHHHHHHHHHH CS
                            Iso_dh 279 apdiagkdkaNpiavilSaalmLr 302
                                        +di + d  Np + i   a +L 
  gi|298674339|ref|YP_003726089.1| 284 FTDIIRHDLLNPASIISGYAKLLI 307
                                       68999*******999988887774 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 3.4e-05
                                       HHHHHHHHHTT.EEEEEEEEE-BCCTTCCSSBTHHHHCT-EEE.EEEE-SSCGGCS.SEEEEETTG..GGGEEEEEE CS
                            Iso_dh  83 ngLlaLrkeld.lfanlrpvkvfeklkvksplkrevveevdlv.ivReltggiYfg.eekekkgsi.fteevavdtk 155
                                       + L+++  + d ++  l ++  f kl++ + ++    e+ d+v i+R  +++  f  ++k+ k++   ++e  + ++
  gi|298674339|ref|YP_003726089.1| 317 QMLKKIQSSNDkIIELLENASEFAKLENTENIE---FENRDIVeIIRKIVDDFQFQlINKNLKTEVlAENEHLCRIN 390
                                       457777777776777788888998888888888...589999989*******76652677777777799999***** PP

                                       EEEHHHHHHHHHHHHHHHHHTTTSEEEEEESTTTT CS
                            Iso_dh 156 lyseeeieriaraafelAlkrgkkkvtlvdKanvl 190
                                       ++ e++i  + + a+++  ++   k++l+dK+n  
  gi|298674339|ref|YP_003726089.1| 391 PMIEQAIANLLSNAIKYSPENSTIKIYLTDKGNFW 425
                                       ********************************975 PP

>> DUF4083  Domain of unknown function (DUF4083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.2    0.0009       2.7       8      25 ..      11      28 ..      10      49 .. 0.75
   2 ?    1.2   0.3      0.12   3.5e+02       8      25 ..     247     264 ..     237     289 .. 0.71
   3 ?    4.8   1.3    0.0091        27      40      55 ..     315     334 ..     305     336 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0009
                           DUF4083  8 liivivLilllvfsftlf 25
                                      ++iv++L++l+v s+ + 
  gi|298674339|ref|YP_003726089.1| 11 YVIVFILTVLIVSSIAFY 28
                                      79**********987664 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.12
                           DUF4083   8 liivivLilllvfsftlf 25 
                                        i++++++ll +  ftlf
  gi|298674339|ref|YP_003726089.1| 247 FILILIVTLLPLSYFTLF 264
                                       355555555556666665 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.0091
                           DUF4083  40 skeleqKL....DkiIeLLe 55 
                                       ++++ +K     DkiIeLLe
  gi|298674339|ref|YP_003726089.1| 315 KIQMLKKIqssnDKIIELLE 334
                                       444444444444*******9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.5      0.27     8e+02      73      82 ..     140     150 ..     114     218 .. 0.61
   2 ?    9.7   0.8   0.00023       0.7      35     100 ..     327     399 ..     321     417 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.27
                   Methyltransf_31  73 ekfDlilsn.e 82 
                                       +kfD+i+ + +
  gi|298674339|ref|YP_003726089.1| 140 KKFDVINEDdQ 150
                                       56666654422 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00023
                   Methyltransf_31  35 DiseeaielArenaqklgldnveFeqgdieelekl.ledekfDlilsn...evl...naladpdkileeierv 100
                                       D   e +e A e a+  + +n+eFe  di e+  + + d +f li+ n   evl    +l+  +  +e+++ +
  gi|298674339|ref|YP_003726089.1| 327 DKIIELLENASEFAKLENTENIEFENRDIVEIIRKiVDDFQFQLINKNlktEVLaenEHLCRINPMIEQAIAN 399
                                       55668999****999999*************555669999****99996665556665555555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (499 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1326  (0.0739584); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 3142.74
//
Query:       gi|298674340|ref|YP_003726090.1|  [L=171]
Description: CheW protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-38  129.8   3.5    6.2e-38  129.6   3.5    1.1  1  CheW      CheW-like domain


Domain annotation for each model (and alignments):
>> CheW  CheW-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.6   3.5   3.4e-42   6.2e-38       1     135 [.      21     156 ..      21     159 .. 0.97

  Alignments for each domain:
  == domain 1  score: 129.6 bits;  conditional E-value: 3.4e-42
                                       EEEEEEETTEEEEEEGGGEEEEEECCT.BTTTTSSTTEEEEEEETTEEEEEEEHHHHCTSSSSTTSTCEEEEEEEET CS
                              CheW   1 qlllfrlgeetyaiplakvreilevppitpipgapgavlgvinlrGevipvidLrellglgpeesrentrvivvelg 77 
                                       ql++f+lg+e++++++++v+ei+++ + t+ip+ap++v+gvin+rG++i vi+L+++l l+ +e+++++r+ivve+g
  gi|298674340|ref|YP_003726090.1|  21 QLVVFQLGGEEFGVDIMQVQEIIRMHQGTRIPQAPDYVKGVINIRGNIIVVINLEKILELPIKEEDDDNRIIVVEIG 97 
                                       789**********************999************************************************* PP

                                       TEEEEEEESEEEEEEEEECCGEETT...TSSTSSTCCCEEEEEECTTSEEEEEE-CCCHHH CS
                              CheW  78 nqvvGllVdevkgiqeivikqiepp...lglssdlagyisGatklgdgrlvliLDveallr 135
                                       ++ +G+ Vd+v+++++i  +++ep+   ++ s++++++i+G+ kl d+rl+++LD+e +l+
  gi|298674340|ref|YP_003726090.1|  98 GNILGMTVDSVSEVLSIAKSNVEPApdmIT-SKINSDFIKGVGKL-DDRLLILLDLENVLT 156
                                       *************************99655.9999**********.***********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1295.99
//
Query:       gi|298674341|ref|YP_003726091.1|  [L=707]
Description: Pas/Pac sensor-containing methyl-accepting chemotaxis sensory transducer [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-54  184.2  69.5    2.6e-50  170.6  26.2    5.2  5  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
      7e-33  113.2   0.0    3.8e-15   56.1   0.0    2.8  2  PAS_4            PAS fold
    3.9e-25   88.1   3.3    3.7e-13   49.6   0.0    3.6  3  PAS_9            PAS domain
    9.5e-17   61.0   0.0      3e-08   33.7   0.0    3.2  2  PAS              PAS fold
    1.9e-09   38.1   5.9       0.01   16.4   0.0    5.5  4  PAS_10           PAS domain
    9.4e-09   35.5  12.2    7.7e-06   26.2   0.1    5.7  4  HAMP             HAMP domain
    5.3e-08   32.9  35.0     0.0031   17.4  10.4    3.5  3  PhageMin_Tail    Phage-related minor tail protein
    1.1e-07   32.0  54.1     0.0079   16.4   8.6    7.6  7  DUF948           Bacterial protein of unknown function (DUF94
      1e-06   28.8  52.0      0.011   15.8   7.9    6.2  7  DUF1664          Protein of unknown function (DUF1664)
    4.2e-05   23.8  52.2       0.48   10.8   4.8    6.7  6  BLOC1_2          Biogenesis of lysosome-related organelles co
    4.5e-05   23.4  35.1      0.035   14.0   8.7    4.6  4  CheZ             Chemotaxis phosphatase, CheZ
    9.8e-05   22.1  41.4     0.0064   16.2  16.3    3.3  2  YkyA             Putative cell-wall binding lipoprotein
     0.0002   21.6  23.9      0.027   14.7   7.0    3.8  3  Med30            Mediator complex subunit 30
    0.00037   18.8  39.4    0.00085   17.6  17.1    2.7  3  EzrA             Septation ring formation regulator, EzrA
    0.00038   19.3   9.8    0.00038   19.3   9.8    3.0  3  DUF773           CDK5 regulatory subunit-associated protein 3
     0.0004   20.3   0.0       0.32   11.1   0.0    2.8  2  PAS_8            PAS domain
     0.0006   20.0  37.5        1.2    9.4   4.0    7.6  7  WXG100           Proteins of 100 residues with WXG
     0.0011   18.7  23.6      0.041   13.6   9.1    2.9  2  Collagen_mid     Bacterial collagen, middle region
     0.0012   18.7  39.1       0.33   10.8   5.9    4.9  4  Sec34            Sec34-like family
     0.0014   18.6  62.7      0.013   15.5   7.0    6.1  6  Laminin_II       Laminin Domain II
     0.0019   16.5  45.8     0.0033   15.7  45.8    1.3  1  FPP              Filament-like plant protein, long coiled-coi
     0.0023   18.2   0.0        3.9    7.8   0.0    2.7  2  PAS_3            PAS fold
     0.0034   16.1  43.4      0.014   14.0  20.4    2.4  2  AAA_13           AAA domain
     0.0067   14.4  39.1     0.0048   14.9  19.3    3.2  3  Prominin         Prominin
     0.0083   15.0  47.0       0.22   10.4  14.4    3.7  3  Spc7             Spc7 kinetochore protein
  ------ inclusion threshold ------
      0.014   15.8   4.1      0.014   15.8   4.1    4.7  4  DUF4200          Domain of unknown function (DUF4200)
      0.015   14.5  44.0       0.14   11.2   4.4    3.7  3  APG17            Autophagy protein Apg17
      0.028   11.9  37.2       0.05   11.1  37.2    1.4  1  DUF3584          Protein of unknown function (DUF3584)
      0.057   11.8  43.8       0.72    8.1  20.6    2.4  2  MAD              Mitotic checkpoint protein
       0.06   12.5  38.2       0.51    9.4   0.8    4.9  5  RmuC             RmuC family
      0.062   13.0   0.2      0.062   13.0   0.2    4.0  3  BAR_3            BAR domain of APPL family
      0.092   12.4  22.6        2.1    8.0   1.3    5.6  4  RPW8             Arabidopsis broad-spectrum mildew resistance
       0.13   12.1  39.3       0.42   10.4  10.8    3.4  3  KASH_CCD         Coiled-coil region of CCDC155 or KASH
       0.21   12.1  46.8        2.8    8.5   1.1    5.3  5  Syntaxin-6_N     Syntaxin 6, N-terminal
       0.27   11.9  35.8        1.5    9.5   2.4    5.3  5  DUF2203          Uncharacterized conserved protein (DUF2203)
       0.31    9.5   6.6       0.94    7.9   1.2    2.2  2  FUSC             Fusaric acid resistance protein family
       0.33   11.4  34.6       0.94   10.0   6.9    3.9  4  FlgN             FlgN protein
       0.34   11.3  50.8       0.99    9.8   6.3    6.5  5  Syntaxin_2       Syntaxin-like protein
       0.34   10.6   3.3       0.39   10.4   0.1    2.7  2  DUF3158          Protein of unknown function (DUF3158)
       0.43   11.1   4.1       0.58   10.7   0.3    3.0  2  TetR_C_18        Tetracyclin repressor-like, C-terminal domai
       0.58   10.4  45.8       0.21   11.9   6.8    5.7  5  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
       0.68   10.4  40.8        6.3    7.3   0.6    8.0  3  H-kinase_dim     Signal transducing histidine kinase, homodim
       0.79    8.5  49.4        1.7    7.4  30.8    2.9  2  DUF812           Protein of unknown function (DUF812)
       0.85   10.1  38.9       0.65   10.5   0.5    5.6  4  Snapin_Pallidin  Snapin/Pallidin
        1.2    9.2  33.3       0.19   11.7   1.4    4.9  5  Serine_rich      Serine rich protein interaction domain
        1.4    9.4  25.7        2.6    8.5   0.6    5.2  4  T7SS_ESX_EspC    Excreted virulence factor EspC, type VII ESX
        1.7    8.5  39.0      0.099   12.4   2.9    8.1  8  DASH_Duo1        DASH complex subunit Duo1
        1.7    7.6  49.7        2.4    7.1  24.0    3.0  3  AIP3             Actin interacting protein 3
        2.2    7.5  48.0      0.036   13.4  12.9    4.3  4  DUF3450          Protein of unknown function (DUF3450)
        2.3    8.3  47.6       0.54   10.3   5.9    4.6  4  GldM_N           GldM N-terminal domain
        3.1    6.6  38.2          2    7.2  17.8    2.6  2  CALCOCO1         Calcium binding and coiled-coil domain (CALC
          4    7.5  41.0       0.13   12.3   2.2    6.1  4  COG2             COG (conserved oligomeric Golgi) complex com
        4.1    7.9  58.0        0.4   11.2   4.2    8.2  7  NPV_P10          Nucleopolyhedrovirus P10 protein
        4.2    6.2  36.8    4.1e+02   -0.4   0.1    4.1  2  DUF677           Protein of unknown function (DUF677)
        4.4    6.2  53.3      0.028   13.4   4.8    4.2  3  IFT57            Intra-flagellar transport protein 57
          5    6.4  23.6        5.1    6.3   2.5    3.8  3  CorA             CorA-like Mg2+ transporter protein
          5    6.9  56.7      0.032   14.1  21.4    4.5  5  Mer2             Mer2
        5.1    7.4  20.0        3.3    8.0   3.1    4.4  3  Rx_N             Rx N-terminal domain
        7.5    5.7  47.0       0.31   10.3   9.0    4.4  5  TMPIT            TMPIT-like protein
        8.4    6.6  49.9        1.2    9.3   7.1    3.8  3  ATG16            Autophagy protein 16 (ATG16)
        8.5    5.9  44.1      0.043   13.4  17.4    3.6  3  Filament         Intermediate filament protein
        9.7    6.9  29.1        9.9    6.8  12.2    4.7  2  ING              Inhibitor of growth proteins N-terminal hist


Domain annotation for each model (and alignments):
>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   6.5   0.00031     0.091      89     169 ..     349     429 ..     326     431 .. 0.64
   2 !   18.5  11.0   4.6e-06    0.0013      86     169 ..     370     450 ..     358     451 .. 0.90
   3 !   16.6  11.3   1.8e-05    0.0053      88     160 ..     432     504 ..     429     506 .. 0.93
   4 !  170.6  26.2   8.9e-53   2.6e-50       8     171 ..     485     648 ..     479     649 .. 0.95
   5 ?    7.4   5.6     0.012       3.6     116     167 ..     642     693 ..     640     698 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00031
                                       HHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHH....HHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  89 keiealiieiqkeindsvesleetrqrveegselveetgealkeiveav....aevadlvqeiaaaseeqsasieev 161
                                       k ++++i    ++ + + ++  +t+   +e ++++ee +++lk++ve++    ++v+++ +e++a+se++++s++++
  gi|298674341|ref|YP_003726091.1| 349 KRVAEAI----ADGDLTQSINVDTKGDLKEFADTIEEMQDNLKNLVENIkesaSQVSSTSEELSASSEQLTSSANQI 421
                                       4444444....222222333345666666677777777777766665551111567777788999999999999999 PP

                                       HHHHHHHH CS
                         MCPsignal 162 nqaveeva 169
                                       +++++e++
  gi|298674341|ref|YP_003726091.1| 422 SDTITEIT 429
                                       99888876 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 4.6e-06
                                       HHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  86 qaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevn 162
                                          ke ++ i+e+q + ++ ve ++e+ ++v+++se+ + + e+l    +++++++d+++ei+  +++qs+ i+ev+
  gi|298674341|ref|YP_003726091.1| 370 GDLKEFADTIEEMQDNLKNLVENIKESASQVSSTSEELSASSEQLT---SSANQISDTITEITNGAQNQSTKIQEVS 443
                                       55689999***************************99999988775...68899*********************** PP

                                       HHHHHHH CS
                         MCPsignal 163 qaveeva 169
                                       ++++ ++
  gi|298674341|ref|YP_003726091.1| 444 STMNDMS 450
                                       *999886 PP

  == domain 3  score: 16.6 bits;  conditional E-value: 1.8e-05
                                       HHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  88 akeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasiee 160
                                       a++ ++ i+e+   +nd  +s++++ ++++++se+v e ++ ++e+ e+ +e+++ +++i+++se+ s+ + e
  gi|298674341|ref|YP_003726091.1| 432 AQNQSTKIQEVSSTMNDMSTSIQDVSSNAQKTSETVTEVNKLVNEVGEQSKELKSKMENIQTTSEQTSEVVRE 504
                                       566677899***********************************************************98876 PP

  == domain 4  score: 170.6 bits;  conditional E-value: 8.9e-53
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHH CS
                         MCPsignal   8 seeAeeggkevanvvkqmeeieksskeisdiieVideiadQTNlLALNAaiEAARAGeqGrGFaVVAdEVrkLAers 84 
                                       +++ e+ +++ +++ + ++e++++sk+i +i++ i++iadQTNlLALNAaiEAARAGeqGrGFaVVAdEVrkLAe+s
  gi|298674341|ref|YP_003726091.1| 485 KSKMENIQTTSEQTSEVVRELDNKSKKIGEIVSMITNIADQTNLLALNAAIEAARAGEQGRGFAVVADEVRKLAEES 561
                                       556666688889999999*********************************************************** PP

                                       HHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  85 aqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieev 161
                                        ++a++i +li+eiq+ + ++v+s+e++ q++e+gs+  +et ++++++v +++e +++vq+ia+++ee+sas+eev
  gi|298674341|ref|YP_003726091.1| 562 SNSAQQIGDLIQEIQNSTGEAVSSMENSSQEIENGSQALDETVNSMSNVVGKTSEADNMVQDIASSAEELSASVEEV 638
                                       ***************************************************************************** PP

                                       HHHHHHHHHH CS
                         MCPsignal 162 nqaveevakv 171
                                       +++veev+++
  gi|298674341|ref|YP_003726091.1| 639 TSSVEEVSSI 648
                                       ******9986 PP

  == domain 5  score: 7.4 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 116 veegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqavee 167
                                       vee s+++ee+ ++ +e +++v+e ++++qe++++++++ + +ee nq+v+ 
  gi|298674341|ref|YP_003726091.1| 642 VEEVSSIAEESSSSTEEASASVEEQTSSMQELSKSAQDLNQMAEELNQSVKS 693
                                       7888889999999999999999999999999999999999999999999876 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   0.0   5.1e-17   1.5e-14       3     109 ..      68     174 ..      66     175 .. 0.97
   2 !   56.1   0.0   1.3e-17   3.8e-15       1     108 [.     187     294 ..     187     296 .. 0.98

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 5.1e-17
                             PAS_4   3 slpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgeer 79 
                                        lp ++  +d++++v+++N ++ae++ + +ee++Gk+++el+ +++    e+  +++++++ + + +++ ++ g++ 
  gi|298674341|ref|YP_003726091.1|  68 LLPTPIMTIDKEFTVTFLNSSGAEVLDMGQEECIGKKCYELFKTPHCNTGECRCDQAMRTGSVGTGETICDPKGKHI 144
                                       6899************************************************************************* PP

                             PAS_4  80 hyelrllPlrdesGevigvlvisrDiTerr 109
                                       +++ +  Pl+d++G + g++++++DiT+++
  gi|298674341|ref|YP_003726091.1| 145 PIQYTGAPLKDSDGNINGAVEYVVDITDTK 174
                                       ***************************986 PP

  == domain 2  score: 56.1 bits;  conditional E-value: 1.3e-17
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       l+++p ++ v+d++++v+++N+a+ae +g + ee+ Gk+++ l+++++     ++++++++ + + ++ ++ +lp +
  gi|298674341|ref|YP_003726091.1| 187 LNNVPTPVMVIDKNMNVQFMNNAGAEAVGKTTEECEGKKCYNLFNTGHCNTENCQVAKAMQKDGTFTDDTVAKLPSG 263
                                       789************************************************************99999999999*** PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTer 108
                                       e ++  +  P++d +Ge++g l++++DiTe+
  gi|298674341|ref|YP_003726091.1| 264 ELPIRYTGAPIKDNKGEIVGGLEYVIDITEE 294
                                       *****************************97 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.0   1.3e-15   3.7e-13       2     104 .]      71     172 ..      70     172 .. 0.88
   2 !   37.3   0.1     9e-12   2.6e-09       2     104 .]     192     293 ..     191     293 .. 0.87
   3 ?   -1.4   0.1        10   2.9e+03      13      66 ..     467     515 ..     457     550 .. 0.63

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 1.3e-15
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetf 76 
                                       ++i+ +++++++++ N + +++l ++ ee +gk++ +lf   +   +++r ++a+++g+  + ++e+++  k g+ +
  gi|298674341|ref|YP_003726091.1|  71 TPIMTIDKEFTVTFLNSSGAEVLDMGQEECIGKKCYELFktPHCNTGECRCDQAMRTGS--VGTGETICDPK-GKHI 144
                                       6788888********************************55555555666666666666..********999.99** PP

                             PAS_9  77 wvlltaspvkdddgelvgiivilrDite 104
                                       +++ t +p+kd+dg++ g++  ++Dit+
  gi|298674341|ref|YP_003726091.1| 145 PIQYTGAPLKDSDGNINGAVEYVVDITD 172
                                       ***************************6 PP

  == domain 2  score: 37.3 bits;  conditional E-value: 9e-12
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfw 77 
                                       +++++++++ ++ ++N+a ++  G + ee  gk++ +lf +  + n + +++ ++++k   +++++v   ++g +++
  gi|298674341|ref|YP_003726091.1| 192 TPVMVIDKNMNVQFMNNAGAEAVGKTTEECEGKKCYNLF-NTGHCNTENCQVAKAMQKdGTFTDDTVAKLPSG-ELP 266
                                       56777789999****************************.777777777777777777756777777777766.9** PP

                             PAS_9  78 vlltaspvkdddgelvgiivilrDite 104
                                       ++ t +p+kd++ge+vg +  ++Dite
  gi|298674341|ref|YP_003726091.1| 267 IRYTGAPIKDNKGEIVGGLEYVIDITE 293
                                       **************************8 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 10
                             PAS_9  13 ilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevev 66 
                                       ++ +N+ ++++ G +++e l  ++++++ t +e  +++ + l++++   + +e+
  gi|298674341|ref|YP_003726091.1| 467 VTEVNKLVNEV-GEQSKE-LKSKMENIQ-TTSEQTSEVVRELDNKS--KKIGEI 515
                                       55666666666.655555.333566666.55555555555555555..333333 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.0     1e-10     3e-08       4     106 ..      63     163 ..      60     169 .. 0.95
   2 !   23.7   0.0   1.3e-07   3.7e-05       6     104 ..     186     282 ..     181     290 .. 0.77

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 1e-10
                                       HHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEE CS
                               PAS   4 raileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfk 80 
                                        +i+e lp+pi+ +D+   +++ N++ +e l   +ee++gk+ ++l+ +++  +   +  q++++g+ ++++ i+ +
  gi|298674341|ref|YP_003726091.1|  63 AEIIELLPTPIMTIDKEFTVTFLNSSGAEVLDMGQEECIGKKCYELFKTPHCNTGECRCDQAMRTGSVGTGETICDP 139
                                       579********************************************9998889*****************999888 PP

                                       CTTSSEEEEEEEEEEEEETTEEEEEE CS
                               PAS  81 lrdgrpihlevraspvrdaggeilgf 106
                                       +  g+ i+++ + +p+ d +g+i g+
  gi|298674341|ref|YP_003726091.1| 140 K--GKHIPIQYTGAPLKDSDGNINGA 163
                                       8..*******************9886 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 1.3e-07
                                       HHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEEC. CS
                               PAS   6 ileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfkl. 81 
                                        l++ p+p++v+D++ ++ ++N a +e  G + ee+ gk+ + l+++      +   e++  ++ ++++g  + ++ 
  gi|298674341|ref|YP_003726091.1| 186 YLNNVPTPVMVIDKNMNVQFMNNAGAEAVGKTTEECEGKKCYNLFNT-----GHCNTENCQVAKAMQKDGTFTDDTv 257
                                       589***************************************99987.....4555555555555555555555555 PP

                                       ..TTSSEEEEEEEEEEEEETTEEEE CS
                               PAS  82 ..rdgrpihlevraspvrdaggeil 104
                                            ++ +++ + +p+ d +gei 
  gi|298674341|ref|YP_003726091.1| 258 akLPSGELPIRYTGAPIKDNKGEIV 282
                                       5546777888888888888888665 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   3.6e-05      0.01      57     106 .]     120     171 ..      64     171 .. 0.67
   2 !   15.6   0.0   6.5e-05     0.019       4     106 .]     186     292 ..     184     292 .. 0.81
   3 ?   -0.3   1.5       5.5   1.6e+03      55      55 ..     470     470 ..     408     527 .. 0.60
   4 ?    3.0   0.1      0.51   1.5e+02      36      75 ..     565     606 ..     558     621 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.6e-05
                            PAS_10  57 eviealrtgekdevevvvpkngkwvlvryl..pyrdedgeiaGvvetfvDit 106
                                       +  +a+rtg   + e+  + +gk++ ++y   p++d dg+i+G+ve++vDit
  gi|298674341|ref|YP_003726091.1| 120 RCDQAMRTGSVGTGETICDPKGKHIPIQYTgaPLKDSDGNINGAVEYVVDIT 171
                                       44578899999999999999999988888444*******************7 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 6.5e-05
                            PAS_10   4 lLnstpieltflDdnlqirrFtpa.akklfklipadvGrpladihpk.kavknveeviealrtgekdevevvvp..k 76 
                                       +Ln++p  ++ +D+n+++ + ++a a+ + k +++  G +  ++ ++ +  ++  +v +a+++  + ++++v +  +
  gi|298674341|ref|YP_003726091.1| 186 YLNNVPTPVMVIDKNMNVQFMNNAgAEAVGKTTEECEGKKCYNLFNTgHCNTENCQVAKAMQKDGTFTDDTVAKlpS 262
                                       79********************964899****************666555555566666666666655555554326 PP

                            PAS_10  77 ngkwvlvrylpyrdedgeiaGvvetfvDit 106
                                        +  +  +  p++d++gei G +e+++Dit
  gi|298674341|ref|YP_003726091.1| 263 GELPIRYTGAPIKDNKGEIVGGLEYVIDIT 292
                                       7777888899*******************7 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 5.5
                            PAS_10  55 v 55 
                                       v
  gi|298674341|ref|YP_003726091.1| 470 V 470
                                       2 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.51
                            PAS_10  36 padvGrpladihpk..kavknveeviealrtgekdevevvvp 75 
                                       ++++G+ +++i+++  +av+++e+  +++ +g +  +e+v +
  gi|298674341|ref|YP_003726091.1| 565 AQQIGDLIQEIQNStgEAVSSMENSSQEIENGSQALDETVNS 606
                                       6899*******8887899999999999999999998887765 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.3    0.0059       1.7      13      52 ..      15      53 ..      13      54 .. 0.92
   2 !   26.2   0.1   2.7e-08   7.7e-06       6      52 ..     341     387 ..     339     388 .. 0.97
   3 ?    1.9   0.0       1.1   3.1e+02      11      52 ..     419     454 ..     411     455 .. 0.69
   4 ?    1.8   0.3       1.1   3.3e+02      41      53 .]     677     689 ..     677     689 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0059
                                      HHHHHHHHTTTBTSSTCCT.TSSSHHHHHHHHHHHHHHHHH CS
                              HAMP 13 LaraarriaaGdldtrlpv.sgrDEiGeLarafNaMldrLr 52
                                      ++++a++i++G ld+rl++ +g D  +e a+++N Mld+L 
  gi|298674341|ref|YP_003726091.1| 15 VVKVANNIQDGKLDARLDTqNGVD--RETAHSVNSMLDNLT 53
                                      7899***************99***..************995 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 2.7e-08
                                       THHHHHHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHHH CS
                              HAMP   6 ilrPLrrLaraarriaaGdldtrlpvsgrDEiGeLarafNaMldrLr 52 
                                       i+ PL++ +r+a++ia+Gdl++++ v+++  + e a ++++M+d+L+
  gi|298674341|ref|YP_003726091.1| 341 IVEPLNETKRVAEAIADGDLTQSINVDTKGDLKEFADTIEEMQDNLK 387
                                       899******************************************96 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHHH CS
                              HAMP  11 rrLaraarriaaGdldtrlpvsgrDEiGeLarafNaMldrLr 52 
                                       +++++++ +i +G  +++        i e+  ++N+M+++++
  gi|298674341|ref|YP_003726091.1| 419 NQISDTITEITNGAQNQS------TKIQEVSSTMNDMSTSIQ 454
                                       556666666666644444......448899999999999987 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHH CS
                              HAMP  41 arafNaMldrLre 53 
                                       a+ +N+M+++L++
  gi|298674341|ref|YP_003726091.1| 677 AQDLNQMAEELNQ 689
                                       788********86 PP

>> PhageMin_Tail  Phage-related minor tail protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.19        56     133     193 ..      40     187 ..      29     190 .. 0.83
   2 !   17.4  10.4   1.1e-05    0.0031      64     188 ..     360     510 ..     328     536 .. 0.77
   3 !   17.2  15.2   1.2e-05    0.0036       4     145 ..     554     694 ..     551     706 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.19
                     PhageMin_Tail 133 eAgtalknllsrltkeaaealkklGist................................................. 160
                                       e + +++++l +ltk+++++ +k  i+                                                  
  gi|298674341|ref|YP_003726091.1|  40 ETAHSVNSMLDNLTKKVSDTESKAEIIEllptpimtidkeftvtflnssgaevldmgqeecigkkcyelfktphcnt 116
                                       45678999999999988888888876633677777777778888888888888999999999999999999999999 PP

                     PhageMin_Tail 161 .....................................kdaqgkmksldeiledlsealkkltda.qraaal 193
                                                                            kd++g++ +++e   d+ +  k l++a q+a++l
  gi|298674341|ref|YP_003726091.1| 117 gecrcdqamrtgsvgtgeticdpkgkhipiqytgaplKDSDGNINGAVEYVVDITDTKKALDEAkQKAEYL 187
                                       9999999999999999999999999999999999999******************9888888886667665 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 1.1e-05
                     PhageMin_Tail  64 alnafglsaa.daeeaaDvlaaaanngatsvedlaealkevgavakaaGlsfee..........taaalallaaag. 128
                                       + +  +++++ d++e+aD + ++++n ++ ve+++e+ ++v+++   +  s e+          t + ++++a++  
  gi|298674341|ref|YP_003726091.1| 360 LTQSINVDTKgDLKEFADTIEEMQDNLKNLVENIKESASQVSSTSEELSASSEQltssanqisdTITEITNGAQNQs 436
                                       3466677766799************************************9999999999999999999999999877 PP

                     PhageMin_Tail 129 ikgseAgtalknllsrl.........tk....eaaealkklGistkdaqgkmksldeiledlsealkkltda.q 188
                                        k  e+  +++ + +++         t     e++++++++G + k+++ km + + ++e++se + +l+++ +
  gi|298674341|ref|YP_003726091.1| 437 TKIQEVSSTMNDMSTSIqdvssnaqkTSetvtEVNKLVNEVGEQSKELKSKMENIQTTSEQTSEVVRELDNKsK 510
                                       99999999999999999777544433113334444444445755677778888888888888888888866633 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 1.2e-05
                     PhageMin_Tail   4 akelgektkysatelaealeelas.aGvsteeilnllegaaklataggaddleeaaeilstalnafglsaadaeeaa 79 
                                       +++l+e+ + sa+++++ ++e+    G +  +++n  + + + ++a + + +++++++++++ +a ++  +d++  a
  gi|298674341|ref|YP_003726091.1| 554 VRKLAEESSNSAQQIGDLIQEIQNsTGEAVSSMENSSQEIENGSQALDET-VNSMSNVVGKTSEADNMV-QDIASSA 628
                                       5666666666999999999999995589999999999999********66.************999999.7999999 PP

                     PhageMin_Tail  80 DvlaaaanngatsvedlaealkevgavakaaGlsfeetaaalallaaagikgseAgtalknllsrl 145
                                         l+a + +  +sve+ +++  e++++   a  s ee++ +++ l+++ ++ ++ +  l++ + + 
  gi|298674341|ref|YP_003726091.1| 629 EELSASVEEVTSSVEEVSSIAEESSSSTEEASASVEEQTSSMQELSKSAQDLNQMAEELNQSVKSF 694
                                       999999999999999999999999999999999999999999999998899999999998888776 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1       1.2   3.6e+02      52      70 ..      41      59 ..      14      75 .. 0.68
   2 ?    4.2   1.0      0.18        51      28      54 ..     372     398 ..     325     402 .. 0.70
   3 !   11.9   9.3   0.00069       0.2      23      88 ..     392     457 ..     366     462 .. 0.76
   4 !   16.4   8.6   2.7e-05    0.0079      28      87 ..     439     501 ..     435     503 .. 0.80
   5 !   13.0   6.2   0.00032     0.092      23      83 ..     462     525 ..     459     530 .. 0.64
   6 !   12.0   1.2   0.00068       0.2      19      81 ..     549     611 ..     546     619 .. 0.91
   7 !   13.2   4.0   0.00029     0.083      24      82 ..     624     682 ..     615     689 .. 0.52

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 1.2
                            DUF948 52 llakvnelledvneklekv 70
                                      + + vn +l+++++k+ + 
  gi|298674341|ref|YP_003726091.1| 41 TAHSVNSMLDNLTKKVSDT 59
                                      3444444444444444333 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.18
                            DUF948  28 ldeaaatieelekqvdpilkevedlla 54 
                                       l+e+a+tiee++++++++++++++  +
  gi|298674341|ref|YP_003726091.1| 372 LKEFADTIEEMQDNLKNLVENIKESAS 398
                                       566667777777777777776666554 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00069
                            DUF948  23 klkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                       ++k+ ++++++t eel    ++++  ++++ +++ e++++ ++++ k++++ + ++d+++s+++++
  gi|298674341|ref|YP_003726091.1| 392 NIKESASQVSSTSEELSASSEQLTSSANQISDTITEITNGAQNQSTKIQEVSSTMNDMSTSIQDVS 457
                                       345555666666666666667777777777777777888888899999999999999999999886 PP

  == domain 4  score: 16.4 bits;  conditional E-value: 2.7e-05
                            DUF948  28 ldeaaatieele...kqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                       ++e+++t++++    ++v +  +++ +++++vn+l+++v e+++++++ +e++++++e+ se+
  gi|298674341|ref|YP_003726091.1| 439 IQEVSSTMNDMStsiQDVSSNAQKTSETVTEVNKLVNEVGEQSKELKSKMENIQTTSEQTSEV 501
                                       6788888888884444444455666788999999*************************9987 PP

  == domain 5  score: 13.0 bits;  conditional E-value: 0.00032
                            DUF948  23 klkktldeaaatieelekqvdpi...lkevedllakvnelledvneklekvdplteavadlges 83 
                                       k ++t++e+++ ++e+++q +++   +++++++ +++ e++ ++ +k++k+ ++++ + +++++
  gi|298674341|ref|YP_003726091.1| 462 KTSETVTEVNKLVNEVGEQSKELkskMENIQTTSEQTSEVVRELDNKSKKIGEIVSMITNIADQ 525
                                       5677888888888888855554411144555555556666677777888888888888887766 PP

  == domain 6  score: 12.0 bits;  conditional E-value: 0.00068
                            DUF948  19 vvllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlg 81 
                                       vv  +++k+++e +++ +++++ +++i + + ++++ +++  +++++ ++++d+ ++++ ++ 
  gi|298674341|ref|YP_003726091.1| 549 VVADEVRKLAEESSNSAQQIGDLIQEIQNSTGEAVSSMENSSQEIENGSQALDETVNSMSNVV 611
                                       6777899*************************************************9999875 PP

  == domain 7  score: 13.2 bits;  conditional E-value: 0.00029
                            DUF948  24 lkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlge 82 
                                       +++ ++e++a++ee+++ v++++  +e+  + ++e  + v+e++ ++++l ++++dl +
  gi|298674341|ref|YP_003726091.1| 624 IASSAEELSASVEEVTSSVEEVSSIAEESSSSTEEASASVEEQTSSMQELSKSAQDLNQ 682
                                       34444555555555555555555555555555555555555555555555555555555 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.9     0.034       9.7      70     121 ..      26      77 ..       9      79 .. 0.88
   2 ?    7.0   0.9     0.019       5.5      40     104 ..     328     401 ..     326     407 .. 0.46
   3 !   15.8   7.9   3.7e-05     0.011      37     123 ..     373     459 ..     368     461 .. 0.95
   4 !   12.5   8.5   0.00038      0.11      44     123 ..     408     487 ..     400     488 .. 0.88
   5 !   10.7   7.1    0.0014      0.42      39     106 ..     449     519 ..     448     529 .. 0.48
   6 !    8.3   1.0    0.0077       2.2      76     118 ..     570     612 ..     548     617 .. 0.79
   7 !   10.5   7.3    0.0017      0.48      50     121 ..     617     688 ..     606     697 .. 0.51

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.034
                           DUF1664  70 rvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                       ++d++ld q+ + +e+++ v+++ ++l++  +d es  e++e l + + +i+
  gi|298674341|ref|YP_003726091.1|  26 KLDARLDTQNGVDRETAHSVNSMLDNLTKKVSDTESKAEIIELLPTPIMTID 77 
                                       79**********************************9999999998888876 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.019
                           DUF1664  40 sdavesvskqleqvseslaatkr........hLssridrvdkk..ldeqkeiskeikeevtevredlseigedve 104
                                       +++++ + + l+ + e l++tkr        +L++ i+ vd+k  l+e +++++e++++++++ e+++e  ++v+
  gi|298674341|ref|YP_003726091.1| 328 RNVIKGINNTLDAIVEPLNETKRvaeaiadgDLTQSIN-VDTKgdLKEFADTIEEMQDNLKNLVENIKESASQVS 401
                                       66777788888888888888886222222223444442.222211334444444444444444444433333333 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 3.7e-05
                           DUF1664  37 rslsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegl 113
                                       + ++d +e++  +l+++ e++++   + ss  +++ ++ ++ +  +++i++ +te+ ++ ++ ++++++v+++++++
  gi|298674341|ref|YP_003726091.1| 373 KEFADTIEEMQDNLKNLVENIKESASQVSSTSEELSASSEQLTSSANQISDTITEITNGAQNQSTKIQEVSSTMNDM 449
                                       5688999********************************************************************** PP

                           DUF1664 114 esklerieek 123
                                        +++++++++
  gi|298674341|ref|YP_003726091.1| 450 STSIQDVSSN 459
                                       ****999875 PP

  == domain 4  score: 12.5 bits;  conditional E-value: 0.00038
                           DUF1664  44 esvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                       +  s+ql++  +++++t  ++++  ++  +k++e++ + ++++  +++v+++ ++++e v++v+++v++++++ +++
  gi|298674341|ref|YP_003726091.1| 408 SASSEQLTSSANQISDTITEITNGAQNQSTKIQEVSSTMNDMSTSIQDVSSNAQKTSETVTEVNKLVNEVGEQSKEL 484
                                       55688999999999999999999999999999999999999999*******************99999999988888 PP

                           DUF1664 121 eek 123
                                       ++k
  gi|298674341|ref|YP_003726091.1| 485 KSK 487
                                       765 PP

  == domain 5  score: 10.7 bits;  conditional E-value: 0.0014
                           DUF1664  39 lsdavesvskqleqvseslaatkr...hLssridrvdkkldeqkeiskeikeevtevredlseigedvesv 106
                                       +s  +++vs++ ++ se+++++ +   +  ++ +++ +k+++ + +s++++e v e+ ++ ++ige v+ +
  gi|298674341|ref|YP_003726091.1| 449 MSTSIQDVSSNAQKTSETVTEVNKlvnEVGEQSKELKSKMENIQTTSEQTSEVVRELDNKSKKIGEIVSMI 519
                                       55555555555555555555443211133344444555555555555555555555555555555555544 PP

  == domain 6  score: 8.3 bits;  conditional E-value: 0.0077
                           DUF1664  76 deqkeiskeikeevtevredlseigedvesvkeavegleskle 118
                                       d  +ei++++ e v+++++  +ei++ +++++e+v+++ + + 
  gi|298674341|ref|YP_003726091.1| 570 DLIQEIQNSTGEAVSSMENSSQEIENGSQALDETVNSMSNVVG 612
                                       556899******************************9988665 PP

  == domain 7  score: 10.5 bits;  conditional E-value: 0.0017
                           DUF1664  50 leqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                        +++ +++a+  ++Ls+ +++v ++++e++ i++e ++  +e++  ++e  + ++++++  ++l++  e+++
  gi|298674341|ref|YP_003726091.1| 617 ADNMVQDIASSAEELSASVEEVTSSVEEVSSIAEESSSSTEEASASVEEQTSSMQELSKSAQDLNQMAEELN 688
                                       355555566666666666666666666665555555555555555555555555555555555444444433 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.33        96      25      73 ..      31      79 ..      26      84 .. 0.85
   2 !   10.2   3.9    0.0025      0.73      11      75 ..     364     429 ..     359     433 .. 0.82
   3 !    8.4   1.9    0.0089       2.6      30      75 ..     433     478 ..     428     479 .. 0.92
   4 !   10.2   6.3    0.0025      0.73      13      81 ..     458     526 ..     456     534 .. 0.82
   5 !   10.8   4.8    0.0017      0.48       6      90 ..     553     637 ..     549     643 .. 0.91
   6 !    9.3   4.5    0.0046       1.3      39      90 ..     642     693 ..     632     697 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.33
                           BLOC1_2 25 LeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekq 73
                                      L + N +  e  +++++++++l+kk++++++k e ++ + + i  i+k+
  gi|298674341|ref|YP_003726091.1| 31 LDTQNGVDRETAHSVNSMLDNLTKKVSDTESKAEIIELLPTPIMTIDKE 79
                                      55677777888889999***************99999888888888876 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0025
                           BLOC1_2  11 leaeleatvedy.klLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvt 75 
                                       ++ ++++  +++ +++e++  +  + ++++k++a+++++++e+l++ +e+l +  +qi +  +++t
  gi|298674341|ref|YP_003726091.1| 364 INVDTKGDLKEFaDTIEEMQDNLKNLVENIKESASQVSSTSEELSASSEQLTSSANQISDTITEIT 429
                                       5556666555543799*************************************9999988666665 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0089
                           BLOC1_2  30 eaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvt 75 
                                       +++s+k++++++ +++++++++++++  ++ ++ +++++++ ++v 
  gi|298674341|ref|YP_003726091.1| 433 QNQSTKIQEVSSTMNDMSTSIQDVSSNAQKTSETVTEVNKLVNEVG 478
                                       7999************************************999985 PP

  == domain 4  score: 10.2 bits;  conditional E-value: 0.0025
                           BLOC1_2  13 aeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeav 81 
                                       ++ + t+e +  ++kl +++ e+ k+lk++++++++++e+++e   el+++ ++i +i   +t + +  
  gi|298674341|ref|YP_003726091.1| 458 SNAQKTSETVTEVNKLVNEVGEQSKELKSKMENIQTTSEQTSEVVRELDNKSKKIGEIVSMITNIADQT 526
                                       667778888888899999999999999999999999999999999999999999999999888877665 PP

  == domain 5  score: 10.8 bits;  conditional E-value: 0.0017
                           BLOC1_2   6 kvskyleaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavs 82 
                                       +v+k+ e+  +++++  +l++++ +++ e + +++++ +++e+ +++l+e+ +++++ + +  + ++ v+++ + ++
  gi|298674341|ref|YP_003726091.1| 553 EVRKLAEESSNSAQQIGDLIQEIQNSTGEAVSSMENSSQEIENGSQALDETVNSMSNVVGKTSEADNMVQDIASSAE 629
                                       678888889999999999*********************************************************** PP

                           BLOC1_2  83 eLDeyske 90 
                                       eL + + e
  gi|298674341|ref|YP_003726091.1| 630 ELSASVEE 637
                                       *9877666 PP

  == domain 6  score: 9.3 bits;  conditional E-value: 0.0046
                           BLOC1_2  39 lkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyske 90 
                                       +++v + +e++++ ++e +++++++ ++++++ k+ ++L ++++eL++ +k+
  gi|298674341|ref|YP_003726091.1| 642 VEEVSSIAEESSSSTEEASASVEEQTSSMQELSKSAQDLNQMAEELNQSVKS 693
                                       45555556667777888888**************************999886 PP

>> CheZ  Chemotaxis phosphatase, CheZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       6.2   1.8e+03      42      62 ..     285     307 ..     276     313 .. 0.76
   2 !   14.0   8.7   0.00012     0.035      21     122 ..     364     470 ..     358     472 .. 0.85
   3 !   13.4   3.0   0.00019     0.055       2     117 ..     472     591 ..     471     595 .. 0.75
   4 !   10.3   7.7    0.0017      0.48       5     118 ..     566     683 ..     562     691 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 6.2
                                       XXXXXXXXX..XXXXXXXXXXXX CS
                              CheZ  42 LeyvielTe..qAAertldavek 62 
                                       Leyvi++Te  qA +++  +v++
  gi|298674341|ref|YP_003726091.1| 285 LEYVIDITEenQAVSEVEGLVDD 307
                                       99******833566666666665 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 0.00012
                                       XXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XX CS
                              CheZ  21 lgld.ekllekaaeeipdardrLeyvielTeqAAertldavekalpladklkeeakeleeewerllerele....ke 92 
                                       +++d +  l++ a++i++ +d L+  +e  +++A+++ ++ e+  +  ++l+++a++++++++++++   +     +
  gi|298674341|ref|YP_003726091.1| 364 INVDtKGDLKEFADTIEEMQDNLKNLVENIKESASQVSSTSEELSASSEQLTSSANQISDTITEITNGAQNqstkIQ 440
                                       55662345788999***********************************************9999876543222267 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              CheZ  93 efrelvkeveaflkeveektealkkqLlei 122
                                       e+ + ++++++ +++v++++++++++++e+
  gi|298674341|ref|YP_003726091.1| 441 EVSSTMNDMSTSIQDVSSNAQKTSETVTEV 470
                                       788889999999999*********999987 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 0.00019
                                       XXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXX..XXX CS
                              CheZ   2 elfeeiGkltReLhdalrelgldekllekaaeeipdardrLeyvielTeqAA.ertldavekalpladklke..eak 75 
                                       +l++e+G+  +eL+  ++++++ +++++++ +e+ + ++++  ++++  + A ++ l a ++a   a++ ++    +
  gi|298674341|ref|YP_003726091.1| 472 KLVNEVGEQSKELKSKMENIQTTSEQTSEVVRELDNKSKKIGEIVSMITNIAdQTNLLALNAAIEAARAGEQgrGFA 548
                                       789**************************************999998666550556888887776665544411567 PP

                                       XXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              CheZ  76 eleeewerllere.lekeefrelvkeveaflkeveektealkk 117
                                        +++e ++l+e++  +++++ +l++e+++ + e+ ++ e+ ++
  gi|298674341|ref|YP_003726091.1| 549 VVADEVRKLAEESsNSAQQIGDLIQEIQNSTGEAVSSMENSSQ 591
                                       8888889988887455777777777777776666555555444 PP

  == domain 4  score: 10.3 bits;  conditional E-value: 0.0017
                                       XXXXXXXXXXX....XXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              CheZ   5 eeiGkltReLh....dalrelgldekllekaaeeipdardrLeyvielTeqAAertldavekalpladklkeeakel 77 
                                       ++iG l  e++    +a+++++  ++++e+ ++++ ++ + ++ v+ +T++A + + d+  +a  l  +++e ++++
  gi|298674341|ref|YP_003726091.1| 566 QQIGDLIQEIQnstgEAVSSMENSSQEIENGSQALDETVNSMSNVVGKTSEADNMVQDIASSAEELSASVEEVTSSV 642
                                       7888888888722224567788889999999***********************99999999999999999999999 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              CheZ  78 eeewerllerelekeefrelvkeveaflkeveektealkkq 118
                                       ee  +   e++ ++ee+ + v+e ++ ++e+++++++l++ 
  gi|298674341|ref|YP_003726091.1| 643 EEVSSIAEESSSSTEEASASVEEQTSSMQELSKSAQDLNQM 683
                                       88877777777889999999999999999999999998875 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2  16.3   2.2e-05    0.0064      36     177 ..     373     513 ..     337     522 .. 0.84
   2 !   10.0  17.0    0.0017       0.5      20     170 ..     547     695 ..     531     699 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.2e-05
                              YkyA  36 elyeeiielgmdefdkikklsdealenveeReellekekesieeakeefekikeeieeiedeelkkeaeelieamee 112
                                       + + ++ie  +d+++++++ ++e  + v+   e+l+   e + ++ +++++  +ei +   +++ ++++e+ ++m++
  gi|298674341|ref|YP_003726091.1| 373 KEFADTIEEMQDNLKNLVENIKESASQVSSTSEELSASSEQLTSSANQISDTITEITNG-AQNQSTKIQEVSSTMND 448
                                       45677777777777777777777777777777777777777777777777777777777.4568999********** PP

                              YkyA 113 ryeaydklykaYkealeldkeLYemLkkeeltleeleeqiekiNesyeevkeaneqFneatkkyn 177
                                         ++++++ ++ +++ e+ +e  ++ ++   + +el+ ++e+i +++e++ e + +++++ kk+ 
  gi|298674341|ref|YP_003726091.1| 449 MSTSIQDVSSNAQKTSETVTEVNKLVNEVGEQSKELKSKMENIQTTSEQTSEVVRELDNKSKKIG 513
                                       **********************99999999999******************99999999988875 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0017
                              YkyA  20 feeqqekLtelekkeqelyeeiielgmdefdkikklsdealenveeReellekekesieeakeefekikeeieeie. 95 
                                       f+  +++  +l ++  +  ++i +      ++i++   ea++++e+  +++e+  ++++e+ + ++++  +++e + 
  gi|298674341|ref|YP_003726091.1| 547 FAVVADEVRKLAEESSNSAQQIGD----LIQEIQNSTGEAVSSMENSSQEIENGSQALDETVNSMSNVVGKTSEADn 619
                                       555566666666666666666643....35679***********************************999999951 PP

                              YkyA  96 .deelkkeaeelieameeryeaydklykaYkealeldkeLYemLkkeeltleeleeqiekiNesyeevkeaneqFn 170
                                         +++ + aeel  ++ee +++ +++ +  +e+ ++ +e     +++  +++el +  +++N+  ee+++ +++F 
  gi|298674341|ref|YP_003726091.1| 620 mVQDIASSAEELSASVEEVTSSVEEVSSIAEESSSSTEEASASVEEQTSSMQELSKSAQDLNQMAEELNQSVKSFK 695
                                       24589999*************************************************************9999995 PP

>> Med30  Mediator complex subunit 30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.3    0.0099       2.9      38      89 ..     360     410 ..     334     424 .. 0.78
   2 !   14.7   7.0   9.3e-05     0.027      33     142 ..     422     527 ..     415     531 .. 0.86
   3 ?    7.3   3.7     0.018       5.2      25     135 ..     570     688 ..     556     695 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0099
                             Med30  38 qskhqaqdrkkklqeqlrqlkvlfkkLrliYekckencqgleevpiesLipy 89 
                                        +++ + d k++l+e  +++++   +L+++ e++ke+ +++ +++ e+L   
  gi|298674341|ref|YP_003726091.1| 360 LTQSINVDTKGDLKEFADTIEEMQDNLKNLVENIKESASQVSSTS-EELSAS 410
                                       389999*******************************99998665.666554 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 9.3e-05
                             Med30  33 pngrtqskhqaqdrkkklqeqlrqlkvlfkkLrliYekckencqgleevpiesLipyvdeekskreerkkseevkql 109
                                       + + t  ++ aq++++k+qe   +++     ++ +  + ++ ++ ++  ++++L+  v e+   +e ++k e++++ 
  gi|298674341|ref|YP_003726091.1| 422 SDTITEITNGAQNQSTKIQEVSSTMNDMSTSIQDVSSNAQKTSETVT--EVNKLVNEVGEQ--SKELKSKMENIQTT 494
                                       55667778999************************999999998777..677***999966..555566679***** PP

                             Med30 110 keerkelleklkeknkqLkeimdqlrkllWdiN 142
                                       +e+  e++ +l++k k++ ei+  ++++  + N
  gi|298674341|ref|YP_003726091.1| 495 SEQTSEVVRELDNKSKKIGEIVSMITNIADQTN 527
                                       *************************99865555 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.018
                             Med30  25 qllkavqlpngrtqskhqaqdr.....kkklqeqlrqlkvlfkkLrliYekckencqgleevp..iesLipyvdeek 94 
                                        l++++q+++g+++s+  ++++     ++ l+e+++ +++   k     + +++  +  ee++  +e+    v+e +
  gi|298674341|ref|YP_003726091.1| 570 DLIQEIQNSTGEAVSSMENSSQeiengSQALDETVNSMSNVVGKTSEADNMVQDIASSAEELSasVEEVTSSVEEVS 646
                                       45555555555554322222111111145677788888888887777777777777666655555777777777775 PP

                             Med30  95 skreerkkseevkqlk.eerkelleklkeknkqLkeimdqlr 135
                                       s +ee+++s e  +++ ee+   +++l++  + L+++ ++l 
  gi|298674341|ref|YP_003726091.1| 647 SIAEESSSSTEEASASvEEQTSSMQELSKSAQDLNQMAEELN 688
                                       555555555444444314555556666666677777776665 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1         5   1.4e+03      94     118 ..      40      64 ..      14      69 .. 0.61
   2 !   17.6  17.1   2.9e-06   0.00085     309     498 ..     335     519 ..     326     524 .. 0.82
   3 !   10.3  10.0    0.0005      0.14     126     279 ..     553     702 ..     548     706 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5
                                       HHHHHTTHHHHHHHHHHHHHHHHHH CS
                              EzrA  94 ykfkkakkklaeleeeldeveekik 118
                                          +++++ l++l+++++++e+k++
  gi|298674341|ref|YP_003726091.1|  40 ETAHSVNSMLDNLTKKVSDTESKAE 64 
                                       4444444444444444444444444 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 2.9e-06
                                       SSSSHHHHT--HHHHTTGGG-TTTS-GGGSSTTTSTTHHHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHH CS
                              EzrA 309 kelkeklehlekqnkelkeeldrlkqsYeLseeeleklrelekelkelekdyeeleekleekkvaYSelqeeleele 385
                                       +++ + + +  +++k + e + + + +  ++ +    l+e+ + ++e+++++++l+e+++e+    S++++  eel+
  gi|298674341|ref|YP_003726091.1| 335 NNTLDAIVEPLNETKRVAEAIADGDLTQSINVDTKGDLKEFADTIEEMQDNLKNLVENIKESA---SQVSSTSEELS 408
                                       445555555555566666666666677778888888999999999999999999999999887...56666666666 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSS-SS-S-TTTHHHHSTTTSTTTHHHHHHHT- CS
                              EzrA 386 ekleeieekqeeileslkslrkdEkrAreqldeikkelkeikrkieksnLPgiPesyleelkeasdeieelakeLek 462
                                        + e++ ++ ++i+++++++ +  ++   +++e++++++++  +i++    +  ++  e ++e+++ ++e+ ++ ++
  gi|298674341|ref|YP_003726091.1| 409 ASSEQLTSSANQISDTITEITNGAQNQSTKIQEVSSTMNDMSTSIQD--VSSNAQKTSETVTEVNKLVNEVGEQSKE 483
                                       67777777888899999999999999999**************9986..67999*********************** PP

                                       TT--HHHHHHHHHTTTTTSGGGTHHHHHHHHHHHHH CS
                              EzrA 463 kpinikevnkrldeardlveklyektneliktAtla 498
                                        + +++ +++  ++++++v +l++k++++ + + ++
  gi|298674341|ref|YP_003726091.1| 484 LKSKMENIQTTSEQTSEVVRELDNKSKKIGEIVSMI 519
                                       ***************************998888876 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.0005
                                       HHHHTTTTTHHHHHHHHHHHHHHHHT--TTTTHHHHHHHHHHHHHHHH----------------HHHHHHHHHHHHH CS
                              EzrA 126 elteseeknreeieklkekYrelrkkllanrfsygealeelekqleniekefsefeeltengdyveakeilkkleee 202
                                       e+++  e++++  +++ +  +e++++  +   s +++ +e+e+  +++++  ++++++   g+ +ea+++++++ ++
  gi|298674341|ref|YP_003726091.1| 553 EVRKLAEESSNSAQQIGDLIQEIQNSTGEAVSSMENSSQEIENGSQALDETVNSMSNVV--GKTSEADNMVQDIASS 627
                                       56677788899999999999999999999999999999999999999999999999886..7789999999999999 PP

                                       HHHHHHHHHHHHHHHTTTTTTSHHHHHHHHHHHHHSTTS--SGGGSSSSSHHHHHHHHHHHHHHHHTT--HHHHHHH CS
                              EzrA 203 ideleevieeiPelleelkkelpkqleelkegykemkeegYaleelniekeieelekkieeilerlkeleledveee 279
                                        +el++ +ee+ + +ee++++  +     +e  +  +e+   ++e  + k  ++l++  ee+ + +k+++++++ ++
  gi|298674341|ref|YP_003726091.1| 628 AEELSASVEEVTSSVEEVSSIAEESSSSTEEASASVEEQTSSMQE--LSKSAQDLNQMAEELNQSVKSFKVDSSDKK 702
                                       999999999999999999999999999999999999999999998..566777777777777777777777776665 PP

>> DUF773  CDK5 regulatory subunit-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   9.8   1.3e-06   0.00038     334     492 ..     351     502 ..     292     515 .. 0.81
   2 ?    3.3   2.3     0.097        28     402     492 ..     560     650 ..     543     656 .. 0.76
   3 ?   -1.1   6.7         2   5.9e+02     402     473 ..     627     694 ..     591     704 .. 0.57

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.3e-06
                            DUF773 334 aaegvakgeealsllddtey.RnkllddLlELeaFLkqRlvElsnestsvlslqqfqsapevlqsqtkeeiekmlsa 409
                                        ae++a+g+ + s+  dt+   +++ d + E++  Lk  lvE  +es     ++q++s++e+l s ++e++++  ++
  gi|298674341|ref|YP_003726091.1| 351 VAEAIADGDLTQSINVDTKGdLKEFADTIEEMQDNLKN-LVENIKES-----ASQVSSTSEEL-SASSEQLTSSANQ 420
                                       6778888888886655555416899***********95.66666664.....45666777666.67889******** PP

                            DUF773 410 veealslltnkklqqLiliktspryvdrlvasLeqklkqeeklkeklkdleekreelqeelselepkleklvkktre 486
                                       +++ ++++tn   +q  +i++ +  ++ + +s+++  ++++k+ e+++++++  +e+ e+ +el++k+e++ + t e
  gi|298674341|ref|YP_003726091.1| 421 ISDTITEITNGAQNQSTKIQEVSSTMNDMSTSIQDVSSNAQKTSETVTEVNKLVNEVGEQSKELKSKMENIQT-TSE 496
                                       ********************************************************************98754.344 PP

                            DUF773 487 lkklie 492
                                         +++ 
  gi|298674341|ref|YP_003726091.1| 497 QTSEVV 502
                                       444443 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.097
                            DUF773 402 eiekmlsaveealslltnkklqqLiliktspryvdrlvasLeqklkqeeklkeklkdleekreelqeelselepkle 478
                                       e  +  +++ +++++++n++ +    + +s++ ++   + L +  ++++ +  k +++++  +++ ++ +el++ +e
  gi|298674341|ref|YP_003726091.1| 560 ESSNSAQQIGDLIQEIQNSTGEAVSSMENSSQEIENGSQALDETVNSMSNVVGKTSEADNMVQDIASSAEELSASVE 636
                                       44556678888889999999999999999999888888888888888888888888888888888888888888888 PP

                            DUF773 479 klvkktrelkklie 492
                                       +++++  e+ +  e
  gi|298674341|ref|YP_003726091.1| 637 EVTSSVEEVSSIAE 650
                                       88877777665555 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 2
                            DUF773 402 eiekmlsaveealslltnkklqqLili.ktspryvdrlvasLeqklkqeeklkeklkdleekreelqeelsel 473
                                       + e+++++vee+ s +     ++   i  +s+   +   as e+++++++ l ++++dl++  eel++++++ 
  gi|298674341|ref|YP_003726091.1| 627 SAEELSASVEEVTSSV-----EEVSSIaEESSSSTEEASASVEEQTSSMQELSKSAQDLNQMAEELNQSVKSF 694
                                       3344444444443333.....3333331356666777777777777777777777777777777777776665 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.042        12       6      35 ..      65      94 ..      62     125 .. 0.77
   2 !   11.1   0.0    0.0011      0.32       7      51 ..     187     232 ..     182     247 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.042
                             PAS_8  6 lfesspdgiavvd.lgdrivdvNqaalellG 35
                                      ++e +p +i+ +d + + +++ N + +e l 
  gi|298674341|ref|YP_003726091.1| 65 IIELLPTPIMTIDkEFT-VTFLNSSGAEVLD 94
                                      7999********96666.**********995 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0011
                             PAS_8   7 fesspdgiavvd.lgdrivdvNqaalellGys.adlkgellgqllpv 51 
                                       ++++p +++v+d + + + ++N+a +e  G + ++  g+++ +l++ 
  gi|298674341|ref|YP_003726091.1| 187 LNNVPTPVMVIDkNMN-VQFMNNAGAEAVGKTtEECEGKKCYNLFNT 232
                                       799*********6666.*************77888888888766665 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       7.4   2.1e+03      49      78 ..     327     356 ..     325     358 .. 0.79
   2 !    9.4   4.0    0.0041       1.2      13      83 ..     369     441 ..     366     444 .. 0.87
   3 !    8.6   5.3    0.0072       2.1       2      82 ..     407     489 ..     406     491 .. 0.89
   4 ?    3.7   2.3      0.25        71       7      57 ..     447     492 ..     441     527 .. 0.53
   5 ?    4.6   0.4      0.13        39       5      34 ..     550     579 ..     546     586 .. 0.64
   6 ?    6.6   2.0     0.032       9.2      12      78 ..     582     646 ..     579     651 .. 0.81
   7 ?    6.8   6.9     0.028         8      10      81 ..     618     694 ..     612     696 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 7.4
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  49 fqaefeewkqaaqklvdaLeeisealkqaa 78 
                                       f+++++ ++++++ +v+ L+e+ +  +++a
  gi|298674341|ref|YP_003726091.1| 327 FRNVIKGINNTLDAIVEPLNETKRVAEAIA 356
                                       777788888889999999999888888777 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0041
                                       HHHHHHHHHHHHHHHHHHHHHHHHC.GCGCT.HHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  13 aarfqkqaeeledelqrlkaevdal.qsgWs.GaaadafqaefeewkqaaqklvdaLeeisealkqaanafed 83 
                                         ++++ a+++e+++++lk+ v+++ +s+ +  +++++  a  e+++ +a+++ d  +ei++  ++ +++ ++
  gi|298674341|ref|YP_003726091.1| 369 KGDLKEFADTIEEMQDNLKNLVENIkESASQvSSTSEELSASSEQLTSSANQISDTITEITNGAQNQSTKIQE 441
                                       57889999*****************877666699999***********************9999988887765 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0072
                                       HCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGCGCT..HHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100   2 ikvdpeelrqaaarfqkqaeeledelqrlkaevdalqsgWs..GaaadafqaefeewkqaaqklvdaLeeisealkq 76 
                                       ++++ e+l+++a++++++ +e+++  q+   ++++++s+ +   ++ +   +  ++  +++++++++ +e++e+ k+
  gi|298674341|ref|YP_003726091.1| 407 LSASSEQLTSSANQISDTITEITNGAQNQSTKIQEVSSTMNdmSTSIQDVSSNAQKTSETVTEVNKLVNEVGEQSKE 483
                                       57889*******************************999993445567889999999999**********9999999 PP

                                       HHHHHH CS
                            WXG100  77 aanafe 82 
                                        ++++e
  gi|298674341|ref|YP_003726091.1| 484 LKSKME 489
                                       999998 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.25
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGCGCTHHHCHHHHHHHHHHH CS
                            WXG100   7 eelrqaaarfqkqaeeledelqrlkaevdalqsgWsGaaadafqaefeewk 57 
                                       +++ +++++++++a++ ++ ++++++ v+++     G+ +++ ++ +e+++
  gi|298674341|ref|YP_003726091.1| 447 NDMSTSIQDVSSNAQKTSETVTEVNKLVNEV-----GEQSKELKSKMENIQ 492
                                       4555555555555555555555555555555.....223333333333333 PP

  == domain 5  score: 4.6 bits;  conditional E-value: 0.13
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100   5 dpeelrqaaarfqkqaeeledelqrlkaev 34 
                                        ++e+r+ a + +++a+++ d++q+++++ 
  gi|298674341|ref|YP_003726091.1| 550 VADEVRKLAEESSNSAQQIGDLIQEIQNST 579
                                       566777777777777777777777777655 PP

  == domain 6  score: 6.6 bits;  conditional E-value: 0.032
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCGCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  12 aaarfqkqaeeledelqrlkaevdalqsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaa 78 
                                       a +++ ++++e+e+  q+l+ +v+++++   G++++a +++ + +  +a++l +  ee+++++++++
  gi|298674341|ref|YP_003726091.1| 582 AVSSMENSSQEIENGSQALDETVNSMSN-VVGKTSEA-DNMVQDIASSAEELSASVEEVTSSVEEVS 646
                                       56789999*****************965.58999887.66667788888888888888888877665 PP

  == domain 7  score: 6.8 bits;  conditional E-value: 0.028
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHCGC.....GCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  10 rqaaarfqkqaeeledelqrlkaevdalqs.....gWsGaaadafqaefeewkqaaqklvdaLeeisealkqaanaf 81 
                                       + + ++++++aeel++ ++++ ++v++++s     + s + a+a  +e++  +q++ k ++ L++++e+l+q+ ++f
  gi|298674341|ref|YP_003726091.1| 618 DNMVQDIASSAEELSASVEEVTSSVEEVSSiaeesSSSTEEASASVEEQTSSMQELSKSAQDLNQMAEELNQSVKSF 694
                                       55666666666666666666666666665533333334444566777777777777777777777777777777666 PP

>> Collagen_mid  Bacterial collagen, middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   9.1   0.00014     0.041      11     149 ..     388     526 ..     378     544 .. 0.81
   2 !   12.2   4.1   0.00038      0.11       5     109 ..     561     663 ..     557     694 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00014
                      Collagen_mid  11 glggvvtsvgnavsalgtgvsaGLGqlgetanpvGtTlastgnvvtelgeavssagslVsaLgtgplaplapvttpv 87 
                                       +l + +++ ++ vs+ ++ +sa   ql ++an +  T++  +n  ++ ++ +++ +s+++++ t  ++ +++ +++ 
  gi|298674341|ref|YP_003726091.1| 388 NLVENIKESASQVSSTSEELSASSEQLTSSANQISDTITEITNGAQNQSTKIQEVSSTMNDMST-SIQDVSSNAQKT 463
                                       4445566778899999**********************************************99.678888888888 PP

                      Collagen_mid  88 ggvvstvgqavtsagttLttals.sgpvqqltqqlssaitPitstvtgttqtvgtatglgapv 149
                                       +++v++v + v+++g++ ++  s   ++q  ++q+s++++ + ++ +++   v   t +    
  gi|298674341|ref|YP_003726091.1| 464 SETVTEVNKLVNEVGEQSKELKSkMENIQTTSEQTSEVVRELDNKSKKIGEIVSMITNIADQT 526
                                       888888888888888887777663457888889999999999998888888888777776654 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00038
                      Collagen_mid   5 ssqvtqglggvvtsvgnavsalgtgvsaGLGqlgetanpvGtTlastgnvvtelgeavssagslVsaLgtgplapla 81 
                                       ss+ +q++g+ ++++ n   ++ + +++   ++ + + ++  T++s++nvv +++ea +   ++ s+  ++  a ++
  gi|298674341|ref|YP_003726091.1| 561 SSNSAQQIGDLIQEIQNSTGEAVSSMENSSQEIENGSQALDETVNSMSNVVGKTSEADNMVQDIASS-AEELSASVE 636
                                       56778999999999999999999999999999*********************99986554444443.333456788 PP

                      Collagen_mid  82 pvttpvggvvstvgqavtsagttLttal 109
                                       +vt+ v + vs++++  +s  +   +++
  gi|298674341|ref|YP_003726091.1| 637 EVTSSVEE-VSSIAEESSSSTEEASASV 663
                                       88887754.3444443333333333332 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   5.9    0.0011      0.33      12      67 ..     376     431 ..     366     452 .. 0.79
   2 !    9.6   5.4    0.0027      0.77       8      67 ..     449     508 ..     442     533 .. 0.70
   3 ?    5.8   0.9      0.04        12       7      60 ..     563     617 ..     557     629 .. 0.73
   4 ?    7.6   5.3     0.011       3.3       4      72 ..     630     695 ..     625     701 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0011
                             Sec34  12 cdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieek 67 
                                        d++ e  d++++++e+++e+ ++vs+ +++l++++eql+++ ++++++  ei++ 
  gi|298674341|ref|YP_003726091.1| 376 ADTIEEMQDNLKNLVENIKESASQVSSTSEELSASSEQLTSSANQISDTITEITNG 431
                                       445555556667777888999999************************99999875 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0027
                             Sec34   8 keeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieek 67 
                                        + +++++ ++++++ e+++e+++ +++v e++++l++++e++ +  ++ +e+++e+++k
  gi|298674341|ref|YP_003726091.1| 449 MSTSIQDVSSNAQKTSETVTEVNKLVNEVGEQSKELKSKMENIQTTSEQTSEVVRELDNK 508
                                       566677777777777777777777777777777777777777777777777777776655 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.04
                             Sec34   7 skeeecdelleqtd.ealeqLeeleekfksvsektsslheaceqlleeqkrleel 60 
                                       ++ +++ +l+++++ ++ e ++++e++ +++++ +++l+e+ +++ +   + +e 
  gi|298674341|ref|YP_003726091.1| 563 NSAQQIGDLIQEIQnSTGEAVSSMENSSQEIENGSQALDETVNSMSNVVGKTSEA 617
                                       66788899999986156789*******************9998876544444433 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.011
                             Sec34   4 qLeskeeecdelleqtdealeqLe.eleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFe 72 
                                       +L+++ ee+++ +e+++++ e+ + + ee   sv+e+tss++    +l ++ ++l+++aee+++ +k F+
  gi|298674341|ref|YP_003726091.1| 630 ELSASVEEVTSSVEEVSSIAEESSsSTEEASASVEEQTSSMQ----ELSKSAQDLNQMAEELNQSVKSFK 695
                                       555555555555555555544433034444455666666655....788889999999999999998886 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.9      0.83   2.4e+02      13      69 ..      13      64 ..       6      70 .. 0.45
   2 !   11.4   4.9   0.00083      0.24      18      80 ..     371     430 ..     361     437 .. 0.52
   3 !   15.5   7.0   4.6e-05     0.013       2      70 ..     387     455 ..     386     459 .. 0.95
   4 !   14.4  13.1   9.7e-05     0.028       6     101 ..     433     521 ..     423     536 .. 0.59
   5 ?    4.0   4.9      0.16        47       3      71 ..     563     631 ..     549     632 .. 0.57
   6 !   10.8  10.0    0.0013      0.37       3      75 ..     619     691 ..     609     703 .. 0.45

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.83
                                      XXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTT CS
                        Laminin_II 13 kevleqlaplsq.nlentkeklseinrsveetnekvkdankairdArrsvkkLeklap 69
                                      + v ++ ++++  +l+   +  ++++r+       +++ n +++   ++v++ e +a+
  gi|298674341|ref|YP_003726091.1| 13 QDVVKVANNIQDgKLDARLDTQNGVDRE------TAHSVNSMLDNLTKKVSDTESKAE 64
                                      3333333333321333333333344333......444555555555555555555554 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00083
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHH CS
                        Laminin_II  18 qlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkq 80 
                                       +l++ +  +e+++++l+++ ++   ++e +++ + + ++ + s+ +L+  a+q+ d + e+ +
  gi|298674341|ref|YP_003726091.1| 371 DLKEFADTIEEMQDNLKNLVEN---IKESASQVSSTSEELSASSEQLTSSANQISDTITEITN 430
                                       4555555555555555555444...44444444444444455555666666666665555555 PP

  == domain 3  score: 15.5 bits;  conditional E-value: 4.6e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTT CS
                        Laminin_II   2 kelaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapq 70 
                                       k+l+++++e+a++v +  ++ls+  e++ +++++i +++ e+++ +++ ++ i+++++ + ++   +++
  gi|298674341|ref|YP_003726091.1| 387 KNLVENIKESASQVSSTSEELSASSEQLTSSANQISDTITEITNGAQNQSTKIQEVSSTMNDMSTSIQD 455
                                       899***********************************************************9987766 PP

  == domain 4  score: 14.4 bits;  conditional E-value: 9.7e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHH CS
                        Laminin_II   6 aeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqle 82 
                                       ++ + +++ev + ++++s+ ++ +++++++  ++v e+n++v++  ++ ++ ++++ +++ + +q  + ++el++++
  gi|298674341|ref|YP_003726091.1| 433 QNQSTKIQEVSSTMNDMSTSIQDVSSNAQKTSETVTEVNKLVNEVGEQSKELKSKMENIQTTSEQTSEVVRELDNKS 509
                                       33345566666666666666666666666666666666666666666666666666666666666666666666665 PP

                                       HH...HHHHHHHHHHHHHH CS
                        Laminin_II  83 eassslsdniseikelIaq 101
                                       ++       i ei  +I  
  gi|298674341|ref|YP_003726091.1| 510 KK-------IGEIVSMITN 521
                                       55.......4444444443 PP

  == domain 5  score: 4.0 bits;  conditional E-value: 0.16
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTT CS
                        Laminin_II   3 elaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqL 71 
                                       + a+++ + ++e+++ + +    +en ++++++  + ++et + +++    + +A + v+++   a++L
  gi|298674341|ref|YP_003726091.1| 563 NSAQQIGDLIQEIQNSTGEAVSSMENSSQEIENGSQALDETVNSMSNVVGKTSEADNMVQDIASSAEEL 631
                                       233334444444444444444455566666666666666666666677777777777777777777665 PP

  == domain 6  score: 10.8 bits;  conditional E-value: 0.0013
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGH CS
                        Laminin_II   3 elaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldkl 75 
                                       ++++++ ++a+e  + ++++   +e++++ ++e  +s ee  + v++ +  +++ ++s ++L++ a++L + +
  gi|298674341|ref|YP_003726091.1| 619 NMVQDIASSAEELSASVEEVTSSVEEVSSIAEESSSSTEEASASVEEQTSSMQELSKSAQDLNQMAEELNQSV 691
                                       3344444444444444444444444444444444444444444444444444444444444444444444433 PP

>> FPP  Filament-like plant protein, long coiled-coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7  45.8   1.2e-05    0.0033     485     828 ..     349     689 ..     326     702 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.2e-05
                               FPP 485 rvalkevneesaeasdslasseeeeedassdek.tlkedslevekeeevseeeksseeeskqkiqqelskaiskiie 560
                                       + + + + + + ++s ++ ++++   ++  d++ +++++ +++ ++++ s +++ss++e+ ++++++l+++ ++i +
  gi|298674341|ref|YP_003726091.1| 349 KRVAEAIADGDLTQSINVDTKGD--LKEFADTIeEMQDNLKNLVENIKESASQVSSTSEELSASSEQLTSSANQISD 423
                                       33333343333222222222222..222233330444445566666666777788888899999999********** PP

                               FPP 561 lveslskealklqdkssksselsevleqFsavvndllsgkadledfvleLssvldeiselkfslldvssmeeeikks 637
                                        ++ +++ a +    s+k +e+s+ +++ s++++d+ s+ ++ ++ v+e+ + ++e+ e   +l+ ++++ ++++++
  gi|298674341|ref|YP_003726091.1| 424 TITEITNGAQNQ---STKIQEVSSTMNDMSTSIQDVSSNAQKTSETVTEVNKLVNEVGEQSKELKSKMENIQTTSEQ 497
                                       999999887555...88999************************************999999999877776665555 PP

                               FPP 638 ddidkvalsenkvaqkgessnecaeisklssekeipselplvsgsneskkeenkllkeeleelksekenleve.... 710
                                          + v  ++nk  + ge  + +++i ++++      + ++ ++  +++     +  +e+++l  e +n + +    
  gi|298674341|ref|YP_003726091.1| 498 -TSEVVRELDNKSKKIGEIVSMITNIADQTNLLAL--NAAIEAARAGEQGRGFAVVADEVRKLAEESSNSAQQigdl 571
                                       .4555667777776666654444444333333333..2233333334443344444555555544444444440111 PP

                               FPP 711 lksatenleslkaqlqesEqllaelkseLeslkeskslaetqlkcmkesyesletrateleaelnelkqkieaLeve 787
                                       +++ +++  ++++ +++s q +++  + L+++ +s s +  +  +   + +++ + a+el a ++e+ + +e++++ 
  gi|298674341|ref|YP_003726091.1| 572 IQEIQNSTGEAVSSMENSSQEIENGSQALDETVNSMSNVVGKTSEADNMVQDIASSAEELSASVEEVTSSVEEVSSI 648
                                       445555666778888888888888899999999999999999999999999999********************999 PP

                               FPP 788 Leeekksheeleakckelqeqlervekkevskssaeeedkk 828
                                        ee ++s ee+ a+++e    ++  +k     ++++ee ++
  gi|298674341|ref|YP_003726091.1| 649 AEESSSSTEEASASVEEQTSSMQELSKSAQDLNQMAEELNQ 689
                                       99999999999999999999999888776666666665554 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0     0.013       3.9       2      82 ..      83     160 ..      82     166 .. 0.91
   2 ?    7.5   0.0     0.018       5.1       3      83 ..     205     282 ..     203     286 .. 0.95

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.013
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       ++++ +  e+l+  +ee +gk  ++++l      +  +   ++a+++g++ +ge  i+ + G+++ ++ ++ +++d+
  gi|298674341|ref|YP_003726091.1|  83 TFLNSSGAEVLDMGQEECIGK--KCYELFKTPHCNTGECRCDQAMRTGSVGTGET-ICDPKGKHIPIQYTGAPLKDS 156
                                       578888899999999999999..999999999999999999********999998.********************* PP

                             PAS_3  79 ngkp 82 
                                       +g++
  gi|298674341|ref|YP_003726091.1| 157 DGNI 160
                                       **97 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.018
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirden 79 
                                       +++++  e +G + ee +gk  ++++l      +  + ++++a++k++ ++ +   + ++Ge   ++ ++ +i+d++
  gi|298674341|ref|YP_003726091.1| 205 FMNNAGAEAVGKTTEECEGK--KCYNLFNTGHCNTENCQVAKAMQKDGTFTDDTVAKLPSGEL-PIRYTGAPIKDNK 278
                                       7899999*************..**************************9*************9.9**********99 PP

                             PAS_3  80 gkpv 83 
                                       g++v
  gi|298674341|ref|YP_003726091.1| 279 GEIV 282
                                       9987 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0  20.4     5e-05     0.014     273     431 ..     372     525 ..     358     544 .. 0.46
   2 !    6.9  15.4    0.0072       2.1     320     470 ..     551     694 ..     515     702 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5e-05
                            AAA_13 273 LeahFddefeekqerLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrk 349
                                       L++ F d+ ee q++L++l+e+++++ s+++   +++s++           e+l++ a++++++++++ +  ++  +
  gi|298674341|ref|YP_003726091.1| 372 LKE-FADTIEEMQDNLKNLVENIKESASQVSSTSEELSAS----------SEQLTSSANQISDTITEITNGAQNQST 437
                                       333.333355555555555555555554444444444444..........444444444444444444444444444 PP

                            AAA_13 350 epfk.svelesvkakiesikklvaeineliakhNekvanleeekeeakkklelhl.....veeleseldeykkkykk 420
                                       ++ + s ++++++  i+ ++++ ++  e++++ N+ v+++ e+ +e+k+k+e         +e+  eld+  kk+ +
  gi|298674341|ref|YP_003726091.1| 438 KIQEvSSTMNDMSTSIQDVSSNAQKTSETVTEVNKLVNEVGEQSKELKSKMENIQttseqTSEVVRELDNKSKKIGE 514
                                       33332224555555555555555555555555555555555555555555555321000034444444444444444 PP

                            AAA_13 421 lekaiekleke 431
                                       +   i++  ++
  gi|298674341|ref|YP_003726091.1| 515 IVSMITNIADQ 525
                                       44444444333 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0072
                            AAA_13 320 eedkeelkaeaealeeqLkglqraleaKrkepfksvelesvkakiesikklvaeineliakhNekvanleeekeeak 396
                                       ++++ +l +e ++ ++q+  l +++++   e ++  ++e+++++ie+++++++e  ++ ++   k+++ ++ +++++
  gi|298674341|ref|YP_003726091.1| 551 ADEVRKLAEESSNSAQQIGDLIQEIQNSTGEAVS--SMENSSQEIENGSQALDETVNSMSNVVGKTSEADNMVQDIA 625
                                       5567888889999999999999999999999998..88899999999999999999999999999988888888888 PP

                            AAA_13 397 kklelhlveeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLkaf 470
                                       ++ e      l + ++e ++ +++++  +e+   + +e++a +++    ++eL k+ +d ++ aee+n+ +k+f
  gi|298674341|ref|YP_003726091.1| 626 SSAEE-----LSASVEEVTSSVEEVSSIAEESSSSTEEASASVEEQTSSMQELSKSAQDLNQMAEELNQSVKSF 694
                                       77766.....3334444445555555555666666677777778888889999999999999999999999988 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9  19.3   1.7e-05    0.0048     189     381 ..     331     522 ..     321     539 .. 0.63
   2 !    6.4   4.1    0.0061       1.8     644     729 ..     547     637 ..     523     652 .. 0.61
   3 ?    1.6   7.7      0.18        53     175     278 ..     597     693 ..     590     704 .. 0.38

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.7e-05
                          Prominin 189 lkdvpqhidhvlvqnyeelekhvsddLddagkhlgldladtlesnvlpaLaelerllenlkeakeqLe....qvnkl 261
                                       +k +++ +d++++   +e++ +v + +   +  l + ++   +  + +  +++e++ +nlk+  e+++    qv+++
  gi|298674341|ref|YP_003726091.1| 331 IKGINNTLDAIVEP-LNETK-RVAEAIA--DGDLTQSINVDTKGDLKEFADTIEEMQDNLKNLVENIKesasQVSST 403
                                       55556666666666.55555.5666553..45677777777777777777777777777776554443222278888 PP

                          Prominin 262 ekeLrksgsqLrdglrgvkrdlnqalsn.lCqseeCskilssleiekldtskcl..dqlpnvdevlealeevletnl 335
                                       ++eL  s++qL ++ +++ + ++++ +  + qs++ ++++s+++   + ts +   ++ ++++e +++++++  +++
  gi|298674341|ref|YP_003726091.1| 404 SEELSASSEQLTSSANQISDTITEITNGaQNQSTKIQEVSSTMND--MSTSIQDvsSNAQKTSETVTEVNKL-VNEV 477
                                       888888888888888888888888777744444555555555555..4444333445566677777777766.4567 PP

                          Prominin 336 ssivkeglarlneipekvknqtaevvpdlkkalakgreqikklakk 381
                                        ++ ke  +++++i+++  +qt+evv++l ++ +k++e ++++++ 
  gi|298674341|ref|YP_003726091.1| 478 GEQSKELKSKMENIQTT-SEQTSEVVRELDNKSKKIGEIVSMITNI 522
                                       77788888888888654.6778888888887777777777766643 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0061
                          Prominin 644 k.......knlkqslkneaqdlraiqqelvlplessvkklkksvkkldeensdlqesikkllaaveraenflkkngs 713
                                               ++l ++  n+aq++ ++ qe+     ++v+++++s +++++ ++ l e+++ + + v ++ +   +n+ 
  gi|298674341|ref|YP_003726091.1| 547 FavvadevRKLAEESSNSAQQIGDLIQEIQNSTGEAVSSMENSSQEIENGSQALDETVNSMSNVVGKTSE--ADNMV 621
                                       1555555566777777777777777777777777777777777777777777777777766666665554..34444 PP

                          Prominin 714 eiinneskklldrile 729
                                       + i++ +++l+++++e
  gi|298674341|ref|YP_003726091.1| 622 QDIASSAEELSASVEE 637
                                       4444444444444443 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.18
                          Prominin 175 ketvkrgledlrtflkdvpqhidhvlvqnyeelekhvsddLddagkhl..gldladtlesnvlpaLaelerllenlk 249
                                       +++++++++++ + + ++++  d++++       +++s +++++ +++  ++ +a++++s+  +a a++e+   +  
  gi|298674341|ref|YP_003726091.1| 597 SQALDETVNSMSNVVGKTSEA-DNMVQD-IASSAEELSASVEEVTSSVeeVSSIAEESSSSTEEASASVEEQTSS-- 669
                                       444444444444444444433.222222.2333334444444444333223344444444433333333333333.. PP

                          Prominin 250 eakeqLeqvnklekeLrksgsqLrdglrg 278
                                            +++++k+ ++L +++++L++++++
  gi|298674341|ref|YP_003726091.1| 670 -----MQELSKSAQDLNQMAEELNQSVKS 693
                                       .....333333333333333333333333 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1  24.2    0.0076       2.2     137     279 ..     379     513 ..     327     569 .. 0.70
   2 ?    4.4  11.2     0.051        15     144     270 ..     470     595 ..     467     603 .. 0.79
   3 !   10.4  14.4   0.00076      0.22     136     262 ..     571     696 ..     569     704 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0076
                              Spc7 137 legLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelka 213
                                       +e+++++l++ +e+++e ++++++  eel++  ++l++  ++++++++++ + a++    ++++++e+ +++++ ++
  gi|298674341|ref|YP_003726091.1| 379 IEEMQDNLKNLVENIKESASQVSSTSEELSASSEQLTSSANQISDTITEITNGAQN----QSTKIQEVSSTMNDMST 451
                                       56666777777777777777777777777777777777777777777777764433....45556666666666666 PP

                              Spc7 214 eieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkale 279
                                        i+  + + ++  e ++e+++ ++e+ eq +el++++++ + +     + +++ v++l ++ k++ 
  gi|298674341|ref|YP_003726091.1| 452 SIQDVSSNAQKTSETVTEVNKLVNEVGEQSKELKSKMENIQTTS----EQTSEVVRELDNKSKKIG 513
                                       66655555555555555555555555555555555555333333....334444455555554444 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.051
                              Spc7 144 leenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesid.keeLeelreelaelkaeieekk 219
                                       +++ ++++ e++++L++++e++++  ++++e   el ++ +k+ e +  +++i  +++L +l  +++++ a   e+ 
  gi|298674341|ref|YP_003726091.1| 470 VNKLVNEVGEQSKELKSKMENIQTTSEQTSEVVRELDNKSKKIGEIVSMITNIAdQTNLLALNAAIEAARAG--EQG 544
                                       566678888999999999999999999999999999999999999999999965599999999999988765..447 PP

                              Spc7 220 kelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsr 270
                                       +  a + +++ +l+e+ ++ ++q+ +l +ei+++        + s++e+++
  gi|298674341|ref|YP_003726091.1| 545 RGFAVVADEVRKLAEESSNSAQQIGDLIQEIQNSTGEAVSSMENSSQEIEN 595
                                       777777777777777777777777777777777777777777777777766 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00076
                              Spc7 136 llegLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelk 212
                                       l+++++++  e ++++e+ ++++e+  + lde ++++++   + +e  ++ q+ a + ++  ++++ee+ ++++e++
  gi|298674341|ref|YP_003726091.1| 571 LIQEIQNSTGEAVSSMENSSQEIENGSQALDETVNSMSNVVGKTSEADNMVQDIASS-AEELSASVEEVTSSVEEVS 646
                                       8999*****************************999999988887776666665544.4445778888888888888 PP

                              Spc7 213 aeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckg 262
                                       +  ee +  ++e  + +ee++++++el+++ ++l++  +e ++ ++  k 
  gi|298674341|ref|YP_003726091.1| 647 SIAEESSSSTEEASASVEEQTSSMQELSKSAQDLNQMAEELNQSVKSFKV 696
                                       88888888888888888888888888888888888888888877776665 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   4.1   4.8e-05     0.014       4     107 ..     368     471 ..     366     474 .. 0.94
   2 ?    1.7   5.6       1.2   3.3e+02       9      51 ..     478     520 ..     472     576 .. 0.71
   3 ?    2.2   0.2      0.78   2.3e+02      34      81 ..     552     599 ..     531     611 .. 0.77
   4 ?   10.2   4.6    0.0025      0.73      19      98 ..     614     693 ..     608     703 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.8e-05
                           DUF4200   4 kkremfevqealeakkeeiqrleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekea 80 
                                       +k ++ e    +e++++++++l e++k+   ++  + +el  + ++++   +++ +  ++    a++++ +++e  +
  gi|298674341|ref|YP_003726091.1| 368 TKGDLKEFADTIEEMQDNLKNLVENIKESASQVSSTSEELSASSEQLTSSANQISDTITEITNGAQNQSTKIQEVSS 444
                                       56678889999****************************************************************** PP

                           DUF4200  81 eikklkaeietlkseiekleekleeyk 107
                                        ++++ ++i+++ s  +k+ e++ e+ 
  gi|298674341|ref|YP_003726091.1| 445 TMNDMSTSIQDVSSNAQKTSETVTEVN 471
                                       ***********************9976 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 1.2
                           DUF4200   9 fevqealeakkeeiqrleealkqreeelekkeqeleedllkfd 51 
                                        e  ++l+ k e+iq++ e+ ++  +el++k +++ e + + +
  gi|298674341|ref|YP_003726091.1| 478 GEQSKELKSKMENIQTTSEQTSEVVRELDNKSKKIGEIVSMIT 520
                                       5566788888888888888888888888888888877765544 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.78
                           DUF4200  34 eelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeae 81 
                                       +e++k  +e  +++++    ++e+++ + +a   +e+ ++++++  + 
  gi|298674341|ref|YP_003726091.1| 552 DEVRKLAEESSNSAQQIGDLIQEIQNSTGEAVSSMENSSQEIENGSQA 599
                                       567777788888888888888888888888888888888877765555 PP

  == domain 4  score: 10.2 bits;  conditional E-value: 0.0025
                           DUF4200  19 keeiqrleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkaeietlkse 95 
                                         e  ++ + +++  eel ++ +e   +++++    +e  + +++a   +ee++   +e  +  ++l++  e+l++ 
  gi|298674341|ref|YP_003726091.1| 614 TSEADNMVQDIASSAEELSASVEEVTSSVEEVSSIAEESSSSTEEASASVEEQTSSMQELSKSAQDLNQMAEELNQS 690
                                       567777888999999**********************************************************9987 PP

                           DUF4200  96 iek 98 
                                        + 
  gi|298674341|ref|YP_003726091.1| 691 VKS 693
                                       665 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   9.3    0.0009      0.26      79     182 ..     330     455 ..     307     459 .. 0.72
   2 ?   11.2   4.4   0.00049      0.14     237     302 ..     460     525 ..     453     536 .. 0.90
   3 ?    1.8  15.9      0.35     1e+02     168     298 ..     563     689 ..     550     707 .] 0.48

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0009
                                       HHHHHHHHHHHHHHHHHTSS-TTS.................STGGGCS-.....-TTTTHHHHHHHHHHHHHHHHHH CS
                             APG17  79 eldaanerLektlekLrktkvepsfrpegee..........ktLlDFvd.....edsveelkealkesidelqaaqk 140
                                        ++  n+ L++++e L++tk  +    +g +            L++F d     +d+ ++l e++kes ++++++ +
  gi|298674341|ref|YP_003726091.1| 330 VIKGINNTLDAIVEPLNETKRVAEAIADG-DltqsinvdtkGDLKEFADtieemQDNLKNLVENIKESASQVSSTSE 405
                                       55666889999999999998777766666.44799999999889999886666667777777777888888888888 PP

                                       HHHTTHH..HHHHHHHHHHH........-------STCCHHHHHHHHHHH CS
                             APG17 141 kldssllefdtdlrelkkel........sksksksessslipellkeles 182
                                       +l+ s +++ ++ +++++++        ++s++ +e ss+++++ ++ ++
  gi|298674341|ref|YP_003726091.1| 406 ELSASSEQLTSSANQISDTIteitngaqNQSTKIQEVSSTMNDMSTSIQD 455
                                       88888888888888888888777665443333333666666666666655 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00049
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHH CS
                             APG17 237 aaeledVvkelqerleemekakkllsekkeeiekllsalkkaleeleevgkklpeylaifkaeeef 302
                                       a+  ++ v+e+++ ++e+ +++k+l++k+e+i++++++++++++el++ +kk+ e++++++++++ 
  gi|298674341|ref|YP_003726091.1| 460 AQKTSETVTEVNKLVNEVGEQSKELKSKMENIQTTSEQTSEVVRELDNKSKKIGEIVSMITNIADQ 525
                                       7788899*****************************************9*******9988888765 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.35
                                       STCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH................S-CCHHHHHHHHHHHHHHHHHHHH CS
                             APG17 168 essslipellkelesleeemAslLesLtnHfDqcvkAvkltegggalrraaaelseeereelleVlekDaaeledVv 244
                                       +s + i +l++e ++   e +s +e+  +  +  ++A+++t +++   +  +  + +e +++++ +   a+el++ v
  gi|298674341|ref|YP_003726091.1| 563 NSAQQIGDLIQEIQNSTGEAVSSMENSSQEIENGSQALDETVNSMS--NVVG--KTSEADNMVQDIASSAEELSASV 635
                                       4444455555555555555555555555544445555554444432..2222..34555577777777777777777 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHH CS
                             APG17 245 kelqerleemekakkllsekkeeiekllsalkkaleeleevgkklpeylaifka 298
                                       +e+++++ee++++ ++ s+ +ee+ +++++ ++ ++el++  + l+++ + +++
  gi|298674341|ref|YP_003726091.1| 636 EEVTSSVEEVSSIAEESSSSTEEASASVEEQTSSMQELSKSAQDLNQMAEELNQ 689
                                       777777777733333333333333333333333333333333333333332222 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1  37.2   0.00017      0.05     233     531 ..     378     675 ..     348     698 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00017
                           DUF3584 233 diqalaaiekvrpeieklqeefeqleslelrLsllkgelkadeerlaekqeevqeakae...lkqqlrtledelkea 306
                                        i+ +++  + ++ +e+++e  +q+ s  ++Ls  + +l +  +++++  +e+ + +++   + q++++  ++++++
  gi|298674341|ref|YP_003726091.1| 378 TIEEMQD--NLKNLVENIKESASQVSSTSEELSASSEQLTSSANQISDTITEITNGAQNqstKIQEVSSTMNDMSTS 452
                                       3333322..34455677777788888888888888888887777777766665554444011456667777888899 PP

                           DUF3584 307 idelnqelsaakaklaakeselealeeqkkkyedadieklkadldqlpsirseleeleeeldaltekhqdvqekydr 383
                                       i+ ++++ +++++ + + ++ ++++ eq k+ +++++e+ +   +q  ++ +el + ++++  + + ++++  +++ 
  gi|298674341|ref|YP_003726091.1| 453 IQDVSSNAQKTSETVTEVNKLVNEVGEQSKE-LKSKMENIQTTSEQTSEVVRELDNKSKKIGEIVSMITNIADQTNL 528
                                       99999999999****************9999.6789*************************************9998 PP

                           DUF3584 384 rkqkikeeleeeleklkerleaireekdrlkaaieealealesql..........rkqleaqkeelneeekelesrl 450
                                       +  ++  e +++ e+ +   +++ +e  +l ++ ++  +++              ++ +e+  +e+++  + l + +
  gi|298674341|ref|YP_003726091.1| 529 LALNAAIEAARAGEQGRGF-AVVADEVRKLAEESSNSAQQIGDLIqeiqnstgeaVSSMENSSQEIENGSQALDETV 604
                                       8888777777766665544.556666555555555555554433300000001112333333333333333333333 PP

                           DUF3584 451 selklrldsatateEeleqieeadealekaqeelekaeaevealqaeeeqlrkkrdeadealqkaerrleqlrqale 527
                                       ++            + + +  ead+ ++   +++e+ +a+ve+ ++  e++ +  +e +   ++a++++e++ + ++
  gi|298674341|ref|YP_003726091.1| 605 NSMS----------NVVGKTSEADNMVQDIASSAEELSASVEEVTSSVEEVSSIAEESSSSTEEASASVEEQTSSMQ 671
                                       3333..........444444455555555555555555555555555555555555555555555555555555555 PP

                           DUF3584 528 elee 531
                                       el +
  gi|298674341|ref|YP_003726091.1| 672 ELSK 675
                                       5443 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1  20.6    0.0025      0.72      40     175 ..     376     515 ..     343     528 .. 0.44
   2 ?    6.7  19.6    0.0068         2      37     220 ..     499     691 ..     494     706 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0025
                               MAD  40 krqleeesdrnqelqkrikllekreeekeealreqiElar.lkkknlealnkkekekesklaearevisalkn...e 112
                                       ++ +ee +d  ++l ++ik+   + +  +e+l++  E+   + ++  +++++ ++  +++ ++++ev+s++++    
  gi|298674341|ref|YP_003726091.1| 376 ADTIEEMQDNLKNLVENIKESASQVSSTSEELSASSEQLTsSANQISDTITEITNGAQNQSTKIQEVSSTMNDmstS 452
                                       22333333333344444444444443333334443333320223333444444444444444444444333321113 PP

                               MAD 113 laelkrqiekqelelsekeseleelqerldllkkklseleqliqqlekkqkelaeaeqrikeL 175
                                       +++   +++k+   ++e ++ ++e+ e+ ++lk k+++++   +q  +  +el ++ ++i e+
  gi|298674341|ref|YP_003726091.1| 453 IQDVSSNAQKTSETVTEVNKLVNEVGEQSKELKSKMENIQTTSEQTSEVVRELDNKSKKIGEI 515
                                       444444444444444444444444444444444444444444444444444444444444443 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0068
                               MAD  37 salkrqleeesdrnqelqkrikllekreeekeealreqi......Elarlkkknlealnkkekekesklaearevis 107
                                       s+  r+l+++s++  e+   i+++ ++ +    al++ i      E+ r      +++ k+++e +++ +++ ++i+
  gi|298674341|ref|YP_003726091.1| 499 SEVVRELDNKSKKIGEIVSMITNIADQTNL--LALNAAIeaaragEQGRGFAVVADEVRKLAEESSNSAQQIGDLIQ 573
                                       556678888888888888888888777643..234444400011255555566789********************* PP

                               MAD 108 alknelaelkrqiekqelelsekeseleelqerldllkkklseleqliqqlekkqkelaeaeqrikeLefeiqs... 181
                                       +++n + e   ++e+  +e+++ ++ l e  +       k+se+++ +q+  ++ +el+++ + +     e++s   
  gi|298674341|ref|YP_003726091.1| 574 EIQNSTGEAVSSMENSSQEIENGSQALDETVNSMSNVVGKTSEADNMVQDIASSAEELSASVEEVTSSVEEVSSiae 650
                                       ***************************9999999999999*******999999999999888887776666666544 PP

                               MAD 182 .qeddslivknsksel.aripelekelerlreenkklnelk 220
                                         +++ ++  +s +e+  ++ el k  + l+++ ++ln++ 
  gi|298674341|ref|YP_003726091.1| 651 eSSSSTEEASASVEEQtSSMQELSKSAQDLNQMAEELNQSV 691
                                       35555566666666666888899999999999999998765 PP

>> RmuC  RmuC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   3.8     0.031       9.1       6      56 ..     378     428 ..     369     438 .. 0.58
   2 ?    7.7   5.9    0.0059       1.7     222     289 ..     433     499 ..     425     501 .. 0.90
   3 ?    7.0   4.0    0.0099       2.9     221     278 ..     460     519 ..     451     528 .. 0.58
   4 ?    9.4   0.8    0.0018      0.51     222     280 ..     559     616 ..     555     630 .. 0.81
   5 ?    5.2   6.0     0.034       9.9       2      61 ..     630     688 ..     629     697 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.031
                              RmuC   6 llkplkeklekfeekveeeskeeaeeleslkeqlkelqelneqlgdeaenL 56 
                                       + ++++++l+++ e+++e+ ++++++ e+l+++ ++l++ ++q++d+ +++
  gi|298674341|ref|YP_003726091.1| 378 TIEEMQDNLKNLVENIKESASQVSSTSEELSASSEQLTSSANQISDTITEI 428
                                       444555566666666666666666666666666666666666666654444 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0059
                              RmuC 222 eaqeknaeeiaellgelydkfekfgedleklgkklekaqksydkavkklegnilrkaeklkelgvkek 289
                                       ++q+ + +e+ ++++++ + ++ +  + +k+ + + +++k +++ v++ ++++ +k+e++++ +++++
  gi|298674341|ref|YP_003726091.1| 433 QNQSTKIQEVSSTMNDMSTSIQDVSSNAQKTSETVTEVNKLVNE-VGEQSKELKSKMENIQTTSEQTS 499
                                       67899999************************************.999999*******9999887765 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0099
                              RmuC 221 qeaqeknaeeiaellgelydkfekfgedleklgkklekaqksydkavkkle..gnilrka 278
                                        ++ ++ ++e+ +l++e+ ++ ++++ ++e++++  e++++ ++++ +k +  g+i++ +
  gi|298674341|ref|YP_003726091.1| 460 AQKTSETVTEVNKLVNEVGEQSKELKSKMENIQTTSEQTSEVVRELDNKSKkiGEIVSMI 519
                                       345555666666666666666666666666666666666666666555555555555555 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.0018
                              RmuC 222 eaqeknaeeiaellgelydkfekfgedleklgkklekaqksydkavkklegnilrkaek 280
                                       e+ ++ a++i +l++e+ +  ++ + ++e+  +++e+ ++++d++v+++++ ++ k  +
  gi|298674341|ref|YP_003726091.1| 559 EESSNSAQQIGDLIQEIQNSTGEAVSSMENSSQEIENGSQALDETVNSMSN-VVGKTSE 616
                                       567789999999999999999999999999999999999999999999964.4444433 PP

  == domain 5  score: 5.2 bits;  conditional E-value: 0.034
                              RmuC   2 qleellkplkeklekfeekveeeskeeaeeleslkeqlkelqelneqlgdeaenLtkaLk 61 
                                       +l++ ++++++++e+++   ee+s++ +e+ +s++eq +++qel+++ +d  +++++ L+
  gi|298674341|ref|YP_003726091.1| 630 ELSASVEEVTSSVEEVSSIAEESSSSTEEASASVEEQTSSMQELSKSAQD-LNQMAEELN 688
                                       688889999999*****9999999*************9999999876665.444444343 PP

>> BAR_3  BAR domain of APPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   0.00022     0.062      33     101 ..     329     397 ..     326     406 .. 0.93
   2 ?    2.7   8.4       0.3        88      25     100 ..     419     491 ..     409     529 .. 0.49
   3 ?    2.9   9.1      0.26        76      17     106 ..     586     692 ..     581     706 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00022
                             BAR_3  33 kllKlckrlieagkaysaaqkqfaqsLrelkkeskgdeetdesLkkfsellqelenehtilldqaqrsi 101
                                       +++K ++++++a  +  + +k +a+ + +    ++ +  t+  Lk+f+++++e+ ++ + l++++++s 
  gi|298674341|ref|YP_003726091.1| 329 NVIKGINNTLDAIVEPLNETKRVAEAIADGDLTQSINVDTKGDLKEFADTIEEMQDNLKNLVENIKESA 397
                                       799**************************************************************9984 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.3
                             BAR_3  25 eelekklkkllKlckrlieagkaysaaqkqfaqsLrelkkeskgdeetdesLkkfsellqelenehtilldqaqrs 100
                                       +++++ + ++++  ++  ++ +++s++++ +++s+++++ + ++ +   e+ +++++l++e+ ++ ++l  ++++ 
  gi|298674341|ref|YP_003726091.1| 419 NQISDTITEITNGAQNQSTKIQEVSSTMNDMSTSIQDVSSNAQKTS---ETVTEVNKLVNEVGEQSKELKSKMENI 491
                                       4455555555555555555555555555555555555555443333...333333333333333333333333322 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.26
                             BAR_3  17 leevEaeleelekklkkllKlckrlieagkaysaaqkqfaqsLrelkkes......kgdeetd.............. 73 
                                       +e+  +e+e+ +++l++ ++++++++ ++ +  ++ + +a+s +el+               +              
  gi|298674341|ref|YP_003726091.1| 586 MENSSQEIENGSQALDETVNSMSNVVGKTSEADNMVQDIASSAEELSASVeevtssV-----Eevssiaeesssste 657
                                       566678888889999999999999999999999999999999999887765444320.....123355666664555 PP

                             BAR_3  74 ...esLkkfsellqelenehtilldqaqrsikkpLe 106
                                          +s ++ ++++qel++  + l +q+++ + ++++
  gi|298674341|ref|YP_003726091.1| 658 easASVEEQTSSMQELSKSAQDL-NQMAEELNQSVK 692
                                       55544444444444444444443.233333333333 PP

>> RPW8  Arabidopsis broad-spectrum mildew resistance protein RPW8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.4      0.26        74      24      68 ..     362     407 ..     348     417 .. 0.70
   2 ?    6.4   0.8     0.023       6.6      13      66 ..     418     471 ..     412     475 .. 0.81
   3 ?    7.2   2.4     0.014       3.9      14      73 ..     461     520 ..     457     524 .. 0.89
   4 ?    8.0   1.3    0.0072       2.1      16      86 ..     579     649 ..     568     692 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.26
                              RPW8  24 kkksldfksilkrLestleritPvvke.ieklnkeldrpreeieeL 68 
                                       +  ++d+k  lk+ ++t+e+++ ++k+ +e++++   +  +  eeL
  gi|298674341|ref|YP_003726091.1| 362 QSINVDTKGDLKEFADTIEEMQDNLKNlVENIKESASQVSSTSEEL 407
                                       5668899999999999999998887763566666656666666655 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.023
                              RPW8  13 lgellkaileakkksldfksilkrLestleritPvvkeieklnkel.drpreeie 66 
                                        +++ + i+e ++ + + + ++++  st+++++++++++ +  ++  +  + e++
  gi|298674341|ref|YP_003726091.1| 418 ANQISDTITEITNGAQNQSTKIQEVSSTMNDMSTSIQDVSSNAQKTsETVT-EVN 471
                                       57889999999999999999*******************988777734443.444 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.014
                              RPW8  14 gellkaileakkksldfksilkrLestleritPvvkeieklnkeldrpreeieeLkklLe 73 
                                       ++  + ++e++k + ++  ++k+L+s +e+i++  ++  ++  eld++ ++i e+ + ++
  gi|298674341|ref|YP_003726091.1| 461 QKTSETVTEVNKLVNEVGEQSKELKSKMENIQTTSEQTSEVVRELDNKSKKIGEIVSMIT 520
                                       6778999999999999999***********************9**999999998877665 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.0072
                              RPW8  16 llkaileakkksldfksilkrLestleritPvvkeieklnkeldrpreeieeLkklLekaekLVekcsklk 86 
                                         +a+   ++ s +++  ++ L++t+++++ vv +  +  + ++   +  eeL    e+  + Ve+ s + 
  gi|298674341|ref|YP_003726091.1| 579 TGEAVSSMENSSQEIENGSQALDETVNSMSNVVGKTSEADNMVQDIASSAEELSASVEEVTSSVEEVSSIA 649
                                       55677777777777777788888888888888877777777777777777777777777777777777664 PP

>> KASH_CCD  Coiled-coil region of CCDC155 or KASH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9  18.9     0.035        10      60     180 ..     374     494 ..     335     504 .. 0.83
   2 ?    6.6   6.9     0.022       6.3       4      71 ..     447     507 ..     444     530 .. 0.66
   3 ?   10.4  10.8    0.0014      0.42      73     186 ..     573     682 ..     546     694 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.035
                          KASH_CCD  60 qkaklleeEleelkalvkeleEkrarlkaqnkqlekenqsLiakiesLqeenikllaekdelkkklkeLlkekaeLk 136
                                       ++a  +ee  ++lk+lv++++E++ +++  +++l    ++L++  +++ + ++ ++  +++  +k++e +++ +++ 
  gi|298674341|ref|YP_003726091.1| 374 EFADTIEEMQDNLKNLVENIKESASQVSSTSEELSASSEQLTSSANQISDTITEITNGAQNQSTKIQEVSSTMNDMS 450
                                       56677888889999999999999999999999999999999999999999999999999999999999999888888 PP

                          KASH_CCD 137 kqlheleellaekealleektkqieeLkltieEyssiieeLrae 180
                                       + ++ + + + +  ++++e +k ++e+  + +E++s +e+++  
  gi|298674341|ref|YP_003726091.1| 451 TSIQDVSSNAQKTSETVTEVNKLVNEVGEQSKELKSKMENIQTT 494
                                       88888888888888888888888888888888887777776654 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.022
                          KASH_CCD   4 sdlistvadLqlnNkkLaeenskLkkavetaeetnakLteeieeLkkklkstQqalqkaklleeElee 71 
                                       +d+ ++++d   n +k +e ++ + k v+ + e         +eLk k+   Q ++++   +  El++
  gi|298674341|ref|YP_003726091.1| 447 NDMSTSIQDVSSNAQKTSETVTEVNKLVNEVGE-------QSKELKSKMENIQTTSEQTSEVVRELDN 507
                                       456666666666666666666666666665555.......5567777777777777777777777765 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.0014
                          KASH_CCD  73 kalvkeleEkrarlkaqnkqlekenqsLiakiesLqeenikllaekdelkkklkeLlkekaeLkkqlheleellaek 149
                                       +++ +++ E   ++++ ++++e   q L + ++s+ +   k         + +++++++ +eL   + e+ + + e 
  gi|298674341|ref|YP_003726091.1| 573 QEIQNSTGEAVSSMENSSQEIENGSQALDETVNSMSNVVGKTSEA----DNMVQDIASSAEELSASVEEVTSSVEEV 645
                                       344566777778888888888888888888888888887775443....3444555555555555555555555555 PP

                          KASH_CCD 150 ealleektkqieeLkltieEyssiieeLraeksrLee 186
                                        +++ee+   +ee  +++eE +s ++eL +  + L++
  gi|298674341|ref|YP_003726091.1| 646 SSIAEESSSSTEEASASVEEQTSSMQELSKSAQDLNQ 682
                                       5555555555555555555555555555554444443 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   3.2     0.012       3.4      35      97 ..     361     423 ..     327     424 .. 0.80
   2 ?    6.8   9.3     0.034       9.7       8      98 ..     412     501 ..     410     502 .. 0.86
   3 ?    5.2   7.2       0.1        30       9      65 ..     441     503 ..     433     521 .. 0.48
   4 ?    8.5   1.1    0.0097       2.8       3      64 ..     547     611 ..     546     633 .. 0.60
   5 ?    8.5   8.6      0.01       2.9       8      69 ..     636     696 ..     625     706 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.012
                      Syntaxin-6_N  35 tseeldetrteLrkalrsiewdledLeetvriveknpskfkidekelsrrrafveevreevke 97 
                                       t++   +t+ +L++  ++ie+  ++L++ v+ ++++ s+++ +++els   + +++  +++++
  gi|298674341|ref|YP_003726091.1| 361 TQSINVDTKGDLKEFADTIEEMQDNLKNLVENIKESASQVSSTSEELSASSEQLTSSANQISD 423
                                       455566889999999***************999*999************99999999999975 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.034
                      Syntaxin-6_N   8 eeVqkslnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLeetvriveknpskfkidekelsrr 84 
                                       e+  +s+n++  ++++ ++  +++s+ + +e+++t++++ +++++++ + +   etv  v+k  ++++ ++kel+++
  gi|298674341|ref|YP_003726091.1| 412 EQLTSSANQISDTITEITNGAQNQST-KIQEVSSTMNDMSTSIQDVSSNAQKTSETVTEVNKLVNEVGEQSKELKSK 487
                                       55677888888888888654555444.599***************************999999999*********** PP

                      Syntaxin-6_N  85 rafveevreevkem 98 
                                        + ++ + e+ +e+
  gi|298674341|ref|YP_003726091.1| 488 MENIQTTSEQTSEV 501
                                       *******9998765 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.1
                      Syntaxin-6_N   9 eVqkslnkaeslyrrwe.rlledtsss.....tseeldetrteLrkalrsiewdledLeetvr 65 
                                       eV +++n + + ++  + + ++++++        +e+ e+++eL++++++i+++ e+  e+vr
  gi|298674341|ref|YP_003726091.1| 441 EVSSTMNDMSTSIQDVSsNAQKTSETVtevnkLVNEVGEQSKELKSKMENIQTTSEQTSEVVR 503
                                       455555555555555531222222221233343444444444444444444444444444444 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.0097
                      Syntaxin-6_N   3 FfevkeeVqkslnkaeslyrrw....erlledtssstseeldetrteLrkalrsiewdledLeetv 64 
                                       F +v++eV+k +++  +  ++     ++++++t +   +++++ ++e+++  + ++++++ + ++v
  gi|298674341|ref|YP_003726091.1| 547 FAVVADEVRKLAEESSNSAQQIgdliQEIQNSTGE-AVSSMENSSQEIENGSQALDETVNSMSNVV 611
                                       88999999999999988888884322343333333.245555555555555555555555555555 PP

  == domain 5  score: 8.5 bits;  conditional E-value: 0.01
                      Syntaxin-6_N   8 eeVqkslnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLeetvrivek 69 
                                       eeV +s++++ s+ ++ ++  e++s ++ ee  + ++eL k+ +++++  e+L+++v+  + 
  gi|298674341|ref|YP_003726091.1| 636 EEVTSSVEEVSSIAEESSSSTEEAS-ASVEEQTSSMQELSKSAQDLNQMAEELNQSVKSFKV 696
                                       5666666666666666655333333.358899999999999999999999999999965443 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.3      0.07        20      11      78 ..     337     402 ..     327     409 .. 0.63
   2 ?    9.5   2.4    0.0052       1.5      13      85 ..     384     455 ..     371     463 .. 0.75
   3 ?    8.0   1.9     0.015       4.4       7      71 ..     462     521 ..     458     531 .. 0.74
   4 ?    3.6   0.6      0.36     1e+02      14      70 ..     553     608 ..     548     613 .. 0.75
   5 ?    9.3   5.1    0.0064       1.9       6      79 ..     615     694 ..     613     704 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.07
                           DUF2203  11 lLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkd 78 
                                       +L  + e l+e +++++ +++   +l+++ +  +k + +e + ++ee+++++++lve+i+e   +v +
  gi|298674341|ref|YP_003726091.1| 337 TLDAIVEPLNETKRVAEAIAD--GDLTQSINVDTKGDLKEFADTIEEMQDNLKNLVENIKESASQVSS 402
                                       333333333333333333333..256666666556669999999999999999999999998777655 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0052
                           DUF2203  13 pllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdleaglvD 85 
                                         lk+l+e++++ ++++ +++eel++++++ ++ +a++   +++e+++ +++  ++i+e+   + d++  + D
  gi|298674341|ref|YP_003726091.1| 384 DNLKNLVENIKESASQVSSTSEELSASSEQLTS-SANQISDTITEITNGAQNQSTKIQEVSSTMNDMSTSIQD 455
                                       467888888888889999999999988888654.488888888888888888888888888877777665555 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.015
                           DUF2203   7 eAnalLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeiee 71 
                                       +  ++++++++l++e+ ++ kel++++e++++++++      +e  +el++ +++i e+v+ i++
  gi|298674341|ref|YP_003726091.1| 462 KTSETVTEVNKLVNEVGEQSKELKSKMENIQTTSEQ-----TSEVVRELDNKSKKIGEIVSMITN 521
                                       556788899999999999999999998888888888.....456666666666666666666655 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.36
                           DUF2203  14 llkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeie 70 
                                       ++++l ee  + ++++ +l +e+++++ ea  s+ ++  +e+e+ ++ ++e+v+ ++
  gi|298674341|ref|YP_003726091.1| 553 EVRKLAEESSNSAQQIGDLIQEIQNSTGEAV-SSMENSSQEIENGSQALDETVNSMS 608
                                       6788888888888888888888888887754.4477778888888888888887765 PP

  == domain 5  score: 9.3 bits;  conditional E-value: 0.0064
                           DUF2203   6 eeAnalLpllkelleelralrkeleeleeeleeakaeaekse......aaeleaeleeleaeieelveeieelGvev 76 
                                        eA ++++ + +  eel a  +e+++ +ee++++ +e+++s+       +e+ ++++el++++++l +  eel   v
  gi|298674341|ref|YP_003726091.1| 615 SEADNMVQDIASSAEELSASVEEVTSSVEEVSSIAEESSSSTeeasasVEEQTSSMQELSKSAQDLNQMAEELNQSV 691
                                       699999************99999999999999888887766667777755666666666666666666666666666 PP

                           DUF2203  77 kdl 79 
                                       k++
  gi|298674341|ref|YP_003726091.1| 692 KSF 694
                                       665 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.6     0.058        17     153     292 ..     402     541 ..     373     559 .. 0.44
   2 ?    7.9   1.2    0.0033      0.94     209     330 ..     560     686 ..     547     700 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.058
                              FUSC 153 svapalrarlrallrdalalaaaalageegaeareaararlaadilalealrsqaayesprirararalrrllsrml 229
                                       s++++l+a+ ++l  +a +    + + + ga++++++ +++ ++++++++ ++ ++   +++++++  ++ l +++ 
  gi|298674341|ref|YP_003726091.1| 402 STSEELSASSEQLTSSANQISDTITEITNGAQNQSTKIQEVSSTMNDMSTSIQDVSSNAQKTSETVTEVNKLVNEVG 478
                                       33333444444444444444444444444444444444444444444444444444444444444444444444444 PP

                              FUSC 230 allallsslarllarlraeeaaavpelaallaelaaleaaaaaealeaalaalrarlralrra 292
                                       + +  l s  ++ ++ +++ ++ v+el++  +++ ++ +     a++++l al a+++a+r+ 
  gi|298674341|ref|YP_003726091.1| 479 EQSKELKSKMENIQTTSEQTSEVVRELDNKSKKIGEIVSMITNIADQTNLLALNAAIEAARAG 541
                                       444444444444444444444444444333333333322222333444444444444444444 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0033
                              FUSC 209 yesprirararalrrllsrmlallallsslarllarlraeeaaavpelaallaelaal.....eaaaaaealeaala 280
                                         s++ ++  + ++++++ + ++++++    ++ ++ +++ +++v ++++++ ++ ++     + a +ae+l a ++
  gi|298674341|ref|YP_003726091.1| 560 ESSNSAQQIGDLIQEIQNSTGEAVSSMENSSQEIENGSQALDETVNSMSNVVGKTSEAdnmvqDIASSAEELSASVE 636
                                       44455555666677888888888888888888888888888888888888888888877777755567888888888 PP

                              FUSC 281 alrarlralrraleadadtaalllarlaellaelaqllaslraleaaiaa 330
                                       +++  ++++++ +e++++  +++ a++ e+ +++++l +s ++l++ +++
  gi|298674341|ref|YP_003726091.1| 637 EVTSSVEEVSSIAEESSSSTEEASASVEEQTSSMQELSKSAQDLNQMAEE 686
                                       88888888888888999999999999999999999999999999998876 PP

>> FlgN  FlgN protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   5.9      0.19        54      48     124 ..     373     449 ..     334     463 .. 0.64
   2 ?    4.1  11.4      0.21        60       4     121 ..     379     502 ..     372     506 .. 0.70
   3 ?   10.0   6.9    0.0033      0.94      32     134 ..     484     592 ..     470     599 .. 0.84
   4 ?    7.2   5.1     0.023       6.7      34     102 ..     625     693 ..     615     696 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.19
                                       HHHHHHHHHHHHHHHHHHHHTT--..SCHHHHHHHHCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                              FlgN  48 qellekleqleqkrakllaelgls..aeeatlsellakeedeelkelwqelkelleelkelnelNgrlieqslefnq 122
                                       +e ++++e++ +++ +l++++++s      t +el a  + e+l +  +++++++ e+ + ++   + i+   ++ +
  gi|298674341|ref|YP_003726091.1| 373 KEFADTIEEMQDNLKNLVENIKESasQVSSTSEELSA--SSEQLTSSANQISDTITEITNGAQNQSTKIQEVSSTMN 447
                                       5566777777777777777777774323333344433..66666666666666666666555555555555555555 PP

                                       HH CS
                              FlgN 123 rl 124
                                        +
  gi|298674341|ref|YP_003726091.1| 448 DM 449
                                       44 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.21
                                       HCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--..SCHHHHH CS
                              FlgN   4 leeLielleeelelleeLlelleeEteaLkagdieaLeelleekqellekleqleqkrakllaelgls..aeeatls 78 
                                       +ee+ ++l++++e ++e ++      e L+a+  e+L++ ++++ +++ +++  +q+ +  ++e++ +  +  ++++
  gi|298674341|ref|YP_003726091.1| 379 IEEMQDNLKNLVENIKESASQVSSTSEELSASS-EQLTSSANQISDTITEITNGAQNQSTKIQEVSSTmnDMSTSIQ 454
                                       677888888888888888888888888888887.8888888888888888888888888888888888774444444 PP

                                       HHHCT.....TCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                              FlgN  79 ellak.....eedeelkelwqelkelleelkelnelNgrlieqslefn 121
                                       ++ ++     e+ +e+++l++e+ e  +elk + e  +++ eq  e +
  gi|298674341|ref|YP_003726091.1| 455 DVSSNaqktsETVTEVNKLVNEVGEQSKELKSKMENIQTTSEQTSEVV 502
                                       444434446666666666666666666666666666666666555555 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.0033
                                       HHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SCHHHHHHHHCT.......TCCHHHHHHHHHHHHHHH CS
                              FlgN  32 LkagdieaLeelleekqellekleqleqkrakllaelglsaeeatlsellak.......eedeelkelwqelkelle 101
                                       Lk +++e ++++ e+  e++++l+   +k+ ++++ + + a+++ l +l a+       e+    + + +e+++l+e
  gi|298674341|ref|YP_003726091.1| 484 LK-SKMENIQTTSEQTSEVVRELDNKSKKIGEIVSMITNIADQTNLLALNAAieaaragEQGRGFAVVADEVRKLAE 559
                                       44.4689************************9999999995555555555545558888****************** PP

                                       HHHHHHHHHHHHHHHCCHHHHHHHHHCCHXXXX CS
                              FlgN 102 elkelnelNgrlieqslefnqrllnllqgaank 134
                                       e  + +++ g li+  ++++ ++++ +  ++++
  gi|298674341|ref|YP_003726091.1| 560 ESSNSAQQIGDLIQEIQNSTGEAVSSMENSSQE 592
                                       ************************999988876 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.023
                                       TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--..SCHHHHHHHHCTTCCHHHHHHHHHHHHHHHH CS
                              FlgN  34 agdieaLeelleekqellekleqleqkrakllaelgls..aeeatlsellakeedeelkelwqelkellee 102
                                       a+ +e+L + +ee ++ +e+++ ++++ + +++e++ s  +++ +++el +  +++ l+++ +el + ++ 
  gi|298674341|ref|YP_003726091.1| 625 ASSAEELSASVEEVTSSVEEVSSIAEESSSSTEEASASveEQTSSMQELSK--SAQDLNQMAEELNQSVKS 693
                                       5678999999**********************9999998888888999987..888888888888887765 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   8.0    0.0065       1.9      22      98 ..     366     444 ..     359     447 .. 0.81
   2 ?    4.0  11.7      0.23        65      14      94 ..     413     492 ..     403     495 .. 0.65
   3 ?    9.8   6.3    0.0034      0.99       1      61 [.     463     524 ..     456     537 .. 0.60
   4 ?    3.5   1.4      0.31        90      28      63 ..     554     590 ..     511     603 .. 0.65
   5 ?    5.0   9.4      0.11        32      14      93 ..     603     694 ..     586     707 .] 0.73

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0065
                        Syntaxin_2  22 Lgtkkdteelreklhelieeinelikktnellkklsqldnsssds..qqkl.qkekLkkdfkealqeFqkiqrqyae 95 
                                       + tk+d +e+ + ++e+++++++l+++++e+ +++s+ ++ +s s  q  + +++ +++ ++e+ +  q+   +++e
  gi|298674341|ref|YP_003726091.1| 366 VDTKGDLKEFADTIEEMQDNLKNLVENIKESASQVSSTSEELSASseQL-TsSANQISDTITEITNGAQNQSTKIQE 441
                                       57999********************************999999886433.247888888888888888888888777 PP

                        Syntaxin_2  96 kek 98 
                                        + 
  gi|298674341|ref|YP_003726091.1| 442 VSS 444
                                       665 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.23
                        Syntaxin_2  14 tleklvkqLgtk.kdteelreklhelieeinelikktnellkklsqldnsssdsqqklqkekLkkdfkealqeFqki 89 
                                       +l +  +q+++  ++ ++  ++  + i+e++ + ++++ +++++s++++++s     ++ +kL++++ e  +e+++ 
  gi|298674341|ref|YP_003726091.1| 413 QLTSSANQISDTiTEITNGAQNQSTKIQEVSSTMNDMSTSIQDVSSNAQKTS--ETVTEVNKLVNEVGEQSKELKSK 487
                                       4444444444442345555555666777777777777777777777777775..67779999999999999988876 PP

                        Syntaxin_2  90 qrqya 94 
                                        ++++
  gi|298674341|ref|YP_003726091.1| 488 MENIQ 492
                                       66665 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0034
                        Syntaxin_2   1 issnlqkinsnvstleklvkqLgtk.kdteelreklhelieeinelikktnellkklsqldn 61 
                                       +s+ ++++n++v++ +++ k L++k  + + + e+  e++ e+ + +kk+ e ++ ++++++
  gi|298674341|ref|YP_003726091.1| 463 TSETVTEVNKLVNEVGEQSKELKSKmENIQTTSEQTSEVVRELDNKSKKIGEIVSMITNIAD 524
                                       35555566666666666666666663345555566666666666666666666666666555 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.31
                        Syntaxin_2  28 teelreklhelieeinelikktnellkk.lsqldnss 63 
                                        ++l e+  ++ ++i +li++++++  + +s+++nss
  gi|298674341|ref|YP_003726091.1| 554 VRKLAEESSNSAQQIGDLIQEIQNSTGEaVSSMENSS 590
                                       4566677777777888888888555444044444443 PP

  == domain 5  score: 5.0 bits;  conditional E-value: 0.11
                        Syntaxin_2  14 tleklvkqLgtkkdteelreklhelieeinelikktnellkklsqldnsssds............qqklqkekLkkd 78 
                                       t +++ + +g+  + +++ + + ++ ee++  +++++++++++s++++ ss+s            + + + +k ++d
  gi|298674341|ref|YP_003726091.1| 603 TVNSMSNVVGKTSEADNMVQDIASSAEELSASVEEVTSSVEEVSSIAEESSSSteeasasveeqtSSMQELSKSAQD 679
                                       33444444788888899999999999999999999999999999999999887888887777654444456666677 PP

                        Syntaxin_2  79 fkealqeFqkiqrqy 93 
                                       +++  +e++++++++
  gi|298674341|ref|YP_003726091.1| 680 LNQMAEELNQSVKSF 694
                                       777777777776665 PP

>> DUF3158  Protein of unknown function (DUF3158)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1    0.0014      0.39      25      60 ..     366     401 ..     354     446 .. 0.88
   2 ?   -0.8   0.1       3.8   1.1e+03     128     152 ..     473     497 ..     460     500 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0014
                           DUF3158  25 fkgkgelealaeqckalrdelialaqevlaqareyp 60 
                                       +++kg+l+++a+++++++d+l +l +++ ++a +  
  gi|298674341|ref|YP_003726091.1| 366 VDTKGDLKEFADTIEEMQDNLKNLVENIKESASQVS 401
                                       79**************************99998754 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 3.8
                           DUF3158 128 llhtilrqaaeCAeklaeaeavylr 152
                                       l++ ++ q++e  +k+++++++  +
  gi|298674341|ref|YP_003726091.1| 473 LVNEVGEQSKELKSKMENIQTTSEQ 497
                                       7899999*********999988665 PP

>> TetR_C_18  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       8.2   2.4e+03      62     102 ..     409     449 ..     403     455 .. 0.77
   2 ?   10.7   0.3     0.002      0.58      20     104 ..     515     602 ..     508     608 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 8.2
                         TetR_C_18  62 aaeasraragelivttlstvGkafseaprspkeieayaeal 102
                                       a++  ++ +++ i +t++ + +   +++ + +e+++  + +
  gi|298674341|ref|YP_003726091.1| 409 ASSEQLTSSANQISDTITEITNGAQNQSTKIQEVSSTMNDM 449
                                       66677788889999999999999999988888887644444 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.002
                         TetR_C_18  20 eaavrvaladaaplyrdapeaqdaraag.drvfqvfmkev..lpsaaeasraragelivttlstvGkafseaprspk 93 
                                        +++ + +ad ++l       ++ara    r f v   ev  l + ++ s ++ g+li +   + G+a+s    s +
  gi|298674341|ref|YP_003726091.1| 515 IVSMITNIADQTNLLALNAAIEAARAGEqGRGFAVVADEVrkLAEESSNSAQQIGDLIQEIQNSTGEAVSSMENSSQ 591
                                       56777888888888776666677777541588999999995456667788899************************ PP

                         TetR_C_18  94 eieayaealad 104
                                       eie+ ++al +
  gi|298674341|ref|YP_003726091.1| 592 EIENGSQALDE 602
                                       ***99988866 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   6.8   0.00071      0.21       3      94 ..     371     464 ..     370     471 .. 0.68
   2 ?    7.2   5.6      0.02       5.8      48     107 ..     466     522 ..     458     525 .. 0.56
   3 ?    5.0   2.1     0.095        28      24      89 ..     547     613 ..     527     627 .. 0.52
   4 ?    8.8   2.0    0.0064       1.8      29      94 ..     581     646 ..     575     654 .. 0.87
   5 ?    4.2   7.3      0.17        48      36     101 ..     626     691 ..     605     695 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00071
                                       -HHHHHH-HHHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCC CS
                      Seryl_tRNA_N   3 DiklirenpeavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkk....edaeeliae 75 
                                       D+k + + +e+++++lk+    ++  ++  ++ +  +el +  e+l +  N++s +I ++ +       +++e+   
  gi|298674341|ref|YP_003726091.1| 371 DLKEFADTIEEMQDNLKNL--VENIKESASQVSSTSEELSASSEQLTSSANQISDTITEITNGAqnqsTKIQEVSST 445
                                       7777888888888888644..667777888999999***********************997652233444444444 PP

                                       CHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  76 vkelkeelkaleaelkele 94 
                                       ++++++ +++++ + ++ +
  gi|298674341|ref|YP_003726091.1| 446 MNDMSTSIQDVSSNAQKTS 464
                                       4444444444444444443 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.02
                                       HHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCTS--- CS
                      Seryl_tRNA_N  48 lqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaeleklllaiPNi 107
                                         +e N+l +e+g+ +k   + ++ ++ +++ +e+++++  el++ ++++ ++++ i Ni
  gi|298674341|ref|YP_003726091.1| 466 TVTEVNKLVNEVGEQSK---ELKSKMENIQTTSEQTSEVVRELDNKSKKIGEIVSMITNI 522
                                       33344444444444443...4566666666666666666666666666666666666666 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.095
                                       CCHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  24 dkadvdelleldekrre.lqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleae 89 
                                       ++   de+ +l e+  + +q+  + +q+ +N+ +++++++ ++ +++e   +  +e  + ++++  +
  gi|298674341|ref|YP_003726091.1| 547 FAVVADEVRKLAEESSNsAQQIGDLIQEIQNSTGEAVSSMENSSQEIENGSQALDETVNSMSNVVGK 613
                                       5555566666555544303333344455566666666666555544444444444444444444444 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.0064
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  29 delleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkele 94 
                                       +++ ++++  +e+++  ++l +  N++s+ +gk +++++  +++  +++el++ +++++  ++e++
  gi|298674341|ref|YP_003726091.1| 581 EAVSSMENSSQEIENGSQALDETVNSMSNVVGKTSEADNMVQDIASSAEELSASVEEVTSSVEEVS 646
                                       67889999999**************************98889999999999999999888888875 PP

  == domain 5  score: 4.2 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  36 ekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelekll 101
                                       +  +el + +ee+ +   e+s   ++ + + e+a++ ++e  +  +el++  ++l+++ +el++ +
  gi|298674341|ref|YP_003726091.1| 626 SSAEELSASVEEVTSSVEEVSSIAEESSSSTEEASASVEEQTSSMQELSKSAQDLNQMAEELNQSV 691
                                       334455566666666666666655555555599999999999999999999999999999888765 PP

>> H-kinase_dim  Signal transducing histidine kinase, homodimeric domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       2.9   8.5e+02      21      45 ..     195     219 ..     193     251 .. 0.82
   2 ?    7.3   0.6     0.022       6.3      25      63 ..     369     408 ..     286     414 .. 0.85
   3 ?   -0.3   0.1       5.1   1.5e+03      27      43 ..     686     702 ..     682     705 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 2.9
                      H-kinase_dim  21 lVitkarLnqsleefrfenglkasv 45 
                                       +Vi+k++  q++++++ e+ +k++ 
  gi|298674341|ref|YP_003726091.1| 195 MVIDKNMNVQFMNNAGAEAVGKTTE 219
                                       79************99666666554 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.022
                      H-kinase_dim  25 karLnqsleefr.fenglkasvtelksslqnlgrisgeLQ 63 
                                       k  L++++++++ ++ +lk++v+++k+s+++++  s+eL 
  gi|298674341|ref|YP_003726091.1| 369 KGDLKEFADTIEeMQDNLKNLVENIKESASQVSSTSEELS 408
                                       555556666555667889********************96 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 5.1
                      H-kinase_dim  27 rLnqsleefrfenglka 43 
                                       +Lnqs+++f++++ +k+
  gi|298674341|ref|YP_003726091.1| 686 ELNQSVKSFKVDSSDKK 702
                                       79*******97777665 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4  30.8    0.0058       1.7     273     480 ..     381     605 ..     342     613 .. 0.49
   2 ?    1.3  19.1      0.41   1.2e+02     269     393 ..     559     689 ..     549     702 .. 0.50

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0058
                            DUF812 273 ksksdlaellsefseksetdslktkgsrfthaeklqftke..elakkaeteeelkkkreeeleelqeqieeleskie 347
                                       + +++l++l++++ ++s+++ + t ++  +++e  q+t++  + + + ++  +  ++++++++e+++ +++++ +i+
  gi|298674341|ref|YP_003726091.1| 381 EMQDNLKNLVENI-KESASQVSSTSEELSASSE--QLTSSanQISDTITEITNGAQNQSTKIQEVSSTMNDMSTSIQ 454
                                       2223334444444.2222222233333333333..333332222344444444455555555555555555555555 PP

                            DUF812 348 eleeeikklessikqveeeleeekeeneelekevk.......lkkktlellpdaeeniekLqalve..asaqrlvel 415
                                        ++++ +k ++++++v++ ++e  e+ +el+++++           ++  l++  + i +  +++   a + +l+ l
  gi|298674341|ref|YP_003726091.1| 455 DVSSNAQKTSETVTEVNKLVNEVGEQSKELKSKMEniqttseQTSEVVRELDNKSKKIGEIVSMITniADQTNLLAL 531
                                       55555555555555555555555555555544443111100045555555555555555555555533345689999 PP

                            DUF812 416 akqWekhRv........plieeyrelkesksekekeaerkleeikklrek.mkevaeelrqkeellkqLvaele 480
                                        +  e++R+         + +e r+l e+ s+ ++++ + ++ei++   + +  +++  ++ e+  + L + ++
  gi|298674341|ref|YP_003726091.1| 532 NAAIEAARAgeqgrgfaVVADEVRKLAEESSNSAQQIGDLIQEIQNSTGEaVSSMENSSQEIENGSQALDETVN 605
                                       99999999633333332466788888888888888888888888765433133333333333444444444444 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.41
                            DUF812 269 ssasksksdlaellsefseksetds........lktkgsrfthaeklqftkeelakkaeteeelkkkreeeleelqe 337
                                       +++s+s++++ +l++e+++++ +          + ++gs+  ++   ++ +     k+++ +++ +    + eel+ 
  gi|298674341|ref|YP_003726091.1| 559 EESSNSAQQIGDLIQEIQNSTGEAVssmenssqEIENGSQALDETVNSMSNV--VGKTSEADNMVQDIASSAEELSA 633
                                       3344455555555555522222222000000002222232222222233333..12333333344444445567777 PP

                            DUF812 338 qieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlellpd 393
                                        +ee+ s++ee+++  ++ +ss+++++ ++ee+ ++ +el k+ +  ++++e l++
  gi|298674341|ref|YP_003726091.1| 634 SVEEVTSSVEEVSSIAEESSSSTEEASASVEEQTSSMQELSKSAQDLNQMAEELNQ 689
                                       77777777777777777777777777777777777777777777776666666654 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   5.4    0.0032      0.92       6      87 ..     381     461 ..     379     464 .. 0.93
   2 ?    5.4   4.2     0.083        24      17      79 ..     462     526 ..     457     530 .. 0.76
   3 ?   10.5   0.5    0.0022      0.65       6      82 ..     574     648 ..     569     654 .. 0.85
   4 ?    2.7   2.7       0.6   1.7e+02      13      47 ..     661     695 ..     648     702 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0032
                   Snapin_Pallidin   6 gllellepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqkl 82 
                                       ++++ l+  +++++e+ +++  + eeL+++ ++l+++ ++++++   e+ + +++   K++++   m+ +++++q +
  gi|298674341|ref|YP_003726091.1| 381 EMQDNLKNLVENIKESASQVSSTSEELSASSEQLTSSANQISDTIT-EITNGAQNQSTKIQEVSSTMNDMSTSIQDV 456
                                       6889999**********************************99888.999************************998 PP

                   Snapin_Pallidin  83 kkRae 87 
                                          a+
  gi|298674341|ref|YP_003726091.1| 457 SSNAQ 461
                                       87665 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.083
                   Snapin_Pallidin  17 eldeklkelrqsQeeLleqldrlnekLkeleeaqe..aevlpdlkeyakKLvnikkrmsslnerl 79 
                                       ++ e++ e+ +  +e+ eq ++l++k+++++ + e  +ev+ +l++  kK+ +i   ++++ +++
  gi|298674341|ref|YP_003726091.1| 462 KTSETVTEVNKLVNEVGEQSKELKSKMENIQTTSEqtSEVVRELDNKSKKIGEIVSMITNIADQT 526
                                       566677777777777777777777777777766554678999***********999999998876 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.0022
                   Snapin_Pallidin   6 gllellepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqkl 82 
                                       ++++    ++  ++++ +e+++  ++L e+++++++ + +++ea++  +++d+ + a+ L++   +++s  e ++++
  gi|298674341|ref|YP_003726091.1| 574 EIQNSTGEAVSSMENSSQEIENGSQALDETVNSMSNVVGKTSEADN--MVQDIASSAEELSASVEEVTSSVEEVSSI 648
                                       566777788999999999999999********************99..**********9999999998766665555 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.6
                   Snapin_Pallidin  13 pkldeldeklkelrqsQeeLleqldrlnekLkele 47 
                                        +++e +++ +el +s ++L+++ ++ln+++k+++
  gi|298674341|ref|YP_003726091.1| 661 ASVEEQTSSMQELSKSAQDLNQMAEELNQSVKSFK 695
                                       56677777778888888888888888877777655 PP

>> Serine_rich  Serine rich protein interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   1.3     0.054        16      77     113 ..     381     414 ..     331     435 .. 0.66
   2 ?    8.8   4.7    0.0051       1.5      34     106 ..     382     456 ..     360     466 .. 0.86
   3 ?    6.1   6.7     0.035        10       6     107 ..     403     509 ..     399     533 .. 0.71
   4 ?   11.7   1.4   0.00067      0.19      58     150 ..     553     646 ..     545     648 .. 0.88
   5 ?    6.8   4.2     0.021       6.1      36     116 ..     622     700 ..     604     706 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.054
                       Serine_rich  77 nlqtkLrkqlqkledsdqilqetsqeLdsceWsleal 113
                                       ++q  L+++++++++s++ +++ts+eL +++ +   l
  gi|298674341|ref|YP_003726091.1| 381 EMQDNLKNLVENIKESASQVSSTSEELSASSEQ---L 414
                                       455555555566666666666555555554222...2 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0051
                       Serine_rich  34 skenleanlqeirlavdrlrtslrefleFargalanaaklsd..knlqtkLrkqlqkledsdqilqetsqeLdsc 106
                                        ++nl++ +++i++++++++++ +e+   +++ +++a ++sd  +++++  ++q  k+++  +++ ++s+++++ 
  gi|298674341|ref|YP_003726091.1| 382 MQDNLKNLVENIKESASQVSSTSEELSASSEQLTSSANQISDtiTEITNGAQNQSTKIQEVSSTMNDMSTSIQDV 456
                                       578999999*********************************888999999999999999999999998887665 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.035
                       Serine_rich   6 AletlarlqqevesavskLlsfvsskWRskenleanlqeirlavdrlrtslrefleFargalanaaklsd.....kn 77 
                                         e+l+   ++++s+ +++ + +++     +n++ ++qe+ + +++++ts++++   a+++  + ++++       +
  gi|298674341|ref|YP_003726091.1| 403 TSEELSASSEQLTSSANQISDTITEITNGAQNQSTKIQEVSSTMNDMSTSIQDVSSNAQKTSETVTEVNKlvnevGE 479
                                       56777777788888888888888888888899999999999999999999999999999999988887654433333 PP

                       Serine_rich  78 lqtkLrkqlqkledsdqilqetsqeLdsce 107
                                        ++ L+ ++++++ + +  +e  +eLd+++
  gi|298674341|ref|YP_003726091.1| 480 QSKELKSKMENIQTTSEQTSEVVRELDNKS 509
                                       344455555555555555555556666655 PP

  == domain 4  score: 11.7 bits;  conditional E-value: 0.00067
                       Serine_rich  58 efleFargalanaaklsd..knlqtkLrkqlqkledsdqilqetsqeLdsceWslealasdkkqekpddlDrlvmva 132
                                       e+ ++a+++  +a+++ d  +++q+   + ++ +e+s q +++ sq+Ld++  s++ ++ ++++  ++ +  + + a
  gi|298674341|ref|YP_003726091.1| 553 EVRKLAEESSNSAQQIGDliQEIQNSTGEAVSSMENSSQEIENGSQALDETVNSMSNVVGKTSEA-DNMVQDIASSA 628
                                       667889999999999***999******************************99999999877665.88889999999 PP

                       Serine_rich 133 rtvpdDvkqlasfiqgna 150
                                        +++  v++++s ++  +
  gi|298674341|ref|YP_003726091.1| 629 EELSASVEEVTSSVEEVS 646
                                       99***9999999998765 PP

  == domain 5  score: 6.8 bits;  conditional E-value: 0.021
                       Serine_rich  36 enleanlqeirlavdrlrtslrefleFargalanaaklsdknlqtkLrkqlqkledsdqilqetsqeLdsceWslea 112
                                       + + + ++e+ ++v+++ +s++e+   a+++ ++  ++s  +++++    +q+l++s+q l ++++eL+++  s ++
  gi|298674341|ref|YP_003726091.1| 622 QDIASSAEELSASVEEVTSSVEEVSSIAEESSSSTEEAS-ASVEEQ-TSSMQELSKSAQDLNQMAEELNQSVKSFKV 696
                                       455666777777777777777777777777666555444.344444.456777778888888888888877555544 PP

                       Serine_rich 113 lasd 116
                                        +sd
  gi|298674341|ref|YP_003726091.1| 697 DSSD 700
                                       4444 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   4.2     0.013       3.9       1      84 [.     382     464 ..     382     472 .. 0.91
   2 ?   -1.1   0.0       9.6   2.8e+03       9      37 ..     488     515 ..     480     543 .. 0.49
   3 ?    8.5   0.6    0.0091       2.6       6      43 ..     548     585 ..     545     616 .. 0.76
   4 ?    1.3   5.2       1.7   4.8e+02      19      75 ..     621     676 ..     591     695 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.013
                     T7SS_ESX_EspC   1 mtdnLsVdpdhlrelaakhdevaaeiasavaaaagasaavldshGpicaatndavaaaeaarraagealaaasteLa 77 
                                       m dnL+   + ++e a+++ ++++e++++ +  +  +++++d+ + i+   ++  ++ ++  +++++++ ++ ++++
  gi|298674341|ref|YP_003726091.1| 382 MQDNLKNLVENIKESASQVSSTSEELSASSEQLTSSANQISDTITEITNGAQNQSTKIQEV-SSTMNDMSTSIQDVS 457
                                       7899999999*********************999****************99999999886.6789********999 PP

                     T7SS_ESX_EspC  78 dkLraAA 84 
                                        + +++ 
  gi|298674341|ref|YP_003726091.1| 458 SNAQKTS 464
                                       9988775 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 9.6
                     T7SS_ESX_EspC   9 pdhlrelaakhdevaaeiasavaaaagas 37 
                                        + +++ +++  ev+ e+++  +   g+ 
  gi|298674341|ref|YP_003726091.1| 488 MENIQTTSEQTSEVVRELDNKSKKI-GEI 515
                                       4555555555555555555544444.333 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0091
                     T7SS_ESX_EspC   6 sVdpdhlrelaakhdevaaeiasavaaaagasaavlds 43 
                                        V++d++r+la++  + a++i ++ +  ++ + + ++s
  gi|298674341|ref|YP_003726091.1| 548 AVVADEVRKLAEESSNSAQQIGDLIQEIQNSTGEAVSS 585
                                       599*********************99996665555555 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 1.7
                     T7SS_ESX_EspC  19 hdevaaeiasavaaaagasaavldshGpicaatndavaaaeaarraagealaaaste 75 
                                       ++++a+ ++ + a++ ++++++++   +i  ++ ++ ++a a+ +++ +++++ s+ 
  gi|298674341|ref|YP_003726091.1| 621 VQDIASSAEELSASV-EEVTSSVEEVSSIAEESSSSTEEASASVEEQTSSMQELSKS 676
                                       344444444444444.77777777777787777777777777766666666654433 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1       0.8   2.3e+02      35      61 ..      40      66 ..      29      67 .. 0.72
   2 ?    1.0   0.0       1.2   3.5e+02       9      31 ..     331     353 ..     325     358 .. 0.60
   3 ?    7.7   1.4      0.01         3       9      42 ..     372     405 ..     369     426 .. 0.88
   4 ?   12.4   2.9   0.00034     0.099       5      45 ..     435     475 ..     432     479 .. 0.93
   5 ?    9.9   3.4    0.0021      0.62       4      43 ..     462     501 ..     461     506 .. 0.92
   6 ?    1.5   0.6      0.86   2.5e+02      15      40 ..     592     617 ..     559     626 .. 0.48
   7 ?    0.5   0.7       1.8   5.3e+02      17      39 ..     629     651 ..     618     676 .. 0.54
   8 ?   -0.8   0.2       4.5   1.3e+03      27      42 ..     667     682 ..     650     692 .. 0.53

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.8
                         DASH_Duo1 35 etvestntLLdkWirIlsqtehtqrll 61
                                      et +s+n++Ld+ ++  s te  ++++
  gi|298674341|ref|YP_003726091.1| 40 ETAHSVNSMLDNLTKKVSDTESKAEII 66
                                      566777777777777777777666665 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 1.2
                         DASH_Duo1   9 LrkinevienviesLkkaksnie 31 
                                       ++ in+++++++e L+++k   e
  gi|298674341|ref|YP_003726091.1| 331 IKGINNTLDAIVEPLNETKRVAE 353
                                       45566666666666666655444 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.01
                         DASH_Duo1   9 LrkinevienviesLkkaksniervketvestnt 42 
                                       L+++ ++ie ++++Lk+  +ni++ +++v+st++
  gi|298674341|ref|YP_003726091.1| 372 LKEFADTIEEMQDNLKNLVENIKESASQVSSTSE 405
                                       8889999999999999999999999999999985 PP

  == domain 4  score: 12.4 bits;  conditional E-value: 0.00034
                         DASH_Duo1   5 EleqLrkinevienviesLkkaksniervketvestntLLd 45 
                                       + ++++++ ++ +++  s+++++sn ++ +etv+++n+L++
  gi|298674341|ref|YP_003726091.1| 435 QSTKIQEVSSTMNDMSTSIQDVSSNAQKTSETVTEVNKLVN 475
                                       6678999********************************98 PP

  == domain 5  score: 9.9 bits;  conditional E-value: 0.0021
                         DASH_Duo1   4 kEleqLrkinevienviesLkkaksniervketvestntL 43 
                                       k  e+++++n+ ++ v e+ k+ ks++e++++t e+t++ 
  gi|298674341|ref|YP_003726091.1| 462 KTSETVTEVNKLVNEVGEQSKELKSKMENIQTTSEQTSEV 501
                                       67799********************************986 PP

  == domain 6  score: 1.5 bits;  conditional E-value: 0.86
                         DASH_Duo1  15 vienviesLkkaksniervketvest 40 
                                        ien  ++L+++ + +++v  +++++
  gi|298674341|ref|YP_003726091.1| 592 EIENGSQALDETVNSMSNVVGKTSEA 617
                                       23333344444444444444443333 PP

  == domain 7  score: 0.5 bits;  conditional E-value: 1.8
                         DASH_Duo1  17 enviesLkkaksniervketves 39 
                                       e + +s ++++s +e+v++  e+
  gi|298674341|ref|YP_003726091.1| 629 EELSASVEEVTSSVEEVSSIAEE 651
                                       44444444444444444433333 PP

  == domain 8  score: -0.8 bits;  conditional E-value: 4.5
                         DASH_Duo1  27 ksniervketvestnt 42 
                                       +s +++++++ ++ n+
  gi|298674341|ref|YP_003726091.1| 667 TSSMQELSKSAQDLNQ 682
                                       3444444444333333 PP

>> AIP3  Actin interacting protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1  24.0    0.0084       2.4      85     245 ..     372     524 ..     335     539 .. 0.60
   2 ?    3.2  20.0      0.14        39      80     217 ..     427     575 ..     424     613 .. 0.67
   3 ?    4.2  18.9     0.066        19      66     225 ..     528     702 ..     519     707 .] 0.51

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0084
                                       XXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXX.........XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              AIP3  85 laslskelkelkssiesqkaslqevserqeeaakekaseslakkelkaqlkevqslrrdLavlrqlysefkseikes 161
                                       l++++++++e+++++++  ++++e s++q ++++e+ s  +++++l+++ +++++   +++   q +s++ +e++++
  gi|298674341|ref|YP_003726091.1| 372 LKEFADTIEEMQDNLKNLVENIKE-SASQVSSTSEELS--ASSEQLTSSANQISDTITEITNGAQNQSTKIQEVSST 445
                                       334444444444444444444444.2222222222222..2345666677777777777777777777777777777 PP

                                       XXXXXXXXXXXXXXXX.XXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXHHHHHHHHH CS
                              AIP3 162 lselrekakkvkeaslastkkssnrayiekgkkkLseesdklvtkvddLqDlvedlrkDVvqRgvrpskkqlesvak 238
                                       ++++++ +++v     + +k+s++ + ++k  +++ e+s++l +k++++q + e+    Vv R+   ++k++ ++ +
  gi|298674341|ref|YP_003726091.1| 446 MNDMSTSIQDVS---SNAQKTSETVTEVNKLVNEVGEQSKELKSKMENIQTTSEQTS-EVV-RELDNKSKKIGEIVS 517
                                       777777777777...224556666677777777777777777777777777766643.344.666666666666666 PP

                                       HHHHHHH CS
                              AIP3 239 eikkakk 245
                                        i+++++
  gi|298674341|ref|YP_003726091.1| 518 MITNIAD 524
                                       6666554 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.14
                                       XXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXX.................XXXXXXXXX.XXX CS
                              AIP3  80 hideslaslskelkelkssiesqkaslqevserqeeaakekasesla........kkelkaqlkevqslrrdL.avl 147
                                       +i+++ ++ s++++e++s++++ ++s+q+vs++ ++++++ ++ +++        +kelk++++++q+  ++  +v+
  gi|298674341|ref|YP_003726091.1| 427 EITNGAQNQSTKIQEVSSTMNDMSTSIQDVSSNAQKTSETVTE-VNKlvnevgeqSKELKSKMENIQTTSEQTsEVV 502
                                       5677777778888888888888888888877766666655554.333566777779999********9987762699 PP

                                       XXXXXXXXX..XXXXXXXXXXXXXXXXX.XXXX.XX...XXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              AIP3 148 rqlysefks..eikeslselrekakkvk.easlast...kkssnrayiekgkkkLseesdklvtkvddLqDlvedl 217
                                       r+l +++k+  ei ++++++ ++++ +  +a+++ +   +++ + a++ +   kL ees++  +++ dL     ++
  gi|298674341|ref|YP_003726091.1| 503 RELDNKSKKigEIVSMITNIADQTNLLAlNAAIEAAragEQGRGFAVVADEVRKLAEESSNSAQQIGDLIQ---EI 575
                                       *9998887644899999999999998777333333300034555578899999999999998888877643...33 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.066
                                       XXXXX...............XXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXX. CS
                              AIP3  66 vLsLn...............iepldevkkhideslaslskelkelkssiesqkaslqevserqeeaakekaseslak 127
                                       +L Ln                 + dev+k + e+ ++ ++++ +l ++i++++ ++ ++ e++++++++ ++   a 
  gi|298674341|ref|YP_003726091.1| 528 LLALNaaieaarageqgrgfAVVADEVRK-LAEESSNSAQQIGDLIQEIQNSTGEAVSSMENSSQEIENGSQ---AL 600
                                       55555555555554444443113444444.444445555666666666655554444444444444443333...23 PP

                                       ........XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXX.XXXXXXHHHHHHHHHHHHHHHH CS
                              AIP3 128 kelkaqlkevqslrrdLavlrqlysefkseikeslselrekakkvk....easlastkkssnrayiekgkkkLsees 200
                                       +e+ +++++v     +   + q  +++ +e+++s++e+++ +++v     e+s ++ + s++ +  +++ ++Ls+ +
  gi|298674341|ref|YP_003726091.1| 601 DETVNSMSNVVGKTSEADNMVQDIASSAEELSASVEEVTSSVEEVSsiaeESSSSTEEASASVEEQTSSMQELSKSA 677
                                       34444555555555555555555555555555555555555555552221111212223333344456777888888 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHX CS
                              AIP3 201 dklvtkvddLqDlvedlrkDVvqRg 225
                                       ++l +  ++L+  v + + D  +++
  gi|298674341|ref|YP_003726091.1| 678 QDLNQMAEELNQSVKSFKVDSSDKK 702
                                       8888888888888888888876665 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   2.2      0.18        53      34      98 ..     350     414 ..     332     417 .. 0.60
   2 ?   13.4  12.9   0.00012     0.036      10     101 ..     410     501 ..     407     512 .. 0.92
   3 ?    3.7   1.5      0.11        32      15      62 ..     548     595 ..     528     598 .. 0.87
   4 ?    4.3  10.8     0.072        21      16     108 ..     598     690 ..     595     695 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.18
                           DUF3450  34 qsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierel 98 
                                       ++ + i + d  ++  ++   +lke ++ +e  +++l++lv++ +++ +++    ee+++ +++l
  gi|298674341|ref|YP_003726091.1| 350 RVAEAIADGDLTQSINVDTKGDLKEFADTIEEMQDNLKNLVENIKESASQVSSTSEELSASSEQL 414
                                       55555555555666666666666666666666666666666666666666666666666666555 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00012
                           DUF3450  10 asgalaatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiaslee 86 
                                       +s  l ++++q+ ++ +++++ a+  ++ki++++   ++++  ++++++ +++++    ++++lv+++ ++ ++l+ 
  gi|298674341|ref|YP_003726091.1| 410 SSEQLTSSANQISDTITEITNGAQNQSTKIQEVSSTMNDMSTSIQDVSSNAQKTSETVTEVNKLVNEVGEQSKELKS 486
                                       455558999******************************************************************** PP

                           DUF3450  87 qieeieeierelvpl 101
                                       ++e+i+ ++++ + +
  gi|298674341|ref|YP_003726091.1| 487 KMENIQTTSEQTSEV 501
                                       *********998765 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.11
                           DUF3450  15 aatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeles 62 
                                       a  +d+++k ae++ ++a+q+   i+++++ + e ++ +++ ++e+e+
  gi|298674341|ref|YP_003726091.1| 548 AVVADEVRKLAEESSNSAQQIGDLIQEIQNSTGEAVSSMENSSQEIEN 595
                                       6678999********************************999999987 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.072
                           DUF3450  16 atldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeie 92 
                                       ++ld++ +  ++ v + +++ + +++++  ++el+a ++++++ +e+ +   e+ +++ +++ +++++ + +++e++
  gi|298674341|ref|YP_003726091.1| 598 QALDETVNSMSNVVGKTSEADNMVQDIASSAEELSASVEEVTSSVEEVSSIAEESSSSTEEASASVEEQTSSMQELS 674
                                       67888888888888889999999999999999999999999999999999888888888888888888888888888 PP

                           DUF3450  93 eierelvpllekmidr 108
                                       + +++l ++ e++ ++
  gi|298674341|ref|YP_003726091.1| 675 KSAQDLNQMAEELNQS 690
                                       8888877665555444 PP

>> GldM_N  GldM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4  18.6      0.24        69      17     140 ..     372     497 ..     360     511 .. 0.74
   2 ?    4.7   7.8       0.1        29      22      91 ..     440     509 ..     435     548 .. 0.73
   3 ?   10.3   5.9    0.0019      0.54      29     130 ..     552     651 ..     513     660 .. 0.56
   4 ?    8.0   4.6    0.0098       2.8      18      75 ..     646     703 ..     638     707 .] 0.81

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.24
                            GldM_N  17 nenasekNaalyasleakaeenpekakewlekAkevkkksdelynyiealKeeivkeaggkdedvgeikakd.nlda 92 
                                        ++++++ +++ ++l++ +e+ +e a ++  +++e+++ s++l++  +++ ++i++ ++g +++ ++i++ +  ++ 
  gi|298674341|ref|YP_003726091.1| 372 LKEFADTIEEMQDNLKNLVENIKESASQVSSTSEELSASSEQLTSSANQISDTITEITNGAQNQSTKIQEVSsTMND 448
                                       567788899999999*********************************************99998888887535666 PP

                            GldM_N  93 aselmlaeg.ksgkGkeLkkkineyreellklvndlakdaklieselst 140
                                       +s+ + +   + +k  e  +++n+  +e+ +  ++l+++ ++i+++ + 
  gi|298674341|ref|YP_003726091.1| 449 MSTSIQDVSsNAQKTSETVTEVNKLVNEVGEQSKELKSKMENIQTTSEQ 497
                                       6665553334667777777777777777777777766666544443332 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.1
                            GldM_N  22 ekNaalyasleakaeenpekakewlekAkevkkksdelynyiealKeeivkeaggkdedvgeikakdnld 91 
                                       ++ +++++++++++++   +a+++ e+ +ev+k+ +e+ ++ ++lK ++++   + ++  + +++ dn+ 
  gi|298674341|ref|YP_003726091.1| 440 QEVSSTMNDMSTSIQDVSSNAQKTSETVTEVNKLVNEVGEQSKELKSKMENIQTTSEQTSEVVRELDNKS 509
                                       5667889999999999999999999999999999999999999999999777766666544444444332 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.0019
                            GldM_N  29 asleakaeenpekakewlekAkevkkksdelynyiealKeeivkeaggkdedvgeikakd.nldaaselmlaegksg 104
                                       ++ ++ aee+ + a+++ +  +e+++ + e ++ +e+  +ei++ +   de v+ + +   ++ +a++ m+++    
  gi|298674341|ref|YP_003726091.1| 552 DEVRKLAEESSNSAQQIGDLIQEIQNSTGEAVSSMENSSQEIENGSQALDETVNSMSNVVgKTSEADN-MVQDI-AS 626
                                       34445556666666666666666666666666666666666666666666666666555424444443.33233.56 PP

                            GldM_N 105 kGkeLkkkineyreellklvndlakd 130
                                        ++eL ++++e  + + ++ + +a++
  gi|298674341|ref|YP_003726091.1| 627 SAEELSASVEEVTSSVEEVSS-IAEE 651
                                       666666666666655555544.3333 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.0098
                            GldM_N  18 enasekNaalyasleakaeenpekakewlekAkevkkksdelynyiealKeeivkeag 75 
                                       ++++e+ ++  ++ +a++ee+   ++e+ + A++++++++el + +++ K +  ++ +
  gi|298674341|ref|YP_003726091.1| 646 SSIAEESSSSTEEASASVEEQTSSMQELSKSAQDLNQMAEELNQSVKSFKVDSSDKKD 703
                                       45566666777788899*********************************98766665 PP

>> CALCOCO1  Calcium binding and coiled-coil domain (CALCOCO1) like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2  17.8    0.0068         2      61     221 ..     369     528 ..     344     540 .. 0.78
   2 ?    3.9  12.9      0.07        20      17     177 ..     542     705 ..     531     707 .] 0.67

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0068
                          CALCOCO1  61 keeykrdreeldrerkelesrveelkeelkesrekveeleekqkelerlseelaeeksalleakeesearirELEeD 137
                                       k + k+  + +++ + +l++ ve++ke ++++    eel++  ++l+++ +++++  + +++ +++++++i+E+   
  gi|298674341|ref|YP_003726091.1| 369 KGDLKEFADTIEEMQDNLKNLVENIKESASQVSSTSEELSASSEQLTSSANQISDTITEITNGAQNQSTKIQEVSST 445
                                       3445555566666777777777777777788888899999999999999999**9999999999************* PP

                          CALCOCO1 138 iktltqralekEteLeRlkerakkalaqrkeeeaerkqlqakleqseeelrslskelqelrnslaerdtqvlqLqdt 214
                                       ++ ++   ++   + ++  e++  + ++  e  ++ k+l++k+e+ ++ +++ s+ ++el n+  ++  ++  +  +
  gi|298674341|ref|YP_003726091.1| 446 MNDMSTSIQDVSSNAQKTSETVTEVNKLVNEVGEQSKELKSKMENIQTTSEQTSEVVRELDNK-SKKIGEIVSMITN 521
                                       **********************99999999999999999999988888887777777777664.3455555555555 PP

                          CALCOCO1 215 ittltqk 221
                                       i+  t+ 
  gi|298674341|ref|YP_003726091.1| 522 IADQTNL 528
                                       5555554 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.07
                          CALCOCO1  17 eegtdmLLVvPrAelLqnrLeeclreraeLlqaqeaan....rqrekekeeykrdreeldrerkelesrveelke.. 87 
                                       e+g ++  V    + L +   ++ ++  +L+q+ + +      + e+  +e ++ +++ld++++ +++ v +  e  
  gi|298674341|ref|YP_003726091.1| 542 EQGRGFAVVADEVRKLAEESSNSAQQIGDLIQEIQNSTgeavSSMENSSQEIENGSQALDETVNSMSNVVGKTSEad 618
                                       55666666666666677777788899999999865544111135688888888888888888888887765544400 PP

                          CALCOCO1  88 .elkesrekveeleekqkelerlseelaeeksalleakeesearirELEeDiktltqralekEteLeRlkerakkal 163
                                         ++      eel++  +e++++ ee++   +  ++ +ee +a + E    ++ l++ a+    +L+ + e+ ++ +
  gi|298674341|ref|YP_003726091.1| 619 nMVQDIASSAEELSASVEEVTSSVEEVSSIAEESSSSTEEASASVEEQTSSMQELSKSAQ----DLNQMAEELNQSV 691
                                       045555568888888888888888888888888888888888888886666666665554....5777777777777 PP

                          CALCOCO1 164 aqrkeeeaerkqlq 177
                                       +  k + +++k+ +
  gi|298674341|ref|YP_003726091.1| 692 KSFKVDSSDKKDKN 705
                                       77777777777655 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.2   0.00046      0.13      62     110 ..     370     418 ..     336     430 .. 0.84
   2 ?    3.8   9.3       0.2        58      31     119 ..     410     505 ..     407     537 .. 0.70
   3 ?    2.7   1.1      0.43   1.2e+02      69     118 ..     570     620 ..     562     634 .. 0.68
   4 ?    4.5   6.4      0.12        33      75     125 ..     621     683 ..     607     691 .. 0.41

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00046
                              COG2  62 ghLvglqeeleevesplaaarkkvesvreklsereeeveskleeakele 110
                                       g L+ + + +ee++ +l+++++++++  +++s ++ee+++  e+ ++ +
  gi|298674341|ref|YP_003726091.1| 370 GDLKEFADTIEEMQDNLKNLVENIKESASQVSSTSEELSASSEQLTSSA 418
                                       6788899999999999999999999999999999999999888877655 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.2
                              COG2  31 lrrdLeaylkllekellelvn..edyad.FvslSghLvglqeeleevesplaaarkkvesvre...klsereeeves 101
                                        +++L + ++++++ + e+ n  ++  +   ++S+ + ++ ++++ v+s+ +++ + v++v++   ++ e+++e++s
  gi|298674341|ref|YP_003726091.1| 410 SSEQLTSSANQISDTITEITNgaQNQSTkIQEVSSTMNDMSTSIQDVSSNAQKTSETVTEVNKlvnEVGEQSKELKS 486
                                       56677777777777777777754455566778999999999999999999888777666665511155667777888 PP

                              COG2 102 kleeakel.eekrellkll 119
                                       k+e+ +   e+++e+++ l
  gi|298674341|ref|YP_003726091.1| 487 KMENIQTTsEQTSEVVREL 505
                                       8877544403334555544 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.43
                              COG2  69 eeleevesplaaarkkvesvreklsereeeveskleeakeleekr.ellkl 118
                                       + ++e++ +  +a++ +e+  +++++ ++++++ ++  +++  k  e  ++
  gi|298674341|ref|YP_003726091.1| 570 DLIQEIQNSTGEAVSSMENSSQEIENGSQALDETVNSMSNVVGKTsEADNM 620
                                       567888888888888888888888888888888888877766555333333 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.12
                              COG2  75 esplaaarkkvesvreklsereeeveskleeakeleekr............ellklllkldev 125
                                        +++a+  +++++ +e++    eev+s  ee ++ +e+             el k+ ++l+++
  gi|298674341|ref|YP_003726091.1| 621 VQDIASSAEELSASVEEVTSSVEEVSSIAEESSSSTEEAsasveeqtssmqELSKSAQDLNQM 683
                                       444444444444444444444444444444433333333333332232222333333333333 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   1.5       1.3   3.8e+02      25      66 ..      13      53 ..       9      72 .. 0.63
   2 ?    0.6   0.1       2.8   8.1e+02      37      61 ..     331     355 ..     289     358 .. 0.71
   3 ?    9.6   5.1    0.0044       1.3       3      66 ..     362     430 ..     360     437 .. 0.73
   4 ?    7.8   4.9     0.015       4.4      12      62 ..     438     492 ..     428     492 .. 0.79
   5 ?   11.2   4.2    0.0014       0.4      12      63 ..     473     524 ..     467     535 .. 0.89
   6 ?   10.1   1.8     0.003      0.88      13      64 ..     597     648 ..     585     656 .. 0.91
   7 ?    0.9   0.6       2.2   6.3e+02      29      58 ..     662     691 ..     654     696 .. 0.56

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 1.3
                           NPV_P10 25 qqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLn 66
                                      q v +v++n++d  +l ++Ld q+    e   +v++  d L+
  gi|298674341|ref|YP_003726091.1| 13 QDVVKVANNIQD-GKLDARLDTQNGVDRETAHSVNSMLDNLT 53
                                      567777777777.66777777776555555555555444444 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 2.8
                           NPV_P10  37 vtelnekLdaqsaqLaeletkvenI 61 
                                       ++ +n+ Lda+ + L+e +   e+I
  gi|298674341|ref|YP_003726091.1| 331 IKGINNTLDAIVEPLNETKRVAEAI 355
                                       5567777777777777766655555 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0044
                           NPV_P10   3 qniLlvIradikavddkVdalqqqvddvqenlp....dvtelnekLdaqsaqLaeletkve.nIqdiLn 66 
                                       q+i +  + d k+  d ++ +q++++++ en++    +v+  +e+L a s+qL++  ++++ +I++i n
  gi|298674341|ref|YP_003726091.1| 362 QSINVDTKGDLKEFADTIEEMQDNLKNLVENIKesasQVSSTSEELSASSEQLTSSANQISdTITEITN 430
                                       666677778999999999999999866666655211168899999999999999988877524777766 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.015
                           NPV_P10  12 dikavddkVdalqqqvddvqenlp....dvtelnekLdaqsaqLaeletkvenIq 62 
                                        i++v++ ++ ++++++dv++n +    +vte+n+ +++  +q +el++k+enIq
  gi|298674341|ref|YP_003726091.1| 438 KIQEVSSTMNDMSTSIQDVSSNAQktseTVTEVNKLVNEVGEQSKELKSKMENIQ 492
                                       5888888888888888888887652222678888888999999999999999997 PP

  == domain 5  score: 11.2 bits;  conditional E-value: 0.0014
                           NPV_P10  12 dikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqd 63 
                                        +++v ++ + l+++++++q+ +++++e+  +Ld+ s+++ e+ + ++nI d
  gi|298674341|ref|YP_003726091.1| 473 LVNEVGEQSKELKSKMENIQTTSEQTSEVVRELDNKSKKIGEIVSMITNIAD 524
                                       58899999999**************************************987 PP

  == domain 6  score: 10.1 bits;  conditional E-value: 0.003
                           NPV_P10  13 ikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdi 64 
                                        +a+d+ V+++++ v + +e  + v+++ +  +++sa+++e+ ++ve++++i
  gi|298674341|ref|YP_003726091.1| 597 SQALDETVNSMSNVVGKTSEADNMVQDIASSAEELSASVEEVTSSVEEVSSI 648
                                       5899*********************************************999 PP

  == domain 7  score: 0.9 bits;  conditional E-value: 2.2
                           NPV_P10  29 dvqenlpdvtelnekLdaqsaqLaeletkv 58 
                                       +v+e+   ++el++  +++++  +el+++v
  gi|298674341|ref|YP_003726091.1| 662 SVEEQTSSMQELSKSAQDLNQMAEELNQSV 691
                                       455555555555555555555555555555 PP

>> DUF677  Protein of unknown function (DUF677)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7  34.2       3.6     1e+03      12     332 ..     348     663 ..     345     667 .. 0.56
   2 ?   -0.4   0.1       1.4   4.1e+02     294     317 ..     667     690 ..     655     702 .. 0.47

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.6
                            DUF677  12 Tnklisslateaktrsls...edslkeltkcllelnqdvvkviieikedvwe.nqdLksLveaYFestkktldlcet 84 
                                       T+++ + +a ++ t+s +      lke+ + + e++++  +++ +ike   +  ++  +L     + t+   ++ +t
  gi|298674341|ref|YP_003726091.1| 348 TKRVAEAIADGDLTQSINvdtKGDLKEFADTIEEMQDNLKNLVENIKESASQvSSTSEELSASSEQLTSSANQISDT 424
                                       66666666666667777733233467777777777777766666666643331233333444444445555555555 PP

                            DUF677  85 lekcveraersellireAlaqFEkek.lekdvGkkkkkyekTleeLkkFkamgdpfdgeefltkFksvykeqvllle 160
                                       +++  + a++    i+e      + +   +dv ++ +k  +T  e++k  +     ++e +  k + ++    +  e
  gi|298674341|ref|YP_003726091.1| 425 ITEITNGAQNQSTKIQEVSSTMNDMStSIQDVSSNAQKTSETVTEVNKLVNEVGEQSKE-LKSKMENIQ----TTSE 496
                                       55555555555555555444443333033666777777777777776654333333444.333332222....2223 PP

                            DUF677 161 klrktkkkldkklrni.ktkraisnvvfvaafvaVlvlSvvlaalaapavvavagalavPleavgkwvasawkkyee 236
                                       + ++  ++ld+k ++i +  ++i+n++  +             al a   +a ag       +v+  v ++ +++ +
  gi|298674341|ref|YP_003726091.1| 497 QTSEVVRELDNKSKKIgEIVSMITNIADQTNLL----------ALNAAIEAARAGEQGRGFAVVADEVRKLAEESSN 563
                                       333333344444444422233334433333332..........2222233334555555555666667788888888 PP

                            DUF677 237 alkrqkeivssmekgievakkdvenisilver....leseiksilktvefAvekeeneaavklaleeikkkveklte 309
                                       + ++  ++++++++ +  a+  +en s+++e+    l+  ++s+++ v    e ++  +++    ee++  ve++t+
  gi|298674341|ref|YP_003726091.1| 564 SAQQIGDLIQEIQNSTGEAVSSMENSSQEIENgsqaLDETVNSMSNVVGKTSEADNMVQDIASSAEELSASVEEVTS 640
                                       88888888888888888888888888888864333377777777777777777777777777778888888888888 PP

                            DUF677 310 kieevgeeaakcskliakarlvv 332
                                        +eev   a++ s+  ++a+  v
  gi|298674341|ref|YP_003726091.1| 641 SVEEVSSIAEESSSSTEEASASV 663
                                       88888888888888877777655 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.4
                            DUF677 294 klaleeikkkvekltekieevgee 317
                                          ++e++k  + l +  ee++++
  gi|298674341|ref|YP_003726091.1| 667 TSSMQELSKSAQDLNQMAEELNQS 690
                                       223333333333333333333333 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   4.8   9.8e-05     0.028     277     336 ..     377     436 ..     358     440 .. 0.82
   2 ?    7.8  11.7    0.0047       1.4     234     318 ..     440     523 ..     432     539 .. 0.86
   3 ?   -0.6  15.5       1.7   4.9e+02     227     344 ..     559     683 ..     545     689 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.8e-05
                             IFT57 277 qeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqemeergssmtDgsplvk 336
                                       +  +e+q++l+++ e++k+  ++vs+ ++el+  se+l++  +++ +  +++t+g++ ++
  gi|298674341|ref|YP_003726091.1| 377 DTIEEMQDNLKNLVENIKESASQVSSTSEELSASSEQLTSSANQISDTITEITNGAQNQS 436
                                       445688999999999999999999999999999999999999999999999999988655 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0047
                             IFT57 234 ksieeslpetksqlkklhedisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelaei 310
                                       ++++++++++++++++++++ +kt e +++  k +n+ + e+ +e++++ e++++++e+ +++ +++ +++++  ei
  gi|298674341|ref|YP_003726091.1| 440 QEVSSTMNDMSTSIQDVSSNAQKTSETVTEVNKLVNE-VGEQSKELKSKMENIQTTSEQTSEVVRELDNKSKKIGEI 515
                                       478999***************************9996.677889999999999999999999999999999999888 PP

                             IFT57 311 seelekvk 318
                                          ++++ 
  gi|298674341|ref|YP_003726091.1| 516 VSMITNIA 523
                                       77666665 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.7
                             IFT57 227 eqmkkhkksieeslpetksqlkklhedisktlekiesrEkylnsqleel...lqeyreaqeelsevkekykqlsegv 300
                                       e+ ++  ++i + ++e++++  +  + ++++ ++ie+  + l++ ++++   + + +ea + ++++  + ++ls++v
  gi|298674341|ref|YP_003726091.1| 559 EESSNSAQQIGDLIQEIQNSTGEAVSSMENSSQEIENGSQALDETVNSMsnvVGKTSEADNMVQDIASSAEELSASV 635
                                       45555666777777777777777777777777777777777765544440004445555666666666777777777 PP

                             IFT57 301 seltrelaeiseelekvkqemeergssmtDgsp....lvkikkaltkl 344
                                       +e t   +e+s   e+ ++  ee ++s+ ++++    l k  + l+++
  gi|298674341|ref|YP_003726091.1| 636 EEVTSSVEEVSSIAEESSSSTEEASASVEEQTSsmqeLSKSAQDLNQM 683
                                       777776666666666666666666666555432100022333334444 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   5.0      0.03       8.6     121     219 ..     373     471 ..     327     480 .. 0.55
   2 ?    6.3   2.5     0.018       5.1     124     226 ..     471     579 ..     461     588 .. 0.72
   3 ?    4.7   2.2     0.054        16     121     222 ..     584     691 ..     579     696 .. 0.58

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.03
                              CorA 121 drlfellekleeeldeledeledstkkeilrelaq.lrrrlvklrralapnrevlkrlla.kaddkllddedkeylr 195
                                       +++++++e++ ++l+ l +++  ++++++++++++ l  +  +l +++++  ++++++ +   ++++  +e +  ++
  gi|298674341|ref|YP_003726091.1| 373 KEFADTIEEMQDNLKNLVENI--KESASQVSSTSEeLSASSEQLTSSANQISDTITEITNgAQNQSTKIQEVSSTMN 447
                                       334444444444444444444..444444444444455566666677777777776666632222222222223345 PP

                              CorA 196 dlldelerllemlealrerleslq 219
                                       d++  ++ ++  ++ ++e ++ ++
  gi|298674341|ref|YP_003726091.1| 448 DMSTSIQDVSSNAQKTSETVTEVN 471
                                       555555555555555555554444 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.018
                              CorA 124 fellekleeeldeledel.....edstkkeilrelaqlrrrlvklrralapnrevlkrlla..kaddkllddedkey 193
                                       ++l+ ++ e+ +el + +      ++++ e +rel +  ++++++ +++++  +   +lla   a +     e+ + 
  gi|298674341|ref|YP_003726091.1| 471 NKLVNEVGEQSKELKSKMeniqtTSEQTSEVVRELDNKSKKIGEIVSMITNIADQT-NLLAlnAAIEAARAGEQGRG 546
                                       444444555555555555544656699999999999999******99999999999.77776555555556666667 PP

                              CorA 194 lrdlldelerllemlealrerleslqdtyssll 226
                                       +  + de+++l+e++++ ++++  l +++++  
  gi|298674341|ref|YP_003726091.1| 547 FAVVADEVRKLAEESSNSAQQIGDLIQEIQNST 579
                                       999999999988888888888887777777654 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.054
                              CorA 121 drlfellekleeeldeledel........edstkkeilrelaqlrrrlvkl.rralapnrevlkrllakaddklldd 188
                                        ++++  +++e   + l++++        ++s+ +++++++a   ++l    +++ +  +ev  ++ +  + +  ++
  gi|298674341|ref|YP_003726091.1| 584 SSMENSSQEIENGSQALDETVnsmsnvvgKTSEADNMVQDIASSAEELSASvEEVTSSVEEVS-SIAE--ESSSSTE 657
                                       555666666666666666666666766688888888888888877774444144444444444.6666..5555555 PP

                              CorA 189 edkeylrdlldelerllemlealrerleslqdty 222
                                       e++   ++  + ++ l++ ++ l +++e l+++ 
  gi|298674341|ref|YP_003726091.1| 658 EASASVEEQTSSMQELSKSAQDLNQMAEELNQSV 691
                                       5544555555555555555555555555555544 PP

>> Mer2  Mer2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.4       0.6   1.7e+02      57     104 ..      12      62 ..       3      84 .. 0.57
   2 ?    1.7   1.0      0.67     2e+02     120     148 ..     370     398 ..     290     405 .. 0.46
   3 ?   14.1  21.4   0.00011     0.032      47     169 ..     401     527 ..     392     530 .. 0.78
   4 ?    3.8  14.4      0.16        46      57     177 ..     554     676 ..     547     691 .. 0.68
   5 ?    0.9   0.3       1.2   3.4e+02      52      83 ..     672     703 ..     670     706 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.6
                              Mer2  57 skeLlkvisklnellidlke...eesdnskekeikdlikdLsvkienqlsk 104
                                        +  +kv +++++  +d +    + +d+++++++ +++ +L+ k+ +  sk
  gi|298674341|ref|YP_003726091.1|  12 KQDVVKVANNIQDGKLDARLdtqNGVDRETAHSVNSMLDNLTKKVSDTESK 62 
                                       444445555444443333321112456666666666666666666554443 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.67
                              Mer2 120 sntdtksnLtellekkeakileeidkkqt 148
                                        ++++  +  e+++++ ++++e+i++  +
  gi|298674341|ref|YP_003726091.1| 370 GDLKEFADTIEEMQDNLKNLVENIKESAS 398
                                       11112222233444444444444444333 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 0.00011
                              Mer2  47 skLinvlkenskeLlkvisklnellidlkeeesdns.kekeikdlikdLsvkien...qlskvskavldklk....v 115
                                       s+ +++l  +s++L+++ +++ + + ++ ++ +++s k++e+ + ++d+s+ i++   + +k+s++v++  k    v
  gi|298674341|ref|YP_003726091.1| 401 SSTSEELSASSEQLTSSANQISDTITEITNGAQNQStKIQEVSSTMNDMSTSIQDvssNAQKTSETVTEVNKlvneV 477
                                       334578999*********************9988873689************9996555556666665544455555 PP

                              Mer2 116 kkhksntdtksnLtellekkeakileeidkkqtkleksvdttqelllnvnkQle 169
                                        +++++++ k +  ++ +++++++++e+d+k++k+ + v     ++ n+ +Q++
  gi|298674341|ref|YP_003726091.1| 478 GEQSKELKSKMENIQTTSEQTSEVVRELDNKSKKIGEIVS----MITNIADQTN 527
                                       55666666666667788999***************99998....9999999985 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.16
                              Mer2  57 skeLlkvisklnellidlkeeesdnskekeikdlikdLsvkienqlskvskavldklk...vkkhksntdt.ksnLt 129
                                        ++L + +s+  ++++dl + e +ns+ + + ++ ++ s +ien ++ + ++v++  +   + ++  n ++ +    
  gi|298674341|ref|YP_003726091.1| 554 VRKLAEESSNSAQQIGDLIQ-EIQNSTGEAVSSM-ENSSQEIENGSQALDETVNSMSNvvgKTSEADNMVQdIASSA 628
                                       45677777777777777777.6777776666554.455666888666665555555552113333333333134456 PP

                              Mer2 130 ellekkeakileeidkkqtkleksvdttqelllnvnkQledvnevllS 177
                                       e+l+   +++++ +++ ++  e+s   t+e   +v +Q+++++e+  S
  gi|298674341|ref|YP_003726091.1| 629 EELSASVEEVTSSVEEVSSIAEESSSSTEEASASVEEQTSSMQELSKS 676
                                       8999999************************************97433 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 1.2
                              Mer2  52 vlkenskeLlkvisklnellidlkeeesdnsk 83 
                                       +l ++ + L ++ ++ln+ + + k ++sd+++
  gi|298674341|ref|YP_003726091.1| 672 ELSKSAQDLNQMAEELNQSVKSFKVDSSDKKD 703
                                       68889999999999999999998887777665 PP

>> Rx_N  Rx N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.3     0.023       6.6      18      85 ..     370     438 ..     349     453 .. 0.80
   2 ?    8.0   3.1     0.011       3.3       2      59 ..     456     517 ..     455     616 .. 0.86
   3 ?    0.7   2.4       2.2   6.4e+02       3      72 ..     639     691 ..     606     707 .] 0.46

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.023
                              Rx_N  18 kllkgvkeeleklkdeLesiqavLe.daeerqikdeavkeWlkelrdlaydaeDvlDefetealrrkss 85 
                                         lk++ + +e+++d+L+++   ++  a++   ++e++ +  ++l   a ++ D + e++  a++++ +
  gi|298674341|ref|YP_003726091.1| 370 GDLKEFADTIEEMQDNLKNLVENIKeSASQVSSTSEELSASSEQLTSSANQISDTITEITNGAQNQSTK 438
                                       567888899999999999665555526888999*************************99888877644 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.011
                              Rx_N   2 vsallqkLadllaeeakllkgvkeeleklkdeLesiqavLedaee..rqi..kdeavkeWlk 59 
                                       vs+  qk ++ ++e  kl+ +v e+ ++lk+++e+iq   e+ +e  r+   k++ + e ++
  gi|298674341|ref|YP_003726091.1| 456 VSSNAQKTSETVTEVNKLVNEVGEQSKELKSKMENIQTTSEQTSEvvRELdnKSKKIGEIVS 517
                                       6777899999999999*********************9999988865333223344555555 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 2.2
                              Rx_N   3 sallqkLadllaeeakllkgvkeeleklkdeLesiqavLedaeerqikdeavkeWlkelrdlaydaeDvl 72 
                                       ++ ++ ++++++e  ++ ++  + +e+  + +                 +++ +  ++l ++a ++   +
  gi|298674341|ref|YP_003726091.1| 639 TSSVEEVSSIAEESSSSTEEASASVEEQTSSM-----------------QELSKSAQDLNQMAEELNQSV 691
                                       23333333333333333333333333333333.................333333333333333333333 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   9.0    0.0011      0.31       6      91 ..     378     462 ..     369     470 .. 0.71
   2 ?    6.6   7.9     0.014       3.9       7      85 ..     442     519 ..     437     539 .. 0.43
   3 ?    3.1   6.5      0.16        46       4      85 ..     467     571 ..     464     586 .. 0.63
   4 ?    5.3   2.7     0.035        10       5      84 ..     559     637 ..     542     640 .. 0.47
   5 ?    6.8   9.2     0.012       3.5       4      82 ..     621     698 ..     618     707 .] 0.76

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0011
                             TMPIT   6 elekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvl 82 
                                       ++e+ +++l++  +++k++  ++s+  +++s + ++ +  +++++++++++++ + ++++++++e++++++++++++
  gi|298674341|ref|YP_003726091.1| 378 TIEEMQDNLKNLVENIKESASQVSSTSEELSASSEQLTSSANQISDTITEITNGA-QNQSTKIQEVSSTMNDMSTSI 453
                                       3444445555556666777777777777777777777777888888888887774.688889999999999999999 PP

                             TMPIT  83 kevesllpk 91 
                                       ++v+s   k
  gi|298674341|ref|YP_003726091.1| 454 QDVSSNAQK 462
                                       999887544 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.014
                             TMPIT   7 lekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlk 83 
                                       +++ +++++++ + + ++ +++s+  +++ k +++  ++ kelks++++++++ +e+++e v+el+++ k++ ++++
  gi|298674341|ref|YP_003726091.1| 442 VSSTMNDMSTSIQDVSSNAQKTSETVTEVNKLVNEVGEQSKELKSKMENIQTT-SEQTSEVVRELDNKSKKIGEIVS 517
                                       33333333333333333333333333333333333333333333333333333.23444444444444444444443 PP

                             TMPIT  84 ev 85 
                                        +
  gi|298674341|ref|YP_003726091.1| 518 MI 519
                                       33 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.16
                             TMPIT   4 weelekefkeleetakeykqkleel...sklqskcskeikkqkkrlkelksslkklkksvk................ 61 
                                       ++e++k ++e+ e+ ke+k+k+e++   s++ s++++e+++++k++ e+ s+++++  +++                
  gi|298674341|ref|YP_003726091.1| 467 VTEVNKLVNEVGEQSKELKSKMENIqttSEQTSEVVRELDNKSKKIGEIVSMITNIADQTNllalnaaieaarageq 543
                                       55556666666666666666655541115666778888999999999999999999988777777777777777777 PP

                             TMPIT  62 ....eeeeeeveelkeelkerkkvlkev 85 
                                           +  ++ev++l+ee ++  +++ ++
  gi|298674341|ref|YP_003726091.1| 544 grgfAVVADEVRKLAEESSNSAQQIGDL 571
                                       7777444555555555555544444444 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.035
                             TMPIT   5 eelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkv 81 
                                       ee +++++++ +  +e+++++ e  ++ ++ s+ei++ ++ l e  +s++++  + ++e ++ v++++++ +e +++
  gi|298674341|ref|YP_003726091.1| 559 EESSNSAQQIGDLIQEIQNSTGEAVSSMENSSQEIENGSQALDETVNSMSNVVGK-TSEADNMVQDIASSAEELSAS 634
                                       2333333444444444444444444444444444444444444444444443333.256666666666666666666 PP

                             TMPIT  82 lke 84 
                                       ++e
  gi|298674341|ref|YP_003726091.1| 635 VEE 637
                                       665 PP

  == domain 5  score: 6.8 bits;  conditional E-value: 0.012
                             TMPIT   4 weelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkk 80 
                                       +++++++++el+++ +e+++++ee+s+  ++ s+++++ +  ++e +ss+++l+ks+ ++ ++ +eel++++k+ k 
  gi|298674341|ref|YP_003726091.1| 621 VQDIASSAEELSASVEEVTSSVEEVSSIAEESSSSTEEASASVEEQTSSMQELSKSA-QDLNQMAEELNQSVKSFKV 696
                                       677888888888888888888888888888888888888888888888888888885.5666777777777777665 PP

                             TMPIT  81 vl 82 
                                         
  gi|298674341|ref|YP_003726091.1| 697 DS 698
                                       54 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   7.1    0.0042       1.2      68     138 ..     364     434 ..     336     456 .. 0.74
   2 ?    4.9   9.3     0.097        28      73     163 ..     439     529 ..     428     543 .. 0.59
   3 ?    5.6  17.0     0.056        16      17     156 ..     547     694 ..     537     699 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0042
                             ATG16  68 snskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletk 138
                                        n +++ ++++ ++++ ++++ l++l     e+a+++ +++eel++  e+l++ ++++ +  +e+++  ++
  gi|298674341|ref|YP_003726091.1| 364 INVDTKGDLKEFADTIEEMQDNLKNLVENIKESASQVSSTSEELSASSEQLTSSANQISDTITEITNGAQN 434
                                       4578889999999*********************************9999999999988877777654443 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.097
                             ATG16  73 sakiqs.leqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelre 148
                                        ++++s +++  +++++  ++++k  +e+ + +++l +e+ ++ ++lk++ e+++  +++ +++ ++l+++ +++ e
  gi|298674341|ref|YP_003726091.1| 439 IQEVSStMNDMSTSIQDVSSNAQK-TSETVTEVNKLVNEVGEQSKELKSKMENIQTTSEQTSEVVRELDNKSKKIGE 514
                                       223333033333334433444444.4556667777777777777777777777777777777777777777777777 PP

                             ATG16 149 keklvqdlqDElsaL 163
                                          ++ ++ D  + L
  gi|298674341|ref|YP_003726091.1| 515 IVSMITNIADQTNLL 529
                                       777777776655544 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.056
                             ATG16  17 faeliqaynrLldrtsaleaenaklekaaasaks..sksskksakekeasasq.......snskqsakiqsleqkla 84 
                                       fa + +  ++L++ +s  +++   l +++++++     ss ++++++ ++ sq       s s+   k+++ ++ ++
  gi|298674341|ref|YP_003726091.1| 547 FAVVADEVRKLAEESSNSAQQIGDLIQEIQNSTGeaV-SSMENSSQEIENGSQaldetvnSMSNVVGKTSEADNMVQ 622
                                       5667778899999999999999999999999998752.333445555555555688889888888899999999999 PP

                             ATG16  85 qlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdl 156
                                        + +  +el  s +e ++++ e+++  ++  ++++e +++++e +++ ++l++  +d+++  +e+++ v+ +
  gi|298674341|ref|YP_003726091.1| 623 DIASSAEELSASVEEVTSSVEEVSSIAEESSSSTEEASASVEEQTSSMQELSKSAQDLNQMAEELNQSVKSF 694
                                       999999999999************************************************999999887765 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4  17.4   0.00015     0.043     155     280 ..     362     490 ..     342     506 .. 0.82
   2 ?   -2.2   7.8       8.1   2.3e+03     210     261 ..     553     605 ..     489     630 .. 0.47
   3 ?    1.4   9.4      0.65   1.9e+02     206     283 ..     616     692 ..     605     703 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00015
                                       XXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHH CS
                          Filament 155 vlvevda.arkldLteilkeiraqyeelaeknreeaeewykskleelqeaaeknsealrsakeeitelrrqiqslei 230
                                        +++vd+ +   + + +++e++++  +l+e+ +e+a +  +s  eel+ ++e+ ++++++    ite+    q+ ++
  gi|298674341|ref|YP_003726091.1| 362 QSINVDTkGDLKEFADTIEEMQDNLKNLVENIKESASQ-VSSTSEELSASSEQLTSSANQISDTITEITNGAQNQST 437
                                       3344444134456999************9987777765.58899********************************* PP

                                       HHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 231 eleslkkqkasleaqlaeleerl...eaeleklqeklseleeelaeireemar 280
                                       +++++ ++ + + ++++++  +    ++ ++++++ ++e+ e+ +e++++m+ 
  gi|298674341|ref|YP_003726091.1| 438 KIQEVSSTMNDMSTSIQDVSSNAqktSETVTEVNKLVNEVGEQSKELKSKMEN 490
                                       ******************986550005667788999***************96 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 8.1
                                       XXXX-HHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 210 alrsakeeitelrrqiqsleieleslkkqk.asleaqlaeleerleaeleklq 261
                                       ++r+  ee +++ +qi  l  e+++  +++ +s+e++ +e+e+  +a  e+++
  gi|298674341|ref|YP_003726091.1| 553 EVRKLAEESSNSAQQIGDLIQEIQNSTGEAvSSMENSSQEIENGSQALDETVN 605
                                       33333333333333333333333333222112333333333322221111111 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.65
                                       XXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 206 knsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerleaeleklqeklseleeelaeireemarql 282
                                       + +++++   +  +el  ++++ ++ +e++ + ++   ++ +e+ + +e++ +++qe  s+  ++l+++ ee+++ +
  gi|298674341|ref|YP_003726091.1| 616 EADNMVQDIASSAEELSASVEEVTSSVEEVSSIAEESSSSTEEASASVEEQTSSMQEL-SKSAQDLNQMAEELNQSV 691
                                       4455566666666666666666666666666666666667777777776666666654.444456666666666555 PP

                                       H CS
                          Filament 283 r 283
                                       +
  gi|298674341|ref|YP_003726091.1| 692 K 692
                                       4 PP

>> ING  Inhibitor of growth proteins N-terminal histone-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8  12.2     0.034       9.9       2      49 ..     372     457 ..     371     512 .. 0.65
   2 ?    0.8   5.0       2.6   7.7e+02      21      71 ..     629     679 ..     550     701 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.034
                                       HHHHHTSGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH................................. CS
                               ING   2 LedyldsvenLPlelqrnltelreiDakvqellkeidskiekfl................................. 45 
                                       L+++ d +e++++ l+ +++ ++e   +v+++ +e++ + e++                                  
  gi|298674341|ref|YP_003726091.1| 372 LKEFADTIEEMQDNLKNLVENIKESASQVSSTSEELSASSEQLTssanqisdtiteitngaqnqstkiqevsstmnd 448
                                       7899********************************888888888888999999**955555555555555555555 PP

                                       .....TS.. CS
                               ING  46 .....kngs 49 
                                            ++ s
  gi|298674341|ref|YP_003726091.1| 449 mstsiQDVS 457
                                       555443333 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 2.6
                                       HHHHHHHHHHHHHHHHHHHHHHHHHTS..S-HHHHHHHHHHHHHHHHHHHH CS
                               ING  21 telreiDakvqellkeidskiekflkngslqknekeeelsriqeelkeaqe 71 
                                       +el +   +v + ++e++s +e+ ++++++++ + ee++s++qe  k aq+
  gi|298674341|ref|YP_003726091.1| 629 EELSASVEEVTSSVEEVSSIAEESSSSTEEASASVEEQTSSMQELSKSAQD 679
                                       222222222222222222222332244444444444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (707 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3298  (0.183948); expected 358.6 (0.02)
Passed bias filter:                      748  (0.0417201); expected 358.6 (0.02)
Passed Vit filter:                       265  (0.0147805); expected 17.9 (0.001)
Passed Fwd filter:                       211  (0.0117686); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              62  [number of targets reported over threshold]
# CPU time: 2.91u 0.44s 00:00:03.35 Elapsed: 00:00:00.80
# Mc/sec: 2658.61
//
Query:       gi|298674342|ref|YP_003726092.1|  [L=366]
Description: histidine kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-23   83.5   0.1    1.4e-23   83.5   0.1    2.1  3  HATPase_c      Histidine kinase-, DNA gyrase B-, and HSP90-li
      1e-08   35.4   0.2    8.9e-08   32.4   0.0    2.4  2  PAS_4          PAS fold
    1.2e-05   25.3   0.1      4e-05   23.6   0.0    2.0  2  HisKA          His Kinase A (phospho-acceptor) domain
    0.00016   21.9   0.2     0.0046   17.2   0.0    2.8  3  PAS_9          PAS domain
     0.0039   17.2   0.0       0.01   15.8   0.0    1.7  1  PAS            PAS fold
  ------ inclusion threshold ------
      0.014   15.4   0.0      0.051   13.5   0.0    2.0  2  HATPase_c_2    Histidine kinase-like ATPase domain
      0.015   15.2   0.3      0.063   13.2   0.0    2.1  2  HATPase_c_5    GHKL domain
      0.024   14.6   0.3       0.21   11.6   0.0    2.4  2  PAS_8          PAS domain
      0.051   13.4   0.1        0.1   12.4   0.1    1.6  1  HATPase_c_3    Histidine kinase-, DNA gyrase B-, and HSP90-li
       0.18   11.9   0.0       0.35   11.0   0.0    1.4  1  Peptidase_S66  LD-carboxypeptidase N-terminal domain


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       6.5   1.2e+04      35      51 ..      58      74 ..      16      90 .. 0.52
   2 ?   -1.7   0.1       2.3   4.1e+03       6      20 ..     223     237 ..     220     250 .. 0.73
   3 !   83.5   0.1   8.1e-27   1.4e-23       6     110 ..     261     364 ..     257     366 .] 0.92

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 6.5
                                      ETEEEEEEEESSSSSTT CS
                         HATPase_c 35 eddlvisveDnGiGipk 51
                                      e+++ ++v D   G + 
  gi|298674342|ref|YP_003726092.1| 58 EETNYLTVCDEATGENS 74
                                      35666666666555555 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.3
                                       HHHHHHHHHHHHHHH CS
                         HATPase_c   6 LrqiisnlvdNavkf 20 
                                       L +ii n++d + + 
  gi|298674342|ref|YP_003726092.1| 223 LGHIIENVIDSLQDK 237
                                       789999999998876 PP

  == domain 3  score: 83.5 bits;  conditional E-value: 8.1e-27
                                       HHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHHH CS
                         HATPase_c   6 LrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsivk 82 
                                       ++q++snl++N++k++++++ei v i  ++d+ +i+v D+G+Gip ++ ++lf++f +  ++  ++ g G+Glsivk
  gi|298674342|ref|YP_003726092.1| 261 IEQAFSNLISNSIKYSPENSEIIVDIVDDNDYWKIRVIDSGPGIPDDEKERLFDRFKR--GSGEKSLGKGIGLSIVK 335
                                       689************99**********7669***************************..4445567********** PP

                                       HHHHHTTTEEEEEEET.TTEEEEEEEEES CS
                         HATPase_c  83 klvelmgGeiwvesep.grGttftftlpl 110
                                       ++vel+gG+i ve++p g+G+ f++t+++
  gi|298674342|ref|YP_003726092.1| 336 NVVELHGGNIGVEDNPeGKGSMFWITVKK 364
                                       ************99999*********986 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0   4.9e-11   8.9e-08       3      99 ..      21     128 ..      19     136 .. 0.77
   2 ?    0.1   0.0      0.52   9.4e+02       6      26 ..     243     263 ..     238     268 .. 0.71

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 4.9e-11
                             PAS_4   3 slpdalavldpdgrvlyaNaaaael...fgappeellGktla....ellpee.......daarleralrrvlegeep 65 
                                        lpd+++v+d+dg++ly+N ++++      +ppe++  +t +    +    e        a+  ++ +r v+ g++ 
  gi|298674342|ref|YP_003726092.1|  21 DLPDNFVVIDTDGTILYVNDSWRDFardNDLPPEHCSEETNYltvcD----EatgenseEAPIAAEGIRNVIHGKRE 93 
                                       58*******************77720003456666666666654442....146668999***************** PP

                             PAS_4  66 iefleelll.pgeerhyelrllPlrdesGevigvl 99 
                                       +++le++ + p ++r+y + ++Pl+de+ +++ ++
  gi|298674342|ref|YP_003726092.1|  94 YFELEYPCHaPNKRRWYIMKVIPLKDEKPRPVLAY 128
                                       999999999***************99877755444 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.52
                             PAS_4   6 dalavldpdgrvlyaNaaaae 26 
                                        ++++++  g + y+N  +++
  gi|298674342|ref|YP_003726092.1| 243 MNIVFVNQGGYYAYVNSIIEQ 263
                                       567777888888888877666 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   2.2e-08     4e-05       5      65 ..     152     211 ..     148     212 .. 0.89
   2 ?   -3.4   0.1       5.9   1.1e+04      51      60 ..     223     232 ..     216     236 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2.2e-08
                                       HHHHHHHHHHHHHHHHHHHHHHH.HC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHH CS
                             HisKA   5 flagvaHELrtPLsailgnaeaL.kregklteelkeyletiesearrldhlvedlLdlsrie 65 
                                       f   + H+L++P+   +g+ae+L k+  +++++  e +e+i+++ +r  +l+e   dl+r e
  gi|298674342|ref|YP_003726092.1| 152 FSDILRHDLKNPVGISKGFAEILyKN--ETDPKKLEIIEKIINNNNRAIDLIEKAGDLARVE 211
                                       566789*****************766..58899999******************99999876 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 5.9
                                       HHHHHHHHHH CS
                             HisKA  51 ldhlvedlLd 60 
                                       l h++e++ d
  gi|298674342|ref|YP_003726092.1| 223 LGHIIENVID 232
                                       7799999865 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.6e-06    0.0046       2      97 ..      24     127 ..      23     134 .. 0.74
   2 ?    1.1   0.1      0.26   4.7e+02      12      74 ..     189     253 ..     171     267 .. 0.68
   3 ?   -0.2   0.0      0.64   1.2e+03       7      41 ..     239     274 ..     233     295 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.6e-06
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlf..............vtdpeanerlraaleqgrkkerev 64 
                                       d ++++++dg+ily+N++++++     +++   ++++                +++p a+e +r+++  +r + +e 
  gi|298674342|ref|YP_003726092.1|  24 DNFVVIDTDGTILYVNDSWRDF--ARDNDLPPEHCSEETnyltvcdeatgensEEAPIAAEGIRNVIHGKR-EYFEL 97 
                                       6678778***************..55677777776666666677888888888888888888888888888.44555 PP

                             PAS_9  65 evvlirkngetfwvlltaspvkdddgelvgiiv 97 
                                       e+ +  +n ++ w+ ++++p+kd++ + v+  +
  gi|298674342|ref|YP_003726092.1|  98 EYPCHAPN-KRRWYIMKVIPLKDEKPRPVL--A 127
                                       55555554.578**********99766665..5 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.26
                             PAS_9  12 rilyaNeaalrllGyspeevlgksitdlf.vtdpeanerlraaleqgrk..kerevevvlirknge 74 
                                       +i+  N+ a++l+  ++ ++    + d + +++ +  + ++++++++++  + ++ ++v+++  g 
  gi|298674342|ref|YP_003726092.1| 189 KIINNNNRAIDLI-EKAGDLARVECMDHIeYEHLDLGHIIENVIDSLQDklTDKNMNIVFVNQGGY 253
                                       5677777777777.4788888888888885555555555556665555555555555555555554 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.64
                             PAS_9   7 dnpdgrilyaNeaalrllGyspeevlgksitdlf....v 41 
                                       ++++ +i+++N++    +    + ++ + +++l+    +
  gi|298674342|ref|YP_003726092.1| 239 TDKNMNIVFVNQGGYYAY---VNSIIEQAFSNLIsnsiK 274
                                       567778889998876665...455666666666655543 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   5.7e-06      0.01       4      33 ..      16      45 ..      13      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.7e-06
                                      HHHHHHSSSEEEEEETTSBEEEECHHHHHH CS
                               PAS  4 raileslpdpifvvDedgrilyvNaaaeel 33
                                      ++i+ +lpd  +v+D dg ilyvN++++++
  gi|298674342|ref|YP_003726092.1| 16 DNIIKDLPDNFVVIDTDGTILYVNDSWRDF 45
                                      6899**********************9876 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       3.3     6e+03      65      84 ..      59      78 ..      45      83 .. 0.75
   2 ?   13.5   0.0   2.9e-05     0.051      39     110 ..     264     339 ..     247     356 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.3
                       HATPase_c_2 65 ealtvevaDsGpgfdpetlp 84
                                      e+  ++v D++ g + e++p
  gi|298674342|ref|YP_003726092.1| 59 ETNYLTVCDEATGENSEEAP 78
                                      45557888888888877766 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 2.9e-05
                       HATPase_c_2  39 actNavehayleap.egpvevrlesdeealtvevaDsGpg.fdpe..tlpdpteeepkeslkegGrGlalikglvD 110
                                       a++N +    +  p + ++ v + +d++  +++v DsGpg  d e   l d+ + ++ e+    G+Gl ++k++v+
  gi|298674342|ref|YP_003726092.1| 264 AFSNLISNSIKYSPeNSEIIVDIVDDNDYWKIRVIDSGPGiPDDEkeRLFDRFKRGSGEKSLGKGIGLSIVKNVVE 339
                                       444555444444454578999999****************97766235567777777999999********99875 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.8   3.3e+03      10      23 ..     223     236 ..     218     250 .. 0.63
   2 ?   13.2   0.0   3.5e-05     0.063       9      89 ..     264     349 ..     257     354 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.8
                       HATPase_c_5  10 lgnlLdNAieacsk 23 
                                       lg +++N i++ ++
  gi|298674342|ref|YP_003726092.1| 223 LGHIIENVIDSLQD 236
                                       46666776666554 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 3.5e-05
                       HATPase_c_5   9 ilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg....ek....kkle.sskskkeehGiGlksire 76 
                                        ++nl+ N+i  +     e+++I + +  +++   i++  s  g    ek    ++++  s +k+  +GiGl+ +++
  gi|298674342|ref|YP_003726092.1| 264 AFSNLISNSIKYSP----ENSEIIVDIVDDNDYWKIRVIDSGPGipddEKerlfDRFKrGSGEKSLGKGIGLSIVKN 336
                                       46677777665544....47789999999999999999999776666544234433333446778899********* PP

                       HATPase_c_5  77 ivkkykgnlsiea 89 
                                       +v+ ++gn+ +e 
  gi|298674342|ref|YP_003726092.1| 337 VVELHGGNIGVED 349
                                       *******998765 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00012      0.21       6      35 ..      18      47 ..      16      72 .. 0.82
   2 ?   -0.1   0.1      0.55   9.9e+02       8      28 ..     232     250 ..     225     253 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                             PAS_8  6 lfesspdgiavvd.lgdrivdvNqaalellG 35
                                      ++  +pd  +v+d +g +i++vN+++ ++  
  gi|298674342|ref|YP_003726092.1| 18 IIKDLPDNFVVIDtDG-TILYVNDSWRDFAR 47
                                      67789999999**555.5********99865 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.55
                             PAS_8   8 esspdgiavvdlgdrivdvNq 28 
                                       +s++d +  +++  +iv+vNq
  gi|298674342|ref|YP_003726092.1| 232 DSLQDKLT-DKNM-NIVFVNQ 250
                                       44444444.4344.4*****9 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   5.8e-05       0.1       4      76 ..     262     330 ..     258     353 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.8e-05
                       HATPase_c_3   4 ekAlaelvdNsldAdaenvkievnknr.gktgeivieDdGkGmseeelknal.rlatsskeakrkstslGkkGiG 76 
                                       e+A   l+ Ns+  + en +i v+  + ++  +i++ D G G++ +e ++ + r+ + s e     +slGk GiG
  gi|298674342|ref|YP_003726092.1| 262 EQAFSNLISNSIKYSPENSEIIVDIVDdNDYWKIRVIDSGPGIPDDEKERLFdRFKRGSGE-----KSLGK-GIG 330
                                       788999*******9999988887744325679*************9988877345444444.....45553.555 PP

>> Peptidase_S66  LD-carboxypeptidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00019      0.35      19      79 ..     194     256 ..     183     276 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00019
                                       HHHHHHHHHHCT..EEEEEGCTC--TTTTCSS-HHHHHHHHHHHHC-TTECEEEES--SS-CH CS
                     Peptidase_S66  19 leraievleelg..levvlgksaaksagylagtdeeRaadLnealadpeikaiicarGGygaa 79 
                                        +rai+++e+ g   +v+  ++++ ++ +l    e+ +++L++ l+d+++++++  +GGy a+
  gi|298674342|ref|YP_003726092.1| 194 NNRAIDLIEKAGdlARVECMDHIEYEHLDLGHIIENVIDSLQDKLTDKNMNIVFVNQGGYYAY 256
                                       56777777776411344455577666668888899999**********************874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2310.99
//
Query:       gi|298674343|ref|YP_003726093.1|  [L=199]
Description: putative PAS/PAC sensor protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-14   52.3   0.0    1.2e-05   25.2   0.0    2.2  2  PAS_8     PAS domain
    9.6e-12   45.1   0.0    5.8e-06   26.5   0.0    2.3  2  PAS_4     PAS fold
    2.3e-09   37.3   0.0    0.00026   21.0   0.0    2.3  2  PAS       PAS fold
    1.3e-07   31.8   0.0     0.0061   16.8   0.0    2.8  2  PAS_9     PAS domain


Domain annotation for each model (and alignments):
>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   2.6e-09   1.2e-05       1      52 [.      12      73 ..      12      89 .. 0.76
   2 !   25.1   0.0   2.8e-09   1.2e-05       3      57 ..     133     188 ..     131     195 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.6e-09
                             PAS_8  1 erlralfesspdgiav....vd.lgd....rivdvNqaalellGys.adlkgellgqllpvl 52
                                      e l ++fes+ +g+++    +d +++    ri+d N+a++ + G++ +d++g++  ++   +
  gi|298674343|ref|YP_003726093.1| 12 ELLNSVFESIKEGVCLheiiYDsNNNpvdyRIIDTNPAYESIIGLKrEDVSGKKASDIYGTI 73
                                      57889**********9888645433377789*************999999998886444333 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 2.8e-09
                             PAS_8   3 lralfesspd.giavvdlgdrivdvNqaalellG.ysadlkgellgqllpvlrplle 57 
                                       l+a++e+sp+ +++ vd ++ri+ +N++a+++ G  s+++kg++ g+ l+ l++l +
  gi|298674343|ref|YP_003726093.1| 133 LEAIYENSPVvSMV-VDSDRRIIKMNKSAEQFAGaISDEVKGMKGGDALRCLHSLDD 188
                                       799*******5555.999999*************666******99988888877665 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   1.3e-09   5.8e-06      14     109 ..      40     127 ..      39     128 .. 0.88
   2 !   16.6   0.0   1.6e-06     0.007       2      42 ..     138     178 ..     137     192 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.3e-09
                             PAS_4  14 dgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgeerhyelrllPlrd 90 
                                       d+r++++N+a+++++g+ +e++ Gk+  +++ +   +++ + +++ +e++e ++f+++  +    +h++++++    
  gi|298674343|ref|YP_003726093.1|  40 DYRIIDTNPAYESIIGLKREDVSGKKASDIYGT-IEPPYLHLYAKTAETGEKAYFETFFPP--LNKHFSISVISP-- 111
                                       89****************************999.***********************8777..888888888555.. PP

                             PAS_4  91 esGevigvlvisrDiTerr 109
                                         G+   ++ i++DiT ++
  gi|298674343|ref|YP_003726093.1| 112 --GR-GMFITIFTDITGQK 127
                                       ..23.56999999999765 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.6e-06
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlae 42 
                                       +++p++  v+d+d r++ +N++a++ +ga  +e+ G++  +
  gi|298674343|ref|YP_003726093.1| 138 ENSPVVSMVVDSDRRIIKMNKSAEQFAGAISDEVKGMKGGD 178
                                       89**************************9999999987665 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   8.3e-06     0.037      22      48 ..      42      68 ..      37      87 .. 0.91
   2 !   21.0   0.0   5.7e-08   0.00026       2      43 ..     132     173 ..     131     180 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.3e-06
                                      BEEEECHHHHHHHSSTHHHCTTSBGGG CS
                               PAS 22 rilyvNaaaeellGlsreevlgkslld 48
                                      ri+ +N+a+e++ Gl+re+v+gk+ +d
  gi|298674343|ref|YP_003726093.1| 42 RIIDTNPAYESIIGLKREDVSGKKASD 68
                                      8999*******************8776 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 5.7e-08
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTT CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlg 43 
                                       +l+ai e++p+  +vvD d ri+ +N++ae++ G   +ev g
  gi|298674343|ref|YP_003726093.1| 132 ELEAIYENSPVVSMVVDSDRRIIKMNKSAEQFAGAISDEVKG 173
                                       799*******************************99999987 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.4e-06    0.0061      10      41 ..      40      73 ..      29     125 .. 0.70
   2 !   11.4   0.0   6.4e-05      0.29       4      35 ..     144     175 ..     141     193 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.4e-06
                             PAS_9 10 dgrilyaNeaalrllGyspeevlgksitdlf..v 41
                                      d ri++ N+a + ++G ++e+v gk+ +d++   
  gi|298674343|ref|YP_003726093.1| 40 DYRIIDTNPAYESIIGLKREDVSGKKASDIYgtI 73
                                      669**************************99642 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 6.4e-05
                             PAS_9   4 ilidnpdgrilyaNeaalrllGyspeevlgks 35 
                                        +++++d ri+++N++a+++ G  ++ev g +
  gi|298674343|ref|YP_003726093.1| 144 SMVVDSDRRIIKMNKSAEQFAGAISDEVKGMK 175
                                       445679****************8899988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1307.95
//
Query:       gi|298674344|ref|YP_003726094.1|  [L=837]
Description: multi-sensor signal transduction histidine kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.3e-41  139.8   6.6    8.2e-16   58.2   0.9    3.8  3  PAS_9        PAS domain
    2.3e-36  124.2   0.0    4.9e-13   49.1   0.0    3.8  3  PAS          PAS fold
    1.3e-32  112.6   0.2    1.1e-31  109.7   0.1    2.2  2  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    4.8e-26   90.9   0.7    4.8e-14   52.4   0.0    4.1  4  PAS_3        PAS fold
    3.1e-20   71.8   0.0    3.5e-06   26.9   0.0    3.6  3  PAS_8        PAS domain
    9.5e-20   70.4   0.2    4.6e-19   68.2   0.1    2.3  2  HisKA        His Kinase A (phospho-acceptor) domain
    1.7e-17   63.6   0.0     0.0002   21.5   0.0    4.0  3  PAS_4        PAS fold
    8.2e-16   58.5   0.0    1.5e-15   57.7   0.0    1.5  1  GAF_2        GAF domain
    7.8e-09   35.7   0.9      4e-06   26.9   0.0    3.6  3  PAS_11       PAS domain
    6.3e-08   32.4   1.3       0.17   11.5   0.0    3.7  3  PAS_12       UPF0242 C-terminal PAS-like domain
    4.7e-07   30.4   3.8      0.054   14.1   0.1    4.0  3  PAS_10       PAS domain
    7.2e-05   23.1   0.0    0.00017   21.9   0.0    1.7  1  GAF_3        GAF domain
    8.5e-05   23.2   0.0    0.00016   22.3   0.0    1.5  1  GAF          GAF domain
    0.00082   19.2   0.0     0.0038   17.1   0.0    2.1  1  HATPase_c_5  GHKL domain
     0.0013   18.8   0.0        2.9    8.1   0.0    3.7  3  PAS_7        PAS fold
  ------ inclusion threshold ------
      0.017   15.1   0.0      0.038   14.0   0.0    1.5  1  HATPase_c_2  Histidine kinase-like ATPase domain


Domain annotation for each model (and alignments):
>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.0   9.9e-14   1.1e-10       6     104 .]      61     168 ..      57     168 .. 0.84
   2 !   58.2   0.9   7.3e-19   8.2e-16       6     104 .]     368     468 ..     364     468 .. 0.88
   3 !   41.0   0.0   1.6e-13   1.8e-10       4     103 ..     494     590 ..     491     591 .. 0.91

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 9.9e-14
                             PAS_9   6 i..dnpdgrilyaNeaalrllGyspeevlgksitdlf........vtdpeanerlraaleqgrkkerevevvlirkn 72 
                                       i   +++g+i+yaN +a+++lG s++++  + ++d+          + p+++  ++ + + ++ ++++v+  +  kn
  gi|298674344|ref|YP_003726094.1|  61 IthLDKSGNIIYANHTAEKVLGLSKNDINRRTYDDVKwkitdydgNDFPQDELPFELVKKYHQ-PVYDVQHAIEWKN 136
                                       335679************************999999999998665444444444444444444.************* PP

                             PAS_9  73 getfwvlltaspvkdddgelvgiivilrDite 104
                                       g++++  ++a+p++d+ g++ g+i+ ++Dit+
  gi|298674344|ref|YP_003726094.1| 137 GKRIYLSINAAPIFDKYGNFDGMIAAIEDITK 168
                                       ******************************95 PP

  == domain 2  score: 58.2 bits;  conditional E-value: 7.3e-19
                             PAS_9   6 i..dnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwv 78 
                                       i  ++++g+i+++N++ +++lGy +eev+g+s+t ++  +   ++ e l+++l+ g    +++e+ ++rk+ge + v
  gi|298674344|ref|YP_003726094.1| 368 ItsVDENGTIVDCNNQIKNILGYEKEEVIGQSMTKIIhpDYVNKSFEILHEILNYGF--SYNKEYKMVRKDGELIDV 442
                                       33588********************************66666666677777777777..****************** PP

                             PAS_9  79 lltaspvkdddgelvgiivilrDite 104
                                       l++ s v   +g++ + i+i++Dit+
  gi|298674344|ref|YP_003726094.1| 443 LINSSGVDKINGNYSRTICIINDITK 468
                                       *******777**************95 PP

  == domain 3  score: 41.0 bits;  conditional E-value: 1.6e-13
                             PAS_9   4 ilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfwvl 79 
                                       i+ ++ dg+ily+N+ a++ lGy+++e+l  +itd+   ++++ e+ r+++  +++ +  + e+   rk+g+ ++++
  gi|298674344|ref|YP_003726094.1| 494 IIAYDFDGNILYVNNLACEKLGYTKNELLSMNITDID--PENNIETYRKYWYGLSQnNSVHIETSRKRKDGSVYPAE 568
                                       344789******************************9..8888888888888888888******************* PP

                             PAS_9  80 ltaspvkdddgelvgiivilrDit 103
                                       l+++ +  +++ +++  +++rD+t
  gi|298674344|ref|YP_003726094.1| 569 LRMTLIDLNGKPVIL--GFSRDMT 590
                                       ******999999999..*****99 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   1.2e-09   1.4e-06       2     113 .]      49     166 ..      48     166 .. 0.88
   2 !   49.1   0.0   4.4e-16   4.9e-13       1     113 []     355     466 ..     355     466 .. 0.92
   3 !   42.5   0.0   4.7e-14   5.2e-11       2     112 ..     482     588 ..     481     589 .. 0.91

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1.2e-09
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH......HHHHHHHHHHHHTT-E CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda......elaelleqlleqgees 72 
                                       +++++ e++p  i  +D++g+i+y+N++ae+ lGls +++ ++++ d+ +  +d+      ++   +e + +  ++ 
  gi|298674344|ref|YP_003726094.1|  49 FFERVAETSPISITHLDKSGNIIYANHTAEKVLGLSKNDINRRTYDDVKWKITDYdgndfpQDELPFELVKKYHQPV 125
                                       689999******************************************99999999996665555666666666677 PP

                                       CCCCEEEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  73 rageisfklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                        ++++ ++ ++g+ i+l ++a+p++d+ g+  g +  + di
  gi|298674344|ref|YP_003726094.1| 126 YDVQHAIEWKNGKRIYLSINAAPIFDKYGNFDGMIAAIEDI 166
                                       7777777779********************99999999997 PP

  == domain 2  score: 49.1 bits;  conditional E-value: 4.4e-16
                                       HHHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCE CS
                               PAS   1 edlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesragei 77 
                                       e++r+i+e++++ i  vDe+g i+ +N  +  +lG++ eev+g+s+   ih+++   +++ +e l e  + + ++++
  gi|298674344|ref|YP_003726094.1| 355 ERYRSIFETAASLITSVDENGTIVDCNNQIKNILGYEKEEVIGQSMTKIIHPDY---VNKSFEILHEILNYGFSYNK 428
                                       68*********************************************9888876...88888888888888888888 PP

                                       EEEC..TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  78 sfkl..rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                         k   +dg+ i ++++ s v  + g+    +++++di
  gi|298674344|ref|YP_003726094.1| 429 EYKMvrKDGELIDVLINSSGVDKINGNYSRTICIINDI 466
                                       7777888******************************8 PP

  == domain 3  score: 42.5 bits;  conditional E-value: 4.7e-14
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       ++r + e+++d i++ D dg+ilyvN  a+e lG++ +e+l+ ++  +i +e + e++++++  l+q+++ +++  +
  gi|298674344|ref|YP_003726094.1| 482 KFRKVTEQAADVIIAYDFDGNILYVNNLACEKLGYTKNELLSMNIT-DIDPENNIETYRKYWYGLSQNNSVHIETSR 557
                                       688999****************************************.88888899****************997777 PP

                                       EECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEE CS
                               PAS  79 fklrdgrpihlevraspvrdaggeilgflgvlrd 112
                                        ++ dg+++++e+r++ +   g+    +lg+ rd
  gi|298674344|ref|YP_003726094.1| 558 KRK-DGSVYPAELRMTLIDLNGKP--VILGFSRD 588
                                       777.************99988776..78888887 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.95   1.1e+03      35      63 ..      87     123 ..      46     158 .. 0.73
   2 !  109.7   0.1   9.4e-35   1.1e-31       2     110 ..     727     835 ..     726     837 .] 0.96

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.95
                                       E......TEEEEEEEE.SSSSSTTHHHT.GTCSTTCH CS
                         HATPase_c  35 e......ddlvisveD.nGiGipkedlk.klfekfsq 63 
                                       +      dd++ +++D +G   p+++l+ +l +k+ q
  gi|298674344|ref|YP_003726094.1|  87 DinrrtyDDVKWKITDyDGNDFPQDELPfELVKKYHQ 123
                                       1333456899999***9**********9655556666 PP

  == domain 2  score: 109.7 bits;  conditional E-value: 9.4e-35
                                       HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTSSSHH CS
                         HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsq.ddstkrggggtGlG 77 
                                       d ++++qi+snl+ Navkf t++g+i++e++++edd+++sv D+GiGipk  ++ +f++f q d++ +r+++gtGlG
  gi|298674344|ref|YP_003726094.1| 727 DYIKIKQILSNLLYNAVKF-TEEGSITLEVSQNEDDVQFSVIDTGIGIPKGSHEAIFDSFKQlDSGPARKYQGTGLG 802
                                       67889**************.***********888******************************************* PP

                                       HHHHHHHHHHTTTEEEEEEETTTEEEEEEEEES CS
                         HATPase_c  78 lsivkklvelmgGeiwvesepgrGttftftlpl 110
                                       l++v+klv+++gG+iwvese ++G++ftft+p 
  gi|298674344|ref|YP_003726094.1| 803 LALVNKLVNMHGGQIWVESEIKKGSRFTFTIPD 835
                                       ******************************997 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.1   5.7e-05     0.064       1      87 [.      70     161 ..      70     163 .. 0.86
   2 !   52.4   0.0   4.3e-17   4.8e-14       2      88 ..     378     462 ..     377     463 .. 0.95
   3 !   20.6   0.0   3.5e-07   0.00039       2      86 ..     504     583 ..     503     586 .. 0.83
   4 ?   -2.8   0.0       7.3   8.2e+03      58      71 ..     809     822 ..     806     824 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.7e-05
                             PAS_3   1 iiyvserveeilGyspeellgk.veswldlvhpeD...rervrealqealkkge.pyegeyRirrkdGeyrwveara 72 
                                       iiy++ + e++lG+s++++  + +++++  +   D    ++ +  ++ + k  + +y++++ i +k+G+ ++++  a
  gi|298674344|ref|YP_003726094.1|  70 IIYANHTAEKVLGLSKNDINRRtYDDVKWKITDYDgndFPQDELPFELVKKYHQpVYDVQHAIEWKNGKRIYLSINA 146
                                       699******************999999999998884334444555667778888999******************** PP

                             PAS_3  73 rvirdengkpvrvig 87 
                                        +i+d+ g+ + +i+
  gi|298674344|ref|YP_003726094.1| 147 APIFDKYGNFDGMIA 161
                                       *********999987 PP

  == domain 2  score: 52.4 bits;  conditional E-value: 4.3e-17
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       + +++++++ilGy++ee++g+  s+ +++hp+  ++ +e l+e+l+ g +y+ ey+++rkdGe + v    + +   
  gi|298674344|ref|YP_003726094.1| 378 VDCNNQIKNILGYEKEEVIGQ--SMTKIIHPDYVNKSFEILHEILNYGFSYNKEYKMVRKDGELIDVLINSSGVDKI 452
                                       78*******************..*********************************************999999999 PP

                             PAS_3  79 ngkpvrvigv 88 
                                       ng+  r i++
  gi|298674344|ref|YP_003726094.1| 453 NGNYSRTICI 462
                                       9999998887 PP

  == domain 3  score: 20.6 bits;  conditional E-value: 3.5e-07
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       +yv++  +e lGy+++ell+   ++ d+     +e +r+ +  + +++ ++++e  ++rkdG+++  e r++ i d 
  gi|298674344|ref|YP_003726094.1| 504 LYVNNLACEKLGYTKNELLSM--NITDIDPENNIETYRKYWYGL-SQNNSVHIETSRKRKDGSVYPAELRMTLI-DL 576
                                       7999999**************..998876555565555555555.566669***********************.** PP

                             PAS_3  79 ngkpvrvi 86 
                                       ngkpv ++
  gi|298674344|ref|YP_003726094.1| 577 NGKPV-IL 583
                                       ****9.44 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 7.3
                             PAS_3  58 irrkdGeyrwvear 71 
                                       +++ +G+ +wve+ 
  gi|298674344|ref|YP_003726094.1| 809 LVNMHGGQIWVESE 822
                                       67889******985 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0     2e-06    0.0023       2      45 ..      49      93 ..      48     114 .. 0.85
   2 !   26.9   0.0   3.1e-09   3.5e-06       1      51 [.     355     406 ..     355     419 .. 0.88
   3 !   22.6   0.0   6.8e-08   7.6e-05       1      47 [.     481     528 ..     481     545 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2e-06
                             PAS_8  2 rlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgell 45
                                      +++ + e+sp +i  +d  g+ i+++N +a++ lG+s +d+ + + 
  gi|298674344|ref|YP_003726094.1| 49 FFERVAETSPISITHLDkSGN-IIYANHTAEKVLGLSkNDINRRTY 93
                                      7999**********9997888.*************99988877665 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 3.1e-09
                             PAS_8   1 erlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellgqllpv 51 
                                       er+r++fe+++  i  vd +g+ ivd+N++   +lGy+ ++++g+ + ++++ 
  gi|298674344|ref|YP_003726094.1| 355 ERYRSIFETAASLITSVDeNGT-IVDCNNQIKNILGYEkEEVIGQSMTKIIHP 406
                                       7*****************8888.*********************999766654 PP

  == domain 3  score: 22.6 bits;  conditional E-value: 6.8e-08
                             PAS_8   1 erlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellgq 47 
                                       e++r + e+++d i+ +d +g+ i++vN+ a+e lGy+ ++l+ + + +
  gi|298674344|ref|YP_003726094.1| 481 EKFRKVTEQAADVIIAYDfDGN-ILYVNNLACEKLGYTkNELLSMNITD 528
                                       79*************9999999.***************88888776643 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       4.9   5.5e+03      26      49 ..     349     369 ..     341     394 .. 0.51
   2 !   68.2   0.1   4.1e-22   4.6e-19       1      67 []     612     680 ..     612     680 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.9
                                       HHHC..T-HSSCHHHHHHHHHHHH CS
                             HisKA  26 aLkregklteelkeyletiesear 49 
                                       aL++     e+ +  +et+ s + 
  gi|298674344|ref|YP_003726094.1| 349 ALEK---SEERYRSIFETAASLIT 369
                                       4433...34555555555544444 PP

  == domain 2  score: 68.2 bits;  conditional E-value: 4.1e-22
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                             HisKA   1 slgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsrieag 67 
                                       ++++ la+v HELrtPL++i+g++++L +   g+l+e++k yl ++++++++l++l+ d+Ldls+ie+g
  gi|298674344|ref|YP_003726094.1| 612 AKSDILANVNHELRTPLTSIIGFSDVLLKGkaGDLNESQKMYLSRVHNNGKHLLDLITDILDLSKIESG 680
                                       5899**********************9777799**********************************97 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   1.8e-07    0.0002       2     109 ..      55     170 ..      54     171 .. 0.93
   2 !   17.4   0.0   3.4e-06    0.0038       5     109 ..     365     470 ..     361     471 .. 0.86
   3 !   20.0   0.0   5.6e-07   0.00063       2     109 ..     488     593 ..     487     594 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.8e-07
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee......daarleralrrvlegeepiefleel 72 
                                       + +p  ++ ld+ g+++yaN +a++++g++  ++  +t+ ++  +       d ++ e + + v + ++p++++++ 
  gi|298674344|ref|YP_003726094.1|  55 ETSPISITHLDKSGNIIYANHTAEKVLGLSKNDINRRTYDDVKWKItdydgnDFPQDELPFELVKKYHQPVYDVQHA 131
                                       568999999*******************************965555788899999999*****************99 PP

                             PAS_4  73 ll..pgeerhyelrllPlrdesGevigvlvisrDiTerr 109
                                           +g++ ++++++ P++d  G  +g ++ + DiT ++
  gi|298674344|ref|YP_003726094.1| 132 IEwkNGKRIYLSINAAPIFDKYGNFDGMIAAIEDITKQK 170
                                       99**********************************986 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 3.4e-06
                             PAS_4   5 pdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pgeerh 80 
                                         +++ +d++g+++++N+++  ++g++ ee++G+++  +  ++      ++l + l  + ++  +  +++ +ge   
  gi|298674344|ref|YP_003726094.1| 365 ASLITSVDENGTIVDCNNQIKNILGYEKEEVIGQSMTKIIHPDYVNKSFEILHEILNYGFSYNKEYKMVRkDGELID 441
                                       5678999******************************9888888888888888888888888888888888899999 PP

                             PAS_4  81 yelrllPlrdesGevigvlvisrDiTerr 109
                                       ++++ + +++ +G    +++i+ DiT  +
  gi|298674344|ref|YP_003726094.1| 442 VLINSSGVDKINGNYSRTICIINDITKSK 470
                                       99999999999999999999999998765 PP

  == domain 3  score: 20.0 bits;  conditional E-value: 5.6e-07
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgee 78 
                                       ++  d++++ d dg++ly+N+ a+e +g++  ell +   ++ pe   + ++ ++  + + + +++++   + +g+ 
  gi|298674344|ref|YP_003726094.1| 488 EQAADVIIAYDFDGNILYVNNLACEKLGYTKNELLSMNITDIDPENNIETYRKYWYGLSQNNSVHIETSRKRKDGSV 564
                                       6778999999***********************************************9999988888888888**** PP

                             PAS_4  79 rhyelrllPlrdesGevigvlvisrDiTerr 109
                                        + elr++ + d +G+   +l++srD+T ++
  gi|298674344|ref|YP_003726094.1| 565 YPAELRMTLI-DLNGK-PVILGFSRDMTVQK 593
                                       **********.99***.889********876 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.7   0.0   1.4e-18   1.5e-15       3     137 ..     205     341 ..     203     342 .. 0.93

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 1.4e-18
                                       HHHHHHHHHHHHHHHS.S..EEEEEEE-TTS-....EEEEEEEES-TTSTT-S-B---TTHHHHHHHHTS-EEES-G CS
                             GAF_2   3 dleelldlvldelvel.gaalgyillvdddgg....lrlaawgeaeeefgaaldrplgeglvgealrtgrpvilndl 74 
                                       d+++ ++ ++d + +l ga +gy+ l+ d g+    l l+  g++   + + +   + +gl +e+ rtg  v+ nd+
  gi|298674344|ref|YP_003726094.1| 205 DFNTAARYIFDSCSRLlGAKAGYVSLLSDTGDeneiLFLEDGGMPCSVDIDLP--IPVRGLSAEVSRTGDVVYDNDF 279
                                       7788999********66*********887777677788889999999999999..779******************9 PP

                                       GG-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  75 eedpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                        ++ + k  p+ h +l + l+ Pl+ +g+++G++++ a k+++f++ d +l+++++e +aia+
  gi|298674344|ref|YP_003726094.1| 280 MNSNRVKYMPECHMNLPNVLISPLTVDGKTLGFMGF-AYKEGGFTDNDAQLAKTFGEYAAIAL 341
                                       999999*****************************7.99***********************8 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.14   1.6e+02       6      41 ..      62      94 ..      60     106 .. 0.89
   2 !   26.9   0.0   3.6e-09     4e-06       4     111 ..     367     470 ..     364     472 .. 0.94
   3 ?    2.4   0.0      0.14   1.6e+02       7      43 ..     496     529 ..     491     562 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.14
                            PAS_11  6 trldidgkIisvDtsaLrasfslglekeelvgrsiy 41
                                      t ld +g+Ii  ++    a+ +lgl+k+++ +r + 
  gi|298674344|ref|YP_003726094.1| 62 THLDKSGNIIYANH---TAEKVLGLSKNDINRRTYD 94
                                      78999*********...9*********999998765 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 3.6e-09
                            PAS_11   4 fttrldidgkIisvDtsaLrasfslglekeelvgrsiydLchpqdlstlkshlrevissngeatsslyRLrlsqdkf 80 
                                       ++t  d +g I+++++    ++  lg+ekee++g s+ +++hp+ + +  + l+e++ + g +    y++  ++++ 
  gi|298674344|ref|YP_003726094.1| 367 LITSVDENGTIVDCNN---QIKNILGYEKEEVIGQSMTKIIHPDYVNKSFEILHEIL-NYGFSYNKEYKMVRKDGEL 439
                                       67899***********...**************************************.99999************** PP

                            PAS_11  81 vkvktksklfknqksneqdfimathtllsee 111
                                       + v  +s   ++ + n +  i +++ + +++
  gi|298674344|ref|YP_003726094.1| 440 IDVLINSSGVDKINGNYSRTICIINDITKSK 470
                                       ****999999999999999999999888776 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.14
                            PAS_11   7 rldidgkIisvDtsaLrasfslglekeelvgrsiydL 43 
                                         d dg+I+ v++    a  +lg++k+el+ + i d+
  gi|298674344|ref|YP_003726094.1| 496 AYDFDGNILYVNN---LACEKLGYTKNELLSMNITDI 529
                                       5688899999999...777788999999988888776 PP

>> PAS_12  UPF0242 C-terminal PAS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0015       1.7      60      93 ..      61      94 ..      45     103 .. 0.82
   2 !    8.9   0.1   0.00095       1.1      54      99 ..     362     408 ..     359     451 .. 0.73
   3 !   11.5   0.0   0.00015      0.17      54     138 ..     488     574 ..     482     578 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0015
                            PAS_12 60 lvysqkenkllfaNaqirallGwssdkflqdfse 93
                                      + +  k   +++aN+  +++lG+s++++ ++  +
  gi|298674344|ref|YP_003726094.1| 61 ITHLDKSGNIIYANHTAEKVLGLSKNDINRRTYD 94
                                      556678889******************9987655 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00095
                            PAS_12  54 EnlgailvysqkenkllfaNaqirallGwssdkfl.qdfseivqegl 99 
                                       E++++++     +  ++  N+qi+++lG+++++++ q++++i+++ +
  gi|298674344|ref|YP_003726094.1| 362 ETAASLITSVDENGTIVDCNNQIKNILGYEKEEVIgQSMTKIIHPDY 408
                                       5556666555666678889***********99977477888988765 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00015
                            PAS_12  54 EnlgailvysqkenkllfaNaqirallGwssdkflqd.fseiv.qegleeWkralaklsskteskirlvlKtKagqe 128
                                       E+++ +++   ++  +l++N+   + lG+ ++++l+   ++i  ++ +e++++    ls+++ ++i+   K K g  
  gi|298674344|ref|YP_003726094.1| 488 EQAADVIIAYDFDGNILYVNNLACEKLGYTKNELLSMnITDIDpENNIETYRKYWYGLSQNNSVHIETSRKRKDGSV 564
                                       78888888889*******************99998751556542456899999999999999999999999999987 PP

                            PAS_12 129 vllncllgii 138
                                        + +  + +i
  gi|298674344|ref|YP_003726094.1| 565 YPAELRMTLI 574
                                       7766666666 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.1   4.8e-05     0.054       6     106 .]      55     167 ..      50     167 .. 0.67
   2 !   11.8   0.2   0.00025      0.28       4     106 .]     360     467 ..     358     467 .. 0.77
   3 ?    2.9   0.0      0.14   1.6e+02      20      80 ..     502     564 ..     481     574 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.8e-05
                            PAS_10   6 nstpieltflDdnlqirrFtpaakklfklipadvGrpl.adih...pk...kavknveeviealrtgekdevevvvp 75 
                                       ++ pi++t lD++ +i++ +++a+k++ l ++d+ r+  +d++   ++   +  ++ e  +e +++  + + +v+ +
  gi|298674344|ref|YP_003726094.1|  55 ETSPISITHLDKSGNIIYANHTAEKVLGLSKNDINRRTyDDVKwkiTDydgNDFPQDELPFELVKKYHQPVYDVQHA 131
                                       7889******************************9876155643332222222233333334444444444444433 PP

                            PAS_10  76 ...kngkw..vlvrylpyrdedgeiaGvvetfvDit 106
                                          kngk     ++  p+ d+ g+++G++  + Dit
  gi|298674344|ref|YP_003726094.1| 132 iewKNGKRiyLSINAAPIFDKYGNFDGMIAAIEDIT 167
                                       55655554114578889****************997 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00025
                            PAS_10   4 lLnstpieltflDdnlqirrFtpaakklfklipad.vGrpladihpkkavknveeviealrtgekdeve.vvv.pkn 77 
                                       ++++++  +t +D+n  i   ++++k+++ + +++ +G ++++i ++++v++  e+++++ +    + + +++  k+
  gi|298674344|ref|YP_003726094.1| 360 IFETAASLITSVDENGTIVDCNNQIKNILGYEKEEvIGQSMTKIIHPDYVNKSFEILHEILNYGFSYNKeYKMvRKD 436
                                       567788889*****************99999876527*******999999999999999888766433303332588 PP

                            PAS_10  78 gkw..vlvrylpyrdedgeiaGvvetfvDit 106
                                       g++  vl++ + + + +g++  ++ ++ Dit
  gi|298674344|ref|YP_003726094.1| 437 GELidVLINSSGVDKINGNYSRTICIINDIT 467
                                       8874456677778888888888888888875 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.14
                            PAS_10  20 qirrFtp.aakklfklipadvGrpladihpkkavknveeviealrtgekdevevvvp.kngkw 80 
                                       +i++ ++ a +kl   +++ +  +++di p+++++  ++    l+++++++ e+ ++ k+g +
  gi|298674344|ref|YP_003726094.1| 502 NILYVNNlACEKLGYTKNELLSMNITDIDPENNIETYRKYWYGLSQNNSVHIETSRKrKDGSV 564
                                       5555555333566666666677799****************************9997566655 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   1.5e-07   0.00017      78     129 .]     293     343 ..     213     343 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.5e-07
                             GAF_3  78 lpdraalavPLvagr.qviGvlalastkprafdaedlelleslArqiataier 129
                                       +++ ++l+ PL++ + +++G++++a+++ + f++ d++l ++++ ++a+a+ +
  gi|298674344|ref|YP_003726094.1| 293 MNLPNVLISPLTV-DgKTLGFMGFAYKE-GGFTDNDAQLAKTFGEYAAIALKN 343
                                       56678999*****.66**********87.55*******************987 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   1.5e-07   0.00016       3     133 .]     207     341 ..     205     341 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.5e-07
                                       HHHHHHHHHHHHHHHTESEEEEEEEEETTEEE........CEEEEECCEEEETTSHHHHHHHHHSSSEEESTGGTST CS
                               GAF   3 eelldtvveelrellgadrvalylpdydGlhy........dipqasrwlfmkngrgicgqvlatgqplvipdstpdp 71 
                                        ++++ + +++++llga  + + l +  G +         + p + +   + ++rg+ ++v +tg+++  +d  +++
  gi|298674344|ref|YP_003726094.1| 207 NTAARYIFDSCSRLLGAKAGYVSLLSDTGDENeilfledgGMPCSVDIDLPIPVRGLSAEVSRTGDVVYDNDFMNSN 283
                                       67777888999999999999997733444211234444444555555566666666555777777777777644555 PP

                                       THHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSSCSHHHHHHHHHHHHHHHHHHH CS
                               GAF  72 rfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsppftreelellqvladqvaval 133
                                       r       +   +m+  ++l  Pl++dg+++G + +  +   ft+++ +l++++++ +a+al
  gi|298674344|ref|YP_003726094.1| 284 RVKY----MPECHMNLPNVLISPLTVDGKTLGFMGFAYKEGGFTDNDAQLAKTFGEYAAIAL 341
                                       5333....455689999*********************7778******************97 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.4e-06    0.0038       6      90 ..     731     822 ..     727     833 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.4e-06
                       HATPase_c_5   6 lcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg...........ekkkless.kskkeehGiG 70 
                                       +  il+nlL NA+   ++      +I+l+v+++++++ +s+  +  g           + k+l s   +k +  G+G
  gi|298674344|ref|YP_003726094.1| 731 IKQILSNLLYNAVKFTEEG-----SITLEVSQNEDDVQFSVIDTGIGipkgsheaifdSFKQLDSGpARKYQGTGLG 802
                                       67899******99776665.....5******************9777666666555542266665556788999*** PP

                       HATPase_c_5  71 lksireivkkykgnlsieae 90 
                                       l  ++++v+ ++g++++e e
  gi|298674344|ref|YP_003726094.1| 803 LALVNKLVNMHGGQIWVESE 822
                                       ***************99876 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0026       2.9       8     114 ..      61     173 ..      55     174 .. 0.70
   2 !    6.3   0.0    0.0093        10       8      49 ..     368     408 ..     361     474 .. 0.82
   3 ?   -1.6   0.0       2.7     3e+03       8      35 ..     494     521 ..     488     572 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0026
                             PAS_7   8 isvfDadlrLvawNrrylelldlpeelvqvgvpleellryn.aer.gefgagdveaeverrlaaaragkphsferer 82 
                                       i+ +D++++++  N+   ++l+l+++ ++  ++++++   +     ++f +++   e+ +  ++   + +h++e + 
  gi|298674344|ref|YP_003726094.1|  61 ITHLDKSGNIIYANHTAEKVLGLSKNDINR-RTYDDVKWKItDYDgNDFPQDELPFELVKKYHQPVYDVQHAIEWKN 136
                                       677899999999999999999999999944.4444443333133303344444333333333344458999*****9 PP

                             PAS_7  83 pdgrvievrgnpl.....pdgGfVttytDiTerrrae 114
                                        +   +++++ p+        G+++  +DiT+++++e
  gi|298674344|ref|YP_003726094.1| 137 GKRIYLSINAAPIfdkygNFDGMIAAIEDITKQKNTE 173
                                       9999*********65554457*************987 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0093
                             PAS_7   8 isvfDadlrLvawNrrylelldlpeelvqvgvpleellryna 49 
                                       i+ +D+++ +v +N+++ ++l++ +e v +g +++++++   
  gi|298674344|ref|YP_003726094.1| 368 ITSVDENGTIVDCNNQIKNILGYEKEEV-IGQSMTKIIHPDY 408
                                       6779**********************99.9999999997555 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.7
                             PAS_7   8 isvfDadlrLvawNrrylelldlpeelv 35 
                                       i+ +D d++++ +N+  +e l+++++ +
  gi|298674344|ref|YP_003726094.1| 494 IIAYDFDGNILYVNNLACEKLGYTKNEL 521
                                       5566667777777766666666655433 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.4e-05     0.038      35     110 ..     734     811 ..     716     822 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.4e-05
                       HATPase_c_2  35 aveEactNavehayleapegpvevrlesdeealtvevaDsGpg.fdpe.tlpdpteeep....keslkegGrGlali 105
                                        ++ +++Nav+       eg+++++++++e+ ++++v D G g  + + ++  +  +++    + + +  G+Glal+
  gi|298674344|ref|YP_003726094.1| 734 ILSNLLYNAVKFTE----EGSITLEVSQNEDDVQFSVIDTGIGiPKGShEAIFDSFKQLdsgpARKYQGTGLGLALV 806
                                       45555666666665....59*********************9965544222222222226777999*********** PP

                       HATPase_c_2 106 kglvD 110
                                       ++lv+
  gi|298674344|ref|YP_003726094.1| 807 NKLVN 811
                                       ***96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (837 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1094  (0.0610185); expected 358.6 (0.02)
Passed bias filter:                      631  (0.0351944); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.85u 0.32s 00:00:01.17 Elapsed: 00:00:00.50
# Mc/sec: 5020.55
//
Query:       gi|298674345|ref|YP_003726095.1|  [L=162]
Description: hypothetical protein Metev_0377 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.1e-14   51.8  11.6    4.8e-10   39.9   1.7    2.4  2  VCBS      Repeat domain in Vibrio, Colwellia, Bradyrhizobium 
    3.6e-06   27.0   4.1      0.011   15.8   0.0    2.8  3  FG-GAP    FG-GAP repeat


Domain annotation for each model (and alignments):
>> VCBS  Repeat domain in Vibrio, Colwellia, Bradyrhizobium and Shewanella
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   1.7   5.3e-14   4.8e-10       1      60 [.      60     117 ..      60     118 .. 0.90
   2 !   23.6   2.8   6.4e-09   5.7e-05       1      34 [.     107     140 ..     107     157 .. 0.80

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 5.3e-14
                              VCBS   1 DldgDGrlDlvvandgglrvyrnngdGtftdvtktslggsgggt.gvavgDlDgDGdlDll 60 
                                       D+++DG  D+vv   g +++y+++ +G+f+    ++++++ ++t ++ v D+++DG  D++
  gi|298674345|ref|YP_003726095.1|  60 DINNDGIKDIVVYKHGVNYLYEGTETGKFEG---YKIHDNSDHTnSLSVCDINRDGNNDIM 117
                                       9***************************985...778886666658*************97 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 6.4e-09
                              VCBS   1 DldgDGrlDlvvandgglrvyrnngdGtftdvtk 34 
                                       D++ DG  D+ ++ndg +++y+++g+G ft   +
  gi|298674345|ref|YP_003726095.1| 107 DINRDGNNDIMAGNDGINYWYEGDGTGEFTRNVA 140
                                       9****************************95433 PP

>> FG-GAP  FG-GAP repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1      0.73   6.5e+03       4      11 ..      21      29 ..      18      30 .. 0.72
   2 !   15.8   0.0   1.3e-06     0.011       3      20 ..      54      71 ..      52      80 .. 0.91
   3 !   12.0   0.4     2e-05      0.18       3      26 ..     101     120 ..      99     134 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.73
                                      SEEEE.STS CS
                            FG-GAP  4 slavg.DvN 11
                                      s++++ D+N
  gi|298674345|ref|YP_003726095.1| 21 SATTAdDIN 29
                                      667776988 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.3e-06
                                      SSEEEESTSSSSS-EEEE CS
                            FG-GAP  3 yslavgDvNGDGyaDLav 20
                                       sl+v+D+N+DG  D++v
  gi|298674345|ref|YP_003726095.1| 54 RSLSVTDINNDGIKDIVV 71
                                      69**************98 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 2e-05
                                       SSEEEESTSSSSS-EEEEEETT-E CS
                            FG-GAP   3 yslavgDvNGDGyaDLavGApesk 26 
                                       +sl+v D+N DG  D+  G    +
  gi|298674345|ref|YP_003726095.1| 101 NSLSVCDINRDGNNDIMAG----N 120
                                       699999**********999....3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1098.65
//
Query:       gi|298674346|ref|YP_003726096.1|  [L=438]
Description: HNH endonuclease [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-69  233.4   1.2      2e-69  232.9   1.2    1.2  1  RRXRR            RRXRR protein
    7.6e-15   54.5   0.9    1.5e-14   53.6   0.9    1.5  1  HNH_5            HNH endonuclease
    1.3e-11   44.2   0.2    3.9e-11   42.7   0.2    1.9  1  HNH_4            HNH endonuclease
    1.6e-11   44.2   1.6    1.6e-11   44.2   1.6    2.2  2  HNH              HNH endonuclease
  ------ inclusion threshold ------
      0.014   14.5   0.0      0.024   13.7   0.0    1.3  1  Glyco_hydro_67M  Glycosyl hydrolase family 67 middle domain
      0.015   15.0   0.2       0.19   11.5   0.1    2.5  2  SH3_2            Variant SH3 domain
      0.067   13.3   0.4        8.2    6.6   0.2    2.7  2  zf-CHCC          Zinc-finger domain
        0.1   12.6   0.0        0.1   12.6   0.0    2.5  2  HLH              Helix-loop-helix DNA-binding domain


Domain annotation for each model (and alignments):
>> RRXRR  RRXRR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  232.9   1.2   8.9e-73     2e-69       1     174 []       2     175 ..       2     175 .. 0.98

  Alignments for each domain:
  == domain 1  score: 232.9 bits;  conditional E-value: 8.9e-73
                             RRXRR   1 VfVldkegkplmPtkpkrarklLkqgkAkvvrrkpftiqLkeesseesvqpvelklDpGskvtGiavvsek.kvllk 76 
                                       VfVl+k++kpl+P++p++ar+lLk gkA++++++pfti+Lke +s++  ++++lk+D Gs++tG+a+ +++ +v++ 
  gi|298674346|ref|YP_003726096.1|   2 VFVLNKNKKPLTPCHPAKARILLKAGKATIHKKYPFTIRLKELKSDDVKDDFRLKIDYGSRYTGLAILKNNkDVIWL 78 
                                       9***********************************************9******************965549**** PP

                             RRXRR  77 aelelrgkdikkkleeRrelRraRRsrktryrqaRfdnRkkkegwLapslqhrvqthlrvvkrlakllpitkivvel 153
                                        ++++r+ dikkkl++Rr++Rr+RRs+++ryr++RfdnRkk+egwL+pslq+rv+++ ++++rl++l+pi+ +++e 
  gi|298674346|ref|YP_003726096.1|  79 DQVHHRT-DIKKKLDDRRNFRRRRRSQNLRYRKPRFDNRKKPEGWLPPSLQSRVDNIQTWITRLRELVPINCLSYEN 154
                                       ******9.********************************************************************* PP

                             RRXRR 154 vkfDiqklenpeisgaeyqqG 174
                                       v+fD+q ++npei+g+eyqqG
  gi|298674346|ref|YP_003726096.1| 155 VNFDTQLMQNPEIKGVEYQQG 175
                                       ********************9 PP

>> HNH_5  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   0.9   6.6e-18   1.5e-14       1      52 [.     194     243 ..     194     246 .. 0.94

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 6.6e-18
                             HNH_5   1 CiyCgkeiaekelseeHIiPeslGGkltisnlvtlCkkCNqkkgqkvdaals 52 
                                       C+yCgk+  + +l++eHI+P+s+GG++ +snl+ +C +CNq+k + + ++++
  gi|298674346|ref|YP_003726096.1| 194 CAYCGKQ--DVQLEIEHIVPRSRGGSNRVSNLTIACHDCNQRKSNLTAEEFG 243
                                       *******..999*******************************999888886 PP

>> HNH_4  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.2   1.7e-14   3.9e-11      17      53 ..     202     238 ..     194     240 .. 0.87

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 1.7e-14
                                       ..SEEEESSTTTT---BSGGGEEEES-GGGGTSSSSS CS
                             HNH_4  17 keydiDHilPrsrskdDsvsNkVLvlrdaNqeKsnrt 53 
                                        +++i+Hi+Prsr+  + vsN++++++d+Nq Ksn t
  gi|298674346|ref|YP_003726096.1| 202 VQLEIEHIVPRSRGGSNRVSNLTIACHDCNQRKSNLT 238
                                       479********************************87 PP

>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       1.2   2.6e+03      15      26 ..      80      91 ..      74      97 .. 0.74
   2 !   44.2   1.6   7.1e-15   1.6e-11       1      46 [.     194     236 ..     194     237 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.2
                               HNH 15 evdHiipisqgg 26
                                      +v+H   i+++ 
  gi|298674346|ref|YP_003726096.1| 80 QVHHRTDIKKKL 91
                                      79**99999644 PP

  == domain 2  score: 44.2 bits;  conditional E-value: 7.1e-15
                               HNH   1 CeyCgrkfhksealevdHiipisqggaddieNlqllCksCHnkkhd 46 
                                       C yCg+++    +le+ Hi+p+s+gg++  +Nl+ +C +C+++k++
  gi|298674346|ref|YP_003726096.1| 194 CAYCGKQD---VQLEIEHIVPRSRGGSNRVSNLTIACHDCNQRKSN 236
                                       9******7...579******************************87 PP

>> Glyco_hydro_67M  Glycosyl hydrolase family 67 middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.1e-05     0.024      60     116 ..     138     194 ..     113     204 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.1e-05
                                       HHHHHHTTT--EEE-S-SS--GGGGSHHHHHHHHHHHHHHGGGT-EEEEEE-TTHHH CS
                   Glyco_hydro_67M  60 yarllasvgingvvlnnvnakaklltkeylekvaaladvlrpygikvylsvnfaapi 116
                                        +rl   v in +  +nvn +++l+++  ++ v+     l+ y+++ yl  +f+   
  gi|298674346|ref|YP_003726096.1| 138 ITRLRELVPINCLSYENVNFDTQLMQNPEIKGVEYQQGTLQGYNVREYLLEKFQRTC 194
                                       5789999******************************************99998665 PP

>> SH3_2  Variant SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.25   5.5e+02      10      27 ..     309     326 ..     304     342 .. 0.74
   2 ?   11.5   0.1   8.4e-05      0.19      17      51 ..     356     390 ..     339     392 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.25
                                       SCGCCB--B-TTEEEEEE CS
                             SH3_2  10 gedkseLsfkkGdvikvl 27 
                                        + ++eL+fk + v+++ 
  gi|298674346|ref|YP_003726096.1| 309 ESTPDELRFKTNSVLHIH 326
                                       356777****99999986 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 8.4e-05
                                       -B-TTEEEEEE..EEEECTTEEEEEE.CCCEEEEEG CS
                             SH3_2  17 sfkkGdvikvlslgskdsdgwwegev.gGrvGlfPs 51 
                                        f+ Gd+ik++ + + +  g w+g+v  +  G+f +
  gi|298674346|ref|YP_003726096.1| 356 GFQSGDIIKAI-VEKGKYKGTWKGAVaCRSNGYFDI 390
                                       69*********.444455566*****99999**965 PP

>> zf-CHCC  Zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.2    0.0036       8.2      24      35 ..     188     199 ..     183     200 .. 0.85
   2 ?    3.7   0.0      0.03        67      11      19 ..     240     248 ..     225     256 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0036
                                       TTSEEEETTTTE CS
                           zf-CHCC  24 kkgpvdCgYCgl 35 
                                       +k + +C YCg+
  gi|298674346|ref|YP_003726096.1| 188 EKFQRTCAYCGK 199
                                       68899******7 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.03
                                       TTSEEEEEE CS
                           zf-CHCC  11 galGHPrvy 19 
                                       +++GHP vy
  gi|298674346|ref|YP_003726096.1| 240 EEFGHPEVY 248
                                       679*****9 PP

>> HLH  Helix-loop-helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -6.9   6.1         8   1.8e+04      10      20 ..      98     108 ..      95     110 .. 0.77
   2 ?   12.6   0.0   4.5e-05       0.1      11      29 ..     129     154 ..     128     200 .. 0.83

  Alignments for each domain:
  == domain 1  score: -6.9 bits;  conditional E-value: 8
                                       HHHHHHHHHHH CS
                               HLH  10 rrRRdriNsal 20 
                                       rrRR++ N ++
  gi|298674346|ref|YP_003726096.1|  98 RRRRRSQNLRY 108
                                       78888888665 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 4.5e-05
                                       HHHHHHHHHHHHHHHCST.......C CS
                               HLH  11 rRRdriNsaleeLrellP.......s 29 
                                        R+d+i +++ +Lrel+P       +
  gi|298674346|ref|YP_003726096.1| 129 SRVDNIQTWITRLRELVPinclsyeN 154
                                       6*****************76655550 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2951.39
//
Query:       gi|298674347|ref|YP_003726097.1|  [L=370]
Description: hypothetical protein Metev_0380 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0013   18.2   0.0      0.033   13.7   0.0    2.5  2  TcfC           E-set like domain
  ------ inclusion threshold ------
      0.016   15.9   0.4        1.2    9.8   0.1    2.6  2  Glyco_hydro_2  Glycosyl hydrolases family 2


Domain annotation for each model (and alignments):
>> TcfC  E-set like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.021   1.9e+02      45      66 ..     104     125 ..     102     126 .. 0.91
   2 !   13.7   0.0   3.7e-06     0.033      39      64 ..     298     324 ..     293     327 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.021
                              TcfC  45 iYeveirvyengqvvrteqqkf 66 
                                       +Y+v  r+++n+ +v +++  f
  gi|298674347|ref|YP_003726097.1| 104 SYKVSARLIQNSSIVDSKNHSF 125
                                       7**************9999876 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 3.7e-06
                              TcfC  39 ssLPsGiYeveirvye.ngqvvrteqq 64 
                                       ++LP+GiY++++++++ +g ++ ++++
  gi|298674347|ref|YP_003726097.1| 298 NTLPKGIYKLTVELVGnDGDLIDKKET 324
                                       58**************55555555444 PP

>> Glyco_hydro_2  Glycosyl hydrolases family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0      0.01        89      30     107 ..      54     125 ..      27     128 .. 0.64
   2 ?    9.8   0.1   0.00014       1.2      51     106 ..     272     325 ..     226     326 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.01
                                       CSSSSCEEEEEEEEETTSTEEEEEEEEEEEESTT-EEEEEEEEEES--BBECCCB-..-EEEEEEEEETTEEEEEEE CS
                     Glyco_hydro_2  30 sdksvevtleteikdaegkkvkeessvlslgngetksiklelevknpklWspetPn..LYtlkveldkdgkvidevs 104
                                       +++ +++ l+ +++d+++ +  ++   + + ++e k+i++         W+  +P    Y++ ++l ++ +++d+++
  gi|298674347|ref|YP_003726097.1|  54 ETTIQNLILSLQLFDDGNFVDEKRLF-IDELEPESKNIRV-------VSWDIKNPDesSYKVSARLIQNSSIVDSKN 122
                                       44444555555555444433333333.3333344444433.......689999987668*******99999***997 PP

                                       EEE CS
                     Glyco_hydro_2 105 trf 107
                                       ++f
  gi|298674347|ref|YP_003726097.1| 123 HSF 125
                                       766 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00014
                                       EE....EEEEEEEESTT-EEEEEEEEEES--BBECCCB-.-EEEEEEE.EETTEEEEEEEEE CS
                     Glyco_hydro_2  51 ke....essvlslgngetksiklelevknpklWspetPn.LYtlkvel.dkdgkvidevstr 106
                                       k      ++  +l  ge+++++          W+   P+  Y+l+vel  +dg+ id+++t 
  gi|298674347|ref|YP_003726097.1| 272 KVvesaVKKSPVLLDGEDETVE--------VIWNNTLPKgIYKLTVELvGNDGDLIDKKETI 325
                                       2222334444444444454444........69******99******************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2388.76
//
Query:       gi|298674348|ref|YP_003726098.1|  [L=385]
Description: hypothetical protein Metev_0381 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-13   52.0   1.4    1.1e-13   52.0   1.4    2.0  2  MacB_PCD  MacB-like periplasmic core domain
    2.8e-13   50.1   4.0    2.8e-13   50.1   4.0    2.5  3  FtsX      FtsX-like permease family


Domain annotation for each model (and alignments):
>> MacB_PCD  MacB-like periplasmic core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.0   1.4   1.2e-17   1.1e-13       1     191 [.      19     225 ..      19     229 .. 0.73
   2 ?   -1.0   0.8      0.21   1.9e+03       8      32 ..     256     280 ..     256     303 .. 0.82

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 1.2e-17
                          MacB_PCD   1 slltvLGiaiGvaaviaivslgeglqasvlsqisdlgnlvtvtpgkgsgeslsdpdve.alrr..evp.veavapvv 73 
                                       ++l+v +i i+v+ +++  ++++g+++ + ++    + l++vt+++ +g++    +++ ++    +++ v++v+p++
  gi|298674348|ref|YP_003726098.1|  19 TFLSVGAIGIAVMMIVISQGFMAGFTEELYDTTV--DELAHVTISPEDGNN-YIHLYKnLINSvgKIEgVTGVSPYL 92 
                                       89*****************************876..778899998744444.2222332222133466799999998 PP

                          MacB_PCD  74 .....tvrgggsgeeevtvvg.vdpdyfkvfgl..klaeGrffteadlrggpnvvvigeelaerlf.pvGdtirl.. 139
                                            +++ ++  +++v + g v + + +v ++  ++ +G   ++++l+  +n++v+g++l  ++  ++Gd++    
  gi|298674348|ref|YP_003726098.1|  93 tgeaiVKHKDD--TQNVILKGiVPERETEVSQInrDIIKG---NFSELKYTKNSIVVGDDLLPEINaKIGDVVDAsf 164
                                       77653223333..677999**9555999999997555779...45899999*************7899*****9999 PP

                          MacB_PCD 140 .....kpftVvGvledppgsgsalgddavylplttlqrrs........itvrlkdgadleaaaae 191
                                            +++++vGv+ d+ g  s+ ++d +y++l+t+q  +        + +r+++  +  ++a+ 
  gi|298674348|ref|YP_003726098.1| 165 pdanpVSLKIVGVY-DT-G--SDDDRDLIYTSLKTAQDFYgtsdvvngVSLRIRNVNNDRKIADN 225
                                       ***9999*******.43.4..3445777****888743334445555577777666665555555 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.21
                          MacB_PCD   8 iaiGvaaviaivslgeglqasvlsq 32 
                                       i++G  ++ia +++++ l+ +vl+ 
  gi|298674348|ref|YP_003726098.1| 256 IMLGLIVIIASFGVVSNLNMTVLEK 280
                                       7999999999999999988777765 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.37   3.3e+03      16      43 ..      29      35 ..      16      63 .. 0.56
   2 ?   -0.8   0.1      0.25   2.3e+03      22      39 ..     252     269 ..     233     277 .. 0.62
   3 !   50.1   4.0   3.1e-17   2.8e-13       1      96 []     281     379 ..     281     379 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.37
                              FtsX 16 qvlllllteillitlvalviGlglglla 43
                                       v+                      +++
  gi|298674348|ref|YP_003726098.1| 29 AVM---------------------MIVI 35
                                      111.....................2222 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.25
                              FtsX  22 lteillitlvalviGlgl 39 
                                       ++ +++++l+ +++++g+
  gi|298674348|ref|YP_003726098.1| 252 MSNNIMLGLIVIIASFGV 269
                                       444444444444444443 PP

  == domain 3  score: 50.1 bits;  conditional E-value: 3.1e-17
                              FtsX   1 kreigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfs...selkisidlitvliiiv 74 
                                       k+eigi+ra+Gm k  ++l++++e+ +++l+++v G+++g+++a  + ++          +++++ + +++v i++ 
  gi|298674348|ref|YP_003726098.1| 281 KKEIGIFRAMGMGKSNIRLIFILESGILGLIGAVTGTIFGIIIALSIGNYPIPAGLYgglTSIPVVVRPLDVTITVT 357
                                       79******************************************9999998888554568***************** PP

                              FtsX  75 lllllallagllsiskilkkep 96 
                                        ++ll l+ag++++ k++  +p
  gi|298674348|ref|YP_003726098.1| 358 AVFLLNLIAGVYPAHKAASLNP 379
                                       ****************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2520.48
//
Query:       gi|298674349|ref|YP_003726099.1|  [L=388]
Description: hypothetical protein Metev_0382 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-16   59.8   3.9    2.8e-16   59.8   3.9    3.0  3  FtsX      FtsX-like permease family
    2.5e-14   54.1   0.4    3.8e-14   53.5   0.4    1.2  1  MacB_PCD  MacB-like periplasmic core domain
  ------ inclusion threshold ------
        1.3    8.8  10.9       0.83    9.5   7.0    2.0  2  CbiM      Cobalt uptake substrate-specific transmembrane regi


Domain annotation for each model (and alignments):
>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.6     0.054   3.3e+02      64      84 ..      20      40 ..      11      51 .. 0.61
   2 ?    0.8   0.8      0.12     7e+02      20      47 ..     250     277 ..     241     280 .. 0.78
   3 !   59.8   3.9   4.6e-20   2.8e-16       1      96 []     281     381 ..     281     381 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.054
                              FtsX 64 idlitvliiivlllllallag 84
                                      +++++v+++i+++++l+++++
  gi|298674349|ref|YP_003726099.1| 20 FSVLSVALAIAMIVVLMSMVS 40
                                      444555555555555555553 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.12
                              FtsX  20 lllteillitlvalviGlglgllaaqll 47 
                                       +l+  ++l+tl+ + +G+g+++ ++ ++
  gi|298674349|ref|YP_003726099.1| 250 QLVFSWILYTLIYITAGFGIANTLITVV 277
                                       6777888999999999988888777665 PP

  == domain 3  score: 59.8 bits;  conditional E-value: 4.6e-20
                              FtsX   1 kreigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfs.....selkisidlitvlii 72 
                                       kreig+l+a+G+++ ++ll++++e+ +++  + ++G++lg+l+a l+ ++  ++ +      + l+++i ++ ++ +
  gi|298674349|ref|YP_003726099.1| 281 KREIGMLKAMGATRSSILLIFISESTILGTAGVLSGCILGYLLAALIDAYSIQIPSEvylglTTLPVNIEIMNFVYA 357
                                       79********************************************8888888855456668*************** PP

                              FtsX  73 ivlllllallagllsiskilkkep 96 
                                        v+++++ ++ag++++ +++k +p
  gi|298674349|ref|YP_003726099.1| 358 TVFAFIINIIAGVYPANRAAKLDP 381
                                       ********************9987 PP

>> MacB_PCD  MacB-like periplasmic core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.4   6.4e-18   3.8e-14       1     189 [.      18     222 ..      18     228 .. 0.69

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 6.4e-18
                          MacB_PCD   1 slltvLGiaiGvaaviaivslgeglqasvlsqisdlgnlvtvtpgkgsgesls..dpdve.alrrevp.veavapvv 73 
                                       s+++vL++a+++a +++++s+++g++  + ++ ++++  ++v+p +   +++   +++++ +++++ + v+a +p+ 
  gi|298674349|ref|YP_003726099.1|  18 SIFSVLSVALAIAMIVVLMSMVSGFRIELIDSTTENSPHIIVNPES--DDEFIhlYRHLDkIIKQH-EgVVATSPYF 91 
                                       6789***********************9999988555534455543..333221245565333444.46999***98 PP

                          MacB_PCD  74 ....tvrgggsgeeevtvvgvdpdyfk.vfgl..klaeGrffteadlrggpnvvvigeelaerlf.pvGdtirl... 139
                                           +  + ++ + +v + gv+pd    v  +  ++ +G+f   +dl + +n++++g++lae+l   +G+++     
  gi|298674349|ref|YP_003726099.1|  92 ekqvALDYKDN-SHGVKLKGVNPDAEMnVMHVddDIIKGSF---TDLSTIRNGIILGDKLAENLEvDLGERVDAssp 164
                                       88542234432.555999**887544446777644588954...88999999***********8899*****99999 PP

                          MacB_PCD 140 ....kpftVvGvledppgsgsalgddavylplttlqrrs........itvrlkdgadleaaa 189
                                           ++f+VvG++++  g+    +++ +y  l ++q  s        i vr++d  +++ +a
  gi|298674349|ref|YP_003726099.1| 165 vsgsVSFKVVGIMDT--GTP--KDETLAYSKLDDVQDFSdendvvtgIGVRVQDIYQADNIA 222
                                       9*9999*******55..322..2355666665554322234456666888888877776665 PP

>> CbiM  Cobalt uptake substrate-specific transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1     0.065   3.9e+02     134     158 ..      14      38 ..       2      57 .. 0.54
   2 ?    9.5   7.0   0.00014      0.83       8     131 ..     254     371 ..     245     381 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.065
                              CbiM 134 kkrvalaaflaallsvvlaallval 158
                                       ++r ++ ++l+ +l++ + ++l+++
  gi|298674349|ref|YP_003726099.1|  14 RRRHSIFSVLSVALAIAMIVVLMSM 38 
                                       3344444444444444444444333 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00014
                              CbiM   8 spavllaayavalallalalrrlrkeldearvpllallaafifaaqminipipggtslHllgavlaaiLlGpwaafl 84 
                                       s+ ++ + y+ a++++a  l  +  e +++++ +l++++a    + +i i+    +++  + +vl + +lG+ +a+l
  gi|298674349|ref|YP_003726099.1| 254 SWILYTLIYITAGFGIANTLITVVME-KKREIGMLKAMGATRSSILLIFISE---STILGTAGVLSGCILGYLLAAL 326
                                       33333333333333333333333333.3455999999999999999998888...88888889999*****999999 PP

                              CbiM  85 avavvlllqallfgdGGitaLGaNilnmavigvllaylvyrllsrla 131
                                       + a  + + + +    G+t+L +Ni +m+++ + ++ ++  ++ + +
  gi|298674349|ref|YP_003726099.1| 327 IDAYSIQIPSEV--YLGLTTLPVNIEIMNFVYATVFAFIINIIAGVY 371
                                       999998888886..89*********************9999776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.25s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2519.66
//
Query:       gi|298674350|ref|YP_003726100.1|  [L=226]
Description: ABC transporter-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-35  121.2   0.0    6.7e-35  120.6   0.0    1.3  1  ABC_tran         ABC transporter
    8.2e-09   35.2   0.4      3e-07   30.1   0.4    2.1  1  SMC_N            RecF/RecN/SMC N terminal domain
    1.2e-08   35.2   0.5    0.00091   19.1   0.3    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    2.3e-05   24.0   0.3    4.9e-05   23.0   0.3    1.5  1  AAA_29           P-loop containing region of AAA domain
    0.00085   19.6   0.3     0.0076   16.5   0.3    2.1  1  AAA_22           AAA domain
     0.0012   18.6   0.2     0.0063   16.3   0.1    1.8  2  AAA_15           AAA ATPase domain
     0.0035   16.9   0.0       0.29   10.7   0.1    2.4  2  AAA_25           AAA domain
     0.0038   17.8   1.4     0.0067   16.9   0.4    1.8  2  AAA_23           AAA domain
     0.0038   17.1   0.1     0.0083   16.0   0.1    1.6  1  RsgA_GTPase      RsgA GTPase
     0.0044   17.4   0.0     0.0081   16.6   0.0    1.6  1  AAA_16           AAA ATPase domain
     0.0055   16.6   0.1      0.023   14.6   0.1    2.0  1  Rad17            Rad17 P-loop domain
     0.0067   15.8   0.0      0.011   15.1   0.0    1.3  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0095   15.7   0.1       0.17   11.6   0.0    2.1  2  AAA_30           AAA domain
  ------ inclusion threshold ------
      0.016   14.6   0.9        2.5    7.4   0.1    2.6  3  ATPase           KaiC
       0.02   15.1   0.6      0.089   12.9   0.6    2.0  1  AAA_33           AAA domain
      0.021   14.5   0.0       0.17   11.6   0.0    2.1  2  IstB_IS21        IstB-like ATP binding protein
      0.043   12.6   0.0      0.058   12.2   0.0    1.3  1  T4SS-DNA_transf  Type IV secretory system Conjugative DNA tra
      0.047   12.4   0.0      0.063   12.0   0.0    1.2  1  RNA12            RNA12 protein
      0.067   13.7   0.0       0.33   11.5   0.0    2.1  2  AAA_18           AAA domain
      0.082   12.8   0.1       0.29   11.1   0.1    1.9  2  NACHT            NACHT domain
      0.096   13.0   0.1       0.15   12.4   0.1    1.4  1  PIN_4            PIN domain
      0.099   12.9   0.0        0.8    9.9   0.0    2.1  2  AAA_28           AAA domain
       0.11   12.1   0.2       0.14   11.7   0.2    1.6  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
       0.11   12.2   0.1       0.39   10.4   0.0    1.9  2  AAA_24           AAA domain
       0.17   11.0   0.7       0.34   10.1   0.2    1.6  2  NB-ARC           NB-ARC domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.6   0.0   9.4e-38   6.7e-35       1     136 [.      25     173 ..      25     174 .. 0.91

  Alignments for each domain:
  == domain 1  score: 120.6 bits;  conditional E-value: 9.4e-38
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpe 73 
                                       l+ v+l++k+ge +aivG++G+GKStLl +l  l +pt+G+i +d+k++++    ++ +  +k +g+++q ++l p+
  gi|298674350|ref|YP_003726100.1|  25 LDGVNLTIKHGEFMAIVGPSGSGKSTLLHILGILDTPTQGSIIIDNKNITSmsdkERSKARNKMLGFIFQYHNLLPD 101
                                       789***********************************************999977777888889************ PP

                                       SBHHHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                        t+ en             e++e ++++l+++gl++    +++++p +LSgGq qrv++aral+++p++++ DEpt
  gi|298674350|ref|YP_003726100.1| 102 FTALENvmipllisgysknEAKESAQNMLKEVGLED----RMYHKPGELSGGQNQRVSVARALVNNPTIVIGDEPT 173
                                       ***************876666666888888888777....556777*****************************9 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.4   4.2e-10     3e-07      21     210 ..      33     217 ..      19     223 .. 0.62

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 4.2e-10
                                       ETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--.......BTTCSSTTEEEEEEEEEETTEES CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  21 pfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk.......skekasvkkaeveitfdnedkkl 90 
                                       + + +f aivGp GSGKs ll     +LG  ++     ++ s +i +        ke++++ +  +  +f+ ++   
  gi|298674350|ref|YP_003726100.1|  33 K-HGEFMAIVGPSGSGKSTLLH----ILGILDT----PTQGSIIIDNknitsmsDKERSKARNKMLGFIFQYHNLL- 99 
                                       4.4469************9875....4554444....222222332222221223455555555666666666665. PP

                                       SSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  91 kiekeevsisrrvkrkgeseykingkevtkkevsellesagiske......lLSgGektLvalaLlfAiqkvkpapl 161
                                       +  +   +++  +  +g s+ +       k+  +++l+++g++        +LSgG+ + v++a       v+   +
  gi|298674350|ref|YP_003726100.1| 100 PDFTALENVMIPLLISGYSKNEA------KESAQNMLKEVGLEDRmyhkpgELSGGQNQRVSVARA----LVNNPTI 166
                                       33333333444444444433333......33344444444444444444449******99988754....4677789 PP

                                       EEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-SCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 162 yllDeidaaLDeknvkkvaellkekskn..aQfivislreemlekadklvg 210
                                       ++ De   +LD k   ++ ell++ + +    fi ++++e+m +k d++ +
  gi|298674350|ref|YP_003726100.1| 167 VIGDEPTGNLDTKTSDRIYELLRKLNRErgQTFILVTHDENMAKKTDRIER 217
                                       999********************776554355899**********999866 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.3   1.3e-06   0.00091       1      24 [.      37      59 ..      37      93 .. 0.73
   2 !   14.8   0.0   2.7e-05     0.019     254     298 ..     159     205 ..      69     209 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.3e-06
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllar 24
                                      +++++Gp gsGKS+LL +l +l +
  gi|298674350|ref|YP_003726100.1| 37 FMAIVGPSGSGKSTLLHILGIL-D 59
                                      789****************888.2 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 2.7e-05
                            AAA_21 254 alkkg.sllliDEpEngLHPkllrrllellkelsrngaQv.iltTHS 298
                                       al  + ++++ DEp  +L+ k   r++ell++l+r+++Q  il+TH+
  gi|298674350|ref|YP_003726100.1| 159 ALVNNpTIVIGDEPTGNLDTKTSDRIYELLRKLNRERGQTfILVTHD 205
                                       44444155555*******************99999777777*****8 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.3   6.8e-08   4.9e-05      12      39 ..      25      52 ..      23      66 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 6.8e-08
                            AAA_29 12 fdghtieidlkgatlltGpsGsGKSTll 39
                                      +dg  ++i+  +++ ++GpsGsGKSTll
  gi|298674350|ref|YP_003726100.1| 25 LDGVNLTIKHGEFMAIVGPSGSGKSTLL 52
                                      577888999666***************9 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.3   1.1e-05    0.0076       4      24 ..      34      54 ..      30     211 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.1e-05
                            AAA_22  4 tagilvvtGesGtGKTtllrr 24
                                      +  +++++G+sG+GK+tll  
  gi|298674350|ref|YP_003726100.1| 34 HGEFMAIVGPSGSGKSTLLHI 54
                                      7889**************975 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   8.8e-06    0.0063      19      74 ..      32      82 ..       7      93 .. 0.77
   2 ?   -0.7   0.0       1.2   8.8e+02     326     368 ..     166     208 ..     157     209 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.8e-06
                            AAA_15 19 idlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifenises 74
                                      i+     ++ ++G+ +sGKS++l++l ++ + +    +  i i+++++  + ++++s
  gi|298674350|ref|YP_003726100.1| 32 IKH--GeFMAIVGPSGSGKSTLLHILGILDTPT----QGSIIIDNKNITSMSDKERS 82
                                      333..259******************9998877....56677777777766666655 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.2
                            AAA_15 326 illiEEPEahLHpqaqkvlikllkelandnktQviitTHSphi 368
                                       i++ +EP  +L ++    +++ll++l ++  +  i+ TH + +
  gi|298674350|ref|YP_003726100.1| 166 IVIGDEPTGNLDTKTSDRIYELLRKLNRERGQTFILVTHDENM 208
                                       5555677777777777777888888888887566789999887 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1    0.0004      0.29      30      50 ..      32      52 ..      25      58 .. 0.88
   2 ?    3.6   0.0     0.059        42     162     188 ..     177     204 ..     167     209 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0004
                            AAA_25 30 lpagelallaGapgtGKttla 50
                                      +  ge+ +++G++g+GK+tl+
  gi|298674350|ref|YP_003726100.1| 32 IKHGEFMAIVGPSGSGKSTLL 52
                                      6789***************97 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.059
                            AAA_25 162 nsdv.galvealeriarrtgaavllvhH 188
                                       ++++ ++++e l+++ r+ g +++lv H
  gi|298674350|ref|YP_003726100.1| 177 DTKTsDRIYELLRKLNRERGQTFILVTH 204
                                       4445699********************9 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.4   9.4e-06    0.0067       2      37 ..       7      53 ..       7      57 .. 0.67
   2 ?   -1.2   0.0       3.5   2.5e+03     116     116 ..     180     180 ..     113     221 .. 0.54

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 9.4e-06
                            AAA_23  2 Lkienfrsf..rdqeidF.........skgltlItGpNGaGKTTild 37
                                      ++i+n++++  +++e+           +  + +I+Gp G+GK+T+l 
  gi|298674350|ref|YP_003726100.1|  7 IEIKNLNKIysDGTEVKAldgvnltikHGEFMAIVGPSGSGKSTLLH 53
                                      67888888887455565523233344333456*************96 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.5
                            AAA_23 116 e 116
                                       +
  gi|298674350|ref|YP_003726100.1| 180 T 180
                                       1 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   1.2e-05    0.0083      86     119 ..      21      55 ..       3      77 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.2e-05
                                       THTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHH CS
                       RsgA_GTPase  86 tkegleelkellkd.ktsvlvGqSGvGKStLinal 119
                                       + ++l+ ++  +k+ +++++vG+SG GKStL+  l
  gi|298674350|ref|YP_003726100.1|  21 EVKALDGVNLTIKHgEFMAIVGPSGSGKSTLLHIL 55 
                                       45666677777777799**************9876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.1e-05    0.0081      20      63 ..      33      75 ..      19     206 .. 0.51

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.1e-05
                            AAA_16 20 rsgrpelvllsGesGvGKsslvrellralekd..ggiflrgkcdql 63
                                      + g  e + ++G+sG+GKs+l+  l   l +   g i +  k+  +
  gi|298674350|ref|YP_003726100.1| 33 KHG--EFMAIVGPSGSGKSTLLHILG-ILDTPtqGSIIIDNKNITS 75
                                      444..7899*************5443.5554444344444444444 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   3.2e-05     0.023      34      86 ..      24      80 ..      20     214 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.2e-05
                             Rad17 34 wlkadvLesrkkriLLisGPsGCgkstvvkvLsk....elgiklrewlnpvslkepd 86
                                      +l+   L  ++ + + i GPsG gkst +++L        g  ++++ n +s+ + +
  gi|298674350|ref|YP_003726100.1| 24 ALDGVNLTIKHGEFMAIVGPSGSGKSTLLHILGIldtpTQGSIIIDNKNITSMSDKE 80
                                      5666667777677999**************997511114455566666666554433 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.5e-05     0.011      22      78 ..      35      91 ..      15     100 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.5e-05
                      Mg_chelatase 22 gHnlllvGppGsGKtmlakrlpsllpplseeealevakiasvagkkeeekllkrrpf 78
                                      g  + +vGp+GsGK+ l + l  l +p + + +++ ++i+s+++k+++++  k+  f
  gi|298674350|ref|YP_003726100.1| 35 GEFMAIVGPSGSGKSTLLHILGILDTPTQGSIIIDNKNITSMSDKERSKARNKMLGF 91
                                      4557899***********999988899999999***********8888777666555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00024      0.17      16      38 ..      33      55 ..      26      71 .. 0.78
   2 ?    2.0   0.0      0.21   1.5e+02      58     114 ..     125     190 ..     119     211 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00024
                            AAA_30 16 sgdrvavltGpAGtGKttalkal 38
                                      ++  +++++Gp G+GK+t+l  l
  gi|298674350|ref|YP_003726100.1| 33 KHGEFMAIVGPSGSGKSTLLHIL 55
                                      344599*************9876 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.21
                            AAA_30  58 aAkvLaeelgieastiakllkrlk........grarlepgtllivDE.agmvdtkqlaallkaaek 114
                                        A+++ +e+g+e +  +k  +  +        +ra +++ t++i DE +g +dtk+ +++ + ++k
  gi|298674350|ref|YP_003726100.1| 125 SAQNMLKEVGLEDRMYHKPGELSGgqnqrvsvARALVNNPTIVIGDEpTGNLDTKTSDRIYELLRK 190
                                       577777777777777777665555777888876566677799999997788999999888777765 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0035       2.5       4      35 ..      21      51 ..      18      54 .. 0.82
   2 ?   -2.0   0.0       2.5   1.8e+03     123     147 ..      66      91 ..      57      98 .. 0.69
   3 ?    4.9   0.0      0.02        14     142     186 ..     182     224 ..     172     225 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0035
                            ATPase  4 gIeglDeilkgGipegrvvlitGepGtGKtif 35
                                       ++ lD + +  i +g+ + i+G +G+GK+++
  gi|298674350|ref|YP_003726100.1| 21 EVKALDGV-NLTIKHGEFMAIVGPSGSGKSTL 51
                                      56666666.46799***************987 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.5
                            ATPase 123 vviDs..itglayeekeavaReilrql 147
                                       ++iD+  it++  +++ ++aR+ +  +
  gi|298674350|ref|YP_003726100.1|  66 IIIDNknITSM-SDKERSKARNKMLGF 91 
                                       67775336666.777777888887665 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.02
                            ATPase 142 eilrqlvrvl.kklgvTailvsekssseeaaggygveefivdgviv 186
                                       + + +l+r l +++g+T ilv+   +++ a+++ ++e  ++dg iv
  gi|298674350|ref|YP_003726100.1| 182 DRIYELLRKLnRERGQTFILVTH--DENMAKKTDRIER-LIDGKIV 224
                                       567899999999**********9..5667788888999.8898885 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.6   0.00012     0.089       4      19 ..      40      55 ..      38     219 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                            AAA_33  4 lvGlpGsGKstlaerl 19
                                      +vG++GsGKstl++ l
  gi|298674350|ref|YP_003726100.1| 40 IVGPSGSGKSTLLHIL 55
                                      79**********9876 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00024      0.17      31      68 ..      18      56 ..       6      81 .. 0.83
   2 ?    0.6   0.0      0.56     4e+02     102     147 ..     156     204 ..     145     216 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00024
                         IstB_IS21 31 dkrkvkeLatlsf.iekkenivllGpsGvGKshlaialg 68
                                      d ++vk+L + +  i++ e ++++GpsG GKs l   lg
  gi|298674350|ref|YP_003726100.1| 18 DGTEVKALDGVNLtIKHGEFMAIVGPSGSGKSTLLHILG 56
                                      5667788877776266778999**********9987777 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.56
                         IstB_IS21 102 alkrllkvdllilDdlgllpldqaeaellfeviekry...errsiiits 147
                                        +++l++   +++ d  + +ld + +  ++e++ k     +++ i++t 
  gi|298674350|ref|YP_003726100.1| 156 VARALVNNPTIVIGDEPTGNLDTKTSDRIYELLRKLNrerGQTFILVTH 204
                                       4556666666667777778889999999999887754101334455555 PP

>> T4SS-DNA_transf  Type IV secretory system Conjugative DNA transfer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.1e-05     0.058      25      96 ..      18      87 ..       2     140 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.1e-05
                   T4SS-DNA_transf 25 ltkdkkalyaggllntdGdfehvlvvAptrsgKgvgvviPnllkwkq.siVvlDpkgElaeltskiRkkqgrk 96
                                       + + kal+  +l  + G+f  + +v+p++sgK++ + i  +l  +    +++D k+ +  +  k R k+ +k
  gi|298674350|ref|YP_003726100.1| 18 DGTEVKALDGVNLTIKHGEF--MAIVGPSGSGKSTLLHILGILDTPTqGSIIIDNKN-ITSMSDKERSKARNK 87
                                      44455577777799999988..*********************98766788889876.445555555554444 PP

>> RNA12  RNA12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   8.7e-05     0.063      15      88 ..      33     105 ..      22     144 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.7e-05
                             RNA12  15 nvntFivvkGPrGSGkkeLvldrvlkdrkk....vlvidCdelvkarndaelisaaAsqlGYfPvFswlnsissliD 87 
                                       +   F+ + GP GSGk+ L+  ++l   ++     ++id ++++ + +d+e  +a  + lG+  +F + n + ++  
  gi|298674350|ref|YP_003726100.1|  33 KHGEFMAIVGPSGSGKSTLL--HILGILDTptqgSIIIDNKNIT-SMSDKERSKARNKMLGF--IFQYHNLLPDFTA 104
                                       56679**************9..54443333336899***99987.56777777888888887..6777776666655 PP

                             RNA12  88 l 88 
                                       l
  gi|298674350|ref|YP_003726100.1| 105 L 105
                                       5 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00047      0.33       3      19 ..      40      56 ..      38     110 .. 0.75
   2 ?   -0.1   0.0       1.7   1.2e+03      50      87 ..     174     209 ..     119     218 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00047
                            AAA_18  3 ltGtpGvGKttlakeLs 19
                                      + G++G+GK+tl + L 
  gi|298674350|ref|YP_003726100.1| 40 IVGPSGSGKSTLLHILG 56
                                      89**********99993 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.7
                            AAA_18  50 krldedkldklldaleenssaleegknlvidghlaele 87 
                                         ld++  d++ ++l++ +  +e g++ ++  h +++ 
  gi|298674350|ref|YP_003726100.1| 174 GNLDTKTSDRIYELLRKLN--RERGQTFILVTHDENMA 209
                                       4555555555666666665..47777777777777665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1    0.0004      0.29       3      18 ..      38      53 ..      36      65 .. 0.89
   2 ?   -1.2   0.0       2.4   1.7e+03     100     126 ..     179     203 ..     151     222 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0004
                                      EEEEC-TTTCHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlq 18
                                      +++ G++GsGK+tLl+
  gi|298674350|ref|YP_003726100.1| 38 MAIVGPSGSGKSTLLH 53
                                      799***********98 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.4
                                       .........HHHHHCTTTTT--EEEEE CS
                             NACHT 100 kekqpvrtlLselirkkllpeaslllt 126
                                       k+  ++ +lL++l r+    ++ +l+t
  gi|298674350|ref|YP_003726100.1| 179 KTSDRIYELLRKLNRE--RGQTFILVT 203
                                       4444555555555555..334444444 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00021      0.15      81     120 ..     164     212 ..      91     216 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00021
                             PIN_4  81 e..........seseknDnrIlavalelkeekpdrkvvLvskDinlrikA 120
                                       +          + ++k+ +rI +   +l++e+  ++ +Lv+ D n+  k 
  gi|298674350|ref|YP_003726100.1| 164 PtivigdeptgNLDTKTSDRIYELLRKLNRER-GQTFILVTHDENMAKKT 212
                                       1344444444322568999************9.99***********9886 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0    0.0011       0.8       3      20 ..      39      56 ..      37      88 .. 0.85
   2 ?    0.7   0.0      0.77   5.5e+02     133     157 ..     180     203 ..     155     216 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0011
                            AAA_28  3 vitGgestGKTtlleaLa 20
                                      +i+G++++GK+tll  L 
  gi|298674350|ref|YP_003726100.1| 39 AIVGPSGSGKSTLLHILG 56
                                      89************9886 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.77
                            AAA_28 133 ereaiderlrealrelgipviivps 157
                                          +i+e+lr++ re+g  +i v +
  gi|298674350|ref|YP_003726100.1| 180 TSDRIYELLRKLNRERGQTFILV-T 203
                                       55678888888888888888887.3 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   0.00019      0.14       3      49 ..      38      85 ..      36     224 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00019
                                      EEEEESTTCCHHHHHHHHH.CT--SS-EEEEESS-SSCHCCCCCCHCC CS
                              cobW  3 tvltGflGsGKTtLlnhll.enraglklavivNefgevsiDaellret 49
                                      + ++G+ GsGK+tLl  l   ++  +   +i N   +   D+e+ +++
  gi|298674350|ref|YP_003726100.1| 38 MAIVGPSGSGKSTLLHILGiLDTPTQGSIIIDNKNITSMSDKERSKAR 85
                                      5799**********9876555555555566666666566666665555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00054      0.39       5      22 ..      38      55 ..      35     126 .. 0.81
   2 ?   -0.9   0.1       1.6   1.2e+03     109     136 ..     182     210 ..     178     220 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00054
                            AAA_24  5 iliyGpsgiGKTtlakel 22
                                      ++i+Gpsg+GK+tl+  l
  gi|298674350|ref|YP_003726100.1| 38 MAIVGPSGSGKSTLLHIL 55
                                      78************9877 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.6
                            AAA_24 109 eefrrllkklqelrk.nvifiahektrkd 136
                                       +++ +ll+kl+  r+ ++i++ h +    
  gi|298674350|ref|YP_003726100.1| 182 DRIYELLRKLNRERGqTFILVTHDENMAK 210
                                       66788999999888899999999765544 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2   0.00047      0.34      21      37 ..      36      52 ..      25      56 .. 0.89
   2 ?   -1.7   0.0       1.9   1.3e+03     127     143 ..     192     208 ..     118     220 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00047
                                      EEEEEEESTTSSHHHHH CS
                            NB-ARC 21 lvvalvGmgGvGKttla 37
                                       ++a+vG  G+GK+tl+
  gi|298674350|ref|YP_003726100.1| 36 EFMAIVGPSGSGKSTLL 52
                                      49*************97 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.9
                                       HCHTTSEEEEEESBCCC CS
                            NB-ARC 127 arenrlrvllTTRdeev 143
                                       +re++   +l T de++
  gi|298674350|ref|YP_003726100.1| 192 NRERGQTFILVTHDENM 208
                                       24444444455555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                       112  (0.00624686); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 1395.63
//
Query:       gi|298674351|ref|YP_003726101.1|  [L=99]
Description: hypothetical protein Metev_0386 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.081   12.1   0.8      0.093   11.9   0.8    1.0  1  CitMHS    Citrate transporter


Domain annotation for each model (and alignments):
>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.8   5.2e-06     0.093       9      66 ..      18      81 ..       6      86 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.2e-06
                                      xxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS  9 lrldvvallvlvll.......vltieealsgiaspii..............llllgamiigaaleetGlfdrlaakllr 66
                                      lrl +        l        ++++          +              +++l++++i++a++e+   +r+ + ++ 
  gi|298674351|ref|YP_003726101.1| 18 LRLGLLI------LiiegiidYIEPDA---------TyssynlliyvlifpIFILFGITIANAMDESKKLNRVMKAIID 81
                                      3333333......22223223333333.........244444455688999****************999999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       941  (0.0524848); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 660.30
//
Query:       gi|298674352|ref|YP_003726102.1|  [L=138]
Description: Insertion element protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-06   27.7   0.0    3.3e-06   26.7   0.0    1.5  1  HTH_23           Homeodomain-like domain
    1.8e-06   27.7   0.0    2.7e-06   27.1   0.0    1.3  1  Terminase_5      Putative ATPase subunit of terminase (gpP-li
    0.00012   22.1   0.0    0.00019   21.5   0.0    1.3  1  HTH_28           Helix-turn-helix domain
     0.0025   17.5   4.7     0.0041   16.8   4.7    1.4  1  Zn_Tnp_IS1       InsA N-terminal domain
     0.0028   17.4   0.0     0.0067   16.2   0.0    1.6  1  HTH_38           Helix-turn-helix domain
     0.0039   17.5   0.0     0.0058   16.9   0.0    1.3  1  HTH_Tnp_1        Transposase
     0.0073   16.4   1.8       0.27   11.4   0.1    2.3  2  Zn-ribbon_8      Zinc ribbon domain
     0.0076   15.9   0.0      0.015   14.9   0.0    1.5  1  Sigma70_r4_2     Sigma-70, region 4
     0.0088   16.0   3.8      0.014   15.4   3.8    1.3  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
     0.0093   16.0   0.0      0.018   15.0   0.0    1.5  1  HTH_29           Winged helix-turn helix
  ------ inclusion threshold ------
      0.017   14.9   3.6      0.035   14.0   3.6    1.4  1  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
      0.041   14.0   0.3      0.083   13.0   0.3    1.5  1  DUF2387          Probable metal-binding protein (DUF2387)
      0.045   14.0   2.4      0.072   13.3   2.4    1.3  1  IBR              IBR domain, a half RING-finger domain
      0.085   13.2   0.7       0.14   12.5   0.7    1.4  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.096   12.8   1.4       0.23   11.6   1.4    1.6  1  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
        0.1   12.2   0.1       0.22   11.1   0.0    1.7  1  HTH_50           Helix-turn-helix domain
       0.91    9.7   5.8       0.99    9.6   0.8    2.2  2  UPF0547          Uncharacterised protein family UPF0547
          1    9.3   4.3        1.7    8.7   2.7    2.0  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
          1   10.0   6.0       0.33   11.5   1.1    2.3  2  zf-C2H2          Zinc finger, C2H2 type
          2    7.8   5.2       0.79    9.1   2.0    2.0  2  zf-TFIIB         Transcription factor zinc-finger
        2.2    8.8   6.4        1.3    9.6   0.6    2.3  2  zf-H2C2_2        Zinc-finger double domain
        2.5    8.8  10.2        1.5    9.6   1.1    2.4  2  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
        3.7    7.3   8.2        5.3    6.8   1.4    2.3  2  Rubredoxin_2     Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   4.3e-09   3.3e-06       7      49 ..      46      87 ..      43      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 4.3e-09
                            HTH_23  7 RlrillllaeGlsvreIAreLgvsrrTvyrwlkryreeGlegl 49
                                      + ++l+l++eGl  r I r Lgvs+  v++w+k++    le+l
  gi|298674352|ref|YP_003726102.1| 46 KRQALQLYLEGLGFRSIGRFLGVSHVSVQKWIKKF-GQELEDL 87
                                      679********************************.4447766 PP

>> Terminase_5  Putative ATPase subunit of terminase (gpP-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   3.5e-09   2.7e-06       2      40 ..      45      83 ..      44      95 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 3.5e-09
                       Terminase_5  2 vRrqArlLYwqGyrvaeIAeelglkeatVysWkkrdewd 40
                                      v+rqA +LY+ G   ++I + lg+++ +V+ W k+++ +
  gi|298674352|ref|YP_003726102.1| 45 VKRQALQLYLEGLGFRSIGRFLGVSHVSVQKWIKKFGQE 83
                                      89*********************************9875 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   2.4e-07   0.00019       2      40 ..      46      83 ..      45      89 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.4e-07
                            HTH_28  2 RleiikllaaGhsvreaArelgisrrtvyrWikryeegG 40
                                      ++++++l+++G   r + r lg+s+ +v++Wik++ +  
  gi|298674352|ref|YP_003726102.1| 46 KRQALQLYLEGLGFRSIGRFLGVSHVSVQKWIKKFGQ-E 83
                                      89*********************************98.4 PP

>> Zn_Tnp_IS1  InsA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   4.7   5.3e-06    0.0041       7      34 ..       2      28 ..       1      29 [. 0.92

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.3e-06
                        Zn_Tnp_IS1  7 hCPrCsstdVyRhGkstagHeRfrCrdC 34
                                       CP+C+s +  ++Gk  +g +R++C dC
  gi|298674352|ref|YP_003726102.1|  2 NCPKCNSFNHKKNGK-VNGRQRYKCHDC 28
                                      6*************9.5799******** PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   8.6e-06    0.0067      13      42 ..      49      78 ..      46      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.6e-06
                            HTH_38 13 IerllaeGlslreIArrLgrspsTIsRElk 42
                                        +l+ eGl++r I+r Lg+s+ ++++ +k
  gi|298674352|ref|YP_003726102.1| 49 ALQLYLEGLGFRSIGRFLGVSHVSVQKWIK 78
                                      5789******************99887666 PP

>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   7.4e-06    0.0058       6      55 ..      40      88 ..      37     110 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7.4e-06
                         HTH_Tnp_1  6 rwsdefKariVreslepgksvsevArrhgvspnqLykWrrqyregeeasp 55
                                       +++ +K ++++++  +g   +++ r +gvs+ +  kW++++ +++e ++
  gi|298674352|ref|YP_003726102.1| 40 AFPQSVKRQALQLY-LEGLGFRSIGRFLGVSHVSVQKWIKKFGQELEDLK 88
                                      69************.7899***********************43333333 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.049        38      29      37 ..       3      12 ..       1      14 [. 0.77
   2 !   11.4   0.1   0.00035      0.27       6      19 ..      23      36 ..      22      45 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.049
                       Zn-ribbon_8 29 CPeCgs.evr 37
                                      CP+C+s + +
  gi|298674352|ref|YP_003726102.1|  3 CPKCNSfNHK 12
                                      ****997765 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00035
                       Zn-ribbon_8  6 YrCeeCghefevlq 19
                                      Y+C++Cg  f v  
  gi|298674352|ref|YP_003726102.1| 23 YKCHDCGYNFSVEL 36
                                      **********9654 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0     2e-05     0.015      16      49 ..      47      79 ..      44      79 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2e-05
                                      HHHHHHHHTS---HHHHHHHHT--HHHHHHHHHH CS
                      Sigma70_r4_2 16 reifllryleglsykEIAellgisegtVksrlsR 49
                                      r+++ l ylegl  + I + lg+s ++V++++++
  gi|298674352|ref|YP_003726102.1| 47 RQALQL-YLEGLGFRSIGRFLGVSHVSVQKWIKK 79
                                      99999*.9***********************975 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   3.8   1.8e-05     0.014      20      45 ..       2      30 ..       1      31 [. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.8e-05
                     Zn_Tnp_IS1595 20 vCPhCgsr...kayriktrglfqCkeCrk 45
                                       CP+C s    k  ++++r++++C +C++
  gi|298674352|ref|YP_003726102.1|  2 NCPKCNSFnhkKNGKVNGRQRYKCHDCGY 30
                                      6*****988889999999*********98 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.4e-05     0.018       2      37 ..      47      81 ..      46      85 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.4e-05
                            HTH_29  2 aqallllaeGvstvsqiAkllglsrrtvyrwlkrfe 37
                                       qal+l+ eG++  + i ++lg+s  +v++w+k f 
  gi|298674352|ref|YP_003726102.1| 47 RQALQLYLEGLG-FRSIGRFLGVSHVSVQKWIKKFG 81
                                      69*********9.********************995 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   3.6   4.4e-05     0.035       4      31 ..       3      32 ..       3      35 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.4e-05
                                      ESTTTSBEEEEECSCCCE..EEESSSS-EE CS
                    RNA_POL_M_15KD  4 CpkCgNlLlpkedkegkn..feCrqCgYee 31
                                      CpkC++    k++k + +  + C  CgY +
  gi|298674352|ref|YP_003726102.1|  3 CPKCNSFNHKKNGKVNGRqrYKCHDCGYNF 32
                                      **************99999*********87 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   0.00011     0.083      11      51 ..       3      43 ..       1      51 [. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                           DUF2387 11 CPrCsemDkirmweedeveyrECvsCgftdelsekgqsvak 51
                                      CP+C++  + +  + ++++   C +Cg+  + + k +++++
  gi|298674352|ref|YP_003726102.1|  3 CPKCNSFNHKKNGKVNGRQRYKCHDCGYNFSVELKSTAFPQ 43
                                      ****************************8777777666655 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   2.4   9.2e-05     0.072      20      50 ..       2      34 ..       1      40 [. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.2e-05
                               IBR 20 wCprpdCeaiiekseg....cksvtCskCgfefCf 50
                                      +Cp  +C+++ +k++g     ++ +C++Cg++f +
  gi|298674352|ref|YP_003726102.1|  2 NCP--KCNSFNHKKNGkvngRQRYKCHDCGYNFSV 34
                                      6*9..******99999776644589*******965 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.7   0.00018      0.14       5      37 ..       2      33 ..       1      51 [. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00018
                   Lar_restr_allev  5 pCPfCggravlersqrvvaeigqcvyCadCga..s 37
                                       CP C++ + +++ + +  +      C+dCg+  s
  gi|298674352|ref|YP_003726102.1|  2 NCPKCNSFNHKKNGKVNGRQ---RYKCHDCGYnfS 33
                                      6*****99988888777775...9*******9431 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.4   0.00029      0.23       2      25 ..       6      31 ..       2      40 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00029
                          zf-Mss51  2 CPvpkhkqt..apkhvdfeCpdCGip 25
                                      C+  +hk++   + +++++C dCG+ 
  gi|298674352|ref|YP_003726102.1|  6 CNSFNHKKNgkVNGRQRYKCHDCGYN 31
                                      444444444778999*********86 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00029      0.22      25      48 ..      58      81 ..      43      83 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00029
                            HTH_50 25 StRklAkrLGvShtaianklrkYg 48
                                       +R +++ LGvSh  + + ++k+g
  gi|298674352|ref|YP_003726102.1| 58 GFRSIGRFLGVSHVSVQKWIKKFG 81
                                      48*******************998 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.4      0.18   1.4e+02       2       7 ..       2       7 ..       2       9 .. 0.80
   2 ?    9.6   0.8    0.0013      0.99      16      25 ..      24      33 ..      23      34 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.18
                           UPF0547 2 vCPeCe 7
                                     +CP C 
  gi|298674352|ref|YP_003726102.1| 2 NCPKCN 7
                                     7***97 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0013
                           UPF0547 16 fCphCGyvFq 25
                                      +C++CGy F+
  gi|298674352|ref|YP_003726102.1| 24 KCHDCGYNFS 33
                                      7*******96 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   2.7    0.0021       1.7      30      56 ..       2      32 ..       1      37 [. 0.84
   2 ?   -0.5   0.0       1.5   1.2e+03       3      27 ..      79     103 ..      77     114 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0021
                    OrfB_Zn_ribbon 30 tCseCgsknke....alsgrtfkCpnCgfea 56
                                      +C++C s n +     + ++++kC +Cg+ +
  gi|298674352|ref|YP_003726102.1|  2 NCPKCNSFNHKkngkVNGRQRYKCHDCGYNF 32
                                      6****9998888886666779*******975 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.5
                    OrfB_Zn_ribbon   3 klkeqleykakeyGikveevnpayT 27 
                                       k+ + le+   e  + ++e ++ +T
  gi|298674352|ref|YP_003726102.1|  79 KFGQELEDLKSENEMDIVELDELHT 103
                                       7788888888888888888887665 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.3       1.4   1.1e+03       3       7 ..       3       7 ..       1      14 [. 0.80
   2 ?   11.5   1.1   0.00043      0.33       1      11 [.      23      33 ..      23      35 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.4
                                     ETTTT CS
                           zf-C2H2 3 CpdCg 7
                                     Cp+C+
  gi|298674352|ref|YP_003726102.1| 3 CPKCN 7
                                     99997 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00043
                                      EEETTTTEEES CS
                           zf-C2H2  1 ykCpdCgksFk 11
                                      ykC+dCg+ F+
  gi|298674352|ref|YP_003726102.1| 23 YKCHDCGYNFS 33
                                      9********97 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   2.0     0.001      0.79       1      26 [.       2      29 ..       2      29 .. 0.86
   2 ?   -1.4   0.1       1.9   1.5e+03       7      13 ..      91      97 ..      81     105 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.001
                          zf-TFIIB  1 kCPkCqd.ele.eserggveidyCpqCr 26
                                      +CPkC++ + +   +++g + ++C++C+
  gi|298674352|ref|YP_003726102.1|  2 NCPKCNSfNHKkNGKVNGRQRYKCHDCG 29
                                      6*****9886648888***********7 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.9
                          zf-TFIIB  7 deleese 13
                                      +e+ ++e
  gi|298674352|ref|YP_003726102.1| 91 NEMDIVE 97
                                      3444444 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.8      0.46   3.6e+02      16      21 ..       2       7 ..       2       9 .. 0.83
   2 ?    9.6   0.6    0.0017       1.3      11      25 ..      19      33 ..      10      33 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.46
                         zf-H2C2_2 16 eCplCd 21
                                      +Cp+C+
  gi|298674352|ref|YP_003726102.1|  2 NCPKCN 7 
                                      5****8 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0017
                         zf-H2C2_2 11 gekpyeCplCdkaFk 25
                                      g  +y+C  C++ F+
  gi|298674352|ref|YP_003726102.1| 19 GRQRYKCHDCGYNFS 33
                                      5568*********95 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.1    0.0019       1.5       5      19 ..       3      17 ..       1      20 [. 0.89
   2 ?    3.9   2.5      0.11        85      39      47 .]      20      28 ..      17      28 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0019
                           zf-ISL3  5 CPnCgsktvvkhgkk 19
                                      CP+C+s +++k+gk+
  gi|298674352|ref|YP_003726102.1|  3 CPKCNSFNHKKNGKV 17
                                      *************85 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.11
                           zf-ISL3 39 krRyrCkeC 47
                                      ++Ry+C +C
  gi|298674352|ref|YP_003726102.1| 20 RQRYKCHDC 28
                                      7*******9 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.7     0.042        33      17      24 ..       3      10 ..       2      10 .. 0.91
   2 ?    6.8   1.4    0.0069       5.3       1      10 [.      23      32 ..      23      34 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.042
                      Rubredoxin_2 17 CpsCgsWn 24
                                      Cp C+s+n
  gi|298674352|ref|YP_003726102.1|  3 CPKCNSFN 10
                                      ******98 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0069
                      Rubredoxin_2  1 YvCsqCGfes 10
                                      Y C++CG+ +
  gi|298674352|ref|YP_003726102.1| 23 YKCHDCGYNF 32
                                      99******86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       910  (0.0507558); expected 358.6 (0.02)
Passed bias filter:                      647  (0.0360868); expected 358.6 (0.02)
Passed Vit filter:                       120  (0.00669307); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 928.34
//
Query:       gi|298674353|ref|YP_003726103.1|  [L=89]
Description: IS1 transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.8e-10   40.2   0.1      4e-10   40.1   0.1    1.0  1  DDE_Tnp_IS1  IS1 transposase
  ------ inclusion threshold ------
      0.038   13.9   0.1      0.041   13.8   0.1    1.1  1  TERT_thumb   Telomerase reverse transcriptase thumb DNA bindi


Domain annotation for each model (and alignments):
>> DDE_Tnp_IS1  IS1 transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.1   4.4e-14     4e-10      53     120 ..       6      73 ..       1      83 [. 0.90

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 4.4e-14
                       DDE_Tnp_IS1  53 llspfdvviltsddwglyerelkkdkhliskiytqriernnltlrtrlkrlarkslsfsksvelhekv 120
                                        l  +d+   ++d w +y + +++d h+ sk  t  +e  n  +r+ l+rl rk+ +++ks+e+ +  
  gi|298674353|ref|YP_003726103.1|   6 KLKGIDIRQGMTDYWKAYAEFIPGDIHIKSKSETFTVEGYNSIFRHFLARLRRKTKCYTKSLEMLKYS 73 
                                       5778899999*****************************************************97655 PP

>> TERT_thumb  Telomerase reverse transcriptase thumb DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   4.6e-06     0.041     121     168 ..      39      85 ..      16      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.6e-06
                                       ---HHHHHHHHHHHHHHHHGGGHHHHHHHHHHHHHHS------S-TTS CS
                        TERT_thumb 121 kvtfqclksiawraflavlkrrteiykglidriksrekltmkfhdgev 168
                                         t++  +si +r fla l+r+t+ y   ++ +k    l mk+++ e+
  gi|298674353|ref|YP_003726103.1|  39 TFTVEGYNSI-FRHFLARLRRKTKCYTKSLEMLKYSILLLMKYRNNEL 85 
                                       4555666666.8*******************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 626.37
//
Query:       gi|298674354|ref|YP_003726104.1|  [L=308]
Description: TM helix repeat-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-21   76.1  18.8    1.7e-10   40.7   3.0    4.8  7  TM_helix  Conserved TM helix
  ------ inclusion threshold ------
       0.21   10.6   0.0       0.66    8.9   0.0    1.7  1  Pex24p    Integral peroxisomal membrane peroxin


Domain annotation for each model (and alignments):
>> TM_helix  Conserved TM helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.6   5.3e-13   4.7e-09       3      49 ..      11      57 ..       9      58 .. 0.94
   2 ?   -2.6   0.5      0.65   5.8e+03      11      23 ..      83      95 ..      76      96 .. 0.66
   3 !   40.7   3.0   1.9e-14   1.7e-10       2      49 ..     103     150 ..     102     151 .. 0.96
   4 ?   -3.6   0.8       1.3   1.2e+04      10      22 ..     178     190 ..     176     192 .. 0.62
   5 !   23.8   1.6   3.7e-09   3.3e-05       3      47 ..     197     241 ..     195     243 .. 0.93
   6 ?   -4.2   1.2         2   1.8e+04      18      27 ..     254     263 ..     248     264 .. 0.64
   7 ?   -5.6   2.1         2   1.8e+04      20      25 ..     286     291 ..     285     291 .. 0.76

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 5.3e-13
                                      XXSXXHHHHTTHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS-H CS
                          TM_helix  3 lnnllnellsflPnLvgAilILlvGwiiAkfvsrlvtkllaktgidd 49
                                      l n  ++++ f+P Lv+ i++L+vG + +k + +l +k+l+k+g+d+
  gi|298674354|ref|YP_003726104.1| 11 LYNAASQFIEFIPMLVAIIVLLIVGKYTGKGLGKLGSKILDKIGLDN 57
                                      567789****************************************8 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.65
                                      HTTHSHHHHHHHH CS
                          TM_helix 11 lsflPnLvgAilI 23
                                      +   + L+ A++I
  gi|298674354|ref|YP_003726104.1| 83 IRWFVYLIFAVII 95
                                      5555668888887 PP

  == domain 3  score: 40.7 bits;  conditional E-value: 1.9e-14
                                       XXXSXXHHHHTTHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS-H CS
                          TM_helix   2 plnnllnellsflPnLvgAilILlvGwiiAkfvsrlvtkllaktgidd 49 
                                        ++++++++++flP +  A+++ ++G+i++ f++++v+k l ++g+dd
  gi|298674354|ref|YP_003726104.1| 103 IVSDFITDVIAFLPLIASAAIVIVIGFIVIDFLADVVKKALSAAGLDD 150
                                       6899*******************************************8 PP

  == domain 4  score: -3.6 bits;  conditional E-value: 1.3
                                       HHTTHSHHHHHHH CS
                          TM_helix  10 llsflPnLvgAil 22 
                                       l+++l  L +A+ 
  gi|298674354|ref|YP_003726104.1| 178 LFGYLLFLAAALN 190
                                       5667766777665 PP

  == domain 5  score: 23.8 bits;  conditional E-value: 3.7e-09
                                       XXSXXHHHHTTHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS CS
                          TM_helix   3 lnnllnellsflPnLvgAilILlvGwiiAkfvsrlvtkllaktgi 47 
                                       + nl+++ + ++PnL + ilILl G +   +  + ++  l+ +++
  gi|298674354|ref|YP_003726104.1| 197 IANLIGQMVEYVPNLAAGILILLAGILALGMFEKYLDGFLKGMNV 241
                                       579*******************************99999999986 PP

  == domain 6  score: -4.2 bits;  conditional E-value: 2
                                       HHHHHHHHHH CS
                          TM_helix  18 vgAilILlvG 27 
                                       v+++l+ +++
  gi|298674354|ref|YP_003726104.1| 254 VLFLLVIFIA 263
                                       4556666665 PP

  == domain 7  score: -5.6 bits;  conditional E-value: 2
                                       HHHHHH CS
                          TM_helix  20 AilILl 25 
                                       Ai+I++
  gi|298674354|ref|YP_003726104.1| 286 AIIIAF 291
                                       899986 PP

>> Pex24p  Integral peroxisomal membrane peroxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   7.4e-05      0.66      55     190 ..      74     280 ..      64     307 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 7.4e-05
                            Pex24p  55 clvpylelvvlplllllfvvmvpaylyrhplrksslik....................................... 92 
                                       ++v +++ v+ ++++l+f+v+++++l +  +   +  +                                       
  gi|298674354|ref|YP_003726104.1|  74 TTVGFFDAVIRWFVYLIFAVIIVDMLNIQIVSDFI--Tdviaflpliasaaivivigfividfladvvkkalsaagl 148
                                       55666777778888888888888777774222222..2345677777777777777777777777777777888877 PP

                            Pex24p  93 ....keesknestsegptldea............................skeivlnLr........dlqnkmedll 129
                                            e+s  +s++e      +                            + +i+ nL         +l     +ll
  gi|298674354|ref|YP_003726104.1| 149 ddkiAESSIGSSMKE------SgtsasglisgfvklfgyllflaaalnilQLDIIANLIgqmveyvpNLAAGILILL 219
                                       665533333333333......23344568999999999999999999999999999999999999999999999999 PP

                            Pex24p 130 npidalekflkelagfkdenlstllfltllltpililllsrlipwrlillvlgailltyHp 190
                                        +i al  f k l gf + +      ++l l+  +++ll+ +i   ++l+ +g++ +++ p
  gi|298674354|ref|YP_003726104.1| 220 AGILALGMFEKYLDGFLKGMNVGSADVLLPLLKGVLFLLVIFIALDTMLVNIGVFNFVIQP 280
                                       9999999999999997666666666666666667777777999999999999988887777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       941  (0.0524848); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2378.55
//
Query:       gi|298674355|ref|YP_003726105.1|  [L=94]
Description: GntR family transcriptional regulator [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.006   16.2   0.1     0.0075   15.9   0.1    1.1  1  ArsR      ArsR transcriptional regulator
  ------ inclusion threshold ------
      0.012   16.0   0.0      0.016   15.6   0.0    1.1  1  Rrf2      Transcriptional regulator
      0.022   14.7   0.0       0.05   13.6   0.0    1.6  1  HTH_11    HTH domain
      0.044   13.4   0.0      0.085   12.5   0.0    1.3  1  GntR      Bacterial regulatory proteins, gntR family
      0.094   12.9   0.0       0.12   12.5   0.0    1.2  1  DUF3782   Protein of unknown function (DUF3782)


Domain annotation for each model (and alignments):
>> ArsR  ArsR transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   2.1e-06    0.0075     105     143 ..      11      49 ..       5      56 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.1e-06
                              ArsR 105 eleelvekiekeveegntsisdlsrklglsplfiralak 143
                                       +++++ ++i+k+++e+++ i+dl++++g+s++f+r + +
  gi|298674355|ref|YP_003726105.1|  11 DYKQIRNDIKKHLKESDITIGDLANRFGVSKVFVREIKR 49 
                                       688999*****************************9876 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.0   4.4e-06     0.016      16      52 ..      18      54 ..      14      60 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.4e-06
                                      HHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHT CS
                              Rrf2 16 yLakeeeeepvsseeiaerqnispsylekilakLrka 52
                                      +++k+ +e+ +++ ++a+r+++s+++++ i ++Lr +
  gi|298674355|ref|YP_003726105.1| 18 DIKKHLKESDITIGDLANRFGVSKVFVREIKRELRTQ 54
                                      5778888899************************986 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.4e-05      0.05       3      33 ..      17      45 ..      15      53 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.4e-05
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvr 33
                                      ++i + L+e  ++i++ +LA +++vS+  vr
  gi|298674355|ref|YP_003726105.1| 17 NDIKKHLKE--SDITIGDLANRFGVSKVFVR 45
                                      566666744..44*************98886 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.4e-05     0.085       6      49 ..      12      52 ..      11      57 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.4e-05
                                      HHHHHHHHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHH CS
                              GntR  6 yerLredIlsgelrpGdkLPsereLaaefgVsrttvReALrrLe 49
                                      y ++r+dI++ +l+ ++ + +  +La +fgVs+  vRe  r+L 
  gi|298674355|ref|YP_003726105.1| 12 YKQIRNDIKK-HLK-ESDI-TIGDLANRFGVSKVFVREIKRELR 52
                                      6788888887.555.4556.799**************9777776 PP

>> DUF3782  Protein of unknown function (DUF3782)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.4e-05      0.12      12      41 ..      11      40 ..       4      61 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.4e-05
                           DUF3782 12 etkedleelekeieklertigaLGaRWGlv 41
                                        k+ +++++k++++ + tig L+ R+G+ 
  gi|298674355|ref|YP_003726105.1| 11 DYKQIRNDIKKHLKESDITIGDLANRFGVS 40
                                      5678888999******************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1247  (0.0695521); expected 358.6 (0.02)
Passed bias filter:                      681  (0.0379832); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 655.74
//
Query:       gi|298674356|ref|YP_003726106.1|  [L=179]
Description: ISA1083-3 transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-23   83.4   0.1    1.9e-23   82.9   0.1    1.2  1  DDE_3     DDE superfamily endonuclease
    4.7e-05   23.1   0.0    7.5e-05   22.4   0.0    1.3  1  DDE_1     DDE superfamily endonuclease
     0.0089   16.2   0.0      0.033   14.4   0.0    1.8  2  rve       Integrase core domain


Domain annotation for each model (and alignments):
>> DDE_3  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.9   0.1   3.1e-27   1.9e-23       4     135 ..       9     133 ..       7     143 .. 0.90

  Alignments for each domain:
  == domain 1  score: 82.9 bits;  conditional E-value: 3.1e-27
                             DDE_3   4 fiDEsgfqlgtvrrrawakkGkrerleeygrrgrvnligaldekgglafvtfeetlnaedfaeflerlletalqakk 80 
                                       f+DE+  q++++  r w+    +     ++ + +vn +g++  +g + ++ f+   ++ed+ efl  + ++ +++ +
  gi|298674356|ref|YP_003726106.1|   9 FLDETSPQNNANTLRFWSFNKPQI---YRNTWIKVNTLGFYALNG-KSVIEFSPHSKKEDVCEFLMNIRKNNPDK-R 80 
                                       99*********9999999987765...789999***********9.6677889999******************8.* PP

                             DDE_3  81 ivlilDnasiHkseslrelveeeadrlellylPpySPelNpiEivwsklkrellk 135
                                       iv+ilDn + H++++++e +++   ++el+ylPpySPelNpiE +w+++ r +  
  gi|298674356|ref|YP_003726106.1|  81 IVIILDNFRSHHAKTVVECAAN--NGIELVYLPPYSPELNPIEFIWKSIRRVISG 133
                                       **********************..************************9998876 PP

>> DDE_1  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.3e-08   7.5e-05      72     111 ..      76     116 ..      63     129 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.3e-08
                             DDE_1  72 aekrkilLlldssrshetvelleselqn.iklvflPassas 111
                                       +++++i+++ld++rsh++ ++ e++ +n i+lv+lP+ s +
  gi|298674356|ref|YP_003726106.1|  76 NPDKRIVIILDNFRSHHAKTVVECAANNgIELVYLPPYSPE 116
                                       7899*************999978877666*******98765 PP

>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   5.5e-06     0.033      40     106 ..      55     119 ..      47     130 .. 0.83
   2 ?   -0.6   0.0      0.24   1.5e+03      69      90 ..     136     157 ..     121     165 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.5e-06
                               rve  40 ealsdemdastvlalleravarfggvepervlsDngseytskafrefladlgirvsftrpgrpqdnG 106
                                       e+ +++ ++++v+++l +  ++    +  +++ Dn ++  +k++ e +a++gi++ + +p++p+ n 
  gi|298674356|ref|YP_003726106.1|  55 EFSPHS-KKEDVCEFLMNIRKNNPD-KRIVIILDNFRSHHAKTVVECAANNGIELVYLPPYSPELNP 119
                                       555566.889999999965555555.5899*********************************9997 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.24
                               rve  69 rvlsDngseytskafrefladl 90 
                                       ++ +D++++ + +af ++ a+ 
  gi|298674356|ref|YP_003726106.1| 136 AIDTDHMKQLIYEAFMQLSANI 157
                                       5789999999999998887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1166.49
//
Query:       gi|298674357|ref|YP_003726107.1|  [L=160]
Description: ISA1083-3 transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.6e-17   61.5   0.4    1.4e-16   60.8   0.4    1.4  1  HTH_32         Homeodomain-like domain
    7.1e-10   38.4   0.0    1.7e-09   37.2   0.0    1.7  2  HTH_33         Winged helix-turn helix
    6.5e-09   35.7   0.1      2e-08   34.1   0.0    1.8  2  HTH_29         Winged helix-turn helix
    3.6e-05   23.4   0.4    0.00037   20.2   0.1    2.5  3  HTH_23         Homeodomain-like domain
    0.00055   20.0   0.4     0.0013   18.8   0.2    1.8  2  HTH_28         Helix-turn-helix domain
     0.0023   18.4   0.1     0.0033   17.9   0.1    1.3  1  LZ_Tnp_IS481   leucine-zipper of insertion element IS481
  ------ inclusion threshold ------
      0.055   13.7   0.0        0.1   12.9   0.0    1.5  1  HTH_Tnp_Tc3_2  Transposase


Domain annotation for each model (and alignments):
>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.8   0.4   5.5e-20   1.4e-16       3      73 .]      61     131 ..      59     131 .. 0.97

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 5.5e-20
                            HTH_32   3 srwlkRyneeGlegLkdrprrgrprklsdevrariiallreeprWsprqlaarlaeregvkvShstvyriL 73 
                                       +rw kR+ne+G+egL +r  +grp+kl+++++++++++l+++  W++ q+++ +  ++gv++   +++riL
  gi|298674357|ref|YP_003726107.1|  61 HRWQKRWNESGYEGLIPRYTGGRPPKLTQQQKDQLKQILKSRNGWTTNQVRELIINEFGVEYCLMQIRRIL 131
                                       8**************************************8888***********9999************8 PP

>> HTH_33  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0         3   7.6e+03      28      34 ..      61      67 ..      55      68 .. 0.64
   2 !   37.2   0.0   6.5e-13   1.7e-09       4      47 ..     104     147 ..     101     160 .] 0.86

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3
                            HTH_33 28 yrlLkrl 34
                                      +r+ kr+
  gi|298674357|ref|YP_003726107.1| 61 HRWQKRW 67
                                      5666666 PP

  == domain 2  score: 37.2 bits;  conditional E-value: 6.5e-13
                            HTH_33   4 rWtlarlaqlieerfgvsysvsgvyrlLkrlGfsyqkPrprapk 47 
                                        Wt+ ++++li  +fgv+y   +++r+Lk+ G+ y kP p+ ++
  gi|298674357|ref|YP_003726107.1| 104 GWTTNQVRELIINEFGVEYCLMQIRRILKEFGMKYAKPYPHDYR 147
                                       6*************************************998754 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   7.9e-12     2e-08       9      62 ..      41      92 ..      37      93 .. 0.94
   2 ?   -1.9   0.0       1.4   3.5e+03      28      36 ..     126     134 ..     121     139 .. 0.73

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 7.9e-12
                            HTH_29  9 aeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsgrprnrlseeqe 62
                                      +eG s v    +++g+s +   rw+kr++e G ++l++r+ +grp + l+++q+
  gi|298674357|ref|YP_003726107.1| 41 YEGNS-VIISSERVGISSPVGHRWQKRWNESGYEGLIPRYTGGRPPK-LTQQQK 92
                                      58997.999*************************************6.9*9997 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.4
                            HTH_29  28 tvyrwlkrf 36 
                                       +++r+lk f
  gi|298674357|ref|YP_003726107.1| 126 QIRRILKEF 134
                                       678888776 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   1.5e-07   0.00037       2      50 .]      28      76 ..      27      76 .. 0.93
   2 ?   -1.4   0.0       0.9   2.3e+03      11      23 ..      98     110 ..      89     114 .. 0.69
   3 ?   -0.1   0.0      0.34   8.8e+02      32      41 ..     125     134 ..     122     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.5e-07
                            HTH_23  2 asereRlrillllaeGlsvreIAreLgvsrrTvyrwlkryreeGlegll 50
                                      a+++ Rl  ++   eG sv   +++ g+s     rw kr++e+G egl+
  gi|298674357|ref|YP_003726107.1| 28 ARVLTRLYFIKYRYEGNSVIISSERVGISSPVGHRWQKRWNESGYEGLI 76
                                      6888999999999999999999*************************95 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.9
                            HTH_23  11 llllaeGlsvreI 23 
                                       +l  ++G+++ ++
  gi|298674357|ref|YP_003726107.1|  98 ILKSRNGWTTNQV 110
                                       5666668887765 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.34
                            HTH_23  32 rTvyrwlkry 41 
                                       ++++r+lk +
  gi|298674357|ref|YP_003726107.1| 125 MQIRRILKEF 134
                                       6889999987 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.2   5.1e-07    0.0013      20      52 .]      51      83 ..      37      85 .. 0.87
   2 ?   -2.7   0.0       2.6   6.7e+03      22      35 ..     118     133 ..     110     135 .. 0.58

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 5.1e-07
                            HTH_28 20 relgisrrtvyrWikryeegGiagLvprrrrpr 52
                                      +++gis+    rW kr++e G +gL pr  ++r
  gi|298674357|ref|YP_003726107.1| 51 ERVGISSPVGHRWQKRWNESGYEGLIPRYTGGR 83
                                      78888888889*****************86554 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.6
                            HTH_28  22 lgi..srrtvyrWikr 35 
                                       +g+  +  +++r +k 
  gi|298674357|ref|YP_003726107.1| 118 FGVeyCLMQIRRILKE 133
                                       5554444466776665 PP

>> LZ_Tnp_IS481  leucine-zipper of insertion element IS481
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   1.3e-06    0.0033      27      71 ..      45      88 ..      23     104 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.3e-06
                      LZ_Tnp_IS481 27 tvaqvarelGvslrtaykwlarfraeGldGlldrssrPrrvPkat 71
                                      +v   ++ +G+s  ++++w  r+   G +Gl+ r +   r Pk t
  gi|298674357|ref|YP_003726107.1| 45 SVIISSERVGISSPVGHRWQKRWNESGYEGLIPRYTGG-RPPKLT 88
                                      45557889************************997533.234444 PP

>> HTH_Tnp_Tc3_2  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     4e-05       0.1      23      49 ..     114     141 ..      92     144 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4e-05
                     HTH_Tnp_Tc3_2  23 lkee.GksvsreTirrrLrkaglkkrkp 49 
                                       + +e G++ + + irr+L+++g+k  kp
  gi|298674357|ref|YP_003726107.1| 114 IINEfGVEYCLMQIRRILKEFGMKYAKP 141
                                       44445*******************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1005.40
//
Query:       gi|298674358|ref|YP_003726108.1|  [L=267]
Description: type 11 methyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-16   60.7   0.0    3.1e-16   59.9   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    7.2e-11   42.6   0.0    1.2e-10   41.9   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    1.1e-10   41.6   0.0    1.3e-10   41.3   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
      2e-09   38.1   0.0    3.5e-09   37.3   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    2.9e-07   30.1   0.1    4.6e-07   29.4   0.1    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    5.4e-07   29.6   0.0    7.5e-07   29.1   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    0.00038   20.1   0.0    0.00055   19.5   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
     0.0021   17.6   0.0      0.003   17.1   0.0    1.2  1  MTS              Methyltransferase small domain
     0.0027   17.1   0.0      0.004   16.6   0.0    1.4  1  TehB             Tellurite resistance protein TehB
  ------ inclusion threshold ------
      0.016   14.7   0.0       0.04   13.4   0.0    1.6  2  CheR             CheR methyltransferase, SAM binding domain
      0.019   14.7   0.0      0.028   14.2   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
       0.02   14.9   0.1       0.11   12.5   0.0    2.2  2  DUF1414          Protein of unknown function (DUF1414)
       0.05   14.2   0.0       0.24   12.1   0.0    2.2  1  Bin3             Bicoid-interacting protein 3 (Bin3)
      0.063   12.9   0.0      0.092   12.4   0.0    1.2  1  UPF0020          Putative RNA methylase family UPF0020
       0.11   12.5   0.0       0.15   12.0   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
       0.11   12.6   0.1       0.27   11.4   0.1    1.6  1  DUF4091          Domain of unknown function (DUF4091)


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9   0.0   2.8e-19   3.1e-16       1      97 []      63     160 ..      63     160 .. 0.95

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 2.8e-19
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSS.STTTEEEEEEEST.GG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpf.edgsfDlvvssga.lh 75 
                                       vLd+++GtG ++ +l++++   +v+  D ++eml++a e+a++ g+ ++ vq+d + +++  ++ fD++++ g+ + 
  gi|298674358|ref|YP_003726108.1|  63 VLDVATGTGFNSVRLLQAG--FEVVSADGNPEMLAKAFENARKYGYLMRTVQADWRWMKQdVHENFDAIICLGNsFT 137
                                       9*****************5..***********************************99853678*********9999 PP

                                       G.SSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  76 h.lsdedlekalkeiarvLkpgG 97 
                                       h ++++d++kal+e++ +Lk +G
  gi|298674358|ref|YP_003726108.1| 138 HlFNERDRRKALAEFYALLKHDG 160
                                       999*****************998 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.0   1.1e-13   1.2e-10       1      95 [.      64     163 ..      64     164 .. 0.91

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 1.1e-13
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCT.SS-TT-EEEEEEES.-CCC-. CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaekl.pfednsfDlvvsse.vlhhv. 74 
                                       Ldv++GtG ++  l ++g +vv  D ++eml+ a e+a++ g  ++ v+ad + + +   + fD++++   +++h+ 
  gi|298674358|ref|YP_003726108.1|  64 LDVATGTGFNSVRLLQAGFEVVSADGNPEMLAKAFENARKYGYLMRTVQADWRWMkQDVHENFDAIICLGnSFTHLf 140
                                       8*********************************9999999998999******88444447*****99877888888 PP

                                       ..CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  75 ..edpekalkeiaRvLkpgGllv 95 
                                          d++kal+e++ +Lk +G+l+
  gi|298674358|ref|YP_003726108.1| 141 neRDRRKALAEFYALLKHDGVLL 163
                                       988*****************997 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.0   1.2e-13   1.3e-10       5     115 ..      61     170 ..      57     237 .. 0.82

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 1.2e-13
                   Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsn 81 
                                       ++vlD+++GtG+ + +l  ++g   evv+ D ++e++ +A ena+k g+  ++  q+d+  ++++++ e+fD i++ 
  gi|298674358|ref|YP_003726108.1|  61 KKVLDVATGTGFNSVRLL-QAG--FEVVSADGNPEMLAKAFENARKYGYL-MRTVQADWRWMKQDVH-ENFDAIICL 132
                                       68****************.655..48***********************6.**********997777.89******6 PP

                   Methyltransf_31  82 evl....naladpdkileeiervlkpggilliedprll 115
                                       +          d  k+l e   +lk +g+ll+++ +  
  gi|298674358|ref|YP_003726108.1| 133 GNSfthlFNERDRRKALAEFYALLKHDGVLLLDQRNYD 170
                                       333443355678899****************9988833 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0   3.2e-12   3.5e-09       1      99 []      64     162 ..      64     162 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 3.2e-12
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvas.nvl 76 
                                       L++ +GtG ++ +ll++  + e++  D +p+++++a e  +k++      v+ +     ++d  + fD+++++ n +
  gi|298674358|ref|YP_003726108.1|  64 LDVATGTGFNSVRLLQA--GFEVVSADGNPEMLAKAFENARKYGY-LMRTVQADW-RWMKQDVHENFDAIICLgNSF 136
                                       89***************..**************666666666554.445555443.345566667********9*** PP

                   Methyltransf_12  77 hhl...kdirevldnirklLkpgGrl 99 
                                        hl   +d+r++l+++++lLk +G+l
  gi|298674358|ref|YP_003726108.1| 137 THLfneRDRRKALAEFYALLKHDGVL 162
                                       ************************87 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.1   4.1e-10   4.6e-07      39     167 ..      51     178 ..      27     241 .. 0.64

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 4.1e-10
                                       HHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-. CS
                   Ubie_methyltran  39 veklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfed. 114
                                       ++++  ++  +kvlDva+Gtg  +++l+   ++ ++vv +D n++mL  + + +++ g+  ++ +qa+   ++ +  
  gi|298674358|ref|YP_003726108.1|  51 IINILKERGVKKVLDVATGTGFNSVRLL---QAGFEVVSADGNPEMLAKAFENARKYGYL-MRTVQADWRWMKQDVh 123
                                       56667777778**********7777775...6789***********************97.5777777666655444 PP

                                       T-EEEE...EEES-.GGG-S-HHHHHHHHHHHEEEEEEEEEEEE----SHHHHHHHH CS
                   Ubie_methyltran 115 dsfDvv...tvsfG.lrnvtDklkaLkeayrvlkpGGrlvvlefskvelpllsqaye 167
                                       + fD +     sf  l n  D+ kaL e y  lk  G l+  +  +    +l+q y+
  gi|298674358|ref|YP_003726108.1| 124 ENFDAIiclGNSFThLFNERDRRKALAEFYALLKHDGVLLL-DQ-RNYDSILDQGYS 178
                                       66665411155775589********************8764.32.333344444443 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   6.7e-10   7.5e-07      24     140 ..      52     211 ..      20     240 .. 0.66

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 6.7e-10
                   Methyltransf_23  24 g.........rvLdiGcGtGillevlrengfsvtgvDlspeaveiae...............kakkaqkdqfdeqea 76 
                                                 +vLd+++GtG ++  l + gf+v+  D +pe+ ++a                  + +++        
  gi|298674358|ref|YP_003726108.1|  52 InilkergvkKVLDVATGTGFNSVRLLQAGFEVVSADGNPEMLAKAFenarkygylmrtvqaDWRWMKQ-------- 120
                                       0444444455**********9999999*****************9856554444444333332222222........ PP

                   Methyltransf_23  77 aepqg...kfdlIvlr.evlehvp...dppellrqiatllkpgGylllseplasl...................... 124
                                           +    fd I++  +++ h+    d  ++l+ +++llk +G+lll   + ++                      
  gi|298674358|ref|YP_003726108.1| 121 ----DvheNFDAIICLgNSFTHLFnerDRRKALAEFYALLKHDGVLLLDQRNYDSildqgysskhahyycgdsvsvy 193
                                       ....14449998877524566665255799******************99987777777766666666666666666 PP

                   Methyltransf_23 125 ..kedrllldwlylvpag 140
                                         + d+ l   +y++ ++
  gi|298674358|ref|YP_003726108.1| 194 peHVDEGLARFRYEFLDN 211
                                       655666666666665555 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   4.9e-07   0.00055       2      60 ..      61     117 ..      60     148 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.9e-07
                   Methyltransf_15   2 rvilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfe 60 
                                       + +lD+ +G+G n++ + + + +v++ + n+e la a +Na+ Yg    + +v++d+  
  gi|298674358|ref|YP_003726108.1|  61 KKVLDVATGTGFNSVRLLQAGFEVVSADGNPEMLAKAFENARKYGYL--MRTVQADWRW 117
                                       679*****************88**********************765..4566666654 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.7e-06     0.003      23     103 ..      51     131 ..      47     169 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.7e-06
                                       HHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-S...TTTTSTTS CS
                               MTS  23 LletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasd...vleeveek 96 
                                       +++ l+++  +kvlD+++G+G+ ++ l+++  e  v+  d + + l+ a en+++ +  +++v+ d   + ++v+ +
  gi|298674358|ref|YP_003726108.1|  51 IINILKERGVKKVLDVATGTGFNSVRLLQAGFE--VVSADGNPEMLAKAFENARKYGYLMRTVQADwrwMKQDVH-E 124
                                       577889988889***************997766..9*******************99985555555221667777.9 PP

                                       -EEEEEE CS
                               MTS  97 kfdlivs 103
                                       +fd+i++
  gi|298674358|ref|YP_003726108.1| 125 NFDAIIC 131
                                       *****98 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   3.5e-06     0.004      31     100 ..      60     130 ..      17     150 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.5e-06
                                       S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHH.HHHHHHHTT-TTEEEEE--GGG----S-EEEEE CS
                              TehB  31 pgkvldlgcgqgrnslylsllgydvtawdknensiaf.leeikekenlknistalydineaklderydfil 100
                                         kvld+  g g ns+ l   g++v + d n + +a  +e+ ++   l     a +   + +++e++d i+
  gi|298674358|ref|YP_003726108.1|  60 VKKVLDVATGTGFNSVRLLQAGFEVVSADGNPEMLAKaFENARKYGYLMRTVQADWRWMKQDVHENFDAII 130
                                       469***************************98777651566666666665555556666778888888876 PP

>> CheR  CheR methyltransferase, SAM binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.9   3.3e+03      64      80 ..      81      97 ..      76     112 .. 0.79
   2 ?   13.4   0.0   3.6e-05      0.04     130     173 ..     119     164 ..     108     169 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.9
                                      -EEEEEEESSCHHHHHH CS
                              CheR 64 kvkilAtDidlkvlekA 80
                                       ++++  D + ++l+kA
  gi|298674358|ref|YP_003726108.1| 81 GFEVVSADGNPEMLAKA 97
                                      58889999999999887 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 3.6e-05
                                       -SGGG--EEEEEE.-S.SGGGC-CHHHHHHHHHHHCCEEEEEEEEE CS
                              CheR 130 kksvlgklDvifc.rn.vliYfdeetqekvlerfaeklkpgglLll 173
                                       k++v++++D i+c  n     f+e +++k l +f+  lk++g+Lll
  gi|298674358|ref|YP_003726108.1| 119 KQDVHENFDAIIClGNsFTHLFNERDRRKALAEFYALLKHDGVLLL 164
                                       48999******99535145579**********************98 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.5e-05     0.028      68     123 ..      54     106 ..      48     130 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.5e-05
                                       HTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTT CS
                              PCMT  68 llelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldl 123
                                        l+ + +++vL+v +G+G++++   rl+++ + vvs +  +e+ ++a +n +k ++
  gi|298674358|ref|YP_003726108.1|  54 ILKERGVKKVLDVATGTGFNSV---RLLQAGFEVVSADGNPEMLAKAFENARKYGY 106
                                       55556689************96...88999********************999876 PP

>> DUF1414  Protein of unknown function (DUF1414)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       2.4   2.7e+03      13      22 ..      48      57 ..      48      58 .. 0.89
   2 ?   12.5   0.0    0.0001      0.11       9      37 ..     129     154 ..     128     156 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.4
                                      HHHHHHHHTT CS
                           DUF1414 13 GNmvTnilns 22
                                      GN + nil++
  gi|298674358|ref|YP_003726108.1| 48 GNTIINILKE 57
                                      9*******86 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.0001
                                       HHHHHHHHHHHHTTTS-CCCHHHHHHHHH CS
                           DUF1414   9 LmvLGNmvTnilnssVpeaqRealAekFa 37 
                                       +++LGN  T+++n++   + R+alAe +a
  gi|298674358|ref|YP_003726108.1| 129 IICLGNSFTHLFNER---DRRKALAEFYA 154
                                       79**********985...77999998765 PP

>> Bin3  Bicoid-interacting protein 3 (Bin3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00021      0.24       1      83 [.     126     208 ..     126     251 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00021
                              Bin3   1 ydvilalSvtkwihLnkgDeglkrlfkkiyellkpgGvlilEpqewksYkkkkklseelkeny.kelklrpedfeev 76 
                                       +d i++l    + hL +  +  ++ ++++y+llk++Gvl+l++++++s  ++   s++++    +++++ pe+++e 
  gi|298674358|ref|YP_003726108.1| 126 FDAIICLG-NSFTHLFNE-RDRRKALAEFYALLKHDGVLLLDQRNYDSILDQGYSSKHAHYYCgDSVSVYPEHVDEG 200
                                       78999998.568898654.445899*********************9998776665554444236688888888888 PP

                              Bin3  77 Lle.evgf 83 
                                       L + ++ f
  gi|298674358|ref|YP_003726108.1| 201 LARfRYEF 208
                                       87733333 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   8.2e-05     0.092      77     127 ..      82     131 ..      48     132 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.2e-05
                                       --EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE CS
                           UPF0020  77 lklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivt 127
                                        +++ +D +++++++a eNa+k+g   +  + ++   k    ++++d+i++
  gi|298674358|ref|YP_003726108.1|  82 FEVVSADGNPEMLAKAFENARKYGYLMRTVQADWRWMKQD-VHENFDAIIC 131
                                       34899*******************9988888887777666.45579**998 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00014      0.15      19      88 ..      53     114 ..      47     153 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                   Methyltransf_32  19 elakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfaels 88 
                                       ++ ke+g ++v+Dv+ G g+ s +l +     +++vv+ d + e+ +ka + a+k+g  +   +++ +++
  gi|298674358|ref|YP_003726108.1|  53 NILKERGVKKVLDVATGTGFNSVRLLQ----AGFEVVSADGNPEMLAKAFENARKYG--Y--LMRTVQAD 114
                                       44677999****************999....69***********************9..5..34444433 PP

>> DUF4091  Domain of unknown function (DUF4091)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00024      0.27      12      62 ..     168     219 ..     157     222 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00024
                           DUF4091  12 fwns...dpltdtsargafpaGDgflvYPgedgkpvsSlRlealrdGiedyeyl 62 
                                       ++ s   + + ++ a+  + +GD++ vYP++ ++ ++  R+e l + + +++++
  gi|298674358|ref|YP_003726108.1| 168 NYDSildQGYSSKHAH--YYCGDSVSVYPEHVDEGLARFRYEFLDNSVYYLNMF 219
                                       5555443334444444..479********7777799999999999988877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 1781.96
//
Query:       gi|298674359|ref|YP_003726109.1|  [L=101]
Description: hypothetical protein Metev_0394 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0055   16.6   0.5      0.012   15.5   0.5    1.6  1  PyrI_C         Aspartate carbamoyltransferase regulatory chai
     0.0084   15.8   1.3       0.04   13.7   0.2    2.2  2  zinc_ribbon_5  zinc-ribbon domain
  ------ inclusion threshold ------
      0.011   15.4   1.4      0.032   13.9   1.4    1.8  1  zf-C2H2_10     C2H2 zinc-finger
      0.013   15.5   7.0        1.4    8.9   7.0    2.3  1  zf-FCS         MYM-type Zinc finger with FCS sequence motif
       0.12   12.3   0.1       0.17   11.9   0.1    1.2  1  APT            Aerolysin/Pertussis toxin (APT) domain
       0.23   11.8   6.1        5.7    7.3   0.9    2.2  2  C1_2           C1 domain


Domain annotation for each model (and alignments):
>> PyrI_C  Aspartate carbamoyltransferase regulatory chain, metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.5   3.9e-06     0.012      28      48 .]       5      25 ..       1      25 [. 0.88

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.9e-06
                                      ETTTTEEEETTT--EEEHHHH CS
                            PyrI_C 28 dkekvklkCkYCekeiseeei 48
                                      ++++ k++C YC+++i+ +ei
  gi|298674359|ref|YP_003726109.1|  5 QNSQKKVRCSYCNQTITVDEI 25
                                      57899************9998 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.2   1.3e-05      0.04      17      33 ..       4      18 ..       1      22 [. 0.82
   2 ?    1.0   0.1      0.12   3.6e+02       7      19 ..      55      67 ..      52      74 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.3e-05
                     zinc_ribbon_5 17 sklKksgkkVrCakCae 33
                                      ++  +s+kkVrC  C +
  gi|298674359|ref|YP_003726109.1|  4 DQ--NSQKKVRCSYCNQ 18
                                      67..9**********86 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.12
                     zinc_ribbon_5  7 dCdtkFklvdskl 19
                                      +C+  Fk+ + k+
  gi|298674359|ref|YP_003726109.1| 55 ECEVFFKIKSYKI 67
                                      69999**998876 PP

>> zf-C2H2_10  C2H2 zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.4   1.1e-05     0.032       3      12 ..      10      19 ..       8      19 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.1e-05
                        zf-C2H2_10  3 kitCSYChet 12
                                      k++CSYC++t
  gi|298674359|ref|YP_003726109.1| 10 KVRCSYCNQT 19
                                      99******97 PP

>> zf-FCS  MYM-type Zinc finger with FCS sequence motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   7.0   0.00046       1.4       2      37 ..       9      56 ..       8      56 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00046
                            zf-FCS  2 vkkrCwfCkkyikgkpeftyvlend...............gvvgqFCStsC 37
                                      +k rC++C++ i++ +    + ++d                  ++FCS +C
  gi|298674359|ref|YP_003726109.1|  9 KKVRCSYCNQTITVDEI---YSSYDimsnlkkmctekdvnTRLQYFCSMEC 56
                                      689*********99997...7777777789999999999999999999999 PP

>> APT  Aerolysin/Pertussis toxin (APT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   5.7e-05      0.17      18      49 ..      10      41 ..       3      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.7e-05
                                      TTB--TTEEE--HHHHHH-HHHHHHHHCC--T CS
                               APT 18 yerCanktRaltvaelrgsaelksylrnvtgg 49
                                      + rC+   +++tv+e+ +s ++ s+l+++ ++
  gi|298674359|ref|YP_003726109.1| 10 KVRCSYCNQTITVDEIYSSYDIMSNLKKMCTE 41
                                      5699999*********************9876 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.4     0.002       5.9      12      33 ..       4      26 ..       1      29 [. 0.77
   2 ?    7.3   0.9    0.0019       5.7      23      41 ..      38      59 ..      37      63 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.002
                              C1_2 12 gedssesfnCsaCgrkidgff.Y 33
                                      +++s+++ +Cs C ++i+ ++ Y
  gi|298674359|ref|YP_003726109.1|  4 DQNSQKKVRCSYCNQTITVDEiY 26
                                      56889999*******97555455 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0019
                              C1_2 23 aCgrk.idgff..YsCse.Cdfs 41
                                       C +k ++  +  Y Cs+ C+++
  gi|298674359|ref|YP_003726109.1| 38 MCTEKdVNT-RlqYFCSMeCEVF 59
                                      688886443.348*****9*965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1347  (0.0751297); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 652.29
//
Query:       gi|298674360|ref|YP_003726110.1|  [L=195]
Description: hypothetical protein Metev_0395 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-08   34.7   2.5      2e-08   34.7   2.5    2.2  2  SNARE_assoc  SNARE associated Golgi protein


Domain annotation for each model (and alignments):
>> SNARE_assoc  SNARE associated Golgi protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   3.0      0.25   4.4e+03      15      35 ..      46      66 ..      17      74 .. 0.60
   2 !   34.7   2.5   1.1e-12     2e-08       8     117 ..      78     186 ..      68     189 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.25
                       SNARE_assoc 15 glllgtlvtslgallGaslay 35
                                      g+  + + ++l a++G++ a+
  gi|298674360|ref|YP_003726110.1| 46 GVHNVYVFAFLLAMIGGVSAF 66
                                      333355556666666666555 PP

  == domain 2  score: 34.7 bits;  conditional E-value: 1.1e-12
                       SNARE_assoc   8 vaaGvlfglllgtlvtslgallGaslayllgrylgrkalrrkllsekrvka.lerlverygflallllrllpivPrd 83 
                                       + aG + ++++  + +s+g +lG++l y+lg++  +++ +r  +  +++   +++  +ry  +++++  l+p +P+d
  gi|298674360|ref|YP_003726110.1|  78 LSAGGA-DPVYIGVFASIGLTLGDLLFYYLGKKGKQYIPERYGWGIRKLSSyVQKIKDRYIGVLIFTYSLTP-LPSD 152
                                       333333.8999***********************98777777777777777455555556667777777777.89** PP

                       SNARE_assoc  84 lvnyvaGltrvsfkrFflatfiGsipwalvyayl 117
                                       ++++++++ ++++k  ++  ++G +  + + a++
  gi|298674360|ref|YP_003726110.1| 153 ILALTLAVIGYPLKYMIIPLLLGNFALISIMATI 186
                                       ***********************98887777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1294.56
//
Query:       gi|298674361|ref|YP_003726111.1|  [L=171]
Description: hypothetical protein Metev_0396 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-16   59.0   5.4    2.4e-05   24.1   0.4    4.3  4  TPR_2         Tetratricopeptide repeat
    1.5e-14   54.2   1.3    8.6e-08   32.6   0.1    3.1  3  TPR_19        Tetratricopeptide repeat
    1.6e-14   53.0   6.3     0.0001   22.0   0.4    4.3  4  TPR_1         Tetratricopeptide repeat
      1e-13   50.6   2.9    6.7e-05   23.0   0.0    3.8  3  TPR_17        Tetratricopeptide repeat
    3.2e-12   45.6   3.9     0.0022   18.0   0.0    4.4  5  TPR_8         Tetratricopeptide repeat
    2.7e-11   43.4   0.0    8.7e-06   25.8   0.0    3.0  3  TPR_9         Tetratricopeptide repeat
    9.6e-11   41.8   8.3    2.6e-05   24.4   1.1    2.9  4  ANAPC3        Anaphase-promoting complex, cyclosome, subunit 
      6e-10   39.1   0.0       0.14   13.0   0.0    4.1  4  TPR_14        Tetratricopeptide repeat
    1.2e-09   38.1   6.0      0.006   16.6   0.1    4.2  4  Fis1_TPR_C    Fis1 C-terminal tetratricopeptide repeat
    4.6e-09   36.8   0.0     0.0031   18.1   0.0    2.3  2  TPR_16        Tetratricopeptide repeat
    1.4e-07   31.7   0.5    0.00024   21.3   0.0    3.3  3  TPR_12        Tetratricopeptide repeat
    1.7e-06   28.3   0.4        5.6    7.8   0.0    4.4  4  TPR_6         Tetratricopeptide repeat
    3.3e-06   27.1   0.4    1.5e-05   24.9   0.3    2.0  1  SRP_TPR_like  Putative TPR-like repeat
    1.4e-05   24.6   9.6      0.056   13.1   0.2    4.2  4  TPR_11        TPR repeat
    0.00054   19.8   2.2        8.5    6.7   0.0    4.2  4  TPR_7         Tetratricopeptide repeat
     0.0011   18.0   2.6      0.016   14.2   0.7    2.2  2  NARP1         NMDA receptor-regulated protein 1
     0.0016   18.3   0.4         11    6.0   0.1    4.1  4  TPR_10        Tetratricopeptide repeat
     0.0035   16.8   3.7        1.1    8.8   0.2    3.1  3  SHNi-TPR      SHNi-TPR
  ------ inclusion threshold ------
      0.056   12.3   0.0      0.076   11.9   0.0    1.2  1  DUF5588       Family of unknown function (DUF5588)


Domain annotation for each model (and alignments):
>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.3     0.013        12      11      33 ..      31      53 ..      29      54 .. 0.90
   2 !   16.5   0.0   6.9e-06    0.0066       8      34 .]      62      88 ..      57      88 .. 0.91
   3 !   12.0   0.0   0.00019      0.18       2      34 .]      90     122 ..      89     122 .. 0.95
   4 !   24.1   0.4   2.5e-08   2.4e-05       2      34 .]     124     156 ..     123     156 .. 0.96

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.013
                             TPR_2 11 yyklgdyeeAleafekAleldPn 33
                                      y+++ ++e+Ale+++  l  +P+
  gi|298674361|ref|YP_003726111.1| 31 YIENEQFEDALELCNGLLDKYPE 53
                                      88999**********99999997 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 6.9e-06
                             TPR_2  8 GlayyklgdyeeAleafekAleldPnn 34
                                      ++++  l +y+eAl  ++k lel+P+n
  gi|298674361|ref|YP_003726111.1| 62 ANVLSFLERYDEALITYDKILELEPEN 88
                                      7888889******************97 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00019
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       ++ly+ +  + klg+y + +  ++  +++dP+n
  gi|298674361|ref|YP_003726111.1|  90 QVLYAKAITLSKLGNYHDSILILNDLISYDPDN 122
                                       589****************************98 PP

  == domain 4  score: 24.1 bits;  conditional E-value: 2.5e-08
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       +++ ++G  yy l+++ +Al++fe A  ldP+n
  gi|298674361|ref|YP_003726111.1| 124 YYWIARGFNYYDLNQFHDALQDFESAQHLDPEN 156
                                       68*****************************97 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   1.7e-08   1.6e-05       2      56 ..      32      86 ..      31      86 .. 0.96
   2 !   32.6   0.1   9.2e-11   8.6e-08       6      62 ..      70     126 ..      69     130 .. 0.96
   3 ?    5.6   0.1     0.024        23       5      28 ..     137     160 ..     133     169 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.7e-08
                            TPR_19  2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedp 56
                                      ++++++++Al+l   +l+++p++  + l  A++l  l ++deA  + d+++e +p
  gi|298674361|ref|YP_003726111.1| 32 IENEQFEDALELCNGLLDKYPEYTPVMLSKANVLSFLERYDEALITYDKILELEP 86
                                      7899**********************************************99775 PP

  == domain 2  score: 32.6 bits;  conditional E-value: 9.2e-11
                            TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                       +y+eAl  + ++l+ +p+n+ ++++ A+ l +lg++ + + +L++l   dpd+++y+
  gi|298674361|ref|YP_003726111.1|  70 RYDEALITYDKILELEPENSQVLYAKAITLSKLGNYHDSILILNDLISYDPDNSYYW 126
                                       8*******************************************************9 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.024
                            TPR_19   5 gdyaeAlalleqalqedpknaear 28 
                                       +++ +Al+ +e+a   dp+n+ + 
  gi|298674361|ref|YP_003726111.1| 137 NQFHDALQDFESAQHLDPENEKLN 160
                                       6899***************99875 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1      0.04        38      11      25 ..      31      45 ..      29      45 .. 0.88
   2 !   19.9   0.0   4.8e-07   0.00045       6      34 .]      60      88 ..      57      88 .. 0.94
   3 !    7.5   0.0    0.0039       3.6       2      21 ..      90     109 ..      89     122 .. 0.78
   4 !   22.0   0.4   1.1e-07    0.0001       3      34 .]     125     156 ..     123     156 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.04
                                      HHHTT-HHHHHHHHH CS
                             TPR_1 11 yfklgkydeAleyye 25
                                      y +++++++Ale ++
  gi|298674361|ref|YP_003726111.1| 31 YIENEQFEDALELCN 45
                                      88999*******986 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 4.8e-07
                                      HHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  6 nlGnayfklgkydeAleyyekALelnPnn 34
                                       ++n++  l++ydeAl  y+k Lel+P+n
  gi|298674361|ref|YP_003726111.1| 60 SKANVLSFLERYDEALITYDKILELEPEN 88
                                      589************************97 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0039
                                       HHHHHHHHHHHHTT-HHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAl 21 
                                       ++ly ++ ++ klg+y + +
  gi|298674361|ref|YP_003726111.1|  90 QVLYAKAITLSKLGNYHDSI 109
                                       689*************9887 PP

  == domain 4  score: 22.0 bits;  conditional E-value: 1.1e-07
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                        +  +G  y+ l+++ +Al+++e A  l+P+n
  gi|298674361|ref|YP_003726111.1| 125 YWIARGFNYYDLNQFHDALQDFESAQHLDPEN 156
                                       689999************************97 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00047      0.44       5      33 ..      47      75 ..      36      76 .. 0.91
   2 !   23.0   0.0   7.1e-08   6.7e-05       1      31 [.      77     107 ..      77     109 .. 0.94
   3 !   14.8   0.2   2.9e-05     0.027       4      34 .]     114     144 ..     111     144 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00047
                            TPR_17  5 aleldPnnadaynnLAelllknGdlmtAr 33
                                       l+++P + +++  +A++l+ + ++++A+
  gi|298674361|ref|YP_003726111.1| 47 LLDKYPEYTPVMLSKANVLSFLERYDEAL 75
                                      68899**********************96 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 7.1e-08
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmt 31 
                                       +y k lel+P n+ +++ +A +l+k+G++ +
  gi|298674361|ref|YP_003726111.1|  77 TYDKILELEPENSQVLYAKAITLSKLGNYHD 107
                                       69**************************976 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 2.9e-05
                            TPR_17   4 kaleldPnnadaynnLAelllknGdlmtArq 34 
                                         + +dP+n++ +  ++  ++ ++++ +A+q
  gi|298674361|ref|YP_003726111.1| 114 DLISYDPDNSYYWIARGFNYYDLNQFHDALQ 144
                                       6799************************987 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       2.5   2.4e+03      17      31 ..      15      29 ..      14      32 .. 0.76
   2 ?   -0.2   0.1       1.7   1.6e+03      11      22 ..      31      42 ..      20      48 .. 0.68
   3 !   18.0   0.0   2.4e-06    0.0022       3      34 .]      57      88 ..      55      88 .. 0.92
   4 !   15.4   0.0   1.7e-05     0.016       2      34 .]      90     122 ..      89     122 .. 0.96
   5 !    9.9   0.1   0.00099      0.93       3      34 .]     125     156 ..     123     156 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.5
                                      HHHHHHHHHHHHHHH CS
                             TPR_8 17 yeeAkeyyekaleld 31
                                       ee +  yek + l+
  gi|298674361|ref|YP_003726111.1| 15 NEEQILLYEKLTNLS 29
                                      578888899988876 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.7
                                      HHHTT-HHHHHH CS
                             TPR_8 11 ylklgdyeeAke 22
                                      y++ +++e A e
  gi|298674361|ref|YP_003726111.1| 31 YIENEQFEDALE 42
                                      666666666655 PP

  == domain 3  score: 18.0 bits;  conditional E-value: 2.4e-06
                                      HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8  3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34
                                      +++ ++++++ l++y+eA  +y k lel+p+n
  gi|298674361|ref|YP_003726111.1| 57 VMLSKANVLSFLERYDEALITYDKILELEPEN 88
                                      67789*************************86 PP

  == domain 4  score: 15.4 bits;  conditional E-value: 1.7e-05
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       +++y ++ +++klg+y+ ++  ++  +++dpdn
  gi|298674361|ref|YP_003726111.1|  90 QVLYAKAITLSKLGNYHDSILILNDLISYDPDN 122
                                       789****************************97 PP

  == domain 5  score: 9.9 bits;  conditional E-value: 0.00099
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       ++   g  y +l++++ A + +e a  ldp+n
  gi|298674361|ref|YP_003726111.1| 125 YWIARGFNYYDLNQFHDALQDFESAQHLDPEN 156
                                       68899999*******************99986 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.24   2.3e+02       5      22 ..      31      48 ..      29      55 .. 0.86
   2 !   12.5   0.0   0.00014      0.13       9      47 ..      69     107 ..      63     115 .. 0.94
   3 !   25.8   0.0   9.2e-09   8.7e-06      19      68 ..     113     162 ..     107     167 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.24
                             TPR_9  5 aireedweralavverll 22
                                      +i++e++e al+ ++ ll
  gi|298674361|ref|YP_003726111.1| 31 YIENEQFEDALELCNGLL 48
                                      89**********998877 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00014
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsa 47 
                                       e++++al +++ +l l P+  + ++  ++ l +lG+++ 
  gi|298674361|ref|YP_003726111.1|  69 ERYDEALITYDKILELEPENSQVLYAKAITLSKLGNYHD 107
                                       799**********************************96 PP

  == domain 3  score: 25.8 bits;  conditional E-value: 9.2e-09
                             TPR_9  19 erllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaeai 68 
                                       + l+  +Pd  + +  RG+ ++ l++++ Al+d+e + +l+p+++    +
  gi|298674361|ref|YP_003726111.1| 113 NDLISYDPDNSYYWIARGFNYYDLNQFHDALQDFESAQHLDPENEKLNEL 162
                                       457778************************************99887666 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.1   0.00012      0.11      33      81 ..      31      80 ..      14      81 .. 0.94
   2 !   20.8   0.1   3.5e-07   0.00033       2      80 ..      34     113 ..      33     115 .. 0.78
   3 !   24.4   1.1   2.7e-08   2.6e-05       3      79 ..      69     146 ..      68     149 .. 0.89
   4 !    7.0   0.2     0.007       6.6      21      54 ..     118     155 ..     110     162 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                                      HHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3 33 lylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81
                                      + +n+q++ A+el++ + +++++   + + +A +l  L++y+eA+ +++k
  gi|298674361|ref|YP_003726111.1| 31 YIENEQFEDALELCNGLlDKYPEYTPVMLSKANVLSFLERYDEALITYDK 80
                                      7789****************************************998876 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 3.5e-07
                                       TT-HHHHHHHHHHHH.HHH--HHH.HHH.HHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHH CS
                            ANAPC3   2 qnnyknAiflaerllaaetesped.ayl.lAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeA 75 
                                       ++++++A+ l++ ll  +++ ++  ++l +A +l  +++y++A+  ++k  +l++++ +++y +A +l kL++y++ 
  gi|298674361|ref|YP_003726111.1|  34 NEQFEDALELCNGLL--DKYPEYTpVMLsKANVLSFLERYDEALITYDKIlELEPENSQVLYAKAITLSKLGNYHDS 108
                                       788999999999999..333333324443599999999999999999999999999999999999999999999998 PP

                                       HHHH- CS
                            ANAPC3  76 iaaLe 80 
                                       i +L 
  gi|298674361|ref|YP_003726111.1| 109 ILILN 113
                                       87775 PP

  == domain 3  score: 24.4 bits;  conditional E-value: 2.7e-08
                                       T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                       ++y++A++ ++++l+ e+e+++ +y++A +l ++g+y+  + +l+++   ++ +  +++  +  +++L+++++A++ 
  gi|298674361|ref|YP_003726111.1|  69 ERYDEALITYDKILELEPENSQVLYAKAITLSKLGNYHDSILILNDLiSYDPDNSYYWIARGFNYYDLNQFHDALQD 145
                                       58*********************************************7777777777777779999********986 PP

                                       H CS
                            ANAPC3  79 L 79 
                                       +
  gi|298674361|ref|YP_003726111.1| 146 F 146
                                       5 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.007
                                       --HHH.HHHH..HHHHHHTT-HHHHHHHHHCT.SHHHC CS
                            ANAPC3  21 esped.ayll..AlclylngqykrAyellrka.klnsk 54 
                                       ++p++  y+   +  +y ++q++ A++ +++a  l+++
  gi|298674361|ref|YP_003726111.1| 118 YDPDNsYYWIarGFNYYDLNQFHDALQDFESAqHLDPE 155
                                       555551555545668************99999555555 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0059       5.5      11      34 ..      31      54 ..      28      62 .. 0.87
   2 !   12.4   0.0   0.00024      0.22       8      42 ..      62      96 ..      57      98 .. 0.90
   3 !   13.0   0.0   0.00015      0.14       3      42 ..      91     130 ..      89     132 .. 0.92
   4 ?    5.8   0.1     0.033        31       4      38 ..     126     160 ..     125     163 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0059
                            TPR_14 11 llalGdpdeAiallrralalaPdd 34
                                      + +++++++A++l++ +l+++P+ 
  gi|298674361|ref|YP_003726111.1| 31 YIENEQFEDALELCNGLLDKYPEY 54
                                      77899*****************86 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00024
                            TPR_14  8 aeallalGdpdeAiallrralalaPddaeawllla 42
                                      a +l  l+++deA+  ++++l+l P++ +++++ a
  gi|298674361|ref|YP_003726111.1| 62 ANVLSFLERYDEALITYDKILELEPENSQVLYAKA 96
                                      77888999*******************99998876 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 0.00015
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       +l+a a  l  lG++ ++i +l+++++ +Pd+  +w++ +
  gi|298674361|ref|YP_003726111.1|  91 VLYAKAITLSKLGNYHDSILILNDLISYDPDNSYYWIARG 130
                                       689999****************************999865 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.033
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeaw 38 
                                       + a++  ++ l ++ +A++ ++ a  l+P+++ ++
  gi|298674361|ref|YP_003726111.1| 126 WIARGFNYYDLNQFHDALQDFESAQHLDPENEKLN 160
                                       55666678999*************999**998765 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1      0.03        28      15      33 ..      35      53 ..      27      57 .. 0.88
   2 !   16.6   0.1   6.4e-06     0.006      14      38 ..      68      92 ..      68      93 .. 0.93
   3 !   11.5   0.0   0.00025      0.23       4      35 ..      92     123 ..      91     125 .. 0.94
   4 !    6.7   0.2    0.0082       7.8      11      47 ..     133     169 ..     124     171 .] 0.88

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.03
                                      T-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C 15 geYseArryvdalLeiEPe 33
                                       ++++A+++++ lL + Pe
  gi|298674361|ref|YP_003726111.1| 35 EQFEDALELCNGLLDKYPE 53
                                      6899**********99997 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 6.4e-06
                                      HT-HHHHHHHHHHHHHHTTS-HHHH CS
                        Fis1_TPR_C 14 lgeYseArryvdalLeiEPenrQaq 38
                                      l +Y+eA+   d +Le+EPen+Q++
  gi|298674361|ref|YP_003726111.1| 68 LERYDEALITYDKILELEPENSQVL 92
                                      579********************85 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00025
                                       HHHHHHHHHHHT-HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C   4 lYylAlGhyklgeYseArryvdalLeiEPenr 35 
                                       lY  A+   klg+Y ++   ++ l++ +P+n+
  gi|298674361|ref|YP_003726111.1|  92 LYAKAITLSKLGNYHDSILILNDLISYDPDNS 123
                                       78889999**********************95 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.0082
                                       HHHHT-HHHHHHHHHHHHHHTTS-HHHHHHHHHHHHH CS
                        Fis1_TPR_C  11 hyklgeYseArryvdalLeiEPenrQaqsLkeliedk 47 
                                       +y l ++ +A++  +   +++Pen+  ++L +l+e++
  gi|298674361|ref|YP_003726111.1| 133 YYDLNQFHDALQDFESAQHLDPENEKLNELVNLLEKE 169
                                       89999*************************9999986 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   3.2e-06    0.0031       6      65 ..      30      86 ..      25      90 .. 0.92
   2 !   16.6   0.0   9.9e-06    0.0094       1      67 [.      93     156 ..      93     157 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.2e-06
                            TPR_16  6 aalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65
                                      +++++ +++dA+++ + +l+++   P+    +l +++++  + r++eA+  y++ l+  p
  gi|298674361|ref|YP_003726111.1| 30 EYIENEQFEDALELCNGLLDKY---PEYTPVMLSKANVLSFLERYDEALITYDKILELEP 86
                                      799*******************...*************************9999987666 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 9.9e-06
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       +a+a  + ++g+y d +  l+ ++ +d   Pd+   + ++g  ++ ++ + +A++ +++a+  +p +
  gi|298674361|ref|YP_003726111.1|  93 YAKAITLSKLGNYHDSILILNDLISYD---PDNSYYWIARGFNYYDLNQFHDALQDFESAQHLDPEN 156
                                       78999999*******************...******************************9999976 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   1.9e-05     0.018      44      73 ..      54      83 ..      31      84 .. 0.54
   2 !   21.3   0.0   2.5e-07   0.00024       5      70 ..      58     114 ..      54     121 .. 0.87
   3 ?    3.8   0.1     0.077        73       8      29 ..     128     149 ..     121     153 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.9e-05
                            TPR_12 44 tattlrnLgrlyralgryeeAlelleeala 73
                                      +  ++   + +++ l+ry+eAl  + + l+
  gi|298674361|ref|YP_003726111.1| 54 YTPVMLSKANVLSFLERYDEALITYDKILE 83
                                      555555555555555555555555555444 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 2.5e-07
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlellee 70 
                                       +l   a+vl  l+rydeAl  ++k le+      p++   +++l++ ++++++lg+y + + +l++
  gi|298674361|ref|YP_003726111.1|  58 ML-SKANVLSFLERYDEALITYDKILELE-----PEN---SQVLYAKAITLSKLGNYHDSILILND 114
                                       55.78************************.....876...88999999999999999999988876 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.077
                            TPR_12   8 nlaavlrrlgrydeAlelleka 29 
                                        ++  ++ l ++++Al+ +e a
  gi|298674361|ref|YP_003726111.1| 128 ARGFNYYDLNQFHDALQDFESA 149
                                       4566777777777777777765 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0062       5.8      10      32 ..      31      53 ..      19      54 .. 0.83
   2 ?    5.3   0.0     0.038        36      14      32 ..      69      87 ..      58      88 .. 0.84
   3 !    7.8   0.0     0.006       5.6       2      33 .]      91     122 ..      90     122 .. 0.91
   4 ?    2.4   0.0      0.32     3e+02       7      28 ..     130     151 ..     123     156 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0062
                                      HHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6 10 yrklgdtdkAlealerlikeYPd 32
                                      y++  + ++Ale+ + l+++YP+
  gi|298674361|ref|YP_003726111.1| 31 YIENEQFEDALELCNGLLDKYPE 53
                                      445359****************6 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.038
                                      HHHHHHHHHHHHHHHH-TT CS
                             TPR_6 14 gdtdkAlealerlikeYPd 32
                                       ++d+Al +++++++  P+
  gi|298674361|ref|YP_003726111.1| 69 ERYDEALITYDKILELEPE 87
                                      489***********99886 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.006
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYPdS 33 
                                       +ly  a  + klg++ +++ +l++li+  Pd+
  gi|298674361|ref|YP_003726111.1|  91 VLYAKAITLSKLGNYHDSILILNDLISYDPDN 122
                                       7888999999999*****************95 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.32
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrklgdtdkAlealerlik 28 
                                       +  y+ l++  +Al+ +e+   
  gi|298674361|ref|YP_003726111.1| 130 GFNYYDLNQFHDALQDFESAQH 151
                                       56688889999**999998765 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.3   1.6e-08   1.5e-05       1      98 [.      33     146 ..      33     166 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.6e-08
                      SRP_TPR_like   1 eneeyekilrlegkelkkf.........kvvaliklekyeeaLkllkkgs...alsedvrfEkaYvlYklkkykkal 65 
                                       ene++e+ l+l +  l+k+         k+  l  le+y+eaL+  +k       +++v + ka  l kl +y+++ 
  gi|298674361|ref|YP_003726111.1|  33 ENEQFEDALELCNGLLDKYpeytpvmlsKANVLSFLERYDEALITYDKILelePENSQVLYAKAITLSKLGNYHDSI 109
                                       589999**********************9999999**********9998733345899******************* PP

                      SRP_TPR_like  66 kilkkveaee..kvk..vlksqvlYrlgsyekAYklL 98 
                                        il+ + + +  ++   + +   +Y l+++++A +  
  gi|298674361|ref|YP_003726111.1| 110 LILNDLISYDpdNSYywIARGFNYYDLNQFHDALQDF 146
                                       ****988776433321133344677888898885544 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.53     5e+02       3      15 ..      30      42 ..      29      43 .. 0.88
   2 !   13.1   0.2   5.9e-05     0.056       8      42 .]      69     103 ..      63     103 .. 0.94
   3 !    7.0   0.4    0.0051       4.8       6      39 ..     101     134 ..      99     135 .. 0.91
   4 !   11.9   0.1   0.00015      0.14       4      28 ..     133     157 ..     130     161 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.53
                            TPR_11  3 ayyeqGkyeeAie 15
                                      +y e  ++e+A+e
  gi|298674361|ref|YP_003726111.1| 30 EYIENEQFEDALE 42
                                      69999******97 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 5.9e-05
                            TPR_11   8 GkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                        +y+eA+  Y k l+l P+n  ++y+ + ++ k+G
  gi|298674361|ref|YP_003726111.1|  69 ERYDEALITYDKILELEPENSQVLYAKAITLSKLG 103
                                       58************************999999988 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0051
                            TPR_11   6 eqGkyeeAieaYkkAlkldPdnaeayynLGlayy 39 
                                       ++G+y ++i  ++  + +dPdn   + ++G+ yy
  gi|298674361|ref|YP_003726111.1| 101 KLGNYHDSILILNDLISYDPDNSYYWIARGFNYY 134
                                       5899999999999****************99888 PP

  == domain 4  score: 11.9 bits;  conditional E-value: 0.00015
                            TPR_11   4 yyeqGkyeeAieaYkkAlkldPdna 28 
                                       yy+++++ +A+++++ A  ldP+n 
  gi|298674361|ref|YP_003726111.1| 133 YYDLNQFHDALQDFESAQHLDPENE 157
                                       9**********************96 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.7   1.6e+03      13      22 ..      35      44 ..      31      50 .. 0.72
   2 !    6.7   0.0     0.009       8.5       6      31 ..      62      87 ..      57      90 .. 0.83
   3 ?    5.3   0.0     0.024        23       2      21 ..      92     111 ..      91     123 .. 0.80
   4 ?    4.1   0.1     0.061        58       9      35 ..     133     157 ..     133     158 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.7
                             TPR_7 13 GdyeeAiely 22
                                       ++e+A+el+
  gi|298674361|ref|YP_003726111.1| 35 EQFEDALELC 44
                                      5788888886 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.009
                             TPR_7  6 arlysrlGdyeeAielyeqsLaltkd 31
                                      a++ s l +y+eA+  y + L+l+ +
  gi|298674361|ref|YP_003726111.1| 62 ANVLSFLERYDEALITYDKILELEPE 87
                                      78888899***********8888754 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.024
                             TPR_7   2 LlnLarlysrlGdyeeAiel 21 
                                       L++ a + s+lG+y + i +
  gi|298674361|ref|YP_003726111.1|  92 LYAKAITLSKLGNYHDSILI 111
                                       788899*********99865 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.061
                             TPR_7   9 ysrlGdyeeAielyeqsLaltkdpeda 35 
                                       y +l+++ +A++ +e   a + dpe++
  gi|298674361|ref|YP_003726111.1| 133 YYDLNQFHDALQDFES--AQHLDPENE 157
                                       568999*********9..999999876 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.7   1.7e-05     0.016      14      73 ..      31      90 ..      13      95 .. 0.85
   2 ?    4.2   0.1     0.017        16      41      76 ..      92     127 ..      89     159 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.7e-05
                                      HHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CH CS
                             NARP1 14 ieeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpensk 73
                                        e ++ e+Ale  +   ++  +   v+  ka++l  L+r++eA  ty ++le  pens+
  gi|298674361|ref|YP_003726111.1| 31 YIENEQFEDALELCNGLLDKYPEYTPVMLSKANVLSFLERYDEALITYDKILELEPENSQ 90
                                      458999****************************************************86 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.017
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHH CS
                             NARP1  41 ketkaelllkLgrkeeAeatyeaLlernpenskYye 76 
                                       + +ka  l kLg+++++  ++++L++  p+ns Y+ 
  gi|298674361|ref|YP_003726111.1|  92 LYAKAITLSKLGNYHDSILILNDLISYDPDNSYYWI 127
                                       557888999999999999999999999999998874 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.42     4e+02      13      32 ..      26      44 ..      25      50 .. 0.75
   2 ?    4.3   0.0     0.043        40       9      23 ..      62      76 ..      58      84 .. 0.79
   3 ?    1.2   0.0      0.39   3.6e+02       9      21 ..      96     108 ..      92     116 .. 0.82
   4 ?    6.0   0.1     0.012        11      11      28 ..     132     149 ..     129     149 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.42
                            TPR_10 13 rqrgrydeAealleealair 32
                                      +++ +y e e++ e+al+++
  gi|298674361|ref|YP_003726111.1| 26 TNLSEYIENEQF-EDALELC 44
                                      566678888888.9999987 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.043
                            TPR_10  9 analrqrgrydeAea 23
                                      an+l+ + rydeA+ 
  gi|298674361|ref|YP_003726111.1| 62 ANVLSFLERYDEALI 76
                                      899999999**9985 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.39
                            TPR_10   9 analrqrgrydeA 21 
                                       a++l+++g+y+++
  gi|298674361|ref|YP_003726111.1|  96 AITLSKLGNYHDS 108
                                       7889999999876 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.012
                            TPR_10  11 alrqrgrydeAealleea 28 
                                        +++++++++A++++e a
  gi|298674361|ref|YP_003726111.1| 132 NYYDLNQFHDALQDFESA 149
                                       69*************976 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.2    0.0028       2.6      12      22 ..      32      42 ..      21      42 .. 0.81
   2 ?   -1.1   0.0       1.4   1.3e+03      15      26 ..      69      80 ..      69      85 .. 0.70
   3 !    8.8   0.2    0.0012       1.1      15      27 ..     137     149 ..     136     152 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0028
                          SHNi-TPR 12 lEnenFpqAve 22
                                      +Ene+F++A+e
  gi|298674361|ref|YP_003726111.1| 32 IENEQFEDALE 42
                                      7********86 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.4
                          SHNi-TPR 15 enFpqAveDlrk 26
                                      e++++A+  ++k
  gi|298674361|ref|YP_003726111.1| 69 ERYDEALITYDK 80
                                      899999855555 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0012
                          SHNi-TPR  15 enFpqAveDlrka 27 
                                       ++F++A++D+++a
  gi|298674361|ref|YP_003726111.1| 137 NQFHDALQDFESA 149
                                       69*********98 PP

>> DUF5588  Family of unknown function (DUF5588)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   8.1e-05     0.076      93     167 ..      60     131 ..      50     152 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.1e-05
                           DUF5588  93 gqarclahlgrhaealeiaad.lenkatntdhlttvlylqlaicsslqnlektilclqklislhpfnpwswgklae 167
                                        +a  l+ l r+ eal    + le    n+     vly +   +s l n + +il l+ lis  p n + w     
  gi|298674361|ref|YP_003726111.1|  60 SKANVLSFLERYDEALITYDKiLELEPENS----QVLYAKAITLSKLGNYHDSILILNDLISYDPDNSYYWIARGF 131
                                       578899999999999865443266666664....699***999****************************76555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1123.80
//
Query:       gi|298674362|ref|YP_003726112.1|  [L=134]
Description: hypothetical protein Metev_0397 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-64  214.4   0.8    3.6e-64  214.3   0.8    1.0  1  DUF1699        Protein of unknown function (DUF1699)
  ------ inclusion threshold ------
       0.06   12.7   0.1      0.069   12.5   0.1    1.2  1  Metalloenzyme  Metalloenzyme superfamily
      0.065   14.0   0.8      0.065   14.0   0.8    1.9  2  VAPB_antitox   Putative antitoxin


Domain annotation for each model (and alignments):
>> DUF1699  Protein of unknown function (DUF1699)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.3   0.8     6e-68   3.6e-64       1     130 []       1     130 [.       1     130 [. 0.99

  Alignments for each domain:
  == domain 1  score: 214.3 bits;  conditional E-value: 6e-68
                           DUF1699   1 mkirvvsskeeietlnenekivHlafrpsntdilslvkkcpklkaiqvpeSykktlsksakmfleiqgiellegdvw 77 
                                       mkirv+ssk+eie+l+ene++vHlafrpsntdi+s+v+kc +lka+++p+Syk+tls+sakmfl++qgi+llegdvw
  gi|298674362|ref|YP_003726112.1|   1 MKIRVLSSKDEIENLDENEEMVHLAFRPSNTDIFSIVSKCTNLKALHIPSSYKRTLSESAKMFLDMQGINLLEGDVW 77 
                                       9**************************************************************************** PP

                           DUF1699  78 ghrkdineyyevseevierikelkseglseeeiaeklsketklspdlikfllk 130
                                       ghrkdiney+evs+++++rikelk+egls++ei++k++ketkl pd+++fl+k
  gi|298674362|ref|YP_003726112.1|  78 GHRKDINEYSEVSDNIYNRIKELKDEGLSDDEIVDKMKKETKLGPDFVEFLIK 130
                                       ***************************************************96 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   1.1e-05     0.069     124     176 ..      56     108 ..       8     111 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.1e-05
                                       HHHH.CC.-SEEEEEE-HHHHHHHTT-HHHHHHHHHHHHHHHHHHHTTS-TTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 124 ldailsgkfdlvvvniknaDmvGHtgdleatiaaieaaDeavkeildaieqvd 176
                                       l++  +   d+  +n+ + D  GH++d++++ ++  ++ +++ke+ d+  ++d
  gi|298674362|ref|YP_003726112.1|  56 LSESAKMFLDMQGINLLEGDVWGHRKDINEYSEVSDNIYNRIKELKDEGLSDD 108
                                       3444455578889*******************************999866665 PP

>> VAPB_antitox  Putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.8   1.1e+04      52      59 ..      10      17 ..       4      26 .. 0.53
   2 ?   14.0   0.8   1.1e-05     0.065       5      34 ..      89     118 ..      88     131 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.8
                      VAPB_antitox 52 eeadeiek 59
                                      +e++++ +
  gi|298674362|ref|YP_003726112.1| 10 DEIENLDE 17
                                      33333333 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.1e-05
                      VAPB_antitox   5 IsdevYekLkklKregeSFsdvIerLlekk 34 
                                       +sd +Y++ k+lK eg S +++++++ +++
  gi|298674362|ref|YP_003726112.1|  89 VSDNIYNRIKELKDEGLSDDEIVDKMKKET 118
                                       89***********************84433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 852.29
//
Query:       gi|298674363|ref|YP_003726113.1|  [L=109]
Description: translation initiation factor eIF-1A [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-17   63.4   0.1    1.7e-17   63.0   0.1    1.2  1  eIF-1a    Translation initiation factor 1A / IF-1


Domain annotation for each model (and alignments):
>> eIF-1a  Translation initiation factor 1A / IF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.0   0.1   9.5e-22   1.7e-17       1      64 []      29      91 ..      29      91 .. 0.97

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 9.5e-22
                                      EEEEEEEEEEETTTEEEEEE.SSSSBEEEEE-HHHHCT----TT-EEEEEE-TT-TTEEEEES- CS
                            eIF-1a  1 gevigkViealgnnlfrVelpdngkevlaeipgkfRnkiwikrGdyVlVelspydltkGrIvyr 64
                                      +ev ++V+ +lg+ +++ +++d g e++++ipg  ++++wi++Gd+V+  +++++++k++++++
  gi|298674363|ref|YP_003726113.1| 29 NEVFATVSTLLGGKRVKLQCMD-GTERMGRIPGSKKKRMWIREGDIVIALPWDFQDEKADVIWK 91
                                      699******************6.***************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 707.79
//
Query:       gi|298674364|ref|YP_003726114.1|  [L=192]
Description: hypothetical protein Metev_0399 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.12   11.7   0.0       0.24   10.7   0.0    1.5  1  mRNA_decap_C  mRNA-decapping enzyme C-terminus


Domain annotation for each model (and alignments):
>> mRNA_decap_C  mRNA-decapping enzyme C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   1.3e-05      0.24      22      38 ..      30      46 ..      26      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 1.3e-05
                      mRNA_decap_C 22 sFLntIHeAYlqslskd 38
                                       FL  I+++Y+qs +k+
  gi|298674364|ref|YP_003726114.1| 30 RFLGDIYNTYIQSGAKS 46
                                      7************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1265.91
//
Query:       gi|298674365|ref|YP_003726115.1|  [L=200]
Description: hypothetical protein Metev_0400 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-08   34.1   4.2    2.7e-08   33.6   4.2    1.2  1  NnrU      NnrU protein
    0.00084   19.7   1.6     0.0013   19.1   0.1    2.0  2  PEMT      Phospholipid methyltransferase


Domain annotation for each model (and alignments):
>> NnrU  NnrU protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   4.2     3e-12   2.7e-08       1     172 [.       8     189 ..       8     197 .. 0.80

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 3e-12
                              NnrU   1 vlilglllFlgaHsvraapalRarliarlGerg...ykilyslvsllglvlliigfgaaryevllWeppawlrhlal 74 
                                       +l+ +l+ F+++Hs  a  ++++rl++ lG ++   y+ +ysl+++l++  li+     +    l+ +p   r++++
  gi|298674365|ref|YP_003726115.1|   8 ILVFCLVAFAVIHSALASLPFKRRLMQFLGSKAdtlYMPVYSLIAVLTISPLIYLLIYNPGP-ILYIVPSPWRWIMV 83 
                                       5899***********99999999*******87555599**********99999888777777.88888888888888 PP

                              NnrU  75 llmlvafillaaallpgnplsvglka..........dlaetgivritrHPmllg..vaiWAlaHllanGdlasvllf 139
                                          ++a i+   all + +   ++++           l+ +gi+r++r P+ll+  ++iW    l +  + + +++ 
  gi|298674365|ref|YP_003726115.1|  84 GGQIIAAIVAPRALLDAPHRFKIHSQlsgpntpeagALNIKGIYRWVRDPFLLSgiIIIW----LTPFMTFNLLVIY 156
                                       8888998888888887655444444457888899988999***********998334456....7777777788888 PP

                              NnrU 140 gglllwalvgviaidrrkrrrlgeewealaart 172
                                       +   ++ ++g ++ ++r+ +++g+e +++++++
  gi|298674365|ref|YP_003726115.1| 157 ALTTIYLYLGSLHWEKRLIAQFGDEYREYQKQV 189
                                       888888889999999999999999988777665 PP

>> PEMT  Phospholipid methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2      0.18   1.6e+03      76      87 ..       9      20 ..       1      63 [. 0.63
   2 !   19.1   0.1   1.5e-07    0.0013      39      99 ..     118     176 ..     100     182 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.18
                              PEMT 76 lllallvllvyl 87
                                      l+++l++++v++
  gi|298674365|ref|YP_003726115.1|  9 LVFCLVAFAVIH 20
                                      333333333332 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 1.5e-07
                              PEMT  39 mdklvtsGiYrylnnPeyvgstlgflGlaLitgsaaglllallvllvylialkfvEephla 99 
                                         +l  +GiYr++++P  + ++++++ + ++t +++ +++al+ +++yl  l  +E++ +a
  gi|298674365|ref|YP_003726115.1| 118 AGALNIKGIYRWVRDPFLLSGIIIIWLTPFMTFNLL-VIYALTTIYLYLGSLH-WEKRLIA 176
                                       448999**************************9999.7777777777777777.9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1280.20
//
Query:       gi|298674366|ref|YP_003726116.1|  [L=278]
Description: CbbQ/NirQ/NorQ domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-32  111.0   0.1    5.6e-32  109.9   0.0    1.6  2  CbbQ_C           CbbQ/NirQ/NorQ C-terminal
    3.2e-31  108.2   0.0    4.4e-31  107.7   0.0    1.2  1  AAA_5            AAA domain (dynein-related subfamily)
    0.00014   21.0   0.1     0.0043   16.1   0.0    2.1  2  AAA_6            Hydrolytic ATP binding site of dynein motor 
     0.0027   17.6   0.0     0.0045   16.8   0.0    1.3  1  AAA_3            ATPase family associated with various cellul
  ------ inclusion threshold ------
      0.015   15.0   0.0      0.034   13.9   0.0    1.5  1  Sigma54_activat  Sigma-54 interaction domain
      0.016   15.5   0.0      0.033   14.5   0.0    1.5  1  AAA_22           AAA domain
      0.017   15.5   0.0      0.029   14.8   0.0    1.4  1  AAA              ATPase family associated with various cellul
      0.043   14.2   0.0      0.094   13.1   0.0    1.6  1  RNA_helicase     RNA helicase
      0.058   13.4   0.0        0.1   12.6   0.0    1.5  1  AAA_14           AAA domain
      0.065   12.8   0.0       0.12   11.8   0.0    1.4  1  AAA_7            P-loop containing dynein motor region


Domain annotation for each model (and alignments):
>> CbbQ_C  CbbQ/NirQ/NorQ C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0         4   7.2e+03      64      73 ..     126     135 ..     118     137 .. 0.78
   2 !  109.9   0.0   3.1e-35   5.6e-32       1      85 []     190     274 ..     190     274 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4
                                       TTCCC---HH CS
                            CbbQ_C  64 lvepltddpe 73 
                                       +++pltd+  
  gi|298674366|ref|YP_003726116.1| 126 VIHPLTDERR 135
                                       7899999976 PP

  == domain 2  score: 109.9 bits;  conditional E-value: 3.1e-35
                                       HHHHHHHHHT--HHHHHHHHHHHHHHHTTBTTTBSS---HHHHHHHHHHHTTT--HHHHHHHHTTCCC---HHHHHH CS
                            CbbQ_C   1 EaeivaresgldeevakkLVklAneiRnlkeggLeegvSTRlLvyaAkLiasglpareacraalvepltddpevrea 77 
                                       E++iva+esg+++++a++LV+++++iRn+k++gLeeg+STRlL+ya+kLi++g+++++acr a++ep+tdd +++ +
  gi|298674366|ref|YP_003726116.1| 190 ETQIVAHESGVSQNTAHSLVEIGHRIRNFKQHGLEEGISTRLLIYAGKLINEGIAPNTACRSAMIEPITDDFDLQMS 266
                                       89*************************************************************************** PP

                                       HHHHHHHH CS
                            CbbQ_C  78 Leelvaav 85 
                                       ++e+++av
  gi|298674366|ref|YP_003726116.1| 267 ISEIISAV 274
                                       *****985 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.7   0.0   2.5e-34   4.4e-31       2     138 .]      44     177 ..      43     177 .. 0.97

  Alignments for each domain:
  == domain 1  score: 107.7 bits;  conditional E-value: 2.5e-34
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG-- CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEverae 78 
                                       v L+Gp+G+gK++++e++a  lnr++ +v++++d+t++dl+gr  ik+g+ ++ d+pl++a+++g+i++lDEv +a+
  gi|298674366|ref|YP_003726116.1|  44 VNLKGPTGCGKTRFMEYMAYHLNRPLITVACHEDLTATDLIGRFIIKGGDVEWNDGPLTKAVKNGAICYLDEVVEAR 120
                                       669************************************************************************** PP

                                       HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
                             AAA_5  79 sevlnsLlslleerrllleeggelvkaknddllerfrviatanpld.rslnelspalrsRf 138
                                       +++l + ++l +err+l+ + ++ v +++++    f++  ++np +    ++l++++r+Rf
  gi|298674366|ref|YP_003726116.1| 121 TDTLVVIHPLTDERRILPIDKQGIVLKAKPE----FMLSISYNPGYqSVIKDLKQSTRQRF 177
                                       *************************999988....***********777799********9 PP

>> AAA_6  Hydrolytic ATP binding site of dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.4e-06    0.0043      25      74 ..      34      83 ..      27      91 .. 0.90
   2 ?    2.8   0.0     0.025        45     126     185 ..     143     203 ..     119     211 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.4e-06
                             AAA_6 25 ltqAlklklggapaGpagtGKtEtvkdLakalakqvvvfncsdqldyksl 74
                                       t A+k +l  +++Gp+g GKt  +  +a +l + ++ + c+++l+++ l
  gi|298674366|ref|YP_003726116.1| 34 FTAAYKNNLPVNLKGPTGCGKTRFMEYMAYHLNRPLITVACHEDLTATDL 83
                                      58899***************************************998755 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.025
                             AAA_6 126 gkeiklnksvgifitmnpgyagr.teLPdnLkalfRpvammvPdlelIaeimLfseGfkea 185
                                       g  +k ++++ + i  npgy+   ++L ++ ++ f  +    P +++ ++i+   +G +++
  gi|298674366|ref|YP_003726116.1| 143 GIVLKAKPEFMLSISYNPGYQSViKDLKQSTRQRFIAIEFNYPSMNTETQIVAHESGVSQN 203
                                       4456678889999*******87537899999999999999999999988888888887765 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.5e-06    0.0045       4     130 ..      46     178 ..      44     179 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.5e-06
                             AAA_3   4 legvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfan.....llladeinrap 75 
                                       l+g  G +kt++++ +a +l+  +  + +  dl  +d++G  +++    ++e + Gp+ +      +   de+  a 
  gi|298674366|ref|YP_003726116.1|  46 LKGPTGCGKTRFMEYMAYHLNRPLITVACHEDLTATDLIGRFIIKG--GDVEWNDGPLTKAvkngaICYLDEVVEAR 120
                                       67889************************************99865..56777889887641112267789999999 PP

                             AAA_3  76 pktqsalleameerqv.tvegethkl..pepflvlatqnPieqeGtyplpeaqldrfl 130
                                       + t   +    +er++  ++++   l  +  f++    nP  q+    l ++   rf+
  gi|298674366|ref|YP_003726116.1| 121 TDTLVVIHPLTDERRIlPIDKQGIVLkaKPEFMLSISYNPGYQSVIKDLKQSTRQRFI 178
                                       9999999999999987346666555511456888889999999999999999988886 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.9e-05     0.034      12     113 ..      31     127 ..      26     146 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.9e-05
                                       HHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBS..SSSSTTTSS-BE CS
                   Sigma54_activat  12 leqikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhe..kGaFtGAekekk 86 
                                       +e  +++ k++l+v ++G +G+GK+ + + +  + +   +p+++v c    e+l +++L G    kG   G  + + 
  gi|298674366|ref|YP_003726116.1|  31 IEIFTAAYKNNLPVNLKGPTGCGKTRFMEYMAYHLN---RPLITVACH---EDLTATDLIGRFiiKG---GDVEWND 98 
                                       56667888999****************999977665...799999885...6788888887531133...4555566 PP

                                       HHHHHT..TTSEEEEETGGGS-HHHHHHH CS
                   Sigma54_activat  87 Glfeka..dgGtlfLDeigelplelQekL 113
                                       G + ka  +g + +LDe+ e  +++ + +
  gi|298674366|ref|YP_003726116.1|  99 GPLTKAvkNGAICYLDEVVEARTDTLVVI 127
                                       87777754566778888887766665555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.8e-05     0.033      10      58 ..      46      85 ..      39      93 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.8e-05
                            AAA_22 10 vtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllr 58
                                      + G++G+GKT+ ++ +++ l         ++++++v + ++ + +dl  
  gi|298674366|ref|YP_003726116.1| 46 LKGPTGCGKTRFMEYMAYHL---------NRPLITVACHEDLTATDLIG 85
                                      56******************.........9********99999999875 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.6e-05     0.029       3      35 ..      46      78 ..      44     119 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.6e-05
                                      EESSTTSSHHHHHHHHHHHHTHEEEEEETTTCS CS
                               AAA  3 lyGppGtGKTllakavakelgvefleisgsell 35
                                      l Gp G+GKT +++ +a +l+++++++ ++e l
  gi|298674366|ref|YP_003726116.1| 46 LKGPTGCGKTRFMEYMAYHLNRPLITVACHEDL 78
                                      78**************************99866 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.2e-05     0.094       3      25 ..      46      68 ..      44      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.2e-05
                      RNA_helicase  3 lyGpsgeGKStlakeLakallkk 25
                                      l Gp+g+GK+++++++a +l + 
  gi|298674366|ref|YP_003726116.1| 46 LKGPTGCGKTRFMEYMAYHLNRP 68
                                      78*************99998765 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.7e-05       0.1       2      76 ..      41     119 ..      40     180 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.7e-05
                            AAA_14   2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelilek.lke..........ekkty 67 
                                       + ++ ++G+  +GKT +++ ++++l    +  + +++ ++ +++        ++i +    e          ++  +
  gi|298674366|ref|YP_003726116.1|  41 NLPVNLKGPTGCGKTRFMEYMAYHLN---RPLITVACHEDLTATDLI----GRFIIKGgDVEwndgpltkavKNGAI 110
                                       567889************99998887...899999998866643322....22333322111223334444557788 PP

                            AAA_14  68 lflDEiqev 76 
                                        +lDE+ e+
  gi|298674366|ref|YP_003726116.1| 111 CYLDEVVEA 119
                                       888888777 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.9e-05      0.12      26      58 ..      34      66 ..      21      82 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.9e-05
                             AAA_7 26 lelllknkkpvllvGptGtGKtviikdllkkld 58
                                      ++   kn+ pv l GptG+GKt  ++ +  +l+
  gi|298674366|ref|YP_003726116.1| 34 FTAAYKNNLPVNLKGPTGCGKTRFMEYMAYHLN 66
                                      5677899*****************998887777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 1922.93
//
Query:       gi|298674367|ref|YP_003726117.1|  [L=1141]
Description: von Willebrand factor type A [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-08   35.6   0.1    4.8e-08   33.6   0.0    2.2  3  VWA_2     von Willebrand factor type A domain
    5.8e-07   29.9   0.0    2.1e-06   28.1   0.0    2.0  1  VWA       von Willebrand factor type A domain


Domain annotation for each model (and alignments):
>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0         2   1.8e+04      17      33 ..     263     279 ..     242     285 .. 0.67
   2 ?   -3.3   0.0       1.6   1.4e+04       4      32 ..     727     751 ..     726     755 .. 0.76
   3 !   33.6   0.0   5.3e-12   4.8e-08       1     107 []     948    1063 ..     948    1063 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2
                             VWA_2  17 gptrleaakdaveallk 33 
                                       ++++++++ ++v+++ k
  gi|298674367|ref|YP_003726117.1| 263 TESEFDQLVNFVIEFAK 279
                                       67899999999999876 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.6
                             VWA_2   4 vlDtSgSmrngdygptrleaakdaveall 32 
                                       ++D S+S+ n+      ++   + +e+++
  gi|298674367|ref|YP_003726117.1| 727 LIDFSKSVLNKM----VFHSESSVIESFV 751
                                       799999999985....6777777776665 PP

  == domain 3  score: 33.6 bits;  conditional E-value: 5.3e-12
                             VWA_2    1 lvfvlDtSgSmrng..dygptrleaakdaveallksl.p.gdrvglvtfsdgpevlipl......tkd.kakiln 64  
                                        ++f++D+S+S + +    g+t l++ k+a++ ++++l + gd++++ +fs++ ++ +        +++  +++++
  gi|298674367|ref|YP_003726117.1|  948 TLFLVDVSASTQKKlgMGGKTILDIEKEALIVMSHALeNiGDKYAIYAFSGTTHRNVEYyvvkkfDEGlSTDMKS 1022
                                        68*********99853338****************99767***********87555554334322333599**** PP

                             VWA_2   65 alrnleakgggtnlaaaLqlarkalkkrrkgekrvivlitDge 107 
                                        ++ +le+   +t+l+ a+++  k  k+    +++ i+li+Dge
  gi|298674367|ref|YP_003726117.1| 1023 RISALEPI-SNTRLGPAIRHSIKKHKDIE-AKTKLIILISDGE 1063
                                        *******7.**************999997.***********96 PP

>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   2.4e-10   2.1e-06       4     156 ..     950    1118 ..     948    1129 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 2.4e-10
                                        EEEE-STTS.......CHHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSS......EEEEEETTSHCHHHHHH CS
                               VWA    4 fvlDgSgsm.......geenfekvkefikklveklevgpegtrvglvqfsse......vktefslndysskeell 65  
                                        f++D+S s        g+  ++  ke+++ +   le  + g+++++  fs++      ++++ ++++    ++++
  gi|298674367|ref|YP_003726117.1|  950 FLVDVSASTqkklgmgGKTILDIEKEALIVMSHALE--NIGDKYAIYAFSGTthrnveYYVVKKFDEG-LSTDMK 1021
                                        9*******9888888555555566777777777777..************996655555555555553.348888 PP

                                        HHHHTGSGGGGSSC-HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CS.S.............HTHHHHHH CS
                               VWA   66 salnnlkysgggttntgkalkyaleklfkssagaRenakkviilltdGksnd.g.............dpkeaane 126 
                                        s +++l  ++ ++t +g a+ + ++k+ + +a+     +k+iil++dG++ d g             d k a++e
  gi|298674367|ref|YP_003726117.1| 1022 SRISAL--EPISNTRLGPAIRHSIKKHKDIEAK-----TKLIILISDGEPYDfGtngppyqgdfaerDTKMAIRE 1089
                                        888887..44455559*****************.....************99889*******9999999999999 PP

                                        HHGCTEEEEEEEESSSHHHHHHHHHSSSSC CS
                               VWA  127 akeqgikvfavGvgnadekelLnkiasepg 156 
                                          e+gi +f+v v++  ++  + +i s+ g
  gi|298674367|ref|YP_003726117.1| 1090 GYEKGIHFFCVTVDKEAKDY-MDSIFSDAG 1118
                                        99***********9888888.888877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.78u 0.30s 00:00:01.08 Elapsed: 00:00:00.47
# Mc/sec: 7233.64
//
Query:       gi|298674368|ref|YP_003726118.1|  [L=281]
Description: hypothetical protein Metev_0404 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-19   69.5  48.8    1.5e-09   38.1  22.4    2.1  2  EamA      EamA-like transporter family
  ------ inclusion threshold ------
      0.061   13.4  12.4       0.14   12.2   0.6    3.2  3  TMEM234   Putative transmembrane family 234


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1  22.4   1.7e-13   1.5e-09       2     136 ..       7     138 ..       6     139 .. 0.93
   2 !   37.6  18.5   2.4e-13   2.1e-09       8     136 ..     155     280 ..     151     281 .] 0.85

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 1.7e-13
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvla 78 
                                       +++++ +++a++w+++ ++  ++ r++s ++++ v+ +++ i + i+a+ + ++l  +sl+++++ ++ g+  ++ +
  gi|298674368|ref|YP_003726118.1|   7 FAVVFGIASAVSWGTGDFVGGYATRRTSAYSVVLVTQIMGVITFPILAFTFSESL--PSLNNLIWGAFAGF-FGASG 80 
                                       57899********************************999999999999999999..********888885.56677 PP

                              EamA  79 fllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                        + ++++l k++ s+++++ +++ ++t ++ ++++   ++++++ g++++++G+++i+
  gi|298674368|ref|YP_003726118.1|  81 LISLYTGLAKGKMSIVAILAAVISMITPVIYSAFYEGIPSIFKITGFIFAFIGIWFIV 138
                                       78999**************************************************997 PP

  == domain 2  score: 37.6 bits;  conditional E-value: 2.4e-13
                              EamA   8 llaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafllffy 84 
                                       lla  ++++ f+ ++ ++++   + lt+ r+  a+i+l  +++l++  + k++   +l+++l gl++t  a  +f  
  gi|298674368|ref|YP_003726118.1| 155 LLAGTLFGLFFISIDNFSATAIYWPLTVSRT-TAFIMLTGFIMLTKTVR-KPTSDVILIVILAGLFNTGGA-AFFAL 228
                                       7899999999999999877777777777676.79****99999999999.677777777777777776666.78888 PP

                              EamA  85 alkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                       a   +   +a++++sl+P++t++l+ +ll+e+l ++q+lg++ +l+++++++
  gi|298674368|ref|YP_003726118.1| 229 ASGAGRLDVATVLSSLSPAVTVLLACILLKEQLASRQWLGVIAALIAIIFLS 280
                                       888899999****************************************987 PP

>> TMEM234  Putative transmembrane family 234
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.9   0.00072       6.4      56     115 ..      79     137 ..      71     138 .. 0.82
   2 ?    1.4   0.6     0.035   3.1e+02      60     109 ..     163     213 ..     156     218 .. 0.71
   3 ?   12.2   0.6   1.6e-05      0.14      52     113 ..     217     277 ..     211     280 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.00072
                           TMEM234  56 sgSvlfflllgkadlslavpiaNslafvfTvltelllgekvlkkktvlgmllvvvgialc 115
                                       sg +  +  l+k ++s++ ++a  + +++T ++ ++  e + +  +++g ++ ++gi  +
  gi|298674368|ref|YP_003726118.1|  79 SGLISLYTGLAKGKMSIVAILAAVI-SMITPVIYSAFYEGIPSIFKITGFIFAFIGIWFI 137
                                       6778889999******987777555.5666666778899*****************9876 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.035
                           TMEM234  60 lfflllgkadls.lavpiaNslafvfTvltelllgekvlkkktvlgmllvv 109
                                       lff+++ +++ + +  p++ s + +f +lt+ ++  k+++k t   +l+v+
  gi|298674368|ref|YP_003726118.1| 163 LFFISIDNFSATaIYWPLTVSRTTAFIMLTGFIMLTKTVRKPTSDVILIVI 213
                                       68999998876526679999999********77666666655544444443 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 1.6e-05
                           TMEM234  52 llNqsgSvlfflllgkadlslavpiaNslafvfTvltelllgekvlkkktvlgmllvvvgia 113
                                       l N  g  +f l+ g   l +a  +  sl+ ++Tvl + +l +++l ++++lg++  +++i+
  gi|298674368|ref|YP_003726118.1| 217 LFNTGGAAFFALASGAGRLDVAT-VLSSLSPAVTVLLACILLKEQLASRQWLGVIAALIAII 277
                                       67888888888888888888876.667***************************98888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1800.12
//
Query:       gi|298674369|ref|YP_003726119.1|  [L=424]
Description: 26S proteasome subunit P45 family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.6e-43  146.5   1.8    1.5e-42  145.1   0.0    2.3  3  AAA              ATPase family associated with various cellul
    9.7e-14   50.9   0.1    3.3e-13   49.2   0.0    1.9  1  AAA_lid_3        AAA+ lid domain
    2.2e-06   27.7   0.0    9.1e-06   25.7   0.0    2.1  1  AAA_5            AAA domain (dynein-related subfamily)
      1e-05   25.4   0.1    4.5e-05   23.3   0.0    2.1  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    2.1e-05   25.0   0.0    0.00017   22.0   0.0    2.2  1  AAA_16           AAA ATPase domain
    8.4e-05   23.0   0.5       0.03   14.7   0.0    2.4  2  AAA_17           AAA domain
    0.00016   21.8   0.0    0.00016   21.8   0.0    2.1  1  AAA_2            AAA domain (Cdc48 subfamily)
    0.00024   21.4   0.0     0.0089   16.3   0.0    2.5  2  AAA_22           AAA domain
     0.0018   18.3   0.1     0.0066   16.5   0.0    1.9  1  AAA_14           AAA domain
     0.0028   18.2   0.4      0.031   14.8   0.0    2.3  2  AAA_18           AAA domain
     0.0073   16.7   0.0      0.018   15.4   0.0    1.7  1  RNA_helicase     RNA helicase
     0.0077   15.6   0.0      0.018   14.4   0.0    1.5  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.008   15.9   0.0      0.018   14.8   0.0    1.6  1  IstB_IS21        IstB-like ATP binding protein
     0.0089   16.2   0.2      0.023   14.8   0.0    1.8  1  AAA_33           AAA domain
  ------ inclusion threshold ------
      0.011   15.0   0.0      0.025   13.8   0.0    1.5  1  TIP49            TIP49 P-loop domain
      0.012   14.9   1.4      0.053   12.9   0.0    2.4  3  ATPase           KaiC
      0.016   14.9   3.0      0.021   14.5   1.1    2.1  2  Prot_ATP_OB_N    Proteasomal ATPase OB N-terminal domain
       0.02   15.0   0.0      0.065   13.3   0.0    1.9  1  Sigma54_activ_2  Sigma-54 interaction domain
      0.023   14.4   0.0      0.082   12.6   0.0    2.0  2  AAA_24           AAA domain
      0.037   13.7   0.0       0.24   11.1   0.0    2.3  3  Sigma54_activat  Sigma-54 interaction domain
      0.041   14.0   1.3        3.1    7.9   0.0    2.3  2  ADK              Adenylate kinase
      0.042   13.2   4.1      0.071   12.4   4.1    1.3  1  DUF3450          Protein of unknown function (DUF3450)
      0.054   12.7   2.8      0.083   12.1   2.8    1.2  1  Taxilin          Myosin-like coiled-coil protein
      0.065   13.1   0.0       0.15   11.9   0.0    1.7  1  AAA_3            ATPase family associated with various cellul
      0.068   12.4   0.0       0.16   11.2   0.0    1.6  1  Zeta_toxin       Zeta toxin
       0.07   13.4   5.4       0.16   12.3   5.4    1.6  1  Tup_N            Tup N-terminal
      0.077   11.6   4.3        0.7    8.5   3.2    2.0  2  AAA_13           AAA domain
      0.093   12.6   0.0       0.89    9.5   0.0    2.3  2  NACHT            NACHT domain
      0.093   12.6   1.6        1.5    8.7   0.0    2.5  3  ATPase_2         ATPase domain predominantly from Archaea
      0.094   12.6   0.0       0.18   11.6   0.0    1.5  1  CPT              Chloramphenicol phosphotransferase-like prot
      0.094   12.7   2.5       0.12   12.4   0.5    2.2  2  Prot_ATP_ID_OB   Proteasomal ATPase OB C-terminal domain
      0.098   12.4   0.9        1.1    9.0   0.0    2.2  2  AAA_11           AAA domain
        0.1   12.1   0.0       0.19   11.2   0.0    1.5  1  AAA_7            P-loop containing dynein motor region
       0.21   11.7   2.1        1.1    9.5   0.1    2.5  2  NYD-SP28_assoc   Sperm tail C-terminal domain
          1    9.8   7.5         20    5.6   0.0    2.4  2  AAA_23           AAA domain
        1.6    8.8   7.8       0.84    9.7   4.8    2.0  2  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
          2    8.7   5.5        0.7   10.2   2.4    1.8  1  ABC_tran_CTD     ABC transporter C-terminal domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.6       3.9   1.9e+03      66     102 ..      22      58 ..      21      96 .. 0.68
   2 ?   -1.0   0.1       4.6   2.2e+03      38      58 ..      69      94 ..      46     151 .. 0.57
   3 !  145.1   0.0   3.2e-45   1.5e-42       1     131 [.     205     337 ..     205     338 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 3.9
                                       TGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSST CS
                               AAA  66 EidalaksrsgseseeeervvnqLlteldgvkkkesk 102
                                       E d+l ks+s+++++ e++ +++L++ ++ ++ ++++
  gi|298674369|ref|YP_003726119.1|  22 EYDELEKSESSDTEDLENKDIDTLISDIKSLRVQNEN 58 
                                       6677777777777788888888888888877776443 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 4.6
                                      STTHHHHHHHHHHHHHHHTS.....T CS
                               AAA 38 yvgesekkirelfkeakeka.....k 58
                                      ++++ e++i++l k++ + +      
  gi|298674369|ref|YP_003726119.1| 69 TISNYEEEIEKLNKQIDQLSkpplfV 94
                                      44555555555555555555322222 PP

  == domain 3  score: 145.1 bits;  conditional E-value: 3.2e-45
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH... CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr... 74 
                                       vllyGppG GKTl+akava++++++f+++sgs+l++k++ge+++ ++++f+ a++k+ psilfiDEida+++ r   
  gi|298674369|ref|YP_003726119.1| 205 VLLYGPPGSGKTLIAKAVASQANATFIRMSGSDLVQKFIGEGARLVKDVFEMARSKS-PSILFIDEIDAVGGMRthd 280
                                       79******************************************************9.****************987 PP

                                       TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  75 sgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                        ++ s e +r++ qLl+e+dg++ k ++v +i+atnr d ldpallr gRfdr iei+
  gi|298674369|ref|YP_003726119.1| 281 GTTGSAEVNRTMLQLLAEMDGFDPK-GEVKIIAATNRADLLDPALLRpGRFDRLIEIP 337
                                       66789999****************7.66***************************997 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.0   6.9e-16   3.3e-13       1      44 [.     360     403 ..     360     405 .. 0.98

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 6.9e-16
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedfe 44 
                                       dvd+ +LA  TeG +GADl al++eA++  lrr   +i+m+df 
  gi|298674369|ref|YP_003726119.1| 360 DVDFTRLADITEGLTGADLMALVKEAGMFVLRRRGNQINMQDFL 403
                                       9*****************************************96 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   1.9e-08   9.1e-06       1     135 [.     204     325 ..     204     327 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.9e-08
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG- CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEvera 77 
                                       +vlL GppG+gK+ +a+ +a+  n+++        ++ +dl+++    +g +  +d   +   ++++il++DE++ +
  gi|298674369|ref|YP_003726119.1| 204 GVLLYGPPGSGKTLIAKAVASQANATFIR------MSGSDLVQKFI-GEGARLVKDVFEMARSKSPSILFIDEIDAV 273
                                       59******************999888765......55578999998.34444455555565666************9 PP

                                       -.HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHH CS
                             AAA_5  78 e.sevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalr 135
                                           + +      e +r +l  + e  ++++++   ++ +ia++n++d     l+pal+
  gi|298674369|ref|YP_003726119.1| 274 GgMRTHDGTTGSAEVNRTMLQLLAEMDGFDPKG---EVKIIAATNRAD----LLDPALL 325
                                       999999999999999999999999999999965...599*******99....7777776 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   9.3e-08   4.5e-05      35      94 ..     204     271 ..     197     277 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 9.3e-08
                            RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgP.vleka.gdlaalltnl......eekdvlfideih 94 
                                        vllyGpPG Gkt +ak +a++ ++++   sg   ++k  g+ a l++++      ++  +lfidei 
  gi|298674369|ref|YP_003726119.1| 204 GVLLYGPPGSGKTLIAKAVASQANATFIRMSGSdLVQKFiGEGARLVKDVfemarsKSPSILFIDEID 271
                                       69********************99987666665155553355555554442212224557******96 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   3.5e-07   0.00017      22      63 ..     200     238 ..     191     299 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 3.5e-07
                            AAA_16  22 grpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63 
                                         p+ vll+G++G+GK+ ++++++ +++++   f+r    +l
  gi|298674369|ref|YP_003726119.1| 200 EPPSGVLLYGPPGSGKTLIAKAVASQANAT---FIRMSGSDL 238
                                       44699*******************988877...777666666 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.3      0.03        15      46     122 ..      26     112 ..      14     123 .. 0.67
   2 !   14.7   0.0   6.3e-05      0.03       1      36 [.     208     245 ..     208     269 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.03
                                       HCTSHHHHHHHHH....HHHHHHHHHHH.HSSE...EEEEE-SEEEETTEEEESSHHHHHHHH..SEEEE..EE--H CS
                            AAA_17  46 mrklpleekkelq....keaaekiaeea.kkkg...vlvdghprikeqagfldglpkevleelkpdaiil..leadp 112
                                       ++k + +++++l     ++++ +i+  + ++++    l+d  ++i + ++++++l k++ +  kp +++   le+++
  gi|298674369|ref|YP_003726119.1|  26 LEKSESSDTEDLEnkdiDTLISDIKSLRvQNENlraNLLDANMTISNYEEEIEKLNKQIDQLSKPPLFVAtvLEIND 102
                                       44433333333331111334444544444333323269*********************999999887766799*** PP

                                       HHHHHHHHHH CS
                            AAA_17 113 eeilerrlkd 122
                                       ++++ r +  
  gi|298674369|ref|YP_003726119.1| 103 DTVVLRQHGN 112
                                       *999998765 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 6.3e-05
                                       EE-TTSSHHHHHHHHHHHHTEEEEEH..HHHHHHHHHT CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsa..Gdllreeakr 36 
                                       +G+PGsGK+ +++ ++ + + t++ +  +dl+ + + +
  gi|298674369|ref|YP_003726119.1| 208 YGPPGSGKTLIAKAVASQANATFIRMsgSDLVQKFIGE 245
                                       7*****************99999855327777665544 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   3.4e-07   0.00016       5     104 ..     204     297 ..     200     313 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.4e-07
                                       -EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHH..HHHHHHTTT-HHHHTTSEEEEETGGG CS
                             AAA_2   5 silllgptgvGktelakalaellfvkkekkliradaselleeeevehlv..srligappgyvgaeegGivllDEidK 79 
                                        +ll gp g+Gkt++aka+a+  ++    ++ir+  s+l +    + +   +rl+     + + +   i+++DEid 
  gi|298674369|ref|YP_003726119.1| 204 GVLLYGPPGSGKTLIAKAVASQANA----TFIRMSGSDLVQ----KFIGegARLVKDVFEMARSKSPSILFIDEIDA 272
                                       57999******************96....9***99999999....44441144444444455555666********* PP

                                       -------------HHHHHHHHHHHH CS
                             AAA_2  80 ihpkessgadvSregVqrdLLqile 104
                                       +   ++      + +V r +Lq+l 
  gi|298674369|ref|YP_003726119.1| 273 VGGMRTHDGTTGSAEVNRTMLQLLA 297
                                       *99877777778889********95 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.8e-05    0.0089       8      42 ..     205     230 ..     200     251 .. 0.83
   2 ?    2.1   0.0      0.44   2.1e+02      82     112 ..     253     296 ..     243     314 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.8e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpev 42 
                                       ++++G++G+GKT+ ++ +++q+         ++++
  gi|298674369|ref|YP_003726119.1| 205 VLLYGPPGSGKTLIAKAVASQA---------NATF 230
                                       689******************9.........4444 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.44
                            AAA_22  82 leqalraravielliiDEaqhlr....s..........eealeeL 112
                                       + + +r+++  ++l iDE++ +     +           ++l+ L
  gi|298674369|ref|YP_003726119.1| 253 VFEMARSKSP-SILFIDEIDAVGgmrtHdgttgsaevnRTMLQLL 296
                                       4455566666.9********9965543134444455555555555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.4e-05    0.0066       5      80 ..     205     277 ..     203     296 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.4e-05
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpewe 80 
                                       +++ G+  +GKT ++k ++++       ++ ++  d  +k + + ++l + ++e+++++  ++lf+DEi  v +++
  gi|298674369|ref|YP_003726119.1| 205 VLLYGPPGSGKTLIAKAVASQAN---ATFIRMSGSDLVQKFIGEGARLVKDVFEMARSKSPSILFIDEIDAVGGMR 277
                                       6899**************98888...999999999977766666667888888875556899*******9987665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.2       1.3   6.4e+02      44      70 ..      38      79 ..      10     128 .. 0.62
   2 !   14.8   0.0   6.4e-05     0.031       1      25 [.     205     237 ..     205     277 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 1.3
                            AAA_18 44 e.........aldeskrldedkldklldaleenss......a 70
                                      e         ++++ ++ +e+ +++llda++ +s+      +
  gi|298674369|ref|YP_003726119.1| 38 EnkdidtlisDIKSLRVQNENLRANLLDANMTISNyeeeieK 79
                                      233333444444777777888888888888777764433330 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 6.4e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf........g 25 
                                       +ll G+pG+GKt +ak++++  +          
  gi|298674369|ref|YP_003726119.1| 205 VLLYGPPGSGKTLIAKAVASQANAtfirmsgsD 237
                                       799***************988643567666543 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   3.8e-05     0.018       1      68 [.     205     263 ..     205     274 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.8e-05
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkdeenps 68 
                                       ++lyGp+g GK+++ak             +++ +++r + +d ++++ g+ + ++ D+ ++  +++ps
  gi|298674369|ref|YP_003726119.1| 205 VLLYGPPGSGKTLIAKA---------VASQANATFIRMSGSDLVQKFIGEGARLVKDVFEMARSKSPS 263
                                       689**************.........345667888899999999999999888888888877665555 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   3.7e-05     0.018      25      43 ..     205     223 ..     198     230 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.7e-05
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll+GppGsGKt++ak+++
  gi|298674369|ref|YP_003726119.1| 205 VLLYGPPGSGKTLIAKAVA 223
                                       79**************986 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   3.6e-05     0.018      46      74 ..     201     229 ..     182     273 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.6e-05
                         IstB_IS21  46 kkenivllGpsGvGKshlaialgveavra 74 
                                          +++l Gp+G GK+ +a a++ +a ++
  gi|298674369|ref|YP_003726119.1| 201 PPSGVLLYGPPGSGKTLIAKAVASQANAT 229
                                       567899****************9998554 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   4.8e-05     0.023       2      34 ..     205     239 ..     205     296 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.8e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlr 34 
                                       vll G+pGsGK+  a+ ++ +    +++ s  +l 
  gi|298674369|ref|YP_003726119.1| 205 VLLYGPPGSGKTLIAKAVASQANatFIRMSGSDLV 239
                                       7899**************99988556666655544 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   5.2e-05     0.025      52      89 ..     204     239 ..     201     254 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.2e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  52 avLlaGpsgtGktalaiaiskelgedvpfvalsgsevy 89 
                                       +vLl Gp+g+Gkt +a a++ + +    f+ +sgs++ 
  gi|298674369|ref|YP_003726119.1| 204 GVLLYGPPGSGKTLIAKAVASQAN--ATFIRMSGSDLV 239
                                       79*****************99866..78******9986 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.3       1.2   5.7e+02      91     148 ..      29      88 ..      16      96 .. 0.67
   2 ?   12.9   0.0   0.00011     0.053       5      38 ..     170     221 ..     168     229 .. 0.88
   3 ?   -3.1   0.0       8.2     4e+03     110     132 ..     252     276 ..     246     301 .. 0.55

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.2
                            ATPase  91 saeesaeekdkedleelieelaea.ikeikakrvviDsitgl.ayeekeavaReilrqlv 148
                                       s++ ++e+ +++d++ li+++++  +++ + ++ ++D   ++ +yee+ +++ ++++ql 
  gi|298674369|ref|YP_003726119.1|  29 SESSDTEDLENKDIDTLISDIKSLrVQNENLRANLLDANMTIsNYEEEIEKLNKQIDQLS 88 
                                       444444556677777777777775355556677777777777677777777777777765 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00011
                            ATPase   5 IeglDeilk..................gGipegrvvlitGepGtGKtifalq 38 
                                       I glD+i++                   Gi   + vl++G pG+GKt++a+ 
  gi|298674369|ref|YP_003726119.1| 170 IGGLDDIIQeviesvqlplteqelfdnIGIEPPSGVLLYGPPGSGKTLIAKA 221
                                       7899999977999999999999999989********************9975 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 8.2
                            ATPase 110 elaeaikeikakrvviDsitgl..a 132
                                       ++ e+ +++  + + iD i+++  +
  gi|298674369|ref|YP_003726119.1| 252 DVFEMARSKSPSILFIDEIDAVggM 276
                                       5556666777777777777765322 PP

>> Prot_ATP_OB_N  Proteasomal ATPase OB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.1   4.2e-05     0.021       2      55 ..      94     146 ..      94     150 .. 0.86
   2 ?   -2.5   0.0       8.8   4.3e+03      31      41 ..     319     329 ..     316     329 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.2e-05
                     Prot_ATP_OB_N   2 yGtflavnsqdgtadVlvggrrmrVavsPlvdaeeLrpGqeVlLnEalvvVeal 55 
                                       ++t+l++n++    + + ++++++ +vs + + ++L+pG +V +n a+ v+ + 
  gi|298674369|ref|YP_003726119.1|  94 VATVLEINDDTVVLRQHGNNQEVVTNVSSDFK-DQLEPGVRVSVNAAFSVISVI 146
                                       58999999766666777788899999****99.*****************9875 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 8.8
                     Prot_ATP_OB_N  31 lvdaeeLrpGq 41 
                                       l+d++ LrpG+
  gi|298674369|ref|YP_003726119.1| 319 LLDPALLRPGR 329
                                       689*******6 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00013     0.065      23      80 ..     204     272 ..     199     278 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00013
                                       -EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-H...........HHHHHHT...TTSEEEEEE-TT CS
                   Sigma54_activ_2  23 pvfltGekGsgkelvArlLhknsgpwleifvverlaklp...........ldlleqa...kggtLylkdiad 80 
                                        v+l G++Gsgk+l+A++ ++++       ++ ++++l            +d++e a   ++ +L++ +i+ 
  gi|298674369|ref|YP_003726119.1| 204 GVLLYGPPGSGKTLIAKAVASQANAT--FIRM-SGSDLVqkfigegarlvKDVFEMArskSPSILFIDEIDA 272
                                       69*****************9998762..2222.333322233455555556666665555889999999876 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       6.7   3.2e+03     107     138 ..      73     104 ..      64     150 .. 0.65
   2 ?   12.6   0.0   0.00017     0.082       5      33 ..     205     235 ..     202     281 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 6.7
                            AAA_24 107 laeefrrllkklqelrknvifiahektrkded 138
                                       ++ee+ +l k++++l k   f+a   + +d++
  gi|298674369|ref|YP_003726119.1|  73 YEEEIEKLNKQIDQLSKPPLFVATVLEINDDT 104
                                       56667777777777777555555554444443 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00017
                            AAA_24   5 iliyGpsgiGKTtlakel..gpkplfidtek 33 
                                       +l+yGp+g+GKT +ak    + ++ fi + +
  gi|298674369|ref|YP_003726119.1| 205 VLLYGPPGSGKTLIAKAVasQANATFIRMSG 235
                                       79*************9997777777776554 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0005      0.24      22      57 ..     202     234 ..     187     246 .. 0.78
   2 ?   -2.5   0.0       7.4   3.6e+03      95     104 ..     263     272 ..     251     275 .. 0.78
   3 ?   -1.7   0.0       4.1     2e+03     134     143 ..     307     316 ..     302     333 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0005
                                       SS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEE CS
                   Sigma54_activat  22 dlsvlitGesGtGKellaraiheaskrkekpfvavn 57 
                                       ++ vl+ G  G+GK+l+a+a+ ++    ++ f+++ 
  gi|298674369|ref|YP_003726119.1| 202 PSGVLLYGPPGSGKTLIAKAVASQA---NATFIRMS 234
                                       5679***************997554...45666665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7.4
                                       SEEEEETGGG CS
                   Sigma54_activat  95 GtlfLDeige 104
                                       ++lf+Dei  
  gi|298674369|ref|YP_003726119.1| 263 SILFIDEIDA 272
                                       79*****975 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 4.1
                                       -EEEEEEESS CS
                   Sigma54_activat 134 dvriiaatne 143
                                       +v+iiaatn+
  gi|298674369|ref|YP_003726119.1| 307 EVKIIAATNR 316
                                       799*****97 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.4     0.068        33      80     141 ..      71     130 ..      29     136 .. 0.69
   2 ?    7.9   0.0    0.0064       3.1       1      45 [.     207     253 ..     207     261 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.068
                                       ESB-SSHHHHHHHHHHHHHHTSEESEE.EEEE--HHHHHHHHHTGSHHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK  80 DGfPRtveqaealeelleeekvkldlv.leldvpeevlveRltgDneetvkkRletykkqtkp 141
                                         +  ++   e+l++ +++ ++   +v   l+++++++v R  g+n+e v +  + +k+q +p
  gi|298674369|ref|YP_003726119.1|  71 SNYEEEI---EKLNKQIDQLSKPPLFVaTVLEINDDTVVLRQHGNNQEVVTNVSSDFKDQLEP 130
                                       4444444...455555555555555541457899*****************999999999887 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0064
                                       EEESTTSSHHHHHHHHHHHH..TSEEEEHHHHHHHHHHCT-HHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK   1 llGaPgaGKGtqaeklvkky..glahlstGdllRaevksgtelGkea 45 
                                       l G+Pg+GK   a+ ++++   +++++s  dl+ + + +g++l k +
  gi|298674369|ref|YP_003726119.1| 207 LYGPPGSGKTLIAKAVASQAnaTFIRMSGSDLVQKFIGEGARLVKDV 253
                                       67*********9999987651167899999**999999988876665 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   4.1   0.00015     0.071      15      92 ..      10      88 ..       1      90 [. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00015
                           DUF3450 15 aatldqalkeaekavaaaaqsqkkidkld.dekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeie 92
                                      +++ +++ +  ++  + +++ ++  ++l+ ++ ++l +++++l+ ++e+l++     +  +++ e+ei++l++qi++++
  gi|298674369|ref|YP_003726119.1| 10 SNPTTNTVNSNNEYDELEKSESSDTEDLEnKDIDTLISDIKSLRVQNENLRANLLDANMTISNYEEEIEKLNKQIDQLS 88
                                      4455555555555555555555555555415679999***************************************987 PP

>> Taxilin  Myosin-like coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.8   0.00017     0.083     250     300 ..      39      89 ..      17      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00017
                           Taxilin 250 tkktkklEketnlwkskfektnkallemaeertekkkeieklkkkiqkLek 300
                                       +k + +l  + ++++ + e+  ++ll++ ++  ++++eiekl+k+i++L+k
  gi|298674369|ref|YP_003726119.1|  39 NKDIDTLISDIKSLRVQNENLRANLLDANMTISNYEEEIEKLNKQIDQLSK 89 
                                       677888999999*************************************87 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00031      0.15       2      36 ..     205     238 ..     204     272 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00031
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdl 36 
                                       vll g PG +ktl++ka+a++ +++f r+   +dl
  gi|298674369|ref|YP_003726119.1| 205 VLLYGPPGSGKTLIAKAVASQANATFIRMS-GSDL 238
                                       7999**********************9985.4555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00033      0.16      14      53 ..     200     237 ..     190     261 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00033
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrldpDd 53 
                                       e P  +ll G pG+GK+ +a++++ +   +  ++r+++ d
  gi|298674369|ref|YP_003726119.1| 200 EPPSGVLLYGPPGSGKTLIAKAVASQA--NATFIRMSGSD 237
                                       568899*****************9997..78888877644 PP

>> Tup_N  Tup N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   5.4   0.00033      0.16      12      75 ..      22      86 ..      19      88 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00033
                             Tup_N 12 Efdalsqeasslkaqkdeyelk.iqsqiqElqqirqtlyeLeea...hrkikqqYEeeiarLkaeLes 75
                                      E+d+l++      + ++++e+k i + i++++++r +  +L ++    +    +YEeei++L++++++
  gi|298674369|ref|YP_003726119.1| 22 EYDELEKS---ESSDTEDLENKdIDTLISDIKSLRVQNENLRANlldANMTISNYEEEIEKLNKQIDQ 86
                                      66666553...234789************************9872224667899************98 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   3.2    0.0014       0.7     376     451 ..      15      89 ..       2      98 .. 0.85
   2 ?    2.0   0.0      0.13        62      20      41 ..     206     227 ..     205     251 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0014
                            AAA_13 376 eliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLek 451
                                       ++++++Ne  ++le+++++ +++le   +  l s+++ +  + ++l +++ +++  +++ e+e++kl+++i +L k
  gi|298674369|ref|YP_003726119.1|  15 NTVNSNNE-YDELEKSESSDTEDLENKDIDTLISDIKSLRVQNENLRANLLDANMTISNYEEEIEKLNKQIDQLSK 89 
                                       45555555.6999999**********99999999999999999999999999999999999999999999999865 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.13
                            AAA_13  20 liYGwNGaGKTtLSrllrslel 41 
                                       l+YG  G+GKT ++++ +s+ +
  gi|298674369|ref|YP_003726119.1| 206 LLYGPPGSGKTLIAKAVASQAN 227
                                       68*************9999754 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0    0.0018      0.89       3      24 ..     205     226 ..     203     232 .. 0.89
   2 ?    0.1   0.0       1.4   6.6e+02      64     115 ..     245     298 ..     225     301 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0018
                                       EEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklalaw 24 
                                       v+l G++GsGKT  ++ +a+++
  gi|298674369|ref|YP_003726119.1| 205 VLLYGPPGSGKTLIAKAVASQA 226
                                       799**************99876 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.4
                                       S--SSS-CCHHHHCCSCCCEEEE..EE-STT-SS-TCH.........HHHHHCT CS
                             NACHT  64 epaapvsevwavllelperlLli..lDglDelvtdlgqkekqpvrtlLselirk 115
                                       e a+ v+ v+++  +   ++L+i  +D++  ++t++g  + ++v++ + +l+ +
  gi|298674369|ref|YP_003726119.1| 245 EGARLVKDVFEMARSKSPSILFIdeIDAVGGMRTHDGTTGSAEVNRTMLQLLAE 298
                                       555667778888888899999998888888999999998888888888888865 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.8      0.45   2.2e+02      54     120 ..      23      84 ..      14     116 .. 0.64
   2 ?    8.7   0.0    0.0031       1.5      18      44 ..     200     226 ..     191     260 .. 0.81
   3 ?   -2.3   0.0       6.9   3.4e+03     114     133 ..     257     276 ..     247     298 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.45
                          ATPase_2  54 yialreesiskldefieeeeekkklekalgiavpkaeleeilkeksklvfkaielllekikkkgkki 120
                                       y++l+++++s +++  e+++ ++ +++ ++ +v++ +l      +  +++  i+++ e+i+k  k+i
  gi|298674369|ref|YP_003726119.1|  23 YDELEKSESSDTEDL-ENKDIDTLISDIKSLRVQNENL----RANLLDANMTISNYEEEIEKLNKQI 84 
                                       455555555555554.4444444444444444444444....4556666666666666666666653 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0031
                          ATPase_2  18 epneiyfiYGpegsGKtaLlkeiienl 44 
                                       ep + +++YGp gsGKt + k ++++ 
  gi|298674369|ref|YP_003726119.1| 200 EPPSGVLLYGPPGSGKTLIAKAVASQA 226
                                       56667899*********8888777655 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 6.9
                          ATPase_2 114 kkkgkkiiiiiDelqklidl 133
                                        +++   i++iDe+  ++ +
  gi|298674369|ref|YP_003726119.1| 257 ARSKSPSILFIDEIDAVGGM 276
                                       34444478999999888744 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00038      0.18       4      38 ..     205     239 ..     203     263 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00038
                                       EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEHHHHH CS
                               CPT   4 ilLnGgsssGKsslaralqevldepwlhlgvDafv 38 
                                       +lL G + sGK+ +a+a+ ++++++++ +    +v
  gi|298674369|ref|YP_003726119.1| 205 VLLYGPPGSGKTLIAKAVASQANATFIRMSGSDLV 239
                                       89*************************99655444 PP

>> Prot_ATP_ID_OB  Proteasomal ATPase OB C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.5   0.00024      0.12       1      47 [.      94     138 ..      94     144 .. 0.87
   2 ?   -1.3   0.1       4.6   2.2e+03      28      40 ..     316     328 ..     314     329 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00024
                                       EEEEEEE-TTSSEEEEE-TT.S-EEEEEE-GGGSSST--TTEEEEEET CS
                    Prot_ATP_ID_OB   1 VatVsEvlddteraiVktss.deevvvslagavpremLrpgDlVavdk 47 
                                       VatV E+ dd   ++  +++  +evv ++++  +++ L pg +V+v+ 
  gi|298674369|ref|YP_003726119.1|  94 VATVLEINDD--TVVLRQHGnNQEVVTNVSSDFKDQ-LEPGVRVSVNA 138
                                       9*******98..88888877588***********55.*********97 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 4.6
                                       E-GGGSSST--TT CS
                    Prot_ATP_ID_OB  28 lagavpremLrpg 40 
                                       +a++++++ Lrpg
  gi|298674369|ref|YP_003726119.1| 316 RADLLDPALLRPG 328
                                       7899********9 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   1.0       0.7   3.4e+02     134     183 ..      28      86 ..       2     106 .. 0.45
   2 ?    9.0   0.0    0.0022       1.1      20      43 ..     205     234 ..     187     272 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.7
                            AAA_11 134 eklakelrafeeeeek................eklkkskekskskleqerrklkkerkelskelee 183
                                       ++++++++       +                + ++++ + +  +++ + ++ ++e+++l+k++++
  gi|298674369|ref|YP_003726119.1|  28 KSESSDTE-------DlenkdidtlisdikslRVQNENLRANLLDANMTISNYEEEIEKLNKQIDQ 86 
                                       11111111.......111123334444444453334444444444444444444444444444443 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0022
                            AAA_11  20 tliqGPPGtgKTktivellsqll......s 43 
                                       +l+ GPPG+gKT    ++ sq++      s
  gi|298674369|ref|YP_003726119.1| 205 VLLYGPPGSGKTLIAKAVASQANatfirmS 234
                                       799*********888888888864444430 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00039      0.19      35      60 ..     204     228 ..     189     273 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00039
                             AAA_7  35 pvllvGptGtGKtviikdllkkldke 60 
                                        vll+Gp G+GKt+i+k + ++ +  
  gi|298674369|ref|YP_003726119.1| 204 GVLLYGPPGSGKTLIAKAVASQAN-A 228
                                       69***************9998887.3 PP

>> NYD-SP28_assoc  Sperm tail C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1    0.0022       1.1      34      56 ..      41      63 ..      40      66 .. 0.86
   2 ?    0.9   0.2         1   4.9e+02      36      53 ..      71      88 ..      68      89 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0022
                    NYD-SP28_assoc 34 eRaklieetesLekqNeeLrnlL 56
                                      +  +li++++sL+ qNe+Lr  L
  gi|298674369|ref|YP_003726119.1| 41 DIDTLISDIKSLRVQNENLRANL 63
                                      6789***************9755 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1
                    NYD-SP28_assoc 36 aklieetesLekqNeeLr 53
                                      +++ ee+e+L kq ++L 
  gi|298674369|ref|YP_003726119.1| 71 SNYEEEIEKLNKQIDQLS 88
                                      678899*******99885 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   5.4      0.16        77     140     196 ..      34      88 ..       3      90 .. 0.45
   2 ?    5.6   0.0     0.041        20      22      39 ..     205     222 ..     193     224 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.16
                            AAA_23 140 qerfeefelkdkkerleelekeleeledekkllekl.....eqekekekeleeleeeleeil 196
                                        e+    e+k     ++ l+ +++ l  +++ l+++       + ++e+e+e+l++++ ++ 
  gi|298674369|ref|YP_003726119.1|  34 TEDL---ENK----DIDTLISDIKSLRVQNENLRANlldanMTISNYEEEIEKLNKQIDQLS 88 
                                       1111...222....222222222222222222222233333566777778888888887765 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.041
                            AAA_23  22 tlItGpNGaGKTTildAi 39 
                                       +l++Gp G+GKT i  A+
  gi|298674369|ref|YP_003726119.1| 205 VLLYGPPGSGKTLIAKAV 222
                                       499*********999886 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.2       4.2     2e+03      34      48 ..      22      36 ..      13      44 .. 0.44
   2 ?    9.7   4.8    0.0017      0.84      34      71 ..      48      85 ..      32      89 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 4.2
                        TMF_DNA_bd 34 tikkLrkknkeleke 48
                                        ++L k ++  +++
  gi|298674369|ref|YP_003726119.1| 22 EYDELEKSESSDTED 36
                                      222233322222222 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0017
                        TMF_DNA_bd 34 tikkLrkknkelekeikelkkkleklekeleeleerlk 71
                                       ik+Lr +n++l  ++ + +  ++++e+e+e+l++  +
  gi|298674369|ref|YP_003726119.1| 48 DIKSLRVQNENLRANLLDANMTISNYEEEIEKLNKQID 85
                                      47777777777777777777777777777777766544 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   2.4    0.0015       0.7       6      54 ..      38      88 ..      34      89 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0015
                      ABC_tran_CTD  6 eqreleeleaeIeaLEeeiaeleaeladpely.sdp.eklaelsaeleele 54
                                      e + +++l ++I +L  + ++l a l d++++ s++ e++ +l++++++l 
  gi|298674369|ref|YP_003726119.1| 38 ENKDIDTLISDIKSLRVQNENLRANLLDANMTiSNYeEEIEKLNKQIDQLS 88
                                      788999************************999999999999999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1571  (0.0876234); expected 358.6 (0.02)
Passed bias filter:                     1008  (0.0562218); expected 358.6 (0.02)
Passed Vit filter:                       209  (0.0116571); expected 17.9 (0.001)
Passed Fwd filter:                        37  (0.0020637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              37  [number of targets reported over threshold]
# CPU time: 0.76u 0.33s 00:00:01.09 Elapsed: 00:00:00.46
# Mc/sec: 2752.15
//
Query:       gi|298674370|ref|YP_003726120.1|  [L=243]
Description: hypothetical protein Metev_0406 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00042   20.6   0.9    0.00066   20.0   0.1    1.7  2  Penicillinase_R  Penicillinase repressor
  ------ inclusion threshold ------
      0.026   14.5  11.5      0.027   14.5  11.5    1.1  1  TFIIA            Transcription factor IIA, alpha/beta subunit


Domain annotation for each model (and alignments):
>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1      0.79   7.1e+03      58      70 ..      59      71 ..      54      86 .. 0.74
   2 !   20.0   0.1   7.3e-08   0.00066      19      77 ..     163     225 ..     159     237 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.79
                                      TEEEEE----XXX CS
                   Penicillinase_R 58 rafiYsplvseee 70
                                      ++++Y+p+ ++  
  gi|298674370|ref|YP_003726120.1| 59 QQYQYYPTNQQPS 71
                                      5799999876644 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 7.3e-08
                                       EHHHHHHT--GGG--.-HHHHHHHHHHHHHTTS-EEEEE..TTEEEEE---.-XXXXXXXXXX CS
                   Penicillinase_R  19 tvkevveeleeekel.aysTVktllrrLvkKgllsreke..grafiYsplv.seeeavasavk 77 
                                       ++++++e+ e+ +   + sTV t l+r+++K+ll+r+ +  +r+++Y   + +e+e+v++ v+
  gi|298674370|ref|YP_003726120.1| 163 SSQDIQEQYEKIYGKiKLSTVSTYLSRMYRKNLLERRGNrtQREYRYIGDMgTEDEYVNENVN 225
                                       6789999999995554*******************9754449999999877346677776665 PP

>> TFIIA  Transcription factor IIA, alpha/beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5  11.5     3e-06     0.027     173     260 ..      41     123 ..      10     227 .. 0.51

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3e-06
                             TFIIA 173 ssvaalqaq.sqqaqalaepqqqlekqqqq.qqqqqqqqqqq.qvqqqqqeesqqaqqasqeqvag.sqvessqtdg 245
                                       ss++++++q ++q+q ++++ q    +qq+ q+q qq+ +q   +qq  q+  q a++    q+++ +q++++ +++
  gi|298674370|ref|YP_003726120.1|  41 SSTESSSSQmPNQNQPISQQYQYYPTNQQPsQTQYQQPVNQPlFTQQPVQQ--QPANT----QFNQpPQYQAPINQQ 111
                                       222222222222222222222221112222233333333333222222111..11111....111111221221111 PP

                             TFIIA 246 aedaleeespvlege 260
                                       + ++ +   pv + +
  gi|298674370|ref|YP_003726120.1| 112 PPQNFA---PVNNQQ 123
                                       111111...111111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1170  (0.0652574); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1574.01
//
Query:       gi|298674371|ref|YP_003726121.1|  [L=76]
Description: hypothetical protein Metev_0407 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.7e-13   47.9   8.0    7.7e-13   47.9   8.0    1.9  2  DUF131    Protein of unknown function DUF131
  ------ inclusion threshold ------
      0.033   13.5   5.1      0.037   13.3   5.1    1.0  1  DUF3273   Protein of unknown function (DUF3273)
        3.6    7.7   7.7         12    6.0   1.8    2.2  2  CrgA      Cell division protein CrgA


Domain annotation for each model (and alignments):
>> DUF131  Protein of unknown function DUF131
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   1.5     0.098   5.9e+02      46      61 ..      12      27 ..       4      28 .. 0.79
   2 !   47.9   8.0   1.3e-16   7.7e-13      19      61 ..      31      73 ..      28      74 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.098
                            DUF131 46 taiiLaIilmilllil 61
                                      ++i+++  +++l +i+
  gi|298674371|ref|YP_003726121.1| 12 LLIFIGFAMVFLGMIF 27
                                      6788888899988887 PP

  == domain 2  score: 47.9 bits;  conditional E-value: 1.3e-16
                            DUF131 19 esrvkgGGVvliGPIPIiFGsdkrlaktaiiLaIilmilllil 61
                                      +++  +GG+++iGPIPI+FG++++++  +++L+++++i++l++
  gi|298674371|ref|YP_003726121.1| 31 TGQNDFGGLIMIGPIPIVFGTSPEITSSMLLLGLLILIVYLLI 73
                                      567899***********************************98 PP

>> DUF3273  Protein of unknown function (DUF3273)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   5.1   6.2e-06     0.037      20      89 ..       4      71 ..       1      75 [. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.2e-06
                           DUF3273 20 nknLrlGfllqllsfillflvsissg..gkglfaldlvklaeevkvgsaptlvvslliglyllGtlllmvfq 89
                                      +++L+lG ll +++f ++fl  i++   g++ f+  ++  + +  +g++p ++ s+    +llG l+l+v+ 
  gi|298674371|ref|YP_003726121.1|  4 SNLLKLGSLLIFIGFAMVFLGMIFTAgtGQNDFGGLIMIGPIPIVFGTSPEITSSM----LLLGLLILIVYL 71
                                      789************999987777651156679999**************966655....455555555544 PP

>> CrgA  Cell division protein CrgA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   1.8     0.002        12      61      84 ..       5      28 ..       1      30 [. 0.84
   2 ?    5.3   0.4    0.0033        20      40      54 ..      58      72 ..      51      75 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.002
                              CrgA 61 fmaelgawNlliGfgliivGllmt 84
                                       + +lg+  ++iGf+++  G++ t
  gi|298674371|ref|YP_003726121.1|  5 NLLKLGSLLIFIGFAMVFLGMIFT 28
                                      567899999************988 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0033
                              CrgA 40 glmllGllwlvvyYl 54
                                       ++llGll l+vy l
  gi|298674371|ref|YP_003726121.1| 58 SMLLLGLLILIVYLL 72
                                      6899********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 493.47
//
Query:       gi|298674372|ref|YP_003726122.1|  [L=44]
Description: hypothetical protein Metev_0408 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 312.74
//
Query:       gi|298674373|ref|YP_003726123.1|  [L=107]
Description: hypothetical protein Metev_0409 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-23   80.4   0.6    5.5e-23   80.4   0.6    2.1  2  DUF131           Protein of unknown function DUF131
  ------ inclusion threshold ------
      0.029   14.6   3.3        5.8    7.3   1.7    2.1  2  Ost5             Oligosaccharyltransferase subunit 5
       0.04   14.9   0.0       0.04   14.9   0.0    2.0  2  DUF4834          Domain of unknown function (DUF4834)
      0.043   13.7   2.7        2.4    8.0   0.4    2.1  2  PMP22_Claudin    PMP-22/EMP/MP20/Claudin family
      0.064   12.9   1.1       0.29   10.7   1.1    1.8  1  SUR7             SUR7/PalI family
      0.076   12.6   1.1       0.13   11.9   0.1    1.8  2  Baculo_11_kDa    Baculovirus 11 kDa family
      0.084   13.5   2.2        1.9    9.2   0.0    2.2  2  OAD_gamma        Oxaloacetate decarboxylase, gamma chain
      0.089   11.5   0.6       0.16   10.7   0.6    1.4  1  DUF2207          Predicted membrane protein (DUF2207)
       0.12   12.6   0.1       0.12   12.6   0.1    2.1  2  Sigma_reg_N      Sigma factor regulator N-terminal
       0.13   13.2   0.7       0.36   11.7   0.0    1.9  2  EphA2_TM         Ephrin type-A receptor 2 transmembrane domai
       0.44   10.7  10.1        1.2    9.3   0.1    2.2  2  SdpI             SdpI/YhfL protein family
       0.59   10.4  12.9         15    5.9   6.5    2.2  2  DUF4064          Protein of unknown function (DUF4064)
        1.5    8.8   8.0        1.1    9.3   0.4    2.3  2  DUF4083          Domain of unknown function (DUF4083)
        4.3    6.5   6.5        8.4    5.5   0.9    2.1  2  Zip              ZIP Zinc transporter


Domain annotation for each model (and alignments):
>> DUF131  Protein of unknown function DUF131
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   8.5       7.6   9.7e+03      46      61 ..      12      27 ..       4      28 .. 0.80
   2 !   80.4   0.6   4.3e-26   5.5e-23       1      61 [.      26     101 ..      23     102 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 7.6
                            DUF131 46 taiiLaIilmilllil 61
                                       +ii++ i++++++i+
  gi|298674373|ref|YP_003726123.1| 12 FVIIIGFIIIAISIII 27
                                      5688888888888886 PP

  == domain 2  score: 80.4 bits;  conditional E-value: 4.3e-26
                            DUF131   1 igvvlkalekeee...............eaekeesrvkgGGVvliGPIPIiFGsdkrlaktaiiLaIilmilllil 61 
                                       i++++k++ekee+               +++k +++vkgGGVv+iGPIP++FGsd++++++++iLaIilm+l +++
  gi|298674373|ref|YP_003726123.1|  26 IINTMKEYEKEEHnyyktpdyqdqhhseNYNKPRTDVKGGGVVMIGPIPLVFGSDNQSLQKLMILAIILMLLGFAF 101
                                       567788888888899**********9999*******************************************9987 PP

>> Ost5  Oligosaccharyltransferase subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0048       6.1      12      37 ..       6      31 ..       2      43 .. 0.79
   2 ?    7.3   1.7    0.0045       5.8      10      29 ..      85     104 ..      82     107 .] 0.85

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0048
                              Ost5 12 qptlafvllligllltalfflyevts 37
                                      + + +++ ++ig++++a+ ++ +  +
  gi|298674373|ref|YP_003726123.1|  6 LIYTGIFVIIIGFIIIAISIIINTMK 31
                                      678899************99886554 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0045
                              Ost5  10 slqptlafvllligllltal 29 
                                       + + +la++l+l+g+++t++
  gi|298674373|ref|YP_003726123.1|  85 QKLMILAIILMLLGFAFTFV 104
                                       56789*************97 PP

>> DUF4834  Domain of unknown function (DUF4834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   3.1e-05      0.04       7      66 ..      11      57 ..       4      69 .. 0.51
   2 ?   -0.1   1.0       1.5   1.9e+03       8      20 ..      88     100 ..      82     107 .] 0.46

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.1e-05
                           DUF4834  7 ilifiiailviglsilsvilrtvfglgsrkkssksaqkqfgnstnsnqqksqsrsetkee 66
                                      i+++ii  ++i++si+ + ++++             +k+++n ++++ +++q++se++++
  gi|298674373|ref|YP_003726123.1| 11 IFVIIIGFIIIAISIIINTMKEY-------------EKEEHNYYKTPDYQDQHHSENYNK 57
                                      56666666666666666655555.............333334444444444333333332 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.5
                           DUF4834   8 lifiiailvigls 20 
                                       +i+ i+++++g++
  gi|298674373|ref|YP_003726123.1|  88 MILAIILMLLGFA 100
                                       3333333333333 PP

>> PMP22_Claudin  PMP-22/EMP/MP20/Claudin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1    0.0071       9.1     101     137 ..       3      38 ..       1      55 [. 0.65
   2 ?    8.0   0.4    0.0019       2.4      71      92 ..      82     103 ..      75     106 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0071
                                       GTTTSSHHHHHHHHHHHHHHHHHHHHHHHHH----SS CS
                     PMP22_Claudin 101 gerfklaGiiflvsgLcvlvgasiYtsriaedlsksl 137
                                       ge    +Gi++++ g+ +++++si ++ ++e ++++ 
  gi|298674373|ref|YP_003726123.1|   3 GEYLIYTGIFVIIIGF-IIIAISIIINTMKEYEKEEH 38 
                                       5555569999999886.46677777666655544433 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0019
                                       TTHHHHHHHHHHHHHHHHHHHH CS
                     PMP22_Claudin  71 qavqalmilsiilgilslivav 92 
                                       q+ q+lmil+iil +l++ + +
  gi|298674373|ref|YP_003726123.1|  82 QSLQKLMILAIILMLLGFAFTF 103
                                       899*************998876 PP

>> SUR7  SUR7/PalI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.1   0.00023      0.29     111     165 ..       6     105 ..       3     107 .] 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00023
                              SUR7 111 ltkalfilhiialvlsfislvvgllaic.............................................vspd 142
                                       l+  +  ++ii++++ +is++++ +                                                ++++
  gi|298674373|ref|YP_003726123.1|   6 LIYTGIFVIIIGFIIIAISIIINTMKEYekeehnyyktpdyqdqhhsenynkprtdvkgggvvmigpiplvfgSDNQ 82 
                                       66677889999999999999999999988999999999999999887777777777777777777777777543333 PP

                              SUR7 143 nsrllsflnlllsvlsflatlla 165
                                       +   l++l+++l +l f +t++ 
  gi|298674373|ref|YP_003726123.1|  83 SLQKLMILAIILMLLGFAFTFVY 105
                                       33458899999999999998876 PP

>> Baculo_11_kDa  Baculovirus 11 kDa family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1    0.0001      0.13      45      72 ..      11      37 ..       5      55 .. 0.69
   2 ?   -0.9   0.2      0.99   1.3e+03      45      51 ..      89      95 ..      79     105 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0001
                     Baculo_11_kDa 45 vfvvivlfilLlvvilknaeaeeaekek 72
                                      +fv+i+ fi++ ++i+ n+ + e+eke+
  gi|298674373|ref|YP_003726123.1| 11 IFVIIIGFIIIAISIIINTMK-EYEKEE 37
                                      799999999988877664433.333332 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.99
                     Baculo_11_kDa 45 vfvvivl 51
                                      ++ +i++
  gi|298674373|ref|YP_003726123.1| 89 ILAIILM 95
                                      2222222 PP

>> OAD_gamma  Oxaloacetate decarboxylase, gamma chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0015       1.9      17      42 ..      12      37 ..       7      71 .. 0.66
   2 ?    3.0   1.7      0.12   1.6e+02       3      16 ..      91     104 ..      89     105 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0015
                         OAD_gamma 17 vLilLslvislfskiikkkakkkkkk 42
                                      + i++ ++i ++s ii++ ++ +k++
  gi|298674373|ref|YP_003726123.1| 12 FVIIIGFIIIAISIIINTMKEYEKEE 37
                                      44555555555555555554444443 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.12
                         OAD_gamma   3 gllltllGmgvVFv 16 
                                       +++l+llG+++ Fv
  gi|298674373|ref|YP_003726123.1|  91 AIILMLLGFAFTFV 104
                                       899**********8 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.6   0.00012      0.16     383     429 ..       6     104 ..       2     107 .] 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00012
                           DUF2207 383 lsalglgliilglilillallllvll................................................... 408
                                       l++ g+++ii+g+i+i ++++  ++                                                    
  gi|298674373|ref|YP_003726123.1|   6 LIYTGIFVIIIGFIIIAISIIINTMKeyekeehnyyktpdyqdqhhsenynkprtdvkgggvvmigpiplvfgsdnq 82 
                                       56667777777777665555544444889999999999999999999999999999999999999999999999888 PP

                           DUF2207 409 .lvfllilllillliaiivlll 429
                                        l  l+il++il+l++++++++
  gi|298674373|ref|YP_003726123.1|  83 sLQKLMILAIILMLLGFAFTFV 104
                                       7555666666666655555554 PP

>> Sigma_reg_N  Sigma factor regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   9.7e-05      0.12      14      47 ..       8      42 ..       4      69 .. 0.59
   2 ?    0.8   1.0      0.49   6.2e+02      11      27 ..      88     104 ..      82     107 .] 0.58

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.7e-05
                       Sigma_reg_N 14 rivlislivlllifvilvvtllyl.aekegnklre 47
                                       + ++++i+ ++i++i+++++ +   eke++++ +
  gi|298674373|ref|YP_003726123.1|  8 YTGIFVIIIGFIIIAISIIINTMKeYEKEEHNYYK 42
                                      56677777777777777555555523333333332 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.49
                       Sigma_reg_N  11 silrivlislivlllif 27 
                                        il i+l  l+++++++
  gi|298674373|ref|YP_003726123.1|  88 MILAIILMLLGFAFTFV 104
                                       45555555555555544 PP

>> EphA2_TM  Ephrin type-A receptor 2 transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00028      0.36       6      50 ..      11      55 ..       6      64 .. 0.42
   2 ?   -0.7   0.5       2.2   2.8e+03      11      18 ..      90      97 ..      84     106 .. 0.43

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00028
                          EphA2_TM  6 vaglvllvilvilvlvlvrrrsknrkqksdlkskeekkeeensgk 50
                                      ++++++  i++++ +++   +++++++++  k+++++ +++ +++
  gi|298674373|ref|YP_003726123.1| 11 IFVIIIGFIIIAISIIINTMKEYEKEEHNYYKTPDYQDQHHSENY 55
                                      444444445455555544334433333333333444433333333 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.2
                          EphA2_TM 11 llvilvil 18
                                      l +il++l
  gi|298674373|ref|YP_003726123.1| 90 LAIILMLL 97
                                      22222222 PP

>> SdpI  SdpI/YhfL protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   6.1     0.059        76      28      58 ..       1      26 [.       1      30 [. 0.65
   2 ?    9.3   0.1   0.00092       1.2      30      67 .]      65     106 ..      54     106 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.059
                              SdpI 28 fagklwiiaGlillllalgavvlvllvlvll 58
                                      +ag ++i +G+ +++++     ++++++ ++
  gi|298674373|ref|YP_003726123.1|  1 MAGEYLIYTGIFVIIIG-----FIIIAISII 26
                                      58899999999999999.....333333222 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00092
                              SdpI  30 gklwiiaGlilllla....lgavvlvllvlvlllvivpiiys 67 
                                       g + +i+ + l++ +    l++++++ ++l+ll ++++++ys
  gi|298674373|ref|YP_003726123.1|  65 GGVVMIGPIPLVFGSdnqsLQKLMILAIILMLLGFAFTFVYS 106
                                       334455555544444999988888999999999999999997 PP

>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   6.5     0.012        15      58      84 ..       3      29 ..       1      35 [. 0.88
   2 ?    5.8  12.1     0.013        16      17      81 ..      11     104 ..       9     107 .] 0.77

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.012
                           DUF4064 58 stllivlgvialiaivlgivgalllkk 84
                                      +++li++g++++i+++++i+ ++++++
  gi|298674373|ref|YP_003726123.1|  3 GEYLIYTGIFVIIIGFIIIAISIIINT 29
                                      6899********************996 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.013
                           DUF4064  17 illglllllflfllssgefsqeltee.............................qalsgedasavleflstllivl 64 
                                       i+ ++++++++ ++++ ++++e+++e                             + ++    + v ++ +++l  l
  gi|298674373|ref|YP_003726123.1|  11 IFVIIIGFIIIAISIIINTMKEYEKEehnyyktpdyqdqhhsenynkprtdvkggGVVMIGPIPLVFGSDNQSLQKL 87 
                                       333333333333344445555555556777889**************99999999999999999999********** PP

                           DUF4064  65 gvialiaivlgivgall 81 
                                       +++a+i+ +lg++++++
  gi|298674373|ref|YP_003726123.1|  88 MILAIILMLLGFAFTFV 104
                                       ***********999886 PP

>> DUF4083  Domain of unknown function (DUF4083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.4   0.00084       1.1       5      29 ..       6      30 ..       3      39 .. 0.85
   2 ?    3.0   1.9      0.08     1e+02       8      24 ..      89     103 ..      84     106 .. 0.49

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00084
                           DUF4083  5 liyliivivLilllvfsftlfiRrv 29
                                      liy+ i +++i+ +++++ ++i  +
  gi|298674373|ref|YP_003726123.1|  6 LIYTGIFVIIIGFIIIAISIIINTM 30
                                      7899999999999999999999765 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.08
                           DUF4083   8 liivivLilllvfsftl 24 
                                        +++i+++l++  +ft+
  gi|298674373|ref|YP_003726123.1|  89 ILAIILMLLGF--AFTF 103
                                       34444444444..4444 PP

>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.5     0.018        23      80     122 ..      12      55 ..       6      67 .. 0.52
   2 ?    5.5   0.9    0.0065       8.4     308     331 ..      81     104 ..      67     106 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.018
                               Zip  80 llvllGflllllveklltmivek..ksshkektpkkasssssesa 122
                                       +++++Gf+++  +  +++ ++e   ++++  ktp+ +++++se++
  gi|298674373|ref|YP_003726123.1|  12 FVIIIGFIII-AISIIINTMKEYekEEHNYYKTPDYQDQHHSENY 55 
                                       3444444443.3445555555554444555555555555555555 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0065
                               Zip 308 gssslkqsllqllglllGfalmll 331
                                       ++s  k+++l+++++llGfa+ ++
  gi|298674373|ref|YP_003726123.1|  81 NQSLQKLMILAIILMLLGFAFTFV 104
                                       45667899************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1368  (0.076301); expected 358.6 (0.02)
Passed bias filter:                      685  (0.0382063); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 716.32
//
Query:       gi|298674374|ref|YP_003726124.1|  [L=664]
Description: excinuclease ABC subunit B [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-32  111.2   0.7    1.1e-31  108.9   0.1    2.6  3  UvrB_inter   UvrB interaction domain
    9.4e-22   76.6   0.8    2.5e-21   75.3   0.8    1.8  1  UvrB         Ultra-violet resistance protein B
    4.1e-18   65.8   0.1    1.3e-17   64.1   0.1    1.9  1  Helicase_C   Helicase conserved C-terminal domain
    1.5e-14   54.3   0.0    2.7e-13   50.3   0.0    2.4  2  ResIII       Type III restriction enzyme, res subunit
    2.8e-10   39.6   4.9    2.8e-10   39.6   4.9    2.4  2  UVR          UvrB/uvrC motif
     0.0005   19.8   0.0       0.03   14.0   0.0    2.5  2  AAA_30       AAA domain
    0.00068   19.6   0.0      0.087   12.8   0.0    2.8  2  Microtub_bd  Microtubule binding
     0.0016   18.3   0.0      0.013   15.2   0.0    2.5  3  DEAD         DEAD/DEAH box helicase
  ------ inclusion threshold ------
      0.038   14.0   0.0       0.18   11.8   0.0    2.3  1  UB2H         Bifunctional transglycosylase second domain
      0.045   12.7   0.0      0.076   11.9   0.0    1.3  1  Kinesin      Kinesin motor domain
       0.05   13.3   0.1       0.39   10.4   0.0    2.4  2  SWI2_SNF2    SWI2/SNF2 ATPase
       0.11   12.6   0.1       0.11   12.6   0.1    2.8  3  DUF87        Helicase HerA, central domain
       0.11   12.7   0.5          1    9.6   0.0    2.7  2  AAA_22       AAA domain
        2.5    8.4  10.0       0.41   10.8   0.3    3.3  3  DUF5446      Family of unknown function (DUF5446)


Domain annotation for each model (and alignments):
>> UvrB_inter  UvrB interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.9   0.1   8.4e-35   1.1e-31       1      91 []     158     250 ..     158     250 .. 0.93
   2 ?   -2.4   0.0       4.3   5.5e+03      47      70 ..     372     394 ..     369     410 .. 0.76
   3 ?   -2.5   0.0       4.8   6.1e+03      52      72 ..     469     489 ..     465     497 .. 0.76

  Alignments for each domain:
  == domain 1  score: 108.9 bits;  conditional E-value: 8.4e-35
                        UvrB_inter   1 lelkvgqkidreellrkLvelqYerndvelkrGtFrvrGdtveifpasaeevairieffgdeiesireidpltgksl 77 
                                       l l+ g+++d+++l + Lv++qYernd+e+++GtFr rGdt+ei+pa+ ee+ irie+fgdeie+i+++dpltgk+ 
  gi|298674374|ref|YP_003726124.1| 158 LFLSPGEEVDKSSLSASLVNMQYERNDIEFTQGTFRSRGDTIEIYPAQ-EEHGIRIELFGDEIEKISYFDPLTGKVQ 233
                                       56899*******************************************.8************************997 PP

                        UvrB_inter  78 ek...leeitifPakhf 91 
                                       ++    e i i+Pakhf
  gi|298674374|ref|YP_003726124.1| 234 NTlneDEYIAIYPAKHF 250
                                       55222778********9 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.3
                        UvrB_inter  47 asaeevairieffgdeiesireid 70 
                                       a+ ++++++++ f++++++i ++ 
  gi|298674374|ref|YP_003726124.1| 372 AY-DNRPLKFDEFENRVNQIIYVS 394
                                       44.789999999999999997765 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 4.8
                        UvrB_inter  52 vairieffgdeiesireidpl 72 
                                       v ir++     i+++++ + +
  gi|298674374|ref|YP_003726124.1| 469 VGIRVKYMHSDIDTLERAEIV 489
                                       678999999999998877665 PP

>> UvrB  Ultra-violet resistance protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3   0.8   1.9e-24   2.5e-21       1      42 [.     552     593 ..     552     594 .. 0.98

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 1.9e-24
                                       EE-SS--HHHHHHHHHHHHHHHHHHHHHHHHT------XXXX CS
                              UvrB   1 lYADkiTdSMkkAideTerRReiQeaYNeehgItPktikKki 42 
                                       lYADk T+SMk+AideT+rRRe+Q+++N+++gI+P+ti+K+i
  gi|298674374|ref|YP_003726124.1| 552 LYADKTTGSMKRAIDETNRRRELQIDFNQRNGIVPQTITKAI 593
                                       8***************************************99 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1   0.1     1e-20   1.3e-17      11     109 ..     441     544 ..     430     546 .. 0.89

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 1e-20
                                       HHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTES CS
                        Helicase_C  11 kleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvn 86 
                                       +  eeg+++l+ + t++++e+ +++lle  gi+v ++h+++ + er ei+++ +kg++dvL+  + + +G+dip+v+
  gi|298674374|ref|YP_003726124.1| 441 EVAEEGYRTLVTTLTKRMAEDlTDYLLE-VGIRVKYMHSDIDTLERAEIVRSLRKGDFDVLVGINLLREGLDIPEVE 516
                                       667899*************998899953.47********************************************** PP

                                       EEEESSSS.....SSHHHHHHHHTTSSS CS
                        Helicase_C  87 lVinfdlp.....rnvtsyiqriGRtgR 109
                                       lV ++d++     r+ +s+iq iGR+ R
  gi|298674374|ref|YP_003726124.1| 517 LVAILDADkegflRSERSLIQTIGRASR 544
                                       ********88888889**********99 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3   0.0   2.1e-16   2.7e-13       2     137 ..      10     137 ..       9     139 .. 0.82
   2 ?    1.5   0.0       0.2   2.6e+02     134     148 ..     331     356 ..     233     399 .. 0.65

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 2.1e-16
                                       -EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGT CS
                            ResIII   2 lelreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkfl 78 
                                       +e+r  Q +ai nl + l+ k+ k+  +   TG+GKT+++a++ie+++k      +l+++++k+l  q+++ef++f+
  gi|298674374|ref|YP_003726124.1|  10 YEPRGDQPSAISNLTNGLN-KGFKHQTLLGVTGSGKTFTMANVIENVQK-----PTLVIAHNKTLAAQLYSEFREFF 80 
                                       678999************9.****************************9.....8********************** PP

                                       GG........GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEE CS
                            ResIII  79 seayke....igkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdvii 137
                                       ++++ e        ++ + +++      +++ ++++++s+++++++ +   ++ l +r dvi+
  gi|298674374|ref|YP_003726124.1|  81 PDNAVEyfvsYYDYYQPEAYIP------TTDTYIEKESSINEEINRLRLSATKSLMERRDVIV 137
                                       *998544444333345555555......99999999999999995545555666666666666 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.2
                                       S...EEEEETGGGTTS.........T CS
                            ResIII 134 d...viiiDEaHrlgak........k 148
                                       +   +i+iDE+H +  +        k
  gi|298674374|ref|YP_003726124.1| 331 PddyLIFIDESHVTIPQiggmyngdK 356
                                       26679999999988776555555441 PP

>> UVR  UvrB/uvrC motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       2.5   3.2e+03       6      18 ..     263     275 ..     259     276 .. 0.81
   2 !   39.6   4.9   2.2e-13   2.8e-10       1      35 [.     626     660 ..     626     661 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.5
                               UVR   6 eLeeemeeAaene 18 
                                       ++e+e+ee ++++
  gi|298674374|ref|YP_003726124.1| 263 SIEKELEEHVSRF 275
                                       7899***999876 PP

  == domain 2  score: 39.6 bits;  conditional E-value: 2.2e-13
                               UVR   1 kklikeLeeemeeAaenedFEkAAklRDqinalkk 35 
                                       ++li +Lee+m+ Aa+n++FEkAA+lRD+in l++
  gi|298674374|ref|YP_003726124.1| 626 ENLIIDLEEDMHLAAKNLEFEKAAELRDKINDLRR 660
                                       699****************************9986 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   2.3e-05      0.03      14      65 ..      27      75 ..      13     138 .. 0.79
   2 ?    3.2   0.0     0.049        63      35      81 ..     436     484 ..     434     562 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.3e-05
                            AAA_30 14 ltsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaee 65
                                      l++g + ++l G+ G+GKt++++ + e ++   ++ +++A++++ A++L  e
  gi|298674374|ref|YP_003726124.1| 27 LNKGFKHQTLLGVTGSGKTFTMANVIENVQ---KPTLVIAHNKTLAAQLYSE 75
                                      345667899**************9988888...5679999999999998765 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.049
                            AAA_30  35 lkalreaweaaggrviglAptgkaAkvLae...elgieastiakllkrlk 81 
                                       ++++re++e +g+r ++ + t+++A++L++   e+gi+ + +++ +++l+
  gi|298674374|ref|YP_003726124.1| 436 IGEVREVAE-EGYRTLVTTLTKRMAEDLTDyllEVGIRVKYMHSDIDTLE 484
                                       567777776.89****************9766677777777666555544 PP

>> Microtub_bd  Microtubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   6.8e-05     0.087      89     108 ..      37      56 ..      34      79 .. 0.70
   2 ?    3.4   0.0     0.052        67       8      26 ..     425     443 ..     419     465 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.8e-05
                                       EES................S CS
                       Microtub_bd  89 ygqTGsGKtyTmegeeeeag 108
                                       +g TGsGKt+Tm +  e+ +
  gi|298674374|ref|YP_003726124.1|  37 LGVTGSGKTFTMANVIENVQ 56 
                                       689**********9444333 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.052
                                       HHHCHHHHHHHCTB-EEEE CS
                       Microtub_bd   8 RrkleNtiqelkGniRvfa 26 
                                        r +eN+i++l G++R  a
  gi|298674374|ref|YP_003726124.1| 425 VRPIENQIDDLIGEVREVA 443
                                       5899************766 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0     1e-05     0.013      15      73 ..      32      82 ..      14     139 .. 0.80
   2 ?   -1.5   0.0       1.4   1.8e+03     159     170 ..     379     398 ..     333     404 .. 0.68
   3 ?   -2.1   0.0       2.1   2.7e+03      46     103 ..     445     502 ..     427     506 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1e-05
                                      CEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 15 gdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkky 73
                                      ++  + + TGsGKT   +  v+++v       ++ +l+++  + La q ++++++f+  
  gi|298674374|ref|YP_003726124.1| 32 KHQTLLGVTGSGKTFT-MANVIENV-------QKPTLVIAHNKTLAAQLYSEFREFFPD 82
                                      55566789******98.78899777.......3356*******************9974 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.4
                                       T........SEEEEEESSBS CS
                                       x........xxxxxxxxxxx RF
                              DEAD 159 q........rqvivlSATlp 170
                                       +        +q+i +SAT+ 
  gi|298674374|ref|YP_003726124.1| 379 KfdefenrvNQIIYVSATPA 398
                                       24444444467999999986 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.1
                                       TS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHHHTT.CSEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                              DEAD  46 tgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlskldng.vdivvg 103
                                       +g ++l+ + t+ +ae+  + l +++  ++  +++ i   ++ + ++ l++g  d++vg
  gi|298674374|ref|YP_003726124.1| 445 EGYRTLVTTLTKRMAEDLTDYLLEVGIRVK-YMHSDIDTLERAEIVRSLRKGdFDVLVG 502
                                       555666666666666666666655555433.2223455566666666666666777776 PP

>> UB2H  Bifunctional transglycosylase second domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00014      0.18       1      43 [.     160     202 ..     160     226 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                              UB2H   1 LypGaalsaaqleqeLellgYrkvsnvtrpGeyavsgnriell 43 
                                       L+pG+++++  l + L +++Y +++   ++G+++++g++ie++
  gi|298674374|ref|YP_003726124.1| 160 LSPGEEVDKSSLSASLVNMQYERNDIEFTQGTFRSRGDTIEIY 202
                                       78**********************9999*************97 PP

>> Kinesin  Kinesin motor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   5.9e-05     0.076      81     103 ..      37      61 ..      17     128 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.9e-05
                                       EESTTSSHHHHHTBC..TTTSBSHH CS
                           Kinesin  81 YGqtgsGKTyTmegk..eeeeeGii 103
                                        G+tgsGKT+Tm     + +++ ++
  gi|298674374|ref|YP_003726124.1|  37 LGVTGSGKTFTMANVieNVQKPTLV 61 
                                       49**********9876533444444 PP

>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0003      0.39      26      74 ..      39      81 ..      16     138 .. 0.81
   2 ?   -0.8   0.1      0.77   9.8e+02      75     109 ..     563     596 ..     553     640 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0003
                         SWI2_SNF2 26 tqGSGKsltmvflakklleeelknpkvvvvtDRkdLdkQlsktfakage 74
                                       +GSGK++tm+ + +++++     p++v +   k L  Ql+++f+++  
  gi|298674374|ref|YP_003726124.1| 39 VTGSGKTFTMANVIENVQK-----PTLV-IAHNKTLAAQLYSEFREFFP 81
                                      58********998887777.....6665.566788********998744 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.77
                         SWI2_SNF2  75 ekpkqaesrkeLkellekesekiifttiqKfeeee 109
                                       ++ +++++r+eL+  + +++++i+  ti K  ++e
  gi|298674374|ref|YP_003726124.1| 563 RAIDETNRRRELQIDF-NQRNGIVPQTITKAIQKE 596
                                       3345788888999999.558889988888875432 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   8.5e-05      0.11      24      48 ..      32      56 ..      27      65 .. 0.85
   2 ?   -2.8   0.1       4.4   5.7e+03     156     181 ..     256     281 ..     218     297 .. 0.60
   3 ?    0.9   0.6      0.32   4.1e+02     130     179 ..     607     662 ..     554     664 .] 0.72

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.5e-05
                             DUF87 24 rHlAilgsTGsGKSntvavLleell 48
                                      +H   lg TGsGK++t+a  +e++ 
  gi|298674374|ref|YP_003726124.1| 32 KHQTLLGVTGSGKTFTMANVIENVQ 56
                                      79999*************9888765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.4
                             DUF87 156 elrklknqaiarlldkledllrkggs 181
                                       +++++ ++++++l+++++++  ++++
  gi|298674374|ref|YP_003726124.1| 256 QIDRAMDSIEKELEEHVSRFEANNQQ 281
                                       34444444444444444444444433 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.32
                             DUF87 130 a.........keekeklssdepveklleelkkekeelrklknqaiarlldkledllrkg 179
                                                 +e+k   +++ ++  l+e+++   + +++l  + +a+l dk++dl rk+
  gi|298674374|ref|YP_003726124.1| 607 TseysetvalAENKSTKDIENLIIDLEEDMH---LAAKNLEFEKAAELRDKINDLRRKY 662
                                       2333333333467777777777777777777...8999999999999999999999987 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00079         1       9      40 ..      35      58 ..      29     128 .. 0.80
   2 ?   -0.5   0.1       1.1   1.4e+03      22      85 ..     590     658 ..     588     664 .] 0.68

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00079
                            AAA_22  9 vvtGesGtGKTtllrrlleqldeeakaeeerp 40
                                      ++ G +G+GKT++++++ e+ +        +p
  gi|298674374|ref|YP_003726124.1| 35 TLLGVTGSGKTFTMANVIENVQ--------KP 58
                                      688***************9974........22 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.1
                            AAA_22  22 lrrlleqldeeakaee...erpevvfvtlpsst.sskdllrellralglelka.erlsseellealeqa 85 
                                        + ++++l+e++++e    e +e+v    ++st + ++l  +l ++++l +k+ e  +  el++++++ 
  gi|298674374|ref|YP_003726124.1| 590 TKAIQKELVEVEYPEPqtsEYSETVALAENKSTkDIENLIIDLEEDMHLAAKNlEFEKAAELRDKINDL 658
                                       566777888888888888867777755555555599999999999999888886555666666666655 PP

>> DUF5446  Family of unknown function (DUF5446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1         2   2.6e+03      38      50 ..     109     121 ..     104     136 .. 0.55
   2 ?   10.8   0.3   0.00032      0.41      16      47 ..     256     287 ..     253     307 .. 0.88
   3 ?    1.7   0.8      0.24     3e+02      16      48 ..     624     656 ..     621     660 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2
                           DUF5446  38 ekeekeeerldll 50 
                                       eke+ ++e +++l
  gi|298674374|ref|YP_003726124.1| 109 EKESSINEEINRL 121
                                       4444444444443 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00032
                           DUF5446  16 eiEeeltevEkelseavneteaekeekeeerl 47 
                                        i + ++++Ekel e v + ea  ++ e +rl
  gi|298674374|ref|YP_003726124.1| 256 QIDRAMDSIEKELEEHVSRFEANNQQLEAQRL 287
                                       6999*******************999998887 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.24
                           DUF5446  16 eiEeeltevEkelseavneteaekeekeeerld 48 
                                       +iE+ +   E+++ +a +++e ek  +  + ++
  gi|298674374|ref|YP_003726124.1| 624 DIENLIIDLEEDMHLAAKNLEFEKAAELRDKIN 656
                                       788888888888888888888888887777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (664 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1175  (0.0655363); expected 358.6 (0.02)
Passed bias filter:                      749  (0.0417759); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.81u 0.30s 00:00:01.11 Elapsed: 00:00:00.51
# Mc/sec: 3925.49
//
Query:       gi|298674375|ref|YP_003726125.1|  [L=94]
Description: rubrerythrin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.4e-09   37.2   2.0    4.1e-09   36.9   2.0    1.1  1  Rubrerythrin  Rubrerythrin
      3e-05   24.3   0.6      3e-05   24.3   0.6    1.6  2  DUF2383       Domain of unknown function (DUF2383)
     0.0019   18.0   0.1     0.0029   17.4   0.1    1.2  1  COQ7          Ubiquinone biosynthesis protein COQ7
     0.0052   17.0   0.1     0.0059   16.8   0.1    1.1  1  Ferritin_2    Ferritin-like domain
  ------ inclusion threshold ------
      0.017   14.9   0.5      0.023   14.6   0.5    1.3  1  DUF2202       Uncharacterized protein domain (DUF2202)
      0.052   13.2   0.6      0.057   13.0   0.6    1.1  1  DUF3231       Protein of unknown function (DUF3231)
        1.8    8.4   6.5        2.2    8.1   0.4    2.4  2  MSL1_dimer    Dimerisation domain of Male-specific-Lethal 1


Domain annotation for each model (and alignments):
>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   2.0   1.6e-12   4.1e-09       1      72 [.      20      88 ..      20      93 .. 0.85

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 1.6e-12
                                      HHHHHHHHHHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS--- CS
                      Rubrerythrin  1 eiLekAiagEssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepelelevkekvreya 72
                                      eiL +Ai++E +a++lY+e+a+ a+  + +i+ +++++A+eE+ H + +  +l k + ++  e +e  ++++
  gi|298674375|ref|YP_003726125.1| 20 EILRAAIIAELDAINLYEEMADLAD--NDEIKSVLLDVAKEEKTHVGEFQTMLLKSDSQQV-EELEAGKKEV 88
                                      89***********************..************************9988776665.4444444444 PP

>> DUF2383  Domain of unknown function (DUF2383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.6   1.2e-08     3e-05      10      58 ..      26      74 ..      17      84 .. 0.87
   2 ?    0.7   0.2      0.26   6.7e+02      82     105 ..      71      92 ..      67      94 .] 0.69

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.2e-08
                                      HHHHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                           DUF2383 10 ietlkdgeegykeaaekvkdpqlktlleriaeereeaaeeLqseiralg 58
                                      i ++ d+++ y+e+a+ ++++++k++l ++a+e + ++ e+q ++ +  
  gi|298674375|ref|YP_003726125.1| 26 IIAELDAINLYEEMADLADNDEIKSVLLDVAKEEKTHVGEFQTMLLKSD 74
                                      66788*************************************9998765 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.26
                                       -----HHHHHHHHHHHHHHHHHHH CS
                           DUF2383  82 ltsndeeaileeleegEdkaleey 105
                                       l+s+++   +eele g + + ee+
  gi|298674375|ref|YP_003726125.1|  71 LKSDSQ--QVEELEAGKKEVEEEL 92 
                                       455554..5999999988887765 PP

>> COQ7  Ubiquinone biosynthesis protein COQ7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   1.1e-06    0.0029       4      60 ..      20      74 ..      18      79 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.1e-06
                              COQ7  4 rllRvdhaGElgAvaiYkgqlavlakkdpelkpllkemleqEkeHlatfeellkerr 60
                                      ++lR     El A  +Y+  ++   +++ e+k++l +++++Ek H+  f+++l + +
  gi|298674375|ref|YP_003726125.1| 20 EILRAAIIAELDAINLYEEMADL--ADNDEIKSVLLDVAKEEKTHVGEFQTMLLKSD 74
                                      789999999************99..6888899*******************998765 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   2.3e-06    0.0059       2      61 ..      18      70 ..       5      86 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.3e-06
                        Ferritin_2  2 dvdiLnfAlnlEyleaafYtaalegaslddkalldaevrevaeeiakheeaHveflkaal 61
                                      d +iL  A+ +E  +++ Y+++++        + ++e++ v+ ++ak+e++Hv  ++++l
  gi|298674375|ref|YP_003726125.1| 18 DKEILRAAIIAELDAINLYEEMAD-------LADNDEIKSVLLDVAKEEKTHVGEFQTML 70
                                      788999999999999999999997.......56788889999999999999998888877 PP

>> DUF2202  Uncharacterized protein domain (DUF2202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.5   8.9e-06     0.023      87     143 ..      19      75 ..       6      93 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.9e-06
                           DUF2202  87 edaLkvgatiedldiaDl.ekalketdnkdikevYenllkGsrnhlRsfvrkleergk 143
                                       ++ L++ a i +ld  +l e++ +  dn++ik+v   + k  + h+  f  +l + + 
  gi|298674375|ref|YP_003726125.1|  19 KEILRA-AIIAELDAINLyEEMADLADNDEIKSVLLDVAKEEKTHVGEFQTMLLKSDS 75 
                                       455664.5688999999989999************************99998766554 PP

>> DUF3231  Protein of unknown function (DUF3231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.6   2.2e-05     0.057      23      74 ..      24      75 ..       9      89 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.2e-05
                           DUF3231 23 ssyianslgialitgFlqvaedkeikelleralelsnkhikelkelLkeenl 74
                                      + +ia+  +i l++ +++ a++ eik++l  + +  + h+ e++++L +++ 
  gi|298674375|ref|YP_003726125.1| 24 AAIIAELDAINLYEEMADLADNDEIKSVLLDVAKEEKTHVGEFQTMLLKSDS 75
                                      56778888999***********************************999875 PP

>> MSL1_dimer  Dimerisation domain of Male-specific-Lethal 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.4   0.00087       2.2      26      34 ..      13      21 ..       7      22 .. 0.89
   2 ?    3.1   1.0     0.031        80      22      36 ..      76      90 ..      67      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00087
                        MSL1_dimer 26 qLqnKnKEI 34
                                      qL nK+KEI
  gi|298674375|ref|YP_003726125.1| 13 QLENKDKEI 21
                                      9*******9 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.031
                        MSL1_dimer 22 QQQqqLqnKnKEIde 36
                                      QQ   L +  KE++e
  gi|298674375|ref|YP_003726125.1| 76 QQVEELEAGKKEVEE 90
                                      9999*********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1043  (0.0581739); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 637.37
//
Query:       gi|298674376|ref|YP_003726126.1|  [L=217]
Description: HAD-superfamily hydrolase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.8e-33  114.5   0.1    8.7e-33  113.9   0.0    1.3  2  HAD_2           Haloacid dehalogenase-like hydrolase
    8.5e-16   58.9   0.0    1.2e-15   58.3   0.0    1.3  1  Hydrolase       haloacid dehalogenase-like hydrolase
    0.00019   21.4   0.0    0.00042   20.3   0.0    1.5  1  Hydrolase_like  HAD-hyrolase-like
  ------ inclusion threshold ------
      0.045   13.6   0.5       0.18   11.7   0.1    2.1  2  NT5C            5' nucleotidase, deoxy (Pyrimidine), cytosoli


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.9   0.0   1.9e-36   8.7e-33       1     178 []       5     183 ..       5     183 .. 0.91
   2 ?   -3.6   0.0       2.3     1e+04     116     127 ..     203     214 ..     195     216 .. 0.62

  Alignments for each domain:
  == domain 1  score: 113.9 bits;  conditional E-value: 1.9e-36
                             HAD_2   1 iiFDlDgTlldteeliiqafnelleeyglselseeelrkliglslrellrklgeseeeee...kieellrkyneekk 74 
                                       iiFD+Dg+l+d+ ++++qa++ ++e+ g+ e++++++ ++ g +   +++ ++++  ++     ++e+ ++ ++   
  gi|298674376|ref|YP_003726126.1|   5 IIFDFDGVLADSMPYHAQAWKIAFEKAGI-EINKDDIYEIEGSNHVGIIQLMFQKMGKSPqphQFDEIAQEKRKIFS 80 
                                       8**************************88.***************99999999998888744444444444444444 PP

                             HAD_2  75 k.kevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklkl 150
                                       +  ++k ++++ + L +L ++++kl++v+  +r+av +++ ++   ++Fdvivt+edv + KP+pe+++kal  l++
  gi|298674376|ref|YP_003726126.1|  81 QiANLKNFEDMDKCLSQL-KNKFKLAVVSGADRNAVFNMVGRFY-PDVFDVIVTGEDVDNGKPSPEPYLKALGMLNV 155
                                       4889**************.88**********************9.7******************************* PP

                             HAD_2 151 kkeeviyvGDsptDieaakkagikviav 178
                                       +k+e+++v+  p ++ +ak+ag+ ++av
  gi|298674376|ref|YP_003726126.1| 156 EKNECLVVENAPLGVDSAKNAGLYCVAV 183
                                       ************************9987 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.3
                             HAD_2 116 lgiesyFdvivt 127
                                        ++++y+++i++
  gi|298674376|ref|YP_003726126.1| 203 SDLKKYLQKIYS 214
                                       455666666665 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   0.0   2.8e-19   1.2e-15       2     210 .]       3     177 ..       2     177 .. 0.91

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 2.8e-19
                                       SEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   2 ktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpewlt 78 
                                       k+++fD+dG+L ++ p + ++++ a                      +  +++++ +++ +++g +++ i +  +++
  gi|298674376|ref|YP_003726126.1|   3 KAIIFDFDGVLADSMPYHAQAWKIA---------------------FEKAGIEINKDDIYEIEGSNHVGIIQL-MFQ 57 
                                       9************************.....................888888999999999999887777666.445 PP

                                       HHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  79 aldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanql 155
                                       ++           s q +  +++ +  + + +f    +lk ++++ +++ +Lk +++++++++g ++   +++ n +
  gi|298674376|ref|YP_003726126.1|  58 KM---------GKSPQPHQFDEIAQ--EKRKIFSQIANLKNFEDMDKCLSQLK-NKFKLAVVSGADR---NAVFNMV 119
                                       55.........69999999999999..99************************.6699********9...7888999 PP

                                       T...GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       x...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 156 G...ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                       G    d fd++++++++  +kpspe +++a+  L+++++e+++V+  + ++  +++Ag
  gi|298674376|ref|YP_003726126.1| 120 GrfyPDVFDVIVTGEDVDNGKPSPEPYLKALGMLNVEKNECLVVENAPLGVDSAKNAG 177
                                       99988999*********************************************99998 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   9.4e-08   0.00042       3      72 ..     139     202 ..     138     205 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 9.4e-08
                                       STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHHHHHHHT---SEE CS
                    Hydrolase_like   3 gKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedleepehkptyvaddl 72 
                                       gKP+pe y  al  l+++++e+l++       + +A+naG+ +v+V t v +pe+l     k+++v++d 
  gi|298674376|ref|YP_003726126.1| 139 GKPSPEPYLKALGMLNVEKNECLVVENA-PLGVDSAKNAGLYCVAVPTYV-DPEKLD----KADVVVEDH 202
                                       9*************************99.899***************988.444433....567777775 PP

>> NT5C  5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   3.9e-05      0.18       4      93 ..       5     112 ..       2     122 .. 0.64
   2 ?   -3.4   0.0       1.7   7.4e+03     128     138 ..     194     204 ..     188     211 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.9e-05
                              NT5C   4 vlvDlDgvladlygkmlevankrfeat...llpeevss.wdleef.............vkPeqreslyrfltepglF 63 
                                       +++D+Dgvlad +  + + +   fe++     ++++   ++ +++              +P q +++ +   ++++F
  gi|298674376|ref|YP_003726126.1|   5 IIFDFDGVLADSMPYHAQAWKIAFEKAgieINKDDIYEiEGSNHVgiiqlmfqkmgksPQPHQFDEIAQ--EKRKIF 79 
                                       789*********************998776667777653333322323333322222223344444433..467777 PP

                              NT5C  64 a...dlepipgarevLeeladegrlvvitaall 93 
                                       +   +l+  ++  + L +l ++ +l v++ a +
  gi|298674376|ref|YP_003726126.1|  80 SqiaNLKNFEDMDKCLSQLKNKFKLAVVSGADR 112
                                       622246677888888888888888888876655 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.7
                              NT5C 128 rgDvlidDapk 138
                                       ++Dv+++D ++
  gi|298674376|ref|YP_003726126.1| 194 KADVVVEDHSD 204
                                       68999999874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1410.76
//
Query:       gi|298674377|ref|YP_003726127.1|  [L=638]
Description: KH-domain/beta-lactamase-domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-29  101.7   2.0    2.4e-28   97.9   0.4    2.8  2  KH_7           KH domain
    2.3e-25   89.0   0.0      7e-25   87.5   0.0    1.9  2  Beta-Casp      Beta-Casp domain
    1.7e-16   59.8   0.1    5.2e-16   58.3   0.0    1.9  2  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    3.4e-15   56.0   0.0    5.8e-15   55.2   0.0    1.4  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
    6.2e-14   52.5   0.4    1.6e-12   47.8   0.5    2.8  2  Lactamase_B    Metallo-beta-lactamase superfamily
    7.9e-10   38.6   0.1    1.6e-09   37.6   0.1    1.5  1  Lactamase_B_2  Beta-lactamase superfamily domain
    1.8e-05   24.5   0.6    0.00013   21.8   0.1    2.7  2  KH_2           KH domain
      0.002   17.9   0.6      0.037   13.9   0.3    2.5  2  KH_1           KH domain
     0.0034   17.3   0.0     0.0081   16.1   0.0    1.6  1  Lactamase_B_3  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.018   14.9   0.0      0.064   13.1   0.0    2.0  1  KH_4           KH domain


Domain annotation for each model (and alignments):
>> KH_7  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.9   0.4   1.4e-31   2.4e-28       1      68 []       4      71 ..       4      71 .. 0.97
   2 ?    2.2   0.1       0.1   1.8e+02       6      55 ..      76     128 ..      74     129 .. 0.81

  Alignments for each domain:
  == domain 1  score: 97.9 bits;  conditional E-value: 1.4e-31
                              KH_7  1 eevleelkekieeklPkevkitdveFEGPelViYtknpklfaengdlirklAkelrkRiviRpDpsvl 68
                                      ee+l +lk+kie+klP++++i+ veFEGP+lV+Yt++p++fa+ng++ir+lAk+lr Riv+RpDp+vl
  gi|298674377|ref|YP_003726127.1|  4 EEMLLDLKKKIESKLPNDTTISTVEFEGPQLVVYTEEPRKFADNGNIIRTLAKDLRTRIVVRPDPKVL 71
                                      578999************************************************************98 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.1
                              KH_7   6 elkekieeklPkevkitdveFEG..PelViYtknpklfa.engdlirklAkel 55 
                                       e ++ki + +P+e+  ++++F     e++i ++ p l++ ++gd +r++ ke+
  gi|298674377|ref|YP_003726127.1|  76 ESMDKIGNIVPEEAATSNYHFDPdvGEVIIEAEKPGLVIgKQGDTLREITKEI 128
                                       66899****************74225888888888888878888888888875 PP

>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       6.2   1.1e+04      30      74 ..     144     188 ..     137     200 .. 0.49
   2 !   87.5   0.0   3.9e-28     7e-25       2     110 .]     422     546 ..     421     546 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 6.2
                                       HHHHHHHHGGGGGGE-SHH.....HHH..H..HHHS-SSEEEEES-TT CS
                         Beta-Casp  30 laskatevYkeyaeveaks.lewmesk..keelnsskgpkvilassgm 74 
                                       +++++ e+ +++ ++e k+ l+ + ++  + e +++k+  v ++s g 
  gi|298674377|ref|YP_003726127.1| 144 TVKNIREFMRNN-HKERKDiLKSVGRQihR-E-TTTKDQWVRITSLGG 188
                                       444444443333.23334444444444322.2.234455555555555 PP

  == domain 2  score: 87.5 bits;  conditional E-value: 3.9e-28
                                       HHHHHHH..HCTT..TTS-S-EEEEE-HHHHHHHHHGGGGGG.........................E-SHH....H CS
                         Beta-Casp   2 qellylLeelwkekkledlklpiyldsplaskatevYkeyae.........................veakslewme 53 
                                       qe++++Le++++++   + ++piyld+ ++ +at+++ +y+e                         v+        
  gi|298674377|ref|YP_003726127.1| 422 QEVMIVLEDAIRKGL--IDDVPIYLDG-MIWEATAIHATYPEylnnelrksifqkgqnpflsdsfkpVD-------- 487
                                       9**********9944..4458******.************99999999999999888887755543333........ PP

                                       HH..H..HHHS-SSEEEEES-TTSSSSHHHHHHHHHTTSTTSEEEESS---TTSHHHHH CS
                         Beta-Casp  54 sk..keelnsskgpkvilassgmlegGrsrellkklledprntvilvgyqaegTlgrkl 110
                                       s+  ++++ +++ p+vila+ gm+++G++ e++k+++++++nt+++vgyqa gTlgr++
  gi|298674377|ref|YP_003726127.1| 488 SNelRQKIIDEPHPCVILATAGMMNAGPILEYFKAFASNENNTLVFVGYQADGTLGRRI 546
                                       3322434557789********************************************97 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       4.1   7.3e+03      41      54 ..       4      17 ..       4      23 .. 0.80
   2 !   58.3   0.0   2.9e-19   5.2e-16       1      59 [.     565     626 ..     565     629 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4.1
                             RMMBL 41 eeatsalarllkee 54
                                      ee++++l+++++++
  gi|298674377|ref|YP_003726127.1|  4 EEMLLDLKKKIESK 17
                                      689999****9766 PP

  == domain 2  score: 58.3 bits;  conditional E-value: 2.9e-19
                             RMMBL   1 tipvkarieeid.fSgHadknellelirklkprn..vilvHGeeeatsalarllkeeegidv 59 
                                       ti+v++ +e +d fSgH+d+ +l+++++k+kpr+  v+  HGee+ + +la+ + ++++i++
  gi|298674377|ref|YP_003726127.1| 565 TINVNMNVEVVDgFSGHSDRKQLMDFVKKMKPRPerVYTEHGEEKFCIDLASSIYKKNKIET 626
                                       699***************************************************99999986 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   0.0   3.2e-18   5.8e-15       2     164 ..     199     355 ..     198     378 .. 0.82

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 3.2e-18
                     Lactamase_B_6   2 LeldnvkiLlDvGwd.eskvslesalkelekv.iptvdliLLshatlehlGayallyakfksklllnipvyatlpvv 76 
                                       L+  + ++++D+G++ +s+ +++  l   e + ++++d+++L+ha l+h G  +lly+     ++ + pvy+tlp+ 
  gi|298674377|ref|YP_003726127.1| 199 LSTPESRVMIDCGVNiGSDENMTPYLYVPEAYpLSQLDAVILTHAHLDHSGFIPLLYK-----YGYQGPVYCTLPTR 270
                                       6677889********54444455555555555689****************5555553.....57899********* PP

                     Lactamase_B_6  77 kLGrvslldlyaskgllgpedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGti..Wkisk 151
                                        L  ++ ld++  +g +g +     e + ++ea ++ +tl ++  +++     ++ +t +n+Gh lG +i  ++i +
  gi|298674377|ref|YP_003726127.1| 271 DLSALLQLDYIDVAGKEGRIVP--YESSQVREALKHTITLDFEEVTDIAP---DIKLTFHNSGHILGSAIahFHIGD 342
                                       *********9999998887654..466899**************999985...89*************98779999* PP

                     Lactamase_B_6 152 esekivYavdwnh 164
                                       +++++v+  d+  
  gi|298674377|ref|YP_003726127.1| 343 GLHNVVFTGDYKY 355
                                       ******9998875 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0       0.4   7.2e+02      58      94 ..     128     164 ..     128     186 .. 0.81
   2 !   47.8   0.5   9.1e-16   1.6e-12       4     161 ..     192     363 ..     189     406 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.4
                                       HTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHC CS
                       Lactamase_B  58 iGglgglveatdvpvgavaeeapalfmeeaddaasrk 94 
                                       iG+ +++v++ +++++ v+ + + ++++++++    k
  gi|298674377|ref|YP_003726127.1| 128 IGWTPKVVRTPPIKSRTVKNIREFMRNNHKERKDILK 164
                                       79999***********************997765554 PP

  == domain 2  score: 47.8 bits;  conditional E-value: 9.1e-16
                                       CSSEEEEEEETTCEEEES--SCHHHHHHHH..HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHH CS
                       Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraal..elaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaee 78 
                                       ++ +++++ ++++ ++iD+G+    +  +   ++  + +++ ++davilTH+HlDH G  + l +     ++++ + 
  gi|298674377|ref|YP_003726127.1| 192 VGRSCFILSTPESRVMIDCGVNIGSDENMTpyLYVPEAYPLSQLDAVILTHAHLDHSGFIPLLYKYGYQGPVYCTLP 268
                                       6789*****************99999998888********************************************* PP

                                       HHCCHCHHHHHHHHHCCHH...........TTCHCGCCEEEEETTTEECCCTEEEEE.HECTTSTSCCEEEEEETTC CS
                       Lactamase_B  79 apalfmeeaddaasrkgll...........lagvsadkpdvdeeeldgnaggrraly.vtggpghghghgvveyggg 143
                                       ++ l      d+    g +           +++  +     +ee++d+  +  ++++   ++ g+   h+++++g  
  gi|298674377|ref|YP_003726127.1| 269 TRDLSALLQLDYIDVAGKEgrivpyessqvREALKHTITLDFEEVTDIAPDIKLTFHnSGHILGSAIAHFHIGDGLH 345
                                       ******99999998888889******998633333333333333333333333333313466778889********* PP

                                       CEEEECTTTSSHHCCCCC CS
                       Lactamase_B 144 kvlftGDallagetgrid 161
                                       +v+ftGD  +   ++ ++
  gi|298674377|ref|YP_003726127.1| 346 NVVFTGDYKYGSTRLFDP 363
                                       *******99955444444 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.1   8.8e-13   1.6e-09       2     165 ..     205     379 ..     204     400 .. 0.70

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 8.8e-13
                                       EEEES--TTHHHH..HTCGG.S--S.SS--..SEEEEE-SS--HHHHGGGGCCCC.C--EEEEEEEEHHHHH..... CS
                     Lactamase_B_2   2 riLiDagpdlrqq..alral.qPve.lrdelppidaVllthaHyDHlaglltlre.lrpkklplyapkgvla..... 68 
                                       r+ iD+g ++     ++++l  P + +   l+++daV+lthaH DH   ++ l + ++  + p+y+++ +++     
  gi|298674377|ref|YP_003726127.1| 205 RVMIDCGVNIGSDenMTPYLyVPEAyP---LSQLDAVILTHAHLDHSGFIPLLYKyGY--QGPVYCTLPTRDlsall 276
                                       89*******877788999998887644...457**************66777777443..479****9998755555 PP

                                       .....HCCTTCGHHHCHTT................TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTT CS
                     Lactamase_B_2  69 .....vleanfvylaleee................pavnvheldwgesfelgdggleitatparhksgrrldrnagd 124
                                            +           ++                +  ++ +ld +e ++++ +++++t++   h  g         
  gi|298674377|ref|YP_003726127.1| 277 qldyiD-----------VAgkegrivpyessqvreALKHTITLDFEEVTDIA-PDIKLTFHNSGHILGS-------A 334
                                       444441...........44434444444444445555566677788888888.5888888776666666.......8 PP

                                       SEEEEEECTTEEEEEESS-S---....HHHHHHHCT-SEEEEE-S CS
                     Lactamase_B_2 125 tlGlriegggkrvyyigDtgyip....eeigerlggadlllldit 165
                                       ++ + i++g ++v+++gD +y +    + + +++  ++ ++ + t
  gi|298674377|ref|YP_003726127.1| 335 IAHFHIGDGLHNVVFTGDYKYGStrlfDPAVNKFPRVETVVTEST 379
                                       9999999*************9884333333356666666666555 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.84   1.5e+03      43      58 ..      47      62 ..       9      72 .. 0.62
   2 !   21.8   0.1   7.1e-08   0.00013      28      67 ..     102     141 ..      82     153 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.84
                                      GGHHHHHHHHHHHHHH CS
                              KH_2 43 gGsnikkigkelrkdi 58
                                      +G  i+++ k+lr +i
  gi|298674377|ref|YP_003726127.1| 47 NGNIIRTLAKDLRTRI 62
                                      4555666666666666 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 7.1e-08
                                       EEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEE CS
                              KH_2  28 iiviresqpgivIGkgGsnikkigkelrkdieklegkkVk 67 
                                       +++i +++pg+vIGk+G ++++i+ke++   ++++  ++k
  gi|298674377|ref|YP_003726127.1| 102 EVIIEAEKPGLVIGKQGDTLREITKEIGWTPKVVRTPPIK 141
                                       799***********************99777777777766 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.17     3e+02      18      40 ..      47      68 ..      46      82 .. 0.77
   2 !   13.9   0.3     2e-05     0.037       4      28 ..     103     127 ..     101     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.17
                                      GGHHHHHHHHHHT-EEEEESSTT CS
                              KH_1 18 gGsnIkeIreetgakIkvpksed 40
                                      +G+ I+ + ++  ++I+v  +++
  gi|298674377|ref|YP_003726127.1| 47 NGNIIRTLAKDLRTRIVVR-PDP 68
                                      79********88*****86.433 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 2e-05
                                       EEEGGGHHHHHHTGGGHHHHHHHHH CS
                              KH_1   4 ilvPsslvgriIGkgGsnIkeIree 28 
                                       +++ +++ g++IGk+G +++eI +e
  gi|298674377|ref|YP_003726127.1| 103 VIIEAEKPGLVIGKQGDTLREITKE 127
                                       67778888**************995 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   4.5e-06    0.0081       5      50 ..     192     248 ..     190     255 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.5e-06
                     Lactamase_B_3   5 lghnsflletagarilvDPf..........ka.nlgyeppaeeaDlvlisqaledHa 50 
                                       +g ++f l+t++ r+++D +           + ++  ++p  + D+v++++a+ dH 
  gi|298674377|ref|YP_003726127.1| 192 VGRSCFILSTPESRVMIDCGvnigsdenmtPYlYVPEAYPLSQLDAVILTHAHLDHS 248
                                       589***************99776666655422455555555***************6 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.6e-05     0.064      32      52 ..     102     122 ..      85     124 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.6e-05
                              KH_4  32 elnvegedlGrvIGkrGrtld 52 
                                       e+ +e e+ G+vIGk+G tl+
  gi|298674377|ref|YP_003726127.1| 102 EVIIEAEKPGLVIGKQGDTLR 122
                                       78999**************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (638 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.73u 0.27s 00:00:01.00 Elapsed: 00:00:00.48
# Mc/sec: 4017.99
//
Query:       gi|298674378|ref|YP_003726128.1|  [L=211]
Description: proteasome endopeptidase complex subunit beta [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      2e-56  190.5   0.3    2.5e-56  190.2   0.3    1.0  1  Proteasome  Proteasome subunit


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.2   0.3   1.4e-60   2.5e-56       3     190 .]       9     190 ..       8     190 .. 0.96

  Alignments for each domain:
  == domain 1  score: 190.2 bits;  conditional E-value: 1.4e-60
                                       HS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGT CS
                        Proteasome   3 kGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpi 79 
                                       kGtt+vGi+++d vvla+++rat+g+ + +++t++Ki++idd+ig+++aG+++Da+++vr++++e +l+++r ++pi
  gi|298674378|ref|YP_003726128.1|   9 KGTTTVGIACSDAVVLATERRATMGNFI-ASKTAKKIYQIDDRIGMTTAGSVGDAQQIVRIISVESKLFKMRRNEPI 84 
                                       7***************************.55559******************************************* PP

                                       CHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHST CS
                        Proteasome  80 pverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeyke 156
                                       +++     ++++l++ +  ++  p++v+l+++gvd++g p  y++dp G  iee ++va+Gsgs   +++le++y++
  gi|298674378|ref|YP_003726128.1|  85 TIK----GITTLLSNLLSGQRYFPLMVQLIVGGVDKTG-PNMYSLDPLGGRIEETNIVATGSGSPITYGLLEDRYHK 156
                                       ***....788888888888888*************999.************************************** PP

                                       TBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEEE CS
                        Proteasome 157 dltleeavelavkalkealerdklsgknievavi 190
                                       d+t +e+ ela++al++a++rd++sg++i+v+vi
  gi|298674378|ref|YP_003726128.1| 157 DMTSDEGAELAIRALHNAMKRDSASGDGIDVVVI 190
                                       ********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1392.83
//
Query:       gi|298674379|ref|YP_003726129.1|  [L=168]
Description: metal dependent phosphohydrolase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.3e-16   58.3   0.4    1.1e-15   57.9   0.4    1.2  1  HD        HD domain
     0.0015   18.0   0.0     0.0092   15.5   0.0    1.9  2  HDOD      HDOD domain


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.9   0.4   1.2e-19   1.1e-15       2     119 ..      21     129 ..      20     132 .. 0.94

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 1.2e-19
                                       HHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHH CS
                                HD   2 leHsleVaklarrlaedlge...eedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlg 75 
                                        eH+ +V  +a + a++l++     d el+++++LlHDiG  +++             ++H+++ga+i++ +++++ 
  gi|298674379|ref|YP_003726129.1|  21 VEHCKAVSSFAVEVAKELKKtgkSVDMELVEIGGLLHDIGRSHTHG------------VKHIVEGAKIAESLGLDS- 84 
                                       79*****************************************775............78****************. PP

                                       HHHHHHHHHHHTTCCHHHHHHHH....H.HHHCCTSCHHHHHHHHHHHH CS
                                HD  76 ldledvaklirehheswegkkrp....r.glaerqlslearivklaDrl 119
                                            ++++i+ h +   ++k+         ++++ ++e++i++ aD+l
  gi|298674379|ref|YP_003726129.1|  85 ----RIVRIIKTHIGAGLTPKEAvnlgFpDDDYMPRTIEEKIIAHADNL 129
                                       ....**************99888876526******************98 PP

>> HDOD  HDOD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0     1e-06    0.0092      94     132 ..      19      61 ..       9      65 .. 0.83
   2 ?    0.4   0.0     0.044   3.9e+02     163     193 ..      63      93 ..      61      95 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1e-06
                                       HHHHHHHHHHHHHHHHHHHTT-S-H....HHHHHHHHTTTHHH CS
                              HDOD  94 klwehslavAlvarelaeelgledp....eeaflaGLLhdiGk 132
                                       +++eh+ av+ +a e+a+el+++ +    e + ++GLLhdiG+
  gi|298674379|ref|YP_003726129.1|  19 HVVEHCKAVSSFAVEVAKELKKTGKsvdmELVEIGGLLHDIGR 61 
                                       57899999*********999555433445*************7 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.044
                                       HHHSS-HHHHHHHHHHHTT--HHHHHHHHHT CS
                              HDOD 163 ellgtdhaevGaallekWnlPeelveaiayh 193
                                       +  g++h   Ga+++e+  l+  +v++i+ h
  gi|298674379|ref|YP_003726129.1|  63 HTHGVKHIVEGAKIAESLGLDSRIVRIIKTH 93 
                                       5678999999****************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      655  (0.036533); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 990.63
//
Query:       gi|298674380|ref|YP_003726130.1|  [L=165]
Description: transcription factor tFIIE subunit alpha [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-17   62.9   1.4    3.4e-17   62.2   0.5    1.7  2  TFIIE_alpha    TFIIE alpha subunit
  ------ inclusion threshold ------
      0.021   14.7   3.8      0.081   12.8   0.1    2.5  2  Rad50_zn_hook  Rad50 zinc hook motif
      0.071   12.5   0.0       0.12   11.8   0.0    1.3  1  RepL           Firmicute plasmid replication protein (RepL)
      0.073   12.6   0.5       0.17   11.4   0.5    1.7  1  TF_Zn_Ribbon   TFIIB zinc-binding
        0.9    9.6   5.3       0.61   10.1   0.3    2.6  3  DUF1610        Domain of unknown function (DUF1610)


Domain annotation for each model (and alignments):
>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2   0.5   9.5e-21   3.4e-17       8     104 ..      14     109 ..       7     110 .. 0.95
   2 ?   -1.0   0.0      0.44   1.6e+03      34      52 ..     144     162 ..     137     165 .] 0.66

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 9.5e-21
                                       HHCS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECCCHCCC CS
                       TFIIE_alpha   8 rkfygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinyeklvdv 84 
                                       ++  g+e  ++++ +  +gevt+e +a+e+++ ln++r+ L+ L e +lv ++r+rd + +w +y wr++   +   
  gi|298674380|ref|YP_003726130.1|  14 KQLVGDEGLKMIENMP-EGEVTDEKIAEETGVLLNIVRRTLFILNEYKLVVCRRERDTSSGWLTYLWRLDLSGIETR 89 
                                       5678999999999988.************************************************************ PP

                                       HHHHHHHHHHHHHHHHCCCT CS
                       TFIIE_alpha  85 vkrkleevvkkLeeklekee 104
                                       + ++ ++++++Le+ le+ee
  gi|298674380|ref|YP_003726130.1|  90 LEKERKKLIQNLEQRLEFEE 109
                                       ******************97 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.44
                                       HHHHTS-HHHHHHHHHHHH CS
                       TFIIE_alpha  34 akelkidlnelrklLnrLy 52 
                                       a++ +  ++++r+ Ln+L+
  gi|298674380|ref|YP_003726130.1| 144 AQDNSKTIENIRSRLNKLK 162
                                       5555556677888888887 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.8      0.05   1.8e+02      32      46 ..      91     106 ..      90     107 .. 0.83
   2 ?   12.8   0.1   2.3e-05     0.081      22      50 ..     135     163 ..     125     163 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.05
                                       HH.HHHHHHHHHHHHH CS
                     Rad50_zn_hook  32 eh.rseLikelqskle 46 
                                       e+ r++Li+ l+++le
  gi|298674380|ref|YP_003726130.1|  91 EKeRKKLIQNLEQRLE 106
                                       4459*******99886 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2.3e-05
                                       -TTT--EE-HHHHHHHHHHHHHHHHHHH. CS
                     Rad50_zn_hook  22 CPlCgReldeehrseLikelqsklerlpe 50 
                                       CPlCg +l   + s+ i+ ++s+l++l++
  gi|298674380|ref|YP_003726130.1| 135 CPLCGEDLVAQDNSKTIENIRSRLNKLKK 163
                                       *************************9975 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.4e-05      0.12      76     105 ..      33      62 ..      24      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.4e-05
                              RepL  76 atnRelaeetgislktvsetlkileeanil 105
                                       +t  ++aeetg+ l+ v++tl il+e  ++
  gi|298674380|ref|YP_003726130.1|  33 VTDEKIAEETGVLLNIVRRTLFILNEYKLV 62 
                                       5889********************997765 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.5   4.8e-05      0.17       2      35 ..     115     148 ..     114     155 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.8e-05
                                       EETTTTCEECHEETSTTCE.EESSSSBEEEECCCC CS
                      TF_Zn_Ribbon   2 kCPnCgstnlveDpergel.vCtdCGlVlednsid 35 
                                        CP+ + + l+++++++ + +C+ CG+ l  ++++
  gi|298674380|ref|YP_003726130.1| 115 ECPEGCLR-LLFNEATNYHfLCPLCGEDLVAQDNS 148
                                       68883334.77887776666******855555555 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0         2     7e+03       1       6 [.      69      74 ..      69      75 .. 0.85
   2 ?    0.9   0.2      0.13   4.7e+02      15      21 ..     112     118 ..     108     119 .. 0.78
   3 ?   10.1   0.3   0.00017      0.61      16      24 .]     132     140 ..     127     140 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2
                           DUF1610  1 CtSCGa 6 
                                      +tS G+
  gi|298674380|ref|YP_003726130.1| 69 DTSSGW 74
                                      79*999 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.13
                           DUF1610  15 vvFpCPN 21 
                                       v F CP+
  gi|298674380|ref|YP_003726130.1| 112 VFFECPE 118
                                       889***7 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00017
                           DUF1610  16 vFpCPNCGE 24 
                                       +F+CP CGE
  gi|298674380|ref|YP_003726130.1| 132 HFLCPLCGE 140
                                       8*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1050  (0.0585643); expected 358.6 (0.02)
Passed bias filter:                      821  (0.0457917); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1074.07
//
Query:       gi|298674381|ref|YP_003726131.1|  [L=406]
Description: hypothetical protein Metev_0417 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-39  135.4   0.0    3.1e-39  134.6   0.0    1.4  1  ATP-grasp_3      ATP-grasp domain
    1.2e-08   34.7   0.0      3e-08   33.5   0.0    1.8  1  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
    6.3e-07   29.1   0.0    3.6e-06   26.6   0.0    2.1  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    5.4e-06   26.1   0.0    1.4e-05   24.7   0.0    1.7  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    0.00065   19.0   0.2     0.0028   17.0   0.0    2.1  3  ATPgrasp_ST      Sugar-transfer associated ATP-grasp
  ------ inclusion threshold ------
      0.033   13.8   0.0        0.2   11.2   0.0    2.0  1  RimK             RimK-like ATP-grasp domain
      0.035   13.7   0.0       0.07   12.8   0.0    1.4  1  Catalase_C       C-terminal domain found in long catalases
        0.1   12.2   0.9        1.2    8.6   0.1    2.2  2  N-Term_TEN       Telomerase reverse transcriptase TEN domain


Domain annotation for each model (and alignments):
>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.6   0.0   1.4e-42   3.1e-39       2     161 .]     109     282 ..     108     282 .. 0.95

  Alignments for each domain:
  == domain 1  score: 134.6 bits;  conditional E-value: 1.4e-42
                                       TSHHHHHHHHTTT.S---.....-EESS--SSSEEEEESS-------B--SS--TTE..................EE CS
                       ATP-grasp_3   2 sdKlktykkLkeagvkvP.tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve...........lv 66 
                                        dK+++++kL+   ++ P t+  ++  + ++++++vKp +++gg ++r++e ++e+e+ i+e+            ++
  gi|298674381|ref|YP_003726131.1| 109 TDKYRFARKLESMDIPHPiTYSANDIKNINDYPIIVKPKRAGGGMFNRKAESFDELESVIDELLetyplwtlddlII 185
                                       7*****************5555555666679******************************99899*********** PP

                                       EE---SEEEEEEEEE.SSSEEEEEEEEEEEET.......TEEEEEEES----HHHHHHHHHHHHHTTSTT--EEEEE CS
                       ATP-grasp_3  67 qefieGkplSvsllsdgekvlvlavnrqliekaeke...fvyaGnvtpietelkeevvelaeevvekleglaGyvGv 140
                                       q+f +G p+Svs++s+g +++ +a+n+qli+  ++    f+y+Gn+tp+et  ++e++++ ++++ +l gl+G++Gv
  gi|298674381|ref|YP_003726131.1| 186 QKFEKGIPVSVSMVSTGDNAYAIAINEQLIGEPWLTdteFAYCGNITPFETLYQDEMYKISKQLMLEL-GLKGSNGV 261
                                       ********************************9998999*****************************.******** PP

                                       EEEESS.SEEEEEEESS--GG CS
                       ATP-grasp_3 141 DlvlkdeepyviEvNPRltts 161
                                       D+++++++p+v+E+NPRl++s
  gi|298674381|ref|YP_003726131.1| 262 DFIITEDGPVVLEINPRLQGS 282
                                       *******************97 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.0   1.3e-11     3e-08      43     125 ..     236     321 ..     179     327 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 1.3e-11
                      ATPgrasp_Ter  43 lekdeelielaerlaeefgldglvnvQvrededgpkLLEiNpRasGGlgys.alaGvnlpylalklllgl..eteev 116
                                       + +++e+ +++++l+ e+gl+g ++v +  +edgp++LEiNpR +G l+   +++ +nl +  +k + g   et++v
  gi|298674381|ref|YP_003726131.1| 236 TLYQDEMYKISKQLMLELGLKGSNGVDFIITEDGPVVLEINPRLQGSLDTVeIATDMNLFDTHVKSFSGIlpETTDV 312
                                       5578999*****************************************87516679*************98777777 PP

                      ATPgrasp_Ter 117 eepeeglrv 125
                                       ++    + v
  gi|298674381|ref|YP_003726131.1| 313 KQFAARAVV 321
                                       666655555 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   1.6e-09   3.6e-06      29     201 ..     130     300 ..     101     309 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.6e-09
                                       HHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS-EEEEE--SSSEEEEEEEEEETTS CS
                       CPSase_L_D2  29 ealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnkqvlvekslkgpkeiEvevlrDakg 105
                                        a +i +   yP+i+k+  ++GG   r a++ +el+ ++ + l++    ++ + + ++k+ kg   + v +++   +
  gi|298674381|ref|YP_003726131.1| 130 SANDIKNINDYPIIVKPKRAGGGMFNRKAESFDELESVIDELLETY-PLWTLDDLIIQKFEKGI-PVSVSMVSTG-D 203
                                       4556666678***************************999988877.5999*********8776.4666666544.4 PP

                                       -EEEEEEEEECCEC......TCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-EEEEEEEEEEETTTTEEEEEEE CS
                       CPSase_L_D2 106 nvitvcerenslql......rtqkvievAPsqtLtdeerqalreaavkvvrevgvvgagtveflldpkskeyyviEv 176
                                       n+  ++  e ++               + P +tL ++   ++ + + +++ e+g++g   v+f++ +  +  +v+E+
  gi|298674381|ref|YP_003726131.1| 204 NAYAIAINEQLIGEpwltdtEFAYCGNITPFETLYQD---EMYKISKQLMLELGLKGSNGVDFIITE--DGPVVLEI 275
                                       4444444444444423322222333344555555544...5777788999***************95..7889**** PP

                                       ESS--CCHHHHHHHHS--HHHHHHH CS
                       CPSase_L_D2 177 NtRlsvesalaekaTGldlvkeaak 201
                                       N+Rl+ +    e aT ++l  + +k
  gi|298674381|ref|YP_003726131.1| 276 NPRLQGSLDTVEIATDMNLFDTHVK 300
                                       *****************99998887 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   6.4e-09   1.4e-05      28     174 ..     131     277 ..     112     279 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 6.4e-09
                                       HHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT-.....SCEEEEE--ESEEEEEEEEETSS..CE CS
                   Dala_Dala_lig_C  28 lekveeelgypvfVKpareGSSvGvskveseeelkeaieeafkyd.....ekvlvEeaiegreievavlgnek..le 97 
                                        +++++ + yp++VKp r+G  +   k+es +el++ i+e ++        + ++ ++ +g  + v+++  ++  + 
  gi|298674381|ref|YP_003726131.1| 131 ANDIKNINDYPIIVKPKRAGGGMFNRKAESFDELESVIDELLETYplwtlDDLIIQKFEKGIPVSVSMVSTGDnaYA 207
                                       567888999*******************************9985322223689999999********9985551144 PP

                                       EEEEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEES CS
                   Dala_Dala_lig_C  98 vsevgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNt 174
                                       ++  ++ + +  + d e  y ++       +  e+  ++++ +++++    l+l+G+  vDf++te+g + + E+N+
  gi|298674381|ref|YP_003726131.1| 208 IAINEQLIGEPWLTDTEFAYCGNI------TPFETLYQDEMYKISKQLMLELGLKGSNGVDFIITEDGPV-VLEINP 277
                                       444444445555666666665333......345666777888899999999**************77765.568885 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0         1   2.3e+03      11      43 ..     100     132 ..      96     153 .. 0.61
   2 !   17.0   0.0   1.3e-06    0.0028     226     281 ..     240     296 ..     199     301 .. 0.86
   3 ?   -1.9   0.0      0.68   1.5e+03      15      39 ..     324     348 ..     313     377 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1
                       ATPgrasp_ST  11 NpraefplvddKlkfkelalraglkvpkllgvi 43 
                                       N+++ +  v dK  f + ++   ++ p ++  +
  gi|298674381|ref|YP_003726131.1| 100 NSQEIMNEVTDKYRFARKLESMDIPHPITYSAN 132
                                       777888888888877776555555555544333 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1.3e-06
                       ATPgrasp_ST 226 eevlelaakaaeklpglgylGwDivldeekgplllElNar..pglaivqiangegllp 281
                                       +e+ ++ +++  +l   g  G+D+ ++e++ p++lE+N r   +l+ v+ia +  l++
  gi|298674381|ref|YP_003726131.1| 240 DEMYKISKQLMLELGLKGSNGVDFIITEDG-PVVLEINPRlqGSLDTVEIATDMNLFD 296
                                       67888888888888888999**********.********9844688999988877776 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.68
                       ATPgrasp_ST  15 efplvddKlkfkelalraglkvpkl 39 
                                       +  ++ +K++ + l+ ++ +++p++
  gi|298674381|ref|YP_003726131.1| 324 QNDVLINKQILNGLIGQNTVDIPDV 348
                                       5567889999999999999999984 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   9.1e-05       0.2      34     183 ..     134     293 ..     117     297 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.1e-05
                                       HHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH........GGG--EEEEE...--SS-S.....EEEEEEE CS
                              RimK  34 iekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea........lkeailvqey...ieeaen.....ediRvlv 94 
                                       i++i+   P++vK   +  G+    a+  ++l++v++         +   +++q++   i  + +      +   + 
  gi|298674381|ref|YP_003726131.1| 134 IKNIN-DYPIIVKPKRAGGGMFNRKAESFDELESVIDElletyplwTLDDLIIQKFekgIPVSVSmvstgDNAYAIA 209
                                       77787.89999999999999999999999999999999666666666666699999444333333444447778888 PP

                                       ETTEEEEEEEEE--SSS----TTTT-EEEE----HHH.HHHHHHHHHHCT-S.EEEEEEEEETTEEEEEEEESS--S CS
                              RimK  95 vddevvaalrrvskeGdFRsnlhrGgvaeklqlseee.kelAikaakamelv.vaGvDllrakrgllvlEvnsspgl 169
                                       ++++ ++    +  + +F    + G+++   +l ++e  ++  +    ++l    GvD + +++g++vlE+n  p l
  gi|298674381|ref|YP_003726131.1| 210 INEQLIGEPWLT--DTEF---AYCGNITPFETLYQDEmYKISKQLMLELGLKgSNGVDFIITEDGPVVLEIN--PRL 279
                                       999999877666..5556...5788888888876554167777777777765357****************9..556 PP

                                       HHHHHHHT--HHHH CS
                              RimK 170 ekiektlgidiakk 183
                                       +++  t++i  +++
  gi|298674381|ref|YP_003726131.1| 280 QGSLDTVEIATDMN 293
                                       66655666655555 PP

>> Catalase_C  C-terminal domain found in long catalases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.1e-05      0.07      56     100 ..      73     116 ..      61     121 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.1e-05
                        Catalase_C  56 aveFDaivvadgaeslfsakataasslfpagrplqllldayrhgK 100
                                        ++FDaiv+++g e + ++ + +++ l+++++ ++ ++d yr++ 
  gi|298674381|ref|YP_003726131.1|  73 EIDFDAIVLDSGFEYINQE-QLPSKVLNNSQEIMNEVTDKYRFAR 116
                                       689*********9999975.5*********************985 PP

>> N-Term_TEN  Telomerase reverse transcriptase TEN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1   0.00056       1.2      20      77 ..      56     113 ..      43     141 .. 0.90
   2 ?    2.0   0.1      0.06   1.3e+02      34     111 ..     261     342 ..     239     349 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00056
                        N-Term_TEN  20 vlkqisalkyvsnlyefllatekivqtseldtqfqefltttiiaseqnlvenykqkyn 77 
                                        +k is+ k v  + ef +  + iv  s ++   qe l + ++   q+++++  +ky 
  gi|298674381|ref|YP_003726131.1|  56 DIKSISCKKVVEWISEFEIDFDAIVLDSGFEYINQEQLPSKVLNNSQEIMNEVTDKYR 113
                                       5899************************************************999996 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.06
                        N-Term_TEN  34 yefllatekivqtseldtqfqefltttiiaseqnlvenykqkynq.....pnfsqltikqviddsiillgnkqnyvq 105
                                        +f++ te      e++ ++q  l t  ia++ nl + + + +        ++ q++ + v+     +l nkq    
  gi|298674381|ref|YP_003726131.1| 261 VDFII-TEDGPVVLEINPRLQGSLDTVEIATDMNLFDTHVKSFSGilpetTDVKQFAARAVVYSQNDVLINKQILNG 336
                                       55554.44444467899999***************999998886511111345555555566555556666666666 PP

                        N-Term_TEN 106 qigttt 111
                                        ig  t
  gi|298674381|ref|YP_003726131.1| 337 LIGQNT 342
                                       666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 2534.80
//
Query:       gi|298674382|ref|YP_003726132.1|  [L=347]
Description: NMD3 family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.6e-56  189.5   0.9    8.3e-56  189.2   0.9    1.1  1  NMD3            NMD3 family
  ------ inclusion threshold ------
      0.026   14.2   2.2        1.5    8.6   0.5    2.6  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
      0.033   13.9   6.4        1.6    8.6   0.1    2.7  2  zinc_ribbon_2   zinc-ribbon domain
      0.036   14.4   1.8       0.41   11.0   0.2    2.9  3  Rpr2            RNAse P Rpr2/Rpp21/SNM1 subunit domain
      0.065   13.4   3.2        2.7    8.2   0.2    2.9  2  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
       0.88    9.6   7.7        8.2    6.5   6.2    2.8  2  DZR             Double zinc ribbon
        1.6    8.3   8.2         15    5.2   4.4    2.8  2  TF_Zn_Ribbon    TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.2   0.9   3.2e-59   8.3e-56       1     243 []       6     238 ..       6     238 .. 0.96

  Alignments for each domain:
  == domain 1  score: 189.2 bits;  conditional E-value: 3.2e-59
                              NMD3   1 CcrCGkeieelinglCedCllkevditegiekievevCkeCgrylpkgkWvkaeleseellaeclkklvekgLkvse 77 
                                       C++CG+e++ l++++C+dC+++++++++ +  i+v++C++Cg+++++g W     +  ++  +++ +lve++L v+e
  gi|298674382|ref|YP_003726132.1|   6 CPKCGNETDVLYENVCKDCFFEQFQLARLPHVIHVKFCSRCGSVYYQGVW-----DDVDSTGDMVIRLVEDELMVHE 77 
                                       *********9****************************************.....5667788899999999****** PP

                              NMD3  78 eveevkvelvdaefiwtephskrikvkvtvqgevrgenetilqqevevevkvkrqqCprCsriaggyyeaivQvRqk 154
                                        +++ ++  ++++   + + s+ ++v+v v+++v+g   + ++qe+e+ev++ r+ C+rCsriaggy+e+ivQ+R++
  gi|298674382|ref|YP_003726132.1|  78 YASDLEIY-FEPQ---QLT-SYMYRVRVIVDARVEG---VPVNQELETEVRIGRESCDRCSRIAGGYFEGIVQIRGT 146
                                       *9999999.8999...777.999***********77...6688********************************** PP

                              NMD3 155 .relteeehkrtfelleqli....lkhdahafiskikevkeGlDfyfgsksaArklveflksevggkvkeseklvse 226
                                        r ++++e + + ++++++i    +k+++ afisk  e k G+D+y+gs ++ r+++++++se ggk++es++l ++
  gi|298674382|ref|YP_003726132.1| 147 nRVPDKNEVEDCIRIANDVIdrmyKKGERFAFISKSVESKHGIDLYIGSSNTSRQICKQIESERGGKFSESPTLFGQ 223
                                       ***************************************************************************** PP

                              NMD3 227 dkksgkevyrltysvrl 243
                                        k+ gke yr+t+s+rl
  gi|298674382|ref|YP_003726132.1| 224 -KD-GKEIYRITFSMRL 238
                                       .88.***********97 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.012        30       6      13 ..       6      13 ..       5      16 .. 0.69
   2 ?    8.6   0.5   0.00058       1.5       4      11 ..      41      48 ..      40      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.012
                     zf-NADH-PPase  6 CgrCGapt 13
                                      C++CG +t
  gi|298674382|ref|YP_003726132.1|  6 CPKCGNET 13
                                      77777666 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00058
                     zf-NADH-PPase  4 rFCgrCGa 11
                                      +FC+rCG+
  gi|298674382|ref|YP_003726132.1| 41 KFCSRCGS 48
                                      5******7 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   3.1    0.0047        12       2       9 ..       6      13 ..       5      24 .. 0.70
   2 ?    8.6   0.1   0.00061       1.6      13      21 ..      40      48 ..      36      49 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0047
                     zinc_ribbon_2  2 CpnCGael 9 
                                      Cp+CG+e 
  gi|298674382|ref|YP_003726132.1|  6 CPKCGNET 13
                                      99999986 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00061
                     zinc_ribbon_2 13 akFCpyCGt 21
                                      +kFC++CG+
  gi|298674382|ref|YP_003726132.1| 40 VKFCSRCGS 48
                                      79*****96 PP

>> Rpr2  RNAse P Rpr2/Rpp21/SNM1 subunit domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   0.00016      0.41      37      59 ..      32      54 ..      16      62 .. 0.86
   2 ?    1.4   0.0      0.16     4e+02      35      54 ..     113     132 ..      93     160 .. 0.80
   3 ?   -3.8   0.0       6.3   1.6e+04      42      49 ..     197     204 ..     191     207 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00016
                                      ---SSTCCCTB-TTT--B--CTT CS
                              Rpr2 37 lrlppsvkrtvCkkCgsvlipgv 59
                                       rlp+ ++ ++C++Cgsv+ +gv
  gi|298674382|ref|YP_003726132.1| 32 ARLPHVIHVKFCSRCGSVYYQGV 54
                                      599****************9997 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.16
                                       CT---SSTCCCTB-TTT--B CS
                              Rpr2  35 aqlrlppsvkrtvCkkCgsv 54 
                                       ++l+ +  + r+ C +C+ +
  gi|298674382|ref|YP_003726132.1| 113 QELETEVRIGRESCDRCSRI 132
                                       55666777899******987 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 6.3
                                       TCCCTB-T CS
                              Rpr2  42 svkrtvCk 49 
                                       + +r++Ck
  gi|298674382|ref|YP_003726132.1| 197 NTSRQICK 204
                                       34566665 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.3     0.012        31      24      33 ..       4      13 ..       1      17 [. 0.84
   2 ?    8.2   0.2     0.001       2.7      10      49 ..      20      66 ..      15      75 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.012
                      NOB1_Zn_bind 24 kFCpkCGnkt 33
                                        CpkCGn+t
  gi|298674382|ref|YP_003726132.1|  4 ILCPKCGNET 13
                                      57******87 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.001
                      NOB1_Zn_bind 10 rChaCfk.......vtkdmtkkFCpkCGnktLkrvavsvdengelkl 49
                                       C  Cf        + +  + kFC++CG+   + v   vd++g++ +
  gi|298674382|ref|YP_003726132.1| 20 VCKDCFFeqfqlarLPHVIHVKFCSRCGSVYYQGVWDDVDSTGDMVI 66
                                      6888887444433223558899******9888877777777777665 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   6.2    0.0032       8.2       1      37 [.       6      49 ..       6      54 .. 0.74
   2 ?   -0.3   0.0      0.43   1.1e+03      28      36 ..     123     131 ..     103     134 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0032
                               DZR  1 CpqCgeelppdar.fCseCgtk......lkavaa...edrCpsCgek 37
                                      Cp+Cg+e++   + +C++C  +      l+   +    ++C++Cg+ 
  gi|298674382|ref|YP_003726132.1|  6 CPKCGNETDVLYEnVCKDCFFEqfqlarLP---HvihVKFCSRCGSV 49
                                      9******98765549****87755543344...35559******975 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.43
                               DZR  28 edrCpsCge 36 
                                        + C++C++
  gi|298674382|ref|YP_003726132.1| 123 RESCDRCSR 131
                                       556777765 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   4.4    0.0058        15       3      25 ..       6      24 ..       4      24 .. 0.78
   2 ?    3.6   0.1     0.018        47      22      28 ..      43      49 ..      42      65 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0058
                                      ETTTTCEECHEETSTTCEEESSS CS
                      TF_Zn_Ribbon  3 CPnCgstnlveDpergelvCtdC 25
                                      CP+Cg++++v+     e vC+dC
  gi|298674382|ref|YP_003726132.1|  6 CPKCGNETDVL----YENVCKDC 24
                                      ******76443....46799999 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.018
                                      ESSSSBE CS
                      TF_Zn_Ribbon 22 CtdCGlV 28
                                      C++CG+V
  gi|298674382|ref|YP_003726132.1| 43 CSRCGSV 49
                                      6777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 2103.40
//
Query:       gi|298674383|ref|YP_003726133.1|  [L=74]
Description: hypothetical protein Metev_0419 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 481.26
//
Query:       gi|298674384|ref|YP_003726134.1|  [L=353]
Description: 4Fe-4S ferredoxin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-41  141.9   0.3    3.7e-41  141.6   0.3    1.1  1  DUF362    Domain of unknown function (DUF362)
    1.2e-08   34.4  11.5    0.00031   20.4   3.3    2.5  2  Fer4      4Fe-4S binding domain
    6.6e-08   32.3   7.7     0.0023   17.9   2.2    2.5  2  Fer4_6    4Fe-4S binding domain
      2e-05   25.0  21.6    0.00012   22.5   8.7    2.2  3  Fer4_7    4Fe-4S dicluster domain
    2.2e-05   24.5   6.6    4.5e-05   23.5   6.6    1.6  1  Fer4_10   4Fe-4S dicluster domain
    3.5e-05   24.6   4.7       0.18   12.8   0.1    2.4  2  Fer4_16   4Fe-4S double cluster binding domain
    5.3e-05   23.1   7.3       0.01   15.9   2.2    2.5  2  Fer4_2    4Fe-4S binding domain
    0.00016   21.7  10.1    0.00038   20.5  10.1    1.7  1  Fer4_21   4Fe-4S dicluster domain
    0.00028   21.0   6.8    0.00058   20.0   6.8    1.5  1  Fer4_9    4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.012   14.7   0.1      0.021   14.0   0.1    1.3  1  Lar_N     Lactate racemase N-terminal domain
      0.017   15.6   9.8          1   10.0   0.3    2.5  2  Fer4_4    4Fe-4S binding domain
      0.085   13.8  11.8        1.5   10.0   0.8    2.6  2  Fer4_3    4Fe-4S binding domain
       0.26   12.0   8.2        3.1    8.6   0.6    2.7  2  Fer4_15   4Fe-4S single cluster domain
        1.1    9.8   8.7         12    6.5   3.7    2.6  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
        1.7    9.1   9.2         91    3.6   9.2    2.4  1  Fer4_8    4Fe-4S dicluster domain
        1.8    9.2   8.5         73    4.0   0.4    2.4  2  Fer4_17   4Fe-4S dicluster domain
        3.6    8.5   9.2         13    6.8   3.2    2.4  2  Fer4_22   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> DUF362  Domain of unknown function (DUF362)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.6   0.3   3.5e-44   3.7e-41       1     203 []      38     309 ..      38     309 .. 0.87

  Alignments for each domain:
  == domain 1  score: 141.6 bits;  conditional E-value: 3.5e-44
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx..xxxxxxxxxxxxxxxxx..xx RF
                            DUF362   1 VaiKpNlgeagnpegatthpevvravvellkeagagkiivgdspglyv.srgka..hrevaeeagydelaega..di 72 
                                       VaiK++ ge+gn+++  +hp++vravv+++k+ g g ++v+d+++ly+  r++a  ++ +a ++g+++ + +a  +i
  gi|298674384|ref|YP_003726134.1|  38 VAIKIHPGEHGNTTH--IHPAIVRAVVDMVKDEG-GIPFVVDTTVLYNgMRFNAadALWTASVNGFTQESMNApvII 111
                                       9*************9..****************9.99*********96667777679999********8886667** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx...... RF
                            DUF362  73 adglegedevvvpvkgkhlkkelkiakavleaDviInlpklKgHalagvtgalKn.lfGcisgsgkaeiHs...... 142
                                        dgl g+++v+v+++g++lk+  ++a+a+++aD++I+l+++KgH  +g++ga+Kn ++Gc+ ++gk+++H       
  gi|298674384|ref|YP_003726134.1| 112 GDGLMGDESVTVEINGEELKQ-TTVASAIAKADSMIVLSHVKGHPATGFGGAVKNlGMGCLDKDGKTDCHEvgipti 187
                                       **************9999988.******************************************************* PP

                                       .......................................................xxx.xxxxxx.xxxxxxxxxxx RF
                            DUF362 143 .......................................................krd.sekfae.kiadlakalkp 162
                                                                                              +++ ++++ e +ia ++++ ++
  gi|298674384|ref|YP_003726134.1| 188 epekcvgcetcidmcawgalkmedgkavvdtelckgegfcvescpegaivppenfTEGlQKRIGEaSIATINSLSGK 264
                                       **************************************************988853345566777677777777445 PP

                                       x..x.xxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DUF362 163 d..l.nvvdgi...kamegegpsggskelglvlaStDpvalDaaaad 203
                                       +  + ++ d +   +++    ps+++ ++g +laS+Dpva+D+a++d
  gi|298674384|ref|YP_003726134.1| 265 IgyInWIFDLTlgcDCFGFYTPSFSK-DVG-ILASKDPVAIDMASID 309
                                       56674555555554333324454443.555.59***********986 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   3.3     3e-07   0.00031       1      22 [.     185     206 ..     185     208 .. 0.85
   2 !   18.8   1.2   9.9e-07     0.001       2      23 ..     215     236 ..     214     237 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3e-07
                                       EEEETTTSSS-THHHHHSTTTE CS
                              Fer4   1 vvideekCigCGaCvevCPvgA 22 
                                       ++i +ekC+gC +C+++C  gA
  gi|298674384|ref|YP_003726134.1| 185 PTIEPEKCVGCETCIDMCAWGA 206
                                       5799**************6665 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 9.9e-07
                                       EEETTTSSS-THHHHHSTTTEE CS
                              Fer4   2 videekCigCGaCvevCPvgAI 23 
                                       v+d+e+C g G Cve CP gAI
  gi|298674384|ref|YP_003726134.1| 215 VVDTELCKGEGFCVESCPEGAI 236
                                       89*******************9 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   2.2   2.2e-06    0.0023       1      24 []     184     207 ..     184     207 .. 0.93
   2 !   17.3   0.3   3.4e-06    0.0036       1      24 []     213     236 ..     213     236 .. 0.96

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.2e-06
                            Fer4_6   1 vveidpdkCigCgdCvrvCPegai 24 
                                       +++i p+kC+gC+ C++ C  ga+
  gi|298674384|ref|YP_003726134.1| 184 IPTIEPEKCVGCETCIDMCAWGAL 207
                                       699****************98886 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 3.4e-06
                            Fer4_6   1 vveidpdkCigCgdCvrvCPegai 24 
                                       ++++d ++C g g Cv  CPegai
  gi|298674384|ref|YP_003726134.1| 213 KAVVDTELCKGEGFCVESCPEGAI 236
                                       689********************8 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   4.9   1.3e-05     0.013      26      52 .]     180     206 ..     165     206 .. 0.79
   2 !   22.5   8.7   1.2e-07   0.00012       1      52 []     191     235 ..     191     235 .. 0.94
   3 !    8.6   0.4    0.0027       2.9       2      21 ..     221     240 ..     220     253 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.3e-05
                            Fer4_7  26 kgtekveidpekClgCgaCvavCPtga 52 
                                        ++  ++i+pekC+gC+ C++ C +ga
  gi|298674384|ref|YP_003726134.1| 180 HEVGIPTIEPEKCVGCETCIDMCAWGA 206
                                       4556779******************97 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 1.2e-07
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       +C+gC+ C ++C ++a+++++        k+++d e C g g Cv+ CP ga
  gi|298674384|ref|YP_003726134.1| 191 KCVGCETCIDMCAWGALKMEDG-------KAVVDTELCKGEGFCVESCPEGA 235
                                       7******************763.......799*****************997 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0027
                            Fer4_7   2 CigCgaCvaaCpvkaielde 21 
                                       C g g+Cv+ Cp +ai  +e
  gi|298674384|ref|YP_003726134.1| 221 CKGEGFCVESCPEGAIVPPE 240
                                       666689******99998766 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   6.6   4.3e-08   4.5e-05       3      56 .]     186     232 ..     184     237 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 4.3e-08
                           Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                        i++++C++C++C ++C +        + ++e+++  ++ e C g g Cve+CP
  gi|298674384|ref|YP_003726134.1| 186 TIEPEKCVGCETCIDMCAW-------GALKMEDGKAVVDTELCKGEGFCVESCP 232
                                       699**************66.......78888888888889*************9 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   2.1    0.0002      0.21       1      28 [.     191     219 ..     191     224 .. 0.78
   2 !   12.8   0.1   0.00017      0.18       2      25 ..     221     244 ..     220     279 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0002
                           Fer4_16   1 rCgtCgkCaevCPtnaikek.kekeiear 28 
                                       +C++C+ C+++C  +a+k++  +++++++
  gi|298674384|ref|YP_003726134.1| 191 KCVGCETCIDMCAWGALKMEdGKAVVDTE 219
                                       5****************988455556655 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00017
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekei 25 
                                       C++ g C+e+CP++ai  +++++ 
  gi|298674384|ref|YP_003726134.1| 221 CKGEGFCVESCPEGAIVPPENFTE 244
                                       777788***********9965554 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   2.2   9.7e-06      0.01       3      20 ..     185     202 ..     183     204 .. 0.90
   2 !    9.7   0.2   0.00088      0.92       2      22 .]     213     233 ..     212     233 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.7e-06
                            Fer4_2   3 vvvdtdrCigCgaCvsaC 20 
                                       + +++++C+gC++C++ C
  gi|298674384|ref|YP_003726134.1| 185 PTIEPEKCVGCETCIDMC 202
                                       7899***********999 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00088
                            Fer4_2   2 pvvvdtdrCigCgaCvsaCPa 22 
                                       ++vvdt+ C g g Cv +CP+
  gi|298674384|ref|YP_003726134.1| 213 KAVVDTELCKGEGFCVESCPE 233
                                       5799*****9879*******5 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5  10.1   3.6e-07   0.00038       2      57 ..     186     236 ..     170     237 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.6e-07
                           Fer4_21   2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57 
                                       +i+++kC+gC+ C+ +C      a+++++  ++ v ++ C G   C++ CP e++i
  gi|298674384|ref|YP_003726134.1| 186 TIEPEKCVGCETCIDMCA---WGALKMEDG-KAVVDTELCKGEGFCVESCP-EGAI 236
                                       699**************9...789998754.55899***************.6877 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   6.8   5.5e-07   0.00058       1      51 []     191     236 ..     191     236 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 5.5e-07
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       kC+gC +C+++C  g+ ++++++  +  +      C g g Cve Cp+gai
  gi|298674384|ref|YP_003726134.1| 191 KCVGCETCIDMCAWGALKMEDGKAVVDTE-----LCKGEGFCVESCPEGAI 236
                                       7**********************999985.....5**9999*******997 PP

>> Lar_N  Lactate racemase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1     2e-05     0.021     145     187 ..     133     175 ..     123     188 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2e-05
                             Lar_N 145 veinklvaeadlviltGfiepHyfaGfsGGrKsilpGvasret 187
                                        ++  ++a+ad +i++  ++ H   Gf+G  K +  G+ +++ 
  gi|298674384|ref|YP_003726134.1| 133 TTVASAIAKADSMIVLSHVKGHPATGFGGAVKNLGMGCLDKDG 175
                                       578899****************************999877665 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   3.9     0.003       3.2       1      14 [.     189     202 ..     189     203 .. 0.92
   2 ?   10.0   0.3   0.00097         1       2      16 ..     219     233 ..     218     242 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.003
                            Fer4_4   1 qerCigCgsCvaaC 14 
                                       +e+C+gC  C++ C
  gi|298674384|ref|YP_003726134.1| 189 PEKCVGCETCIDMC 202
                                       69*********988 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00097
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       e C g g Cv +CP 
  gi|298674384|ref|YP_003726134.1| 219 ELCKGEGFCVESCPE 233
                                       67************6 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   4.3    0.0063       6.6       1      15 []     192     206 ..     192     206 .. 0.96
   2 ?   10.0   0.8    0.0014       1.5       7      15 .]     227     235 ..     219     235 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0063
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+gC++C + C +gA
  gi|298674384|ref|YP_003726134.1| 192 CVGCETCIDMCAWGA 206
                                       ***********9998 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0014
                            Fer4_3   7 CvevCPvgA 15 
                                       Cve+CP+gA
  gi|298674384|ref|YP_003726134.1| 227 CVESCPEGA 235
                                       ********9 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   8.4     0.062        65       3      34 ..     187     218 ..     186     237 .. 0.70
   2 ?    8.6   0.6    0.0029       3.1       2      20 ..     215     233 ..     214     244 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.062
                           Fer4_15   3 vDrdaCigcglCvaeapevfeldedglasvll 34 
                                       ++ ++C gc+ C++ +     + edg+a+v++
  gi|298674384|ref|YP_003726134.1| 187 IEPEKCVGCETCIDMCAWGALKMEDGKAVVDT 218
                                       78899999999999997777777799996663 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0029
                           Fer4_15   2 vvDrdaCigcglCvaeape 20 
                                       vvD ++C g g Cv+ +pe
  gi|298674384|ref|YP_003726134.1| 215 VVDTELCKGEGFCVESCPE 233
                                       69***************86 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   3.7     0.011        12       1      16 [.     187     202 ..     187     204 .. 0.92
   2 ?    5.4   0.2     0.026        27       1      18 [.     216     233 ..     216     234 .. 0.96

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.011
                           Fer4_13   1 VDrdtCiacgaCvela 16 
                                       ++ ++C++c++C +++
  gi|298674384|ref|YP_003726134.1| 187 IEPEKCVGCETCIDMC 202
                                       6789***********9 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.026
                           Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                       VD + C + g Cve +P+
  gi|298674384|ref|YP_003726134.1| 216 VDTELCKGEGFCVESCPE 233
                                       899**************7 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   9.2     0.086        91       3      23 ..     190     209 ..     188     235 .. 0.57

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.086
                            Fer4_8   3 ekCieCgaCqsaCpvlrrtkk 23 
                                       ekC++C+ C ++C  + + k+
  gi|298674384|ref|YP_003726134.1| 190 EKCVGCETCIDMCA-WGALKM 209
                                       79***********5.333332 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   9.0      0.48   5.1e+02       1      16 [.     191     206 ..     191     235 .. 0.79
   2 ?    4.0   0.4     0.069        73       2      16 ..     221     235 ..     220     256 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.48
                           Fer4_17   1 rCiqCgyClpeCpsye 16 
                                       +C +C+ C+++C  ++
  gi|298674384|ref|YP_003726134.1| 191 KCVGCETCIDMCAWGA 206
                                       699*******998655 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.069
                           Fer4_17   2 CiqCgyClpeCpsye 16 
                                       C + g+C+++Cp ++
  gi|298674384|ref|YP_003726134.1| 221 CKGEGFCVESCPEGA 235
                                       666677777777665 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   3.2     0.012        13      78      93 ..     188     203 ..     180     206 .. 0.85
   2 ?    5.4   0.3     0.033        34      69      94 ..     208     233 ..     203     235 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.012
                           Fer4_22  78 gesgCvGCgRCieacp 93 
                                       + ++CvGC  Ci++c 
  gi|298674384|ref|YP_003726134.1| 188 EPEKCVGCETCIDMCA 203
                                       5679***********7 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.033
                           Fer4_22  69 klsefkekfgesgCvGCgRCieacpv 94 
                                       k+++ k+ ++++ C G g C+e+cp+
  gi|298674384|ref|YP_003726134.1| 208 KMEDGKAVVDTELCKGEGFCVESCPE 233
                                       7777788899**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2596.36
//
Query:       gi|298674385|ref|YP_003726135.1|  [L=469]
Description: CO dehydrogenase/acetyl-CoA synthase subunit delta [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.6e-146  488.0   0.0   1.9e-146  487.7   0.0    1.0  1  CdhD      CO dehydrogenase/acetyl-CoA synthase delta subunit
    8.2e-13   47.8   0.9    1.4e-12   47.0   0.9    1.4  1  FeS       Putative Fe-S cluster
  ------ inclusion threshold ------
      0.061   13.3   0.5        1.2    9.2   0.1    3.0  4  DUF5608   Domain of unknown function (DUF5608)


Domain annotation for each model (and alignments):
>> CdhD  CO dehydrogenase/acetyl-CoA synthase delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  487.7   0.0  3.2e-150  1.9e-146       1     385 [.      68     459 ..      68     460 .. 0.97

  Alignments for each domain:
  == domain 1  score: 487.7 bits;  conditional E-value: 3.2e-150
                                       EEEESSGCG-EEEE----SSTTTS---S--EEEEEEESSS-HHHHHHHHHHHTT-EEE....ETTEEEE--EEEEE- CS
                              CdhD   1 evvlGaeekavkiGgeevLyrfeltffnptaiaidvsDelseellkalaerieevvddwakkrvgekltldaiairl 77 
                                       ev +G+++kav+iGg++vLyr++ltffn+ta+++dv+D+++e+    laer++++++ ++k++vge+l+ daiair 
  gi|298674385|ref|YP_003726135.1|  68 EVDIGVGDKAVTIGGDDVLYRHKLTFFNKTALTYDVWDTMDEN---DLAERVNHIEN-FQKFYVGEFLNPDAIAIRS 140
                                       799*************************************996...78888888888.999**************** PP

                                       -SSST.HHHHHHHHHHHCC--SEEEEE-SSHHHHHHHHTTTCCC--EEEEE-TTTHHHHHHHHHHTT--EEEE-.SS CS
                              CdhD  78 istdPakkfakavekvakavkvplvlggsdpevlkaalevvederpllyaAtkddykeiaelaleykvpvvllsind 154
                                        s+dP  +f ++v+kv + +++p+vl++++pevl+a+lev  d++pl+yaA+kd+++e+a++a +y+vpv+l++  d
  gi|298674385|ref|YP_003726135.1| 141 VSDDP-TQFSETVKKVIEITNLPMVLCSFNPEVLRAGLEVSSDRNPLIYAANKDNWQEVADIANDYGVPVTLFAPGD 216
                                       *****.*********************************************************************** PP

                                       HHHHHHHHHHHHCTT---EEEE---SH.....HHHHHHHHHHHHHHHHS-TTS-S-BEEE---SSHHHHHHHHH... CS
                              CdhD 155 leelkelarkllkagvkdivldPttaalGegleetidnvvriRraaikgdkdlafPilslttnawlaresdeve... 228
                                       l+ lk++a +++k+g++++vldP+t++ G  l +t++n++++Rra+i+gd+++afP++s+++++wl+  +d+v+   
  gi|298674385|ref|YP_003726135.1| 217 LDLLKSMALTFTKMGMENLVLDPGTYPTGTQLRDTFNNFIKLRRAGINGDREIAFPLMSVPLTSWLVY-EDTVSasy 292
                                       *******************************************************************7.66777788 PP

                                       ........HHHTT-SEEEES---HHHHHHHHHHHHHHTS-SSS--B--SSEEEESS--TTS-EEEEESBHHHHHHHH CS
                              CdhD 229 ........lvvrYadililrslekeellPvltlrqniYtDPrkPvavdpglyeigdrdensPvflttnfsLtyYtve 297
                                               ++++Y+di++l+s+e +++lP+l++r++iYtDPrkPv vdpg+ye+g +  +sPv++ttnf+LtyYtve
  gi|298674385|ref|YP_003726135.1| 293 wetvlactFIIKYGDIMLLHSTEPYAMLPELHMRDTIYTDPRKPVMVDPGVYEVGSPTADSPVIITTNFALTYYTVE 369
                                       88899999********************************************************************* PP

                                       HHHHHTTS-EEEEEE-SSS--HHHHHHTTSSSHHHHHHHHHHTTHHHH..SSS-EEEE-GGGGGGHHHHHHHHTSEE CS
                              CdhD 298 gdlesdkitayLLvldteGlgvevslaggqleaekvkdlieetgieek..vkhrflilPglvavlkgkiedltgwkv 372
                                       +dl s++i +yL ++dteG+gve+++aggql+a+k+k+ +ee++++ k  ++h++l+lPgl+a+l+g++ed+tg++v
  gi|298674385|ref|YP_003726135.1| 370 SDLASNDIDCYLAAIDTEGIGVEAAVAGGQLTASKIKKGLEESEFDLKeqTNHKTLMLPGLAARLQGDVEDETGANV 446
                                       ******************************************99887766*************************** PP

                                       EE--SSGGGHHHH CS
                              CdhD 373 lvgprdsseivav 385
                                       + gp+ds++i+++
  gi|298674385|ref|YP_003726135.1| 447 VIGPADSGRIPGW 459
                                       **********988 PP

>> FeS  Putative Fe-S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.9   2.3e-16   1.4e-12       1      32 [.      13      44 ..      13      45 .. 0.97

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 2.3e-16
                               FeS  1 LPgtNCgaCGypgCmafAealvegeaqledCp 32
                                      LPg NCg CG+ +CmafA+ l+e +a+l+dC 
  gi|298674385|ref|YP_003726135.1| 13 LPGDNCGICGESTCMAFASRLIERSAELTDCE 44
                                      9******************************6 PP

>> DUF5608  Domain of unknown function (DUF5608)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1    0.0002       1.2      24      46 ..      67      90 ..      63      96 .. 0.85
   2 ?   -3.8   0.0       2.3   1.3e+04      39      51 ..     306     318 ..     305     319 .. 0.81
   3 ?   -0.9   0.0      0.29   1.7e+03      25      33 ..     338     346 ..     335     350 .. 0.88
   4 ?   -0.8   0.0      0.27   1.6e+03       8      29 ..     387     408 ..     381     413 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0002
                                      EEEEE-SSEEEEXETTE.EEEEEG CS
                           DUF5608 24 rlidiGvyevlvevGGd.iiyihk 46
                                      r +diGv +  v +GGd ++y hk
  gi|298674385|ref|YP_003726135.1| 67 REVDIGVGDKAVTIGGDdVLYRHK 90
                                      789************954899998 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2.3
                                       TEEEEEEGGG-SE CS
                           DUF5608  39 Gdiiyihkdlvya 51 
                                       Gdi+ +h    ya
  gi|298674385|ref|YP_003726135.1| 306 GDIMLLHSTEPYA 318
                                       9***999877776 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.29
                                       EEEE-SSEE CS
                           DUF5608  25 lidiGvyev 33 
                                       ++d Gvyev
  gi|298674385|ref|YP_003726135.1| 338 MVDPGVYEV 346
                                       6899****9 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 0.27
                                       TTSEEEEEETTEEEEEEEEEE- CS
                           DUF5608   8 kGiGvtvylanGrvqGrlidiG 29 
                                        GiGv   +a G++    i  G
  gi|298674385|ref|YP_003726135.1| 387 EGIGVEAAVAGGQLTASKIKKG 408
                                       79****9999999877766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3275.81
//
Query:       gi|298674386|ref|YP_003726136.1|  [L=442]
Description: CO dehydrogenase/acetyl-CoA synthase subunit delta [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.9e-86  289.2   1.2    1.6e-78  264.1   0.1    3.1  3  CdhD          CO dehydrogenase/acetyl-CoA synthase delta subu
  ------ inclusion threshold ------
      0.039   13.4   0.1      0.065   12.7   0.1    1.3  1  His_biosynth  Histidine biosynthesis protein


Domain annotation for each model (and alignments):
>> CdhD  CO dehydrogenase/acetyl-CoA synthase delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  264.1   0.1   1.8e-82   1.6e-78       1     226 [.     119     368 ..     119     370 .. 0.97
   2 !   10.6   0.0   1.9e-05      0.17     263     288 ..     371     393 ..     369     399 .. 0.90
   3 !   12.5   0.0   4.8e-06     0.043     347     384 ..     402     440 ..     394     442 .] 0.90

  Alignments for each domain:
  == domain 1  score: 264.1 bits;  conditional E-value: 1.8e-82
                                       EEEESS.......GCG-EEEE----S.STTTS---S--EEEEEEESSS-HHHHHHHHHHHTT-EEE.......ETTE CS
                              CdhD   1 evvlGa.......eekavkiGgeevL.yrfeltffnptaiaidvsDelseellkalaerieevvdd...wakkrvge 66 
                                       ev+lGa       +++++++Gge++L y f++++++++ +++dv+D + +  +k+++ ++e+v+dd   wakk v+e
  gi|298674386|ref|YP_003726136.1| 119 EVTLGAtssdggsRGNTITLGGENALpYYFDAEMPHRNYVTMDVFDLPIS-MAKSVRTNYEDVMDDpaeWAKKVVNE 194
                                       67777777777779************888*****************9987.6************************* PP

                                       EEE--EEEEE--SSST.......HHHHHHHHHHHCC--SEEEEE-S.....SHHHHHHHHTTTCCC--EEEEE-TT. CS
                              CdhD  67 kltldaiairlistdP......akkfakavekvakavkvplvlggs.....dpevlkaalevvederpllyaAtkd. 131
                                        +++d+++i+l stdP      ak++ k+ve+v++av+vplv+ggs     dpevl++a+ev+e+er ll++A+++ 
  gi|298674386|ref|YP_003726136.1| 195 -YNADMVTIHLVSTDPniedtsAKEASKVVEDVLQAVDVPLVIGGSgnpdkDPEVLEKAAEVAEGERALLASASLNl 270
                                       .**************************************************************************** PP

                                       THHHHHHHHHHTT--EEEE-.SSHHHHHHHHHHHHC.TT-..--EEEE---SH.....HHHHHHHHHHHHHHHHS-T CS
                              CdhD 132 dykeiaelaleykvpvvllsindleelkelarkllk.agv..kdivldPttaalGegleetidnvvriRraaikgdk 205
                                       dy++ia++a +y+++++++++ +++++kel+rkl+  ++v  ++i++dPttaalG+gl+++++n++riR+a++ gd+
  gi|298674386|ref|YP_003726136.1| 271 DYERIAKAATDYGHAILSWTQLEINAQKELNRKLMTqCNVprDSILMDPTTAALGYGLDYAYTNMERIRLAGLTGDD 347
                                       **********************************98799999*********************************** PP

                                       TS-S-BEEE---SSHHHHHHH CS
                              CdhD 206 dlafPilslttnawlaresde 226
                                       +l+fP++s+ttnaw+ares++
  gi|298674386|ref|YP_003726136.1| 348 ELTFPMSSGTTNAWGARESWM 368
                                       ********************8 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 1.9e-05
                                       S--B--SSEEEESS--TTS-EEEEES CS
                              CdhD 263 kPvavdpglyeigdrdensPvflttn 288
                                       +P+++d ++   g+r++++P++++ +
  gi|298674386|ref|YP_003726136.1| 371 SPIQNDSDW---GPREYRGPIWEIST 393
                                       8********...***********987 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 4.8e-06
                                       SS-EEEE.-GGGGGGHHHHHHHHTSEEEE--SSGGGHHH CS
                              CdhD 347 khrflil.Pglvavlkgkiedltgwkvlvgprdsseiva 384
                                       ++ f+++ P++v+vlk++++ l+g+k +++++ s++i+a
  gi|298674386|ref|YP_003726136.1| 402 NDLFMMMhPTSVQVLKETTQSLFGTKEAEDIDISNWIGA 440
                                       6779*******************************9987 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   7.2e-06     0.065      16      80 ..     169     238 ..     158     288 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.2e-06
                                       ECTTCSTCEEEETTSHHHHHHHH.HHHT-SE..EEEEEHHHHC..TTHHHHHHHHHHHHHH-SSEEEEES CS
                      His_biosynth  16 lvkGdrfqelryagdpvelakry.eeegade..lhvvDldaak..egreanldlveeiaeevfipvqvGG 80 
                                       + k +r +++++ +dp+e ak+  +e +ad+  +h+v  d     ++ ++  ++ve ++++v++p+ +GG
  gi|298674386|ref|YP_003726136.1| 169 MAKSVRTNYEDVMDDPAEWAKKVvNEYNADMvtIHLVSTDPNIedTSAKEASKVVEDVLQAVDVPLVIGG 238
                                       6788999999********99999666666652267776666663344555669***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2962.26
//
Query:       gi|298674387|ref|YP_003726137.1|  [L=250]
Description: cobyrinic acid ac-diamide synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.3e-18   64.7   0.0    1.1e-17   64.3   0.0    1.1  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    7.8e-15   55.2   0.0    1.3e-14   54.6   0.0    1.2  1  AAA_31       AAA domain
    5.4e-10   39.2   0.5    7.9e-09   35.3   0.5    2.0  1  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
    5.6e-09   35.6   1.5      3e-08   33.2   1.5    2.3  1  ArsA_ATPase  Anion-transporting ATPase
    8.6e-08   31.9   0.0    6.4e-05   22.5   0.0    2.4  2  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
      1e-07   31.7   0.6    4.6e-07   29.5   0.6    1.9  1  ParA         NUBPL iron-transfer P-loop NTPase
    0.00014   22.1   0.1     0.0068   16.6   0.0    2.3  2  Toprim       Toprim domain
    0.00021   21.7   0.0    0.00036   20.9   0.0    1.6  1  AAA_16       AAA ATPase domain
     0.0018   18.0   0.9      0.037   13.8   0.9    2.7  1  AAA_24       AAA domain
      0.002   17.8   1.6        1.4    8.6   0.1    2.2  2  SRP54        SRP54-type protein, GTPase domain
     0.0082   16.4   0.0      0.029   14.6   0.0    1.8  2  AAA_22       AAA domain
  ------ inclusion threshold ------
      0.013   15.4   1.7        3.4    7.6   0.2    2.3  2  NTPase_1     NTPase
      0.016   15.7   0.1       0.09   13.3   0.1    2.1  2  Toprim_4     Toprim domain
      0.025   14.4   0.9        2.3    8.0   0.1    2.2  2  AAA_26       AAA domain
      0.031   14.8   0.0      0.072   13.6   0.0    1.6  1  AAA_18       AAA domain
      0.046   13.8   0.2       0.12   12.4   0.1    1.8  2  DUF87        Helicase HerA, central domain
      0.059   12.5   0.0      0.089   11.9   0.0    1.3  1  PIF1         PIF1-like helicase
      0.069   12.7   0.0       0.16   11.5   0.0    1.5  1  AAA_7        P-loop containing dynein motor region
       0.07   12.2   0.0       0.14   11.2   0.0    1.5  1  T2SSE        Type II/IV secretion system protein
      0.077   12.9   0.1        0.2   11.5   0.0    1.8  2  APS_kinase   Adenylylsulphate kinase
       0.11   12.8   0.1       0.11   12.8   0.1    2.0  2  AAA_19       AAA domain
       0.13   12.3   0.0       0.43   10.6   0.0    2.0  1  AAA_14       AAA domain
       0.15   11.3   2.0        4.1    6.6   0.2    2.6  3  MipZ         ATPase MipZ
       0.19   11.3   0.0       0.28   10.8   0.0    1.2  1  PP2C_2       Protein phosphatase 2C
        0.2   10.3   0.1       0.32    9.6   0.1    1.2  1  PEPCK_ATP    Phosphoenolpyruvate carboxykinase
       0.28   10.7   1.7        0.4   10.2   0.3    2.2  3  AAA_25       AAA domain


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.3   0.0   1.6e-20   1.1e-17       1     128 []       4     228 ..       4     228 .. 0.91

  Alignments for each domain:
  == domain 1  score: 64.3 bits;  conditional E-value: 1.6e-20
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       i+++ +kGG+GKT ++a L+r l ++ + Vl+vDaDp++n+   + g e+d+                         
  gi|298674387|ref|YP_003726137.1|   4 IIAVTGKGGTGKTAITAMLMRHLVKDDNLVLAVDADPDTNLPD-ALGCEIDHTLgemrefmlnerdnfppdsnkesv 79 
                                       68899***********************************999.666666666677777999*************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|298674387|ref|YP_003726137.1|  80 leskvyeainemddydllvmgrpegpgcycyvnnllrgimtrlvtnydaviidteaglehfsrklipeiddlivvtd 156
                                       ***************************************************************************** PP

                                       ....CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS- CS
                                       ....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ....dlkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeapargep 127
                                           +++  +e +++l+++++ ++k + vv+n+v ++  +++l+e+ ++ +    +++lg +p d+ + e + +g+p
  gi|298674387|ref|YP_003726137.1| 157 gskrGMQT-GERIRQLVGELETKVKNVYVVANKVTES--NRELIEQNAKDL---DLRLLGAVPVDKIIEERDLKGLP 227
                                       99987755.77778888888777************99..555555555555...9************9999999987 PP

                                       H CS
                                       x RF
                              CbiA 128 v 128
                                       +
  gi|298674387|ref|YP_003726137.1| 228 L 228
                                       5 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   0.0   1.8e-17   1.3e-14       2     172 ..       3     180 ..       2     185 .. 0.87

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 1.8e-17
                            AAA_31   2 kvIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekneiektlyevli.eeknikeaiiktk 77 
                                       ++Ia++  KGG GKT+ + +l   l k ++ vL vD+Dp +n+  +lg+e +++  ++ e ++ e+ n     +k++
  gi|298674387|ref|YP_003726137.1|   3 RIIAVT-GKGGTGKTAITAMLMRHLVKDDNLVLAVDADPDTNLPDALGCEIDHTLGEMREFMLnERDNFPPDSNKES 78 
                                       677765.7****************************************97777777777777547777776677677 PP

                            AAA_31  78 venldlipssidLaeaeielvelekk.......eeilkellekvkdeYDyiiiDcpPsLglltenaLvasdsviipv 147
                                       v + ++  +  ++ +++  +++  +        ++ l+ +++++  +YD +iiD+   L+ + ++ +   d +i+++
  gi|298674387|ref|YP_003726137.1|  79 VLESKVYEAINEMDDYDLLVMGRPEGpgcycyvNNLLRGIMTRLVTNYDAVIIDTEAGLEHFSRKLIPEIDDLIVVT 155
                                       7778888998999999988888777799999988889**************************************** PP

                            AAA_31 148 qaeayaleGleqllktieevkkkln 172
                                       + +++ +++ e++ + + e+++k++
  gi|298674387|ref|YP_003726137.1| 156 DGSKRGMQTGERIRQLVGELETKVK 180
                                       *******999999999998888765 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.5   1.2e-11   7.9e-09       1     243 [.       3     247 ..       3     249 .. 0.80

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 1.2e-11
                         Fer4_NifH   1 rkiaiyGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggkaqetvld....tlrekgav.edvkved 72 
                                       r ia+ GkGG Gk+  ++ l+  l+++ + vl v  DP ++     lg  + +t+ +    +l+e++    d + e+
  gi|298674387|ref|YP_003726137.1|   3 RIIAVTGKGGTGKTAITAMLMRHLVKDDNLVLAVDADPDTNLP-DALGCEIDHTLGEmrefMLNERDNFpPDSNKES 78 
                                       679***********************************98877.568888888886622334677777667777777 PP

                         Fer4_NifH  73 vvk.kGyggvkcve.....sGGPepGvGCaGrgvitaielleelgayddlDfvlyDvLGDvvCGGfalPiredkaqe 143
                                       v+  k y+ ++ ++       G + G GC  ++      ++ +l   +++D v+ D         f+  +     ++
  gi|298674387|ref|YP_003726137.1|  79 VLEsKVYEAINEMDdydllVMGRPEGPGCYCYVNNLLRGIMTRL--VTNYDAVIIDTEA--GLEHFSRKLI-PEIDD 150
                                       76424566666655222333455568999888765555566655..578999*999754..4568999988.57899 PP

                         Fer4_NifH 144 vyivtsgelmalyaanniakgiekyaksggvrlgGliinsrkvddereliekfaeelgtkvlevvPrdeivrkaelr 220
                                       +++vt+g    + +  +i + + +     +v+   ++ n + ++++relie+ a++l++++l +vP d+i+++ +l+
  gi|298674387|ref|YP_003726137.1| 151 LIVVTDGSKRGMQTGERIRQLVGELE--TKVKNVYVVAN-KVTESNRELIEQNAKDLDLRLLGAVPVDKIIEERDLK 224
                                       ********************999875..46777789999.88999******************************** PP

                         Fer4_NifH 221 kktvieyapeseqakeyrelark 243
                                          +++  +es   ke +++a++
  gi|298674387|ref|YP_003726137.1| 225 GLPLFDLPDESVAIKEINNIAND 247
                                       *****999999999999999986 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   1.5   4.3e-11     3e-08       1      61 [.       2      62 ..       2     250 .] 0.78

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 4.3e-11
                                      -EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEETSS CS
                       ArsA_ATPase  1 lkvilvgGKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklgkeptkvkeN 61
                                      +++i v+GKGG GKt++ a +  +l + ++ vl +  DP  +l D++  ++ ++   ++e 
  gi|298674387|ref|YP_003726137.1|  2 TRIIAVTGKGGTGKTAITAMLMRHLVKDDNLVLAVDADPDTNLPDALGCEIDHTLGEMREF 62
                                      699************************************************9998777654 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   9.3e-08   6.4e-05       3      59 ..       4      59 ..       1      74 [. 0.87
   2 !    7.1   0.0     0.005       3.4     105     147 ..     115     157 ..     103     248 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 9.3e-08
                          CBP_BcsQ  3 vlalqGvRGGvGttsllaaLawalhelgesvlviDlspdnlLrlhFnvdieqregwa 59
                                      ++a++G +GG+G+t+++a+L + l + ++ vl++D+ pd  L      +i+++ g +
  gi|298674387|ref|YP_003726137.1|  4 IIAVTG-KGGTGKTAITAMLMRHLVKDDNLVLAVDADPDTNLPDALGCEIDHTLGEM 59
                                      678888.8*******************************999888888888877755 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.005
                          CBP_BcsQ 105 llaalkelkeqyrwillDlpagasaltrellaladlvllvvep 147
                                       l   +++l ++y+ +++D  ag ++  r+l+   d  + v+  
  gi|298674387|ref|YP_003726137.1| 115 LRGIMTRLVTNYDAVIIDTEAGLEHFSRKLIPEIDDLIVVTDG 157
                                       555689999***********************99999999864 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.6   6.7e-10   4.6e-07       5     245 ..       4     248 ..       1     249 [. 0.73

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 6.7e-10
                              ParA   5 viavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgvee........ekpeqsekkliPvea..k 71 
                                       +i  + gKGG GK+ +++ l  +L k +  v  +DaD    ++p+ lg+e         e + ++++++ P ++  +
  gi|298674387|ref|YP_003726137.1|   4 II-AVTGKGGTGKTAITAMLMRHLVKDDNLVLAVDADP-DTNLPDALGCEIdhtlgemrEFMLNERDNFPPDSNkeS 78 
                                       44.457******************************84.34555555554433333331444444444555554543 PP

                              ParA  72 gikvmSigfllesedea..vvwr..Gpmkskaikqllkdvew...gelDyLiiDlPPGtgDeqltvaqklplagavi 141
                                        ++    + + e +d    v+ r  Gp     +++ll+ +      + D +iiD+  G    +  ++   ++++ ++
  gi|298674387|ref|YP_003726137.1|  79 VLESKVYEAINEMDDYDllVMGRpeGPGCYCYVNNLLRGIMTrlvTNYDAVIIDTEAGLEHFSRKLIP--EIDDLIV 153
                                       355555556655554441044445589888899999887765223689*******8877555555555..568**** PP

                              ParA 142 VttpqevaladvkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeirea 218
                                       Vt   +  ++  ++  +++ ++++kv    +N+ +++ + ++++      +  e+ a++l+++llg++p+d+ i e 
  gi|298674387|ref|YP_003726137.1| 154 VTDGSKRGMQTGERIRQLVGELETKV----KNVYVVANKVTESNR-----ELIEQNAKDLDLRLLGAVPVDKIIEER 221
                                       **********************9995....676666655555554.....5567889******************** PP

                              ParA 219 sdegkplvlkepeseaakaleeiaekv 245
                                         +g pl+   +es a k++++ia+++
  gi|298674387|ref|YP_003726137.1| 222 DLKGLPLFDLPDESVAIKEINNIANDL 248
                                       *******999999999******99876 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.17   1.1e+02      50      75 ..      16      41 ..       4      43 .. 0.80
   2 !   16.6   0.0   9.8e-06    0.0068      28     100 ..     115     184 ..     105     187 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.17
                                      HHHHHHHHHHHHHHSEEEEECSSSHH CS
                            Toprim 50 kkvlkalkelakradeiilatDpDre 75
                                      + + ++l + + + d+++la D+D +
  gi|298674387|ref|YP_003726137.1| 16 TAITAMLMRHLVKDDNLVLAVDADPD 41
                                      4555667777899**********975 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 9.8e-06
                                       ESSSSEEEHSTTEEEEE.ECTTTHHHHHHHHHHH.HHHSEEEEECSSSHHHHHHHHHHHHHHTHHHTTTEEEEEE CS
                            Toprim  28 slGhildletefkpvye.eiedkkkvlkalkela.kradeiilatDpDreGeaiawellevlkellenkigrvef 100
                                       ++G ++ l+t    +y+ +i d++  l+ + + +  + d +i+ tD+ + G +++ +++++++el  + +++v++
  gi|298674387|ref|YP_003726137.1| 115 LRGIMTRLVT----NYDaVIIDTEAGLEHFSRKLiPEIDDLIVVTDGSKRGMQTGERIRQLVGELETK-VKNVYV 184
                                       5788888888....777766677777777655555****************************77776.999987 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   5.3e-07   0.00036      25      63 ..       3      41 ..       1     131 [. 0.85

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 5.3e-07
                            AAA_16 25 elvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                      +++ ++G  G+GK+++  +l+r+l kd+ ++l+ ++d  
  gi|298674387|ref|YP_003726137.1|  3 RIIAVTGKGGTGKTAITAMLMRHLVKDDNLVLAVDADPD 41
                                      799************************877755555544 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.9   5.3e-05     0.037       4     135 ..       4     192 ..       1     204 [. 0.72

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.3e-05
                            AAA_24   4 kiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie.........swedfldevvel............ 59 
                                        i+++G+ g+GKT + ++l  + l+ d +  + ++dad   +++         ++ ++++++               
  gi|298674387|ref|YP_003726137.1|   4 IIAVTGKGGTGKTAITAML-MRHLVKDDNL-VLAVDADPDTNLPdalgceidhTLGEMREFMLNErdnfppdsnkes 78 
                                       699****************.5555554333.3344444444444566663446444444444333778888888888 PP

                            AAA_24  60 .........................................aaeladyktlviDt...ideleelclaevirqneka 92 
                                                                                 +   +y+ ++iDt   ++++ +  + e+++   + 
  gi|298674387|ref|YP_003726137.1|  79 vleskvyeainemddydllvmgrpegpgcycyvnnllrgimTRLVTNYDAVIIDTeagLEHFSRKLIPEIDDLIVVT 155
                                       88888888888889999999999999999999999999999999999999999995555566666666666655553 PP

                            AAA_24  93 eskedkgdgkGygelaeefrrllkklqelrknvifiahektrk 135
                                       ++     + +G ++ +e++r+l+  l+   knv+++a   t+ 
  gi|298674387|ref|YP_003726137.1| 156 DG-----SKRG-MQTGERIRQLVGELETKVKNVYVVANKVTES 192
                                       22.....3344.7889999999999999999999999877765 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.2    0.0021       1.4       2      38 ..       3      39 ..       2      40 .. 0.87
   2 !    8.6   0.1     0.002       1.4      80     112 ..     122     155 ..     110     205 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0021
                                      EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54  2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                      ++i++ G  G+GKT  +a L ++l k+ + vl v aD
  gi|298674387|ref|YP_003726137.1|  3 RIIAVTGKGGTGKTAITAMLMRHLVKDDNLVLAVDAD 39
                                      57999*******************9998877776665 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.002
                                       HHTTSSEEEEEE.--SSTTHHHHHHHHHHHHHHH CS
                             SRP54  80 keekidvvlvDT.aGrlqndkelmeelkkikkvv 112
                                          ++d+v++DT aG  +  ++l+ e++++  v+
  gi|298674387|ref|YP_003726137.1| 122 LVTNYDAVIIDTeAGLEHFSRKLIPEIDDLIVVT 155
                                       5579********99*************9988777 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   4.2e-05     0.029       6      66 ..       3      58 ..       2      99 .. 0.68
   2 ?   -1.4   0.0       3.8   2.6e+03      39      67 ..     178     207 ..     157     225 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.2e-05
                            AAA_22  6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralgl 66
                                      +i++vtG  GtGKT   ++l++ l+++      +  v+ v++  +t  ++ l  e+ + lg+
  gi|298674387|ref|YP_003726137.1|  3 RIIAVTGKGGTGKTAITAMLMRHLVKD------DNLVLAVDADPDTnLPDALGCEIDHTLGE 58
                                      699*********************875......66666888888884444445555555555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.8
                            AAA_22  39 rpevvfvtlpsst.sskdllrellralgle 67 
                                       +++ v+v +++ t s ++l ++ +++l+l+
  gi|298674387|ref|YP_003726137.1| 178 KVKNVYVVANKVTeSNRELIEQNAKDLDLR 207
                                       444555555555556666666666555554 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.2    0.0049       3.4       2      26 ..       5      29 ..       4      35 .. 0.86
   2 ?    7.0   0.1    0.0072         5      88     165 ..     118     199 ..     106     201 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0049
                                      EEEE--TTSSHHHHHHHHHHHH... CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkss 26
                                      +++TG+ G+GKt +   +++ l ++
  gi|298674387|ref|YP_003726137.1|  5 IAVTGKGGTGKTAITAMLMRHLVKD 29
                                      78*************9999988765 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0072
                                       HHHHHHHHH-EEEE---STTGGG-HHHHHHHHHHHT...TTSEEEEE--SS--SHHHHHHHT-TT...-EEEE--TT CS
                          NTPase_1  88 alrkalseadviviDEiGkmElkskkfkeaveevLk...sekpvlavihrrkdlalveeirerkd...vkvfevtee 158
                                       ++++ +++ d ++iD    +E +s+k++ ++++++     +k  + +  r    +lv e++ + +   v+  +vte+
  gi|298674387|ref|YP_003726137.1| 118 IMTRLVTNYDAVIIDTEAGLEHFSRKLIPEIDDLIVvtdGSKRGMQTGERI--RQLVGELETKVKnvyVVANKVTES 192
                                       555666889999***7777*************9774323667777777776..578999888766332333449999 PP

                                       TTTTHHH CS
                          NTPase_1 159 nrdalle 165
                                       nr+ + +
  gi|298674387|ref|YP_003726137.1| 193 NRELIEQ 199
                                       9997765 PP

>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       2.7   1.9e+03      50      64 ..      25      39 ..       6      41 .. 0.77
   2 ?   13.3   0.1   0.00013      0.09      34      88 ..     137     182 ..     119     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.7
                          Toprim_4 50 aekkvkevilaldgD 64
                                      ++ k ++++la+d+D
  gi|298674387|ref|YP_003726137.1| 25 HLVKDDNLVLAVDAD 39
                                      56677999*****98 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00013
                          Toprim_4  34 ldgirpeklktenlveaekkvkevilaldgDaeGeataerlaellleegvkvtrl 88 
                                       l++ +++ +++         ++ +i+++dg+++G +t er+ +l++e ++kv+++
  gi|298674387|ref|YP_003726137.1| 137 LEHFSRKLIPE---------IDDLIVVTDGSKRGMQTGERIRQLVGELETKVKNV 182
                                       45666666666.........8**********************777888888776 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.029        20      10      25 ..      11      26 ..       3      33 .. 0.79
   2 ?    8.0   0.1    0.0033       2.3     155     195 ..     177     219 ..     147     221 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.029
                            AAA_26 10 tgvGKTvvslgLvral 25
                                       g GKT+++++L+r l
  gi|298674387|ref|YP_003726137.1| 11 GGTGKTAITAMLMRHL 26
                                      479***********98 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0033
                            AAA_26 155 knvrvlGvilNkvrnpenvetlekksg...ipvlGvvPylpdle 195
                                       ++v+ + v++Nkv  + n+e +e++ +   +++lG+vP ++ +e
  gi|298674387|ref|YP_003726137.1| 177 TKVKNVYVVANKV-TESNRELIEQNAKdldLRLLGAVPVDKIIE 219
                                       46677789****6.55567777777666669*******998765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0    0.0001     0.072       1      68 [.       5      74 ..       5     101 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.0001
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe....aldeskrldedkldklldaleens 68
                                      I++tG+ G+GKt ++  L ++l  +   + v++ +   +++ p+    ++d ++ + ++++ +  d++   s
  gi|298674387|ref|YP_003726137.1|  5 IAVTGKGGTGKTAITAMLMRHL--VKDDNLVLAVDADPDTNLPDalgcEIDHTLGEMREFMLNERDNFPPDS 74
                                      89****************9997..444444444444444444446666666666666666666666666654 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00018      0.12      23      56 ..       2      34 ..       1      41 [. 0.81
   2 ?   -1.9   0.0       4.2   2.9e+03     137     151 ..     162     176 ..     115     209 .. 0.49

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00018
                             DUF87 23 trHlAilgsTGsGKSntvavLleellekkgatil 56
                                      tr +A+ g+ G+GK+  +a L++ l+++++  +l
  gi|298674387|ref|YP_003726137.1|  2 TRIIAVTGKGGTGKTAITAMLMRHLVKDDN-LVL 34
                                      6779**********************5444.444 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.2
                             DUF87 137 lssdepveklleelk 151
                                       +++ e + +l  el+
  gi|298674387|ref|YP_003726137.1| 162 MQTGERIRQLVGELE 176
                                       333333333333333 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00013     0.089      23      56 ..       3      36 ..       1      39 [. 0.92

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                                      S-EEEEESTTSSCHHHHHHHHHHCHCTCCCEEEE CS
                              PIF1 23 klfFvtGsgGtgKtflwkallkklrsegkivlav 56
                                      +++ vtG gGtgKt +   l+  l + ++ vlav
  gi|298674387|ref|YP_003726137.1|  3 RIIAVTGKGGTGKTAITAMLMRHLVKDDNLVLAV 36
                                      67889**************************998 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00023      0.16      36      68 ..       5      37 ..       2      46 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00023
                             AAA_7 36 vllvGptGtGKtviikdllkkldkekylsltin 68
                                      + ++G+ GtGKt+i+  l+++l k++ l+l + 
  gi|298674387|ref|YP_003726137.1|  5 IAVTGKGGTGKTAITAMLMRHLVKDDNLVLAVD 37
                                      5689******************99998888765 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0002      0.14     131     166 ..       4      38 ..       1      53 [. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0002
                             T2SSE 131 lilvsGgTgsGKttllyallkeinksderivtvEDp 166
                                       +i v+G  g+GKt ++ +l+  + k+ +++v++ D+
  gi|298674387|ref|YP_003726137.1|   4 IIAVTGKGGTGKTAITAMLMRHLVKD-DNLVLAVDA 38 
                                       799**********************9.888877665 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00029       0.2       4      39 ..       4      39 ..       1      60 [. 0.88
   2 ?   -1.8   0.0       3.7   2.5e+03     109     122 ..     212     226 ..     166     227 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00029
                                      EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHH CS
                        APS_kinase  4 vvwltGlsgsGKstianalekkLvekgisvylLdGd 39
                                      ++ +tG  g+GK++i+ +l ++Lv++   v  +d d
  gi|298674387|ref|YP_003726137.1|  4 IIAVTGKGGTGKTAITAMLMRHLVKDDNLVLAVDAD 39
                                      7889**********************9999998877 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.7
                                       --HH.HHHHHTTTSH CS
                        APS_kinase 109 tple.vceerDpkgl 122
                                       +p++ + eerD kgl
  gi|298674387|ref|YP_003726137.1| 212 VPVDkIIEERDLKGL 226
                                       333313466666665 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   0.00016      0.11      11      38 ..       3      30 ..       1      40 [. 0.88
   2 ?   -2.3   0.0       7.3     5e+03      34      45 ..     171     182 ..     131     215 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00016
                            AAA_19 11 kvllvtaGpGtGKTrvlkhivallvelg 38
                                      ++++vt+  GtGKT ++ + +++lv+  
  gi|298674387|ref|YP_003726137.1|  3 RIIAVTGKGGTGKTAITAMLMRHLVKDD 30
                                      6899********************9876 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7.3
                            AAA_19  34 lvelggvkpeei 45 
                                       lv + + k++++
  gi|298674387|ref|YP_003726137.1| 171 LVGELETKVKNV 182
                                       333333333333 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00062      0.43       3      46 ..       3      44 ..       1     185 [. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00062
                            AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkl 46
                                      +i+++tG   +GKT +   l+++l   k++ l +++d ++d++l
  gi|298674387|ref|YP_003726137.1|  3 RIIAVTGKGGTGKTAITAMLMRHLV--KDDNLVLAVDADPDTNL 44
                                      799******************9999..66677777777666543 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.2    0.0059       4.1       3      38 ..       4      39 ..       2      44 .. 0.89
   2 ?    3.7   0.1     0.047        32      89     127 ..     115     153 ..     108     206 .. 0.83
   3 ?   -1.6   0.0       1.9   1.3e+03     189     205 ..     192     208 ..     162     246 .. 0.56

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0059
                                      EEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE-- CS
                              MipZ  3 ivlgnekGGsGksttavhvavaLlkkGarvaaidld 38
                                      i+    kGG+Gk++++  ++  L+k    v a+d d
  gi|298674387|ref|YP_003726137.1|  4 IIAVTGKGGTGKTAITAMLMRHLVKDDNLVLAVDAD 39
                                      566678**************************9988 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.047
                                       HHHHHHHHHHH-SEEEEE--SS--HHHHHHHHT-SEEEE CS
                              MipZ  89 leelvadleaeldfividtPGsdsalsrlahsladtlvt 127
                                       l+ ++++l +++d ++idt    ++ sr    + d l+ 
  gi|298674387|ref|YP_003726137.1| 115 LRGIMTRLVTNYDAVIIDTEAGLEHFSRKLIPEIDDLIV 153
                                       567899999**********98888887777666666654 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHHHHHHH CS
                              MipZ 189 rnkkkveealeeLskrv 205
                                        n++ +e++ ++L  r+
  gi|298674387|ref|YP_003726137.1| 192 SNRELIEQNAKDLDLRL 208
                                       45555555555555554 PP

>> PP2C_2  Protein phosphatase 2C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0004      0.28     153     195 ..     138     178 ..     119     192 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0004
                            PP2C_2 153 eelrirrlkledgdalllmTDGlanslrdeerfaelleellrv 195
                                       e++ ++ ++  ++d l+++TDG   ++++ er ++l+ el + 
  gi|298674387|ref|YP_003726137.1| 138 EHFSRKLIP--EIDDLIVVTDGSKRGMQTGERIRQLVGELETK 178
                                       444554445..89***********************9998554 PP

>> PEPCK_ATP  Phosphoenolpyruvate carboxykinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00046      0.32     217     242 ..       9      34 ..       5      38 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00046
                                       E-TTSSHHHHH-BTTB-EEESSEEEE CS
                         PEPCK_ATP 217 GLSGtGKTtLsadperkligdDehgw 242
                                       G  GtGKT+++a   r+l+ dD+ ++
  gi|298674387|ref|YP_003726137.1|   9 GKGGTGKTAITAMLMRHLVKDDNLVL 34 
                                       567*******************9987 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.3   0.00058       0.4      35      62 ..       4      31 ..       1     100 [. 0.85
   2 ?   -3.2   0.0       7.6   5.2e+03     142     150 ..     125     133 ..     113     142 .. 0.76
   3 ?   -1.6   0.0       2.4   1.7e+03      76     116 ..     152     195 ..     148     224 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00058
                            AAA_25 35 lallaGapgtGKttlaldlalavatGkp 62
                                      +++++G +gtGKt+++  l+ +++++++
  gi|298674387|ref|YP_003726137.1|  4 IIAVTGKGGTGKTAITAMLMRHLVKDDN 31
                                      6789****************99987665 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 7.6
                            AAA_25 142 gvrlvviDp 150
                                       +++ v+iD+
  gi|298674387|ref|YP_003726137.1| 125 NYDAVIIDT 133
                                       478899998 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.4
                            AAA_25  76 yvsaEdsedelr..rRlravgeal.rddarllvldlagv.eslpL 116
                                       +v++++s  +++  +R+r++  +l +  ++++v+   +v es++ 
  gi|298674387|ref|YP_003726137.1| 152 IVVTDGSKRGMQtgERIRQLVGELeTKVKNVYVVA-NKVtESNRE 195
                                       55666665544433777777777755566666664.344444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      720  (0.0401584); expected 358.6 (0.02)
Passed Vit filter:                       134  (0.00747392); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 1523.48
//
Query:       gi|298674388|ref|YP_003726138.1|  [L=469]
Description: CO dehydrogenase/acetyl-CoA synthase complex subunit beta [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-64  216.1   0.0      3e-64  215.6   0.0    1.2  1  CdhC      CO dehydrogenase/acetyl-CoA synthase complex beta s


Domain annotation for each model (and alignments):
>> CdhC  CO dehydrogenase/acetyl-CoA synthase complex beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.6   0.0   1.7e-68     3e-64       1     155 []       4     158 ..       4     158 .. 0.99

  Alignments for each domain:
  == domain 1  score: 215.6 bits;  conditional E-value: 1.7e-68
                              CdhC   1 ipvevspafeGeriRkedlyvelggkktkafElvkvkeadevedgkieviGpdideveegsrlplailvevaGkkle 77 
                                       +p+e+sp+feGeriRk+d+yvel+g k+k+fElv+++++de+edgk+++iGpdi+e+eegsr+p+a+l+++ G+ +e
  gi|298674388|ref|YP_003726138.1|   4 FPLEISPMFEGERIRKNDMYVELAGPKSKGFELVRATDSDEIEDGKFTLIGPDISEMEEGSRYPFAMLYKIGGELVE 80 
                                       699**********************99************************************************** PP

                              CdhC  78 edlEpvlERriHeflnyieGvmHlgqRdiiwvRiskeavekGl.rlkhigevlyaklkeefeaivdkvevtlitdee 153
                                       +dlE+++ERr+H+f+ny++GvmHl+qR++iwvR+sk+av+kGl ++++++ ++++++k+e+ ++++k+e  +itd+e
  gi|298674388|ref|YP_003726138.1|  81 PDLEAIVERRNHDFYNYMQGVMHLNQRYDIWVRLSKDAVNKGLnSFEQMAAAMMSLFKNEL-SFIEKIEAVYITDPE 156
                                       *******************************************99****************.**************9 PP

                              CdhC 154 kv 155
                                       ++
  gi|298674388|ref|YP_003726138.1| 157 EI 158
                                       86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       894  (0.0498633); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3349.21
//
Query:       gi|298674389|ref|YP_003726139.1|  [L=171]
Description: CO dehydrogenase/acetyl-CoA synthase complex subunit epsilon [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-33  114.8   0.1    4.2e-33  114.5   0.1    1.0  1  CO_dh         CO dehydrogenase beta subunit/acetyl-CoA syntha
    1.3e-05   24.9   0.1    2.4e-05   24.1   0.1    1.4  1  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
  ------ inclusion threshold ------
       0.11   12.5   0.1       0.23   11.5   0.1    1.5  1  Adhesin_P1_N  Adhesin P1 N-terminal domain


Domain annotation for each model (and alignments):
>> CO_dh  CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.5   0.1     7e-37   4.2e-33      15     167 ..      15     167 ..       8     168 .. 0.87

  Alignments for each domain:
  == domain 1  score: 114.5 bits;  conditional E-value: 7e-37
                                       XXX--EEE--SHHHHHHHHHSSSEEEEE-S--.-HH.HHHHHHHHH.TSSSEEEEET.....HHHTT-G..GGSE.- CS
                             CO_dh  15 nskkatleealkvvakmikkakrPllivGpqvlkaeneeakekkil.ekklkvvata.....lkeaglkdyekkn.k 84 
                                       + k+a+ +++ kv+ak i+kakrPl+ivG ++lk+ +   +++ i+    ++v+at+     l ++g+   + k+  
  gi|298674389|ref|YP_003726139.1|  15 GTKNAKPVQP-KVAAKTISKAKRPLMIVGAELLKNKEVLDRAVTIAkTAGIPVAATGhsikeLVDKGV---NAKYiN 87 
                                       6789999***.******************999888766666665551578*******66444444444...566669 PP

                                       HHHHHHHHHSTT--TTTSS---SEEEEES--HHHHHHHHHHHHHH-TT-EEEE-SSS--TTSSEEE---GGGHHHHH CS
                             CO_dh  85 lveltkllkdpepkgfdgegeydlvlfiGviyYyasqalsslkkftdkittiaidkyyhpdAdvslanlskeeeeyl 161
                                       ++ l   l dp++ g dg+g yd+++++G   Yy +q ls lk+ft +++ti+idk y ++A +s++nl++e+  + 
  gi|298674389|ref|YP_003726139.1|  88 IHSLGLYLCDPNWGGLDGNGCYDMAIILGHKKYYINQVLSGLKNFT-NLKTISIDKHYLQNATMSFGNLNDEK--HI 161
                                       9*********************************************.*************************9..88 PP

                                       HHHHHH CS
                             CO_dh 162 emleel 167
                                       e l+el
  gi|298674389|ref|YP_003726139.1| 162 EALDEL 167
                                       988886 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.1     4e-09   2.4e-05       4      53 ..      27      78 ..      25      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 4e-09
                                      HHHHHHH-SSEEEEE-CHHCHT.TGHHHHHHHHHHHT-EEEEEGGG.TTSS- CS
                      TPP_enzyme_M  4 aaellkaakrpvilvGggvars.gaseelrelaeklgiPvvttlmg.kgvip 53
                                      aa+ +++akrp+++vG +   + ++ + ++  a++ giPv+ t +  k +++
  gi|298674389|ref|YP_003726139.1| 27 AAKTISKAKRPLMIVGAELLKNkEVLDRAVTIAKTAGIPVAATGHSiKELVD 78
                                      899***************998879****************999887565555 PP

>> Adhesin_P1_N  Adhesin P1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   3.8e-05      0.23       2      29 ..      49      81 ..      48      85 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.8e-05
                      Adhesin_P1_N  2 tskLDqAvkeAkeaGveV.....ekdatvDkGt 29
                                      ++ LD+Av+ Ak aG+ V     +  + vDkG+
  gi|298674389|ref|YP_003726139.1| 49 KEVLDRAVTIAKTAGIPVaatghSIKELVDKGV 81
                                      678*************99222222345677776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1064.60
//
Query:       gi|298674390|ref|YP_003726140.1|  [L=801]
Description: CO dehydrogenase/acetyl-CoA synthase complex subunit epsilon [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   8.4e-112  374.5   0.3    2.1e-92  310.5   0.0    2.0  2  Prismane      Prismane/CO dehydrogenase family
    2.2e-08   33.6  23.1    4.8e-06   26.2   3.5    3.5  3  Fer4          4Fe-4S binding domain
    3.8e-08   33.3  20.6      2e-06   27.8  11.3    3.1  2  Fer4_10       4Fe-4S dicluster domain
    6.9e-08   33.0  23.0    1.5e-06   28.6  13.1    3.1  2  Fer4_7        4Fe-4S dicluster domain
    1.9e-07   31.4   7.5     0.0015   18.9   0.1    3.1  2  Fer4_8        4Fe-4S dicluster domain
    2.1e-07   31.0   9.5    2.1e-07   31.0   9.5    2.8  2  Fer4_9        4Fe-4S dicluster domain
    2.5e-06   27.4   0.0    9.9e-06   25.5   0.0    2.1  1  CODH_A_N      Carbon monoxide dehydrogenase subunit alpha N-t
    9.1e-06   25.7  10.7    9.1e-06   25.7  10.7    2.7  2  Fer4_21       4Fe-4S dicluster domain
    9.7e-06   26.0  18.1     0.0022   18.5   0.6    3.6  3  Fer4_17       4Fe-4S dicluster domain
    5.6e-05   23.0  13.9      0.001   19.1   4.2    3.2  2  Fer4_6        4Fe-4S binding domain
     0.0001   22.2  24.1    0.00081   19.3   1.8    3.8  3  Fer4_2        4Fe-4S binding domain
    0.00026   21.3  12.8     0.0032   17.9   1.6    3.3  2  Fer4_4        4Fe-4S binding domain
    0.00079   19.6   9.0      0.037   14.2   0.7    2.8  2  Fer4_18       4Fe-4S dicluster domain
     0.0012   19.8  15.8       0.14   13.1   2.0    3.2  4  Fer4_16       4Fe-4S double cluster binding domain
     0.0017   18.1   7.3       0.03   14.1   7.2    2.5  2  Fer4_20       Dihydroprymidine dehydrogenase domain II, 4Fe-4
     0.0028   18.5   3.6     0.0028   18.5   3.6    3.6  2  Fer4_3        4Fe-4S binding domain
  ------ inclusion threshold ------
       0.02   14.9   0.1      0.049   13.7   0.1    1.6  1  BRCT_3        BRCA1 C Terminus (BRCT) domain
      0.027   15.3   3.3      0.027   15.3   3.3    2.9  2  Fer4_22       4Fe-4S dicluster domain
      0.066   12.4   0.1       0.14   11.4   0.1    1.5  1  Ribosomal_S2  Ribosomal protein S2
       0.14   12.7  10.4        1.6    9.3   2.5    2.7  2  Fer4_13       4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> Prismane  Prismane/CO dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   2.6   2.4e-19   2.1e-16       2      58 ..      70     126 ..      69     134 .. 0.96
   2 !  310.5   0.0   2.3e-95   2.1e-92     113     504 ..     144     681 ..     132     688 .. 0.88

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 2.4e-19
                                       EE-SSTCT-ECSCS.SS-TTS-BHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane   2 fCrqCengpCritknkrGvCGkdadtavardlliavlkgaaahaahareladtliak 58 
                                       +C++C++g+C++++nk+G+CG+d+++++ar++l++v++ga+ah+ h+r+l+++li+k
  gi|298674390|ref|YP_003726140.1|  70 QCCYCTFGKCDLSGNKEGACGIDMKAHQAREFLLRVITGASAHTGHGRHLLHHLIEK 126
                                       7****************************************************9987 PP

  == domain 2  score: 310.5 bits;  conditional E-value: 2.3e-95
                                       HHHHHHCCCHHHHHHHHHHHCHHTT-HHHHHHHHHHHCCCCTTSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane 113 dirslkellpkglkglyaehaivlgyadeevveflaktlaglesdpldllskalrlGlldlkgmelldeantslfGt 189
                                        ++++++++p++l +l    ++vl y++e+++++la++++g+e++++d++skal+ G+ld++gme++d+a++s++  
  gi|298674390|ref|YP_003726140.1| 144 VMQTVTGYKPETLGDL----EKVLDYVEEQITQLLATIHMGQEGEAIDFESKALHGGMLDHVGMEISDIAQISCLKM 216
                                       4789999999999999....********************************************************* PP

                                       -....--EEEEECGCG-.SSSEEEEEESS-HHHHHHHHHHHCTTCCCCCCCGCCCCCCHHHHHH.HHHCC......E CS
                                       x....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx......x RF
                          Prismane 190 P....eppltevnlgvldkdkvnIlvsGHdladleelleqtegkglnvythgemLpghcctalk.lkyrh......l 255
                                       P    e pl+e+++g++d +k+++l +GH++  ++++++++ ++ l + ++   ++g+ccta + ++y++       
  gi|298674390|ref|YP_003726140.1| 217 PksdaESPLAEIGMGCIDSSKPMLLTIGHNVSGVTNIMDYIDEQSLSDDIE---IAGLCCTAIDmTRYNTdegdepK 290
                                       ****9999*******************************************...**********999999******* PP

                                       EEEECSSGGGHHHHHCCHECEEEESSSS--TTHHHHHHCHCCEEEEECTTB-TTSEEE--CTTCH............ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............ RF
                          Prismane 256 vgnvGnawqqekaeftgavdaivvdtnCivpplasvaekyktrlittsevakpgakhieeeekad............ 320
                                       ++++G+++++ k++++g++d+ivvd++C+++++ ++a+k+ +++i+t++++++g+k+ + +++ d            
  gi|298674390|ref|YP_003726140.1| 291 AKVIGSLAKELKMIRSGVPDVIVVDEQCVRADILREAQKLSIPVISTNDKIMYGLKDRS-SDDVDdiledlksgiep 366
                                       **********************************************************9.23332234445556666 PP

                                       ........HHHHHHHHHHHCCHCCTTCGG.-.............................................. CS
                                       ........xxxxxxxxxxxxxxxxxxxxxxx.............................................. RF
                          Prismane 321 ........kdaseiiekAielakareekkve.............................................. 343
                                               k  + + + A+++a++reek ++                                              
  gi|298674390|ref|YP_003726140.1| 367 galildfdKLGELAPRLAMDMAPIREEKGIKslptseelqeltercvhckecelvcptnlsisdamsaaetgdfapf 443
                                       6666666699999999*********998888999*999999999999999988888888888777777777666666 PP

                                       .......................HHH...................................HHTTSS-EEEEE-B-- CS
                                       .......................xxx...................................xxxxxxxxxxxxxxxx RF
                          Prismane 344 .......................ida...................................iksGtIkgvvlvvGCd 362
                                                              + +                                   ++ Gt++g++++vGC+
  gi|298674390|ref|YP_003726140.1| 444 eelhdkcigcgrceqvcpkdipvL-NvieksaqrvireekgtlragrgqvsdpeireegvnLVLGTTPGIIALVGCS 519
                                       666666666666666666555551.05555666666667777777777777777777777799************** PP

                                       -TTCGCCHHHHHHHHCHHTTEEEEEECHHHHHC...CCTTTTEC...GHHHHSTHCEESEEEEESCCCHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane 363 nakkgrdyytelakelikrdvlvltaGCakyal...nklglgti...eaaelagegiPrvLdvGsCvdnyrivvial 433
                                       n+++g+++ + +a+e++kr+++v+++GC++++l    ++++ t+   ++ ++  ++   +L+vGsCv+n++i++ a+
  gi|298674390|ref|YP_003726140.1| 520 NYPEGTKDLYRIADEMLKRNYIVVVSGCSAMDLgmyRNEDGNTLyeeYPGKFIKGN---LLNVGSCVSNSHITGTAI 593
                                       ********************************999988888888888999999966...****************** PP

                                       HHHHHT.......TS.SGGGSSE...EEEECC-..-SHHHHHHHHHHHHTT-CEEECSS-TTTT-HHHHHHHHCH.. CS
                                       xxxxxx.......xx.xxxxxxx...xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                          Prismane 434 klaeal.......gv.dindLpl...aalalew..yeqKAvailltllalGinihlgptlpafgspnvlkvlved.. 495
                                       k+a+++       +  +i+d++l   +a+ ++w  y+qKA +i+++++++Gi++++gp++++++++ + k +++d  
  gi|298674390|ref|YP_003726140.1| 594 KVASIFaqrnvtgNFeEIADYILnrvGAVGVAWgaYSQKASSIATGCNRFGIPVIVGPHGSKYRRALIGKPYEKDkw 670
                                       ************7788*********99*********************************************99988 PP

                                       ..HHHHHCEEE CS
                                       ..xxxxxxxxx RF
                          Prismane 496 ..fedriggiv 504
                                         +++r g+++
  gi|298674390|ref|YP_003726140.1| 671 tvYDARNGEEL 681
                                       77777777766 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   2.5       5.3   4.8e+03       7      14 ..      67      74 ..      62      75 .. 0.83
   2 !   19.9   1.9     5e-07   0.00045       5      21 ..     409     425 ..     408     426 .. 0.94
   3 !   26.2   3.5   5.4e-09   4.8e-06       6      22 ..     448     464 ..     446     466 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 5.3
                                      TSSS-THH CS
                              Fer4  7 kCigCGaC 14
                                      +C  C +C
  gi|298674390|ref|YP_003726140.1| 67 MCDQCCYC 74
                                      69999999 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 5e-07
                                       TTTSSS-THHHHHSTTT CS
                              Fer4   5 eekCigCGaCvevCPvg 21 
                                       +e+C++C++C+ vCP++
  gi|298674390|ref|YP_003726140.1| 409 TERCVHCKECELVCPTN 425
                                       59*************98 PP

  == domain 3  score: 26.2 bits;  conditional E-value: 5.4e-09
                                       TTSSS-THHHHHSTTTE CS
                              Fer4   6 ekCigCGaCvevCPvgA 22 
                                       +kCigCG+C++vCP + 
  gi|298674390|ref|YP_003726140.1| 448 DKCIGCGRCEQVCPKDI 464
                                       9*************986 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8  11.3   2.2e-09     2e-06       6      56 .]     409     461 ..     405     461 .. 0.86
   2 !   19.8   1.8   7.2e-07   0.00065       7      29 ..     448     476 ..     444     494 .. 0.72

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 2.2e-09
                           Fer4_10   6 ddtCirCgkCvkaCPadl.tsvgakgeaseeeavrk.kvekCtgcgaCveaCP 56 
                                       +++C++C++C  +CP++l  s+  +++++++ a  +   +kC+gcg C ++CP
  gi|298674390|ref|YP_003726140.1| 409 TERCVHCKECELVCPTNLsISDAMSAAETGDFAPFEeLHDKCIGCGRCEQVCP 461
                                       589*************998777777777777777665999************9 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 7.2e-07
                           Fer4_10   7 dtCirCgkCvkaCPadl........tsvgak 29 
                                       d+Ci+Cg+C ++CP d+        +   ++
  gi|298674390|ref|YP_003726140.1| 448 DKCIGCGRCEQVCPKDIpvlnviekS--AQR 476
                                       89*************88877776442..222 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   2.2   2.1e-06    0.0019      20      51 ..     388     425 ..     380     426 .. 0.68
   2 !   28.6  13.1   1.7e-09   1.5e-06       1      52 []     411     464 ..     411     464 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.1e-06
                            Fer4_7  20 deeenekgt......ekveidpekClgCgaCvavCPtg 51 
                                        +  +ekg+      e+++   e+C++C++C+ vCPt+
  gi|298674390|ref|YP_003726140.1| 388 APIREEKGIkslptsEELQELTERCVHCKECELVCPTN 425
                                       55555555433333355577789*************97 PP

  == domain 2  score: 28.6 bits;  conditional E-value: 1.7e-09
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgt...ekveidpekClgCgaCvavCPtga 52 
                                       rC++C+ C+ +Cp++    d  +  ++t   +  e  ++kC+gCg+C++vCP+++
  gi|298674390|ref|YP_003726140.1| 411 RCVHCKECELVCPTNLSISDAMSA-AETgdfAPFEELHDKCIGCGRCEQVCPKDI 464
                                       8************88665555433.3331224457779**************985 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.4e-05     0.012      44      64 ..     398     425 ..     351     426 .. 0.78
   2 !   18.9   0.1   1.7e-06    0.0015       3      17 ..     448     469 ..     429     519 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-05
                            Fer4_8  44 e.......eealwsCttcgaCtevCpvg 64 
                                       +       +e  ++C++c++C+ vCp++
  gi|298674390|ref|YP_003726140.1| 398 SlptseelQELTERCVHCKECELVCPTN 425
                                       1334444578899*************97 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 1.7e-06
                            Fer4_8   3 ekCieCgaCqsaCp.......v 17 
                                       +kCi+Cg+C++ Cp       v
  gi|298674390|ref|YP_003726140.1| 448 DKCIGCGRCEQVCPkdipvlnV 469
                                       4666666666666555554441 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   1.4      0.73   6.5e+02       2      12 ..      68      79 ..      44     101 .. 0.74
   2 !   31.0   9.5   2.4e-10   2.1e-07       1      49 [.     411     463 ..     411     465 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.73
                            Fer4_9  2 CtgCgaCvea.C 12
                                      C +C +C+   C
  gi|298674390|ref|YP_003726140.1| 68 CDQCCYCTFGkC 79
                                      777777753325 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 2.4e-10
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase.....eaCigCgaCveaCpkg 49 
                                       +C+ C++C+ +Cp+++ + da       + a       ++CigCg+C+++Cpk+
  gi|298674390|ref|YP_003726140.1| 411 RCVHCKECELVCPTNLSISDAMSAAETGDFA-PfeelhDKCIGCGRCEQVCPKD 463
                                       5************999877665544444333.2356999*************98 PP

>> CODH_A_N  Carbon monoxide dehydrogenase subunit alpha N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   1.1e-08   9.9e-06       3      69 ..     119     185 ..     117     195 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.1e-08
                          CODH_A_N   3 alekaikkygkdkkvefPdTAYylPviyaltGekvktlgdleevLerarsllkeeetLedaldaGla 69 
                                       +l++ i+kyg+d+++       + Pv+  +tG k +tlgdle+vL+ +++++++  +  ++ + G+a
  gi|298674390|ref|YP_003726140.1| 119 LLHHLIEKYGRDHPIDVGPSNLKTPVMQTVTGYKPETLGDLEKVLDYVEEQITQLLATIHMGQEGEA 185
                                       57889************************************************99888777777776 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   2.7   0.00025      0.22      34      54 ..     405     425 ..     398     430 .. 0.80
   2 !   25.7  10.7     1e-08   9.1e-06       6      52 ..     410     461 ..     406     471 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00025
                           Fer4_21  34 lkvvedeCvGCnlCssvCPve 54 
                                       l+ ++++Cv C+ C  vCP++
  gi|298674390|ref|YP_003726140.1| 405 LQELTERCVHCKECELVCPTN 425
                                       5567899***********985 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 1e-08
                           Fer4_21   6 dkCigCgkCliaCedt..shqaieidakt...vlkvvedeCvGCnlCssvCP 52 
                                       ++C++C++C ++C+++    +a++ ++      ++ ++d+C+GC  C +vCP
  gi|298674390|ref|YP_003726140.1| 410 ERCVHCKECELVCPTNlsISDAMSAAETGdfaPFEELHDKCIGCGRCEQVCP 461
                                       79************752235666554443111446679************** PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   4.4       9.4   8.4e+03       2      12 ..      68      79 ..      67     104 .. 0.78
   2 !   18.1   0.5   3.3e-06     0.003      37      60 ..     403     426 ..     378     427 .. 0.76
   3 !   18.5   0.6   2.4e-06    0.0022      41      60 ..     445     464 ..     429     465 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 9.4
                           Fer4_17  2 CiqCgyClp.eC 12
                                      C qC yC+  +C
  gi|298674390|ref|YP_003726140.1| 68 CDQCCYCTFgKC 79
                                      999999985345 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 3.3e-06
                           Fer4_17  37 aekeekaslCieCgeCerkCPqgl 60 
                                       +e +e  ++C++C+eCe +CP +l
  gi|298674390|ref|YP_003726140.1| 403 EELQELTERCVHCKECELVCPTNL 426
                                       3445789**************998 PP

  == domain 3  score: 18.5 bits;  conditional E-value: 2.4e-06
                           Fer4_17  41 ekaslCieCgeCerkCPqgl 60 
                                       e  ++Ci+Cg+Ce++CP+++
  gi|298674390|ref|YP_003726140.1| 445 ELHDKCIGCGRCEQVCPKDI 464
                                       56689*************98 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   2.1     2e-06    0.0018       7      22 ..     410     425 ..     409     428 .. 0.92
   2 !   19.1   4.2   1.1e-06     0.001       7      22 ..     448     463 ..     447     466 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2e-06
                            Fer4_6   7 dkCigCgdCvrvCPeg 22 
                                       ++C++C +C+ vCP++
  gi|298674390|ref|YP_003726140.1| 410 ERCVHCKECELVCPTN 425
                                       79************97 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 1.1e-06
                            Fer4_6   7 dkCigCgdCvrvCPeg 22 
                                       dkCigCg+C+ vCP +
  gi|298674390|ref|YP_003726140.1| 448 DKCIGCGRCEQVCPKD 463
                                       8*************75 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   5.3       5.6     5e+03       7      18 ..      65      76 ..      62      79 .. 0.79
   2 !   15.2   2.0   1.9e-05     0.017       7      22 .]     409     424 ..     404     424 .. 0.92
   3 !   19.3   1.8   9.1e-07   0.00081       8      21 ..     448     461 ..     441     462 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 5.6
                            Fer4_2  7 tdrCigCgaCvs 18
                                      t +C +C  C+ 
  gi|298674390|ref|YP_003726140.1| 65 TPMCDQCCYCTF 76
                                      679****99985 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.9e-05
                            Fer4_2   7 tdrCigCgaCvsaCPa 22 
                                       t+rC++C+ C  +CP+
  gi|298674390|ref|YP_003726140.1| 409 TERCVHCKECELVCPT 424
                                       89*************7 PP

  == domain 3  score: 19.3 bits;  conditional E-value: 9.1e-07
                            Fer4_2   8 drCigCgaCvsaCP 21 
                                       d+CigCg C ++CP
  gi|298674390|ref|YP_003726140.1| 448 DKCIGCGRCEQVCP 461
                                       8************9 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   3.8   4.6e-06    0.0041       2      17 .]     410     425 ..     409     425 .. 0.93
   2 !   17.9   1.6   3.5e-06    0.0032       2      16 ..     448     462 ..     447     473 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.6e-06
                            Fer4_4   2 erCigCgsCvaaCPqg 17 
                                       erC++C+ C+ +CP++
  gi|298674390|ref|YP_003726140.1| 410 ERCVHCKECELVCPTN 425
                                       8*************86 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 3.5e-06
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       ++CigCg+C+ +CP 
  gi|298674390|ref|YP_003726140.1| 448 DKCIGCGRCEQVCPK 462
                                       89************5 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.7   4.1e-05     0.037      50      81 ..     402     432 ..     387     438 .. 0.77
   2 !    8.6   2.0    0.0023       2.1      57      77 ..     446     466 ..     433     473 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.1e-05
                           Fer4_18  50 keerkekgagdcidcescvkvcPtgidirkGl 81 
                                       +ee  ++ +  c++c+ c  vcPt++ i + +
  gi|298674390|ref|YP_003726140.1| 402 SEE-LQELTERCVHCKECELVCPTNLSISDAM 432
                                       333.4677889****************99876 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0023
                           Fer4_18  57 gagdcidcescvkvcPtgidi 77 
                                        + +ci c+ c +vcP +i +
  gi|298674390|ref|YP_003726140.1| 446 LHDKCIGCGRCEQVCPKDIPV 466
                                       5679************99976 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       5.9   5.3e+03      56      60 ..      67      71 ..      25      76 .. 0.58
   2 !   13.1   2.0   0.00016      0.14      35      67 .]     393     425 ..     378     425 .. 0.76
   3 !   13.0  13.3   0.00017      0.16       1      66 [.     411     462 ..     411     463 .. 0.74
   4 !   12.6   3.0   0.00023       0.2       1      16 [.     449     464 ..     449     500 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 5.9
                           Fer4_16 56 gCdiC 60
                                       Cd C
  gi|298674390|ref|YP_003726140.1| 67 MCDQC 71
                                      34444 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00016
                           Fer4_16  35 taekkdlaedeekckkqeaitgCdiCqdvCPan 67 
                                       +++ k+l+++ee ++  e++  C+ C+ vCP n
  gi|298674390|ref|YP_003726140.1| 393 EKGIKSLPTSEELQELTERCVHCKECELVCPTN 425
                                       566677777777777788999999999999987 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 0.00017
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCPa 66 
                                       rC+ C++C  vCPtn   ++          +s+  ae+ d+a+ ee ++   +++gC++C++vCP 
  gi|298674390|ref|YP_003726140.1| 411 RCVHCKECELVCPTNLSISD---------AMSA--AETGDFAPFEELHD---KCIGCGRCEQVCPK 462
                                       6*************987777.........2333..34455555554444...699**********5 PP

  == domain 4  score: 12.6 bits;  conditional E-value: 0.00023
                           Fer4_16   1 rCgtCgkCaevCPtna 16 
                                       +C++Cg+C +vCP + 
  gi|298674390|ref|YP_003726140.1| 449 KCIGCGRCEQVCPKDI 464
                                       5999999999999865 PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   7.2   3.3e-05      0.03      13      78 ..     401     463 ..     391     464 .. 0.84
   2 ?    5.0   1.2     0.023        20      22      54 ..     448     478 ..     443     487 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.3e-05
                                       -HHHHHHHHTT----TT-HHHHCSTT---HHHHHHHHHTT-HHHHHHHHHHH-S-HHHHHHHS-GG CS
                           Fer4_20  13 teeealeeAsRClqCkkapcvkgCPveidipefikkiaegnleeaakiiketnslpavcgrvCpqe 78 
                                       t+ee +e  +RC++C  ++c+  CP++++i + +++ ++g+++  ++ ++++ +    c +vCp++
  gi|298674390|ref|YP_003726140.1| 401 TSEELQELTERCVHC--KECELVCPTNLSISDAMSAAETGDFAP-FEELHDKCIGCGRCEQVCPKD 463
                                       667788889******..789999******************975.7777788888889*****986 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.023
                                       TT----TT-HHHHCSTT---HHHHHHHHHTT-H CS
                           Fer4_20  22 sRClqCkkapcvkgCPveidipefikkiaegnl 54 
                                       ++C+ C    c++ CP +i + + i+k a++ +
  gi|298674390|ref|YP_003726140.1| 448 DKCIGC--GRCEQVCPKDIPVLNVIEKSAQRVI 478
                                       58****..78***********999999877655 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   6.2    0.0018       1.6       1      14 [.     412     425 ..     412     425 .. 0.95
   2 !   18.5   3.6   3.1e-06    0.0028       1      14 [.     450     463 ..     450     464 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0018
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       C++C  C+ vCP++
  gi|298674390|ref|YP_003726140.1| 412 CVHCKECELVCPTN 425
                                       ************86 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 3.1e-06
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       C+gCg+C++vCP++
  gi|298674390|ref|YP_003726140.1| 450 CIGCGRCEQVCPKD 463
                                       ************97 PP

>> BRCT_3  BRCA1 C Terminus (BRCT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   5.5e-05     0.049      30      75 ..     291     337 ..     288     339 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.5e-05
                            BRCT_3  30 aavvkkekseaeeislgkldvvvtdsscp.eevlkkaeqlkipvvSt 75 
                                       a+v+ +  +e ++i  g+ dv+v d++c  +++l +a++l+ipv+St
  gi|298674390|ref|YP_003726140.1| 291 AKVIGSLAKELKMIRSGVPDVIVVDEQCVrADILREAQKLSIPVIST 337
                                       5666777777888999***********75278**************8 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   3.1     0.007       6.3       1      16 [.     411     426 ..     411     439 .. 0.84
   2 ?   15.3   3.3     3e-05     0.027      79      96 .]     447     464 ..     429     464 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.007
                           Fer4_22   1 rClsCgaCtlvCptCs 16 
                                       rC++C +C lvCpt  
  gi|298674390|ref|YP_003726140.1| 411 RCVHCKECELVCPTNL 426
                                       7************965 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 3e-05
                           Fer4_22  79 esgCvGCgRCieacpvki 96 
                                       + +C+GCgRC+++cp++i
  gi|298674390|ref|YP_003726140.1| 447 HDKCIGCGRCEQVCPKDI 464
                                       568************987 PP

>> Ribosomal_S2  Ribosomal protein S2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00016      0.14     136     179 ..     298     339 ..     273     342 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                      Ribosomal_S2 136 eknlggikkmkklPdlvvvldpkkekiavkEakklgipviaivD 179
                                        k+l+ i+  + +Pd++vv ++     +++Ea+kl ipvi+  D
  gi|298674390|ref|YP_003726140.1| 298 AKELKMIR--SGVPDVIVVDEQCVRADILREAQKLSIPVISTND 339
                                       33333333..589***************************9877 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   1.1    0.0093       8.3       4      28 ..     410     434 ..     409     439 .. 0.85
   2 ?    9.3   2.5    0.0018       1.6       4      18 ..     448     462 ..     447     463 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0093
                           Fer4_13   4 dtCiacgaCvelaPdvFeeddegga 28 
                                       ++C+ c+ C  ++P    + d  +a
  gi|298674390|ref|YP_003726140.1| 410 ERCVHCKECELVCPTNLSISDAMSA 434
                                       79************99998887665 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0018
                           Fer4_13   4 dtCiacgaCvelaPd 18 
                                       d+Ci+cg C +++P+
  gi|298674390|ref|YP_003726140.1| 448 DKCIGCGRCEQVCPK 462
                                       89************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (801 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.81u 0.33s 00:00:01.14 Elapsed: 00:00:00.51
# Mc/sec: 4692.50
//
Query:       gi|298674391|ref|YP_003726141.1|  [L=195]
Description: resolvase domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-19   70.4   0.1    1.9e-19   70.2   0.1    1.1  1  Resolvase  Resolvase, N terminal domain
     0.0032   17.6   0.0      0.006   16.8   0.0    1.5  1  HTH_17     Helix-turn-helix domain
  ------ inclusion threshold ------
      0.067   12.0   0.0      0.098   11.5   0.0    1.2  1  Trp_syntA  Tryptophan synthase alpha chain
      0.082   13.0   0.0       0.18   11.9   0.0    1.6  1  HTH_7      Helix-turn-helix domain of resolvase


Domain annotation for each model (and alignments):
>> Resolvase  Resolvase, N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.2   0.1   4.3e-23   1.9e-19       2     135 ..      56     187 ..      55     195 .] 0.83

  Alignments for each domain:
  == domain 1  score: 70.2 bits;  conditional E-value: 4.3e-23
                                       EEEEEES-----THHHHHHHHHHHH-S--..SE...EEEE.S-TT-TT.-HHHHHHHHHHTT-EE.EEEESSCCCC- CS
                         Resolvase   2 igYaRvSteeqddslerQkealrayakenglkivkefeDkgvSGakle.RpglkrllaalregkgdvlvvekldRLa 77 
                                       ++YaRvSt++q+++le+Q+++l+ +a + g+++  +++D  +SG + e R+++ ++l+++++ k++ +++   dRL+
  gi|298674391|ref|YP_003726141.1|  56 VIYARVSTSKQKKDLENQVQMLKTWAFNSGYQVNHVYSDV-ASGISFEkRKDFFKMLDEITNYKVENVIISYKDRLS 131
                                       89*******************************9******.*****555**************************** PP

                                       S...S-HHHHHHHHHTT-EEEESS..SS----H.HHHHHHHHHHHHHHHHHHHHCT-TT CS
                         Resolvase  78 Rsvrdlltlleelrekgvslvsldegidtstpm.grlllqilaalaeferelirertke 135
                                       R  ++l+  ++ +++ g +++++++ i  ++    +++ +i + l  +  +l ++  ++
  gi|298674391|ref|YP_003726141.1| 132 RVGFELF--YHLFSKYGTNIIVVSD-IGSKKLDdEEVFSEIKSLLHCYSMKLYSKTRAK 187
                                       *999998..789************9.443333325677777776666655555555555 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.3e-06     0.006       5      50 ..       4      50 ..       1      51 [. 0.87

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.3e-06
                            HTH_17  5 eEaAelLgvsrstvyrlirrgelpaak.iGrrwriprsdleewlekr 50
                                       ++ + L++ r t+yr++ +g ++ +   ++++ ++ +++ ++l+k+
  gi|298674391|ref|YP_003726141.1|  4 GDVLKTLRITRPTLYRYVENGYIKRTSlPNGQYEYDDESVYAFLNKD 50
                                      577788*****************999777788*****9999999985 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.2e-05     0.098      72     128 ..     105     159 ..      94     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.2e-05
                                       HHHHHHHHHHHHHCSSS-EEEEE-CHHHCCC-HHHHCHHHHHCTEEEEEETTSBCCC CS
                         Trp_syntA  72 ekvlelveevrkkevevPivlltylnlvlsygeerflaelkeagvdglivpDlPlee 128
                                       ++++++++e++  + +v  v+++y + + ++g e f++ + + g + ++v D+  ++
  gi|298674391|ref|YP_003726141.1| 105 KDFFKMLDEIT--NYKVENVIISYKDRLSRVGFELFYHLFSKYGTNIIVVSDIGSKK 159
                                       67999*****9..667777999******************************97654 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.9e-05      0.18      22      42 ..       1      21 [.       1      24 [. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.9e-05
                                      --STTTSSSS---SSSS--SS CS
                             HTH_7 22 isiskIAkevnisRsTvYRyl 42
                                      +++ ++ k + i+R T+YRy 
  gi|298674391|ref|YP_003726141.1|  1 MKAGDVLKTLRITRPTLYRYV 21
                                      5678999*************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1095  (0.0610742); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1240.32
//
Query:       gi|298674392|ref|YP_003726142.1|  [L=400]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-24   87.1   0.1    2.3e-24   85.9   0.1    1.6  1  OrfB_IS605      Probable transposase
      2e-11   43.7   0.0    4.9e-11   42.4   0.0    1.8  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0002   20.8   0.7    0.00032   20.1   0.7    1.3  1  Glyco_hydro_97  Glycoside hydrolase 97
  ------ inclusion threshold ------
      0.023   14.7   0.1      0.059   13.4   0.1    1.6  1  Dynamin_N       Dynamin family
       0.13   12.6   1.8        0.6   10.6   0.3    2.7  3  ACP_PD          Acyl carrier protein phosphodiesterase
        9.7    6.4   6.4        3.3    7.9   0.1    3.2  2  DUF3885         Domain of unknown function (DUF3885)


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.9   0.1   7.6e-28   2.3e-24       2     117 ..     167     281 ..     166     284 .. 0.95

  Alignments for each domain:
  == domain 1  score: 85.9 bits;  conditional E-value: 7.6e-28
                        OrfB_IS605   2 ipvevevelpkpkgnkaagiDlGinnLatvvtedgtw.flykgrrlksdykylakeiaelqsklkksknykkasrkl 77 
                                       i+++++ +++k ++n+ a+iDlGinn++t+v++ g+  +++kg  +ks ++y++k++ +  s+++k +     +++l
  gi|298674392|ref|YP_003726142.1| 167 IVYKQKIIHNKLDENNIASIDLGINNIITMVNNIGEKpIVIKGGGVKSINQYYNKKKSQWKSFYDKRG--FDETKRL 241
                                       67888888999*************************99*****************************9..7888899 PP

                        OrfB_IS605  78 arlhrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                        ++++kr++++++++hk+++++i+++ e++++tL+vg+  
  gi|298674392|ref|YP_003726142.1| 242 EKIYQKRNNKINDFFHKVSKKIINYCIENNIGTLIVGYNE 281
                                       9************************************986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.0   1.6e-14   4.9e-11       1      69 []     302     376 ..     302     376 .. 0.91

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 1.6e-14
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke......alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f klk+q+eyk +++Gikv   +++yTSk +    + +++      ++  r +  +n g ++++Dvn+a+Nilk+
  gi|298674392|ref|YP_003726142.1| 302 FFKLKKQIEYKSEDAGIKVLFQEESYTSKCSFLDDEPVEKrtsylgKRIMRGLFKSNTGKVINADVNGAYNILKK 376
                                       789*************************98877777777789999988888888999****************96 PP

>> Glyco_hydro_97  Glycoside hydrolase 97
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.7   1.1e-07   0.00032      28     110 ..     251     332 ..     212     358 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.1e-07
                    Glyco_hydro_97  28 fkhgantetvkryiDfAaengleyvlvegwdegWee..kkkkekefdftkpypdfdleelvaYakekgvgvelwlhs 102
                                       + + +  +  k+ i+++ en++ +++v g++egW++  +  k+ +++ + ++p f+l++ ++Y  e   g++++ ++
  gi|298674392|ref|YP_003726142.1| 251 KINDFFHKVSKKIINYCIENNIGTLIV-GYNEGWKQecNIGKK-NNQNFVQIPFFKLKKQIEYKSEDA-GIKVLFQE 324
                                       44555567789****************.*******98655544.55555689***********66554.88888888 PP

                    Glyco_hydro_97 103 etsgnvan 110
                                       e ++++ +
  gi|298674392|ref|YP_003726142.1| 325 ESYTSKCS 332
                                       87665544 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1     2e-05     0.059      35      96 ..     204     269 ..     188     276 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2e-05
                                       -EEEEECCT---C..CS...SSEEEE..T-EB--CHHHHHHHHHHHHHHHTSSSS--SS-EEEEEE CS
                         Dynamin_N  35 plelqlgeeeeas..eravkeelkek..ekkledfsevreeieketekiagankgiskkvillkil 96 
                                       p++++ g  ++++   ++ k ++k++  ++ +++ +++++ ++k+++ki++   ++skk+i+++i 
  gi|298674392|ref|YP_003726142.1| 204 PIVIKGGGVKSINqyYNKKKSQWKSFydKRGFDETKRLEKIYQKRNNKINDFFHKVSKKIINYCIE 269
                                       5556555444444334567888999999***********************************987 PP

>> ACP_PD  Acyl carrier protein phosphodiesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.3    0.0002       0.6      34      92 ..      22      83 ..      11      90 .. 0.71
   2 ?   -2.2   0.0       1.8   5.5e+03      80     101 ..     210     231 ..     191     234 .. 0.82
   3 ?   -3.0   0.0       3.3   9.8e+03      85     102 ..     241     258 ..     235     265 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0002
                            ACP_PD 34 alPerlqrllprmieedwLesY..aelegieralqrma.rrlkrasklaeaieeleenyael 92
                                      +++++l + ++++i+++wL+ Y   + e +++ l++ + + +  ++  +++++ +++n + +
  gi|298674392|ref|YP_003726142.1| 22 HISKNLYNQANYIIRQNWLNGYgyTKYEKVNEELKGTEnYSILPSQTAQQTLKMVDRNWKSF 83
                                      6678888999*********9762267889999999999444444444666666665555544 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.8
                            ACP_PD  80 eaieeleenyaeleadFleffp 101
                                       + ++ +++ y++ ++++++f+ 
  gi|298674392|ref|YP_003726142.1| 210 GGVKSINQYYNKKKSQWKSFYD 231
                                       5678889999999999999996 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 3.3
                            ACP_PD  85 leenyaeleadFleffpe 102
                                       le+ y++ +++ ++ff +
  gi|298674392|ref|YP_003726142.1| 241 LEKIYQKRNNKINDFFHK 258
                                       444455555555555544 PP

>> DUF3885  Domain of unknown function (DUF3885)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   2.4       1.2   3.5e+03       4      30 ..      13      40 ..      10      44 .. 0.62
   2 ?    7.9   0.1    0.0011       3.3       4      33 ..     230     255 ..     229     259 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.2
                           DUF3885  4 YDDRGcdvisnnketlke.lYekyndWI 30
                                      YDDR   +   +k+ +++ +Y  +++W+
  gi|298674392|ref|YP_003726142.1| 13 YDDRLSRLCHISKNLYNQaNYIIRQNWL 40
                                      8888666666666655432566666666 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0011
                           DUF3885   4 YDDRGcdvisnnketlkelYekyndWIlDY 33 
                                       YD RG d    ++++l+++Y+k+n+ I D+
  gi|298674392|ref|YP_003726142.1| 230 YDKRGFD----ETKRLEKIYQKRNNKINDF 255
                                       8888865....99************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1161  (0.0647554); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 2429.18
//
Query:       gi|298674393|ref|YP_003726143.1|  [L=299]
Description: rhomboid family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.2e-33  113.5  17.9    8.2e-33  113.5  17.9    1.8  2  Rhomboid         Rhomboid family
    1.6e-11   44.1   7.6    2.4e-11   43.6   7.6    1.2  1  zf-AN1           AN1-like Zinc finger
    1.2e-06   29.0   2.1    1.2e-06   29.0   2.1    2.7  3  DUF1751          Eukaryotic integral membrane protein (DUF175
     0.0072   16.1   0.1      0.022   14.5   0.1    1.8  1  Flavi_M          Flavivirus envelope glycoprotein M
  ------ inclusion threshold ------
      0.014   15.5   0.3      0.014   15.5   0.3    4.3  6  ATPase_gene1     Putative F0F1-ATPase subunit Ca2+/Mg2+ trans
      0.026   14.7   1.7      0.039   14.1   1.7    1.3  1  FYVE             FYVE zinc finger
      0.038   14.4   6.0      0.075   13.4   6.0    1.5  1  Transp_Tc5_C     Tc5 transposase C-terminal domain
        0.1   13.1   0.6       0.21   12.1   0.6    1.5  1  Antimicrobial_2  Frog antimicrobial peptide
       0.13   11.0   0.0       0.19   10.5   0.0    1.1  1  Pneumo_ncap      Pneumovirus nucleocapsid protein
       0.15   12.2   5.5       0.26   11.5   5.5    1.4  1  C5HCH            NSD Cys-His rich domain
          3    6.7  27.5        1.1    8.1  17.1    2.7  2  MFS_1            Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> Rhomboid  Rhomboid family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.3      0.72   1.2e+03     103     130 ..     100     127 ..      79     131 .. 0.49
   2 !  113.5  17.9     5e-36   8.2e-33       6     147 ..     141     282 ..     138     285 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.72
                                       C...CCCCCCCCCCHHHCTSSSTTTHHH CS
                          Rhomboid 103 allllllfillnlvlgllpraggvsnlA 130
                                       + + ++ ++++ ++  +++   g++++A
  gi|298674393|ref|YP_003726143.1| 100 MAIIIICVASYIIGNLIITNVIGINYFA 127
                                       2344444445555555555546666666 PP

  == domain 2  score: 113.5 bits;  conditional E-value: 5e-36
                                       -TTHHHHGGG--SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-S...-EESSHHHHHHH CS
                          Rhomboid   6 elwrlltsmflHagwlHllfNmlallvfGsplerrlGslrflllyllsglagsllsllfsaesesplvGaSGaifgl 82 
                                       + w+++t++f+H +++Hl++Nm++l++fG+++e+r+G+ rfl++++l+g+++s++++l++     plvGaSGa+ g+
  gi|298674393|ref|YP_003726143.1| 141 KPWTIVTHIFVHSNFAHLFLNMFVLFFFGNEFEKRFGKQRFLTVFFLAGIIASIGFALITTTP-FPLVGASGAVIGI 216
                                       57********************************************************99995.6************ PP

                                       HHHHHHHHHCCCCGS----HC....CCCCCCCCCCHHHCTSSSTTTHHHHHHHHHHHHHHHHHHCC CS
                          Rhomboid  83 lgallvlvprnrkllrkliia.llllllfillnlvlgllpraggvsnlAHlgGllaGlllgllllr 147
                                       +++l++lvp  ++ ++++++    ++ll+i +++++ +++ ++ ++++AHl+G+++G+l+g+++ +
  gi|298674393|ref|YP_003726143.1| 217 FASLAILVPDLPIFVFFIPMRiKHAILLLIGIEFLFFIINTQDMIAHSAHLMGMAVGILMGFWIKK 282
                                       ***************99999977889999999******9999********************9977 PP

>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   7.6   1.5e-14   2.4e-11       1      39 [.       5      41 ..       5      42 .. 0.93

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 1.5e-14
                            zf-AN1  1 CsfksCkkkdflpfkCryCgkvFClkHrlpedHdCkkla 39
                                      C +  C+k+d++ f+Cr+Cgk+FC +Hrlpe H+C++l+
  gi|298674393|ref|YP_003726143.1|  5 CWI--CGKQDSTLFRCRFCGKTFCVEHRLPERHACEGLE 41
                                      665..******************************9875 PP

>> DUF1751  Eukaryotic integral membrane protein (DUF1751)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.2       3.6   5.9e+03      67      67 ..     111     111 ..      88     129 .. 0.53
   2 !   29.0   2.1   7.3e-10   1.2e-06       3      68 ..     137     202 ..     136     224 .. 0.89
   3 ?    3.9   0.9     0.049        80      50      95 ..     233     280 ..     226     283 .. 0.64

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.6
                           DUF1751  67 l 67 
                                       +
  gi|298674393|ref|YP_003726143.1| 111 I 111
                                       1 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 7.3e-10
                           DUF1751   3 allpypwtlltasfveqnvwkvlvslltlllggkylErlWgskEllkFilvvnvitnllvvlltll 68 
                                       ++l+ pwt++t+ fv +n+ ++ ++++ l+++g+  E+  g++ +l  +++ ++i+++  +l+t+ 
  gi|298674393|ref|YP_003726143.1| 137 QILVKPWTIVTHIFVHSNFAHLFLNMFVLFFFGNEFEKRFGKQRFLTVFFLAGIIASIGFALITTT 202
                                       67889*****************************************99999**9999988888765 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.049
                           DUF1751  50 Filvvnvitnllvvlltlllylvtkseelll.vpisGl.agilagflv 95 
                                       Fi +    + ll + + +l++++ +++ +   +++ G+ +gil+gf +
  gi|298674393|ref|YP_003726143.1| 233 FIPMRIKHAILLLIGIEFLFFIINTQDMIAHsAHLMGMaVGILMGFWI 280
                                       444444555566667777777777777766677787762477787766 PP

>> Flavi_M  Flavivirus envelope glycoprotein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   1.3e-05     0.022      24      61 ..      83     121 ..      72     133 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.3e-05
                           Flavi_M  24 aekqlqkverWalrnPffavialtla.ylvGssitqkvv 61 
                                       a   l k+ rWa   P +a+i + +a y++G  i   v+
  gi|298674393|ref|YP_003726143.1|  83 AFSFLNKIKRWATTSPTMAIIIICVAsYIIGNLIITNVI 121
                                       666799****************99985777776665554 PP

>> ATPase_gene1  Putative F0F1-ATPase subunit Ca2+/Mg2+ transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       1.6   2.6e+03      25      41 ..      90     106 ..      88     109 .. 0.75
   2 ?   -1.5   0.4       1.8     3e+03      11      24 ..     102     115 ..      96     133 .. 0.58
   3 ?   15.5   0.3   8.9e-06     0.014      10      48 ..     157     194 ..     156     200 .. 0.90
   4 ?   -1.3   0.2       1.5   2.5e+03      38      47 ..     210     219 ..     195     224 .. 0.66
   5 ?   -2.6   0.6       3.9   6.3e+03       4      15 ..     243     254 ..     241     255 .. 0.61
   6 ?    4.4   0.1     0.027        43      14      27 ..     269     282 ..     265     290 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.6
                      ATPase_gene1  25 LDkkfgtspwfliigll 41 
                                       + ++  tsp + ii + 
  gi|298674393|ref|YP_003726143.1|  90 IKRWATTSPTMAIIIIC 106
                                       56788889988888775 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.8
                      ATPase_gene1  11 lvapillggllGyw 24 
                                       ++++ ++++ +G++
  gi|298674393|ref|YP_003726143.1| 102 IIIICVASYIIGNL 115
                                       45555555666655 PP

  == domain 3  score: 15.5 bits;  conditional E-value: 8.9e-06
                      ATPase_gene1  10 elvapillggllGywLDkkfgtspwfliiglllGlaaGf 48 
                                       +l + +++ ++ G+ ++k+fg +  fl++++l+G++a++
  gi|298674393|ref|YP_003726143.1| 157 HLFLNMFVLFFFGNEFEKRFG-KQRFLTVFFLAGIIASI 194
                                       567789***************.679***********986 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 1.5
                      ATPase_gene1  38 iglllGlaaG 47 
                                        g ++G++a+
  gi|298674393|ref|YP_003726143.1| 210 SGAVIGIFAS 219
                                       4556666665 PP

  == domain 5  score: -2.6 bits;  conditional E-value: 3.9
                      ATPase_gene1   4 asqiGielvapi 15 
                                       ++ iGie++ +i
  gi|298674393|ref|YP_003726143.1| 243 LLLIGIEFLFFI 254
                                       455777777665 PP

  == domain 6  score: 4.4 bits;  conditional E-value: 0.027
                      ATPase_gene1  14 pillggllGywLDk 27 
                                       ++++g+l+G+w+ k
  gi|298674393|ref|YP_003726143.1| 269 GMAVGILMGFWIKK 282
                                       67788888888776 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.7   2.4e-05     0.039       9      40 ..       2      38 ..       1      88 [. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.4e-05
                                      -SB-TTT--B--SSS--EE-TTT--EE-........STTS CS
                              FYVE  9 vkkCeiCakkFsllrrrhhCrlCGkvvC........ekCs 40
                                      +++C iC k+ s+l r   Cr CGk +C        ++C 
  gi|298674393|ref|YP_003726143.1|  2 SNNCWICGKQDSTLFR---CRFCGKTFCvehrlperHACE 38
                                      5789999999977554...*********666666665554 PP

>> Transp_Tc5_C  Tc5 transposase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   6.0   4.6e-05     0.075      27      63 .]       2      37 ..       1      37 [. 0.92

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.6e-05
                      Transp_Tc5_C 27 sedCkiegCselafikCarCkellCFdHfvvsekhlC 63
                                      s++C i g +++++ +C +C +++C +H +  e h C
  gi|298674393|ref|YP_003726143.1|  2 SNNCWICGKQDSTLFRCRFCGKTFCVEHRL-PERHAC 37
                                      689*************************98.588888 PP

>> Antimicrobial_2  Frog antimicrobial peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.6   0.00013      0.21       5      26 ..      70      91 ..      67      91 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                   Antimicrobial_2  5 tlKgvAKgvAKglAksgLdtls 26
                                       +K  AK ++KglA s L++++
  gi|298674393|ref|YP_003726143.1| 70 MFKETAKQASKGLAFSFLNKIK 91
                                      79*****************997 PP

>> Pneumo_ncap  Pneumovirus nucleocapsid protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00012      0.19     123     180 ..      66     123 ..      49     127 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00012
                       Pneumo_ncap 123 ivveiekearksykkllkessGevaqeqrhdapdtgiillcvaalvitklaatievGl 180
                                       i +++ ke+ k   k l  s  +  +     +p  +ii++cva+ +i  l  t+ +G+
  gi|298674393|ref|YP_003726143.1|  66 IFKNMFKETAKQASKGLAFSFLNKIKRWATTSPTMAIIIICVASYIIGNLIITNVIGI 123
                                       4556667777777777777777778889999*******************99988886 PP

>> C5HCH  NSD Cys-His rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   5.5   0.00016      0.26       3      27 ..       4      30 ..       3      42 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00016
                             C5HCH  3 qCsvCgkaats..fCefCPssFCkeHe 27
                                      +C +Cgk+ +   +C fC ++FC eH+
  gi|298674393|ref|YP_003726143.1|  4 NCWICGKQDSTlfRCRFCGKTFCVEHR 30
                                      6999*987554238************6 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   3.3     0.025        40     267     312 ..      86     131 ..      78     150 .. 0.88
   2 ?    8.1  17.1   0.00069       1.1     201     345 ..     136     279 ..     132     280 .. 0.57

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.025
                             MFS_1 267 lsdrlgrrrrlllallllllaalglallavtssavllllvlvliGf 312
                                       ++++++r+ ++  ++++++++++++++ +++ ++v+++  ++l+G+
  gi|298674393|ref|YP_003726143.1|  86 FLNKIKRWATTSPTMAIIIICVASYIIGNLIITNVIGINYFALLGL 131
                                       5689999**********************************99998 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00069
                             MFS_1 201 kallkdpvlwillialllf.ffgfsglltllply....lqevlglsglllaglllallalvgailallagrlsdrlg 272
                                       +++l +p  w +++++++   f++ +l +++ ++    + +++g    +l++  + l+++++   ++ ++ + +   
  gi|298674393|ref|YP_003726143.1| 136 SQILVKP--WTIVTHIFVHsNFAHLFLNMFVLFFfgneFEKRFGKQ-RFLTV--FFLAGIIA---SIGFALITTT-- 202
                                       5666666..6344444443222222233333333111114444444.34444..56666665...4334444444.. PP

                             MFS_1 273 rrrrlllallllllaalglallavtssavllll........vlvliGfglgfvfpsllalasdlappeeagtasglf 341
                                         ++l+ a ++++ ++++la+l +   ++++ +        +l+liG+ + f+ +  + +++++a  + +g+a+g+ 
  gi|298674393|ref|YP_003726143.1| 203 -PFPLVGASGAVIGIFASLAILVPD-LPIFVFFipmrikhaILLLIGIEFLFFIINTQDMIAHSA--HLMGMAVGIL 275
                                       .356777777777777777777777.4444444688888888888***66667788888888999..9*******99 PP

                             MFS_1 342 ntag 345
                                       + ++
  gi|298674393|ref|YP_003726143.1| 276 MGFW 279
                                       8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1035  (0.0577277); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2178.27
//
Query:       gi|298674394|ref|YP_003726144.1|  [L=135]
Description: hypothetical protein Metev_0430 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.033   14.1   0.0      0.048   13.6   0.0    1.3  1  Ferritin  Ferritin-like domain


Domain annotation for each model (and alignments):
>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.7e-06     0.048      31      71 ..      69     109 ..      62     132 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.7e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHH CS
                          Ferritin  31 eglaeffdeqaeeerehadklaerilalGgtpvltraelee 71 
                                        + +e + e + eer+++++ +e +l+ Gg+   tr+++++
  gi|298674394|ref|YP_003726144.1|  69 ISGHESLIELSNEERKQFEETMELLLKYGGEIRYTRKKVGR 109
                                       566899999*********************99999888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1018.14
//
Query:       gi|298674395|ref|YP_003726145.1|  [L=178]
Description: hypothetical protein Metev_0431 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-22   80.0   0.0    3.1e-22   79.7   0.0    1.1  1  NYN              NYN domain
  ------ inclusion threshold ------
      0.046   13.7   0.1        2.7    7.9   0.0    2.1  2  Chal_sti_synt_C  Chalcone and stilbene synthases, C-terminal 
       0.11   12.6   0.1       0.24   11.4   0.0    1.4  1  MMR_HSR1_Xtn     C-terminal region of MMR_HSR1 domain


Domain annotation for each model (and alignments):
>> NYN  NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.7   0.0   5.1e-26   3.1e-22       2     146 ..      26     156 ..      25     157 .. 0.91

  Alignments for each domain:
  == domain 1  score: 79.7 bits;  conditional E-value: 5.1e-26
                               NYN   2 vavfiDgenlpvpakgkevdyrklleeirskgelvraraygnwedeeqnkfqdalsstgi.kvkhkplkkrggsgkk 77 
                                       +++++Dg n+    k+ +v+++++++ ++++g++++  +++n+++   +k+ +a++++g+ +v              
  gi|298674395|ref|YP_003726145.1|  26 IGLLVDGPNVLR--KEFNVNLEAIRDVLKEYGNVKIGLVFLNQYA--SEKLVEAIENNGFePVICS----------S 88 
                                       789********9..6568****************999*****443..48999********888433..........6 PP

                               NYN  78 avDvelavdalelaydnkydtivLvsgDgDFaplveklrergkrVevllaeeastsseLisaadefisl 146
                                       +vDv+lav+ +e++ ++++dti Lv++D+DF pl++k++++gk+++++++e +  s++L+++ad++i l
  gi|298674395|ref|YP_003726145.1|  89 DVDVRLAVEGTEMVCNPNIDTITLVTRDADFKPLLNKANKHGKETILFGVE-PGFSPALKNSADYVIML 156
                                       7************************************************66.9************9965 PP

>> Chal_sti_synt_C  Chalcone and stilbene synthases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0   0.00046       2.7      86     106 ..      43      63 ..      32      82 .. 0.81
   2 ?    3.9   0.0    0.0081        48      16      90 ..      89     164 ..      81     171 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00046
                   Chal_sti_synt_C  86 kleasrkvlseyGnvssatvl 106
                                       +lea r+vl+eyGnv    v+
  gi|298674395|ref|YP_003726145.1|  43 NLEAIRDVLKEYGNVKIGLVF 63 
                                       6999***********877665 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0081
                   Chal_sti_synt_C  16 vidgklteeGltfkllrdlPekieenieeflkklleklGieefndlfwivhPG.Gpaildrleaklklekekleas 90 
                                        +d +l+ eG ++ +  ++ +      +   k ll+k+  +  + +++ v PG  pa+ +  +  + l+ e ++ +
  gi|298674395|ref|YP_003726145.1|  89 DVDVRLAVEGTEMVCNPNIDTITLVTRDADFKPLLNKANKHGKETILFGVEPGfSPALKNSADYVIMLNTEEMKLT 164
                                       57888888899999998888777777777889999999999999********966999999999999999999877 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0     4e-05      0.24      15      52 ..      42      79 ..      32      89 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4e-05
                      MMR_HSR1_Xtn 15 ldeetvkkilkeykihnaevliredvtvDdlidviegn 52
                                      ++ e ++++lkey+ ++  +++ +++  ++l+++ie+n
  gi|298674395|ref|YP_003726145.1| 42 VNLEAIRDVLKEYGNVKIGLVFLNQYASEKLVEAIENN 79
                                      66799******************************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1199.46
//
Query:       gi|298674396|ref|YP_003726146.1|  [L=394]
Description: pyruvate carboxyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.5e-79  267.2   1.2    2.6e-79  266.5   1.2    1.4  1  HMGL-like  HMGL-like


Domain annotation for each model (and alignments):
>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  266.5   1.2   1.5e-83   2.6e-79       2     264 .]      25     281 ..      24     281 .. 0.99

  Alignments for each domain:
  == domain 1  score: 266.5 bits;  conditional E-value: 1.5e-83
                                       -EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHH CS
                         HMGL-like   2 vkivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdi 78 
                                       ++i+d+tLRDGeq++++ ++ eek++i ++Ld +gv++iE+gfp+ s d+ + v++i + + +ar ++l ra  +d+
  gi|298674396|ref|YP_003726146.1|  25 IEICDVTLRDGEQTPGVVFTKEEKMNISNQLDSLGVEVIETGFPVVSSDEKDTVKQISNMGLNARTCCLSRALTSDV 101
                                       79*************************************************************************** PP

                                       HHHHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHHH CS
                         HMGL-like  79 kaavealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkdvelsledasrtdleflaevveaa 155
                                       + a +    +++++v +f+a+s+lhl +k++k+ ee+++ a + +++a+++g +v++ +edasrt++++l +v  +a
  gi|298674396|ref|YP_003726146.1| 102 DSALD----CNVDMVSIFVAMSDLHLIHKYNKSCEEMISCALDTIEYAKDHGLEVRFAAEDASRTNVDTLKNVFLRA 174
                                       *****....******************************************************************** PP

                                       HHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS--SSBB CS
                         HMGL-like 156 eeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGlGeraG 232
                                       +++G++++++aDtvGvl+P+  ++l++++ + v+  +++ +HcHndlG+A+antl+A+eaGa+++ +tvnG+GeraG
  gi|298674396|ref|YP_003726146.1| 175 QDYGVDYVSLADTVGVLNPSTTYHLVNEINKSVE--TPICIHCHNDLGMATANTLMAAEAGAKQLHTTVNGIGERAG 249
                                       **********************************..***************************************** PP

                                       B-BHHHHHHHHHHTT-B----HHHHHHHHHHH CS
                         HMGL-like 233 naaleelvaalealgvdtgldlqklrsiaalv 264
                                       na+lee+ + l +      +d++ l++++++v
  gi|298674396|ref|YP_003726146.1| 250 NAPLEEVLMGLLVEYNIDRYDTTGLTDLSRMV 281
                                       **************99999******9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 2927.14
//
Query:       gi|298674397|ref|YP_003726147.1|  [L=257]
Description: 1-(5-phosphoribosyl)-5-amino-4-imidazole-carboxylate (AIR) carboxylase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-17   61.1   4.9    1.6e-16   60.2   4.9    1.5  1  AIRC      AIR carboxylase


Domain annotation for each model (and alignments):
>> AIRC  AIR carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.2   4.9   9.2e-21   1.6e-16       2     128 ..     122     249 ..     121     256 .. 0.86

  Alignments for each domain:
  == domain 1  score: 60.2 bits;  conditional E-value: 9.2e-21
                                       EEEEESSGGGHHHHHHHHHHHHHTT-....EEEEEE--TTTSHHHHHHHHHHCHTTTEEEEEEEEESS--HHHHHHH CS
                              AIRC   2 VgiimGSdsDlevmkkaaeilkelgv....eyevrvvSahrtpeelleyaeeaeerglkviIagAGgaahLpgvvas 74 
                                       Vgi+ G + D+ v+++a  + +e+g     +y+v v+  hr   ++ +     +e g++++I++AG++  Lp +v++
  gi|298674397|ref|YP_003726147.1| 122 VGILSGGTTDVGVAEEANIVASEMGCktitAYDVGVAGIHRLFPQISR----LKETGVDAVIVAAGREGTLPTIVSG 194
                                       99*********************9997777899*******98776655....566899******************* PP

                                       HSSS-EEEEEE--...STTCCHHHHHHHHT--TTS--EE-SSTHHHHHHHHHHHHHT CS
                              AIRC  75 lttlPVigvPvks...kalkgldsllSivqmPsgvpvatvaigkaknAallAaqila 128
                                       l ++PVig Pv++       g  +l+S++q +s ++v++++   +  A+ +Aaqi  
  gi|298674397|ref|YP_003726147.1| 195 LIDVPVIGLPVSTgygAGGLGQAALMSMLQSCSVISVVNID--AGFVAGAFAAQIAN 249
                                       ************94323456889*************98877..88888888888854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2012.92
//
Query:       gi|298674398|ref|YP_003726148.1|  [L=280]
Description: ATP-NAD/AcoX kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.1e-55  188.0   0.9    2.6e-55  187.7   0.9    1.2  1  NAD_kinase  ATP-NAD kinase
     0.0023   17.6   0.0     0.0038   16.8   0.0    1.4  1  DAGK_cat    Diacylglycerol kinase catalytic domain
  ------ inclusion threshold ------
       0.11   11.8   0.0       0.16   11.3   0.0    1.2  1  PFK         Phosphofructokinase


Domain annotation for each model (and alignments):
>> NAD_kinase  ATP-NAD kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.7   0.9   4.4e-59   2.6e-55      65     291 ..      42     265 ..       5     266 .. 0.90

  Alignments for each domain:
  == domain 1  score: 187.7 bits;  conditional E-value: 4.4e-59
                                       .........EEECCC-TTTTTSSSEEEEEE-HHHHHHHHHHHHHCT-EEEEEESSS--SS-SEEGGGHHHHHHHHHH CS
                        NAD_kinase  65 d........dtrkaleafadagvdliivvGGDGTaldvarllqkaeiPvlgvnaGvkgfltefepeaaaelleklle 133
                                       +          ++a+e++ + gv+++ivvGGDGT+l   + + +  iP+lg+n+G++gfl + epe+a +++ek l+
  gi|298674398|ref|YP_003726148.1|  42 KeigieddvIRIEAIEDMRNTGVEFLIVVGGDGTVLLTLSRMYD-PIPILGINMGKVGFLVDTEPEEALSTIEKALH 117
                                       13334444456899*********************999888886.9******************************* PP

                                       T-SEEEEEEEEEEEEEETTE......EEEEEEESSEEEEEESSSSS-EEEEEEETTEEEEEEEESEEEEE-TGGGGT CS
                        NAD_kinase 134 geirvekrevldavimrskgeediadiviensvlnevviirgpgstlielelyvdtelleadqldglivstPtGsta 210
                                        +++ ++ ++l ++++ +        i+  + + ne+v+++g++++++++++++d+  le++++dg++ stPtGsta
  gi|298674398|ref|YP_003726148.1| 118 -GFTYNEQIRLGVKLNGD--------IL--PPATNEIVLMTGRPAKILTTKVKIDDYELEELRSDGIVFSTPTGSTA 183
                                       .9**********888544........34..5679******************************************* PP

                                       HHHHTT--EE-TT---EEEEEESESSS----EEE-TT-EEEEEE-.SS--EEEEETTTEEEEE-TT-EEEEEEESSE CS
                        NAD_kinase 211 yslsaGgplisPgvlailivpicPhslssrpiVvssssklrirva.srseallaldGseelelspgdevrvtasdkk 286
                                       y++saGgp+i+P+v+a livp+ P++lssrp+Vv+ +  ++++    ++ea+l++dG++++++ ++ +v++t++d++
  gi|298674398|ref|YP_003726148.1| 184 YAMSAGGPIIDPRVNAALIVPLAPFKLSSRPLVVPADCVINVETTiPEKEAILVIDGQHTYKIHENHVVTLTKADQP 260
                                       *******************************************99******************************** PP

                                       EEEEE CS
                        NAD_kinase 287 fklir 291
                                       +++++
  gi|298674398|ref|YP_003726148.1| 261 ARFVK 265
                                       ***98 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   6.3e-07    0.0038      45      77 ..      53      85 ..      15     116 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.3e-07
                                      HHHHHHHHHCC-SEEEEEESHHHHHHHHHHHCT CS
                          DAGK_cat 45 kelakeakeegvdlivvaGGDGtvsevlnglle 77
                                       e +++++++gv++++v+GGDGtv   l+ + +
  gi|298674398|ref|YP_003726148.1| 53 IEAIEDMRNTGVEFLIVVGGDGTVLLTLSRMYD 85
                                      4568889999**************998888887 PP

>> PFK  Phosphofructokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.6e-05      0.16      79     105 ..      51      77 ..       7      94 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.6e-05
                                       HHHHHHHHHHHHT--EEEEEESHHHHH CS
                               PFK  79 grkkaaenlkklgidaLvviGGdgslk 105
                                        r +a+e +++ g++ L+v+GGdg++ 
  gi|298674398|ref|YP_003726148.1|  51 IRIEAIEDMRNTGVEFLIVVGGDGTVL 77 
                                       38899*******************963 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1938.27
//
Query:       gi|298674399|ref|YP_003726149.1|  [L=268]
Description: inositol monophosphatase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.7e-30  105.8   0.0    3.4e-30  105.5   0.0    1.1  1  Inositol_P  Inositol monophosphatase family
    9.4e-05   22.0   0.0    0.00015   21.3   0.0    1.3  1  FBPase      Fructose-1-6-bisphosphatase, N-terminal domain
  ------ inclusion threshold ------
       0.11   12.2   0.1       0.21   11.4   0.1    1.4  1  HTH_38      Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Inositol_P  Inositol monophosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.5   0.0   5.7e-34   3.4e-30      40     260 ..      42     257 ..       9     266 .. 0.79

  Alignments for each domain:
  == domain 1  score: 105.5 bits;  conditional E-value: 5.7e-34
                                       HHHHHHHHHHHHHHHHHHHHHHSTTSEEEHHCHHHHCCCT.SSSSSEEEEEEEEETHHHHHHT-SG-EEEEEEEE.. CS
                        Inositol_P  40 edlvtaadeaveelilealaekfpshkilgeetlakgekseltedgltwivDPiDGTknFvrgipqvaVsigllv.. 114
                                       +d  + +d ++e++i+e+l++   s +i++ee + k+    +++ ++t+i+DPiDGT+n    ip + Vsi++    
  gi|298674399|ref|YP_003726149.1|  42 TD-TKLIDDVAERAIIEVLKKDGRSMRIISEEMGVKIL---GNNPEFTIIIDPIDGTYNASFCIPFYSVSIAIGSpd 114
                                       33.3479****************************999...67767*************999999999999998866 PP

                                       TTEEEEEEEEETTTTEEECEETTTEEEETCEEEEECTTSEGGGTEEEEEESSSSSSHHHHCHHHHHHHCCCCCHEEE CS
                        Inositol_P 115 egkpvlGviaqPllgqlysaakgkGaflngeklplsrappiseallvtlfavssrkdtseasllekvesavsaegvr 191
                                          + +G + +   + +y a  gkGa+lng++++ s++++++e++      + ++++t +       +s++ ++ +r
  gi|298674399|ref|YP_003726149.1| 115 LSYIWAGYVKNISSKDIYYAESGKGAYLNGKRISPSKKSELNECCASVYGYRLHVERTVD-------LSRNIRR-MR 183
                                       889999*********************************999998544344445555555.......5556666.79 PP

                                       BESSHHHHHHHHHHTSTSEEEEEC..EBHHHHHHHHHHHHHTTEEEEESSSC.....SSSTTSSEEEEESCHHHH CS
                        Inositol_P 192 svgssalklaavaeGkadaylefg.rekkWDhAAGeaileeaGGvvtdakge.....grlllargiiaanqkela 260
                                        +g   l++++va+G++da+++ + ++   D+AAG +i+ e GG+vtd   +      + + +  +ia+n +  +
  gi|298674399|ref|YP_003726149.1| 184 ILGCVSLEICYVASGRFDAFVDVRgSLRLTDVAAGKFIVDESGGRVTDGFADsielqDNSIYHVYMIASN-GIVH 257
                                       99*********************9999999******************9888565553333334444444.4444 PP

>> FBPase  Fructose-1-6-bisphosphatase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   2.5e-08   0.00015      54     116 ..      37      96 ..      10     106 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.5e-08
                            FBPase  54 eNvtGdeqkklDvladeiliealkaseevkvlvSEEeeelivlerekegkyvvafDPlDGSSn 116
                                       +  +G + k +D +a+  +ie+lk+ ++   ++SEE+  +++l   ++ ++++++DP+DG  n
  gi|298674399|ref|YP_003726149.1|  37 TGADGTDTKLIDDVAERAIIEVLKKDGRSMRIISEEMG-VKIL--GNNPEFTIIIDPIDGTYN 96 
                                       4568999999*************************996.7888..67789**********877 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   3.6e-05      0.21       8      32 ..      51      75 ..      49      76 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.6e-05
                            HTH_38  8 eeReeIerllaeGlslreIArrLgr 32
                                      +eR  Ie l + G s+r I  ++g+
  gi|298674399|ref|YP_003726149.1| 51 AERAIIEVLKKDGRSMRIISEEMGV 75
                                      7********************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2012.75
//
Query:       gi|298674400|ref|YP_003726150.1|  [L=338]
Description: glyceraldehyde-3-phosphate dehydrogenase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-25   89.4   0.0    2.8e-25   88.8   0.0    1.3  1  Gp_dh_C          Glyceraldehyde 3-phosphate dehydrogenase, C-
    7.2e-13   48.8   0.8    1.4e-12   47.8   0.8    1.5  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
      3e-07   30.7   1.0    6.7e-07   29.6   0.2    2.0  2  Gp_dh_N          Glyceraldehyde 3-phosphate dehydrogenase, NA
    1.1e-05   24.9   0.2      0.011   15.1   0.1    2.3  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
     0.0018   19.1   0.1     0.0037   18.1   0.1    1.5  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
     0.0038   17.6   0.1     0.0077   16.7   0.1    1.5  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
     0.0053   17.0   0.1      0.013   15.7   0.1    1.7  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
      0.023   15.3   0.4       0.18   12.5   0.1    2.4  2  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain
      0.034   14.7   0.1      0.087   13.4   0.1    1.7  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent


Domain annotation for each model (and alignments):
>> Gp_dh_C  Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.8   0.0   1.4e-28   2.8e-25       1     158 []     146     298 ..     146     298 .. 0.95

  Alignments for each domain:
  == domain 1  score: 88.8 bits;  conditional E-value: 1.4e-28
                                       HHHHHHHHHHHHEEEEEEEEEEEECTTTSBSSSS--.SSTTTTSBTT..CSSEEEE-THHHHHHHHSGGGTTTEEEE CS
                           Gp_dh_C   1 LaplakvlndkfgikkglmttvhaytndQkllDgpskkdlrraraaa..eniiptstgaakavglVlpelkgkldgl 75 
                                       L++l+  ++ ++g+kk ++t++++++++         +d++++++++   ++++ +++++++v++V+p  +++++++
  gi|298674400|ref|YP_003726150.1| 146 LCRLISNIDREYGVKKCRVTLIRRAADP---------SDIKKGPINSivADPVKLPSHHGPDVQSVIP--SIDISTM 211
                                       89**************************.........8*********99*******************..699**** PP

                                       EEEESSSSEEEEEEEEEESSTS-HHHHHHHHHHHHH..TTTTTTEEEEHSHHHGGGGTTGCS..SEEEEGGGCEEET CS
                           Gp_dh_C  76 AvrVPtpnvsvvdlvvelekevtveevnaalkeaae..galkgilsyteeelvssDlvgdph..ssifdaketivve 148
                                       Av+VP + ++++ + +el+++ ++++++++l + ++    + gi+s++e ++ ++Dl + ++   ++  ++ +i   
  gi|298674400|ref|YP_003726150.1| 212 AVKVPNTMMHIHTVNMELKNDCSADDIKNLLAKNPRmhYLEPGITSTSETMELARDLGRPRNdmWENCIWEDSIDFY 288
                                       ************************************866678****************998888999*******999 PP

                                       TTEEEEEEEE CS
                           Gp_dh_C 149 enlvkvvawy 158
                                       e ++++++++
  gi|298674400|ref|YP_003726150.1| 289 EGELYLLQAV 298
                                       9999999875 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.8   7.2e-16   1.4e-12       1      95 [.       4     107 ..       4     118 .. 0.89

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 7.2e-16
                                       EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTC..STTTTTBHH........HHSSSS--S-BEBSSHHHHHHH CS
                            DapB_N   1 ikvavvGasGrmGkevvkaveeaedlelvaavdrke..selegkdag........ellglgklgvavtddleevlek 67 
                                       +kv+++G+ G++Gk+v++av+++ed+el +  ++k+  +++ ++ +g        +  +++  g++v  ++e+++++
  gi|298674400|ref|YP_003726150.1|   4 VKVGINGY-GTIGKRVADAVHQQEDMELIGISKTKPnyEAVMAQRMGynvytpsdKTSKMKDGGIKVAGTVEDMVNE 79 
                                       69******.************************99966666777777*******9999999**************** PP

                                       -SEEEE-S-HHHHHHHHHHHHHT.T-EEE CS
                            DapB_N  68 advliDFTtpeavlenlklalek.gvklV 95 
                                       adv++D T p++v e+ k ++ek gvk++
  gi|298674400|ref|YP_003726150.1|  80 ADVIVDAT-PKGVGEKNKELYEKaGVKAI 107
                                       ********.88888888877777688876 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.2   3.4e-10   6.7e-07       1      75 [.       4      79 ..       4      91 .. 0.75
   2 ?   -2.9   0.0       4.3   8.6e+03      31      48 ..     217     234 ..     206     247 .. 0.63

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 3.4e-10
                                      CEEEEESTSHHHHHHHHHHHHHTTCEEEEEE-TS-HHHHHHHHHEE..TTTEC-SS-EEEETTEEEETTEEEEEE-- CS
                           Gp_dh_N  1 vkvainGfGRIGrlvlralleekelevvaindltdletlayllkyD..svhgrfkgeveaeeealvvngkkikvlae 75
                                      vkv+inG+G IG+ v+ a+ +++++e++ i + t++++ a + ++    v+   +++ ++++  + v g+   +++e
  gi|298674400|ref|YP_003726150.1|  4 VKVGINGYGTIGKRVADAVHQQEDMELIGISK-TKPNYEAVMAQRMgyNVYTPSDKTSKMKDGGIKVAGTVEDMVNE 79
                                      69*****************************9.55555555555431145666677777778888888765555555 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.3
                                       E-TS-HHHHHHHHHEETT CS
                           Gp_dh_N  31 ndltdletlayllkyDsv 48 
                                       n++++++t+ + lk D  
  gi|298674400|ref|YP_003726150.1| 217 NTMMHIHTVNMELKNDCS 234
                                       336666777666666654 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   5.6e-06     0.011      36      71 ..       3      39 ..       1      44 [. 0.85
   2 !    7.8   0.0   0.00098       1.9      54     110 ..      44     100 ..      40     110 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.6e-06
                                      TSEEEEES-SHHHHHHHHHHH.HTT-EEEEESSSHHH CS
                      2-Hacid_dh_C 36 gktvGiiGlGrIGqavakrlk.afgmkviaydrskkk 71
                                      + +vGi G+G IG++va+ ++ + +m++i+++++k +
  gi|298674400|ref|YP_003726150.1|  3 KVKVGINGYGTIGKRVADAVHqQEDMELIGISKTKPN 39
                                      568***************9986899*****9998664 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00098
                                       HHHHTT-EEEEESSSHHHHHCHHHHTCEEC.SHHHHHHH-SEEEE-S-..-STTTTTSBS CS
                      2-Hacid_dh_C  54 rlkafgmkviaydrskkkeeeeeelgvelv.sleellaesDivslhlp..ltpetrhlin 110
                                       +++ +g +v+  + + +   ++++ g++++ ++e++++e+D+++ ++p  + +++++l +
  gi|298674400|ref|YP_003726150.1|  44 MAQRMGYNVYTPSDKTS---KMKDGGIKVAgTVEDMVNEADVIVDATPkgVGEKNKELYE 100
                                       55666666654444433...58899998888*************9998444566666655 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   1.9e-06    0.0037       1      76 [.       4      93 ..       4     107 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.9e-06
                                      EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESS.................HHHHHTCTT CS
                      GFO_IDH_MocA  1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysd.................leelladpe 62
                                      ++v+i G+G ig++ + +++++ ++ e++++ +++++    +a+++g ++y+                  +e++++  e
  gi|298674400|ref|YP_003726150.1|  4 VKVGINGYGTIGKRVADAVHQQ-EDMELIGISKTKPNYEAVMAQRMGYNVYTPsdktskmkdggikvagtVEDMVN--E 79
                                      589*************666666.9*******99999888888*******999888999999999998888888888..8 PP

                                      ESEEEE-S-GGGHH CS
                      GFO_IDH_MocA 63 idavivatpngthe 76
                                      +d+++ atp g +e
  gi|298674400|ref|YP_003726150.1| 80 ADVIVDATPKGVGE 93
                                      99999999984433 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   3.9e-06    0.0077       1      94 [.       5     107 ..       5     109 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.9e-06
                                       EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSG........GGTTTECEBEEE..GGGGGCTT- CS
                    Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavk........aleegkdlkved..vdeeelkev 67 
                                       kv+i G  G +G++++  ++++ ++el+ ++ ++ +    +a++++        ++++ kd  ++   + e+ ++e+
  gi|298674400|ref|YP_003726150.1|   5 KVGING-YGTIGKRVADAVHQQEDMELIGISKTKPNYEAVMAQRMGynvytpsdKTSKMKDGGIKVagTVEDMVNEA 80 
                                       688888.899*********************9999888888888889999999955555555555444888888*** PP

                                       SEEEE-SCHHHHHHHHHHHHHTTSEEE CS
                    Semialdhyde_dh  68 divflalpagvskelapklaeagvkvi 94 
                                       d+++ a+p+gv ++  + + +agvk i
  gi|298674400|ref|YP_003726150.1|  81 DVIVDATPKGVGEKNKELYEKAGVKAI 107
                                       ***********************9876 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   6.6e-06     0.013       2      79 ..       7      89 ..       6     106 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.6e-06
                                      EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH.......TTTCEEEEE--TTTHHHHHHHHHTTSSEE CS
                   Sacchrp_dh_NADP  2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka.......lgvrfeaialdaenyeavLaallkegdlv 73
                                       i G+G +G+ va+ +++++d+  e++ ++++k + ea+ a+         + + ++++    +++ +++ +++e+d++
  gi|298674400|ref|YP_003726150.1|  7 GINGYGTIGKRVADAVHQQEDM--ELIGISKTKPNYEAVMAQRmgynvytPSDKTSKMKDGGIKVAGTVEDMVNEADVI 83
                                      567*******************..9***************999999888866666666666667777899999999999 PP

                                      EE-SSG CS
                   Sacchrp_dh_NADP 74 vnlspp 79
                                      v+++p 
  gi|298674400|ref|YP_003726150.1| 84 VDATPK 89
                                      999885 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1     9e-05      0.18       1      69 [.      10      89 ..      10     102 .. 0.75
   2 ?   -0.3   0.0      0.83   1.7e+03      75      95 ..     293     313 ..     291     329 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9e-05
                                      --SHHHHHHHHHHHH---SSEEEEEEEEESS.EEE-TT................HHHHHT--CB---HHHHHHHHS-EE CS
                     NAD_binding_3  1 GlGaiGsavleqlkrqqseielelvavadrd.sllskd................rkallasealtldlddliahldpdv 62
                                      G+G+iG++v++++ +q++   +el ++ + +   ++                   k + +  ++   ++d+++  ++dv
  gi|298674400|ref|YP_003726150.1| 10 GYGTIGKRVADAVHQQED---MELIGISKTKpNYEA-VmaqrmgynvytpsdktSKMKDGGIKVAGTVEDMVN--EADV 82
                                      99**************97...677777777632222.246666666777777655566667788889999999..**** PP

                                      EEE-S-- CS
                     NAD_binding_3 63 vVEcass 69
                                      +V+++++
  gi|298674400|ref|YP_003726150.1| 83 IVDATPK 89
                                      ***9975 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.83
                                       THHHHHHTTEEEE-S--CGGG CS
                     NAD_binding_3  75 lvlkaLkagkdvvtankgala 95 
                                       ++l+a+ +  dvv  n +a+ 
  gi|298674400|ref|YP_003726150.1| 293 YLLQAVHQEADVVPENIDAIR 313
                                       5789999******99999986 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   4.4e-05     0.087       1      70 [.       5      88 ..       5     102 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.4e-05
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.................-EEECECHHHHHHH- CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.................vkvtavdneeaaeea 62
                                      k+gi G+G +g+ +a  + ++   + e++ +++ +p+  + +a+++g                 +kv + + e++++ea
  gi|298674400|ref|YP_003726150.1|  5 KVGINGYGTIGKRVADAVHQQE--DMELIGISKTKPNYEAVMAQRMGynvytpsdktskmkdggIKVAG-TVEDMVNEA 80
                                      68999***********999987..5555546588888888899999999******************99.********* PP

                                      SEEEE-S- CS
                     F420_oxidored 63 dvvvlavk 70
                                      dv+v a +
  gi|298674400|ref|YP_003726150.1| 81 DVIVDATP 88
                                      ***97765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2084.25
//
Query:       gi|298674401|ref|YP_003726151.1|  [L=738]
Description: amino acid permease [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.8e-52  177.2  56.1    6.1e-52  176.9  56.1    1.1  1  AA_permease_2   Amino acid permease
    1.4e-42  145.9  48.6    2.1e-42  145.3  48.6    1.2  1  AA_permease     Amino acid permease
    6.6e-17   62.3   0.4    4.3e-08   33.8   0.0    4.0  3  Usp             Universal stress protein family
    4.8e-10   38.8  20.5    4.8e-10   38.8  20.5    2.3  2  Spore_permease  Spore germination protein
  ------ inclusion threshold ------
      0.014   14.9   0.7       0.59    9.5   0.3    2.1  2  ABC_transp_aux  ABC-type uncharacterized transport system
       0.27   11.1   0.7          3    7.7   0.0    2.4  2  NPBW            Neuropeptides B and W
        1.5    9.0   9.9        0.1   12.7   3.2    2.7  2  AA_permease_C   C-terminus of AA_permease


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.9  56.1   2.4e-55   6.1e-52       1     404 [.      18     410 ..      18     427 .. 0.88

  Alignments for each domain:
  == domain 1  score: 176.9 bits;  conditional E-value: 2.4e-55
                     AA_permease_2   1 lsllsafalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkk 75 
                                       l+++s+fa+ +g++ig+gifv +  ++a++gpa+il+++++ li  +a ++  aEl++ +pr gG y ++++a+g +
  gi|298674401|ref|YP_003726151.1|  18 LGFFSTFAIGTGTMIGAGIFVLPgmATAAAGPAAILSFIFGGLIA-MATAISAAELATGMPRAGGSYYFVSRAMGAV 93 
                                       79*********************888888***************9.6999999***999****************** PP

                     AA_permease_2  76 vaflsawfnwfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilki 152
                                       ++ + ++ +w++ v+  ++ l+ ++ y+ +++ p+      ++++ a +i +l+ +in++g k s+ +qn+++i+ +
  gi|298674401|ref|YP_003726151.1|  94 FGTIIGIGAWIGLVFKGSFALVGFGDYFYTLF-PS------PVLITATIIGLLLLFINYKGAKSSGFLQNVIVIILF 163
                                       ***************99888888999988865.54......6999999999************************** PP

                     AA_permease_2 153 llpliiliilglitvdgggfsslstetdtffpngwpgvllgllivlwsfdGfesaanvseevkk..kdvpkaifigl 227
                                        ++l ++ii g +++d++  +        ++p g ++++ + + ++ s+ G+   a +seevk   k++p+a + ++
  gi|298674401|ref|YP_003726151.1| 164 -IILSVFIIKGAFIIDPNKYH-------PVVPYGYSSIFTTTGLIFISYLGIIKLAAISEEVKDpsKNLPRAFIGSV 232
                                       .899************99775.......79*******************************887779********** PP

                     AA_permease_2 228 livlvlyllvniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealar 304
                                       ++v+vly+++++++ gv+p +   n+++   ++  ++e + g++++ii+++++ l+ l  +n+a+++ssr+ +a++r
  gi|298674401|ref|YP_003726151.1| 233 ATVIVLYTGIMVVVNGVLPFEDAVNTET---PLVDVAEVMLGPTGQIIIILAGLLATLSTANAAIMSSSRFPFAMGR 306
                                       ********************99988776...34455555555999******************************** PP

                     AA_permease_2 305 dgvlPrffakvn.kfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigalilrkkrphlk 380
                                       d+  P++f +++ k+++p+rai++t ++ +ill  f++    ++  l+ ++s ++i+++ l+ ++a+ilr+   ++ 
  gi|298674401|ref|YP_003726151.1| 307 DDLVPHWFIHIHgKYNTPYRAIVITGLLMVILL--FIF----NVEQLAKLGSAFNILVFVLVNLSAIILRRSAVNWY 377
                                       ****************************87765..555....489*************************9988886 PP

                     AA_permease_2 381 rpgk.....ilvaiigalfllfll....valff 404
                                       +p++     +++ i+g+ ++l+ll    v++f+
  gi|298674401|ref|YP_003726151.1| 378 KPAFkdpfyPVTQIFGIAGSLVLLpvigVLPFI 410
                                       644444553667788877777776544433333 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.3  48.6   8.3e-46   2.1e-42       5     426 ..      26     401 ..      23     428 .. 0.88

  Alignments for each domain:
  == domain 1  score: 145.3 bits;  conditional E-value: 8.3e-46
                       AA_permease   5 ialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGln 81 
                                       i  g +iG+g+fv  g ++++aGp +a+l+++++g++ +++++s +e+at +p++gg y+++sr +g  +G  iG+ 
  gi|298674401|ref|YP_003726151.1|  26 IGTGTMIGAGIFVLPGMATAAAGP-AAILSFIFGGLIAMATAISAAELATGMPRAGGSYYFVSRAMGAVFGTIIGIG 101
                                       67799*******************.888************************************************* PP

                       AA_permease  82 ylfswitvlaleltaasiliqfwelvtdlpkawvtgavflvvlliinlvgvkvygeaefilalikiiaiiafiivgi 158
                                        ++  ++   ++l++ + ++  +  +++     +t++++ ++ll+in+ g+k +g+ + ++ +i++i++  fii g 
  gi|298674401|ref|YP_003726151.1| 102 AWIGLVFKGSFALVGFGDYFYTL--FPSPV--LITATIIGLLLLFINYKGAKSSGFLQNVIVIILFIILSVFIIKG- 173
                                       99999999999999999999999..88777..789999***********************************999. PP

                       AA_permease 159 illaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPka 235
                                        ++++ ++ +                 +p g         ++++     ++ ++ Gi+ +a+i++EvkdP+k++P+a
  gi|298674401|ref|YP_003726151.1| 174 AFIIDPNKYHP---------------VVPYG--------YSSIFTTTGLIFISYLGIIKLAAISEEVKDPSKNLPRA 227
                                       46677777777...............34445........799*********************************** PP

                       AA_permease 236 ilqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssansslysas 312
                                       ++  v +++++Y+++++++  ++p  d  +++      +++ ++ +++g  +   +i a+ l+a+ls+an++++s+s
  gi|298674401|ref|YP_003726151.1| 228 FIGSVATVIVLYTGIMVVVNGVLPFEDAVNTE-----TPLVDVAEVMLGPTGQIIIILAG-LLATLSTANAAIMSSS 298
                                       ******************************99.....45777788888887776666666.6689************ PP

                       AA_permease 313 RvlyslakdglaP.kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliilsyl 388
                                       R  +++ +d+l P ++   ++k++ P+rai+++ ++ +++l++  +n++       l  +  + +++v++l++ls +
  gi|298674401|ref|YP_003726151.1| 299 RFPFAMGRDDLVPhWFIHIHGKYNTPYRAIVITGLLMVILLFI--FNVE------QLAKLGSAFNILVFVLVNLSAI 367
                                       ********************************99999888844..4444......5688889999************ PP

                       AA_permease 389 rfRkalkyqgrsieelgfkaallplgvilvlaaliiil 426
                                        +R++      ++ +  fk +++p + i+++a  + +l
  gi|298674401|ref|YP_003726151.1| 368 ILRRS---AVNWY-KPAFKDPFYPVTQIFGIAGSLVLL 401
                                       99998...33334.678999999999999987555554 PP

>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.15   3.9e+02     115     139 ..     222     246 ..     219     247 .. 0.91
   2 !   20.9   0.0   1.6e-07    0.0004       4     141 .]     454     582 ..     451     582 .. 0.81
   3 !   33.8   0.0   1.7e-11   4.3e-08       4     141 .]     591     710 ..     588     710 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.15
                                       STTTTCSSBHHHHHHHHHTSSEEEE CS
                               Usp 115 sglsrlllGSvseyvlrhapcpVlv 139
                                       ++l r+++GSv+  ++  + ++V+v
  gi|298674401|ref|YP_003726151.1| 222 KNLPRAFIGSVATVIVLYTGIMVVV 246
                                       57889**************999998 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 1.6e-07
                                       EEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTC CS
                               Usp   4 rIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggv 80 
                                       +IlV++  ++e +  l +  e+    g+++  lhv + +++++  +a++e  e+  e     + +   ++   +g +
  gi|298674401|ref|YP_003726151.1| 454 KILVPI-ANPEHESDLVYLSENI---GDDILGLHVRKVPNQTSLQAARDEYHEHKPEIDSLLENQF-RRCSVMEGCE 525
                                       788888.5555555454555554...555999****999999988888888888877777766555.599999999* PP

                                       EEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  81 kvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       +  +v  ++d++ +i+e  + e++dliV+G++   g s  ++G+ +e+vl  a ++  v +
  gi|298674401|ref|YP_003726151.1| 526 HQYIVAFDHDVSNSIIEQGRIENVDLIVIGWHE--GYS--FIGDIAEKVLSCARKDIAVLK 582
                                       *********************************..555..69********99999988865 PP

  == domain 3  score: 33.8 bits;  conditional E-value: 1.7e-11
                                       EEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTC CS
                               Usp   4 rIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggv 80 
                                        I Va+ + e++++Al    ++ak++ga++ l++vi p+   + ++ + e+ +e +++ e e               
  gi|298674401|ref|YP_003726151.1| 591 SITVAYNNKENTRYALYLVKQFAKRTGAKIKLVRVINPDLEVYQKNREIEMIKETAQDDELEF-------------- 653
                                       699*************************************99999999999999999999754.............. PP

                                       EEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  81 kvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                           + e+ + +e+i+e a++   dl+V+G +   ++s++llG  s+++++ ++ pV++V+
  gi|298674401|ref|YP_003726151.1| 654 -NYEINESYHTKEAIIESAKK--SDLLVIGDSS-QRFSKALLGTLSQNIAQDCDRPVMIVK 710
                                       .56677788888999998887..8*********.999***********************8 PP

>> Spore_permease  Spore germination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8  20.5   1.9e-13   4.8e-10       5     253 ..      21     269 ..      17     294 .. 0.85
   2 ?   -1.4   7.9      0.32   8.1e+02     111     180 ..     322     390 ..     314     418 .. 0.74

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 1.9e-13
                    Spore_permease   5 kqlfvlivsfqlGvgiltlprsvaeqatpdgWisvllagiiililvllmlkllkkfpek.tliellkkilgkwLGsl 80 
                                       + +f +   +++G+gi +lp++++++a+p + +s +++g+i++  ++ + +l   +p     + +++  +g + G +
  gi|298674401|ref|YP_003726151.1|  21 FSTFAIGTGTMIGAGIFVLPGMATAAAGPAAILSFIFGGLIAMATAISAAELATGMPRAgGSYYFVSRAMGAVFGTI 97 
                                       667888899**********************************************99751678889999******** PP

                    Spore_permease  81 lsilfilyFlllaafelRefseliqvflledtplwiiilllllvilYlvvkGieslareflfiivilliilllillf 157
                                       ++i   +  ++  +f l  f++ + +  l   p+ i   ++ l+ l++ +kG +s   +  +i++il+iil ++++ 
  gi|298674401|ref|YP_003726151.1|  98 IGIGAWIGLVFKGSFALVGFGDYFYT--LFPSPVLITATIIGLLLLFINYKGAKSSGFLQNVIVIILFIILSVFIIK 172
                                       *********************97644..3334444444444455555666676665534456777777777777888 PP

                    Spore_permease 158 slklaeiknlrPvlgngikpvlkslkttslsflgveillllvpflkdkkkvk.kaallgvlistllyllttlivilv 233
                                          +++++   Pv+  g+++++  +  + +s+lg++ l  + + +kd+ k + +a + +v+++++ly+ ++++v +v
  gi|298674401|ref|YP_003726151.1| 173 GAFIIDPNKYHPVVPYGYSSIFTTTGLIFISYLGIIKLAAISEEVKDPSKNLpRAFIGSVATVIVLYTGIMVVVNGV 249
                                       88899******************************************9776615555668888999*********** PP

                    Spore_permease 234 lsveqlkkatwptlsllkvi 253
                                       l  e +  +  p++++++v+
  gi|298674401|ref|YP_003726151.1| 250 LPFEDAVNTETPLVDVAEVM 269
                                       **************998875 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.32
                    Spore_permease 111 dtplwiiilllllvilYlvvkGieslareflfiivilliilllillfslklaeiknlrPvlgngikpvlk 180
                                       +tp  +i+++ ll++++l +  +e+la+ +  ++ il+++l+ ++ ++l+   ++  +P +++ + pv +
  gi|298674401|ref|YP_003726151.1| 322 NTPYRAIVITGLLMVILLFIFNVEQLAK-LGSAFNILVFVLVNLSAIILRRSAVNWYKPAFKDPFYPVTQ 390
                                       6888888888888888888888*****6.77778888888888888888888888889999988888765 PP

>> ABC_transp_aux  ABC-type uncharacterized transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1    0.0048        12     189     235 ..     584     630 ..     569     652 .. 0.76
   2 ?    9.5   0.3   0.00023      0.59     146     220 ..     626     700 ..     620     710 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0048
                    ABC_transp_aux 189 ilpedidvlviakptkdlseeelykldqflmnGgkllvfldpvaeeq 235
                                       +lp++i+ + +a + k+ + ++ly ++qf ++ g  ++++  ++ + 
  gi|298674401|ref|YP_003726151.1| 584 KLPSKINSITVAYNNKENTRYALYLVKQFAKRTGAKIKLVRVINPDL 630
                                       36899999999999999999999999999999999988887777554 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00023
                    ABC_transp_aux 146 kkpkvgfltghgelslsspse.adfleeleenYnveevdldsedil..pedidvlviakptkdlseeelykldqflm 219
                                        +p+  + + + e +     +  +  +ele nY+++e  +++e+i+   ++ d+lvi + ++++s+  l  l+q + 
  gi|298674401|ref|YP_003726151.1| 626 INPDLEVYQKNREIEMI---KeTAQDDELEFNYEINESYHTKEAIIesAKKSDLLVIGDSSQRFSKALLGTLSQNIA 699
                                       55666677777776665...22445799999**************754678****************9999999776 PP

                    ABC_transp_aux 220 n 220
                                       +
  gi|298674401|ref|YP_003726151.1| 700 Q 700
                                       5 PP

>> NPBW  Neuropeptides B and W
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.15   3.8e+02      23      38 ..      78      93 ..      61      97 .. 0.85
   2 ?    7.7   0.0    0.0012         3       3      34 ..     360     391 ..     357     403 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.15
                              NPBW 23 aagpsyysVGRAsGLL 38
                                       ag syy V RA G  
  gi|298674401|ref|YP_003726151.1| 78 RAGGSYYFVSRAMGAV 93
                                      6999********9976 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0012
                              NPBW   3 vavalallllaspaeaWYkqaagpsyysVGRA 34 
                                       v+v l+ ++l ++a  WYk+a    +y+V   
  gi|298674401|ref|YP_003726151.1| 360 VLVNLSAIILRRSAVNWYKPAFKDPFYPVTQI 391
                                       566777799******************99765 PP

>> AA_permease_C  C-terminus of AA_permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.5       6.2   1.6e+04      13      24 ..     327     338 ..     323     344 .. 0.49
   2 ?   12.7   3.2     4e-05       0.1       1      49 [.     381     429 ..     381     431 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 6.2
                     AA_permease_C  13 sIlvNiyLmlqL 24 
                                       +I++   Lm+ L
  gi|298674401|ref|YP_003726151.1| 327 AIVITGLLMVIL 338
                                       444444444433 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 4e-05
                     AA_permease_C   1 FkvPlvPflPalsIlvNiyLmlqLdsltwirfgvwmliglliYflYgir 49 
                                       Fk P++P+  +++I+  + L+  +++l +i +++++++g++ Y +Yg+ 
  gi|298674401|ref|YP_003726151.1| 381 FKDPFYPVTQIFGIAGSLVLLPVIGVLPFIFAVAVIIAGIIWYNAYGKA 429
                                       888*******************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (738 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1063  (0.0592894); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 5009.65
//
Query:       gi|298674402|ref|YP_003726152.1|  [L=63]
Description: RNA-binding protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-21   75.9   1.5    2.3e-21   75.8   1.5    1.0  1  CooT      CO dehydrogenase accessory protein CooT


Domain annotation for each model (and alignments):
>> CooT  CO dehydrogenase accessory protein CooT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.8   1.5   1.3e-25   2.3e-21       1      60 [.       1      59 [.       1      60 [. 0.95

  Alignments for each domain:
  == domain 1  score: 75.8 bits;  conditional E-value: 1.3e-25
                              CooT  1 MCeanvyllkngkeeelvmedVdkiepeedgvvltdifGeekevegkIkeidLvehkiil 60
                                      MCe+n++l+  g+e++++me+V+++  +++ ++lt+ifG++k+++g+Ike+d+++++ i+
  gi|298674402|ref|YP_003726152.1|  1 MCELNAVLE-TGNERQVIMESVTRMVNNDGDIELTGIFGDKKTIKGTIKEVDFSKGETII 59
                                      *******95.66688*******************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.22s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 519.46
//
Query:       gi|298674403|ref|YP_003726153.1|  [L=293]
Description: hypothetical protein Metev_0439 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-56  189.8   0.0    7.6e-56  189.6   0.0    1.0  1  DUF89     Protein of unknown function DUF89
  ------ inclusion threshold ------
       0.12   11.5   0.0       0.19   10.9   0.0    1.2  1  DUF2099   Uncharacterized protein conserved in archaea (DUF20


Domain annotation for each model (and alignments):
>> DUF89  Protein of unknown function DUF89
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.6   0.0   8.5e-60   7.6e-56       3     346 ..       5     278 ..       3     284 .. 0.96

  Alignments for each domain:
  == domain 1  score: 189.6 bits;  conditional E-value: 8.5e-60
                                       HTHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHCTTCGHHH-HHHHT-BTTBSBHHHHHHHHHHHHHHH CS
                             DUF89   3 eerlpciltqviddlekakdekeeelkkiieelselkeelqtdkpltpledeeekrswfnapwlfaecylyrrllel 79 
                                       ++++ c+lt+v+ +++ ++d+++   k++++ + el ++ +  kp  ++                  + ++++++e+
  gi|298674403|ref|YP_003726153.1|   5 PRCAHCLLTRVHYEARLSTDDEQLLHKAVMTGIDELNRTYKPGKPAGEI-----------------STAVHQKVYEV 64 
                                       79*******************9999999*********************.................*********** PP

                                       HTHSGGGTTS-TTHHHHHHHHHHHHHHHHHHHHH.HHHCCSHHHHHHHHHHHHHHHCG--CCCHTSHHCHHHHHHHH CS
                             DUF89  80 fglskelknyDpFkeqKeesnksalkaveelakr.leeledekelfkellkislwGNaiDlsllateediqkdqeee 155
                                       +g      ++Dp+ e+K+ snk a++ ++  +kr +e+  ++kelf++ + +s++GN++D+++ +  ++ ++   e+
  gi|298674403|ref|YP_003726153.1|  65 LG------DEDPYLELKKLSNKTAEDIFPVAQKRvYEDDVSDKELFRRSVLASVIGNTFDFGVVG-FDVAPEIFDET 134
                                       **......**************************77777888***********************.*********** PP

                                       HHHHHHCTESEE-HHHHHHHHCTCHTSEEEEE--BTTHHHHHHHHHHHHHHHCTTTSEEEEEEBSS--TTTB-BHHH CS
                             DUF89 156 arkaleknilvddleklweklkkkkakrvdivlDNaGfElvfDlllaeeLlesglatkVvlhvkaiPwfvsDvtpeD 232
                                       +++ +e+ + vdd+++++e l      +v++v+DN+G E+++D ++ + +++  l+ k++l+v++ P +++D+t++D
  gi|298674403|ref|YP_003726153.1| 135 FKQTFENGLDVDDTSSMFEML-----DNVVYVADNCG-EILLDTIVFDIIKK--LGGKITLVVRGAP-ILNDATLDD 202
                                       *********************.....***********.**************..*************.********* PP

                                       HHHHHHHHH-TTTSHHHHCHTTHHHHHHTSEEEEESSCGGSSS--CCGSSSHHHHHHHHHC-SEEEEEHHHHHHHHT CS
                             DUF89 233 fewlleqladsksfelsalgagldellkegklvlrgssfwttglsysempeapelyeelekadLvifKGdlNyrkLt 309
                                       +                    g+d+  k+++l+++gs+   +g++++e+  + el+e++++a+L+i+KG++Ny++L+
  gi|298674403|ref|YP_003726153.1| 203 VY-----------------DYGIDK--KVDRLLTTGSN--AIGVNFEEA--PNELFEAFDNASLIISKGMANYETLS 256
                                       **.................9*****..***********..*********..*************************8 PP

                                       TSCTTTTTSEHHHHTGTSS--EEEEEE--SHHHHHHH CS
                             DUF89 310 gdrkwppttpfttalgfspvpvlaLrtvKadvvagll 346
                                       + +  p               +++L+++K++ va +l
  gi|298674403|ref|YP_003726153.1| 257 EYNLGP---------------IAYLLKTKCESVASDL 278
                                       777766...............************9876 PP

>> DUF2099  Uncharacterized protein conserved in archaea (DUF2099)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   2.1e-05      0.19      88     128 ..     153     195 ..     147     212 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2.1e-05
                           DUF2099  88 glidaavivcdgaGtvivtnp..elvqglggrisGlveTePie 128
                                       +++d +v v+d +G +++++   ++++ lgg+i+ +v+  Pi 
  gi|298674403|ref|YP_003726153.1| 153 EMLDNVVYVADNCGEILLDTIvfDIIKKLGGKITLVVRGAPIL 195
                                       69***************99853389**************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2304.06
//
Query:       gi|298674404|ref|YP_003726154.1|  [L=383]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.4e-28   97.4   2.6    1.4e-27   96.2   2.6    1.5  1  OrfB_IS605      Probable transposase
    1.7e-23   82.3   0.2    3.6e-23   81.3   0.2    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    4.1e-20   71.0   1.4    9.3e-20   69.8   1.4    1.6  1  HTH_OrfB_IS605  Helix-turn-helix domain
  ------ inclusion threshold ------
      0.013   15.6   0.3       0.03   14.5   0.3    1.6  1  zf-piccolo      Piccolo Zn-finger
       0.05   13.5   1.9       0.31   10.9   0.3    2.3  2  LemA            LemA family
       0.11   12.3   7.0       0.42   10.4   4.0    2.3  2  Phage_GP20      Phage minor structural protein GP20


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.2   2.6   4.9e-31   1.4e-27      10     117 ..     180     284 ..     167     286 .. 0.91

  Alignments for each domain:
  == domain 1  score: 96.2 bits;  conditional E-value: 4.9e-31
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsr 86 
                                       +++  + +++g+D+Gi+++a++++++   ++ ++r lk+  ++l+  +++l++k+k+s+ny+k + ++a++h+k+++
  gi|298674404|ref|YP_003726154.1| 180 KQTFYEVNTVGVDVGIKDFAVTSDGE---KIDNPRYLKNSIERLKVLQKRLSRKKKGSNNYRKLKHQIAKYHEKIAN 253
                                       45555789******************...************************************************ PP

                        OrfB_IS605  87 rrkhllhklathliktlkevgvetLnvgnmk 117
                                       +r +++hkl+++li ++++v++etLnv+++ 
  gi|298674404|ref|YP_003726154.1| 254 QREDFQHKLSNKLISENQAVALETLNVKGLL 284
                                       ****************************986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.3   0.2   1.2e-26   3.6e-23       1      68 [.     298     367 ..     298     368 .. 0.98

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 1.2e-26
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpay.TSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       ++++ ++leyka++yG++++++ ++  +Sk C++Cg+ +++ +l++r+++Cp+C++ +drD+nA++Ni k
  gi|298674404|ref|YP_003726154.1| 298 WGSFVQKLEYKAEWYGKNIIKIGRFDpSSKICHVCGYYHQDlELKDREWECPDCKTIHDRDINASVNIKK 367
                                       99******************************************************************87 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.8   1.4   3.1e-23   9.3e-20       1      47 []       9      54 ..       9      54 .. 0.98

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 3.1e-23
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeegk 47
                                      M lkaykyr yP++ Q+e++a+++G++Rf+YN+aL+ +++ ye+ gk
  gi|298674404|ref|YP_003726154.1|  9 M-LKAYKYRMYPNQIQQELIAKHIGACRFIYNWALENKIKSYEQDGK 54
                                      8.******************************************997 PP

>> zf-piccolo  Piccolo Zn-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.3     1e-05      0.03      28      55 ..     326     353 ..     322     356 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1e-05
                        zf-piccolo  28 kqvCnlCGFnptphltekkeWlclnCQt 55 
                                       +++C +CG+  ++   + +eW c  C t
  gi|298674404|ref|YP_003726154.1| 326 SKICHVCGYYHQDLELKDREWECPDCKT 353
                                       79***********999**********86 PP

>> LemA  LemA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1     0.075   2.2e+02      34      82 ..      64     112 ..      42     116 .. 0.81
   2 ?   10.9   0.3    0.0001      0.31      55     108 ..     208     262 ..     180     272 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.075
                              LemA  34 leevteaRakaaeaesveekaeaenqlssalsrllavaEnYPdLkanen 82 
                                         +v +  ++  ++ + ++ + a  +l++a+ +++     +P++k+++n
  gi|298674404|ref|YP_003726154.1|  64 QIRVLKQDHEWLKEINSQSLQGATLNLENAFTKFFREKSGFPKFKSKKN 112
                                       555666666667888899999999**********************987 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0001
                              LemA  55 eaenqlssalsrllavaEnY.PdLkanenfleLqeelegtEnriavaRrrYneav 108
                                       ++ + l+++++rl +++ +   + k ++n+++L++++++  ++ia++R++++++ 
  gi|298674404|ref|YP_003726154.1| 208 DNPRYLKNSIERLKVLQKRLsRKKKGSNNYRKLKHQIAKYHEKIANQREDFQHKL 262
                                       5556677777777777776414567899***********************8765 PP

>> Phage_GP20  Phage minor structural protein GP20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.045   1.4e+02     113     136 ..      51      77 ..      27      90 .. 0.66
   2 ?   10.4   4.0   0.00014      0.42      32      95 ..     218     281 ..     205     289 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.045
                        Phage_GP20 113 edgelkg...LdeqikkLkesdkyLFe 136
                                       +dg+ +    L++qi  Lk+++++L e
  gi|298674404|ref|YP_003726154.1|  51 QDGKAISrfeLNKQIRVLKQDHEWLKE 77 
                                       444444333377777777777776654 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00014
                        Phage_GP20  32 eqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeyeakiadlkldnaielaLkeakak 95 
                                       e+lk  +k L+  kk +++  +L+ qi+++ +k++++ ++ + k+++  +++    aL++ ++k
  gi|298674404|ref|YP_003726154.1| 218 ERLKVLQKRLSRKKKGSNNYRKLKHQIAKYHEKIANQREDFQHKLSNKLISENQAVALETLNVK 281
                                       6788889999999**********************************99999988899888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1585  (0.0884043); expected 358.6 (0.02)
Passed bias filter:                      662  (0.0369234); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2756.13
//
Query:       gi|298674405|ref|YP_003726155.1|  [L=428]
Description: gluconate transporter [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-64  218.2  27.0      2e-64  218.0  27.0    1.0  1  GntP_permease   GntP family permease
    2.8e-08   33.3  26.7    4.3e-08   32.7  26.7    1.3  1  CitMHS          Citrate transporter
  ------ inclusion threshold ------
      0.011   15.9   0.6        3.2    8.0   0.0    2.7  2  Chordopox_A13L  Chordopoxvirus A13L protein
       0.16   12.1   0.0       0.16   12.1   0.0    4.7  5  AzlD            Branched-chain amino acid transport protein (


Domain annotation for each model (and alignments):
>> GntP_permease  GntP family permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.0  27.0   4.4e-68     2e-64       2     436 ..       3     422 ..       2     426 .. 0.92

  Alignments for each domain:
  == domain 1  score: 218.0 bits;  conditional E-value: 4.4e-68
                     GntP_permease   2 pllivligvilllllviklklnafvaLllvsllvglvsGmpldkvvksiekGlGgtlGslaiiiglGamlGklleds 78 
                                       p++i li++i +l++++kl++++f++L+ +s++vg++ G pld  ++s++ GlG ++ + aiii+ G ++G +l ++
  gi|298674405|ref|YP_003726155.1|   3 PVIIFLIALITVLVMTTKLRVHPFLSLITASIVVGILDGNPLDA-LNSVSLGLGRVFSQFAIIITCGSIIGLILFQT 78 
                                       68999**********************************99976.79****************************** PP

                     GntP_permease  79 GaaerialtlikklgkkkvqwalvlagfivgialFfev.glvlLiplvfaiakeakisllklgiplvaalavvhgll 154
                                       G+   ia  li+    +k  +al l gf++++++   + + v++ip+++ i+ + +i+   ++ +l  + ++   ++
  gi|298674405|ref|YP_003726155.1|  79 GGTAIIADDLIRFS--RKPLFALNLLGFLFAVPVMCSIlAYVIFIPIAKDIGSRLNIPKASVAASLGLGTLASFNMV 153
                                       ***********965..44689*************999669************************************* PP

                     GntP_permease 155 pPhPgplavaellgadiGkvllyGlivaiptviiagpllkkflkevvkeeeelaeeaeeksreekelPsfgl..sll 229
                                        P P    +ae+lga+ G++ll+Gl va+ ++i+ g  ++k+  ++ +         +e +++++ lP +    + +
  gi|298674405|ref|YP_003726155.1| 154 YPSPVIFSAAEELGANTGEILLTGLPVAVIVTIV-GYYYAKISCNFGPPPVINP---SEAEDNTQGLPRINRieAYS 226
                                       ****************************988776.6788898888887776633...34444678899886422678 PP

                     GntP_permease 230 tillPvvlmlvktiaelllpkesaalevvefiGnpvvalliallvaiytlglrrgksikkvldileealksiaiill 306
                                        i +Pv+l+l   i++       + + +++fi n  +alli +++a+     +r   ++++ + +++a++  +++ll
  gi|298674405|ref|YP_003726155.1| 227 PICIPVILILSGVIIN-------EQTPLINFISNRNIALLIGVMLAFI---SARSLGLEQIKNRTDKAVRRSGVVLL 293
                                       99*******9999886.......445689***************9975...6899********************** PP

                     GntP_permease 307 iigaGGafkqvlvdsgvgkalaellsnlelspillaflvaallrialGsatVaaltaaglvapiiaqlpgvnlallv 383
                                        + +GGa++ +l  +g+gk l++++++l+l+ i+++f+va++++ ++Gs  V++l a ++v+p + +l+     +  
  gi|298674405|ref|YP_003726155.1| 294 DMCGGGALGTTLSMTGIGKDLGQMFTTLNLPDIIIPFMVAVAIQSVQGSRIVTMLVAPSIVVPFLPELN-LPASITL 369
                                       ********************************************************************5.5556667 PP

                     GntP_permease 384 laigaGslilshvnDagFWlvkeylgltvketlktwtvletilsvvgliivll 436
                                       l++++G+ ++shvnD+ FW++ e ++l ++e ++++t+  ++++++gl+++ +
  gi|298674405|ref|YP_003726155.1| 370 LSMASGTFLISHVNDPYFWIFGELIELKTTEIFRSYTIGGVLMGFTGLVLTYI 422
                                       78889********************************************9976 PP

>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7  26.7   9.6e-12   4.3e-08       2     298 ..      14     373 ..       1     375 [. 0.61

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 9.6e-12
                                       xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................xxxxxxxxxxxxxxxx RF
                            CitMHS   2 vllilek.lrldvvallvlvllvltieealsgiaspii.......................llllgamiigaaleet 54 
                                       vl++++k +  ++ +l+++             i ++i+                       +++  + iig +l +t
  gi|298674405|ref|YP_003726155.1|  14 VLVMTTKlRVHPFLSLITA------------SIVVGILdgnpldalnsvslglgrvfsqfaIIITCGSIIGLILFQT 78 
                                       3344444422223333222............222222244444444555555558888888**************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                            CitMHS  55 Glfdrlaakllrlaggkrdllvllvlltallsafvsn.dgvvlimipivlslakrlkklppl.lliplalaanigga 129
                                       G+   +a+ l+r++++    l++l ll +l++  v     + +i+ipi+ +++ r  ++p + +  +++l+ ++  +
  gi|298674405|ref|YP_003726155.1|  79 GGTAIIADDLIRFSRK--P-LFALNLLGFLFAVPVMCsILAYVIFIPIAKDIGSR-LNIPKAsV--AASLGLGTLAS 149
                                       ***************8..3.566777777774444443555*************9.66666623..33333333333 PP

                                       xxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxx..................................... RF
                            CitMHS 130 ltpiGtpttraa........arpglslpnllllalllvgl..................................... 161
                                       + ++  +++  +        a+ g +l+ +l +a++++++                                     
  gi|298674405|ref|YP_003726155.1| 150 FNMVYPSPV--IfsaaeelgANTGEILLTGLPVAVIVTIVgyyyakiscnfgpppvinpseaedntqglprinriea 224
                                       444443333..233688888777777777777777666556666666666666666666666666666666666666 PP

                                       .....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxx..................xxxxxx RF
                            CitMHS 162 .....lplvllfmfgvalalpvnapkvkkqkaiieaiarsllpv..atillla..................ykkveW 213
                                            +p++l++                +q+ +i+ i+ + +    +++l  a                    + + 
  gi|298674405|ref|YP_003726155.1| 225 yspicIPVILIL----------SGVIINEQTPLINFISNRNIALliGVML--AfisarslgleqiknrtdkAVRRSG 289
                                       666444444443..........2223344555555555543322112222..1345666666666666533222223 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxx.xxxxxxxxxxxxxxxxxxxx.xxxx RF
                            CitMHS 214 svlllfaGvfllvgaleqtGilealadllgaggplval....alvlglial.lsafisnvavaalmapialg.mapa 284
                                        vll  +G + l++ l+ tGi++ l++++++      l    +++ +++a+ + +++++  v++l+ap ++   +p 
  gi|298674405|ref|YP_003726155.1| 290 VVLLDMCGGGALGTTLSMTGIGKDLGQMFTT------LnlpdIIIPFMVAVaIQSVQGSRIVTMLVAPSIVVpFLPE 360
                                       335668999999*****************43......223445677777887***************9876504446 PP

                                       xxxxxxxxxxxxxx RF
                            CitMHS 285 lgllspsplalala 298
                                       l+ l++s+ +l +a
  gi|298674405|ref|YP_003726155.1| 361 LN-LPASITLLSMA 373
                                       66.77777788777 PP

>> Chordopox_A13L  Chordopoxvirus A13L protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.6    0.0068        31       3      20 ..      59      76 ..      57      78 .. 0.90
   2 ?    8.0   0.0   0.00072       3.2       3      46 ..     171     213 ..     170     218 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0068
                    Chordopox_A13L  3 adlllliiCvaivglivY 20
                                      ++++++i C  i+gli++
  gi|298674405|ref|YP_003726155.1| 59 SQFAIIITCGSIIGLILF 76
                                      7899************97 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00072
                    Chordopox_A13L   3 adlllliiCvaivglivYgiYnrkketqttnpstveeyeeedni 46 
                                       +++ll  + va+++ iv   Y +++ +  ++p  +++ e edn+
  gi|298674405|ref|YP_003726155.1| 171 GEILLTGLPVAVIVTIVGYYYAKISCNFGPPPV-INPSEAEDNT 213
                                       689999***********8888888777666665.7999999987 PP

>> AzlD  Branched-chain amino acid transport protein (AzlD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   1.7      0.27   1.2e+03      68      90 ..       8      31 ..       3      40 .. 0.44
   2 ?   -0.9   0.1      0.43   1.9e+03      66      78 ..      99     111 ..      81     149 .. 0.59
   3 ?   -0.6   0.0      0.35   1.6e+03      34      49 ..     173     188 ..     156     194 .. 0.64
   4 ?   12.1   0.0   3.7e-05      0.16      30      84 ..     217     271 ..     206     275 .. 0.88
   5 ?    1.5   0.3     0.072   3.2e+02      26      55 ..     321     356 ..     299     382 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.27
                              AzlD 68 llaalvavlvalltr.nlllsilv 90
                                      l+a+++++++  + r + +ls ++
  gi|298674405|ref|YP_003726155.1|  8 LIALITVLVMTTKLRvHPFLSLIT 31
                                      333444444333333334444444 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.43
                              AzlD  66 arllaalvavlva 78 
                                        +ll++l+av v+
  gi|298674405|ref|YP_003726155.1|  99 LNLLGFLFAVPVM 111
                                       4444444443332 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.35
                              AzlD  34 rllryvPiavLaalia 49 
                                        ll  +P+av++ ++ 
  gi|298674405|ref|YP_003726155.1| 173 ILLTGLPVAVIVTIVG 188
                                       4566788888888875 PP

  == domain 4  score: 12.1 bits;  conditional E-value: 3.7e-05
                              AzlD  30 pwlqrllryvPiavLaaliapellaetgklsaslglarllaalvavlvalltrnl 84 
                                       p+++r+  y Pi++ ++li+  ++ ++++   ++   r +a+l++v++a+++ + 
  gi|298674405|ref|YP_003726155.1| 217 PRINRIEAYSPICIPVILILSGVIINEQTPLINFISNRNIALLIGVMLAFISARS 271
                                       78999************************99999999999999999999988754 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.072
                              AzlD  26 lklppwlqrllryvPi......avLaaliapellae 55 
                                       l+lp+ +  ++ +v+i       + ++l+ap+++ +
  gi|298674405|ref|YP_003726155.1| 321 LNLPDIIIPFMVAVAIqsvqgsRIVTMLVAPSIVVP 356
                                       455555555555555555555567777888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2967.41
//
Query:       gi|298674406|ref|YP_003726156.1|  [L=525]
Description: choline/carnitine/betaine transporter [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.3e-194  647.2  48.1   1.4e-194  647.1  48.1    1.0  1  BCCT      BCCT, betaine/carnitine/choline family transporter


Domain annotation for each model (and alignments):
>> BCCT  BCCT, betaine/carnitine/choline family transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  647.1  48.1    8e-199  1.4e-194       1     484 [.       9     491 ..       9     492 .. 0.99

  Alignments for each domain:
  == domain 1  score: 647.1 bits;  conditional E-value: 8e-199
                              BCCT   1 vflvslliivlfvllalvfpealeevlsslnswilekfgwlylllvllflvfllvlafskygkikLGkddekpefst 77 
                                       vf+vs+++iv+fv+l+ +f+e +++++++l++ i+++fgw+y+l+v++fl+f+++l++s+yg+ikLGkdd+ p fs+
  gi|298674406|ref|YP_003726156.1|   9 VFFVSATVIVMFVVLGSLFTEFMKQFFNTLQNSIISYFGWFYILSVAFFLIFIIWLYLSPYGNIKLGKDDDVPVFSN 85 
                                       89*************************************************************************** PP

                              BCCT  78 lsWfamlfaaglgigllfwgvaEplahylspppgaeagteeaaqeAlaytffhwGlhaWaiyalvalalayfayrkg 154
                                       +sWfamlf+ag+gigllf++vaEp+ h+ +pp g ++++ eaa++A+++tffhwGlhaWaiy++++l layf yr++
  gi|298674406|ref|YP_003726156.1|  86 TSWFAMLFSAGMGIGLLFYSVAEPVLHFSNPPGGIAPESIEAAKQAINLTFFHWGLHAWAIYIIIGLSLAYFGYRHD 162
                                       ******************************99999****************************************** PP

                              BCCT 155 lpltissalypllgeringllgkvvDvlavlatvfGvatslGlgvlqinaglselfgieesltvqlaiivvitalat 231
                                       lpl+i+s+lyp++g+ri+g++g++v+v+a+++tvfGvatslGlgvlqin+gl++l  ++es++ q+++i+ it++at
  gi|298674406|ref|YP_003726156.1| 163 LPLSIRSTLYPMIGDRIYGFIGNIVEVMAIFGTVFGVATSLGLGVLQINSGLNYLGVLPESTFNQILLIIGITLAAT 239
                                       ***************************************************************************** PP

                              BCCT 232 vsavsGldkGikrlSnlnlvlalllllfvllvGptlfilntfvqslgdylqnlvalslatdaaeeaeewlasWTvFy 308
                                       +s+vsGl kGi++lS++nl++ +ll++f+++vGpt+f+l++fvq++gdylqnl++l+++tda++  e w++sWT+F+
  gi|298674406|ref|YP_003726156.1| 240 MSVVSGLTKGIRILSEMNLAFGFLLMMFIIIVGPTIFLLSSFVQGMGDYLQNLISLTFNTDAYQGIE-WQKSWTMFF 315
                                       ****************************************************************998.********* PP

                              BCCT 309 WawwiawapfvGlFiAriSrGRtiRefilgvllvptlvtflwftvlGgtaielelegeaelaeaaeasveaalfall 385
                                       W+wwi+w+pfvG+FiAriSrGRtiRefi g+l+vpt+vtf+w++ +G+ta+++el g++ l++++++sv+ +lfall
  gi|298674406|ref|YP_003726156.1| 316 WGWWISWSPFVGMFIARISRGRTIREFIRGILIVPTIVTFIWVIAFGNTALYIELFGSGGLVQIVSESVPISLFALL 392
                                       ***************************************************************************** PP

                              BCCT 386 eqlplgsilsvlavvliiiffvTsaDSatlvlatltsggdenpprkqrvfWgvllgavaavlllagglealqsasii 462
                                       e+lpl+ ++s+la+v++++ffvTsaDS++lv++ l++ggd +p++ qrvfW++ +gavaavlll+ggl+alq+a+i+
  gi|298674406|ref|YP_003726156.1| 393 ENLPLTVLTSTLATVVVATFFVTSADSGSLVVCILATGGDPEPSVYQRVFWAFSQGAVAAVLLLTGGLAALQTAAIT 469
                                       ***************************************************************************** PP

                              BCCT 463 aalPftlvlllmvvsllkalre 484
                                       +alPf++++l+m+ sl+k lr+
  gi|298674406|ref|YP_003726156.1| 470 TALPFCIIMLFMCRSLVKGLRA 491
                                       ******************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (525 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1154  (0.064365); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.72u 0.34s 00:00:01.06 Elapsed: 00:00:00.51
# Mc/sec: 3118.44
//
Query:       gi|298674407|ref|YP_003726157.1|  [L=71]
Description: hypothetical protein Metev_0445 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-39  134.5   5.1    1.2e-39  134.3   5.1    1.0  1  DUF5371   Family of unknown function (DUF5371)


Domain annotation for each model (and alignments):
>> DUF5371  Family of unknown function (DUF5371)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.3   5.1   6.8e-44   1.2e-39       1      65 []       1      65 [.       1      65 [. 0.99

  Alignments for each domain:
  == domain 1  score: 134.3 bits;  conditional E-value: 6.8e-44
                           DUF5371  1 mvKivHAqtvLaeeeLeeLKkKtnesstkdAlsiAveHYleCeYtdlneemwtkKlEkvvqKKkk 65
                                      mvKivHAqtvLaee+L++LK+K+n sstkdAlsiAv+HYleCeYt+++++mwt+KlEkv+qKK++
  gi|298674407|ref|YP_003726157.1|  1 MVKIVHAQTVLAEEDLNSLKEKCNVSSTKDALSIAVQHYLECEYTNTDDDMWTHKLEKVMQKKNQ 65
                                      89*************************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1079  (0.0601818); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 550.35
//
Query:       gi|298674408|ref|YP_003726158.1|  [L=165]
Description: hypothetical protein Metev_0446 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-25   88.5   3.2      4e-25   88.5   3.2    1.6  2  Pilin_N   Archaeal Type IV pilin, N-terminal
  ------ inclusion threshold ------
      0.015   15.0   0.2      0.021   14.5   0.2    1.2  1  MtrD      Tetrahydromethanopterin S-methyltransferase, subuni


Domain annotation for each model (and alignments):
>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.5   3.2   4.5e-29     4e-25       1      79 [.      14      91 ..      14      93 .. 0.86
   2 ?   -1.9   0.0      0.75   6.7e+03      29      29 ..     132     132 ..      96     158 .. 0.65

  Alignments for each domain:
  == domain 1  score: 88.5 bits;  conditional E-value: 4.5e-29
                           Pilin_N  1 eAVSpViGviLmvaitvIlaAviaafvlglasneekapqasievkidssastgknavslehkgGdsidt..kdlkivln 77
                                      +AVSpViGviLmvaitvIlaAvi++fv+g+ + +e+apqasi  + ++ +s  +n++++eh+gG+ i++  +++ki++ 
  gi|298674408|ref|YP_003726158.1| 14 DAVSPVIGVILMVAITVILAAVIGSFVFGM-GSPEQAPQASIRGSAETIDS--NNSIKIEHQGGEGIELdsASTKITVA 89
                                      69****************************.9**********666555554..356***********996677788877 PP

                           Pilin_N 78 se 79
                                      ++
  gi|298674408|ref|YP_003726158.1| 90 GD 91
                                      65 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.75
                           Pilin_N  29 g 29 
                                       g
  gi|298674408|ref|YP_003726158.1| 132 G 132
                                       2 PP

>> MtrD  Tetrahydromethanopterin S-methyltransferase, subunit D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2   2.3e-06     0.021      72     127 ..      17      78 ..       8      91 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.3e-06
                              MtrD  72 sGavgamlmlaitmlvgnli..yvygvGvva....asakvekdpitgdkqekyvsqGteGhg 127
                                       s  +g  lm+ait++++ +i  +v+g+G +     as + + + i  ++  k   qG eG  
  gi|298674408|ref|YP_003726158.1|  17 SPVIGVILMVAITVILAAVIgsFVFGMGSPEqapqASIRGSAETIDSNNSIKIEHQGGEGIE 78 
                                       66799************998779*****8751111555566677777777777777777755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1020  (0.0568911); expected 358.6 (0.02)
Passed bias filter:                      711  (0.0396564); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 978.18
//
Query:       gi|298674409|ref|YP_003726159.1|  [L=185]
Description: nuclease [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-26   93.3   0.1    1.5e-26   92.9   0.1    1.1  1  SNase     Staphylococcal nuclease homologue


Domain annotation for each model (and alignments):
>> SNase  Staphylococcal nuclease homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.9   0.1   8.6e-31   1.5e-26       1     106 [.      62     179 ..      62     181 .. 0.95

  Alignments for each domain:
  == domain 1  score: 92.9 bits;  conditional E-value: 8.6e-31
                                       EEEETTEE-STSSBTTT...........TTSTTHHHHHHHHHHHHHHCSSEEEEE-S..SBSTTSEEEEEEEET.TE CS
                             SNase   1 kvrLvgidaPetakpkk...........tvqpfgkeAkeflkklvlqkkvvvleldk..kkDkygrllayvyln.kk 63 
                                       +vrL+g+d+Pet+  +k           +++++g +A++++++ +  k+v+++ +d+  ++++ygrllayvyl+ ++
  gi|298674409|ref|YP_003726159.1|  62 RVRLLGVDTPETHAENKpeefegidndsYLHEWGVKANNYTSNILEDKEVRLEYDDIsdRRGYYGRLLAYVYLKnDT 138
                                       79***********9999*****************************99999999999999*************9899 PP

                                       EHHHHHHHTTSSEE---BTTSTTTHHHHHHHHHHHHHTT-GGG CS
                             SNase  64 nineeLvkeGlArvyevyekneekkkellkaeeeAkkkrkglW 106
                                       + n  L+k+G+Arvy     + e+ +e+l++e+eA++++kglW
  gi|298674409|ref|YP_003726159.1| 139 MYNRMLIKDGYARVYDEA--EIEYMDEFLELEKEARENKKGLW 179
                                       9************87744..579******************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1224.48
//
Query:       gi|298674410|ref|YP_003726160.1|  [L=147]
Description: hypothetical protein Metev_0449 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.015   15.1   0.4      0.025   14.4   0.4    1.4  1  Acetyltransf_16  GNAT acetyltransferase, Mec-17


Domain annotation for each model (and alignments):
>> Acetyltransf_16  GNAT acetyltransferase, Mec-17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.4   1.4e-06     0.025     148     175 .]     107     134 ..      98     134 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.4e-06
                                       HHHHHHHHH---SEE--SSSEEEEGGGT CS
                   Acetyltransf_16 148 llsFlekhynlkktvpqvnnFvvfegff 175
                                       ++s ++ +y+lk+++ +v+n+++f+ +f
  gi|298674410|ref|YP_003726160.1| 107 MVSIIKEKYGLKTYIYKVDNYIIFDTYF 134
                                       788899*********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 965.24
//
Query:       gi|298674411|ref|YP_003726161.1|  [L=88]
Description: hypothetical protein Metev_0450 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.017   15.2   0.2      0.019   15.0   0.2    1.1  1  DUF3939   Protein of unknown function (DUF3939)


Domain annotation for each model (and alignments):
>> DUF3939  Protein of unknown function (DUF3939)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.2   1.1e-06     0.019      52      94 ..      18      56 ..       8      84 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-06
                           DUF3939 52 kqkFymskeTfeifeeeekdivkeiDkvQkAvdqYvkeekklP 94
                                      + ++ m ++ + ++ee++ di+ ++  +Q+A+d+Y k++   P
  gi|298674411|ref|YP_003726161.1| 18 NSPYPMEQNAYFLVEEDDVDIA-IVNDIQEAIDEYKKNN---P 56
                                      566779999*********9986.67789*******7765...4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 597.42
//
Query:       gi|298674412|ref|YP_003726162.1|  [L=40]
Description: hypothetical protein Metev_0451 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 282.38
//
Query:       gi|298674413|ref|YP_003726163.1|  [L=545]
Description: phage/plasmid primase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-16   61.4   0.6    2.2e-16   60.5   0.6    1.5  1  D5_N             D5 N terminal like
      7e-08   32.9   2.9    1.3e-07   32.0   0.1    2.6  3  Pox_D5           Poxvirus D5 protein-like
    0.00018   22.1   0.0     0.0013   19.3   0.0    2.3  2  RFX_DNA_binding  RFX DNA-binding domain
  ------ inclusion threshold ------
       0.11   11.6   3.9       0.52    9.4   1.3    2.4  2  Adenyl_transf    Streptomycin adenylyltransferase


Domain annotation for each model (and alignments):
>> D5_N  D5 N terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.5   0.6   4.9e-20   2.2e-16      55     149 ..     172     264 ..     103     266 .. 0.87

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 4.9e-20
                              D5_N  55 aksalkalkkfakssrskkkvdnvlreaaelprldleideldadplllafaNGvldlktgelrdhepedyltkitpv 131
                                        +++ k+ ++++ ++  k+ +++v++++++     ++ + ++ +++ ++ +NG +d ++g++ +h+p+++ t ++pv
  gi|298674413|ref|YP_003726163.1| 172 IDEISKQVQDKLDEHYRKSYKKEVIDYIKTK--ALVDRESINNNKYIINLKNGLYDVSKGKFLPHSPKYMSTIQLPV 246
                                       4677888889999999*************99..******************************************** PP

                              D5_N 132 dydpdadcptfkewlddi 149
                                        y+p+a+cp ++++l d+
  gi|298674413|ref|YP_003726163.1| 247 YYKPEAECPNIEKFLSDV 264
                                       ***************997 PP

>> Pox_D5  Poxvirus D5 protein-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.7   7.7e+03      55      78 ..     143     170 ..     137     177 .. 0.70
   2 ?   -0.4   0.2      0.38   1.7e+03      45      78 ..     171     207 ..     159     215 .. 0.63
   3 !   32.0   0.1   2.9e-11   1.3e-07       3      56 ..     472     523 ..     470     536 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.7
                            Pox_D5  55 kileeg..fekkkkk..kgqqpneyley 78 
                                       +il e+  f+ k +k  +++q+ +yl++
  gi|298674413|ref|YP_003726163.1| 143 EILRENhfFTLKDTKevYYYQNGVYLPN 170
                                       4666645788888887777777777765 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.38
                            Pox_D5  45 skrtFqkrlkkileegfekkkkk...kgqqpneyley 78 
                                       +  +  k+ +  l e+++k  kk   ++ +++  +  
  gi|298674413|ref|YP_003726163.1| 171 GIDEISKQVQDKLDEHYRKSYKKeviDYIKTKALVDR 207
                                       5556667778888888888888855545555554444 PP

  == domain 3  score: 32.0 bits;  conditional E-value: 2.9e-11
                            Pox_D5   3 nDpvldFveelfeeekstrvpsdvlYeaYkafcekngykpvlskrtFqkrlkki 56 
                                       ++pv++F++e++  e  +++ +  +Y+aY ++cek++++p l+k++F+k++k+ 
  gi|298674413|ref|YP_003726163.1| 472 SNPVAKFADECVG-ESNEYTFKVDMYNAYVEWCEKEDIVP-LKKNEFGKQFKNL 523
                                       79*********99.6777888899****************.**********975 PP

>> RFX_DNA_binding  RFX DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.64   2.9e+03       7      40 ..     106     139 ..     101     144 .. 0.80
   2 !   19.3   0.0   2.8e-07    0.0013      21      75 ..     491     542 ..     479     545 .] 0.79

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.64
                   RFX_DNA_binding   7 wlnanfeeaedvsvprqevYaeYlsicsklklkp 40 
                                        + + +e+ e +  ++++ Y++Y s   k  +k 
  gi|298674413|ref|YP_003726163.1| 106 IIDEVLENTEPTRAKKDDPYNKYFSKKGKFVVKY 139
                                       6788899999999999*******98877766665 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 2.8e-07
                   RFX_DNA_binding  21 prqevYaeYlsicsklklkplnaasFgKlirsvFpnvktrRLgtrgqskYhyvGi 75 
                                        + ++Y+ Y++ c+k+++ pl++ +FgK  +++    +  RL+  g  +Y++ G+
  gi|298674413|ref|YP_003726163.1| 491 FKVDMYNAYVEWCEKEDIVPLKKNEFGKQFKNL--GYRDSRLN-TGDRSYCWDGV 542
                                       5789************************87765..45555884.47777877776 PP

>> Adenyl_transf  Streptomycin adenylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.021        96     112     175 ..      10      73 ..       4      85 .. 0.72
   2 ?    9.4   1.3   0.00012      0.52     204     277 ..     126     200 ..     104     202 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.021
                                       HHH-----..--EEEESS--S-------GGGTEE----HHHHHHHHHHHHHHHHHHHHHHHTT-HH CS
                     Adenyl_transf 112 evleedsl..vkvLlDKdgllkelpepsdedylvkkPseqeFedccneFwwvstyVakglwRkell 175
                                       ++ +ed+   +k+  DK+  ++++p+ +  +    + +++ F++ cn +  ++ y   g +R+ ++
  gi|298674413|ref|YP_003726163.1|  10 NYSTEDKTtySKITNDKKVETSNIPDLTVMK--RCRQNNEFFDSLCNGYITELGYTQEGAVREFIT 73 
                                       4444444423777778877777776666555..55557899********************99776 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00012
                                       EEE--GGGTTGGGTS-HHHHHH.HHTT---SSHHHHHHHHHHHHHHHHHHHHHHHHHHT----.SHHHHHHHHHH CS
                     Adenyl_transf 204 svsvgkngkylkkyLeeelwek.llktysdsdyeeiwealfkmlelFrelakevaeklgyeypeeedekvskYlk 277
                                       +    k+gk++ kyL ee+ ++    t++d++     ++ +   +  +e++k+v +kl+ +y+++++++v +Y+k
  gi|298674413|ref|YP_003726163.1| 126 NKYFSKKGKFVVKYLAEEILREnHFFTLKDTKEVYYYQNGVYLPNGIDEISKQVQDKLDEHYRKSYKKEVIDYIK 200
                                       556789***********998651344555555555678888889999**************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (545 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 3527.66
//
Query:       gi|298674414|ref|YP_003726164.1|  [L=709]
Description: signal transduction histidine kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-42  144.5  10.1    1.1e-12   48.2   0.3    5.0  5  PAS_9            PAS domain
    3.6e-41  139.9   0.0    5.6e-21   74.8   0.0    4.5  4  PAS_4            PAS fold
    6.2e-32  109.9   0.0    1.6e-08   34.5   0.0    4.6  4  PAS              PAS fold
    2.1e-29  101.4   1.5    2.1e-29  101.4   1.5    2.5  1  HisKA_2          Histidine kinase
    1.6e-20   72.7   0.0    4.3e-06   26.6   0.2    4.5  4  PAS_8            PAS domain
    6.1e-12   45.7   0.4    2.3e-05   24.6   0.0    4.9  5  PAS_3            PAS fold
    1.4e-07   32.0   0.3    3.9e-06   27.3   0.0    3.1  2  HATPase_c        Histidine kinase-, DNA gyrase B-, and HSP90-
    6.9e-06   26.7   1.8    7.3e-06   26.6   0.0    2.0  1  HWE_HK           HWE histidine kinase
    4.2e-05   23.9   1.9      0.023   15.1   0.0    3.7  3  sCache_3_3       Single cache domain 3
    5.3e-05   22.6   5.2    0.00074   18.9   0.1    3.0  3  Cache_3-Cache_2  Cache 3/Cache 2 fusion domain
      8e-05   23.2   0.7       0.26   11.9   0.0    3.9  3  PAS_10           PAS domain
    0.00031   20.9   2.1        6.7    6.9   0.2    4.7  4  PAS_7            PAS fold
    0.00032   20.8   0.1       0.68   10.1   0.0    3.1  2  sCache_3_2       Single cache domain 3
     0.0011   18.9   0.0     0.0028   17.6   0.0    1.6  1  HATPase_c_2      Histidine kinase-like ATPase domain
     0.0013   18.8   0.2        1.9    8.7   0.0    2.8  3  PAS_11           PAS domain
     0.0066   16.1   0.3       0.58    9.8   0.0    3.3  3  PAS_12           UPF0242 C-terminal PAS-like domain
  ------ inclusion threshold ------
        6.6    7.2  13.2        8.3    6.9   0.7    3.7  3  YgaB             YgaB-like protein


Domain annotation for each model (and alignments):
>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.1e-05     0.012      13     104 .]      23     105 ..       5     105 .. 0.82
   2 !   42.6   0.5   5.5e-14   5.8e-11       2     104 .]     129     228 ..     128     228 .. 0.89
   3 !   40.7   0.0   2.1e-13   2.2e-10       6     104 .]     256     355 ..     251     355 .. 0.85
   4 !   48.2   0.3     1e-15   1.1e-12       7     104 .]     384     476 ..     378     476 .. 0.92
   5 ?   -2.7   0.0       6.7   7.1e+03      48      80 ..     675     707 ..     661     708 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.1e-05
                             PAS_9  13 ilyaNeaalrllGyspeevlgksitdlf.vtdpeanerlraaleqgrkkerevevvlirkngetfwvlltaspvkdd 88 
                                       i+++N+a + ++G ++ ev+g++ ++++ +++p   ++ +++ e+g+  +  +e+ +   +    +  +++s++  +
  gi|298674414|ref|YP_003726164.1|  23 ITDCNPAYESIIGLKRHEVIGQKASEVYgAGEPPYLSTYAKVAETGE--QTYFETYFPPFDK---Y--FKISAISPE 92 
                                       56***************************999999999999999999..9999998888887...6..455556445 PP

                             PAS_9  89 dgelvgiivilrDite 104
                                       +g++v    i++Dite
  gi|298674414|ref|YP_003726164.1|  93 KGKFV---TIFNDITE 105
                                       66655...58999987 PP

  == domain 2  score: 42.6 bits;  conditional E-value: 5.5e-14
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetf 76 
                                       d+ ++ + +g+il++Ne+a + lGys++e+l  +i+d+   ++++  n+++ ++ e+g+   + +e v+i++ng+++
  gi|298674414|ref|YP_003726164.1| 129 DALFVGDLEGNILDVNETAVKRLGYSKQELLSMNIKDIDelYDEDGINDNILNLPENGK---QKFESVHITNNGTRI 202
                                       56777669*********************999996666655588888999988888888...9************** PP

                             PAS_9  77 wvlltaspvkdddgelvgiivilrDite 104
                                       +v+++   +k ++++ v+  +++r+it+
  gi|298674414|ref|YP_003726164.1| 203 PVEINSNLIKYKEKTAVL--SVVRNITD 228
                                       **********99999999..******96 PP

  == domain 3  score: 40.7 bits;  conditional E-value: 2.1e-13
                             PAS_9   6 idnpdgrilyaNeaalrllGyspeevlgksitdlf...vtdpeanerlraaleqgrkkerevevvlirkngetfwvl 79 
                                       + +++ + l aN+a++++ G+s e + gk+ +d++   + ++++ ++ + +  ++  + ++ e  +++++ge  w+l
  gi|298674414|ref|YP_003726164.1| 256 LKDSKLNYLTANDAFCKVVGFSIENIKGKNDFDFLpekEAEKYRSDDTSVMESRK--PIYNLEEKYTTSEGEIRWAL 330
                                       5567888999*************************77555555555555555555..5******************* PP

                             PAS_9  80 ltaspvkdddgelvgiivilrDite 104
                                        + +p +d++g+++gi++ + Dite
  gi|298674414|ref|YP_003726164.1| 331 TSKVPYFDTEGNVIGIVGSSLDITE 355
                                       ************************8 PP

  == domain 4  score: 48.2 bits;  conditional E-value: 1e-15
                             PAS_9   7 dnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwvllt 81 
                                        + +g+il++N+aa +++G + ++++g+++  l+  +++  +n+ + +++++g+   +e++v++++k       +++
  gi|298674414|ref|YP_003726164.1| 384 HDLEGKILWCNKAATKFTGLNCRDMIGQYCYKLLynKSEICDNCPIYEIVKTGK--HYEETVTFTNK-----ILNVK 453
                                       56899*****************************99999999999999999999..***********.....778** PP

                             PAS_9  82 aspvkdddgelvgiivilrDite 104
                                         pv++++g ++gii + +Dit+
  gi|298674414|ref|YP_003726164.1| 454 KDPVRNTSGDIIGIITVTNDITD 476
                                       *********************96 PP

  == domain 5  score: -2.7 bits;  conditional E-value: 6.7
                             PAS_9  48 erlraaleqgrkkerevevvlirkngetfwvll 80 
                                       ++l  +l +    + +++ +  + ng++f +++
  gi|298674414|ref|YP_003726164.1| 675 NTLGLQLVNSLVDQINGDFEAETINGTKFVIEF 707
                                       444444444444578888899999999998765 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   1.8e-07   0.00019      15     107 ..      21     105 ..      19     108 .. 0.89
   2 !   11.8   0.0    0.0002      0.21       1     109 [.     124     230 ..     124     231 .. 0.77
   3 !   74.8   0.0   5.3e-24   5.6e-21       1     110 []     247     358 ..     247     358 .. 0.98
   4 !   26.2   0.0   7.1e-09   7.5e-06       1     109 [.     374     478 ..     374     479 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.8e-07
                             PAS_4  15 grvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgeerhyelrllPlrde 91 
                                       + ++++N+a+++++g+ ++e++G++  e++ +   +++ + +++v+e++e  +f+++  +   ++++ ++++    e
  gi|298674414|ref|YP_003726164.1|  21 YLITDCNPAYESIIGLKRHEVIGQKASEVYGA-GEPPYLSTYAKVAETGEQTYFETYFPP--FDKYFKISAISP--E 92 
                                       56899*************************99.999*****************9997666..899999999777..6 PP

                             PAS_4  92 sGevigvlvisrDiTe 107
                                       +G+   ++ i+ DiTe
  gi|298674414|ref|YP_003726164.1|  93 KGK---FVTIFNDITE 105
                                       788...9999999998 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0002
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pg 76 
                                       +ds+ dal+v d +g++l++N++a + +g++ +ell +   ++    d +++ +++  + e ++  +f+ ++ + +g
  gi|298674414|ref|YP_003726164.1| 124 FDSMEDALFVGDLEGNILDVNETAVKRLGYSKQELLSMNIKDIDELYDEDGINDNILNLPENGKQ-KFESVHITnNG 199
                                       7999*********************************9999864444778888888888777744.44444444488 PP

                             PAS_4  77 eerhyelrllPlrdesGevigvlvisrDiTerr 109
                                        + ++e++ + ++  + +  +vl ++r iT+r+
  gi|298674414|ref|YP_003726164.1| 200 TRIPVEINSNLIKYKEKT--AVLSVVRNITDRK 230
                                       888888888777654444..7777777777776 PP

  == domain 3  score: 74.8 bits;  conditional E-value: 5.3e-24
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll..p 75 
                                       l+s+p++++ +d+ +++l aN a+++++g++ e + Gk ++++lpe  a+ ++++++ v+e+++pi+ lee  +  +
  gi|298674414|ref|YP_003726164.1| 247 LSSTPAYVYLKDSKLNYLTANDAFCKVVGFSIENIKGKNDFDFLPEKEAEKYRSDDTSVMESRKPIYNLEEKYTtsE 323
                                       6799*****************************************************************999999** PP

                             PAS_4  76 geerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                       ge r+ +++++P +d++G vig+++ s DiTer+r
  gi|298674414|ref|YP_003726164.1| 324 GEIRWALTSKVPYFDTEGNVIGIVGSSLDITERKR 358
                                       *********************************97 PP

  == domain 4  score: 26.2 bits;  conditional E-value: 7.1e-09
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       l+s+++++++ d +g++l++N+aa +  g+   +++G+ ++ ll   +     +++ + +++++++e++ + +    
  gi|298674414|ref|YP_003726164.1| 374 LNSTSEIVVYHDLEGKILWCNKAATKFTGLNCRDMIGQYCYKLLYNKSEICDNCPIYEIVKTGKHYEETVTFTN--- 447
                                       67899999999******************************877764333334566677777788887776666... PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerr 109
                                        +++++ + P+r++sG++ig++ ++ DiT+r+
  gi|298674414|ref|YP_003726164.1| 448 -KILNVKKDPVRNTSGDIIGIITVTNDITDRV 478
                                       .9****************************97 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   4.4e-05     0.046      22      50 ..      22      50 ..      19      70 .. 0.89
   2 !   24.6   0.0   1.8e-08   1.9e-05       6     101 ..     123     216 ..     118     226 .. 0.71
   3 !   34.5   0.0   1.5e-11   1.6e-08       4     111 ..     244     351 ..     241     353 .. 0.95
   4 !   31.5   0.0   1.3e-10   1.4e-07       2     113 .]     369     474 ..     368     474 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.4e-05
                                      BEEEECHHHHHHHSSTHHHCTTSBGGGGB CS
                               PAS 22 rilyvNaaaeellGlsreevlgkslldli 50
                                       i+ +N+a+e++ Gl+r ev+g++ ++++
  gi|298674414|ref|YP_003726164.1| 22 LITDCNPAYESIIGLKRHEVIGQKASEVY 50
                                      5999*******************998876 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 1.8e-08
                                       HHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEEEC CS
                               PAS   6 ileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda.elaelleqlleqgeesrageisfkl 81 
                                       +++s+ d+ fv D  g+il vN++a + lG+s +e+l+ ++  +i e +d+   ++ +++l e+g+++    + ++ 
  gi|298674414|ref|YP_003726164.1| 123 LFDSMEDALFVGDLEGNILDVNETAVKRLGYSKQELLSMNIK-DIDELYDEdGINDNILNLPENGKQKFE-SVHITN 197
                                       7899*************************************9.666655544444444444444433333.333344 PP

                                       TTSSEEEEEEEEEEEEETTE CS
                               PAS  82 rdgrpihlevraspvrdagg 101
                                        +g+ i++e++ + +  +++
  gi|298674414|ref|YP_003726164.1| 198 -NGTRIPVEINSNLIKYKEK 216
                                       .8899999999887766655 PP

  == domain 3  score: 34.5 bits;  conditional E-value: 1.5e-11
                                       HHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEE CS
                               PAS   4 raileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfk 80 
                                       +a+l+s+p+ + + D + + l +N+a+++  G+s e + gk+ +d+++e++ ++ ++  + ++e++++  + e + +
  gi|298674414|ref|YP_003726164.1| 244 KALLSSTPAYVYLKDSKLNYLTANDAFCKVVGFSIENIKGKNDFDFLPEKEAEKYRSDDTSVMESRKPIYNLEEKYT 320
                                       6899*********************************************998899999999**************** PP

                                       CTTSSEEEEEEEEEEEEETTEEEEEEEEEEE CS
                               PAS  81 lrdgrpihlevraspvrdaggeilgflgvlr 111
                                       +  g+++++++  +p++d +g+++g++g   
  gi|298674414|ref|YP_003726164.1| 321 TSEGEIRWALTSKVPYFDTEGNVIGIVGSSL 351
                                       **************************99655 PP

  == domain 4  score: 31.5 bits;  conditional E-value: 1.3e-10
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       + ra+l+s+ + ++  D  g+il++N+aa++++Gl++ +++g+  + l+        ++++  ++   e  ++g++ 
  gi|298674414|ref|YP_003726164.1| 369 EKRALLNSTSEIVVYHDLEGKILWCNKAATKFTGLNCRDMIGQYCYKLLY------NKSEICDNCPIYEIVKTGKHY 439
                                       679**********************************************6......778888888888888888888 PP

                                       EECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  79 fklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       ++++  + + l v   pvr+ +g i+g++ v +di
  gi|298674414|ref|YP_003726164.1| 440 EETVTFTNKILNVKKDPVRNTSGDIIGIITVTNDI 474
                                       8888888899*****************99999987 PP

>> HisKA_2  Histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.4   1.5     2e-32   2.1e-29       1      75 [.     519     593 ..     519     594 .. 0.98

  Alignments for each domain:
  == domain 1  score: 101.4 bits;  conditional E-value: 2e-32
                           HisKA_2   1 EihHRvkNnLqvisslLslqarkakdeevkealresqnRvlsialiheeLyksedletvdfseylekLvenlfks 75 
                                       E+hHR+kNnLqvisslLslq++k++d+evk+a+ ++qnRv+s++l+h++Ly++++le+v+ ++y+e+Lv++l+ +
  gi|298674414|ref|YP_003726164.1| 519 ELHHRIKNNLQVISSLLSLQSEKFTDDEVKDAFIDTQNRVKSMSLVHNKLYQTKGLENVNSKDYIEDLVDHLVGL 593
                                       99*********************************************************************9876 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   8.4e-05     0.088      17      54 ..      12      56 ..       1      69 [. 0.66
   2 !   26.6   0.2   4.1e-09   4.3e-06       4      56 ..     121     173 ..     118     183 .. 0.85
   3 !    7.0   0.0    0.0056       5.9       7      48 ..     247     285 ..     243     304 .. 0.62
   4 !   19.9   0.0   5.2e-07   0.00054       4      48 ..     371     416 ..     370     429 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.4e-05
                             PAS_8 17 vd.lgd....rivdvNqaalellGys.adlkgellg.qllpvlrp 54
                                      +d  g     +i+d+N+a++ + G++  +++g++   +++ + +p
  gi|298674414|ref|YP_003726164.1| 12 YDkKGSpvdyLITDCNPAYESIIGLKrHEVIGQKASeVYGAGEPP 56
                                      44333366667*************998889888876555555555 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 4.1e-09
                             PAS_8   4 ralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellgqllpvlrpll 56 
                                         lf+s+ d+++v d +g+ i+dvN++a + lGys ++l+ + + +++++l+++ 
  gi|298674414|ref|YP_003726164.1| 121 NYLFDSMEDALFVGDlEGN-ILDVNETAVKRLGYSkQELLSMNI-KDIDELYDED 173
                                       579*********9785666.***************999999888.8888888775 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0056
                             PAS_8   7 fesspdgiavvdlgd..rivdvNqaalellGys.adlkgellgql 48 
                                       + s p  + + d     + + +N+a+++  G+s + +kg    + 
  gi|298674414|ref|YP_003726164.1| 247 LSSTPAYVYLKD--SklNYLTANDAFCKVVGFSiENIKG----KN 285
                                       555566666444..2346899**********88444444....33 PP

  == domain 4  score: 19.9 bits;  conditional E-value: 5.2e-07
                             PAS_8   4 ralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgql 48 
                                       ral++s ++ ++  dl ++i+++N+aa +++G++  d++g+ + +l
  gi|298674414|ref|YP_003726164.1| 371 RALLNSTSEIVVYHDLEGKILWCNKAATKFTGLNcRDMIGQYCYKL 416
                                       899*********8885555*********************998655 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.093        98       2      22 ..      24      44 ..      23      76 .. 0.81
   2 !   11.0   0.0   0.00039      0.41       2      80 ..     141     216 ..     140     223 .. 0.85
   3 !   24.6   0.0   2.2e-08   2.3e-05       2      87 ..     264     348 ..     263     350 .. 0.96
   4 ?   -1.0   0.0       2.1   2.2e+03       2      31 ..     391     418 ..     390     448 .. 0.67
   5 ?   -1.0   0.1       2.1   2.3e+03      34      65 ..     476     509 ..     475     518 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.093
                             PAS_3  2 iyvserveeilGyspeellgk 22
                                      + +++++e i+G+ ++e++g+
  gi|298674414|ref|YP_003726164.1| 24 TDCNPAYESIIGLKRHEVIGQ 44
                                      679***************998 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00039
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvird 77 
                                       + v+e+  + lGys++ell+   +++d+    D + +++++ ++ ++g+ ++  e   ++ +G+ + ve   + i++
  gi|298674414|ref|YP_003726164.1| 141 LDVNETAVKRLGYSKQELLSM--NIKDIDELYDEDGINDNILNLPENGKqKF--ESVHITNNGTRIPVEINSNLIKY 213
                                       6799999**************..9****9999*************9999555..55559999999999999999966 PP

                             PAS_3  78 eng 80 
                                       ++ 
  gi|298674414|ref|YP_003726164.1| 214 KEK 216
                                       554 PP

  == domain 3  score: 24.6 bits;  conditional E-value: 2.2e-08
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvird 77 
                                       +++++++++++G+s e ++gk  +  d++   + e++r++   ++++++  y+ e ++ +  Ge+rw  ++ ++++d
  gi|298674414|ref|YP_003726164.1| 264 LTANDAFCKVVGFSIENIKGK--NDFDFLPEKEAEKYRSDDTSVMESRKpIYNLEEKYTTSEGEIRWALTSKVPYFD 338
                                       689******************..99************************777************************* PP

                             PAS_3  78 engkpvrvig 87 
                                        +g+++ ++g
  gi|298674414|ref|YP_003726164.1| 339 TEGNVIGIVG 348
                                       ********99 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 2.1
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvh 31 
                                       + ++++  + +G+ + +++g+   +++l++
  gi|298674414|ref|YP_003726164.1| 391 LWCNKAATKFTGLNCRDMIGQ--YCYKLLY 418
                                       578899999999999999998..6666555 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 2.1
                             PAS_3  34 Drervrealqealkkge..pyegeyRirrkdGey 65 
                                       Dr +++e++++++++ e   +e e+R+r++  ++
  gi|298674414|ref|YP_003726164.1| 476 DRVKTEEKIEKYAEELEkiNIELEHRVRKQTEDI 509
                                       7888888999999777734667789999987666 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.75   7.9e+02      38      57 ..     191     210 ..     158     238 .. 0.80
   2 !   27.3   0.0   3.7e-09   3.9e-06       5     108 ..     617     707 ..     613     709 .] 0.84

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.75
                                       EEEEEEESSSSSTTHHHTGT CS
                         HATPase_c  38 lvisveDnGiGipkedlkkl 57 
                                        ++ +++nG  ip+e+  +l
  gi|298674414|ref|YP_003726164.1| 191 ESVHITNNGTRIPVEINSNL 210
                                       57889999999999876644 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 3.7e-09
                                       HHHHHHHHHHHHHHHHHS...TTTEEEEEEEEEE.TEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHH CS
                         HATPase_c   5 rLrqiisnlvdNavkfat...kageieveikase.ddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlG 77 
                                        L  ii +l++N++k+a    ++ge+ + + ++e +++++ v DnG+G ++++                  + + lG
  gi|298674414|ref|YP_003726164.1| 617 PLGMIITELLSNSLKYAFfddEQGEVYIGLYRNEeGNYKLIVADNGKGFSEDIDI------E---------EPNTLG 678
                                       67789***********55545888889988875469**************96655......2.........4778** PP

                                       HHHHHHHHHHTTTEEEEEEETTTEEEEEEEE CS
                         HATPase_c  78 lsivkklvelmgGeiwvesepgrGttftftl 108
                                       l +v++lv++++G+++ e+    Gt+f++++
  gi|298674414|ref|YP_003726164.1| 679 LQLVNSLVDQINGDFEAETIN--GTKFVIEF 707
                                       *****************8888..**999865 PP

>> HWE_HK  HWE histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   6.9e-09   7.3e-06       1      53 [.     519     573 ..     519     605 .. 0.69

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 6.9e-09
                                       HHHHHHHHHHHHHHHHHHHHSSS..XS-HHHHHHHHHHHHHHHHHHHHHHHHCTT CS
                            HWE_HK   1 ElnHRvKNlLavvqsiarqtlrs..aesleefaeklsgRLqALsaahdllsreew 53 
                                       El+HR+KN L v++s+ +  +++   ++++++  + ++R++++s +h+ l +++ 
  gi|298674414|ref|YP_003726164.1| 519 ELHHRIKNNLQVISSLLSLQSEKftDDEVKDAFIDTQNRVKSMSLVHNKLYQTKG 573
                                       9****************988664112344555556689**********9887764 PP

>> sCache_3_3  Single cache domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.2       2.7   2.8e+03      61      82 ..      60      81 ..      37      89 .. 0.78
   2 ?    5.5   0.0     0.021        22      72     105 ..     328     361 ..     305     363 .. 0.86
   3 !   15.1   0.0   2.2e-05     0.023      50      98 ..     426     475 ..     419     483 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.7
                        sCache_3_3 61 tysgraeilgkkyltaYePlkd 82
                                      ty + ae   + y+  Y P +d
  gi|298674414|ref|YP_003726164.1| 60 TYAKVAETGEQTYFETYFPPFD 81
                                      5668889999999999999777 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.021
                        sCache_3_3  72 kyltaYePlkdadgkviGmlfvGlpeeevqalik 105
                                       + lt  +P +d +g+viG++  +l+++e + +++
  gi|298674414|ref|YP_003726164.1| 328 WALTSKVPYFDTEGNVIGIVGSSLDITERKRMYE 361
                                       6677779**************9999999888765 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 2.2e-05
                        sCache_3_3  50 e.vaeavlkkGetysgraeilgkkyltaYePlkdadgkviGmlfvGlpee 98 
                                       + ++++++k G+ y+++++  +k      +P+++ +g++iG++ v  +++
  gi|298674414|ref|YP_003726164.1| 426 NcPIYEIVKTGKHYEETVTFTNKILNVKKDPVRNTSGDIIGIITVTNDIT 475
                                       4488999************************************9987776 PP

>> Cache_3-Cache_2  Cache 3/Cache 2 fusion domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.3   1.3e+03     152     177 ..     328     353 ..     327     370 .. 0.74
   2 !   18.9   0.1   7.1e-07   0.00074     128     183 ..     425     480 ..     410     488 .. 0.88
   3 ?    4.4   0.7     0.019        20       7      62 ..     493     559 ..     489     588 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.3
                   Cache_3-Cache_2 152 wYvTaYePikdadgkViGilyVgvdq 177
                                       w +T   P  d +g+ViGi+   +d+
  gi|298674414|ref|YP_003726164.1| 328 WALTSKVPYFDTEGNVIGIVGSSLDI 353
                                       7788999999*********9544444 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 7.1e-07
                   Cache_3-Cache_2 128 asspvykavlagetYvGrakvfgkwYvTaYePikdadgkViGilyVgvdqsealks 183
                                       ++ p+y+ v+ g+ Y  ++++ +k    + +P+++ +g++iGi+ V  d+++ +k+
  gi|298674414|ref|YP_003726164.1| 425 DNCPIYEIVKTGKHYEETVTFTNKILNVKKDPVRNTSGDIIGIITVTNDITDRVKT 480
                                       444***********************************************988764 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.019
                   Cache_3-Cache_2   7 evnklieeelekevedlaetletqdellrekverdlnvfakllsn...........ewrvdnqetvk 62 
                                       ++n + e++++k++ed+ +  +t++  l+ +++++l+v+++lls            ++ +d+q++vk
  gi|298674414|ref|YP_003726164.1| 493 KINIELEHRVRKQTEDIINAERTRELELHHRIKNNLQVISSLLSLqsekftddevkDAFIDTQNRVK 559
                                       56778899***********************************998888885544444444444444 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1       2.1   2.2e+03      39      85 ..     159     206 ..     120     240 .. 0.67
   2 !    7.0   0.0    0.0084       8.9      45     106 .]     288     354 ..     243     354 .. 0.63
   3 !   11.9   0.0   0.00025      0.26       3     106 .]     372     475 ..     371     475 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.1
                            PAS_10  39 vGrpladihpkkavknvee.viealrtgekdevevvvpkngkwvlvry 85 
                                       +  +++di +   ++ +++ +++   +g+++ ++v++++ng+ + v++
  gi|298674414|ref|YP_003726164.1| 159 LSMNIKDIDELYDEDGINDnILNLPENGKQKFESVHITNNGTRIPVEI 206
                                       555666776665555555514444467788888888998888766655 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0084
                            PAS_10  45 dihpkkavknveeviealrtgek...devevvvp..kngkwvlvrylpyrdedgeiaGvvetfvDit 106
                                       d+ p+k+ ++ +++  ++ +++k   + +e++ +   + +w l    py d++g++ G+v   +Dit
  gi|298674414|ref|YP_003726164.1| 288 DFLPEKEAEKYRSDDTSVMESRKpiyNLEEKYTTseGEIRWALTSKVPYFDTEGNVIGIVGSSLDIT 354
                                       55555555555444444444444333444555543366799*********************99997 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00025
                            PAS_10   3 nlLnstpieltflDdnlqirrFtpaakklfklipad.vGrpladihpk.kavknveeviealrtgekdevevvvpkn 77 
                                        lLnst   +++ D + +i++ ++aa+k+  l+  d +G    ++  + +++ +   + e ++tg+  ++e  v+  
  gi|298674414|ref|YP_003726164.1| 372 ALLNSTSEIVVYHDLEGKILWCNKAATKFTGLNCRDmIGQYCYKLLYNkSEICDNCPIYEIVKTGKH-YEE-TVTFT 446
                                       599***************************99966538***99997662555555556666666655.454.45677 PP

                            PAS_10  78 gkwvlvrylpyrdedgeiaGvvetfvDit 106
                                       +k+  v+  p+r + g+i G++ +  Dit
  gi|298674414|ref|YP_003726164.1| 447 NKILNVKKDPVRNTSGDIIGIITVTNDIT 475
                                       9**************************97 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0063       6.7      87     112 ..      83     108 ..      41     111 .. 0.75
   2 ?    2.9   0.1      0.11   1.2e+02       2      51 ..     125     173 ..     124     234 .. 0.69
   3 ?   -1.8   0.0       3.1   3.3e+03      99     112 ..     345     358 ..     340     361 .. 0.85
   4 !    6.9   0.2    0.0063       6.7      73     115 .]     435     482 ..     380     482 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0063
                             PAS_7  87 vievrgnplpdgGfVttytDiTerrr 112
                                         ++ +   ++g fVt+++DiTe+++
  gi|298674414|ref|YP_003726164.1|  83 YFKISAISPEKGKFVTIFNDITEYKN 108
                                       5555555667788**********986 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.11
                             PAS_7   2 enmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaer 51 
                                       ++m++++ v D +++++ +N+  ++ l+++++ +   ++++++ +   e 
  gi|298674414|ref|YP_003726164.1| 125 DSMEDALFVGDLEGNILDVNETAVKRLGYSKQEL-LSMNIKDIDELYDED 173
                                       7888888888888888888888888888888776.666666665555444 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 3.1
                             PAS_7  99 GfVttytDiTerrr 112
                                       G+V +  DiTer+r
  gi|298674414|ref|YP_003726164.1| 345 GIVGSSLDITERKR 358
                                       8888899*****98 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.0063
                             PAS_7  73 gkphsfererpdgrvievrgnpl.....pdgGfVttytDiTerrraee 115
                                         +h+ e  + ++++++v++ p+     +  G++t+ +DiT+r+++ee
  gi|298674414|ref|YP_003726164.1| 435 TGKHYEETVTFTNKILNVKKDPVrntsgDIIGIITVTNDITDRVKTEE 482
                                       5567777788888899999998855544557*************9986 PP

>> sCache_3_2  Single cache domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0055       5.8      96     122 ..     321     347 ..     306     363 .. 0.80
   2 !   10.1   0.0   0.00065      0.68      84     124 ..     430     470 ..     427     478 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0055
                        sCache_3_2  96 tvtgtlgpslrvklPvfdadgrviGiv 122
                                       t  g +  +l+ k+P+fd +g viGiv
  gi|298674414|ref|YP_003726164.1| 321 TSEGEIRWALTSKVPYFDTEGNVIGIV 347
                                       455666668999**************8 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00065
                        sCache_3_2  84 aaalkagrayvgtvtgtlgpslrvklPvfdadgrviGivsv 124
                                       ++++k g++y +tvt+t       k Pv+  +g++iGi+ v
  gi|298674414|ref|YP_003726164.1| 430 YEIVKTGKHYEETVTFTNKILNVKKDPVRNTSGDIIGIITV 470
                                       68999***********7666666789************987 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   2.7e-06    0.0028      32     113 ..     618     690 ..     608     705 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.7e-06
                       HATPase_c_2  32 irlaveEactNavehayleapegpvevrlesdeea.ltvevaDsGpgfdpetlpdpteeepkeslkegGrGlalikg 107
                                       + + ++E+++N  ++a  ++++g+v + l ++ee   ++ vaD+G+gf              + ++++ +Gl l+++
  gi|298674414|ref|YP_003726164.1| 618 LGMIITELLSNSLKYAFFDDEQGEVYIGLYRNEEGnYKLIVADNGKGFSEDI----------DIEEPNTLGLQLVNS 684
                                       67899***********************66665555************9974..........6778999******** PP

                       HATPase_c_2 108 lvDeve 113
                                       lvD+++
  gi|298674414|ref|YP_003726164.1| 685 LVDQIN 690
                                       ***984 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0018       1.9       8      97 ..     134     218 ..     128     231 .. 0.87
   2 !    7.2   0.0    0.0052       5.5       2      46 ..     378     419 ..     377     445 .. 0.87
   3 ?   -3.1   0.0       8.1   8.5e+03      51      84 ..     501     513 ..     460     540 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0018
                            PAS_11   8 ldidgkIisvDtsaLrasfslglekeelvgrsiydLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvkvk 84 
                                        d++g+I++v++    a  +lg++k+el+ + i+d+    d   +++   +   +ng+++  +++++  +++ + v 
  gi|298674414|ref|YP_003726164.1| 134 GDLEGNILDVNE---TAVKRLGYSKQELLSMNIKDIDELYDEDGINDNILNLP-ENGKQKFESVHITN-NGTRIPVE 205
                                       5899********...9999**********************999999999999.99999999999876.99999999 PP

                            PAS_11  85 tksklfknqksne 97 
                                        +s l k +++  
  gi|298674414|ref|YP_003726164.1| 206 INSNLIKYKEKTA 218
                                       9999998766554 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0052
                            PAS_11   2 eqfttrldidgkIisvDtsaLrasfslglekeelvgrsiydLchp 46 
                                       ++  + +d++gkI+ +++    a+  +gl+  +++g + y+L+  
  gi|298674414|ref|YP_003726164.1| 378 SEIVVYHDLEGKILWCNK---AATKFTGLNCRDMIGQYCYKLLYN 419
                                       567788************...99999**************99865 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 8.1
                            PAS_11  51 tlkshlrevissngeatsslyRLrlsqdkfvkvk 84 
                                       +++++ +++i                     ++ 
  gi|298674414|ref|YP_003726164.1| 501 RVRKQTEDII---------------------NAE 513
                                       3333333333.....................222 PP

>> PAS_12  UPF0242 C-terminal PAS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.21   2.2e+02      63     101 ..     134     172 ..     112     212 .. 0.73
   2 ?   -0.3   0.0      0.69   7.3e+02      69      88 ..     263     282 ..     247     308 .. 0.77
   3 !    9.8   0.0   0.00055      0.58      56      88 ..     377     409 ..     371     418 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.21
                            PAS_12  63 sqkenkllfaNaqirallGwssdkflqdfseivqeglee 101
                                          e  +l +N+   + lG+s++++l+   + ++e ++e
  gi|298674414|ref|YP_003726164.1| 134 GDLEGNILDVNETAVKRLGYSKQELLSMNIKDIDELYDE 172
                                       566788999**************9998877777776655 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.69
                            PAS_12  69 llfaNaqirallGwssdkfl 88 
                                        l aN+ + +++G+s +++ 
  gi|298674414|ref|YP_003726164.1| 263 YLTANDAFCKVVGFSIENIK 282
                                       3679************9985 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00055
                            PAS_12  56 lgailvysqkenkllfaNaqirallGwssdkfl 88 
                                       ++ i+vy   e k+l+ N+   +++G++  +++
  gi|298674414|ref|YP_003726164.1| 377 TSEIVVYHDLEGKILWCNKAATKFTGLNCRDMI 409
                                       689************************988876 PP

>> YgaB  YgaB-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.7    0.0079       8.3      28      66 ..     205     243 ..     202     248 .. 0.93
   2 ?    3.1   1.4      0.12   1.3e+02      44      73 ..     479     512 ..     469     516 .. 0.71
   3 ?    3.4   0.2     0.094        99       6      45 ..     524     563 ..     519     581 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0079
                              YgaB  28 eiekeLlklekeaklesiqeeikrkkkeLkeiqkvFekQ 66 
                                       ei+++L+k ++++ + s+  +i+ +k+  k iq+  ++Q
  gi|298674414|ref|YP_003726164.1| 205 EINSNLIKYKEKTAVLSVVRNITDRKNAEKLIQRKIQEQ 243
                                       899*************************999*9999988 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.12
                              YgaB  44 siqeeikrkkkeLkei....qkvFekQteevirs 73 
                                       + +e+i++  +eL++i    ++   kQte++i++
  gi|298674414|ref|YP_003726164.1| 479 KTEEKIEKYAEELEKInielEHRVRKQTEDIINA 512
                                       56677888888888772222456689******97 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.094
                              YgaB   6 VseQmktmdkLLflQselerCqeiekeLlklekeaklesi 45 
                                       +++ ++++  LL lQse     e++   + +++  k  s+
  gi|298674414|ref|YP_003726164.1| 524 IKNNLQVISSLLSLQSEKFTDDEVKDAFIDTQNRVKSMSL 563
                                       678999***********88888888888888877776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (709 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1132  (0.0631379); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.70u 0.30s 00:00:01.00 Elapsed: 00:00:00.47
# Mc/sec: 4578.10
//
Query:       gi|298674415|ref|YP_003726165.1|  [L=67]
Description: deoxyribonuclease/rho motif-like TRAM protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-14   52.2   0.4    4.7e-14   52.1   0.4    1.0  1  TRAM      TRAM domain


Domain annotation for each model (and alignments):
>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   0.4   2.6e-18   4.7e-14       3      61 ..      11      65 ..       9      66 .. 0.95

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 2.6e-18
                                      XXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEE CS
                              TRAM  3 yvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGel 61
                                        G+ ++V++e  + s+g+gi+r+  g+v+fvp+++   Gd+V++ +tkv  ++++Ge+
  gi|298674415|ref|YP_003726165.1| 11 RSGERYDVEIENIA-SKGDGIARVG-GFVIFVPDTSV--GDEVTIAVTKVMDNFAFGEI 65
                                      579**********9.**********.********999..******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.29u 0.23s 00:00:00.52 Elapsed: 00:00:00.34
# Mc/sec: 584.67
//
Query:       gi|298674416|ref|YP_003726166.1|  [L=447]
Description: deoxyribonuclease I [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-22   79.1   4.0      3e-22   79.1   4.0    3.2  3  LTD            Lamin Tail Domain
    5.8e-10   39.1   0.1    8.2e-10   38.6   0.1    1.4  1  Exo_endo_phos  Endonuclease/Exonuclease/phosphatase family


Domain annotation for each model (and alignments):
>> LTD  Lamin Tail Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.2     0.014   1.3e+02       8      37 ..      96     124 ..      91     161 .. 0.83
   2 ?   -1.5   0.1      0.34     3e+03      64      85 ..     309     332 ..     308     355 .. 0.58
   3 !   79.1   4.0   3.3e-26     3e-22       7     108 ..     350     444 ..     337     446 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.014
                               LTD   8 vvIsevmedgagnnan.efvelyNtsskavd 37 
                                       + I e+ +++  +n+  + vel+N ++   d
  gi|298674416|ref|YP_003726166.1|  96 IAIQEIRDKS--ENSLpQLVELVNEGDYNYD 124
                                       6788999877..33346********998665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.34
                               LTD  64 yvvvwsgsgttsasngskas..ss 85 
                                       y+++w++++ ++ ++ ++ s  + 
  gi|298674416|ref|YP_003726166.1| 309 YATFWTNKDDDNITSNYTPSeqTL 332
                                       788999988886666655553222 PP

  == domain 3  score: 79.1 bits;  conditional E-value: 3.3e-26
                               LTD   7 dvvIsevmedgagnnanefvelyNtsskavdLsgwkledasge.ytfpngtgtlaageyvvvwsgsgttsasngska 82 
                                       dv Is    +       e+v+++N+++++vdL++wk+ed++++ y f++   tl ++ +v++++++gt++ ++ +++
  gi|298674416|ref|YP_003726166.1| 350 DVYISDLSLED------EWVKITNPGETSVDLNNWKIEDEANHaYEFTDF--TLGPNNTVTLYTDEGTDAENQLYWG 418
                                       45555555544......******************************999..5************************ PP

                               LTD  83 sssavwnnggdavaLydasgevvdsv 108
                                       s++a+wnn+gd+++Lyd++ge+vds+
  gi|298674416|ref|YP_003726166.1| 419 SGRAIWNNDGDNAYLYDSTGELVDSY 444
                                       ************************98 PP

>> Exo_endo_phos  Endonuclease/Exonuclease/phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.1   9.2e-14   8.2e-10       3     159 ..      67     233 ..      65     348 .. 0.78

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 9.2e-14
                                       EEESTGCHHHHTHHHHHHHHHHHHHHCTTSEEEEEEEBSCTCHHHHHHHHHTTCEEEEECCHECSSSTTSSEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Exo_endo_phos   3 wNvngqaspalgssrrsdrladlltaydaDvlgLQEvdddelsriplllalggflgasstsptgggggggnggavls 79 
                                       +N++ ++ ++++ +  +  +a+++++y  D++++QE++d +++ +p+l     ++ +          +  +  ++  
  gi|298674416|ref|YP_003726166.1|  67 FNIQVFGTSKASEPETMNTIAKIIRNY--DIIAIQEIRDKSENSLPQLV--ELVNEG----------DYNYDFVMSE 129
                                       9*****9********************..********************..666665..........4457777777 PP

                                       CSTEEEEEEEEEEETSSSSGCEEEEEEEEEEEEEEE........................CCCHHGHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................xxxxxxxxxxxxxxxxx RF
                     Exo_endo_phos  80 rfpltslfrrtfiefndlvaalrreplaakleqlni........................ashrdhdlvrdlqllal 132
                                       r   t  +  + + +n   + + ++p +++++  ++                         +  +     +  +l+ 
  gi|298674416|ref|YP_003726166.1| 130 RLGRTVSKEQYAYIYNTATVDISNNPHTYPEPEGTDpfhrqpyiasfeavngnfdatfitVHTDPDEATEEINALDS 206
                                       88888888888888888888888888888888888888888888***************666666666777778889 PP

                                       HHHHHHHHHHTTSEEEEEEE-SSSTSG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Exo_endo_phos 133 llqvealnadrgapvivaGDfNarpsd 159
                                       + +       + + +iv+GD+Na+ s 
  gi|298674416|ref|YP_003726166.1| 207 VVEYTHEKYSEERDFIVMGDLNADGSY 233
                                       999999999999***********3332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 3068.88
//
Query:       gi|298674417|ref|YP_003726167.1|  [L=178]
Description: hypothetical protein Metev_0456 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0061   16.8   0.1     0.0099   16.1   0.1    1.3  1  BTB       BTB/POZ domain


Domain annotation for each model (and alignments):
>> BTB  BTB/POZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   5.5e-07    0.0099      36     100 ..      77     139 ..      73     148 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.5e-07
                                       HHHHHHTSTTTTTCCCEEEEETTSGHHHHHHHHHHHHHSEEEC-CGGGHHHHHHHHHHHT-HHHH CS
                               BTB  36 yFkalftskeieessvseielddvepeafealLefiYtgeleitseenleelLaaadllqiprlk 100
                                        Fk++++ + ++++ +   +ld +   +   +L+fiY+++++i  +  ++e+L+   +l+ ++ +
  gi|298674417|ref|YP_003726167.1|  77 TFKEMLKAE-DDAKLSILCQLDGIGVPTASTILHFIYPERFPII-DYRVMEVLNNFGYLNTKNAT 139
                                       699999999.56666667999**********************7.999****9998888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1121.69
//
Query:       gi|298674418|ref|YP_003726168.1|  [L=145]
Description: group 1 glycosyl transferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 896.81
//
Query:       gi|298674419|ref|YP_003726169.1|  [L=327]
Description: hypothetical protein Metev_0458 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.7e-16   58.4   2.6    1.6e-15   57.7   2.6    1.4  1  PDDEXK_4  PD-(D/E)XK nuclease superfamily
  ------ inclusion threshold ------
      0.037   14.3   0.0       0.13   12.6   0.0    1.9  1  DUF4854   Domain of unknown function (DUF4854)
       0.34   10.8   1.6        5.2    7.0   0.1    2.9  4  DUF4907   Domain of unknown function (DUF4907)


Domain annotation for each model (and alignments):
>> PDDEXK_4  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.7   2.6   2.7e-19   1.6e-15       2     163 ..       2     195 ..       1     224 [. 0.73

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 2.7e-19
                          PDDEXK_4   2 nifdvlgk...gskelrhSallAwlLnpeethgqgdsflkafldllrerlfssdeisasvadlesaevere...... 69 
                                       nif++l+    + +e  +Sa+l +lL pe++hg++d flk+fl+ ++e ++ +  + ++  +l ++e++ e      
  gi|298674419|ref|YP_003726169.1|   2 NIFTALSQgrgSLNEENMSAMLGYLLSPEQSHGLNDVFLKKFLSSVAEIKDGQLHDLDN-LLLSKDEIKVEvnfeqp 77 
                                       99999999987779*****************************7776666666666666.46666666666669896 PP

                          PDDEXK_4  70 ..nasekng....riDlll....qenkivvlIEnKva.AkdqkeQlarYeefakkka......kkkdivvvyLtldg 129
                                         +           iD+ +     ++ + ++IEnK+  A+ + +Q++  +e++ + +         ++++++Lt+ g
  gi|298674419|ref|YP_003726169.1|  78 ysYHG---YsryvDIDIRIfdnhYNELYRLIIENKIKpASSSSNQFKEEYEAVISDIeensenSHPKVIMIFLTPTG 151
                                       53333...234467788889997778888********999999***9988855555445556688889999**9999 PP

                          PDDEXK_4 130 .........eapsedsleedekeayktisy....eqilewleecvkk 163
                                                e+ s+d l++   ++ + + +    ++i  +l++++k 
  gi|298674419|ref|YP_003726169.1| 152 rhsqllneyENLSQDMLGK---NEKVWVYWaddeNTITDLLRQILKD 195
                                       7777773333333333333...4444444477777888888777776 PP

>> DUF4854  Domain of unknown function (DUF4854)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.2e-05      0.13      59      98 ..     113     152 ..      94     157 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.2e-05
                           DUF4854  59 laesldsqastfeslakqlkkevkvenpivvvrvltsdGk 98 
                                       +++s+++ ++ +e + ++++++ +++ p+v++++lt++G 
  gi|298674419|ref|YP_003726169.1| 113 ASSSSNQFKEEYEAVISDIEENSENSHPKVIMIFLTPTGR 152
                                       6789999*******************************96 PP

>> DUF4907  Domain of unknown function (DUF4907)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.043   2.6e+02      19      41 ..     104     126 ..      99     128 .. 0.90
   2 ?   -4.0   0.0       2.4   1.4e+04      11      22 ..     252     263 ..     249     265 .. 0.78
   3 ?   -2.0   0.0      0.57   3.4e+03      43      58 ..     273     288 ..     259     292 .. 0.79
   4 ?    7.0   0.1   0.00088       5.2      36      56 ..     297     317 ..     294     327 .] 0.83

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.043
                           DUF4907  19 vlIkQpfIPaisgkkpFkteedA 41 
                                       ++I+ ++ Pa s+ + Fk+e +A
  gi|298674419|ref|YP_003726169.1| 104 LIIENKIKPASSSSNQFKEEYEA 126
                                       78999999************998 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 2.4
                           DUF4907  11 YqIllnekvlIk 22 
                                       Y+I + e+++Ik
  gi|298674419|ref|YP_003726169.1| 252 YKIEKYESTTIK 263
                                       888888888875 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.57
                           DUF4907  43 kvgklVvekLkkgenp 58 
                                       +v+k +++k ++++n 
  gi|298674419|ref|YP_003726169.1| 273 EVAKPILRKVNDEKNL 288
                                       7999999999998875 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.00088
                           DUF4907  36 kteedArkvgklVvekLkkge 56 
                                       ++e+++r  g++V++kLk+++
  gi|298674419|ref|YP_003726169.1| 297 NNERNTRSLGNMVIKKLKQQN 317
                                       58999*************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1099  (0.0612973); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2187.62
//
Query:       gi|298674420|ref|YP_003726170.1|  [L=129]
Description: hypothetical protein Metev_0459 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.012   15.8   1.1       0.67   10.2   0.3    2.2  2  TrbC           TrbC/VIRB2 family
      0.031   13.5   2.8        1.6    7.9   0.6    2.0  2  MIG-14_Wnt-bd  Wnt-binding factor required for Wnt secretion
       0.12   12.1   3.9        4.6    6.9   3.8    2.0  1  BPD_transp_1   Binding-protein-dependent transport system inn
        0.4   10.8   2.5       0.58   10.3   0.4    2.1  2  ETRAMP         Malarial early transcribed membrane protein (E


Domain annotation for each model (and alignments):
>> TrbC  TrbC/VIRB2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.3   0.00015      0.67      16      73 ..      24      83 ..      11      85 .. 0.74
   2 ?    4.4   0.0    0.0099        44      43      74 ..      90     120 ..      84     127 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00015
                              TrbC 16 alalvllllaspalAqaagg..dpvetvlqnivdfltgplakviatiaiivaGimlafgr 73
                                      + +++++l  +   A ++++  ++++t ++++   +  ++  ++++i+i  ++ +l+ g+
  gi|298674420|ref|YP_003726170.1| 24 VFIAIIILTVQRMGAKSSSSnqKDWNTDINKFKEKILPNFKVIVIVIGITEISNGLILGY 83
                                      2344444445555555555599**************************988887777775 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0099
                              TrbC  43 qnivdfltgplakviatiaiivaGimlafgrl 74 
                                        n+  +l+  + +vi+t+ai+  ++ la +  
  gi|298674420|ref|YP_003726170.1|  90 PNWALSLSY-ITYVISTLAILLFSYWLAKHAF 120
                                       577889999.99*********99998876655 PP

>> MIG-14_Wnt-bd  Wnt-binding factor required for Wnt secretion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   2.9   0.00037       1.7     202     289 ..      17     114 ..       5     114 .. 0.68
   2 ?    7.9   0.6   0.00035       1.6      46      84 ..      85     123 ..      82     128 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00037
                     MIG-14_Wnt-bd 202 ilavlyflyLlylifrsfseirskrvk.............egdi.Rfkflilltllvlavlvifiilglvselspts 264
                                        +++ly +++ ++i+++ +   +++ +             e ++ +fk++++++ ++ ++ ++ +  g+    + + 
  gi|298674420|ref|YP_003726170.1|  17 TVGALYGVFIAIIILTVQRMGAKSSSSnqkdwntdinkfkEKILpNFKVIVIVIGITEISNGLILGYGI----NHKL 89 
                                       678899999999999866655555544777886666655544445666655555555555555555555....5666 PP

                     MIG-14_Wnt-bd 265 dssaqflgvygllNlyvytlaylYa 289
                                        + a  l++++++   + +l++ Y+
  gi|298674420|ref|YP_003726170.1|  90 PNWALSLSYITYVISTLAILLFSYW 114
                                       8888888888888888888888887 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00035
                     MIG-14_Wnt-bd  46 inpgftlfeisfrtvfliisliililflfslrklsfrdw 84 
                                       in++  ++ +s+ ++  +is +++ lf+++l k+ f d+
  gi|298674420|ref|YP_003726170.1|  85 INHKLPNWALSLSYITYVISTLAILLFSYWLAKHAFDDF 123
                                       688889999***********************9999875 PP

>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   3.8     0.001       4.6     137     177 ..      33     117 ..       7     119 .. 0.53

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.001
                      BPD_transp_1 137 lgtllleailgydyseis............................................nggvlalviavllln 169
                                       ++++   ++++++ ++++                                              +++++vi++l+++
  gi|298674420|ref|YP_003726170.1|  33 VQRMGAKSSSSNQKDWNTdinkfkekilpnfkvivivigiteisnglilgyginhklpnwalSLSYITYVISTLAIL 109
                                       55555555555555555555555555555555555555555555555555555555555555555666666666666 PP

                      BPD_transp_1 170 lvadilqr 177
                                       l++++l++
  gi|298674420|ref|YP_003726170.1| 110 LFSYWLAK 117
                                       66666555 PP

>> ETRAMP  Malarial early transcribed membrane protein (ETRAMP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.4   0.00013      0.58      12      80 ..      25      88 ..      15      91 .. 0.68
   2 ?    0.1   0.1      0.19   8.6e+02       4      18 ..     100     114 ..      98     123 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00013
                            ETRAMP 12 fLlavnlltpeslcdevnkkkekakkaikkiddkiekkkkkkKliiistiatalallvasalGlgiykk 80
                                      f+ ++ l ++ + ++ +  ++++ + +i+k+++ki  +    K i+i  i  +  +  +++lG+gi++k
  gi|298674420|ref|YP_003726170.1| 25 FIAIIILTVQRMGAKSSSSNQKDWNTDINKFKEKILPN---FKVIVIV-I-GITEISNGLILGYGINHK 88
                                      55555555555666666666688888888888888877...6644443.3.333479999*******98 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.19
                            ETRAMP   4 tkvllffafLlavnl 18 
                                       t v + +a+Ll+   
  gi|298674420|ref|YP_003726170.1| 100 TYVISTLAILLFSYW 114
                                       555666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1091  (0.0608511); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 832.83
//
Query:       gi|298674421|ref|YP_003726171.1|  [L=197]
Description: hypothetical protein Metev_0460 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.033   14.1   0.9        1.7    8.7   1.0    2.7  2  DUF2335   Predicted membrane protein (DUF2335)


Domain annotation for each model (and alignments):
>> DUF2335  Predicted membrane protein (DUF2335)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.0   9.2e-05       1.7      23      42 ..      71      90 ..      70      97 .. 0.89
   2 ?    2.1   0.0     0.011   1.9e+02       8      18 ..     104     114 ..     100     115 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 9.2e-05
                           DUF2335 23 maekEqehRheleeklldaq 42
                                       +ekE++ R ++e+k++d++
  gi|298674421|ref|YP_003726171.1| 71 TFEKESKNREKIEQKQQDIE 90
                                      59***************976 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.011
                           DUF2335   8 qYesilPGaAe 18 
                                       +Y++il ++Ae
  gi|298674421|ref|YP_003726171.1| 104 KYNQILINTAE 114
                                       8********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1323  (0.0737911); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.22s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1359.36
//
Query:       gi|298674422|ref|YP_003726172.1|  [L=365]
Description: radical SAM domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-05   25.3   0.0    3.4e-05   24.0   0.0    1.7  1  Fer4_14      4Fe-4S single cluster domain
    2.4e-05   24.7   0.0    8.2e-05   23.0   0.0    1.8  2  Radical_SAM  Radical SAM superfamily
    4.7e-05   23.7   0.0    9.9e-05   22.6   0.0    1.6  1  Fer4_12      4Fe-4S single cluster domain
  ------ inclusion threshold ------
       0.13   12.6   0.5       0.52   10.6   0.6    1.9  2  FRD2         Bacteriophage FRD2 protein


Domain annotation for each model (and alignments):
>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   7.5e-09   3.4e-05       2      96 ..      32     137 ..      31     158 .. 0.64

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 7.5e-09
                           Fer4_14   2 fvrlsgCnlsCkgCdnke..twkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkell.....klv 71 
                                       ++r   CnlsC  C+ +     + +     +   le+ +++l++ + +i  + + GGePL+  + ++       +++
  gi|298674422|ref|YP_003726172.1|  32 VLRYRDCNLSCYLCYFQPyaYLNRTTSRRPVTSSLETCVNQLNNLDRSIGWVRIQGGEPLLNDSRSKSTsilagEVL 108
                                       678899*********6651033445555556666779999999999999***********87655543311122445 PP

                           Fer4_14  72 krlkeey....pekkiwletngtleiele 96 
                                       ++++ +     ++ +i ++tng +  +  
  gi|298674422|ref|YP_003726172.1| 109 NHIVSNNlssyENPRIIIQTNGIWLGNAS 137
                                       55555442222457888888888764444 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   1.8e-08   8.2e-05       4     130 ..      35     189 ..      32     213 .. 0.84
   2 ?   -1.6   0.0      0.67     3e+03      57      89 ..     245     274 ..     241     285 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.8e-08
                                       ESEESS--TTTSCCTT....HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC.. CS
                                       xxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                       Radical_SAM   4 trgCnlrCsfCarpet....vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla.. 74 
                                       +r Cnl C  C++         + +r+ + s+e  ++++  l  +  ++ v + ggepll++   + +  la +   
  gi|298674422|ref|YP_003726172.1|  35 YRDCNLSCYLCYFQPYaylnRTTSRRPVTSSLETCVNQLNNL-DRS-IGWVRIQGGEPLLNDSRSKSTSILAGEVln 109
                                       688*************99999999999999999999999999.576.************************999999 PP

                                       .........CCTEEEEEEECSSCHG.......HHHHHHHHHTT......-SEEEEEEBSSSHH...HHHHHHTCTSH CS
                                       .........xxxxxxxxxxxxxxxx.......xxxxxxxxxxx......xxxxxxxxxxxxxx...xxxxxxxxxxx RF
                       Radical_SAM  75 .........vpgiritvetngtlpd.......eeklerllelg......vdrvslgleaadde...kvlklmnrght 126
                                                 ++ ri + tng+++        +e++++++e+         +++++ +  + e    + k +  + +
  gi|298674422|ref|YP_003726172.1| 110 hivsnnlssYENPRIIIQTNGIWLGnasvdkiDEFVQKIVEYLenvgygKIVLEISFKGSNREmanSYAKSI-NTTN 185
                                       9**********************999**99997777666666555447777777787777777666666666.4455 PP

                                       HHHH CS
                                       xxxx RF
                       Radical_SAM 127 feev 130
                                       +++v
  gi|298674422|ref|YP_003726172.1| 186 VDDV 189
                                       5555 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.67
                                       GGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  57 pllypdfvellerlaklavpgiritvetngtlp 89 
                                       p+++pd  ++ + ++     ++r+t++tn+ + 
  gi|298674422|ref|YP_003726172.1| 245 PIFHPDTWDENFSRVID---DFRNTLSTNESVY 274
                                       77777777777777776...9999999998765 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   2.2e-08   9.9e-05       3      72 ..      26      99 ..      22     155 .. 0.67

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2.2e-08
                           Fer4_12  3 GeGvrlslfvsgCnlsCkgCfnketwsfk...sgkeftkelleeiiedlkk..esiegltllGGEPllpenaeal 72
                                      G+ + l+l+  +CnlsC  C+ +     +   s +++t+  le  +++l++  +si  + + GGEPll   +++ 
  gi|298674422|ref|YP_003726172.1| 26 GQHGALVLRYRDCNLSCYLCYFQPYAYLNrttSRRPVTSS-LETCVNQLNNldRSIGWVRIQGGEPLLNDSRSKS 99
                                      4448899*************98877644422155555544.45666677655599999**********6555433 PP

>> FRD2  Bacteriophage FRD2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.3   5.7e+03      47      95 ..      32      81 ..      20      85 .. 0.55
   2 ?   10.6   0.6   0.00012      0.52       5      96 ..     125     215 ..     123     218 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.3
                              FRD2 47 yfelseeefycfreykeptseedevkdkvsgvtki.hcivdennvdeiie 95
                                       +   + ++ c+  y +p +  +    +    + +  c+ + nn+d  i 
  gi|298674422|ref|YP_003726172.1| 32 VLRYRDCNLSCYLCYFQPYAYLNRTTSRRPVTSSLeTCVNQLNNLDRSIG 81
                                      55555566666666666666555554444333333147777788887765 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00012
                              FRD2   5 iiqenggwfevksissldgfdyvteiicangeiynddgmgddyfelseeef.ycfreykeptseedevkdkvsgvtk 80 
                                       iiq ng w+   s+  +d f  v +i+    ++     + +  f+ s+ e+   + +  + t+ +d +  ++sg  k
  gi|298674422|ref|YP_003726172.1| 125 IIQTNGIWLGNASVDKIDEF--VQKIVEYLENVGYGKIVLEISFKGSNREMaNSYAKSINTTNVDDVLATQISGYNK 199
                                       89*********999999976..677776555555555555666777777761466677777788888899******* PP

                              FRD2  81 ihcivdennvdeiiel 96 
                                       +h  + +n  d+ i+ 
  gi|298674422|ref|YP_003726172.1| 200 LHESIKNNAWDNDINR 215
                                       ******9999987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2427.75
//
Query:       gi|298674423|ref|YP_003726173.1|  [L=223]
Description: hypothetical protein Metev_0462 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1359  (0.075799); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1660.35
//
Query:       gi|298674424|ref|YP_003726174.1|  [L=679]
Description: N-6 DNA methylase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-63  213.6   1.6    4.2e-63  213.5   0.1    1.5  2  N6_Mtase       N-6 DNA Methylase
    1.1e-21   77.9   9.8    1.3e-20   74.4   0.4    2.7  2  HsdM_N         HsdM N-terminal domain
      0.007   16.1   0.1       0.11   12.2   0.2    2.7  2  UPF0020        Putative RNA methylase family UPF0020
  ------ inclusion threshold ------
      0.014   15.0   0.0      0.034   13.7   0.0    1.6  1  MTS            Methyltransferase small domain
      0.016   15.4   9.2      0.024   14.9   7.1    2.3  2  DUF4355        Domain of unknown function (DUF4355)
      0.038   13.5   0.0       0.08   12.4   0.0    1.5  1  AviRa          RRNA methyltransferase AviRa
      0.074   12.7   0.1         12    5.7   0.0    2.8  2  CRM1_repeat_2  CRM1 / Exportin repeat 2


Domain annotation for each model (and alignments):
>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.5   0.1   1.6e-66   4.2e-63       3     284 ..     152     457 ..     150     466 .. 0.90
   2 ?   -2.9   0.1       1.2   3.1e+03     249     293 ..     509     553 ..     484     566 .. 0.54

  Alignments for each domain:
  == domain 1  score: 213.5 bits;  conditional E-value: 1.6e-66
                          N6_Mtase   3 kdllGdvYEyllrkfaeeegksgGeffTPrevsklivell.........epksgesvyDpacGsggllvqaekvlke 70 
                                       ++ +G ++E l+r+f e   ++ Ge fTPrev++l+v+l+         ++ + +++yDpacG+gg+l  a++++ +
  gi|298674424|ref|YP_003726174.1| 152 NHEMGYIFEELIRRFNEDVNENPGEHFTPREVIRLMVNLIfyqdeaklgHNTPIRTIYDPACGTGGMLTIANDHILK 228
                                       6889***************************************9998886666778********************* PP

                          N6_Mtase  71 edgktkelsiyGqeknettyrLakmNlllhgieykkvkirlgdtlekpkfekdkkfdvvvaNppfnqkew....... 140
                                       e +++ ++ ++Gqe+n++t+++ak  ++l+g + +  +i++g+ ++++ +  +++f+++++Nppf+++ w       
  gi|298674424|ref|YP_003726174.1| 229 EINSNADIWLFGQEVNPETFAIAKSDMMLKGNDRDAENIKMGSVFSNDGHP-NETFNYMLSNPPFGKD-Wkkeqnfi 303
                                       ***************************************************.**************99.*8665555 PP

                          N6_Mtase 141 kektlekderfreavapksnadlafllhiieslk...pkG.raavvlangvLfr...ggkegkIrkalvekdlveav 210
                                        e+ +   +rf+ +++ k+  +l fl+h+i+++k   ++G r+avv +   Lf    g+ e +Ir+ ++e+d +ea+
  gi|298674424|ref|YP_003726174.1| 304 LEEAKSASSRFTAGLPRKDDGQLLFLQHMISKMKrpeDGGsRIAVVTNGSPLFTgdaGSGESEIRRWIIENDWLEAI 380
                                       4455566679*********************99733234469999999999**855567899*************** PP

                          N6_Mtase 211 ialpeklFyntsiptcilvlkkekae.rkgkvlfidaseefkkkd....rkknklteediekildtykekskevdkf 282
                                       +alpe+lFynt+i+t +++++  k++ rkgk+ ++da+e ++k+     +k+++++ e+i++i++  +++  ++ ++
  gi|298674424|ref|YP_003726174.1| 381 VALPEQLFYNTGINTYVWIVTNRKEDhRKGKIQLVDARECYQKMRkslgEKRHEISSEQIDTITNLHNNF--NEGQY 455
                                       ********************9988778************99998766778999**************999..44455 PP

                          N6_Mtase 283 sk 284
                                       s+
  gi|298674424|ref|YP_003726174.1| 456 SQ 457
                                       54 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.2
                          N6_Mtase 249 efkkkdrkknklteediekildtykek.skevdkfskvveleeiae 293
                                       e +k++ + +kl++  ie + ++  ek +k+ d+f kv   +++++
  gi|298674424|ref|YP_003726174.1| 509 EKEKEEAEGQKLQDSIIEMLSEMDSEKfYKNRDEFWKV-LNDNLKK 553
                                       22223344445555555555554444456777777443.3455555 PP

>> HsdM_N  HsdM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.4   0.4   5.2e-24   1.3e-20       3     137 .]       9     140 ..       7     140 .. 0.88
   2 !    6.6   3.6    0.0046        12      38     105 ..     508     576 ..     476     598 .. 0.63

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 5.2e-24
                                       HHHHHHH.HHHHHS-SHHHHHHHHHHHHHHHHHHHHHHHHHHCC...........--..--------....S-CCCS CS
                            HsdM_N   3 sklwkaa.diLRgkvdaseykeyilgLlFlKrlddveeereekllee...yken.aleeleeklkskeafyipeelr 74 
                                       +++w++a + LR+++++ +y+++il++++l+r+++v+e++++ ++++   +k++ ++ +++ + ++++ fy+++++ 
  gi|298674424|ref|YP_003726174.1|   9 NFIWSVAdEVLRDDFKRGKYRDVILPFTVLRRVECVLEPTKDNVIQTyenVKDKvKDPHNALCHAAGHSFYNTSPYD 85 
                                       89*****778**99******************************999665444464456899999************ PP

                                       HHHHHHS--HHHHHHHHHHCHHHHCT--STHHHHHHHS......S-----SSHHHHHHHHHHH CS
                            HsdM_N  75 WkelakkkdddelgenlnkafpaleelnkslkgvfmkddfnafalgeitkkspalLskviekf 137
                                       +k+l +++++  +g+n++ ++++++e+    +++f+  +f+   + ++++++++lL+ ++ekf
  gi|298674424|ref|YP_003726174.1|  86 LKKLLDDPSN--IGQNFKSYINSFSEN---MRDIFD--KFYLW-NYIDQLIEDNLLYMLLEKF 140
                                       ******6555..**************9...999995..45555.668899**********998 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0046
                                       HHHHHHCC............--...--------....S-CCCSHHHHHHS..--HHHHHHHHHH.CHHHHCT--STH CS
                            HsdM_N  38 eeereeklleeyken.....al.eeleeklkskeafyipeelrWkelakk..kdddelgenlnk.afpaleelnksl 105
                                       ee+++e++      +     +   e   +++s e+fy   +  Wk l ++  k++ +++++++k ++++++e + ++
  gi|298674424|ref|YP_003726174.1| 508 EEKEKEEA------EgqklqDSiIEMLSEMDS-EKFYKNRDEFWKVLNDNlkKHGININNTVEKaILDSMSERD-ET 576
                                       12222222......022222112233334444.56999999******9999888889*******5666666664.33 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.2   4.2e-05      0.11      28     139 ..     204     300 ..     198     307 .. 0.59
   2 ?   -2.7   0.0       1.6   4.1e+03     146     173 ..     330     357 ..     324     366 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.2e-05
                                       TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHHHHHHHTT-G.. CS
                           UPF0020  28 pgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvvqgareNaekagvg.. 102
                                       p ++++DP CG+G++l  a     + +                 + +a++ l+g + +++  + a++     g +  
  gi|298674424|ref|YP_003726174.1| 204 PIRTIYDPACGTGGMLTIANDHILKEI-----------------NSNADIWLFGQEVNPETFAIAKSDMMLKGNDrd 263
                                       5679**********9954433333333.................223444455555555555555555444443310 PP

                                       .GGEEEEE--GGG--STTS---EEEE----------HH CS
                           UPF0020 103 .dliefsqadaakLrlkegevdvivtnpPYGerlgskk 139
                                        + i++ +    + + +++ ++ +++npP+G+  ++++
  gi|298674424|ref|YP_003726174.1| 264 aENIKMGSVFSNDGH-PNETFNYMLSNPPFGKDWKKEQ 300
                                       022222222223334.7889999********9988876 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.6
                                       HHHHHHHHHH-TT..-EEEEEESSHHHH CS
                           UPF0020 146 seflrelkrvlrgggrlvlltsenkale 173
                                       +++ +++kr  +gg+r++++t+++  ++
  gi|298674424|ref|YP_003726174.1| 330 QHMISKMKRPEDGGSRIAVVTNGSPLFT 357
                                       56888999999999*****999988776 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.3e-05     0.034      34     125 ..     207     310 ..     198     330 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.3e-05
                                       EEEEET-TTS.HHHHH....HHHHTTC.EEEE....EESBHHHHHHHHHHHHHTTGC.EEEEE-STTTT..STTS-E CS
                               MTS  34 kvlDlGcGaG.vlgaa....lakespeaevtl....vdvdarAlesakenleankle.vevvasdvlee..veekkf 98 
                                       ++ D +cG+G +l++a    l++ +++a++ l    v+ ++ A++ +   l+ n+ +  ++   +v+++   +++ f
  gi|298674424|ref|YP_003726174.1| 207 TIYDPACGTGgMLTIAndhiLKEINSNADIWLfgqeVNPETFAIAKSDMMLKGNDRDaENIKMGSVFSNdgHPNETF 283
                                       5677778875245543222244445555554411113334567777777888888887555666666542156899* PP

                                       EEEEE---STTTCHCHHHHHHHHHHHH CS
                               MTS  99 dlivsNPPfhagkatelavaeeliaeA 125
                                       ++++sNPPf ++ ++e++ + e  ++A
  gi|298674424|ref|YP_003726174.1| 284 NYMLSNPPFGKDWKKEQNFILEEAKSA 310
                                       *********999988877766555555 PP

>> DUF4355  Domain of unknown function (DUF4355)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.2   3.2e+03      97     116 ..     433     452 ..     426     458 .. 0.82
   2 ?   14.9   7.1   9.3e-06     0.024      51     117 ..     487     553 ..     479     557 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.2
                           DUF4355  97 aeetkknvetfkelfnkave 116
                                        e  +++++t+++l+n+ +e
  gi|298674424|ref|YP_003726174.1| 433 HEISSEQIDTITNLHNNFNE 452
                                       57788999******999877 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 9.3e-06
                           DUF4355  51 eleklqkeleelkaelarkelkaearkvlaekkipiellnlvvgedaeetkknvetfkelfnkavek 117
                                       e  k+qk++ +l   ++rk+ +++ ++ ++ +k++ +++++++ +d e+ +kn + f +++n+ ++k
  gi|298674424|ref|YP_003726174.1| 487 EQLKEQKAFKNLAVSKKRKNTEEKEKEEAEGQKLQDSIIEMLSEMDSEKFYKNRDEFWKVLNDNLKK 553
                                       67799********************************************************998877 PP

>> AviRa  RRNA methyltransferase AviRa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.1e-05      0.08      51     101 ..     201     257 ..     182     268 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.1e-05
                             AviRa  51 egapl.tlyDpCCGgayLltvlgllhgkkikk.....vlasDvdeevlelakkNLsL 101
                                       +++p+ t+yDp CG++ +lt+      k+i++     +++ +v+ e+ ++ak+ + L
  gi|298674424|ref|YP_003726174.1| 201 HNTPIrTIYDPACGTGGMLTIANDHILKEINSnadiwLFGQEVNPETFAIAKSDMML 257
                                       4445438*************9865444444432333388999999999999988876 PP

>> CRM1_repeat_2  CRM1 / Exportin repeat 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.019        48      15      25 ..     331     341 ..     328     351 .. 0.89
   2 ?    5.7   0.0    0.0045        12      26      57 ..     397     428 ..     395     431 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.019
                     CRM1_repeat_2  15 vlierMakPeE 25 
                                        +i++M++Pe+
  gi|298674424|ref|YP_003726174.1| 331 HMISKMKRPED 341
                                       6********96 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0045
                     CRM1_repeat_2  26 VliveneeGeivretvkdtdtialYktmretL 57 
                                       V iv+n + +  + +++ +d+ + Y++mr+ L
  gi|298674424|ref|YP_003726174.1| 397 VWIVTNRKEDHRKGKIQLVDARECYQKMRKSL 428
                                       789**************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (679 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1835  (0.102348); expected 358.6 (0.02)
Passed bias filter:                      712  (0.0397122); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.72u 0.29s 00:00:01.01 Elapsed: 00:00:00.44
# Mc/sec: 4663.70
//
Query:       gi|298674425|ref|YP_003726175.1|  [L=461]
Description: restriction modification system DNA specificity domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-36  125.8  12.5    5.6e-18   65.7   0.6    2.1  2  Methylase_S  Type I restriction modification DNA specificity 
  ------ inclusion threshold ------
       0.14   11.9   0.6        4.7    6.9   0.1    2.5  2  Spo7_2_N     Sporulation protein family 7
       0.35   10.7   6.4        2.2    8.1   0.5    2.8  3  DSPc         Dual specificity phosphatase, catalytic domain
          3    8.2   9.6        5.2    7.4   1.5    3.3  2  Osmo_CC      Osmosensory transporter coiled coil


Domain annotation for each model (and alignments):
>> Methylase_S  Type I restriction modification DNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.5   5.6   2.9e-21   1.3e-17       1     162 [.      36     213 ..      36     219 .. 0.86
   2 !   65.7   0.6   1.2e-21   5.6e-18       1     167 [.     254     435 ..     254     436 .. 0.91

  Alignments for each domain:
  == domain 1  score: 64.5 bits;  conditional E-value: 2.9e-21
                                       ETT-EEEEHHHHEEE.EE-----TTGGTTT--EEEE-HH.HCCT......EE-HHHHCCTT---B-TT-EEEE-S.. CS
                       Methylase_S   1 pedwevvkLgdvfei.kkgktpkkkelkengkypyirag.ilnn......kvvkdglgykkkyilpkgdilissr.. 67 
                                       pe w+v++L  v++  k+g+t ++  +    +yp+ r++ i+n+       ++ +  + +k yil+k+dilis +  
  gi|298674425|ref|YP_003726175.1|  36 PEHWDVKQLRRVIKSlKNGTTAPQ-LDSGTTNYPVTRIEtISNGyinynnVGYLKENDVDKRYILNKDDILISHIns 111
                                       799************888888887.9*************7777799998777777788889999*********99** PP

                                       .SSTT-EEEESS-BEE-TTEEEEEEST.TT--HHHHHHHHH...HCHHHHHHHCCSSTTT---HHHHCC-EEEE--H CS
                       Methylase_S  68 .atiGkvayrdkkyylnqsvivlipkn.kkkineflylyll...lklkklkslsvgstqpkltkenlkkikIplPpl 139
                                        ++iG+ a+ + + +l ++++ l++++ ++ i  fl++yl+   +k+++ ++ + + +q++++ + lk++k++ P+ 
  gi|298674425|ref|YP_003726175.1| 112 lEYIGNCAIYKDNETLVHGMNLLRLIPdDNIIPDFLIYYLKsknFKYSARIHAKPAINQASVSSTVLKSLKFSYPSN 188
                                       ***************************888889*******954434444444499********************** PP

                                       .HHHHHHHHHHHHHHH.HHHHHHHH CS
                       Methylase_S 140 .eeQkkIakiLsqldn.tielekki 162
                                        +eQk Ia +L++ +    +l++k+
  gi|298674425|ref|YP_003726175.1| 189 fNEQKSIANFLDKETHkIDKLIEKK 213
                                       ************9888444455544 PP

  == domain 2  score: 65.7 bits;  conditional E-value: 1.2e-21
                                       ETT-EEEEHHHHEEEEE-----TT.GGTTT--EEEE-HH.HCCT.........EE-HHHHCCTT---B-TT-EEEE- CS
                       Methylase_S   1 pedwevvkLgdvfeikkgktpkkk.elkengkypyirag.ilnn.........kvvkdglgykkkyilpkgdiliss 66 
                                       pe w+vvkL+ +   k +  p  + ++ +ng  p+++a  i+n+           ++d + y+ k++ +k d+l+++
  gi|298674425|ref|YP_003726175.1| 254 PEHWDVVKLKYLLRSKVTDGPHESpAFVDNGI-PFLSADsIQNGklkfencryVPYEDHIRYIRKCKPEKYDLLLGK 329
                                       799************99999999978888776.******99999*******99999********************* PP

                                       SSSTT-EEEESS-..BEE-TTEEEEEESTTT--HHHHHHHHH..HCHHHHHHHCCSSTTT---HHHHCC-EEEE--H CS
                       Methylase_S  67 ratiGkvayrdkk..yylnqsvivlipknkkkineflylyll..lklkklkslsvgstqpkltkenlkkikIplPpl 139
                                        a++Gkva+ d++  +   + +  ++p + +++++ ly+ l   + +k++  l+   tq +l +++++++kI lP+ 
  gi|298674425|ref|YP_003726175.1| 330 AASVGKVALVDVDfeFSIWSPLALIKPDTRELNSKLLYYVLRsrYVQKQIDMLNHTNTQDNLGMKEIENLKIILPSV 406
                                       ************6226888889999997666776888888889999999999999********************** PP

                                       HHHHHHHHHHHHHHH.HHHHHHHHHHHHH CS
                       Methylase_S 140 eeQkkIakiLsqldn.tielekkikneie 167
                                       +eQk+Ia++L+q ++   el++ki+ +ie
  gi|298674425|ref|YP_003726175.1| 407 SEQKQIADYLDQRTSkIDELINKINHQIE 435
                                       ***************999**********9 PP

>> Spo7_2_N  Sporulation protein family 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1    0.0011       4.7      31      52 ..      32      53 ..      29      59 .. 0.88
   2 ?    2.5   0.1     0.026   1.2e+02      31      38 ..     250     257 ..     247     269 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0011
                          Spo7_2_N 31 LGgIPelWlqeqrksiyksllk 52
                                      LG+IPe+W  +q ++++ksl++
  gi|298674425|ref|YP_003726175.1| 32 LGEIPEHWDVKQLRRVIKSLKN 53
                                      9*******99999999999865 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.026
                          Spo7_2_N  31 LGgIPelW 38 
                                       LG+IPe+W
  gi|298674425|ref|YP_003726175.1| 250 LGEIPEHW 257
                                       9******* PP

>> DSPc  Dual specificity phosphatase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       2.2     1e+04      60      79 ..     110     129 ..      82     131 .. 0.54
   2 ?    5.2   0.2    0.0039        17      37      75 ..     177     215 ..     148     217 .. 0.75
   3 ?    8.1   0.5   0.00048       2.2      23      72 ..     382     429 ..     370     443 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.2
                                       HHHHHHHHHH.HHTT-EEEEE CS
                              DSPc  60 eeavefidka.kqkgkkvlVH 79 
                                       +++ e+i ++   k ++ lVH
  gi|298674425|ref|YP_003726175.1| 110 NSL-EYIGNCaIYKDNETLVH 129
                                       332.22332224455555555 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0039
                                       TTTSEEEEECCESSTTSCCGGGHHHHHHHHHHHHHTT-E CS
                              DSPc  37 kseieklripvedehetkiskyleeavefidkakqkgkk 75 
                                         +  k+++p + ++++ i+++l++ +  idk+ +k+++
  gi|298674425|ref|YP_003726175.1| 177 VLKSLKFSYPSNFNEQKSIANFLDKETHKIDKLIEKKQR 215
                                       3467889999999*******************9888765 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.00048
                                       EEESSSSSECECCTTTTSEEEEECCES.STTSCCGGGHHHHHHHHHHHHHT CS
                              DSPc  23 invtkevpnanalkkseieklripved.ehetkiskyleeavefidkakqk 72 
                                       +n t++++n   l ++eie+l+i +   +++++i++yl++ ++ id++ +k
  gi|298674425|ref|YP_003726175.1| 382 LNHTNTQDN---LGMKEIENLKIILPSvSEQKQIADYLDQRTSKIDELINK 429
                                       567777776...678899999998655599****************99776 PP

>> Osmo_CC  Osmosensory transporter coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   1.4     0.023     1e+02      26      40 ..     204     218 ..     194     230 .. 0.71
   2 ?    7.4   1.5    0.0012       5.2      10      39 ..     416     445 ..     407     447 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.023
                                       HHHHHHHHHHHHHHH CS
                           Osmo_CC  26 eeIaaLeekRqrLvd 40 
                                       + I +L ek+qrLv+
  gi|298674425|ref|YP_003726175.1| 204 HKIDKLIEKKQRLVE 218
                                       457777777777775 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0012
                                       XXXXXTHHHHHHHHHHHHHHHHHHHHHHHH CS
                           Osmo_CC  10 LqehYdnIEqkvedideeIaaLeekRqrLv 39 
                                       L ++  +I + ++ i+++I+ L+e R+ L+
  gi|298674425|ref|YP_003726175.1| 416 LDQRTSKIDELINKINHQIEYLKEYRTALI 445
                                       667778999******************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1027  (0.0572815); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 3177.56
//
Query:       gi|298674426|ref|YP_003726176.1|  [L=988]
Description: hypothetical protein Metev_0465 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.9e-26   91.1   1.1    3.1e-25   89.2   1.1    2.0  1  SWI2_SNF2  SWI2/SNF2 ATPase
    3.8e-17   62.9   5.1    4.7e-17   62.6   2.3    2.5  2  HSDR_N     Type I restriction enzyme R protein N terminus (HS
    4.1e-16   59.4   0.1    1.4e-15   57.7   0.1    1.9  1  ResIII     Type III restriction enzyme, res subunit
    5.3e-09   36.1   0.5    2.9e-08   33.7   0.1    2.4  3  DEAD       DEAD/DEAH box helicase
  ------ inclusion threshold ------
      0.037   14.1   0.8        1.4    9.0   0.0    2.8  2  YopX       YopX protein
       0.11   12.6  10.6       0.16   12.0   0.0    4.1  4  DUF87      Helicase HerA, central domain
       0.87   10.1   3.8        2.2    8.8   0.2    2.6  2  DUF3106    Protein of unknown function (DUF3106)


Domain annotation for each model (and alignments):
>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.2   1.1   1.2e-28   3.1e-25       1     203 [.     269     516 ..     269     530 .. 0.77

  Alignments for each domain:
  == domain 1  score: 89.2 bits;  conditional E-value: 1.2e-28
                         SWI2_SNF2   1 qQyravekavervke.gdrkgGviWHtqGSGKsltmvflakklle.eelknp....kvvvvtDRkdLdkQlsktfak 71 
                                       +Q+ av++++e+++  g  +  ++ H +GSGKs+t ++l++kl   ++ +n      ++v+tDR+ Ld+Qls+t+ +
  gi|298674426|ref|YP_003726176.1| 269 HQLKAVNSMIENARLnGPGHRYLVQHSTGSGKSFTIAWLCNKLSGlHDENNNrifdSIIVITDRRVLDQQLSSTMFE 345
                                       8**********99864778999*********************9876555541222589**************9888 PP

                         SWI2_SNF2  72 a.....geekpkqaesrkeLkellekesekiifttiqKfe..eeekeklevlsereniivlvDEaHRsqyg...... 135
                                       +     + e  ++ +++++Lk+ l +++++ii++t+q f       ++ ++ls+r+ + ++vDEaH sq+g      
  gi|298674426|ref|YP_003726176.1| 346 FeqvrgTVEWIDSNKKSEQLKQAL-ESNKEIIVVTLQTFPflV---DEANQLSDRN-FAIVVDEAHSSQSGetargs 417
                                       733332233446888999******.6699**********7542...2357788776.99****************** PP

                         SWI2_SNF2 136 ......................elakklrkal...pnaafigFTGTPilkkdkktkevFg........eyidkYtik 179
                                                              ++++++k++   +n ++++FT TP +    kt e Fg        e  + Y++k
  gi|298674426|ref|YP_003726176.1| 418 rkvlvsaddvqyedemekdvedVINSEIEKTVgpaKNISYFAFTATPKQ----KTLELFGtkmpdgsyEPYHLYSMK 490
                                       ******************99995555666554333899*********66....577788766666666678****** PP

                         SWI2_SNF2 180 eaveDgavvp..ilYesrlaklelke 203
                                       +a+e g +++    Y+   +  elk+
  gi|298674426|ref|YP_003726176.1| 491 QAIEEGFILNplENYTTFETYFELKK 516
                                       ******99984223444444444444 PP

>> HSDR_N  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.6   2.3   1.8e-20   4.7e-17       3     179 ..       6     193 ..       4     208 .. 0.71
   2 ?   -0.7   0.0      0.45   1.1e+03     164     187 ..     738     764 ..     715     837 .. 0.68

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 1.8e-20
                                       SHHHHHH.HHHHHHHHTT-EE...............----SHHHHHHHHHHHHHHHH-HHHHHHHH..TT--HHH.. CS
                            HSDR_N   3 sEaeleqelidellrelGyqvlskkdveiegrrpevrkskaevaleknlreqlgalnikkltkrla..lsdgnke.. 75 
                                       sE++ e++ +  l+++ Gy + +++d   e   +    ++  +a+++++ e+l++ + +++++r+   l +++++  
  gi|298674426|ref|YP_003726176.1|   6 SENTFENDIVQTLVNQKGYIHRKNSDYDKELCMDPEMVIEFIWATQSKEWEKLEKQYGEQVKERFLerLQKNIERrg 82 
                                       89999999999999********9999998887666334445677777777777777778888888877333333311 PP

                                       HHHHHHTS.-EE.EE.....TS-EEEEESS-SSSGGGS-EEEEE----SSSS---EEEEEEETTEEEEEEEE--T.. CS
                            HSDR_N  76 fyellkeg.kvk.fk.....egrkknikLiDkknlenNrfqvvnQvtvtgnqkrrpDivlfvnglplvviElKrp.. 143
                                        +++lk+g k    +      + + + ++   +  ++Nrf+v++Q+ ++ ++++ +D+vlf+nglp+++ ElK+p  
  gi|298674426|ref|YP_003726176.1|  83 TLDVLKKGiKDRgCRfdlvyFKPETTLNVEHQDRYKANRFSVIQQLHYNTKNEKSIDLVLFINGLPIITSELKNPln 159
                                       3444444444333333365644555555567777888***************************************8 PP

                                       .T-HHHHHHHHTSS---.---S.SSGGGGG--EEEEE- CS
                            HSDR_N 144 .gtieeAinQikryrkeksdvs.ipqlfrYlqfgvisn 179
                                        +++e Ai+Q++++r++k   + +   + +++f  +++
  gi|298674426|ref|YP_003726176.1| 160 eQNVEHAIHQYRKDRSPK--EPlLSPRRCFVHF--AVD 193
                                       66************9996..2245555555544..344 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.45
                                       S...SSGGGGG--EEEEE-SS-EEEEE CS
                            HSDR_N 164 s...ipqlfrYlqfgvisngketrfya 187
                                       +   +++  +++q ++++ g+++++y+
  gi|298674426|ref|YP_003726176.1| 738 RiftEDDVEKFAQEYFSTSGTQAKLYS 764
                                       345555566666666666666666654 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.7   0.1   5.4e-19   1.4e-15       4     170 ..     266     465 ..     264     466 .. 0.73

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 5.4e-19
                                       E-HHHHHHHHHHT......TTS.EEEEEESTTSTHHHHHHHHHHHH-S...........-EEEEESSHHHHHHHH.. CS
                            ResIII   4 lreyQeeaienlleklkskrdk.rglikmaTGtGKTlvaaklierllkkgkee......kflflvprkslleqtl.. 71 
                                       +r++Q +a+++++e+   ++   r+l+++ TG+GK++++a l+ +l+  ++e+       ++++ +r+ l +q+   
  gi|298674426|ref|YP_003726176.1| 266 PRYHQLKAVNSMIENARLNGPGhRYLVQHSTGSGKSFTIAWLCNKLSGLHDENnnrifdSIIVITDRRVLDQQLSst 342
                                       69***********8887666655999*********************999888999**99************99944 PP

                                       .HHGGGGTGG.....GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS CS
                            ResIII  72 .eefkkflseayke.igkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlga 146
                                         ef+++  +      ++k+s++ k+     ++nk+i+v+t q++         ++  +l+dr+  i++DEaH +++
  gi|298674426|ref|YP_003726176.1| 343 mFEFEQVRGTVE-WiDSNKKSEQLKQ---ALESNKEIIVVTLQTFPFLV-----DEANQLSDRNFAIVVDEAHSSQS 410
                                       445555555543.2223333333333...579*************9999.....778888999999*********** PP

                                       ............T............TTHHHHHT---...........SEEEEEESS-S CS
                            ResIII 147 k...........k............swreilekfke...........avllglTATpe 170
                                                   +             ++ +   +++              +++TATp+
  gi|298674426|ref|YP_003726176.1| 411 GetargsrkvlvSaddvqyedemekDVEDV---INSeiektvgpaknISYFAFTATPK 465
                                       966666555555055565556444433332...2112223344444488999999998 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.3   5.8e+03      97     152 ..      95     150 ..      57     157 .. 0.55
   2 !   33.7   0.1   1.1e-11   2.9e-08      13     170 ..     286     465 ..     268     471 .. 0.67
   3 ?   -2.7   0.0       1.6   4.2e+03     150     176 .]     588     615 ..     555     615 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.3
                                       T..CSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHH CS
                                       x..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  97 g..vdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqi 152
                                       g   d+v+  p+  +++ ++ +  ++  rf V+   +   +++ s ++   +n lp i
  gi|298674426|ref|YP_003726176.1|  95 GcrFDLVYFKPETTLNVEHQDR--YKANRFSVIQQLHYNTKNEKSIDLVLFINGLPII 150
                                       1337777777777777555555..6777777777777666666666666556655555 PP

  == domain 2  score: 33.7 bits;  conditional E-value: 1.1e-11
                                       TTCEEEEEESTTSSHHHH..HHHHHHHHHHHS.TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSS CS
                                       xxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  13 gggdvlvaaeTGsGKTla..flipvlqivyet.kgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggva 86 
                                        g+  lv+  TGsGK+    +l   l+ + ++ +++    +++++  r L +q  +++ +f +  + +v++i ++++
  gi|298674426|ref|YP_003726176.1| 286 PGHRYLVQHSTGSGKSFTiaWLCNKLSGLHDEnNNRIFDSIIVITDRRVLDQQLSSTMFEFEQVRG-TVEWIDSNKK 361
                                       56899**********765114455555554445566666788888889999999999999999644.5665555555 PP

                                       HHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEE.EEEETHHHHHHTTTHHHHHHHHHHSHHHCTTST.TT.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.. RF
                              DEAD  87 ardqlskldngvdivvgtpgrlddllstgklnlsqvrf.lVlDEadrlldqgfsdfinrilnqlpqitcdgk.lq.. 159
                                        ++ +++l+++ +i+v t + +  l+++ + +ls+ +f +V+DEa+  ++ +  +  +++l + ++ + + + ++  
  gi|298674426|ref|YP_003726176.1| 362 SEQLKQALESNKEIIVVTLQTFPFLVDEAN-QLSDRNFaIVVDEAHSSQSGETARGSRKVLVSADDVQYEDEmEKdv 437
                                       56666667899***********99995333.699999989*******999877777777666554443333323356 PP

                                       .................SEEEEEESSBS CS
                                       .................xxxxxxxxxxx RF
                              DEAD 160 .................rqvivlSATlp 170
                                                            +++AT++
  gi|298674426|ref|YP_003726176.1| 438 edvinseiektvgpaknISYFAFTATPK 465
                                       6666666666666665444666666666 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.6
                                       HHHCTTSTTTSEEEEEESSBS.HHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                              DEAD 150 pqitcdgklqrqvivlSATlp.kdvkkl 176
                                       +qi+++g   + ++++S T++ +dv+k+
  gi|298674426|ref|YP_003726176.1| 588 KQINDNGYPFEALVAFSGTVEgNDVEKV 615
                                       4455554433458899999999998875 PP

>> YopX  YopX protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1     0.063   1.6e+02      66      94 ..      10      38 ..       6      63 .. 0.82
   2 ?    9.0   0.0   0.00053       1.4      52     117 ..     309     375 ..     261     378 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.063
                                      ETTEEEEETTTSTTCEC.EEEEEECCCCE CS
                              YopX 66 yegDivkvslkrkyivkkevvkykdgkfv 94
                                      +e+Div++ +++k + +++ ++y+++ ++
  gi|298674426|ref|YP_003726176.1| 10 FENDIVQTLVNQKGYIHRKNSDYDKELCM 38
                                      9********99999999999999877665 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00053
                                       EEEEEEE-TTS-EEETTEEEEETTTSTTCEC....EEEEEECCCCEECCEEES-SS--SHHCCCTTTTE CS
                              YopX  52 mqytGlkDkngkeIyegDivkvslkrkyivkk...evvkykdgkfvvtvekesakkdliqllwfevktf 117
                                        +  Gl+D+n   I++  iv +  +r   +++   ++ ++++ +  v+++++++k + +++    +k++
  gi|298674426|ref|YP_003726176.1| 309 NKLSGLHDENNNRIFDSIIVIT-DRRVL-DQQlssTMFEFEQVRGTVEWIDSNKKSEQLKQALESNKEI 375
                                       6789***********9866555.33333.3334669999**********98777776666666655555 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       2.2   5.8e+03     131     179 ..      55     102 ..      40     143 .. 0.59
   2 ?   12.0   0.0   6.3e-05      0.16      31      51 ..     295     318 ..     288     333 .. 0.77
   3 ?   -4.1   0.0       5.4   1.4e+04     185     210 ..     357     382 ..     335     389 .. 0.60
   4 ?    0.4   3.8      0.23   5.8e+02     102     102 ..     862     862 ..     693     971 .. 0.59

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.2
                             DUF87 131 keekeklssdepveklleelkkekeelrklknqaiarlldkledllrkg 179
                                       +e+ ek  +++  e++le l+ ++ e+r   + ++++++d+  ++++ +
  gi|298674426|ref|YP_003726176.1|  55 WEKLEKQYGEQVKERFLERLQ-KNIERRGTLDVLKKGIKDRGCRFDLVY 102
                                       555555556666666666666.333555566666666655555555444 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 6.3e-05
                             DUF87  31 sTGsGKSntvavLleelle...kk 51 
                                       sTGsGKS+t+a L+++l     ++
  gi|298674426|ref|YP_003726176.1| 295 STGSGKSFTIAWLCNKLSGlhdEN 318
                                       8****************9876633 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 5.4
                             DUF87 185 sstdliallleklekegkitiidlsg 210
                                       +s++  ++l + le++++i ++ l+ 
  gi|298674426|ref|YP_003726176.1| 357 DSNKKSEQLKQALESNKEIIVVTLQT 382
                                       44444555556667777777776665 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.23
                             DUF87 102 l 102
                                       l
  gi|298674426|ref|YP_003726176.1| 862 L 862
                                       1 PP

>> DUF3106  Protein of unknown function (DUF3106)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.4       0.2   5.1e+02      51      74 ..      51      74 ..      47      85 .. 0.71
   2 ?    8.8   0.2   0.00087       2.2      11      78 ..     765     832 ..     758     835 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.2
                           DUF3106 51 rmeewakLspeqreqarenyqklk 74
                                      + +ew+kL+++  eq++e++ +  
  gi|298674426|ref|YP_003726176.1| 51 QSKEWEKLEKQYGEQVKERFLERL 74
                                      557888888888888888886554 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00087
                           DUF3106  11 aLaplaeewnelspeqreklleiaerykkltpeeqkrlqermeewakLspeqreqarenyqklkqLpp 78 
                                       +L+p+ +ew++ ++e+r+ + +  +++ +l +   + +  r +e +kL +  r  +++    +k+Lp+
  gi|298674426|ref|YP_003726176.1| 765 ILEPVIQEWESRPEEERKDFKKQMQSFTRLYAFLSHIMTFRDTELEKLYQFSRFLVKKLKIGYKRLPT 832
                                       78999999999999999999999999999988888888888888888888888888777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (988 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1049  (0.0585086); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.81u 0.29s 00:00:01.10 Elapsed: 00:00:00.47
# Mc/sec: 6358.90
//
Query:       gi|298674427|ref|YP_003726177.1|  [L=172]
Description: TATA-box-binding family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.1e-34  115.4   0.1      2e-17   62.9   0.0    2.0  2  TBP              Transcription factor TFIID (or TATA-binding 
  ------ inclusion threshold ------
      0.039   14.2   1.0      0.077   13.3   1.0    1.5  1  Antimicrobial15  Ocellatin family
      0.044   14.2   0.3      0.085   13.3   0.1    1.6  2  DUF1048          Protein of unknown function (DUF1048)


Domain annotation for each model (and alignments):
>> TBP  Transcription factor TFIID (or TATA-binding protein, TBP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.1   1.9e-17   1.2e-13       3      84 ..       2      81 ..       1      82 [. 0.92
   2 !   62.9   0.0   3.3e-21     2e-17       3      79 ..      92     166 ..      90     170 .. 0.94

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 1.9e-17
                                      EEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHH CS
                               TBP  3 kiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiapi 81
                                      +i+Nvva+++l++ ldL  l+  +  ++++        l +rl+ +++++ +++sGk+ itG+ks+e++ +  +++++i
  gi|298674427|ref|YP_003726177.1|  2 EIVNVVATVKLNSYLDLASLEDAL--QDTQVVSTSKVWLKMRLMPENYYVAFYKSGKFLITGVKSTEDISTISNRVLDI 78
                                      8*******************8777..7777777777789999999********************************** PP

                                      HHH CS
                               TBP 82 lkk 84
                                      lk+
  gi|298674427|ref|YP_003726177.1| 79 LKN 81
                                      *97 PP

  == domain 2  score: 62.9 bits;  conditional E-value: 3.3e-21
                                       EEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHH CS
                               TBP   3 kiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkia 79 
                                        iqN+va  +++++  Lek+ +++++ +++Yepe+fpgl+y+  ++ +++l+FssGkvvitG+k e+ l++ + k+ 
  gi|298674427|ref|YP_003726177.1|  92 YIQNIVAVDKIEMNSTLEKIIYNLDPSKSSYEPEQFPGLIYK--NWGASFLLFSSGKVVITGVKDENYLDDLITKFK 166
                                       59*********************99****************9..79**********************999999886 PP

>> Antimicrobial15  Ocellatin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.0   1.3e-05     0.077       1      11 [.      75      85 ..      75      86 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.3e-05
                   Antimicrobial15  1 VlDILKgAAKd 11
                                      VlDILK+A+ d
  gi|298674427|ref|YP_003726177.1| 75 VLDILKNAGID 85
                                      9*******955 PP

>> DUF1048  Protein of unknown function (DUF1048)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   1.4e-05     0.085      18      74 ..      41     100 ..      29     112 .. 0.80
   2 ?   -3.0   0.0       1.7     1e+04      70      87 ..     149     166 ..     147     169 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.4e-05
                                       HHS-HHHHHHHHHHHHHHCCCTB-SHHHHHHHHHHHHHHHHHHHHT....T--HHHHH-S- CS
                           DUF1048  18 kaLPedYqtvykeiqkylwkvgategadlleilkevldLfEeaaad....gkevkevvGed 74 
                                       + +Pe+Y++++ +  k+l++ g+ + +d+ +i + vld++ +a +d    ++ ++++v  d
  gi|298674427|ref|YP_003726177.1|  41 RLMPENYYVAFYKSGKFLIT-GVKSTEDISTISNRVLDILKNAGIDvdieDTYIQNIVAVD 100
                                       568*************9985.789999***************9764222266777776655 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.7
                                       HH-S-HHHHHHHCCTTSH CS
                           DUF1048  70 vvGedvaaFadelvkdsk 87 
                                       ++G + +++ d+l+++ k
  gi|298674427|ref|YP_003726177.1| 149 ITGVKDENYLDDLITKFK 166
                                       567777778888887666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1333.36
//
Query:       gi|298674428|ref|YP_003726178.1|  [L=242]
Description: hypothetical protein Metev_0467 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-10   39.8   0.4    5.5e-10   39.2   0.4    1.2  1  PLDc_2          PLD-like domain
     0.0012   18.1   0.1      0.002   17.3   0.1    1.3  1  Regulator_TrmB  Archaeal transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.038   13.8   0.6      0.038   13.8   0.6    3.3  3  zf-CpG_bind_C   CpG binding protein zinc finger C terminal do
       0.68   10.0  14.6        2.7    8.1  10.4    3.3  2  DZR             Double zinc ribbon
        8.7    6.3  12.0         15    5.6   6.0    2.9  2  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)


Domain annotation for each model (and alignments):
>> PLDc_2  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.4   1.5e-13   5.5e-10       2     125 ..      15     128 ..      14     136 .. 0.74

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 1.5e-13
                            PLDc_2   2 iqliksAkksidiatyyfvsdreildallkaakrgvkvrilldskkddagavdeaslkelkellleagvevrvfetl 78 
                                        q ik+A +++ i+++y++ ++ + d + ++ + + ++r++ ++   +  + + +++++lk+l   + ++  ++   
  gi|298674428|ref|YP_003726178.1|  15 EQIIKNADDKLIIVSPYLQINERLKDLIQDKDRMKIDIRVIYGK---N--DLKPEENNWLKSL---NSIRTNFC--- 80 
                                       689***************77777555555577777********9...3..3445678888888...34553343... PP

                            PLDc_2  79 lgslHaKlylidgktvivGSsNltkrgldlnlElnvviedk...elakel 125
                                        + lHaK+yl d k ++++S+N+ + +  +n E+++ +++    +l++ +
  gi|298674428|ref|YP_003726178.1|  81 -KNLHAKCYLND-KEALITSMNMYRYSEVHNNEMGIYVSKDsdpKLYSDI 128
                                       .347******97.678999*****************99877333444433 PP

>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   5.7e-07     0.002      10     113 ..       9     118 ..       5     132 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.7e-07
                                       HHHHHHHHHHHH-SSEEEEEE-GGGHHHHHHHHHHHHHT.T-EEEEEESS.----GGGSSSSEEEEEE-S---S..E CS
                    Regulator_TrmB  10 tvierieelIesAenelivslpselLeelreeliaaaer.gvtVllliyp.dedleeldleevatevrvrrsga.pl 83 
                                        v   +e++I++A+  li+  p+ +++e  ++li+ ++r ++ + +++ + d ++ee+++++  + +r++  +    
  gi|298674428|ref|YP_003726178.1|   9 GVSHHLEQIIKNADDKLIIVSPYLQINERLKDLIQDKDRmKIDIRVIYGKnDLKPEENNWLKSLNSIRTNFCKNlHA 85 
                                       5777899*******************9988888888774245555444449999**************986665433 PP

                                       EEEETTTEEEEE-SSS-...EEEE--HHHHHHH CS
                    Regulator_TrmB  84 lvivDrkrgvvaprevl...rdkeeeyaiifke 113
                                           + k++++ + ++    + +++e +i++++
  gi|298674428|ref|YP_003726178.1|  86 KCYLNDKEALITSMNMYrysEVHNNEMGIYVSK 118
                                       344444444554444555666666666666665 PP

>> zf-CpG_bind_C  CpG binding protein zinc finger C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2       0.3   1.1e+03     134     157 ..      73      96 ..      58     111 .. 0.75
   2 ?   13.8   0.6     1e-05     0.038      65     108 ..     151     194 ..     126     199 .. 0.77
   3 ?    3.0   3.2     0.021        75      78     114 ..     200     238 ..     193     240 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.3
                     zf-CpG_bind_C 134 naktktYCkRLkvlCpEHtkepkv 157
                                       n+    +Ck L++ C    ke+ +
  gi|298674428|ref|YP_003726178.1|  73 NSIRTNFCKNLHAKCYLNDKEALI 96 
                                       666778999999988766666655 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1e-05
                     zf-CpG_bind_C  65 lslkeeeeeeedeedselsvaCvtCgheislkkalkHmekCfak 108
                                       + + ++++++++++++  + +C+ Cg +isl+ +    +kCf+ 
  gi|298674428|ref|YP_003726178.1| 151 SDVFKKQSNTKNNSNKSDNGYCIRCGDSISLNPMYPYCKKCFST 194
                                       25555666666788888899**********************75 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.021
                     zf-CpG_bind_C  78 edselsvaCvtCgh..eislkkalkHmekCfakyEsqts 114
                                       +++ ++ aC +Cg+  + +++ka      C++ky     
  gi|298674428|ref|YP_003726178.1| 200 DENIEESACHICGKsnKSNISKAKPTCYNCYKKYKDTYE 238
                                       45556789*****9556777788889999***9987665 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.63   2.3e+03      39      47 ..      74      82 ..      70      87 .. 0.74
   2 ?    8.1  10.4   0.00074       2.7       1      48 [.     172     229 ..     159     239 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.63
                               DZR 39 dpearfCpe 47
                                      + +++fC++
  gi|298674428|ref|YP_003726178.1| 74 SIRTNFCKN 82
                                      567788875 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00074
                               DZR   1 CpqCgee..lppdarfCseCgtklkavaa....edrCpsCgekvdpearf....CpeC 48 
                                       C +Cg    l+p   +C++C ++ k+  +    e +C  Cg++++++ +     C +C
  gi|298674428|ref|YP_003726178.1| 172 CIRCGDSisLNPMYPYCKKCFSTWKKKGDenieESACHICGKSNKSNISKakptCYNC 229
                                       8888888444555558999999888766699999999999999777644334447666 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   6.0    0.0041        15      25      46 ..     187     214 ..     164     218 .. 0.83
   2 ?    2.6   0.3     0.035   1.2e+02      25      34 ..     225     234 ..     222     238 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0041
                                       E-HHHHHHHHH......TT-B-TTT--B CS
                        zf-C3HC4_3  25 lCeeCaekllk......rkkkCpiCrrp 46 
                                       +C++C+++++k      ++  C+iC ++
  gi|298674428|ref|YP_003726178.1| 187 YCKKCFSTWKKkgdeniEESACHICGKS 214
                                       8********999*************986 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.035
                                       E-HHHHHHHH CS
                        zf-C3HC4_3  25 lCeeCaekll 34 
                                       +C++C +k++
  gi|298674428|ref|YP_003726178.1| 225 TCYNCYKKYK 234
                                       6888888874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1536  (0.0856713); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1691.04
//
Query:       gi|298674429|ref|YP_003726179.1|  [L=54]
Description: hypothetical protein Metev_0468 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.022   14.5   2.0       0.24   11.1   0.5    2.2  2  zinc_ribbon_2  zinc-ribbon domain


Domain annotation for each model (and alignments):
>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.006   1.1e+02       2      15 ..      12      25 ..      12      25 .. 0.90
   2 ?   11.1   0.5   1.4e-05      0.24       7      19 ..      34      46 ..      33      46 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.006
                     zinc_ribbon_2  2 CpnCGaelqdnakF 15
                                      C +C   l+d++++
  gi|298674429|ref|YP_003726179.1| 12 CVRCDVDLKDDDTY 25
                                      999*999*999986 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 1.4e-05
                     zinc_ribbon_2  7 aelqdnakFCpyC 19
                                      + ++++a +C++C
  gi|298674429|ref|YP_003726179.1| 34 NSIKKGAMYCENC 46
                                      7899********* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.44
# Mc/sec: 370.60
//
Query:       gi|298674430|ref|YP_003726180.1|  [L=55]
Description: hypothetical protein Metev_0469 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 375.40
//
Query:       gi|298674431|ref|YP_003726181.1|  [L=184]
Description: hypothetical protein Metev_0470 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1193.86
//
Query:       gi|298674432|ref|YP_003726182.1|  [L=60]
Description: E1-like enzyme family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.05   14.0   0.8       0.68   10.4   0.1    2.5  2  TPR_17        Tetratricopeptide repeat
      0.059   12.9   0.1      0.098   12.2   0.1    1.4  1  TF_Zn_Ribbon  TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   7.6e-05      0.68       2      16 ..      20      34 ..      19      48 .. 0.77
   2 ?   -1.3   0.1      0.43   3.9e+03      13      18 ..      52      57 ..      50      58 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 7.6e-05
                            TPR_17  2 ylkaleldPnnaday 16
                                      y+ +le++P+n+d y
  gi|298674432|ref|YP_003726182.1| 20 YKHFLEKHPSNPDYY 34
                                      999*********965 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.43
                            TPR_17 13 adaynn 18
                                      +++y+n
  gi|298674432|ref|YP_003726182.1| 52 SYSYYN 57
                                      789998 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   1.1e-05     0.098       2      14 ..       4      17 ..       3      23 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.1e-05
                                      EETTTTCEE.CHEE CS
                      TF_Zn_Ribbon  2 kCPnCgstn.lveD 14
                                       CP+Cg+++ +v D
  gi|298674432|ref|YP_003726182.1|  4 FCPECGTSSyVVSD 17
                                      5******8867777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       931  (0.051927); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 421.28
//
Query:       gi|298674433|ref|YP_003726183.1|  [L=282]
Description: integrase family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-17   62.9   0.3    1.6e-14   54.1   0.1    2.3  2  Phage_integrase  Phage integrase family
  ------ inclusion threshold ------
      0.036   14.0   0.3       0.11   12.4   0.1    2.0  2  zinc_ribbon_4    zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0   0.00067         6      22      42 ..      41      61 ..      18      65 .. 0.76
   2 !   54.1   0.1   1.8e-18   1.6e-14      42     168 ..     112     231 ..     110     234 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.00067
                                      HHHHHHHHHHHHT--HHHHTT CS
                   Phage_integrase 22 rdklllellyetGlRisElls 42
                                         ll++ll+ tG+RisE+++
  gi|298674433|ref|YP_003726183.1| 41 DYSLLVRLLFFTGARISEIVG 61
                                      456789************986 PP

  == domain 2  score: 54.1 bits;  conditional E-value: 1.8e-18
                                       T-BGGGEECTTTEEEEEEEECSSSSE..EEEECTHHHHHHHHHHHHHHCHCCTTTSBSSBETTSSB--HHHHHHHHH CS
                   Phage_integrase  42 sLrvkdldlengvilvheregKgske..ravplseealellkellskaleeaeksellfaskrgkplsrqtvrkafk 116
                                       ++rvkd+ ++++ i +  +  K++    r+v + ++ l  ++e +++          l +  +   l+++ ++ +++
  gi|298674433|ref|YP_003726183.1| 112 GIRVKDIAFKDRLIAIYGKSVKTEELkpRTVVVDQKTLDIIQEHINRY--------SLKPDDKIINLNENGAKVFIN 180
                                       689*************766666543255******************99........4444445555678******** PP

                                       HHHHHCT-SSC--TTHHHHHHHHHHHHHCTSHHHHHHHHT-SSCCHHHHHHC CS
                   Phage_integrase 117 raveeagiekpltpHtlRhsfataLleagvdlrvvqkllGHssisttqiYth 168
                                       ++++e++i   l+ H++Rh +a   +++g+d+r++q  lGH++++tt iY +
  gi|298674433|ref|YP_003726183.1| 181 KLKKESKIP-WLSAHKFRHGHAIYCIQNGMDIRTLQLQLGHTDLATTAIYLQ 231
                                       ********9.****************************************86 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.1   9.5e+03      11      17 ..     231     237 ..     231     240 .. 0.84
   2 ?   12.4   0.1   1.3e-05      0.11       3      16 ..     254     267 ..     253     271 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.1
                     zinc_ribbon_4  11 kyeidde 17 
                                       +++idd+
  gi|298674433|ref|YP_003726183.1| 231 QFAIDDR 237
                                       699*996 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 1.3e-05
                     zinc_ribbon_4   3 itCpsCkakyeidd 16 
                                        +CpsC+++y+i  
  gi|298674433|ref|YP_003726183.1| 254 LQCPSCGFQYKIKK 267
                                       79*********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.20s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2139.25
//
Query:       gi|298674434|ref|YP_003726184.1|  [L=151]
Description: hypothetical protein Metev_0474 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-25   88.5   1.9    8.7e-25   87.5   1.9    1.6  1  Pilin_N   Archaeal Type IV pilin, N-terminal


Domain annotation for each model (and alignments):
>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.5   1.9   4.9e-29   8.7e-25       2      80 ..       2      79 ..       1      80 [. 0.89

  Alignments for each domain:
  == domain 1  score: 87.5 bits;  conditional E-value: 4.9e-29
                           Pilin_N  2 AVSpViGviLmvaitvIlaAviaafvlglasneekapqasievkidssastgknavslehkgGdsidt.kdlkivlnse 79
                                      + SpViGviLmvaitvIlaAvi++fv+g+ +n+e+apqasi+ +  s+++ g++ v + h+gG+ id+ ++++i+++++
  gi|298674434|ref|YP_003726184.1|  2 GLSPVIGVILMVAITVILAAVIGSFVFGM-ENPESAPQASIQGSAYSDSD-GDDIVMISHQGGEEIDLhNNVRITMSGN 78
                                      78***************************.9**********777444444.4677*************9******9987 PP

                           Pilin_N 80 g 80
                                      +
  gi|298674434|ref|YP_003726184.1| 79 D 79
                                      5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       874  (0.0487478); expected 358.6 (0.02)
Passed bias filter:                      635  (0.0354175); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1129.53
//
Query:       gi|298674435|ref|YP_003726185.1|  [L=191]
Description: hypothetical protein Metev_0475 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-07   29.5   2.7    8.1e-07   29.4   2.1    1.4  1  PDDEXK_3  PD-(D/E)XK nuclease superfamily
  ------ inclusion threshold ------
      0.029   14.6   0.0        1.2    9.4   0.0    2.1  2  DUF3669   Zinc finger protein


Domain annotation for each model (and alignments):
>> PDDEXK_3  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   2.1     9e-11   8.1e-07      14     112 ..      58     155 ..      44     164 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 9e-11
                          PDDEXK_3  14 VhnelGegllEsvYekaLaveLkkrglkveeqvelpvvYkgkevgeeyrlDllveekvivElKave...elkeehea 87 
                                        + + G+  +E+ Y++ L+ +L+     ++e + +++ Y+    + +yr+D++ve+ v +E+K  +   +++e+   
  gi|298674435|ref|YP_003726185.1|  58 TYFRHGKHKTEKDYQQNLEGKLEV----LTERHGYNIKYEAVPKNGKYRVDFVVENLVGIEMKFYQgghKIEEQLCR 130
                                       566778889999999999999875....5677889****************************96533389999999 PP

                          PDDEXK_3  88 qllnYlkltklklGlliNFnkkklk 112
                                       q++nY k +   +Gl++N  +k+ k
  gi|298674435|ref|YP_003726185.1| 131 QIINYSKYYPKMIGLVLNSTNKNDK 155
                                       ******************8774333 PP

>> DUF3669  Zinc finger protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00013       1.2       8      61 ..      32      88 ..      25      98 .. 0.75
   2 ?    3.3   0.0     0.011        95      19      35 ..     124     141 ..     103     163 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00013
                           DUF3669  8 acrkmtleetgiae...avkafwdndpYyPrPlseetavelgpqdeklWevfktrY.l 61
                                       + k++l++t ++     v  f +n+ Y+   ++++t  ++++ +e++ ev+ +r  +
  gi|298674435|ref|YP_003726185.1| 32 VVVKIKLSQTKTDRvfnNVSEFLENETYFRH-GKHKTEKDYQQNLEGKLEVLTERHgY 88
                                      55666777666555555799*******9998.66666689************998744 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.011
                           DUF3669  19 iae.avkafwdndpYyPr 35 
                                       i+e +++ ++   +YyP+
  gi|298674435|ref|YP_003726185.1| 124 IEEqLCRQIINYSKYYPK 141
                                       555599***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1579  (0.0880696); expected 358.6 (0.02)
Passed bias filter:                      742  (0.0413855); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1215.63
//
Query:       gi|298674436|ref|YP_003726186.1|  [L=188]
Description: glycerophosphoryl diester phosphodiesterase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.1e-08   31.4  12.5    3.1e-07   29.5   5.6    2.1  2  GPDPase_memb    Membrane domain of glycerophosphoryl diester 
    9.2e-06   25.6  10.8    2.9e-05   24.0   4.8    2.4  3  UPF0259         Uncharacterised protein family (UPF0259)
    0.00023   19.6   2.5    0.00036   19.0   2.5    1.2  1  SpecificRecomb  Site-specific recombinase
  ------ inclusion threshold ------
      0.012   15.7   2.0       0.14   12.2   0.2    2.1  2  UPF0242         Uncharacterised protein family (UPF0242) N-te
      0.039   13.9   0.8      0.039   13.9   0.8    3.2  3  OppC_N          N-terminal TM domain of oligopeptide transpor
        4.9    7.1  16.2       0.46   10.4   9.5    2.0  2  DUF5453         Family of unknown function (DUF5453)
        7.2    7.3  17.1       0.33   11.6   3.7    3.1  3  DUF2627         Protein of unknown function (DUF2627)


Domain annotation for each model (and alignments):
>> GPDPase_memb  Membrane domain of glycerophosphoryl diester phosphodiesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   3.3    0.0033       8.4     199     261 ..       6      71 ..       1      86 [. 0.62
   2 !   29.5   5.6   1.2e-10   3.1e-07     162     238 ..      82     158 ..      73     175 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0033
                      GPDPase_memb 199 AlkeSwqltkknflrlllklllliliivivltv..ilsllllllqllldkl.pkkvslilaiinlt 261
                                        lk++w + + nf+++++++++ ++  ++++t+  ++++l++++   ++ + ++ + ++ ++  ++
  gi|298674436|ref|YP_003726186.1|   6 LLKNTWYVFRDNFVAFVVGSIVAVIGSILIVTIapLFYGLTYMALKGVKGVkVEINDVFEGFHHFA 71 
                                       689999*********999998877777776666234666777776666665444444555544444 PP

  == domain 2  score: 29.5 bits;  conditional E-value: 1.2e-10
                      GPDPase_memb 162 ilivllylifylivfylaiRliftLPliilekkslkeAlkeSwqltkknflrlllklllliliivivltvilsllll 238
                                       +l+ ++y++f++  ++l+i l+++LPl+++++++  +A++eS ++ ++n+  +l++ ++  +i ++   + + ++l 
  gi|298674436|ref|YP_003726186.1|  82 VLLFIGYMAFVIPGVILSILLVYALPLLVIKDYNSIDAIRESISFSRENLADTLVIFVIGAFINFVGGAITFGFILS 158
                                       456789***********************************************666555555555554444444433 PP

>> UPF0259  Uncharacterised protein family (UPF0259)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.1    0.0049        12       5      51 ..       3      48 ..       1      71 [. 0.69
   2 !   24.0   4.8   1.1e-08   2.9e-05     129     191 ..      69     131 ..      54     147 .. 0.81
   3 ?   -1.6   0.2      0.75   1.9e+03     143     171 ..     137     168 ..     130     175 .. 0.50

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0049
                           UPF0259  5 vnslyrDtinflrnkiaailllsllsafitvlidsiilPnaeellil 51
                                      v+ l+++t+  +r++++a ++ s+++ +i +++  +i P    l+ +
  gi|298674436|ref|YP_003726186.1|  3 VEGLLKNTWYVFRDNFVAFVVGSIVA-VIGSILIVTIAPLFYGLTYM 48
                                      6779999*********9988877765.55555556777755555555 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 1.1e-08
                           UPF0259 129 llPklliLiflttlliqlGllllliPGiivaillslsPiillkekksildsikasvnitfkni 191
                                        + k  i   +t +l+ +G + ++iPG+i++ill ++  +l++++ + +d+i+ s+  + +n+
  gi|298674436|ref|YP_003726186.1|  69 HFAKSWIFAIITGVLLFIGYMAFVIPGVILSILLVYALPLLVIKDYNSIDAIRESISFSRENL 131
                                       45677788899************************996666666666679*****99988776 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.75
                           UPF0259 143 liqlGllllliPGiiva.illsl..sPiillk 171
                                       +  +G  + ++ G i+   +lsl  + i+ +k
  gi|298674436|ref|YP_003726186.1| 137 IFVIGAFINFVGGAITFgFILSLpfATILYTK 168
                                       33466666666665542134443114555554 PP

>> SpecificRecomb  Site-specific recombinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   2.5   1.4e-07   0.00036     407     480 ..      15      86 ..       6      93 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.4e-07
                    SpecificRecomb 407 velvvallRsqlaAvlGNvlvvipvalliallilallgapliseekaeallesldplgslallyAaitGvlLFl 480
                                        + +va +   ++Av+G +l+v ++ l+  l ++al g + +++ +++ ++e ++ +++ + ++A itGvlLF+
  gi|298674436|ref|YP_003726186.1|  15 RDNFVAFVVGSIVAVIGSILIVTIAPLFYGLTYMALKGVKGVKV-EINDVFEGFHHFAK-SWIFAIITGVLLFI 86 
                                       566666667789****************************9987.5899********99.*************7 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1     0.037        95      31      54 ..       9      39 ..       3      53 .. 0.80
   2 ?   12.2   0.2   5.6e-05      0.14       4      73 ..      96     177 ..      95     185 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.037
                           UPF0242 31 ksWs.......llsiGlllaaaGsLllllll 54
                                      + W+        +++G ++a++Gs+l++ ++
  gi|298674436|ref|YP_003726186.1|  9 NTWYvfrdnfvAFVVGSIVAVIGSILIVTIA 39
                                      5677777777799************877655 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 5.6e-05
                           UPF0242   4 llisiiflYllPllllaiy.siqllseqksWs.........llsiGlllaaaGsLlllllllkw..ekalkekleks 68 
                                       +++si+++Y lPll++  y si  + e+ s s         +++iG ++  +G  + +  +l +   + l +k  ks
  gi|298674436|ref|YP_003726186.1|  96 VILSILLVYALPLLVIKDYnSIDAIRESISFSrenladtlvIFVIGAFINFVGGAITFGFILSLpfATILYTKATKS 172
                                       5789**********998763689999999999********************9888776655540044444444555 PP

                           UPF0242  69 kleek 73 
                                        ++e 
  gi|298674436|ref|YP_003726186.1| 173 LIKEH 177
                                       55554 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.8   1.5e-05     0.039       2      39 ..       6      43 ..       5      54 .. 0.83
   2 ?   -5.8   7.8         7   1.8e+04      29      34 ..      89      94 ..      68     131 .. 0.61
   3 ?   -3.3   2.4       3.8   9.7e+03      32      32 ..     144     144 ..     134     167 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.5e-05
                            OppC_N  2 lwqdawrrFkrNklAvvglvillll..lliaifaPliaPy 39
                                      l++ +w+ F+ N +A+v   i++++  +li+ +aPl+  y
  gi|298674436|ref|YP_003726186.1|  6 LLKNTWYVFRDNFVAFVVGSIVAVIgsILIVTIAPLF--Y 43
                                      7899*************99999997446667779999..5 PP

  == domain 2  score: -5.8 bits;  conditional E-value: 7
                            OppC_N 29 iaifaP 34
                                      +a++ P
  gi|298674436|ref|YP_003726186.1| 89 MAFVIP 94
                                      333322 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 3.8
                            OppC_N  32 f 32 
                                       +
  gi|298674436|ref|YP_003726186.1| 144 I 144
                                       2 PP

>> DUF5453  Family of unknown function (DUF5453)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   9.5   0.00018      0.46      39     110 ..      32     107 ..       9     127 .. 0.78
   2 ?    0.8   0.8      0.16     4e+02      33      71 ..     128     166 ..     105     170 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00018
                           DUF5453  39 qariliitallGvvlgivlyff.dvkfflkdypykkfhfdkkytrvylsGvivf...llnillgvlllvllvnflt 110
                                       +  i+ i++l+ ++  ++l +   vk  ++d +    hf k +    ++Gv++f   ++ ++ gv+l +llv+ l 
  gi|298674436|ref|YP_003726186.1|  32 SILIVTIAPLFYGLTYMALKGVkGVKVEINDVFEGFHHFAKSWIFAIITGVLLFigyMAFVIPGVILSILLVYALP 107
                                       3445556688888888888876369********9999**************875222678999*********9875 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.16
                           DUF5453  33 lsrvtlqariliitallGvvlgivlyffdvkfflkdypy 71 
                                        ++ +    i++i a++  v g++ ++f +   ++   y
  gi|298674436|ref|YP_003726186.1| 128 RENLADTLVIFVIGAFINFVGGAITFGFILSLPFATILY 166
                                       455666677889999999999999999977665555555 PP

>> DUF2627  Protein of unknown function (DUF2627)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.2      0.18   4.7e+02      33      55 ..      12      34 ..       4      37 .. 0.74
   2 ?   11.6   3.7   0.00013      0.33      13      56 ..      49      92 ..      33     100 .. 0.83
   3 ?    1.6   2.5      0.17   4.3e+02      20      61 ..     117     157 ..      96     159 .. 0.61

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.18
                           DUF2627 33 spfsslwlqflaGlllfaiglgf 55
                                        f++ ++ f++G ++++ig  +
  gi|298674436|ref|YP_003726186.1| 12 YVFRDNFVAFVVGSIVAVIGSIL 34
                                      56778889999999999988655 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00013
                           DUF2627 13 gllaayGiklmrdalfgilsspfsslwlqflaGlllfaiglgfi 56
                                      +l +++G+k+  + +f+ +++ ++s++  +++G+llf++ ++f+
  gi|298674436|ref|YP_003726186.1| 49 ALKGVKGVKVEINDVFEGFHHFAKSWIFAIITGVLLFIGYMAFV 92
                                      45567777777799***************************996 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.17
                           DUF2627  20 iklmrdalfgilsspfsslwlqflaGlllfaiglgfiaGfil 61 
                                       i ++r+++  + ++ ++ +++ f++G  +  +g ++  Gfil
  gi|298674436|ref|YP_003726186.1| 117 IDAIRESISFSRENLAD-TLVIFVIGAFINFVGGAITFGFIL 157
                                       55555555544444444.455566666666666667778887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1024  (0.0571142); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1165.04
//
Query:       gi|298674437|ref|YP_003726187.1|  [L=486]
Description: hypothetical protein Metev_0477 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-05   25.4   0.9    0.00059   20.7   0.3    2.7  2  Pilin_N   Archaeal Type IV pilin, N-terminal


Domain annotation for each model (and alignments):
>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.3   3.3e-08   0.00059       1      26 [.      10      35 ..      10      92 .. 0.77
   2 ?    2.4   0.0     0.017   3.1e+02      27      69 ..     288     331 ..     284     347 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3.3e-08
                           Pilin_N  1 eAVSpViGviLmvaitvIlaAviaaf 26
                                      +AVS+V+G++L++ it+I ++   ++
  gi|298674437|ref|YP_003726187.1| 10 DAVSSVVGMVLILGITMISISAMMVY 35
                                      69****************99876554 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.017
                           Pilin_N  27 vlglasneekapqasievkidssastgkna..vslehkgGdsidt 69 
                                       v+ l ++++++p+ ++++++ +++s++ n   ++++ ++G+ + t
  gi|298674437|ref|YP_003726187.1| 288 VGAL-NTSKDEPMYDFSFDLVAEGSQKLNPsdFKIKASSGNKTLT 331
                                       4555.7899999999999966666665554689999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (486 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 2808.39
//
Query:       gi|298674438|ref|YP_003726188.1|  [L=256]
Description: hypothetical protein Metev_0478 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.036   15.0   4.1        0.2   12.6   4.1    2.3  1  Pilin_N   Archaeal Type IV pilin, N-terminal
      0.047   14.1   0.2       0.11   12.8   0.2    1.8  1  Ly49      Ly49-like protein, N-terminal region


Domain annotation for each model (and alignments):
>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   4.1   2.2e-05       0.2       2      64 ..      12      84 ..      11     100 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.2e-05
                           Pilin_N  2 AVSpViGviLmvaitvIlaAviaafvlgl.asneekapqasievkidssastgkna.........vslehkgG 64
                                      AVS+V+  ++++ + +++++vi++  + l +  +e +   +i+ +++  a + ++          ++l++ gG
  gi|298674438|ref|YP_003726188.1| 12 AVSEVVDFVILLGVMLLAVSVIGVAGFPLlDHMQEVEHTENIKQSYTVLAANINEIvfgnapsqsIELQMRGG 84
                                      9***********************9999987777777777776665544444333344445555555555555 PP

>> Ly49  Ly49-like protein, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   1.3e-05      0.11       8      57 ..      16      65 ..      13     139 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.3e-05
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXX CS
                              Ly49  8 vvalgILclllLvtvavLvtkifqysqekheleetlnlsqnysimqndin 57
                                      vv + IL  ++L++v+v+++  f    + +e e t n++q y+++  +in
  gi|298674438|ref|YP_003726188.1| 16 VVDFVILLGVMLLAVSVIGVAGFPLLDHMQEVEHTENIKQSYTVLAANIN 65
                                      68889**************************************9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       810  (0.0451782); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1584.07
//
Query:       gi|298674439|ref|YP_003726189.1|  [L=154]
Description: hypothetical protein Metev_0479 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.075   14.0   4.0       0.22   12.5   4.0    2.0  1  Pilin_N   Archaeal Type IV pilin, N-terminal


Domain annotation for each model (and alignments):
>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   4.0   1.2e-05      0.22       1      48 [.      10      58 ..      10     147 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.2e-05
                           Pilin_N  1 eAVSpViGviLmvaitvIlaAviaafvlgl.asneekapqasievkids 48
                                      +AVS  +G iL+ +i v+++ ++  + +++ +++ee+ ++ ++e+  ++
  gi|298674439|ref|YP_003726189.1| 10 SAVSVSVGSILIFSISVLAFIMVMNSFFSMmDQTEETVTREEFETYGND 58
                                      69****************************8999999998888544333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1320  (0.0736237); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 953.03
//
Query:       gi|298674440|ref|YP_003726190.1|  [L=283]
Description: hypothetical protein Metev_0480 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       854  (0.0476323); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1767.67
//
Query:       gi|298674441|ref|YP_003726191.1|  [L=205]
Description: hypothetical protein Metev_0481 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1038  (0.057895); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1301.93
//
Query:       gi|298674442|ref|YP_003726192.1|  [L=156]
Description: hypothetical protein Metev_0482 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       916  (0.0510904); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1065.27
//
Query:       gi|298674443|ref|YP_003726193.1|  [L=1048]
Description: flagella protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-28   97.9   0.2    1.9e-27   95.0   0.2    2.7  1  Arch_fla_DE      Archaeal flagella protein
    0.00031   20.2   5.9    0.00031   20.2   5.9    6.3  6  GAS              Growth-arrest specific micro-tubule binding
     0.0024   18.2   1.3     0.0024   18.2   1.3    9.1  9  FlaC_arch        Flagella accessory protein C (FlaC)
  ------ inclusion threshold ------
      0.011   15.7   0.2      0.011   15.7   0.2    6.2  6  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
      0.089   12.7   0.1        2.1    8.3   0.0    2.7  2  Erythro-docking  Erythronolide synthase, docking
        0.1   12.5   0.1        0.1   12.5   0.1    6.8  6  HSBP1            Heat shock factor binding protein 1
       0.14   12.4  20.3        1.7    8.9   0.9    5.9  4  ABC_tran_CTD     ABC transporter C-terminal domain
       0.17   11.9  32.5       0.18   11.8   2.0    5.5  5  DUF1664          Protein of unknown function (DUF1664)
       0.17   12.1  20.2       0.22   11.8   0.3    5.2  6  DUF948           Bacterial protein of unknown function (DUF94
       0.17   12.4   0.7        1.3    9.6   0.0    3.0  1  HisKA_3          Histidine kinase
       0.18   11.8   9.8         14    5.8   0.1    5.3  6  PilJ             Type IV pili methyl-accepting chemotaxis tra
       0.19   10.6   5.5       0.15   10.9   3.3    1.9  2  DUF2397          Protein of unknown function (DUF2397)
       0.36   10.9  26.4       0.17   12.0   4.0    5.0  5  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
       0.42   11.0  42.0      0.043   14.1   7.9    6.4  7  BLOC1_2          Biogenesis of lysosome-related organelles co
       0.53   10.3  14.3       0.68    9.9   1.4    3.7  3  DUF489           Protein of unknown function (DUF489)
       0.92    9.4  15.2        3.3    7.6   0.2    6.1  5  DASH_Dam1        DASH complex subunit Dam1
        5.9    6.8   9.3        0.2   11.5   0.6    3.0  3  DUF720           Protein of unknown function (DUF720)
        7.3    6.6   7.3      1e+02    2.9   0.2    4.8  4  ApoO             Apolipoprotein O
        8.2    6.9  27.7          1    9.8   2.1    5.4  4  T3SSipB          Type III cell invasion protein SipB
        9.2    6.8  36.0        1.6    9.2   3.1    7.2  5  NPV_P10          Nucleopolyhedrovirus P10 protein


Domain annotation for each model (and alignments):
>> Arch_fla_DE  Archaeal flagella protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.0   0.2   2.1e-30   1.9e-27       2      95 .]     937    1026 ..     936    1026 .. 0.96

  Alignments for each domain:
  == domain 1  score: 95.0 bits;  conditional E-value: 2.1e-30
                       Arch_fla_DE    2 ekpyLeelpedyaaelvvleWlefLvervgvenaaealdyYeeigWiseevreeLlkylkgikledeekeelkks 76  
                                        ++++L  +p++++++ +++eWl++L++rvg +n+ e+l+yY+e+ Wis++vr+eLl+y+ gi++ + ek+++k  
  gi|298674443|ref|YP_003726193.1|  937 QNVQLGYIPKNSVSMRICMEWLKYLMNRVGGNNLDEVLTYYKELSWISDDVRQELLRYSAGISH-NGEKSDWK-- 1008
                                        6899**********************************************************97.88889998.. PP

                       Arch_fla_DE   77 eltvedHvkSllyieklag 95  
                                         lt +dH+kS+++i+klag
  gi|298674443|ref|YP_003726193.1| 1009 -LTKTDHIKSIWFIQKLAG 1026
                                        .****************96 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   4.7      0.98   8.8e+02      44     120 ..     268     343 ..     253     355 .. 0.72
   2 ?    0.8   0.7       0.3   2.7e+02     107     140 ..     434     467 ..     406     475 .. 0.79
   3 ?   -3.2   7.1       4.8   4.3e+03      29      48 ..     556     575 ..     514     627 .. 0.65
   4 ?    5.3   1.8     0.013        11      79     140 ..     708     769 ..     660     771 .. 0.82
   5 !   20.2   5.9   3.5e-07   0.00031      30     153 ..     736     862 ..     724     866 .. 0.83
   6 !    6.1   5.9     0.007       6.3      24      81 ..     859     916 ..     854     929 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.98
                               GAS  44 rnekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvek 120
                                       +  k+  +  ++ ++l ++L++a+ e + L k +++   + + l+  k + ++ + e  +l+++ ++l++++++ + 
  gi|298674443|ref|YP_003726193.1| 268 SSLKNKFKSITQRRNLFDELEEAQSEDQPLAKPVNKSVDEEKPLEPFKDKFQNITHE-GNLTESFDQLRKKVDEFQT 343
                                       445555566677788888889999988888888888888888888888888888777.4566666666666666555 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.3
                               GAS 107 ehevleqrfekvekerdelykkfeaaiqevqqkt 140
                                       ++++ e + ++  +++++l+++f+++++ ++qk+
  gi|298674443|ref|YP_003726193.1| 434 KSDSSERKNAEYAEKFNDLTASFKNKFKNIRQKA 467
                                       4566677778888999999999999999999996 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 4.8
                               GAS  29 kslKeeieelkkkeerneke 48 
                                       +slK+++e++k++ e+ e+e
  gi|298674443|ref|YP_003726193.1| 556 RSLKNQMEQMKEEIEEEEQE 575
                                       34555555555555544443 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.013
                               GAS  79 nyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdelykkfeaaiqevqqkt 140
                                       n ++ +++ + + +r++++++ l++l+   + l +r++++++  +++++k +++ + ++ ++
  gi|298674443|ref|YP_003726193.1| 708 NLQELQSKVNGSVTRVEKVTDDLQNLSDTVDELDDRIKEIQRRNEDFESKIDNSYYSTSDRI 769
                                       55566666777778889999999999999999999999999999999999888888776665 PP

  == domain 5  score: 20.2 bits;  conditional E-value: 3.5e-07
                               GAS  30 slKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkw 106
                                       +  e   ++k+ ++rne   s+i +   + ++ + ++e ++++L+  l   ++  ++l+++ +r+ ele+ l +++ 
  gi|298674443|ref|YP_003726193.1| 736 TVDELDDRIKEIQRRNEDFESKIDNSYYSTSDRIDNLEYQLKNLQDSLGISNESDSKLNSIGTRVDELESALDSTQS 812
                                       444444556777888888889999999************************************************** PP

                               GAS 107 ehevleqrfekvekerdelykkfeaa...iqevqqktglknllLekklka 153
                                       +++  + +++++++++ ++y+++++    ++ev ++ + k   L  kl++
  gi|298674443|ref|YP_003726193.1| 813 DNQEIKSELSNIQQSISDMYDSYKDLlshLNEVNEDYESKFSDLYDKLSK 862
                                       ************************98555667777777776666666665 PP

  == domain 6  score: 6.1 bits;  conditional E-value: 0.007
                               GAS  24 NLelIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknye 81 
                                        L++I++  +++ +++k+ ++ +  ls++++e   +k  +k+  +e++ L + l++ +
  gi|298674443|ref|YP_003726193.1| 859 KLSKIDTVESKLSQIDKNTKERDEILSKVEEELPVIKNAIKRNHKENQVLANSLEELK 916
                                       5666666666666666666666666666666666666666666666666666666544 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.72   6.5e+02      18      38 ..     326     346 ..     317     347 .. 0.85
   2 ?    1.5   0.8      0.44   3.9e+02      17      32 ..     556     571 ..     547     575 .. 0.81
   3 !   14.5   2.2   3.8e-05     0.034       3      40 ..     710     747 ..     708     748 .. 0.95
   4 ?    0.7   0.1      0.79   7.1e+02      15      29 ..     768     782 ..     750     791 .. 0.61
   5 !   18.2   1.3   2.6e-06    0.0024       2      44 ..     793     835 ..     792     846 .. 0.69
   6 ?    2.2   0.2      0.26   2.4e+02      15      29 ..     862     876 ..     847     886 .. 0.67
   7 ?    3.7   0.8     0.094        84       1      38 [.     862     899 ..     862     900 .. 0.79
   8 ?    5.7   1.4     0.022        20       4      35 ..     886     917 ..     883     922 .. 0.93
   9 ?   -2.6   0.2       8.3   7.4e+03      24      35 ..    1035    1046 ..    1032    1047 .. 0.52

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.72
                         FlaC_arch  18 tvkkeneelsksveelkenVk 38 
                                       ++ +++++l+k+v+e + n++
  gi|298674443|ref|YP_003726193.1| 326 NLTESFDQLRKKVDEFQTNIQ 346
                                       56678899*******999997 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.44
                         FlaC_arch  17 etvkkeneelsksvee 32 
                                        ++k+++e++++++ee
  gi|298674443|ref|YP_003726193.1| 556 RSLKNQMEQMKEEIEE 571
                                       6899999***999998 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 3.8e-05
                         FlaC_arch   3 delEnklsklsteletvkkeneelsksveelkenVkdl 40 
                                       +el++k++   t++e v +++++ls++v+el++++k++
  gi|298674443|ref|YP_003726193.1| 710 QELQSKVNGSVTRVEKVTDDLQNLSDTVDELDDRIKEI 747
                                       79*********************************985 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.79
                         FlaC_arch  15 eletvkkeneelsks 29 
                                       ++++++ ++++l++s
  gi|298674443|ref|YP_003726193.1| 768 RIDNLEYQLKNLQDS 782
                                       555555555555554 PP

  == domain 5  score: 18.2 bits;  conditional E-value: 2.6e-06
                         FlaC_arch   2 idelEnklsklsteletvkkeneelsksveelkenVkdllsLY 44 
                                       ++++ +++++l++ l++ +++n+e+++++ ++++++ d+ + Y
  gi|298674443|ref|YP_003726193.1| 793 LNSIGTRVDELESALDSTQSDNQEIKSELSNIQQSISDMYDSY 835
                                       6667777777777777777777777777777777776654433 PP

  == domain 6  score: 2.2 bits;  conditional E-value: 0.26
                         FlaC_arch  15 eletvkkeneelsks 29 
                                       +++tv+++++++ k+
  gi|298674443|ref|YP_003726193.1| 862 KIDTVESKLSQIDKN 876
                                       667777777777665 PP

  == domain 7  score: 3.7 bits;  conditional E-value: 0.094
                         FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelkenVk 38 
                                       +id++E+kls+++ + +   + ++++++++  +k  +k
  gi|298674443|ref|YP_003726193.1| 862 KIDTVESKLSQIDKNTKERDEILSKVEEELPVIKNAIK 899
                                       8999*******999887777777777777777777666 PP

  == domain 8  score: 5.7 bits;  conditional E-value: 0.022
                         FlaC_arch   4 elEnklsklsteletvkkeneelsksveelke 35 
                                       ++E++l+ ++  ++   ken+ l +s+eelk 
  gi|298674443|ref|YP_003726193.1| 886 KVEEELPVIKNAIKRNHKENQVLANSLEELKS 917
                                       79****************************96 PP

  == domain 9  score: -2.6 bits;  conditional E-value: 8.3
                         FlaC_arch   24 eelsksveelke 35  
                                        ++++++v+++ke
  gi|298674443|ref|YP_003726193.1| 1035 QSIENDVNQIKE 1046
                                        455555555554 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   5.2       1.9   1.7e+03      28     109 ..     210     291 ..     186     299 .. 0.85
   2 ?    0.1   0.1      0.88   7.9e+02      70      93 ..     328     351 ..     314     358 .. 0.58
   3 ?   -2.6   2.5       5.9   5.3e+03      67      83 ..     443     459 ..     414     487 .. 0.40
   4 ?   -0.0   3.6      0.96   8.6e+02      61      80 ..     557     576 ..     550     603 .. 0.48
   5 ?   15.7   0.2   1.3e-05     0.011      32     110 ..     703     781 ..     693     784 .. 0.95
   6 ?   14.0  12.3   4.5e-05      0.04       5     129 .]     788     915 ..     786     915 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.9
                        TPR_MLP1_2  28 qedlekqaeiakeaqqkYerelvkhaedvkelqalreel.nelkaeiaelkaeaesakaeleeseesweeqkeelek 103
                                        +d  +q  ++ e +q++e+ l   ++++++ q++ +++    k+e +e +++  + +++l+++ +s++++++ + +
  gi|298674443|ref|YP_003726193.1| 210 TKDNSSQDISLGEIEQSFETDLKDSESETDNNQTVESDItYPEKTEETEPQSDKSDDSSSLKNKFKSITQRRNLF-D 285
                                       5788999999999***********************999445778888888888899999999999998777655.5 PP

                        TPR_MLP1_2 104 elsele 109
                                       el+e++
  gi|298674443|ref|YP_003726193.1| 286 ELEEAQ 291
                                       677766 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.88
                        TPR_MLP1_2  70 kaeiaelkaeaesakaeleesees 93 
                                       ++   +l++++++ +++++++e s
  gi|298674443|ref|YP_003726193.1| 328 TESFDQLRKKVDEFQTNIQNEEGS 351
                                       344445555555555555555544 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 5.9
                        TPR_MLP1_2  67 nelkaeiaelkaeaesa 83 
                                       +e+ ++ ++l+a+ ++ 
  gi|298674443|ref|YP_003726193.1| 443 AEYAEKFNDLTASFKNK 459
                                       22222222222222221 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 0.96
                        TPR_MLP1_2  61 alreelnelkaeiaelkaea 80 
                                       +l+++++++k+ei+e ++e 
  gi|298674443|ref|YP_003726193.1| 557 SLKNQMEQMKEEIEEEEQEE 576
                                       34444444444444433333 PP

  == domain 5  score: 15.7 bits;  conditional E-value: 1.3e-05
                        TPR_MLP1_2  32 ekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaeleeseesweeqkeelekelsel 108
                                       ++q+  ++e q k    ++  ++ +++lq+l + ++el ++i+e++ ++e+ ++++++s  s + + ++le +l++l
  gi|298674443|ref|YP_003726193.1| 703 TNQTGNLQELQSKVNGSVTRVEKVTDDLQNLSDTVDELDDRIKEIQRRNEDFESKIDNSYYSTSDRIDNLEYQLKNL 779
                                       6789999*******************************************************************999 PP

                        TPR_MLP1_2 109 ek 110
                                       + 
  gi|298674443|ref|YP_003726193.1| 780 QD 781
                                       86 PP

  == domain 6  score: 14.0 bits;  conditional E-value: 4.5e-05
                        TPR_MLP1_2   5 sleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeae 81 
                                       + +++++s+ ++ +e+e++l + q+d ++ ++++++ qq+ +      ++ +  l++++e++++  +++ +  ++ +
  gi|298674443|ref|YP_003726193.1| 788 ESDSKLNSIGTRVDELESALDSTQSDNQEIKSELSNIQQSISDMYDSYKDLLSHLNEVNEDYESKFSDLYDKLSKID 864
                                       5678999999******************************************************************* PP

                        TPR_MLP1_2  82 sakaeleeseesweeqkeel...ekelselekriedlneqNklLhdQlEsl 129
                                       +++++l++  ++ +e+ e l   e+el  +++ i+   + N++L + lE+l
  gi|298674443|ref|YP_003726193.1| 865 TVESKLSQIDKNTKERDEILskvEEELPVIKNAIKRNHKENQVLANSLEEL 915
                                       ***************998763337899999*******************85 PP

>> Erythro-docking  Erythronolide synthase, docking
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.48   4.3e+02      10      27 ..     767     784 ..     764     787 .. 0.86
   2 ?    8.3   0.0    0.0024       2.1       7      22 ..     795     810 ..     789     816 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.48
                                       HHHHHHHHHHHHHTTSS- CS
                   Erythro-docking  10 dRLDeLekaLeaLsdedG 27 
                                       dR+D+Le  L  L d  G
  gi|298674443|ref|YP_003726193.1| 767 DRIDNLEYQLKNLQDSLG 784
                                       9**********9998765 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0024
                                       TTHHHHHHHHHHHHHH CS
                   Erythro-docking   7 dvGdRLDeLekaLeaL 22 
                                        +G R+DeLe aL+  
  gi|298674443|ref|YP_003726193.1| 795 SIGTRVDELESALDST 810
                                       59***********975 PP

>> HSBP1  Heat shock factor binding protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       7.3   6.5e+03      13      23 ..     269     279 ..     268     283 .. 0.85
   2 ?   12.5   0.1   0.00011       0.1      11      45 ..     311     347 ..     308     353 .. 0.87
   3 ?   -3.2   0.2         9     8e+03      27      37 ..     560     570 ..     557     573 .. 0.61
   4 ?   -0.0   5.7      0.92   8.2e+02      32      48 ..     765     781 ..     707     784 .. 0.75
   5 ?    7.9   0.7     0.003       2.7      21      48 ..     785     812 ..     776     815 .. 0.79
   6 ?    0.6   0.3      0.59   5.3e+02      15      42 ..     850     876 ..     837     880 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 7.3
                             HSBP1  13 qlqdkFqtmsd 23 
                                        l++kF+++++
  gi|298674443|ref|YP_003726193.1| 269 SLKNKFKSITQ 279
                                       589****9986 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00011
                             HSBP1  11 LqqlqdkFqtm..sdqilsriDdMssriDdLEksiad 45 
                                       L+  +dkFq++  + ++++  D++ +++D+ +++i++
  gi|298674443|ref|YP_003726193.1| 311 LEPFKDKFQNIthEGNLTESFDQLRKKVDEFQTNIQN 347
                                       66679******66678*******************97 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 9
                             HSBP1  27 sriDdMssriD 37 
                                       +++++M + i+
  gi|298674443|ref|YP_003726193.1| 560 NQMEQMKEEIE 570
                                       45666666665 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 0.92
                             HSBP1  32 MssriDdLEksiadlmt 48 
                                        s riD+LE ++++l +
  gi|298674443|ref|YP_003726193.1| 765 TSDRIDNLEYQLKNLQD 781
                                       57888888888888766 PP

  == domain 5  score: 7.9 bits;  conditional E-value: 0.003
                             HSBP1  21 msdqilsriDdMssriDdLEksiadlmt 48 
                                       +s++  s+++ +++r+D+LE  +++  +
  gi|298674443|ref|YP_003726193.1| 785 ISNESDSKLNSIGTRVDELESALDSTQS 812
                                       6777779*************99987665 PP

  == domain 6  score: 0.6 bits;  conditional E-value: 0.59
                             HSBP1  15 qdkFqtmsdqilsriDdMssriDdLEks 42 
                                       ++kF+++ d+ ls+iD  +s++ +++k+
  gi|298674443|ref|YP_003726193.1| 850 ESKFSDLYDK-LSKIDTVESKLSQIDKN 876
                                       5788888887.59999999999999888 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   2.9     0.011       9.5      13      50 ..     558     596 ..     549     603 .. 0.85
   2 ?    8.9   0.9    0.0019       1.7      14      58 ..     766     808 ..     724     813 .. 0.70
   3 ?    4.6   0.5     0.043        39      10      61 ..     800     853 ..     798     861 .. 0.80
   4 ?   -0.5   0.5       1.7   1.5e+03      16      48 ..     862     889 ..     847     916 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.011
                      ABC_tran_CTD  13 leaeIeaLEeeiaeleaeladpelysdp.eklaelsael 50 
                                       l +++e++ eei+e e+e ++pe+   + ++  e+ +e+
  gi|298674443|ref|YP_003726193.1| 558 LKNQMEQMKEEIEEEEQEESSPEFVPSFeQETEETEEEK 596
                                       7899********************977757777777665 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0019
                      ABC_tran_CTD  14 eaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLe 58 
                                        ++I+ LE ++++l++ l   +  + + kl+ + ++ +ele++L+
  gi|298674443|ref|YP_003726193.1| 766 SDRIDNLEYQLKNLQDSLGISN--ESDSKLNSIGTRVDELESALD 808
                                       4677777777777777777655..555677777777777777776 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.043
                      ABC_tran_CTD  10 leeleaeIeaLEeeiaeleaeladpely.sdp.eklaelsaeleeleaeLeely 61 
                                        +ele+ +++ + + +e+  el++ +   sd  +  ++l   l+e++++ e ++
  gi|298674443|ref|YP_003726193.1| 800 VDELESALDSTQSDNQEIKSELSNIQQSiSDMyDSYKDLLSHLNEVNEDYESKF 853
                                       577888888888888888888888777777777888888888888888888887 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 1.7
                      ABC_tran_CTD  16 eIeaLEeeiaeleaeladpelysdpeklaelsa 48 
                                       +I+  E +++++++   + +     e l+++ +
  gi|298674443|ref|YP_003726193.1| 862 KIDTVESKLSQIDKNTKERD-----EILSKVEE 889
                                       33333333333333332222.....22333333 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1         2   1.8e+03      64      77 ..     327     340 ..     268     358 .. 0.62
   2 ?    0.1   0.1      0.88   7.9e+02      44      63 ..     556     575 ..     551     628 .. 0.66
   3 ?    7.9   4.5    0.0034         3      78     122 ..     705     749 ..     657     762 .. 0.66
   4 ?   11.8   2.0    0.0002      0.18      40     121 ..     766     846 ..     762     859 .. 0.75
   5 ?    7.9   3.6    0.0034       3.1      41     122 ..     833     917 ..     830     919 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2
                           DUF1664  64 Lssridrvdkklde 77 
                                       L++  d++ kk+de
  gi|298674443|ref|YP_003726193.1| 327 LTESFDQLRKKVDE 340
                                       22222222222222 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.88
                           DUF1664  44 esvskqleqvseslaatkrh 63 
                                        s+ +q+eq++e++++  ++
  gi|298674443|ref|YP_003726193.1| 556 RSLKNQMEQMKEEIEEEEQE 575
                                       45666666666666655444 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0034
                           DUF1664  78 qkeiskeikeevtevredlseigedvesvkeavegleskleriee 122
                                       q+   +e++++v+     ++++ +d+++++++v +l+ ++++i+ 
  gi|298674443|ref|YP_003726193.1| 705 QTGNLQELQSKVNGSVTRVEKVTDDLQNLSDTVDELDDRIKEIQR 749
                                       334455666667666677777777777777777777777777764 PP

  == domain 4  score: 11.8 bits;  conditional E-value: 0.0002
                           DUF1664  40 sdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesk 116
                                       sd ++++  ql+++++sl    ++  s+++++++++de + +  +++++ +e++++ls+i++ ++ + +  ++l s+
  gi|298674443|ref|YP_003726193.1| 766 SDRIDNLEYQLKNLQDSLGIS-NESDSKLNSIGTRVDELESALDSTQSDNQEIKSELSNIQQSISDMYDSYKDLLSH 841
                                       677888889999999998654.4457777778888888888888888888888888888877777777777777777 PP

                           DUF1664 117 lerie 121
                                       l++++
  gi|298674443|ref|YP_003726193.1| 842 LNEVN 846
                                       66664 PP

  == domain 5  score: 7.9 bits;  conditional E-value: 0.0034
                           DUF1664  41 davesvskqleqvseslaatkrhLs...sridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                       d  +++ ++l++v e+ ++   +L    s+id+v++kl +  + +ke +e +++v+e+l  i++ ++  ++  + l+
  gi|298674443|ref|YP_003726193.1| 833 DSYKDLLSHLNEVNEDYESKFSDLYdklSKIDTVESKLSQIDKNTKERDEILSKVEEELPVIKNAIKRNHKENQVLA 909
                                       56666667777777766666666652225688889999999999999999999999999999999999999999999 PP

                           DUF1664 115 skleriee 122
                                       ++le++++
  gi|298674443|ref|YP_003726193.1| 910 NSLEELKS 917
                                       99998865 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       3.7   3.3e+03      57      77 ..     326     345 ..     285     354 .. 0.63
   2 ?   -3.0   0.2        10   8.9e+03      32      50 ..     457     475 ..     443     488 .. 0.40
   3 ?   -1.5   0.1       3.4     3e+03      56      70 ..     666     680 ..     653     691 .. 0.48
   4 ?    8.0   4.7    0.0037       3.3      50      87 ..     703     740 ..     666     756 .. 0.80
   5 ?    2.8   0.2      0.15   1.4e+02      24      70 ..     733     779 ..     732     819 .. 0.54
   6 ?   11.8   0.3   0.00025      0.22      29      83 ..     815     876 ..     793     882 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3.7
                            DUF948  57 nelledvneklekvdplteav 77 
                                       n  +e   +  +kvd++ +++
  gi|298674443|ref|YP_003726193.1| 326 NL-TESFDQLRKKVDEFQTNI 345
                                       33.333333333333333333 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 10
                            DUF948  32 aatieelekqvdpilkeve 50 
                                       ++  +++++++++ +++++
  gi|298674443|ref|YP_003726193.1| 457 KNKFKNIRQKATGSTEQTK 475
                                       2233333333333333333 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 3.4
                            DUF948  56 vnelledvneklekv 70 
                                       vn+ l+d ++++++v
  gi|298674443|ref|YP_003726193.1| 666 VNKKLNDHQKQVKDV 680
                                       333333333333222 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.0037
                            DUF948  50 edllakvnelledvneklekvdplteavadlgesvsel 87 
                                       ++ + + +el++ vn+ + +v+++t+ +++l+++v el
  gi|298674443|ref|YP_003726193.1| 703 TNQTGNLQELQSKVNGSVTRVEKVTDDLQNLSDTVDEL 740
                                       44566778888889999999999999999999988887 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.15
                            DUF948  24 lkktldeaaatieele..............kqvdpilkevedllakvnelledvneklekv 70 
                                       l++t+de+ ++i+e++                              + +  ++++ +l+++
  gi|298674443|ref|YP_003726193.1| 733 LSDTVDELDDRIKEIQrrnedfeskidnsyY--------------STSDRIDNLEYQLKNL 779
                                       7788888888888888444444433333331..............3333333333333322 PP

  == domain 6  score: 11.8 bits;  conditional E-value: 0.00025
                            DUF948  29 deaaatieelekqvdpilkevedllakvnelledvne.......klekvdplteavadlges 83 
                                       +e+++ + ++++ +  + +  +dll++ ne+ ed ++       kl k+d++ +++ ++ ++
  gi|298674443|ref|YP_003726193.1| 815 QEIKSELSNIQQSISDMYDSYKDLLSHLNEVNEDYESkfsdlydKLSKIDTVESKLSQIDKN 876
                                       45666677777888888888888888888877777774444444777777777777766666 PP

>> HisKA_3  Histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0015       1.3      24      65 ..     803     844 ..     795     847 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0015
                                       HHHHHHHTTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                           HisKA_3  24 lelakrllekdpekaaeqlreieelarealqevRrllhnLrp 65 
                                       le a  ++++d+++++ +l +i++ +++ ++  ++ll++L +
  gi|298674443|ref|YP_003726193.1| 803 LESALDSTQSDNQEIKSELSNIQQSISDMYDSYKDLLSHLNE 844
                                       78889999*******************************986 PP

>> PilJ  Type IV pili methyl-accepting chemotaxis transducer N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.018        17      39      75 ..     326     362 ..     316     374 .. 0.82
   2 ?   -3.2   0.0       9.4   8.4e+03      76      98 ..     444     466 ..     426     484 .. 0.57
   3 ?    0.8   0.0      0.52   4.7e+02      41      80 ..     552     588 ..     540     597 .. 0.78
   4 ?   -1.2   0.0       2.2   1.9e+03      43      63 ..     612     632 ..     602     650 .. 0.76
   5 ?    5.8   0.1     0.015        14      13      95 ..     703     783 ..     698     797 .. 0.69
   6 ?    0.2   0.0      0.82   7.4e+02      71      95 ..     810     835 ..     787     852 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.018
                              PilJ  39 daaearaqlretiaqfdrtlaalrlgdpapgllvpae 75 
                                       + +e+++qlr+++++f++++++ + ++++ +   p+e
  gi|298674443|ref|YP_003726193.1| 326 NLTESFDQLRKKVDEFQTNIQNEEGSADNSSSIEPDE 362
                                       57999****************9999988877777765 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9.4
                              PilJ  76 avraqleaveqlWqelkkpaeaa 98 
                                       +  ++++++++ +++  k++++ 
  gi|298674443|ref|YP_003726193.1| 444 EYAEKFNDLTASFKNKFKNIRQK 466
                                       66666666666666666666222 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.52
                              PilJ  41 aearaqlretiaqfdrtlaalrlgdpapgllvpaeavraq 80 
                                       ++ r++l+++++q+ + +++ ++ +++ + +vp  ++ ++
  gi|298674443|ref|YP_003726193.1| 552 SSGRRSLKNQMEQMKEEIEEEEQEESS-PEFVP--SFEQE 588
                                       788999**************9999999.68888..45555 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 2.2
                              PilJ  43 araqlretiaqfdrtlaalrl 63 
                                       +r +lr++++qf+++l+  ++
  gi|298674443|ref|YP_003726193.1| 612 QRGRLRKRMKQFRENLTGSKQ 632
                                       677888888888888876554 PP

  == domain 5  score: 5.8 bits;  conditional E-value: 0.015
                              PilJ  13 INvAGslRMqsqRlakeallaaagaydaaearaqlretiaqfdrtlaalrlgdpapgllvpae..avraqleaveql 87 
                                        N++G l+ +  ++  +++++         + ++l++t++++d+++++ ++ +++   +  ++  +++++++++e +
  gi|298674443|ref|YP_003726193.1| 703 TNQTGNLQELQSKVNGSVTRVEKVT----DDLQNLSDTVDELDDRIKEIQRRNEDFESKIDNSyySTSDRIDNLEYQ 775
                                       5888888888888886666555555....799********************9995554444455555555555555 PP

                              PilJ  88 Wqelkkpa 95 
                                        ++l++++
  gi|298674443|ref|YP_003726193.1| 776 LKNLQDSL 783
                                       55555555 PP

  == domain 6  score: 0.2 bits;  conditional E-value: 0.82
                              PilJ  71 lvpae.avraqleaveqlWqelkkpa 95 
                                        + ++ +++++l++++q  + + ++ 
  gi|298674443|ref|YP_003726193.1| 810 TQSDNqEIKSELSNIQQSISDMYDSY 835
                                       22222377777777777776665554 PP

>> DUF2397  Protein of unknown function (DUF2397)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.5   1.4e+03     147     171 ..     325     349 ..     284     356 .. 0.81
   2 ?   10.9   3.3   0.00017      0.15      38     177 ..     711     852 ..     688     923 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.5
                           DUF2397 147 relferfekLaenaadFlasLqrvl 171
                                        +l+e+f++L++++ +F++++q++ 
  gi|298674443|ref|YP_003726193.1| 325 GNLTESFDQLRKKVDEFQTNIQNEE 349
                                       579999***********99999865 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00017
                           DUF2397  38 rlkedpefedyteeqlqadLdqLveW.gnLea.sqdtsrvttieefkrkrfrYqltpagveveraveeleealgegg 112
                                       +l+++  +   ++e++++dL++L +    L+  +++ +r +   e k  ++ Y+ +     +e ++++l+  lg + 
  gi|298674443|ref|YP_003726193.1| 711 ELQSKVNGSVTRVEKVTDDLQNLSDTvDELDDrIKEIQRRNEDFESKIDNSYYSTSDRIDNLEYQLKNLQDSLGISN 787
                                       567777778888899999999998765555543666666666666666799*******************9999966 PP

                           DUF2397 113 slervlleriaarLraLaelaeedeadd.evaellrelferfekLaenaadFlasLqrvlaeedmd 177
                                       + + + l  i +r  +L+ ++++ ++d+ e+ + l++++++ +++ ++++d l++L++v + ++ +
  gi|298674443|ref|YP_003726193.1| 788 E-SDSKLNSIGTRVDELESALDSTQSDNqEIKSELSNIQQSISDMYDSYKDLLSHLNEVNEDYESK 852
                                       5.66779**************99997777*****************************99876544 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.32   2.9e+02      28      56 ..     319     347 ..     301     355 .. 0.66
   2 ?   -3.2   0.1       8.5   7.6e+03      52      69 ..     447     464 ..     423     480 .. 0.55
   3 ?    9.8   4.3   0.00083      0.74      44     108 ..     706     783 ..     690     784 .. 0.64
   4 ?   12.0   4.0   0.00019      0.17      39     118 ..     768     845 ..     764     852 .. 0.62
   5 ?    2.2   1.0      0.19   1.7e+02       4      63 ..     842     900 ..     839     935 .. 0.57

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.32
                      Baculo_PEP_C  28 qnvqilaqlatlldaietqLnalsedlks 56 
                                       qn++  ++l++ +d++ ++++++++++++
  gi|298674443|ref|YP_003726193.1| 319 QNITHEGNLTESFDQLRKKVDEFQTNIQN 347
                                       55555555555555555555555555554 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8.5
                      Baculo_PEP_C  52 edlksllaeldtrldtll 69 
                                       e++++l a++++++++  
  gi|298674443|ref|YP_003726193.1| 447 EKFNDLTASFKNKFKNIR 464
                                       333333333333333332 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00083
                      Baculo_PEP_C  44 etqLnalsedlksllaeldt......rldtlltnLtdalnalq.......dtlrneLtnlnsiltnLlssvtNinst 107
                                        ++L++l+++++ +++ +++      +l++++++L+d ++++q        +++n   ++   + nL  ++ N++ +
  gi|298674443|ref|YP_003726193.1| 706 TGNLQELQSKVNGSVTRVEKvtddlqNLSDTVDELDDRIKEIQrrnedfeSKIDNSYYSTSDRIDNLEYQLKNLQDS 782
                                       34455555555555555555555555777778888888888877775555666666667777888888888887766 PP

                      Baculo_PEP_C 108 L 108
                                       L
  gi|298674443|ref|YP_003726193.1| 783 L 783
                                       5 PP

  == domain 4  score: 12.0 bits;  conditional E-value: 0.00019
                      Baculo_PEP_C  39 lldaietqLnalsedlksllaeldtrldtlltnLtdalnalq......dtlrneLtnlnsiltnLlssvtNinstLn 109
                                        +d++e qL++l+++l   ++e d++l++  t++++   al       ++++       s+l+n++ s+  +  + +
  gi|298674443|ref|YP_003726193.1| 768 RIDNLEYQLKNLQDSLGI-SNESDSKLNSIGTRVDELESALDstqsdnQEIK-------SELSNIQQSISDMYDSYK 836
                                       579999999999999986.777888777776666666666652224445555.......555555555555555555 PP

                      Baculo_PEP_C 110 nllqalnnl 118
                                        ll+ ln +
  gi|298674443|ref|YP_003726193.1| 837 DLLSHLNEV 845
                                       555555544 PP

  == domain 5  score: 2.2 bits;  conditional E-value: 0.19
                      Baculo_PEP_C   4 vqqLnggggnqfldLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldt 63 
                                       ++++n    ++f dL + L+ i + ++++ +q+ +  ++ ++ L++++e+l    +++++
  gi|298674443|ref|YP_003726193.1| 842 LNEVNEDYESKFSDLYDKLSKIDTVESKL-SQIDKNTKERDEILSKVEEELPVIKNAIKR 900
                                       55556666666777777777776666666.666666666666666666666554444333 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1       2.4   2.1e+03      46      64 ..     327     345 ..     312     350 .. 0.56
   2 ?    1.4   0.4      0.46   4.1e+02      36      77 ..     446     487 ..     425     489 .. 0.69
   3 ?   -2.9   0.2       9.6   8.6e+03      46      57 ..     558     569 ..     546     576 .. 0.59
   4 ?   11.4   3.0   0.00033      0.29      46      93 ..     702     749 ..     659     752 .. 0.80
   5 ?    4.4   0.2     0.053        48      36      80 ..     762     806 ..     755     812 .. 0.72
   6 ?    5.4   1.1     0.026        23      30      69 ..     787     826 ..     771     831 .. 0.87
   7 ?   14.1   7.9   4.8e-05     0.043      25      94 ..     821     890 ..     807     892 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.4
                           BLOC1_2  46 lekkleklnekyeelqpyl 64 
                                       l++++++l++k +e+q ++
  gi|298674443|ref|YP_003726193.1| 327 LTESFDQLRKKVDEFQTNI 345
                                       3344444444444444333 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.46
                           BLOC1_2  36 ykklkdvaaslekkleklnekyeelqpylqqidqiekqvteL 77 
                                        +k +d +as+++k++++++k     ++ +  ++ e+ v++L
  gi|298674443|ref|YP_003726193.1| 446 AEKFNDLTASFKNKFKNIRQKATGSTEQTKDSEKTETAVDDL 487
                                       345566677778888888888877777777777777777766 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 9.6
                           BLOC1_2  46 lekkleklneky 57 
                                       l++++e+++e+ 
  gi|298674443|ref|YP_003726193.1| 558 LKNQMEQMKEEI 569
                                       344444444432 PP

  == domain 4  score: 11.4 bits;  conditional E-value: 0.00033
                           BLOC1_2  46 lekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEa 93 
                                       ++++  +l+e++ +++  +++++++ ++++ L ++v+eLD  +ke++ 
  gi|298674443|ref|YP_003726193.1| 702 ATNQTGNLQELQSKVNGSVTRVEKVTDDLQNLSDTVDELDDRIKEIQR 749
                                       3456778889999********************************986 PP

  == domain 5  score: 4.4 bits;  conditional E-value: 0.053
                           BLOC1_2  36 ykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeea 80 
                                       y + +d++++le +l++l+      ++  ++++ i ++v+eLe+a
  gi|298674443|ref|YP_003726193.1| 762 YYSTSDRIDNLEYQLKNLQDSLGISNESDSKLNSIGTRVDELESA 806
                                       556667777777777777777777777777888888888888765 PP

  == domain 6  score: 5.4 bits;  conditional E-value: 0.026
                           BLOC1_2  30 eaasekykklkdvaaslekkleklnekyeelqpylqqidq 69 
                                       +++ +k +++ +++++le+ l+ +++ ++e+++ l++i+q
  gi|298674443|ref|YP_003726193.1| 787 NESDSKLNSIGTRVDELESALDSTQSDNQEIKSELSNIQQ 826
                                       5677899999****************99999999999986 PP

  == domain 7  score: 14.1 bits;  conditional E-value: 4.8e-05
                           BLOC1_2  25 LeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEak 94 
                                       L ++ ++ s  y+++kd +++l++  e++++k   l  +l++id +e +++++ ++ +e De+ ++ E+ 
  gi|298674443|ref|YP_003726193.1| 821 LSNIQQSISDMYDSYKDLLSHLNEVNEDYESKFSDLYDKLSKIDTVESKLSQIDKNTKERDEILSKVEEE 890
                                       7788899999*******************************************************99986 PP

>> DUF489  Protein of unknown function (DUF489)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.6     0.014        13      43     120 ..     683     759 ..     660     767 .. 0.73
   2 ?    9.9   1.4   0.00076      0.68      52     137 ..     769     853 ..     760     861 .. 0.85
   3 ?    2.8   1.0      0.11     1e+02      42     113 ..     850     920 ..     841     934 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.014
                                       SSHHHHTTSGGGGHHHHHHHHHHHHT--SCHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHTTHHHHTTS-TTS CS
                            DUF489  43 estedvygglanlklGletlleqlekekkkkdaeltryalsllalerkLsknkealaklgerieqierqlehfdllh 119
                                       +++++v++++    ++ +   +q ++ ++  + ++   +  + +++  L++ ++++++l++ri++i+r+ e f+   
  gi|298674443|ref|YP_003726193.1| 683 KKIDKVFNKEYMDYIASRVATNQTGNLQE-LQSKVNGSVTRVEKVTDDLQNLSDTVDELDDRIKEIQRRNEDFESKI 758
                                       55666666533333444445555555555.67788888888999999**********************99996554 PP

                                       H CS
                            DUF489 120 e 120
                                       +
  gi|298674443|ref|YP_003726193.1| 759 D 759
                                       4 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00076
                                       GGGGHHHHHHHHHHHHT--SCHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHTTHHHHTTS-TTSHHHHHHHHH CS
                            DUF489  52 lanlklGletlleqlekekkkkdaeltryalsllalerkLsknkealaklgerieqierqlehfdllhenvlanlas 128
                                       ++nl+  l+ l+++l+ +++ +d +l +    + +le+ L ++++  +++++++++i++  + +  + +++l++l++
  gi|298674443|ref|YP_003726193.1| 769 IDNLEYQLKNLQDSLGISNE-SDSKLNSIGTRVDELESALDSTQSDNQEIKSELSNIQQSISDMYDSYKDLLSHLNE 844
                                       7899999*********9999.79**************************************9887777778888887 PP

                                       HHHHHTGGG CS
                            DUF489 129 iYsdtiSkl 137
                                       + +d  Sk+
  gi|298674443|ref|YP_003726193.1| 845 VNEDYESKF 853
                                       766655544 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.11
                                       -SSHHHHTTSGGGGHHHHHHHHHHHHT--SCHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHTTHHHHT CS
                            DUF489  42 pestedvygglanlklGletlleqlekekkkkdaeltryalsllalerkLsknkealaklgerieqierqle 113
                                       ++++ d+y++l+++ +  e  l+q++k++k++d  l +   +l  +++ +++n++  + l++++e++++ ++
  gi|298674443|ref|YP_003726193.1| 850 ESKFSDLYDKLSKIDTV-ESKLSQIDKNTKERDEILSKVEEELPVIKNAIKRNHKENQVLANSLEELKSSST 920
                                       56778889988888765.445566677777688888999999999999999999999999999999998766 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.21   1.8e+02       1      20 [.     327     346 ..     327     348 .. 0.90
   2 ?    7.6   0.2    0.0036       3.3       2      28 ..     727     753 ..     723     762 .. 0.79
   3 ?   -0.5   0.1       1.2   1.1e+03      21      35 ..     775     789 ..     765     807 .. 0.66
   4 ?    0.0   0.3      0.85   7.6e+02       2      33 ..     825     843 ..     813     847 .. 0.44
   5 ?    4.1   0.1     0.044        40       2      31 ..     850     879 ..     849     885 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.21
                         DASH_Dam1   1 lepafaeLaDsletLdknle 20 
                                       l+++f +L ++++++++n++
  gi|298674443|ref|YP_003726193.1| 327 LTESFDQLRKKVDEFQTNIQ 346
                                       6799**************97 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0036
                         DASH_Dam1   2 epafaeLaDsletLdknledLqqihes 28 
                                       ++ +++L+D +++Ld++++++q+ +e+
  gi|298674443|ref|YP_003726193.1| 727 TDDLQNLSDTVDELDDRIKEIQRRNED 753
                                       567889999999999999998877665 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.2
                         DASH_Dam1  21 dLqqihesLsdfNeS 35 
                                       +L+++++sL   NeS
  gi|298674443|ref|YP_003726193.1| 775 QLKNLQDSLGISNES 789
                                       455555566555555 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 0.85
                         DASH_Dam1   2 epafaeLaDsletLdknledLqqihesLsdfN 33 
                                       +++++++ Ds ++L ++             +N
  gi|298674443|ref|YP_003726193.1| 825 QQSISDMYDSYKDLLSH-------------LN 843
                                       23333333333333333.............33 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.044
                         DASH_Dam1   2 epafaeLaDsletLdknledLqqihesLsd 31 
                                       e +f++L D+l+++d+  ++L+qi+++ ++
  gi|298674443|ref|YP_003726193.1| 850 ESKFSDLYDKLSKIDTVESKLSQIDKNTKE 879
                                       579*********************998665 PP

>> DUF720  Protein of unknown function (DUF720)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.2       2.6   2.3e+03      53      97 ..     261     304 ..     236     309 .. 0.74
   2 ?   -2.9   0.1       6.3   5.6e+03      94     107 ..     701     714 ..     688     741 .. 0.54
   3 ?   11.5   0.6   0.00022       0.2      54      97 ..     802     845 ..     778     870 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.6
                            DUF720  53 saneseiqavqssNqavsAsReaiqdqlsaarqraqvisssvntn 97 
                                       s +++    ++++ + ++ +R ++ d+l  a+ + q   + vn  
  gi|298674443|ref|YP_003726193.1| 261 SDKSDDSSSLKNKFKSIT-QRRNLFDELEEAQSEDQPLAKPVNKS 304
                                       555666666666666665.77788899999999999888888765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.3
                            DUF720  94 vntnsniiqqilqa 107
                                       v tn++   q lq 
  gi|298674443|ref|YP_003726193.1| 701 VATNQTGNLQELQS 714
                                       44444443333332 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00022
                            DUF720  54 aneseiqavqssNqavsAsReaiqdqlsaarqraqvisssvntn 97 
                                       + es +   qs Nq++  + ++iq+ +s + +  +  +s++n  
  gi|298674443|ref|YP_003726193.1| 802 ELESALDSTQSDNQEIKSELSNIQQSISDMYDSYKDLLSHLNEV 845
                                       458999**********************9999888888888865 PP

>> ApoO  Apolipoprotein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.7   1.5e+03      11      39 ..     322     350 ..     309     359 .. 0.79
   2 ?    1.6   0.2      0.29   2.6e+02      29      63 ..     444     478 ..     423     499 .. 0.59
   3 ?    1.6   0.1      0.28   2.5e+02      26      62 ..     739     775 ..     700     786 .. 0.69
   4 ?    2.9   0.2      0.11     1e+02       9      61 ..     810     862 ..     794     872 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.7
                              ApoO  11 eptdrLeegvrslRkslepytsavqdeln 39 
                                       +++++L e++ +lRk + +  + +q+e  
  gi|298674443|ref|YP_003726193.1| 322 THEGNLTESFDQLRKKVDEFQTNIQNEEG 350
                                       56789999999999999888887777655 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.29
                              ApoO  29 pytsavqdelnkvkskvetaeqsvtdtiasLkepp 63 
                                       +y+++++d + ++k+k+++  q+ t + ++ k+++
  gi|298674443|ref|YP_003726193.1| 444 EYAEKFNDLTASFKNKFKNIRQKATGSTEQTKDSE 478
                                       45555555555666666666665555555555542 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.28
                              ApoO  26 slepytsavqdelnkvkskvetaeqsvtdtiasLkep 62 
                                       +l + ++++q + ++++sk+++++ s++d i++L  +
  gi|298674443|ref|YP_003726193.1| 739 ELDDRIKEIQRRNEDFESKIDNSYYSTSDRIDNLEYQ 775
                                       4555566666667778888888888888888877765 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.11
                              ApoO   9 seeptdrLeegvrslRkslepytsavqdelnkvkskvetaeqsvtdtiasLke 61 
                                       ++++ +++++  +++ +s+++ ++ ++d l+++++  e+ e++++d ++ L++
  gi|298674443|ref|YP_003726193.1| 810 TQSDNQEIKSELSNIQQSISDMYDSYKDLLSHLNEVNEDYESKFSDLYDKLSK 862
                                       35667788888888888888888888888888888888888888888888865 PP

>> T3SSipB  Type III cell invasion protein SipB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.7     0.014        12      25     100 ..     279     365 ..     266     380 .. 0.75
   2 ?   -2.5   2.4       7.2   6.4e+03      32      74 ..     433     476 ..     415     488 .. 0.56
   3 ?    6.4   0.9     0.013        12      41      79 ..     723     761 ..     701     815 .. 0.43
   4 ?    9.8   2.1    0.0012         1      35      92 ..     822     879 ..     804     927 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.014
                                       HHHHHHHHHHHHTTTTT----STHHHHHHHHHHHH..HHHHHHHHHHHHHHHHHHHHHHHHHHHHH..........H CS
                           T3SSipB  25 nrlaawkamskaqqeaasklSdelqtalseakgat..ddleaaiekadqaksaadaatkkvdeaqk..........r 89 
                                       +r + +    +aq  + + l + +++ ++e k +   +d  + i +  ++    d++ kkvde q+           
  gi|298674443|ref|YP_003726193.1| 279 QRRNLFDELEEAQ-SEDQPLAKPVNKSVDEEKPLEpfKDKFQNITHEGNLTESFDQLRKKVDEFQTniqneegsadN 354
                                       5555555555554.4456677788888888776542256667899999******************88888888888 PP

                                       HTT-------- CS
                           T3SSipB  90 lkeLaPdePek 100
                                        ++++PdePe 
  gi|298674443|ref|YP_003726193.1| 355 SSSIEPDEPES 365
                                       88899999986 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7.2
                                       HHHHHTTTTT----STHHHHHHHHHHHHHHH.HHHHHHHHHHHH CS
                           T3SSipB  32 amskaqqeaasklSdelqtalseakgatddl.eaaiekadqaks 74 
                                        +s + + ++ +  +++++++   k+  +++ ++a   ++q k 
  gi|298674443|ref|YP_003726193.1| 433 EKSDSSERKNAEYAEKFNDLTASFKNKFKNIrQKATGSTEQTKD 476
                                       55666667777777777777766655433330333344444333 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.013
                                       T----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           T3SSipB  41 asklSdelqtalseakgatddleaaiekadqaksaadaa 79 
                                        +k+ d lq++ +  +++ d +++ + + ++ +s++d+ 
  gi|298674443|ref|YP_003726193.1| 723 VEKVTDDLQNLSDTVDELDDRIKEIQRRNEDFESKIDNS 761
                                       333333333333333333333333333333333333322 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.0012
                                       HHTTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                           T3SSipB  35 kaqqeaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlke 92 
                                          q+  s + d  +++ls  +++ +d+e +   + +  s++d ++ k++++ k  ke
  gi|298674443|ref|YP_003726193.1| 822 SNIQQSISDMYDSYKDLLSHLNEVNEDYESKFSDLYDKLSKIDTVESKLSQIDKNTKE 879
                                       556899999*************************99999*************995444 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1      0.57   5.1e+02      40      60 ..     327     347 ..     301     361 .. 0.71
   2 ?    0.0   2.5       1.3   1.2e+03      16      38 ..     666     687 ..     658     718 .. 0.51
   3 ?    9.2   3.1    0.0018       1.6      23      62 ..     709     748 ..     697     753 .. 0.79
   4 ?    1.7   9.0       0.4   3.6e+02      17      62 ..     766     811 ..     756     900 .. 0.70
   5 ?   -2.3   0.1         7   6.3e+03      50      62 ..    1033    1045 ..    1031    1046 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.57
                           NPV_P10  40 lnekLdaqsaqLaeletkven 60 
                                       l+e +d++ ++++e++t+++n
  gi|298674443|ref|YP_003726193.1| 327 LTESFDQLRKKVDEFQTNIQN 347
                                       556666666666666665554 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.3
                           NPV_P10  16 vddkVdalqqqvddvqenlpdvt 38 
                                       v++k++  q+qv+dv ++  d +
  gi|298674443|ref|YP_003726193.1| 666 VNKKLNDHQKQVKDVVDKKID-K 687
                                       566666666666666654443.2 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0018
                           NPV_P10  23 lqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIq 62 
                                       lq+   +v+  +  v+++++ L+++s++++el++ +++Iq
  gi|298674443|ref|YP_003726193.1| 709 LQELQSKVNGSVTRVEKVTDDLQNLSDTVDELDDRIKEIQ 748
                                       444445566666777788899*************999998 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.4
                           NPV_P10  17 ddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIq 62 
                                       +d++d l+ q++++q+ l   +e  +kL+++ + ++ele+++++ q
  gi|298674443|ref|YP_003726193.1| 766 SDRIDNLEYQLKNLQDSLGISNESDSKLNSIGTRVDELESALDSTQ 811
                                       5666666666666666666666666666666666666666444332 PP

  == domain 5  score: -2.3 bits;  conditional E-value: 7
                           NPV_P10   50 qLaeletkvenIq 62  
                                        +L+++e+ v++I+
  gi|298674443|ref|YP_003726193.1| 1033 ALQSIENDVNQIK 1045
                                        5777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1048 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2876  (0.160411); expected 358.6 (0.02)
Passed bias filter:                      639  (0.0356406); expected 358.6 (0.02)
Passed Vit filter:                       143  (0.0079759); expected 17.9 (0.001)
Passed Fwd filter:                        81  (0.00451782); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 1.77u 0.38s 00:00:02.15 Elapsed: 00:00:00.65
# Mc/sec: 4854.66
//
Query:       gi|298674444|ref|YP_003726194.1|  [L=276]
Description: diaminopimelate epimerase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-54  182.5   0.4    7.7e-30  103.6   0.0    2.0  2  DAP_epimerase  Diaminopimelate epimerase
  ------ inclusion threshold ------
      0.019   14.0   0.0      0.034   13.2   0.0    1.3  1  Pro_racemase   Proline racemase
       0.14   11.9   0.0       0.29   10.9   0.0    1.5  1  Adenosine_kin  Adenosine specific kinase


Domain annotation for each model (and alignments):
>> DAP_epimerase  Diaminopimelate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.6   0.0   1.3e-33   7.7e-30       1     118 [.       4     126 ..       4     128 .. 0.98
   2 !   77.4   0.1   1.7e-25     1e-21       2     120 ..     155     268 ..     154     269 .. 0.92

  Alignments for each domain:
  == domain 1  score: 103.6 bits;  conditional E-value: 1.3e-33
                                       EEEECSSEEEEEEECCTTCSSHHH...HHHHHHHHTTTTSTT-SEEEEEEEEETTEEEEEEEETTTEEESTTHCCHH CS
                     DAP_epimerase   1 fakshGnpndvvvvddveaelvle...aelvaalcdreagpgadgvlfvkpsgeediklryfnrdgseaemCGnGvr 74 
                                       f+k hGn+nd++v+d++e+e v e   a+++ + c+r++g+gadg+l +  s+++d+k+r    d+seaemCGnG+r
  gi|298674444|ref|YP_003726194.1|   4 FTKLHGNGNDFIVIDEFENEIVPEnqkADFAVKYCRRKFGIGADGILYISGSDKADMKMRLLQPDASEAEMCGNGIR 80 
                                       899*****************99999999************************************************* PP

                                       HHHHHHHCTTS-S-SEEEEEETTEEEEEEEECTTSS..EEEEEE-- CS
                     DAP_epimerase  75 vfaaylreggletkkevtvetlgGeleievkddgek..vkvdmGka 118
                                       + ++y++++g  +  e tvet +    +++++d+    vkv+mGk+
  gi|298674444|ref|YP_003726194.1|  81 CLVKYAYDNGYINLGESTVETIADVYNVKTRKDDGGfwVKVNMGKP 126
                                       ******************************9999989*******98 PP

  == domain 2  score: 77.4 bits;  conditional E-value: 1.7e-25
                                       EEECSSEEEEEEECCTTCSSHHHHHHHHHHHTTTTSTT-SEEEEEEEEETTEEEEE.EEETTTEEESTTHCC.HHHH CS
                     DAP_epimerase   2 akshGnpndvvvvddveaelvleaelvaalcdreagpgadgvlfvkpsgeediklr.yfnrdgseaemCGnG.vrvf 76 
                                       ++++G+p++v++v++++  ++++  +++++   e++p++ +v+fv  +++++i++r y++++++e+ +CG+G v+ +
  gi|298674444|ref|YP_003726194.1| 155 VVNTGVPHAVIFVENLDF-NIQN--TAPKIRFDETFPNGANVNFVRIDSNDEITIRtYERGVEDETLSCGTGsVASA 228
                                       699**************7.6666..7******************************7777889*********99999 PP

                                       HHHHHCTTS-S-SEEEEEETTEEEEEEEECTTSSEEEEEE--EE CS
                     DAP_epimerase  77 aaylreggletkkevtvetlgGeleievkddgekvkvdmGkasl 120
                                             g+   +++v v+t+gG l ie+  +g    ++ G+a+ 
  gi|298674444|ref|YP_003726194.1| 229 YISNLLGK--VNNPVLVHTKGGMLNIELDGKGF--LYMEGPAET 268
                                       99999998..68****************99995..9****9975 PP

>> Pro_racemase  Proline racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.7e-06     0.034      58     127 ..      49     115 ..      42     135 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.7e-06
                                       EEE--SSTTSSEEEEEEESSSB.-SSTHHHHHHHHHHHHHTTSS-SEEEECEEEEEETTEEEEEEEECTST CS
                      Pro_racemase  58 llvppkepdadlgvifletsgy.lpmcGsntigvvtvlletGlvevqepetklsletpaGlvevtaecrdg 127
                                       +l+ + +++ad+ + +l+++     mcG++  ++v+ + ++G ++  e +    +et a + +v+++++dg
  gi|298674444|ref|YP_003726194.1|  49 ILYISGSDKADMKMRLLQPDASeAEMCGNGIRCLVKYAYDNGYINLGEST----VETIADVYNVKTRKDDG 115
                                       78889999*********99865267*********************9999....88888888888888777 PP

>> Adenosine_kin  Adenosine specific kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   4.8e-05      0.29      14      61 ..     159     206 ..     146     233 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.8e-05
                                       EEESSTTHHHHHHHHHHCCSTTSEEEEEEE--STT-EEEEEESSHHHH CS
                     Adenosine_kin  14 gqshfiktvedlyealvtsvpgikfglafcEasgkrLvrvegndeelv 61 
                                       g  h +  ve+l   + +++p+i+f  +f + ++   vr+++nde  +
  gi|298674444|ref|YP_003726194.1| 159 GVPHAVIFVENLDFNIQNTAPKIRFDETFPNGANVNFVRIDSNDEITI 206
                                       77899999************************************9655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1731.40
//
Query:       gi|298674445|ref|YP_003726195.1|  [L=98]
Description: acylphosphatase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-29  102.4   0.1    1.5e-29  102.2   0.1    1.0  1  Acylphosphatase  Acylphosphatase
  ------ inclusion threshold ------
      0.032   13.9   0.1      0.056   13.1   0.1    1.5  1  NdhS             NAD(P)H dehydrogenase subunit S


Domain annotation for each model (and alignments):
>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.2   0.1   1.6e-33   1.5e-29       2      85 .]      13      96 ..      12      96 .. 0.98

  Alignments for each domain:
  == domain 1  score: 102.2 bits;  conditional E-value: 1.6e-33
                   Acylphosphatase  2 rllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppkarvdeveveeleeeeef 80
                                      +++v+GrVQgv+FR+f+ ++A+ lgl+Gyv+Nl+dg+V++vaeg++ek++k++++l+sgp  a+v++v+v+++e ++ef
  gi|298674445|ref|YP_003726195.1| 13 EIYVSGRVQGVFFRQFTNDAATHLGLTGYVQNLPDGRVRVVAEGSQEKMNKLIDKLHSGPSLANVENVNVNWYEPTNEF 91
                                      799**************************************************************************** PP

                   Acylphosphatase 81 kdFei 85
                                      +dF++
  gi|298674445|ref|YP_003726195.1| 92 RDFKV 96
                                      ***85 PP

>> NdhS  NAD(P)H dehydrogenase subunit S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   6.2e-06     0.056      10      38 ..      29      57 ..      17      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.2e-06
                              NdhS 10 knpkdiYygfeGlvQrvsdgkaaVlFeGG 38
                                      +n   ++ g +G+vQ + dg++ V+ eG 
  gi|298674445|ref|YP_003726195.1| 29 TNDAATHLGLTGYVQNLPDGRVRVVAEGS 57
                                      6888899999*****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 638.36
//
Query:       gi|298674446|ref|YP_003726196.1|  [L=637]
Description: threonyl-tRNA synthetase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-53  179.3   0.2    6.3e-53  178.5   0.2    1.4  1  tRNA-Thr_ED      Archaea-specific editing domain of threonyl-
      3e-19   68.9   0.2    8.5e-19   67.5   0.2    1.8  1  HGTP_anticodon   Anticodon binding domain
    3.8e-19   69.4   0.5    7.1e-19   68.5   0.5    1.4  1  tRNA-synt_2b     tRNA synthetase class II core domain (G, H, 
  ------ inclusion threshold ------
      0.088   12.5   0.2       0.63    9.7   0.1    2.4  2  Retrotran_gag_2  gag-polypeptide of LTR copia-type
       0.17   12.2   0.5         18    5.7   0.0    3.7  4  DUF424           Protein of unknown function (DUF424)


Domain annotation for each model (and alignments):
>> tRNA-Thr_ED  Archaea-specific editing domain of threonyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.5   0.2   1.8e-56   6.3e-53       1     137 []       1     137 [.       1     137 [. 0.99

  Alignments for each domain:
  == domain 1  score: 178.5 bits;  conditional E-value: 1.8e-56
                                       -EEEEEEEEEEEEEEEEESSSS-...SS---EEEESSEEEEEEE-BTT--H...HHHHHHHHHHHHHHHHHT-SEEE CS
                       tRNA-Thr_ED   1 mrlLlihadeleyeakkkalkeae..eeeekegrleealvvFiavEkeDeeekekvvekavkeikkvakkvkakkvv 75 
                                       mrlLl+h+d++eye+kk++ ++ae  +e++k+grleeal+vF+avEk De++ +++v+++v+eik+v+ ++++++++
  gi|298674446|ref|YP_003726196.1|   1 MRLLLVHSDYIEYEVKKST-PVAEkvDESQKSGRLEEALTVFLAVEKPDESDIDEIVKRTVDEIKNVMGQINTDRIM 76 
                                       9*****************9.99998999************************************************* PP

                                       EEE-STS-SSB--HHHHHHHHHHHHHHHHTT.-EEEE--SSEEEEEEEEE--STTSEEEEE- CS
                       tRNA-Thr_ED  76 lypyaHLssslaspevakeilkkleeklkekglevkraPFGwykefeisckGhpLaelsrei 137
                                       lypyaHLs++l+sp++a+++lkk+e++l++k +evkraPFGwyk+f+i+ckGhpL+elsr+i
  gi|298674446|ref|YP_003726196.1|  77 LYPYAHLSNELSSPDTAVKALKKIEKELSDK-YEVKRAPFGWYKSFNINCKGHPLSELSRTI 137
                                       ******************************8.****************************97 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.5   0.2   2.4e-22   8.5e-19       1      92 [.     523     613 ..     523     615 .. 0.93

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 2.4e-22
                                       SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEET... CS
                    HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdr... 74 
                                       qv +ip++e    + ++a+k++e+L+   +rv++dd+++++gkkirea + +ip++vv+G++e+e+g+++v  r   
  gi|298674446|ref|YP_003726196.1| 523 QVRIIPVHE---HHFDFAEKIYEQLN---CRVDIDDREDTVGKKIREAGREWIPYVVVIGDREIESGKLNVTIRses 593
                                       89*******...9************9...88*******************************************888 PP

                                       ..TTCEEEEEETTHHHHHHH CS
                    HGTP_anticodon  75 ..dtreqervsldelveklk 92 
                                         ++ +  +++++el + + 
  gi|298674446|ref|YP_003726196.1| 594 lpKKPKSSEMTVEELNNRVL 613
                                       76666779******988775 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.5   0.5     2e-22   7.1e-19       1     179 []     293     503 ..     293     503 .. 0.90

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 2e-22
                                       EEEEETTSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEE.EBTTTS.TBCTTTB-SEEEEEEEEEEES.GG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx.xxxxxxxxxxxxxxxxxxxxx.xx RF
                      tRNA-synt_2b   1 YkledrndreyiLkPtneetfvelirdevlrskrLPlklyqiqtk.yRdEks.dsrGLlRvreFhqkdgyvfha.ea 74 
                                       Y +e++ +r++ L+  ++ +   +  d ++  k+LPlk++++++  +R+E++ ++ G+ R+r F++ d + f+   +
  gi|298674446|ref|YP_003726196.1| 293 YSIESD-KRRLFLRFAACFGQFLMSHDMTISYKNLPLKMVEMTRYsFRKEQRgELVGMKRLRSFTMPDMHTFCEdMD 368
                                       566666.599******************8888*********99854******8999******************88* PP

                                       GHHHHHHHHHHHHHHHHHHTT.SCEEEEEEGTTSCBTTSEEEEEEEEETT........................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
                      tRNA-synt_2b  75 slddslrdlikaisriferlglefraiielmsaksadykdkkefeavses........................... 124
                                       ++ +++ d  k   + + ++g+ +   +   +++  +y++ k+f   + +                           
  gi|298674446|ref|YP_003726196.1| 369 QSISEFDDQYKMCINTLDNIGVDVDDYEVAIRFTRDFYENNKDFITEMAKtvnkpvlvemwdtrffyfvlkfefnfi 445
                                       **********************9844444444444589999999887777889999999999999999999999999 PP

                                       ..TSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEEEEEEE.EE.HHHHHHHHHHHH CS
                                       ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxxxxxxxxx RF
                      tRNA-synt_2b 125 ..ltkgieigtiqklgtrlserlgatvldennreksvimicaa.ig.veRllsaileqn 179
                                         l+k+  ++t+q +  + +e+ +++++d+n+++k++ m++ +  g +eR + a+le+n
  gi|298674446|ref|YP_003726196.1| 446 daLGKASALSTVQID-VENAETYDISYIDRNGESKRPTMLHCSpSGaIERCIYALLEKN 503
                                       99*************.999************************9999**********87 PP

>> Retrotran_gag_2  gag-polypeptide of LTR copia-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.41   1.5e+03      24      44 ..      87     107 ..      71     113 .. 0.61
   2 ?    9.7   0.1   0.00018      0.63      51     114 ..     355     418 ..     339     429 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.41
                   Retrotran_gag_2  24 vkeektakevWdkLkelyekk 44 
                                       + +++ta+++ +k++++   k
  gi|298674446|ref|YP_003726196.1|  87 LSSPDTAVKALKKIEKELSDK 107
                                       445555555555555544433 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00018
                   Retrotran_gag_2  51 tlrkklfslkmkegesvadhinkleelvneLsalgvkiddedkvvllLasLPesyetfvtaies 114
                                       + + +++++  + ++s++++ ++ +  +n L ++gv++dd ++++   + + e+ ++f+t + +
  gi|298674446|ref|YP_003726196.1| 355 FTMPDMHTFCEDMDQSISEFDDQYKMCINTLDNIGVDVDDYEVAIRFTRDFYENNKDFITEMAK 418
                                       45556777777778899999999999*******************9999999999999998876 PP

>> DUF424  Protein of unknown function (DUF424)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0         1   3.6e+03      37      53 ..      84     100 ..      82     123 .. 0.84
   2 ?   -0.4   0.0      0.38   1.4e+03      30      76 ..     205     269 ..     195     274 .. 0.80
   3 ?    5.7   0.0    0.0049        18      18      56 ..     388     426 ..     376     452 .. 0.77
   4 ?    0.5   0.0       0.2   7.2e+02      20      53 ..     578     611 ..     575     619 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1
                                       --EEE-HHHHHHHHHHH CS
                            DUF424  37 ggelaseeeaikeLeka 53 
                                       ++el s ++a+k+L+k+
  gi|298674446|ref|YP_003726196.1|  84 SNELSSPDTAVKALKKI 100
                                       67889999999999997 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.38
                                       E--HHHH--EEE-HHHHHHHHHHH..................EEEEEESHHHHHHHHHTTSS-GG CS
                            DUF424  30 nvsegfyggelaseeeaikeLeka..................tiaNivgeeavvlavkaGlvdpd 76 
                                       ++se+ +  +   + e++k+L  a                   i +++++ + ++a++ G  + +
  gi|298674446|ref|YP_003726196.1| 205 EISESRVVDKTPPHVELMKRLGIAdyeqgsdsgnlryyprgrFIKSLLENYVLDEAIRSGAMEVE 269
                                       56666666666667888888888888889988899999999899999999999999999987765 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0049
                                       TT-EEEETTEEEE--HHHH--EEE-HHHHHHHHHHHEEE CS
                            DUF424  18 lgktfkegelllnvsegfyggelaseeeaikeLekatia 56 
                                       +g  ++++e+ +  ++ fy ++++   e+ k+ +k   +
  gi|298674446|ref|YP_003726196.1| 388 IGVDVDDYEVAIRFTRDFYENNKDFITEMAKTVNKPVLV 426
                                       68899******************9666666665555555 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.2
                                       -EEEETTEEEE--HHHH--EEE-HHHHHHHHHHH CS
                            DUF424  20 ktfkegelllnvsegfyggelaseeeaikeLeka 53 
                                       ++++ g+l++++  +  +++ +s e++++eL++ 
  gi|298674446|ref|YP_003726196.1| 578 REIESGKLNVTIRSESLPKKPKSSEMTVEELNNR 611
                                       678999*************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (637 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.50
# Mc/sec: 3811.54
//
Query:       gi|298674447|ref|YP_003726197.1|  [L=437]
Description: transposase IS605 OrfB [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-15   56.3   4.6    2.2e-15   56.3   4.6    1.8  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
       0.65   10.3  10.1        1.8    8.9   6.9    2.9  2  Rpr2            RNAse P Rpr2/Rpp21/SNM1 subunit domain


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1      0.71   6.3e+03       2      25 ..      46      69 ..      45      70 .. 0.77
   2 !   56.3   4.6   2.5e-19   2.2e-15       3      69 .]     337     403 ..     335     403 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.71
                    OrfB_Zn_ribbon  2 rklkeqleykakeyGikveevnpa 25
                                      + l  ++ey  k  G   +++n++
  gi|298674447|ref|YP_003726197.1| 46 NYLYDMVEYDYKYNGSRNKLINKY 69
                                      677889999999888888888876 PP

  == domain 2  score: 56.3 bits;  conditional E-value: 2.5e-19
                    OrfB_Zn_ribbon   3 klkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       kl+  +e+ + + G+++++v++ +T k+C  C  + k++++ rtf+C++Cg ++ rD+n+a+Ni+k+
  gi|298674447|ref|YP_003726197.1| 337 KLRGTIEWVCDKSGKTFKKVDEKNTTKKCCICEDVEKKDPEVRTFTCKKCGQTLSRDINSAVNIAKK 403
                                       8999*************************************************************96 PP

>> Rpr2  RNAse P Rpr2/Rpp21/SNM1 subunit domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.19   1.7e+03       3      32 ..      46      97 ..      45     108 .. 0.68
   2 ?    8.9   6.9    0.0002       1.8      36      70 ..     371     405 ..     277     418 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.19
                                      HHHHHHHH.......................HHHHH-HHHHHHHHHHHHHHH CS
                              Rpr2  3 nfLyqaahl......................qlaeaspalsrylakqlrevs 32
                                      n+Ly++ ++                      +l+e+ p l   +++ l++v+
  gi|298674447|ref|YP_003726197.1| 46 NYLYDMVEYdykyngsrnklinkynlrnqvpRLKEEKPFLKTVYSSVLKNVA 97
                                      8888888887777777777777776666666556666666666666666654 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0002
                                       T---SSTCCCTB-TTT--B--CTTTEEEEEE-SSS CS
                              Rpr2  36 qlrlppsvkrtvCkkCgsvlipgvtcsvrvenksk 70 
                                       + + +p+v+  +CkkCg+ l   +++ v++ +k+ 
  gi|298674447|ref|YP_003726197.1| 371 VEKKDPEVRTFTCKKCGQTLSRDINSAVNIAKKEM 405
                                       33489*************************87554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       818  (0.0456244); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 2616.31
//
Query:       gi|298674448|ref|YP_003726198.1|  [L=361]
Description: hypothetical protein Metev_0489 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-45  154.1  44.5    5.9e-45  153.8  44.5    1.0  1  AI-2E_transport  AI-2E family transporter
  ------ inclusion threshold ------
       0.19   11.3   5.7       0.72    9.4   5.7    2.0  1  Saf_2TM          SAVED-fused 2TM effector domain


Domain annotation for each model (and alignments):
>> AI-2E_transport  AI-2E family transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.8  44.5   6.6e-49   5.9e-45       4     326 ..      22     339 ..      19     340 .. 0.91

  Alignments for each domain:
  == domain 1  score: 153.8 bits;  conditional E-value: 6.6e-49
                   AI-2E_transport   4 ilvllllllalypfiselllplliAlvlayllnpvvkfL.kkrgvkrvlavllvlllllvllvllvlllvplliaql 79 
                                        ++ +l+ la+++++++l   ++++lv+ay+  p++ +L k ++v + +a++++++ ++ +l + +l ++    +q+
  gi|298674448|ref|YP_003726198.1|  22 AIAVALFFLAIIFILRPLADGIILGLVFAYISRPIYLKLnKNKRVGALVATICIVIPIIFILGMGILEII----QQI 94 
                                       5678899999999999***********************8888888888888887777666666666666....*** PP

                   AI-2E_transport  80 tqlvkslpayidslqnilnelpslleelenliqalkqslskilsnilssi.lnsllsllasllglilslvlvllllf 155
                                       t +v++   +i+sl  ++n+++ + ++l   +  ++qs+++i ++i + +    ++s++++l+ ++l+lv+++++++
  gi|298674448|ref|YP_003726198.1|  95 TWIVQNQNEVISSLTGFINNVE-IPDFL---HTGIEQSIQDISQSIIPILrEIGIVSYAKDLVIFLLNLVISIIVCY 167
                                       *********************9.77777...46777777777777777775557999******************** PP

                   AI-2E_transport 156 fllldgeklrqgilkllpervrervkailrelektlsgylrgqvlvaliigvlvfigllilgvpyalllailvglan 232
                                       fll dg +l+q++l + p+++++ +++++ el+k+l+g+++g++  al+++++++i+++++g+ + l l+ l+++a+
  gi|298674448|ref|YP_003726198.1| 168 FLLSDGNTLYQKVLDITPSNYQKTFQNYVTELDKILGGIFIGNAYAALFVSIMSAIVFYVFGFSHILALSALIFIAA 244
                                       ***************************************************************************** PP

                   AI-2E_transport 233 liPyiGavivlipiaiialltggikevlivlivvllvqli.egnilePklmgkrlglhplvillsllaggklfGlvG 308
                                       ++P++ +++vl+p+a++ ++ +gi+++li+++v+ +v ++  + + +P+l + + ++hpl+i+l++++g+ ++G+ G
  gi|298674448|ref|YP_003726198.1| 245 VVPLFAGYMVLLPLALLRYFNQGIEAALIFFLVASIVIYLpPELFMRPYLASLKSKVHPLLIMLAFIGGAFVGGIAG 321
                                       **************999999999*999999999887766626889******************************** PP

                   AI-2E_transport 309 lilavpltavikaileay 326
                                       ++ a++l++++ a++++y
  gi|298674448|ref|YP_003726198.1| 322 FFAAPILLGALIAAYRVY 339
                                       **************9988 PP

>> Saf_2TM  SAVED-fused 2TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   5.7     8e-05      0.72      21      90 ..      23      93 ..      12     106 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 8e-05
                           Saf_2TM 21 aelllftigvalllailgtdwalkialklaggslevsfssse.ipeivlaiilvigvllivvGavllilry 90
                                      ++ +lf +++  +l  l+  ++l +++   ++ + +++++++ + ++v++i++vi +++i++  +l i++ 
  gi|298674448|ref|YP_003726198.1| 23 IAVALFFLAIIFILRPLADGIILGLVFAYISRPIYLKLNKNKrVGALVATICIVIPIIFILGMGILEIIQQ 93
                                      567799999999***9**************************999****************9999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1189  (0.0663171); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 2169.63
//
Query:       gi|298674449|ref|YP_003726199.1|  [L=513]
Description: phenylalanyl-tRNA synthetase subunit alpha [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      9e-93  310.3   0.0    1.2e-92  309.9   0.0    1.1  1  tRNA-synt_2d     tRNA synthetases class II core domain (F)
    2.1e-08   33.9   0.0    4.4e-05   23.0   0.0    2.2  2  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
     0.0011   18.2   0.6      0.082   12.0   0.0    2.9  3  tRNA-synt_2      tRNA synthetases class II (D, K and N)
  ------ inclusion threshold ------
      0.049   13.6   0.6          2    8.5   0.2    2.5  2  HTH_45           Winged helix-turn-helix
       0.06   13.1   0.4       0.69    9.6   0.2    2.2  2  DUF4364          Domain of unknown function (DUF4364)
       0.13   12.1   1.9       0.76    9.7   0.2    2.4  2  TrmB             Sugar-specific transcriptional regulator Trm


Domain annotation for each model (and alignments):
>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  309.9   0.0   3.9e-96   1.2e-92       2     244 ..     240     507 ..     239     508 .. 0.98

  Alignments for each domain:
  == domain 1  score: 309.9 bits;  conditional E-value: 3.9e-96
                                       .-TSSCTSCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-.. CS
                      tRNA-synt_2d   2 idvtlpgkrieagklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpeka.. 76 
                                       ++++ p k+i+ +k+hp++++++++++if+e+gf+e++g+ ++s+f+nfdaL++pqdhpaRdmqdtF l++ +++  
  gi|298674449|ref|YP_003726199.1| 240 YNIHTPPKPIYGAKIHPYQRLINQMRQIFIEMGFTEIKGEIIQSSFWNFDALFQPQDHPARDMQDTFHLESTSEIde 316
                                       89*******************************************************************777777** PP

                                       ............................ECESEEE-SSTHHHHHHHH.TTS-SSEEEEEEEEEEBSST-SSSB-SEE CS
                      tRNA-synt_2d  77 ............................veekllLRthttavqirtl.ekkkppikiisigrvfRrdavDathlaeF 124
                                                                   ++++++LRthttav+i++l ++++pp+k ++i+r++Rr+++D thl+eF
  gi|298674449|ref|YP_003726199.1| 317 eckdnvcamhehggdisstgwggrwdenIARRNVLRTHTTAVTIKYLaDNPEPPVKAFCIDRAYRRETIDPTHLPEF 393
                                       ****************************999****************9999************************** PP

                                       EEEEEEEEETT--HHHHHHHHHHHHHHHCTSTEEEEEEECEETTEEEEEEEEEEECCSSSSEEEEEEEEEE-HHHHH CS
                      tRNA-synt_2d 125 hqveglvvdenvsladlkgvleellkklfgaevkvrfrpsyfpftePsaevdvylvekkkkwlEllgaGmvrpevle 201
                                        q+eg+v+d+n+s+a+l+g+l e+++++ g+e +vrfrp yfp+tePs+e +vy+  ++ +w+El+gaG++r+ev++
  gi|298674449|ref|YP_003726199.1| 394 EQLEGVVMDKNMSFANLLGCLAEFYHRM-GFE-NVRFRPGYFPYTEPSVEPEVYI--DGMGWIELGGAGIFRKEVTD 466
                                       ****************************.***.**********************..******************** PP

                                       HTT-.TTSEEEEEEEEHHHHHHHHHT-SSGHHHHTT.HHHHGG CS
                      tRNA-synt_2d 202 avgideevsgfafGlGveRlamlkygieDiRelvendlrflrq 244
                                       ++gi  + +++a+GlGv R+amlk+g+ D+Rel+++d++++r+
  gi|298674449|ref|YP_003726199.1| 467 PLGI--KHPVLAWGLGVSRVAMLKLGLRDLRELYQSDINWIRK 507
                                       ****..**********************************986 PP

>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0   0.00042       1.3       6      48 ..     245     291 ..     243     312 .. 0.72
   2 !   23.0   0.0   1.5e-08   4.4e-05      72     209 ..     349     476 ..     345     480 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00042
                   tRNA_synthFbeta   6 PkapttegelnkeqklrrklrdllagaGlnEv....itysfvsekel 48 
                                       P  p+ +++ ++ q+l +++r++ +++G++E+    i +sf + + l
  gi|298674449|ref|YP_003726199.1| 245 PPKPIYGAKIHPYQRLINQMRQIFIEMGFTEIkgeiIQSSFWNFDAL 291
                                       55566667799******************986222255666555555 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 1.5e-08
                   tRNA_synthFbeta  72 svlRtsLlpglLevlarNlargnedvrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlk 147
                                       +vlRt  ++  ++ la N    ++ v++F i + ++ +  + +   e ++l +v++ k+           ++f++l 
  gi|298674449|ref|YP_003726199.1| 349 NVLRTHTTAVTIKYLADN---PEPPVKAFCIDRAYRREtIDPTHLPEFEQLEGVVMDKN-----------MSFANLL 411
                                       567777766666666665...667788***********97778899*************...........******* PP

                   tRNA_synthFbeta 148 givealleslgiekvefepaehpalhpgrsAeikvdgk...evGvlGelhpevleafdlkqrvyv 209
                                       g + ++  ++g+e+v+f+p   p+ +p    e+++dg    e+G +G + +ev + +++k++v +
  gi|298674449|ref|YP_003726199.1| 412 GCLAEFYHRMGFENVRFRPGYFPYTEPSVEPEVYIDGMgwiELGGAGIFRKEVTDPLGIKHPVLA 476
                                       *************************************8899********************9986 PP

>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.013        39      23      52 ..     255     284 ..     233     295 .. 0.82
   2 !   12.0   0.0   2.7e-05     0.082      93     119 ..     372     397 ..     371     420 .. 0.84
   3 ?   -2.0   0.0      0.49   1.5e+03     287     307 ..     477     497 ..     473     498 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.013
                                       HHHHHHHHHHHHHHHHTT-EE----SEESS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  23 rlrstvtkavrkyleengfieietPiLsks 52 
                                          +++++++r+++ e gf+ei+  i+++s
  gi|298674449|ref|YP_003726199.1| 255 HPYQRLINQMRQIFIEMGFTEIKGEIIQSS 284
                                       5567899***************98877765 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 2.7e-05
                                       EEEEEEEEE--S--BTTB-S-CEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  93 rvfqiaraFRaEdsrtdrhlaEFtqie 119
                                       + f+i ra+R E ++ ++ + EF q+e
  gi|298674449|ref|YP_003726199.1| 372 KAFCIDRAYRRETIDPTHLP-EFEQLE 397
                                       68***************999.***997 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.49
                                       EEEEHHHHHHHHCT-SSGGGC CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 287 lglGldRlvmlllgsesIrdv 307
                                       +glG++R+ ml lg+++ r++
  gi|298674449|ref|YP_003726199.1| 477 WGLGVSRVAMLKLGLRDLREL 497
                                       79***********99999875 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.045   1.4e+02      43      66 ..      55      81 ..      39      85 .. 0.81
   2 ?    8.5   0.2   0.00067         2      37      68 ..     177     211 ..     164     219 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.045
                            HTH_45 43 Lvekgli...kkskekYvlTekGlell 66
                                      L e+gl    ++ + +Y++T +G e+ 
  gi|298674449|ref|YP_003726199.1| 55 LEEEGLAkvdEEVSVNYTITREGVEYA 81
                                      6677774445667899*******9986 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00067
                            HTH_45  37 nkYLdmLvekglikkskekYv...lTekGlellek 68 
                                       ++ L+ L++++l+ k++ekY+   +T++G+el+++
  gi|298674449|ref|YP_003726199.1| 177 KSALKDLLKRKLVIKNEEKYRyvsITNQGRELVSQ 211
                                       566999******9777777743359*******987 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0       0.1   3.1e+02      43      71 ..      55      82 ..      47      99 .. 0.75
   2 ?    9.6   0.2   0.00023      0.69      37      90 ..     177     228 ..     165     251 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.1
                           DUF4364 43 LvesglieeeekenktlykiTekGketle 71
                                      L+e+gl  + ++e +  y+iT +G e ++
  gi|298674449|ref|YP_003726199.1| 55 LEEEGL-AKVDEEVSVNYTITREGVEYAD 82
                                      445555.4557799999*******98775 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00023
                           DUF4364  37 qqalseLvesglieeeekenktlykiTekGketlelfenripksirekideylk 90 
                                       ++al++L++ +l+ + ++e+  + +iT++G+e +++   +i ++i + + + lk
  gi|298674449|ref|YP_003726199.1| 177 KSALKDLLKRKLVIK-NEEKYRYVSITNQGRELVSQ-GIEIGEEITQLTSQLLK 228
                                       579***********8.569999**********9985.44556666555555555 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.2   0.00025      0.76       3      57 ..      12      66 ..      10      75 .. 0.83
   2 ?    1.2   0.1      0.11   3.3e+02      41      61 ..     178     198 ..     172     203 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00025
                                      HCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                              TrmB  3 klGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57
                                      +++Ls +E kv +aL +l++ t +++ae++ +    + ++   Le+ Gl ++ ++
  gi|298674449|ref|YP_003726199.1| 12 DYNLSINEKKVLIALGELESTTPETLAEKTSLKPEAAMQSAFLLEEEGLAKVDEE 66
                                      699**************************99877777777777777777777665 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.11
                                       HHHHHHHHCTSEEEESSTTTE CS
                              TrmB  41 evLrsLedkGlVerekgrpkl 61 
                                       ++L+ L+++ lV ++++++++
  gi|298674449|ref|YP_003726199.1| 178 SALKDLLKRKLVIKNEEKYRY 198
                                       57999*********9887664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3705.51
//
Query:       gi|298674450|ref|YP_003726200.1|  [L=442]
Description: tryptophanyl-tRNA synthetase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-37  129.6   0.0    3.4e-21   75.8   0.0    2.1  2  tRNA-synt_1b  tRNA synthetases class I (W and Y)


Domain annotation for each model (and alignments):
>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.8   0.0   1.9e-25   3.4e-21       3     177 ..      65     233 ..      62     271 .. 0.86
   2 !   52.0   0.0   3.5e-18   6.2e-14     165     293 .]     286     416 ..     276     416 .. 0.93

  Alignments for each domain:
  == domain 1  score: 75.8 bits;  conditional E-value: 1.9e-25
                                       HS--EEEEEEETSSS-BGGGHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHH.HHHHHHHHHHHHHH CS
                      tRNA-synt_1b   3 erplrvysGidPTgklHlGylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkr.eevlenaikaqlak 78 
                                        +p++v sG++P+g +HlG  +++  +++ q++g ++f+ iaD +A+ ++    ++ k r+   +++  +   ++a 
  gi|298674450|ref|YP_003726200.1|  65 GEPFSVISGFMPSGMVHLGGKMVMDEIIWHQQMGADAFVGIADREAYAVRGL--SWDKCRELgINEYILS---LIAL 136
                                       689****************6666666777777*******************9..5666655414556666...99** PP

                                       TCHTTTEEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHHCCHHCSS..SC--BHHHHHHHHHHHHHHHHTCHSE CS
                      tRNA-synt_1b  79 gldpekaevvlqsewlehlelaellrdlgklgslnrmlqfksvkkrlee..gegislgeftYplLqaaDilllkadl 153
                                       g++p + ++++qs+  + +++a  l + ++  +l+ ++ f   ++++++  ++  + ++++ p+L + D    k+++
  gi|298674450|ref|YP_003726200.1| 137 GFEP-DGHIYFQSKCDNVKNMAFELGSKTNYSELSAIYGFGG-ETNVSHmiSTLTQSADILQPQLKEFDGP--KPTV 209
                                       ****.789**********************************.777777433567899***********99..**** PP

                                       EEEEGGGHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1b 154 vpgGsDQkqnielgrdlarrfnkk 177
                                       vp+G DQ+ +i+l+r la ++n  
  gi|298674450|ref|YP_003726200.1| 210 VPVGADQDPHIRLTRGLAHKMNML 233
                                       *******************99976 PP

  == domain 2  score: 52.0 bits;  conditional E-value: 3.5e-18
                                       HHHHHHHHHHHHH...STTSS-EEEEET-BBSTTSSSBTTCETTCGC-BTTCCHHHHHHHHHHCHCSTTC..SHHHH CS
                      tRNA-synt_1b 165 elgrdlarrfnkk...evfkkpegltvplltgldGekKmSKSagnsaIfLddekesvkkkiqkavtdsde..evekl 236
                                       e+  d++r+++ +     f +p+++++++++gl+G+ KmS+S++ s+I L++++++  kk+++ +t      e +k 
  gi|298674450|ref|YP_003726200.1| 286 EAILDIVRQVELEaggYSFVPPVATYHRFMSGLQGG-KMSSSDPDSYIALTEDPKEGAKKVKRSKTGGCVslEEQKK 361
                                       555688888888888889******************.*******************************998889999 PP

                                       HHHHHTHHHCHHHHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1b 237 lklktelsnelierleavsgkkpkreaeellaeevtklvhggdlkkalaealnelle 293
                                       l ++++ +  ++e l+ ++  ++ +++ e++ e+v+++ ++g +kk +ae + e+l+
  gi|298674450|ref|YP_003726200.1| 362 LGGNPKNCS-VYELLMFHLIDDD-KQLTEIYDECVSGTRMCGSCKKYTAELMSEFLK 416
                                       999999999.***********99.9****************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3056.54
//
Query:       gi|298674451|ref|YP_003726201.1|  [L=405]
Description: radical SAM domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.8e-15   55.5   0.1    1.6e-14   54.7   0.1    1.4  1  Radical_SAM  Radical SAM superfamily
    1.2e-09   38.5   0.5    2.9e-09   37.3   0.5    1.6  1  SPASM        Iron-sulfur cluster-binding domain
     0.0072   16.6   0.0      0.015   15.6   0.0    1.5  1  Fer4_12      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.081   13.1   0.7       0.23   11.6   0.7    1.8  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.7   0.1   3.5e-18   1.6e-14       2     146 ..     111     244 ..     110     257 .. 0.89

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 3.5e-18
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgi 78 
                                       ++tr C  +C +C ++      g + +l+v+ i++ ++e+  ++g+  ++++ g+pll+ ++ el++   k      
  gi|298674451|ref|YP_003726201.1| 111 EITRECKCNCEHCVVS------GGEGDLDVDTIKRTIDEA-LDMGAFIITFTEGDPLLREEIFELIDYVDKD---RA 177
                                       789*************......7999**************.8****************88887777777776...9* PP

                                       EEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  79 ritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvv 146
                                        + + t+gt +++e ++rl+e g+  + +++ ++d+ek+    +  +  e  l+a++++ +ag+ + +
  gi|298674451|ref|YP_003726201.1| 178 IVNIFTPGTELTPETAKRLKESGLHNLLISIYSTDSEKHDSVRRLDGAHEMALNAIKNAVDAGLLV-T 244
                                       *************************************5555555889****************994.3 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.5   6.5e-13   2.9e-09       1      53 [.     324     371 ..     324     383 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 6.5e-13
                             SPASM   1 CfapsrslfInsdGdVvpCcvdkktyveelklGnireesleeIwnse.eyqefr 53 
                                       C+a++r + + +dG V pC  +  ++  ++ +Gni+++sl++Iwn+   y  f+
  gi|298674451|ref|YP_003726201.1| 324 CMAGQRWMHVCVDGSVKPC--P--YI--PFEFGNIQNDSLKDIWNNIrNYSHFK 371
                                       99*****************..2..34..6***************9987888888 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   3.3e-06     0.015      13      96 ..     114     188 ..     106     223 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.3e-06
                           Fer4_12  13 sgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiw 89 
                                         C+ +C+ C+        ++ + + +++++ i+++ +   + +t++ G+Pll   +e++ el+++v +     + +
  gi|298674451|ref|YP_003726201.1| 114 RECKCNCEHCV-----VSGGEGDLDVDTIKRTIDEALDMGAFIITFTEGDPLL---REEIFELIDYVDKDRA-IVNI 181
                                       67999999999.....455666788899999999999****************...9999999999998877.4555 PP

                           Fer4_12  90 lytgytl 96 
                                        + g+ l
  gi|298674451|ref|YP_003726201.1| 182 FTPGTEL 188
                                       5555555 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.7   5.2e-05      0.23       5      89 ..     113     185 ..     110     208 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.2e-05
                           Fer4_14   5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypek 81 
                                       +  C+++C  C  +       +   + +++++ +  +++ ++ +  +++t G+PL+    +e+++l++++ +     
  gi|298674451|ref|YP_003726201.1| 113 TRECKCNCEHCVVSG-----GEGDLDVDTIKRTI--DEALDMGAFIITFTEGDPLLR---EEIFELIDYVDKDR--A 177
                                       568********9877.....34444455666777..55556666779********65...89999999999988..6 PP

                           Fer4_14  82 kiwletng 89 
                                        + + t g
  gi|298674451|ref|YP_003726201.1| 178 IVNIFTPG 185
                                       66666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2766.74
//
Query:       gi|298674452|ref|YP_003726202.1|  [L=211]
Description: translation initiation factor aIF-2 subunit beta [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-37  128.5   0.0    1.6e-37  127.9   0.0    1.2  1  eIF-5_eIF-2B  Domain found in IF2B/IF5
    2.7e-12   46.5   0.5    6.2e-12   45.3   0.5    1.6  1  TRAM          TRAM domain
  ------ inclusion threshold ------
        0.1   12.2   0.1        0.1   12.2   0.1    1.8  2  zf_C2H2_13    Zinc finger domain
        0.2   11.0   0.0        0.2   11.0   0.0    1.6  2  zf-RanBP      Zn-finger in Ran binding protein and others
       0.26   11.2   1.2          2    8.4   0.1    2.2  2  DUF35_N       Rubredoxin-like zinc ribbon domain (DUF35_N)


Domain annotation for each model (and alignments):
>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.9   0.0   4.5e-41   1.6e-37       5     117 .]      26     136 ..      23     136 .. 0.97

  Alignments for each domain:
  == domain 1  score: 127.9 bits;  conditional E-value: 4.5e-41
                                       CSSSS--SSTT--EEEETT.EEEETTHHHHHHHHTTSHHHHHHHHHHHHTSEEEESETTEEEESSSSSCCHHHHHHH CS
                      eIF-5_eIF-2B   5 edkkerykmpklqvkvegkkktvivNfeeiakaLnrdpehvlkyllkelgtqgsidengrlilngkfeakkleklld 81 
                                       e++++r+++p+++v +egk +t++ Nf +i++ Lnrdpehvlkyl +elgt+g+i e++r++++g+f ++ +++ ld
  gi|298674452|ref|YP_003726202.1|  26 ETSDDRFTIPEPKVLQEGK-TTILDNFGNIVDVLNRDPEHVLKYLNRELGTAGKI-EGSRAVFQGRFPKELIKSNLD 100
                                       56789**************.***********************************.999****************** PP

                                       HHHHHHTSTSSSTSTCEEECCSSSCEEEEESSSTCE CS
                      eIF-5_eIF-2B  82 kyieeyVlCkeCkspetelekeerllvlkCkaCgak 117
                                       +y++eyVlC+eC++p+t+lek +r+lv+kC aCga+
  gi|298674452|ref|YP_003726202.1| 101 SYLNEYVLCTECGRPDTQLEKVDRVLVMKCLACGAH 136
                                       **********************************85 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.5   1.7e-15   6.2e-12       3      60 ..     155     208 ..     153     210 .. 0.96

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 1.7e-15
                                       XXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEE CS
                              TRAM   3 yvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGe 60 
                                       ++G++++V ++ ++ s+g+gi+++d ++++fvpg+ +  G+ V+VkI +   + +++e
  gi|298674452|ref|YP_003726202.1| 155 EEGKVYDVQITAVG-SKGDGIAKLD-KFTIFVPGAAK--GQNVKVKINRISGNLAFAE 208
                                       79************.**********.***********..****************998 PP

>> zf_C2H2_13  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   2.9e-05       0.1       5      26 ..      93     115 ..      91     120 .. 0.91
   2 ?   -2.8   0.3       1.4   4.9e+03      20      27 ..     130     139 ..     130     141 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.9e-05
                        zf_C2H2_13   5 rliedpLdtn.lnYRvCnkCGkP 26 
                                       +li+  Ld+   +Y +C +CG+P
  gi|298674452|ref|YP_003726202.1|  93 ELIKSNLDSYlNEYVLCTECGRP 115
                                       689999***9889*********9 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.4
                        zf_C2H2_13  20 CnkCG..kPi 27 
                                       C +CG  +Pi
  gi|298674452|ref|YP_003726202.1| 130 CLACGahRPI 139
                                       8899944465 PP

>> zf-RanBP  Zn-finger in Ran binding protein and others
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.5       1.1     4e+03       7      11 ..     109     113 ..     108     113 .. 0.82
   2 ?   11.0   0.0   5.7e-05       0.2      19      29 ..     128     138 ..     125     139 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.1
                                       -SSS- CS
                          zf-RanBP   7 CskCl 11 
                                       C+ C+
  gi|298674452|ref|YP_003726202.1| 109 CTECG 113
                                       99996 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 5.7e-05
                                       SB-TTT--BTS CS
                          zf-RanBP  19 tkCvaCqapkp 29 
                                       +kC+aC+a++p
  gi|298674452|ref|YP_003726202.1| 128 MKCLACGAHRP 138
                                       7*********9 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.2       0.1   3.6e+02      28      34 ..     109     115 ..     107     118 .. 0.59
   2 ?    8.4   0.1   0.00056         2       8      21 ..     124     137 ..     119     139 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.1
                           DUF35_N  28 CphCgsd 34 
                                       C+ Cg+ 
  gi|298674452|ref|YP_003726202.1| 109 CTECGRP 115
                                       5555554 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00056
                           DUF35_N   8 rLvgqrCpdCGtvq 21 
                                       r+++++C +CG+++
  gi|298674452|ref|YP_003726202.1| 124 RVLVMKCLACGAHR 137
                                       899********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      640  (0.0356964); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1344.67
//
Query:       gi|298674453|ref|YP_003726203.1|  [L=172]
Description: 50S ribosomal protein L10 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-31  108.9   0.3    2.1e-31  108.7   0.3    1.0  1  Ribosomal_L16  Ribosomal protein L16p/L10e
     0.0032   17.4   0.0     0.0046   16.9   0.0    1.2  1  GvpL_GvpF      Gas vesicle synthesis protein GvpL/GvpF


Domain annotation for each model (and alignments):
>> Ribosomal_L16  Ribosomal protein L16p/L10e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.7   0.3   2.3e-35   2.1e-31       2     132 .]      13     163 ..      12     163 .. 0.95

  Alignments for each domain:
  == domain 1  score: 108.7 bits;  conditional E-value: 2.3e-35
                                       XSSXXBSSSXXSSTSXX.XSXXXXXESX........EEEEESSXEEEEHHHHHHHHHHHCTCCCCTSXC...EEXXS CS
                     Ribosomal_L16   2 krkkyrKsrkryirgvs.tkgtklefgd........ygLvalekgqltaealeaariainrylkkkrgk...klwir 66 
                                       k++ y++++  y+ gv+ ++  ++++g+        ++L+a+e++ ++++ale+ar+ +nr+l k  g+   +l++r
  gi|298674453|ref|YP_003726203.1|  13 KKRSYTRRE--YMGGVPgSQVIHYDMGNktaqfpvkLSLIAEEDCHIRHTALESARVSANRKLMKAAGRagyHLKVR 87 
                                       8899****9..***********************9999**************************9999999****** PP

                                       XXXXEEEEE-.....SS-TTTSSSS....XEEEEEEEEEXSSCEEEEETTXXXSH...HHHHHHHHHHHTSSSXEEE CS
                     Ribosomal_L16  67 vfphhpvtkk.....agedRmgkGk....Gkpegwvarvkigqiifeikagvnee...iakealrraasKlpiktki 131
                                       v+ph +++++     ag+dR+++G+    Gk  g++arv++gq +f+  + vn++    ak+al ra +K+p++ +i
  gi|298674453|ref|YP_003726203.1|  88 VYPHEVLRENkqatgAGADRVSSGMrqafGKNVGTAARVSAGQKVFTA-S-VNKDdfgAAKDALWRAGQKIPTPFRI 162
                                       ************************************************.3.44444559****************99 PP

                                       E CS
                     Ribosomal_L16 132 v 132
                                       v
  gi|298674453|ref|YP_003726203.1| 163 V 163
                                       7 PP

>> GvpL_GvpF  Gas vesicle synthesis protein GvpL/GvpF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   5.1e-07    0.0046      70     148 ..      36     112 ..      29     140 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.1e-07
                         GvpL_GvpF  70 m.aegtvlPlrFgtvlkdeeav.relLeeeadelreaLerlagkvEygvkvlwdeealleelleedpelrelreeie 144
                                       m  ++   P+++ ++++++  +   +Le+ +   +++L++ ag++ y++kv++ +    +e+l+e++++  + +++ 
  gi|298674453|ref|YP_003726203.1|  36 MgNKTAQFPVKLSLIAEEDCHIrHTALESARVSANRKLMKAAGRAGYHLKVRVYP----HEVLRENKQATGAGADRV 108
                                       55677889**************99*******************************....888888888777776666 PP

                         GvpL_GvpF 145 aase 148
                                       +++ 
  gi|298674453|ref|YP_003726203.1| 109 SSGM 112
                                       5554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 1075.19
//
Query:       gi|298674454|ref|YP_003726204.1|  [L=356]
Description: hypothetical protein Metev_0495 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-90  302.2   0.0    4.9e-90  301.2   0.0    1.5  2  DUF1786   Putative pyruvate format-lyase activating enzyme (D


Domain annotation for each model (and alignments):
>> DUF1786  Putative pyruvate format-lyase activating enzyme (DUF1786)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.13   2.3e+03      18      45 ..      27      54 ..      16      56 .. 0.81
   2 !  301.2   0.0   2.7e-94   4.9e-90       1     252 []      60     313 ..      60     313 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.13
                           DUF1786 18 lkvvateeaAltlrddlekvkemGieiv 45
                                        v++ ++    ++d ++k  + Gi+iv
  gi|298674454|ref|YP_003726204.1| 27 SPVMIMPSPTVMVADKIRKATSQGIDIV 54
                                      4688889999999999999999999986 PP

  == domain 2  score: 301.2 bits;  conditional E-value: 2.7e-94
                           DUF1786   1 MGGGavtkavkehlkaGlkvvateeaAltlrddlekvkemGieivee.....apeeaekielkDvdlealkealeaf 72 
                                       MGGG++tkavk+hlk+Gl+v+ate+aAlt++d+++k+++mG++i +e      pe++++i+l+D++l+a+k+a+ +f
  gi|298674454|ref|YP_003726204.1|  60 MGGGPSTKAVKDHLKKGLNVYATENAALTIHDNPDKIRSMGVKIIDEhelksLPENLQRINLQDLTLDAIKNAYYQF 136
                                       ********************************************777677779999********************* PP

                           DUF1786  73 glelpekvavavqDHGyspgesnrkfRfelleelleeggkleelvfeee.vpeeftRlkavaeslkeegkvvvmDtg 148
                                       g+++p+++avavqDHGysp++snr++Rf+++e+ ++egg +e++ ++++ +p+++tRl + ++ +   ++ v+mDtg
  gi|298674454|ref|YP_003726204.1| 137 GITAPSNFAVAVQDHGYSPESSNRVYRFKHFENAIREGGGIEQFSYKNKdIPPYLTRLVDTSRIIG-GTQSVFMDTG 212
                                       *****************************************************************9.459******* PP

                           DUF1786 149 aaavlGalldpeveklsgalvvnvGngHtlaalvkegrivgvfEhHTsaltkekleelieklaegeltneevfedgG 225
                                       +aa++G l d++  +  + +vvn+GngHtl+alv ++++v++fEhHTs+lt+ +l+++i +l eg+l +ee+f+d+G
  gi|298674454|ref|YP_003726204.1| 213 PAAIFGSLKDSSSYQ--PSVVVNIGNGHTLGALVIDNKVVALFEHHTSQLTSYRLQDYIIRLSEGDLAFEEIFNDKG 287
                                       ***********9986..************************************************************ PP

                           DUF1786 226 HGvlaaaekeeaeevekvvvtGPrrel 252
                                       HG ++ ++k  ++++++v+vtGPrre+
  gi|298674454|ref|YP_003726204.1| 288 HG-CYINRKIGFDNIKSVMVTGPRREM 313
                                       **.8888899***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2177.98
//
Query:       gi|298674455|ref|YP_003726205.1|  [L=181]
Description: molybdenum cofactor synthesis domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.4e-35  119.9   0.1    7.4e-35  119.7   0.1    1.0  1  MoCF_biosynth  Probable molybdopterin binding domain


Domain annotation for each model (and alignments):
>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.7   0.1   4.1e-39   7.4e-35       3     143 ..      24     173 ..      22     174 .. 0.91

  Alignments for each domain:
  == domain 1  score: 119.7 bits;  conditional E-value: 4.1e-39
                                       EEE-HHHH........TTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTS.SEEEEESS-SSST CS
                     MoCF_biosynth   3 itvGdell........sgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleea.dviittGGtGptp 70 
                                       it++++++        +++++Dt+g ++++ l+  g++v++y+++ Dd ++i++++ +a+ ++ d++ittGGtG+t+
  gi|298674455|ref|YP_003726205.1|  24 ITISSSRYykygdvtnPEEADDTSGNTIKNILTTNGHKVIHYKLINDDFTAIQNTVNSAVYSNaDIVITTGGTGLTS 100
                                       78888888888888889999************************************55543335************* PP

                                       T--HHHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EE.....TTEEEEE-SSHHHHHHHHHHHHHGGH CS
                     MoCF_biosynth  71 dDvtpealaklfekelegfeeafrrvslkpgkpvgvapgailsrav.....gktiigLPGspkavkealeeillpal 142
                                        Dvt ea+++lf+ke++gf+e+fr  sl+      +++ +il ra+      k++++LPGs +av+ a++ei++p+ 
  gi|298674455|ref|YP_003726205.1| 101 HDVTIEAVQPLFDKEIPGFGELFRFKSLED-----IGTSVILTRATagvvrTKPVFCLPGSNNAVRLAIREIIIPET 172
                                       *****************************8.....999999****9***96666*******************9987 PP

                                       H CS
                     MoCF_biosynth 143 e 143
                                       +
  gi|298674455|ref|YP_003726205.1| 173 D 173
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1202.30
//
Query:       gi|298674456|ref|YP_003726206.1|  [L=86]
Description: hypothetical protein Metev_0497 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.8e-19   68.0   0.2    6.4e-19   67.9   0.2    1.0  1  CRS1_YhbY  CRS1 / YhbY (CRM) domain
  ------ inclusion threshold ------
      0.053   12.8   0.2      0.067   12.5   0.2    1.0  1  DUF915     Alpha/beta hydrolase of unknown function (DUF915)


Domain annotation for each model (and alignments):
>> CRS1_YhbY  CRS1 / YhbY (CRM) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.9   0.2   7.1e-23   6.4e-19       1      84 []       1      86 []       1      86 [] 0.95

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 7.1e-23
                         CRS1_YhbY  1 LtekelrrLrhlairlkpkvkiGkaGvtkevvdeiheklkteelvkvkc..egppalnmkrmaeiLeektgglviqrsg 77
                                      + +k+l +L++ a +lkp+++iGk+G+t+ v++e+++++k++ lvkvk+     + ++  +  ++++++t+ ++++++g
  gi|298674456|ref|YP_003726206.1|  1 MDKKQLYKLKSEASQLKPVIHIGKSGLTEPVIEELKKQIKANRLVKVKIlkSTFESEDTFQFSQKIADATNTTLVDVRG 79
                                      5789*********************************************9945568889******************** PP

                         CRS1_YhbY 78 tsivLYR 84
                                      + +vLYR
  gi|298674456|ref|YP_003726206.1| 80 NNVVLYR 86
                                      ******9 PP

>> DUF915  Alpha/beta hydrolase of unknown function (DUF915)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   7.5e-06     0.067       4      72 ..       9      77 ..       7      81 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.5e-06
                            DUF915  4 lksekkkeiPtifihGyggtaeslnemvkqlenkegkkkkvltvdvskdgevsvkgkiskdaknPiikv 72
                                      lkse+++  P+i i  +g t+  ++e+ kq++ ++ +k k+l+++ +++ + +++ ki+   + +++ v
  gi|298674456|ref|YP_003726206.1|  9 LKSEASQLKPVIHIGKSGLTEPVIEELKKQIKANRLVKVKILKSTFESEDTFQFSQKIADATNTTLVDV 77
                                      6899999*************************9999***************************999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 564.44
//
Query:       gi|298674457|ref|YP_003726207.1|  [L=108]
Description: hypothetical protein Metev_0498 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.5e-35  119.9   0.2    5.1e-35  119.7   0.2    1.0  1  DUF190       Uncharacterized ACR, COG1993
  ------ inclusion threshold ------
      0.091   12.9   0.0       0.11   12.6   0.0    1.2  1  DUF3240      Protein of unknown function (DUF3240)
       0.16   11.9   0.0       0.21   11.5   0.0    1.2  1  Cas_APE2256  CRISPR-associated protein (Cas_APE2256)


Domain annotation for each model (and alignments):
>> DUF190  Uncharacterized ACR, COG1993
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.7   0.2   8.5e-39   5.1e-35       2      97 .]       5     100 ..       4     100 .. 0.99

  Alignments for each domain:
  == domain 1  score: 119.7 bits;  conditional E-value: 8.5e-39
                                       EEEEEEETT-EETTEEHHHHHHHHHHHTT-S--EEEE-S---------------------EEEEEEEE-HHHHHHHH CS
                            DUF190   2 lLrIyigesdrlegkplyeaivelareeglagatvlrGieGfgassrihtakllelsedlPvvieivdteekieafl 78 
                                       +LrIy+++sd+++gk  ++a++e+++++g+agatv++GieG+g +++ihta++l+l  dlPv++e++d+eek+++++
  gi|298674457|ref|YP_003726207.1|   5 ILRIYMNQSDTYKGKTSHDAVLEYLKDSGIAGATVIHGIEGYGTHNEIHTANVLRLGVDLPVIVEVIDDEEKVRNVI 81 
                                       69*************************************************************************** PP

                                       HHHHT----SEEEEEEEE- CS
                            DUF190  79 pelkelvkeglvtlekvev 97 
                                       p+lke++  +l+tl+++e+
  gi|298674457|ref|YP_003726207.1|  82 PHLKEMLPGALMTLQDIEI 100
                                       *****************96 PP

>> DUF3240  Protein of unknown function (DUF3240)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.9e-05      0.11      16      86 ..      22      91 ..      10     101 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.9e-05
                           DUF3240 16 kddlvDlLlelpdllsGFtlldakghsrevslatiaEkvrGradkvvveivleeaalerllaeLrkavakt 86
                                      +d+++ +L +  +++    ++ ++g++ + +  t++    G    v+ve++  e+++++++ +L+++++++
  gi|298674457|ref|YP_003726207.1| 22 HDAVLEYLKDS-GIAGATVIHGIEGYGTHNEIHTANVLRLGVDLPVIVEVIDDEEKVRNVIPHLKEMLPGA 91
                                      56777777776.6555555678**********99999999*************************999875 PP

>> Cas_APE2256  CRISPR-associated protein (Cas_APE2256)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.5e-05      0.21      24      55 ..       7      39 ..       2      64 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.5e-05
                       Cas_APE2256 24 elvllssdTaaGklvaeilkeyleeegae.vev 55
                                      ++++  sdT++Gk + +++ eyl+ +g++  +v
  gi|298674457|ref|YP_003726207.1|  7 RIYMNQSDTYKGKTSHDAVLEYLKDSGIAgATV 39
                                      578889*******************88773444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 743.23
//
Query:       gi|298674458|ref|YP_003726208.1|  [L=399]
Description: molybdenum cofactor synthesis domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      7e-42  142.9   0.1    1.1e-41  142.2   0.1    1.3  1  MoeA_N         MoeA N-terminal region (domain I and II)
      4e-25   88.2   0.0    7.1e-25   87.4   0.0    1.4  1  MoCF_biosynth  Probable molybdopterin binding domain
    3.5e-16   59.1   3.9    2.4e-15   56.4   0.0    3.6  5  MoeA_C         MoeA C-terminal region (domain IV)
  ------ inclusion threshold ------
      0.065   13.1   0.0       0.14   12.0   0.0    1.5  1  UEV            UEV domain
      0.083   11.5   0.0       0.14   10.7   0.0    1.3  1  MutL           MutL protein


Domain annotation for each model (and alignments):
>> MoeA_N  MoeA N-terminal region (domain I and II)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.2   0.1   3.1e-45   1.1e-41       2     157 .]      10     165 ..       9     165 .. 0.93

  Alignments for each domain:
  == domain 1  score: 142.2 bits;  conditional E-value: 3.1e-45
                                       -HHHHHHHHHHH-.HH-EEE.EEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--...........-S CS
                            MoeA_N   2 sveealaiilaal.eleeee.vplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeepsaageepe 76 
                                       +v++a++i+l+a+  +e++e v++  e+ gr+l + v+A+++vP+++++amDGYAvr++++ gas+++p+  + ++e
  gi|298674458|ref|YP_003726208.1|  10 PVNQARKIFLNAFnSIENTEqVSI-DECSGRILSDSVTANRNVPHYRRAAMDGYAVRSSDTVGASPDNPIMLQIDDE 85 
                                       799**********88888888***.99********************************************999*** PP

                                       ---TT-EEEE-TTSB--TT--EEEEGGGE..E....EETTE.S--STTTTEE-TTSSB-TTSEEE-TTBB--CCCHH CS
                            MoeA_N  77 rllpggavrimTGaplPegadaVvpvEdte.eeeaketvev.kavkpgenvrraGedikaGevllragtrltpaeig 151
                                       ++++g++vr++TG+ +P+gadaVv+vEdt+      + ve+ ++v+p+++v  +Gedi++++++++ g++l+p +++
  gi|298674458|ref|YP_003726208.1|  86 EVVEGTCVRVHTGSSIPDGADAVVMVEDTTpV---GDMVEIlTHVHPNKHVGIIGEDIEKNDTVFTDGHMLRPCDLA 159
                                       ****************************9542...333444699********************************* PP

                                       HHHHCT CS
                            MoeA_N 152 llasvG 157
                                       +las+G
  gi|298674458|ref|YP_003726208.1| 160 VLASLG 165
                                       ****98 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.4   0.0     2e-28   7.1e-25       2     143 ..     179     315 ..     178     316 .. 0.93

  Alignments for each domain:
  == domain 1  score: 87.4 bits;  conditional E-value: 2e-28
                                       EEEE-HHHH.........TTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSS CS
                     MoCF_biosynth   2 vitvGdell.........sgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGpt 69 
                                       vi +G+e++         +gk++ tng + a+++++ g   ++  +v Dd+e i +a+ ++le+ d+ii++GGt+++
  gi|298674458|ref|YP_003726208.1| 179 VIPTGNEVVprtsssqlqPGKVVETNGLMTAKYVEKWGGLPEHCDIVSDDPELIISAIQSQLES-DIIILCGGTSVG 254
                                       789999999999999999****************************************888666.************ PP

                                       TT--HHHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHHHHGGHH CS
                     MoCF_biosynth  70 pdDvtpealaklfekelegfeeafrrvslkpgkpvgvapgailsravgktiigLPGspkavkealeeillpale 143
                                       ++D++p++++ l++       +++++vs+ pgkp+ ++++   ++    ++++LPG+p+a+  +l  + +pal+
  gi|298674458|ref|YP_003726208.1| 255 ERDHVPDVVKSLGN-------VLVHGVSMSPGKPIALGMI---DN---VPVVCLPGYPVAAFIGLFMFARPALR 315
                                       **************.......8************999988...43...47**********99999999999987 PP

>> MoeA_C  MoeA C-terminal region (domain IV)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.12   4.2e+02       4      23 ..      41      60 ..      39      70 .. 0.85
   2 ?   -0.9   0.0      0.52   1.9e+03      52      70 ..      78      96 ..      77      97 .. 0.86
   3 ?   -2.5   0.1       1.7     6e+03      48      69 ..     105     123 ..     104     125 .. 0.77
   4 ?   -2.6   0.0       1.9   6.7e+03      59      68 ..     193     202 ..     179     207 .. 0.64
   5 !   56.4   0.0   6.7e-19   2.4e-15       1      71 [.     329     397 ..     329     398 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.12
                                      ESS-EE--SSS-EEEEEEEE CS
                            MoeA_C  4 laedlksdpgrreflRvilt 23
                                      l+++++++++ +++ R+ ++
  gi|298674458|ref|YP_003726208.1| 41 LSDSVTANRNVPHYRRAAMD 60
                                      8999*************998 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.52
                                      EEE-TT--EE-TT-EEEEE CS
                            MoeA_C 52 ivipegtegleaGeeVevi 70
                                      i+++ + e++ +G++V v+
  gi|298674458|ref|YP_003726208.1| 78 IMLQIDDEEVVEGTCVRVH 96
                                      678889999*******986 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.7
                                       --EEEEE-TT--EE-TT-EEEE CS
                            MoeA_C  48 AnglivipegtegleaGeeVev 69 
                                       A++ ++++  t    +G+ Ve+
  gi|298674458|ref|YP_003726208.1| 105 ADAVVMVEDTTP---VGDMVEI 123
                                       999999998886...7777776 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 1.9
                                       -EE-TT-EEE CS
                            MoeA_C  59 egleaGeeVe 68 
                                        +l++G++Ve
  gi|298674458|ref|YP_003726208.1| 193 SQLQPGKVVE 202
                                       3466777766 PP

  == domain 5  score: 56.4 bits;  conditional E-value: 6.7e-19
                                       EEEESS-EE--SSS-EEEEEEEES-S-EEEEEE-S---TT-GGGCTT--EEEEE-TT--EE-TT-EEEEEE CS
                            MoeA_C   1 karlaedlksdpgrreflRvilteedgeyvaeptgkqgSglLsslaeAnglivipegtegleaGeeVevil 71 
                                       ka+l+++++s++g ++f Rv+++   g  +a+p+ ++g g+Lss a++ngl+++pe+ eg+e+Ge+V++ l
  gi|298674458|ref|YP_003726208.1| 329 KAELSDKIPSKEGYMTFSRVVVD--FGSSTAHPVMTSGAGVLSSVAKSNGLVIVPENIEGYEKGEKVDIFL 397
                                       699********************..5899***************************************865 PP

>> UEV  UEV domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.9e-05      0.14      64      99 ..     174     217 ..     167     239 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.9e-05
                                       --EEEE-GCC--........TSGGGGGB-TTSBB--HHHHS--T CS
                               UEV  64 aPivyvkptksm........vikknenvdaqGlvylpyLeeWkr 99 
                                       +P+v v pt ++        ++++++ v+++Gl++ +y+e+W  
  gi|298674458|ref|YP_003726208.1| 174 KPHVSVIPTGNEvvprtsssQLQPGKVVETNGLMTAKYVEKWGG 217
                                       66666666666666666666**********************86 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   3.9e-05      0.14     117     148 ..     238     269 ..     225     293 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.9e-05
                              MutL 117 relrpdiiLLaGGtDgGnkevllenAellaea 148
                                        +l++dii+L+GGt  G+++++    + l ++
  gi|298674458|ref|YP_003726208.1| 238 SQLESDIIILCGGTSVGERDHVPDVVKSLGNV 269
                                       4899*****************99888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2610.58
//
Query:       gi|298674459|ref|YP_003726209.1|  [L=94]
Description: MoaD family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-19   70.2   0.0    2.1e-19   69.9   0.0    1.1  1  ThiS         ThiS family
     0.0025   17.5   0.0     0.0059   16.3   0.0    1.6  1  XPC-binding  XPC-binding domain


Domain annotation for each model (and alignments):
>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9   0.0   2.4e-23   2.1e-19       1      77 []       6      94 .]       6      94 .] 0.97

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 2.4e-23
                                      EEETTCCHHHHTCEEEEESSTSBHHHHHHHHHHHTCHHG............TTTTEEEEETTEEEGC.CTTTSB--TTC CS
                              ThiS  1 vllfaelrelageeelelaegstvaelleaLgerypela............lerrvavavNgeivpr.lwldtelkdgD 66
                                      v+lfa+lre ag   ++  +g+ v+++l++Lg++yp+l+            l   ++v++Nge++++ ++l+t+lkd D
  gi|298674459|ref|YP_003726209.1|  6 VKLFANLREYAG-VSEVTISGDIVSDILNSLGQQYPQLKelifenpeyedeLQGYINVLLNGENIQHlEGLSTQLKDYD 83
                                      89**********.7778889*******************************99**************99********** PP

                                      EEEEEESTTC- CS
                              ThiS 67 evailppVaGG 77
                                      e+ailppV+GG
  gi|298674459|ref|YP_003726209.1| 84 EIAILPPVSGG 94
                                      **********9 PP

>> XPC-binding  XPC-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   6.6e-07    0.0059      24      47 ..      28      51 ..      24      52 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.6e-07
                       XPC-binding 24 LqplLqqlaqsnPqllqlIqqnqe 47
                                       +++L+ l+q+ Pql +lI +n+e
  gi|298674459|ref|YP_003726209.1| 28 VSDILNSLGQQYPQLKELIFENPE 51
                                      6789*******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 594.46
//
Query:       gi|298674460|ref|YP_003726210.1|  [L=185]
Description: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-25   89.1   0.1      3e-25   88.8   0.1    1.1  1  Flavoprotein  Flavoprotein
  ------ inclusion threshold ------
       0.17   12.1   0.1       0.53   10.6   0.0    1.7  2  FISNA         Fish-specific NACHT associated domain


Domain annotation for each model (and alignments):
>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.8   0.1   3.4e-29     3e-25       2     124 ..       3     164 ..       2     175 .. 0.88

  Alignments for each domain:
  == domain 1  score: 88.8 bits;  conditional E-value: 3.4e-29
                                       EEEEEE-SSCGGGCHHHHHHHHHH.TTEEEEEEESCHHHHCCHHG.GS....TCSSHHHHHHCT............. CS
                      Flavoprotein   2 killgiTGsvaaikalellekLkk.egievqvvltkaAkkfiske.klklaaredpilhielrr............. 63 
                                       +i++gi+G++++ ++++l+e L   +++ +++v+t++Akk+i  e +        ++l+ie                
  gi|298674460|ref|YP_003726210.1|   3 EIAIGISGASGVHYGIRLVEILSGmDNVFTHLVITESAKKLIGIEsE-------YSVLEIEDMAsraynekdftapi 72 
                                       699*********************99*****************8843.......44444444222345556888888 PP

                                       .....TESEEEEEEEEHHHHHHHHTT--SSHH..............................HHHHHTHCCTTEEEE CS
                      Flavoprotein  64 .....wadllviaPasantlakianGiadnll..............................tlilratakkpilia 105
                                            ++ ++++aP+s++tl+ +anGi+dnll                              +l++   ++ +++i+
  gi|298674460|ref|YP_003726210.1|  73 asgshRFAGMIVAPCSMKTLGSVANGITDNLLtrsadvcmkerrslvlmtretplnqihienMLKA---TQSGATIL 146
                                       88888***************************************************9999777666...88****** PP

                                       E.--HHCCTCSTCHHHHHH CS
                      Flavoprotein 106 Pamnpamyenpqtlknlek 124
                                       P + p +y+npqt+++l +
  gi|298674460|ref|YP_003726210.1| 147 P-ACPGFYSNPQTIEDLLN 164
                                       *.*************9865 PP

>> FISNA  Fish-specific NACHT associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   5.9e-05      0.53      25      58 ..      27      62 ..      14      73 .. 0.79
   2 ?   -1.7   0.0      0.38   3.4e+03      22      30 ..     124     132 ..     112     141 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.9e-05
                             FISNA 25 LnsiYTeLyitegesge..vneeHEvlqiekasrkk 58
                                      +++++T+L ite  ++   ++ e  vl+ie +++++
  gi|298674460|ref|YP_003726210.1| 27 MDNVFTHLVITESAKKLigIESEYSVLEIEDMASRA 62
                                      5799*********99974477788899999888766 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.38
                             FISNA  22 ktlLnsiYT 30 
                                       +t+Ln+i  
  gi|298674460|ref|YP_003726210.1| 124 ETPLNQIHI 132
                                       455555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1328.90
//
Query:       gi|298674461|ref|YP_003726211.1|  [L=119]
Description: hypothetical protein Metev_0502 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.076   13.0   0.1       0.11   12.5   0.1    1.2  1  Borrelia_REV  Borrelia burgdorferi REV protein


Domain annotation for each model (and alignments):
>> Borrelia_REV  Borrelia burgdorferi REV protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1     6e-06      0.11     130     174 .]      70     117 ..      60     117 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6e-06
                                       HHHHHHHHHHTT---TT......HHHHHHHHH.HHH..HHHHHHHHH- CS
                      Borrelia_REV 130 klkirsiaklvGvntsgialhainikklskdv.veq..idkvikylee 174
                                        +ki s +  + v  +gi l  i ++++ k v v +  +d+ ikylee
  gi|298674461|ref|YP_003726211.1|  70 ARKISSCTHRTTVFMAGIHLDDITGEEINKIVeVSDiiVDRFIKYLEE 117
                                       69************************99986534442269*******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 760.27
//
Query:       gi|298674462|ref|YP_003726212.1|  [L=398]
Description: metal dependent phosphohydrolase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.9e-15   55.2   2.4    1.9e-14   53.9   2.1    1.9  2  HD        HD domain
  ------ inclusion threshold ------
      0.016   15.7   0.1      0.048   14.2   0.1    1.8  1  DUF2482   Hypothetical protein of unknown function (DUF2482)
      0.062   13.0   0.1       0.14   11.9   0.1    1.5  1  PDEase_I  3'5'-cyclic nucleotide phosphodiesterase


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   2.1   3.2e-18   1.9e-14       1     121 [.      50     163 ..      50     164 .. 0.78
   2 ?   -3.5   0.0       1.9   1.2e+04      79      93 ..     349     363 ..     334     383 .. 0.70

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 3.2e-18
                                       HHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHTTTTHHHHTS..HHH....HHHCTCCHHHHHHHHHHHHHHH CS
                                HD   1 rleHsleVaklarrlaedlge..eedrellllaaLlHDiGkgpfgdafekk....eeefekflaHekvgaeilreve 71 
                                       r+eHsl+V++la  l ++l+   + +++ l++aaLlHDiG+gp ++  e +    +    +  + +++ + +l++  
  gi|298674462|ref|YP_003726212.1|  50 RFEHSLGVMHLATILMNQLDNisDNEKNGLKAAALLHDIGHGPYSHVTEGTvkyyT----R--KKHDDVRDVLKK-- 118
                                       79*********************999*****************9995554432210....1..223333333333.. PP

                                       HHHHHHHHHHHHHHHTTCCHHHHHHHH.H.HHHCCTSCHHHHHHHHHHHHHH CS
                                HD  72 krlgldledvaklirehheswegkkrp.r.glaerqlslearivklaDrlaa 121
                                              e++a++ reh  + e+  ++ + + a  q+ +++++v+++D+l +
  gi|298674462|ref|YP_003726212.1| 119 -------EEIANILREHDIDPETVAKHiKgETALGQILNSEIDVDRMDYLVR 163
                                       .......4889999999999987777763688999**************976 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.9
                                       HHHHHHHHTTCCHHH CS
                                HD  79 edvaklirehheswe 93 
                                       + va l  +h++ w 
  gi|298674462|ref|YP_003726212.1| 349 QVVATLEQAHRDNWK 363
                                       457777777877776 PP

>> DUF2482  Hypothetical protein of unknown function (DUF2482)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1     8e-06     0.048       6      67 ..     116     176 ..     110     188 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 8e-06
                           DUF2482   6 mtqeeikdllaeKskeLyelieeikeetdFdillfsaigvsdgdaqvsssslvvGkivglan 67 
                                       +++eei ++l e + +   ++++ik+et    +l+s i v+  d ++      +G ++gl++
  gi|298674462|ref|YP_003726212.1| 116 LKKEEIANILREHDIDPETVAKHIKGETALGQILNSEIDVDRMD-YLVRDAHYTGVTFGLVD 176
                                       4689****************************************.77777777899988875 PP

>> PDEase_I  3'5'-cyclic nucleotide phosphodiesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   2.3e-05      0.14       4      46 ..      51      90 ..      49      95 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.3e-05
                                      HHHHHHHHHHHHHHHHCCHCCCCS-HHHHHHHHHHHHHTTTT- CS
                          PDEase_I  4 frHAadVlqalfyllkkeklkeeltpleilalliaalcHDvdH 46
                                      f H++ V++   +l+++ +   ++++ e+  l  aal HD++H
  gi|298674462|ref|YP_003726212.1| 51 FEHSLGVMHLATILMNQLD---NISDNEKNGLKAAALLHDIGH 90
                                      78*******9999997765...68******************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2583.28
//
Query:       gi|298674463|ref|YP_003726213.1|  [L=308]
Description: LPPG domain-containing protein containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-45  155.2   0.1    2.5e-45  155.0   0.1    1.0  1  UPF0052   Uncharacterised protein family UPF0052


Domain annotation for each model (and alignments):
>> UPF0052  Uncharacterised protein family UPF0052
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.0   0.1   1.4e-49   2.5e-45       2     260 ..       2     269 ..       1     299 [. 0.84

  Alignments for each domain:
  == domain 1  score: 155.0 bits;  conditional E-value: 1.4e-49
                                       EEEE-CHHHHHHHHHHCCSS..CEEEEEE-----SHHHHHHHHHHTS---HHHHHHHHHH--S-C.......HHHHH CS
                           UPF0052   2 vvlgGGtGlskllrglkevt..aeltavvtvaDdggssGelrrelgllaigDirnvlvalidder.......lleeL 69 
                                       +vl+GGtG++kll+gl+++   +++t+vv++++d+++sG        l+ +D+++vl+  +d+ +       + + +
  gi|298674463|ref|YP_003726213.1|   2 IVLSGGTGTPKLLNGLRNIIpeEDITVVVNTGEDIRISG-------NLISPDVDTVLYLFSDKLDtdkwwgvANDTF 71 
                                       79*****************9999****************.......99************77666555777644445 PP

                                       CH-B-SS...........SSSSTT-BHHHHHHHHHHHHHS.-HHHHHHHHHHHTT-SSEEEES-SS--EEEEEETTS CS
                           UPF0052  70 fqyRfkg...........dgdlaghslgnllLaalaeltg.sleeaiealskilkvrgrvlPatddpvelsaeledG 134
                                         +   +           d d a+h+++  +L++     g  l++a+ +l++ +++r+++lP++dd++++ +++  G
  gi|298674463|ref|YP_003726213.1|  72 TTHETMKtngydegmmlgDIDRATHIMRSEYLRN-----GdILTQATSKLANNFGIRANILPMSDDTATTIIKTPSG 143
                                       555333377788889998889*************.....8789********************************** PP

                                       -EEE.STTTGGGG-S...-EEEEEE.ESTT----HHHHHHHHH-SEEEE-SS-IIIIIHHHHTSCCHHHHHHH-SSE CS
                           UPF0052 135 eeit.geskisearklkapikrvfl.epegaeaapevleaikeAdlivlgpGslytSiiPiLlvpgiaealreskak 209
                                       + ++ ++ +i+e++  + ++ +vf+ + ++a++ p vl+a ++ d +++gp++++tSi+PiL +p ++e l  +++k
  gi|298674463|ref|YP_003726213.1| 144 N-LHfQDFWIKEKG--ELDVYDVFIdGISNASISPAVLDAFENEDEVLIGPSNPITSIGPILSLPTMKEIL--KDKK 215
                                       *.555*****5554..599***6662578889***************************************..569* PP

                                       EEEE--SB--TTTSTT-BHHHHHHHHHHCH-........SS....S...-SEEEEE-S.---H CS
                           UPF0052 210 kvlvsnimtqkGetdgfsvsdhvkaieravg........kgvakay...vdavlvnts.evpe 260
                                       +v+vs+i++      + +vs++++++++a          +   k y   ++a++++++ +++e
  gi|298674463|ref|YP_003726213.1| 216 VVAVSPIIG------HEPVSGPIAKLMHANDmevssigvA---KCYkefLNAFIIDKTdHFKE 269
                                       ********9......************9998777774443...4445659****988823333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2251.53
//
Query:       gi|298674464|ref|YP_003726214.1|  [L=194]
Description: CDP-alcohol phosphatidyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-12   48.5   1.8    1.1e-12   48.5   1.8    2.5  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase


Domain annotation for each model (and alignments):
>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   1.8     6e-17   1.1e-12       2      66 .]      23      86 ..      22      86 .. 0.91
   2 ?   -0.6   2.2      0.13   2.4e+03      26      35 ..     109     125 ..      88     184 .. 0.54

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 6e-17
                                      -HHHHHHHHHHHHHHHHHGGGS-H..HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                   CDP-OH_P_transf  2 lPnaiTllrlllsvlailllltyyplvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                       Pn++T+++l +s++a++++ t + ++++ +l+l+ +++D+lDG +AR+ +  + +G llDs++D
  gi|298674464|ref|YP_003726214.1| 23 SPNLLTVIGLGISIIAAVMFGTGR-VFIGGILILLNGFFDILDGAVARENGWMTPFGGLLDSVCD 86
                                      5****************9886666.58888889999***************9999*********9 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.13
                                       .........HHHHHHHH CS
                   CDP-OH_P_transf  26 p.......lvlaillll 35 
                                       p       ++++i+ l+
  gi|298674464|ref|YP_003726214.1| 109 PvllniplWLWCIIALI 125
                                       34444444333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1175.71
//
Query:       gi|298674465|ref|YP_003726215.1|  [L=169]
Description: shikimate kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.7e-34  117.1   0.2    9.4e-34  116.8   0.2    1.0  1  SKI              Shikimate kinase
    2.6e-07   31.0   0.8    1.1e-06   28.9   0.8    2.0  1  Cytidylate_kin2  Cytidylate kinase-like family
    9.6e-07   28.8   1.5      0.014   15.3   0.1    2.2  2  dNK              Deoxynucleoside kinase
    1.4e-06   28.9   0.2    3.7e-06   27.5   0.1    1.8  1  AAA_18           AAA domain
    1.9e-06   27.8   0.1    3.5e-06   26.9   0.0    1.5  2  Cytidylate_kin   Cytidylate kinase
      4e-06   27.3   0.3    2.6e-05   24.7   0.3    2.1  1  AAA_17           AAA domain
    1.7e-05   25.0   0.0    3.7e-05   23.9   0.0    1.8  1  AAA_33           AAA domain
     0.0014   18.3   0.0     0.0027   17.4   0.0    1.5  1  CoaE             Dephospho-CoA kinase
     0.0016   18.9   0.1     0.0082   16.6   0.0    2.0  2  AAA              ATPase family associated with various cellul
     0.0061   15.8   0.4      0.047   12.9   0.1    2.1  2  NB-ARC           NB-ARC domain
     0.0098   16.0   0.2        2.3    8.3   0.1    2.2  2  ADK              Adenylate kinase
  ------ inclusion threshold ------
      0.012   14.9   0.3       0.02   14.2   0.3    1.4  1  ATP_bind_2       P-loop ATPase protein family
      0.017   15.4   1.2      0.035   14.3   0.2    1.8  2  PHM7_cyt         Cytosolic domain of 10TM putative phosphate 
      0.027   15.0   0.9      0.051   14.1   0.9    1.8  1  ABC_tran         ABC transporter
      0.033   13.9   0.4      0.046   13.4   0.4    1.4  1  AAA_24           AAA domain
      0.039   13.6   0.4        3.2    7.4   0.1    2.1  2  Thymidylate_kin  Thymidylate kinase
      0.043   14.1   0.0      0.085   13.1   0.0    1.5  2  AAA_22           AAA domain
      0.095   12.9   0.0       0.11   12.7   0.0    1.4  1  AAA_28           AAA domain
      0.096   13.1   0.0      0.099   13.0   0.0    1.2  1  AAA_16           AAA ATPase domain
       0.13   12.4   0.0       0.29   11.2   0.0    1.6  1  HHH_2            Helix-hairpin-helix motif
       0.93    9.4   5.9        2.3    8.2   0.1    3.0  3  Rsd_AlgQ         Regulator of RNA polymerase sigma(70) subuni


Domain annotation for each model (and alignments):
>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.8   0.2   1.1e-36   9.4e-34       2     155 ..      10     164 ..       9     166 .. 0.92

  Alignments for each domain:
  == domain 1  score: 116.8 bits;  conditional E-value: 1.1e-36
                                       TSSHHHHHHHHHHHHTSEEEEHHHHHHHHHTS-HHHHHHHHHHHHHHHHHHHHHHHHCCCS..SEEEEE-TTGGGSH CS
                               SKI   2 GaGKstvGkllAkklglefiDlDeliekrtgksiaeifeeegeegFrelEsevlkelleee..glViatGGGavlse 76 
                                       GaGKst+Gk +Akklg++fiD+D+l+ek+  k+ +e+++ +g ++  elE++++ el  ++  +++i+ GG++v s+
  gi|298674465|ref|YP_003726215.1|  10 GAGKSTIGKSMAKKLGYRFIDIDKLVEKKSDKNLQELIDTHGDNALLELEEQTVLELRLNTedECIISPGGSIVYSD 86 
                                       9***************************************************99998777668************** PP

                                       HHHHHHHHHSEEEEEE--HHHHHHHHHHTTSSGGGCSCHHHHHHHHHHH.HHHHHHCCSSCEEEECTSSHH.HHHHH CS
                               SKI  77 enrellkekgiviyLdvsleellerlkadkeRPllqekskeeelleela.ereplyeeaadvvvdeseesk.eevae 151
                                        ++e+l +  ++++Ldvs++++ +rl++  +R ++  k+k    le+l+ er++ly+++a+++v+ ++++  +e ++
  gi|298674465|ref|YP_003726215.1|  87 SAMEFLDKYSTIVFLDVSFDVITKRLSNSATRGMVGIKNK---SLEDLFrERRKLYNKYANITVKLNKHNRvSETVN 160
                                       ***********************************99999...6677777***********9998877765488888 PP

                                       HHHH CS
                               SKI 152 eile 155
                                       +i++
  gi|298674465|ref|YP_003726215.1| 161 KIIK 164
                                       8876 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.8   1.3e-09   1.1e-06       1      52 [.       2      53 ..       2     155 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.3e-09
                   Cytidylate_kin2  1 iITIsreyGsgGetigeaLAekLglpfydreiieevakelglseeeveevde 52
                                      +ITI +  G+g++tig+  A+kLg++f+d + + e  ++++l+e +  + d+
  gi|298674465|ref|YP_003726215.1|  2 NITIIGMAGAGKSTIGKSMAKKLGYRFIDIDKLVEKKSDKNLQELIDTHGDN 53
                                      59***************************98888777777777777666666 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.1   9.8e-05     0.083       1      27 [.       3      29 ..       3      51 .. 0.85
   2 !   15.3   0.1   1.6e-05     0.014     114     182 ..      86     154 ..      80     165 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.8e-05
                                      EEEEESTTSSHHHHHHHHHCCSTCEEE CS
                               dNK  1 ivveGnIgaGKstlvklLskklgvkvf 27
                                      i++ G  gaGKst+ k ++kklg+ ++
  gi|298674465|ref|YP_003726215.1|  3 ITIIGMAGAGKSTIGKSMAKKLGYRFI 29
                                      7899*******************8765 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.6e-05
                                       HHHHHHCCH-SEEEEEE--HHHHHHHHHHCTTCCCTTS-HHHHHHHHHHHHHHHTSGGCS-EEEEETSS CS
                               dNK 114 dnlleelakpdlliYLkasletclerikkRgreeekkieldYlekLhekyeewlkklnevpvlvidvee 182
                                       d ++e l+k + +++L++s +++ +r+ + +     +i+ + le L ++  + ++k+ +++v     ++
  gi|298674465|ref|YP_003726215.1|  86 DSAMEFLDKYSTIVFLDVSFDVITKRLSNSATRGMVGIKNKSLEDLFRERRKLYNKYANITVKLNKHNR 154
                                       45666677899*********************9999************************998776666 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.1   4.3e-09   3.7e-06       1     115 [.       3     117 ..       3     132 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 4.3e-09
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskrldedkldklldaleenss..aleegk 75 
                                       I + G++G+GK+t++k  +k+l  g++ +d+ k    ++   ++  + ++ +d++ +++ll++ e+     +l  ++
  gi|298674465|ref|YP_003726215.1|   3 ITIIGMAGAGKSTIGKSMAKKL--GYRFIDIDKL---VEKKSDK--NLQELIDTHGDNALLELEEQTVLelRLNTED 72 
                                       89********************..7777777554...5555555..5777888888888888888877788777778 PP

                            AAA_18  76 nlvidghlaeleseaakdikk.....vvLtaspeelleRlekRgy 115
                                        ++i+   +  +s++a +        v+L++s ++  +Rl++  +
  gi|298674465|ref|YP_003726215.1|  73 ECIISPGGSIVYSDSAMEFLDkystiVFLDVSFDVITKRLSNSAT 117
                                       88888777777766555433357788*************998664 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   4.2e-09   3.5e-06       1      66 [.       3      68 ..       3      90 .. 0.91
   2 ?   -2.1   0.0       3.1   2.7e+03     158     170 ..     123     135 ..      95     163 .. 0.52

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 4.2e-09
                                      EEEE-STTSSHHHHHHHHHHHHT-EEEEHHHHHHHHHHHHHHTT--TT-HHHHHHHHHT--EEEEE CS
                    Cytidylate_kin  1 iaiDGPagsGKssvaralaeklglkyldtgalYRalalaalrrkvdlldeaalvelakevelsfea 66
                                      i+i G ag+GKs++++ +a+klg++++d  +l    +   l++ +d+   +al+el +++ l+++ 
  gi|298674465|ref|YP_003726215.1|  3 ITIIGMAGAGKSTIGKSMAKKLGYRFIDIDKLVEKKSDKNLQELIDTHGDNALLELEEQTVLELRL 68
                                      8999****************************************************9999887764 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.1
                                       --HHHHHHHHHHH CS
                    Cytidylate_kin 158 vsleellaeikeR 170
                                        + ++l+   +eR
  gi|298674465|ref|YP_003726215.1| 123 IKNKSLEDLFRER 135
                                       3333333333333 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.3     3e-08   2.6e-05       1     128 [.       6     121 ..       6     131 .. 0.62

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 3e-08
                                       EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTS.HSSHHHHCTSHHHHHHHHHHHHHHHHHHHH..HSSEE CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrggl.akardemrklpleekkelqkeaaekiaeea..kkkgv 74 
                                       +G+ G+GK+t+ + +++k+g+ ++    l+ e  ++++l +  + + +++ le ++++  e+  + ++e+  + +g 
  gi|298674465|ref|YP_003726215.1|   6 IGMAGAGKSTIGKSMAKKLGYRFIDIDKLV-EKKSDKNLqELIDTHGDNALLELEEQTVLELRLNTEDECiiSPGGS 81 
                                       69***********************75555.5556666622222333333333333333333333444444333333 PP

                                       EEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHTTST-T CS
                            AAA_17  75 lvdghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdrtrgrd 128
                                       +v            +++   e+l+++  ++i++l+++ ++i++r+ +  trg  
  gi|298674465|ref|YP_003726215.1|  82 IV------------YSDSAMEFLDKY--STIVFLDVSFDVITKRLSNSATRGMV 121
                                       33............222233444555..99****************99999974 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   4.3e-08   3.7e-05       3      50 ..       4      50 ..       3     155 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 4.3e-08
                            AAA_33  3 llvGlpGsGKstlaerllkklgavllssdtlrrrlfgtdqqsktdytr 50
                                       ++G++G+GKst  ++++kklg+ +++ d+l ++   +  q +   t+
  gi|298674465|ref|YP_003726215.1|  4 TIIGMAGAGKSTIGKSMAKKLGYRFIDIDKLVEKKSDKNLQEL-IDTH 50
                                      579***************************9998776433322.2233 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   3.1e-06    0.0027       3      58 ..       3      56 ..       1      67 [. 0.86

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.1e-06
                                      EEEEESTTSSHHHHHHHHHH.TT-EEEEHHHHHHHTTCCTHHHHHHHHHHHGGGCB. CS
                              CoaE  3 vgltGgiasGKstvanlfad.lgvpivDaDlvArqvvepgsealkkiveeFgeeild 58
                                      + + G  ++GKst+ + +a+ lg+  +D D++   v ++  + l+++ +++g++ l 
  gi|298674465|ref|YP_003726215.1|  3 ITIIGMAGAGKSTIGKSMAKkLGYRFIDIDKL---VEKKSDKNLQELIDTHGDNALL 56
                                      67889999*********9999*********87...5667788999999999999876 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   9.6e-06    0.0082       3      52 ..       5      49 ..       3      66 .. 0.78
   2 ?    0.0   0.0       1.2   1.1e+03      32      54 ..     115     136 ..      84     149 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9.6e-06
                                      EESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfke 52
                                      ++G  G GK+++ k++ak+lg +f+ i+   l+    ++s k+++el+++
  gi|298674465|ref|YP_003726215.1|  5 IIGMAGAGKSTIGKSMAKKLGYRFIDIDK--LV---EKKSDKNLQELIDT 49
                                      789*********************99875..44...23677777777665 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.2
                                       TTCSSSSTTHHHHHHHHHHHHHH CS
                               AAA  32 sellskyvgesekkirelfkeak 54 
                                       s  +  +vg ++k++++lf+e +
  gi|298674465|ref|YP_003726215.1| 115 SATR-GMVGIKNKSLEDLFRERR 136
                                       2222.367777777777777654 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.1   5.5e-05     0.047      23      43 ..       3      23 ..       1      50 [. 0.90
   2 ?    1.5   0.0      0.17   1.4e+02     212     250 ..     130     167 ..      87     169 .] 0.62

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.5e-05
                                      EEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC 23 valvGmgGvGKttlakqilnk 43
                                      +++ Gm+G GK+t+ k++ +k
  gi|298674465|ref|YP_003726215.1|  3 ITIIGMAGAGKSTIGKSMAKK 23
                                      79************9999887 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.17
                                       CSCCHHHHHHHHHHCTGCCTS--SSSSSSSHHHHHHHHH CS
                            NB-ARC 212 ktveewkkvlekleskllevekstskslesvasilqlsy 250
                                       +++ e +k+++k  +  ++   +++   e v +i++l++
  gi|298674465|ref|YP_003726215.1| 130 DLFRERRKLYNKYANITVK-LNKHNRVSETVNKIIKLCF 167
                                       4444444444444433333.1122223455666666665 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.013        11       1      31 [.       5      35 ..       5      71 .. 0.86
   2 !    8.3   0.1    0.0027       2.3     102     131 ..      94     148 ..      84     164 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.013
                                      EEESTTSSHHHHHHHHHHHHTSEEEEHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK  1 llGaPgaGKGtqaeklvkkyglahlstGdll 31
                                      ++G  gaGK t  ++++kk+g+  +    l+
  gi|298674465|ref|YP_003726215.1|  5 IIGMAGAGKSTIGKSMAKKLGYRFIDIDKLV 35
                                      689****************998877666555 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0027
                                       EESEEEEEE--HHHHHHHHHT.........................GSHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx.........................xxxxxxxxx RF
                               ADK 102 kldlvleldvpeevlveRltg.........................DneetvkkR 131
                                       k  +++ ldv+ +v+++Rl++                         ++  ++  +
  gi|298674465|ref|YP_003726215.1|  94 KYSTIVFLDVSFDVITKRLSNsatrgmvgiknksledlfrerrklyNKYANITVK 148
                                       67899****************9999999999985554444444444333333333 PP

>> ATP_bind_2  P-loop ATPase protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.3   2.3e-05      0.02       4     127 ..       3     140 ..       1     165 [. 0.71

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.3e-05
                                       EEEEESTTSSHHHHHHHH.HHHTXEEEB..SXXG....GGHHHHHHHHH...TTTXXEEEEESTTTSXSSHHHHHHH CS
                        ATP_bind_2   4 vivsGlsGaGksvalral.edlGyyvvd..nlPl....sllpklvdllkeansreskvavvldvrnreesaelleqa 73 
                                       + + G++GaGks+  +++   lGy  +d   l      + l +l+d+  +++  e +   vl++r   e + +++  
  gi|298674465|ref|YP_003726215.1|   3 ITIIGMAGAGKSTIGKSMaKKLGYRFIDidKLVEkksdKNLQELIDTHGDNALLELEEQTVLELRLNTEDECIISPG 79 
                                       4567*********999983579*976542256441111567888888877777778888999999888877777643 PP

                                       HHTSXT.......TSEEEEEEEEXXHHHHHHHCTSSSXSSTTSXXXSSHHHHHHHHHHTHH CS
                        ATP_bind_2  74 eellek.......aitprilfleadddtlvrryedtrrshPlsakdlslegiakerellep 127
                                        +++ +            i+fl+ + d++ +r +++     +  k+ sle + +er+ l +
  gi|298674465|ref|YP_003726215.1|  80 GSIVYSdsameflDKYSTIVFLDVSFDVITKRLSNSATRGMVGIKNKSLEDLFRERRKLYN 140
                                       3332221100012234579*****************99999**********9999998864 PP

>> PHM7_cyt  Cytosolic domain of 10TM putative phosphate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.4   1.2e+03      36      53 ..      23      40 ..      13      61 .. 0.75
   2 ?   14.3   0.2   4.1e-05     0.035      36      83 ..     120     167 ..     106     169 .] 0.84

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.4
                          PHM7_cyt 36 qivrdvkkldklveerek 53
                                       + +++ ++dklve++ +
  gi|298674465|ref|YP_003726215.1| 23 KLGYRFIDIDKLVEKKSD 40
                                      577888899999988754 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 4.1e-05
                          PHM7_cyt  36 qivrdvkkldklveerekavrkleaalskykkngkklpkkrpthklgf 83 
                                       ++  + k l++l +er k+++k+  ++ k++k+++ +++ ++  kl+f
  gi|298674465|ref|YP_003726215.1| 120 MVGIKNKSLEDLFRERRKLYNKYANITVKLNKHNRVSETVNKIIKLCF 167
                                       56667899**************************99988877777776 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.9     6e-05     0.051      14      37 ..       3      26 ..       1     161 [. 0.70

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6e-05
                                      EEEEESTTSSHHHHHHHHTTSS-- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 14 vaivGenGaGKStLlkllagllkp 37
                                      + i+G  GaGKSt+ k +a++l  
  gi|298674465|ref|YP_003726215.1|  3 ITIIGMAGAGKSTIGKSMAKKLGY 26
                                      68****************998755 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.4   5.4e-05     0.046       4      42 ..       2      42 ..       1     110 [. 0.66

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.4e-05
                            AAA_24  4 kiliyGpsgiGKTtlakel..gpkplfidtekGlksldadk 42
                                      +i i+G +g+GK+t+ k++  +    fid++k + +  +++
  gi|298674465|ref|YP_003726215.1|  2 NITIIGMAGAGKSTIGKSMakKLGYRFIDIDKLVEKKSDKN 42
                                      799****************6644556888888444444444 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0038       3.2       3      26 ..       7      30 ..       5      66 .. 0.81
   2 ?    4.9   0.0     0.021        18     121     179 ..      98     157 ..      80     163 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0038
                                      ESTTSSHHHHHHHHHHHHHHTTE. CS
                   Thymidylate_kin  3 GlDGaGKttqaellkerlkeegik 26
                                      G+ GaGK+t+ + ++++l  + i 
  gi|298674465|ref|YP_003726215.1|  7 GMAGAGKSTIGKSMAKKLGYRFID 30
                                      899**************9877766 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.021
                                       EEEEESSHHHHHTSCCTTSS...TTTSHHHHHHHHHHHHHHHHHHHHTTSTEEEEETTS-HH CS
                   Thymidylate_kin 121 tflldvdpevalkRlakrde...ldeeeeeqldflrkvrerylelakederiliidasksie 179
                                       +++ldv+ +v  kRl+  ++      + +  +d +r+ r+ y++ a  + +++ ++ ++  e
  gi|298674465|ref|YP_003726215.1|  98 IVFLDVSFDVITKRLSNSATrgmVGIKNKSLEDLFRERRKLYNKYA--NITVKLNKHNRVSE 157
                                       789************9988844233445555677888888888888..56666664444333 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0    0.0001     0.085       8      56 ..       3      46 ..       1      77 [. 0.69
   2 ?   -2.9   0.0       8.6   7.3e+03      78      81 ..     131     134 ..     108     156 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0001
                            AAA_22  8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv....fvtlpsstsskdl 56
                                      ++++G +G+GK+t  + ++++l         + +++    +v+ +s++++++l
  gi|298674465|ref|YP_003726215.1|  3 ITIIGMAGAGKSTIGKSMAKKL---------GYRFIdidkLVEKKSDKNLQEL 46
                                      79*******************9.........7777744444444444344443 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 8.6
                            AAA_22  78 llea 81 
                                       l++ 
  gi|298674465|ref|YP_003726215.1| 131 LFRE 134
                                       2222 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00013      0.11       2      79 ..       3      78 ..       2     148 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                            AAA_28  2 ivitGgestGKTtlleaLaar.gypvvpEaareileeklakgedalpwvedllafaervleeqleeeaaaaankvlfcD 79
                                      i i+G  ++GK+t+ + +a++ gy+ +     +++e+k++k+ ++l ++    +   +++e+ + e++ +++++++++ 
  gi|298674465|ref|YP_003726215.1|  3 ITIIGMAGAGKSTIGKSMAKKlGYRFID--IDKLVEKKSDKNLQELIDT-HGDNALLELEEQTVLELRLNTEDECIISP 78
                                      89*****************988***996..6777777777777777665.33444444455555556666666666654 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00012     0.099      27      91 ..       3      62 ..       1     154 [. 0.70

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00012
                            AAA_16 27 vllsGesGvGKsslvrellralekdggif......lrgkcdqlesaipysalaqalareellrqlldeaes 91
                                      + ++G++G GKs++ ++ ++ l  +   f      ++ k d++     ++ l+++    +  + l+ e+++
  gi|298674465|ref|YP_003726215.1|  3 ITIIGMAGAGKSTIGKSMAKKLGYR---FididklVEKKSDKN-----LQELIDTH---GDNALLELEEQT 62
                                      679*****************99998...333444577777777.....33355555...444444444333 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00034      0.29      10      35 ..      15      40 ..       9      51 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00034
                             HHH_2 10 hVGektAklLakrFksldaLkkasle 35
                                       +G+++Ak+L  rF ++d+L + + +
  gi|298674465|ref|YP_003726215.1| 15 TIGKSMAKKLGYRFIDIDKLVEKKSD 40
                                      69******************877654 PP

>> Rsd_AlgQ  Regulator of RNA polymerase sigma(70) subunit, Rsd/AlgQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.9      0.36   3.1e+02     125     146 ..      52      75 ..      28      77 .. 0.61
   2 ?    1.2   0.0      0.37   3.1e+02     103     129 ..      86     113 ..      83     118 .. 0.76
   3 ?    8.2   0.1    0.0027       2.3      11      58 ..     120     166 ..     112     168 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.36
                          Rsd_AlgQ 125 dedLsklge..aLeeRfelEDkLi 146
                                       d++L +l e  +Le R+++ED+ i
  gi|298674465|ref|YP_003726215.1|  52 DNALLELEEqtVLELRLNTEDECI 75 
                                       455666654227999999999876 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.37
                          Rsd_AlgQ 103 eaaldfndkyee.aadedeleeldedLs 129
                                       ++a++f dky++ +  + +++ ++++Ls
  gi|298674465|ref|YP_003726215.1|  86 DSAMEFLDKYSTiVFLDVSFDVITKRLS 113
                                       789*******996666666666666666 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0027
                          Rsd_AlgQ  11 rwggvselidrwLeeRqqllvaycklaglkpkkeekelpseealqefc 58 
                                        +g +++ ++++ +eR++l  +y +++ +k +k+++  ++ +++ ++c
  gi|298674465|ref|YP_003726215.1| 120 MVGIKNKSLEDLFRERRKLYNKYANIT-VKLNKHNRVSETVNKIIKLC 166
                                       5778899999****************8.77788888888888888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       858  (0.0478554); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 1017.35
//
Query:       gi|298674466|ref|YP_003726216.1|  [L=82]
Description: phosphoribosylformylglycinamidine synthase PurS [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-27   96.1   0.0    1.1e-27   96.0   0.0    1.0  1  PurS      Phosphoribosylformylglycinamidine (FGAM) synthase
     0.0006   19.3   0.0    0.00075   19.0   0.0    1.1  1  DUF2184   Uncharacterized protein conserved in bacteria (DUF2
  ------ inclusion threshold ------
       0.11   12.4   0.2       0.13   12.2   0.2    1.2  1  MRP-S26   Mitochondrial ribosome subunit S26


Domain annotation for each model (and alignments):
>> PurS  Phosphoribosylformylglycinamidine (FGAM) synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.0   0.0   1.8e-31   1.1e-27       2      76 ..       5      78 ..       4      79 .. 0.97

  Alignments for each domain:
  == domain 1  score: 96.0 bits;  conditional E-value: 1.8e-31
                                      EEEEEEE-TTS--HHHHHHHHHHHHTTHTTEEEEEEEEEEEEEEE-SSHHHHHHHHHHHHHHTTS-TTTEEEEEE CS
                              PurS  2 akveVtlKkgvlDpqGkavkkalkslgyeevedvrvgkyieleleaedeeeaeeeveemceklLaNpviedyeie 76
                                      a v+V+lK+g+lDp+G+++k+al +lgye  +dv+++k ++++l+ae+ ++a+++v+emc+kl+aNp+i++y+i+
  gi|298674466|ref|YP_003726216.1|  5 ADVTVELKSGMLDPEGNTIKRALGHLGYE-TNDVKTAKKFTIDLDAESFDDARQNVDEMCQKLIANPIIHNYTID 78
                                      78**************************9.*******************************************97 PP

>> DUF2184  Uncharacterized protein conserved in bacteria (DUF2184)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.3e-07   0.00075      21      70 ..      17      66 ..       8      68 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.3e-07
                           DUF2184 21 eketakvkligasygytvqElraaqalGrsLdtrkadaarraadkkinki 70
                                      ++e +++k++   +gy++ ++++a+++ ++Ld++  d+ar+++d++ +k+
  gi|298674466|ref|YP_003726216.1| 17 DPEGNTIKRALGHLGYETNDVKTAKKFTIDLDAESFDDARQNVDEMCQKL 66
                                      567789999999*********************************99987 PP

>> MRP-S26  Mitochondrial ribosome subunit S26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   2.2e-05      0.13     142     165 ..      56      79 ..      35      80 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.2e-05
                           MRP-S26 142 eeNLdeaIeeaLdnpvnYNfaidl 165
                                       ++N+de  ++ ++np+ +N+ idl
  gi|298674466|ref|YP_003726216.1|  56 RQNVDEMCQKLIANPIIHNYTIDL 79 
                                       78*********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 653.81
//
Query:       gi|298674467|ref|YP_003726217.1|  [L=232]
Description: phosphoribosylformylglycinamidine synthase I [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.3e-47  160.1   0.0    6.2e-47  159.9   0.0    1.1  1  GATase_5       CobB/CobQ-like glutamine amidotransferase doma
    3.2e-10   40.0   0.0      5e-10   39.4   0.0    1.3  1  DJ-1_PfpI      DJ-1/PfpI family
    8.5e-09   35.3   0.0    1.5e-08   34.5   0.0    1.4  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    2.1e-06   27.6   0.0    5.1e-06   26.4   0.0    1.7  1  GATase         Glutamine amidotransferase class-I
    0.00019   21.3   0.0     0.0005   20.0   0.0    1.6  2  SNO            SNO glutamine amidotransferase family
      0.005   16.6   0.0     0.0097   15.7   0.0    1.5  1  Peptidase_C26  Peptidase C26


Domain annotation for each model (and alignments):
>> GATase_5  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.9   0.0   2.1e-50   6.2e-47       3     259 ..       2     227 ..       1     228 [. 0.91

  Alignments for each domain:
  == domain 1  score: 159.9 bits;  conditional E-value: 2.1e-50
                          GATase_5   3 kvailreeGvngeyemaaafeka.GfeavdvhmsdllegrvslddfqilalpGGfsygDelgsgkgwakslllnekl 78 
                                       ++ai+ + G+n+++++ + +++   ++a+ v ++d      +ld+f + ++pGGfsygD l +g+++a+     + +
  gi|298674467|ref|YP_003726217.1|   2 RIAIIQFGGTNCDRDVLHVLKNVmNVDAELVWFKDK-----NLDRFDGAVIPGGFSYGDYLRAGAIAAR-----TPI 68 
                                       89******************9852566666877665.....9**********************99994.....467 PP

                          GATase_5  79 realekflnredtlaLGiCnGfqlLvklglvpggeieeaeksptltrNksgrfesrlvsv.vvsekspsvfl.kgme 153
                                        ++++k++++ ++ ++GiCnGfq+L++ gl++g          +lt N+  +f ++++++ v ++++p     ++++
  gi|298674467|ref|YP_003726217.1|  69 MDSVRKMVSE-GKPVIGICNGFQVLTESGLLDG----------ALTTNSYPKFLCEWTHLrVDNTDTPFTSRfEKGD 134
                                       8999999999.**********************..........9****************7777788888767999* PP

                          GATase_5 154 glslpvahGeGrfvfkseevlkeleangqvalrYvdeegkpteeyplNPNgSpegiagitspdGRvlalmpHpervv 230
                                       ++++p+ah eG f + +++++++l++n+qv++rYvde+g  t++ + NPNgS+e+iagit+ +  v++lmpHper++
  gi|298674467|ref|YP_003726217.1| 135 VIQIPIAHKEGYFYA-DQSAISDLNKNNQVVFRYVDEDG--TSDDESNPNGSKENIAGITNSSKNVIGLMPHPERAS 208
                                       ***************.999******************77..667889****************************** PP

                          GATase_5 231 eavqksiipeeeeeevspwlrlFenavky 259
                                       e+v  s          +++l++F+++v+y
  gi|298674467|ref|YP_003726217.1| 209 EKVLGS----------EDGLKIFQSMVDY 227
                                       **9999..........4689999999988 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.0   1.7e-13     5e-10      54     119 ..      34     104 ..      13     120 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 1.7e-13
                                       GGGCTCCG-SEEEE--BHHHHHHHHTSH.....HHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTTSEE- CS
                         DJ-1_PfpI  54 lddvkaaeyDalvlpGGragperlrene.....kvvelvkefaekgklvaaICagpqlLaaagvlkgrrvT 119
                                       ++d + +++D  v+pGG +  ++lr+ +      +++ v++++++gk+v  IC g q+L + g+l+g  +T
  gi|298674467|ref|YP_003726217.1|  34 FKDKNLDRFDGAVIPGGFSYGDYLRAGAiaartPIMDSVRKMVSEGKPVIGICNGFQVLTESGLLDGALTT 104
                                       4688999***************99975433333899******************************98877 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.0     5e-12   1.5e-08      16      91 ..      18      95 ..       2     106 .. 0.87

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 5e-12
                          GATase_3 16 ldpLeaepevrvrfvplkdeslgedadlvilpGgkdt...iqdlallresgldeaikeaaeaggpvlgiCGGlqmLGee 91
                                      l++L++  +v+ + v +kd++l++  d  ++pGg+++   +++ a+++++ + +++++++++g+pv+giC G+q+L e+
  gi|298674467|ref|YP_003726217.1| 18 LHVLKNVMNVDAELVWFKDKNLDR-FDGAVIPGGFSYgdyLRAGAIAARTPIMDSVRKMVSEGKPVIGICNGFQVLTES 95
                                      678999999*************76.*********9751116677889999**************************986 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   1.7e-09   5.1e-06      21      87 ..      26      95 ..      13     215 .. 0.61

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 1.7e-09
                                      T-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.........TTTHHHHHHHHCTSTS-EEEETHHHHHHHHH CS
                            GATase 21 gvkvevvpidasaeeilellknpdgilvsgGpgspg.........vegkieaikearenkiPiLGICLGmQllaie 87
                                      +v+ e+v+++ +      +l+ +dg +++gG+ +           ++  ++ ++++ ++++P++GIC G+Q+l+++
  gi|298674467|ref|YP_003726217.1| 26 NVDAELVWFKDK------NLDRFDGAVIPGGFSYGDylragaiaaRTPIMDSVRKMVSEGKPVIGICNGFQVLTES 95
                                      455566665533......35679*********999999555554433333334444448*************9876 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.7e-07    0.0005      25      83 ..      34      94 ..      14     105 .. 0.78
   2 ?   -2.0   0.0      0.89   2.7e+03     155     174 ..     190     209 ..     151     219 .. 0.65

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.7e-07
                                      E-SGGGGCC-SEEEE-SS-HHH....HHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCC CS
                               SNO 25 vkrkedlaevdaliiPGGesta....mskliertglyedllefvknsekvvlGtCaGlillsk 83
                                       k  ++l++ d+ +iPGG s       + ++ rt ++++++++v ++ k+v+G C G+ +l++
  gi|298674467|ref|YP_003726217.1| 34 FK-DKNLDRFDGAVIPGGFSYGdylrAGAIAARTPIMDSVRKMVSEG-KPVIGICNGFQVLTE 94
                                      34.467***********998642222689*****************9.*********988765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.89
                                       EEEEETTEEEESS-GGGSTT CS
                               SNO 155 vvakqkkilatsfhPelaed 174
                                       ++   k+++++  hPe a +
  gi|298674467|ref|YP_003726217.1| 190 ITNSSKNVIGLMPHPERASE 209
                                       33345688888888887765 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   3.2e-06    0.0097      98     119 ..      72      93 ..      34     124 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.2e-06
                     Peptidase_C26  98 iraalergvPilgiCrGlqlln 119
                                       +r+++++g+P++giC G+q+l 
  gi|298674467|ref|YP_003726217.1|  72 VRKMVSEGKPVIGICNGFQVLT 93 
                                       7899****************93 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1532.83
//
Query:       gi|298674468|ref|YP_003726218.1|  [L=218]
Description: ribonuclease HII [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      1e-50  172.3   0.1    1.2e-50  172.1   0.1    1.0  1  RNase_HII   Ribonuclease HII
  ------ inclusion threshold ------
      0.046   14.0   0.5         14    6.1   0.2    3.1  3  Ish1        Putative stress-responsive nuclear envelope prote
      0.085   12.8   1.4       0.93    9.4   0.0    2.3  2  Peroxin-22  Peroxisomal biogenesis protein family
      0.097   12.8   0.3        0.3   11.2   0.0    1.9  2  AsiA        Anti-Sigma Factor A
       0.15   12.1   0.5        1.9    8.5   0.0    2.0  2  eIF3_p135   Translation initiation factor eIF3 subunit 135


Domain annotation for each model (and alignments):
>> RNase_HII  Ribonuclease HII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.1   0.1   3.3e-54   1.2e-50       1     197 [.       4     208 ..       4     209 .. 0.88

  Alignments for each domain:
  == domain 1  score: 172.1 bits;  conditional E-value: 3.3e-54
                                       EEEEEE-TT-SBS-EEEEEEEECGHHHHHHHCTTGTTGTTS-HHHHHHHHHHHHSEEEEE...EE-HHHHH.HHTTT CS
                         RNase_HII   1 iGiDEaGrGpvlGplvvaavavekereeelkklgvkDSKkLskqkreeLaklikkkiekr...klvaeeikyasene 74 
                                       +GiDEaG+Gpv+G++ +a+v+v++++++ lk+lgv DSKk s++kreeLa++ikk++ +    ++  ++i+ +  n 
  gi|298674468|ref|YP_003726218.1|   4 AGIDEAGKGPVIGSMCIAGVVVDEAKINSLKNLGVTDSKKISPRKREELAHKIKKYVDNYfifEITPSQID-ELRNV 79 
                                       6*****************************************************99987521155666666.78999 PP

                                       S-HHHHHHHHHHHHHHHHHHTCEECCECCCE--SSHHHHHHHHHHHHC.....CEEEEETTGGGT-HHHHHHHHHHH CS
                         RNase_HII  75 inlneikaaltlaviklleklgvkvdeilvdgvttpeslkkkleqiik.....ikvtvekkadekyllvaaASiiAk 146
                                       ++ n+i +  +++v + l+++ v+vd+ +v+  + +e++  +  +  k     ik++ e+ ad  y +v+aASiiAk
  gi|298674468|ref|YP_003726218.1|  80 MSMNDIMVLGFSRVVENLNPELVYVDSADVKPERFAEKIRSEYSKSNKtasenIKIISEHEADVVYSVVSAASIIAK 156
                                       ******************************9655544433333332223347999********************** PP

                                       HHHHHHHHHHHHHCSH.--TTSSTTSHHHHHHHHHHHHH..S--TTB-TTSHH CS
                         RNase_HII 147 verdeelellkrkpgtldkgsGyasdektrallkkgats..klpdivrlsfkt 197
                                       v+rde +++lk++ g +d+gsGy+sd+kt+++l ++++    lpdivr+s+kt
  gi|298674468|ref|YP_003726218.1| 157 VRRDELVNNLKEEFG-VDFGSGYPSDPKTKQFLLDWVKRygSLPDIVRHSWKT 208
                                       *************96.************************9***********8 PP

>> Ish1  Putative stress-responsive nuclear envelope protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.2    0.0039        14      17      37 .]      37      59 ..      33      59 .. 0.81
   2 ?    4.2   0.0     0.015        54      25      36 ..     152     168 ..     144     168 .. 0.73
   3 ?   -1.0   0.0      0.64   2.3e+03      18      37 .]     178     195 ..     176     195 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0039
                              Ish1 17 Gipvskaas..tRdeLlklardn 37
                                      G+ +sk+ s  +R+eL ++ +++
  gi|298674468|ref|YP_003726218.1| 37 GVTDSKKISprKREELAHKIKKY 59
                                      66666777799**********98 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.015
                              Ish1  25 s.....tRdeLlklard 36 
                                       s      RdeL++ +++
  gi|298674468|ref|YP_003726218.1| 152 SiiakvRRDELVNNLKE 168
                                       4444558******9986 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.64
                              Ish1  18 ipvskaastRdeLlklardn 37 
                                       +p  + ++t+  Ll+ ++++
  gi|298674468|ref|YP_003726218.1| 178 YP--SDPKTKQFLLDWVKRY 195
                                       55..5678888899988887 PP

>> Peroxin-22  Peroxisomal biogenesis protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00026      0.93      69      93 ..      88     112 ..      49     121 .. 0.85
   2 ?    2.2   0.4     0.047   1.7e+02      48      91 ..     120     163 ..     114     173 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00026
                        Peroxin-22  69 dglsavvkqLkpsslivdedelese 93 
                                        g s vv++L+p+ ++vd+ +++ e
  gi|298674468|ref|YP_003726218.1|  88 LGFSRVVENLNPELVYVDSADVKPE 112
                                       6899*****************9877 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.047
                        Peroxin-22  48 ddl.eeevsskneyKiilcdssdglsavvkqLkpsslivdedele 91 
                                       +++ +++ + +++ Kii+   +d +++vv    + +  v +del 
  gi|298674468|ref|YP_003726218.1| 120 SEYsKSNKTASENIKIISEHEADVVYSVVSA-ASIIAKVRRDELV 163
                                       455466777788899*999988888888754.3334445555555 PP

>> AsiA  Anti-Sigma Factor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       1.1     4e+03       3      28 ..      72      96 ..      71     109 .. 0.74
   2 ?   11.2   0.0   8.3e-05       0.3       3      30 ..     140     167 ..     138     175 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.1
                                      HHHHHHHHHHHHHHHHHTTTHHHHTS CS
                              AsiA  3 tielvldiiavaslLvklsrdeiven 28
                                      +i+  ++++++  ++v l++  +ven
  gi|298674468|ref|YP_003726218.1| 72 QIDELRNVMSMNDIMV-LGFSRVVEN 96
                                      5677788888888777.677777877 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 8.3e-05
                                       HHHHHHHHHHHHHHHHHTTTHHHHTSHH CS
                              AsiA   3 tielvldiiavaslLvklsrdeivenrk 30 
                                       + ++v  +++ as++ k+ rde+v+n k
  gi|298674468|ref|YP_003726218.1| 140 EADVVYSVVSAASIIAKVRRDELVNNLK 167
                                       579999*******************976 PP

>> eIF3_p135  Translation initiation factor eIF3 subunit 135
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0   0.00053       1.9     116     156 ..      41      80 ..      19      89 .. 0.75
   2 ?    2.1   0.1     0.049   1.8e+02      98     140 ..     116     175 ..      81     189 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00053
                         eIF3_p135 116 esewtkltpeslweqiekevkarfryeleedsieeelkkis 156
                                       +++++  ++e+l ++i+k v ++f +e++ ++i+ el+++ 
  gi|298674468|ref|YP_003726218.1|  41 SKKISPRKREELAHKIKKYVDNYFIFEITPSQID-ELRNVM 80 
                                       4577888999*******************99999.666554 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.049
                         eIF3_p135  98 ellkklykkkkkkknkkk.....................esewtkltpeslweqiekevkarfr 140
                                       e ++++y+k++k     +                     +s ++k+ +++l++++++e    f 
  gi|298674468|ref|YP_003726218.1| 116 EKIRSEYSKSNKT----AsenikiiseheadvvysvvsaASIIAKVRRDELVNNLKEEFGVDFG 175
                                       3333333322222....12235677788888888888777778888888888888888877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1563.37
//
Query:       gi|298674469|ref|YP_003726219.1|  [L=750]
Description: type II secretion system F domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-35  121.8   0.6    4.7e-18   65.3   0.4    4.3  5  T2SSF     Type II secretion system (T2SS), protein F
  ------ inclusion threshold ------
       0.19   10.5  22.1       0.12   11.1   1.3    3.9  3  DUF2207   Predicted membrane protein (DUF2207)
       0.78    8.7   5.1        8.3    5.3   0.0    2.8  2  Pex24p    Integral peroxisomal membrane peroxin


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.4   1.6         3   1.8e+04     101     124 ..     131     154 ..     128     155 .. 0.68
   2 !   63.4   0.0   3.2e-21   1.9e-17       2     124 ..     226     354 ..     225     355 .. 0.96
   3 ?   -7.0   6.1         3   1.8e+04     107     124 ..     375     392 ..     360     393 .. 0.73
   4 ?   -2.6   1.5      0.84     5e+03     102     120 ..     471     489 ..     469     491 .. 0.54
   5 !   65.3   0.4   7.9e-22   4.7e-18       1     123 [.     542     667 ..     542     669 .. 0.95

  Alignments for each domain:
  == domain 1  score: -4.4 bits;  conditional E-value: 3
                                       HHHTTXXXXXXXXXXXXXXXXXXX CS
                             T2SSF 101 allepllllvvallvllillaill 124
                                       a+++ +++ +++++++++   +l+
  gi|298674469|ref|YP_003726219.1| 131 AIFYSVVSGLTGAILGIFAAYMLI 154
                                       566777777777777777777765 PP

  == domain 2  score: 63.4 bits;  conditional E-value: 3.2e-21
                                       HHHHHHHHHTT--HHHHHHHHHHHHS.SHHHHHHHHHHHHHHHTTS.SHHHHHC....T-TT.TS-HHHHHHHHHHH CS
                             T2SSF   2 lrqlatllsaGvplveaLellaeeae.ngplaeelkriarrlraGg.slseale....rtpssefpelvvqlirage 72 
                                       ++ ++ l+++G+++  ++++l++++  +g+ ++e++ i+r++++ g +l++a++     tps+ f +l+ +l+++++
  gi|298674469|ref|YP_003726219.1| 226 VTFMYALSKGGMNIINVFDSLSRSSNtYGEASKEVETIIREMDYFGhDLRTAISnvseMTPSDRFQDLLHNLLTVID 302
                                       56799**************************************9887889999999989999*************** PP

                                       HHT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXXX CS
                             T2SSF  73 eggnLaevLerlaeyleeerelrrkllaallepllllvvallvllillaill 124
                                       +gg++++++++ ++++ +++   +k ++++l+ l++ +v+++v+++l++i++
  gi|298674469|ref|YP_003726219.1| 303 SGGSISKYFQDKSDQYLKKAIDDQKGFLETLGLLAESYVTAFVAGPLFIIIM 354
                                       **************************************************98 PP

  == domain 3  score: -7.0 bits;  conditional E-value: 3
                                       XXXXXXXXXXXXXXXXXX CS
                             T2SSF 107 lllvvallvllillaill 124
                                       ++l++++++++++++i+ 
  gi|298674469|ref|YP_003726219.1| 375 AVLPIGSVMFVVMISIMA 392
                                       567777777777777775 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 0.84
                                       HHTTXXXXXXXXXXXXXXX CS
                             T2SSF 102 llepllllvvallvllill 120
                                       ll+++++ +va+++lli++
  gi|298674469|ref|YP_003726219.1| 471 LLSVAVTSPVAVILLLIFV 489
                                       3455555555555555554 PP

  == domain 5  score: 65.3 bits;  conditional E-value: 7.9e-22
                                       HHHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHC....T-TT.TS-HHHHHHHHHHHH CS
                             T2SSF   1 flrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGgslseale....rtpssefpelvvqliragee 73 
                                       fl  la+ +++G++l+++++l+ +++ n  l++e ++i +++++G+ l++al     r ++ + ++ ++ ++ a e+
  gi|298674469|ref|YP_003726219.1| 542 FLKKLASTVETGMTLQDSIKLMVKTD-NEGLSDETRKIWKDISWGMELNDALVrfanRLKTQVVSRSMTLITKANES 617
                                       8999**********************.**************************88875555566************* PP

                                       HT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXX CS
                             T2SSF  74 ggnLaevLerlaeyleeerelrrkllaallepllllvvallvllillail 123
                                       +g+++evL+ +a++   e+e++r++  +++ +++++++  +v++ ++ ++
  gi|298674469|ref|YP_003726219.1| 618 SGDIGEVLMVAARDASSEEEMKRERSMNMMIYIVIIYISYMVFVGVIYVI 667
                                       *********************************************99887 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.3   2.1e-05      0.12     309     427 ..      33     198 ..      10     248 .. 0.62
   2 ?    8.3   0.9   0.00014      0.86     351     432 ..     309     390 ..     265     405 .. 0.65
   3 ?    0.0   5.5     0.047   2.8e+02     303     409 ..     547     710 ..     405     750 .] 0.60

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.1e-05
                           DUF2207 309 kkndeeldpyEkal.ldlLfdkseeg.ks......lkeikkyakkskk...................kakkfkkalk 358
                                       +++  + ++yEk+l ++ L++  +++ ++      +++i +++++ +                    k k+ kk+++
  gi|298674469|ref|YP_003726219.1|  33 NTESPDTSEYEKRLsFKNLKNRFQSNnHQdnerglSDKISSRINNLDRqarlfltifkkipfallgeKMKEKKKKYA 109
                                       33444448888888766666555555444566777555555555544456666668888888887778888888888 PP

                           DUF2207 359 kwksavkk....kergyfdkkgkkklkklsalglgliilglilillallllvll....................... 408
                                       +++ ++k+    ++++ + ++    ++++ + gl ++ilg++++ +++++++ l                       
  gi|298674469|ref|YP_003726219.1| 110 RLQLQLKQaripTSYEMYISN---AIFYSVVSGLTGAILGIFAAYMLIAVIG-Lpdnltnltfgpstawllnfkeif 182
                                       888888889888666666666...3444444444444444444433333333.247889*******99999877544 PP

                           DUF2207 409 .lvfllilllillliaiivl 427
                                        +    ++++++  i ++ +
  gi|298674469|ref|YP_003726219.1| 183 lS----LFIVVFTTITLGGM 198
                                       31....33333322222222 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00014
                           DUF2207 351 kkfkkalkkwksavkkkergyfdkkgkkklkklsalglgliilglilillallllvlllvfllilllillliaiivl 427
                                       k f+++ +++ ++  ++++g++++ g     ++ a+  g +++++++i++++++ +++l+ ++++  +l++ +++++
  gi|298674469|ref|YP_003726219.1| 309 KYFQDKSDQYLKKAIDDQKGFLETLGLLAESYVTAFVAGPLFIIIMGIMMTVMGSGSILMVYAVIYAVLPIGSVMFV 385
                                       33444444444444446777777777666667777777777777777777777777645555555555555555555 PP

                           DUF2207 428 llfsr 432
                                       +++s+
  gi|298674469|ref|YP_003726219.1| 386 VMISI 390
                                       55443 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.047
                           DUF2207 303 d.............tltilkkndeeldpyEkalldlLfdkseegkslkeikkyakkskkkakkfkkalkkwksavkk 366
                                                     +   +k+++e l+++ +++++ +  ++e +   +++ ++a+    k + ++++++ +++a ++
  gi|298674469|ref|YP_003726219.1| 547 AstvetgmtlqdsiK-LMVKTDNEGLSDETRKIWKDISWGMELN---DALVRFANR--LKTQVVSRSMTLITKANES 617
                                       033333333333322.4556666666666666666665333222...233333332..1666777777777776666 PP

                           DUF2207 367 ...............kergyfdkkgkkklkklsalglgliilglilillallllvll.................... 408
                                                      ++++ ++++ + +++++++++ +   ++++++++++ + +l+                    
  gi|298674469|ref|YP_003726219.1| 618 sgdigevlmvaardaSSEEEMKRERSMNMMIYIVIIYIS-YMVFVGVIYVISTTFLTemaeageqmtssgaqqmgml 693
                                       777777777776666555555555444433332222222.2222222222222222245566666666666555555 PP

                           DUF2207 409 ................l 409
                                                       +
  gi|298674469|ref|YP_003726219.1| 694 gsfdldkytrifkhsaV 710
                                       55555555555555550 PP

>> Pex24p  Integral peroxisomal membrane peroxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0014       8.3      92     196 ..     220     387 ..     159     459 .. 0.58
   2 ?    1.6   4.4     0.019   1.1e+02     140     180 ..     633     673 ..     363     676 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0014
                            Pex24p  92 k............................................keesknestsegptldea.............. 110
                                       +                                            +                +              
  gi|298674469|ref|YP_003726219.1| 220 ShlpyavtfmyalskggmniinvfdslsrssntygeaskevetiiR----------------Emdyfghdlrtaisn 280
                                       0444455555555555555555554433332333333333332330................133333333333333 PP

                            Pex24p 111 .........skeivlnLr...........dlqnkmedllnpidalekflkelagfkdenlstllfltllltpilill 167
                                                 +++++nL             +q+k +++l+     +k + e+ g+ +e++ t ++ + l ++i+ ++
  gi|298674469|ref|YP_003726219.1| 281 vsemtpsdrFQDLLHNLLtvidsggsiskYFQDKSDQYLKKAIDDQKGFLETLGLLAESYVTAFVAGPLFIIIMGIM 357
                                       33344433344777776688888888888899999999987666666777777888888888888887777777666 PP

                            Pex24p 168 lsrlipwrlillvlg.ailltyHpsvkkvl 196
                                       ++++   + +++ +   ++l + + +  v+
  gi|298674469|ref|YP_003726219.1| 358 MTVMGSGSILMVYAViYAVLPIGSVMFVVM 387
                                       655555554444444344444444444444 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.019
                            Pex24p 140 kelagfkdenlstllfltllltpililllsrlipwrlillv 180
                                       ++   +k+e+   ++++++++ ++++++++++  +++++l+
  gi|298674469|ref|YP_003726219.1| 633 SSEEEMKRERSMNMMIYIVIIYISYMVFVGVIYVISTTFLT 673
                                       33344999*********************999999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (750 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1397  (0.0779185); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.79u 0.32s 00:00:01.11 Elapsed: 00:00:00.47
# Mc/sec: 4820.13
//
Query:       gi|298674470|ref|YP_003726220.1|  [L=692]
Description: type II secretion system protein E [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-49  168.6   0.0    2.2e-49  167.9   0.0    1.2  1  T2SSE        Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.012   15.3   0.0      0.031   14.0   0.0    1.7  1  AAA_29       P-loop containing region of AAA domain
      0.069   11.7  27.2       0.12   10.9  27.2    1.4  1  TFIIF_alpha  Transcription initiation factor IIF, alpha subun


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.9   0.0   3.7e-53   2.2e-49       6     256 ..     315     571 ..     312     584 .. 0.92

  Alignments for each domain:
  == domain 1  score: 167.9 bits;  conditional E-value: 3.7e-53
                             T2SSE   6 eallddekvsdihvekper.vkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpekgvrlr 81 
                                       ++l++d+ + di  + ++  +++  r+ + ++++    ++++l  +i r+a+  +++is  +p++da++p +g r++
  gi|298674470|ref|YP_003726220.1| 315 DPLMNDDYIEDISGNGHNIpLFLYHRIYH-NIATNIAFTEDELDSFIIRLAQKCGKHISLAEPMVDASMP-DGSRVQ 389
                                       67888999999999999999999999999.788888888899999999**********************.888888 PP

                             T2SSE  82 vvllPvvag..ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinks 156
                                       + l  ++ +   +++iRk s+  +t  dl+  ++++ ++ + l   ++++++++ +GgT sGKt +l+a+  +++++
  gi|298674470|ref|YP_003726220.1| 390 MTLSTTITThgSTFTIRKFSEVPITPIDLIDWGTFSSEQMAYLWLCIENNKSLIYAGGTASGKTSSLNAVSLFVPEK 466
                                       8777776665599**************************************************************** PP

                             T2SSE 157 derivtvEDpvEiqleganqvqlnak.......kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGHlg 226
                                         ++vt+ED++Ei+l + n +  +++       ++ v++ dllraaLR+rP  ++vGE+R+ke+l++ +A++TGH  
  gi|298674470|ref|YP_003726220.1| 467 -AKVVTLEDTREIKLPHTNWIPGVTRdsftadeRGAVDMYDLLRAALRQRPEYLIVGEVRGKEALTLFQAMSTGHTT 542
                                       .********************999999*****99******************************************* PP

                             T2SSE 227 slsTlHansaagalerLeqlgaeveaaelk 256
                                        +sT+Ha+s+ +a++rLe+    v++++++
  gi|298674470|ref|YP_003726220.1| 543 -FSTMHADSVPSAIHRLENPPISVPRNMIQ 571
                                       .*****************977666666665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.2e-06     0.031       3      50 ..     415     466 ..     413     470 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.2e-06
                            AAA_29   3 rlqlvNWgtfdghtie.....idlkgatlltGpsGsGKSTllDAiqalLvpak 50 
                                        ++l++Wgtf+ +++      i+ + + + +G + sGK++ l A++ l+vp+k
  gi|298674470|ref|YP_003726220.1| 415 PIDLIDWGTFSSEQMAylwlcIENNKSLIYAGGTASGKTSSLNAVS-LFVPEK 466
                                       589*********6654222225545477779***********9985.777776 PP

>> TFIIF_alpha  Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9  27.2     2e-05      0.12     260     370 ..      59     172 ..       8     190 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2e-05
                                       XXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXX.XX CS
                       TFIIF_alpha 260 kkrgsdddadeydsddGddegrEldyisDdsasendpeeredkkseEeeekkeieqdedeeekeeekke..eeg.kl 333
                                          +++ d+ +y     +d +    ++sD+ +s++++ee+ d + +E++  +++e++++++ ke+e++e  + g +l
  gi|298674470|ref|YP_003726220.1|  59 DANDENFDKEDYILTPSEDVENTSLWLSDKHESDEEHEENFDILTPESGFETNKEKSDESGIKENESEEsdKSGkNL 135
                                       223444466666677789999999**************************999999999976655554400333146 PP

                                       XXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXX CS
                       TFIIF_alpha 334 skkkkkakklkkkkkekdkkdSddeedsddsDideed 370
                                        k+   +kk kk   + ++++S+++e+ ++s ++e +
  gi|298674470|ref|YP_003726220.1| 136 VKSLIHEKKSKKLRPGAEESSSKSDESFEESASEELT 172
                                       6777778888888888888888888888888887754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (692 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       868  (0.0484132); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.49
# Mc/sec: 4222.47
//
Query:       gi|298674471|ref|YP_003726221.1|  [L=540]
Description: phenylalanyl-tRNA synthetase subunit beta [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.5e-41  139.9   0.1    1.5e-40  138.9   0.1    1.5  2  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    1.4e-19   70.1   2.5    3.3e-19   68.9   0.2    2.7  3  B5               tRNA synthetase B5 domain
    1.4e-17   63.9   0.0      3e-17   62.8   0.0    1.6  1  B3_4             B3/4 domain
    0.00055   20.1   0.1      0.093   13.0   0.0    3.0  2  PhetRS_B1        Phe-tRNA synthetase beta subunit B1 domain
  ------ inclusion threshold ------
      0.022   14.2   0.3      0.047   13.2   0.3    1.5  1  tRNA-synt_2d     tRNA synthetases class II core domain (F)
      0.042   13.8   0.1        6.7    6.7   0.0    3.7  5  DUF4265          Domain of unknown function (DUF4265)
       0.11   12.4   0.0       0.97    9.3   0.2    2.3  2  AAA_lid_2        AAA lid domain


Domain annotation for each model (and alignments):
>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.9   4.8e+03      67      90 ..      86     109 ..      51     111 .. 0.68
   2 !  138.9   0.1   5.9e-44   1.5e-40       1     213 [.     344     536 ..     344     537 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.9
                   tRNA_synthFbeta  67 lsedqsvlRtsLlpglLevlarNl 90 
                                        +ed +++R+ L   ++ +++ N 
  gi|298674471|ref|YP_003726221.1|  86 KDEDIEHIRPYLACAVIRNVNFNA 109
                                       456777777777777777777775 PP

  == domain 2  score: 138.9 bits;  conditional E-value: 5.9e-44
                   tRNA_synthFbeta   1 IpstlPkapttegelnkeqklrrklrdllagaGlnEvitysfvsekeldklleddderkavelanPlsedqsvlRts 77 
                                       I++ +P+ +t +   ++   +++++ ++++g+G++Ev+++++ +e +  + + ++  +++  + +P+sedq+++Rt+
  gi|298674471|ref|YP_003726221.1| 344 IQPEFPESATFGS-AHEVSVTSDNICEIMTGLGYSEVMSFTLSNERVHFDNMCRNRTDDVTYVMHPISEDQTMVRTT 419
                                       7889999999999.88******************************98888877789999***************** PP

                   tRNA_synthFbeta  78 LlpglLevlarNlargnedvrlFEigkvflkdseeelpeeerhlaivltgkreeeswsekaravdfydlkgiveall 154
                                       +lp+l+e l+ N++r+++   +FE+g+v++++      + +r+la+v  +++           v+f d+ +iv+a++
  gi|298674471|ref|YP_003726221.1| 420 ILPNLMEILSMNQHRELP-QSIFEFGDVVINN------KIHRNLAAVSIHPE-----------VNFTDIREIVDAVM 478
                                       ******************.*************......889***********...........************** PP

                   tRNA_synthFbeta 155 eslgiekvefepaehpalhpgrsAeikvdgkevGvlGelhpevleafdlkqrvyvfEld 213
                                       ++  + ++e+e++++pa+  gr A+i v+gk+vGv+Ge+ p+v  +f+l ++v++fE++
  gi|298674471|ref|YP_003726221.1| 479 RERMV-EYEVEESDDPAFIGGRRADILVNGKKVGVMGEIYPQVITNFGLGEPVIGFEME 536
                                       *****.***************************************************97 PP

>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       2.2   5.6e+03      36      56 ..      18      38 ..       9      53 .. 0.70
   2 !   68.9   0.2   1.3e-22   3.3e-19       2      67 .]     276     341 ..     275     341 .. 0.98
   3 ?   -0.7   0.0      0.71   1.8e+03      15      32 ..     361     395 ..     356     452 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.2
                                      STTCEEEE--TT-TT--SHHH CS
                                      xxxxxxxxxxxxxxxxxxxxx RF
                                B5 36 dkdlllVtvPswRsDlereeD 56
                                      d d++  ++P +  D+er eD
  gi|298674471|ref|YP_003726221.1| 18 DRDTIVEQIPMMGADIERIED 38
                                      555666667777667776665 PP

  == domain 2  score: 68.9 bits;  conditional E-value: 1.3e-22
                                       EEEHHHHHHHHTS---HHHHHHHHHHTT-E.EESSTTCEEEE--TT-TT--SHHHHHHHHHHHH-G CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                B5   2 slrvekinkllGidlseeeiikiLkrlgceriekdkdlllVtvPswRsDlereeDliEEvaRlyGY 67 
                                       +l+v++in+l+G++ls++ei k L+r+ + ++ k+++ ++V+vP++R D+++  D++E++a+ yGY
  gi|298674471|ref|YP_003726221.1| 276 ELEVSEINSLIGTELSQDEILKQLQRMRYGADIKNNKSIEVKVPPYRADILHNYDIVEDIAIGYGY 341
                                       6899*************************************************************9 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.71
                                       ---HHHHHHHHHHTT-E.................. CS
                                       xxxxxxxxxxxxxxxxx.................x RF
                                B5  15 dlseeeiikiLkrlgce.................r 32 
                                       ++++++i++i++ lg+                   
  gi|298674471|ref|YP_003726221.1| 361 SVTSDNICEIMTGLGYSevmsftlsnervhfdnmC 395
                                       57789999999999987555555555555555551 PP

>> B3_4  B3/4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.8   0.0   1.2e-20     3e-17       2     129 ..      94     232 ..      93     258 .. 0.92

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 1.2e-20
                                       SSEEEEEEEES--.-----HHHHHHHHHTT-----HHHHHHHHHHHHHT-.....-EEEEEGGGTBTEEEEEE--TT CS
                              B3_4   2 cpryaarvlrgvkktapspewlqrrLrragirpinnvVDitNyvmlelgq.....PlhafDldkiqgdivvrlakeg 73 
                                       +p+ a++v+r+v+++a+s               i+++ D+++ ++  +g+      ++++Dl++i+++++   a  +
  gi|298674471|ref|YP_003726221.1|  94 RPYLACAVIRNVNFNANS---------------IKSLMDLQEDLHWGVGRdrkkvSIGVHDLSNITPPFRYMAADPD 155
                                       89****************...............******************************************** PP

                                       EEEEBTTS-EEEE.-T...................TSEEEETEEEEE.EETTTEEBTTTB--TT--EEEEEEEE--H CS
                              B3_4  74 eklvtldgkerel.de...................edlviadsekpv.slagvmggeeskvsedTknvfleaaafdp 129
                                        k+++ld +e    ++                   e+++i d++++v s ++++++ +++++e+T++ f+ ++++++
  gi|298674471|ref|YP_003726221.1| 156 TKFIPLDFTEPMSmNQilekhpkgmkfayilegfnEYPIILDADDNVlSFPPIINSTRTQITENTTDLFIDVTGLSE 232
                                       *******9988874559****************************999*************************9776 PP

>> PhetRS_B1  Phe-tRNA synthetase beta subunit B1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   3.6e-05     0.093      49      82 ..      34      67 ..      16      68 .. 0.85
   2 ?    3.7   0.0     0.029        74      27      78 ..     282     336 ..     270     340 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.6e-05
                         PhetRS_B1 49 kkseeviykidipAnryDLLcleglaralkvFlg 82
                                      ++ e++++ i+    r+DL ++eg+aral+ Fl+
  gi|298674471|ref|YP_003726221.1| 34 ERIEDEYIDIEFFPDRPDLYSVEGVARALRGFLN 67
                                      567889999*********************9985 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.029
                         PhetRS_B1  27 llfefGlEl..Deiveeeekkk.adkkseeviykidipAnryDLLcleglaralk 78 
                                       +    G El  Dei ++ ++ +  ++ ++++ + + +p  r D+L    +++ ++
  gi|298674471|ref|YP_003726221.1| 282 INSLIGTELsqDEILKQLQRMRyGADIKNNKSIEVKVPPYRADILHNYDIVEDIA 336
                                       455556676557777777755436677888999************8888777665 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   1.8e-05     0.047       9     112 ..     350     448 ..     343     492 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.8e-05
                                       SCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-ECESEEE-S CS
                      tRNA-synt_2d   9 krieagklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpekaveekllLRt 85 
                                       ++ + g+ h ++ ++++i ei++ lg++ev +  + +e   fd +  +        +d+ y+ +p +  e+++++Rt
  gi|298674471|ref|YP_003726221.1| 350 ESATFGSAHEVSVTSDNICEIMTGLGYSEVMSFTLSNERVHFDNMCRN------RTDDVTYVMHPIS--EDQTMVRT 418
                                       55677999***************************9999999987654......3456667768888..889***** PP

                                       STHHHHHHHH...TTS-SSEEEEEEEEEEB CS
                      tRNA-synt_2d  86 httavqirtl...ekkkppikiisigrvfR 112
                                          +  +  l   +++++p+ i+ +g v  
  gi|298674471|ref|YP_003726221.1| 419 TILPNLMEILsmnQHRELPQSIFEFGDVVI 448
                                       **998888877788999******9998755 PP

>> DUF4265  Domain of unknown function (DUF4265)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       0.7   1.8e+03      67      92 ..      20      45 ..      10      67 .. 0.79
   2 ?   -2.3   0.0       1.7   4.3e+03      89     106 ..      81      98 ..      45     100 .. 0.81
   3 ?    0.7   0.0       0.2   5.1e+02      57      92 ..     258     290 ..     233     302 .. 0.66
   4 ?    0.7   0.0      0.19   4.8e+02      63      94 ..     289     320 ..     282     325 .. 0.86
   5 ?    6.7   0.0    0.0026       6.7      85     114 ..     454     483 ..     434     485 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.7
                           DUF4265 67 sevreeLealgceveglsakllavdv 92
                                      + ++e++ ++g+++e ++++++ ++ 
  gi|298674471|ref|YP_003726221.1| 20 DTIVEQIPMMGADIERIEDEYIDIEF 45
                                      789999999******99999988775 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.7
                           DUF4265  89 avdvpadvdleaikelLa 106
                                        +++ +d d+e+i+ +La
  gi|298674471|ref|YP_003726221.1|  81 NIEIEKDEDIEHIRPYLA 98 
                                       578999999999999986 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.2
                           DUF4265  57 lvdekaelgesevreeLealgceveglsa.kllavdv 92 
                                       +  ++     ++ +  Le l ce+e+++  +l+  + 
  gi|298674471|ref|YP_003726221.1| 258 IDSDGN----EKTLPDLEPLSCELEVSEInSLIGTEL 290
                                       333322....689999*********998866665555 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.19
                           DUF4265  63 elgesevreeLealgceveglsakllavdvpa 94 
                                       el+++e++++L+++    +  ++k + v+vp+
  gi|298674471|ref|YP_003726221.1| 289 ELSQDEILKQLQRMRYGADIKNNKSIEVKVPP 320
                                       445589************************98 PP

  == domain 5  score: 6.7 bits;  conditional E-value: 0.0026
                           DUF4265  85 akllavdvpadvdleaikelLaeleeegvi 114
                                        +l av+++++v++  i+e+ +++ +e ++
  gi|298674471|ref|YP_003726221.1| 454 RNLAAVSIHPEVNFTDIREIVDAVMRERMV 483
                                       5899*****************997776655 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.57   1.5e+03       6      21 ..     311     326 ..     308     327 .. 0.87
   2 ?    9.3   0.2   0.00038      0.97      27      61 ..     454     489 ..     450     504 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.57
                         AAA_lid_2   6 hlaielgvsgrRadla 21 
                                       +++ie+ v + Rad+ 
  gi|298674471|ref|YP_003726221.1| 311 NKSIEVKVPPYRADIL 326
                                       6789**********95 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00038
                         AAA_lid_2  27 rAlAalegrdyVtpeDvkeaaplVLaHRlr.repea 61 
                                       r lAa+    +V+  D++e++  V++ R++ +e e+
  gi|298674471|ref|YP_003726221.1| 454 RNLAAVSIHPEVNFTDIREIVDAVMRERMVeYEVEE 489
                                       668999999********************9533332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (540 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.58u 0.22s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3879.73
//
Query:       gi|298674472|ref|YP_003726222.1|  [L=446]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-26   92.1   0.1    5.4e-26   91.2   0.1    1.5  1  OrfB_IS605      Probable transposase
    7.5e-23   80.2   0.8    1.8e-22   79.0   0.8    1.7  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      2e-08   33.6   0.0    5.2e-08   32.2   0.0    1.7  1  HTH_OrfB_IS605  Helix-turn-helix domain
     0.0026   17.4   1.0       0.95    9.3   0.2    2.8  2  zinc_ribbon_2   zinc-ribbon domain
     0.0036   16.8   0.4        1.4    8.5   0.1    2.7  2  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0082   15.5   0.6        5.1    6.6   0.2    2.8  2  zf-ribbon_3     zinc-ribbon domain
  ------ inclusion threshold ------
      0.022   14.8   0.7      0.051   13.6   0.7    1.6  1  DZR             Double zinc ribbon
       0.04   13.9   1.1      0.088   12.8   1.1    1.6  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.14   11.7   4.2       0.26   10.8   4.2    1.4  1  Vps5            Vps5 C terminal like
       0.14   11.5   0.6       0.53    9.7   0.6    2.0  1  Vps36-NZF-N     Vacuolar protein sorting 36 NZF-N zinc-finger
       0.24   11.1   2.1          1    9.1   2.1    2.0  1  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.2   0.1   3.3e-29   5.4e-26       3     117 ..     204     315 ..     202     318 .. 0.97

  Alignments for each domain:
  == domain 1  score: 91.2 bits;  conditional E-value: 3.3e-29
                        OrfB_IS605   3 pvevevelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklar 79 
                                        ve+++++ + ++++a+giD+G++ ++t+++ d   f+  +r+l++++k+lake+++l++   ks+ny k+++k+ r
  gi|298674472|ref|YP_003726222.1| 204 TVELPDNPVPSTPTNAVGIDIGLKSFITTSDDD---FVEPPRFLRKAEKRLAKEQQKLAKMEFKSNNYNKQKQKVNR 277
                                       699999999************************...***************************************** PP

                        OrfB_IS605  80 lhrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       +hrk++  r+h+ h l++ l+++++ ++ e+L+++n++
  gi|298674472|ref|YP_003726222.1| 278 IHRKVASARNHFSHCLSKLLVERYDLIVFEDLKIKNLV 315
                                       ***********************************997 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.0   0.8   1.1e-25   1.8e-22       1      69 []     329     399 ..     329     399 .. 0.98

  Alignments for each domain:
  == domain 1  score: 79.0 bits;  conditional E-value: 1.1e-25
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke..alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       ++kl + + yka e+G+ v +v+p +T + Cs Cg k+ke  +l++rtf+C+nCg+e+drD+nA+ Nil +
  gi|298674472|ref|YP_003726222.1| 329 WNKLVQHVTYKAAERGKIVDKVDPDNTTQVCSYCGTKKKEklKLEDRTFHCSNCGLEIDRDLNASANILTK 399
                                       99******************************************************************975 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0   3.2e-11   5.2e-08       5      44 ..      11      50 ..       9      52 .. 0.93

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 3.2e-11
                    HTH_OrfB_IS605  5 aykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayee 44
                                        ++ +  TpeQe kl  t++ +R+++N+ L+ + e y +
  gi|298674472|ref|YP_003726222.1| 11 NLRFKIHITPEQEKKLDDTLEYCRLIWNHLLSIKVELYDR 50
                                      67999*******************************9987 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.2   0.00058      0.95      11      22 ..     353     365 ..     349     366 .. 0.68
   2 !    5.7   0.0    0.0079        13       2       9 ..     379     386 ..     370     391 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00058
                     zinc_ribbon_2  11 dnakF.CpyCGtp 22 
                                       dn +  C+yCGt+
  gi|298674472|ref|YP_003726222.1| 353 DNTTQvCSYCGTK 365
                                       333335*****97 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0079
                     zinc_ribbon_2   2 CpnCGael 9  
                                       C+nCG e+
  gi|298674472|ref|YP_003726222.1| 379 CSNCGLEI 386
                                       77777666 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.1   0.00089       1.4      13      27 ..     350     364 ..     346     370 .. 0.89
   2 !    5.7   0.0    0.0064        10      19      33 ..     376     390 ..     372     395 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00089
                                       EETSTTCEEESSSSB CS
                      TF_Zn_Ribbon  13 eDpergelvCtdCGl 27 
                                       +Dp++++ vC+ CG+
  gi|298674472|ref|YP_003726222.1| 350 VDPDNTTQVCSYCGT 364
                                       79************7 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0064
                                       CEEESSSSBEEEECC CS
                      TF_Zn_Ribbon  19 elvCtdCGlVledns 33 
                                       ++ C++CGl ++ + 
  gi|298674472|ref|YP_003726222.1| 376 TFHCSNCGLEIDRDL 390
                                       678******998765 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.2    0.0031       5.1      17      25 ..     357     365 ..     351     368 .. 0.74
   2 !    6.1   0.0    0.0047       7.6       2       9 ..     376     383 ..     372     389 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0031
                       zf-ribbon_3  17 nvCpyCGtk 25 
                                       +vC yCGtk
  gi|298674472|ref|YP_003726222.1| 357 QVCSYCGTK 365
                                       567777765 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0047
                       zf-ribbon_3   2 tvrCPnCG 9  
                                       t +C+nCG
  gi|298674472|ref|YP_003726222.1| 376 TFHCSNCG 383
                                       56788887 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.7   3.1e-05     0.051       9      41 ..     353     389 ..     349     394 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.1e-05
                               DZR   9 ppdarfCseCgtklkavaa....edrCpsCgekvdpe 41 
                                       ++  ++Cs+Cgtk k+  +      +C++Cg ++d +
  gi|298674472|ref|YP_003726222.1| 353 DNTTQVCSYCGTKKKEKLKledrTFHCSNCGLEIDRD 389
                                       567789*******7765557777999****9887765 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.1   5.4e-05     0.088      18      44 ..     356     383 ..     352     385 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.4e-05
                     Zn_Tnp_IS1595  18 gfvCPhCgsr..kayriktrglfqCkeCr 44 
                                       ++vC +Cg +  +  ++++ + f+C+ C+
  gi|298674472|ref|YP_003726222.1| 356 TQVCSYCGTKkkEKLKLED-RTFHCSNCG 383
                                       589*******889999998.********7 PP

>> Vps5  Vps5 C terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   4.2   0.00016      0.26     137     208 ..     244     309 ..     241     318 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00016
                              Vps5 137 wqsaeqelskkkeqleKlekaaksqqdklqqlkkeveelerkvqeaekeFeeisetikkElerFetervedf 208
                                       + +ae+ l+k +++l+K+e ++    +  ++ k+ v+ ++rkv++a+++F++  +++   +er++   +ed+
  gi|298674472|ref|YP_003726222.1| 244 LRKAEKRLAKEQQKLAKMEFKS----NNYNKQKQKVNRIHRKVASARNHFSHCLSKL--LVERYDLIVFEDL 309
                                       5689*****************3....35789999****************9864433..3444444444444 PP

>> Vps36-NZF-N  Vacuolar protein sorting 36 NZF-N zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.6   0.00033      0.53       7      59 ..     354     402 ..     348     408 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00033
                       Vps36-NZF-N   7 tatWvCpICsfsNevpsnfdpnastplPpClaCGvkpdlelikksikasassk 59 
                                       ++t vC  C  + + + ++    ++ +  C +CG + d++l  ++ + ++ss 
  gi|298674472|ref|YP_003726222.1| 354 NTTQVCSYCGTKKKEKLKL----EDRTFHCSNCGLEIDRDLNASANILTKSSY 402
                                       5666788888776666544....467778***********9999888777765 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   2.1   0.00063         1       2      30 ..     355     385 ..     354     386 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00063
                     zf-NADH-PPase   2 thrFCgrCGaptepaeg..gwarvCpaCgle 30 
                                       t++ C+ CG++ + +    ++  +C++Cgle
  gi|298674472|ref|YP_003726222.1| 355 TTQVCSYCGTKKKEKLKleDRTFHCSNCGLE 385
                                       899*******9876666669********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1410  (0.0786435); expected 358.6 (0.02)
Passed bias filter:                      669  (0.0373138); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 2644.46
//
Query:       gi|298674473|ref|YP_003726223.1|  [L=252]
Description: hypothetical protein Metev_0515 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.7e-46  156.5  39.0    9.9e-46  156.3  39.0    1.0  1  TauE             Sulfite exporter TauE/SafE
  ------ inclusion threshold ------
       0.16   11.5   0.3       0.16   11.5   0.3    2.6  2  ATP1G1_PLM_MAT8  ATP1G1/PLM/MAT8 family


Domain annotation for each model (and alignments):
>> TauE  Sulfite exporter TauE/SafE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.3  39.0   1.1e-49   9.9e-46       2     236 .]       7     247 ..       5     247 .. 0.94

  Alignments for each domain:
  == domain 1  score: 156.3 bits;  conditional E-value: 1.1e-49
                              TauE   2 llagllaGfvagllGiGggliavPlLll.llppavavatsllavvatslsgalahrrrgnvdwrlllllllgsliGa 77 
                                       ++++++  ++ +++G Gg++i+vPlL++ +++ +++++t ll++++ + s+++ + +++ vd++++++l+l s++Ga
  gi|298674473|ref|YP_003726223.1|   7 AIIVFFLAILFSIIGTGGSTIYVPLLYWiGIDLHIVIPTVLLINTFATGSATIFYTKKKMVDFKTAIPLILTSVAGA 83 
                                       78899999********************559********************************************** PP

                              TauE  78 llGallllllpsellkllfgvlllllallmllrkkr...srak..grerrptaillvligglvGllsGllGiGgGfl 149
                                       ++Ga++++++p++ll l+f+vllll+++ m+++++r      k  gr +r++ i++++ g+++G+++GllG +gG++
  gi|298674473|ref|YP_003726223.1|  84 PIGAYFSKSTPQDLLILIFAVLLLLIGIHMVFTSSRighL--KctGRGTRKNVIISLISGFMIGIVAGLLGLSGGVF 158
                                       ******************************9977765542..25578899999988888888*************** PP

                              TauE 150 lvpllllllglplkkavatslllilvislagalgyal..agavdwpllllllpgallGallGar.larrlsertlrr 223
                                       +vpll++ lg+++k+a atsl++i+++s++g+lg++   +g++d  ll++  ++++lGa++G++ +  rl+ +t+ +
  gi|298674473|ref|YP_003726223.1| 159 IVPLLVY-LGYNIKTASATSLFIIVFTSISGFLGHIGtsTGSLDAGLLVYSSLAGFLGAQVGSYfMIYRLKSKTINQ 234
                                       ******9.6**************************7777********999**************8899********* PP

                              TauE 224 lfallllvlgvkl 236
                                       +f+++l v++++l
  gi|298674473|ref|YP_003726223.1| 235 MFGIVLWVVAIRL 247
                                       **********986 PP

>> ATP1G1_PLM_MAT8  ATP1G1/PLM/MAT8 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3   1.7e-05      0.16      18      40 ..     100     126 ..     100     133 .. 0.76
   2 ?   -1.0   0.5      0.14   1.3e+03      19      30 ..     146     157 ..     142     172 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.7e-05
                                       HHHHHHHHHHHHHHHHCCHH....HCC CS
                   ATP1G1_PLM_MAT8  18 LifAglLfivGiliilSkkc....kCk 40 
                                       LifA+lL ++Gi ++++ +     kC 
  gi|298674473|ref|YP_003726223.1| 100 LIFAVLLLLIGIHMVFTSSRighlKCT 126
                                       8***********999865443566774 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHH CS
                   ATP1G1_PLM_MAT8  19 ifAglLfivGil 30 
                                       i+AglL + G +
  gi|298674473|ref|YP_003726223.1| 146 IVAGLLGLSGGV 157
                                       667777555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1087  (0.060628); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1849.19
//
Query:       gi|298674474|ref|YP_003726224.1|  [L=200]
Description: nitroreductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.9e-35  120.2   0.0      1e-34  120.0   0.0    1.0  1  Nitroreductase  Nitroreductase family
    3.6e-16   59.4   0.0    3.5e-07   30.0   0.0    3.1  3  TM1586_NiRdase  Putative TM nitroreductase
  ------ inclusion threshold ------
      0.019   15.3   1.5        1.1    9.7   0.0    2.5  2  FAM25           FAM25 family


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.0   0.0   1.7e-38     1e-34       1     170 []      15     177 ..      15     177 .. 0.94

  Alignments for each domain:
  == domain 1  score: 120.0 bits;  conditional E-value: 1.7e-38
                                       HHH--B---B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHHHHHHHHHHHHHTT-SS-GGGGGG CS
                    Nitroreductase   1 irkRrSiRkFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelryklaeaalelllkaeaqaelaqryrke 77 
                                       i++RrS+R + d++v+++++ ++++a+ +aP+a +lqpw+fvv++ k++++++ ++++  +++  ++ +++  ++ +
  gi|298674474|ref|YP_003726224.1|  15 IKSRRSVRDYIDKQVSEDTVNQVIDAGIHAPTALGLQPWNFVVISGKDIIKEISDHIKPMVQEHLKDSTEQLAKDLK 91 
                                       89*******************************************9****999999999999999999988888877 PP

                                       .HHHHHHHHHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHH..HHH CS
                    Nitroreductase  78 .elklkaqkalagapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaae..evr 151
                                        ++k+k   ++++ap+l+++           ++r++  a  d++++a+n++LaA++lGlgsc+ig+    ++  e+ 
  gi|298674474|ref|YP_003726224.1|  92 eKMKNKDFNLFYDAPILVLV----------MHNRDDKLADYDCALCAENMMLAAHSLGLGSCWIGAGAFIQQspELL 158
                                       789999999***********..........9**********************************999666656*** PP

                                       HHHT-S..SEEEEEEEEE- CS
                    Nitroreductase 152 kllglpdeeeivvliavGy 170
                                       + l++p + eiv+ i +Gy
  gi|298674474|ref|YP_003726224.1| 159 DDLDIPHDFEIVAPIILGY 177
                                       ******99*********99 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.3   1.5e-06    0.0089       2      27 ..      11      36 ..      10      37 .. 0.91
   2 !   15.2   0.0     2e-06     0.012     158     190 ..      32      64 ..      30      76 .. 0.77
   3 !   30.0   0.0   5.9e-11   3.5e-07      22     136 ..      61     181 ..      59     198 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.5e-06
                                      HHHHHHH--B---B--S---HHHHHH CS
                    TM1586_NiRdase  2 lyeaiekRhsvRkYkdealeeellee 27
                                      ++eai+ R+svR+Y d++++e+++++
  gi|298674474|ref|YP_003726224.1| 11 VIEAIKSRRSVRDYIDKQVSEDTVNQ 36
                                      589******************98876 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 2e-06
                                       HHHHHHHHHHHTS--GGG----EEE.E-SSEE. CS
                    TM1586_NiRdase 158 ewfkeileaarlAPsAlNqqpwrfelkdddeik 190
                                       + ++++++a + AP+Al  qpw f + + ++i 
  gi|298674474|ref|YP_003726224.1|  32 DTVNQVIDAGIHAPTALGLQPWNFVVISGKDII 64 
                                       67899*******************976665553 PP

  == domain 3  score: 30.0 bits;  conditional E-value: 5.9e-11
                                       HHHHHHHHH-----S.....S-----EE.E.............-SSSSEEEE----SS.HHHHHHHHHHHHHHHHHH CS
                    TM1586_NiRdase  22 eelleelkeaieeinkes..glelqlvidenkafkskvaklgkfkgvpnyialvgekk.edleekaGYygeqlvLkl 95 
                                       +++++e+ + i+ + +e+  +   ql  d ++  k+k + ++ f ++p  ++++ + + + ++  +  + e+++L +
  gi|298674474|ref|YP_003726224.1|  61 KDIIKEISDHIKPMVQEHlkDSTEQLAKDLKE--KMKNKDFNLFYDAPILVLVMHNRDdKLADYDCALCAENMMLAA 135
                                       56788888888888888873444445554444..455677888999998776666555488999************* PP

                                       HHTT-EEEEES--S.ST...............T-S-EEEEE-BS-- CS
                    TM1586_NiRdase  96 talGlgtcWvggty.kk....kkakvelkkgeklvivIalGyaktk 136
                                        +lGlg+cW+g+    +        ++++++ ++v+ I lGy++++
  gi|298674474|ref|YP_003726224.1| 136 HSLGLGSCWIGAGAfIQqspeLLDDLDIPHDFEIVAPIILGYPRST 181
                                       **********964312211122234688999999999999999876 PP

>> FAM25  FAM25 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00018       1.1      21      62 ..       8      49 ..       3      51 .. 0.91
   2 ?    4.0   0.5     0.011        64       6      37 ..      61      88 ..      57      98 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00018
                             FAM25 21 EKAiadalKkAqesgekvvKevtekvtntvtnavtHAaEgLg 62
                                      E  + +a+K  +   + + K+v+e   n v +a +HA  +Lg
  gi|298674474|ref|YP_003726224.1|  8 ENPVIEAIKSRRSVRDYIDKQVSEDTVNQVIDAGIHAPTALG 49
                                      667889*******************************99887 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.011
                             FAM25  6 eevvkevveHaKeaGEKAiadalKkAqesgek 37
                                      ++++ke+ +H+K      + + lK   e   k
  gi|298674474|ref|YP_003726224.1| 61 KDIIKEISDHIKPM----VQEHLKDSTEQLAK 88
                                      45667777777654....33334333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1284  (0.0716158); expected 358.6 (0.02)
Passed bias filter:                     1009  (0.0562775); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1239.12
//
Query:       gi|298674475|ref|YP_003726225.1|  [L=197]
Description: hypothetical protein Metev_0517 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.11   12.9   0.4       0.26   11.7   0.1    1.7  2  Lipoprotein_17  Lipoprotein associated domain


Domain annotation for each model (and alignments):
>> Lipoprotein_17  Lipoprotein associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   1.4e-05      0.26      23      79 ..      27      95 ..      12      96 .. 0.75
   2 ?   -2.4   0.0      0.34   6.2e+03      72      72 ..     163     163 ..     142     178 .. 0.49

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.4e-05
                                      -GGGS-HHH........EEE-S..-TTTEEEEEEEE-.T.HHHHHTEEEEEEEE..TTT--EEEEEEEE CS
                    Lipoprotein_17 23 vtnsnlknd........nfitfpntkngvsfsikivs.s.anDeeGtLkvkvtl..sknnksetktiti 79
                                      +++++l++         +   f++++n   ++i+  + + +n+++G++ ++v +  s n+++e+ ++t+
  gi|298674475|ref|YP_003726225.1| 27 ISKKTLSEPrevvedgeKHLIFYDNSNKRILTISMLYhQgYNNKTGEIPLRVAAshSENTVIESMDLTV 95
                                      555555333666666667778999**********999648************99655555557777665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.34
                                       E CS
                    Lipoprotein_17  72 s 72 
                                       s
  gi|298674475|ref|YP_003726225.1| 163 S 163
                                       1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1311.91
//
Query:       gi|298674476|ref|YP_003726226.1|  [L=116]
Description: iron dependent repressor, partial [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-08   34.4   0.0    2.5e-08   34.1   0.0    1.1  1  FeoA           FeoA domain
    4.9e-05   23.3   0.1    8.1e-05   22.6   0.1    1.4  1  Fe_dep_repr_C  Iron dependent repressor, metal binding and di


Domain annotation for each model (and alignments):
>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   2.7e-12   2.5e-08       1      73 [.      43     112 ..      43     113 .. 0.94

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 2.7e-12
                                       EEGGG--TT-EEEEEEE-TT.SSHHHHHHHHT--TT-EEEEEEE-TTS-SEEEEETTEEEEE-HHHHTTEEEE CS
                              FeoA   1 vpLsdlkeGergeiarisdedpellrrLremGlvpGarievvarapfggplvvrvgdtrvaLgreeAqaIlVe 73 
                                       +pLs lk +++g+ia +  +d   l++L++mG+ pG  ++ ++ +     +v  +++tr a+++e+ + ++V+
  gi|298674476|ref|YP_003726226.1|  43 RPLSALKLNQKGKIAYFVIQDNGKLQKLMSMGILPGMPVTQLQ-SY--PSYVFDLDQTRYAVDKEMEDYVFVR 112
                                       69****************************************5.43..47*****************999998 PP

>> Fe_dep_repr_C  Iron dependent repressor, metal binding and dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.1   9.1e-09   8.1e-05      44      69 ..       1      26 [.       1      27 [. 0.92

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 9.1e-09
                                      S-HHHHHHHHHHCT-.SB-TTS-B-- CS
                     Fe_dep_repr_C 44 lseelierldellgfpeecPhgdpip 69
                                      +++ + ++++ ll++p+ cPhg+pip
  gi|298674476|ref|YP_003726226.1|  1 MHDGVDDKVCILLSHPRACPHGNPIP 26
                                      5788899******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 755.27
//
Query:       gi|298674477|ref|YP_003726227.1|  [L=919]
Description: hypothetical protein Metev_0519 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   3.7e-284  944.6  13.9   4.3e-284  944.4  13.9    1.0  1  UPF0182          Uncharacterised protein family (UPF0182)
  ------ inclusion threshold ------
      0.082   13.2   0.1       0.18   12.1   0.1    1.6  1  FliS             Flagellar protein FliS


Domain annotation for each model (and alignments):
>> UPF0182  Uncharacterised protein family (UPF0182)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  944.4  13.9  4.8e-288  4.3e-284       4     758 .]       9     779 ..       6     779 .. 0.96

  Alignments for each domain:
  == domain 1  score: 944.4 bits;  conditional E-value: 4.8e-288
                           UPF0182   4 llavlavlllllellarlytellwfkelgylsvfltrlltrlllfvvvflllalllllnlllaerlelleklerlre 80 
                                       l+++l++++l +  l+ +y+++lwf  ++y+svf+t l +++++++  f+l++++l++n+++a+++   + l+  + 
  gi|298674477|ref|YP_003726227.1|   9 LFIALLAIILGIGPLLGIYMDYLWFGMVDYTSVFTTILQWKIVTVIPGFILAFIFLYINIKFARNS-IDKILTDKQI 84 
                                       455666677779999**************************************************9.5577888899 PP

                           UPF0182  81 alekklkllllaialvlsllvglvassqwekvllflnstsfgvkDpifgkDisFYvFklPflelllslllalvllal 157
                                       a ek   +l+l+ +++ls+l+glv+s++w+++ll+lnst+fg++Dpi  +D++FY+F+lPf+++l+++ll+lv+++l
  gi|298674477|ref|YP_003726227.1|  85 AYEKIDYRLFLIGTVFLSFLFGLVFSGNWRTILLYLNSTPFGIQDPILLNDVGFYIFQLPFFHMLRGVLLGLVIITL 161
                                       9999999999999**************************************************************** PP

                           UPF0182 158 iavllvyllsgesl..girl..................kfaelskaarrhlsvllallllllalsywLdryellysk 214
                                       i++ ++y++  + +  +                      + ++ k++ +h+svlla++++l+a++++L+rye+l+++
  gi|298674477|ref|YP_003726227.1| 162 IIAGALYVYRLQPVllT--QrddteepydinpeiniknIMDKVPKRVLVHVSVLLAFIFALIAVGFFLNRYEILFTQ 236
                                       **999999888776432..246889999*9****99997899*********************************** PP

                           UPF0182 215 rgvvtGagYtdvnavlpaktilavialvvavlllvaivlkklklplialallvllaillgvvlpalvqkfiVkPnel 291
                                       +g+v+GagYtdv ++lp+ til+v+++++av+ll++i+lk++k+pli+++l+vl+++ +++++p+++q++ V+P el
  gi|298674477|ref|YP_003726227.1| 237 QGAVAGAGYTDVFVRLPIFTILTVLSALTAVALLANIKLKNIKVPLIGIGLIVLFVL-ASAFVPSVYQQYAVEPTEL 312
                                       ***************************************************999988.9****************** PP

                           UPF0182 292 ekEkpYiernIeaTreAygLdkveveefeaeaeltaedleenaetienirLlDprplletfrqlqqirnYYkFedld 368
                                       ++E+p++e++I++TreAygL++ +v+++++++++t++d+een++ i+nir++D+r+l +++rqlqqir+YY+F+d+d
  gi|298674477|ref|YP_003726227.1| 313 QREEPFLEHSINFTREAYGLSDADVNQLDVDTNITNRDIEENEDIISNIRIWDHRALRQSYRQLQQIRTYYTFNDVD 389
                                       ***************************************************************************** PP

                           UPF0182 369 vdrYtidgeerqvviaaREldysalpeeaktwvnkhlvYTHGyGvvaspvnkvteeGlpeflvkdipseeeeslkie 445
                                       +drY++d++++q+++a+REld ++lp +a++wvn++l+YTHG+G+v++pv++ t++G+pe+ ++dip+  +++++ie
  gi|298674477|ref|YP_003726227.1| 390 IDRYRTDENYQQYMLAVRELDIDGLPPQARNWVNERLIYTHGFGMVMNPVSTKTADGQPELALQDIPP--RGDFEIE 464
                                       *******************************************************************9..9****** PP

                           UPF0182 446 epriYfGeltndyvivgtkvkEfdypsge.envyntYdGkgGvkigsllrrllfaiklkdlklllsseitseskilf 521
                                       +pr+Y+Ge+tn+y iv+t  +Efdyp++e  nv ++YdGkgGv+++s+++rl++a++++++k++ls++it++s++++
  gi|298674477|ref|YP_003726227.1| 465 NPRVYYGESTNEYKIVNTLRQEFDYPRSEgGNVLTNYDGKGGVQMDSFFKRLAYAFRFGEPKFILSEYITDDSRVMY 541
                                       ******************99******999679********************************************* PP

                           UPF0182 522 rRnikeRvekvaPfLtlDsdpYlvvadgrlyWivDaYTtsdrYPySepeeatsgeeevnYiRNSVKvvvDAydGtvk 598
                                       +++i+eR +k+aPfL++DsdpY+v++dgr+ Wi+DaYTt++rYPyS++    s+ + +nY++N+VKvv+D+ydG+v+
  gi|298674477|ref|YP_003726227.1| 542 HQHIEERTDKIAPFLEYDSDPYPVIHDGRIHWIIDAYTTASRYPYSDTYYG-SEMSGINYLQNPVKVVIDSYDGSVD 617
                                       **********************************************99333.56799******************** PP

                           UPF0182 599 lYvvdeeDPiikawskiFpglfkplsempeeLrshlrYPedlFkvqsellakYHvtdpevFYnredlWevpke...e 672
                                       +Y+++ e+P+++++skiFp+lfk++++mpe+L++h+rYP d+F+vq+el+++YH+tdp +FYnred W++p+e    
  gi|298674477|ref|YP_003726227.1| 618 YYIIE-EEPVVETYSKIFPDLFKSYEQMPENLKQHIRYPVDYFEVQMELYRNYHMTDPVTFYNREDSWDIPEEqyrG 693
                                       ****9.79*****************************************************************8877 PP

                           UPF0182 673 eeqpvePyYlilklpgeekeefillspftpssrenliawlaarsdgenygklllyelpkqelvyGpeqiearinqdp 749
                                       +++++ePyY+i++lpg+++ e+ill+pftp++r+n+i+w+aarsd+ +yg+++ y++ k elvyGp+qieari+q+p
  gi|298674477|ref|YP_003726227.1| 694 TSTKMEPYYMITRLPGSDELEYILLQPFTPRERQNMISWIAARSDEPHYGEIKDYRMQKGELVYGPTQIEARIDQNP 770
                                       7778************************************************************************* PP

                           UPF0182 750 eisqqlsLw 758
                                       eis+ql+Lw
  gi|298674477|ref|YP_003726227.1| 771 EISEQLTLW 779
                                       ********* PP

>> FliS  Flagellar protein FliS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1     2e-05      0.18      20      63 ..     867     910 ..     863     919 .] 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2e-05
                                       HHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHTCC CS
                              FliS  20 mLydgalkflkrakeaieekdiekkgeaiskaqdIiseLrasLd 63 
                                        L ++al++ + a+e++++++  + ge+i+++ d++++L++ L+
  gi|298674477|ref|YP_003726227.1| 867 QLAQQALEHYETAQEHLRAGNWSAYGEEIEQMRDVLNQLSQELE 910
                                       68899***********************************9994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (919 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       947  (0.0528195); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.83u 0.36s 00:00:01.19 Elapsed: 00:00:00.52
# Mc/sec: 5319.02
//
Query:       gi|298674478|ref|YP_003726228.1|  [L=134]
Description: beta-Ig-H3/fasciclin, partial [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.4e-31  107.0   0.0    8.4e-31  106.8   0.0    1.0  1  Fasciclin  Fasciclin domain
  ------ inclusion threshold ------
      0.066   13.4   0.6       0.12   12.6   0.6    1.5  1  DUF211     Uncharacterized ArCR, COG1888
      0.073   13.1   0.0      0.098   12.7   0.0    1.2  1  Phage_SSB  Lactococcus phage single-stranded DNA binding prot


Domain annotation for each model (and alignments):
>> Fasciclin  Fasciclin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.8   0.0   1.4e-34   8.4e-31       2     128 .]      13     133 ..      12     133 .. 0.96

  Alignments for each domain:
  == domain 1  score: 106.8 bits;  conditional E-value: 1.4e-34
                                       GGHHHHHHHHTTTCCCCCTCSSSSEEEEEE-HHHHCCCHHHHHHHHHTCHHHHHHHHHTTEEESSS-HHHHHHHHEE CS
                         Fasciclin   2 dlstfvsllekaglaeeLnkkdgglTvFaPtneAfaklppellakllndkkklkeiLkyHvvpetvsssalkkaset 78 
                                        ++t+ ++le+agl++ L +k g++T+ aP ++Af+ +++++l++ll+dk++lk+iL+yH++ ++ + ++ ++  ++
  gi|298674478|ref|YP_003726228.1|  13 SFKTLLNALETAGLKDLLINK-GPFTLYAPDDDAFSTFSEKELDNLLADKEELKQILLYHITGGKAMLQDAVQL-KS 87 
                                       699***************555.9*************************************************99.9* PP

                                       EECCTTSSEEEEEEEGGTTEEEETTEEEEEEEEEEESSEEEEEESS-TSX CS
                         Fasciclin  79 latllegaklrvniekgngtvtvngkarvvrsdieatngvihvidkvLlp 128
                                       ++t l+g ++  +++  +++v vn+ a+vv+sdie+tngvih id++L p
  gi|298674478|ref|YP_003726228.1|  88 MRT-LQGGDIIAEES--GDDVNVNN-AKVVHSDIECTNGVIHSIDRLLNP 133
                                       ***.**********9..99******.*********************977 PP

>> DUF211  Uncharacterized ArCR, COG1888
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.6     2e-05      0.12      57      78 ..     109     130 ..      75     133 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2e-05
                                       -HHHHHHHHHCTT-EEEEEEEE CS
                            DUF211  57 dyeeieeaieelggvihSiDev 78 
                                       + + +++ ie ++gvihSiD++
  gi|298674478|ref|YP_003726228.1| 109 NAKVVHSDIECTNGVIHSIDRL 130
                                       23568899************86 PP

>> Phage_SSB  Lactococcus phage single-stranded DNA binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.6e-05     0.098      41      78 ..      72     110 ..      55     122 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.6e-05
                         Phage_SSB  41 vaiGsiflpdsvqlGdivtv.idrvkakekGekvyynav 78 
                                       ++ G ++l d vql  + t+  + + a+e+G+ v+ n +
  gi|298674478|ref|YP_003726228.1|  72 ITGGKAMLQDAVQLKSMRTLqGGDIIAEESGDDVNVNNA 110
                                       456899**************8899**********99864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.55
# Mc/sec: 736.93
//
Query:       gi|298674479|ref|YP_003726229.1|  [L=944]
Description: DEAD/DEAH box helicase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.2e-33  115.0   0.0    1.1e-32  113.3   0.0    1.9  1  DEAD        DEAD/DEAH box helicase
    1.8e-32  112.7   0.0    3.3e-32  111.8   0.0    1.4  1  DEAD_assoc  DEAD/H associated
    3.8e-23   82.0   0.3    7.5e-20   71.3   0.0    3.8  4  Helicase_C  Helicase conserved C-terminal domain
    1.1e-08   35.2   0.0    2.3e-08   34.2   0.0    1.5  1  ResIII      Type III restriction enzyme, res subunit
     0.0024   16.6   0.0      0.015   14.0   0.0    1.9  2  SNF2_N      SNF2 family N-terminal domain
     0.0039   17.4   0.1          4    7.7   0.0    2.7  2  DUF2551     Protein of unknown function (DUF2551)
  ------ inclusion threshold ------
       0.11   12.9   0.0        2.8    8.3   0.0    2.9  2  AAA_19      AAA domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.3   0.0   4.1e-36   1.1e-32       1     170 [.      27     196 ..      27     201 .. 0.92

  Alignments for each domain:
  == domain 1  score: 113.3 bits;  conditional E-value: 4.1e-36
                                       -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS..TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet..kgktgpkalivePtreLaeqtlnnlkkfkkyid 75 
                                       t+ Q++a+p il++++ l+ a+TGsGKT+a ++pv+++++e+  ++++g  al+++P+r+L +++l+++k +++y++
  gi|298674479|ref|YP_003726229.1|  27 TEPQEKAFPVILKDNNTLLIAPTGSGKTEASVLPVFNKILEKsdDERKGVSALYITPLRALNRDMLSRIKWWGEYLG 103
                                       577**************************************9998999***************************** PP

                                       SEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHH..HCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  76 lrvlliiggvaardqlskldngvdivvgtpgrlddll..stgklnlsqvrflVlDEadrlldqgfsdfinrilnqlp 150
                                       +rv++  g++++++ +++ +n +d++++tp+ l+ ++  ++ + nl+ v+ +++DE++++  ++++ ++   l++l 
  gi|298674479|ref|YP_003726229.1| 104 IRVMVRHGDTSKHERQKQSQNPPDMLITTPETLQAMFtgKRLRGNLEYVTHVIVDEIHEMGTSKRGSQLTLGLERLV 180
                                       ****999988888888888777*************9955333345*******************************9 PP

                                       HHCTTSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                              DEAD 151 qitcdgklqrqvivlSATlp 170
                                       +i+ + k     i lSAT+ 
  gi|298674479|ref|YP_003726229.1| 181 EISGNFK----RIGLSATVG 196
                                       8888877....9******86 PP

>> DEAD_assoc  DEAD/H associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.8   0.0   1.3e-35   3.3e-32       1     190 [.     612     784 ..     612     785 .. 0.96

  Alignments for each domain:
  == domain 1  score: 111.8 bits;  conditional E-value: 1.3e-35
                        DEAD_assoc   1 lPtdrtllvErfrdelgdwrlvvhspfGrrvnealalllaarlsrrfgidvqvaanDdgivlllpleerlpllldel 77 
                                       lP+ rt+++E+  de     ++++s+fG+  ne++a +l++ l++rfg++v+  +++++i l lp++ ++ +l++++
  gi|298674479|ref|YP_003726229.1| 612 LPDSRTVVIEEDVDED---AVIINSCFGHTTNETFAKVLTSLLAARFGSSVGQEIDPYRIKLKLPKRVSA-DLVKDM 684
                                       8***********9999...9******************************************99776666.46899* PP

                        DEAD_assoc  78 lellspdeleedleaalnaselfkrrFrevAaralllprrypgkrkplwqqrlraaqLldvareypdfpllleavre 154
                                       +  ++p+++e ++e  l+++ ++k+++ +vA+++++l+++ +         r+++++Lld+++   ++ +++e vre
  gi|298674479|ref|YP_003726229.1| 685 ILGIQPEHIEPIIEMTLKNTTVMKWKMVHVAKKFGALSKDIDY-------DRISMKKLLDIYE---ETWMYDEVVRE 751
                                       *****************************************99.......***********99...*********** PP

                        DEAD_assoc 155 vledqlDlerlaellrriaageirvvevetprpSpf 190
                                       +++d+l++++++++l+++++gei +     ++p+p+
  gi|298674479|ref|YP_003726229.1| 752 IFHDMLNVDGAKDILTKLNSGEISILV---SEPTPI 784
                                       *************************97...778886 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.015        37      28      60 ..      91     123 ..      61     135 .. 0.70
   2 !   71.3   0.0   2.9e-23   7.5e-20       8     108 ..     258     355 ..     249     357 .. 0.88
   3 ?    0.3   0.0      0.33   8.4e+02      45      72 ..     752     779 ..     704     793 .. 0.79
   4 ?   -1.4   0.0       1.2     3e+03      11      31 ..     810     830 ..     800     916 .. 0.54

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.015
                                       HHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHH CS
                        Helicase_C  28 rlekvklllekkgikvavlhgelpqnereeile 60 
                                       +l+++k+  e  gi+v v hg++++ er++  +
  gi|298674479|ref|YP_003726229.1|  91 MLSRIKWWGEYLGIRVMVRHGDTSKHERQKQSQ 123
                                       444456666666****************99765 PP

  == domain 2  score: 71.3 bits;  conditional E-value: 2.9e-23
                                       HHHHHTTTTSEEEEEESSHHHHHHHHHHHHHT...TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSST CS
                        Helicase_C   8 ellkleeeggkilifvntidrlekvklllekk...gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGid 81 
                                       ++    e+++ +lifvnt++++e+   l + +   +  + v+hg+l+ + r+e+ ++f++g+ + Li+t+ +e Gid
  gi|298674479|ref|YP_003726229.1| 258 DI---VEKHESTLIFVNTRQSAES---LASGFniiDAPISVHHGSLSFEARLEAEDSFKNGNLKGLICTSSMELGID 328
                                       34...48999**********9964...43333456899*************************************** PP

                                       STTESEEEESSSSSSHHHHHHHHTTSS CS
                        Helicase_C  82 ipkvnlVinfdlprnvtsyiqriGRtg 108
                                       i ++++Vi+++ pr+v+++ qr+GR+g
  gi|298674479|ref|YP_003726229.1| 329 IGNIDHVIQYGSPRQVSRLLQRVGRAG 355
                                       **************************8 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.33
                                       EESTTSTHHHHHHHHHHHHTTSSSEEEE CS
                        Helicase_C  45 vlhgelpqnereeileqfnkgesdvLia 72 
                                       ++h  l+ +  ++il++ n+ge+ +L++
  gi|298674479|ref|YP_003726229.1| 752 IFHDMLNVDGAKDILTKLNSGEISILVS 779
                                       6677788888899*************97 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 1.2
                                       HHTTTTSEEEEEESSHHHHHH CS
                        Helicase_C  11 kleeeggkilifvntidrlek 31 
                                       k++  ++++++f+ ++++  +
  gi|298674479|ref|YP_003726229.1| 810 KERIMNDRVILFCVNCKKWTS 830
                                       666677777777777763322 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   9.2e-12   2.3e-08      22     169 ..      38     195 ..      10     197 .. 0.78

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 9.2e-12
                                       .TTSEEEEEESTTSTHHHHH.HHHHHHH-S.........-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS- CS
                            ResIII  22 krdkrglikmaTGtGKTlva.aklierllkkgkee....kflflvprkslleqtleefkkflseaykeigkkvsgdk 93 
                                        +d++ l+ ++TG+GKT  + + +  ++l+k + e     +l + p ++l   +l+++k + +        + +gd+
  gi|298674479|ref|YP_003726229.1|  38 LKDNNTLLIAPTGSGKTEASvLPVFNKILEKSDDErkgvSALYITPLRALNRDMLSRIKWWGEYL-GIRVMVRHGDT 113
                                       4788999*************8889999999988889999****************9887766533.22333333333 PP

                                       B--.........-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T.......TTHHHHHT---SE CS
                            ResIII  94 kka..kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk.......swreilekfkeav 161
                                        k+  ++++++  ++l+tt ++l+a     + ++ +   ++   +i+DE H +g +k         ++++e   +++
  gi|298674479|ref|YP_003726229.1| 114 SKHerQKQSQNPPDMLITTPETLQAMF---TGKRLRGNLEYVTHVIVDEIHEMGTSKrgsqltlGLERLVEISGNFK 187
                                       3333344688999**************...7777777777888************86666777789998999999** PP

                                       EEEEESS- CS
                            ResIII 162 llglTATp 169
                                       ++gl+AT 
  gi|298674479|ref|YP_003726229.1| 188 RIGLSATV 195
                                       *******6 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   5.9e-06     0.015      58     199 ..      43     173 ..      20     194 .. 0.71
   2 ?   -0.2   0.1      0.13   3.3e+02     266     313 ..     888     939 ..     842     942 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.9e-06
                                       EEE---TTS--HHHHHHHHH...HHTTTS---.......S-EEEE--H.HHHHHHHHHHHHH-TTS-EEE--SSHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N  58 GiLaDemGLGKTvqvlalilaqrakeekdkekkrkdtlagptLivvPa.slldqWeneierhvsssalrvlvyggqk 133
                                        +L   +G GKT  ++  +  ++  e++d e     +  + +L + P  +l +   + i+ + +   +rv+v +g++
  gi|298674479|ref|YP_003726229.1|  43 TLLIAPTGSGKTEASVLPVF-NKILEKSDDE-----RKGVSALYITPLrALNRDMLSRIKWWGEYLGIRVMVRHGDT 113
                                       56666677777777776666.3333333332.....3467789999998889999999*****************87 PP

                                       H-----------------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--TTSHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 134 kmkkkntkvapklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlknstskaaea 199
                                           ++++ +++ ++  d +itt ++l+     +  r  l+      v++DE h ++ s++  + +
  gi|298674479|ref|YP_003726229.1| 114 ----SKHERQKQSQNPPDMLITTPETLQAMFTGKRLRGNLEY--VTHVIVDEIHEMGTSKRGSQLT 173
                                       ....334558889999************66644444444444..679**********997444333 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.13
                                       TTEE---GGGT....--S---EEEEEEEEE--HHHHHHHH............ CS
                                       xxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 266 rlmlrrakkdv....eknlPpkteeiiflklskverksYnrllevlrkkala 313
                                       +++l + kk v    ++ + p t   +  k+ + e+ +Y +++e++rk a+ 
  gi|298674479|ref|YP_003726229.1| 888 SIVLTHGKKAVialaSRGIGPDTASRVIQKMRQDEEAFYRDIMEAERKYART 939
                                       57778888888888888999999999999**************999998776 PP

>> DUF2551  Protein of unknown function (DUF2551)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0    0.0032       8.3      15      58 ..     405     448 ..     400     471 .. 0.77
   2 !    7.7   0.0    0.0016         4       7      56 ..     558     605 ..     555     607 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0032
                           DUF2551  15 evLklfleakkltveeiyeklkekfdvsykgvasmvGliasrlG 58 
                                       ++  ++l+ +++tv++i+e +++ +  +  ++  + G+++  +G
  gi|298674479|ref|YP_003726229.1| 405 QICGIVLDFGEITVDKIHEIVTRAYPFKDLKIEVLNGVVSQLIG 448
                                       5667999****************998777777666666665555 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0016
                           DUF2551   7 rDksGiRrevLklfleakkltveeiyeklkekfdvsykgvasmvGliasr 56 
                                       +D  GiR+ + + +  ++++  ++i ++l+e++++++++v  ++Gl+  +
  gi|298674479|ref|YP_003726229.1| 558 QDVGGIRERISSYI--KQDCDDSTISKNLRENYTINTNAVLNVIGLVREQ 605
                                       68889999887766..4567778999********************9866 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0011       2.8       1      62 [.      30      95 ..      30     172 .. 0.56
   2 ?    0.8   0.0      0.22   5.6e+02      41      90 ..     262     309 ..     249     358 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0011
                            AAA_19  1 qreave.alkekvllvtaGpGtGKTr..vlkhivallvelggvkp.eeillvaftgrAakelrerl 62
                                      q++a    lk+++ l++a+ G+GKT+  vl    ++l++  ++    + l +++ +   + +  r+
  gi|298674479|ref|YP_003726229.1| 30 QEKAFPvILKDNNTLLIAPTGSGKTEasVLPVFNKILEKSDDERKgVSALYITPLRALNRDMLSRI 95
                                      677776689999*************73244444455544443321244555555555455555555 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.22
                            AAA_19  41 kpeeillvaftgrAakelrerlaalgaeatTiHrlalldfddlltealel 90 
                                       k e+ l+   t+++a+ l+   + ++a+++  H+   l f+ +l+ + ++
  gi|298674479|ref|YP_003726229.1| 262 KHESTLIFVNTRQSAESLASGFNIIDAPISVHHGS--LSFEARLEAEDSF 309
                                       4588999999***********************88..8888877555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (944 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.88u 0.35s 00:00:01.23 Elapsed: 00:00:00.55
# Mc/sec: 5144.27
//
Query:       gi|298674480|ref|YP_003726230.1|  [L=276]
Description: metallophosphoesterase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.2e-09   36.6   0.9    7.9e-09   36.3   0.9    1.1  1  Metallophos    Calcineurin-like phosphoesterase
    3.6e-05   24.0   0.0    5.4e-05   23.4   0.0    1.3  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
  ------ inclusion threshold ------
      0.021   14.2   0.0      0.079   12.3   0.0    1.9  1  Metallophos_3  Metallophosphoesterase, calcineurin superfamil
       0.16   10.8   0.0       0.27   10.1   0.0    1.4  1  Epimerase_2    UDP-N-acetylglucosamine 2-epimerase


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.9   1.8e-12   7.9e-09       2     166 ..      21     206 ..      20     223 .. 0.67

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 1.8e-12
                                       EEEEEESBTB..........TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS...HHHHHHHHH.HHHHHHH. CS
                       Metallophos   2 rilvigDlHl..........algggqlddllkllddllreekpdlvllaGDlvdrg...dlekellel.laalvky. 63 
                                       ++lv++D+Hl             + q ++ l+ l+  +++ +pd ++l+GD+ +     ++++   ++ + ++++  
  gi|298674480|ref|YP_003726230.1|  21 KVLVVADIHLgiewdlyksgITIPSQTEKRLERLKGYAEQTDPDRIVLLGDVKHNVprtSWQE---KNeVPYFLDAl 94 
                                       89***************999888899999999999999999**********666553334444...22222222224 PP

                                       ..TSEEEEEC-TTS...CHHHHHHHHHHHHHHH..HHHHEHHHCEE..ETSEEEEEETTEEEEEEEESE.CEEE... CS
                       Metallophos  64 ..pipvylllGNHe...gfeeellnkygylgif..sepwrsdaevf..nnlplaslgsgslkvlllhGg.spel... 127
                                         +  v +l+GNH+       +ll+ + +++    ++   + +++f    +p ++l  +  +v+++h++ + ++   
  gi|298674480|ref|YP_003726230.1|  95 teHASVDILPGNHDsgiE---SLLHENNDIKVHssKGAVIDGVGYFhgHTWPAFELLQT-EYVVTAHNHpTVRFtds 167
                                       5578999*******5330...33333333333333222222222222255666665555.78999999963333556 PP

                                       ....THHHHHHHHHHHSCHHHHCC...HHHHHHHHHHTTCSEEEEE CS
                       Metallophos 128 ....lvsldklgslnleleapepg...dewlkdlekrekadwvivl 166
                                           + ++++++s+  ++e ++ +   ++ +++       ++v+v+
  gi|298674480|ref|YP_003726230.1| 168 lghpTIEPSWIRSEFNFDELSRYQsldYQSWNN-------PIVFVM 206
                                       677777777777777777777777777777776.......566655 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   1.2e-08   5.4e-05       2      75 ..      21     119 ..      21     171 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.2e-08
                     Metallophos_2   2 klaiiSDlH................snldaleavlealkevgvdaiihaGD.........leeeep......evlee 47 
                                       k+++++D+H                +  ++le++   ++++++d+i+++GD         +    +       +l++
  gi|298674480|ref|YP_003726230.1|  21 KVLVVADIHlgiewdlyksgitipsQTEKRLERLKGYAEQTDPDRIVLLGDvkhnvprtsW----QeknevpYFLDA 93 
                                       799*******************998888899999999999***********5555554442....044322248888 PP

                     Metallophos_2  48 llelapvlaVrGNnD.......eevveedvlreaa 75 
                                       l e a v + +GN+D                 e++
  gi|298674480|ref|YP_003726230.1|  94 LTEHASVDILPGNHDsgiesllH---------ENN 119
                                       88888**********22222220.........222 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.8e-05     0.079      19      53 ..      49      82 ..      42     140 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.8e-05
                                      GGHHHHHHHHHHH--SEEEEES-----HHHHHHHH CS
                     Metallophos_3 19 ellerlveviedkdpDllvlvGdlvkaeakadeye 53
                                       +lerl++ +e+ dpD +vl+Gd+ k +     ++
  gi|298674480|ref|YP_003726230.1| 49 KRLERLKGYAEQTDPDRIVLLGDV-KHNVPRTSWQ 82
                                      689*********************.5555445555 PP

>> Epimerase_2  UDP-N-acetylglucosamine 2-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   5.9e-05      0.27      33      78 ..      29      73 ..      15      88 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 5.9e-05
                                      T----SEEE---S--HHHHHHHHHHHHHHHHHHH--SEEEEESSSH CS
                       Epimerase_2 33 eiekpdydlnsdsqslakstgrvligleevleeekpDlvlvlGDtn 78
                                      ++  +++dl +++ ++  +t + l++l+ + e+++pD +++lGD  
  gi|298674480|ref|YP_003726230.1| 29 HL-GIEWDLYKSGITIPSQTEKRLERLKGYAEQTDPDRIVLLGDVK 73
                                      34.67888889999******************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.38s 00:00:00.97 Elapsed: 00:00:00.57
# Mc/sec: 1462.27
//
Query:       gi|298674481|ref|YP_003726231.1|  [L=653]
Description: acetate/CoA ligase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-89  300.0   0.0    2.6e-89  299.7   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    1.6e-24   86.6   0.1    4.4e-24   85.3   0.1    1.8  1  AMP-binding_C  AMP-binding enzyme C-terminal domain
    1.1e-20   73.3   3.3    1.1e-20   73.3   3.3    2.5  2  ACAS_N         Acetyl-coenzyme A synthetase N-terminus


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  299.7   0.0   4.4e-93   2.6e-89       2     422 ..      89     526 ..      88     527 .. 0.85

  Alignments for each domain:
  == domain 1  score: 299.7 bits;  conditional E-value: 4.4e-93
                                       HHHHHHSTTSEEEEE...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEE CS
                       AMP-binding   2 eeqaaktpdkvalvd...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvv 75 
                                       +++ +k+ +k+a+ +   +g+ +++TY+el e+++r+A++L++ Gv+kgd V i++p+ pe v+a+la++++Ga ++
  gi|298674481|ref|YP_003726231.1|  89 DRHINKRGEKTAILWegeKGDIRKYTYNELLEATSRFANALKNQGVEKGDIVTIYMPMIPEAVIAMLACARIGAPHS 165
                                       57889999*****99**9999*********************99********************************* PP

                                       EEETTS-HHHHHHHHHHHTESEEE.........E..TCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHC CS
                       AMP-binding  76 plnptltaeelayiledseakvli.........a..tvdsel.leklleaaakleavklvivldadellkeeelkee 140
                                       ++ ++++a++la  ++++e+k++i         +  +  +++  ++  +   k e+v++viv+ + +     e +++
  gi|298674481|ref|YP_003726231.1| 166 VVFAGFSADALADRINNAESKYVIttdgyyrrgKilE--HKNkTDEGIS---KAETVEKVIVVNHLDN----EIEIK 233
                                       ************************9988886441221..2222333333...3444555555554332....23333 PP

                                       CCCSCTTS.......-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEH.HHHHHHHHHHHHHHC.SCCTTT-EEEES CS
                       AMP-binding 141 eeseekae.......kpeeeeelkpddlayiiYTSGTTGkPKGVmlsh.rnlvanvaslkletr.fklkeddvvlsi 208
                                        + + +++         +e+e+ +++d+++++YTSGTTG PKG+++++ +++v +  ++  +   f+lkedd +++ 
  gi|298674481|ref|YP_003726231.1| 234 PGRDVWWHeiiesadSTCEPEKMDSEDMLFLMYTSGTTGSPKGIVHTTgGYMVGTHVTA--N-WvFDLKEDDIYWCS 307
                                       3333333234455667889999**************************66666665554..2.3488999******* PP

                                       S-TTSCHHHHHHHHHHHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGT CS
                       AMP-binding 209 lplahifglilelllallsGatvvllpkdaa.ldpklllelieklkvtviagvPrvlealle.sgalkaakkakdls 283
                                       +++ +i+g+++ ++++l++G+t+ ++++ ++ +d+++++e+iek+k+t+++++P++++a+++  ++     +++dls
  gi|298674481|ref|YP_003726231.1| 308 ADVGWITGHSYIVYGPLSNGSTIFMYEGAPDyPDKDRFWEMIEKHKITIFYTAPTAVRAFMKwGSEW---PEKHDLS 381
                                       *******************************8889999************************65433...4688*** PP

                                       T-SEEEEESS-EBHHHHHHHHHHHTC...EEEEEEEEGGGSSECEE.CHCTTTCTSTTS-BEE-TTEEEEEE-TTTS CS
                       AMP-binding 284 slrlvllggeplspellrffralfge...evlegYGlTEttgvvtv.lpleedkkklgsvGkplpgvevkivDeetg 356
                                       slrl+ ++gep++p+ + ++++  g    ++++++++TEt++++++ lp  ++  k+gs   p+pg+++ ++D+e g
  gi|298674481|ref|YP_003726231.1| 382 SLRLLGTVGEPINPDPWWWYYKNIGYekcPIVDTWWQTETGMILITpLPGITP-MKPGSPTNPFPGIKASVLDDE-G 456
                                       *****************888888776999***************885454444.678999**************9.9 PP

                                       CBEETTSEEEEEEEET..TS-SEBTT-HHHHHHHEEET..CCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 357 epvpdgeeGellvrgp..gvmkgYlkkpeataeafdse..grwlrTGDlgrldedGyleivgRkkdlikl 422
                                       + +++g+ G l +  p  ++ +  ++++e+   +++s+  ++ + T D +rld d y++i+gR +d+i++
  gi|298674481|ref|YP_003726231.1| 457 NKIEPGHGGYLAIERPwpSMIRTVYGDEERFINTYWSKwgPDKYMTEDAARLDNDNYFWILGRVDDVINV 526
                                       99*************9778*****************8454569*************************97 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.3   0.1   7.3e-28   4.4e-24       1      76 []     535     613 ..     535     613 .. 0.94

  Alignments for each domain:
  == domain 1  score: 85.3 bits;  conditional E-value: 7.3e-28
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE----.--..HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TT CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgs.ea..leeeLkahvrkelgpyavpkkvvfvdelpktrs 74 
                                       e+Esal shp+V eaaV G++de+kGea+ ++V+l++gs e+  l++eL++++ k +gp+a+pk +vf+d+lpktrs
  gi|298674481|ref|YP_003726231.1| 535 ELESALESHPDVVEAAVEGIKDEIKGEAVFGYVILSSGSkEDekLKQELRDKIVKDIGPIAKPKGIVFTDDLPKTRS 611
                                       89*********************************888433357********************************* PP

                                       S- CS
                     AMP-binding_C  75 GK 76 
                                       GK
  gi|298674481|ref|YP_003726231.1| 612 GK 613
                                       *9 PP

>> ACAS_N  Acetyl-coenzyme A synthetase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.3   3.3   1.9e-24   1.1e-20       3      55 .]      36      87 ..      35      87 .. 0.98
   2 ?    1.1   0.4     0.066   3.9e+02      11      33 ..     341     365 ..     332     376 .. 0.76

  Alignments for each domain:
  == domain 1  score: 73.3 bits;  conditional E-value: 1.9e-24
                                      HHHHHHHH-HHHHHHHHHCCS--SB--S-SECSTTTCT-EESTT-EE-HHHHH CS
                            ACAS_N  3 elykeSiedpeaFWaeqakeldWekpfdkvldgskgpfikWFeGGklNicyNc 55
                                      e+yk++ ++pe+FW+e a+++dW++++++vl + ++p++kWF+GGklN++yNc
  gi|298674481|ref|YP_003726231.1| 36 EVYKRAEDNPEKFWEELAEHIDWFEKWKRVLGW-EPPHAKWFVGGKLNASYNC 87
                                      79*******************************.999**************** PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.066
                                       -HHHHHHHHHCC.S-.-SB--S-SE CS
                            ACAS_N  11 dpeaFWaeqake.ld.Wekpfdkvl 33 
                                       d ++FW+ + k+ ++ +++ ++ v 
  gi|298674481|ref|YP_003726231.1| 341 DKDRFWEMIEKHkITiFYTAPTAVR 365
                                       789******9988663667777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (653 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.75u 0.37s 00:00:01.12 Elapsed: 00:00:00.55
# Mc/sec: 3584.64
//
Query:       gi|298674482|ref|YP_003726232.1|  [L=321]
Description: deoxyhypusine synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.3e-102  343.0   0.1   1.5e-102  342.8   0.1    1.0  1  DS        Deoxyhypusine synthase


Domain annotation for each model (and alignments):
>> DS  Deoxyhypusine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  342.8   0.1  8.3e-107  1.5e-102       1     287 [.      31     312 ..      31     313 .. 0.97

  Alignments for each domain:
  == domain 1  score: 342.8 bits;  conditional E-value: 8.3e-107
                                DS   1 ellesyekigfqatslgeaidilnkmrkdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDlika 77 
                                       el++  + ++f a +l+ea+di+ +m   +++t f+gl+++++++G+r+i++dl++++++dv+vtT++++ +Dl++a
  gi|298674482|ref|YP_003726232.1|  31 ELIKGISGCAFGAGRLSEAVDIYCEML-TKDTTKFFGLAGAMVPAGMRKIVVDLIRDGYIDVLVTTGANMVHDLVEA 106
                                       6899999*******************5.6789********************************************* PP

                                DS  78 lgkktylgdfelddeeLrekginRignllvpnenyckfedwvreildkleeeqkvwspselikelGkeindeeSily 154
                                       lg ++y+g+ + +d+eL++++inRi+++++p++++ +fe+ +++il++++ee    s++++++++G++++d++Sil+
  gi|298674482|ref|YP_003726232.1| 107 LGLHHYKGSAHSNDTELKNEEINRIYDVYLPENHFTEFEEKMQSILEDVSEE--PVSIRQFLTHIGNHLEDDDSILK 181
                                       **************************************************96..68********************* PP

                                DS 155 wAykndipvfcpaltDgslGdqlllfhsvkekkklkldivkDirelndialkakktgaiilGGGvpKhhilnanlm. 230
                                        A++ ++p++cpa++D+++G+q++l++   +++kl++d+++D++el di+++a+k+ga+++GGGvpK++i +++l+ 
  gi|298674482|ref|YP_003726232.1| 182 VAADMNVPIYCPAIQDSMIGLQAWLYK---QTNKLNVDAFDDMKELIDICYDAEKSGAMLIGGGVPKNYIFQSMLVt 255
                                       **************************9...7889****************************************663 PP

                                DS 231 rngadyavyittaqefdGslsgatldEavSwgkikaeaksvkvyaDaTivlPLlvaa 287
                                        +++dya+++t++++++G+lsga+ldEa+Swgk+ + a+s +v+aDaTi+lP++vaa
  gi|298674482|ref|YP_003726232.1| 256 PKELDYAIQLTMDTPETGGLSGASLDEARSWGKVGEYAQSLTVHADATITLPIIVAA 312
                                       689****************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 1839.18
//
Query:       gi|298674483|ref|YP_003726233.1|  [L=217]
Description: orotidine 5'-phosphate decarboxylase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.5e-42  145.7   0.4    1.8e-42  145.4   0.4    1.1  1  OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS famil


Domain annotation for each model (and alignments):
>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.4   0.4     1e-46   1.8e-42       2     224 ..       6     208 ..       5     209 .. 0.89

  Alignments for each domain:
  == domain 1  score: 145.4 bits;  conditional E-value: 1e-46
                                       EEEEEE-SSSHHHHHHHHHHHGGGSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHTSEEEEEEEE-S-HHHHHHHHHS CS
                         OMPdecase   2 nLclalDvatarelleladkvgpsivvlKthydlvegwgfegtgaklaalarkhgflifeDrKfaDIGntvekqata 78 
                                       +L+lalDv++++++l++a+kv ++++ +K++y+lv + g       +++ + ++ +++++D+K+aDI+nt +++++ 
  gi|298674483|ref|YP_003726233.1|   6 QLILALDVTEKNKALDVAEKVYEYVDAVKIGYPLVLKTG-----IGIIEDISSR-VPVIADFKVADIPNTNRLICE- 75 
                                       79*************************************.....9******999.8*******************9. PP

                                       TCHHHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHHSHHHHHHHHHHHHHHHTTESEE CS
                         OMPdecase  79 gsarikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqekgytqacveaarehkaedfvmGf 155
                                           + ++ad+v+vh++ G +s+ a++ +a++++ r+++++a ms++g+ ++ +     ++ e++++++ + +v G+
  gi|298674483|ref|YP_003726233.1|  76 --QVFNSGADAVIVHGFTGRDSLDACVATANEYN-RQVFVVADMSHPGATEFFQ-----QVSEKIAKMSLDTGVSGV 144
                                       ..567****************************6.**************99999.....88999999999999**** PP

                                       ECCCHTH....HHHHH.TTCSCEEEHHHTTEEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHHH CS
                         OMPdecase 156 vaqetln....ateed.addfihltpgigleqggdgkgqqyntpekligiagadiiivGRgIlkagdpveeaer 224
                                       va +t+     +++++ ++++ ++ pg+g+ qgg +         ++i+ +gad +i GR+I++++ p +ea++
  gi|298674483|ref|YP_003726233.1| 145 VAPATRTnsveNIRKIiGNELAIISPGVGA-QGGSA--------SDVIN-KGADWVITGRSIYQSDSPDTEAKK 208
                                       *****9954443333377777777777776.55554........45556.78********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1400.01
//
Query:       gi|298674484|ref|YP_003726234.1|  [L=579]
Description: oxaloacetate decarboxylase subunit alpha [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.2e-56  188.7   1.4    2.1e-55  187.6   0.8    1.9  2  PYC_OADA         Conserved carboxylase domain
    2.9e-50  171.3   0.0      4e-50  170.8   0.0    1.2  1  HMGL-like        HMGL-like
      7e-20   70.6   3.4    1.8e-19   69.3   1.8    2.2  2  Biotin_lipoyl    Biotin-requiring enzyme
    7.8e-08   32.0   0.1     0.0014   18.4   0.0    2.7  2  Biotin_lipoyl_2  Biotin-lipoyl like
      6e-07   30.1   0.2     0.0088   16.7   0.0    2.7  2  HlyD_3           HlyD family secretion protein
     0.0004   19.7   0.3       0.37   10.0   0.0    2.4  2  HlyD_D23         Barrel-sandwich domain of CusB or HlyD membr
  ------ inclusion threshold ------
      0.032   14.1   1.2      0.074   13.0   0.4    2.0  2  GCV_H            Glycine cleavage H-protein
      0.081   12.1   0.2        1.1    8.3   0.0    2.2  2  DUF561           Protein of unknown function (DUF561)
       0.23   11.4   3.7       0.72    9.8   1.0    3.0  4  RnfC_N           RnfC Barrel sandwich hybrid domain
        1.2    7.9   3.4        5.4    5.7   0.5    2.7  3  YqfD             Putative stage IV sporulation protein YqfD


Domain annotation for each model (and alignments):
>> PYC_OADA  Conserved carboxylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.6   2.8e+03     129     162 ..      67     105 ..      58     140 .. 0.58
   2 !  187.6   0.8   1.2e-58   2.1e-55       1     196 [.     291     483 ..     291     485 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.6
                                       HHHHHTTTTSS....SHHHHHHHHHSHHHH.HHHHHHHH CS
                          PYC_OADA 129 klrkeleekak....teedvlsyalypkva.ekflkfre 162
                                       +l+k++++ +       ++++ y  yp+++ ekf+++  
  gi|298674484|ref|YP_003726234.1|  67 ELKKHMHNTQAqmllRGQNLVGYRHYPDDVvEKFVTKAY 105
                                       444444443322333558888888888754155655433 PP

  == domain 2  score: 187.6 bits;  conditional E-value: 1.2e-58
                                       HHCCT--CCHHHHHHHHHHHTT-GGGHHHHHHHHHHHHHHTT----STTHHHHHHHHHHHHHHH........TS.TT CS
                          PYC_OADA   1 VykheiPGGqltnlkeqakeqglldkfeevlkeyaevnkllGdivkVTPsSkvvgdlAvfnvlnklteedvleegry 77 
                                       V+ +++PGG+l+nl +q+keq++l k+++vl+e+++v+++lG++++VTP+S++vg++Av+nv +        +e ry
  gi|298674484|ref|YP_003726234.1| 291 VLIYQVPGGMLSNLVSQLKEQNALGKYKDVLAEIPKVRAELGYPPLVTPTSQIVGTQAVLNVVM--------GE-RY 358
                                       789*************************************************************........86.** PP

                                       SS--HHHHHHHTTSS---SS---HHHHHHHHT.-----S-GGGG---.-HHHHHHHTTTTS..SSHHHHHHHHHSHH CS
                          PYC_OADA  78 kdipdsvvdllkGelGkppggfpeelvkkvlkgeepitsrpadslepedleklrkeleeka..kteedvlsyalypk 152
                                       k +p++v+d+++G +G+pp ++  e+++k++++eep+t+rpad+lep ++e+ +ke+e+    ++eedvl+y+lyp 
  gi|298674484|ref|YP_003726234.1| 359 KMVPKEVKDYVRGFYGQPPQPISSEMIAKIIENEEPFTGRPADLLEP-EYEEKKKEAEDLGlvRNEEDVLTYILYPS 434
                                       ***********************************************.***********77556************* PP

                                       HHHHHHHHHHHHHHHH..CTTTS...........-SEEEEEETTEEEE. CS
                          PYC_OADA 153 vaekflkfreeygdvsvlptkvffeglkv.....geeveveveggkyli 196
                                       +a kfl+ ++e ++++ ++t++  ++ +      ++e++v+++++ y++
  gi|298674484|ref|YP_003726234.1| 435 IAPKFLRGEAEEEQLAPVETEKPPQKSSSpdtgiPTEFKVTIDQEVYNV 483
                                       *******9998888887777666554443466669**********9985 PP

>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.8   0.0   2.3e-53     4e-50       1     263 [.       2     268 ..       2     269 .. 0.96

  Alignments for each domain:
  == domain 1  score: 170.8 bits;  conditional E-value: 2.3e-53
                                       B-EEEE-TTTHHHHTS.SS---HHHHHHHHHHHHHHT-SEE--........TSGGGT.THHHHHHHS---TT-B... CS
                         HMGL-like   1 kvkivdttLRDGeqal.kaalsveeklaiakaLdeagvdeiEv........gfpaaseddfevvraiakavkkar.. 66 
                                       +vk++dt LRD++q+l ++++++ ++l+i+++Lde+g++++E+        +++ + ed++e++r+++k++++++  
  gi|298674484|ref|YP_003726234.1|   2 RVKLTDTILRDAHQSLlATRMRTRNMLPIVDKLDEVGYHSLEMwggatfdsCIRYLNEDPWERLRELKKHMHNTQaq 78 
                                       589************99******************************************************999555 PP

                                       ........--EE-SSHHHHHHHHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-E..TT CS
                         HMGL-like  67 .......ilalvrarekdikaavealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkd..ve 134
                                              +++++++ +++++++v ++ ++g +++++f+a+++              ++++e a++ a +lg++   +
  gi|298674484|ref|YP_003726234.1|  79 mllrgqnLVGYRHYPDDVVEKFVTKAYENGIDIFRIFDAVND--------------VRNMETAINTANKLGAHvqGT 141
                                       6666778***********************************..............9****************5556 PP

                                       T-BTTTBS--HHHHHHHHHHHHHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHH CS
                         HMGL-like 135 lsledasrtdleflaevveaaeeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantla 211
                                       + ++ ++ ++ e+ +e+++++e+  ++++ i+D+ G+l+P++a eli+ +k++v+  +++s+HcH + G+A +  +a
  gi|298674484|ref|YP_003726234.1| 142 ICYTISPVHTTEKYVELAKELEQRECDSLCIKDMAGLLSPHAAEELIKSIKKKVS--LPISLHCHCTSGMAPMTYMA 216
                                       78999**************************************************..******************** PP

                                       HHHTT--EEEEBTTS--SSBBB-BHHHHHHHHHHTT-B----HHHHHHHHHH CS
                         HMGL-like 212 AveaGadrvdgtvnGlGeraGnaaleelvaalealgvdtgldlqklrsiaal 263
                                       A eaG+d++d++++  ++++  +++e +vaal+++++dtgldl+ +++ia++
  gi|298674484|ref|YP_003726234.1| 217 ACEAGVDVLDTALSPFSGGSSQPPTESMVAALQGTPYDTGLDLEAFTEIAEY 268
                                       *************************************************986 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.55   9.9e+02      29      64 ..     445     480 ..     444     483 .. 0.83
   2 !   69.3   1.8     1e-22   1.8e-19       3      73 .]     513     578 ..     511     578 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.55
                                       TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE CS
                     Biotin_lipoyl  29 agqvlaeveamKmemeieapkaGvvkeilvkeGdtv 64 
                                       +++ la ve+ K   + ++p++G+ +e +v  +++v
  gi|298674484|ref|YP_003726234.1| 445 EEEQLAPVETEKPPQKSSSPDTGIPTEFKVTIDQEV 480
                                       68999*******999999999998777777766665 PP

  == domain 2  score: 69.3 bits;  conditional E-value: 1e-22
                                       EEESSSEEEEEE.ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEEE CS
                     Biotin_lipoyl   3 iksPmiGesveegvvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllaki 73 
                                       ++s m G++       v+++vGd+V++g++++++eamKme +i+a + Gvvkei+v+eGd++++gdlla i
  gi|298674484|ref|YP_003726234.1| 513 VTSSMQGTVLS-----VHMNVGDTVNEGDPVCVIEAMKMESTITASHGGVVKEIYVSEGDAISSGDLLASI 578
                                       45556666666.....****************************************************987 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00019      0.34       5      33 ..     513     541 ..     511     548 .. 0.87
   2 !   18.4   0.0     8e-07    0.0014       4      33 ..     549     578 ..     545     578 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00019
                   Biotin_lipoyl_2   5 IaapvsGrVaqlnVkdGqrVkaGdvLael 33 
                                       ++++  G+V ++++  G+ V++Gd   ++
  gi|298674484|ref|YP_003726234.1| 513 VTSSMQGTVLSVHMNVGDTVNEGDPVCVI 541
                                       78999*******************86666 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 8e-07
                   Biotin_lipoyl_2   4 sIaapvsGrVaqlnVkdGqrVkaGdvLael 33 
                                       +I+a+  G+V++++V +G+ +  Gd+La +
  gi|298674484|ref|YP_003726234.1| 549 TITASHGGVVKEIYVSEGDAISSGDLLASI 578
                                       799999**********************87 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00037      0.66       2      31 ..     513     542 ..     512     546 .. 0.92
   2 !   16.7   0.0   4.9e-06    0.0088       1      31 [.     549     579 .]     549     579 .] 0.97

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00037
                            HlyD_3   2 lrApvdGvvvelnveegevvqagdelleii 31 
                                       ++++ +G+v +++ ++g+ v++gd++  i 
  gi|298674484|ref|YP_003726234.1| 513 VTSSMQGTVLSVHMNVGDTVNEGDPVCVIE 542
                                       899***********************9885 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 4.9e-06
                            HlyD_3   1 tlrApvdGvvvelnveegevvqagdelleii 31 
                                       t++A+ +Gvv+e+ v+eg+ +++gd l++i+
  gi|298674484|ref|YP_003726234.1| 549 TITASHGGVVKEIYVSEGDAISSGDLLASIV 579
                                       79***************************96 PP

>> HlyD_D23  Barrel-sandwich domain of CusB or HlyD membrane-fusion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.1   0.00087       1.6     111     141 ..     513     543 ..     506     546 .. 0.66
   2 !   10.0   0.0   0.00021      0.37     106     139 ..     545     578 ..     542     579 .] 0.81

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00087
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          HlyD_D23 111 vkapisGvVteknvreGqyvqpgdtlftiad 141
                                       v+++++G+V++ +++ G++v++gd++  i  
  gi|298674484|ref|YP_003726234.1| 513 VTSSMQGTVLSVHMNVGDTVNEGDPVCVIEA 543
                                       5666777777777777777777776666654 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00021
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          HlyD_D23 106 qktvtvkapisGvVteknvreGqyvqpgdtlfti 139
                                       + + t++a+  GvV e  v eG+ ++ gd l++i
  gi|298674484|ref|YP_003726234.1| 545 KMESTITASHGGVVKEIYVSEGDAISSGDLLASI 578
                                       5567889999999999999999999999988877 PP

>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.8     5e+03      30      42 ..     477     489 ..     416     502 .. 0.66
   2 ?   13.0   0.4   4.1e-05     0.074      28      74 ..     516     561 ..     511     566 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.8
                                       H-SEEEEE---TT CS
                             GCV_H  30 lgdvvfvelpevg 42 
                                         +v++v++ +vg
  gi|298674484|ref|YP_003726234.1| 477 DQEVYNVKVEPVG 489
                                       3334444444444 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 4.1e-05
                                       HHH-SEEEEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEEE CS
                             GCV_H  28 eelgdvvfvelpevgtkvkkgeslaavEsvKaasevyapvsGevvev 74 
                                       ++ g v++v++ +vg++v++g+++ ++E+ K+ s++ a   G v e+
  gi|298674484|ref|YP_003726234.1| 516 SMQGTVLSVHM-NVGDTVNEGDPVCVIEAMKMESTITASHGGVVKEI 561
                                       56678888876.69*************************99999886 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0       0.1   1.9e+02     119     148 ..     140     169 ..     120     174 .. 0.84
   2 ?    8.3   0.0   0.00063       1.1      48      86 ..     183     226 ..     171     228 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.1
                            DUF561 119 tdlsvtiPyiLkleeqvkLakkLeslgvdl 148
                                        +++ ti  + + e+ v+Lak+Le+ + d 
  gi|298674484|ref|YP_003726234.1| 140 GTICYTISPVHTTEKYVELAKELEQRECDS 169
                                       4799********************988775 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00063
                            DUF561  48 adpklvkkvksvsniPi.....CvsaveakllleavkaGadlve 86 
                                       a+++l+k++k+ +++Pi     C s++ + + + a  aG+d+++
  gi|298674484|ref|YP_003726234.1| 183 AAEELIKSIKKKVSLPIslhchCTSGMAPMTYMAACEAGVDVLD 226
                                       7889************9999999******************986 PP

>> RnfC_N  RnfC Barrel sandwich hybrid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.81   1.5e+03      30      51 ..     336     357 ..     320     360 .. 0.85
   2 ?   -2.4   0.0       2.7   4.8e+03      72      88 ..     487     503 ..     476     513 .. 0.80
   3 ?    9.8   1.0    0.0004      0.72      39      81 ..     519     562 ..     496     571 .. 0.86
   4 ?    2.7   0.1     0.068   1.2e+02      36      60 ..     553     577 ..     548     578 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.81
                            RnfC_N  30 lvlplsqhiGapakplvkvgdk 51 
                                       lv p sq +G++a + v  g++
  gi|298674484|ref|YP_003726234.1| 336 LVTPTSQIVGTQAVLNVVMGER 357
                                       899**********999998886 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.7
                            RnfC_N  72 svsGtVkaiekrlvahg 88 
                                       +v G V+++++  ++h+
  gi|298674484|ref|YP_003726234.1| 487 PVGGSVVSVTEEDTSHT 503
                                       89999999999888775 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0004
                            RnfC_N  39 GapakplvkvgdkVlkGqkiaeaeg.fvsapvhasvsGtVkaie 81 
                                       G+  ++ ++vgd+V++G+ +   e+  + + + as  G Vk+i 
  gi|298674484|ref|YP_003726234.1| 519 GTVLSVHMNVGDTVNEGDPVCVIEAmKMESTITASHGGVVKEIY 562
                                       666677889***********999886679************995 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.068
                            RnfC_N  36 qhiGapakplvkvgdkVlkGqkiae 60 
                                        h G   ++ v++gd +  G+++a+
  gi|298674484|ref|YP_003726234.1| 553 SHGGVVKEIYVSEGDAISSGDLLAS 577
                                       68999999************99985 PP

>> YqfD  Putative stage IV sporulation protein YqfD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.092   1.6e+02      16      62 ..      97     143 ..      94     147 .. 0.87
   2 ?    0.5   0.1      0.12   2.1e+02     166     212 ..     492     537 ..     479     540 .. 0.82
   3 ?    5.7   0.5     0.003       5.4     177     205 ..     540     568 ..     513     576 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.092
                              YqfD  16 perflnllarrgIelwdikrkkdgeleakislkdfkklrkiarktgc 62 
                                       +e+f+ +++++gI+++ i    ++   +++ ++  +kl   ++ t c
  gi|298674484|ref|YP_003726234.1|  97 VEKFVTKAYENGIDIFRIFDAVNDVRNMETAINTANKLGAHVQGTIC 143
                                       79**************9999888888999999999999888887776 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.12
                              YqfD 166 ivevvekeeppeieekdepcnivAkkdGvItkvivesGeplvkegdt 212
                                       +v v+e ++  +++ ++  + + ++++G++ +v +  G   v+egd 
  gi|298674484|ref|YP_003726234.1| 492 VVSVTEEDTSHTPDPENVEGAVTSSMQGTVLSVHMNVGDT-VNEGDP 537
                                       578899998889999999999**********999999975.566665 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.003
                              YqfD 177 eieekdepcnivAkkdGvItkvivesGep 205
                                        ie  +  + i A+  Gv+++++v++G +
  gi|298674484|ref|YP_003726234.1| 540 VIEAMKMESTITASHGGVVKEIYVSEGDA 568
                                       5556666789****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (579 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.66u 0.35s 00:00:01.01 Elapsed: 00:00:00.51
# Mc/sec: 3399.98
//
Query:       gi|298674485|ref|YP_003726235.1|  [L=493]
Description: acetyl-CoA carboxylase biotin carboxylase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-77  259.9   0.2    2.3e-77  259.3   0.2    1.3  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    1.9e-48  163.6   0.0    9.8e-48  161.3   0.0    2.3  1  Biotin_carb_N    Biotin carboxylase, N-terminal domain
    4.7e-44  148.9   0.0    1.2e-43  147.6   0.0    1.8  1  Biotin_carb_C    Biotin carboxylase C-terminal domain
    7.8e-14   51.7   1.2    1.5e-13   50.8   0.2    1.9  2  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    2.1e-07   31.1   0.2    3.9e-07   30.3   0.2    1.5  1  ATP-grasp_3      ATP-grasp domain
    2.2e-07   30.6   0.1    4.4e-07   29.6   0.1    1.4  1  ATP-grasp        ATP-grasp domain
      3e-07   30.2   0.4    2.7e-06   27.1   0.4    2.2  1  RimK             RimK-like ATP-grasp domain
    0.00021   20.9   0.2    0.00039   20.1   0.2    1.5  1  ATP-grasp_4      ATP-grasp domain
    0.00037   20.3   0.1    0.00073   19.4   0.1    1.6  1  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
     0.0046   16.7   0.0     0.0093   15.7   0.0    1.5  1  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
  ------ inclusion threshold ------
      0.054   13.7   0.1      0.097   12.9   0.1    1.4  1  Archease         Archease protein family (MTH1598/TM1083)
       0.12   11.8   0.3       0.23   10.9   0.0    1.6  2  ATP-grasp_5      ATP-grasp domain


Domain annotation for each model (and alignments):
>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  259.3   0.2   1.5e-80   2.3e-77       2     209 ..     116     321 ..     115     323 .. 0.99

  Alignments for each domain:
  == domain 1  score: 259.3 bits;  conditional E-value: 1.5e-80
                                       HHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2   2 kesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaaf 78 
                                       k sa++++ +++vpvvp+++ p+e++++a++ia++ig+Pviika++g+GG Gm++++++e++++++++ ++ a++af
  gi|298674485|ref|YP_003726235.1| 116 KISARNIMIDAGVPVVPGTEEPIEDVNTAIDIAESIGFPVIIKASAGGGGIGMKIVHSREDFEKALNSIQSIASSAF 192
                                       7899************************************************************************* PP

                                       STS-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCECTCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-E CS
                       CPSase_L_D2  79 gnkqvlvekslkgpkeiEvevlrDakgnvitvcerenslqlrtqkvievAPsqtLtdeerqalreaavkvvrevgvv 155
                                       g+++v++ek++++p++iE+++l+D++gn+i++ +re+s+q+r+qk+ie+APs+ +t+e r++++eaavk+++++g++
  gi|298674485|ref|YP_003726235.1| 193 GDSTVFIEKYVEEPRHIEIQILSDKYGNTIYISDRECSIQRRHQKLIEEAPSPIMTPELRKEMGEAAVKAAKAIGYE 269
                                       ***************************************************************************** PP

                                       EEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GC CS
                       CPSase_L_D2 156 gagtveflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLe 209
                                       +agtvefl++  ++e+y++EvNtRl+ve++++e++ G+d+vk ++ ia gekL+
  gi|298674485|ref|YP_003726235.1| 270 NAGTVEFLYS--KGEFYFLEVNTRLQVEHTITEMINGIDIVKDQLYIACGEKLP 321
                                       **********..5***************************************97 PP

>> Biotin_carb_N  Biotin carboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.3   0.0   6.6e-51   9.8e-48       1     110 []       1     110 [.       1     110 [. 0.99

  Alignments for each domain:
  == domain 1  score: 161.3 bits;  conditional E-value: 6.6e-51
                                       ---EEEE---HHHHHHHHHHHHHTT-EEEEEEEGGGTTSHHHHHSSEEEEEESSTTCCGGG-HHHHHHHHHHTT-SE CS
                     Biotin_carb_N   1 kikkvlianrGeiAvriiravrelgietvavyseedanslhvreadeavelgpasasesYlniekivkaakesgada 77 
                                       ++kk+l+anrGeiA+ri+ra+rel+i tvavyse+d+n+l++++ade++ +gpa++s+sYl+i+ki+++a+esgad 
  gi|298674485|ref|YP_003726235.1|   1 MFKKILVANRGEIAIRIMRACRELDIPTVAVYSEADKNALFAKYADESYPIGPAPSSKSYLDINKILDVAEESGADG 77 
                                       79*************************************************************************** PP

                                       EE--SSTTTT-HHHHHHHHHTT-EESSS-HHHH CS
                     Biotin_carb_N  78 vhpGyGflsEnaefaeaveeagivfiGPsaeal 110
                                       +hpGyGflsEn+efa+++e++gi+fiGPs++++
  gi|298674485|ref|YP_003726235.1|  78 IHPGYGFLSENPEFARECEKRGITFIGPSSDVI 110
                                       *****************************9986 PP

>> Biotin_carb_C  Biotin carboxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.6   0.0   8.2e-47   1.2e-43       1     107 [.     335     441 ..     335     442 .. 0.99

  Alignments for each domain:
  == domain 1  score: 147.6 bits;  conditional E-value: 8.2e-47
                                       EEEEESEETTTTTEE--CE-SEEE---STTEEEEE---TT-EE-TTS-SEEEEEEEEESSHHHHHHHHHHHHHT-EE CS
                     Biotin_carb_C   1 eaRinaEdpeknflpssGkvtelelpegpgvRvdsgveegsevspyyDsllaKlivhgetreealarlrraLaelri 77 
                                       e+RinaEdp ++f+ps+Gk+++++  +gpgvRvdsgv+ g+++spyyDs+++Kl+v+g++r+ea++r++raL e+++
  gi|298674485|ref|YP_003726235.1| 335 ECRINAEDPLNDFAPSPGKIRRYRSAGGPGVRVDSGVHMGYTISPYYDSMISKLCVWGKNRDEAINRMKRALFEYVV 411
                                       8**************************************************************************** PP

                                       ESS-BSHHHHHHHHH-HHHHHT---TTTCC CS
                     Biotin_carb_C  78 eGvktnieflrailedeefakgeldtkfle 107
                                        Gv+tni+f++aile+++f++gel+t+f++
  gi|298674485|ref|YP_003726235.1| 412 VGVTTNIPFHKAILENDAFRRGELTTHFID 441
                                       *****************************8 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.2   9.9e-17   1.5e-13      27     174 ..     143     290 ..     123     292 .. 0.79
   2 ?   -2.2   0.1       1.6   2.5e+03      89     142 ..     423     478 ..     397     487 .. 0.60

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 9.9e-17
                                       HHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT......-SCEEEEE--.ESEEEEEEEEETSSC CS
                   Dala_Dala_lig_C  27 llekveeelgypvfVKpareGSSvGvskveseeelkeaieeafky......dekvlvEeai.egreievavlgnekl 96 
                                       +  ++ e++g+pv++K++  G  +G++ v+s+e++++a+++  +       d++v++E+++ e r ie+ +l +   
  gi|298674485|ref|YP_003726235.1| 143 TAIDIAESIGFPVIIKASAGGGGIGMKIVHSREDFEKALNSIQSIassafgDSTVFIEKYVeEPRHIEIQILSDKYG 219
                                       4557999******************************988644322223349*********999*********6555 PP

                                       EEEEEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEE CS
                   Dala_Dala_lig_C  97 evsevgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvN 173
                                       ++  + ++    ++ + ++k ++++        +++e ++++ e+a+ka ka++ +  + v f+++ +ge+++ EvN
  gi|298674485|ref|YP_003726235.1| 220 NTIYISDREC--SIQRRHQKLIEEA-P---SPIMTPELRKEMGEAAVKAAKAIGYENAGTVEFLYS-KGEFYFLEVN 289
                                       5544444333..5566677776332.2...22357899999*********************9997.9********* PP

                                       S CS
                   Dala_Dala_lig_C 174 t 174
                                       t
  gi|298674485|ref|YP_003726235.1| 290 T 290
                                       9 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.6
                                       EEEETSSCEEEEEEEEE-SS.SSS-HHHHHC..TT-EEESS----HHHHHHHHHHH CS
                   Dala_Dala_lig_C  89 avlgneklevsevgeivvkk.gfydyeakysd.dkaqlevpaklekeveekiqela 142
                                       a+l+n++++  e+  +  ++ ++ +  +k +d ++ + +  a+  +++++k+ ++ 
  gi|298674485|ref|YP_003726235.1| 423 AILENDAFRRGELTTHFIDThDILEDVEKIVDkEAKRNMTLASALDNQNQKVAAVT 478
                                       67777777777666655444366666677766333333333444455555555443 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.2   2.6e-10   3.9e-07      21     159 ..     142     293 ..     114     295 .. 0.87

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 2.6e-10
                                       ...-EESS--SSSEEEEESS-------B--SS--TTE...................EEEE---.SEEEEEEEEE.SS CS
                       ATP-grasp_3  21 kleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve............lvqefie.GkplSvsllsdge 84 
                                       ++  + +e+   ++++K + G+gg ++ +v+ +e+ e+a+++++             + +++e  +++ +++lsd+ 
  gi|298674485|ref|YP_003726235.1| 142 NTAIDIAESIGFPVIIKASAGGGGIGMKIVHSREDFEKALNSIQsiassafgdstvFIEKYVEePRHIEIQILSDKY 218
                                       4556667777889***************************9999999********98889996369********999 PP

                                       SEEEEEEEEEEEET....TEEEEEEES----H.HHHHHHHHHHHHTTSTT--EEEEEEEEESS.SEEEEEEESS-- CS
                       ATP-grasp_3  85 kvlvlavnrqliekaekefvyaGnvtpietel.keevvelaeevvekleglaGyvGvDlvlkdeepyviEvNPRlt 159
                                        + +    r+   +++++       +pi t + ++e+ e+a ++ +++ g      v+++++++e y++EvN Rl+
  gi|298674485|ref|YP_003726235.1| 219 GNTIYISDRECSIQRRHQKLIEEAPSPIMTPElRKEMGEAAVKAAKAI-GYENAGTVEFLYSKGEFYFLEVNTRLQ 293
                                       998888888888777888888999999999877***************.9999999******************97 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.1     3e-10   4.4e-07      14     159 ..     138     291 ..     126     294 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 3e-10
                                       ECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC........GTTCEEEEE----SEEEEEEE CS
                         ATP-grasp  14 veskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal........keekvivEefvpfekElsvlv 82 
                                       +e+ + + ++ae++g+pv++K +  g  G G ++v+s+ed e+al+ +        ++ +v +E++v+  + + + +
  gi|298674485|ref|YP_003726235.1| 138 IEDVNTAIDIAESIGFPVIIK-ASAGGGGIGMKIVHSREDFEKALNSIqsiassafGDSTVFIEKYVEEPRHIEIQI 213
                                       7888899999***********.677779*****************9999999*9999*****************99* PP

                                       EEETTC-EEE-.-EEEEEEETTEEEEEEECEE.-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEEEEE CS
                         ATP-grasp  83 vrsaeGetafy.pvvetvqedgilrlsvapae.vsekaqkkaeeiakkiveeLggvGvfavElFvledgellvnEla 157
                                         ++ G+t  + +    +q++    +  ap++ ++ +  k+  e a k+++++g+    +vE+ +  +ge ++ E+ 
  gi|298674485|ref|YP_003726235.1| 214 LSDKYGNTIYIsDRECSIQRRHQKLIEEAPSPiMTPELRKEMGEAAVKAAKAIGYENAGTVEFLYS-KGEFYFLEVN 289
                                       ******9665515555677766666666666615667899999*******************8777.8999999988 PP

                                       SS CS
                         ATP-grasp 158 pR 159
                                        R
  gi|298674485|ref|YP_003726235.1| 290 TR 291
                                       77 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.4   1.8e-09   2.7e-06      28     182 ..     139     309 ..     116     314 .. 0.73

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1.8e-09
                                       S-HHHHHHTT-..-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH.........GGG--EEEEE--SS-SEEEEEEE CS
                              RimK  28 edaekliekik.lrfPvvvKsvegsqGikvvlakkeqklkqvlea.........lkeailvqeyieeaenediRvlv 94 
                                       ed++  i+  + ++fPv++K + g  Gi++ + + +++ ++ l++          + ++++ +y+ee    +i +l 
  gi|298674485|ref|YP_003726235.1| 139 EDVNTAIDIAEsIGFPVIIKASAGGGGIGMKIVHSREDFEKALNSiqsiassafGDSTVFIEKYVEEPRHIEIQIL- 214
                                       55556666655679***********999999998888888887775544444444445599999998877666665. PP

                                       ETTEEEEEEEEE--SSS----TTT..T-EEEE-...---HHHHHHHHHHHHHCT-SEEE.EEEEEETTEEEEEEEES CS
                              RimK  95 vddevvaalrrvskeGdFRsnlhr..Ggvaekl...qlseeekelAikaakamelvvaG.vDllrakrgllvlEvns 165
                                         d+   ++    +e       ++    + +++   +l +e  e A+kaaka++   aG v+ l +k ++++lEvn+
  gi|298674485|ref|YP_003726235.1| 215 -SDKYGNTIYISDRECSIQRRHQKliEEAPSPImtpELRKEMGEAAVKAAKAIGYENAGtVEFLYSKGEFYFLEVNT 290
                                       .77777777777777766444333112333333223688888999*************9678*************** PP

                                       S--SHH..HHHHHT--HHH CS
                              RimK 166 spglek..iektlgidiak 182
                                         ++e+   e+  gidi k
  gi|298674485|ref|YP_003726235.1| 291 RLQVEHtiTEMINGIDIVK 309
                                       9998762258888999866 PP

>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.2   2.6e-07   0.00039       1     150 [.     151     290 ..     151     300 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.6e-07
                       ATP-grasp_4   1 islPvviKPsvgffSlGVykinneeewkaavaaieeeleqakeeykeevveeesflvEeyieG.eEfavdayfdeeG 76 
                                       i +Pv+iK s g + +G+ +++++e++++a+++i++    a++     +  ++++ +E+y+e    + + ++ d+ G
  gi|298674485|ref|YP_003726235.1| 151 IGFPVIIKASAGGGGIGMKIVHSREDFEKALNSIQSI---ASS-----AFGDSTVFIEKYVEEpRHIEIQILSDKYG 219
                                       579********************************66...333.....44566778999997525678888998888 PP

                       ATP-grasp_4  77 epvilnilkkefaseedvsdrlyvtsakvie.etlealeellkevnallglknfpvHiElrvsedgkiipiEvnp 150
                                       +++   i ++e + ++  ++ +   ++ +++ e  +++ e+  ++++++g +n  + +E+  s+ g+ + +Evn 
  gi|298674485|ref|YP_003726235.1| 220 NTIY--ISDRECSIQRRHQKLIEEAPSPIMTpELRKEMGEAAVKAAKAIGYENAGT-VEFLYSK-GEFYFLEVNT 290
                                       8754..55666666666666776666665542666777777777777888777654.7777664.6777777776 PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   4.9e-07   0.00073       1      91 [.     114     205 ..     114     279 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 4.9e-07
                                       HBHHHHHHHHHHTT--B-..-EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHH...HHHHHHHHCT CS
                            GARS_A   1 asKsfakdllkkagipta..eyeaftdpeeakeyieeatakalVvKadglaagKgvivakseee...alkavkeile 72 
                                       +sK  a++++ +ag+p    + e ++d+++a ++ e+ ++++ ++Ka+   +g g+++++s+e+   al+ +++i  
  gi|298674485|ref|YP_003726235.1| 114 GSKISARNIMIDAGVPVVpgTEEPIEDVNTAIDIAESIGFPV-IIKASAGGGGIGMKIVHSREDfekALNSIQSIA- 188
                                       589999**********975677889*****************.****************77665111555566555. PP

                                       S-TTCCCCSSEEEEE---S CS
                            GARS_A  73 kkkfGeagekvviEelleG 91 
                                       + +fG   ++v iE+++e 
  gi|298674485|ref|YP_003726235.1| 189 SSAFG--DSTVFIEKYVEE 205
                                       58999..889*****9974 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   6.2e-06    0.0093      42     114 ..     248     320 ..     209     336 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.2e-06
                      ATPgrasp_Ter  42 elekdeelielaerlaeefgldglvnvQvrededgpkLLEiNpRasGGlgys.alaGvnlpylalklllglete 114
                                       + e ++e+ e+a + a+++g +    v + + +++ + LE+N+R +    ++ +  G+++++  l  + g++  
  gi|298674485|ref|YP_003726235.1| 248 TPELRKEMGEAAVKAAKAIGYENAGTVEFLYSKGEFYFLEVNTRLQVEHTITeMINGIDIVKDQLYIACGEK-L 320
                                       556788999************************************988777624569999999988888843.2 PP

>> Archease  Archease protein family (MTH1598/TM1083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   6.5e-05     0.097      12      94 ..     388     477 ..     386     493 .] 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.5e-05
                                       EEEE-SSSHHHHHHHHHHHHHHHS-.-TT---S-EEEEEEEESSSHHHHHHHHHHHHHHHHHT--S----EE..... CS
                          Archease  12 ieawGksleeafesaalalfeymtd.lskvepkeekeieveaedledlLfdfLdellylfdteyfvfkevkv..... 82 
                                       + +wGk+ +ea+ ++ +alfey++  + +  p ++  +e +a  + +l  +f+d   +l d+e++v ke+k      
  gi|298674485|ref|YP_003726235.1| 388 LCVWGKNRDEAINRMKRALFEYVVVgVTTNIPFHKAILENDAFRRGELTTHFIDTHDILEDVEKIVDKEAKRnmtla 464
                                       569********************554677777777899****************************99998766665 PP

                                       ...EE.E-SSSEEEE CS
                          Archease  83 ...deeeeeeelele 94 
                                          d  ++++++ + 
  gi|298674485|ref|YP_003726235.1| 465 salD--NQNQKVAAV 477
                                       4431..333333333 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00015      0.23      13      54 ..     117     160 ..     111     205 .. 0.87
   2 ?   -4.2   0.1       6.2   9.2e+03      36      48 ..     257     269 ..     253     271 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00015
                       ATP-grasp_5  13 aeakelleaygipvvetrl..assaeeaveaaeeigypvvlKiv 54 
                                         a++++ + g+pvv+     +++++ a+++ae+ig+pv +K  
  gi|298674485|ref|YP_003726235.1| 117 ISARNIMIDAGVPVVPGTEepIEDVNTAIDIAESIGFPVIIKAS 160
                                       56899999*******987667*********************86 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 6.2
                       ATP-grasp_5  36 eeaveaaeeigyp 48 
                                       e+av+aa++igy 
  gi|298674485|ref|YP_003726235.1| 257 EAAVKAAKAIGYE 269
                                       6899*****9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 3083.07
//
Query:       gi|298674486|ref|YP_003726236.1|  [L=325]
Description: biotin--acetyl-CoA-carboxylase ligase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-17   63.5   0.0    7.3e-17   61.5   0.0    1.9  2  BPL_LplA_LipB    Biotin/lipoate A/B protein ligase family
      3e-17   62.3   0.1    6.2e-17   61.3   0.1    1.6  1  HTH_11           HTH domain
    6.2e-08   32.4   0.0    1.2e-07   31.5   0.0    1.5  1  BPL_LplA_LipB_2  Biotin/lipoate A/B protein ligase family
    1.3e-07   31.4   0.0    2.6e-07   30.4   0.0    1.5  1  BPL_C            Biotin protein ligase C terminal domain
    5.1e-07   29.1   0.0    9.5e-07   28.3   0.0    1.5  1  HTH_24           Winged helix-turn-helix DNA-binding
     0.0037   17.3   0.1       0.43   10.6   0.0    2.6  2  Put_DNA-bind_N   Putative DNA-binding protein N-terminus
     0.0053   17.1   0.0       0.01   16.2   0.0    1.4  1  Rrf2             Transcriptional regulator
  ------ inclusion threshold ------
      0.013   15.7   0.0      0.028   14.6   0.0    1.6  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
      0.035   14.0   0.0      0.071   13.0   0.0    1.4  1  TrmB             Sugar-specific transcriptional regulator Trm
      0.036   14.0   0.0      0.076   13.0   0.0    1.5  1  HTH_Crp_2        Crp-like helix-turn-helix domain
      0.063   13.0   0.0       0.15   11.8   0.0    1.6  1  HTH_39           Helix-turn-helix domain
      0.073   13.0   0.0       0.14   12.1   0.0    1.4  1  MarR             MarR family
      0.094   12.5   0.0        0.2   11.5   0.0    1.5  1  HTH_10           HTH DNA binding domain


Domain annotation for each model (and alignments):
>> BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.1   1.6e+03      67      83 ..      28      51 ..       9      74 .. 0.64
   2 !   61.5   0.0   5.3e-20   7.3e-17       9     131 .]      93     210 ..      86     210 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.1
                                      H...HHHHHHHHHHHH........ CS
                     BPL_LplA_LipB 67 y...vsllvlavlealg...y.rd 83
                                           +++v++++++l+   y ++
  gi|298674486|ref|YP_003726236.1| 28 QlgiSRTMVWKYIKSLKddgYnIT 51
                                      335578899999999976653422 PP

  == domain 2  score: 61.5 bits;  conditional E-value: 5.3e-20
                                       HHHHH..GCGGG--TT-EEEEEEESS-B....-B--B-TTSEEEEEEEEESS...-CCGTHHHHHHHHHHHHHHH.. CS
                     BPL_LplA_LipB   9 ntllkeslnsselesgglvvvrrqtgGr....nvwhspkgeltyslllspeqktfqnrvlelyvsllvlavlealgy 81 
                                       +t+ + ++   + + g++ + ++q +Gr    + w sp g++++s++l+p+   ++ + + +++++  +av++a+  
  gi|298674486|ref|YP_003726236.1|  93 STNEEAKRLAPDEDEGTVIISETQKSGRgrmgRDWTSPRGGIYMSVILKPT---IPASHAYHLTLVAGIAVANAI-- 164
                                       455566677777788999999****************************55...699999999************.. PP

                                       ....HHTT-TTEEEETTTEEEETTEEEEEEEEEEEE.TTS-EEEEEEEEEE CS
                     BPL_LplA_LipB  82 rdskpgiegipvfikwpnDlyvngrKlaGiavtstr.gktlhhivigvgvn 131
                                            ++ gi++ ikwpnD+++n+rK+ Gi+++ +  ++++ +iv+g+g+n
  gi|298674486|ref|YP_003726236.1| 165 -----RNLGINACIKWPNDILINNRKVCGILTEINAeIEKIDYIVLGMGIN 210
                                       .....99*****************************99***********99 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.3   0.1   4.5e-20   6.2e-17       1      55 []       4      59 ..       4      59 .. 0.98

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 4.5e-20
                            HTH_11  1 RllqilelLleargp.isgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepgrGYr 55
                                      R+++il +L++++++ +sgeeL e+L++Sr+ v+++Ik+L++ g+ I+s+ + GY+
  gi|298674486|ref|YP_003726236.1|  4 RKEDILNILKNSDQKpVSGEELGEQLGISRTMVWKYIKSLKDDGYNITSSTKTGYI 59
                                      899****************************************************6 PP

>> BPL_LplA_LipB_2  Biotin/lipoate A/B protein ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   8.5e-11   1.2e-07      42     181 ..     134     270 ..      89     271 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 8.5e-11
                   BPL_LplA_LipB_2  42 leaAlvlaPevplakAaamlpvlmvalqdAlgalaPPevavhlewpgtilvngarvGgvrlaaseadeeevPdwlvv 118
                                       + ++++l+P+ p ++A ++  v+++a+++A++ l+       ++wp++il+n+ +v g+  ++  ++e e+ d++v+
  gi|298674486|ref|YP_003726236.1| 134 IYMSVILKPTIPASHAYHLTLVAGIAVANAIRNLGI---NACIKWPNDILINNRKVCGILTEI--NAEIEKIDYIVL 205
                                       6789******************************95...77899******9877665554444..4567778***** PP

                   BPL_LplA_LipB_2 119 glelalekese..epGetpdetaLeeEGcaeveavalleslarhllawinrweedGfrpvhaewl 181
                                       g+ ++++ ++   +   +  +t+L++E  + ve+v+ ++ l   + +   +++++ f+ + +ew 
  gi|298674486|ref|YP_003726236.1| 206 GMGINANVDTGmfSSELKEGSTSLKSELGKPVERVSFVQNLLYEFEQEYIKFKSKPFNDIVDEWI 270
                                       *******99996667777778***************99999988888888899999999888885 PP

>> BPL_C  Biotin protein ligase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   1.9e-10   2.6e-07       1      45 [.     275     319 ..     275     321 .. 0.96

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 1.9e-10
                                       STTSEEEEEETSCEEEEEEEEE-TTSEEEEEETTE.EEEESSCCE CS
                             BPL_C   1 hsGqeVtlededgkveGiavGIdddGaLllktddglqpdinsGdi 45 
                                       ++G+eV + ++ + veG+a G++  GaL++k ddg+ + i +G +
  gi|298674486|ref|YP_003726236.1| 275 TIGKEVSIMTPSKMVEGKAIGVTKNGALIVKKDDGEKEEIIAGRC 319
                                       69****************************************988 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   6.9e-10   9.5e-07       2      46 ..       2      48 ..       1      48 [. 0.92

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 6.9e-10
                            HTH_24  2 detdrkILelLqk.npr.isqreLAerlglSpstvnrrlkrLeeeGl 46
                                      ++ + +IL++L+  + +  s  eL e+lg+S++ v++++k L+++G+
  gi|298674486|ref|YP_003726236.1|  2 SDRKEDILNILKNsDQKpVSGEELGEQLGISRTMVWKYIKSLKDDGY 48
                                      677889********6666****************************8 PP

>> Put_DNA-bind_N  Putative DNA-binding protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00031      0.43      16      44 ..       8      36 ..       6      38 .. 0.90
   2 ?    4.4   0.0     0.028        39      15      32 ..      38      55 ..      37      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00031
                                      HHHHHHHTT--EE-HHHHHHHCTS-HHHH CS
                    Put_DNA-bind_N 16 yLeelkeegveriSSteLaealgvtaaqv 44
                                      +L+ lk+++++ +S +eL+e+lg++ + v
  gi|298674486|ref|YP_003726236.1|  8 ILNILKNSDQKPVSGEELGEQLGISRTMV 36
                                      6899********************98877 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.028
                                      HHHHHHHHTT--EE-HHH CS
                    Put_DNA-bind_N 15 ryLeelkeegveriSSte 32
                                      +y+++lk++g +++SSt+
  gi|298674486|ref|YP_003726236.1| 38 KYIKSLKDDGYNITSSTK 55
                                      699*************97 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   7.3e-06      0.01      17      72 ..      11      65 ..       7      74 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.3e-06
                                      HHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEEESSHCC CS
                              Rrf2 17 LakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyrLakppe 72
                                      + k+++++pvs ee+ e+ +is++++ k ++ L+  g+  +    + Gy L+ +p+
  gi|298674486|ref|YP_003726236.1| 11 ILKNSDQKPVSGEELGEQLGISRTMVWKYIKSLKDDGYNITSST-KTGYILNSSPD 65
                                      456777789****************************9555554.48899988886 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.1e-05     0.028       4      55 ..       3      52 ..       1      56 [. 0.85

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.1e-05
                                      HHHHHHHHHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                    Fe_dep_repress  4 estEdYLetIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyveye 55
                                      +++Ed L  I+++s ++k+v+  +l e L++s   V + +k L++dGy +++
  gi|298674486|ref|YP_003726236.1|  3 DRKEDIL-NILKNS-DQKPVSGEELGEQLGISRTMVWKYIKSLKDDGYNITS 52
                                      5666666.477777.9********************************8876 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.1e-05     0.071      21      51 ..      18      48 ..      11      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.1e-05
                                      CCCHHCHHCCCTTSSCHCHHHHHHHHHHCTS CS
                              TrmB 21 gpatadeiaeelgvprskvYevLrsLedkGl 51
                                      +p + +e+ e+lg++r+ v ++++sL+d G+
  gi|298674486|ref|YP_003726236.1| 18 KPVSGEELGEQLGISRTMVWKYIKSLKDDGY 48
                                      678899**********************997 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.5e-05     0.076      21      52 ..      19      51 ..       3      68 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.5e-05
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTS.EE CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkregl.is 52
                                      p++ eel++ lG++r  v + ++ Lk++g+ i+
  gi|298674486|ref|YP_003726236.1| 19 PVSGEELGEQLGISRTMVWKYIKSLKDDGYnIT 51
                                      8999*************************8555 PP

>> HTH_39  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00011      0.15       5      49 ..       7      55 ..       4      60 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                            HTH_39  5 rilaaLrqhgs..ittleamrelditr..laaRIkeLrekGyeIkterv 49
                                       il++L++  +  ++  e+ ++l+i r    ++Ik L+++Gy+I+  ++
  gi|298674486|ref|YP_003726236.1|  7 DILNILKNSDQkpVSGEELGEQLGISRtmVWKYIKSLKDDGYNITSSTK 55
                                      68999998544449*9*********986689*************98875 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0    0.0001      0.14       7      46 ..       7      48 ..       2      56 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0001
                                      HHHHHHHHSTTEEHH..HHHHHHTS-HHHHHHHHHHHHHTTS CS
                              MarR  7 viLrilyeqgplsvs..eLakklgvskstvtrvldrLekkGl 46
                                      +iL il+++++  vs  eL+++lg+s+++v + ++ L ++G+
  gi|298674486|ref|YP_003726236.1|  7 DILNILKNSDQKPVSgeELGEQLGISRTMVWKYIKSLKDDGY 48
                                      68999*****9999999********************99996 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00014       0.2      22      46 ..      18      42 ..      15      45 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                            HTH_10 22 RrvtlkeLAkelGIskstlsehLrk 46
                                      + v+ +eL ++lGIs++ +++++++
  gi|298674486|ref|YP_003726236.1| 18 KPVSGEELGEQLGISRTMVWKYIKS 42
                                      56899****************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2424.63
//
Query:       gi|298674487|ref|YP_003726237.1|  [L=192]
Description: hypothetical protein Metev_0529 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-13   48.6   0.5      7e-13   48.2   0.5    1.1  1  S-layer   S-layer protein
  ------ inclusion threshold ------
      0.044   13.6   0.0      0.067   13.0   0.0    1.3  1  SurA_N_3  SurA N-terminal domain


Domain annotation for each model (and alignments):
>> S-layer  S-layer protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.2   0.5   7.8e-17     7e-13     101     206 ..      37     133 ..      21     144 .. 0.88

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 7.8e-17
                           S-layer 101 LskvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevdskvissskadstyvyekdlgdeddv 177
                                       +  v++ + ++  +ks++s +  +gY+l+ik ++ ++++ wleL+ +g++v s+v+++    + ++y++d       
  gi|298674487|ref|YP_003726237.1|  37 V-PVVLINGTKIFIKSDESHSFYQGYKLQIKGVNQEDERLWLELSLNGRSVKSDVVHE---GEHFTYKRD-----ST 104
                                       4.44444569999*********************************************...******975.....68 PP

                           S-layer 178 viiavhvdevfrgtedslvviegifqisd 206
                                       vi+   vd+++++ e++lv+++ ++q  d
  gi|298674487|ref|YP_003726237.1| 105 VILNATVDKIYSNPENELVTFKSVYQYLD 133
                                       9************************9766 PP

>> SurA_N_3  SurA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.5e-06     0.067       5      51 ..       1      49 [.       1      81 [. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.5e-06
                          SurA_N_3  5 lrknakswiakillgliilaFvl.wGvgsylsgsgns....vakVngekIsr 51
                                      +r+n+k   +k ++ l+i+ ++l  Gv  ++s+s+++    v+ +ng+kI  
  gi|298674487|ref|YP_003726237.1|  1 MRQNTK---LKTFVSLLIILMILhSGVTVVSSQSEEDdsvpVVLINGTKIFI 49
                                      788988...777777777788877***99999998445789********964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1415.69
//
Query:       gi|298674488|ref|YP_003726238.1|  [L=306]
Description: phosphoserine phosphatase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.9e-05   22.5  13.9    5.9e-05   22.5  13.9    3.8  4  DUF3450          Protein of unknown function (DUF3450)
    0.00016   21.6  15.7    0.00016   21.6  15.7    3.7  4  DUF724           Protein of unknown function (DUF724)
    0.00033   20.9  46.7      0.049   13.9  20.0    4.6  4  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
     0.0023   17.7  42.5     0.0057   16.4  14.9    2.2  2  Laminin_I        Laminin Domain I
     0.0047   14.5  42.4      0.006   14.2  42.4    1.0  1  DUF3584          Protein of unknown function (DUF3584)
     0.0048   17.1  47.9     0.0056   16.9  19.7    3.2  3  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
     0.0076   15.8  52.1      0.036   13.6  27.1    3.9  4  MscS_porin       Mechanosensitive ion channel porin domain
     0.0081   16.2  23.5     0.0081   16.2  23.5    3.1  3  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
     0.0087   14.3   1.2     0.0087   14.3   1.2    1.4  1  DUF1633          Protein of unknown function (DUF1633)
     0.0096   15.8  41.6      0.081   12.7  25.8    2.6  2  ERM              Ezrin/radixin/moesin family
  ------ inclusion threshold ------
      0.011   15.9   4.6      0.011   15.9   4.6    3.9  4  ADIP             Afadin- and alpha -actinin-Binding
      0.011   15.5   7.4      0.011   15.5   7.4    3.8  3  DUF4201          Domain of unknown function (DUF4201)
      0.013   15.8   1.8      0.013   15.8   1.8    5.3  5  BLOC1_2          Biogenesis of lysosome-related organelles co
      0.019   15.5  41.4       0.49   10.8  20.8    2.6  3  Fez1             Fez1
      0.021   15.1   0.1      0.056   13.8   0.1    1.7  1  DUF1871          Domain of unknown function (DUF1871)
       0.03   13.2  50.5       0.28   10.0  15.0    3.1  3  Spc7             Spc7 kinetochore protein
      0.036   13.6  47.7       0.16   11.6  47.7    2.2  1  Filament         Intermediate filament protein
      0.038   14.3  11.7      0.054   13.8   3.3    2.9  2  IL5              Interleukin 5
      0.041   13.7  45.4      0.033   14.0   9.8    2.6  2  KASH_CCD         Coiled-coil region of CCDC155 or KASH
      0.061   13.2   4.5       0.12   12.3   0.0    2.5  2  PhageMin_Tail    Phage-related minor tail protein
      0.097   13.0  43.8        3.4    7.9   1.4    4.9  4  DUF5082          Domain of unknown function (DUF5082)
       0.15   12.5   4.0         29    5.1   0.0    4.0  4  HsbA             Hydrophobic surface binding protein A
       0.16   12.5  27.0        1.5    9.4   7.1    5.3  4  YtxH             YtxH-like protein
       0.18   11.8  37.1        3.2    7.8  10.6    3.6  3  Laminin_II       Laminin Domain II
       0.19   12.1  48.3      0.068   13.5  12.6    4.6  3  Syntaxin_2       Syntaxin-like protein
       0.24   10.6  37.8      0.037   13.3  13.1    3.5  5  TMPIT            TMPIT-like protein
       0.26   11.5  40.8        2.2    8.5   5.1    3.5  3  ATG16            Autophagy protein 16 (ATG16)
       0.41   10.9  19.6        3.1    8.1   0.5    4.6  4  DUF948           Bacterial protein of unknown function (DUF94
       0.52   10.3  11.3        1.4    8.8   0.1    4.1  3  ApoO             Apolipoprotein O
       0.64   10.4  55.2       0.31   11.4  21.1    4.6  3  DUF4200          Domain of unknown function (DUF4200)
       0.66   10.3  55.0       0.24   11.7   9.4    4.1  4  OmpH             Outer membrane protein (OmpH-like)
       0.67   10.4  31.8          2    8.9  14.4    3.2  3  T3SSipB          Type III cell invasion protein SipB
       0.77    9.5  25.1       0.78    9.4   4.6    2.5  2  DUF745           Protein of unknown function (DUF745)
       0.85    9.9  37.8        6.1    7.1   6.0    4.7  3  FliJ             Flagellar FliJ protein
       0.92    9.9  16.2        3.3    8.1   0.4    3.5  3  HCMV_UL139       Human Cytomegalovirus UL139 protein
          1    9.4  32.6          1    9.4   4.1    4.5  4  DUF1664          Protein of unknown function (DUF1664)
        1.1    9.3  53.0       0.22   11.6  10.5    4.4  4  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
        1.2    9.3  38.8          1    9.5   0.4    6.4  6  bZIP_1           bZIP transcription factor
        1.3    9.2  56.0       0.55   10.4   7.9    4.3  4  Tropomyosin_1    Tropomyosin like
        1.4    9.4  30.3         19    5.8  11.2    5.6  4  NPV_P10          Nucleopolyhedrovirus P10 protein
        1.7    8.4  39.6      0.097   12.5   2.2    4.0  4  Bacillus_HBL     Bacillus haemolytic enterotoxin (HBL)
        2.1    8.7  37.2          2    8.8   4.7    4.5  4  DUF641           Plant protein of unknown function (DUF641)
        2.5    8.2  10.6        0.2   11.7   1.7    3.1  2  PilJ             Type IV pili methyl-accepting chemotaxis tra
        2.6    6.1  53.7        1.4    7.0  27.7    2.0  2  HOOK             HOOK protein
        2.7    7.0  54.5       0.42    9.7  21.3    2.1  2  DUF4686          Domain of unknown function (DUF4686)
        3.1    5.9  53.1        3.3    5.8  27.8    2.5  2  EzrA             Septation ring formation regulator, EzrA
        3.1    6.3  47.0        4.2    5.9  20.1    2.1  2  AAA_13           AAA domain
        3.3    6.7  47.9       0.16   11.0   8.5    3.2  3  Atg14            Vacuolar sorting 38 and autophagy-related su
        3.5    8.3  45.2         11    6.7   7.9    5.0  4  YabA             Initiation control protein YabA
        3.8    7.7  45.5       0.37   11.0  10.2    4.3  4  Fib_alpha        Fibrinogen alpha/beta chain family
          4    6.7  36.3    1.8e+04   -8.3  36.3    2.6  0  DUF4407          Domain of unknown function (DUF4407)
          4    7.6  20.7        0.6   10.2   0.2    5.5  4  DUF1192          Protein of unknown function (DUF1192)
        4.2    5.6  50.9        1.2    7.4  31.3    2.1  2  MAD              Mitotic checkpoint protein
        4.9    6.5  57.0        2.7    7.3  38.5    3.4  3  GAS              Growth-arrest specific micro-tubule binding
        6.4    6.3  42.3       0.28   10.7   4.7    3.1  3  HAUS-augmin3     HAUS augmin-like complex subunit 3
        6.5    6.2  48.2         17    4.8  35.9    2.4  2  Leu_zip          Leucine zipper
        7.2    6.0  52.7       0.38   10.2  18.5    2.6  2  HMMR_N           Hyaluronan mediated motility receptor N-term
        7.4    7.1  32.3        5.3    7.5   2.4    6.3  4  LPP              Lipoprotein leucine-zipper
        8.2    6.7  39.7       0.19   11.9   0.7    5.1  3  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
        8.2    6.9  27.5        8.5    6.9   0.0    6.1  3  FlaC_arch        Flagella accessory protein C (FlaC)
        8.3    5.7  39.7        3.3    7.0  21.9    2.6  2  FAM76            FAM76 protein
        8.9    5.1  47.2        3.1    6.6  24.7    2.5  2  DUF812           Protein of unknown function (DUF812)


Domain annotation for each model (and alignments):
>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   3.9     0.059        17      54     111 ..      15      72 ..       2      73 .. 0.63
   2 !   22.5  13.9   2.1e-07   5.9e-05      27     138 ..      51     164 ..      45     167 .. 0.92
   3 ?    6.0   5.7     0.022       6.3      17      90 ..     156     230 ..     155     238 .. 0.87
   4 ?    1.8   5.4      0.44   1.3e+02      19      86 ..     215     284 ..     212     303 .. 0.51

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.059
                           DUF3450  54 ralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvpllekmidrLeq 111
                                       r+lk+++++l+ + +q e+ +++  ++++  +++i+e++e ++el    ++++++ ++
  gi|298674488|ref|YP_003726238.1|  15 RELKDKINQLRTQISQKEKNLNTIFKDLKLYRNNIDELKEKRNELNTKVKDLVSQAQD 72 
                                       5566666666666666666666666666666666666666666666666666655554 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 2.1e-07
                           DUF3450  27 kavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvplle 103
                                       +  +++ + ++k+++l  ++q+ +++  + ++++ +l+ ++++ +++ +s  +eia+l+++ +e++ i+++ +  l 
  gi|298674488|ref|YP_003726238.1|  51 ELKEKRNELNTKVKDLVSQAQDFKSKRDENNKKITELKSKRDEIQKQNKSKANEIAQLKKKRNELNDISKGTEETLS 127
                                       667889999******************************************************************** PP

                           DUF3450 104 kmid.rLeqfveldlPflle.eRqarlakLkelmdra 138
                                       k  + +L++f ++d+P + e +  +rl++Lk+ ++ a
  gi|298674488|ref|YP_003726238.1| 128 KAYSqELNKFLNEDIPLNHEiDLFERLENLKKRLEAA 164
                                       998527***********99988899999999887765 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.022
                           DUF3450  17 tldqalkeaekavaaaaqsqkkidkl.ddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqiee 90 
                                       +l++ l++a++a+++  ++q+ ++ + dd+ +el +++++l +e ++  ++  ++ +  +++++e +s  e+i++
  gi|298674488|ref|YP_003726238.1| 156 NLKKRLEAAQEANNIHHKIQEIYNTSfDDNINELNDQIQQLADESQQYHLQMVEYFNKADEVRAEADSYHEDIKN 230
                                       5677789999***********999752677899**************9999999999999999999999888875 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.44
                           DUF3450  19 dqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyne..qlerlvasqeqeiaslee 86 
                                       d++++ea + ++  +   + ++ l+ + + l+ e+ +l+eel++  ++ +  ql++  ++q+++ ++ +e
  gi|298674488|ref|YP_003726238.1| 215 DEVRAEADSYHEDIKNKYSLMSPLKSKIDPLKTEISQLREELDRYLKQLDdiQLQKDEKNQDEKYTEAKE 284
                                       4455555555555555555555555555555555555555555555554422333333444444444444 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.3       1.8   5.3e+02     123     146 ..      12      35 ..       2      43 .. 0.59
   2 !   21.6  15.7   5.4e-07   0.00016      95     185 ..      40     130 ..      33     133 .. 0.91
   3 ?    5.8   4.4     0.038        11     100     176 ..     157     230 ..     144     236 .. 0.76
   4 ?    4.3   7.8      0.11        32     100     180 ..     189     269 ..     186     293 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.8
                            DUF724 123 sekrkleeeidelekkilelerql 146
                                       +++r+l+++i++l  +i++ e++l
  gi|298674488|ref|YP_003726238.1|  12 MSERELKDKINQLRTQISQKEKNL 35 
                                       344556666666666666655554 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 5.4e-07
                            DUF724  95 nkLlslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekle 171
                                       ++L   +++ ++l+e+r++l+ k+++  s+ + ++++ de++kki el+ +++ ++++++++++eia+lk++ ++l+
  gi|298674488|ref|YP_003726238.1|  40 KDLKLYRNNIDELKEKRNELNTKVKDLVSQAQDFKSKRDENNKKITELKSKRDEIQKQNKSKANEIAQLKKKRNELN 116
                                       6677789999******************************************************************* PP

                            DUF724 172 eeledveqeFeava 185
                                       +  + +e+  ++  
  gi|298674488|ref|YP_003726238.1| 117 DISKGTEETLSKAY 130
                                       99999888877665 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.038
                            DUF724 100 lkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeled 176
                                       lk ++ ++++e +++++ki+e    +++++++i+el+ +i++l  ++++   ++ +  ++  ++++ea++++e++++
  gi|298674488|ref|YP_003726238.1| 157 LK-KRLEAAQEANNIHHKIQE--IYNTSFDDNINELNDQIQQLADESQQYHLQMVEYFNKADEVRAEADSYHEDIKN 230
                                       44.344555666677777775..4457899**************999999999999889999999988888888876 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.11
                            DUF724 100 lkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeled 176
                                       l+d+ ++l++e+++++ ++ e  ++  ++ +e d   + i++       lk+k +  + ei++l+ e +++ ++l+d
  gi|298674488|ref|YP_003726238.1| 189 LNDQIQQLADESQQYHLQMVEYFNKADEVRAEADSYHEDIKNKYSLMSPLKSKIDPLKTEISQLREELDRYLKQLDD 265
                                       67788888888888888888888888888888888888888888888888888888888888888888888888777 PP

                            DUF724 177 veqe 180
                                       ++ +
  gi|298674488|ref|YP_003726238.1| 266 IQLQ 269
                                       7655 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.9     0.068        20      77     101 ..      15      39 ..       2      42 .. 0.69
   2 !   13.9  20.0   0.00017     0.049       3     101 ..      41     138 ..      40     143 .. 0.86
   3 ?    7.0   4.2     0.023       6.7      32      93 ..     148     210 ..     139     220 .. 0.82
   4 !   11.7   0.4    0.0008      0.23      43     102 ..     212     268 ..     206     270 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.068
                                       HHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  77 kelkeelkaleaelkeleaelekll 101
                                       +elk+++++l ++ ++ e++l+++ 
  gi|298674488|ref|YP_003726238.1|  15 RELKDKINQLRTQISQKEKNLNTIF 39 
                                       5677777777777777777777664 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 0.00017
                                       -HHHHHH-HHHHHHHHCCCT.CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHH CS
                      Seryl_tRNA_N   3 DiklirenpeavkeklkkRg.edkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevke 78 
                                       D+kl r+n++++kek ++ + + k +v +  +  +kr e ++++ el+++r e++k+ +++    +++++l+++ +e
  gi|298674488|ref|YP_003726238.1|  41 DLKLYRNNIDELKEKRNELNtKVKDLVSQAQDFKSKRDENNKKITELKSKRDEIQKQNKSKA---NEIAQLKKKRNE 114
                                       99************9988887899999****************************9844444...48999******* PP

                                       HHHHHHHHHHHHHHH.HHHHHHHH CS
                      Seryl_tRNA_N  79 lkeelkaleaelkel.eaelekll 101
                                       l++  k +e++l+++ ++el+k+l
  gi|298674488|ref|YP_003726238.1| 115 LNDISKGTEETLSKAySQELNKFL 138
                                       *********999776256677766 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.023
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT..S-TCCCCCCCHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  32 leldekrrelqveleelqaerNelskeIgkakkkk..edaeeliaevkelkeelkaleaelkel 93 
                                       ++l e+ ++l+++le++q+  N++  +I+++ +    ++++el +++++l +e +++  ++ e 
  gi|298674488|ref|YP_003726238.1| 148 IDLFERLENLKKRLEAAQE-ANNIHHKIQEIYNTSfdDNINELNDQIQQLADESQQYHLQMVEY 210
                                       5677888889999998875.6889999*****99999999999999999999999988877765 PP

  == domain 4  score: 11.7 bits;  conditional E-value: 0.0008
                                       HHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                      Seryl_tRNA_N  43 veleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaeleklll 102
                                       ++++e++ae  +  + I+++       + l+ +++ lk+e+++l +el+   ++l+++ l
  gi|298674488|ref|YP_003726238.1| 212 NKADEVRAEADSYHEDIKNKYS---LMSPLKSKIDPLKTEISQLREELDRYLKQLDDIQL 268
                                       6788888888888888888886...57999999999999999999999999999999876 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0  19.8     0.014       4.2      15     114 ..      15     117 ..      10     140 .. 0.88
   2 !   16.4  14.9     2e-05    0.0057      19     156 ..     152     285 ..     138     292 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.014
                         Laminin_I  15 ykinanledltkeLqeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaeki 91 
                                       +++  ++++l++++++k+++ +   +++++  +++ +L++  +eL +k++    +aq+ + + ++ +++++eL+ k 
  gi|298674488|ref|YP_003726238.1|  15 RELKDKINQLRTQISQKEKNLNTIFKDLKLYRNNIDELKEKRNELNTKVKDLVSQAQDFKSKRDENNKKITELKSKR 91 
                                       678899*********************************************************************** PP

                         Laminin_I  92 kkladnikeilekvatlne...neea 114
                                        +++++ k   + +a+l +   + ++
  gi|298674488|ref|YP_003726238.1|  92 DEIQKQNKSKANEIAQLKKkrnELND 117
                                       *****999999999999995543333 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 2e-05
                         Laminin_I  19 anledltkeLqeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaekikkla 95 
                                       + le+l+k L+     ++a+++  +i+e  ++s   +++eL  + +q  ++ q+   ++ + +n+a e  +++   +
  gi|298674488|ref|YP_003726238.1| 152 ERLENLKKRLEAA---QEANNIHHKIQEIYNTSFDDNINELNDQIQQLADESQQYHLQMVEYFNKADEVRAEADSYH 225
                                       5688888888765...55566666777777*********************************************** PP

                         Laminin_I  96 dnikeilekvatlneneealpssklseelaeaqrlLeelrsRdftkqleeaeaelkaAqkL 156
                                       ++ik   + ++ l   + ++ ++++s+  +e +r L++l   +++k  ++ +++  +A++ 
  gi|298674488|ref|YP_003726238.1| 226 EDIKNKYSLMSPLKS-KIDPLKTEISQLREELDRYLKQLDDIQLQKDEKNQDEKYTEAKEK 285
                                       **********99998.89999******************9999**********99999975 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2  42.4   2.1e-05     0.006     599     861 ..      12     288 ..       4     303 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.1e-05
                           DUF3584 599 aseeeLrerlqaleealqsaeakqkqaeeelkqlnaeleeakravaeaatalknardtlerlqnekesekdklek.. 673
                                        se eL+ ++++l +++ ++e++ + + + lk  +++++e+k++  e +t++k    + +  ++++++ ++k+++  
  gi|298674488|ref|YP_003726238.1|  12 MSERELKDKINQLRTQISQKEKNLNTIFKDLKLYRNNIDELKEKRNELNTKVKDLVSQAQDFKSKRDENNKKITElk 88 
                                       5788***********************************************99988888888887777777766411 PP

                           DUF3584 674 ....aiaerkqqaeeqlqkldaqlkqleeqqkaaleelkedlseerlekkakwqevvgeld..eqlaelkkaieaar 744
                                            i+++ +++ +++ +l+++ + l+   k  +e l + +s+e +++ ++   +  e+d  e l++lkk +eaa+
  gi|298674488|ref|YP_003726238.1|  89 skrdEIQKQNKSKANEIAQLKKKRNELNDISKGTEETLSKAYSQELNKFLNEDIPLNHEIDlfERLENLKKRLEAAQ 165
                                       1111455556666667777777777777777778888888888888888888776666666559999*******999 PP

                           DUF3584 745 tqakarlkeleeaykreLkskdvD.petvkelkrkieeLe....kkieriekrreevreYraflqetwlkvdslaee 816
                                       ++++ +  +++e y+++ +++  + ++++++l+ + ++ +    +  +++ + r+e+ +Y++ ++++++ +  l+ +
  gi|298674488|ref|YP_003726238.1| 166 EANNIHH-KIQEIYNTSFDDNINElNDQIQQLADESQQYHlqmvEYFNKADEVRAEADSYHEDIKNKYSLMSPLKSK 241
                                       8887654.466667766666533323566677777766551111455677888899999****************** PP

                           DUF3584 817 rpalkeqveelesaaeeleqeltrl..iedtklerkklekerkalek 861
                                        + lk++ ++l++++ +  ++l  +  ++d k++ +k  ++++ l+k
  gi|298674488|ref|YP_003726238.1| 242 IDPLKTEISQLREELDRYLKQLDDIqlQKDEKNQDEKYTEAKEKLDK 288
                                       ****************9999998651155566666666666555555 PP

>> Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9  19.7     2e-05    0.0056      46     152 ..       8     117 ..       2     121 .. 0.85
   2 !   11.2   6.8    0.0011      0.33      55     138 ..     150     226 ..     133     243 .. 0.75
   3 ?    1.0   5.9       1.6   4.6e+02      44      77 ..     248     281 ..     238     303 .. 0.46

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2e-05
                     Jnk-SapK_ap_N  46 eeeeaeleelreeleqLeteyerekelrkraeeeleeie...dqweeerkelqekveqleeenrelelkaknaadql 119
                                       +  +  ++el+++++qL+t+ +++ +  +   ++l ++    d+++e+r+el++kv++l ++ + ++ k ++ ++++
  gi|298674488|ref|YP_003726238.1|   8 DISNMSERELKDKINQLRTQISQKEKNLNTIFKDLKLYRnniDELKEKRNELNTKVKDLVSQAQDFKSKRDENNKKI 84 
                                       55678899************988777777666666655422278899****************************** PP

                     Jnk-SapK_ap_N 120 srleekeaelkkeysklheretellkklkelve 152
                                       ++l++k +e +k+++++ ++  +l kk  el +
  gi|298674488|ref|YP_003726238.1|  85 TELKSKRDEIQKQNKSKANEIAQLKKKRNELND 117
                                       *******************99999999888876 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0011
                     Jnk-SapK_ap_N  55 lreeleqLeteyerekelrkraeeeleeiedqweeerkelqekveqleeenrelelkaknaadqlsrleekeaelkk 131
                                       l e le+L++++e  +e+++ + +  e + ++++++ +el+++++ql +e ++++l++ ++ +++ +       ++ 
  gi|298674488|ref|YP_003726238.1| 150 LFERLENLKKRLEAAQEANNIHHKIQEIYNTSFDDNINELNDQIQQLADESQQYHLQMVEYFNKADE-------VRA 219
                                       5578999************************************************665555544444.......444 PP

                     Jnk-SapK_ap_N 132 eysklhe 138
                                       e ++ he
  gi|298674488|ref|YP_003726238.1| 220 EADSYHE 226
                                       4444444 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 1.6
                     Jnk-SapK_ap_N  44 rneeeeaeleelreeleqLeteyerekelrkrae 77 
                                       +  +  +el++  ++l++++++++++++++k +e
  gi|298674488|ref|YP_003726238.1| 248 EISQLREELDRYLKQLDDIQLQKDEKNQDEKYTE 281
                                       2222333333333333334443333333333333 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   3.0    0.0041       1.2      69     116 ..       3      50 ..       1      55 [. 0.86
   2 !   13.6  27.1   0.00012     0.036       2     155 ..      49     206 ..      48     214 .. 0.82
   3 ?    4.5   1.2     0.076        22     100     135 ..     185     220 ..     180     231 .. 0.70
   4 ?    2.1   6.7      0.41   1.2e+02      31      77 ..     241     288 ..     237     302 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0041
                        MscS_porin  69 easkeilaklsleeLeqrllqtssqlqelqeqlaqlnsqlvelqtrpe 116
                                       ++ + +++++s +eL  +++q   q ++ +++l+++ ++l  +++ ++
  gi|298674488|ref|YP_003726238.1|   3 ATENSDISNMSERELKDKINQLRTQISQKEKNLNTIFKDLKLYRNNID 50 
                                       5678899****************************9988877776665 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.00012
                        MscS_porin   2 LdelekakldeaeqkallqdLeqalnlLdkidkskkkaeelqkaiddaPkelrelqqelealqkkkeeaskeilakl 78 
                                       +del+++   ++ ++++++   qa+++  k+d+++kk+ el+ + d+ +k+ ++  +e+++l  kk+ +  ++++k 
  gi|298674488|ref|YP_003726238.1|  49 IDELKEKR--NELNTKVKDLVSQAQDFKSKRDENNKKITELKSKRDEIQKQNKSKANEIAQL--KKKRNELNDISKG 121
                                       78888888..899*************************************************..999999******* PP

                        MscS_porin  79 sleeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltear..qrlqei.....rnrLnstaaage.als 147
                                       + e+L + + q++++ +++   l+ + +++  l++   r+ +++ +++   ++qei      +++n++ ++ +    
  gi|298674488|ref|YP_003726238.1| 122 TEETLSKAYSQELNKFLNEDIPLNHEIDLFERLENLKKRLEAAQEANNihHKIQEIyntsfDDNINELNDQIQqLAD 198
                                       ****************************9999999999999999887633789999544442222222211122444 PP

                        MscS_porin 148 qaqrtalq 155
                                       ++q+  lq
  gi|298674488|ref|YP_003726238.1| 199 ESQQYHLQ 206
                                       44444444 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.076
                        MscS_porin 100 qlaqlnsqlvelqtrperaqqqltearqrlqeirnr 135
                                       ++++ln+q+++l +  ++ + q+ e   + +e+r++
  gi|298674488|ref|YP_003726238.1| 185 NINELNDQIQQLADESQQYHLQMVEYFNKADEVRAE 220
                                       567777777777777777777777777777777664 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.41
                        MscS_porin  31 kidkskkkaeelqkaiddaPkelrelqqeleal.qkkkeeaskeilak 77 
                                       kid  k ++ +l++ +d++ k+l+++q + ++  q++k ++ ke+l+k
  gi|298674488|ref|YP_003726238.1| 241 KIDPLKTEISQLREELDRYLKQLDDIQLQKDEKnQDEKYTEAKEKLDK 288
                                       678889999999999999999999999999999644444444444433 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2  23.5   2.8e-05    0.0081      19     135 ..      14     130 ..       7     136 .. 0.94
   2 ?    5.8  11.7     0.046        13      22     132 ..     150     264 ..     144     273 .. 0.81
   3 ?    5.3   3.8     0.064        19      51      87 ..     239     275 ..     218     299 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.8e-05
                    CENP-F_leu_zip  19 adsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqer 95 
                                       +  Lkdk+++L  ++ + e+n++ +  +    ++ + +lke+ +el+++ ++l ++ ++++s ++e +k++ + +++
  gi|298674488|ref|YP_003726238.1|  14 ERELKDKINQLRTQISQKEKNLNTIFKDLKLYRNNIDELKEKRNELNTKVKDLVSQAQDFKSKRDENNKKITELKSK 90 
                                       568************************************************************************** PP

                    CENP-F_leu_zip  96 vseLeslnsslenlleekEqekvqmkeeskaaveeLqtql 135
                                        +e ++ n s  n + ++ +++ ++++ sk + e L++  
  gi|298674488|ref|YP_003726238.1|  91 RDEIQKQNKSKANEIAQLKKKRNELNDISKGTEETLSKAY 130
                                       ***************************9999999998765 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.046
                    CENP-F_leu_zip  22 LkdkvenLerelemseenqe..kvileaEts..kaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqe 94 
                                       L ++ enL++ le ++e ++  + i e  +      +++l+++i++la e ++ +l++v+  +  +e+  e     e
  gi|298674488|ref|YP_003726238.1| 150 LFERLENLKKRLEAAQEANNihHKIQEIYNTsfDDNINELNDQIQQLADESQQYHLQMVEYFNKADEVRAEADSYHE 226
                                       556889999999888775541144444444312467899************************************** PP

                    CENP-F_leu_zip  95 rvseLeslnsslenlleekEqekvqmkeeskaaveeLq 132
                                        +++  sl s l++ +  +  e  q++ee ++ +++L 
  gi|298674488|ref|YP_003726238.1| 227 DIKNKYSLMSPLKSKIDPLKTEISQLREELDRYLKQLD 264
                                       ******************************99999995 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.064
                    CENP-F_leu_zip  51 kaevetlkeeieelaeelreleldLvalrsekeeLek 87 
                                       k ++  lk+ei +l+eel +   +L++++ +k+e ++
  gi|298674488|ref|YP_003726238.1| 239 KSKIDPLKTEISQLREELDRYLKQLDDIQLQKDEKNQ 275
                                       4455556666666666666666666666655554333 PP

>> DUF1633  Protein of unknown function (DUF1633)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   1.2     3e-05    0.0087     598     645 ..      27      74 ..      14      90 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3e-05
                           DUF1633 598 kikimeqefrGleadkqtarsqihrleekkdelskkvldltsiaqGvk 645
                                       +i   e++++ +  d ++ r++i  l+ek++el  kv dl s aq  k
  gi|298674488|ref|YP_003726238.1|  27 QISQKEKNLNTIFKDLKLYRNNIDELKEKRNELNTKVKDLVSQAQDFK 74 
                                       56667888888889999****************************876 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7  25.8   0.00028     0.081      15     137 ..      15     152 ..       2     190 .. 0.81
   2 ?    5.2  11.4     0.055        16      26     128 ..     184     288 ..     162     294 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00028
                               ERM  15 kqlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerklreaelea 91 
                                       ++l++++++ + + +++e+  +   + ++  +++ ++L++k++e++++ + l  +a++ ++++++ ++k++e +++ 
  gi|298674488|ref|YP_003726238.1|  15 RELKDKINQLRTQISQKEKNLNTIFKDLKLYRNNIDELKEKRNELNTKVKDLVSQAQDFKSKRDENNKKITELKSKR 91 
                                       57788899999999999999999999*************************************************** PP

                               ERM  92 arleeeserkeeeaerLkeeleeareaeeeakekllealstpsks...............e 137
                                        +++++++ k++e  +Lk++  e ++  + ++e l +a s++ ++               e
  gi|298674488|ref|YP_003726238.1|  92 DEIQKQNKSKANEIAQLKKKRNELNDISKGTEETLSKAYSQELNKflnediplnheidlfE 152
                                       *************************************999997666666655555544441 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.055
                               ERM  26 eaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerklreaeleaarleeeser.. 100
                                       ++ +e ++++++La ++++   ++ +  +ka e+++e +   e+ +++ +  + l+ k++  + e+++l+ee +r  
  gi|298674488|ref|YP_003726238.1| 184 DNINELNDQIQQLADESQQYHLQMVEYFNKADEVRAEADSYHEDIKNKYSLMSPLKSKIDPLKTEISQLREELDRyl 260
                                       56677889999**************************************************************9977 PP

                               ERM 101 keeeaerLkeeleeareaeeeakeklle 128
                                       k+ +  +L+++ ++  e+ +eakekl +
  gi|298674488|ref|YP_003726238.1| 261 KQLDDIQLQKDEKNQDEKYTEAKEKLDK 288
                                       77888899999999999999****9975 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0  25.2    0.0046       1.3      56     150 ..      15     112 ..       7     114 .. 0.90
   2 ?    3.6  11.6      0.22        63      72     122 ..      80     130 ..      72     141 .. 0.53
   3 ?   -1.1   4.7       6.1   1.8e+03      77     117 ..     155     199 ..     144     216 .. 0.45
   4 ?   15.9   4.6   3.6e-05     0.011      52     120 ..     218     288 ..     207     298 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0046
                              ADIP  56 eslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktl...eqklknekeelqrlknalqqik 129
                                        +l+++i++l++ i++++++ +   + l+ +++ ++ +++k ++l++k+k+l    q  k++++e+++  + l++ +
  gi|298674488|ref|YP_003726238.1|  15 RELKDKINQLRTQISQKEKNLNTIFKDLKLYRNNIDELKEKRNELNTKVKDLvsqAQDFKSKRDENNKKITELKSKR 91 
                                       4689******************************************999986211566799**************** PP

                              ADIP 130 tqyahelkkkdreiekLkekl 150
                                          +   k k  ei++Lk+k 
  gi|298674488|ref|YP_003726238.1|  92 DEIQKQNKSKANEIAQLKKKR 112
                                       ******************985 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.22
                              ADIP  72 lqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlk 122
                                        ++ki  lk +  + ++++++  ++ +ql+kk  +l++  k++ e l++ +
  gi|298674488|ref|YP_003726238.1|  80 NNKKITELKSKRDEIQKQNKSKANEIAQLKKKRNELNDISKGTEETLSKAY 130
                                       345555555555555555555555555555555555555555555555543 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 6.1
                              ADIP  77 erlktqleqlerelalvqake....rqlekklktleqklknekee 117
                                       e lk++le+ +  +  +++ +    ++   ++ +l+++++++++e
  gi|298674488|ref|YP_003726238.1| 155 ENLKKRLEAAQEANNIHHKIQeiynTSFDDNINELNDQIQQLADE 199
                                       444444444444444333332011122222333333333333333 PP

  == domain 4  score: 15.9 bits;  conditional E-value: 3.6e-05
                              ADIP  52 leqreslnetirkleaeierlqskierlktqleqlerela..lvqakerqlekklktleqklknekeelqr 120
                                       +++  s++e+i+++ + ++ l+ski+ lkt+ +ql+ el+  l q ++ ql+k+ k++++k  + ke+l +
  gi|298674488|ref|YP_003726238.1| 218 RAEADSYHEDIKNKYSLMSPLKSKIDPLKTEISQLREELDryLKQLDDIQLQKDEKNQDEKYTEAKEKLDK 288
                                       5667899*********************************878888999******************9988 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   7.4   3.7e-05     0.011      80     138 ..      15      73 ..       4      75 .. 0.94
   2 ?    4.0  16.3      0.12        36      71     136 ..      62     127 ..      61     169 .. 0.79
   3 ?    4.0  14.9      0.12        36      48     146 ..     176     271 ..     153     298 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.7e-05
                           DUF4201  80 thlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqggll 138
                                        +lk+k + l+++ s+++k+l+++ ++l+ +r ++ ++k++r+ l ++ ++l +q +++
  gi|298674488|ref|YP_003726238.1|  15 RELKDKINQLRTQISQKEKNLNTIFKDLKLYRNNIDELKEKRNELNTKVKDLVSQAQDF 73 
                                       579****************************************************9987 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.12
                           DUF4201  71 kttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqgg 136
                                       k+++ v + ++ k k+++++++  elk++ +e++++ ++   e+ ++k++r+ l +  +  ++ + 
  gi|298674488|ref|YP_003726238.1|  62 KVKDLVSQAQDFKSKRDENNKKITELKSKRDEIQKQNKSKANEIAQLKKKRNELNDISKGTEETLS 127
                                       5677789999******************************************99887766655555 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.12
                           DUF4201  48 qienqalnkkIeernkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdkl 124
                                       +i n++++++I+e n+++++l + +++   ++ ++ +k++++++e    ++++k+k      l+ ++  +k+e ++l
  gi|298674488|ref|YP_003726238.1| 176 EIYNTSFDDNINELNDQIQQLADESQQYHLQMVEYFNKADEVRAEADSYHEDIKNKYSLMSPLKSKIDPLKTEISQL 252
                                       6889********************************************99999999888888888888888888888 PP

                           DUF4201 125 rkqneklkqqggllrvPaLlkD 146
                                       r++ ++  +q+ ++   +L kD
  gi|298674488|ref|YP_003726238.1| 253 REELDRYLKQLDDI---QLQKD 271
                                       88877777776664...44444 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   5.3     0.027       7.8      37      84 ..      19      66 ..       8      78 .. 0.70
   2 ?    2.3  13.1      0.72   2.1e+02      13      92 ..      40     123 ..      36     137 .. 0.86
   3 ?    3.5   3.6       0.3        87      42      86 ..     153     198 ..     145     206 .. 0.60
   4 ?   15.8   1.8   4.4e-05     0.013      34      92 ..     209     264 ..     200     267 .. 0.87
   5 ?   -0.8   0.1       6.7   1.9e+03      26      45 ..     269     288 ..     265     301 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.027
                           BLOC1_2 37 kklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseL 84
                                      +k+++   ++++k ++ln   + l+ y ++id+++++ +eL + v+ L
  gi|298674488|ref|YP_003726238.1| 19 DKINQLRTQISQKEKNLNTIFKDLKLYRNNIDELKEKRNELNTKVKDL 66
                                      345555556666666777777788888888888888888888888777 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.72
                           BLOC1_2  13 aeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekq....vteLeeavseLD 85 
                                       ++l+  +++++ L++  ++ ++k+k+l ++a+++++k ++ n+k  el+++ ++i++ +k+    +++L++  +eL+
  gi|298674488|ref|YP_003726238.1|  40 KDLKLYRNNIDELKEKRNELNTKVKDLVSQAQDFKSKRDENNKKITELKSKRDEIQKQNKSkaneIAQLKKKRNELN 116
                                       688999999999999999*************************************9987533333888888888888 PP

                           BLOC1_2  86 eyskeLE 92 
                                        +sk  E
  gi|298674488|ref|YP_003726238.1| 117 DISKGTE 123
                                       8888666 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.3
                           BLOC1_2  42 vaaslekkleklnekyeelqpylqqi..dqiekqvteLeeavseLDe 86 
                                       ++++l+k le+ +e  ++++ ++q+i    ++++++eL + +++L  
  gi|298674488|ref|YP_003726238.1| 153 RLENLKKRLEAAQE-ANNIHHKIQEIynTSFDDNINELNDQIQQLAD 198
                                       55666666666655.56666666666323456666666666666644 PP

  == domain 4  score: 15.8 bits;  conditional E-value: 4.4e-05
                           BLOC1_2  34 ekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLE 92 
                                       e ++k ++v a++ +  e++++ky  ++p++++id +++++++L e   eLD y k+L 
  gi|298674488|ref|YP_003726238.1| 209 EYFNKADEVRAEADSYHEDIKNKYSLMSPLKSKIDPLKTEISQLRE---ELDRYLKQLD 264
                                       55677888889999999***************************96...9*******96 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 6.7
                           BLOC1_2  26 eklNeaasekykklkdvaas 45 
                                       +k  +++ eky++ k+++++
  gi|298674488|ref|YP_003726238.1| 269 QKDEKNQDEKYTEAKEKLDK 288
                                       55557777778777777654 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8  20.8    0.0017      0.49      48     164 ..      15     136 ..       5     142 .. 0.66
   2 ?    7.5  22.4     0.018       5.2      19     152 ..      52     204 ..      51     212 .. 0.65
   3 ?    9.9  12.5    0.0032      0.94      33     134 ..     186     287 ..     154     303 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0017
                              Fez1  48 eekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeeaalesdeakaqr 124
                                       +e  ++i++l++++++k+++l+++ ++l+  +++ + l+ek ++l++++k+l +++++ +++++e++++ +e k +r
  gi|298674488|ref|YP_003726238.1|  15 RELKDKINQLRTQISQKEKNLNTIFKDLKLYRNNIDELKEKRNELNTKVKDLVSQAQDFKSKRDENNKKITELKSKR 91 
                                       34456777888888888888888888888888888888888888888888887777777777777776666666666 PP

                              Fez1 125 qe....aeeleelkreverlraeLkeerq.kkeeqassFeqERrt 164
                                       +e    +++ +++ +++++ r+eL+   + ++e+  +++ qE ++
  gi|298674488|ref|YP_003726238.1|  92 DEiqkqNKSKANEIAQLKKKRNELNDISKgTEETLSKAYSQELNK 136
                                       663222233333445566667788876551555667788888666 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.018
                              Fez1  19 Lkdsqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleee 95 
                                       Lk+ ++e+++k++++v   +q ++ ++k +e++++i+el+++++e +++++   ne+++ k++ + l++  + +ee 
  gi|298674488|ref|YP_003726238.1|  52 LKEKRNELNTKVKDLV---SQAQDFKSKRDENNKKITELKSKRDEIQKQNKSKANEIAQLKKKRNELNDISKGTEET 125
                                       9************999...5888889999999999999999999999999999999999999999999988877777 PP

                              Fez1  96 lkel.reelselsleeeeaa.....................lesdeakaqrqe..........aeeleelkreverl 140
                                       l++   +el++  +e+   +                     +          +          +++ ++  +e++  
  gi|298674488|ref|YP_003726238.1| 126 LSKAySQELNKFLNEDIPLNheidlferlenlkkrleaaqeA----------NnihhkiqeiyNTSFDDNINELNDQ 192
                                       765525667776555444447777876666555444433221..........0222223323333333333333333 PP

                              Fez1 141 raeLkeerqkke 152
                                        ++L+ e q+ +
  gi|298674488|ref|YP_003726238.1| 193 IQQLADESQQYH 204
                                       335555555544 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0032
                              Fez1  33 ivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsle 109
                                       i +l  q+++l  + ++   ++ e+ ++++e  +e + +++++++k s  + l+ k++ l++e+++lreel +  ++
  gi|298674488|ref|YP_003726238.1| 186 INELNDQIQQLADESQQYHLQMVEYFNKADEVRAEADSYHEDIKNKYSLMSPLKSKIDPLKTEISQLREELDRYLKQ 262
                                       3345666666666666666677777778888888899999999999999************************9888 PP

                              Fez1 110 eeeaalesdeakaqrqe.aeeleelk 134
                                        ++ +l++de k+q ++ +e+ e+l+
  gi|298674488|ref|YP_003726238.1| 263 LDDIQLQKDE-KNQDEKyTEAKEKLD 287
                                       8888777777.444433133333333 PP

>> DUF1871  Domain of unknown function (DUF1871)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   0.00019     0.056      30      55 ..     161     186 ..     151     200 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00019
                                       HTT-S-HHHHHHHHHHHHHHHHSS-- CS
                           DUF1871  30 vyelddpkklakkiqeiyevsFeqli 55 
                                       ++ +++++++ +kiqeiy++sF++ i
  gi|298674488|ref|YP_003726238.1| 161 LEAAQEANNIHHKIQEIYNTSFDDNI 186
                                       56778999***************987 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2  24.0    0.0017       0.5     178     283 ..      16     120 ..       2     135 .. 0.56
   2 ?    2.4  10.8       0.2        58     156     252 ..     106     202 ..     103     208 .. 0.68
   3 ?   10.0  15.0   0.00097      0.28     155     273 ..     183     302 ..     165     305 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0017
                              Spc7 178 eleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeae 254
                                       el++++++l+++  +    ++++L+++ ++l+   ++i+e+k++ +el++++++l ++ ++ k++++e +++i e +
  gi|298674488|ref|YP_003726238.1|  16 ELKDKINQLRTQISQ----KEKNLNTIFKDLKLYRNNIDELKEKRNELNTKVKDLVSQAQDFKSKRDENNKKITELK 88 
                                       555555555554433....4555666666666666666666666666666666666666666666666666655554 PP

                              Spc7 255 rvl...eeckgwsesevsrlkeevkaleeltg 283
                                       + +   +++ +++++e+ +lk++ ++l ++++
  gi|298674488|ref|YP_003726238.1|  89 SKRdeiQKQNKSKANEIAQLKKKRNELNDISK 120
                                       43311144555566666666666666665554 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.2
                              Spc7 156 elLekqeeeldellpeleeeka.eleeeleklqeaaeeles.id.keeLeelreelaelkaeieekkkelaelqeql 229
                                       ++L+k+++el+++ + +ee  + + ++el+k  ++   l+  id  e+Le+l+++l+++++  +    +++e     
  gi|298674488|ref|YP_003726238.1| 106 AQLKKKRNELNDISKGTEETLSkAYSQELNKFLNEDIPLNHeIDlFERLENLKKRLEAAQEANN-IHHKIQEIY--N 179
                                       799**********9999998874678888887664444443399899*********99987665.444444433..3 PP

                              Spc7 230 eeleekieelkeqkseleeeiae 252
                                       ++ +++i+el++q+++l +e ++
  gi|298674488|ref|YP_003726238.1| 180 TSFDDNINELNDQIQQLADESQQ 202
                                       44555555555555555555443 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00097
                              Spc7 155 kelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqlee 231
                                       ++++++ ++++++l +e ++++ ++ e ++k  e ++e +++ +e++++  + ++ lk++i+ +k+e+++l+e+l++
  gi|298674488|ref|YP_003726238.1| 183 DDNINELNDQIQQLADESQQYHLQMVEYFNKADEVRAE-ADSYHEDIKNKYSLMSPLKSKIDPLKTEISQLREELDR 258
                                       35789999999***************999999998888.6678999******************************* PP

                              Spc7 232 leekieelkeqksele..eeiaeaervleeckgwsesevsrlke 273
                                         +++++++ qk+e +  e+  ea++ l++  + s ++++ l+e
  gi|298674488|ref|YP_003726238.1| 259 YLKQLDDIQLQKDEKNqdEKYTEAKEKLDKSGRLSLEDLKILME 302
                                       *********99998762246778888888888888888777766 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6  47.7   0.00054      0.16      27     267 ..      14     286 ..      11     302 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00054
                                       XXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......... CS
                          Filament  27 nkeLeakieeleekksaevsklkelyekeleelrkqldeltkerarlqleldnlreeledlrkkyeke......... 94 
                                       ++eL+ ki++l+ + s+++++l+ + +k l+  r+++del+++r+ l+  +++l  +++d+++k +++         
  gi|298674488|ref|YP_003726238.1|  14 ERELKDKINQLRTQISQKEKNLNTI-FKDLKLYRNNIDELKEKRNELNTKVKDLVSQAQDFKSKRDENnkkitelks 89 
                                       689***********76666656555.578***********************************9988899999999 PP

                                       .....XXXXXXXXXXXXXXX.........XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXX.... CS
                          Filament  95 .....lnkreevEaelkalr.........kdldeatlarvdLekkvesLkeelaflkkvhe.eEvkelqkqvs.... 152
                                            +++ ++  +e+++l+          +  e+tl+++  ++  + L+e++ +  ++   e +++l+k+++    
  gi|298674488|ref|YP_003726238.1|  90 krdeiQKQNKSKANEIAQLKkkrnelndiSKGTEETLSKAYSQELNKFLNEDIPLNHEIDLfERLENLKKRLEaaqe 166
                                       99998444555556666666666666555445678999999999999999999998876431558888888876544 PP

                                       .XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHH CS
                          Filament 153 .eqvlvevdaarkldLteilkeiraqyeelaeknreeaeew..ykskleelqeaaeknsealrsakeeitelrrqiq 226
                                        ++++  +++  ++  +  ++e+ +q  +la+++++   ++  y +k +e++ +a++ +e++++  + ++ l+ +i+
  gi|298674488|ref|YP_003726238.1| 167 aNNIHHKIQEIYNTSFDDNINELNDQIQQLADESQQYHLQMveYFNKADEVRAEADSYHEDIKNKYSLMSPLKSKID 243
                                       444555666677777***************9998876554334899******************************* PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHH CS
                          Filament 227 sleieleslkkqkasleaqlaeleerle..aeleklqeklsel 267
                                        l++e+++l+++ + + +ql +++ + +  ++ ek+ e+ ++l
  gi|298674488|ref|YP_003726238.1| 244 PLKTEISQLREELDRYLKQLDDIQLQKDekNQDEKYTEAKEKL 286
                                       ********************99875544003444444444444 PP

>> IL5  Interleukin 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   3.3   0.00019     0.054      45     101 ..      16      73 ..       7      80 .. 0.88
   2 ?    5.1   0.2      0.09        26      32     100 ..     196     265 ..     184     270 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00019
                                       HHHHHHHHHHTTS--SS.THHHHHHHHHHHHHHHHHHHHTTTSSEEEHHHHHHHHHHH CS
                               IL5  45 eifqGidtlknqtvqge.aveklfqnlslikkyidlqkkkcgeerrrvkqfldylqef 101
                                       e+   i+ l++q+ q+e  ++++f++l+l ++ id  k+k  e   +vk+++   q+f
  gi|298674488|ref|YP_003726238.1|  16 ELKDKINQLRTQISQKEkNLNTIFKDLKLYRNNIDELKEKRNELNTKVKDLVSQAQDF 73 
                                       6667899*****99865279******************************99998888 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.09
                                       E--SSS-GGGGHHHHHHHHHHHHTTS.--SSTHHHHHHHHHHHHHHHHHHHHTTTSSEEEHHHHHHHHHH CS
                               IL5  32 svPvhknhqlcieeifqGidtlknqt.vqgeaveklfqnlslikkyidlqkkkcgeerrrvkqfldylqe 100
                                          + ++++l + e f+  d +++     +e +++ +  +s +k  id  k + ++ r + +++l  l++
  gi|298674488|ref|YP_003726238.1| 196 LADESQQYHLQMVEYFNKADEVRAEAdSYHEDIKNKYSLMSPLKSKIDPLKTEISQLREELDRYLKQLDD 265
                                       5556778889999999999999987625578899999***************************998875 PP

>> KASH_CCD  Coiled-coil region of CCDC155 or KASH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7  26.1     0.019       5.6      46     169 ..      15     140 ..       1     150 [. 0.81
   2 ?   14.0   9.8   0.00011     0.033      66     171 ..     151     253 ..     143     270 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.019
                          KASH_CCD  46 eeLkkklks.tQqalqkaklleeEleelk...alvkeleEkrarlkaqnkqlekenqsLiakiesLqeenikllaek 118
                                        eLk k+     q +qk+k l+    +lk   +++ el+Ekr++l+++ k l    q  ++k ++ + +++ l++ +
  gi|298674488|ref|YP_003726238.1|  15 RELKDKINQlRTQISQKEKNLNTIFKDLKlyrNNIDELKEKRNELNTKVKDLVSQAQDFKSKRDENNKKITELKSKR 91 
                                       467777754145788999999988888752227889999************************************** PP

                          KASH_CCD 119 delkkklkeLlkekaeLkkqlheleellaekealleektkqieeLkltieE 169
                                       de +k+ k  ++e+a+Lkk+  el+ +    e++l++     +eL+  ++E
  gi|298674488|ref|YP_003726238.1|  92 DEIQKQNKSKANEIAQLKKKRNELNDISKGTEETLSKAY--SQELNKFLNE 140
                                       ***************************999999887654..4566666665 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 0.00011
                          KASH_CCD  66 eeEleelkalvkeleEkrarlkaqnkqlekenqsLiakiesLqeenikllaekdelkkklkeLlkekaeLkkqlhel 142
                                        e le+lk+ ++  +E ++    + k  e  n s   +i++L++++++l+ e ++ + ++ e +++ +e++ +++++
  gi|298674488|ref|YP_003726238.1| 151 FERLENLKKRLEAAQEANN---IHHKIQEIYNTSFDDNINELNDQIQQLADESQQYHLQMVEYFNKADEVRAEADSY 224
                                       5778999999998888876...456667889********************************************** PP

                          KASH_CCD 143 eellaekealleektkqieeLkltieEys 171
                                       +e + +k +l++  + +i+ Lk+ i  ++
  gi|298674488|ref|YP_003726238.1| 225 HEDIKNKYSLMSPLKSKIDPLKTEISQLR 253
                                       **999999999999999999998665544 PP

>> PhageMin_Tail  Phage-related minor tail protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   2.3         2   5.8e+02     149     187 ..      28      69 ..       6     104 .. 0.62
   2 ?   12.3   0.0    0.0004      0.12      24     103 ..     136     214 ..     112     288 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 2
                     PhageMin_Tail 149 aaealkklGistkdaq...gkmksldeiledlsealkkltda 187
                                        +++ k+l  ++kd++   +++  l+e  ++l++++k+l ++
  gi|298674488|ref|YP_003726238.1|  28 ISQKEKNLNTIFKDLKlyrNNIDELKEKRNELNTKVKDLVSQ 69 
                                       233444444455666665455566666666666666666444 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.0004
                     PhageMin_Tail  24 elasaGvsteeilnllegaaklataggaddleeaaeilstalnafgls.aadaeeaaDvlaaaanngatsvedlaea 99 
                                        +   ++ ++  ++l+e   +l +  +   ++ea +i  ++ + ++ s +++++e+ D++ ++a++++    ++ e+
  gi|298674488|ref|YP_003726238.1| 136 KFLNEDIPLNHEIDLFERLENLKKRLE-A-AQEANNIHHKIQEIYNTSfDDNINELNDQIQQLADESQQYHLQMVEY 210
                                       4444566777799999***********.8.9*****************777******************99999999 PP

                     PhageMin_Tail 100 lkev 103
                                       ++++
  gi|298674488|ref|YP_003726238.1| 211 FNKA 214
                                       9874 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   1.4     0.012       3.4      91     115 ..      15      39 ..       7      47 .. 0.84
   2 ?    5.5   0.1      0.07        20      95     122 ..      47      74 ..      43      75 .. 0.90
   3 ?    5.5  22.7     0.067        19       2     121 ..      60     196 ..      59     197 .. 0.79
   4 ?    5.1  11.0     0.088        26      14     114 ..     162     266 ..     149     271 .. 0.51

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.012
                           DUF5082  91 daieeEIerLenqiseaqgvldtlq 115
                                       ++++++I++L++qis+++++l+t+ 
  gi|298674488|ref|YP_003726238.1|  15 RELKDKINQLRTQISQKEKNLNTIF 39 
                                       6799999*********999999875 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.07
                           DUF5082  95 eEIerLenqiseaqgvldtlqsqlnslk 122
                                       + I +L+++++e+ ++++ l sq +++k
  gi|298674488|ref|YP_003726238.1|  47 NNIDELKEKRNELNTKVKDLVSQAQDFK 74 
                                       579999**************99999987 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.067
                           DUF5082   2 ktkisklqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnssesWkGkeennydgirs..... 73 
                                        tk ++l +q+ + +s+++ +++kI++Lk+ +++++++++s  +++ +l+k+ n+ +   + +e++ + ++s     
  gi|298674488|ref|YP_003726238.1|  60 NTKVKDLVSQAQDFKSKRDENNKKITELKSKRDEIQKQNKSKANEIAQLKKKRNELNDISKGTEETLSKAYSqelnk 136
                                       57778899***********************************************9988888888888888877778 PP

                           DUF5082  74 ......nlessyqtyvdkldelidaie..eEIerLenqiseaqg.....vldtlqsqlnsl 121
                                              l ++++ + ++l++l++++e  +E +++  +i+e ++     +++ l+ q+++l
  gi|298674488|ref|YP_003726238.1| 137 flnediPLNHEIDLF-ERLENLKKRLEaaQEANNIHHKIQEIYNtsfddNINELNDQIQQL 196
                                       666655455555544.578899998876678888888888877533333677777777776 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.088
                           DUF5082  14 elrseiaaleekIerLk..eaktklsdekeslkqkkkklekplnssesWkGkeennydgirs...nlessyqtyvdk 85 
                                       e+ +e++ +  kI++ +  +  + + + + +++q   +++++ +++ ++ +k+++   ++ s   +++ +y+   + 
  gi|298674488|ref|YP_003726238.1| 162 EAAQEANNIHHKIQEIYntSFDDNINELNDQIQQLADESQQYHLQMVEYFNKADEVRAEADSyheDIKNKYSL-MSP 237
                                       4445666666666666633334556666666666666666666666655555444333333333455555543.345 PP

                           DUF5082  86 ldelidaieeEIerLenqiseaqgvldtl 114
                                       l++ id +++EI++L++++    + ld +
  gi|298674488|ref|YP_003726238.1| 238 LKSKIDPLKTEISQLREELDRYLKQLDDI 266
                                       56666666666666666655555555544 PP

>> HsbA  Hydrophobic surface binding protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1         1     3e+02      71     118 ..      14      63 ..       3      65 .. 0.74
   2 ?    3.2   0.5      0.39   1.1e+02      10      53 ..      58     106 ..      47     129 .. 0.77
   3 ?    1.0   0.0       1.9   5.6e+02       6      46 ..     184     229 ..     180     234 .. 0.65
   4 ?    5.1   0.0       0.1        29       4      63 ..     238     297 ..     235     302 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 1
                                       H.HCHHHHHHHHHHHHHTHHHHHHH.T-HHHHHHHHHHHHHHHHHHHHHH CS
                              HsbA  71 q.tLepdvkaaldaliaKkpafdka.gltslvlssLqdlkaasdaLsdal 118
                                       + +L+++++++ +++  K   + ++    +l ++++++lk + ++L + +
  gi|298674488|ref|YP_003726238.1|  14 ErELKDKINQLRTQISQKEKNLNTIfKDLKLYRNNIDELKEKRNELNTKV 63 
                                       44688888888888888888888664557888888888888888888766 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.39
                                       HHHHHHHHHHHHHHH--S....H...HHHHHHHHHHHHHHHHHHHHHHH CS
                              HsbA  10 tistavtaldtavnafnG....g.asalpilsasnalvsaikkattdaq 53 
                                        ++t+v++l ++ + f+     + +++++++s+ +++++ +k+ ++ + 
  gi|298674488|ref|YP_003726238.1|  58 ELNTKVKDLVSQAQDFKSkrdeNnKKITELKSKRDEIQKQNKSKANEIA 106
                                       5778888888888888667777667888888888888888887666554 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHHHHHHHHH--S....H...HHHHHHHHHHHHHHHH CS
                              HsbA   6 sdittistavtaldtavnafnG....g.asalpilsasnalvsaik 46 
                                       ++i+ +++++++l +  ++++       ++a ++   +++ + +ik
  gi|298674488|ref|YP_003726238.1| 184 DNINELNDQIQQLADESQQYHLqmveYfNKADEVRAEADSYHEDIK 229
                                       5678888888888888888844556523456666666666666666 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.1
                                       HHHHHHHHHHHHHHHHHHHHH--SH..HHHHHHHHHHHHHHHHHHHHHHHTS----HHHH CS
                              HsbA   4 visdittistavtaldtavnafnGgasalpilsasnalvsaikkattdaqasapltdeea 63 
                                       ++s i+ ++t +++l + ++ +  +++ ++++++  +   + ++a  + ++s+ l++e+ 
  gi|298674488|ref|YP_003726238.1| 238 LKSKIDPLKTEISQLREELDRYLKQLDDIQLQKDEKNQDEKYTEAKEKLDKSGRLSLEDL 297
                                       578999****************553557****************************9995 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.2      0.77   2.2e+02      36      68 ..      16      33 ..       2      55 .. 0.48
   2 ?    9.4   7.1    0.0052       1.5      24      72 ..      53     107 ..      46     110 .. 0.84
   3 ?    6.1   0.5     0.057        17      32      69 ..     165     199 ..     107     204 .. 0.72
   4 ?    5.2   1.9      0.11        32      33      70 ..     213     256 ..     206     298 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.77
                              YtxH 36 dlkekakelleeakekakekaedlkekvkekad 68
                                      +l               k+k+++l++++++k +
  gi|298674488|ref|YP_003726238.1| 16 EL---------------KDKINQLRTQISQKEK 33
                                      33...............3333333333333322 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0052
                              YtxH  24 ketRkdlkekaddlkekakelleeakeka......kekaedlkekvkekadelke 72 
                                       ke R++l+ k++dl  +a++++ +  e+       k+k ++++++ k+ka+e+++
  gi|298674488|ref|YP_003726238.1|  53 KEKRNELNTKVKDLVSQAQDFKSKRDENNkkitelKSKRDEIQKQNKSKANEIAQ 107
                                       567888888888888888888777777779*********************9975 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.057
                              YtxH  32 ekaddlkekakelleeakeka...........kekaedlkekvkekade 69 
                                       ++a+++                           +++++l +++++ ade
  gi|298674488|ref|YP_003726238.1| 165 QEANNI--------------HhkiqeiyntsfDDNINELNDQIQQLADE 199
                                       122222..............13334444445799999999999999988 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.11
                              YtxH  33 kaddlkekakelleeakeka......kekaedlkekvkekadel 70 
                                       kad+++  a++++e++k+k       k+k++ lk+++++  +el
  gi|298674488|ref|YP_003726238.1| 213 KADEVRAEADSYHEDIKNKYslmsplKSKIDPLKTEISQLREEL 256
                                       78899999999999999999999999666666666666655543 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8  10.6     0.011       3.2      20      96 ..      15      88 ..       2      95 .. 0.82
   2 ?    7.4  11.2     0.014       4.1       3      95 ..      82     177 ..      80     180 .. 0.89
   3 ?    7.3   3.4     0.016       4.6       4      84 ..     185     272 ..     180     289 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.011
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHHHHHH CS
                        Laminin_II 20 aplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdniseik 96
                                       +l+ ++++++ ++s+ +++++ + +++k + + i++ +++  +L+ ++ +L+++ +  k ++++++   ++i e+k
  gi|298674488|ref|YP_003726238.1| 15 RELKDKINQLRTQISQKEKNLNTIFKDLKLYRNNIDELKEKRNELNTKVKDLVSQAQDFKSKRDENN---KKITELK 88
                                      5778888899999999999999999999999999999999999999999999999999999999966...5555555 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.014
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXX--TTTTTGGGHHHH CS
                        Laminin_II   3 elaaeanetakevleqlaplsqnlentkeklseinrsveetnekvk.dankairdArrsvkkLeklapqLldklkel 78 
                                       ++++e +++  e+++q +  ++++ ++k+k +e+n+  + t+e ++ ++++ ++   ++   L+++++ L+++l++l
  gi|298674488|ref|YP_003726238.1|  82 KKITELKSKRDEIQKQNKSKANEIAQLKKKRNELNDISKGTEETLSkAYSQELNKFLNEDIPLNHEID-LFERLENL 157
                                       6789999999999***9999**************9999999999986889999999999999999995.9******* PP

                                       HHHHHH......HHHHHHHH CS
                        Laminin_II  79 kqleeasss...lsdnisei 95 
                                       k++ ea +    + ++i+ei
  gi|298674488|ref|YP_003726238.1| 158 KKRLEAAQEannIHHKIQEI 177
                                       **999977678899999998 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.016
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.......XXXXXXXXXXXXXXXX--TTTTTGG CS
                        Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvk.......dankairdArrsvkkLeklapqLld 73 
                                       +++e n+++++  +  ++ + ++ +  +k+ e++++++  +e++k        ++  i+  ++++++L +++++ l+
  gi|298674488|ref|YP_003726238.1| 185 NINELNDQIQQLADESQQYHLQMVEYFNKADEVRAEADSYHEDIKnkyslmsPLKSKIDPLKTEISQLREELDRYLK 261
                                       56777777777778888888888888888888888888888887733322222344566667777777777777777 PP

                                       GHHHHHHHHHH CS
                        Laminin_II  74 klkelkqleea 84 
                                       +l  ++ ++++
  gi|298674488|ref|YP_003726238.1| 262 QLDDIQLQKDE 272
                                       77777655554 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5  12.6   0.00024     0.068       7      77 ..      20      91 ..      15      92 .. 0.93
   2 ?    5.1  14.0       0.1        30       7      86 ..      58     137 ..      57     140 .. 0.80
   3 ?   -0.1  15.5       4.1   1.2e+03      10      76 ..     184     287 ..     144     303 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00024
                        Syntaxin_2  7 kinsnvstleklvkqLgtk.kdteelreklhelieeinelikktnellkklsqldnsssdsqqklqkekLkk 77
                                      kin++ +++ ++ k L+t  kd + +r++++el e+ nel +k+++l+++ +  + + + +++k+++ k k+
  gi|298674488|ref|YP_003726238.1| 20 KINQLRTQISQKEKNLNTIfKDLKLYRNNIDELKEKRNELNTKVKDLVSQAQDFKSKRDENNKKITELKSKR 91
                                      89****************989*********************************999988899998877766 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.1
                        Syntaxin_2   7 kinsnvstleklvkqLgtkkdteelreklhelieeinelikktnellkklsqldnsssds..qqklqkekLkkdfke 81 
                                       ++n++v+ l ++ ++ ++k+d  e ++k+ el ++  e+ k+ +++ ++++ql+++ +      k ++e L+k +++
  gi|298674488|ref|YP_003726238.1|  58 ELNTKVKDLVSQAQDFKSKRD--ENNKKITELKSKRDEIQKQNKSKANEIAQLKKKRNELndISKGTEETLSKAYSQ 132
                                       678888888888888999988..5558888888888888888888888888888777554557778*********** PP

                        Syntaxin_2  82 alqeF 86 
                                        l++F
  gi|298674488|ref|YP_003726238.1| 133 ELNKF 137
                                       ****9 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 4.1
                        Syntaxin_2  10 snvstleklvkqLgtkkdteelr.................................eklhelieeinelikktnell 53 
                                        n+++l+ +++qL +  ++ +l+                                 +k++ l +ei++l ++  + l
  gi|298674488|ref|YP_003726238.1| 184 DNINELNDQIQQLADESQQYHLQmveyfnkadevraeadsyhediknkyslmsplkSKIDPLKTEISQLREELDRYL 260
                                       34444444444444443333333333443333333555555555555566666666666666666666666666666 PP

                        Syntaxin_2  54 kklsqldnsssds...qqkl.qkekLk 76 
                                       k+l+ ++ +++ +    +++ +kekL 
  gi|298674488|ref|YP_003726238.1| 261 KQLDDIQLQKDEKnqdEKYTeAKEKLD 287
                                       666666666655555322224556655 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.6      0.38   1.1e+02      22      59 ..      11      48 ..       2      51 .. 0.64
   2 ?   13.3  13.1   0.00013     0.037       4     101 ..      42     138 ..      39     149 .. 0.90
   3 ?    0.9   1.9      0.73   2.1e+02       7      52 ..     157     199 ..     129     214 .. 0.43
   4 ?    2.8   3.0      0.19        55       3      46 ..     185     228 ..     151     234 .. 0.59
   5 ?    9.4   7.1     0.002      0.58       3      88 ..     185     269 ..     183     295 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.38
                             TMPIT 22 kqkleelsklqskcskeikkqkkrlkelksslkklkks 59
                                      + + +el+  +++++++i++++k+l+ + ++lk ++++
  gi|298674488|ref|YP_003726238.1| 11 NMSERELKDKINQLRTQISQKEKNLNTIFKDLKLYRNN 48
                                      44556677777777777777777777777777766554 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00013
                             TMPIT   4 weelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkk 80 
                                       ++  +++++el+e+ +e+++k+++l ++ ++++++ ++++k+++elks+ ++++k+ ++++++e+++lk++ +e + 
  gi|298674488|ref|YP_003726238.1|  42 LKLYRNNIDELKEKRNELNTKVKDLVSQAQDFKSKRDENNKKITELKSKRDEIQKQ-NKSKANEIAQLKKKRNELND 117
                                       556678999*********************************************99.5799999************* PP

                             TMPIT  81 vlkevesllpkknglylklvl 101
                                       + k +e++l k  +  l+ +l
  gi|298674488|ref|YP_003726238.1| 118 ISKGTEETLSKAYSQELNKFL 138
                                       ********9998776666665 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.73
                             TMPIT   7 lekefkeleetakeykqkleelsklqskcskeikkqkkrlkelkss 52 
                                       l+k++++ +e++ ++++k++e+ +  +++  +i++ + ++++l ++
  gi|298674488|ref|YP_003726238.1| 157 LKKRLEAAQEAN-NIHHKIQEIYN--TSFDDNINELNDQIQQLADE 199
                                       223333333222.22222222211..11222222222222222222 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.19
                             TMPIT   3 eweelekefkeleetakeykqkleelsklqskcskeikkqkkrl 46 
                                       +++el++++++l ++ ++y+ ++ e+++  ++++ e+++ ++++
  gi|298674488|ref|YP_003726238.1| 185 NINELNDQIQQLADESQQYHLQMVEYFNKADEVRAEADSYHEDI 228
                                       45555666666666666666666666666655555555555444 PP

  == domain 5  score: 9.4 bits;  conditional E-value: 0.002
                             TMPIT   3 eweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerk 79 
                                       +++el++++++l ++ ++y+ ++ e+++  ++++ e+++ ++++k+  s ++ lk++++   ++e+++l+eel++  
  gi|298674488|ref|YP_003726238.1| 185 NINELNDQIQQLADESQQYHLQMVEYFNKADEVRAEADSYHEDIKNKYSLMSPLKSKID-PLKTEISQLREELDRYL 260
                                       67888999999999999999999999999999999999999999998888888888875.55667788888888888 PP

                             TMPIT  80 kvlkevesl 88 
                                       k+l++++  
  gi|298674488|ref|YP_003726238.1| 261 KQLDDIQLQ 269
                                       888877644 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   5.1    0.0075       2.2      96     146 ..      20      70 ..      10      75 .. 0.65
   2 ?    5.9   9.5     0.045        13      95     146 ..      75     126 ..      69     132 .. 0.89
   3 ?    7.0  12.7     0.021         6      27     157 ..     150     267 ..     121     288 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0075
                             ATG16  96 srgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeel 146
                                       + ++l +++ ++++ l +  + lk  +++++el+++r++l+tk+kd+  + 
  gi|298674488|ref|YP_003726238.1|  20 KINQLRTQISQKEKNLNTIFKDLKLYRNNIDELKEKRNELNTKVKDLVSQA 70 
                                       345666777777777777777777777777777777777777777766554 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.045
                             ATG16  95 ksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeel 146
                                        +r e++++++el+++ ++ +++ k++++++a+l+++r++l++  k  ee+l
  gi|298674488|ref|YP_003726238.1|  75 SKRDENNKKITELKSKRDEIQKQNKSKANEIAQLKKKRNELNDISKGTEETL 126
                                       57899************************************99888887776 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.021
                             ATG16  27 Lldrtsaleaenaklekaaasakssksskksakekeasasq.....snskqsakiqsleqklaqlreelaelyksrg 98 
                                       L++r + l+++ +++++a ++ +                        n++ +++i++l+++++ql +e ++ + +  
  gi|298674488|ref|YP_003726238.1| 150 LFERLENLKKRLEAAQEA-NNIH-----------------HkiqeiYNTSFDDNINELNDQIQQLADESQQYHLQMV 208
                                       666666666665555322.1111.................0111123445578999999999999999999999999 PP

                             ATG16  99 elaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlq 157
                                       e  ++  e+ +e +   e +k++ + +  l++++  l+t++++++eel    k ++d+q
  gi|298674488|ref|YP_003726238.1| 209 EYFNKADEVRAEADSYHEDIKNKYSLMSPLKSKIDPLKTEISQLREELDRYLKQLDDIQ 267
                                       99999999999999999999999999999999999999999999999998888887665 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   2.4     0.014       3.9      23      79 ..      16      72 ..      11      81 .. 0.72
   2 ?    3.5   1.7       0.3        85      26      68 ..      82     123 ..      73     140 .. 0.77
   3 ?    8.1   0.5     0.011       3.1      28      87 ..     186     252 ..     152     254 .. 0.76
   4 ?    3.2   0.0      0.36   1.1e+02      24      52 ..     238     266 ..     233     288 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.014
                            DUF948 23 klkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavad 79
                                      +lk+ +++++++i + ek+++ i k+++   +++ el e  ne   kv+ l+++++d
  gi|298674488|ref|YP_003726238.1| 16 ELKDKINQLRTQISQKEKNLNTIFKDLKLYRNNIDELKEKRNELNTKVKDLVSQAQD 72
                                      466667777777777777777777777777777777777777777777777777776 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.3
                            DUF948  26 ktldeaaatieelekqvdpilkevedllakvnelledvnekle 68 
                                       k ++e+++  +e++kq ++  +e+++l +k ne l+d+++ +e
  gi|298674488|ref|YP_003726238.1|  82 KKITELKSKRDEIQKQNKSKANEIAQLKKKRNE-LNDISKGTE 123
                                       556677777778888888888888888888888.777766544 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.011
                            DUF948  28 ldeaaatieele.......kqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                       ++e++++i++l         q+ ++ ++++++ a++    ed+++k   + pl +++  l + +s+l
  gi|298674488|ref|YP_003726238.1| 186 INELNDQIQQLAdesqqyhLQMVEYFNKADEVRAEADSYHEDIKNKYSLMSPLKSKIDPLKTEISQL 252
                                       4455555555552222222677777777777777777799999999999999999999999999988 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.36
                            DUF948  24 lkktldeaaatieelekqvdpilkevedl 52 
                                       lk+ +d +++ i +l++++d +lk+++d+
  gi|298674488|ref|YP_003726238.1| 238 LKSKIDPLKTEISQLREELDRYLKQLDDI 266
                                       34444555555555555555555555543 PP

>> ApoO  Apolipoprotein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   3.1       1.3   3.7e+02      16      52 ..      17      52 ..       4     137 .. 0.63
   2 ?    2.5   0.2      0.47   1.4e+02      24      64 ..     160     201 ..     153     210 .. 0.77
   3 ?    8.8   0.1     0.005       1.4       4      47 ..     233     281 ..     230     289 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 1.3
                              ApoO 16 LeegvrslRkslepytsavqdelnkvkskvetaeqsv 52
                                      L+ ++++lR +++++ + ++  ++++k  + +    +
  gi|298674488|ref|YP_003726238.1| 17 LKDKINQLRTQISQKEKNLNTIFKDLKL-YRNNIDEL 52
                                      5555566666655555555555533322.12222222 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.47
                              ApoO  24 Rkslepytsavqdelnkvks.kvetaeqsvtdtiasLkeppe 64 
                                       R+++ ++++ ++++++++++ ++++  + ++d+i++L+++++
  gi|298674488|ref|YP_003726238.1| 160 RLEAAQEANNIHHKIQEIYNtSFDDNINELNDQIQQLADESQ 201
                                       778888888888888887652567788999999999998764 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.005
                              ApoO   4 svrtpseeptdrLeegvrslRkslepytsavqdel.....nkvkskvet 47 
                                       s  +p +++ d L++ +++lR++l +y+++++d       +++ +k+ +
  gi|298674488|ref|YP_003726238.1| 233 SLMSPLKSKIDPLKTEISQLREELDRYLKQLDDIQlqkdeKNQDEKYTE 281
                                       5555667789********************9997755555555555554 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   2.3      0.21        60      82     105 ..      14      37 ..       2      47 .. 0.73
   2 ?   11.4  21.1    0.0011      0.31      24     106 ..      47     129 ..      40     140 .. 0.87
   3 ?   10.3   9.1    0.0025      0.71       9     108 ..     162     261 ..     154     267 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.21
                           DUF4200  82 ikklkaeietlkseiekleeklee 105
                                        ++lk++i++l+++i++ e++l+ 
  gi|298674488|ref|YP_003726238.1|  14 ERELKDKINQLRTQISQKEKNLNT 37 
                                       567888888888888888887764 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0011
                           DUF4200  24 rleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkaeietlkseiekle 100
                                       +  ++lk++++el+ k + l  +++ f+    en++k ++   k +e +k++k+k++ei++lk++ ++l+   + +e
  gi|298674488|ref|YP_003726238.1|  47 NNIDELKEKRNELNTKVKDLVSQAQDFKSKRDENNKKITELKSKRDEIQKQNKSKANEIAQLKKKRNELNDISKGTE 123
                                       55678999**************************************************************9999999 PP

                           DUF4200 101 ekleey 106
                                       e+l + 
  gi|298674488|ref|YP_003726238.1| 124 ETLSKA 129
                                       999864 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.0025
                           DUF4200   9 fevqealeakkeeiqrleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikkl 85 
                                       + +qea +   +  +  + ++++  +el+++ q+l ++ +++   + e  +k  + + +a++ ++ +k+k + +  l
  gi|298674488|ref|YP_003726238.1| 162 EAAQEANNIHHKIQEIYNTSFDDNINELNDQIQQLADESQQYHLQMVEYFNKADEVRAEADSYHEDIKNKYSLMSPL 238
                                       333333333333333467799999***************************************************** PP

                           DUF4200  86 kaeietlkseiekleekleeykk 108
                                       k++i+ lk+ei++l e+l++y k
  gi|298674488|ref|YP_003726238.1| 239 KSKIDPLKTEISQLREELDRYLK 261
                                       ********************976 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   9.4   0.00084      0.24      19      82 ..      12      75 ..       2      82 .. 0.81
   2 ?    7.0  14.7     0.025       7.1      26      96 ..      71     139 ..      69     143 .. 0.81
   3 ?    6.2   5.2     0.042        12      12      94 ..     162     238 ..     144     244 .. 0.49
   4 ?    3.2   7.5      0.36   1.1e+02      22      74 ..     236     284 ..     219     301 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00084
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS..-HHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH 19 aaqeqlekkfkklqaeleakekelqklqeelqkkakkl.ekeekeqelqkkeqelqqkqqqkaqe 82
                                        + +l++k+++l++++ +kek+l++  ++l+ + ++  e +ek++el++k+++l   q+q+++ 
  gi|298674488|ref|YP_003726238.1| 12 MSERELKDKINQLRTQISQKEKNLNTIFKDLKLYRNNIdELKEKRNELNTKVKDLVS-QAQDFKS 75
                                      55789**************************98888876799999*********999.7766543 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.025
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  26 kkfkklqaeleakekelqklqeelqkkakklekeekeqelqkkeqelqqkqqqkaqelqkkqqellkpild 96 
                                       ++fk+ ++e ++k +el+++++e+qk++k+  k+++  +l+kk++el++  + +++ l k+  ++l+++l+
  gi|298674488|ref|YP_003726238.1|  71 QDFKSKRDENNKKITELKSKRDEIQKQNKS--KANEIAQLKKKRNELNDISKGTEETLSKAYSQELNKFLN 139
                                       5789999999**************977666..666666699999999997777778899999888888765 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.042
                                       HHSHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  12 eespegkaaqeqlekkf.kklqaeleakekelqklqeelqkkakklekeekeqelqkkeqelqqkqqqkaqelqkkq 87 
                                       e+ +e++++  ++++ + +++++ ++++++++q+l++e q++  +        e+ +k +e++++++   +++++k 
  gi|298674488|ref|YP_003726238.1| 162 EAAQEANNIHHKIQEIYnTSFDDNINELNDQIQQLADESQQYHLQ------MVEYFNKADEVRAEADSYHEDIKNKY 232
                                       333344444444444333345555555555555555555444443......44455555555553333335555555 PP

                                       HHHHHHH CS
                              OmpH  88 qellkpi 94 
                                         l+ p+
  gi|298674488|ref|YP_003726238.1| 233 -SLMSPL 238
                                       .555555 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.36
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHHHHHHHHHHHH CS
                              OmpH  22 eqlekkfkklqaeleakekelqklqeelqkkakklekeekeqelqkkeqelqq 74 
                                       + l++k+ +l++e+ ++++el++  ++l++ + ++    +e+  ++k +e ++
  gi|298674488|ref|YP_003726238.1| 236 SPLKSKIDPLKTEISQLREELDRYLKQLDDIQLQK----DEKNQDEKYTEAKE 284
                                       34556666666666666666666666665444443....22223333333322 PP

>> T3SSipB  Type III cell invasion protein SipB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9  14.4    0.0069         2      15     128 ..       9     113 ..       7     141 .. 0.77
   2 ?    3.0   5.6      0.46   1.3e+02      21     111 ..     106     197 ..     101     202 .. 0.70
   3 ?    5.6   7.3     0.073        21      31     135 ..     194     288 ..     179     297 .. 0.43

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0069
                                       HHHHCHHHHHHHHHHHHHHHHHTTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                           T3SSipB  15 lgnkSLsqLenrlaawkamskaqqeaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlk 91 
                                       ++n S  +L+++++  + ++  +++++  + + l+   ++ ++++++ ++   k++++ s+a++ + k de  k++ 
  gi|298674488|ref|YP_003726238.1|   9 ISNMSERELKDKINQLRTQISQKEKNLNTIFKDLKLYRNNIDELKEKRNELNTKVKDLVSQAQDFKSKRDENNKKIT 85 
                                       689999*********************************************************************** PP

                                       T---------CHHHHHHHHH..HHHHHHHHHHHHHHH CS
                           T3SSipB  92 eLaPdePekakleaaeqQagaaadalqadealqKkld 128
                                       eL        k +++e+Q +++  a +  + l+Kk +
  gi|298674488|ref|YP_003726238.1|  86 EL--------KSKRDEIQKQNKSKANEIAQ-LKKKRN 113
                                       **........66677777776655555555.444432 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.46
                                       HHHHHHHHHHHHHHHHTTTTT--.--STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---- CS
                           T3SSipB  21 sqLenrlaawkamskaqqeaask.lSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPd 96 
                                        qL+++ +  +  sk+++e +sk  S+el++ l+e   +  ++ +  e+++++k+  +aa++ ++++ ++++e+   
  gi|298674488|ref|YP_003726238.1| 106 AQLKKKRNELNDISKGTEETLSKaYSQELNKFLNEDIPLNHEI-DLFERLENLKKRLEAAQE-ANNIHHKIQEIYNT 180
                                       799999999999****999887538**********99998876.467888888888887765.57788888888443 PP

                                       -..----CHHHHHHHHH CS
                           T3SSipB  97 e..PekakleaaeqQag 111
                                       +   +  +l+ + qQ++
  gi|298674488|ref|YP_003726238.1| 181 SfdDNINELNDQIQQLA 197
                                       30023334444444443 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.073
                                       HHHHHHTTTTT----STHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---------CHH CS
                           T3SSipB  31 kamskaqqeaasklSdelqtals...eakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPdePekakle 104
                                       ++     q+  +++ + +++a +   ea+   +d++++   +  +ks++d ++  +++  + l+         ++l 
  gi|298674488|ref|YP_003726238.1| 194 QQLADESQQYHLQMVEYFNKADEvraEADSYHEDIKNKYSLMSPLKSKIDPLKTEISQLREELDRY------LKQL- 263
                                       333344455556666666665331112222222333333333444555555555555555544433......1222. PP

                                       HHHHHHH..HHHHHHHHHHHHHHHHHHHHHH CS
                           T3SSipB 105 aaeqQagaaadalqadealqKkldaasklse 135
                                        + +Q++  +d  ++de   K ++a +kl +
  gi|298674488|ref|YP_003726238.1| 264 -DDIQLQ--KDEKNQDE---KYTEAKEKLDK 288
                                       .222333..33333333...44455555443 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3  12.5     0.049        14      70     168 ..      13     111 ..       8     114 .. 0.96
   2 ?    9.4   4.6    0.0027      0.78      71     164 ..     164     258 ..     152     263 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.049
                            DUF745  70 elreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkk 146
                                       + re ++ +++  +++++ e+n+++  k  k  +++++ lk+  ++ +++++++ + a+  +++ +e ++ +++ k+
  gi|298674488|ref|YP_003726238.1|  13 SERELKDKINQLRTQISQKEKNLNTIFKDLKLYRNNIDELKEKRNELNTKVKDLVSQAQDFKSKRDENNKKITELKS 89 
                                       56899999********************************************************************* PP

                            DUF745 147 RveeLkkqlkearkdlektkka 168
                                       + +e++kq k+  ++ ++ kk+
  gi|298674488|ref|YP_003726238.1|  90 KRDEIQKQNKSKANEIAQLKKK 111
                                       ****************999986 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0027
                            DUF745  71 lreaeavvqeekkslqss.eanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkk 146
                                        +ea+++ +++++ +++s   n++  ++  +q   + ++ +  + ++ ++++++++ a++  +++++k +l+   k+
  gi|298674488|ref|YP_003726238.1| 164 AQEANNIHHKIQEIYNTSfDDNINELNDQIQQLADESQQYHLQMVEYFNKADEVRAEADSYHEDIKNKYSLMSPLKS 240
                                       3455555555555555554578999999999998888888888888889999999999999**************** PP

                            DUF745 147 RveeLkkqlkearkdlek 164
                                       +++ Lk+++++ r++l++
  gi|298674488|ref|YP_003726238.1| 241 KIDPLKTEISQLREELDR 258
                                       ***************987 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   4.1      0.03       8.8      48     110 ..      15      77 ..       2      81 .. 0.73
   2 ?    7.1   6.0     0.021       6.1       9      71 ..      72     129 ..      64     136 .. 0.84
   3 ?    6.8   9.4     0.026       7.4       4      90 ..     197     278 ..     180     296 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.03
                              FliJ  48 rnyqafisaldeaiaqqkqelaqaekqvekareewqearqerkklekLkerekkeeqkeenrr 110
                                       r ++  i++l+++i+q +++l+   k+++ +r++  e + +r+ l +  +    ++q    +r
  gi|298674488|ref|YP_003726238.1|  15 RELKDKINQLRTQISQKEKNLNTIFKDLKLYRNNIDELKEKRNELNTKVKDLVSQAQDFKSKR 77 
                                       556677899999999999999999999999999988888888887765555555555555555 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.021
                              FliJ   9 eaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqa 71 
                                         + +++++++k++el++ r+e qkq +++a     +e+ ++++ ++ l++  + ++++l++a
  gi|298674488|ref|YP_003726238.1|  72 DFKSKRDENNKKITELKSKRDEIQKQNKSKA-----NEIAQLKKKRNELNDISKGTEETLSKA 129
                                       5678899***********************9.....888888888888888888888888776 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.026
                              FliJ   4 areLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekare 80 
                                       a e ++ + +  ++ +k +e++ + ++y++ +++++     + +  +++ i+ l+++i+q+++el++  kq++  + 
  gi|298674488|ref|YP_003726238.1| 197 ADESQQYHLQMVEYFNKADEVRAEADSYHEDIKNKY-----SLMSPLKSKIDPLKTEISQLREELDRYLKQLDDIQL 268
                                       455556666667777888888888888888888888.....888888888888888888888888888888888888 PP

                              FliJ  81 ewqearqerk 90 
                                       +  e++q +k
  gi|298674488|ref|YP_003726238.1| 269 QKDEKNQDEK 278
                                       8777777766 PP

>> HCMV_UL139  Human Cytomegalovirus UL139 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   1.1     0.043        12      43      88 ..      18      61 ..      12      77 .. 0.82
   2 ?    2.8   5.0      0.49   1.4e+02      42      85 ..      59     102 ..      55     140 .. 0.73
   3 ?    8.1   0.4     0.011       3.3      42      93 ..     238     285 ..     234     291 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.043
                        HCMV_UL139 43 nsrilslrseidaldakyvaisrdlrslkgeveeaerkeeereryy 88
                                        +i  lr++i + +   ++i +dl+  + +++e+++k +e    +
  gi|298674488|ref|YP_003726238.1| 18 KDKINQLRTQISQKEKNLNTIFKDLKLYRNNIDELKEKRNE--LNT 61
                                      568999******************************99998..334 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.49
                        HCMV_UL139  42 lnsrilslrseidaldakyvaisrdlrslkgeveeaerkeeere 85 
                                       ln ++  l s+ ++ ++k++   +++ +lk+  +e++++++ + 
  gi|298674488|ref|YP_003726238.1|  59 LNTKVKDLVSQAQDFKSKRDENNKKITELKSKRDEIQKQNKSKA 102
                                       67888888888888888888888888888888888888777653 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.011
                        HCMV_UL139  42 lnsrilslrseidaldakyvaisrdlrslkgeveeaerkeeereryyeakrk 93 
                                       l s+i  l++ei +l+   + + ++l +++ + +e   k+++ e+y+eak k
  gi|298674488|ref|YP_003726238.1| 238 LKSKIDPLKTEISQLREELDRYLKQLDDIQLQKDE---KNQD-EKYTEAKEK 285
                                       5689999*********************9988333...3333.489999976 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   4.1    0.0036         1      60     120 ..      13      73 ..       4      77 .. 0.81
   2 ?    3.5   6.5      0.24        70      48      91 ..      85     128 ..      71     165 .. 0.60
   3 ?    5.7   1.9     0.049        14      55     106 ..     152     203 ..     144     217 .. 0.49
   4 ?    3.6   0.7      0.22        63      46      96 ..     238     286 ..     229     295 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0036
                           DUF1664  60 tkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                         r+L+++i+++ +++ + ++  + i ++++  r++++e++e+ +++++ v++l s+ ++ 
  gi|298674488|ref|YP_003726238.1|  13 SERELKDKINQLRTQISQKEKNLNTIFKDLKLYRNNIDELKEKRNELNTKVKDLVSQAQDF 73 
                                       4688999999999999999999999999999999999999999999999999887776655 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.24
                           DUF1664  48 kqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevte 91 
                                       ++l++  ++++++ +  +++i+++ kk +e ++isk ++e +++
  gi|298674488|ref|YP_003726238.1|  85 TELKSKRDEIQKQNKSKANEIAQLKKKRNELNDISKGTEETLSK 128
                                       23344445555555555555555555555555555555555554 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.049
                           DUF1664  55 eslaatkrhLs..sridrvdkkldeqkeiskeikeevtevredlseigedvesv 106
                                       e l++ k++L+  ++ +++ +k++e  +  ++ +++++e++++++++ +++++ 
  gi|298674488|ref|YP_003726238.1| 152 ERLENLKKRLEaaQEANNIHHKIQEIYN--TSFDDNINELNDQIQQLADESQQY 203
                                       3344444444311333344444433332..334555555555555555555554 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.22
                           DUF1664  46 vskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredl 96 
                                       + ++++ +++++++ +++L + ++++d+ + +  e  k+ +e+ te++e+l
  gi|298674488|ref|YP_003726238.1| 238 LKSKIDPLKTEISQLREELDRYLKQLDDIQLQKDE--KNQDEKYTEAKEKL 286
                                       56778888888888888888888888875444333..33345555555555 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   6.3     0.017       4.8      75     125 ..      16      69 ..       3      72 .. 0.56
   2 ?   11.6  10.5   0.00075      0.22      57     120 ..      40      99 ..      33     100 .. 0.71
   3 ?    1.7   8.9      0.85   2.5e+02      52     123 ..     101     172 ..      99     177 .. 0.84
   4 ?    8.1  12.3    0.0088       2.5       2     103 ..     185     288 ..     184     298 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.017
                        TPR_MLP1_2  75 elkaeaesakaeleeseeswe...eqkeelekelselekriedlneqNklLhdQ 125
                                       elk++ ++++++++++e++++   +  + ++++++el++++++ln++ k L +Q
  gi|298674488|ref|YP_003726238.1|  16 ELKDKINQLRTQISQKEKNLNtifKDLKLYRNNIDELKEKRNELNTKVKDLVSQ 69 
                                       455555555555555554444111345556666666666666666665555555 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00075
                        TPR_MLP1_2  57 kelqalreelnelkaeiaelkaeaesakaeleeseesweeqkeelekelselekriedlneqNk 120
                                       k+l+ +r+ ++elk++++el++++++    l  + +  +++++e  k+++el+++++++++qNk
  gi|298674488|ref|YP_003726238.1|  40 KDLKLYRNNIDELKEKRNELNTKVKD----LVSQAQDFKSKRDENNKKITELKSKRDEIQKQNK 99 
                                       45555566666666666666665554....45566778889999999****************8 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.85
                        TPR_MLP1_2  52 haedvkelqalreelnelkaeiaelkaeaesakaeleeseesweeqkeelekelselekriedlneqNklLh 123
                                       +a+++ +l++ r+eln++ +  +e  ++a s + +   +e    +++  l ++l++l+kr+e  +e N++ h
  gi|298674488|ref|YP_003726238.1| 101 KANEIAQLKKKRNELNDISKGTEETLSKAYSQELNKFLNEDIPLNHEIDLFERLENLKKRLEAAQEANNIHH 172
                                       5778888888888888888888888888888888888899999999999*******************9855 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.0088
                        TPR_MLP1_2   2 elksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelka 78 
                                       ++++l+++i++l +e++++  ++ ++ ++  + +++a   +++ ++   + +    ++  l++e+++l++e+    +
  gi|298674488|ref|YP_003726238.1| 185 NINELNDQIQQLADESQQYHLQMVEYFNKADEVRAEADSYHEDIKNKYSLMSPLKSKIDPLKTEISQLREELDRYLK 261
                                       6899************************************************************************* PP

                        TPR_MLP1_2  79 eaesakael..eeseesweeqkeelek 103
                                       ++++ + +   +++ e+ +e ke+l+k
  gi|298674488|ref|YP_003726238.1| 262 QLDDIQLQKdeKNQDEKYTEAKEKLDK 288
                                       *99876554005556777788888776 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.9       1.1     3e+02      44      62 ..      16      34 ..      11      43 .. 0.75
   2 ?    9.4   5.1    0.0039       1.1      25      62 ..      53      90 ..      46      92 .. 0.93
   3 ?    5.9   8.8     0.049        14      26      62 ..      82     118 ..      77     120 .. 0.90
   4 ?    0.4   0.2       2.5   7.2e+02      45      57 ..     150     162 ..     144     177 .. 0.69
   5 ?    3.8   0.1      0.22        62      42      62 ..     179     199 ..     165     201 .. 0.86
   6 ?    9.5   0.4    0.0035         1      28      59 ..     235     266 ..     229     271 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 1.1
                                      HHHHHHHHHHHHHHHHHHH CS
                            bZIP_1 44 sLkseleelkkevekLksk 62
                                      +Lk+++++l+ ++++++++
  gi|298674488|ref|YP_003726238.1| 16 ELKDKINQLRTQISQKEKN 34
                                      5778888888887776655 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0039
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1 25 qaeieeLerrvkaLekeNksLkseleelkkevekLksk 62
                                      +++ +eL ++vk L ++ ++ ks+ +e +k++ +Lksk
  gi|298674488|ref|YP_003726238.1| 53 KEKRNELNTKVKDLVSQAQDFKSKRDENNKKITELKSK 90
                                      566789******************************98 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.049
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  26 aeieeLerrvkaLekeNksLkseleelkkevekLksk 62 
                                       ++i eL+++ ++++k+Nks ++e+ +lkk++++L + 
  gi|298674488|ref|YP_003726238.1|  82 KKITELKSKRDEIQKQNKSKANEIAQLKKKRNELNDI 118
                                       7899***************************999765 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 2.5
                                       HHHHHHHHHHHHH CS
                            bZIP_1  45 Lkseleelkkeve 57 
                                       L ++le+lkk  e
  gi|298674488|ref|YP_003726238.1| 150 LFERLENLKKRLE 162
                                       5666777776655 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.22
                                       HHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  42 NksLkseleelkkevekLksk 62 
                                       N+s  + ++el++++++L ++
  gi|298674488|ref|YP_003726238.1| 179 NTSFDDNINELNDQIQQLADE 199
                                       8899999*********99876 PP

  == domain 6  score: 9.5 bits;  conditional E-value: 0.0035
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  28 ieeLerrvkaLekeNksLkseleelkkevekL 59 
                                       ++ L+++ + L++e ++L++el+++ k+ +  
  gi|298674488|ref|YP_003726238.1| 235 MSPLKSKIDPLKTEISQLREELDRYLKQLDDI 266
                                       66799999999999999999999999987765 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5  11.6       4.2   1.2e+03      77     136 ..      16      75 ..       1      83 [. 0.38
   2 ?    4.8  18.7     0.098        28       4      99 ..      72     164 ..      69     167 .. 0.75
   3 ?    8.9   7.0    0.0056       1.6       2      81 ..     154     231 ..     153     235 .. 0.73
   4 ?   10.4   7.9    0.0019      0.55       9      77 ..     214     282 ..     211     298 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 4.2
                     Tropomyosin_1  77 altrkiqlLEeeleesdkkLkettekLretdvkaeelERkvkaLeqerdewekkyeelee 136
                                       +l+ ki++L  ++ + +k+L++  + L+    + +el  k+++L+++ ++  ++ +++++
  gi|298674488|ref|YP_003726238.1|  16 ELKDKINQLRTQISQKEKNLNTIFKDLKLYRNNIDELKEKRNELNTKVKDLVSQAQDFKS 75 
                                       333333333333333333333333333333333333333333333333333333333322 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.098
                     Tropomyosin_1   4 sLkleaeeaqekaeeleekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakekaeesekkktnne..al 78 
                                         k   +e  +k  el++k  e +++n++k +ei++L+kk ++l++    +ee+l++a ++   + +k   ne   l
  gi|298674488|ref|YP_003726238.1|  72 DFKSKRDENNKKITELKSKRDEIQKQNKSKANEIAQLKKKRNELNDISKGTEETLSKAYSQ---ELNK-FLNEdiPL 144
                                       57888999************************************99999999999865433...2222.22222466 PP

                     Tropomyosin_1  79 trkiqlLEeeleesdkkLket 99 
                                       +  i+l E  le+  k+L+ +
  gi|298674488|ref|YP_003726238.1| 145 NHEIDLFE-RLENLKKRLEAA 164
                                       66666654.466666666555 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0056
                     Tropomyosin_1   2 lnsLkleaeeaqekaeeleekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakekaeese.kkktnnea 77 
                                       l++Lk   e+aqe   + + + K +e  n++ +++i++L+ ++qql +e  ++  ++ e+ +ka+e   ++++  e 
  gi|298674488|ref|YP_003726238.1| 154 LENLKKRLEAAQE---ANNIHHKIQEIYNTSFDDNINELNDQIQQLADESQQYHLQMVEYFNKADEVRaEADSYHED 227
                                       5555555555533...2333557788899******************************999998865144555666 PP

                     Tropomyosin_1  78 ltrk 81 
                                       ++ k
  gi|298674488|ref|YP_003726238.1| 228 IKNK 231
                                       6555 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.0019
                     Tropomyosin_1   9 aeeaqekaeeleekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakekaeesekkktnnea 77 
                                       a+e  + a+ ++e++K++ +      ++i  L++ ++ql ee++++ ++l + + +++e++++++  ea
  gi|298674488|ref|YP_003726238.1| 214 ADEVRAEADSYHEDIKNKYSLMSPLKSKIDPLKTEISQLREELDRYLKQLDDIQLQKDEKNQDEKYTEA 282
                                       788899999********************************************9999999998887774 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.4       0.2        57      15      37 ..      16      38 ..      13      44 .. 0.84
   2 ?    5.8  11.2     0.065        19       8      63 ..      44      96 ..      40     181 .. 0.96
   3 ?    1.9   1.3       1.1   3.2e+02      17      35 ..     183     201 ..     168     223 .. 0.72
   4 ?    5.7   0.5     0.069        20      14      55 ..     229     267 ..     223     290 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.2
                           NPV_P10 15 avddkVdalqqqvddvqenlpdv 37
                                      +++dk++ l +q+ + ++nl+++
  gi|298674488|ref|YP_003726238.1| 16 ELKDKINQLRTQISQKEKNLNTI 38
                                      78999999999999999999885 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.065
                           NPV_P10  8 vIradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqd 63
                                      + r++i ++++k + l+++v+d+ ++ +d    ++k d+ +++++el++k ++Iq+
  gi|298674488|ref|YP_003726238.1| 44 LYRNNIDELKEKRNELNTKVKDLVSQAQD---FKSKRDENNKKITELKSKRDEIQK 96
                                      6699*************************...669**************9999985 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 1.1
                           NPV_P10  17 ddkVdalqqqvddvqenlp 35 
                                       dd ++ l++q+++++++++
  gi|298674488|ref|YP_003726238.1| 183 DDNINELNDQIQQLADESQ 201
                                       5666666666666666555 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.069
                           NPV_P10  14 kavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaele 55 
                                       k+  + ++ l++++d +++++    +l e+Ld+  +qL++++
  gi|298674488|ref|YP_003726238.1| 229 KNKYSLMSPLKSKIDPLKTEIS---QLREELDRYLKQLDDIQ 267
                                       5555555556666666666433...36666666666666665 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   2.2   0.00034     0.097      98     137 ..      12      51 ..       4      54 .. 0.90
   2 ?    3.5  11.4      0.19        56     107     172 ..      49     117 ..      47     122 .. 0.82
   3 ?    0.4   0.4       1.7   4.9e+02      89     128 ..     136     177 ..     127     191 .. 0.59
   4 ?    4.0  11.1      0.14        40      56     174 ..     179     256 ..     156     298 .. 0.50

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00034
                      Bacillus_HBL  98 kdkaellellekLqeeiqqnqkevkqlikeLkklklklak 137
                                           el++++++L+++i q++k+ ++  k+Lk +++++++
  gi|298674488|ref|YP_003726238.1|  12 MSERELKDKINQLRTQISQKEKNLNTIFKDLKLYRNNIDE 51 
                                       56789*******************************9985 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.19
                      Bacillus_HBL 107 lekLqeeiqqnqkevkqlikeLkklklklakdsk...nFktdvdeltsilagdsgvisqlqneiedlqg 172
                                       + +L+e+ ++ + +vk+l+ + +++k+k ++++k   ++k++ de+++  +++  +i+ql+++ ++l++
  gi|298674488|ref|YP_003726238.1|  49 IDELKEKRNELNTKVKDLVSQAQDFKSKRDENNKkitELKSKRDEIQKQNKSKANEIAQLKKKRNELND 117
                                       78999999999***************99887765111567777999999999999******99888775 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1.7
                      Bacillus_HBL  89 ktlveavdkkdkaellellekLqeeiqqnqk..evkqlikeL 128
                                       k l+e +  +   +l e+le+L++ +   q+  +++++i+e+
  gi|298674488|ref|YP_003726238.1| 136 KFLNEDIPLNHEIDLFERLENLKKRLEAAQEanNIHHKIQEI 177
                                       455666666667778888888887755554400444444443 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.14
                      Bacillus_HBL  56 kanakewlnevkPqliktiqdiigYstkFqsyyktlveav........dkkdkaellellekLqeeiqqnqkevkql 124
                                        +  +  +ne++ q+++++ +  +Y  +  +y ++ +e          d                            
  gi|298674488|ref|YP_003726238.1| 179 NTSFDDNINELNDQIQQLADESQQYHLQMVEYFNKADEVRaeadsyheD---------------------------- 227
                                       3334444566666666666666666666555555544433444554443............................ PP

                      Bacillus_HBL 125 ikeLkklklklakdsknFktdvdeltsilagdsgvisqlqneiedlqgki 174
                                                            +++  s ++  + +i+ l+ ei++l++++
  gi|298674488|ref|YP_003726238.1| 228 ---------------------IKNKYSLMSPLKSKIDPLKTEISQLREEL 256
                                       .....................44444444444444444444444444332 PP

>> DUF641  Plant protein of unknown function (DUF641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   4.2    0.0083       2.4      69     124 ..      10      65 ..       1      69 [. 0.86
   2 ?    5.2   8.8     0.084        24      71     124 ..      68     121 ..      56     125 .. 0.83
   3 ?    8.8   4.7    0.0069         2      51     121 ..     194     262 ..     148     268 .. 0.84
   4 ?   -0.1   0.3       3.7   1.1e+03      96     119 ..     267     290 ..     263     295 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0083
                            DUF641  69 seaeeseleaeiqeqrsllktyeitvkkleaelkakdseieeLkekLeeaeksnkk 124
                                       s+++e+el+ +i+++r  +   e+ ++ + ++lk  +++i+eLkek +e++ + k 
  gi|298674488|ref|YP_003726238.1|  10 SNMSERELKDKINQLRTQISQKEKNLNTIFKDLKLYRNNIDELKEKRNELNTKVKD 65 
                                       258999****************************************9998887665 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.084
                            DUF641  71 aeeseleaeiqeqrsllktyeitvkkleaelkakdseieeLkekLeeaeksnkk 124
                                        + + ++++ +e+ +++  ++   ++++++ k+k +ei +Lk+k +e++  +k 
  gi|298674488|ref|YP_003726238.1|  68 SQAQDFKSKRDENNKKITELKSKRDEIQKQNKSKANEIAQLKKKRNELNDISKG 121
                                       678889999*********************************998887766555 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0069
                            DUF641  51 kklselkrlyrkkqkkkaseaeeseleaeiqeqrsllktyeitvkkleaelkakdseieeLkekLeeaeks 121
                                       ++l++  ++y  +  +    ++  e++ae++  ++ +k     ++ l+++++  ++ei++L+e+L++  k+
  gi|298674488|ref|YP_003726238.1| 194 QQLADESQQYHLQMVEY-F-NKADEVRAEADSYHEDIKNKYSLMSPLKSKIDPLKTEISQLREELDRYLKQ 262
                                       55555556665543322.3.6889999999999999999999***********************987765 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 3.7
                            DUF641  96 kleaelkakdseieeLkekLeeae 119
                                       +l+++ k++d++ +e kekL+++ 
  gi|298674488|ref|YP_003726238.1| 267 QLQKDEKNQDEKYTEAKEKLDKSG 290
                                       68999999************9875 PP

>> PilJ  Type IV pili methyl-accepting chemotaxis transducer N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   1.2       2.2   6.4e+02      51      74 ..      42      65 ..      12     132 .. 0.56
   2 ?   11.7   1.7   0.00069       0.2      22     109 ..     192     277 ..     180     282 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 2.2
                              PilJ 51 iaqfdrtlaalrlgdpapgllvpa 74
                                      ++++++++++l+++ ++ + +v +
  gi|298674488|ref|YP_003726238.1| 42 LKLYRNNIDELKEKRNELNTKVKD 65
                                      334444444444443333333322 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00069
                              PilJ  22 qsqRlakeallaaagaydaaearaqlretiaqfdrtlaalrlg.dpapgllvpaeavraqleaveqlWqelkkpaea 97 
                                       q q+la e  ++  +     e++++++e +a+ d  ++  +++ +++ +l++  ++ ++++++++++ ++++k+++ 
  gi|298674488|ref|YP_003726238.1| 192 QIQQLADESQQYHLQM---VEYFNKADEVRAEADSYHEDIKNKySLMSPLKSKIDPLKTEISQLREELDRYLKQLDD 265
                                       6688887777777666...9*********************99455555555545********************98 PP

                              PilJ  98 alaqqddaayla 109
                                       +  q+d +++++
  gi|298674488|ref|YP_003726238.1| 266 IQLQKDEKNQDE 277
                                       888888887765 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0  27.7    0.0049       1.4     464     586 ..       5     124 ..       3     136 .. 0.89
   2 ?    2.9  20.7     0.085        25     440     583 ..     132     288 ..     120     292 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0049
                              HOOK 464 ENKmLklkqegseeekltelqelledanrrkneLetenrlanqrileLeaqveelqkalqeqgskaedssllkkkle 540
                                       EN  ++   e++ ++k+++l +++ ++++++n++ ++ +l ++ i eL+++ +el+++ ++  s+a+d    k+k +
  gi|298674488|ref|YP_003726238.1|   5 ENSDISNMSERELKDKINQLRTQISQKEKNLNTIFKDLKLYRNNIDELKEKRNELNTKVKDLVSQAQD---FKSKRD 78 
                                       888899999999*******************************************************9...888889 PP

                              HOOK 541 ehleklkevqeelqkkkeqleelepklssnkqkieeleeaLkkkde 586
                                       e  +k++e+++++ + ++q  + ++++ + k+k +el+++ k  +e
  gi|298674488|ref|YP_003726238.1|  79 ENNKKITELKSKRDEIQKQNKSKANEIAQLKKKRNELNDISKGTEE 124
                                       9999999999999999999999999999999999999877655554 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.085
                              HOOK 440 ssgenlaaellpaev.reklirLqhENKmLklkqegse.eekltel.....qelledanrrkneLetenrlanqril 509
                                       ++ ++  +e +p +   + + rL++  K+L+ +qe+++ ++k++e+      + +++ n ++++L +e+++ + ++ 
  gi|298674488|ref|YP_003726238.1| 132 QELNKFLNEDIPLNHeIDLFERLENLKKRLEAAQEANNiHHKIQEIyntsfDDNINELNDQIQQLADESQQYHLQMV 208
                                       34444445555554426789999999****99999864266776651111144556667888889999888888888 PP

                              HOOK 510 eLeaqveelqkalqe..qgskaed..ssllkkkleehleklkevqeelqkkkeqleelepklssnk..qkieeleea 580
                                       e  ++ +e++ + ++  ++ k++    s lk+k++ +  +++++ eel +  +ql++++ + ++++  +k +e +e+
  gi|298674488|ref|YP_003726238.1| 209 EYFNKADEVRAEADSyhEDIKNKYslMSPLKSKIDPLKTEISQLREELDRYLKQLDDIQLQKDEKNqdEKYTEAKEK 285
                                       8888888887765541133333334557899*************************987655443335999999999 PP

                              HOOK 581 Lkk 583
                                       L k
  gi|298674488|ref|YP_003726238.1| 286 LDK 288
                                       987 PP

>> DUF4686  Domain of unknown function (DUF4686)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4  32.0       1.6   4.7e+02     106     259 ..      11     166 ..       1     180 [. 0.83
   2 ?    9.7  21.3    0.0015      0.42     162     288 ..     162     288 ..     152     300 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.6
                           DUF4686 106 lksqnsLqeklaqekskvaeaeekileLqqkLeqahkvrltearilekkqLeekikeaseneaklkqqlqeeqqkrk 182
                                         s+  L++k++q ++++ ++e+ +  + + L+  ++    +    ++++L+ k+k++ ++++  k++ +e+ +k  
  gi|298674488|ref|YP_003726238.1|  11 NMSERELKDKINQLRTQISQKEKNLNTIFKDLKLYRNN--IDELKEKRNELNTKVKDLVSQAQDFKSKRDENNKKIT 85 
                                       567889***************99999999999999433..34557789***************************** PP

                           DUF4686 183 lLdqnveeLqqqvrslrdkeaqlertnsqqqlriqqqeaqlkk.lenekrk.sdehl..ksnqeLsekLsslqqeke 255
                                        L+ + +e+q+q +s  +  aql+    +++   +  e  l+k   +e +k  +e +  + + +L e+L +l++  e
  gi|298674488|ref|YP_003726238.1|  86 ELKSKRDEIQKQNKSKANEIAQLKKKRNELNDISKGTEETLSKaYSQELNKfLNEDIplNHEIDLFERLENLKKRLE 162
                                       ******************99*****9999987777776666553788999998999866666778899999888777 PP

                           DUF4686 256 alqe 259
                                       a qe
  gi|298674488|ref|YP_003726238.1| 163 AAQE 166
                                       7665 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0015
                           DUF4686 162 easeneaklkqqlqeeqqkrklLdqnveeLqqqvrslrdkeaqlertnsqqqlriqqqeaqlkklenekrksdehlk 238
                                       ea ++++++  ++qe        d n++eL  q++ l d  +q +   ++   + ++  a      +++    ++  
  gi|298674488|ref|YP_003726238.1| 162 EAAQEANNIHHKIQEI--YNTSFDDNINELNDQIQQLADESQQYHLQMVEYFNKADEVRAEADSYHEDI---KNKYS 233
                                       4555566667777765..45679**************99999999999998766666555555544444...45567 PP

                           DUF4686 239 snqeLsekLsslqqekealqeelqqvLkqldahv.....rkynekqehhkaklrr 288
                                           L+ k+  l+ e  +l+eel ++Lkqld        ++ +ek+++ k kl +
  gi|298674488|ref|YP_003726238.1| 234 LMSPLKSKIDPLKTEISQLREELDRYLKQLDDIQlqkdeKNQDEKYTEAKEKLDK 288
                                       778999************************9755111114555555666666655 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7  19.2     0.049        14      76     162 ..      20     108 ..       5     114 .. 0.61
   2 ?    5.8  27.8     0.011       3.3     252     428 ..     113     291 ..     109     299 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.049
                                       HTHHHHHT-GGGT--S-S..HHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHH CS
                              EzrA  76 klpeieellfeaeelldk..ykfkkakkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrk 150
                                       k++++  ++ + e+ l++  +++k ++++++el+e+ +e+ +k+k++ ++ ++++++  +n ++i++lk+k +e++k
  gi|298674488|ref|YP_003726238.1|  20 KINQLRTQISQKEKNLNTifKDLKLYRNNIDELKEKRNELNTKVKDLVSQAQDFKSKRDENNKKITELKSKRDEIQK 96 
                                       55555555555555555432356666666666666666666666666666666666677777777777777777777 PP

                                       T--TTTTHHHHH CS
                              EzrA 151 kllanrfsygea 162
                                       + +++ ++  + 
  gi|298674488|ref|YP_003726238.1|  97 QNKSKANEIAQL 108
                                       766666655444 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.011
                                       SHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHHTTTSSSSSH.HHHT--HHHHTT CS
                              EzrA 252 keieelekkieeilerlkeleledveeelktieeeidsL..yddlekEveAkkeveknlkelke.klehlekqnkel 325
                                       +e+++++k  ee+l++  + el++  +e   ++ eid +   + l+k  eA +e ++  ++++e + +  +++++el
  gi|298674488|ref|YP_003726238.1| 113 NELNDISKGTEETLSKAYSQELNKFLNEDIPLNHEIDLFerLENLKKRLEAAQEANNIHHKIQEiYNTSFDDNINEL 189
                                       67889999999999999999999999998888888884422455556666666666665555541334567777777 PP

                                       GGG-TTT...S-GGGSSTTTSTTHHHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHH CS
                              EzrA 326 keeldrl...kqsYeLseeeleklrelekelkelekdyeeleekleekkvaYSelqeeleeleekleeieekqeeil 399
                                       ++++++l   +q+Y+L     + ++ + ++ +e++++ ++ +e++++k    S l+++++ l+ +++++ e+++++l
  gi|298674488|ref|YP_003726238.1| 190 NDQIQQLadeSQQYHL-----QMVEYF-NKADEVRAEADSYHEDIKNKYSLMSPLKSKIDPLKTEISQLREELDRYL 260
                                       7777777222577888.....444444.4778********************************************* PP

                                       HHHH..HHHHHHHHHHHHHHHHHHHHHHHHH CS
                              EzrA 400 eslk..slrkdEkrAreqldeikkelkeikr 428
                                       ++l+  +l+kdEk+  e+ +e k++l ++ r
  gi|298674488|ref|YP_003726238.1| 261 KQLDdiQLQKDEKNQDEKYTEAKEKLDKSGR 291
                                       ***934579*****************98765 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4  24.3     0.041        12     326     440 ..       9     123 ..       2     139 .. 0.75
   2 ?    5.9  20.1     0.014       4.2     298     472 ..     110     291 ..     108     302 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.041
                            AAA_13 326 lkaea.ealeeqLkglqraleaKrkepfksve.lesvkakiesikklvaeineliakhNekvanleeekeeakkkle 400
                                       +++   ++l++++++l+ ++++K k++ + ++ l+ + ++i+++k++ +e+n+ +++   + +++++++ e +kk+ 
  gi|298674488|ref|YP_003726238.1|   9 ISNMSeRELKDKINQLRTQISQKEKNLNTIFKdLKLYRNNIDELKEKRNELNTKVKDLVSQAQDFKSKRDENNKKIT 85 
                                       444333789999***************9988779999*************************************999 PP

                            AAA_13 401 lhlveeleseldeykkkykklekaieklekelkeeeaelk 440
                                          +++ ++e+++ +k +++  ++++k  +el+++++ ++
  gi|298674488|ref|YP_003726238.1|  86 E--LKSKRDEIQKQNKSKANEIAQLKKKRNELNDISKGTE 123
                                       8..6666888886665555555555555555444444333 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.014
                            AAA_13 298 kkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksvelesvkakiesikklvaei 374
                                       kk+++l+ + ++++ +++ +a+ ++ +++ +e   l+ +++  + +le+ +k++ +  e +++  ki++i +  +++
  gi|298674488|ref|YP_003726238.1| 110 KKRNELNDISKGTE-ETLSKAYSQELNKFLNEDIPLNHEIDLFE-RLENLKKRLEAAQEANNIHHKIQEIYN--TSF 182
                                       56667777766666.44566777778888888888888887654.466666677777777788888876655..689 PP

                            AAA_13 375 neliakhNekvanleeekeeakkklelhl..veeleseldeykkkykklekaieklekelkeeeaelkkleee.... 445
                                        ++i++ N ++++l++e ++   ++  ++  + e+++e d y++++k+    ++ l+ +++  ++e+ +l+ee    
  gi|298674488|ref|YP_003726238.1| 183 DDNINELNDQIQQLADESQQYHLQMVEYFnkADEVRAEADSYHEDIKNKYSLMSPLKSKIDPLKTEISQLREEldry 259
                                       99999999999999999998887776666355788899999998888877777777777777777777777774444 PP

                            AAA_13 446 .....ikeLekqlrdekpaaeeinkeLkafGl 472
                                              +L+k  +++ +  +e  ++L + G+
  gi|298674488|ref|YP_003726238.1| 260 lkqldDIQLQKDEKNQDEKYTEAKEKLDKSGR 291
                                       44444346777777777777777777777774 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   8.5   0.00056      0.16      50     116 ..       2      68 ..       1      71 [. 0.90
   2 ?    3.9  19.5     0.081        23      56     168 ..      57     170 ..      56     180 .. 0.89
   3 ?    2.5  13.2      0.22        63      30     157 ..     153     289 ..     144     298 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00056
                             Atg14  50 egkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrs 116
                                       e +e+++ +++ ++ +k+k+++l+++i++++++l+++ ++l+  +  i+e k+k  +l+ k+k+  s
  gi|298674488|ref|YP_003726238.1|   2 EATENSDISNMSERELKDKINQLRTQISQKEKNLNTIFKDLKLYRNNIDELKEKRNELNTKVKDLVS 68 
                                       66777788999999***********************************************997655 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.081
                             Atg14  56 eqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdleslqneleerrkkq 132
                                       ++l++k+k +  ++++ ks++ + ++++ elk k+++ +k+++ k +++a+l++k  + +   + +++ l+++  ++
  gi|298674488|ref|YP_003726238.1|  57 NELNTKVKDLVSQAQDFKSKRDENNKKITELKSKRDEIQKQNKSKANEIAQLKKKRNELNDISKGTEETLSKAYSQE 133
                                       578899999999*******************************************99999999999999******** PP

                             Atg14 133 iaklqdaikrieqklsslsskt.lesrsslcselakl 168
                                       ++k++++ ++  + ++ ++++  l++r++ ++e++++
  gi|298674488|ref|YP_003726238.1| 134 LNKFLNEDIPLNHEIDLFERLEnLKKRLEAAQEANNI 170
                                       *****99999999999998864266699999988886 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.22
                             Atg14  30 rlaklksekeslk..kkiekalegke......eaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeie 98 
                                       rl +lk++ e+ +  + i  ++++ +      + ++l+d+i+++++  ++   ++ +  ++  e+++  ++  + i+
  gi|298674488|ref|YP_003726238.1| 153 RLENLKKRLEAAQeaNNIHHKIQEIYntsfddNINELNDQIQQLADESQQYHLQMVEYFNKADEVRAEADSYHEDIK 229
                                       33444444333331123334444444555677667777777777777777777777777777777777777777777 PP

                             Atg14  99 ekkkklaklsdklkkRrsdleslqneleerrkkqia.klqdaikrieqklsslssktles 157
                                       +k   ++ l++k+   + +++ l++el  + k++ + +lq++ k++++k+++ + k+ +s
  gi|298674488|ref|YP_003726238.1| 230 NKYSLMSPLKSKIDPLKTEISQLREELDRYLKQLDDiQLQKDEKNQDEKYTEAKEKLDKS 289
                                       776666666666666666666666666665443322245555556666666666666665 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   7.9     0.038        11       1      66 [.      12      77 ..      12      83 .. 0.65
   2 ?    6.3  10.0     0.051        15       4      76 ..      64     137 ..      61     147 .. 0.87
   3 ?    2.4   0.3      0.85   2.5e+02       5      35 ..     149     178 ..     145     182 .. 0.67
   4 ?    3.1  10.3       0.5   1.4e+02       9      72 ..     220     285 ..     179     304 .. 0.45

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.038
                                      X-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXX CS
                              YabA  1 mdkkelfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkel 66
                                      m ++el dk+++l +q+++  ++l+++ ++l+   ++ +eL+   ++l +++++  +++++ k++ 
  gi|298674488|ref|YP_003726238.1| 12 MSERELKDKINQLRTQISQKEKNLNTIFKDLKLYRNNIDELKEKRNELNTKVKDLVSQAQDFKSKR 77
                                      778899999999999999999888888888877777777777776666666643333333333322 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.051
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXX.XXXXXX CS
                              YabA   4 kelfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegk.enLarl 76 
                                       k+l+++ ++++++ +e +++++elk++  e+ ++n++   e  +l+++ +e ++ +k ++++ls+++ ++L++ 
  gi|298674488|ref|YP_003726238.1|  64 KDLVSQAQDFKSKRDENNKKITELKSKRDEIQKQNKSKANEIAQLKKKRNELNDISKGTEETLSKAYsQELNKF 137
                                       78999******************************************998888888888888888762456665 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.85
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA   5 elfdkleeleeqleelleeleelkeelaell 35 
                                       +lf++le+l+++le+  +e ++++++++e++
  gi|298674488|ref|YP_003726238.1| 149 DLFERLENLKKRLEAA-QEANNIHHKIQEIY 178
                                       6778888888777654.45566777666654 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.5
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.........XXXXXXXXXXXXXXXXXXXX CS
                              YabA   9 kleeleeqleelleeleelkeelaelleenaeLeleneklrerl.........eeeekkekekkkelsegken 72 
                                       + ++ +e++++ ++ ++ lk+++  l  e ++L+ e       l          + +k+ek+++++  e+ke+
  gi|298674488|ref|YP_003726238.1| 220 EADSYHEDIKNKYSLMSPLKSKIDPLKTEISQLREE-------LdrylkqlddIQLQKDEKNQDEKYTEAKEK 285
                                       222223333333333333333333333333333333.......244444445522333333333444444444 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   7.5      0.15        42      75     130 ..       6      61 ..       2      72 .. 0.57
   2 ?    0.9  13.1       1.7   4.9e+02      28     111 ..      75     161 ..      69     176 .. 0.69
   3 ?   11.0  10.2    0.0013      0.37      29     128 ..     178     273 ..     169     279 .. 0.85
   4 ?    3.8   1.5      0.21        60      46      88 ..     248     288 ..     247     293 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  75 ndnvikksskeleeeilrlketidaqesnirvLqnvlesneqkiqkLeqdidqker 130
                                       n+ + + s++el+++i++l+ +i+++e+n++ + + l+  +++i +L+++ ++++ 
  gi|298674488|ref|YP_003726238.1|   6 NSDISNMSERELKDKINQLRTQISQKEKNLNTIFKDLKLYRNNIDELKEKRNELNT 61 
                                       44555555666666666666666666666666666666666666666655544433 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.7
                                       CCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHCCCHHHHHHHCCH.. CS
                         Fib_alpha  28 kyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn.dnvikksskeleeeilrlketidaqe.. 101
                                       +++ + +k++++l+++ +ei++++k+  + + ++k++ +e +  +k++ +++ k +s+el+ + l+ +  +++++  
  gi|298674488|ref|YP_003726238.1|  75 SKRDENNKKITELKSKRDEIQKQNKSKANEIAQLKKKRNELNDISKGTeETLSKAYSQELN-KFLNEDIPLNHEIdl 150
                                       456678999***************************9999888888775666677888888.333333333333211 PP

                                       .HHHHHHHHHH CS
                         Fib_alpha 102 .snirvLqnvl 111
                                        +++++L++ l
  gi|298674488|ref|YP_003726238.1| 151 fERLENLKKRL 161
                                       14444554444 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.0013
                                       CCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHH CS
                         Fib_alpha  29 yekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnir 105
                                       y++++++++++l++++++++++   ++++  ++ ++ +++ +  ++ d++ ++++++    ++ lk +id   ++i 
  gi|298674488|ref|YP_003726238.1| 178 YNTSFDDNINELNDQIQQLADE---SQQYHLQMVEYFNKADEVRAEADSYHEDIKNKYS-LMSPLKSKIDPLKTEIS 250
                                       88999********998888765...5667778999999999999999999999999999.9999************* PP

                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 106 vLqnvlesneqkiqkLeqdidqk 128
                                       +L++ l++  +++ +++ + d+k
  gi|298674488|ref|YP_003726238.1| 251 QLREELDRYLKQLDDIQLQKDEK 273
                                       *****999999998877665555 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.21
                                       CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  46 eisnstkeaeelvkeikdslrekqkskkdndnvikksskelee 88 
                                       eis+  +e +++ k+++d+  +k ++++  d+ +++ +++l++
  gi|298674488|ref|YP_003726238.1| 248 EISQLREELDRYLKQLDDIQLQKDEKNQ--DEKYTEAKEKLDK 288
                                       68889999999******99666555555..8999999999995 PP

>> DUF4407  Domain of unknown function (DUF4407)
   [No individual domains that satisfy reporting thresholds (although complete target did)]

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.2    0.0021       0.6      14      40 ..       6      32 ..       2      38 .. 0.84
   2 ?    0.9   0.1       1.7   4.9e+02      12      33 ..      37      60 ..      29      78 .. 0.74
   3 ?    2.1   0.0       0.7     2e+02      22      35 ..     186     199 ..     185     207 .. 0.91
   4 ?    6.5   0.1      0.03       8.7      25      45 ..     238     258 ..     213     264 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0021
                           DUF1192 14 gqDLslLSveELeerIalLeaEIaRle 40
                                        D+s++S  EL++ I +L+  I   e
  gi|298674488|ref|YP_003726238.1|  6 NSDISNMSERELKDKINQLRTQISQKE 32
                                      68*****************99887655 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.7
                           DUF1192 12 eigqDLslL..SveELeerIalLe 33
                                      +i +DL+l+  +++EL+e   +L 
  gi|298674488|ref|YP_003726238.1| 37 TIFKDLKLYrnNIDELKEKRNELN 60
                                      566777776668999999988886 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.7
                           DUF1192  22 veELeerIalLeaE 35 
                                       ++EL++ I++L +E
  gi|298674488|ref|YP_003726238.1| 186 INELNDQIQQLADE 199
                                       89*********998 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.03
                           DUF1192  25 LeerIalLeaEIaRleaaiak 45 
                                       L+  I  L+ EI  l++++++
  gi|298674488|ref|YP_003726238.1| 238 LKSKIDPLKTEISQLREELDR 258
                                       8899999*********99987 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4  31.3    0.0043       1.2     102     243 ..       9     167 ..       2     175 .. 0.71
   2 ?    1.1  20.7      0.33        95      53     201 ..     138     281 ..     119     302 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0043
                               MAD 102 arev.isalknelaelkrqiekqelelsekeseleelqerldllkkklseleqli....qqlekkqkelaeaeqrik 173
                                       ++++ +++lk+++++l++qi ++e +l++  ++l+  +++ d+lk+k +el+ ++    +q +  ++++ e++++i 
  gi|298674488|ref|YP_003726238.1|   9 ISNMsERELKDKINQLRTQISQKEKNLNTIFKDLKLYRNNIDELKEKRNELNTKVkdlvSQAQDFKSKRDENNKKIT 85 
                                       5554146899*****************99999999999999999999999999995555444444556667788888 PP

                               MAD 174 eLef...eiqsqedds....livknskselaripeleke.ler..lreenkklnelke.nkel.LkEevedlkkkLe 238
                                       eL+    eiq+q++++    + +k+ ++el  i++  +e l +   +e nk+lne +  n e+ L E +e+lkk+Le
  gi|298674488|ref|YP_003726238.1|  86 ELKSkrdEIQKQNKSKaneiAQLKKKRNELNDISKGTEEtLSKaySQELNKFLNEDIPlNHEIdLFERLENLKKRLE 162
                                       887522268887766522114688888889888875554133211467799999976436677788**********9 PP

                               MAD 239 reEka 243
                                          +a
  gi|298674488|ref|YP_003726238.1| 163 AAQEA 167
                                       76655 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.33
                               MAD  53 lqkrikllekre.eekeealreqiElarlkkknlealnkkekekesklaearevisalknelaelkrqiekqelels 128
                                       l+++i l ++ +  e+ e+l++++E a+      +++++k +e    +++  + i++l++++++l+ + ++  l++ 
  gi|298674488|ref|YP_003726238.1| 138 LNEDIPLNHEIDlFERLENLKKRLEAAQ----EANNIHHKIQE--IYNTSFDDNINELNDQIQQLADESQQYHLQMV 208
                                       5555555555555666777777777777....44445555554..5556788999999******************* PP

                               MAD 129 ekeseleelqerldllkkklseleqliqqlekkqkelaeaeqrikeLefeiqsqeddslivknskselaripe 201
                                       e  ++  e++ + d +++ +++   l++ l++k + l+++  +++e   +  +q dd +  k+ k++ ++  e
  gi|298674488|ref|YP_003726238.1| 209 EYFNKADEVRAEADSYHEDIKNKYSLMSPLKSKIDPLKTEISQLREELDRYLKQLDDIQLQKDEKNQDEKYTE 281
                                       ***************************************9999998666667777777777777766555555 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3  38.5    0.0094       2.7      30     200 .]      16     196 ..      13     196 .. 0.80
   2 ?    0.3   9.4       1.3   3.6e+02      61     139 ..     152     231 ..     123     238 .. 0.59
   3 ?    2.3  10.1      0.31        90      34     101 ..     220     286 ..     200     299 .. 0.53

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0094
                               GAS  30 slKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlk....arlkelekelk 102
                                       +lK++i++l+++  ++ek+l+ i ++ k ++ ++ +++e+++eL+ ++k+  ++ q++k+ +    ++++el+++  
  gi|298674488|ref|YP_003726238.1|  16 ELKDKINQLRTQISQKEKNLNTIFKDLKLYRNNIDELKEKRNELNTKVKDLVSQAQDFKSKRdennKKITELKSKRD 92 
                                       79*******************************************98887777766666544111166777888888 PP

                               GAS 103 dlkwehevleqrfekvekerdelykkfeaa.......iqevqqktglknllLekklkalqeelEkkeaqleevlaaa 172
                                       +++ +++++  ++++++k+r+el++  + +         +   k  ++ + L   ++ l e+lE+ +++le++ +a+
  gi|298674488|ref|YP_003726238.1|  93 EIQKQNKSKANEIAQLKKKRNELNDISKGTeetlskaYSQELNKFLNEDIPLNHEID-LFERLENLKKRLEAAQEAN 168
                                       899999999999999999999997655444222222133333455566677777775.6799*************** PP

                               GAS 173 nldpaalsavsekleevlesKnqeIkdL 200
                                       n+ ++  +  + ++++ +++ n++I++L
  gi|298674488|ref|YP_003726238.1| 169 NIHHKIQEIYNTSFDDNINELNDQIQQL 196
                                       ***9999999****************98 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.3
                               GAS  61 epLkkaeeeveeLrkqlknyekdkqslkn.lkarlkelekelkdlkwehevleqrfekvekerdelykkfeaaiqev 136
                                       e L+++++ +e  +++ + ++k ++ ++     +++el++++++l  e+++ + ++ +  ++ de++++ ++  +++
  gi|298674488|ref|YP_003726238.1| 152 ERLENLKKRLEAAQEANNIHHKIQEIYNTsFDDNINELNDQIQQLADESQQYHLQMVEYFNKADEVRAEADSYHEDI 228
                                       34444444444444444433333333332134455666666666666666666666666666666666666666666 PP

                               GAS 137 qqk 139
                                       + k
  gi|298674488|ref|YP_003726238.1| 229 KNK 231
                                       665 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.31
                               GAS  34 eieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekel 101
                                       e     +  + +  ++s ++++   lk ++ +++ee+++  kql + + +k + kn+ ++++e++++l
  gi|298674488|ref|YP_003726238.1| 220 EADSYHEDIKNKYSLMSPLKSKIDPLKTEISQLREELDRYLKQLDDIQLQKDE-KNQDEKYTEAKEKL 286
                                       44444444444455555555555555555555555555555555555444433.34444444444443 PP

>> HAUS-augmin3  HAUS augmin-like complex subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3  18.6     0.089        26      46     163 ..      14     140 ..       2     150 .. 0.72
   2 ?    0.4   9.8       1.4     4e+02      72     165 ..     119     215 ..     107     224 .. 0.69
   3 ?   10.7   4.7   0.00095      0.28      63     124 ..     225     286 ..     217     296 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.089
                      HAUS-augmin3  46 geaLeeaLktie......psdlkq..edvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqe 114
                                       +++L+++ +++       +++l++  +d +l++  ++e++e+ ++L++++++L ++ +   +++++ +  +++l+++
  gi|298674488|ref|YP_003726238.1|  14 ERELKDKINQLRtqisqkEKNLNTifKDLKLYRNNIDELKEKRNELNTKVKDLVSQAQDFKSKRDENNKKITELKSK 90 
                                       56666666666644433333344478888899999999999999999999999999999999999999999999999 PP

                      HAUS-augmin3 115 lrkleeeekeakk...klkeaqeelraenaetnavLqqlteeakqlaeyfee 163
                                       + + ++++k++++   +lk+  +el+  ++ t++ L++  +  ++l ++++e
  gi|298674488|ref|YP_003726238.1|  91 RDEIQKQNKSKANeiaQLKKKRNELNDISKGTEETLSKAYS--QELNKFLNE 140
                                       99999998888872224566666666667777777777776..777777765 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.4
                      HAUS-augmin3  72 ileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkklkeaqeelraenaetnavLq 148
                                       +   ee+  +a+ qel++  +e+  ++++ +  + +  +l+++l++ +e+++   k  +  + ++  +++e+n + q
  gi|298674488|ref|YP_003726238.1| 119 SKGTEETLSKAYSQELNKFLNEDIPLNHEIDLFERL-ENLKKRLEAAQEANNIHHKIQEIYNTSFDDNINELNDQIQ 194
                                       444455778899999999999988888888877765.4566666666666666666667778899999999999999 PP

                      HAUS-augmin3 149 qlteeakq....laeyfeeae 165
                                       ql++e++q    ++eyf++a+
  gi|298674488|ref|YP_003726238.1| 195 QLADESQQyhlqMVEYFNKAD 215
                                       999998863322677777766 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00095
                      HAUS-augmin3  63 qedvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeeke 124
                                       +ed +   + ++ +++++  L++e+++L++e ++ lk+l+ +q+q  + +q +++ e++ek 
  gi|298674488|ref|YP_003726238.1| 225 HEDIKNKYSLMSPLKSKIDPLKTEISQLREELDRYLKQLDDIQLQKDEKNQDEKYTEAKEKL 286
                                       46666666777778899999**************************************9986 PP

>> Leu_zip  Leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8  35.9     0.058        17      81     275 ..       7     194 ..       4     202 .. 0.64
   2 ?    1.2  14.8      0.72   2.1e+02      93     216 ..     152     275 ..     144     298 .. 0.59

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.058
                           Leu_zip  81 aDiselenReLlEkiaefEekefkssnkkeseelkkkkLePlnegGgaeLLkkeierLkeenekLkerlkelEkqat 157
                                       +Dis++  ReL +ki+++  +           ++k+k L+ + +    +L +++i++Lke+ + L++++k+l +qa+
  gi|298674488|ref|YP_003726238.1|   7 SDISNMSERELKDKINQLRTQ----------ISQKEKNLNTIFK--DLKLYRNNIDELKEKRNELNTKVKDLVSQAQ 71 
                                       677777777777777776433..........3344566777877..589***************************9 PP

                           Leu_zip 158 saleeksklekalkelqkelge...kkdeke.nskeiskleeklaelkldlektleek..tasaksleedlastkhe 228
                                       +  +++ + +k++ el+++ +e   ++++k+ + ++++k +++l+++    e+tl++   ++ +k l+ed+    he
  gi|298674488|ref|YP_003726238.1|  72 DFKSKRDENNKKITELKSKRDEiqkQNKSKAnEIAQLKKKRNELNDISKGTEETLSKAysQELNKFLNEDI-PLNHE 147
                                       98876666666666555444431003333322445555566666667777777665543244555666665.45566 PP

                           Leu_zip 229 lLkvqeqLelaekeLekkfqqtaayknlkeml.tkkneqikelRkrLs 275
                                       +  + e+Le  +k Le   +  + ++ ++e+  t+ ++ i el  +++
  gi|298674488|ref|YP_003726238.1| 148 I-DLFERLENLKKRLEAAQEANNIHHKIQEIYnTSFDDNINELNDQIQ 194
                                       4.6777888888888877777777777777752334566666666554 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.72
                           Leu_zip  93 EkiaefEekefkssnkkeseelkkkkLePlneg...GgaeLLkkeierLkeenekLkerlkelEkqatsaleekskl 166
                                       E++ ++ ++  ++    +++++ ++k++ + ++     ++ L+ +i++L +e ++ + ++ e+ ++a ++  e    
  gi|298674488|ref|YP_003726238.1| 152 ERLENLKKRLEAA----QEANNIHHKIQEIYNTsfdDNINELNDQIQQLADESQQYHLQMVEYFNKADEVRAEADSY 224
                                       3333333332222....233334455555544322245666788888888888888888888888888888888888 PP

                           Leu_zip 167 ekalkelqkelgekkdeke.nskeiskleeklaelkldlektleektasak 216
                                       ++++k++ + ++  k++ +  ++eis+l+e+l     +l+  + +k ++++
  gi|298674488|ref|YP_003726238.1| 225 HEDIKNKYSLMSPLKSKIDpLKTEISQLREELDRYLKQLDDIQLQKDEKNQ 275
                                       888888877777776665546677777777777766666653333222221 PP

>> HMMR_N  Hyaluronan mediated motility receptor N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6  22.0      0.13        39     232     334 ..       5     111 ..       2     112 .. 0.69
   2 ?   10.2  18.5    0.0013      0.38     172     309 ..     153     288 ..     148     302 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.13
                            HMMR_N 232 yieelsnvseqlekykldiaqleellkekndeiesLkssLe...ekeqelskqvkdlnekckllekekeelvreeee 305
                                       +++ +sn+se+    k +i+ql+  +++k+++++++ ++L+   ++ +el+++ ++ln+k+k l ++ +   + ++ 
  gi|298674488|ref|YP_003726238.1|   5 ENSDISNMSERE--LKDKINQLRTQISQKEKNLNTIFKDLKlyrNNIDELKEKRNELNTKVKDLVSQAQ-DFKSKRD 78 
                                       677899999885..7999999999999999999999998864447788888888888888888887776.3444444 PP

                            HMMR_N 306 keqtlsaEle....elkeklklkeqeaqklqqk 334
                                        +++  +El+    e++++ k+k +e+ +l++k
  gi|298674488|ref|YP_003726238.1|  79 ENNKKITELKskrdEIQKQNKSKANEIAQLKKK 111
                                       444455555511114555556666777777666 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0013
                            HMMR_N 172 kleakekevsvkQedmeaklqvtqknLeeskakvaqLkeklvslekekieekseteklleyieelsnvseqlekykl 248
                                       +le  +k + + Qe  ++  +  +   +++  ++ +L++++++l +e    ++   +++ey ++  +v+ +++ y++
  gi|298674488|ref|YP_003726238.1| 153 RLENLKKRLEAAQEANNIHHKIQEIYNTSFDDNINELNDQIQQLADE---SQQYHLQMVEYFNKADEVRAEADSYHE 226
                                       566667777777877776666666666678999*****999777777...444456789999999999999999*** PP

                            HMMR_N 249 diaqleellkekndeiesLkssLeekeqelskqvkdlne.kckllekekeelvreeeekeqt 309
                                       di++  +l++  +++i  Lk+++++  +el++  k+l+  +++  ek+++e+ +e++ek ++
  gi|298674488|ref|YP_003726238.1| 227 DIKNKYSLMSPLKSKIDPLKTEISQLREELDRYLKQLDDiQLQKDEKNQDEKYTEAKEKLDK 288
                                       ************************************97548999999999999999988654 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.7       0.1        29       8      26 ..      20      38 ..       7      54 .. 0.54
   2 ?   -0.8   7.8       7.3   2.1e+03      10      34 ..      50      74 ..      42     132 .. 0.71
   3 ?    7.5   2.4     0.018       5.3       8      26 ..     185     203 ..     180     229 .. 0.65
   4 ?    5.8   0.3     0.061        18       5      26 ..     238     259 ..     234     277 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.1
                               LPP  8 qVsqLkskvdqlssdvnsa 26
                                       ++qL ++++q ++++n +
  gi|298674488|ref|YP_003726238.1| 20 KINQLRTQISQKEKNLNTI 38
                                      3333333333333333333 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 7.3
                               LPP 10 sqLkskvdqlssdvnsakaaaqaak 34
                                       +Lk+k ++l+ +v+++ ++aq+ k
  gi|298674488|ref|YP_003726238.1| 50 DELKEKRNELNTKVKDLVSQAQDFK 74
                                      4444444444444444444433332 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.018
                               LPP   8 qVsqLkskvdqlssdvnsa 26 
                                       ++++L+++++ql+++ ++ 
  gi|298674488|ref|YP_003726238.1| 185 NINELNDQIQQLADESQQY 203
                                       5667777777777665443 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.061
                               LPP   5 LssqVsqLkskvdqlssdvnsa 26 
                                       L s +  Lk++++ql ++++  
  gi|298674488|ref|YP_003726238.1| 238 LKSKIDPLKTEISQLREELDRY 259
                                       5555666666666666665544 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2  11.9       1.4   4.1e+02      13      77 ..      20      88 ..       3      97 .. 0.50
   2 ?    5.0   0.6     0.091        26      28      64 ..     186     222 ..     179     231 .. 0.67
   3 ?   11.9   0.7   0.00066      0.19       8      46 ..     229     267 ..     223     299 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 1.4
                       TMF_TATA_bd 13 lverlsseirrlEgElas.......lkeelerleaerdeareeivklmkeneelkelkkeleelekeleelq 77
                                       +++l ++i ++E  l++       +++++ +l+++r+e++  + +l+++ ++ k++ +e+++   +++el+
  gi|298674488|ref|YP_003726238.1| 20 KINQLRTQISQKEKNLNTifkdlklYRNNIDELKEKRNELNTKVKDLVSQAQDFKSKRDENNK---KITELK 88
                                      456666666666666555111111135555666666666666666666555544443333222...222222 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.091
                       TMF_TATA_bd  28 laslkeelerleaerdeareeivklmkeneelkelkk 64 
                                       +++l++++++l+ e ++   ++v+  ++ +e++++++
  gi|298674488|ref|YP_003726238.1| 186 INELNDQIQQLADESQQYHLQMVEYFNKADEVRAEAD 222
                                       5666777777777777777777777777777766655 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00066
                       TMF_TATA_bd   8 gpsvqlverlsseirrlEgElaslkeelerleaerdear 46 
                                       +++ +l++ l+s+i  l +E+++l+eel r  ++ d+++
  gi|298674488|ref|YP_003726238.1| 229 KNKYSLMSPLKSKIDPLKTEISQLREELDRYLKQLDDIQ 267
                                       67889999**********************999988765 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   4.9     0.049        14       6      42 ..      32      68 ..       6      69 .. 0.75
   2 ?    1.9   0.8         1   2.9e+02      24      38 ..     180     194 ..     149     198 .. 0.44
   3 ?    6.9   0.0     0.029       8.5       5      32 ..     238     265 ..     232     269 .. 0.57

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.049
                         FlaC_arch  6 EnklsklsteletvkkeneelsksveelkenVkdlls 42
                                      E+ l+ +   l+  +++++el+++ +el+ +Vkdl+s
  gi|298674488|ref|YP_003726238.1| 32 EKNLNTIFKDLKLYRNNIDELKEKRNELNTKVKDLVS 68
                                      5555555557777788888888888888888888875 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 1
                         FlaC_arch  24 eelsksveelkenVk 38 
                                        +  ++++el+++++
  gi|298674488|ref|YP_003726238.1| 180 TSFDDNINELNDQIQ 194
                                       222345555555555 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.029
                         FlaC_arch   5 lEnklsklsteletvkkeneelsksvee 32 
                                       l +k++ l+te++ +++e++   k++++
  gi|298674488|ref|YP_003726238.1| 238 LKSKIDPLKTEISQLREELDRYLKQLDD 265
                                       4455555556666666665555555555 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4  17.0     0.069        20     222     300 .]      15      99 ..       1      99 [. 0.62
   2 ?    7.0  21.9     0.011       3.3     144     295 ..      79     259 ..      71     265 .. 0.56

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.069
                             FAM76 222 tqLkeeiaslkkqleqkdqellekdkkitelka..e.llekekelreklke...lekeakekieklekkirellkev 292
                                        +Lk++i++l+ q++qk+++l +  k +   +   + l ek++el++k+k+   + +++k+k ++ +kki+el+ + 
  gi|298674488|ref|YP_003726238.1|  15 RELKDKINQLRTQISQKEKNLNTIFKDLKLYRNniDeLKEKRNELNTKVKDlvsQAQDFKSKRDENNKKITELKSKR 91 
                                       46788888888888888777766444433333211213344455566655411145567889999999999999999 PP

                             FAM76 293 aelskkkk 300
                                        e++k++k
  gi|298674488|ref|YP_003726238.1|  92 DEIQKQNK 99 
                                       99999876 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.011
                             FAM76 144 ekrskskkkkskskkskkskekskekkaskkkskkh......kkrss................rlevskleeek... 195
                                       e+++k  + ksk+++ +k+++++ +++a+ kk++++          +                +         +   
  gi|298674488|ref|YP_003726238.1|  79 ENNKKITELKSKRDEIQKQNKSKANEIAQLKKKRNElndiskG---TeetlskaysqelnkflN---------Edip 143
                                       3333333333333333332222222222222222222222110...111112122222223330.........0334 PP

                             FAM76 196 ....................laeekesnetskksldsnssdhlvavtqLkeeiaslkkqleqkdqellekdkkitel 252
                                                           ++e+++ ++++++  +++  d   ++++L+++i++l  + +q   +++e   k  e+
  gi|298674488|ref|YP_003726238.1| 144 lnheidlferlenlkkrleaAQEANNIHHKIQEIYNTSFDD---NINELNDQIQQLADESQQYHLQMVEYFNKADEV 217
                                       44445555555555553332333444444444445555555...589****************************** PP

                             FAM76 253 kaellekekelreklkelekeakekieklekkirellkevael 295
                                       +ae  + ++++++k++ + +  k+ki+ l+++i++l+ e+ + 
  gi|298674488|ref|YP_003726238.1| 218 RAEADSYHEDIKNKYSLM-SPLKSKIDPLKTEISQLREELDRY 259
                                       **************9766.67899*************998665 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6  24.7     0.011       3.1     357     475 ..      11     129 ..       2     143 .. 0.81
   2 ?    3.4  14.3     0.098        28     258     383 ..     162     286 ..     153     293 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.011
                            DUF812 357 essikqveeeleeekeeneelekevklkkktlellpdaeeniekLqa...lveasaqrlvelakqWekhRvplieey 430
                                       ++s +++++++++++++ +++ek++++  k l+l     +ni +L++   +++++ ++lv+ a+ ++++R    +++
  gi|298674488|ref|YP_003726238.1|  11 NMSERELKDKINQLRTQISQKEKNLNTIFKDLKLY---RNNIDELKEkrnELNTKVKDLVSQAQDFKSKRDENNKKI 84 
                                       56678899999999999999999999999999999...556666655111566677777777888************ PP

                            DUF812 431 relkesksekekeaerkleeikklrekmkevaeelrqkeellkqL 475
                                        elk++ +e +k+ ++k +ei++l++k  e+ +  +  ee l++ 
  gi|298674488|ref|YP_003726238.1|  85 TELKSKRDEIQKQNKSKANEIAQLKKKRNELNDISKGTEETLSKA 129
                                       ******************************999999999887654 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.098
                            DUF812 258 rkaalkseeaessasksksdlaellsefseksetdslktkgsrfthaeklqftke..elakkaeteeelkkkreeel 332
                                       + a  ++++ ++ ++  + ++++ ++e+   + + ++++ +s+  h + +++ ++  e++++a++  e  k++   +
  gi|298674488|ref|YP_003726238.1| 162 EAAQEANNIHHKIQEIYNTSFDDNINEL---NDQIQQLADESQQYHLQMVEYFNKadEVRAEADSYHEDIKNKYSLM 235
                                       3332223333333333444444544444...4444445566666666666443331233455566655566666789 PP

                            DUF812 333 eelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevkl 383
                                       + l+++i+ l+ +i++l+ee++++ +++  ++ + +e+++  + +e++ kl
  gi|298674488|ref|YP_003726238.1| 236 SPLKSKIDPLKTEISQLREELDRYLKQLDDIQLQKDEKNQDEKYTEAKEKL 286
                                       999999999999999999999999999988877777766666655555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      4225  (0.235652); expected 358.6 (0.02)
Passed bias filter:                      716  (0.0399353); expected 358.6 (0.02)
Passed Vit filter:                       235  (0.0131073); expected 17.9 (0.001)
Passed Fwd filter:                       161  (0.00897987); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              62  [number of targets reported over threshold]
# CPU time: 2.26u 0.44s 00:00:02.70 Elapsed: 00:00:00.68
# Mc/sec: 1358.00
//
Query:       gi|298674489|ref|YP_003726239.1|  [L=215]
Description: hypothetical protein Metev_0531 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00084   18.3  24.8       0.03   13.2  17.3    2.0  2  Spc7             Spc7 kinetochore protein
     0.0016   17.9   2.3     0.0039   16.6   1.7    1.9  1  Med14            Mediator complex subunit MED14
     0.0078   16.1  17.7       0.02   14.8  10.5    2.2  2  Sec34            Sec34-like family
     0.0087   16.3   9.6        2.7    8.3   4.1    3.6  4  DUF948           Bacterial protein of unknown function (DUF94
  ------ inclusion threshold ------
      0.017   14.5  11.5       0.42    9.9   7.1    2.1  2  DUF4407          Domain of unknown function (DUF4407)
      0.023   14.9  22.4      0.082   13.1  11.9    2.3  2  End3             Actin cytoskeleton-regulatory complex protei
      0.027   13.6   1.1      0.051   12.7   0.9    1.6  1  DUF5129          Domain of unknown function (DUF5129)
      0.056   13.1  12.7       0.12   11.9   6.0    2.1  2  Phage_GPO        Phage capsid scaffolding protein (GPO) serin
      0.092   12.9  18.7        1.2    9.3  10.0    3.1  3  Uds1             Up-regulated During Septation
      0.093   12.1  25.3       0.34   10.2   5.4    2.6  3  GAS              Growth-arrest specific micro-tubule binding
       0.11   13.0  16.6        1.2    9.7   3.9    2.7  3  Spectrin         Spectrin repeat
       0.12   12.5  20.8        2.4    8.2   6.2    3.4  3  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
       0.15   12.5  12.1         35    4.9   5.8    3.3  2  NPV_P10          Nucleopolyhedrovirus P10 protein
       0.15   12.4   0.5       0.15   12.4   0.5    4.8  5  Csm1_N           Csm1 N-terminal domain
       0.16   12.4   0.2       0.16   12.4   0.2    3.8  3  CLZ              C-terminal leucine zipper domain of cyclic n
       0.17   12.0  25.3        1.3    9.2   5.6    2.4  2  Fib_alpha        Fibrinogen alpha/beta chain family
       0.17   11.9  22.6       0.12   12.5   2.7    3.7  4  DHR10            Designed helical repeat protein 10 domain
       0.18   12.5  15.1       0.46   11.2   0.5    3.1  2  DUF2203          Uncharacterized conserved protein (DUF2203)
       0.18   12.4  11.7        2.9    8.6   0.2    4.2  4  SlyX             SlyX
       0.23   11.6   8.5        4.8    7.3   0.6    3.5  2  Erf4             Golgin subfamily A member 7/ERF4 family
       0.28   11.2  17.6        1.6    8.8   9.0    2.6  2  DUF1664          Protein of unknown function (DUF1664)
       0.38   11.4  17.8        2.4    8.8   9.6    2.6  2  HIP1_clath_bdg   Clathrin-binding domain of Huntingtin-intera
        0.5   10.8  12.8        2.8    8.4   0.7    3.5  2  DUF4140          N-terminal domain of unknown function (DUF41
        0.5   10.1   3.5        0.4   10.4   0.5    2.0  2  DUF2785          Protein of unknown function (DUF2785)
       0.51   10.1  11.0       0.66    9.8   5.1    2.8  2  SKA2             Spindle and kinetochore-associated protein 2
       0.52   10.4   5.1        2.6    8.2   1.2    2.3  2  Lipase_GDSL_3    GDSL-like Lipase/Acylhydrolase family
       0.61   10.3   7.2        3.2    8.0   0.7    3.7  3  WXG100           Proteins of 100 residues with WXG
       0.63   10.4  16.4       0.29   11.5   1.1    4.1  4  KxDL             Uncharacterized conserved protein
       0.74   10.6  21.5        5.5    7.8   9.4    3.3  3  Occludin_ELL     Occludin homology domain
       0.74    9.9  10.0         12    6.1   2.5    3.3  3  DUF2730          Protein of unknown function (DUF2730)
       0.84   10.5  25.4        3.9    8.3   0.6    4.3  3  Rho_Binding      Rho Binding
       0.92    9.8  27.2        5.1    7.4   2.4    3.3  3  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
        1.1    9.7  19.7        5.1    7.6   2.0    3.5  4  Snapin_Pallidin  Snapin/Pallidin
        1.2    9.6  24.5        1.5    9.2   0.6    5.2  5  FlaC_arch        Flagella accessory protein C (FlaC)
        1.4    9.3  12.0        1.9    8.9   0.4    4.1  5  Val_tRNA-synt_C  Valyl tRNA synthetase tRNA binding arm
        1.4    8.1  22.6        4.3    6.5   1.8    2.7  3  TMPIT            TMPIT-like protein
        1.9    7.7  13.4        2.5    7.3  11.7    2.0  2  CorA             CorA-like Mg2+ transporter protein
          2    8.1  14.5       0.72    9.5   1.4    2.9  2  RPW8             Arabidopsis broad-spectrum mildew resistance
        2.2    6.1  19.9       0.42    8.5  10.1    2.0  2  V_ATPase_I       V-type ATPase 116kDa subunit family
        2.4    8.9   5.9         12    6.6   0.2    3.1  3  Sulfatase_C      C-terminal region of aryl-sulfatase
        2.5    8.5   7.4        4.1    7.8   0.2    3.9  3  HalX             HalX domain
        2.7    7.7  11.8        9.4    5.9   4.7    2.4  3  DUF745           Protein of unknown function (DUF745)
        3.4    7.5   8.9        2.2    8.1   0.4    3.3  4  Glutaredoxin2_C  Glutaredoxin 2, C terminal domain
        3.5    7.5   7.7        1.7    8.5   5.2    1.7  2  GvpL_GvpF        Gas vesicle synthesis protein GvpL/GvpF
        4.3    7.5   8.7          2    8.5   0.2    3.6  3  Mst1_SARAH       C terminal SARAH domain of Mst1
        5.8    5.6  14.1        7.6    5.2  14.1    1.2  1  ALMT             Aluminium activated malate transporter
         10    5.7  23.1         21    4.7  23.0    1.6  1  DUF4795          Domain of unknown function (DUF4795)


Domain annotation for each model (and alignments):
>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2  17.3   7.8e-05      0.03     134     258 ..      21     149 ..      20     160 .. 0.88
   2 !    9.4   1.5    0.0011      0.44     197     244 ..     161     208 ..     147     215 .] 0.57

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.8e-05
                              Spc7 134 mqllegLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreela. 209
                                       ++l++g+ e+ ++ l++ +++ e+L+++ e ++e +++ +++k+ +  + + l+e+++++    ++ L+el+++++ 
  gi|298674489|ref|YP_003726239.1|  21 SELVSGVIEKHQNFLNKYRQEFEQLNERIESINEQMESAKKNKEYVVGRRDVLREKRQQILYQAQKTLNELQSSIKd 97 
                                       7899***********************************************************************72 PP

                              Spc7 210 .elkaeieekkkelaelqeql..eeleekieelkeqkseleeeiaeaervle 258
                                        e+k+ +++  +++++l++ +  +e ++ ++e+++++se+  + + a+r l 
  gi|298674489|ref|YP_003726239.1|  98 sEHKEILSSVDEKISKLKTSIssDEEKQIVDEINDSISEISLNDETANRKLS 149
                                       24566689999******9987224566779**********999999998765 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0011
                              Spc7 197 dkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqks 244
                                       +++e+e+++ + ++ ++e++++kkel++l+ + ++le++i++ +e+++
  gi|298674489|ref|YP_003726239.1| 161 TSNEIESIKGSDKQYEKEYDKLKKELNDLNPRYKWLEKRISSHEESIE 208
                                       245666666666666666666666666666666666666666655554 PP

>> Med14  Mediator complex subunit MED14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   1.7     1e-05    0.0039      63     152 ..      21     112 ..      17     154 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1e-05
                                       HHHCCHHH.HHHHHHHHHHHCCCCCHCCCCCHHHHHHCCHHHHHHHHCHHCHCTTCHCHCCCCCCSCSH.--S---S CS
                             Med14  63 aekvskli.dllaflrqqneafedaadalkelkeslanaklpnpdlktAleVLstGrysrlpslikeey.ppkplta 137
                                       +e vs +i + ++fl++ ++ fe++ +++ +++e++++ak ++  + +  +VL ++r + l +++k  +  + ++++
  gi|298674489|ref|YP_003726239.1|  21 SELVSGVIeKHQNFLNKYRQEFEQLNERIESINEQMESAKKNKEYVVGRRDVLREKRQQILYQAQKTLNeLQSSIKD 97 
                                       667777887889***********************************************9*9999877447888899 PP

                                       HHHHHHHHHHHHHHH CS
                             Med14 138 keilktlkdlnelir 152
                                       +e ++ l+ ++e i+
  gi|298674489|ref|YP_003726239.1|  98 SEHKEILSSVDEKIS 112
                                       998888888888776 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8  10.5   5.3e-05      0.02       3     106 ..      33     135 ..      31     147 .. 0.90
   2 ?    5.7   1.2     0.032        12      10      75 ..     149     214 ..     135     215 .] 0.66

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.3e-05
                             Sec34   3 dqLeskeeecdelleqtdealeqLeeleekfksvsektsslheaceq.lleeqkrleelaeeieekLkyFeeldpit 78 
                                       + L+++++e+++l e++++++eq+e+ +++ + v  +   l+e+ +q l++ qk l+el+ +i++  ++ e l ++ 
  gi|298674489|ref|YP_003726239.1|  33 NFLNKYRQEFEQLNERIESINEQMESAKKNKEYVVGRRDVLREKRQQiLYQAQKTLNELQSSIKDS-EHKEILSSVD 108
                                       56999*************************************99988356899**********987.6669999999 PP

                             Sec34  79 rkLnspgsslvksesFlemLkklDecle 106
                                       +k+++ ++s ++s++ ++++++++++++
  gi|298674489|ref|YP_003726239.1| 109 EKISKLKTS-ISSDEEKQIVDEINDSIS 135
                                       999999999.999999*********997 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.032
                             Sec34  10 eecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFeeld 75 
                                       + +++ ++++ e+ +++e+++ + k+ +++  +l+++ ++l    k le+   + ee ++y+++++
  gi|298674489|ref|YP_003726239.1| 149 SDIKSKIDSVIETSNEIESIKGSDKQYEKEYDKLKKELNDLNPRYKWLEKRISSHEESIEYWKNVE 214
                                       334444555556666777777777777777777777777777777777777777777777777665 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1     0.012       4.4      46      79 ..      28      61 ..       7      67 .. 0.58
   2 !    8.1   1.4    0.0084       3.2      21      60 ..      35      95 ..      32     120 .. 0.57
   3 !    8.3   4.1     0.007       2.7      21      87 ..      81     168 ..      76     171 .. 0.83
   4 ?    5.6   0.6     0.049        19      45      86 ..     126     167 ..     124     205 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.012
                            DUF948 46 lkevedllakvnelledvneklekvdplteavad 79
                                      +++ ++ l+k ++  e++ne++e++++ +e++++
  gi|298674489|ref|YP_003726239.1| 28 IEKHQNFLNKYRQEFEQLNERIESINEQMESAKK 61
                                      5555555555555555555555555555555543 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0084
                            DUF948 21 llklkktldeaaatieele.....................kqvdpilkevedllakvnell 60
                                      l+k ++ +++++++ie+++                     ++ ++il +++++l++ +   
  gi|298674489|ref|YP_003726239.1| 35 LNKYRQEFEQLNERIESINeqmesakknkeyvvgrrdvlrEKRQQILYQAQKTLNELQSSI 95
                                      6788888889999999999444444444444444444444555555555555555555544 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.007
                            DUF948  21 llklkktldeaaatieele.....................kqvdpilkevedllakvnelledvneklekvdpltea 76 
                                       l +++ktl+e++++i++ e                     ++ ++i++e++d ++++    e  n+kl ++++ +++
  gi|298674489|ref|YP_003726239.1|  81 LYQAQKTLNELQSSIKDSEhkeilssvdekisklktsissDEEKQIVDEINDSISEISLNDETANRKLSDIKSKIDS 157
                                       67788888888888888888888888888888888999998889999999999998887778899999999999999 PP

                            DUF948  77 vadlgesvsel 87 
                                       v ++++ ++++
  gi|298674489|ref|YP_003726239.1| 158 VIETSNEIESI 168
                                       99999888776 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.049
                            DUF948  45 ilkevedllakvnelledvneklekvdplteavadlgesvse 86 
                                       i++e++d ++++    e  n+kl ++++ +++v ++++ +++
  gi|298674489|ref|YP_003726239.1| 126 IVDEINDSISEISLNDETANRKLSDIKSKIDSVIETSNEIES 167
                                       444555555544444444555555555555555555554444 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   7.1    0.0011      0.42     131     233 ..      24     125 ..       2     145 .. 0.74
   2 ?    7.0   0.4    0.0085       3.2     130     161 ..     158     205 ..     128     209 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0011
                           DUF4407 131 ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaq.ldaaqaelaelkakl 206
                                        +  +++ ++ +++ ++e++++++r++  ++++++  ++    + + v G+ ++ +ek++q l +aq++l+el++++
  gi|298674489|ref|YP_003726239.1|  24 VSGVIEKHQNFLNKYRQEFEQLNERIESINEQMESAKKN----K-EYVVGRRDVLREKRQQiLYQAQKTLNELQSSI 95 
                                       556677777778888888888888888777777755554....3.3488999999887666268************9 PP

                           DUF4407 207 d...atarlaalraelaeleaerakeraas 233
                                       +    ++ l++ ++++++l++ ++++++++
  gi|298674489|ref|YP_003726239.1|  96 KdseHKEILSSVDEKISKLKTSISSDEEKQ 125
                                       999978888888888888888877776654 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0085
                           DUF4407 130 a................ltaelaeleaqiaalqaeidaaearldalra 161
                                                        +++e+++l++++++l+  ++ +e+r++  ++
  gi|298674489|ref|YP_003726239.1| 158 VietsneiesikgsdkqYEKEYDKLKKELNDLNPRYKWLEKRISSHEE 205
                                       233344445555555559999999999999999999999998887765 PP

>> End3  Actin cytoskeleton-regulatory complex protein END3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1  11.9   0.00022     0.082      99     182 ..      35     119 ..       5     125 .. 0.86
   2 ?    6.6   3.7     0.021       7.8      83     123 ..     157     203 ..     120     214 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00022
                              End3  99 evrLkreLaeLeeklekveeeaekrkekereessksalvkreleqLLkYKeeqlreleegegkske.knlksvkedi 174
                                        ++ ++e ++L+e++e+++e++e+ k+++++   ++++++++ +q+L   +++l+el+++ ++s++ + l+sv e i
  gi|298674489|ref|YP_003726239.1|  35 LNKYRQEFEQLNERIESINEQMESAKKNKEYVVGRRDVLREKRQQILYQAQKTLNELQSSIKDSEHkEILSSVDEKI 111
                                       567899*****************999999999**************************999999986679******* PP

                              End3 175 etveeqVe 182
                                       +++++ ++
  gi|298674489|ref|YP_003726239.1| 112 SKLKTSIS 119
                                       *9998876 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.021
                              End3  83 s..ekgtdfsatk....gtdweevrLkreLaeLeeklekveeeaekr 123
                                       s  e++ ++++ k    + + e ++Lk+eL++L+ + + +e++ +++
  gi|298674489|ref|YP_003726239.1| 157 SviETSNEIESIKgsdkQYEKEYDKLKKELNDLNPRYKWLEKRISSH 203
                                       23434444444331102445567889999999988888888776654 PP

>> DUF5129  Domain of unknown function (DUF5129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.9   0.00013     0.051     188     242 ..      15      70 ..       7     144 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                           DUF5129 188 atiPeassyalellerfrkfkakyreateek.drlealtekelsraenvrlarefk 242
                                        ti ++s+  + ++e++++f++kyr+ +e+  +r+e++ e+  s ++n   +   +
  gi|298674489|ref|YP_003726239.1|  15 VTIMDKSELVSGVIEKHQNFLNKYRQEFEQLnERIESINEQMESAKKNKEYVVGRR 70 
                                       689999********************999752699*99999988888776665444 PP

>> Phage_GPO  Phage capsid scaffolding protein (GPO) serine peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   6.7      0.14        53     158     254 ..      27     101 ..       4     126 .. 0.46
   2 ?   11.9   6.0   0.00032      0.12     138     254 ..      85     206 ..      78     213 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.14
                         Phage_GPO 158 avetalefeeeeeeeegeslferikallskkkksddarfadveeavelvAeevkelsekveallaleael.aalkke 233
                                        +e + +f ++                         ++f +++e +e + e++++++++ e ++  ++ l ++ ++ 
  gi|298674489|ref|YP_003726239.1|  27 VIEKHQNFLNKY-----------------------RQEFEQLNERIESINEQMESAKKNKEYVVGRRDVLrEKRQQI 80 
                                       333333333333.......................344555555555555555555544444442222220222333 PP

                         Phage_GPO 234 veklkaeleaLkekLsktdak 254
                                       + ++++ l++L+++++  ++k
  gi|298674489|ref|YP_003726239.1|  81 LYQAQKTLNELQSSIKDSEHK 101
                                       344444555555555444432 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00032
                         Phage_GPO 138 kakanplak..rkqspenlftaavetalefeeeeeeeegeslferikallskkkksd...darfadveeavelvAee 209
                                       +++ n l++  + ++++++++   e   +++++ +++e+++++++i+  +s+ + +d   + + +d+++ ++ v e+
  gi|298674489|ref|YP_003726239.1|  85 QKTLNELQSsiKDSEHKEILSSVDEKISKLKTSISSDEEKQIVDEINDSISEISLNDetaNRKLSDIKSKIDSVIET 161
                                       4445555541134456678888888888888888888888888888888666554443338999************* PP

                         Phage_GPO 210 vkelsekveallaleaelaalkkeveklkaeleaLkekLsktdak 254
                                        +e+++   + ++ e+e  +lkke+++l+ +++ L++++s+ +++
  gi|298674489|ref|YP_003726239.1| 162 SNEIESIKGSDKQYEKEYDKLKKELNDLNPRYKWLEKRISSHEES 206
                                       ****99999999***************************999874 PP

>> Uds1  Up-regulated During Septation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.39   1.5e+02      25      43 ..      37      55 ..      28      57 .. 0.72
   2 ?    9.3  10.0    0.0032       1.2      21     112 ..      54     148 ..      52     168 .. 0.66
   3 ?    7.2   0.3     0.014       5.4      21      46 ..     177     202 ..     172     207 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.39
                              Uds1 25 elkkelkaLeerlealrkk 43
                                      + ++e ++L+er+e+++++
  gi|298674489|ref|YP_003726239.1| 37 KYRQEFEQLNERIESINEQ 55
                                      5677788888888887765 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0032
                              Uds1  21 eeVeelkkelkaLeerlealrkkLaletklrdaarsLsrlyssskksak...............ssaarsnskssre 82 
                                       e++e++kk+ + +  r + lr+k   ++ l +a ++L++l+ss k s++               +          + 
  gi|298674489|ref|YP_003726239.1|  54 EQMESAKKNKEYVVGRRDVLREK--RQQILYQAQKTLNELQSSIKDSEHkeilssvdekisklkT----------SI 118
                                       899********************..999999**********999999886666543333322220..........22 PP

                              Uds1  83 slakaeeelaeserkvdelaselekleera 112
                                       s++++++ ++e + ++ e++ + e++++++
  gi|298674489|ref|YP_003726239.1| 119 SSDEEKQIVDEINDSISEISLNDETANRKL 148
                                       333333334444444444444444444444 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.014
                              Uds1  21 eeVeelkkelkaLeerlealrkkLal 46 
                                       +e ++lkkel+ L+ r + l+k+++ 
  gi|298674489|ref|YP_003726239.1| 177 KEYDKLKKELNDLNPRYKWLEKRISS 202
                                       699****************9999875 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   9.0    0.0074       2.8      81     139 ..      29      87 ..      26      97 .. 0.70
   2 ?    3.7   4.0      0.09        34      61     105 ..      79     122 ..      75     129 .. 0.84
   3 ?   10.2   5.4    0.0009      0.34      30     106 ..     129     205 ..     120     213 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0074
                               GAS  81 ekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdelykkfeaaiqevqqk 139
                                       ek+++ l++ +++ ++l++ ++++ ++ e+ ++  e v   rd l++k ++ ++++q+ 
  gi|298674489|ref|YP_003726239.1|  29 EKHQNFLNKYRQEFEQLNERIESINEQMESAKKNKEYVVGRRDVLREKRQQILYQAQKT 87 
                                       56666777777777777777777777777777777777777777777777777777654 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.09
                               GAS  61 epLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlk 105
                                       + L +a++ ++eL+  +k+ e+ k+ l ++ +++++l+  +++ +
  gi|298674489|ref|YP_003726239.1|  79 QILYQAQKTLNELQSSIKDSEH-KEILSSVDEKISKLKTSISSDE 122
                                       568899***********99887.9999999999999999888755 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.0009
                               GAS  30 slKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkw 106
                                       +  + i e+  ++e ++++ls+i+++  +  e+ ++ e  +   ++  k+y+k k++l+ l+ r+k lek +++ ++
  gi|298674489|ref|YP_003726239.1| 129 EINDSISEISLNDETANRKLSDIKSKIDSVIETSNEIESIKGSDKQYEKEYDKLKKELNDLNPRYKWLEKRISSHEE 205
                                       45556677777777777777777777777777777777777777777777777777777777777777777776655 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   4.8    0.0086       3.3      37     104 ..      28      92 ..       4      93 .. 0.72
   2 ?    1.0   1.9       1.6   5.9e+02      40      70 ..      85     118 ..      76     139 .. 0.54
   3 ?    9.7   3.9    0.0031       1.2      17     103 ..     111     207 ..      98     208 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0086
                                       HHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  37 qallk.khkaleaelaaqqervkalnelaeklldeghsaseeieerleelnerWeeLkelaaerkqkLe 104
                                        ++++  +  +++e+++  er++++ne+ e+  ++    +e++  r + l+e+ ++++ +a+++ ++L+
  gi|298674489|ref|YP_003726239.1|  28 IEKHQnFLNKYRQEFEQLNERIESINEQMESAKKN----KEYVVGRRDVLREKRQQILYQAQKTLNELQ 92 
                                       33333244556667777777777777666666444....7********************999999987 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHHHH..HHHHHHHHHHHHHHH.HHT CS
                          Spectrin  40 lkkhkaleaelaa..qqervkalnelaekl.lde 70 
                                       +k++ +l+  +++  ++e + +++e  +kl ++ 
  gi|298674489|ref|YP_003726239.1|  85 QKTLNELQSSIKDseHKEILSSVDEKISKLkTSI 118
                                       4455555555555445666666666666663333 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0031
                                       HHHHHHHHCCSSCSSSHHHHHHHHH....HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTH......HHHHHHHH CS
                          Spectrin  17 ieekeellssedlgkdleevqallk....khkaleaelaaqqervkalnelaeklldeghsas......eeieerle 83 
                                       i++ ++ +ss++  + ++e+ + +       ++  + l++ + +++++ e+++++++ ++s++      +++++ l+
  gi|298674489|ref|YP_003726239.1| 111 ISKLKTSISSDEEKQIVDEINDSISeislNDETANRKLSDIKSKIDSVIETSNEIESIKGSDKqyekeyDKLKKELN 187
                                       55556666666666666666666666655667778889999999999999999996666433334555699****** PP

                                       HHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  84 elnerWeeLkelaaerkqkL 103
                                       +ln r++ L++++ ++++++
  gi|298674489|ref|YP_003726239.1| 188 DLNPRYKWLEKRISSHEESI 207
                                       *************9998865 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   6.2    0.0063       2.4      59     116 ..      35      92 ..      29      97 .. 0.82
   2 ?    1.0   3.7       1.1     4e+02      57     105 ..      79     130 ..      69     138 .. 0.55
   3 ?    4.4   9.4     0.099        38      15     122 ..     102     196 ..      86     208 .. 0.49

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0063
                        TPR_MLP1_2  59 lqalreelnelkaeiaelkaeaesakaeleeseesweeqkeelekelselekriedln 116
                                       l+++r+e+++l+++i++++++ esak++ e      +  +e+ ++ l +++k +++l+
  gi|298674489|ref|YP_003726239.1|  35 LNKYRQEFEQLNERIESINEQMESAKKNKEYVVGRRDVLREKRQQILYQAQKTLNELQ 92 
                                       899***********************99887777777777777777777777777776 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 1.1
                        TPR_MLP1_2  57 kelqalreelnelkaeia..elkaeaesakaeleeseeswee.qkeelekel 105
                                       + l ++ + lnel++ i+  e k+ + s+ +++++ + s+++ +++++ +e+
  gi|298674489|ref|YP_003726239.1|  79 QILYQAQKTLNELQSSIKdsEHKEILSSVDEKISKLKTSISSdEEKQIVDEI 130
                                       5556666666666666651133444566666666666665431444555555 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.099
                        TPR_MLP1_2  15 eekeeaeaklqklqedle..kqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaelee 89 
                                       e  ++ ++k++kl++ +   ++++i+ e +++ ++  ++ +++ ++l++++++++++ ++ +e++            
  gi|298674489|ref|YP_003726239.1| 102 EILSSVDEKISKLKTSISsdEEKQIVDEINDSISEISLNDETANRKLSDIKSKIDSVIETSNEIE------------ 166
                                       44566666666666655411455666666666666666666666666666666655554444443............ PP

                        TPR_MLP1_2  90 seesweeqkeelekelselekriedlneqNklL 122
                                          s++   +++eke ++l+k ++dln   k L
  gi|298674489|ref|YP_003726239.1| 167 ---SIKGSDKQYEKEYDKLKKELNDLNPRYKWL 196
                                       ...333333333333333333333333333333 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   5.5       0.1        39       3      63 ..      32      93 ..      30     136 .. 0.71
   2 ?    4.9   5.8     0.093        35      14      63 ..     105     153 ..     101     202 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.1
                           NPV_P10  3 qniLlvIradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaq.LaeletkvenIqd 63
                                      qn L   r++ ++++++++++++q+++ ++n + v    + L +  +q L + ++++++ q+
  gi|298674489|ref|YP_003726239.1| 32 QNFLNKYRQEFEQLNERIESINEQMESAKKNKEYVVGRRDVLREKRQQiLYQAQKTLNELQS 93
                                      78899999999999999999999999999988877655555543333314444444444444 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.093
                           NPV_P10  14 kavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqd 63 
                                       + vd+k++ l++++ +  e+ + v+e+n+ + ++s + ++ + k+++I++
  gi|298674489|ref|YP_003726239.1| 105 SSVDEKISKLKTSISSD-EEKQIVDEINDSISEISLNDETANRKLSDIKS 153
                                       57999999999999764.44566778888888888888888888887776 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.5   0.00041      0.15      36      65 ..      35      64 ..      23      67 .. 0.87
   2 ?    1.2   1.1       1.2   4.7e+02      37      64 ..      75     102 ..      70     106 .. 0.80
   3 ?    4.0   0.7      0.16        62      36      57 ..     104     125 ..      97     136 .. 0.70
   4 ?    1.0   0.2       1.5   5.6e+02      37      63 ..     142     168 ..     134     174 .. 0.80
   5 ?    7.3   0.3     0.015       5.9      38      69 ..     174     205 ..     170     206 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00041
                            Csm1_N 36 letkdqeiesLkeqlaeleekvkeleerrk 65
                                      l+++ qe e+L e++++++e++++++++++
  gi|298674489|ref|YP_003726239.1| 35 LNKYRQEFEQLNERIESINEQMESAKKNKE 64
                                      67889******************9999875 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 1.2
                            Csm1_N  37 etkdqeiesLkeqlaeleekvkeleerr 64 
                                       e+++q + + +++l+el++ +k++e+++
  gi|298674489|ref|YP_003726239.1|  75 EKRQQILYQAQKTLNELQSSIKDSEHKE 102
                                       5677777889999999999999988775 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.16
                            Csm1_N  36 letkdqeiesLkeqlaeleekv 57 
                                       l++ d++i++Lk  + + eek 
  gi|298674489|ref|YP_003726239.1| 104 LSSVDEKISKLKTSISSDEEKQ 125
                                       5566777777777777777764 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 1.5
                            Csm1_N  37 etkdqeiesLkeqlaeleekvkeleer 63 
                                       et +++++ +k +++++ e ++e+e+ 
  gi|298674489|ref|YP_003726239.1| 142 ETANRKLSDIKSKIDSVIETSNEIESI 168
                                       677889999999999999999888765 PP

  == domain 5  score: 7.3 bits;  conditional E-value: 0.015
                            Csm1_N  38 tkdqeiesLkeqlaeleekvkeleerrkkqeE 69 
                                       ++++e  +Lk++l+ l+ + k le+r +++eE
  gi|298674489|ref|YP_003726239.1| 174 QYEKEYDKLKKELNDLNPRYKWLEKRISSHEE 205
                                       6899**********************999998 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   4.1       1.9   7.1e+02      15      30 ..      45      60 ..      25     101 .. 0.54
   2 ?    0.6   1.1       1.9   7.2e+02      24      39 ..     102     117 ..      73     124 .. 0.48
   3 ?   12.4   0.2   0.00041      0.16      19      61 ..     165     207 ..     154     209 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1.9
                               CLZ 15 LDeeaakagaeqkele 30
                                      L e+ ++ +++ ++++
  gi|298674489|ref|YP_003726239.1| 45 LNERIESINEQMESAK 60
                                      3333334444444444 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.9
                               CLZ  24 aeqkeleekverLess 39 
                                       +   +++ek+++L++s
  gi|298674489|ref|YP_003726239.1| 102 EILSSVDEKISKLKTS 117
                                       2223455555555554 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00041
                               CLZ  19 aakagaeqkeleekverLessLeaLqtrlarLlaeyessqrkL 61 
                                        ++ +   k+ e+  ++L+++L+ L+ r+++L +  +s ++ +
  gi|298674489|ref|YP_003726239.1| 165 IESIKGSDKQYEKEYDKLKKELNDLNPRYKWLEKRISSHEESI 207
                                       566678899************************9999988765 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0  13.1    0.0079         3      32     130 ..      23     123 ..      12     125 .. 0.64
   2 ?    9.2   5.6    0.0035       1.3      35     120 ..     125     209 ..     119     215 .] 0.68

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0079
                                       CCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCH.HHHH.. CS
                         Fib_alpha  32 dvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqe.snir.. 105
                                        v+  +ek +n l++++++ ++ +e +++i++++++++k+k+      +++ +e +++il+  ++  ++  s+i+  
  gi|298674489|ref|YP_003726239.1|  23 LVSGVIEKHQNFLNKYRQEFEQLNERIESINEQMESAKKNKEY-VVGRRDVLREKRQQILYQAQKTLNELqSSIKds 98 
                                       5666777888888888888888888888888888877777773.333334444444455555444444444777522 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 106 vLqnvlesneqkiqkLeqdidqker 130
                                       + +++l+s ++ki+kL++ i++ e+
  gi|298674489|ref|YP_003726239.1|  99 EHKEILSSVDEKISKLKTSISSDEE 123
                                       4577888888888888888776655 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0035
                                       HHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHH CS
                         Fib_alpha  35 kdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvl 111
                                       + +++++++++eis + ++a++  ++ik+++ +  ++++ + + ik s k+ e+e+ +lk+++++   + + L + +
  gi|298674489|ref|YP_003726239.1| 125 QIVDEINDSISEISLNDETANRKLSDIKSKIDSVIETSN-EIESIKGSDKQYEKEYDKLKKELNDLNPRYKWLEKRI 200
                                       556777777777777777777777777777777777776.3666777777777777777777777777777777777 PP

                                       HHHHHHHHH CS
                         Fib_alpha 112 esneqkiqk 120
                                       +s e++i+ 
  gi|298674489|ref|YP_003726239.1| 201 SSHEESIEY 209
                                       777766654 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   9.0      0.27     1e+02      53     114 ..      29      90 ..      15      93 .. 0.50
   2 ?    1.0   4.0       1.1   4.1e+02      49      88 ..      78     119 ..      72     125 .. 0.43
   3 ?    2.6   2.0      0.36   1.4e+02      60     101 ..     121     162 ..      96     167 .. 0.59
   4 ?   12.5   2.7    0.0003      0.12       5      95 ..     121     208 ..     117     212 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.27
                             DHR10  53 eeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaeekreaakarlee 114
                                       e+ +  l++ r++ e+++++ + ++ + e  ++  e    + + lre++++   +a+++l e
  gi|298674489|ref|YP_003726239.1|  29 EKHQNFLNKYRQEFEQLNERIESINEQMESAKKNKEYVVGRRDVLREKRQQILYQAQKTLNE 90 
                                       33444444445555555555555555555555555555555555555555555555555555 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 1.1
                             DHR10  49 lakleeakkklkelrdaleekeie..lrelerkeerlqrqle 88 
                                       ++ l +a+k+l+el+  +++ e++  l+ ++ k++ l+  ++
  gi|298674489|ref|YP_003726239.1|  78 QQILYQAQKTLNELQSSIKDSEHKeiLSSVDEKISKLKTSIS 119
                                       334444555555555555444433123344444444444444 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.36
                             DHR10  60 kelrdaleekeielrelerkeerlqrqlenaeeklerlreqa 101
                                       +e ++ ++e +   +e++ + e  +r+l+  + k++ + e++
  gi|298674489|ref|YP_003726239.1| 121 DEEKQIVDEINDSISEISLNDETANRKLSDIKSKIDSVIETS 162
                                       455555666666666666666666666666666666665554 PP

  == domain 4  score: 12.5 bits;  conditional E-value: 0.0003
                             DHR10   5 aeekeelaelErkarelqakidalqvvekdlrsciklleeieaelakleeakkklkelrdaleekeielrelerkee 81 
                                       +eek+ ++e    + e++   ++ ++   d++s i+ + e ++e+++ + ++k+ +   ++++++++el++l+ + +
  gi|298674489|ref|YP_003726239.1| 121 DEEKQIVDEINDSISEISLNDETANRKLSDIKSKIDSVIETSNEIESIKGSDKQYE---KEYDKLKKELNDLNPRYK 194
                                       57888888888888888888888888888899999999999999999998888765...578888889999999999 PP

                             DHR10  82 rlqrqlenaeekle 95 
                                        l+++++++ee +e
  gi|298674489|ref|YP_003726239.1| 195 WLEKRISSHEESIE 208
                                       99999999999887 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   8.3      0.48   1.8e+02      21      78 ..      37      97 ..      22     141 .. 0.58
   2 ?   11.2   0.5    0.0012      0.46       6      69 ..     142     207 ..     138     214 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.48
                           DUF2203 21 elralrkeleeleeeleeakaeaekse......aaeleaeleeleaeieelveeieelGvevkd 78
                                      ++r+  ++l+e+ e+++e+ ++a+k++      +  l+++ +++     ++ ++++el   +kd
  gi|298674489|ref|YP_003726239.1| 37 KYRQEFEQLNERIESINEQMESAKKNKeyvvgrRDVLREKRQQIL---YQAQKTLNELQSSIKD 97
                                      333333333333333333333333333554344333333333333...3444444444444444 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0012
                           DUF2203   6 eeAnalLpllkelleelralrkeleeleeeleeakaeaekse..aaeleaeleeleaeieelveei 69 
                                       e+An+ L  +k++++ ++++ +e+e+++ + ++ ++e++k +   + l+ +++ le++i+++ e i
  gi|298674489|ref|YP_003726239.1| 142 ETANRKLSDIKSKIDSVIETSNEIESIKGSDKQYEKEYDKLKkeLNDLNPRYKWLEKRISSHEESI 207
                                       78************************9988887777766555555666666666666666555555 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.2    0.0076       2.9      25      59 ..      27      61 ..      21      65 .. 0.76
   2 ?    2.4   1.0      0.66   2.5e+02      23      50 ..      78      98 ..      71     124 .. 0.65
   3 ?    3.1   0.2      0.39   1.5e+02       3      55 ..     109     163 ..     107     174 .. 0.75
   4 ?    3.9   0.0      0.22        83      28      55 ..     174     201 ..     163     209 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0076
                                      HHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXXX CS
                              SlyX 25 vvaeqqqqidrlqrqlrllaerlkeleessgasea 59
                                      v+ ++q  + + ++++++l+er+++++e+++++++
  gi|298674489|ref|YP_003726239.1| 27 VIEKHQNFLNKYRQEFEQLNERIESINEQMESAKK 61
                                      66678888888999999999999999888876554 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.66
                                      HHHHHHHHHHHHHHHHHHHHHHHT-XXX CS
                              SlyX 23 ndvvaeqqqqidrlqrqlrllaerlkel 50
                                      ++++++ q+++ +lq  ++         
  gi|298674489|ref|YP_003726239.1| 78 QQILYQAQKTLNELQSSIKD-------S 98
                                      35555555555555555443.......3 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.39
                                       HHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXX CS
                              SlyX   3 erleeLEiklafqe..dtieeLndvvaeqqqqidrlqrqlrllaerlkeleessg 55 
                                       e++ +L + ++  e  + ++e nd + e     +   r+l  ++ ++ ++ e+s+
  gi|298674489|ref|YP_003726239.1| 109 EKISKLKTSISSDEekQIVDEINDSISEISLNDETANRKLSDIKSKIDSVIETSN 163
                                       56666666666555225899*******9999999999999999999977766654 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.22
                                       HHHHHHHHHHHHHHHHHHT-XXXXXXXX CS
                              SlyX  28 eqqqqidrlqrqlrllaerlkeleessg 55 
                                       + +++ d+l+++l+ l+ r k le++ +
  gi|298674489|ref|YP_003726239.1| 174 QYEKEYDKLKKELNDLNPRYKWLEKRIS 201
                                       5678899999999999988888777654 PP

>> Erf4  Golgin subfamily A member 7/ERF4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.6     0.012       4.8      76     100 ..      36      61 ..      15      75 .. 0.75
   2 ?    5.6   1.9     0.043        16      23      48 ..     112     137 ..      66     206 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.012
                              Erf4  76 thykkklkklekyieelNeel.fker 100
                                       ++y++++++l++ ie++Ne++  +++
  gi|298674489|ref|YP_003726239.1|  36 NKYRQEFEQLNERIESINEQMeSAKK 61 
                                       68999***************963333 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.043
                              Erf4  23 peLsgyiseeefeeiinkiNeilaea 48 
                                       ++L+  is +e ++i+++iN+ + e 
  gi|298674489|ref|YP_003726239.1| 112 SKLKTSISSDEEKQIVDEINDSISEI 137
                                       56788888888888888888776553 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   9.0    0.0041       1.6      43     124 .]      42     125 ..      32     125 .. 0.91
   2 ?    7.1   1.6     0.014       5.4      41     117 ..     132     207 ..     124     212 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0041
                           DUF1664  43 vesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlse..igedvesvkeavegleskl 117
                                        e++ +++e++ e+++++k++ +  + r d   ++ ++i  + ++ ++e+++ +++   +e ++sv+e +++l++++
  gi|298674489|ref|YP_003726239.1|  42 FEQLNERIESINEQMESAKKNKEYVVGRRDVLREKRQQILYQAQKTLNELQSSIKDseHKEILSSVDEKISKLKTSI 118
                                       6789999*********************************************99761157889************** PP

                           DUF1664 118 erieekQ 124
                                       ++ eekQ
  gi|298674489|ref|YP_003726239.1| 119 SSDEEKQ 125
                                       **99998 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.014
                           DUF1664  41 davesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskl 117
                                       d ++++s + e+   +l++ k ++ s i++  +++++ k   k+ ++e ++++++l++++   + +++ +++ e+++
  gi|298674489|ref|YP_003726239.1| 132 DSISEISLNDETANRKLSDIKSKIDSVIET-SNEIESIKGSDKQYEKEYDKLKKELNDLNPRYKWLEKRISSHEESI 207
                                       333444444444444555555555444443.3455555566666666666777777666666666666666666655 PP

>> HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   9.6    0.0063       2.4      16      82 ..      36     102 ..      30     117 .. 0.88
   2 ?    7.1   0.5     0.022       8.5      25      85 ..     148     210 ..     138     213 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0063
                    HIP1_clath_bdg  16 svarqaqeeverekkeleeelerlkeeaerkleeqkeelekLkreleakraelarlkssLesseqsg 82 
                                          rq+ e+++   + ++e++e++k+++e  +  +    ek ++ l + ++ l++l+ss+++se+++
  gi|298674489|ref|YP_003726239.1|  36 NKYRQEFEQLNERIESINEQMESAKKNKEYVVGRRDVLREKRQQILYQAQKTLNELQSSIKDSEHKE 102
                                       5679999*******************************************************99876 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.022
                    HIP1_clath_bdg  25 verekkeleeelerlkeeaerkle..eqkeelekLkreleakraelarlkssLesseqsgeql 85 
                                       +   k++++  +e  +e ++ k +  + ++e +kLk+el++ + + + l++ ++s+e+s e +
  gi|298674489|ref|YP_003726239.1| 148 LSDIKSKIDSVIETSNEIESIKGSdkQYEKEYDKLKKELNDLNPRYKWLEKRISSHEESIEYW 210
                                       455566666666666666666655223346789999999999999999999999999887766 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.7    0.0073       2.8      66      96 ..      34      64 ..       6      77 .. 0.65
   2 ?    3.3   6.4      0.29   1.1e+02      48      97 ..     147     209 ..      67     210 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0073
                           DUF4140 66 elkalraeleeledelaaledelaaaearla 96
                                       l++ r+e e+l+++++ +++++++a++ ++
  gi|298674489|ref|YP_003726239.1| 34 FLNKYRQEFEQLNERIESINEQMESAKKNKE 64
                                      2667777777777777777777777777665 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.29
                           DUF4140  48 tildvqvervpnreaeee.............elkalraeleeledelaaledelaaaearlaf 97 
                                       +++d++ + +   e+ +e             e+++l++el+ l+ + + le++++++e+++++
  gi|298674489|ref|YP_003726239.1| 147 KLSDIKSKIDSVIETSNEiesikgsdkqyekEYDKLKKELNDLNPRYKWLEKRISSHEESIEY 209
                                       555555555555555555667777666666568888888888888888888888888888876 PP

>> DUF2785  Protein of unknown function (DUF2785)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.2       1.2   4.7e+02     124     151 ..      33      60 ..       1      77 [. 0.50
   2 ?   10.4   0.5    0.0011       0.4      86     148 ..      94     158 ..      84     174 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.2
                           DUF2785 124 alleknkleeetllawleelrqelakke 151
                                       + l+k + e e+l++ +e+++++++  +
  gi|298674489|ref|YP_003726239.1|  33 NFLNKYRQEFEQLNERIESINEQMESAK 60 
                                       3444444444555555555544443322 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0011
                           DUF2785  86 elkradailllelivkkltrtqsvlaadEdeRlatailalleknkleeetllawleelrqel..a 148
                                        +k ++  ++l  + +k++++++    dE++ ++  i   +++  l++et ++ l++++ ++  +
  gi|298674489|ref|YP_003726239.1|  94 SIKDSEHKEILSSVDEKISKLKTSISSDEEKQIVDEINDSISEISLNDETANRKLSDIKSKIdsV 158
                                       577899999*************************************************8877432 PP

>> SKA2  Spindle and kinetochore-associated protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   5.1    0.0017      0.66      40      94 ..      42      96 ..      29     115 .. 0.83
   2 ?    2.9   0.2      0.24        92      13      60 ..     143     199 ..     132     208 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0017
                              SKA2 40 pvkLlerlkkvkeelqaLkeqceellaekkelidkirttlvanrellqqLqasae 94
                                        +L er++ ++e++++ k++ e +  ++  l +k ++ l + +++l +Lq s++
  gi|298674489|ref|YP_003726239.1| 42 FEQLNERIESINEQMESAKKNKEYVVGRRDVLREKRQQILYQAQKTLNELQSSIK 96
                                      468999*********************************************9983 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.24
                              SKA2  13 kaesdLdyvqhrLekefqqsypdna.........eNpvkLlerlkkvkeelqaLkeq 60 
                                       +a+++L  ++++ ++ +++s + +          ++  kL ++l++++ +++ L+++
  gi|298674489|ref|YP_003726239.1| 143 TANRKLSDIKSKIDSVIETSNEIESikgsdkqyeKEYDKLKKELNDLNPRYKWLEKR 199
                                       677777777777777777666655555444455555556666666666666655555 PP

>> Lipase_GDSL_3  GDSL-like Lipase/Acylhydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   1.2    0.0067       2.6     102     154 ..      27      79 ..      19      87 .. 0.88
   2 ?    3.7   0.1      0.16        62      32      86 ..     107     161 ..      98     168 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0067
                     Lipase_GDSL_3 102 lsttkglvdeklekeveaknkaleelvkklkkekekklylisskellgkdeea 154
                                       +  +++ + +k ++e e+ n+ +e++ +++++ k++k y++  +++l+++ ++
  gi|298674489|ref|YP_003726239.1|  27 VIEKHQNFLNKYRQEFEQLNERIESINEQMESAKKNKEYVVGRRDVLREKRQQ 79 
                                       56678899999*********************************999987765 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.16
                     Lipase_GDSL_3  32 lgrevvnLgfsGnalleaeladvlaevdasvfvldllpNasaeeirerleyfvkt 86 
                                       +++++  L +s ++  e++++d +++  +++ + d  +N++ + i+ +++ +++t
  gi|298674489|ref|YP_003726239.1| 107 VDEKISKLKTSISSDEEKQIVDEINDSISEISLNDETANRKLSDIKSKIDSVIET 161
                                       66777788888888899*********************************99986 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.7    0.0084       3.2      49      79 ..      31      61 ..      29      64 .. 0.86
   2 ?    0.3   0.1       2.1   8.2e+02      28      40 ..      82      94 ..      73     119 .. 0.61
   3 ?    2.9   0.0      0.34   1.3e+02      45      64 ..     171     190 ..     126     208 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0084
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100 49 fqaefeewkqaaqklvdaLeeisealkqaan 79
                                       q+++++++q++++l++  e+i+e++++a++
  gi|298674489|ref|YP_003726239.1| 31 HQNFLNKYRQEFEQLNERIESINEQMESAKK 61
                                      6788999999999999999999999999987 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 2.1
                                      HHHHHHHHHCGCG CS
                            WXG100 28 qrlkaevdalqsg 40
                                       + ++++++lqs+
  gi|298674489|ref|YP_003726239.1| 82 YQAQKTLNELQSS 94
                                      3333333333332 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.34
                                       HCHHHHHHHHHHHHHHHHHH CS
                            WXG100  45 aadafqaefeewkqaaqklv 64 
                                       + +++++e++++k+++++l+
  gi|298674489|ref|YP_003726239.1| 171 SDKQYEKEYDKLKKELNDLN 190
                                       44566666666666666665 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.1   0.00075      0.29      20      70 ..      12      62 ..       2      65 .. 0.90
   2 ?    2.4   2.4      0.49   1.9e+02      38      80 ..      76     120 ..      71     125 .. 0.67
   3 ?    3.0   0.3      0.33   1.3e+02      19      60 ..     124     165 ..     119     191 .. 0.77
   4 ?    1.7   0.1       0.8   3.1e+02      51      79 ..     173     201 ..     159     209 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00075
                              KxDL 20 qtsgrlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkk 70
                                      +ts ++ +k++ ++ ++++ q+ l+k+r++f+q  + + ++++++es +k+
  gi|298674489|ref|YP_003726239.1| 12 NTSVTIMDKSELVSGVIEKHQNFLNKYRQEFEQLNERIESINEQMESAKKN 62
                                      788899999999*********************************999885 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.49
                              KxDL  38 lsqerlaklrarfkqgtkllk..evkkdLesifkkirslkaklak 80 
                                       + q+ l ++++ +++ +  +k  e k+ L s+ +ki++lk+ +++
  gi|298674489|ref|YP_003726239.1|  76 KRQQILYQAQKTLNELQSSIKdsEHKEILSSVDEKISKLKTSISS 120
                                       555666666666666666665224577789999999999988776 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.33
                              KxDL  19 aqtsgrlnkknreLlelnalsqerlaklrarfkqgtkllkev 60 
                                       +q+++++n++  e++   + ++++l+++++++ + +++++e+
  gi|298674489|ref|YP_003726239.1| 124 KQIVDEINDSISEISLNDETANRKLSDIKSKIDSVIETSNEI 165
                                       677788888888888888888888888888888887777766 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.8
                              KxDL  51 kqgtkllkevkkdLesifkkirslkakla 79 
                                       kq+ k   ++kk+L+ ++ + + l+++++
  gi|298674489|ref|YP_003726239.1| 173 KQYEKEYDKLKKELNDLNPRYKWLEKRIS 201
                                       44444555555555555555555555444 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   9.4     0.014       5.5      15      97 ..      32     119 ..      27     122 .. 0.73
   2 ?    4.9   0.8      0.12        45      34      72 ..     100     140 ..      87     158 .. 0.58
   3 ?    7.7   1.6     0.016         6      19      59 ..     173     214 ..     159     215 .] 0.81

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.014
                      Occludin_ELL  15 aeFnkeY.keYkelhaeleevskkfseLerelkelkegsk....eykkieeeilqeykklkkdpeyqekkkrceyLk 86 
                                       ++F ++Y +e+ +l++++e+++++++  +++ +    +++    + ++i  + ++++++l+++ +  e+k+ +    
  gi|298674489|ref|YP_003726239.1|  32 QNFLNKYrQEFEQLNERIESINEQMESAKKNKEYVVGRRDvlreKRQQILYQAQKTLNELQSSIKDSEHKEILSSVD 108
                                       4566666346777777777777777777766666655555566666677777777888888888888999999999* PP

                      Occludin_ELL  87 ekLshiKklik 97 
                                       ek s +K+ i+
  gi|298674489|ref|YP_003726239.1| 109 EKISKLKTSIS 119
                                       *******9997 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.12
                      Occludin_ELL  34 vskkfseLerelkelkegsk..eykkieeeilqeykklkkd 72 
                                        ++ +s +++++++lk++ +  e+k+i++ei ++ ++++ +
  gi|298674489|ref|YP_003726239.1| 100 HKEILSSVDEKISKLKTSISsdEEKQIVDEINDSISEISLN 140
                                       33445666666666666554457777777777777776443 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.016
                      Occludin_ELL  19 keY.keYkelhaeleevskkfseLerelkelkegskeykkie 59 
                                       k+Y keY +l++el++++ + + Le+++++++e+ + +k++e
  gi|298674489|ref|YP_003726239.1| 173 KQYeKEYDKLKKELNDLNPRYKWLEKRISSHEESIEYWKNVE 214
                                       556358999999999999999999999999988888777765 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   1.3      0.12        45      32      65 ..      39      72 ..      23     102 .. 0.71
   2 ?    6.1   2.5     0.031        12      31      98 ..      96     160 ..      75     166 .. 0.87
   3 ?    2.6   0.0      0.37   1.4e+02      63      88 ..     177     202 ..     174     209 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.12
                           DUF2730 32 redleklaekveendkrlteletkvenLPtakdl 65
                                      r++ e+l+e +e++++++++++ + e++  ++d+
  gi|298674489|ref|YP_003726239.1| 39 RQEFEQLNERIESINEQMESAKKNKEYVVGRRDV 72
                                      8999999999999999999999888877777776 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.031
                           DUF2730  31 kredleklaekveendkrlteletkvenLPtakdlekLkllladlrgelkaleaevrqlshqvdLLLe 98 
                                       k ++++++   +++ d+++++l+t++++   ++ +++++  ++++  + ++++++++ ++ ++d  +e
  gi|298674489|ref|YP_003726239.1|  96 KDSEHKEI---LSSVDEKISKLKTSISSDEEKQIVDEINDSISEISLNDETANRKLSDIKSKIDSVIE 160
                                       44555555...888899999999999999999999************************999998877 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.37
                           DUF2730  63 kdlekLkllladlrgelkaleaevrq 88 
                                       k+ +kLk++l+dl+ + k le+++++
  gi|298674489|ref|YP_003726239.1| 177 KEYDKLKKELNDLNPRYKWLEKRISS 202
                                       66778888888888888888777765 PP

>> Rho_Binding  Rho Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2  13.1       4.7   1.8e+03       6      34 ..      36      64 ..      32     131 .. 0.92
   2 ?    8.3   0.6      0.01       3.9       4      50 ..     133     178 ..     130     180 .. 0.85
   3 ?    7.4   0.6      0.02       7.7       2      35 ..     176     209 ..     175     215 .] 0.80

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 4.7
                       Rho_Binding  6 enlakekeelnkklkkleeelekakeeee 34
                                      +++++e e+ln+++++++e++e ak+++e
  gi|298674489|ref|YP_003726239.1| 36 NKYRQEFEQLNERIESINEQMESAKKNKE 64
                                      67899*******************96555 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.01
                       Rho_Binding   4 dvenlakekeelnkklkkleeelekakeeeeeieklkasyekqLktE 50 
                                       ++ +++ + e  n+kl+++++++    e+++eie++k   +kq ++E
  gi|298674489|ref|YP_003726239.1| 133 SISEISLNDETANRKLSDIKSKIDSVIETSNEIESIK-GSDKQYEKE 178
                                       5678899999**************************9.666666555 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.02
                       Rho_Binding   2 tkdvenlakekeelnkklkkleeelekakeeeee 35 
                                       +k+ ++l+ke ++ln + k le++++  +e+ e 
  gi|298674489|ref|YP_003726239.1| 176 EKEYDKLKKELNDLNPRYKWLEKRISSHEESIEY 209
                                       588999************9999999988755444 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   2.4     0.013       5.1      39      67 ..      36      64 ..      19      69 .. 0.83
   2 ?    6.4   6.7     0.026        10      35     103 ..      71     136 ..      67     140 .. 0.78
   3 ?    6.9   3.9     0.018         7      48      94 ..     158     204 ..     128     210 .. 0.54

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.013
                                      HHHHHHHHHHHHHHHHHHHHCCCCCCTTS CS
                      Seryl_tRNA_N 39 relqveleelqaerNelskeIgkakkkke 67
                                       + ++e+e+l+++  ++++++++akk+ke
  gi|298674489|ref|YP_003726239.1| 36 NKYRQEFEQLNERIESINEQMESAKKNKE 64
                                      5778999******************9986 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.026
                                       HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                      Seryl_tRNA_N  35 dekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelekllla 103
                                       d  r++ q+ l ++q+  Nel+ +I+    k e  +++ +++++lk+ ++  e+  k++ +e+++ +++
  gi|298674489|ref|YP_003726239.1|  71 DVLREKRQQILYQAQKTLNELQSSIKDSEHK-EILSSVDEKISKLKTSISSDEE--KQIVDEINDSISE 136
                                       556888999999***************9986.79999**********9987665..4444444444433 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.018
                                       HHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  48 lqaerNelskeIgkakkkk....edaeeliaevkelkeelkaleaelkele 94 
                                       + +     s+eI+++k ++    ++ ++l++e ++l+ + k le++ +  e
  gi|298674489|ref|YP_003726239.1| 158 VIE----TSNEIESIKGSDkqyeKEYDKLKKELNDLNPRYKWLEKRISSHE 204
                                       333....34444444444333335666666666666666666666555555 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   7.7      0.24        92      10      53 ..      23      65 ..      21     101 .. 0.72
   2 ?    2.8   2.7      0.41   1.6e+02      27      67 ..      76     116 ..      71     120 .. 0.68
   3 ?    3.9   3.3      0.19        71      11      77 ..     107     170 ..      98     182 .. 0.47
   4 ?    7.6   2.0     0.013       5.1      15      87 ..     127     201 ..     120     202 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.24
                   Snapin_Pallidin 10 llepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeae 53
                                      l++ +++++++ l++ rq+ e+L+e++++ ne+++++++++e  
  gi|298674489|ref|YP_003726239.1| 23 LVSGVIEKHQNFLNKYRQEFEQLNERIESINEQMESAKKNKE-Y 65
                                      66778999999999999999**************99999888.3 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.41
                   Snapin_Pallidin  27 qsQeeLleqldrlnekLkeleeaqe.aevlpdlkeyakKLvn 67 
                                       + Q+ L +  ++ln +L++  ++ e +e+l+ ++e + KL++
  gi|298674489|ref|YP_003726239.1|  76 KRQQILYQAQKTLN-ELQSSIKDSEhKEILSSVDEKISKLKT 116
                                       45666666555555.555555555559999999999999975 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.19
                   Snapin_Pallidin  11 lepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslne 77 
                                       +  k+ +l++++++ +++Q    ++++   +++  l++++ +  l+d+k+ ++ +++  ++++s++ 
  gi|298674489|ref|YP_003726239.1| 107 VDEKISKLKTSISSDEEKQ--IVDEINDSISEIS-LNDETANRKLSDIKSKIDSVIETSNEIESIKG 170
                                       3334444444444333333..3345555555554.22222235566666666666666666666655 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.013
                   Snapin_Pallidin  15 ldeldeklkelrqsQeeLleqldrlnekLkeleeaqe..aevlpdlkeyakKLvnikkrmsslnerlqklkkRae 87 
                                       +de++++++e+  + e  + +l+  ++k++++ e+ +  +++    k+y k   ++kk+++ ln r + l+kR++
  gi|298674489|ref|YP_003726239.1| 127 VDEINDSISEISLNDETANRKLSDIKSKIDSVIETSNeiESIKGSDKQYEKEYDKLKKELNDLNPRYKWLEKRIS 201
                                       788889999999999999999999999999888877764444445578999999999999999999999999985 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.6     0.004       1.5       9      37 ..      28      56 ..      24      66 .. 0.88
   2 ?    1.2   5.5       1.3   5.1e+02       4      33 ..     106     137 ..      78     140 .. 0.79
   3 ?    7.1   2.4     0.019       7.4       2      36 ..     127     161 ..     126     165 .. 0.93
   4 ?    4.7   0.3      0.11        40      13      40 ..     162     189 ..     157     196 .. 0.57
   5 ?   -1.0   0.0       6.1   2.3e+03       4      18 ..     195     209 ..     192     213 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.004
                         FlaC_arch  9 lsklsteletvkkeneelsksveelkenV 37
                                      ++k++  l+  ++e+e+l++ +e ++e+ 
  gi|298674489|ref|YP_003726239.1| 28 IEKHQNFLNKYRQEFEQLNERIESINEQM 56
                                      5777888999****************986 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 1.3
                         FlaC_arch   4 elEnklsklsteletvkken..eelsksveel 33 
                                       ++++k+skl+t++++ ++++  +e+++s+ e+
  gi|298674489|ref|YP_003726239.1| 106 SVDEKISKLKTSISSDEEKQivDEINDSISEI 137
                                       56788888888888766553337777777777 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.019
                         FlaC_arch   2 idelEnklsklsteletvkkeneelsksveelken 36 
                                       +de+   +s++s + et+ +++++++++++ + e+
  gi|298674489|ref|YP_003726239.1| 127 VDEINDSISEISLNDETANRKLSDIKSKIDSVIET 161
                                       89****************************98665 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.11
                         FlaC_arch  13 steletvkkeneelsksveelkenVkdl 40 
                                       s e+e++k + ++ +k+ ++lk++ +dl
  gi|298674489|ref|YP_003726239.1| 162 SNEIESIKGSDKQYEKEYDKLKKELNDL 189
                                       4455555555555555555555555444 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 6.1
                         FlaC_arch   4 elEnklsklstelet 18 
                                        lE+++s+++ ++e 
  gi|298674489|ref|YP_003726239.1| 195 WLEKRISSHEESIEY 209
                                       589999999988875 PP

>> Val_tRNA-synt_C  Valyl tRNA synthetase tRNA binding arm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0      0.05        19      40      65 ..      27      52 ..      25      53 .. 0.89
   2 ?   -1.5   0.3       8.5   3.2e+03      44      64 ..      59      79 ..      54      92 .. 0.64
   3 ?   -0.4   0.2       3.8   1.4e+03      10      26 ..      85     101 ..      71     105 .. 0.79
   4 ?   -1.6   0.0       9.2   3.5e+03      45      62 ..     101     118 ..      96     120 .. 0.64
   5 ?    8.9   0.4    0.0049       1.9       3      29 ..     176     202 ..     174     204 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.05
                   Val_tRNA-synt_C 40 VVeeekaklaeleeqaeklkerLskL 65
                                      V+e+ ++ l +++++ e+l+er++++
  gi|298674489|ref|YP_003726239.1| 27 VIEKHQNFLNKYRQEFEQLNERIESI 52
                                      99999999999999999999999876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 8.5
                   Val_tRNA-synt_C 44 ekaklaeleeqaeklkerLsk 64
                                       k++++ +   +++l+e+ ++
  gi|298674489|ref|YP_003726239.1| 59 AKKNKEYVVGRRDVLREKRQQ 79
                                      555555555666666666555 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 3.8
                   Val_tRNA-synt_C  10 eKeLaklekeiervqkK 26 
                                       +K+L++l++ i+  + K
  gi|298674489|ref|YP_003726239.1|  85 QKTLNELQSSIKDSEHK 101
                                       68888888888776665 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 9.2
                   Val_tRNA-synt_C  45 kaklaeleeqaeklkerL 62 
                                       k+ l ++ e+  klk+ +
  gi|298674489|ref|YP_003726239.1| 101 KEILSSVDEKISKLKTSI 118
                                       555666667777776665 PP

  == domain 5  score: 8.9 bits;  conditional E-value: 0.0049
                   Val_tRNA-synt_C   3 ekeraRLeKeLaklekeiervqkKLan 29 
                                       eke ++L+KeL+ l+   + ++k+++ 
  gi|298674489|ref|YP_003726239.1| 176 EKEYDKLKKELNDLNPRYKWLEKRISS 202
                                       8999************99999999986 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   7.9     0.038        15      20      86 ..      23      99 ..       4     102 .. 0.56
   2 ?    0.0  20.0       1.1     4e+02      16     127 ..      75     185 ..      32     187 .. 0.53
   3 ?    6.5   1.8     0.011       4.3       5      56 ..     159     210 ..     145     215 .] 0.72

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.038
                             TMPIT 20 eykqkleelsklqskcskeikkqkkrlkelksslkklkksvk..........eeeeeeveelkeelkerkkvlkeve 86
                                       +   +e+ +++ +k ++e ++ ++r++++++++++ kk+++          e++++++ + +++l+e ++++k+ e
  gi|298674489|ref|YP_003726239.1| 23 LVSGVIEKHQNFLNKYRQEFEQLNERIESINEQMESAKKNKEyvvgrrdvlrEKRQQILYQAQKTLNELQSSIKDSE 99
                                      33444444444444555555555555555555555544443355555555556667777777777777777777665 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.1
                             TMPIT  16 eta.keykqkleelsklqskcskeikkqkkrlkelksslkklkksvk.eeeeeeveelkeelkerkkvlkevesllp 90 
                                       e+  + + q  ++l++lqs+++ +  ++k+ l++++++++klk+s++ +ee+++v+e++++++e++ + +  +  l 
  gi|298674489|ref|YP_003726239.1|  75 EKRqQILYQAQKTLNELQSSIKDS--EHKEILSSVDEKISKLKTSISsDEEKQIVDEINDSISEISLNDETANRKLS 149
                                       222011222222333333333322..233445555555555555533466666777777777777777777777777 PP

                             TMPIT  91 kknglylklvlGnvnvsllnkqdkfkyKdeYekFklk 127
                                         ++   +++ ++ +++ ++ +dk +y +eY+k k+ 
  gi|298674489|ref|YP_003726239.1| 150 DIKSKIDSVIETSNEIESIKGSDK-QYEKEYDKLKKE 185
                                       777777777777777777766666.577777777765 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.011
                             TMPIT   5 eelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkkl 56 
                                        e ++e+++++ + k+y+++ ++l+k  +++  + k  +kr+++ ++s++  
  gi|298674489|ref|YP_003726239.1| 159 IETSNEIESIKGSDKQYEKEYDKLKKELNDLNPRYKWLEKRISSHEESIEYW 210
                                       4566777777777777777777777777777777777777777777777654 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3  11.7    0.0066       2.5     119     222 ..      34     155 ..      19     168 .. 0.65
   2 ?    3.4   3.0       0.1        39     124     204 ..     101     189 ..      98     208 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0066
                              CorA 119 ivdrlfellekleeeldeledel.............edstkkeilrelaqlrrrlvklrralap..nrevlkrlla. 179
                                       ++++++++ e+l+e+++ + +++             +d  +++  + l+q +++l +l++++++  ++e+l+++ + 
  gi|298674489|ref|YP_003726239.1|  34 FLNKYRQEFEQLNERIESINEQMesakknkeyvvgrRDVLREKRQQILYQAQKTLNELQSSIKDseHKEILSSVDEk 110
                                       678999*****************888888888888666666666666777888888888888752256777644445 PP

                              CorA 180 .kaddkllddedkey.lrdlldelerllemlealrerleslqdty 222
                                        ++++  ++++++++  +++ d ++ ++   e+  ++l+ +++ +
  gi|298674489|ref|YP_003726239.1| 111 iSKLKTSISSDEEKQiVDEINDSISEISLNDETANRKLSDIKSKI 155
                                       555666665555222244444444443333333333333333333 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.1
                              CorA 124 fellekleeeldeledel....edstkkeilrelaqlrrrlvklrralapnrevlkrlla.kaddkllddedkey.. 193
                                        e+l+ ++e++ +l + +    e+++ +ei ++++++  +  +  r l++ +  ++++++ +++ + ++  dk+y  
  gi|298674489|ref|YP_003726239.1| 101 KEILSSVDEKISKLKTSIssdeEKQIVDEINDSISEISLNDETANRKLSDIKSKIDSVIEtSNEIESIKGSDKQYek 177
                                       67888899999999999966655666666666666666666666777777777777777767777777777755544 PP

                              CorA 194 .lrdlldelerl 204
                                        ++ l  el+ l
  gi|298674489|ref|YP_003726239.1| 178 eYDKLKKELNDL 189
                                       455555555554 PP

>> RPW8  Arabidopsis broad-spectrum mildew resistance protein RPW8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   5.7      0.37   1.4e+02      52      91 ..      36      73 ..      24     120 .. 0.55
   2 ?    9.5   1.4    0.0019      0.72      12      74 ..     126     188 ..     123     191 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.37
                              RPW8 52 eklnkeldrpreeieeLkklLekaekLVekcsklkrynvl 91
                                      +k ++e+++ +e ie++++++e+a+k  +k   + r++vl
  gi|298674489|ref|YP_003726239.1| 36 NKYRQEFEQLNERIESINEQMESAKK--NKEYVVGRRDVL 73
                                      45556666666666666666666665..333333333333 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0019
                              RPW8  12 algellkaileakkksldfksilkrLestleritPvvkeieklnkeldrpreeieeLkklLek 74 
                                       +++e+ + i e + +  + + +l +++s + ++    +eie+++   ++ ++e ++Lkk+L++
  gi|298674489|ref|YP_003726239.1| 126 IVDEINDSISEISLNDETANRKLSDIKSKIDSVIETSNEIESIKGSDKQYEKEYDKLKKELND 188
                                       78889999999999999999************************999*************975 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5  10.1    0.0011      0.42      61     137 ..      25     102 ..       6     128 .. 0.63
   2 ?    2.0   4.5     0.098        37      59     117 ..     131     197 ..     103     215 .] 0.38

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0011
                        V_ATPase_I  61 esleapeekeldeleeelekleeelkelnenleklkkelnelvelkavlekakefleee.eeeeeeeeseeeeeeke 136
                                       +   +++++ l+++ +e+e+l+e+++++ne++e+ kk+++ +v  + vl++ ++ +  + +++ +e +s+ +++e++
  gi|298674489|ref|YP_003726239.1|  25 SGVIEKHQNFLNKYRQEFEQLNERIESINEQMESAKKNKEYVVGRRDVLREKRQQILYQaQKTLNELQSSIKDSEHK 101
                                       44556778889999999999999999999999999999999999999998776665544233333322222222211 PP

                        V_ATPase_I 137 e 137
                                       e
  gi|298674489|ref|YP_003726239.1| 102 E 102
                                       1 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.098
                        V_ATPase_I  59 a........eesleapeekeldeleeelekleeelkelnenleklkkelnelvelkavlekakefle 117
                                       +        ++++++++ +++++  +++ ++ +e+++++ + ++ +ke+ +l+++ + l+   + le
  gi|298674489|ref|YP_003726239.1| 131 NdsiseislNDETANRKLSDIKSKIDSVIETSNEIESIKGSDKQYEKEYDKLKKELNDLNPRYKWLE 197
                                       2344443332222222222222222333333333333333333333333333333333333333333 PP

>> Sulfatase_C  C-terminal region of aryl-sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.2     0.032        12      73     108 ..      27      63 ..      17      70 .. 0.82
   2 ?    3.0   0.2      0.41   1.6e+02      59      98 ..      84     122 ..      70     138 .. 0.68
   3 ?    0.4   0.1       2.7     1e+03      74      98 ..     173     197 ..     140     213 .. 0.55

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.032
                                       T.CCHHHHHHHHHHHHHHHCCC------TCCHHCHS. CS
                       Sulfatase_C  73 s.peykevlkeikkaveehkktlkpvpnqlakgellp 108
                                         +++++ l++ +++ e+++++++  ++q++++++++
  gi|298674489|ref|YP_003726239.1|  27 ViEKHQNFLNKYRQEFEQLNERIESINEQMESAKKNK 63 
                                       458999************************9997654 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.41
                                       TTT-TT--S-TTSTTCCHHHHHHHHHHHHHHHCCC----- CS
                       Sulfatase_C  59 lerDpsEkyplsaespeykevlkeikkaveehkktlkpvp 98 
                                        ++  +E +    +++e+ke+l+++ + + ++k +++  +
  gi|298674489|ref|YP_003726239.1|  84 AQKTLNELQSSI-KDSEHKEILSSVDEKISKLKTSISSDE 122
                                       444444433322.347899999999999999988887654 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 2.7
                                       CCHHHHHHHHHHHHHHHCCC----- CS
                       Sulfatase_C  74 peykevlkeikkaveehkktlkpvp 98 
                                       ++y++  +++kk++++++ + k  +
  gi|298674489|ref|YP_003726239.1| 173 KQYEKEYDKLKKELNDLNPRYKWLE 197
                                       3333333333333333333333333 PP

>> HalX  HalX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.2     0.011       4.1      35      57 ..      40      62 ..      38      71 .. 0.87
   2 ?    0.7   0.7       1.8   6.8e+02      14      30 ..     106     122 ..      69     166 .. 0.73
   3 ?    1.5   0.1         1   3.9e+02      34      50 ..     190     206 ..     176     211 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.011
                              HalX 35 eeYqeLearleelraqldetlde 57
                                      +e+++L +r+e++ +q +    +
  gi|298674489|ref|YP_003726239.1| 40 QEFEQLNERIESINEQMESAKKN 62
                                      89**************9987665 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.8
                              HalX  14 aLasKravLeaekseae 30 
                                       ++ +K ++L+++ s++e
  gi|298674489|ref|YP_003726239.1| 106 SVDEKISKLKTSISSDE 122
                                       44455566666555544 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 1
                              HalX  34 seeYqeLearleelraq 50 
                                       + +Y  Le r+ + ++ 
  gi|298674489|ref|YP_003726239.1| 190 NPRYKWLEKRISSHEES 206
                                       55566666666665555 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.4     0.035        13     127     161 ..      28      62 ..      13      68 .. 0.61
   2 ?    5.9   4.7     0.025       9.4      60     168 ..      77     185 ..      65     188 .. 0.80
   3 ?    4.4   0.6     0.071        27      74     134 ..     123     179 ..     109     209 .. 0.52

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.035
                            DUF745 127 aagaqqelaektqlleaAkkRveeLkkqlkearkd 161
                                        ++ q+ l++ +q  e+ ++R+e++++q+++a+k+
  gi|298674489|ref|YP_003726239.1|  28 IEKHQNFLNKYRQEFEQLNERIESINEQMESAKKN 62 
                                       44455555555555555666666666666666654 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.025
                            DUF745  60 Kqqlveqleqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelae 136
                                        qq++ q ++ l+e ++ +++ +++   s+   k+ +   +    + +++ + ++ + ++++  +++a+   +++++
  gi|298674489|ref|YP_003726239.1|  77 RQQILYQAQKTLNELQSSIKDSEHKEILSSVDEKISKLKTSISSDEEKQIVDEINDSISEISLNDETANRKLSDIKS 153
                                       47888899999999998888777666666666666666666666666677777777777777888888999999999 PP

                            DUF745 137 ktqlleaAkkRveeLkkqlkearkdlektkka 168
                                       k + + +  + +e++k   k+  k+++k kk+
  gi|298674489|ref|YP_003726239.1| 154 KIDSVIETSNEIESIKGSDKQYEKEYDKLKKE 185
                                       *99999**********************9986 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.071
                            DUF745  74 aeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqel 134
                                        +++v+e+++s+++ + n ++a++  ++++++++++ ++ +++++    ++   ++ ++e 
  gi|298674489|ref|YP_003726239.1| 123 EKQIVDEINDSISEISLNDETANRKLSDIKSKIDSVIETSNEIES----IKGSDKQYEKEY 179
                                       555555555555555555555555555555555444433333222....222222222222 PP

>> Glutaredoxin2_C  Glutaredoxin 2, C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.3      0.24        92      39      69 ..      28      58 ..      22      61 .. 0.67
   2 ?    8.1   0.4    0.0059       2.2      40      87 ..      61     108 ..      58     120 .. 0.86
   3 ?   -1.9   0.0       7.2   2.7e+03      55      71 ..     122     138 ..     109     151 .. 0.69
   4 ?   -0.0   0.1       1.9   7.2e+02      50      75 ..     169     194 ..     158     209 .. 0.62

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.24
                   Glutaredoxin2_C 39 tkkkeksigdfeellaktpeliaelnalLee 69
                                      ++k+++++ ++ + +++ +e i+ +n+++e 
  gi|298674489|ref|YP_003726239.1| 28 IEKHQNFLNKYRQEFEQLNERIESINEQMES 58
                                      4566666677777777777777777776665 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0059
                   Glutaredoxin2_C  40 kkkeksigdfeellaktpeliaelnalLeelepliksseavngelSvd 87 
                                       k+ke  +g  + l +k+++++ + ++ L+el++ ik se+ +   Svd
  gi|298674489|ref|YP_003726239.1|  61 KNKEYVVGRRDVLREKRQQILYQAQKTLNELQSSIKDSEHKEILSSVD 108
                                       689999999999***********************8887776544454 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 7.2
                   Glutaredoxin2_C  55 ktpeliaelnalLeele 71 
                                       ++++++ e+n+ + e++
  gi|298674489|ref|YP_003726239.1| 122 EEKQIVDEINDSISEIS 138
                                       55688888888877765 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 1.9
                   Glutaredoxin2_C  50 eellaktpeliaelnalLeeleplik 75 
                                       +   ++ ++ + +l+++L++l+p  k
  gi|298674489|ref|YP_003726239.1| 169 KGSDKQYEKEYDKLKKELNDLNPRYK 194
                                       55555566666777777777776654 PP

>> GvpL_GvpF  Gas vesicle synthesis protein GvpL/GvpF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   5.2    0.0045       1.7     114     221 ..      23     132 ..      15     150 .. 0.77
   2 ?   -1.1   0.0       3.7   1.4e+03     123     144 ..     180     201 ..     137     214 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0045
                         GvpL_GvpF 114 ygvkvlwdeealleelleedpelrelreeieaasesgtayllrkrlgqrleealeerreelaeeleeaLaplaeevr 190
                                       +   v ++++++l++  +e ++l+e  e+i ++ e   +  ++k++    ++ l+e+r+++  + +++L++l ++++
  gi|298674489|ref|YP_003726239.1|  23 LVSGVIEKHQNFLNKYRQEFEQLNERIESINEQME---SAKKNKEYVVGRRDVLREKRQQILYQAQKTLNELQSSIK 96 
                                       55556666666666666666666666666666655...467788888889999************************ PP

                         GvpL_GvpF 191 erepqd.....eemvlnaafLvdrdreeefgeavee 221
                                         e ++     +e + ++   +++d+e+++ +++++
  gi|298674489|ref|YP_003726239.1|  97 DSEHKEilssvDEKISKLKTSISSDEEKQIVDEIND 132
                                       999999999998889999888888888877766655 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3.7
                         GvpL_GvpF 123 ealleelleedpelrelreeie 144
                                       ++l++el + +p+ + l+++i+
  gi|298674489|ref|YP_003726239.1| 180 DKLKKELNDLNPRYKWLEKRIS 201
                                       3344444444444444444444 PP

>> Mst1_SARAH  C terminal SARAH domain of Mst1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.2    0.0053         2       8      25 ..      41      58 ..      33      60 .. 0.84
   2 ?   -1.2   0.0       5.8   2.2e+03      12      30 ..     148     168 ..     139     177 .. 0.68
   3 ?    2.5   0.1      0.42   1.6e+02      22      35 ..     181     194 ..     172     199 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0053
                        Mst1_SARAH  8 svdeLqqrlasLDpeMEq 25
                                       +++L++r++s+ ++ME 
  gi|298674489|ref|YP_003726239.1| 41 EFEQLNERIESINEQMES 58
                                      589*************95 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 5.8
                        Mst1_SARAH  12 LqqrlasLDpeME..qEieel 30 
                                       L +  +++D+ +E  +Eie +
  gi|298674489|ref|YP_003726239.1| 148 LSDIKSKIDSVIEtsNEIESI 168
                                       455556777777733477766 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.42
                        Mst1_SARAH  22 eMEqEieelrkrYq 35 
                                       ++ +E+++l+ rY+
  gi|298674489|ref|YP_003726239.1| 181 KLKKELNDLNPRYK 194
                                       46789999999996 PP

>> ALMT  Aluminium activated malate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2  14.1      0.02       7.6     269     412 ..      44     186 ..      13     214 .. 0.56

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.02
                              ALMT 269 qcaytvealhgci...lseiqapeelrkkfkeelqrvslesakvlrelaesvkkmkklskveellkevkvaaeeLqs 342
                                       q + ++e+++  +   +++ +     r  ++e+ q++  ++ k l+el+ s+k+ +++    e+l++v   + +L++
  gi|298674489|ref|YP_003726239.1|  44 QLNERIESINEQMesaKKNKEYVVGRRDVLREKRQQILYQAQKTLNELQSSIKDSEHK----EILSSVDEKISKLKT 116
                                       4455555555555332334444455677777777777777777777777777766554....346777777777777 PP

                              ALMT 343 kldskskLlvnsekweaakkkekaeeveekkeeekeseskkeeaeaveeaeseseksllkeskrslklsk 412
                                       ++ s  + ++  e ++ +++ + ++e+ ++k ++ +s+ ++  ++++e ++ + ++++ +++  +lk++ 
  gi|298674489|ref|YP_003726239.1| 117 SISSDEEKQIVDEINDSISEISLNDETANRKLSDIKSKIDSVIETSNEIESIKGSDKQYEKEYDKLKKEL 186
                                       7777666666666655555555555555555555444444444444444444444443333333333332 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7  23.0     0.054        21       9     145 ..      42     196 ..      20     213 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.054
                           DUF4795   9 lkklqeaieklqeelekleekvkelekrl....edkekklealkkqieelekvkadkeeveeelaekadkeaLatkv 81 
                                       +++l+e ie + e++e+ ++ ++ + +r     e++++ l   +k ++el+++ +d+e+ e   ++    ++L+t +
  gi|298674489|ref|YP_003726239.1|  42 FEQLNERIESINEQMESAKKNKEYVVGRRdvlrEKRQQILYQAQKTLNELQSSIKDSEHKEILSSVDEKISKLKTSI 118
                                       799***************999999999871111344444445566677777788999999999999999******** PP

                           DUF4795  82 srdq....fDeakkeLekml...eellekleeqeealkkaldtLq..eelkekld...rlelepLkeqle...erlk 143
                                       s d+    +De  + ++++    e +  kl+   ++++++++t +  e++k   d   ++e ++Lk++l+    r k
  gi|298674489|ref|YP_003726239.1| 119 SSDEekqiVDEINDSISEISlndETANRKLSDIKSKIDSVIETSNeiESIKG-SDkqyEKEYDKLKKELNdlnPRYK 194
                                       ***9555544444444444455555566666666666666666664433332.235667777777777775554444 PP

                           DUF4795 144 el 145
                                        l
  gi|298674489|ref|YP_003726239.1| 195 WL 196
                                       44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3027  (0.168833); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                       127  (0.0070835); expected 17.9 (0.001)
Passed Fwd filter:                        75  (0.00418317); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              47  [number of targets reported over threshold]
# CPU time: 1.13u 0.41s 00:00:01.53 Elapsed: 00:00:00.62
# Mc/sec: 1040.67
//
Query:       gi|298674490|ref|YP_003726240.1|  [L=96]
Description: hypothetical protein Metev_0532 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.7e-30  103.0   0.4    8.6e-30  102.9   0.4    1.0  1  DUF424    Protein of unknown function (DUF424)


Domain annotation for each model (and alignments):
>> DUF424  Protein of unknown function (DUF424)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.9   0.4   4.8e-34   8.6e-30       8      91 ..      12      95 ..       6      96 .] 0.96

  Alignments for each domain:
  == domain 1  score: 102.9 bits;  conditional E-value: 4.8e-34
                                      EEEEEEEGGGTT-EEEETTEEEE--HHHH--EEE-HHHHHHHHHHHEEEEEESHHHHHHHHHTTSS-GGG-EEETTEEE CS
                            DUF424  8 klvavcdkellgktfkegelllnvsegfyggelaseeeaikeLekatiaNivgeeavvlavkaGlvdpdsVlvidgvph 86
                                       +vavcd+++lgkt+keg+l++++se+fy+g+ ase+e+i++L  at aNi+gee+v++a+k+  vdp++V++i++vph
  gi|298674490|ref|YP_003726240.1| 12 YVVAVCDEDILGKTLKEGNLTVEISEQFYKGKTASENEVIEALSVATTANIFGEESVACAIKCSAVDPENVIRINDVPH 90
                                      69***************************************************************************** PP

                                      EEEEE CS
                            DUF424 87 aqigk 91
                                      aqi++
  gi|298674490|ref|YP_003726240.1| 91 AQIFR 95
                                      ***98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.35s 00:00:00.90 Elapsed: 00:00:00.55
# Mc/sec: 525.21
//
Query:       gi|298674491|ref|YP_003726241.1|  [L=1056]
Description: MCM family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.5e-90  299.7   0.0    4.8e-59  199.2   0.0    2.3  2  MCM           MCM P-loop domain
      2e-37  127.8   0.4    4.3e-37  126.8   0.4    1.5  1  MCM_OB        MCM OB domain
    4.1e-25   88.0   0.5    1.2e-24   86.5   0.5    1.9  1  MCM_lid       MCM AAA-lid domain
    5.5e-10   39.8   0.3    2.8e-09   37.5   0.3    2.2  1  MCM_N         MCM N-terminal domain
    4.6e-08   33.3   0.1     0.0011   19.2   0.0    2.7  2  LAGLIDADG_3   LAGLIDADG-like domain
    0.00033   20.7   0.0    0.00087   19.3   0.0    1.7  1  AAA_5         AAA domain (dynein-related subfamily)
  ------ inclusion threshold ------
      0.044   14.2   0.2       0.18   12.1   0.0    2.1  2  AAA_16        AAA ATPase domain
      0.084   12.5   0.1       0.17   11.5   0.1    1.4  1  Zn_ribbon_17  Zinc-ribbon, C4HC2 type


Domain annotation for each model (and alignments):
>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.2   0.0   2.2e-62   4.8e-59       1     149 [.     263     412 ..     263     414 .. 0.97
   2 !   98.3   0.0   1.5e-31   3.3e-28     148     224 .]     767     843 ..     763     843 .. 0.98

  Alignments for each domain:
  == domain 1  score: 199.2 bits;  conditional E-value: 2.2e-62
                                       HHHHHHHHHTSSTHHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHH CS
                               MCM   1 eveeikelakekdiieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyv 77 
                                       ++eei el+k+++i+ek++ksi psiyg+e++k+a++lqlf+gv+k+l+d++++rgdi++l+vgdpg+aKsq+L+y+
  gi|298674491|ref|YP_003726241.1| 263 DEEEILELSKDPQIYEKVAKSISPSIYGYENIKEALALQLFSGVTKALPDSSRVRGDIHILIVGDPGIAKSQMLRYM 339
                                       5799************************************************************************* PP

                                       HHHSSSEEEEESSSSSSSHSSSEEEEESSSSS.EEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSE CS
                               MCM  78 eklapravytsgkgssaagLtaavvrdeetge.fvleaGalvladkGvcciDefdkmkeedrsalhEamEqqt 149
                                       eklapr+v+tsgk++s++gLta+ vrde  +  ++leaGalv+ad Gv+++De+dkm++ed+s+lhEamEqq 
  gi|298674491|ref|YP_003726241.1| 340 EKLAPRGVFTSGKSASSSGLTASAVRDELGDGrWTLEAGALVMADMGVAAVDELDKMSSEDKSSLHEAMEQQC 412
                                       ***************************986655**************************************96 PP

  == domain 2  score: 98.3 bits;  conditional E-value: 1.5e-31
                                       SEEEEESSSCEEEEE--EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHHHHHHHHH CS
                               MCM 148 qtisiaKaGivatLnartsvlaAanpkagrydkkksvaeninlsaalLsrFDlifvllDkvdeekDeelaehivslh 224
                                       +t+s+aKaGi+atL++r+++l Aanpk+gr+d+ + +a +in+++al+srFDlifvllD +d++kD+++a+hi++ h
  gi|298674491|ref|YP_003726241.1| 767 NTVSVAKAGIIATLKSRCALLGAANPKYGRFDRYEGIATQINMPPALISRFDLIFVLLDVPDDDKDRRIANHILKAH 843
                                       79************************************************************************987 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.8   0.4   1.9e-40   4.3e-37       2     125 ..      98     226 ..      97     227 .. 0.96

  Alignments for each domain:
  == domain 1  score: 126.8 bits;  conditional E-value: 1.9e-40
                                       XGG--GGGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EEE.....S----SB-..TTT-HHH-EEE-GGGSE CS
                            MCM_OB   2 lRdlrsehigklvkveGivtrasevkpklkkavfeckkcgktvev.....eleePrkCeekeCeskdpfkleteksk 73 
                                       +R+lrs+h+ + v veG++ +a+ev+pk+++a+f+c +c++++ +     +++eP++Ce+++C++k+pfk  ++ks+
  gi|298674491|ref|YP_003726241.1|  98 IRNLRSKHLMQSVAVEGMIRKATEVRPKITNAAFYCMRCEHVTYIpqtsqKFTEPHECENETCGRKGPFKTLVDKST 174
                                       8***************************************98878888888999*********************** PP

                                       EEEEEEEEEE-------------EEEEEEEGGGTT---TT-EEEEEEEEEEE CS
                            MCM_OB  74 fvdfqklklQEspeevpaGelPrslevileddlvdkvkPGdrvevtGiyral 125
                                       fvd qkl++QEspe++  Ge P+sl++ ++ddl   v+PGdrv + G++r+ 
  gi|298674491|ref|YP_003726241.1| 175 FVDAQKLQIQESPENLRGGEQPQSLDIDVDDDLAGIVTPGDRVIINGVLRSH 226
                                       ************************************************9975 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.5   0.5   5.4e-28   1.2e-24       1      86 [.     879     963 ..     879     964 .. 0.95

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 5.4e-28
                                       HHHHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHH CS
                           MCM_lid   1 ellrkYiayarekikPklseeakeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedve 77 
                                       e+lrkY+ayar+++ P+l+++a+++l e+Y++lRk+ ed+ +  +p+t+RqLe+l+RL+e++A++rls+v+t ed++
  gi|298674491|ref|YP_003726241.1| 879 EKLRKYVAYARRNVYPILEDDARNHLIEFYMNLRKMGEDK-DAPVPVTARQLEALVRLTESSARVRLSSVATLEDAK 954
                                       68**********************************9766.99********************************** PP

                                       HHHHHHHHH CS
                           MCM_lid  78 eairllkes 86 
                                       + ++l+ ++
  gi|298674491|ref|YP_003726241.1| 955 RTTNLVYTC 963
                                       ***999776 PP

>> MCM_N  MCM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.3   1.2e-12   2.8e-09       2      74 ..       8      70 ..       7     102 .. 0.88

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 1.2e-12
                             MCM_N  2 ekFedFLeefkddsededgekkYrdqlqemaer..ekttLevdlddLaafdeeLaeailenpkeylplleealke 74
                                      e+F +F++ +            Y d++ ++a++  e+++L+v++ d+++fd+eLa++++ np e++p+ ee+l+e
  gi|298674491|ref|YP_003726241.1|  8 ERFGTFFRRY------------YWDEILHLANEypEQRSLTVNYYDIENFDQELADELIVNPDEIIPAAEEVLRE 70
                                      6666677665............*********9999**************************************97 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00019      0.42       8      50 ..     557     599 ..     554     622 .. 0.93
   2 !   19.2   0.0   4.9e-07    0.0011       6      58 ..     644     694 ..     640     716 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00019
                                       HHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.H CS
                       LAGLIDADG_3   8 rGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIe 50 
                                        G++  +Gsv   ++   s+ +t++    ++++q+ L rlG +
  gi|298674491|ref|YP_003726241.1| 557 LGYYLPEGSVKYMNGIPYSVQITQKTSGKIQKIQNSLDRLGFK 599
                                       59************99888**********************76 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 4.9e-07
                                       HHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.HSCEEEE.EE CS
                       LAGLIDADG_3   6 fLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIestiyek.kk 58 
                                       f  ++  +DG+++ + +    + + +ssk+l++d+q+l l+ G  ++ y   +k
  gi|298674491|ref|YP_003726241.1| 644 FVDAMVLGDGYIRCETGQ---MAYITSSKRLADDMQELALKMGYSANNYVVvNK 694
                                       7778889*********99...**************************9998433 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   3.9e-07   0.00087       1      94 [.     321     413 ..     321     430 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 3.9e-07
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEE...E--TT--HHHHH--B--.........--------G-SEEEEESG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyv...qltrdtteedlkgrreikngttslvdsplvraaregeilvlDEv 74 
                                       ++l+vG+pG++Ks++ +++ ++  r v++    + ++++t++ ++ ++   +g+  l+ ++lv  +    ++ +DE+
  gi|298674491|ref|YP_003726241.1| 321 HILIVGDPGIAKSQMLRYMEKLAPRGVFTSgksASSSGLTASAVRDELG--DGRWTLEAGALV--MADMGVAAVDEL 393
                                       689********************99999852226677888888888888..9999********..99999******* PP

                                       GG--HHHHHHHHHHHHSSEE CS
                             AAA_5  75 eraesevlnsLlslleerrl 94 
                                       ++++se  +sL+  +e++ +
  gi|298674491|ref|YP_003726241.1| 394 DKMSSEDKSSLHEAMEQQCY 413
                                       ************99998765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   8.2e-05      0.18      26     124 ..     321     409 ..     306     417 .. 0.68
   2 ?   -2.0   0.1       1.8   4.1e+03      75     132 ..     995    1048 ..     978    1055 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.2e-05
                            AAA_16  26 lvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekle 102
                                        +l++G++G+ Ks ++r     l  + g+f++gk  ++          + l++ + +r++l + + ++ + +    +
  gi|298674491|ref|YP_003726241.1| 321 HILIVGDPGIAKSQMLRYME-KLAPR-GVFTSGKSASS----------SGLTA-SAVRDELGDGRWTLEAGALVMAD 384
                                       799*************9988.57777.9*******999..........67755.66777777744433333333333 PP

                            AAA_16 103 eala...avpelagaeasrllellk 124
                                         +a   + ++++++++s+l+e++ 
  gi|298674491|ref|YP_003726241.1| 385 MGVAavdELDKMSSEDKSSLHEAME 409
                                       3333222444555555577777765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.8
                            AAA_16   75 alareellrqlldeaesaeleawrekleealaavpelagaeasrllellkrllallsr 132 
                                        ++ r e+++ l+de+++++ ++  e   +a  +  ++++++a+ l   ++r  +lls+
  gi|298674491|ref|YP_003726241.1|  995 VI-R-EIIQSLADEHSDKKGAPVEEVYSRA--EEEQIDREHAEELVTRMRRQGDLLSP 1048
                                        45.4.7777777776665555554433332..34677777778888888877777766 PP

>> Zn_ribbon_17  Zinc-ribbon, C4HC2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   7.5e-05      0.17      14      52 ..     126     163 ..     122     168 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.5e-05
                      Zn_ribbon_17  14 vkgrvvlcgvCeHvlHasCarewfenddlaeCps.GCGck 52 
                                       ++   ++c +CeHv+     ++ f++ +  eC    CG k
  gi|298674491|ref|YP_003726241.1| 126 ITNAAFYCMRCEHVTYIPQTSQKFTEPH--ECENeTCGRK 163
                                       78889*******************9999..9988789866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1056 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       965  (0.0538234); expected 358.6 (0.02)
Passed bias filter:                      782  (0.0436165); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.95u 0.34s 00:00:01.29 Elapsed: 00:00:00.54
# Mc/sec: 5919.94
//
Query:       gi|298674492|ref|YP_003726242.1|  [L=232]
Description: RNA methyltransferase, TrmH family, group 1 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.3e-34  116.6   0.0    1.3e-33  116.2   0.0    1.2  1  SpoU_methylase   SpoU rRNA Methylase family
      0.001   19.0   0.0       0.01   15.7   0.0    2.1  1  Methyltrn_RNA_4  SAM-dependent RNA methyltransferase
  ------ inclusion threshold ------
      0.029   14.5   0.0      0.059   13.5   0.0    1.5  1  Ldh_1_N          lactate/malate dehydrogenase, NAD binding do


Domain annotation for each model (and alignments):
>> SpoU_methylase  SpoU rRNA Methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.2   0.0   2.1e-37   1.3e-33       2     142 .]       5     156 ..       4     156 .. 0.89

  Alignments for each domain:
  == domain 1  score: 116.2 bits;  conditional E-value: 2.1e-37
                                       EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHH.EEEESSHHHHHHHHCCCTEE CS
                    SpoU_methylase   2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevle.lkvvdsleealkelkeegfa 77 
                                       + +vlve+ ++gN+G+iaR++k+fg+ elvlv+p++    + ea++++++a+++le +kv ++++ea+k+   + + 
  gi|298674492|ref|YP_003726242.1|   5 IKIVLVEPLYQGNVGSIARVMKNFGLCELVLVNPCKL---KGEARAMSSHARDILEnAKVTNTFKEAVKDASLV-VG 77 
                                       679******************************8875...99*******************************9.66 PP

                                       EEEEST..T-SEGCCSHHH............TTEEEEEEBTTTBS-HHHHCTSSEEEE----TTSSS--HHHHHHHH CS
                    SpoU_methylase  78 lvatsl..kgkslseidlk............ekvalvfGnEdkGlsnelleladrlvkIpmsgeveSLNvavAvail 140
                                       ++++++  +++++++ +++            +kva++fG+Ed+G +n++l+l+d +v+Ip ++e++ +N+++++a++
  gi|298674492|ref|YP_003726242.1|  78 TTGMTSskDDEHIRNPSYTpkelknrlegmdGKVAILFGREDNGFTNDELRLCDMIVHIPANEEYPIMNISHSAAVI 154
                                       6555554466777766555555667888999*********************************************9 PP

                                       HH CS
                    SpoU_methylase 141 ly 142
                                       +y
  gi|298674492|ref|YP_003726242.1| 155 FY 156
                                       98 PP

>> Methyltrn_RNA_4  SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.7e-06      0.01      65     176 ..      42     154 ..       8     159 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.7e-06
                                       TSGGGGT-SSSHHHHTTEEEESSHHHHHHHHHHHHSS--EEEE--SS.--SS-B-HHHHHHHHHH--S-EEEEE--. CS
                   Methyltrn_RNA_4  65 egagaeynpdRkealslvkvvesleealeeiekeegkkplvvatsAr.kkentvsyeelrelleeeekpvlllfGt. 139
                                       +g+ +++  + ++ l++ kv+++++ea+++ +   g++ ++   + +  ++ +++ +el+++le  + +v +lfG  
  gi|298674492|ref|YP_003726242.1|  42 KGEARAMSSHARDILENAKVTNTFKEAVKDASLVVGTTGMTSSKDDEhIRNPSYTPKELKNRLEGMDGKVAILFGRe 118
                                       566777778888999****************9999999888777666356779999*******************73 PP

                                       TT---HHHHTT-SEEB--TTTTSS-----HHHHHHHH CS
                   Methyltrn_RNA_4 140 gwGlaeevlekadyiLepirgaseynHLsvrsAvaii 176
                                         G++++ l+ +d+i++ i +++ey  + +   +a+i
  gi|298674492|ref|YP_003726242.1| 119 DNGFTNDELRLCDMIVH-IPANEEYPIMNISHSAAVI 154
                                       58***********9875.8999999888888777777 PP

>> Ldh_1_N  lactate/malate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   9.9e-06     0.059      10      80 ..      16      82 ..       6      89 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.9e-06
                                      SHHHHHHHHHHHHTTSSSEEEEE-SSHHHHHHHHHHHHHCHCCSTS-EEEEESSGGGGTTESEEEE--S-S CS
                           Ldh_1_N 10 GgiGqslalllankkladelaLlDiakekleGvaldlshistflsvkvkvsekeeealkdadvvvitagvp 80
                                      G++G+ +a  ++n +l++ l+L+  ++ kl+G+a  +s  +  ++ ++kv+++ +ea+kda++vv t g++
  gi|298674492|ref|YP_003726242.1| 16 GNVGS-IARVMKNFGLCE-LVLV--NPCKLKGEARAMSSHARDILENAKVTNTFKEAVKDASLVVGTTGMT 82
                                      55653.555666667776.6665..5559********99999999********************999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.34s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1355.61
//
Query:       gi|298674493|ref|YP_003726243.1|  [L=65]
Description: 4Fe-4S ferredoxin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-11   42.5  14.6    1.2e-05   24.9   4.5    2.1  2  Fer4      4Fe-4S binding domain
      9e-10   38.2  12.2    6.6e-05   22.8   2.0    2.1  2  Fer4_6    4Fe-4S binding domain
    1.4e-09   38.4  22.5    1.8e-07   31.6  11.8    1.8  2  Fer4_7    4Fe-4S dicluster domain
    2.9e-09   36.9   6.1    3.4e-09   36.7   6.1    1.1  1  Fer4_21   4Fe-4S dicluster domain
      6e-09   35.9  21.2    9.8e-08   32.0   9.3    1.4  2  Fer4_9    4Fe-4S dicluster domain
    1.1e-08   34.6  12.6    9.6e-06   25.4   1.8    2.2  2  Fer4_2    4Fe-4S binding domain
    2.6e-07   30.6  11.9    5.4e-07   29.6  11.9    1.5  1  Fer4_10   4Fe-4S dicluster domain
    1.8e-06   28.6   6.3      1e-05   26.2   0.2    2.0  2  Fer4_15   4Fe-4S single cluster domain
    2.3e-06   27.7  15.1     0.0058   17.0   4.3    2.1  2  Fer4_4    4Fe-4S binding domain
    4.3e-05   24.0   7.0    0.00031   21.2   0.2    2.1  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    7.4e-05   23.1  11.6    0.00019   21.8  11.6    1.6  1  Fer4_8    4Fe-4S dicluster domain
    9.2e-05   23.3   8.4      0.024   15.6   0.4    2.1  2  Fer4_16   4Fe-4S double cluster binding domain
    0.00023   21.9  18.5      0.024   15.5   4.5    2.2  2  Fer4_3    4Fe-4S binding domain
     0.0019   19.0   9.2      0.066   14.1   2.2    2.1  2  Fer4_22   4Fe-4S dicluster domain
     0.0039   17.7  13.5        1.3    9.6  13.6    2.1  1  Fer4_17   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.057   13.4   0.8      0.074   13.1   0.8    1.2  1  NapB      Nitrate reductase cytochrome c-type subunit (NapB)
       0.66   10.2   9.2        0.3   11.3   0.9    2.0  2  Fer4_18   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   4.5   1.1e-08   1.2e-05       1      18 [.       3      20 ..       3      20 .. 0.96
   2 !   23.6   2.5   2.8e-08     3e-05       4      24 .]      42      62 ..      39      62 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.1e-08
                                      EEEETTTSSS-THHHHHS CS
                              Fer4  1 vvideekCigCGaCvevC 18
                                      ++id++kC+gCGaC ++C
  gi|298674493|ref|YP_003726243.1|  3 ITIDKNKCTGCGACRKAC 20
                                      68**************** PP

  == domain 2  score: 23.6 bits;  conditional E-value: 2.8e-08
                                      ETTTSSS-THHHHHSTTTEEE CS
                              Fer4  4 deekCigCGaCvevCPvgAIt 24
                                      +++ C gC  Cv+vC  gAIt
  gi|298674493|ref|YP_003726243.1| 42 NPSYCLGCRMCVSVCKPGAIT 62
                                      89*****************97 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   2.0   6.2e-08   6.6e-05       2      19 ..       3      20 ..       2      23 .. 0.93
   2 !   21.0   2.9   2.3e-07   0.00024       5      24 .]      42      61 ..      42      61 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 6.2e-08
                            Fer4_6  2 veidpdkCigCgdCvrvC 19
                                      ++id++kC+gCg+C ++C
  gi|298674493|ref|YP_003726243.1|  3 ITIDKNKCTGCGACRKAC 20
                                      89************9999 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 2.3e-07
                            Fer4_6  5 dpdkCigCgdCvrvCPegai 24
                                      +p+ C+gC+ Cv+vC  gai
  gi|298674493|ref|YP_003726243.1| 42 NPSYCLGCRMCVSVCKPGAI 61
                                      7999***********99997 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   2.9   3.5e-06    0.0036      30      50 ..       2      22 ..       1      24 [. 0.84
   2 !   31.6  11.8   1.7e-10   1.8e-07       1      52 []       9      60 ..       9      60 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.5e-06
                            Fer4_7 30 kveidpekClgCgaCvavCPt 50
                                      +++id +kC+gCgaC ++C +
  gi|298674493|ref|YP_003726243.1|  2 EITIDKNKCTGCGACRKACLK 22
                                      678999999999999999965 PP

  == domain 2  score: 31.6 bits;  conditional E-value: 1.7e-10
                            Fer4_7  1 rCigCgaCvaaCp..vkaieldeeenekgtekv.eidpekClgCgaCvavCPtga 52
                                      +C+gCgaC +aC    k + l++++   g++ + +++p++ClgC++Cv+vC  ga
  gi|298674493|ref|YP_003726243.1|  9 KCTGCGACRKACLkgPKIFLLKDRN---GKKVAeVGNPSYCLGCRMCVSVCKPGA 60
                                      7***********7445666676664...444441568**************8776 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   6.1   3.2e-12   3.4e-09       2      58 ..       4      62 ..       3      63 .. 0.80

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 3.2e-12
                           Fer4_21  2 ridedkCigCgkCliaCedtshqai..eidaktvlkv.vedeCvGCnlCssvCPvedcie 58
                                      +id++kC gCg C +aC ++    +  + ++k+v++v   + C GC +C+svC   ++i+
  gi|298674493|ref|YP_003726243.1|  4 TIDKNKCTGCGACRKACLKGPKIFLlkDRNGKKVAEVgNPSYCLGCRMCVSVCK-PGAIT 62
                                      59****************87766664444567888884479************7.57776 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   4.0   1.9e-05      0.02      34      48 ..       8      22 ..       2      24 .. 0.75
   2 !   32.0   9.3   9.3e-11   9.8e-08       1      51 []       9      61 ..       9      61 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.9e-05
                            Fer4_9 34 eaCigCgaCveaCpk 48
                                      ++C+gCgaC +aC k
  gi|298674493|ref|YP_003726243.1|  8 NKCTGCGACRKACLK 22
                                      479999999999966 PP

  == domain 2  score: 32.0 bits;  conditional E-value: 9.3e-11
                            Fer4_9  1 kCtgCgaCveaC...pagvv.vedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      kCtgCgaC +aC   p+    +++++++ a++ + s+  C+gC+ Cv +C+ gai
  gi|298674493|ref|YP_003726243.1|  9 KCTGCGACRKAClkgPKIFLlKDRNGKKVAEVGNPSY--CLGCRMCVSVCKPGAI 61
                                      7***********9996665536777777777777776..************9987 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   1.8   9.1e-09   9.6e-06       3      20 ..       3      20 ..       2      24 .. 0.93
   2 !   14.7   3.4   2.3e-05     0.024       7      20 ..      43      56 ..      40      58 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 9.1e-09
                            Fer4_2  3 vvvdtdrCigCgaCvsaC 20
                                      + +d ++C+gCgaC++aC
  gi|298674493|ref|YP_003726243.1|  3 ITIDKNKCTGCGACRKAC 20
                                      679*************** PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.3e-05
                            Fer4_2  7 tdrCigCgaCvsaC 20
                                      +  C+gC+ Cvs+C
  gi|298674493|ref|YP_003726243.1| 43 PSYCLGCRMCVSVC 56
                                      566*********** PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6  11.9   5.1e-10   5.4e-07       2      55 ..       3      56 ..       2      57 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 5.1e-10
                           Fer4_10  2 vvidddtCirCgkCvkaCPadl.tsvgakgeaseeeavrkkvekCtgcgaCveaC 55
                                      + id+++C++Cg+C+kaC  +  +    k+ + ++ a+ ++++ C gc +Cv++C
  gi|298674493|ref|YP_003726243.1|  3 ITIDKNKCTGCGACRKAC-LKGpKIFLLKDRNGKKVAEVGNPSYCLGCRMCVSVC 56
                                      689***************.444556666666666666677*************** PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.2   9.5e-09     1e-05       1      31 [.       3      37 ..       3      44 .. 0.85
   2 ?    5.8   1.6     0.022        23       7      19 ..      45      58 ..      40      65 .] 0.80

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 9.5e-09
                           Fer4_15  1 VvvDrdaCigcglCvaea...pevfelded.glas 31
                                      +++D+++C+gcg+C +++   p++f l+++ g+++
  gi|298674493|ref|YP_003726243.1|  3 ITIDKNKCTGCGACRKAClkgPKIFLLKDRnGKKV 37
                                      89************************999636664 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.022
                           Fer4_15  7 aCigcglCvaea.p 19
                                       C gc +Cv ++ p
  gi|298674493|ref|YP_003726243.1| 45 YCLGCRMCVSVCkP 58
                                      6**********955 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   4.3   5.5e-06    0.0058       1      14 [.       7      20 ..       7      23 .. 0.93
   2 !   16.4   3.1   8.7e-06    0.0092       2      15 ..      44      57 ..      42      59 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.5e-06
                            Fer4_4  1 qerCigCgsCvaaC 14
                                      +++C+gCg+C+ aC
  gi|298674493|ref|YP_003726243.1|  7 KNKCTGCGACRKAC 20
                                      689*********** PP

  == domain 2  score: 16.4 bits;  conditional E-value: 8.7e-06
                            Fer4_4  2 erCigCgsCvaaCP 15
                                      + C+gC+ Cv++C+
  gi|298674493|ref|YP_003726243.1| 44 SYCLGCRMCVSVCK 57
                                      57***********7 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.2     3e-07   0.00031       1      30 [.       5      37 ..       5      44 .. 0.86
   2 ?    6.3   1.9     0.013        14       4      16 ..      44      56 ..      40      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3e-07
                           Fer4_13  1 VDrdtCiacgaCvela...PdvFeeddeggasv 30
                                      +D+++C++cgaC++++   P++F  +d  g+ v
  gi|298674493|ref|YP_003726243.1|  5 IDKNKCTGCGACRKAClkgPKIFLLKDRNGKKV 37
                                      8***************99999998888887755 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.013
                           Fer4_13  4 dtCiacgaCvela 16
                                      + C +c  Cv+++
  gi|298674493|ref|YP_003726243.1| 44 SYCLGCRMCVSVC 56
                                      56**********9 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8  11.6   1.8e-07   0.00019       3      62 ..       8      57 ..       6      60 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.8e-07
                            Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCp 62
                                      +kC++CgaC++aC  l+  k +ll+ r++  + ++ e +     +  +C++c++C++vC+
  gi|298674493|ref|YP_003726243.1|  8 NKCTGCGACRKAC--LKGPKIFLLKDRNG--K-KVAEVG-----NPSYCLGCRMCVSVCK 57
                                      79***********..55555444444444..4.344444.....379************7 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   2.2   0.00028       0.3      52      64 ..       8      20 ..       2      24 .. 0.68
   2 !   15.6   0.4   2.3e-05     0.024       2      19 ..      46      63 ..      28      65 .] 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00028
                           Fer4_16 52 eaitgCdiCqdvC 64
                                      +++tgC++C ++C
  gi|298674493|ref|YP_003726243.1|  8 NKCTGCGACRKAC 20
                                      5666666666666 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 2.3e-05
                           Fer4_16  2 CgtCgkCaevCPtnaike 19
                                      C +C+ C++vC  +ai+ 
  gi|298674493|ref|YP_003726243.1| 46 CLGCRMCVSVCKPGAITL 63
                                      777777777777777776 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   4.5   2.3e-05     0.024       1      14 [.      10      23 ..      10      23 .. 0.93
   2 !   12.5   6.1   0.00021      0.23       1      15 []      46      60 ..      46      60 .. 0.97

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.3e-05
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      CtgCgaC ++C +g
  gi|298674493|ref|YP_003726243.1| 10 CTGCGACRKACLKG 23
                                      ***********876 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00021
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+gC+ Cv vC +gA
  gi|298674493|ref|YP_003726243.1| 46 CLGCRMCVSVCKPGA 60
                                      ****99******998 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   2.2   6.3e-05     0.066      77      94 ..       5      22 ..       1      24 [. 0.86
   2 !    9.8   0.7    0.0014       1.5      78      93 ..      42      57 ..      27      60 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.3e-05
                           Fer4_22 77 fgesgCvGCgRCieacpv 94
                                      +++++C+GCg C +ac +
  gi|298674493|ref|YP_003726243.1|  5 IDKNKCTGCGACRKACLK 22
                                      6899************86 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0014
                           Fer4_22 78 gesgCvGCgRCieacp 93
                                      + s C GC  C+++c+
  gi|298674493|ref|YP_003726243.1| 42 NPSYCLGCRMCVSVCK 57
                                      5678999999999996 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6  13.6    0.0013       1.3       1      57 [.       9      57 ..       9      61 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0013
                           Fer4_17  1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCP 57
                                      +C++Cg+C+++C  + ++       l++ +    +++ +  + s C++C++C+++C 
  gi|298674493|ref|YP_003726243.1|  9 KCTGCGACRKACLKGPKIFL-----LKDRN---GKKVAEVGNPSYCLGCRMCVSVCK 57
                                      6***********98766443.....22211...222333357789***********5 PP

>> NapB  Nitrate reductase cytochrome c-type subunit (NapB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.8     7e-05     0.074      58     112 ..       1      51 [.       1      61 [. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7e-05
                              NapB  58 yqidknaNkClsCHsrekakevkatkisvtHfvdregkelaevsprryfCtqCHv 112
                                       ++i+ ++NkC  C + +ka   k +ki    + dr+gk++aev +  y C+ C  
  gi|298674493|ref|YP_003726243.1|   1 MEITIDKNKCTGCGACRKAC-LKGPKIFL--LKDRNGKKVAEVGNPSY-CLGCRM 51 
                                       68***********9998875.67788875..789*********99887.666654 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   1.6     0.039        41      58      72 ..       7      21 ..       2      27 .. 0.72
   2 ?   11.3   0.9   0.00028       0.3      55      73 ..      40      58 ..      22      65 .] 0.67

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.039
                           Fer4_18 58 agdcidcescvkvcP 72
                                      +++c+ c++c k c 
  gi|298674493|ref|YP_003726243.1|  7 KNKCTGCGACRKACL 21
                                      567888888877775 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00028
                           Fer4_18 55 ekgagdcidcescvkvcPt 73
                                        + + c+ c++cv+vc  
  gi|298674493|ref|YP_003726243.1| 40 VGNPSYCLGCRMCVSVCKP 58
                                      334456***********43 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      173  (0.00964917); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.53u 0.34s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 368.00
//
Query:       gi|298674494|ref|YP_003726244.1|  [L=220]
Description: nitrite and sulfite reductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-29  102.7   0.0    1.9e-29  102.2   0.0    1.2  1  NIR_SIR       Nitrite and sulphite reductase 4Fe-4S domain
    1.1e-16   60.4   0.0    1.7e-16   59.8   0.0    1.3  1  NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half 
  ------ inclusion threshold ------
      0.026   14.6   0.0      0.064   13.3   0.0    1.6  1  DUF2059       Uncharacterized protein conserved in bacteria (


Domain annotation for each model (and alignments):
>> NIR_SIR  Nitrite and sulphite reductase 4Fe-4S domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.2   0.0   3.2e-33   1.9e-29       3     152 ..      86     219 ..      84     220 .] 0.96

  Alignments for each domain:
  == domain 1  score: 102.2 bits;  conditional E-value: 3.2e-33
                                       SSCCCCCCSTCCCTBSS-SS-THHHHHHHHHHHCTCCCCTSSSS-BEEEEESSTCSTSSGGGSSEEEEEEEETTCEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           NIR_SIR   3 anlrnvtlcpgaglceeallDttelakaiedelepeygetylPrKfKiavsgcpnncvaveanDiglvgvkkdekei 79 
                                        ++r+v++cpg+++c+    D+  l  +++    ++y+ ++lP K+K+ v+gc n c +  ++Dig++g+ k     
  gi|298674494|ref|YP_003726244.1|  86 VCVRSVKFCPGTTFCKRGQQDSVALGLKLD----EKYHGMELPGKMKMGVAGCMNSCSEPAVKDIGIMGTSK----- 153
                                       589***************************....**************************************..... PP

                                       EEEEEE--B-SSSTC-TCEEEEEEEEEGGGHHHHHHHHHHHHHHHS-CSSGGG-SHHHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           NIR_SIR  80 gfnilvGGglgrthgakktsarlgfvpeeevlevveaivevyrdhgdrknrkkeRlkylverlGvekFrekve 152
                                       g+++++GG++g +++ + t a  + + eeev+++v+ i+e+y+     ++  k+Rl+ +++++G+ekF+e+v+
  gi|298674494|ref|YP_003726244.1| 154 GYTLMLGGSAGLKPRIANTVA--TELSEEEVIQYVDRIIEFYK-----SQTSKKRLGQVIDNMGIEKFKEEVG 219
                                       *********************..6777888*************.....9999*******************95 PP

>> NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   0.0   2.8e-20   1.7e-16       3      67 ..      14      77 ..      12      79 .. 0.95

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 2.8e-20
                      NIR_SIR_ferr  3 qkdgkgyymvrlrvpnGritaeqlraladiaekygsgeirlTtrQnlqlhgvpeedleeileeLa 67
                                      q+d+++y ++  ++p+G+++a++l+++ad+aeky+   +++T+ Q + + g++eedl+++++eL+
  gi|298674494|ref|YP_003726244.1| 14 QRDKETY-AIAPHIPGGIVSADMLKKIADVAEKYDAQALKVTSSQRIAIVGLNEEDLDDVWSELE 77
                                      8998887.*******************************************************97 PP

>> DUF2059  Uncharacterized protein conserved in bacteria (DUF2059)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.1e-05     0.064       3      34 ..     165     200 ..     164     205 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.1e-05
                                       HHHHHHHHHHHHS-HHH....HHHHHHHHHSHHHHH CS
                           DUF2059   3 mkdllaaiyaktfteae....lkailaFYkSPlGkk 34 
                                       +k+++a+  a +++e+e    +++i++FYkS + kk
  gi|298674494|ref|YP_003726244.1| 165 LKPRIANTVATELSEEEviqyVDRIIEFYKSQTSKK 200
                                       6899************99999**********88877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1243.92
//
Query:       gi|298674495|ref|YP_003726245.1|  [L=865]
Description: S-layer protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.6e-202  669.7  38.7   5.7e-102  340.2  14.1    2.6  2  S-layer          S-layer protein
      4e-08   33.4  15.0    0.00024   21.3   0.5    4.6  4  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    1.5e-06   28.0   8.3      0.012   15.5   0.7    4.5  3  PEGA             PEGA domain
    8.6e-06   25.7  10.5      0.054   13.5   0.5    4.6  4  CarbopepD_reg_2  CarboxypepD_reg-like domain
    0.00021   21.7   1.9        1.6    9.1   0.1    3.5  3  DUF4198          Domain of unknown function (DUF4198)
    0.00026   21.2   2.5       0.31   11.3   0.1    2.9  2  DUF4362          Domain of unknown function (DUF4362)
  ------ inclusion threshold ------
      0.042   14.0  23.5       0.87    9.8   1.0    4.2  3  Big_3_5          Bacterial Ig-like domain (group 3)
      0.066   13.3   3.0         25    5.1   0.0    3.8  3  PrcB_C           PrcB C-terminal
      0.081   13.3   0.8       0.56   10.6   0.2    2.5  2  A2M_BRD          Alpha-2-macroglobulin bait region domain
       0.17   12.5   8.5         12    6.5   0.4    4.5  3  YtkA             YtkA-like
        0.3   11.1   7.0        3.1    7.8   0.0    4.5  5  Y_Y_Y            Y_Y_Y domain
       0.51    9.7   4.4       0.22   10.9   1.1    1.9  2  DUF1616          Protein of unknown function (DUF1616)
        5.2    6.9   9.4       0.66    9.8   0.1    4.1  3  Big_4            Bacterial Ig-like domain (group 4)
        8.7    6.3  11.0        2.5    8.0   0.9    3.9  3  PKD              PKD domain


Domain annotation for each model (and alignments):
>> S-layer  S-layer protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  334.8  16.6    2e-103  2.6e-100       2     258 .]      38     291 ..      37     291 .. 0.98
   2 !  340.2  14.1  4.4e-105  5.7e-102       2     258 .]     313     565 ..     312     565 .. 0.98

  Alignments for each domain:
  == domain 1  score: 334.8 bits;  conditional E-value: 2e-103
                           S-layer   2 eneeeseeltwtasnFsgfyydiddglssEsltlelesksdrtieegelvYsttpvekefefeewgsYevigflaek 78 
                                       +ne+ s ++twta ++sgfyyd+d+++ssE+lt++l+s ++r++++g+l+Y+t+p+e+efe++e+gsYevigf+ae+
  gi|298674495|ref|YP_003726245.1|  38 ANENVSRDYTWTAMSYSGFYYDLDTNESSETLTINLDS-DSRNVNDGDLEYTTKPIETEFEYNEFGSYEVIGFMAER 113
                                       5788899****************************997.99************************************ PP

                           S-layer  79 Yfagy.dnsaetsddvsllsdekLskvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevdsk 154
                                       Yfagy dn+++t++dvsl+sd++L+kvl+d+d+++++++gs+leLeegY+++i ++D++gd+v++eL+kdg+++ds 
  gi|298674495|ref|YP_003726245.1| 114 YFAGYtDNTTFTDEDVSLMSDGQLAKVLTDTDDRESFFAGSELELEEGYSIHIIEVDINGDSVFVELRKDGDQIDSG 190
                                       *****88888******************************************************************* PP

                           S-layer 155 vissskadstyvyekdlgdeddvviiavhvdevfrgtedslvviegifqisddvleieegdefgkmevksvseneie 231
                                       ++s     + y+yekdlg++ddv+iiav++d++frgte+++v++egifqis+d++e+++gd++gkmev+sv++nei+
  gi|298674495|ref|YP_003726245.1| 191 IVSG---GDVYTYEKDLGSADDVPIIAVNFDNIFRGTETNAVFVEGIFQISEDYTEVDDGDNYGKMEVDSVTSNEIT 264
                                       ****...********************************************************************** PP

                           S-layer 232 menddsitLsrdktieimddlkfkvaD 258
                                       m+nddsitL ++++i+im++l+f vaD
  gi|298674495|ref|YP_003726245.1| 265 MSNDDSITLGQGDDINIMGRLNFIVAD 291
                                       **************************8 PP

  == domain 2  score: 340.2 bits;  conditional E-value: 4.4e-105
                           S-layer   2 eneeeseeltwtasnFsgfyydiddglssEsltlelesksdrtieegelvYsttpvekefefeewgsYevigflaek 78 
                                       ++++e+e+++wt+ nF+gfyydid+gl++Es++++   +++r+i++g+l Y+t+p+e+efef ++gsYevigf+aek
  gi|298674495|ref|YP_003726245.1| 313 GTVTENENFEWTPLNFEGFYYDIDEGLKTESIEVT---RDKRNIDDGDLLYTTEPAEVEFEFGDFGSYEVIGFMAEK 386
                                       578999****************************9...378************************************ PP

                           S-layer  79 Yfagy..dnsaetsddvsllsdekLskvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevds 153
                                       Yfagy  dn++++++dvsl+sd++Lskvlid+de+k+ +sgssl LeegY+l+i ++D++gd+v++eL+kdge++ds
  gi|298674495|ref|YP_003726245.1| 387 YFAGYteDNTTFSDEDVSLMSDGQLSKVLIDDDETKSTFSGSSLVLEEGYRLRIVEVDLEGDSVFVELHKDGEQIDS 463
                                       *****8666679***************************************************************** PP

                           S-layer 154 kvissskadstyvyekdlgdeddvviiavhvdevfrgtedslvviegifqisddvleieegdefgkmevksvsenei 230
                                        v+s     + y+yekd+g++ddv+iiav+++++frg+e+++v++egifqis+d++e+++gd++gkmev+svs+nei
  gi|298674495|ref|YP_003726245.1| 464 GVVSG---GDVYTYEKDVGSADDVPIIAVNFEDIFRGSETNAVFVEGIFQISEDYTEVDDGDNYGKMEVDSVSSNEI 537
                                       *****...********************************************************************* PP

                           S-layer 231 emenddsitLsrdktieimddlkfkvaD 258
                                        m+nddsitL +d+ti+im++++fkvaD
  gi|298674495|ref|YP_003726245.1| 538 SMSNDDSITLGQDDTISIMGNINFKVAD 565
                                       ***************************9 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   2.2   3.3e-05     0.042       8      79 ..     605     670 ..     599     673 .. 0.77
   2 !   21.3   0.5   1.9e-07   0.00024       2      70 ..     683     746 ..     682     777 .. 0.76
   3 ?    3.4   0.0     0.073        94      48      80 ..     784     815 ..     776     817 .. 0.85
   4 ?    2.7   0.3      0.12   1.6e+02      22      53 ..     805     838 ..     793     842 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.3e-05
                   CarboxypepD_reg   8 dasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagqtttldi 79 
                                        + ga++ +a V+v       +   tt ++G+   +   +gt++vt++++G+ +a++ e+++   q++++ +
  gi|298674495|ref|YP_003726245.1| 605 ESRGAAVQNAVVMVD-----DENIGTTTREGTIEYTPEDTGTFTVTAEKQGFVSASK-EIEVIGQQENRMSV 670
                                       3579***********.....34445566788877775667****************7.69999777776654 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 1.9e-07
                   CarboxypepD_reg   2 isGrVtda.sgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtlt 70 
                                       i+ +Vt a  ++pi++a+Vt  +   ++     t adG+ + +   pg ++vt+s++Gy+  +  ++++ 
  gi|298674495|ref|YP_003726245.1| 683 ITITVTEAiGNEPIENAEVTYDD---ESI--GDTSADGTINYTTNDPGVHKVTASKDGYQDGEE-NIEIL 746
                                       7889****7889**********3...444..456667766666679***************996.55553 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.073
                   CarboxypepD_reg  48 gtysvtvsapGyatatreevtltagqtttldit 80 
                                       g+y+++   +G  + + e++ l+ag++tt+++t
  gi|298674495|ref|YP_003726245.1| 784 GDYTIELMVNGTMEDS-EQINLDAGNSTTVEFT 815
                                       8899999888888888.57***********997 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.12
                   CarboxypepD_reg  22 tnadtgtvasttt.dadGafrlrglpp..gtysvt 53 
                                        + +++tv  t t ++ G+++++ +    gty+vt
  gi|298674495|ref|YP_003726245.1| 805 DAGNSTTVEFTHTeNEPGNYSVE-VDGqtGTYTVT 838
                                       44333444444442666777776.43335777776 PP

>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.7   9.2e-06     0.012       2      65 ..     600     671 ..     599     676 .. 0.78
   2 !   11.6   0.1   0.00016       0.2      11      55 ..     697     746 ..     693     758 .. 0.82
   3 ?    2.1   0.0      0.14   1.8e+02      32      65 ..     782     815 ..     772     820 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 9.2e-06
                              PEGA   2 gtltirSn...peGatVyidGkylGkT....Pvtls.leaGnyslrvekeGYedlektvtvtagetvklnlt 65 
                                       +t+ti+S+    ++a V++d +++G T     ++++  ++G+ +++ ek G+  ++k+++v  +++ ++++ 
  gi|298674495|ref|YP_003726245.1| 600 VTITIESRgaaVQNAVVMVDDENIGTTtregTIEYTpEDTGTFTVTAEKQGFVSASKEIEVIGQQENRMSVD 671
                                       57778776333689***********662222577888889*********************98877776665 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00016
                              PEGA  11 eGatVyidGkylGkTP....vtls.leaGnyslrvekeGYedlektvtvt 55 
                                       e+a+V+ d +++G T     ++++  ++G ++++ +k+GY+d e+ +++ 
  gi|298674495|ref|YP_003726245.1| 697 ENAEVTYDDESIGDTSadgtINYTtNDPGVHKVTASKDGYQDGEENIEIL 746
                                       6999*********77522226777789*****************999975 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.14
                              PEGA  32 eaGnyslrvekeGYedlektvtvtagetvklnlt 65 
                                       + G+y++++   G ++ +++++++ag  ++++ t
  gi|298674495|ref|YP_003726245.1| 782 MGGDYTIELMVNGTMEDSEQINLDAGNSTTVEFT 815
                                       689*********************9999988654 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       5.3   6.7e+03      11      39 ..     207     238 ..     203     242 .. 0.76
   2 !   13.5   0.5   4.2e-05     0.054       5      78 ..     602     674 ..     601     681 .. 0.84
   3 !   13.0   0.3   6.1e-05     0.078       4      66 ..     686     747 ..     683     766 .. 0.83
   4 ?    2.8   0.1     0.089   1.1e+02      44      80 ..     784     820 ..     778     838 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5.3
                   CarbopepD_reg_2  11 keplpgatVyvkgtkkgtvTde...nGnFelk 39 
                                        + +p + V + +  +gt T++   +G F+++
  gi|298674495|ref|YP_003726245.1| 207 ADDVPIIAVNFDNIFRGTETNAvfvEGIFQIS 238
                                       56788899999999999999975556777775 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 4.2e-05
                   CarbopepD_reg_2   5 VvdketkeplpgatVyvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvskektldvnillke 78 
                                       ++ ++ + ++  a V+v + + gt+T  +G+ e +  + g++t++++  G+ +++k+++v ++++  +++  ++
  gi|298674495|ref|YP_003726245.1| 602 ITIESRGAAVQNAVVMVDDENIGTTT-REGTIEYTPEDTGTFTVTAEKQGFVSASKEIEVIGQQENRMSVDISP 674
                                       666778899***************98.68*999999999********************987766665555554 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 6.1e-05
                   CarbopepD_reg_2   4 tVvdketkeplpgatVyvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvsk 66 
                                       tV+++ ++ep++ a V++ + + g  T ++G+ + ++ ++g +++++s  Gy+  e+++++ +
  gi|298674495|ref|YP_003726245.1| 686 TVTEAIGNEPIENAEVTYDDESIGD-TSADGTINYTTNDPGVHKVTASKDGYQDGEENIEILE 747
                                       7999999************999996.56788877778899*******************9844 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.089
                   CarbopepD_reg_2  44 gkytLvvsyvGyktqekkvtvskektldvnillkeea 80 
                                       g+yt+   + G  +++++++++ +++++v+++ +e++
  gi|298674495|ref|YP_003726245.1| 784 GDYTIELMVNGTMEDSEQINLDAGNSTTVEFTHTENE 820
                                       89********************999999999988765 PP

>> DUF4198  Domain of unknown function (DUF4198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.1    0.0032       4.1     144     204 ..     591     651 ..     578     655 .. 0.92
   2 !    9.1   0.1    0.0012       1.6     144     204 ..     674     736 ..     672     737 .. 0.91
   3 ?    1.8   0.0       0.2   2.6e+02      47      89 ..     795     837 ..     757     849 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0032
                           DUF4198 144 pydlkageelevqvlldGkPlagaeveveyggtryrdapdeikvktdadGvvtftlpkaGl 204
                                       p ++ ++ ++++++  +G  +++a v v  ++ +  + +++i+++  + G +t+t +k+G+
  gi|298674495|ref|YP_003726245.1| 591 PDTITQDSTVTITIESRGAAVQNAVVMVDDENIGTTTREGTIEYTPEDTGTFTVTAEKQGF 651
                                       778889999999999******************99999999999*************9996 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0012
                           DUF4198 144 pydlkageelevqvl..ldGkPlagaeveveyggtryrdapdeikvktdadGvvtftlpkaGl 204
                                       p +++ag+ ++++v+  +  +P ++aev+   ++ ++  a ++i ++t++ Gv ++t +k G+
  gi|298674495|ref|YP_003726245.1| 674 PDEIFAGDIITITVTeaIGNEPIENAEVTYDDESIGDTSADGTINYTTNDPGVHKVTASKDGY 736
                                       788999999999999888899********99999999999999999***********999986 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.2
                           DUF4198  47 lapdgektdlg.kylstfdvallkpekegtyklaaakkpgdwke 89 
                                       +  d e+++l  ++ +t+++++++ +++g y +++  + g+++ 
  gi|298674495|ref|YP_003726245.1| 795 TMEDSEQINLDaGNSTTVEFTHTE-NEPGNYSVEVDGQTGTYTV 837
                                       444445666664566777888855.668******9888898886 PP

>> DUF4362  Domain of unknown function (DUF4362)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.3    0.0017       2.1      26      68 ..     158     200 ..     142     216 .. 0.82
   2 !   11.3   0.1   0.00024      0.31      31      68 ..     437     474 ..     431     489 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0017
                           DUF4362  26 qkkkdkirivsyTeeGdpiledleydgkklkyilDnrrDefas 68 
                                        ++   i i++  ++Gd ++ +l +dg+++ +   +  D ++ 
  gi|298674495|ref|YP_003726245.1| 158 LEEGYSIHIIEVDINGDSVFVELRKDGDQIDSGIVSGGDVYTY 200
                                       4555689***********************9988888888775 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00024
                           DUF4362  31 kirivsyTeeGdpiledleydgkklkyilDnrrDefas 68 
                                       ++riv+   eGd ++ +l++dg+++ + + +  D ++ 
  gi|298674495|ref|YP_003726245.1| 437 RLRIVEVDLEGDSVFVELHKDGEQIDSGVVSGGDVYTY 474
                                       68************************999988888875 PP

>> Big_3_5  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   4.1     0.041        52       7      66 ..     595     647 ..     586     650 .. 0.66
   2 ?    9.8   1.0   0.00068      0.87      12      66 ..     683     732 ..     679     740 .. 0.87
   3 ?    9.3   3.6     0.001       1.3       1      65 [.     761     828 ..     761     841 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.041
                                       TSEEEEEEE--CCCCTTS--EEEEEETTEE-SS-EE--TTSEEEEEEE-SS-EEEEEEEE CS
                           Big_3_5   7 gqtvtltatVtaasggtptGtVtftdggttlgtavllsanGtAtltvsalaaGthsitAt 66 
                                        q+ t+t+t+ +  g++++  V  ++++ ++gt++    +Gt  +t +++  Gt ++tA+
  gi|298674495|ref|YP_003726245.1| 595 TQDSTVTITIESR-GAAVQNAVV-MVDDENIGTTT--R-EGTIEYTPEDT--GTFTVTAE 647
                                       4455555555555.335555554.55667788866..4.58888888876..******96 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00068
                                       EEEE--CCCCTTS--EEEEEETTEE-SS-EE--TTSEEEEEEE-SS-EEEEEEEE CS
                           Big_3_5  12 ltatVtaasggtptGtVtftdggttlgtavllsanGtAtltvsalaaGthsitAt 66 
                                       +t+tVt+a g+ p  + ++t ++ ++g++++   +Gt ++t+++  +G h++tA+
  gi|298674495|ref|YP_003726245.1| 683 ITITVTEAIGNEPIENAEVTYDDESIGDTSA---DGTINYTTND--PGVHKVTAS 732
                                       799*****99******************773...6888887777..6*******7 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.001
                                       -S-EETTSEEEEEEE--CCCCTTS--..EEEEEETTEE-SS-EE--TTS...EEEEEEE-SS-EEEEEEE CS
                           Big_3_5   1 ptsvtagqtvtltatVtaasggtptG..tVtftdggttlgtavllsanG...tAtltvsalaaGthsitA 65 
                                       p++v+ag++v++t++ t    g++ G  t++++++gt   + + + ++G   t+ +t++  ++G++s+ +
  gi|298674495|ref|YP_003726245.1| 761 PSEVEAGNPVSITVNATNI--GNMGGdyTIELMVNGTMEDSEQINLDAGnstTVEFTHTENEPGNYSVEV 828
                                       578999*******999999..55555559*******9998766665455555888999999999999975 PP

>> PrcB_C  PrcB C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.024        30      13      34 ..     160     181 ..     152     193 .. 0.88
   2 ?    5.1   0.0      0.02        25      13      34 ..     434     455 ..     432     467 .. 0.88
   3 ?    0.8   0.1      0.43   5.5e+02      13      24 ..     822     833 ..     818     837 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.024
                            PrcB_C  13 gGYsievdkvyetenaiyvktt 34 
                                       +GYsi + +v  +++++ v+++
  gi|298674495|ref|YP_003726245.1| 160 EGYSIHIIEVDINGDSVFVELR 181
                                       7*****************9986 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.02
                            PrcB_C  13 gGYsievdkvyetenaiyvktt 34 
                                       +GY++++ +v ++++++ v++ 
  gi|298674495|ref|YP_003726245.1| 434 EGYRLRIVEVDLEGDSVFVELH 455
                                       7*****************9975 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.43
                            PrcB_C  13 gGYsievdkvye 24 
                                       g+Ys+evd+ + 
  gi|298674495|ref|YP_003726245.1| 822 GNYSVEVDGQTG 833
                                       89******9775 PP

>> A2M_BRD  Alpha-2-macroglobulin bait region domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   0.00043      0.56      10     123 ..     594     690 ..     539     703 .. 0.75
   2 ?   -0.2   0.0       0.9   1.2e+03      37     104 ..     791     814 ..     717     845 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00043
                                       --TTSEEEEEEE-SS-EE-TT-....BSS-----.-S...S....-EEEEEE--TT-----EEEEEE..E--CEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           A2M_BRD  10 ykvGetakltvkstfatverdstlylvlsrgnivssgekveeidsstsfsfpvtadmaPnarvvvyyirrdgevvad 86 
                                       +  ++t+++t++s+ a+v+++    ++++  ni           ++++ +++ t++    ++v      +++ +v+ 
  gi|298674495|ref|YP_003726245.1| 594 ITQDSTVTITIESRGAAVQNAV---VMVDDENIG---------TTTREGTIEYTPEDTGTFTVT--A--EKQGFVSA 654
                                       3444555555555554333333...344444442.........234567888888888888873..3..56899*** PP

                                       EEE----.-GGGB-EEEEEEE...-SSSEEEEEEE.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           A2M_BRD  87 svqlpvekdfenklsvslesynetrPgeevtlkvkas 123
                                       s +++v   +en+ sv++ s +e   g+ +t++v+ +
  gi|298674495|ref|YP_003726245.1| 655 SKEIEVIGQQENRMSVDI-SPDEIFAGDIITITVTEA 690
                                       ******************.999************943 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.9
                                       SS-----.-S...S....-EEEEEE--TT-----EEEEEE..E--CEEEEEEE----.-GGGB-EEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           A2M_BRD  37 lsrgnivssgekveeidsstsfsfpvtadmaPnarvvvyyirrdgevvadsvqlpvekdfenklsvsl 104
                                       + +g +                                           ds q++ +  + n  +v++
  gi|298674495|ref|YP_003726245.1| 791 MVNGTM------------------------------------------EDSEQINLD--AGNSTTVEF 814
                                       333322..........................................344444444..344444444 PP

>> YtkA  YtkA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.2     0.079     1e+02      18      67 ..     594     640 ..     583     647 .. 0.69
   2 ?    4.3   0.2     0.047        60       3      43 ..     664     704 ..     662     732 .. 0.71
   3 ?    6.5   0.4    0.0096        12      51      84 ..     806     838 ..     759     840 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.079
                              YtkA  18 kagentivvtvtqggkpVedadvkvefwmpameGmeemttkvelkesedG 67 
                                        +++ t+++t +  g++V++a+v+v+ +     G  + +  +e +++  G
  gi|298674495|ref|YP_003726245.1| 594 ITQDSTVTITIESRGAAVQNAVVMVDDENI---GTTTREGTIEYTPEDTG 640
                                       677889999999**********99875444...55555555555555555 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.047
                              YtkA   3 esddlevelvspeepkagen.tivvtvtqggkpVedadvkve 43 
                                       + +   v+++++ e+ ag+  ti+vt   g++p+e+a+v+ +
  gi|298674495|ref|YP_003726245.1| 664 QENRMSVDISPD-EIFAGDIiTITVTEAIGNEPIENAEVTYD 704
                                       566777888876.5666666589999************8754 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0096
                              YtkA  51 GmeemttkvelkesedGvYeaevnfsmeGtWqvq 84 
                                       +++ +t++ +++e e+G Y++ev+  + Gt++v+
  gi|298674495|ref|YP_003726245.1| 806 AGNSTTVEFTHTENEPGNYSVEVDG-QTGTYTVT 838
                                       45556888889999*********95.89999997 PP

>> Y_Y_Y  Y_Y_Y domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.2       7.2   9.2e+03      18      42 ..      82     105 ..      81     106 .. 0.75
   2 ?    2.2   0.0      0.14   1.8e+02      23      45 ..     625     646 ..     619     651 .. 0.78
   3 ?    1.3   0.1      0.27   3.4e+02      20      45 ..     707     731 ..     701     747 .. 0.71
   4 ?   -2.1   0.0         3   3.8e+03      39      47 ..     784     792 ..     775     802 .. 0.80
   5 ?    7.8   0.0    0.0024       3.1      19      45 ..     799     828 ..     795     833 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 7.2
                                       ESSEEEESSTS.EEEEES--SEEEE CS
                             Y_Y_Y  18 dkeWveasdysqeasytnlppGdYt 42 
                                       d++ +++++   e ++  ++ G+Y+
  gi|298674495|ref|YP_003726245.1|  82 DGDLEYTTKPI-ETEFEYNEFGSYE 105
                                       67777777777.8888888888886 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.14
                                       EESSTS.EEEEES--SEEEEEEE CS
                             Y_Y_Y  23 easdysqeasytnlppGdYtlkV 45 
                                       +++  + +++yt+   G++t+++
  gi|298674495|ref|YP_003726245.1| 625 TTTREG-TIEYTPEDTGTFTVTA 646
                                       444555.9************875 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.27
                                       SEEEESSTS.EEEEES--SEEEEEEE CS
                             Y_Y_Y  20 eWveasdysqeasytnlppGdYtlkV 45 
                                       +  ++s+ + +++yt + pG  ++++
  gi|298674495|ref|YP_003726245.1| 707 SIGDTSADG-TINYTTNDPGVHKVTA 731
                                       455677777.**********877664 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 3
                                       EEEEEEEEE CS
                             Y_Y_Y  39 GdYtlkVka 47 
                                       GdYt+++ +
  gi|298674495|ref|YP_003726245.1| 784 GDYTIELMV 792
                                       9****9876 PP

  == domain 5  score: 7.8 bits;  conditional E-value: 0.0024
                                       SSEEEESSTS....EEEEES--SEEEEEEE CS
                             Y_Y_Y  19 keWveasdysq...easytnlppGdYtlkV 45 
                                        e +++++ ++   e++ t+++pG+Y ++V
  gi|298674495|ref|YP_003726245.1| 799 SEQINLDAGNSttvEFTHTENEPGNYSVEV 828
                                       55566666655679*************999 PP

>> DUF1616  Protein of unknown function (DUF1616)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1      0.98   1.3e+03     194     248 ..     595     649 ..     580     687 .. 0.60
   2 ?   10.9   1.1   0.00017      0.22     187     260 ..     760     831 ..     740     838 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.98
                           DUF1616 194 gesqevivgieNhEheevnYtvvvllqevtdeeevevlerteldrrevtladnet 248
                                       +++++v+++ie ++   +n  v v  ++  ++++  ++e t  d+ ++t+ ++++
  gi|298674495|ref|YP_003726245.1| 595 TQDSTVTITIESRGAAVQNAVVMVDDENIGTTTREGTIEYTPEDTGTFTVTAEKQ 649
                                       4556677777777766666666665555533333333445555555555555544 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00017
                           DUF1616 187 ypteltagesqevivgieNhEheevnYtvvvllqevtdeeevevlerteldrrevtladnetweqelevepeat 260
                                        p+e++ag++ +++v  +N ++   +Yt+++ ++ +   e+ e+++ +  ++++v+  + e +  +++ve++ +
  gi|298674495|ref|YP_003726245.1| 760 SPSEVEAGNPVSITVNATNIGNMGGDYTIELMVNGT--MEDSEQINLDAGNSTTVEFTHTENEPGNYSVEVDGQ 831
                                       599******************************984..333444455566666777777777777777777664 PP

>> Big_4  Bacterial Ig-like domain (group 4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00052      0.66      40      57 ..     299     316 ..     297     318 .. 0.91
   2 ?   -2.9   0.1       4.6   5.9e+03       4      21 ..     576     595 ..     576     595 .. 0.76
   3 ?    0.2   0.4       0.5   6.5e+02      33      53 ..     700     720 ..     684     736 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00052
                             Big_4  40 paedtskpGtytveGtve 57 
                                       p++d+s++Gty++ Gtv 
  gi|298674495|ref|YP_003726245.1| 299 PYVDISESGTYELRGTVT 316
                                       79**************95 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.6
                             Big_4   4 vevtvtvgtsp..nLPttVe 21 
                                       vevt+  g+ +  +LP+t++
  gi|298674495|ref|YP_003726245.1| 576 VEVTTGPGDMLtiDLPDTIT 595
                                       67888888886669999986 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.5
                             Big_4  33 kVtWdkipaedtskpGtytve 53 
                                       +Vt d++   dts+ Gt  ++
  gi|298674495|ref|YP_003726245.1| 700 EVTYDDESIGDTSADGTINYT 720
                                       444444444444444444332 PP

>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.9     0.002       2.5      32      60 ..     618     646 ..     589     649 .. 0.86
   2 ?   -2.3   0.2       3.2   4.1e+03      34      59 ..     705     730 ..     702     731 .. 0.77
   3 ?    3.0   0.4     0.072        92      41      60 ..     809     828 ..     803     838 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.002
                                       --SS--EEEEETTEEEEEE-SSEEEEEEE CS
                               PKD  32 fgdgsvvqvlseptvthtYlspGeYeVtv 60 
                                       ++d+  +++++e t+ +t++ +G+++Vt 
  gi|298674495|ref|YP_003726245.1| 618 VDDENIGTTTREGTIEYTPEDTGTFTVTA 646
                                       6788999********************95 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.2
                                       SS--EEEEETTEEEEEE-SSEEEEEE CS
                               PKD  34 dgsvvqvlseptvthtYlspGeYeVt 59 
                                       d+s + ++   t+++t + pG + Vt
  gi|298674495|ref|YP_003726245.1| 705 DESIGDTSADGTINYTTNDPGVHKVT 730
                                       5566667777788888888**99998 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.072
                                       EETTEEEEEE-SSEEEEEEE CS
                               PKD  41 lseptvthtYlspGeYeVtv 60 
                                       ++  ++tht ++pG+Y V v
  gi|298674495|ref|YP_003726245.1| 809 STTVEFTHTENEPGNYSVEV 828
                                       666789************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (865 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.77u 0.36s 00:00:01.12 Elapsed: 00:00:00.55
# Mc/sec: 4743.67
//
Query:       gi|298674496|ref|YP_003726246.1|  [L=213]
Description: HAD-superfamily hydrolase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      5e-33  114.7   0.2    5.9e-33  114.4   0.2    1.1  1  HAD_2           Haloacid dehalogenase-like hydrolase
    4.6e-13   50.0   0.1    2.8e-12   47.4   0.1    1.9  1  Hydrolase       haloacid dehalogenase-like hydrolase
    0.00032   21.2   0.0    0.00057   20.3   0.0    1.4  1  HAD             haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
       0.04   14.0   0.0      0.085   12.9   0.0    1.6  1  Hydrolase_like  HAD-hyrolase-like
       0.05   13.3   0.2       0.12   12.2   0.2    1.6  1  DUF2179         Uncharacterized protein conserved in bacteria


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.4   0.2   1.6e-36   5.9e-33       2     178 .]       6     183 ..       5     183 .. 0.97

  Alignments for each domain:
  == domain 1  score: 114.4 bits;  conditional E-value: 1.6e-36
                             HAD_2   2 iFDlDgTlldteeliiqafnelleeyglselseeelrkliglslrellrklgeseeeee...kieellrkyneekkk 75 
                                       +FD+Dg+l+++ +++++a++ ++++ g+ +++++++ ++ g  + +++r l ++++++    +++ ++++y++e +k
  gi|298674496|ref|YP_003726246.1|   6 MFDMDGVLVNSMPYHVEAMKVAFDNIGV-QINKQDIYEHEGSRTIDIVRDLLIKDNKNPdsfNLDGIIQQYEQEFNK 81 
                                       8***********************9998.************************988877999999999********9 PP

                             HAD_2  76 .kevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklklk 151
                                         +++p++g+k+lL+ L +++y l +v+  +++ v++ le+l   ++Fdvi+t++dve+ KP pe++++a+ek +++
  gi|298674496|ref|YP_003726246.1|  82 iVKLEPFEGLKDLLDAL-KNKYILCVVSGAEDSIVKDILEKLY-PDVFDVIITANDVENGKPVPEPYLRAVEKSGVE 156
                                       9999*************.88**********************9.7******************************** PP

                             HAD_2 152 keeviyvGDsptDieaakkagikviav 178
                                       k e+i+++    ++e+ak+ag+ ++a+
  gi|298674496|ref|YP_003726246.1| 157 KGECIVFENAMLGVESAKRAGLYCVAI 183
                                       **********************99985 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4   0.1   7.7e-16   2.8e-12       2     210 .]       3     177 ..       2     177 .. 0.83

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 7.7e-16
                                       SEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   2 ktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpewlt 78 
                                       k+++fD+dG+L+++ p ++++++ a                         +++++ +++ + +g  ++ i +  +++
  gi|298674496|ref|YP_003726246.1|   3 KALMFDMDGVLVNSMPYHVEAMKVA---------------------FDNIGVQINKQDIYEHEGSRTIDIVRDLLIK 58 
                                       89***********************.....................6666667777888885555567777777777 PP

                                       HHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  79 aldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanql 155
                                       ++              s   + +++  ++ ++f    +l++++++++++ +Lk + i +++++g + + ++ ++++l
  gi|298674496|ref|YP_003726246.1|  59 DN----------KNPDSFNLDGIIQ--QYEQEFNKIVKLEPFEGLKDLLDALKNKYI-LCVVSGAEDSIVKDILEKL 122
                                       77..........5555555555555..44444444444458************9999.******************7 PP

                                       TGGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 156 GddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                         d fd++i++ +++ +kp pe +++a+++ ++++ e+++++  + +++ +++Ag
  gi|298674496|ref|YP_003726246.1| 123 YPDVFDVIITANDVENGKPVPEPYLRAVEKSGVEKGECIVFENAMLGVESAKRAG 177
                                       779*************************************************998 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.6e-07   0.00057       2     130 ..       6     133 ..       5     166 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.6e-07
                               HAD   2 lfDfDgTLldgdsle.....lllrfllrrgaprl.wralreklllalfrellrldraglaelleallaglseelaae 72 
                                        fD+Dg L+++ +++     + +++++ +  +++ ++    ++  ++ r+ll+ d++  + +      g  ++ ++e
  gi|298674496|ref|YP_003726246.1|   6 MFDMDGVLVNSMPYHveamkVAFDNIGVQINKQDiYEHEGSRTIDIV-RDLLIKDNKNPDSFNL---DGIIQQYEQE 78 
                                       59999999999888888887556656666555553444444444444.5555555554444444...3555666677 PP

                               HAD  73 lerfvaevirpklldp..galellaahraaGdrvvvvSgglrplvepll.aelg..adevlat 130
                                       ++++v      k l p  g+++ll+ ++++ + ++vvSg+ + +v+ +l +++   +d ++  
  gi|298674496|ref|YP_003726246.1|  79 FNKIV------K-LEPfeGLKDLLD-ALKNKYILCVVSGAEDSIVKDILeKLYPdvFDVIITA 133
                                       77777......3.33333*******.6688899****************44555866666544 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.4e-05     0.085       3      55 ..     139     190 ..     137     203 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.4e-05
                                       STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-T CS
                    Hydrolase_like   3 gKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrp 55 
                                       gKP pe y +a+e+ g++++e+++        +++A++aG+ +v++ t + r+
  gi|298674496|ref|YP_003726246.1| 139 GKPVPEPYLRAVEKSGVEKGECIVFENA-MLGVESAKRAGLYCVAIPTYIDRN 190
                                       9************************999.99************9998866555 PP

>> DUF2179  Uncharacterized protein conserved in bacteria (DUF2179)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   3.3e-05      0.12      17      53 ..     100     136 ..      95     138 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.3e-05
                           DUF2179  17 kkvlytvvsrkelsklkeiikeiDpkAFiivsdvsev 53 
                                        k +++vvs  e s +k+i ++  p+ F ++ ++++v
  gi|298674496|ref|YP_003726246.1| 100 NKYILCVVSGAEDSIVKDILEKLYPDVFDVIITANDV 136
                                       5789****************************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1252.96
//
Query:       gi|298674497|ref|YP_003726247.1|  [L=242]
Description: hypothetical protein Metev_0539 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-62  211.8   0.7    1.5e-62  211.6   0.7    1.0  1  DUF72     Protein of unknown function DUF72


Domain annotation for each model (and alignments):
>> DUF72  Protein of unknown function DUF72
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.6   0.7   8.2e-67   1.5e-62       1     217 [.      22     236 ..      22     237 .. 0.94

  Alignments for each domain:
  == domain 1  score: 211.6 bits;  conditional E-value: 8.2e-67
                                       B.TT..CCCHHHHHCCT-SEEEE-HHCCSSS-HHHHHHHHCTS-TT-EEEEE--CCCCCS.G-.SCHHHHHHHHHH. CS
                             DUF72   1 YpeglkkkerLeyYarhfntVEinstFYalpspetvakwaaqtpedFrFavKapraitherne.daeealerflesa 76 
                                       Ype+l kk++L+yYa++fntVE+nstFY + +p+t+++w+++tp++F+F++K +r ith ++  d+e+++++f+e+ 
  gi|298674497|ref|YP_003726247.1|  22 YPEKLGKKKWLSYYAERFNTVEVNSTFYNPIKPKTFSRWYNETPSNFKFTIKGYRVITHFKKLhDVEDDIKAFYER- 97 
                                       9**********************************************************753347**********8. PP

                                       CHHHCT-EEEEEEE--TT--S.HHHHHHHHHHTTTS-...SEEEE--BGGGH.H.HHHHHHHTT-EEEEE--SSC-- CS
                             DUF72  77 lepLgeklgpllfQlppsfkfdeenlerLeaflaalp...llavEvRhrswf.e.llellrehgvavvldepkkpkl 148
                                        +pL++klg++l+Qlp ++   ++n+e Le+f+++l    + ++E+Rh swf e + +ll+++++++++   ++p+l
  gi|298674497|ref|YP_003726247.1|  98 AAPLQHKLGCVLWQLPSNL---HKNMELLEEFCKNLDkrkNNVIEFRHVSWFtEdVQSLLQKYKIGYCII--SSPEL 169
                                       *******************...5589******998888845***********956***********8884..58999 PP

                                       ------SSTEEEEEE--SHHTTB----HHHHHHHHHHHHHHHTCSSEEEEEE-SBCCCHHHHHHHHHHH CS
                             DUF72 149 pledvttadfvyvRlhgreeryayrYseeelaewaerikawaaegrevyvffnndaegqaplnaraLae 217
                                       p   ++t++  y+R+hg +++y ++Y +e+l++ a++ik+  a  ++vy++fnnd +g+a+++a +L+e
  gi|298674497|ref|YP_003726247.1| 170 PEIITVTSNILYMRFHGINNWYTEKYGKEKLKDYASKIKKTDA--KKVYCYFNNDENGYAVHDAYNLRE 236
                                       *999999**********88*********************987..89*****************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       961  (0.0536003); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.55
# Mc/sec: 1329.23
//
Query:       gi|298674498|ref|YP_003726248.1|  [L=259]
Description: CoB--CoM heterodisulfide reductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0044   16.3  17.2      0.011   15.1  17.2    1.6  1  O_anti_polymase  Putative O-antigen polymerase
     0.0058   16.2  19.2      0.014   15.0  13.7    2.7  2  Nitrate_red_gam  Nitrate reductase gamma subunit


Domain annotation for each model (and alignments):
>> O_anti_polymase  Putative O-antigen polymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1  17.2   1.2e-06     0.011      26     158 ..      19     199 ..       3     252 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.2e-06
                   O_anti_polymase  26 lliilillglisfilgall.........................................lsklvlsieellvknnk 61 
                                       +++il ++++ +f++g++l                                         l+ lvl i  +    + 
  gi|298674498|ref|YP_003726248.1|  19 QVMILSVIAIGIFLYGMYLnikkwglgttgyaqepggggitvfpktfasqvakkgdwkiiLKTLVLDIILQRRIIRI 95 
                                       44555588888888888889999999999999999999999999999888888888777755555544443333344 PP

                   O_anti_polymase  62 kkleikfnekkvekiglilvliGillfiinllivggiPlfdpslraklntkltalsylflpsiailva........k 130
                                       +k   ++++++++ + ++l+l+++l+f+i+ll+++g+ +  + +r+ l++   ++sy++l++i+i ++         
  gi|298674498|ref|YP_003726248.1|  96 SKFRWFMHISIFVGW-MTLFLLSLLMFLIELLSLSGVNIHPEAIRQMLQPWNDLFSYILLLGIGIAIFrrlfvkraR 171
                                       677788888887755.789*************************************************99*998876 PP

                   O_anti_polymase 131 varlrnlilfiiglvllallgYrttvla 158
                                          +++ ++++ gl +++++g+ ++ + 
  gi|298674498|ref|YP_003726248.1| 172 ESTISYDAVLLAGLTFIVITGFVAQGIR 199
                                       667888889999999******9888775 PP

>> Nitrate_red_gam  Nitrate reductase gamma subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.2      0.82   7.3e+03     127     139 ..      19      31 ..      13      47 .. 0.57
   2 !   15.0  13.7   1.6e-06     0.014      91     209 ..     146     250 ..      87     254 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 0.82
                   Nitrate_red_gam 127 lllLllqillGll 139
                                        +++l +i++G++
  gi|298674498|ref|YP_003726248.1|  19 QVMILSVIAIGIF 31 
                                       4444444444443 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.6e-06
                   Nitrate_red_gam  91 GliagvlalvGlllLllRRltnkrvraatsasDkvvlllLllqillGllttlvsaldygseretispwlrslltlqp 167
                                         ++  ++l+G+ + ++RRl++kr r++t   D v+l+ L++ +++G+++  +   d+         w+ ++     
  gi|298674498|ref|YP_003726248.1| 146 NDLFSYILLLGIGIAIFRRLFVKRARESTISYDAVLLAGLTFIVITGFVAQGIRIGDF---------WAFGI----- 208
                                       45678999*****************************************999987766.........66555..... PP

                   Nitrate_red_gam 168 daellaevplifklHvllglll.falfPFtrLvHvlsapleYl 209
                                       d+  ++ +p +  +H+++ ll  +a +PF++ +H++++pl+ l
  gi|298674498|ref|YP_003726248.1| 209 DW-GINAAPQMALFHAVVSLLFcIAYIPFSKYIHMIATPLTIL 250
                                       43.467788888889888766426889************9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       922  (0.0514251); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.37s 00:00:00.99 Elapsed: 00:00:00.54
# Mc/sec: 1439.68
//
Query:       gi|298674499|ref|YP_003726249.1|  [L=412]
Description: CoB--CoM heterodisulfide reductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-34  116.1   2.4    8.3e-17   61.2   0.0    2.8  2  CCG       Cysteine-rich domain
    2.6e-11   43.8   2.7    2.6e-11   43.8   2.7    3.0  3  Fer4_8    4Fe-4S dicluster domain
    3.4e-08   33.9   3.5    3.4e-08   33.9   3.5    3.1  3  Fer4_17   4Fe-4S dicluster domain
    1.6e-06   28.9   3.1    1.6e-06   28.9   3.1    2.3  2  Fer4_16   4Fe-4S double cluster binding domain
    5.8e-06   26.8  18.6    1.3e-05   25.6   8.3    2.9  3  Fer4_7    4Fe-4S dicluster domain
    2.5e-05   24.3   9.6    2.5e-05   24.3   9.6    3.8  3  Fer4_10   4Fe-4S dicluster domain
    3.5e-05   23.9  22.2    7.7e-05   22.8  11.3    3.3  4  Fer4_9    4Fe-4S dicluster domain
    4.8e-05   23.5   2.3       0.31   11.2   0.4    2.6  2  Fer4_18   4Fe-4S dicluster domain
     0.0025   17.8   1.8     0.0025   17.8   1.8    3.4  4  Fer4_2    4Fe-4S binding domain
     0.0053   17.6   7.3       0.86   10.5   0.4    3.5  3  Fer4_22   4Fe-4S dicluster domain
     0.0098   16.0  11.0       0.23   11.6   0.6    3.4  3  Fer4_21   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.027   15.4   3.8      0.027   15.4   3.8    3.2  2  Fer4_3    4Fe-4S binding domain
      0.033   14.0   1.8      0.033   14.0   1.8    3.5  4  Fer4      4Fe-4S binding domain
        0.6   10.3  21.2       0.11   12.6   1.4    3.4  3  Fer4_6    4Fe-4S binding domain
       0.82   10.4   9.7        2.1    9.2   0.2    3.5  3  Fer4_15   4Fe-4S single cluster domain
        6.2    7.6  23.7       0.18   12.4   2.6    3.7  4  Fer4_4    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   1.2   2.6e-17   2.9e-14       2      81 ..     166     248 ..     165     251 .. 0.95
   2 !   61.2   0.0   7.4e-20   8.3e-17       1      84 [.     293     380 ..     293     381 .. 0.95

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 2.6e-17
                               CCG   2 ayfdgChllraaypevrkalkkllealgveleel.ekesCCGagggrsgkee...laealakrnvetaeetgadaiv 74 
                                       +y+ gC  +++++ ++  a++++l++lg+++  l e+e CCG++  r+g+ e   +a++ + +nve+++ +ga +++
  gi|298674499|ref|YP_003726249.1| 166 VYYGGC-TAEYKQTKLAVATARVLNKLGIDFAMLgEDELCCGSPLLRTGQSElenIARDCTIKNVENIKAKGASKVL 241
                                       799***.*******************************************87777999******************* PP

                               CCG  75 tacpgCl 81 
                                        ac+gC+
  gi|298674499|ref|YP_003726249.1| 242 YACAGCY 248
                                       ******8 PP

  == domain 2  score: 61.2 bits;  conditional E-value: 7.4e-20
                               CCG   1 vayfdgChllraa..ypevrkalkkllealgveleel.ekesCCGagggrsgkee.laealakrnvetaeetgadai 73 
                                       v+y+d+Ch++r+   y+++r +l+++++ +++e+++  + + CCGaggg +   + la++++++++e a et+ad++
  gi|298674499|ref|YP_003726249.1| 293 VTYHDPCHMGRHVgtYDAPRYVLENIPGIKLIEMDRIkDYSRCCGAGGGMKAGIPdLALKVGEERIEDALETDADIL 369
                                       89**********99***********************999******9998888667********************* PP

                               CCG  74 vtacpgCllql 84 
                                        +acp+C+ +l
  gi|298674499|ref|YP_003726249.1| 370 SSACPFCKRNL 380
                                       *******9876 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   2.7   2.3e-14   2.6e-11       2      65 .]      21     104 ..      20     104 .. 0.78
   2 ?   -0.4   0.3       1.4   1.6e+03      38      55 ..     231     248 ..     201     249 .. 0.59
   3 ?    0.2   0.0      0.96   1.1e+03      13      31 ..     371     390 ..     368     405 .. 0.63

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 2.3e-14
                            Fer4_8   2 lekCieCgaCqsaCpvlrrtkkhlldargeaae....dvqeeqvlee.....................eealwsCtt 53 
                                       l++C++Cg C + Cp+++++++++  a+ +++     +     ++++                        l++Ctt
  gi|298674499|ref|YP_003726249.1|  21 LDSCTRCGECVQWCPTYSASGQEPGLAPRDKILrwrdY-----MNKSyglraklfgpkeiseeeldefSSDLYQCTT 92 
                                       789******************88777777767734441.....33335555677777777777777799******** PP

                            Fer4_8  54 cgaCtevCpvgi 65 
                                       cg C++vC  gi
  gi|298674499|ref|YP_003726249.1|  93 CGICETVCESGI 104
                                       ********9887 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.4
                            Fer4_8  38 eeqvleeeealwsCttcg 55 
                                       + +++ + + l++C +c 
  gi|298674499|ref|YP_003726249.1| 231 NIKAKGASKVLYACAGCY 248
                                       333333367799999885 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.96
                            Fer4_8  13 saCpvlrrtk.khlldarge 31 
                                       saCp+++r   + + +   +
  gi|298674499|ref|YP_003726249.1| 371 SACPFCKRNLaDARDSVDAK 390
                                       68**9999873333333333 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   3.5   3.1e-11   3.4e-08       2      61 .]      24     105 ..      23     105 .. 0.66
   2 ?    1.6   0.5      0.38   4.2e+02      16      49 ..     211     247 ..     203     249 .. 0.74
   3 ?   -3.0   0.0       9.8   1.1e+04      11      19 ..     372     380 ..     370     390 .. 0.68

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 3.1e-11
                           Fer4_17   2 CiqCgyClpeCpsyeaydnepk.....kllraakl...............glleeaeke...ekaslCieCgeCerk 55 
                                       C++Cg C++ Cp+y a ++ep      k+lr   +               ++ ee+  +   +   +C++Cg Ce++
  gi|298674499|ref|YP_003726249.1|  24 CTRCGECVQWCPTYSASGQEPGlaprdKILRWRDYmnksyglraklfgpkEISEEEL-DefsSDLYQCTTCGICETV 99 
                                       ****************88864432222333333224555566666677742333322.235489************* PP

                           Fer4_17  56 CPqgld 61 
                                       C +g+d
  gi|298674499|ref|YP_003726249.1| 100 CESGID 105
                                       ***997 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.38
                           Fer4_17  16 eaydnepkkllraaklglleeaeke...ekaslCieC 49 
                                       +  ++e ++++r+ +++ +e+++++   ++   C++C
  gi|298674499|ref|YP_003726249.1| 211 RTGQSELENIARDCTIKNVENIKAKgasKVLYACAGC 247
                                       455566778999999999999877777679999*999 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 9.8
                           Fer4_17  11 eCpsyeayd 19 
                                       +Cp+++++ 
  gi|298674499|ref|YP_003726249.1| 372 ACPFCKRNL 380
                                       477777654 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   3.1   1.4e-09   1.6e-06       2      64 ..      24     100 ..      23     103 .. 0.76
   2 ?   -2.3   0.2         8   8.9e+03      49      57 ..     239     247 ..     214     249 .. 0.49

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.4e-09
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisy.............ntaekkdlaedeekckkq..eaitgCdiCqdv 63 
                                       C++Cg+C++ CPt   +++ e+ +++r++i               +  + k+++e+e  + +   +++t C+iC++v
  gi|298674499|ref|YP_003726249.1|  24 CTRCGECVQWCPTYSASGQ-EPGLAPRDKILRwrdymnksyglraKLFGPKEISEEELDEFSSdlYQCTTCGICETV 99 
                                       **************99999.677777774333355555566999978888888888766663334999********* PP

                           Fer4_16  64 C 64 
                                       C
  gi|298674499|ref|YP_003726249.1| 100 C 100
                                       * PP

  == domain 2  score: -2.3 bits;  conditional E-value: 8
                           Fer4_16  49 kkqeaitgC 57 
                                       k  +a++gC
  gi|298674499|ref|YP_003726249.1| 239 KVLYACAGC 247
                                       223444444 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   2.6   3.1e-05     0.034      33      50 ..      19      36 ..       3      39 .. 0.75
   2 !   25.6   8.3   1.2e-08   1.3e-05       1      52 []      23     104 ..      23     104 .. 0.63
   3 ?   -2.8   0.2       9.4   1.1e+04      37      42 ..     243     248 ..     223     250 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.1e-05
                            Fer4_7 33 idpekClgCgaCvavCPt 50
                                      ++ ++C+ Cg+Cv+ CPt
  gi|298674499|ref|YP_003726249.1| 19 MELDSCTRCGECVQWCPT 36
                                      468999999999999997 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 1.2e-08
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenek..............................gtekveidpekClgCgaCvav 47 
                                       +C+ Cg Cv+ Cp++  + +e   ++                              + ++   d  +C++Cg C++v
  gi|298674499|ref|YP_003726249.1|  23 SCTRCGECVQWCPTYSASGQEPGLAPrdkilrwrdymnksyglraklfgpkeiseeELDEFSSDLYQCTTCGICETV 99 
                                       5************999998863222223333333333333444444443333322244566888889********** PP

                            Fer4_7  48 CPtga 52 
                                       C +g+
  gi|298674499|ref|YP_003726249.1| 100 CESGI 104
                                       *9885 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 9.4
                            Fer4_7  37 kClgCg 42 
                                        C gC+
  gi|298674499|ref|YP_003726249.1| 243 ACAGCY 248
                                       566665 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   9.6   2.2e-08   2.5e-05       5      55 ..      20     100 ..      17     101 .. 0.82
   2 ?   -0.3   0.2       1.1   1.2e+03      33      49 ..     232     248 ..     221     251 .. 0.73
   3 ?   -0.3   0.0         1   1.2e+03      42      49 ..     370     377 ..     348     394 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 2.2e-08
                           Fer4_10   5 dddtCirCgkCvkaCPadl.............................tsvgakgeaseeeavrk..kvekCtgcga 50 
                                       + d+C+rCg+Cv+ CP++                              +  g  +e+seee ++   ++++Ct+cg 
  gi|298674499|ref|YP_003726249.1|  20 ELDSCTRCGECVQWCPTYSasgqepglaprdkilrwrdymnksyglraKLFG-PKEISEEELDEFssDLYQCTTCGI 95 
                                       679**************99************************999963333.3444444333333589******** PP

                           Fer4_10  51 CveaC 55 
                                       C  +C
  gi|298674499|ref|YP_003726249.1|  96 CETVC 100
                                       ***** PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.1
                           Fer4_10  33 seeeavrkkvekCtgcg 49 
                                        + +  +k++++C gc 
  gi|298674499|ref|YP_003726249.1| 232 IKAKGASKVLYACAGCY 248
                                       55566778889999985 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1
                           Fer4_10  42 vekCtgcg 49 
                                       +++C++c 
  gi|298674499|ref|YP_003726249.1| 370 SSACPFCK 377
                                       55566654 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   3.1   2.2e-05     0.025      31      48 ..      19      36 ..       4      40 .. 0.72
   2 !   22.8  11.3   6.9e-08   7.7e-05       2      49 ..      24     103 ..      23     104 .. 0.95
   3 ?   -1.5   0.2       2.5   2.8e+03      34      39 ..     242     247 ..     218     249 .. 0.60
   4 ?   -2.3   0.0       4.7   5.2e+03      34      40 ..     371     377 ..     349     381 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.2e-05
                            Fer4_9 31 aseeaCigCgaCveaCpk 48
                                       + ++C+ Cg+Cv+ Cp+
  gi|298674499|ref|YP_003726249.1| 19 MELDSCTRCGECVQWCPT 36
                                      33368************7 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 6.9e-08
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase................................eaCigCgaCveaC 46 
                                       Ct+Cg+Cv+ Cp+  +++++ +   r ++ ++                                 +C++Cg C+ +C
  gi|298674499|ref|YP_003726249.1|  24 CTRCGECVQWCPTYSASGQEPGLAPRDKILRWrdymnksyglraklfgpkeiseeeldefssdlYQCTTCGICETVC 100
                                       ****************9999999999999999999*****************************99*********** PP

                            Fer4_9  47 pkg 49 
                                       ++g
  gi|298674499|ref|YP_003726249.1| 101 ESG 103
                                       998 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.5
                            Fer4_9  34 eaCigC 39 
                                        aC gC
  gi|298674499|ref|YP_003726249.1| 242 YACAGC 247
                                       356666 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 4.7
                            Fer4_9  34 eaCigCg 40 
                                       +aC +C+
  gi|298674499|ref|YP_003726249.1| 371 SACPFCK 377
                                       5677775 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.4   0.00028      0.31      43      73 ..       6      36 ..       1      39 [. 0.79
   2 !   11.2   0.1   0.00029      0.33      55      77 ..      84     106 ..      64     119 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00028
                           Fer4_18 43 ekkalkekeerkekgagdcidcescvkvcPt 73
                                       + ++k     +  +   c+ c+ cv+ cPt
  gi|298674499|ref|YP_003726249.1|  6 PSIDTKGITAVQLMELDSCTRCGECVQWCPT 36
                                      555666667777788899************9 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00029
                           Fer4_18  55 ekgagdcidcescvkvcPtgidi 77 
                                       +++  +c++c+ c +vc  gid 
  gi|298674499|ref|YP_003726249.1|  84 SSDLYQCTTCGICETVCESGIDT 106
                                       455678***************95 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   1.8   2.3e-06    0.0025       6      22 .]      20      36 ..      15      36 .. 0.88
   2 !   10.7   2.5   0.00041      0.45       9      20 ..      89     100 ..      83     102 .. 0.89
   3 ?   -2.1   0.1       4.9   5.5e+03       9      13 ..     243     247 ..     241     249 .. 0.78
   4 ?   -2.5   0.1       6.4   7.1e+03      18      21 ..     371     374 ..     370     375 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.3e-06
                            Fer4_2  6 dtdrCigCgaCvsaCPa 22
                                      + d+C++Cg Cv+ CP+
  gi|298674499|ref|YP_003726249.1| 20 ELDSCTRCGECVQWCPT 36
                                      679*************7 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00041
                            Fer4_2   9 rCigCgaCvsaC 20 
                                        C+ Cg+C ++C
  gi|298674499|ref|YP_003726249.1|  89 QCTTCGICETVC 100
                                       5*********** PP

  == domain 3  score: -2.1 bits;  conditional E-value: 4.9
                            Fer4_2   9 rCigC 13 
                                       +C gC
  gi|298674499|ref|YP_003726249.1| 243 ACAGC 247
                                       59999 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 6.4
                            Fer4_2  18 saCP 21 
                                       saCP
  gi|298674499|ref|YP_003726249.1| 371 SACP 374
                                       79*9 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.4   0.00077      0.86      73      94 ..      15      36 ..       3      40 .. 0.77
   2 !    8.6   0.2     0.003       3.4      78      95 ..      86     103 ..      60     104 .. 0.79
   3 ?   -0.2   0.1       1.7   1.9e+03      78      88 ..     240     250 ..     212     255 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00077
                           Fer4_22 73 fkekfgesgCvGCgRCieacpv 94
                                       ++ ++  +C+ Cg C+++cp+
  gi|298674499|ref|YP_003726249.1| 15 AVQLMELDSCTRCGECVQWCPT 36
                                      5566677889999999999986 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.003
                           Fer4_22  78 gesgCvGCgRCieacpvk 95 
                                       + ++C+ Cg C+++c ++
  gi|298674499|ref|YP_003726249.1|  86 DLYQCTTCGICETVCESG 103
                                       556788888888888765 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1.7
                           Fer4_22  78 gesgCvGCgRC 88 
                                         ++C GC R 
  gi|298674499|ref|YP_003726249.1| 240 VLYACAGCYRT 250
                                       45679999885 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.6   0.00021      0.23      35      53 ..      17      36 ..       4      40 .. 0.67
   2 !    9.6   0.4   0.00086      0.97       7      26 ..      89     107 ..      80     119 .. 0.71
   3 ?   -0.7   0.3       1.5   1.7e+03      30      46 ..     233     249 ..     220     253 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00021
                           Fer4_21 35 kvve.deCvGCnlCssvCPv 53
                                      +++e d+C+ C  C++ CP+
  gi|298674499|ref|YP_003726249.1| 17 QLMElDSCTRCGECVQWCPT 36
                                      44433788888888888886 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00086
                           Fer4_21   7 kCigCgkCliaCedtshqai 26 
                                       +C  Cg C ++Ce ++++ i
  gi|298674499|ref|YP_003726249.1|  89 QCTTCGICETVCE-SGIDTI 107
                                       5667777777776.466666 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.5
                           Fer4_21  30 aktvlkvvedeCvGCnl 46 
                                       +++ +  v   C GC  
  gi|298674499|ref|YP_003726249.1| 233 KAKGASKVLYACAGCYR 249
                                       44444555668999965 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   3.8   2.4e-05     0.027       1      13 [.      24      36 ..      24      39 .. 0.91
   2 ?    6.4   3.6     0.019        21       1      14 [.      90     103 ..      90     104 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.4e-05
                            Fer4_3  1 CtgCgaCvevCPv 13
                                      Ct Cg Cv++CP+
  gi|298674499|ref|YP_003726249.1| 24 CTRCGECVQWCPT 36
                                      ************6 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.019
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       Ct Cg C+ vC +g
  gi|298674499|ref|YP_003726249.1|  90 CTTCGICETVCESG 103
                                       ***********665 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.8   2.9e-05     0.033       6      20 ..      22      36 ..      20      38 .. 0.92
   2 ?   12.4   2.2   9.8e-05      0.11       7      20 ..      89     102 ..      85     104 .. 0.85
   3 ?   -2.4   0.3       4.5     5e+03       3      10 ..     330     337 ..     329     337 .. 0.81
   4 ?   -2.5   0.3       4.9   5.5e+03      16      20 ..     371     375 ..     370     377 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.9e-05
                                      TTSSS-THHHHHSTT CS
                              Fer4  6 ekCigCGaCvevCPv 20
                                      + C++CG+Cv+ CP+
  gi|298674499|ref|YP_003726249.1| 22 DSCTRCGECVQWCPT 36
                                      89***********98 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 9.8e-05
                                       TSSS-THHHHHSTT CS
                              Fer4   7 kCigCGaCvevCPv 20 
                                        C+ CG+C+ vC  
  gi|298674499|ref|YP_003726249.1|  89 QCTTCGICETVCES 102
                                       6***********65 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 4.5
                                       EETTTSSS CS
                              Fer4   3 ideekCig 10 
                                        d+++C g
  gi|298674499|ref|YP_003726249.1| 330 KDYSRCCG 337
                                       6999**76 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 4.9
                                       HHSTT CS
                              Fer4  16 evCPv 20 
                                       ++CP+
  gi|298674499|ref|YP_003726249.1| 371 SACPF 375
                                       57885 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.4    0.0001      0.11       7      22 ..      22      37 ..      19      39 .. 0.89
   2 ?   10.5   2.4   0.00045       0.5       9      22 ..      90     103 ..      86     104 .. 0.89
   3 ?   -1.4   0.4       2.7   3.1e+03       8      14 ..     243     249 ..     243     249 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0001
                            Fer4_6  7 dkCigCgdCvrvCPeg 22
                                      d+C+ Cg+Cv  CP++
  gi|298674499|ref|YP_003726249.1| 22 DSCTRCGECVQWCPTY 37
                                      89************84 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00045
                            Fer4_6   9 CigCgdCvrvCPeg 22 
                                       C+ Cg C++vC  g
  gi|298674499|ref|YP_003726249.1|  90 CTTCGICETVCESG 103
                                       9**********876 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.7
                            Fer4_6   8 kCigCgd 14 
                                       +C gC++
  gi|298674499|ref|YP_003726249.1| 243 ACAGCYR 249
                                       5999985 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.2    0.0018       2.1       4      22 ..      20      38 ..      18      54 .. 0.84
   2 ?    2.9   0.8      0.16   1.8e+02       5      20 ..      87     102 ..      84     112 .. 0.85
   3 ?    2.4   0.1      0.24   2.7e+02      27      61 ..     344     375 ..     325     376 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0018
                           Fer4_15  4 DrdaCigcglCvaeapevf 22
                                      + d C+ cg Cv+ +p++ 
  gi|298674499|ref|YP_003726249.1| 20 ELDSCTRCGECVQWCPTYS 38
                                      5699************985 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.16
                           Fer4_15   5 rdaCigcglCvaeape 20 
                                         +C+ cg C ++++ 
  gi|298674499|ref|YP_003726249.1|  87 LYQCTTCGICETVCES 102
                                       568*******999975 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.24
                           Fer4_15  27 dglasvllddgeiaegevpddeeeaaqeAaraCPv 61 
                                       +g++++ l+   ++e++++d +e++a+   +aCP 
  gi|298674499|ref|YP_003726249.1| 344 AGIPDLALK---VGEERIEDALETDADILSSACPF 375
                                       566666665...5679***********99999995 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   2.6   0.00016      0.18       2      16 ..      22      36 ..      21      42 .. 0.91
   2 ?    8.3   2.7    0.0033       3.7       4      17 .]      90     103 ..      84     103 .. 0.91
   3 ?   -1.6   0.1       4.7   5.3e+03       3       7 ..     243     247 ..     241     249 .. 0.67
   4 ?   -1.7   0.4       5.1   5.7e+03       7      10 ..     373     376 ..     371     378 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00016
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      ++C++Cg Cv  CP+
  gi|298674499|ref|YP_003726249.1| 22 DSCTRCGECVQWCPT 36
                                      89***********96 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0033
                            Fer4_4   4 CigCgsCvaaCPqg 17 
                                       C+ Cg C+ +C++g
  gi|298674499|ref|YP_003726249.1|  90 CTTCGICETVCESG 103
                                       ***********975 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 4.7
                            Fer4_4   3 rCigC 7  
                                        C gC
  gi|298674499|ref|YP_003726249.1| 243 ACAGC 247
                                       47777 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 5.1
                            Fer4_4   7 CgsC 10 
                                       C+ C
  gi|298674499|ref|YP_003726249.1| 373 CPFC 376
                                       6666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.54
# Mc/sec: 2281.83
//
Query:       gi|298674500|ref|YP_003726250.1|  [L=81]
Description: hypothetical protein Metev_0543 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.019   15.0   0.0      0.038   14.1   0.0    1.5  1  UBA_2     Ubiquitin associated domain (UBA)


Domain annotation for each model (and alignments):
>> UBA_2  Ubiquitin associated domain (UBA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.1e-06     0.038      32      46 .]      42      56 ..      31      56 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.1e-06
                             UBA_2 32 ssneIkDAYlLmkEN 46
                                        ne++DAYlL+  N
  gi|298674500|ref|YP_003726250.1| 42 ILNEVRDAYLLLDSN 56
                                      57**********988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 557.59
//
Query:       gi|298674501|ref|YP_003726251.1|  [L=143]
Description: hypothetical protein Metev_0544 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00072   19.8   0.4    0.00098   19.4   0.4    1.1  1  MecA_N          NTF2-like N-terminal transpeptidase domain
     0.0031   17.8   0.0     0.0046   17.2   0.0    1.3  1  DUF4878         Domain of unknown function (DUF4878)
  ------ inclusion threshold ------
      0.043   13.6   0.2      0.069   12.9   0.2    1.4  1  Ig_mannosidase  Ig-fold domain
      0.089   13.6   0.2       0.14   13.0   0.2    1.4  1  DUF3887         Protein of unknown function (DUF3887)


Domain annotation for each model (and alignments):
>> MecA_N  NTF2-like N-terminal transpeptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.4   2.2e-07   0.00098       1     103 [.      34     135 ..      34     135 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.2e-07
                                       HHHHHHHHHHHHHHTT-HHHHHC.TB--BSSBSS-HHHHHHHHHHHCCCTT-EEEEEEEEEEEEEETTEEEEEEEEE CS
                            MecA_N   1 saeeaaetFldawakgdykkaas.llseqskkeisekeavekyqaiydglqvkklkieakkvkkdkentaeipykvs 76 
                                       ++ee+ +++++  ++ +++++++ lls+++k ++++ e+++      +   +++ +i   +  +d+++ + ++  v 
  gi|298674501|ref|YP_003726251.1|  34 TPEETLDDYISYYNSSEFNNIYDeLLSSDVKDDYTRDEFHNLNRISEATFRINGYEI---TGSSDENGSVILTVDVI 107
                                       599*******************73578888***********99999999********...788888999999999** PP

                                       EEETTEEE.EEEEEEEEEEEETTEEEE- CS
                            MecA_N  77 mntpagki.ktldskltltkeeeewkid 103
                                       +n++a  i +t   + +++ e+++wk +
  gi|298674501|ref|YP_003726251.1| 108 WNVNAFDIqRTKTHTIEFVVEDNRWKMN 135
                                       ********777777889********975 PP

>> DUF4878  Domain of unknown function (DUF4878)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0     1e-06    0.0046       5     111 ..      31     134 ..      25     135 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1e-06
                           DUF4878   5 ekqtpeeavknFleavkeGdvedaikyltestreedalaeklkgkfkelkakaekkkekqgnlkeveikdeeesgdt 81 
                                        + tpee+++++++  +++++++  + l  s+ + d + ++    f +     ++ +e++  ++ +ei  + +++++
  gi|298674501|ref|YP_003726251.1|  31 PESTPEETLDDYISYYNSSEFNNIYDELLSSDVKDDYTRDE----FHN----LNRISEATFRINGYEITGSSDENGS 99 
                                       345*******************9988888888888888888....665....99*********************** PP

                           DUF4878  82 AvvtVkv.....tlkdGkekkeeieliKedgkWkv 111
                                       ++ tV v     +++   +k+ +ie + ed++Wk 
  gi|298674501|ref|YP_003726251.1| 100 VILTVDViwnvnAFDIQRTKTHTIEFVVEDNRWKM 134
                                       *****98332222334567888999999*****97 PP

>> Ig_mannosidase  Ig-fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   1.5e-05     0.069      33      61 ..     103     129 ..      74     141 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.5e-05
                    Ig_mannosidase  33 elsgvdgrFsdNgFdLlpgesktvtftv.n 61 
                                       +   vd+++  N+Fd+   ++ t++f+v +
  gi|298674501|ref|YP_003726251.1| 103 T---VDVIWNVNAFDIQRTKTHTIEFVVeD 129
                                       3...899999******************32 PP

>> DUF3887  Protein of unknown function (DUF3887)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   3.2e-05      0.14       2      41 ..      40      80 ..      39     116 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.2e-05
                           DUF3887  2 eeiiellnsgdyeeaqdlf.sedlkealseetleeawkalk 41
                                      +++i+++ns+++ +++d + s+d+k+ ++ +++ + +  ++
  gi|298674501|ref|YP_003726251.1| 40 DDYISYYNSSEFNNIYDELlSSDVKDDYTRDEFHNLNRISE 80
                                      689**************999*********999987765544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1029.99
//
Query:       gi|298674502|ref|YP_003726252.1|  [L=215]
Description: hypothetical protein Metev_0545 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-46  155.7  10.0    7.6e-46  155.4  10.0    1.1  1  DUF116    Protein of unknown function DUF116
  ------ inclusion threshold ------
        5.6    6.1   5.6        8.4    5.5   5.6    1.1  1  Zip       ZIP Zinc transporter


Domain annotation for each model (and alignments):
>> DUF116  Protein of unknown function DUF116
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.4  10.0   8.5e-50   7.6e-46       3     154 ..      56     206 ..      54     207 .. 0.97

  Alignments for each domain:
  == domain 1  score: 155.4 bits;  conditional E-value: 8.5e-50
                            DUF116   3 lkllgrllgldkdklkrvfievnnklvrkkfkkvppekrllllPhClraadCpaklte.eglnCkrCgkCkigelkk 78 
                                       +kl++r+++++++ +++++iev n+++ ++fk+v + k +++lP+Clr+ +C+a++++ +g++C++Cg C+ig++++
  gi|298674502|ref|YP_003726252.1|  56 AKLICRTCSIKESIVDDIIIEVGNAVMLERFKQV-NGKCAVILPQCLRHPNCKARCDPiTGYECEKCGLCDIGTICE 131
                                       799******************************7.8999************************************** PP

                            DUF116  79 laeklgykvyivtggtlarkiikekkpkaiigvaCerdltegiqdlkklpvigqlvllekggCinTkvdveeleel 154
                                       +aek+++kv++v+g++++rkiik+++p+a+igvaC+++lte++q+++k  +++q+v l k+gC+nT+vdv+e+ ++
  gi|298674502|ref|YP_003726252.1| 132 AAEKYNFKVFVVPGDSFVRKIIKSYRPHACIGVACHMELTESMQEVSK-YMPVQGVWLLKDGCYNTEVDVDEVIRK 206
                                       ***********************************************9.99*********************9875 PP

>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   5.6   0.00093       8.4       4      43 ..      12      51 ..      10      52 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.00093
                               Zip  4 kilaiiaililsllgllgpllvpkiskllsklllslllaf 43
                                       +++++a++il+l++ll+ +++ k++k+l+ ++++++l+f
  gi|298674502|ref|YP_003726252.1| 12 FVYLVVAVIILTLISLLIGIYSYKKNKSLFPNFIFFMLYF 51
                                      689*************************999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1147  (0.0639746); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1535.24
//
Query:       gi|298674503|ref|YP_003726253.1|  [L=232]
Description: hypothetical protein Metev_0546 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-42  143.7   0.8    3.8e-42  143.4   0.8    1.1  1  DUF116    Protein of unknown function DUF116


Domain annotation for each model (and alignments):
>> DUF116  Protein of unknown function DUF116
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.4   0.8   2.1e-46   3.8e-42       4     154 ..      54     201 ..      51     202 .. 0.96

  Alignments for each domain:
  == domain 1  score: 143.4 bits;  conditional E-value: 2.1e-46
                            DUF116   4 kllgrllgldkdklkrvfievnnklvrkkfkkvppekrllllPhClraadCpaklteeglnCkrCgkCkigelkkla 80 
                                       k+l++ ++ d++kl++ +++++n++++++fkk  +++rl+l+PhC+r+ dCpa+ t+ g++C +C+kC ++++kk a
  gi|298674503|ref|YP_003726253.1|  54 KILFQKFS-DSSKLDKLMVSLRNTANKSSFKK--TRNRLILAPHCMRSLDCPASSTRFGIKCISCNKCILASIKKDA 127
                                       66777676.899********************..8****************************************** PP

                            DUF116  81 eklgykvyivtggtlarkiikekkpkaiigvaCerdltegiqdlkklpvigqlvllekggCinTkvdveeleel 154
                                       e+++yk+yiv g++++r+i+k++ +++ +  aC+++l++ ++ lk+ ++++++v+l ++gC+nT++d+++l+++
  gi|298674503|ref|YP_003726253.1| 128 ENYNYKLYIVAGSSYIRHIVKKEPVDGALLLACYYELNKVMRYLKQKNIVTYGVPLLEDGCYNTTIDYNNLKKT 201
                                       ***********************************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1092  (0.0609069); expected 358.6 (0.02)
Passed bias filter:                      623  (0.0347482); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1321.53
//
Query:       gi|298674504|ref|YP_003726254.1|  [L=381]
Description: methanogenesis marker protein 9 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.5e-19   68.0   0.2    1.7e-18   66.8   0.2    1.5  1  Dus            Dihydrouridine synthase (Dus)
    1.5e-08   34.1   1.0    2.3e-08   33.5   1.0    1.2  1  IMPDH          IMP dehydrogenase / GMP reductase domain
      7e-08   32.2   0.5    6.2e-07   29.1   0.1    2.1  2  His_biosynth   Histidine biosynthesis protein
     0.0028   17.8   0.0        0.2   11.8   0.0    2.3  2  Fer4_14        4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.021   14.1   0.1       0.12   11.6   0.0    2.2  3  Oxidored_FMN   NADH:flavin oxidoreductase / NADH oxidase fami
      0.027   14.2   0.2        0.1   12.3   0.0    2.0  2  TPP_enzyme_M   Thiamine pyrophosphate enzyme, central domain
       0.21   11.1   0.7        6.3    6.3   0.1    2.1  2  PP_kinase_C_1  Polyphosphate kinase C-terminal domain 1


Domain annotation for each model (and alignments):
>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.8   0.2   6.8e-22   1.7e-18      35     231 ..      68     257 ..      20     273 .. 0.81

  Alignments for each domain:
  == domain 1  score: 66.8 bits;  conditional E-value: 6.8e-22
                                       SS---HHHHHHH-GGGGGT..SCEEEEEE-S-HHHHHHHHHHHHHTT-SCEEEEESSTTEEETTEEEGGGGGGSHHH CS
                               Dus  35 aivreekvrirmlseeeee..tplavQlggsdpallaeaAklvadlgadeIdlNvGCPskkvtrggaGaaLlrkpdl 109
                                       ++++++  ++++ + ++ +  + +av + ++ p+ l eaA+++++    + +l + C ++++ + g+G aL+++   
  gi|298674504|ref|YP_003726254.1|  68 EFITDNPLQFLKEEINNVDtgSVVAVNVRSATPEPLIEAAQIAKE-SDAILELDAHCRQEEMVNIGVGEALMHDTSR 143
                                       556666666665555555566899*********************.67789************************** PP

                                       HHHHHHHHHCCSSS-EEEEEESESSTTTC.HHHHHHHHHHCT-SEEEEESSECCCTT-CG--CHHHHHHHHH-SS-E CS
                               Dus 110 vaqivkavvkaveiPvtvkirigiddeeenalelakiveaaGaqaltvHgRtraqnyegtadweaIkevkqavsipv 186
                                       +a+ +++++  +++ ++vkir  + d     +el + +e aGa+ l + +     + + tad++aI++++++v+ ++
  gi|298674504|ref|YP_003726254.1| 144 LADWIQKIK-ETGVVLSVKIRANVVD----DVELSRQIESAGADILHIDAT---LEGKNTADLKAIRKIRDSVRMTL 212
                                       *******96.58999******99985....477************999763...344559***************** PP

                                       EEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHH.HHHHHH CS
                               Dus 187 iaNGdIkdaedaqaileetGadgvmigrgalgnPwlfae.stavkt 231
                                       i+N  I++++da++i ++ Gad v ++rg   nP+l++e ++ v+ 
  gi|298674504|ref|YP_003726254.1| 213 IGNNSITEFSDAKDIFSR-GADLVSVSRGVMDNPYLIDElVESVND 257
                                       ******************.******************987666655 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   1.0   8.9e-12   2.3e-08      29     175 ..      11     240 ..       4     241 .. 0.87

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 8.9e-12
                                       TTEEESSSEEE-SSTTT-SHHHHHHHHHTTSEEEE-SSS-HHHHHHHHHHHHTS....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                             IMPDH  29 kkiklniPlvsaamdtvtesemAialareGgigvihknlsieeqaeevkkvkrs....................... 82 
                                       ++i+l+ P+   +m  vt+s+ A + a++ g+ ++      ++  e  +++ +                        
  gi|298674504|ref|YP_003726254.1|  11 DNISLKNPIALGPMAGVTDSNFANKYAKNAGLVILGGFNLDDKTNEAASRMAERgreefitdnplqflkeeinnvdt 87 
                                       79******************************99988777777777777776667889******************* PP

                                       ............................................................TTSXBXTTSXB-EEEEE CS
                                       ............................................................xxxxxxxxxxxxxxxxx RF
                             IMPDH  83 ............................................................pnaakdekgrllvgaav 99 
                                                                                                    ++ k++   l v    
  gi|298674504|ref|YP_003726254.1|  88 gsvvavnvrsatpeplieaaqiakesdaileldahcrqeemvnigvgealmhdtsrladwIQKIKETGVVLSVKIRA 164
                                       *****************************************************998776555555555555555555 PP

                                       -SSTTHHHHHHHHHHTT-SEEEEE-S.TSSSHHHHHHHHHHHHHTTTSEEEEEE.E-SHHHHHHHHHTT-SEEEE-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 100 gvkedalervkalveagvdvlvvdsa.hghsekvleavkeikkkveeveviaGn.vataegakaLieagadavkvGi 174
                                       +v  d+ e  +++ +ag+d+l +d++ +g+++  l+a+++i+++v ++++i+ n +++ + ak++++ gad v v  
  gi|298674504|ref|YP_003726254.1| 165 NVV-DDVELSRQIESAGADILHIDATlEGKNTADLKAIRKIRDSV-RMTLIGNNsITEFSDAKDIFSRGADLVSVSR 239
                                       555.567788899***********6549*****************.799998874666799************9965 PP

                                       S CS
                                       x RF
                             IMPDH 175 G 175
                                       G
  gi|298674504|ref|YP_003726254.1| 240 G 240
                                       5 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.099   2.5e+02      98     133 ..     130     165 ..     109     168 .. 0.81
   2 !   29.1   0.1   2.4e-10   6.2e-07      30     120 ..     168     256 ..     159     260 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.099
                                       EEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEEC CS
                      His_biosynth  98 kviigtaavknpelikelaekfgsqkivvaiDarrg 133
                                       ++ +g a +++ + + ++++k+ +  +v+++ +r++
  gi|298674504|ref|YP_003726254.1| 130 NIGVGEALMHDTSRLADWIQKIKETGVVLSVKIRAN 165
                                       567899999999999999999999999999988875 PP

  == domain 2  score: 29.1 bits;  conditional E-value: 2.4e-10
                                       SHHHHHHHHHHHT-SEEEEEEHHHHCTTHH.HHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHH CS
                      His_biosynth  30 dpvelakryeeegadelhvvDldaakegre.anldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaa 105
                                       d vel ++ e++gad lh   +da+ eg++ a+l+++++i+++v++++     I +++d+++++++gad v+++  +
  gi|298674504|ref|YP_003726254.1| 168 DDVELSRQIESAGADILH---IDATLEGKNtADLKAIRKIRDSVRMTLIGNNSITEFSDAKDIFSRGADLVSVSRGV 241
                                       669999*********999...5888877661578***************99************************** PP

                                       HH-THHHHHHHHHHC CS
                      His_biosynth 106 vknpelikelaekfg 120
                                       ++np li+el+e ++
  gi|298674504|ref|YP_003726254.1| 242 MDNPYLIDELVESVN 256
                                       ***********9887 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.025        65      39      77 ..      29      68 ..       7      93 .. 0.77
   2 !   11.8   0.0   7.8e-05       0.2      37      99 ..     116     176 ..     101     193 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.025
                           Fer4_14 39 k.dlkkseikiqglvltGGePLhyenkkellklvkrlkee 77
                                      + ++ +++ k +glv++GG  L  + +++  ++ +r +ee
  gi|298674504|ref|YP_003726254.1| 29 DsNFANKYAKNAGLVILGGFNLDDKTNEAASRMAERGREE 68
                                      44678899999********887666666666666665555 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 7.8e-05
                           Fer4_14  37 ilkdlkkseikiqglvltG.GePLhyenkkellklvkrlkeeypekkiwletngtleielektp 99 
                                       il    + +++++++v  G Ge L++ +++ l + ++++ke +  +++++  n + ++el +  
  gi|298674504|ref|YP_003726254.1| 116 IL--ELDAHCRQEEMVNIGvGEALMH-DTSRLADWIQKIKETGVVLSVKIRANVVDDVELSRQI 176
                                       44..3344555667888888****88.9*****************************9998433 PP

>> Oxidored_FMN  NADH:flavin oxidoreductase / NADH oxidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.92   2.4e+03       6      28 ..       8      30 ..       5      40 .. 0.81
   2 ?   -0.8   0.0      0.29   7.3e+02     285     336 ..      93     152 ..      78     158 .. 0.64
   3 ?   11.6   0.0   4.6e-05      0.12     281     338 ..     198     254 ..     135     257 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.92
                                      EEETTEEESSSEEE----S-TTT CS
                      Oxidored_FMN  6 ikignmtLknRivmapmtrlral 28
                                      +++ n  Lkn i+ +pm  +  +
  gi|298674504|ref|YP_003726254.1|  8 LQVDNISLKNPIALGPMAGVTDS 30
                                      689999**********9877654 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.29
                                       HHHCCCHSSEEEE-SS--SHHHHHHHHHT....TS-SEEEESTHHHH-....TTHHHHHH CS
                      Oxidored_FMN 285 efvkevwkkplitvgriadeekaaeivae....geadLvamgReflad....pdlveklk 336
                                        +v++   +pli + +ia+e++a   +      +e   +++g +++ d    +d+++k+k
  gi|298674504|ref|YP_003726254.1|  93 VNVRSATPEPLIEAAQIAKESDAILELDAhcrqEEMVNIGVGEALMHDtsrlADWIQKIK 152
                                       578889999999999999999543322222311444445666677766433345666665 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 4.6e-05
                                       THHHHHHCCCHSSEEEE-SS--SHHHHHHHHHTTS-SEEEESTHHHH-TTHHHHHHCC CS
                      Oxidored_FMN 281 ekntefvkevwkkplitvgriadeekaaeivaegeadLvamgRefladpdlveklkkg 338
                                        k   +++  + + li+ ++i++ ++a++i ++g adLv++ R ++ +p l++ l + 
  gi|298674504|ref|YP_003726254.1| 198 LKAIRKIRDSVRMTLIGNNSITEFSDAKDIFSRG-ADLVSVSRGVMDNPYLIDELVES 254
                                       2556899******************888888876.8***************9887665 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     4e-05       0.1      53     100 ..      14      61 ..       9      96 .. 0.82
   2 ?   -1.4   0.1      0.71   1.8e+03      81     134 ..     157     208 ..     136     210 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4e-05
                                       -TTSTTEEE.ESGGGSCHHHHHHHHH-SEEEEES-SSSTCCCTTTTTTT CS
                      TPP_enzyme_M  53 pedhplylg.mlglhgskaanealeeaDlvlalGarfddirttgsepef 100
                                       + ++p  lg m+g++ s+ an+ +++a lv++ G ++dd  t +  +++
  gi|298674504|ref|YP_003726254.1|  14 SLKNPIALGpMAGVTDSNFANKYAKNAGLVILGGFNLDD-KTNEAASRM 61 
                                       5679999********************************.444433344 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.71
                                       EEEES-SSSTCCCTTTTTTTTTT-.EEEEEESSCCCCTTCC--SEEEECTHHHHH CS
                      TPP_enzyme_M  81 vlalGarfddirttgsepefapea.kiihididpaeigknyqvdlaivgdvketl 134
                                       vl +  r + +  ++ ++++ + +  i+hid  ++  gkn  +dl  + ++++++
  gi|298674504|ref|YP_003726254.1| 157 VLSVKIRANVVDDVELSRQIESAGaDILHID--ATLEGKNT-ADLKAIRKIRDSV 208
                                       5555555555544554445555555777777..33335554.7787777777776 PP

>> PP_kinase_C_1  Polyphosphate kinase C-terminal domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1    0.0024       6.3      49      89 ..      96     138 ..      80     145 .. 0.83
   2 ?    3.3   0.1     0.021        54      58      97 ..     146     185 ..     141     214 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0024
                                       --HHHHHHHHHHHTT-EEEEEES--S..SS--HHHHHHHHHHH CS
                     PP_kinase_C_1  49 dskivkaLieAaengkqvtvlvElkA..rfdeenNiewakkle 89 
                                       +s+  + LieAa+  k+  +++El A  r +e  Ni + ++l 
  gi|298674504|ref|YP_003726254.1|  96 RSATPEPLIEAAQIAKESDAILELDAhcRQEEMVNIGVGEALM 138
                                       6677788*****************9855678888999888876 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.021
                                       HHHHTT-EEEEEES--SSS--HHHHHHHHHHHHHT-EEEE CS
                     PP_kinase_C_1  58 eAaengkqvtvlvElkArfdeenNiewakkleeagvkvvy 97 
                                       +  ++ k+  v++ +k r +  + +e+++++e+ag+++++
  gi|298674504|ref|YP_003726254.1| 146 DWIQKIKETGVVLSVKIRANVVDDVELSRQIESAGADILH 185
                                       55677899999*************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.71u 0.38s 00:00:01.08 Elapsed: 00:00:00.57
# Mc/sec: 2020.10
//
Query:       gi|298674505|ref|YP_003726255.1|  [L=315]
Description: triphosphoribosyl-dephospho-CoA protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.2e-76  255.2   0.0      1e-75  255.0   0.0    1.0  1  CitG      ATP:dephospho-CoA triphosphoribosyl transferase
     0.0038   17.3   0.1       0.46   10.6   0.1    2.2  2  ADIP      Afadin- and alpha -actinin-Binding


Domain annotation for each model (and alignments):
>> CitG  ATP:dephospho-CoA triphosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  255.0   0.0   1.2e-79     1e-75       2     281 .]      23     308 ..      22     308 .. 0.93

  Alignments for each domain:
  == domain 1  score: 255.0 bits;  conditional E-value: 1.2e-79
                                       XXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXHHHHHHHHHTTHHHHHHHH...........HH--HHHHHHHHHHH CS
                              CitG   2 elavlAlllEvsatpKPGlVdrrdsgahdDmdfetFlaSaealapyfeeaaaaGleakalfeelrsiGelaekamla 78 
                                       ++a+l+++lEvsa+pKPG+Vdr++++   D+ +e+F+aSa+ ++p++e+a+          ++  +iG+l+++ + +
  gi|298674505|ref|YP_003726255.1|  23 RCAQLSMVLEVSAFPKPGNVDRDHNY--IDTYYEHFMASAIGVYPVIEDAS----------KSSHGIGKLIKRSVSE 87 
                                       79************************..***********************..........899************* PP

                                       H...------HHHHHHHHHHHHTTTTS-.......SHHHHHHHHHHHHHT--HHHHHHH.HHHHHH--......... CS
                              CitG  79 a...tggvNThkGaifllgllaaaagrraaeeeeasleelveeaaevlaeltvedavaf.rairlakv......... 142
                                       +   ++g+NTh+Ga++ll++l +aag+ +a+++++sl+el++ a++++++++v dav+f + +rla v         
  gi|298674505|ref|YP_003726255.1|  88 SvnwQKGGNTHFGAFILLIPLTMAAGKIMAHKSQFSLNELINCAHDLVKNTDVLDAVDFyESFRLAGVrvnnvddfd 164
                                       ********************************************************************999887554 PP

                                       ..---..HHHHHH.TT--HHHHHHTS-TT-HHHHHHHHTSHHHHHHHH........HH-SSHHHHHHHHHHHHHHS- CS
                              CitG 143 ..eel..kdelvekksltlgevlelsygvdgirgeaasgFpsvfeialpalrealasgadlndalvqallallaelp 215
                                         + +  +d+l e +++tl++ +e++ ++d +++e+++gF+++ ++a   ++++ ++ +++n+ +v+a+l++l+e++
  gi|298674505|ref|YP_003726255.1| 165 lqD-EnsIDSLYE-QNITLYDLMEIAKNYDIVANEWSEGFNRCSQCAEIIIEKMKNNYNNINNTIVYAFLKILSENK 239
                                       432.145666666.9*********************************9999987666******************* PP

                                       -HHHHHHHHHHHHHHHHHHHH............H-.SHHHHHHHHHHHHHHT---HHHHHHHHHHHHHH CS
                              CitG 216 DtnilrrgGaegaeevqeeArallaa..ggvaaea.glealeeldrelvernisPGgsADllaatlfla 281
                                       Dt+i ++++ e+a +v+ +A ++++a  ++  + +     ++++drel +++i+PG++AD+++a+l++a
  gi|298674505|ref|YP_003726255.1| 240 DTFIETKFDTETAVYVSTKASEIISAleEQNTDFEsMIPDIQKFDRELLDKKINPGSTADITIAGLYIA 308
                                       **************************8844455555999***************************985 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.5   0.0    0.0039        35      27      49 ..     117     139 ..      91     140 .. 0.84
   2 !   10.6   0.1   5.1e-05      0.46      13     103 ..     199     291 ..     198     297 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0039
                              ADIP  27 tekveeniaaiinviysLlqard 49 
                                       + k++ +++++in+ ++L++ +d
  gi|298674505|ref|YP_003726255.1| 117 AHKSQFSLNELINCAHDLVKNTD 139
                                       568999*************9875 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 5.1e-05
                              ADIP  13 srGylrskllfdtatekveeniaaiinv.iysLlqardrdleqreslnetirkleaeierlqskierlktqleqler 88 
                                       s G++r ++  + + ek ++n+++i n+ +y+ l+ +++++++  +++ + ++  + +++ +  i+ l++q++++e+
  gi|298674505|ref|YP_003726255.1| 199 SEGFNRCSQCAEIIIEKMKNNYNNINNTiVYAFLKILSENKDTFIETKFDTETAVYVSTKASEIISALEEQNTDFES 275
                                       5677777777777778889999999995269************9999999999999999999**************9 PP

                              ADIP  89 ela.lvqakerqlekk 103
                                        +   ++++   l kk
  gi|298674505|ref|YP_003726255.1| 276 MIPdIQKFDRELLDKK 291
                                       9985666665555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1076  (0.0600145); expected 358.6 (0.02)
Passed bias filter:                      624  (0.0348039); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.38s 00:00:01.00 Elapsed: 00:00:00.55
# Mc/sec: 1729.48
//
Query:       gi|298674506|ref|YP_003726256.1|  [L=199]
Description: hypothetical protein Metev_0549 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.1e-49  165.8   0.2    9.2e-49  165.6   0.2    1.0  1  DUF447    Protein of unknown function (DUF447)
  ------ inclusion threshold ------
      0.028   14.8   1.9       0.18   12.2   0.3    2.2  2  RPM2      Mitochondrial ribonuclease P subunit (RPM2)


Domain annotation for each model (and alignments):
>> DUF447  Protein of unknown function (DUF447)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.6   0.2     1e-52   9.2e-49       1     175 [.      18     192 ..      18     193 .. 0.98

  Alignments for each domain:
  == domain 1  score: 165.6 bits;  conditional E-value: 1e-52
                                       EEEEEEEE-TT-EEEEEEEEEESSSEEEEEEETTSHHHHHHHHHSEEEEEE---HHHHHHHHHS---GGGEEEETTT CS
                            DUF447   1 yEvivtTksekrpnaaPiGvivkgdkvvlrlfkgsrTleNllengelvinvtdDpllfakaalgdleesdfdsetkp 77 
                                       +E+i+tT  ++ pnaaP+G+i+k+d + +rlfkgs+T+eN+++++ lv+nv+ Dp++fa++++ +l +++fd   ++
  gi|298674506|ref|YP_003726256.1|  18 SETIITTGTDS-PNAAPMGLIRKDDRIQIRLFKGSQTYENVVNEKCLVANVVIDPVVFARSTFTNLCDEEFDTVSVN 93 
                                       6******9977.****************************************************************9 PP

                                       C.TT.EETT-SEEEEEEEEEECTCECCEEEEEEEEEEEEETTB---B-HHHHHHHHHHHHHHCCCCSHHHHHHHHHH CS
                            DUF447  78 a.kiavlksaeawveveveevegdsealelelepvkeeileervkpfnRgdaaviEaaVlatRldiedkeklleeie 153
                                       + k ++lk+a ++v +e+ +++ +++ l++ + p+ + i+++++k+ nRg++av++a+++atR+ + d+ek+l+ + 
  gi|298674506|ref|YP_003726256.1|  94 NrKHPFLKNALSYVIFECSDIRYTKNTLVADVLPLYACINRNVIKAPNRGFNAVLDALIHATRYRVFDDEKYLNMVY 170
                                       98888************************************************************************ PP

                                       HHHHHHHHH--HHHHHHHHHHH CS
                            DUF447 154 ylssvikktggerekealellk 175
                                       +l++++kk+gg++ek+a+++l+
  gi|298674506|ref|YP_003726256.1| 171 ELNNTVKKCGGSKEKRAMKILY 192
                                       *******************996 PP

>> RPM2  Mitochondrial ribonuclease P subunit (RPM2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1     0.035   3.1e+02      49      84 ..      61      96 ..      36     106 .. 0.78
   2 ?   12.2   0.3     2e-05      0.18      37      89 ..     118     174 ..      99     185 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.035
                              RPM2 49 ksLkrneivpslelfekvLksivkrdlDnedidnkl 84
                                      k L  n +++++      ++ ++  ++D   ++n+ 
  gi|298674506|ref|YP_003726256.1| 61 KCLVANVVIDPVVFARSTFTNLCDEEFDTVSVNNRK 96
                                      788999999999999999999999999998888875 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 2e-05
                              RPM2  37 ekkeynkinalyksLkrneivpslelfekvLksivk....rdlDnedidnklveLLt 89 
                                       +++    + +ly  + rn i  +   f+ vL+++++    r +D+e   n ++eL +
  gi|298674506|ref|YP_003726256.1| 118 KNTLVADVLPLYACINRNVIKAPNRGFNAVLDALIHatryRVFDDEKYLNMVYELNN 174
                                       445567899***********999999*****99975444478999999998888866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.55
# Mc/sec: 1099.12
//
Query:       gi|298674507|ref|YP_003726257.1|  [L=223]
Description: PHP domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.3e-17   61.1   0.0      2e-16   59.5   0.0    1.8  2  PHP_C       PHP-associated
    6.3e-11   42.9   0.0    6.8e-11   42.7   0.0    1.2  1  PHP         PHP domain
      0.001   19.0   0.1      0.033   14.2   0.0    2.4  2  DbpA        DbpA RNA binding domain
  ------ inclusion threshold ------
      0.042   13.2   0.1       0.06   12.7   0.1    1.3  1  TatD_DNase  TatD related DNase


Domain annotation for each model (and alignments):
>> PHP_C  PHP-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0         1   4.5e+03       9      19 ..      26      36 ..      22      37 .. 0.80
   2 !   59.5   0.0   4.5e-20     2e-16       4      55 ..     142     193 ..     140     194 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1
                             PHP_C  9 rfAeklglpgt 19
                                      +fAek+gl ++
  gi|298674507|ref|YP_003726257.1| 26 SFAEKNGLDAV 36
                                      69***999766 PP

  == domain 2  score: 59.5 bits;  conditional E-value: 4.5e-20
                             PHP_C   4 NrrArrfAeklglpgtgGSDAHrleeVGrayTefeepiatpdelleairegr 55 
                                       N++Arr+A+ +++p  gGSD+H++++VG+ yT +e +++tp+++++ai++g+
  gi|298674507|ref|YP_003726257.1| 142 NDEARRAAQLHNIPEAGGSDSHIPDTVGQTYTIVEVSENTPEAIISAIKNGT 193
                                       9*************************************************96 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.0   1.5e-14   6.8e-11       1      74 [.       6      83 ..       6     209 .. 0.76

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 1.5e-14
                                      EEEE--CCC--.S-H..HHHHHHHHHCT-SEEEEEEEEBTTHHHHHHHHHHHHTTTTSEEEEEEE.............. CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...... RF
                               PHP  1 dlHvHteyslldgalsieelvkkakelglkaiaiTDhgnlfgyvefykaakkkykagikpiiGleayvaddse...... 73
                                      d HvH+ +s   ++ ++e ++  a++ gl+a+ai Dh+ + g +e  k akk   ++i++i G+e++ ++++       
  gi|298674507|ref|YP_003726257.1|  6 DVHVHSCFSKD-SNSKLESIISFAEKNGLDAVAICDHDTVEGGIEGLKVAKKLG-SKITVIPGIEVTSTKGHIlvlgvd 82
                                      78*******66.67777*********************************7655.89********66655554445444 PP

                                      . CS
                                      x RF
                               PHP 74 k 74
                                      k
  gi|298674507|ref|YP_003726257.1| 83 K 83
                                      0 PP

>> DbpA  DbpA RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.044     2e+02      27      56 ..     121     150 ..     116     154 .. 0.87
   2 !   14.2   0.0   7.4e-06     0.033      37      70 ..     168     203 ..     167     205 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.044
                                       B-GGGEEEEEE-SS-EEEEE-TT-HHHHHH CS
                              DbpA  27 lsgkdIGkIdildkfSfvevpkekaeevlk 56 
                                       ++g dI ++++l++ +f + p+++a+++ +
  gi|298674507|ref|YP_003726257.1| 121 VDGIDIDAVEVLNSRCFTDKPNDEARRAAQ 150
                                       6899*****************999998765 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 7.4e-06
                                       E-SS-EEEEE-TT-HHHHHHHHTT--SS..S----E CS
                              DbpA  37 ildkfSfvevpkekaeevlkalkkkkik..Grkvrv 70 
                                       + ++++ vev+++ +e +++a+k+++i   G+kv v
  gi|298674507|ref|YP_003726257.1| 168 VGQTYTIVEVSENTPEAIISAIKNGTISagGKKVPV 203
                                       6789********************998766888766 PP

>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   1.3e-05      0.06       1      67 [.       5      73 ..       5     109 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.3e-05
                                      EEEEE-TTS.CCCTTTHHHHHHHHHHTTEEEEEEE-SSGG.GHHHHHHHHTT.TTTEEEEE---GGGGG CS
                        TatD_DNase  1 iDaHcHlds.kefeedreeileraeeagvaavvvvgtssk.dskavlelakkypnkvyavlGiHPnevd 67
                                      iD H+H  + k+ +++ e+i++ ae++g+ av+ ++ +++    + l++akk  +k+ +  Gi +++ +
  gi|298674507|ref|YP_003726257.1|  5 IDVHVHSCFsKDSNSKLESIISFAEKNGLDAVAICDHDTVeGGIEGLKVAKKLGSKITVIPGIEVTSTK 73
                                      8********9999999****************8888888746679999999999999999999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.38s 00:00:00.95 Elapsed: 00:00:00.56
# Mc/sec: 1189.45
//
Query:       gi|298674508|ref|YP_003726258.1|  [L=418]
Description: GTP-binding protein HflX [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-24   87.0   0.0    2.1e-24   86.0   0.0    1.6  1  GTP-bdg_N      GTP-binding GTPase N-terminal
    3.5e-22   78.6   0.1    8.3e-22   77.4   0.1    1.7  1  MMR_HSR1       50S ribosome-binding GTPase
    8.3e-17   61.6   2.0    1.8e-16   60.5   2.0    1.6  1  GTP-bdg_M      GTP-binding GTPase Middle Region
    4.6e-10   39.2   0.8    7.7e-10   38.5   0.1    1.8  2  FeoB_N         Ferrous iron transport protein B
    3.4e-09   36.8   0.4    0.00087   19.2   0.1    2.4  2  RsgA_GTPase    RsgA GTPase
    3.8e-07   30.1   0.1      1e-06   28.7   0.1    1.7  1  MMR_HSR1_Xtn   C-terminal region of MMR_HSR1 domain
    1.4e-06   28.0   0.0    0.00016   21.3   0.0    2.5  2  GTP_EFTU       Elongation factor Tu GTP binding domain
    8.9e-05   21.9   0.7     0.0098   15.3   0.0    2.4  2  Gtr1_RagA      Gtr1/RagA G protein conserved region
     0.0026   17.8   0.8      0.029   14.4   0.0    2.5  3  Dynamin_N      Dynamin family
     0.0038   16.8   2.6       0.25   10.9   0.4    3.2  3  cobW           CobW/HypB/UreG, nucleotide-binding domain
     0.0099   16.1   0.0      0.021   15.0   0.0    1.5  1  MnmE_helical   MnmE helical domain
  ------ inclusion threshold ------
      0.068   13.4   0.1         22    5.3   0.0    2.6  2  Roc            Ras of Complex, Roc, domain of DAPkinase
      0.077   13.1   0.8       0.18   11.9   0.1    2.0  2  AHH            A nuclease family of the HNH/ENDO VII superfam
      0.084   13.4   0.1       0.38   11.3   0.0    2.1  2  ABC_tran       ABC transporter
       0.14   12.7  12.3        5.5    7.4   6.4    2.9  3  AAA_23         AAA domain


Domain annotation for each model (and alignments):
>> GTP-bdg_N  GTP-binding GTPase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.0   0.0   1.8e-27   2.1e-24       3      89 .]      22     107 ..      20     107 .. 0.97

  Alignments for each domain:
  == domain 1  score: 86.0 bits;  conditional E-value: 1.8e-27
                         GTP-bdg_N   3 sleEleeLaktaglevvgevvqkrekpdpatyiGkGkveeikelveeeeadlvifddeLspsqqrnLekelevkViD 79 
                                       +l EleeLak+ag+ +vge++q+ ++pd+++ +G+Gkv+e+++lv+e +a+ vif ++Ls+ q+ n++++++++ViD
  gi|298674508|ref|YP_003726258.1|  22 KLFELEELAKSAGYCIVGEITQS-KNPDRRYQVGRGKVDELASLVNEYNAEKVIFYNQLSTIQIYNVSETCKCEVID 97 
                                       788*******************9.59*************************************************** PP

                         GTP-bdg_N  80 RtqLILdIFA 89 
                                       + +LIL+IFA
  gi|298674508|ref|YP_003726258.1|  98 KFHLILEIFA 107
                                       *********8 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.4   0.1   6.9e-25   8.3e-22       2     114 .]     193     311 ..     192     311 .. 0.84

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 6.9e-25
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC... CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee... 75 
                                       va++G++N+GKStL+n++++e ++v+d+ +tT+ ++++ ++l+g+++ l+Dt+G+ie  +  +++ +af++  +   
  gi|298674508|ref|YP_003726258.1| 193 VALAGYTNAGKSTLFNTIVDEDVRVEDMLFTTLSPVTRSLNLGGRHVLLTDTVGFIE--DLPHWMIDAFRSTLDeif 267
                                       89****************************************************998..566689999999665577 PP

                                       .TSEEEEEEETTTTCSHHHHHHHHHHHHH......TTSEEEEEEES CS
                          MMR_HSR1  76 .adlillvvdaseeklkpldeeleellee......akkplilvlnk 114
                                        +d+illvvd++ e+ ++++++l+    e      ++ p+i vlnk
  gi|298674508|ref|YP_003726258.1| 268 lTDVILLVVDVA-EDAEKIRKKLATSH-EilwnksEGAPIITVLNK 311
                                       78********88.44555555554443.22444569999*****98 PP

>> GTP-bdg_M  GTP-binding GTPase Middle Region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.5   2.0   1.5e-19   1.8e-16       1      79 []     109     185 ..     109     185 .. 0.88

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 1.5e-19
                                       H--SHHHHHHHHHHHHHHHHHHHCXXXXXXXXX..X..XXXXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHH.... CS
                         GTP-bdg_M   1 rArtkeaklQVelAqlkyllprLeglgkelsrqgGgigtrGpGetkleldrrlireriaklkkeLekvkkkrelqrk 77 
                                       rA+tk aklQVelAql+y+lp+ ++  + l++ +   g++  Ge++ +++++ i++ri+++k+eL+  kk re +rk
  gi|298674508|ref|YP_003726258.1| 109 RATTKRAKLQVELAQLEYELPKAKNIVSLLKQEE-RPGFMSLGEYE-DSYEQDIKNRISRIKNELKTAKKDRESLRK 183
                                       9**********************75554444443.3469*******.*****************************9 PP

                                       .T CS
                         GTP-bdg_M  78 kR 79 
                                        R
  gi|298674508|ref|YP_003726258.1| 184 FR 185
                                       76 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       2.5     3e+03      77     111 ..      97     131 ..      81     142 .. 0.65
   2 !   38.5   0.1   6.4e-13   7.7e-10       3     156 .]     193     352 ..     191     352 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.5
                                       TSSSEEEEEEEGGGHHHHHHHHHHHHHTTSSEEEE CS
                            FeoB_N  77 eepdvvvnvvdatnlernLyLtlqllelgvpvvla 111
                                       +++++++++  +    +   L ++l++l+ ++  a
  gi|298674508|ref|YP_003726258.1|  97 DKFHLILEIFATRATTKRAKLQVELAQLEYELPKA 131
                                       46667777777777777777777777776665555 PP

  == domain 2  score: 38.5 bits;  conditional E-value: 6.4e-13
                                       EEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----.SSSSSSSHHH..HHHHHHHHC CS
                            FeoB_N   3 valvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGi.Yslsayseee..kvardflle 76 
                                       val+G  n+Gk+tlfn++ + + +v     +t    + +l+l g++v ++D  G   +l +  ++   +   +++l+
  gi|298674508|ref|YP_003726258.1| 193 VALAGYTNAGKSTLFNTIVDEDVRVEDMLFTTLSPVTRSLNLGGRHVLLTDTVGFiEDLPHWMIDAfrSTLDEIFLT 269
                                       89****************************************************73457666666421344556666 PP

                                       TSSSEEEEEE.EGGGHHHHHHHHHHHH...HTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTH CS
                            FeoB_N  77 eepdvvvnvv.datnlernLyLtlqll...elgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegi 149
                                       + + +vv+v+ da++++++L    ++l     g+p++ +ln++d++++++++  l+k++     p v +sak++ g+
  gi|298674508|ref|YP_003726258.1| 270 DVILLVVDVAeDAEKIRKKLATSHEILwnkSEGAPIITVLNKVDAIKSDELNKKLDKIEYLAPNP-VFISAKSGYGL 345
                                       7777999997689************9833345699**********************98755555.679******** PP

                                       HHHHHHH CS
                            FeoB_N 150 eellkai 156
                                       ++l+k+i
  gi|298674508|ref|YP_003726258.1| 346 DNLKKQI 352
                                       ****987 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0     1e-05     0.012      66     128 ..     158     218 ..     107     238 .. 0.83
   2 !   19.2   0.1   7.2e-07   0.00087      38     101 ..     294     356 ..     260     357 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1e-05
                                       HHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT-----S CS
                       RsgA_GTPase  66 eelkeelealgyevllvsaktkegleelkellkdktsvlvGqSGvGKStLinallpelelktg 128
                                       +++k++++++  e l++ +k++e+l++ ++    ++++l+G + +GKStL n+++ e +++++
  gi|298674508|ref|YP_003726258.1| 158 QDIKNRISRIKNE-LKTAKKDRESLRKFRHDKGFSLVALAGYTNAGKSTLFNTIVDE-DVRVE 218
                                       4566667777444.455577788899998888889*******************998.55554 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 7.2e-07
                                       HHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTTSE CS
                       RsgA_GTPase  38 fLvlaeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkellkdkt 101
                                        ++  +++g++++ vlnK+D ++++e l++  +++e l  +++++sak++ gl++lk+++++++
  gi|298674508|ref|YP_003726258.1| 294 EILWNKSEGAPIITVLNKVDAIKSDE-LNKKLDKIEYLAPNPVFISAKSGYGLDNLKKQINQQV 356
                                       34555678888899************.********************************99875 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.1   8.7e-10     1e-06      56     103 ..     303     355 ..     293     357 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 8.7e-10
                      MMR_HSR1_Xtn  56 ipclyvlNKiDlisleeldelare.....pnsvviSaekelnldeLkekiwee 103
                                        p ++vlNK+D+i+ +el++   +     pn v+iSa+++++ld+Lk++i ++
  gi|298674508|ref|YP_003726258.1| 303 APIITVLNKVDAIKSDELNKKLDKieylaPNPVFISAKSGYGLDNLKKQINQQ 355
                                       589**********99999765554467779*******************9765 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.021        25       6      24 ..     193     211 ..     131     220 .. 0.69
   2 !   21.3   0.0   1.4e-07   0.00016      91     185 ..     266     349 ..     225     369 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.021
                                       EEEEESTTSSHHHHHHHHH CS
                          GTP_EFTU   6 igiighvDhGKtTLtdrLl 24 
                                       ++++g +++GK+TL  +++
  gi|298674508|ref|YP_003726258.1| 193 VALAGYTNAGKSTLFNTIV 211
                                       3445555666666665555 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 1.4e-07
                                       HHT-SEEEEEEETTTB.....STHHHHHHHHHHHHTTTEEEEEEESCGST.HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          GTP_EFTU  91 lrvlDgavlvvdaveG.....vepqteevlrlalkegvpiivfiNKmDrl.kaelkeiveevkqklsrkeeklekyg 161
                                       +  +D+ +lvvd++e+      +  t   +   ++eg pii+++NK+D +  +el++  +++++             
  gi|298674508|ref|YP_003726258.1| 266 IFLTDVILLVVDVAEDaekirKKLATSHEILWNKSEGAPIITVLNKVDAIkSDELNKKLDKIEYLA----------- 331
                                       5689***********9888777788999999999****************8889999998888443........... PP

                                       HTTTTTEEEEEEBTTTTBTHHHHH CS
                          GTP_EFTU 162 ekgekevpvvfgSalkgegvktll 185
                                              + vf+Sa++g g+++l 
  gi|298674508|ref|YP_003726258.1| 332 -P-----NPVFISAKSGYGLDNLK 349
                                       .1.....23455555555555554 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.2     0.014        16     184     218 ..      59      93 ..      57     106 .. 0.79
   2 !   15.3   0.0   8.2e-06    0.0098       4     134 ..     195     325 ..     192     333 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.014
                         Gtr1_RagA 184 elLkklaeaieaeevlLferstflviatvsskeae 218
                                       ++L++l+++ +ae+v+ +++ + + i +vs++ + 
  gi|298674508|ref|YP_003726258.1|  59 DELASLVNEYNAEKVIFYNQLSTIQIYNVSETCKC 93 
                                       5799**********************999965554 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 8.2e-06
                         Gtr1_RagA   4 LmGksgsGKtsmrsiiFdnylardtlrlgatidveksevrflgnltlnlwDcgGqea....fveeylssqkeeifrn 76 
                                       L G  ++GK+++ + i d+ +  +   l +t +    ++ +lg  ++ l D  G  +     + ++++s  +eif +
  gi|298674508|ref|YP_003726258.1| 195 LAGYTNAGKSTLFNTIVDEDVRVED-MLFTTLSPVTRSL-NLGGRHVLLTDTVGFIEdlphWMIDAFRSTLDEIFLT 269
                                       7888999999887666655443333.3557777777777.4555566677777754411114555889999999975 PP

                         Gtr1_RagA  77 vgvliyVfDvesreleedletlkeilealrqyspeakvfvlihKmDliqedereeife 134
                                        +v++ V+Dv  ++ e+  ++l ++ e l + s+ a +   ++K+D i++de ++ ++
  gi|298674508|ref|YP_003726258.1| 270 -DVILLVVDVA-EDAEKIRKKLATSHEILWNKSEGAPIITVLNKVDAIKSDELNKKLD 325
                                       .99*******9.67888888888888889999999*************9988766655 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       3.7   4.5e+03      67      87 ..     155     175 ..     110     187 .. 0.57
   2 !   14.4   0.0   2.4e-05     0.029       1      36 [.     193     228 ..     193     238 .. 0.90
   3 ?    0.9   0.0      0.35   4.2e+02     129     167 ..     269     311 ..     230     312 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.7
                                       HHHHHHHHHHHHHHTSSSS-- CS
                         Dynamin_N  67 evreeieketekiagankgis 87 
                                        +++ i+++ ++i++++k+ +
  gi|298674508|ref|YP_003726258.1| 155 SYEQDIKNRISRIKNELKTAK 175
                                       333444444444444444443 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2.4e-05
                                       EEEEEBTTTTHHHHHHHHHTS--S---SSS---S-E CS
                         Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrrpl 36 
                                       +a+ G +++GKS++ n ++ ed+ + +   tT  p+
  gi|298674508|ref|YP_003726258.1| 193 VALAGYTNAGKSTLFNTIVDEDVRVEDMLFTTLSPV 228
                                       6889*******************9999999998876 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.35
                                       TEEEEEEEETTS-CCC-.CHHHHHHHHSTTBTT...EEEEEE- CS
                         Dynamin_N 129 adiilavtsanhdlsns.ealflarevdpkgkr...tivvltk 167
                                        d+il+v++   d+ +  ++l  ++e+  +++    +i vl+k
  gi|298674508|ref|YP_003726258.1| 269 TDVILLVVDVAEDAEKIrKKLATSHEILWNKSEgapIITVLNK 311
                                       69999**999999986546666677777777777778888887 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0         2   2.4e+03      26      48 ..     161     183 ..     156     187 .. 0.82
   2 ?    4.3   0.0     0.022        27       3      23 ..     193     213 ..     191     221 .. 0.84
   3 !   10.9   0.4   0.00021      0.25      84     163 ..     238     325 ..     216     334 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2
                                       SS-EEEEESS-SSCHCCCCCCHC CS
                              cobW  26 glklavivNefgevsiDaellre 48 
                                       ++++  i Ne+++ + D+e lr+
  gi|298674508|ref|YP_003726258.1| 161 KNRISRIKNELKTAKKDRESLRK 183
                                       56788899999999999998876 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.022
                                       EEEEESTTCCHHHHHHHHHCT CS
                              cobW   3 tvltGflGsGKTtLlnhllen 23 
                                       + l+G+  +GK+tL n+++++
  gi|298674508|ref|YP_003726258.1| 193 VALAGYTNAGKSTLFNTIVDE 213
                                       5799*************9954 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00021
                                       SEEEEEECTTTTHHHH.HTT..SHHHHHCCCECEEEEEEETTTH.....CCHCCHHHHHHHHHHTSSEE.EEE-HHH CS
                              cobW  84 dviliEttGlaePapv.aft..eeelksdltldavvavvDaknl....eaeeekieekaedqlaaadll.vlnKtDl 152
                                        v+l  t+G  e  p  ++    ++l + +  d+++ vvD+++      ++  +++e + ++ + a ++ vlnK+D 
  gi|298674508|ref|YP_003726258.1| 238 HVLLTDTVGFIEDLPHwMIDafRSTLDEIFLTDVILLVVDVAEDaekiRKKLATSHEILWNKSEGAPIItVLNKVDA 314
                                       67888999977777763444778999999***********9554444444444455555555566665547888888 PP

                                       HCHC..HHHHH CS
                              cobW 153 ldeeallekle 163
                                       +++++l +kl+
  gi|298674508|ref|YP_003726258.1| 315 IKSDELNKKLD 325
                                       88776655554 PP

>> MnmE_helical  MnmE helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.8e-05     0.021      60     131 ..     153     356 ..     146     375 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.8e-05
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxx...................................... RF
                      MnmE_helical  60 eelseeelaekleelkeelekllatakrgellr..eGik...................................... 96 
                                       e+  e++++++++++k+el++  ++ ++ +  r  +G++                                      
  gi|298674508|ref|YP_003726258.1| 153 EDSYEQDIKNRISRIKNELKTAKKDRESLRKFRhdKGFSlvalagytnagkstlfntivdedvrvedmlfttlspvt 229
                                       34566789***************9999998888668999************************************** PP

                                       ............................................................................. RF
                      MnmE_helical  97 ............................................................................. 96 
                                                                                                                    
  gi|298674508|ref|YP_003726258.1| 230 rslnlggrhvlltdtvgfiedlphwmidafrstldeifltdvillvvdvaedaekirkklatsheilwnksegapii 306
                                       ***********************************************888888888888888888888888888888 PP

                                       ...........xxxxxxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxx.x RF
                      MnmE_helical  97 ...........Dllkekeekeeeevl...............kiSaktgegieeLeeaike.l 131
                                                  D     e       l                iSak+g g+++L+++i++ +
  gi|298674508|ref|YP_003726258.1| 307 tvlnkvdaiksD-----E-------LnkkldkieylapnpvFISAKSGYGLDNLKKQINQqV 356
                                       777777444442.....3.......02222233444556668****************8844 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.018        22       2      27 ..     193     218 ..     192     243 .. 0.83
   2 ?    5.3   0.0     0.018        22      72     119 ..     263     313 ..     256     314 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.018
                                       EEEESSTTSSHHHHHHCHCT-CCC-E CS
                               Roc   2 vvlvGdsgvGKtsllkrfvedkfsek 27 
                                       v l G +++GK++l++ +v+++++ +
  gi|298674508|ref|YP_003726258.1| 193 VALAGYTNAGKSTLFNTIVDEDVRVE 218
                                       568899*************9988655 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.018
                                       T-HHHHCTSCEEEEEEE..GHHH...HCHHHHHHHHHHHCSSS-EEEEEE-TT CS
                               Roc  72 lhplylreaalailvyd..srss...enlkeWlkelkkvagkspvilvgnkiD 119
                                       l +++l++   ++lv+d  ++ +   ++l +  + l ++++ +p+i v nk+D
  gi|298674508|ref|YP_003726258.1| 263 LDEIFLTDV--ILLVVDvaEDAEkirKKLATSHEILWNKSEGAPIITVLNKVD 313
                                       567777765..55555532222211245566666667778889*********9 PP

>> AHH  A nuclease family of the HNH/ENDO VII superfamily with conserved AHH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00015      0.18      36     104 ..     115     182 ..     100     194 .. 0.73
   2 ?   -3.6   0.1       9.3   1.1e+04      74      92 ..     386     404 ..     385     409 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
                               AHH  36 kk...llkkygydindaeNgvlLPekkeaslklglpgHrgsHteeYsklVrerldeikkeakekklkkealk 104
                                       +k    l + +y++ +a+N+v L   k+++    +++ +   + +Y++++++r+++ik+e k+ k+ +e l+
  gi|298674508|ref|YP_003726258.1| 115 AKlqvELAQLEYELPKAKNIVSL--LKQEERPGFMSLGE--YEDSYEQDIKNRISRIKNELKTAKKDRESLR 182
                                       22334788999999999999999..34444444444444..479********************99888754 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 9.3
                               AHH  74 HteeYsklVrerldeikke 92 
                                       H+ +Y ++++ +l++ +++
  gi|298674508|ref|YP_003726258.1| 386 HNIDYGDYIEVDLEARDEI 404
                                       8899999998888876655 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       2.2   2.6e+03      28      94 ..     103     173 ..     101     186 .. 0.54
   2 ?   11.3   0.0   0.00031      0.38      12      35 ..     191     214 ..     187     294 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.2
                                       HHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S-TTSBHHHH......HHHTCHHHHHHHSTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx......xxxxxxxxxxxxxxx RF
                          ABC_tran  28 lkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe..pqlfpeltvren......esdeeiekalsklgl 94 
                                       l+++a   + +  +++++ ++l++ el+++++ ++ l+qe  p + +   ++e       + +++i+++ ++l+ 
  gi|298674508|ref|YP_003726258.1| 103 LEIFATRATTKRAKLQVELAQLEY-ELPKAKNIVSLLKQEerPGFMS---LGEYedsyeqDIKNRISRIKNELKT 173
                                       566666666666677777777777.7788888888888884322221...2222222333444445555555544 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00031
                                       SEEEEEESTTSSHHHHHHHHTTSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  12 ekvaivGenGaGKStLlkllagll 35 
                                       ++va+ G + aGKStL++++  + 
  gi|298674508|ref|YP_003726258.1| 191 SLVALAGYTNAGKSTLFNTIVDED 214
                                       579*****************9875 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   6.4    0.0046       5.5      89     198 ..      36     177 ..       5     179 .. 0.66
   2 ?    7.2   0.0    0.0054       6.5      20      39 ..     191     210 ..     180     211 .. 0.84
   3 ?   -0.4   0.1       1.2   1.4e+03     169     193 ..     317     353 ..     262     358 .. 0.50

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0046
                            AAA_23  89 siererelskkkgkttkkaklelleideleqfisellgskkiilnlilflgqer.............feefelkdkk 152
                                       +i  e++ sk+  ++++   ++  e + l ++ + +  +++++l+ i+++  ++              e f++ ++ 
  gi|298674508|ref|YP_003726258.1|  36 CIVGEITQSKNPDRRYQVGRGKVDELASLVNEYNAEKVIFYNQLSTIQIYNVSEtckcevidkfhliLEIFATRATT 112
                                       45444444444333333333333333666666666777777788777777777789999988866663333333322 PP

                            AAA_23 153 e......rleelekeleeledekkllekl.............eqekekekeleeleeeleeilke 198
                                       +      +l++le el +++++ +ll+++               e++ +++++ +++el++++k+
  gi|298674508|ref|YP_003726258.1| 113 KraklqvELAQLEYELPKAKNIVSLLKQEerpgfmslgeyedSYEQDIKNRISRIKNELKTAKKD 177
                                       345556699*****************************998888899999999*****9999887 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0054
                            AAA_23  20 gltlItGpNGaGKTTildAi 39 
                                        l+++ G + aGK+T+++ i
  gi|298674508|ref|YP_003726258.1| 191 SLVALAGYTNAGKSTLFNTI 210
                                       478999***********976 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.2
                            AAA_23 169 kkllekleqekekek............eleeleeele 193
                                        ++l+k++++ e+ +             l++l+++++
  gi|298674508|ref|YP_003726258.1| 317 SDELNKKLDKIEYLApnpvfisaksgyGLDNLKKQIN 353
                                       1222222222222224444444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1127  (0.0628591); expected 358.6 (0.02)
Passed bias filter:                      703  (0.0392102); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.72u 0.39s 00:00:01.10 Elapsed: 00:00:00.55
# Mc/sec: 2282.05
//
Query:       gi|298674509|ref|YP_003726259.1|  [L=130]
Description: hypothetical protein Metev_0552 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-55  185.8   1.1    3.2e-55  185.6   1.1    1.0  1  DUF2209        Uncharacterized protein conserved in archaea (
  ------ inclusion threshold ------
       0.17   12.1   0.8       0.22   11.8   0.8    1.5  1  Peptidase_Prp  Cysteine protease Prp


Domain annotation for each model (and alignments):
>> DUF2209  Uncharacterized protein conserved in archaea (DUF2209)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.6   1.1   3.6e-59   3.2e-55       1     120 [.       5     123 ..       5     124 .. 0.99

  Alignments for each domain:
  == domain 1  score: 185.6 bits;  conditional E-value: 3.6e-59
                           DUF2209   1 vavDiSGRHkekdgeylmvcaaVslevsadriekveqvkilvvaseeepkledvvklieeaveelkeegtivaEkGe 77 
                                       +avDiSGRHk+k+g y+mvcaaVs+  sad++ekv+qvki++++++++p+++dvv++ie++v+e+k +gtivaEkG+
  gi|298674509|ref|YP_003726259.1|   5 IAVDISGRHKIKNG-YYMVCAAVSVVSSADHVEKVNQVKIKPFWMDSAPQVTDVVRIIEDTVKEIKYDGTIVAEKGD 80 
                                       8***********99.************************************************************** PP

                           DUF2209  78 lynepewlveailkkefkyqeslgEreaielAHhvslsarkll 120
                                       +yn+pew+++++++k+fkyqesl+Er aie+AHh+slsar+ll
  gi|298674509|ref|YP_003726259.1|  81 MYNKPEWVATSMFSKNFKYQESLSERLAIEMAHHISLSARNLL 123
                                       *****************************************99 PP

>> Peptidase_Prp  Cysteine protease Prp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.8   2.4e-05      0.22      16      41 ..       7      31 ..       3     111 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.4e-05
                                      EEEESTSS-SSHHHHHHHHHHHHHHH CS
                     Peptidase_Prp 16 fevsGHAgyaeaGeDiVCAavSalvi 41
                                      +++sG  + + +G+ +VCAavS+++ 
  gi|298674509|ref|YP_003726259.1|  7 VDISGRHKIK-NGYYMVCAAVSVVSS 31
                                      5566655555.7999*******9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       737  (0.0411066); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.34s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 748.76
//
Query:       gi|298674510|ref|YP_003726260.1|  [L=351]
Description: tRNA intron endonuclease [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-48  161.4   0.2    3.7e-26   91.0   0.1    2.4  2  tRNA_int_endo    tRNA intron endonuclease, catalytic C-termin
    4.2e-39  132.1   1.1    7.6e-20   70.3   0.4    2.5  2  tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain
     0.0017   18.6   0.0     0.0045   17.3   0.0    1.7  2  Sen15            Sen15 protein
  ------ inclusion threshold ------
      0.049   13.4   0.0        0.1   12.4   0.0    1.5  1  RnlA_toxin       RNase LS, bacterial toxin


Domain annotation for each model (and alignments):
>> tRNA_int_endo  tRNA intron endonuclease, catalytic C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.2   0.0   1.1e-22   4.9e-19       1      85 []      75     158 ..      75     158 .. 0.98
   2 !   91.0   0.1   8.2e-30   3.7e-26       1      81 [.     257     340 ..     257     343 .. 0.96

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 1.1e-22
                                       HHHHHHHHHHHHHTT-EEEECGGGTSSEEEE..TSCTTTSSCSEEEEEEETTSEEEHHHHHHHHHHHHHTTSEEEEE CS
                     tRNA_int_endo   1 falkyavyrdLrekGyvvrsGlkFGadFrvY..qrrpslehseylVvvvsedeeldwpdlsaavrlahsvkKklila 75 
                                       f+lky+vy+d re+G+++++G    +dFrvY  +++p++++ ++ ++v se+ +l+++dl++ +++a +v K+lila
  gi|298674510|ref|YP_003726260.1|  75 FELKYIVYKDIRERGLYIQPG---VTDFRVYprGGHPGKSQPRSYIHVHSERIPLSLKDLQKLLETADNVHKQLILA 148
                                       89*******************...78*************************************************** PP

                                       EETTTSCEEE CS
                     tRNA_int_endo  76 ivdaegdvty 85 
                                       ivd+e d+t+
  gi|298674510|ref|YP_003726260.1| 149 IVDEESDITF 158
                                       ********96 PP

  == domain 2  score: 91.0 bits;  conditional E-value: 8.2e-30
                                       HHHHHHHHHHHHHTT-EEEECGGGTSSEEEE...TSCTTTSSCSEEEEEEETTSEEEHHHHHHHHHHHHHTTSEEEE CS
                     tRNA_int_endo   1 falkyavyrdLrekGyvvrsGlkFGadFrvY...qrrpslehseylVvvvsedeeldwpdlsaavrlahsvkKklil 74 
                                       f +k++vy dLr++G+v+++G+kFG++FrvY   +++ +  hseylV+ +++d e+ +p +s+a+rla+svkK++++
  gi|298674510|ref|YP_003726260.1| 257 FPRKCRVYSDLRNRGLVPKTGFKFGTHFRVYkqvESSNNIPHSEYLVHALPNDYEFILPVMSRAIRLANSVKKRMLF 333
                                       779*****************************9999***************************************** PP

                                       EEETTTS CS
                     tRNA_int_endo  75 aivdaeg 81 
                                       a+++++g
  gi|298674510|ref|YP_003726260.1| 334 AVEKEKG 340
                                       **98765 PP

>> tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.3   0.4   1.7e-23   7.6e-20       1      67 []       1      65 [.       1      65 [. 0.97
   2 !   60.1   0.0   2.7e-20   1.2e-16       3      66 ..     181     246 ..     179     247 .. 0.94

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 1.7e-23
                                      EEEEEETTEEEESSHHHHHHHHHTTT-SEECCTSSEEEEHHHHHHHHHTTSEEEETTSEEE-HHHHH CS
                   tRNA_int_endo_N  1 vegeLsgdrvlvedeeaakrlyekgfYGkplidepLqLslvEAlYLlekGklevvkggeplsfeell 67
                                      + geL +drvlv  e+++ +ly++g++G+  ++++L+LslvEA+YLl+++k++ +++++ l+f +++
  gi|298674510|ref|YP_003726260.1|  1 MIGELTNDRVLVD-EKGIDELYKSGYFGR-PKGNKLELSLVEAAYLLYRNKIKAQENEKGLDFTDFF 65
                                      78**********9.6**************.8********************************9986 PP

  == domain 2  score: 60.1 bits;  conditional E-value: 2.7e-20
                                       EEEETTEEEESSHHHHHHHHHTTT-SEECCTSSEEEEHHHHHHHHHTTSEEEE..TTSEEE-HHHH CS
                   tRNA_int_endo_N   3 geLsgdrvlvedeeaakrlyekgfYGkplidepLqLslvEAlYLlekGklevv..kggeplsfeel 66 
                                       + L +drvl++d e +++++e+gfYGk+l+ e LqLslvE+ YLle+++++v   k+g  l+f e+
  gi|298674510|ref|YP_003726260.1| 181 ASLMEDRVLIWDGESSNTIHENGFYGKLLDPEHLQLSLVESGYLLENNIIQVNdrKNGNHLNFSEF 246
                                       6799************************************************99889999999887 PP

>> Sen15  Sen15 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0     1e-06    0.0045      40      92 ..     115     163 ..      82     169 .. 0.80
   2 ?   -3.1   0.0       2.2     1e+04      27      46 ..     302     317 ..     283     330 .. 0.56

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1e-06
                             Sen15  40 elvlPlelteklslekldkvfkelkeekserkkrivLaivddDsTvvYYkvtd 92 
                                        ++   + +  lsl++l+k++++ ++      k+++Laivd++s + +Y+ ++
  gi|298674510|ref|YP_003726260.1| 115 SYIHVHSERIPLSLKDLQKLLETADNV----HKQLILAIVDEESDITFYEAKK 163
                                       5555555567899**********8877....599***************9765 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.2
                             Sen15  27 llkGrpkkklsed.elvlPle 46 
                                       l++++p+     d e++lP+ 
  gi|298674510|ref|YP_003726260.1| 302 LVHALPN-----DyEFILPVM 317
                                       3344433.....136777764 PP

>> RnlA_toxin  RNase LS, bacterial toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.3e-05       0.1      39      85 ..     139     186 ..     127     220 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.3e-05
                                       EEEEEE.EETTTTEEEEEEEETTTEEEEEE-SSHHHHHHHHHHGGG-- CS
                        RnlA_toxin  39 kkkyki.isskykdkititlysnkklliqGrplslyrelitalselld 85 
                                        +++k+ i  + +++ +it+y+ kk+ i G   +ly  l+t +s + d
  gi|298674510|ref|YP_003726260.1| 139 DNVHKQlILAIVDEESDITFYEAKKVNIKGDMKKLYPDLTTSASLMED 186
                                       467888889999999************************996554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 2101.93
//
Query:       gi|298674511|ref|YP_003726261.1|  [L=491]
Description: cobyrinic acid a,c-diamide synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.5e-39  133.4   0.8    1.1e-38  132.8   0.8    1.3  1  GATase_3  CobB/CobQ-like glutamine amidotransferase domain
    1.2e-16   61.1   0.1    5.9e-13   49.1   0.0    3.0  3  AAA_26    AAA domain
    3.2e-16   59.5   0.0    5.7e-16   58.7   0.0    1.4  1  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain
  ------ inclusion threshold ------
       0.16   11.9   0.0       0.69    9.9   0.0    2.1  2  HTH_11    HTH domain


Domain annotation for each model (and alignments):
>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.8   0.8   2.5e-42   1.1e-38       1     190 [.     269     470 ..     269     476 .. 0.88

  Alignments for each domain:
  == domain 1  score: 132.8 bits;  conditional E-value: 2.5e-42
                          GATase_3   1 kiavirlpaisnyt..dldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeag 75 
                                       +i+++ ++a+++y+  ++++Le e++   +f+p++d  l++ +d ++++Gg+++++  +l+ +++++++ikea+ +g
  gi|298674511|ref|YP_003726261.1| 269 TIGIALDEAFNFYYhnNIELLELEGARIKYFSPIHDAHLPK-VDGLYIGGGYPELFGDELESNESIRNDIKEASGQG 344
                                       699************************************66.*********************************** PP

                          GATase_3  76 gpvlgiCGGlqmLGeeiedpegveg.........eageveglglLdietefekekltgqvegevel....aaegeev 139
                                        p++++CGGl++L e++++  ++ +         ++++++++g L+ +t ++++++++   g  +      ++g+ +
  gi|298674511|ref|YP_003726261.1| 345 LPIYAECGGLMYLTEKMTTGVQNKHkgkyhmaemQESTYNMVGALPGHTLMGHTRVVSYNIGMFKCdsviGKAGNSF 421
                                       *****************77655544689999987778********************99999988899998899*** PP

                          GATase_3 140 kGyEiHsGrtilkekakpllkvkv..ggnng.ekdGavkksedgnvlGtYlHgl 190
                                       +G+E+H+++ ++ +  +  +++k   g+++  + dG+  +    n++G+Y H+ 
  gi|298674511|ref|YP_003726261.1| 422 RGHEFHHSEITNLP-SNSNFAIKLsrGTGIVsGWDGLTVN----NTMGSYAHLE 470
                                       ********655444.4444555443355555799999988....********85 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0   0.00046         2       3      31 ..      18      46 ..      17      54 .. 0.83
   2 !   49.1   0.0   1.3e-16   5.9e-13      95     193 ..      92     198 ..      56     201 .. 0.78
   3 ?   -0.7   0.0      0.23     1e+03      19      70 ..     206     260 ..     202     270 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00046
                            AAA_26  3 ifvtgtdtgvGKTvvslgLvralkrkgvk 31
                                      +++++ + ++GKT+++ gL++al+ +g++
  gi|298674511|ref|YP_003726261.1| 18 VLLAADRSSSGKTTITSGLLAALTFQGYR 46
                                      577788899**************777766 PP

  == domain 2  score: 49.1 bits;  conditional E-value: 1.3e-16
                            AAA_26  95 lekdadivvVEGagglgvp..itee.llnadiaknlgapvilVargglgtinqllltiealr.qknvrvlGvilNkv 167
                                        +++ad+ v+EG+ gl ++  ++++  ++a+iak+l++pv+l++++++ t  ++++   ++  + +v+++GvilN++
  gi|298674511|ref|YP_003726261.1|  92 ESEKADLAVIEGVRGLFEGleSFSDtGSTAQIAKTLDCPVVLIINARSITRSAAAIVNGYVNfDPDVNIAGVILNNI 168
                                       46789***********99866666669*******************99764444333333333669**********7 PP

                            AAA_26 168 rnp....envetlekksgipvlGvvPylpd 193
                                              ++ +++e ++g+pvlG++P +++
  gi|298674511|ref|YP_003726261.1| 169 GGGrhakKAKDAIEYYTGVPVLGIIPRDDS 198
                                       55544445999***************9876 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.23
                            AAA_26  19 lgLvralkrkgvkvgyfKPiqtgie...ededselikellgldqtyelpeplals 70 
                                       lgLv a++ ++    + K i +  +   e+ d+e i e+ ++ ++ e pe ++++
  gi|298674511|ref|YP_003726261.1| 206 LGLVPAIEGRQKDSEFRKRIYSIESiikENVDIEKIIEISHNASPVEKPEYTLFK 260
                                       7899999999999999998754444222666777777777776666666555554 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.7   0.0   1.3e-19   5.7e-16       2     124 ..      19     204 ..      18     209 .. 0.89

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 1.3e-19
                                       EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.........HTTEB-HHHH............... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxx............... RF
                              CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai.........leglendiep............... 54 
                                       ++a+  + +GKTt++ +L++al  +g+r ++++++ +    ++                  +               
  gi|298674511|ref|YP_003726261.1|  19 LLAADRSSSGKTTITSGLLAALTFQGYRPQPFKVGLDYIDPSYhseitgikaR--------Nldgylmdddkildvf 87 
                                       56788899*************************99997777765453333330........25577777777***** PP

                                       ................................................CCHCCCHHHHHHCHCHHHH.....EEEEE CS
                                       ................................................xxxxxxxxxxxxxxxxxxx...xxxxxxx RF
                              CbiA  55 ................................................dlkrllellealgkkkall...lkiagvv 80 
                                                                                       ++ ++ ++++a+++++ ++   ++iagv+
  gi|298674511|ref|YP_003726261.1|  88 thafesekadlaviegvrglfeglesfsdtgstaqiaktldcpvvliiNARSITRSAAAIVNGYVNFdpdVNIAGVI 164
                                       ****************************************************************999********** PP

                                       EEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  81 lnrvdgeneetllkealeelkqrygvpvlgviprdeavaeapar 124
                                       ln ++g ++ ++ k+a+e +    gvpvlg+iprd++  ++ +r
  gi|298674511|ref|YP_003726261.1| 165 LNNIGGGRHAKKAKDAIEYYT---GVPVLGIIPRDDSM-QISMR 204
                                       *******************98...***********986.55555 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.2   5.4e+03      33      46 ..     283     296 ..     283     297 .. 0.88
   2 ?    9.9   0.0   0.00015      0.69      28      51 ..     329     352 ..     326     355 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.2
                            HTH_11  33 rrdIkaLeelgvpI 46 
                                       ++ I+ Le  g++I
  gi|298674511|ref|YP_003726261.1| 283 HNNIELLELEGARI 296
                                       6899****999998 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00015
                            HTH_11  28 SrrtvrrdIkaLeelgvpIesepg 51 
                                       S   +r+dIk+ + +g+pI++e g
  gi|298674511|ref|YP_003726261.1| 329 SNESIRNDIKEASGQGLPIYAECG 352
                                       7789*****************966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.35s 00:00:01.01 Elapsed: 00:00:00.53
# Mc/sec: 2766.12
//
Query:       gi|298674512|ref|YP_003726262.1|  [L=293]
Description: nitrogenase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.2e-92  307.3   1.7    1.1e-91  307.0   1.7    1.0  1  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
    4.9e-12   45.8   0.3    1.3e-11   44.5   0.3    1.7  1  ParA         NUBPL iron-transfer P-loop NTPase
    1.7e-10   41.0   0.0    6.7e-10   39.1   0.0    2.0  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
      6e-08   32.8   0.5    2.3e-07   30.9   0.0    2.1  3  AAA_31       AAA domain
    8.6e-07   28.4   0.8    2.7e-06   26.8   0.2    2.0  2  ArsA_ATPase  Anion-transporting ATPase
    8.1e-05   21.7   0.0    0.00014   21.0   0.0    1.3  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
     0.0001   22.1   0.0    0.00017   21.3   0.0    1.5  2  AAA_24       AAA domain
     0.0007   19.0   0.2      0.021   14.1   0.0    2.2  2  MipZ         ATPase MipZ
      0.003   17.2   0.0     0.0088   15.7   0.0    1.8  1  SRP54        SRP54-type protein, GTPase domain
  ------ inclusion threshold ------
      0.011   15.0   0.0      0.017   14.3   0.0    1.3  1  DAP3         Mitochondrial ribosomal death-associated protein
      0.015   14.9   0.2      0.038   13.6   0.0    1.7  3  AAA_25       AAA domain
      0.027   14.9   0.1      0.068   13.6   0.0    1.7  2  AAA_16       AAA ATPase domain
      0.036   13.6   0.0      0.062   12.8   0.0    1.3  1  AAA_7        P-loop containing dynein motor region
      0.037   13.7   0.0        1.8    8.2   0.0    2.2  2  AAA_30       AAA domain
      0.079   13.2   0.1        3.4    8.0   0.0    2.4  2  AAA_22       AAA domain
      0.088   12.5   0.3       0.22   11.2   0.1    1.7  2  IstB_IS21    IstB-like ATP binding protein
      0.095   12.5   0.2        4.8    6.9   0.1    2.5  2  ATP_bind_1   Conserved hypothetical ATP binding protein
       0.12   11.7   0.5       0.95    8.7   0.0    2.4  3  DUF1611      Domain of unknown function (DUF1611_C) P-loop do


Domain annotation for each model (and alignments):
>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  307.0   1.7   1.1e-94   1.1e-91       2     267 ..      14     275 ..      13     279 .. 0.95

  Alignments for each domain:
  == domain 1  score: 307.0 bits;  conditional E-value: 1.1e-94
                         Fer4_NifH   2 kiaiyGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggkaqetvldtlrekgavedvkvedvvkkGy 78 
                                       +ia+yGkGGiGks t++n++aa a+ g kv+i+GCDPk+Ds  +llggk ++t+ld+lr+    e ++ edvv++Gy
  gi|298674512|ref|YP_003726262.1|  14 RIALYGKGGIGKSSTASNVAAACADEGYKVMIIGCDPKSDSSITLLGGKRIPTILDLLRDG---EGLNEEDVVFEGY 87 
                                       79********************************************************986...579********** PP

                         Fer4_NifH  79 ggvkcvesGGPepGvGCaGrgvitaielleelgayd.dlDfvlyDvLGDvvCGGfalPiredkaqevyivtsgelma 154
                                       +gvkcve GGPepG+GCaGrg+i ai+ l++ +    ++D+++yDv GD+vCGGf +P+r+++ +e yi+tsge m 
  gi|298674512|ref|YP_003726262.1|  88 NGVKCVEVGGPEPGIGCAGRGIIVAINQLKRISDSMkEMDLIIYDVPGDIVCGGFVAPVRKGMVNESYIITSGEYMP 164
                                       ******************************98755528*************************************** PP

                         Fer4_NifH 155 lyaanniakgiekyaksggvrlgGliinsrkvddereliekfaeelgtkvlevvPrdeivrkaelrkktvieyapes 231
                                       +yaanni+ g+ k +      l G+++nsr+v++e+e++e+fa+e+g+++l ++P+++iv+  e +   v++ ap+s
  gi|298674512|ref|YP_003726262.1| 165 MYAANNICSGLSKIN----TPLNGIVCNSRDVTNEKEIVEEFAHEIGSELLSFIPKEQIVQDCEREGYSVMDIAPDS 237
                                       ***********9986....4799****************************************************** PP

                         Fer4_NifH 232 eqakeyrelarkilenk..klviPkplsedeLeellee 267
                                       ++a+ yrela+ki+++   + v+P+ + +++L el  +
  gi|298674512|ref|YP_003726262.1| 238 KIAQVYRELAQKIMSKTepDSVLPNSMDDEQLRELARK 275
                                       *************99763378*************9876 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.3   1.3e-14   1.3e-11       8     246 .]      16     251 ..       9     251 .. 0.79

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 1.3e-14
                              ParA   8 vlSgKGGVGKStvavnlAlaLakkglkvgllDaD.........iyGpsiprllgveeekpeqsekkliPveakgikv 75 
                                        l gKGG+GKS++a+n+A+a a++g+kv ++  D         + G  ip++l++ ++    +e+ ++    +g+k+
  gi|298674512|ref|YP_003726262.1|  16 ALYGKGGIGKSSTASNVAAACADEGYKVMIIGCDpksdssitlLGGKRIPTILDLLRDGEGLNEEDVVFEGYNGVKC 92 
                                       567****************************988555555443447777777777666556666667766779**** PP

                              ParA  76 mSigfllesedeavvwrGpmkskaikqllkdv.ewgelDyLiiDlPPGtgDeq....ltvaqklplagaviVttpqe 147
                                       + +g   +        rG  +  ai+ql +   + +e+D++i D+P   gD+     ++ + k  +++  i+t+ + 
  gi|298674512|ref|YP_003726262.1|  93 VEVGGPEP--GIGCAGRG--IIVAINQLKRISdSMKEMDLIIYDVP---GDIVcggfVAPVRKGMVNESYIITSGEY 162
                                       99997444..55555555..55689998775514699********9...555411113344444688999******* PP

                              ParA 148 valadvkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkp 224
                                       + +  ++  ++ ++k+++++ G+v N   ++ +          k+ +e++a+e+g +ll+ ip ++ ++++  eg +
  gi|298674512|ref|YP_003726262.1| 163 MPMYAANNICSGLSKINTPLNGIVCNSRDVTNE----------KEIVEEFAHEIGSELLSFIPKEQIVQDCEREGYS 229
                                       ************************997666554..........4567999***************99999999**** PP

                              ParA 225 lvlkepeseaakaleeiaekvl 246
                                       ++  +p+s++a++++e+a+k++
  gi|298674512|ref|YP_003726262.1| 230 VMDIAPDSKIAQVYRELAQKIM 251
                                       *******************985 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.0   6.7e-13   6.7e-10       4     125 ..      17     227 ..      15     287 .. 0.88

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 6.7e-13
                                       EESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.......................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................... RF
                              CbiA   4 astkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.......................... 54 
                                         +kGG GK+++a n a+a a++g++V  + +Dp + ++     l +++ p                          
  gi|298674512|ref|YP_003726262.1|  17 LYGKGGIGKSSTASNVAAACADEGYKVMIIGCDPKSDSSI--TLLGGKRIPtildllrdgeglneedvvfegyngvk 91 
                                       579********************************66664..44444444456899999****************** PP

                                       ...........................................................................CC CS
                                       ...........................................................................xx RF
                              CbiA  55 ...........................................................................dl 56 
                                                                                                                   +
  gi|298674512|ref|YP_003726262.1|  92 cvevggpepgigcagrgiivainqlkrisdsmkemdliiydvpgdivcggfvapvrkgmvnesyiitsgeympmyAA 168
                                       ************************************************************************77666 PP

                                       HCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  57 krllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeaparg 125
                                         +   l+++ ++      + g+v n  d  ne++  +e+  e+    g ++l +ip+ + v +++ +g
  gi|298674512|ref|YP_003726262.1| 169 NNICSGLSKINTP------LNGIVCNSRDVTNEKEIVEEFAHEI----GSELLSFIPKEQIVQDCEREG 227
                                       6655556666655......78*****988876555555555554....*********999998877766 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   2.3e-10   2.3e-07       9      48 ..      19      58 ..      12      88 .. 0.82
   2 ?   -1.0   0.0       1.5   1.5e+03     111     128 ..     119     136 ..     108     183 .. 0.75
   3 ?   -2.4   0.0       3.8   3.8e+03      89      99 ..     238     248 ..     191     281 .. 0.56

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 2.3e-10
                            AAA_31  9 qKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattgl 48
                                       KGG+GK+ t+ n+aaa a +g+kv+++ +Dp + ++++l
  gi|298674512|ref|YP_003726262.1| 19 GKGGIGKSSTASNVAAACADEGYKVMIIGCDPKSDSSITL 58
                                      5********************************9999854 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.5
                            AAA_31 111 lekvkdeYDyiiiDcpPs 128
                                       +++  +e D+ii D+p +
  gi|298674512|ref|YP_003726262.1| 119 ISDSMKEMDLIIYDVPGD 136
                                       344456789999998855 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 3.8
                            AAA_31  89 dLaeaeielve 99 
                                       ++a++  el++
  gi|298674512|ref|YP_003726262.1| 238 KIAQVYRELAQ 248
                                       33333333333 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.2   2.7e-09   2.7e-06       3      40 ..      14      51 ..      12      56 .. 0.92
   2 ?   -1.2   0.0      0.88   8.8e+02     211     249 ..     156     196 ..     148     211 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 2.7e-09
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STT CS
                       ArsA_ATPase  3 vilvgGKGGVGKttvsaatavklsekgkkvllistDPA 40
                                       i + GKGG+GK++ ++ +a+ ++++g+kv++i  DP 
  gi|298674512|ref|YP_003726262.1| 14 RIALYGKGGIGKSSTASNVAAACADEGYKVMIIGCDPK 51
                                      57889********************************5 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.88
                                       EEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEE..E-TTC CS
                       ArsA_ATPase 211 lVvipEklslkEteRaikeLkkygikvdavivNk..llpee 249
                                       +++  E ++++  +  ++ L+k++   + ++ N   + +e+
  gi|298674512|ref|YP_003726262.1| 156 IITSGEYMPMYAANNICSGLSKINTPLNGIVCNSrdVTNEK 196
                                       6778899999999999999***9999999999975454444 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.4e-07   0.00014      28      72 ..      11      55 ..       3      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.4e-07
                                      -SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE------- CS
                              MeaB 28 raqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspft 72
                                      + +++ l G  G Gks + +++++  +++G++v ++  DP s  +
  gi|298674512|ref|YP_003726262.1| 11 KQKRIALYGKGGIGKSSTASNVAAACADEGYKVMIIGCDPKSDSS 55
                                      6789*************************************9865 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   1.7e-07   0.00017       2      53 ..      12      71 ..      11     132 .. 0.87
   2 ?   -3.7   0.0         8   7.9e+03      26      47 ..     218     240 ..     210     259 .. 0.61

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.7e-07
                            AAA_24  2 klkiliyGpsgiGKTtlakel.......gpkplfidtek.Glksldadkfpdieswedfl 53
                                      +++i++yG+ giGK+++a++        g+k+ +i ++  +  s+    +++i+++ d+l
  gi|298674512|ref|YP_003726262.1| 12 QKRIALYGKGGIGKSSTASNVaaacadeGYKVMIIGCDPkSDSSITLLGGKRIPTILDLL 71
                                      689**********************************98677777777777777666655 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 8
                            AAA_24  26 plfidtek.Glksldadkfpdie 47 
                                        ++ d+e+ G+  +d +   +i 
  gi|298674512|ref|YP_003726262.1| 218 QIVQDCEReGYSVMDIAPDSKIA 240
                                       55666776666666666655553 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   2.2e-05     0.021       9      44 ..      20      55 ..      15      65 .. 0.88
   2 ?    2.5   0.0     0.076        75      92     110 ..     118     136 ..     110     139 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.2e-05
                                      STTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HH CS
                              MipZ  9 kGGsGksttavhvavaLlkkGarvaaidldlrqrtl 44
                                      kGG Gks ta  va a +++G +v  i  d +  ++
  gi|298674512|ref|YP_003726262.1| 20 KGGIGKSSTASNVAAACADEGYKVMIIGCDPKSDSS 55
                                      9**************************999877665 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.076
                                       HHHHHHHH-SEEEEE--SS CS
                              MipZ  92 lvadleaeldfividtPGs 110
                                        ++d ++e+d+i+ d+PG 
  gi|298674512|ref|YP_003726262.1| 118 RISDSMKEMDLIIYDVPGD 136
                                       4578899**********96 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   8.8e-06    0.0088       3      38 ..      14      49 ..      12      56 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 8.8e-06
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                       i+l G  G+GK +t++ +aa + +eg+kv+++ +D
  gi|298674512|ref|YP_003726262.1| 14 RIALYGKGGIGKSSTASNVAAACADEGYKVMIIGCD 49
                                      6899*******************************9 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.7e-05     0.017      16      54 ..       5      43 ..       1      48 [. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.7e-05
                                      TS-SSS---EEEEE-SSSSSTTTTHHHHHHHGGGS--EE CS
                              DAP3 16 kadkkkkvkrlvltGekgsGKSvlLlqalayAlekgwvv 54
                                       +d+++k+kr+ l+G+ g GKS + + + a ++++g+ v
  gi|298674512|ref|YP_003726262.1|  5 TNDNNQKQKRIALYGKGGIGKSSTASNVAAACADEGYKV 43
                                      459**************************9999997654 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.8e-05     0.038      33      60 ..      12      40 ..       9      54 .. 0.85
   2 ?   -4.0   0.0       9.2   9.1e+03     130     149 ..     113     132 ..     111     132 .. 0.77
   3 ?   -3.5   0.0       6.5   6.5e+03     118     139 ..     231     252 ..     220     259 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.8e-05
                            AAA_25 33 gelallaGapgtGKttlaldlalava.tG 60
                                      ++ ++l+G +g GK+  a+++a+a+a +G
  gi|298674512|ref|YP_003726262.1| 12 QKRIALYGKGGIGKSSTASNVAAACAdEG 40
                                      67899*********************555 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 9.2
                            AAA_25 130 vdaleaaieevegvrlvviD 149
                                       +++l +  +++++ +l++ D
  gi|298674512|ref|YP_003726262.1| 113 INQLKRISDSMKEMDLIIYD 132
                                       77888888888888888855 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 6.5
                            AAA_25 118 akdrggtlltadvdaleaaiee 139
                                       ++++ ++++++++++l+++i +
  gi|298674512|ref|YP_003726262.1| 231 MDIAPDSKIAQVYRELAQKIMS 252
                                       5667778888999999988876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   6.8e-05     0.068      25      63 ..      13      51 ..       4     116 .. 0.76
   2 ?   -1.7   0.0       3.4   3.4e+03      72      88 ..     239     253 ..     197     283 .. 0.48

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.8e-05
                            AAA_16 25 elvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                        + l+G  G+GKss +  ++ a  ++g  ++   cd  
  gi|298674512|ref|YP_003726262.1| 13 KRIALYGKGGIGKSSTASNVAAACADEGYKVMIIGCDPK 51
                                      5688*****************655555555555555544 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.4
                            AAA_16  72 laqalareellrqllde 88 
                                       +aq+  r el +++ ++
  gi|298674512|ref|YP_003726262.1| 239 IAQVY-R-ELAQKIMSK 253
                                       33333.2.333333333 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.3e-05     0.062      31      75 ..      10      54 ..       5      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.3e-05
                             AAA_7 31 knkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsa 75
                                      +++k + l+G+ G GK+++++++  ++ +e y++++i +  + ++
  gi|298674512|ref|YP_003726262.1| 10 QKQKRIALYGKGGIGKSSTASNVAAACADEGYKVMIIGCDPKSDS 54
                                      68999******************************9998877666 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0018       1.8      21      52 ..      15      46 ..       8      65 .. 0.87
   2 ?    3.3   0.0     0.059        58      38      64 ..     219     245 ..     216     284 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0018
                            AAA_30 21 avltGpAGtGKttalkalreaweaaggrvigl 52
                                       +l G  G GK+ + + +++a +++g++v+++
  gi|298674512|ref|YP_003726262.1| 15 IALYGKGGIGKSSTASNVAAACADEGYKVMII 46
                                      578899*********************99875 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.059
                            AAA_30  38 lreaweaaggrviglAptgkaAkvLae 64 
                                       +++  e++g++v+ +Ap +k A+v +e
  gi|298674512|ref|YP_003726262.1| 219 IVQDCEREGYSVMDIAPDSKIAQVYRE 245
                                       56678999***************9775 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0034       3.4       4      56 ..      11      59 ..       7      88 .. 0.68
   2 ?    2.9   0.0      0.12   1.2e+02      37      86 ..     217     277 ..     187     287 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0034
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaee.erpevvfvtlpsstsskdl 56
                                      +++ ++++G  G+GK+ ++ +++         +e  ++ ++ ++++s++s + l
  gi|298674512|ref|YP_003726262.1| 11 KQKRIALYGKGGIGKSSTASNVAAACA-----DEgYKVMIIGCDPKSDSSITLL 59
                                      677799***************998752.....2224555555555555555555 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.12
                            AAA_22  37 e......erpevvfvtlpsstsskdllrellralglelka.....erlsseellealeqal 86 
                                       e      er ++  ++++ +++ ++++rel++++ ++++      +  + e+l+e+ ++++
  gi|298674512|ref|YP_003726262.1| 217 EqivqdcEREGYSVMDIAPDSKIAQVYRELAQKIMSKTEPdsvlpNSMDDEQLRELARKQS 277
                                       0444456677777899999999999999999999998888766664444444444444444 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00022      0.22      45      79 ..      10      44 ..       4      49 .. 0.89
   2 ?   -2.5   0.0       3.8   3.7e+03      97     115 ..     114     132 ..     112     135 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                         IstB_IS21 45 ekkenivllGpsGvGKshlaialgveavraglsvl 79
                                      +k++ i+l G  G+GKs  a  ++ + + +g++v+
  gi|298674512|ref|YP_003726262.1| 10 QKQKRIALYGKGGIGKSSTASNVAAACADEGYKVM 44
                                      67889*********************999****97 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.8
                         IstB_IS21  97 gklaralkrllkvdllilD 115
                                       ++l+r+ +++ ++dl+i D
  gi|298674512|ref|YP_003726262.1| 114 NQLKRISDSMKEMDLIIYD 132
                                       578999999999***9988 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1    0.0048       4.8       3      36 ..      19      52 ..      17      55 .. 0.92
   2 ?    2.9   0.0     0.082        82      69     102 ..     110     137 ..      93     146 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0048
                        ATP_bind_1  3 GpaGsGKttfvgalseilelrgrsvavvNLDPAa 36
                                      G  G GK++  ++++  + ++g++v ++  DP +
  gi|298674512|ref|YP_003726262.1| 19 GKGGIGKSSTASNVAAACADEGYKVMIIGCDPKS 52
                                      888****************************966 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.082
                        ATP_bind_1  69 vvaleflresldwldeelekeeddyllfDtPGQi 102
                                       +va++ l+      ++++  +e d++++D+PG i
  gi|298674512|ref|YP_003726262.1| 110 IVAINQLKRI----SDSM--KEMDLIIYDVPGDI 137
                                       5555533332....3333..2449********76 PP

>> DUF1611  Domain of unknown function (DUF1611_C) P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00095      0.95       8      51 ..       8      50 ..       3      57 .. 0.87
   2 ?   -1.4   0.0       1.2   1.2e+03     157     185 ..     181     207 ..     164     220 .. 0.71
   3 ?   -0.7   0.0      0.72   7.2e+02     131     178 ..     225     274 ..     210     285 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00095
                           DUF1611  8 revkakrvlvvGTdcavGKrttaleleealeerGlkaafvaTgq 51
                                      ++ k kr++  G +  +GK +ta ++++a+ ++G+k+ +++ ++
  gi|298674512|ref|YP_003726262.1|  8 NNQKQKRIALYGKG-GIGKSSTASNVAAACADEGYKVMIIGCDP 50
                                      56789999999987.69********************9999876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.2
                           DUF1611 157 kvvgislNtknlseeeakealeeleeelg 185
                                        + gi  N+++++  + ke++ee+++e+g
  gi|298674512|ref|YP_003726262.1| 181 PLNGIVCNSRDVT--NEKEIVEEFAHEIG 207
                                       5789999999999..33566666666665 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.72
                           DUF1611 131 irglpeialppleeeieliealaakk..kvvgislNtknlseeeakeale 178
                                       ++g++ +++ p ++  +++++la+k   k    s+  + +++e+++e ++
  gi|298674512|ref|YP_003726262.1| 225 REGYSVMDIAPDSKIAQVYRELAQKImsKTEPDSVLPNSMDDEQLRELAR 274
                                       56677788888888888888888877664444444455555555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       823  (0.0459033); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.71u 0.33s 00:00:01.04 Elapsed: 00:00:00.55
# Mc/sec: 1611.23
//
Query:       gi|298674513|ref|YP_003726263.1|  [L=373]
Description: methanogenesis marker 13 metalloprotein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.7e-17   60.8   0.0    1.3e-16   60.3   0.0    1.3  1  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
  ------ inclusion threshold ------
      0.016   14.9   0.3      0.032   14.0   0.3    1.5  1  SHOCT           Short C-terminal domain
      0.045   13.8   0.0      0.078   13.0   0.0    1.3  1  GvpG            Gas vesicle protein G


Domain annotation for each model (and alignments):
>> Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.0   2.2e-20   1.3e-16      17     137 ..      34     148 ..      19     293 .. 0.83

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 2.2e-20
                                       EEEEES-HHHHHCCCCHHHCHHSS-HS-EEEE--HHHHSSSSHHHHHHHHHHHHHHC-TSEEEEEE-HHHHHTTTTH CS
                    Oxidored_nitro  17 lplvhGpqGCatyaralltrhfrepiplastdltekdavfGgeekLkeaikeivkrykpkaIgVittClteliGdDi 93 
                                       + ++hGp GC++ + +ll     + i +++t+l+e+  vfGg + L++ i ++v+ ++p +Ig++ tC++ +iG+D+
  gi|298674513|ref|YP_003726263.1|  34 VAILHGPPGCSFKHARLLEE---DGIHVLTTALDENCFVFGGHDELVNVINKAVDLFNPGLIGIVGTCASMIIGEDL 107
                                       789*********99999954...4569************************************************** PP

                                       HHHHHHHHHHHTSSEEEEEE--TTSSSHHHHHHHHHHHHHHHCT CS
                    Oxidored_nitro  94 eavareaeeelgeipvipvstpgfggsqseGydaalealvrklv 137
                                       +  +  a+ +    pvi v++     + ++G   ale+ +++ +
  gi|298674513|ref|YP_003726263.1| 108 HEPVLDANLDI---PVIEVEVHAGYSDNTKGVLFALESALDAGI 148
                                       *9887776554...9*****999999999999999988887655 PP

>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   5.3e-06     0.032       6      24 ..     140     158 ..     137     158 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.3e-06
                             SHOCT   6 LkeLyarGeIteEEFeakK 24 
                                       L + +++G+I++ EFe++K
  gi|298674513|ref|YP_003726263.1| 140 LESALDAGIIDRTEFERQK 158
                                       78899************99 PP

>> GvpG  Gas vesicle protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.3e-05     0.078      32      58 ..     132     158 ..     121     178 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.3e-05
                              GvpG  32 nlrkeLaaLqqeLdaGeIdeeeFdrrE 58 
                                       n +  L aL+ +LdaG Id +eF+r+ 
  gi|298674513|ref|YP_003726263.1| 132 NTKGVLFALESALDAGIIDRTEFERQK 158
                                       5566799*****************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 2074.16
//
Query:       gi|298674514|ref|YP_003726264.1|  [L=463]
Description: Mur ligase middle domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00013   22.0   0.1    0.00059   19.9   0.1    2.1  1  Mur_ligase_M  Mur ligase middle domain
     0.0046   16.3   0.0      0.027   13.8   0.0    2.1  2  HEM4          Uroporphyrinogen-III synthase HemD


Domain annotation for each model (and alignments):
>> Mur_ligase_M  Mur ligase middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   6.6e-08   0.00059       1     143 [.     119     268 ..     119     313 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 6.6e-08
                                       EESSS-HHHHHHHHHHHHHCT..EEEEETTC..................SS-THHHHHHHHHHHHHTT-SEEEEE-- CS
                      Mur_ligase_M   1 vTGtnGKTTtteliaaileka..gkvigtvg..................ttnneiglpktlaemekkeaeyavlEvs 57 
                                       vTGt  KT+t++l+a il+++  + ++++ g                  t  n +++     + +  + +++++Evs
  gi|298674514|ref|YP_003726264.1| 119 VTGTRAKTSTSSLLADILSRKldVVLHSSRGveywkeglpetiydglsiTPGNILQVMDRSFSEKL-NPDAYIFEVS 194
                                       9*****************99987778888889*********9999999887888888877776666.9********* PP

                                       HCHHHCTTTCCHCBESEEEE---TSTTHHHHSSHHHHHHHHHHHHHTSETTCEEEEETTSC...CHHHHHCTCCTCE CS
                      Mur_ligase_M  58 shglgekrlegllkpdvavitnispdHldfhgtlenyaeaKaelferlkeegiavinaddpyakelikklkkakvkv 134
                                                 g++  d  +it +++d     ++      aK ++++  k+++ ++in d +    li++++k+ +++
  gi|298674514|ref|YP_003726264.1| 195 LG------GTGIA--DFNIITTLEQDY-KIAKENRWASSAKTQMINYAKSGSKLLINTDTK---GLINHSAKKFNSI 259
                                       99......44554..445799999984.555666667889999999999999999999999...9999999988888 PP

                                       EEEESSSTS CS
                      Mur_ligase_M 135 vtfglekea 143
                                       ++f   k  
  gi|298674514|ref|YP_003726264.1| 260 FEFNDGKYP 268
                                       888776655 PP

>> HEM4  Uroporphyrinogen-III synthase HemD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0     3e-06     0.027     118     158 ..       9      48 ..       1      60 [. 0.76
   2 ?   -0.7   0.0     0.081   7.2e+02      25      61 ..     122     157 ..     116     167 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3e-06
                                       EEEEE-SS.S--HHHHHHHHHTTEEEEEE-SEEEEE-HHHH CS
                              HEM4 118 krvlllrgeiarddlaegLeergaevdevevYetvpaeeep 158
                                       k++ +l   ++ +++a++L+e g++v++v+vY t  ++++ 
  gi|298674514|ref|YP_003726264.1|   9 KNIAVLDLTHGGAIIARKLSELGYNVHAVDVYNT-EDDDTL 48 
                                       5677777778899*********************.333333 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.081
                                       CCHHHHHHHHHT.....--SEEEE--HHHHHHHHHHH CS
                              HEM4  25 aedraelraalddleagkydwliftSanavealfeal 61 
                                       ++ + + +++l d+ ++k d +++ S+++ve++ e l
  gi|298674514|ref|YP_003726264.1| 122 TRAKTSTSSLLADILSRKLD-VVLHSSRGVEYWKEGL 157
                                       55556666666555556666.5677888888876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.36s 00:00:01.00 Elapsed: 00:00:00.54
# Mc/sec: 2569.49
//
Query:       gi|298674515|ref|YP_003726265.1|  [L=134]
Description: cobalamin (vitamin B12) biosynthesis protein CbiX [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-28   99.3   0.0    1.6e-28   99.1   0.0    1.0  1  CbiX            CbiX
    1.1e-06   28.2   0.0    1.1e-06   28.2   0.0    1.0  1  CbiK            Cobalt chelatase (CbiK)
     0.0034   16.5   0.0     0.0042   16.2   0.0    1.1  1  Ferrochelatase  Ferrochelatase
  ------ inclusion threshold ------
       0.17   12.1   0.0       0.24   11.6   0.0    1.2  1  DUF1380         Protein of unknown function (DUF1380)


Domain annotation for each model (and alignments):
>> CbiX  CbiX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.1   0.0   3.6e-32   1.6e-28       1     106 [.      14     126 ..      14     127 .. 0.98

  Alignments for each domain:
  == domain 1  score: 99.1 bits;  conditional E-value: 3.6e-32
                                       -STSSCCHHHHHHHHHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTHHHHHCT CS
                              CbiX   1 HGSrdpesneeveklaeelrekgpfkpvelgfleleepsleealrelaeqgvkrivvvPlflfaGvhvkeDIpeele 77 
                                       HGS++p+ ++ v+++a+++  k++ + v+ gf+e +ep++eeal++++  g+++i++vP+fl++Gvh+++DIpe+l+
  gi|298674515|ref|YP_003726265.1|  14 HGSKLPYNKQVVTDIANRIADKHEDVVVRAGFMEKNEPTVEEALQSFEGTGISKIAAVPVFLASGVHITQDIPEILG 90 
                                       ***************************************************************************** PP

                                       --SSSS-.......TTEEEEE---CCCSCCHHHHHH CS
                              CbiX  78 eaeeahp.......kdveieytepLGthplvaevlk 106
                                        +++ ++        ++ i+y++pLG+++l+ae++ 
  gi|298674515|ref|YP_003726265.1|  91 IDPDSKEgsiklngTEIPIVYGNPLGSDDLLAELVY 126
                                       99999999****9999*****************986 PP

>> CbiK  Cobalt chelatase (CbiK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   2.5e-10   1.1e-06     144     260 ..       9     132 ..       1     134 [] 0.78

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 2.5e-10
                                       EEEEE---SCHHHH.HHHHHHHHHHHCT-S.EEE..EETT.SSS-HHHHHHHHHHHT--EEEEEE-SSS--HHHHCC CS
                              CbiK 144 lvfvgHGtehesna.vyaeldkvlkekdfkqvvv..gtve.gyPeveevieelkkkgikevkliPlmlvAGdHaknD 216
                                       ++ +gHG++ + n+ v + + + + +k+ ++vvv  g +e   P+vee +++ +++gi ++  +P++l  G H ++D
  gi|298674515|ref|YP_003726265.1|   9 ILAIGHGSKLPYNKqVVTDIANRIADKH-EDVVVraGFMEkNEPTVEEALQSFEGTGISKIAAVPVFLASGVHITQD 84 
                                       6779*****9987625566766666654.44444226665278********************************** PP

                                       CCS...SSTTSHHHHHHHTT--EEE.----GGGSHHHHHHHHHHHHHH CS
                              CbiK 217 mas...deedswkealeaaGikvei.ilkgLGeieeirsifikhikea 260
                                       + +    + ds    ++ +G ++ i + + LG+++ ++++  ++ +ea
  gi|298674515|ref|YP_003726265.1|  85 IPEilgIDPDSKEGSIKLNGTEIPIvYGNPLGSDDLLAELVYNRAQEA 132
                                       864222699**************6537899****99999888887776 PP

>> Ferrochelatase  Ferrochelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   9.4e-07    0.0042      64     123 ..      15      74 ..       3      85 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.4e-07
                                       S-SHHHHHHHHHHHHHHHHHHH---EEEEEE.ESSSSSBHHHHHHHHHCTT-SEEEEEES- CS
                    Ferrochelatase  64 gSPlneitrkqaealekelaergidvkvyla.mrywePsiedaleelkadgvervvvlply 123
                                       gS  + ++++  + +++++a+++ dv v  + m+  eP +e+al+ ++ +g+ ++ ++p +
  gi|298674515|ref|YP_003726265.1|  15 GSK-LPYNKQVVTDIANRIADKHEDVVVRAGfMEKNEPTVEEALQSFEGTGISKIAAVPVF 74 
                                       554.46899*********************9557799*********************986 PP

>> DUF1380  Protein of unknown function (DUF1380)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.4e-05      0.24      71     122 ..      23      74 ..      19      86 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.4e-05
                           DUF1380  71 aavmelieqvkenrktvtvpadllatllrtaeqalwkrewaardaglavPes 122
                                       ++v ++ + + + ++ v+v a+++++   t e+al + e++   + +avP  
  gi|298674515|ref|YP_003726265.1|  23 QVVTDIANRIADKHEDVVVRAGFMEKNEPTVEEALQSFEGTGISKIAAVPVF 74 
                                       57899999**********************************9999999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.34s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 792.41
//
Query:       gi|298674516|ref|YP_003726266.1|  [L=423]
Description: group 1 glycosyl transferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.8e-32  110.2   0.0    1.5e-31  109.2   0.0    1.4  1  Glycos_transf_1  Glycosyl transferases group 1
    7.9e-27   94.3   1.3    1.3e-26   93.6   1.3    1.4  1  Glyco_transf_4   Glycosyltransferase Family 4
    4.4e-25   88.7   0.0    1.2e-24   87.2   0.0    1.8  1  Glyco_trans_1_4  Glycosyl transferases group 1
    2.4e-18   67.1   0.0    3.4e-18   66.6   0.0    1.2  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    3.9e-17   62.8   0.9    2.4e-14   53.6   0.9    2.3  1  Glyco_transf_5   Starch synthase catalytic domain
    9.3e-10   38.7   0.0    1.8e-09   37.7   0.0    1.4  1  Glyco_trans_4_2  Glycosyl transferase 4-like
     0.0082   16.5   0.0      0.017   15.5   0.0    1.4  1  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
      0.073   12.9   0.0       0.17   11.8   0.0    1.5  1  PDZ_3            PDZ domain
      0.089   12.1   0.0       0.14   11.5   0.0    1.3  1  Marek_SORF3      Marek's disease-like virus SORF3 protein


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.2   0.0   7.6e-35   1.5e-31       7     156 ..     240     384 ..     237     398 .. 0.92

  Alignments for each domain:
  == domain 1  score: 109.2 bits;  conditional E-value: 7.6e-35
                                       HHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHS CS
                   Glycos_transf_1   7 kklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsr 83 
                                       kk+g+    +i+l++gr++++Kg+dll+++++ +    +++v++v++G+g+++   ++lae l++sd ++flg+ s+
  gi|298674516|ref|YP_003726266.1| 240 KKYGIHPLAPIVLFIGRMNYQKGPDLLVESVPMILNH-RQDVQFVFIGEGDMRSHCEYLAETLGVSDSCHFLGYASD 315
                                       6777777789************************976.*************************************** PP

                                       SSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHH CS
                   Glycos_transf_1  84 edleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairkll 156
                                       e+ + ++++++++++ps++E+fGiv+lEA  ag+pv+as+a    ++v + ++G++v ++ +e++a +++ ++
  gi|298674516|ref|YP_003726266.1| 316 EAAIDWYNACNVVCMPSRNEPFGIVVLEAWDAGKPVVASDA---VKLVDNFKNGVVVYKY-PESIAWGVNYVV 384
                                       ****************************************6...5678888888899999.999999998876 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.6   1.3   6.6e-30   1.3e-26       1     168 [.      53     226 ..      53     228 .. 0.81

  Alignments for each domain:
  == domain 1  score: 93.6 bits;  conditional E-value: 6.6e-30
                    Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeev...elvvrvprvpl..pllkrllrslaflrrlrrllkre. 71 
                                       vGG++ hv eL++aLa++GheV++vt++d+ + +      ++++r+++ p   ++++ ++   a+++ + ++ +++ 
  gi|298674516|ref|YP_003726266.1|  53 VGGIAPHVTELSEALAEKGHEVHIVTRNDGNHDAHDIingVHYHRIVYDPSgdVIHQMNKMCDAMYSTFLEVRDEYg 129
                                       7***************************9999999886554444444444211222222233333444444444448 PP

                    Glyco_transf_4  72 kpDvvHahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrl..lrradrviavSeatad 146
                                       ++Dv+H h+++++  +l +l+++lg+p+Vlt+H+++ +++ ++r++p  ++ +   r +     +  vi++S+ + d
  gi|298674516|ref|YP_003726266.1| 130 EFDVLHGHDWHPV-TVLCRLKHELGLPFVLTYHSTE-WGRNGNRHNPDPIAQEITQREWlgGYESSEVIVTSQVLYD 204
                                       ************8.677888889*************.9***************9999996777899*********** PP

                    Glyco_transf_4 147 elrerygvppekitVipnGvDl 168
                                       e++ +y++p  ki ++pnG  +
  gi|298674516|ref|YP_003726266.1| 205 EVVYLYQIPDYKISIVPNGTHI 226
                                       *******************865 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.2   0.0   6.2e-28   1.2e-24       2     125 ..     249     377 ..     248     385 .. 0.82

  Alignments for each domain:
  == domain 1  score: 87.2 bits;  conditional E-value: 6.2e-28
                                       EEEEEES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---...HHHHHHHT..T-T.TEEEE---..THHHHHHH CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk..dvrlvivGdgp.rpeeleelaa..gleerveftGfv..edlaella 71 
                                       p++lf+Gr+   +kg dll+e vp ++++  dv++v++G+g+ r+ ++e la+  g++++++f+G+   e   ++++
  gi|298674516|ref|YP_003726266.1| 249 PIVLFIGRM-NYQKGPDLLVESVPMILNHrqDVQFVFIGEGDmRS-HCEYLAEtlGVSDSCHFLGYAsdEAAIDWYN 323
                                       89*******.567**********999966435*********9665.7775555679***********6444****** PP

                                       H-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--.T.TSSEE--TT-HHHHH CS
                   Glyco_trans_1_4  72 aadvfvaPs..egfglkllEamaaglpvVatdvggiaevv.g.engllvppgdpeala 125
                                       a++v+++Ps  e fg+++lEa  ag+pvVa+d+     +v + +ng++v  + pe++a
  gi|298674516|ref|YP_003726266.1| 324 ACNVVCMPSrnEPFGIVVLEAWDAGKPVVASDAVK---LVdNfKNGVVVY-KYPESIA 377
                                       *********999*******************9955...444448998885.3466666 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.6   0.0   1.7e-21   3.4e-18       1     160 []      54     223 ..      54     223 .. 0.82

  Alignments for each domain:
  == domain 1  score: 66.6 bits;  conditional E-value: 1.7e-21
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpspladla.alralrrll...rqrrer 73 
                                       gGi+ +v el++aLa+ GheV+++t+++ + + +   +gv++hr+   ++++    +  ++ a+ +++   r +   
  gi|298674516|ref|YP_003726266.1|  54 GGIAPHVTELSEALAEKGHEVHIVTRNDGNHDAHDIINGVHYHRIVYDPSGDVIHQMNkMCDAMYSTFlevRDEYGE 130
                                       8*************************999999988899*******9999998666554266666665556578899* PP

                   Glyco_trans_4_4  74 pdvvhahspt.aglaarlarrrrgiplvvtlhgll.lrrg.sgavrrlyral.errllrr..adavlvvseaeaeel 144
                                       +dv+h h+++    ++rl     g+p+v+t+h+++ +r g  +   ++++++ +r  l +     v+v+s+ + +e+
  gi|298674516|ref|YP_003726266.1| 131 FDVLHGHDWHpVTVLCRLKH-ELGLPFVLTYHSTEwGRNGnRHNPDPIAQEItQREWLGGyeSSEVIVTSQVLYDEV 206
                                       *********63677777777.99*********855255555556777888886554444445999************ PP

                   Glyco_trans_4_4 145 ra.lgvpadrvvvvpng 160
                                       +  + +p+ ++ +vpng
  gi|298674516|ref|YP_003726266.1| 207 VYlYQIPDYKISIVPNG 223
                                       **788***********8 PP

>> Glyco_transf_5  Starch synthase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   0.9   1.2e-17   2.4e-14       1     182 [.      39     173 ..      39     211 .. 0.78

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 1.2e-17
                    Glyco_transf_5   1 kilfvasEvaplaktGGLadvvgaLpkaLaklghdvrvilPrygaikeekkeleevaelskaaedevevevekvkva 77 
                                       +i ++++E    +k+GG+a +v++L++aLa++gh+v++++ + g+ ++     +++++                   
  gi|298674516|ref|YP_003726266.1|  39 RIGMFSWESLHAVKVGGIAPHVTELSEALAEKGHEVHIVTRNDGNHDA-----HDIIN------------------- 91 
                                       6889************************************87744443.....34444................... PP

                    Glyco_transf_5  78 klkkdgvdvyfldnpeffdreglYgdkgedyednaerfalfsraalellekl..gw.kpdvihahDWhtalvpallk 151
                                            gv+++ +          +Y     +  d  +++  ++ a+  +  ++  ++ ++dv+h hDWh + v + lk
  gi|298674516|ref|YP_003726266.1|  92 -----GVHYHRI----------VYD----PSGDVIHQMNKMCDAMYSTFLEVrdEYgEFDVLHGHDWHPVTVLCRLK 149
                                       .....8888863..........452....34567777888888888888887666645******************* PP

                    Glyco_transf_5 152 el.ykerglfkkiktvftiHNlayqgrfpkde 182
                                       +            ++v+t H++++ ++ +++ 
  gi|298674516|ref|YP_003726266.1| 150 HElG--------LPFVLTYHSTEWGRNGNRHN 173
                                       *955........*************9999654 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.0   9.2e-13   1.8e-09      11     110 ..      58     164 ..      51     187 .. 0.80

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 9.2e-13
                   Glyco_trans_4_2  11 vhtlrlakeLakrgyeVhvitpkkga.kdeleaegihvhrlkvd.....rkg..pleylkafklkklikki.kPDvv 78 
                                       +h+++l ++La++g+eVh++t+++g  + +++ +g+h hr+  d     ++   ++ ++++ ++ ++ ++  ++Dv+
  gi|298674516|ref|YP_003726266.1|  58 PHVTELSEALAEKGHEVHIVTRNDGNhDAHDIINGVHYHRIVYDpsgdvIHQmnKMCDAMYSTFLEVRDEYgEFDVL 134
                                       79********************7776699************55544455333356666666788899888636**** PP

                   Glyco_trans_4_2  79 hahyakpygllgslaarlsgvipvvlsvwGld 110
                                       h h   p+ +l +l +  +g  p+vl+ + + 
  gi|298674516|ref|YP_003726266.1| 135 HGHDWHPVTVLCRL-KHELG-LPFVLTYHSTE 164
                                       ********999988.56666.9*****99776 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   8.3e-06     0.017       4      85 ..     330     408 ..     325     414 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.3e-06
                   Glyco_trans_1_2   4 npsrsespnlrlfEaaacGafaltddaegleelftpgkevilfedleelaekiryllanpeerraiaeaarervlae 80 
                                        psr+e +  +++Ea  +G +++++da  l + f++g  v++++ +e++a  ++y+++  ++ +++++ +re v+++
  gi|298674516|ref|YP_003726266.1| 330 MPSRNEPFGIVVLEAWDAGKPVVASDAVKLVDNFKNG--VVVYKYPESIAWGVNYVVDGLGD-DSMGNFGRELVETK 403
                                       499********************************99..***************99877777.78999999999999 PP

                   Glyco_trans_1_2  81 htydh 85 
                                       ++++ 
  gi|298674516|ref|YP_003726266.1| 404 YNWTT 408
                                       98875 PP

>> PDZ_3  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   8.5e-05      0.17      32      94 ..     162     230 ..     151     234 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.5e-05
                             PDZ_3  32 gkdwakkapirlldralygilee......edqevvlLsqvLaselntGyenianlqlkkv.NgtkvknLk 94 
                                       +++w ++ +++  d ++++i ++      e++ev++ sqvL +e+ + y +i + +++ v Ngt++++++
  gi|298674516|ref|YP_003726266.1| 162 STEWGRNGNRHNPDPIAQEITQRewlggyESSEVIVTSQVLYDEVVYLY-QIPDYKISIVpNGTHINKIR 230
                                       4555555666666666666665566667799******************.99999999887999998876 PP

>> Marek_SORF3  Marek's disease-like virus SORF3 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0     7e-05      0.14     107     168 ..      32      91 ..      13     129 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7e-05
                       Marek_SORF3 107 ltetGkleilyrlwdvrdalkikvlGpklmalfsavlenatailsiainkGydrhntrsmdm 168
                                       +++ Gk++i  + w+   a+k+  + p++  l  a +e    +  +++n G   h+++++  
  gi|298674516|ref|YP_003726266.1|  32 IVKEGKYRIGMFSWESLHAVKVGGIAPHVTELSEALAEKGHEVHIVTRNDGN--HDAHDIIN 91 
                                       6788**********************************************85..44444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.66u 0.36s 00:00:01.02 Elapsed: 00:00:00.55
# Mc/sec: 2313.37
//
Query:       gi|298674517|ref|YP_003726267.1|  [L=212]
Description: hypothetical protein Metev_0560 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-73  246.4  12.5    2.3e-73  246.2  12.5    1.0  1  DUF2150   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2150  Uncharacterized protein conserved in archaea (DUF2150)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.2  12.5   1.3e-77   2.3e-73       1     188 []      14     203 ..      14     203 .. 0.99

  Alignments for each domain:
  == domain 1  score: 246.2 bits;  conditional E-value: 1.3e-77
                           DUF2150   1 eFYteeRwqNWlnrvkeedldleedseele..aavllnlqdDvilavlkiikaveeeelskeeAleeleevreivle 75 
                                       eFYt++Rw+NW+n+vke+ ++++e++ee+e  +a+++++qdDvila+lk+i+++e++ lske++l+ ++++reivle
  gi|298674517|ref|YP_003726267.1|  14 EFYTQKRWNNWINKVKESGFEFKESDEETEkeSAIFVYMQDDVILACLKVIAQYERNILSKEDTLDIISQIREIVLE 90 
                                       7**********************888888889********************************************* PP

                           DUF2150  76 eveeddeekeeliesvqtsllvvfaaaeeyieggvakekdieelvkaaaeaeaeedleaaleivaqiGakvidgekl 152
                                       e+++++e+++ +ies+qtsl++++aa+e yi+++++ke++i+el+kaa++ae++edl+ a++++a++Ga+vi ge+l
  gi|298674517|ref|YP_003726267.1|  91 EIDSISEDIDLMIESLQTSLMAAIAACEVYIMDEYDKEAKIDELIKAAVDAEDSEDLQVAMQFIAETGARVIGGEQL 167
                                       ***************************************************************************** PP

                           DUF2150 153 pekvledleyglvaewldgidslaaamsssesveee 188
                                       pe+++++l+yglvaewldgids+aaam++++s++e+
  gi|298674517|ref|YP_003726267.1| 168 PENIFDELPYGLVAEWLDGIDSIAAAMVGADSYKED 203
                                       **********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1369  (0.0763567); expected 358.6 (0.02)
Passed bias filter:                      704  (0.039266); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 1222.61
//
Query:       gi|298674518|ref|YP_003726268.1|  [L=149]
Description: hypothetical protein Metev_0561 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.3e-51  173.3   5.2    2.6e-51  173.2   5.2    1.0  1  UPF0179      Uncharacterised protein family (UPF0179)
  ------ inclusion threshold ------
       0.23   11.7   2.4        0.5   10.6   0.2    2.0  2  DDE_Tnp_1_6  Transposase DDE domain


Domain annotation for each model (and alignments):
>> UPF0179  Uncharacterised protein family (UPF0179)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.2   5.2   2.9e-55   2.6e-51       1     140 []       8     147 ..       8     147 .. 0.99

  Alignments for each domain:
  == domain 1  score: 173.2 bits;  conditional E-value: 2.9e-55
                           UPF0179   1 kitLigkklAkeGteFiylgeaeeCekCklkkvClnLekgrkYrivevrekteheCavheegvvaveveeapieali 77 
                                       k+tL+g +lAkeG+eFiy ge+++C++Ck+k +C nLe grkYr+ ++r+ t+h C +h++gv++vev+++p++a+i
  gi|298674518|ref|YP_003726268.1|   8 KVTLVGCRLAKEGQEFIYWGESPDCSGCKIKGTCNNLEAGRKYRVEKIRNGTVHGCYLHDQGVMVVEVSRTPVVATI 84 
                                       69*************************************************************************** PP

                           UPF0179  78 eskkavegskitleseeCdevecesyelcepeglkegekvkivevlgeieeckkgrslkkvel 140
                                       eskkav g+ki++e+ +C+e++ce y +c p+glk+g+k++iv+v+++++ec +g+slkkvel
  gi|298674518|ref|YP_003726268.1|  85 ESKKAVPGAKINFEPIKCSEINCEFYGYCYPKGLKSGDKCTIVNVMDDVDECLRGKSLKKVEL 147
                                       *************************************************************96 PP

>> DDE_Tnp_1_6  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   5.6e-05       0.5      28      55 ..      27      54 ..       5      62 .. 0.80
   2 ?    1.2   0.2     0.046   4.2e+02      28      55 ..      97     128 ..      78     144 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.6e-05
                       DDE_Tnp_1_6 28 yrlkdCrgCplreqCtkkkkgrqltirp 55
                                       +  dC gC+ +  C + ++gr+ ++++
  gi|298674518|ref|YP_003726268.1| 27 GESPDCSGCKIKGTCNNLEAGRKYRVEK 54
                                      5789**************9999988876 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.046
                       DDE_Tnp_1_6  28 yrlkdCr..gCplreqCtkk..kkgrqltirp 55 
                                       ++  +C   +C++   C+ k  k+g + ti +
  gi|298674518|ref|YP_003726268.1|  97 FEPIKCSeiNCEFYGYCYPKglKSGDKCTIVN 128
                                       6677776337*******999887787777754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.36s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 871.67
//
Query:       gi|298674519|ref|YP_003726269.1|  [L=356]
Description: 3-dehydroquinate synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.7e-73  245.5   4.5    8.8e-73  245.1   4.5    1.1  1  Fe-ADH_2      Iron-containing alcohol dehydrogenase
    3.5e-23   82.0   3.5    1.1e-22   80.4   3.5    1.7  1  Fe-ADH        Iron-containing alcohol dehydrogenase
    4.1e-07   29.4   0.2    1.6e-06   27.5   0.2    1.9  1  DHQ_synthase  3-dehydroquinate synthase


Domain annotation for each model (and alignments):
>> Fe-ADH_2  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  245.1   4.5   1.5e-76   8.8e-73       2     250 .]      20     277 ..      19     277 .. 0.93

  Alignments for each domain:
  == domain 1  score: 245.1 bits;  conditional E-value: 1.5e-76
                          Fe-ADH_2   2 igegaleklgellkelel.kkvllvadentkkaagekveeslkeagikvevveeveeeadleeveklvealreketd 77 
                                       +g g+++++ +++++l+l +++l+v++  t k+ag+ v+++l+++g +ve+++  + +a+++ev+++ +++++ + +
  gi|298674519|ref|YP_003726269.1|  20 VGTGVINDITDVCNDLKLgDNALIVTGDSTRKIAGDIVHDELEDKGRSVEMYT--SSSATMDEVRRVEDEAMKYGSN 94 
                                       899*************9637******************************997..78******************** PP

                          Fe-ADH_2  78 lvvavGgGtiiDiakyvsaklnvpyvsvpTaaSvDGfaspgaslvvdgkkrtvakaaaPlaviaDldvlaeAPrrll 154
                                        +++vG+G+ iDiak+++++l++p++svpTaaS+DG+ s+ as+++d k++++ + +aP+av+aD++++a+AP rll
  gi|298674519|ref|YP_003726269.1|  95 YLLGVGSGNSIDIAKLAATELDIPFLSVPTAASHDGIVSSRASIIHDSKTTSI-QSNAPMAVVADTEIIANAPYRLL 170
                                       ***********************************************988888.99********************* PP

                          Fe-ADH_2 155 asGvGDllgkytaladwklan........evseplaklsaamvqeaaeklvedkke..tealeellea.lalsgigi 220
                                       a+G+GD++++yta+ dw+la+        e++++l++++a+++ ++a+++  + ++  + ++++l+++ +a+s++g+
  gi|298674519|ref|YP_003726269.1| 171 AAGCGDIVSNYTAVLDWELASrlknesfsEYAASLSRMTAKILIDSADSIKPELESsaRLVVKALVSSgVAMSIAGS 247
                                       *********************999998888899***************9987433222555566665536******* PP

                          Fe-ADH_2 221 srpaSGsEHliSHaldmlalkqalHGeqVG 250
                                       srpaSGsEH++SHald +a+ +alHGeq+G
  gi|298674519|ref|YP_003726269.1| 248 SRPASGSEHMFSHALDSIAPGSALHGEQCG 277
                                       *****************************9 PP

>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.4   3.5   1.8e-26   1.1e-22       1     276 [.      15     278 ..      15     343 .. 0.86

  Alignments for each domain:
  == domain 1  score: 80.4 bits;  conditional E-value: 1.8e-26
                                       -SEEEEETTGGGGHHHHHTTT-...EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTT CS
                            Fe-ADH   1 Ptrivfgkgaleelgellkklg.akralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaal 76 
                                       P+ +v g+g+++++ + + +l+  ++alivt+ ++  k  + d v ++le++g +v++++  ++  t +ev+++ + 
  gi|298674519|ref|YP_003726269.1|  15 PRDVVVGTGVINDITDVCNDLKlGDNALIVTGDSTR-KI-AGDIVHDELEDKGRSVEMYT--SSSATMDEVRRVEDE 87 
                                       889****************997337********965.54.89999*************99..6799*********** PP

                                       S-TT.--EEEEEESHHHHHHHHHHHHHTT..................--EEEEESS-S-S-TT-SEEEEE.-TTSEE CS
                            Fe-ADH  77 areegadvviavGGGsviDtAKaialllanpevedylgegkakkkkalpliaiPTtaGtGsevtplavitdeeegek 153
                                       a + g +++++vG G +iD+AK++a  l                   +p+  +PT a+ +  v++ a i  +++ + 
  gi|298674519|ref|YP_003726269.1|  88 AMKYGSNYLLGVGSGNSIDIAKLAATELD------------------IPFLSVPTAASHDGIVSSRASII-HDS-KT 144
                                       *****************************..................************99999999888.444.46 PP

                                       EEE-..SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHH....HHHHT---TTSSB--HHHHHHHHHHHHHHHH CS
                            Fe-ADH 154 lsifdpellPdlaivDpeltltlPkrvtaatglDalahalEa....yvskkanplsdalaleairliaknleravad 226
                                       +si   +  P +++ D+e+++++P r++aa+ +D+++ +       ++s+ +n+    +a +  r+ ak l ++ + 
  gi|298674519|ref|YP_003726269.1| 145 TSIQ--SNAPMAVVADTEIIANAPYRLLAAGCGDIVSNYTAVldweLASRLKNESFSEYAASLSRMTAKILIDSADS 219
                                       7777..889**************************998877733333336666655567777777777777777776 PP

                                       HH.HHHHHHHHHHHHHH.HHHHHHSS---.....HHHHHHHHHHC.C.GGG.GGS-HHH CS
                            Fe-ADH 227 ge.dleareqmllastl.aglafsnaglg.....avHalahalgalf.gip.hglanai 276
                                        +  le  ++++  +++ +g+a+s ag +       H+++hal ++  g + hg+ +++
  gi|298674519|ref|YP_003726269.1| 220 IKpELESSARLVVKALVsSGVAMSIAGSSrpasgSEHMFSHALDSIApGSAlHGEQCGV 278
                                       445889999999999999***999999998888899*******9966555568888776 PP

>> DHQ_synthase  3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.2   2.6e-10   1.6e-06      31     216 ..      93     288 ..      70     324 .. 0.73

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 2.6e-10
                                       T-EEEEEESHHHHHHHHHHHHHBTT--EEEEEE-SHHHHHTTTSSSEEEEEETTEEEEEEEE---SEEEEEGGGGGG CS
                      DHQ_synthase  31 ksllialGGGvvgDlaGfvAatylRGvrfvqvPttllaqvDssvGgKtainlplgKNliGafaqPkavlidlevLkt 107
                                       +++l+ +G G   D+a ++A  +   + f+ vPt+  a  D  v  + +i ++ +   i +   P av++d+e+++ 
  gi|298674519|ref|YP_003726269.1|  93 SNYLLGVGSGNSIDIAKLAATELD--IPFLSVPTA--ASHDGIVSSRASIIHDSKTTSIQS-NAPMAVVADTEIIAN 164
                                       6799**************998875..********7..999************999999976.78************* PP

                                       S-HHHHHHHHHHHH.HHHHHT-HHHHHHHHHHHHHHHC...........TTTHHHHHHHH.....HHHHHHHHHHHH CS
                      DHQ_synthase 108 LperelraGlaEvi.Kyalikdeelfelleenaeallk...........eeeeealeeli.....arsievkaevve 167
                                        p r l+aG+++++  y+++ d el ++l++++ +  +                           +  +e  a+ v 
  gi|298674519|ref|YP_003726269.1| 165 APYRLLAAGCGDIVsNYTAVLDWELASRLKNESFSEYAaslsrmtakilI---------DsadsiKPELESSARLVV 232
                                       ************9846999*************999988666665544441.........032222333444444444 PP

                                       HCCTT........TTGGGGGGTTHHHHHHHHHHHTTTTS-HHHHHHHHHHHHHHHHH CS
                      DHQ_synthase 168 eDeke........kglralLnlGHtigHaiEallgyekllHGeaVaiGmvlaaelse 216
                                       +             + r +    H ++Ha+++++   + lHGe   +G ++ ++l  
  gi|298674519|ref|YP_003726269.1| 233 KALVSsgvamsiaGSSRPASGSEHMFSHALDSIAPG-SALHGEQCGVGTIMMMYLHG 288
                                       44444000001114556667788**********987.9***********99998863 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 2066.42
//
Query:       gi|298674520|ref|YP_003726270.1|  [L=283]
Description: hypothetical protein Metev_0563 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   6.6e-106  354.5  26.0   7.4e-106  354.3  26.0    1.0  1  DUF63      Membrane protein of unknown function DUF63


Domain annotation for each model (and alignments):
>> DUF63  Membrane protein of unknown function DUF63
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  354.3  26.0  4.1e-110  7.4e-106       1     272 []       8     283 .]       8     283 .] 0.99

  Alignments for each domain:
  == domain 1  score: 354.3 bits;  conditional E-value: 4.1e-110
                             DUF63   1 iseFiykyYidpivykegYnivntltyaiiLivavyliykllkklkikidekfvlatipyvilgsslRvveDagllk 77 
                                       i+eFi++yYidpi+ ++gYn+vnt+t+ai L+++++ ++kl+k+l+i++d++f+l++ip++++gsslRvveDag+++
  gi|298674520|ref|YP_003726270.1|   8 IWEFIQNYYIDPIIFDTGYNPVNTITWAIFLGIFLFGVIKLFKRLNISVDDRFILSIIPFILAGSSLRVVEDAGIFN 84 
                                       89*************************************************************************** PP

                             DUF63  78 pplsyllitPliyflvflitlavlliskklekk.lkkdykklyaavGvvlvlvvlllLllteevvnlevlllvllla 153
                                       +p++yllitP+iyflvf+i++++l++sk l +k ++kdy+ l+a +G++++++++ +Ll+ e+vvnl+v+ +v+++a
  gi|298674520|ref|YP_003726270.1|  85 APVNYLLITPIIYFLVFAIVILTLVVSKWLYNKeFIKDYHILVASIGSLWFIFNVSILLYFENVVNLYVPYFVIGAA 161
                                       *******************************999******************************************* PP

                             DUF63 154 avltalvllllrklklellsdklnlllllahllDasatfvgidllgYvEqHvvpsfLidltGtalvmyplkllvlip 230
                                       ++l+++v+ +l++  l++ls++ln+++++ahllDas+t+vgidllgY+E+Hvvps+Li+lt+ta+vmyplk+l++ip
  gi|298674520|ref|YP_003726270.1| 162 TLLVFIVYKILKYSGLDILSTNLNFAIMWAHLLDASSTIVGIDLLGYHEKHVVPSYLIELTNTATVMYPLKILIFIP 238
                                       ***************************************************************************** PP

                             DUF63 231 vlyildkevkeeee...lrnlvklailvlGlaPgiRnllrmvlgv 272
                                       vlyild++++e++e   l+++vk++il+lGlaP++Rn++rm+lg+
  gi|298674520|ref|YP_003726270.1| 239 VLYILDSYFNEDREsrnLKTFVKIVILILGLAPACRNTIRMTLGI 283
                                       ***********999899**************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.36s 00:00:00.99 Elapsed: 00:00:00.57
# Mc/sec: 1500.95
//
Query:       gi|298674521|ref|YP_003726271.1|  [L=202]
Description: hypothetical protein Metev_0564 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-35  120.6  20.2    7.3e-35  120.3  20.2    1.1  1  SpoIIM    Stage II sporulation protein M
  ------ inclusion threshold ------
      0.028   14.4   0.1       0.11   12.5   0.1    2.0  1  JmjN      jmjN domain
       0.16   11.8   1.0       0.22   11.3   0.2    1.6  2  ATG27     Autophagy-related protein 27


Domain annotation for each model (and alignments):
>> SpoIIM  Stage II sporulation protein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.3  20.2   1.2e-38   7.3e-35       2     156 .]      28     195 ..      19     195 .. 0.92

  Alignments for each domain:
  == domain 1  score: 120.3 bits;  conditional E-value: 1.2e-38
                            SpoIIM   2 lllflvgillgallaasnfa...eqis......seskensalslflaifanNlrvalllfllGllllgiptilvlli 69 
                                       ++lf+ +i++ga++++ n++   ++++      +  k+ ++ +++l+if+nN+  +l+++llG+  +gi+++ ++++
  gi|298674521|ref|YP_003726271.1|  28 VALFISSIIIGAVYSSMNPEiaqQSMEefrnmiDFIKSLPPYAIMLFIFVNNTVKTLIALLLGI-GFGIIPFAFIAY 103
                                       679*************66666543333777888899999999*********************8.************ PP

                            SpoIIM  70 nGfvlGavaalvaefgglllflllilPhgilelpaiiiagaaglrlgkal.....rsrrkalkeakrellklllllv 141
                                       nG+++G++++++a  +gl++++ ++lPhgi+elp+++i++a+gl+lg ++      ++ + ++e+ r +  +++++v
  gi|298674521|ref|YP_003726271.1| 104 NGYIIGIFGFITAMEKGLFYLVTALLPHGIIELPMVFISAAIGLKLGHEMfnsvtGRKANIKEELSRGIRFYFYWIV 180
                                       ********999999988***********************************99877788888899999******** PP

                            SpoIIM 142 pllliAaliEafvtp 156
                                       pll++Aa +E+f+tp
  gi|298674521|ref|YP_003726271.1| 181 PLLFVAAAVETFITP 195
                                       **************8 PP

>> JmjN  jmjN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   1.9e-05      0.11       6      24 ..      52      70 ..      52      72 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.9e-05
                                      -HHHHC-HHHHHHHHHHHH CS
                              JmjN  6 TeeEFkdplkYiekieplg 24
                                      ++eEF++ + +i++  p++
  gi|298674521|ref|YP_003726271.1| 52 SMEEFRNMIDFIKSLPPYA 70
                                      7*************99886 PP

>> ATG27  Autophagy-related protein 27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   3.7e-05      0.22     193     255 ..      18      80 ..       5      84 .. 0.77
   2 ?   -2.3   0.0      0.55   3.3e+03     197     210 ..     175     188 ..     160     189 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.7e-05
                             ATG27 193 sgwGfFtwlfiilflataaYlifgsw..lNynryGargwDllphgdtirdlPyllkDvvrkvlgt 255
                                       ++++f  +l+ii+ l++++ +i+ ++  +N +  ++++ ++++  d+i++lP  +  +  +v +t
  gi|298674521|ref|YP_003726271.1|  18 NSISF--YLLIIVALFISSIIIGAVYssMNPEIAQQSMEEFRNMIDFIKSLPPYAIMLFIFVNNT 80 
                                       67888..899999999999998776622677788999***************8766555555555 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.55
                             ATG27 197 fFtwlfiilflata 210
                                       +F w++ +lf+a+a
  gi|298674521|ref|YP_003726271.1| 175 YFYWIVPLLFVAAA 188
                                       69999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1089  (0.0607396); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.37s 00:00:00.98 Elapsed: 00:00:00.55
# Mc/sec: 1104.78
//
Query:       gi|298674522|ref|YP_003726272.1|  [L=383]
Description: IMP biosynthesis enzyme PurP domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-78  260.6   0.0    8.5e-78  260.2   0.0    1.2  1  DUF1297   Domain of unknown function (DUF1297)
    2.1e-42  143.9   0.0    3.6e-42  143.2   0.0    1.4  1  DUF1246   Protein of unknown function (DUF1246)
  ------ inclusion threshold ------
       0.11   12.4   0.0        1.6    8.6   0.0    2.3  2  TnpW      Transposon-encoded protein TnpW


Domain annotation for each model (and alignments):
>> DUF1297  Domain of unknown function (DUF1297)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  260.2   0.0   1.4e-81   8.5e-78       1     188 []     189     383 .]     189     383 .] 0.98

  Alignments for each domain:
  == domain 1  score: 260.2 bits;  conditional E-value: 1.4e-81
                                       HHHHHHHHHHCTTSSSHHHHCCEEEEE---SEEEEEEEEEETTT...TEEEEEEEEEEEEEECCCHCCS-HHHHHCC CS
                           DUF1297   1 efeekleellekglieeedlkkasieeyvvGanfnlnyfysplk...eevellgidrRyesnldglvrlpakeqlel 74 
                                       e+ +k+++ll++g+i++++l++a+ie+y++G  fn+++fysp++   +++ellgid+R+e++ldg+vrlpa +q++l
  gi|298674522|ref|YP_003726272.1| 189 EYLDKANNLLDRGIITQDALDNAVIEKYIIGPVFNFDMFYSPIEdemNKLELLGIDWRFETSLDGHVRLPAPQQMTL 265
                                       6889****************************************888899*************************99 PP

                                       T-...---EEEEEEEEEEE-GGGHHHHHHHHHHHHHHHHHHSTT---EEEEEEEEE-TTS-EEEEEEESSB-GGGGG CS
                           DUF1297  75 ev...epeyvvvGnipvvlREsllekvfelgekfveaakklvppGiiGpFcLqsvvtkdlelvvfdvsaRivggtnv 148
                                       ++   +pey+v+G+++ +lREsll+k+fel+ek+vea++k+++pGiiGpFcLq++++kdl+++++dv++Ri+ggtnv
  gi|298674522|ref|YP_003726272.1| 266 SEhqmNPEYTVCGHNSSTLRESLLDKIFELSEKYVEATQKYYDPGIIGPFCLQTCIDKDLNFHIYDVAPRIGGGTNV 342
                                       887789*********************************************************************** PP

                                       GTT.--CCHHHTTSS---HHHHHHHHHHHHHHCT-GGGCEE CS
                           DUF1297 149 yme.gspyskllfgeplsmGrrialEikeaiekdrleeivt 188
                                       +m+ g++y ++l+++p+s+Grr+a+Eik+aie+++l++ivt
  gi|298674522|ref|YP_003726272.1| 343 HMSvGHSYGNTLWRKPMSTGRRVAFEIKRAIETEQLDKIVT 383
                                       ****************************************8 PP

>> DUF1246  Protein of unknown function (DUF1246)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.2   0.0   6.1e-46   3.6e-42       1     121 [.      21     155 ..      21     156 .. 0.98

  Alignments for each domain:
  == domain 1  score: 143.2 bits;  conditional E-value: 6.1e-46
                                       EEEESSTTHHHHHHHHHHTT--EEEEC-CCCHHHHHTT.............TT-SEEEE.S.S..TTSS--HHHHHH CS
                           DUF1246   1 iatlaSHsalqilkgAkkegfrtlavcekgreklYekf.............kvidevivldkfkdilkeevqeklre 64 
                                       ++t++SHsal++++gA +egf+t+a c++grek+Y+++             +++de  v+++f+dil+++  +kl++
  gi|298674522|ref|YP_003726272.1|  21 VGTVGSHSALDVFDGAVEEGFNTFAACKSGREKTYNQYfkakrdsegnvirGIVDEASVFSRFDDILNHQ--QKLVD 95 
                                       79************************************************99***************775..***** PP

                                       TTCEE--BTTHHHHC-HHHHH.C-SS-EES-TTHHHHHCSHHHHHHH..HHHTT-BB--B CS
                           DUF1246  65 enailvPhgsfveYvgiekie.elkvpifGnrkllrwEerrekkrky..LekAgiriPkk 121
                                       +n+++vP++sf++Y+gie++e ++kvp++G+r+llr+Eer  + ++y  L+kAg+++P++
  gi|298674522|ref|YP_003726272.1|  96 DNVLFVPNRSFTTYCGIENVEnNFKVPLVGSRNLLRSEERGMDYDYYwiLDKAGLPYPER 155
                                       **********************************************99**********97 PP

>> TnpW  Transposon-encoded protein TnpW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.056   3.4e+02      13      32 ..     179     198 ..     179     200 .. 0.90
   2 ?    8.6   0.0   0.00027       1.6       9      29 ..     273     293 ..     271     295 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.056
                              TnpW  13 rvhFsetatETiaDKikRli 32 
                                       r++F   + E + DK + l+
  gi|298674522|ref|YP_003726272.1| 179 RGFFTAASYEEYLDKANNLL 198
                                       689999999********997 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00027
                              TnpW   9 TYvVrvhFsetatETiaDKik 29 
                                        Y+V++h s t +E++ DKi 
  gi|298674522|ref|YP_003726272.1| 273 EYTVCGHNSSTLRESLLDKIF 293
                                       5******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 2170.34
//
Query:       gi|298674523|ref|YP_003726273.1|  [L=410]
Description: protein synthesis factor GTP-binding protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-31  108.8   0.1    3.1e-31  107.5   0.1    1.8  1  eIF2_C        Initiation factor eIF2 gamma, C terminal
    1.2e-31  109.8   1.6    8.4e-31  107.0   1.6    2.0  1  GTP_EFTU      Elongation factor Tu GTP binding domain
    5.1e-07   30.0   0.3    1.7e-06   28.3   0.3    1.9  1  GTP_EFTU_D2   Elongation factor Tu domain 2
    3.1e-05   24.0   0.0     0.0001   22.3   0.0    1.9  1  MMR_HSR1      50S ribosome-binding GTPase
      7e-05   22.8   1.0    0.00093   19.1   0.2    2.2  2  RsgA_GTPase   RsgA GTPase
     0.0019   18.2   0.2     0.0036   17.3   0.2    1.5  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
     0.0042   16.8   2.9        1.9    8.2   0.0    2.9  3  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
  ------ inclusion threshold ------
      0.051   13.6   2.6        0.1   12.7   2.6    1.4  1  Nop10p        Nucleolar RNA-binding protein, Nop10p family
      0.079   10.8   0.2       0.11   10.4   0.2    1.1  1  PolC_DP2      DNA polymerase II large subunit DP2
      0.097   12.2   1.3         13    5.3   0.0    2.8  2  FeoB_N        Ferrous iron transport protein B


Domain annotation for each model (and alignments):
>> eIF2_C  Initiation factor eIF2 gamma, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.5   0.1   1.7e-34   3.1e-31       2      86 .]     322     408 ..     321     408 .. 0.97

  Alignments for each domain:
  == domain 1  score: 107.5 bits;  conditional E-value: 1.7e-34
                                       EEEEEEEE-SBESSSSSCCC..-----TTEEEEEEETTEEEEEEEEEEESSEEEEEEEEEEE-STTEEEEEEEEETT CS
                            eIF2_C   2 eleieyellerlvgvkeekk..veklkkkEvLmlniGsastggvvtsvkkdeakvkLkkPvcaekgekialsRrvek 76 
                                       +l++e++l++++vgv+ee++  + ++k++E+Lmln+G+a+t+g+vts+++d+a+vkLk+Pvcae g+ +a+sRr+++
  gi|298674523|ref|YP_003726273.1| 322 SLKLELHLFDKIVGVTEETNadIGNIKTSEPLMLNVGTATTVGIVTSARSDVAEVKLKRPVCAEAGSMVAISRRIGS 398
                                       6899*************97778******************************************************* PP

                                       SEEEEEEEEE CS
                            eIF2_C  77 rWrLiGwGei 86 
                                       rWrLiG G i
  gi|298674523|ref|YP_003726273.1| 399 RWRLIGAGAI 408
                                       ********87 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.0   1.6   4.7e-34   8.4e-31       3     193 ..       5     197 ..       3     198 .. 0.84

  Alignments for each domain:
  == domain 1  score: 107.0 bits;  conditional E-value: 4.7e-34
                                       EEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE............... CS
                          GTP_EFTU   3 irnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle............... 64 
                                        +nig++ghvDhGKtTL+ +L                   +D+++eE +rgi+i    +                  
  gi|298674523|ref|YP_003726273.1|   5 CVNIGLVGHVDHGKTTLVRALSGIW---------------TDRHSEEMKRGISIRLGYADATlrecsdcpvpncytv 66 
                                       68*****************998333...............5666666666666666666666666666666666666 PP

                                       .........TTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB.STHHHHHHHHHHHHTTTE.EEEEEE CS
                          GTP_EFTU  65 .........ketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveG.vepqteevlrlalkegvp.iivfiN 130
                                                ++t+ ++i+++D+PGH+  + ++  g++++Dgavlv++a+e  ++pqt+e+l  ++  g++ ii++ N
  gi|298674523|ref|YP_003726273.1|  67 entcpecdsETTELRKISFVDSPGHETLMATMLSGAAIMDGAVLVIAANEKcPQPQTKEHLMALNIIGIKnIIIVQN 143
                                       777777766699*************************************8879*****************9****** PP

                                       SCGST.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHSH CS
                          GTP_EFTU 131 KmDrl.kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvellp 193
                                       K+D + ++++ e  +++k+ +         +g+ +e + pv+++Sa ++ +++ l++a+ + +p
  gi|298674523|ref|YP_003726273.1| 144 KIDLVtRDKMVEHYHQIKDFV---------AGTVAE-DAPVIPISAQQNINIDVLIKAMEDIIP 197
                                       *****9999999999999444.........444443.68********************99988 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.3   9.8e-10   1.7e-06       1      65 [.     229     300 ..     229     310 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 9.8e-10
                                       EEEEEEEEEESEEETTEEEEEEC.TCTTSEE.......EEEEEEEEEEETEEESEEETTSEEEEEEEESSCCS CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskke.......ivtrissletfhededeavaganaGvivaikgled 65 
                                       G+v++g++ +G+l+ Gde++i++  ++ ++e       i+t +s l++  e+++e+ +g+ + v++ +++  +
  gi|298674523|ref|YP_003726273.1| 229 GGVIGGTLKDGKLNSGDELEIRPgRKV-ESEgsvkwepITTNVSMLLAGTERLEEVTPGGLIAVGTTLDPSLT 300
                                       89*********************6655.6668********************************999987665 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   5.8e-08    0.0001       1     114 []       7     144 ..       7     144 .. 0.64

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 5.8e-08
                                       EEEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEE..ETTEE........................... CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvk..lkgke........................... 47 
                                       ++++vG+   GK+tL++al+g  + + s++    + i+ g  +  l+  e                           
  gi|298674523|ref|YP_003726273.1|   7 NIGLVGHVDHGKTTLVRALSGIwTDRHSEEMKRGISIRLGYADatLR--Ecsdcpvpncytventcpecdsettelr 81 
                                       589*****************966555556555555555554442233..1333455555555555555666666666 PP

                                       .EEEEECGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHHHHH.TTSEEEEEEES CS
                          MMR_HSR1  48 .ielvDtpGliegaseekglgkaflalee.adlillvvdaseeklkpldeeleellee.akkplilvlnk 114
                                        i +vD pG  e       l  ++l+    +d ++lv+ a+e+  +p+ +e    l+    k++i+v nk
  gi|298674523|ref|YP_003726273.1|  82 kISFVDSPG-HE------TLMATMLSGAAiMDGAVLVIAANEKCPQPQTKEHLMALNIiGIKNIIIVQNK 144
                                       6********.55......7889999877768*******98855455555554444433234556666665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.11     2e+02     104     136 ..      10      39 ..       6      43 .. 0.76
   2 !   19.1   0.2   5.2e-07   0.00093      12      99 ..      98     194 ..      78     198 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.11
                                       EECSTTSSHHHHHHHHCTT-----S-------- CS
                       RsgA_GTPase 104 lvGqSGvGKStLinallpelelktgevseklgr 136
                                       lvG+   GK+tL+ al +     t   se+++r
  gi|298674523|ref|YP_003726273.1|  10 LVGHVDHGKTTLVRALSGI---WTDRHSEEMKR 39 
                                       7899999*********985...55555555555 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 5.2e-07
                                       T...EES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-.EEEEEEE-GGG--HHH......HHHHHHHHHHHTTSE CS
                       RsgA_GTPase  12 k...vaNvdqllivvslkepelslnlldrfLvlaeekgi.epvivlnKiDlleeee......eleelkeelealgye 78 
                                           +a +d +++v++++ +++ + + +  L++++  gi +++iv nKiDl+++++      +++++ + + a + +
  gi|298674523|ref|YP_003726273.1|  98 MlsgAAIMDGAVLVIAAN-EKCPQPQTKEHLMALNIIGIkNIIIVQNKIDLVTRDKmvehyhQIKDFVAGTVAEDAP 173
                                       15558999**********.677777778888999999995778889********99888777777777788888999 PP

                                       EEE--TTTHTTHHHHHHHCTT CS
                       RsgA_GTPase  79 vllvsaktkegleelkellkd 99 
                                       v+ +sa+++ +++ l ++++d
  gi|298674523|ref|YP_003726273.1| 174 VIPISAQQNINIDVLIKAMED 194
                                       999999999999999888765 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.2     2e-06    0.0036      57     100 ..     137     192 ..      94     196 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2e-06
                      MMR_HSR1_Xtn  57 pclyvlNKiDlisleeldelare............pnsvviSaekelnldeLkeki 100
                                       + ++v NKiDl++ +++ e +++              +++iSa++++n+d L +++
  gi|298674523|ref|YP_003726273.1| 137 NIIIVQNKIDLVTRDKMVEHYHQikdfvagtvaedAPVIPISAQQNINIDVLIKAM 192
                                       568999*****99999888888668899999997668999***********99876 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0011       1.9       4      23 ..       8      27 ..       6      38 .. 0.88
   2 !    6.9   0.7    0.0027       4.8      40     142 ..      85     193 ..      75     194 .. 0.56
   3 ?   -0.6   0.0      0.56     1e+03      92     137 ..     333     376 ..     324     387 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0011
                         PduV-EutP  4 illiGkvgsGKttLtqalkg 23
                                      i l+G+v+ GKttL +al+g
  gi|298674523|ref|YP_003726273.1|  8 IGLVGHVDHGKTTLVRALSG 27
                                      669***************97 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0027
                         PduV-EutP  40 viDtPGeylenrklysalivtsaeadvialvqdateeesvfppgfasvfnkeviGi......itkidlaedeeniea 110
                                       ++D+PG      ++ s  +++   + via        ++  p++  ++++ ++iGi        kidl++ ++ +e 
  gi|298674523|ref|YP_003726273.1|  85 FVDSPGHETLMATMLSGAAIMDGAVLVIAANE-----KCPQPQTKEHLMALNIIGIkniiivQNKIDLVTRDKMVEH 156
                                       57888854444444444444433333444333.....4445555555555555553222111679****88888877 PP

                         PduV-EutP 111 veelLk.saGa....ekifevsavekegieellkyle 142
                                        ++     aG     + ++ +sa ++++i+ l+k +e
  gi|298674523|ref|YP_003726273.1| 157 YHQIKDfVAGTvaedAPVIPISAQQNINIDVLIKAME 193
                                       55543323453222134799**********9999876 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.56
                         PduV-EutP  92 viGiitkidlaedeenieaveelLksaGaekifevsavekegieel 137
                                       ++G+   ++ a d  ni+++e l+ ++G ++   + +  ++++ e+
  gi|298674523|ref|YP_003726273.1| 333 IVGVTEETN-A-DIGNIKTSEPLMLNVGTATTVGIVTSARSDVAEV 376
                                       555443333.2.4667777777777777777666666655555554 PP

>> Nop10p  Nucleolar RNA-binding protein, Nop10p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.6   5.7e-05       0.1       4      28 ..      51      78 ..      49      80 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.7e-05
                                      --EE-TTT-...-EESSSB-TTT-SB-B CS
                            Nop10p  4 ylrkcgkcr...vYTLkkvcpecggptk 28
                                      +lr+c++c     YT +++cpec ++t+
  gi|298674523|ref|YP_003726273.1| 51 TLRECSDCPvpnCYTVENTCPECDSETT 78
                                      6899999987778************996 PP

>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   6.1e-05      0.11     616     757 ..      50     194 ..      31     198 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 6.1e-05
                          PolC_DP2 616 iarrkCkkC...gketlearCeeCgekteeklvCkkceeeveeekcekcekeakavkkkkidlkellekaleklger 689
                                        + r+C++C   +  t+e++C+eC+++t+e  + + +++  +e  +  + + a  ++   + + +  +  + + +e 
  gi|298674523|ref|YP_003726273.1|  50 ATLRECSDCpvpNCYTVENTCPECDSETTELRKISFVDSPGHETLMATMLSGAAIMDGAVLVIAANEKCPQPQTKE- 125
                                       566788888433568999************9999999998877666666666666666655555555555555565. PP

                          PolC_DP2 690 eekleelkgvkglts.kekipEpleKgilRakhdvsvfkdgtvRyDmtdlplthfrpkeigvsveklre 757
                                       +    ++ g+k+++  ++ki       ++   h++  f  gtv  D+  +p+++ +  +i+v ++ +++
  gi|298674523|ref|YP_003726273.1| 126 HLMALNIIGIKNIIIvQNKIDLVTRDKMVEHYHQIKDFVAGTVAEDAPVIPISAQQNINIDVLIKAMED 194
                                       44666777888876515555555566789999********************99999999998887765 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0073        13       2      23 ..       7      28 ..       6      31 .. 0.90
   2 ?    4.7   0.6     0.011        20     106     155 ..     136     191 ..      62     192 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0073
                                      EEEEEESTTSSHHHHHHHHHTT CS
                            FeoB_N  2 tvalvGnpnvGkttlfnaltga 23
                                      ++ lvG  + Gkttl+ al+g 
  gi|298674523|ref|YP_003726273.1|  7 NIGLVGHVDHGKTTLVRALSGI 28
                                      689****************985 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.011
                                       SSEEEEEETHHHHHHTTEEE-HHHHHHHH......TS-EEEEBTTTTBTHHHHHHH CS
                            FeoB_N 106 vpvvlalnmideaekkgieidlkkLsekL......gvpvvktsakkkegieellka 155
                                       ++++++ n+id ++++++  + +++++ +      + pv+++sa+++ +i+ l+ka
  gi|298674523|ref|YP_003726273.1| 136 KNIIIVQNKIDLVTRDKMVEHYHQIKDFVagtvaeDAPVIPISAQQNINIDVLIKA 191
                                       46888899999999999998888888766433344689************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2842.32
//
Query:       gi|298674524|ref|YP_003726274.1|  [L=122]
Description: nucleotide-binding protein PInc [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-46  157.6   1.0    1.5e-46  157.4   1.0    1.0  1  PIN_9          PIN like domain
     0.0003   21.1   0.9     0.0006   20.1   0.9    1.6  1  PIN_4          PIN domain
  ------ inclusion threshold ------
      0.015   15.5   0.0      0.032   14.4   0.0    1.6  2  PIN_10         PIN like domain
      0.031   14.0   0.4       0.12   12.1   0.3    2.1  2  DUF5615        Domain of unknown function (DUF5615)
      0.038   13.4   0.2        2.9    7.3   0.2    2.1  2  PIN_5          PINc domain ribonuclease
      0.038   13.6   0.4      0.059   13.0   0.3    1.3  1  DUF188         Uncharacterized BCR, YaiI/YqxD family COG1671
      0.096   12.5   0.2       0.11   12.3   0.2    1.3  1  RNase_Zc3h12a  Zc3h12a-like Ribonuclease NYN domain


Domain annotation for each model (and alignments):
>> PIN_9  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.4   1.0     6e-50   1.5e-46       1     116 []       3     115 ..       3     115 .. 0.99

  Alignments for each domain:
  == domain 1  score: 157.4 bits;  conditional E-value: 6e-50
                             PIN_9   1 vilDtnaLmipvqfgvdifeelerllgsvelvvpkavleELerlakagkgkertaakvalsLaerceiveaeeekaD 77 
                                       vi+DtnaLmipvqf+vdif+el+rl g+++++vpkavl+EL++l+k+ kg++++aakva+sL ++cei++++ + aD
  gi|298674524|ref|YP_003726274.1|   3 VIIDTNALMIPVQFNVDIFQELKRL-GYNKFLVPKAVLNELDTLVKKSKGSDKAAAKVACSLGNKCEIINQT-GIAD 77 
                                       8************************.**********************************************.**** PP

                             PIN_9  78 dailelakeldaavlvTnDreLkkrllekgipvilLRqk 116
                                       ++i++la+eld avl TnD+eLkkrl++k+ipvi+LRqk
  gi|298674524|ref|YP_003726274.1|  78 EVIIKLANELDSAVL-TNDIELKKRLIDKNIPVIYLRQK 115
                                       ***************.**********************8 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.9   2.3e-07    0.0006       1      79 [.       3      89 ..       3     121 .. 0.58

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.3e-07
                             PIN_4  1 fVlDTnvlLhdpealksf......keehdvviPitVleELdklKkgsse..relarlarqanrlldel...lekesgrl 68
                                      +++DTn l+  +++   +       + ++  +P  Vl+ELd l k+s+   +   ++a+ a +l +++    +    + 
  gi|298674524|ref|YP_003726274.1|  3 VIIDTNALMIPVQFNVDIfqelkrLGYNKFLVPKAVLNELDTLVKKSKGsdK---AAAKVACSLGNKCeiiNQTGIADE 78
                                      589******988775555677788799***************9777763221...222222233333321122223333 PP

                             PIN_4 69 kvqtsaeelpe 79
                                      ++ ++a+el++
  gi|298674524|ref|YP_003726274.1| 79 VIIKLANELDS 89
                                      44444444443 PP

>> PIN_10  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.8   7.1e+03       1       9 [.       1       9 [.       1      15 [. 0.84
   2 ?   14.4   0.0   1.2e-05     0.032      11      65 ..      36     101 ..      33     114 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.8
                            PIN_10 1 MkfflDenl 9
                                     Mk+ +D n 
  gi|298674524|ref|YP_003726274.1| 1 MKVIIDTNA 9
                                     999999885 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 1.2e-05
                            PIN_10  11 palakaLrelleeeghevvhlrdkf...........aagtkDeeWiaalaeggwvvltkDrrirkr 65 
                                       +a+   L++l+++++ +    +++            + g +De  i++++e +++vlt+D +++kr
  gi|298674524|ref|YP_003726274.1|  36 KAVLNELDTLVKKSKGSDKAAAKVAcslgnkceiinQTGIADEVIIKLANELDSAVLTNDIELKKR 101
                                       556666666666555333333333333333346777999*************************99 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.9   7.4e+03       8      22 ..      15      29 ..      10      35 .. 0.68
   2 ?   12.1   0.3   4.8e-05      0.12      30      59 ..      70      99 ..      65     115 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.9
                           DUF5615  8 nlsprlvellreagh 22
                                      +++ ++ ++l+++g+
  gi|298674524|ref|YP_003726274.1| 15 QFNVDIFQELKRLGY 29
                                      566666667766666 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 4.8e-05
                           DUF5615 30 lglegasDeeileyAkeedriivTkDkDFg 59
                                      +++ g+ De i+++A+e d +++T+D    
  gi|298674524|ref|YP_003726274.1| 70 INQTGIADEVIIKLANELDSAVLTNDIELK 99
                                      46789*********************6555 PP

>> PIN_5  PINc domain ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0    0.0058        15      44      79 ..      31      66 ..       5      81 .. 0.80
   2 ?    7.3   0.2    0.0011       2.9     162     182 ..      80     100 ..      69     116 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0058
                             PIN_5 44 scyippsvykElkeflkreeveeeviakldtwlvkk 79
                                      ++ +p++v +El +++k+++ +++  ak+   l  k
  gi|298674524|ref|YP_003726274.1| 31 KFLVPKAVLNELDTLVKKSKGSDKAAAKVACSLGNK 66
                                      456889999999999999999999999998877666 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0011
                             PIN_5 162 vllLAkELdaavvssDeGikk 182
                                       ++ LA+ELd+av+++D  +kk
  gi|298674524|ref|YP_003726274.1|  80 IIKLANELDSAVLTNDIELKK 100
                                       456*************88876 PP

>> DUF188  Uncharacterized BCR, YaiI/YqxD family COG1671
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   2.3e-05     0.059      37      74 ..      72     110 ..      55     115 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.3e-05
                            DUF188  37 gadaaDdaIveraeagD.lvvTqDipLAarvlekgaaal 74 
                                       +   aD+ I++ a++ D  v T+Di L +r+++k++ ++
  gi|298674524|ref|YP_003726274.1|  72 QTGIADEVIIKLANELDsAVLTNDIELKKRLIDKNIPVI 110
                                       5567*********99883688*************99988 PP

>> RNase_Zc3h12a  Zc3h12a-like Ribonuclease NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   4.3e-05      0.11      78     111 ..      71      96 ..      18     121 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.3e-05
                     RNase_Zc3h12a  78 pskyldgkksvsyddrlilelAeekdGvivsndn 111
                                       ++            d++i++lA+e d  +++nd 
  gi|298674524|ref|YP_003726274.1|  71 NQTG--------IADEVIIKLANELDSAVLTNDI 96 
                                       3333........44******************93 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 891.29
//
Query:       gi|298674525|ref|YP_003726275.1|  [L=188]
Description: DNA-directed RNA polymerase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-18   67.1   0.0    2.2e-18   66.4   0.0    1.4  1  SHS2_Rpb7-N    SHS2 domain found in N terminus of Rpb7p/Rpc25
    8.2e-11   42.1   0.4    2.8e-10   40.4   0.0    1.9  2  S1             S1 RNA binding domain
  ------ inclusion threshold ------
       0.14   12.4   0.1       0.33   11.2   0.1    1.7  1  RNA_pol_Rbc25  RNA polymerase III subunit Rpc25


Domain annotation for each model (and alignments):
>> SHS2_Rpb7-N  SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.4   0.0   3.7e-22   2.2e-18       2      70 .]       9      77 ..       8      77 .. 0.98

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 3.7e-22
                                      EEEEE-GGGTTSTHHHHHHHHHHHHHTTBEETTTEEEEEEEEEEEECCEEE-TTTSSEEEEEEEEEEEE CS
                       SHS2_Rpb7-N  2 dtvrlePsylgstledallerllekyegkvvpslGvivavldiaeysegkvlggsGsvyvrVtfralvF 70
                                      dtvr+ P  lg++ + +++++l++k+eg+++++ G iva++di++++eg+++ g+G+vy++Vtf+a+vF
  gi|298674525|ref|YP_003726275.1|  9 DTVRISPDRLGDDETLSVKDALKNKLEGRIDKKNGSIVAITDIESIGEGHIIMGDGAVYYDVTFKAIVF 77
                                      9***********9999****************************************************9 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       0.4   2.4e+03      47      72 ..      21      46 ..      19      49 .. 0.71
   2 !   40.4   0.0   4.6e-14   2.8e-10       5      64 ..      82     150 ..      79     160 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.4
                                      HHCEETTEEEEEEEEEEETTTTEEEE CS
                                S1 47 devlkvGdevkvkvlkvdkdrrriil 72
                                      de+l+v+d +k k+++  +++++ i+
  gi|298674525|ref|YP_003726275.1| 21 DETLSVKDALKNKLEGRIDKKNGSIV 46
                                      67888888888888876666665655 PP

  == domain 2  score: 40.4 bits;  conditional E-value: 4.6e-14
                                       TCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSS..........CEESCHHHCEETTEEEEEEEEEEE CS
                                S1   5 gevveGeVtsvtkgGafVelgngvegfvpaselsrd..........arvedpdevlkvGdevkvkvlkvd 64 
                                        ev+eG+V++++++Gaf+ +g  ++g++++s++ +d             +++++ l +Gd +++++  v 
  gi|298674525|ref|YP_003726275.1|  82 QEVIEGKVVEIVDFGAFISFG-AMDGLLHVSQITDDfmsydgknarLISKNSNRALAEGDYLRARIVAVS 150
                                       59*******************.*********************9998889999*******9999999886 PP

>> RNA_pol_Rbc25  RNA polymerase III subunit Rpc25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   5.5e-05      0.33       1      90 [.      79     165 ..      79     187 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.5e-05
                                       -STTSEEEEEEEEEETTCEEEEBTTBSEEEEECCCCSTTEEEECCCTCEEEEESSSEEEEE-TTSEEEEEEEEEEE- CS
                     RNA_pol_Rbc25   1 PfvgevltgkiksstregikvslgffddifvpkelLfepsefdeeeqawvweveeeeelyldvgeeirfrveeeifv 77 
                                       P+++ev++gk+ +    g ++s g +d ++   +   + +++d ++   + +    ++  l  g+ +r r++ ++ +
  gi|298674525|ref|YP_003726275.1|  79 PMMQEVIEGKVVEIVDFGAFISFGAMDGLLHVSQITDDFMSYDGKNARLISKN---SNRALAEGDYLRARIVAVSIN 152
                                       99**************************9999999999999999998877766...6777889*************9 PP

                                       ------HHHHHCH CS
                     RNA_pol_Rbc25  78 dvkpkspkeaele 90 
                                       +++p+++k   + 
  gi|298674525|ref|YP_003726275.1| 153 ERDPRESKIGLTM 165
                                       9999888755444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1398.53
//
Query:       gi|298674526|ref|YP_003726276.1|  [L=61]
Description: DNA-directed RNA polymerase subunit E [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.2e-14   52.1   0.2    6.2e-14   51.8   0.2    1.1  1  Spt4            Spt4/RpoE2 zinc finger
    0.00085   19.3   0.2     0.0015   18.5   0.2    1.4  1  Nop10p          Nucleolar RNA-binding protein, Nop10p family
     0.0052   16.4   2.9       0.17   11.6   0.1    2.1  2  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII
  ------ inclusion threshold ------
      0.016   14.8   3.0      0.023   14.3   3.0    1.2  1  RecR            RecR protein
      0.016   14.6   2.3       0.03   13.7   0.3    2.0  2  zf-ribbon_3     zinc-ribbon domain
      0.021   14.9   1.4      0.029   14.5   1.4    1.2  1  DUF1272         Protein of unknown function (DUF1272)
      0.035   13.8   1.9      0.044   13.5   1.9    1.1  1  TackOD1         Thaumarchaeal output domain 1
      0.036   13.6   3.2       0.15   11.6   0.3    2.5  3  TF_Zn_Ribbon    TFIIB zinc-binding
      0.039   13.8   1.8      0.059   13.2   1.8    1.2  1  Prok-RING_4     Prokaryotic RING finger family 4
       0.12   10.3   0.1      0.094   10.6   0.1    1.1  1  PolC_DP2        DNA polymerase II large subunit DP2
       0.15   10.8   1.1       0.18   10.5   1.1    1.1  1  NRDD            Anaerobic ribonucleoside-triphosphate reducta
       0.35   11.0   3.7        5.3    7.3   3.7    2.1  1  Zn-ribbon_8     Zinc ribbon domain
        1.8    8.6   5.4        1.2    9.2   0.2    2.1  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
        6.9    7.0   6.4        2.7    8.3   0.8    2.1  2  Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase


Domain annotation for each model (and alignments):
>> Spt4  Spt4/RpoE2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.2   4.9e-17   6.2e-14       2      77 .]       4      61 .]       3      61 .] 0.96

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 4.9e-17
                              Spt4  2 rACllCklvktedqFeeegCpnCeilelkgdkekvsectseefeGlvaildpekSwvAkwqrldkkvpglYAlkve 77
                                      + C++C++++ ++      Cp+C           +s+++s++++Glv+i+dp+kS++A++  ++ ++p++YAlkv+
  gi|298674526|ref|YP_003726276.1|  4 QVCRECHRITLNQV-----CPVC-----------GSSNLSTDWSGLVIIIDPKKSKIAEK--IGIEMPDKYALKVR 61
                                      68*******99888.....****...........**************************..************96 PP

>> Nop10p  Nucleolar RNA-binding protein, Nop10p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.2   1.2e-06    0.0015       6      26 ..       4      24 ..       1      29 [. 0.87

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.2e-06
                                      EE-TTT--EESSSB-TTT-SB CS
                            Nop10p  6 rkcgkcrvYTLkkvcpecggp 26
                                      ++c++c++ TL++vcp cg+ 
  gi|298674526|ref|YP_003726276.1|  4 QVCRECHRITLNQVCPVCGSS 24
                                      58*****************86 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.6     0.011        15      23      28 ..       5      10 ..       3      12 .. 0.91
   2 !   11.6   0.1   0.00013      0.17       4      15 ..      15      30 ..      13      31 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.011
                           zf-RRN7 23 yCrrCh 28
                                      +Cr+Ch
  gi|298674526|ref|YP_003726276.1|  5 VCRECH 10
                                      8***** PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00013
                           zf-RRN7  4 gppCgvCgc....rsf 15
                                      + +C+vCg+    +++
  gi|298674526|ref|YP_003726276.1| 15 NQVCPVCGSsnlsTDW 30
                                      679******7666666 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   3.0   1.8e-05     0.023      18      36 ..       5      23 ..       4      25 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.8e-05
                                      E-TTT--EESSSS-CCCCS CS
                              RecR 18 hCsrCgnlteedlCaICsd 36
                                       C++C+ +t + +C++C +
  gi|298674526|ref|YP_003726276.1|  5 VCRECHRITLNQVCPVCGS 23
                                      5****************76 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.37   4.7e+02      17      22 ..       4       9 ..       2       9 .. 0.78
   2 ?   13.7   0.3   2.3e-05      0.03       4      16 ..      17      30 ..      15      31 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.37
                       zf-ribbon_3 17 nvCpyC 22
                                      +vC  C
  gi|298674526|ref|YP_003726276.1|  4 QVCREC 9 
                                      789999 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2.3e-05
                       zf-ribbon_3  4 rCPnCGa.plssdd 16
                                       CP CG+ +ls+d+
  gi|298674526|ref|YP_003726276.1| 17 VCPVCGSsNLSTDW 30
                                      7******99**998 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.4   2.3e-05     0.029      32      48 ..       6      22 ..       3      27 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.3e-05
                           DUF1272 32 CaeCaeevlenvCPncg 48
                                      C+eC+  +l++vCP cg
  gi|298674526|ref|YP_003726276.1|  6 CRECHRITLNQVCPVCG 22
                                      ****************9 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.9   3.4e-05     0.044      73     100 ..       3      28 ..       1      31 [. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.4e-05
                           TackOD1  73 irlCpsCksghlnvrevCpkCkSidiee 100
                                        ++C++C+   ln  +vCp C+S+++++
  gi|298674526|ref|YP_003726276.1|   3 EQVCRECHRITLN--QVCPVCGSSNLST 28 
                                       579****876665..79********986 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.14   1.7e+02       2       8 ..       5      11 ..       4      15 .. 0.78
   2 ?   11.6   0.3   0.00012      0.15       2      14 ..      17      29 ..      16      32 .. 0.85
   3 ?   -1.1   0.0       1.1   1.4e+03      33      42 ..      36      45 ..      32      46 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.14
                                      EETTTTC CS
                      TF_Zn_Ribbon  2 kCPnCgs 8 
                                      +C +C+ 
  gi|298674526|ref|YP_003726276.1|  5 VCRECHR 11
                                      7999975 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00012
                                      EETTTTCEECHEE CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveD 14
                                      +CP+Cgs+nl +D
  gi|298674526|ref|YP_003726276.1| 17 VCPVCGSSNLSTD 29
                                      8******998666 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.1
                                      CCCCCCHHHH CS
                      TF_Zn_Ribbon 33 sidegpewre 42
                                      +id+++ +++
  gi|298674526|ref|YP_003726276.1| 36 IIDPKKSKIA 45
                                      6899888876 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.8   4.6e-05     0.059      20      38 ..       5      23 ..       4      29 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.6e-05
                       Prok-RING_4 20 vCkeCfdskdlssCPlCqr 38
                                      vC+eC   + ++ CP+C +
  gi|298674526|ref|YP_003726276.1|  5 VCRECHRITLNQVCPVCGS 23
                                      8****************86 PP

>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   7.4e-05     0.094     617     640 ..       2      25 ..       1      56 [. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 7.4e-05
                          PolC_DP2 617 arrkCkkCgketlearCeeCgekt 640
                                       +++ C++C++ tl++ C+ Cg++ 
  gi|298674526|ref|YP_003726276.1|   2 SEQVCRECHRITLNQVCPVCGSSN 25 
                                       6789*****************975 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.1   0.00014      0.18     508     529 ..       4      25 ..       2      32 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00014
                                       EEETT.--EESSSB-TTT--BE CS
                              NRDD 508 dvCnecgykgeiekCpkCgsee 529
                                       +vC+ec++  + + Cp+Cgs++
  gi|298674526|ref|YP_003726276.1|   4 QVCRECHRITLNQVCPVCGSSN 25 
                                       59******888888*****876 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   3.7    0.0041       5.3      26      36 ..      14      26 ..       1      28 [. 0.67

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0041
                       Zn-ribbon_8 26 lta.CPeCgs.ev 36
                                      l + CP Cgs ++
  gi|298674526|ref|YP_003726276.1| 14 LNQvCPVCGSsNL 26
                                      4444*****9776 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.7      0.14   1.8e+02      19      25 ..       4      10 ..       2      16 .. 0.71
   2 ?    9.2   0.2   0.00092       1.2      19      28 ..      16      25 ..      11      32 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.14
                     Zn_Tnp_IS1595 19 fvCPhCg 25
                                      +vC  C+
  gi|298674526|ref|YP_003726276.1|  4 QVCRECH 10
                                      6788887 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00092
                     Zn_Tnp_IS1595 19 fvCPhCgsrk 28
                                      +vCP Cgs+ 
  gi|298674526|ref|YP_003726276.1| 16 QVCPVCGSSN 25
                                      79*****984 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.4      0.16     2e+02      26      31 ..       4       9 ..       2      17 .. 0.82
   2 ?    8.3   0.8    0.0021       2.7       6      12 ..      18      24 ..      13      30 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.16
                                      EEETTT CS
                    Prim_Zn_Ribbon 26 wfCrqC 31
                                       +Cr+C
  gi|298674526|ref|YP_003726276.1|  4 QVCREC 9 
                                      69**** PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0021
                                      -TTTT-T CS
                    Prim_Zn_Ribbon  6 CPvCGGr 12
                                      CPvCG++
  gi|298674526|ref|YP_003726276.1| 18 CPVCGSS 24
                                      *****86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 460.19
//
Query:       gi|298674527|ref|YP_003726277.1|  [L=193]
Description: hypothetical protein Metev_0570 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-42  143.5   0.2    3.4e-42  143.0   0.2    1.2  1  DUF359           Protein of unknown function (DUF359)
  ------ inclusion threshold ------
      0.094   12.1   0.0       0.64    9.4   0.0    1.9  2  Astro_capsid_p2  C-terminal tail of astrovirus capsid project


Domain annotation for each model (and alignments):
>> DUF359  Protein of unknown function (DUF359)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.0   0.2   3.8e-46   3.4e-42       1     124 [.      51     169 ..      51     171 .. 0.94

  Alignments for each domain:
  == domain 1  score: 143.0 bits;  conditional E-value: 3.8e-46
                            DUF359   1 vtknllkagikPdlaivDgktkReeveeeekeeekekekekevievkNpaGtiteelieaikealeseekvlilVdG 77 
                                       +t +l+++gi+Pd+ ++D++t+R+++ ++ ++     ++++++++v+Np Gtite+l++ i++a+ s+++v+i+V+G
  gi|298674527|ref|YP_003726277.1|  51 TTFHLIESGIIPDVYLIDNRTNRKPTPDRVDK-----NHRFTQVTVDNPSGTITEDLVNNIENAVLSDKNVRIFVNG 122
                                       799*********************76664444.....4589************************************ PP

                            DUF359  78 EEDLavlpaillapegsvvvYGqpdeGvvlvkvteeakeeaeellek 124
                                       EEDLa+lpaillap +s+v+YGqp+eGvvlv++te++kee+++l+++
  gi|298674527|ref|YP_003726277.1| 123 EEDLAALPAILLAPINSIVLYGQPGEGVVLVEITESKKEEIRDLMNN 169
                                       ********************************************987 PP

>> Astro_capsid_p2  C-terminal tail of astrovirus capsid projection or spike
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0     0.041   3.7e+02     107     142 ..      13      51 ..       8      55 .. 0.65
   2 ?    9.4   0.0   7.2e-05      0.64      76     128 ..     138     188 ..     119     192 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.041
                   Astro_capsid_p2 107 paikkyypg...ttnldeelkqrlklaegdpvislgdtt 142
                                       p+++ky+ +    t  d   k   +l +   +is+gd+t
  gi|298674527|ref|YP_003726277.1|  13 PTLRKYFGElflGTGNDTIKKMEQQLKNSTKLISVGDVT 51 
                                       667777654221233354556667788889999999987 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 7.2e-05
                   Astro_capsid_p2  76 qtgvlfgqpklgvgviqtmktlkqhikdytepaikkyypgttnldeelkqrlk 128
                                       ++ vl+gqp  gv +++   + k+ i+d  +  i+  + +t n  ++l+ +l+
  gi|298674527|ref|YP_003726277.1| 138 NSIVLYGQPGEGVVLVEITESKKEEIRDLMNNIIE--FQNTNNSLNKLRRKLN 188
                                       5679**************************99997..7788888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1104  (0.0615762); expected 358.6 (0.02)
Passed bias filter:                      665  (0.0370907); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.20s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1534.74
//
Query:       gi|298674528|ref|YP_003726278.1|  [L=99]
Description: 30S ribosomal protein S24e [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-26   91.0   0.0    4.1e-26   90.7   0.0    1.1  1  Ribosomal_S24e  Ribosomal protein S24e
  ------ inclusion threshold ------
      0.081   13.1   0.0      0.083   13.1   0.0    1.1  1  DUF1510         Domain of unknown function (DUF1510)


Domain annotation for each model (and alignments):
>> Ribosomal_S24e  Ribosomal protein S24e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.7   0.0   4.6e-30   4.1e-26       2      78 ..      21      96 ..      20      97 .. 0.98

  Alignments for each domain:
  == domain 1  score: 90.7 bits;  conditional E-value: 4.6e-30
                                      EEEE-SSS-S--HHHHHHHHHHHHTS-CTTEEEEEEEE-SSSSEEEEEEEEES-HHHHHHHS-HHHHHHTTSS---S CS
                    Ribosomal_S24e  2 vdvlHpgkatpskteireklakmykvdpdlvvvfgfrthfGggkttGfakiYdsleaakkfEpkhrlaRnglaekkk 78
                                      +++ ++g atps++ei++kla+m++++++l+vv+ +++++G+ ++ G+akiYd+++++k++E +++++Rn+++e+++
  gi|298674528|ref|YP_003726278.1| 21 FTIKFDG-ATPSRNEIKNKLAAMMDISSELIVVQDIDNQYGKKEARGYAKIYDDANTLKSVECDYIIERNKPPEETE 96
                                      7899***.******************************************************************987 PP

>> DUF1510  Domain of unknown function (DUF1510)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   9.2e-06     0.083      14      65 ..      18      69 ..       5      94 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.2e-06
                           DUF1510 14 tgehtssydkgsvDwnEmekavskatglsednmivwwlgnggspqkaigtvs 65
                                      + + t ++d  +  +nE+++ +++ +++s++ ++v  + n+ ++++a g  +
  gi|298674528|ref|YP_003726278.1| 18 KIDFTIKFDGATPSRNEIKNKLAAMMDISSELIVVQDIDNQYGKKEARGYAK 69
                                      5567899*********************************955566766544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 780.45
//
Query:       gi|298674529|ref|YP_003726279.1|  [L=50]
Description: 30S ribosomal protein S27a [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-22   78.5   3.7    3.5e-22   78.3   3.7    1.0  1  Ribosomal_S27   Ribosomal protein S27a
    1.2e-05   25.3   0.8    1.5e-05   25.0   0.8    1.2  1  Ribosomal_L37e  Ribosomal protein L37e
    0.00068   19.2   8.8     0.0053   16.4   8.8    2.0  1  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
     0.0014   18.5   6.7      0.017   15.0   4.3    2.6  2  Nudix_N_2       Nudix N-terminal
     0.0033   17.1   2.7       0.15   11.9   0.1    2.3  2  zinc_ribbon_2   zinc-ribbon domain
     0.0046   17.3   1.0      0.019   15.3   0.2    1.9  2  GFA             Glutathione-dependent formaldehyde-activating
     0.0068   16.5   0.2     0.0075   16.4   0.2    1.2  1  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito
     0.0096   15.9   1.6      0.018   15.1   1.6    1.4  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.017   15.0   0.4      0.019   14.9   0.4    1.1  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.021   14.8   0.7      0.078   13.0   0.7    1.9  1  PriA_CRR        PriA DNA helicase Cys-rich region (CRR) domai
      0.021   14.5   0.5        1.9    8.3   0.0    2.2  2  A2L_zn_ribbon   A2L zinc ribbon domain
      0.024   14.0   2.5       0.53    9.8   0.1    2.2  2  zf-ribbon_3     zinc-ribbon domain
      0.041   13.9   0.7      0.043   13.9   0.7    1.0  1  DUF1451         Zinc-ribbon containing domain
      0.052   13.5   2.5      0.091   12.8   2.5    1.4  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
      0.063   13.2   2.6       0.29   11.1   0.2    2.2  2  DUF1936         Domain of unknown function (DUF1936)
      0.085   13.0   2.9       0.25   11.5   0.4    2.2  2  zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ri
       0.17   12.1   5.2       0.48   10.6   0.5    2.0  2  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
       0.17   11.8   5.5       0.91    9.5   5.5    1.9  1  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
       0.52    9.9   4.3        1.4    8.5   4.1    1.8  2  TF_Zn_Ribbon    TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> Ribosomal_S27  Ribosomal protein S27a
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.3   3.7   3.7e-25   3.5e-22       1      45 []       4      46 ..       4      46 .. 0.98

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 3.7e-25
                                      SSSSCCESSSSSEEESS-B-SS-S-TTSBEEECTTEEEESSTTTE CS
                     Ribosomal_S27  1 vlkyYkvddsgkverlrkeCpreCGaGvfMAehkdRkyCGkCglT 45
                                      v++yYkvd+ +++er+++ Cpr CG Gvf+AehkdR +CGkCg+T
  gi|298674529|ref|YP_003726279.1|  4 VYEYYKVDG-DNIERTHQFCPR-CGVGVFLAEHKDRLSCGKCGYT 46
                                      799******.9***********.*********************9 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.8   1.6e-08   1.5e-05      13      43 ..      16      49 ..      10      50 .] 0.80

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.6e-08
                    Ribosomal_L37e 13 kktHilCrrCgkrsy...hvqkktCascGypsak 43
                                      ++tH +C rCg   +   h  + +C++cGy + k
  gi|298674529|ref|YP_003726279.1| 16 ERTHQFCPRCGVGVFlaeHKDRLSCGKCGYTEFK 49
                                      679************555666669******7654 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   8.8   5.7e-06    0.0053       1      32 []      17      48 ..      17      48 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.7e-06
                     zf-NADH-PPase  1 rthrFCgrCGaptepaeggwarvCpaCglehY 32
                                      rth+FC+rCG  + +ae+   + C  Cg+  +
  gi|298674529|ref|YP_003726279.1| 17 RTHQFCPRCGVGVFLAEHKDRLSCGKCGYTEF 48
                                      8**********999999988899999998665 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   2.5    0.0059       5.6      16      29 ..      11      26 ..       4      27 .. 0.67
   2 !   15.0   4.3   1.8e-05     0.017       2      32 ..      21      47 ..      20      49 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0059
                                      TT-SS-EE..EETTTT CS
                         Nudix_N_2 16 dgDnreRl..vCpaCg 29
                                      dgDn eR    Cp+Cg
  gi|298674529|ref|YP_003726279.1| 11 DGDNIERThqFCPRCG 26
                                      6777777522588887 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.8e-05
                                      B-TTT--B-EEE--TT-SS-EEEETTTTEEE CS
                         Nudix_N_2  2 FCsqCGtpvelripdgDnreRlvCpaCgtih 32
                                      FC+ CG  v l+    +++ Rl C +Cg++ 
  gi|298674529|ref|YP_003726279.1| 21 FCPRCGVGVFLA----EHKDRLSCGKCGYTE 47
                                      *******98776....69**********975 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   0.00015      0.15      13      20 ..      19      26 ..      12      29 .. 0.76
   2 ?    5.9   0.3     0.011        11      16      21 ..      40      45 ..      33      46 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
                     zinc_ribbon_2 13 akFCpyCG 20
                                       +FCp+CG
  gi|298674529|ref|YP_003726279.1| 19 HQFCPRCG 26
                                      57999998 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.011
                     zinc_ribbon_2 16 CpyCGt 21
                                      C +CG+
  gi|298674529|ref|YP_003726279.1| 40 CGKCGY 45
                                      888886 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2     2e-05     0.019      37      65 ..       7      35 ..       1      40 [. 0.67
   2 ?    2.9   0.1      0.15   1.4e+02      46      59 ..      34      47 ..      31      50 .] 0.77

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2e-05
                               GFA 37 ykktadsgnkvtrsfCpeCgsplyseesa 65
                                      y k    + + t++fCp+Cg+ ++  e++
  gi|298674529|ref|YP_003726279.1|  7 YYKVDGDNIERTHQFCPRCGVGVFLAEHK 35
                                      33344445566779*********985444 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.15
                               GFA 46 kvtrsfCpeCgspl 59
                                      +++r  C +Cg + 
  gi|298674529|ref|YP_003726279.1| 34 HKDRLSCGKCGYTE 47
                                      678899****9765 PP

>> MqsA_antitoxin  Antitoxin component of bacterial toxin-antitoxin system, MqsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.2   7.9e-06    0.0075      33      57 ..      18      42 ..       3      50 .] 0.76

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.9e-06
                    MqsA_antitoxin 33 tgdfCarCGegvldeeeedrlseel 57
                                      t +fC+rCG gv+ +e++drls   
  gi|298674529|ref|YP_003726279.1| 18 THQFCPRCGVGVFLAEHKDRLSCGK 42
                                      569*****************98765 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   1.6   1.9e-05     0.018       7      36 ..      14      45 ..      12      49 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.9e-05
                               DZR  7 elppdarfCseCgtklkavaa..edrCpsCge 36
                                      +++   +fC++Cg  +  +++     C +Cg+
  gi|298674529|ref|YP_003726279.1| 14 NIERTHQFCPRCGVGVFLAEHkdRLSCGKCGY 45
                                      6788899******9965444455999****98 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.4     2e-05     0.019      24      55 ..      15      46 ..       5      49 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2e-05
                    OrfB_Zn_ribbon 24 payTSktCseCgsknkealsgrtfkCpnCgfe 55
                                       + T + C++Cg  +  a +++++ C +Cg++
  gi|298674529|ref|YP_003726279.1| 15 IERTHQFCPRCGVGVFLAEHKDRLSCGKCGYT 46
                                      5568899******999999***********97 PP

>> PriA_CRR  PriA DNA helicase Cys-rich region (CRR) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.7   8.2e-05     0.078       1      26 [.      22      47 ..      22      47 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.2e-05
                          PriA_CRR  1 CpnCdvsltyHksrnrLrCHyCgyte 26
                                      Cp+C v   +  ++ rL C  Cgyte
  gi|298674529|ref|YP_003726279.1| 22 CPRCGVGVFLAEHKDRLSCGKCGYTE 47
                                      ****87655555555*********97 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.021        20      20      28 ..      18      26 ..      11      27 .. 0.83
   2 ?    8.3   0.0     0.002       1.9      19      31 ..      35      47 ..      28      49 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.021
                     A2L_zn_ribbon 20 gylvCieCg 28
                                       + +C+ Cg
  gi|298674529|ref|YP_003726279.1| 18 THQFCPRCG 26
                                      5779****9 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.002
                     A2L_zn_ribbon 19 qgylvCieCgasf 31
                                      ++ l+C +Cg+++
  gi|298674529|ref|YP_003726279.1| 35 KDRLSCGKCGYTE 47
                                      6889*******86 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00057      0.53      16      23 ..      19      26 ..      12      29 .. 0.62
   2 ?    4.7   0.3     0.022        21      18      24 ..      39      45 ..      35      46 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00057
                       zf-ribbon_3 16 dnvCpyCG 23
                                       ++Cp CG
  gi|298674529|ref|YP_003726279.1| 19 HQFCPRCG 26
                                      45555555 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.022
                       zf-ribbon_3 18 vCpyCGt 24
                                       C +CG+
  gi|298674529|ref|YP_003726279.1| 39 SCGKCGY 45
                                      6999997 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.7   4.5e-05     0.043     106     144 ..      11      49 ..       2      50 .] 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.5e-05
                           DUF1451 106 sGevvglGtlvCekCgkelalkkteeippCpkCgateFr 144
                                        G+ +   +  C +Cg  + l + +    C kCg teF+
  gi|298674529|ref|YP_003726279.1|  11 DGDNIERTHQFCPRCGVGVFLAEHKDRLSCGKCGYTEFK 49 
                                       48888899999***************************7 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   2.5   9.6e-05     0.091      18      46 .]      19      46 ..      15      46 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.6e-05
                     Zn_Tnp_IS1595 18 gfvCPhCgsrkayriktrglfqCkeCrkq 46
                                      ++ CP+Cg+  +   ++  ++ C +C+++
  gi|298674529|ref|YP_003726279.1| 19 HQFCPRCGVGVFLA-EHKDRLSCGKCGYT 46
                                      456*****763333.3357*******985 PP

>> DUF1936  Domain of unknown function (DUF1936)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2    0.0003      0.29       2       9 ..      22      29 ..      21      32 .. 0.89
   2 ?    2.3   0.2      0.17   1.6e+02      27      34 .]      40      47 ..      36      47 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0003
                                      -TTTSSSB CS
                           DUF1936  2 CPKCnvGk 9 
                                      CP+C+vG+
  gi|298674529|ref|YP_003726279.1| 22 CPRCGVGV 29
                                      *******9 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.17
                                      -TT---EE CS
                           DUF1936 27 redCdYiE 34
                                         C+Y E
  gi|298674529|ref|YP_003726279.1| 40 CGKCGYTE 47
                                      34577765 PP

>> zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.22     2e+02       2       8 ..      22      28 ..      21      36 .. 0.78
   2 ?   11.5   0.4   0.00026      0.25      36      46 ..      38      48 ..      29      50 .] 0.89

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.22
                    zinc_ribbon_13  2 CpKCgnt 8 
                                      Cp+Cg  
  gi|298674529|ref|YP_003726279.1| 22 CPRCGVG 28
                                      9999975 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00026
                    zinc_ribbon_13 36 vsCknCgYtel 46
                                       sC +CgYte+
  gi|298674529|ref|YP_003726279.1| 38 LSCGKCGYTEF 48
                                      59********8 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.5   0.00051      0.48      21      30 ..      17      26 ..       8      32 .. 0.85
   2 ?    8.4   5.1    0.0025       2.3       1      35 [.      15      49 ..      15      50 .] 0.76

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00051
                      NOB1_Zn_bind 21 mtkkFCpkCG 30
                                       t +FCp+CG
  gi|298674529|ref|YP_003726279.1| 17 RTHQFCPRCG 26
                                      689******9 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0025
                      NOB1_Zn_bind  1 ikrvkswvlrChaCfkvtkdmtkkFCpkCGnktLk 35
                                      i+r++++  rC   + + +++++  C kCG    k
  gi|298674529|ref|YP_003726279.1| 15 IERTHQFCPRCGVGVFLAEHKDRLSCGKCGYTEFK 49
                                      67788888888888888888888888888877665 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   5.5   0.00096      0.91       2      31 ..      20      47 ..      20      48 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00096
                                      EBESTTTS..BEEEEECSCCCEEEESSSS-EE CS
                    RNA_POL_M_15KD  2 kFCpkCgN..lLlpkedkegknfeCrqCgYee 31
                                      +FCp Cg    L   +d++     C +CgY e
  gi|298674529|ref|YP_003726279.1| 20 QFCPRCGVgvFLAEHKDRLS----CGKCGYTE 47
                                      7*****86225555555555....******75 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.5      0.01       9.7      20      26 ..      20      26 ..      11      29 .. 0.69
   2 ?    8.5   4.1    0.0015       1.4       2      27 ..      21      45 ..      20      47 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.01
                                      EEESSSS CS
                      TF_Zn_Ribbon 20 lvCtdCG 26
                                       +C++CG
  gi|298674529|ref|YP_003726279.1| 20 QFCPRCG 26
                                      4677777 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0015
                                      EETTTTCEECHEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGl 27
                                       CP Cg   ++ +++   l C++CG+
  gi|298674529|ref|YP_003726279.1| 21 FCPRCGVGVFLAEHK-DRLSCGKCGY 45
                                      6*****953444444.456******6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 390.21
//
Query:       gi|298674530|ref|YP_003726280.1|  [L=161]
Description: hypothetical protein Metev_0573 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1150.45
//
Query:       gi|298674531|ref|YP_003726281.1|  [L=99]
Description: rubrerythrin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.4e-08   33.6   1.0    5.2e-08   33.4   1.0    1.1  1  Rubrerythrin  Rubrerythrin
    0.00074   19.8   0.4    0.00096   19.5   0.4    1.1  1  DUF2383       Domain of unknown function (DUF2383)
    0.00084   19.2   0.2    0.00099   18.9   0.2    1.1  1  COQ7          Ubiquinone biosynthesis protein COQ7
      0.001   19.3   0.0     0.0012   19.0   0.0    1.1  1  Ferritin_2    Ferritin-like domain
  ------ inclusion threshold ------
      0.013   15.4   0.3      0.015   15.2   0.3    1.1  1  DUF2202       Uncharacterized protein domain (DUF2202)
      0.037   14.0   1.3      0.044   13.7   1.3    1.1  1  Ferritin      Ferritin-like domain
      0.039   12.9   0.3      0.041   12.9   0.3    1.0  1  Mn_catalase   Manganese containing catalase


Domain annotation for each model (and alignments):
>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   1.0     2e-11   5.2e-08       1      54 [.      30      81 ..      30      94 .. 0.92

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 2e-11
                                      HHHHHHHHHHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  1 eiLekAiagEssarrlYkelaekakegypqiaelFeelAeeEreHakilnklle 54
                                      e L +Ai++E +a +lY+e+a  ++  +++++ +++++A+eE+ H +++  +l 
  gi|298674531|ref|YP_003726281.1| 30 ETLRAAIIAELDAVNLYEEMANLTE--NEDLKTILLDIAKEEKVHVAMFQSVLI 81
                                      789**********************..********************9998775 PP

>> DUF2383  Domain of unknown function (DUF2383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.4   3.7e-07   0.00096       5      57 ..      31      83 ..      28      87 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3.7e-07
                                      HHHHHHHHHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                           DUF2383  5 aLndLietlkdgeegykeaaekvkdpqlktlleriaeereeaaeeLqseiral 57
                                      +L   i ++ d+++ y+e+a   ++++lkt+l +ia+e + +++ +qs + + 
  gi|298674531|ref|YP_003726281.1| 31 TLRAAIIAELDAVNLYEEMANLTENEDLKTILLDIAKEEKVHVAMFQSVLIEA 83
                                      5666677889*************************************998765 PP

>> COQ7  Ubiquinone biosynthesis protein COQ7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.2   3.9e-07   0.00099       4      58 ..      30      82 ..      27      87 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.9e-07
                              COQ7  4 rllRvdhaGElgAvaiYkgqlavlakkdpelkpllkemleqEkeHlatfeellke 58
                                      + lR     El Av +Y+  +    +++++lk++l +++++Ek H+a+f+++l e
  gi|298674531|ref|YP_003726281.1| 30 ETLRAAIIAELDAVNLYEEMANL--TENEDLKTILLDIAKEEKVHVAMFQSVLIE 82
                                      678888899*********99999..6888999******************98876 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   4.9e-07    0.0012      65     135 ..      10      81 ..       3      82 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4.9e-07
                        Ferritin_2  65 aavakptfdf.afdpfadeksflalaavlEdvgvsAYlgaapllsnkelltaaasIlsvEArHaavirtllg 135
                                       + ++++ +d+   ++ +  k+ l++a + E  +v+ Y   a+l +n++l+t  + I+  E  H a+++++l 
  gi|298674531|ref|YP_003726281.1|  10 SVLSEIPIDLeRIKQGDVNKETLRAAIIAELDAVNLYEEMANLTENEDLKTILLDIAKEEKVHVAMFQSVLI 81 
                                       55556666662223333467899999999999********************************99999875 PP

>> DUF2202  Uncharacterized protein domain (DUF2202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.3   5.8e-06     0.015      79     144 ..      22      86 ..       8      93 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.8e-06
                           DUF2202  79 vekgsksledaLkvgatiedldiaDl.ekalketdnkdikevYenllkGsrnhlRsfvrkleergke 144
                                       +++g+ + ++ L++ a i +ld  +l e++ + t+n+d+k++   + k  + h+  f + l e + e
  gi|298674531|ref|YP_003726281.1|  22 IKQGDVN-KETLRA-AIIAELDAVNLyEEMANLTENEDLKTILLDIAKEEKVHVAMFQSVLIEADDE 86 
                                       5566665.778886.56889*****9999****************************9999877766 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.3   1.7e-05     0.044      82     136 ..      29      80 ..       9      84 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.7e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin  82 eevleaalehekkvteslrelielaeeegDpatadfledfleeqeeheweleall 136
                                       +e l+aa+ +e ++++ ++e+++l+e e    +  +l d+ +e+  h+++++++l
  gi|298674531|ref|YP_003726281.1|  29 KETLRAAIIAELDAVNLYEEMANLTENE---DLKTILLDIAKEEKVHVAMFQSVL 80 
                                       789999999*****************87...788899*************99987 PP

>> Mn_catalase  Manganese containing catalase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   1.6e-05     0.041     143     199 ..      32      89 ..      22      98 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.6e-05
                       Mn_catalase 143 lranlaaEakarlqverlyeltddpgvrdmlsfLlaRelvHqlafekAleeleeee.t 199
                                       lra + aE  a   +e + +lt++ +++  l  + + e vH  +f+  l e+++e+ +
  gi|298674531|ref|YP_003726281.1|  32 LRAAIIAELDAVNLYEEMANLTENEDLKTILLDIAKEEKVHVAMFQSVLIEADDEFlK 89 
                                       7888899999999999999999999999999999999999999999988888888733 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       818  (0.0456244); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.56u 0.36s 00:00:00.92 Elapsed: 00:00:00.56
# Mc/sec: 535.01
//
Query:       gi|298674532|ref|YP_003726282.1|  [L=67]
Description: hypothetical protein Metev_0575 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      9e-06   25.6   1.3     0.0081   16.1   0.0    2.3  2  ADK_lid         Adenylate kinase, active site lid
    2.6e-05   23.4   1.9      0.025   14.0   0.2    2.2  2  zf-ribbon_3     zinc-ribbon domain
      8e-05   22.5   2.5      0.067   13.2   0.1    2.1  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
     0.0002   20.9   3.7      0.032   14.0   0.8    2.5  2  zinc_ribbon_2   zinc-ribbon domain
    0.00059   19.3   0.7       0.19   11.3   0.2    2.4  2  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0018   18.2   1.1      0.079   12.9   0.0    2.3  2  zinc_ribbon_4   zinc-ribbon domain
     0.0032   17.3   3.3     0.0056   16.6   3.3    1.5  1  Zn_ribbon_SprT  SprT-like zinc ribbon domain
     0.0034   17.1   3.0     0.0046   16.7   3.0    1.3  1  zf-RING_4       RING/Ubox like zinc-binding domain
     0.0048   16.5   0.8        0.7    9.5   0.2    2.2  2  zf_C2H2_13      Zinc finger domain
     0.0064   16.4   0.5        2.4    8.2   0.1    2.2  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
     0.0069   16.4   0.1     0.0069   16.4   0.1    1.1  1  Elf1            Transcription elongation factor Elf1 like
      0.009   15.9   1.4        1.4    8.9   0.0    2.2  2  zf-C2HC_2       zinc-finger of a C2HC-type
  ------ inclusion threshold ------
      0.011   15.7   1.0       0.32   11.1   1.1    2.0  1  Zn_Tnp_IS91     Transposase zinc-binding domain
      0.012   15.9   4.4      0.022   15.0   4.4    1.5  1  Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
      0.012   15.2   0.9        3.7    7.3   0.1    2.2  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
      0.016   15.2   2.5      0.079   13.0   2.5    1.9  1  DZR             Double zinc ribbon
      0.022   14.7   1.1      0.068   13.1   1.1    1.7  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.022   15.0   2.5        1.8    8.9   0.2    2.2  2  zinc_ribbon_9   zinc-ribbon
      0.032   14.3   3.2       0.88    9.7   0.4    2.2  2  UPF0547         Uncharacterised protein family UPF0547
       0.05   13.7   1.5        7.8    6.7   0.1    2.2  2  Zn-ribbon_8     Zinc ribbon domain
      0.051   13.7   1.5          1    9.5   0.1    2.1  2  DUF2387         Probable metal-binding protein (DUF2387)
      0.057   13.5   2.4        7.8    6.7   0.1    2.6  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain
      0.067   13.0   0.4        1.5    8.7   0.0    2.3  2  zf-C2H2_3       zinc-finger of acetyl-transferase ESCO
      0.072   13.1   5.5       0.77    9.8   1.1    2.3  2  DUF1610         Domain of unknown function (DUF1610)
      0.074   11.8   0.9      0.093   11.5   0.9    1.0  1  NRDD            Anaerobic ribonucleoside-triphosphate reducta
      0.083   13.0   1.0       0.17   12.0   1.0    1.5  1  TerY_C          TerY-C metal binding domain
      0.092   12.5   3.0        3.8    7.3   0.2    2.2  2  A2L_zn_ribbon   A2L zinc ribbon domain
        0.1   13.3   1.6        3.4    8.4   0.2    2.2  2  zf-ISL3         zinc-finger of transposase IS204/IS1001/IS109
       0.12   12.5   0.5       0.15   12.2   0.5    1.1  1  PknG_rubred     Protein kinase G rubredoxin domain
       0.19   12.3   1.9       0.67   10.6   1.9    1.8  1  Trm112p         Trm112p-like protein
       0.23   11.5   1.9         13    5.9   0.1    2.1  2  DUF2752         Protein of unknown function (DUF2752)
       0.27   11.2   5.2        5.9    6.9   0.3    2.2  2  Prok-RING_1     Prokaryotic RING finger family 1
       0.43   10.4   5.2        1.5    8.6   5.2    1.8  1  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
       0.44   10.8   3.6          3    8.2   0.6    2.1  2  Ribosomal_L32p  Ribosomal L32p protein family
        8.1    5.9   7.7    1.9e+02    1.5   7.8    2.1  1  zf_Rg           Reverse gyrase zinc finger


Domain annotation for each model (and alignments):
>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.7     0.005       2.5       2      16 ..      10      26 ..      10      32 .. 0.72
   2 !   16.1   0.0   1.6e-05    0.0081       3      14 ..      38      49 ..      37      61 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.005
                                      EE-TTT--..EEETTTB CS
                           ADK_lid  2 rvCpkCGr..sYhvvfn 16
                                      r+Cp+CG    +h+ f+
  gi|298674532|ref|YP_003726282.1| 10 RICPNCGYkkGFHLCFK 26
                                      8*****95447777764 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.6e-05
                                      E-TTT--EEETT CS
                           ADK_lid  3 vCpkCGrsYhvv 14
                                      +Cp+CG sY++ 
  gi|298674532|ref|YP_003726282.1| 38 ICPSCGQSYNID 49
                                      9*********65 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.2   4.9e-05     0.025      12      25 ..       5      18 ..       2      18 .. 0.78
   2 !    9.3   0.1    0.0015      0.77       5      10 ..      39      44 ..      37      52 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.9e-05
                       zf-ribbon_3 12 lssddnvCpyCGtk 25
                                      ++++ ++Cp+CG+k
  gi|298674532|ref|YP_003726282.1|  5 PDDEFRICPNCGYK 18
                                      4788899*****96 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0015
                       zf-ribbon_3  5 CPnCGa 10
                                      CP+CG+
  gi|298674532|ref|YP_003726282.1| 39 CPSCGQ 44
                                      777776 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.6   0.00093      0.48      19      31 ..      10      25 ..       4      29 .. 0.72
   2 !   13.2   0.1   0.00013     0.067       6      30 ..      24      46 ..      22      53 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00093
                     Zn_Tnp_IS1595 19 fvCPhCgsr...kayr 31
                                      ++CP+Cg++   ++++
  gi|298674532|ref|YP_003726282.1| 10 RICPNCGYKkgfHLCF 25
                                      56*****996666665 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00013
                     Zn_Tnp_IS1595  6 aralLealrWpngfvCPhCgsrkay 30
                                      +++  e+ r++ g +CP Cg  ++y
  gi|298674532|ref|YP_003726282.1| 24 CFKKTENSRFRIGLICPSCG--QSY 46
                                      77778999************..555 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.8   6.2e-05     0.032       7      22 ..       2      18 ..       2      19 .. 0.77
   2 !    7.6   0.1    0.0063       3.2       2       6 ..      39      43 ..      28      47 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.2e-05
                     zinc_ribbon_2  7 aelq.dnakFCpyCGtp 22
                                      +e++ d+ + Cp+CG++
  gi|298674532|ref|YP_003726282.1|  2 KENPdDEFRICPNCGYK 18
                                      5775368899*****97 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0063
                     zinc_ribbon_2  2 CpnCG 6 
                                      Cp+CG
  gi|298674532|ref|YP_003726282.1| 39 CPSCG 43
                                      66666 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.2   0.00036      0.19      14      39 ..       4      29 ..       2      33 .. 0.71
   2 ?    6.6   0.0     0.011       5.5      21      26 ..      38      43 ..      34      59 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00036
                                      ETSTTCEEESSSSBEEEECCCCCCCH CS
                      TF_Zn_Ribbon 14 DpergelvCtdCGlVlednsidegpe 39
                                      +p+    +C++CG+    + + ++ e
  gi|298674532|ref|YP_003726282.1|  4 NPDDEFRICPNCGYKKGFHLCFKKTE 29
                                      66666679999999877777776666 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.011
                                      EESSSS CS
                      TF_Zn_Ribbon 21 vCtdCG 26
                                      +C++CG
  gi|298674532|ref|YP_003726282.1| 38 ICPSCG 43
                                      566665 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.2      0.11        56       5       9 ..      12      16 ..      11      18 .. 0.62
   2 !   12.9   0.0   0.00015     0.079       4      15 ..      38      49 ..      37      52 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.11
                     zinc_ribbon_4  5 CpsCk 9 
                                      Cp+C+
  gi|298674532|ref|YP_003726282.1| 12 CPNCG 16
                                      66665 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00015
                     zinc_ribbon_4  4 tCpsCkakyeid 15
                                       CpsC+  y+id
  gi|298674532|ref|YP_003726282.1| 38 ICPSCGQSYNID 49
                                      6**********8 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   3.3   1.1e-05    0.0056       7      35 ..      12      47 ..      11      50 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.1e-05
                    Zn_ribbon_SprT  7 CtgCgreythhlsi.rrhn......YrCrrCkgtLr 35
                                      C++Cg + ++hl + +++n       +C+ C++  +
  gi|298674532|ref|YP_003726282.1| 12 CPNCGYKKGFHLCFkKTENsrfrigLICPSCGQSYN 47
                                      *******************************98665 PP

>> zf-RING_4  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   3.0   9.1e-06    0.0046      10      48 .]       4      47 ..       1      47 [. 0.81

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 9.1e-06
                         zf-RING_4 10 etdkdlkpC.eCgyqi.ClfCyhrileee...egrCPaCreeYk 48
                                      + d++++ C +Cgy+   + C+++  ++    + +CP C + Y+
  gi|298674532|ref|YP_003726282.1|  4 NPDDEFRICpNCGYKKgFHLCFKKTENSRfriGLICPSCGQSYN 47
                                      5699*****88***853789***999843444999*****9995 PP

>> zf_C2H2_13  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.2    0.0014       0.7      16      24 ..       8      16 ..       2      18 .. 0.85
   2 ?    5.6   0.0     0.023        12      14      26 ..      30      45 ..      27      54 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0014
                        zf_C2H2_13 16 nYRvCnkCG 24
                                      ++R+C +CG
  gi|298674532|ref|YP_003726282.1|  8 EFRICPNCG 16
                                      8*******9 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.023
                        zf_C2H2_13 14 nlnYR...vCnkCGkP 26
                                      n+ +R   +C +CG+ 
  gi|298674532|ref|YP_003726282.1| 30 NSRFRiglICPSCGQS 45
                                      577774446*****85 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.1    0.0048       2.4      16      27 ..       6      17 ..       5      18 .. 0.80
   2 ?    6.8   0.0     0.013       6.4      20      26 ..      37      43 ..      34      47 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0048
                    PhnA_Zn_Ribbon 16 dgallvCpeCah 27
                                      d++  +Cp+C++
  gi|298674532|ref|YP_003726282.1|  6 DDEFRICPNCGY 17
                                      666679****97 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.013
                    PhnA_Zn_Ribbon 20 lvCpeCa 26
                                      l+Cp C+
  gi|298674532|ref|YP_003726282.1| 37 LICPSCG 43
                                      89****8 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   1.3e-05    0.0069      18      59 ..       5      50 ..       1      66 [. 0.80

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.3e-05
                              Elf1 18 lptkFd.CpfCnheksvevkldkkek...iaevsCkvCgesfetkv 59
                                       + +F+ Cp+C+ +k  +  ++k+e+   +  + C +Cg+s+++++
  gi|298674532|ref|YP_003726282.1|  5 PDDEFRiCPNCGYKKGFHLCFKKTENsrfRIGLICPSCGQSYNIDW 50
                                      5666755*****************9999967788*******99763 PP

>> zf-C2HC_2  zinc-finger of a C2HC-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.4     0.023        12       2       9 ..       9      16 ..       8      16 .. 0.84
   2 !    8.9   0.0    0.0027       1.4       4      15 ..      38      49 ..      37      49 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.023
                         zf-C2HC_2  2 lvpCpkCg 9 
                                       + Cp+Cg
  gi|298674532|ref|YP_003726282.1|  9 FRICPNCG 16
                                      678****9 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0027
                         zf-C2HC_2  4 pCpkCgRsFnpd 15
                                       Cp Cg s+n d
  gi|298674532|ref|YP_003726282.1| 38 ICPSCGQSYNID 49
                                      6*******9965 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.1   0.00062      0.32      59      74 ..      38      53 ..      10      60 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00062
                       Zn_Tnp_IS91 59 hCpsCqkkateewlek 74
                                       CpsC++ ++ +w+ +
  gi|298674532|ref|YP_003726282.1| 38 ICPSCGQSYNIDWITS 53
                                      5************976 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   4.4   4.4e-05     0.022       6      32 ..      12      43 ..      10      49 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.4e-05
                                      -TTTT-TTTEE..ETT.......S-EEETTTT CS
                    Prim_Zn_Ribbon  6 CPvCGGrDrFr..fddkdgr...GtwfCrqCg 32
                                      CP+CG + +F   f++++++    + +C +Cg
  gi|298674532|ref|YP_003726282.1| 12 CPNCGYKKGFHlcFKKTENSrfrIGLICPSCG 43
                                      ************88888888999899*****4 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1    0.0073       3.7      22      28 ..      10      16 ..       4      18 .. 0.72
   2 ?    6.8   0.1      0.01       5.4      22      29 ..      37      44 ..      35      46 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0073
                     zf-NADH-PPase 22 rvCpaCg 28
                                      r Cp+Cg
  gi|298674532|ref|YP_003726282.1| 10 RICPNCG 16
                                      5566666 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.01
                     zf-NADH-PPase 22 rvCpaCgl 29
                                      + Cp+Cg+
  gi|298674532|ref|YP_003726282.1| 37 LICPSCGQ 44
                                      56888886 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   2.5   0.00015     0.079       9      40 ..       6      48 ..       2      53 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00015
                               DZR  9 ppdarfCseCgtk......lkavaa.......edrCpsCgekvdp 40
                                      +++ r C++Cg k       k+  +          CpsCg++ + 
  gi|298674532|ref|YP_003726282.1|  6 DDEFRICPNCGYKkgfhlcFKK--TensrfriGLICPSCGQSYNI 48
                                      5778999999999777744333..25689999999****998665 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.1   0.00013     0.068      30      61 ..      11      51 ..       4      53 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00013
                    OrfB_Zn_ribbon 30 tCseCgsknke.........alsgrtfkCpnCgfeadrDvn 61
                                       C++Cg+k+           ++ +  + Cp+Cg +++ D+ 
  gi|298674532|ref|YP_003726282.1| 11 ICPNCGYKKGFhlcfkktenSRFRIGLICPSCGQSYNIDWI 51
                                      7*******99889998655555555678********99985 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.2    0.0035       1.8      18      28 ..       5      16 ..       2      21 .. 0.59
   2 ?    6.5   0.2      0.02        10      23      29 ..      38      44 ..      23      46 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0035
                     zinc_ribbon_9 18 edsd.vlCPhCg 28
                                       d++  +CP+Cg
  gi|298674532|ref|YP_003726282.1|  5 PDDEfRICPNCG 16
                                      3333347****8 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.02
                     zinc_ribbon_9 23 lCPhCgg 29
                                      +CP+Cg+
  gi|298674532|ref|YP_003726282.1| 38 ICPSCGQ 44
                                      6****96 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.4    0.0017      0.88      15      22 ..      10      17 ..       9      18 .. 0.89
   2 ?    5.2   0.1     0.043        22      16      21 ..      38      43 ..      37      47 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0017
                           UPF0547 15 qfCphCGy 22
                                      ++Cp CGy
  gi|298674532|ref|YP_003726282.1| 10 RICPNCGY 17
                                      79*****9 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.043
                           UPF0547 16 fCphCG 21
                                      +Cp CG
  gi|298674532|ref|YP_003726282.1| 38 ICPSCG 43
                                      566666 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1     0.015       7.8      23      33 ..       6      16 ..       1      20 [. 0.72
   2 ?    6.7   0.1     0.015       7.8      28      34 ..      38      44 ..      22      48 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.015
                       Zn-ribbon_8 23 dapltaCPeCg 33
                                      d++   CP+Cg
  gi|298674532|ref|YP_003726282.1|  6 DDEFRICPNCG 16
                                      55566699998 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.015
                       Zn-ribbon_8 28 aCPeCgs 34
                                       CP+Cg+
  gi|298674532|ref|YP_003726282.1| 38 ICPSCGQ 44
                                      4999997 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.2       0.1        52      27      39 ..       6      18 ..       1      31 [. 0.76
   2 ?    9.5   0.1     0.002         1       3      25 ..      31      53 ..      29      59 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.1
                           DUF2387 27 eveyrECvsCgft 39
                                      ++e+r C +Cg+ 
  gi|298674532|ref|YP_003726282.1|  6 DDEFRICPNCGYK 18
                                      4788889999986 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.002
                           DUF2387  3 krFiAGavCPrCsemDkirmwee 25
                                       rF  G +CP C +  +i + ++
  gi|298674532|ref|YP_003726282.1| 31 SRFRIGLICPSCGQSYNIDWITS 53
                                      59999*******99888877655 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.3     0.021        11      18      26 .]       7      15 ..       4      15 .. 0.88
   2 ?    6.7   0.1     0.015       7.8       4       9 ..      39      44 ..      38      50 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.021
                            zf-ACC 18 rnlyVCPkC 26
                                      + + +CP+C
  gi|298674532|ref|YP_003726282.1|  7 DEFRICPNC 15
                                      67899**** PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.015
                            zf-ACC  4 CpsCge 9 
                                      CpsCg+
  gi|298674532|ref|YP_003726282.1| 39 CPSCGQ 44
                                      9***98 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1       0.2     1e+02      11      20 ..       9      16 ..       2      18 .. 0.77
   2 ?    8.7   0.0    0.0029       1.5      15      26 ..      32      49 ..      21      55 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.2
                         zf-C2H2_3 11 fgasqCkeCg 20
                                      f+   C++Cg
  gi|298674532|ref|YP_003726282.1|  9 FRI--CPNCG 16
                                      444..****9 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0029
                         zf-C2H2_3 15 q......CkeCgMvYnpg 26
                                      +      C+ Cg +Yn +
  gi|298674532|ref|YP_003726282.1| 32 RfrigliCPSCGQSYNID 49
                                      2345667********975 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.1    0.0015      0.77      18      23 ..      11      16 ..      10      17 .. 0.93
   2 ?    5.4   0.2     0.035        18      18      23 ..      38      43 ..      37      44 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0015
                           DUF1610 18 pCPNCG 23
                                      +CPNCG
  gi|298674532|ref|YP_003726282.1| 11 ICPNCG 16
                                      6****9 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.035
                           DUF1610 18 pCPNCG 23
                                      +CP CG
  gi|298674532|ref|YP_003726282.1| 38 ICPSCG 43
                                      6****9 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.9   0.00018     0.093     506     534 ..       8      51 ..       5      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00018
                                       -EEEETT.--.EESS..............SB-TTT--BE.EEEE CS
                              NRDD 506 kidvCnecgy.kgei..............ekCpkCgseeevevi 534
                                       ++ +C++cgy kg +                Cp+Cg++ ++++i
  gi|298674532|ref|YP_003726282.1|   8 EFRICPNCGYkKGFHlcfkktensrfrigLICPSCGQSYNIDWI 51 
                                       588*******88888***********99966*****76657766 PP

>> TerY_C  TerY-C metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.0   0.00034      0.17      76     124 ..      11      60 ..       7      63 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00034
                            TerY_C  76 gCPhCgnalafavCeCgkllCidgeeeatCpwCgkevkfgeasee..gfdv 124
                                        CP Cg + +f +C          +   +Cp Cg++ +++   ++  ++dv
  gi|298674532|ref|YP_003726282.1|  11 ICPNCGYKKGFHLCFKKT-ENSRFRIGLICPSCGQSYNIDWITSDipELDV 60 
                                       5*************7544.4445677789******9999876665566776 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.2    0.0074       3.8      19      29 ..       7      17 ..       4      18 .. 0.80
   2 ?    5.6   0.3     0.025        13      22      31 ..      37      46 ..      35      48 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0074
                     A2L_zn_ribbon 19 qgylvCieCga 29
                                      +  ++C++Cg+
  gi|298674532|ref|YP_003726282.1|  7 DEFRICPNCGY 17
                                      55689*****7 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.025
                     A2L_zn_ribbon 22 lvCieCgasf 31
                                      l+C+ Cg s+
  gi|298674532|ref|YP_003726282.1| 37 LICPSCGQSY 46
                                      89*****887 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.2    0.0067       3.4       4      12 ..      11      19 ..       8      35 .. 0.73
   2 ?    4.5   0.1      0.11        58       5      10 ..      39      44 ..      37      49 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0067
                           zf-ISL3  4 rCPnCgskt 12
                                       CPnCg k+
  gi|298674532|ref|YP_003726282.1| 11 ICPNCGYKK 19
                                      7*****995 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.11
                           zf-ISL3  5 CPnCgs 10
                                      CP Cg+
  gi|298674532|ref|YP_003726282.1| 39 CPSCGQ 44
                                      *****8 PP

>> PknG_rubred  Protein kinase G rubredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.5    0.0003      0.15      93     125 ..      10      47 ..       3      54 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0003
                                       -B-TTT--B-S.....---SS----SEEE-TTT--EEE CS
                       PknG_rubred  93 RfCwrCGrpvG.....RsekerkgaseGtCpkCgspys 125
                                       R C +CG + G     + +++++ +   +Cp+Cg++y+
  gi|298674532|ref|YP_003726282.1|  10 RICPNCGYKKGfhlcfKKTENSRFRIGLICPSCGQSYN 47 
                                       99******999444434455556666668********8 PP

>> Trm112p  Trm112p-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.9    0.0013      0.67      41      66 ..       8      49 ..       2      49 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0013
                                      S.............CHHTTEECCC...CEEEETTTTEEEEEE CS
                           Trm112p 41 y.............ellleldiee...geLvCpncgraYpIk 66
                                                    +l+++  + +     L+Cp+cg+ Y I+
  gi|298674532|ref|YP_003726282.1|  8 EfricpncgykkgfHLCFKKTENSrfrIGLICPSCGQSYNID 49
                                      44455555555555555544444444467**********995 PP

>> DUF2752  Protein of unknown function (DUF2752)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.2     0.038        19      11      23 ..      12      24 ..      10      27 .. 0.84
   2 ?    5.9   0.1     0.025        13       7      15 ..      35      43 ..      31      45 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.038
                           DUF2752 11 CPGCGltRavhal 23
                                      CP CG    +h  
  gi|298674532|ref|YP_003726282.1| 12 CPNCGYKKGFHLC 24
                                      *****99988875 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.025
                           DUF2752  7 tGipCPGCG 15
                                       G+ CP CG
  gi|298674532|ref|YP_003726282.1| 35 IGLICPSCG 43
                                      5999****9 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.6     0.013       6.6      17      38 ..       6      28 ..       2      33 .. 0.67
   2 ?    6.9   0.3     0.012       5.9      22      30 ..      38      46 ..      31      49 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.013
                       Prok-RING_1 17 edDiVvCpeCgtpy.HraCyeka 38
                                      +d   +Cp+Cg       C++k+
  gi|298674532|ref|YP_003726282.1|  6 DDEFRICPNCGYKKgFHLCFKKT 28
                                      667779****9643223466665 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.012
                       Prok-RING_1 22 vCpeCgtpy 30
                                      +Cp Cg +y
  gi|298674532|ref|YP_003726282.1| 38 ICPSCGQSY 46
                                      899999988 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   5.2    0.0029       1.5      24      52 ..      11      44 ..       3      47 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0029
                    zinc_ribbon_10 24 ICskChshnGlap...keeleev..kyrCpkCga 52
                                      IC++C  + G      k e++++    +Cp+Cg+
  gi|298674532|ref|YP_003726282.1| 11 ICPNCGYKKGFHLcfkKTENSRFriGLICPSCGQ 44
                                      9*********998844333333322457****96 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.6    0.0059         3      40      50 ..      10      20 ..       9      26 .. 0.89
   2 ?    3.9   0.1      0.12        63      41      49 ..      38      47 ..      28      53 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0059
                                      C-BTTTTBSSS CS
                    Ribosomal_L32p 40 rvcpscGyYkg 50
                                      r+cp+cGy kg
  gi|298674532|ref|YP_003726282.1| 10 RICPNCGYKKG 20
                                      89*****9998 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.12
                                      -BTTTT.BSS CS
                    Ribosomal_L32p 41 vcpscG.yYk 49
                                      +cpscG  Y+
  gi|298674532|ref|YP_003726282.1| 38 ICPSCGqSYN 47
                                      7999985665 PP

>> zf_Rg  Reverse gyrase zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   7.8      0.38   1.9e+02       9      31 ..      11      42 ..       9      43 .. 0.58

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.38
                             zf_Rg  9 lCPNCg...G......disdeRlekGLpCkrC 31
                                       CPNCg   G      + ++ R   GL C +C
  gi|298674532|ref|YP_003726282.1| 11 ICPNCGykkGfhlcfkKTENSRFRIGLICPSC 42
                                      79999833323222223456677777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        35  (0.00195214); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              35  [number of targets reported over threshold]
# CPU time: 0.55u 0.36s 00:00:00.91 Elapsed: 00:00:00.56
# Mc/sec: 360.85
//
Query:       gi|298674533|ref|YP_003726283.1|  [L=276]
Description: hypothetical protein Metev_0576 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-87  292.3   1.2    3.4e-87  292.1   1.2    1.0  1  SDH_sah        Serine dehydrogenase proteinase
     0.0014   18.0   0.0      0.006   15.9   0.0    1.9  2  ECH_1          Enoyl-CoA hydratase/isomerase
     0.0032   17.4   0.2     0.0076   16.2   0.0    1.7  2  CLP_protease   Clp protease
     0.0097   16.3   0.1      0.014   15.8   0.1    1.2  1  PBP_dimer      Penicillin-binding Protein dimerisation domain
  ------ inclusion threshold ------
      0.024   14.6   0.0      0.074   13.0   0.0    1.7  2  Peptidase_S49  Peptidase family S49
       0.05   13.4   0.5      0.076   12.9   0.5    1.2  1  KbaA           KinB-signalling pathway activation in sporulat
       0.14   12.5   0.0       0.33   11.3   0.0    1.7  1  DUF3864        Domain of Unknown Function with PDB structure 


Domain annotation for each model (and alignments):
>> SDH_sah  Serine dehydrogenase proteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  292.1   1.2   1.3e-90   3.4e-87      10     272 ..      11     275 ..       3     276 .] 0.94

  Alignments for each domain:
  == domain 1  score: 292.1 bits;  conditional E-value: 1.3e-90
                           SDH_sah  10 lssllwfllflylllapqlkrkqlllarlkvlrkleekrksrvitmihrqesigflGipiykfitiedseevlrair 86 
                                       ++++l ++++ly l++pq+++k++ ++rl +++k+e++ +++v+t+ihr+e+++++G+p+y++i+ied+e +lr ir
  gi|298674533|ref|YP_003726283.1|  11 ILTVLAIVFVLYALVYPQYQMKKVKTQRLSMIKKMEQEWGTKVLTLIHRKEAVSMFGLPVYQYIDIEDAESILRGIR 87 
                                       567888999******************************************************************** PP

                           SDH_sah  87 ltpkdkpidliihtpGGlvlaatqiakalkehkaktrvivphyamsGGtlialaadeiildenavlGpvdpqlgq.. 161
                                        t +++pid+i htpGG v  + qia+alk+h+ +trv++phy+msGGt+ialaadeii+d++av+Gp+dpqlg+  
  gi|298674533|ref|YP_003726283.1|  88 NTANNRPIDIIAHTPGGQVHPSIQIARALKNHNGHTRVMIPHYSMSGGTIIALAADEIIMDDDAVIGPIDPQLGDli 164
                                       ************************************************************************97544 PP

                           SDH_sah 162 ...ypaasilkvvekkeakdiddktliladiakkaikqveefvyellkdky.deekakeiakklteGrwthdypltv 234
                                          ypa+s +++v +k+  ++ d t++l+di++k++k ++++  ell  k+ deek + + +kl +G++ h  p++ 
  gi|298674533|ref|YP_003726283.1| 165 rgtYPAPSWINAVSQKG-ANAADTTIVLSDISEKTMKLMRKVANELLEGKIeDEEKRNYVVEKLVSGEMVHITPISA 240
                                       4449*************.56789************************9998245677889***************** PP

                           SDH_sah 235 eelkelGlevntnvpeevyellelyeqplgqrpsveyi 272
                                       +e+ ++Gl+v+tn+p++v+e++++y+     ++sveyi
  gi|298674533|ref|YP_003726283.1| 241 SEAADIGLPVSTNLPDKVHEFMKFYRS---VKSSVEYI 275
                                       *************************85...45556665 PP

>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.4e-06     0.006      98     151 ..     130     184 ..     114     200 .. 0.90
   2 ?   -0.7   0.0      0.28   7.1e+02     156     172 ..     235     251 ..     220     265 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.4e-06
                                       EEETHHHHHHHHSSEEEEETTTEEE-GGGGGT.S--CTTCHHHHHHHHHHHHHHH CS
                             ECH_1  98 aaigGGlelalacDiviaadnasfglnelklG.lipgaggtqilarkvGkskAee 151
                                       +++ GG  +ala+D +i++d+a++g    +lG li g +  + ++++v ++ A+ 
  gi|298674533|ref|YP_003726283.1| 130 YSMSGGTIIALAADEIIMDDDAVIGPIDPQLGdLIRGTYPAPSWINAVSQKGANA 184
                                       8899****************************88999999999999999988875 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.28
                                       T-EEEHHHHHHCTSSSE CS
                             ECH_1 156 gkkisaqealkvGlvdk 172
                                        ++isa ea+++Gl+  
  gi|298674533|ref|YP_003726283.1| 235 ITPISASEAADIGLPVS 251
                                       4689*********9654 PP

>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0     3e-06    0.0076      41      98 ..      87     144 ..      58     148 .. 0.87
   2 ?   -2.2   0.0       1.3   3.3e+03     149     155 ..     219     225 ..     185     248 .. 0.44

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3e-06
                                       HHH-SSS-EEEEEEE--B-HHHHHHHHHHHHHSSS-EEEEEEEEEETHHHHHHHTS-T CS
                      CLP_protease  41 eaedpdkdillyinspGGsvtaglaIydtmqyikpdvsticlGlaaSmgslllaagek 98 
                                        +++++++i ++ ++pGG+v+ ++ I+ +++ ++ +  ++     +S g+++++a+++
  gi|298674533|ref|YP_003726283.1|  87 RNTANNRPIDIIAHTPGGQVHPSIQIARALKNHNGHTRVMIPHYSMSGGTIIALAADE 144
                                       5668999***********************************************9975 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.3
                                       S-HHHHH CS
                      CLP_protease 149 qslekie 155
                                       +    +e
  gi|298674533|ref|YP_003726283.1| 219 KRNYVVE 225
                                       2222233 PP

>> PBP_dimer  Penicillin-binding Protein dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   5.4e-06     0.014      35     120 ..      43     232 ..      22     246 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.4e-06
                                       HHHHHHHHHHHHHHCHHHTTS-H........HHHHH......................................... CS
                         PBP_dimer  35 kkkalekikklaklleseenldd........erlee......................................... 62 
                                       kk ++e+  k+  l++ +e ++         +++e+                                         
  gi|298674533|ref|YP_003726283.1|  43 KKMEQEWGTKVLTLIHRKEAVSMfglpvyqyIDIEDaesilrgirntannrpidiiahtpggqvhpsiqiaralknh 119
                                       44444444444444433333333343333334444466777777777777777777788888888888888888888 PP

                                       .......................................................HHCCCCTSSTTSCECCCCCEEC CS
                         PBP_dimer  63 .......................................................lalkknsykaykpvviaedise 84 
                                                                                              +a ++++++a  ++ + +dise
  gi|298674533|ref|YP_003726283.1| 120 nghtrvmiphysmsggtiialaadeiimdddavigpidpqlgdlirgtypapswiNAVSQKGANAADTTIVLSDISE 196
                                       8888888888888888888888888888888888888888888888888888888889999999999999******* PP

                                       HHHCCCHHHHHCSTT-EEEEEEEEEETTTSTTHHHH CS
                         PBP_dimer  85 eevarikenakdlpGinievepkRyYpkgelaahvl 120
                                       ++++ +++ a++l   +ie+e+kR+Y  ++l++  +
  gi|298674533|ref|YP_003726283.1| 197 KTMKLMRKVANELLEGKIEDEEKRNYVVEKLVSGEM 232
                                       ***************************999887555 PP

>> Peptidase_S49  Peptidase family S49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.9e-05     0.074      11      41 ..     125     155 ..     117     156 .. 0.91
   2 ?   -2.5   0.0       1.7   4.3e+03      51      87 ..     224     261 ..     220     263 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.9e-05
                                       EEEEEEEETHHHHHHTTSSEEEE-TT-EEE- CS
                     Peptidase_S49  11 asaenvaaSggYylasaadkivanpstivgs 41 
                                       +++  ++ Sgg  +a aad+i+++  +++g 
  gi|298674533|ref|YP_003726283.1| 125 VMIPHYSMSGGTIIALAADEIIMDDDAVIGP 155
                                       567789***********************95 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.7
                                       -HHHHHHTT-EEEEEESSTTCCCC.CTTSS--HHHHHH CS
                     Peptidase_S49  51 lenlldklgvevqvvkaGeyksav.slrrelteeerei 87 
                                       +e+l+    v+++ ++a+e ++++  ++ +l+++  e+
  gi|298674533|ref|YP_003726283.1| 224 VEKLVSGEMVHITPISASEAADIGlPVSTNLPDKVHEF 261
                                       66666677799999999999999955556666666665 PP

>> KbaA  KinB-signalling pathway activation in sporulation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.5   2.9e-05     0.076      64     100 ..       2      38 ..       1      47 [. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.9e-05
                              KbaA  64 ifrsaklWnavQvvlilfvlfdlvylrylafakeees 100
                                       +f    +W+ + v+ i+fvl+ lvy +y++   + + 
  gi|298674533|ref|YP_003726283.1|   2 VFEDVGTWDILTVLAIVFVLYALVYPQYQMKKVKTQR 38 
                                       6888899*********************977666554 PP

>> DUF3864  Domain of Unknown Function with PDB structure (DUF3864)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00013      0.33      38      79 ..     169     208 ..     148     209 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                                       ---B----SSB-TT--SGGGS-B-GGGS-HHHHHHHHHH-GG CS
                           DUF3864  38 pakdwsllnkinqkglrpqdkpvlldklekedqdlirkyype 79 
                                       pa +w  +n + qkg    d+ ++l++++++  +l+rk   e
  gi|298674533|ref|YP_003726283.1| 169 PAPSW--INAVSQKGANAADTTIVLSDISEKTMKLMRKVANE 208
                                       56666..9****************************998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       806  (0.0449551); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.63u 0.38s 00:00:01.01 Elapsed: 00:00:00.55
# Mc/sec: 1499.41
//
Query:       gi|298674534|ref|YP_003726284.1|  [L=303]
Description: methanogenesis marker protein 11 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-10   41.0   0.0    3.8e-07   30.2   0.0    3.4  2  DUF1743   Domain of unknown function (DUF1743)
  ------ inclusion threshold ------
       0.01   16.0   0.0      0.039   14.1   0.0    2.1  2  YorP      YorP protein


Domain annotation for each model (and alignments):
>> DUF1743  Domain of unknown function (DUF1743)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   4.3e-11   3.8e-07       1     114 [.     153     243 ..     153     245 .. 0.91
   2 ?    2.5   0.0     0.016   1.4e+02       1      13 [.     276     288 ..     276     297 .. 0.80

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 4.3e-11
                                       TTHHHHHHHHHH-..-TT....S-EEEEEEEE-GGGTT---EEHHHHHHHHHHHTTCECTSEBTTTTCECCS-STTS CS
                           DUF1743   1 grgiiGAtaalganiale....dstyEllaYreperwgerevdeesvieadektypetfdnvDlshklvvlvPhtpd 73 
                                       +++++GAt++l++nia++    +s y                                     lsh++v+l+P ++ 
  gi|298674534|ref|YP_003726284.1| 153 DTKEKGATWTLTHNIADAlncsESVY-------------------------------------LSHSIVQLYP-VSS 191
                                       799************99766655666.....................................**********.777 PP

                                       S........EEEEEEES-H.HHHHHHHHCSEE..S-EEC..EEEEEESTTS- CS
                           DUF1743  74 p........vlfGirgedp.eallkaakeilskeeesee..mavfrtnqgtd 114
                                       +        ++fG+ +e++ +++l+++k++l k+++s++  m+ f+++++ d
  gi|298674534|ref|YP_003726284.1| 192 KtqncvstvLEFGCVDENAkNKILQEIKSALLKYSVSDKtgMVAFSGFDAVD 243
                                       77***************9989**************************99876 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.016
                                       TTHHHHHHHHHH- CS
                           DUF1743   1 grgiiGAtaalga 13 
                                       g g+iGA+aal +
  gi|298674534|ref|YP_003726284.1| 276 GEGVIGALAALPW 288
                                       689*******988 PP

>> YorP  YorP protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0         1     9e+03      27      36 ..      24      33 ..      12      40 .. 0.63
   2 ?   14.1   0.0   4.4e-06     0.039      20      55 ..     202     236 ..     183     243 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1
                                      -SSEEEEEEE CS
                              YorP 27 vgrkgkiieh 36
                                        r   iieh
  gi|298674534|ref|YP_003726284.1| 24 NNRYAEIIEH 33
                                      3455566666 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 4.4e-06
                                       TTTSTT--SSEEEEEEE---SS-SEEEEETTS-EEE CS
                              YorP  20 rygcphhvgrkgkiiehlhsatydyavsdetgdity 55 
                                        +gc      k ki++ ++sa   y+vsd+tg +++
  gi|298674534|ref|YP_003726284.1| 202 EFGCVDE-NAKNKILQEIKSALLKYSVSDKTGMVAF 236
                                       5777765.4689********************8875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 1673.85
//
Query:       gi|298674535|ref|YP_003726285.1|  [L=518]
Description: Indolepyruvate ferredoxin oxidoreductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.5e-11   41.9   0.2    1.7e-10   40.9   0.2    1.5  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
      1e-05   25.2   0.0     0.0045   16.6   0.0    2.4  2  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
  ------ inclusion threshold ------
      0.011   15.5   0.0      0.022   14.5   0.0    1.4  1  POR_N         Pyruvate flavodoxin/ferredoxin oxidoreductase, 
      0.029   14.7   0.0      0.084   13.2   0.0    1.8  1  PFOR_II       Pyruvate:ferredoxin oxidoreductase core domain 


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.2   3.7e-14   1.7e-10      28      98 ..     400     466 ..     381     503 .. 0.82

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 3.7e-14
                                       S-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEEEEEEE-SBCCCHHHHHHHHTCC CS
                      TPP_enzyme_C  28 gtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpitvvvlnNegygmtggqqepfggk 98 
                                        ++G +++ A+G        + +a++GD g++++ l+ l++av+ + +++v+vl+Ne+ +mtggq +p+  +
  gi|298674535|ref|YP_003726285.1| 400 FALGSAIGTACGFNN-----KGIAVIGDFGLAHSgLMSLINAVYGGFDVLVIVLQNEVAAMTGGQDTPELTD 466
                                       556666666666654.....79*******************************************9987654 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   9.9e-07    0.0045       2     160 ..      15     170 ..      14     180 .. 0.87
   2 !    6.2   0.0    0.0016       7.1      78     131 ..     428     479 ..     401     510 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9.9e-07
                                       EHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT...TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHH CS
                      TPP_enzyme_N   2 tvaealvraLkalgvehvfgvpGsrilplldalseeq..girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGa 76 
                                       t+ +al+ a  + gv+++ gv G  +++++ ++ ++q  + +   + +E +   +  g + + ++  ++  ++g ++
  gi|298674535|ref|YP_003726285.1|  15 TGLDALFSAVVDSGVKTINGVAGFPVTEIMQKFLDNQngRYNARWVTNEKTGLEIVLGSSISGHRSLMITKHVGMNV 91 
                                       7889*********************************9988888999***********9888887888888889999 PP

                                       HHCHHHHHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS-- CS
                      TPP_enzyme_N  77 tnaltalaeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtkyaervtspeelpealrrAirtalsgrpg 153
                                       ++      + ++ ++ +++++gd p++l +q+ +       +++++v   ++ +++pe++   +r+A++t+ ++ + 
  gi|298674535|ref|YP_003726285.1|  92 LSDPLITSTTHSIGSGVVIITGDDPEALASQNEQ--DSRWYGIIAEVP--VYDPSTPENAYLSIRKAFETS-EKIKA 163
                                       887777778888899***************4433..346788889999..99*******************.88888 PP

                                       EEEEEEE CS
                      TPP_enzyme_N 154 Pvylelp 160
                                       P+ + + 
  gi|298674535|ref|YP_003726285.1| 164 PAIVRIT 170
                                       8888775 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0016
                                       HCHHHHHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSEEEE-S CS
                      TPP_enzyme_N  78 naltalaeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtkyaervt 131
                                       ++l++l++A + ++ +lv++ +++++     + q++ + ++++++++ ++   +
  gi|298674535|ref|YP_003726285.1| 428 SGLMSLINAVYGGFDVLVIVLQNEVAAMT--GGQDTPELTDVVKSIVDDVSIYN 479
                                       4799*********************9999..44445566666666664433333 PP

>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   4.8e-06     0.022      22     152 ..      40     168 ..      36     197 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.8e-06
                                       HHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCCHHHHHHTT--EEEEEEEEE- CS
                             POR_N  22 iaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmienlglaageelPvvivvvaRal 98 
                                       + e ++++l++ + g+ +   + +E    + v+G++++G r++  T   G+   ++ l+   ++ +   +v+++   
  gi|298674535|ref|YP_003726285.1|  40 VTEIMQKFLDNQN-GRYNARWVTNEKTGLEIVLGSSISGHRSLMITKHVGMNVLSDPLITSTTHSIGSGVVIITGDD 115
                                       6788899999999.58999*****************************************99999998888887666 PP

                                       STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEEEE CS
                             POR_N  99 pstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAekvrvPvivl 152
                                       p   l+ +++q    + +  ++ v  +++ + a+  + +Af ++ek++ P+iv 
  gi|298674535|ref|YP_003726285.1| 116 PEA-LASQNEQDSRWYGIIAEVPVYDPSTPENAYLSIRKAFETSEKIKAPAIVR 168
                                       665.***********************************************985 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.9e-05     0.084       2      63 ..     240     299 ..     239     318 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.9e-05
                                       SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S-- CS
                           PFOR_II   2 evvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnis 63 
                                       +v i+  G+ ++ + ++ d+   +  k   + l +++P P+++l+e++k+ ++v+v++ +  
  gi|298674535|ref|YP_003726285.1| 240 DVGIISSGTPSNLVYKILDKTGFN--KFSHFSLNMVYPLPKKKLNEFIKNHDRVLVIEESEP 299
                                       566777777777777777776666..777899**************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (518 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.69u 0.35s 00:00:01.04 Elapsed: 00:00:00.54
# Mc/sec: 2911.03
//
Query:       gi|298674536|ref|YP_003726286.1|  [L=51]
Description: hypothetical protein Metev_0581 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0031   17.8   2.2      0.004   17.4   2.2    1.2  1  C1_2           C1 domain
     0.0049   16.7   1.0     0.0064   16.4   1.0    1.2  1  C1_1           Phorbol esters/diacylglycerol binding domain (
  ------ inclusion threshold ------
      0.025   14.3   3.8       0.39   10.5   0.5    2.2  2  A2L_zn_ribbon  A2L zinc ribbon domain
      0.031   14.4   0.1      0.034   14.3   0.1    1.2  1  zf-UDP         Zinc-binding RING-finger
      0.035   13.3   1.0      0.037   13.3   1.0    1.0  1  Baculo_ME53    Baculoviridae ME53
        3.7    7.3   7.5       0.36   10.6   2.7    1.7  2  Rubredoxin_2   Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   2.2   1.3e-06     0.004      15      41 ..       4      36 ..       2      40 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.3e-06
                              C1_2 15 ssesfnCsaCgrk.....idgff..YsCseCdfs 41
                                      +++++ C++C+ +     i + +  Y+C+ C f+
  gi|298674536|ref|YP_003726286.1|  4 KHNQKLCKLCRSPierelIGS-YmvYYCQNCGFT 36
                                      567899*******77776433.359***99**97 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   1.0   2.1e-06    0.0064      10      37 ..       6      36 ..       2      40 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.1e-06
                                      S--B-TTT-SB-..-S.SSS-EEEETTT--E CS
                              C1_1 10 qptfCkhCgefl..wg.kekqglkCswCkll 37
                                      +++ Ck C++++  +  +++  + C++C+++
  gi|298674536|ref|YP_003726286.1|  6 NQKLCKLCRSPIerELiGSYMVYYCQNCGFT 36
                                      6789********8655688999******986 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2    0.0068        20       2      12 ..       6      16 ..       5      18 .. 0.86
   2 ?   10.5   0.5   0.00013      0.39      22      31 ..      28      37 ..      24      38 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0068
                     A2L_zn_ribbon  2 nlkvCsvCggn 12
                                      n+k C+ C+++
  gi|298674536|ref|YP_003726286.1|  6 NQKLCKLCRSP 16
                                      899*****986 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00013
                     A2L_zn_ribbon 22 lvCieCgasf 31
                                      ++C++Cg+++
  gi|298674536|ref|YP_003726286.1| 28 YYCQNCGFTT 37
                                      89*****985 PP

>> zf-UDP  Zinc-binding RING-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   1.1e-05     0.034       4      37 ..       3      37 ..       1      47 [. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.1e-05
                            zf-UDP  4 kdlngqiCqiCgddvgltedgelFv.acnecafpv 37
                                      ++ n+++C++C   ++ +  g   v  c++c+f  
  gi|298674536|ref|YP_003726286.1|  3 RKHNQKLCKLCRSPIERELIGSYMVyYCQNCGFTT 37
                                      57899****************998846*****975 PP

>> Baculo_ME53  Baculoviridae ME53
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.0   1.2e-05     0.037     263     294 ..       3      37 ..       1      43 [. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.2e-05
                       Baculo_ME53 263 kkedkeycklckk...tklytknPvlscskcGftn 294
                                       +k++++ cklc+      l+    v++c  cGft 
  gi|298674536|ref|YP_003726286.1|   3 RKHNQKLCKLCRSpieRELIGSYMVYYCQNCGFTT 37 
                                       4566677****9422245668899*********96 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.2      0.66     2e+03      17      21 ..      10      14 ..       9      15 .. 0.59
   2 ?   10.6   2.7   0.00012      0.36       1      10 [.      28      37 ..      28      39 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.66
                      Rubredoxin_2 17 CpsCg 21
                                      C+ C+
  gi|298674536|ref|YP_003726286.1| 10 CKLCR 14
                                      66665 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00012
                      Rubredoxin_2  1 YvCsqCGfes 10
                                      Y C++CGf++
  gi|298674536|ref|YP_003726286.1| 28 YYCQNCGFTT 37
                                      88******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.35s 00:00:00.85 Elapsed: 00:00:00.53
# Mc/sec: 287.41
//
Query:       gi|298674537|ref|YP_003726287.1|  [L=45]
Description: hypothetical protein Metev_0582 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00055   19.7   0.7     0.0006   19.6   0.7    1.2  1  Cys_rich_CPCC   Cysteine-rich CPCC
     0.0073   16.9   0.4     0.0076   16.8   0.4    1.1  1  RPA_interact_C  Replication protein A interacting C-terminal
  ------ inclusion threshold ------
       0.01   15.7   0.8      0.013   15.3   0.8    1.2  1  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
      0.015   15.0   1.7       0.02   14.6   1.7    1.2  1  A2L_zn_ribbon   A2L zinc ribbon domain
      0.017   15.3   0.4      0.019   15.2   0.4    1.0  1  PHF5            PHF5-like protein
      0.019   14.9   0.5      0.025   14.5   0.5    1.2  1  Prok-RING_1     Prokaryotic RING finger family 1
      0.022   14.8   0.3      0.062   13.3   0.3    1.8  1  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
      0.045   13.8   0.3      0.064   13.3   0.3    1.3  1  DZR             Double zinc ribbon
       0.06   13.3   0.5        1.1    9.3   0.1    2.0  2  ADK_lid         Adenylate kinase, active site lid
      0.063   13.2   3.1       0.12   12.3   3.1    1.5  1  zf-C3HC4_5      Zinc finger, C3HC4 type (RING finger)
      0.077   13.2   4.4          5    7.3   4.4    2.1  1  zf-piccolo      Piccolo Zn-finger
       0.38   10.5   4.0       0.41   10.3   0.1    2.0  2  DUF2225         Uncharacterized protein conserved in bacteria
       0.53    9.9   4.5        4.4    7.0   0.3    2.1  2  RecR            RecR protein


Domain annotation for each model (and alignments):
>> Cys_rich_CPCC  Cysteine-rich CPCC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.7   4.3e-07    0.0006       3      27 ..       7      31 ..       5      44 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 4.3e-07
                     Cys_rich_CPCC  3 CpcCgyltleeeegsydiCpvC.fWe 27
                                      Cp+C  + +++e  +++iC+vC +W 
  gi|298674537|ref|YP_003726287.1|  7 CPVCKSQLINRE-YKIQICNVCgYWT 31
                                      *********999.99*******6676 PP

>> RPA_interact_C  Replication protein A interacting C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.4   5.5e-06    0.0076       1      26 [.       6      33 ..       6      42 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.5e-06
                    RPA_interact_C  1 lCPvCkkrklketsevifCe.Cg.lrle 26
                                      +CPvCk++ ++++ ++ +C+ Cg  +++
  gi|298674537|ref|YP_003726287.1|  6 ICPVCKSQLINREYKIQICNvCGyWTIK 33
                                      7*******************9*965655 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.8   9.7e-06     0.013       4      29 ..       7      29 ..       4      31 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9.7e-06
                                      ESTTTSBEEEEECSCCCEEEESSSS- CS
                    RNA_POL_M_15KD  4 CpkCgNlLlpkedkegknfeCrqCgY 29
                                      Cp C++ L+++e k      C  CgY
  gi|298674537|ref|YP_003726287.1|  7 CPVCKSQLINREYKIQI---CNVCGY 29
                                      ****************5...****** PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   1.7   1.4e-05      0.02       2      29 ..       3      29 ..       2      32 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.4e-05
                     A2L_zn_ribbon  2 nlkvCsvCggngilnseqgylvCieCga 29
                                      +l +C vC+++ i  +e  + +C+ Cg+
  gi|298674537|ref|YP_003726287.1|  3 SLEICPVCKSQLIN-REYKIQICNVCGY 29
                                      6789*******998.************8 PP

>> PHF5  PHF5-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.4   1.4e-05     0.019      30      55 ..       7      33 ..       2      38 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.4e-05
                              PHF5 30 cpicdslv.kpatkvricdecsfgkle 55
                                      cp+c s++ +++ k++ic+ c + + +
  gi|298674537|ref|YP_003726287.1|  7 CPVCKSQLiNREYKIQICNVCGYWTIK 33
                                      *****98658999********987665 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.5   1.8e-05     0.025       5      27 ..       5      28 ..       2      31 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.8e-05
                       Prok-RING_1  5 kkCpvCgkel.keedDiVvCpeCg 27
                                      ++CpvC+ +l + e  i +C +Cg
  gi|298674537|ref|YP_003726287.1|  5 EICPVCKSQLiNREYKIQICNVCG 28
                                      68****9886267799*******9 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   4.5e-05     0.062       2      12 ..       7      18 ..       7      35 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.5e-05
                    DNA_ligase_ZBD  2 CPvCGsavv.Re 12
                                      CPvC s ++ Re
  gi|298674537|ref|YP_003726287.1|  7 CPVCKSQLInRE 18
                                      ********9665 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   4.6e-05     0.064      14      36 ..       6      29 ..       2      37 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.6e-05
                               DZR 14 fCseCgtklkavaa.edrCpsCge 36
                                       C+ C+++l + +   + C  Cg+
  gi|298674537|ref|YP_003726287.1|  6 ICPVCKSQLINREYkIQICNVCGY 29
                                      577777776543334677777776 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1   0.00081       1.1      22      35 ..       5      18 ..       2      18 .. 0.88
   2 ?    2.7   0.0     0.089   1.2e+02      23      28 ..      23      28 ..      20      32 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00081
                                      TB-TTT--.-B--G CS
                           ADK_lid 22 glCDkCGepLvqRs 35
                                       +C +C ++L+ R+
  gi|298674537|ref|YP_003726287.1|  5 EICPVCKSQLINRE 18
                                      69**********96 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.089
                                      B-TTT- CS
                           ADK_lid 23 lCDkCG 28
                                      +C +CG
  gi|298674537|ref|YP_003726287.1| 23 ICNVCG 28
                                      788887 PP

>> zf-C3HC4_5  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   3.1   8.5e-05      0.12       2      25 ..       5      27 ..       4      35 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.5e-05
                        zf-C3HC4_5  2 eiCPvCkssrYlnpdleflinpeC 25
                                      eiCPvCks+  +n++ ++ i   C
  gi|298674537|ref|YP_003726287.1|  5 EICPVCKSQ-LINREYKIQICNVC 27
                                      89*****96.79999999887777 PP

>> zf-piccolo  Piccolo Zn-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   4.4    0.0036         5       2      36 ..       6      29 ..       5      36 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0036
                        zf-piccolo  2 lCplCktelnvgskeppnyntCteCkkqvCnlCGF 36
                                      +Cp+Ck +l              e k q+Cn+CG+
  gi|298674537|ref|YP_003726287.1|  6 ICPVCKSQLINR-----------EYKIQICNVCGY 29
                                      688888887655...........335567777775 PP

>> DUF2225  Uncharacterized protein conserved in bacteria (DUF2225)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.4     0.061        84       8      15 ..       7      14 ..       2      18 .. 0.79
   2 ?   10.3   0.1    0.0003      0.41      45      60 ..      18      33 ..      12      41 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.061
                           DUF2225  8 CPvCeekf 15
                                      CPvC+++ 
  gi|298674537|ref|YP_003726287.1|  7 CPVCKSQL 14
                                      ****9875 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0003
                           DUF2225 45 fYevvvCpkCgYaalk 60
                                       Y++++C+ CgY ++k
  gi|298674537|ref|YP_003726287.1| 18 EYKIQICNVCGYWTIK 33
                                      6***********8876 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.5    0.0086        12      28      36 ..       4      12 ..       1      14 [. 0.78
   2 ?    7.0   0.3    0.0032       4.4      15      26 ..      20      31 ..      12      34 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0086
                                      SSS-CCCCS CS
                              RecR 28 edlCaICsd 36
                                       ++C++C++
  gi|298674537|ref|YP_003726287.1|  4 LEICPVCKS 12
                                      589999986 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0032
                                      H-EE-TTT--EE CS
                              RecR 15 kvrhCsrCgnlt 26
                                      k++ C +Cg  t
  gi|298674537|ref|YP_003726287.1| 20 KIQICNVCGYWT 31
                                      899*****9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.54
# Mc/sec: 249.17
//
Query:       gi|298674538|ref|YP_003726288.1|  [L=224]
Description: HAD-superfamily hydrolase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.4e-17   62.5   0.5    9.3e-17   61.7   0.5    1.4  1  HAD_2           Haloacid dehalogenase-like hydrolase
    1.1e-05   25.9   0.0    8.4e-05   23.0   0.0    2.0  1  Hydrolase       haloacid dehalogenase-like hydrolase
    1.2e-05   25.3   0.0      2e-05   24.6   0.0    1.3  1  Hydrolase_like  HAD-hyrolase-like
  ------ inclusion threshold ------
      0.071   13.2   0.0       0.12   12.4   0.0    1.4  1  Type_III_YscG   Bacterial type II secretion system chaperone 


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   0.5   2.1e-20   9.3e-17       1     174 [.      10     206 ..      10     210 .. 0.77

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 2.1e-20
                             HAD_2   1 iiFDlDgTlld..teeliiqaf...nelleeyglselseeelrkliglslrellrklgeseeeee............ 60 
                                       iiFD   Tl+d  t e +++++    ++l  yg+ ++s+e+l+  +  +  ++++ +++++ e +            
  gi|298674538|ref|YP_003726288.1|  10 IIFDCYKTLIDieTDEDSLETYdivSKWLLYYGV-QISPEKLKGEYKKKISKSFELSEQDYPEVKvedifseicqen 85 
                                       6777777777644445554444000445544544.666666666666666666666666555444566777777777 PP

                             HAD_2  61 ..........kieellrkyneekkkkevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivt 127
                                                  ie+  r +++   + ++  y++  elLe    ++y   iv++ +r   e +l+ lg+ +yFd+++ 
  gi|298674538|ref|YP_003726288.1|  86 aiwdideeilGIETA-RLFRAASIQ-NIGTYSESLELLEIF--EDYPKCIVSNAQRVFSELELKYLGLYKYFDFVIF 158
                                       777776666545544.667777777.999999999999998..89******************************** PP

                             HAD_2 128 sedvekkKPdpeviekaleklklkkeeviyvGDsp.tDieaakkagik 174
                                       s+d++ kKPd ++++ a ++l++++ee++ +GD++ +D+e  +k+g++
  gi|298674538|ref|YP_003726288.1| 159 SSDFGYKKPDERLFKIAQKRLDINPEEILSIGDTTeNDVEPPQKLGMR 206
                                       **********************************************98 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   1.9e-08   8.4e-05     120     204 ..     114     198 ..       7     204 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.9e-08
                                       HTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT.GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 120 kpeaaeavasLkaagievvlltgdnpetaeraanqlG.ddyfdaviasdietvakpspegkvaaireLqgkpeevam 195
                                       + e  e+++ +    ++ +++++ ++ + e  ++ lG  +yfd+vi s++ + +kp+ + ++ a ++L ++pee++ 
  gi|298674538|ref|YP_003726288.1| 114 YSESLELLEIFE--DYPKCIVSNAQRVFSELELKYLGlYKYFDFVIFSSDFGYKKPDERLFKIAQKRLDINPEEILS 188
                                       666666666666..667899**********99999****************************************** PP

                                       EESSHH.HHH CS
                                       xxxxxx.xxx RF
                         Hydrolase 196 VGDgvn.Daa 204
                                       +GD+   D++
  gi|298674538|ref|YP_003726288.1| 189 IGDTTEnDVE 198
                                       ***9876875 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   4.4e-09     2e-05       2      47 ..     164     209 ..     163     212 .. 0.95

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 4.4e-09
                                       .STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEE CS
                    Hydrolase_like   2 lgKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvL 47 
                                       + KP   +++ a ++l+++pee+l iGD+ + D++  ++ G+++v 
  gi|298674538|ref|YP_003726288.1| 164 YKKPDERLFKIAQKRLDINPEEILSIGDTTENDVEPPQKLGMRGVH 209
                                       68*****************************************986 PP

>> Type_III_YscG  Bacterial type II secretion system chaperone protein (type_III_yscG)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.7e-05      0.12      40      71 ..      98     130 ..      82     141 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.7e-05
                                       HHHHHHHHHHHHHTT-HHHHHHHHTTS.--GGG CS
                     Type_III_YscG  40 eavrlirlssLmnkGkyeealalaekl.ayPdL 71 
                                       e++rl r++s+ n G+y e+l+l+e    yP+ 
  gi|298674538|ref|YP_003726288.1|  98 ETARLFRAASIQNIGTYSESLELLEIFeDYPKC 130
                                       89*********************9987688875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.38s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 1235.64
//
Query:       gi|298674539|ref|YP_003726289.1|  [L=314]
Description: Mn2+dependent serine/threonine protein kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.5e-12   46.1   0.0    6.9e-12   45.8   0.0    1.1  1  APH             Phosphotransferase enzyme family
    4.5e-06   26.4   3.2     0.0099   15.5   0.6    2.2  2  RIO1            RIO1 family
      4e-05   23.3   2.6     0.0007   19.2   2.6    2.3  1  Choline_kinase  Choline/ethanolamine kinase
  ------ inclusion threshold ------
      0.043   13.2   0.0      0.073   12.4   0.0    1.3  1  APH_6_hur       Aminoglycoside/hydroxyurea antibiotic resista
      0.044   13.7   0.1       0.12   12.3   0.0    1.8  2  Hemopexin       Hemopexin
        0.2   11.7   1.9       0.48   10.4   1.9    1.7  1  MSA-2c          Merozoite surface antigen 2c


Domain annotation for each model (and alignments):
>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.0   2.3e-15   6.9e-12      53     211 ..      95     243 ..      50     269 .. 0.79

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 2.3e-15
                                       B--B-CTTBS-EEETTEEEEEEE----EE-SS.HHHHHHHHHHHHHHHHHHCCHHCH.-STTTB-SHHCHTCCHHHH CS
                               APH  53 pvPevlagdtddeeigllfalieyvpgrsllr.klsaaqlpellealgeflaalhqvdpaalpladflaqdlellrq 128
                                        + +++a   + +++   + +ieyv g+sl   ++++++l+  l +++e+l++lh+    + + +++ ++  +++++
  gi|298674539|ref|YP_003726289.1|  95 NTSKPIA--RNKDFNC--VIVIEYVSGKSLMWyMEHEKHLDSRLSEIAELLRKLHDN---TKMNFYDKKKEFDDFQW 164
                                       6667777..4444444..89************9************************...77777777776666665 PP

                                       HHCHHHCCCGCCTCCHHHHHHHHHHHHHHHH--S.SS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-EEEECCHH CS
                               APH 129 lesatarllaselldlleeleeqvlaalaallpg.elptvllHgDlhpgNllvdpddgrvtGviDfedaglgpplyD 204
                                         ++    l+++ +  + +++e +l +++   +  e+   l+H+D  p N +++  +++v + iDfe +g+ ++++D
  gi|298674539|ref|YP_003726289.1| 165 NLDY----LHLDAHT-RNKFDE-LLGKWWNSPQVnEECSYLIHRDVTPLNYIFQ--NDKV-YAIDFESSGYRNRIHD 232
                                       5555....7888888.89****.9****999999999999**************..9999.**************** PP

                                       HHCCH....HH CS
                               APH 205 lavll....rs 211
                                       l+vl+    ++
  gi|298674539|ref|YP_003726289.1| 233 LGVLCaeikNH 243
                                       *****444433 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.6   3.3e-06    0.0099       9     102 ..      29     127 ..      22     157 .. 0.63
   2 !   11.4   0.1   5.9e-05      0.18     106     152 ..     178     224 ..     160     247 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.3e-06
                                       TTEEEEEEEE-S---SS-H.....HHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEEET CS
                              RIO1   9 dgkevaiKiyktstteFkk.....rkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpielkr 80 
                                       ++ke+a+ +yk ++++ +      +++  s  ++f  + +   + +    + e+Ef+nLk+++e+ ++  kpi+ ++
  gi|298674539|ref|YP_003726289.1|  29 QNKECAVNVYKFNISSHTVcryelVDEGFSVVAKFLGEPKGETREYNPCDVMENEFENLKKVNEI-INTSKPIARNK 104
                                       6779999999988877554200115555555566666654445555556689*************.*********98 PP

                                       T...EEEEE--EETTEEGGBHHHCG CS
                              RIO1  81 h...vlvmefigedgvaapklkdve 102
                                       +   v+v e+++ +   ++   + e
  gi|298674539|ref|YP_003726289.1| 105 DfncVIVIEYVSGK--SLMWYMEHE 127
                                       655599******44..333333333 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 5.9e-05
                                       HHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE--GTTE CS
                              RIO1 106 eaeelyeevleemrklykeaglvHaDLSeyNvlvdedkvviIDvsQa 152
                                       + +el+ +  ++ ++  ++  l+H D+   N ++++dkv+ ID+  +
  gi|298674539|ref|YP_003726289.1| 178 KFDELLGKWWNSPQVNEECSYLIHRDVTPLNYIFQNDKVYAIDFESS 224
                                       5555555555555556667789*********************9765 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   2.6   2.4e-07    0.0007     143     191 ..     195     241 ..      81     247 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.4e-07
                                       G-EEEE-S--SGGGEEE.-CTTEEEE--GTT-EEEEHHHHHHHHHHHTT CS
                    Choline_kinase 143 spvvfcHnDlqegNillnkeekklvlIDFEYagynyrgfDlanhfiEwa 191
                                       +   + H D+ + N ++  +++k++ IDFE +gy  r  Dl+   +E+ 
  gi|298674539|ref|YP_003726289.1| 195 ECSYLIHRDVTPLNYIF--QNDKVYAIDFESSGYRNRIHDLGVLCAEIK 241
                                       335667***********..99*********************9998875 PP

>> APH_6_hur  Aminoglycoside/hydroxyurea antibiotic resistance kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.4e-05     0.073      67     109 ..     106     148 ..     100     154 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.4e-05
                         APH_6_hur  67 eesalLLErlsgersltslvaegdDdeAtrilaellarLhaps 109
                                        + ++ +E++sg+ ++  +++e++ d  + ++aell++Lh + 
  gi|298674539|ref|YP_003726289.1| 106 FNCVIVIEYVSGKSLMWYMEHEKHLDSRLSEIAELLRKLHDNT 148
                                       466899**********************************875 PP

>> Hemopexin  Hemopexin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       3.2   9.7e+03      17      25 ..     160     168 ..     160     174 .. 0.82
   2 ?   12.3   0.0   4.1e-05      0.12      13      42 ..     209     234 ..     208     237 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.2
                                       TTEEEEEET CS
                         Hemopexin  17 GdkYWrfdp 25 
                                       +d++W +d+
  gi|298674539|ref|YP_003726289.1| 160 DDFQWNLDY 168
                                       799998886 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 4.1e-05
                                       EEEETTEEEEEETTEETTTEEEEHHHHSTT CS
                         Hemopexin  13 YFFkGdkYWrfdpqkvepgypklisdswpg 42 
                                       Y+F++dk++  d++  ++gy+++i+d+  g
  gi|298674539|ref|YP_003726289.1| 209 YIFQNDKVYAIDFE--SSGYRNRIHDL--G 234
                                       9*************..9********98..5 PP

>> MSA-2c  Merozoite surface antigen 2c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.9   0.00016      0.48       7      86 ..      80     157 ..      75     179 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00016
                            MSA-2c   7 akdtlkaLkkvkalikeeapf.etslfdaevl.eelstkddeellkallesikgmkiileklnkflkelrknsdkle 81 
                                        ++ +++Lkkv+ +i +  p+ + ++f+  ++ e++s+k+    l   +e  k ++ +l ++ + l++l  n++   
  gi|298674539|ref|YP_003726289.1|  80 MENEFENLKKVNEIINTSKPIaRNKDFNCVIViEYVSGKS----LMWYMEHEKHLDSRLSEIAELLRKLHDNTKMNF 152
                                       67789************999846789**987526777775....566677777777777777777777777777666 PP

                            MSA-2c  82 eDkek 86 
                                        Dk+k
  gi|298674539|ref|YP_003726289.1| 153 YDKKK 157
                                       66664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.53
# Mc/sec: 1792.66
//
Query:       gi|298674540|ref|YP_003726290.1|  [L=880]
Description: ATP-dependent chaperone ClpB [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-59  200.2   4.5    1.6e-56  191.1   0.0    3.4  2  AAA_2            AAA domain (Cdc48 subfamily)
    2.7e-36  123.6   2.3    2.7e-36  123.6   2.3    3.9  2  AAA_lid_9        AAA lid domain
    2.8e-32  110.6   0.9    7.4e-15   54.8   0.1    3.3  3  Clp_N            Clp amino terminal domain, pathogenicity isl
    3.2e-25   89.1   0.1    4.6e-12   46.5   0.0    3.1  2  AAA              ATPase family associated with various cellul
    4.1e-25   87.7   1.9    1.5e-24   85.8   0.8    2.7  1  ClpB_D2-small    C-terminal, D2-small domain, of ClpB protein
    5.4e-18   65.3   0.7    7.7e-13   48.6   0.0    3.6  2  AAA_5            AAA domain (dynein-related subfamily)
    4.9e-11   43.3   6.3     0.0001   22.7   0.1    4.7  3  AAA_16           AAA ATPase domain
    4.8e-08   32.9   0.0      4e-05   23.4   0.0    2.6  2  Sigma54_activat  Sigma-54 interaction domain
    9.9e-08   32.6   1.6     0.0091   16.5   0.0    3.8  3  AAA_18           AAA domain
    1.6e-07   31.7   2.9       0.11   12.8   0.0    5.2  4  AAA_22           AAA domain
    3.9e-07   30.2   0.0       0.03   14.4   0.0    3.0  2  AAA_14           AAA domain
    7.9e-07   29.0   0.0      0.015   15.0   0.0    2.9  2  IstB_IS21        IstB-like ATP binding protein
    1.8e-06   28.0   0.0     0.0095   15.9   0.0    3.4  2  NACHT            NACHT domain
    2.6e-06   27.0   0.0     0.0024   17.3   0.0    3.6  2  TniB             Bacterial TniB protein
    2.7e-06   27.0   0.0      0.026   14.1   0.0    2.6  2  AAA_7            P-loop containing dynein motor region
    2.3e-05   24.6   0.0       0.24   11.6   0.0    3.3  2  Roc              Ras of Complex, Roc, domain of DAPkinase
    4.5e-05   23.4   0.0       0.73    9.7   0.0    3.4  3  RsgA_GTPase      RsgA GTPase
    6.4e-05   23.3   0.0       0.17   12.3   0.0    3.3  2  RNA_helicase     RNA helicase
    0.00023   21.1  12.2       0.64    9.9   0.1    5.0  3  ATPase_2         ATPase domain predominantly from Archaea
    0.00048   20.6   3.7       0.66   10.5   0.0    4.3  3  ABC_tran         ABC transporter
    0.00073   19.3   1.6       0.21   11.3   0.0    4.1  3  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00085   19.4   0.0     0.0043   17.1   0.0    2.1  1  Torsin           Torsin
    0.00092   18.5   0.0      0.036   13.4   0.0    2.7  2  Zeta_toxin       Zeta toxin
    0.00093   19.4   0.0        0.2   11.8   0.0    2.9  2  AAA_33           AAA domain
     0.0011   18.9   0.3        1.6    8.7   0.0    2.9  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
     0.0015   18.8   1.6       0.69   10.1   0.0    3.9  3  AAA_28           AAA domain
     0.0022   17.4   0.1       0.82    9.0   0.1    3.6  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0029   16.8   2.5       0.22   10.7   0.1    3.5  2  DUF815           Protein of unknown function (DUF815)
     0.0046   16.8   0.9        1.7    8.5   0.0    3.5  2  Bac_DnaA         Bacterial dnaA  protein
      0.005   16.3   0.0       0.76    9.2   0.0    2.8  2  PhoH             PhoH-like protein
     0.0068   16.2   0.0       0.54   10.0   0.0    2.8  2  DNA_pol3_delta2  DNA polymerase III, delta subunit
     0.0081   15.9   0.0        1.9    8.1   0.0    2.7  2  AAA_24           AAA domain
  ------ inclusion threshold ------
       0.01   15.4   1.1        1.7    8.1   0.0    3.0  3  AAA_25           AAA domain
       0.02   14.6   0.0        2.3    7.9   0.0    3.0  2  AAA_30           AAA domain
      0.021   14.4   0.3         18    4.9   0.0    3.8  3  Ras              Ras family
      0.069   12.9   0.0        9.8    6.0   0.0    2.4  2  AAA_29           P-loop containing region of AAA domain
      0.069   12.9   0.1        4.2    7.1   0.0    3.1  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
      0.085   12.5   0.0         10    5.7   0.0    2.8  2  SRP54            SRP54-type protein, GTPase domain
      0.096   12.5   0.2          4    7.3   0.1    3.0  2  AAA_3            ATPase family associated with various cellul
        0.2   11.7   8.5       0.83    9.6   0.0    4.5  3  ResIII           Type III restriction enzyme, res subunit
       0.23   11.5  16.6        1.1    9.3   0.1    4.9  4  DUF87            Helicase HerA, central domain
        0.9   10.0  36.6        0.1   13.1   0.2    4.5  2  AAA_23           AAA domain
        3.7    6.5  12.6          8    5.5  12.6    1.5  1  Atg14            Vacuolar sorting 38 and autophagy-related su
        4.7    5.9   6.9        9.4    4.9   6.9    1.4  1  ALMT             Aluminium activated malate transporter
          5    5.9   4.0         11    4.9   4.0    1.6  1  LMBR1            LMBR1-like membrane protein
        5.7    4.7   8.7        4.2    5.2   6.9    1.8  2  V_ATPase_I       V-type ATPase 116kDa subunit family
          6    7.4  26.7       0.29   11.6  13.6    4.7  3  KELK             KELK-motif containing domain of MRCK Ser/Thr


Domain annotation for each model (and alignments):
>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.1    0.0028       1.1       5     102 ..     203     304 ..     199     330 .. 0.73
   2 !  191.1   0.0   4.2e-59   1.6e-56       1     171 []     600     765 ..     600     765 .. 0.97

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0028
                                       -EEEE--TTSSHHHHHHHHHHHTT-..........-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS.EEEE CS
                             AAA_2   5 silllgptgvGktelakalaellfv......kkekkliradaselleeeevehlvsrligappgyvgaeegG.ivll 74 
                                       +  l+g+ gvGkt + + la+            +k++i +d+ +l+ + + +   +  + +    v+  eg  i+++
  gi|298674540|ref|YP_003726290.1| 203 NPVLIGEAGVGKTAIVEGLAQRVANgdvpedMANKRIIALDMGALIAGAKYRGEFEDRLKSVLKEVSESEGQiILFI 279
                                       567899********9999999887788899888999***********888777776666665555555554448899 PP

                                       ETGGG-------------HHHHHHHHHH CS
                             AAA_2  75 DEidKihpkessgadvSregVqrdLLqi 102
                                       DE+  +     +ga   + +  ++L ++
  gi|298674540|ref|YP_003726290.1| 280 DELHTVVG---AGAAEGSMDASNLLKPM 304
                                       *9988877...44444444555555555 PP

  == domain 2  score: 191.1 bits;  conditional E-value: 4.2e-59
                                       -----EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS....... CS
                             AAA_2   1 rpiisilllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG....... 70 
                                       +pi+s+++lgptgvGktelakala  lf ++e++++r+d+se++e    +h+vsr igappgyvg+eegG       
  gi|298674540|ref|YP_003726290.1| 600 KPIGSFIFLGPTGVGKTELAKALAADLF-DNENNMVRLDMSEYME----KHTVSRMIGAPPGYVGYEEGGqlteair 671
                                       689*************************.****************....**************************** PP

                                       .....EEEEETGGG-------------HHHHHHHHHHHH--EE-------EE-TT-EEEEEE--TTHHHHTTTS-ST CS
                             AAA_2  71 .....ivllDEidKihpkessgadvSregVqrdLLqileggtltdkqgrkvdtknilfImtgafgsskisdesrske 142
                                            ++l+DEi+K+h+           +V++++Lqil++g+ltd+qgr+vd+kn+++Imt+++ ++   ++ + + 
  gi|298674540|ref|YP_003726290.1| 672 rrpysVILFDEIEKAHH-----------DVFNIMLQILDDGRLTDAQGRTVDFKNTIIIMTSNIFVDYVHEQLE-NG 736
                                       *****************...........*****************************************99544.59 PP

                                       TTTSGGG--HHHHHHTT--HHHHTT--EE CS
                             AAA_2 143 eeeekkkeeveeelkkglipEllgRlpei 171
                                       ++++k+k+++++el+k+++pE+l+R++e+
  gi|298674540|ref|YP_003726290.1| 737 ADYSKMKSMAQNELSKHFRPEFLNRIDEV 765
                                       **************************985 PP

>> AAA_lid_9  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.6   2.3   7.2e-39   2.7e-36       2     103 ..     345     446 ..     344     447 .. 0.98
   2 ?    3.4   1.8      0.18        69      65     101 ..     468     504 ..     453     507 .. 0.68

  Alignments for each domain:
  == domain 1  score: 123.6 bits;  conditional E-value: 7.2e-39
                         AAA_lid_9   2 eeetieiLrglkekyekhHgvkisdealeaavklSkrYisdrflPdkAIDllDeaaarvrlkkeskpeeleklekel 78 
                                       +e+ti+iLrglke+ye hHgv+i+d+al++a+ lS+rYis+rflPdkAIDl+Deaaa+vr++ +skp++l+++++++
  gi|298674540|ref|YP_003726290.1| 345 VEDTISILRGLKERYEVHHGVRIKDSALVEAAVLSDRYISERFLPDKAIDLVDEAAANVRTQIDSKPTQLDEVDRKI 421
                                       79*************************************************************************** PP

                         AAA_lid_9  79 aklekekealekeeekekaerlkel 103
                                       ++le e+eal+ke++ +++erl++l
  gi|298674540|ref|YP_003726290.1| 422 TQLEIEREALKKETDPASKERLESL 446
                                       *******************999876 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.18
                         AAA_lid_9  65 eskpeeleklekelaklekekealekeeekekaerlk 101
                                       ++  +el+++++++++++++ e++e+++++e a+rlk
  gi|298674540|ref|YP_003726290.1| 468 KEIISELRSFKEQIEDTKTQLERAENDNDFELASRLK 504
                                       2223457777788888888888888888899988886 PP

>> Clp_N  Clp amino terminal domain, pathogenicity island component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.1   9.8e-17   3.7e-14       4      52 ..      20      68 ..      18      69 .. 0.96
   2 !   54.8   0.1   1.9e-17   7.4e-15       1      53 []      95     147 ..      95     147 .. 0.97
   3 ?   -1.8   0.0       9.5   3.6e+03      32      46 ..     161     175 ..     157     176 .. 0.83

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 9.8e-17
                                      HHHHTTCSSB-HHHHHHHHHHSCTSHHHHHHHHTTSSHHHHHHHHHHHH CS
                             Clp_N  4 lAkslghqyistEHLLlALleeddGlaarlLkkaGvdldalrkaiekll 52
                                      +A +++hq+i+ EHLLlALle++dGl+ r+L+k+ ++++++ k +ek+l
  gi|298674540|ref|YP_003726290.1| 20 IAARYRHQQIDCEHLLLALLEQKDGLIPRILQKMDISPETIIKKVEKAL 68
                                      7999******************************************997 PP

  == domain 2  score: 54.8 bits;  conditional E-value: 1.9e-17
                                       HHHHHHHTTCSSB-HHHHHHHHHHSCTSHHHHHHHHTTSSHHHHHHHHHHHHC CS
                             Clp_N   1 AqelAkslghqyistEHLLlALleeddGlaarlLkkaGvdldalrkaiekllg 53 
                                       A ++A ++g++y+s+EHLL +Ll+e+d+   ++L +aGv+ + l++ +++++g
  gi|298674540|ref|YP_003726290.1|  95 AGKEAEQMGDEYVSVEHLLFGLLKESDSSSGKILSNAGVTREYLQQVLKEIRG 147
                                       568************************************************97 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 9.5
                                       HHHHHTTSSHHHHHH CS
                             Clp_N  32 rlLkkaGvdldalrk 46 
                                       ++L+k G+d  +l k
  gi|298674540|ref|YP_003726290.1| 161 EALEKYGIDFTELAK 175
                                       789******988876 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.0   1.2e-14   4.6e-12       2     112 ..     205     322 ..     204     339 .. 0.79
   2 !   39.0   0.0   2.6e-12   9.9e-10       2     118 ..     606     732 ..     605     741 .. 0.84

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 1.2e-14
                                       EEESSTTSSHHHHHHHHHHHH..........THEEEEEETTTCS..SSSTTHHHHHHHHHHHHHHHTSTSEEEEEET CS
                               AAA   2 llyGppGtGKTllakavakel..........gvefleisgsell..skyvgesekkirelfkeakekakpsilfiDE 66 
                                       +l+G  G+GKT++++ +a+ +          + +++ +++  l+   ky ge e++++ ++ke++e++++ ilfiDE
  gi|298674540|ref|YP_003726290.1| 205 VLIGEAGVGKTAIVEGLAQRVangdvpedmaNKRIIALDMGALIagAKYRGEFEDRLKSVLKEVSESEGQIILFIDE 281
                                       599*****************54444444444799********997778***************9999877******* PP

                                       GGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS...G CS
                               AAA  67 idalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr...p 112
                                       ++ ++++    + e ++++ n L ++l + +       +igat+     
  gi|298674540|ref|YP_003726290.1| 282 LHTVVGAG---AAEGSMDASNLLKPMLARGEL-----HCIGATTLdeyR 322
                                       ********...777778888888888877766.....688888864433 PP

  == domain 2  score: 39.0 bits;  conditional E-value: 2.6e-12
                                       EEESSTTSSHHHHHHHHHHHH...THEEEEEETTTCSSS............STTHHHH.HHHHHHHHHHHTSTS.EE CS
                               AAA   2 llyGppGtGKTllakavakel...gvefleisgsellsk............yvgesek.kirelfkeakekakp.si 61 
                                       ++ Gp G+GKT laka+a +l   + +++++++se ++k            yvg  e  ++ e +++      p s+
  gi|298674540|ref|YP_003726290.1| 606 IFLGPTGVGKTELAKALAADLfdnENNMVRLDMSEYMEKhtvsrmigappgYVGYEEGgQLTEAIRR---R--PySV 677
                                       789*****************9776699**********999*********998886554155555544...3..559* PP

                                       EEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS........SSTEEEEEEESS.GGGSTHH CS
                               AAA  62 lfiDEidalaksrsgseseeeervvnqLlteldgvkkk........eskvivigatnr.pdkldpa 118
                                       +++DEi++ + +             n +l+ ld+ +           +++i+i+++n  +d + ++
  gi|298674540|ref|YP_003726290.1| 678 ILFDEIEKAHHDV-----------FNIMLQILDDGRLTdaqgrtvdFKNTIIIMTSNIfVDYVHEQ 732
                                       *********8777...........**********9999999****955599999999866666555 PP

>> ClpB_D2-small  C-terminal, D2-small domain, of ClpB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.8   0.8   4.1e-27   1.5e-24       1      81 []     771     851 ..     771     851 .. 0.98

  Alignments for each domain:
  == domain 1  score: 85.8 bits;  conditional E-value: 4.1e-27
                                       SCHHHHHHHHHHHHHHHHHHSCTTTEEEEEHHHHHHHHHHHTSBTTTBTCCHHHHHHHHTHHHHHHHHHTTSSSTTS CS
                     ClpB_D2-small   1 LtkeelkkIvdlalkklekrlkergvelevtdealdalaekgydpeyGARpLrriiqreiedplaeeilsgelkegd 77 
                                       Ltke+l++Ivd+++++l++rl +++++le+td+a+++lae+gy++ yGARpL+r+iq+e+e+++a+ i+sg + e +
  gi|298674540|ref|YP_003726290.1| 771 LTKEQLVEIVDIKVQDLAERLIHQRLKLEITDKAKQYLAEEGYSETYGARPLQRVIQNEVETEVAKSIISGYVPERS 847
                                       89************************************************************************999 PP

                                       EEEE CS
                     ClpB_D2-small  78 tvrv 81 
                                       tv+v
  gi|298674540|ref|YP_003726290.1| 848 TVKV 851
                                       9986 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   0.00024      0.09       3      75 ..     205     283 ..     203     291 .. 0.62
   2 !   48.6   0.0     2e-15   7.7e-13       2     121 ..     605     723 ..     604     735 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00024
                                       EEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--HHH...HH--B--.........--------..G-S.EEEEE CS
                             AAA_5   3 lLvGppGtgKselaerlaaal.nreveyvqltrdtteed...lkgrreikngttslvdsplvraar..ege.ilvlD 72 
                                       +L+G+ G+gK+ ++e la+++ n  v + + ++++ + d   l+ + +++++ + + +s+l+ ++   eg+ il++D
  gi|298674540|ref|YP_003726290.1| 205 VLIGEAGVGKTAIVEGLAQRVaNGDVPEDMANKRIIALDmgaLIAGAKYRGEFEDRLKSVLK-EVSesEGQiILFID 280
                                       79*******************97776666666665554411134444443333333334444.44446555234677 PP

                                       SGG CS
                             AAA_5  73 Eve 75 
                                       E++
  gi|298674540|ref|YP_003726290.1| 281 ELH 283
                                       766 PP

  == domain 2  score: 48.6 bits;  conditional E-value: 2e-15
                                       EEEE--SSSSHHHHHHHGGGGB...S--EEEEE--TT--HHHHH--B--..........--------..G-SEEEEE CS
                             AAA_5   2 vlLvGppGtgKselaerlaaal...nreveyvqltrdtteedlkgrreikngttsl.vdsplvraar..egeilvlD 72 
                                       ++ +Gp+G+gK+ela+ laa l   +++++   +++++++ ++   +   +g   + + + l++a+r    +++++D
  gi|298674540|ref|YP_003726290.1| 605 FIFLGPTGVGKTELAKALAADLfdnENNMVRLDMSEYMEKHTVSRMIGAPPGYVGYeEGGQLTEAIRrrPYSVILFD 681
                                       799*****************9999888888889999999999998888776655550557899999998889***** PP

                                       SGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEES CS
                             AAA_5  73 EveraesevlnsLlslleerrllleeggelvkaknddllerfrviatan 121
                                       E+e+a+ +v+n++l++l++ rl  +  g+ v++kn      + +i+t+n
  gi|298674540|ref|YP_003726290.1| 682 EIEKAHHDVFNIMLQILDDGRLT-DAQGRTVDFKN------TIIIMTSN 723
                                       **********************9.77888888999......78999988 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1   2.7e-07    0.0001       2      48 ..     182     225 ..     181     231 .. 0.81
   2 ?    3.9   0.0      0.17        64     118     149 ..     256     292 ..     229     313 .. 0.72
   3 !   16.3   0.0   2.5e-05    0.0096       1      51 [.     573     629 ..     573     687 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 2.7e-07
                            AAA_16   2 lvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellral 48 
                                       ++GR++e+++   +l+r r++ p   +l+Ge+GvGK+++v+ l++++
  gi|298674540|ref|YP_003726290.1| 182 VIGRDREIRHTVKILSRRRKNNP---VLIGEAGVGKTAIVEGLAQRV 225
                                       78******777777776666655...899***********9998765 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.17
                            AAA_16 118 rllellkrllallsrderplvlvlDdlq.....wade 149
                                        + + lk+ l+  s+ e +++l++D+l+      a e
  gi|298674540|ref|YP_003726290.1| 256 EFEDRLKSVLKEVSESEGQIILFIDELHtvvgaGAAE 292
                                       5778888888555555777********9666654444 PP

  == domain 3  score: 16.3 bits;  conditional E-value: 2.5e-05
                            AAA_16   1 rlvGReeeleqLlsalervrsgrp......elvllsGesGvGKsslvrellralekd 51 
                                       r+vG +e ++++ +a+ r+++g        ++ ++ G+ GvGK+ l+++l+  l ++
  gi|298674540|ref|YP_003726290.1| 573 RVVGQDEAVKAVSDAVVRAHAGIKdpdkpiGSFIFLGPTGVGKTELAKALAADLFDN 629
                                       579*************9999998888999*********************9888766 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.013       4.8       3      60 ..     184     246 ..     182     288 .. 0.67
   2 !   23.4   0.0     1e-07     4e-05      24     138 ..     604     718 ..     574     737 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.013
                                       --SHHHHHHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHH.......HSTTTTS-EEEEETTT CS
                   Sigma54_activat   3 gesealkelleqikkvaktdlsvlitGesGtGKellaraihe.......askrkekpfvavncaa 60 
                                       g++++++++++ +++  +++ +vl  Ge G+GK+ + + + +        ++ ++k+++a++++a
  gi|298674540|ref|YP_003726290.1| 184 GRDREIRHTVKILSRR-RKNNPVL-IGEAGVGKTAIVEGLAQrvangdvPEDMANKRIIALDMGA 246
                                       5566666666555554.3344555.5*********999888844434333334455555555554 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 1e-07
                                       -EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BE..HHHHHTTTSEEE CS
                   Sigma54_activat  24 svlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekk..GlfekadgGtlf 98 
                                       s + +G +G+GK+ la+a+ +    +e+++v+++++++ e+   s++ G   G + G e+  +   ++++   ++++
  gi|298674540|ref|YP_003726290.1| 604 SFIFLGPTGVGKTELAKALAADLFDNENNMVRLDMSEYMEKHTVSRMIGAPPG-YVGYEEGGQltEAIRRRPYSVIL 679
                                       56789*********************************************998.88877765544667777889*** PP

                                       EETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEE CS
                   Sigma54_activat  99 LDeigelplelQekLlrvlqegevervGsskeikvdvrii 138
                                       +Dei++   ++ + +l++l++g+++   +++    ++ ii
  gi|298674540|ref|YP_003726290.1| 680 FDEIEKAHHDVFNIMLQILDDGRLTDAQGRTVDFKNT-II 718
                                       *********************9987654433333333.33 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00048      0.18       3      75 ..     206     274 ..     205     291 .. 0.76
   2 ?   -1.1   0.3       6.6   2.5e+03      45      83 ..     434     475 ..     414     494 .. 0.60
   3 !   16.5   0.0   2.4e-05    0.0091       3      43 ..     607     645 ..     606     672 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00048
                            AAA_18   3 ltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe.aldeskrldedkldklldaleenssaleegk 75 
                                       l G +GvGKt + + L++r ++g++  d+a ++ + l+  +  a  +++ + ed+l+++l+++ e+     eg+
  gi|298674540|ref|YP_003726290.1| 206 LIGEAGVGKTAIVEGLAQRVANGDVPEDMANKRIIALDMGALiAGAKYRGEFEDRLKSVLKEVSES-----EGQ 274
                                       7899***************999*************9999999666666666666655555555554.....333 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 6.6
                            AAA_18  45 aldeskrldedkldklldaleenss....aleegknlvidghl 83 
                                       ++d+  +++ + l+k l++++e+s+     ++++k  +i+ ++
  gi|298674540|ref|YP_003726290.1| 434 ETDPASKERLESLEKELSNIREQSKtlreQWQKEKE-IISELR 475
                                       334444444444444444444444477667888877.665555 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 2.4e-05
                            AAA_18   3 ltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdp 43 
                                         G+ GvGKt+lak+L+  l   +n + +++ +++++++ +
  gi|298674540|ref|YP_003726290.1| 607 FLGPTGVGKTELAKALAADL--FDNENNMVRLDMSEYMEKH 645
                                       67***************999..9999999999888887665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       6.5   2.5e+03      19      90 ..      18      96 ..      18     109 .. 0.66
   2 !   12.8   0.0   0.00028      0.11       4     104 ..     200     286 ..     197     320 .. 0.65
   3 !   12.6   0.2   0.00031      0.12       7     118 ..     604     700 ..     600     725 .. 0.72
   4 ?   -1.6   0.0       7.6   2.9e+03      74     114 ..     738     781 ..     719     794 .. 0.56

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 6.5
                            AAA_22 19 Ttllrrlleqldeeakaee.......erpevvfvtlpsst.sskdllrellralglelka.erlsseell.ealeqalr 87
                                      Tt ++r+++q    ++ e+       ++++++   l++   s++++ +++ +al ++ +   ++s++ ++ ++l + l+
  gi|298674540|ref|YP_003726290.1| 18 TTIAARYRHQQ---IDCEHlllalleQKDGLIPRILQKMDiSPETIIKKVEKALSESPSVsGPGSEQVYMsQRLKRVLD 93
                                      56666666664...22222445667667777766666666688899999999998877766566666666677777776 PP

                            AAA_22 88 ara 90
                                      +++
  gi|298674540|ref|YP_003726290.1| 94 TAG 96
                                      655 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00028
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelkaerlsseell 79 
                                       +++  v++Ge+G+GKT  ++ l+++              +  ++p+++ + + ++ ++   +   + + +  +++l 
  gi|298674540|ref|YP_003726290.1| 200 RKNNPVLIGEAGVGKTAIVEGLAQRV-------------ANGDVPEDMaNKRIIALDMGALIAGAKYR-GEFEDRLK 262
                                       677789**************999985.............45567777744444466666666654444.44444444 PP

                            AAA_22  80 ealeqalraravielliiDEaqhlr 104
                                       + l + +++ +   +l iDE + + 
  gi|298674540|ref|YP_003726290.1| 263 SVLKEVSESEGQ-IILFIDELHTVV 286
                                       555555555555.777777777754 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.00031
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseelleale 83 
                                       + +  G++G+GKT l++ l+  l        ++   v+ ++++ ++  ++ r++      +  +      e   +l+
  gi|298674540|ref|YP_003726290.1| 604 SFIFLGPTGVGKTELAKALAADLFD------NENNMVRLDMSEYMEKHTVSRMIG----APPGY---VGYEEGGQLT 667
                                       56778**************998832......377778888888887766655554....44444...4445667788 PP

                            AAA_22  84 qalraravielliiDEaqhlrseealeeLrsllnl 118
                                       +a+r+r   ++++ DE+++  ++++++   ++l++
  gi|298674540|ref|YP_003726290.1| 668 EAIRRRPY-SVILFDEIEKA-HHDVFNIMLQILDD 700
                                       88888888.89999999998.88888888888776 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 7.6
                            AAA_22  74 sseellealeqalraraviell.iiDEaqhlr..seealeeLrs 114
                                       + + + ++ ++ l++++++e+l  iDE+  +r  ++e+l e+++
  gi|298674540|ref|YP_003726290.1| 738 DYSKMKSMAQNELSKHFRPEFLnRIDEVAIFRplTKEQLVEIVD 781
                                       44555566666666666633331466666664333555544443 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00032      0.12       6      79 ..     205     288 ..     201     327 .. 0.74
   2 !   14.4   0.0   7.8e-05      0.03       6      90 ..     606     701 ..     603     751 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00032
                            AAA_14   6 vitGaRrvGKTtllkqlikell.......vkkesilyinldderd.kkla.dpekllelileklke.ekktylflDE 72 
                                       v+ G   vGKT +++ l+++         + +++i+ +++      +k++ ++e+ l+ +l++++e e++ +lf+DE
  gi|298674540|ref|YP_003726290.1| 205 VLIGEAGVGKTAIVEGLAQRVAngdvpedMANKRIIALDMGALIAgAKYRgEFEDRLKSVLKEVSEsEGQIILFIDE 281
                                       5778889***********988899999777777777777666443444444566666666666544489999***** PP

                            AAA_14  73 iqevpew 79 
                                        + v ++
  gi|298674540|ref|YP_003726290.1| 282 LHTVVGA 288
                                       **99544 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 7.8e-05
                            AAA_14   6 vitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe..............kllelileklkeekktyl 68 
                                       +  G+  vGKT l+k l+ +l+ ++++++ +++ +  +k                    +l e+i+++      +++
  gi|298674540|ref|YP_003726290.1| 606 IFLGPTGVGKTELAKALAADLFDNENNMVRLDMSEYMEKHTVSRMigappgyvgyeeggQLTEAIRRR----PYSVI 678
                                       567999****************8889999999988777443322233343444333333444444443....3457* PP

                            AAA_14  69 flDEiqev.pewekalkslvdeg 90 
                                       ++DEi ++  ++++++ +++d+g
  gi|298674540|ref|YP_003726290.1| 679 LFDEIEKAhHDVFNIMLQILDDG 701
                                       *****998445777777777655 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00092      0.35      45     107 ..     199     265 ..     185     284 .. 0.76
   2 !   15.0   0.0     4e-05     0.015      50      78 ..     605     633 ..     600     652 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00092
                         IstB_IS21  45 ekkenivllGpsGvGKshlaialgveavr....aglsvlfvrvedLveelkrarrdgklaralkrll 107
                                       ++k+n vl+G +GvGK+ +   l+++ ++    ++++   + + d+ + ++ a+  g+++ +lk++l
  gi|298674540|ref|YP_003726290.1| 199 RRKNNPVLIGEAGVGKTAIVEGLAQRVANgdvpEDMANKRIIALDMGALIAGAKYRGEFEDRLKSVL 265
                                       68999*************9999999876522225555566666777777777777777777777665 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 4e-05
                         IstB_IS21  50 ivllGpsGvGKshlaialgveavraglsv 78 
                                       +++lGp+GvGK+ la al+ +   ++ ++
  gi|298674540|ref|YP_003726290.1| 605 FIFLGPTGVGKTELAKALAADLFDNENNM 633
                                       799****************9988766554 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.5e-05    0.0095       4      33 ..     205     234 ..     204     308 .. 0.89
   2 !    8.0   0.0    0.0067       2.5       4      33 ..     606     635 ..     604     660 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.5e-05
                                       EEEC-TTTCHHHHHHHHHHHHCTS-SCCCC CS
                             NACHT   4 ilqGeaGsGKTtLlqklalawaegklpqga 33 
                                       +l GeaG+GKT+ +++la+  a g+ p+++
  gi|298674540|ref|YP_003726290.1| 205 VLIGEAGVGKTAIVEGLAQRVANGDVPEDM 234
                                       689**********************99875 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0067
                                       EEEC-TTTCHHHHHHHHHHHHCTS-SCCCC CS
                             NACHT   4 ilqGeaGsGKTtLlqklalawaegklpqga 33 
                                       i  G+ G+GKT L++ la ++ +++ + ++
  gi|298674540|ref|YP_003726290.1| 606 IFLGPTGVGKTELAKALAADLFDNENNMVR 635
                                       678***************999887766655 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   6.4e-06    0.0024      24     183 ..     190     339 ..     186     342 .. 0.74
   2 ?    0.5   0.0      0.91   3.5e+02      36      57 ..     603     624 ..     581     638 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 6.4e-06
                              TniB  24 eeLleypkrkrmpnlllvGdsnnGKtmivekFarlhppek.dedaekvpvlvvqappkpdekrlyaaiLealgaplk 99 
                                       ++ ++  +r r +n +l+G+  +GKt+ive  a++  + +  ed ++ +++++++               al a +k
  gi|298674540|ref|YP_003726290.1| 190 RHTVKILSRRRKNNPVLIGEAGVGKTAIVEGLAQRVANGDvPEDMANKRIIALDMG--------------ALIAGAK 252
                                       566677789999999***************99988776651455666677777664..............4555555 PP

                              TniB 100 ararvskleqqvlrl.lrelkvrvLiiDEihnll.agsarkqreflnalksLgnelkipivlvGtee.alralrtDp 173
                                        r + ++  + vl+   ++ +  +L iDE+h ++ ag a+    + n+lk +  + ++  +++ t +   + +++D+
  gi|298674540|ref|YP_003726290.1| 253 YRGEFEDRLKSVLKEvSESEGQIILFIDELHTVVgAGAAEGSMDASNLLKPMLARGELHCIGATTLDeYRKNIEKDA 329
                                       55555544444444404444555899*****9874788899999*****************99986515678***** PP

                              TniB 174 qlasRFepia 183
                                        l++RF p+ 
  gi|298674540|ref|YP_003726290.1| 330 ALERRFMPVM 339
                                       ******9975 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.91
                              TniB  36 pnlllvGdsnnGKtmivekFar 57 
                                        + +++G++ +GKt +++  a+
  gi|298674540|ref|YP_003726290.1| 603 GSFIFLGPTGVGKTELAKALAA 624
                                       567889*********9987765 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0    0.0011      0.42      32      58 ..     200     226 ..     187     287 .. 0.74
   2 !   14.1   0.0   6.8e-05     0.026      36      82 ..     605     651 ..     600     654 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0011
                             AAA_7  32 nkkpvllvGptGtGKtviikdllkkld 58 
                                       +k++ +l+G++G+GKt+i++ l +++ 
  gi|298674540|ref|YP_003726290.1| 200 RKNNPVLIGEAGVGKTAIVEGLAQRVA 226
                                       45567899***********99888765 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 6.8e-05
                             AAA_7  36 vllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdii 82 
                                       +++ GptG+GKt ++k l   l +++ +++ + +s +++ +++ ++i
  gi|298674540|ref|YP_003726290.1| 605 FIFLGPTGVGKTELAKALAADLFDNENNMVRLDMSEYMEKHTVSRMI 651
                                       689**************9999999****************9999998 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0046       1.7       3      23 ..     205     225 ..     204     241 .. 0.85
   2 !   11.6   0.0   0.00062      0.24       3      36 ..     606     638 ..     604     650 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0046
                                       EEESSTTSSHHHHHHCHCT-C CS
                               Roc   3 vlvGdsgvGKtsllkrfvedk 23 
                                       vl+G++gvGKt +++ + ++ 
  gi|298674540|ref|YP_003726290.1| 205 VLIGEAGVGKTAIVEGLAQRV 225
                                       79************9888765 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00062
                                       EEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEE CS
                               Roc   3 vlvGdsgvGKtsllkrfvedkfsekekstigvdf 36 
                                       +++G +gvGKt l+k +  d f++++ +++ +d+
  gi|298674540|ref|YP_003726290.1| 606 IFLGPTGVGKTELAKALAADLFDNEN-NMVRLDM 638
                                       79********************8764.5555555 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0    0.0019      0.73      89     122 ..     191     224 ..     158     240 .. 0.80
   2 ?   -2.2   0.0       9.1   3.5e+03      64     101 ..     536     574 ..     526     580 .. 0.73
   3 !    8.9   0.0    0.0035       1.3     102     123 ..     605     626 ..     592     652 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0019
                                       THHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  89 gleelkellkdktsvlvGqSGvGKStLinallpe 122
                                       ++ ++ ++ +++  vl+G+ GvGK+++++ l+++
  gi|298674540|ref|YP_003726290.1| 191 HTVKILSRRRKNNPVLIGEAGVGKTAIVEGLAQR 224
                                       45566677778889**************999876 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 9.1
                                       HHHHHHHHHHHTT.SEEEE--TTTHTTHHHHHHHCTTSE CS
                       RsgA_GTPase  64 eleelkeelealg.yevllvsaktkegleelkellkdkt 101
                                       + e+++e ++++  ++v+++ + ++e+l++l+++l++++
  gi|298674540|ref|YP_003726290.1| 536 DEEDIAEVVSEWTsIPVTKLMEGEREKLTHLEDRLHNRV 574
                                       345555555555436888898999999****99999986 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0035
                                       EEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase 102 svlvGqSGvGKStLinallpel 123
                                        +++G++GvGK+ L +al+ +l
  gi|298674540|ref|YP_003726290.1| 605 FIFLGPTGVGKTELAKALAADL 626
                                       68***************99864 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.019       7.3       3      24 ..     206     227 ..     205     243 .. 0.86
   2 !   12.3   0.0   0.00045      0.17       2      25 ..     606     629 ..     605     651 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.019
                      RNA_helicase   3 lyGpsgeGKStlakeLakallk 24 
                                       l G++g+GK+ +++ La+++++
  gi|298674540|ref|YP_003726290.1| 206 LIGEAGVGKTAIVEGLAQRVAN 227
                                       78****************9984 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00045
                      RNA_helicase   2 wlyGpsgeGKStlakeLakallkk 25 
                                       ++ Gp+g+GK+ lak La++l ++
  gi|298674540|ref|YP_003726290.1| 606 IFLGPTGVGKTELAKALAADLFDN 629
                                       689*****************9844 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.1    0.0017      0.64       4      43 ..     185     224 ..     183     232 .. 0.90
   2 !    8.9   0.0    0.0033       1.3     102     134 ..     257     289 ..     232     306 .. 0.80
   3 ?    6.8   0.1     0.015       5.7      25      70 ..     606     652 ..     597     806 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0017
                          ATPase_2   4 RekelkeleeilerepneiyfiYGpegsGKtaLlkeiien 43 
                                       R++e++   +il+r +++  ++ G  g+GKta++  ++++
  gi|298674540|ref|YP_003726290.1| 185 RDREIRHTVKILSRRRKNNPVLIGEAGVGKTAIVEGLAQR 224
                                       99*************99999999*********99887776 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0033
                          ATPase_2 102 vfkaielllekikkkgkkiiiiiDelqklidlg 134
                                        +  ++++l++++++  +ii++iDel  ++  g
  gi|298674540|ref|YP_003726290.1| 257 FEDRLKSVLKEVSESEGQIILFIDELHTVVGAG 289
                                       567899********************9999555 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.015
                          ATPase_2  25 iY.GpegsGKtaLlkeiienledkdkyviyyialreesiskldefie 70 
                                       i+ Gp g+GKt L k ++  l d + + + ++  +  + ++++++i+
  gi|298674540|ref|YP_003726290.1| 606 IFlGPTGVGKTELAKALAADLFDNENNMVRLDMSEYMEKHTVSRMIG 652
                                       444**************999977666666555555555555555555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.056        21      15      42 ..     205     230 ..     196     279 .. 0.83
   2 ?    1.3   1.2       1.2   4.5e+02      46      96 ..     435     492 ..     409     563 .. 0.65
   3 !   10.5   0.0    0.0017      0.66      16      51 ..     607     643 ..     603     710 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.056
                                       EEEESTTSSHHHHHHHHTTSS--SEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  15 aivGenGaGKStLlkllagllkpteGei 42 
                                       +++Ge G GK+ +++ la+ +   +G++
  gi|298674540|ref|YP_003726290.1| 205 VLIGEAGVGKTAIVEGLAQRVA--NGDV 230
                                       79*************9999874..5655 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 1.2
                                       TCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.......HHHTCHHHHHHHSTTGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxx RF
                          ABC_tran  46 gkdlkeqeleslrkeigvlpqepqlfpeltvren.......esdeeiekalsklglke 96 
                                        ++ ++++lesl+ke++ + ++++  +e   +e+         +e+ie+  ++l+  e
  gi|298674540|ref|YP_003726290.1| 435 TDPASKERLESLEKELSNIREQSKTLREQWQKEKeiiselrSFKEQIEDTKTQLERAE 492
                                       3333336666666666666666333333323333566666655555555555555444 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.0017
                                       EEESTTSSHHHHHHHHTTSS.--SEEEEEETTCEGGG CS
                                       xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                          ABC_tran  16 ivGenGaGKStLlkllagll.kpteGeilldgkdlke 51 
                                       ++G++G GK+ L+k+la  l ++++  ++ld+ +  e
  gi|298674540|ref|YP_003726290.1| 607 FLGPTGVGKTELAKALAADLfDNENNMVRLDMSEYME 643
                                       79**************875516677777777655444 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.3      0.21        80      73      95 ..     259     284 ..     178     290 .. 0.65
   2 !   11.3   0.0   0.00056      0.21       8      57 ..     573     626 ..     566     639 .. 0.72
   3 ?   -1.3   0.0       4.2   1.6e+03      84     113 ..     674     703 ..     664     715 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.21
                            RuvB_N  73 gdlaalltnleekd...vlfideihr 95 
                                         l ++l++++e++   +lfide+h 
  gi|298674540|ref|YP_003726290.1| 259 DRLKSVLKEVSESEgqiILFIDELHT 284
                                       34555666555543334788888886 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00056
                            RuvB_N   8 eyigqekvkeklk.ifieaa...kkreealdhvllyGpPGlGkttlakiiakel 57 
                                         +gq++  + ++  +++a    k  ++++   ++ Gp G+Gkt lak +a++l
  gi|298674540|ref|YP_003726290.1| 573 RVVGQDEAVKAVSdAVVRAHagiKDPDKPIGSFIFLGPTGVGKTELAKALAADL 626
                                       567887655555413343321225567788899******************987 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 4.2
                            RuvB_N  84 ekdvlfideihrlsraveevlysamedfrl 113
                                       +  v++ dei + ++ v +++ + ++d rl
  gi|298674540|ref|YP_003726290.1| 674 PYSVILFDEIEKAHHDVFNIMLQILDDGRL 703
                                       5678999**************999999876 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.1e-05    0.0043      15      80 ..     562     629 ..     555     645 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.1e-05
                                       -HHHHHHHHHHH--S-HHHHHHHHHH.HHHHHT-SS-SS-E.EEEEEE-TTSSHHHHHHHHHHHHSTT CS
                            Torsin  15 nleeLekdlekklfGqhlvkklvvks.vkaylenekpkkpL.vlsfhGwtGtGknfvaeiiaenlyrd 80 
                                       +l++Le  l+++++Gq  + k v  + v+a+   ++p+kp+  + f G tG Gk  +a+ +a +l+ +
  gi|298674540|ref|YP_003726290.1| 562 KLTHLEDRLHNRVVGQDEAVKAVSDAvVRAHAGIKDPDKPIgSFIFLGPTGVGKTELAKALAADLFDN 629
                                       6899*************999999987369***********9558899*****************9975 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0       0.3   1.1e+02      11      41 ..     196     226 ..     186     231 .. 0.76
   2 !   13.4   0.0   9.4e-05     0.036      20      58 ..     606     645 ..     586     658 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.3
                        Zeta_toxin  11 psqerPklillgGqpGAGKselaellkdele 41 
                                        s++r+   +l G  G GK+++ e l+++++
  gi|298674540|ref|YP_003726290.1| 196 LSRRRKNNPVLIGEAGVGKTAIVEGLAQRVA 226
                                       566677777788************9999874 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 9.4e-05
                        Zeta_toxin  20 llgGqpGAGKselaellkdele.rqgnvvrldpDdlRelh 58 
                                       +  G +G GK+ela++l+++l  +++n+vrld  ++ e h
  gi|298674540|ref|YP_003726290.1| 606 IFLGPTGVGKTELAKALAADLFdNENNMVRLDMSEYMEKH 645
                                       345899**************998999*******9998887 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0      0.11        42       4      24 ..     206     226 ..     205     277 .. 0.79
   2 !   11.8   0.0   0.00052       0.2       3      39 ..     606     647 ..     605     698 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.11
                            AAA_33   4 lvGlpGsGKstlaerllkklg 24 
                                       l+G +G+GK+  +e+l+++ +
  gi|298674540|ref|YP_003726290.1| 206 LIGEAGVGKTAIVEGLAQRVA 226
                                       799*************98755 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00052
                            AAA_33   3 llvGlpGsGKstlaerllkklg.....avllssdtlrrrlfg 39 
                                       ++ G+ G+GK+ la+ l++ l      +v+l+  ++++++++
  gi|298674540|ref|YP_003726290.1| 606 IFLGPTGVGKTELAKALAADLFdnennMVRLDMSEYMEKHTV 647
                                       899**************9999889999999999888887765 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0042       1.6      13      43 ..     195     225 ..     184     231 .. 0.75
   2 ?    7.2   0.0     0.013       4.9      22      43 ..     605     626 ..     575     635 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0042
                                       HHHHCHTEEEEEEESTTSSHHHHHHHHHHHT CS
                              TsaE  13 klakalgdvilLeGdLGaGKTtlvrglakal 43 
                                        l +  ++  +L G+ G+GKT++v gla+ +
  gi|298674540|ref|YP_003726290.1| 195 ILSRRRKNNPVLIGEAGVGKTAIVEGLAQRV 225
                                       444444566799****************986 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.013
                                       EEEEESTTSSHHHHHHHHHHHT CS
                              TsaE  22 ilLeGdLGaGKTtlvrglakal 43 
                                       +++ G+ G+GKT l+++la+ l
  gi|298674540|ref|YP_003726290.1| 605 FIFLGPTGVGKTELAKALAADL 626
                                       7788**************9876 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.076        29       3      23 ..     205     227 ..     203     243 .. 0.83
   2 ?   -1.5   0.1       7.1   2.7e+03      29      71 ..     390     433 ..     375     443 .. 0.63
   3 !   10.1   0.0    0.0018      0.69       2      23 ..     605     630 ..     604     656 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.076
                            AAA_28   3 vitGgestGKTtlleaLaar..g 23 
                                       v++G  + GKT ++e La+r  +
  gi|298674540|ref|YP_003726290.1| 205 VLIGEAGVGKTAIVEGLAQRvaN 227
                                       899***************98542 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 7.1
                            AAA_28  29 Eaareileeklakgedalpwv.edllafaervleeqleeeaaaa 71 
                                       + a ++++e +a+ + ++++   +l ++ +++ + ++e+ea  +
  gi|298674540|ref|YP_003726290.1| 390 DKAIDLVDEAAANVRTQIDSKpTQLDEVDRKITQLEIEREALKK 433
                                       45555566666555555555556777777777777777666553 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.0018
                            AAA_28   2 ivitGgestGKTtlleaLaar....g 23 
                                       ++++G+ + GKT l++aLaa+    +
  gi|298674540|ref|YP_003726290.1| 605 FIFLGPTGVGKTELAKALAADlfdnE 630
                                       6899***************8755443 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.12        45      23      61 ..     202     240 ..     179     264 .. 0.77
   2 !    9.0   0.1    0.0021      0.82      24      49 ..     604     629 ..     571     776 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.12
                      Mg_chelatase  23 HnlllvGppGsGKtmlakrlpsllpplseeealevakia 61 
                                        n +l+G +G GKt + + l++ +++ +  e +  ++i 
  gi|298674540|ref|YP_003726290.1| 202 NNPVLIGEAGVGKTAIVEGLAQRVANGDVPEDMANKRII 240
                                       56789***********99998877777666666666655 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0021
                      Mg_chelatase  24 nlllvGppGsGKtmlakrlpsllppl 49 
                                       +++++Gp G GKt lak+l++ l + 
  gi|298674540|ref|YP_003726290.1| 604 SFIFLGPTGVGKTELAKALAADLFDN 629
                                       589***************98765443 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1   0.00057      0.22      41     116 ..     189     282 ..     172     285 .. 0.71
   2 ?    3.1   0.3      0.11        43      55      93 ..     604     642 ..     553     820 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00057
                            DUF815  41 venteqfleglpannvLLwGarGtGKSslvkallneyaeeg.......Lrlievekedl...........kelpklv 99 
                                       ++ t + l+ ++ nn +L+G+ G+GK ++v  l +++a+          r+i ++   l           + l++++
  gi|298674540|ref|YP_003726290.1| 189 IRHTVKILSRRRKNNPVLIGEAGVGKTAIVEGLAQRVANGDvpedmanKRIIALDMGALiagakyrgefeDRLKSVL 265
                                       5678888999999**********************999877677777744544444333111111111124577777 PP

                            DUF815 100 ellrerperfilfvDDL 116
                                       ++++e++ ++ilf+D L
  gi|298674540|ref|YP_003726290.1| 266 KEVSESEGQIILFIDEL 282
                                       77778888888888876 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.11
                            DUF815  55 nvLLwGarGtGKSslvkallneyaeegLrlievekedlk 93 
                                         ++ G  G+GK  l kal +++ +++  ++ ++ ++  
  gi|298674540|ref|YP_003726290.1| 604 SFIFLGPTGVGKTELAKALAADLFDNENNMVRLDMSEYM 642
                                       457788888999999998888888877666655554443 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.055        21      32      59 ..     200     226 ..     182     245 .. 0.80
   2 !    8.5   0.0    0.0043       1.7      28      65 ..     596     633 ..     560     652 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.055
                                       T.S--EEEE-SSSSSHHHHHHHHHHHHH CS
                          Bac_DnaA  32 kkynPlfiygevGlGktHLlkaignevl 59 
                                       +k nP++i ge G+Gkt +++ ++++v 
  gi|298674540|ref|YP_003726290.1| 200 RKNNPVLI-GEAGVGKTAIVEGLAQRVA 226
                                       46799988.**********999988775 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0043
                                       HSTTT.S--EEEE-SSSSSHHHHHHHHHHHHHHHSSSS CS
                          Bac_DnaA  28 eapgkkynPlfiygevGlGktHLlkaignevlenapel 65 
                                       + p+k    +++ g++G+Gkt L ka++  + +n++++
  gi|298674540|ref|YP_003726290.1| 596 KDPDKPIGSFIFLGPTGVGKTELAKALAADLFDNENNM 633
                                       5577777778899*****************99988775 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.093        36      10      38 ..     190     220 ..     182     242 .. 0.74
   2 !    9.2   0.0     0.002      0.76      23      47 ..     606     630 ..     595     655 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.093
                                       HHHHHHHH..H-SEEEEE--TTSSTTHHHHH CS
                              PhoH  10 keylealk..kndivfaiGpaGtGKtylava 38 
                                       ++++++l+  +++  + iG+aG GKt +   
  gi|298674540|ref|YP_003726290.1| 190 RHTVKILSrrRKNNPVLIGEAGVGKTAIVEG 220
                                       56666666655667789*********98544 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.002
                                       EEE--TTSSTTHHHHHHHHHHHHTT CS
                              PhoH  23 faiGpaGtGKtylavalavealkkk 47 
                                       + +Gp+G GKt la ala++++ ++
  gi|298674540|ref|YP_003726290.1| 606 IFLGPTGVGKTELAKALAADLFDNE 630
                                       578*****************99875 PP

>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0    0.0014      0.54      20      50 ..     603     633 ..     587     653 .. 0.85
   2 ?    2.8   0.0      0.24        90     100     128 ..     671     699 ..     660     704 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0014
                   DNA_pol3_delta2  20 hayLfeGdegigkkelalnlakallceekne 50 
                                        +++f G++g+gk ela++la  l+ +e+n 
  gi|298674540|ref|YP_003726290.1| 603 GSFIFLGPTGVGKTELAKALAADLFDNENNM 633
                                       579**********************999875 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.24
                   DNA_pol3_delta2 100 reskkkiiiiedaekmtksAaNalLktlE 128
                                       r   + +i+ +++ek ++   N++L++l 
  gi|298674540|ref|YP_003726290.1| 671 RRRPYSVILFDEIEKAHHDVFNIMLQILD 699
                                       556789********************997 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.053        20       3      24 ..     202     223 ..     200     283 .. 0.82
   2 !    8.1   0.0    0.0051       1.9       7      83 ..     607     692 ..     604     708 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.053
                            AAA_24   3 lkiliyGpsgiGKTtlakelgp 24 
                                       ++ +++G++g+GKT ++  l +
  gi|298674540|ref|YP_003726290.1| 202 NNPVLIGEAGVGKTAIVEGLAQ 223
                                       56689*********99987744 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0051
                            AAA_24   7 iyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdieswedfldevvel...........aaeladyktlviD 72 
                                         Gp g+GKT lak l   + ++d e+ + +ld  ++ + +++  ++ +               a   ++y+++ +D
  gi|298674540|ref|YP_003726290.1| 607 FLGPTGVGKTELAKAL--AADLFDNENNMVRLDMSEYMEKHTVSRMIGAPPGYvgyeeggqlteAIRRRPYSVILFD 681
                                       57**************..66778889888888888887666555555554444777888888888888999999999 PP

                            AAA_24  73 tideleelcla 83 
                                        i+++   +++
  gi|298674540|ref|YP_003726290.1| 682 EIEKAHHDVFN 692
                                       99998777665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0046       1.7      37     105 ..     205     276 ..     179     306 .. 0.72
   2 ?   -1.9   0.1       5.5   2.1e+03      82     157 ..     518     594 ..     514     606 .. 0.57
   3 ?    4.6   0.1     0.055        21      37      57 ..     606     626 ..     601     635 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0046
                            AAA_25  37 llaGapgtGKttlaldlalavatGkpwlg.....pvapeqgkVlyvsaEdsedelrrRlravgealrddarllv 105
                                       +l+G  g+GKt+++  la  va G+ +++     ++    +  l+  a  +  e++ Rl+ v++++++ ++  +
  gi|298674540|ref|YP_003726290.1| 205 VLIGEAGVGKTAIVEGLAQRVANGD-VPEdmankRIIALDMGALIAGAKYRG-EFEDRLKSVLKEVSESEGQII 276
                                       799*******************998.66634433111234444444444444.777777777777766555555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.5
                            AAA_25  82 sedelrrRlravgealrddarllvldlagv.eslpLfakdrggtl.ltadvdaleaaieevegvrlvviDplsralg 156
                                       +e+el++   +++   ++ +++++  ++++ +s+p+++++ g+   lt   d+l +++    +++  v D + ra++
  gi|298674540|ref|YP_003726290.1| 518 KEEELHQMQDEMLLR-EEVDEEDIAEVVSEwTSIPVTKLMEGEREkLTHLEDRLHNRVVGQDEAVKAVSDAVVRAHA 593
                                       555555555544433.4556666666666667788777766665556666566666555534455555566666666 PP

                            AAA_25 157 g 157
                                       g
  gi|298674540|ref|YP_003726290.1| 594 G 594
                                       5 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.055
                            AAA_25  37 llaGapgtGKttlaldlalav 57 
                                       ++ G++g+GKt la  la+++
  gi|298674540|ref|YP_003726290.1| 606 IFLGPTGVGKTELAKALAADL 626
                                       778***************986 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0061       2.3      20      44 ..     203     227 ..     190     299 .. 0.81
   2 ?    3.3   0.0      0.16        60      22      49 ..     606     634 ..     602     705 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0061
                            AAA_30  20 vavltGpAGtGKttalkalreawea 44 
                                         vl G AG GKt ++++l++ +++
  gi|298674540|ref|YP_003726290.1| 203 NPVLIGEAGVGKTAIVEGLAQRVAN 227
                                       46899*************9887664 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.16
                            AAA_30  22 vltGpAGtGKttalkal.reaweaaggrv 49 
                                       +  Gp G GKt + kal ++++++++  v
  gi|298674540|ref|YP_003726290.1| 606 IFLGPTGVGKTELAKALaADLFDNENNMV 634
                                       5679***********99444555444444 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0         4   1.5e+03      51      60 ..      90      99 ..      80     111 .. 0.78
   2 ?    4.9   0.0     0.047        18       3      17 ..     205     219 ..     203     227 .. 0.88
   3 ?    4.6   0.0     0.057        22       2      29 ..     605     632 ..     604     649 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 4
                                      EEEEETTSGG CS
                               Ras 51 eiwDTAGqee 60
                                      +++DTAG+e 
  gi|298674540|ref|YP_003726290.1| 90 RVLDTAGKEA 99
                                      689****996 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.047
                                       EEEESTTSSHHHHHH CS
                               Ras   3 vlvGdsavGKtslll 17 
                                       vl+G+ +vGKt+++ 
  gi|298674540|ref|YP_003726290.1| 205 VLIGEAGVGKTAIVE 219
                                       89**********985 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.057
                                       EEEEESTTSSHHHHHHHHHHSSCSSSCT CS
                               Ras   2 lvlvGdsavGKtslllrfvkdkFkeeye 29 
                                       ++++G ++vGKt l    + d F++e +
  gi|298674540|ref|YP_003726290.1| 605 FIFLGPTGVGKTELAKALAADLFDNENN 632
                                       589******************9998865 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.026       9.8      21      41 ..     200     220 ..     190     225 .. 0.78
   2 ?    4.1   0.0       0.1        39      23      44 ..     603     624 ..     597     632 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.026
                            AAA_29  21 lkgatlltGpsGsGKSTllDA 41 
                                       +k++ +l+G+ G+GK++++  
  gi|298674540|ref|YP_003726290.1| 200 RKNNPVLIGEAGVGKTAIVEG 220
                                       445889***********9965 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.1
                            AAA_29  23 gatlltGpsGsGKSTllDAiqa 44 
                                       g++++ Gp+G+GK+ l  A++a
  gi|298674540|ref|YP_003726290.1| 603 GSFIFLGPTGVGKTELAKALAA 624
                                       57899********998877765 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.41   1.6e+02       5      23 ..     205     223 ..     201     232 .. 0.85
   2 ?    7.1   0.0     0.011       4.2       4      23 ..     605     624 ..     602     657 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.41
                         PduV-EutP   5 lliGkvgsGKttLtqalkg 23 
                                       +liG+ g+GKt++ + l +
  gi|298674540|ref|YP_003726290.1| 205 VLIGEAGVGKTAIVEGLAQ 223
                                       79*********99877765 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.011
                         PduV-EutP   4 illiGkvgsGKttLtqalkg 23 
                                        +++G++g+GKt L++al  
  gi|298674540|ref|YP_003726290.1| 605 FIFLGPTGVGKTELAKALAA 624
                                       589**************986 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0      0.12        45       5      27 ..     205     227 ..     201     244 .. 0.84
   2 ?    5.7   0.0     0.027        10       4      31 ..     605     632 ..     603     638 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.12
                                       EEEESTTSSHHHHHHHHHHHHHH CS
                             SRP54   5 llvGlqGaGKTttlaKLaallkk 27 
                                       +l+G  G+GKT  +  La+++ +
  gi|298674540|ref|YP_003726290.1| 205 VLIGEAGVGKTAIVEGLAQRVAN 227
                                       799***************98765 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.027
                                       EEEEESTTSSHHHHHHHHHHHHHHTTS- CS
                             SRP54   4 illvGlqGaGKTttlaKLaallkkegkk 31 
                                       ++++G++G+GKT  +  Laa l +++++
  gi|298674540|ref|YP_003726290.1| 605 FIFLGPTGVGKTELAKALAADLFDNENN 632
                                       5899**********99999887766544 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       1.1     4e+02       4      23 ..     206     225 ..     204     230 .. 0.85
   2 ?    7.3   0.1     0.011         4      63     109 ..     675     722 ..     605     729 .. 0.59

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.1
                             AAA_3   4 legvPGlaktllvkalakal 23 
                                       l g  G++kt +v+ la+ +
  gi|298674540|ref|YP_003726290.1| 206 LIGEAGVGKTAIVEGLAQRV 225
                                       56788************987 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.011
                             AAA_3  63 anllladeinrappktqsalleameerqvt.vegethklpepflvlat 109
                                        +++l dei++a   +   +l+++++ ++t ++g+t +++++ ++++ 
  gi|298674540|ref|YP_003726290.1| 675 YSVILFDEIEKAHHDVFNIMLQILDDGRLTdAQGRTVDFKNTIIIMTS 722
                                       4799**********************9999456788888887776654 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.25        94      12      49 ..     189     226 ..     135     232 .. 0.81
   2 ?   -0.2   0.0       2.3   8.8e+02     124     146 ..     265     287 ..     251     303 .. 0.77
   3 ?    9.6   0.0    0.0022      0.83       8      53 ..     577     631 ..     561     645 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.25
                                       HHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH- CS
                            ResIII  12 ienlleklkskrdkrglikmaTGtGKTlvaaklierll 49 
                                       i+ +++ l+ +r+++ ++  + G+GKT +   l++r++
  gi|298674540|ref|YP_003726290.1| 189 IRHTVKILSRRRKNNPVLIGEAGVGKTAIVEGLAQRVA 226
                                       44444445546777888999********9988888776 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.3
                                       ...HHHTTT-SEEEEETGGGTTS CS
                            ResIII 124 eseellrdrfdviiiDEaHrlga 146
                                        +e  +++ + +++iDE H + +
  gi|298674540|ref|YP_003726290.1| 265 LKEVSESEGQIILFIDELHTVVG 287
                                       455666777889*******8776 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0022
                                       HHHHHHHHT............TTS...EEEEEESTTSTHHHHHHHHHHHH-S... CS
                            ResIII   8 Qeeaienlleklks......krdk...rglikmaTGtGKTlvaaklierllkkgk 53 
                                       Q ea++++ +++        + dk    +++  +TG+GKT +a +l++ l+ +++
  gi|298674540|ref|YP_003726290.1| 577 QDEAVKAVSDAVVRahagikDPDKpigSFIFLGPTGVGKTELAKALAADLFDNEN 631
                                       77777777755554555554223345688999***********999999998754 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       4.2   1.6e+03     116     190 ..      87     160 ..      51     181 .. 0.63
   2 ?    3.6   0.0      0.16        63      29      60 ..     207     244 ..     205     246 .. 0.90
   3 ?    1.2   5.8      0.84   3.2e+02     115     213 ..     411     516 ..     386     525 .. 0.60
   4 ?    9.3   0.1     0.003       1.1      29     173 ..     608     755 ..     604     800 .. 0.55

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 4.2
                             DUF87 116 vqrsvleealdqakakeekeklssdepveklleelkkekeelrklknqaiarlldkledllrkggsfsnsstdli 190
                                       ++++vl+ a ++a+ +  +e +s+++++  ll+e  +++ ++ +++  +++ l++ l+++  +++  ++ +++++
  gi|298674540|ref|YP_003726290.1|  87 RLKRVLDTAGKEAE-QMGDEYVSVEHLLFGLLKESDSSSGKILSNAGVTREYLQQVLKEIRGDKKVTTENPEETY 160
                                       45555555555555.455555666666666666666444455555555555555555555544444444444443 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.16
                             DUF87  29 lgsTGsGKSntvavLleelle......kkgatililDp 60 
                                       +g++G+GK+  v  L +++++        + +i+ lD+
  gi|298674540|ref|YP_003726290.1| 207 IGEAGVGKTAIVEGLAQRVANgdvpedMANKRIIALDM 244
                                       799*****************999998877889999997 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.84
                             DUF87 115 avqrsvleealdqakakeekeklssdepveklleelk......kekeelrklknqaiarlldkledllrkggsf..s 183
                                       ++q + ++++++q++ ++e  k  +d   ++ le+l+      +e+++  +++ q ++++++ l++++++ ++   +
  gi|298674540|ref|YP_003726290.1| 411 PTQLDEVDRKITQLEIEREALKKETDPASKERLESLEkelsniREQSKTLREQWQKEKEIISELRSFKEQIEDTktQ 487
                                       44555566666666555555555555555555555554444644444666666666677777777777776666554 PP

                             DUF87 184 nsstdliallleklekegkitiidlsgvde 213
                                        + ++++++  e++++ +  t i+l+   e
  gi|298674540|ref|YP_003726290.1| 488 LERAENDNDF-ELASRLKYGTLIPLQRQYE 516
                                       4444444444.6677777777777766555 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.003
                             DUF87  29 lgsTGsGKSntvavLleellekkgatililDpHGEYgkal..............ekllsekvkvitpspsakdkelk 91 
                                       lg TG+GK+ +++ L + l  ++  +++ lD+ +EY                  ++++ + ++ i+ +p        
  gi|298674540|ref|YP_003726290.1| 608 LGPTGVGKTELAKALAADLF-DNENNMVRLDM-SEYMEKHtvsrmigappgyvgYEEGGQLTEAIRRRP-----YSV 677
                                       899*****************.99999999999.688777655555555555444333333334444332.....223 PP

                             DUF87  92 inpwsldp..eelldllee..ddkpaaavqrsvleealdqakakeekeklssdepveklleelkkekeelrklknqa 164
                                       i +++++   +++++++    dd  ++++q + ++        k+ +  ++s+ +v +++e+l+   ++++k+k++a
  gi|298674540|ref|YP_003726290.1| 678 ILFDEIEKahHDVFNIMLQilDDGRLTDAQGRTVDF-------KNTIIIMTSNIFVDYVHEQLE-NGADYSKMKSMA 746
                                       333333320022222222223333333333332222.......455666777777777777777.555666666666 PP

                             DUF87 165 iarlldkle 173
                                       +++l+++++
  gi|298674540|ref|YP_003726290.1| 747 QNELSKHFR 755
                                       666666655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5  20.7      0.23        89      24     200 .]     206     489 ..     200     489 .. 0.51
   2 ?   13.1   0.2   0.00027       0.1      20     143 ..     603     758 ..     597     875 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.23
                            AAA_23  24 ItGpNGaGKTTildAikl.aLygetprlsrks.......grgfeksdveiesegkvkayveltfenkdgry...... 86 
                                       ++G+ G GKT+i++ +   +  g++p+   ++       g  +  ++++ e+e+  k++++   e+++ +       
  gi|298674540|ref|YP_003726290.1| 206 LIGEAGVGKTAIVEGLAQrVANGDVPEDMANKriialdmGALIAGAKYRGEFEDRLKSVLKEVSESEGQIIlfidel 282
                                       56777777777777777534456665555555566666655555555555555444444333333333333455555 PP

                            AAA_23  87 ............................................................................. 86 
                                                                                                                    
  gi|298674540|ref|YP_003726290.1| 283 htvvgagaaegsmdasnllkpmlargelhcigattldeyrkniekdaalerrfmpvmvgepdvedtisilrglkery 359
                                       55566666666666666666666666666666666666666666666666666666666444444333333332222 PP

                            AAA_23  87 ....trsiererelskkkgkttkkaklellei.....deleqfisellgskkiilnlilflgqer............ 142
                                            ++i+++  +     + ++ ++++l ++     de   +++++++sk  +                       
  gi|298674540|ref|YP_003726290.1| 360 evhhGVRIKDSALVEAAVLSDRYISERFLPDKaidlvDEAAANVRTQIDSKPTQ----------Ldevdrkitqlei 426
                                       222211111111111111111111111111112222233333333333333333..........1333333333334 PP

                            AAA_23 143 ....feefelkdkkerleelekeleeledekkllekl.eqekekekeleeleeeleeilkele 200
                                            +++ + + kerle+lekel  + ++ k l+++ ++eke   el   +e++e+++ +le
  gi|298674540|ref|YP_003726290.1| 427 ereaLKKETDPASKERLESLEKELSNIREQSKTLREQwQKEKEIISELRSFKEQIEDTKTQLE 489
                                       444445555577777********9998876665555559*****************9999986 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00027
                            AAA_23  20 gltlItGpNGaGKTTildAiklaLygetprlsrks.grgfeksdveiese...........gkvkayvelt...... 78 
                                       g +++ Gp+G GKT +  A+   L+   +++ r + ++ +ek+ v+   +           g+  + ++++      
  gi|298674540|ref|YP_003726290.1| 603 GSFIFLGPTGVGKTELAKALAADLFDNENNMVRLDmSEYMEKHTVSRMIGappgyvgyeegGQLTEAIRRRpysvil 679
                                       679***********************988888888766888999985555556666666654444445555666666 PP

                            AAA_23  79 fenkdgry......trsiererelskkkgkttkkaklellei.deleqfisellgskkiilnlilflgqer...... 142
                                       f  + +          +i ++  l++ +g+t++++++ ++ + +   +++ e+l++  + +++ ++ + e       
  gi|298674540|ref|YP_003726290.1| 680 FDEIEKAHhdvfniMLQILDDGRLTDAQGRTVDFKNTIIIMTsNIFVDYVHEQLENGADYSKMKSMAQNELskhfrp 756
                                       55555555666777556667888888888888888777776646667777777777776667777766666333322 PP

                            AAA_23 143 .f 143
                                        f
  gi|298674540|ref|YP_003726290.1| 757 eF 758
                                       20 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  12.6     0.021         8      21     128 ..     411     525 ..     401     568 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.021
                             Atg14  21 perlyelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkei 97 
                                       p +l e   ++++l +e+e+lkk+ + a +++       + ++++  +++e+ ++ +++ ++ +e+   l++ k++i
  gi|298674540|ref|YP_003726290.1| 411 PTQLDEVDRKITQLEIEREALKKETDPASKER------LESLEKELSNIREQSKTLREQWQKEKEIISELRSFKEQI 481
                                       45555555566666666666666655444444......466777778888888888888888999999999999999 PP

                             Atg14  98 eekkkklaklsdklk....................kRrsdleslqneleer 128
                                       e++k +l++  +++                     +        ++el++ 
  gi|298674540|ref|YP_003726290.1| 482 EDTKTQLERAENDNDfelasrlkygtliplqrqyeE-------KEEELHQM 525
                                       999999999999988888888666666655333333.......33333333 PP

>> ALMT  Aluminium activated malate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   6.9     0.025       9.4     328     448 ..     391     509 ..     379     528 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.025
                              ALMT 328 ellkevkvaaeeLqskldskskLlvnsekweaakkkekaeeveekkeeekeseskkeea...eaveeaeseseksll 401
                                       + ++ v  aa ++++++dsk++     + +e  +k ++ e ++e  ++e++  sk++ +   ++ ++ +++s++   
  gi|298674540|ref|YP_003726290.1| 391 KAIDLVDEAAANVRTQIDSKPT-----QLDEVDRKITQLEIEREALKKETDPASKERLEsleKELSNIREQSKTLRE 462
                                       67788999*************4.....44444444444444444444444444444433232455555555555555 PP

                              ALMT 402 keskrslklskkesapaeesleekqlskeeelkelelaealslatfa 448
                                       + +k++  +s+ +s +++ + +++ql+++e+ ++ ela+ l+  t++
  gi|298674540|ref|YP_003726290.1| 463 QWQKEKEIISELRSFKEQIEDTKTQLERAENDNDFELASRLKYGTLI 509
                                       566667777888888888899999**************999988876 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   4.0     0.028        11     245     328 ..     415     499 ..     328     549 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.028
                             LMBR1 245 kyleeilkkvPeeiaeklks..............nenkteeslaklekqlikalqkrertekqwkrllekaleledi 307
                                       + ++               +              ++++++e+l +lek+l + +++++  ++qw++  e + el   
  gi|298674540|ref|YP_003726290.1| 415 DEVDR--------------KitqleierealkkeTDPASKERLESLEKELSNIREQSKTLREQWQKEKEIISELRSF 477
                                       22222..............1333333344444446677888999999888888888888888888888888888888 PP

                             LMBR1 308 iknksskekefksses.srrge 328
                                        ++ +++++++++ e+ ++ + 
  gi|298674540|ref|YP_003726290.1| 478 KEQIEDTKTQLERAENdNDFEL 499
                                       8888888888887776444443 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   6.9     0.011       4.2      49     131 ..     414     496 ..     352     588 .. 0.63
   2 ?   -3.5   0.0       4.6   1.8e+03     282     334 ..     781     833 ..     750     841 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.011
                        V_ATPase_I  49 lekavikeeeaeesleapeekeldeleeelekleeelkelnenleklkkelnelvelkavlekakefleeeeeeeee 125
                                       l+++ +k ++ e ++ea ++++    +e+le+le+el++++e++++l+++ ++ +e  + l++ ke +e+++++ e+
  gi|298674540|ref|YP_003726290.1| 414 LDEVDRKITQLEIEREALKKETDPASKERLESLEKELSNIREQSKTLREQWQKEKEIISELRSFKEQIEDTKTQLER 490
                                       23333333332223333333333344556666666666666666666666666666666666666666544333222 PP

                        V_ATPase_I 126 eeseee 131
                                       +e++++
  gi|298674540|ref|YP_003726290.1| 491 AENDND 496
                                       222222 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.6
                        V_ATPase_I 282 ewklkvkkekaiyhtLnlfnldvtkkvliaegWvpkeeleeiqkalkeatees 334
                                       ++k++   e+ i++ L l  +d++k++l  eg+  +   + +q+++++  e++
  gi|298674540|ref|YP_003726290.1| 781 DIKVQDLAERLIHQRLKLEITDKAKQYLAEEGYSETYGARPLQRVIQNEVETE 833
                                       44455557889999999999999999999999999999999999998876544 PP

>> KELK  KELK-motif containing domain of MRCK Ser/Thr protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       4.7   1.8e+03      24      52 ..     255     283 ..     251     286 .. 0.80
   2 ?   11.6  13.6   0.00077      0.29       4      67 ..     416     480 ..     413     496 .. 0.67
   3 ?    1.2   0.2       1.4   5.2e+02      68      79 ..     511     522 ..     508     527 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 4.7
                              KELK  24 aeaqErlksqkkeLkdaisqrklamqefs 52 
                                        e+++rlks  ke  +   q  l ++e++
  gi|298674540|ref|YP_003726290.1| 255 GEFEDRLKSVLKEVSESEGQIILFIDELH 283
                                       6899*********9999888777777765 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00077
                              KELK   4 eLekqlrllkqEkeelqkelae.aqErlksqkkeLkdaisqrklamqefsevneklselrsqkqk 67 
                                       e+++++ +l+ E+e l+ke    ++Erl s +keL +  +q k+ ++++++ +e +selrs k++
  gi|298674540|ref|YP_003726290.1| 416 EVDRKITQLEIEREALKKETDPaSKERLESLEKELSNIREQSKTLREQWQKEKEIISELRSFKEQ 480
                                       66777777777777777777641457777777777777777777777777777777777776654 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 1.4
                              KELK  68 lsRqlrdkeeEl 79 
                                       l Rq  +keeEl
  gi|298674540|ref|YP_003726290.1| 511 LQRQYEEKEEEL 522
                                       78*********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (880 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1690  (0.0942607); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                       127  (0.0070835); expected 17.9 (0.001)
Passed Fwd filter:                        58  (0.00323498); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              47  [number of targets reported over threshold]
# CPU time: 1.09u 0.34s 00:00:01.43 Elapsed: 00:00:00.53
# Mc/sec: 4989.63
//
Query:       gi|298674541|ref|YP_003726291.1|  [L=122]
Description: membrane-bound metal-dependent hydrolase, partial [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-14   53.3   1.4    3.6e-13   49.2   1.4    2.0  1  YdjM         LexA-binding, inner membrane-associated putative
  ------ inclusion threshold ------
      0.034   14.1   0.1      0.052   13.6   0.1    1.2  1  Zn_dep_PLPC  Zinc dependent phospholipase C
      0.065   12.7   0.6       0.25   10.8   0.1    2.0  2  SieB         Super-infection exclusion protein B
      0.075   12.8   0.1      0.094   12.5   0.1    1.2  1  PH_4         Pleckstrin homology domain
        2.5    8.6   5.5         45    4.6   5.5    2.0  1  DUF2085      Predicted membrane protein (DUF2085)


Domain annotation for each model (and alignments):
>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   1.4     1e-16   3.6e-13       4     122 ..       5     122 .]       1     122 [] 0.81

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 1e-16
                              YdjM   4 ltHallGaalglalaallgaake........avllavavlgAllPDiDhpsstlgrklgllskklaklvgHRgftHS 72 
                                       +tH++ Ga+ gl+++  lg+           ++++++ v+g++lPD          k+ ++++      +HR f+HS
  gi|298674541|ref|YP_003726291.1|   5 KTHITAGAISGLIVLLILGKIHSitispllsIIAILFSVMGSTLPD----------KIEPAKN-----SKHRKFFHS 66 
                                       6******************987777776666666666666666665..........6678788.....78******* PP

                              YdjM  73 llflallalvlllllrlfgrsa.....lrlgll.lllgvlsHlllDlltkyGvpll 122
                                        + l++ +++l+ ++++  +       l+l ++ +l+g+lsHl+lD+ t++G pl+
  gi|298674541|ref|YP_003726291.1|  67 KIILIATSYLLYEIFNTGTTAYfneniLSLYTGfILAGYLSHLILDATTPSGLPLF 122
                                       ***********999988887767777644444447777****************98 PP

>> Zn_dep_PLPC  Zinc dependent phospholipase C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.4e-05     0.052      30     107 ..      43     115 ..      30     115 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.4e-05
                                       HHHHHGGGG...-TT-GGG--BTTTTB-HHHHS......-HHHHHHHHHHHHHHHHHC.....T-HHHHHHHHHHHH CS
                       Zn_dep_PLPC  30 llGsvaPDl.eylfnasshsykthtkagllged......hhweetgkfllllikklrelyksegslklaafllGvls 99 
                                       ++Gs++PD  e+ +++s+h  ++h+k  l++ +      ++ + t ++++++i +l             ++l G+ls
  gi|298674541|ref|YP_003726291.1|  43 VMGSTLPDKiEP-AKNSKHRKFFHSKIILIATSyllyeiFN-TGTTAYFNENILSLYT----------GFILAGYLS 107
                                       68*******522.3357777777774444444455444322.4566777777777755..........499****** PP

                                       HHHHHHTS CS
                       Zn_dep_PLPC 100 HyvaDvft 107
                                       H++ D++t
  gi|298674541|ref|YP_003726291.1| 108 HLILDATT 115
                                       *****987 PP

>> SieB  Super-infection exclusion protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.21   7.4e+02      98     120 ..       5      27 ..       3      30 .. 0.81
   2 ?   10.8   0.1   7.1e-05      0.25       3      57 ..      33      87 ..      31      96 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.21
                              SieB  98 tlplndpavkeLlekgiltkasn 120
                                       +++++ +a+++L+ + il k  +
  gi|298674541|ref|YP_003726291.1|   5 KTHITAGAISGLIVLLILGKIHS 27 
                                       68999999999999998887655 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 7.1e-05
                              SieB  3 aLiiasglllllPdslleklnlgkfleeyglwiglvflisiayllaqvvskllae 57
                                      +L+i+  l+ ++  +l+ k+  +k  ++ +++   ++li+++yll  +++ + + 
  gi|298674541|ref|YP_003726291.1| 33 LLSIIAILFSVMGSTLPDKIEPAKNSKHRKFFHSKIILIATSYLLYEIFNTGTTA 87
                                      68999999999999*******9999***********************9988765 PP

>> PH_4  Pleckstrin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   2.6e-05     0.094       8      43 ..      56      91 ..      54     108 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.6e-05
                              PH_4  8 kkkkhsafkkyfvvLipGflllfklfkrsktgaskk 43
                                      k++kh +f +  ++Li+   ll+++f+  +t + ++
  gi|298674541|ref|YP_003726291.1| 56 KNSKHRKFFHSKIILIATSYLLYEIFNTGTTAYFNE 91
                                      99************************9988665554 PP

>> DUF2085  Predicted membrane protein (DUF2085)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   5.5     0.013        45      39      84 ..      47     103 ..       5     110 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.013
                           DUF2085  39 k...........aklsklsllllvllllpmaiDgltqllglyestnllRlitGllaG 84 
                                       +           ++ + ++  +++++   ++ + ++   + y ++n+l l tG++ +
  gi|298674541|ref|YP_003726291.1|  47 TlpdkiepaknsKHRKFFHSKIILIATSYLLYEIFNTGTTAYFNENILSLYTGFILA 103
                                       033334454344444555666688888888999999999999***********8754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 698.26
//
Query:       gi|298674542|ref|YP_003726292.1|  [L=329]
Description: methanogenesis marker protein 12 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0047   16.1   0.7     0.0066   15.6   0.7    1.4  1  DUF1464   Protein of unknown function (DUF1464)
  ------ inclusion threshold ------
      0.015   15.3   0.0      0.025   14.5   0.0    1.3  1  DUF1910   Domain of unknown function (DUF1910)


Domain annotation for each model (and alignments):
>> DUF1464  Protein of unknown function (DUF1464)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.7   7.3e-07    0.0066       1     190 [.       4     193 ..       4     321 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7.3e-07
                           DUF1464   1 GiDPGtksydvvvvdd.lgkvvlekeiptdevek.dpsvlvkaieea......radivalpSGyGlPlkriselaer 69 
                                       GiD Gt++  ++++++  +    + e+p+d+ +  + s ++ +i ++      +++++a+    G  +  i+++++ 
  gi|298674542|ref|YP_003726292.1|   4 GIDHGTNAIRFASITEdEDTDSYRFELPRDNAASmNESDIIDYIMDSfdvskeNVELMAVTYSMGDDINSIENIKNV 80 
                                       9************998345567789*****98762667899***999999999999********************9 PP

                           DUF1464  70 eillltlaeeseeglvGLrellkelaskelnaftiPgVieLptvPewRKvnkiDmGtA.DKlasavlavadeaeeee 145
                                       +   +  +e   +++ G +++  ++++++++a++iPg+ +  +  ++ ++n+    t  +K+ +a       a+  +
  gi|298674542|ref|YP_003726292.1|  81 DSRGVRSIEGAGKKTGGGAKIFDAIKNSDIPAVVIPGI-HTGSN-TDQRMNIFSHSTSpEKVGIAYH-----ARCLN 150
                                       9887776666666666999******************5.65554.3445676666665345555544.....22222 PP

                           DUF1464 146 yrelsFilvEvGsgfnaviaVknGkivDGlGgti.lpGflsaGalD 190
                                        ++ +Fi+ ++ s+ +  + V n ki   + + i  pG l+ G +D
  gi|298674542|ref|YP_003726292.1| 151 -HDDDFIVSDISSN-TVTLGVSNKKIAGAIDACIfAPG-LQHGPMD 193
                                       .2335666666554.44455666666666666664455.5566665 PP

>> DUF1910  Domain of unknown function (DUF1910)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.8e-06     0.025      38      73 ..      37      76 ..      14      80 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.8e-06
                           DUF1910 38 siqae....ikilklsifkykleliiakYSlGesieelea 73
                                      s+ +     + + ++++ k+++el+ ++YS+G++i+++e+
  gi|298674542|ref|YP_003726292.1| 37 SMNESdiidYIMDSFDVSKENVELMAVTYSMGDDINSIEN 76
                                      34444555557888999********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.37s 00:00:01.00 Elapsed: 00:00:00.55
# Mc/sec: 1813.64
//
Query:       gi|298674543|ref|YP_003726293.1|  [L=119]
Description: hypothetical protein Metev_0589 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-37  127.3   0.9    2.1e-37  127.1   0.9    1.1  1  DUF2103   Predicted metal-binding protein (DUF2103)


Domain annotation for each model (and alignments):
>> DUF2103  Predicted metal-binding protein (DUF2103)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.1   0.9   1.2e-41   2.1e-37       2      98 .]      16     114 ..      15     114 .. 0.96

  Alignments for each domain:
  == domain 1  score: 127.1 bits;  conditional E-value: 1.2e-41
                           DUF2103   2 pkeklggsHstiiggreGkkllekiakhpevkkviPgvikakg..sssggglrvkvtraderGnlrlllrdgssvQe 76 
                                       p +klggsHstiiggr+G+++++ i +hpevkk+iP+vi++k+   ++gg +++k++r+d+rGnlrl++++g+s+Qe
  gi|298674543|ref|YP_003726293.1|  16 PYDKLGGSHSTIIGGRQGRRIIHIIGSHPEVKKIIPAVIQVKAkkGVPGGAFSAKALRCDKRGNLRLVVSQGTSTQE 92 
                                       789************************************887755799***************************** PP

                           DUF2103  77 vfivttakdreegeriaeeLne 98 
                                       ++i+tt++d+ eg+r+++eLne
  gi|298674543|ref|YP_003726293.1|  93 LRIITTVGDTVEGKRVMDELNE 114
                                       ********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 666.55
//
Query:       gi|298674544|ref|YP_003726294.1|  [L=147]
Description: amino acid-binding ACT domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-15   55.2   0.3    2.1e-06   27.4   0.1    2.2  2  ACT             ACT domain
    3.3e-09   37.2   1.1    5.8e-05   23.6   0.1    2.2  2  ACT_4           ACT domain
    5.2e-05   22.9   0.1       0.21   11.4   0.0    2.7  2  ACT_7           ACT domain
  ------ inclusion threshold ------
      0.056   12.5   0.3       0.23   10.5   0.1    1.8  2  Glyco_hydro_28  Glycosyl hydrolases family 28


Domain annotation for each model (and alignments):
>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   1.2e-09   5.6e-06       2      51 ..      10      57 ..       9      64 .. 0.83
   2 !   27.4   0.1   4.6e-10   2.1e-06       2      58 ..      76     130 ..      75     134 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.2e-09
                                      EEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEE CS
                               ACT  2 vlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvd 51
                                       ++++++++PG La+++  l ++++Ni+  ++++ ++   gi+ +v+   
  gi|298674544|ref|YP_003726294.1| 10 QISIFAENKPGRLADIADKLKNADVNIRAFNIAEAGE--FGIIRMVVDNP 57
                                      589********************************99..55555554443 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 4.6e-10
                                       EEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHH CS
                               ACT   2 vlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleev 58 
                                       vl ++++D+PG L+ +++ l++rgiNid    + ++    +   +v v d +++ +v
  gi|298674544|ref|YP_003726294.1|  76 VLGIEMEDVPGSLSNIANSLGKRGINIDYSYAFVTKT--EKALLIVRVDDIKGAISV 130
                                       6889*******************************99..588888888887776555 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.1   1.3e-08   5.8e-05       8      54 ..      10      54 ..       4      59 .. 0.89
   2 !   12.5   0.1   3.8e-05      0.17       9      45 ..      77     113 ..      72     131 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.3e-08
                             ACT_4  8 rleveaedrkglLaditqviseekanivsvnaktrkkdglaeikitv 54
                                      ++++ ae+++g Ladi++ ++++++ni++ n+ +  + ++  i++ v
  gi|298674544|ref|YP_003726294.1| 10 QISIFAENKPGRLADIADKLKNADVNIRAFNIAE--AGEFGIIRMVV 54
                                      799*****************************99..57788877765 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 3.8e-05
                             ACT_4   9 leveaedrkglLaditqviseekanivsvnaktrkkd 45 
                                       l +e+ed +g L++i++ + + ++ni    a  +k++
  gi|298674544|ref|YP_003726294.1|  77 LGIEMEDVPGSLSNIANSLGKRGINIDYSYAFVTKTE 113
                                       56999*********************87776665533 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   4.7e-05      0.21      19      41 ..      17      39 ..       2      66 .. 0.72
   2 !    9.1   0.1   0.00024       1.1      16      63 ..      81     131 ..      70     133 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.7e-05
                                      SS--HHHHHHHHHHTTT---EEE CS
                             ACT_7 19 dvtGivaklaspLaeagIsifqi 41
                                      + +G++a +a +L +a+++i ++
  gi|298674544|ref|YP_003726294.1| 17 NKPGRLADIADKLKNADVNIRAF 39
                                      589**********8888888554 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00024
                                       ---SS--HHHHHHHHHHTTT---EEEE-SS-....EEEEEEGGGHHHHHHHH CS
                             ACT_7  16 lpfdvtGivaklaspLaeagIsifqiStyrt....dyiLVpeedlekAveaL 63 
                                       +  dv+G ++ +a+ L + gI+i ++  + t      ++V+ +d++ A+++L
  gi|298674544|ref|YP_003726294.1|  81 ME-DVPGSLSNIANSLGKRGINIDYSYAFVTktekALLIVRVDDIKGAISVL 131
                                       53.69******************88774443111145677888888888887 PP

>> Glyco_hydro_28  Glycosyl hydrolases family 28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   5.2e-05      0.23     108     178 ..      29     102 ..      21     108 .. 0.84
   2 ?    1.5   0.0     0.027   1.2e+02     242     273 ..      94     125 ..      87     132 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 5.2e-05
                    Glyco_hydro_28 108 lniknspvfhfsvesgkdltisditidasagd....hNtDgidvgsskgvtisntnikngDDciainsgsknisi 178
                                       l+  + +  +f++ ++ ++ i  +++d+++++    hNt g+ v++++   i+   +     +ia   g++ i+i
  gi|298674544|ref|YP_003726294.1|  29 LKNADVNIRAFNIAEAGEFGIIRMVVDNPDKAyeslHNT-GFTVSETNVLGIEMEDVPGSLSNIANSLGKRGINI 102
                                       4445566789****************************9.9*******999999888877777777777766665 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.027
                    Glyco_hydro_28 242 knvaypividqdYenkeptgkptsgvkisdvt 273
                                       +  +++i id  Y  + +t k+   v++ d++
  gi|298674544|ref|YP_003726294.1|  94 SLGKRGINIDYSYAFVTKTEKALLIVRVDDIK 125
                                       444689****************9999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.36s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 813.50
//
Query:       gi|298674545|ref|YP_003726295.1|  [L=433]
Description: phenylacetate--CoA ligase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-33  114.2   1.9      3e-32  110.8   1.4    2.3  2  AMP-binding_C_2  AMP-binding enzyme C-terminal domain
    2.3e-12   46.2   0.7    3.2e-11   42.5   0.0    2.4  2  AMP-binding      AMP-binding enzyme
  ------ inclusion threshold ------
      0.029   13.2   0.0       0.36    9.6   0.0    2.1  2  GH3              GH3 auxin-responsive promoter


Domain annotation for each model (and alignments):
>> AMP-binding_C_2  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.071   4.2e+02      22      71 ..     184     231 ..     176     236 .. 0.75
   2 !  110.8   1.4     5e-36     3e-32       1      96 []     335     431 ..     335     431 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.071
                                       EEEEEEEEETTEEEEEEEEEE-TT----HHHHHHHHHHHHHHHHHHHSS- CS
                   AMP-binding_C_2  22 eYqivvtregelDelevkvEvkegfsdelkelealekkiakklksklgvs 71 
                                        Y+++++  +   ++++++  ++++  ++   e  +++++k+++++ g++
  gi|298674545|ref|YP_003726295.1| 184 SYMLYMN--EAAKKMNINIKKDTDLKIGILGAEPWSEEMRKRIEDTTGIK 231
                                       5555554..45677888888888877788888889999999999999887 PP

  == domain 2  score: 110.8 bits;  conditional E-value: 5e-36
                                       TEEE-HHHHHHHHHT-TTEEEEEEEEEEEETTEEEEEEEEEE-T.T----HHHHHHHHHHHHHHHHHHHSS--EEEE CS
                   AMP-binding_C_2   1 GvnvfPsqieevlkeieevepeYqivvtregelDelevkvEvke.gfsdelkelealekkiakklksklgvsvkvel 76 
                                       GvnvfP qie+vl++i+ev++++qi+v+r +e+D ++v++E+++ +fsd++++  +lekk++++lks+l+vsvkvel
  gi|298674545|ref|YP_003726295.1| 335 GVNVFPGQIEAVLMNIPEVGEHFQIIVDRVNEMDMMNVQIEMTDtAFSDKVNDIISLEKKVESALKSVLNVSVKVEL 411
                                       9*******************************************899****************************** PP

                                       E-TT-S---------EEE-S CS
                   AMP-binding_C_2  77 vepgtlprsegKakrviDkR 96 
                                       ve+g+lpr+ gK+k+viD+R
  gi|298674545|ref|YP_003726295.1| 412 VEQGSLPRTVGKSKKVIDNR 431
                                       *******************9 PP

>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.0   5.3e-15   3.2e-11     168     370 ..      92     286 ..      91     289 .. 0.68
   2 ?   -3.1   0.2      0.36   2.1e+03     411     423 .]     322     334 ..     320     334 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 5.3e-15
                                       --SSSS-EEEEEEHHHH...HHHHHHHH..HHHCSCCTTT-EE.EESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCG CS
                       AMP-binding 168 SGTTGkPKGVmlshrnl...vanvaslk..letrfklkeddvv.lsilplahifglilelllallsGatvvllpkda 238
                                       SGT GkP  V ++ + +   +    sl+  l+   +++++d + +s+    +  g  l+l +     ++ vl++   
  gi|298674545|ref|YP_003726295.1|  92 SGTSGKPTVVGYTRNDIngwA---NSLAraLT-SIGIGRGDNMqVSYGYGLFTGG--LGLHYGAEEVSASVLPTSAG 162
                                       777777777777666663332...33322122.2334456666233333333333..23333333333444544333 PP

                                       CCHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEE CS
                       AMP-binding 239 aldpklllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllggeplspellrffralfgeevleg 314
                                           ++ +el+++l+ +via++P+ + ++ e +++ +   + k+   l++ +lg+ep s+e+ +++++++g + +++
  gi|298674545|ref|YP_003726295.1| 163 N--TGRQIELMQDLGTSVIACTPSYMLYMNEaAKKMN--INIKKDTDLKIGILGAEPWSEEMRKRIEDTTGIKAYDI 235
                                       3..45668*********************88454444..34444455****************************** PP

                                       EEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEE CS
                       AMP-binding 315 YGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvr 370
                                       +G +E +g ++  +++ +      +        v+i+D++tg+ +pdge Gel++ 
  gi|298674545|ref|YP_003726295.1| 236 FGTSELSGPLF-TECKYQ----DGIHIWADQFLVEIIDPDTGKALPDGERGELVIT 286
                                       *********98.453333....33667778999*********************96 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.36
                                       EEEEECCCEEEET CS
                       AMP-binding 411 eivgRkkdliklr 423
                                       +i+gR +d++++r
  gi|298674545|ref|YP_003726295.1| 322 RITGRVDDMLVVR 334
                                       79*******9985 PP

>> GH3  GH3 auxin-responsive promoter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   6.1e-05      0.36      73     116 ..      82     129 ..      16     199 .. 0.78
   2 ?    1.7   0.0     0.015        90     357     381 ..     278     306 ..     271     409 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 6.1e-05
                                       SSS-SEEEEECCEETTEEEEEEESHHHHHHHHHH.HHHHHHHH.....H CS
                               GH3  73 sepiklfalsSGTtsgksKliPvteeslkelallvlallaall.....s 116
                                       ++++++f  sSGT+ gk+ ++ +t++  + +a+ ++++l ++      +
  gi|298674545|ref|YP_003726295.1|  82 NTQLVRFHASSGTS-GKPTVVGYTRNDINGWANSLARALTSIGigrgdN 129
                                       567899********.***********99998776444444433433332 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.015
                                       TSEEEEEEESTT....S-SSEEECEEEEE CS
                               GH3 357 GkeYelvvTtfa....GLyRYrigDvvrv 381
                                       G++ elv+Tt +     L RYr+gD+   
  gi|298674545|ref|YP_003726295.1| 278 GERGELVITTLSkealPLIRYRVGDLTAL 306
                                       78889999997644447********8654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.69u 0.31s 00:00:01.00 Elapsed: 00:00:00.55
# Mc/sec: 2381.36
//
Query:       gi|298674546|ref|YP_003726296.1|  [L=322]
Description: phosphoesterase RecJ domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-12   47.7   0.1    3.3e-12   46.5   0.1    1.6  1  DHH       DHH family
    6.6e-11   42.8   0.2    1.1e-10   42.1   0.2    1.4  1  DHHA1     DHHA1 domain


Domain annotation for each model (and alignments):
>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.1   3.7e-16   3.3e-12       2     101 .]      18     150 ..      17     150 .. 0.87

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 3.7e-16
                                       EEEE-ECSSSHHHHHHHHHHHH.......................................CECS--TCGGCGCCHH CS
                                       xxxxxxxxxxxxxxxxxxxxxx.......................................xxxxxxxxxxxxxxxx RF
                               DHH   2 ilivghknpDtDsigSaialan.......................................llvDhneksqavegea 39 
                                       il ++h+n D D++ Sa+al++                                       ++vD++++sq  +   
  gi|298674546|ref|YP_003726296.1|  18 ILFLCHRNADPDAVSSAFALSEavggtvglvegcnrlaallvdrlnievvdepdpqsyefvVVVDTSTSSQLNDI-- 92 
                                       78889*****************9999988888888888888888888888888888888888*********9976.. PP

                                       CCCSEEEEEEE-S---SS---SS--EEEE-SSS-HHHHHHHHHHHTT----HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH  40 keeaedviiiDHHrlgeefetlapilflnepvgstaeivaelleekkeeiskeiaellllgi 101
                                         e  +  +iDHH     +++    ++l++ + staeiv+++l+  ++ i++++a  l++gi
  gi|298674546|ref|YP_003726296.1|  93 --ELPNYCVIDHHSTT-ALTEK-ADFYLHTRATSTAEIVFKVLKSMGAPITRRTAIGLISGI 150
                                       ..778899*******8.44444.568889**************************9999998 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.2   1.2e-14   1.1e-10      53     131 ..     221     301 ..     180     308 .. 0.82

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 1.2e-14
                                       HHHHHHHHHHHHTHGBTTCEEEEEEEECTEEEEEEEESSH....SS-HHHHHHHHHHHTTCCEEEETCEEEEEEEHC CS
                             DHHA1  53 agalgiaadklksklkkpvivfvakeegdkvkvsarskkd....gvdagelakeaaaklgggGGGHdlAaGagipae 125
                                           g+aa+ ++ +++  v++++++ +g  ++vsar+++d    gv++g++++++++   g GGGH+ AaG  +   
  gi|298674546|ref|YP_003726296.1| 221 VSSFGGAASSMLINIGADVAFVATTCDG-SIRVSARARRDavnsGVNLGKIMEDISENYCGTGGGHPGAAGIDV-VT 295
                                       4667888888888888888888888888.******************************************877.34 PP

                                       HHHHHH CS
                             DHHA1 126 kleeal 131
                                       +++++l
  gi|298674546|ref|YP_003726296.1| 296 DVNQIL 301
                                       455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 1826.97
//
Query:       gi|298674547|ref|YP_003726297.1|  [L=122]
Description: prefoldin subunit beta [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.4e-25   86.6  24.3    1.1e-24   86.4  24.3    1.0  1  Prefoldin_2      Prefoldin subunit
    9.8e-05   22.3  14.7     0.0083   16.0   4.1    2.3  2  Prefoldin        Prefoldin subunit
  ------ inclusion threshold ------
      0.029   13.7   5.4      0.041   13.2   5.4    1.3  1  ADPrib_exo_Tox   ADP-ribosyltransferase exoenzyme
      0.068   13.6  11.8       0.16   12.4   2.9    2.4  2  FlaC_arch        Flagella accessory protein C (FlaC)
       0.08   12.8   1.5        6.4    6.7   0.0    2.6  3  DUF4041          Domain of unknown function (DUF4041)
       0.17   11.1  27.4       0.39   10.0  11.3    2.0  2  DUF3450          Protein of unknown function (DUF3450)
       0.55   10.3   4.8       0.22   11.6   0.6    2.2  2  UPF0147          Uncharacterised protein family (UPF0147)
       0.72    8.7  22.9       0.44    9.4   6.5    2.0  2  Spc7             Spc7 kinetochore protein
        0.8    8.2  12.8        1.1    7.8  12.8    1.3  1  FapA             Flagellar Assembly Protein A
       0.91    8.8  23.9        5.1    6.4  23.9    1.8  1  GAS              Growth-arrest specific micro-tubule binding
        1.5    9.1   8.2        5.1    7.4   4.4    2.3  2  DUF948           Bacterial protein of unknown function (DUF94
        1.6    8.6  13.7          2    8.3   3.2    2.1  2  Sec34            Sec34-like family
        2.3    8.4   6.8        6.8    6.9   6.9    1.7  1  DUF2852          Protein of unknown function (DUF2852)
        2.5    7.5  25.1       0.84    9.0   7.8    2.0  2  DUF3552          Domain of unknown function (DUF3552)
        2.5    5.5  23.3        2.7    5.4  23.3    1.0  1  DUF3584          Protein of unknown function (DUF3584)
        2.5    7.6  24.9          1    8.9  10.2    2.0  2  HAUS-augmin3     HAUS augmin-like complex subunit 3
        2.6    8.0  15.0       0.44   10.5   3.2    2.0  2  DUF4509          Domain of unknown function (DUF4509)
        2.8    8.0  24.4        6.1    6.9  24.4    1.5  1  UPF0242          Uncharacterised protein family (UPF0242) N-t
        2.9    7.2  16.8          3    7.1  16.8    1.0  1  DUF4407          Domain of unknown function (DUF4407)
        2.9    7.9  17.6         39    4.3  17.6    2.0  1  Laminin_II       Laminin Domain II
          3    8.2  16.9        3.7    7.9   5.7    2.3  2  BLOC1_2          Biogenesis of lysosome-related organelles co
        3.5    7.3  13.8        3.8    7.2  13.8    1.0  1  AAA_11           AAA domain
        4.3    6.9  20.6         32    4.1  20.8    2.0  1  DUF4795          Domain of unknown function (DUF4795)
        4.4    7.8  13.6        1.8    9.1   2.0    2.3  2  DUF4140          N-terminal domain of unknown function (DUF41
        4.7    7.5  20.6        1.8    8.8   6.3    2.2  2  Spc24            Spc24 subunit of Ndc80
        5.9    6.9  13.3        5.3    7.0   1.6    2.2  2  AAA_lid_9        AAA lid domain
          6    7.0  19.5        2.2    8.5   7.8    2.1  2  PilO             Pilus assembly protein, PilO
        6.3    7.1  10.3        0.7   10.1   2.1    2.2  2  XhlA             Haemolysin XhlA
          8    5.2  11.1        9.9    4.9  11.1    1.0  1  LMBR1            LMBR1-like membrane protein


Domain annotation for each model (and alignments):
>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.4  24.3   1.8e-27   1.1e-24       1     106 []      10     115 ..      10     115 .. 0.98

  Alignments for each domain:
  == domain 1  score: 86.4 bits;  conditional E-value: 1.8e-27
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EEEEETTEEEEE-HHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2   1 qelinkfqqlqqqlqqlaqqikqletqlkelelvleelelldedtkvyklvGdvlvkqdkeevkeeLeerketleke 77 
                                       q++  ++qqlqqq q la q++q+e   ke e++leel++l+ed++vy++vG+v vk+++++++e+Lee+ke+l+ +
  gi|298674547|ref|YP_003726297.1|  10 QNQMSQLQQLQQQAQSLAVQKNQVESSQKETEKALEELNKLPEDATVYRMVGNVQVKTTRDDAIEKLEEQKENLSLR 86 
                                       89999************************************************************************ PP

                                       HHHHHHHHHHHHHHHHHHHHHHHCCTS-- CS
                       Prefoldin_2  78 iktlekqleklekeleelkeelqkklqqq 106
                                       ++++++q+e++ k++++l+e+lq+ +++q
  gi|298674547|ref|YP_003726297.1|  87 LQSINRQEERISKRFKQLQEQLQQSMGKQ 115
                                       ************************99886 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   2.8   0.00022      0.14       1      34 [.      19      52 ..      19      61 .. 0.91
   2 !   16.0   4.1   1.4e-05    0.0083      68     117 ..      62     111 ..      58     114 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00022
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                         Prefoldin  1 lkeeleslqaelaqlkeaieelektletlktlkk 34
                                      l+++++sl+ + +q++++++e ek+le l++l +
  gi|298674547|ref|YP_003726297.1| 19 LQQQAQSLAVQKNQVESSQKETEKALEELNKLPE 52
                                      689****************************987 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.4e-05
                                       TEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  68 gyyveksleeAiellkkkleelekqlekleeeleklkdqittleanlaql 117
                                       ++ v+ + ++Aie l++++e+l+  l++++ + e ++++ ++l+++l+q 
  gi|298674547|ref|YP_003726297.1|  62 NVQVKTTRDDAIEKLEEQKENLSLRLQSINRQEERISKRFKQLQEQLQQS 111
                                       89**********************************************95 PP

>> ADPrib_exo_Tox  ADP-ribosyltransferase exoenzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   5.4   6.6e-05     0.041      40      93 ..      20      91 ..      10     117 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.6e-05
                                      HCTTTSGGGS-SCHHHHHHHHHHHHCCT-.B-SS-EEEEEEE-GGGG-HHHHTT..................- CS
                    ADPrib_exo_Tox 40 rqnkgerndldkselekkiknldsaleks.ripeniivYRrvdeaelgleldsk..................n 93
                                      +q + +   ++k+++e++ k+ ++ale+  ++pe+ +vYR v++ + +++ d+                   n
  gi|298674547|ref|YP_003726297.1| 20 QQ-QAQSLAVQKNQVESSQKETEKALEELnKLPEDATVYRMVGNVQVKTTRDDAiekleeqkenlslrlqsiN 91
                                      33.33566677789999999************************99999988876666665555555555540 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   1.7     0.019        12       3      35 ..      17      49 ..       9      65 .. 0.85
   2 ?   12.4   2.9   0.00026      0.16       2      39 ..      73     110 ..      72     113 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.019
                         FlaC_arch  3 delEnklsklsteletvkkeneelsksveelke 35
                                      ++l+++ ++l ++ + v+++++e +k +eel++
  gi|298674547|ref|YP_003726297.1| 17 QQLQQQAQSLAVQKNQVESSQKETEKALEELNK 49
                                      678899999999999999999999999999986 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00026
                         FlaC_arch   2 idelEnklsklsteletvkkeneelsksveelkenVkd 39 
                                       i++lE++ ++ls +l+++ ++ e +sk  ++l+e+ ++
  gi|298674547|ref|YP_003726297.1|  73 IEKLEEQKENLSLRLQSINRQEERISKRFKQLQEQLQQ 110
                                       799******************************99875 PP

>> DUF4041  Domain of unknown function (DUF4041)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0      0.01       6.4      18      41 ..      28      51 ..      26      57 .. 0.90
   2 ?   -2.2   0.0       6.3   3.9e+03      22      26 ..      72      76 ..      62      84 .. 0.56
   3 ?    4.6   0.3     0.048        29      19      39 ..      86     106 ..      70     113 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.01
                           DUF4041 18 VkynnietlekRIeksfeainklg 41
                                      V  n +e+++k  ek+ e +nkl 
  gi|298674547|ref|YP_003726297.1| 28 VQKNQVESSQKETEKALEELNKLP 51
                                      78899*****************95 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.3
                           DUF4041 22 nietl 26
                                       ie+l
  gi|298674547|ref|YP_003726297.1| 72 AIEKL 76
                                      22222 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.048
                           DUF4041  19 kynnietlekRIeksfeaink 39 
                                       + + i++ e+RI k f++++ 
  gi|298674547|ref|YP_003726297.1|  86 RLQSINRQEERISKRFKQLQE 106
                                       677899999*******99975 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0  11.3   0.00062      0.39      43      92 ..       6      55 ..       2      64 .. 0.88
   2 ?    7.1   8.5    0.0047       2.9      36      77 ..      70     111 ..      61     120 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00062
                           DUF3450 43 ddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeie 92
                                        ++q+  +++++l+++++sl+v+++q+e+++++ e+ +++l++  e+++
  gi|298674547|ref|YP_003726297.1|  6 PPQAQNQMSQLQQLQQQAQSLAVQKNQVESSQKETEKALEELNKLPEDAT 55
                                      568999************************************98766665 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0047
                           DUF3450  36 qkkidklddekqellaeyralkeeleslevyneqlerlvasq 77 
                                          i+kl+++k++l+ ++++++++ e++++  +ql++++++ 
  gi|298674547|ref|YP_003726297.1|  70 DDAIEKLEEQKENLSLRLQSINRQEERISKRFKQLQEQLQQS 111
                                       456778888888888888888888888888887777777654 PP

>> UPF0147  Uncharacterised protein family (UPF0147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.2       1.6   9.9e+02      32      47 ..      15      30 ..       8      35 .. 0.67
   2 ?   11.6   0.6   0.00035      0.22       2      47 ..      37      87 ..      36      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.6
                                      HHHHHT-TTS-HHHHH CS
                           UPF0147 32 akekLkdekeslavra 47
                                       +++L+++ +slav+ 
  gi|298674547|ref|YP_003726297.1| 15 QLQQLQQQAQSLAVQK 30
                                      4567777777777765 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00035
                                      HHHHHHHHHHHHHHHT-TTS-H.....HHHHHHHHHHHHHT-TTS-HHHHH CS
                           UPF0147  2 eekikevielLeeiiedtsvPr.....niRraakeakekLkdekeslavra 47
                                      +++ ++++e L+++ ed +v r      ++ + ++a+ekL+++ke+l++r 
  gi|298674547|ref|YP_003726297.1| 37 QKETEKALEELNKLPEDATVYRmvgnvQVKTTRDDAIEKLEEQKENLSLRL 87
                                      5778999**************94443234677899**************96 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   8.4    0.0086       5.3     216     258 ..      10      52 ..       3      59 .. 0.84
   2 ?    9.4   6.5   0.00071      0.44     139     190 ..      64     115 ..      56     121 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0086
                              Spc7 216 eekkkelaelqeqleeleekieelkeqkseleeeiaeaervle 258
                                       ++++ +l++lq+q ++l+ + ++++++ +e+e++++e +++ e
  gi|298674547|ref|YP_003726297.1|  10 QNQMSQLQQLQQQAQSLAVQKNQVESSQKETEKALEELNKLPE 52 
                                       6678899999999999999999999999999999999998765 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00071
                              Spc7 139 gLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaa 190
                                       ++k++ ++ +e+lee+ke+L+ + + +++  +++++++++l+e+l++   ++
  gi|298674547|ref|YP_003726297.1|  64 QVKTTRDDAIEKLEEQKENLSLRLQSINRQEERISKRFKQLQEQLQQSMGKQ 115
                                       6788889999********************************9999866555 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8  12.8    0.0018       1.1     334     414 ..      27     106 ..       4     118 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0018
                              FapA 334 elkekl.keleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeele 409
                                       ++++++ +  ++e e+  eel+kl ++ +  ++   + q++ ++ + ++kl+e+ke+l+ +l++++++ ++++++++
  gi|298674547|ref|YP_003726297.1|  27 AVQKNQvESSQKETEKALEELNKLPEDATVYRM-VGNVQVKTTRDDAIEKLEEQKENLSLRLQSINRQEERISKRFK 102
                                       222222233333334444444444444666666.4468899999*****************************9999 PP

                              FapA 410 skkee 414
                                       +  +e
  gi|298674547|ref|YP_003726297.1| 103 QL-QE 106
                                       98.33 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4  23.9    0.0083       5.1      40     143 ..       7     115 ..       3     118 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0083
                               GAS  40 kkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkel.....ekelkdlkwehevl 111
                                        +++ +  +l++++q+ ++l  + +++e   +e +k+l++ +k  ++ +  ++  +++     ++ +++l++++e+l
  gi|298674547|ref|YP_003726297.1|   7 PQAQNQMSQLQQLQQQAQSLAVQKNQVESSQKETEKALEELNKLPEDATVYRMVGNVQvkttrDDAIEKLEEQKENL 83 
                                       566666677777777777776666666666666666666666666555555544443311112568999******** PP

                               GAS 112 eqrfekvekerdelykkfeaaiqevqqktglk 143
                                       + r++++ ++ ++++k+f++  +++qq +g +
  gi|298674547|ref|YP_003726297.1|  84 SLRLQSINRQEERISKRFKQLQEQLQQSMGKQ 115
                                       ***************************99976 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   4.4    0.0082       5.1      28      64 ..      19      55 ..       8      85 .. 0.76
   2 ?    3.2   0.6      0.17     1e+02      37      65 ..      82     110 ..      63     118 .. 0.46

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0082
                            DUF948 28 ldeaaatieelekqvdpilkevedllakvnelledvn 64
                                      l++ a+++++ ++qv++  ke+e++l++ n+l ed +
  gi|298674547|ref|YP_003726297.1| 19 LQQQAQSLAVQKNQVESSQKETEKALEELNKLPEDAT 55
                                      5666777777789******************766654 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.17
                            DUF948  37 elekqvdpilkevedllakvnelledvne 65 
                                       +l  ++++i ++ e++ +  ++l+e++++
  gi|298674547|ref|YP_003726297.1|  82 NLSLRLQSINRQEERISKRFKQLQEQLQQ 110
                                       33333333333333333333333333333 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   2.9     0.015       9.4      18      59 ..       8      49 ..       2      58 .. 0.53
   2 ?    8.3   3.2    0.0033         2       8      56 ..      69     117 ..      63     121 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.015
                             Sec34 18 qtdealeqLeeleekfksvsektsslheaceqlleeqkrlee 59
                                      q+++ ++qL++l+++ +s + + ++++++ ++  +  ++l++
  gi|298674547|ref|YP_003726297.1|  8 QAQNQMSQLQQLQQQAQSLAVQKNQVESSQKETEKALEELNK 49
                                      455555555555555555555555554444444444444443 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0033
                             Sec34   8 keeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkr 56 
                                       + + +++l eq +++   L++++ + +++s++ ++l+e+ +q + +q++
  gi|298674547|ref|YP_003726297.1|  69 RDDAIEKLEEQKENLSLRLQSINRQEERISKRFKQLQEQLQQSMGKQQQ 117
                                       5577899999999****************************99999886 PP

>> DUF2852  Protein of unknown function (DUF2852)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   6.9     0.011       6.8      41     108 ..      27     111 ..       8     117 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.011
                           DUF2852  41 kaakeeveekvkelfskakrereaaraskraaassGNaaFdeyreeeLerLeeeqr..................eFe 99 
                                         +k++ve++ ke+ +++ +e ++  +  + ++  GN+     r++ +e+Lee+++                   F+
  gi|298674547|ref|YP_003726297.1|  27 AVQKNQVESSQKETEKAL-EELNKLPEDATVYRMVGNVQVKTTRDDAIEKLEEQKEnlslrlqsinrqeeriskRFK 102
                                       233333433333333333.33335777888999*********************99666666666666666666666 PP

                           DUF2852 100 eflerLrrA 108
                                       +  e+L+++
  gi|298674547|ref|YP_003726297.1| 103 QLQEQLQQS 111
                                       666666665 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   7.8    0.0014      0.84     110     168 ..      14      72 ..       2      74 .. 0.86
   2 ?    4.3  10.4     0.037        23      85     126 ..      74     115 ..      66     121 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0014
                           DUF3552 110 ekekelkqkeqsleekeeeleelveeqrqeLerisgLtkeeAkeilleeveeelkheaA 168
                                       ++ ++l+q+ qsl  +++++e+ ++e ++ Le++ +L ++     ++ +v+ +++++ A
  gi|298674547|ref|YP_003726297.1|  14 SQLQQLQQQAQSLAVQKNQVESSQKETEKALEELNKLPEDATVYRMVGNVQVKTTRDDA 72 
                                       567899*******************************9998888888888888888776 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.037
                           DUF3552  85 kRllqkeetLdrkeeslekkeesleekekelkqkeqsleeke 126
                                       ++l++++e+L  + +s++++ee+++++ k+l+++ q+   k+
  gi|298674547|ref|YP_003726297.1|  74 EKLEEQKENLSLRLQSINRQEERISKRFKQLQEQLQQSMGKQ 115
                                       467777777888888888888888887777777766544444 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4  23.3    0.0044       2.7     602     702 ..      15     117 ..       3     122 .] 0.79

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0044
                           DUF3584 602 e..eLrerlqaleealqsaeakqkqaeeelkqlnaeleeakravaeaatalknar.dtlerlqnekesekdklekai 675
                                       +  +L++++q l  + ++ e++qk++e++l++ln+  e+a       + ++k +r d +e+l+++ke+++ +l+ +i
  gi|298674547|ref|YP_003726297.1|  15 QlqQLQQQAQSLAVQKNQVESSQKETEKALEELNKLPEDATVYRMVGNVQVKTTRdDAIEKLEEQKENLSLRLQ-SI 90 
                                       34499999999999999999999999999999999999999887777777776651557899999999999996.68 PP

                           DUF3584 676 aerkqqaeeqlqkldaqlkqleeqqka 702
                                       +++ + + ++ ++l++ql+q   +q++
  gi|298674547|ref|YP_003726297.1|  91 NRQEERISKRFKQLQEQLQQSMGKQQQ 117
                                       888889999999999999998777776 PP

>> HAUS-augmin3  HAUS augmin-like complex subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9  10.2    0.0016         1      88     134 ..       3      49 ..       1      55 [. 0.94
   2 ?    5.2   6.6     0.022        13      67     114 ..      67     114 ..      51     121 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0016
                      HAUS-augmin3  88 qeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkklkeaqe 134
                                       qeL  + + + ++l++Lq qa sl+ +++++e+++ke++k l+e+++
  gi|298674547|ref|YP_003726297.1|   3 QELPPQAQNQMSQLQQLQQQAQSLAVQKNQVESSQKETEKALEELNK 49 
                                       8999999************************************9975 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.022
                      HAUS-augmin3  67 ellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqe 114
                                       +  +  +e++ee++e+L   lq   ++++++ kr+++Lq q  +   +
  gi|298674547|ref|YP_003726297.1|  67 TTRDDAIEKLEEQKENLSLRLQSINRQEERISKRFKQLQEQLQQSMGK 114
                                       445567888899999999999999999999999999999877665544 PP

>> DUF4509  Domain of unknown function (DUF4509)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   3.2   0.00071      0.44     115     161 ..       3      50 ..       1      65 [. 0.86
   2 ?    4.5   3.6     0.048        30     122     166 ..      68     112 ..      51     119 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00071
                           DUF4509 115 aeleas.veevdkvkhlqwLngklrlqlkslsslqkeqcallhkihsy 161
                                       +el+ + +++++++++lq +   l +q  ++ s+qke ++ l++++  
  gi|298674547|ref|YP_003726297.1|   3 QELPPQaQNQMSQLQQLQQQAQSLAVQKNQVESSQKETEKALEELNKL 50 
                                       6677777899**********************************9954 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.048
                           DUF4509 122 eevdkvkhlqwLngklrlqlkslsslqkeqcallhkihsytqgak 166
                                       ++ d +++l+ ++  l l+l+s++ ++++ +++ ++++++ q++ 
  gi|298674547|ref|YP_003726297.1|  68 TRDDAIEKLEEQKENLSLRLQSINRQEERISKRFKQLQEQLQQSM 112
                                       455667788888888888888888888888888888887666654 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9  24.4    0.0098       6.1      66     150 ..       8     111 ..       1     121 [. 0.75

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0098
                           UPF0242  66 ekskleekeaklteldeglktkeealeelqeeeeeLkee...................ldakeeelerlkeenqqLq 123
                                       ++++  ++ ++l+++ ++l+++++++e +q+e+e+  ee                      ++ ++e+l+e++++L+
  gi|298674547|ref|YP_003726297.1|   8 QAQNQMSQLQQLQQQAQSLAVQKNQVESSQKETEKALEElnklpedatvyrmvgnvqvKTTRDDAIEKLEEQKENLS 84 
                                       56666677778888888999999999999999888777779999999999999998877778899999999999999 PP

                           UPF0242 124 ekleaiaedfeelkleleeqLaekqel 150
                                        +l+ i ++ e+ ++  ++  ++ q+ 
  gi|298674547|ref|YP_003726297.1|  85 LRLQSINRQEERISKRFKQLQEQLQQS 111
                                       999999998877777666433333333 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1  16.8    0.0048         3     130     231 ..      14     116 ..       1     122 [] 0.71

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0048
                           DUF4407 130 altaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelaelkakl 206
                                       +  ++l++  + +a  ++++++ +++ +++ +e++k  +    ++  ++ G+ ++ +++++++++++++ ++l+ +l
  gi|298674547|ref|YP_003726297.1|  14 SQLQQLQQQAQSLAVQKNQVESSQKETEKALEELNKLPED---ATVYRMVGNVQVKTTRDDAIEKLEEQKENLSLRL 87 
                                       2445666666666688899999999999999999999885...5556799999999999999999999999999999 PP

                           DUF4407 207 d....atarlaalraelaeleaerakera 231
                                       +    +++r++++ ++l+e  ++   +++
  gi|298674547|ref|YP_003726297.1|  88 QsinrQEERISKRFKQLQEQLQQSMGKQQ 116
                                       98888677777776666554444333333 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3  17.6     0.062        39      16     101 ..      30     110 ..       2     113 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.062
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHH CS
                        Laminin_II  16 leqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdni 92 
                                       ++q++  ++++e+  e+l+++ +++     + +   k++r   +++ kLe++ ++L  +l++++ +ee    +s+  
  gi|298674547|ref|YP_003726297.1|  30 KNQVESSQKETEKALEELNKLPEDATVYRMVGNVQVKTTR--DDAIEKLEEQKENLSLRLQSINRQEER---ISKRF 101
                                       2344555555555555555555552222222222233333..468999*********************...***** PP

                                       HHHHHHHHH CS
                        Laminin_II  93 seikelIaq 101
                                       ++++e+ +q
  gi|298674547|ref|YP_003726297.1| 102 KQLQEQLQQ 110
                                       *****9998 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   5.7    0.0059       3.7      30      72 ..      10      52 ..       5      65 .. 0.86
   2 ?    6.2   3.5     0.021        13      50      76 ..      73      99 ..      57     117 .. 0.50

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0059
                           BLOC1_2 30 eaasekykklkdvaaslekkleklnekyeelqpylqqidqiek 72
                                      ++++++ ++l+++a+sl+++ +++++ ++e ++ l++++++ +
  gi|298674547|ref|YP_003726297.1| 10 QNQMSQLQQLQQQAQSLAVQKNQVESSQKETEKALEELNKLPE 52
                                      678889999999**************999***99999999855 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.021
                           BLOC1_2 50 leklnekyeelqpylqqidqiekqvte 76
                                      +ekl+e++e+l+  lq+i++ e+++++
  gi|298674547|ref|YP_003726297.1| 73 IEKLEEQKENLSLRLQSINRQEERISK 99
                                      344444444444444444443333332 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2  13.8    0.0062       3.8     103     194 ..      10     114 ..       1     117 [. 0.72

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0062
                            AAA_11 103 avksvsleekvekrlekeekaqlakeiskeleklakelrafeeeeek.............eklkkskekskskleqe 166
                                       +++  +l++ +++ ++   + +++++ +ke+ek  +el++  e+++              +   ++ e++k++l+ +
  gi|298674547|ref|YP_003726297.1|  10 QNQMSQLQQLQQQAQSLAVQKNQVESSQKETEKALEELNKLPEDATVyrmvgnvqvkttrDDAIEKLEEQKENLSLR 86 
                                       33333444444444444445566666666666666666666666666************988999999999999999 PP

                            AAA_11 167 rrklkkerkelskeleeaeesleeevld 194
                                       ++ ++++ +++sk++++ +e+l++++ +
  gi|298674547|ref|YP_003726297.1|  87 LQSINRQEERISKRFKQLQEQLQQSMGK 114
                                       9999999999999999999999988755 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1  20.8     0.051        32      13     124 ..      10     114 ..       2     117 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.051
                           DUF4795  13 qeaieklqeelekleekvkelekrledkekklealkkqieelekvkadkeeveeelaekadkeaLatkvsrdq..fD 87 
                                       q+++++lq    +l++++++l  ++++ e++ +  +k++eel+k  +d ++  +     ++  +++t+ ++    ++
  gi|298674547|ref|YP_003726297.1|  10 QNQMSQLQ----QLQQQAQSLAVQKNQVESSQKETEKALEELNKLPEDATVYRM-----VGNVQVKTTRDDAIekLE 77 
                                       44444444....667888888888888888888888888888888888665555.....444455555544435578 PP

                           DUF4795  88 eakkeLekmleellekleeqeealkkaldtLqeelke 124
                                       e k+ L+  l+++  + e  +++ k++ ++Lq+++++
  gi|298674547|ref|YP_003726297.1|  78 EQKENLSLRLQSINRQEERISKRFKQLQEQLQQSMGK 114
                                       8888888888888888888888888888888888876 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   4.2     0.087        54      59      96 ..       8      45 ..       1      47 [. 0.74
   2 ?    9.1   2.0    0.0029       1.8      57      96 ..      63     102 ..      50     111 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.087
                           DUF4140 59 nreaeeeelkalraeleeledelaaledelaaaearla 96
                                      + +++ ++l++l+++ ++l  +++++e++++  e+ l+
  gi|298674547|ref|YP_003726297.1|  8 QAQNQMSQLQQLQQQAQSLAVQKNQVESSQKETEKALE 45
                                      33333337999999999999999999999999888776 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0029
                           DUF4140  57 vpnreaeeeelkalraeleeledelaaledelaaaearla 96 
                                       v+ +++ ++++++l+++ e+l  +l+ ++++ +++++r +
  gi|298674547|ref|YP_003726297.1|  63 VQVKTTRDDAIEKLEEQKENLSLRLQSINRQEERISKRFK 102
                                       3444455555777777777777777777777777766654 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   6.3    0.0029       1.8      12      63 ..       8      60 ..       2      74 .. 0.69
   2 ?    4.8   6.6     0.055        34       1      43 [.      75     117 ..      67     122 .] 0.74

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0029
                             Spc24 12 elsdleselesleselaelkeeleeleeeseekeserve.detllklklYrsL 63
                                      +++++ s+l++l+++ ++l  + +++e++++e e++++e ++    + +Yr +
  gi|298674547|ref|YP_003726297.1|  8 QAQNQMSQLQQLQQQAQSLAVQKNQVESSQKETEKALEElNKLPEDATVYRMV 60
                                      56667778888888888888888888888888666665545555666666666 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.055
                             Spc24   1 kldnekfriakelsdleselesleselaelkeeleeleeesee 43 
                                       kl+++k +++  l++++++ e+++++ ++l+e+l++   ++++
  gi|298674547|ref|YP_003726297.1|  75 KLEEQKENLSLRLQSINRQEERISKRFKQLQEQLQQSMGKQQQ 117
                                       5677777777777777778888888888888877777666655 PP

>> AAA_lid_9  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   4.4     0.027        17      64      98 ..       9      43 ..       2      50 .. 0.78
   2 ?    7.0   1.6    0.0085       5.3      47      92 ..      70     115 ..      61     122 .] 0.67

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.027
                         AAA_lid_9 64 keskpeeleklekelaklekekealekeeekekae 98
                                       +++ ++l++l+++ ++l  +k+++e+++++++++
  gi|298674547|ref|YP_003726297.1|  9 AQNQMSQLQQLQQQAQSLAVQKNQVESSQKETEKA 43
                                      56677899***************999988865543 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0085
                         AAA_lid_9  47 dkAIDllDeaaarvrlkkeskpeeleklekelaklekekealekee 92 
                                       d AI+ l+e   +++l+ +s +++ e+++k++++l+++ ++   ++
  gi|298674547|ref|YP_003726297.1|  70 DDAIEKLEEQKENLSLRLQSINRQEERISKRFKQLQEQLQQSMGKQ 115
                                       6677777777777777777777777777777777777776665555 PP

>> PilO  Pilus assembly protein, PilO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   7.8    0.0035       2.2       7      60 ..       8      64 ..       3      72 .. 0.76
   2 ?    4.7   3.9     0.049        31      12      46 ..      74     108 ..      65     115 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0035
                              PilO  7 kekeLkkefeekkekaanLeklkkqleeleeeleellk...qLPskkeipsLLedin 60
                                      + ++  +++++ +++a++L   k+q+e+ ++e e++l+   +LP+++ +  ++ +++
  gi|298674547|ref|YP_003726297.1|  8 QAQNQMSQLQQLQQQAQSLAVQKNQVESSQKETEKALEelnKLPEDATVYRMVGNVQ 64
                                      556667788888999999999999999888888887651116899999999988876 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.049
                              PilO  12 kkefeekkekaanLeklkkqleeleeeleellkqL 46 
                                       +k  e+k++   +L+++ +q e++ +++++l +qL
  gi|298674547|ref|YP_003726297.1|  74 EKLEEQKENLSLRLQSINRQEERISKRFKQLQEQL 108
                                       444567888899999***************99999 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   1.3      0.51   3.1e+02      14      45 ..      17      48 ..      10      53 .. 0.68
   2 ?   10.1   2.1    0.0011       0.7       4      42 ..      71     109 ..      70     113 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.51
                              XhlA 14 dnleervdkleekaaeaeekiknleedlkkle 45
                                        l+++ + l   ++ +e++ k++e+ l++l 
  gi|298674547|ref|YP_003726297.1| 17 QQLQQQAQSLAVQKNQVESSQKETEKALEELN 48
                                      55666666666777777777777777777664 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0011
                              XhlA   4 erlerietkldnleervdkleekaaeaeekiknleedlk 42 
                                       + +e++e++ +nl+ r++ +++ +++  ++ k+l+e+l 
  gi|298674547|ref|YP_003726297.1|  71 DAIEKLEEQKENLSLRLQSINRQEERISKRFKQLQEQLQ 109
                                       56999********************************96 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9  11.1     0.016       9.9     197     301 ..      11     115 ..       7     121 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.016
                             LMBR1 197 dldeelkklyfeaaklntekeeaereledllkevkklrksisesdplrkyleeilkkvPeeiaeklksnenkteesl 273
                                       +  ++l++l+ +a++l  +k++ e   +++ k++++l+k  ++   +r + +  +k++  ++ ekl++++++   +l
  gi|298674547|ref|YP_003726297.1|  11 NQMSQLQQLQQQAQSLAVQKNQVESSQKETEKALEELNKLPEDATVYRMVGNVQVKTTRDDAIEKLEEQKENLSLRL 87 
                                       66678999999999999999999999999999999997777777757777777777888888888888666666666 PP

                             LMBR1 274 aklekqlikalqkrertekqwkrlleka 301
                                       ++ ++q  + +++ ++ ++q+++ + k+
  gi|298674547|ref|YP_003726297.1|  88 QSINRQEERISKRFKQLQEQLQQSMGKQ 115
                                       6666666666666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      4267  (0.237994); expected 358.6 (0.02)
Passed bias filter:                      977  (0.0544927); expected 358.6 (0.02)
Passed Vit filter:                       167  (0.00931452); expected 17.9 (0.001)
Passed Fwd filter:                        66  (0.00368119); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.86u 0.34s 00:00:01.20 Elapsed: 00:00:00.55
# Mc/sec: 670.21
//
Query:       gi|298674548|ref|YP_003726298.1|  [L=91]
Description: hypothetical protein Metev_0594 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-08   35.1   0.1    1.3e-08   34.8   0.1    1.2  1  Pcc1      Transcription factor Pcc1
  ------ inclusion threshold ------
       0.12   11.5   0.0       0.12   11.5   0.0    1.0  1  Wap1      Wap1 domain


Domain annotation for each model (and alignments):
>> Pcc1  Transcription factor Pcc1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.1   1.5e-12   1.3e-08      13      72 ..      18      78 ..       7      80 .. 0.93

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 1.5e-12
                                      HHHHHHHHHHHHCHC-TTE.CEEEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHHHHHHH CS
                              Pcc1 13 lAsialrtLqvDkelspla.vkrslslegnvLqveykAttnrmLRvavngfleslglvlet 72
                                      +A+ ++r++ ++ e ++ + + +++s++++ L ++++A++  ++R a+n++l++++++ e+
  gi|298674548|ref|YP_003726298.1| 18 DAENIYRAVLPESESNDFErSVVDISVTDTGLLLNITANDSVSMRSALNTWLRLVQIAYEI 78
                                      79***************999************************************99875 PP

>> Wap1  Wap1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   1.4e-05      0.12     268     312 ..      35      79 ..       8      87 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.4e-05
                                       --HHHHHHHHHHHHHHHHHHTT-HHHHTCH...GGGHHHHHHHHH CS
                              Wap1 268 ledakidiliLhLGLcLNvvseedislkldesllsklkkifsklq 312
                                        e + +di +   GL+LN+ ++++ s++   +++ +l +i+ ++ 
  gi|298674548|ref|YP_003726298.1|  35 FERSVVDISVTDTGLLLNITANDSVSMRSALNTWLRLVQIAYEIG 79 
                                       345589**********************9999*****99998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.36s 00:00:00.88 Elapsed: 00:00:00.55
# Mc/sec: 497.44
//
Query:       gi|298674549|ref|YP_003726299.1|  [L=157]
Description: Brix domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.037   13.8   0.0       0.29   10.8   0.0    1.9  2  Cytidylate_kin  Cytidylate kinase
      0.051   13.8   0.1       0.08   13.2   0.1    1.3  1  Hat1_N          Histone acetyl transferase HAT1 N-terminus


Domain annotation for each model (and alignments):
>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0     0.038   3.4e+02      12      31 ..      14      33 ..       9      35 .. 0.87
   2 ?   10.8   0.0   3.2e-05      0.29       6      52 ..      94     140 ..      92     154 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.038
                                      HHHHHHHHHHHT-EEEEHHH CS
                    Cytidylate_kin 12 ssvaralaeklglkyldtga 31
                                       ++++ l++ l++ y++ g+
  gi|298674549|ref|YP_003726299.1| 14 RTLCKHLSRFLNCDYVNRGK 33
                                      599*************9885 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 3.2e-05
                                       STTSSHHHHHHHHHHHHT-EEEEHHHHHHHHHHHHHHTT--TT-HHH CS
                    Cytidylate_kin   6 PagsGKssvaralaeklglkyldtgalYRalalaalrrkvdlldeaa 52 
                                       Pa sG   +a+++a++l+++y++ +    +    + + ++d++d  +
  gi|298674549|ref|YP_003726299.1|  94 PAVSGDNNIAKTIAKTLSFEYIENSGQCNTRCISVDKDSIDFMDSGE 140
                                       9*********************8766556666666666777776655 PP

>> Hat1_N  Histone acetyl transferase HAT1 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   8.9e-06      0.08      57     134 ..      66     152 ..      60     155 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.9e-06
                                       EEETTT--EEEEEE-SEE--.STTS-.........-HHHHHHTTS-T..ES-HHHHHHHHH...HHH.H--GGSEEE CS
                            Hat1_N  57 yfaagslkpylkvsyseklkdkskte.k.......dvekklkeflpeeafkskeeFekale...ekaksfkppGeli 122
                                       +f   +l+ y++v+y +++k+ + ++ +       ++ k++ + l  e++++  + + ++    +++ +f   Geli
  gi|298674549|ref|YP_003726299.1|  66 QFGNYKLSVYMNVDYPQNFKSVNRKKeVpavsgdnNIAKTIAKTLSFEYIENSGQCNTRCIsvdKDSIDFMDSGELI 142
                                       688899**************9998874499*******************9999988876544447777777779999 PP

                                       EEETTEE..EEE CS
                            Hat1_N 123 hsytrekkefei 134
                                        s++ ++  + +
  gi|298674549|ref|YP_003726299.1| 143 FSFRIKS--YRV 152
                                       9999887..665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.35s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 871.29
//
Query:       gi|298674550|ref|YP_003726300.1|  [L=45]
Description: RNA polymerase Rbp10 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-08   33.2   8.7    4.3e-08   32.7   8.7    1.3  1  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
    0.00012   21.3   0.6     0.0079   15.6   0.1    2.1  2  zf-ribbon_3      zinc-ribbon domain
    0.00015   21.6   2.3    0.00022   21.1   2.3    1.4  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
    0.00053   19.5   5.4       0.25   11.0   0.0    2.5  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
     0.0031   17.5   0.3     0.0031   17.5   0.3    1.1  1  HypA             Hydrogenase/urease nickel incorporation, met
     0.0043   17.0   2.0     0.0058   16.6   2.0    1.3  1  zinc_ribbon_6    Zinc-ribbon
     0.0044   16.7   2.4     0.0082   15.8   2.4    1.5  1  zinc_ribbon_2    zinc-ribbon domain
  ------ inclusion threshold ------
       0.01   15.7   3.0       0.11   12.5   0.2    2.0  2  DUF951           Bacterial protein of unknown function (DUF95
      0.011   15.9   3.1      0.019   15.1   3.1    1.5  1  Zn-ribbon_8      Zinc ribbon domain
      0.018   15.3   0.5      0.018   15.3   0.5    1.1  1  DUF2072          Zn-ribbon containing protein
      0.021   14.8   0.2      0.024   14.6   0.2    1.1  1  zf-C2HC5         Putative zinc finger motif, C2HC5-type
      0.025   14.5   3.6       0.69    9.9   3.6    2.1  1  zinc_ribbon_4    zinc-ribbon domain
       0.03   14.3   4.6       0.13   12.2   0.2    2.1  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.037   13.8   3.5      0.049   13.4   0.6    2.0  2  zf-HYPF          HypF finger
      0.038   14.0   0.8      0.063   13.3   0.8    1.4  1  DZR              Double zinc ribbon
      0.038   13.5   3.0       0.11   12.0   3.2    1.6  2  TF_Zn_Ribbon     TFIIB zinc-binding
      0.039   13.8   2.7        4.2    7.3   0.1    2.2  2  TFIIS_C          Transcription factor S-II (TFIIS)
      0.048   13.6   0.2      0.048   13.6   0.2    1.9  2  Cys_rich_CPXG    Cysteine-rich CPXCG
       0.05   13.9   1.1      0.067   13.5   1.1    1.2  1  zinc_ribbon_9    zinc-ribbon
      0.054   13.6   2.0        7.3    6.8   0.1    2.2  2  zf-ACC           Acetyl-coA carboxylase zinc finger domain
       0.12   12.5   1.3       0.67   10.0   0.1    2.0  2  CpXC             CpXC protein
       0.31   11.6   4.2         10    6.8   0.1    2.2  2  zf-C2H2          Zinc finger, C2H2 type
        1.3    8.7   6.2        1.6    8.4   1.2    2.1  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain


Domain annotation for each model (and alignments):
>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   8.7   5.5e-11   4.3e-08       1      32 []       3      35 ..       3      35 .. 0.91

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 5.5e-11
                                      -B-SSS--B--.--SSS----SSS-----B--- CS
                    DNA_RNApol_7kD  1 YiCgeCgaevs.lkkgdpiRCkeCGhRilYKkR 32
                                      Y+C +C++ v+ + +   iRC +CGhRil K+R
  gi|298674550|ref|YP_003726300.1|  3 YKCTRCKKVVEiDYHYTGIRCPYCGHRILVKER 35
                                      9**********4457788**************9 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0      0.03        24       3      14 ..       3      14 ..       1      15 [. 0.77
   2 !   15.6   0.1     1e-05    0.0079       3      12 ..      21      32 ..      20      37 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.03
                       zf-ribbon_3  3 vrCPnCGaplss 14
                                      ++C +C+++++ 
  gi|298674550|ref|YP_003726300.1|  3 YKCTRCKKVVEI 14
                                      689999997775 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1e-05
                       zf-ribbon_3  3 vrCPnCGa.p.l 12
                                      +rCP+CG+ + +
  gi|298674550|ref|YP_003726300.1| 21 IRCPYCGHrIlV 32
                                      799999998844 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   2.3   2.8e-07   0.00022      10      38 ..       3      30 ..       1      43 [. 0.83

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.8e-07
                    OrfB_Zn_ribbon 10 ykakeyGikveevnpayTSktCseCgskn 38
                                      yk++ + +kv+e++ +yT  +C+ Cg++ 
  gi|298674550|ref|YP_003726300.1|  3 YKCT-RCKKVVEIDYHYTGIRCPYCGHRI 30
                                      7887.6689******************86 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   2.7    0.0015       1.2       3      14 ..       3      14 ..       2      17 .. 0.88
   2 !   11.0   0.0   0.00031      0.25       3      18 ..      21      36 ..      19      37 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0015
                            zf_UBZ  3 ylCerCgkeipe 14
                                      y C rC+k +++
  gi|298674550|ref|YP_003726300.1|  3 YKCTRCKKVVEI 14
                                      99*******987 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00031
                            zf_UBZ  3 ylCerCgkeipeselq 18
                                      + C+ Cg++i++ e++
  gi|298674550|ref|YP_003726300.1| 21 IRCPYCGHRILVKERP 36
                                      68**********9997 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.3     4e-06    0.0031      71     101 ..       3      33 ..       1      44 [. 0.73

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4e-06
                                       EEETTTS-EEECHHH..HHS-TTTSSS-EEEEE CS
                              HypA  71 vrCreCgkefeleek..alrCpkCgsadveivs 101
                                       ++C++C+k +e++ +   +rCp Cg++   +v+
  gi|298674550|ref|YP_003726300.1|   3 YKCTRCKKVVEIDYHytGIRCPYCGHRI--LVK 33 
                                       68*********99744678******953..344 PP

>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   2.0   7.5e-06    0.0058      31      54 ..       4      27 ..       1      28 [. 0.94

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 7.5e-06
                     zinc_ribbon_6 31 lCnDCekksevkfhvlglkCkeCg 54
                                       C  C+k  e+++h+ g++C  Cg
  gi|298674550|ref|YP_003726300.1|  4 KCTRCKKVVEIDYHYTGIRCPYCG 27
                                      5999*******************7 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   2.4     1e-05    0.0082       1      22 [.       4      29 ..       4      30 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1e-05
                     zinc_ribbon_2  1 fCpnCGaelqdnakF....CpyCGtp 22
                                      +C++C + ++ +  +    CpyCG+ 
  gi|298674550|ref|YP_003726300.1|  4 KCTRCKKVVEIDYHYtgirCPYCGHR 29
                                      8*********999999********96 PP

>> DUF951  Bacterial protein of unknown function (DUF951)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.3     0.041        32      32      42 ..       4      14 ..       1      18 [. 0.84
   2 ?   12.5   0.2   0.00014      0.11      30      52 ..      20      43 ..      17      45 .] 0.87

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.041
                            DUF951 32 kClgcgrevml 42
                                      kC++c+++v +
  gi|298674550|ref|YP_003726300.1|  4 KCTRCKKVVEI 14
                                      9******9976 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00014
                            DUF951 30 klkClgcgrevm.lpRskfekkik 52
                                       ++C  cg+ ++  +R +  k+ik
  gi|298674550|ref|YP_003726300.1| 20 GIRCPYCGHRILvKERPTTIKRIK 43
                                      69**********557999999999 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   3.1   2.4e-05     0.019       6      34 ..       3      28 ..       2      34 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.4e-05
                       Zn-ribbon_8  6 YrCeeCghefevlqsisdapltaCPeCgs 34
                                      Y+C++C+++ e+    +    + CP Cg+
  gi|298674550|ref|YP_003726300.1|  3 YKCTRCKKVVEIDYHYT---GIRCPYCGH 28
                                      9**********555444...899*****8 PP

>> DUF2072  Zn-ribbon containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.5   2.3e-05     0.018       2      29 ..       3      30 ..       2      44 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.3e-05
                           DUF2072  2 HkCtkCekvfedgskeilkGCpsCGgkk 29
                                       kCt+C+kv e   +     Cp CG + 
  gi|298674550|ref|YP_003726300.1|  3 YKCTRCKKVVEIDYHYTGIRCPYCGHRI 30
                                      59*********999999999*****875 PP

>> zf-C2HC5  Putative zinc finger motif, C2HC5-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.2   3.1e-05     0.024      19      49 ..       4      35 ..       1      40 [. 0.85

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.1e-05
                          zf-C2HC5 19 nClnCGkiiCakegls.kpCsfCgspllssee 49
                                       C+ C k++ +  +++  +C++Cg+ +l +e 
  gi|298674550|ref|YP_003726300.1|  4 KCTRCKKVVEIDYHYTgIRCPYCGHRILVKER 35
                                      6********999888889*******9998876 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   3.6   0.00088      0.69       4      35 ..       4      30 ..       1      31 [. 0.85

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00088
                     zinc_ribbon_4  4 tCpsCkakyeiddeklpakgvkvrCskCghvF 35
                                       C +Ck++ eid      + + +rC+ Cgh +
  gi|298674550|ref|YP_003726300.1|  4 KCTRCKKVVEIDY-----HYTGIRCPYCGHRI 30
                                      7999999999999.....78899******976 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.7     0.057        44      38      45 ..       3      10 ..       2      11 .. 0.89
   2 ?   12.2   0.2   0.00017      0.13      18      33 ..      20      40 ..      17      44 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.057
                     Zn_Tnp_IS1595 38 fqCkeCrk 45
                                      ++C +C+k
  gi|298674550|ref|YP_003726300.1|  3 YKCTRCKK 10
                                      89****97 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00017
                     Zn_Tnp_IS1595 18 gfvCPhCgsr.....kayrik 33
                                      g +CP+Cg+r     ++++ik
  gi|298674550|ref|YP_003726300.1| 20 GIRCPYCGHRilvkeRPTTIK 40
                                      789*****9976655555555 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1      0.38     3e+02       2       5 ..       5       8 ..       3      14 .. 0.69
   2 ?   13.4   0.6   6.3e-05     0.049      17      30 ..      16      29 ..      15      32 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.38
                                     -HHH CS
                           zf-HYPF 2 CedC 5
                                     C +C
  gi|298674550|ref|YP_003726300.1| 5 CTRC 8
                                     5555 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 6.3e-05
                                      TT-TT---TTTS-- CS
                           zf-HYPF 17 fhaqfisCtnCGPr 30
                                      +h+ +i C+ CG r
  gi|298674550|ref|YP_003726300.1| 16 YHYTGIRCPYCGHR 29
                                      9***********66 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.8   8.1e-05     0.063      15      36 ..       5      28 ..       2      36 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.1e-05
                               DZR 15 CseCgtklkavaa..edrCpsCge 36
                                      C +C++ ++   +   +rCp Cg+
  gi|298674550|ref|YP_003726300.1|  5 CTRCKKVVEIDYHytGIRCPYCGH 28
                                      555555554444455555555555 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   3.2   0.00014      0.11       1      27 [.       3      28 ..       3      30 .. 0.93
   2 ?    9.2   0.2    0.0011      0.84       2      12 ..      22      32 ..      21      38 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                                      EEETTTTCEECHEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon  1 ykCPnCgstnlveDpergelvCtdCGl 27
                                      ykC  C+   ++ D+  + ++C+ CG 
  gi|298674550|ref|YP_003726300.1|  3 YKCTRCKKV-VEIDYHYTGIRCPYCGH 28
                                      89*****87.89*************95 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0011
                                      EETTTTCEECH CS
                      TF_Zn_Ribbon  2 kCPnCgstnlv 12
                                      +CP+Cg++ lv
  gi|298674550|ref|YP_003726300.1| 22 RCPYCGHRILV 32
                                      7*****98554 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.6     0.008       6.2      29      36 ..       3      10 ..       1      12 [. 0.87
   2 ?    7.3   0.1    0.0053       4.2       1       9 [.      21      29 ..      21      33 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.008
                           TFIIS_C 29 ykCtkCgh 36
                                      ykCt C++
  gi|298674550|ref|YP_003726300.1|  3 YKCTRCKK 10
                                      99****98 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0053
                           TFIIS_C  1 akCpkCgsr 9 
                                      ++Cp Cg+r
  gi|298674550|ref|YP_003726300.1| 21 IRCPYCGHR 29
                                      579999998 PP

>> Cys_rich_CPXG  Cysteine-rich CPXCG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.2      0.89     7e+02       2      12 ..       4      14 ..       3      19 .. 0.61
   2 ?   13.6   0.2   6.2e-05     0.048       1      11 [.      21      31 ..      21      33 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.89
                     Cys_rich_CPXG  2 qCPyCgeeiev 12
                                      +C  C + +e+
  gi|298674550|ref|YP_003726300.1|  4 KCTRCKKVVEI 14
                                      67777665554 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 6.2e-05
                     Cys_rich_CPXG  1 iqCPyCgeeie 11
                                      i CPyCg++i 
  gi|298674550|ref|YP_003726300.1| 21 IRCPYCGHRIL 31
                                      78******986 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.1   8.6e-05     0.067       5      30 ..       5      29 ..       3      33 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.6e-05
                     zinc_ribbon_9  5 ChqCdrfVsvspdedsdvlCPhCggg 30
                                      C +C++ V++  + + +  CP+Cg  
  gi|298674550|ref|YP_003726300.1|  5 CTRCKKVVEIDYHYTGIR-CPYCGHR 29
                                      779*******99999999.****986 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.3      0.01       8.1       3      11 ..       4      12 ..       3      12 .. 0.89
   2 ?    6.8   0.1    0.0093       7.3       2      15 ..      21      34 ..      21      34 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.01
                            zf-ACC  3 KCpsCgeml 11
                                      KC++C+ ++
  gi|298674550|ref|YP_003726300.1|  4 KCTRCKKVV 12
                                      9*****886 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0093
                            zf-ACC  2 tKCpsCgemlykke 15
                                      ++Cp Cg+ ++ ke
  gi|298674550|ref|YP_003726300.1| 21 IRCPYCGHRILVKE 34
                                      78*****9888776 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1      0.13     1e+02      39      51 ..       4      16 ..       2      20 .. 0.59
   2 ?   10.0   0.1   0.00086      0.67      36      50 ..      19      33 ..      14      45 .] 0.74

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.13
                              CpXC 39 tCpkCgataklea 51
                                      +C +C + +++++
  gi|298674550|ref|YP_003726300.1|  4 KCTRCKKVVEIDY 16
                                      5666666555555 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00086
                              CpXC 36 featCpkCgatakle 50
                                      + ++Cp+Cg+++ ++
  gi|298674550|ref|YP_003726300.1| 19 TGIRCPYCGHRILVK 33
                                      6689*****999875 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.8     0.016        12       1       9 [.       3      11 ..       3      19 .. 0.89
   2 ?    6.8   0.1     0.013        10       2       8 ..      22      28 ..      21      34 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.016
                                      EEETTTTEE CS
                           zf-C2H2  1 ykCpdCgks 9 
                                      ykC+ C+k+
  gi|298674550|ref|YP_003726300.1|  3 YKCTRCKKV 11
                                      9******97 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.013
                                      EETTTTE CS
                           zf-C2H2  2 kCpdCgk 8 
                                      +Cp+Cg 
  gi|298674550|ref|YP_003726300.1| 22 RCPYCGH 28
                                      8****95 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.2    0.0021       1.6       7      18 ..       3      14 ..       2      20 .. 0.94
   2 ?    3.6   0.3     0.068        53       8      18 ..      22      32 ..      17      35 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0021
                                      EE-TTT--EEEE CS
                   Desulfoferrod_N  7 YkCevCGniVeV 18
                                      YkC+ C  +Ve+
  gi|298674550|ref|YP_003726300.1|  3 YKCTRCKKVVEI 14
                                      **********98 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.068
                                      E-TTT--EEEE CS
                   Desulfoferrod_N  8 kCevCGniVeV 18
                                      +C  CG  + V
  gi|298674550|ref|YP_003726300.1| 22 RCPYCGHRILV 32
                                      8*****86655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.52u 0.35s 00:00:00.87 Elapsed: 00:00:00.55
# Mc/sec: 248.24
//
Query:       gi|298674551|ref|YP_003726301.1|  [L=96]
Description: 50S ribosomal protein L37a [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-33  114.4   6.7    2.2e-33  114.2   6.7    1.0  1  Ribosomal_L37ae  Ribosomal L37ae protein family
     0.0072   16.2   8.3      0.079   12.9   7.1    2.5  2  HalOD2           Halobacterial output domain 2
  ------ inclusion threshold ------
      0.012   15.5   1.3      0.018   14.9   1.3    1.3  1  DUF951           Bacterial protein of unknown function (DUF95
      0.012   15.6   4.1      0.021   14.8   4.1    1.4  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.015   15.2   1.5      0.026   14.5   1.5    1.4  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.017   15.1   3.7       0.55   10.2   0.3    2.4  2  zinc_ribbon_4    zinc-ribbon domain
      0.031   14.4   0.8        2.5    8.3   0.1    2.3  2  Zn-ribbon_8      Zinc ribbon domain
      0.063   13.1   2.2        1.8    8.5   0.4    2.3  2  TFIIS_C          Transcription factor S-II (TFIIS)
      0.081   13.4   3.2        2.8    8.5   0.1    2.2  2  zf-H2C2_2        Zinc-finger double domain
       0.11   12.3   3.3        4.2    7.2   0.3    2.3  2  Rubredoxin_2     Rubredoxin metal binding domain
       0.31   10.8   3.4        9.9    6.0   0.2    2.3  2  zinc_ribbon_5    zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.2   6.7   1.4e-36   2.2e-33       2      83 ..       9      90 ..       8      92 .. 0.97

  Alignments for each domain:
  == domain 1  score: 114.2 bits;  conditional E-value: 1.4e-36
                                      XXXXX-GGGGTTSS-HHHHHHHHHHHHHHHS-BEESSSSSSEEEEEETTEEEETTTTEEEE-BSSSSS-HHHHHHHH-X CS
                   Ribosomal_L37ae  2 tkkvgiaGkygtrYGaslrkrvkkieisqhakytCpfcgktkvkRkavgiwkCkkcgktvaGgAytpettsaktvksai 80
                                       +++++aG++gtrYG++ rk +++ie+++h+k++C++c + +v+R+++giw+C+kcg+t+aGg+ytp+t+ +ktv +ai
  gi|298674551|ref|YP_003726301.1|  9 GRVTRSAGRFGTRYGRKDRKLIANIEEQMHKKHRCSNCARVSVRRTGTGIWECTKCGHTFAGGTYTPQTSVGKTVPRAI 87
                                      57899************************************************************************** PP

                                      XXX CS
                   Ribosomal_L37ae 81 rrl 83
                                      r++
  gi|298674551|ref|YP_003726301.1| 88 RKA 90
                                      *97 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.7       0.1   1.7e+02      33      38 ..      42      47 ..       9      52 .. 0.76
   2 !   12.9   7.1   4.8e-05     0.079      24      45 ..      51      72 ..      39      78 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.1
                            HalOD2 33 kCtrCG 38
                                      +C++C 
  gi|298674551|ref|YP_003726301.1| 42 RCSNCA 47
                                      555555 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 4.8e-05
                            HalOD2 24 yrqLGayvWkCtrCGevqaaAd 45
                                      +r+ G+ +W Ct+CG++ a+ +
  gi|298674551|ref|YP_003726301.1| 51 VRRTGTGIWECTKCGHTFAGGT 72
                                      78899************99876 PP

>> DUF951  Bacterial protein of unknown function (DUF951)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   1.3   1.1e-05     0.018       8      40 ..      36      68 ..      34      83 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.1e-05
                            DUF951  8 emKKpHPC.gsneweilRvGadiklkClgcgrev 40
                                      +m K+H C  + +  + R+G+ i  +C++cg+ +
  gi|298674551|ref|YP_003726301.1| 36 QMHKKHRCsNCARVSVRRTGTGI-WECTKCGHTF 68
                                      79******889***********9.6*******86 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   4.1   1.3e-05     0.021      18      46 .]      40      67 ..      34      67 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.3e-05
                     Zn_Tnp_IS1595 18 gfvCPhCgsrkayriktrglfqCkeCrkq 46
                                      +++C +C+  +++r+ t g ++C +C+++
  gi|298674551|ref|YP_003726301.1| 40 KHRCSNCARVSVRRTGT-GIWECTKCGHT 67
                                      578*****778888887.********996 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.5   1.6e-05     0.026      30      56 ..      42      68 ..      28      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.6e-05
                    OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfea 56
                                      +Cs+C +++ ++  +  ++C++Cg+++
  gi|298674551|ref|YP_003726301.1| 42 RCSNCARVSVRRTGTGIWECTKCGHTF 68
                                      7**********99***********985 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.2    0.0078        13      22      33 ..      37      48 ..      25      49 .. 0.82
   2 ?   10.2   0.3   0.00034      0.55      27      35 ..      60      68 ..      53      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0078
                     zinc_ribbon_4 22 kgvkvrCskCgh 33
                                       ++k rCs+C  
  gi|298674551|ref|YP_003726301.1| 37 MHKKHRCSNCAR 48
                                      567889****75 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00034
                     zinc_ribbon_4 27 rCskCghvF 35
                                       C+kCgh+F
  gi|298674551|ref|YP_003726301.1| 60 ECTKCGHTF 68
                                      5*******9 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1      0.02        32      26      38 ..      39      53 ..      28      54 .. 0.71
   2 ?    8.3   0.1    0.0015       2.5       7      15 ..      60      68 ..      58      79 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.02
                       Zn-ribbon_8 26 lta.CPeCgs.evrr 38
                                      +++ C +C    vrr
  gi|298674551|ref|YP_003726301.1| 39 KKHrCSNCARvSVRR 53
                                      444599998888887 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0015
                       Zn-ribbon_8  7 rCeeCghef 15
                                      +C++Cgh+f
  gi|298674551|ref|YP_003726301.1| 60 ECTKCGHTF 68
                                      7*******9 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1     0.025        41      22      35 ..      34      47 ..      32      49 .. 0.85
   2 ?    8.5   0.4    0.0011       1.8      29      38 ..      59      68 ..      55      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.025
                           TFIIS_C 22 DEpmtvfykCtkCg 35
                                      +E m   ++C +C 
  gi|298674551|ref|YP_003726301.1| 34 EEQMHKKHRCSNCA 47
                                      68899999*****6 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0011
                           TFIIS_C 29 ykCtkCghrW 38
                                       +CtkCgh++
  gi|298674551|ref|YP_003726301.1| 59 WECTKCGHTF 68
                                      58*****998 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.3     0.012        20      13      24 ..      39      50 ..      34      52 .. 0.81
   2 ?    8.5   0.1    0.0017       2.8      10      25 ..      54      69 ..      50      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.012
                         zf-H2C2_2 13 kpyeCplCdkaF 24
                                      k++ C+ C+ + 
  gi|298674551|ref|YP_003726301.1| 39 KKHRCSNCARVS 50
                                      78******9865 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0017
                         zf-H2C2_2 10 tgekpyeCplCdkaFk 25
                                      tg  ++eC +C+ +F+
  gi|298674551|ref|YP_003726301.1| 54 TGTGIWECTKCGHTFA 69
                                      677899*******995 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.2    0.0066        11       1      12 [.      41      52 ..      41      56 .. 0.78
   2 ?    7.2   0.3    0.0026       4.2       1      10 [.      59      68 ..      59      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0066
                      Rubredoxin_2  1 YvCsqCGfesak 12
                                      ++Cs+C  +s +
  gi|298674551|ref|YP_003726301.1| 41 HRCSNCARVSVR 52
                                      69****988766 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0026
                      Rubredoxin_2  1 YvCsqCGfes 10
                                      ++C +CG+++
  gi|298674551|ref|YP_003726301.1| 59 WECTKCGHTF 68
                                      79*****997 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.3    0.0079        13      23      34 ..      38      49 ..      31      51 .. 0.85
   2 ?    6.0   0.2    0.0061       9.9      28      35 ..      61      68 ..      56      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0079
                     zinc_ribbon_5 23 gkkVrCakCaev 34
                                       kk rC  Ca v
  gi|298674551|ref|YP_003726301.1| 38 HKKHRCSNCARV 49
                                      6899******98 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0061
                     zinc_ribbon_5 28 CakCaevF 35
                                      C kC++ F
  gi|298674551|ref|YP_003726301.1| 61 CTKCGHTF 68
                                      99999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       842  (0.046963); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.52u 0.34s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 552.15
//
Query:       gi|298674552|ref|YP_003726302.1|  [L=260]
Description: 3' exoribonuclease [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.2e-30  105.3   0.0      6e-30  104.5   0.0    1.4  2  RNase_PH    3' exoribonuclease family, domain 1
    1.1e-10   41.3   0.2      2e-10   40.6   0.2    1.4  1  RNase_PH_C  3' exoribonuclease family, domain 2


Domain annotation for each model (and alignments):
>> RNase_PH  3' exoribonuclease family, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.5   0.0   6.7e-34     6e-30       1     132 []      31     166 ..      31     166 .. 0.95
   2 ?   -3.1   0.0       1.2   1.1e+04       9      19 ..     212     222 ..     202     243 .. 0.71

  Alignments for each domain:
  == domain 1  score: 104.5 bits;  conditional E-value: 6.7e-34
                                       EEEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG.--CCEEEECCCCECCCCEC-C...S...HHHH CS
                          RNase_PH   1 elRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseer.ddaegaldveveyapfasgerrregrpsdeei 76 
                                       e+R++siet+++ +a+GSa +  Gdt+++++v++++ e p++++ d  +g + +  e+ p+as++++  g p++ +i
  gi|298674552|ref|YP_003726302.1|  31 EIRDISIETDIIGNAEGSAKVYWGDTQLIVGVKLQVGE-PFPDTpD--KGIIITSLELNPIASPDFEA-GPPKEDAI 103
                                       79**********************************99.8888744..578***************55.9******* PP

                                       HHHHHHHHHHCCTC-C........CGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
                          RNase_PH  77 elsrlleralrpsill........ekkpkstididitvlssdggslldalinaaslALadagip 132
                                       e++r+++r +r+s+ +        e++  +t+ id+ vl++dg +++da++++a++AL+++ ip
  gi|298674552|ref|YP_003726302.1| 104 EIARVVDRGIRESGAIdlnklcitEGEEVWTVFIDVNVLNDDG-NIMDAASIGAIAALMTTNIP 166
                                       ***************8899999999999***************.*******************9 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.2
                                       ESSSSTTSEEE CS
                          RNase_PH   9 tgvlsqanGSa 19 
                                       + v+s+ +GS 
  gi|298674552|ref|YP_003726302.1| 212 ITVVSNQDGSI 222
                                       44555555554 PP

>> RNase_PH_C  3' exoribonuclease family, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.2   2.2e-14     2e-10       1      65 [.     182     246 ..     182     248 .. 0.95

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 2.2e-14
                                       S--EEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSCEEHHHHHHHHHHHH CS
                        RNase_PH_C   1 apviavtvgkvddqfvlDptkeEedlsegdltlavagtkevvtlmkeggsqldeetlleaielAk 65 
                                       +++++++   + +++++Dpt++Ee++++ ++t++ + ++++ +++k+g ++l+ee++l+a  +A 
  gi|298674552|ref|YP_003726302.1| 182 DIPVGISLVDISGELMVDPTYNEESVCDTKITVVSNQDGSISAMQKSGTGSLTEEKVLQAANIAR 246
                                       589999******************************************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 1438.39
//
Query:       gi|298674553|ref|YP_003726303.1|  [L=333]
Description: exosome complex exonuclease 1 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      6e-33  114.2   0.3    2.7e-32  112.1   0.0    2.0  2  RNase_PH    3' exoribonuclease family, domain 1
      3e-17   62.4   0.7    5.5e-17   61.5   0.7    1.5  1  RNase_PH_C  3' exoribonuclease family, domain 2


Domain annotation for each model (and alignments):
>> RNase_PH  3' exoribonuclease family, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.1   0.0     3e-36   2.7e-32       1     132 []      23     152 ..      23     152 .. 0.96
   2 ?   -0.3   0.2      0.16   1.4e+03      51      82 ..     241     274 ..     224     313 .. 0.68

  Alignments for each domain:
  == domain 1  score: 112.1 bits;  conditional E-value: 3e-36
                                       EEEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG.--CCEEEECCCCECCCCEC-C...S...HHHH CS
                          RNase_PH   1 elRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseer.ddaegaldveveyapfasgerrregrpsdeei 76 
                                       e+R++++ +gvls+a+GS+yle G++k++ +v+gp+e +p++++ +da  ++  ++++a+f+ ++r+r   ps+++ 
  gi|298674553|ref|YP_003726303.1|  23 EIRPMKVDIGVLSRADGSCYLEWGNNKIISAVYGPRELHPRRMQrPDA-AVIRYKYNMASFSVEDRQR-PGPSRRSS 97 
                                       79************************************9999998888.589999*******999955.56****** PP

                                       HHHHHHHHHHCCTC-CCGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
                          RNase_PH  77 elsrlleralrpsillekkpkstididitvlssdggslldalinaaslALadagip 132
                                       e+s++  +a++p+++++ +p++ id++ +vl++d  ++  a+inaa+lAL+dagip
  gi|298674553|ref|YP_003726303.1|  98 EISKVSSEAFEPVVMTQFYPNTVIDVFSEVLEADA-GTRTAAINAATLALIDAGIP 152
                                       ***********************************.*******************9 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.16
                                       EECCCCECCCCEC-C...S.....HHHHHHHHHH CS
                          RNase_PH  51 ldveveyapfasgerrregr..psdeeielsrll 82 
                                        d+e++  p+ +++ ++e     +++++++s+ +
  gi|298674553|ref|YP_003726303.1| 241 ADTEIQSVPLTETSSKQETEsvDTESSELISSNI 274
                                       5667777777777775542222555555555544 PP

>> RNase_PH_C  3' exoribonuclease family, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.5   0.7   6.2e-21   5.5e-17       2      66 ..     156     218 ..     155     219 .. 0.96

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 6.2e-21
                                       --EEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSCEEHHHHHHHHHHHHH CS
                        RNase_PH_C   2 pviavtvgkvddqfvlDptkeEedlsegdltlavagtkevvtlmkeggsqldeetlleaielAkk 66 
                                       +v+a++vgkvd+q+vlD++k+E++ +e+dl++a++ ++e+ tl++++g  l+e+++++a+el k+
  gi|298674553|ref|YP_003726303.1| 156 LVSACAVGKVDGQLVLDLNKKEDNEGEADLPVAITQDGEI-TLLQMDGH-LTEDEIKQAMELVKN 218
                                       79*********************************99999.********.***********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1428  (0.0796475); expected 358.6 (0.02)
Passed bias filter:                      631  (0.0351944); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.35s 00:00:01.00 Elapsed: 00:00:00.51
# Mc/sec: 1953.75
//
Query:       gi|298674554|ref|YP_003726304.1|  [L=230]
Description: ribosome maturation protein SBDS-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-25   88.5   0.9    4.1e-25   87.7   0.9    1.5  1  SBDS      Shwachman-Bodian-Diamond syndrome (SBDS) protein
    1.4e-23   83.1   0.3    2.2e-23   82.5   0.3    1.3  1  SBDS_C    SBDS protein C-terminal domain
  ------ inclusion threshold ------
      0.057   13.5   0.0       0.11   12.5   0.0    1.4  1  EFG_C     Elongation factor G C-terminus


Domain annotation for each model (and alignments):
>> SBDS  Shwachman-Bodian-Diamond syndrome (SBDS) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.7   0.9   6.9e-29   4.1e-25       3      88 .]       8      93 ..       6      93 .. 0.98

  Alignments for each domain:
  == domain 1  score: 87.7 bits;  conditional E-value: 6.9e-29
                                      EEEEEEETTEEEEEEE-HHHHHHHHCTT---HHHHBSSSS-EEETTTTEE--HHHHHHHHS---HHHHHHHHHHHSEEE CS
                              SBDS  3 sivrykkgkkrFeiavyknklleyregkeidLsevlqsekiFtnaskGetaskselekafgteskdeiikeILkkGeiq 81
                                      +i+rykkg+k+Fe++v+++ +l+ ++g++i++++++++e++F++a+kG+ as+s+++++fgt+++ eii  I+k+G+iq
  gi|298674554|ref|YP_003726304.1|  8 VIARYKKGGKQFEVFVDPDGALDIKRGEDINIEDIIAVESVFEDANKGNLASESDIQEIFGTDEVYEIIYNIIKHGDIQ 86
                                      799**************************************************************************** PP

                                      --HHHHH CS
                              SBDS 82 vsaeerk 88
                                      +++e+rk
  gi|298674554|ref|YP_003726304.1| 87 LTKEQRK 93
                                      ****997 PP

>> SBDS_C  SBDS protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.5   0.3   3.7e-27   2.2e-23       2     115 ..     100     217 ..      99     218 .. 0.84

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 3.7e-27
                                       HHHHHHHHHHHEEBTTTTB---HHHHHHHHHHTT----TTS-CCCCHHHHHHHHTTTS--EE-EEEEEEEE-..... CS
                            SBDS_C   2 ekeiieivaeklvnpqtkrpytttmIekalkelgtsvktnksaksQalevikaLiqeipiqrarmrlritcptsi.. 76 
                                       +k++++i+a++++npqtk+p+++++Ie+a++e+++++++ ks+++Q+  ++ka++ +ipi+++++++++++p s   
  gi|298674554|ref|YP_003726304.1| 100 RKQVVNIIAQNAINPQTKTPHPPSRIESAMEEAKVNIDLLKSVDEQVNTALKAIRPIIPIRFEEVQVAVKIPASYaa 176
                                       79**********************************************************************76633 PP

                                       .CCCHHHHHHHHHH......S.EEEEEEEEGGGHHHHHHHH CS
                            SBDS_C  77 .kdkilklieqvesqkvae.kewevvvliePgaykeleefv 115
                                            ++ + +ve++++++ ++w  vv i++g+++++ +++
  gi|298674554|ref|YP_003726304.1| 177 kSYGEISRFGTVEKEEWQNdGSWVAVVRIPAGLQNDFYSLI 217
                                       2222234445566666666444778888******9998877 PP

>> EFG_C  Elongation factor G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.9e-05      0.11       8      70 ..     165     226 ..     163     229 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.9e-05
                                       EEEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-E CS
                             EFG_C   8 kveievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegs 70 
                                       +v +++p +y +k ++++s r G++e+ e +++g  +   +iP+    +f++ ++ lTkGe++
  gi|298674554|ref|YP_003726304.1| 165 QVAVKIPASYAAKSYGEIS-RFGTVEKEEWQNDGSWVAVVRIPAGLQNDFYSLINRLTKGEAE 226
                                       7899***********9997.66888888877677777789****9999*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       868  (0.0484132); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1686.34
//
Query:       gi|298674555|ref|YP_003726305.1|  [L=255]
Description: proteasome endopeptidase complex subunit alpha [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-60  202.9   0.4    4.7e-60  202.3   0.4    1.2  1  Proteasome      Proteasome subunit
    1.2e-14   53.6   0.5    4.3e-14   51.9   0.1    2.1  2  Proteasome_A_N  Proteasome subunit A N-terminal signature
  ------ inclusion threshold ------
        2.4    8.4   6.2        2.8    8.2   1.6    2.6  3  Synuclein       Synuclein


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.3   0.4   7.8e-64   4.7e-60       1     190 []      33     217 ..      33     217 .. 0.98

  Alignments for each domain:
  == domain 1  score: 202.3 bits;  conditional E-value: 7.8e-64
                                       HHHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSS CS
                        Proteasome   1 vkkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygr 77 
                                       vk+Gtt+ Gik+kdgvvl +dkr+t  s l++ +++eKif+id higva++Gl+aDartlv+rar+eaq  r+++++
  gi|298674555|ref|YP_003726305.1|  33 VKRGTTAAGIKAKDGVVLLVDKRIT--SRLIEAESIEKIFQIDAHIGVATSGLVADARTLVDRARVEAQVNRVSFDE 107
                                       79***********************..************************************************** PP

                                       GTCHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHH CS
                        Proteasome  78 pipverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekey 154
                                       pi ve++++++++++q ytq +g+rp+g ++liag+d+++ p+L+++dpsG+++e++ a+aiG g+++ ++ +e++y
  gi|298674555|ref|YP_003726305.1| 108 PIGVEVIAKKICDHKQTYTQFGGVRPYGTAVLIAGIDDNK-PRLFETDPSGALLEYR-ATAIGAGRNSFMETFEANY 182
                                       *************************************665.***************5.******************* PP

                                       STTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEEE CS
                        Proteasome 155 kedltleeavelavkalkealerdklsgknievavi 190
                                       ++d++ ++a+ l   al++++e+ kl  +++ev++i
  gi|298674555|ref|YP_003726305.1| 183 SDDMDIDSAIMLGMDALYNVTEG-KLDASTLEVGII 217
                                       **********************5.599999999987 PP

>> Proteasome_A_N  Proteasome subunit A N-terminal signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   0.1   7.1e-18   4.3e-14       1      23 []      10      32 ..      10      32 .. 0.99
   2 ?   -0.9   0.0      0.24   1.4e+03      13      18 ..      68      73 ..      68      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 7.1e-18
                    Proteasome_A_N  1 YDrslttFSPdGRLfQVEYAmkA 23
                                      YDr++t+FSPdGRLfQVEYA +A
  gi|298674555|ref|YP_003726305.1| 10 YDRAITVFSPDGRLFQVEYAREA 32
                                      *********************99 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.24
                    Proteasome_A_N 13 RLfQVE 18
                                      ++fQ++
  gi|298674555|ref|YP_003726305.1| 68 KIFQID 73
                                      79**97 PP

>> Synuclein  Synuclein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   1.6   0.00046       2.8      18      51 ..      29      63 ..      25     104 .. 0.73
   2 ?    0.5   0.1      0.11   6.5e+02      44      87 ..      80     124 ..      74     132 .. 0.63
   3 ?    0.8   0.2      0.09   5.4e+02      70     130 ..     192     251 ..     172     255 .] 0.61

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00046
                         Synuclein 18 aaEKtKqGvteAAektKeGv.lyvGsktkegvvqs 51
                                      a E  K+G t A  k K+Gv l v +++ ++++++
  gi|298674555|ref|YP_003726305.1| 29 AREAVKRGTTAAGIKAKDGVvLLVDKRITSRLIEA 63
                                      77999**************7367999999998764 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.11
                         Synuclein  44 tkegvvqsvttvaekt..keqasvvgeavvtsvnavaektvegaen 87 
                                       t+   v    t ++++  + q++ v+     +v+ +a+k  + +++
  gi|298674555|ref|YP_003726305.1|  80 TSGL-VADARTLVDRArvEAQVNRVSFDEPIGVEVIAKKICDHKQT 124
                                       4444.44444444554115688899988889999999998776665 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.09
                         Synuclein  70 vvtsvnavaektvegaeniaaatGlvkkedlekdlpeeegeease.vedealldeeeesaee 130
                                       ++ +++a+ + t  + +  +  +G++  +  +k+ ++ ++ee+++ v++e ++++ ee++e+
  gi|298674555|ref|YP_003726305.1| 192 IMLGMDALYNVTEGKLDASTLEVGIITTD--TKQFRKFSNEEVENyVNKELEKHKGEEPEES 251
                                       55566666666767778888889999988..3344444555555534444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1916.85
//
Query:       gi|298674556|ref|YP_003726306.1|  [L=127]
Description: ribonuclease P [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-19   69.3   0.1    3.3e-19   69.0   0.1    1.1  1  RNase_P_Rpp14  Rpp14/Pop5 family


Domain annotation for each model (and alignments):
>> RNase_P_Rpp14  Rpp14/Pop5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.0   0.1   1.9e-23   3.3e-19       1     102 [.      13     107 ..      13     108 .. 0.94

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 1.9e-23
                                       EEEEEEEEESS......-HHHHHHHHHHHHHHHHHHHHHHH--..EEEEEETTTTEEEEEEEGGGHHHHHHHHHT-- CS
                     RNase_P_Rpp14   1 RYllveilypdeeeelteksllkairesvqelfGdyglgklgsslsvkyfspatstaiiRcsresyrlvwaaLtlit 77 
                                       RYl++e+++++   e+++++l+k++ + +++l Gd+g+++++   ++ +f++  s +iiRc+++ +++ +a+L++++
  gi|298674556|ref|YP_003726306.1|  13 RYLAFELISEK---EVSRDDLIKEVFSCASSLIGDLGSSECNI--RLLSFEN--SKGIIRCNHNTTDKTRAVLATVS 82 
                                       9**********...4789***********************99..6667776..9********************** PP

                                       EETTEEEEEEEEEEESSHHHHHHHT CS
                     RNase_P_Rpp14  78 kiegrpvvfrvvrvsGTikkaeeea 102
                                       +i g+++v++++++sGT+k a +++
  gi|298674556|ref|YP_003726306.1|  83 NISGTQAVIHILGISGTVKGATKKY 107
                                       *********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 908.78
//
Query:       gi|298674557|ref|YP_003726307.1|  [L=241]
Description: ribonuclease P [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.8e-48  163.5   0.0    6.4e-48  163.1   0.0    1.1  1  RNase_P_p30   RNase P subunit p30
     0.0011   19.3   0.1     0.0019   18.6   0.1    1.2  1  PHP           PHP domain
  ------ inclusion threshold ------
      0.093   12.5   0.0        2.7    7.7   0.0    2.6  2  Amidohydro_2  Amidohydrolase


Domain annotation for each model (and alignments):
>> RNase_P_p30  RNase P subunit p30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.1   0.0   1.1e-51   6.4e-48       1     213 [.       7     208 ..       7     209 .. 0.95

  Alignments for each domain:
  == domain 1  score: 163.1 bits;  conditional E-value: 1.1e-51
                                       EEEEE-SH.........HHHHHHHHH-SEEEEEEEEEESS---HHHHH.......HHHHHHHH..HHSSEEEEEEES CS
                       RNase_P_p30   1 ydlnipwpsddskkksrtiktlaelgytgvainftveaekekkpnasepikeelkelkkelsglkllsRvtlvvsdp 77 
                                       yd+n++  +d++++ ++ +  +++lg+ g ai+++ + e++  + + +              g+++++ v++vvs+p
  gi|298674557|ref|YP_003726307.1|   7 YDFNVHTVPDGKDTVKDVMAFAKHLGFGGFAITNHSNVEESYPEGSMQ-------------DGIDVYKAVEIVVSNP 70 
                                       8*************999********************55555555555.............78************** PP

                                       -H..HHHHHHHHH--EEEEE--SHHHHHHHHHT.T-SEEE-TTTTSSS-S--HHHHHHHHHHT-EEEEESHHHHHS- CS
                       RNase_P_p30  78 skl.qrlskvrqkfdllavrPttekalraacenldvDiisidltsrlpfglkhktiraAvergvafEinyspllrds 153
                                       skl + + k+r+ +d++av++++e+++raa+e++ vDi+ ++ ts ++ g++h+++++A++++va+E+n+  +++++
  gi|298674557|ref|YP_003726307.1|  71 SKLnGLVGKYRKNVDVVAVHGGNEEINRAAVETPAVDILAHPQTS-KNGGINHVLAKSASHNNVAIEFNLDSIIKGR 146
                                       **99****************************************9.8899*************************** PP

                                       HHHHHHHHHHHHHHHHHHHH..--EEEE--BSSGGG---HHHHHHHHHHHT--HHHHHHTTT CS
                       RNase_P_p30 154 glaRrnfisnarkllrltrg..kgvviSSgAesplelRnpydiinLlktlGLeedrakeavs 213
                                       g++R++++s ++k+l+l+r+   + +++S+A + ++lR+p ++i+L k++G+  ++a  ++s
  gi|298674557|ref|YP_003726307.1| 147 GGKRVHTLSFFSKNLELARKynVPTILTSNAFNCFDLRAPEEMIALSKLFGMGREEAITSLS 208
                                       ********************************************************988776 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   3.1e-07    0.0019       3      74 ..      10      93 ..       8     177 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 3.1e-07
                                      EE--CCC--.S-H..HHHHHHHHHCT-SEEEEEEEEBTT.HHHHHHHHHHHHTTTTSEEEEEEE............... CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
                               PHP  3 HvHteyslldgalsieelvkkakelglkaiaiTDhgnlf.gyvefykaakkkykagikpiiGleayvaddse....... 73
                                       vHt   ++ +++  +++++ ak lg+  +aiT h+n+  +y+e         ++gi +   +e+ v + s+       
  gi|298674557|ref|YP_003726307.1| 10 NVHTVPDGK-DTV--KDVMAFAKHLGFGGFAITNHSNVEeSYPEGS------MQDGIDVYKAVEIVVSNPSKlnglvgk 79
                                      566666666.566..**********************994344433......345788888888777776665555555 PP

                                      .............. CS
                                      .............x RF
                               PHP 74 .............k 74
                                                   +
  gi|298674557|ref|YP_003726307.1| 80 yrknvdvvavhggN 93
                                      55555555555550 PP

>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0   0.00046       2.7      83     137 ..       5      65 ..       3     152 .. 0.66
   2 ?    0.9   0.0     0.052   3.1e+02     132     181 ..     158     220 ..     142     225 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00046
                                       TCBECEEECTSSHCHHHHHHHHHHHHTTECEEEEESSTTTCCTTTCGGH......HHHHHH CS
                      Amidohydro_2  83 rfvggaavvpldpedaaaeleraveelgfkGvrlnphvggddllgdrld......rpifea 137
                                       rf  + + +++d++d+++  +  +++lgf G+ +  h + ++ ++++        ++ +e+
  gi|298674557|ref|YP_003726307.1|   5 RFYDFNVHTVPDGKDTVKDVMAFAKHLGFGGFAITNHSNVEESYPEGSMqdgidvYKAVEI 65 
                                       5666666678899******************998766655555554444225444333332 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.052
                                       HHHHHHHHHHT-EEEEE...................CHHHCHHHHHHHHHHHHHHHCCHHHHCTT CS
                      Amidohydro_2 132 rpifealeelglpvdihtGps...............pewlfggpqettraiqplllsgvarkfPn 181
                                        + +e+++++++p  +   ++                + lfg+ +e+++++++ + ++++ k  n
  gi|298674557|ref|YP_003726307.1| 158 SKNLELARKYNVPTILT--SNafncfdlrapeemiaLSKLFGMGREEAITSLSDIPESIITKNRN 220
                                       488999*******9999..5568999999999999999**********99999999988888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1486.55
//
Query:       gi|298674558|ref|YP_003726308.1|  [L=148]
Description: hypothetical protein Metev_0605 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-32  112.7   0.8    1.4e-32  112.4   0.8    1.0  1  RNA_binding  RNA binding


Domain annotation for each model (and alignments):
>> RNA_binding  RNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.4   0.8   7.9e-37   1.4e-32       1     119 []       4     129 ..       4     129 .. 0.97

  Alignments for each domain:
  == domain 1  score: 112.4 bits;  conditional E-value: 7.9e-37
                                       EEEEEEEE-TTC-HHHHHHHHHTTSTTS......E---EEEEEE-CCC-EEEEEEEEESSHHH.HHHHHHHHHHHCC CS
                       RNA_binding   1 kievrafvhaTEdeekVlealsnllpee......eveieeeeaeGhygnpitileaelekkka.kkvlkkllellre 70 
                                       +i++ra  haTE++++V+++l+ +l ++      ++ +e+ ++eGhygn i +++ael++k++ k+++++++e+l++
  gi|298674558|ref|YP_003726308.1|   4 YITLRATSHATEEKSRVKTSLDLFLLNSasnantDEIVEVLDVEGHYGNLISLCSAELTRKSEcKRLVEFIKENLSS 80 
                                       69***********************9999****97688*************************************** PP

                                       CCHHHHHHCCHCCB-TTSEEEEEEEHHHHHTT---BESSSSEEEEEEEE CS
                       RNA_binding  71 eeikeLlkeleervdekgklylrldKQaaylgklslvegddvIkvkikv 119
                                       +++  ++ke+++r+d++++++lr++KQ+aylg+l l++++d+I +kik+
  gi|298674558|ref|YP_003726308.1|  81 QDLATVYKEIPDRLDDEQVFHLRFNKQEAYLGRLLLSTSSDAIIIKIKI 129
                                       ***********************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1080.60
//
Query:       gi|298674559|ref|YP_003726309.1|  [L=185]
Description: 50S ribosomal protein L15e [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.8e-81  270.8  14.2    6.5e-81  270.6  14.2    1.0  1  Ribosomal_L15e  Ribosomal L15
  ------ inclusion threshold ------
       0.19   11.5   1.3       0.69    9.7   1.3    1.8  1  YjbF            Group 4 capsule polysaccharide lipoprotein gf


Domain annotation for each model (and alignments):
>> Ribosomal_L15e  Ribosomal L15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  270.6  14.2   7.3e-85   6.5e-81       2     184 ..       5     184 ..       4     185 .] 0.98

  Alignments for each domain:
  == domain 1  score: 270.6 bits;  conditional E-value: 7.3e-85
                                       SHHHHHHHTTSTTSHHHHHHHHHHHHHHTTS-SEEEESS-SSHHHHHHHT--SSTTEEEEEEEEE-SS---..---S CS
                    Ribosomal_L15e   2 aykylrelwkkkqsdvlrellrerlweyrqepavvrverptrldrArrLGYkakqGivvvrvrvrrGgrkkkvskgk 78 
                                       +y+y+re+w+k++++++++l ++rl+e+r++ ++++++rptrldrAr+LGYkakqGi+vvr++vrrGg++k  s+++
  gi|298674559|ref|YP_003726309.1|   5 FYNYIREAWRKPEETYVNNLRWQRLQEWRRQGSITKINRPTRLDRARTLGYKAKQGIIVVRAKVRRGGMRK--SRYN 79 
                                       69*********************************************************************..**** PP

                                       S---GGGG-SSS---SS-HHHHHHHHHHHHSTTSEEEEEEEEEEESSEEEEEEEEE-TTSHHHHT-TTTGGGGSGGG CS
                    Ribosomal_L15e  79 tgrkpkrqgvnklkpakslqaiaeervgrklpnlrvLnSYwvgeDgtykyyEvilvDpshkairndkkinwickkvh 155
                                       +gr++kr+g nk+++ ks+q+iaeer+ rk+pn++vLnSYwv+eDg+ k+yE+ilvDp+h++i++dk++nw+c++++
  gi|298674559|ref|YP_003726309.1|  80 AGRRTKRMGKNKITTGKSIQRIAEERAYRKYPNMEVLNSYWVAEDGKSKWYEIILVDPNHPVIKSDKDLNWVCSNKQ 156
                                       ***************************************************************************** PP

                                       TTGGGGT-SHHHHHHTT-S-SS.TT-TTT CS
                    Ribosomal_L15e 156 khRelrGltsagkksRGlrkkglkgaeki 184
                                       k+R+ rG+tsa++k+RG+rk+g kg+ek+
  gi|298674559|ref|YP_003726309.1| 157 KGRAHRGKTSASRKGRGIRKSG-KGTEKT 184
                                       ********************99.888876 PP

>> YjbF  Group 4 capsule polysaccharide lipoprotein gfcB, YjbF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.3   7.7e-05      0.69     109     167 ..      32     125 ..       6     128 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 7.7e-05
                                       E........................................EETTEEEEEEEEEEEEEEEEEEEETTEEEEEEEEEE CS
                              YjbF 109 w........................................qekyrygyladstfrragketvtilektvettrieE 145
                                       w                                        +  ++ +y+a  +++r+gk+++t+ ++ +     eE
  gi|298674559|ref|YP_003726309.1|  32 WrrqgsitkinrptrldrartlgykakqgiivvrakvrrggM--RKSRYNAGRRTKRMGKNKITTGKSIQR--IAEE 104
                                       555555555555555555555555555555555555554332..456788999999999999977665443..3445 PP

                                       EEEETTTTEEEEEEEEEETTT- CS
                              YjbF 146 svevpaleaefqNqYwvdsqsg 167
                                       +   +  ++e+ N+Ywv +++g
  gi|298674559|ref|YP_003726309.1| 105 RAYRKYPNMEVLNSYWV-AEDG 125
                                       55555589*********.6666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1451.13
//
Query:       gi|298674560|ref|YP_003726310.1|  [L=301]
Description: hypothetical protein Metev_0607 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1019  (0.0568353); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2155.17
//
Query:       gi|298674561|ref|YP_003726311.1|  [L=390]
Description: integrase family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.6e-24   84.1   0.5    1.9e-23   83.1   0.5    1.5  1  Phage_integrase  Phage integrase family
    3.9e-06   27.2   0.1    1.1e-05   25.8   0.1    1.8  1  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
    8.5e-05   22.1   2.2    0.00017   21.2   2.2    1.5  1  zinc_ribbon_2    zinc-ribbon domain
    0.00015   21.7   0.6    0.00027   20.9   0.6    1.3  1  DZR              Double zinc ribbon
     0.0014   18.2   3.1      0.066   12.9   0.2    2.4  2  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
     0.0017   18.2   0.8      0.003   17.4   0.8    1.3  1  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
  ------ inclusion threshold ------
      0.011   15.1   1.9       0.02   14.3   1.9    1.4  1  zf-ribbon_3      zinc-ribbon domain
      0.016   14.5   1.6      0.029   13.7   1.6    1.4  1  zf-RanBP         Zn-finger in Ran binding protein and others
      0.017   15.8   0.5      0.036   14.8   0.5    1.5  1  zinc_ribbon_15   zinc-ribbon family
      0.093   12.9   0.2       0.24   11.6   0.2    1.7  1  NOB1_Zn_bind     Nin one binding (NOB1) Zn-ribbon like
       0.11   12.5   2.0       0.65   10.0   0.9    2.6  3  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
       0.11   12.9   0.3       0.22   11.9   0.3    1.5  1  mono-CXXC        single CXXC unit
       0.16   11.9   0.0       0.16   11.9   0.0    1.9  2  Nudix_N_2        Nudix N-terminal


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.1   0.5   1.4e-26   1.9e-23       3     169 ..     130     294 ..     128     297 .. 0.87

  Alignments for each domain:
  == domain 1  score: 83.1 bits;  conditional E-value: 1.4e-26
                                       HHHHHHHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECTHHHHHH CS
                   Phage_integrase   3 ltedeverllaaleeslkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgskeravplseealel 79 
                                       +t +ev+++++a+++   +rdk+l+++ly+tG+R+sE+ +L++kdl++++    + +  gK++  r+  +    +++
  gi|298674561|ref|YP_003726311.1| 130 ITTEEVKQMIEAADY---VRDKALIAVLYDTGARVSEIGNLKIKDLNFDQYGGVI-KVDGKTGMRRIRII--FSVPY 200
                                       799************...******************************9855555.33888888776665..46899 PP

                                       HHHHHHHH..CHCCTTTSBSSBET..TSSB--HHHHHHHHHHHHHHCT-SSC--TTHHHHHHHHHHHHHCTSHHHHH CS
                   Phage_integrase  80 lkellska..leeaeksellfask..rgkplsrqtvrkafkraveeagiekpltpHtlRhsfataLleagvdlrvvq 152
                                       + ++l+++   +++++  ++ +s+  + ++l   ++++ +k ++++agi+k++  H +Rhs at+L+++   +   +
  gi|298674561|ref|YP_003726311.1| 201 INMWLNTHplRDNQDSYLWVTLSRraKCSQLRYHSINDNLKIIAKRAGINKKIYNHLFRHSRATELANHL-TQAQME 276
                                       9*******655555555677777788889***************************************98.67789* PP

                                       HHHT-SSCCHH.HHHHCC CS
                   Phage_integrase 153 kllGHssistt.qiYthv 169
                                       + lG+ + s   q+Y+h 
  gi|298674561|ref|YP_003726311.1| 277 EHLGWIHGSNMpQTYIHM 294
                                       ******999999***996 PP

>> Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.1     8e-09   1.1e-05       5      81 ..      33     107 ..      29     110 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 8e-09
                   Phage_int_SAM_4   5 frealrlaglserTiksYlsaikrflrflkkkapeeltkedieaYlnyLanerklsastqknalnalsffykkvler 81 
                                       + +++ ++gl+++Ti+++l+    +   ++ k++ +++k+die+Y+ yL  ++  s s+ ++++  l+ f+k++ + 
  gi|298674561|ref|YP_003726311.1|  33 YENHMFMNGLKKSTIRNHLYGMHYISGIIN-KPFPQVQKRDIESYIGYLE-RNIDSESSKSTKKTQLKKFFKWYHGS 107
                                       5678999**************999999999.******************9.444599999999**********8765 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   2.2   1.2e-07   0.00017       2      23 .]     324     345 ..     323     345 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.2e-07
                     zinc_ribbon_2   2 CpnCGaelqdnakFCpyCGtpl 23 
                                       Cp+C + + +++kFC++CG+ l
  gi|298674561|ref|YP_003726311.1| 324 CPRCDEMNGPTSKFCSRCGAAL 345
                                       *******************976 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.6     2e-07   0.00027       1      23 [.     324     346 ..     313     362 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2e-07
                               DZR   1 CpqCgeelppdarfCseCgtklk 23 
                                       Cp+C e + p ++fCs+Cg++l+
  gi|298674561|ref|YP_003726311.1| 324 CPRCDEMNGPTSKFCSRCGAALD 346
                                       88888888888888888888876 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.3     0.011        15      21      29 ..     321     329 ..     319     330 .. 0.87
   2 !   12.9   0.2   4.8e-05     0.066       2      13 ..     334     345 ..     334     350 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.011
                     zf-NADH-PPase  21 arvCpaCgl 29 
                                       ar+Cp C++
  gi|298674561|ref|YP_003726311.1| 321 ARQCPRCDE 329
                                       9******86 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 4.8e-05
                     zf-NADH-PPase   2 thrFCgrCGapt 13 
                                       t++FC+rCGa+ 
  gi|298674561|ref|YP_003726311.1| 334 TSKFCSRCGAAL 345
                                       679******986 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.8   2.2e-06     0.003       5      33 ..     315     343 ..     312     347 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.2e-06
                           DUF35_N   5 aegrLvgqrCpdCGtvqfPPravCphCgs 33 
                                       ++++L +++Cp C+    P   +C++Cg+
  gi|298674561|ref|YP_003726311.1| 315 TQPELTARQCPRCDEMNGPTSKFCSRCGA 343
                                       589************************97 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   1.9   1.5e-05      0.02       3      24 ..     322     343 ..     321     345 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.5e-05
                       zf-ribbon_3   3 vrCPnCGa.plssddnvCpyCGt 24 
                                       ++CP+C++ +  +  ++C  CG+
  gi|298674561|ref|YP_003726311.1| 322 RQCPRCDEmN-GPTSKFCSRCGA 343
                                       58********.***********7 PP

>> zf-RanBP  Zn-finger in Ran binding protein and others
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.6   2.1e-05     0.029       6      26 ..     323     343 ..     323     344 .. 0.96

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.1e-05
                                       E-SSS--EEESSSSB-TTT-- CS
                          zf-RanBP   6 dCskClvqNfawstkCvaCqa 26 
                                       +C+ C  +N ++s  C +C+a
  gi|298674561|ref|YP_003726311.1| 323 QCPRCDEMNGPTSKFCSRCGA 343
                                       8*******************9 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.5   2.6e-05     0.036      55      86 .]     311     342 ..     288     342 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.6e-05
                    zinc_ribbon_15  55 keiekkessekkeCknCgkeveeefkyCpkCg 86 
                                       k+ e++ + ++++C++C++   + +k+C++Cg
  gi|298674561|ref|YP_003726311.1| 311 KDEETQPELTARQCPRCDEMNGPTSKFCSRCG 342
                                       23333344449********************9 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00018      0.24      10      46 ..     323     358 ..     316     371 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                      NOB1_Zn_bind  10 rChaCfkvtkdmtkkFCpkCGnktLkrvavsvdenge 46 
                                       +C  C + ++  t kFC++CG +  +++a+ +de+ +
  gi|298674561|ref|YP_003726311.1| 323 QCPRCDE-MNGPTSKFCSRCGAALDTQIAMELDEKKS 358
                                       5777766.4567889*******999999999999955 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       6.1   8.4e+03       2      18 ..     234     250 ..     233     255 .. 0.78
   2 ?   10.0   0.9   0.00047      0.65      20      58 ..     313     347 ..     305     350 .. 0.81
   3 ?    6.7   0.1    0.0047       6.5      27      40 ..     334     347 ..     329     357 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 6.1
                    OrfB_Zn_ribbon   2 rklkeqleykakeyGik 18 
                                       +++   l+  ak++Gi+
  gi|298674561|ref|YP_003726311.1| 234 HSINDNLKIIAKRAGIN 250
                                       66777899999999996 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00047
                    OrfB_Zn_ribbon  20 eevnpayTSktCseCgsknkealsgrtfkCpnCgfeadr 58 
                                       ee +p+ T  +C++C + n +        C++Cg+ +d 
  gi|298674561|ref|YP_003726311.1| 313 EETQPELTARQCPRCDEMNGP----TSKFCSRCGAALDT 347
                                       567888999999999999999....55579999988875 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0047
                    OrfB_Zn_ribbon  27 TSktCseCgsknke 40 
                                       TSk Cs+Cg+ +++
  gi|298674561|ref|YP_003726311.1| 334 TSKFCSRCGAALDT 347
                                       9********98776 PP

>> mono-CXXC  single CXXC unit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   0.00016      0.22       6      31 ..     322     347 ..     319     362 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00016
                         mono-CXXC   6 rvCAacreddkpaasapdRsrlavDd 31 
                                       r C +c+e + p+++  +R+  a D 
  gi|298674561|ref|YP_003726311.1| 322 RQCPRCDEMNGPTSKFCSRCGAALDT 347
                                       78******************888775 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.5       6.3   8.7e+03      25      28 ..     324     327 ..     323     329 .. 0.70
   2 ?   11.9   0.0   0.00011      0.16       1      15 [.     336     350 ..     336     357 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 6.3
                                       ETTT CS
                         Nudix_N_2  25 CpaC 28 
                                       Cp+C
  gi|298674561|ref|YP_003726311.1| 324 CPRC 327
                                       7777 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00011
                                       -B-TTT--B-EEE-- CS
                         Nudix_N_2   1 kFCsqCGtpvelrip 15 
                                       kFCs CG+++ ++i 
  gi|298674561|ref|YP_003726311.1| 336 KFCSRCGAALDTQIA 350
                                       9*********99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1258  (0.0701657); expected 358.6 (0.02)
Passed bias filter:                      687  (0.0383178); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2609.79
//
Query:       gi|298674562|ref|YP_003726312.1|  [L=200]
Description: hypothetical protein Metev_0610 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.05   13.5   0.6       0.05   13.5   0.6    2.2  2  DUF2678        Protein of unknown function (DUF2678)
      0.097   12.3   0.2      0.097   12.3   0.2    1.9  2  Sgf11          Sgf11 (transcriptional regulation protein)
       0.12   11.7   2.9       0.24   10.7   0.2    2.0  2  S_4TM          SMODS-associating 4TM effector domain
       0.53   10.2   3.6       0.54   10.2   0.2    2.6  3  Deltameth_res  Deltamethrin resistance


Domain annotation for each model (and alignments):
>> DUF2678  Protein of unknown function (DUF2678)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.3     0.066   2.9e+02      38      54 ..      15      31 ..       3      68 .. 0.55
   2 ?   13.5   0.6   1.1e-05      0.05      23      74 ..     116     169 ..     101     193 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.066
                           DUF2678 38 tsllvlvtvvssfvfps 54
                                        +lv +t vs +++  
  gi|298674562|ref|YP_003726312.1| 15 VGILVAITFVSLVLLFA 31
                                      23444444444433222 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.1e-05
                           DUF2678  23 tsardriinlvvggltsllvlvtvvssfvfpslppkpln..iffavcillisss 74 
                                        + ++r in++   +t +l++ t    +vf  l p+ +n  +ff++++ +i++ 
  gi|298674562|ref|YP_003726312.1| 116 IYGHKRYINFIQNKMTNILLVLTFFVYMVFTPLIPHYINsaVFFVLVMTFITIN 169
                                       5678899*************************9999998668999888777654 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   2.2e-05     0.097       2      17 ..     100     115 ..      99     117 .. 0.87
   2 ?   -1.3   0.2      0.37   1.7e+03      15      20 ..     170     175 ..     170     176 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.2e-05
                                       C-EEE-TTTSSEEEGG CS
                             Sgf11   2 seyvtCpnCgRqiaas 17 
                                       + y+ C+nC+++i  +
  gi|298674562|ref|YP_003726312.1| 100 TSYFICKNCKKPIGIN 115
                                       579**********876 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.37
                                       EGGGHH CS
                             Sgf11  15 aasRFA 20 
                                       a++R+A
  gi|298674562|ref|YP_003726312.1| 170 ASNRYA 175
                                       68***9 PP

>> S_4TM  SMODS-associating 4TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   5.4e-05      0.24     164     237 ..       7      79 ..       4      98 .. 0.81
   2 ?    1.4   0.3     0.034   1.5e+02      32     209 ..     126     166 ..     115     190 .. 0.45

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.4e-05
                             S_4TM 164 rryaklllfalvlwillvlvvgliknlslsdlllsvivpllpllllalkeyreqresakelerlkeeiesllnd 237
                                       ++++  l++++++ i++v +v l+++l++ + + ++++ ++++++++l+ +r+ ++  k+l   k e  ++l+ 
  gi|298674562|ref|YP_003726312.1|   7 QKFNIRLVVGILVAITFVSLVLLFADLNIIESM-FFVAAVAGIITMVLNDARKLTDREKNLIASKLEPYNKLKH 79 
                                       78999999************************9.99999*********99999888777766555555555555 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.034
                             S_4TM  32 lrvilsvvlaivlsvlav.lvpslktylallgllwllldvlvldrlqkkekekAAkiQeqFDtkvfdlpwneilags 107
                                       ++  ++ +l ++  ++ + + p +  y++ +++++l++                                       
  gi|298674562|ref|YP_003726312.1| 126 IQNKMTNILLVLTFFVYMvFTPLIPHYINSAVFFVLVMT-------------------------------------- 164
                                       333333333333222222133333333333333333333...................................... PP

                             S_4TM 108 kideeeiarlakkykkkkkdeerlkdWYpeevedlprplavllCqrqNlsWdsrlrrryaklllfalvlwillvlvv 184
                                                                                                                    
  gi|298674562|ref|YP_003726312.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                             S_4TM 185 gliknlslsdlllsvivpllpllll 209
                                                              ++
  gi|298674562|ref|YP_003726312.1| 165 -----------------------FI 166
                                       .......................22 PP

>> Deltameth_res  Deltamethrin resistance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.2   0.00012      0.54      17      34 ..       5      22 ..       4      38 .. 0.81
   2 ?   -1.2   0.0      0.43   1.9e+03      26      42 ..      41      57 ..      34      65 .. 0.66
   3 ?   -1.3   0.1      0.46   2.1e+03      31      44 ..     160     173 ..     155     177 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00012
                     Deltameth_res 17 kqrkYNavLaaGivilig 34
                                      kq+k+N  L++Gi++ i 
  gi|298674562|ref|YP_003726312.1|  5 KQQKFNIRLVVGILVAIT 22
                                      8************98764 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.43
                     Deltameth_res 26 aaGiviligTialakes 42
                                      +++ v+ i+T++l  + 
  gi|298674562|ref|YP_003726312.1| 41 FVAAVAGIITMVLNDAR 57
                                      55667777777776555 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.46
                     Deltameth_res  31 iligTialakesgl 44 
                                       +l++T++++++s+ 
  gi|298674562|ref|YP_003726312.1| 160 VLVMTFITINASNR 173
                                       57788888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1436  (0.0800937); expected 358.6 (0.02)
Passed bias filter:                      640  (0.0356964); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1338.65
//
Query:       gi|298674563|ref|YP_003726313.1|  [L=609]
Description: hypothetical protein Metev_0611 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.2e-08   32.6   4.2    0.00019   21.6   0.2    3.7  4  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    4.7e-05   23.3   0.1     0.0026   17.8   0.0    3.1  3  bMG3             Bacterial alpha-2-macroglobulin MG3 domain
     0.0003   21.5   2.5     0.0003   21.5   2.5    2.4  2  Big_7            Bacterial Ig domain
     0.0039   17.0   1.5      0.063   13.2   0.1    2.9  2  FlgD_ig          FlgD Ig-like domain
  ------ inclusion threshold ------
      0.013   15.5   1.9        1.6    8.8   0.3    3.8  3  CarbopepD_reg_2  CarboxypepD_reg-like domain
       0.02   14.8   0.8         10    6.1   0.1    2.7  2  PEGA             PEGA domain
        3.5    8.2   6.5         14    6.3   1.6    2.5  2  baeRF_family12   Bacterial archaeo-eukaryotic release factor 


Domain annotation for each model (and alignments):
>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       2.4   6.1e+03      18      28 ..      32      42 ..      20      60 .. 0.49
   2 ?    2.6   0.1     0.064   1.6e+02       1      24 [.     155     179 ..     155     193 .. 0.80
   3 !    7.3   0.0    0.0022       5.7      44      71 ..     204     230 ..     201     237 .. 0.84
   4 !   21.6   0.2   7.6e-08   0.00019       6      69 ..     260     324 ..     259     332 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.4
                   CarboxypepD_reg 18 tVtvtnadtgt 28
                                      ++t+++ ++gt
  gi|298674563|ref|YP_003726313.1| 32 SITISSPSNGT 42
                                      33333333332 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.064
                   CarboxypepD_reg   1 tisGrVtda.sgapiagatVtvtna 24 
                                       +i  +V+d+ + +p+++ ++ ++n 
  gi|298674563|ref|YP_003726313.1| 155 SIWVQVVDEdTTNPVSNPNIKIQNP 179
                                       58899***8789*******999963 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0022
                   CarboxypepD_reg  44 glppgtysvtvsapGyatatreevtlta 71 
                                       +l pg+y v ++a+Gy   ++  v l++
  gi|298674563|ref|YP_003726313.1| 204 QLDPGKYMVSITAEGYNKEEY-LVNLEE 230
                                       699**************9998.577766 PP

  == domain 4  score: 21.6 bits;  conditional E-value: 7.6e-08
                   CarboxypepD_reg   6 Vtda.sgapiagatVtvtnadtgtv.astttdadGafrlrglppgtysvtvsapGyatatreevtl 69 
                                       V d+ +g+p++ at+   +++++tv +s +t + G+  +    +g ++v+vs+pGy+  t  +v++
  gi|298674563|ref|YP_003726313.1| 260 VMDSeTGEPVEDATIKMVDKESNTViRSEKTTDYGEVYWHWDIAGYFTVVVSKPGYDKETT-SVRV 324
                                       789779**********99987776439999******99998888****************6.5776 PP

>> bMG3  Bacterial alpha-2-macroglobulin MG3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.22   5.7e+02      35      95 ..      14      76 ..      11      77 .. 0.73
   2 ?    0.0   0.0      0.34   8.7e+02      11      56 ..     152     195 ..     133     228 .. 0.72
   3 !   17.8   0.0     1e-06    0.0026      12      54 ..     253     296 ..     244     330 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.22
                              bMG3 35 lldkkgevlaegtTDaqGvarfaallar.gkegaapylvsAr.kdedlaflkldwergldlsr 95
                                      l+++   +la  ++  ++ ++++++++  + e+ + + v A+ +d d++  +l+++++l +++
  gi|298674563|ref|YP_003726313.1| 14 LISAALVLLAGSASATNESITISSPSNGtTFEHGETVTVYAQtTDPDMTKPMLQTSNNLGTWD 76
                                      5666666777777777888888888665455777788888887899**998888888777775 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.34
                              bMG3  11 grdkllvwvtsLdsgkPvagaeVrlldkkgevlaegtTDaqGvarf 56 
                                        + +++v v   d+++Pv++ ++++ +     l + +  ++G++++
  gi|298674563|ref|YP_003726313.1| 152 INGSIWVQVVDEDTTNPVSNPNIKIQNP--SILNTYEGTESGLVKL 195
                                       4666777778888999999988887543..3455555555555555 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 1e-06
                              bMG3  12 rdkllvwvtsLdsgkPvagaeVrlld.kkgevlaegtTDaqGva 54 
                                       ++k ++wv   ++g+Pv++a+++++d +++ v+ + +T + G +
  gi|298674563|ref|YP_003726313.1| 253 NSKTDIWVMDSETGEPVEDATIKMVDkESNTVIRSEKTTDYGEV 296
                                       7899**********************788899999988888776 PP

>> Big_7  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   2.5   1.2e-07    0.0003       2      66 ..      32     100 ..      32     106 .. 0.84
   2 ?   -1.8   0.1       2.2   5.6e+03      10      24 ..     146     161 ..     140     188 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.2e-07
                                       EEEEEE--TT--EB.TSEEEEEEEEE-SS-EEEEEEEETTEE.....EEEE-SSSEEEEEE--...SEEE CS
                             Big_7   2 tvtitsPangatvs.ggtvtisasAsddggvskVefyvdgtl.g...lgtdtsapysltwtttaltagth 66 
                                       ++ti+sP+ng+t++ g+tvt+ a+++d+  ++k  +   ++l +   +++  ++ +  tw+t++l++++ 
  gi|298674563|ref|YP_003726313.1|  32 SITISSPSNGTTFEhGETVTVYAQTTDP-DMTKPMLQTSNNLgTwdpMDQIDNNLFVKTWNTSSLENKNE 100
                                       58**************************.88888888888885578888888899999999999666554 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.2
                                       TT--EB.TSEEEEEEE CS
                             Big_7  10 ngatvs.ggtvtisas 24 
                                       +g+t++ +g++ +++ 
  gi|298674563|ref|YP_003726313.1| 146 DGNTYNiNGSIWVQVV 161
                                       5666666666666554 PP

>> FlgD_ig  FlgD Ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.1   2.5e-05     0.063      43      76 ..     186     217 ..     147     219 .. 0.84
   2 ?    1.6   0.2       0.1   2.6e+02      20      55 ..     267     301 ..     251     305 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.5e-05
                                       EESSSEEEEEEE-SB-TTS-B--SEEEEEEEEEE CS
                           FlgD_ig  43 gaqsaGvvsftWdGtdndGnkladGaYtvkvtat 76 
                                       +  ++G v+++W   + dG++l +G+Y v++ta+
  gi|298674563|ref|YP_003726313.1| 186 EGTESGLVKLDWM--NLDGEQLDPGKYMVSITAE 217
                                       55789*******9..*****************97 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.1
                                       SSSEEEEEEEE-S.S--EEEEEEEEESSSEEEEEEE- CS
                           FlgD_ig  20 eaadevtvtikDa.sGevVrtidlgaqsaGvvsftWd 55 
                                       e+++ +t++  D+ s++v+r+   ++ + G+v + Wd
  gi|298674563|ref|YP_003726313.1| 267 EPVEDATIKMVDKeSNTVIRSE--KTTDYGEVYWHWD 301
                                       7899999**99*9555555666..5577888999998 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1      0.46   1.2e+03       4      24 ..     159     179 ..     159     189 .. 0.87
   2 ?    2.7   0.0     0.049   1.3e+02      41      69 ..     205     233 ..     201     247 .. 0.85
   3 ?    8.8   0.3   0.00062       1.6       5      70 ..     260     330 ..     259     344 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.46
                   CarbopepD_reg_2   4 tVvdketkeplpgatVyvkgt 24 
                                       +Vvd++t +p+   ++ +++ 
  gi|298674563|ref|YP_003726313.1| 159 QVVDEDTTNPVSNPNIKIQNP 179
                                       69***********99999875 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.049
                   CarbopepD_reg_2  41 lpagkytLvvsyvGyktqekkvtvskekt 69 
                                       l++gky + +++ Gy+++e  v++++ ++
  gi|298674563|ref|YP_003726313.1| 205 LDPGKYMVSITAEGYNKEEYLVNLEEPEE 233
                                       679****************9999987654 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00062
                   CarbopepD_reg_2   5 VvdketkeplpgatVyvkgtkkgtv.....TdenGnFelknlpagkytLvvsyvGyktqekkvtvskektl 70 
                                       V+d+et+ep++ at+ + +++ +tv     T + G+   +   ag +t+vvs  Gy++++ +v v  e+ +
  gi|298674563|ref|YP_003726313.1| 260 VMDSETGEPVEDATIKMVDKESNTVirsekTTDYGEVYWHWDIAGYFTVVVSKPGYDKETTSVRVVHESDI 330
                                       89***************99998888887788888986666667899****************999877655 PP

>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1     0.004        10      31      55 ..     205     229 ..     200     235 .. 0.81
   2 ?    6.0   0.0    0.0042        11      33      55 ..     303     325 ..     301     331 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.004
                              PEGA  31 leaGnyslrvekeGYedlektvtvt 55 
                                       l++G+y + + +eGY   e  v+++
  gi|298674563|ref|YP_003726313.1| 205 LDPGKYMVSITAEGYNKEEYLVNLE 229
                                       789************8766666665 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0042
                              PEGA  33 aGnyslrvekeGYedlektvtvt 55 
                                       aG+ ++ v+k+GY   ++ v v 
  gi|298674563|ref|YP_003726313.1| 303 AGYFTVVVSKPGYDKETTSVRVV 325
                                       6999*********9999999886 PP

>> baeRF_family12  Bacterial archaeo-eukaryotic release factor family 12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.2     0.027        70      31      87 ..     326     382 ..     314     403 .. 0.71
   2 ?    6.3   1.6    0.0055        14      17      88 ..     481     547 ..     471     549 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.027
                    baeRF_family12  31 fkreqdrpsdregssdrpGrsssggagrsameetdfkeqeeerFakeladeLkkrak 87 
                                       ++ + + ++d + s  ++ + ssg+ +++  ++td+++++e+  ++e++++L++  k
  gi|298674563|ref|YP_003726313.1| 326 HESDIGTHPDFDDSESTSSDDSSGSDNGNDGSDTDTQDKDEDLTLREVQQYLDENHK 382
                                       55555666666666666655677777777778********************97544 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0055
                    baeRF_family12  17 neegdieelelveefkreqdrpsdregssdrpGr.sssggagrsameetdfkeqeeerFakeladeLkkrake 88 
                                       n ++d+ +++   ++k eq+  +d++   +++G+ ++ ++++     ++d+ e++eer++  l  + kk++++
  gi|298674563|ref|YP_003726313.1| 481 N-NEDVPDIQIPYTSKPEQSSTDDNNEEDQSTGKeQEETQQH-----SSDTDEKTEERLMELLTPKQKKELLK 547
                                       5.5555555555556777777777777777778855555555.....888888899**999999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (609 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1819  (0.101456); expected 358.6 (0.02)
Passed bias filter:                      704  (0.039266); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.86u 0.33s 00:00:01.19 Elapsed: 00:00:00.50
# Mc/sec: 3658.70
//
Query:       gi|298674564|ref|YP_003726314.1|  [L=106]
Description: hypothetical protein Metev_0612 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 686.29
//
Query:       gi|298674565|ref|YP_003726315.1|  [L=263]
Description: hypothetical protein Metev_0613 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1888.34
//
Query:       gi|298674566|ref|YP_003726316.1|  [L=275]
Description: hypothetical protein Metev_0614 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       854  (0.0476323); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2165.65
//
Query:       gi|298674567|ref|YP_003726317.1|  [L=321]
Description: hypothetical protein Metev_0615 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.6e-06   25.4   0.1    0.00025   20.8   0.0    2.2  2  Zot          Zonular occludens toxin (Zot)
     0.0045   17.4   0.0      0.041   14.3   0.0    2.3  3  AAA_16       AAA ATPase domain
  ------ inclusion threshold ------
      0.046   12.8   0.0      0.072   12.1   0.0    1.2  1  T2SSE        Type II/IV secretion system protein
      0.078   13.1   0.0        1.5    9.0   0.0    2.4  2  Hydrolase_6  Haloacid dehalogenase-like hydrolase
       0.11   12.6   0.0         22    5.2   0.0    2.4  2  AD           Anticodon-binding domain
       0.12   11.9   0.2       0.21   11.1   0.2    1.4  1  Tenui_N      Tenuivirus/Phlebovirus nucleocapsid protein
       0.13   11.7   0.1       0.49    9.8   0.1    2.0  1  Pox_A32      Poxvirus A32 protein
        0.2   11.8   0.3       0.48   10.6   0.1    1.9  2  AAA_33       AAA domain


Domain annotation for each model (and alignments):
>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.046     1e+02       3      31 ..      94     120 ..      92     123 .. 0.76
   2 !   20.8   0.0   1.1e-07   0.00025      73     135 ..     138     200 ..     129     239 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.046
                               Zot   3 slvtGapGsgKtsgavkkdllpalkegRk 31 
                                        l  G +GsgKt+    ++ll al+++ k
  gi|298674567|ref|YP_003726317.1|  94 ILISGSKGSGKTYE--GWRLLHALRKEYK 120
                                       6789*********8..4667777777655 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 1.1e-07
                               Zot  73 akwatidkgallviDEcqeifpvrakegrkdpevinaftehRhlgwDivlltqdiskihkevr 135
                                       a+ +  +++a+ ++DE   + + r+   ++  e+ + ++ +Rh g  ++++tq+ s+ ++ + 
  gi|298674567|ref|YP_003726317.1| 138 ATLDHLPQNAVGLVDESAIFMNSRRSMSKDNVESTELLAVARHQGRKVIFITQNTSRSDNSLT 200
                                       5556678*********99888888887777788889********************9888765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.53   1.2e+03      69      99 ..      22      49 ..       6      61 .. 0.74
   2 !   14.3   0.0   1.8e-05     0.041      20      55 ..      87     123 ..      78     155 .. 0.84
   3 ?   -2.5   0.0       2.6   5.9e+03      43      66 ..     176     198 ..     171     238 .. 0.61

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.53
                            AAA_16 69 ysalaqalareellrqlldeaesaeleawre 99
                                      y  ++ +l +e+l+r l+++    e+e++++
  gi|298674567|ref|YP_003726317.1| 22 YRKWLFQLHKEHLIRYLDER---WEPEEHST 49
                                      45588889999*****9988...45555554 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.8e-05
                            AAA_16  20 rsgrpelvllsGesGvGKsslvrellralekdg.gif 55 
                                       r+++  ++l+sG +G+GK+   ++ll+al+k++ +++
  gi|298674567|ref|YP_003726317.1|  87 RKPGQDVILISGSKGSGKTYEGWRLLHALRKEYkVYW 123
                                       5556689**********************99965665 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 2.6
                            AAA_16  43 ellralekdggiflrgkcdqlesa 66 
                                       +++r+  ++ +if+++++ +++ +
  gi|298674567|ref|YP_003726317.1| 176 AVARHQGRK-VIFITQNTSRSDNS 198
                                       444333333.77777776666333 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.2e-05     0.072     117     156 ..      81     118 ..      63     130 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.2e-05
                             T2SSE 117 kiaevlrkavrerglilvsGgTgsGKttllyallkeinks 156
                                       k+ +v+rk+   + +il+sG  gsGKt     ll+ + k+
  gi|298674567|ref|YP_003726317.1|  81 KMINVIRKP--GQDVILISGSKGSGKTYEGWRLLHALRKE 118
                                       567899999..999*************9988888888776 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.16   3.6e+02      14      39 ..      74      99 ..      65     118 .. 0.81
   2 ?    9.0   0.0   0.00067       1.5      19      45 ..     171     197 ..     168     202 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.16
                                      EE-TTHHHHHHHHHHTT-EEEEEE-- CS
                       Hydrolase_6 14 kaipgaaealnalraagkpvvllTNn 39
                                      ++ ++  +++n++r+ g +v+l++ +
  gi|298674567|ref|YP_003726317.1| 74 DPTKNFWKMINVIRKPGQDVILISGS 99
                                      566667799*************9965 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00067
                                       HHHHHHHHHHTT-EEEEEE---SS-HH CS
                       Hydrolase_6  19 aaealnalraagkpvvllTNnssksee 45 
                                       + e+l + r +g +v+++T n+s+s +
  gi|298674567|ref|YP_003726317.1| 171 STELLAVARHQGRKVIFITQNTSRSDN 197
                                       5799********************965 PP

>> AD  Anticodon-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0      0.01        22      25      56 ..      99     129 ..      96     132 .. 0.88
   2 ?    4.7   0.0     0.015        33      50      69 ..     194     213 ..     176     224 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.01
                                AD  25 sigkgvskeaqalFdalsktlpdvrWkgkeIv 56 
                                       s+g+g + e+ +l +al+k ++ v W g+ I 
  gi|298674567|ref|YP_003726317.1|  99 SKGSGKTYEGWRLLHALRKEYK-VYWVGPPIN 129
                                       56788999*************9.****99886 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.015
                                AD  50 WkgkeIvVldeviIspPYkv 69 
                                        +++++ ++ +v I +PY++
  gi|298674567|ref|YP_003726317.1| 194 RSDNSLTIWADVHIIKPYTS 213
                                       5788999***********97 PP

>> Tenui_N  Tenuivirus/Phlebovirus nucleocapsid protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   9.5e-05      0.21      17      60 ..     270     315 ..     263     318 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.5e-05
                           Tenui_N  17 itehkaeivefvneieYqgfdaakilkllkekg..kgddlkkDvkk 60 
                                       + e+++  ++++++++ qg+ a+ i k+++ kg  kg+d+ +D+ +
  gi|298674567|ref|YP_003726317.1| 270 VFENEDMAMQYAEAMAEQGYGAKSIQKVMRMKGmdKGQDFWQDIID 315
                                       55789999*************************99********976 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00022      0.49      17      60 ..      95     138 ..      77     204 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00022
                           Pox_A32  17 alvGgsGsGktvyLlsLlrtlvkkykhifLltpvknseYdkyvw 60 
                                        + G  GsGkt     Ll+ l k+yk  ++  p++ +e+ +yv 
  gi|298674567|ref|YP_003726317.1|  95 LISGSKGSGKTYEGWRLLHALRKEYKVYWVGPPINLPEWAGYVA 138
                                       455788********************9999999*99*****995 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       6.3   1.4e+04      42      57 ..      16      31 ..       8      41 .. 0.59
   2 ?   10.6   0.1   0.00021      0.48       1      25 [.      93     119 ..      93     205 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 6.3
                            AAA_33 42 qqsktdytrvldrlyq 57
                                      q+ k++y ++l++l++
  gi|298674567|ref|YP_003726317.1| 16 QKGKNWYRKWLFQLHK 31
                                      4455566666665443 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00021
                            AAA_33   1 lvllvGlpGsGKstlaerllkklg..a 25 
                                       ++l+ G +GsGK++  +rll +l   +
  gi|298674567|ref|YP_003726317.1|  93 VILISGSKGSGKTYEGWRLLHALRkeY 119
                                       79999**************98887552 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2153.79
//
Query:       gi|298674568|ref|YP_003726318.1|  [L=154]
Description: hypothetical protein Metev_0616 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00052   20.2   0.4     0.0018   18.5   0.0    2.0  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0032   17.3   1.4     0.0054   16.6   0.1    1.9  2  DUF3116         Protein of unknown function (DUF3116)
     0.0042   17.2   0.4      0.013   15.6   0.0    1.9  2  HTH_34          Winged helix DNA-binding domain
     0.0062   16.5   0.4      0.025   14.5   0.0    2.1  2  HTH_36          Helix-turn-helix domain
  ------ inclusion threshold ------
       0.02   15.4   0.0      0.049   14.1   0.0    1.6  1  HTH_27          Winged helix DNA-binding domain
       0.03   14.2   0.0      0.055   13.3   0.0    1.4  1  HxlR            HxlR-like helix-turn-helix
      0.031   14.3   1.0      0.064   13.3   0.1    2.0  2  HTH_54          ParA helix turn helix domain
      0.061   12.2   1.3      0.084   11.8   1.3    1.2  1  DUF3375         Protein of unknown function (DUF3375)
       0.41   11.1   8.7       0.24   11.8   3.5    2.2  2  DUF4600         Domain of unknown function (DUF4600)
        1.1    9.7   4.8        7.8    7.0   0.1    2.4  2  DUF2533         Protein of unknown function (DUF2533)


Domain annotation for each model (and alignments):
>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   9.8e-07    0.0018      26      57 ..      36      67 ..      27      69 .. 0.90
   2 ?   -1.0   0.2       1.2   2.1e+03       5      21 ..     117     133 ..     113     151 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 9.8e-07
                                      HHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                    Fe_dep_repress 26 kdlaerLnvspssVsemlkkLekdGyveyeky 57
                                        l +rL+vs+ s  ++l+k+++ Gy++ +ky
  gi|298674568|ref|YP_003726318.1| 36 NTLHKRLDVSKNSLVKTLNKMANYGYLIRKKY 67
                                      56779************************999 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHHHHS CS
                    Fe_dep_repress   5 stEdYLetIYtlseekk 21 
                                       + E+Y++   ++ e+kk
  gi|298674568|ref|YP_003726318.1| 117 TSEEYIKKRIQILEDKK 133
                                       67888886555555544 PP

>> DUF3116  Protein of unknown function (DUF3116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1     3e-06    0.0054      34      84 ..      39      92 ..      16      93 .. 0.83
   2 ?   -0.7   0.1      0.71   1.3e+03       9      21 ..     122     134 ..     105     151 .. 0.54

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3e-06
                           DUF3116 34 ksvkkltkneLLytvYWLElkgyilRkeeka...nnkkrYelTekGellykelk 84
                                      +++ +++kn+L  t+  +  +gy++Rk++ +   n k +Y l e G++++ +l+
  gi|298674568|ref|YP_003726318.1| 39 HKRLDVSKNSLVKTLNKMANYGYLIRKKYITprnNCKNYYVLGEVGKKVFPKLH 92
                                      445688*********************985322156778899*****9999887 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.71
                           DUF3116   9 ilevLelvkdpnf 21 
                                       i+  +++ +d++ 
  gi|298674568|ref|YP_003726318.1| 122 IKKRIQILEDKKK 134
                                       3333333333333 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   7.4e-06     0.013      12      77 ..      30      96 ..      28      98 .. 0.87
   2 ?   -0.8   0.1      0.96   1.7e+03      23      40 ..     114     131 ..     107     148 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7.4e-06
                            HTH_34 12 vdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtll.riTpeGreafkkyvkaLk 77
                                      +d+ad ++l + l +++  L + l+k+ + gY+ ++k    +  +  +  + + G++ f k  + +k
  gi|298674568|ref|YP_003726318.1| 30 ADKADLNTLHKRLDVSKNSLVKTLNKMANYGYLIRKKYITPRNNCKNYyVLGEVGKKVFPKLHEKMK 96
                                      599***********************************99999887651567789998888887776 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.96
                            HTH_34  23 aleatdgnLsvhlkkLek 40 
                                        +++++  + + +++Le+
  gi|298674568|ref|YP_003726318.1| 114 YIRTSEEYIKKRIQILED 131
                                       455555555555555554 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.4e-05     0.025      28      55 .]      35      62 ..      13      62 .. 0.91
   2 ?   -0.2   0.1      0.56     1e+03      37      51 ..     117     131 ..      84     145 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.4e-05
                            HTH_36 28 qetlakrlglsknTvsraikeLeqlGyi 55
                                        tl krl +skn+ ++ +++ + +Gy+
  gi|298674568|ref|YP_003726318.1| 35 LNTLHKRLDVSKNSLVKTLNKMANYGYL 62
                                      689************************8 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.56
                            HTH_36  37 lsknTvsraikeLeq 51 
                                        s++ + + i+ Le+
  gi|298674568|ref|YP_003726318.1| 117 TSEEYIKKRIQILED 131
                                       444444444444443 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.7e-05     0.049      18      52 ..      32      66 ..      30      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.7e-05
                            HTH_27 18 rkkladlcgrlnvedshisyslkkLtekGLvertg 52
                                      ++ l  l++rl+v++ + ++ l+k+ ++G++ r++
  gi|298674568|ref|YP_003726318.1| 32 KADLNTLHKRLDVSKNSLVKTLNKMANYGYLIRKK 66
                                      5567889************************6665 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.1e-05     0.055      23      84 ..      37      99 ..      29     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.1e-05
                                      HHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEE..SSSS-EEEEEE-TCGGGGHHHHHHHHHHHH CS
                              HxlR 23 elkralpkisqkmLaqrLreLeqdglierevy..pevPpkveYsltekGrslepvlqelkkwge 84
                                       l+++l ++s++ L+++L ++ + g + r+ y  p+   k  Y l e G+++ p l+e +k ge
  gi|298674568|ref|YP_003726318.1| 37 TLHKRL-DVSKNSLVKTLNKMANYGYLIRKKYitPRNNCKNYYVLGEVGKKVFPKLHEKMKNGE 99
                                      566777.89**************998888876447788999***************98777665 PP

>> HTH_54  ParA helix turn helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   3.6e-05     0.064      17      62 ..      22      67 ..       7      81 .. 0.81
   2 ?   -1.0   0.1       1.1   1.9e+03       7      15 ..     131     139 ..     107     151 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.6e-05
                            HTH_54 17 kElkedeyyqtyskaalaklpklsrrkvdkavsemeaeGyefekke 62
                                      +E k+d +  +   ++l+k+  +s++++ k++++m + Gy ++kk 
  gi|298674568|ref|YP_003726318.1| 22 EERKKDPFADKADLNTLHKRLDVSKNSLVKTLNKMANYGYLIRKKY 67
                                      55666777777778999*************************9984 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.1
                            HTH_54   7 elteqiqkq 15 
                                       +  ++i++q
  gi|298674568|ref|YP_003726318.1| 131 DKKKEIDDQ 139
                                       222333333 PP

>> DUF3375  Protein of unknown function (DUF3375)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.3   4.7e-05     0.084     131     161 ..     117     147 ..     109     153 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.7e-05
                           DUF3375 131 etepDpeeRlaeLeaeiaeidaeidrlrage 161
                                        +e+  ++R++ Le +++eid++i++l +++
  gi|298674568|ref|YP_003726318.1| 117 TSEEYIKKRIQILEDKKKEIDDQIEKLNQEK 147
                                       56666799*******************9854 PP

>> DUF4600  Domain of unknown function (DUF4600)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.6      0.11     2e+02      39      64 ..      33      58 ..       7     103 .. 0.56
   2 ?   11.8   3.5   0.00014      0.24      26      76 ..      91     143 ..      75     149 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.11
                           DUF4600 39 drlasirvleklteeelnqllkqLek 64
                                       +l++++   ++++++l ++l+++ +
  gi|298674568|ref|YP_003726318.1| 33 ADLNTLHKRLDVSKNSLVKTLNKMAN 58
                                      22344444444445555555555443 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00014
                           DUF4600  26 lkeklekir..gnpsdrlasirvleklteeelnqllkqLekekkslenqlkdl 76 
                                       l+ek+++    + ++ + + i ++ + +ee ++++++ Le+ kk+++ q+ +l
  gi|298674568|ref|YP_003726318.1|  91 LHEKMKNGEslNLRNPKEEKISSYIRTSEEYIKKRIQILEDKKKEIDDQIEKL 143
                                       445554444443344455899****************************9865 PP

>> DUF2533  Protein of unknown function (DUF2533)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0044       7.8      51      74 ..      47      70 ..       4      78 .. 0.79
   2 ?    3.6   1.5     0.051        92       5      45 ..     109     149 ..     107     153 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0044
                           DUF2533 51 NevTkeiNelakkgivptRklVtk 74
                                      N + k +N++a+ g++  +k++t+
  gi|298674568|ref|YP_003726318.1| 47 NSLVKTLNKMANYGYLIRKKYITP 70
                                      8999******************96 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.051
                           DUF2533   5 kaitahvkkqnaalkqfleLeqkREaaIeeavelckkgkpf 45 
                                       ++i+  ++  ++ +k+ +++ + + + I++ +e+ +++k++
  gi|298674568|ref|YP_003726318.1| 109 EKISSYIRTSEEYIKKRIQILEDKKKEIDDQIEKLNQEKAL 149
                                       679999999999999999998889999*****999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1923  (0.107256); expected 358.6 (0.02)
Passed bias filter:                      662  (0.0369234); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1114.88
//
Query:       gi|298674569|ref|YP_003726319.1|  [L=288]
Description: hypothetical protein Metev_0617 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-18   67.3   0.9    8.1e-18   65.1   0.1    2.3  2  Pilin_N   Archaeal Type IV pilin, N-terminal
  ------ inclusion threshold ------
      0.017   16.0   0.8      0.069   14.0   0.2    2.1  2  DUF4065   Protein of unknown function (DUF4065)


Domain annotation for each model (and alignments):
>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.1   0.1   9.1e-22   8.1e-18       1      80 [.      12      86 ..      12      87 .. 0.96
   2 ?   -0.1   0.1       0.2   1.8e+03      56      67 ..     198     212 ..     171     237 .. 0.55

  Alignments for each domain:
  == domain 1  score: 65.1 bits;  conditional E-value: 9.1e-22
                           Pilin_N  1 eAVSpViGviLmvaitvIlaAviaafvlglasneekapqasievkidssastgknavslehkgGdsidtkdlkivlnse 79
                                      eAVS++iG+iLm+ i v+++A+ia++v+++  ++ ++p+++++ + ++ +++    + ++h+gG+ ++t+dlk++++ +
  gi|298674569|ref|YP_003726319.1| 12 EAVSSIIGEILMTGIAVLIFAIIAVSVFSM-LDPVEEPHIDVDGWPNNYTDK----IHIRHEGGEKLSTEDLKLIVEVN 85
                                      69****************************.99************9999987....*******************9987 PP

                           Pilin_N 80 g 80
                                      +
  gi|298674569|ref|YP_003726319.1| 86 D 86
                                      6 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.2
                           Pilin_N  56 a...vslehkgGdsi 67 
                                       a   +s+  + G+++
  gi|298674569|ref|YP_003726319.1| 198 AnfnFSFSVNEGEVT 212
                                       123455555555543 PP

>> DUF4065  Protein of unknown function (DUF4065)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   7.7e-06     0.069      67     114 .]      60     107 ..      41     107 .. 0.77
   2 ?   -0.1   0.0      0.19   1.7e+03      27      60 ..     221     243 ..     185     260 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.7e-06
                           DUF4065  67 keveeleddkeaelseeekevidkvikkykdlsaseLselthkeeaWk 114
                                       +++   + ++  +ls e++++i +v ++ k+++++e+ +  h+++ W+
  gi|298674569|ref|YP_003726319.1|  60 TDKIHIRHEGGEKLSTEDLKLIVEVNDTRKSYTGNEIKDDFHNKDTWQ 107
                                       2223333344445**********************************6 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.19
                           DUF4065  27 awkyGPVvpevydeikelgskpieekeeeisdek 60 
                                         + GPV    y++ik +        e+e+++e+
  gi|298674569|ref|YP_003726319.1| 221 VNEDGPV---GYNNIKIN--------EREFTNEN 243
                                       5566777...77766533........33333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.36s 00:00:00.97 Elapsed: 00:00:00.56
# Mc/sec: 1539.30
//
Query:       gi|298674570|ref|YP_003726320.1|  [L=98]
Description: hypothetical protein Metev_0618 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       905  (0.0504769); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 723.23
//
Query:       gi|298674571|ref|YP_003726321.1|  [L=205]
Description: hypothetical protein Metev_0619 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       812  (0.0452898); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1491.02
//
Query:       gi|298674572|ref|YP_003726322.1|  [L=61]
Description: hypothetical protein Metev_0620 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.22s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 503.75
//
Query:       gi|298674573|ref|YP_003726323.1|  [L=437]
Description: PEGA domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.1e-07   31.6   2.5    1.1e-07   31.6   2.5    2.8  2  PEGA       PEGA domain
    8.9e-07   28.7   5.7    1.4e-06   28.1   5.7    1.3  1  PGF-CTERM  PGF-CTERM motif
    3.4e-06   27.0   0.0    6.8e-05   22.8   0.0    2.7  3  BiPBP_C    Penicillin-Binding Protein C-terminus Family
     0.0049   16.3   0.0       0.02   14.4   0.0    2.0  2  TcfC       E-set like domain
  ------ inclusion threshold ------
      0.064   13.0   0.4       0.47   10.2   0.1    2.5  2  PKD_3      PKD-like domain
        2.6    8.5   6.0       0.45   11.0   1.4    2.1  2  DUF5104    Domain of unknown function (DUF5104)
        7.1    7.0   6.7        8.4    6.8   0.1    3.1  4  PCC_BT     Propionyl-coenzyme A carboxylase BT domain


Domain annotation for each model (and alignments):
>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.2      0.18   4.7e+02       6      24 ..      98     115 ..      95     125 .. 0.71
   2 !   31.6   2.5   4.5e-11   1.1e-07       2      68 ..     205     277 ..     204     279 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.18
                              PEGA   6 irSnpeGatVyidGkylGk 24 
                                       i  +peG+ V+++ +++G 
  gi|298674573|ref|YP_003726323.1|  98 IGYTPEGSDVTVN-VDIGG 115
                                       55689*******5.57774 PP

  == domain 2  score: 31.6 bits;  conditional E-value: 4.5e-11
                              PEGA   2 gtltirSnpeGatVyidGkylGkTP......vtlsleaGnyslrvekeGYedlektvtvtagetvklnltLek 68 
                                       gt+  +++p Ga Vy+dG y G+T       +t++l +G++s +v++  Ye+ + t +vtaget  ++  Le+
  gi|298674573|ref|YP_003726323.1| 205 GTVEFYTDPVGAAVYVDGDYKGQTSsysygvLTMELYEGSHSYTVSANDYETETGTFSVTAGETNAVTASLEE 277
                                       677889****************9965555534555*********************************99987 PP

>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   5.7   5.5e-10   1.4e-06       1      22 [.     413     434 ..     413     435 .. 0.96

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 5.5e-10
                         PGF-CTERM   1 tPGFGavlAlaGLLaaalLaRR 22 
                                       +PGF+av+AlaGL  ++lLaRR
  gi|298674573|ref|YP_003726323.1| 413 IPGFEAVFALAGLVIVVLLARR 434
                                       7********************9 PP

>> BiPBP_C  Penicillin-Binding Protein C-terminus Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.33   8.4e+02      11      38 ..      95     123 ..      87     125 .. 0.87
   2 ?   -2.1   0.0       1.5     4e+03      48      62 ..     218     232 ..     204     252 .. 0.71
   3 !   22.8   0.0   2.7e-08   6.8e-05      31      86 ..     312     374 ..     297     379 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.33
                           BiPBP_C  11 plrIafPadGailaldpdip.krqrlqlk 38 
                                        + I + ++G+ + +  di+ + q ++l+
  gi|298674573|ref|YP_003726323.1|  95 RVAIGYTPEGSDVTVNVDIGgSSQTVTLS 123
                                       57899999************999999996 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.5
                           BiPBP_C  48 Wlldgeplaetkrgr 62 
                                        ++dg + ++t++ +
  gi|298674573|ref|YP_003726323.1| 218 VYVDGDYKGQTSSYS 232
                                       588999998887755 PP

  == domain 3  score: 22.8 bits;  conditional E-value: 2.7e-08
                           BiPBP_C  31 krqrlqlkarggea.....plrWlldgeplaetkrgrelawqp.epGrhrLtv..vDaaGrvdd 86 
                                       ++ +++++ + +++     + +W+l+gep+ +t+++ +++ +  ++G++ +++  +D++G++++
  gi|298674573|ref|YP_003726323.1| 312 SETNIVFTSESSDPdgqitKQEWFLNGEPV-STGDQYQMETSNmNSGTYVVELdvTDDQGATST 374
                                       677888888888555888899*********.99***************9888776*****9987 PP

>> TcfC  E-set like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.4   3.7e+03       9      20 ..     201     212 ..     199     213 .. 0.85
   2 !   14.4   0.0   7.7e-06      0.02      17      66 ..     329     379 ..     313     381 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.4
                              TcfC   9 lpragrveiyRd 20 
                                        p+ g ve+y d
  gi|298674573|ref|YP_003726323.1| 201 SPSTGTVEFYTD 212
                                       7999******77 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 7.7e-06
                              TcfC  17 iyRdgqLlstqnvnaGnq.eidtssLPsGiYeveirvyengqvvrteqqkf 66 
                                       i++ +  l+   v+ G q +++ts++ sG+Y ve+ v ++++ ++t + k+
  gi|298674573|ref|YP_003726323.1| 329 ITKQEWFLNGEPVSTGDQyQMETSNMNSGTYVVELDVTDDQGATSTAKYKV 379
                                       677777899999999987589***********************9988776 PP

>> PKD_3  PKD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.36   9.3e+02      43      65 ..     136     158 ..     119     161 .. 0.82
   2 ?   10.2   0.1   0.00018      0.47      35      67 ..     332     366 ..     312     367 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.36
                             PKD_3  43 ivsteptytfteeelgsyevtle 65 
                                       +v t  +++ + +  g++evt++
  gi|298674573|ref|YP_003726323.1| 136 VVNTGLNLEHVDDGDGQVEVTIK 158
                                       78999999999999******997 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00018
                             PKD_3  35 faWtieGkivsteptytfteeel..gsyevtleve 67 
                                        +W ++G+ vst  +y+   +++  g+y v l v+
  gi|298674573|ref|YP_003726323.1| 332 QEWFLNGEPVSTGDQYQMETSNMnsGTYVVELDVT 366
                                       58**************9877654339999999875 PP

>> DUF5104  Domain of unknown function (DUF5104)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.2       3.5     9e+03      60      60 ..     242     242 ..     218     270 .. 0.46
   2 ?   11.0   1.4   0.00018      0.45      24      97 ..     320     393 ..     314     398 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.5
                           DUF5104  60 s 60 
                                       +
  gi|298674573|ref|YP_003726323.1| 242 E 242
                                       1 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00018
                           DUF5104  24 kesddldeeidelidfykGdivsyeeasssseessesgktktktlsaiysiktdkdkYviaievvlkdeknedn 97 
                                        es+d d +i++   f++G+ vs+++++++++++++sg++  +   +  +  t + kY + i+++ k  ++e++
  gi|298674573|ref|YP_003726323.1| 320 SESSDPDGQITKQEWFLNGEPVSTGDQYQMETSNMNSGTYVVELDVTDDQGATSTAKYKVTIDETKKVVESEEK 393
                                       577888999999999*****************99****999966666677888899999999988776666655 PP

>> PCC_BT  Propionyl-coenzyme A carboxylase BT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0033       8.4      18      61 ..      68     112 ..      63     125 .. 0.75
   2 ?   -0.7   0.1      0.68   1.7e+03      37      62 ..     145     170 ..     113     183 .. 0.67
   3 ?   -3.1   0.0       3.8   9.7e+03      49      64 ..     254     268 ..     234     279 .. 0.46
   4 ?    2.3   0.1     0.081   2.1e+02      30      75 ..     355     396 ..     327     413 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0033
                            PCC_BT  18 qisnqlr.tkeakeekdwvvtvdgedetvtvkveeaadevevkvd 61 
                                       +++n  r t + +++++++ ++++e+ +v + ++ ++++v+v+vd
  gi|298674573|ref|YP_003726323.1|  68 RFQNSVRgTVTYENSNSFDTSMKNENFRVAIGYTPEGSDVTVNVD 112
                                       678888867777899999999999999999999988887766654 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.68
                            PCC_BT  37 tvdgedetvtvkveeaadevevkvdg 62 
                                       +vd++d +v+v+++++++e  vk+++
  gi|298674573|ref|YP_003726323.1| 145 HVDDGDGQVEVTIKHSSSEKSVKIHE 170
                                       34555666666666666666666555 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 3.8
                            PCC_BT  49 veeaadevevkvdgks 64 
                                       +e +++++ v+  g++
  gi|298674573|ref|YP_003726323.1| 254 YETETGTFSVT-AGET 268
                                       22333444444.3333 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.081
                            PCC_BT  30 eekdwvvtvdgedetvtvkveeaadevevkvdgksvkvssdwklgq 75 
                                       ++ ++vv++d++d +       ++ +++v++d+++  v+s+ k g+
  gi|298674573|ref|YP_003726323.1| 355 NSGTYVVELDVTDDQGA----TSTAKYKVTIDETKKVVESEEKSGD 396
                                       23344444444444322....3345788999998888887766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.35
# Mc/sec: 3748.01
//
Query:       gi|298674574|ref|YP_003726324.1|  [L=609]
Description: hypothetical protein Metev_0622 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.7   0.0        3.6    7.9   0.0    2.6  2  PCC_BT    Propionyl-coenzyme A carboxylase BT domain
        6.8    7.2  10.9         31    5.1   0.0    4.5  5  CBM60     Ca-dependent carbohydrate-binding module xylan-bind


Domain annotation for each model (and alignments):
>> PCC_BT  Propionyl-coenzyme A carboxylase BT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0004       3.6       1      91 [.      13     112 ..      13     122 .. 0.82
   2 ?    1.5   0.0     0.039   3.5e+02      26      59 ..     334     367 ..     317     376 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0004
                            PCC_BT   1 LaAvAaavharrqaRarqisnqlrtkeakeekdwvvtvdgedetvtvkveeaadevevkvdgksvk.........vs 68 
                                       L+A+A+ +  + +  ++ is+ ++  + ++ +d    +d+++ +++ +v++ ++e+ ++vd++++k         ++
  gi|298674574|ref|YP_003726324.1|  13 LLAAAVSLSGCLDLSTTGISEPMPVRSVDYTEDNPGNIDNNYWRISTTVDGTGEEYVLEVDEEQLKdgdtqaqnsLR 89 
                                       56667777777777777777777777777777777788888999999*****************9888888888899 PP

                            PCC_BT  69 sdwklgqplirgtvdgesvtvqv 91 
                                         +++ qp +++++ + s  +q+
  gi|298674574|ref|YP_003726324.1|  90 LYFRPTQPYWDANCYEPSNKLQY 112
                                       9***********99887777777 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.039
                            PCC_BT  26 keakeekdwvvtvdgedetvtvkveeaadevevk 59 
                                       +++ ++ d v tv+ge ++++v+v+++++  +v+
  gi|298674574|ref|YP_003726324.1| 334 SPDINKLDSVTTVEGESVNFKVTVDNKGTGGDVE 367
                                       5555566778899999999999999887765554 PP

>> CBM60  Ca-dependent carbohydrate-binding module xylan-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1      0.67     6e+03      55      82 ..      40      65 ..      39      93 .. 0.64
   2 ?    5.1   0.0    0.0035        31      22      59 ..     153     196 ..     141     201 .. 0.81
   3 ?   -0.1   0.1      0.14   1.3e+03      13      48 ..     348     404 ..     342     408 .. 0.60
   4 ?    4.1   0.6    0.0071        63      10      55 ..     408     453 ..     399     460 .. 0.83
   5 ?    1.3   0.0     0.051   4.6e+02      36      64 ..     508     537 ..     474     541 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.67
                             CBM60 55 irylNDlyvgagqDRnLevdsitvngkt 82
                                      + y++D  ++  +D n    s tv+g+ 
  gi|298674574|ref|YP_003726324.1| 40 VDYTEDNPGN--IDNNYWRISTTVDGTG 65
                                      5666665444..6666555555555554 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0035
                             CBM60  22 vdGqkvg.....eadvasteaktytftadltag.ahklqirylN 59 
                                       +dG++v      ++  ++te+ t+t++a+ ++g  h++ i+  N
  gi|298674574|ref|YP_003726324.1| 153 ADGEEVAsgtvtNFATDDTESGTLTMEAEGPDGrDHTIYITLNN 196
                                       688888777766444599***************9****998665 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.14
                             CBM60  13 deppefrllvdGqkvg.....................eadvasteaktytftadlta 48 
                                       +e ++f++ vd +  g                     +  + s+e++ + ftad+++
  gi|298674574|ref|YP_003726324.1| 348 GESVNFKVTVDNKGTGgdveltavsdalknigtigdqKRYIPSGESESFMFTADVAD 404
                                       557788888888777766655555555555555555322355666666777766665 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.0071
                             CBM60  10 qagdeppefrllvdGqkvgeadvasteaktytftadltagahklqi 55 
                                        +g+e   +++++dG + g++  ++t+  ++ ++  +ta++ +l+i
  gi|298674574|ref|YP_003726324.1| 408 DYGEESFDVKVQADGGVSGQFGTTDTQTFELVVKSSDTAQKGTLKI 453
                                       67999999***********999788888888888888877777776 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.051
                             CBM60  36 eaktytftadltag.ahklqirylNDlyvg 64 
                                         ++  + +++++g  ++++i++++D  + 
  gi|298674574|ref|YP_003726324.1| 508 YTQEEPYLVTVEPGgMEEVTIKFAEDRPGS 537
                                       3344445567777779**********7655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (609 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.38
# Mc/sec: 4810.46
//
Query:       gi|298674575|ref|YP_003726325.1|  [L=53]
Description: hypothetical protein Metev_0623 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 404.84
//
Query:       gi|298674576|ref|YP_003726326.1|  [L=239]
Description: hypothetical protein Metev_0624 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        2.6    8.3   9.1       0.91    9.8   0.2    3.3  3  DUF2304   Uncharacterized conserved protein (DUF2304)
        3.3    8.1   9.8         94    3.4   9.8    2.5  1  CRCB      CrcB-like protein, Camphor Resistance (CrcB)


Domain annotation for each model (and alignments):
>> DUF2304  Uncharacterized conserved protein (DUF2304)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.2    0.0001      0.91      46      73 ..      35      62 ..      11      66 .. 0.92
   2 ?    1.9   0.8     0.028   2.5e+02      26      44 ..      81      99 ..      77     111 .. 0.76
   3 ?   -0.4   0.1      0.15   1.3e+03      54      70 ..     197     213 ..     190     227 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0001
                           DUF2304 46 lfpqiltvlanllGvgrgtnllfllgiv 73
                                      lfp+i++ l+n + ++ +++llfl++++
  gi|298674576|ref|YP_003726326.1| 35 LFPNIADTLTNTIDFYLPMTLLFLVVLL 62
                                      8**********************99875 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.028
                           DUF2304 26 lkleysllwlllalilivl 44
                                      l  +y++++++++++ ++l
  gi|298674576|ref|YP_003726326.1| 81 LVRNYAFWFIVFWIGTFLL 99
                                      5567888899999887665 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.15
                           DUF2304  54 lanllGvgrgtnllfll 70 
                                       la  lG+ + +  +f+l
  gi|298674576|ref|YP_003726326.1| 197 LAISLGFAYIAFTVFYL 213
                                       33344444443333333 PP

>> CRCB  CrcB-like protein, Camphor Resistance (CrcB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   9.8      0.01        94      24      92 ..     137     209 ..      17     218 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.01
                                       E......BHHHHHHHHHHHHHHHHHHHHHTTTHHHHHS-SHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHHHHH CS
                              CRCB  24 r......plgtlavNvlGsfllglllallttGflGglTTfStfvlelvslleegellaallyvllsvvlgllavv 92 
                                              p + +a N+ Gs ++  +++ +  G++ +l+ +S + +++   +++      ++++++s+ ++++a++
  gi|298674576|ref|YP_003726326.1| 137 LalvmvaP-ALFAFNLGGSGVVSKIIEYVPAGVVAALSHVSVYWTQTQLQIQKT-GGDPVTNLAISLGFAYIAFT 209
                                       13444445.7899999999999999999**************999988777443.35555677777766665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1926.80
//
Query:       gi|298674577|ref|YP_003726327.1|  [L=392]
Description: hypothetical protein Metev_0625 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 3014.07
//
Query:       gi|298674578|ref|YP_003726328.1|  [L=442]
Description: FG-GAP repeat-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    9.3e-68  224.7  64.9    1.6e-14   54.2   2.4    7.1  7  VCBS        Repeat domain in Vibrio, Colwellia, Bradyrhizobiu
    3.6e-28   97.3  23.8     0.0005   20.1   0.0    7.5  7  FG-GAP      FG-GAP repeat
    7.2e-07   28.3  21.7       0.42   10.3   0.0    8.3  9  EF-hand_1   EF hand
    1.4e-05   25.1   5.5         10    6.2   0.0    6.2  7  BBS2_Mid    Ciliary BBSome complex subunit 2, middle region
    7.7e-05   22.0  28.8        1.6    8.4   0.1    7.9  8  EF-hand_5   EF hand
    0.00023   20.9   6.1        6.2    6.6   0.1    5.9  7  PliI        Periplasmic lysozyme inhibitor of I-type lysozyme
  ------ inclusion threshold ------
      0.013   16.0   0.6        7.7    7.1   0.0    3.5  3  Phage_pRha  Phage regulatory protein Rha (Phage_pRha)
      0.095   12.5   6.6        1.4    8.8   0.1    4.0  4  DUF1391     Protein of unknown function (DUF1391)
        2.7    6.7   6.4        8.9    5.0   0.9    2.6  2  LptF_LptG   Lipopolysaccharide export system permease LptF/Lp


Domain annotation for each model (and alignments):
>> VCBS  Repeat domain in Vibrio, Colwellia, Bradyrhizobium and Shewanella
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.2   1.9e-07   0.00038      17      60 ..      89     138 ..      80     139 .. 0.72
   2 !   47.6   3.5   9.6e-16   1.9e-12       1      61 []     128     187 ..     128     187 .. 0.83
   3 !   54.2   2.4   7.9e-18   1.6e-14       1      61 []     176     234 ..     176     234 .. 0.88
   4 !   47.7   3.3   8.8e-16   1.8e-12       1      60 [.     223     282 ..     223     283 .. 0.84
   5 !   47.2   6.0   1.2e-15   2.4e-12       1      61 []     272     331 ..     272     331 .. 0.92
   6 !   39.4   1.9   3.4e-13   6.7e-10       1      60 [.     320     378 ..     320     379 .. 0.85
   7 !   46.7   4.1   1.8e-15   3.7e-12       1      61 []     368     427 ..     368     427 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.9e-07
                              VCBS  17 glrvyrnngdGtftdvtkt.....slggsgggt.gvavgDlDgDGdlDll 60 
                                       ++++ + +g G +++ t +     +++++++ t ++ v+D+++DG+lD++
  gi|298674578|ref|YP_003726328.1|  89 TVNLEEKSGGGGWSEKTLIftnahEIHSYNNDTkSMKVADMNNDGHLDVI 138
                                       56666667778777666643333377777777769*************98 PP

  == domain 2  score: 47.6 bits;  conditional E-value: 9.6e-16
                              VCBS   1 DldgDGrlDlvvandgglrv.yrnngdGtftdvtktslggsgggtgvavgDlDgDGdlDllv 61 
                                       D+++DG+lD++++n+g++   y+nn dGtft   ++ +++  +++++a+ Dl++DG+lD+++
  gi|298674578|ref|YP_003726328.1| 128 DMNNDGHLDVIAGNNGQIDCwYENNSDGTFTA-HEININSE-WANSIAIYDLNNDGYLDIIC 187
                                       9*************999555388999****84.45555554.7779**************86 PP

  == domain 3  score: 54.2 bits;  conditional E-value: 7.9e-18
                              VCBS   1 DldgDGrlDlvvandgglrvyrnngdGtftdvtktslgg.sgggtgvavgDlDgDGdlDllv 61 
                                       Dl++DG+lD+++++ g + +y+nngdGtft+   +++++   +  ++ v+D++ DG++D++v
  gi|298674578|ref|YP_003726328.1| 176 DLNNDGYLDIICGTGGVNSWYENNGDGTFTP---HDIHShEKDTQAIKVADMNKDGHPDIIV 234
                                       9****************************96...344442556779**************98 PP

  == domain 4  score: 47.7 bits;  conditional E-value: 8.8e-16
                              VCBS   1 DldgDGrlDlvvan.d.gglrvyrnngdGtftdvtktslgg.sgggtgvavgDlDgDGdlDll 60 
                                       D++ DG++D++v+n    ++++y+nn dGtft    ++++  + + +++ ++Dl++DG+lD++
  gi|298674578|ref|YP_003726328.1| 223 DMNKDGHPDIIVGNaFeYKNYWYENNSDGTFTA---HEIHNnAKNTYAIELADLNNDGYLDYI 282
                                       9************864488************84...445552556779*************98 PP

  == domain 5  score: 47.2 bits;  conditional E-value: 1.2e-15
                              VCBS   1 DldgDGrlDlvvandgglrvyrnngdGtftdvtktslggsgggt.gvavgDlDgDGdlDllv 61 
                                       Dl++DG+lD++++n + +++y+n+gd+  t+ t+++++++ ++t +v+v+D++gD + D+l+
  gi|298674578|ref|YP_003726328.1| 272 DLNNDGYLDYIAGNGNENYWYENSGDN--TKFTAHEIHTNPDWTkSVDVADMNGDNRIDILI 331
                                       9***********************987..57789999998888879**************85 PP

  == domain 6  score: 39.4 bits;  conditional E-value: 3.4e-13
                              VCBS   1 DldgDGrlDlvvan.dgglrvyrnngdGtftdvtktslgg.sgggtgvavgDlDgDGdlDll 60 
                                       D++gD r D++++n   ++ +y+n+gd tf +   +++++ s + +++ v D+++DG+lD++
  gi|298674578|ref|YP_003726328.1| 320 DMNGDNRIDILIGNsGYKNCWYENSGDDTFHE---HEIHSkSEYTRSLKVNDINNDGHLDVI 378
                                       9************95577999*********97...44555355678**************97 PP

  == domain 7  score: 46.7 bits;  conditional E-value: 1.8e-15
                              VCBS   1 DldgDGrlDlvva.ndgglrvyrnngdGtftdvtktslggsgggtgvavgDlDgDGdlDllv 61 
                                       D+++DG+lD++ + n++++++y+nng++tft     + +   + +++ v D+++DG  D++v
  gi|298674578|ref|YP_003726328.1| 368 DINNDGHLDVITGvNNDSNYFYENNGNNTFTAHK--MHSNKKRTYSIEVIDFNNDGIKDIIV 427
                                       9***********9679*************98543..333356677***************98 PP

>> FG-GAP  FG-GAP repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2     5e-06      0.01       7      28 ..     126     143 ..     123     155 .. 0.89
   2 !   18.2   0.7   9.9e-07     0.002       3      27 ..     170     193 ..     168     204 .. 0.75
   3 !   20.1   0.0   2.5e-07    0.0005       7      27 ..     221     242 ..     217     251 .. 0.78
   4 !   11.0   0.2   0.00018      0.37       3      21 ..     266     284 ..     264     296 .. 0.80
   5 !   14.4   0.0   1.5e-05      0.03       4      29 ..     315     336 ..     312     344 .. 0.85
   6 !   15.7   0.4     6e-06     0.012       9      30 ..     368     390 ..     361     396 .. 0.71
   7 !   13.3   0.1   3.4e-05     0.067       3      21 ..     410     428 ..     409     437 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5e-06
                                       EESTSSSSS-EEEEEETT-ETC CS
                            FG-GAP   7 vgDvNGDGyaDLavGApeskgg 28 
                                       v+D+N+DG+ D++ G    ++g
  gi|298674578|ref|YP_003726328.1| 126 VADMNNDGHLDVIAG----NNG 143
                                       89*************....776 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 9.9e-07
                                       SSEEEESTSSSSS-EEEEEETT-ET CS
                            FG-GAP   3 yslavgDvNGDGyaDLavGApeskg 27 
                                       +s+a  D+N+DGy D++ G ++  +
  gi|298674578|ref|YP_003726328.1| 170 NSIAIYDLNNDGYLDIICGTGG-VN 193
                                       79999**************633.33 PP

  == domain 3  score: 20.1 bits;  conditional E-value: 2.5e-07
                                       EESTSSSSS-EEEEEE.TT-ET CS
                            FG-GAP   7 vgDvNGDGyaDLavGA.peskg 27 
                                       v+D+N DG++D++vG  +e+k+
  gi|298674578|ref|YP_003726328.1| 221 VADMNKDGHPDIIVGNaFEYKN 242
                                       9**************5444454 PP

  == domain 4  score: 11.0 bits;  conditional E-value: 0.00018
                                       SSEEEESTSSSSS-EEEEE CS
                            FG-GAP   3 yslavgDvNGDGyaDLavG 21 
                                       y++ ++D+N+DGy D + G
  gi|298674578|ref|YP_003726328.1| 266 YAIELADLNNDGYLDYIAG 284
                                       78889*********96666 PP

  == domain 5  score: 14.4 bits;  conditional E-value: 1.5e-05
                                       SEEEESTSSSSS-EEEEEETT-ETCS CS
                            FG-GAP   4 slavgDvNGDGyaDLavGApeskgga 29 
                                       s+ v+D+NGD   D+++G    + g+
  gi|298674578|ref|YP_003726328.1| 315 SVDVADMNGDNRIDILIG----NSGY 336
                                       899***************....4443 PP

  == domain 6  score: 15.7 bits;  conditional E-value: 6e-06
                                       STSSSSS-EEEEEE.TT-ETCST CS
                            FG-GAP   9 DvNGDGyaDLavGA.peskggay 30 
                                       D+N+DG+ D+++G  + s++++ 
  gi|298674578|ref|YP_003726328.1| 368 DINNDGHLDVITGVnNDSNYFYE 390
                                       *************8622444433 PP

  == domain 7  score: 13.3 bits;  conditional E-value: 3.4e-05
                                       SSEEEESTSSSSS-EEEEE CS
                            FG-GAP   3 yslavgDvNGDGyaDLavG 21 
                                       ys+ v D+N+DG  D++vG
  gi|298674578|ref|YP_003726328.1| 410 YSIEVIDFNNDGIKDIIVG 428
                                       899999************* PP

>> EF-hand_1  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.1    0.0029       5.8       5      18 ..     123     136 ..     121     137 .. 0.88
   2 !   10.0   0.0   0.00025       0.5       3      18 ..     169     184 ..     167     185 .. 0.84
   3 ?   -2.1   0.1       1.9   3.8e+03      12      20 ..     199     207 ..     198     210 .. 0.79
   4 ?    3.6   0.0     0.028        56       4      16 ..     217     229 ..     216     229 .. 0.89
   5 ?   -3.6   0.0       5.7   1.1e+04      12      21 ..     248     257 ..     247     258 .. 0.82
   6 !   10.3   0.0   0.00021      0.42       5      19 ..     267     281 ..     266     281 .. 0.92
   7 ?    2.5   0.4     0.064   1.3e+02       7      18 ..     317     328 ..     311     329 .. 0.84
   8 ?    2.9   0.1      0.05        99       9      18 ..     367     376 ..     360     377 .. 0.85
   9 ?    0.8   0.0      0.23   4.5e+02       6      15 ..     412     421 ..     410     422 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0029
                                       HHHHHTTTSSSEEE CS
                         EF-hand_1   5 iFrefDkDgdGkId 18 
                                        ++++D ++dG++d
  gi|298674578|ref|YP_003726328.1| 123 SMKVADMNNDGHLD 136
                                       5899********98 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00025
                                       HHHHHHHTTTSSSEEE CS
                         EF-hand_1   3 keiFrefDkDgdGkId 18 
                                        + ++++D ++dG++d
  gi|298674578|ref|YP_003726328.1| 169 ANSIAIYDLNNDGYLD 184
                                       567899*********9 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.9
                                       TSSSEEEHH CS
                         EF-hand_1  12 DgdGkIdfe 20 
                                       +gdG+ +  
  gi|298674578|ref|YP_003726328.1| 199 NGDGTFTPH 207
                                       9***98765 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.028
                                       HHHHHHTTTSSSE CS
                         EF-hand_1   4 eiFrefDkDgdGk 16 
                                       ++++++D ++dG+
  gi|298674578|ref|YP_003726328.1| 217 QAIKVADMNKDGH 229
                                       689*********5 PP

  == domain 5  score: -3.6 bits;  conditional E-value: 5.7
                                       TSSSEEEHHH CS
                         EF-hand_1  12 DgdGkIdfeE 21 
                                       + dG+ +  E
  gi|298674578|ref|YP_003726328.1| 248 NSDGTFTAHE 257
                                       789*999887 PP

  == domain 6  score: 10.3 bits;  conditional E-value: 0.00021
                                       HHHHHTTTSSSEEEH CS
                         EF-hand_1   5 iFrefDkDgdGkIdf 19 
                                       +++++D ++dG++d+
  gi|298674578|ref|YP_003726328.1| 267 AIELADLNNDGYLDY 281
                                       789**********97 PP

  == domain 7  score: 2.5 bits;  conditional E-value: 0.064
                                       HHHTTTSSSEEE CS
                         EF-hand_1   7 refDkDgdGkId 18 
                                       +++D +gd +Id
  gi|298674578|ref|YP_003726328.1| 317 DVADMNGDNRID 328
                                       689********9 PP

  == domain 8  score: 2.9 bits;  conditional E-value: 0.05
                                       HTTTSSSEEE CS
                         EF-hand_1   9 fDkDgdGkId 18 
                                        D ++dG++d
  gi|298674578|ref|YP_003726328.1| 367 NDINNDGHLD 376
                                       59******98 PP

  == domain 9  score: 0.8 bits;  conditional E-value: 0.23
                                       HHHHTTTSSS CS
                         EF-hand_1   6 FrefDkDgdG 15 
                                       ++++D ++dG
  gi|298674578|ref|YP_003726328.1| 412 IEVIDFNNDG 421
                                       6789*****9 PP

>> BBS2_Mid  Ciliary BBSome complex subunit 2, middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.025        51      78     107 ..     119     147 ..     107     148 .. 0.76
   2 ?    2.5   0.0     0.074   1.5e+02      81     100 ..     170     189 ..     161     193 .. 0.77
   3 ?    3.3   0.0     0.041        81      80      99 ..     216     235 ..     208     240 .. 0.74
   4 ?   -1.6   0.0       1.4   2.7e+03      79      99 ..     264     284 ..     255     289 .. 0.71
   5 ?   -0.2   0.0      0.51     1e+03       2      28 ..     316     342 ..     315     357 .. 0.71
   6 ?    4.5   0.0     0.018        35      74     102 ..     354     383 ..     346     387 .. 0.84
   7 !    6.2   0.0    0.0052        10      75     100 ..     404     429 ..     396     434 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.025
                          BBS2_Mid  78 nevvalaaydingdgtkelivgwsnGkldv 107
                                       n   ++++ d+n+dg+ ++i g +nG++d+
  gi|298674578|ref|YP_003726328.1| 119 NDTKSMKVADMNNDGHLDVIAG-NNGQIDC 147
                                       4466788899999999999988.5888885 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.074
                          BBS2_Mid  81 valaaydingdgtkelivgw 100
                                        ++a yd+n+dg+ ++i+g 
  gi|298674578|ref|YP_003726328.1| 170 NSIAIYDLNNDGYLDIICGT 189
                                       56788888888888888874 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.041
                          BBS2_Mid  80 vvalaaydingdgtkelivg 99 
                                         a+++ d+n+dg+ ++ivg
  gi|298674578|ref|YP_003726328.1| 216 TQAIKVADMNKDGHPDIIVG 235
                                       56777888888888888888 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 1.4
                          BBS2_Mid  79 evvalaaydingdgtkelivg 99 
                                       +  a+ + d+n+dg+ + i g
  gi|298674578|ref|YP_003726328.1| 264 NTYAIELADLNNDGYLDYIAG 284
                                       456777788888888777776 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 0.51
                          BBS2_Mid   2 laladvdgdgeneLvvgsddfeirvfk 28 
                                       + +ad++gd++ ++++g   ++   ++
  gi|298674578|ref|YP_003726328.1| 316 VDVADMNGDNRIDILIGNSGYKNCWYE 342
                                       568999999999999998887766655 PP

  == domain 6  score: 4.5 bits;  conditional E-value: 0.018
                          BBS2_Mid  74 vkskne.vvalaaydingdgtkelivgwsn 102
                                       + sk+e   +l+++din+dg+ ++i+g +n
  gi|298674578|ref|YP_003726328.1| 354 IHSKSEyTRSLKVNDINNDGHLDVITGVNN 383
                                       677887456899**************9876 PP

  == domain 7  score: 6.2 bits;  conditional E-value: 0.0052
                          BBS2_Mid  75 ksknevvalaaydingdgtkelivgw 100
                                       ++k++  ++ ++d+n+dg k++ivg 
  gi|298674578|ref|YP_003726328.1| 404 SNKKRTYSIEVIDFNNDGIKDIIVGN 429
                                       45667888888888888888888884 PP

>> EF-hand_5  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.1   0.00078       1.6       5      17 ..     124     136 ..     122     137 .. 0.85
   2 !    5.7   0.1    0.0057        11       8      17 ..     175     184 ..     171     185 .. 0.88
   3 ?   -3.0   0.8       3.1   6.2e+03      11      15 ..     199     203 ..     198     203 .. 0.87
   4 !    5.2   0.0     0.008        16       5      15 ..     219     229 ..     216     229 .. 0.84
   5 !    6.9   0.0    0.0024       4.7       6      17 ..     269     280 ..     266     281 .. 0.86
   6 !    7.1   1.0     0.002         4       7      18 ..     318     329 ..     317     330 .. 0.88
   7 ?    2.3   0.5     0.065   1.3e+02       9      17 ..     368     376 ..     365     377 .. 0.91
   8 ?    1.5   0.1      0.12   2.4e+02       6      14 ..     413     421 ..     411     422 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00078
                                       HHHH-SS-SSCE- CS
                         EF-hand_5   5 FqaiDlNgDGkIs 17 
                                        + +D+N+DG+++
  gi|298674578|ref|YP_003726328.1| 124 MKVADMNNDGHLD 136
                                       5789*******98 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0057
                                       H-SS-SSCE- CS
                         EF-hand_5   8 iDlNgDGkIs 17 
                                        DlN+DG+++
  gi|298674578|ref|YP_003726328.1| 175 YDLNNDGYLD 184
                                       6*******98 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 3.1
                                       S-SSC CS
                         EF-hand_5  11 NgDGk 15 
                                       NgDG+
  gi|298674578|ref|YP_003726328.1| 199 NGDGT 203
                                       9***6 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.008
                                       HHHH-SS-SSC CS
                         EF-hand_5   5 FqaiDlNgDGk 15 
                                        + +D+N+DG+
  gi|298674578|ref|YP_003726328.1| 219 IKVADMNKDGH 229
                                       6789******5 PP

  == domain 5  score: 6.9 bits;  conditional E-value: 0.0024
                                       HHH-SS-SSCE- CS
                         EF-hand_5   6 qaiDlNgDGkIs 17 
                                       + +DlN+DG+++
  gi|298674578|ref|YP_003726328.1| 269 ELADLNNDGYLD 280
                                       679******998 PP

  == domain 6  score: 7.1 bits;  conditional E-value: 0.002
                                       HH-SS-SSCE-H CS
                         EF-hand_5   7 aiDlNgDGkIsk 18 
                                        +D+NgD +I++
  gi|298674578|ref|YP_003726328.1| 318 VADMNGDNRIDI 329
                                       68********95 PP

  == domain 7  score: 2.3 bits;  conditional E-value: 0.065
                                       -SS-SSCE- CS
                         EF-hand_5   9 DlNgDGkIs 17 
                                       D N+DG+++
  gi|298674578|ref|YP_003726328.1| 368 DINNDGHLD 376
                                       99*****98 PP

  == domain 8  score: 1.5 bits;  conditional E-value: 0.12
                                       HHH-SS-SS CS
                         EF-hand_5   6 qaiDlNgDG 14 
                                       + iD N+DG
  gi|298674578|ref|YP_003726328.1| 413 EVIDFNNDG 421
                                       679****** PP

>> PliI  Periplasmic lysozyme inhibitor of I-type lysozyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.17   3.3e+02      51      76 ..     113     138 ..     102     144 .. 0.83
   2 ?   -2.1   0.0       1.5   3.1e+03      61      77 ..     171     187 ..     149     195 .. 0.71
   3 !    6.6   0.1    0.0031       6.2      50      78 ..     207     235 ..     171     239 .. 0.84
   4 ?   -1.1   0.0      0.77   1.5e+03      48      73 ..     254     279 ..     240     285 .. 0.67
   5 ?    2.7   0.0     0.051     1e+02      43      77 ..     297     331 ..     290     336 .. 0.82
   6 ?    2.8   0.0     0.046        91      45      77 ..     347     379 ..     335     388 .. 0.84
   7 ?    4.4   0.1     0.015        30      45      78 ..     395     428 ..     386     433 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.17
                                       EEEEESSEEEEEEEE-SSSSSS-EEE CS
                              PliI  51 lvlsRdGsveevkladvngdkkkelv 76 
                                       +++s +   +++k+ad+n+d++ +++
  gi|298674578|ref|YP_003726328.1| 113 EIHSYNNDTKSMKVADMNNDGHLDVI 138
                                       577777888899*********99988 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.5
                                       EEEEE-SSSSSS-EEEE CS
                              PliI  61 evkladvngdkkkelvv 77 
                                       ++ + d+n+d+  +++ 
  gi|298674578|ref|YP_003726328.1| 171 SIAIYDLNNDGYLDIIC 187
                                       47788888888888875 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0031
                                       EEEEEESSEEEEEEEE-SSSSSS-EEEEE CS
                              PliI  50 GlvlsRdGsveevkladvngdkkkelvvl 78 
                                         ++s +   + +k+ad+n d++++++v 
  gi|298674578|ref|YP_003726328.1| 207 HDIHSHEKDTQAIKVADMNKDGHPDIIVG 235
                                       456666667777***************95 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 0.77
                                       EEEEEEEESSEEEEEEEE-SSSSSS- CS
                              PliI  48 vaGlvlsRdGsveevkladvngdkkk 73 
                                        a +++        ++lad+n+d+  
  gi|298674578|ref|YP_003726328.1| 254 TAHEIHNNAKNTYAIELADLNNDGYL 279
                                       44555555555566899999999765 PP

  == domain 5  score: 2.7 bits;  conditional E-value: 0.051
                                       TTSSEEEEEEEEESSEEEEEEEE-SSSSSS-EEEE CS
                              PliI  43 dldefvaGlvlsRdGsveevkladvngdkkkelvv 77 
                                       d ++f a ++++     ++v +ad+ngd++ ++++
  gi|298674578|ref|YP_003726328.1| 297 DNTKFTAHEIHTNPDWTKSVDVADMNGDNRIDILI 331
                                       445788999999999999***********999876 PP

  == domain 6  score: 2.8 bits;  conditional E-value: 0.046
                                       SSEEEEEEEEESSEEEEEEEE-SSSSSS-EEEE CS
                              PliI  45 defvaGlvlsRdGsveevkladvngdkkkelvv 77 
                                       d f + +++s+     ++k+ d+n+d++ +++ 
  gi|298674578|ref|YP_003726328.1| 347 DTFHEHEIHSKSEYTRSLKVNDINNDGHLDVIT 379
                                       458888999999999*************99985 PP

  == domain 7  score: 4.4 bits;  conditional E-value: 0.015
                                       SSEEEEEEEEESSEEEEEEEE-SSSSSS-EEEEE CS
                              PliI  45 defvaGlvlsRdGsveevkladvngdkkkelvvl 78 
                                       + f a +++s      +++++d n+d+ k+++v 
  gi|298674578|ref|YP_003726328.1| 395 NTFTAHKMHSNKKRTYSIEVIDFNNDGIKDIIVG 428
                                       45888889999999999***************95 PP

>> Phage_pRha  Phage regulatory protein Rha (Phage_pRha)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0039       7.7       1      63 [.     121     185 ..     121     239 .. 0.85
   2 ?   -0.7   0.0       1.1   2.2e+03       4      59 ..     219     277 ..     216     289 .. 0.60
   3 ?    4.7   0.1     0.022        44       2      69 ..     314     383 ..     313     428 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0039
                        Phage_pRha   1 tsSleiAelfgkrHknVlrdIrkliedleefgke..lnfe..eseykdsngretkvylltrdgftll 63 
                                       t+S+++A++ +  H +V+   +  i+ + e++++  +     e +   +  +++ +y+l+ dg   +
  gi|298674578|ref|YP_003726328.1| 121 TKSMKVADMNNDGHLDVIAGNNGQIDCWYENNSDgtF--TahEININSEWANSIAIYDLNNDGYLDI 185
                                       68*****************999999999999999653..3325555555558999999999997655 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.1
                        Phage_pRha   4 leiAelfgkrHknVlr.dIrkliedleefgke..lnfe..eseykdsngretkvylltrdg 59 
                                       +++A++ +  H +++  +  ++++++ e++++  +     e ++  +n+  ++ ++l+ dg
  gi|298674578|ref|YP_003726328.1| 219 IKVADMNKDGHPDIIVgNAFEYKNYWYENNSDgtF--TahEIHNNAKNTYAIELADLNNDG 277
                                       56777777777666654555666667777766432..322444444444566667777666 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.022
                        Phage_pRha   2 sSleiAelfgkrHknVlrdIrkliedleefgkelnfe..eseykdsngretkvylltrdgftllvmgftg 69 
                                       +S ++A++ g +  ++l     +++ + e++ +  f+  e ++k + +r+ kv +++ dg   +++g ++
  gi|298674578|ref|YP_003726328.1| 314 KSVDVADMNGDNRIDILIGNSGYKNCWYENSGDDTFHehEIHSKSEYTRSLKVNDINNDGHLDVITGVNN 383
                                       6888888888888888888888888888877774444335555555567888888888887777777764 PP

>> DUF1391  Protein of unknown function (DUF1391)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1    0.0007       1.4       6      25 ..     140     159 ..     135     163 .. 0.91
   2 ?    0.4   0.0      0.29   5.7e+02      18      24 ..     199     205 ..     177     209 .. 0.87
   3 ?    3.4   0.0     0.033        67      18      25 ..     248     255 ..     245     265 .. 0.88
   4 ?   -1.1   0.1      0.85   1.7e+03      18      35 ..     392     411 ..     387     414 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0007
                           DUF1391   6 GnnesLvCGvfPnqDGtfta 25 
                                       Gnn  + C    n DGtfta
  gi|298674578|ref|YP_003726328.1| 140 GNNGQIDCWYENNSDGTFTA 159
                                       9******************9 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.29
                           DUF1391  18 nqDGtft 24 
                                       n DGtft
  gi|298674578|ref|YP_003726328.1| 199 NGDGTFT 205
                                       88****9 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.033
                           DUF1391  18 nqDGtfta 25 
                                       n DGtfta
  gi|298674578|ref|YP_003726328.1| 248 NSDGTFTA 255
                                       89*****9 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 0.85
                           DUF1391  18 nqDGtfta..mtytksktfk 35 
                                       n + tfta  m   k +t+ 
  gi|298674578|ref|YP_003726328.1| 392 NGNNTFTAhkMHSNKKRTYS 411
                                       56779999556667777776 PP

>> LptF_LptG  Lipopolysaccharide export system permease LptF/LptG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.5    0.0068        14     144     216 ..     147     227 ..      85     309 .. 0.82
   2 ?    5.0   0.9    0.0044       8.9     141     185 ..     384     427 ..     358     434 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0068
                         LptF_LptG 144 vfikdgdgyiiyvgsmddeggelqdvtiydltegkgltsiitAksgv..lvksadelqlrLfngeiyevgddek... 215
                                        +++++ + ++ + +++ + ++ + + iydl +++g+ +ii    gv  +++++++ +++ ++ +++e + +     
  gi|298674578|ref|YP_003726328.1| 147 CWYENNSDGTFTAHEININSEWANSIAIYDL-NNDGYLDIICGTGGVnsWYENNGDGTFTPHDIHSHEKDTQAIkva 222
                                       589999999**********************.888999999888886447777779999999999988755433555 PP

                         LptF_LptG 216 ....k 216
                                            
  gi|298674578|ref|YP_003726328.1| 223 dmnkD 227
                                       44440 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0044
                         LptF_LptG 141 kpgvfikdgdgyiiyvgsmddeggelqdvtiydltegkgltsiit 185
                                       +++ f++++ ++++ + +m +++++   + ++d+ +++g+++ii+
  gi|298674578|ref|YP_003726328.1| 384 DSNYFYENNGNNTFTAHKMHSNKKRTYSIEVIDF-NNDGIKDIIV 427
                                       6799******************************.8989999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2963.46
//
Query:       gi|298674579|ref|YP_003726329.1|  [L=197]
Description: hypothetical protein Metev_0627 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-16   61.4   3.0    5.5e-16   59.2   1.2    2.1  2  Pilin_N   Archaeal Type IV pilin, N-terminal
      0.003   18.0   0.0     0.0039   17.6   0.0    1.2  1  DUF4198   Domain of unknown function (DUF4198)
     0.0068   16.4   0.1      0.013   15.5   0.0    1.7  2  SL4P      Uncharacterized Strongylid L4 protein
  ------ inclusion threshold ------
      0.062   13.0   0.0       0.22   11.2   0.0    1.9  2  DUF3481   C-terminal domain of neuropilin glycoprotein
      0.085   12.8   0.1       0.56   10.2   0.1    2.0  2  DUF3290   Protein of unknown function (DUF3290)


Domain annotation for each model (and alignments):
>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.2   1.2   1.5e-19   5.5e-16       1      70 [.      14      89 ..      14      96 .. 0.85
   2 ?    1.7   0.0      0.14     5e+02      52      71 ..     130     149 ..     103     155 .. 0.68

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 1.5e-19
                           Pilin_N  1 eAVSpViGviLmvaitvIlaAviaafvlgl.asneekapqasievkidssastgkna.....vslehkgGdsidtk 70
                                      ++VSpViGviLmvaitvIlaAvi+++v  +  +  ek  qa++e+++ ++   ++++     +++++  Gd+++++
  gi|298674579|ref|YP_003726329.1| 14 KGVSPVIGVILMVAITVILAAVIGSIVYDTdTKYLEKPSQAAFETSTVNGIHRDTEEmtvpvIKINKVAGDTLSQE 89
                                      59****************************6667777788***9996666655555567899**********9875 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.14
                           Pilin_N  52 tgknavslehkgGdsidtkd 71 
                                       ++ + + +eh++G+   t++
  gi|298674579|ref|YP_003726329.1| 130 ESFYIFHFEHDDGNYWMTNN 149
                                       2234499******9877754 PP

>> DUF4198  Domain of unknown function (DUF4198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.1e-06    0.0039      31      94 ..      89     165 ..      67     188 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.1e-06
                           DUF4198  31 pfead.heplkleklkvlapdg.........ektdlg.....kylstfdvallkpekegtyklaaakk...pgdwke 89 
                                       ++e++ h  +kl+k+++++pdg         +          ++++ f + +++ ++ g y ++  kk    +dw++
  gi|298674579|ref|YP_003726329.1|  89 EYEEGvHSGIKLNKVYLFDPDGnkyevnnsdT----MegsiiETGESFYIFHFEHDD-GNYWMTNNKKrvkKADWEF 160
                                       4555579999************8887744442....3556669*********99887.666666633347799**** PP

                           DUF4198  90 ygdpk 94 
                                        g+p+
  gi|298674579|ref|YP_003726329.1| 161 EGQPR 165
                                       99999 PP

>> SL4P  Uncharacterized Strongylid L4 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   3.6e-06     0.013      40      79 ..      96     136 ..      66     153 .. 0.84
   2 ?   -3.6   0.0       3.5   1.2e+04      49      60 ..     181     192 ..     178     195 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.6e-06
                              SL4P  40 lgipldevywvdedgdrilirnaddLl.eavkdnavvklyv 79 
                                        gi+l++vy  d dg++++++n d++  ++++  ++ +++ 
  gi|298674579|ref|YP_003726329.1|  96 SGIKLNKVYLFDPDGNKYEVNNSDTMEgSIIETGESFYIFH 136
                                       699**********************9966666666666655 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3.5
                              SL4P  49 wvdedgdrilir 60 
                                        vd+++d il++
  gi|298674579|ref|YP_003726329.1| 181 IVDDKRDLILVD 192
                                       567777777766 PP

>> DUF3481  C-terminal domain of neuropilin glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   6.2e-05      0.22      17      42 ..      19      44 ..       4      72 .. 0.81
   2 ?   -1.4   0.0      0.53   1.9e+03      58      72 ..      90     104 ..      83     111 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.2e-05
                           DUF3481 17 litiiamsalGvllGaicGvvlycac 42
                                      +i +i m a+ v+l a+ G ++y + 
  gi|298674579|ref|YP_003726329.1| 19 VIGVILMVAITVILAAVIGSIVYDTD 44
                                      4899******************9765 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.53
                           DUF3481  58 ynfelvdGvklkkek 72 
                                       y+  +  G+kl+k+ 
  gi|298674579|ref|YP_003726329.1|  90 YEEGVHSGIKLNKVY 104
                                       66667789**99975 PP

>> DUF3290  Protein of unknown function (DUF3290)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.15   5.4e+02      20      34 ..      22      36 ..       4      74 .. 0.68
   2 ?   10.2   0.1   0.00016      0.56     100     134 ..     114     148 ..     108     156 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.15
                           DUF3290 20 yililvlllllivvl 34
                                      +il++++ ++l++v+
  gi|298674579|ref|YP_003726329.1| 22 VILMVAITVILAAVI 36
                                      444444444333322 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00016
                           DUF3290 100 lvnstslkdglivkidkkyYrvtlnsdnnsYtlek 134
                                        vn++   +g i+++ +++Y  ++++d  +Y +++
  gi|298674579|ref|YP_003726329.1| 114 EVNNSDTMEGSIIETGESFYIFHFEHDDGNYWMTN 148
                                       589999*************************8875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       939  (0.0523733); expected 358.6 (0.02)
Passed bias filter:                      711  (0.0396564); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1180.76
//
Query:       gi|298674580|ref|YP_003726330.1|  [L=164]
Description: hypothetical protein Metev_0628 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0089   15.3   0.0      0.011   15.0   0.0    1.1  1  LYTB           LytB protein
  ------ inclusion threshold ------
      0.015   16.2   0.9      0.095   13.6   0.7    2.3  1  Pilin_N        Archaeal Type IV pilin, N-terminal
       0.15   11.9   2.3       0.12   12.2   1.0    1.5  1  Inhibitor_I71  Falstatin, cysteine peptidase inhibitor


Domain annotation for each model (and alignments):
>> LYTB  LytB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.9e-06     0.011     174     235 ..      29      90 ..      15     110 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.9e-06
                                       C-S--CHHHHHHHHHHHHHGHSSEEEEES-TT-HHHHHHHHHHHHCSCTEEEESSGGG--HH CS
                              LYTB 174 kdtiCkatqeRqeavkelakevdlvivvGgknSsNtkkLveiakeknkktyliesaeeldee 235
                                       +d+  ++t ++qe+   + k++  + +vGg++S N++k++++ ++ + k+ +++ ++ ++ +
  gi|298674580|ref|YP_003726330.1|  29 SDDTTNQTDDNQEQSDGIPKQAPQLSIVGGSESINGNKIIKLEHRGGDKVTFVKGETTVEVN 90 
                                       6777799**********************************************999988754 PP

>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.7   1.6e-05     0.095      33      77 ..      46      90 ..       5     100 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.6e-05
                           Pilin_N 33 neekapqasievkidssastgkna.vslehkgGdsidt..kdlkivln 77
                                       +++apq si   ++ s+s ++n+ ++leh gGd ++    ++++ +n
  gi|298674580|ref|YP_003726330.1| 46 IPKQAPQLSI---VGGSESINGNKiIKLEHRGGDKVTFvkGETTVEVN 90
                                      5678899999...444444433446**********9985545555444 PP

>> Inhibitor_I71  Falstatin, cysteine peptidase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.0     2e-05      0.12     101     141 ..      26      70 ..      18      81 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2e-05
                     Inhibitor_I71 101 skdvdeekesggqnesdsnkfkk..PkeqlvGGssmlr..svika 141
                                       ++d+d+  +++++n+++s+  +k  P+  +vGGs+ ++   +ik 
  gi|298674580|ref|YP_003726330.1|  26 ENDSDDTTNQTDDNQEQSDGIPKqaPQLSIVGGSESINgnKIIKL 70 
                                       344444444455555555544442289999*****9962246664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1040  (0.0580066); expected 358.6 (0.02)
Passed bias filter:                      703  (0.0392102); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.35s 00:00:00.91 Elapsed: 00:00:00.53
# Mc/sec: 935.38
//
Query:       gi|298674581|ref|YP_003726331.1|  [L=86]
Description: hypothetical protein Metev_0629 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0076   14.9   0.1     0.0091   14.7   0.1    1.0  1  H_PPase   Inorganic H+ pyrophosphatase
  ------ inclusion threshold ------
       0.02   14.2   0.7        2.2    7.5   0.1    2.2  2  PorA      Porin PorA
        9.3    6.5   9.6        8.4    6.6   0.6    2.3  2  DUF350    Domain of Unknown Function (DUF350)


Domain annotation for each model (and alignments):
>> H_PPase  Inorganic H+ pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   1.5e-06    0.0091     448     492 ..       6      73 ..       3      80 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.5e-06
                                       HHHHHHHHHHHHHHHHHHHT.......................HHCS--BTTSHHHHHHHHHHHHHHH CS
                           H_PPase 448 faigsAalaalaLfaaylee.......................aklekvdllnpevlvglliGamlvf 492
                                       + igsA l+a +L+  y+++                       ++ +++++++    +g++iG+++  
  gi|298674581|ref|YP_003726331.1|   6 IIIGSAILVASLLLNMYVSDqidemnqygvfdeivreiddeskEEYQTMKIIKYGSTAGIVIGGIILL 73 
                                       679**************************************998899*****************9864 PP

>> PorA  Porin PorA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1   0.00036       2.2       5      28 ..       5      28 ..       3      32 .. 0.89
   2 ?    5.3   0.1    0.0017        10     267     300 .]      45      77 ..      34      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00036
                              PorA  5 llalGvallvlAillptyvvpklk 28
                                      ++++G a lv+++ll+ yv++++ 
  gi|298674581|ref|YP_003726331.1|  5 AIIIGSAILVASLLLNMYVSDQID 28
                                      699*****************9976 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0017
                              PorA 267 eqakegrdklkllgrtlpivllvlGlvllvaglv 300
                                       ++ ke+ +++k++ ++  ++ +v+G+++l++g+v
  gi|298674581|ref|YP_003726331.1|  45 DESKEEYQTMKII-KYGSTAGIVIGGIILLVGFV 77 
                                       6678888899999.99****************86 PP

>> DUF350  Domain of Unknown Function (DUF350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   2.7    0.0072        43      38      52 ..       2      16 ..       1      18 [. 0.87
   2 ?    6.6   0.6    0.0014       8.4      25      49 ..      54      77 ..      27      80 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0072
                            DUF350 38 vlagviiglaiivaa 52
                                      + +++iig ai+va+
  gi|298674581|ref|YP_003726331.1|  2 DAGAIIIGSAILVAS 16
                                      6799*********97 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0014
                            DUF350 25 gelIkqgnnAaaivlagviiglaii 49
                                       ++Ik g   a+iv +g+i+ ++++
  gi|298674581|ref|YP_003726331.1| 54 MKIIKYGS-TAGIVIGGIILLVGFV 77
                                      44555554.8999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       813  (0.0453455); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.37s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 469.79
//
Query:       gi|298674582|ref|YP_003726332.1|  [L=222]
Description: hypothetical protein Metev_0630 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-06   28.5   0.0    0.00019   21.2   0.0    2.1  2  Phage_integrase  Phage integrase family
  ------ inclusion threshold ------
       0.18   12.0   0.0       0.28   11.3   0.0    1.3  1  NitrOD2          Nitrososphaera output domain 2


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.0    0.0017        15       7      43 ..      53      86 ..      47     122 .. 0.80
   2 !   21.2   0.0   2.2e-08   0.00019     114     167 ..     148     202 ..     143     205 .. 0.95

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0017
                                      HHHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT- CS
                   Phage_integrase  7 everllaaleeslkirdklllellyetGlRisEllsL 43
                                      e+++l + +++    + ++++e+l+ +G+R  El +L
  gi|298674582|ref|YP_003726332.1| 53 EYDALSEQIPK---DYLRTIFEILFWSGMRYVELQRL 86
                                      66666666666...68899***************998 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 2.2e-08
                                       HHHHHHHHCT-S.SC--TTHHHHHHHHHHHHHCTSHHHHHHHHT-SSCCHHHHHH CS
                   Phage_integrase 114 afkraveeagie.kpltpHtlRhsfataLleagvdlrvvqkllGHssisttqiYt 167
                                        +kr++e+a+ + k ++  t R+s+ ++++ +g++l  +    GH ++ + ++Y 
  gi|298674582|ref|YP_003726332.1| 148 NMKRWAEKADMDpKGFSAKTTRKSIESWMVTSGMPLTSICLRQGHDNLTSMRHYQ 202
                                       689*********99***************************************95 PP

>> NitrOD2  Nitrososphaera output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   3.1e-05      0.28       6      38 ..      36      68 ..      31      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.1e-05
                           NitrOD2  6 kladailddlkeilGpevfdalmeliaedylgg 38
                                      k+++ il +  +i+Gp  +dal e+i +dyl +
  gi|298674582|ref|YP_003726332.1| 36 KISEDILVKGTKIIGPFEYDALSEQIPKDYLRT 68
                                      78899999999*******************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 1291.65
//
Query:       gi|298674583|ref|YP_003726333.1|  [L=139]
Description: hypothetical protein Metev_0631 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.015   15.8   0.6      0.024   15.1   0.5    1.4  1  DUF2340   Uncharacterized conserved protein (DUF2340)


Domain annotation for each model (and alignments):
>> DUF2340  Uncharacterized conserved protein (DUF2340)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.5   1.3e-06     0.024      38     103 ..      12      81 ..       4      92 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.3e-06
                           DUF2340  38 eeiktesglkpfrnvkydtlKiytkahgsKttnlvinlddddelilkd....eektLaelgvenEtelsl 103
                                       ++i  +s++k+f ++++  lK y+++  sKttn  i  d+  + + +d    + ++L++++++ E++l +
  gi|298674583|ref|YP_003726333.1|  12 DNIVAKSHVKTFEDINFCILKGYKNSKFSKTTNFYITADELSKCFANDreiiRASKLEHFNFKPESNLVI 81 
                                       5788999*********************************998888887887788999999999988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 818.67
//
Query:       gi|298674584|ref|YP_003726334.1|  [L=45]
Description: hypothetical protein Metev_0632 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 283.09
//
Query:       gi|298674585|ref|YP_003726335.1|  [L=60]
Description: hypothetical protein Metev_0633 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0022   17.9   2.8     0.0034   17.3   2.8    1.3  1  Ogr_Delta  Ogr/Delta-like zinc finger
  ------ inclusion threshold ------
      0.059   13.0   0.7      0.059   13.0   0.7    2.1  2  FeS        Putative Fe-S cluster


Domain annotation for each model (and alignments):
>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   2.8   3.7e-07    0.0034       2      42 ..       6      49 ..       5      52 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.7e-07
                         Ogr_Delta  2 CPhCga.paaartsrnlskdvre..ryyqCsnfeCgatfvaaee 42
                                      C +Cg+ + +  ++   s d+ e  +y +C+ ++Cg +fv+  e
  gi|298674585|ref|YP_003726335.1|  6 CNNCGSsNCRQFRKPVVSSDGDEvcIYWECQEPNCGKRFVTGYE 49
                                      8889863689999999************************9766 PP

>> FeS  Putative Fe-S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.7   6.6e-06     0.059       6      23 ..       6      23 ..       3      32 .. 0.83
   2 ?    1.9   0.6      0.02   1.8e+02       8      14 ..      34      40 ..      34      42 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.6e-06
                               FeS  6 CgaCGypgCmafAealve 23
                                      C  CG  +C+ f + +v+
  gi|298674585|ref|YP_003726335.1|  6 CNNCGSSNCRQFRKPVVS 23
                                      9***********988876 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.02
                               FeS  8 aCGypgC 14
                                      +C +p+C
  gi|298674585|ref|YP_003726335.1| 34 ECQEPNC 40
                                      5999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.53
# Mc/sec: 343.15
//
Query:       gi|298674586|ref|YP_003726336.1|  [L=59]
Description: hypothetical protein Metev_0634 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       894  (0.0498633); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 445.05
//
Query:       gi|298674587|ref|YP_003726337.1|  [L=45]
Description: hypothetical protein Metev_0635 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.23s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 370.44
//
Query:       gi|298674588|ref|YP_003726338.1|  [L=122]
Description: hypothetical protein Metev_0636 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 982.40
//
Query:       gi|298674589|ref|YP_003726339.1|  [L=176]
Description: hypothetical protein Metev_0637 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1376.01
//
Query:       gi|298674590|ref|YP_003726340.1|  [L=65]
Description: hypothetical protein Metev_0638 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.49
# Mc/sec: 402.13
//
Query:       gi|298674591|ref|YP_003726341.1|  [L=59]
Description: hypothetical protein Metev_0639 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.013   15.8   1.5      0.015   15.7   1.5    1.1  1  CCDC-167        Coiled-coil domain-containing protein 167
      0.045   13.6   0.1      0.046   13.6   0.1    1.1  1  Apolipoprotein  Apolipoprotein A1/A4/E domain
       0.05   13.6   1.1      0.089   12.8   1.1    1.5  1  DUF2205         Short coiled-coil protein


Domain annotation for each model (and alignments):
>> CCDC-167  Coiled-coil domain-containing protein 167
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   1.5   2.4e-06     0.015      31      67 ..       3      40 ..       1      45 [. 0.89

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.4e-06
                          CCDC-167 31 elseeeResleeEeaslkeqleenekeLk.sLrkeNrk 67
                                      +ls+e+Re++e+  ++lke ++++  eLk  L++  +k
  gi|298674591|ref|YP_003726341.1|  3 SLSSEDREKIEQKAKTLKESIRPHIIELKtDLHELKQK 40
                                      79**********************99999778887776 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   7.8e-06     0.046     123     161 ..       5      39 ..       1      48 [. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.8e-06
                                       HHHHHHHHHHHHHHHHH-----..-----SSSHHHHHHH CS
                    Apolipoprotein 123 veelrqklaerleelkeslaphaeeveerlssrveelre 161
                                       + e r+k++++++ lkes++ph  e++      + el++
  gi|298674591|ref|YP_003726341.1|   5 SSEDREKIEQKAKTLKESIRPHIIELK----TDLHELKQ 39 
                                       566689999999999999999999999....45555555 PP

>> DUF2205  Short coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.1   1.5e-05     0.089      10      33 ..       1      24 [.       1      43 [. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.5e-05
                           DUF2205 10 veklerearerLqqqakeLqssLq 33
                                      ++ l++e+re+++q+ak+L++s +
  gi|298674591|ref|YP_003726341.1|  1 MNSLSSEDREKIEQKAKTLKESIR 24
                                      577889999999999999998864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1393  (0.0776954); expected 358.6 (0.02)
Passed bias filter:                      767  (0.0427799); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 472.49
//
Query:       gi|298674592|ref|YP_003726342.1|  [L=168]
Description: integrase catalytic subunit [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-21   76.7   0.1      2e-21   76.3   0.1    1.2  1  DDE_3     DDE superfamily endonuclease
    9.7e-05   22.1   0.1    0.00012   21.8   0.1    1.3  1  DDE_1     DDE superfamily endonuclease
    0.00031   20.9   0.0    0.00046   20.4   0.0    1.2  1  rve       Integrase core domain


Domain annotation for each model (and alignments):
>> DDE_3  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.3   0.1   3.4e-25     2e-21       5     144 ..       1     133 [.       1     135 [. 0.87

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 3.4e-25
                             DDE_3   5 iDEsgfqlgtvrrrawakkGkrerleeygrrgrvnligaldekgglafvtfeetlnaedfaeflerlletalqakki 81 
                                       +DEs  q++++ +r w+       +++++   + n++++++ +g   ++ f+++ +++d+ efle++ +      +i
  gi|298674592|ref|YP_003726342.1|   1 MDESSPQTRANTQRLWSFDKPV--IYKNTDYIKANAFAFYSING-NNLIEFKDSSKSDDVCEFLEEISRINHGR-PI 73 
                                       6****************97555..66666667888999999988.4567789999*****************98.** PP

                             DDE_3  82 vlilDnasiHkseslrelveeeadrlellylPpySPelNpiEivwsklkrellkrrsfkslde 144
                                       vli+Dna+ H++ + + ++++   ++ l++lPpySP+lNp+E +w+++kre+   r+++s++ 
  gi|298674592|ref|YP_003726342.1|  74 VLIMDNARAHHALKTTMKAKQ--LGIILVFLPPYSPDLNPVEFIWKSIKREISV-RFVQSKQH 133
                                       **********98666666555..*****************************99.88888765 PP

>> DDE_1  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   1.9e-08   0.00012      72     163 ..      68     155 ..      24     167 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.9e-08
                             DDE_1  72 aekrkilLlldssrshetvel.leselqniklvflPassasllqPldqgvvselKarYrrqllqalleeqnrlskeq 147
                                       + +r i+L++d++r+h++++  ++ ++  i lvflP+ s + l P++  +++ +K++    ++q  ++ ++ ++   
  gi|298674592|ref|YP_003726342.1|  68 NHGRPIVLIMDNARAHHALKTtMKAKQLGIILVFLPPYSPD-LNPVEF-IWKSIKREISVRFVQSKQHMRSIIKT-- 140
                                       57899************888879999999*******88876.689985.9*********9999999998888887.. PP

                             DDE_1 148 kkltlldalkfikkAw 163
                                         + + + l f +kAw
  gi|298674592|ref|YP_003726342.1| 141 VFMKIGNSLSF-AKAW 155
                                       44444555444.3344 PP

>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   7.7e-08   0.00046      44     118 ..      50     122 ..      43     123 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 7.7e-08
                               rve  44 demdastvlalleravarfggvepervlsDngseytskafrefladlgirvsftrpgrpqdnGkvErfhrtlkde 118
                                       d++++++v+++le+  +  +g+ p ++++Dn+++  + +++  +++lgi + f +p++p+ n  vE +++ +k+e
  gi|298674592|ref|YP_003726342.1|  50 DSSKSDDVCEFLEEISRINHGR-PIVLIMDNARAHHALKTTMKAKQLGIILVFLPPYSPDLNP-VEFIWKSIKRE 122
                                       455899*******999999999.**********99999**********************997.67777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1296.39
//
Query:       gi|298674593|ref|YP_003726343.1|  [L=189]
Description: ISA1083-3 transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.8e-11   42.6   0.1    1.3e-10   41.7   0.1    1.5  1  HTH_32         Homeodomain-like domain
    4.7e-08   32.6   0.2    1.5e-07   31.0   0.0    1.9  2  HTH_23         Homeodomain-like domain
    2.3e-07   30.3   0.3    1.7e-06   27.6   0.1    2.4  2  HTH_33         Winged helix-turn helix
    7.6e-07   29.2   0.0    2.2e-06   27.7   0.0    1.8  1  HTH_28         Helix-turn-helix domain
    8.9e-06   25.6   0.0    1.9e-05   24.6   0.0    1.5  1  HTH_29         Winged helix-turn helix
     0.0027   17.5   0.4     0.0078   16.1   0.1    1.8  2  DUF559         Protein of unknown function (DUF559)
     0.0034   17.4   0.7     0.0055   16.7   0.3    1.6  1  HTH_Tnp_IS630  Transposase
  ------ inclusion threshold ------
      0.037   14.8   0.4      0.053   14.3   0.2    1.6  1  Tau95          RNA polymerase III transcription factor (TF)II
       0.53   10.4   5.6       0.52   10.4   0.3    2.8  3  U3_assoc_6     U3 small nucleolar RNA-associated protein 6


Domain annotation for each model (and alignments):
>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.1   6.7e-14   1.3e-10       1      72 [.      80     151 ..      80     152 .. 0.95

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 6.7e-14
                            HTH_32   1 TvsrwlkRyneeGlegLkdrprrgrprklsdevrariiallreeprWsprqlaarlaeregvkvShstvyri 72 
                                       T + w  R+n++G+e+L +  ++gr +kl++++ ++++++l+e++ W++ ++++ + +++gv++S  +++ i
  gi|298674593|ref|YP_003726343.1|  80 TGYYWQDRWNKGGYEALVPMVSKGREHKLTQQQFDELKDILKERSLWTTNEVRQLVIQKYGVEYSLKQIRII 151
                                       889*****************9********************8889*********999999********9966 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   7.6e-11   1.5e-07       9      49 ..      50      96 ..      43      97 .. 0.79
   2 ?   -1.7   0.0       1.4   2.9e+03       5      23 ..     130     148 ..     126     151 .. 0.76

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 7.6e-11
                            HTH_23  9 rilllla..e....GlsvreIAreLgvsrrTvyrwlkryreeGlegl 49
                                      r+l+ l   +    G+sv+e+A++ g++++T y w  r++++G e+l
  gi|298674593|ref|YP_003726343.1| 50 RMLRRLYfcKfrylGDSVSEAADKVGITKMTGYYWQDRWNKGGYEAL 96
                                      44444444423355*****************************9998 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.4
                            HTH_23   5 reRlrillllaeGlsvreI 23 
                                       + R+++++ + + +s ++I
  gi|298674593|ref|YP_003726343.1| 130 EVRQLVIQKYGVEYSLKQI 148
                                       6789999988777777776 PP

>> HTH_33  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.44   8.8e+02       6      21 ..      35      50 ..      33      54 .. 0.85
   2 !   27.6   0.1   8.4e-10   1.7e-06       2      41 ..     123     162 ..     122     171 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.44
                            HTH_33  6 tlarlaqlieerfgvs 21
                                      tl++l +li+++++ +
  gi|298674593|ref|YP_003726343.1| 35 TLDQLNTLIKTETNAR 50
                                      9999******998865 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 8.4e-10
                            HTH_33   2 fgrWtlarlaqlieerfgvsysvsgvyrlLkrlGfsyqkP 41 
                                         +Wt+ +++ql+ +++gv+ys ++++ ++   G+   kP
  gi|298674593|ref|YP_003726343.1| 123 RSLWTTNEVRQLVIQKYGVEYSLKQIRIIMIQFGMKHSKP 162
                                       579************************9999999988887 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   1.1e-09   2.2e-06      12      49 ..      64     103 ..      57     106 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.1e-09
                            HTH_28  12 GhsvreaArelgisrrtvyrWikryeegGiagLvp..rrr 49 
                                       G+sv+eaA ++gi+  t y W  r+++gG ++Lvp   ++
  gi|298674593|ref|YP_003726343.1|  64 GDSVSEAADKVGITKMTGYYWQDRWNKGGYEALVPmvSKG 103
                                       789*******************************964444 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   9.6e-09   1.9e-05      11      61 ..      64     112 ..      62     113 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 9.6e-09
                            HTH_29  11 GvstvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsgrprnrlseeq 61 
                                       G s vs++A  +g+++ t y w++r+++gG +al +  ++gr  ++l+++q
  gi|298674593|ref|YP_003726343.1|  64 GDS-VSEAADKVGITKMTGYYWQDRWNKGGYEALVPMVSKGRE-HKLTQQQ 112
                                       666.********************************8888987.4799887 PP

>> DUF559  Protein of unknown function (DUF559)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.1   2.1e+03      75      88 ..      49      62 ..      18      75 .. 0.62
   2 !   16.1   0.1   3.9e-06    0.0078      20      75 ..     115     170 ..     101     177 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.1
                                      HHHHHHTT-EEEEE CS
                            DUF559 75 telLeslGftvlRf 88
                                      +++L +l f  +R+
  gi|298674593|ref|YP_003726343.1| 49 ARMLRRLYFCKFRY 62
                                      33444444444444 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 3.9e-06
                                       HHHHHHGGGTTTT--EEEEEEETTEEEEEEETTTTEEEEEE-----------HHHH CS
                            DUF559  20 kLWqllrnrrlsglkfrRqkpigsYivDfvclkaklivelDGaqhdeeeeyDaeRt 75 
                                       +L   l++r l      Rq +i++Y v++  ++ ++i+   G +h++  +yD ++ 
  gi|298674593|ref|YP_003726343.1| 115 ELKDILKERSLWTTNEVRQLVIQKYGVEYSLKQIRIIMIQFGMKHSKPYTYDYRKP 170
                                       57778999999999999***********************************8875 PP

>> HTH_Tnp_IS630  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.3   2.8e-06    0.0055      13      97 ..      59     151 ..      48     171 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.8e-06
                     HTH_Tnp_IS630  13 dyiesGggitkaskvfkvgratvyrWlkreela......atkvetrkrkidrkelke..dvkknpdallkerakkfg 81 
                                       ++   G+++ +a    ++++ t y W +r + +      ++  + r++k+ +++++e  d+ k+      + ++++ 
  gi|298674593|ref|YP_003726343.1|  59 KFRYLGDSVSEAADKVGITKMTGYYWQDRWNKGgyealvPMVSKGREHKLTQQQFDElkDILKERSLWTTNEVRQLV 135
                                       556679*********************997766111111556799*****999887444999999999999****** PP

                     HTH_Tnp_IS630  82 vtpasllyalkklkit 97 
                                       ++   + y lk+++i 
  gi|298674593|ref|YP_003726343.1| 136 IQKYGVEYSLKQIRII 151
                                       *************985 PP

>> Tau95  RNA polymerase III transcription factor (TF)IIIC subunit HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   2.7e-05     0.053      55     100 ..     100     147 ..      27     158 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.7e-05
                                       ----...HHHHHHHHHHHHHHHH-SEEEHHHHHTTS-GGGT..TTHHH CS
                             Tau95  55 vkelkekkelqkaveelkklfeerPiwtrraLknklekker..kklkl 100
                                       v++  e+k  q++++elk++++er +wt++++++ + +k    ++lk+
  gi|298674593|ref|YP_003726343.1| 100 VSKGREHKLTQQQFDELKDILKERSLWTTNEVRQLVIQKYGveYSLKQ 147
                                       4555667999*********************99988866655655554 PP

>> U3_assoc_6  U3 small nucleolar RNA-associated protein 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.2      0.14   2.7e+02      25      69 ..      19      62 ..       7      78 .. 0.73
   2 ?   10.4   0.3   0.00026      0.52       6      38 ..     114     147 ..     110     155 .. 0.86
   3 ?   -1.2   0.0       1.1   2.2e+03      22      37 ..     173     188 ..     169     189 .] 0.81

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.14
                        U3_assoc_6 25 IvkkrrkfEyklqrrgkkkedflkYieyElnLeklrkkRrkrlkl 69
                                      ++k+rrk    +  ++ ++++  + i+ E+n   lr+ +  + ++
  gi|298674593|ref|YP_003726343.1| 19 LMKQRRKDQIDI-EHHVTLDQLNTLIKTETNARMLRRLYFCKFRY 62
                                      567777777776.45667778888899999999999988877776 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00026
                        U3_assoc_6   6 peled.leekglFtkeEikeIvkkrrkfEyklqr 38 
                                       +el+d l+e+ l t +E++++v +    Ey+l++
  gi|298674593|ref|YP_003726343.1| 114 DELKDiLKERSLWTTNEVRQLVIQKYGVEYSLKQ 147
                                       566664799**********************985 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.1
                        U3_assoc_6  22 ikeIvkkrrkfEyklq 37 
                                         eI+kk r + y+l+
  gi|298674593|ref|YP_003726343.1| 173 ADEILKKPRRHTYSLK 188
                                       5789999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       829  (0.0462379); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1428.26
//
Query:       gi|298674594|ref|YP_003726344.1|  [L=88]
Description: hypothetical protein Metev_0642 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.032   14.3   0.0      0.042   13.9   0.0    1.2  1  DUF2288   Protein of unknown function (DUF2288)


Domain annotation for each model (and alignments):
>> DUF2288  Protein of unknown function (DUF2288)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.3e-06     0.042       5      45 ..      28      68 ..      25      81 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.3e-06
                                      HHTT---EE-GGGGHHHHHTT-EEEE-SSS-HHHHHHHHHT CS
                           DUF2288  5 kLneetaeieWeeLephfargavivVaeeldLvevavaiae 45
                                      +++e++++ + ee+++hfar ++++ +++ d+v+      +
  gi|298674594|ref|YP_003726344.1| 28 EIQESIENSDDEEVQQHFARSNIVYLTANQDVVDCTNFTRD 68
                                      67899999999**********************98655444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.38
# Mc/sec: 688.76
//
Query:       gi|298674595|ref|YP_003726345.1|  [L=184]
Description: hypothetical protein Metev_0643 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
        0.2   10.8   0.0       0.27   10.4   0.0    1.1  1  AI-2E_transport  AI-2E family transporter


Domain annotation for each model (and alignments):
>> AI-2E_transport  AI-2E family transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   1.5e-05      0.27      73     110 ..       8      46 ..       2      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 1.5e-05
                   AI-2E_transport  73 plliaqltqlvkslpayidslqnilnelpslleele.nl 110
                                       + + + lt+l++++p ++++ ++ ln+l++++++++ ++
  gi|298674595|ref|YP_003726345.1|   8 TTIKNALTELFEKMPVWVQESKDMLNDLENRYNVEKlEW 46 
                                       467899***************************996443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1351.74
//
Query:       gi|298674596|ref|YP_003726346.1|  [L=238]
Description: radical SAM domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.4e-08   33.7   0.0    5.6e-08   33.3   0.0    1.1  1  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
      0.025   14.9   0.1      0.047   14.0   0.1    1.4  1  Fer4_12      4Fe-4S single cluster domain
      0.076   13.1   0.0       0.12   12.5   0.0    1.4  1  Fer4_14      4Fe-4S single cluster domain
      0.085   12.6   5.7        1.8    8.2   6.2    2.2  2  DUF1848      Domain of unknown function (DUF1848)
      0.089   12.2   0.0       0.24   10.9   0.0    1.7  2  DUF5131      Protein of unknown function (DUF5131)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   1.6e-11   5.6e-08       2     167 .]      20     192 ..      19     192 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.6e-11
                                       EEESEESS--TTTSCCTT..HHHHHHHHHHHHHHHHHHHHHHH.HHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTC CS
                                       xxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpet..vrregrgrslsveeileevkelk.aekg.vkevilgggepllypdfvellerlakla 74 
                                       +++rgC+++C++C+ p     +r++ +  ++  +i++++k  + ++   ++ v+l+     ++p + el + + +++
  gi|298674596|ref|YP_003726346.1|  20 NIYRGCSHGCKYCYAPAAtrTSRRDFQNPVPRKDIIRHLKNDAeKNGYwIDKVLLSFISDPYQPIERELGLTRQAIE 96 
                                       689*************9999888889999999999999999996666699888888665455443333333333333 PP

                                       ...CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSET.EE CS
                                       ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx.xx RF
                       Radical_SAM  75 ...vpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikr.vv 146
                                          +++i +++ t   l   +  + l+  + + v ++l   d+   ++  +   + + ++  al+ ++ +gi   v+
  gi|298674596|ref|YP_003726346.1|  97 ilnENNIPVRILTKSNLF-LRDFDVLKGHPENEVGMTLAVRDES-LRRQWEpNAPKYFDRFMALKEAHHRGIYTwVS 171
                                       68889************9.************************9.99999886666666668889999999999*** PP

                                       EEEEEBTTTSHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 147 drivglpGendeeleellell 167
                                          v+ p e+++ ++++ e++
  gi|298674596|ref|YP_003726346.1| 172 LEPVIYPTETFQIIDDTHEFV 192
                                       ***************999986 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.3e-05     0.047      12      50 ..      22      60 ..      10      75 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.3e-05
                           Fer4_12 12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkk 50
                                        gC++ Ck+C+++++ + ++ +  +    + ii++lk+
  gi|298674596|ref|YP_003726346.1| 22 YRGCSHGCKYCYAPAATRTSRRDFQNPVPRKDIIRHLKN 60
                                      68**********999887665444443344445555544 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.3e-05      0.12       6      50 ..      23      71 ..      19     126 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.3e-05
                           Fer4_14  6 sgCnlsCkgCd...nketwkselgkpqteelleqilk.dlkkseikiqg 50
                                       gC++ Ck C+    + t + + ++p  ++++ + lk d++k+ + i++
  gi|298674596|ref|YP_003726346.1| 23 RGCSHGCKYCYapaATRTSRRDFQNPVPRKDIIRHLKnDAEKNGYWIDK 71
                                      69*********66544444555556666666666665555555555555 PP

>> DUF1848  Domain of unknown function (DUF1848)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   6.2    0.0005       1.8     252     265 .]      21      34 ..      10      34 .. 0.88
   2 ?    1.4   0.0      0.06   2.1e+02     133     167 ..      55      90 ..      45     117 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0005
                           DUF1848 252 ayntClhgCvYCYA 265
                                        y  C+hgC+YCYA
  gi|298674596|ref|YP_003726346.1|  21 IYRGCSHGCKYCYA 34 
                                       699**********9 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.06
                           DUF1848 133 lekfeklaeelkgytekvviSfvdl.ykkvkrnlkk 167
                                       ++++++ ae+    ++kv++Sf+   y+ ++r+l  
  gi|298674596|ref|YP_003726346.1|  55 IRHLKNDAEKNGYWIDKVLLSFISDpYQPIERELGL 90 
                                       5555555666666799******9766*****99953 PP

>> DUF5131  Protein of unknown function (DUF5131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   6.6e-05      0.24       5      38 ..      13      42 ..      11     116 .. 0.81
   2 ?   -1.3   0.0      0.34   1.2e+03     162     175 ..     168     181 ..     152     210 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.6e-05
                           DUF5131  5 ewtdatwnpvtGCtkvspgCdnCyaerlakrlka 38
                                      e++  + n  +GC   s gC+ Cya + ++ +++
  gi|298674596|ref|YP_003726346.1| 13 EYCSFALNIYRGC---SHGCKYCYAPAATR-TSR 42
                                      789999999****...68*******88543.333 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.34
                           DUF5131 162 rflSvEPlLgpvdl 175
                                        ++S+EP++ p + 
  gi|298674596|ref|YP_003726346.1| 168 TWVSLEPVIYPTET 181
                                       69999999988743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1810.46
//
Query:       gi|298674597|ref|YP_003726347.1|  [L=247]
Description: hypothetical protein Metev_0645 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-08   32.8   0.0    6.5e-08   32.2   0.0    1.2  1  N6_Mtase  N-6 DNA Methylase


Domain annotation for each model (and alignments):
>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0   3.6e-12   6.5e-08      23     120 ..     132     233 ..     123     241 .. 0.86

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 3.6e-12
                          N6_Mtase  23 ksgGeffTPrevsklivell....epksgesv..yDpacGsggllvqaekvlkee.dgktkelsiyGqeknettyrL 92 
                                       k gG+ffTP e+sk+ ++++    ++ ++e++    pa+G+g++ + + ++l+e+  + +++l++  q+++ + + +
  gi|298674597|ref|YP_003726347.1| 132 KFGGQFFTPYELSKFAAQVTfsdyDSDTDEVIefNEPAVGAGSFVIAVCEMLHEKgVNFQNRLKVTAQDSDYMVFCM 208
                                       779*******************99777787764369****************998445578899************* PP

                          N6_Mtase  93 akmNlllhgieykkvkirlgdtlekpkf 120
                                       a + l l g   +     +g+tl+ +++
  gi|298674597|ref|YP_003726347.1| 209 AYTQLSLIGCPAQ---LVHGNTLKLENK 233
                                       *******999888...788999876554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1854.94
//
Query:       gi|298674598|ref|YP_003726348.1|  [L=72]
Description: LuxR family transcriptional regulator [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-07   30.7   0.2    4.4e-07   29.4   0.2    1.8  1  GerE             Bacterial regulatory proteins, luxR family
    6.4e-06   25.8   0.0    1.1e-05   25.1   0.0    1.4  1  HTH_23           Homeodomain-like domain
     0.0001   22.0   0.5     0.0007   19.3   0.1    2.0  2  HTH_38           Helix-turn-helix domain
    0.00013   21.9   0.2    0.00018   21.5   0.2    1.4  1  HTH_7            Helix-turn-helix domain of resolvase
    0.00049   20.0   0.1    0.00076   19.4   0.1    1.3  1  HTH_11           HTH domain
     0.0015   18.5   0.2      0.003   17.5   0.2    1.5  2  Phage_terminase  Phage terminase small subunit
     0.0028   17.6   0.0     0.0045   17.0   0.0    1.3  1  HTH_29           Winged helix-turn helix
     0.0046   17.0   0.0      0.007   16.5   0.0    1.4  1  HTH_28           Helix-turn-helix domain
     0.0049   16.5   0.0     0.0077   15.9   0.0    1.3  1  Sigma70_r4_2     Sigma-70, region 4
     0.0052   17.2   0.1      0.009   16.4   0.0    1.4  2  HTH_40           Helix-turn-helix domain
  ------ inclusion threshold ------
      0.014   15.0   0.0       0.02   14.4   0.0    1.3  1  HTH_24           Winged helix-turn-helix DNA-binding
      0.017   14.1   0.0      0.017   14.1   0.0    1.1  1  TnsD             Tn7-like transposition protein D
      0.019   14.8   0.5       0.17   11.8   0.0    2.2  2  Terminase_5      Putative ATPase subunit of terminase (gpP-li
      0.029   14.4   0.2      0.056   13.5   0.2    1.5  1  HTH_3            Helix-turn-helix
      0.055   13.4   0.0      0.057   13.3   0.0    1.2  1  Sigma70_ECF      ECF sigma factor
      0.062   13.4   0.2      0.095   12.8   0.2    1.6  1  Trp_repressor    Trp repressor protein
      0.083   12.9   0.0        0.1   12.6   0.0    1.2  1  HTH_36           Helix-turn-helix domain
        0.2   11.1   0.0       0.24   10.8   0.0    1.2  1  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil


Domain annotation for each model (and alignments):
>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.2   4.4e-10   4.4e-07       9      39 ..      37      67 ..      21      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 4.4e-10
                                      HHHHHHCTTS-HHHHHHHHTS-HHHHHHHHH CS
                              GerE  9 evLrllaeGksnkeIAeelniSekTVkvhks 39
                                      +  r+l eGk n eI+eel+iS++TV  +k+
  gi|298674598|ref|YP_003726348.1| 37 QLYRMLQEGKNNREISEELGISNRTVVKYKA 67
                                      55699*********************88876 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   1.1e-08   1.1e-05      12      41 ..      40      69 ..      31      70 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.1e-08
                            HTH_23 12 lllaeGlsvreIAreLgvsrrTvyrwlkry 41
                                      ++l+eG++ reI++eLg+s rTv +++  +
  gi|298674598|ref|YP_003726348.1| 40 RMLQEGKNNREISEELGISNRTVVKYKAEW 69
                                      57788******************9998877 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1      0.29   2.9e+02       4      23 ..       4      23 ..       2      30 .. 0.81
   2 !   19.3   0.1     7e-07    0.0007      11      37 ..      36      62 ..      26      64 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.29
                            HTH_38  4 hLsleeReeIerllaeGlsl 23
                                      +L++ee e+ + + ++ +sl
  gi|298674598|ref|YP_003726348.1|  4 KLTPEEYERFQNMQQKRESL 23
                                      79999999999998877776 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 7e-07
                            HTH_38 11 eeIerllaeGlslreIArrLgrspsTI 37
                                      e+++r+l+eG+++reI  +Lg s  T+
  gi|298674598|ref|YP_003726348.1| 36 EQLYRMLQEGKNNREISEELGISNRTV 62
                                      789********************9998 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.2   1.8e-07   0.00018      10      45 .]      34      69 ..       3      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.8e-07
                                      HHGGGGSSTTTT--STTTSSSS---SSSS--SS--S CS
                             HTH_7 10 dinrvvkLleeGisiskIAkevnisRsTvYRyladn 45
                                      +++++ ++l+eG   ++I +e++is  Tv +y+a++
  gi|298674598|ref|YP_003726348.1| 34 KQEQLYRMLQEGKNNREISEELGISNRTVVKYKAEW 69
                                      599******************************987 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   7.7e-07   0.00076       2      35 ..      35      65 ..      34      67 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 7.7e-07
                            HTH_11  2 llqilelLleargpisgeeLAeeLnvSrrtvrrd 35
                                      ++q++++L e +++    e++eeL++S rtv+++
  gi|298674598|ref|YP_003726348.1| 35 QEQLYRMLQEGKNN---REISEELGISNRTVVKY 65
                                      89999***888876...**************997 PP

>> Phage_terminase  Phage terminase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       2.5   2.4e+03      37      44 ..      28      35 ..      21      37 .. 0.77
   2 !   17.5   0.2     3e-06     0.003      13      45 ..      36      68 ..      28      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.5
                   Phage_terminase 37 stvrkWKa 44
                                      +++ +WK 
  gi|298674598|ref|YP_003726348.1| 28 QQIPEWKQ 35
                                      68899995 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 3e-06
                   Phage_terminase 13 yelykEsggtlklkdIAkvLdvsestvrkWKak 45
                                       +ly+     +++++I ++L++s++tv k+Ka+
  gi|298674598|ref|YP_003726348.1| 36 EQLYRMLQEGKNNREISEELGISNRTVVKYKAE 68
                                      577777778899*******************95 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   4.5e-06    0.0045       5      35 ..      39      68 ..      37      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.5e-06
                            HTH_29  5 llllaeGvstvsqiAkllglsrrtvyrwlkr 35
                                       ++l eG  + ++i + lg+s rtv +++  
  gi|298674598|ref|YP_003726348.1| 39 YRMLQEGK-NNREISEELGISNRTVVKYKAE 68
                                      68999**9.9****************99876 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   7.1e-06     0.007       8      31 ..      41      64 ..      37      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.1e-06
                            HTH_28  8 llaaGhsvreaArelgisrrtvyr 31
                                       l++G++ re+++elgis rtv +
  gi|298674598|ref|YP_003726348.1| 41 MLQEGKNNREISEELGISNRTVVK 64
                                      467899***************965 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   7.8e-06    0.0077      15      43 ..      35      62 ..      32      66 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.8e-06
                                      HHHHHHHHHTS---HHHHHHHHT--HHHH CS
                      Sigma70_r4_2 15 qreifllryleglsykEIAellgisegtV 43
                                      q + + +   eg+  +EI+e+lgis +tV
  gi|298674598|ref|YP_003726348.1| 35 QEQLYRM-LQEGKNNREISEELGISNRTV 62
                                      5666666.4699****************9 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       8.3   8.2e+03      61      61 ..      17      17 ..       5      31 .. 0.53
   2 !   16.4   0.0     9e-06     0.009       2      32 ..      35      65 ..      34      69 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 8.3
                            HTH_40 61 i 61
                                       
  gi|298674598|ref|YP_003726348.1| 17 Q 17
                                      1 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 9e-06
                            HTH_40  2 aeetlelleeglsieeIAkerglkesTIegH 32
                                      +e+ +++l+eg++  eI++e g++  T++++
  gi|298674598|ref|YP_003726348.1| 35 QEQLYRMLQEGKNNREISEELGISNRTVVKY 65
                                      57789***********************987 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0     2e-05      0.02      17      34 ..      45      62 ..      35      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2e-05
                            HTH_24 17 risqreLAerlglSpstv 34
                                      + ++re++e+lg+S  tv
  gi|298674598|ref|YP_003726348.1| 45 GKNNREISEELGISNRTV 62
                                      679***********9998 PP

>> TnsD  Tn7-like transposition protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.7e-05     0.017     188     222 ..      35      68 ..       8      72 .] 0.71

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.7e-05
                              TnsD 188 eerlkeLveeeglslkeiAkelgvdiktVlryakk 222
                                       +e+l ++++ eg++ +ei++elg++ +tV++y+ +
  gi|298674598|ref|YP_003726348.1|  35 QEQLYRMLQ-EGKNNREISEELGISNRTVVKYKAE 68 
                                       233334444.9*********************876 PP

>> Terminase_5  Putative ATPase subunit of terminase (gpP-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.37   3.7e+02      40      57 ..      11      28 ..       8      29 .. 0.80
   2 ?   11.8   0.0   0.00017      0.17      17      35 ..      49      67 ..      44      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.37
                       Terminase_5 40 ddldplsrveeaieaRlv 57
                                      ++ ++++++ e++++R +
  gi|298674598|ref|YP_003726348.1| 11 ERFQNMQQKRESLSNRGQ 28
                                      6678899999****9966 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00017
                       Terminase_5 17 aeIAeelglkeatVysWkk 35
                                      +eI+eelg++++tV  +k 
  gi|298674598|ref|YP_003726348.1| 49 REISEELGISNRTVVKYKA 67
                                      79************99985 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   5.6e-05     0.056       5      29 ..      40      65 ..      35      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.6e-05
                                      HH.HTTHHHHHHHHHHTSSHHHHHHH CS
                             HTH_3  5 Rk.qlglsqeeLAeklGvsrstisri 29
                                      R  q g   +e++e+lG+s +t+ ++
  gi|298674598|ref|YP_003726348.1| 40 RMlQEGKNNREISEELGISNRTVVKY 65
                                      55599******************998 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.8e-05     0.057     140     170 ..      34      64 ..       6      72 .] 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.8e-05
                       Sigma70_ECF 140 qarlvelrkleGlsveEiAeklgvskrtver 170
                                       + +++  +  eG  + Ei+e+lg+s+rtv +
  gi|298674598|ref|YP_003726348.1|  34 KQEQLYRMLQEGKNNREISEELGISNRTVVK 64 
                                       45556667779*****************976 PP

>> Trp_repressor  Trp repressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   9.6e-05     0.095      41      66 ..      38      62 ..       8      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.6e-05
                     Trp_repressor 41 vvkeLLkeelsqreIaeelgvSiAtI 66
                                       ++ +L+e++  reI+eelg+S  t+
  gi|298674598|ref|YP_003726348.1| 38 LYR-MLQEGKNNREISEELGISNRTV 62
                                      567.******************8776 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0    0.0001       0.1      28      48 ..      48      68 ..      22      68 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0001
                            HTH_36 28 qetlakrlglsknTvsraike 48
                                      ++ +++ lg+s +Tv+++++e
  gi|298674598|ref|YP_003726348.1| 48 NREISEELGISNRTVVKYKAE 68
                                      899***************975 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00024      0.24      18      45 ..      36      63 ..      24      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00024
                      HTH_Tnp_ISL3 18 ayilelllesrsvkavArqlgvSwtTVw 45
                                      ++ +++l+e+++ ++++++lg+S +TV 
  gi|298674598|ref|YP_003726348.1| 36 EQLYRMLQEGKNNREISEELGISNRTVV 63
                                      677899********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1208  (0.0673769); expected 358.6 (0.02)
Passed bias filter:                      651  (0.0363099); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 540.06
//
Query:       gi|298674599|ref|YP_003726349.1|  [L=210]
Description: hypothetical protein Metev_0647 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   12.4   0.0        0.2   11.8   0.0    1.3  1  DUF2794   Protein of unknown function (DUF2794)


Domain annotation for each model (and alignments):
>> DUF2794  Protein of unknown function (DUF2794)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.1e-05       0.2       9      44 ..     134     169 ..     128     189 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.1e-05
                           DUF2794   9 eailrlygrmvaagewrDYaidllrdvavFsvFrra 44 
                                       e + +ly + +    ++D  ++ ++ +a+F+ F r+
  gi|298674599|ref|YP_003726349.1| 134 EDLTDLYQQLPERTRFKDIPLKYQKAKAIFEYFNRH 169
                                       56779****************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1629.60
//
Query:       gi|298674600|ref|YP_003726350.1|  [L=47]
Description: hypothetical protein Metev_0648 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.40
# Mc/sec: 354.42
//
Query:       gi|298674601|ref|YP_003726351.1|  [L=708]
Description: MCM family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-84  281.7   0.0    4.1e-84  281.2   0.0    1.2  1  MCM           MCM P-loop domain
    7.3e-31  106.6   1.4    1.2e-30  106.0   1.4    1.3  1  MCM_OB        MCM OB domain
    6.5e-27   93.8   0.0      2e-26   92.2   0.0    1.9  1  MCM_lid       MCM AAA-lid domain
     0.0008   18.9   0.0     0.0019   17.6   0.0    1.6  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.005   16.2   0.1      0.011   15.0   0.1    1.6  1  EAP30         EAP30/Vps36 family
  ------ inclusion threshold ------
       0.14   12.1   0.0        0.4   10.7   0.0    1.9  1  AAA_5         AAA domain (dynein-related subfamily)


Domain annotation for each model (and alignments):
>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  281.2   0.0   1.4e-87   4.1e-84       2     224 .]     273     497 ..     272     497 .. 0.97

  Alignments for each domain:
  == domain 1  score: 281.2 bits;  conditional E-value: 1.4e-87
                                       HHHHHHHHTSSTHHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHH CS
                               MCM   2 veeikelakekdiieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyve 78 
                                       +e++ el+++++i ++++ s+a siyg+++ kkai++qlf+gv+k++ed++ +rgdi+vl v+dpg++Ks+lL+y++
  gi|298674601|ref|YP_003726351.1| 273 EEQVLELSRDPNIKDRIAGSMATSIYGYQNLKKAIAVQLFSGVSKTHEDGAYTRGDIHVLAVSDPGMSKSKLLNYAA 349
                                       78999************************************************************************ PP

                                       HHSSSEEEEESSSSSSSHSSSEEEEES..SSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEE CS
                               MCM  79 klapravytsgkgssaagLtaavvrde..etgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisia 153
                                       +l+p+++ tsgkg saagLta+v +++  + ++f+leaGal ladkG+cciDe+dkm+eedrsalh+am qq++ i+
  gi|298674601|ref|YP_003726351.1| 350 TLSPKSIITSGKGNSAAGLTASVIKNDpdMDDQFALEAGALPLADKGLCCIDELDKMSEEDRSALHDAMAQQKLPIN 426
                                       **********************99875224456******************************************** PP

                                       SSSCEEEEE--EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHHHHHHHHH CS
                               MCM 154 KaGivatLnartsvlaAanpkagrydkkksvaeninlsaalLsrFDlifvllDkvdeekDeelaehivslh 224
                                       Ka i+ tL++rtsvl Aanpk+gr+d+ +s+++++++ ++l+srFDlif++lDk+d+ kD+el++hi+ +h
  gi|298674601|ref|YP_003726351.1| 427 KANIHLTLSTRTSVLGAANPKYGRFDEYESLSRQVQMAPSLISRFDLIFLMLDKPDDVKDRELSDHIIATH 497
                                       ********************************************************************987 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.0   1.4   3.9e-34   1.2e-30       4     124 ..     110     234 ..     107     236 .. 0.95

  Alignments for each domain:
  == domain 1  score: 106.0 bits;  conditional E-value: 3.9e-34
                                       G--GGGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EEE.....S----SB-..TTT-HHH-EEE-GGGSEEE CS
                            MCM_OB   4 dlrsehigklvkveGivtrasevkpklkkavfeckkcgktvev.....eleePrkCeekeCeskdpfkletekskfv 75 
                                       + rs+h+ k+v+++G+v ++s+vkp +++a+f+c +c++ + +     +++eP++Ce++ C++k+pfk  ++ks+++
  gi|298674601|ref|YP_003726351.1| 110 SFRSDHLMKFVSIPGVVKKVSKVKPMIVNAAFYCMRCEHITYIpqtgsKFTEPHECENEVCGRKGPFKTLVDKSSYR 186
                                       689***********************************97777899999999************************* PP

                                       EEEEEEEE-------------EEEEEEEGGGTT---TT-EEEEEEEEEE CS
                            MCM_OB  76 dfqklklQEspeevpaGelPrslevileddlvdkvkPGdrvevtGiyra 124
                                       d+q +++QE+pe++ + + P++l ++++dd+v+++kPGd++ v G++++
  gi|298674601|ref|YP_003726351.1| 187 DVQIIEIQENPEDIEKSQ-PETLICYAYDDMVQTCKPGDKILVNGVLQS 234
                                       **************9865.***************************986 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.2   0.0   6.8e-30     2e-26       1      87 []     530     613 ..     530     613 .. 0.96

  Alignments for each domain:
  == domain 1  score: 92.2 bits;  conditional E-value: 6.8e-30
                                       HHHHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHH CS
                           MCM_lid   1 ellrkYiayarekikPklseeakeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedve 77 
                                       +ll+kYi+yar+++ P+l  e k+ ++e++++lR+++    ++sip+t+R+Les+iR+seA+A++rl++ v+e+dv+
  gi|298674601|ref|YP_003726351.1| 530 DLLQKYISYARHNVVPVLPVELKDRITEFWMNLRHNKG---DDSIPVTPRKLESIIRVSEAFARMRLDNRVNEQDVQ 603
                                       589********************************773...689********************************* PP

                                       HHHHHHHHHH CS
                           MCM_lid  78 eairllkesl 87 
                                       +ai+l++esl
  gi|298674601|ref|YP_003726351.1| 604 DAIDLIQESL 613
                                       *******986 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   6.3e-07    0.0019      97     159 ..     385     447 ..     380     473 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 6.3e-07
                      Mg_chelatase  97 pkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpc 159
                                        + G++ la +G+  +DEl +++++   +L + + ++++ i++a+ +++  +r+ ++ a+Np 
  gi|298674601|ref|YP_003726351.1| 385 LEAGALPLADKGLCCIDELDKMSEEDRSALHDAMAQQKLPINKANIHLTLSTRTSVLGAANPK 447
                                       568999*******************************************************95 PP

>> EAP30  EAP30/Vps36 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   3.8e-06     0.011      97     233 ..     550     698 ..     548     702 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.8e-06
                             EAP30  97 eLavqivevclatraeng............glisleelyalvnrarggvalvspdDllraiekl.lvlg........ 152
                                       eL  +i e+ ++ r+ +g            ++i ++e +a++   r   + v+++D++ ai++  + l+        
  gi|298674601|ref|YP_003726351.1| 550 ELKDRITEFWMNLRHNKGddsipvtprkleSIIRVSEAFARM---R-LDNRVNEQDVQDAIDLIqESLKqsavdpqt 622
                                       8899999****99999999********555666666655555...5.2369*************8667655555555 PP

                             EAP30 153 ..sglsvlqvggkkvvrSvptelntdqvevlevakrlvsllaekssgggvtaselaeeeenlgwsvarakeaLeele 227
                                             +l++g        +++++++   ++ v+ +l++  a+ ++++gv+  ++ ee++++g+s + ++ea+ ++ 
  gi|298674601|ref|YP_003726351.1| 623 gkLDTDILETGT-------SNSQRSKIKDLYWVIYDLEDANAQMGRQKGVSIHDIYEEAQKEGISNDQVDEAIGRMR 692
                                       443334444222.......233333333444566666666666666699******999999**************** PP

                             EAP30 228 reGllw 233
                                       ++G l+
  gi|298674601|ref|YP_003726351.1| 693 KQGDLM 698
                                       ***987 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00013       0.4      50     125 ..     375     455 ..     330     492 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00013
                                       .......--------....G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS CS
                             AAA_5  50 gttslvdsplvraar....egeilvlDEveraesevlnsLlslleerrllleeggelvkaknddllerfrviatanp 122
                                        +  + d+ + +a+      + ++++DE+++++ e  ++L+  + +++l++++ +     +       ++v+++anp
  gi|298674601|ref|YP_003726351.1| 375 NDPDMDDQFALEAGAlplaDKGLCCIDELDKMSEEDRSALHDAMAQQKLPINKANIHLTLSTR-----TSVLGAANP 446
                                       4444455555555556666899****************************9999988877775.....899999999 PP

                                       --....... CS
                             AAA_5 123 ld......r 125
                                        +       
  gi|298674601|ref|YP_003726351.1| 447 KYgrfdeyE 455
                                       885544430 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (708 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.66u 0.26s 00:00:00.92 Elapsed: 00:00:00.44
# Mc/sec: 4872.33
//
Query:       gi|298674602|ref|YP_003726352.1|  [L=136]
Description: hypothetical protein Metev_0650 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0038   17.2   0.0      0.009   16.0   0.0    2.0  1  GPAT_N     Glycerol-3-phosphate acyltransferase N-terminal
     0.0072   15.7   0.1     0.0082   15.6   0.1    1.0  1  DUF3458_C  Domain of unknown function (DUF3458_C) ARM repeats


Domain annotation for each model (and alignments):
>> GPAT_N  Glycerol-3-phosphate acyltransferase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     1e-06     0.009      26      49 ..      62      85 ..      17     116 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1e-06
                            GPAT_N 26 LpanvaagmeelYqNYknAVlqsG 49
                                      +p++++  + el++N+++ Vlqs 
  gi|298674602|ref|YP_003726352.1| 62 VPKDMDDHLMELFDNFRDSVLQSL 85
                                      599*******************95 PP

>> DUF3458_C  Domain of unknown function (DUF3458_C) ARM repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   9.2e-07    0.0082      61     153 ..      26     125 ..       5     133 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 9.2e-07
                                       HHHHTS---HHHHCTT-SSB...-HHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHC......--SHHHHHHHHHH CS
                         DUF3458_C  61 kaeaLtlPseaelaeqlkev...dpdaihaarealrkalaealedellalyealaaeg......ayspdaaaagrRa 128
                                         +++++Ps+++la+ +k+    +pd      + l++ + + + d+l +l+++ +++       +y+ + a     a
  gi|298674602|ref|YP_003726352.1|  26 ERMMVKIPSNSYLADFIKNEkekNPDLT--YNQILERLVPKDMDDHLMELFDNFRDSVlqslatDYRGSDAYYQMEA 100
                                       567999***********99744455543..34556666678888888888888766655555568888888899*** PP

                                       HHHHHHHHHHHCTTTHHHHHHHHHH CS
                         DUF3458_C 129 LknlaLsylaaaddeeaaelavaqf 153
                                       L+ l L+yl++ ++++  +++++ +
  gi|298674602|ref|YP_003726352.1| 101 LRTLFLKYLVQRQNPKNPDKILKTL 125
                                       ****************999988665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1022.56
//
Query:       gi|298674603|ref|YP_003726353.1|  [L=177]
Description: hypothetical protein Metev_0651 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       154  (0.00858944); expected 358.6 (0.02)
Passed bias filter:                      149  (0.00831056); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 1292.00
//
Query:       gi|298674604|ref|YP_003726354.1|  [L=123]
Description: hypothetical protein Metev_0652 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 938.80
//
Query:       gi|298674605|ref|YP_003726355.1|  [L=59]
Description: hypothetical protein Metev_0653 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0025   17.7   4.6     0.0039   17.1   4.6    1.2  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
     0.0076   16.2   0.9      0.017   15.1   0.9    1.7  1  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
      0.009   16.1   4.4      0.099   12.8   0.5    2.2  2  Zn-ribbon_8     Zinc ribbon domain
  ------ inclusion threshold ------
      0.011   15.4   1.4      0.013   15.1   1.4    1.1  1  TackOD1         Thaumarchaeal output domain 1
      0.014   14.9   4.5       0.02   14.4   4.5    1.2  1  TF_Zn_Ribbon    TFIIB zinc-binding
       0.33   11.5   2.4        7.5    7.2   0.7    2.4  2  zf-H2C2_2       Zinc-finger double domain


Domain annotation for each model (and alignments):
>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   4.6   1.3e-06    0.0039      19      43 ..       6      30 ..       2      32 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.3e-06
                     Zn_Tnp_IS1595 19 fvCPhCgsrkayriktrglfqCkeC 43
                                      ++CP Cgs+++++ ++   ++C+eC
  gi|298674605|ref|YP_003726355.1|  6 QCCPECGSSQIRKRTRMMDYRCSEC 30
                                      68*******99999999******** PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.9   5.8e-06     0.017       2      21 ..       8      28 ..       7      31 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.8e-06
                    DNA_ligase_ZBD  2 CPvCGsavvReeg.eaiyRCt 21
                                      CP+CGs  +R+     +yRC+
  gi|298674605|ref|YP_003726355.1|  8 CPECGSSQIRKRTrMMDYRCS 28
                                      *********97753888***7 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.5   3.3e-05     0.099      27      39 ..       5      19 ..       1      20 [. 0.81
   2 !    5.0   0.3    0.0088        26       5      11 ..      24      30 ..      23      32 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.3e-05
                       Zn-ribbon_8 27 ta.CPeCgs.evrrv 39
                                      ++ CPeCgs + r++
  gi|298674605|ref|YP_003726355.1|  5 IQcCPECGSsQIRKR 19
                                      566******999985 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0088
                       Zn-ribbon_8  5 eYrCeeC 11
                                      +YrC eC
  gi|298674605|ref|YP_003726355.1| 24 DYRCSEC 30
                                      8****** PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   1.4   4.5e-06     0.013      86     111 ..       4      29 ..       2      36 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.5e-06
                           TackOD1  86 vrevCpkCkSidieeqelihhftCgn 111
                                       ++++Cp+C+S++i++++ +  ++C +
  gi|298674605|ref|YP_003726355.1|   4 FIQCCPECGSSQIRKRTRMMDYRCSE 29 
                                       789*****************999975 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   4.5   6.7e-06      0.02       3      25 ..       8      30 ..       6      30 .. 0.96

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.7e-06
                                      ETTTTCEECHEETSTTCEEESSS CS
                      TF_Zn_Ribbon  3 CPnCgstnlveDpergelvCtdC 25
                                      CP+Cgs+++   +   +++C++C
  gi|298674605|ref|YP_003726355.1|  8 CPECGSSQIRKRTRMMDYRCSEC 30
                                      ********9999999******** PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.7    0.0025       7.5      11      22 ..       2      13 ..       1      14 [. 0.81
   2 ?    3.8   0.0      0.03        89      14      20 ..      24      30 ..      16      31 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0025
                         zf-H2C2_2 11 gekpyeCplCdk 22
                                      +e++ +Cp+C+ 
  gi|298674605|ref|YP_003726355.1|  2 NEFIQCCPECGS 13
                                      57888*****86 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.03
                         zf-H2C2_2 14 pyeCplC 20
                                       y C++C
  gi|298674605|ref|YP_003726355.1| 24 DYRCSEC 30
                                      49***** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 474.11
//
Query:       gi|298674606|ref|YP_003726356.1|  [L=45]
Description: hypothetical protein Metev_0654 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      185  (0.0103185); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 323.71
//
Query:       gi|298674607|ref|YP_003726357.1|  [L=64]
Description: hypothetical protein Metev_0655 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.083   12.9  10.1        0.1   12.6  10.1    1.2  1  Zn_Tnp_IS1595  Transposase zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6  10.1   5.8e-06       0.1      19      44 ..       7      32 ..       2      34 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.8e-06
                     Zn_Tnp_IS1595 19 fvCPhCgsrkayriktrglfqCkeCr 44
                                       +CP C s ++++ ++ + ++C++C+
  gi|298674607|ref|YP_003726357.1|  7 MCCPVCSSCEVRFRTRSRDYKCYSCH 32
                                      69*****9989888889********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       908  (0.0506442); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 486.04
//
Query:       gi|298674608|ref|YP_003726358.1|  [L=68]
Description: hypothetical protein Metev_0656 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       228  (0.0127168); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.26s 00:00:00.58 Elapsed: 00:00:00.38
# Mc/sec: 531.21
//
Query:       gi|298674609|ref|YP_003726359.1|  [L=100]
Description: hypothetical protein Metev_0657 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 707.65
//
Query:       gi|298674610|ref|YP_003726360.1|  [L=60]
Description: hypothetical protein Metev_0658 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.02   15.3   1.0        5.5    7.6   0.1    2.2  2  zf-H2C2_2       Zinc-finger double domain
      0.035   13.8   0.5       0.37   10.5   0.1    2.1  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
      0.037   14.1   0.3      0.041   13.9   0.3    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.36   10.3   4.3       0.91    9.0   0.1    2.2  2  zf-ribbon_3     zinc-ribbon domain
        3.2    7.8   6.0        5.3    7.1   0.2    2.5  3  Zn_Tnp_IS1595   Transposase zinc-ribbon domain


Domain annotation for each model (and alignments):
>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1    0.0015       5.5      16      24 ..       6      14 ..       2      15 .. 0.84
   2 ?    6.8   0.1    0.0027       9.5      12      20 ..      19      31 ..      17      34 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0015
                         zf-H2C2_2 16 eCplCdkaF 24
                                       Cp+C++ +
  gi|298674610|ref|YP_003726360.1|  6 RCPVCGYDY 14
                                      7*****987 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0027
                         zf-H2C2_2 12 ekpy....eCplC 20
                                      e py    eCp+C
  gi|298674610|ref|YP_003726360.1| 19 EDPYadpaECPAC 31
                                      77777777***** PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1    0.0001      0.37      15      25 ..       2      12 ..       1      13 [. 0.90
   2 ?    1.6   0.0     0.062   2.2e+02       9      23 ..      17      31 ..      15      32 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0001
                                      SS----SSS-- CS
                    DNA_RNApol_7kD 15 gdpiRCkeCGh 25
                                      +d iRC  CG+
  gi|298674610|ref|YP_003726360.1|  2 SDTIRCPVCGY 12
                                      599*******8 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.062
                                      B----SSS----SSS CS
                    DNA_RNApol_7kD  9 evslkkgdpiRCkeC 23
                                      +v++   dp  C  C
  gi|298674610|ref|YP_003726360.1| 17 SVEDPYADPAECPAC 31
                                      678888899999999 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.3   1.1e-05     0.041      70     100 ..       4      39 ..       1      45 [. 0.75

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.1e-05
                                       EEEETTTS-EEECHH.HHH.....S-TTTSSS-EEEE CS
                              HypA  70 kvrCreCgkefelee.kal.....rCpkCgsadveiv 100
                                       ++rC +Cg+++ ++  +       +Cp+C +a++e  
  gi|298674610|ref|YP_003726360.1|   4 TIRCPVCGYDYGISVeD-PyadpaECPACIEAEMEAE 39 
                                       689*******9966532.1234559****99998865 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   0.00025      0.91       2       9 ..       4      11 ..       3      13 .. 0.90
   2 ?    2.6   0.8     0.028        99       4       8 ..      27      31 ..      26      31 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00025
                       zf-ribbon_3  2 tvrCPnCG 9 
                                      t+rCP CG
  gi|298674610|ref|YP_003726360.1|  4 TIRCPVCG 11
                                      799****9 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.028
                       zf-ribbon_3  4 rCPnC 8 
                                      +CP+C
  gi|298674610|ref|YP_003726360.1| 27 ECPAC 31
                                      79999 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.2    0.0015       5.3      18      27 ..       4      13 ..       2      23 .. 0.78
   2 ?    3.8   0.5     0.015        55      17      26 ..      24      33 ..      20      39 .. 0.77
   3 ?   -1.9   0.0      0.95   3.4e+03       2       8 ..      40      46 ..      35      48 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0015
                     Zn_Tnp_IS1595 18 gfvCPhCgsr 27
                                      + +CP Cg++
  gi|298674610|ref|YP_003726360.1|  4 TIRCPVCGYD 13
                                      578*****86 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.015
                     Zn_Tnp_IS1595 17 ngfvCPhCgs 26
                                      +   CP+C  
  gi|298674610|ref|YP_003726360.1| 24 DPAECPACIE 33
                                      6678****65 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.95
                     Zn_Tnp_IS1595  2 dEeeara 8 
                                      dE++a++
  gi|298674610|ref|YP_003726360.1| 40 DEAKAER 46
                                      6777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 440.52
//
Query:       gi|298674611|ref|YP_003726361.1|  [L=62]
Description: hypothetical protein Metev_0659 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.04   13.8   0.4      0.047   13.6   0.4    1.0  1  PhaP_Bmeg  Polyhydroxyalkanoic acid inclusion protein (PhaP_B


Domain annotation for each model (and alignments):
>> PhaP_Bmeg  Polyhydroxyalkanoic acid inclusion protein (PhaP_Bmeg)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.4   2.6e-06     0.047      46      89 ..       8      50 ..       3      56 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.6e-06
                         PhaP_Bmeg 46 vkeltkalselekeskqltaeledqlqktvenlrskaGnkvedn 89
                                      +++   +l+++ kes+++ +++    ++t++ l +++Gn+ + n
  gi|298674611|ref|YP_003726361.1|  8 NQSQSTNLDSISKESRKIASQICSDDKDTLDYL-EQFGNEFDRN 50
                                      6778889************************99.8999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1031  (0.0575046); expected 358.6 (0.02)
Passed bias filter:                      661  (0.0368676); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 461.75
//
Query:       gi|298674612|ref|YP_003726362.1|  [L=55]
Description: hypothetical protein Metev_0660 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      181  (0.0100954); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 388.59
//
Query:       gi|298674613|ref|YP_003726363.1|  [L=74]
Description: putative CopG/Arc/MetJ family transcriptional regulator [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.5e-05   22.9   0.0    8.2e-05   22.8   0.0    1.1  1  RHH_8     Ribbon-Helix-Helix transcriptional regulator family


Domain annotation for each model (and alignments):
>> RHH_8  Ribbon-Helix-Helix transcriptional regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   4.6e-09   8.2e-05      17      45 ..      17      45 ..      12      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 4.6e-09
                             RHH_8 17 qiDlLveeGfYsnRtDlirtairaqLakh 45
                                      +iD Lve+ +Y nR+D++r+ +r+ L  +
  gi|298674613|ref|YP_003726363.1| 17 EIDELVENNYYKNRSDVVRSLVRTCLMIN 45
                                      79**********************98654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 518.17
//
Query:       gi|298674614|ref|YP_003726364.1|  [L=114]
Description: hypothetical protein Metev_0662 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.021   15.2   0.2      0.029   14.8   0.2    1.3  1  PhoU       PhoU domain
      0.046   13.5   0.7      0.094   12.5   0.7    1.6  1  ScsC_N     Copper resistance protein ScsC N-terminal domain
      0.067   13.1   0.1       0.14   12.1   0.1    1.6  1  Ectatomin  Ectatomin


Domain annotation for each model (and alignments):
>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.2   4.9e-06     0.029       2      40 ..      34      76 ..      33      99 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.9e-06
                                      HHHHHHHHHHHHHHHHHHHCT-H....HHHHHHHHHHHHHHHH CS
                              PhoU  2 rrmaeiveemlddalealeekdt....elarevierddeidrl 40
                                      ++m+++v+++l++ +  +e+kd+    +++r++ie+d ei++ 
  gi|298674614|ref|YP_003726364.1| 34 SSMSDLVSQALSEFIANYEKKDKeditDIVRDIIENDPEINKV 76
                                      68********************76666888999999*999985 PP

>> ScsC_N  Copper resistance protein ScsC N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.7   1.6e-05     0.094       1      19 [.      55      73 ..      55      73 .. 0.97

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.6e-05
                            ScsC_N  1 QkaaiekivrdYLleNPEi 19
                                      +k++i +ivrd + + PEi
  gi|298674614|ref|YP_003726364.1| 55 DKEDITDIVRDIIENDPEI 73
                                      79****************9 PP

>> Ectatomin  Ectatomin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   2.4e-05      0.14       2      19 ..       5      22 ..       4      26 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.4e-05
                         Ectatomin  2 skkvklTvCPTlksmAKK 19
                                      sk  k T+C T+ ++ KK
  gi|298674614|ref|YP_003726364.1|  5 SKRKKNTICATVSPYVKK 22
                                      577799***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1350  (0.075297); expected 358.6 (0.02)
Passed bias filter:                      606  (0.0338); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 694.07
//
Query:       gi|298674615|ref|YP_003726365.1|  [L=124]
Description: hypothetical protein Metev_0663 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.021   15.2   0.1      0.052   13.9   0.1    1.6  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.055   13.8   0.1      0.082   13.2   0.1    1.3  1  OKR_DC_1_C       Orn/Lys/Arg decarboxylase, C-terminal domain


Domain annotation for each model (and alignments):
>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   5.8e-06     0.052       5      44 ..       7     112 ..       5     121 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.8e-06
                   Lar_restr_allev   5 pCPfCggravlersqrvvaeigq...................................................... 27 
                                        CP Cg+ + +   q+ v++++                                                       
  gi|298674615|ref|YP_003726365.1|   7 ECPVCGNLNFVNIKQKIVEHYENghlvgtdfmdaklketvsadklvddilsslaehlyngitikklckmlhdiygiv 83 
                                       6******************9999****************************************************** PP

                   Lar_restr_allev  28 ...............cvyCad.Cgastpwfkia 44 
                                                      c+yC d C      +  +
  gi|298674615|ref|YP_003726365.1|  84 edfccdmiqkikyelCMYCPDrCHL----YFVD 112
                                       *******************999*98....3333 PP

>> OKR_DC_1_C  Orn/Lys/Arg decarboxylase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   9.2e-06     0.082       8      30 ..      60      82 ..      55     120 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.2e-06
                                      SHHHHTT-BHHHHHHHHHHHHHH CS
                        OKR_DC_1_C  8 kperYegmtlrdLcqemhdlyke 30
                                       ++ Y+g+t+++Lc+ +hd+y  
  gi|298674615|ref|YP_003726365.1| 60 AEHLYNGITIKKLCKMLHDIYGI 82
                                      5678****************964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1002  (0.0558871); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 751.79
//
Query:       gi|298674616|ref|YP_003726366.1|  [L=155]
Description: hypothetical protein Metev_0664 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1177  (0.0656478); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 980.49
//
Query:       gi|298674617|ref|YP_003726367.1|  [L=265]
Description: hypothetical protein Metev_0665 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-25   88.8   1.8    2.2e-25   88.8   0.3    1.8  2  DUF1828   Domain of unknown function DUF1828


Domain annotation for each model (and alignments):
>> DUF1828  Domain of unknown function DUF1828
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.8   0.3   1.2e-29   2.2e-25       1      91 []      38     128 ..      38     128 .. 0.98
   2 ?   -2.3   0.1      0.32   5.7e+03       2      18 ..     167     184 ..     167     186 .. 0.76

  Alignments for each domain:
  == domain 1  score: 88.8 bits;  conditional E-value: 1.2e-29
                           DUF1828   1 TPfldedgDsiqiyvkkkegdeirLtDdGltlmdLsysgidldl.skkRkellesilakfgvtledgelsvkvteen 76 
                                       TPf+++dgD +++++k++   ++++tD+G+tlm+Lsy+++d +l ++kRk+++++il++++++++dgel ++v++e+
  gi|298674617|ref|YP_003726367.1|  38 TPFTFDDGDFLNVVLKYD-YPYWYFTDEGDTLMHLSYDDLDEKLeKGKRKDMFDTILKTHDIKNKDGELKLNVDDEK 113
                                       9**************777.6********************************************************* PP

                           DUF1828  77 laaakhrllqallav 91 
                                       +++  ++++q l+++
  gi|298674617|ref|YP_003726367.1| 114 FGDCYFTFIQGLVKI 128
                                       *************98 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.32
                           DUF1828   2 PfldedgDs.iqiyvkkk 18 
                                       P++d+dg + i++yv++k
  gi|298674617|ref|YP_003726367.1| 167 PVYDPDGKYvIDCYVENK 184
                                       788999987358999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       967  (0.053935); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1559.45
//
Query:       gi|298674618|ref|YP_003726368.1|  [L=313]
Description: hypothetical protein Metev_0666 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-15   58.1   1.7    1.2e-14   54.9   1.7    2.2  1  AbiTii    AbiTii


Domain annotation for each model (and alignments):
>> AbiTii  AbiTii
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   1.7   6.5e-19   1.2e-14       3     182 ..      19     169 ..      17     172 .. 0.77

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 6.5e-19
                            AbiTii   3 veelqedaldes.sslsslLrkakvlArklgskelreWvksElnGYpsddelPeYRkvlkalngsssgwipvqleee 78 
                                       +e+l +  ld+s + l+s+L k k+lA+++++ +  +W+++ElnGY s++++P+YR+ +k+ n  s+g+        
  gi|298674618|ref|YP_003726368.1|  19 IENLHNCNLDNSmHFLNSILIKYKHLAKLVEDTDEIKWINCELNGY-SNEKVPSYRI-IKYGN--SYGY-------- 83 
                                       7889999999997889******************************.8999******.55555..4688........ PP

                            AbiTii  79 ereeleelklrqsiseleellekekdssgslslplpaelvallnkllnklqitrlylevsksalegildqVrnklld 155
                                                ++ si  l e+++++k +s  ++  +p+e++    ++ + + ++    ++ k +++ i+  ++nk ++
  gi|298674618|ref|YP_003726368.1|  84 ---------IKYSIYDLMEWINNYKRKSFLIRSLNPNESI----DVPQ-IPVS--PYILKKIMYKIIFIVIHNKTIN 144
                                       .........6677888888888888888888888888888....7777.6666..7777777777777777777777 PP

                            AbiTii 156 wvleLeee.gilgegddfskeekekaks 182
                                       +   L++  +   e d+f +++k ++++
  gi|298674618|ref|YP_003726368.1| 145 I---LYNSkFGKIESDIFDENHKHVDNK 169
                                       7...555555566777777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       973  (0.0542696); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 1859.07
//
Query:       gi|298674619|ref|YP_003726369.1|  [L=512]
Description: hypothetical protein Metev_0667 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00043   20.7   0.2     0.0012   19.2   0.2    1.9  1  NERD      Nuclease-related domain


Domain annotation for each model (and alignments):
>> NERD  Nuclease-related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.2   6.9e-08    0.0012       2      88 ..     223     308 ..     222     335 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 6.9e-08
                              NERD   2 gaegEravakeLkelkedeylvlhdvrlrpgtgeiDhlvispkgifviEvKnwsGwifgdkegrwtqki.kkgfk.. 75 
                                       g   E  v+k Lk+++++ ++ ++++++++   e D+lv ++k  f+iE+K+ +  i+ + +  w +   k+++k  
  gi|298674619|ref|YP_003726369.1| 223 GDHLEDLVEKKLKDFLPN-FVTFKNYYINEF--EKDILVTHKKMGFCIECKSVK--IRPS-SFDWSKLNlKNDIKsd 293
                                       666788899999977666.666******777..*******************77..6666.5557666664444311 PP

                              NERD  76 ..npleqakrhakal 88 
                                         + l+q+ +  ++l
  gi|298674619|ref|YP_003726369.1| 294 vsHALNQISKPLNIL 308
                                       236666666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (512 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       796  (0.0443973); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 3037.09
//
Query:       gi|298674620|ref|YP_003726370.1|  [L=434]
Description: hypothetical protein Metev_0668 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.7e-05   24.3   0.0      8e-05   23.2   0.0    1.5  1  AAA_assoc_C  C-terminal AAA-associated domain


Domain annotation for each model (and alignments):
>> AAA_assoc_C  C-terminal AAA-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   4.5e-09     8e-05      18     109 ..     327     423 ..     325     427 .. 0.69

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 4.5e-09
                       AAA_assoc_C  18 veaaelLglv.eveegdielTelGrkfveadi.kerKeifreqllklvplaaairrvLder..enkrlpeerfldeL 90 
                                       ++aa++Lg++ ++++g+ +lTe+G+k++++   +er  if +qllk+  ++++i + L++   e  +l+ + + +++
  gi|298674620|ref|YP_003726370.1| 327 ANAARYLGFLtKTNNGEFRLTETGKKLAHSVYrSERNYIFLQQLLKRPTFHEIIIS-LKDYdfELSNLDDNLISSII 402
                                       689*****973579**************99761578889*******8888888877.54431133455555666666 PP

                       AAA_assoc_C  91 eekls..eeeaertletaieW 109
                                       +++ s  +   +r  +t+ +W
  gi|298674620|ref|YP_003726370.1| 403 SKHTSltSGTPKRRASTVKSW 423
                                       666444455555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 2494.03
//
Query:       gi|298674621|ref|YP_003726371.1|  [L=317]
Description: DNA adenine methylase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.3e-59  199.2   6.8    1.1e-58  199.0   6.8    1.0  1  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
  ------ inclusion threshold ------
       0.09   12.3   0.2       0.15   11.6   0.2    1.3  1  LuxQ-periplasm   LuxQ, periplasmic
        0.3   11.6   2.0        2.9    8.4   0.1    2.4  2  DUF1493          Protein of unknown function (DUF1493)


Domain annotation for each model (and alignments):
>> MethyltransfD12  D12 class N6 adenine-specific DNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.0   6.8   1.8e-62   1.1e-58       1     259 [.      21     294 ..      21     295 .. 0.93

  Alignments for each domain:
  == domain 1  score: 199.0 bits;  conditional E-value: 1.8e-62
                                       STTTSCTTHHHHHCCS-......--SEEEETT-TTSCCHHCS.....SSCEEEEES-HHHHHHHHHHCCHSHHHHHH CS
                   MethyltransfD12   1 YiGgKrkllpeIkelipkd....kgktfvepFaGggaVffeakk..qgkkvlinDinedlinlykaliknnveelik 71 
                                       ++GgK++l++e+++ +p+d    k k++vepF+GggaVff++ +  ++k++ i D+ne+li  y+ ++kn+ve lik
  gi|298674621|ref|YP_003726371.1|  21 WAGGKKQLIEEFEKRFPDDldtvKLKKYVEPFVGGGAVFFHVIQnyDFKECHIYDLNEELILAYR-VVKNDVEYLIK 96 
                                       9*****************9****99*******************9********************.99999****** PP

                                       HHH.T....CTTGGC.TSHHHHHHHHHHHH...HHH-HHHH.......HHHHHHHHCCBGGG---B-TTS-B---B- CS
                   MethyltransfD12  72 elekl....lekeelenereyfyelreefnkkidaireaee.......aidflylnrllfsglervnkkgnfnvpyg 137
                                       +l++l    l +++  n++e++y +r++fnk++ +i++          a+++++ln+++++gl rvn+kg+fnvp g
  gi|298674621|ref|YP_003726371.1|  97 RLKTLqseyLALDH-SNRKEFYYSIRKSFNKNKPDIDFSTYsnkwverAAQLIFLNKTCYNGLFRVNSKGEFNVPIG 172
                                       ***99877654544.49*************666666655556779999***************************** PP

                                       S-SS-....HHHHHHHHHHHHHCCEEEC-CHHHHTT--TTE.EEEE--S-T.S...TS--GGGG.CS-HHHHHHHHH CS
                   MethyltransfD12 138 aykkpkkvaekelklrseklknakiecgdfdavllkakieddivYlDPPYnprqytanytlyetlafsdedevrlae 214
                                         k+p++ + ++l+++s+ l+ + i+ gdf + +  + +++ +vY+DPPY+p+++t+++ +y+++ f+d+++ rl  
  gi|298674621|ref|YP_003726371.1| 173 SHKNPTILDDENLRSVSRVLQGVYIHLGDFSDCEPVV-DSNTFVYIDPPYRPLNQTSSFNSYSKDCFDDNEQYRLCR 248
                                       *************************************.8888*********************************** PP

                                       HHHHH.HHTT-EEEEEEES.....EESHHHHHHCTT...SEEEEECCCCH CS
                   MethyltransfD12 215 vlkslsskfgvkvllsnsf.....kdtklfrelyksYnnesileveelra 259
                                       +++ l+ + g+k++lsns       d ++f++ly +   ++i +v+++r 
  gi|298674621|ref|YP_003726371.1| 249 FYHRLD-SMGSKIMLSNSDpknenPDDDFFDNLYTD---YNIERVKATRM 294
                                       *****7.**************999999*********...67777777765 PP

>> LuxQ-periplasm  LuxQ, periplasmic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   2.5e-05      0.15      43     105 ..     100     160 ..      96     167 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.5e-05
                                       HHHHHHHTT-CCCHHHHHHHHHHCCCCCS-SEEEEEETTEEEEE-SHHHHCT--HHHHHHHHH CS
                    LuxQ-periplasm  43 alaealssgdeealdafflsvdqkepsntpdlrfissqegllWddgNaqfyglneseLkklik 105
                                       +l+  +   d+++ ++f++s+ ++  +n pd+ f + +++  W++  aq+  ln+++ + l +
  gi|298674621|ref|YP_003726371.1| 100 TLQSEYLALDHSNRKEFYYSIRKSFNKNKPDIDFSTYSNK--WVERAAQLIFLNKTCYNGLFR 160
                                       788889999999999************************9..***********9999988876 PP

>> DUF1493  Protein of unknown function (DUF1493)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1   0.00048       2.9      46      76 ..      26      56 ..      22      74 .. 0.81
   2 ?    2.2   0.3     0.041   2.5e+02      36      71 ..     104     139 ..      70     163 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00048
                           DUF1493 46 edllekffkrfnVdrgnfkiktYfvpdtpll 76
                                      ++l+e+f+krf  d + +k+k+Y +p+++  
  gi|298674621|ref|YP_003726371.1| 26 KQLIEEFEKRFPDDLDTVKLKKYVEPFVGGG 56
                                      6899********************9976644 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.041
                           DUF1493  36 edlkldeddaedllekffkrfnVdrgnfkiktYfvp 71 
                                       e l ld  + +++     k fn ++ +++++tY + 
  gi|298674621|ref|YP_003726371.1| 104 EYLALDHSNRKEFYYSIRKSFNKNKPDIDFSTYSNK 139
                                       4588999999999999*****************755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1967.60
//
Query:       gi|298674622|ref|YP_003726372.1|  [L=162]
Description: hypothetical protein Metev_0670 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 952.63
//
Query:       gi|298674623|ref|YP_003726373.1|  [L=86]
Description: hypothetical protein Metev_0671 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.085   13.0   0.1       0.52   10.4   0.1    1.9  1  DUF3898   Domain of unknown function (DUF3898)


Domain annotation for each model (and alignments):
>> DUF3898  Domain of unknown function (DUF3898)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   2.9e-05      0.52      16      59 ..       9      53 ..       2      79 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 2.9e-05
                           DUF3898 16 aqiveqkPeielklkldeievkalladfGeklh.iakvndrYvll 59
                                      + +ve++Pe el++++ +  +     +f ++   + +++d Y++l
  gi|298674623|ref|YP_003726373.1|  9 TVLVEKTPEYELRFRIKKDYLEQNNIEFSHTSKvLNEIDDEYLML 53
                                      679*************99999988888887765245677777664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 526.77
//
Query:       gi|298674624|ref|YP_003726374.1|  [L=83]
Description: hypothetical protein Metev_0672 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 507.47
//
Query:       gi|298674625|ref|YP_003726375.1|  [L=134]
Description: hypothetical protein Metev_0673 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.4e-60  200.8   1.0      6e-60  200.6   1.0    1.0  1  DUF1699      Protein of unknown function (DUF1699)
  ------ inclusion threshold ------
      0.023   13.9   0.1       0.31   10.2   0.0    1.9  2  HIGH_NTase1  HIGH Nucleotidyl Transferase


Domain annotation for each model (and alignments):
>> DUF1699  Protein of unknown function (DUF1699)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.6   1.0   6.7e-64     6e-60       1     130 []       1     130 [.       1     130 [. 0.99

  Alignments for each domain:
  == domain 1  score: 200.6 bits;  conditional E-value: 6.7e-64
                           DUF1699   1 mkirvvsskeeietlnenekivHlafrpsntdilslvkkcpklkaiqvpeSykktlsksakmfleiqgiellegdvw 77 
                                       mkirv+s+k++i++lnene++vHlafrps++d+ls+++k+p++k++qvp+Sy+++lsksakmfl++++i+llegdvw
  gi|298674625|ref|YP_003726375.1|   1 MKIRVISTKDDIDNLNENEEMVHLAFRPSDEDLLSIINKSPNIKVVQVPTSYMRSLSKSAKMFLDLRNITLLEGDVW 77 
                                       9**************************************************************************** PP

                           DUF1699  78 ghrkdineyyevseevierikelkseglseeeiaeklsketklspdlikfllk 130
                                       ghrkdineyye+++ v++ri+el++eg+s++ei++k++ketkl+p++i+fl++
  gi|298674625|ref|YP_003726375.1|  78 GHRKDINEYYEIPNGVYKRINELMDEGFSKDEIIDKVDKETKLEPEFIRFLIE 130
                                       ***************************************************96 PP

>> HIGH_NTase1  HIGH Nucleotidyl Transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   3.5e-05      0.31     317     377 ..       7      66 ..       1      71 [. 0.84
   2 ?    1.9   0.0     0.012     1e+02     262     297 ..      80     115 ..      69     120 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 3.5e-05
                       HIGH_NTase1 317 ikkedlkklkkkkpylrvLGfnkkgrelLkeikkksklplitklskakkklkeeakkllel 377
                                        +k+d+++l+++ + +  L+f+ + ++lL+ i+k+ ++++++  ++++++l+++ak +l+l
  gi|298674625|ref|YP_003726375.1|   7 STKDDIDNLNEN-EEMVHLAFRPSDEDLLSIINKSPNIKVVQVPTSYMRSLSKSAKMFLDL 66 
                                       578999999876.455559******************************999988877765 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.012
                       HIGH_NTase1 262 keelkkildvsegLenrikkalkkaesleelleklk 297
                                       ++++++++++ +g  +ri + +++  s +e+++k+ 
  gi|298674625|ref|YP_003726375.1|  80 RKDINEYYEIPNGVYKRINELMDEGFSKDEIIDKVD 115
                                       46799******************9999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 861.85
//
Query:       gi|298674626|ref|YP_003726376.1|  [L=405]
Description: hypothetical protein Metev_0675 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-07   32.3   4.9      1e-07   32.3   4.9    2.9  3  FtsX      FtsX-like permease family


Domain annotation for each model (and alignments):
>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.6     0.023   4.2e+02      65      87 ..      27      47 ..      10      62 .. 0.63
   2 ?   -0.3   0.5     0.087   1.6e+03      27      42 ..     279     294 ..     262     303 .. 0.52
   3 !   32.3   4.9   5.6e-12     1e-07       1      95 [.     304     397 ..     304     398 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.023
                              FtsX 65 dlitvliiivlllllallaglls 87
                                       +  +++++++++l ++++  +s
  gi|298674626|ref|YP_003726376.1| 27 TFAVIILVLAMSFLSVTFF--AS 47
                                      3344444444444444444..33 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.087
                              FtsX  27 litlvalviGlglgll 42 
                                       ++++v+l+i+++  ++
  gi|298674626|ref|YP_003726376.1| 279 ITGVVGLLIAFATIYI 294
                                       4455555555333222 PP

  == domain 3  score: 32.3 bits;  conditional E-value: 5.6e-12
                              FtsX   1 kreigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlll 77 
                                       +++ig+l+a+G kk  +l+ +++++l +++++ +iG ++  l+++++s + l++   +e+ + +    ++ + + + 
  gi|298674626|ref|YP_003726376.1| 304 RSQIGVLKAIGIKKEIILGSYIIQSLSYGVIGVAIGNVIMQLLLWFMSMYPLEVPI-GEVVPILTNQRIISTSITIA 379
                                       689*********************************99999999997777766654.77777777777777777777 PP

                              FtsX  78 llallagllsiskilkke 95 
                                       +  ++ag++++ +++k +
  gi|298674626|ref|YP_003726376.1| 380 MASVIAGYFPSNRAAKEN 397
                                       7777788******99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       901  (0.0502538); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 2360.27
//
Query:       gi|298674627|ref|YP_003726377.1|  [L=383]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.8e-27   94.3   1.9    1.3e-26   93.2   1.9    1.5  1  OrfB_IS605      Probable transposase
    1.7e-23   82.3   0.3    3.6e-23   81.3   0.3    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    4.3e-20   70.9   1.4    9.3e-20   69.8   1.4    1.6  1  HTH_OrfB_IS605  Helix-turn-helix domain
  ------ inclusion threshold ------
      0.012   15.8   0.3       0.03   14.5   0.3    1.7  1  zf-piccolo      Piccolo Zn-finger
      0.019   14.7   4.5       0.29   10.9   1.7    2.4  2  Phage_GP20      Phage minor structural protein GP20
      0.039   13.8   1.1       0.32   10.8   0.1    2.3  2  LemA            LemA family
       0.51   10.6   6.7       0.21   11.8   1.3    2.3  2  MapZ_EC1        MapZ extracellular domain 1


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.2   1.9   5.1e-30   1.3e-26      10     117 ..     180     284 ..     167     286 .. 0.91

  Alignments for each domain:
  == domain 1  score: 93.2 bits;  conditional E-value: 5.1e-30
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsr 86 
                                       +++  + +++g+D+Gi+++a++++++   ++ ++r lk+  ++l+  +++l++k+k+s+ny+k + ++a++h+k+++
  gi|298674627|ref|YP_003726377.1| 180 KQTFYEVNTVGVDVGIKDFAVTSDGE---KIDNPRYLKNSIERLKVLQKRLSRKKKGSNNYRKLKHQIAKYHEKIAN 253
                                       45555789******************...************************************************ PP

                        OrfB_IS605  87 rrkhllhklathliktlkevgvetLnvgnmk 117
                                       +r +++hkl+++li ++++v++e Lnv+++ 
  gi|298674627|ref|YP_003726377.1| 254 QREDFQHKLSSRLISENQAVALECLNVKGLL 284
                                       ****************************986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.3   0.3   1.4e-26   3.6e-23       1      68 [.     298     367 ..     298     368 .. 0.98

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 1.4e-26
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpay.TSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       ++++ ++leyka++yG++++++ ++  +Sk C++Cg+ +++ +l++r+++Cp+C++ +drD+nA++Ni k
  gi|298674627|ref|YP_003726377.1| 298 WSSFVQKLEYKAEWYGKNIIKIGRFDpSSKICHVCGYYHQDlELKDREWECPDCKTIHDRDINASVNIKK 367
                                       99******************************************************************87 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.8   1.4   3.7e-23   9.3e-20       1      47 []       9      54 ..       9      54 .. 0.98

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 3.7e-23
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeegk 47
                                      M lkaykyr yP++ Q+e++a+++G++Rf+YN+aL+ +++ ye+ gk
  gi|298674627|ref|YP_003726377.1|  9 M-LKAYKYRMYPNQIQQELIAKHIGACRFIYNWALENKIKSYEQDGK 54
                                      8.******************************************997 PP

>> zf-piccolo  Piccolo Zn-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.3   1.2e-05      0.03      28      55 ..     326     353 ..     322     356 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.2e-05
                        zf-piccolo  28 kqvCnlCGFnptphltekkeWlclnCQt 55 
                                       +++C +CG+  ++   + +eW c  C t
  gi|298674627|ref|YP_003726377.1| 326 SKICHVCGYYHQDLELKDREWECPDCKT 353
                                       79***********999**********86 PP

>> Phage_GP20  Phage minor structural protein GP20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.016        40     113     136 ..      51      77 ..      22      87 .. 0.76
   2 ?   10.9   1.7   0.00011      0.29      32      90 ..     218     276 ..     205     286 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.016
                        Phage_GP20 113 edgelkg...LdeqikkLkesdkyLFe 136
                                       +dg+ +    L++qi  Lke++++L e
  gi|298674627|ref|YP_003726377.1|  51 QDGKAISrfeLNKQIRVLKEDHEWLKE 77 
                                       566665444499999999999999976 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00011
                        Phage_GP20  32 eqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeyeakiadlkldnaielaLk 90 
                                       e+lk  +k L+  kk +++  +L+ qi+++ +k++++ ++ + k++ + +++    aL+
  gi|298674627|ref|YP_003726377.1| 218 ERLKVLQKRLSRKKKGSNNYRKLKHQIAKYHEKIANQREDFQHKLSSRLISENQAVALE 276
                                       6788889999999********************************99888776666666 PP

>> LemA  LemA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1      0.11   2.8e+02      36      82 ..      66     112 ..      41     116 .. 0.80
   2 ?   10.8   0.1   0.00013      0.32      55     107 ..     208     261 ..     180     268 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.11
                              LemA  36 evteaRakaaeaesveekaeaenqlssalsrllavaEnYPdLkanen 82 
                                       +v +  ++  ++ + ++ + a  +l++a+ +++     +P++k+++n
  gi|298674627|ref|YP_003726377.1|  66 RVLKEDHEWLKEINSQSLQGATLNLENAFTKFFREKSGFPKFKSKKN 112
                                       45555555577778899999999********************9987 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00013
                              LemA  55 eaenqlssalsrllavaEnY.PdLkanenfleLqeelegtEnriavaRrrYnea 107
                                       ++ + l+++++rl +++ +   + k ++n+++L++++++  ++ia++R++++++
  gi|298674627|ref|YP_003726377.1| 208 DNPRYLKNSIERLKVLQKRLsRKKKGSNNYRKLKHQIAKYHEKIANQREDFQHK 261
                                       5556677777777777776414567899**********************9876 PP

>> MapZ_EC1  MapZ extracellular domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.4      0.15   3.8e+02      48      84 ..      42      81 ..      39      93 .. 0.74
   2 ?   11.8   1.3   8.3e-05      0.21      37      78 ..     213     254 ..     173     277 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.15
                          MapZ_EC1 48 LekkLeklk.gskeYk..klkkkldslkkqisaieavNsq 84
                                      Le+k++ ++ + k  +  +l+k++  lk+  + ++++Nsq
  gi|298674627|ref|YP_003726377.1| 42 LENKIKSYEqDGKAISrfELNKQIRVLKEDHEWLKEINSQ 81
                                      5666666654333332227999999999999999999997 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 8.3e-05
                          MapZ_EC1  37 lknsefaklseLekkLeklk.gskeYkklkkkldslkkqisai 78 
                                       lkns ++ l+ L+k L   k gs++Y+klk+++++  ++i+ +
  gi|298674627|ref|YP_003726377.1| 213 LKNS-IERLKVLQKRLSRKKkGSNNYRKLKHQIAKYHEKIANQ 254
                                       4443.688999*****98777*****************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1486  (0.0828825); expected 358.6 (0.02)
Passed bias filter:                      671  (0.0374254); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 2330.61
//
Query:       gi|298674628|ref|YP_003726378.1|  [L=112]
Description: cupin 2 conserved barrel domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-14   52.4   0.2    4.4e-14   51.9   0.2    1.2  1  Cupin_2          Cupin domain
    9.9e-05   22.3   0.1    0.00011   22.1   0.1    1.1  1  MannoseP_isomer  Mannose-6-phosphate isomerase
      0.005   16.7   0.0     0.0058   16.5   0.0    1.1  1  AraC_binding     AraC-like ligand binding domain
     0.0056   17.0   0.0     0.0071   16.7   0.0    1.1  1  Pirin_C          Pirin C-terminal cupin domain
      0.009   15.6   0.0      0.015   14.9   0.0    1.5  1  Cupin_1          Cupin
  ------ inclusion threshold ------
      0.033   14.2   0.0       0.18   11.8   0.0    1.9  2  DUF4585          Domain of unknown function (DUF4585)


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   0.2   1.5e-17   4.4e-14       2      70 ..      33     100 ..      32     101 .. 0.97

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 1.5e-17
                                       EEEEETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEE CS
                           Cupin_2   2 lvelppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllvv 70 
                                       ++el+pGes   h+ p    ffyVleG++++++++e+ ++e++ +v  pa+ pHr+ N+g+  +r++vv
  gi|298674628|ref|YP_003726378.1|  33 HIELKPGESLRKHITPVD-VFFYVLEGTATIEIGEETEDVEKDNLVESPAKIPHRVMNNGESNVRFIVV 100
                                       5799*************8.***********************************************998 PP

>> MannoseP_isomer  Mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   3.6e-08   0.00011      61     137 ..      27     102 ..       5     108 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 3.6e-08
                   MannoseP_isomer  61 eryqvkritvkPgeklslqkhhhrae.hWvvvkGtakvtvddevlllkenestyiplgaihrlenpGkiplelievq 136
                                       ++ q  +i++kPge  sl+kh    +  + v++Gta +++++e+  +++++ +  p+   hr+ n G+ ++++i v+
  gi|298674628|ref|YP_003726378.1|  27 DHGQAVHIELKPGE--SLRKHITPVDvFFYVLEGTATIEIGEETEDVEKDNLVESPAKIPHRVMNNGESNVRFIVVK 101
                                       4456678999**99..5689988877256799****************************************99987 PP

                   MannoseP_isomer 137 s 137
                                       +
  gi|298674628|ref|YP_003726378.1| 102 M 102
                                       6 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.9e-06    0.0058       7      77 ..      33     103 ..      27     106 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.9e-06
                                       EETTSTT-SEEEETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-TTSEEEEEEEEE- CS
                      AraC_binding   7 ieagypdhsfpphvhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesdsedgweyrwlyfe 77 
                                       +    p++s ++h  +  v+ yv+eGt++++++++t d++++ l+  p   pH+    +e + ++ +++++
  gi|298674628|ref|YP_003726378.1|  33 HIELKPGESLRKHITPVDVFFYVLEGTATIEIGEETEDVEKDNLVESPAKIPHRVMNNGESNVRFIVVKMP 103
                                       5555688888899999999***********************************99999999998888886 PP

>> Pirin_C  Pirin C-terminal cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   2.4e-06    0.0071       2      68 ..      32     100 ..      31     107 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.4e-06
                                       EEEEE-TT-EEEEE--TT-EEEEEEEES-E..EESSTTEEE-TTEEEEE-.SSSEEEEE--SS-EEEEEE CS
                           Pirin_C   2 ldltleagaelelplpegleaavyvleGel..evggerseieeeqlavlg.dgdslvvkaeekgarvlLl 68 
                                       ++++l++g++l+      ++++ yvleG++  e+g+e++ +e+++l+    +  + v++ +e+++r++++
  gi|298674628|ref|YP_003726378.1|  32 VHIELKPGESLRKH-ITPVDVFFYVLEGTAtiEIGEETEDVEKDNLVESPaKIPHRVMNNGESNVRFIVV 100
                                       799*********99.6679*********963377888899*****9987755455555666689999886 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   4.9e-06     0.015      31     123 ..      27     110 ..       5     112 .] 0.79

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.9e-06
                                       STEEEEEEEE.TTEEEEEEEESSS-EEEEEEESEEEEEEEETTSS.EEEEEEEETTEEEEE-TT-EEEEEEESSSSE CS
                           Cupin_1  31 lgisaarvdlepgglllPhyhpnateiayvlqGegrvgfvvpgngnrdfhkklreGdvfvvPaglvhfqynsgdepa 107
                                        ++ a+ + l+pg  l  h++      +yvl+G++++++         ++ ++++  ++  Pa ++h ++n+g e++
  gi|298674628|ref|YP_003726378.1|  27 DHGQAVHIELKPGESLRKHIT-PVDVFFYVLEGTATIEIG-------EETEDVEKDNLVESPAKIPHRVMNNG-ESN 94 
                                       566777777777777777888.788889999999994432.......3456799999999************9.*** PP

                                       EEEEEEESSSTT-EEH CS
                           Cupin_1 108 vaivvfdtnnpgnqsv 123
                                       v ++v++  +p + ++
  gi|298674628|ref|YP_003726378.1|  95 VRFIVVKMPKPTESTQ 110
                                       *******999977765 PP

>> DUF4585  Domain of unknown function (DUF4585)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.2e-05      0.18      24      61 ..      15      52 ..      10      59 .. 0.89
   2 ?    0.1   0.0      0.29   8.8e+02      21      49 ..      77     107 ..      75     111 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.2e-05
                           DUF4585 24 PvqpktktlFDPetgqYvevlvpssesqssqaspvelp 61
                                      P  ++ ++l+D + gq v + ++  es  ++++pv++ 
  gi|298674628|ref|YP_003726378.1| 15 PHGVNARKLYDMDHGQAVHIELKPGESLRKHITPVDVF 52
                                      8889******************9999999999999875 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.29
                           DUF4585  21 vdlPvqpktktlFDPetg.qYvevlvps.se 49 
                                       v+ P +   + +   e+  +++ v +p+ +e
  gi|298674628|ref|YP_003726378.1|  77 VESPAKIPHRVMNNGESNvRFIVVKMPKpTE 107
                                       6777777777777777643677777776444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 714.70
//
Query:       gi|298674629|ref|YP_003726379.1|  [L=563]
Description: hybrid cluster protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.9e-180  600.3   0.0   3.5e-180  600.1   0.0    1.0  1  Prismane  Prismane/CO dehydrogenase family
  ------ inclusion threshold ------
       0.16   12.4   0.2       0.43   11.0   0.2    1.7  1  PHtD_u1   Unstructured region on Pneumococcal histidine triad


Domain annotation for each model (and alignments):
>> Prismane  Prismane/CO dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  600.1   0.0  3.9e-184  3.5e-180       1     511 []       1     560 [.       1     560 [. 0.96

  Alignments for each domain:
  == domain 1  score: 600.1 bits;  conditional E-value: 3.9e-184
                                       -EE-SST....CT-ECSCS.SS-TTS-BHHHHHHHHHHHHHHHHHHHHHHHHHHC......HHHHHHHHHCHTSTTT CS
                                       xxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxx RF
                          Prismane   1 mfCrqCe....ngpCritknkrGvCGkdadtavardlliavlkgaaahaaharel......adtliakalfktltnv 67 
                                       mfC+qCe    +++C+ +    GvCGk+ ++a+++d l++vlkg+a ++++are       +d+++++alf+t+tnv
  gi|298674629|ref|YP_003726379.1|   1 MFCYQCEetakGEGCTKK----GVCGKSNEVANLQDELMYVLKGIAFYNTKAREHglndekTDRFMLDALFATVTNV 73 
                                       9****************9....******************************************************* PP

                                       B-SHHHHHHHHHHHHCHHHCC.........................................SSHHHHHHHHC..CH CS
                                       xxxxxxxxxxxxxxxxxxxxx.........................................xxxxxxxxxxx..xx RF
                          Prismane  68 nfddekklkrlaealgieeel.........................................kdieelaakva..ev 101
                                       nf+ +++ +++++a+ i+++                                          +   ++ ++    + 
  gi|298674629|ref|YP_003726379.1|  74 NFSADDFRDMINDAFSIRDQVkdklvqnnidpvegrdisltdqikskllhkntidgssspdiA---TVTSQNLdnNE 147
                                       ********************************************************9885542...33322211245 PP

                                       HHCGGGS-SSHHHHHHHCCCHHHHHHH..HHHHCHHTT-HHHHHHHHHHHCCCCTTSTHHH...HHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxx RF
                          Prismane 102 aledlskeenedirslkellpkglkgl..yaehaivlgyadeevveflaktlaglesdpld...llskalrlGlldl 173
                                       +++ l+++ +ed+rsl+ell++g+kg+  ya+ha+vlgy d+e+++f+++ l ++ +d+l+   l++++l++G++ +
  gi|298674629|ref|YP_003726379.1| 148 NIGVLATK-DEDVRSLRELLTYGMKGMaaYAHHAHVLGYSDDEIFKFMERGLLATVDDNLSaddLTNLVLECGSIGV 223
                                       78888866.7**************************************************9999************* PP

                                       HHHHHHHHHHHHHH-----EEEEECGCG-.SSSEEEEEESS-HHHHHHHHHHHCTTCCCCCCCGCCCCCCHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane 174 kgmelldeantslfGtPeppltevnlgvldkdkvnIlvsGHdladleelleqtegkglnvythgemLpghcctalkl 250
                                       k+m +ldea+ts +G+Pep  te+nlgv+  + ++Il+sGHd++d+e+ll+qteg+g++vythgemLp+++++++k 
  gi|298674629|ref|YP_003726379.1| 224 KTMSILDEAHTSNYGNPEP--TEINLGVR-DN-PGILISGHDMKDMEQLLKQTEGTGVDVYTHGEMLPANAYPEFK- 295
                                       *******************..********.66.9******************************************. PP

                                       HHCCEEEEECSSGGGHHHHHCCHECEEEESSSS--TTHHHHHHCHCCEEEEECTTB-TTSEEE--CTTCHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane 251 kyrhlvgnvGnawqqekaeftgavdaivvdtnCivpplasvaekyktrlittsevakpgakhieeeekadkdaseii 327
                                       ky+h+vgn+G +w+++k+ef++++++i+++tnCivpp+++    y +rl+tts v++ ga+hi+++e+ +kd+s+ii
  gi|298674629|ref|YP_003726379.1| 296 KYDHFVGNYGGSWWKQKEEFEKFNGPILMTTNCIVPPKDT----YINRLYTTSIVGYDGATHIKADENGNKDFSQII 368
                                       *************************************766....********************99999******** PP

                                       HHHHCCHCCTTCGG.-.................HHHHHTTSS-EEEEE-B---TTCGCCHHHHHHHHCHHTTEEEEE CS
                                       xxxxxxxxxxxxxxxx.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane 328 ekAielakareekkve.................idaiksGtIkgvvlvvGCdnakkgrdyytelakelikrdvlvlt 387
                                       e+A++ +++++ ++ +                 +da+k+G+I ++v+++GCd++kk+r+yyt++ak+l ++d+++lt
  gi|298674629|ref|YP_003726379.1| 369 EQAKNTNPPQQLEEGKimggfahnaalsvadkiVDAVKNGQISRFVVMAGCDGRKKEREYYTDFAKQL-PEDTVILT 444
                                       **********88666688**************************************************.******** PP

                                       ECHHHHHCCCTTTTECGHHHHSTHCEESEEEEESCCCHHHHHHHHHHHHHHTTS.SGGGSSEEEEECC--SHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane 388 aGCakyalnklglgtieaaelagegiPrvLdvGsCvdnyrivvialklaealgv.dindLplaalalewyeqKAvai 463
                                       aGCaky++nkl+lg+i      g giPr+Ld+G+C+d+y++vvia+klaea+++ din+Lp+ +++++wyeqKAv +
  gi|298674629|ref|YP_003726379.1| 445 AGCAKYRYNKLDLGEI------G-GIPRILDAGQCNDSYSLVVIAQKLAEAFELdDINELPV-SYNIAWYEQKAVLV 513
                                       ****************......8.*****************************99*******.************** PP

                                       HHHHHHTT-.CEEECSS-TTTT-HHHHHHHHCHHHHHHCEEEECHCHHH CS
                                       xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane 464 lltllalGi.nihlgptlpafgspnvlkvlvedfedriggivtveedpe 511
                                       ll ll+lG+ ni lgp+lpaf+spn+l+vlv++f  +i++ +tveed+e
  gi|298674629|ref|YP_003726379.1| 514 LLSLLSLGVkNITLGPSLPAFVSPNMLNVLVDKF--NIAPNSTVEEDME 560
                                       **********************************..***********96 PP

>> PHtD_u1  Unstructured region on Pneumococcal histidine triad protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   4.8e-05      0.43      19      44 ..     132     162 ..     123     168 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.8e-05
                           PHtD_u1  19 qP.....tntrlSnNsnlnsqpsQgedidSL 44 
                                        P     t  +l nN n+ + ++  ed+ SL
  gi|298674629|ref|YP_003726379.1| 132 SPdiatvTSQNLDNNENIGVLATKDEDVRSL 162
                                       455554477799******************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (563 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 3509.71
//
Query:       gi|298674630|ref|YP_003726380.1|  [L=142]
Description: HxlR family transcriptional regulator [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-23   82.1   0.6    2.4e-23   81.8   0.6    1.1  1  HxlR          HxlR-like helix-turn-helix
    0.00029   20.7   0.1    0.00049   20.0   0.1    1.4  1  PadR          Transcriptional regulator PadR-like family
    0.00097   19.4   0.3     0.0027   18.0   0.3    1.6  2  DUF2513       Hypothetical protein (DUF2513)
      0.003   17.4   0.1     0.0044   16.9   0.1    1.3  1  MarR          MarR family
     0.0038   15.7   0.2     0.0043   15.5   0.2    1.0  1  DUF505        Protein of unknown function (DUF505)
     0.0049   17.0   0.1     0.0087   16.2   0.1    1.4  1  HTH_34        Winged helix DNA-binding domain
      0.007   15.9   0.0      0.013   15.0   0.0    1.4  1  HTH_24        Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.014   15.4   0.0      0.022   14.7   0.0    1.4  1  HTH_12        Ribonuclease R winged-helix domain
      0.014   15.2   0.1      0.018   14.8   0.1    1.3  1  DUF4423       Domain of unknown function (DUF4423)
      0.023   14.6   0.0      0.029   14.2   0.0    1.2  1  MarR_2        MarR family
      0.035   14.2   0.0       0.05   13.7   0.0    1.2  1  HTH_20        Helix-turn-helix domain
      0.041   14.2   0.0       0.06   13.7   0.0    1.2  1  Rrf2          Transcriptional regulator
      0.044   13.8   0.2       0.11   12.5   0.2    1.7  1  HTH_45        Winged helix-turn-helix
      0.085   12.9   0.0      0.099   12.7   0.0    1.1  1  Replic_Relax  Replication-relaxation
       0.11   12.4   0.0       0.18   11.8   0.0    1.4  1  HTH_Crp_2     Crp-like helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.8   0.6     2e-26   2.4e-23       1      87 [.      32     122 ..      32     126 .. 0.92

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 2e-26
                                       HHHSTTHHHHHHHHTTS-...EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEE.SSSS-EEEEEE-TCGGGGH CS
                              HxlR   1 liggkWkllilvellkgk...kRfselkralpkisqkmLaqrLreLeqdglierevy.pevPpkveYsltekGrsle 73 
                                       +ig++W+l il el kg+   k f+elk+ l +i+ k+L++rLreLeq+gl+ ++v  +++P k +Y+lt+ G++  
  gi|298674630|ref|YP_003726380.1|  32 IIGKRWTLCILLELYKGQneeKQFNELKNMLQNITPKTLTTRLRELEQQGLVRKKVDdSSIPIKCKYTLTDSGEDFI 108
                                       79*************98644489*****************************999862679**************** PP

                                       HHHHHHHHHHHHHH CS
                              HxlR  74 pvlqelkkwgeeyl 87 
                                       +++q++kkwg ++ 
  gi|298674630|ref|YP_003726380.1| 109 EIIQQIKKWGLKWK 122
                                       **********9996 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   4.1e-07   0.00049      20      73 ..      56     108 ..      46     116 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 4.1e-07
                                       HCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHH CS
                              PadR  20 eelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrel 73 
                                       +el + l ++ + +l + L++Le++glv ++ ++s + p +  Y+lTd G++ +
  gi|298674630|ref|YP_003726380.1|  56 NELKNMLQNITPKTLTTRLRELEQQGLVRKKVDDS-SIPIKCKYTLTDSGEDFI 108
                                       555555566777789999*************9996.9999999*******9876 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       2.1   2.6e+03      78      95 ..      14      31 ..      10      40 .. 0.79
   2 !   18.0   0.3   2.3e-06    0.0027      10      91 ..      41     117 ..      35     126 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.1
                           DUF2513 78 GhdFLdsiRddtvWkkvk 95
                                      G  ++d+++d t++k+v 
  gi|298674630|ref|YP_003726380.1| 14 GSFYVDTMKDCTLYKTVD 31
                                      556899999999998875 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 2.3e-06
                           DUF2513  10 iLltleeletkeeslddeeeklsaidgyskeeiiyhlkllaeagLieaekkkakssiislvvkrLtweGhdFLdsiR 86 
                                       iLl+l + +++e++++  +   + +++ + +++   l+ l+++gL++ + + ++   +  + + Lt +G dF++ i+
  gi|298674630|ref|YP_003726380.1|  41 ILLELYKGQNEEKQFNELK---NMLQNITPKTLTTRLRELEQQGLVRKKVDDSSI--PIKCKYTLTDSGEDFIEIIQ 112
                                       7777777777777776644...389999999***************987766554..5777889************* PP

                           DUF2513  87 ddtvW 91 
                                       + + W
  gi|298674630|ref|YP_003726380.1| 113 QIKKW 117
                                       *9999 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   3.7e-06    0.0044      28      51 ..      64      87 ..      41      91 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.7e-06
                                      TS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR 28 gvskstvtrvldrLekkGlieRsk 51
                                      ++++ t+t+ l++Le++Gl++++ 
  gi|298674630|ref|YP_003726380.1| 64 NITPKTLTTRLRELEQQGLVRKKV 87
                                      799*****************9975 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   3.6e-06    0.0043     343     413 ..      48     116 ..      32     127 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.6e-06
                            DUF505 343 keeiakkfeeakdlekWyednfdlreaLysLesfeLieseveekg...kevyvlTeyGekvledqekklrevsa 413
                                        ++ +k+f+e+k++        +l++ L +Le  +L++++v++     k  y+lT+ Ge  +e     +++++ 
  gi|298674630|ref|YP_003726380.1|  48 GQNEEKQFNELKNML-QNITPKTLTTRLRELEQQGLVRKKVDDSSipiKCKYTLTDSGEDFIEI----IQQIKK 116
                                       455566777777775.233455788888888888888888876666778888888888888873....344444 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   7.3e-06    0.0087       5      67 ..      41     106 ..      38     117 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.3e-06
                            HTH_34   5 vlsyLas..vdeadfvelkeale.atdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGre 67 
                                       +l  L++  ++e +f+elk+ l+ +t   L + l+ Le++g +  + + ++   +  +++T+ G +
  gi|298674630|ref|YP_003726380.1|  41 ILLELYKgqNEEKQFNELKNMLQnITPKTLTTRLRELEQQGLVRKKVDDSSIPIKCKYTLTDSGED 106
                                       6666777779***********954899**************8876666666555678999999965 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.1e-05     0.013      28      48 .]      64      84 ..      63      84 .. 0.96

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-05
                            HTH_24 28 glSpstvnrrlkrLeeeGlIk 48
                                      +++p t+++rl++Le++Gl++
  gi|298674630|ref|YP_003726380.1| 64 NITPKTLTTRLRELEQQGLVR 84
                                      89*****************96 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.8e-05     0.022      22      64 ..      57     106 ..      47     108 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.8e-05
                            HTH_12  22 eLkkrgydigeravRyrLrkleergltrrvgya.......greltEkGle 64 
                                       eLk+   +i  +++  rLr le++gl+r++          + +lt+ G++
  gi|298674630|ref|YP_003726380.1|  57 ELKNMLQNITPKTLTTRLRELEQQGLVRKKVDDssipikcKYTLTDSGED 106
                                       78888899999*****************9877656777777777777766 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   1.5e-05     0.018      19      74 ..      35      89 ..      28     117 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.5e-05
                           DUF4423 19 ssWyypvirellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedg 74
                                      ++W   +++el + ++++++ +el+++l+ +i+ +   + l+ L++ gl++k+ d+
  gi|298674630|ref|YP_003726380.1| 35 KRWTLCILLELYKGQNEEKQFNELKNMLQ-NITPKTLTTRLRELEQQGLVRKKVDD 89
                                      579**************************.*********************99875 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.5e-05     0.029      32      55 ..      64      87 ..      41      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.5e-05
                                      TSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2 32 glsksavsrilkrLvaaGLverrp 55
                                      ++++ +++ +l++L+++GLv+++ 
  gi|298674630|ref|YP_003726380.1| 64 NITPKTLTTRLRELEQQGLVRKKV 87
                                      58999***************9984 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.2e-05      0.05      27      55 ..      55      84 ..      40      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.2e-05
                                      HHHHHHHH.TS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20 27 aselaerl.dlskntlsyHLrvLeeagLve 55
                                      ++el+  l  ++++tl  +Lr+Le+ gLv+
  gi|298674630|ref|YP_003726380.1| 55 FNELKNMLqNITPKTLTTRLRELEQQGLVR 84
                                      6677777866*******************8 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     5e-05      0.06       9      56 ..      37      84 ..      34      87 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5e-05
                                      HHHHHHHHHHHSSTCC-B-HHHHHH.HHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2  9 yalhallyLakeeeeepvsseeiae.rqnispsylekilakLrkaglvk 56
                                        l +ll+L k ++ee  + +e+ +  qni p+ l   l++L+++glv+
  gi|298674630|ref|YP_003726380.1| 37 WTLCILLELYKGQNEE-KQFNELKNmLQNITPKTLTTRLRELEQQGLVR 84
                                      56899****9999988.999***99457********************8 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   9.1e-05      0.11      30      74 ..      64     116 ..      45     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.1e-05
                            HTH_45  30 nLsykllnkYLdmLvekgli........kkskekYvlTekGlelleklkelee 74 
                                       n++ k+l   L  L ++gl+           k kY+lT+ G++++e ++++++
  gi|298674630|ref|YP_003726380.1|  64 NITPKTLTTRLRELEQQGLVrkkvddssIPIKCKYTLTDSGEDFIEIIQQIKK 116
                                       6777888889999******976654322223679**************99986 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   8.3e-05     0.099      25      82 ..      65     121 ..      51     136 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.3e-05
                      Replic_Relax  25 a...tarrrLarLrelgllsr.lrkrvggarggsepyvYaLtpkGarllaaqraepeprskr 82 
                                           t+ +rL++L+++gl+++ ++ +  ++     +  Y+Lt  G+++++  ++ +++  k+
  gi|298674630|ref|YP_003726380.1|  65 ItpkTLTTRLRELEQQGLVRKkVDDS--SIPI---KCKYTLTDSGEDFIEIIQQIKKWGLKW 121
                                       23347999*************88888..7777...89***********95555455555444 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00015      0.18      32      54 ..      64      86 ..      41      95 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                                      TSSHHHHHHHHHHHHHTTSEEET CS
                         HTH_Crp_2 32 GltretvsrilseLkreglisrg 54
                                      ++t+ t++  l+eL+++gl++++
  gi|298674630|ref|YP_003726380.1| 64 NITPKTLTTRLRELEQQGLVRKK 86
                                      49******************953 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1249  (0.0696637); expected 358.6 (0.02)
Passed bias filter:                      688  (0.0383736); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 883.90
//
Query:       gi|298674631|ref|YP_003726381.1|  [L=314]
Description: PP-loop domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.9e-15   55.5   0.0    9.1e-15   54.9   0.0    1.3  1  ATP_bind_3     PP-loop family
    0.00028   21.0   0.0    0.00055   20.0   0.0    1.4  1  PAPS_reduct    Phosphoadenosine phosphosulfate reductase fami
    0.00057   19.1   0.0    0.00078   18.6   0.0    1.2  1  NAD_synthase   NAD synthase
     0.0025   16.7   0.0     0.0036   16.1   0.0    1.2  1  tRNA_Me_trans  tRNA methyl transferase
  ------ inclusion threshold ------
       0.01   15.3   7.1       0.01   15.3   7.1    3.0  3  zn-ribbon_14   Zinc-ribbon
      0.065   12.9   0.0       0.11   12.1   0.0    1.3  1  Asn_synthase   Asparagine synthase
       0.91    9.1  10.6       0.32   10.6   4.3    2.9  3  RecR           RecR protein


Domain annotation for each model (and alignments):
>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   0.0   3.5e-18   9.1e-15       2     156 ..      62     227 ..      61     245 .. 0.84

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 3.5e-18
                                       EEEE--SCHHHHHHHHHHHHHCTTT.TTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H......... CS
                        ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkkl.giklvaihvdhglreeskeeaelvkelckklnikleiekvdv......... 68 
                                       +++A+SgG DS++Ll++l+k   +   i+lvai++d g++    +  +  kel ++l+ik++i ++           
  gi|298674631|ref|YP_003726381.1|  62 IAIALSGGKDSTVLLYILNKIFGDRpDINLVAITIDEGISGYRLDTIQKSKELTDNLGIKHVIRSFADeygmtldel 138
                                       689***************9987665156*************************************998887777666 PP

                                       .HHCTTSTCCCHHHHHHHHHHHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--CCHHH-S-SEEEETTCCE.E-C CS
                        ATP_bind_3  69 .akkkgknleeaARelRYevlkealkkegievlllAhhadDqaEtfllrlargsglaglagikeaseiasirl.vRP 143
                                        +k+++ +       +R ++l++++k+eg++ l+++h+ dD a t+ll++ +g     l+ +++ ++i++ +l + P
  gi|298674631|ref|YP_003726381.1| 139 tQKQRSYGACSYCGVFRKKLLNKTAKEEGATRLAIGHNLDDEAQTILLNHLKGDIS-RLVRLDPPKKIEGLTLrIKP 214
                                       5445555556666679************************************9875.77778888888884443788 PP

                                       CCT--HHHHHHHH CS
                        ATP_bind_3 144 lLkvskeeleeyl 156
                                       l  +  +e+  y+
  gi|298674631|ref|YP_003726381.1| 215 LRSIPEKEVALYA 227
                                       8888777776665 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   2.1e-07   0.00055       2     154 ..      62     233 ..      61     235 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.1e-07
                                       EEEE--SSCTCHHHHHHHHHHCTTH.....EEEEEE-STB..-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHH CS
                       PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpv.....pvvfvdtghe..fpetiefvdeleeryglrlkvyepeeevaekinae 71 
                                       ++++ sgGkds+Vll ++ k+f ++       + +d g      +ti+  +el++++g++  + +  +e    + + 
  gi|298674631|ref|YP_003726381.1|  62 IAIALSGGKDSTVLLYILNKIFGDRpdinlVAITIDEGISgyRLDTIQKSKELTDNLGIKHVIRSFADEYGMTLDEL 138
                                       68899*******************87787678899999872245899999**********88889999999999999 PP

                                       H-S-THHHC.HHHHHHTHHHHHHHHHCTTECEEE----CCCTTTTTTSSSEEECTTT-S.............CEEE- CS
                       PAPS_reduct  72 khgsslyee.aaeriaKveplkkaLekldedalltGaRrdesksraklpiveidedfek.............slrvf 134
                                       ++ ++ y    ++ + + + l+k+ ++ +++ l +G   d++++   l+ ++ d +  +             +lr+ 
  gi|298674631|ref|YP_003726381.1| 139 TQKQRSYGAcSYCGVFRKKLLNKTAKEEGATRLAIGHNLDDEAQTILLNHLKGDIS--RlvrldppkkieglTLRIK 213
                                       999999999999****************************9998888877766655..4458899999999999999 PP

                                       CCCT--HHHHHHHHHHCT-- CS
                       PAPS_reduct 135 PllnWteedvwqyilrenip 154
                                       Pl    e++v  y+  +++p
  gi|298674631|ref|YP_003726381.1| 214 PLRSIPEKEVALYAIVNELP 233
                                       **999999999999988887 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0     3e-07   0.00078       4     119 ..      45     165 ..      42     182 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 3e-07
                                       HHHHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCG...EEEEEE--SSST..THHHHHHHHHHHHHHTSE CS
                      NAD_synthase   4 elvdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgke...nvlalllPssvs..seedvedalalaenlgie 75 
                                       +++  ++++ + +  + + + lSGG DS++  ++  k++g+    n +a+ + +  s    + ++++++l +nlgi+
  gi|298674631|ref|YP_003726381.1|  45 KIKLTIRKHYNINRNETIAIALSGGKDSTVLLYILNKIFGDRpdiNLVAITIDEGISgyRLDTIQKSKELTDNLGIK 121
                                       677888999999999999*********************8653348899999954441145679************* PP

                                       EEE---HHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHH CS
                      NAD_synthase  76 vktidikpivrafeqelkeakedlakgNlkaRiRmailyaiank 119
                                           + ++ + +  +el++++    +   +   R ++l + a++
  gi|298674631|ref|YP_003726381.1| 122 HVIRSFADEYGMTLDELTQKQRSYGACSYCGVFRKKLLNKTAKE 165
                                       *9999999999888888877766666666666666666666655 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.4e-06    0.0036       2     124 ..      61     175 ..      60     192 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.4e-06
                     tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfekeykekv 78 
                                       ++++alSgG DS+v +++l++ + +   + l  ++  de   +    + +++ ++  ++lgi++ + +f++ey  ++
  gi|298674631|ref|YP_003726381.1|  61 TIAIALSGGKDSTVLLYILNKIFGDRPDINLVAITI-DEGI-SGYRLDTIQKSKELTDNLGIKHVIRSFADEYGMTL 135
                                       799**************************9998887.4444.45667889***********************8876 PP

                     tRNA_Me_trans  79 feefleeyeeGrTPnPdvlCNkeiKfgallekakeelgadalatGH 124
                                        e + ++ + G     +  C    K  +ll+k  +e ga  la GH
  gi|298674631|ref|YP_003726381.1| 136 DELTQKQRSYGA----CSYCGVFRK--KLLNKTAKEEGATRLAIGH 175
                                       655555555553....667764433..3444444447777777777 PP

>> zn-ribbon_14  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.6      0.17   4.4e+02       2       7 ..      14      19 ..      13      22 .. 0.83
   2 ?   -1.2   0.3      0.57   1.5e+03       1       8 [.     146     153 ..     146     154 .. 0.81
   3 ?   15.3   7.1   3.9e-06      0.01       2      21 ..     292     311 ..     291     313 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.17
                      zn-ribbon_14  2 kCerCG 7 
                                      +C++C+
  gi|298674631|ref|YP_003726381.1| 14 QCTKCD 19
                                      8****6 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.57
                      zn-ribbon_14   1 gkCerCGy 8  
                                       g C+ CG 
  gi|298674631|ref|YP_003726381.1| 146 GACSYCGV 153
                                       57****96 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 3.9e-06
                      zn-ribbon_14   2 kCerCGylSSqkiCkACvLL 21 
                                        C+ CG l+  ++C+AC LL
  gi|298674631|ref|YP_003726381.1| 292 ECSVCGDLCTGSLCQACKLL 311
                                       7******************9 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.3e-05      0.11      19      83 ..      61     131 ..      45     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.3e-05
                      Asn_synthase  19 pvGalLSGGlDSSliaalaarqsk..splktFsigfee....kgsdeakyakevaehlgtehtelvlteee 83 
                                        +++ LSGG DS+++ +++++     ++++ ++i+ +e     + d ++  ke+ + lg++h+   +  e 
  gi|298674631|ref|YP_003726381.1|  61 TIAIALSGGKDSTVLLYILNKIFGdrPDINLVAITIDEgisgYRLDTIQKSKELTDNLGIKHVIRSFADEY 131
                                       67899****************98888999999999966676688899**************9877666655 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.49   1.3e+03      17      24 ..      13      20 ..       4      22 .. 0.79
   2 ?    0.6   0.0      0.17   4.3e+02       9      25 ..     138     154 ..     135     157 .. 0.73
   3 ?   10.6   4.3   0.00012      0.32      15      35 ..     289     309 ..     287     310 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.49
                                      EE-TTT-- CS
                              RecR 17 rhCsrCgn 24
                                      r+C +C n
  gi|298674631|ref|YP_003726381.1| 13 RQCTKCDN 20
                                      57888866 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.17
                                       HHHHHHH-EE-TTT--E CS
                              RecR   9 LqeakekvrhCsrCgnl 25 
                                       L++  ++ + Cs Cg +
  gi|298674631|ref|YP_003726381.1| 138 LTQKQRSYGACSYCGVF 154
                                       5666667788****976 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00012
                                       H-EE-TTT--EESSSS-CCCC CS
                              RecR  15 kvrhCsrCgnlteedlCaICs 35 
                                       k+  Cs+Cg l++  lC+ C+
  gi|298674631|ref|YP_003726381.1| 289 KLNECSVCGDLCTGSLCQACK 309
                                       7789****************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       849  (0.0473534); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 1887.39
//
Query:       gi|298674632|ref|YP_003726382.1|  [L=442]
Description: hypothetical protein Metev_0682 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-74  251.5  38.1    1.4e-74  251.3  38.1    1.0  1  TctA             Tripartite tricarboxylate transporter TctA f


Domain annotation for each model (and alignments):
>> TctA  Tripartite tricarboxylate transporter TctA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  251.3  38.1   7.8e-79   1.4e-74       1     408 [.      13     430 ..      13     431 .. 0.93

  Alignments for each domain:
  == domain 1  score: 251.3 bits;  conditional E-value: 7.8e-79
                              TctA   1 LllvllGvllGtliGllPGlhatlavalllpltf.....gldpeaalilllgiyvgaifggsipaillgvPGtpssv 72 
                                       Ll++l+G++lG+++Gl+PG+h+++++++l+ l+      g+  ++a++++ + +++++f+++ip+i+lg+P +++++
  gi|298674632|ref|YP_003726382.1|  13 LLSILAGYILGVISGLIPGIHTNNFAMVLVYLSSvmadyGITTIYAAVIISSNSITHTFHDVIPSIFLGAP-SEDMA 88 
                                       899******************************9999999999****************************.***** PP

                              TctA  73 atvldgyplakqGrageAlrlaaigSfiGglvsvllllllapllakvalkfgpaeyfalillglvliailse..... 144
                                       ++vl+g++l ++G ++eA++l+aigS+ ++++s++l+l++a +++  +++   ++y+ +ill+++l+++ +e     
  gi|298674632|ref|YP_003726382.1|  89 LAVLPGHQLSLEGSGAEAIKLSAIGSAGSIIFSLILVLPVAGVFS--TMYPIIQNYMGWILLVIILLMVATEkgesv 163
                                       *********************************************..****************************** PP

                              TctA 145 .........ksllkglialllglllgtvgldpnsgtpRftfgsielldgislvpvliGlFgiselltsleskskip. 211
                                                k+ + +++++ll++llg++++++++ ++     ++++ +   l+p+l+GlFg+s+l+ sl+s+++ip 
  gi|298674632|ref|YP_003726382.1| 164 agqgqlvpyKHKFYAFVIFLLSGLLGYFAFETEYLIE----PVVDIGSPSILLPLLSGLFGASQLVISLMSRTDIPp 236
                                       *********************************9666....799**************************9999987 PP

                              TctA 212 .......lslkdlkkslptilrgsliGtivGilPgvGasiaaflayavakr.ls.kkpekfgkgaiegvaapeaann 279
                                              l+++++++    i+ gs++G+iv+++Pg+++sia++++  +    ++ k+ e   + ++e++++++++n+
  gi|298674632|ref|YP_003726382.1| 237 qkysipkLERSKISR---GIAMGSVAGSIVAWIPGISSSIATVISRLFITDnFNnKNTEDELDSSKEFIVSVSGVNT 310
                                       776654334444444...5888***********************998776454133344456************** PP

                              TctA 280 aaaggaliplltlgipgsgvaavllgallihglqpgpeLftenpelvyallasllianvlllvlgllliklfakll. 355
                                       ++a++ l  l+++  ++sg+++++++++        ++    n ++v+++++++l a++l+++ ++++++ + ++l 
  gi|298674632|ref|YP_003726382.1| 311 SNAVFGLLSLVVIEKTRSGAMVAFNKLI-----DASQL----NGQFVILFFCIILAAAFLSYLSTIVIGNNAYRILs 378
                                       **************************75.....45555....99******************************998 PP

                              TctA 356 kipkelLlpiilvllvigayalnnslfdvlvmlifgvlGlllrrlgvplaplv 408
                                       ki+++ L++ +++ l+++++++++  +++l+++i++ +G++   + v++++++
  gi|298674632|ref|YP_003726382.1| 379 KIDYYKLCISVILGLALLVFLFTGL-YGLLIFIIATPIGMMAPFMTVKKSNAM 430
                                       *************************.**********************99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       865  (0.0482459); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 2687.08
//
Query:       gi|298674633|ref|YP_003726383.1|  [L=185]
Description: hypothetical protein Metev_0683 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-48  162.4   0.1    4.4e-48  162.1   0.1    1.1  1  Trm56           tRNA ribose 2'-O-methyltransferase, aTrm56
     0.0017   18.5   0.0     0.0024   18.0   0.0    1.2  1  SpoU_methylase  SpoU rRNA Methylase family


Domain annotation for each model (and alignments):
>> Trm56  tRNA ribose 2'-O-methyltransferase, aTrm56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.1   0.1   4.9e-52   4.4e-48       1     119 []      57     174 ..      57     174 .. 0.99

  Alignments for each domain:
  == domain 1  score: 162.1 bits;  conditional E-value: 4.9e-52
                                       H-S--EEE.E--HHHHHHC-S...SEEEEE-TTSEEHHHHHHHHHC-SE.EEEEE------TCHHHHSSEEEESSSS CS
                             Trm56   1 wGgefkvevakslkklikefkkeggivvhltmyGenieevieeikkkekdllvvvGaekvprevyeladynvsvgnq 77 
                                       wGg+f v++++++kk i+++k++gg+v+hl+myG+n+++v ++ik+ +k ++++vGaekvp evy++ad nv+vgnq
  gi|298674633|ref|YP_003726383.1|  57 WGGNFYVKNNVNWKKEIQSWKNNGGKVCHLSMYGLNLSDVESDIKNWHK-IMIIVGAEKVPPEVYDMADLNVAVGNQ 132
                                       *********************************************9988.*************************** PP

                                       ---HHHHHHHHHHHHC.--TTT---TT-SSEEE--SSS-EEE CS
                             Trm56  78 PhsevaalaifldrllegkelekefedaklkviPsergkkvv 119
                                       Phsevaa+++++dr+ + + l++ef da+l+++P++rgkkv+
  gi|298674633|ref|YP_003726383.1| 133 PHSEVAAISVTMDRISDYDPLKQEFGDAELSIVPTSRGKKVI 174
                                       ****************************************96 PP

>> SpoU_methylase  SpoU rRNA Methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.7e-07    0.0024      21     122 ..      28     129 ..      23     145 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.7e-07
                                       HHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEEEESTT-SEGCCSHHH... CS
                    SpoU_methylase  21 takafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegfalvatslkgkslseidlk... 94 
                                       ta+afga++l+l ++++a  +n e ++   g  ++++     ++++ ++ +k++g +++ +s +g +ls+++ +   
  gi|298674633|ref|YP_003726383.1|  28 TARAFGAEGLLLASDDRAIADNIESVARRWGGNFYVK--NNVNWKKEIQSWKNNGGKVCHLSMYGLNLSDVESDikn 102
                                       789***********99998899888888899999998..6779*************************977555557 PP

                                       .TTEEEEEEBTTTBS-HHHHCTSSEEEE- CS
                    SpoU_methylase  95 .ekvalvfGnEdkGlsnelleladrlvkI 122
                                         k+++++G E+  +++e+ + ad  v +
  gi|298674633|ref|YP_003726383.1| 103 wHKIMIIVGAEK--VPPEVYDMADLNVAV 129
                                       89*********6..677777777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1318.11
//
Query:       gi|298674634|ref|YP_003726384.1|  [L=506]
Description: AMP phosphorylase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-16   59.1   0.1    6.2e-16   58.0   0.1    1.6  1  Glycos_trans_3N  Glycosyl transferase family, helical bundle 
    1.5e-12   47.0   0.6    8.9e-12   44.5   0.1    2.4  2  PYNP_C           Pyrimidine nucleoside phosphorylase C-termin
    6.7e-12   45.5   1.3    7.7e-11   42.1   1.3    2.2  1  Glycos_transf_3  Glycosyl transferase family, a/b domain
    1.5e-05   25.0   0.1    4.5e-05   23.5   0.0    1.7  2  Molydop_binding  Molydopterin dinucleotide binding domain
  ------ inclusion threshold ------
       0.02   15.0   0.1      0.043   14.0   0.1    1.6  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
       0.03   13.2   0.0      0.044   12.6   0.0    1.2  1  DUF2254          Predicted membrane protein (DUF2254)
       0.28   11.0   2.4       0.68    9.8   0.1    2.9  3  Biotin_lipoyl    Biotin-requiring enzyme


Domain annotation for each model (and alignments):
>> Glycos_trans_3N  Glycosyl transferase family, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   0.1   2.4e-19   6.2e-16       2      63 .]      89     150 ..      88     150 .. 0.97

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 2.4e-19
                                       HHHHHHHTT.---HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHHHHHHHHHHS CS
                   Glycos_trans_3N   2 diikklrdgeeLtaeeirfaihgilkgevtdaqiaAfLmAlrlkGetaeEiaalaeAmresg 63 
                                       ++ikkl+++++Lt+eei+ +++gi++ +++d++++Af++A +++ ++ +E+  l++Am++ g
  gi|298674634|ref|YP_003726384.1|  89 QVIKKLMNKQKLTQEEIYLLVNGIVDESLSDIELSAFMTASYINDMSDDETEWLTRAMIDTG 150
                                       68********************************************************9875 PP

>> PYNP_C  Pyrimidine nucleoside phosphorylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.36   9.3e+02      18      29 ..     371     382 ..     360     393 .. 0.79
   2 !   44.5   0.1   3.5e-15   8.9e-12       2      74 ..     425     490 ..     424     491 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.36
                                       TTSBSSTTS--- CS
                            PYNP_C  18 GAGRakkeDpid 29 
                                       G GR+++eD++ 
  gi|298674634|ref|YP_003726384.1| 371 GQGRKVAEDTLR 382
                                       779******986 PP

  == domain 2  score: 44.5 bits;  conditional E-value: 3.5e-15
                                       EEEE-HHHHHHHHHHTTTSBSSTTS---TT-EEEES--TT-EEBTTSEEEEEEESSSCHHHHHHHHHHHHEEE CS
                            PYNP_C   2 vseidareiGlaaveLGAGRakkeDpidlavGielhkklGdkVkkGeplatiYankeekleeavkklkkaiki 74 
                                       + e++++++  +a+ +GA       p d+++G+ +hkk G++Vkk+++++ti+++ke kl++avk ++ +  i
  gi|298674634|ref|YP_003726384.1| 425 LIEFNNKRLIEIARLAGA-------PNDKGAGVLIHKKRGESVKKDQAVLTIHSEKEYKLKSAVKSAQMNSPI 490
                                       567899999999******.......******************************************999876 PP

>> Glycos_transf_3  Glycosyl transferase family, a/b domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   1.3     3e-14   7.7e-11       3     252 ..     159     386 ..     157     387 .. 0.84

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 3e-14
                                       TBEEEEESS-SSSTHHHHHHHHHHHHHHTT-BEEEEE-STCTTCS-HHHHHCTST--ST--HHHHHHHHHHHSEEEE CS
                   Glycos_transf_3   3 dlvDivgTGGdgantfNiStaaaivvAaaGvkvakhgnrsvssksGsaDvLealgvnleltpeeveklleevgvgfl 79 
                                       +++D+++ GG+  n   iS+   ++vAa G+ ++k + r+++  +G++D++e l   +e t++ev+++ e+vg +++
  gi|298674634|ref|YP_003726384.1| 159 PVMDKHSIGGVPGNK--ISLLVVPIVAANGLMIPKTSSRAITGAGGTSDLMEVL-APVEFTASEVRSMTEKVGGVLV 232
                                       689***********9..***********************************99.589*************997777 PP

                                       E..HHSSSSHHHHHHHHHHHHTT.-SSHHHCHHHHHT..SEE.EEHHHHHHHHTCHSEEEEEEEESTTSSCCSTSHH CS
                   Glycos_transf_3  80 f..apeyhkamkhvapvrrelgirTvfnlLGPLinparvkkq.llgvyskelaeklaevlkelgveralvvhgdGld 153
                                          a++  +a ++ + +              PL     ++ q l ++++k+   ++++v+ +++++++  +++  + 
  gi|298674634|ref|YP_003726384.1| 233 WggATNIAPADDKLIRIEY------------PLSID--PHCQlLASIMAKKGSVGADQVVIDIPTGEGTKIKN--VQ 293
                                       4114444444444444433............55332..34440559***************************..** PP

                                       HHHHHHHHHHHHHH.TTEEEEEEEEEGSSTSSSEEESHHHHSSHHHHHHHHTTHHTSCHHHHHHHHHHHHHHHHHHH CS
                   Glycos_transf_3 154 evsllakttvaelk.dgeiteytlepedfglkraelealeggepkenaeilkavlegkksaakrdlvllnagaalvl 229
                                       e + la  ++   +  g   e +l+  + +++r  + ale+   +e++++l+++ eg++s +  +  +  ag++l  
  gi|298674634|ref|YP_003726384.1| 294 EGRKLARDLINLGErLGMNIECALTYGSSPVGRTVGPALEV---REALKVLESM-EGPNSLI--EKSTSIAGMLLE- 363
                                       **************99999**********************...9******999.9999997..444445555555. PP

                                       TTSSSSHHHHHHHHHHHHHTSHH CS
                   Glycos_transf_3 230 agkadslkegvakaeevidsGkA 252
                                        g +    +g++ ae+++++G A
  gi|298674634|ref|YP_003726384.1| 364 MGGVAIKGQGRKVAEDTLRNGYA 386
                                       55599999*************98 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   1.7e-08   4.5e-05      31      82 ..      16      67 ..       4      87 .. 0.85
   2 ?   -2.8   0.0       2.5   6.5e+03      64      82 ..     455     473 ..     444     488 .. 0.60

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.7e-08
                                      EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESS.B-TTEEEEESSHCC CS
                   Molydop_binding 31 vveinpedAaalGikdGdlVevesrrGsvevrakvter.vrpGvvfmpfgwwe 82
                                       v +n  dA++lG+++Gd+V+v+ ++ s+++ +  te+ + pG+v +++   e
  gi|298674634|ref|YP_003726384.1| 16 KVVLNSVDAKELGVNEGDRVRVR-DHDSLTAIVDFTEDmISPGMVGLYHEVQE 67
                                      6889******************9.778999999776666*******9997655 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.5
                                       EEESSB-TTEEEEESSHCC CS
                   Molydop_binding  64 kvtervrpGvvfmpfgwwe 82 
                                       k  e+v++++++++ + ++
  gi|298674634|ref|YP_003726384.1| 455 KRGESVKKDQAVLTIHSEK 473
                                       4445555666665555555 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.7e-05     0.043       2      83 ..       3      82 ..       2      84 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.7e-05
                                      EEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTST.TTTEEEE-HHHHHHHT--TTEEEE CS
                           CDC48_N  2 LrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepede.gkgiIrmdgvtRknagvsiGdkVt 79
                                      L+V+ ++   vg+ +v++++ d +elg+++gd v+++ + +  aiv  + +ed  ++g + +   + + ++    ++V 
  gi|298674634|ref|YP_003726384.1|  3 LKVQPLN-IKVGKYKVVLNSVDAKELGVNEGDRVRVRDHDSLTAIV--DFTEDMiSPGMVGLYHEVQEKLQREWTETVD 78
                                      5666665.359**************************988644444..3333333788888877777777777777777 PP

                                      EEEE CS
                           CDC48_N 80 Vrka 83
                                      +++a
  gi|298674634|ref|YP_003726384.1| 79 ISPA 82
                                      7766 PP

>> DUF2254  Predicted membrane protein (DUF2254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.7e-05     0.044     184     254 ..     406     481 ..     374     493 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.7e-05
                           DUF2254 184 eeeseeeeatpiraersGylqaidveaLvklae......ehdlvielevrpGdfvvkgeplakvwgeeddeelaekl 254
                                       ++ ++ e +++++a+++Gyl + + ++L+++a+      ++++ + ++++ G+ v k++ ++++++e+ + +l+ ++
  gi|298674634|ref|YP_003726384.1| 406 DDINAGEYTHKLTAPTDGYLIEFNNKRLIEIARlagapnDKGAGVLIHKKRGESVKKDQAVLTIHSEK-EYKLKSAV 481
                                       344566789999*******************9744444477899********************9988.33344333 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       1.1   2.8e+03      17      29 ..      25      37 ..      10      40 .. 0.65
   2 ?   -3.0   0.0       2.6   6.6e+03      24      36 ..     270     281 ..     262     289 .. 0.64
   3 ?    9.8   0.1   0.00026      0.68      15      40 ..     447     473 ..     440     481 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.1
                                      CSESSSTTCEE-T CS
                     Biotin_lipoyl 17 vevlvkvGdkVka 29
                                       e  v++Gd V  
  gi|298674634|ref|YP_003726384.1| 25 KELGVNEGDRVRV 37
                                      4555666666654 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.6
                                       TCEE-TTSEEEEE CS
                     Biotin_lipoyl  24 GdkVkagqvlaev 36 
                                       G +V a+qv++ +
  gi|298674634|ref|YP_003726384.1| 270 G-SVGADQVVIDI 281
                                       3.46677776665 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00026
                                       ..ECSESSSTTCEE-TTSEEEEEECTT CS
                     Biotin_lipoyl  15 g.vvevlvkvGdkVkagqvlaeveamK 40 
                                       g  v +++k G++Vk++q ++++ + K
  gi|298674634|ref|YP_003726384.1| 447 GaGVLIHKKRGESVKKDQAVLTIHSEK 473
                                       44566899***************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (506 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.52
# Mc/sec: 2918.24
//
Query:       gi|298674635|ref|YP_003726385.1|  [L=623]
Description: nitrite and sulfite reductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-36  126.0   0.0    2.9e-36  124.6   0.0    1.7  1  FrhB_FdhB_C   Coenzyme F420 hydrogenase/dehydrogenase, beta s
    1.2e-29  102.8   0.1    2.2e-29  102.0   0.1    1.4  1  NIR_SIR       Nitrite and sulphite reductase 4Fe-4S domain
    7.6e-16   58.0   0.0    1.5e-15   57.0   0.0    1.5  1  FrhB_FdhB_N   Coenzyme F420 hydrogenase/dehydrogenase, beta s
    2.2e-11   43.0  46.9    1.9e-06   27.4   4.2    5.1  4  Fer4          4Fe-4S binding domain
    5.3e-10   39.7  26.7    0.00023   21.7   0.4    4.4  4  Fer4_7        4Fe-4S dicluster domain
    1.5e-09   37.6   0.0    4.2e-09   36.1   0.0    1.8  1  NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half 
    3.1e-09   36.8  27.0      8e-05   22.7   1.3    4.0  4  Fer4_10       4Fe-4S dicluster domain
    2.5e-08   33.9  27.6     0.0054   16.8   5.0    3.6  3  Fer4_21       4Fe-4S dicluster domain
    3.6e-08   33.0  37.8    0.00076   19.4   3.0    5.6  5  Fer4_2        4Fe-4S binding domain
    6.2e-08   32.7  29.7    7.5e-07   29.2  11.4    3.6  3  Fer4_9        4Fe-4S dicluster domain
      2e-07   31.9  28.6     0.0061   17.5   0.5    5.8  5  Fer4_16       4Fe-4S double cluster binding domain
    7.4e-07   29.0  37.8    0.00074   19.5   3.2    5.1  5  Fer4_6        4Fe-4S binding domain
    1.2e-06   28.8  18.4       0.11   12.9   0.2    4.6  5  Fer4_8        4Fe-4S dicluster domain
    5.2e-06   26.6  35.5     0.0026   18.1   1.7    6.0  6  Fer4_4        4Fe-4S binding domain
      9e-05   22.6  14.6      0.013   15.7   4.4    2.7  2  Fer4_18       4Fe-4S dicluster domain
    0.00012   22.6  26.1      0.061   13.9   1.8    4.8  5  Fer4_17       4Fe-4S dicluster domain
    0.00091   20.0  23.4      0.041   14.7   1.6    4.2  3  Fer4_22       4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.014   16.3   4.4      0.014   16.3   4.4    5.4  4  Fer4_3        4Fe-4S binding domain
       0.15   12.1   0.1       0.32   11.0   0.1    1.5  1  DUF237        Domain of unknown function (DUF237)
          1    9.9  27.4       0.22   12.1   0.3    5.3  5  Fer4_13       4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.6   0.0   3.2e-39   2.9e-36       2     153 ..     152     312 ..     151     313 .. 0.93

  Alignments for each domain:
  == domain 1  score: 124.6 bits;  conditional E-value: 3.2e-39
                       FrhB_FdhB_C   2 kkvavvGtPCqiaalrklqk................kklkekilltiglfCggnfspealrklleelgvdpedvkkl 62 
                                       ++vavvG+PCqi++lrklq                 + +  +i ++iglfC++ f++++l+++l++++vd e+v+k+
  gi|298674635|ref|YP_003726385.1| 152 ENVAVVGLPCQINGLRKLQYfeylakhgeelgsngkPANLPDIQYLIGLFCTEKFEYDSLKNILQKYNVDIENVEKF 228
                                       78*****************8889999999******9899999*********************************** PP

                       FrhB_FdhB_C  63 efrgkgkfrvelkd...ekeislkeleefirpsCkvCkdktaelADisvGdvwgpekkgdddegvstvlvrtekgee 136
                                       ++  kgk++++ ++   +++i+l+e++  i p+C+vC+d+ a++AD+svG++      g +++g+stv+vrtekg++
  gi|298674635|ref|YP_003726385.1| 229 DI-LKGKLVAYSNKknaSVKIPLDEID--ITPGCRVCRDFDANMADVSVGSA------G-SSDGYSTVVVRTEKGDD 295
                                       **.8******88877666667777776..9**********************......8.***************** PP

                       FrhB_FdhB_C 137 llekaveageleleeld 153
                                       + ++++ ++e++l +++
  gi|298674635|ref|YP_003726385.1| 296 IKNAIELHDEINLDAVS 312
                                       *****999999998775 PP

>> NIR_SIR  Nitrite and sulphite reductase 4Fe-4S domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.0   0.1   2.5e-32   2.2e-29       2     156 ..     422     617 ..     421     620 .. 0.95

  Alignments for each domain:
  == domain 1  score: 102.0 bits;  conditional E-value: 2.5e-32
                                       SSSCCCCCCSTCCCTBSS-SS-THHHHHHHHHHHCTCCCCTSSSS-BEEEEESSTCSTSSGGGSSEEEEEEEETTCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           NIR_SIR   2 ganlrnvtlcpgaglceeallDttelakaiedelepeygetylPrKfKiavsgcpnncvaveanDiglvgvkkdeke 78 
                                       g  +r++ +cpg g c   l++tt +++ +e    +e+ e   P+KfKiavsgcpn+cv+ +++Dig++gv  ++ +
  gi|298674635|ref|YP_003726385.1| 422 GPLVRATLACPGEGECGSGLINTTRICELME----DEFTEKPEPYKFKIAVSGCPNKCVRPHIHDIGFYGVRYPKVN 494
                                       6679***************************....99999999******************************9999 PP

                                       E...................................................EEEEEE--B-SSSTC-TCEEEEEEE CS
                                       x...................................................xxxxxxxxxxxxxxxxxxxxxxxxx RF
                           NIR_SIR  79 i...................................................gfnilvGGglgrthgakktsarlgf 104
                                                                                           g+  lvGG+ gr+  +++ +    +
  gi|298674635|ref|YP_003726385.1| 495 DncngcgrcadvckleaisvrgttsytnynvcigcgkcikacpndardiekeGYMALVGGKSGREIVEATNMG---M 568
                                       9*****************************************************************9999887...6 PP

                                       EEGGGHHHHHHHHHHHHHHHS-CSSGGG-SHHHHHHHHHHHHHHHHHHHCCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           NIR_SIR 105 vpeeevlevveaivevyrdhgdrknrkkeRlkylverlGvekFrekveeelg 156
                                       + e+e++++v ++++vy+   ++++ ++eRl  ++e++G   F+++v+ +++
  gi|298674635|ref|YP_003726385.1| 569 MGEDELVDFVNGVMKVYE--KYADKPQRERLSSVMEKIGKGSFLSEVK-DFK 617
                                       89999*************..9999***********************5.454 PP

>> FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.0   0.0   1.7e-18   1.5e-15      14      74 ..      83     141 ..      76     144 .. 0.92

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 1.7e-18
                       FrhB_FdhB_N  14 kaqsGGivtallkylLeegiidgvivvapskdpwrpkpviattkeellaaaGskYtlspnl 74 
                                        +q+GG+vta lkylL++ +i+g+ivv  +   w+p+ +++++++ l+++a+skYt+s + 
  gi|298674635|ref|YP_003726385.1|  83 DGQDGGVVTAFLKYLLDNEKIEGAIVVGDE--CWKPVSMVVKDEKGLMDTAKSKYTISTLD 141
                                       69**************************55..8***********************99864 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   3.6     6e-07   0.00054       2      21 ..      10      29 ..       9      32 .. 0.91
   2 ?    3.8   0.6     0.063        57      12      19 ..      49      56 ..      49      58 .. 0.91
   3 !   21.2   3.0     2e-07   0.00018       4      24 .]     493     513 ..     490     513 .. 0.88
   4 !   27.4   4.2   2.1e-09   1.9e-06       4      23 ..     522     541 ..     520     542 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 6e-07
                                      EEETTTSSS-THHHHHSTTT CS
                              Fer4  2 videekCigCGaCvevCPvg 21
                                      ++d  +C +CG+C+ vCP++
  gi|298674635|ref|YP_003726385.1| 10 IVDNGMCARCGTCAVVCPND 29
                                      699***************98 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.063
                                      THHHHHST CS
                              Fer4 12 GaCvevCP 19
                                      G C evCP
  gi|298674635|ref|YP_003726385.1| 49 GMCLEVCP 56
                                      89****** PP

  == domain 3  score: 21.2 bits;  conditional E-value: 2e-07
                                       ETTTSSS-THHHHHSTTTEEE CS
                              Fer4   4 deekCigCGaCvevCPvgAIt 24 
                                         + C gCG+C++vC  +AI+
  gi|298674635|ref|YP_003726385.1| 493 VNDNCNGCGRCADVCKLEAIS 513
                                       5799***********999995 PP

  == domain 4  score: 27.4 bits;  conditional E-value: 2.1e-09
                                       ETTTSSS-THHHHHSTTTEE CS
                              Fer4   4 deekCigCGaCvevCPvgAI 23 
                                       +++ CigCG+C+++CP++A 
  gi|298674635|ref|YP_003726385.1| 522 NYNVCIGCGKCIKACPNDAR 541
                                       8899**************95 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   7.2   0.00012      0.11       2      49 ..      16      56 ..      15      59 .. 0.83
   2 !   11.9   5.7   0.00028      0.25      10      49 ..     469     508 ..     468     511 .. 0.72
   3 !   13.9   2.7   7.2e-05     0.064       2      20 ..     497     515 ..     496     523 .. 0.86
   4 !   21.7   0.4   2.6e-07   0.00023       2      22 ..     526     546 ..     525     571 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00012
                            Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCga..CvavCP 49
                                      C  Cg C+++Cp++ +++++           +  ++Cl  g+  C +vCP
  gi|298674635|ref|YP_003726385.1| 16 CARCGTCAVVCPNDLLDFKNG---------PVLKDECLRKGHgmCLEVCP 56
                                      99****************764.........46789999655444*****9 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00028
                            Fer4_7  10 aaCpvkaieldeeenekgtekveidpekClgCgaCvavCP 49 
                                       + Cp+k+++ + ++      ++  + ++C gCg+C++vC 
  gi|298674635|ref|YP_003726385.1| 469 SGCPNKCVRPHIHDIGFYGVRYPKVNDNCNGCGRCADVCK 508
                                       679999999887633333355666789************7 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 7.2e-05
                            Fer4_7   2 CigCgaCvaaCpvkaield 20 
                                       C gCg+C+++C+ +ai+++
  gi|298674635|ref|YP_003726385.1| 497 CNGCGRCADVCKLEAISVR 515
                                       ************9999875 PP

  == domain 4  score: 21.7 bits;  conditional E-value: 2.6e-07
                            Fer4_7   2 CigCgaCvaaCpvkaieldee 22 
                                       CigCg+C +aCp++a+++++e
  gi|298674635|ref|YP_003726385.1| 526 CIGCGKCIKACPNDARDIEKE 546
                                       ****************99876 PP

>> NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.0   4.7e-12   4.2e-09       4      67 ..     351     412 ..     348     414 .. 0.90

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 4.7e-12
                      NIR_SIR_ferr   4 kdgkgyymvrlrvp.nGritaeqlraladiaekygsgeirlTtrQnlqlhgvpeedleeileeLa 67 
                                        d ++y ++r+r + +G++ a++ + + +iae+y  g ++lT r ++++h+++  d+ee+  +L+
  gi|298674635|ref|YP_003726385.1| 351 AD-DSY-FIRIRAKpSGWYEADEIEYVSKIAEEYN-GKLKLTNRGGIEIHDISGFDAEEVALKLK 412
                                       44.555.******989*******************.***********************987776 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   4.9   5.3e-06    0.0047       4      56 .]      11      56 ..       8      56 .. 0.84
   2 ?    4.8   6.9     0.034        30      41      55 ..     493     507 ..     468     508 .. 0.63
   3 !   20.6  14.2     4e-07   0.00036       6      56 .]     494     537 ..     488     537 .. 0.86
   4 !   22.7   1.3   8.9e-08     8e-05       5      24 ..     522     546 ..     518     570 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.3e-06
                           Fer4_10  4 idddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtg..cgaCveaCP 56
                                      +d   C rCg+C  +CP           + ++++v k  ++C +  +g+C e+CP
  gi|298674635|ref|YP_003726385.1| 11 VDNGMCARCGTCAVVCPN-------DLLDFKNGPVLK--DECLRkgHGMCLEVCP 56
                                      57778*************.......888888888888..777774478******9 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.034
                           Fer4_10  41 kvekCtgcgaCveaC 55 
                                       + ++C gcg C+++C
  gi|298674635|ref|YP_003726385.1| 493 VNDNCNGCGRCADVC 507
                                       445555555555555 PP

  == domain 3  score: 20.6 bits;  conditional E-value: 4e-07
                           Fer4_10   6 ddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                        d C +Cg+C ++C       + +++  ++ +  +++  C+gcg+C++aCP
  gi|298674635|ref|YP_003726385.1| 494 NDNCNGCGRCADVC-------KLEAISVRGTTSYTNYNVCIGCGKCIKACP 537
                                       589***********.......56666667777777***************9 PP

  == domain 4  score: 22.7 bits;  conditional E-value: 8.9e-08
                           Fer4_10   5 dddtCirCgkCvkaCPadl.....t 24 
                                       + + Ci+CgkC kaCP d+     +
  gi|298674635|ref|YP_003726385.1| 522 NYNVCIGCGKCIKACPNDArdiekE 546
                                       7899*************66554430 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   5.0     6e-06    0.0054       3      52 ..      11      56 ..       9      60 .. 0.86
   2 !   12.3   4.0   0.00015      0.14      16      57 ..     473     512 ..     466     514 .. 0.70
   3 !   15.7   3.0   1.3e-05     0.012       5      24 ..     523     542 ..     519     553 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6e-06
                           Fer4_21  3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCv..GCnlCssvCP 52
                                      +d+ +C  Cg C+++C++   + ++++     +v++deC   G  +C++vCP
  gi|298674635|ref|YP_003726385.1| 11 VDNGMCARCGTCAVVCPN---DLLDFK---NGPVLKDECLrkGHGMCLEVCP 56
                                      7999*************5...888885...55899****6559********* PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00015
                           Fer4_21  16 iaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57 
                                         C    +  i + + ++ + v+d+C GC  C++vC + ++i
  gi|298674635|ref|YP_003726385.1| 473 NKCVRPHIHDIGFYGVRY-PKVNDNCNGCGRCADVCKL-EAI 512
                                       555555555555555555.7889*************86.666 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 1.3e-05
                           Fer4_21   5 edkCigCgkCliaCedtshq 24 
                                        + CigCgkC++aC++ + +
  gi|298674635|ref|YP_003726385.1| 523 YNVCIGCGKCIKACPNDARD 542
                                       578***********986654 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   4.4   6.1e-05     0.054       5      22 .]      11      28 ..       9      28 .. 0.87
   2 ?    3.8   0.2     0.077        69      13      21 ..      48      56 ..      38      57 .. 0.74
   3 ?   -0.2   0.2       1.5   1.3e+03      12      18 ..     258     264 ..     257     265 .. 0.85
   4 !   13.8   4.2   5.4e-05     0.048       4      20 ..     492     507 ..     489     508 .. 0.81
   5 !   19.4   3.0   8.4e-07   0.00076       6      22 .]     522     538 ..     520     538 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.1e-05
                            Fer4_2  5 vdtdrCigCgaCvsaCPa 22
                                      vd  +C +Cg+C  +CP+
  gi|298674635|ref|YP_003726385.1| 11 VDNGMCARCGTCAVVCPN 28
                                      56679************5 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.077
                            Fer4_2 13 CgaCvsaCP 21
                                       g C+ +CP
  gi|298674635|ref|YP_003726385.1| 48 HGMCLEVCP 56
                                      689****** PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1.5
                            Fer4_2  12 gCgaCvs 18 
                                       gC+ C++
  gi|298674635|ref|YP_003726385.1| 258 GCRVCRD 264
                                       8****86 PP

  == domain 4  score: 13.8 bits;  conditional E-value: 5.4e-05
                            Fer4_2   4 vvdtdrCigCgaCvsaC 20 
                                       +v+ d+C+gCg C ++C
  gi|298674635|ref|YP_003726385.1| 492 KVN-DNCNGCGRCADVC 507
                                       555.67*********** PP

  == domain 5  score: 19.4 bits;  conditional E-value: 8.4e-07
                            Fer4_2   6 dtdrCigCgaCvsaCPa 22 
                                       + + CigCg+C++aCP+
  gi|298674635|ref|YP_003726385.1| 522 NYNVCIGCGKCIKACPN 538
                                       7899************5 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   2.5   0.00038      0.34      35      49 ..      15      29 ..       4      31 .. 0.73
   2 !    9.4   7.7    0.0013       1.2       2      48 ..      16      57 ..      15      60 .. 0.78
   3 !   29.2  11.4   8.3e-10   7.5e-07       1      50 [.     496     540 ..     496     541 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00038
                            Fer4_9 35 aCigCgaCveaCpkg 49
                                       C  Cg+C+ +Cp++
  gi|298674635|ref|YP_003726385.1| 15 MCARCGTCAVVCPND 29
                                      588899999999886 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0013
                            Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCig..CgaCveaCpk 48
                                      C++Cg+C  +Cp+++   ++++            C+    g C+e+Cp+
  gi|298674635|ref|YP_003726385.1| 16 CARCGTCAVVCPNDLLDFKNGPVLKDE-------CLRkgHGMCLEVCPR 57
                                      ***************998888877663.......644114559999997 PP

  == domain 3  score: 29.2 bits;  conditional E-value: 8.3e-10
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                       +C+gCg+C ++C+ ++++ +  + + +++      CigCg+C++aCp++a
  gi|298674635|ref|YP_003726385.1| 496 NCNGCGRCADVCKLEAISVRGTTSYTNYNV-----CIGCGKCIKACPNDA 540
                                       6*****************999999999865.....************985 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   6.6    0.0022         2       2      29 ..      16      42 ..      15      81 .. 0.82
   2 ?   -0.7   0.0       3.2   2.8e+03      32      62 ..     237     264 ..     216     265 .. 0.58
   3 ?   -1.4   0.2       5.4   4.8e+03      15      51 ..     298     332 ..     297     337 .. 0.63
   4 !   14.1   1.0   7.5e-05     0.067       1      20 [.     496     515 ..     496     523 .. 0.86
   5 !   17.5   0.5   6.8e-06    0.0061       2      17 ..     526     541 ..     525     561 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0022
                           Fer4_16  2 CgtCgkCaevCPtnaikekkekeieare 29
                                      C +Cg Ca vCP + ++ k+ ++++ +e
  gi|298674635|ref|YP_003726385.1| 16 CARCGTCAVVCPNDLLDFKNGPVLK-DE 42
                                      ***************9999655544.44 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3.2
                           Fer4_16  32 syntaekkdlaedeekckkqeaitgCdiCqd 62 
                                       +y+++++ ++++   + +    + gC++C d
  gi|298674635|ref|YP_003726385.1| 237 AYSNKKNASVKIPLDEID---ITPGCRVCRD 264
                                       454444444444444444...3468888875 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 5.4
                           Fer4_16  15 naikekkekeiearecisyntaekkdlaedeekckkq 51 
                                       nai+     ei+ ++  + ++++ ++++++++++k++
  gi|298674635|ref|YP_003726385.1| 298 NAIELHD--EINLDAVSKLKNIKSERFNKEIKRRKEY 332
                                       6777774..4444444445568888888888877755 PP

  == domain 4  score: 14.1 bits;  conditional E-value: 7.5e-05
                           Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                       +C +Cg+Ca+vC  +ai+ +
  gi|298674635|ref|YP_003726385.1| 496 NCNGCGRCADVCKLEAISVR 515
                                       6***************9876 PP

  == domain 5  score: 17.5 bits;  conditional E-value: 6.8e-06
                           Fer4_16   2 CgtCgkCaevCPtnai 17 
                                       C++CgkC+++CP +a 
  gi|298674635|ref|YP_003726385.1| 526 CIGCGKCIKACPNDAR 541
                                       ************9984 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   3.4   0.00014      0.12       4      20 ..      11      27 ..      10      31 .. 0.88
   2 ?    2.3   0.2      0.23     2e+02      13      20 ..      49      56 ..      43      65 .. 0.86
   3 ?   -2.4   0.3       6.8   6.1e+03      11      17 ..     470     477 ..     469     477 .. 0.69
   4 !   14.2   4.5   3.9e-05     0.035       7      20 ..     495     508 ..     493     512 .. 0.89
   5 !   19.5   3.2   8.2e-07   0.00074       5      22 ..     522     539 ..     519     542 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                            Fer4_6  4 idpdkCigCgdCvrvCP 20
                                      +d   C  Cg C++vCP
  gi|298674635|ref|YP_003726385.1| 11 VDNGMCARCGTCAVVCP 27
                                      68889************ PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.23
                            Fer4_6 13 gdCvrvCP 20
                                      g C  vCP
  gi|298674635|ref|YP_003726385.1| 49 GMCLEVCP 56
                                      67****** PP

  == domain 3  score: -2.4 bits;  conditional E-value: 6.8
                            Fer4_6  11 gC.gdCvr 17 
                                       gC ++Cvr
  gi|298674635|ref|YP_003726385.1| 470 GCpNKCVR 477
                                       67777875 PP

  == domain 4  score: 14.2 bits;  conditional E-value: 3.9e-05
                            Fer4_6   7 dkCigCgdCvrvCP 20 
                                       d+C+gCg+C++vC 
  gi|298674635|ref|YP_003726385.1| 495 DNCNGCGRCADVCK 508
                                       99***********6 PP

  == domain 5  score: 19.5 bits;  conditional E-value: 8.2e-07
                            Fer4_6   5 dpdkCigCgdCvrvCPeg 22 
                                       +++ CigCg+C+++CP +
  gi|298674635|ref|YP_003726385.1| 522 NYNVCIGCGKCIKACPND 539
                                       5678************65 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.5   0.00027      0.24      50      64 ..      15      29 ..       3      34 .. 0.82
   2 ?    2.1   0.0       0.3   2.7e+02       9      17 ..      49      57 ..      39      94 .. 0.71
   3 !    7.8   4.8    0.0052       4.6       4      62 ..     496     508 ..     473     511 .. 0.76
   4 ?    4.2  13.4     0.066        59       3      63 ..     495     538 ..     492     540 .. 0.72
   5 !   12.9   0.2   0.00013      0.11       4      17 ..     525     543 ..     522     596 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00027
                            Fer4_8 50 sCttcgaCtevCpvg 64
                                       C  cg C++vCp++
  gi|298674635|ref|YP_003726385.1| 15 MCARCGTCAVVCPND 29
                                      688888999998875 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.3
                            Fer4_8  9 gaCqsaCpv 17
                                      g+C + Cp 
  gi|298674635|ref|YP_003726385.1| 49 GMCLEVCPR 57
                                      456666654 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0052
                            Fer4_8   4 kCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCp 62 
                                       +C++Cg+C + C                                              +
  gi|298674635|ref|YP_003726385.1| 496 NCNGCGRCADVC----------------------------------------------K 508
                                       555555555555..............................................4 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.066
                            Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63 
                                       ++C++Cg+C + C        +  + rg  +     +       + + C +cg+C ++Cp+
  gi|298674635|ref|YP_003726385.1| 495 DNCNGCGRCADVCK------LEAISVRGTTSY----T-------NYNVCIGCGKCIKACPN 538
                                       68*********993......344555666333....1.......24679999999999997 PP

  == domain 5  score: 12.9 bits;  conditional E-value: 0.00013
                            Fer4_8   4 kCieCgaCqsaCp.....v 17 
                                        Ci+Cg C +aCp     +
  gi|298674635|ref|YP_003726385.1| 525 VCIGCGKCIKACPndardI 543
                                       5999999999999554440 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   1.0   0.00076      0.68       3      15 ..      15      27 ..       9      33 .. 0.91
   2 ?    1.0   0.2      0.91   8.2e+02       2      15 ..      41      56 ..      40      67 .. 0.82
   3 ?    2.3   0.2      0.33     3e+02       6      13 ..     258     265 ..     257     265 .. 0.91
   4 ?   -2.0   0.3       8.4   7.5e+03       6      11 ..     470     476 ..     468     477 .. 0.54
   5 !   15.4   2.3   2.1e-05     0.019       2      15 ..     495     508 ..     494     515 .. 0.92
   6 !   18.1   1.7   2.9e-06    0.0026       2      15 ..     524     537 ..     523     548 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00076
                            Fer4_4  3 rCigCgsCvaaCP 15
                                       C +Cg C  +CP
  gi|298674635|ref|YP_003726385.1| 15 MCARCGTCAVVCP 27
                                      5************ PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.91
                            Fer4_4  2 erCigCg..sCvaaCP 15
                                      + C++ g   C  +CP
  gi|298674635|ref|YP_003726385.1| 41 DECLRKGhgMCLEVCP 56
                                      7888887667*****9 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.33
                            Fer4_4   6 gCgsCvaa 13 
                                       gC++C+++
  gi|298674635|ref|YP_003726385.1| 258 GCRVCRDF 265
                                       8****997 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 8.4
                            Fer4_4   6 gCg.sCv 11 
                                       gC+ +Cv
  gi|298674635|ref|YP_003726385.1| 470 GCPnKCV 476
                                       4554555 PP

  == domain 5  score: 15.4 bits;  conditional E-value: 2.1e-05
                            Fer4_4   2 erCigCgsCvaaCP 15 
                                       ++C+gCg+C ++C+
  gi|298674635|ref|YP_003726385.1| 495 DNCNGCGRCADVCK 508
                                       89***********8 PP

  == domain 6  score: 18.1 bits;  conditional E-value: 2.9e-06
                            Fer4_4   2 erCigCgsCvaaCP 15 
                                       + CigCg+C+ aCP
  gi|298674635|ref|YP_003726385.1| 524 NVCIGCGKCIKACP 537
                                       78************ PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   2.5   0.00025      0.23      57      98 ..      12      58 ..       3      68 .. 0.78
   2 !   15.7   4.4   1.5e-05     0.013      56     102 ..     492     543 ..     479     552 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00025
                           Fer4_18 57 gagdcidcescvkvcPtg.idirkG..lqlecisc..llcidacdkv 98
                                      ++g c  c++c  vcP + +d ++G  l+ ec+    + c++ c +v
  gi|298674635|ref|YP_003726385.1| 12 DNGMCARCGTCAVVCPNDlLDFKNGpvLKDECLRKghGMCLEVCPRV 58
                                      6789************9846****95556689975225799999877 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.5e-05
                           Fer4_18  56 kgagdcidcescvkvcPt.gidirkGlqle....ciscllcidacdkvmekl 102
                                       k + +c  c+ c +vc    i +r    +     ci c++ci ac +    +
  gi|298674635|ref|YP_003726385.1| 492 KVNDNCNGCGRCADVCKLeAISVRGTTSYTnynvCIGCGKCIKACPNDARDI 543
                                       56789***********973699998877644446***********8755555 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.7    0.0002      0.18      44      60 ..      14      30 ..       3      31 .. 0.87
   2 ?    2.3   0.1      0.28   2.5e+02       6      16 ..      49      59 ..      42      87 .. 0.73
   3 !    7.5   3.3    0.0066       5.9      43      56 ..     494     507 ..     476     511 .. 0.77
   4 ?    6.6   3.3     0.012        11       1      14 [.     496     509 ..     496     521 .. 0.78
   5 !   13.9   1.8   6.8e-05     0.061      37      59 ..     517     539 ..     508     541 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0002
                           Fer4_17 44 slCieCgeCerkCPqgl 60
                                      + C+ Cg C+ +CP++l
  gi|298674635|ref|YP_003726385.1| 14 GMCARCGTCAVVCPNDL 30
                                      57************997 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.28
                           Fer4_17  6 gyClpeCpsye 16
                                      g+Cl++Cp+  
  gi|298674635|ref|YP_003726385.1| 49 GMCLEVCPRVS 59
                                      68999999854 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0066
                           Fer4_17  43 aslCieCgeCerkC 56 
                                        ++C++Cg+C+ +C
  gi|298674635|ref|YP_003726385.1| 494 NDNCNGCGRCADVC 507
                                       56777777777777 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.012
                           Fer4_17   1 rCiqCgyClpeCps 14 
                                       +C++Cg C+++C  
  gi|298674635|ref|YP_003726385.1| 496 NCNGCGRCADVCKL 509
                                       58888888888875 PP

  == domain 5  score: 13.9 bits;  conditional E-value: 6.8e-05
                           Fer4_17  37 aekeekaslCieCgeCerkCPqg 59 
                                       +   ++ + Ci+Cg+C ++CP++
  gi|298674635|ref|YP_003726385.1| 517 TTSYTNYNVCIGCGKCIKACPND 539
                                       445578899************97 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   1.2      0.01         9       2      13 ..      16      27 ..       5      30 .. 0.75
   2 !   12.0   1.4   0.00031      0.28      79      93 ..     494     508 ..     443     511 .. 0.87
   3 !   14.7   1.6   4.6e-05     0.041      76      94 ..     520     538 ..     513     540 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.01
                           Fer4_22  2 ClsCgaCtlvCp 13
                                      C +Cg+C++vCp
  gi|298674635|ref|YP_003726385.1| 16 CARCGTCAVVCP 27
                                      777777777776 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00031
                           Fer4_22  79 esgCvGCgRCieacp 93 
                                       +  C GCgRC ++c+
  gi|298674635|ref|YP_003726385.1| 494 NDNCNGCGRCADVCK 508
                                       578***********8 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 4.6e-05
                           Fer4_22  76 kfgesgCvGCgRCieacpv 94 
                                        ++ ++C+GCg+Ci+acp+
  gi|298674635|ref|YP_003726385.1| 520 YTNYNVCIGCGKCIKACPN 538
                                       457899***********97 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   5.7     0.044        40       1      13 [.      16      28 ..      15      29 .. 0.85
   2 ?    5.4   0.5     0.047        42       5      12 ..      49      56 ..      41      60 .. 0.76
   3 ?    8.7   4.0    0.0042       3.7       1      11 [.     497     507 ..     497     511 .. 0.93
   4 ?   16.3   4.4   1.6e-05     0.014       1      15 []     526     540 ..     526     540 .. 0.97

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.044
                            Fer4_3  1 CtgCgaCvevCPv 13
                                      C  Cg+C +vCP+
  gi|298674635|ref|YP_003726385.1| 16 CARCGTCAVVCPN 28
                                      5669********7 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.047
                            Fer4_3  5 gaCvevCP 12
                                      g C+evCP
  gi|298674635|ref|YP_003726385.1| 49 GMCLEVCP 56
                                      46****** PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0042
                            Fer4_3   1 CtgCgaCvevC 11 
                                       C+gCg+C +vC
  gi|298674635|ref|YP_003726385.1| 497 CNGCGRCADVC 507
                                       *********** PP

  == domain 4  score: 16.3 bits;  conditional E-value: 1.6e-05
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+gCg C ++CP++A
  gi|298674635|ref|YP_003726385.1| 526 CIGCGKCIKACPNDA 540
                                       ************998 PP

>> DUF237  Domain of unknown function (DUF237)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00036      0.32       2      94 ..     303     389 ..     302     399 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00036
                            DUF237   2 Rdelkkkanikl.klkkvkvkgkkedeekvwiapesikwnkekggiekrktkpykfkfeveleyegsyklkwwtail 77 
                                        de++  a  kl ++k+ +++++ +   k ++ p s+ w +e gg+ kr + +y   + ++ + +g+y++  ++ + 
  gi|298674635|ref|YP_003726385.1| 303 HDEINLDAVSKLkNIKSERFNKEIKRR-KEYNEPVSLYWLAEHGGVSKRADDSYF--IRIRAKPSGWYEADEIEYVS 376
                                       577888888899888888888887777.99*********************9875..67999**********99987 PP

                            DUF237  78 aklggiPgeWkGklklk 94 
                                           +i  e++Gklkl+
  gi|298674635|ref|YP_003726385.1| 377 ----KIAEEYNGKLKLT 389
                                       ....9*********997 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   3.2     0.015        13       1      18 [.      11      28 ..      11      30 .. 0.94
   2 ?    0.7   0.1      0.91   8.1e+02       8      19 ..      47      58 ..      40      60 .. 0.79
   3 ?   -1.3   0.0       3.7   3.3e+03      44      56 ..     464     476 ..     453     477 .. 0.80
   4 ?    2.2   4.3       0.3   2.7e+02       1      16 [.     493     507 ..     493     508 .. 0.92
   5 ?   12.1   0.3   0.00024      0.22       5      18 ..     525     538 ..     522     564 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.015
                           Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                      VD+  C  cg+C+ ++P+
  gi|298674635|ref|YP_003726385.1| 11 VDNGMCARCGTCAVVCPN 28
                                      89999************6 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.91
                           Fer4_13  8 acgaCvelaPdv 19
                                      ++g C e++P v
  gi|298674635|ref|YP_003726385.1| 47 GHGMCLEVCPRV 58
                                      6899******87 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 3.7
                           Fer4_13  44 aeeAadaCPvesI 56 
                                        + A+ +CP +++
  gi|298674635|ref|YP_003726385.1| 464 FKIAVSGCPNKCV 476
                                       567999***9986 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.3
                           Fer4_13   1 VDrdtCiacgaCvela 16 
                                       V+ d+C +cg C++++
  gi|298674635|ref|YP_003726385.1| 493 VN-DNCNGCGRCADVC 507
                                       67.9**********99 PP

  == domain 5  score: 12.1 bits;  conditional E-value: 0.00024
                           Fer4_13   5 tCiacgaCvelaPd 18 
                                        Ci+cg+C +++P+
  gi|298674635|ref|YP_003726385.1| 525 VCIGCGKCIKACPN 538
                                       6************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (623 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.74u 0.33s 00:00:01.07 Elapsed: 00:00:00.51
# Mc/sec: 3670.29
//
Query:       gi|298674636|ref|YP_003726386.1|  [L=281]
Description: prephenate dehydratase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.6e-58  196.8   0.1    3.5e-58  196.4   0.1    1.2  1  PDT        Prephenate dehydratase
    2.7e-09   36.6   0.0    4.5e-09   35.9   0.0    1.4  1  ACT        ACT domain
     0.0011   19.4   0.0       0.52   10.8   0.0    2.4  2  OAM_dimer  Dimerisation domain of d-ornithine 4,5-aminomutase
     0.0023   18.5   0.0     0.0047   17.5   0.0    1.5  1  ACT_4      ACT domain


Domain annotation for each model (and alignments):
>> PDT  Prephenate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.4   0.1   7.9e-62   3.5e-58       1     181 [.       3     182 ..       3     184 .. 0.93

  Alignments for each domain:
  == domain 1  score: 196.4 bits;  conditional E-value: 7.9e-62
                                       EEEES-TTSHHHHHHCCCS........EE.EEES-HHHHHHHHCTTS-SEEEEEEEESSS-B-HHHHHHHHH.SSEE CS
                               PDT   1 vaylGpegtyshqAalkvf...kaedvel.ipvasieevfeavekgeadyavvPiENsteGsVnetlDlLlkesdlk 73 
                                       v++lGp g+ys++Aa+k +   +++dv +   ++ i++ f+av ++++dy+vvP+ENs+eGsV  tlD L + +++ 
  gi|298674636|ref|YP_003726386.1|   3 VGVLGPAGSYSEKAAKKWAkkmEHTDVPVfNYYEDITDTFSAVVNKTVDYGVVPVENSIEGSVGITLDQLFE-NEIT 78 
                                       789*************9997554444444245799*************************************.99** PP

                                       EEEEEEEE---EEEE-TT--TTT--EEEE-HHHHHHTHHHHHH-.TTSEEEE-S-HHHHHHHHHHCT-TTEEEEE-H CS
                               PDT  74 ivgEvvlpiehcLlakpktkleeikkvyShpqalgQcrkfLeehlpqvervavestaeAakkveassdkdaaaiase 150
                                       i+ E+v+piehcLl+k +  l++ik ++Shpqal+Qcr+fL++h+++ e +++ st++Aa    a + +++aaias+
  gi|298674636|ref|YP_003726386.1|  79 ITSEIVVPIEHCLLSKGS--LSDIKIILSHPQALAQCRNFLKTHFKNTELRTTGSTSHAATL--ATEFDEMAAIASR 151
                                       *************97754..6*****************************************..999999******* PP

                                       HHHHHTT-EEEECS-SS-S--EEEEEEEEET CS
                               PDT 151 vaaelyglkvleeniedkknntTRFlvlake 181
                                         ae+yglk+l  ni+d+++n+TRFlv++++
  gi|298674636|ref|YP_003726386.1| 152 SSAEMYGLKILIPNIQDHNENYTRFLVIKSK 182
                                       ****************************986 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.0     1e-12   4.5e-09       2      66 ..     200     265 ..     199     266 .. 0.94

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 1e-12
                                       EEEEEEE.SSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTTC CS
                               ACT   2 vlrvgvp.DrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkle 66 
                                       +++v++  +rPG+L +++  +a+  iN+++ie+r+s+  ++++ f ++ ++  ++e+++ al +l+
  gi|298674636|ref|YP_003726386.1| 200 SIIVYLDqNRPGALYEILEEFAKKEINLTKIESRPSKKALGDYLFYIDFEGSIQDETIKSALDNLG 265
                                       67788888******************************************************9986 PP

>> OAM_dimer  Dimerisation domain of d-ornithine 4,5-aminomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00012      0.52      25      60 ..      10      46 ..       6      58 .. 0.80
   2 !    6.0   0.0    0.0036        16      18      65 ..     136     183 ..     125     191 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00012
                                      CHHHHHHHHHHHHCTTSEEEEEEE.EEEEETTEEEEE CS
                         OAM_dimer 25 eeeAeeAAlelakkmGledpeVvh.keelheeftffv 60
                                      ++ +e+AA+++akkm  +d+ V +  e++++ f+ +v
  gi|298674636|ref|YP_003726386.1| 10 GSYSEKAAKKWAKKMEHTDVPVFNyYEDITDTFSAVV 46
                                      6789*****************9862577877777665 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0036
                                       EEESS-SCHHHHHHHHHHHHCTTSEEEEEEEEEEEETTEEEE.EEEEE- CS
                         OAM_dimer  18 ftLPvpaeeeAeeAAlelakkmGledpeVvhkeelheeftff.vvyGkv 65 
                                        tL ++ +e A  A +  a+  Gl+ + + + ++ +e++t+f v++ k+
  gi|298674636|ref|YP_003726386.1| 136 ATLATEFDEMAAIASRSSAEMYGLK-ILIPNIQDHNENYTRFlVIKSKY 183
                                       58999*******************7.899999**999**9762556665 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0     1e-06    0.0047       4      58 ..     196     254 ..     193     273 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1e-06
                             ACT_4   4 sytvrlevea.edrkglLaditqviseekanivsvnaktrkk...dglaeikitveVkd 58 
                                        y++++ v+  ++r+g+L +i++ ++++++n+++++++  kk   d l+ i+++ +++d
  gi|298674636|ref|YP_003726386.1| 196 LYKTSIIVYLdQNRPGALYEILEEFAKKEINLTKIESRPSKKalgDYLFYIDFEGSIQD 254
                                       588889898889***************************99888888888888777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1688.73
//
Query:       gi|298674637|ref|YP_003726387.1|  [L=296]
Description: hypothetical protein Metev_0689 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.055   12.4   2.8      0.034   13.1   1.1    1.4  2  MFS_1     Major Facilitator Superfamily
       0.22   11.4   1.9       0.25   11.2   0.2    2.0  2  DUF5337   Family of unknown function (DUF5337)
        4.6    6.5   8.9        0.2   11.0   2.9    1.8  3  TMEM43    Transmembrane protein 43


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.1   5.6e-06     0.034     211     274 ..      32     104 ..       8     109 .. 0.70
   2 ?   -3.2   0.0      0.51     3e+03      68      75 ..     162     169 ..     145     179 .. 0.44

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.6e-06
                             MFS_1 211 illialllf.ffgfsg..lltllpl...ylqevlgls...glllaglllallalvgailallagrlsdrlgrr 274
                                       i++ ++l++ f++f++  +++ + +   y+  +++++    l+++ +l+ ++  +++il+l++ ++sd++++ 
  gi|298674637|ref|YP_003726387.1|  32 IAISVFLYTiFVIFNIdtIFSSIKSfelYTGRQFHFAgfsILFETIGLIVISLTIALILSLIIHKYSDKTNAI 104
                                       233333333133344444555444467789**********99***************************8864 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.51
                             MFS_1  68 glllfalg 75 
                                        ++l a++
  gi|298674637|ref|YP_003726387.1| 162 IAVLVAVS 169
                                       11111111 PP

>> DUF5337  Family of unknown function (DUF5337)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   4.2e-05      0.25      36      65 ..      18      47 ..      16      49 .. 0.92
   2 ?   -3.7   0.1       1.8   1.1e+04      15      23 ..     161     169 ..     154     175 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.2e-05
                           DUF5337 36 qlglsnRyalLfdLaAlAaliwalvvtyql 65
                                      +l +  R   L+d++A+  + + + v++ +
  gi|298674637|ref|YP_003726387.1| 18 RLKWFRRLYRLLDFIAISVFLYTIFVIFNI 47
                                      678999**********************87 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.8
                           DUF5337  15 lvalviavt 23 
                                       ++a+ +av+
  gi|298674637|ref|YP_003726387.1| 161 IIAVLVAVS 169
                                       456666655 PP

>> TMEM43  Transmembrane protein 43
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.9   3.3e-05       0.2     165     245 ..       2      89 ..       1      96 [. 0.81
   2 ?   -3.4   0.1      0.83   4.9e+03     224     241 ..     157     174 ..     139     176 .. 0.73
   3 ?   -3.9   0.0       1.2   7.3e+03     144     167 ..     249     272 ..     248     274 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.3e-05
                            TMEM43 165 eegevsaeemfakeksenklltwllRllGfllmfl...glllllsplsvlvslipll.....gelvglglalvalll 233
                                       +eg++  e++++k++s  k++ +l+Rll f+ + +   +++++++ + +++s i+       +++  +g++++  ++
  gi|298674637|ref|YP_003726387.1|   2 AEGNFNIEHFVEKHESRLKWFRRLYRLLDFIAISVflyTIFVIFN-IDTIFSSIKSFelytgRQFHFAGFSILFETI 77 
                                       68999*********************9998877653334444444.4777777777677999999999999999999 PP

                            TMEM43 234 slslsllviala 245
                                       +l++ +l+ial+
  gi|298674637|ref|YP_003726387.1|  78 GLIVISLTIALI 89 
                                       999999999986 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.83
                            TMEM43 224 lglalvalllslslsllv 241
                                       ++ +++a+l+++sl++++
  gi|298674637|ref|YP_003726387.1| 157 FASSIIAVLVAVSLFSVI 174
                                       566677777777777665 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 1.2
                            TMEM43 144 kqkgntlepYstkngdeielleeg 167
                                       +q+gn  +p++ +++++i++++++
  gi|298674637|ref|YP_003726387.1| 249 RQEGNDNQPFEPSSAYDINVISSK 272
                                       688888899999999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1001  (0.0558313); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1749.28
//
Query:       gi|298674638|ref|YP_003726388.1|  [L=324]
Description: ATPase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-62  209.4   0.1    2.2e-62  208.7   0.1    1.3  1  AAA_3            ATPase family associated with various cellul
    1.9e-17   62.8   0.0    3.4e-17   62.0   0.0    1.4  1  AAA_lid_2        AAA lid domain
    2.8e-10   40.4   0.0    1.3e-09   38.2   0.0    2.0  2  AAA_5            AAA domain (dynein-related subfamily)
    1.3e-05   25.6   0.2      4e-05   24.0   0.0    2.0  3  AAA              ATPase family associated with various cellul
     0.0018   17.4   0.0     0.0031   16.6   0.0    1.4  1  MCM              MCM P-loop domain
     0.0038   17.0   0.1      0.027   14.2   0.1    2.1  1  Sigma54_activat  Sigma-54 interaction domain
  ------ inclusion threshold ------
      0.024   14.0   0.1        0.6    9.5   0.0    2.2  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.033   14.5   0.7          2    8.7   0.1    2.6  3  AAA_19           AAA domain


Domain annotation for each model (and alignments):
>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.7   0.1   9.7e-66   2.2e-62       1     131 []      52     184 ..      52     184 .. 0.98

  Alignments for each domain:
  == domain 1  score: 208.7 bits;  conditional E-value: 9.7e-66
                             AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeeke..kefefkkGpvfanllladeinrap 75 
                                       h l+e+ PGl+ktl+++++ak+ +l+f+riq+tpdl+P+di+Gt+++ee++  k f+f++Gpvfan++lade+nra+
  gi|298674638|ref|YP_003726388.1|  52 HALVESNPGLGKTLTISTIAKITELDFSRIQCTPDLMPADITGTHIIEESDgkKMFKFEQGPVFANIVLADEVNRAS 128
                                       99**********************************************9986688********************** PP

                             AAA_3  76 pktqsalleameerqvtvegethklpepflvlatqnPieqeGtyplpeaqldrfll 131
                                       pktqsalle+m+e+qvtv+++t+kl++pf+vlatqnPie+eGtyplpeaqldrf++
  gi|298674638|ref|YP_003726388.1| 129 PKTQSALLESMQEKQVTVGNDTYKLDRPFFVLATQNPIEMEGTYPLPEAQLDRFMF 184
                                       ******************************************************96 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.0   0.0   1.5e-20   3.4e-17       8      73 .]     253     319 ..     247     319 .. 0.93

  Alignments for each domain:
  == domain 1  score: 62.0 bits;  conditional E-value: 1.5e-20
                         AAA_lid_2   8 aielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlr..repeaegetteeiveei 73 
                                        ie+g+s+r a++ l+ a++A+A+++gr+yV+ eD++++a ++L+HR++   e e+ g+++++++++i
  gi|298674638|ref|YP_003726388.1| 253 HIEYGASPR-ASIGLILASKARALIHGRNYVSHEDIETMAYPILRHRIIltFESERRGVSKDQVIKKI 319
                                       79*******.***************************************8878888889999999875 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.0   5.8e-13   1.3e-09       7     138 .]      58     182 ..      52     182 .. 0.89
   2 ?   -0.9   0.1      0.69   1.5e+03      74     104 ..     200     228 ..     192     253 .. 0.54

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 5.8e-13
                                       -SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.............--------G-SEEEEESGGG--H CS
                             AAA_5   7 ppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik....ngttslvdsplvraaregeilvlDEveraes 79 
                                       +pG gK+  +  +a+ ++  +  +q+t d+ ++d++g   i+    ++  +++++p+      + i++ DEv+ra++
  gi|298674638|ref|YP_003726388.1|  58 NPGLGKTLTISTIAKITELDFSRIQCTPDLMPADITGTHIIEesdgKKMFKFEQGPVF-----ANIVLADEVNRASP 129
                                       79***************************************99987777899999999.....9************* PP

                                       HHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
                             AAA_5  80 evlnsLlslleerrllleeggelvkaknddllerfrviatanpld.rslnelspalrsRf 138
                                       +++++Ll  + e+++ + + +     +++     f v+at np +  +  +l +a ++Rf
  gi|298674638|ref|YP_003726388.1| 130 KTQSALLESMQEKQVTVGNDTYKL--DRP-----FFVLATQNPIEmEGTYPLPEAQLDRF 182
                                       ****************55554444..443.....99********9888888888888888 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.69
                                       GGG--HHHHHHHHHHHHSSEEE..-SSSEEE CS
                             AAA_5  74 veraesevlnsLlslleerrllleeggelvk 104
                                       v+r  ++ ++ +++++++++ll   +++l +
  gi|298674638|ref|YP_003726388.1| 200 VNRYTTAETPQVNRIIDKNTLLE--LQKLSR 228
                                       34444555667888888888873..333322 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       4.2   9.3e+03      63      72 ..      25      34 ..       9      48 .. 0.59
   2 !   24.0   0.0   1.8e-08     4e-05       2     128 ..      54     186 ..      53     190 .. 0.71
   3 ?   -2.8   0.0       3.5   7.9e+03      99     111 ..     236     248 ..     205     251 .. 0.67

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4.2
                                      EEETGGGHHH CS
                               AAA 63 fiDEidalak 72
                                      ++DEi +++ 
  gi|298674638|ref|YP_003726388.1| 25 IFDEIGKVIV 34
                                      3455555544 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 1.8e-08
                                       EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS.......STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHH CS
                               AAA   2 llyGppGtGKTllakavakelgvefleisgsellsk.......yvgesekkirelfkeakekakpsilfiDEidala 71 
                                       l+  +pG GKTl+++ +ak ++ +f +i+++  l         +++es  k    f++    a   i++ DE+ +  
  gi|298674638|ref|YP_003726388.1|  54 LVESNPGLGKTLTISTIAKITELDFSRIQCTPDLMPaditgthIIEESDGKKMFKFEQGPVFA--NIVLADEVNRAS 128
                                       56678***********************99654422468886556665555555555544444..9*********** PP

                                       HHHTTCCCHHHHHHHHHHHHHHHHTTTS........SSTEEEEEEESS.....GGGSTHHHHSTTSSEEE CS
                               AAA  72 ksrsgseseeeervvnqLlteldgvkkk........eskvivigatnr.....pdkldpallrgRfdrki 128
                                       ++            +++Ll+ +++ +          +++++v+++ n         l++a l +Rf  ki
  gi|298674638|ref|YP_003726388.1| 129 PKT-----------QSALLESMQEKQVTvgndtyklDRPFFVLATQNPiemegTYPLPEAQL-DRFMFKI 186
                                       999...........999999999999999999999766666666666533222223555555.6666666 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 3.5
                                       SSSTEEEEEEESS CS
                               AAA  99 keskvivigatnr 111
                                        + +vi i++t+r
  gi|298674638|ref|YP_003726388.1| 236 LKTRVIKIVMTTR 248
                                       2566777888777 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.4e-06    0.0031      52     175 ..      45     167 ..      19     186 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.4e-06
                                       SBBCSS-EEEEEESSTSTHHHHHHHHHHHSS..SEEEEESSSSSSSHSSSEEEEESSSSS..EEEEETHHHHTTTSE CS
                               MCM  52 tklrgdinvllvgdpgtaKsqlLkyveklap..ravytsgkgssaagLtaavvrdeetge..fvleaGalvladkGv 124
                                       + +  d + l+ ++pg++K+  + +++k+++   +   +      a++t +   +e+ g+  f +e G +      +
  gi|298674638|ref|YP_003726388.1|  45 IAILCDGHALVESNPGLGKTLTISTIAKITEldFSRIQCTPDLMPADITGTHIIEESDGKkmFKFEQGPVFA---NI 118
                                       457788999999********9999999987621455666777788899766554444443359999999775...49 PP

                                       EEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--SS CS
                               MCM 125 cciDefdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpka 175
                                       ++ De+++ + +++sal+E m ++++++      ++L+    vla  np++
  gi|298674638|ref|YP_003726388.1| 119 VLADEVNRASPKTQSALLESMQEKQVTVGNDT--YKLDRPFFVLATQNPIE 167
                                       ***************************98776..88999999999999973 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   1.2e-05     0.027      12     145 ..      40     166 ..      33     172 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.2e-05
                                       HHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEHH CS
                   Sigma54_activat  12 leqikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekkGl 88 
                                       +eqi  ++  d + l++ + G GK+l  ++i + ++     f +++c+   ++l+ +++ G++      ++ +k+ +
  gi|298674638|ref|YP_003726388.1|  40 VEQIIIAILCDGHALVESNPGLGKTLTISTIAKITE---LDFSRIQCT---PDLMPADITGTHI--IEESDGKKMFK 108
                                       555666666666666666666666666666554433...456666664...4555555554432..33444444455 PP

                                       HHHTT..TSEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEEEEESS-H CS
                   Sigma54_activat  89 fekad..gGtlfLDeigelplelQekLlrvlqegevervGsskeikvdvriiaatnedl 145
                                       fe+      +++ De+++ ++++Q+ Ll+ +qe++v+ vG+++ +     ++ at++ +
  gi|298674638|ref|YP_003726388.1| 109 FEQGPvfANIVLADEVNRASPKTQSALLESMQEKQVT-VGNDTYKLDRPFFVLATQNPI 166
                                       5553211457788*********************996.887766655566677776655 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00027       0.6       5      45 ..      33      73 ..      30      81 .. 0.92
   2 ?    2.2   0.0     0.045     1e+02     109     158 ..     118     165 ..     113     176 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00027
                      Mg_chelatase  5 vkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsl 45
                                      ++Gq+++ + + ia+    + l+  +pG GKt+ ++ ++++
  gi|298674638|ref|YP_003726388.1| 33 IVGQKNTVEQIIIAILCDGHALVESNPGLGKTLTISTIAKI 73
                                      89***************9999************99999877 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.045
                      Mg_chelatase 109 vLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNp 158
                                       +++ DE+   + k+  +L e +++++vt+   ++k++ p  f ++a+ Np
  gi|298674638|ref|YP_003726388.1| 118 IVLADEVNRASPKTQSALLESMQEKQVTVGNDTYKLDRP--FFVLATQNP 165
                                       5677*************************9888887765..777777777 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1    0.0009         2       7      34 ..      47      74 ..      41      85 .. 0.82
   2 ?    3.5   0.0     0.036        80      97     135 ..     111     146 ..      78     151 .. 0.74
   3 ?   -2.4   0.0       2.5   5.5e+03      23      40 ..     237     254 ..     237     298 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0009
                            AAA_19  7 alkekvllvtaGpGtGKTrvlkhivall 34
                                       l +++ lv   pG GKT ++ +i ++ 
  gi|298674638|ref|YP_003726388.1| 47 ILCDGHALVESNPGLGKTLTISTIAKIT 74
                                      566788999*************998765 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.036
                            AAA_19  97 ekklqeeellivDEfqdvd.elqyrLlkallgekkklllv 135
                                       + ++  +++++ DE+   + ++q +Ll+ +  ek+  + v
  gi|298674638|ref|YP_003726388.1| 111 QGPV-FANIVLADEVNRASpKTQSALLESMQ-EKQ--VTV 146
                                       4455.466999********99*******999.444..345 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.5
                            AAA_19  23 KTrvlkhivallvelggv 40 
                                       KTrv+k +++  ++ +++
  gi|298674638|ref|YP_003726388.1| 237 KTRVIKIVMTTRQWGEHI 254
                                       888888888777766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 1910.05
//
Query:       gi|298674639|ref|YP_003726389.1|  [L=294]
Description: hypothetical protein Metev_0691 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.6e-21   74.4   0.0    1.2e-20   73.5   0.0    1.5  1  DUF58     Protein of unknown function DUF58
    1.2e-05   25.9   0.0    2.2e-05   25.0   0.0    1.5  1  VWA_2     von Willebrand factor type A domain
     0.0018   17.7   0.1     0.0052   16.2   0.1    1.7  1  VWA_CoxE  VWA domain containing CoxE-like protein
  ------ inclusion threshold ------
      0.037   14.3   0.1      0.082   13.2   0.1    1.6  1  VWA       von Willebrand factor type A domain


Domain annotation for each model (and alignments):
>> DUF58  Protein of unknown function DUF58
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.5   0.0   2.7e-24   1.2e-20       1      84 [.      43     127 ..      43     129 .. 0.93

  Alignments for each domain:
  == domain 1  score: 73.5 bits;  conditional E-value: 2.7e-24
                             DUF58   1 gldfaglReYvpgDplrrIdWkatARtgelyvrefeaerartvllvldlspemslgstg.dekletavsaaaslarq 76 
                                       g+d  g R+Y pgD++r+IdW+++ARt +lyvr++e+e++ t+ ++ld s++m+ + ++  +k+e+ + +aa  a+ 
  gi|298674639|ref|YP_003726389.1|  43 GIDTVGYRPYYPGDEIRSIDWNVYARTEKLYVRQYEEEKSLTTHILLDSSKSMDYRGNNnTSKFEYGAMIAAGFAYL 119
                                       68999************************************************8766656****************9 PP

                             DUF58  77 lldegdrv 84 
                                       + + +d++
  gi|298674639|ref|YP_003726389.1| 120 VTKDNDKF 127
                                       99999876 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0     5e-09   2.2e-05       3     105 ..      87     188 ..      85     200 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 5e-09
                             VWA_2   3 fvlDtSgSmrngdy.gptrleaakdaveallk..slpgdrvglvtfsdgpevlipltkdkakilnalrnleak..gg 74 
                                       ++lD+S+Sm  +   +++++e+ + ++  +    + ++d++++ tfs+++  +++++++++ + + +++l ++  gg
  gi|298674639|ref|YP_003726389.1|  87 ILLDSSKSMDYRGNnNTSKFEYGAMIAAGFAYlvTKDNDKFAISTFSENVD-IAKPKRGREYLIRTIDRLSETelGG 162
                                       89*******766442566666666655555552155799**********99.68999**************99**** PP

                             VWA_2  75 gtnlaaaLqlarkalkkrrkgekrvivlitD 105
                                       +t++ + + + + a+++r+      +v+i+D
  gi|298674639|ref|YP_003726389.1| 163 QTSIRESMIQYTPAISSRS-----LVVIISD 188
                                       ********99999999775.....9999998 PP

>> VWA_CoxE  VWA domain containing CoxE-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   1.2e-06    0.0052     109     164 ..     142     193 ..      58     204 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-06
                          VWA_CoxE 109 erDpaeaLarvsaaved.lgGgTrigaalaeflelvtrpaLsrravvvlvsDglerg 164
                                       +r ++ +++ + +  e  lgG T i +++ +       pa+s+r++vv++sD+l+  
  gi|298674639|ref|YP_003726389.1| 142 KRGREYLIRTIDRLSETeLGGQTSIRESMIQYT-----PAISSRSLVVIISDFLDNP 193
                                       556677777776555555999999999987654.....5666799********9864 PP

>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.8e-05     0.082       4      83 ..      87     168 ..      86     207 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.8e-05
                                       EEEE-STTSCHHHHHHHHHHHHHHHHHHT....BTTTTEEEEEEEESSSEEEEEETTSHCHHHHHHHHHHTG.SGGG CS
                               VWA   4 fvlDgSgsmgeenfekvkefikklvekle....vgpegtrvglvqfssevktefslndysskeellsalnnl.kysg 75 
                                       ++lD+S+sm+++  +++ +f    +        v ++++++++ +fs++v +  + +    +e l++ +++l +++ 
  gi|298674639|ref|YP_003726389.1|  87 ILLDSSKSMDYRGNNNTSKFEYGAMIAAGfaylVTKDNDKFAISTFSENVDIAKPKR---GREYLIRTIDRLsETEL 160
                                       79*******9999998888877666555545555***************99874433...45889999999887777 PP

                                       GSSC-HHH CS
                               VWA  76 ggttntgk 83 
                                       gg+t++ +
  gi|298674639|ref|YP_003726389.1| 161 GGQTSIRE 168
                                       77776765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1777.68
//
Query:       gi|298674640|ref|YP_003726390.1|  [L=625]
Description: hypothetical protein Metev_0692 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.2e-15   55.6   4.4    5.2e-15   55.6   4.4    2.3  2  BatA            Aerotolerance regulator N-terminal
    2.5e-05   24.9   1.1    0.00012   22.7   0.7    2.4  2  VWA_2           von Willebrand factor type A domain
     0.0013   18.2   1.1      0.015   14.8   1.2    2.2  1  ABC_transp_aux  ABC-type uncharacterized transport system
  ------ inclusion threshold ------
      0.089   13.2   0.6          7    7.2   0.0    3.8  5  DUF4350         Domain of unknown function (DUF4350)


Domain annotation for each model (and alignments):
>> BatA  Aerotolerance regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   4.4   1.2e-18   5.2e-15       2      77 .]       3      81 ..       1      81 [. 0.97
   2 ?    0.9   0.1      0.14   6.1e+02       9      30 ..     603     623 ..     601     624 .. 0.78

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 1.2e-18
                              BatA  2 lpFlnPllLlallllplpiillyllkrrpqevvfsslrlleevekdeea....lqrlkknllllLrllalallvlalAr 76
                                      +pF n  +L+ ll +++ +i+lyll+++p+ ++++sl++l++vek++++    ++r+ k+ l+l++l +l++l +a A+
  gi|298674640|ref|YP_003726390.1|  3 IPFDNLFALASLLSVIP-LIILYLLRPKPRVARIPSLMFLMKVEKEKKKiyssITRIIKDPLFLIQLFVLIFLSVASAG 80
                                      68************999.************************************************************9 PP

                              BatA 77 P 77
                                      P
  gi|298674640|ref|YP_003726390.1| 81 P 81
                                      9 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.14
                              BatA   9 lLlallllplpiillyllkrrp 30 
                                       +L+a++ll + i  +y++k+r 
  gi|298674640|ref|YP_003726390.1| 603 YLIAAALLLI-ITEIYIIKKRG 623
                                       6777777777.89999999985 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.7   2.7e-08   0.00012       1     106 [.      94     186 ..      94     188 .. 0.92
   2 ?   -2.0   0.0       1.3   5.8e+03      27      61 ..     435     470 ..     419     473 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 2.7e-08
                             VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallkslpgdrvglvtfsdgpevlipltkdkakilnalrnleakgggtn 77 
                                       +v+v+D+S+Sm+++     r++ a + +++++++  +++v l   ++++ v +  + + ++ +n l++l++k+   +
  gi|298674640|ref|YP_003726390.1|  94 TVIVIDSSASMQTDG----RFDDAISKAKSYISQ--ENTVIL---AENVPVTALENAGASDARNLLDKLNPKATVAD 161
                                       79*********9996....**************9..777777...899999999999******************** PP

                             VWA_2  78 laaaLqlarkalkkrrkgekrvivlitDg 106
                                       l +a++  + +l++    +  +iv+i+D 
  gi|298674640|ref|YP_003726390.1| 162 LSSAISSGMRILSN----QGGRIVVISDF 186
                                       *************4....47*******95 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.3
                             VWA_2  27 aveallkslpgd.rvglvtfsdgpevlipltkdkak 61 
                                       av ++l+s p++   +l++ +++   l+ +t++ ++
  gi|298674640|ref|YP_003726390.1| 435 AVYKYLNSTPRSgSTTLISTENNIPMLTYWTSGEGT 470
                                       667778888866699999999999999999988776 PP

>> ABC_transp_aux  ABC-type uncharacterized transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   1.2   3.4e-06     0.015     183     227 ..     340     383 ..      90     396 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.4e-06
                    ABC_transp_aux 183 dldsedilpedidvlviakptkdlseeelykldqflmnGgkllvf 227
                                       + +  +++ +++dv+v+ +++++++++e+ +l+ + +nGg +++ 
  gi|298674640|ref|YP_003726390.1| 340 SENIPTQI-NNYDVVVLSNNERSFNDDEISRLETYTNNGGEMVFI 383
                                       33344456.79******************************9886 PP

>> DUF4350  Domain of unknown function (DUF4350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.18     8e+02      29      67 ..      86     129 ..      76     131 .. 0.61
   2 ?   -2.8   0.0         2     9e+03      60      68 ..     175     183 ..     164     184 .. 0.74
   3 ?   -1.7   0.0      0.93   4.2e+03      34      52 ..     311     328 ..     297     336 .. 0.75
   4 ?    7.2   0.0    0.0016         7      36      68 ..     351     383 ..     330     384 .. 0.85
   5 ?   -0.6   0.0      0.43   1.9e+03      37      68 ..     449     474 ..     411     475 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.18
                           DUF4350  29 dalegedgtllvvapdlrlte.....eelaallewvarGntlvl 67 
                                       ++  ++++t++v+++  +  +     + + +   + ++ nt++l
  gi|298674640|ref|YP_003726390.1|  86 EEPLSSEHTVIVIDSSASMQTdgrfdDAISKAKSYISQENTVIL 129
                                       34445899999999997755555553333355556666666665 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2
                           DUF4350  60 arGntlvla 68 
                                        +G+++v++
  gi|298674640|ref|YP_003726390.1| 175 NQGGRIVVI 183
                                       388888885 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.93
                           DUF4350  34 edgtllvvapdlrlteeel 52 
                                        +++llv++ d ++++e++
  gi|298674640|ref|YP_003726390.1| 311 DNDVLLVTDKD-NTPSETA 328
                                       68999999999.8888765 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.0016
                           DUF4350  36 gtllvvapdlrlteeelaallewvarGntlvla 68 
                                       +++++ +++ +++++e+ +l+ ++ +G+  v +
  gi|298674640|ref|YP_003726390.1| 351 DVVVLSNNERSFNDDEISRLETYTNNGGEMVFI 383
                                       57889999999*****************88865 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 0.43
                           DUF4350  37 tllvvapdlrlteeelaallewvarGntlvla 68 
                                       t l+ + +       +  l +w++  +t+v++
  gi|298674640|ref|YP_003726390.1| 449 TTLISTEN------NIPMLTYWTSGEGTVVYL 474
                                       44444444......455899999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (625 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.50
# Mc/sec: 3771.56
//
Query:       gi|298674641|ref|YP_003726391.1|  [L=825]
Description: von Willebrand factor type A [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-11   45.4   4.4    2.8e-09   37.5   0.5    2.9  2  VWA           von Willebrand factor type A domain
    2.4e-10   41.0   0.2    2.7e-09   37.6   0.0    2.6  2  VWA_2         von Willebrand factor type A domain
    6.4e-06   25.8   0.1      0.014   14.9   0.0    2.2  2  GATase1_like  Putative glutamine amidotransferase
    0.00026   20.4   0.0     0.0083   15.5   0.0    2.8  3  VWA_CoxE      VWA domain containing CoxE-like protein
  ------ inclusion threshold ------
      0.015   15.2   0.0       0.14   12.1   0.0    2.3  2  VWA_3         von Willebrand factor type A domain


Domain annotation for each model (and alignments):
>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.3   0.00063       2.3     103     139 ..     125     162 ..      91     201 .. 0.74
   2 !   37.5   0.5   7.8e-13   2.8e-09       1     164 [.     371     543 ..     371     554 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00063
                                       SEEEEEEEESS--CSS.HTHHHHHHHHGCTEEEEEEEE CS
                               VWA 103 akkviilltdGksndg.dpkeaaneakeqgikvfavGv 139
                                         + i+++tdG++n g ++k a++ a +   +v+av  
  gi|298674641|ref|YP_003726391.1| 125 GDNQIVIVTDGNNNNGeSLKSALEFADNTETNVYAVQP 162
                                       467799*******9984666666666666888887765 PP

  == domain 2  score: 37.5 bits;  conditional E-value: 7.8e-13
                                       EEEEEEE-STTSCHHHHH.HHHHHHHHHHHHHTBTTTTEEEEEEEESSS....EEEEEETTSHCHHHHHHHHHHTGS CS
                               VWA   1 DivfvlDgSgsmgeenfe.kvkefikklveklevgpegtrvglvqfsse....vktefslndysskeellsalnnlk 72 
                                       +iv+vlD+S+s  ++  +  ++  + +l+++ +   +++++g++ f++e        + l   s++e l ++++nl 
  gi|298674641|ref|YP_003726391.1| 371 NIVLVLDVSQSTAAHGTQsDILGNAVNLIQNEN--LKDANLGVIAFGTEgedvSNGLVYLGIPSNRERLENKIRNL- 444
                                       8***********99999999**********999..89999*******9977744445888888899*********8. PP

                                       GGGGSSC-HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CSS..HTHHHHHHHHGCTEEEEEEEE........ CS
                               VWA  73 ysgggttntgkalkyaleklfkssagaRenakkviilltdGksndg..dpkeaaneakeqgikvfavGv........ 139
                                         +++t+ ++ +l+ + ++ ++++ g     k  +i+++dG   ++  + ++ a+ +k++g++++ v +        
  gi|298674641|ref|YP_003726391.1| 445 KTETDTS-LNLGLS-VSQEWLQGETG-----KLEVIVISDGAIGSSyqKSLDIADDMKKKGVNFYFVNIepsdpsie 514
                                       2233333.555555.44556666666.....999******88855446999************************** PP

                                       ......SSSHHHHHHHHHSSSSCHHCEEEES CS
                               VWA 140 ......gnadekelLnkiasepgeghvftvt 164
                                             gn + k ++++i ++++  ++f+ +
  gi|298674641|ref|YP_003726391.1| 515 grydnrGNLYAKRFIQEIEGSTD--TYFQIQ 543
                                       99999999999999999988887..777766 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.44   1.6e+03      94     107 .]     123     136 ..      95     137 .. 0.76
   2 !   37.6   0.0   7.4e-13   2.7e-09       1     106 [.     372     478 ..     372     479 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.44
                             VWA_2  94 kgekrvivlitDge 107
                                       +g  ++iv++tDg+
  gi|298674641|ref|YP_003726391.1| 123 SGGDNQIVIVTDGN 136
                                       36788999999995 PP

  == domain 2  score: 37.6 bits;  conditional E-value: 7.4e-13
                             VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallksl.pgdrvglvtfsdgpevlipl....t..kdkakilnalrnle 70 
                                       +v+vlD+S+S ++     t+ +++ +av+ + +++ ++ ++g+++f+++ e +++        +++++++n++rnl+
  gi|298674641|ref|YP_003726391.1| 372 IVLVLDVSQSTAAH---GTQSDILGNAVNLIQNENlKDANLGVIAFGTEGEDVSNGlvylGipSNRERLENKIRNLK 445
                                       79*********998...5999************884677*********754444322222355************** PP

                             VWA_2  71 akgggtnlaaaLqlarkalkkrrkgekrvivlitDg 106
                                       ++  +t+l+ +L+  +++l+ ++   k ++++i+Dg
  gi|298674641|ref|YP_003726391.1| 446 TE-TDTSLNLGLSVSQEWLQGET--GKLEVIVISDG 478
                                       86.*****************996..9*********9 PP

>> GATase1_like  Putative glutamine amidotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0   0.00031       1.1      93     139 ..     317     359 ..     293     365 .. 0.75
   2 !   14.9   0.0   3.9e-06     0.014     160     226 ..     575     643 ..     557     661 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00031
                      GATase1_like  93 vPnrlkllkdyvaeGggllmvGGylsfqGidgkarykktpvedvlPv 139
                                         n ++ l++yv++G gl++vGG  s+        y +++ e+ lPv
  gi|298674641|ref|YP_003726391.1| 317 SQNEVEKLNNYVTDGNGLVVVGGDQSYS----FGGYLNSTFEELLPV 359
                                       45788999***************87764....233556666666665 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 3.9e-06
                      GATase1_like 160 asehpvlkglssewPkllGyneveakdnaevlatvsedshPllvvGeygkGrtaaftsdis....phwlsp 226
                                       +s+h +++ ++    ++ Gyn+v++k +a+ l  ++ +++P++   ++g Gr++ +t+d +    + w s 
  gi|298674641|ref|YP_003726391.1| 575 NSNHFITRDINI-TGNVSGYNDVTPKAGAQRLV-ITTNGKPIVTSWRFGLGRVVSYTTDNGygsgNRWASQ 643
                                       567888888874.46889***********9986.666779*******************751111456555 PP

>> VWA_CoxE  VWA domain containing CoxE-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.11     4e+02      50      73 ..      62      85 ..      52      89 .. 0.77
   2 ?   -0.7   0.0      0.21   7.6e+02     152     189 ..     127     163 ..     116     180 .. 0.74
   3 !   15.5   0.0   2.3e-06    0.0083      57     198 ..     369     518 ..     349     529 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.11
                          VWA_CoxE 50 rkprerkprelvllvDvSgSmaay 73
                                      ++ r +++ +lv+++D   Sm+ +
  gi|298674641|ref|YP_003726391.1| 62 SETRTNENPNLVVISDETSSMELF 85
                                      444666555************975 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.21
                          VWA_CoxE 152 avvvlvsDglergdreellaelarlvrrarrlvwlnpl 189
                                         +v+v+Dg + ++ e l+++l+   +   ++  + p+
  gi|298674641|ref|YP_003726391.1| 127 NQIVIVTDG-NNNNGESLKSALEFADNTETNVYAVQPE 163
                                       579******.7888888888888777777777777776 PP

  == domain 3  score: 15.5 bits;  conditional E-value: 2.3e-06
                          VWA_CoxE  57 prelvllvDvSgSmaaysaiflallhAllqqlp......rtevfaFdtrlvdlTralrerDpaeaLarvsaaved.. 125
                                        r++vl++DvS S aa+ +    l +A+    +      +  v+aF+t+  d+++ l      +  +r+++++ +  
  gi|298674641|ref|YP_003726391.1| 369 GRNIVLVLDVSQSTAAHGTQSDILGNAVNLIQNenlkdaNLGVIAFGTEGEDVSNGLVYLGIPSNRERLENKIRNlk 445
                                       5689************877666666666422223356788899*************988888888888855554425 PP

                          VWA_CoxE 126 lgGgTrigaalaeflelvtrpaLsrravvvlvsDglergdreellaelarlvrrarrlvwln..plsdagtpgyd 198
                                        +  T ++ +l   +e+ + ++   +  v+++sDg  + + +++l+  ++++++++++  +n  p ++   ++yd
  gi|298674641|ref|YP_003726391.1| 446 TETDTSLNLGLSVSQEWLQGET--GKLEVIVISDGAIGSSYQKSLDIADDMKKKGVNFYFVNiePSDPSIEGRYD 518
                                       7778889999999999999999..9999*****************************998882244445555555 PP

>> VWA_3  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.22   7.7e+02      95     112 ..     124     141 ..     109     165 .. 0.73
   2 ?   12.1   0.0     4e-05      0.14       2     113 ..     371     486 ..     370     511 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.22
                             VWA_3  95 gevrsvilltDgssaqge 112
                                       g   +++++tDg+  +ge
  gi|298674641|ref|YP_003726391.1| 124 GGDNQIVIVTDGNNNNGE 141
                                       566789999999966655 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 4e-05
                             VWA_3   2 evvivvDvsssmsaen...klvkdaLsvalrqLptndkiavllfgtkprplfpgsravs.aaelqealqkikelels 74 
                                       ++v+v+Dvs+s+ a++   + + +a +++  +  +   + v++fgt+ + ++ g + +  ++ +++++ ki  l+  
  gi|298674641|ref|YP_003726391.1| 371 NIVLVLDVSQSTAAHGtqsDILGNAVNLIQNENLKDANLGVIAFGTEGEDVSNGLVYLGiPSNRERLENKIRNLKT- 446
                                       79*********888866677777777776666555669****************998875899**********999. PP

                             VWA_3  75 lgasnlegaLkealrqp..akpgevrsvilltDgss.aqgee 113
                                          +++   L   ++q+  +  +   +vi+++Dg++  ++++
  gi|298674641|ref|YP_003726391.1| 447 --ETDTSLNLGLSVSQEwlQGETGKLEVIVISDGAIgSSYQK 486
                                       ..45555555555666666777888999*****997544442 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (825 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       922  (0.0514251); expected 358.6 (0.02)
Passed bias filter:                      621  (0.0346366); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.80u 0.33s 00:00:01.13 Elapsed: 00:00:00.52
# Mc/sec: 4769.62
//
Query:       gi|298674642|ref|YP_003726392.1|  [L=167]
Description: PfpI family intracellular protease [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.8e-59  197.8   0.0    1.1e-58  197.7   0.0    1.0  1  DJ-1_PfpI      DJ-1/PfpI family
      3e-05   23.9   0.0      4e-05   23.5   0.0    1.3  1  GATase         Glutamine amidotransferase class-I
     0.0074   15.9   0.0      0.011   15.4   0.0    1.3  1  Catalase_C     C-terminal domain found in long catalases
  ------ inclusion threshold ------
      0.032   13.3   0.0      0.046   12.8   0.0    1.3  1  GATase_5       CobB/CobQ-like glutamine amidotransferase doma
      0.036   13.8   0.0      0.053   13.3   0.0    1.2  1  Peptidase_C26  Peptidase C26
      0.044   13.5   0.0        4.4    6.9   0.0    2.4  2  ThiJ_like      ThiJ/PfpI family-like
      0.046   13.3   0.0      0.065   12.8   0.0    1.2  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma


Domain annotation for each model (and alignments):
>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.7   0.0   4.3e-62   1.1e-58       1     164 [.       1     163 [.       1     164 [. 0.99

  Alignments for each domain:
  == domain 1  score: 197.7 bits;  conditional E-value: 4.3e-62
                                       EEEEEEEETTBEHHHHHHHHHHHHHTTEEEEEEESSTSEEEETTSEEEE-SEEGGGCTCCG-SEEEE--BHHHHHHH CS
                         DJ-1_PfpI   1 kkvlvlladgvedvElivpvdvlkragikvdvvsvdkeevkgsrGlkvtvdaslddvkaaeyDalvlpGGragperl 77 
                                       +k+l++ adg+ed+El++p+++lk++g++v+++s++k++++g++G+   vd ++d+++++++D+lv+ GG+a pe++
  gi|298674642|ref|YP_003726392.1|   1 MKALIISADGFEDLELFYPLNRLKEEGVDVKIASMEKGTITGKHGYPADVDLTFDEINPDDFDMLVISGGKA-PEKV 76 
                                       699*********************************************************************.**** PP

                                       HTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTTSEE--SGGGHHHHHHTTSEE-SSSEEEETTEEEESSGGG CS
                         DJ-1_PfpI  78 renekvvelvkefaekgklvaaICagpqlLaaagvlkgrrvTsypavkdklekagakyvdkrvvvdgnlvTsrgpga 154
                                       r +ek+++++k+f++k+k+va+IC+g+q+L++agv+kgr++T+y++v+d+l+ +ga+y+dk+vvvdgnl+Tsr+p++
  gi|298674642|ref|YP_003726392.1|  77 RLDEKAIKITKHFFDKNKPVASICHGAQILISAGVVKGRKATCYIGVRDDLKVSGANYEDKEVVVDGNLITSRNPND 153
                                       ***************************************************************************** PP

                                       HHHHHHHHHH CS
                         DJ-1_PfpI 155 aiefalelle 164
                                       +++f++e+++
  gi|298674642|ref|YP_003726392.1| 154 LYAFGREIVK 163
                                       ********98 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   1.6e-08     4e-05      33      87 ..      54     109 ..      21     152 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.6e-08
                                       HHHHHHTHHSTSEEEEEEESSCTT...TTTHHHHHHHHCTSTS-EEEETHHHHHHHHH CS
                            GATase  33 aeeilellknpdgilvsgGpgspg...vegkieaikearenkiPiLGICLGmQllaie 87 
                                       ++ei  + +++d +++sgG    +    e++i+++k+++++++P+  IC G Q+l+ +
  gi|298674642|ref|YP_003726392.1|  54 FDEI--NPDDFDMLVISGGKAPEKvrlDEKAIKITKHFFDKNKPVASICHGAQILISA 109
                                       3444..36799********666666699**************************9875 PP

>> Catalase_C  C-terminal domain found in long catalases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   4.3e-06     0.011      26     119 ..      22     113 ..       7     127 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.3e-06
                        Catalase_C  26 alaaegvdvtvvaeklg...saeg....vnrTYstadaveFDaivvadgaeslfsakataasslfpagrplqlllda 95 
                                       +l++egvdv++   + g   +++g    v+ T+   +  +FD +v+ +g+         a+++   +++++++ +  
  gi|298674642|ref|YP_003726392.1|  22 RLKEEGVDVKIASMEKGtitGKHGypadVDLTFDEINPDDFDMLVISGGK---------APEKVRLDEKAIKITKHF 89 
                                       6888999999887555534444446667*********************2.........34566789********** PP

                        Catalase_C  96 yrhgKpigalGsgaealkaagisa 119
                                       +   Kp++ + +ga++l +ag+ +
  gi|298674642|ref|YP_003726392.1|  90 FDKNKPVASICHGAQILISAGVVK 113
                                       *****************9999876 PP

>> GATase_5  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.8e-05     0.046      63     113 ..      67     116 ..      51     125 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.8e-05
                          GATase_5  63 gsgkgwakslllneklrealekflnredtlaLGiCnGfqlLvklglvpgge 113
                                        sg  + + ++l ek+ +  ++f+++ ++ +  iC G q+L+  g+v g +
  gi|298674642|ref|YP_003726392.1|  67 ISGGKAPEKVRLDEKAIKITKHFFDK-NKPVASICHGAQILISAGVVKGRK 116
                                       56667777899999***********9.999****************99854 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.1e-05     0.053      91     119 ..      79     107 ..      56     118 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.1e-05
                     Peptidase_C26  91 dalelaLiraalergvPilgiCrGlqlln 119
                                       d+  +++ ++  ++++P+ +iC G q+l 
  gi|298674642|ref|YP_003726392.1|  79 DEKAIKITKHFFDKNKPVASICHGAQILI 107
                                       8889999********************94 PP

>> ThiJ_like  ThiJ/PfpI family-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.012        30       2      32 ..       7      37 ..       6      56 .. 0.81
   2 ?    6.9   0.0    0.0017       4.4      83     142 ..      60     110 ..      44     121 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.012
                         ThiJ_like  2 adeGydvtevaipwkvlkdagfsveFvtekg 32
                                      +  G++  e+  p++ lk++g+ v+ ++ + 
  gi|298674642|ref|YP_003726392.1|  7 SADGFEDLELFYPLNRLKEEGVDVKIASMEK 37
                                      67899999*****************998653 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0017
                         ThiJ_like  83 eeydlvllpGGsdkavrelleserlhsllveylklvkrekepskvlgaicqgvlalafak 142
                                       +++d++ + GG+ +     l+++ + +  ++++       +++k +++ic+g+  l  a 
  gi|298674642|ref|YP_003726392.1|  60 DDFDMLVISGGKAPEK-VRLDEKAI-KITKHFF-------DKNKPVASICHGAQILISAG 110
                                       5678888888877643.12333333.3334444.......7899*********9998875 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.5e-05     0.065      12      89 ..      16     107 ..      10     123 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.5e-05
                          GATase_3  12 nytdldpLeaepevrvrfvplkdeslg..................edadlvilpGgkdtiqdlallresgldeaike 70 
                                        ++ l+ L++e+ v+v+++++++ +++                  +d d++++ Ggk  ++    +++    +  k+
  gi|298674642|ref|YP_003726392.1|  16 LFYPLNRLKEEG-VDVKIASMEKGTITgkhgypadvdltfdeinpDDFDMLVISGGKAPEKVRLDEKA---IKITKH 88 
                                       566666666655.5566666566666666666666666677777788**********87765544444...444466 PP

                          GATase_3  71 aaeaggpvlgiCGGlqmLG 89 
                                       +  +++pv  iC G q+L 
  gi|298674642|ref|YP_003726392.1|  89 FFDKNKPVASICHGAQILI 107
                                       77899************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1021.45
//
Query:       gi|298674643|ref|YP_003726393.1|  [L=46]
Description: hypothetical protein Metev_0695 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1042  (0.0581181); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.32s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 284.46
//
Query:       gi|298674644|ref|YP_003726394.1|  [L=255]
Description: peptidase A24B, FlaK domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-31  107.9   0.0    2.8e-31  107.9   0.0    2.1  2  Arc_PepC_II    Archaeal Peptidase A24 C-terminus Type II
    2.8e-15   56.6   6.4    2.8e-15   56.6   6.4    1.7  2  Peptidase_A24  Type IV leader peptidase family


Domain annotation for each model (and alignments):
>> Arc_PepC_II  Archaeal Peptidase A24 C-terminus Type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.7      0.39   3.5e+03      63      84 ..      27      48 ..      19      68 .. 0.63
   2 !  107.9   0.0   3.1e-35   2.8e-31       2      92 .]     152     242 ..     151     242 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.39
                       Arc_PepC_II 63 ieetvWvtygvPflipitaGfi 84
                                      + ++ W    vP +i+++  +i
  gi|298674644|ref|YP_003726394.1| 27 VPNKLWSFMLVPGMIFVIYDLI 48
                                      5556666666666666654443 PP

  == domain 2  score: 107.9 bits;  conditional E-value: 3.1e-35
                       Arc_PepC_II   2 kllymligyrvkvkellkkflflleefeekdgkikrkfisvekeldeelrkelkkykkkglieetvWvtygvPflip 78 
                                       k++ym++gy+++v e   ++++llee+ee++++i+  f +++k++d+e+++el++y +k+li++++Wvt+g+Pf+ip
  gi|298674644|ref|YP_003726394.1| 152 KPWYMFLGYKTSVYESIPDHIRLLEEYEETNEGIRAGFSRSGKKIDSETIEELRNYADKNLISKRIWVTPGLPFMIP 228
                                       89*************************************************************************** PP

                       Arc_PepC_II  79 itaGfiialvlGDl 92 
                                       it+Gf++++v+GDl
  gi|298674644|ref|YP_003726394.1| 229 ITVGFLTTVVYGDL 242
                                       *************6 PP

>> Peptidase_A24  Type IV leader peptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   6.4   3.1e-19   2.8e-15       2     103 ..       9     125 ..       8     134 .. 0.83
   2 ?   -3.0   0.1       1.1   9.9e+03      51      61 ..     227     237 ..     211     247 .. 0.58

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 3.1e-19
                     Peptidase_A24   2 vlltillvlsviDldtrtlpdeltlpllllgvlfa..qllllglpnlaqavlgalvgalvlllislvdeqamGgGDv 76 
                                       ++l +ll+ +++Dl+tr++p++l+ ++l+ g++f   +l++ g+++l   +++++ +++++++  l+  +a+Gg+D+
  gi|298674644|ref|YP_003726394.1|   9 FFLPFLLYSCYSDLKTRRVPNKLWSFMLVPGMIFViyDLINYGFAHLVHLLISFVFIFGFVYV--LFSFNAFGGADA 83 
                                       6899*******************************9988899*********************..************ PP

                     Peptidase_A24  77 klaavlgaflgwerl...............llavlvaillga 103
                                       kl+++++++++ +                 + ++ +++++ a
  gi|298674644|ref|YP_003726394.1|  84 KLMIIISIIIPAFPEidmfgytlplnpvppINLFAFSVFANA 125
                                       *********995544456666667777776333333334444 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.1
                     Peptidase_A24  51 lgalvgalvll 61 
                                       + + vg+l ++
  gi|298674644|ref|YP_003726394.1| 227 IPITVGFLTTV 237
                                       33333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       830  (0.0462937); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 1521.16
//
Query:       gi|298674645|ref|YP_003726395.1|  [L=426]
Description: dimethylmenaquinone methyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.2e-42  143.8   2.5    4.2e-42  143.8   2.5    1.8  2  RraA-like     Aldolase/RraA
    5.1e-20   72.0   3.1      2e-19   70.1   3.1    1.9  1  OMPdecase     Orotidine 5'-phosphate decarboxylase / HUMPS fa
    4.3e-08   32.6   4.6    8.7e-08   31.6   1.3    2.8  3  NanE          Putative N-acetylmannosamine-6-phosphate epimer
    3.4e-07   30.0   0.7    2.3e-05   24.0   0.4    2.4  2  His_biosynth  Histidine biosynthesis protein
    1.2e-05   24.7   1.2    7.3e-05   22.2   1.2    2.4  1  TMP-TENI      Thiamine monophosphate synthase
    0.00041   20.0   0.2       0.11   12.1   0.0    2.3  2  HMGL-like     HMGL-like
    0.00054   19.5   6.2        0.1   12.0   0.3    2.8  3  PcrB          PcrB family
     0.0008   18.8   0.4     0.0022   17.4   0.1    1.8  2  ThiG          Thiazole biosynthesis protein ThiG
     0.0025   17.0   0.4      0.011   14.9   0.1    2.0  2  Dus           Dihydrouridine synthase (Dus)
     0.0043   15.9   3.2      0.036   12.9   0.9    2.5  2  Trp_syntA     Tryptophan synthase alpha chain
     0.0059   16.1   0.2        0.7    9.3   0.0    2.3  2  PEP_mutase    Phosphoenolpyruvate phosphomutase
     0.0091   15.6   0.1      0.058   13.0   0.1    2.0  2  DeoC          DeoC/LacD family aldolase
     0.0094   15.4   2.2      0.026   13.9   2.2    1.7  1  NMO           Nitronate monooxygenase
  ------ inclusion threshold ------
      0.041   13.0   0.3      0.065   12.4   0.3    1.3  1  IGPS          Indole-3-glycerol phosphate synthase
       0.46    9.6   5.1       0.65    9.1   0.4    2.9  4  DUF561        Protein of unknown function (DUF561)


Domain annotation for each model (and alignments):
>> RraA-like  Aldolase/RraA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       5.4   6.5e+03     122     132 ..     158     168 ..     147     192 .. 0.68
   2 !  143.8   2.5   3.5e-45   4.2e-42       1     150 []     235     381 ..     235     381 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5.4
                                       SEESS-EEETT CS
                         RraA-like 122 gevnvpveigg 132
                                        +vnvpv+++g
  gi|298674645|ref|YP_003726395.1| 158 DAVNVPVAVAG 168
                                       46788888854 PP

  == domain 2  score: 143.8 bits;  conditional E-value: 3.5e-45
                                       HHHHHHHCEE-SSBSTB.TT.EE.S.EEEEEEEEEESS.BGHHHHHHHTS--TTEEEEEESTT.SSSSSECE-HHHH CS
                         RraA-like   1 tadvsDalkklggrsggirpler.s.fvGpavTvkvveadnslvkealeeagpgdvlVvdgggdeslraallGglla 75 
                                       t+++sDa+++ g  + +i pl + + +vG+avTv+++e+d+++  +a++ a+pgdv+V+ +++  +  a++ Ggl +
  gi|298674645|ref|YP_003726395.1| 235 TPNISDAMHRKGAMR-KIIPLVQdTkMVGKAVTVQTFEGDWAKPVQAIDIAKPGDVIVIYNSS--KDIACW-GGLAT 307
                                       789******444444.699966634699*******************************9888..558888.***** PP

                                       HHHHHTTBSEEEEEEEES-HHHHTTSSSEEEEEEE-SSB-B-S.STSEESS-EEETTEEE-TTSEEEEETTEEEE CS
                         RraA-like  76 taakangvaGvvvdGavRDvaelreldfpvfargvtprkkpkkkgkgevnvpveiggvtvkpgdlivaDedGvvv 150
                                        ++ ++g+aGvvvdGavRDv+++ ++++p+fa +++p++   k g ge+n ++++g + v+pgd+iv+D++Gvvv
  gi|298674645|ref|YP_003726395.1| 308 FSCLNKGIAGVVVDGAVRDVDDITNIGLPIFAGNTVPNAGDPK-GFGEINSEITCGSQNVRPGDYIVGDNNGVVV 381
                                       **************************************95555.******************************8 PP

>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.1   3.1   1.7e-22     2e-19       3     224 ..       5     204 ..       3     205 .. 0.87

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 1.7e-22
                                       EEEEE-SSSHHHHHHHHHHHGG.GSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHT..SEEEEEEEE-S-HHHHHHHH CS
                         OMPdecase   3 LclalDvatarelleladkvgp.sivvlKthydlvegwgfegtgaklaalarkhg..flifeDrKfaDIGntvekqa 76 
                                       +++alD+ + ++++++a+++ +  +++++++++l++++g     +++++++rk++    +++D+K+ D G+++ ++a
  gi|298674645|ref|YP_003726395.1|   5 VQVALDLLEIDRAVQIAKEALEgGVDWIEVGTPLIKSEG-----MSAIRRIRKEFpgYTVLADMKTIDTGSIEVEMA 76 
                                       79******************999****************.....**********888******************** PP

                                       HSTCHHHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHH..H..SHHHHHHHHHHHHHHH CS
                         OMPdecase  77 tagsarikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqe..k..gytqacveaarehkae 149
                                             +k++adiv + +  + +++   ++ a ++g    l+ + ms  +  +++   +  g+++  v+   +++ +
  gi|298674645|ref|YP_003726395.1|  77 ------AKSGADIVMILGGSDNSTIDDSVRSAHQYG--VKLMADLMSVNDPVERAIqlEkmGIDYINVHVGIDQQMQ 145
                                       ......69***************************8..89999*******998888442466666666666666622 PP

                                       TTESEEECCCHTHHHHHHTTCSCEEEHHHTTEEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHHH CS
                         OMPdecase 150 dfvmGfvaqetlnateedaddfihltpgigleqggdgkgqqyntpekligiagadiiivGRgIlkagdpveeaer 224
                                           G+      +    +   ++ ++  +++   ++++g+ ++   ++++  gadi+ivG  I+++++   +a+ 
  gi|298674645|ref|YP_003726395.1| 146 ----GYD-----P----I-YLLKDVVDAVNV-PVAVAGGIDEQRSSEIVN-TGADIVIVGGNITRSDNVSRAAKT 204
                                       ....322.....2....2.456667777777.*********998888888.88***************9999986 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.66   7.9e+02     158     180 ..      20      42 ..      15      48 .. 0.84
   2 !   31.6   1.3   7.3e-11   8.7e-08      56     184 ..      72     200 ..      50     207 .. 0.82
   3 ?   -0.8   0.0       0.6   7.1e+02     162     183 ..     310     331 ..     306     339 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.66
                                       HHHHHHTT--SEEEE-HHHH-HH CS
                              NanE 158 kakkaieiGvdavvvGsaitrle 180
                                        ak+a+e Gvd + vG+ + + e
  gi|298674645|ref|YP_003726395.1|  20 IAKEALEGGVDWIEVGTPLIKSE 42 
                                       6999************9887665 PP

  == domain 2  score: 31.6 bits;  conditional E-value: 7.3e-11
                                       HHHHHHTTT-SEEEEE--SS--T--HHHHHHHHHHH--EEEEE-SSHHH....HHHHHHTT-SEEE-TTTTSSTTS- CS
                              NanE  56 dideLaaagadiialDatdrerpvtieelikkikekyqllmaDistlee....glvakklGvdivGttlsGytkeee 128
                                       +++  a+ gadi+ + + + +   ti++ +++ ++ ++ lmaD+ ++++    +++ +k+G+d++     G  ++ +
  gi|298674645|ref|YP_003726395.1|  72 EVEMAAKSGADIVMILGGSDN--STIDDSVRSAHQYGVKLMADLMSVNDpverAIQLEKMGIDYINVH-VGIDQQMQ 145
                                       7888999999*9999888765..6899****************988755333378999*******865.58888877 PP

                                       .SS--HHHHHHHHHT.T--EEEES---SHHHHHHHHTT--SEEEE-HHHH-HHHHHH CS
                              NanE 129 kaepDfalvkalsea.glkviaeGrintPekakkaieiGvdavvvGsaitrleeiak 184
                                         +p + l+k++++a ++ v + G i+  +++ +++++G+d v+vG+ itr +++ +
  gi|298674645|ref|YP_003726395.1| 146 GYDPIY-LLKDVVDAvNVPVAVAGGIDE-QRSSEIVNTGADIVIVGGNITRSDNVSR 200
                                       788866.666666653899*******97.5678999***************999864 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.6
                                       HHTT--SEEEE-HHHH-HHHHH CS
                              NanE 162 aieiGvdavvvGsaitrleeia 183
                                       +++ G++ vvv +a+  +++i+
  gi|298674645|ref|YP_003726395.1| 310 CLNKGIAGVVVDGAVRDVDDIT 331
                                       6677888888888887777666 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.031        38      84     132 ..      17      65 ..      16     108 .. 0.74
   2 !   24.0   0.4   1.9e-08   2.3e-05      27     120 ..     115     206 ..     105     229 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.031
                                       SHHHHHHHHHCT-SEEEESHHHHH-..THHHHHHHHHHCGGGEEEEEEEEE CS
                      His_biosynth  84 sledveelleagadkviigtaavkn..pelikelaekfgsqkivvaiDarr 132
                                        ++ ++e+le g+d + +gt  +k+   + i+++ ++f++  + +  D++ 
  gi|298674645|ref|YP_003726395.1|  17 AVQIAKEALEGGVDWIEVGTPLIKSegMSAIRRIRKEFPGYTVLA--DMKT 65 
                                       567789*****************98334569*******9944444..4443 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 1.9e-08
                                       ETTSHHHHHHHHHHHT-SEEEE.EEHHHHCTTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEES CS
                      His_biosynth  27 yagdpvelakryeeegadelhv.vDldaakegreanldlveeiaeevfipvqvGGGIrsledveelleagadkviig 102
                                         +dpve a ++e+ g+d++ v v +d  ++g    + l++ ++++v++pv v GGI +     e+++ gad vi+g
  gi|298674645|ref|YP_003726395.1| 115 SVNDPVERAIQLEKMGIDYINVhVGIDQQMQG-YDPIYLLKDVVDAVNVPVAVAGGIDEQR-SSEIVNTGADIVIVG 189
                                       679*****************876899988755.5567899*****************9887.99************* PP

                                       HHHHH-THHHHHHHHHHC CS
                      His_biosynth 103 taavknpelikelaekfg 120
                                           ++ + ++++a+ + 
  gi|298674645|ref|YP_003726395.1| 190 GNITRS-DNVSRAAKTIR 206
                                       876555.45566666554 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   1.2   6.1e-08   7.3e-05     101     177 ..     114     188 ..       4     192 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 6.1e-08
                          TMP-TENI 101 lSvhslee.aeeaealgadYigvGpifpTdtKkdaeplgleglkelaealeiPvvaiGGitlenvaevleagadgva 176
                                       +Sv+++ e a ++e++g+dYi v   +     +++    + +lk++++a+++Pv + GGi++++  e++++gad v 
  gi|298674645|ref|YP_003726395.1| 114 MSVNDPVErAIQLEKMGIDYINV---HVGIDQQMQGYDPIYLLKDVVDAVNVPVAVAGGIDEQRSSEIVNTGADIVI 187
                                       58898888899**********76...4566777778888999********************************998 PP

                          TMP-TENI 177 v 177
                                       v
  gi|298674645|ref|YP_003726395.1| 188 V 188
                                       7 PP

>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   8.9e-05      0.11      15      95 ..       7      86 ..       5     104 .. 0.75
   2 !    5.9   0.1    0.0071       8.4      16      73 ..     110     193 ..      93     215 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.9e-05
                                      TSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE.-SSHHHHHHHHH....TT-SE CS
                         HMGL-like 15 alkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalv.rarekdikaavealkgagakr 92
                                       + + l++++ ++iak+  e gvd iEvg p    + + ++r i k+ +  ++la + + +   i++ ++   + ga++
  gi|298674645|ref|YP_003726395.1|  7 VALDLLEIDRAVQIAKEALEGGVDWIEVGTPLIKSEGMSAIRRIRKEFPGYTVLADMkTIDTGSIEVEMA--AKSGADI 83
                                      56677999**************************************998887554430344444444444..4466666 PP

                                      EEE CS
                         HMGL-like 93 vhv 95
                                      v +
  gi|298674645|ref|YP_003726395.1| 84 VMI 86
                                      655 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0071
                                       SSS---HHHHHHHHHHHHHHT-SEE--..........................TSGGGT.THHHHHHHS---TT-B. CS
                         HMGL-like  16 lkaalsveeklaiakaLdeagvdeiEv..........................gfpaaseddfevvraiakavkkar 66 
                                       +++ +sv++ ++ a +L+++g+d+i v                           +++a+  d ++  +i++++ +  
  gi|298674645|ref|YP_003726395.1| 110 MADLMSVNDPVERAIQLEKMGIDYINVhvgidqqmqgydpiyllkdvvdavnvPVAVAGGIDEQRSSEIVNTGADIV 186
                                       57889999*******************88554444444444444444444433333444444444444444443333 PP

                                       .--EE-S CS
                         HMGL-like  67 ilalvra 73 
                                       i++  + 
  gi|298674645|ref|YP_003726395.1| 187 IVGGNIT 193
                                       4444444 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.3   8.7e-05       0.1      22      52 ..      72     103 ..      48     121 .. 0.84
   2 !    9.5   0.7    0.0005       0.6     171     221 ..     150     204 ..     122     209 .. 0.61
   3 ?   -2.6   0.0       2.5     3e+03      39      61 ..     315     337 ..     310     343 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.7e-05
                                       HHHHHHCTT-SEEEE.ECSTCHHHHHHHHHHH CS
                              PcrB  22 iveiviesgtDavmi.gGsqsvtldntvrllk 52 
                                        ve++++sg+D vmi gGs+++t d+ vr  +
  gi|298674645|ref|YP_003726395.1|  72 EVEMAAKSGADIVMIlGGSDNSTIDDSVRSAH 103
                                       58999********9759999******998755 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0005
                                       HHHHHHHHSSSE..EEEESS--SHHHHHHHHCCSSEEEE-CHHHHHH..HCHHHH CS
                              PcrB 171 vialkkklekar..livGGGirsaEkAkevveaADvivvGnvveekd..erkida 221
                                       +  lk +++  +  + v GGi+++ + + v + AD+++vG  +  +d   r+ ++
  gi|298674645|ref|YP_003726395.1| 150 IYLLKDVVDAVNvpVAVAGGIDEQRSSEIVNTGADIVIVGGNITRSDnvSRAAKT 204
                                       455566666655225789***998766555555**99998777766634555555 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 2.5
                                       STCHHHHHHHHHHHHHCTSSS-E CS
                              PcrB  39 sqsvtldntvrllkkvsriklPi 61 
                                         +v  d +vr + ++++i+lPi
  gi|298674645|ref|YP_003726395.1| 315 IAGVVVDGAVRDVDDITNIGLPI 337
                                       55788899999999999999998 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   1.8e-06    0.0022     137     226 ..     123     211 ..      98     227 .. 0.82
   2 ?   -2.8   0.0       2.5     3e+03     193     215 ..     310     332 ..     307     337 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.8e-06
                                       HHHHHHTT-SEBEEBSSSTTS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSH CS
                              ThiG 137 arrleevGcaavmPlaapiGsglGllnkealkiiieeakvPvivDAGigspsdaaqamelGadavllntavaeakdp 213
                                       a +le++G+  +          +G    + lk +++ ++vPv v  Gi +     + ++ Gad v++   ++++++ 
  gi|298674645|ref|YP_003726395.1| 123 AIQLEKMGIDYINVHVGIDQQMQGYDPIYLLKDVVDAVNVPVAVAGGIDEQ-RSSEIVNTGADIVIVGGNITRSDNV 198
                                       556666666666555555556688889999******************875.567889******************* PP

                                       HHHHHHHHHHHHH CS
                              ThiG 214 vamArafklavea 226
                                        + A++++ +v++
  gi|298674645|ref|YP_003726395.1| 199 SRAAKTIRSSVDS 211
                                       *******999986 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.5
                                       HHHTT-SEEEESHHHHTSSSHHH CS
                              ThiG 193 amelGadavllntavaeakdpva 215
                                        ++ G+ +v+++ av   +d+ +
  gi|298674645|ref|YP_003726395.1| 310 CLNKGIAGVVVDGAVRDVDDITN 332
                                       5778999*******999999876 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.33     4e+02     172     212 ..      44      86 ..       9      94 .. 0.67
   2 !   14.9   0.1   8.9e-06     0.011     138     268 ..     117     252 ..      93     271 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.33
                                       CHHHHHHHHH-S.S-EEEESS--SHHHHH.HHHHHH--SEEEE CS
                               Dus 172 weaIkevkqavs.ipviaNGdIkdaedaq.aileetGadgvmi 212
                                        +aI+ ++++++  +v+a     d+ +++ ++ +++Gad vmi
  gi|298674645|ref|YP_003726395.1|  44 MSAIRRIRKEFPgYTVLADMKTIDTGSIEvEMAAKSGADIVMI 86 
                                       4678888888888888887766666666536778899999998 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 8.9e-06
                                       C.HHHHHHHHHHCT-SEEEEESSECCCTT-CG--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESC CS
                               Dus 138 enalelakiveaaGaqaltvHgRtraqnyegtadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigr 214
                                       ++ +e a  +e+ G++ + vH    +q  +g + +   k+v +av++pv + G+I + ++ + i  +tGad v++g 
  gi|298674645|ref|YP_003726395.1| 117 NDPVERAIQLEKMGIDYINVHVGIDQQ-MQGYDPIYLLKDVVDAVNVPVAVAGGIDEQRSSE-I-VNTGADIVIVGG 190
                                       556788889999*********976555.456666667889999999*********9866544.4.467********9 PP

                                       HHCCSTTHHHHHHHHHHSC------.HHHH......HHHH.HHHHHHCHHTTCCCCCCHHHH CS
                               Dus 215 galgnPwlfaestavktgeaepapp.laee......aeiv.eehlkkleeelgedkglrkir 268
                                          +  +++++ ++++ + ++p+   + ++       e++ +   +++ + ++++ ++rki 
  gi|298674645|ref|YP_003726395.1| 191 NITRSDNVSRAAKTIRSSVDSPSKFqVSKQslddeiYELLtSTSTPNISDAMHRKGAMRKII 252
                                       99999999998889999888888774444455555533330344556666666666666665 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.046        55      21      47 ..      12      38 ..       3      42 .. 0.85
   2 !   12.9   0.9     3e-05     0.036     189     243 ..     152     208 ..     104     223 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.046
                                      S-HHHHHHHHHHHHHCT-SSEEEE--- CS
                         Trp_syntA 21 pdleqsleilkalekagadviElGlpf 47
                                       ++++ ++i k+  ++g+d iE+G p 
  gi|298674645|ref|YP_003726395.1| 12 LEIDRAVQIAKEALEGGVDWIEVGTPL 38
                                      5688999*****************995 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 3e-05
                                       HHHHHHHCTSS-EEEESSS-SHHHHHHHHTT-SEEEE-HHHHH..HHHCTTTSHHHH CS
                         Trp_syntA 189 lverlkkltavPvavGFGistkeqvkqvakvadGvivGSalvk..kieeeaeekeqa 243
                                       l++ + ++ +vPvav  Gi ++   + v+++ad vivG  + +  ++ ++a++ ++ 
  gi|298674645|ref|YP_003726395.1| 152 LLKDVVDAVNVPVAVAGGIDEQRSSEIVNTGADIVIVGGNITRsdNVSRAAKTIRSS 208
                                       5778888899*****************************998621355555555544 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00058       0.7     164     220 ..      75     137 ..      71     146 .. 0.71
   2 !    6.7   0.1    0.0036       4.4     155     226 ..     116     195 ..     112     207 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00058
                        PEP_mutase 164 aYaeAGAdgvfvpglqkdaeiaelvaav.dvplnvvp.l.kgt...lsvaelaelGvarislg 220
                                       + a+ GAd v++ g++++++i + v+   +  + +++ l + +       +l+++G+  i ++
  gi|298674645|ref|YP_003726395.1|  75 MAAKSGADIVMILGGSDNSTIDDSVRSAhQYGVKLMAdLmSVNdpvERAIQLEKMGIDYINVH 137
                                       6789*****************999988856444444422221223355667888888887765 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0036
                        PEP_mutase 155 leeaieRaraYaeAGAdgvfvpgl.......qkdae.iaelvaavdvplnvvplkgtlsvaelaelGvarislgnhl 223
                                       +++ +eRa    + G d + v+ +        ++   ++++v+av+vp+ v  + ++   +e+ + G+ ++++g ++
  gi|298674645|ref|YP_003726395.1| 116 VNDPVERAIQLEKMGIDYINVHVGidqqmqgYDPIYlLKDVVDAVNVPVAVAGGIDEQRSSEIVNTGADIVIVGGNI 192
                                       5677899999999999999999887877654333334688999999***99997667999***************99 PP

                        PEP_mutase 224 lra 226
                                        r+
  gi|298674645|ref|YP_003726395.1| 193 TRS 195
                                       987 PP

>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.29   3.5e+02      85     218 ..      72     103 ..      15     117 .. 0.62
   2 !   13.0   0.1   4.9e-05     0.058     161     216 ..     127     181 ..      54     193 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.29
                                       HHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEEEEE-CTTBSSTTCHHHHHHHHHHHHT CS
                              DeoC  85 sveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplilelylrdeaikdekvdpdlvaeAarvsa 161
                                       +ve a + GA                                                                   
  gi|298674645|ref|YP_003726395.1|  72 EVEMAAKSGA------------------------------------------------------------------- 81 
                                       3333333333................................................................... PP

                                       CCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTEEEEETTSSHHHHHHHHHHHH CS
                              DeoC 162 elGaDiiKvevpkevvnateedaevfkdvikaapvpgvvlsGGvseedfletvedAv 218
                                                                          + v++ GG+++ ++ + v+ A+
  gi|298674645|ref|YP_003726395.1|  82 -----------------------------------DIVMILGGSDNSTIDDSVRSAH 103
                                       ...................................3466666666666666666665 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 4.9e-05
                                       TCCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTEEEEETTSSHHHHHHHHHH CS
                              DeoC 161 aelGaDiiKvevpkevvnateedaevfkdvikaapvpgvvlsGGvseedfletved 216
                                        ++G+D i v v+   + ++++ ++  kdv++a++vp v ++GG++e+  +e v++
  gi|298674645|ref|YP_003726395.1| 127 EKMGIDYINVHVGIDQQMQGYDPIYLLKDVVDAVNVP-VAVAGGIDEQRSSEIVNT 181
                                       369999999****9999********************.*******88877777665 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   2.2   2.1e-05     0.026     127     223 ..      97     190 ..      39     210 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.1e-05
                               NMO 127 evvarlkeagvvliptiss....vkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavdiPviAa 199
                                       + v + ++ gv l+    s    v+ a ++e++G D + v  +    +qG       + + L++ v+dav++Pv  a
  gi|298674645|ref|YP_003726395.1|  97 DSVRSAHQYGVKLMADLMSvndpVERAIQLEKMGIDYINVHVGIDQQMQG------YDPIYLLKDVVDAVNVPVAVA 167
                                       45556666666555555541111345666777777777665444445666......35679**************** PP

                               NMO 200 GGiidrrgvaaaLalGAsgvqigt 223
                                       GGi ++r    +   GA  v +g 
  gi|298674645|ref|YP_003726395.1| 168 GGIDEQRSS-EIVNTGADIVIVGG 190
                                       ***888874.46678888888776 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   5.5e-05     0.065      99     253 ..      45     204 ..      10     205 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.5e-05
                                       CHHHHHHHH-SS-EEE...ES---SHHHHHHHHHCT-SEEEEECCCS-HHHHHHHHHHHCCTT-EEEEEESSHHH.H CS
                              IGPS  99 edLrevrqavslpvlr...KdFiideyqieearalgadaiLLivkvledeeleelaeaakslglevLvEvhdeee.l 171
                                       + +r++r++    ++    K     + ++e a + gad+++++    +++++ + ++ a+++g++ + +  + ++ +
  gi|298674645|ref|YP_003726395.1|  45 SAIRRIRKEFPGYTVLadmKTIDTGSIEVEMAAKSGADIVMIL-GGSDNSTIDDSVRSAHQYGVKLMADLMSVNDpV 120
                                       4566666666554444122444445678899*******98765.55699999***********99999987755449 PP

                                       HHHHHTT-SEEEEESEETTTTEE-CHHHHH.....HCHCC-TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC CS
                              IGPS 172 eralklgakiiGvNnRnLktlevdlnttee.....LaklvpkdvllvaeSGiktredveklkeegvnafLvGeslmr 243
                                       era++l+   +G+   n +   +d + +       L+++v++  + va  G  +++  +++ ++g++ ++vG  ++r
  gi|298674645|ref|YP_003726395.1| 121 ERAIQLEK--MGIDYINVHV-GIDQQMQGYdpiylLKDVVDAVNVPVAVAGGIDEQRSSEIVNTGADIVIVGGNITR 194
                                       9***9987..6888888873.33333221122222566666667888888888888889999999************ PP

                                       -TTHHHHHHH CS
                              IGPS 244 qedvekaire 253
                                       +++v++a ++
  gi|298674645|ref|YP_003726395.1| 195 SDNVSRAAKT 204
                                       ***9998775 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.3   2.7e+03      75      88 ..      22      35 ..       7      46 .. 0.65
   2 ?    1.1   0.0      0.16   1.9e+02     128     152 ..     113     137 ..     107     147 .. 0.84
   3 ?    9.1   0.4   0.00054      0.65      52      88 ..     152     189 ..     147     198 .. 0.89
   4 ?   -3.2   0.0       3.2   3.8e+03     151     186 ..     231     266 ..     217     268 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.3
                            DUF561 75 leavkaGadlveiG 88
                                       ea   G+d +e+G
  gi|298674645|ref|YP_003726395.1| 22 KEALEGGVDWIEVG 35
                                      34555556666655 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.16
                            DUF561 128 iLkleeqvkLakkLeslgvdliqte 152
                                       ++++++ v+ a +Le++g+d+i   
  gi|298674645|ref|YP_003726395.1| 113 LMSVNDPVERAIQLEKMGIDYINVH 137
                                       6788999**************9875 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00054
                            DUF561  52 lvkkvksvsniPiCvs.aveakllleavkaGadlveiG 88 
                                       l+k v +++n+P+ v+ +++ +   e v +Gad+v +G
  gi|298674645|ref|YP_003726395.1| 152 LLKDVVDAVNVPVAVAgGIDEQRSSEIVNTGADIVIVG 189
                                       67899999******9746*****************998 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 3.2
                            DUF561 151 teGkitsiskakkvndliekslstlastyeiskkvs 186
                                       t  ++ +is+a + ++ ++k+++ +  t  + k+v+
  gi|298674645|ref|YP_003726395.1| 231 TSTSTPNISDAMHRKGAMRKIIPLVQDTKMVGKAVT 266
                                       556677788888888888888887777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.72u 0.32s 00:00:01.04 Elapsed: 00:00:00.51
# Mc/sec: 2506.56
//
Query:       gi|298674646|ref|YP_003726396.1|  [L=150]
Description: hypothetical protein Metev_0698 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-45  152.8   2.0    6.3e-45  152.6   2.0    1.0  1  LDcluster4       SLOG cluster4 family
    3.1e-08   33.8   0.1    4.5e-08   33.3   0.1    1.2  1  Lysine_decarbox  Possible lysine decarboxylase
    4.1e-06   26.2   2.2    0.00044   19.5   0.6    2.0  2  DNA_processg_A   DNA recombination-mediator protein A
  ------ inclusion threshold ------
      0.027   13.7   0.1      0.045   13.0   0.1    1.4  1  LSDAT_prok       SLOG in TRPM, prokaryote
       0.12   12.0   0.7          3    7.5   0.0    2.3  2  DAGK_cat         Diacylglycerol kinase catalytic domain


Domain annotation for each model (and alignments):
>> LDcluster4  SLOG cluster4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.6   2.0   1.7e-48   6.3e-45       2     138 ..       4     136 ..       3     147 .. 0.91

  Alignments for each domain:
  == domain 1  score: 152.6 bits;  conditional E-value: 1.7e-48
                        LDcluster4   2 lkigVmGsaeteakeealelaeelGrliAkegavlltGgrtGvmeaaskGakeagGltvGilpassekehsnkyvdi 78 
                                        +igV+G+++  ++ + l lae++G++iA+++ +l++G+ +GvmeaaskGake++G+t+Gilp+ ++++++n+y+di
  gi|298674646|ref|YP_003726396.1|   4 AQIGVIGAGD--CDARILALAENVGKCIARRNGILICGALGGVMEAASKGAKEENGTTLGILPG-KKRDEANPYIDI 77 
                                       69********..****************************************************.566669999*** PP

                        LDcluster4  79 iiyTGlglagRnlilvlssdvviaiggrsGTlsEialaleegkpvivlkgtdellseiie 138
                                       +++++lg a Rn ++++ssdv+ia++g++GTlsEia++l+ gk+v+vl+++++++ +  +
  gi|298674646|ref|YP_003726396.1|  78 AVVSDLGEA-RNALIARSSDVLIAVSGGYGTLSEIAMSLKMGKKVVVLESQWDIKGTYRA 136
                                       *******99.***************************************88876655444 PP

>> Lysine_decarbox  Possible lysine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.1   1.2e-11   4.5e-08       1      72 [.      45     114 ..      45     124 .. 0.88

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.2e-11
                                       HHHHHHHHHHTTS-EEEEEECCHHHHHCCTTT-SEEEEESSHHHHHHHHHHHESEEEE-S-SHHHHHHHHHH CS
                   Lysine_decarbox   1 meavakgaleaggrviGiipkillaeeapneevnelvivedmeeRkealveladafvilPGGiGTleEllei 72 
                                       mea++kga e +g+++Gi p +   e  +n++++  v+ +  e R++ +++ +d ++++ GG+GTl E+   
  gi|298674646|ref|YP_003726396.1|  45 MEAASKGAKEENGTTLGILPGKKRDE--ANPYIDIAVVSDLGEARNALIARSSDVLIAVSGGYGTLSEIAMS 114
                                       9*****************88877655..5999998888888899************************9655 PP

>> DNA_processg_A  DNA recombination-mediator protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.6   1.2e-07   0.00044      41     104 ..       2      65 ..       1      85 [. 0.93
   2 !    6.6   0.0    0.0011         4     145     190 ..      86     129 ..      84     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.2e-07
                    DNA_processg_A  41 ekravaiVGtRkaseygkevakklakelaeagitivSGlAlGiDaaahraaleaggktvavlgt 104
                                       ++ +++++G+ ++ ++  ++a+++ k +a+++ + + G   G+ +aa ++a e++g+t+++l++
  gi|298674646|ref|YP_003726396.1|   2 NRAQIGVIGAGDCDARILALAENVGKCIARRNGILICGALGGVMEAASKGAKEENGTTLGILPG 65 
                                       6789*********************************************************986 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0011
                    DNA_processg_A 145 eRnriiaglseavlvveaaekSGalitaelAlelgrevfavpgdit 190
                                       +Rn +ia  s+ ++ v  +   G+l  + + l++g++v++++++ +
  gi|298674646|ref|YP_003726396.1|  86 ARNALIARSSDVLIAVSGGY--GTLSEIAMSLKMGKKVVVLESQWD 129
                                       69*****9999999998775..9*****************987765 PP

>> LSDAT_prok  SLOG in TRPM, prokaryote
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   1.3e-05     0.045     121     154 ..      92     125 ..      54     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.3e-05
                        LSDAT_prok 121 ekkpsvtvlvnGgeitlkdiresvkagrpilvva 154
                                       ++ + v + v Gg  tl++i++s+k g++++v++
  gi|298674646|ref|YP_003726396.1|  92 ARSSDVLIAVSGGYGTLSEIAMSLKMGKKVVVLE 125
                                       4457889*************************96 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.024        85      59      89 ..      35      64 ..      20      65 .. 0.66
   2 ?    7.5   0.0   0.00083         3      48      76 ..      90     116 ..      66     125 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.024
                                      EEEEESHHHHHHHHHHHCT..HHCTTSEEEEEE CS
                          DAGK_cat 59 ivvaGGDGtvsevlnglle..elatkpplgiiP 89
                                      i+++G     + v+++  +  ++++ + lgi+P
  gi|298674646|ref|YP_003726396.1| 35 ILICGAL---GGVMEAASKgaKEENGTTLGILP 64
                                      5555544...44444444455599********9 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00083
                                       HHHHHHCC-SEEEEEESHHHHHHHHHHHC CS
                          DAGK_cat  48 akeakeegvdlivvaGGDGtvsevlngll 76 
                                       +   ++++  li v GG Gt+se++ +l 
  gi|298674646|ref|YP_003726396.1|  90 LI--ARSSDVLIAVSGGYGTLSEIAMSLK 116
                                       33..33344788999*********98886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 911.58
//
Query:       gi|298674647|ref|YP_003726397.1|  [L=742]
Description: DNA topoisomerase I [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   3.8e-131  437.9   0.1   5.5e-131  437.4   0.1    1.2  1  Topoisom_bac     DNA topoisomerase
    3.2e-15   56.2   2.0    7.9e-15   54.9   1.4    2.0  2  Toprim           Toprim domain
    4.7e-14   51.9   1.1    4.7e-14   51.9   1.1    2.3  2  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
    5.1e-08   33.4   0.0    1.9e-07   31.6   0.0    2.0  1  HHH_5            Helix-hairpin-helix domain
    0.00036   20.8   0.0    0.00092   19.4   0.0    1.7  1  DUF4332          Domain of unknown function (DUF4332)
    0.00042   20.5   0.0     0.0012   19.0   0.0    1.8  1  Cdd1             Pathogenicity locus
    0.00046   20.0   0.0     0.0011   18.7   0.0    1.7  1  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
    0.00099   19.3   0.0     0.0025   18.1   0.0    1.7  1  IMS_HHH          IMS family HHH motif
  ------ inclusion threshold ------
       0.03   14.7   0.0      0.096   13.1   0.0    1.9  1  BAF              Barrier to autointegration factor
      0.031   13.5   0.2      0.031   13.5   0.2    2.6  4  OMS28_porin      OMS28 porin
       0.15   12.0   0.0       0.43   10.5   0.0    1.8  1  HHH              Helix-hairpin-helix motif
        1.2    9.1   3.4        5.2    7.1   0.0    3.1  3  hnRNP_Q_AcD      Heterogeneous nuclear ribonucleoprotein Q ac
        4.4    7.3   7.0       0.35   10.8   0.2    2.6  3  Homeobox_KN      Homeobox KN domain


Domain annotation for each model (and alignments):
>> Topoisom_bac  DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  437.4   0.1    4e-134  5.5e-131       2     413 .]     154     558 ..     153     558 .. 0.94

  Alignments for each domain:
  == domain 1  score: 437.4 bits;  conditional E-value: 4e-134
                      Topoisom_bac   2 inenlvdaaeaRrelDwliGinlsrlltkklkg..kkvlsaGRVqtptLaliveRereienFvpeeyweveatl.kk 75 
                                       +++nl+da+++R+++D+++G++l+r++++++ +  k +ls+GRVq+ptLaliv+Re+e+e+Fvp +ywev atl ++
  gi|298674647|ref|YP_003726397.1| 154 VDFNLADAGHSRQVIDLVWGASLTRYISLSAGRlgKMFLSVGRVQSPTLALIVDREKEREAFVPDPYWEVYATLaNS 230
                                       589**************************555566899************************************777 PP

                      Topoisom_bac  76 ekkekekkkkkkkerikdkeeaeaileklkk.keakvesvekkekkkppplpfdtttLqkeasrklglsakktlsia 151
                                       +++e+    ++k +r++dk+++++++ klk+ k+a+v+svek++k+++pp pf+tt++ ++a++  g++a+++++ia
  gi|298674647|ref|YP_003726397.1| 231 NGEEF--VTQHKTQRFWDKNQVNSVVDKLKDcKTAEVTSVEKSTKQDKPPSPFNTTEFISAANSV-GFTASNAMRIA 304
                                       77777..59********************99779******************************8.*********** PP

                      Topoisom_bac 152 qkLYekaglitYpRTdstrlseeaelkailealakkygkeylefaekllkktkkksvvknkkveaHeAIrPteelpk 228
                                       + LY++ g+i+YpRTd+t+++++ +l+++++++++    +++++a+ ll+k++   ++++k++++H++I+Pt  ++ 
  gi|298674647|ref|YP_003726397.1| 305 ETLYTN-GYISYPRTDNTVYPDSLDLRNLIAMFKSG---QFKQYAQYLLNKSNLVPTRGKKETQDHPPIYPTSAAK- 376
                                       *****7.****************77*********96...477777788876664448889999*********6655. PP

                      Topoisom_bac 229 lkelsddekklYelIvrrflaslmkdakyeettvkleveeeefkasgktilekGfkkvykeekkeeeeeelpelkeg 305
                                       ++el++de+k+Ye++vrrf+a+++++ak+e+++vk++++ eef+a+g +++++G++ +y++++ e++   lp+lk+g
  gi|298674647|ref|YP_003726397.1| 377 KSELNEDEWKIYEMVVRRFFATFADPAKWETMKVKFDIGSEEFRAKGARLISPGWRWFYPYNSPEDK--ILPPLKKG 451
                                       69**************************************************************998..6******* PP

                      Topoisom_bac 306 eevkvkeveleekkTkppkryteasLikamekagiGtpaTraeiieklvergYverkkkslvptelGkalvellekf 382
                                       e ++vk+ ++ +k+T+pp ry +++L++ me+ g+Gt+aTr+eii+kl++r Yv+++   l+pt++++a++++le++
  gi|298674647|ref|YP_003726397.1| 452 EVLTVKSSKVADKETQPPGRYGQGRLVRIMEELGLGTKATRHEIISKLFSRAYVHSNP--LQPTKTAFAVIDALENY 526
                                       ********************************************************66..**************999 PP

                      Topoisom_bac 383 .kdlvspelTaeleekLdeIaegkadakevld 413
                                        +++++ e+T++lee++++I+egk++++evl+
  gi|298674647|ref|YP_003726397.1| 527 aPTITKHEMTSKLEEDMEKISEGKIKEDEVLK 558
                                       9****************************985 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   1.4   5.8e-18   7.9e-15       2     103 .]       3     139 ..       2     139 .. 0.89
   2 ?   -3.2   0.0       7.1   9.8e+03      13      52 ..     343     379 ..     340     390 .. 0.70

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 5.8e-18
                                       EEEESSHHHHHHHHHTHT....................STEEEEEEESSSSEEEHS..........TTEEEEE.... CS
                            Toprim   2 lvivEgpsdaktiakalg....................sgfqavtaslGhildlet..........efkpvye.... 44 
                                       l+i+E+  +ak ia +l                     +++++v+ ++Ghi++l++          +          
  gi|298674647|ref|YP_003726397.1|   3 LIIAEKHIAAKRIAAILApkkpkkvrvsgvdtyeyednEDDKIVMGLSGHIVELDFpkeynnwqkvN-----Aedli 74 
                                       8*************************************99****************76666444441.....26666 PP

                                       .....ECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHHHHHHTHHHTT.TEEEEEESSS CS
                            Toprim  45 .....eiedkkkvlkalkelakradeiilatDpDreGeaiawellevlkellen.kigrvefsei 103
                                             ++++ k+++alk+l k+a+++ +atD D eGe i+ e+l+ +k+ +++ ++ rv+ s i
  gi|298674647|ref|YP_003726397.1|  75 daeliTKPTQVKIVAALKKLGKKASKVTIATDYDGEGELIGVEALDIIKKVNQDiQFDRVKYSAI 139
                                       6766588888999999*********************************9999999999998865 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 7.1
                                       HHHHTHTSTEEEEEEESSSSEEEHSTTEEEEEECTTTHHH CS
                            Toprim  13 tiakalgsgfqavtaslGhildletefkpvyeeiedkkkv 52 
                                       + a++l  ++ + ++++G+  ++++  +p+y     kk+ 
  gi|298674647|ref|YP_003726397.1| 343 QYAQYLL-NKSNLVPTRGKKETQDH--PPIYPTSAAKKSE 379
                                       5677777.77888999999999999..7777744444444 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   1.1   3.4e-17   4.7e-14       2      38 ..     593     630 ..     592     631 .. 0.95
   2 ?    0.2   0.1      0.48   6.6e+02      28      37 ..     664     673 ..     661     675 .. 0.70

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 3.4e-17
                                       EE-SSS--EEEEEE-SSS.EEEEESST.T----EEB-G CS
                    zf-C4_Topoisom   2 ekCPkCggdLvlkrgkkG.kFvGCsnYPeCkftkklkk 38 
                                       ++CP+C + L+++r+k+G +F+GC+ YP+C+f  +l+k
  gi|298674647|ref|YP_003726397.1| 593 GTCPECESRLMVRRSKRGsRFIGCDGYPDCTFSLPLPK 630
                                       79*********************************998 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.48
                                       .T----EEB- CS
                    zf-C4_Topoisom  28 PeCkftkklk 37 
                                       P C+f+++ k
  gi|298674647|ref|YP_003726397.1| 664 PHCNFIEWQK 673
                                       6788888876 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   1.4e-10   1.9e-07       3      52 ..     689     738 ..     687     740 .. 0.94

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1.4e-10
                                       HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHH CS
                             HHH_5   3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAerii 52 
                                       ++++++GiG++tA +l +aG++sve+la+ad+ eL+k + ++ k+ +++ 
  gi|298674647|ref|YP_003726397.1| 689 SITEINGIGKVTAEKLENAGVSSVEELANADAVELSKQTNLSVKKIKNWQ 738
                                       6799*************************************999999986 PP

>> DUF4332  Domain of unknown function (DUF4332)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   6.6e-07   0.00092      57      92 ..     692     727 ..     689     741 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 6.6e-07
                           DUF4332  57 rikgigeeyaeLLeaaGvdsvaeLaqrnpanLhqkl 92 
                                        i+gig+  ae Le aGv+sv+eLa+  + +L +++
  gi|298674647|ref|YP_003726397.1| 692 EINGIGKVTAEKLENAGVSSVEELANADAVELSKQT 727
                                       68999999*****************99999999886 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   8.7e-07    0.0012       5      46 ..     687     728 ..     683     736 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 8.7e-07
                              Cdd1   5 lkelqdiPniGkalaedlvelGirsveelkgedpeelyekle 46 
                                        k++++i +iGk +ae+l + G++sveel++ d+ el ++ +
  gi|298674647|ref|YP_003726397.1| 687 PKSITEINGIGKVTAEKLENAGVSSVEELANADAVELSKQTN 728
                                       67899*******************************998865 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   8.2e-07    0.0011       3      44 ..     690     732 ..     688     738 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 8.2e-07
                   DNA_pol_lambd_f   3 FtkvyGVGpktAkkwyakGirtledlra.krakLtreqqiGlk 44 
                                        t++ G+G +tA+k+ ++G+ ++e+l + +  +L+++  + +k
  gi|298674647|ref|YP_003726397.1| 690 ITEINGIGKVTAEKLENAGVSSVEELANaDAVELSKQTNLSVK 732
                                       58899***********************866888888766655 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.8e-06    0.0025      10      32 .]     687     709 ..     686     709 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.8e-06
                           IMS_HHH  10 plpitkipGiGgklgekLeklGi 32 
                                       p +it+i GiG++++ekLe+ G+
  gi|298674647|ref|YP_003726397.1| 687 PKSITEINGIGKVTAEKLENAGV 709
                                       568****************9996 PP

>> BAF  Barrier to autointegration factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     7e-05     0.096      17      44 ..     687     714 ..     667     729 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7e-05
                               BAF  17 dKevtalaGigevlgkkLeekGfdkAyv 44 
                                        K++t+++Gig+v ++kLe++G++  ++
  gi|298674647|ref|YP_003726397.1| 687 PKSITEINGIGKVTAEKLENAGVSSVEE 714
                                       69********************987765 PP

>> OMS28_porin  OMS28 porin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       3.2   4.4e+03      56      69 ..     117     130 ..     116     153 .. 0.72
   2 ?   -0.8   0.6      0.53   7.3e+02      33      69 ..     229     266 ..     225     274 .. 0.78
   3 ?   -3.4   0.3       3.1   4.3e+03     174     220 ..     530     577 ..     524     580 .. 0.71
   4 ?   13.5   0.2   2.2e-05     0.031      28      89 ..     660     721 ..     651     732 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.2
                       OMS28_porin  56 qaldtinkvtedvs 69 
                                       +ald i+kv +d+ 
  gi|298674647|ref|YP_003726397.1| 117 EALDIIKKVNQDIQ 130
                                       58999999999985 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.53
                       OMS28_porin  33 qsnvlehsdqkdnkkldqkdqvnqaldtinkv.tedvs 69 
                                       +sn  e   q+  +++ +k+qvn  +d ++   t +v+
  gi|298674647|ref|YP_003726397.1| 229 NSNGEEFVTQHKTQRFWDKNQVNSVVDKLKDCkTAEVT 266
                                       57888899999999999*********998754244454 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 3.1
                       OMS28_porin 174 ltkeef.akveqvketlmaseraldetvqeaqkvlnmvnglnpsnkdq 220
                                       +tk e+ +k+e+  e +   +   de ++e++ +l+ +     sn+d+
  gi|298674647|ref|YP_003726397.1| 530 ITKHEMtSKLEEDMEKISEGKIKEDEVLKESRDMLKSMFSELESNRDN 577
                                       566665257888888887778888899999988887666666677776 PP

  == domain 4  score: 13.5 bits;  conditional E-value: 2.2e-05
                       OMS28_porin  28 nilkpqsnvlehsdqkdnkkldqkdqvnqaldtinkvtedvssklegvresslelvesndag 89 
                                       n+  p  n +e   +++n+k  qkd   +++  in + +  + kle    ss+e +   da 
  gi|298674647|ref|YP_003726397.1| 660 NLGCPHCNFIEWQKEQENNKNKQKDTTPKSITEINGIGKVTAEKLENAGVSSVEELANADAV 721
                                       5667999**********************************************988888875 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00031      0.43       5      26 ..     682     703 ..     679     704 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00031
                                       HHTSSHHHHHTSTT-SHHHHHH CS
                               HHH   5 lipasreeLlalPGVGpktAea 26 
                                        ++ +++ ++++ G+G+ tAe+
  gi|298674647|ref|YP_003726397.1| 682 QKDTTPKSITEINGIGKVTAEK 703
                                       67889***************97 PP

>> hnRNP_Q_AcD  Heterogeneous nuclear ribonucleoprotein Q acidic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       1.6   2.2e+03      39      57 ..     249     267 ..     246     270 .. 0.81
   2 ?    0.8   0.3      0.36     5e+02       7      35 ..     540     567 ..     534     571 .. 0.79
   3 ?    7.1   0.0    0.0038       5.2      11      61 ..     691     740 ..     687     742 .] 0.84

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.6
                       hnRNP_Q_AcD  39 gAlaVlkqfkesdlskvsN 57 
                                       +  +V++++k+++  +v +
  gi|298674647|ref|YP_003726397.1| 249 QVNSVVDKLKDCKTAEVTS 267
                                       55789*******9999876 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.36
                       hnRNP_Q_AcD   7 aekLdelfrsgkltasdlDeraleaLksl 35 
                                        e ++++  +gk++++++ + + ++Lks+
  gi|298674647|ref|YP_003726397.1| 540 EEDMEKI-SEGKIKEDEVLKESRDMLKSM 567
                                       5556554.689****************98 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0038
                       hnRNP_Q_AcD  11 delfrsgkltasdlDeraleaLkslpeegAlaVlkqfkesdlskvsNksay 61 
                                       +e+   gk+ta++l+++ +++ ++l  ++A++  kq  +++ +k++N  +y
  gi|298674647|ref|YP_003726397.1| 691 TEINGIGKVTAEKLENAGVSSVEELANADAVELSKQ-TNLSVKKIKNWQEY 740
                                       5677789*************************8887.55778888888777 PP

>> Homeobox_KN  Homeobox KN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.3       1.6   2.2e+03       4      17 ..     362     377 ..     361     383 .. 0.74
   2 ?   -2.9   0.1         5   6.9e+03       8      16 ..     435     443 ..     433     457 .. 0.77
   3 ?   10.8   0.2   0.00025      0.35      14      33 ..     718     737 ..     716     737 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.6
                       Homeobox_KN   4 ahlhnP..YPseedKe 17 
                                       ++ ++P  YP+ + K+
  gi|298674647|ref|YP_003726397.1| 362 ETQDHPpiYPTSAAKK 377
                                       57778778**988875 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5
                       Homeobox_KN   8 nPYPseedK 16 
                                       +PY s edK
  gi|298674647|ref|YP_003726397.1| 435 YPYNSPEDK 443
                                       699999999 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00025
                       Homeobox_KN  14 edKeeLlkeTglsvkqitnW 33 
                                       +d  eL k+T+lsvk i+nW
  gi|298674647|ref|YP_003726397.1| 718 ADAVELSKQTNLSVKKIKNW 737
                                       56679*************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (742 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1107  (0.0617435); expected 358.6 (0.02)
Passed bias filter:                      641  (0.0357521); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.77u 0.33s 00:00:01.10 Elapsed: 00:00:00.52
# Mc/sec: 4332.39
//
Query:       gi|298674648|ref|YP_003726398.1|  [L=412]
Description: RNA-metabolising metallo-beta-lactamase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-13   49.7   0.0    2.7e-09   36.8   0.0    2.7  2  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    2.5e-12   47.0   0.0    5.9e-12   45.9   0.0    1.6  1  Beta-Casp      Beta-Casp domain
    2.6e-09   36.9   0.0    4.4e-09   36.1   0.0    1.3  1  Lactamase_B_2  Beta-lactamase superfamily domain
    1.2e-07   31.9   0.4    5.6e-07   29.8   0.4    2.0  1  Lactamase_B    Metallo-beta-lactamase superfamily
    1.2e-06   28.1   0.0    4.1e-06   26.4   0.0    1.8  2  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
    4.4e-05   23.4   0.1    0.00011   22.2   0.1    1.6  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00022      0.65      27      57 ..      40      70 ..      38      74 .. 0.87
   2 !   36.8   0.0     9e-13   2.7e-09       3      62 .]     344     404 ..     342     404 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00022
                             RMMBL 27 rklkprnvilvHGeeeatsalarllkeeegi 57
                                      + l p+ v + HG+ +++ al +l++++++i
  gi|298674648|ref|YP_003726398.1| 40 NNLHPKSVLVTHGHLDHCGALTNLIHDNSEI 70
                                      67889********************887775 PP

  == domain 2  score: 36.8 bits;  conditional E-value: 9e-13
                             RMMBL   3 pvkarieeidfSgHadknellelirklkprn...vilvHGeeeatsalarllkeeegidvfiP 62 
                                       +++++ie++dfS+H + +el++l++ +  r    vi  HG+    + +ar++ ++ g+++++P
  gi|298674648|ref|YP_003726398.1| 344 KLQTEIEQYDFSAHCGDRELKQLVKDFCDRGterVITMHGDN--SEGFARWIVDKIGVEAYAP 404
                                       5799**************************************..899*****9999****998 PP

>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   0.0     2e-15   5.9e-12      31     108 ..     243     328 ..     223     329 .. 0.68

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 2e-15
                                       HHHHHHHGGGGGG...........E-SHH.....HHHH..HHHS-SSEEEEES-TTSSSSHHHHHHHHHTTSTTSEE CS
                         Beta-Casp  31 askatevYkeyae...........veaks.lewmeskkeelnsskgpkvilassgmlegGrsrellkklledprntv 95 
                                       + +a ++ k+y++               +  + ++ kk+  + +++ +vi+++ gml+gG++ ++l k+ +dp++ +
  gi|298674648|ref|YP_003726398.1| 243 GLDAYSIMKKYPDyiknikhlkkaF---RdASVVKGKKR-EKLPRDSSVIVTTAGMLNGGPVLQYLDKVYKDPKSKI 315
                                       4444444444444444666564331...22223344432.2356799****************************** PP

                                       EESS---TTSHHH CS
                         Beta-Casp  96 ilvgyqaegTlgr 108
                                       +l+gyq+egT gr
  gi|298674648|ref|YP_003726398.1| 316 MLTGYQVEGTNGR 328
                                       ************9 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.0   1.5e-12   4.4e-09      31     174 ..      44     192 ..      23     216 .. 0.73

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 1.5e-12
                                       EEEEE-SS--HHHHGGGGCCCC......C--EE..EEEEEEHHHHHHCCTTCGHHHCHTT....TTEEEEEE-TTSE CS
                     Lactamase_B_2  31 idaVllthaHyDHlaglltlre......lrpkk..lplyapkgvlavleanfvylaleee....pavnvheldwges 95 
                                        + Vl+th+H DH+  l  l +      ++p    ++ +  +++l++ e++ ++ a + e    +  +++++d+g++
  gi|298674648|ref|YP_003726398.1|  44 PKSVLVTHGHLDHCGALTNLIHdnseifMTPPTadFTEMLAEDTLKIAENENIPPAYNLEdlkyFMNRTNKVDTGME 120
                                       356***********777777774444442222223333344555555555555555555589877778889999999 PP

                                       EEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEE.CTTEEEEEESS-S---HHHH...HHHCT-SEEEEE-S-SS CS
                     Lactamase_B_2  96 felgdggleitatparhksgrrldrnagdtlGlrie.gggkrvyyigDtgyipeeig...erlggadllllditaye 168
                                       f+ +  g ++++  a h  g           ++ ie ++g++++y+gD+++i+ ++    + + +ad l+++ t++ 
  gi|298674648|ref|YP_003726398.1| 121 FSTN--GYKVHFYDAGHIPGS---------SSVYIEtKEGESICYTGDVNTIDTRLLygaDVFPDADTLIIESTYFG 186
                                       9998..789****99999999.........8899998****************775445566777*********999 PP

                                       TTHHHH CS
                     Lactamase_B_2 169 ddemir 174
                                       +d   r
  gi|298674648|ref|YP_003726398.1| 187 EDHTPR 192
                                       987655 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.4   1.9e-10   5.6e-07      17     162 ..      22     169 ..      11     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 1.9e-10
                                       EEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHH CS
                       Lactamase_B  17 viLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasr 93 
                                        iLiD G+ + +  +        l+ + ++ v++TH+HlDH+G+l  l++     +++ + +a   +m ++d+   +
  gi|298674648|ref|YP_003726398.1|  22 EILIDYGMKPGEIAQY------PLNNLHPKSVLVTHGHLDHCGALTNLIHDNSE-IFMTPPTADFTEMLAEDTLKIA 91 
                                       599***********98......7**************************98775.5556666666666666555544 PP

                                       CCHH.........TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCC CS
                       Lactamase_B  94 kgll.........lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgrid 161
                                       +            l+++  + + vd+  + ++ g  + +y  g+ + ++++++ + +g+++++tGD+  +  +++ +
  gi|298674648|ref|YP_003726398.1|  92 ENENippaynledLKYFMNRTNKVDTGMEFSTNGYKVHFYDAGHIPGSSSVYIETKEGESICYTGDVNTIDTRLLYG 168
                                       4444699**999999999999999999999999999999**999999999999999**********97777666666 PP

                                       C CS
                       Lactamase_B 162 l 162
                                        
  gi|298674648|ref|YP_003726398.1| 169 A 169
                                       6 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   1.4e-09   4.1e-06       8     178 ..      22     174 ..      19     184 .. 0.80
   2 ?   -2.4   0.0      0.92   2.8e+03      99     128 ..     256     285 ..     209     299 .. 0.60

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 1.4e-09
                     Lactamase_B_6   8 kiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakfksklllnipvyatlpvvkLGrvsll 84 
                                       +iL+D G++  ++    a  +l++  p    +L++h  l+h Ga++ l++        n +++ t p++   +++  
  gi|298674648|ref|YP_003726398.1|  22 EILIDYGMKPGEI----AQYPLNNLHP--KSVLVTHGHLDHCGALTNLIH-------DNSEIFMTPPTADFTEMLAE 85 
                                       6999999998755....3456666666..589************866654.......5789**************** PP

                     Lactamase_B_6  85 dlyaskgllgpedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGtiWki.skesekivYav 160
                                       d+ + ++ ++       +led +  +++ +++     + ++ +++g  +  y aGh +G +   i +ke e+i Y  
  gi|298674648|ref|YP_003726398.1|  86 DTLKIAENENIP--PAYNLEDLKYFMNRTNKVD----TGMEFSTNGYKVHFYDAGHIPGSSSVYIeTKEGESICYTG 156
                                       998876555332..34689***99999999985....34444568899999*********99889567899****** PP

                     Lactamase_B_6 161 dwnhakeshLngaallds 178
                                       d+n    ++L ga+++  
  gi|298674648|ref|YP_003726398.1| 157 DVNTIDTRLLYGADVFPD 174
                                       *************99864 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.92
                     Lactamase_B_6  99 eeleledideafdkiktlkYsQklelkskl 128
                                          +++  ++af   + +k + + +l+ + 
  gi|298674648|ref|YP_003726398.1| 256 YIKNIKHLKKAFRDASVVKGKKREKLPRDS 285
                                       233445555555555555555555555544 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.1   3.6e-08   0.00011      17     119 ..      21     163 ..      13     181 .. 0.68

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 3.6e-08
                     Lactamase_B_3  17 arilvDPfka...nlgyeppaeeaDlvlisqaledHahletlkql....................aenvkvlee... 67 
                                        +il+D++ +    ++y  ++ ++  vl+++++ dH+ + t   l                    a       e   
  gi|298674648|ref|YP_003726398.1|  21 DEILIDYGMKpgeIAQYPLNNLHPKSVLVTHGHLDHCGALTN--LihdnseifmtpptadftemlA-------Edtl 88 
                                       579****95445577899999****************87654..3335566666666655444442.......1444 PP

                     Lactamase_B_3  68 ........geslevggleiravatsh...............davggsergenngflleqdgltiyhlGhlahels 119
                                               + ++++++l++   +t++                   g+ +g  ++++ +++g +i++ G++ +  +
  gi|298674648|ref|YP_003726398.1|  89 kiaeneniPPAYNLEDLKYFMNRTNKvdtgmefstngykvhFYDAGHIPGSSSVYIETKEGESICYTGDVNTIDT 163
                                       444344443447777777777777775556565555554443335667799******************998544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.52
# Mc/sec: 2374.35
//
Query:       gi|298674649|ref|YP_003726399.1|  [L=63]
Description: hypothetical protein Metev_0701 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.33   11.3   2.9       0.39   11.0   2.9    1.1  1  2TM       2TM domain


Domain annotation for each model (and alignments):
>> 2TM  2TM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.9   2.2e-05      0.39       8      64 ..       7      63 .]       3      63 .] 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.2e-05
                               2TM  8 keikgFyrhlvvYli.vniflilinlgsswflwpilfWgiglllhalkvFgtekffgk 64
                                       +i gF + l+vY++ vn++li    + s f+++     igl+  ++  +++ +f++k
  gi|298674649|ref|YP_003726399.1|  7 SQILGFITFLIVYFAgVNLWLISTG-STSSFIYVPGTLIIGLAGYWIGGYVYTEFLNK 63
                                      6889999999999875788999885.77788889999999999999999998888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.49
# Mc/sec: 390.59
//
Query:       gi|298674650|ref|YP_003726400.1|  [L=632]
Description: peptidase S8 and S53 subtilisin kexin sedolisin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.3e-20   71.4   2.8    1.6e-15   57.1   0.0    2.6  3  Peptidase_S8  Subtilase family
  ------ inclusion threshold ------
      0.055   12.9   0.1       0.34   10.3   0.0    2.3  2  BIRC6         Baculoviral IAP repeat-containing protein 6
      0.081   12.9   7.6        3.2    7.8   0.1    3.0  3  Smg4_UPF3     Smg-4/UPF3 family
       0.39   10.8   1.5       0.64   10.1   0.0    2.0  2  PGF-CTERM     PGF-CTERM motif


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       1.1   4.7e+03     109     131 ..     162     186 ..     150     209 .. 0.58
   2 !   14.1   0.1   4.6e-06      0.02     110     170 ..     240     299 ..     221     318 .. 0.79
   3 !   57.1   0.0   3.6e-19   1.6e-15     174     298 .]     425     543 ..     375     543 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHCT-S..EEEE-EES CS
                                       xxxxxxxxxxxxxxx..xxxxxxxx RF
                      Peptidase_S8 109 eliraieeaaedkvd..vinmslge 131
                                       + +r ++ +  ++++  vi+ s+ +
  gi|298674650|ref|YP_003726400.1| 162 DRVREMYNQYGSGIKigVISDSVDG 186
                                       5555555555555554455555552 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 4.6e-06
                                       HHHHHHHHHHCT-SEEEE-EESCETTCHHCHHHHHHHHHHHH.CCT-EEEEE--SS-T-HH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 110 liraieeaaedkvdvinmslgestslpktgrsiealainravnkkgvlvviSaGNngktgs 170
                                         +a++  +++++++i   +g     p ++ ++ a  + + v+++++l+v++aGN+gk++ 
  gi|298674650|ref|YP_003726400.1| 240 FNSAVDTLVNSGCRIIVDDIG-WKREPYFEHGVVASHVANVVENNEILYVTAAGNDGKKHY 299
                                       56788888999999*******.66666666666656788888899************6654 PP

  == domain 3  score: 57.1 bits;  conditional E-value: 3.6e-19
                                       -TTCEECTTTSTTCEEEEEESTTSSB-TT--B-TT.............-EEEE-S-CCCCCCCCCHHHTTTHHEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 174 agspvgtpstsknvitvgayttegkiapfSsrGpssd......gklkpdivapGgnivstwsrqsnnsaglssyqsm 244
                                       + s +g p+  + v+tvga++ +++i pfSs+Gp++          kpd+v   g  vs ++  s         +++
  gi|298674650|ref|YP_003726400.1| 425 SDSIYGHPA-IRDVVTVGAISIDSDIEPFSSQGPVTHyhpdyeMISKPDVVGVNGINVSGAGGFS---------KKF 491
                                       455567777.678**********************985555544556666644444455555555.........699 PP

                                       -SHHHCHHHHHHHHHHHHHHHTT--HHHHHHHHHCCS-EE......SSSSSSTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 245 sGTSmAsPnaagaaAlllsalpkltpetvraallntAqdlgkadniesfaqGaG 298
                                       +GTS+++P++a++aAll+s +p+++++++r+a+  +A d+g++    ++ +G+G
  gi|298674650|ref|YP_003726400.1| 492 YGTSASAPHVAAVAALLWSSFPSMKAQDIREAIYYSAVDMGAE--NYDYTYGYG 543
                                       *************************************998666..889999998 PP

>> BIRC6  Baculoviral IAP repeat-containing protein 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   7.6e-05      0.34      11      54 ..     480     522 ..     475     531 .. 0.81
   2 ?   -1.4   0.1       0.3   1.3e+03     129     171 ..     580     626 ..     552     630 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 7.6e-05
                             BIRC6  11 rrigagasssrelgLlapsPshlhCvaailWqsyelpveydlld 54 
                                       +++gag+ s++ +g +a++P h+  vaa+lW s+     +d+ +
  gi|298674650|ref|YP_003726400.1| 480 NVSGAGGFSKKFYGTSASAP-HVAAVAALLWSSFPSMKAQDIRE 522
                                       56678888988889888888.9************9888887765 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.3
                             BIRC6 129 dqeelr...sltDDskeaesekdsqsssv.vqdishvalsesqLatl 171
                                       + ++++   s +D +  +++++++ +++v +  ++ + l+ s L  +
  gi|298674650|ref|YP_003726400.1| 580 ETSNKSsmkSPADTQSGQSESQNHSPEEVeTPGFEAIYLTASLLIAI 626
                                       22222222133444333443446666666678899999998887655 PP

>> Smg4_UPF3  Smg-4/UPF3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1     0.054   2.4e+02     145     173 ..      50      78 ..      32      79 .. 0.77
   2 ?    7.8   0.1   0.00071       3.2      45      91 ..      76     122 ..      74     153 .. 0.85
   3 ?    7.0   1.4    0.0012       5.5     106     160 ..     560     607 ..     550     619 .. 0.67

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.054
                         Smg4_UPF3 145 eaeekekekeakkekktttpLleylkekk 173
                                       ++ e++ke+++ +e+k +tpL+  l+ k+
  gi|298674650|ref|YP_003726400.1|  50 SYLENKKENTTCIEEKCSTPLVSLLERKN 78 
                                       344556666899***********999875 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00071
                         Smg4_UPF3  45 kdslkeskysrayinfkdpedlvqfakkfdghvFvDskgnespaive 91 
                                       ++++ ++ y  +yi fk+  d+ ++++++ +++ +D+k+n  +  v+
  gi|298674650|ref|YP_003726400.1|  76 RKNNSSNNYVCVYIYFKQSVDIKTIESHITNVTNRDEKNNLIVGWVN 122
                                       6788999999****************************997766665 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0012
                         Smg4_UPF3 106 kdakqgtIekDpeylaFleslekeeeekeseseeeklaeeaeekekekeakkekk 160
                                       +  ++ t ++D+ey++F ++  ++++  +s +++++ ++e ++++        ++
  gi|298674650|ref|YP_003726400.1| 560 SSVQKKTYDNDTEYKTFEKQETSNKSSMKSPADTQSGQSESQNHS-------PEE 607
                                       566889***********8877766655555555555554443333.......333 PP

>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.8      0.59   2.7e+03       7      14 ..     501     508 ..     501     509 .. 0.76
   2 ?   10.1   0.0   0.00014      0.64       1      22 [.     610     631 ..     610     631 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.59
                         PGF-CTERM   7 vlAlaGLL 14 
                                       v A+a+LL
  gi|298674650|ref|YP_003726400.1| 501 VAAVAALL 508
                                       67888887 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00014
                         PGF-CTERM   1 tPGFGavlAlaGLLaaalLaRR 22 
                                       tPGF+a++  a LL a++ a++
  gi|298674650|ref|YP_003726400.1| 610 TPGFEAIYLTASLLIAIYYAKK 631
                                       9*******99999999998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (632 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1158  (0.0645881); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 4126.88
//
Query:       gi|298674651|ref|YP_003726401.1|  [L=207]
Description: molybdopterin-guanine dinucleotide biosynthesis protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-30  105.5   0.0      4e-30  105.3   0.0    1.1  1  NTP_transf_3     MobA-like NTP transferase domain
    0.00017   20.8   0.0    0.00033   19.9   0.0    1.4  1  CofC             Guanylyl transferase CofC like
    0.00059   19.5   0.0    0.00078   19.1   0.0    1.2  1  NTP_transferase  Nucleotidyl transferase
     0.0057   16.6   0.0      0.012   15.6   0.0    1.4  1  CTP_transf_3     Cytidylyltransferase
  ------ inclusion threshold ------
      0.023   14.5   0.1       0.03   14.1   0.1    1.3  1  Glycos_transf_2  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.3   0.0   1.1e-33     4e-30       1     144 [.       9     151 ..       9     171 .. 0.89

  Alignments for each domain:
  == domain 1  score: 105.3 bits;  conditional E-value: 1.1e-33
                                       EEEEEESS-TTTTT.THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSHCHHHHHHTTC..TS-EEE-TTSS-SHHH CS
                      NTP_transf_3   1 aviLAGGrSsRmgg.dKallplggkpllervldalraagvdevvvvggdeevlaalarl..gvrvvededpgkgpla 74 
                                       ++iLAGG++sR+   +Kal+p+g+ +l+e+++d+l+ + vd+v+++++de  ++ l+++  + ++v+d+++g gpla
  gi|298674651|ref|YP_003726401.1|   9 GLILAGGEGSRLEYaEKALIPFGKYTLIEHIIDTLENS-VDDVIISVRDEIQKQKLKQYvgNRTIVTDKYKGVGPLA 84 
                                       69***********77**********************9.**********97778888886568999*********** PP

                                       HHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEEEECCEEEGGGHHHHHHH CS
                      NTP_transf_3  75 slaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvptyegerghpllfrarllsalaal 144
                                       +++ + + a ++++v+v+acDmPl+++++v+ l++ a+  g+d++ p+++++  +pl +++r+ + + ++
  gi|298674651|ref|YP_003726401.1|  85 GILEGFKVA-RSEYVFVAACDMPLINTDVVDLLFEYAE--GHDAALPQWDDGNLEPLHAVYRVYPLVFEI 151
                                       *******98.9************************986..8999*************9999988777655 PP

>> CofC  Guanylyl transferase CofC like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   9.1e-08   0.00033      33     118 ..      35     125 ..      30     138 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 9.1e-08
                              CofC  33 mlldvidalkr.ldvlvvsedeevleyalde.l.gvevvkekekdln..tavekafeeieekeviiipsdiPlikke 104
                                       ++  +id+l++ +d +++s  +e+ + +l++   +  +v +k+k++   + + + f     + v +  +d+Pli+ +
  gi|298674651|ref|YP_003726401.1|  35 LIEHIIDTLENsVDDVIISVRDEIQKQKLKQyVgNRTIVTDKYKGVGplAGILEGFKVARSEYVFVAACDMPLINTD 111
                                       566899***999**9999999999887764314145678899*9976224566678999999*************** PP

                              CofC 105 dvkdllelekradv 118
                                       +v+ l+e ++  d 
  gi|298674651|ref|YP_003726401.1| 112 VVDLLFEYAEGHDA 125
                                       *******9987775 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   2.2e-07   0.00078       2      66 ..       9      68 ..       8     100 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.2e-07
                                      EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHT CS
                   NTP_transferase  2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlk 66
                                      ++ILaGG+G+RL     + a k++   gk++li++ + +l ns  + ii v  + +++ ++++++
  gi|298674651|ref|YP_003726401.1|  9 GLILAGGEGSRL-----EYAEKALIPFGKYTLIEHIIDTLENSVDDVIISVRDEIQKQKLKQYVG 68
                                      79*********9.....7999999999999***********966666666666666666666655 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   3.3e-06     0.012       5     114 ..      12     119 ..       9     136 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.3e-06
                                       EE-SSSSSST..TGGGSEETTEEHHHHHHHHHHHTTTTSEEEEEES-HHHHHHHHHTTSEEEE--TTCSSHHHHHHH CS
                      CTP_transf_3   5 pARsgSkRlp..gKnlldlggkpliayvleaalkskafekvivaTDseeiknvakefgasvlvtrsslesdterfle 79 
                                       +A  + +Rl+  +K+l+++g  +li+++++ + +   +++vi++  +e  k+ +k++  + + + ++  ++   ++ 
  gi|298674651|ref|YP_003726401.1|  12 LAGGEGSRLEyaEKALIPFGKYTLIEHIIDTLEN--SVDDVIISVRDEIQKQKLKQYV-GNRTIVTDKYKGVGPLAG 85 
                                       5555556665448*********************..789*********9999999995.444444444555556666 PP

                                       HHHHHTTT.TTSEEEEE-TT-TT--HHHHHHHHHH CS
                      CTP_transf_3  80 vvkaflmseneeiivnlqGdnPllqeevikkaiet 114
                                        ++ f++    e++     d Pl++  v++ ++e+
  gi|298674651|ref|YP_003726401.1|  86 ILEGFKVA-RSEYVFVAACDMPLINTDVVDLLFEY 119
                                       66666666.44455555557777776666666666 PP

>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   8.5e-06      0.03      43     127 ..      60     141 ..      33     169 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.5e-06
                                       HHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEE CS
                   Glycos_transf_2  43 veileelakedprvrvirreenvGkagalnaglraatgdyilflDaDdepdpdwleklvealekdgadvvlgqrpri 119
                                       ++ l++++  + r +v  + ++vG+ +++ +g++ a+++y+++   D      ++ +l+ ++ + g+d++l+q++  
  gi|298674651|ref|YP_003726401.1|  60 KQKLKQYV--GNRTIVTDKYKGVGPLAGILEGFKVARSEYVFVAACDMPLINTDVVDLLFEYAE-GHDAALPQWDDG 133
                                       66777777..4666777777788*************************8888888888888888.8888****9999 PP

                                       ECCCCCCC CS
                   Glycos_transf_2 120 fgetdeie 127
                                       + e+ +  
  gi|298674651|ref|YP_003726401.1| 134 NLEPLHAV 141
                                       98887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1625.22
//
Query:       gi|298674652|ref|YP_003726402.1|  [L=183]
Description: hypothetical protein Metev_0704 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-31  106.8   0.5    7.3e-31  106.0   0.5    1.4  1  DUF2148   Uncharacterized protein containing a ferredoxin dom
    0.00077   19.1   1.4     0.0015   18.2   1.4    1.4  1  FeS       Putative Fe-S cluster


Domain annotation for each model (and alignments):
>> DUF2148  Uncharacterized protein containing a ferredoxin domain (DUF2148)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.0   0.5   8.1e-35   7.3e-31       1      68 []     117     183 .]     117     183 .] 0.99

  Alignments for each domain:
  == domain 1  score: 106.0 bits;  conditional E-value: 8.1e-35
                           DUF2148   1 agplCafkaiDlGiAlgsavkvaadlrvDnRvmysvGaaAkslgllkeasvvlgiplsvsgKsifFDR 68 
                                       +gp C +k++DlGiA+g+a ++a+dl++DnR+my++G aAk+ gl++ a++v+gipls++g+sifFDR
  gi|298674652|ref|YP_003726402.1| 117 EGPRCSIKYVDLGIAVGAATAKAKDLCIDNRIMYTIGSAAKNSGLID-ADMVYGIPLSIKGRSIFFDR 183
                                       59*********************************************.*******************9 PP

>> FeS  Putative Fe-S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   1.4   1.6e-07    0.0015       4      24 ..      90     110 ..      89     113 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.6e-07
                               FeS   4 tNCgaCGypgCmafAealveg 24 
                                       ++CgaCG+ +C ++ + l eg
  gi|298674652|ref|YP_003726402.1|  90 LDCGACGFSTCAEMLQYLKEG 110
                                       69**********987777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1409.95
//
Query:       gi|298674653|ref|YP_003726403.1|  [L=416]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.1e-25   87.2   1.0    2.3e-24   85.9   0.0    2.1  2  OrfB_IS605      Probable transposase
    4.7e-12   45.6   0.1    1.6e-11   43.9   0.0    2.0  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.055   13.9   0.0       0.11   12.9   0.0    1.4  1  RuvX            Holliday junction resolvase


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.3      0.46   2.7e+03      47      84 ..      10      29 ..       2      40 .. 0.53
   2 !   85.9   0.0   3.9e-28   2.3e-24      15     119 ..     192     294 ..     178     295 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.46
                        OrfB_IS605 47 ksdykylakeiaelqsklkksknykkasrklarlhrkr 84
                                      k+d+++                   ++ +++++l++++
  gi|298674653|ref|YP_003726403.1| 10 KADKQK------------------YEVLKRITKLSKNL 29
                                      333333..................34444444444444 PP

  == domain 2  score: 85.9 bits;  conditional E-value: 3.9e-28
                        OrfB_IS605  15 gnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsrrrkhl 91 
                                        nk+++iDlG+nn+at v+++gt+f+++gr lks +++++k +  lqs ++k++   k  +kl  l++kr+++++++
  gi|298674653|ref|YP_003726403.1| 192 YNKHLSIDLGVNNFATSVDTNGTAFIIEGRGLKSYNRWWNKVKSGLQSVYDKQG--IKSGQKLNWLFEKRKNKLNDF 266
                                       699**************************************************9..9******************** PP

                        OrfB_IS605  92 lhklathliktlkevgvetLnvgnmkdi 119
                                       +++ ++++ik++ +++++++++g++kdi
  gi|298674653|ref|YP_003726403.1| 267 MNQSVNYIIKHCIDNNIGNIIIGELKDI 294
                                       *************************998 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.6   9.7e+03       9      23 ..     167     181 ..     166     182 .. 0.84
   2 !   43.9   0.0   2.7e-15   1.6e-11       1      69 []     313     387 ..     313     387 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.6
                    OrfB_Zn_ribbon   9 eykakeyGikveevn 23 
                                       +y  +++ i++++ +
  gi|298674653|ref|YP_003726403.1| 167 KYNGQWFEIEYVYRD 181
                                       688999999999876 PP

  == domain 2  score: 43.9 bits;  conditional E-value: 2.7e-15
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke......alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f+k+k++l+ k++ yGik +ev++ayTSkt +   +  ++      ++ +r +  ++ g  +++Dvn+a+Nil++
  gi|298674653|ref|YP_003726403.1| 313 FGKFKQKLRSKCEYYGIKHIEVDEAYTSKTDALALEPIEKhqkymgKRVKRGLFQSSTGKLLNADVNGALNILRK 387
                                       89****************************887776666666688977788888888***************986 PP

>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.8e-05      0.11      36     107 ..     265     348 ..     243     364 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.8e-05
                                       H..HHHHHHHHHHHHHTT--EEEEE--......---..-SSS---SSTTHHHHHHHHHT....T-EEEEE--S---- CS
                              RuvX  36 k..ekdleelkelvkeeeveeiVvGlP......lnl..dgsegesakkvrkfaeeLakrl..kklpvelvDErlttv 100
                                       +  +++++ + + + ++++ +i++G         n+  +++++ ++  + kf ++L++++  ++++ + vDE +t++
  gi|298674653|ref|YP_003726403.1| 265 DfmNQSVNYIIKHCIDNNIGNIIIGELkdikqnSNMgkKNNQTFQTIPFGKFKQKLRSKCeyYGIKHIEVDEAYTSK 341
                                       1447899999999************88677776444114455555556699*******997788999*********9 PP

                                       XXXXXXX CS
                              RuvX 101 eaerilr 107
                                       + + +l+
  gi|298674653|ref|YP_003726403.1| 342 TDALALE 348
                                       8776664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1074  (0.059903); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 3342.26
//
Query:       gi|298674654|ref|YP_003726404.1|  [L=217]
Description: transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-10   40.6   0.1    4.8e-10   39.8   0.1    1.4  1  DDE_Tnp_IS240    DDE domain
    0.00024   20.7   0.0    0.00037   20.1   0.0    1.2  1  DDE_Tnp_IS66     Transposase IS66 family
    0.00074   19.3   0.0     0.0013   18.5   0.0    1.4  1  DDE_Tnp_ISL3     Transposase
     0.0042   16.9   0.0        0.1   12.4   0.0    2.6  4  DDE_3            DDE superfamily endonuclease
  ------ inclusion threshold ------
      0.021   13.7   0.1        1.6    7.5   0.0    2.3  2  Transposase_mut  Transposase, Mutator family
      0.063   13.7   0.0       0.16   12.4   0.0    1.8  1  HAD              haloacid dehalogenase-like hydrolase
       0.11   12.4   0.0        2.9    7.8   0.0    2.3  2  UvrC_HhH_N       UvrC Helix-hairpin-helix N-terminal


Domain annotation for each model (and alignments):
>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   0.1   1.9e-13   4.8e-10       5     112 ..      83     183 ..      79     193 .. 0.89

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 1.9e-13
                     DDE_Tnp_IS240   5 rvDETyvkikGkwaYlyravDkegr.ildflvskrRdtkaakaflrkalkkeklepeeivtDkasayasalkelkre 80 
                                        vDET v+   +  +ly+a++ +++ i+ + +   R+   +k f++ + k + + p+ +v+D+ + + +al++l+ +
  gi|298674654|ref|YP_003726404.1|  83 VVDETKVQLGSEYWFLYAAINPDSKkIVYARIYPTRNYLTTKSFFKDLKKMYAQLPQMVVVDGGP-WYKALERLGVK 158
                                       69********************9999*************************************99.6689****993 PP

                     DDE_Tnp_IS240  81 gelfdevshvqvkylnnriEsdhrtlKkrlrp 112
                                                +     +n iE++++++K+r+++
  gi|298674654|ref|YP_003726404.1| 159 ------RVVISGD-FRNYIERWYKEFKRRIKV 183
                                       ......3334444.499************976 PP

>> DDE_Tnp_IS66  Transposase IS66 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   1.4e-07   0.00037      14     145 ..      32     158 ..      25     162 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.4e-07
                      DDE_Tnp_IS66  14 vlkyadhlPlyRqeeilarlGvelsrgtlanwvkraaelleplvealkaallasevihaDETtlrvlkpgrgkgkks 90 
                                       +l y+++l+l++ +e+l+ l  ++s   ++ wv++ ++ l+p   +l ++      i +DET+++         + +
  gi|298674654|ref|YP_003726404.1|  32 ILLYQQGLSLRKTSELLSYLAEPISYRGVHYWVQKFGWCLQPYDGELPDT------IVVDETKVQ------LGSEYW 96 
                                       6789*****************************************99765......68*******......556889 PP

                      DDE_Tnp_IS66  91 ylWvyvtdkrkpavlfeyspsRggevaealLag.......fkGvlvsDgyagYnklaeeqvt 145
                                        l+++++ ++k++v+ ++ p+R+  ++++++++          ++v+Dg   Y++l++ +v+
  gi|298674654|ref|YP_003726404.1|  97 FLYAAINPDSKKIVYARIYPTRNYLTTKSFFKDlkkmyaqLPQMVVVDGGPWYKALERLGVK 158
                                       9999999999********************88876675545579999999999999875554 PP

>> DDE_Tnp_ISL3  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   5.1e-07    0.0013       1      69 [.      82     152 ..      82     166 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 5.1e-07
                      DDE_Tnp_ISL3   1 lgiDEislkkghkyvtvvvdllvdggrlld..ilpgRkketlkafleslsekerekveavvmDmsaayksa 69 
                                       + +DE++++ g++y   ++ +  d +++++  i p+R+  t k+f+++l++  ++  ++vv+D+ ++yk++
  gi|298674654|ref|YP_003726404.1|  82 IVVDETKVQLGSEYWFLYAAINPDSKKIVYarIYPTRNYLTTKSFFKDLKKMYAQLPQMVVVDGGPWYKAL 152
                                       78************99*****9999999864489***************99999999***********986 PP

>> DDE_3  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.2     3e+03       2      14 ..      81      93 ..      80      96 .. 0.83
   2 !   12.4   0.0   3.9e-05       0.1      38      93 ..      96     151 ..      85     154 .. 0.92
   3 ?    1.1   0.1      0.12     3e+02     120     135 ..     168     183 ..     163     193 .. 0.83
   4 ?   -2.6   0.1       1.6   4.2e+03      35      50 ..     194     209 ..     173     213 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.2
                             DDE_3  2 vvfiDEsgfqlgt 14
                                      ++++DE+++qlg+
  gi|298674654|ref|YP_003726404.1| 81 TIVVDETKVQLGS 93
                                      6899****99975 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 3.9e-05
                             DDE_3  38 vnligaldekgglaf.vtfeetlnaedfaeflerlletalqakkivlilDnasiHks 93 
                                       + l++a++++ ++++ + ++ t+n   ++ f+++l++ + q  ++++++D+ +++k+
  gi|298674654|ref|YP_003726404.1|  96 WFLYAAINPDSKKIVyARIYPTRNYLTTKSFFKDLKKMYAQL-PQMVVVDGGPWYKA 151
                                       5689*************************************8.********998875 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.12
                             DDE_3 120 NpiEivwsklkrellk 135
                                       N iE++++ +kr+++ 
  gi|298674654|ref|YP_003726404.1| 168 NYIERWYKEFKRRIKV 183
                                       8999999999999875 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 1.6
                             DDE_3  35 rgrvnligaldekggl 50 
                                         ++++ig+++ ++++
  gi|298674654|ref|YP_003726404.1| 194 SFSISIIGSICTSRII 209
                                       3478899999887765 PP

>> Transposase_mut  Transposase, Mutator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0   0.00064       1.6      93     129 ..      18      53 ..      14      61 .. 0.75
   2 ?    3.7   0.0    0.0088        23     337     362 ..     167     193 ..     156     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00064
                   Transposase_mut  93 lerykRrekaleavvielyvkGvstrkveklveelyg 129
                                       +e +kRr+ + +a  i ly++G+s rk ++l+  l  
  gi|298674654|ref|YP_003726404.1|  18 VE-RKRRDVKAIALSILLYQQGLSLRKTSELLSYLAE 53 
                                       44.555555556666779***********99988876 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0088
                   Transposase_mut 337 tNllErLNkeirRrtrvv.giFPnees 362
                                        N +Er  ke +Rr +v  + FP +e 
  gi|298674654|ref|YP_003726404.1| 167 RNYIERWYKEFKRRIKVFdKYFPHKEG 193
                                       499************996368999875 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.1e-05      0.16      69     139 ..     126     189 ..      61     207 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.1e-05
                               HAD  69 laaelerfvaevirpklldp.galellaahraaGdrvvvvSgglrplvepllaelg.adevlatelevddrlt 139
                                       + ++l++++a+  +  + d   ++++l+   + G++ vv+Sg +r ++e++ +e+   + v +       ++ 
  gi|298674654|ref|YP_003726404.1| 126 FFKDLKKMYAQLPQMVVVDGgPWYKALE---RLGVKRVVISGDFRNYIERWYKEFKrRIKVFDK------YFP 189
                                       3344444442222222444446668888...999*********************998888888......443 PP

>> UvrC_HhH_N  UvrC Helix-hairpin-helix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.054   1.4e+02      74      92 ..      50      92 ..      12     100 .. 0.67
   2 ?    7.8   0.0    0.0011       2.9      68      88 ..     127     147 ..     117     163 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.054
                                      ...........................---SEEEESSSHHHHH CS
                                      x........................xxxxxxxxxxxxxxxxxx RF
                        UvrC_HhH_N 74 e........................fsklPdLiliDGGkgqln 92
                                                               + +lPd i++D  k ql 
  gi|298674654|ref|YP_003726404.1| 50 YlaepisyrgvhywvqkfgwclqpyDGELPDTIVVDETKVQLG 92
                                      05555555555555555666666667899*******9999986 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0011
                                       HTTS.....---SEEEESSSH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                        UvrC_HhH_N  68 fkrllkefsklPdLiliDGGk 88 
                                       fk l+k  ++lP+++++DGG 
  gi|298674654|ref|YP_003726404.1| 127 FKDLKKMYAQLPQMVVVDGGP 147
                                       788899999***********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1674.75
//
Query:       gi|298674655|ref|YP_003726405.1|  [L=665]
Description: hypothetical protein Metev_0707 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-48  163.8   0.2    6.2e-48  162.1   0.2    1.9  1  DUF460         Protein of unknown function (DUF460)
     0.0006   20.1   0.0     0.0015   18.8   0.0    1.7  1  acVLRF1        Actinobacteria/chloroflexi VLRF1 release facto
     0.0037   17.8  20.3     0.0037   17.8  20.3    2.5  4  AAA_23         AAA domain
  ------ inclusion threshold ------
      0.028   14.8   0.1        5.9    7.3   0.0    3.4  3  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
      0.079   12.4   3.5       0.13   11.7   0.0    2.5  2  DUF4392        Domain of unknown function (DUF4392)
       0.15   11.4   8.8       0.29   10.5   8.8    1.4  1  DUF4407        Domain of unknown function (DUF4407)
        0.4   10.0  22.4       0.77    9.1  22.4    1.4  1  FAM76          FAM76 protein
       0.51   10.7  18.3        2.1    8.7   4.1    2.8  2  CC2-LZ         Leucine zipper of domain CC2 of NEMO, NF-kappa
        1.4    9.4   6.6         16    6.0   1.1    2.7  2  MitMem_reg     Maintenance of mitochondrial structure and fun
        1.5    9.0   7.4       0.23   11.6   0.3    2.4  2  Phage_lysis    Bacteriophage Rz lysis protein
        2.2    8.6   6.7       0.15   12.3   1.0    2.1  1  Nse4_C         Nse4 C-terminal
        3.7    7.9  24.6       0.45   10.9   9.6    2.8  3  DUF641         Plant protein of unknown function (DUF641)
        4.7    6.0   7.4        8.7    5.1   7.4    1.5  1  LMBR1          LMBR1-like membrane protein
        7.7    7.0   8.3        1.4    9.4   0.8    2.8  2  DUF4094        Domain of unknown function (DUF4094)


Domain annotation for each model (and alignments):
>> DUF460  Protein of unknown function (DUF460)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.1   0.2   4.9e-51   6.2e-48       5     141 .]     226     359 ..     223     359 .. 0.95

  Alignments for each domain:
  == domain 1  score: 162.1 bits;  conditional E-value: 4.9e-51
                            DUF460   5 kdvkvevesvekdkiefeplkkkr...kkklivGiDPGittgiavldldgevlalkssreldreevieliselGkpv 78 
                                        dv+v+v+ ve+dki++ pl+k++   +k++ivGiDPG+t+giavl+ld+e+l+lks r+++++ev++l+se+Gkpv
  gi|298674655|ref|YP_003726405.1| 226 GDVQVKVKGVERDKIKYIPLDKHDeqkRKYTIVGIDPGTTVGIAVLSLDAELLYLKSFRGISHDEVVKLVSEYGKPV 302
                                       7****************77754433349************************************************* PP

                            DUF460  79 ivAtDvspppetvkklarslkavlyvPeedlsveeKeelaeklsekekvkykddHeRDalaAA 141
                                       i+AtDv p+p++v+k++rs+ka+   P+++ls eeK++l +       + y++dHeRDalaAA
  gi|298674655|ref|YP_003726405.1| 303 IIATDVIPTPNSVEKIRRSFKAIEGRPDTRLSSEEKITLSKP------YGYSNDHERDALAAA 359
                                       ******************************************......999***********9 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.2e-06    0.0015      38      69 ..     154     185 ..     127     230 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.2e-06
                           acVLRF1  38 aaGGwSqqRfaRrrenqadalleavaeaaarl 69 
                                        +GGwSq+R++R++ + +++  +++  ++++ 
  gi|298674655|ref|YP_003726405.1| 154 GRGGWSQNRYHRKVHGAVKEKCRDIDTTLKNF 185
                                       57*****************9999988877765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       6.7   8.6e+03     154     175 ..      62      83 ..      34     117 .. 0.64
   2 ?   -3.4   0.0         9   1.1e+04      78     101 ..     128     156 ..      93     200 .. 0.53
   3 !   17.8  20.3   2.9e-06    0.0037      37     197 ..     354     522 ..     306     525 .. 0.65
   4 ?   -2.5   0.2       4.6   5.9e+03     146     170 ..     624     648 ..     583     660 .. 0.53

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 6.7
                            AAA_23 154 rleelekeleeledekkllekl 175
                                       +l+++ +  e +++ +++le+l
  gi|298674655|ref|YP_003726405.1|  62 ALDNVFELAENKKNLIQFLERL 83 
                                       5666666666666666666665 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 9
                            AAA_23  78 t..........fenkdgrytrsiererelskkkg 101
                                                  fen+++     i+ +r +s + g
  gi|298674655|ref|YP_003726405.1| 128 AamgvgsevslFENITK-----IKVSRARSLGRG 156
                                       44444444445566555.....333443333333 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 2.9e-06
                            AAA_23  37 dAiklaLygetprlsrksgrgfeksdveiesegkvkayveltfenkdgry..trsiererelskkkgkttkkaklel 111
                                       dA+  aLy   +  +    ++ ek+++     + +k  v+l + + d+++   ++++  +++ ++k + +kk+  e+
  gi|298674655|ref|YP_003726405.1| 354 DALAAALYSYRNYKNV--FSKVEKRSPY----DVDKDHVKLYVMHGDTIEdaIEKVKTPKKEEESKRELVKKQYVEE 424
                                       6888888875332222..2233333333....366677999988877755444444444444444444445555555 PP

                            AAA_23 112 leideleqfisellgskkiil.nlilflgqerfeefelkdkke............rleelekeleeledekkllekl 175
                                        ++d+ ++++++ ++++k+++ ++ ++++q +++++++ +k +            r +e++ke+e +         +
  gi|298674655|ref|YP_003726405.1| 425 EKPDDYQKLVET-INRQKSQIkHMQDYIDQLKKDKKKKDKKISslefkidnlmseRNKEIKKEKEIKI--------R 492
                                       556888888886.7777776637777888888754444333336666444444433333333333333........2 PP

                            AAA_23 176 ........eqekekekeleeleeeleeilk 197
                                                ++k+k+k l++l+++++++++
  gi|298674655|ref|YP_003726405.1| 493 dnkisklkSELKNKNKSLKKLKSQINKLKQ 522
                                       444544457899999999999999999865 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 4.6
                            AAA_23 146 felkdkkerleelekeleeledekk 170
                                       +el++  +r++e+ ke+  +e+ek+
  gi|298674655|ref|YP_003726405.1| 624 EELESAISRWNEFAKEKYMEEKEKE 648
                                       3334444444444444333333322 PP

>> Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.096   1.2e+02      69      94 ..     379     404 ..     335     405 .. 0.83
   2 ?    7.3   0.0    0.0046       5.9      37      81 ..     564     609 ..     551     617 .. 0.83
   3 ?   -0.7   0.0       1.4   1.8e+03      10      27 ..     613     630 ..     610     651 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.096
                                       HHHCTTTSEEEES-SSBHHHHHHHHH CS
                     Nitro_FeMo-Co  69 akleaagievykgaggtveealkevl 94 
                                         +++  ++ y+  g t+e+a+++v+
  gi|298674655|ref|YP_003726405.1| 379 YDVDKDHVKLYVMHGDTIEDAIEKVK 404
                                       56677889***************986 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0046
                                       CTSSCSSTHHHHHHHHTT-SEEEESSS.CHHHHHHHCTTTSEEEES CS
                     Nitro_FeMo-Co  37 daegggggklaqllaeegvdvvivgki.Gpralakleaagievykg 81 
                                       ++++ggg ++a++l ++g+++viv+      a++++ +++i ++k 
  gi|298674655|ref|YP_003726405.1| 564 EDASGGGASTASMLINAGIKAVIVSDDlSHAAFEAFFENNIPILKE 609
                                       566799**************99998755999999999999988874 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.4
                                       CC-SEEEEEEESSSCEEE CS
                     Nitro_FeMo-Co  10 GrapyFaiyeveegevki 27 
                                        ra+ Fai++ ee e  i
  gi|298674655|ref|YP_003726405.1| 613 QRADDFAIVDPEELESAI 630
                                       5899******99765444 PP

>> DUF4392  Domain of unknown function (DUF4392)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   1.5      0.49   6.2e+02      95     177 ..     381     459 ..     364     468 .. 0.58
   2 ?   11.7   0.0    0.0001      0.13      60     102 ..     569     612 ..     564     659 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.49
                           DUF4392  95 vlktevpllelqdrsaeaaivfltkdgdkkeaeaeelleklkpdhliaiErpGra.adGnyynmrgeniselvapld 170
                                       v k++v+l  ++ ++ e ai++++  ++++e++ e + ++      +  E+p    +  ++ n ++ +i+++++ +d
  gi|298674655|ref|YP_003726405.1| 381 VDKDHVKLYVMHGDTIEDAIEKVKTPKKEEESKRELVKKQ-----YVEEEKPDDYqKLVETINRQKSQIKHMQDYID 452
                                       4555555556666666666666666665554443333333.....35556665441345566667777777777777 PP

                           DUF4392 171 dlfeaak 177
                                       +l +  k
  gi|298674655|ref|YP_003726405.1| 453 QLKKDKK 459
                                       7666554 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0001
                           DUF4392  60 GAialaraLqalgkkvvivtdelnekiveaaveqgvlkte.vpl 102
                                       G ++ a +L   g+k+viv d+l++++ ea++e ++++ + v++
  gi|298674655|ref|YP_003726405.1| 569 GGASTASMLINAGIKAVIVSDDLSHAAFEAFFENNIPILKeVSI 612
                                       778899****************************7766653222 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   8.8   0.00022      0.29     121     205 ..     435     523 ..     398     553 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00022
                           DUF4407 121 kelkeqlaaa......ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk..gtgttgvaGkgpaakekk 189
                                       +++++    +      +++ +++l+++ ++ +++i+++e ++d+l+ e +ke++ +k  + + +++     + k+k+
  gi|298674655|ref|YP_003726405.1| 435 ETINR----QksqikhMQDYIDQLKKDKKKKDKKISSLEFKIDNLMSERNKEIKKEKeiKIRDNKISKLKSELKNKN 507
                                       22222....12233449999**********************************97766333333455556666666 PP

                           DUF4407 190 aqldaaqaelaelkak 205
                                       + l++++ ++++lk+ 
  gi|298674655|ref|YP_003726405.1| 508 KSLKKLKSQINKLKQI 523
                                       6666666666666554 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1  22.4    0.0006      0.77     183     298 ..     406     520 ..     351     522 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0006
                             FAM76 183 ssrlevskleeeklaeekesnetskksldsnssdhlvavtqLkeeiaslkkqleqkdqellekdkkitelkaellek 259
                                       +++ e sk e  k++  +e++ +  ++l  + + +  +++++++ i +lkk  ++kd+++++ + ki +l +e  + 
  gi|298674655|ref|YP_003726405.1| 406 PKKEEESKRELVKKQYVEEEKPDDYQKLVETINRQKSQIKHMQDYIDQLKKDKKKKDKKISSLEFKIDNLMSERNK- 481
                                       2222222222111222222223334466677788999*********************************998754. PP

                             FAM76 260 ekelreklkelekeakekieklekkirellkevaelskk 298
                                       e + ++ +k +++++++  ++l++k+++l+k +++++k 
  gi|298674655|ref|YP_003726405.1| 482 EIKKEKEIKIRDNKISKLKSELKNKNKSLKKLKSQINKL 520
                                       4555566777777788888999**********9999986 PP

>> CC2-LZ  Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   6.2    0.0067       8.6       6      54 ..     420     468 ..     410     477 .. 0.83
   2 ?    8.7   4.1    0.0017       2.1       3      44 ..     483     524 ..     479     537 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0067
                            CC2-LZ   6 keaekvkkeeieeLkaqlqaaeealaakqeeidelkeeikkkeeeleti 54 
                                       +  e+ k +++++L + ++    +++++q+ id+lk++ kkk++++  +
  gi|298674655|ref|YP_003726405.1| 420 QYVEEEKPDDYQKLVETINRQKSQIKHMQDYIDQLKKDKKKKDKKISSL 468
                                       4445556799*********************************977643 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0017
                            CC2-LZ   3 lkakeaekvkkeeieeLkaqlqaaeealaakqeeidelkeei 44 
                                        k+++  k++ ++i++Lk +l++++++l++ +++i++lk+  
  gi|298674655|ref|YP_003726405.1| 483 IKKEKEIKIRDNKISKLKSELKNKNKSLKKLKSQINKLKQIR 524
                                       445555566688999999999999999999999999998744 PP

>> MitMem_reg  Maintenance of mitochondrial structure and function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.6     0.019        24      19      45 ..     426     456 ..     409     487 .. 0.73
   2 ?    6.0   1.1     0.013        16      14      45 ..     490     522 ..     473     543 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.019
                        MitMem_reg  19 s....stlstglnrqyyslkilqerldlikd 45 
                                       +    ++l++ +nrq +++k +q+ +d++k+
  gi|298674655|ref|YP_003726405.1| 426 KpddyQKLVETINRQKSQIKHMQDYIDQLKK 456
                                       2455578888888888888888888887775 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.013
                        MitMem_reg  14 siqdas.stlstglnrqyyslkilqerldlikd 45 
                                       +i+d++ s+l ++l+++ +slk+l++ ++++k+
  gi|298674655|ref|YP_003726405.1| 490 KIRDNKiSKLKSELKNKNKSLKKLKSQINKLKQ 522
                                       45666689*******************999887 PP

>> Phage_lysis  Bacteriophage Rz lysis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   0.00018      0.23      95     123 ..     425     453 ..     418     456 .. 0.89
   2 ?   -0.2   1.9      0.81     1e+03       7      35 ..     494     522 ..     471     529 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                       Phage_lysis  95 aaerdyftLrerideveeqlkglQdyira 123
                                       +   dy++L+e i+  ++q+k +Qdyi +
  gi|298674655|ref|YP_003726405.1| 425 EKPDDYQKLVETINRQKSQIKHMQDYIDQ 453
                                       6668**********************975 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.81
                       Phage_lysis   7 rqvekdnaelraakaeieelqtrqravae 35 
                                       +++ k ++el+++++ +++l+ ++ ++ +
  gi|298674655|ref|YP_003726405.1| 494 NKISKLKSELKNKNKSLKKLKSQINKLKQ 522
                                       44556666666666666666666665544 PP

>> Nse4_C  Nse4 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.0   0.00012      0.15      44      91 .]     399     446 ..     377     446 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                            Nse4_C  44 vleeteeeeeekakeeeakkkqavlsldmetWkelieafdikepliph 91 
                                       ++e+++++++e+++++e  kkq v + + +++++l+e+++ +++ i+h
  gi|298674655|ref|YP_003726405.1| 399 AIEKVKTPKKEEESKRELVKKQYVEEEKPDDYQKLVETINRQKSQIKH 446
                                       45778889999999999****************************997 PP

>> DUF641  Plant protein of unknown function (DUF641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   9.6   0.00035      0.45      58     124 ..     414     481 ..     403     486 .. 0.79
   2 ?    3.1   6.7     0.087   1.1e+02      84     118 ..     486     520 ..     479     529 .. 0.59
   3 ?   -3.5   0.0       9.7   1.2e+04      66      66 ..     639     639 ..     610     660 .. 0.45

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00035
                            DUF641  58 rlyrkkqkkkas.eaeeseleaeiqeqrsllktyeitvkkleaelkakdseieeLkekLeeaeksnkk 124
                                       r  +kkq  +++ + + ++l   i++q+s +k ++  +++l+++ k+kd++i++L+ k++++ ++++k
  gi|298674655|ref|YP_003726405.1| 414 RELVKKQYVEEEkPDDYQKLVETINRQKSQIKHMQDYIDQLKKDKKKKDKKISSLEFKIDNLMSERNK 481
                                       5555555444442356788999**************************************99887665 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.087
                            DUF641  84 rsllktyeitvkkleaelkakdseieeLkekLeea 118
                                        + +k  +  ++kl++elk+k++ +++Lk++++++
  gi|298674655|ref|YP_003726405.1| 486 EKEIKIRDNKISKLKSELKNKNKSLKKLKSQINKL 520
                                       33455555666666666666666666666666655 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 9.7
                            DUF641  66 k 66 
                                       +
  gi|298674655|ref|YP_003726405.1| 639 E 639
                                       1 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   7.4    0.0068       8.7     221     301 ..     425     520 ..     358     577 .. 0.52

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0068
                             LMBR1 221 reledllkevkklrksisesdplrkyleeilk..............kvPeeiaeklks.nenkteeslaklekqlik 282
                                       ++ +d+ k v+++++++s+ +++++y++++ k              k+ + ++e++k+ +++k  +   +  ++l++
  gi|298674655|ref|YP_003726405.1| 425 EKPDDYQKLVETINRQKSQIKHMQDYIDQLKKdkkkkdkkisslefKIDNLMSERNKEiKKEKEIKIRDNKISKLKS 501
                                       22223333333333333333333344444443333333333333332322222222222111111111111122222 PP

                             LMBR1 283 alqkrertekqwkrlleka 301
                                       +l++++++ k++k  ++k 
  gi|298674655|ref|YP_003726405.1| 502 ELKNKNKSLKKLKSQINKL 520
                                       2222222222222222222 PP

>> DUF4094  Domain of unknown function (DUF4094)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.8    0.0011       1.4      34      82 ..     409     472 ..     395     481 .. 0.79
   2 ?    0.6   1.2      0.59   7.6e+02      64      84 ..     485     505 ..     472     522 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0011
                           DUF4094  34 sk.eelklvsedcdskdaesrskdilgevskthkaiqtL..............dktissLemeL 82 
                                       ++ ++ +lv++++ ++++  + +++++ ++++++ i+ +              dk+issLe ++
  gi|298674655|ref|YP_003726405.1| 409 EEeSKRELVKKQYVEEEKPDDYQKLVETINRQKSQIKHMqdyidqlkkdkkkkDKKISSLEFKI 472
                                       22467778998988877777788999999999999997777778889999999*******9876 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.59
                           DUF4094  64 thkaiqtLdktissLemeLaa 84 
                                       ++k+i+  d++is+L  eL  
  gi|298674655|ref|YP_003726405.1| 485 KEKEIKIRDNKISKLKSELKN 505
                                       333444446666666666653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (665 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3407  (0.190027); expected 358.6 (0.02)
Passed bias filter:                      793  (0.04423); expected 358.6 (0.02)
Passed Vit filter:                       137  (0.00764125); expected 17.9 (0.001)
Passed Fwd filter:                        43  (0.00239835); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.90u 0.25s 00:00:01.14 Elapsed: 00:00:00.45
# Mc/sec: 4459.04
//
Query:       gi|298674656|ref|YP_003726406.1|  [L=295]
Description: Non-specific serine/threonine protein kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.2e-45  152.5   0.3    1.4e-44  152.0   0.3    1.2  1  RIO1      RIO1 family
    8.6e-25   86.8   0.0    1.7e-24   85.8   0.0    1.5  1  Rio2_N    Rio2, N-terminal
     0.0009   19.2   0.1      0.037   13.9   0.0    2.1  2  APH       Phosphotransferase enzyme family
     0.0093   15.3   0.1        3.1    7.1   0.0    2.2  2  Kdo       Lipopolysaccharide kinase (Kdo/WaaP) family
  ------ inclusion threshold ------
      0.025   14.0   0.2      0.045   13.1   0.0    1.6  2  Pkinase   Protein kinase domain
      0.069   13.1   0.0       0.17   11.9   0.0    1.6  1  Tfb5      Transcription factor TFIIH complex subunit Tfb5


Domain annotation for each model (and alignments):
>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.0   0.3   4.5e-48   1.4e-44      12     181 ..     124     281 ..     107     288 .. 0.93

  Alignments for each domain:
  == domain 1  score: 152.0 bits;  conditional E-value: 4.5e-48
                                       EEEEEEE-S---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEEETTEEEEE-- CS
                              RIO1  12 evaiKiyktstteFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpielkrhvlvmefi 88 
                                       +v+iK+++ ++++Fk++k+ ++   +    ++++++ + ++l+a++E++ L+ l+   v+vP+p++ +r+++vm f 
  gi|298674656|ref|YP_003726406.1| 124 SVVIKFHREGISSFKSVKRIRDHLVD----REHYSWVYASRLSARREYEVLTNLYPD-VSVPEPVDQNRNAVVMHFA 195
                                       799******************99999....789***********************9.******************* PP

                                       EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE--GTTEEETTSTTHHHHHH CS
                              RIO1  89 gedgvaapklkdveeeeeaeelyeevleemrklykeaglvHaDLSeyNvlvdedkvviIDvsQaveldhpnalefLe 165
                                       +  g +++k k +e     +  ++e++++++  y   g++HaDLSeyN++v+ ++v iID++Q+++++hp+a+e+L+
  gi|298674656|ref|YP_003726406.1| 196 K--GSELTKTKLLE----PDWFFNEIIQQIKNSY-SLGIIHADLSEYNIFVHPEGVEIIDWPQYITPEHPHAAELLK 265
                                       9..99999999999....5678************.****************************************** PP

                                       HHHHHHHHHHHTTC-- CS
                              RIO1 166 rDveniikfFrrkgve 181
                                       rDv+n+ ++F+rk+  
  gi|298674656|ref|YP_003726406.1| 266 RDVSNVLTYFNRKYKV 281
                                       ************9865 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.8   0.0   5.7e-28   1.7e-24       2      82 .]      10      90 ..       9      90 .. 0.98

  Alignments for each domain:
  == domain 1  score: 85.8 bits;  conditional E-value: 5.7e-28
                            Rio2_N  2 ryLskedfrvLtavEmgmrnhevVptelieeisrlkeeevkkrlsrllkaklisrktakydGYkLtyeGyDyLALktlv 80
                                      ++L+++d r+Lt++E+gm+++++Vp e+i +++++ ++e+ +rl++l+k++ +  + ++y+GY++ ++GyD+LAL++lv
  gi|298674656|ref|YP_003726406.1| 10 KNLDNKDIRILTGIEVGMKHYKWVPLEEIVKYTKIPSDELFYRLDNLVKEDVVIGTRTPYEGYHIYFNGYDTLALNALV 88
                                      789**************************************************************************** PP

                            Rio2_N 81 kr 82
                                      kr
  gi|298674656|ref|YP_003726406.1| 89 KR 90
                                      98 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.024        72      34      60 ..     160     185 ..     156     207 .. 0.80
   2 !   13.9   0.0   1.2e-05     0.037     163     202 ..     222     259 ..     196     261 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.024
                                       HHHHHHHHHHHHHHHHTT-B--B-CTT CS
                               APH  34 aeeirrevallrlLakagvpvPevlag 60 
                                         ++rre+++l++L    v+vPe+++ 
  gi|298674656|ref|YP_003726406.1| 160 RLSARREYEVLTNLYPD-VSVPEPVDQ 185
                                       56899***********9.99*****92 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.2e-05
                                       SS-EEEE-SS-SGGGEEEC..TTEEEEE---.TT-EEEECC CS
                               APH 163 elptvllHgDlhpgNllvdpddgrvtGviDf.edaglgppl 202
                                       + + +++H Dl+  N+ v+p++ +   +iD+ ++ ++ +p+
  gi|298674656|ref|YP_003726406.1| 222 SYSLGIIHADLSEYNIFVHPEGVE---IIDWpQYITPEHPH 259
                                       66789**************88777...8***7777777665 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0     0.002         6      44      82 ..     148     186 ..     138     196 .. 0.84
   2 !    7.1   0.0     0.001       3.1     126     165 ..     214     248 ..     190     290 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.002
                               Kdo  44 lskdlyrfk.lgrtravrEfrllkrLeeagvavpkpvaag 82 
                                       + +++y++  ++r+ a+rE+++l +L+   v vp+pv  +
  gi|298674656|ref|YP_003726406.1| 148 VDREHYSWVyASRLSARREYEVLTNLYP-DVSVPEPVDQN 186
                                       4699**********************96.79999999765 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.001
                               Kdo 126 avgrliaklhragvnHadlyaknillqqeeeeeaeiwliD 165
                                       ++ + i++  ++g+ Hadl   ni+++ e+     + +iD
  gi|298674656|ref|YP_003726406.1| 214 EIIQQIKNSYSLGIIHADLSEYNIFVHPEG-----VEIID 248
                                       566778888999****************98.....55555 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0         2   5.9e+03       5      20 ..      98     113 ..      96     116 .. 0.81
   2 ?   13.1   0.0   1.5e-05     0.045     102     142 ..     210     249 ..     137     253 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2
                                       EEEEEESSEEEEEEEE CS
                           Pkinase   5 eklGeGsfGkVykave 20 
                                        ++G G+ ++V ++++
  gi|298674656|ref|YP_003726406.1|  98 DEIGYGKESVVHEGIK 113
                                       6899999999999886 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1.5e-05
                                       HHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SG CS
                           Pkinase 102 kiakqilegleylHskgiiHrDlKpeNiLidekgelKitDF 142
                                        ++++i++ ++  +s giiH Dl   Ni+++  + + i+D+
  gi|298674656|ref|YP_003726406.1| 210 WFFNEIIQQIKNSYSLGIIHADLSEYNIFVH-PEGVEIIDW 249
                                       578999999**********************.777899987 PP

>> Tfb5  Transcription factor TFIIH complex subunit Tfb5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   5.7e-05      0.17       8      52 ..     204     247 ..     199     248 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.7e-05
                              Tfb5   8 vLveCDpaikqlilkldeqepsqkfiiedLDethlfvkeevveel 52 
                                        L+e D    ++i ++ ++  s  +i  dL e  +fv++e ve +
  gi|298674656|ref|YP_003726406.1| 204 KLLEPDWFFNEIIQQIKNSY-SLGIIHADLSEYNIFVHPEGVEII 247
                                       6888999999*********8.99*****************99977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2101.92
//
Query:       gi|298674657|ref|YP_003726407.1|  [L=131]
Description: hypothetical protein Metev_0710 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.3e-36  121.8   1.1    1.2e-35  121.4   1.1    1.1  1  DUF2111   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2111  Uncharacterized protein conserved in archaea (DUF2111)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.4   1.1   6.8e-40   1.2e-35       1      83 []      22     103 ..      22     103 .. 0.98

  Alignments for each domain:
  == domain 1  score: 121.4 bits;  conditional E-value: 6.8e-40
                           DUF2111   1 vhelvgklPvtirsknkkGvriekgkvvdedYtgpvLeevleegkvikkvpkeGaYkGvpvvvaPikekegkviaai 77 
                                       +h+l+g +P+tirsknk+G+r+e+g+vvd+dYtgp+Le+v++++k+i++vp+eG+YkG pvvv+P+++++g+ +aa+
  gi|298674657|ref|YP_003726407.1|  22 MHTLIG-IPITIRSKNKNGIRMERGEVVDRDYTGPILEQVIKTDKTIRDVPQEGVYKGRPVVVTPLHSSDGNLVAAL 97 
                                       699***.********************************************************************** PP

                           DUF2111  78 GvVDit 83 
                                       G+VD++
  gi|298674657|ref|YP_003726407.1|  98 GIVDLV 103
                                       ****86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 1006.11
//
Query:       gi|298674658|ref|YP_003726408.1|  [L=302]
Description: thioredoxin reductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-53  181.8   0.2      2e-53  181.6   0.2    1.0  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    5.1e-28   98.2   3.9    1.2e-20   74.0   0.1    2.1  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    4.7e-16   59.1   3.7    4.7e-13   49.5   0.1    2.9  3  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    1.1e-07   31.6   0.1    1.1e-07   31.6   0.1    2.3  2  FAD_oxidored   FAD dependent oxidoreductase
    1.2e-07   31.2   4.9     0.0014   17.7   0.5    3.9  4  FAD_binding_2  FAD binding domain
      2e-07   30.1   1.0     0.0027   16.5   0.2    2.8  3  HI0933_like    HI0933-like protein
    2.4e-06   27.4   6.2      0.017   14.8   0.0    2.9  3  DAO            FAD dependent oxidoreductase
    2.2e-05   23.7   7.5     0.0017   17.5   0.5    3.6  4  GIDA           Glucose inhibited division protein A
    6.2e-05   23.1   0.9    0.00012   22.2   0.1    1.8  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    8.8e-05   21.8   2.9      0.028   13.7   0.4    2.5  3  Thi4           Thi4 family
    0.00034   20.0   2.6     0.0068   15.7   0.2    2.5  2  FAD_binding_3  FAD binding domain
     0.0011   18.1   1.0        1.5    7.8   0.4    2.9  3  Lycopene_cycl  Lycopene cyclase protein
     0.0015   18.6   0.9       0.17   11.9   0.0    2.6  3  NAD_binding_9  FAD-NAD(P)-binding


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.6   0.2   1.4e-56     2e-53       2     291 ..       3     285 ..       2     288 .. 0.89

  Alignments for each domain:
  == domain 1  score: 181.6 bits;  conditional E-value: 1.4e-56
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH........HHHHCHHHHCCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias........evvkklnqgiell 70 
                                       d+++iGgGpAG+aa +++ ++g++++l+  e+t  +g+++ s+++++++++ +i                 ++i + 
  gi|298674658|ref|YP_003726408.1|   3 DLIIIGGGPAGIAAGIYAVRYGLDTYLL--ERTAIGGQISSSQEVENYPGFSSINGmelmntfkA----HAESIGVP 73 
                                       79**************************..999*******************9999*89844443....33345554 PP

                                       HCCT.CEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSEEE CS
                                       xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  71 lgee.vvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllpkriv 146
                                        +++ v+++ p+  k++l+++   ++ +i+++++++AtG++pr+lgipG+ +++g++v+++++++a  +k+++  ++
  gi|298674658|ref|YP_003726408.1|  74 IENKgVTGVRPEDDKIVLSTD---ENVDIEAKAVIIATGAKPRKLGIPGEDTYYGRGVSYCATCDAPFYKERD--VI 145
                                       554559*******99999654...5668*******************************************99..** PP

                                       EES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHT.TEEEEESCEEEEEEETTE....EEE. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx....xxx. RF
                       Pyr_redox_2 147 vvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealeke.Gvevklgtsvkeidgnge....kle. 217
                                       vvGgG++++  A  l++++ +v+ v++rd+l       +s+ le++ + + ++e+ + t+ +e++gn+      l+ 
  gi|298674658|ref|YP_003726408.1| 146 VVGGGNTAISDALILSNVANKVYQVHRRDELR------ASKVLEDRARSRdNIEFLWDTVLEEVKGNNFvesaLLRd 216
                                       *******************************7......9999999999988*****************987765558 PP

                                       EEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS--HHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 218 vvledgeeidadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDvaggkggpelaqaAv 291
                                       + +++ +ei  d v++ vG+ p+t+l+     +e de g+i ++ef++t+v+giya+GD+  +   ++ ++aA+
  gi|298674658|ref|YP_003726408.1| 217 LNTNELSEISIDGVFIYVGIDPNTDLI----DVEKDESGFIITNEFMETSVEGIYAAGDCR-KSPLWQVITAAS 285
                                       99999999****************997....9*****************************.555555555554 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   1.3   6.9e-09   9.5e-06       1      36 [.       5      39 ..       5      49 .. 0.90
   2 !   74.0   0.1   8.4e-24   1.2e-20      78     305 .]      54     270 ..      39     270 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 6.9e-09
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgnignsi 36
                                      iIiG+GPaG+aa+i + + gl++y  lE+ +ig  i
  gi|298674658|ref|YP_003726408.1|  5 IIIGGGPAGIAAGIYAVRYGLDTY-LLERTAIGGQI 39
                                      8********************765.9*****99776 PP

  == domain 2  score: 74.0 bits;  conditional E-value: 8.4e-24
                       Pyr_redox_3  78 lsrkealeYlrevaksfelpiklfeeVesvkkedegfevetske.tyeAkkviiAtGefdkPnklnipGeek...lv 150
                                       ++++e+++ +++ a+s  +pi+ ++ V+ v +ed++ +++t+++ ++eAk viiAtG   kP+kl+ipGe+      
  gi|298674658|ref|YP_003726408.1|  54 INGMELMNTFKAHAESIGVPIE-NKGVTGVRPEDDKIVLSTDENvDIEAKAVIIATGA--KPRKLGIPGEDTyygRG 127
                                       5677777777788888888886.678*****************989***********9..***********853234 PP

                       Pyr_redox_3 151 khyskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvke..e 225
                                       + y    ++  y++++v+V+Gg+n+a+  Al l +  ++V  v+r++e+++++   +   +++ ++++e l+++  e
  gi|298674658|ref|YP_003726408.1| 128 VSYCATCDAPFYKERDVIVVGGGNTAISDALILSNVANKVYQVHRRDELRASKVLED---RARSRDNIEFLWDTvlE 201
                                       5555556776799**********************************9999874444...44445555554443112 PP

                       Pyr_redox_3 226 kikvlfnaevkeikekeeeykvktedgkkvevkddvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpglf 302
                                         +v  n+ v++        +++t++ +++++ d v++ +G +p++++++   +e+de+g++ +t+e +et v+g++
  gi|298674658|ref|YP_003726408.1| 202 --EVKGNNFVESAL----LRDLNTNELSEISI-DGVFIYVGIDPNTDLID---VEKDESGFI-ITNEFMETSVEGIY 267
                                       ..355554444443....34678888888777.5556669*********9...888888876.56789********* PP

                       Pyr_redox_3 303 laG 305
                                        aG
  gi|298674658|ref|YP_003726408.1| 268 AAG 270
                                       *99 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.3    0.0011       1.6       2      31 ..       4      33 ..       3      37 .. 0.94
   2 ?   -1.3   0.0       2.4   3.4e+03      59      72 ..      75      88 ..      53     115 .. 0.58
   3 !   49.5   0.1   3.4e-16   4.7e-13       2      71 ..     144     208 ..     143     218 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0011
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvvers 31
                                      ++++GgG  g+ ++ ++ ++g +++++er 
  gi|298674658|ref|YP_003726408.1|  4 LIIIGGGPAGIAAGIYAVRYGLDTYLLERT 33
                                      68*************************995 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.4
                                      CSEEEEEEEEETTS CS
                         Pyr_redox 59 lntkveeiegsedg 72
                                       n+ v+ ++ ++d+
  gi|298674658|ref|YP_003726408.1| 75 ENKGVTGVRPEDDK 88
                                      34444444444444 PP

  == domain 3  score: 49.5 bits;  conditional E-value: 3.4e-16
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHT.TEEEECSEEEEEEEEETT CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekn.gievllntkveeiegsed 71 
                                       v+vvGgG++++  A +l++ ++kV+ v+r+d+l+      ask+l+++ + + +ie+l++t++ee++g++ 
  gi|298674658|ref|YP_003726408.1| 144 VIVVGGGNTAISDALILSNVANKVYQVHRRDELR------ASKVLEDRARSRdNIEFLWDTVLEEVKGNNF 208
                                       89********************************......*********9999**************9975 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.1   7.9e-11   1.1e-07       1      40 [.       3      41 ..       3      58 .. 0.92
   2 ?    0.1   0.9      0.28   3.8e+02       1      19 [.     143     161 ..     143     176 .. 0.71

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 7.9e-11
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGllts 40
                                      D++++GGgpaG+aA i A r G  + L+e++  +GG+ +s
  gi|298674658|ref|YP_003726408.1|  3 DLIIIGGGPAGIAAGIYAVRYGLDTYLLERT-AIGGQISS 41
                                      99**************************987.58999887 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.28
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAa 19 
                                       Dv+VvGGg   +  A+   
  gi|298674658|ref|YP_003726408.1| 143 DVIVVGGGNTAISDALILS 161
                                       9*******99988776555 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.5     1e-06    0.0014       1      42 [.       3      43 ..       3      50 .. 0.90
   2 !    9.8   0.0   0.00027      0.37     159     204 ..      64     113 ..      45     125 .. 0.81
   3 ?    0.8   0.0      0.15     2e+02       1      19 [.     143     161 ..     143     179 .. 0.77
   4 ?    1.8   0.0     0.074     1e+02     378     404 ..     255     275 ..     251     285 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1e-06
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG-- CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsq 42
                                      D+i+iG+G AG aA++ a + Gl++ ++e +   gg++  sq
  gi|298674658|ref|YP_003726408.1|  3 DLIIIGGGPAGIAAGIYAVRYGLDTYLLERTAI-GGQISSSQ 43
                                      89***************************9984.77776665 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00027
                                       EESEEEEEEEECTTEEEEEEEEET....TTTCEEEEEESEEEE-----GG CS
                     FAD_binding_2 159 qerteadeLivedgrvtGavvenp....esgrevrirakavvlatgGfgr 204
                                        +++e   + +e+++vtG+  e++    ++ ++v i+akav++atg+ +r
  gi|298674658|ref|YP_003726408.1|  64 KAHAESIGVPIENKGVTGVRPEDDkivlSTDENVDIEAKAVIIATGAKPR 113
                                       44444444556999********99**********************9776 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.15
                                       SEEEE--SHHHHHHHHHHH CS
                     FAD_binding_2   1 DviViGsGlAGLaAAleaa 19 
                                       DviV+G+G    + Al ++
  gi|298674658|ref|YP_003726408.1| 143 DVIVVGGGNTAISDALILS 161
                                       9*******88777776555 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.074
                                       BETTSBESTTEEESSBTEEE-STCEES CS
                     FAD_binding_2 378 tdengrvldadgqpipGLYAaGevaag 404
                                       t+e +++       ++G YAaG +  +
  gi|298674658|ref|YP_003726408.1| 255 TNEFMET------SVEGIYAAGDCRKS 275
                                       6677777......9********99855 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2   1.9e-06    0.0027       2      33 ..       3      34 ..       2      42 .. 0.88
   2 !   10.8   0.0   0.00011      0.15     109     165 ..      57     111 ..      51     116 .. 0.87
   3 ?   -0.7   0.0      0.31   4.3e+02       2      26 ..     143     167 ..     142     181 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.9e-06
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekak 33
                                      d+i+iGgG+AG+ a i a + g ++ lle++ 
  gi|298674658|ref|YP_003726408.1|  3 DLIIIGGGPAGIAAGIYAVRYGLDTYLLERTA 34
                                      79***************************973 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----S CS
                       HI0933_like 109 edivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGl 165
                                        ++++++++++++ gv ++ ++ v++v+ e+d+ + ++t+++  +ea+++++AtG +
  gi|298674658|ref|YP_003726408.1|  57 MELMNTFKAHAESIGVPIE-NKGVTGVRPEDDK-IVLSTDENVDIEAKAVIIATGAK 111
                                       5788899999999999997.578****888888.9999999**************86 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.31
                                       SEEEE--SHHHHHHHHHHHHTT--E CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrV 26 
                                       dviv+GgG   +  A+ +++  ++V
  gi|298674658|ref|YP_003726408.1| 143 DVIVVGGGNTAISDALILSNVANKV 167
                                       89******98877777776666665 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   3.4   0.00018      0.25       1      34 [.       3      38 ..       3      46 .. 0.85
   2 !   14.8   0.0   1.2e-05     0.017     137     207 ..      48     115 ..      43     138 .. 0.75
   3 ?    0.8   0.0       0.2   2.8e+02       1      19 [.     143     161 ..     143     180 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00018
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiags 34
                                      d++iiGGG +G+++  ++ r g  + lle+  i g+
  gi|298674658|ref|YP_003726408.1|  3 DLIIIGGGPAGIAAGIYAVRYGldTYLLERTAIGGQ 38
                                      789****************************55554 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.2e-05
                                       ETTEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEE.EEEEEEEE--GGGHHHH CS
                               DAO 137 ypdtgqvdpakltaalaraaealGveilegtevtgleeedgkvwgverttpgen.daadavVnaaGawsdll 207
                                       yp+   ++  +l++ + + ae+ Gv i ++  vtg++ ed+k++ +   t++++  +a+av++a+Ga  ++l
  gi|298674658|ref|YP_003726408.1|  48 YPGFSSINGMELMNTFKAHAESIGVPIENK-GVTGVRPEDDKIV-L--STDENVdIEAKAVIIATGAKPRKL 115
                                       56667889999**************99998.*****77765533.3..333333346799******987744 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.2
                                       EEEEECTSHHHHHHHHHHH CS
                               DAO   1 dvviiGGGiiGlstAyeLa 19 
                                       dv+++GGG + +s A+ L+
  gi|298674658|ref|YP_003726408.1| 143 DVIVVGGGNTAISDALILS 161
                                       8*******98888887775 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.5   1.3e-06    0.0017       1      29 [.       3      39 ..       3      70 .. 0.77
   2 !    7.2   0.1    0.0017       2.3     111     150 ..      72     110 ..      57     136 .. 0.74
   3 ?    0.5   0.0      0.18   2.5e+02       1      26 [.     143     168 ..     143     181 .. 0.81
   4 ?   -0.1   0.0      0.28   3.9e+02     349     391 ..     258     301 ..     253     302 .] 0.73

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.3e-06
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEE........E CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi........t 29
                                      d+i+iGgG AG++A + a r G+++ L+         
  gi|298674658|ref|YP_003726408.1|  3 DLIIIGGGPAGIAAGIYAVRYGLDTYLLertaiggqI 39
                                      689************************9665555443 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0017
                                       EEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                              GIDA 111 leiieeeveeliveekkvkgvvtedgetikakavviatGt 150
                                       + i ++ v+ + +e++k+ ++ t+++  i+akav+iatG+
  gi|298674658|ref|YP_003726408.1|  72 VPIENKGVTGVRPEDDKI-VLSTDENVDIEAKAVIIATGA 110
                                       557788889998866666.578889999***********9 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.18
                                       CEEEE-SSHHHHHHHHHHHHTT--EE CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGakvl 26 
                                       dviV+GgG   +  Al +++   kv 
  gi|298674658|ref|YP_003726408.1| 143 DVIVVGGGNTAISDALILSNVANKVY 168
                                       79******998888888888777765 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.28
                                       TSBBSSSBTEEE-CGGGTB..-SHHHHHHHHHHHHHHHHHHHCTS CS
                              GIDA 349 tLetkkvkgLflAGqinGt..eGYeEaaaqGllAGinaarkakgk 391
                                        +et+ v+g+++AG+      +  + aa+ G +A+  a  ++++k
  gi|298674658|ref|YP_003726408.1| 258 FMETS-VEGIYAAGDCRKSplWQVITAASDGAIAAAKAYEYIRNK 301
                                       46676.999999999765433656778888999998888888775 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.1   8.6e-08   0.00012       1      54 [.       6      62 ..       6      69 .. 0.81
   2 ?   -1.9   0.0         3   4.2e+03       1      16 [.     146     161 ..     146     171 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 8.6e-08
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECE....TTCEECTS---EEE CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyev....pgvrvdygahifhg 54
                                      I+G+G +G +a  ++ ++g+d  lle+ + +GG+++s +     pg+    g+  +++
  gi|298674658|ref|YP_003726408.1|  6 IIGGGPAGIAAGIYAVRYGLDTYLLER-TAIGGQISSSQEvenyPGFSSINGMELMNT 62
                                      9************************98.59******9966555666655556666555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3
                                       EE--SHHHHHHHHHHH CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLa 16 
                                       +vG+G ++ + A  L+
  gi|298674658|ref|YP_003726408.1| 146 VVGGGNTAISDALILS 161
                                       89**988877666665 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.4     2e-05     0.028      18      56 ..       2      38 ..       1      45 [. 0.88
   2 ?   -3.7   0.0         4   5.5e+03     156     167 ..      98     109 ..      76     111 .. 0.73
   3 !    8.1   0.0     0.001       1.4      15      39 ..     139     163 ..     128     173 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2e-05
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TT CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspGGG 56
                                       D++i+G+G++G++a+ y  +  +l + +ler  ++GG 
  gi|298674658|ref|YP_003726408.1|  2 NDLIIIGGGPAGIAAGIYAVRY-GLDTYLLERT-AIGGQ 38
                                      69**************999998.********85.77775 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4
                                       EEEEEEEEE--G CS
                              Thi4 156 virakvvvdatG 167
                                        i+ak+v+ atG
  gi|298674658|ref|YP_003726408.1|  98 DIEAKAVIIATG 109
                                       378888888887 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.001
                                       HTEEEEEEE--SHHHHHHHHHHHHC CS
                              Thi4  15 yaesDvvivGaGssGLtaayylakk 39 
                                       y e Dv++vG+G + ++ a +l++ 
  gi|298674658|ref|YP_003726408.1| 139 YKERDVIVVGGGNTAISDALILSNV 163
                                       899****************999875 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   4.9e-06    0.0068       4      34 ..       4      34 ..       2      47 .. 0.92
   2 ?    3.7   0.2     0.022        31       3      33 ..     143     173 ..     141     188 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.9e-06
                                      EEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                     FAD_binding_3  4 VlIVGaGpaGlmlallLseaGvrvvlvekrs 34
                                       +I+G+GpaG+ ++    ++G ++ l+e+ +
  gi|298674658|ref|YP_003726408.1|  4 LIIIGGGPAGIAAGIYAVRYGLDTYLLERTA 34
                                      68**************************975 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.022
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekr 33 
                                       dV++VG+G + ++ al+Ls+   +v  v +r
  gi|298674658|ref|YP_003726408.1| 143 DVIVVGGGNTAISDALILSNVANKVYQVHRR 173
                                       8999999999999999998765555555554 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.4    0.0011       1.5       1      31 [.       3      31 ..       3      37 .. 0.76
   2 !    6.6   0.0    0.0024       3.3      88     148 ..      58     116 ..      38     135 .. 0.72
   3 ?    0.7   0.0      0.15   2.1e+02       1      27 [.     143     167 ..     143     203 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0011
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlie 31
                                      D+++iG+GpAg++  a + + ++gl   l+e
  gi|298674658|ref|YP_003726408.1|  3 DLIIIGGGPAGIA--AGIYAVRYGLDTYLLE 31
                                      9**********75..5555577777777665 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0024
                     Lycopene_cycl  88 rlkeellerlvengvklleakvesveeeeageslvvleggrkirarlvvdarglaslkkar 148
                                       +l +  + +  + gv   +  v+ v++e++ + +  +++++ i+a++v+ a+g a+++k  
  gi|298674658|ref|YP_003726408.1|  58 ELMNTFKAHAESIGVPIENKGVTGVRPEDD-KIVLSTDENVDIEAKAVIIATG-AKPRKLG 116
                                       555555555556677888888999999999.7777888888************.5555443 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.15
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkv 27 
                                       Dv+v+G+G   +s A  l  ++ + kv
  gi|298674658|ref|YP_003726408.1| 143 DVIVVGGGNTAISDALIL--SNVANKV 167
                                       99******9888877766..5555555 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.2      0.02        28       2      39 ..       6      37 ..       5      48 .. 0.69
   2 !   11.9   0.0   0.00012      0.17     111     155 ..      66     110 ..      57     111 .. 0.84
   3 ?   -2.3   0.0       2.8   3.8e+03       2      16 ..     146     160 ..     145     190 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.02
                     NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdpsepgag 39
                                      i+G+Gp+G+a+    ++       l+  l +++ +g g
  gi|298674658|ref|YP_003726408.1|  6 IIGGGPAGIAAGIYAVRY-----GLDTYLLERTAIG-G 37
                                      9********987766665.....3566666666665.5 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00012
                     NAD_binding_9 111 lpegvtvevhraevvdleeradgqavlladgaslaadaVvLAlGh 155
                                         e++ v + ++ v+ +++++d+  + ++++  ++a+aV++A+G 
  gi|298674658|ref|YP_003726408.1|  66 HAESIGVPIENKGVTGVRPEDDKIVLSTDENVDIEAKAVIIATGA 110
                                       3466888899999**********9999999999**********95 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.8
                     NAD_binding_9   2 ivGaGprGlavlerL 16 
                                       +vG+G ++++ +  L
  gi|298674658|ref|YP_003726408.1| 146 VVGGGNTAISDALIL 160
                                       678887777655444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2159.98
//
Query:       gi|298674659|ref|YP_003726409.1|  [L=80]
Description: thioredoxin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-10   41.3   0.0    1.2e-10   41.3   0.0    1.0  1  Thioredoxin_3  Thioredoxin domain
    9.2e-06   25.6   0.0    9.8e-06   25.5   0.0    1.1  1  Thioredoxin    Thioredoxin
    1.6e-05   25.0   0.0    2.1e-05   24.6   0.0    1.2  1  Glutaredoxin   Glutaredoxin
     0.0093   15.8   0.1      0.012   15.4   0.1    1.3  1  DSBA           DSBA-like thioredoxin domain
  ------ inclusion threshold ------
      0.029   14.8   0.0      0.034   14.5   0.0    1.1  1  DUF836         Glutaredoxin-like domain (DUF836)
       0.12   12.7   0.0       0.14   12.5   0.0    1.2  1  ArsD           Arsenical resistance operon trans-acting repre


Domain annotation for each model (and alignments):
>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.0     4e-14   1.2e-10       7      74 ..       9      78 ..       1      80 [] 0.83

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 4e-14
                                      SSSSTTCHHHHHHHHHHCHCCTCEC...EEECCTTHHHHHHCT-SSSSEEECTTCEEEESS---CCHHHHH CS
                     Thioredoxin_3  7 gpgCakCpklekavkeaaaekgika...evekvtdfeeiekygVmsvPalvidgkvvvsGkvpseeeirkl 74
                                       + C+ Cp + k+++ +  + ++++   +v+  +  + i+++g++ vPa+++dg+v + G vp++++  k 
  gi|298674659|ref|YP_003726409.1|  9 AKWCHVCPSAIKLWEDLHSKYDFEYkelDVDSEEGQDVISEHGIRGVPATIVDGEVAFIG-VPDKDKAIKA 78
                                      455******************999977778888888888*********************.****996554 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   3.3e-09   9.8e-06      25      77 ..       7      59 ..       2      79 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 3.3e-09
                                      EE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEE CS
                       Thioredoxin 25 FyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlk 77
                                       yA+wC  C +    +e+l +++  + k + vd +e +d+ ++++++g+P+ +
  gi|298674659|ref|YP_003726409.1|  7 LYAKWCHVCPSAIKLWEDLHSKYDFEYKELDVDSEEGQDVISEHGIRGVPATI 59
                                      6***********************9*************************864 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   7.1e-09   2.1e-05       7      59 ..      10      64 ..       2      65 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 7.1e-09
                                      TSSHHHHHHHHHHHHTT....GGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEETTEE CS
                      Glutaredoxin  7 ptCpyCkkakrlLkelg....vkfeeidvdkdeeireelkelsgvrtvPqvfidgkh 59
                                      ++C  C+ a++l ++l     ++++e dvd + e ++ + e  g+r vP   +dg++
  gi|298674659|ref|YP_003726409.1| 10 KWCHVCPSAIKLWEDLHskydFEYKELDVDSE-EGQDVISEH-GIRGVPATIVDGEV 64
                                      89***********8887442244555555553.555555555.************96 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   3.9e-06     0.012     160     188 ..      47      75 ..      28      80 .] 0.81

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.9e-06
                                       HHHTT-SSSSEEEETTCEEEESSSSHHHH CS
                              DSBA 160 aqslgvtGvPtvvvdgkrmvfGadrldtl 188
                                         + g++GvP+++vdg++++ G+++ d+ 
  gi|298674659|ref|YP_003726409.1|  47 ISEHGIRGVPATIVDGEVAFIGVPDKDKA 75 
                                       5678*************999999987765 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.2e-05     0.034       1      38 [.       3      42 ..       3      58 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.2e-05
                                      -EEEEE-TT-HHHHHHHHHHHHHCCCTTEEEEEEETT..T CS
                            DUF836  1 kltLyskpgChlCeqakekLkelkleegleleviDIa..k 38
                                      k+tL+  + Ch+C +a ++ ++l+ + ++e ++ D++  +
  gi|298674659|ref|YP_003726409.1|  3 KVTLLYAKWCHVCPSAIKLWEDLHSKYDFEYKELDVDseE 42
                                      68999999****************************9443 PP

>> ArsD  Arsenical resistance operon trans-acting repressor ArsD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.6e-05      0.14      59      87 ..      41      69 ..      32      80 .] 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.6e-05
                              ArsD 59 kavkellekkgaeaLPlvlvdgeivktgr 87
                                      ++ +++++++g   +P ++vdge++  g 
  gi|298674659|ref|YP_003726409.1| 41 EEGQDVISEHGIRGVPATIVDGEVAFIGV 69
                                      566889******************98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.75
# Mc/sec: 323.53
//
Query:       gi|298674660|ref|YP_003726410.1|  [L=235]
Description: N-acetyltransferase GCN5 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-11   45.1   0.0    1.5e-11   44.5   0.0    1.3  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    6.4e-09   36.1   0.1    1.4e-08   35.0   0.0    1.6  2  Acetyltransf_7   Acetyltransferase (GNAT) domain
    1.7e-07   31.2   0.0    3.2e-07   30.3   0.0    1.4  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    0.00057   20.0   0.0    0.00095   19.3   0.0    1.3  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
     0.0011   18.9   0.1     0.0043   17.0   0.0    2.0  2  FR47             FR47-like protein
     0.0011   19.6   0.0     0.0017   19.1   0.0    1.3  1  Acetyltransf_3   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.0   5.1e-15   1.5e-11      17     117 .]      43     135 ..      28     135 .. 0.78

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 5.1e-15
                                       HHHHHHHHHHHHHSTTCEEEE.EEET.TEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHH CS
                    Acetyltransf_1  17 edaseeefeesfsleaegllv.aeed.geliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerare 91 
                                         ++++ f +s s++ ++++v a  + + l+Gf ++   ++    ++ ++s+ ++++yr kG+G++Ll a++++++ 
  gi|298674660|ref|YP_003726410.1|  43 FATPYRFFLKS-SIDSGHIIVvAFSIpNVLVGFTRFEYTNQ----CCLLRSIEINSSYRQKGIGKTLLSAALQYLLG 114
                                       33333334444.56666666645555688*****9999999....*******************************9 PP

                                       TTESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  92 egikkivlaveedndaairlYeklGF 117
                                         +  i   + +dn++a+++++klGF
  gi|298674660|ref|YP_003726410.1| 115 S-C--I--VTKPDNERAQNFFKKLGF 135
                                       9.3..3..35788********88**9 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.0   4.8e-12   1.4e-08       3      75 ..      58     136 ..      55     137 .. 0.71
   2 ?   -3.7   0.0       5.8   1.7e+04      66      74 ..     179     187 ..     169     188 .. 0.76

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 4.8e-12
                                       EEEEEEEET..TEEEEEEEEEEES.TCTEE.EEE-GGGTTSSHHHHHHHHTT...SE.EEEEEEEETHHHHHHHHHH CS
                    Acetyltransf_7   3 gevfVaedd..gkivGfialslld.aeitr.laVdpeyrgkGiGraLleaae...kg.iileqlelnaekaikfYek 71 
                                       g+++V+     +  vGf +++ ++ +++ r + ++ +yr kGiG+ Ll aa     g +i++  + ++e+a++f++k
  gi|298674660|ref|YP_003726410.1|  58 GHIIVVAFSipNVLVGFTRFEYTNqCCLLRsIEINSSYRQKGIGKTLLSAALqylLGsCIVT--KPDNERAQNFFKK 132
                                       555554444456668*99999998755555799***************97333455545422..334459******* PP

                                       TTEE CS
                    Acetyltransf_7  72 lGFe 75 
                                       lGF+
  gi|298674660|ref|YP_003726410.1| 133 LGFI 136
                                       ***7 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 5.8
                                       HHHHHHTTE CS
                    Acetyltransf_7  66 ikfYeklGF 74 
                                       ik+Ye l F
  gi|298674660|ref|YP_003726410.1| 179 IKLYEDLQF 187
                                       789998877 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   1.1e-10   3.2e-07      22     110 ..      51     139 ..      32     147 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 1.1e-10
                   Acetyltransf_10  22 lrerieegealllvaeeggkivGvielrdgshisll...fVdpeyrgqGigkaLleaveeeaekdgikleltvnasp 95 
                                       l++ i++g+ +++++   + +vG+ + + +++ +ll    ++++yr++Gigk Ll a+++++   g+   +t   + 
  gi|298674660|ref|YP_003726410.1|  51 LKSSIDSGHIIVVAFSIPNVLVGFTRFEYTNQCCLLrsiEINSSYRQKGIGKTLLSAALQYLL--GSC-IVTKPDNE 124
                                       577887778878888888*********6666666655559*********************83..222.45555555 PP

                   Acetyltransf_10  96 yavpfYeklGFkavg 110
                                        a++f++klGF + +
  gi|298674660|ref|YP_003726410.1| 125 RAQNFFKKLGFIRAN 139
                                       ***********8865 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   3.2e-07   0.00095      11      53 ..      71     112 ..      64     132 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 3.2e-07
                   Acetyltransf_CG  11 evafleYevrkegvldfthTeVpeelrGkGiAkkLvkaaldda 53 
                                        v+f ++e   ++   +  +e++ ++r kGi+k L  aal++ 
  gi|298674660|ref|YP_003726410.1|  71 LVGFTRFE-YTNQCCLLRSIEINSSYRQKGIGKTLLSAALQYL 112
                                       68999999.8888***************************997 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.4e-06    0.0043      19      80 ..      81     138 ..      78     142 .. 0.84
   2 ?   -2.6   0.0       1.8   5.4e+03      69      79 ..     179     189 ..     179     192 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.4e-06
                                       -TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  19 kdggelgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGfeki 80 
                                       ++   l +++++ + r++G g+ l +a  + +      + +v++++N++++++++klGf  +
  gi|298674660|ref|YP_003726410.1|  81 NQCCLLRSIEINSSYRQKGIGKTLLSAALQYLL----GSCIVTKPDNERAQNFFKKLGFIRA 138
                                       566778899999999******998887777665....46899*****************976 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.8
                                       HHHHHHHT-EE CS
                              FR47  69 irlyeklGfek 79 
                                       i+lye l f++
  gi|298674660|ref|YP_003726410.1| 179 IKLYEDLQFRL 189
                                       589*****997 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   5.6e-07    0.0017      66     137 ..      72     135 ..      38     136 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 5.6e-07
                    Acetyltransf_3  66 iGsvglrdleeedeeaelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGf 137
                                       +G+ ++ + ++    +  ++ +++s+++kG+++  ++a+l+y+         ++v++++Ne+ ++ ++klGf
  gi|298674660|ref|YP_003726410.1|  72 VGFTRFEYTNQCC--LLRSIEINSSYRQKGIGKTLLSAALQYLL------GSCIVTKPDNERAQNFFKKLGF 135
                                       5555555444432..4445779999******************3......3579*****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1523.04
//
Query:       gi|298674661|ref|YP_003726411.1|  [L=490]
Description: hypothetical protein Metev_0714 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00064   19.8  32.0     0.0053   16.8   4.0    4.3  4  DUF1664          Protein of unknown function (DUF1664)
     0.0008   18.4  40.5       0.19   10.6   8.4    3.3  3  Spc7             Spc7 kinetochore protein
  ------ inclusion threshold ------
       0.06   14.0   0.5       0.06   14.0   0.5    3.2  3  AKNA             AT-hook-containing transcription factor
        0.2   11.7   0.1        0.2   11.7   0.1    3.3  4  PilJ             Type IV pili methyl-accepting chemotaxis tra
        0.2   11.2  43.0        0.1   12.2   3.5    3.8  4  DUF4795          Domain of unknown function (DUF4795)
       0.28    9.8  44.3      0.058   12.0   9.9    3.2  3  AAA_13           AAA domain
       0.43    9.8  31.3       0.63    9.3   3.9    3.6  3  DUF3450          Protein of unknown function (DUF3450)
       0.43   11.0  33.5        1.1    9.7   1.6    3.3  3  Fez1             Fez1
       0.49   10.9  47.0        7.1    7.2   1.4    7.3  5  NPV_P10          Nucleopolyhedrovirus P10 protein
       0.67    9.5  27.6        0.3   10.6   1.1    3.1  3  Exonuc_VII_L     Exonuclease VII, large subunit
       0.93    9.8  43.0       0.39   11.0   8.2    5.0  5  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
          1    9.0  13.8        5.1    6.7   0.5    3.9  3  GARP             Glutamic acid/alanine-rich protein of Trypan
        1.1    8.3  39.4       0.24   10.4  20.0    3.1  3  AIP3             Actin interacting protein 3
        1.2    9.2  40.1        2.6    8.1   3.4    5.0  5  Laminin_II       Laminin Domain II
        1.4    9.4  36.9      0.046   14.3   2.8    4.1  2  APG6_N           Apg6 coiled-coil region
        1.6    8.7  40.0      0.062   13.3   7.4    4.2  4  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
        1.7    9.3  33.4       0.49   11.0   4.7    4.8  4  HIP1_clath_bdg   Clathrin-binding domain of Huntingtin-intera
        2.1    8.5  26.7        2.4    8.3   2.0    5.0  6  COG2             COG (conserved oligomeric Golgi) complex com
        2.2    7.9  36.6       0.98    9.1   1.7    4.6  4  GrpE             GrpE
        2.3    7.7  12.7       0.51    9.9   0.6    3.6  3  DUF3053          Protein of unknown function (DUF3053)
          4    6.8  23.8       0.95    8.9   1.8    4.1  4  DUF4349          Domain of unknown function (DUF4349)
        4.1    8.1  18.4        4.5    8.0   0.4    5.2  4  SlyX             SlyX
        4.2    7.6  48.7       0.21   11.8   5.1    4.8  4  Fib_alpha        Fibrinogen alpha/beta chain family
        4.7    8.0  30.9       0.57   10.9   2.9    5.5  4  Occludin_ELL     Occludin homology domain
        6.2    7.7   6.5        8.4    7.3   1.3    4.2  1  M                M protein repeat
        6.4    7.3  44.6      0.068   13.7   7.8    4.9  2  DUF16            Protein of unknown function DUF16
        8.3    5.6  35.0      0.076   12.2   4.9    3.9  4  TMPIT            TMPIT-like protein
        8.7    6.8  28.4        8.5    6.9   1.6    6.8  5  LPP              Lipoprotein leucine-zipper
        9.7    5.2  33.7        3.3    6.7   5.2    3.4  3  Atg14            Vacuolar sorting 38 and autophagy-related su


Domain annotation for each model (and alignments):
>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   2.9    0.0029       1.8      44     121 ..      35     112 ..      31     115 .. 0.64
   2 !   16.8   4.0   8.6e-06    0.0053      36     121 ..     233     324 ..     226     326 .. 0.77
   3 !    7.8   5.4     0.005       3.1      44     102 ..     352     412 ..     345     429 .. 0.78
   4 ?   -0.5   0.1         2   1.2e+03      62      77 ..     456     471 ..     431     481 .. 0.41

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0029
                           DUF1664  44 esvskqleqvs.eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskler 119
                                       ++v++ +++   ++l++   +L+sr++++++ +de ++  +++ +++++   ++++  +d+++++  ++++ ++l+r
  gi|298674661|ref|YP_003726411.1|  35 KNVTEYMDRSDkKELENEISDLKSRLENLQQYVDERTDSNSQTISQLKD-DVKTKTNYDDFNQLNYSFNSFSKRLKR 110
                                       5566666665425666777777777777777777776666666555543.233445567888888888888888888 PP

                           DUF1664 120 ie 121
                                       i 
  gi|298674661|ref|YP_003726411.1| 111 IA 112
                                       86 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 8.6e-06
                           DUF1664  36 krslsdavesvs...kqleqvseslaatkr...hLssridrvdkkldeqkeiskeikeevtevredlseigedvesv 106
                                         sl+ av++v+   ++l+++ +sl + k+   +Ls++++++++ +++q+e + + +e++++++++++e+ + ++  
  gi|298674661|ref|YP_003726411.1| 233 TGSLEYAVDKVTiheTKLNELNDSLIDLKDktsNLSRDLESINEIQNKQSESIDNNSENISAINNQIEEMTNAINLH 309
                                       56788888888733345777777766555422268899999999999999999999999999999999999999999 PP

                           DUF1664 107 keaveglesklerie 121
                                        +a+++l+++l++i+
  gi|298674661|ref|YP_003726411.1| 310 TRAIKTLNKRLADIQ 324
                                       999999999999887 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.005
                           DUF1664  44 esvskqleqvseslaatkrhLssridrvdkkldeqkei..skeikeevtevredlseiged 102
                                        ++ ++++++ ++l++ k+++ + ++++++ l++  +    ++i++e+++++ ++s+i++ 
  gi|298674661|ref|YP_003726411.1| 352 MEMDEKIQNMNNDLTSFKQEILESLENIQSVLENKVDDdkLTKIEDELSSIKTQISNIQDT 412
                                       5678899999999999999999999999999999876511456788999999999999875 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 2
                           DUF1664  62 rhLssridrvdkklde 77 
                                       + +s+++ ++ +kl++
  gi|298674661|ref|YP_003726411.1| 456 NTISKNLSEILDKLEN 471
                                       2222222222233333 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   3.2   0.00034      0.21     234     277 ..      44      87 ..       5     122 .. 0.62
   2 !   10.6   8.4   0.00031      0.19     160     242 ..     248     326 ..     231     341 .. 0.64
   3 !    8.6  13.9    0.0012      0.75     152     283 ..     345     474 ..     331     481 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00034
                              Spc7 234 ekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevka 277
                                       ++ +el++++s+l++++++ +++++e+ +++++ +s+lk+ vk+
  gi|298674661|ref|YP_003726411.1|  44 SDKKELENEISDLKSRLENLQQYVDERTDSNSQTISQLKDDVKT 87 
                                       33456666777777777777777777777777777777776665 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00031
                              Spc7 160 kqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleeki 236
                                        + +el++ l +l+ + ++l++ le+++e    +++ ++e++ +  e++++++++iee  + ++  ++ +++l++++
  gi|298674661|ref|YP_003726411.1| 248 TKLNELNDSLIDLKDKTSNLSRDLESINE----IQNKQSESIDNNSENISAINNQIEEMTNAINLHTRAIKTLNKRL 320
                                       45667777777777777777777777777....44445566666666666666666666666666666666666666 PP

                              Spc7 237 eelkeq 242
                                       ++++++
  gi|298674661|ref|YP_003726411.1| 321 ADIQNS 326
                                       655554 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0012
                              Spc7 152 eedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeq 228
                                       +++++ L++  e+++++ ++l++ k+e+ e le++q+  e+  ++d ++L ++ +el+++k++i++ ++  ++ q +
  gi|298674661|ref|YP_003726411.1| 345 KAERNDLMEMDEKIQNMNNDLTSFKQEILESLENIQSVLEN--KVDDDKLTKIEDELSSIKTQISNIQD--TSIQPD 417
                                       789999*******************************7776..9*********************6665..455666 PP

                              Spc7 229 leeleekieelkeqkseleeeiaeae.rvleeckgwsesevsr.lkeevkaleeltg 283
                                       +++ + ++++ +    e+ ++++ a  + le++ +++ + +s+ l e +++le+++ 
  gi|298674661|ref|YP_003726411.1| 418 INNTDGELDNDDLTVFETLKNMETATfKQLEKQSDSDGNTISKnLSEILDKLENQSH 474
                                       666666666666666666666666653566666666666665326666777777765 PP

>> AKNA  AT-hook-containing transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.5   9.7e-05      0.06      39      79 ..      44      84 ..      16     105 .. 0.80
   2 ?   -0.1   0.1       2.4   1.5e+03      54      76 ..     249     271 ..     241     290 .. 0.62
   3 ?   -1.9   0.1       8.6   5.3e+03      27      76 ..     325     372 ..     297     386 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9.7e-05
                              AKNA 39 dpsreleaeIyqlgqrleeLkdqtdqlkqkveefskdiaqd 79
                                      + ++ele eI+ l+ rle L+  +d       +  ++++ d
  gi|298674661|ref|YP_003726411.1| 44 SDKKELENEISDLKSRLENLQQYVDERTDSNSQTISQLKDD 84
                                      45699****************99998766666655555555 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2.4
                              AKNA  54 rleeLkdqtdqlkqkveefskdi 76 
                                       +l+eL d    lk k+ + s+d+
  gi|298674661|ref|YP_003726411.1| 249 KLNELNDSLIDLKDKTSNLSRDL 271
                                       45555555555555555555554 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 8.6
                              AKNA  27 klssskgqpgkfdpsreleaeIyqlgqrleeLkdqtdqlkqkveefskdi 76 
                                       ++++  ++  + d ++ l a+    +  l e+ +++ ++ +   +f ++i
  gi|298674661|ref|YP_003726411.1| 325 NSPDNDTETYETDLESRLDAK--AERNDLMEMDEKIQNMNNDLTSFKQEI 372
                                       444444445555566666666..334445555666655555555555554 PP

>> PilJ  Type IV pili methyl-accepting chemotaxis transducer N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00032       0.2      10     104 ..      20     117 ..      14     130 .. 0.67
   2 ?   -0.5   0.1         2   1.2e+03      85      85 ..     285     285 ..     242     338 .. 0.52
   3 ?   -0.5   0.2         2   1.2e+03      45      45 ..     336     336 ..     287     397 .. 0.51
   4 ?   -0.6   0.1       2.2   1.3e+03      58      92 ..     373     410 ..     346     427 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00032
                              PilJ  10 aaaINvAGslRMqsqRlakeallaaagaydaaearaqlretiaqfdrtlaalrlgdpapgllvpae........... 75 
                                        + +  +G    qsq+ ++e        y + +++++l++ i+++  +l++l+++ ++++    ++           
  gi|298674661|ref|YP_003726411.1|  20 TKNVDSSGNPETQSQKNVTE--------YMDRSDKKELENEISDLKSRLENLQQYVDERTDSNSQTisqlkddvktk 88 
                                       56677888888999999955........4556677777777777777777777776666666666566666668554 PP

                              PilJ  76 avraqleaveqlWqelkkpaeaalaqqdd 104
                                       +  +++++++  ++ + k ++++++++d+
  gi|298674661|ref|YP_003726411.1|  89 TNYDDFNQLNYSFNSFSKRLKRIAKEEDA 117
                                       44455556666677777777777777776 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2
                              PilJ  85 e 85 
                                       +
  gi|298674661|ref|YP_003726411.1| 285 I 285
                                       2 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 2
                              PilJ  45 a 45 
                                       +
  gi|298674661|ref|YP_003726411.1| 336 T 336
                                       1 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 2.2
                              PilJ  58 laalrlgdpapgllvpae...avraqleaveqlWqelk 92 
                                       l++l++ ++    +v ++   ++ ++l+++ ++ ++ +
  gi|298674661|ref|YP_003726411.1| 373 LESLENIQSVLENKVDDDkltKIEDELSSIKTQISNIQ 410
                                       34444444444444443344444455544444444444 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   3.5   0.00017       0.1      82     150 ..      45     116 ..      29     125 .. 0.84
   2 ?    2.7   0.4      0.13        83      98     136 ..     237     276 ..     186     286 .. 0.60
   3 ?    1.6  30.8      0.29   1.8e+02       6     150 ..     268     444 ..     249     464 .. 0.65
   4 ?    0.7   0.4      0.55   3.4e+02      83     109 ..     448     474 ..     426     479 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                           DUF4795  82 srdqfDeakkeLekmleellekleeqeealkkaldtLqeelkekldrlelepLkeqle...erlkelqkelq 150
                                       +++++++ +++L+  le l + ++e  ++  + +++L++++k+k + +++++L   ++   +rlk ++ke +
  gi|298674661|ref|YP_003726411.1|  45 DKKELENEISDLKSRLENLQQYVDERTDSNSQTISQLKDDVKTKTNYDDFNQLNYSFNsfsKRLKRIAKEED 116
                                       445599999*********************************************999977777777776544 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.13
                           DUF4795  98 eellekleeqeealkkaldtLqeelkekld..rlelepLke 136
                                       e +++k++ +e +l+++ d L  +lk k      +le++ e
  gi|298674661|ref|YP_003726411.1| 237 EYAVDKVTIHETKLNELNDSLI-DLKDKTSnlSRDLESINE 276
                                       5556666666666666666666.555554433333333333 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.29
                           DUF4795   6 aellkklqeaieklqeelekleekvkelekrledkekklealkkqieelekvkadkeev..eeelaekadke.aLat 79 
                                       ++ l+ ++e   k +e++++++e  + +++++e+    ++ ++ +i+ l+k+ ad ++   ++ +++  d e  L++
  gi|298674661|ref|YP_003726411.1| 268 SRDLESINEIQNKQSESIDNNSENISAINNQIEEMTNAINLHTRAIKTLNKRLADIQNSpdNDTETYETDLEsRLDA 344
                                       44478888888888999999999999999**********************99998777336678999997526999 PP

                           DUF4795  80 kvsrdq...fDeakkeLekmleellekleeqeealkkaldtLqeelkekld.......rlelepLkeqle....... 139
                                       k++r++   +       +++++ + + l++  +++ + l+++q+ l++k+d       ++el+++k+q+        
  gi|298674661|ref|YP_003726411.1| 345 KAERNDlmeM-------DEKIQNMNNDLTSFKQEILESLENIQSVLENKVDddkltkiEDELSSIKTQISniqdtsi 414
                                       9999885445.......555555555555555555555555665556666644444444455555555443333333 PP

                           DUF4795 140 ...................erlkelqkelq 150
                                                          e+lk+++++  
  gi|298674661|ref|YP_003726411.1| 415 qpdinntdgeldnddltvfETLKNMETATF 444
                                       333335555555555555555555554444 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.55
                           DUF4795  83 rdqfDeakkeLekmleellekleeqee 109
                                       ++q D+  + ++k+l+e+l+kle+q++
  gi|298674661|ref|YP_003726411.1| 448 EKQSDSDGNTISKNLSEILDKLENQSH 474
                                       445567777778888999999998876 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   6.3   0.00075      0.46     312     393 ..      35     116 ..      11     123 .. 0.65
   2 ?   12.0   9.9   9.4e-05     0.058     332     457 ..     199     331 ..     138     336 .. 0.75
   3 ?    0.2  13.3      0.37   2.3e+02     316     407 ..     344     433 ..     328     480 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00075
                            AAA_13 312 easensafeedkeelkaeaealeeqLkglqraleaKrkepfksvelesvkakiesikklvaeineliakhNekvanl 388
                                       ++  +   ++dk+el++e++ l+++L++lq+ ++++ +  ++++++ + + k++   ++ +++n + +++ ++ +++
  gi|298674661|ref|YP_003726411.1|  35 KNVTEYMDRSDKKELENEISDLKSRLENLQQYVDERTDSNSQTISQLKDDVKTKTNYDDFNQLNYSFNSFSKRLKRI 111
                                       33333446789**************************9999966643333333333555555555555555555555 PP

                            AAA_13 389 eeeke 393
                                       ++e+ 
  gi|298674661|ref|YP_003726411.1| 112 AKEED 116
                                       55554 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 9.4e-05
                            AAA_13 332 aleeqLkglqraleaKrkepfksvelesvkaki.....esikklvaeineliakhNekvanleeekeeakkklelhl 403
                                       + ++q+ g + +l +K    + s e  ++ + +     e + ++v+  ++  ++ N    +l+++++++  +le   
  gi|298674661|ref|YP_003726411.1| 199 VSRKQIHGTYVELYNKLSVYVPSYEGRDFRSFVetgslEYAVDKVTIHETKLNELNDSLIDLKDKTSNLSRDLESIN 275
                                       44556666666666666666666666666555533222455667777788889999999999999999999999743 PP

                            AAA_13 404 ..veeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdek 457
                                          ++  + +d+  +++++++++ie+++++++ +++++k+l+++ ++++++  + +
  gi|298674661|ref|YP_003726411.1| 276 eiQNKQSESIDNNSENISAINNQIEEMTNAINLHTRAIKTLNKRLADIQNSPDNDT 331
                                       21577778899999999999999999999999999999999999999999877665 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.37
                            AAA_13 316 nsafeedkeelkaeaealeeqLkglqraleaKrkepfksvelesvkakiesikklvaeineliakhNekvanleeek 392
                                        +a ++d  e++++++++++ L++ ++++ +  +++ + +e ++ ++k+++i++++++i+++i++   + ++++ + 
  gi|298674661|ref|YP_003726411.1| 344 AKAERNDLMEMDEKIQNMNNDLTSFKQEILESLENIQSVLENKVDDDKLTKIEDELSSIKTQISNI--QDTSIQPDI 418
                                       345677899999999*********************9999999999999**********9999854..444555555 PP

                            AAA_13 393 eeakkklelhlveel 407
                                       ++   +l  + +  +
  gi|298674661|ref|YP_003726411.1| 419 NNTDGELDNDDLTVF 433
                                       555555555444433 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   3.9     0.001      0.63      31      83 ..      29      83 ..       8     120 .. 0.75
   2 ?    9.3   5.1     0.001      0.65      36      93 ..     247     304 ..     236     326 .. 0.88
   3 ?    2.7   6.4       0.1        64      21      95 ..     344     413 ..     337     417 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.001
                           DUF3450 31 aaaqsqkkidkldd..ekqellaeyralkeeleslevyneqlerlvasqeqeias 83
                                       + qsqk+++++ d  +k+el++e+ +lk++le+l+ y ++ +++ ++  +++++
  gi|298674661|ref|YP_003726411.1| 29 PETQSQKNVTEYMDrsDKKELENEISDLKSRLENLQQYVDERTDSNSQTISQLKD 83
                                      456778888777662247789*****************99998887776666554 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.001
                           DUF3450  36 qkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeiee 93 
                                       ++k ++l+d   +l+++  +l++ les++  ++++++++++  ++i+ +++qiee+++
  gi|298674661|ref|YP_003726411.1| 247 ETKLNELNDSLIDLKDKTSNLSRDLESINEIQNKQSESIDNNSENISAINNQIEEMTN 304
                                       678999999999******************************************9876 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.1
                           DUF3450  21 alkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeie 95 
                                       a++e +  ++ ++++q+  ++l+  kqe+l+ ++++++ le     n+  ++ +++ e e++s+++qi++i+ ++
  gi|298674661|ref|YP_003726411.1| 344 AKAERNDLMEMDEKIQNMNNDLTSFKQEILESLENIQSVLE-----NKVDDDKLTKIEDELSSIKTQISNIQDTS 413
                                       56667777788888888888888888888888888887765.....6777777888999************9885 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.6    0.0017       1.1      37     150 ..      43     114 ..      12     171 .. 0.59
   2 ?    6.1   4.8     0.023        14      45     112 ..     248     315 ..     225     340 .. 0.57
   3 ?    8.3  11.5    0.0048         3      15     141 ..     316     470 ..     312     487 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0017
                              Fez1  37 kaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeea 113
                                       +++ +el++++++  +++++l++ ++e+t+++ +                                           
  gi|298674661|ref|YP_003726411.1|  43 RSDKKELENEISDLKSRLENLQQYVDERTDSNSQTI----------------------------------------- 78 
                                       333344444444444444444444444444433333......................................... PP

                              Fez1 114 alesdeakaqrqeaeeleelkreverlraeLkeerqk 150
                                        ++ ++  + +++ ++ ++l+ + +   ++Lk   ++
  gi|298674661|ref|YP_003726411.1|  79 -SQLKDDVKTKTNYDDFNQLNYSFNSFSKRLKRIAKE 114
                                       .333333333333444444444444444444443333 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.023
                              Fez1  45 akleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeee 112
                                       +kl+e ++++ +l++++++ +++le +++  ++++++ ++ +e++++++++++e+ ++++ +++  ++
  gi|298674661|ref|YP_003726411.1| 248 TKLNELNDSLIDLKDKTSNLSRDLESINEIQNKQSESIDNNSENISAINNQIEEMTNAINLHTRAIKT 315
                                       45566666666666666666666666554444455555666666666666666666655543332222 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0048
                              Fez1  15 LKqQLkdsqa...evtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrek 88 
                                       L + L d+q+   + t+  +  ++ + + +  r++l e +e+i+++++ l++ ++e+ +  +++q    e+++ ++k
  gi|298674661|ref|YP_003726411.1| 316 LNKRLADIQNspdNDTETYETDLESRLDAKAERNDLMEMDEKIQNMNNDLTSFKQEILESLENIQSVL-ENKVDDDK 391
                                       55666677762212233333447889999********************9998888766666666654.777889** PP

                              Fez1  89 vekleeelkelreelselsleeeeaa..........................lesdeakaqrqe....aeeleelkr 135
                                       ++k+e+el+++++++s+ + ++ +                                 ++ ++q+    ++ +++l++
  gi|298674661|ref|YP_003726411.1| 392 LTKIEDELSSIKTQISNIQDTSIQPDinntdgeldnddltvfetlknmetatF----KQLEKQSdsdgNTISKNLSE 464
                                       *************9999776655554667777777777766666544322111....11222221122222233333 PP

                              Fez1 136 everlr 141
                                        +++l+
  gi|298674661|ref|YP_003726411.1| 465 ILDKLE 470
                                       333333 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   1.4     0.011       7.1      11      48 ..      51      89 ..      47     134 .. 0.75
   2 ?    1.9  10.8      0.51   3.2e+02      14      66 ..     251     307 ..     233     328 .. 0.68
   3 ?    4.7   6.2     0.066        41      29      66 ..     343     384 ..     308     389 .. 0.57
   4 ?    5.9   9.7     0.029        18      11      73 ..     356     418 ..     351     420 .. 0.73
   5 ?    2.1   1.4      0.43   2.7e+02       8      66 ..     413     470 ..     412     477 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.011
                           NPV_P10 11 adikavddkVdalqqqvdd.vqenlpdvtelnekLdaqs 48
                                      ++i++++++++ lqq vd+  ++n++++++l++ +   +
  gi|298674661|ref|YP_003726411.1| 51 NEISDLKSRLENLQQYVDErTDSNSQTISQLKDDVKTKT 89
                                      578999999999999996526778888888888765544 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.51
                           NPV_P10  14 kavddkVdalqqqvddvqenlpdvtelnek....LdaqsaqLaeletkvenIqdiLn 66 
                                       ++++d +  l+++  +++ +l+ ++e+++k    +d+ s+++ ++++++e+ ++  n
  gi|298674661|ref|YP_003726411.1| 251 NELNDSLIDLKDKTSNLSRDLESINEIQNKqsesIDNNSENISAINNQIEEMTNAIN 307
                                       556666666666667777777777777654444467777777777777777766665 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.066
                           NPV_P10  29 dvqenlpdvtelnekLdaqsaqLaelet....kvenIqdiLn 66 
                                       d +++ +d+ e+ ek++++++ L+++++    ++enIq++L 
  gi|298674661|ref|YP_003726411.1| 343 DAKAERNDLMEMDEKIQNMNNDLTSFKQeileSLENIQSVLE 384
                                       344555666666677777777766666666667777777776 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.029
                           NPV_P10  11 adikavddkVdalqqqv....ddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLnpdevPdl 73 
                                       + i+++++ +++ +q++    +++q+ l++ +   +kL ++ ++L +++t+++nIqd+      Pd+
  gi|298674661|ref|YP_003726411.1| 356 EKIQNMNNDLTSFKQEIleslENIQSVLEN-KVDDDKLTKIEDELSSIKTQISNIQDTSI---QPDI 418
                                       678888888888888885555555555555.44479********************9633...4555 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.43
                           NPV_P10   8 vIradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaq.LaeletkvenIqdiLn 66 
                                        I  di+++d  +d  +  v +  +n+++ t   ++L++qs++  +++++++++I d L 
  gi|298674661|ref|YP_003726411.1| 413 SIQPDINNTDGELDNDDLTVFETLKNMETAT--FKQLEKQSDSdGNTISKNLSEILDKLE 470
                                       5777888888888887777877777777744..677888887523566666666666554 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.1   0.00048       0.3     171     249 ..      34     118 ..      10     150 .. 0.58
   2 ?    7.8   9.1    0.0034       2.1     147     261 ..     248     363 ..     186     367 .. 0.64
   3 ?    2.1   6.4      0.19   1.1e+02     144     257 ..     353     470 ..     344     486 .. 0.38

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00048
                      Exonuc_VII_L 171 leklasrlk.speellerkrqrldeleerleralkkqlkkkrerleelkerlk.....ekleekkerlkklkerlel 241
                                        +++++ +  s ++ le++ + l++  e+l++ ++++++++++++++lk+ +k     +++++ + ++++ ++rl++
  gi|298674661|ref|YP_003726411.1|  34 QKNVTEYMDrSDKKELENEISDLKSRLENLQQYVDERTDSNSQTISQLKDDVKtktnyDDFNQLNYSFNSFSKRLKR 110
                                       33333334325555666666666666666666666667777777777776663233332233333333333333333 PP

                      Exonuc_VII_L 242 leekkerl 249
                                       +++++++l
  gi|298674661|ref|YP_003726411.1| 111 IAKEEDAL 118
                                       33333333 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0034
                      Exonuc_VII_L 147 eqleelerrlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkqlkkkrerleelkerl.k 222
                                        +l+el+++l +    + ++ ++ le++++  ++++e +++++++++ +++++e+ ++++++ +++++++l++rl  
  gi|298674661|ref|YP_003726411.1| 248 TKLNELNDSLIDLK-DKTSNLSRDLESINEIQNKQSESIDNNSENISAINNQIEE-MTNAINLHTRAIKTLNKRLaD 322
                                       33333333333322.2233344445555433346666777777777777777777.777788888888888877743 PP

                      Exonuc_VII_L 223 ..ekleekkerl.kklkerlelleekkerleeleeklealsp 261
                                         ++ ++ +e++ ++l++rl+ +++++++l e+ ek+++++ 
  gi|298674661|ref|YP_003726411.1| 323 iqNSPDNDTETYeTDLESRLD-AKAERNDLMEMDEKIQNMNN 363
                                       542222222222344455555.77788888888888887764 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.19
                      Exonuc_VII_L 144 eleeqleelerrlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkq....lkkkrerlee 216
                                       e+ e+++++++ l++  ++ le+ ++  + l++++   +++l++ +++l+++++++++ ++++    +++   +l++
  gi|298674661|ref|YP_003726411.1| 353 EMDEKIQNMNNDLTSFKQEILESLENIQSVLENKVD--DDKLTKIEDELSSIKTQISNIQDTSiqpdINNTDGELDN 427
                                       444444444444444444444333322222233332..234444444444444444442222233344455555554 PP

                      Exonuc_VII_L 217 lkerlkekleekk.erlkklkerle.lleekkerleeleekle 257
                                          ++ e+l++++ +++k+l+++ +   ++ +++l+e+ +kle
  gi|298674661|ref|YP_003726411.1| 428 DDLTVFETLKNMEtATFKQLEKQSDsDGNTISKNLSEILDKLE 470
                                       4433322333332122344443333422223333333333333 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   2.2     0.032        20      54     101 ..      32      78 ..      12      83 .. 0.81
   2 ?    2.7   0.5      0.24   1.5e+02      34      91 ..      83     116 ..      69     124 .. 0.48
   3 ?   11.0   8.2   0.00064      0.39      24     100 ..     250     323 ..     239     329 .. 0.82
   4 ?    8.3   7.4    0.0042       2.6       9      88 ..     329     411 ..     328     417 .. 0.86
   5 ?   -0.3   0.2       2.1   1.3e+03      51      67 ..     454     470 ..     429     484 .. 0.49

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.032
                                       HHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  54 elskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelekll 101
                                       + +k++ + +++  d++el +e+++lk +l++l++ ++e ++   + +
  gi|298674661|ref|YP_003726411.1|  32 QSQKNVTEYMDRS-DKKELENEISDLKSRLENLQQYVDERTDSNSQTI 78 
                                       6678999999986.9999999999999999999999888777666555 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.24
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  34 ldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelk 91 
                                        d k ++   ++++l+   N+ sk  +++ k++                        +
  gi|298674661|ref|YP_003726411.1|  83 DDVKTKTNYDDFNQLNYSFNSFSKRLKRIAKEE------------------------D 116
                                       233334444455555555556665555555543........................2 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00064
                                       CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  24 dkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelekl 100
                                        +++ d+l++l +k  +l  +le++++ +N+ s++I + ++   +++++ ++++e+ + ++  + + k+l+++l ++
  gi|298674661|ref|YP_003726411.1| 250 LNELNDSLIDLKDKTSNLSRDLESINEIQNKQSESIDNNSE---NISAINNQIEEMTNAINLHTRAIKTLNKRLADI 323
                                       567889*******************************9995...577777888888888777777777777777665 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.0042
                                       H-HHHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT...S-TCCCCCCCHHHHHH CS
                      Seryl_tRNA_N   9 enpeavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkk...edaeeliaevkelkee 82 
                                       +++e+++  l++R ++ka+  +l+e+dek ++++++l ++++e  e  ++I++  ++k   ++ +++ +e +++k++
  gi|298674661|ref|YP_003726411.1| 329 NDTETYETDLESRLDAKAERNDLMEMDEKIQNMNNDLTSFKQEILESLENIQSVLENKvddDKLTKIEDELSSIKTQ 405
                                       689999****************************************************6555555666677777777 PP

                                       HHHHHH CS
                      Seryl_tRNA_N  83 lkalea 88 
                                       ++++++
  gi|298674661|ref|YP_003726411.1| 406 ISNIQD 411
                                       777655 PP

  == domain 5  score: -0.3 bits;  conditional E-value: 2.1
                                       HHHHHHHHCCCCCCTTS CS
                      Seryl_tRNA_N  51 erNelskeIgkakkkke 67 
                                         N++sk+ +++ +k e
  gi|298674661|ref|YP_003726411.1| 454 DGNTISKNLSEILDKLE 470
                                       22333333333333332 PP

>> GARP  Glutamic acid/alanine-rich protein of Trypanosoma
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.5    0.0082       5.1     143     182 ..      32      71 ..      30      77 .. 0.88
   2 ?    5.0   0.1     0.029        18     137     177 ..      74     114 ..      68     122 .. 0.89
   3 ?    2.3   4.0      0.19   1.2e+02      60     175 ..     289     410 ..     250     415 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0082
                              GARP 143 ealealakltdednaeelreeaneaaeeLeeLekaaeeak 182
                                       +  +++++++d ++ +el++e  ++ ++Le+L++ ++e  
  gi|298674661|ref|YP_003726411.1|  32 QSQKNVTEYMDRSDKKELENEISDLKSRLENLQQYVDERT 71 
                                       5678999***************************998865 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.029
                              GARP 137 TseSLeealealakltdednaeelreeaneaaeeLeeLeka 177
                                       +s+++++ +++++ +t+ d++++l    n+++++L++  k+
  gi|298674661|ref|YP_003726411.1|  74 NSQTISQLKDDVKTKTNYDDFNQLNYSFNSFSKRLKRIAKE 114
                                       799********************************998765 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.19
                              GARP  60 kelvkrakeaaaeateAaeaAetaasevegeaanlkavaeeylesldksLkslaes.......ansdedvreaAkkC 129
                                        e  +    + +e t+A +    a++ ++++ a+++ ++++ +e++++ L+s  +         ++de+++++  + 
  gi|298674661|ref|YP_003726411.1| 289 SENISAINNQIEEMTNAINLHTRAIKTLNKRLADIQNSPDNDTETYETDLESRLDAkaerndlMEMDEKIQNMNNDL 365
                                       45678888899999999999999999999999999999998888888888774444444566667788888888888 PP

                              GARP 130 tetaenVTseSLeealealakltdednaeelreeaneaaeeLeeLe 175
                                       t  ++++  eSLe+    l++++d d+++++++e  ++  ++++ +
  gi|298674661|ref|YP_003726411.1| 366 TSFKQEI-LESLENIQSVLENKVDDDKLTKIEDELSSIKTQISNIQ 410
                                       7777776.59999999999999999999999999999888887766 PP

>> AIP3  Actin interacting protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   5.3     0.006       3.7     108     171 ..      25      87 ..       5     121 .. 0.54
   2 ?   10.4  20.0   0.00039      0.24      42     198 ..     258     427 ..     246     439 .. 0.73
   3 ?   -1.3   7.4       1.4   8.8e+02      83     182 ..     385     480 ..     370     490 .] 0.48

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.006
                                       XXXXXXXXXXXXXXXXXXX.........XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              AIP3 108 evserqeeaakekaseslakkelkaqlkevqslrrdLavlrqlysefkseikeslselrekakk 171
                                       + s + e++++++ +e + ++++k+  +e+++l+  L+ l+q  +e +++ ++++s+l++ +k+
  gi|298674661|ref|YP_003726411.1|  25 S-SGNPETQSQKNVTEYMDRSDKKELENEISDLKSRLENLQQYVDERTDSNSQTISQLKDDVKT 87 
                                       2.22222333333333444566666666666666666666666666666666666666666553 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00039
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXX...XXXXXXXXXXX...XXXXXXXXXXX CS
                              AIP3  42 iyiqDpksgvrYeLedlsdvkdrsvLsLn..iepldevkkhideslasl...skelkelkssiesqkaslqevserq 113
                                       i ++D++s+ +  Le +++++++   s+    e+++ ++++i+e+++ +   ++ +k l++++ + ++s ++ +e+ 
  gi|298674661|ref|YP_003726411.1| 258 IDLKDKTSNLSRDLESINEIQNKQSESIDnnSENISAINNQIEEMTNAInlhTRAIKTLNKRLADIQNSPDNDTETY 334
                                       7899****************999876665337799999999999998887777888888888888888888877888 PP

                                       XXXXXXXXXXXXX.........XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXX......XXXX.XXXX CS
                              AIP3 114 eeaakekaseslakkelkaqlkevqslrrdLavlrqlysefkseikeslselre..kakkvk......easlastkk 182
                                       e++ +++ + ++++++l +  +++q++++dL++ +q   e+ ++i++ l++  +  k++k++      ++++++++ 
  gi|298674661|ref|YP_003726411.1| 335 ETDLESRLDAKAERNDLMEMDEKIQNMNNDLTSFKQEILESLENIQSVLENKVDddKLTKIEdelssiKTQISNIQD 411
                                       88888888877788899999999999999999999988888888887766533201233333333333366666666 PP

                                       XXHHHHHHHHHHHHHH CS
                              AIP3 183 ssnrayiekgkkkLse 198
                                       +s +  i+++  +L++
  gi|298674661|ref|YP_003726411.1| 412 TSIQPDINNTDGELDN 427
                                       6666666666666665 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.4
                                       XXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXX.........XXXXXXXXXXXXXXXXXXXXXXXX CS
                              AIP3  83 eslaslskelkelkssiesqkaslqevserqeeaakekaseslakkelkaqlkevqslrrdLavlrqlysefkseik 159
                                       +++    ++l++++++++s k++++++++++ +   ++++  l  +++ + +++++++  + a+ +ql++++ s+ +
  gi|298674661|ref|YP_003726411.1| 385 NKVD--DDKLTKIEDELSSIKTQISNIQDTSIQPDINNTDGELD-NDDLTVFETLKNM--ETATFKQLEKQSDSDGN 456
                                       3322..23455555555555555555555555554444443333.5555666777766..45777777777776655 PP

                                       XXXXXXXXXXXXXX.XXXX.XXXX CS
                              AIP3 160 eslselrekakkvk.easlastkk 182
                                       ++ ++l+e ++k++ ++++ s+kk
  gi|298674661|ref|YP_003726411.1| 457 TISKNLSEILDKLEnQSHIYSQKK 480
                                       555555555555542223333333 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   3.4    0.0042       2.6      17      84 ..      44     117 ..      20     124 .. 0.71
   2 ?    7.6   8.1    0.0058       3.6      11      74 ..     242     305 ..     234     326 .. 0.69
   3 ?    6.8   6.2      0.01       6.3      10      71 ..     262     323 ..     256     344 .. 0.68
   4 ?    3.2   7.6      0.13        82      27      96 ..     345     410 ..     318     415 .. 0.68
   5 ?    4.0   7.0     0.076        47      17      95 ..     390     465 ..     374     471 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0042
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXX.....XXX--TTTTTGGGHHHHHHHHHH CS
                        Laminin_II  17 eqlaplsqnlentkeklseinrsveetnekvk.dankairdArrsv.....kkLeklapqLldklkelkqleea 84 
                                       +++++l+++++ +k+ l+++++ v+e ++  +   ++  +d++++       +L+   +   ++lk++ + e+a
  gi|298674661|ref|YP_003726411.1|  44 SDKKELENEISDLKSRLENLQQYVDERTDSNSqTISQLKDDVKTKTnyddfNQLNYSFNSFSKRLKRIAKEEDA 117
                                       46778888888888888888888877666555255555666666542222268888888888888888888877 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0058
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGG CS
                        Laminin_II  11 takevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldk 74 
                                       +++  + +l++l+  l  +k+k s++ r++e +ne  ++ ++ i+  +++++ ++++++++ + 
  gi|298674661|ref|YP_003726411.1| 242 KVTIHETKLNELNDSLIDLKDKTSNLSRDLESINEIQNKQSESIDNNSENISAINNQIEEMTNA 305
                                       5555566778888888888888888888888888888888888888888888888887776654 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.01
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTT CS
                        Laminin_II  10 etakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqL 71 
                                       +++++  ++l+ +++  ++ +e++ +  +++  +n++++++++ai++  r++k+L+k + ++
  gi|298674661|ref|YP_003726411.1| 262 DKTSNLSRDLESINEIQNKQSESIDNNSENISAINNQIEEMTNAINLHTRAIKTLNKRLADI 323
                                       45555555556665555556666666666666666667777777777777777777766655 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.13
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXX--TTTTTGGGHHHHHHHHHH...HHHHHHHHH CS
                        Laminin_II  27 entkeklseinrsveetnekvkdankairdArrsv.kkLeklapqLldklkelkqleeassslsdniseik 96 
                                       + ++++l e++++++++n+++ ++++ i +  +++ + Le+++++  dkl +++   +    ++ +is+i+
  gi|298674661|ref|YP_003726411.1| 345 KAERNDLMEMDEKIQNMNNDLTSFKQEILESLENIqSVLENKVDD--DKLTKIEDELSS---IKTQISNIQ 410
                                       456777888888888888888887776665555541557778877..777777666666...777777775 PP

  == domain 5  score: 4.0 bits;  conditional E-value: 0.076
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH....HHHHH CS
                        Laminin_II  17 eqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeasss.lsdni 92 
                                       ++l++++ +l+ +k ++s+i+++   ++ ++++    ++   +     e l +   + +k+l+++++  ++ +s+n+
  gi|298674661|ref|YP_003726411.1| 390 DKLTKIEDELSSIKTQISNIQDT--SIQPDINNTDGELDN--DDLTVFETLKNMETATFKQLEKQSDSDGNtISKNL 462
                                       34667777777777777777777..666666665555554..444445555555567888999999999999***** PP

                                       HHH CS
                        Laminin_II  93 sei 95 
                                       sei
  gi|298674661|ref|YP_003726411.1| 463 SEI 465
                                       **9 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   6.3    0.0082       5.1      44     123 ..      35     119 ..      15     122 .. 0.81
   2 ?   14.3   2.8   7.4e-05     0.046      11     130 ..     191     331 ..     187     334 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0082
                            APG6_N  44 k......qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlelle 114
                                       k      ++++ +ele+e+++l++  e+l++  +e  + +++  ++l++  +++ + ++  ++   ++n+++  l++
  gi|298674661|ref|YP_003726411.1|  35 KnvteymDRSDKKELENEISDLKSRLENLQQYVDERTDSNSQTISQLKDDVKTKTNYDDF-NQLNYSFNSFSKRLKR 110
                                       033455588999***********************************9998888777765.5666789999999999 PP

                            APG6_N 115 leeeldsle 123
                                         +e d+l+
  gi|298674661|ref|YP_003726411.1| 111 IAKEEDALN 119
                                       999999887 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 7.4e-05
                            APG6_N  11 leeldkqleqaekerdaYeeflkklkkekkeeek.....................qdeeleeleeeleklekeeeel 66 
                                        e ++++l + ++ + +Y e  +kl  + ++ e                      ++++l+el+++l +l+++ ++l
  gi|298674661|ref|YP_003726411.1| 191 SEAVESKLVSRKQIHGTYVELYNKLSVYVPSYEGrdfrsfvetgsleyavdkvtiHETKLNELNDSLIDLKDKTSNL 267
                                       56666666666777777777888888777776557888888888888888889999********************* PP

                            APG6_N  67 leeLkelekereeleaelaaleeelealeeeeerfwreynelqlelleleeeldsleaqyehaq 130
                                        + L+ + + + +  + + + +e  +a++++ e+  +  n + +  + l+++l+ ++++ + ++
  gi|298674661|ref|YP_003726411.1| 268 SRDLESINEIQNKQSESIDNNSENISAINNQIEEMTNAINLHTRAIKTLNKRLADIQNSPDNDT 331
                                       ******************************************************9999877765 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   4.9     0.038        24      13      88 ..      47     121 ..      33     124 .. 0.87
   2 ?   13.3   7.4    0.0001     0.062      10      85 ..     248     323 ..     241     340 .. 0.86
   3 ?    2.6   9.3       0.2   1.2e+02      37     108 ..     335     404 ..     328     415 .. 0.64
   4 ?   -1.1   4.1       2.8   1.7e+03      66     135 ..     390     462 ..     374     469 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.038
                    CENP-F_leu_zip  13 KeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLeke 88 
                                       Ke e + + Lk + enL++ + +   +++++i +  +  ++ +t  +  ++l+ + + ++  L+ + +e + L+k+
  gi|298674661|ref|YP_003726411.1|  47 KELENEISDLKSRLENLQQYVDERTDSNSQTISQLKDDVKT-KTNYDDFNQLNYSFNSFSKRLKRIAKEEDALNKK 121
                                       88999999999999999999999999999999999887665.4556789999999999999999999999999986 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.0001
                    CENP-F_leu_zip  10 ekLKeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeL 85 
                                        kL e + +   Lkdk  nL r+le ++e q+k     +++ + +++++++iee+++  +  +  +++l +   ++
  gi|298674661|ref|YP_003726411.1| 248 TKLNELNDSLIDLKDKTSNLSRDLESINEIQNKQSESIDNNSENISAINNQIEEMTNAINLHTRAIKTLNKRLADI 323
                                       577777777778*********************************************9998888888887766555 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.2
                    CENP-F_leu_zip  37 eenqekvileaEtskaevetlkeeieelaeelreleldL.valrsekeeLekelqkkqervseLeslnsslen 108
                                       e ++e   l+a  +++ + ++ e+i+++++ l+ +++++ ++l + +  Le+++ +  ++    e   ss++ 
  gi|298674661|ref|YP_003726411.1| 335 ETDLE-SRLDAKAERNDLMEMDEKIQNMNNDLTSFKQEIlESLENIQSVLENKVDD--DKLTKIEDELSSIKT 404
                                       55544.36899999999999*************99999614555445555555443..333444444444444 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 2.8
                    CENP-F_leu_zip  66 eelreleldLvalrsekeeLek.elqkk.qervseLeslnsslenlleekEqe.kvqmkeeskaaveeLqtql 135
                                        +l+++e +L++++ +  +++  ++q   +++  eL++  +++ ++l++ E    +q++++s++  + ++++l
  gi|298674661|ref|YP_003726411.1| 390 DKLTKIEDELSSIKTQISNIQDtSIQPDiNNTDGELDNDDLTVFETLKNMETAtFKQLEKQSDSDGNTISKNL 462
                                       7889999999999999999965145554255556899999999999999999844556666666666666655 PP

>> HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   4.7    0.0008      0.49      18      84 ..      42     110 ..      27     121 .. 0.79
   2 ?    1.6   4.1       0.7   4.3e+02      32      94 ..     260     325 ..     239     351 .. 0.68
   3 ?    7.7   3.5    0.0086       5.3      13      74 ..     353     412 ..     345     422 .. 0.85
   4 ?    3.5   0.4      0.18   1.1e+02       7      46 ..     437     476 ..     435     484 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0008
                    HIP1_clath_bdg  18 arqaqeeverekkeleeelerlkeeaerkleeqkeelekLkreleakr..aelarlkssLesseqsgeq 84 
                                        r  ++e+e+e ++l+ +le+l++  +++++  ++++ +Lk ++++k   +++++l+ s +s  +  ++
  gi|298674661|ref|YP_003726411.1|  42 DRSDKKELENEISDLKSRLENLQQYVDERTDSNSQTISQLKDDVKTKTnyDDFNQLNYSFNSFSKRLKR 110
                                       478899*************************************98875225778888777776665555 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.7
                    HIP1_clath_bdg  32 leeelerlkeeaerkle...eqkeelekLkreleakraelarlkssLesseqsgeqlssqlaaLqa 94 
                                       l+++  +l+++ e+  e   +q+e +++  +++ a +++++++ ++++ ++++ ++l+++la++q+
  gi|298674661|ref|YP_003726411.1| 260 LKDKTSNLSRDLESINEiqnKQSESIDNNSENISAINNQIEEMTNAINLHTRAIKTLNKRLADIQN 325
                                       444444444444333332225566666666677777777888888888777777777777777764 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0086
                    HIP1_clath_bdg  13 kqlsvarqaqeeverekkeleeelerlkeeaerkleeqkeelekLkreleakraelarlkss 74 
                                        +    ++  +++   k+e+ e+le++++  e+k+++ k  l k++ el + ++++++++ +
  gi|298674661|ref|YP_003726411.1| 353 EMDEKIQNMNNDLTSFKQEILESLENIQSVLENKVDDDK--LTKIEDELSSIKTQISNIQDT 412
                                       55566788999************************9765..678899999999999999876 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.18
                    HIP1_clath_bdg   7 KnAevtkqlsvarqaqeeverekkeleeelerlkeeaerk 46 
                                       Kn e+++  +  +q+ ++ ++  k+l+e l++l+++++  
  gi|298674661|ref|YP_003726411.1| 437 KNMETATFKQLEKQSDSDGNTISKNLSEILDKLENQSHIY 476
                                       999*****************************99998654 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   1.8     0.017        11      65     126 ..      47     108 ..      34     120 .. 0.78
   2 ?   -2.4   0.0       7.5   4.7e+03      87     110 ..     182     205 ..     179     218 .. 0.70
   3 ?    7.7   1.5    0.0058       3.6      63     114 ..     256     307 ..     247     327 .. 0.48
   4 ?    8.3   2.0    0.0038       2.4      63     111 ..     350     391 ..     345     412 .. 0.54
   5 ?    0.7   0.3      0.81     5e+02      69      90 ..     390     411 ..     387     471 .. 0.69
   6 ?   -0.9   0.1       2.7   1.7e+03      77     113 ..     443     479 ..     430     487 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.017
                              COG2  65 vglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekrellklllkldevv 126
                                       + l++e++ ++s l+++++ v++ +++ s++++++++ ++ +++  + ++l  +  ++++++
  gi|298674661|ref|YP_003726411.1|  47 KELENEISDLKSRLENLQQYVDERTDSNSQTISQLKDDVKTKTNYDDFNQLNYSFNSFSKRL 108
                                       568999999999************************99999998877765555555555555 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 7.5
                              COG2  87 svreklsereeeveskleeakele 110
                                       ++r  +++ +e+veskl  +k++ 
  gi|298674661|ref|YP_003726411.1| 182 NNRFMVKKLSEAVESKLVSRKQIH 205
                                       555667777888888888777765 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0058
                              COG2  63 hLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekre 114
                                       +L++l+++ ++++ +l+++ +  ++  e++++++e++++  ++ +e++++ +
  gi|298674661|ref|YP_003726411.1| 256 SLIDLKDKTSNLSRDLESINEIQNKQSESIDNNSENISAINNQIEEMTNAIN 307
                                       5555555555555555554444444444444443333333333333333332 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.0038
                              COG2  63 hLvglqeeleevesplaaarkkvesvreklsereeeveskleeakelee 111
                                        L+ ++e++++++ +l+++++++ +  e+++       s le++ +  +
  gi|298674661|ref|YP_003726411.1| 350 DLMEMDEKIQNMNNDLTSFKQEILESLENIQ-------SVLENKVDDDK 391
                                       4556666666666666666666655555554.......44444444444 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 0.81
                              COG2  69 eeleevesplaaarkkvesvre 90 
                                       ++l ++e +l++++++++++++
  gi|298674661|ref|YP_003726411.1| 390 DKLTKIEDELSSIKTQISNIQD 411
                                       4555555555555555554443 PP

  == domain 6  score: -0.9 bits;  conditional E-value: 2.7
                              COG2  77 plaaarkkvesvreklsereeeveskleeakeleekr 113
                                        ++++ k+ +s  + +s++ +e+ +kle+++++ +++
  gi|298674661|ref|YP_003726411.1| 443 TFKQLEKQSDSDGNTISKNLSEILDKLENQSHIYSQK 479
                                       4566666666777778888888888888887776655 PP

>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   1.7    0.0016      0.98       4      71 ..      43     111 ..      24     162 .. 0.78
   2 ?    3.7   5.8     0.072        45      12      81 ..     241     315 ..     233     325 .. 0.60
   3 ?    1.1  17.1      0.44   2.7e+02       8     105 ..     279     409 ..     275     434 .. 0.79
   4 ?    4.3   0.6     0.046        29      42      81 ..     436     475 ..     424     486 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0016
                                       ...CTTTHHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTT.THHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              GrpE   4 eeeeeeeedeeeeleeeleelekevkelkekllrllaefe.nlrkrtekekeeakkfaiekfakdLLpv 71 
                                       +++++e+e+e+ +l+++le+l++ v+e +++  ++  +++  ++ +t+ +  +  +++  +f k L  +
  gi|298674661|ref|YP_003726411.1|  43 RSDKKELENEISDLKSRLENLQQYVDERTDSNSQTISQLKdDVKTKTNYDDFNQLNYSFNSFSKRLKRI 111
                                       467788889999999999999999998888888888888878888888888888888888888877554 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.072
                                       HHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHHHHHHH.....HHHHHHHHHHHHHHHHHHHHHHC CS
                              GrpE  12 deeeeleeeleelekevkelkekllrllaefenlrkrtekekeeakk.....faiekfakdLLpvlDnleralks 81 
                                       d+ +  e++l+el++ + +lk+k  +l  ++e +++  +k+ e + +     +ai + ++++ + ++   ra+k+
  gi|298674661|ref|YP_003726411.1| 241 DKVTIHETKLNELNDSLIDLKDKTSNLSRDLESINEIQNKQSESIDNnseniSAINNQIEEMTNAINLHTRAIKT 315
                                       556666777778888777777777777777777766666666654431112245555566666666555555554 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.44
                                       TTTHHHHCCCCCCTTCHHHCTTSCCCCCC.................................TTTTTTTTHHHHHHH CS
                              GrpE   8 eeeedeeeeleeeleelekevkelkekll.................................rllaefenlrkrtek 51 
                                       +++ + ++++ e++++++++++e++++++                                 rl a++e       +
  gi|298674661|ref|YP_003726411.1| 279 NKQSESIDNNSENISAINNQIEEMTNAINlhtraiktlnkrladiqnspdndtetyetdlesRLDAKAERNDLMEMD 355
                                       55556666666666666666666666666666666666666667777777888888888889999999988888899 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHC..HHH-HHHHHHHHHHHHHHHHHH CS
                              GrpE  52 ekeeakkfaiekfakdLLpvlDnleralksakeneeekslleGvemtlkqllki 105
                                       ek +  +  +++f +++L+ l+n++ +l+++ +++++ ++ + ++ ++ q+ +i
  gi|298674661|ref|YP_003726411.1| 356 EKIQNMNNDLTSFKQEILESLENIQSVLENKVDDDKLTKIEDELSSIKTQISNI 409
                                       999999999*********************999999999999999999998877 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.046
                                       TTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                              GrpE  42 fenlrkrtekekeeakkfaiekfakdLLpvlDnleralks 81 
                                       ++n++  t k++e+ +++    + k+L ++lD+le + + 
  gi|298674661|ref|YP_003726411.1| 436 LKNMETATFKQLEKQSDSDGNTISKNLSEILDKLENQSHI 475
                                       7899999***************************988655 PP

>> DUF3053  Protein of unknown function (DUF3053)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.5     0.093        58      66     114 ..      61     109 ..      17     156 .. 0.61
   2 ?    1.3   0.6      0.34   2.1e+02      46     121 ..     200     279 ..     172     328 .. 0.54
   3 ?    9.9   0.6   0.00083      0.51      66     118 ..     359     411 ..     348     430 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.093
                           DUF3053  66 qqlnqavetslepvvdalqsirspqdyltrrdelrqaagalneleqqlq 114
                                       ++l+q v++      +++++++      t+ d+++q + + n ++++l+
  gi|298674661|ref|YP_003726411.1|  61 ENLQQYVDERTDSNSQTISQLKDDVKTKTNYDDFNQLNYSFNSFSKRLK 109
                                       2334444444444444444444444444444555555555555555555 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.34
                           DUF3053  46 aqkkafGdYasdYailtaf.....sqqlnqavet.slepvvdalqsirspqdyltrrdelrqaagalneleqqlqna 116
                                         k+  G Y++ Y+ l+ +     ++ + + vet sle  vd++  i+    + +  d+l   +++ ++l+ +l++ 
  gi|298674661|ref|YP_003726411.1| 200 SRKQIHGTYVELYNKLSVYvpsyeGRDFRSFVETgSLEYAVDKV-TIHE-TKLNELNDSLIDLKDKTSNLSRDLESI 274
                                       45666777777777777663222234455555441344444444.3332.223344445555555555555555544 PP

                           DUF3053 117 kaqad 121
                                       ++  +
  gi|298674661|ref|YP_003726411.1| 275 NEIQN 279
                                       43333 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00083
                           DUF3053  66 qqlnqavetslepvvdalqsirspqdyltrrdelrqaagalneleqqlqnaka 118
                                       q++n+ + +  ++++++l++i+s+ ++ +  d+l + +++l+ +++q+ n + 
  gi|298674661|ref|YP_003726411.1| 359 QNMNNDLTSFKQEILESLENIQSVLENKVDDDKLTKIEDELSSIKTQISNIQD 411
                                       8999999999*************************************998765 PP

>> DUF4349  Domain of unknown function (DUF4349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.5     0.016        10     101     148 ..      33      73 ..      23     113 .. 0.61
   2 ?    8.9   1.8    0.0015      0.95      40     146 ..     203     320 ..     157     322 .. 0.78
   3 ?    2.4   3.6      0.15        91      89     150 ..     336     391 ..     324     393 .. 0.64
   4 ?    5.2   1.5      0.02        13     100     136 ..     374     410 ..     364     414 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.016
                           DUF4349 101 sedrllallekaksvedlleiereLsevqaeieslegqlryLdnqvay 148
                                       s+++++++++++++     e+e+e+s+ ++++e+l++   y d++++ 
  gi|298674661|ref|YP_003726411.1|  33 SQKNVTEYMDRSDKK----ELENEISDLKSRLENLQQ---YVDERTDS 73 
                                       555566666554443....567777777777777753...44444444 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0015
                           DUF4349  40 rsgtegdersasltlRvPaarldafldelael......gkvtsrstsaeDVTeqyvDleaRlkaleasedrllalle 110
                                       +  ++  e + +l + vP+ +  +f + +++        kvt ++t+  ++ ++++Dl+ + ++l    +++ ++ +
  gi|298674661|ref|YP_003726411.1| 203 QIHGTYVELYNKLSVYVPSYEGRDFRSFVETGsleyavDKVTIHETKLNELNDSLIDLKDKTSNLSRDLESINEIQN 279
                                       45566666778899999995555555555532334444899999*******************************96 PP

                           DUF4349 111 kak.....svedlleiereLsevqaeieslegqlryLdnqv 146
                                       k++     + e + +i+++++e +  i+  ++ +++L+++ 
  gi|298674661|ref|YP_003726411.1| 280 KQSesidnNSENISAINNQIEEMTNAINLHTRAIKTLNKRL 320
                                       64446666788999999999999999999999999998875 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.15
                           DUF4349  89 vDleaRlkaleasedrllallekaksvedlleiereLsevqae.ieslegqlryLdnqvayst 150
                                       +Dle+Rl a+  +++    l+e +++++ +   +++L++ ++e +esle  +  L+n+v+  +
  gi|298674661|ref|YP_003726411.1| 336 TDLESRLDAKA-ERND---LMEMDEKIQNM---NNDLTSFKQEiLESLENIQSVLENKVDDDK 391
                                       68999998764.4444...55555554433...556666555526999999999999988665 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.02
                           DUF4349 100 asedrllallekaksvedlleiereLsevqaeiesle 136
                                       +s ++++++le++ + + l +ie+eLs+++++i +++
  gi|298674661|ref|YP_003726411.1| 374 ESLENIQSVLENKVDDDKLTKIEDELSSIKTQISNIQ 410
                                       678999999*999999*****************9988 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.4      0.49     3e+02      30      54 ..      50      74 ..      44      88 .. 0.59
   2 ?    8.0   0.4    0.0072       4.5      11      53 ..     242     284 ..     241     291 .. 0.81
   3 ?    6.8   0.2     0.017        10      18      57 ..     291     330 ..     287     337 .. 0.82
   4 ?    0.1   1.2       2.1   1.3e+03      15      41 ..     354     380 ..     349     419 .. 0.63

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.49
                                      HHHHHHHHHHHHHHHHT-XXXXXXX CS
                              SlyX 30 qqqidrlqrqlrllaerlkeleess 54
                                      + +i+ l+ +l+ l++ + e+ +s+
  gi|298674661|ref|YP_003726411.1| 50 ENEISDLKSRLENLQQYVDERTDSN 74
                                      3455555555555555555554444 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0072
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXX CS
                              SlyX  11 klafqedtieeLndvvaeqqqqidrlqrqlrllaerlkelees 53 
                                       k++ +e  ++eLnd +++  ++ + l r l+ ++e  ++ +es
  gi|298674661|ref|YP_003726411.1| 242 KVTIHETKLNELNDSLIDLKDKTSNLSRDLESINEIQNKQSES 284
                                       67889999**********************9998876555544 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.017
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXX CS
                              SlyX  18 tieeLndvvaeqqqqidrlqrqlrllaerlkeleessgas 57 
                                        i + n+++ e    i   +r ++ l++rl+++++s  ++
  gi|298674661|ref|YP_003726411.1| 291 NISAINNQIEEMTNAINLHTRAIKTLNKRLADIQNSPDND 330
                                       6888999999999999999999999999999999886544 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 2.1
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SlyX  15 qedtieeLndvvaeqqqqidrlqrqlr 41 
                                       +++ i+ +n+ ++   q+i +  + ++
  gi|298674661|ref|YP_003726411.1| 354 MDEKIQNMNNDLTSFKQEILESLENIQ 380
                                       566677777777766666644333333 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   5.1   0.00034      0.21      52     130 ..      14      90 ..       8     120 .. 0.78
   2 ?   11.3   9.4   0.00048       0.3      33     115 ..     246     324 ..     237     329 .. 0.90
   3 ?    3.4  12.0      0.13        81      34     114 ..     310     390 ..     301     412 .. 0.69
   4 ?   -1.5   6.2       4.3   2.7e+03      35     112 ..     390     467 ..     382     480 .. 0.46

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00034
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  52 keaeelvkeikdslrekqkskkdndnvikks.skeleeeilrlketidaqesnirvLqnvlesneqkiqkLeqdidq 127
                                       ++a++ +k++++s +++ +s+k+ ++++ +s +kele+ei++lk ++ +     ++  +  +sn+q i++L+ d+++
  gi|298674661|ref|YP_003726411.1|  14 SSAYNETKNVDSSGNPETQSQKNVTEYMDRSdKKELENEISDLKSRLENLQ---QYVDERTDSNSQTISQLKDDVKT 87 
                                       677788888888888888888866777766635678888888887774333...45567788999999999999998 PP

                                       HHH CS
                         Fib_alpha 128 ker 130
                                       k++
  gi|298674661|ref|YP_003726411.1|  88 KTN 90 
                                       875 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00048
                                       CCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHH CS
                         Fib_alpha  33 vkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqn 109
                                        +++l++l+++l +++++t++ ++  ++i+++ +++ +s ++n++ i+ +++++e    ++ + i+ + + i+ L +
  gi|298674661|ref|YP_003726411.1| 246 HETKLNELNDSLIDLKDKTSNLSRDLESINEIQNKQSESIDNNSENISAINNQIE----EMTNAINLHTRAIKTLNK 318
                                       5789***********************************9999999999998888....899999999999999999 PP

                                       HHHHHH CS
                         Fib_alpha 110 vlesne 115
                                        l + +
  gi|298674661|ref|YP_003726411.1| 319 RLADIQ 324
                                       988766 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.13
                                       CHHHCCCCCCCCCCCCH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHH.HHH CS
                         Fib_alpha  34 kkdlekleneleeisns.tkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnir.vLq 108
                                       ++ +++l+++l++i+ns  +++e++ +++++ l +k + ++     + +  ++++++ + +k++i +  +ni+ vL 
  gi|298674661|ref|YP_003726411.1| 310 TRAIKTLNKRLADIQNSpDNDTETYETDLESRLDAKAERND-L-MEMDEKIQNMNNDLTSFKQEILESLENIQsVLE 384
                                       5789************9456788888888888887777766.3.344444444455777********9999973566 PP

                                       HHHHHH CS
                         Fib_alpha 109 nvlesn 114
                                       n +++ 
  gi|298674661|ref|YP_003726411.1| 385 NKVDDD 390
                                       666542 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 4.3
                                       HHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HCCCHHHHHHHCCHHHH.HHHHH CS
                         Fib_alpha  35 kdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskele.eeilrlketidaqesni.rvLqn 109
                                       ++l+k+e+el++i+ + +++++++  i+  ++++  + ++ d ++ +  k++e     +l+++ d+  ++i ++L +
  gi|298674661|ref|YP_003726411.1| 390 DKLTKIEDELSSIKTQISNIQDTS--IQPDINNTDGELDNDDLTVFETLKNMEtATFKQLEKQSDSDGNTIsKNLSE 464
                                       456677777777776666666653..332222222222222333333333333023333444444444333123444 PP

                                       HHH CS
                         Fib_alpha 110 vle 112
                                       +l+
  gi|298674661|ref|YP_003726411.1| 465 ILD 467
                                       443 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   5.1       0.1        65      25      92 ..      47     111 ..      28     114 .. 0.61
   2 ?    5.3   6.6     0.054        33      26      98 ..     301     374 ..     242     377 .. 0.91
   3 ?   10.9   2.9   0.00093      0.57      38      98 ..     348     408 ..     332     411 .. 0.78
   4 ?    1.3   0.5      0.91   5.6e+02      44      82 ..     443     483 ..     424     486 .. 0.53

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.1
                      Occludin_ELL  25 kelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpeyqekkkrceyLkekLshi 92 
                                       kel++e++++++++++L++ ++e    ++  +++++++ ++ k +++  ++ +    ++  +++L+ i
  gi|298674661|ref|YP_003726411.1|  47 KELENEISDLKSRLENLQQYVDER---TDSNSQTISQLKDDVKTKTNYDDFNQLNYSFNSFSKRLKRI 111
                                       455666666666666666555543...22444555555666777777777777777777777777766 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.054
                      Occludin_ELL  26 elhaeleevskkfseLerelkelkegsk.eykkieeeilqeykklkkdpeyqekkkrceyLkekLshiKklike 98 
                                       e+ + ++  ++ ++ L+++l + +++ +  +++ e ++ +++  + + ++ +e+ ++++ +++ L+  K+ i e
  gi|298674661|ref|YP_003726411.1| 301 EMTNAINLHTRAIKTLNKRLADIQNSPDnDTETYETDLESRLDAKAERNDLMEMDEKIQNMNNDLTSFKQEILE 374
                                       6677788888999999999999988877688888999999******************************9975 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00093
                      Occludin_ELL  38 fseLerelkelkegskeykkieeeilqeykklkkdpeyqekkkrceyLkekLshiKklike 98 
                                        ++L ++ ++ ++ ++  ++ ++eil++++++++  e + +  ++++++++Ls iK++i++
  gi|298674661|ref|YP_003726411.1| 348 RNDLMEMDEKIQNMNNDLTSFKQEILESLENIQSVLENKVDDDKLTKIEDELSSIKTQISN 408
                                       3444444444555567889999*************************************97 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.91
                      Occludin_ELL  44 elkelkegsk.eykkieeeilqeykklkk.dpeyqekkkrc 82 
                                         k+l+++s+   ++i +++ + + kl++ ++ y +kk r 
  gi|298674661|ref|YP_003726411.1| 443 TFKQLEKQSDsDGNTISKNLSEILDKLENqSHIYSQKKGRY 483
                                       34444444444444444444444444444366677777665 PP

>> M  M protein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   1.3     0.014       8.4       2      20 ..      45      63 ..      44      64 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.014
                                 M  2 akkeLEaelqeLeeelqaL 20
                                       kkeLE e ++L++ l++L
  gi|298674661|ref|YP_003726411.1| 45 DKKELENEISDLKSRLENL 63
                                      59*************9998 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   6.4     0.007       4.3      22     101 ..      34     117 ..      19     120 .. 0.72
   2 ?   13.7   7.8   0.00011     0.068      32     102 ..     253     323 ..     185     325 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.007
                                       HHHHHHB-..BHHHHHHHHHHHH...HHHHHHHHHHHHHH....HHHHHHHHHHHHHH..H.......HHHHHHHHH CS
                             DUF16  22 rkqlnefkdsnkqrLkkieakvdklgeqinkleqkvekqg....ekikelkveqkaqg..eelnkvdetleliletL 92 
                                       +k+  e+ d  ++  k++e++++ l+ ++++l+q v++ +    + i++lk ++k++   +++n+++ ++++  + L
  gi|298674661|ref|YP_003726411.1|  34 QKNVTEYMDRSDK--KELENEISDLKSRLENLQQYVDERTdsnsQTISQLKDDVKTKTnyDDFNQLNYSFNSFSKRL 108
                                       6788888865544..78899999888888888888876541111678999877766551157888888888888888 PP

                                       HHHHHHHHH CS
                             DUF16  93 qkinkRlDs 101
                                       ++i k  D 
  gi|298674661|ref|YP_003726411.1| 109 KRIAKEEDA 117
                                       888876665 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00011
                                       BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHHH CS
                             DUF16  32 nkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkRlDsi 102
                                        +  L+++++k + l   ++ ++++ +kq e i++ ++++ a +++++++ ++++l  ++++++nkRl  i
  gi|298674661|ref|YP_003726411.1| 253 LNDSLIDLKDKTSNLSRDLESINEIQNKQSESIDNNSENISAINNQIEEMTNAINLHTRAIKTLNKRLADI 323
                                       35568888888889999999999*********************************************877 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   4.2      0.04        25      10      80 ..      19      90 ..      13     119 .. 0.74
   2 ?   12.2   4.9   0.00012     0.076       3      83 ..     249     328 ..     247     342 .. 0.89
   3 ?    5.0   5.2      0.02        13      22      88 ..     345     412 ..     328     423 .. 0.66
   4 ?   -0.5   0.3      0.93   5.8e+02      54      98 ..     445     485 ..     412     489 .. 0.59

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.04
                             TMPIT 10 efkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk...eeeeeeveelkeelkerkk 80
                                      e+k++ ++ +  +q+ +++++  ++  k  k+ ++++++lks+l++l++ v+   +++++++++lk+++k++++
  gi|298674661|ref|YP_003726411.1| 19 ETKNVDSSGNPETQSQKNVTEYMDRSDK--KELENEISDLKSRLENLQQYVDertDSNSQTISQLKDDVKTKTN 90
                                      6666666666667777777777776544..56778888888888888888665557788889999999887665 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00012
                             TMPIT   3 eweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerk 79 
                                       +++el++++ +l+++ +++ ++le++++ q+k s++i+++++++++++++++++++++ + + +++++l+++l++++
  gi|298674661|ref|YP_003726411.1| 249 KLNELNDSLIDLKDKTSNLSRDLESINEIQNKQSESIDNNSENISAINNQIEEMTNAI-NLHTRAIKTLNKRLADIQ 324
                                       678999************************************************9997.689999999*99999998 PP

                             TMPIT  80 kvlk 83 
                                       ++ +
  gi|298674661|ref|YP_003726411.1| 325 NSPD 328
                                       8655 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.02
                             TMPIT  22 kqkleelsklqskcskeikkqkkrlkelksslkklkksvk.eeeeeeveelkeelkerkkvlkevesl 88 
                                       k++ ++l ++ +k+++  +  +   +e+ +sl+++++ ++ + ++++++++++el+++k+++++++++
  gi|298674661|ref|YP_003726411.1| 345 KAERNDLMEMDEKIQNMNNDLTSFKQEILESLENIQSVLEnKVDDDKLTKIEDELSSIKTQISNIQDT 412
                                       4444555555555555555555555555555555555433278999*****************99875 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.93
                             TMPIT  54 kklkksvkeeeeeeveelkeelkerkkvlkevesllpkknglylk 98 
                                       k+    +++++++  ++++++l+e+   l++ +++  +k+g+y +
  gi|298674661|ref|YP_003726411.1| 445 KQ----LEKQSDSDGNTISKNLSEILDKLENQSHIYSQKKGRYKR 485
                                       12....234444555566666666666666666666666666655 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   3.5      0.38   2.3e+02       3      25 ..      47      69 ..      46     119 .. 0.81
   2 ?    6.9   1.6     0.014       8.5       1      28 [.     249     276 ..     249     284 .. 0.86
   3 ?    4.3   0.3     0.087        54       2      32 ..     285     315 ..     284     325 .. 0.83
   4 ?    2.6   0.1       0.3   1.8e+02       7      30 ..     349     372 ..     348     379 .. 0.79
   5 ?    3.3   0.3      0.18   1.1e+02       1      32 [.     391     420 ..     390     425 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.38
                               LPP  3 deLssqVsqLkskvdqlssdvns 25
                                      +eL +++s+Lks  ++l++ v++
  gi|298674661|ref|YP_003726411.1| 47 KELENEISDLKSRLENLQQYVDE 69
                                      58999999999999999988443 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.014
                               LPP   1 kldeLssqVsqLkskvdqlssdvnsaka 28 
                                       kl+eL++ + +Lk+k ++ls d++s+++
  gi|298674661|ref|YP_003726411.1| 249 KLNELNDSLIDLKDKTSNLSRDLESINE 276
                                       899*******************999875 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.087
                               LPP   2 ldeLssqVsqLkskvdqlssdvnsakaaaqa 32 
                                       +d+ s+++s+ +++++++++ +n    a+++
  gi|298674661|ref|YP_003726411.1| 285 IDNNSENISAINNQIEEMTNAINLHTRAIKT 315
                                       5677999999*******99999887777765 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.3
                               LPP   7 sqVsqLkskvdqlssdvnsakaaa 30 
                                       +++ ++ +k++++++d++s k+++
  gi|298674661|ref|YP_003726411.1| 349 NDLMEMDEKIQNMNNDLTSFKQEI 372
                                       577788889999999988887765 PP

  == domain 5  score: 3.3 bits;  conditional E-value: 0.18
                               LPP   1 kldeLssqVsqLkskvdqlssdvnsakaaaqa 32 
                                       kl+++ +++s+ k++++++++  +s++ ++++
  gi|298674661|ref|YP_003726411.1| 391 KLTKIEDELSSIKTQISNIQD--TSIQPDINN 420
                                       678888999999999999887..355555555 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   5.0     0.013         8      61     126 ..      38     102 ..      13     122 .. 0.64
   2 ?    4.2   8.6      0.03        19      57     138 ..     245     321 ..     186     347 .. 0.67
   3 ?    6.7   5.2    0.0054       3.3      20      81 ..     347     411 ..     336     479 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.013
                             Atg14  61 kiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklk..kRrsdleslqnele 126
                                        +  ++ + +el ++i+dl++rl++l++ ++++++++   ++++++l+d++k  + + d + l+++ +
  gi|298674661|ref|YP_003726411.1|  38 TEYMDRSDKKELENEISDLKSRLENLQQYVDERTDSN---SQTISQLKDDVKtkTNYDDFNQLNYSFN 102
                                       3444555556677777777777887777777777766...6789999999995533344444444443 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.03
                             Atg14  57 qledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdleslqneleerrkkqi 133
                                         e+k+  ++++l +lk +++ l++ l+ +++ + ++ ++i++ ++++++ ++++ +++  +++++  ++       
  gi|298674661|ref|YP_003726411.1| 245 IHETKLNELNDSLIDLKDKTSNLSRDLESINEIQNKQSESIDNNSENISAINNQIEEMTNAINLHTRAIKTL----- 316
                                       445566666777777777777777777777777777777777777777777777766666655555544433..... PP

                             Atg14 134 aklqd 138
                                       +k + 
  gi|298674661|ref|YP_003726411.1| 317 NKRLA 321
                                       33333 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0054
                             Atg14  20 gperlyelrerlaklksekeslkkkiekalegke...eaeqledkiknkkakleelksliadlre 81 
                                       ++++l e  e++++++ +  s+k++i + le+ +   e++ ++dk+ +  + l+++k++i+ +++
  gi|298674661|ref|YP_003726411.1| 347 ERNDLMEMDEKIQNMNNDLTSFKQEILESLENIQsvlENKVDDDKLTKIEDELSSIKTQISNIQD 411
                                       4669******************************8887777777777777788888877776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2995  (0.167048); expected 358.6 (0.02)
Passed bias filter:                      633  (0.0353059); expected 358.6 (0.02)
Passed Vit filter:                       121  (0.00674884); expected 17.9 (0.001)
Passed Fwd filter:                        80  (0.00446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 1.12u 0.28s 00:00:01.40 Elapsed: 00:00:00.48
# Mc/sec: 3075.67
//
Query:       gi|298674662|ref|YP_003726412.1|  [L=256]
Description: hypothetical protein Metev_0715 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.051   13.7   0.2       0.29   11.3   0.1    2.2  2  Importin_rep_6  Importin repeat 6
      0.062   12.5   0.0      0.085   12.0   0.0    1.1  1  p31comet        Mad1 and Cdc20-bound-Mad2 binding


Domain annotation for each model (and alignments):
>> Importin_rep_6  Importin repeat 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       0.2   1.8e+03      26      43 ..      57      74 ..      50      77 .. 0.82
   2 ?   11.3   0.1   3.3e-05      0.29      13      59 ..     127     174 ..     119     203 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.2
                    Importin_rep_6 26 lakftkgvsanlsdvyer 43
                                      + +ft+ +++nl ++ ++
  gi|298674662|ref|YP_003726412.1| 57 IFEFTNVINNNLRHISQQ 74
                                      6789999****9988765 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 3.3e-05
                    Importin_rep_6  13 leilganalsedqlakftkgvsanlsdvyerv.kereneddeynedvd 59 
                                       l+i+++ +++ dql+++++ v+++l  + +rv +e + +  ey+ +++
  gi|298674662|ref|YP_003726412.1| 127 LHIFEQRPMTSDQLSQYSEDVANELRALSKRVfDEMYTQSSEYKKNME 174
                                       7899999************************84567899999988764 PP

>> p31comet  Mad1 and Cdc20-bound-Mad2 binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   9.5e-06     0.085      62     168 ..     120     223 ..      94     229 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.5e-06
                                       HHHHHHHHHHHHHTTSSSS-HHHHTS-----------------------HHHHHHHHHHHHHHHHHHHHHHHHHS-- CS
                          p31comet  62 qftcellkhilyqrqqlplpyeqlkhfyrksspqaedmlkkkaraiteassrkcqqalaelesvlshledlfartlv 138
                                         t e++ hi+ qr   p+  +ql ++ ++ + +    l k+ +    ++s  +++ ++ l+ + s++ +++ r  v
  gi|298674662|ref|YP_003726412.1| 120 DTTREVMLHIFEQR---PMTSDQLSQY-SEDVANELRALSKRVFDEMYTQSSEYKKNMEILDDIKSKISSVMGRGEV 192
                                       45677888887666...9******985.555777777888888888889999999********************** PP

                                       SEEEEEE.SS-SSS-SEEEEEE-TTS----- CS
                          p31comet 139 prvlill.ggsalspkefyeldlsrlapssv 168
                                        +vl +     a spk + e +  +l  + +
  gi|298674662|ref|YP_003726412.1| 193 DQVLTMAfNEIASSPKWMTENEWILLVEMVI 223
                                       ****876145567899888877777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1129  (0.0629706); expected 358.6 (0.02)
Passed bias filter:                      664  (0.037035); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1762.97
//
Query:       gi|298674663|ref|YP_003726413.1|  [L=358]
Description: putative circadian clock protein KaiC [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-47  161.5   0.0    3.7e-47  160.6   0.0    1.4  2  ATPase           KaiC
    1.8e-08   34.2   0.0    2.7e-08   33.6   0.0    1.3  1  AAA_25           AAA domain
    0.00018   20.3   0.1     0.0025   16.5   0.1    2.1  1  GvpD             GvpD gas vesicle protein
    0.00025   20.9   0.0    0.00056   19.7   0.0    1.6  1  AAA_24           AAA domain
    0.00027   20.4   0.0    0.00043   19.7   0.0    1.4  1  DnaB_C           DnaB-like helicase C terminal domain
    0.00045   19.6   0.0    0.00066   19.0   0.0    1.2  1  Rad51            Rad51
    0.00047   20.2   0.0     0.0017   18.4   0.0    2.0  2  AAA_14           AAA domain
     0.0046   16.7   0.0     0.0096   15.6   0.0    1.4  1  AAA_29           P-loop containing region of AAA domain
     0.0059   16.5   0.0      0.011   15.5   0.0    1.5  1  MEDS             MEDS: MEthanogen/methylotroph, DcmR Sensory 
     0.0074   15.4   0.0      0.012   14.7   0.0    1.3  1  T2SSE            Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.012   15.4   0.0      0.023   14.4   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
      0.016   15.4   0.0      0.039   14.1   0.0    1.7  1  AAA_33           AAA domain
      0.017   15.4   0.0      0.036   14.3   0.0    1.5  1  AAA_22           AAA domain
      0.017   14.8   0.0      0.038   13.7   0.0    1.5  1  Sigma54_activat  Sigma-54 interaction domain
       0.03   13.8   1.2      0.048   13.2   0.0    1.8  2  AAA_7            P-loop containing dynein motor region
      0.034   14.7   0.1        0.1   13.1   0.0    1.9  2  ABC_tran         ABC transporter
      0.057   13.8   0.1       0.27   11.6   0.1    1.9  2  AAA_16           AAA ATPase domain
      0.078   13.0   0.1       0.65   10.0   0.0    2.2  2  AAA_5            AAA domain (dynein-related subfamily)
       0.11   11.9   0.1       0.18   11.2   0.1    1.3  1  FtsK_SpoIIIE     FtsK/SpoIIIE family


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.6   0.0   3.9e-50   3.7e-47       1     225 [.       6     223 ..       6     230 .. 0.89
   2 ?   -3.3   0.0         5   4.7e+03     112     131 ..     248     267 ..     233     303 .. 0.67

  Alignments for each domain:
  == domain 1  score: 160.6 bits;  conditional E-value: 3.9e-50
                            ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekl 77 
                                       ++tgI glD++++gG+ ++++ l++G++GtGK++fa+q+++ g+e+ ge+ ++v++eep+e++ e+a++lG d++k+
  gi|298674663|ref|YP_003726413.1|   6 IPTGIAGLDRVIEGGLRDNTTLLVVGSSGTGKSTFAMQYIMYGLEN-GENALYVSLEEPPEQILEEAEKLGFDMKKY 81 
                                       69*****************************************999.****************************** PP

                            ATPase  78 eeegklaiidasesaeesaeekdkedleelieelaeaikeika.krvviDsitgl.ayeekeavaReilrqlvrvlk 152
                                        e++++++    e+         k+ +ee +  l ea k++ + +rvviD++t+l   ++++++ Re + +l+++lk
  gi|298674663|ref|YP_003726413.1|  82 HERELFFFHTKGEDF--------KQLVEEQLPALVEANKDYSVrTRVVIDPLTPLiWSISDKKEQRELITKLFYTLK 150
                                       ***777765554444........5678888888899999999989**********99******************** PP

                            ATPase 153 klgvTailvsekss.seeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegik 225
                                       +lg + + ++e s  +e+  +   +  +++dg+++L+++ i + + R+lei+kmR t+h  +++p+   + gi 
  gi|298674663|ref|YP_003726413.1| 151 QLGAVLVTTEEHSApGETIGEDVLIPVYLSDGAVHLTYRPIGGAFNRSLEIIKMRATRHGEEVYPYIFVR-GIG 223
                                       ****99999997774444444556789**************************************96554.444 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 5
                            ATPase 112 aeaikeikakrvviDsitgl 131
                                        +  ++++a+ + +D+i  +
  gi|298674663|ref|YP_003726413.1| 248 IKTASDLGASEMFLDKIRYV 267
                                       44556677788888887766 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.0   2.9e-11   2.7e-08      14     175 ..       5     152 ..       1     163 [. 0.78

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 2.9e-11
                            AAA_25  14 dlaapppprrwlvkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrR 89 
                                       ++ + ++ ++ +++g l+ +++ l++G +gtGK+t+a++     +  G+           + lyvs+E++ +++ + 
  gi|298674663|ref|YP_003726413.1|   5 RIPTGIAGLDRVIEGGLRDNTTLLVVGSSGTGKSTFAMQYIMYGLeNGE-----------NALYVSLEEPPEQILEE 70 
                                       566677788899999999**********************998884444...........89*************** PP

                            AAA_25  90 lravgeal..rddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsr.algg.densn 162
                                       ++++g ++   + ++l++ + +g+         +  +l+++++ al +a +++     vviDpl+  +++  d++++
  gi|298674663|ref|YP_003726413.1|  71 AEKLGFDMkkYHERELFFFHTKGE---------DFKQLVEEQLPALVEANKDYSVRTRVVIDPLTPlIWSIsDKKEQ 138
                                       *****9996544566666665554.........5567788988888888888554667*******966666777777 PP

                            AAA_25 163 sdv.galvealeri 175
                                       ++  ++l+  l+++
  gi|298674663|ref|YP_003726413.1| 139 RELiTKLFYTLKQL 152
                                       77557777777765 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   2.6e-06    0.0025      11     210 ..      25     223 ..      20     264 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.6e-06
                              GvpD  11 ktllikGaPGtGktlftlrgl.dvlrresdvlyvstrvddetvseayfsgeaeldktalldllkdpleldldvdvPi 86 
                                        tll+ G  GtGk +f+++++   l++ ++ lyvs     e + e    ++  +d  +   + +  l +   +   +
  gi|298674663|ref|YP_003726413.1|  25 TTLLVVGSSGTGKSTFAMQYImYGLENGENALYVSLEEPPEQILEEA--EKLGFDMKK---YHERELFFFHTKGEDF 96 
                                       69****************9862579***********99999998753..333344333...3444444444455678 PP

                              GvpD  87 ekldlesllefvdeiaaiatkliialdswelvyeylaerydsPediktvkndlvvlaresgvrlvlvletaan.... 159
                                       ++l  e l   v++ +  + +  + +d    ++  ++ + ++ e i  +   l     + g+ lv   e  a+    
  gi|298674663|ref|YP_003726413.1|  97 KQLVEEQLPALVEANKDYSVRTRVVIDPLTPLIWSISDKKEQRELITKLFYTLK----QLGAVLVTTEEHSAPgeti 169
                                       88888999999999999999999999*988888888888888777665555444....5566666666554431111 PP

                              GvpD 160 ..srl..eyivdGvvtlnvkeddrgrlrrdlrleklrGvrignrlqPftladGkf 210
                                         + l   y+ dG v l  +    g   r+l + k+r  r g+ ++P+ +  G  
  gi|298674663|ref|YP_003726413.1| 170 geDVLipVYLSDGAVHLTYRPI-GGAFNRSLEIIKMRATRHGEEVYPYIFVRGIG 223
                                       104444459********99987.899*********************88777643 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0     6e-07   0.00056       3      77 ..      25     128 ..      23     143 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 6e-07
                            AAA_24   3 lkiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie..........................swedfl 53 
                                         +l++G+sg+GK+t+a ++    ++  +e+G ++l++   + +e                          + edf+
  gi|298674663|ref|YP_003726413.1|  25 TTLLVVGSSGTGKSTFAMQY----IMYGLENGENALYVSLEEPPEqileeaeklgfdmkkyherelfffhtKGEDFK 97 
                                       6789****************....66666666666655554433344444444445555555566666766666666 PP

                            AAA_24  54 devvel.......aaeladyktlviDtidel 77 
                                       + v+e        +++++    +viD ++ l
  gi|298674663|ref|YP_003726413.1|  98 QLVEEQlpalveaNKDYSVRTRVVIDPLTPL 128
                                       6666667777665666666666888877765 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   4.5e-07   0.00043       2      66 ..       6      70 ..       5     154 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 4.5e-07
                                      BXSSTHHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHH CS
                                      xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  2 lstgfkdLDklts.GlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqR 66
                                      ++tg + LD++++ Gl++++ +++ + +++Gk+++a++ +    + +  + +++sle + eq+++ 
  gi|298674663|ref|YP_003726413.1|  6 IPTGIAGLDRVIEgGLRDNTTLLVVGSSGTGKSTFAMQYIMYGLE-NGENALYVSLEEPPEQILEE 70
                                      799******9885279999999****************9998775.56689***********9764 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0     7e-07   0.00066      19     131 ..       6     111 ..       4     153 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 7e-07
                                       E--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGGHHHHHHT CS
                             Rad51  19 lttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrperlveiaery 95 
                                       + tG   lD++++GG++  +   ++G +++Gk+ ++++  ++  l+   +G  ++a+y++ e    pe+++e ae+ 
  gi|298674663|ref|YP_003726413.1|   6 IPTGIAGLDRVIEGGLRDNTTLLVVGSSGTGKSTFAMQY-IMYGLE---NG--ENALYVSLEE--PPEQILEEAEKL 74 
                                       78***********************************97.455554...34..4689999998..5999*******9 PP

                                       T--HHHHGGGEEEEE--STTHHHHHHH.HTHHHHHHS CS
                             Rad51  96 kldkeevlenvayaRaytiehqeellq.qaaallaed 131
                                       + d ++  e+       + e+ ++l++ q++al+  +
  gi|298674663|ref|YP_003726413.1|  75 GFDMKKYHERELFFFHTKGEDFKQLVEeQLPALVEAN 111
                                       9999999888877666666788888876777766544 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.8e-06    0.0017       3      52 ..      25      74 ..      23     108 .. 0.80
   2 ?   -2.6   0.0       5.4   5.1e+03      63      78 ..     254     269 ..     233     274 .. 0.61

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.8e-06
                            AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekl 52
                                        l+++G   +GK+t++ q+i   l + e+ ly++l++++++ l++ ekl
  gi|298674663|ref|YP_003726413.1| 25 TTLLVVGSSGTGKSTFAMQYIMYGLENGENALYVSLEEPPEQILEEAEKL 74
                                      67899****************998899************99877765422 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.4
                            AAA_14  63 ekktylflDEiqevpe 78 
                                        + + +flD i +v++
  gi|298674663|ref|YP_003726413.1| 254 LGASEMFLDKIRYVKK 269
                                       3445589999998876 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0     1e-05    0.0096      24      48 ..      26      48 ..      14      54 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1e-05
                            AAA_29 24 atlltGpsGsGKSTllDAiqalLvp 48
                                      + l++G sG+GKST+  A+q+++++
  gi|298674663|ref|YP_003726413.1| 26 TLLVVGSSGTGKSTF--AMQYIMYG 48
                                      6799**********9..79999997 PP

>> MEDS  MEDS: MEthanogen/methylotroph, DcmR Sensory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.2e-05     0.011      17     108 ..      41     124 ..      15     143 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.2e-05
                              MEDS  17 lvpfikaglargekvlyvasastldelrealrkagldvdaalesgqleildaeetylrgggfdpermlealrralak 93 
                                       ++++i  gl++ge  lyv  ++  ++++e+ +k g d  ++ e++         ++ +  g d ++ +e+   al +
  gi|298674663|ref|YP_003726413.1|  41 AMQYIMYGLENGENALYVSLEEPPEQILEEAEKLGFDMKKYHERE--------LFFFHTKGEDFKQLVEEQLPALVE 109
                                       789**************999************************9........345555556666688888888888 PP

                              MEDS  94 aladgyaglrvigem 108
                                       a +d   + rv++++
  gi|298674663|ref|YP_003726413.1| 110 ANKDYSVRTRVVIDP 124
                                       887767777777776 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.2e-05     0.012     118     182 ..      13      79 ..       7     105 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-05
                             T2SSE 118 iaevlrkavrerglilvsGgTgsGKttll..yallkeinksderivtvEDpvEiqleganqvqlnak 182
                                       +++v++  +r + ++lv G  g+GK+t++  y++    n ++   v +E p E  le+a+++    k
  gi|298674663|ref|YP_003726413.1|  13 LDRVIEGGLRDNTTLLVVGSSGTGKSTFAmqYIMYGLENGENALYVSLEEPPEQILEEAEKLGFDMK 79 
                                       67899999999*****************97666666666667778999*****99998887766655 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.4e-05     0.023      45      89 ..      22      66 ..      17      86 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.4e-05
                         IstB_IS21 45 ekkenivllGpsGvGKshlaialgveavraglsvlfvrvedLvee 89
                                      +++  ++++G sG+GKs +a+   + + ++g + l+v++e+  e+
  gi|298674663|ref|YP_003726413.1| 22 RDNTTLLVVGSSGTGKSTFAMQYIMYGLENGENALYVSLEEPPEQ 66
                                      5678899******************************99875555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.2e-05     0.039       3      20 ..      28      45 ..      27     121 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.2e-05
                            AAA_33  3 llvGlpGsGKstlaerll 20
                                      l+vG +G+GKst+a +++
  gi|298674663|ref|YP_003726413.1| 28 LVVGSSGTGKSTFAMQYI 45
                                      79*************984 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.8e-05     0.036       5     104 ..      24     129 ..      21     162 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.8e-05
                            AAA_22   5 agilvvtGesGtGKTtllrrl.leqldeeakaee....erpevvfvtlpsst.sskdllrellralglelkaerlss 75 
                                        + l+v+G sGtGK+t + ++ ++ l++ ++a +    e+pe+++ ++ +++ + k+  ++ l +++ ++++     
  gi|298674663|ref|YP_003726413.1|  24 NTTLLVVGSSGTGKSTFAMQYiMYGLENGENALYvsleEPPEQILEEAEKLGfDMKKYHERELFFFHTKGED----F 96 
                                       56799*********9976655155666665555588888888888888877777777766666666654444....3 PP

                            AAA_22  76 eell.ealeqalrarav...ielliiDEaqhlr 104
                                       ++l+ e+l   ++a ++   +  ++iD    l+
  gi|298674663|ref|YP_003726413.1|  97 KQLVeEQLPALVEANKDysvRTRVVIDPLTPLI 129
                                       333322222222222223335666776666655 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.1e-05     0.038      20      67 ..      22      69 ..       9      77 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.1e-05
                                      TSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHH CS
                   Sigma54_activat 20 ktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelle 67
                                      + ++++l++G sGtGK+++a ++     ++ ++ + v   + pe++le
  gi|298674663|ref|YP_003726413.1| 22 RDNTTLLVVGSSGTGKSTFAMQYIMYGLENGENALYVSLEEPPEQILE 69
                                      567899**************9988777777777777777777777776 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.1e-05     0.048      29      58 ..      20      50 ..      11      61 .. 0.80
   2 ?   -2.0   0.3       2.3   2.2e+03      55      85 ..     303     333 ..     299     340 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.1e-05
                             AAA_7 29 llknkkpvllvGptGtGKtviikd.llkkld 58
                                       l+ +  +l+vG++GtGK++ +++ ++  l+
  gi|298674663|ref|YP_003726413.1| 20 GLRDNTTLLVVGSSGTGKSTFAMQyIMYGLE 50
                                      5778899**************9997777776 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.3
                             AAA_7  55 kkldkekylsltinfsaqtsanqlqdiiesk 85 
                                       +++dk++++s + + s++ s++q+ + ++++
  gi|298674663|ref|YP_003726413.1| 303 ENVDKDNTSSSQSEQSSNESSQQTTESFDKS 333
                                       5788999999999999999999999988765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00011       0.1       7      36 ..      20      51 ..      15     159 .. 0.76
   2 ?   -1.2   0.1       2.8   2.6e+03      43      60 ..     304     321 ..     258     352 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                                      EEETTSEEEEEESTTSSHHHHHH..HHTTSS- CS
                                      xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxx RF
                          ABC_tran  7 klkegekvaivGenGaGKStLlk..llagllk 36
                                       l+ ++++ +vG++G+GKSt+++  +++gl++
  gi|298674663|ref|YP_003726413.1| 20 GLRDNTTLLVVGSSGTGKSTFAMqyIMYGLEN 51
                                      67788999************975335555554 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.8
                                       EETTCEGGGB-HHHCCHC CS
                                       xxxxxxxxxxxxxxxxxx RF
                          ABC_tran  43 lldgkdlkeqeleslrke 60 
                                       ++d++++++ + e++++e
  gi|298674663|ref|YP_003726413.1| 304 NVDKDNTSSSQSEQSSNE 321
                                       222222222222222222 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00028      0.27      17      42 ..      14      42 ..      10      47 .. 0.78
   2 ?   -2.1   0.0       4.8   4.5e+03      18      39 ..     206     229 ..     200     262 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00028
                            AAA_16 17 ervrsgrp...elvllsGesGvGKsslvr 42
                                      +rv +g+      +l++G sG+GKs+ + 
  gi|298674663|ref|YP_003726413.1| 14 DRVIEGGLrdnTTLLVVGSSGTGKSTFAM 42
                                      5666666666689************9875 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.8
                            AAA_16  18 rvrsgrp..elvllsGesGvGKss 39 
                                       ++r g++  ++++++G   v K++
  gi|298674663|ref|YP_003726413.1| 206 ATRHGEEvyPYIFVRGIGVVAKTT 229
                                       566777788899999999999987 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00069      0.65       2      20 ..      27      45 ..      26      73 .. 0.79
   2 ?    0.4   0.1      0.62   5.8e+02      26      58 ..     284     316 ..     278     354 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00069
                                      EEEE--SSSSHHHHHHHGG CS
                             AAA_5  2 vlLvGppGtgKselaerla 20
                                      +l+vG +GtgKs++a+++ 
  gi|298674663|ref|YP_003726413.1| 27 LLVVGSSGTGKSTFAMQYI 45
                                      799************9975 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.62
                                       -EEEEE--TT--HHHHH--B--.........-- CS
                             AAA_5  26 eveyvqltrdtteedlkgrreikngttslvdsp 58 
                                        +e++ lt+ ++++d+ g+ ++++++ts ++s+
  gi|298674663|ref|YP_003726413.1| 284 LFETYGLTQAIKKDDVSGSENVDKDNTSSSQSE 316
                                       578889999999999999999998888877664 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00019      0.18      30      60 ..      16      45 ..       5      49 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00019
                                      EEEEEGGGS-.SEEEE--TTSSHHHHHHHHH CS
                      FtsK_SpoIIIE 30 plvldlkkmashllvaGatgsGKStalntLi 60
                                      +++  l+ ++  llv+G++g+GKSt+ +  i
  gi|298674663|ref|YP_003726413.1| 16 VIEGGLRDNT-TLLVVGSSGTGKSTFAMQYI 45
                                      5555567777.89************988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1391  (0.0775838); expected 358.6 (0.02)
Passed bias filter:                      758  (0.0422779); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 2479.16
//
Query:       gi|298674664|ref|YP_003726414.1|  [L=105]
Description: hypothetical protein Metev_0717 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00042   20.0   0.1    0.00056   19.5   0.1    1.2  1  LSM       LSM domain
  ------ inclusion threshold ------
      0.043   13.4   0.1      0.051   13.1   0.1    1.0  1  Gemin6    Gemin6 protein


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   6.3e-08   0.00056       2      65 ..      12      74 ..      11      76 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 6.3e-08
                                      HHHHTTTSEEEEEETTSEEEEEEEEEEE.TTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEE CS
                               LSM  2 flkklinkkvtvelkngrelrGtLkgfD.qfmNlvLedveetlkdkkekrklglvliRGnnivli 65
                                       l +++++ ++v++ ++  +rG  + +D  + N+ L+d++    ++  k+  +lv+iRG++i +i
  gi|298674664|ref|YP_003726414.1| 12 SLTNFLGNYIRVIT-DNAHYRGYCEKVDySYTNILLKDAVQKTVNG-WKHISNLVMIRGESIESI 74
                                      57888888899886.5678*********779**********99999.8888889********987 PP

>> Gemin6  Gemin6 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   5.7e-06     0.051       9      90 ..      10      97 ..       3     104 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.7e-06
                            Gemin6  9 llefedyvekevkvllsekeikGwlltvdpvsksvvl...vnfledG..alsvsv.vlGhavktveiiseleyrkrekl 81
                                       +  +++    ++v+  + +++G+   vd    +++l   v+ + +G   +s+ v + G +++ + i +   +   e l
  gi|298674664|ref|YP_003726414.1| 10 CESLTNFLGNYIRVITDNAHYRGYCEKVDYSYTNILLkdaVQKTVNGwkHISNLVmIRGESIESIYIEKAYPFDDDEDL 88
                                      57789*******************************933334455563345665525599***9999999999999999 PP

                            Gemin6 82 myvyaslea 90
                                      +    ++e+
  gi|298674664|ref|YP_003726414.1| 89 ILSIEKGEV 97
                                      888777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 806.95
//
Query:       gi|298674665|ref|YP_003726415.1|  [L=317]
Description: hypothetical protein Metev_0718 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-07   30.0   0.9      9e-07   28.8   0.9    1.6  1  V4R              V4R domain
  ------ inclusion threshold ------
        3.9    7.3   9.4        5.7    6.8   9.4    1.2  1  Folliculin       Vesicle coat protein involved in Golgi to pl
        7.1    7.7   9.5         13    6.9   9.5    1.3  1  DUF4834          Domain of unknown function (DUF4834)
        9.5    5.5   7.8    1.1e+02    2.1   7.0    2.1  2  GNAT_acetyltr_2  GNAT acetyltransferase 2


Domain annotation for each model (and alignments):
>> V4R  V4R domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.9     2e-10     9e-07       5      60 ..     103     159 ..     100     161 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 2e-10
                                       EEEES-S-TT--.-SS---HHHHHHHHHHHHHHHSSEEEEEEEE-GGGT-SSEEEEE CS
                               V4R   5 ieespelaglpg.keePvCyleaGllagalsellgkrveveEveCaaeGhdhCeFev 60 
                                       + ++p+++ +p+ ++++vC +   +l+++++e l+ ++ veE+eC   G++ C+F+v
  gi|298674665|ref|YP_003726415.1| 103 VPNCPVCSLYPAlENQKVCVATSDALHRFFTEDLELECTVEEIECVKDGDKLCKFKV 159
                                       568********95679***************************************98 PP

>> Folliculin  Vesicle coat protein involved in Golgi to plasma membrane transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   9.4    0.0013       5.7      83     142 ..     246     303 ..     237     317 .] 0.56

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0013
                        Folliculin  83 kawsfiveafeklaaeiqalaeaelereskeeeassaassssalkadgsglsrregssfs 142
                                       ++ + + +af ++a+++q++++++++++++++++s ++++ +++++++++ +++++++ +
  gi|298674665|ref|YP_003726415.1| 246 SKKKTFGAAFGEMAQKVQNESDTQQSQSQSQSQSSDTQTQDNESDKSKEA-KEESKDT-Q 303
                                       556677899****************9998866544433333332222222.2221221.1 PP

>> DUF4834  Domain of unknown function (DUF4834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   9.5    0.0028        13      29      77 ..     254     303 ..     237     313 .. 0.40

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0028
                           DUF4834  29 vfg.lgsrkkssksaqkqfgnstnsnqqksqsrsetkeegeiieeersek 77 
                                        fg + ++ ++++  q+++++s++++++ +++++e+++++e++ee+++++
  gi|298674665|ref|YP_003726415.1| 254 AFGeMAQKVQNESDTQQSQSQSQSQSSDTQTQDNESDKSKEAKEESKDTQ 303
                                       33322222222222222222222222222223333333333333333333 PP

>> GNAT_acetyltr_2  GNAT acetyltransferase 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.025   1.1e+02      17      32 ..      88     103 ..      85     145 .. 0.89
   2 ?    2.1   7.0     0.023   1.1e+02     118     175 ..     257     315 ..     242     317 .] 0.52

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.025
                   GNAT_acetyltr_2  17 DLqllsDaPahklfvL 32 
                                       D+ql+s aP h +f+ 
  gi|298674665|ref|YP_003726415.1|  88 DMQLVSYAPMHYIFAV 103
                                       9************986 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.023
                   GNAT_acetyltr_2 118 ellekyyegklssleeeeekeeeeeeekeeeee.klsleeeklkprkelpplllklsee 175
                                       e+ +k  +++ ++++++++++++++++++++e+ k+++ +e+ k++++ ++l+ k++++
  gi|298674665|ref|YP_003726415.1| 257 EMAQKVQNESDTQQSQSQSQSQSSDTQTQDNESdKSKEAKEESKDTQSFAELFEKMKKK 315
                                       33333334443444444444334444433333347777778888888888888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3035  (0.169279); expected 358.6 (0.02)
Passed bias filter:                     1036  (0.0577835); expected 358.6 (0.02)
Passed Vit filter:                       191  (0.0106531); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.46
# Mc/sec: 2064.14
//
Query:       gi|298674666|ref|YP_003726416.1|  [L=197]
Description: hypothetical protein Metev_0719 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.011   15.4   0.0      0.028   14.2   0.1    1.7  1  CheF-arch  Chemotaxis signal transduction system protein F fr
       0.14   12.1   0.0       0.41   10.5   0.0    1.8  2  GRAM       GRAM domain


Domain annotation for each model (and alignments):
>> CheF-arch  Chemotaxis signal transduction system protein F from archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   3.1e-06     0.028      21      69 ..      29      77 ..      17     122 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.1e-06
                         CheF-arch 21 dvkWekgrilLsnkrlvlasedkkitiplssvedvggevPrklkdifdd 69
                                        +Wekg ++L+n  l +   ++  tipl+++  +g e  +++k  ++ 
  gi|298674666|ref|YP_003726416.1| 29 SNNWEKGVMYLTNINLWFSVGNGWETIPLKNITMIGREPTSSIKTKAQR 77
                                      568*****************************88888777777765544 PP

>> GRAM  GRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   4.6e-05      0.41      31      71 ..      33      68 ..       5      92 .. 0.80
   2 ?   -1.6   0.0      0.26   2.3e+03      10      26 ..     107     123 ..     100     140 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.6e-05
                                      EEEEEEEESSEEEEEE-STT---EEEEEGGGEEEEEE.... CS
                              GRAM 31 vqGrlyltnyrlcFrskplgsskkvvlpladikriekstsa 71
                                       +G++yltn +l F+  + g++   ++pl+ i+ i + +++
  gi|298674666|ref|YP_003726416.1| 33 EKGVMYLTNINLWFSVGN-GWE---TIPLKNITMIGR-EPT 68
                                      58************9888.***...599999998888.333 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.26
                                       --TT--EEEEEEEEEES CS
                              GRAM  10 llpeEkllatykCyllr 26 
                                       l+ +E +++t+k yl++
  gi|298674666|ref|YP_003726416.1| 107 LAGNESIINTLKNYLQP 123
                                       34488888888877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1550.74
//
Query:       gi|298674667|ref|YP_003726417.1|  [L=267]
Description: hypothetical protein Metev_0720 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      7e-06   26.3   0.0    1.6e-05   25.1   0.0    1.7  2  Acetyltransf_1  Acetyltransferase (GNAT) family


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.26   4.6e+03      82      99 ..       1      17 [.       1      42 [. 0.72
   2 !   25.1   0.0   8.7e-10   1.6e-05      19      83 ..      43     111 ..      25     139 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.26
                                      HHHHHHHHHHT.TESEEEE CS
                    Acetyltransf_1 82 lealeeraree.gikkivl 99
                                      ++++++ a+++ g   +++
  gi|298674667|ref|YP_003726417.1|  1 MTTMIDLAKSNnGM--VYC 17
                                      67788888888554..244 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 8.7e-10
                                       HHHHHHHHHHHSTTC.EEEEEEETTEEEEEEEEEEEET...TSTTEEEEEEEEESGGGTTSSHHHHHHH CS
                    Acetyltransf_1  19 aseeefeesfsleae.gllvaeedgeliGfisllkipd...ekggvayieslaVspeyrgkGlGsaLle 83 
                                       +++   ++s+++  +  ++  +  ++++G+ ++ k  +   ++++v++++++ +s++  g+G+G+ Ll+
  gi|298674667|ref|YP_003726417.1|  43 SDYSKNFKSWINRQNvVFITTLLKNTVVGWTMAEKWSHtstNSKPVYVLRGIEISSSKKGNGYGKILLD 111
                                       4444455555555552555599999******************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       882  (0.049194); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2049.16
//
Query:       gi|298674668|ref|YP_003726418.1|  [L=454]
Description: histone deacetylase superfamily protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.1e-80  268.4   0.0    1.5e-79  267.7   0.0    1.3  1  Hist_deacetyl  Histone deacetylase domain
  ------ inclusion threshold ------
       0.81    9.3   3.5        1.6    8.3   3.5    1.5  1  SUR7           SUR7/PalI family


Domain annotation for each model (and alignments):
>> Hist_deacetyl  Histone deacetylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  267.7   0.0   1.6e-83   1.5e-79       3     300 ..     114     395 ..     112     402 .. 0.92

  Alignments for each domain:
  == domain 1  score: 267.7 bits;  conditional E-value: 1.6e-83
                                       CGTHHHHHHHHHHHHT.THHHHCCE..EE-----HHHHTTTS-HHHHHHHHCHHHHCHHT.TTHCCHHHCCTSTSSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl   3 enpkRlsaileslaesvglldelel.liqpseatkeellkvHskeYlelleslsnelkkkeeakekeleeiasklld 78 
                                       e+p+Rl+ + + l++++   d+ +  + +  +a +++llk+H+k+Y+ ++++ s   kk                l 
  gi|298674668|ref|YP_003726418.1| 114 EKPERLIDAFQYLKDNKIFNDDRCNlVTDIDKALEKDLLKIHTKSYVSFIKNYS---KKGG------------GFLG 175
                                       899************8444444333478889999****************9654...4443............2467 PP

                                       SSTHCTTTCCHHHHHHHHHHHHHHHHHHTTSSSEEEETTSS--TT-BTTB-BTTBSS-HHHHHHHHHHHCC-SS-EE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl  79 ddtpvspktlkaallavgavleavdavlsgsvkaafvlvrPpgHHakaseasGFClvNnvaiaikylqakhelkrva 155
                                       d+t+v+++t+++a++++ga+++ +++v++++++  f+l rPpgHHa +s+ +GFC++Nn+ai ++ylq+k ++++v+
  gi|298674668|ref|YP_003726418.1| 176 DSTYVTKDTYDVAKMSAGAAIRSAELVIDNNYSYSFALLRPPGHHAGKSRYGGFCIFNNAAILARYLQQKKGIEKVM 252
                                       88*************************************************************************** PP

                                       EEE-SSS--HHHHHHCTT-TTEEEEEEEE-CCTSTTSS--TT---SGGGTTSEEEEEE-TT-BHHHHHHHHHHCHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl 156 ilDvDvHhGnGteeafysdpdvltlSiHryegifyPgtgaledlgegkgkgfnlnvpleegtgdeeylkvfeeilrp 232
                                       i+D+D+H GnGt ++fy+dpdv+tlSiHr+++ fyP tg ++++geg+g+g+n+n++++ g+++ ey  +f+e+++p
  gi|298674668|ref|YP_003726418.1| 253 IVDWDAHAGNGTMDIFYDDPDVITLSIHRSPHDFYPRTGFMSQIGEGAGEGYNINIEMPVGSENVEYKLAFDEVIIP 329
                                       ***************************************************************************** PP

                                       HHCCH--SEEEEEE-STTBTTSTT-S-BB-HHHHHHHHHHHCCCHGS-G.EEEEE-S---HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl 233 vleefkPdlilvsaGfDalkgdplgelnlsvegykeltkklaeladkvkkvvllleGGYnlealarav 300
                                       ++++++Pd+++  +GfD++ +++  ++nl+ +gy+++++++++++ +  ++v+l+eGGY++ +++ + 
  gi|298674668|ref|YP_003726418.1| 330 LIKRHSPDFLICCCGFDGYYQEKTVQMNLTSKGYYQMIRSIKSVFPE--NFVILMEGGYHKHNGKLCH 395
                                       *********************************************94..8**********98877665 PP

>> SUR7  SUR7/PalI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   3.5   0.00017       1.6      47     107 ..      27      87 ..      13     163 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00017
                              SUR7  47 qigladvysfgvwgyC.dnsdvnytkCsk.pkagypfdp.leelnsesngkvdlPsnlrktlsk 107
                                       qi + ++ ++g++gyC  n d++++ C++ p+++  ++  l+++n++s++k   P ++   l+ 
  gi|298674668|ref|YP_003726418.1|  27 QILMDNFKDYGYYGYCsVNIDDEKSVCTNvPEPND-LKSeLNNINQNSETK--NPTDVSTELNQ 87 
                                       556678899*******888999999***9445543.332378888888877..78888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 3347.47
//
Query:       gi|298674669|ref|YP_003726419.1|  [L=313]
Description: hypothetical protein Metev_0722 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0096   16.1   0.1      0.022   14.9   0.1    1.6  1  Transglut_C  Transglutaminase family, C-terminal ig like doma
  ------ inclusion threshold ------
       0.02   14.3   0.0       0.13   11.6   0.1    2.2  2  TRAP_beta    Translocon-associated protein beta (TRAPB)
        2.6    8.8   7.5       0.55   10.9   0.4    2.6  2  DUF3139      Protein of unknown function (DUF3139)


Domain annotation for each model (and alignments):
>> Transglut_C  Transglutaminase family, C-terminal ig like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   3.7e-06     0.022      11      80 ..     220     283 ..     214     296 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.7e-06
                                       EBTTSEEEEEEEEEE-SSS-BEEEEEEEEEEEEECTTTEEEEEEEEEEEEEE-TTEEEEEEEEE-HHSHE CS
                       Transglut_C  11 avlgqdltvsvllkNplseelkdvklnlcaqtveynGvlaaefkkksleltLePkeeksvrlkilpskyG 80 
                                        ++g++ ++ v +kNp++++ ++   n  + +v+ n +  + ++ + +++t+ P+++++ + +++p+ +G
  gi|298674669|ref|YP_003726419.1| 220 NKVGKKSKIDVWVKNPSKKP-YN---NFKVVAVYCNTL--KVKNPTLDFGTIAPGQTVKQTWEVIPEASG 283
                                       589*****************.78...788999999999..46888999*******************997 PP

>> TRAP_beta  Translocon-associated protein beta (TRAPB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.12   7.1e+02     147     163 ..     164     180 ..     144     201 .. 0.82
   2 ?   11.6   0.1   2.2e-05      0.13      72     111 ..     257     296 ..     221     305 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.12
                         TRAP_beta 147 dwvafaviilpvvgipl 163
                                       ++v ++ ii++v+g+++
  gi|298674669|ref|YP_003726419.1| 164 NYVLYILIIFSVIGVLV 180
                                       58899999999888765 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 2.2e-05
                         TRAP_beta  72 slsakwerlapgenvshsfvvepkksgsfngtaavvtYre 111
                                       + ++ + ++apg++v+ + +v+p +sg+ ++   +v +++
  gi|298674669|ref|YP_003726419.1| 257 NPTLDFGTIAPGQTVKQTWEVIPEASGIVSINKPTVVFEN 296
                                       6778899***********************9999998854 PP

>> DUF3139  Protein of unknown function (DUF3139)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.4   9.2e-05      0.55       1      76 [.       1      72 [.       1      87 [. 0.76
   2 ?    0.8   1.6      0.14   8.2e+02       8      28 ..     167     185 ..     164     249 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 9.2e-05
                           DUF3139  1 mkkiiiililliillvivkvflglvgskpikkylankkldkylqekgykeddIksikpkydskkgsyya..kVvFKDe 76
                                      mkk+ +il++++il  i   + g+  +k++k   +n+ + ++l  ++ ++ d k+  + y   k  y    k +F+De
  gi|298674669|ref|YP_003726419.1|  1 MKKWVFILTIFFILASI--CLSGCSENKQVKP--VNETILSFL--DKVNKTDFKNAHSFYEGGKYPYPEvmKQIFRDE 72
                                      8*********9999998..5669999999964..788888888..677777777766666655555543446666665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.14
                           DUF3139   8 lilliillvivkvflglvgsk 28 
                                       l +lii++vi  v++ ++++k
  gi|298674669|ref|YP_003726419.1| 167 LYILIIFSVI-GVLV-YTKNK 185
                                       5667777776.4444.44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       933  (0.0520386); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2299.85
//
Query:       gi|298674670|ref|YP_003726420.1|  [L=242]
Description: hypothetical protein Metev_0723 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.03   14.6   2.5        1.6    9.0   0.9    2.5  2  Chi-conotoxin  chi-Conotoxin or t superfamily


Domain annotation for each model (and alignments):
>> Chi-conotoxin  chi-Conotoxin or t superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0    0.0024        44       3      13 ..       5      15 ..       3      38 .. 0.67
   2 ?    9.0   0.9   9.1e-05       1.6       4      18 ..     220     234 ..     217     240 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0024
                     Chi-conotoxin  3 clpVFvILLLL 13
                                       + VF+ILL  
  gi|298674670|ref|YP_003726420.1|  5 IFTVFIILLFT 15
                                      678*****974 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 9.1e-05
                     Chi-conotoxin   4 lpVFvILLLLiaSaP 18 
                                       ++ Fv+LL+LiaSa 
  gi|298674670|ref|YP_003726420.1| 220 ISLFVLLLVLIASAS 234
                                       678**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1005  (0.0560544); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1908.43
//
Query:       gi|298674671|ref|YP_003726421.1|  [L=235]
Description: flagellin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-36  126.5   7.6    1.5e-36  126.1   7.6    1.2  1  Arch_flagellin  Archaebacterial flagellin
     0.0015   18.8   1.0       0.55   10.4   0.2    2.2  2  DUF4330         Domain of unknown function (DUF4330)
  ------ inclusion threshold ------
       0.04   13.3   0.3       0.05   13.0   0.3    1.2  1  Adap_comp_sub   Adaptor complexes medium subunit family
      0.044   13.8   0.0       0.18   11.8   0.0    1.9  2  CbtA_toxin      CbtA_toxin of type IV toxin-antitoxin system


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.1   7.6   3.3e-40   1.5e-36       1     164 []      14     219 ..      14     219 .. 0.95

  Alignments for each domain:
  == domain 1  score: 126.1 bits;  conditional E-value: 3.3e-40
                                       X--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEE.....EEE-SSSSSEEEEE CS
                    Arch_flagellin   1 GfvgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvg.....dsatngtineitiy 72 
                                       G+vgigtlI+fIAmVlVAAvaa vli+t+g lqq+aqstg+e+t++vss+++i  + g     +s+ ++ti+++ i 
  gi|298674671|ref|YP_003726421.1|  14 GQVGIGTLIIFIAMVLVAAVAAAVLIQTSGNLQQRAQSTGQEATAEVSSNMDIKAIEGirannTSGLSNTIDYLKIR 90 
                                       89********************************************************998877777788888**** PP

                                       EE--TTS--EEGGG-EEEEEESS--EE--E.................................T-EE-TT-EEEEEE CS
                    Arch_flagellin  73 vklnaGsspidlnkttisvtddgqetlltad...............efgivvisdtdgsltngdevlekgekvelev 134
                                         ++aG++++dl++ +i+++d+++ ++l  +               +f++++i d+d+s++++++v+++g++v+l+v
  gi|298674671|ref|YP_003726421.1|  91 TGVSAGATAMDLSQLIITISDSDERNVLEHNesglngsntmnyskeHFSLNSIRDEDNSFSKTNPVMNRGDLVTLNV 167
                                       ***********************888888889********************************************* PP

                                       E--......................TTT---TT-EEEEEEE-SSS--EEEEE CS
                    Arch_flagellin 135 nvn......................eddgitagdevsvevvpenGasttief 164
                                        +                          ++++++ vs++++pe+G s  i+f
  gi|298674671|ref|YP_003726421.1| 168 STLtettakasymvngmsvpnnpvdSELKLDTRTSVSITLTPESGTSKQIDF 219
                                       9779*******************9966679****************999986 PP

>> DUF4330  Domain of unknown function (DUF4330)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.2   0.00012      0.55      19      65 ..      24      70 ..       9     124 .. 0.72
   2 !    7.3   0.0    0.0011         5      48      88 ..     170     212 ..     156     221 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00012
                           DUF4330 19 llailvilavivgiflkpgts.gsvaqaeaaatkpvevdvvvrglevp 65
                                      ++a++++ av++++++ ++ + ++ aq ++ ++++ ev+  + +++++
  gi|298674671|ref|YP_003726421.1| 24 FIAMVLVAAVAAAVLIQTSGNlQQRAQSTG-QEATAEVSSNMDIKAIE 70
                                      456666666666666666666666677776.67777887777766664 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0011
                           DUF4330  48 aatkpvevdvvvrglevpeelak.v.kegektniiirnqPagd 88 
                                        ++ + +++++v g +vp++ ++ + k + +t+++i+  P + 
  gi|298674671|ref|YP_003726421.1| 170 LTETTAKASYMVNGMSVPNNPVDsElKLDTRTSVSITLTPESG 212
                                       45677889***************878**********9999854 PP

>> Adap_comp_sub  Adaptor complexes medium subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   1.1e-05      0.05     128     218 ..      64     175 ..      41     217 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.1e-05
                                       SEEEEEEEEE..E-S-T.T-EEEEEEEEEE--TT-EEEEEEESSTT-EEEEETTEEEEEE--EETT-EE..EE.EEE CS
                     Adap_comp_sub 128 vrveielklk..enfkk.kltlenvkisiplpkevsnlaiktskGkakynpeenaleWtikklpggnesslsg.ele 200
                                       ++++    ++  +++   ++t++ +ki+  +++ ++++++++ ++++    e+n+le +  +l+g+n++++s   ++
  gi|298674671|ref|YP_003726421.1|  64 MDIKAIEGIRanNTS-GlSNTIDYLKIRTGVSAGATAMDLSQLIITISDSDERNVLEHNESGLNGSNTMNYSKeHFS 139
                                       444433333321333.3589*****************************************************9*** PP

                                       EE--------------...................E CS
                     Adap_comp_sub 201 leaesekkeenprdgkl..................v 218
                                       l++++ +++++ + +++                  +
  gi|298674671|ref|YP_003726421.1| 140 LNSIRDEDNSFSKTNPVmnrgdlvtlnvstltettA 175
                                       ***********9988877777666655544444444 PP

>> CbtA_toxin  CbtA_toxin of type IV toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.33   1.5e+03      79      97 ..      71      89 ..      54     104 .. 0.66
   2 ?   11.8   0.0     4e-05      0.18      44      98 ..     112     166 ..      98     179 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.33
                        CbtA_toxin 79 gfsaqeqspyisavdilra 97
                                      g+ a + s + +++d l+ 
  gi|298674671|ref|YP_003726421.1| 71 GIRANNTSGLSNTIDYLKI 89
                                      4444455555555555555 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 4e-05
                        CbtA_toxin  44 adeavikehidagitladavnflvekyelvridrkgfsaqeqspyisavdilrar 98 
                                       +de+ + eh ++g+  ++++n+  e++ l  i  +  s+ +  p+++  d++   
  gi|298674671|ref|YP_003726421.1| 112 SDERNVLEHNESGLNGSNTMNYSKEHFSLNSIRDEDNSFSKTNPVMNRGDLVTLN 166
                                       79******************************999999999*****999987654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1028  (0.0573373); expected 358.6 (0.02)
Passed bias filter:                      640  (0.0356964); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1778.11
//
Query:       gi|298674672|ref|YP_003726422.1|  [L=244]
Description: flagellin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-32  112.8  15.1    4.1e-32  111.6  15.1    1.6  1  Arch_flagellin   Archaebacterial flagellin
  ------ inclusion threshold ------
       0.47   10.5   2.3        1.5    8.8   2.3    1.8  1  Methyltransf_21  Methyltransferase FkbM domain


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.6  15.1   4.6e-36   4.1e-32       1     163 [.      14     227 ..      14     228 .. 0.91

  Alignments for each domain:
  == domain 1  score: 111.6 bits;  conditional E-value: 4.6e-36
                                       X--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSE......EEE CS
                    Arch_flagellin   1 GfvgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvgdsatngtine......iti 71 
                                       G+vgigtlI+fIAmVlVAAvaa vli+t+g lqq+aqstg+e+t++vss+l+i  + g  a++g++n       + i
  gi|298674672|ref|YP_003726422.1|  14 GQVGIGTLIIFIAMVLVAAVAAAVLIQTSGNLQQRAQSTGQEATAEVSSNLDIKTIEGIRADSGDNNLtpyidyLKI 90 
                                       89********************************************************7777766666677777999 PP

                                       EEE--TTS--EEGGG-EEEEEESS--EE--E......................................T-EE-TT- CS
                    Arch_flagellin  72 yvklnaGsspidlnkttisvtddgqetlltad....................efgivvisdtdgsltngdevlekge 128
                                           +aG++++dl++ +i+++d+++ ++l++                     +++++++ d+dgs++++++v+++g+
  gi|298674672|ref|YP_003726422.1|  91 RTGISAGAQAMDLSQLVITISDSNERNVLKYYgndtyepdgydiinnnnsteQYSMSATRDEDGSFSKSNPVMNRGD 167
                                       99999*******************888888878******************999*********************** PP

                                       EEEEEEE--.........................TTT---TT-EEEEEEE-SSS--EEEE CS
                    Arch_flagellin 129 kvelevnvn.........................eddgitagdevsvevvpenGasttie 163
                                       +ve++v +                             +++++++vs+  +pe G +  ++
  gi|298674672|ref|YP_003726422.1| 168 LVEINVSTItsdsldynniddidistvnssntteSGLELDTRTTVSISMTPEAGTTKQLD 227
                                       *******88999999999999999999999888766668899999999999999887665 PP

>> Methyltransf_21  Methyltransferase FkbM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   2.3   0.00016       1.5      55     116 ..     126     191 ..       2     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00016
                   Methyltransf_21  55 v...glyelivegksggkyfpfavgdtngfsts..svlggedaryievpvvtldsf.leeikksridl 116
                                       +   + y+ i +++s ++y   a+ d++g+++    v+ + d ++i+v+++t ds+   +  + +id+
  gi|298674672|ref|YP_003726422.1| 126 TyepDGYDIINNNNSTEQYSMSATRDEDGSFSKsnPVMNRGDLVEINVSTITSDSLdYNN--IDDIDI 191
                                       1555778877777777***********999999777777999999999999999884444..477775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1083  (0.0604049); expected 358.6 (0.02)
Passed bias filter:                      665  (0.0370907); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1616.63
//
Query:       gi|298674673|ref|YP_003726423.1|  [L=242]
Description: hypothetical protein Metev_0726 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.15   12.0   0.3       0.15   12.0   0.3    3.0  3  Herpes_UL73  UL73 viral envelope glycoprotein
        4.3    7.0  28.9        1.5    8.5   5.5    3.0  2  Yip1         Yip1 domain


Domain annotation for each model (and alignments):
>> Herpes_UL73  UL73 viral envelope glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.3      0.51   4.6e+03      35      47 ..      14      26 ..       9      26 .. 0.80
   2 ?   12.0   0.3   1.7e-05      0.15      35      64 ..      36      65 ..      33      76 .. 0.90
   3 ?   -1.7   0.4      0.34     3e+03      36      58 ..     139     161 ..     133     166 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.51
                       Herpes_UL73 35 slslsSFssiwal 47
                                      ++ +sSF   w+l
  gi|298674673|ref|YP_003726423.1| 14 AITVSSFTLAWVL 26
                                      5788999988876 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 1.7e-05
                       Herpes_UL73 35 slslsSFssiwallnvlvvivalliylryl 64
                                      ++sl S  s+w+l++v  +++++ i+  yl
  gi|298674673|ref|YP_003726423.1| 36 KPSLWSLISLWFLIGVTYLTISIGIFAEYL 65
                                      6899**********************9997 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.34
                       Herpes_UL73  36 lslsSFssiwallnvlvvivall 58 
                                       +s+s   +i++++ +l +i  ++
  gi|298674673|ref|YP_003726423.1| 139 ISVSGDLTIYMYIIALFIIPTSM 161
                                       66677778888877766665544 PP

>> Yip1  Yip1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   5.5   0.00017       1.5      16      80 ..      35      98 ..      27      99 .. 0.80
   2 ?    7.6  10.7   0.00031       2.8      28     137 ..     111     222 ..     103     227 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00017
                              Yip1 16 ppilrapdlallllalltlllgllaslnlgqtlasg.eevqgltlssllgaiiggylglllgllll 80
                                      +    +++  + l++l+++ +++++ ++++ +l+ +    ++l+l+s+ +a+++ +l+++++++++
  gi|298674673|ref|YP_003726423.1| 35 NK--PSLWSLISLWFLIGVTYLTISIGIFAEYLQHQyLNTAMLNLGSVSFAFVSVPLVFFITYVII 98
                                      33..57999999**************9999999999866668888888888888888888888887 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00031
                              Yip1  28 llalltlllgllas........lnlgqtlasg.....eevqgltlssllgaiiggylglllgllllalllhliakll 91 
                                       ++++  l               +   +  a +       + +lt  +++ a+++++  ++lgllll ll++l     
  gi|298674673|ref|YP_003726423.1| 111 FAIFSILY-----LnyfhsinaG---NLGATDhssiiSVSGDLTIYMYIIALFIIPTSMILGLLLLLLLQKL----- 174
                                       23333333.....2344434331...222222555655578888999999999999999*************..... PP

                              Yip1  92 ggkgsfkqtlsvvgyallP..lilgaliaillllllgtllllvgllal 137
                                         ++++k+tl +vg +l+   ++l +l +   + l+  ++++vg++++
  gi|298674673|ref|YP_003726423.1| 175 PRSTHYKKTLPLVGMSLVFdfMMLDVLTLTETMQLSARIFIVVGIVLT 222
                                       ****************55311333333333333333335555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1046  (0.0583412); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1729.52
//
Query:       gi|298674674|ref|YP_003726424.1|  [L=120]
Description: hypothetical protein Metev_0727 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.026   14.6   0.0       0.93    9.7   0.0    2.3  2  Mrr_N       Mrr N-terminal domain
      0.045   14.0   0.0      0.063   13.6   0.0    1.4  1  TFIIE_beta  TFIIE beta subunit core domain


Domain annotation for each model (and alignments):
>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.017   1.6e+02       6      25 ..      32      53 ..      30      56 .. 0.86
   2 ?    9.7   0.0    0.0001      0.93      61      82 ..      72      93 ..      68      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.017
                             Mrr_N  6 lplLealad..gsehrlkeire 25
                                      + +L++l++  g++++ +eir+
  gi|298674674|ref|YP_003726424.1| 32 RVILKVLKKndGNVTSFSEIRS 53
                                      569****9889********986 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0001
                             Mrr_N 61 LkkagllespkrgvwkiTekGr 82
                                       + +gl+++ k g ++iT+kGr
  gi|298674674|ref|YP_003726424.1| 72 FQLEGLVNKVKWGGYTITDKGR 93
                                      5678*****************9 PP

>> TFIIE_beta  TFIIE beta subunit core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     7e-06     0.063       8      53 ..      34      83 ..      32     115 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7e-06
                        TFIIE_beta  8 iveylKkkdg.plsleeIlsylsl...qldlsdknwllleaLknnpkiey 53
                                      i + lKk+dg   s++eI sy++l   + ++++k ++++++    +k+++
  gi|298674674|ref|YP_003726424.1| 34 ILKVLKKNDGnVTSFSEIRSYTDLfadRGSIGSKMKTVFQLEGLVNKVKW 83
                                      5667999888799**********966666666888888888777788877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 800.16
//
Query:       gi|298674675|ref|YP_003726425.1|  [L=264]
Description: indole-3-glycerol-phosphate synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.6e-71  238.1   1.8    9.8e-71  237.9   1.8    1.0  1  IGPS          Indole-3-glycerol phosphate synthase
    9.3e-05   21.7   1.1     0.0011   18.2   0.1    2.9  3  NanE          Putative N-acetylmannosamine-6-phosphate epimer
    0.00043   19.8   0.1     0.0013   18.3   0.0    1.8  2  His_biosynth  Histidine biosynthesis protein
    0.00084   19.1   0.3     0.0016   18.3   0.3    1.4  1  QRPTase_C     Quinolinate phosphoribosyl transferase, C-termi
     0.0081   15.6   1.7      0.013   14.9   0.4    2.0  2  PcrB          PcrB family
  ------ inclusion threshold ------
      0.021   13.7   2.0      0.054   12.3   0.3    2.5  3  Trp_syntA     Tryptophan synthase alpha chain
      0.033   13.2   0.0       0.08   11.9   0.0    1.6  1  IMPDH         IMP dehydrogenase / GMP reductase domain
      0.042   13.2   0.0       0.15   11.3   0.0    1.9  2  ThiG          Thiazole biosynthesis protein ThiG
      0.096   12.7   0.7       0.24   11.4   0.1    2.0  3  DUF61         Protein of unknown function DUF61


Domain annotation for each model (and alignments):
>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.9   1.8   4.9e-74   9.8e-71       3     254 .]       7     259 ..       5     259 .. 0.90

  Alignments for each domain:
  == domain 1  score: 237.9 bits;  conditional E-value: 4.9e-74
                                       HCHHHHHHHHHHHHCCS-GGCCCCG..-SS-SS-HHHHCHCH..TTS-EEEEEE-SEETTT..EESBSS--HHHHHH CS
                              IGPS   3 kivaekkeevaeakkrqsladleaavklakpkrsfaeaLres..ekklaliaEvKkaSPsk..gliredfdpaeiAk 75 
                                       +i++++k++v++ kk++s + ++++     + r++ + ++e+    k+ +iaE+K aSPs+    i    d+a+iAk
  gi|298674675|ref|YP_003726425.1|   7 NIIDSTKKRVDDLKKNNSYSGIDKT-----DIRNIETIINETkkYYKVPVIAEIKPASPSTfyREISP-PDAASIAK 77 
                                       6888899999999999987777664.....5666666666664367899***********92122333.37889*** PP

                                       HHTTT.-SEEEEE--CCCC---CCHHHHHHHH-SS-EEEES---SHHHHHHHHHCT-SEEEEECCCS-HHHHHHHHH CS
                              IGPS  76 kyeeagAsaiSVLteekyFqGsledLrevrqavslpvlrKdFiideyqieearalgadaiLLivkvledeeleelae 152
                                       ++e+agA+aiSVLte++yF+Gs+++L  vr++  lpvlrKdFiide q++     + d+iLLi++vl +++ e++++
  gi|298674675|ref|YP_003726425.1|  78 EMEKAGAAAISVLTEPDYFHGSIDNLDYVRNESTLPVLRKDFIIDETQMD---EQQTDLILLIASVLGNQL-ENFVS 150
                                       **************************************************...6799**********9876.***** PP

                                       HHCCTT-EEEEEESSHHHHHHHHHTT-SEEEEESEETTTTEE-CHHHHHHCHCC-.......TTSEEEEESSS-SHH CS
                              IGPS 153 aakslglevLvEvhdeeeleralklgakiiGvNnRnLktlevdlntteeLaklvp.......kdvllvaeSGiktre 222
                                       +a+s g+++LvEvhd++ele+al+  akiiG+NnRnL+t+e+dl+tt +La+ ++       ++ ++++eSGi ++e
  gi|298674675|ref|YP_003726425.1| 151 TAQSKGIQPLVEVHDRNELEKALQTSAKIIGINNRNLNTFEIDLQTTYDLAPIIKqydiennTNHIVISESGIDSQE 227
                                       ****************************************************99988887655699*********** PP

                                       HHHHHCCTT-SEEEESHHHHC-TTHHHHHHHH CS
                              IGPS 223 dveklkeegvnafLvGeslmrqedvekairel 254
                                       dv++l ++g++a+L+G+s+++++d   +++el
  gi|298674675|ref|YP_003726425.1| 228 DVKQLINSGADALLIGSSIIKSDDIYSKTKEL 259
                                       ************************99999986 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.3      0.19   3.7e+02      24      43 ..      40      59 ..      19      92 .. 0.67
   2 ?   -0.6   0.0      0.33   6.5e+02       4      35 ..      75     114 ..      72     129 .. 0.69
   3 !   18.2   0.1   5.6e-07    0.0011     119     189 ..     186     259 ..     138     262 .. 0.61

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.19
                                      HHHHHTT--S-EEEE-B--- CS
                              NanE 24 ikaikavvdlPiiGivkrdl 43
                                      i+++k+  ++P+i  +k   
  gi|298674675|ref|YP_003726425.1| 40 INETKKYYKVPVIAEIKPAS 59
                                      45667777788877777544 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.33
                                       HHHHHHHHT-SEEEE........ESHHHHHHHHTT--S-E CS
                              NanE   4 makaaeqaGavgiri........egvedikaikavvdlPi 35 
                                       +ak  e+aGa++i +         +++++  ++++ +lP+
  gi|298674675|ref|YP_003726425.1|  75 IAKEMEKAGAAAISVltepdyfhGSIDNLDYVRNESTLPV 114
                                       6677777777777653333222247888888888888887 PP

  == domain 3  score: 18.2 bits;  conditional E-value: 5.6e-07
                                       TTTTSSTTS-.SS--HHHHHHH...HHTT--EEEES---SHHHHHHHHTT--SEEEE-HHHH-HHHHHHHHHHH CS
                              NanE 119 tlsGytkeeekaepDfalvkal...seaglkviaeGrintPekakkaieiGvdavvvGsaitrleeiakkfvea 189
                                        l  +  + + + +   ++k++   ++++  vi e  i++ e  k+ i++G+da+ +Gs+i + ++i +k  e 
  gi|298674675|ref|YP_003726425.1| 186 NLNTFEIDLQTTYDLAPIIKQYdieNNTNHIVISESGIDSQEDVKQLINSGADALLIGSSIIKSDDIYSKTKEL 259
                                       3444433333333333356655211345556***********************************99987665 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.6   3.1e+03     148     164 ..      71      87 ..      65      91 .. 0.72
   2 !   18.3   0.0   6.3e-07    0.0013      68     116 ..     209     257 ..     193     263 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.6
                                       EHHHHHHHHHHTT-SEE CS
                      His_biosynth 148 davelakkleelgagei 164
                                       da ++ak++e++ga++i
  gi|298674675|ref|YP_003726425.1|  71 DAASIAKEMEKAGAAAI 87 
                                       56777888888887766 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 6.3e-07
                                       HHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHH CS
                      His_biosynth  68 iaeevfipvqvGGGIrsledveelleagadkviigtaavknpelikela 116
                                       i ++++  v   +GI s edv++l+++gad + ig++ +k+ ++ ++  
  gi|298674675|ref|YP_003726425.1| 209 IENNTNHIVISESGIDSQEDVKQLINSGADALLIGSSIIKSDDIYSKTK 257
                                       5566667777889**************************9999877665 PP

>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.3   7.9e-07    0.0016      70     158 ..     149     246 ..     133     252 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 7.9e-07
                                       HHHHHHHHTTTSEEEEEESSHHHHHHHHHHT-SEEEEES-..........-HHHHHHHHHHHHHHSTT..SEEEEES CS
                         QRPTase_C  70 vksvreavdkevkievevesleeleevleaeadiimLDnf..........sveelkkaveelkeknkr..vlievSG 134
                                       v++++++    ++  vev+  +ele++l++ a ii + n           ++ +l+ ++++ +  n++  ++i+ SG
  gi|298674675|ref|YP_003726425.1| 149 VSTAQSKG---IQPLVEVHDRNELEKALQTSAKIIGINNRnlntfeidlqTTYDLAPIIKQYDIENNTnhIVISESG 222
                                       33333333...3347**********************999888888877666777777777644444366******* PP

                                       S--TTTHHHHHCTT-SEEEECHHC CS
                         QRPTase_C 135 gvtlenveeyaksgvdvisvgalt 158
                                         ++e+v+++ +sg d++ +g+ +
  gi|298674675|ref|YP_003726425.1| 223 IDSQEDVKQLINSGADALLIGSSI 246
                                       ******************999866 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.41   8.2e+02      38      64 ..      27      54 ..       8      67 .. 0.72
   2 !   14.9   0.4   6.7e-06     0.013      48     217 ..      76     252 ..      70     263 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.41
                                      CSTCHHHHHHHHHHHHHCT.SSS-EEEE CS
                              PcrB 38 Gsqsvtldntvrllkkvsr.iklPivle 64
                                      G ++ +  n+ +++++ ++ +k+P++ e
  gi|298674675|ref|YP_003726425.1| 27 GIDKTDIRNIETIINETKKyYKVPVIAE 54
                                      5555566666677766655279999976 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 6.7e-06
                                       HHHHHHHCTSSS-EEEEESSGGG--TTSSEEEEEEETTBSSTTTTTH...HHHHHHHHHHHHHHCTEEEEEEEEEBT CS
                              PcrB  48 vrllkkvsriklPivlepsnvegvvryaDalFvmsllnsanadWivg...ahalglkkvkklieseeilaegYlvve 121
                                       ++ ++k     + ++ ep   +g   ++D++   s l     d+i+    ++++    +  + +++  + e ++   
  gi|298674675|ref|YP_003726425.1|  76 AKEMEKAGAAAISVLTEPDYFHGSIDNLDYVRNESTLPVLRKDFIIDetqMDEQQTDLILLIASVLGNQLENFVSTA 152
                                       67777777778888888888888888888888888888888888887655666666667777777778888887777 PP

                                       TTSHHHHHTTB-..B-TTHHHHHHHHHHHHHHTT-SEEEEE-TTSSS-HHHHHHHHHH.HSSSEEEEESS--SHHHH CS
                              PcrB 122 Pdskvaavteak..vdlnkediaayallaakllglrliYlEasGaledveevialkkk.lekarlivGGGirsaEkA 195
                                         + +  + e++   +l+k   +++ +++ +  +l  + ++   +++    +++      ++ ++i   Gi+s+E+ 
  gi|298674675|ref|YP_003726425.1| 153 QSKGIQPLVEVHdrNELEKALQTSAKIIGINNRNLNTFEIDLQTTYDLAPIIKQYDIEnNTNHIVISESGIDSQEDV 229
                                       777777777776556677777888888888888888888888777666566666554404456677889******** PP

                                       HHHHCC.SSEEEE-CHHHHHHHC CS
                              PcrB 196 kevvea.ADvivvGnvveekder 217
                                       k+ ++  AD++++G  + ++d+ 
  gi|298674675|ref|YP_003726425.1| 230 KQLINSgADALLIGSSIIKSDDI 252
                                       *****99*******998887742 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0         1   2.1e+03     179     201 ..      29      51 ..      25      53 .. 0.75
   2 ?   -3.5   0.0       1.9   3.7e+03      27      41 ..      73      87 ..      70      89 .. 0.79
   3 ?   12.3   0.3   2.7e-05     0.054     194     232 ..     210     249 ..     135     263 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1
                                       TSSB-TTHHHHHHHHHHCTSS-E CS
                         Trp_syntA 179 enavaaevdelverlkkltavPv 201
                                        ++  +++++++++ kk+ +vPv
  gi|298674675|ref|YP_003726425.1|  29 DKTDIRNIETIINETKKYYKVPV 51 
                                       55666788888999999988887 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.9
                                      HHHHHHHHHCT-SSE CS
                         Trp_syntA 27 leilkalekagadvi 41
                                      ++i k++ekaga +i
  gi|298674675|ref|YP_003726425.1| 73 ASIAKEMEKAGAAAI 87
                                      568899999999887 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 2.7e-05
                                       HHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHHH CS
                         Trp_syntA 194 kkltavPvavGFGistkeqvkqva.kvadGvivGSalvkk 232
                                       ++ t+  v    Gi ++e+vkq++ ++ad+ ++GS ++k 
  gi|298674675|ref|YP_003726425.1| 210 ENNTNHIVISESGIDSQEDVKQLInSGADALLIGSSIIKS 249
                                       555566666677**********999*************85 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     4e-05      0.08     196     240 ..     203     247 ..     196     259 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4e-05
                                       HHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 196 vaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGslla 240
                                       +++ +++ ++++  vi+  Gi +++d+ + +  Gada+++Gs + 
  gi|298674675|ref|YP_003726425.1| 203 IIKQYDIENNTNHIVISESGIDSQEDVKQLINSGADALLIGSSII 247
                                       7777888999999****************************9875 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.68   1.4e+03     135     152 ..      74      91 ..      70     115 .. 0.76
   2 ?   11.3   0.0   7.7e-05      0.15     175     215 ..     214     254 ..     194     263 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.68
                                       HHHHHHHHTT-SEBEEBS CS
                              ThiG 135 vlarrleevGcaavmPla 152
                                        +a+ +e++G+aa+  l+
  gi|298674675|ref|YP_003726425.1|  74 SIAKEMEKAGAAAISVLT 91 
                                       578889999998886655 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 7.7e-05
                                       SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHH CS
                              ThiG 175 kvPvivDAGigspsdaaqamelGadavllntavaeakdpva 215
                                       +  vi + Gi s +d+ q ++ Gada+l+ +++ +++d+ +
  gi|298674675|ref|YP_003726425.1| 214 NHIVISESGIDSQEDVKQLINSGADALLIGSSIIKSDDIYS 254
                                       4558889*****************************99865 PP

>> DUF61  Protein of unknown function DUF61
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00012      0.24      35      80 ..      20      64 ..      11      81 .. 0.89
   2 ?   -2.2   0.0         2     4e+03      19      45 ..     166     194 ..     156     211 .. 0.52
   3 ?   -2.2   0.0       1.9   3.9e+03      66      86 ..     202     222 ..     181     254 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                                      .TTS-EEE--HHHHHHHHTTS-GGGGGT-EESEEEEE-SSSSE..E CS
                             DUF61 35 tkdgsehrfdkeeleklkeilpeelwdklkLPIllemdpelgesvy 80
                                      +k++s+  +dk ++++++ i++e  ++  k+P++ e++p + + +y
  gi|298674675|ref|YP_003726425.1| 20 KKNNSYSGIDKTDIRNIETIINET-KKYYKVPVIAEIKPASPSTFY 64
                                      58999999*************999.699***********9888777 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2
                                       -EEHHHHHHT--EEE..B.TTS-EEE--H CS
                             DUF61  19 rktLkelLeeekpti..vtkdgsehrfdk 45 
                                       r  L+++L+   ++i    ++ +++++d 
  gi|298674675|ref|YP_003726425.1| 166 RNELEKALQTSAKIIgiNNRNLNTFEIDL 194
                                       45555555554444311223334444444 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.9
                                       SEEEEE-SSSSE..EEEES-H CS
                             DUF61  66 PIllemdpelgesvylvrgka 86 
                                       PI+ ++d e ++  ++++++ 
  gi|298674675|ref|YP_003726425.1| 202 PIIKQYDIENNTNHIVISESG 222
                                       666666666666666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       974  (0.0543254); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 1997.23
//
Query:       gi|298674676|ref|YP_003726426.1|  [L=398]
Description: tryptophan synthase subunit beta [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-40  139.8   0.6    1.6e-40  139.4   0.6    1.1  1  PALP      Pyridoxal-phosphate dependent enzyme
  ------ inclusion threshold ------
      0.023   15.2   1.0      0.058   13.9   1.0    1.6  1  SF3A3     Pre-mRNA-splicing factor SF3A3, of SF3a complex, Pr


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.4   0.6   1.7e-44   1.6e-40       4     294 .]      51     379 ..      49     379 .. 0.81

  Alignments for each domain:
  == domain 1  score: 139.4 bits;  conditional E-value: 1.7e-44
                                       CSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHH.HHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT- CS
                              PALP   4 gigpTPlvrlprlskelgvplflKlEslnptgSfKdRgae.yllarlkegtgaktvveassGNhgralAaaaallGl 79 
                                       + ++TPl  +++ls+++g++++lK+E+l ++g++K++     +l++   g + + v+e+++G+hg a+A+a+a+lGl
  gi|298674676|ref|YP_003726426.1|  51 AGRETPLYFARNLSEKYGIKIYLKREDLLHGGAHKINNTLgQALLARYMG-KHRIVAETGAGQHGTATAMAGAALGL 126
                                       5789**********************************994444445555.9999999999**************** PP

                                       EEEEEEETTS-...HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHH...........STTCEE--TTTSHHHHHH CS
                              PALP  80 kvtivvpadas...pekvallrllGaevvevggdydeavaaaaelaae...........gegaylvsqfdnptvieg 142
                                       + ++++ +++    + +v ++++lGa+v+ v  + ++ ++a++e++++           +++++  +++  p ++  
  gi|298674676|ref|YP_003726426.1| 127 DTVVYMGEKDVerqKTNVYRMEMLGAKVHPVSAGSKTLKDAINEALRDwvsnvdsthylIGSVVGPHPY--PMIVRD 201
                                       ***********6655****************99999999999999999999997444444444444444..557777 PP

                                       .HHTHHHHHH....HHTTTTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.. CS
                              PALP 143 .ygtiglEil....eqlggkpdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvs. 213
                                        +  ig E++    e+ g+ pd +v+++GgG++++G+ +++ ++ + v++i ve+ g +   +s +a +  ++ v+ 
  gi|298674676|ref|YP_003726426.1| 202 fQCVIGNEVKkqiiEKEGKYPDSIVACTGGGSNAMGTFHPFVDDTG-VKLISVEAGGESMKSTSKAALHSASLCVGe 277
                                       7********966677777************************8555.9*****998555555555333333333336 PP

                                       ......................SSS.CCSTCS..CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HH CS
                              PALP 214 ......................dtiadglavg..spselafelldrlvdeivtvsdeealeamrllarregivveps 266
                                                             ++i  gl+ +   p+   ++  +rl++     sd+ea++a  +l++ egi++   
  gi|298674676|ref|YP_003726426.1| 278 egilhgaktrilqdkygqilesHSISAGLDYSgvGPELSYLKDSERLNT--AVASDKEAIDAFHELCHLEGIIPALE 352
                                       67788888888888999999999******99944444444444455555..999**********************9 PP

                                       HHHHHHHH.HHHHHHCCTTCEEEEEEE-B CS
                              PALP 267 saaalaal.klreagelkegdrvvviltg 294
                                       s +a+a + k ++ gel++   vv+ l+g
  gi|298674676|ref|YP_003726426.1| 353 SSHAIAHVlKKAKTGELGNI--VVINLSG 379
                                       99999999677777777776..8888876 PP

>> SF3A3  Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.0   6.5e-06     0.058      40      75 ..      22      57 ..       4      60 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.5e-06
                             SF3A3 40 kfseipkkqkkskeYkeYlkeLleYLesfikrtqpL 75
                                      ++se+++k + +k+  ++lk+L+ YL++f  r  pL
  gi|298674676|ref|YP_003726426.1| 22 AISELERKYEYYKNNPDFLKDLHYYLNDFAGRETPL 57
                                      33444444444455559******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 3139.53
//
Query:       gi|298674677|ref|YP_003726427.1|  [L=269]
Description: tryptophan synthase subunit alpha [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      6e-89  297.3   0.1    7.4e-89  297.0   0.1    1.0  1  Trp_syntA     Tryptophan synthase alpha chain
    9.1e-05   22.0   0.2    0.00021   20.8   0.1    1.6  2  His_biosynth  Histidine biosynthesis protein
     0.0022   17.2   0.0       0.01   15.0   0.0    1.8  2  IGPS          Indole-3-glycerol phosphate synthase
     0.0045   16.2   0.1      0.008   15.4   0.1    1.5  1  NanE          Putative N-acetylmannosamine-6-phosphate epimer
  ------ inclusion threshold ------
      0.012   15.1   0.6       0.25   10.8   0.2    2.6  3  PcrB          PcrB family
      0.016   14.0   0.6      0.048   12.4   0.4    1.8  2  Pneumo_ncap   Pneumovirus nucleocapsid protein
      0.048   13.0   0.0      0.071   12.5   0.0    1.4  1  NMO           Nitronate monooxygenase
      0.059   13.6   0.0       0.92    9.8   0.0    2.3  2  PucR          Purine catabolism regulatory protein-like famil


Domain annotation for each model (and alignments):
>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  297.0   0.1   3.3e-92   7.4e-89       6     250 ..      11     252 ..       7     260 .. 0.94

  Alignments for each domain:
  == domain 1  score: 297.0 bits;  conditional E-value: 3.3e-92
                                       CTTB-EEEEEEETTSS-HHHHHHHHHHHHHCT-SSEEEE---S--TTS-HHHHHHHHCCCCTT--HHHHHHHHHHHH CS
                         Trp_syntA   6 aenraafvpyvtagdpdleqsleilkalekagadviElGlpfsdPladGPvIqaanlraLakgvtlekvlelveevr 82 
                                       +en+aa++ yv agdp+ + + +i+++l ++gad+iElGlpfsdP+adGP Iqaa++r++++g++++  +elv+++ 
  gi|298674677|ref|YP_003726427.1|  11 DENEAALISYVCAGDPSPDATKNIVSSLVRGGADIIELGLPFSDPMADGPSIQAASKRSIEAGMNPDLYFELVSSIS 87 
                                       799************************************************************************** PP

                                       HHCSSS-EEEEE-CHHHCCC-HHHHCHHHHHCTEEEEEETTSBCCCHHHHHHHHHHTT-EEEEEE-TTS-HHHHHHH CS
                         Trp_syntA  83 kkevevPivlltylnlvlsygeerflaelkeagvdglivpDlPleeaeelveaakkkglelvflvapttsderlkev 159
                                        ++ ++P v++ty+nl++++g+e+f++++++ g+ g+ivpDlP+ee++el +a++k++++l+ +++p t +er k++
  gi|298674677|ref|YP_003726427.1|  88 -DKFNIPFVCMTYYNLIYKRGTEKFVQDCAQSGISGVIVPDLPVEESDELANACQKNDVDLILIITPVTGKERTKKI 163
                                       .99************************************************************************** PP

                                       HHH--S-EEEESTTC-SSTTSSB-TTHHHHHHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHHHHHC CS
                         Trp_syntA 160 veqaegfvYvvsraGvTgaenavaaevdelverlkkltavPvavGFGistkeqvkqva.kvadGvivGSalvkkiee 235
                                       +e+++gf Y+vsr GvTga++ +a+++ +l++ +++    P+avGFGist+eqvk+v+ ++a+GvivGSa v++i++
  gi|298674677|ref|YP_003726427.1| 164 TEKSSGFLYIVSRLGVTGARSDIAENTGQLLKMVNSS--IPKAVGFGISTPEQVKNVVlSGANGVIVGSAFVNIIAS 238
                                       ********************************99865..6******************9*****************5 PP

                                       TTTSHHHHHHHHHHH CS
                         Trp_syntA 236 eaeekeqalekleel 250
                                         ++  + +ek+++ 
  gi|298674677|ref|YP_003726427.1| 239 -NDDIYNRTEKFTAE 252
                                       .45555555555544 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.6   3.5e+03      88     118 ..     112     142 ..     108     150 .. 0.66
   2 !   20.8   0.1   9.4e-08   0.00021      52     109 ..     180     236 ..     160     253 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.6
                                       HHHHHHCT-SEEEESHHHHH-THHHHHHHHH CS
                      His_biosynth  88 veelleagadkviigtaavknpelikelaek 118
                                       v++  ++g++ vi+    v++++ + ++++k
  gi|298674677|ref|YP_003726427.1| 112 VQDCAQSGISGVIVPDLPVEESDELANACQK 142
                                       4556666777777777777777777666665 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 9.4e-08
                                       HHHCTTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-T CS
                      His_biosynth  52 daakegreanldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknp 109
                                       ++a++   +n+  + +++++ +ip  vG GI++ e+v++++ +ga+ vi+g+a v+  
  gi|298674677|ref|YP_003726427.1| 180 TGARSDIAENTGQLLKMVNS-SIPKAVGFGISTPEQVKNVVLSGANGVIVGSAFVNII 236
                                       67777777777666677776.7*******************************88654 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.28   6.3e+02     128     154 ..     141     167 ..     123     171 .. 0.79
   2 !   15.0   0.0   4.5e-06      0.01     197     243 ..     188     234 ..     184     244 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.28
                                       HHCT-SEEEEECCCS-HHHHHHHHHHH CS
                              IGPS 128 ralgadaiLLivkvledeeleelaeaa 154
                                       ++   d+iL+i  v  +e+ ++++e +
  gi|298674677|ref|YP_003726427.1| 141 QKNDVDLILIITPVTGKERTKKITEKS 167
                                       556789999999999888888887766 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 4.5e-06
                                       HHHHHHCHCC-TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC CS
                              IGPS 197 ntteeLaklvpkdvllvaeSGiktredveklkeegvnafLvGeslmr 243
                                       ++t +L k+v++++      Gi+t+e+v+++  +g+n+++vG+++++
  gi|298674677|ref|YP_003726427.1| 188 ENTGQLLKMVNSSIPKAVGFGISTPEQVKNVVLSGANGVIVGSAFVN 234
                                       6899*********99999**************************975 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   3.6e-06     0.008     111     177 ..     168     233 ..     131     248 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.6e-06
                                       TT-SEEE-TTTTSSTTS-..SS--HHHHHHHHHTT--EEEES---SHHHHHHHHTT--SEEEE-HHHH CS
                              NanE 111 lGvdivGttlsGytkeeek.aepDfalvkalseaglkviaeGrintPekakkaieiGvdavvvGsait 177
                                        G+ ++ + l G t+  ++ ae+  +l+k +++  +   +   i tPe+ k+++ +G++ v+vGsa  
  gi|298674677|ref|YP_003726427.1| 168 SGFLYIVSRL-GVTGARSDiAENTGQLLKMVNS-SIPKAVGFGISTPEQVKNVVLSGANGVIVGSAFV 233
                                       5555665555.6666666668899999986655.5555555569**********************75 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.086   1.9e+02       8      36 ..      20      48 ..      12      52 .. 0.87
   2 ?   -1.3   0.0      0.56   1.3e+03      19      65 ..     108     153 ..     105     165 .. 0.73
   3 ?   10.8   0.2   0.00011      0.25     161     213 ..     179     234 ..     162     249 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.086
                                      EEEEE-TTSS-CHHHHHHHHCTT-SEEEE CS
                              PcrB  8 hltklDPeeenpdEiveiviesgtDavmi 36
                                      ++   DP  + + +iv  ++++g+D + +
  gi|298674677|ref|YP_003726427.1| 20 YVCAGDPSPDATKNIVSSLVRGGADIIEL 48
                                      77778********************8866 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.56
                                       CHHHHHHHHCTT-SEEEEECSTCHHHHHHHHHHHHHCTSSS-EEEEE CS
                              PcrB  19 pdEiveiviesgtDavmigGsqsvtldntvrllkkvsriklPivlep 65 
                                       ++  v+  ++sg  +v++      + d+ +++ +k+  ++l +++ p
  gi|298674677|ref|YP_003726427.1| 108 TEKFVQDCAQSGISGVIVPDLPVEESDELANACQKN-DVDLILIITP 153
                                       566777778888888888888888888888888888.4555444444 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00011
                                       -TTSSS-H.HHHHHHHHHHSSSE.EEEESS--SHHHHHHHHCC.SSEEEE-CHHHH CS
                              PcrB 161 asGaledv.eevialkkklekar.livGGGirsaEkAkevvea.ADvivvGnvvee 213
                                         Ga  d+ e++ +l k +++++   vG Gi  +E+ k+vv   A+ ++vG +  +
  gi|298674677|ref|YP_003726427.1| 179 VTGARSDIaENTGQLLKMVNSSIpKAVGFGISTPEQVKNVVLSgANGVIVGSAFVN 234
                                       579999999999888887766542789***************99*******87554 PP

>> Pneumo_ncap  Pneumovirus nucleocapsid protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.12   2.6e+02      64      94 ..     167     198 ..     144     201 .. 0.71
   2 ?   12.4   0.4   2.1e-05     0.048     304     368 ..     196     263 ..     179     268 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.12
                       Pneumo_ncap  64 eiGilyissalGredv.ikilkdaGsevkvvd 94 
                                         G+lyi+s+lG   +   i  ++G+ +k+v+
  gi|298674677|ref|YP_003726427.1| 167 SSGFLYIVSRLGVTGArSDIAENTGQLLKMVN 198
                                       35899999999976541568888888777765 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 2.1e-05
                       Pneumo_ncap 304 llqs..pkasllslaqfpnfasvvlGnaaGlGiiGeyrG.rvrntelydaakayakslkesnkinysv 368
                                       + +s  pka  + ++   +   vvl  a G+ +   +    + n ++y+ ++ ++ +lk++  inys 
  gi|298674677|ref|YP_003726427.1| 196 MVNSsiPKAVGFGISTPEQVKNVVLSGANGVIVGSAFVNiIASNDDIYNRTEKFTAELKNNCYINYSK 263
                                       5544448888888888889999********9655556541568***********************95 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.2e-05     0.071     180     228 ..     189     235 ..     137     256 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.2e-05
                               NMO 180 glfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrfLlt 228
                                       ++ +L++ v +  +iP     Gi + ++v+ +   GA+gv +g++f+  
  gi|298674677|ref|YP_003726427.1| 189 NTGQLLKMVNS--SIPKAVGFGISTPEQVKNVVLSGANGVIVGSAFVNI 235
                                       45555555544..47776666*************************754 PP

>> PucR  Purine catabolism regulatory protein-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.17   3.8e+02      35      74 ..       6      46 ..       1      70 [. 0.74
   2 ?    9.8   0.0   0.00041      0.92      47     104 ..      97     154 ..      87     166 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.17
                              PucR 35 iaellrggeLllttglal.kddpealaelvrelaeagvaaL 74
                                       ++ l ++e  l++ +   + +p+a +++v +l++ g+  +
  gi|298674677|ref|YP_003726427.1|  6 KFDNLDENEAALISYVCAgDPSPDATKNIVSSLVRGGADII 46
                                      55778899988888888867799**********99998654 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00041
                              PucR  47 ttglalkddpealaelvrelaeagvaaLviklgr.eipeelieaadelglPlielpeev 104
                                        t ++l   +   +++v+++a++g++++++   + e ++el +a++++++ li + + v
  gi|298674677|ref|YP_003726427.1|  97 MTYYNLI-YKRGTEKFVQDCAQSGISGVIVPDLPvEESDELANACQKNDVDLILIITPV 154
                                       5666663.3556799***************99766889********9999888775554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1916.65
//
Query:       gi|298674678|ref|YP_003726428.1|  [L=359]
Description: signal recognition particle-docking protein FtsY [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-71  239.8   0.3    2.7e-71  239.3   0.3    1.2  1  SRP54            SRP54-type protein, GTPase domain
      6e-10   39.2   6.9    6.1e-10   39.2   1.1    2.6  2  SRP54_N          SRP54-type protein, helical bundle domain
    2.3e-05   24.8   0.0    4.7e-05   23.8   0.0    1.5  1  AAA_17           AAA domain
    2.5e-05   24.1   0.1    4.7e-05   23.2   0.1    1.4  1  AAA_30           AAA domain
    5.2e-05   22.6   0.1    8.6e-05   21.9   0.1    1.3  1  Zeta_toxin       Zeta toxin
    8.2e-05   22.0   0.8    0.00024   20.4   0.3    1.8  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    0.00049   19.7   0.0     0.0015   18.1   0.0    1.8  1  AAA_7            P-loop containing dynein motor region
    0.00064   20.0   0.0     0.0015   18.8   0.0    1.6  1  AAA_22           AAA domain
    0.00066   20.0   0.0     0.0012   19.1   0.0    1.5  1  AAA_28           AAA domain
    0.00082   19.8   0.3     0.0069   16.8   0.3    2.3  1  AAA              ATPase family associated with various cellul
     0.0017   18.0   0.3      0.018   14.7   0.1    2.4  1  Thymidylate_kin  Thymidylate kinase
     0.0028   17.8   0.0     0.0057   16.8   0.0    1.5  1  AAA_33           AAA domain
     0.0041   17.6   0.0      0.011   16.3   0.0    1.7  1  ABC_tran         ABC transporter
     0.0053   17.2   0.0      0.015   15.7   0.0    1.7  1  AAA_16           AAA ATPase domain
     0.0086   16.1   1.0      0.028   14.5   0.5    2.1  2  MMR_HSR1         50S ribosome-binding GTPase
     0.0091   16.0   0.0      0.018   15.0   0.0    1.6  1  AAA_5            AAA domain (dynein-related subfamily)
  ------ inclusion threshold ------
      0.014   15.4   0.4      0.014   15.4   0.4    1.9  2  ResIII           Type III restriction enzyme, res subunit
      0.015   15.2   0.0      0.025   14.5   0.0    1.4  1  APS_kinase       Adenylylsulphate kinase
      0.016   15.2   0.2       0.04   14.0   0.2    1.9  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
      0.016   15.1   0.5      0.094   12.6   0.1    2.1  2  NTPase_1         NTPase
      0.021   14.3   0.1       0.04   13.4   0.1    1.5  1  KTI12            Chromatin associated protein KTI12
      0.021   14.5   0.1      0.053   13.2   0.0    1.8  2  AAA_24           AAA domain
      0.022   13.9   0.1      0.039   13.0   0.1    1.4  1  T2SSE            Type II/IV secretion system protein
      0.024   15.0   0.1      0.059   13.7   0.1    1.6  1  AAA_19           AAA domain
      0.031   13.4   0.0      0.048   12.8   0.0    1.4  1  LpxK             Tetraacyldisaccharide-1-P 4'-kinase
      0.032   13.7   0.0      0.065   12.7   0.0    1.4  1  Arf              ADP-ribosylation factor family
      0.034   14.0   0.7       0.05   13.5   0.7    1.3  1  FCP1_C           FCP1, C-terminal
       0.05   12.5   0.0       0.11   11.3   0.0    1.5  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
      0.058   13.1   0.1      0.058   13.1   0.1    2.1  2  AAA_15           AAA ATPase domain
      0.083   12.8   0.3       0.26   11.2   0.1    1.9  1  MobB             Molybdopterin guanine dinucleotide synthesis
      0.092   11.9   0.7       0.13   11.4   0.0    1.6  2  G-alpha          G-protein alpha subunit
        0.1   12.2   1.5       0.17   11.5   0.5    1.8  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
       0.42   10.7   2.9       0.82    9.8   0.0    2.5  3  PTPlike_phytase  Inositol hexakisphosphate


Domain annotation for each model (and alignments):
>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  239.3   0.3     5e-74   2.7e-71       2     195 ..     165     358 ..     164     359 .] 0.99

  Alignments for each domain:
  == domain 1  score: 239.3 bits;  conditional E-value: 5e-74
                                       EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHH CS
                             SRP54   2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavek 78 
                                         i++vG++G+GKTtt+aK+a+ll++++++++++a DtfRa+A++Q++ +a+k++ ++ik++e  dpaav+++av+ 
  gi|298674678|ref|YP_003726428.1| 165 VHIVFVGVNGTGKTTTIAKMANLLQNDNYSTVIAAGDTFRAGAIDQIESHANKINTKLIKHQEMGDPAAVVYDAVQY 241
                                       5799************************************************************************* PP

                                       HHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSS CS
                             SRP54  79 akeekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgdak 155
                                       ak+++idvvl DTaGr++++ +lm++l+k+ +v +pd +++v +a++g++av+ a++F++++ i+g iltk D+d+k
  gi|298674678|ref|YP_003726428.1| 242 AKSRSIDVVLSDTAGRMHTNVNLMSQLEKVCRVSSPDLIIFVDEAVAGNDAVERAQQFNDNIPIDGSILTKADADSK 318
                                       ***************************************************************************** PP

                                       TTHHHHHHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHH CS
                             SRP54 156 gGaalsiaaelklPikfigvGekiedleefdperlvsrll 195
                                       gGaa+sia+ +++Pi ++g+G+ +edl++fdp+++v++l+
  gi|298674678|ref|YP_003726428.1| 319 GGAAISIAYITGKPILYLGIGQGYEDLKKFDPQWFVDQLF 358
                                       **************************************97 PP

>> SRP54_N  SRP54-type protein, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.5      0.29   1.6e+02       6      30 ..       5      29 ..       3      32 .. 0.60
   2 !   39.2   1.1   1.1e-12   6.1e-10      14      75 .]      79     143 ..      70     143 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.29
                                      HHHHHHHCCSSCGHHHHHHHHHHHH CS
                           SRP54_N  6 nsalkklsgkskideedleealkel 30
                                      n++  kls+ +k  e++++e   e+
  gi|298674678|ref|YP_003726428.1|  5 NKLKEKLSSFKKSAEDTIDEKAVEV 29
                                      4455556667777777777755455 PP

  == domain 2  score: 39.2 bits;  conditional E-value: 1.1e-12
                                       CSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTS...S-HHHHHHHHHHHHH CS
                           SRP54_N  14 gkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekk...lkpkqqvkkivkdeL 75 
                                       +  ++de+d++++l++le+ Lle+D++++v + ++e+vk++ vg ++     +++ v++++k++L
  gi|298674678|ref|YP_003726428.1|  79 REFVLDEDDIQDTLWDLEMGLLENDIALSVSEAIVESVKNELVGTRRrigSDTGKIVEDALKKSL 143
                                       35589***************************************666776668888888888765 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   8.7e-08   4.7e-05       1     109 [.     170     284 ..     170     298 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 8.7e-08
                                       EE-TTSSHHHHHHHHHHHH....TEEEEEHHHHHHHHHHTT.TS..HSSHHHHC.TSHHHHHHHHHHHHHHHHHHHH CS
                            AAA_17   1 lGgPGsGKgtqceklveky....gfthlsaGdllreeakrg.gl..akardemr.klpleekkelqkeaaekiaeea 69 
                                       +G+ G GK+t ++k++  +      t++ aGd +r+ a ++ ++  +k + ++    ++ +  ++   a +  +  +
  gi|298674678|ref|YP_003726428.1| 170 VGVNGTGKTTTIAKMANLLqndnYSTVIAAGDTFRAGAIDQiEShaNKINTKLIkHQEMGDPAAVVYDAVQYAKS-R 245
                                       79*************97665554678999******9987775331123222222133444444444455443333.3 PP

                                       HSSEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE CS
                            AAA_17  70 kkkgvlvdghprikeqagfldglpkevleelkpdaiille 109
                                       + + vl d+  r+ ++  ++++l+k v++  +pd+ii+++
  gi|298674678|ref|YP_003726428.1| 246 SIDVVLSDTAGRMHTNVNLMSQLEK-VCRVSSPDLIIFVD 284
                                       557899*********9999999985.9***********98 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.1   8.7e-08   4.7e-05      21     102 ..     167     260 ..     158     303 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 8.7e-08
                            AAA_30  21 avltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlk.............gra 84 
                                        v +G+ GtGKtt+++++++++++++++ +++A     A ++  +++ +a+ i+  l +++             + a
  gi|298674678|ref|YP_003726428.1| 167 IVFVGVNGTGKTTTIAKMANLLQNDNYSTVIAAGDTFRAGAID-QIESHANKINTKLIKHQemgdpaavvydavQYA 242
                                       5789**********************99999999999999998.778899999888888887888888888775222 PP

                            AAA_30  85 rlepg.tllivDEagmvdt 102
                                       + + + ++++ D ag + t
  gi|298674678|ref|YP_003726428.1| 243 KSR-SiDVVLSDTAGRMHT 260
                                       223.236666666666533 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.1   1.6e-07   8.6e-05      10     119 ..     158     270 ..     149     301 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.6e-07
                        Zeta_toxin  10 ypsqerPklillgGqpGAGKselaellkdele.rqgnvvrldpDdlRe.lhPeyeeilka.dpkkaseltqkdasel 83 
                                        ++ e+P+ i+ +G  G GK+++++++++ l+  + + v   +D++R+  + + e++ ++ + k    +   d   +
  gi|298674678|ref|YP_003726428.1| 158 LKNAEKPVHIVFVGVNGTGKTTTIAKMANLLQnDNYSTVIAAGDTFRAgAIDQIESHANKiNTKLIKHQEMGDPAAV 234
                                       34559**************************977777888999****835666666666544444444445566789 PP

                        Zeta_toxin  84 vekllqeaiengyniivegtlrspdvvkklaealkk 119
                                       v  ++q+a ++ +++++  t    ++  +l+ +l+k
  gi|298674678|ref|YP_003726428.1| 235 VYDAVQYAKSRSIDVVLSDTAGRMHTNVNLMSQLEK 270
                                       999999999999999999998888888888877766 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.42   2.3e+02      34      93 ..     103     169 ..      96     170 .. 0.86
   2 !   20.4   0.3   4.5e-07   0.00024       4     132 ..     168     285 ..     163     299 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.42
                           DUF2075  34 avylsvNhplvlvlrealakke......ekkkkkeafeklssfinnlsef.kkaeekkeepkedvvi 93 
                                        + lsv+++ v+ ++++l +++      ++k  ++a++k+   i+++++f  +++ k++e+++++v 
  gi|298674678|ref|YP_003726428.1| 103 DIALSVSEAIVESVKNELVGTRrrigsdTGKIVEDALKKSLYNIMSANTFdFDEYLKNAEKPVHIVF 169
                                       6789999999999999999999999998899999999999999999999998888888888888875 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 4.5e-07
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnlsefkka 80 
                                       v+  Gv GtGKt    ++++ l   +++++++++     +++    ++++++  +k+++++ k +++  ++   ++a
  gi|298674678|ref|YP_003726428.1| 168 VF-VGVNGTGKTTTIAKMANLL---QNDNYSTVIAAGDTFRAGAIDQIESHA--NKINTKLIKHQEMGDPAAVVYDA 238
                                       34.4*****************9...888888888999999999999**9999..9999999999999999997799* PP

                           DUF2075  81 eekkeepkedvvivDEAhrlltksdqaekqseenqlkelmkr.akvvvalvDe 132
                                        + ++++ +dvv+ D A r+ t      + +   ql+++ +  +  ++++vDe
  gi|298674678|ref|YP_003726428.1| 239 VQYAKSRSIDVVLSDTAGRMHT------NVNLMSQLEKVCRVsSPDLIIFVDE 285
                                       **********************......4455788999998855577888887 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   2.7e-06    0.0015      32      66 ..     163     197 ..     147     225 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.7e-06
                             AAA_7  32 nkkpvllvGptGtGKtviikdllkkldkekylslt 66 
                                       +  ++++vG  GtGKt++i ++ + l++++y++++
  gi|298674678|ref|YP_003726428.1| 163 KPVHIVFVGVNGTGKTTTIAKMANLLQNDNYSTVI 197
                                       456899*********************99998865 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   2.8e-06    0.0015       7     100 ..     166     286 ..     161     301 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.8e-06
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee........................erpevvfvtlpsstsskdllre 59 
                                       ++v +G  GtGKTt+++++++ l+++++ +                         +     +++ ++ ++++ +  +
  gi|298674678|ref|YP_003726428.1| 166 HIVFVGVNGTGKTTTIAKMANLLQNDNYSTViaagdtfragaidqieshankintK-----LIKHQEMGDPAAVVYD 237
                                       7999*******************977666556666666666666666554222220.....3333333333333222 PP

                            AAA_22  60 llralglelka...........erlsseellealeqalraravielliiDEa 100
                                        ++  ++   +           + +++  l+++le+ +r  +   ++ +DEa
  gi|298674678|ref|YP_003726428.1| 238 AVQYAKS---RsidvvlsdtagRMHTNVNLMSQLEKVCRVSSPDLIIFVDEA 286
                                       2222222...133355555555667788888888888887777667777877 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   2.3e-06    0.0012       2      87 ..     167     256 ..     166     306 .. 0.61

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.3e-06
                            AAA_28   2 ivitGgestGKTtlleaLaar....gypvvpEaareileeklakgedalpwv.edllafaervleeqleeeaaaaan 73 
                                       iv++G  +tGKTt+++++a+     +y++v  a+ ++     ++ e ++++   +l++ +e + + ++  + a +  
  gi|298674678|ref|YP_003726428.1| 167 IVFVGVNGTGKTTTIAKMANLlqndNYSTVIAAGDTFRAGAIDQIESHANKInTKLIKHQE-MGDPAAVVYDAVQYA 242
                                       9**************99994444469**998888888877777777777777344444444.333333222222333 PP

                            AAA_28  74 kvlfcDrglldtla 87 
                                       k   +D  l dt+ 
  gi|298674678|ref|YP_003726428.1| 243 KSRSIDVVLSDTAG 256
                                       33334444444444 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.3   1.3e-05    0.0069       1      47 [.     167     263 ..     167     318 .. 0.55

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.3e-05
                                       EEEESSTTSSHHHHHHHHHHHHT...HEEEEEETTTCSSS..................................... CS
                               AAA   1 vllyGppGtGKTllakavakelg...vefleisgsellsk..................................... 37 
                                       ++++G  GtGKT+++  +a+ l+    + +   g +++                                       
  gi|298674678|ref|YP_003726428.1| 167 IVFVGVNGTGKTTTIAKMANLLQndnYSTVIAAGDTFRAGaidqieshankintklikhqemgdpaavvydavqyak 243
                                       5799*****************95332333333444444333333333333344444444533333333333333333 PP

                                       ..........STTHHHHHHH CS
                               AAA  38 ..........yvgesekkir 47 
                                                 + g +  +++
  gi|298674678|ref|YP_003726428.1| 244 srsidvvlsdTAGRMHTNVN 263
                                       33333333333333333333 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   3.4e-05     0.018       3      84 ..     171     250 ..     169     303 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.4e-05
                                       ESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHHHHHHHTTHHHHHHHHHT CS
                   Thymidylate_kin   3 GlDGaGKttqaellkerlkeegikvvltrepggteiGekirelllkeeeleeqteallfaadriehleekikpalkq 79 
                                       G++G+GKtt ++++++ l++  +++v+    g+t  +  i+++ +++++++ + +    + d +  +++ ++ a ++
  gi|298674678|ref|YP_003726428.1| 171 GVNGTGKTTTIAKMANLLQNDNYSTVI--AAGDTFRAGAIDQIESHANKINTKLIKHQEMGDPAAVVYDAVQYAKSR 245
                                       9*********************98544..467888888888888888888777766666666655555555555555 PP

                                       T-EEE CS
                   Thymidylate_kin  80 gktvi 84 
                                       +  v+
  gi|298674678|ref|YP_003726428.1| 246 SIDVV 250
                                       55554 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0     1e-05    0.0057       2     104 ..     167     283 ..     167     310 .. 0.58

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklg.....avllssdtlrrrlfg......tdqqskt.dytrvldrlyqilnelarka 66 
                                       +++vG++G+GK+t + ++++ l+     +v+ + dt+r           ++ ++k  + ++  d   + + + ++ a
  gi|298674678|ref|YP_003726428.1| 167 IVFVGVNGTGKTTTIAKMANLLQndnysTVIAAGDTFRAGAIDqieshaNKINTKLiKHQEMGD-PAAVVYDAVQYA 242
                                       68**************998665566675555666775553333243232222222222222333.334666777888 PP

                            AAA_33  67 lsagrnvildat....nlsrrerarflklarrlgvpvrivvv 104
                                        s+ ++v+l  t     ++ + ++++ k+ r  ++p++i++v
  gi|298674678|ref|YP_003726428.1| 243 KSRSIDVVLSDTagrmHTNVNLMSQLEKVCR-VSSPDLIIFV 283
                                       8888888886664443222344444444444.4446666654 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.9e-05     0.011      14      80 ..     167     242 ..     160     287 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.9e-05
                                       EEEEESTTSSHHHHHHHHTTSS--SEEEEEET.TCEGGG.....B-HHHCCHCEEEE-SS--S-TTSBHHHH...H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxx...x RF
                          ABC_tran  14 vaivGenGaGKStLlkllagllkpteGeilld.gkdlke.....qeleslrkeigvlpqepqlfpeltvren...e 80 
                                       +++vG nG+GK+t ++ +a+ll++++ +  +  g+ ++      +e +  + + + +++++  +p   v++    +
  gi|298674678|ref|YP_003726428.1| 167 IVFVGVNGTGKTTTIAKMANLLQNDNYSTVIAaGDTFRAgaidqIESHANKINTKLIKHQEMGDPAAVVYDAvqyA 242
                                       789*******************997655544435555554442233333333333343333333433344445553 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.8e-05     0.015      22     143 ..     162     285 ..     153     292 .. 0.53

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.8e-05
                            AAA_16  22 grpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawr 98 
                                         p  ++++G  G+GK++ + + ++ l+ d+  ++ +  d +++       ++++ + +  +++++++ +  +++  
  gi|298674678|ref|YP_003726428.1| 162 EKPVHIVFVGVNGTGKTTTIAKMANLLQNDNYSTVIAAGDTFRA-----GAIDQI-E-SHANKINTKLIK--HQEMG 229
                                       4568899*****************88888854444444444411.....244444.2.333333333111..11111 PP

                            AAA_16  99 ekleeala.............avpelagaea...srllellkrllallsrderp.lvlvlDd 143
                                       +      a             +++ + ++ a   +   +l+++l + ++  ++p l++++D+
  gi|298674678|ref|YP_003726428.1| 230 DP-----AavvydavqyaksrSIDVVLSDTAgrmHTNVNLMSQLEKVCRV-SSPdLIIFVDE 285
                                       11.....1112222223333322222233335566666677777777777.44448888887 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       5.4   2.9e+03      15      44 ..       3      32 ..       3      46 .. 0.81
   2 !   14.5   0.5   5.1e-05     0.028       2      87 ..     167     290 ..     166     313 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 5.4
                                      HHHHHHTSTEEESSSTTSSSSEEEEEEEET CS
                          MMR_HSR1 15 LinaltgekaivsdkpgtTrdinegrvklk 44
                                      L+n+l ++ +  ++ +  T+d +  +v+++
  gi|298674678|ref|YP_003726428.1|  3 LFNKLKEKLSSFKKSAEDTIDEKAVEVEEQ 32
                                      789999888899999999999888888744 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 5.1e-05
                                       EEEEESTTSSHHHHHHHHHT.................STEEESSSTTSSSSEEEEEEEETTEE.............. CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg.................ekaivsdkpgtTrdinegrvklkgke.............. 47 
                                       +++vG   +GK+t i ++ +                 ++  + ++     +in++ +k+   +              
  gi|298674678|ref|YP_003726428.1| 167 IVFVGVNGTGKTTTIAKMANllqndnystviaagdtfRAGAIDQIESHANKINTKLIKH---Qemgdpaavvydavq 240
                                       89*****************8777777766665554332234455555555555555542...134445666666666 PP

                                       ........EEEEECGGCSSHHHHHHHHHHHHHHHHC...TSEEEEEEETT..T CS
                          MMR_HSR1  48 ........ielvDtpGliegaseekglgkaflalee...adlillvvdas..e 87 
                                               ++l Dt+G ++   ++ +l  +++++ +    dli++v +a   +
  gi|298674678|ref|YP_003726428.1| 241 yaksrsidVVLSDTAGRMH---TNVNLMSQLEKVCRvssPDLIIFVDEAVagN 290
                                       66666777********555...4444444444433332159999998766331 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   3.3e-05     0.018       1      46 [.     166     212 ..     166     268 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.3e-05
                                       EEEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--HHHHH--B- CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaal.nreveyvqltrdtteedlkgrre 46 
                                       +++ vG  GtgK++ + ++a +l n+++ +v    dt ++  + ++e
  gi|298674678|ref|YP_003726428.1| 166 HIVFVGVNGTGKTTTIAKMANLLqNDNYSTVIAAGDTFRAGAIDQIE 212
                                       6889********************99999998888876666665555 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.3       5.7   3.1e+03      71      96 ..       8      36 ..       3      80 .. 0.50
   2 ?   15.4   0.4   2.6e-05     0.014      21      81 ..     154     218 ..     109     303 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 5.7
                                      HHHGGGGTGG.......GEEEESSS-B-- CS
                            ResIII 71 leefkkflseayke...igkkvsgdkkka 96
                                      +e++++f+++a +    +  +v++++ ++
  gi|298674678|ref|YP_003726428.1|  8 KEKLSSFKKSAEDTideKAVEVEEQNTQP 36
                                      44444444444433211333344444443 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 2.6e-05
                                       .........TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG. CS
                            ResIII  21 s.......krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflsea 81 
                                               ++  +++++   GtGKT ++ak++  l++ ++     +++ + +    +++++++ +++ 
  gi|298674678|ref|YP_003726428.1| 154 FdeylknaEKPVHIVFVGVNGTGKTTTIAKMANLLQNDNY---STVIAAGDTFRAGAIDQIESHANKI 218
                                       04444433455599*****************999999766...4667777777777777776666655 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   4.7e-05     0.025       2      48 ..     164     210 ..     163     230 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.7e-05
                                       -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT CS
                        APS_kinase   2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkd 48 
                                       +v + + G+ g+GK+t   ++++ L+++++s+++  Gd+ R g   +
  gi|298674678|ref|YP_003726428.1| 164 PVHIVFVGVNGTGKTTTIAKMANLLQNDNYSTVIAAGDTFRAGAIDQ 210
                                       67899***********9999*********************986655 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   7.4e-05      0.04       9      36 ..     174     201 ..     167     334 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.4e-05
                                       TSSHHHHHHHHHHHHHHTT--EEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA   9 GvGKTtlaanLaralarrglrVllvDaD 36 
                                       G+GKTt+ a++a +l+++++ ++    D
  gi|298674678|ref|YP_003726428.1| 174 GTGKTTTIAKMANLLQNDNYSTVIAAGD 201
                                       9****************99998776555 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00017     0.094       1      29 [.     166     194 ..     166     199 .. 0.91
   2 ?    0.0   0.0       1.3     7e+02      87     135 ..     237     286 ..     213     305 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00017
                                       EEEEE--TTSSHHHHHHHHHHHH...GGG CS
                          NTPase_1   1 kvfiTGppGvGKtTlvkkvlellkssgvk 29 
                                       +++  G  G+GKtT + k+++ll++++++
  gi|298674678|ref|YP_003726428.1| 166 HIVFVGVNGTGKTTTIAKMANLLQNDNYS 194
                                       6778899******************9986 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.3
                                       HHHHHHH.HHH-EEEE---STTGGG-HHHHHHHHHHHT.TTSEEEEE--SS CS
                          NTPase_1  87 ealrkal.seadviviDEiGkmElkskkfkeaveevLk.sekpvlavihrr 135
                                       +a++ a  ++ dv++ D  G+m  +++ + +++e+v + s++ +++ + ++
  gi|298674678|ref|YP_003726428.1| 237 DAVQYAKsRSIDVVLSDTAGRMHTNVNLM-SQLEKVCRvSSPDLIIFVDEA 286
                                       55555554677899999999998877654.557777776666666655555 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   7.3e-05      0.04       4      84 ..     167     244 ..     165     274 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.3e-05
                                       EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH.TTSSS--GGGHHHHHHHHHHHHHHHHTT.SEEEE-S-- CS
                             KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvviddeslgiekdsykdsakekalRsslrsavkrdLskekvVIvDsln 80 
                                       +v+ G+  +GK+t  +++a+ l++ ++s v+   ++++    +  +s++ k + ++l++  ++++     V+ D++ 
  gi|298674678|ref|YP_003726428.1| 167 IVFVGVNGTGKTTTIAKMANLLQNDNYSTVIAAGDTFRAGAIDQIESHANK-INTKLIK--HQEMGDPAAVVYDAVQ 240
                                       899**********************************97777656665554.3444443..4778888888888888 PP

                                       -SHH CS
                             KTI12  81 yikg 84 
                                       y k+
  gi|298674678|ref|YP_003726428.1| 241 YAKS 244
                                       8887 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       7.2   3.9e+03      88     111 ..      52      75 ..      43      76 .. 0.73
   2 ?   13.2   0.0   9.8e-05     0.053       3      76 ..     165     257 ..     163     275 .. 0.55

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 7.2
                            AAA_24  88 qnekaeskedkgdgkGygelaeef 111
                                        +++ e++++ ++g+G+g+ a+ f
  gi|298674678|ref|YP_003726428.1|  52 TSNNLEQETGSKSGTGFGQKAKAF 75 
                                       445567888999999999888776 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 9.8e-05
                            AAA_24   3 lkiliyGpsgiGKTtlakel.......gpkplfi..dtek.Glksldadkfpdieswedfldevvel.......... 59 
                                       + i+ +G +g+GKTt+++++        +++++   dt++ G+  +d           ++ + ++++          
  gi|298674678|ref|YP_003726428.1| 165 VHIVFVGVNGTGKTTTIAKManllqndNYSTVIAagDTFRaGA--ID-----------QIESHANKIntklikhqem 228
                                       67999***************55544443333333332222111..11...........1111111112222333333 PP

                            AAA_24  60 ............aaeladyktlviDtide 76 
                                                   +a+ + ++++  Dt++ 
  gi|298674678|ref|YP_003726428.1| 229 gdpaavvydavqYAKSRSIDVVLSDTAGR 257
                                       34444445556666666677777666665 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   7.2e-05     0.039     106     166 ..     142     202 ..     133     230 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.2e-05
                             T2SSE 106 ddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinks.derivtvEDp 166
                                       + + ++ a++ +++e l++a ++   i++ G  g+GKtt++  + + ++++    ++ + D+
  gi|298674678|ref|YP_003726428.1| 142 SLYNIMSANTFDFDEYLKNA-EKPVHIVFVGVNGTGKTTTIAKMANLLQNDnYSTVIAAGDT 202
                                       55777888888999******.9999****************999999988844556666665 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   0.00011     0.059      12     111 ..     166     286 ..     156     303 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00011
                            AAA_19  12 vllvtaGpGtGKTrvlkhivallvelggvkpeeillv..aftgrAakelrerlaalgae.................. 68 
                                       +++ ++  GtGKT+++ ++ +ll++ +     +++++  +f   A ++++   ++++ +                  
  gi|298674678|ref|YP_003726428.1| 166 HIVFVGVNGTGKTTTIAKMANLLQNDN-Y--STVIAAgdTFRAGAIDQIESHANKINTKlikhqemgdpaavvydav 239
                                       45567889********99888887776.3..4566662244445677777777666655555555555554444433 PP

                            AAA_19  69 atTiHrlal..........ldfddlltealelleeaeeekklqeee.llivDEf 111
                                                           d+ +++++ ++l+ + e+   + + + +++vDE+
  gi|298674678|ref|YP_003726428.1| 240 Q-------YaksrsidvvlSDTAGRMHTNVNLMSQLEKVCRVSSPDlIIFVDEA 286
                                       0.......0444444444455556666666666666666677677767778875 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   8.8e-05     0.048      23      70 ..     154     197 ..     141     255 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.8e-05
                                       HHTTSS--B--SS-EEEEEESBSS-HSHHHHHHHHHHHTTTS..-EEE CS
                              LpxK  23 yragllkserlpvpVivVGNitvGGtGKTPlvialvkllqarglkvgv 70 
                                       +  + lk+ + pv ++ VG   v GtGKT +++ +++llq+ ++  ++
  gi|298674678|ref|YP_003726428.1| 154 F-DEYLKNAEKPVHIVFVG---VNGTGKTTTIAKMANLLQNDNYSTVI 197
                                       4.456888899*******9...99*****************9988765 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00012     0.065       8      36 ..     158     186 ..     153     210 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                                       GTT.TTEEEEEEEESTTSSHHHHHHHHHH CS
                               Arf   8 lklkkkelrilllGLDnaGKtTilkklkl 36 
                                       lk+++k ++i+++G  ++GKtT + k+ +
  gi|298674678|ref|YP_003726428.1| 158 LKNAEKPVHIVFVGVNGTGKTTTIAKMAN 186
                                       677899****************9988765 PP

>> FCP1_C  FCP1, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.7   9.1e-05      0.05     137     221 ..       1      81 [.       1     111 [. 0.71

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.1e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXX...XXXXXXXXXXXXXXXXXXXXXX CS
                            FCP1_C 137 mPLYtLCkeDLesmDkevDDilGeesDesdsekkkkeeeeeeeeeeeqerkpealeakeeeklastssserslaesv 213
                                       mPL+   ke L s  k  +D + e++ e +++++++ e+ e e   +++++p++++ + e++++s+s +   + +++
  gi|298674678|ref|YP_003726428.1|   1 MPLFNKLKEKLSSFKKSAEDTIDEKAVEVEEQNTQPAETSEPE---PVKTEPSKTSNNLEQETGSKSGT--GFGQKA 72 
                                       9*****************************9999999877765...66666666665555544433322..222222 PP

                                       .XXXXXXXX CS
                            FCP1_C 214 .prGhkRkl 221
                                        +   kR +
  gi|298674678|ref|YP_003726428.1|  73 kAFVFKREF 81 
                                       244556655 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00021      0.11      15      48 ..     164     197 ..     157     202 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00021
                     TrwB_AAD_bind  15 tqhilivGttGsGKtqalekllrairargdraiv 48 
                                         hi++vG  G+GKt+++ k+ + +++ +   ++
  gi|298674678|ref|YP_003726428.1| 164 PVHIVFVGVNGTGKTTTIAKMANLLQNDNYSTVI 197
                                       57******************99888877776666 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   1.5       2.3   1.2e+03     238     300 ..       7      69 ..       3      91 .. 0.44
   2 ?   13.1   0.1   0.00011     0.058      25      55 ..     166     213 ..     148     270 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.3
                            AAA_15 238 lteklkeiqeklkeidkklaeelkkilkkkidkikkfnykgkkneeieik...........ddeelplnknGsG 300
                                       l+ekl++++++ ++++++ a e ++  +++ ++++ +                        ++e  + +  G+G
  gi|298674678|ref|YP_003726428.1|   7 LKEKLSSFKKSAEDTIDEKAVEVEEQNTQPAETSEPEP-----------VktepsktsnnlEQETGSKSGTGFG 69 
                                       33333333333333333333333333333333332222...........1233333332335555554555555 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00011
                            AAA_15  25 ltvliGkNnsGKSsilealdlFlnnkekkn..................k 55 
                                         v++G N++GK++ +  +  +l+n+ +++                  +
  gi|298674678|ref|YP_003726428.1| 166 HIVFVGVNGTGKTTTIAKMANLLQND-NYStviaagdtfragaidqieS 213
                                       579*************9999999999.3335887665544333332221 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00048      0.26       2      29 ..     167     194 ..     166     203 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00048
                              MobB   2 lgivgksgsGKTtLleklipelkarglr 29 
                                       + +vg +g+GKTt + k+ + l++ +++
  gi|298674678|ref|YP_003726428.1| 167 IVFVGVNGTGKTTTIAKMANLLQNDNYS 194
                                       679********************99986 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.4       2.2   1.2e+03     119     120 ..      32      73 ..       4     160 .. 0.43
   2 ?   11.4   0.0   0.00025      0.13      19      74 ..     159     218 ..     145     303 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.2
                                       .........................................H CS
                           G-alpha 119 e........................................q 120
                                       +                                        +
  gi|298674678|ref|YP_003726428.1|  32 QntqpaetsepepvktepsktsnnleqetgsksgtgfgqkaK 73 
                                       223333333332222222222222333333333333333330 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00025
                                       XE...EEEEEEEESTTSSHHHHHHHHH.HHCS----HHHH..HCCHHHHHHHHHHHHHHH CS
                           G-alpha  19 kk.krevkllllGqseSGKsTilkqlk.llykkgfseeel..atwraviqlnivrsikti 74 
                                       k+ +++v+++++G ++ GK+T++ ++  ll ++++s+  +   t+ra  + +i +++++i
  gi|298674678|ref|YP_003726428.1| 159 KNaEKPVHIVFVGVNGTGKTTTIAKMAnLLQNDNYSTVIAagDTFRAGAIDQIESHANKI 218
                                       334679***************999988466666677652211224444444444444443 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       5.3   2.9e+03      27      53 ..      95     120 ..      92     140 .. 0.80
   2 ?   11.5   0.5   0.00031      0.17       3     151 ..     167     314 ..     165     325 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 5.3
                                       S-EEEEESS-SSCHCCCCCCHCCCT.E CS
                              cobW  27 lklavivNefgevsiDaellretgvei 53 
                                       l++ +++N++  +s+ ++++++ ++e+
  gi|298674678|ref|YP_003726428.1|  95 LEMGLLENDIA-LSVSEAIVESVKNEL 120
                                       67888999999.999999998776654 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00031
                                       EEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT.EEEETTTTECCH.CTT-HHHHHHHH CS
                              cobW   3 tvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgveivelenGciCct.lredllkeleal 76 
                                       +v++G  G+GKTt + ++    +++++++ +  ++       a  +++ ++++ ++++  i ++ + + +  + +a+
  gi|298674678|ref|YP_003726428.1| 167 IVFVGVNGTGKTTTIAKMAnlLQNDNYSTVIAAGDTFR----AGAIDQIESHANKINTKLIKHQeMGDPAAVVYDAV 239
                                       6899************9997666677777777788774....34444444556788888888885666555555555 PP

                                       HHHH.TT-SEEEEEECTTTTHHHH.HTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HH CS
                              cobW  77 eere.erldviliEttGlaePapv.afteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtD 151
                                       +  + +++dv+l  t G ++ +   + + e++++    d +++v +a +  ++  + +++++d +   d  +l+K+D
  gi|298674678|ref|YP_003726428.1| 240 QYAKsRSIDVVLSDTAGRMHTNVNlMSQLEKVCRVSSPDLIIFVDEAVA-GNDAVERAQQFNDNIPI-DGSILTKAD 314
                                       4433458999999999966655552555677777777777777666644.46666677777777654.555566666 PP

>> PTPlike_phytase  Inositol hexakisphosphate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.5       8.4   4.6e+03      59      76 ..      25      42 ..       5      63 .. 0.41
   2 ?    9.8   0.0    0.0015      0.82     121     155 ..     154     188 ..     145     189 .. 0.88
   3 ?    0.1   0.0       1.4   7.6e+02      37      79 ..     209     249 ..     202     275 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 8.4
                                      HHHHTT-CCG-EEE-S-. CS
                   PTPlike_phytase 59 grvlvhdeteegkdvktl 76
                                      + v v++++++  + ++ 
  gi|298674678|ref|YP_003726428.1| 25 KAVEVEEQNTQPAETSEP 42
                                      222222222222222222 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0015
                                       HHHHHHTS-TT-EEEEE-SSSSHHHHHHHHHHHHH CS
                   PTPlike_phytase 121 lvsilkeapektalvfnCqmGrgRTTtamviatLl 155
                                       + ++lk+a++   +vf   +G+g+TTt   +a Ll
  gi|298674678|ref|YP_003726428.1| 154 FDEYLKNAEKPVHIVFVGVNGTGKTTTIAKMANLL 188
                                       5678899*99*********************9997 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHT-SEEEEEEEHHHHHTT-CCG-EEE-S-.... CS
                   PTPlike_phytase  37 eeleklearlkeevlaeakksegrvlvhdeteegkdvktlqev 79 
                                       +++e+  +++   +++ ++ +++  +v+d +++ k +++ ++v
  gi|298674678|ref|YP_003726428.1| 209 DQIESHANKINTKLIKHQEMGDPAAVVYDAVQYAK-SRS-IDV 249
                                       67888888999999999999999999999999886.333.333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1031  (0.0575046); expected 358.6 (0.02)
Passed bias filter:                      650  (0.0362541); expected 358.6 (0.02)
Passed Vit filter:                       115  (0.00641419); expected 17.9 (0.001)
Passed Fwd filter:                        33  (0.00184059); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              33  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.41
# Mc/sec: 2599.94
//
Query:       gi|298674679|ref|YP_003726429.1|  [L=156]
Description: prefoldin subunit alpha [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-25   87.8   4.1    6.2e-25   87.4   4.1    1.1  1  Prefoldin        Prefoldin subunit
      5e-09   36.1  13.3    9.1e-05   22.4   0.8    2.3  2  Prefoldin_2      Prefoldin subunit
     0.0018   18.3   7.2       0.21   11.6   2.3    2.1  2  DUF1043          Protein of unknown function (DUF1043)
     0.0018   18.7   2.5      0.044   14.1   0.6    2.1  2  Gp-FAR-1         Nematode fatty acid retinoid binding protein
     0.0028   16.0   5.1     0.0034   15.7   5.1    1.0  1  FPP              Filament-like plant protein, long coiled-coi
      0.003   17.7   2.5        1.9    8.6   1.3    2.4  2  DUF2433          Protein of unknown function (DUF2433)
     0.0031   17.9  10.2       0.11   12.9  10.2    2.3  1  Syntaxin_2       Syntaxin-like protein
     0.0031   17.8   8.6       0.63   10.3   3.4    2.3  2  DUF5082          Domain of unknown function (DUF5082)
     0.0033   17.8   0.3     0.0033   17.8   0.3    1.7  2  DUF3510          Domain of unknown function (DUF3510)
     0.0055   16.5  11.5      0.084   12.7   0.9    2.2  2  CdvA             CdvA-like coiled-coil domain
     0.0095   15.5  14.9       0.03   13.9  14.9    1.7  1  PI3K_P85_iSH2    Phosphatidylinositol 3-kinase regulatory sub
  ------ inclusion threshold ------
      0.011   15.7   6.5        1.1    9.2   1.7    2.4  2  BORCS8           BLOC-1-related complex sub-unit 8
      0.011   15.2   9.0       0.34   10.4   3.5    2.1  2  MscS_porin       Mechanosensitive ion channel porin domain
      0.015   14.2   8.2       0.24   10.3   3.8    2.1  2  Spc7             Spc7 kinetochore protein
       0.02   14.9   7.3       0.66   10.1   0.8    2.2  2  DASH_Dad3        DASH complex subunit Dad3
      0.021   14.9   7.6        1.2    9.2   0.2    2.2  2  DUF2959          Protein of unknown function (DUF2959)
      0.023   13.4   9.6      0.078   11.7   5.0    2.0  2  Tektin           Tektin family
      0.025   14.9   4.7        1.2    9.5   1.6    2.3  2  KxDL             Uncharacterized conserved protein
      0.029   14.5   3.5        4.3    7.5   0.0    2.1  2  CREPT            Cell-cycle alteration and expression-elevate
       0.03   15.0   3.7      0.043   14.5   3.7    1.3  1  AATF-Che1        Apoptosis antagonizing transcription factor
       0.03   15.0   7.4        1.4    9.6   0.4    2.1  2  Plk4_PB2         Polo-like Kinase 4 Polo Box 2
       0.03   13.7  13.3       0.21   10.9   0.8    2.1  2  GAS              Growth-arrest specific micro-tubule binding
       0.03   14.6   0.6        8.5    6.7   0.2    2.2  2  DUF948           Bacterial protein of unknown function (DUF94
      0.033   14.2   0.7        6.7    6.8   0.1    2.2  2  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
       0.04   14.1   8.0       0.44   10.7   2.6    2.1  2  Fib_alpha        Fibrinogen alpha/beta chain family
      0.041   13.5   7.8      0.077   12.6   3.3    2.1  2  PspA_IM30        PspA/IM30 family
      0.053   13.4   4.5        2.4    8.1   0.4    2.2  2  SLATT_1          SMODS and SLOG-associating 2TM effector doma
      0.056   13.4   5.6        2.3    8.2   1.2    2.2  2  DUF4446          Protein of unknown function (DUF4446)
      0.057   12.6   3.3       0.42    9.7   3.0    2.0  1  phiKZ_IP         phiKZ-like phage internal head proteins
       0.06   12.0  10.8       0.13   10.8   5.7    2.0  2  FapA             Flagellar Assembly Protein A
      0.064   12.2   3.1      0.079   11.9   3.1    1.0  1  LMBR1            LMBR1-like membrane protein
      0.067   13.3  12.7       0.11   12.6   0.6    2.1  2  RasGAP_C         RasGAP C-terminus
      0.068   13.2   7.8       0.28   11.2   2.4    2.1  2  DUF1664          Protein of unknown function (DUF1664)
       0.07   13.7   0.8       0.32   11.6   0.2    2.2  2  DUF883           Bacterial protein of unknown function (DUF88
      0.075   13.0   2.6        6.8    6.7   0.1    2.3  2  ApoO             Apolipoprotein O
      0.078   13.2   5.4        1.5    9.0   1.5    2.3  2  DUF4047          Domain of unknown function (DUF4047)
      0.078   13.1   8.8       0.31   11.1   3.6    2.2  2  ApoLp-III        Apolipophorin-III precursor (apoLp-III)
      0.086   13.1   8.2        1.1    9.6   2.6    2.5  2  WXG100           Proteins of 100 residues with WXG
      0.088   13.3   6.5       0.27   11.8   3.2    2.3  2  YtxH             YtxH-like protein
        0.1   12.9  13.3       0.21   11.9   7.1    2.1  2  OmpH             Outer membrane protein (OmpH-like)
       0.14   12.6   2.9         13    6.2   0.0    2.1  2  L31              Mitochondrial ribosomal protein L31
       0.14   12.1  12.0      0.089   12.8   0.8    2.4  2  FlxA             FlxA-like protein
       0.15   12.0   8.4       0.53   10.2   2.7    2.1  2  Ax_dynein_light  Axonemal dynein light chain
       0.15   12.6  11.4        1.8    9.2   0.4    2.9  3  DUF5344          Family of unknown function (DUF5344)
       0.16   12.0   5.7        1.5    8.8   2.0    2.2  2  Laminin_II       Laminin Domain II
       0.17   12.3   5.5        1.5    9.2   0.1    3.4  3  FlaC_arch        Flagella accessory protein C (FlaC)
       0.23   11.6   5.2        5.3    7.1   0.8    2.2  2  COG2             COG (conserved oligomeric Golgi) complex com
       0.33   10.0  10.1        1.7    7.7   0.8    2.1  2  APG17            Autophagy protein Apg17
       0.35    8.8   7.7       0.82    7.6   7.7    1.5  1  Prominin         Prominin
       0.38    9.7  15.6        1.3    8.0   5.6    2.0  2  IFT57            Intra-flagellar transport protein 57
       0.43   10.5  11.0       0.97    9.3  11.0    1.5  1  STAT_alpha       STAT protein, all-alpha domain
       0.64    9.7  10.9       0.73    9.5   6.2    2.1  2  GrpE             GrpE
       0.73    9.0  12.9       0.61    9.3   1.3    2.0  2  TMPIT            TMPIT-like protein
       0.77    9.8   7.2        1.9    8.5   0.2    2.6  2  SOAR             STIM1 Orai1-activating region
       0.78    9.3  10.0        4.1    7.0  10.0    1.9  1  DUF4795          Domain of unknown function (DUF4795)
       0.83   10.4   4.5        7.2    7.4   1.2    2.1  2  Sulfatase_C      C-terminal region of aryl-sulfatase
       0.87    9.9   0.1       0.87    9.9   0.1    2.5  2  DUF3135          Protein of unknown function (DUF3135)
        0.9    9.6  14.2         19    5.3  14.2    2.2  1  Mod_r            Modifier of rudimentary (Mod(r)) protein
        1.1    9.3  11.9          1    9.4   5.6    2.1  2  ADIP             Afadin- and alpha -actinin-Binding
        1.3    8.9  11.1        6.5    6.6  11.3    1.8  1  FTA4             Kinetochore complex Fta4 of Sim4 subunit, or
        1.3    8.6  15.9       0.64    9.6   8.3    2.0  2  Filament         Intermediate filament protein
        1.4    8.2   7.8        3.8    6.8   7.5    1.7  1  DUF4407          Domain of unknown function (DUF4407)
        1.4    9.2  12.8       0.16   12.3   0.5    2.7  3  T4SS             Type IV secretion system proteins
          2    7.8  12.7       0.23   10.9   6.0    2.0  2  DUF3552          Domain of unknown function (DUF3552)
          2    8.8  13.1        2.8    8.3   0.8    2.3  2  BLOC1_2          Biogenesis of lysosome-related organelles co
        3.9    6.7  15.4       0.95    8.7   0.7    2.0  2  DUF3450          Protein of unknown function (DUF3450)
        6.5    7.2   9.4         15    6.0   0.5    3.0  3  LPP              Lipoprotein leucine-zipper
          8    6.5   9.7         16    5.5   1.7    2.6  2  Nore1-SARAH      Novel Ras effector 1 C-terminal SARAH (Sav/R
        9.9    6.7  15.3         12    6.4   6.1    2.1  2  APG6_N           Apg6 coiled-coil region


Domain annotation for each model (and alignments):
>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.4   4.1   2.4e-27   6.2e-25       1     118 [.      25     142 ..      25     144 .. 0.98

  Alignments for each domain:
  == domain 1  score: 87.4 bits;  conditional E-value: 2.4e-27
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.-TT-EEEEEEETTEEEEEE--STTEEEEEEETTEEEEEEHHH CS
                         Prefoldin   1 lkeeleslqaelaqlkeaieelektletlktlkkedegkevlvplgaglyvkaevkdtdkvlvdlGagyyvekslee 77 
                                       +k +les+ + ++ + ++ ee+ k+l+t+++l+  +eg+e +vp+g+g y+ a+  d +++++d+Gag++vek+ e+
  gi|298674679|ref|YP_003726429.1|  25 YKNQLESIKQHIDMVYTSSEECVKALNTIESLESLEEGTESMVPIGSGTYMHAQFNDLNRFVIDIGAGISVEKNRED 101
                                       899************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  78 Aiellkkkleelekqlekleeeleklkdqittleanlaqly 118
                                       A+e+l+k++ee++++ e l+e+  +  ++++++e+++++ +
  gi|298674679|ref|YP_003726429.1| 102 AKETLNKRKEEMDNAYERLNESYSQVVQNMQEIERQFNEYQ 142
                                       ************************************99866 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.8   3.5e-07   9.1e-05       2      43 ..      17      58 ..      16      69 .. 0.93
   2 !   18.3   5.9   6.6e-06    0.0017      56     103 ..      95     142 ..      92     150 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 3.5e-07
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-T CS
                       Prefoldin_2  2 elinkfqqlqqqlqqlaqqikqletqlkelelvleelellde 43
                                      +l  ++qq+++ql+ ++q i++++t  +e+ ++l+++e+l++
  gi|298674679|ref|YP_003726429.1| 17 QLSTQYQQYKNQLESIKQHIDMVYTSSEECVKALNTIESLES 58
                                      6779**********************************9986 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 6.6e-06
                                       EEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCT CS
                       Prefoldin_2  56 vkqdkeevkeeLeerketlekeiktlekqleklekeleelkeelqkkl 103
                                       v++++e++ke+L++rke+++  +++l+++++++ ++++e++ + ++ +
  gi|298674679|ref|YP_003726429.1|  95 VEKNREDAKETLNKRKEEMDNAYERLNESYSQVVQNMQEIERQFNEYQ 142
                                       7899*************************************9988766 PP

>> DUF1043  Protein of unknown function (DUF1043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.2    0.0032      0.84      27      63 ..      16      52 ..       8      79 .. 0.85
   2 !   11.6   2.3   0.00079      0.21      28      81 ..      94     147 ..      88     156 .] 0.80

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0032
                           DUF1043 27 kklekelekakaeleeqkqeledHfaqsaelLetlae 63
                                      ++l ++ ++ k++le  kq+++   ++s e ++ l++
  gi|298674679|ref|YP_003726429.1| 16 RQLSTQYQQYKNQLESIKQHIDMVYTSSEECVKALNT 52
                                      5789999***************999999999999864 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00079
                           DUF1043  28 klekelekakaeleeqkqeledHfaqsaelLetlaedyqkLyqhlaksseeLlp 81 
                                       ++ek+ e+ak++l++ k+e+++  ++ +e  ++  +++q++ ++++++++++ +
  gi|298674679|ref|YP_003726429.1|  94 SVEKNREDAKETLNKRKEEMDNAYERLNESYSQVVQNMQEIERQFNEYQSKMQS 147
                                       678889999999999999999999999999999999999998888888888744 PP

>> Gp-FAR-1  Nematode fatty acid retinoid binding protein (Gp-FAR-1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1      0.15        38      28      64 ..      13      50 ..       6      69 .. 0.70
   2 !   14.1   0.6   0.00017     0.044      35      80 ..      92     140 ..      73     153 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.15
                          Gp-FAR-1 28 evvkn.ykgyknedellaalKkkspaLyekaeklqakl 64
                                      + +++ + +y+ +++ l+ +K+  + +y+  e+  + l
  gi|298674679|ref|YP_003726429.1| 13 QYFRQlSTQYQQYKNQLESIKQHIDMVYTSSEECVKAL 50
                                      45566555677777778888888888888877766665 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 0.00017
                          Gp-FAR-1  35 g...yknedellaalKkkspaLyekaeklqaklkekvdkLspeakeFvk 80 
                                       g    kn +++ + l k+++++ + +e+l++ + + v+++++  ++F +
  gi|298674679|ref|YP_003726429.1|  92 GisvEKNREDAKETLNKRKEEMDNAYERLNESYSQVVQNMQEIERQFNE 140
                                       444579************************************9999965 PP

>> FPP  Filament-like plant protein, long coiled-coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   5.1   1.3e-05    0.0034     620     744 ..      18     150 ..       9     155 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.3e-05
                               FPP 620 lkfslldvssmeeeikksddidkvalsenkvaqkgessnecaeisklssekeipselplvsgsnesk.......... 686
                                       l  + ++++++ e ik++  id v  s ++ +++    n++ ++++l++ +e  s +p+ sg++ +           
  gi|298674679|ref|YP_003726429.1|  18 LSTQYQQYKNQLESIKQH--IDMVYTSSEECVKA---LNTIESLESLEEGTE--SMVPIGSGTYMHAqfndlnrfvi 87 
                                       566788999999999998..66655666666555...456666666555555..4789999988888899999**** PP

                               FPP 687 .....keenkllkeeleelksekenlevelksatenleslkaqlqesEqllaelkseLeslke 744
                                             +++k+ ++  e l+ +ke+++   ++ +e+  +++  +qe+E++ +e +s+++s ++
  gi|298674679|ref|YP_003726429.1|  88 digagISVEKNREDAKETLNKRKEEMDNAYERLNESYSQVVQNMQEIERQFNEYQSKMQSQQD 150
                                       ***9989999999999*******************************************9886 PP

>> DUF2433  Protein of unknown function (DUF2433)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0     0.011       2.9      12      57 ..       9      52 ..       4      80 .. 0.75
   2 !    8.6   1.3    0.0071       1.9       8      48 ..      93     133 ..      89     146 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.011
                           DUF2433 12 psleayrsklakskakfaevwetvkkeveaaid..eaqrklLenalev 57
                                       ++e+y  +l+++ +++++  e++k++++++ +  e+      +al+ 
  gi|298674679|ref|YP_003726429.1|  9 GDTEQYFRQLSTQYQQYKNQLESIKQHIDMVYTssEECV----KALNT 52
                                      688999999999999999999999999998877333333....33333 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0071
                           DUF2433   8 fsvnpsleayrsklakskakfaevwetvkkeveaaideaqr 48 
                                       +sv+++ e  ++ l+k+k+++++ +e++++++ +++++ q+
  gi|298674679|ref|YP_003726429.1|  93 ISVEKNREDAKETLNKRKEEMDNAYERLNESYSQVVQNMQE 133
                                       79********************************9996554 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9  10.2   0.00042      0.11      16     100 ..      12     145 ..       9     146 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00042
                        Syntaxin_2  16 eklvkqLgtkkdteelreklhelieeinelikktnellkklsqldnsssds.......................... 66 
                                       e++++qL+t+   ++++++l+++ ++i  + +  +e +k l++++  +s +                          
  gi|298674679|ref|YP_003726429.1|  12 EQYFRQLSTQ--YQQYKNQLESIKQHIDMVYTSSEECVKALNTIESLESLEegtesmvpigsgtymhaqfndlnrfv 86 
                                       799999*998..89******************************9999888999*********************** PP

                        Syntaxin_2  67 .........................qqklqkekLkkdfkealqeFqkiqrqyaekekqi 100
                                                                    + e+L++++++++q+ q+i rq++e + ++
  gi|298674679|ref|YP_003726429.1|  87 idigagisveknredaketlnkrkeEMDNAYERLNESYSQVVQNMQEIERQFNEYQSKM 145
                                       ********************998554455*************************99876 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.2    0.0025      0.64      73      95 ..      15      38 ..       5      59 .. 0.82
   2 !   10.3   3.4    0.0024      0.63      59     103 ..     104     148 ..      93     154 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0025
                           DUF5082 73 s.nlessyqtyvdkldelidaiee 95
                                        +l ++yq+y+ +l++++++i++
  gi|298674679|ref|YP_003726429.1| 15 FrQLSTQYQQYKNQLESIKQHIDM 38
                                      258999************999986 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0024
                           DUF5082  59 sWkGkeennydgirsnlessyqtyvdkldelidaieeEIerLenq 103
                                       +  +k++++ d++++ l +sy+++v+++ e++++ +e  +++++q
  gi|298674679|ref|YP_003726429.1| 104 ETLNKRKEEMDNAYERLNESYSQVVQNMQEIERQFNEYQSKMQSQ 148
                                       556889999******************999998877655555554 PP

>> DUF3510  Domain of unknown function (DUF3510)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       9.7   2.5e+03      67      86 ..      15      33 ..       9      38 .. 0.46
   2 !   17.8   0.3   1.3e-05    0.0033       5     103 ..      44     149 ..      41     156 .] 0.75

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 9.7
                           DUF3510 67 leevtsrYletisevlssvk 86
                                      +++++++Y +  ++ l+s+k
  gi|298674679|ref|YP_003726429.1| 15 FRQLSTQYQQ-YKNQLESIK 33
                                      3333444433.333333333 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 1.3e-05
                           DUF3510   5 ercceaLkqvssiprlyRrtnkevptepSkyvseilkplktf............kkesekklseevleewlaevlee 69 
                                       e+c++aL+ ++s+ +l   t+  vp    +y++  ++ l++f            + +  +k + + ++e +++++e+
  gi|298674679|ref|YP_003726429.1|  44 EECVKALNTIESLESLEEGTESMVPIGSGTYMHAQFNDLNRFvidigagisvekN-REDAKETLNKRKEEMDNAYER 119
                                       89***************************************99****99986421.222223333467888888999 PP

                           DUF3510  70 vtsrYletisevlssvkkteesLkrlkkarkgaa 103
                                       + ++Y +    v++++++ e + +  + + ++++
  gi|298674679|ref|YP_003726429.1| 120 LNESYSQ----VVQNMQEIERQFNEYQSKMQSQQ 149
                                       9999988....66666666666665555544433 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.9   0.00032     0.084      78     118 ..      23      63 ..      21      67 .. 0.92
   2 !    8.5   3.8    0.0064       1.7      24      63 ..      99     138 ..      93     150 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00032
                              CdvA  78 eaYksaieairellesaleekeeikklleklskleleeeev 118
                                       ++Yk++ e+i+++++++  + ee  k+l+++++le+ ee  
  gi|298674679|ref|YP_003726429.1|  23 QQYKNQLESIKQHIDMVYTSSEECVKALNTIESLESLEEGT 63 
                                       68********************************9988765 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0064
                              CdvA  24 kekleealkklkekakelkeklkkrlkeledqikslekal 63 
                                       +e  +e+l+k ke++++  e+l+++ +++ ++++++e+ +
  gi|298674679|ref|YP_003726429.1|  99 REDAKETLNKRKEEMDNAYERLNESYSQVVQNMQEIERQF 138
                                       5566666677777777777777777777777776666654 PP

>> PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9  14.9   0.00012      0.03      29     134 ..      11     147 ..       8     150 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00012
                     PI3K_P85_iSH2  29 kskeydqlkeeynkiseeiqlkrqaleaFneaikmFeeqiklqekfskeaq.......................... 79 
                                       +++ + ql+++y++ +++++  +q+++      + +   ++++e++++  +                          
  gi|298674679|ref|YP_003726429.1|  11 TEQYFRQLSTQYQQYKNQLESIKQHIDMVYTSSEECVKALNTIESLESLEEgtesmvpigsgtymhaqfndlnrfvi 87 
                                       45666677777777777777777777655555555556666666666655334455557777777788888888888 PP

                     PI3K_P85_iSH2  80 ......ehEieklqenleqlksrlkelhsskekLeedlkqqkeeereleReinalkpellq 134
                                             + E+++ ++  e l++r +e+ ++ e+L+e+  q +++ +e+eR+ n+ ++ +++
  gi|298674679|ref|YP_003726429.1|  88 digagiSVEKNR-EDAKETLNKRKEEMDNAYERLNESYSQVVQNMQEIERQFNEYQSKMQS 147
                                       888876555544.7788999**********************************9998875 PP

>> BORCS8  BLOC-1-related complex sub-unit 8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.2     0.006       1.6      44      82 ..      22      59 ..      13      68 .. 0.83
   2 ?    9.2   1.7    0.0043       1.1      47      91 ..     102     147 ..      94     150 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.006
                            BORCS8 44 lvekkkevkeleeelqgacydveyaisavksikesessf 82
                                        + k++++++++++   +   e++++a+++i+  e s+
  gi|298674679|ref|YP_003726429.1| 22 YQQYKNQLESIKQHIDMVYTSSEECVKALNTIESLE-SL 59
                                      56789***************************9988.44 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0043
                            BORCS8  47 kkkevkeleeelqgacydveyais.avksikesessfeniqelLkn 91 
                                        k+ +++ +ee+ +a++ ++++ s  v++++e+e +f++ q+ +++
  gi|298674679|ref|YP_003726429.1| 102 AKETLNKRKEEMDNAYERLNESYSqVVQNMQEIERQFNEYQSKMQS 147
                                       577788889999999999999975278*************999875 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.3    0.0062       1.6      39      84 ..      15      60 ..       8      68 .. 0.65
   2 ?   10.4   3.5    0.0013      0.34      61     119 ..      98     156 .]      92     156 .] 0.79

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0062
                        MscS_porin 39 aeelqkaiddaPkelrelqqelealqkkkeeaskeilaklsleeLe 84
                                       ++l ++ +++ ++l++++q+++    ++ee +k+  +  sle Le
  gi|298674679|ref|YP_003726429.1| 15 FRQLSTQYQQYKNQLESIKQHIDMVYTSSEECVKALNTIESLESLE 60
                                      4566667777777777777777777666666666666666666666 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0013
                        MscS_porin  61 ealqkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaq 119
                                       +++++k++ + +++      e L+  + q+ +++qe ++q ++++s+ +++q+   raq
  gi|298674679|ref|YP_003726429.1|  98 NREDAKETLNKRKEEMDNAYERLNESYSQVVQNMQEIERQFNEYQSKMQSQQDGAYRAQ 156
                                       55555666666666666677899999999999999999999999999999999998887 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1     0.013       3.5     213     256 ..      13      56 ..       8      81 .. 0.75
   2 ?   10.3   3.8   0.00092      0.24     154     195 ..     102     143 ..      93     154 .. 0.55

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.013
                              Spc7 213 aeieekkkelaelqeqleeleekieelkeqkseleeeiaeaerv 256
                                       +  +++++++++ ++qle++++ i+ + ++ +e+ ++++  e++
  gi|298674679|ref|YP_003726429.1|  13 QYFRQLSTQYQQYKNQLESIKQHIDMVYTSSEECVKALNTIESL 56 
                                       45566777788888888888888888888888888777766554 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00092
                              Spc7 154 dkelLekqeeeldellpeleeekaeleeeleklqeaaeeles 195
                                        ke+L+k++ee+d+++++l+e ++++ +++++++++ +e +s
  gi|298674679|ref|YP_003726429.1| 102 AKETLNKRKEEMDNAYERLNESYSQVVQNMQEIERQFNEYQS 143
                                       345555566666666666666666555555555554444433 PP

>> DASH_Dad3  DASH complex subunit Dad3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.8    0.0025      0.66      10      46 ..      20      55 ..      14      61 .. 0.89
   2 ?    8.3   0.9    0.0092       2.4      14      48 ..     105     138 ..      97     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0025
                         DASH_Dad3 10 deYerLaenlktLaselkeLasnsteeildgLReLEr 46
                                      ++Y++ +++l+++++++ ++  +s+ee ++ L  +E 
  gi|298674679|ref|YP_003726429.1| 20 TQYQQYKNQLESIKQHI-DMVYTSSEECVKALNTIES 55
                                      69***************.9999999999999999996 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0092
                         DASH_Dad3  14 rLaenlktLaselkeLasnsteeildgLReLErki 48 
                                       +L++  +++++  ++L+++  ++++++++e+Er+ 
  gi|298674679|ref|YP_003726429.1| 105 TLNKRKEEMDNAYERLNES-YSQVVQNMQEIERQF 138
                                       5677777788888888877.899**********96 PP

>> DUF2959  Protein of unknown function (DUF2959)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.2    0.0048       1.2      49      86 ..       8      45 ..       5      66 .. 0.88
   2 ?    8.2   2.9    0.0093       2.4      22      79 ..     101     140 ..      93     155 .. 0.48

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0048
                           DUF2959 49 ggeLekeyeklnkeyeesekaaeevrerieaveevaea 86
                                      +g+ e+ +++l+++y++ +++ e++++ i+ v + +e+
  gi|298674679|ref|YP_003726429.1|  8 KGDTEQYFRQLSTQYQQYKNQLESIKQHIDMVYTSSEE 45
                                      5889999***********************99887765 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0093
                           DUF2959  22 kardsqeeakeqfksALerfkavvefdggeLekeyeklnkeyeesekaaeevreriea 79 
                                       +a+++ ++ ke++++A er+++                  +y +  ++ +e++++ ++
  gi|298674679|ref|YP_003726429.1| 101 DAKETLNKRKEEMDNAYERLNE------------------SYSQVVQNMQEIERQFNE 140
                                       4555555555555555555444..................444444333333333322 PP

>> Tektin  Tektin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1      0.05        13     244     284 ..      10      50 ..       3      61 .. 0.68
   2 ?   11.7   5.0    0.0003     0.078     239     292 ..      96     149 ..      93     156 .] 0.79

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.05
                            Tektin 244 avnealrkrieetedaknkleeqlkkvleeiaeleknieeL 284
                                       ++++ +r+  +++++ kn+le+ ++++    ++ e+ +++L
  gi|298674679|ref|YP_003726429.1|  10 DTEQYFRQLSTQYQQYKNQLESIKQHIDMVYTSSEECVKAL 50 
                                       57777777777777777777777776665555555544444 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0003
                            Tektin 239 raqaeavnealrkrieetedaknkleeqlkkvleeiaeleknieeLekairdke 292
                                       ++ +e+  e l+kr ee+ +a + l+e  ++v+++++e+e++ +e ++++++++
  gi|298674679|ref|YP_003726429.1|  96 EKNREDAKETLNKRKEEMDNAYERLNESYSQVVQNMQEIERQFNEYQSKMQSQQ 149
                                       566777788888888999999999999999999999888888888888777655 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1     0.048        12      41      66 ..      13      38 ..       9      60 .. 0.64
   2 ?    9.5   1.6    0.0045       1.2      27      73 ..     101     147 ..      92     153 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.048
                              KxDL 41 erlaklrarfkqgtkllkevkkdLes 66
                                      + + +l+++++q+++ l ++k+ +++
  gi|298674679|ref|YP_003726429.1| 13 QYFRQLSTQYQQYKNQLESIKQHIDM 38
                                      44455555555555555555555444 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0045
                              KxDL  27 kknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirs 73 
                                       + +++L +  +++++ +++l++ + q ++ ++e+ ++ +  ++k++s
  gi|298674679|ref|YP_003726429.1| 101 DAKETLNKRKEEMDNAYERLNESYSQVVQNMQEIERQFNEYQSKMQS 147
                                       55678888888888888888888888888888888888888888765 PP

>> CREPT  Cell-cycle alteration and expression-elevated protein in tumour
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0     0.016       4.3      82     138 ..      12      68 ..       3      75 .. 0.85
   2 ?    6.1   2.5     0.045        12      72     122 ..      97     147 ..      88     150 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.016
                             CREPT  82 edfleaqkellakaeekleelkeklekvksvrkelkshiqsLPdLtelpdvtgglap 138
                                       e++++++ ++ ++ +++le++k+ ++ v +  +e  + ++ + +L++l + t+++ p
  gi|298674679|ref|YP_003726429.1|  12 EQYFRQLSTQYQQYKNQLESIKQHIDMVYTSSEECVKALNTIESLESLEEGTESMVP 68 
                                       678888999999999*************99999999999988888888887777666 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.045
                             CREPT  72 eeRkklakmledfleaqkellakaeekleelkeklekvksvrkelkshiqs 122
                                       ++R+  +++l++ +e + ++ ++ +e ++++ + +++++ + +e +s++qs
  gi|298674679|ref|YP_003726429.1|  97 KNREDAKETLNKRKEEMDNAYERLNESYSQVVQNMQEIERQFNEYQSKMQS 147
                                       567778888888888888888888888888888888888888888888876 PP

>> AATF-Che1  Apoptosis antagonizing transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   3.7   0.00017     0.043      34     131 ..      17     144 ..      10     149 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 0.00017
                         AATF-Che1  34 qLp.qpetlkeflesseefeealeeaekalkklleslleLreelleqne.ikkla...................... 86 
                                       qL+ q++++k+ les ++  +++ + ++++ k l+++ +L +      e ++++                       
  gi|298674679|ref|YP_003726429.1|  17 QLStQYQQYKNQLESIKQHIDMVYTSSEECVKALNTIESLESLE----EgTESMVpigsgtymhaqfndlnrfvidi 89 
                                       55546666666666644445555555555555555555554444....33343336668889999999999****** PP

                         AATF-Che1  87 .......eskeeeekkkskrkrkkk...kkeetsleelwkeleklekalkpfrna 131
                                              ++ e+ +++ +krk++ +   ++ ++s++++ +++++ e+++++++++
  gi|298674679|ref|YP_003726429.1|  90 gagisveKNREDAKETLNKRKEEMDnayERLNESYSQVVQNMQEIERQFNEYQSK 144
                                       ****976444434444444444433555666777777999*********999876 PP

>> Plk4_PB2  Polo-like Kinase 4 Polo Box 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.4    0.0054       1.4      56     103 ..      24      69 ..       6      73 .. 0.69
   2 ?    9.1   1.5    0.0077         2      27      97 ..      77     146 ..      70     151 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0054
                          Plk4_PB2  56 eseeeleslsselkkllehaeeclkqclklesalsslekekseslFPv 103
                                       + +++les++++++ +++  eec k    +es+  sle+  +es+ P+
  gi|298674679|ref|YP_003726429.1|  24 QYKNQLESIKQHIDMVYTSSEECVKALNTIESLE-SLEE-GTESMVPI 69 
                                       2335778888999999999999999888888844.4443.56666665 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0077
                          Plk4_PB2  27 asFydgakvtkssgekvkiieksg.ksltleseeeleslsselkkllehaeeclkqclklesalsslekeks 97 
                                       a+F d  ++    g ++++ ++ +  + tl++  + e++++++++l e ++++ +++ ++e+++++ +++ +
  gi|298674679|ref|YP_003726429.1|  77 AQFNDLNRFVIDIGAGISVEKNREdAKETLNK--RKEEMDNAYERLNESYSQVVQNMQEIERQFNEYQSKMQ 146
                                       55666555555444467776655424444444..47899999999999999999999999999999988743 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.8   0.00081      0.21      96     136 ..      10      50 ..       8      59 .. 0.91
   2 ?    7.6   5.7    0.0086       2.2      95     137 ..     104     146 ..      93     153 .. 0.42

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00081
                               GAS  96 elekelkdlkwehevleqrfekvekerdelykkfeaaiqev 136
                                       ++e+++++l+ ++++ + ++e++++++d +y + e++++ +
  gi|298674679|ref|YP_003726429.1|  10 DTEQYFRQLSTQYQQYKNQLESIKQHIDMVYTSSEECVKAL 50 
                                       589*********************************99876 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0086
                               GAS  95 kelekelkdlkwehevleqrfekvekerdelykkfeaaiqevq 137
                                       ++l+k  +++   +e l++ +++v +  +e++++f++   ++q
  gi|298674679|ref|YP_003726429.1| 104 ETLNKRKEEMDNAYERLNESYSQVVQNMQEIERQFNEYQSKMQ 146
                                       2333333333334444444444444444444444443333333 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.041        11      21      59 ..      15      53 ..      12      71 .. 0.77
   2 ?    6.7   0.2     0.033       8.5      37      76 ..     101     140 ..      79     151 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.041
                            DUF948 21 llklkktldeaaatieelekqvdpilkevedllakvnel 59
                                      +++l+   ++ ++++e++++++d + + +e+ ++  n++
  gi|298674679|ref|YP_003726429.1| 15 FRQLSTQYQQYKNQLESIKQHIDMVYTSSEECVKALNTI 53
                                      567788888999999999999999999999999999982 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.033
                            DUF948  37 elekqvdpilkevedllakvnelledvneklekvdpltea 76 
                                       + ++ +++  +e++++ +  ne  ++v + ++++++ +++
  gi|298674679|ref|YP_003726429.1| 101 DAKETLNKRKEEMDNAYERLNESYSQVVQNMQEIERQFNE 140
                                       4444555555555555555555555555555555555544 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1     0.038        10      34      66 ..      16      48 ..       8      66 .. 0.67
   2 ?    6.8   0.1     0.026       6.7      55      97 ..      96     141 ..      72     150 .. 0.54

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.038
                      Baculo_PEP_C 34 aqlatlldaietqLnalsedlksllaeldtrld 66
                                       ql+t+ ++ ++qL+++++++  + ++ ++ ++
  gi|298674679|ref|YP_003726429.1| 16 RQLSTQYQQYKNQLESIKQHIDMVYTSSEECVK 48
                                      578888888888888888888776665554222 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.026
                      Baculo_PEP_C  55 ksllaeldtrldtlltnLtdalnalq...dtlrneLtnlnsiltnL 97 
                                       ++  ++ ++ l++  +++++a  +l+    ++ ++++ ++ + ++ 
  gi|298674679|ref|YP_003726429.1|  96 EKNREDAKETLNKRKEEMDNAYERLNesySQVVQNMQEIERQFNEY 141
                                       3344455556666666666666666633333444444444444444 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.3     0.029       7.6      26      61 ..      18      53 ..       9      68 .. 0.63
   2 ?   10.7   2.6    0.0017      0.44      70     120 ..      97     147 ..      73     152 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.029
                                      CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHH CS
                         Fib_alpha 26 llkyekdvkkdlekleneleeisnstkeaeelvkei 61
                                      l+++ +++k++le+++++++ +  s++e  +  ++i
  gi|298674679|ref|YP_003726429.1| 18 LSTQYQQYKNQLESIKQHIDMVYTSSEECVKALNTI 53
                                      555666666666666666666666666555555554 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0017
                                       HHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  70 kskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesneqkiqk 120
                                       k+ +d +++++k ++e+++ ++rl+e+ ++ ++n++++   +++ ++k+q 
  gi|298674679|ref|YP_003726429.1|  97 KNREDAKETLNKRKEEMDNAYERLNESYSQVVQNMQEIERQFNEYQSKMQS 147
                                       344446888999999999999999999988889999999999999999985 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1       0.2        52     100     122 ..      15      37 ..       6      66 .. 0.53
   2 ?   12.6   3.3   0.00029     0.077      18      76 ..      96     154 ..      90     155 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.2
                         PspA_IM30 100 aealetqlaqqrsaveqlrkqle 122
                                        ++l+tq++q + + e +++ ++
  gi|298674679|ref|YP_003726429.1|  15 FRQLSTQYQQYKNQLESIKQHID 37 
                                       33444444444444444444333 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00029
                         PspA_IM30  18 ldkaeDPekileqairdmqselakarqalaqviarqkqlerkleeqkeqakklekkAka 76 
                                         + eD++  l++  ++m+++++++ ++  qv+ + ++ er+ +e + ++++ ++ A  
  gi|298674679|ref|YP_003726429.1|  96 EKNREDAKETLNKRKEEMDNAYERLNESYSQVVQNMQEIERQFNEYQSKMQSQQDGAYR 154
                                       56679*********************************************999988765 PP

>> SLATT_1  SMODS and SLOG-associating 2TM effector domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.4    0.0094       2.4      74     112 ..      15      54 ..      11      63 .. 0.76
   2 ?    7.0   0.3      0.02       5.1      73     101 ..     116     144 ..     114     154 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0094
                           SLATT_1  74 yeelaaaYslaaeeLeiiraalea.eateeewaklVadaE 112
                                       +++l+++Y++  ++Le+i+++++    + ee  k+ ++ E
  gi|298674679|ref|YP_003726429.1|  15 FRQLSTQYQQYKNQLESIKQHIDMvYTSSEECVKALNTIE 54 
                                       6899*******************86444555555555555 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.02
                           SLATT_1  73 qyeelaaaYslaaeeLeiiraaleaeate 101
                                        ye+l ++Ys++ +++++i++++++ +++
  gi|298674679|ref|YP_003726429.1| 116 AYERLNESYSQVVQNMQEIERQFNEYQSK 144
                                       5899******************9984333 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.2     0.013       3.5      39      82 ..       7      50 ..       1      54 [. 0.87
   2 ?    8.2   1.2    0.0089       2.3      38      82 ..      97     145 ..      73     154 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.013
                           DUF4446 39 dgksleellkekleeveelkeeseelekeieeleeklkkslqkv 82
                                       + + e+ +++  +++++ k++ e+++++i+ ++++ +++++ +
  gi|298674679|ref|YP_003726429.1|  7 GKGDTEQYFRQLSTQYQQYKNQLESIKQHIDMVYTSSEECVKAL 50
                                      45688999999***************************999865 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0089
                           DUF4446  38 kdgksleellkekleeveelkeesee....lekeieeleeklkkslqkv 82 
                                       k++++ +e+l+++ ee++++ e+ +e    + ++++e+e+++++  +k+
  gi|298674679|ref|YP_003726429.1|  97 KNREDAKETLNKRKEEMDNAYERLNEsysqVVQNMQEIERQFNEYQSKM 145
                                       4566666666666666655444443322225555555555555555554 PP

>> phiKZ_IP  phiKZ-like phage internal head proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   3.0    0.0016      0.42      48     104 ..      91     147 ..      21     152 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0016
                          phiKZ_IP  48 iavsledlkeklkeagkkakelikkiietlkdaavritsgierlskridkLeerlks 104
                                       +++s+e   e +ke+ +k ke    ++e l+++++++ ++++ +++++++ +++ +s
  gi|298674679|ref|YP_003726429.1|  91 AGISVEKNREDAKETLNKRKEEMDNAYERLNESYSQVVQNMQEIERQFNEYQSKMQS 147
                                       344666888999**************************************9999887 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.7     0.029       7.5     337     374 ..      13      49 ..       5      69 .. 0.61
   2 ?   10.8   5.7    0.0005      0.13     333     415 ..      73     151 ..      43     156 .] 0.66

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.029
                              FapA 337 eklkeleeeleeleeeleklkkkikklpklkaekqles 374
                                       + +++l +++++++++le +k+ i+ +   + e+++++
  gi|298674679|ref|YP_003726429.1|  13 QYFRQLSTQYQQYKNQLESIKQHIDMVYT-SSEECVKA 49 
                                       44577777788888888888877777766.44444433 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0005
                              FapA 333 pelkeklkeleeeleel......eeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelke 403
                                         +++++++l++ + ++      e++ e+ k++++k          ++e+ + +++l e++ + +++++e+e++++e
  gi|298674679|ref|YP_003726429.1|  73 TYMHAQFNDLNRFVIDIgagisvEKNREDAKETLNKR---------KEEMDNAYERLNESYSQVVQNMQEIERQFNE 140
                                       5566667777777777755333333333333333333.........457889************************* PP

                              FapA 404 lkeeleskkeea 415
                                        +++++s+ +++
  gi|298674679|ref|YP_003726429.1| 141 YQSKMQSQ-QDG 151
                                       ******99.554 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   3.1    0.0003     0.079     225     324 ..      13     146 ..       5     155 .. 0.43

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0003
                             LMBR1 225 dllkevkklrksisesdp.lrkyleeilk........................kvPeeiaeklksnenktee..... 271
                                       ++ +++++++++++++ + ++++++++ +                                                
  gi|298674679|ref|YP_003726429.1|  13 QYFRQLSTQYQQYKNQLEsIKQHIDMVYTsseecvkalntieslesleegtesM-----------------Vpigsg 72 
                                       444455555555555544333444444442222222222222233333333331.................033333 PP

                             LMBR1 272 .....................slaklekqlikalqkrertekqwkrllekalelediiknksskekefksses..s 324
                                                            s+ k++++ +++l+kr+++ ++ ++ l++     ++++n++++e++f++ +s  +
  gi|298674679|ref|YP_003726429.1|  73 tymhaqfndlnrfvidigagiSVEKNREDAKETLNKRKEEMDNAYERLNES--YSQVVQNMQEIERQFNEYQSkmQ 146
                                       333333444444444444444555555555555555555544444444444..35666666666666665544321 PP

>> RasGAP_C  RasGAP C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.6   0.00044      0.11      55     123 ..      11      77 ..       9      83 .. 0.69
   2 ?    5.3   5.8     0.077        20      56     106 ..     100     147 ..      96     156 .] 0.66

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00044
                          RasGAP_C  55 leetlktLseknnylesqlesYkayienvleqlkkkkgklpfskqyfkkrel.kksgklpkfgsykysak 123
                                       +e+ +++Ls + +++++qles k++i+ v   +++  ++l++ +   + ++l + ++++   gs  y ++
  gi|298674679|ref|YP_003726429.1|  11 TEQYFRQLSTQYQQYKNQLESIKQHIDMVYTSSEECVKALNTIE---SLESLeEGTESMVPIGSGTYMHA 77 
                                       5788899**********************999988854444333...33333334444445555555555 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.077
                          RasGAP_C  56 eetlktLseknnylesqlesYkayienvleqlkkkkgklpfskqyfkkrel 106
                                       e++ +tL+++++ + +  e +++  ++v++++++ +++ +  + y +k+++
  gi|298674679|ref|YP_003726429.1| 100 EDAKETLNKRKEEMDNAYERLNESYSQVVQNMQEIERQFN--E-YQSKMQS 147
                                       5677888899999999999999999999999988863322..2.2222222 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.3     0.064        17      49      86 ..      17      54 ..       8      88 .. 0.62
   2 ?   11.2   2.4    0.0011      0.28      53     105 ..      95     147 ..      74     152 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.064
                           DUF1664 49 qleqvseslaatkrhLssridrvdkkldeqkeiskeik 86
                                      ql + +++ +++ + ++++id v ++ +e+ ++ + i+
  gi|298674679|ref|YP_003726429.1| 17 QLSTQYQQYKNQLESIKQHIDMVYTSSEECVKALNTIE 54
                                      33333333333333344556666666666666555443 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0011
                           DUF1664  53 vseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedves 105
                                       v ++ +++k+ L++r +++d+  +  +e  +++ ++++e++++ +e +++++s
  gi|298674679|ref|YP_003726429.1|  95 VEKNREDAKETLNKRKEEMDNAYERLNESYSQVVQNMQEIERQFNEYQSKMQS 147
                                       44555667777777777777777777777777777777777777777777765 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       3.9     1e+03      52      64 ..      23      35 ..       5      64 .. 0.58
   2 ?   11.6   0.2    0.0012      0.32      29      67 ..      95     133 ..      77     153 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 3.9
                            DUF883 52 eavaerakeaaea 64
                                      ++++++ +++ ++
  gi|298674679|ref|YP_003726429.1| 23 QQYKNQLESIKQH 35
                                      2222222222222 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.0012
                            DUF883  29 aeelRerleerlerarerlrdaeeavaerakeaaeaadd 67 
                                       +e+ Re ++e+l++ +e++++a+e++ e+ ++++++ ++
  gi|298674679|ref|YP_003726429.1|  95 VEKNREDAKETLNKRKEEMDNAYERLNESYSQVVQNMQE 133
                                       566677777777777777777777777777777766654 PP

>> ApoO  Apolipoprotein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1     0.026       6.8      16      59 ..      11      56 ..       4      70 .. 0.63
   2 ?    6.2   0.6     0.036       9.3      15      55 ..     101     141 ..      90     154 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.026
                              ApoO 16 LeegvrslRkslepytsavqdelnkvkskvetaeqsvt..dtiasL 59
                                       e+++r+l  + ++y +++++  +++   + ++e+ v+  +ti+sL
  gi|298674679|ref|YP_003726429.1| 11 TEQYFRQLSTQYQQYKNQLESIKQHIDMVYTSSEECVKalNTIESL 56
                                      5666666666666666666666666666666666665533455555 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.036
                              ApoO  15 rLeegvrslRkslepytsavqdelnkvkskvetaeqsvtdt 55 
                                         +e  ++  +++ + ++ +++++++v + +++ e+++++ 
  gi|298674679|ref|YP_003726429.1| 101 DAKETLNKRKEEMDNAYERLNESYSQVVQNMQEIERQFNEY 141
                                       34455566666666777777777777777777777766655 PP

>> DUF4047  Domain of unknown function (DUF4047)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1     0.047        12      61      96 ..      14      49 ..       6      80 .. 0.75
   2 ?    9.0   1.5    0.0058       1.5      71     104 ..     101     134 ..      85     152 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.047
                           DUF4047 61 eieqalsvwkqgrekikaerealqkvyteieepynq 96
                                        +q  ++++q ++++ + ++ +  vyt+ ee  + 
  gi|298674679|ref|YP_003726429.1| 14 YFRQLSTQYQQYKNQLESIKQHIDMVYTSSEECVKA 49
                                      556777777777888888888888888888887654 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0058
                           DUF4047  71 qgrekikaerealqkvyteieepynqvqeelkvn 104
                                       + +e ++  +e + + y+ ++e y qv+++++  
  gi|298674679|ref|YP_003726429.1| 101 DAKETLNKRKEEMDNAYERLNESYSQVVQNMQEI 134
                                       467889999*******************998754 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.2      0.11        28     108     144 ..      16      51 ..       9      60 .. 0.79
   2 ?   11.1   3.6    0.0012      0.31      51      94 ..      97     147 ..      92     150 .. 0.48

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.11
                         ApoLp-III 108 eslkensqeakeklakaikqayddaveaaqklakqLk 144
                                        +l+ + q+ k++l+  ikq +d +  ++++  k+L+
  gi|298674679|ref|YP_003726429.1|  16 RQLSTQYQQYKNQLE-SIKQHIDMVYTSSEECVKALN 51 
                                       578888888888887.488888888888888888876 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0012
                         ApoLp-III  51 kksdeleealkevkkkieetadklse.......enPevkkkaqelqekvQs 94 
                                       k+ + ++e+l+  k+++ ++ + l+e       +  e++++ +e+q+k+Qs
  gi|298674679|ref|YP_003726429.1|  97 KNREDAKETLNKRKEEMDNAYERLNEsysqvvqNMQEIERQFNEYQSKMQS 147
                                       444455555555555555555555551111111444456666666666665 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.3     0.041        11      51      75 ..      13      37 ..       4      46 .. 0.68
   2 ?    9.6   2.6    0.0041       1.1      47      84 ..     111     148 ..     101     150 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.041
                                      HHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100 51 aefeewkqaaqklvdaLeeisealk 75
                                      + f ++  + q+++++Le+i + ++
  gi|298674679|ref|YP_003726429.1| 13 QYFRQLSTQYQQYKNQLESIKQHID 37
                                      4555666777777777777766655 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0041
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  47 dafqaefeewkqaaqklvdaLeeisealkqaanafeda 84 
                                       ++ ++++e+++++  ++v++++ei+++ ++  ++++++
  gi|298674679|ref|YP_003726429.1| 111 EEMDNAYERLNESYSQVVQNMQEIERQFNEYQSKMQSQ 148
                                       6778999********************99999999875 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1      0.77     2e+02      29      47 ..      17      35 ..      10      67 .. 0.71
   2 ?   11.8   3.2     0.001      0.27      25      64 ..      97     146 ..      94     152 .. 0.68

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.77
                              YtxH 29 dlkekaddlkekakellee 47
                                      +l+ +++++k++++++++ 
  gi|298674679|ref|YP_003726429.1| 17 QLSTQYQQYKNQLESIKQH 35
                                      6788888888888776443 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.001
                              YtxH  25 etRkdlkekaddlkekakelleeakeka..........kekaedlkekvk 64 
                                       + R+d+ke++++ ke +++++e+++e            +++++++++k++
  gi|298674679|ref|YP_003726429.1|  97 KNREDAKETLNKRKEEMDNAYERLNESYsqvvqnmqeiERQFNEYQSKMQ 146
                                       78999999999999999999999988885554444544444555555544 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.4      0.11        27      22      43 ..      16      37 ..       6      64 .. 0.67
   2 ?   11.9   7.1   0.00082      0.21      24      80 ..      95     149 ..      86     156 .] 0.61

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.11
                                      HHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH 22 eqlekkfkklqaeleakekelq 43
                                       ql +++++++++le+ ++ ++
  gi|298674679|ref|YP_003726429.1| 16 RQLSTQYQQYKNQLESIKQHID 37
                                      4566666666666666666555 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00082
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  24 lekkfkklqaeleakekelqklqeelqkkakklekeekeqelqkkeqelqqkqqqka 80 
                                       +ek +++ +++l+++++e+++++e+l+++ ++    +  qe++++ +e+q k+q ++
  gi|298674679|ref|YP_003726429.1|  95 VEKNREDAKETLNKRKEEMDNAYERLNESYSQ--VVQNMQEIERQFNEYQSKMQSQQ 149
                                       56677777777777777777777777644444..34555555555555555444443 PP

>> L31  Mitochondrial ribosomal protein L31
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.051        13      17      56 ..      19      58 ..      12      80 .. 0.71
   2 ?    5.6   1.8     0.081        21      19      67 ..     102     150 ..      95     155 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.051
                               L31 17 ktqkarqrkRlkavDevieavkeslkkkgvslkalekaka 56
                                      +tq ++ ++ l+++ + i++v++s ++    l+++e+ ++
  gi|298674679|ref|YP_003726429.1| 19 STQYQQYKNQLESIKQHIDMVYTSSEECVKALNTIESLES 58
                                      57889999****************5544333355554444 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.081
                               L31  19 qkarqrkRlkavDevieavkeslkkkgvslkalekakaelpkesemspk 67 
                                        k  + kR +++D+  e ++es ++  ++++++e++ +e++++ + ++ 
  gi|298674679|ref|YP_003726429.1| 102 AKETLNKRKEEMDNAYERLNESYSQVVQNMQEIERQFNEYQSKMQSQQD 150
                                       5788899***************999999999999988877766665555 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.8   0.00034     0.089      10      40 ..       6      37 ..       1      58 [. 0.79
   2 ?    3.9   4.5       0.2        51      11      52 ..     109     149 ..      94     155 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00034
                              FlxA 10 ssssgsasqiasLqkQiknlqkqLkelses.d 40
                                      s + +++++ ++L  Q++++++qL+++++  d
  gi|298674679|ref|YP_003726429.1|  6 SGKGDTEQYFRQLSTQYQQYKNQLESIKQHiD 37
                                      55678999*******************99852 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.2
                              FlxA  11 sssgsasqiasLqkQiknlqkqLkelses..deltkeekkkqqq 52 
                                       +++++++  ++L++ ++++ + ++e+  +  +    + k++ qq
  gi|298674679|ref|YP_003726429.1| 109 RKEEMDNAYERLNESYSQVVQNMQEIERQfnE---YQSKMQSQQ 149
                                       44556666666666666666666666666322...222333333 PP

>> Ax_dynein_light  Axonemal dynein light chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.3     0.063        16     120     163 ..       7      50 ..       3      61 .. 0.84
   2 ?   10.2   2.7     0.002      0.53     116     168 ..      98     150 ..      77     155 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.063
                   Ax_dynein_light 120 gkselekkikeLeeekeelekqvaelkaklealekrekerrqee 163
                                       gk ++e+  ++L ++ ++ ++q++++k+ ++ +  +++e  ++ 
  gi|298674679|ref|YP_003726429.1|   7 GKGDTEQYFRQLSTQYQQYKNQLESIKQHIDMVYTSSEECVKAL 50 
                                       78899999999**************9999999988888876655 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.002
                   Ax_dynein_light 116 qaeqgkselekkikeLeeekeelekqvaelkaklealekrekerrqeeekkhe 168
                                       ++e+ k+ l+k+ +e+++  e+l++  +++ ++++++e++++e +++ +++++
  gi|298674679|ref|YP_003726429.1|  98 NREDAKETLNKRKEEMDNAYERLNESYSQVVQNMQEIERQFNEYQSKMQSQQD 150
                                       68899999999999999999999999999999999999999999998888775 PP

>> DUF5344  Family of unknown function (DUF5344)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.4     0.007       1.8       7      55 ..      21      66 ..      11      68 .. 0.78
   2 ?    6.5   4.9     0.048        13      36      71 ..      97     135 ..      80     148 .. 0.65
   3 ?    3.8   0.7      0.33        86      45      66 ..     127     148 ..     122     155 .. 0.52

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.007
                           DUF5344  7 nqaeVeqkLselktaaeelktsipetisgknsldvvekineleeeleel 55
                                      ++++ +++L+++k++++ + ts +e  +    l+++e++++lee  e++
  gi|298674679|ref|YP_003726429.1| 21 QYQQYKNQLESIKQHIDMVYTSSEECVKA---LNTIESLESLEEGTESM 66
                                      6788899**********998888888888...66666666666665555 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.048
                           DUF5344  36 knsldvvekineleee....leellkaYktlllknvedte 71 
                                       kn+ d+ e++n+++ee    +e l ++Y +++++ + ++e
  gi|298674679|ref|YP_003726429.1|  97 KNREDAKETLNKRKEEmdnaYERLNESYSQVVQNMQ-EIE 135
                                       566666666666666511116777788888887654.444 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.33
                           DUF5344  45 ineleeeleellkaYktlllkn 66 
                                       + ++++e+e +++ Y++ ++++
  gi|298674679|ref|YP_003726429.1| 127 VVQNMQEIERQFNEYQSKMQSQ 148
                                       3344555555555555555554 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1      0.11        28      19      62 ..      15      44 ..       6      67 .. 0.45
   2 ?    8.8   2.0    0.0059       1.5      10      54 ..     100     145 ..      94     152 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.11
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II 19 laplsqnlentkeklseinrsveetnekvkdankairdArrsvk 62
                                        +ls++ ++ k++l++i+++++ +               +s+ 
  gi|298674679|ref|YP_003726429.1| 15 FRQLSTQYQQYKNQLESIKQHIDMV--------------YTSSE 44
                                      3444444444444444444443322..............22222 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0059
                                       XXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II  10 etakevl.eqlaplsqnlentkeklseinrsveetnekvkdankai 54 
                                       e ake+l + ++++++  e+++e++s++ ++++e++ + ++++  +
  gi|298674679|ref|YP_003726429.1| 100 EDAKETLnKRKEEMDNAYERLNESYSQVVQNMQEIERQFNEYQSKM 145
                                       5666666256889**********************99999766554 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1    0.0059       1.5       6      33 ..      12      39 ..       9      58 .. 0.84
   2 ?    1.8   0.5       1.2   3.2e+02      18      40 ..     105     127 ..      94     134 .. 0.61
   3 ?    2.0   0.1         1   2.7e+02       2      21 ..     131     150 ..     130     152 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0059
                         FlaC_arch  6 Enklsklsteletvkkeneelsksveel 33
                                      E+ + +lst+ +  k+++e++++ ++++
  gi|298674679|ref|YP_003726429.1| 12 EQYFRQLSTQYQQYKNQLESIKQHIDMV 39
                                      7778889999999999999999999987 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 1.2
                         FlaC_arch  18 tvkkeneelsksveelkenVkdl 40 
                                       t+ k  ee+ +  e+l+e+  ++
  gi|298674679|ref|YP_003726429.1| 105 TLNKRKEEMDNAYERLNESYSQV 127
                                       55555566666666666554444 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 1
                         FlaC_arch   2 idelEnklsklsteletvkk 21 
                                       ++e+E ++++ ++++++ ++
  gi|298674679|ref|YP_003726429.1| 131 MQEIERQFNEYQSKMQSQQD 150
                                       78999999999999999876 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.2     0.031         8      68     112 ..      12      56 ..       9      67 .. 0.81
   2 ?    7.1   0.8     0.021       5.3      66     108 ..     101     143 ..      88     154 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.031
                              COG2  68 qeeleevesplaaarkkvesvreklsereeeveskleeakeleek 112
                                       ++  ++++++ ++ ++++es+++++++  +  e+++++ + +e+ 
  gi|298674679|ref|YP_003726429.1|  12 EQYFRQLSTQYQQYKNQLESIKQHIDMVYTSSEECVKALNTIESL 56 
                                       667788999999999999999999999999999999988888765 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.021
                              COG2  66 glqeeleevesplaaarkkvesvreklsereeeveskleeake 108
                                       + +e l++ + ++ +a +++++  +++ ++++e+e + +e ++
  gi|298674679|ref|YP_003726429.1| 101 DAKETLNKRKEEMDNAYERLNESYSQVVQNMQEIERQFNEYQS 143
                                       5567777777888888888888888888888888888877654 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.8    0.0064       1.7     244     286 ..      15      57 ..       8      69 .. 0.75
   2 ?    6.4   2.9     0.016       4.3     124     294 ..     102     143 ..      79     154 .. 0.47

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0064
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH... CS
                             APG17 244 vkelqerleemekakkllsekkeeiekllsalkkaleeleevg 286
                                       +++l +++++ +++ ++++++ + + +++++ +kal+++e+++
  gi|298674679|ref|YP_003726429.1|  15 FRQLSTQYQQYKNQLESIKQHIDMVYTSSEECVKALNTIESLE 57 
                                       5678888888888888888888888888888888888888763 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.016
                                       HHHHHHHHHHHHHHHHHHHHTTHH..HHHHHHHHHHH-------STCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             APG17 124 lkealkesidelqaaqkkldssllefdtdlrelkkelsksksksessslipellkelesleeemAslLesLtnHfDq 200
                                        ke l++ ++e+++a+++l++s ++  ++++e+++++                                        
  gi|298674679|ref|YP_003726429.1| 102 AKETLNKRKEEMDNAYERLNESYSQVVQNMQEIERQF---------------------------------------- 138
                                       3333333333333333333333333333333333333........................................ PP

                                       HHHH................S-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             APG17 201 cvkAvkltegggalrraaaelseeereelleVlekDaaeledVvkelqerleemekakkllsekkeeiekllsalkk 277
                                                                                                                    
  gi|298674679|ref|YP_003726429.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       HHHHHH....HHHHHHH CS
                             APG17 278 aleeleevgkklpeyla 294
                                         +e++          +
  gi|298674679|ref|YP_003726429.1| 139 --NEYQ----------S 143
                                       ..2222..........2 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   7.7    0.0031      0.82     270     410 ..      16     147 ..       8     155 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0031
                          Prominin 270 sqLrdglrgvkrdlnqalsnlCqseeCskilssleiekldtskcldqlpnvdevlealeevletnlssivkeglarl 346
                                       +qL++  ++ k++l+++ ++ +       +  +++ e ++  +++++l++++e  e++  +    + ++  ++l+r+
  gi|298674679|ref|YP_003726429.1|  16 RQLSTQYQQYKNQLESIKQH-ID------MVYTSSEECVKALNTIESLESLEEGTESMVPIGSGTYMHAQFNDLNRF 85 
                                       44444444444444444333.11......112222223444444455666666666666666666655555555555 PP

                          Prominin 347 neipekvknqtaevvpdlkkalakgreqikklakkiprealdavisdlenterssktfddvvek 410
                                         i   +   +++  +d k++l+k +e++++  +++ +e  ++v+++++++er+ ++++ +++ 
  gi|298674679|ref|YP_003726429.1|  86 V-IDIGAGISVEKNREDAKETLNKRKEEMDNAYERL-NESYSQVVQNMQEIERQFNEYQSKMQS 147
                                       3.555666689999**********************.*********************998874 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   2.3    0.0072       1.9     270     311 ..      13      54 ..      10      67 .. 0.83
   2 ?    8.0   5.6    0.0048       1.3     252     304 ..      97     149 ..      91     154 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0072
                             IFT57 270 sqleellqeyreaqeelsevkekykqlsegvseltrelaeis 311
                                       + +++l ++y++ +++l+++k++++++ ++ +e+ + l++i+
  gi|298674679|ref|YP_003726429.1|  13 QYFRQLSTQYQQYKNQLESIKQHIDMVYTSSEECVKALNTIE 54 
                                       568899999999999999999999999999999999999985 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0048
                             IFT57 252 edisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvselt 304
                                       ++ + + e +++r + +++ +e l + y+++ ++++e+++++++ ++++++++
  gi|298674679|ref|YP_003726429.1|  97 KNREDAKETLNKRKEEMDNAYERLNESYSQVVQNMQEIERQFNEYQSKMQSQQ 149
                                       55566667777777777777777777777777777777777777777777665 PP

>> STAT_alpha  STAT protein, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3  11.0    0.0038      0.97       3      94 ..      17     146 ..       8     149 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0038
                        STAT_alpha   3 eieqrleelrskvqeteqdirkLedeqeeFdfqyqelqkl..................................... 42 
                                       +++++ ++ +++ + ++q+i  +    ee +   +++++l                                     
  gi|298674679|ref|YP_003726429.1|  17 QLSTQYQQYKNQLESIKQHIDMVYTSSEECVKALNTIESLesleegtesmvpigsgtymhaqfndlnrfvidigagi 93 
                                       34444444444444444444444444444444444444448888888888888888888899999999999999999 PP

                        STAT_alpha  43 .eqeraesekkelkkqkellqqmlnaLdqkRkelvdklkellnlleslqekll 94 
                                         ++++e +k++l+k+ke++++  ++L+++  ++v++++e+  ++++ q+k+ 
  gi|298674679|ref|YP_003726429.1|  94 sVEKNREDAKETLNKRKEEMDNAYERLNESYSQVVQNMQEIERQFNEYQSKMQ 146
                                       845566666666*****************************999999999875 PP

>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1      0.32        84      21      43 ..      15      37 ..       5      66 .. 0.61
   2 ?    9.5   6.2    0.0028      0.73       6      58 ..      95     147 ..      92     152 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.32
                                      TTCHHHCTTSCCCCCCTTTTTTT CS
                              GrpE 21 leelekevkelkekllrllaefe 43
                                      + +l ++++++k++l+  ++ ++
  gi|298674679|ref|YP_003726429.1| 15 FRQLSTQYQQYKNQLESIKQHID 37
                                      44555555555555555555444 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0028
                                       .CTTTHHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHHHHHHH CS
                              GrpE   6 eeeeeedeeeeleeeleelekevkelkekllrllaefenlrkrtekekeeakk 58 
                                       +e++ ed++e+l+++ ee+++ ++ l+e++ +  ++++++++++++ ++++++
  gi|298674679|ref|YP_003726429.1|  95 VEKNREDAKETLNKRKEEMDNAYERLNESYSQVVQNMQEIERQFNEYQSKMQS 147
                                       678899999********************************999988887765 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   1.3    0.0024      0.61       8      58 ..      12      61 ..       8      89 .. 0.81
   2 ?    4.9   4.6     0.049        13       3      42 ..     109     148 ..      92     155 .. 0.37

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0024
                             TMPIT  8 ekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkk 58
                                      e+ f++l+++ ++yk++le+++++++ + ++ +++ k l+ ++s l++l++
  gi|298674679|ref|YP_003726429.1| 12 EQYFRQLSTQYQQYKNQLESIKQHIDMVYTSSEECVKALNTIES-LESLEE 61
                                      67789999999999999999999999999999999999988764.555554 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.049
                             TMPIT   3 eweelekefkeleetakeykqkleelsklqskcskeikkq 42 
                                       + ee+ + +++l+e+ +++ q+++e++++ ++ ++++++q
  gi|298674679|ref|YP_003726429.1| 109 RKEEMDNAYERLNESYSQVVQNMQEIERQFNEYQSKMQSQ 148
                                       1222233333333333333333333333333333333322 PP

>> SOAR  STIM1 Orai1-activating region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.2    0.0073       1.9      59      98 ..      19      58 ..      15      60 .. 0.91
   2 ?    3.3   2.3       0.3        77      62      92 ..     110     140 ..      93     150 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0073
                              SOAR 59 ssslddvdkkileakqaleevtkelkerqeRWqqieklcg 98
                                      s++ ++  +++ ++kq++++v ++++e+ +  + ie+l +
  gi|298674679|ref|YP_003726429.1| 19 STQYQQYKNQLESIKQHIDMVYTSSEECVKALNTIESLES 58
                                      67889999****************************9966 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.3
                              SOAR  62 lddvdkkileakqaleevtkelkerqeRWqq 92 
                                        +++d++  ++ +++++v ++++e ++ +++
  gi|298674679|ref|YP_003726429.1| 110 KEEMDNAYERLNESYSQVVQNMQEIERQFNE 140
                                       4555555555556666666666655555544 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0  10.0     0.016       4.1      21     157 ..      13     146 ..       7     153 .. 0.46

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.016
                           DUF4795  21 eelekleekvkelekrledkekklealkkqieelekvkadkeeveeelaekadkeaLatkvsrdqfDeakkeLekml 97 
                                       ++  +l+ + ++ +++le  ++++++++ + ee+ k+    +++e  +++  ++e +    s + + + +++L++ +
  gi|298674679|ref|YP_003726429.1|  13 QYFRQLSTQYQQYKNQLESIKQHIDMVYTSSEECVKAL---NTIESLESLEEGTESMVPIGSGTYMHAQFNDLNRFV 86 
                                       34444555555555555555555555555555554333...335666666666666666666666666666666666 PP

                           DUF4795  98 eellek..leeqeealkkaldtLqeelkekldrlelepLkeqleerlkelqkelqeameked 157
                                        ++     +e++ e+ k+ l++ +ee+++  +rl+  +  +q+ ++++e++ + +e+ +k +
  gi|298674679|ref|YP_003726429.1|  87 IDIGAGisVEKNREDAKETLNKRKEEMDNAYERLN--ESYSQVVQNMQEIERQFNEYQSKMQ 146
                                       44443311334444444444444455555544332..2222333344444444444444433 PP

>> Sulfatase_C  C-terminal region of aryl-sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1      0.25        66      68     103 ..      17      52 ..       8      67 .. 0.68
   2 ?    7.4   1.2     0.028       7.2      64     107 ..     103     144 ..      96     153 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.25
                                       -TTSTTCCHHHHHHHHHHHHHHHCCC------TCCH CS
                       Sulfatase_C  68 plsaespeykevlkeikkaveehkktlkpvpnqlak 103
                                       +ls++ ++yk+ l++ik+ ++++  + ++  + l++
  gi|298674679|ref|YP_003726429.1|  17 QLSTQYQQYKNQLESIKQHIDMVYTSSEECVKALNT 52 
                                       455555778888888888888777776665555555 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.028
                                       T--S-TTSTTCCHHHHHHHHHHHHHHHCCC------TCCHHCHS CS
                       Sulfatase_C  64 sEkyplsaespeykevlkeikkaveehkktlkpvpnqlakgell 107
                                       +E   l++ ++e++++ +++++ + ++ +++++ + q+++++++
  gi|298674679|ref|YP_003726429.1| 103 KE--TLNKRKEEMDNAYERLNESYSQVVQNMQEIERQFNEYQSK 144
                                       44..466667999*************************999654 PP

>> DUF3135  Protein of unknown function (DUF3135)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1    0.0034      0.87      35      67 ..      22      54 ..      12      60 .. 0.86
   2 ?    2.3   1.1       0.8   2.1e+02      36      79 ..     100     143 ..      94     149 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0034
                           DUF3135 35 peemqrrLrglqfqiDmqlsraknPvaacvals 67
                                       ++++++L++++ +iDm+  +++  v+a ++++
  gi|298674679|ref|YP_003726429.1| 22 YQQYKNQLESIKQHIDMVYTSSEECVKALNTIE 54
                                      57899***************9999999988875 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.8
                           DUF3135  36 eemqrrLrglqfqiDmqlsraknPvaacvalsrmmqeklvelrr 79 
                                       e+ ++ L + + + D   +r +  + ++v+ +++ + ++ e ++
  gi|298674679|ref|YP_003726429.1| 100 EDAKETLNKRKEEMDNAYERLNESYSQVVQNMQEIERQFNEYQS 143
                                       55555555555566666666666666666666666666665544 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3  14.2     0.075        19      28      94 ..      22     144 ..       8     153 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.075
                             Mod_r  28 vkqlkeekeellaenesla........................................................ek 48 
                                        +q+k+++e++ ++ +++                                                         ek
  gi|298674679|ref|YP_003726429.1|  22 YQQYKNQLESI-KQHIDMVytsseecvkalntieslesleegtesmvpigsgtymhaqfndlnrfvidigagisvEK 97 
                                       44555555544.33333333555555555555555556666666666777777777777777777777777777766 PP

                             Mod_r  49 nlsl.epeleelrselqekleelkelekefeekeqeldellqkfspd 94 
                                       n ++ +++l++ ++e+ +++e l+e ++++ +  qe ++ +++++++
  gi|298674679|ref|YP_003726429.1|  98 NREDaKETLNKRKEEMDNAYERLNESYSQVVQNMQEIERQFNEYQSK 144
                                       66666777777777777777777777777777777766666665544 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.4      0.22        57      77      95 ..      16      34 ..       8      60 .. 0.51
   2 ?    9.4   5.6    0.0039         1      53     101 ..     101     149 ..      93     155 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.22
                              ADIP 77 erlktqleqlerelalvqa 95
                                      ++l+tq++q++++l++ ++
  gi|298674679|ref|YP_003726429.1| 16 RQLSTQYQQYKNQLESIKQ 34
                                      3444444444444443333 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0039
                              ADIP  53 eqreslnetirkleaeierlqskierlktqleqlerelalvqakerqle 101
                                       +++e+ln++ +++++ +erl+ +++++ ++ ++ er+   +q+k ++++
  gi|298674679|ref|YP_003726429.1| 101 DAKETLNKRKEEMDNAYERLNESYSQVVQNMQEIERQFNEYQSKMQSQQ 149
                                       3688999999999999999999999999999999999999988887765 PP

>> FTA4  Kinetochore complex Fta4 of Sim4 subunit, or CENP-50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6  11.3     0.025       6.5      68     152 ..      13     147 ..      11     150 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.025
                              FTA4  68 qairhvaeQidklYlea.edekleie.....vnedltkeelIkeLPeswe........................... 111
                                       q  r+ ++Q ++ Y ++ e+ k++i+      +e     ++I++L   +e                           
  gi|298674679|ref|YP_003726429.1|  13 QYFRQLSTQYQQ-YKNQlESIKQHIDmvytsSEECVKALNTIESLESLEEgtesmvpigsgtymhaqfndlnrfvid 88 
                                       566666666666.4444433333331222223333333555555555555777999999999999999999999999 PP

                              FTA4 112 ..................veekeaeeepleallerYaelrarLielserrqqlqarlar 152
                                                         +++ke+ ++  e l+e+Y +++++++e++++ ++ q++++ 
  gi|298674679|ref|YP_003726429.1|  89 igagisveknredaketlNKRKEEMDNAYERLNESYSQVVQNMQEIERQFNEYQSKMQS 147
                                       999999999999998888777788888889*************************9985 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   1.0      0.14        36      44     227 ..      17      55 ..       8      67 .. 0.46
   2 ?    9.6   8.3    0.0025      0.64     182     237 ..      95     150 ..      75     155 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.14
                                       XXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament  44 evsklkelyekeleelrkqldeltkerarlqleldnlreeledlrkkyekelnkreevEaelkalrkdldeatlarv 120
                                       + s  ++ y+++le                                                               
  gi|298674679|ref|YP_003726429.1|  17 QLSTQYQQYKNQLE--------------------------------------------------------------- 30 
                                       33333333333333............................................................... PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament 121 dLekkvesLkeelaflkkvheeEvkelqkqvseqvlvevdaarkldLteilkeiraqyeelaeknreeaeewykskl 197
                                                                                                                    
  gi|298674679|ref|YP_003726429.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       XXXXXXXXXXXXXXXX-HHHHHHHHHHHHH CS
                          Filament 198 eelqeaaeknsealrsakeeitelrrqiqs 227
                                            +++++ +++ ++ ee  ++  +i+s
  gi|298674679|ref|YP_003726429.1|  31 -----SIKQHIDMVYTSSEECVKALNTIES 55 
                                       .....3444444444444444444444444 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0025
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 182 aeknreeaeewykskleelqeaaeknsealrsakeeitelrrqiqsleieleslkk 237
                                       +eknre+a+e+ +++ ee+ +a e+ +e+ +++ ++++e+ rq ++ +++++s++ 
  gi|298674679|ref|YP_003726429.1|  95 VEKNREDAKETLNKRKEEMDNAYERLNESYSQVVQNMQEIERQFNEYQSKMQSQQD 150
                                       78999999999999999999999999999999999999999999999999999885 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   7.5     0.015       3.8     125     235 ..      12     147 ..       2     153 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.015
                           DUF4407 125 eqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk...gtgttgvaGkgpaake........... 187
                                       eq+  +l++++++ ++q++++++ id   +  ++  ++++   + ++   gt+     G g+++++           
  gi|298674679|ref|YP_003726429.1|  12 EQYFRQLSTQYQQYKNQLESIKQHIDMVYTSSEECVKALNTIESLESleeGTESMVPIGSGTYMHAqfndlnrfvid 88 
                                       44445588899999999998888888888777777777764444444666888888899999999999999999999 PP

                           DUF4407 188 .............kkaqldaaqaelaelkakldatarlaalraelaeleaerakeraasqa 235
                                                    +k+ l+++++e++++ ++   ++  ++  ++++e+e++ ++ +++ q+
  gi|298674679|ref|YP_003726429.1|  89 igagisveknredAKETLNKRKEEMDNAYER--LNESYSQVVQNMQEIERQFNEYQSKMQS 147
                                       9999997777666666666666666666666..4444444444444444444333333333 PP

>> T4SS  Type IV secretion system proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.5   0.00063      0.16      22      47 ..      13      38 ..       5      64 .. 0.74
   2 ?   -1.0   0.0       7.6     2e+03      15      35 ..      97     117 ..      86     122 .. 0.50
   3 ?    1.7   4.4       1.1   2.9e+02       9      36 ..     123     150 ..     121     155 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00063
                              T4SS 22 qqltqlkqqleqakqqlesltgargl 47
                                      q + ql  q++q+k+qles+++  ++
  gi|298674679|ref|YP_003726429.1| 13 QYFRQLSTQYQQYKNQLESIKQHIDM 38
                                      45566667777777777776665544 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 7.6
                              T4SS  15 kqvkeaaqqltqlkqqleqak 35 
                                       k+ + a+++l++ k+++++a 
  gi|298674679|ref|YP_003726429.1|  97 KNREDAKETLNKRKEEMDNAY 117
                                       444444445555555555544 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 1.1
                              T4SS   9 aiaqaikqvkeaaqqltqlkqqleqakq 36 
                                       ++ q +++++e ++q++++++ ++ +++
  gi|298674679|ref|YP_003726429.1| 123 SYSQVVQNMQEIERQFNEYQSKMQSQQD 150
                                       78899999*************9997765 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.5      0.86   2.2e+02     107     146 ..      17      56 ..       9      65 .. 0.53
   2 ?   10.9   6.0   0.00088      0.23      86     138 ..      98     150 ..      93     154 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.86
                           DUF3552 107 sleekekelkqkeqsleekeeeleelveeqrqeLerisgL 146
                                       +l+++ ++ k++ +s+++  + + +  ee  + L+ i  L
  gi|298674679|ref|YP_003726429.1|  17 QLSTQYQQYKNQLESIKQHIDMVYTSSEECVKALNTIESL 56 
                                       4444444444445555555444444455555555555555 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00088
                           DUF3552  86 RllqkeetLdrkeeslekkeesleekekelkqkeqsleekeeeleelveeqrq 138
                                         ++ +etL++++e++++  e+l+e  +++ q+ q++e++ +e ++ +++q++
  gi|298674679|ref|YP_003726429.1|  98 NREDAKETLNKRKEEMDNAYERLNESYSQVVQNMQEIERQFNEYQSKMQSQQD 150
                                       5556679*************************************999999985 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.8     0.011       2.8      31      71 ..      17      57 ..       8      67 .. 0.75
   2 ?    5.1   5.5       0.1        27      23      65 ..     104     146 ..      94     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.011
                           BLOC1_2 31 aasekykklkdvaaslekkleklnekyeelqpylqqidqie 71
                                      + s++y+++k++++s+++ ++ +   +ee  + l+ i+ +e
  gi|298674679|ref|YP_003726429.1| 17 QLSTQYQQYKNQLESIKQHIDMVYTSSEECVKALNTIESLE 57
                                      55677888888888888888888888888877777777776 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.1
                           BLOC1_2  23 klLeklNeaasekykklkdvaaslekkleklnekyeelqpylq 65 
                                       ++L+k  e++ + y+ l+++ +++ +++++++++ +e q+++q
  gi|298674679|ref|YP_003726429.1| 104 ETLNKRKEEMDNAYERLNESYSQVVQNMQEIERQFNEYQSKMQ 146
                                       5677888888899999999999999999999999999988877 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.7    0.0037      0.95      63     118 ..      11      68 ..       5      86 .. 0.80
   2 ?    2.8   8.2      0.24        62      25      78 ..      96     149 ..      88     155 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0037
                           DUF3450  63 levyneqlerlvasqeqeiasleeqieeieeierelvpllekm..idrLeqfveldlP 118
                                       +e y +ql+ + ++ +++++s+++ i+ +   ++e v  l ++  +++Le+  e+ +P
  gi|298674679|ref|YP_003726429.1|  11 TEQYFRQLSTQYQQYKNQLESIKQHIDMVYTSSEECVKALNTIesLESLEEGTESMVP 68 
                                       5778899999999999999999999999999999999999754225566666666555 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.24
                           DUF3450  25 aekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqe 78 
                                       +++  +a++  +k+++++d+  + l + y ++ +  +++e + +++++ ++sq+
  gi|298674679|ref|YP_003726429.1|  96 EKNREDAKETLNKRKEEMDNAYERLNESYSQVVQNMQEIERQFNEYQSKMQSQQ 149
                                       566677778888888888888888888888888888888888887777777776 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.065        17       4      26 ..      17      39 ..      15      51 .. 0.79
   2 ?    0.8   0.5       2.5   6.4e+02      20      45 ..      96     121 ..      77     125 .. 0.80
   3 ?    6.0   0.5     0.058        15       5      40 ..     120     155 ..     117     156 .] 0.82

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.065
                               LPP  4 eLssqVsqLkskvdqlssdvnsa 26
                                      +Ls+q +q k++ +++++ ++ +
  gi|298674679|ref|YP_003726429.1| 17 QLSTQYQQYKNQLESIKQHIDMV 39
                                      89999999999999999887655 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 2.5
                               LPP  20 ssdvnsakaaaqaakeEAaRANqRlD 45 
                                       +++ ++ak+ +++ keE   A +Rl+
  gi|298674679|ref|YP_003726429.1|  96 EKNREDAKETLNKRKEEMDNAYERLN 121
                                       55567788888888999888888886 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.058
                               LPP   5 LssqVsqLkskvdqlssdvnsakaaaqaakeEAaRA 40 
                                       L++  sq  +++++++ + n+ ++ +q+ ++ A RA
  gi|298674679|ref|YP_003726429.1| 120 LNESYSQVVQNMQEIERQFNEYQSKMQSQQDGAYRA 155
                                       556667777888899999999999999999999999 PP

>> Nore1-SARAH  Novel Ras effector 1 C-terminal SARAH (Sav/Rassf/Hpo) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   1.7      0.06        16      19      37 ..      12      30 ..      12      31 .. 0.91
   2 ?    4.9   1.3     0.093        24      21      38 ..     130     147 ..     128     148 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.06
                       Nore1-SARAH 19 eeeiqqikrkYtalrqklq 37
                                      e++ +q+ ++Y++++++l+
  gi|298674679|ref|YP_003726429.1| 12 EQYFRQLSTQYQQYKNQLE 30
                                      6899*************97 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.093
                       Nore1-SARAH  21 eiqqikrkYtalrqklqq 38 
                                        +q+i+r+++ +++k+q 
  gi|298674679|ref|YP_003726429.1| 130 NMQEIERQFNEYQSKMQS 147
                                       68**************96 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   1.7     0.076        20      16      64 ..      13      61 ..      10      67 .. 0.76
   2 ?    6.4   6.1     0.046        12      70     117 ..     103     150 ..      93     154 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.076
                            APG6_N 16 kqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeee 64
                                      + ++q+  + ++Y++ l+ +k++ +   ++ ee+ ++ + +e le+ ee
  gi|298674679|ref|YP_003726429.1| 13 QYFRQLSTQYQQYKNQLESIKQHIDMVYTSSEECVKALNTIESLESLEE 61
                                      5578888888888888888888877666578888888888888887776 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.046
                            APG6_N  70 Lkelekereeleaelaaleeelealeeeeerfwreynelqlellelee 117
                                        + l k +ee++++ + l e  +++ ++ ++  r++ne+q ++++ ++
  gi|298674679|ref|YP_003726429.1| 103 KETLNKRKEEMDNAYERLNESYSQVVQNMQEIERQFNEYQSKMQSQQD 150
                                       456777788888888888888888888888888888888877777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3243  (0.18088); expected 358.6 (0.02)
Passed bias filter:                     1097  (0.0611858); expected 358.6 (0.02)
Passed Vit filter:                       164  (0.00914719); expected 17.9 (0.001)
Passed Fwd filter:                        73  (0.00407162); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              69  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.40
# Mc/sec: 1160.05
//
Query:       gi|298674680|ref|YP_003726430.1|  [L=58]
Description: 50S ribosomal LX protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.5e-11   42.6   0.4    6.3e-11   42.4   0.4    1.1  1  Ribosomal_L18A  Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
  ------ inclusion threshold ------
      0.079   12.4   0.1      0.087   12.2   0.1    1.0  1  Coatomer_E      Coatomer epsilon subunit


Domain annotation for each model (and alignments):
>> Ribosomal_L18A  Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.4     7e-15   6.3e-11      67     120 ..       2      55 ..       1      56 [. 0.97

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 7e-15
                                       ............TEEEEEEEEEEESSHHHHHHHHHHHHHHHS---GGGEEEEEE CS
                    Ribosomal_L18A  67 knygiwlrydsrsgthnfykeyrdlteegaveqvYselgsrhrakrssIqIekv 120
                                       kny +  +++  + +++f k++++ +e++a e++Ys +gs+h +kr +I+I+++
  gi|298674680|ref|YP_003726430.1|   2 KNYLVKGKFKAGHYWEKFSKYVESQNEKNATEKTYSLFGSKHGVKRFDIKIDSI 55 
                                       9**************************************************998 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   9.7e-06     0.087       6      60 ..       4      57 ..       2      58 .] 0.92

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.7e-06
                                      HHHHHHHHTT-HHHHHHHHHS---SHHHHHHHHHHHHHHHHHTT-HHHHHHHS-T CS
                        Coatomer_E  6 fdvrnefYlGaYqkaineadvaslseeekeerdvylyrsylAlgsaqiviseIke 60
                                      + v+ +f  G Y + + +  v+s++e++++e+   l+ s+  +++  i i++I e
  gi|298674680|ref|YP_003726430.1|  4 YLVKGKFKAGHYWEKF-SKYVESQNEKNATEKTYSLFGSKHGVKRFDIKIDSITE 57
                                      779999**********.577*******************************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 449.60
//
Query:       gi|298674681|ref|YP_003726431.1|  [L=217]
Description: translation initiation factor eIF-6 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-68  229.1   6.3    3.7e-68  228.8   6.3    1.0  1  eIF-6     eIF-6 family


Domain annotation for each model (and alignments):
>> eIF-6  eIF-6 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  228.8   6.3     2e-72   3.7e-68       2     197 .]       5     196 ..       4     196 .. 0.98

  Alignments for each domain:
  == domain 1  score: 228.8 bits;  conditional E-value: 2e-72
                                       E-BTTB--HHHH-EE-SSEEEE-TTS-HHHHHHHHHHHT-EEEE--BTTBS-HHHH-EE-SSEEEEETT--HHHHHH CS
                             eIF-6   2 lsiegsseiGvfarltnkyalvpegveeefvkaieeeLkvevvettiagsrlvGslvvgNsngllvpstvtdeelek 78 
                                       l+i +++ iGvfa++t+++a+vp+g++e+++k ie+ L+v+v++t i+gs++vGslv gNs+gll+p++ ++++l+ 
  gi|298674681|ref|YP_003726431.1|   5 LNILDNPVIGVFATCTEELAIVPTGTKEKTIKSIEDSLQVQVISTLISGSTVVGSLVSGNSHGLLIPRYGNEDDLKD 81 
                                       67899********************************************************************9998 PP

                                       HHHHHH---EEE--SS--HHHHEEE-SSEEEE-GGGGG.GHHHHHHHHTSEEEE--BTTBS-TTTSEEE-SSEEEE- CS
                             eIF-6  79 lkeslkleverleekltAlGNvilaNDkvAlvhpdlsketveiiadvLgvevvrgtiagiktvGsaavvtnkgllvh 155
                                        +    ++v++++++ltA+GN++laND++Alvhp++s++++e+i+++Lgv+ +rgtiagik vG+a+v++n+g+lvh
  gi|298674681|ref|YP_003726431.1|  82 TD----VTVSTVPSNLTAIGNTVLANDSAALVHPNFSDKSIEVISETLGVNAERGTIAGIKAVGMAGVANNNGILVH 154
                                       87....78********************************************************************* PP

                                       TT--HHHHHHHHHHHT-SEEE--BTTTBS-GGGTEEE-SS-E CS
                             eIF-6 156 pkateeeleeleellkveveagTvNrGsklvgsglvaNdkga 197
                                       p++t +e+++le+l+++++++gTvN+Gs++vgsg++aN++g+
  gi|298674681|ref|YP_003726431.1| 155 PNTTPSEMSQLEKLFDLPIDVGTVNYGSQMVGSGVIANTSGY 196
                                       ***************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1770.27
//
Query:       gi|298674682|ref|YP_003726432.1|  [L=88]
Description: 50S ribosomal protein L31e [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-09   36.4   0.2    5.7e-09   36.1   0.2    1.1  1  Ribosomal_L31e  Ribosomal protein L31e
  ------ inclusion threshold ------
      0.058   13.3   0.1       0.12   12.3   0.1    1.6  1  A1_Propeptide   A1 Propeptide


Domain annotation for each model (and alignments):
>> Ribosomal_L31e  Ribosomal protein L31e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.2   6.3e-13   5.7e-09       6      71 ..      10      76 ..       5      82 .. 0.88

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 6.3e-13
                    Ribosomal_L31e  6 eytInihkrihgvgfkkraprAlkeikkfamkemg.tpdv.ridtrLnkavwakgirnvpyrirvrls 71
                                       ytI   ++++++ + kr ++A+  i++f  ++++  p   +id ++n+ vw++g +++p  irvr +
  gi|298674682|ref|YP_003726432.1| 10 IYTIP-LRKVKSAPRWKRSHKAMALIRQFLIRHTKsLPSQiKIDRTVNEKVWERGSEKPPSSIRVRAA 76
                                      59999.6778999999*******************855555************************965 PP

>> A1_Propeptide  A1 Propeptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.3e-05      0.12       1      12 [.      10      21 ..      10      21 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.3e-05
                                      -EEEEEEE---H CS
                     A1_Propeptide  1 ivRIPLkKvKSm 12
                                      i+ IPL+KvKS+
  gi|298674682|ref|YP_003726432.1| 10 IYTIPLRKVKSA 21
                                      678********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 678.89
//
Query:       gi|298674683|ref|YP_003726433.1|  [L=51]
Description: 50S ribosomal protein L39e [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-20   71.4  11.4    3.8e-20   71.2  11.4    1.1  1  Ribosomal_L39  Ribosomal L39 protein


Domain annotation for each model (and alignments):
>> Ribosomal_L39  Ribosomal L39 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.2  11.4   2.1e-24   3.8e-20       2      42 .]       9      49 ..       8      49 .. 0.98

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 2.1e-24
                     Ribosomal_L39  2 KlrLaKalkqNrpvPaWvrlktdrkvrynpkrRhWRrtkLk 42
                                      K+rLaKa kqN +vP Wv++k++r+v ++pkrR+WRr++Lk
  gi|298674683|ref|YP_003726433.1|  9 KKRLAKAHKQNHRVPTWVIMKSNREVVTHPKRRNWRRNDLK 49
                                      9***************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 416.44
//
Query:       gi|298674684|ref|YP_003726434.1|  [L=200]
Description: ATP-binding protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.04   13.4   0.0      0.081   12.4   0.0    1.6  1  QueC      Queuosine biosynthesis protein QueC
       0.14   12.4   1.6       0.59   10.4   0.1    2.2  2  DUF2654   Protein of unknown function (DUF2654)


Domain annotation for each model (and alignments):
>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     9e-06     0.081       1      33 [.       2      33 ..       2      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9e-06
                                      EEEEE--SSHHHHHHHHHHHHH-SEEEEEEEES CS
                              QueC  1 kavvllSGGlDSttvlalakkegkevealtfdY 33
                                      ka vl+SGG DS+   a+ ++ + e+e++tf++
  gi|298674684|ref|YP_003726434.1|  2 KASVLFSGGKDSSLS-AILLEPFFEIELITFSF 33
                                      5779********976.56678999*******87 PP

>> DUF2654  Protein of unknown function (DUF2654)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.2     0.062   5.6e+02      31      47 ..      78      96 ..      60     103 .. 0.69
   2 ?   10.4   0.1   6.6e-05      0.59      32      58 ..     163     186 ..     148     198 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.062
                           DUF2654 31 nkaqYvY..aikklRdilk 47
                                      n  +Y +  aikkl +i  
  gi|298674684|ref|YP_003726434.1| 78 NAINYIHynAIKKLASIKS 96
                                      44455422499**999965 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 6.6e-05
                           DUF2654  32 kaqYvYaikklRdilkqtvnDelleiL 58 
                                       ka+Y+     lR+i++qt++D+ ++ +
  gi|298674684|ref|YP_003726434.1| 163 KADYE---TELREIIRQTYGDDKVSQI 186
                                       56665...479***********88865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1532.33
//
Query:       gi|298674685|ref|YP_003726435.1|  [L=116]
Description: DNA-binding TFAR19-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-27   95.5  20.8    2.8e-27   95.2  20.8    1.0  1  dsDNA_bind      Double-stranded DNA-binding domain
  ------ inclusion threshold ------
       0.15   11.4   2.0       0.24   10.7   2.0    1.3  1  Pkinase         Protein kinase domain
       0.18   11.9  11.3       0.29   11.3  11.3    1.4  1  F_actin_bund_C  F actin bundling C terminal


Domain annotation for each model (and alignments):
>> dsDNA_bind  Double-stranded DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.2  20.8   4.7e-31   2.8e-27       1     106 [.       8     113 ..       8     115 .. 0.93

  Alignments for each domain:
  == domain 1  score: 95.2 bits;  conditional E-value: 4.7e-31
                                       XXXXXXXXXXXXXXXXXXXX...XXXX--SS..S--SSHHHHTTS--HHHHHHHHHHTTT-HHHHHHHHHHHHHHHH CS
                        dsDNA_bind   1 irkarlaelqaqagsssgsggaseqqeqqqeaseeeakqaiLsqiLepeAreRLsrirlvkperaeavenrLiqlaq 77 
                                       ir+++ +++q+q++++++ g ++  ++q+q++++ee+k++iL+qiL+p+AreRL+r++++++e  e++e++Li laq
  gi|298674685|ref|YP_003726435.1|   8 IRRKKREQIQQQQQAAQQPGIDQYANQQEQAERMEEEKKKILRQILTPDARERLTRLKMSRNELGEQLESQLISLAQ 84 
                                       8*************9999995566666666668******************************************** PP

                                       --SS-----HHHHHHHHHHHS---XXXXX CS
                        dsDNA_bind  78 sGqlrskvteeqLkeLLeqvaekkketki 106
                                       sG+++s +++e+Lk+LL+q++ kk++t+i
  gi|298674685|ref|YP_003726435.1|  85 SGRIQSVIDDEKLKQLLSQIQPKKHDTNI 113
                                       **************************999 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   2.0     4e-05      0.24     207     258 ..      13      66 ..       3      71 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4e-05
                                       HHHHHTHHHHHHHCT..SHH...HHHTTS-HHHHHHHHHHT-SSGCCSTTHHHH CS
                           Pkinase 207 ekeldqlekilkilg..etkeklpeaseiseeakdllkkllkkdpkkRltaeel 258
                                       +++++q ++ ++  g  ++ ++ ++a+ ++ee k++l+++l+ d ++Rlt  ++
  gi|298674685|ref|YP_003726435.1|  13 REQIQQQQQAAQQPGidQYANQQEQAERMEEEKKKILRQILTPDARERLTRLKM 66 
                                       22333323333333355777889999999********************96554 PP

>> F_actin_bund_C  F actin bundling C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3  11.3   4.9e-05      0.29       6      75 ..       4      73 ..       2      85 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.9e-05
                    F_actin_bund_C  6 efqaqkrareakmkeLeakaalgGVkgmaAkneLaqmkseDqlelnkaeltaeaakrkAeKavkeedala 75
                                      e+++ +r++ +++++++++a++ G+ + a ++e a   +e++++  ++ lt  a+ r +  +++ +++ +
  gi|298674685|ref|YP_003726435.1|  4 ELEEIRRKKREQIQQQQQAAQQPGIDQYANQQEQAERMEEEKKKILRQILTPDARERLTRLKMSRNELGE 73
                                      77788999999********************************************999987777666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3008  (0.167773); expected 358.6 (0.02)
Passed bias filter:                      922  (0.0514251); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 882.58
//
Query:       gi|298674686|ref|YP_003726436.1|  [L=149]
Description: 30S ribosomal protein S19e [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.3e-56  187.5   0.0    9.3e-56  187.3   0.0    1.0  1  Ribosomal_S19e  Ribosomal protein S19e
  ------ inclusion threshold ------
      0.042   13.9   0.0      0.085   13.0   0.0    1.5  1  Vault_4         Major Vault Protein repeat domain
      0.075   12.7   0.1       0.19   11.4   0.1    1.7  1  GntR            Bacterial regulatory proteins, gntR family


Domain annotation for each model (and alignments):
>> Ribosomal_S19e  Ribosomal protein S19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.3   0.0   1.6e-59   9.3e-56       1     136 [.       3     137 ..       3     138 .. 0.97

  Alignments for each domain:
  == domain 1  score: 187.3 bits;  conditional E-value: 1.6e-59
                                       TSSSHHHHHHHHHS--S---S-SSS-SSSS-SS-S-SS-SSTTTHHHHHHHHHHHTS--TTSGGGGS----SS-SSS CS
                    Ribosomal_S19e   1 tvkdVpaeelikalaeeLkksgklevPewadlvKtgsakelapededWfyvRaAsilRkvylrgpvGverlrkvYGg 77 
                                       t++dVpa++li+++ae+Lk+++++++Pewa++vKtg++++l+p ++dW+y+R+A++lR +y++gpvGverlr++YGg
  gi|298674686|ref|YP_003726436.1|   3 TAYDVPANDLINKVAEKLKENEHVNPPEWASYVKTGVFNDLPPAEDDWWYTRCAAVLRSIYMDGPVGVERLRSMYGG 79 
                                       689************************************************************************** PP

                                       -------THHHHHHHHHTTSSS--SSS---SS-HHHHHTHHHHH--SS--S--XXXXXX CS
                    Ribosomal_S19e  78 kkrrgvrpshfvkasgsvirkilqqLeklglvkkekkkgrrltkkGqrlldriaeevak 136
                                       k  rgv p h+ k+sgs++rk+lqqLe++g+v++  k+gr+++++Gq++ld++a+ev++
  gi|298674686|ref|YP_003726436.1|  80 KLTRGVVPAHKLKGSGSILRKALQQLENAGYVRTL-KTGRVVSSQGQAFLDNVAYEVKN 137
                                       ********************************888.55******************976 PP

>> Vault_4  Major Vault Protein repeat domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.4e-05     0.085       9      29 ..     109     128 ..     101     140 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.4e-05
                           Vault_4   9 GiYvRdiktGkvrvviGetYm 29 
                                       G YvR  ktG+v +  G++++
  gi|298674686|ref|YP_003726436.1| 109 G-YVRTLKTGRVVSSQGQAFL 128
                                       4.*****************97 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   3.2e-05      0.19      32      57 ..      89     114 ..      88     120 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.2e-05
                                       HHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              GntR  32 aefgVsrttvReALrrLeaeglverr 57 
                                        +++ s + +R+AL++Le +g+v   
  gi|298674686|ref|YP_003726436.1|  89 HKLKGSGSILRKALQQLENAGYVRTL 114
                                       567889999*************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1088.32
//
Query:       gi|298674687|ref|YP_003726437.1|  [L=80]
Description: hypothetical protein Metev_0740 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 571.24
//
Query:       gi|298674688|ref|YP_003726438.1|  [L=424]
Description: adenylosuccinate synthetase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.9e-162  541.0   0.0   2.2e-162  540.8   0.0    1.0  1  Adenylsucc_synt  Adenylosuccinate synthetase
     0.0046   17.2   0.1        0.1   12.9   0.0    2.3  2  Fer4_12          4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Adenylsucc_synt  Adenylosuccinate synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  540.8   0.0  2.4e-166  2.2e-162       1     418 [.       3     420 ..       3     421 .. 0.97

  Alignments for each domain:
  == domain 1  score: 540.8 bits;  conditional E-value: 2.4e-166
                                       .EEEE-SSS-S-HHHHHHHHHTT-SEEEE-SB-TTSSEEEEETTEEEEESSS-GGGGSTT-EEEE-TTBEE-HHHHH CS
                   Adenylsucc_synt   1 vvvvGaqwGDEGKGkivDllaeeadvvvRfqGGanAGHtvvvdgkkyklhllpSGilnpgvvnviGngvvvdpeall 77 
                                       +v+ Gaq+GDEGKGkivDl+++++d++vRfqGG+nAGHtv v++  yklhl+pSG l+ +++ +iG+gvv++pe+l+
  gi|298674688|ref|YP_003726438.1|   3 TVLTGAQFGDEGKGKIVDLMSKDYDIIVRFQGGDNAGHTVTVGDDVYKLHLIPSGFLY-NARVLIGPGVVLNPEVLA 78 
                                       5899*****************************************************7.7888************** PP

                                       HHHTTSS-TT......TEEEETTSEE--HHHHHHHHHHHHH----------TTHHHHHHHHHTT---BGGGGGSHHH CS
                   Adenylsucc_synt  78 eEieeleakgvelskerllisdrahlvlpyhkalDkleeaakgkkkiGtTkkGiGpayadkvarrgirvgdlldeee 154
                                       +Ei++le++g++++ e+l +++++ +++pyh++lD+l+e+a + +kiGtTk+GiG ay dkvar+ i++ dl d+++
  gi|298674688|ref|YP_003726438.1|  79 DEIDMLEKSGCNVEPEKLGVDSKTSVIMPYHIELDNLRESALT-EKIGTTKRGIGFAYVDKVARNEIQFSDLTDKNK 154
                                       *************99*************************964.8******************************** PP

                                       HHHHHHHHHHHTHHHHHHT......T-----HHHHHHHHHHHHGGGEE-HHHHHHHHHHTT--EEEE--S-GGG-TT CS
                   Adenylsucc_synt 155 leeklekllelknkllekldk...eeleveelleellkyaerlkpyvvdtvallnealkegkkvLfEGaqgtllDid 228
                                       l ekl++l+ +k++ +e l       ++ eel++++ k+ ++l+py++d+++++n+a+++gk+v+ EGaqgt+lD+ 
  gi|298674688|ref|YP_003726438.1| 155 LIEKLSELAPQKKNDIEFLGGdpsIVMD-EELIDKYVKLGKKLEPYMADVSYEVNKAIDNGKSVMAEGAQGTHLDVI 230
                                       *********8887777776556544444.89********************************************** PP

                                       TSSTTSS-SS--SHHHHHHHTT--GGGEEEEEEEEESSEEESSSS--TTB--SHHHHHHHHHTT-B-TTT--B-EEE CS
                   Adenylsucc_synt 229 hGtYPfvTsSnttaggaltglglapkkidevlgvvKAyttrvGeGpfptelkdevgeklrekGkEfgtttgrpRrcG 305
                                       hGt  +vTsS+t+ag+a++  g++p+k+++vlg+vK+y+trvGeGp+ptel+devg++ +++G+EfgtttgrpRrcG
  gi|298674688|ref|YP_003726438.1| 231 HGTQKYVTSSSTIAGSACSSIGVGPTKVTNVLGIVKSYITRVGEGPLPTELNDEVGKHFQDVGREFGTTTGRPRRCG 307
                                       ***************************************************************************** PP

                                       -EEHHHHHHHHHHHT-SEEEEE-GGGGTT-SEEEEEEEEEETTEEESS--S.....-GEEEEEEEEE--.S--TT-- CS
                   Adenylsucc_synt 306 wlDlvllryavrvngvtelaltklDvldgldeikvcvaYkldgkeldefpasleelekvepvyeelpgWkedisgvr 382
                                       w+Dl+l+ +++++ng+t++altklDvl++ld ik+cv+Ykldg+ +++ p+ +++l+++epvyeelpgWk+d+++v+
  gi|298674688|ref|YP_003726438.1| 308 WIDLPLILKSINLNGYTGIALTKLDVLSELDPIKICVGYKLDGEYMEYPPQLTSDLSRCEPVYEELPGWKQDLTHVT 384
                                       ***************************************************************************** PP

                                       -GGGS-HHHHHHHHHHHHHHTS-EEEEE-SSSTT-E CS
                   Adenylsucc_synt 383 sfedlpenakkyvefieellgvpvkiisvGpereqt 418
                                       +f dlpe+a+kyv+++eel+gvpv++isvGp+r+qt
  gi|298674688|ref|YP_003726438.1| 385 EFGDLPEKAQKYVKRLEELMGVPVEYISVGPGRAQT 420
                                       *********************************998 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.032   2.9e+02      33      62 ..       7      36 ..       3      44 .. 0.88
   2 !   12.9   0.0   1.1e-05       0.1      32      81 ..     146     195 ..     133     215 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.032
                           Fer4_12 33 gkeftkelleeiiedlkkesiegltllGGE 62
                                      g +f +e + +i++ ++k++++ + + GG+
  gi|298674688|ref|YP_003726438.1|  7 GAQFGDEGKGKIVDLMSKDYDIIVRFQGGD 36
                                      66777888899******************9 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 1.1e-05
                           Fer4_12  32 sgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevke 81 
                                        ++ ++k+ l e + +l+ ++++++ +lGG+P+  +  e + + vk  k+
  gi|298674688|ref|YP_003726438.1| 146 FSDLTDKNKLIEKLSELAPQKKNDIEFLGGDPSIVMDEELIDKYVKLGKK 195
                                       556666555555566777999*************8888877777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 3013.14
//
Query:       gi|298674689|ref|YP_003726439.1|  [L=353]
Description: cellulase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.7e-111  371.9   2.7     2e-111  371.7   2.7    1.0  1  Peptidase_M42  M42 glutamyl aminopeptidase
      2e-11   44.0   0.1    2.8e-11   43.5   0.1    1.2  1  Peptidase_M20  Peptidase family M20/M25/M40
    3.1e-06   27.0   0.1    0.00067   19.4   0.0    2.3  2  Peptidase_M28  Peptidase family M28


Domain annotation for each model (and alignments):
>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  371.7   2.7  3.4e-115    2e-111       1     292 []      45     341 ..      45     341 .. 0.99

  Alignments for each domain:
  == domain 1  score: 371.7 bits;  conditional E-value: 3.4e-115
                                       S-EEEEEESSTTSSEEEEEEE--B-EEEEEEEETTSEEEEEEESS--GGGTTTEEEEEEETTEEEEEEEEE--CGGC CS
                     Peptidase_M42   1 GnliakkkgkekepkvmiaAHmDeiGfmVkeIkedGflrfekvGGvdpkvlegqrvkiltkkgkisGvigskppHll 77 
                                       Gnlia+kkg  ++p +m+aAHmDeiG+mVk I+++Gf+rf kvGG+ +++l +qrv i t++g i+Gvig+kppH++
  gi|298674689|ref|YP_003726439.1|  45 GNLIATKKG--SGPTIMLAAHMDEIGLMVKYIDDNGFIRFVKVGGWFDQTLYNQRVVIDTENGPIKGVIGAKPPHVM 119
                                       9********..****************************************************************** PP

                                       HHHHHHCT--GCGEEEEGSGSSHHHHHHTTS-TT-EEEES---EEETTECEEETTHHHHHHHHHHHHHHHHHCTSS- CS
                     Peptidase_M42  78 keeerkkaleikelfiDigakskeeaeelGisvGdivvfdkefvelangkivskalDdragvavllellkelkeeel 154
                                       ++e++kk+++ +++fiD+gak+ke+ae+lG++vG ++++d++f+ lang++++ka+D+ragvav +e++k+l+e ++
  gi|298674689|ref|YP_003726439.1| 120 SDEDKKKPIKAEDMFIDVGAKDKEDAENLGVQVGSTISLDRDFEPLANGFMTGKAFDNRAGVAVTIEIMKQLSEMDV 196
                                       **************************************************************************999 PP

                                       S..SEEEEEEESTCTTTSHHHHHHHHHH--SEEEEEEEEEE-CSTTSTTTTSS..TTS-CEEEEEETT...CCSHHH CS
                     Peptidase_M42 155 e..atvylvatvqEEvGlrGaktsaekikpdiaiavDvtaagdtpgskekeak..lgkGpvirvkDas...giyhpk 224
                                       +   t+y+v+tvqEEvGl+Ga+tsa+ ++pd+aia+D+t+ gd+pg ++k+++  +g+G vi+v+Da+   +i++++
  gi|298674689|ref|YP_003726439.1| 197 DikPTIYAVGTVQEEVGLKGARTSAFGLNPDAAIAIDTTIPGDHPGIEKKDSAleIGEGCVITVMDAGgrgLIADKN 273
                                       97789**********************************************9899***********998889***** PP

                                       HHHHHHHHHHHTT--EEEEEESSSSSTHHHHHTSTTTSEEEEEEEEEBSTTSTTEEEEHHHHHHHHHH CS
                     Peptidase_M42 225 lrkkllelAkknnipyqlevlsgggtDAgaihltgegvptalisiptryiHspvevahlddleatvkL 292
                                       ++k+l+e+ ++n+ipyq++v  gg+tDA+aih+t+eg+p+ +isi+tryiHspve++++dd++++++L
  gi|298674689|ref|YP_003726439.1| 274 IVKWLKETGNENDIPYQMDVSDGGTTDATAIHITREGIPSSTISIATRYIHSPVELLSIDDMKSAADL 341
                                       ***************************************************************99987 PP

>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   0.1   4.7e-15   2.8e-11      21     206 ..     162     347 ..     150     348 .. 0.77

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 4.7e-15
                                       TSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHHHHHHHHHHTTTCESEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20  21 fslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgGakallegleerekvdavfel 97 
                                       f++   +G++ G  a d+ +gv+  +e++++l +  ++ k ti  + ++ EE+g +Ga+  +     + ++da++++
  gi|298674689|ref|YP_003726439.1| 162 FEPL-ANGFMTGK-AFDNRAGVAVTIEIMKQLSEMDVDIKPTIYAVGTVQEEVGLKGARTSAF----GLNPDAAIAI 232
                                       5555.57*****9.**************************************88899999998....5667775522 PP

                                       EEESSSBTCHSTETEEEE.........E.EEEEEEEEESHEEECCHHHHHHHHHHHHHHHTSC.EEEEEESSSBHTH CS
                                       xxxxxxxxxxxxxxxxxx.........x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                     Peptidase_M20  98 hieepgileagklaigvv.........k.vevelleggapvtlndsplvkalaeaaeelfgek.velivsgpggtda 163
                                          +++i+  +  ++g+          + + ++   +g    + d+ +vk+l+e+  e      ++++  g g+tda
  gi|298674689|ref|YP_003726439.1| 233 ---DTTIPG-D--HPGIEkkdsaleigEgCVITVMDAGGRGLIADKNIVKWLKETGNEN-DIPyQMDVSDG-GTTDA 301
                                       ...244444.2..23333444444455669999887777777777**********9985.44433444677.***** PP

                                       HHH....TTTEEEEEEESSGGCTTSTTTEEEHHHHHHHHHHHHHHHH CS
                                       xxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 164 rff....agiptvmifgpgsglaHspnEyvdledlekgikvlarlle 206
                                         +    +gip+  i       +Hsp E ++++d++ ++++++++++
  gi|298674689|ref|YP_003726439.1| 302 TAIhitrEGIPSSTISIAT-RYIHSPVELLSIDDMKSAADLVTKAIL 347
                                       ***9999999966444434.79********************99987 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.0    0.0023        14       1      39 [.      46      78 ..      46      80 .. 0.76
   2 !   19.4   0.0   1.1e-07   0.00067      35     163 ..     174     316 ..     160     344 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0023
                                      EEEEEESTTCESEEEEEEEE--B-TTTTCCT---TTTTH CS
                     Peptidase_M28  1 NviatlegkatdevlllgAHyDsvgvgrgpifvGAdDnA 39
                                      N+iat +g+    +++l+AH+D +g   +     +dDn+
  gi|298674689|ref|YP_003726439.1| 46 NLIATKKGSG--PTIMLAAHMDEIGLMVK----YIDDNG 78
                                      8888888888..69********9998433....366665 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 1.1e-07
                                       TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSCSGSSHHHHHHHH.HHC.CCTTEEEEEEECS-SSSS--EEE CS
                     Peptidase_M28  35 AdDnAsgvaalLelarvlaasgsrpkrgvrflffdaEEagllGSkafak.akp.elkkiaavlnlDmvgsggkellf 109
                                       A Dn +gva+ +e++++l ++  + k ++  + +  EE gl G++  a   +p ++ +i++ +  D  g ++k    
  gi|298674689|ref|YP_003726439.1| 174 AFDNRAGVAVTIEIMKQLSEMDVDIKPTIYAVGTVQEEVGLKGARTSAFgLNPdAAIAIDTTIPGDHPGIEKKDSAL 250
                                       88******************99999********************99987556588889999999988888777777 PP

                                       .........HHHHHHCHHH.HHHHHHHHHHTT-TTSCCEEEEES.STT-STTHHHH..TTT--EEEE CS
                     Peptidase_M28 110 .........esgdksssel.ekelkalakpvgraaaedpfders.grgrsDhspfl..kagvpvldl 163
                                                ++  +++  +  k + +  k++g++    p + ++   g++D+++++  ++g+p  ++
  gi|298674689|ref|YP_003726439.1| 251 eigegcvitVMDAGGRGLIaDKNIVKWLKETGNE-NDIPYQMDVsDGGTTDATAIHitREGIPSSTI 316
                                       7788888862222222222123344555555554.23444444435566887776665888888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2618.21
//
Query:       gi|298674690|ref|YP_003726440.1|  [L=493]
Description: isopropylmalate/citramalate/homocitrate synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.7e-81  271.7   0.3    1.1e-80  271.1   0.3    1.3  1  HMGL-like   HMGL-like
    1.5e-35  122.0   2.2    2.6e-35  121.2   2.2    1.4  1  LeuA_dimer  LeuA allosteric (dimerisation) domain
     0.0002   20.5   0.7     0.0002   20.5   0.7    1.9  2  IMPDH       IMP dehydrogenase / GMP reductase domain


Domain annotation for each model (and alignments):
>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  271.1   0.3   1.8e-84   1.1e-80       2     264 .]       6     263 ..       5     263 .. 0.99

  Alignments for each domain:
  == domain 1  score: 271.1 bits;  conditional E-value: 1.8e-84
                                       -EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHH CS
                         HMGL-like   2 vkivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdi 78 
                                       ++++dttLRDGeq++++al++e+k+ ia++Lde+g+d iE+g +  se+++e+++ai ++  +a+i++++r + +d+
  gi|298674690|ref|YP_003726440.1|   6 IRFLDTTLRDGEQTPGVALTTEDKVSIAQKLDELGIDIIEAGSAITSEGERESIKAITAENINAEICSYCRIKNSDV 82 
                                       899************************************************************************** PP

                                       HHHHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHHH CS
                         HMGL-like  79 kaavealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkdvelsledasrtdleflaevveaa 155
                                       + a e    + ++++h+++++s+lh+ aklkkdr+ev+++a e++++a+++g  vels edasr+d efl  ++   
  gi|298674690|ref|YP_003726440.1|  83 DYALE----CDVDSIHLVVPVSDLHITAKLKKDRDEVRQIASEVTEYAKDHGLIVELSGEDASRADHEFLKSLYSDG 155
                                       *****....******************************************************************** PP

                                       HHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS--SSBB CS
                         HMGL-like 156 eeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGlGeraG 232
                                       ++aGa+r+   DtvG+l P++ +e++s +++ ++  ++lsvHcH+d+GlAvan++aA++aGa++   tvnG+GeraG
  gi|298674690|ref|YP_003726440.1| 156 ISAGADRLCYCDTVGMLIPEKTREIFSDMSSSLD--APLSVHCHDDFGLAVANSVAAINAGARECHMTVNGIGERAG 230
                                       **********************************..***************************************** PP

                                       B-BHHHHHHHHHHTT.-B----HHHHHHHHHHH CS
                         HMGL-like 233 naaleelvaalealg.vdtgldlqklrsiaalv 264
                                       n++lee+++ le l  +dtg++l++l++++++v
  gi|298674690|ref|YP_003726440.1| 231 NTSLEEVIMILEWLYnYDTGIKLEELYKTSRTV 263
                                       ************9988*************9987 PP

>> LeuA_dimer  LeuA allosteric (dimerisation) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.2   2.2   4.4e-39   2.6e-35       2     133 .]     359     491 ..     358     491 .. 0.97

  Alignments for each domain:
  == domain 1  score: 121.2 bits;  conditional E-value: 4.4e-39
                                       XXXXXXXXXXXXXXXXXX.--EEEEEEEEEEETTCEEEEEEEEEE.TTEEEEEEEE-SSHHHHHHHHHHHHHHH..T CS
                        LeuA_dimer   2 vtdedlealvkdelleae.erlkleklqvssgedelstatvklevkdgeekeasaeGnGpvdAllnAlrkalgv..d 75 
                                       v+d+d++++++++l   +  ++kle+l+v+sg++ ++ta+ kl+v +g++ +++++GnGpvdA+++ +rka++   d
  gi|298674690|ref|YP_003726440.1| 359 VSDADIQSIAETVLEIYRePKVKLEELTVVSGNTVTPTASTKLNV-NGQDIVEAGVGNGPVDAAIQGVRKAISGvaD 434
                                       89*************9888**************************.**************************9889* PP

                                       -EEEEEEEE--TT-TT--EEEEEEEE--GGGEEEEEEEESSHHHHHHHHHHHHHHHHS CS
                        LeuA_dimer  76 ikLldYsvhaitegtdaqaevrVelevddgkkvsgvGvdsdiveASlkAlisalnrll 133
                                       i+L++Y+v+ait+gtda++ev V+l+ +dgk+++ +G+++di++AS++A+++++n+ll
  gi|298674690|ref|YP_003726440.1| 435 IQLQEYHVDAITGGTDALVEVLVKLS-KDGKIITSRGARTDIIMASVEAVLNGINYLL 491
                                       **************************.99999***********************986 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1     0.093   5.5e+02      96     146 ..      21      69 ..      12      97 .. 0.70
   2 !   20.5   0.7   3.4e-08    0.0002     104     179 ..     344     418 ..     253     483 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.093
                                       EEEE-SSTTHHHHHHHHHHTT-SEEEEE-STSSSHHHHHHHHHHHHHTTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH  96 gaavgvkedalervkalveagvdvlvvdsahghsekvleavkeikkkveev 146
                                       g a+ ++ d+ + +++l e g+d++   sa   se+  e +k+i ++  + 
  gi|298674690|ref|YP_003726440.1|  21 GVALTTE-DKVSIAQKLDELGIDIIEAGSAI-TSEGERESIKAITAENINA 69 
                                       5555555.78888999999999999887775.4666677777776665555 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 3.4e-08
                                       THHHHHHHHHHTT-SEEEEE-STSSSHHHHHHHHHHHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEEEE-SS-STT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 104 dalervkalveagvdvlvvdsahghsekvleavkeikkkveeveviaGnvataegakaLieagadavkvGiGpGsi 179
                                       + l+rvk l+++g  v   d+ +   e+vle  +e k k+ee++v++Gn +t  + ++L  +g d+v  G+G+G +
  gi|298674690|ref|YP_003726440.1| 344 EILSRVKVLADKGKRVSDADI-QSIAETVLEIYREPKVKLEELTVVSGNTVTPTASTKLNVNGQDIVEAGVGNGPV 418
                                       567788888888888877776.56788999999*******99********************************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.22s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 3778.19
//
Query:       gi|298674691|ref|YP_003726441.1|  [L=561]
Description: acetolactate synthase large subunit, biosynthetic type [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-58  195.9   0.1    4.6e-57  192.4   0.1    2.3  2  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
    2.3e-56  189.8   0.1    1.4e-54  184.1   0.0    2.8  3  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    1.2e-53  180.5   0.0    2.4e-53  179.5   0.0    1.5  1  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
  ------ inclusion threshold ------
      0.042   13.6   3.3       0.03   14.1   1.2    1.9  2  POR_N         Pyruvate flavodoxin/ferredoxin oxidoreductase, 
      0.094   11.7   0.0        6.5    5.6   0.0    2.2  2  Bmp           ABC transporter substrate-binding protein PnrA-
       0.34    9.8   2.0        2.7    6.9   0.1    2.6  3  E1_dh         Dehydrogenase E1 component


Domain annotation for each model (and alignments):
>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.4   0.1   1.5e-60   4.6e-57       1     169 [.       8     174 ..       8     176 .. 0.99
   2 ?    0.7   0.0      0.11   3.4e+02      83     145 ..     451     526 ..     439     535 .. 0.69

  Alignments for each domain:
  == domain 1  score: 192.4 bits;  conditional E-value: 1.5e-60
                                       EEHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHH CS
                      TPP_enzyme_N   1 mtvaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGat 77 
                                       mt+a+al+++L +++v+++fg+pG+ +lp++d++ +++ ++++l+rhEq+aa+aAdgyaratgk gv+++tsgpGat
  gi|298674691|ref|YP_003726441.1|   8 MTGARALIECLYKENVDTIFGYPGGAVLPIYDEIYKSD-LNHILTRHEQSAAHAADGYARATGKTGVCVATSGPGAT 83 
                                       89***********************************6.************************************** PP

                                       HCHHHHHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--E CS
                      TPP_enzyme_N  78 naltalaeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtkyaervtspeelpealrrAirtalsgrpgP 154
                                       n++t++a+A+ d+iP+++++g++pt ++g +++q e +++++  p+tk+++ v+++++lp+++++A+ +a +gr+gP
  gi|298674691|ref|YP_003726441.1|  84 NLVTGIATAYMDSIPMVAITGQVPTFMIGNDAFQ-EANITGITLPITKHNYLVQDANDLPRIIKEAFHIASTGRKGP 159
                                       **********************************.****************************************** PP

                                       EEEEEEHHHCC-EEE CS
                      TPP_enzyme_N 155 vylelpkdvlleevd 169
                                       v++++pkdv  +e+d
  gi|298674691|ref|YP_003726441.1| 160 VLIDIPKDVTAQEID 174
                                       ************997 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.11
                                       HHHHHHHT--EEEEEEE--CCCHH.............S..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHH CS
                      TPP_enzyme_N  83 laeAkvdriPllvlsgdrptslrg.............qgvlqqeldqlalfrpvtkyaervtspeelpealrrAir 145
                                       la+A + +iP++v + ++ +                 +  l++ +d ++l++ +     r ++pe++++++++A++
  gi|298674691|ref|YP_003726441.1| 451 LATAVQHNIPVIVAVINNCYLGMVrqwqelffeqrysCTCLEESVDFVKLAEAYGALGLRAEKPEDVRPVIDEALA 526
                                       7778888888887776665444443555555555555666666667777777777777888888888888887765 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.57   1.7e+03      37      62 ..      86     112 ..      57     129 .. 0.70
   2 ?    2.3   0.0     0.043   1.3e+02     127     153 .]     135     164 ..     116     164 .. 0.86
   3 !  184.1   0.0   4.5e-58   1.4e-54       2     153 .]     388     535 ..     387     535 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.57
                                       HHHHHHHST.TSEEEEEEEHHHHHHTG CS
                      TPP_enzyme_C  37 AiGaklakp.drevvaivGDGgflmil 62 
                                        +G++ a+  + ++vai+G   ++mi+
  gi|298674691|ref|YP_003726441.1|  86 VTGIATAYMdSIPMVAITGQVPTFMIG 112
                                       356666654135777777777777774 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.043
                                       ESSH.HHHHHHHHHHHH.....CSSSEEEEEE CS
                      TPP_enzyme_C 127 vekadveeleealkeal.....ekkgpaliev 153
                                       v++a  ++l +++kea+      +kgp+li++
  gi|298674691|ref|YP_003726441.1| 135 VQDA--NDLPRIIKEAFhiastGRKGPVLIDI 164
                                       4445..99********999999999*****97 PP

  == domain 3  score: 184.1 bits;  conditional E-value: 4.5e-58
                                       SSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEEE CS
                      TPP_enzyme_C   2 iGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitvv 78 
                                       +G++++wa++++k+k+pr+++tsgglgtmGyg+paA+Gak+ kp++ v+ i+GDG+f+m++qelatav++n+p++v 
  gi|298674691|ref|YP_003726441.1| 388 VGQHQMWASQYFKFKEPRTFITSGGLGTMGYGFPAALGAKIGKPEKVVFDIAGDGSFQMNCQELATAVQHNIPVIVA 464
                                       9**************************************************************************** PP

                                       EEE-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                      TPP_enzyme_C  79 vlnNegygmtggqqepfggkrksgpagkdlkpvdfaklaealGakgarvekadveeleealkealekkgpaliev 153
                                       v+nN ++gm++++qe f+++r+s++    +++vdf+klaea+Ga g+r ek+  e+++++++eal++++p++i++
  gi|298674691|ref|YP_003726441.1| 465 VINNCYLGMVRQWQELFFEQRYSCTC--LEESVDFVKLAEAYGALGLRAEKP--EDVRPVIDEALASERPTVIDF 535
                                       ************************99..699*****************8888..*******************95 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.5   0.0   8.1e-57   2.4e-53       1     137 []     197     332 ..     197     332 .. 0.98

  Alignments for each domain:
  == domain 1  score: 179.5 bits;  conditional E-value: 8.1e-57
                                       HHHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHHHH CS
                      TPP_enzyme_M   1 iekaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylgmlglhgskaanealee 77 
                                       ++ka e+++++k+pvi++Ggg+++s+as+el+e+aek+++Pv+ttl g g++p+dhp+++gmlg+hg+k+an a++e
  gi|298674691|ref|YP_003726441.1| 197 VKKASEYIERSKKPVIYAGGGIINSNASDELKEFAEKINAPVTTTLTGIGCFPDDHPQNMGMLGMHGTKYANYAIQE 273
                                       68999************************************************************************ PP

                                       -SEEEEES-SSSTCCCTTTTTTTTTT-EEEEEESSCCCCTTCC--SEEEECTHHHHHHHH CS
                      TPP_enzyme_M  78 aDlvlalGarfddirttgsepefapeakiihididpaeigknyqvdlaivgdvketleaL 137
                                       +Dl++a+Garfdd r+tg+  +fap+a iihididpaei+kn +v+++ivgd+k +l++L
  gi|298674691|ref|YP_003726441.1| 274 SDLIIAVGARFDD-RVTGKIAAFAPNADIIHIDIDPAEISKNIKVSVPIVGDAKWILKSL 332
                                       *************.****************************************999876 PP

>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.2   9.9e-06      0.03      36      95 ..      44     105 ..      33     235 .. 0.85
   2 ?   -2.7   0.0       1.3     4e+03     132     152 ..     444     464 ..     442     467 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.9e-06
                                       EE.EEEE-SSHHHHHHHHHH.HHCTT-E.EEEEEECCHHHHCCCCHHHHHHTT--EEEEEEE CS
                             POR_N  36 gdvevvqmesEigaisaviG.AaaaGar.aaTaTSgqGllLmienlglaageelPvvivvva 95 
                                        d + + +  E +a+ a+ G A a+G   + +aTSg+G    +  +  a ++ +P+v +  +
  gi|298674691|ref|YP_003726441.1|  44 SDLNHILTRHEQSAAHAADGyARATGKTgVCVATSGPGATNLVTGIATAYMDSIPMVAITGQ 105
                                       556777888999******99677888762479*************************98765 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHHHCTSEEEEE CS
                             POR_N 132 fdlalvAfnlAekvrvPvivl 152
                                       f++  + +++A++ ++Pviv+
  gi|298674691|ref|YP_003726441.1| 444 FQMNCQELATAVQHNIPVIVA 464
                                       566677788999999999986 PP

>> Bmp  ABC transporter substrate-binding protein PnrA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0    0.0022       6.5     166     220 ..       4      56 ..       1      69 [. 0.83
   2 ?    3.7   0.0    0.0083        25      55      91 ..     268     305 ..     262     341 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0022
                                       SSS-HHHHHHHHHHHHHCT--EEEEE-GGGHHHHHHHHHHHCHCTEEEEEES--C CS
                               Bmp 166 tfsDakkgkslAsslykegvdvifpaagkagkgvieaakelglsnyvIgvdkdqs 220
                                       ++++ + +++l + lyke vd if+  g+a+ ++++++ +  l+   I    +qs
  gi|298674691|ref|YP_003726441.1|   4 STEKMTGARALIECLYKENVDTIFGYPGGAVLPIYDEIYKSDLN--HILTRHEQS 56 
                                       6677778899999************************9999888..566666665 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0083
                                       HHHCTT-SEEEEESCCHHH.HHHHHHHH-TTS-EEEES CS
                               Bmp  55 nlkeegsdlivatgfalqd.alqevssdfpkvkFliiD 91 
                                       n + ++sdli+a+g ++ d ++ ++++  p+   ++iD
  gi|298674691|ref|YP_003726441.1| 268 NYAIQESDLIIAVGARFDDrVTGKIAAFAPNADIIHID 305
                                       677899************95566888888887777777 PP

>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1     0.037   1.1e+02      94     137 ..      47      85 ..      17     117 .. 0.73
   2 ?   -2.9   0.0      0.86   2.6e+03     202     219 ..     195     212 ..     189     236 .. 0.65
   3 ?    6.9   0.1   0.00089       2.7      99     163 ..     409     470 ..     369     479 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.037
                                       ..BEEE-SSTTTHHHHHHHHHHHHHHHTS---EEEEEEGGGTT- CS
                             E1_dh  94 srilggngivgaqvplvaGialaakiegkkevailliGDgAanq 137
                                       ++il+++  ++a    + G a+a    gk+ v++++ G gA+n 
  gi|298674691|ref|YP_003726441.1|  47 NHILTRHEQSAAH--AADGYARA---TGKTGVCVATSGPGATNL 85 
                                       4666666666666..55577666...69999999999*999985 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.86
                                       HHHHHHHHHHHTTT--EE CS
                             E1_dh 202 eAvkfAaeraregkgpll 219
                                       + vk A e+ ++ k+p++
  gi|298674691|ref|YP_003726441.1| 195 QQVKKASEYIERSKKPVI 212
                                       345556666666665554 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.00089
                                       E-SSTTTHHHHHHHHHHHHHHHTS---EEEEEEGGG.TT-HHHHHHHHHHHHTT--EEEEEEEESE CS
                             E1_dh  99 gngivgaqvplvaGialaakiegkkevailliGDgA.anqGdvyealnlaalwklpvifvveNNky 163
                                       ++g +g+    +  +al aki + ++v++ + GDg+   + +    l  a  +++pvi  v NN y
  gi|298674691|ref|YP_003726441.1| 409 TSGGLGTM-GYGFPAALGAKIGKPEKVVFDIAGDGSfQMNCQE---LATAVQHNIPVIVAVINNCY 470
                                       55555555.34445899******************96444443...4447889***********88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (561 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 4126.65
//
Query:       gi|298674692|ref|YP_003726442.1|  [L=161]
Description: acetolactate synthase small subunit [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-32  110.9   4.6    1.2e-31  108.7   1.6    2.1  2  ALS_ss_C  Small subunit of acetolactate synthase
    1.5e-16   59.9   0.3    3.5e-15   55.6   0.1    2.4  2  ACT_5     ACT domain
      2e-16   59.4   1.1    4.6e-16   58.3   0.1    2.0  2  ACT       ACT domain
    0.00017   22.1   0.5    0.00017   22.1   0.5    1.9  2  ACT_4     ACT domain
  ------ inclusion threshold ------
      0.041   13.7   3.1       0.45   10.3   3.3    1.9  2  SLS       Mitochondrial inner-membrane-bound regulator
       0.11   12.3   0.1         18    5.3   0.0    2.9  3  NIL       NIL domain


Domain annotation for each model (and alignments):
>> ALS_ss_C  Small subunit of acetolactate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1     0.039   1.2e+02      23      54 ..      42      73 ..      34      78 .. 0.88
   2 !  108.7   1.6     4e-35   1.2e-31       1      74 []      84     157 ..      84     157 .. 0.99

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.039
                                      HHTT-EEEEEETTEEEEEEEE-HHHHHHHHHH CS
                          ALS_ss_C 23 eifrakivdvspdsliieltgteekidaliel 54
                                      +i r+ iv  ++d ++ ++t++ +k+ ++i++
  gi|298674692|ref|YP_003726442.1| 42 DISRMSIVVHGDDHVLEQVTKQLNKLVDVIRV 73
                                      678999***************99999988875 PP

  == domain 2  score: 108.7 bits;  conditional E-value: 4e-35
                                       EEEEEEEEE.-SCHHHHHHHHHHHTT-EEEEEETTEEEEEEEE-HHHHHHHHHHS-GGGEEEEEEEEEEEEEST CS
                          ALS_ss_C   1 RElaLiKVkaekeerseileiaeifrakivdvspdsliieltgteekidaliellkpfgilevvRtGrvAleRG 74 
                                       RElaLiKV +++++r+ei++i+++fra++vdv+ +s++ie+tg+e+ki+a+ +ll+pfgi+e+vRtG++A++RG
  gi|298674692|ref|YP_003726442.1|  84 RELALIKVTTDTKTRPEIMQIVDVFRARTVDVAAKSMTIEITGNEDKINAIEQLLRPFGIKEMVRTGKIAMTRG 157
                                       9************************************************************************8 PP

>> ACT_5  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   0.1   1.2e-18   3.5e-15       4      62 .]      14      73 ..      11      73 .. 0.97
   2 ?    2.1   0.0     0.057   1.7e+02       9      30 ..     104     127 ..      98     135 .. 0.66

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 1.2e-18
                             ACT_5  4 gvLeRvlrvvrrrgFevkslnmsttedggtvrieltVes.ersvelLsnQleKLidVlkV 62
                                      gvL Rv ++++rrg++++sl +  t+d + +r+ ++V + +  +e++++Ql+KL+dV++V
  gi|298674692|ref|YP_003726442.1| 14 GVLARVAGLFSRRGYNIDSLAVGITDDPDISRMSIVVHGdDHVLEQVTKQLNKLVDVIRV 73
                                      9**************************************99****************998 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.057
                             ACT_5   9 vlrvvrrrgFevk..slnmstted 30 
                                       +  v+r r ++v+  s++++ t++
  gi|298674692|ref|YP_003726442.1| 104 IVDVFRARTVDVAakSMTIEITGN 127
                                       778999999988611455555444 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   0.1   1.5e-19   4.6e-16       1      66 [.       3      68 ..       3      69 .. 0.97
   2 ?   -0.6   0.1       0.4   1.2e+03      40      60 ..     116     136 ..      86     139 .. 0.64

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 1.5e-19
                                      EEEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTTC CS
                               ACT  1 tvlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkle 66
                                      ++l v+v+++ G+Larv+g++++rg+Nids+ ++ ++d   +++ +v+++d+ +le+v ++l+kl 
  gi|298674692|ref|YP_003726442.1|  3 HTLAVLVENKYGVLARVAGLFSRRGYNIDSLAVGITDDPDISRMSIVVHGDDHVLEQVTKQLNKLV 68
                                      67889***********************************************************96 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.4
                                       ECEEEEEEEEEEHHHHHHHHH CS
                               ACT  40 vagivfvvivvdeedleevle 60 
                                        a+ +++ i+++e+ + ++++
  gi|298674692|ref|YP_003726442.1| 116 AAKSMTIEITGNEDKINAIEQ 136
                                       345555555566655555555 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.5   5.7e-08   0.00017       8      79 ..       4      74 ..       1      74 [. 0.88
   2 ?   -1.3   0.1       1.2   3.5e+03      39      39 ..     117     117 ..      87     139 .. 0.60

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 5.7e-08
                             ACT_4  8 rleveaedrkglLaditqviseekanivsvnaktrkkdglaeikitveVkdveh.LsrviakLraipgVisVe 79
                                      +l v +e++ g+La+++ ++s  + ni s+ +  ++       ++++ V+  +h L++v ++L+++ +Vi+V+
  gi|298674692|ref|YP_003726442.1|  4 TLAVLVENKYGVLARVAGLFSRRGYNIDSLAVGITD--DPDISRMSIVVHGDDHvLEQVTKQLNKLVDVIRVT 74
                                      7999*****************************965..466778888888777769***************95 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.2
                             ACT_4  39 a 39 
                                       a
  gi|298674692|ref|YP_003726442.1| 117 A 117
                                       2 PP

>> SLS  Mitochondrial inner-membrane-bound regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   3.3   0.00015      0.45      62     162 ..      42     138 ..      22     139 .. 0.73
   2 ?    5.4   0.2    0.0049        15      55      85 ..     109     139 ..      98     152 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00015
                               SLS  62 nrsenklritAtkstaeyieasineilknittetvdlsellklskvdklkdl.lseelleelgrltntvievseddn 137
                                       ++s+  + + ++ ++ e++ +++n+++  i+++++d+++ ++  +   l ++  + ++  e++++ +++      ++
  gi|298674692|ref|YP_003726442.1|  42 DISRMSIVVHGDDHVLEQVTKQLNKLVDVIRVTDLDAKDSVE--RELALIKVtTDTKTRPEIMQIVDVFRA----RT 112
                                       567788999***************************777774..444455566788888888888888877....33 PP

                               SLS 138 nknskselkisalged.radlakRlL 162
                                        +  ++ ++i+ +g++ +++ +++lL
  gi|298674692|ref|YP_003726442.1| 113 VDVAAKSMTIEITGNEdKINAIEQLL 138
                                       22334444444444333666666665 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0049
                               SLS  55 hgakielnrsenklritAtkstaeyieasin 85 
                                       + +++++  ++ ++ it+++ ++++ie+ ++
  gi|298674692|ref|YP_003726442.1| 109 RARTVDVAAKSMTIEITGNEDKINAIEQLLR 139
                                       56899**********************9875 PP

>> NIL  NIL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.029        87      39      67 ..      39      67 ..      29      73 .. 0.80
   2 ?   -0.1   0.0      0.28   8.4e+02      54      71 ..      98     115 ..      86     117 .. 0.76
   3 ?    5.3   0.0    0.0059        18      45      66 ..     119     140 ..     118     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.029
                                      TTEEEEEEEEEEES-HHHHHHHHHHHHHT CS
                               NIL 39 qgtpfGqlvielsgsqesiaaalqylrkr 67
                                      ++  + ++ i + g+++ ++++ + l+k 
  gi|298674692|ref|YP_003726442.1| 39 DDPDISRMSIVVHGDDHVLEQVTKQLNKL 67
                                      56667899999999999999999988875 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.28
                                       HHHHHHHHHHHHHTT-EE CS
                               NIL  54 qesiaaalqylrkrnvdv 71 
                                       + +i ++++ +r r vdv
  gi|298674692|ref|YP_003726442.1|  98 RPEIMQIVDVFRARTVDV 115
                                       457899999999999998 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.0059
                                       EEEEEEES-HHHHHHHHHHHHH CS
                               NIL  45 qlvielsgsqesiaaalqylrk 66 
                                       +++ie++g++++i+a+ q lr 
  gi|298674692|ref|YP_003726442.1| 119 SMTIEITGNEDKINAIEQLLRP 140
                                       69***********999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       875  (0.0488036); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1291.27
//
Query:       gi|298674693|ref|YP_003726443.1|  [L=330]
Description: ketol-acid reductoisomerase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-77  258.4   0.9    3.2e-77  257.8   0.9    1.3  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
    2.9e-61  206.0   0.3    4.4e-61  205.4   0.3    1.3  1  IlvC            Acetohydroxy acid isomeroreductase, catalytic
    5.4e-07   29.1   0.0      1e-06   28.3   0.0    1.4  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    1.6e-06   28.6   0.2    3.2e-06   27.6   0.2    1.6  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    4.4e-06   26.9   0.0    9.6e-06   25.9   0.0    1.5  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    0.00069   19.7   0.0     0.0011   19.0   0.0    1.3  1  AdoHcyase_NAD   S-adenosyl-L-homocysteine hydrolase, NAD bind
     0.0087   16.5   0.1      0.023   15.2   0.1    1.7  1  CoA_binding_2   CoA binding domain
       0.01   15.5   0.2      0.018   14.7   0.2    1.5  1  ApbA            Ketopantoate reductase PanE/ApbA
  ------ inclusion threshold ------
      0.027   15.1   0.1      0.063   14.0   0.1    1.6  1  CoA_binding     CoA binding domain
      0.083   12.9   0.0       0.16   12.0   0.0    1.4  1  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
       0.11   11.1   0.0       0.29    9.8   0.0    1.6  2  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
       0.17   11.9   0.3        2.2    8.2   0.5    2.2  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen


Domain annotation for each model (and alignments):
>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  257.8   0.9   2.1e-80   3.2e-77       2     165 .]      15     178 ..      14     178 .. 0.99

  Alignments for each domain:
  == domain 1  score: 257.8 bits;  conditional E-value: 2.1e-80
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHH CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevye 78 
                                       lk+k+iaviGyGsqGhaqa+nl+dsgl+v++glregs+ +k+A+++g+ev++++ea+k+adv+ il+PDe+q++vye
  gi|298674693|ref|YP_003726443.1|  15 LKDKTIAVIGYGSQGHAQAQNLHDSGLNVIIGLREGSSRWKQAENDGLEVKSISEAAKAADVIQILMPDEVQANVYE 91 
                                       89*************************************************************************** PP

                                       HHTGGG--TT-EEEESSSHHHHTTSS---TTSEEEEEEESS-SHHHHHHHHTT----EEEEEEE-SSS-HHHHHHHH CS
                              IlvN  79 eeiepnlkegkalafahGfnihfglikppkdvdvvlvAPkgpGhlvreeyeegkGvpaliaveqdasgkakelalay 155
                                       ++i+p ++ g+a++f+hGfnih+++i+p kd+dv++vAPk+pGhlvr+++eeg Gvp liav+qda+g+ak+lala+
  gi|298674693|ref|YP_003726443.1|  92 SHIKPGIEPGNAIVFSHGFNIHYNQIVPSKDIDVYMVAPKSPGHLVRRTFEEGAGVPGLIAVYQDATGDAKNLALAH 168
                                       ***************************************************************************** PP

                                       HHHTTHHHH- CS
                              IlvN 156 akgiGatraG 165
                                       akgiG+traG
  gi|298674693|ref|YP_003726443.1| 169 AKGIGCTRAG 178
                                       *********9 PP

>> IlvC  Acetohydroxy acid isomeroreductase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.4   0.3   2.9e-64   4.4e-61       1     144 []     184     327 ..     184     327 .. 0.99

  Alignments for each domain:
  == domain 1  score: 205.4 bits;  conditional E-value: 2.9e-64
                                       HHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHTT--HHHHHHHHTHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHH CS
                              IlvC   1 FkeEtetDlfgEqavLcGgvselveagFetlveaGyspelAyfeclhelklivdliyegGiakmresiSdtaeygdl 77 
                                       F+eEtetDlfgEq+ LcGgvs+l++++Fetlv+aGy+pe+Ayfe++helklivdliyegG++km++s+S+taeyg+l
  gi|298674693|ref|YP_003726443.1| 184 FREETETDLFGEQVDLCGGVSTLIKTAFETLVDAGYQPEMAYFETFHELKLIVDLIYEGGLEKMWSSVSNTAEYGGL 260
                                       99*************************************************************************** PP

                                       HHHHHHS-HHHHHHHHHHHHHHHTTHHHHHHHHHHHTTSHHHHHHHHHHHTSHHHHHHHHHHHCHTT CS
                              IlvC  78 tagprviteevkeemkeileeiqsGefakevieenkagrpelkklrkeeaeheiekvgkklralmpw 144
                                       t+gp++i+e+++e+m+e le+iqsGefa+e+++en+++ p l++l+k+e+eh  e+vgk+lr+ +pw
  gi|298674693|ref|YP_003726443.1| 261 TVGPKIINEQSREAMYEALERIQSGEFAREFVLENQTNSPVLSALEKKEKEHLAENVGKELRSKIPW 327
                                       ***************************************************************9988 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   6.7e-10     1e-06      29     101 ..      10      83 ..       3      90 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 6.7e-10
                                       GSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.CHHHHTCEECSHHHHHHH-SEEEE-S-- CS
                      2-Hacid_dh_C  29 llgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee.eeeelgvelvsleellaesDivslhlpl 101
                                         +  l++kt+++iG+G+ G+a a+ l+  g++vi+  r  +++  ++e+ g+e+ s+ e+ + +D++ + +p 
  gi|298674693|ref|YP_003726443.1|  10 ANIDALKDKTIAVIGYGSQGHAQAQNLHDSGLNVIIGLREGSSRWkQAENDGLEVKSISEAAKAADVIQILMPD 83 
                                       567789****************************9998888765568899999*****************9995 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.2   2.2e-09   3.2e-06       1      80 [.      19      92 ..      19     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 2.2e-09
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHH CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevls 79
                                      +i++iG+G++g+a a++l  +g    +++++  r+ +++ + ae+ g +v++   +eaa+ adv+ + ++ e+ ++v +
  gi|298674693|ref|YP_003726443.1| 19 TIAVIGYGSQGHAQAQNLHDSG---LNVIIG-LREGSSRWKQAENDGLEVKS--ISEAAKAADVIQILMPDEVQANVYE 91
                                      59********************...****88.88888888888888877777..99*********99999888777765 PP

                                      H CS
                     F420_oxidored 80 e 80
                                      +
  gi|298674693|ref|YP_003726443.1| 92 S 92
                                      5 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   6.4e-09   9.6e-06       1      88 [.      19     106 ..      19     118 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 6.4e-09
                                       EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHC CS
                     NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdeviegll 77 
                                       +i++iG G  G+  a+nl ++g +v++  r+ ++  + +++    ++si+e+++++dv+ ++++++ + +   + ++
  gi|298674693|ref|YP_003726443.1|  19 TIAVIGYGSQGHAQAQNLHDSGLNVIIGLREGSSRWKQAENDGLEVKSISEAAKAADVIQILMPDEVQANVYESHIK 95 
                                       59*************************9999888888888888899******************98887655555** PP

                                       CC--TT-EEEE CS
                     NAD_binding_2  78 ealkkgdilid 88 
                                       + +++g+ ++ 
  gi|298674693|ref|YP_003726443.1|  96 PGIEPGNAIVF 106
                                       ******99985 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   7.6e-07    0.0011      22      82 ..      16      77 ..       9      96 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 7.6e-07
                                      TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHH.HHHHHCTT-EE--HHHCTTT-SEE CS
                     AdoHcyase_NAD 22 aGkvavvaGyGdvGkGcaaslkglGarvivtevdPic.alqaameGfevvtleevvkkadiv 82
                                        k++ v+GyG  G   a+ l+  G  vi+   +  +   qa  +G+ev+ + e++k ad++
  gi|298674693|ref|YP_003726443.1| 16 KDKTIAVIGYGSQGHAQAQNLHDSGLNVIIGLREGSSrWKQAENDGLEVKSISEAAKAADVI 77
                                      57999*************************98776651579*******************97 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   1.5e-05     0.023       1     105 [.      18     125 ..      18     134 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.5e-05
                                       --EEEET--S-TTSHHHHHHHHHHHHT--EEEESSS-SEETTEE......S----T....T--EEEE-S-HHHHGGG CS
                     CoA_binding_2   1 rtiaVvGasdnpgkfgykvlryllehglpvvpVnpkeeeilgek......vyaslaedpepvdlvdvftppeatpei 71 
                                       +tiaV+G     g+ g+  +++l+++gl+v+ +  +e++   ++      +++s++e+ ++ d++ +++p e+++++
  gi|298674693|ref|YP_003726443.1|  18 KTIAVIG----YGSQGHAQAQNLHDSGLNVI-IGLREGSSRWKQaendglEVKSISEAAKAADVIQILMPDEVQANV 89 
                                       79*****....7788************8876.556664444433356667999***967****************** PP

                                       HHHHHHH-..-SEEEE-TT---HHHHHHHHHTT-EE CS
                     CoA_binding_2  72 vkealalg..akavwlqpgsedeeaaelaeeagirv 105
                                       +++ ++ g  +  ++++++ ++    +++ +++i+v
  gi|298674693|ref|YP_003726443.1|  90 YESHIKPGiePGNAIVFSHGFNIHYNQIVPSKDIDV 125
                                       ***999875577888887777766666666666665 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.2   1.2e-05     0.018       1      51 [.      20      72 ..      20     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-05
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH..HHHHHHHHCEEEEETTCEEE CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr..rlealkknGlrltseggeei 51
                                      ia++G G++G   a +L+  g +v++ lr+   r ++ +++Gl+++s ++  +
  gi|298674693|ref|YP_003726443.1| 20 IAVIGYGSQGHAQAQNLHDSGLNVIIGLREGssRWKQAENDGLEVKSISEAAK 72
                                      89*********************999999886788888999999999984433 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   4.2e-05     0.063       2      89 ..      16     100 ..      15     107 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.2e-05
                                       TTEEEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTT...CEETTEEEESCHHHHHHHCTTTEEEEES-HHHH CS
                       CoA_binding   2 kdtkviviGagglgiaglyhfkeklkygikavfgvnprkvg...tevlglpvyksvdeleektevdvavitvPaesa 75 
                                       kd+ ++viG g +g+a + + ++    g+++++g  ++       e +gl+v+ s++e+ +   +dv  i++P e  
  gi|298674693|ref|YP_003726443.1|  16 KDKTIAVIGYGSQGHAQAQNLHDS---GLNVIIGLREGSSRwkqAENDGLEVK-SISEAAKA--ADVIQILMPDEVQ 86 
                                       7899******99988877666665...9999***99994432124445*****.********..***99******99 PP

                                       HHHHHHHHHTT-SE CS
                       CoA_binding  76 qeavdelveagikg 89 
                                       +++ +  ++ gi++
  gi|298674693|ref|YP_003726443.1|  87 ANVYESHIKPGIEP 100
                                       99999999999975 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00011      0.16       7      78 ..      12      76 ..       8      83 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                                      HS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SE CS
                      Shikimate_DH  7 leslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadv 78
                                      ++ lk+k++ +iG G  ++  a++L+++g++ v++  R+ +  ++ ae+ +      l++++++e+ ++adv
  gi|298674693|ref|YP_003726443.1| 12 IDALKDKTIAVIGYGSQGHAQAQNLHDSGLN-VIIGLREGSSRWKQAENDG------LEVKSISEAAKAADV 76
                                      6789**************************9.8888887777666665542......234444444444444 PP

>> Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00019      0.29     269     356 ..      14      95 ..       7     115 .. 0.79
   2 ?   -2.0   0.0      0.74   1.1e+03     228     228 ..     243     243 ..     151     284 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00019
                                       HHTT-EEEEECSSHHHHHHHHHHHHHT-EEEEEEESSS-HHHHHHHHHHS.TT.SEEEES.CHHHHHHHHHHHT-SE CS
                    Oxidored_nitro 269 ylagkrvaiygdpdrvvalarllkelGmevvaagtetahrddeerlkaeleegepeviddadleeleelikelkpdl 345
                                        l+ k++a++g++++ +a a+ l++ G +v+ +g +++++++++  ++    g  ev   ++  + ++ i+ l+pd 
  gi|298674693|ref|YP_003726443.1|  14 ALKDKTIAVIGYGSQGHAQAQNLHDSGLNVI-IGLREGSSRWKQAEND----G-LEVKSISEAAKAADVIQILMPDE 84 
                                       5899*************************86.6888888888854444....2.35555566777888888888888 PP

                                       EEE-CCHHHHH CS
                    Oxidored_nitro 346 llggskeryia 356
                                       + ++++e +i 
  gi|298674693|ref|YP_003726443.1|  85 VQANVYESHIK 95 
                                       88888887775 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.74
                                       S CS
                    Oxidored_nitro 228 G 228
                                       G
  gi|298674693|ref|YP_003726443.1| 243 G 243
                                       3 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.5    0.0015       2.2       2      31 ..      20      49 ..      19      89 .. 0.72
   2 ?    1.6   0.0      0.16   2.4e+02      61     103 ..      65     107 ..      59     120 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0015
                                      EEEE--SHHHHHHHHHHHTTT--EEEE-S- CS
                    NAD_Gly3P_dh_N  2 iavlGaGswGtalAkvlaenghevrlwvre 31
                                      iav+G Gs G a A+ l++ g +v +  re
  gi|298674693|ref|YP_003726443.1| 20 IAVIGYGSQGHAQAQNLHDSGLNVIIGLRE 49
                                      9********************777664444 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.16
                                       S-HHHHHTT--EEEE---HHHHHHHHHHHCCC--TT-EEEE-- CS
                    NAD_Gly3P_dh_N  61 tdlaealkgadiivlvvPsqalrevlkklkgllkkkailvsli 103
                                       + + ea+k ad+i + +P ++ ++v +++ +   +   ++  +
  gi|298674693|ref|YP_003726443.1|  65 KSISEAAKAADVIQILMPDEVQANVYESHIKPGIEPGNAIVFS 107
                                       67899****************9999987544333333444445 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 2406.84
//
Query:       gi|298674694|ref|YP_003726444.1|  [L=180]
Description: nitroreductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-35  122.4   0.3    5.1e-19   68.9   0.0    2.1  2  Nitroreductase  Nitroreductase family
    2.6e-17   63.1   0.2    5.1e-06   26.2   0.0    3.0  3  TM1586_NiRdase  Putative TM nitroreductase


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.9   0.0   5.7e-23   5.1e-19       1      54 [.       7      60 ..       7      69 .. 0.95
   2 !   52.4   0.1   6.8e-18   6.1e-14      82     170 .]      64     146 ..      59     146 .. 0.95

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 5.7e-23
                                      HHH--B---B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHH CS
                    Nitroreductase  1 irkRrSiRkFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelrykla 54
                                      i+ RrSiRkF+++pv+ke++++il+ +r+aPs+ n qpwrf+v+qdke++++l 
  gi|298674694|ref|YP_003726444.1|  7 IKARRSIRKFENTPVEKEDIDTILDSGRWAPSGLNNQPWRFIVIQDKETIKNLS 60
                                      799**********************************************98875 PP

  == domain 2  score: 52.4 bits;  conditional E-value: 6.8e-18
                                       HHHHHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHHHHHHHHT-S. CS
                    Nitroreductase  82 kaqkalagapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaaeevrkllglpd 158
                                       ++ + ++gap+liv+      + + +   +y  +++++ga ++n+lLa+++lGlg++++g + ++ae v+++l+ p+
  gi|298674694|ref|YP_003726444.1|  64 HYSEIVEGAPLLIVV------YLYHEVLYNYVKDIQSIGASIENMLLACHELGLGAVWLGEILNQAESVNTILETPE 134
                                       577899*********......999999999**********************************************9 PP

                                       .SEEEEEEEEE- CS
                    Nitroreductase 159 eeeivvliavGy 170
                                         e+++++a+G+
  gi|298674694|ref|YP_003726444.1| 135 SFELMAVVAIGH 146
                                       9**********7 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.1   5.7e-06     0.052       3      29 ..       4      30 ..       2      32 .. 0.89
   2 !   24.6   0.0   1.7e-09   1.6e-05     158     202 ..      24      68 ..      23      75 .. 0.82
   3 !   26.2   0.0   5.7e-10   5.1e-06      84     161 ..      95     173 ..      81     175 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.7e-06
                                      HHHHHH--B---B--S---HHHHHHHH CS
                    TM1586_NiRdase  3 yeaiekRhsvRkYkdealeeelleelk 29
                                      +++i+ R+s+Rk++++++e+e ++++ 
  gi|298674694|ref|YP_003726444.1|  4 LDTIKARRSIRKFENTPVEKEDIDTIL 30
                                      689******************999886 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 1.7e-09
                                       HHHHHHHHHHHTS--GGG----EEE.E-SSEE......EEE-S-HH CS
                    TM1586_NiRdase 158 ewfkeileaarlAPsAlNqqpwrfelkdddeikika.svlgklski 202
                                       e++++il+  r APs lN+qpwrf + + d+ +ik+ s+  ++s+i
  gi|298674694|ref|YP_003726444.1|  24 EDIDTILDSGRWAPSGLNNQPWRFIVIQ-DKETIKNlSTCTHYSEI 68 
                                       67899*******************9666.56667666777888887 PP

  == domain 3  score: 26.2 bits;  conditional E-value: 5.7e-10
                                       HHHHHHHHHHHHHHTT-EEEEES--SST..............T-S-EEEEE-BS----.-----HHHHBSS-GGGS- CS
                    TM1586_NiRdase  84 aGYygeqlvLkltalGlgtcWvggtykk...kkakvelkkgeklvivIalGyaktklveakrkpleelcevkeeelp 157
                                       +G   e+++L + +lGlg  W+g   ++   +++ +e++++ +l++v+a+G +++k++  +rk++ el++ ++   +
  gi|298674694|ref|YP_003726444.1|  95 IGASIENMLLACHELGLGAVWLGEILNQaesVNTILETPESFELMAVVAIGHPAEKST-SERKEIHELVYSEK-FGN 169
                                       666789*****************98877545666678889999***********9986.57899999996665.446 PP

                                       HHHH CS
                    TM1586_NiRdase 158 ewfk 161
                                       +w++
  gi|298674694|ref|YP_003726444.1| 170 RWIE 173
                                       7765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1243.04
//
Query:       gi|298674695|ref|YP_003726445.1|  [L=772]
Description: DNA topoisomerase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.8e-113  379.7   0.4   2.4e-113  379.3   0.4    1.2  1  Topoisom_bac    DNA topoisomerase
    1.5e-15   56.7  16.0    1.2e-10   41.0   2.2    3.1  3  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
    2.3e-14   53.5   0.1      1e-13   51.4   0.0    2.1  2  Toprim          Toprim domain
  ------ inclusion threshold ------
      0.061   12.7   0.0       0.11   11.8   0.0    1.3  1  DUF2113         Uncharacterized protein conserved in archaea 
       0.29   10.9   3.5        7.4    6.4   0.1    3.4  3  Rubredoxin_2    Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> Topoisom_bac  DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  379.3   0.4  6.6e-117  2.4e-113       2     408 ..     154     564 ..     153     569 .. 0.92

  Alignments for each domain:
  == domain 1  score: 379.3 bits;  conditional E-value: 6.6e-117
                      Topoisom_bac   2 inenlvdaaeaRrelDwliGinlsrlltk....klkg..kkvlsaGRVqtptLaliveRereienFvpeeyweveat 72 
                                       ++ nl+++a+aR++lD+ +G++++r++t+    k     k+vls+G++qtpt ++++eRe++i++F+p+++w++ea 
  gi|298674695|ref|YP_003726445.1| 154 PDVNLANSAKARQILDLKMGVAFTRYITLsvqqK--ArtKGVLSIGPCQTPTCGFVYEREKAIKEFEPRDFWKIEAV 228
                                       688**************************77544..2459************************************9 PP

                      Topoisom_bac  73 lkkekkekekkkkkkkerikdkeeaeaileklkk.keakvesvekkekkkppplpfdtttLqkeasrklglsakktl 148
                                       +++++  +  + +++ ++++dk++a+a+++k+++ k+ +v++ + ke+k++pp p++t++++k+as+ lgl+++++l
  gi|298674695|ref|YP_003726445.1| 229 FTHNDIDF--QGTHRTGKFFDKQKADAVYNKISDcKTGQVTNKKVKETKSSPPYPLNTNEFLKRASKFLGLNSDRAL 303
                                       96666666..69********************99779**************************************** PP

                      Topoisom_bac 149 siaqkLYekaglitYpRTdstrlseeaelkailealakkygkeylefaekllkktkkksvvknkkveaHeAIrPtee 225
                                       +ia++LY + g+ +YpRT+++++ +++++++ ++ l+kk +ke++  + k+ +++ ++   + k+ ++H++I+P+++
  gi|298674695|ref|YP_003726445.1| 304 EIAEQLYLS-GFTSYPRTETNKYANDFDFQSRVAELTKKAHKELALEVFKNSEDGFNP-RNGTKDAQDHPPIHPIKS 378
                                       ********7.****************99**********98887777777777666554.34444559********99 PP

                      Topoisom_bac 226 lp..klkels......ddekklYelIvrrflaslmkdakyeettvkleveeeefkasgktilekGfkkvykeekkee 294
                                       ++  +    +      ++ +++Y+lIvr+fla lm++a++e+t+++++v++e f+a+g++ +e G+  vy+ e k++
  gi|298674695|ref|YP_003726445.1| 379 ANkgD----InnavndSKGWDVYDLIVRHFLANLMQPAVFEKTRIEISVNDEIFDATGTVKKESGWIWVYPFEAKND 451
                                       88542....12235668999***************************************************999998 PP

                      Topoisom_bac 295 eeeelpelkegeevkvkeveleekkTkppkryteasLikamekagiGtpaTraeiieklvergYverkkkslvptel 371
                                       +   lpe++ +e++k+++++ ++ +T+ppkr+te++L+++m+k+giGt+aT  ++ie+ ++rgY e k+ks+   ++
  gi|298674695|ref|YP_003726445.1| 452 K--ILPEIEINEKLKINKITNTNSQTTPPKRLTESELLTLMDKNGIGTKATAPTHIETNKKRGYFETKGKSISILDT 526
                                       7..6***************************************************************98******** PP

                      Topoisom_bac 372 Gkalvell.ekfkdlvspelTaeleekLdeIaegkada 408
                                       G++l+++l + ++ +v+pe++a++e+ ++++++gk++ 
  gi|298674695|ref|YP_003726445.1| 527 GFTLMDALdKSVPLIVKPEIRARVEQLIQDVEDGKKSL 564
                                       ********6555***********************986 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   2.2   3.2e-14   1.2e-10       2      39 .]     611     648 ..     610     648 .. 0.96
   2 !   23.7   2.2   8.3e-09     3e-05       2      38 ..     698     732 ..     697     733 .. 0.94
   3 ?   -2.7   0.1       1.5   5.4e+03       6      19 ..     744     757 ..     742     762 .. 0.74

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 3.2e-14
                                       EE-SSS--EEEEEE-SSSEEEEESST.T----EEB-GG CS
                    zf-C4_Topoisom   2 ekCPkCggdLvlkrgkkGkFvGCsnYPeCkftkklkkn 39 
                                       +kC +C   L + ++ +G+FvGC+ YPeCk+t++l+k+
  gi|298674695|ref|YP_003726445.1| 611 GKCSECSRVLRIVTTDNGRFVGCTGYPECKNTYPLPKK 648
                                       79*********************************985 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 8.3e-09
                                       EE-SSS--EEEEEE-SSSEEEEESST.T----EEB-G CS
                    zf-C4_Topoisom   2 ekCPkCggdLvlkrgkkGkFvGCsnYPeCkftkklkk 38 
                                       ++CP C g + l ++k  +F+GC+n  +C +t + +k
  gi|298674695|ref|YP_003726445.1| 698 GQCPNCDGYMFLIKTKDSRFLGCTN--KCGYTQSVPK 732
                                       79***********************..******9987 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.5
                                       SS--EEEEEE-SSS CS
                    zf-C4_Topoisom   6 kCggdLvlkrgkkG 19 
                                       +Cg ++v+ + k +
  gi|298674695|ref|YP_003726445.1| 744 ECGWNIVRVKEKEK 757
                                       79988888777665 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.4   0.0   2.8e-17     1e-13       5     102 ..       7     138 ..       4     139 .. 0.88
   2 ?   -2.2   0.0       1.3   4.8e+03      49      84 ..     210     246 ..     186     272 .. 0.71

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 2.8e-17
                                       ESSHHHHHHHHHTHT....................STEEEEEEESSSSEEEHS..............TTEEEEEECT CS
                            Toprim   5 vEgpsdaktiakalg....................sgfqavtaslGhildlet..............efkpvyeeie 47 
                                       +E++++a++ia++l+                    +++ +++ ++Ghi++ +                ++ + e+  
  gi|298674695|ref|YP_003726445.1|   7 AEKNKAAAQIASILSegnferttlegvnvyefkkdGKQWRIMGLSGHIMTYDYpqeynnwkdvdpgvLIDTMPEQFI 83 
                                       8**************9******************99999**********9999666665555555554444444888 PP

                                       TTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHHHHHHTHHHTTTEEEEEESS CS
                            Toprim  48 dkkkvlkalkelakradeiilatDpDreGeaiawellevlkellenkigrvefse 102
                                       +k+   +a+ +lak+ deiila+D DreGe+i++e+ + +++ +++ i+r++fs+
  gi|298674695|ref|YP_003726445.1|  84 TKQAFANAISRLAKDSDEIILACDYDREGENIGFEAKSIAEKVCNSPIKRARFSS 138
                                       99999999*********************************************97 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.3
                                       THHHHHHHHHHH.HHHSEEEEECSSSHHHHHHHHHHH CS
                            Toprim  49 kkkvlkalkela.kradeiilatDpDreGeaiawell 84 
                                        +k++k+++++   + + ++   D D  G + + + +
  gi|298674695|ref|YP_003726445.1| 210 REKAIKEFEPRDfWKIEAVFTHNDIDFQGTHRTGKFF 246
                                       4567777777767777777777777777776665555 PP

>> DUF2113  Uncharacterized protein conserved in archaea (DUF2113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     3e-05      0.11       6      58 ..     389     441 ..     385     462 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3e-05
                           DUF2113   6 tdeegaeaYeeiirdilqDlnllrsierlkvyidpeeplFiiavllrktsspi 58 
                                       +d +g ++Y+ i+r+ l +l   ++ e+ ++ i  ++ +F ++++++k s  i
  gi|298674695|ref|YP_003726445.1| 389 NDSKGWDVYDLIVRHFLANLMQPAVFEKTRIEISVNDEIFDATGTVKKESGWI 441
                                       6899*******************************************998766 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.021        76      10      21 ..     606     617 ..     604     618 .. 0.81
   2 ?    6.4   0.1    0.0021       7.4      13      21 ..     696     704 ..     694     706 .. 0.81
   3 ?   -1.2   0.1       0.5   1.8e+03       4      10 ..     722     728 ..     722     730 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.021
                      Rubredoxin_2  10 sakwfGrCpsCg 21 
                                       s  + G+C +C 
  gi|298674695|ref|YP_003726445.1| 606 SDNYIGKCSECS 617
                                       66799******5 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0021
                      Rubredoxin_2  13 wfGrCpsCg 21 
                                        +G+Cp+C 
  gi|298674695|ref|YP_003726445.1| 696 IVGQCPNCD 704
                                       68******7 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.5
                      Rubredoxin_2   4 sqCGfes 10 
                                       ++CG+++
  gi|298674695|ref|YP_003726445.1| 722 NKCGYTQ 728
                                       68***97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (772 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       817  (0.0455686); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.71u 0.26s 00:00:00.97 Elapsed: 00:00:00.43
# Mc/sec: 5406.86
//
Query:       gi|298674696|ref|YP_003726446.1|  [L=153]
Description: hypothetical protein Metev_0749 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1290.97
//
Query:       gi|298674697|ref|YP_003726447.1|  [L=427]
Description: thiamine biosynthesis protein ThiC [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   1.1e-182  607.5   0.4   1.2e-182  607.3   0.4    1.0  1  ThiC_Rad_SAM  Radical SAM ThiC family


Domain annotation for each model (and alignments):
>> ThiC_Rad_SAM  Radical SAM ThiC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  607.3   0.4  6.8e-187  1.2e-182       1     417 [.       2     418 ..       2     419 .. 0.98

  Alignments for each domain:
  == domain 1  score: 607.3 bits;  conditional E-value: 6.8e-187
                      ThiC_Rad_SAM   1 tqleaarkgiiteemeevaekenvepefvreevaeGrivipanknhkekpvaiGkglrtkvnaniGtsadasdieeE 77 
                                       t +e+a+kgiit+ +++vaeke+++ e+vr+ vaeG i ip+n+n +++p++iGk ++tkvnaniGts+d++di++E
  gi|298674697|ref|YP_003726447.1|   2 TLMEDAKKGIITPLIKNVAEKEGIDSETVRSCVAEGLITIPKNVNSSSNPCGIGKYMSTKVNANIGTSRDYVDIDTE 78 
                                       789************************************************************************** PP

                      ThiC_Rad_SAM  78 veKlkvalkagadtvmdLstggdideirekileespvpvgtvpiYqaleekekkveelteeellevieeqaedGvdf 154
                                       veK+k a+++g dt+mdLstgg++d++r+ki+++ ++++gtvpiYqa++  +k+v++++++++++++ ++a+dGvdf
  gi|298674697|ref|YP_003726447.1|  79 VEKAKSAERYGVDTLMDLSTGGELDKVRKKIMDSINMSFGTVPIYQAAS-PHKSVVDMSSDDMFNAVLKHAKDGVDF 154
                                       ***********************************************98.789************************ PP

                      ThiC_Rad_SAM 155 ltiHagvtlellellkkekRltgivSrgGsllaawmlanekenplyeefdelleilkeydvtlSlgdglRpGsiaDa 231
                                       +tiHag +l++l++l++++R+t++vSrgG++++awm++ne+enp+y+efd+llei++eyd+tlSlgdg+RpG+i+Da
  gi|298674697|ref|YP_003726447.1| 155 VTIHAGANLNALDRLRNSNRITDVVSRGGAFTIAWMVHNEQENPFYSEFDYLLEIAHEYDMTLSLGDGMRPGCINDA 231
                                       ***************************************************************************** PP

                      ThiC_Rad_SAM 232 tdeaqlaelivlgelvkrareagvqvmveGPGHvpldeieanvklqkklckeaPfyvlGplvtDiapgYDhitsaiG 308
                                       +d  +++e+i+lgel+k+ar+++vq++veGPGHvp+deie +v+ +kklc++aP+y+lGplvtDiapgYDhit+aiG
  gi|298674697|ref|YP_003726447.1| 232 SDGPKFMEFITLGELIKKARNQNVQMFVEGPGHVPVDEIELSVQGMKKLCDGAPLYLLGPLVTDIAPGYDHITGAIG 308
                                       ***************************************************************************** PP

                      ThiC_Rad_SAM 309 aalaaaaGadllCyvtpaEHlglPdeedvkeGviaakiaahaadlakg..lkkarerdkalskaRkeldwekqfela 383
                                       ++la+++Gad+lC+ tp+EHl+lP++ed+keG ++++iaah adl+k   +++a++ d++++ aRk+ldw++q++la
  gi|298674697|ref|YP_003726447.1| 309 GTLAGMYGADFLCMTTPSEHLALPSVEDIKEGAMVTRIAAHSADLVKDgqKERAHSVDTEMAYARKNLDWNTQYNLA 385
                                       ***********************************************8446678899******************** PP

                      ThiC_Rad_SAM 384 ldpekareireeklpeeeeaCsmCgekCavkive 417
                                       +d+ekar+ire++ + e++aCsmCg+ Ca++iv+
  gi|298674697|ref|YP_003726447.1| 386 IDSEKARSIRESRVT-ESDACSMCGDLCAMEIVK 418
                                       ***********9985.99*************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      588  (0.032796); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3230.25
//
Query:       gi|298674698|ref|YP_003726448.1|  [L=123]
Description: hypothetical protein Metev_0751 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 916.28
//
Query:       gi|298674699|ref|YP_003726449.1|  [L=130]
Description: methionine-R-sulfoxide reductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-58  196.1   0.2    1.7e-58  195.9   0.2    1.0  1  SelR            SelR domain
      0.008   16.4   0.1      0.016   15.4   0.1    1.6  1  Yippee-Mis18    Yippee zinc-binding/DNA-binding /Mis18, centr
  ------ inclusion threshold ------
       0.04   13.4   0.5        5.1    6.7   0.2    2.6  2  TF_Zn_Ribbon    TFIIB zinc-binding
      0.041   13.8   0.6        2.6    8.0   0.1    2.3  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
      0.053   13.4   0.1         13    5.8   0.0    2.2  2  ADD_ATRX        Cysteine Rich ADD domain
      0.053   13.2   1.3        4.4    7.1   0.1    2.2  2  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
      0.066   13.4   2.3        4.1    7.7   0.2    2.3  2  Ribosomal_L37e  Ribosomal protein L37e
      0.081   12.7   0.4       0.96    9.2   0.1    2.2  2  Ribosomal_S27e  Ribosomal protein S27
      0.085   11.7   0.3        1.6    7.5   0.1    2.0  2  HECT_2          HECT-like Ubiquitin-conjugating enzyme (E2)-b
       0.52   10.4   2.3        9.4    6.4   0.0    2.9  3  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
       0.56   10.2   3.4        4.5    7.3   0.4    2.3  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain


Domain annotation for each model (and alignments):
>> SelR  SelR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.9   0.2   1.1e-61   1.7e-58       1     120 [.      10     128 ..      10     129 .. 0.99

  Alignments for each domain:
  == domain 1  score: 195.9 bits;  conditional E-value: 1.1e-61
                                       HHHCTSHCCHHHHHHHTT-SSTTSSSTSS--SSCEEEETTTS-EEEECCCCE-STTSSSEESS-STTTTEEEEEEEC CS
                              SelR   1 elkkkLtpeqyevlrekgterpftgeyekekekGvyecavcgepLfssetkfdsgcGwpsFaeaikeeavkekkdts 77 
                                       e+kk+Ltpeqy+vlrekgte+pftg+y+++k+kG+y+ca+cg++Lfssetk+dsg+GwpsF+++i+e+++++k+d s
  gi|298674699|ref|YP_003726449.1|  10 EWKKELTPEQYYVLREKGTEPPFTGKYYQNKRKGIYRCAGCGQELFSSETKYDSGTGWPSFWAPISEDRIETKTDYS 86 
                                       7**************************************************************************** PP

                                       TTSEEEEEEETTCECEEEEEECTSSSSS.SEEEEE-CCCEEEE CS
                              SelR  78 lgmertevvcakcdahlGhvFedgpkpttgkrycinsvslkfk 120
                                       ++mertev+c++c++hlGhvF+dgp+pt gkryc+nsv+l+fk
  gi|298674699|ref|YP_003726449.1|  87 FSMERTEVMCSRCGGHLGHVFNDGPQPT-GKRYCLNSVALDFK 128
                                       **************************95.*************8 PP

>> Yippee-Mis18  Yippee zinc-binding/DNA-binding /Mis18, centromere assembly
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1     1e-05     0.016       3      86 ..      45     121 ..      43     129 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1e-05
                                       EEETTTS-EEEECCCEEEEECCCEEEES---CCCEEEECEEEETTSTTEEEEEEEETTT--EEEEEEEECSCCCCCC CS
                      Yippee-Mis18   3 fqCkkCktilgdslqlvsegralnivvlkkvtrnvvvgkelvtdeegkctystlsCkgCnsvlGwkYksteeelkyk 79 
                                       ++C+ C ++l  s    ++g+ +  +     ++++ +++  + +     + +++ C+ C+ +lG ++++ ++  + k
  gi|298674699|ref|YP_003726449.1|  45 YRCAGCGQELFSSETKYDSGTGWPSFWAPISEDRIETKTDYSFS----MERTEVMCSRCGGHLGHVFNDGPQP-TGK 116
                                       68999999999999999999998888888888889988888888....66799***************98876.233 PP

                                       CTCEEEE CS
                      Yippee-Mis18  80 rglfile 86 
                                       r  ++l+
  gi|298674699|ref|YP_003726449.1| 117 R--YCLN 121
                                       3..4444 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.015        24      16      28 ..      41      53 ..      33      70 .. 0.63
   2 ?    6.7   0.2    0.0031       5.1      16      26 ..      90     100 ..      81     104 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.015
                                      STTCEEESSSSBE CS
                      TF_Zn_Ribbon 16 ergelvCtdCGlV 28
                                        g ++C  CG  
  gi|298674699|ref|YP_003726449.1| 41 RKGIYRCAGCGQE 53
                                      567799****743 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0031
                                       STTCEEESSSS CS
                      TF_Zn_Ribbon  16 ergelvCtdCG 26 
                                       er+e+ C++CG
  gi|298674699|ref|YP_003726449.1|  90 ERTEVMCSRCG 100
                                       89********7 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1    0.0016       2.6      25      34 ..      45      54 ..      27      58 .. 0.76
   2 ?    4.1   0.1     0.027        45      26      35 ..      95     104 ..      81     106 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0016
                    Zn_ribbon_SprT 25 YrCrrCkgtL 34
                                      YrC  C+++L
  gi|298674699|ref|YP_003726449.1| 45 YRCAGCGQEL 54
                                      7777777766 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.027
                    Zn_ribbon_SprT  26 rCrrCkgtLr 35 
                                        C rC+g+L+
  gi|298674699|ref|YP_003726449.1|  95 MCSRCGGHLG 104
                                       6999999997 PP

>> ADD_ATRX  Cysteine Rich ADD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0077        13       6      23 ..      39      56 ..      35      61 .. 0.79
   2 ?    5.5   0.0    0.0094        15       8      25 ..      91     107 ..      85     110 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0077
                          ADD_ATRX  6 keleeivsCtaCgqqvnh 23
                                      ++++ i  C+ Cgq+++ 
  gi|298674699|ref|YP_003726449.1| 39 NKRKGIYRCAGCGQELFS 56
                                      55678899******9975 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0094
                          ADD_ATRX   8 leeivsCtaCgqqvnhfq 25 
                                       +   v C+ Cg ++ h+ 
  gi|298674699|ref|YP_003726449.1|  91 R-TEVMCSRCGGHLGHVF 107
                                       3.359*********9975 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.2     0.011        18      40      52 ..      40      52 ..      33      54 .. 0.77
   2 ?    7.1   0.1    0.0027       4.4      17      43 ..      88     114 ..      81     122 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.011
                    zinc_ribbon_10 40 leevkyrCpkCga 52
                                      +++  yrC+ Cg+
  gi|298674699|ref|YP_003726449.1| 40 KRKGIYRCAGCGQ 52
                                      55668******96 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0027
                    zinc_ribbon_10  17 aknryalICskChshnGlapkeeleev 43 
                                        ++r  + Cs C  h G + ++ ++++
  gi|298674699|ref|YP_003726449.1|  88 SMERTEVMCSRCGGHLGHVFNDGPQPT 114
                                       5678999**********9977766666 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.2    0.0025       4.1      11      41 ..      39      69 ..      25      70 .. 0.76
   2 ?    5.5   0.1     0.012        19      14      25 ..      91     102 ..      86     109 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0025
                    Ribosomal_L37e 11 qkkktHilCrrCgkrsyhvqkktCascGyps 41
                                      +k+k   +C  Cg++ +  ++k+ +  G+ps
  gi|298674699|ref|YP_003726449.1| 39 NKRKGIYRCAGCGQELFSSETKYDSGTGWPS 69
                                      45566789*************9999999986 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.012
                    Ribosomal_L37e  14 ktHilCrrCgkr 25 
                                       +t ++C rCg +
  gi|298674699|ref|YP_003726449.1|  91 RTEVMCSRCGGH 102
                                       57899****976 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.17   2.7e+02      28      36 ..      46      54 ..      40      58 .. 0.75
   2 ?    9.2   0.1   0.00059      0.96      19      37 ..      86     104 ..      81     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.17
                                      EESSSTCEE CS
                    Ribosomal_S27e 28 kCisCgkvL 36
                                       C  Cg+ L
  gi|298674699|ref|YP_003726449.1| 46 RCAGCGQEL 54
                                      588888766 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00059
                                       EESS-SS-EEESSSTCEEE CS
                    Ribosomal_S27e  19 vFshaatvvkCisCgkvLv 37 
                                        Fs   t v+C  Cg  L+
  gi|298674699|ref|YP_003726449.1|  86 SFSMERTEVMCSRCGGHLG 104
                                       59999**********9886 PP

>> HECT_2  HECT-like Ubiquitin-conjugating enzyme (E2)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.024        39     102     130 ..      30      61 ..       3      77 .. 0.68
   2 ?    7.5   0.1     0.001       1.6     205     226 ..      86     107 ..      74     129 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.024
                            HECT_2 102 vpWsakdlsa..etslrCrsCknvllks.rki 130
                                        p + k  ++  +   rC  C+++l++s +k+
  gi|298674699|ref|YP_003726449.1|  30 PPFTGKYYQNkrKGIYRCAGCGQELFSSeTKY 61 
                                       46666666665347789******999984444 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.001
                            HECT_2 205 tkpkkeeslsCkrCkatlGeed 226
                                       + ++++++++C+rC+ +lG++ 
  gi|298674699|ref|YP_003726449.1|  86 SFSMERTEVMCSRCGGHLGHVF 107
                                       4568999************875 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1      0.25   4.1e+02      28      46 ..       6      22 ..       3      29 .. 0.71
   2 ?    6.4   0.0    0.0058       9.4      10      35 ..      38      63 ..      29      66 .. 0.80
   3 ?    1.0   0.0      0.28   4.6e+02      13      23 ..      90     100 ..      73     103 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.25
                          zf-Mss51 28 cseehwedDyeahleicdt 46
                                       see+w+++ +   e ++ 
  gi|298674699|ref|YP_003726449.1|  6 KSEEEWKKELT--PEQYYV 22
                                      69*****9887..333444 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0058
                          zf-Mss51 10 tapkhvdfeCpdCGiptycseehwed 35
                                      +++++  + C  CG   + se ++ +
  gi|298674699|ref|YP_003726449.1| 38 QNKRKGIYRCAGCGQELFSSETKYDS 63
                                      45777789*************99875 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.28
                          zf-Mss51  13 khvdfeCpdCG 23 
                                       ++ ++ C +CG
  gi|298674699|ref|YP_003726449.1|  90 ERTEVMCSRCG 100
                                       677889****9 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.4    0.0028       4.5      28      45 ..      35      52 ..      31      53 .. 0.87
   2 ?    3.7   0.2     0.037        61      19      27 ..      94     102 ..      81     119 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0028
                     Zn_Tnp_IS1595 28 kayriktrglfqCkeCrk 45
                                      k+y+ k+ g ++C+ C+ 
  gi|298674699|ref|YP_003726449.1| 35 KYYQNKRKGIYRCAGCGQ 52
                                      78999999********86 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.037
                     Zn_Tnp_IS1595  19 fvCPhCgsr 27 
                                       + C +Cg+ 
  gi|298674699|ref|YP_003726449.1|  94 VMCSRCGGH 102
                                       457777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 921.49
//
Query:       gi|298674700|ref|YP_003726450.1|  [L=66]
Description: hypothetical protein Metev_0753 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.13   12.5   0.0       0.14   12.5   0.0    1.0  1  Glyco_hydro_67N  Glycosyl hydrolase family 67 N-terminus


Domain annotation for each model (and alignments):
>> Glyco_hydro_67N  Glycosyl hydrolase family 67 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   7.8e-06      0.14      29      79 ..       3      55 ..       1      64 [. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.8e-06
                                      -SHHHHHHHHHHHHHHHHHHTS---EE-SS--SSEEEEE-TTT-HH..HHHT- CS
                   Glyco_hydro_67N 29 atstievakqELkeglkgilgkelkvsseekkessilvgtleelae..iesla 79
                                      +++ i  +k+EL+eg+k +   +  + +++ +++s l++t+++ +    ++++
  gi|298674700|ref|YP_003726450.1|  3 ESNSIGKIKSELQEGIKFVKCYKCGCMENTLQNCSHLIATIDTDEPleLRNKR 55
                                      56788899*********************************987763344444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 483.73
//
Query:       gi|298674701|ref|YP_003726451.1|  [L=264]
Description: type 11 methyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-38  131.0   0.1    4.8e-38  130.3   0.1    1.3  1  Methyltransf_31  Methyltransferase domain
    3.8e-23   81.9   0.6    7.9e-23   80.9   0.0    1.8  1  Methyltransf_11  Methyltransferase domain
    2.5e-22   79.4   0.2    5.4e-22   78.3   0.0    1.7  1  Methyltransf_25  Methyltransferase domain
    4.8e-19   68.6   0.8    2.5e-18   66.3   0.3    2.2  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    4.2e-13   49.9   0.1    8.3e-13   48.9   0.1    1.5  1  Methyltransf_12  Methyltransferase domain
    1.9e-10   40.8   0.0    3.6e-10   39.9   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
      3e-10   40.2   0.0    4.8e-10   39.6   0.0    1.4  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    6.8e-09   35.5   0.2    9.2e-09   35.1   0.2    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    6.3e-06   25.9   0.1    1.3e-05   24.8   0.1    1.5  1  MTS              Methyltransferase small domain
      2e-05   24.4   0.1    8.5e-05   22.3   0.1    1.8  2  UPF0020          Putative RNA methylase family UPF0020
    2.4e-05   23.8   0.0    3.3e-05   23.3   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
    2.4e-05   24.3   0.5    5.2e-05   23.2   0.5    1.7  1  Methyltransf_8   Hypothetical methyltransferase
    0.00012   21.1   0.0    0.00027   20.0   0.0    1.5  1  Methyltransf_9   Protein of unknown function (DUF1698)
     0.0018   17.6   0.0     0.0026   17.1   0.0    1.2  1  Methyltransf_2   O-methyltransferase domain
     0.0022   18.0   0.0     0.0041   17.1   0.0    1.4  1  Methyltransf_32  Methyltransferase domain
     0.0041   16.3   0.0      0.015   14.4   0.0    1.9  2  Fibrillarin      Fibrillarin
     0.0054   15.9   0.1     0.0074   15.4   0.1    1.2  1  DREV             DREV methyltransferase
     0.0075   15.8   0.0      0.019   14.4   0.0    1.7  2  Methyltransf_4   Putative methyltransferase
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.023   14.7   0.0    1.6  1  ADH_zinc_N       Zinc-binding dehydrogenase
      0.037   13.8   0.1      0.061   13.1   0.1    1.4  1  Met_10           Met-10+ like-protein
      0.057   12.6   0.0      0.081   12.1   0.0    1.3  1  Methyltransf_3   O-methyltransferase
      0.091   12.2   0.2       0.58    9.6   0.1    2.1  2  CheR             CheR methyltransferase, SAM binding domain
       0.11   11.9   0.7       0.21   11.0   0.4    1.5  1  TehB             Tellurite resistance protein TehB


Domain annotation for each model (and alignments):
>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.3   0.1   6.1e-41   4.8e-38       2     152 .]      74     220 ..      73     220 .. 0.96

  Alignments for each domain:
  == domain 1  score: 130.3 bits;  conditional E-value: 6.1e-41
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDli 78 
                                       +kg +vlDlG+G+G+++f +a+++ +++ v+G+D++++++e+A++na k +++nveF+ g+ie+l+  l d+++D++
  gi|298674701|ref|YP_003726451.1|  74 KKGEVVLDLGSGAGFDCFLAADKVDEDGLVIGVDMTPDMVEKAKNNAVKDNYTNVEFRLGEIENLP--LDDNSVDVV 148
                                       7899**************************************************************..99******* PP

                   Methyltransf_31  79 lsnevlnaladpdkileeiervlkpggilliedprllaelpakveeeskay.evvegakigtqkdelyelleeag 152
                                       +sn+v+n+ +d++k+++ + rvlkp+g+l+++d+ ll++lp++++++ +ay ++++ga     k+++ +l+e+ag
  gi|298674701|ref|YP_003726451.1| 149 ISNCVINLSPDKEKVFNDVYRVLKPDGRLVVSDIVLLQDLPESIRNSIEAYvGCISGAL---KKEDYLDLIEKAG 220
                                       *************************************************9999998888...8988888888876 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.9   0.0     1e-25   7.9e-23       1      96 []      80     179 ..      80     179 .. 0.97

  Alignments for each domain:
  == domain 1  score: 80.9 bits;  conditional E-value: 1e-25
                                       EEET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg...arvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhh 73 
                                       Ld+G+G+G  +   a+++   + v+gvD+++ m++ ak++a++++  +vef+ +++e+lp+ dns+D+v+s+ v++ 
  gi|298674701|ref|YP_003726451.1|  80 LDLGSGAGFDCFLAADKVdedGLVIGVDMTPDMVEKAKNNAVKDNYtNVEFRLGEIENLPLDDNSVDVVISNCVINL 156
                                       8**************8888889*********************999******************************* PP

                                       -CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  74 vedpekalkeiaRvLkpgGllvi 96 
                                        +d ek+++ ++RvLkp+G+lv+
  gi|298674701|ref|YP_003726451.1| 157 SPDKEKVFNDVYRVLKPDGRLVV 179
                                       ********************996 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.3   0.0   6.9e-25   5.4e-22       1      97 []      79     175 ..      79     175 .. 0.93

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 6.9e-25
                                       EEEET-TTSHHHHHHHCTS.TSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEEST.G CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrl.gkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssga.l 74 
                                       vLdlG G G +++ +a+++ +++ v+gvD++++m+e+a+++a ++++ nvef+ g++e+lp++d+s+D+v+s ++ +
  gi|298674701|ref|YP_003726451.1|  79 VLDLGSGAGFDCFLAADKVdEDGLVIGVDMTPDMVEKAKNNAVKDNYtNVEFRLGEIENLPLDDNSVDVVIS-NCvI 154
                                       9******************669********************998889************************.5735 PP

                                       GGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  75 hhlsdedlekalkeiarvLkpgG 97 
                                       ++ s +d ek+++ ++rvLkp+G
  gi|298674701|ref|YP_003726451.1| 155 NL-S-PDKEKVFNDVYRVLKPDG 175
                                       55.5.6889*************9 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   0.3   3.2e-21   2.5e-18      44     152 ..      72     180 ..      68     200 .. 0.92
   2 ?    0.0   0.0      0.57   4.5e+02     201     217 ..     209     225 ..     192     231 .. 0.83

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 3.2e-21
                                       -S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEE CS
                   Ubie_methyltran  44 avkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvv 120
                                       + k+g+ vlD+ +G+g   f  +d+v+e g v+++D+ ++m++ +++ + ++ ++n+ef  ++ e+Lp +d+s Dvv
  gi|298674701|ref|YP_003726451.1|  72 SLKKGEVVLDLGSGAGFDCFLAADKVDEDGLVIGVDMTPDMVEKAKNNAVKDNYTNVEFRLGEIENLPLDDNSVDVV 148
                                       5689***********************************************************************98 PP

                                       EEES-GGG-S-HHHHHHHHHHHEEEEEEEEEE CS
                   Ubie_methyltran 121 tvsfGlrnvtDklkaLkeayrvlkpGGrlvvl 152
                                            +   +Dk+k+++++yrvlkp Grlvv 
  gi|298674701|ref|YP_003726451.1| 149 ISNCVINLSPDKEKVFNDVYRVLKPDGRLVVS 180
                                       6666666678*******************985 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.57
                                       HHHHHHHHHHTTEEEEE CS
                   Ubie_methyltran 201 qetlkeliedaGfksve 217
                                       +e++ +lie+aGfk ++
  gi|298674701|ref|YP_003726451.1| 209 KEDYLDLIEKAGFKDIQ 225
                                       577889*******9886 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.1   1.1e-15   8.3e-13       1      99 []      80     177 ..      80     177 .. 0.81

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 1.1e-15
                   Methyltransf_12   1 LeiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvvasnv 75 
                                       L++G+G G   +  ++k  +d  ++gvD  p+++e+ak+   k +  n   ve++  ++++l+   +s+D+v++++v
  gi|298674701|ref|YP_003726451.1|  80 LDLGSGAGFDCFLAADKVdEDGLVIGVDMTPDMVEKAKNNAVKDNYTN---VEFRLGEIENLPLDdNSVDVVISNCV 153
                                       8*****************8888888*********77777766666544...4444444333333345********** PP

                   Methyltransf_12  76 lhhlkdirevldnirklLkpgGrl 99 
                                       ++  +d+++v++ ++++Lkp+Grl
  gi|298674701|ref|YP_003726451.1| 154 INLSPDKEKVFNDVYRVLKPDGRL 177
                                       **********************97 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.0   4.6e-13   3.6e-10      19     161 ..      72     222 ..      64     226 .. 0.72

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 4.6e-13
                   Methyltransf_23  19 klraggrvLdiGcGtGillevlrengf...svtgvDlspeaveiae...kakkaqkdqfdeqeaae...pqgkfdlI 86 
                                        l++g  vLd+G G G  + ++++++     v+gvD+ p +ve+a+    ++++ ++ f+  e+++   ++++ d++
  gi|298674701|ref|YP_003726451.1|  72 SLKKGEVVLDLGSGAGFDCFLAADKVDedgLVIGVDMTPDMVEKAKnnaVKDNYTNVEFRLGEIENlplDDNSVDVV 148
                                       489999**********98888888877665699***********9776655555555554445554777888***** PP

                   Methyltransf_23  87 vlrevlehvpdppellrqiatllkpgGylllseplaslkedrllldwlylvpagrhisffsarslkelleeaGle 161
                                       +++ v++  pd +++++ +++ lkp+G+l++s++   +   +++++   ++  g  +     +++ +l e+aG++
  gi|298674701|ref|YP_003726451.1| 149 ISNCVINLSPDKEKVFNDVYRVLKPDGRLVVSDIVLLQDLPESIRN-SIEAYVGCISGALKKEDYLDLIEKAGFK 222
                                       *********************************7444334444332.3333332222334445555566666665 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.0   6.1e-13   4.8e-10      68     132 ..      69     134 ..      62     179 .. 0.94

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 6.1e-13
                                       HTT.--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES- CS
                              PCMT  68 lle.lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgD 132
                                       +l  lkkg+ vL++GsG+G+   + a  v e+g+v++++ ++++ve+ak+n  k++++nv ++ g+
  gi|298674701|ref|YP_003726451.1|  69 YLAsLKKGEVVLDLGSGAGFDCFLAADKVDEDGLVIGVDMTPDMVEKAKNNAVKDNYTNVEFRLGE 134
                                       5666*********************************************************99885 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.2   1.2e-11   9.2e-09     159     264 ..      73     185 ..      68     220 .. 0.80

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 1.2e-11
                              PrmA 159 vkegeevlDvGtGSGiLa.iaaakLgak.kvvavDiDevAvkvakeNaelNkvea.klevalseell.keekadviv 231
                                       +k+ge vlD+G G+G    +aa k++ +  v++vD+ +  v+ ak+Na + + ++ ++++   e+l+ +++++dv++
  gi|298674701|ref|YP_003726451.1|  73 LKKGEVVLDLGSGAGFDCfLAADKVDEDgLVIGVDMTPDMVEKAKNNAVKDNYTNvEFRLGEIENLPlDDNSVDVVI 149
                                       68999**********96538999998762699***************9887777769988777777754799***** PP

                              PrmA 232 aNILaevl...ielaedikklvkeggllilSGilke 264
                                       +N + +      +  +d+++++k++g+l++S i+  
  gi|298674701|ref|YP_003726451.1| 150 SNCVINLSpdkEKVFNDVYRVLKPDGRLVVSDIVLL 185
                                       **977654222789*****************99643 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.1   1.6e-08   1.3e-05      24     137 ..      70     179 ..      51     197 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.6e-08
                                       HHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTT.TSTTS- CS
                               MTS  24 letlpkelsgkvlDlGcGaGvlgaalakespeae.vtlvdvdarAlesakenleankle.vevvasdvle.eveekk 97 
                                       l  l+k   + vlDlG+GaG+    +a++ +e   v  vd     +e ak+n+ + +   ve++  ++ +  +++++
  gi|298674701|ref|YP_003726451.1|  70 LASLKK--GEVVLDLGSGAGFDCFLAADKVDEDGlVIGVDMTPDMVEKAKNNAVKDNYTnVEFRLGEIENlPLDDNS 144
                                       555655..6679*********99999999988876889*************987766665***9999987356799* PP

                                       EEEEEE---STTTCHCHHHHHHHHHHHHHHHEEEEEEEEE CS
                               MTS  98 fdlivsNPPfhagkatelavaeeliaeAkeaLkegGeLli 137
                                       +d+++sN  +  + +      e+++++  ++Lk++G+L++
  gi|298674701|ref|YP_003726451.1| 145 VDVVISNCVINLSPD-----KEKVFNDVYRVLKPDGRLVV 179
                                       *******99998888.....78999999999999999975 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.97   7.6e+02      89     143 ..      28      81 ..       2      87 .. 0.71
   2 !   22.3   0.1   1.1e-07   8.5e-05      78     129 ..     102     152 ..      90     173 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.97
                                       HHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----------HHHHHH CS
                           UPF0020  89 vqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerlgskkalek 143
                                       v ++ +  +  ++++l+ + + d ++++ ++++ ++  +np Y  +l++ + + +
  gi|298674701|ref|YP_003726451.1|  28 VSCCGSRESPEEISKLVGYTEEDLKNVP-RDSNLGLGCGNPVYLASLKKGEVVLD 81 
                                       6666777777788888899999999999.66688999999999999888776655 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 1.1e-07
                                       -EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE-- CS
                           UPF0020  78 klygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnp 129
                                        ++g+D+ + +v++a++Na k + +  +ef+  ++ +L+l++++vdv+++n 
  gi|298674701|ref|YP_003726451.1| 102 LVIGVDMTPDMVEKAKNNAVKDNYT-NVEFRLGEIENLPLDDNSVDVVISNC 152
                                       389*****************98876.69***********9999*******95 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   4.3e-08   3.3e-05      59     176 ..      72     191 ..      68     253 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 4.3e-08
                                       T--TT-EEEEES-TTSHHHHHHHHHH--E..EEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---...--SE CS
                              CMAS  59 elkpGmtlLdiGcGWGslvrraverydvk..vvglTlSkeqaklakkrvdeldlerkvevklldyedlde...kvdr 130
                                       +lk+G+ +Ld+G G G  +  a+++ d +  v+g+ +  +  ++ak++  + d+  +ve +l + e+l+     vd 
  gi|298674701|ref|YP_003726451.1|  72 SLKKGEVVLDLGSGAGFDCFLAADKVDEDglVIGVDMTPDMVEKAKNNAVK-DNYTNVEFRLGEIENLPLddnSVDV 147
                                       79***************999999987654339*******999999887554.5678899999999998543468999 PP

                                       EEEES-GGGTSGGGHHHHHHHHHHHS-TT-EEEEEEEEE--HHHHH CS
                              CMAS 131 vvsvgafehvgkenydtffkklkkllkedGllllhtitslhkkela 176
                                       v+s  +++    +  ++ f+ ++++lk+dG+l++  i+ l+    +
  gi|298674701|ref|YP_003726451.1| 148 VISNCVINLSP-D-KEKVFNDVYRVLKPDGRLVVSDIVLLQDLPES 191
                                       99988887543.3.46889***************999987765444 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.5   6.7e-08   5.2e-05     111     159 ..     133     182 ..      68     197 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 6.7e-08
                                       S-TTS-S--TT-EEEEEE.ES---SS-HHHHHHHHHHHEEEEEEEEEEEE CS
                    Methyltransf_8 111 cdlakvPledesvdvavf.clslmgtnladflkeanrvlkvGGllkvaev 159
                                        ++ ++Pl+d+svdv++  c+  ++ + ++  ++++rvlk+ G l v+++
  gi|298674701|ref|YP_003726451.1| 133 GEIENLPLDDNSVDVVISnCVINLSPDKEKVFNDVYRVLKPDGRLVVSDI 182
                                       5789************954999999*********************9987 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   3.4e-07   0.00027     115     270 ..      75     231 ..      67     237 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3.4e-07
                                       TT-EEEEET-TTSHHHHHHHH..CT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---.GGGS-T.---EEEEE CS
                    Methyltransf_9 115 kgrtildvGcgnGyhlwrmvg..egaklvvGidPselfliqfeavrkllgedqrahllplg.ieqlpe.leafdtvf 187
                                       kg ++ld+G g+G+  +  +   ++  lv+G+d +   +   +a ++ + ++  ++++ lg ie+lp   ++ d+v 
  gi|298674701|ref|YP_003726451.1|  75 KGEVVLDLGSGAGFDCFLAADkvDEDGLVIGVDMTPDMVE--KAKNNAVKDNYTNVEFRLGeIENLPLdDNSVDVVI 149
                                       6899**********99987652256779****98776654..34444455555555566655*****9889****** PP

                                       EES-GGG-S-HHHHHHHHHCTEEEEEEEEEEEE-BSS-TT-EE--SS-BTTBSS---EEBHHHHHHHHHHTT-EEEE CS
                    Methyltransf_9 188 smGvlyhrrsPldhllqlkdqlvkgGelvletlvieGdenavlvPedryakmrnvyfiPsaaalkvWlekvgfvdvr 264
                                       s  v+         + ++   l+ +G lv+  +v+  d  + +  +   a +  +      +     +ek+gf+d++
  gi|298674701|ref|YP_003726451.1| 150 SNCVINLSPDKEKVFNDVYRVLKPDGRLVVSDIVLLQDLPESIR-NSIEAYVGCISGALKKEDYLDLIEKAGFKDIQ 225
                                       *****988777888999*****************9999876543.23333333333333444455568999999999 PP

                                       EEEEEE CS
                    Methyltransf_9 265 ivdesv 270
                                       i+des 
  gi|298674701|ref|YP_003726451.1| 226 IIDESE 231
                                       999875 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.4e-06    0.0026      64     210 .]      77     222 ..      65     222 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.4e-06
                                       SEEEEET-TTSHHHHHHHHH-TT.-EEEEEE-.HHHHHHHHHHS-----TTEEEEES-TTTS---..--SEEEEESS CS
                    Methyltransf_2  64 kslvDvGGGtGalakaivsayPt.ikvivfDl.peVveaAkehlsageeervefvgGdffkdslP..eaDaillkrv 136
                                       ++++D+G G+G     ++ +  +   vi  D+ p+ ve+Ak+  + ++ ++vef  G++ + +l   + D+++ + v
  gi|298674701|ref|YP_003726451.1|  77 EVVLDLGSGAGFDCFLAADKVDEdGLVIGVDMtPDMVEKAKNNAVKDNYTNVEFRLGEIENLPLDdnSVDVVISNCV 153
                                       5677888888765554444444313344567659*********9999************955554534455555555 PP

                                       GGGS-HHHHHHHHHHHHHH--TT-EEEEEE----TTS---HHHHHHHHHHHHCSS-----HHHHHHHHHHCT-E CS
                    Methyltransf_2 137 lhDwsdekcvklLkrvkkalpagGkvivveavlgadpsgeletelvdlimlvqteGkeRteaeyeellseaGfs 210
                                       +   s +k  k+ ++v++ l+++G+++v + vl +d  ++ ++ + + ++  +  G  + +++y +l+++aGf+
  gi|298674701|ref|YP_003726451.1| 154 I-NLSPDK-EKVFNDVYRVLKPDGRLVVSDIVLLQDLPESIRNSI-EAYVGCI-SGALK-KEDYLDLIEKAGFK 222
                                       5.555444.6899*******************9988888888887.5566555.57665.46899999999996 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   5.3e-06    0.0041      25      91 ..      75     137 ..      61     169 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.3e-06
                   Methyltransf_32  25 galtvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfaelsiee 91 
                                       + + v+D+G+G g+  f  a+ +++    v+g+d+  ++veka++ a k +  + ++++f  ++ie+
  gi|298674701|ref|YP_003726451.1|  75 KGEVVLDLGSGAGFDCFLAAD-KVDEDGLVIGVDMTPDMVEKAKNNAVKDN--Y-TNVEFRLGEIEN 137
                                       56789**********999999.666799****************9999988..7.788887777765 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   1.9e-05     0.015      50     110 ..      55     115 ..      34     129 .. 0.87
   2 ?   -1.7   0.0       1.7   1.3e+03     172     207 ..     146     182 ..     140     190 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.9e-05
                                       TTTSHHHHHHHTT-S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHHH CS
                       Fibrillarin  50 pfrsKlaaailkglkelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlre 110
                                       p+ s l+ +  + +    +kkg+ vL lG+++G      +D v+e+g+v +v+++p ++ +
  gi|298674701|ref|YP_003726451.1|  55 PRDSNLGLGCGNPVYLASLKKGEVVLDLGSGAGFDCFLAADKVDEDGLVIGVDMTPDMVEK 115
                                       677888888888999999************************************9988765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.7
                                       EEEEEHHHHHSSSSHHHHHHHHHHHHHHTT.EEEEEE CS
                       Fibrillarin 172 lisikarsidvtkepeevfkeeveklkeeg.lkvleq 207
                                        ++i    i+   + e+vf++  + lk +g l v + 
  gi|298674701|ref|YP_003726451.1| 146 DVVISNCVINLSPDKEKVFNDVYRVLKPDGrLVVSDI 182
                                       4566667778888888888888888886431444555 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   9.5e-06    0.0074      91     190 ..      72     183 ..      65     222 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9.5e-06
                              DREV  91 sdqedkklldlGaGdGeitkrvaptfee.......vyatelsetmrdrlkkkky.nv...lsale.lqetdvkldli 155
                                       s ++ + +ldlG+G G      a+ ++e         + ++ e+ +++  k +y nv   l+++e l   d   d++
  gi|298674701|ref|YP_003726451.1|  72 SLKKGEVVLDLGSGAGFDCFLAADKVDEdglvigvDMTPDMVEKAKNNAVKDNYtNVefrLGEIEnLPLDDNSVDVV 148
                                       56677889********999999999999999555312223444444445566663334446778768888999**** PP

                              DREV 156 lclnlldrcfdplklledirsalepngrvivalvl 190
                                        +  +++   d  k+++d++ +l+p+gr +v+ ++
  gi|298674701|ref|YP_003726451.1| 149 ISNCVINLSPDKEKVFNDVYRVLKPDGRLVVSDIV 183
                                       *******************************9654 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   2.5e-05     0.019       3      60 ..      77     135 ..      75     151 .. 0.84
   2 ?   -2.5   0.0       3.9     3e+03      98     118 ..     162     181 ..     160     203 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.5e-05
                                       EEEEEET-TTS.HHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-C CS
                    Methyltransf_4   3 pvvleiGcGkG.eflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgda 60 
                                        vvl++G+G G +  +a  k + d +++G+++  ++v+k+ +++ +++++N++   g+ 
  gi|298674701|ref|YP_003726451.1|  77 EVVLDLGSGAGfDCFLAADKVDEDGLVIGVDMTPDMVEKAKNNAVKDNYTNVEFRLGEI 135
                                       689********556666667788999**************************9877775 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.9
                                       HHHHHHHHHEEEEEEEEEEES CS
                    Methyltransf_4  98 ellkelarvLkkgGvlelaTD 118
                                       ++ +++ rvLk+ G l++ +D
  gi|298674701|ref|YP_003726451.1| 162 KVFNDVYRVLKPDGRLVV-SD 181
                                       566788899999999864.45 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.9e-05     0.023      17      88 ..     103     180 ..      97     218 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.9e-05
                                       EEEEESSHHHHHHHHHTT.ESEEEETTTCHHHHHHHHHTT.TSSEEEEEESSC......SHHHHHHHHHCEEEEEEE CS
                        ADH_zinc_N  17 viavdsseeklelakklG.adevinykeadlverikeltg.gegvdvvfecvG......sgatleaalkllkpgGrl 85 
                                       vi+vd +++ +e+ak +   d + n  e     +i+ l   ++ vdvv+           ++++++ +++lkp+Grl
  gi|298674701|ref|YP_003726451.1| 103 VIGVDMTPDMVEKAKNNAvKDNYTNV-E-FRLGEIENLPLdDNSVDVVISNCVinlspdKEKVFNDVYRVLKPDGRL 177
                                       9***************9966777777.4.47788999985599****775433255557799*************** PP

                                       EEC CS
                        ADH_zinc_N  86 vvv 88 
                                       vv 
  gi|298674701|ref|YP_003726451.1| 178 VVS 180
                                       *96 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   7.8e-05     0.061      98     147 ..      73     123 ..      68     176 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.8e-05
                                       --TT-EEEETT-TTTCCH.HHCCHHTTSSEEEEEES-HHHHHHHHHHHHHT CS
                            Met_10  98 veegevVvdvfAGiGpfa.ipiakyskakrvlaidlnPesvkylkeniklN 147
                                        ++gevV+d+  G G+   +++ k  ++  v+++d+ P+ v+  k+n    
  gi|298674701|ref|YP_003726451.1|  73 LKKGEVVLDLGSGAGFDCfLAADKVDEDGLVIGVDMTPDMVEKAKNNAVKD 123
                                       689************854278889999************999888775443 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0    0.0001     0.081      43     106 ..      71     133 ..      59     185 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0001
                                       HHHHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES CS
                    Methyltransf_3  43 vklvnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekielieg 106
                                        +l     vl++G   G+  +  a ++ eDG ++ +d+ ++ +e a++   k  +   +e++ g
  gi|298674701|ref|YP_003726451.1|  71 ASLKKGEVVLDLGSGAGFDCFLAADKVDEDGLVIGVDMTPDMVEKAKNNAVKDNYT-NVEFRLG 133
                                       566777789***********************************999987776654.4666665 PP

>> CheR  CheR methyltransferase, SAM binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.35   2.7e+02      65      88 ..     101     124 ..      91     131 .. 0.80
   2 ?    9.6   0.1   0.00074      0.58     119     173 ..     127     179 ..     112     195 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.35
                                       EEEEEEESSCHHHHHHHHTEEECC CS
                              CheR  65 vkilAtDidlkvlekAkagvykee 88 
                                         ++++D+   ++ekAk+  +k++
  gi|298674701|ref|YP_003726451.1| 101 GLVIGVDMTPDMVEKAKNNAVKDN 124
                                       5689*************9887765 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00074
                                       TEEEEE--TTT-SGGG--EEEEEE-SSGGGC-CHHHHHHHHHHHCCEEEEEEEEE CS
                              CheR 119 lvkFeklnllekksvlgklDvifcrnvliYfdeetqekvlerfaeklkpgglLll 173
                                       +v+F+  ++ +     +++Dv+++ n +i ++ +++ekv +++++ lkp+g+L++
  gi|298674701|ref|YP_003726451.1| 127 NVEFRLGEIENLPLDDNSVDVVIS-NCVINLS-PDKEKVFNDVYRVLKPDGRLVV 179
                                       577777777663444567898876.8889887.5799****************98 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.4   0.00027      0.21      33     107 ..      78     156 ..      69     196 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00027
                                       EEEEES-TTSHHHHHHHHTT-E....EEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----S-.EEEEEEESS CS
                              TehB  33 kvldlgcgqgrnslylsllgyd....vtawdknensiafleeikekenlknistalydineaklder.ydfilstvv 104
                                        vldlg g g +  +l++   d    v  +d   + ++  ++ + k+n +n++ +l +i+++ ld++  d ++s  v
  gi|298674701|ref|YP_003726451.1|  78 VVLDLGSGAGFDC-FLAADKVDedglVIGVDMTPDMVEKAKNNAVKDNYTNVEFRLGEIENLPLDDNsVDVVISNCV 153
                                       589*******875.788777774455668999999*****************************9763799999988 PP

                                       GGG CS
                              TehB 105 lmf 107
                                       + +
  gi|298674701|ref|YP_003726451.1| 154 INL 156
                                       754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       777  (0.0433376); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 1808.90
//
Query:       gi|298674702|ref|YP_003726452.1|  [L=444]
Description: FAD-dependent pyridine nucleotide-disulfide oxidoreductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-54  185.0   0.5    2.2e-54  184.7   0.5    1.1  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.9e-21   76.4   0.0      3e-21   75.7   0.0    1.4  1  Pyr_redox_dim   Pyridine nucleotide-disulphide oxidoreductase
    1.1e-18   67.6   1.5    2.6e-14   53.5   0.1    3.3  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    1.1e-12   47.8   1.7    2.4e-10   40.1   0.1    2.1  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    4.3e-09   35.6   0.5     0.0019   17.0   0.1    3.0  3  HI0933_like     HI0933-like protein
    9.9e-07   28.2   0.8    1.7e-05   24.1   0.6    2.3  2  FAD_binding_2   FAD binding domain
    1.5e-06   27.9   0.0      0.002   17.5   0.0    2.4  2  FAD_oxidored    FAD dependent oxidoreductase
    2.2e-05   24.2   3.8    0.00062   19.4   3.8    2.5  1  DAO             FAD dependent oxidoreductase
    0.00017   21.8   0.2     0.0011   19.1   0.1    2.4  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    0.00026   20.4   0.6      0.033   13.5   0.2    2.4  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
     0.0003   20.0   1.7     0.0019   17.4   0.6    2.4  2  GIDA            Glucose inhibited division protein A
     0.0019   18.1   0.2       0.05   13.5   0.0    2.3  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
  ------ inclusion threshold ------
      0.014   14.4   0.1      0.025   13.6   0.1    1.4  1  Lycopene_cycl   Lycopene cyclase protein
      0.016   15.8   0.2        1.2    9.7   0.1    2.8  2  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
      0.025   14.8   0.0        0.1   12.9   0.0    2.1  1  TrkA_N          TrkA-N domain
      0.053   12.8   0.1       0.16   11.2   0.1    1.9  1  Thi4            Thi4 family
      0.068   12.4   0.0       0.25   10.6   0.0    1.8  2  FAD_binding_3   FAD binding domain
      0.083   12.3   0.1       0.43    9.9   0.0    2.1  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
       0.14   11.2   0.4         44    3.1   0.0    3.0  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
        0.2   10.5   1.1        1.1    8.0   0.1    2.0  2  Trp_halogenase  Tryptophan halogenase


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.7   0.5   2.4e-57   2.2e-54       1     294 []       4     318 ..       4     318 .. 0.94

  Alignments for each domain:
  == domain 1  score: 184.7 bits;  conditional E-value: 2.4e-57
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEE...TTHCHHHCSHHHHCHHHHHHHHHHHHH................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx................. RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve...legtclnggcllskallgvaedaeias................. 57 
                                       +dvvviG G AG ++a++ + ag +v++++    +gtc ++gc ++k+l+g ae  +                    
  gi|298674702|ref|YP_003726452.1|   4 YDVVVIGTGTAGSTVAHKCNSAGKNVAIIDhrpFGGTCALRGCDPKKVLVGGAELVDWNNrmketagldrdttinwt 80 
                                       69****************************9*********************99988777899************** PP

                                       .......HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECC CS
                                       .......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 .......evvkklnqgielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklv 127
                                                ++ +   ie+  ++++++ ++g +++ + k+ e    +i+ d++v+AtGs+pr l+i G+ e      
  gi|298674702|ref|YP_003726452.1|  81 slisfkrTFTQAFPDMIEKNFTSHGIDAYHGLACFSDDKTIEVGDDQIEGDYIVIATGSKPRELNILGE-E------ 150
                                       *****9855567788899999999*************999998888***********************.3...... PP

                                       SECHHHHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 128 rtldsaealklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgt 204
                                       ++++s+e ++l++lp ++v  GgGyi+ E+A  +a++g++  ++++++++l+++d+++ + + ea ++ G++v +g+
  gi|298674702|ref|YP_003726452.1| 151 HIITSDEFMELENLPGNVVFLGGGYISFEFANIAARAGSKPLILQRGENPLKTFDSDMVDVAVEASKDAGIDVLTGH 227
                                       4599************************************************************************* PP

                                       EEEEEEETTE..EEEEEETTSCEEEESEEEE-S-EEES-HHCS.HCCT-EEEETTEEE--TTSBES.STTEEE-GGG CS
                                       xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                       Pyr_redox_2 205 svkeidgnge..klevvledgeeidadlvvvavGvrpstelle.eklglelderggivvdeflrtn.vpgiyaiGDv 277
                                       +v++i+++g+  ++++++e+++++ +dlvv + G++++ + l+ +k ++e+ ++ gi v+e++++   p +ya+GD+
  gi|298674702|ref|YP_003726452.1| 228 KVTKIEKKGNlyEVTTENEKQNTFTTDLVVHGGGRSANIDELGlDKGNVEV-HKKGIAVNEYMQSPsNPRVYAAGDC 303
                                       **********6666677777777****************************.************955********** PP

                                       CTECCSS--HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 278 aggkggpelaqaAvqqG 294
                                       +  ++gp+l+++A  qG
  gi|298674702|ref|YP_003726452.1| 304 T--EEGPQLTPVAGLQG 318
                                       *..**********9887 PP

>> Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.7   0.0   3.4e-24     3e-21       1     107 [.     338     441 ..     338     444 .] 0.93

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 3.4e-24
                                       BEEEEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHH CS
                     Pyr_redox_dim   1 iptvvftdpevasvGlteeeAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgageliq 77 
                                       ip+vvft p++asvG+t++++k+ +   +v+  + ++ + ++  ++++   K+++d++t+k+lGahi+Gp+a+e+i+
  gi|298674702|ref|YP_003726452.1| 338 IPAVVFTLPPLASVGITKDDVKDTH---EVIYNDRSSWYSSKRLNFNHAASKIIIDKQTDKILGAHILGPEAEEVIN 411
                                       79***********************...88888888888888888999***************************** PP

                                       HHHHHHHTTSBHHHHHTSBSSSSSTGGGGH CS
                     Pyr_redox_dim  78 elavaikagltvedladtihihPtlsealk 107
                                        +a+a+++gl ++d+ + ++++P++   ++
  gi|298674702|ref|YP_003726452.1| 412 IFAMAMRYGLNASDVKNAVFTYPSVCSDIE 441
                                       ***********************9876665 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.2    0.0005      0.45       2      32 ..       6      36 ..       5      39 .. 0.94
   2 ?   -1.6   0.0       4.5     4e+03      29      55 ..      84     106 ..      80     111 .. 0.53
   3 !   53.5   0.1   2.9e-17   2.6e-14       1      80 [.     167     245 ..     167     248 .. 0.96

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0005
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversd 32
                                      vvv+G G+ g  +A   +  gk+V +++ ++
  gi|298674702|ref|YP_003726452.1|  6 VVVIGTGTAGSTVAHKCNSAGKNVAIIDHRP 36
                                      8**************************9875 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.5
                                       ESSSSSSTTSSHHHHHHHHHHHHHTTE CS
                         Pyr_redox  29 ersdkllrllDeeaskilqeklekngi 55 
                                         + ++     +++ ++++++++ +gi
  gi|298674702|ref|YP_003726452.1|  84 SFKRTFT----QAFPDMIEKNFTSHGI 106
                                       4444444....4455555555555555 PP

  == domain 3  score: 53.5 bits;  conditional E-value: 2.9e-17
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEE CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgvesvk 77 
                                       +vv++GgGyi  E+A+++a+ g+k  +++r++++l+ +D ++ ++  e  ++ gi+vl+++kv++ie++++ +++v+
  gi|298674702|ref|YP_003726452.1| 167 NVVFLGGGYISFEFANIAARAGSKPLILQRGENPLKTFDSDMVDVAVEASKDAGIDVLTGHKVTKIEKKGN-LYEVT 242
                                       59*****************************************************************9998.89999 PP

                                       EET CS
                         Pyr_redox  78 lkd 80 
                                       +++
  gi|298674702|ref|YP_003726452.1| 243 TEN 245
                                       975 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.1    0.0031       2.8       1      30 [.       7      35 ..       1      42 [. 0.64
   2 !   40.1   0.1   2.7e-13   2.4e-10     115     305 .]     120     301 ..     113     301 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0031
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg 30
                                      ++iG G aG ++a++++ ag  ++ i++  
  gi|298674702|ref|YP_003726452.1|  7 VVIGTGTAGSTVAHKCNSAGK-NVAIIDHR 35
                                      466666666666666666665.56666654 PP

  == domain 2  score: 40.1 bits;  conditional E-value: 2.7e-13
                       Pyr_redox_3 115 evetsketyeAkkviiAtGefdkPnklnipGeeklvkhyskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVt 191
                                       ++e   +++e ++++iAtG   kP+ lni Gee + + + ++ e++++   +vv  Gg+  +++ A   +r+g++  
  gi|298674702|ref|YP_003726452.1| 120 TIEVGDDQIEGDYIVIATGS--KPRELNILGEE-HIITSDEFMELENLP-GNVVFLGGGYISFEFANIAARAGSKPL 192
                                       67777899***********9..**********9.899999999997765.578889999999*************** PP

                       Pyr_redox_3 192 vvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeykvktedgkkvevkddvvla.tGy 267
                                       ++ rg+       +p  +   d+ +   e++k   i+vl+ ++v++i++k + y+v+te++k+ + ++d v+   G 
  gi|298674702|ref|YP_003726452.1| 193 ILQRGE-------NPLKTFDSDMVDVAVEASKDAGIDVLTGHKVTKIEKKGNLYEVTTENEKQNTFTTDLVVHgGGR 262
                                       ****97.......4556666777777777777766****************************99999999994455 PP

                       Pyr_redox_3 268 kpdlsf..lkkslfeldedgrpvlteeteetnvpglflaG 305
                                       + +++   l+k  +e   ++ ++++e  ++   p ++ aG
  gi|298674702|ref|YP_003726452.1| 263 SANIDElgLDKGNVEV-HKKGIAVNEYMQSPSNPRVYAAG 301
                                       5667772345566666.6777899999999999***9998 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   2.1e-06    0.0019       1      32 [.       4      35 ..       4      42 .. 0.94
   2 ?    0.2   0.0      0.26   2.4e+02     144     165 ..     120     140 ..     108     142 .. 0.85
   3 !   14.5   0.0   1.2e-05     0.011     109     167 ..     206     264 ..     196     303 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.1e-06
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVllleka 32
                                      +dv+viG G AG   A +++++gk+V+++++ 
  gi|298674702|ref|YP_003726452.1|  4 YDVVVIGTGTAGSTVAHKCNSAGKNVAIIDHR 35
                                      59****************************97 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.26
                                       EEEE.TTEEEEESEEEE----S CS
                       HI0933_like 144 rvktkseeeleadklvlAtGGl 165
                                       ++++ +++++e d++v+AtG++
  gi|298674702|ref|YP_003726452.1| 120 TIEV-GDDQIEGDYIVIATGSK 140
                                       6777.899************86 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 1.2e-05
                                       HHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE..TTEEEEESEEEE----SS- CS
                       HI0933_like 109 edivdallkelkeagvklrletevksvekeedgkfrvkt.kseeeleadklvlAtGGlSi 167
                                       +d+vd+ +++ k+ag+++ + ++v+++ek+ +  ++v+t +++++  ++ lv+  GG S+
  gi|298674702|ref|YP_003726452.1| 206 SDMVDVAVEASKDAGIDVLTGHKVTKIEKKGNL-YEVTTeNEKQNTFTTDLVVHGGGRSA 264
                                       68899999*******************886666.*****7777888899999999**995 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.6   1.9e-08   1.7e-05       1      37 [.       5      40 ..       5      45 .. 0.90
   2 ?    2.2   0.0     0.083        74     142     203 ..     207     263 ..      56     321 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.9e-08
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgga 37
                                      Dv+ViG+G AG + A++++ aG++va+++  +  gg+
  gi|298674702|ref|YP_003726452.1|  5 DVVVIGTGTAGSTVAHKCNSAGKNVAIIDHRPF-GGT 40
                                      9***************************99874.665 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.083
                                       HHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----G CS
                     FAD_binding_2 142 allarlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfg 203
                                        ++ + ve+ ++ag+d+++ ++++++   +g  + ++ e   +++ +    + +v++ gG +
  gi|298674702|ref|YP_003726452.1| 207 DMVDVAVEASKDAGIDVLTGHKVTKIEK-KGNLYEVTTE---NEK-QNTFTTDLVVHGGGRS 263
                                       68889999999999*********99966.5555555555...222.2222345666666665 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.3e-06     0.002       1      36 [.       5      39 ..       5     104 .. 0.91
   2 !    8.0   0.0    0.0018       1.6      83     139 ..     203     256 ..     168     262 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.3e-06
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGG 36
                                      DvvV+G g+aG + A  +  aG++v++++ r++  G
  gi|298674702|ref|YP_003726452.1|  5 DVVVIGTGTAGSTVAHKCNSAGKNVAIIDHRPFG-G 39
                                      9******************************984.4 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0018
                      FAD_oxidored  83 tfepevakavleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvf 139
                                       tf+ +++  v+ e  ++ag++vl++++++++ek+g ++ +vt+e+ e++ t++ +++
  gi|298674702|ref|YP_003726452.1| 203 TFDSDMV-DVAVEASKDAGIDVLTGHKVTKIEKKG-NLYEVTTEN-EKQNTFTTDLV 256
                                       6666554.4555666888****************8.9******86.55777766655 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   3.8     7e-07   0.00062       1     203 [.       5     263 ..       5     299 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 7e-07
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSE....EEEESSSSTHHSTH................ CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrns....gllhsglrylpeas................ 55 
                                       dvv+iG G +G+++A+    +g  V++++ +  +g g+    +    ++l +g +   ++                 
  gi|298674702|ref|YP_003726452.1|   5 DVVVIGTGTAGSTVAHKCNSAGknVAIIDHR-PFG-GTCALRGcdpkKVLVGGAELVDWNNrmketagldrdttinw 79 
                                       9*****************888899*******.888.66665555887888887754444446667777889999999 PP

                                       ....HHHHHHHHHH.HHHHHHHHHHSST.....TSEEEEEEEEEESSHHHHHHHHHHHHHH...HHTTT..TEEEEE CS
                               DAO  56 ....elarlsleal.eelreleeelgid.....idyrrtGllslaadeeelealdkllall...leagl..daelld 117
                                            + r   +a+ +++++   ++gid       +    ++ +++d+ e +++   +a +   +e+++  ++++++
  gi|298674702|ref|YP_003726452.1|  80 tsliSFKRTFTQAFpDMIEKNFTSHGIDayhglACFSDDKTIEVGDDQIEGDYI--VIATGskpRELNIlgEEHIIT 154
                                       988844455555542333333333344222122568889999998776555554..4444444755666645579** PP

                                       HHHHHHHSTTSTTTSEEEEETTEEEEEHHHHHHH...........................HHHHHHHTT-EEEESE CS
                               DAO 118 aeevrelepalpgllgalfypdtgqvdpakltaa...........................laraaealGveilegt 167
                                       ++e +ele     l g +++ ++g +  + +  a                             +a +++G+++l+g+
  gi|298674702|ref|YP_003726452.1| 155 SDEFMELEN----LPGNVVFLGGGYISFEFANIAaragskplilqrgenplktfdsdmvdvAVEASKDAGIDVLTGH 227
                                       *99*****4....5566666666666444444445667778****************9996556668889******* PP

                                       CEEEEEEEETCEEEEEEECT.EEE.E.EEEEEEE--GGG CS
                               DAO 168 evtgleeedgkvwgverttp.gen.d.aadavVnaaGaw 203
                                       +vt++e+  g +++v  tt+ + + + + d vV   G  
  gi|298674702|ref|YP_003726452.1| 228 KVTKIEK-KGNLYEV--TTEnEKQnTfTTDLVVHGGGRS 263
                                       *****76.4678888..5543444222435566655544 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   1.3e-06    0.0011       1      35 [.       8      42 ..       8      62 .. 0.84
   2 ?   -1.1   0.0       2.6   2.3e+03       3      30 ..     172     199 ..     171     200 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.3e-06
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGra 35
                                      ++G+G +G++ A+ +  ag++v ++++r+  G +a
  gi|298674702|ref|YP_003726452.1|  8 VIGTGTAGSTVAHKCNSAGKNVAIIDHRPFGGTCA 42
                                      8**************************97555554 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.6
                                       --SHHHHHHHHHHHCCTEEEEEE-SSSS CS
                     NAD_binding_8   3 GaGlsGlvaAylLakagfdvlllekrdr 30 
                                       G+G  +  +A  +a+ag + l+l++++ 
  gi|298674702|ref|YP_003726452.1| 172 GGGYISFEFANIAARAGSKPLILQRGEN 199
                                       999999999999*********9999875 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.2   3.7e-05     0.033      30      61 ..       5      36 ..       1      40 [. 0.93
   2 ?    4.9   0.0     0.016        14      28      78 ..     165     239 ..     161     260 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.7e-05
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSH CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrp 61
                                       v+viG G+aG   ++ +++ g +V ++D rp
  gi|298674702|ref|YP_003726452.1|  5 DVVVIGTGTAGSTVAHKCNSAGKNVAIIDHRP 36
                                      79***************************986 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.016
                                       --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTTCECEE.......................H CS
                       AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgakVtvlDvrparleqles.lgakfvev.......................l 78 
                                       p++v+ +GgG    + +++a++ g k  +l   ++ l+ ++s +    ve+                       +
  gi|298674702|ref|YP_003726452.1| 165 PGNVVFLGGGYISFEFANIAARAGSKPLILQRGENPLKTFDSdMVDVAVEAskdagidvltghkvtkiekkgnlY 239
                                       899************************999999999999998655444555555555555555555555555544 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.6   2.1e-06    0.0019       1      53 [.       5      59 ..       5      70 .. 0.88
   2 ?    0.8   0.0      0.22     2e+02     137     151 ..     126     158 ..     118     256 .. 0.59

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.1e-06
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEE..ES-GGGTT--SSSSEEE-TTHHHHH CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi..thkldtiaelsCnpsiggiakgllv 53
                                      dv+ViG G AG+  A ++  +G +v++i   +  +t+a  +C p    ++ ++lv
  gi|298674702|ref|YP_003726452.1|  5 DVVVIGTGTAGSTVAHKCNSAGKNVAIIdhRPFGGTCALRGCDPKKVLVGGAELV 59
                                      79**************************6666789*******9988877766665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.22
                                       -EEEECEEEE--TT..................- CS
                              GIDA 137 etikakavviatGt..................f 151
                                        +i+ + +viatG+                  f
  gi|298674702|ref|YP_003726452.1| 126 DQIEGDYIVIATGSkprelnilgeehiitsdeF 158
                                       567778888888883333333333333333333 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   5.6e-05      0.05       2      31 ..       6      35 ..       5      91 .. 0.94
   2 ?    2.4   0.0      0.14   1.2e+02       2      82 ..     168     256 ..     167     258 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.6e-05
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S- CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdis 31
                                      v viG+Gt G+ +a+ + sag +V ++d +
  gi|298674702|ref|YP_003726452.1|  6 VVVIGTGTAGSTVAHKCNSAGKNVAIIDHR 35
                                      89*************************986 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.14
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S........-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEE CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdi........seealekalekieksleklvekgklkeeeveaalarisft 70 
                                       v  +G G +  + a+++a+ag +  ++++        +++ ++ a e+ ++    +   +k+++ e +  l +++++
  gi|298674702|ref|YP_003726452.1| 168 VVFLGGGYISFEFANIAARAGSKPLILQRgenplktfDSDMVDVAVEASKDAGIDVLTGHKVTKIEKKGNLYEVTTE 244
                                       7789******************9999999444444444444455555555544444444555555555566666666 PP

                                       S-HHHHHC-SEE CS
                           3HCDH_N  71 tdleeavdadlv 82 
                                       ++ ++   +dlv
  gi|298674702|ref|YP_003726452.1| 245 NEKQNTFTTDLV 256
                                       666666666665 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   2.8e-05     0.025       1      32 [.       5      34 ..       5      40 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.8e-05
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvliea 32
                                      DvvviG G Ag  +A++   + +g +v +i+ 
  gi|298674702|ref|YP_003726452.1|  5 DVVVIGTGTAGSTVAHKC--NSAGKNVAIIDH 34
                                      9*****************..999999999975 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1    0.0014       1.2       2      34 ..       6      35 ..       5      44 .. 0.89
   2 ?    3.3   0.0      0.14   1.2e+02       2      45 ..     168     207 ..     167     246 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0014
                                      EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEES CS
                     F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansr 34
                                      + +iG+G  g+++a+++ +ag   +++ ++ +r
  gi|298674702|ref|YP_003726452.1|  6 VVVIGTGTAGSTVAHKCNSAG---KNVAIIDHR 35
                                      679******************...999988655 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.14
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHH CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaee 45 
                                       + ++G+G + + +a+ +++ag   ++ ++  +r ++ ++ + ++
  gi|298674702|ref|YP_003726452.1| 168 VVFLGGGYISFEFANIAARAG---SKPLIL-QRGENPLKTFDSD 207
                                       78*******************...665534.7777766666544 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00011       0.1       1      31 [.       6      36 ..       6      37 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                                      EEEES-SHHHHHHHHHHHHTTEEEEEEESSH CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidkde 31
                                      +++iG G+ G+++a++ +++gk+v +id+++
  gi|298674702|ref|YP_003726452.1|  6 VVVIGTGTAGSTVAHKCNSAGKNVAIIDHRP 36
                                      79*****************7768*****975 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00018      0.16      17      62 ..       3      46 ..       1      57 [. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
                                      EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTST CS
                              Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGq 62
                                      + Dvv++G+G++G t a+    + + +vai++++  +GG   l G 
  gi|298674702|ref|YP_003726452.1|  3 KYDVVVIGTGTAGSTVAHKCNSA-GKNVAIIDHR-PFGGTCALRGC 46
                                      57*****************9999.999****976.67887777665 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00027      0.25       2      33 ..       4      35 ..       3      37 .. 0.94
   2 ?   -1.2   0.0         1   9.2e+02     113     175 ..     214     272 ..     171     314 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00027
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                      +dV+++G+G aG + a+   +aG +v +++ r
  gi|298674702|ref|YP_003726452.1|  4 YDVVVIGTGTAGSTVAHKCNSAGKNVAIIDHR 35
                                      79***************************976 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1
                                       HHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--GTT-HHHHHHTGG CS
                     FAD_binding_3 113 ehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaDGgrStvrktlgie 175
                                       e+ + +g++v  +++v+ +e+ ++    ev+  e+++++t++ + +v   GgrS+  ++lg++
  gi|298674702|ref|YP_003726452.1| 214 EASKDAGIDVLTGHKVTKIEKKGNLY--EVTT-ENEKQNTFTTDLVVH-GGGRSANIDELGLD 272
                                       44455566666666666444444433..3332.344566778787775.46677777777766 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00048      0.43      38      68 ..       5      35 ..       1      50 [. 0.90
   2 ?   -0.8   0.0      0.94   8.5e+02      38      73 ..     167     202 ..     148     225 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00048
                                      EEEEES-SHHHHHHHHHHHHTT-EEEEESSS CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrs 68
                                       v +iG+G  G++va+++++ g +v ++d++
  gi|298674702|ref|YP_003726452.1|  5 DVVVIGTGTAGSTVAHKCNSAGKNVAIIDHR 35
                                      689***********************99987 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.94
                                       EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH CS
                      2-Hacid_dh_C  38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkee 73 
                                        v  +G G I  ++a++++  g k ++ +r +++ +
  gi|298674702|ref|YP_003726452.1| 167 NVVFLGGGYISFEFANIAARAGSKPLILQRGENPLK 202
                                       577899999999999999999999999888877655 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.049        44     190     217 ..       2      29 ..       1      36 [. 0.82
   2 ?    1.8   0.0      0.12   1.1e+02     145     207 ..     126     181 ..     110     217 .. 0.66
   3 ?    2.9   0.1     0.055        49     292     337 ..     218     259 ..     202     264 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.049
                       K_oxygenase 190 akkriaVvGsGqSaaeifedllrrqkkv 217
                                       +k +++V+G G  ++ +++++ +  k+v
  gi|298674702|ref|YP_003726452.1|   2 KKYDVVVIGTGTAGSTVAHKCNSAGKNV 29 
                                       578899*****99999999998876654 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.12
                       K_oxygenase 145 eelearnlvlgvGtepkiPevleklegkervvHsseylerkeellakkriaVvGsGqSaaeif 207
                                       +++e   +v+++G++p     l+ l  +e+++ s+e++e +   + + +++  G+G    e +
  gi|298674702|ref|YP_003726452.1| 126 DQIEGDYIVIATGSKP---RELNILG-EEHIITSDEFMELE---NLPGNVVFLGGGYISFEFA 181
                                       4566677888888875...5666555.58888888888876...5677788888887766644 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.055
                       K_oxygenase 292 eerlrllpnrevesaeaegkgeveltlrneesgeeetlevdavvlA 337
                                       ++ + +l+ ++v+++e++g+  +e+t++n   ++++t ++d vv  
  gi|298674702|ref|YP_003726452.1| 218 DAGIDVLTGHKVTKIEKKGN-LYEVTTEN---EKQNTFTTDLVVHG 259
                                       45688899999999999996.99999988...45556666777655 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1    0.0012       1.1       1      29 [.       5      30 ..       5      38 .. 0.83
   2 ?    1.0   0.1      0.17   1.5e+02     163     216 ..     215     269 ..     204     297 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0012
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEE CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevt 29
                                      ++v++G GtaG+++A  ++ a+k+   v 
  gi|298674702|ref|YP_003726452.1|  5 DVVVIGTGTAGSTVAHKCNSAGKN---VA 30
                                      69****************999954...33 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.17
                                       HHHHCT-EEEE--EEEEEE-TTS-EEEEEETT..S-EEE-SEEEE-SGGG-IIIII CS
                    Trp_halogenase 163 vaearGvtrvegkvvevqldedgrveslrled..greveadlfiDcsGfrgllieq 216
                                        ++++G++++ g+ v ++++++g+  ++++e+   +++  dl++   G  + + e 
  gi|298674702|ref|YP_003726452.1| 215 ASKDAGIDVLTGHKV-TKIEKKGNLYEVTTENekQNTFTTDLVVHGGGRSANIDEL 269
                                       577889999999874.68899********99844567999***9988876665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.39
# Mc/sec: 3380.51
//
Query:       gi|298674703|ref|YP_003726453.1|  [L=146]
Description: PEBP family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-40  137.1   0.0      5e-40  136.9   0.0    1.0  1  PBP       Phosphatidylethanolamine-binding protein


Domain annotation for each model (and alignments):
>> PBP  Phosphatidylethanolamine-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.9   0.0   2.8e-44     5e-40       1     132 []      16     143 ..      16     143 .. 0.96

  Alignments for each domain:
  == domain 1  score: 136.9 bits;  conditional E-value: 2.8e-44
                                       B--GGG..CSBGGS-EEEEES--TTSSEEEEEEEETTSCCTCTTEEEEEEEEEETTSSEE-TTC...EE-B-TTSSC CS
                               PBP   1 klpkky..egentsPplswsdvpegtksyalvviDpDapkvsetflHwvvtnipasvtslpega...vqgknslgee 72 
                                       ++pkky  +ge+++P l++s+vp+gt+s++l++ DpDap v++ f+Hwvv+ni    +s++e++   vqg ns+g+ 
  gi|298674703|ref|YP_003726453.1|  16 EIPKKYscDGEDINPDLQFSNVPSGTESLVLIMDDPDAP-VGT-FTHWVVWNID-PSSSIKENSvpgVQGANSFGK- 88 
                                       5899*999*******************************.888.*********9.6777999999***********. PP

                                       CCCS---B--STTS..EEEEEEEEEESSSG--BGSS-SHHHHHHHHCTTEEEEEEEEEEE CS
                               PBP  73 sesgYlgpcPpkgdgkHrYvfllyaldvealdlkagftraelgaaiaghvlakatlagnY 132
                                         s+Y+gpcPp g+  HrY+f +yald++  d ++g+t++e+++a++ghv++k +l+gnY
  gi|298674703|ref|YP_003726453.1|  89 --SSYGGPCPPSGT--HRYFFRVYALDTKL-DKSEGATKKEVEKAMEGHVVGKGELMGNY 143
                                       ..************..************95.77999999********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1085.83
//
Query:       gi|298674704|ref|YP_003726454.1|  [L=208]
Description: phosphoribosyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.2e-23   80.7   0.0    1.9e-22   79.5   0.0    1.5  1  Pribosyltran    Phosphoribosyl transferase domain
  ------ inclusion threshold ------
      0.011   15.2   0.2      0.015   14.7   0.2    1.4  1  UPRTase         Uracil phosphoribosyltransferase
      0.016   14.3   0.0      0.029   13.5   0.0    1.4  1  DREV            DREV methyltransferase
      0.028   14.5   0.3      0.059   13.4   0.3    1.4  1  Unstab_antitox  Putative addiction module component


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.5   0.0   4.2e-26   1.9e-22      14     155 ..       7     188 ..       1     190 [. 0.94

  Alignments for each domain:
  == domain 1  score: 79.5 bits;  conditional E-value: 4.2e-26
                                       EEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE................... CS
                      Pribosyltran  14 avarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes........... 79 
                                       ++ + +a++l++y+++ ++v++i+rgGv +++++a++L+++l  + ++k   + ++ea  g++ e            
  gi|298674704|ref|YP_003726454.1|   7 DAGKQLAKLLDKYRNEDVLVLAIPRGGVEIGYQVANYLDAELSLLVSRKLPFPYNPEAGFGAVTEDgssfineiaar 83 
                                       567779999999**************************999999999998888888888888888888********* PP

                                       ............................EE----TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HH CS
                      Pribosyltran  80 ............................rlledpagkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpa 128
                                                                   ++l+d ++++V++ DD+l+ G+T+ a ++l k+kg+ ++ +av+v+ ++
  gi|298674704|ref|YP_003726454.1|  84 elsedmieqikkeqvdeikrrievlrngEPLPDMKNRTVILTDDGLAMGSTMSASVKLCKNKGAGKIVVAVPVAGKQ 160
                                       ***************************************************************************** PP

                                       HHHHHHHH-TTS......EEEEEEE-SE CS
                      Pribosyltran 129 teeevdknakrvfsls.pdnfvavvgfe 155
                                        +   dk ++ ++ l  p +f+av++++
  gi|298674704|ref|YP_003726454.1| 161 VADMIDKVVDDIIVLDiPPFFHAVAQVY 188
                                       *************************997 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.2   3.3e-06     0.015     115     170 ..     114     166 ..      17     176 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.3e-06
                           UPRTase 115 LPkkiaertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrla 170
                                       LP ++++rtv+l+D  +a G+++ a ++l k++g+g  kI+v+  +a ++ ++ + 
  gi|298674704|ref|YP_003726454.1| 114 LP-DMKNRTVILTDDGLAMGSTMSASVKLCKNKGAG--KIVVAVPVAGKQVADMID 166
                                       44.4699*************************8875..999999999888776555 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   6.5e-06     0.029     103     137 ..      64      98 ..      60     112 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.5e-06
                              DREV 103 aGdGeitkrvaptfeevyatelsetmrdrlkkkky 137
                                       aG G +t+  +++++e+ a else m++++kk + 
  gi|298674704|ref|YP_003726454.1|  64 AGFGAVTEDGSSFINEIAARELSEDMIEQIKKEQV 98 
                                       899****************************9876 PP

>> Unstab_antitox  Putative addiction module component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   1.3e-05     0.059      17      45 ..      84     112 ..      82     114 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.3e-05
                    Unstab_antitox  17 SLdeeadpelpaawkaElerRlaeyeaGk 45 
                                        L+e++++++ +++ +E++rR++ +++G+
  gi|298674704|ref|YP_003726454.1|  84 ELSEDMIEQIKKEQVDEIKRRIEVLRNGE 112
                                       578899*********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1086  (0.0605723); expected 358.6 (0.02)
Passed bias filter:                      788  (0.0439511); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1566.60
//
Query:       gi|298674705|ref|YP_003726455.1|  [L=246]
Description: short-chain dehydrogenase/reductase SDR [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-62  210.6   0.3    1.6e-62  210.4   0.3    1.0  1  adh_short        short chain dehydrogenase
    3.7e-48  164.1   0.0    5.7e-48  163.5   0.0    1.3  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    3.7e-14   53.0   0.1    4.7e-14   52.7   0.1    1.1  1  KR               KR domain
     0.0014   18.1   0.0     0.0036   16.8   0.0    1.7  1  Epimerase        NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
      0.017   14.1   0.3      0.022   13.8   0.3    1.3  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
      0.023   13.9   0.1      0.025   13.7   0.1    1.2  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
      0.029   14.6   0.0       0.15   12.3   0.0    2.0  2  Pyr_redox_dim    Pyridine nucleotide-disulphide oxidoreductas


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.4   0.3   6.4e-66   1.6e-62       1     191 [.      22     211 ..      22     215 .. 0.98

  Alignments for each domain:
  == domain 1  score: 210.4 bits;  conditional E-value: 6.4e-66
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSS CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgk 77 
                                       ++++vtG+++GIG+ i+ +lakeGa+++ ++r+e+++e+++ e++e g++ +a+++Dvt++e+v++lv+k ++ +g+
  gi|298674705|ref|YP_003726455.1|  22 QTAVVTGGGKGIGKSICLALAKEGANIIPAARTESDIEKTKREVEEIGTQSMAVKTDVTKEEDVKNLVSKSIDTFGG 98 
                                       589************************************************************************** PP

                                       ESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHH CS
                         adh_short  78 ldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKa 154
                                       +d++vnNAG+  ++pf e+s +e+e+vievNl+gvfl ++++lp+m  ++sG+I+n+sS agk + +++++YsAsK+
  gi|298674705|ref|YP_003726455.1|  99 IDIFVNNAGVGLRKPFIETSLDEFEKVIEVNLKGVFLGMKHALPHMQYNNSGKIINISSGAGKSGIPELSVYSASKF 175
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHC CS
                         adh_short 155 avagltrslakelaptgirvnavaPGlvdTdmakelr 191
                                       +v+glt+s a+e+ + ++++ av+PG+vdTdm ++  
  gi|298674705|ref|YP_003726455.1| 176 GVIGLTESTAREVGS-NVQIYAVCPGGVDTDMYRSMF 211
                                       *************99.5***************98776 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.5   0.0   2.2e-51   5.7e-48       4     182 ..      31     210 ..      26     242 .. 0.92

  Alignments for each domain:
  == domain 1  score: 163.5 bits;  conditional E-value: 2.2e-51
                                       TSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSE..EEE--TTSHHHHHHHHHHHHHHHSSEEEEEE--- CS
                      adh_short_C2   4 sgIGraiAkalaeeGaevvltdlneeakkrveelaeelgae..vlecDVtdeeqvealveevvekfgklDilvnnag 78 
                                       +gIG+ i  ala+eGa+++ + + e++ +++++ +ee+g++  ++++DVt+ee+v++lv++  ++fg++Di+vnnag
  gi|298674705|ref|YP_003726455.1|  31 KGIGKSICLALAKEGANIIPAARTESDIEKTKREVEEIGTQsmAVKTDVTKEEDVKNLVSKSIDTFGGIDIFVNNAG 107
                                       8**************************77888888889977645********************************* PP

                                       --EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHH CS
                      adh_short_C2  79 iapklkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnynaygaaKaalealtr 153
                                       +  +  +pf+ets +ef+++++vnl+++fl +k+alp+m+ +  g+i+n+ss +++ ++p+ ++y+a+K ++++lt 
  gi|298674705|ref|YP_003726455.1| 108 VGLR--KPFIETSLDEFEKVIEVNLKGVFLGMKHALPHMQYNnsGKIINISSGAGKSGIPELSVYSASKFGVIGLTE 182
                                       ****..*******************************9987668********************************* PP

                                       HHHHHHGGGTEEEEEEEE--BHCTGGGGS CS
                      adh_short_C2 154 ylAvelgpkgiRvNavspgpikTlaasgi 182
                                       + A+e+g+ ++++ av+pg ++T++ +++
  gi|298674705|ref|YP_003726455.1| 183 STAREVGS-NVQIYAVCPGGVDTDMYRSM 210
                                       ********.****************6654 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7   0.1   1.8e-17   4.7e-14       3     152 ..      24     173 ..      22     189 .. 0.91

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 1.8e-17
                                       EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHS CS
                                KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaee 79 
                                        ++tGG  g+G++++  la++ga +++  +R+   ++d +++ +e+e+ g++ ++v+ Dv+++++v++l+++  +++
  gi|298674705|ref|YP_003726455.1|  24 AVVTGGGKGIGKSICLALAKEGA-NIIPAART---ESDIEKTKREVEEIGTQSMAVKTDVTKEEDVKNLVSKSIDTF 96 
                                       68********************8.68888999...566777889********************************* PP

                                       S---EEEE---------TTT--HHHHHHHHTTTTHHHHH.HHHHTTT...S--SEEEEEEEHHHHH--TT-HHHHHH CS
                                KR  80 ppikGvihaAgvlrdklleemtaedleqvlapKvkGawn.Lhelled...esldffvlfSSiagllgsagqanYaaa 152
                                       + i   ++ Agv   k++ e++ +++e+v++  +kG+   ++++l++   ++   ++ +SS ag  g ++ + Y+a 
  gi|298674705|ref|YP_003726455.1|  97 GGIDIFVNNAGVGLRKPFIETSLDEFEKVIEVNLKGVFLgMKHALPHmqyNNSGKIINISSGAGKSGIPELSVYSAS 173
                                       ************************************8643888888866678889*******************985 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.4e-06    0.0036       2     164 ..      25     192 ..      24     199 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.4e-06
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC......EEEE--TT-HHHHHHH....HHHH.T-SE CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl......elveldltdrsalerl....fkee.qpda 67 
                                       +VtG+   iG+ ++ al+++g ++i  +r +s+ ++ ++e          v+ d+t+++++++l    ++++ ++d+
  gi|298674705|ref|YP_003726455.1|  25 VVTGGGKGIGKSICLALAKEGANIIPAARTESDIEKTKREVEeigtqsMAVKTDVTKEEDVKNLvsksIDTFgGIDI 101
                                       79*********************999999977777666665579***9999******99766661111555667888 PP

                                       EEE--S--....-HHHHHHSHHHHHHHHTHHH....HHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS-- CS
                         Epimerase  68 vihlAavg....gvaassedpadfieknlqgt....lnlleaarkagvkrllflsSsevYGkdaeqpkeettltgpl 136
                                        ++ A+vg     +++s ++ +++ie nl+g+     + l  ++ ++  +++++sS    G++++           +
  gi|298674705|ref|YP_003726455.1| 102 FVNNAGVGlrkpFIETSLDEFEKVIEVNLKGVflgmKHALPHMQYNNSGKIINISS----GAGKS----------GI 164
                                       88888887222235566666666666666543100033344444445556666666....43333..........33 PP

                                       --SSHHHHHHHHHHHHHHHHHHHHT-EE CS
                         Epimerase 137 kpnspYaaaKlageklveayaaqyglna 164
                                       +  s Y+a+K  +  l+e+ a++ g n+
  gi|298674705|ref|YP_003726455.1| 165 PELSVYSASKFGVIGLTESTAREVGSNV 192
                                       5567777777777777777777776665 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3   8.6e-06     0.022       1      66 [.      25      91 ..      25     157 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.6e-06
                         3Beta_HSD  1 vvtGgaGFlGralvkeLvrleelkevrvlDlres.pelleelskvnvkk.viegDvtdkdkleealeg 66
                                      vvtGg+  +G++++ +L +++  + + ++  + + ++++ e++++++++  +++Dvt+++++++ + +
  gi|298674705|ref|YP_003726455.1| 25 VVTGGGKGIGKSICLALAKEGA-NIIPAARTESDiEKTKREVEEIGTQSmAVKTDVTKEEDVKNLVSK 91
                                      79****99************96.5555554433314556678888888888***********997754 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   9.8e-06     0.025       2      75 ..      25      91 ..      24     176 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.8e-06
                                      EEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT. CS
                   Polysacc_synt_2  2 lvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekalee 75
                                      +vtG+g  iG++++  ++k+  ++ii   r+E  + + ++e+e e+ ++++ v+     +dv+++e +++++++
  gi|298674705|ref|YP_003726455.1| 25 VVTGGGKGIGKSICLALAKEG-ANIIPAARTESDIEKTKREVE-EIGTQSMAVK-----TDVTKEEDVKNLVSK 91
                                      69************9988765.6799999***********995.5555566555.....899999999888773 PP

>> Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       0.8     2e+03      75      94 ..      67      86 ..      61      90 .. 0.74
   2 ?   12.3   0.0   5.8e-05      0.15       5      44 ..     169     208 ..     165     228 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.8
                                      HHHHHHHHHHTTSBHHHHHT CS
                     Pyr_redox_dim 75 liqelavaikagltvedlad 94
                                       i   ++a+k ++t+e++ +
  gi|298674705|ref|YP_003726455.1| 67 EIGTQSMAVKTDVTKEEDVK 86
                                      56777999999999995544 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 5.8e-05
                                       EESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHT CS
                     Pyr_redox_dim   5 vftdpevasvGlteeeAkaagieikvgkfpfkangralay 44 
                                       v++  +++ +Glte  A++ g +++++ + +  ++  ++ 
  gi|298674705|ref|YP_003726455.1| 169 VYSASKFGVIGLTESTAREVGSNVQIYAVCPGGVDTDMYR 208
                                       899999*********************9988755555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1630.12
//
Query:       gi|298674706|ref|YP_003726456.1|  [L=190]
Description: type 11 methyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-20   71.9   0.0    6.1e-20   71.6   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    5.2e-18   65.5   0.0    7.6e-18   65.0   0.0    1.2  1  Methyltransf_25  Methyltransferase domain
    4.7e-16   59.2   0.0    7.5e-16   58.6   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    1.6e-15   57.1   0.0    2.1e-15   56.7   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    3.7e-12   46.4   0.0    4.5e-12   46.1   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    1.5e-11   44.9   0.0    2.2e-11   44.4   0.0    1.2  1  Methyltransf_12  Methyltransferase domain
    3.1e-09   36.9   0.0    3.9e-09   36.6   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    4.2e-09   36.1   0.0    5.2e-09   35.8   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
    6.3e-09   35.6   0.0    8.4e-09   35.2   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    2.8e-08   33.5   0.0    3.8e-08   33.0   0.0    1.2  1  MTS              Methyltransferase small domain
      1e-06   29.0   0.0    1.2e-06   28.8   0.0    1.3  1  FtsJ             FtsJ-like methyltransferase
    3.8e-06   26.8   0.0    4.7e-06   26.4   0.0    1.1  1  Methyltransf_16  Lysine methyltransferase
    4.3e-06   26.7   0.0      7e-06   26.0   0.0    1.3  1  Methyltransf_18  Methyltransferase domain
    6.2e-06   26.0   0.0    9.3e-06   25.4   0.0    1.2  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    1.7e-05   24.3   0.0    2.3e-05   23.9   0.0    1.1  1  TehB             Tellurite resistance protein TehB
    7.2e-05   22.6   0.1    8.5e-05   22.4   0.1    1.1  1  Met_10           Met-10+ like-protein
     0.0001   22.1   0.0    0.00013   21.7   0.0    1.1  1  GCD14            tRNA methyltransferase complex GCD14 subunit
    0.00029   20.0   0.0    0.00035   19.7   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
    0.00041   19.5   0.0    0.00072   18.7   0.0    1.3  1  Fibrillarin      Fibrillarin
     0.0034   16.7   0.0     0.0043   16.4   0.0    1.1  1  Rsm22            Mitochondrial small ribosomal subunit Rsm22
     0.0037   16.8   0.0      0.013   15.1   0.1    1.7  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
      0.004   16.4   0.0      0.045   12.9   0.0    1.9  2  NNMT_PNMT_TEMT   NNMT/PNMT/TEMT family
     0.0042   16.3   0.0     0.0052   16.0   0.0    1.2  1  Methyltransf_3   O-methyltransferase
     0.0054   16.5   0.0      0.017   14.8   0.0    1.7  2  N6_N4_Mtase      DNA methylase
      0.006   16.1   0.0     0.0094   15.4   0.0    1.3  1  Methyltransf_4   Putative methyltransferase
     0.0096   14.9   0.0     0.0096   14.9   0.0    1.1  1  Methyltransf_9   Protein of unknown function (DUF1698)
  ------ inclusion threshold ------
      0.016   15.2   0.0      0.017   15.1   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
      0.046   13.4   0.3       0.39   10.4   0.3    2.2  1  UPF0020          Putative RNA methylase family UPF0020
       0.16   11.0   0.0       0.19   10.8   0.0    1.2  1  DREV             DREV methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.6   0.0   9.8e-23   6.1e-20       4     114 ..      36     146 ..      34     182 .. 0.91

  Alignments for each domain:
  == domain 1  score: 71.6 bits;  conditional E-value: 9.8e-23
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlil 79 
                                       g +v+D GCG G++t+ +a+ +g +++v+ +D++e+++e  +++++k gl+ +v+ +q + e++   ++ ek+D++l
  gi|298674706|ref|YP_003726456.1|  36 GQTVMDFGCGPGTYTIDMAQMVGRNGKVIAVDFQEKMLEILEKKCKKEGLEsRVKIHQNNPESIG--VS-EKVDFVL 109
                                       678**************************************************************..77.9****** PP

                   Methyltransf_31  80 snevlnaladpdkileeiervlkpggilliedpr..l 114
                                       ++ v++ l++ d+++ e++  +kp+g+ll+ +p   +
  gi|298674706|ref|YP_003726456.1| 110 AFYVIHELPAIDNFFAELKTIVKPEGRLLVVEPEvhV 146
                                       ********************************99322 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.0   0.0   1.2e-20   7.6e-18       1      97 []      39     135 ..      39     135 .. 0.95

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 1.2e-20
                                       EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgal 74 
                                       v+d+GcG+G++t+++a+ +g ++kv++vD++e+mle+ ++++++egl  +v+++q + e++   + ++D+v++++++
  gi|298674706|ref|YP_003726456.1|  39 VMDFGCGPGTYTIDMAQMVGrNGKVIAVDFQEKMLEILEKKCKKEGLesRVKIHQNNPESIGVSE-KVDFVLAFYVI 114
                                       89*****************779***************************************9876.*******9999 PP

                                       GGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  75 hhlsdedlekalkeiarvLkpgG 97 
                                       h l+   ++++++e++ ++kp+G
  gi|298674706|ref|YP_003726456.1| 115 HELP--AIDNFFAELKTIVKPEG 135
                                       9887..789************99 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   0.0   1.2e-18   7.5e-16       2      96 .]      41     139 ..      40     139 .. 0.96

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 1.2e-18
                                       EET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CCC CS
                   Methyltransf_11   2 dvGcGtGrlaealakrg...arvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlhh 73 
                                       d+GcG G ++ ++a+ +   ++v++vD+ ++ml++ ++k ++egl  +v++++ + e++ + + ++D+v+++ v+h 
  gi|298674706|ref|YP_003726456.1|  41 DFGCGPGTYTIDMAQMVgrnGKVIAVDFQEKMLEILEKKCKKEGLesRVKIHQNNPESIGVSE-KVDFVLAFYVIHE 116
                                       99************7777889***************************************988.************* PP

                                       -CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  74 vedpekalkeiaRvLkpgGllvi 96 
                                       ++  + +++e++ ++kp+G+l++
  gi|298674706|ref|YP_003726456.1| 117 LPAIDNFFAELKTIVKPEGRLLV 139
                                       ********************975 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.7   0.0   3.4e-18   2.1e-15      44     154 ..      32     142 ..      15     156 .. 0.91

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 3.4e-18
                                       -S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT-TTS-T-EEE CS
                   Ubie_methyltran  44 avkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqanaeeLpfeddsfDv 119
                                        vk+g++v+D  +G g ++++++++vg++gkv+ +D++e+mL++ ekk k+eg   +++  q n e +  ++   D+
  gi|298674706|ref|YP_003726456.1|  32 YVKPGQTVMDFGCGPGTYTIDMAQMVGRNGKVIAVDFQEKMLEILEKKCKKEGLEsRVKIHQNNPESIGVSE-KVDF 107
                                       5799*************************************************9879999999999998875.68** PP

                                       EEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE CS
                   Ubie_methyltran 120 vtvsfGlrnvtDklkaLkeayrvlkpGGrlvvlef 154
                                       v   + +  ++ +++ + e+  ++kp Grl+v+e 
  gi|298674706|ref|YP_003726456.1| 108 VLAFYVIHELPAIDNFFAELKTIVKPEGRLLVVEP 142
                                       ********************************994 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.0   7.2e-15   4.5e-12      11     125 ..      23     145 ..      14     179 .. 0.75

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 7.2e-15
                   Methyltransf_23  11 dklerllpk.lraggrvLdiGcGtGillevlren.gf..svtgvDlspeaveiae........kakkaqkdqfdeqe 75 
                                       +k e++l++  ++g+ v+d+GcG G+ +  +++  g   +v++vD  +++ ei+e        +          + +
  gi|298674706|ref|YP_003726456.1|  23 HKPEQILDNyVKPGQTVMDFGCGPGTYTIDMAQMvGRngKVIAVDFQEKMLEILEkkckkeglE---------SRVK 90 
                                       566667766348999**********777777665255779**************6555444441.........3444 PP

                   Methyltransf_23  76 aaepqg.......kfdlIvlrevlehvpdppellrqiatllkpgGylllseplaslk 125
                                       + +++        k d++ +++v++ +p     ++ ++t++kp+G+ll+ ep +  +
  gi|298674706|ref|YP_003726456.1|  91 IHQNNPesigvseKVDFVLAFYVIHELPAIDNFFAELKTIVKPEGRLLVVEPEV--H 145
                                       4443334555677**************************************965..3 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.0   3.6e-14   2.2e-11       1      99 []      40     137 ..      40     137 .. 0.87

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 3.6e-14
                   Methyltransf_12   1 LeiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvl 76 
                                       +++GcG G+++  +++   ++ ++++vD++++++e  ++k +k++ ++  +v++ +++ ++   ++++D v+a+ v+
  gi|298674706|ref|YP_003726456.1|  40 MDFGCGPGTYTIDMAQMVgRNGKVIAVDFQEKMLEILEKKCKKEGLES--RVKIHQNNPESIGVSEKVDFVLAFYVI 114
                                       69************99999***************77777777777755..7777777765444448*********** PP

                   Methyltransf_12  77 hhlkdirevldnirklLkpgGrl 99 
                                       h l+ i+ ++++++  +kp+Grl
  gi|298674706|ref|YP_003726456.1| 115 HELPAIDNFFAELKTIVKPEGRL 137
                                       *********************97 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   6.4e-12   3.9e-09      70     141 ..      30     105 ..      23     174 .. 0.76

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 6.4e-12
                                       T..--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC.SEEEEES-G.GGTTGGG- CS
                              PCMT  70 e..lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle.nvivvvgDG.rkGyeeka 141
                                       +  +k+g+ v++ G+G G  t  +a++vg++g+v++++ ++++ e  +++ kk++le +v+++       G+ ek 
  gi|298674706|ref|YP_003726456.1|  30 DnyVKPGQTVMDFGCGPGTYTIDMAQMVGRNGKVIAVDFQEKMLEILEKKCKKEGLEsRVKIHQNNPeSIGVSEKV 105
                                       45589**************************************************998898887654134666654 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.0   8.4e-12   5.2e-09      59     164 ..      32     139 ..      19     164 .. 0.86

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 8.4e-12
                                       T--TT-EEEEES-TTSHHHHHHHHHH..--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-..----SEE CS
                              CMAS  59 elkpGmtlLdiGcGWGslvrravery..dvkvvglTlSkeqaklakkrvdeldlerkvevklldyedl..dekvdrv 131
                                        +kpG+t++d GcG G+ ++ +++    + kv+++ + ++  +  +k++++++le +v+++  + e +  +ekvd v
  gi|298674706|ref|YP_003726456.1|  32 YVKPGQTVMDFGCGPGTYTIDMAQMVgrNGKVIAVDFQEKMLEILEKKCKKEGLESRVKIHQNNPESIgvSEKVDFV 108
                                       489**************98888876511578*******************************9998752278***** PP

                                       EEES-GGGTSGGGHHHHHHHHHHHS-TT-EEEE CS
                              CMAS 132 vsvgafehvgkenydtffkklkkllkedGllll 164
                                        ++ ++  +     d+ff++lk+++k++G+ll+
  gi|298674706|ref|YP_003726456.1| 109 LAFYVIHEL--PAIDNFFAELKTIVKPEGRLLV 139
                                       **9999887..5689***************997 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.0   1.4e-11   8.4e-09     153     257 ..      27     138 ..      26     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 1.4e-11
                              PrmA 153 ealeklvkegeevlDvGtGSGiLaiaaakL.g.akkvvavDiDevAvkvakeNaelNkveakleva..lseellkee 225
                                       ++l+++vk+g++v+D+G+G G  +i  a++ g   kv+avD  e  +++ ++  ++ ++e++++++  ++e++  +e
  gi|298674706|ref|YP_003726456.1|  27 QILDNYVKPGQTVMDFGCGPGTYTIDMAQMvGrNGKVIAVDFQEKMLEILEKKCKKEGLESRVKIHqnNPESIGVSE 103
                                       689**********************76655252469*************************9999622345554589 PP

                              PrmA 226 kadvivaNILae...vlielaedikklvkegglli 257
                                       k+d ++a  + +   ++ ++  ++k +vk++g+l+
  gi|298674706|ref|YP_003726456.1| 104 KVDFVLAFYVIHelpAIDNFFAELKTIVKPEGRLL 138
                                       *******8765423368999************986 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   6.2e-11   3.8e-08      31     140 ..      35     142 ..      24     162 .. 0.88

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 6.2e-11
                                       TCSEEEEET-TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTSTTS-EEEEEE- CS
                               MTS  31 lsgkvlDlGcGaGvlgaalakespeae.vtlvdvdarAlesakenleankle..vevvasdvleeveekkfdlivsN 104
                                         ++v+D+GcG G  ++ +a++  ++  v +vd + + le+ ++ +++++le  v++++++  +    +k+d+++  
  gi|298674706|ref|YP_003726456.1|  35 PGQTVMDFGCGPGTYTIDMAQMVGRNGkVIAVDFQEKMLEILEKKCKKEGLEsrVKIHQNNPESIGVSEKVDFVLAF 111
                                       5788******************998766************************99999**999998889*******98 PP

                                       --STTTCHCHHHHHHHHHHHHHHHEEEEEEEEEEEE CS
                               MTS 105 PPfhagkatelavaeeliaeAkeaLkegGeLliVan 140
                                         +h+  a     +++++ae k + k++G+Ll+V  
  gi|298674706|ref|YP_003726456.1| 112 YVIHELPA-----IDNFFAELKTIVKPEGRLLVVEP 142
                                       88887766.....99*****************9964 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   1.9e-09   1.2e-06       4      68 ..      20      94 ..      18     158 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1.9e-09
                                      CHHHHHHHHHHHHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS............HHH.TTEEEECS CS
                              FtsJ  4 RsayKLleidekfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm............apl.pgvttiqg 68
                                      +s +K ++i++ +   kpg+tv+D g++PG ++  ++q +g +gkv+avD q+               l ++v+++q 
  gi|298674706|ref|YP_003726456.1| 20 KSIHKPEQILDNYV--KPGQTVMDFGCGPGTYTIDMAQMVGRNGKVIAVDFQEKmleilekkckkeG-LeSRVKIHQN 94
                                      6889999*****96..9************************9*********8765766655433211.1345555544 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   7.7e-09   4.7e-06      46     171 ..      35     154 ..      12     157 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 7.7e-09
                   Methyltransf_16  46 sklsvlELGsGtGlvGlavaell.peakviltDlee.llellkknielnknalkskvkvevLdWgeeleedllekee 120
                                        +++v++ G G G   + +a+++  + kvi  D +e +le+l+k  +   + l+s+vk+++ +      e +  +e+
  gi|298674706|ref|YP_003726456.1|  35 PGQTVMDFGCGPGTYTIDMAQMVgRNGKVIAVDFQEkMLEILEKKCKK--EGLESRVKIHQNNP-----ESIGVSEK 104
                                       5689******************9899*******8777*********99..56******987554.....44455678 PP

                   Methyltransf_16 121 vDlilaaDcvYledslelLvkvLkellkkeskvlvaykkrreaekkFfkll 171
                                       vD++la  ++    +++   + Lk ++k+e+ +lv+  + +   k+Ff+++
  gi|298674706|ref|YP_003726456.1| 105 VDFVLAFYVIHELPAIDNFFAELKTIVKPEGRLLVVEPEVH-VRKHFFDSI 154
                                       ******************************99888766555.557888876 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   1.1e-08     7e-06       9      73 ..      30      95 ..      26     110 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.1e-08
                   Methyltransf_18  9 aslvekgsrvaDiGtDHgylpiylvke.gkakkviasDinegplekakeniekagledkievrlsd 73
                                       ++v++g++v+D G+  g  +i +++  g+  kvia+D +e+ le  +++++k+gle++++++ ++
  gi|298674706|ref|YP_003726456.1| 30 DNYVKPGQTVMDFGCGPGTYTIDMAQMvGRNGKVIAVDFQEKMLEILEKKCKKEGLESRVKIHQNN 95
                                      5799******************9997548999****************************998766 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   1.5e-08   9.3e-06       7      63 ..      34      91 ..      28     110 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.5e-08
                                      -TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--.SEEE CS
                   Methyltr_RsmB-F  7 qeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvt.ntiv 63
                                      ++++t++D  ++PG  T  +a+++  +g+v+Avd +++ l+ +++  k+ g++  +++
  gi|298674706|ref|YP_003726456.1| 34 KPGQTVMDFGCGPGTYTIDMAQMVGRNGKVIAVDFQEKMLEILEKKCKKEGLEsRVKI 91
                                      6789******************************************999999822333 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   3.8e-08   2.3e-05      28     133 ..      32     140 ..      17     144 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 3.8e-08
                                       CS-S-E.EEEES-TTSHHHHHHH.HTT-E..EEEEES-HHHHHHHHHHHHHTT-TT.EEEEE--GGG----S-EEEE CS
                              TehB  28 ivkpgk.vldlgcgqgrnslyls.llgyd..vtawdknensiafleeikekenlkn.istalydineaklderydfi 99 
                                        vkpg+ v+d+gcg g  ++ ++ ++g +  v a+d +e+ ++ le+  +ke l++ ++    + +++ ++e+ df+
  gi|298674706|ref|YP_003726456.1|  32 YVKPGQtVMDFGCGPGTYTIDMAqMVGRNgkVIAVDFQEKMLEILEKKCKKEGLESrVKIHQNNPESIGVSEKVDFV 108
                                       689997368********9997762567644499*********************9436667777788999******* PP

                                       EEESSGGGS-GGGHHHHHHHHHHTEEEEEEEEEE CS
                              TehB 100 lstvvlmfleaeripsiienmqectkvggynliv 133
                                       l+  v+  l   +i +  +++++  k+ g  l+v
  gi|298674706|ref|YP_003726456.1| 109 LAFYVIHEL--PAIDNFFAELKTIVKPEGRLLVV 140
                                       *98887655..57999999999999999988877 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1   1.4e-07   8.5e-05      93     177 ..      28     113 ..      19     164 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.4e-07
                                       HHHTT--TT-EEEETT-TTTCCHHHCCHH.TTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---TT- CS
                            Met_10  93 rlaklveegevVvdvfAGiGpfaipiaky.skakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevireql 168
                                        l + v++g++V+d   G G ++i +a++ +++ +v+a+d + +  + l++  k   +e++vk  ++  + +  +++
  gi|298674706|ref|YP_003726456.1|  28 ILDNYVKPGQTVMDFGCGPGTYTIDMAQMvGRNGKVIAVDFQEKMLEILEKKCKKEGLESRVKIHQNNPESIGVSEK 104
                                       45567*******************999753899*****************************766666565555888 PP

                                       EEEEEE--T CS
                            Met_10 169 adrvvmnlp 177
                                       +d v+  ++
  gi|298674706|ref|YP_003726456.1| 105 VDFVLAFYV 113
                                       884433333 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   2.1e-07   0.00013      38     142 ..      33     137 ..      26     160 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.1e-07
                             GCD14  38 lkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrDvckeGfdeevsgk. 113
                                       +kpG  v++ G G g+ +  +a+ v+  G++ +++f e+  e   ++ ++++l++ v++++ +  + G +e+v+ + 
  gi|298674706|ref|YP_003726456.1|  33 VKPGQTVMDFGCGPGTYTIDMAQMVGRNGKVIAVDFQEKMLEILEKKCKKEGLESRVKIHQNNPESIGVSEKVDFVl 109
                                       89*******************************************************************99996541 PP

                             GCD14 114 vDavfLDlPaPweaiphaakalkkeggrl 142
                                       +  v  +lPa ++   ++++ +k e grl
  gi|298674706|ref|YP_003726456.1| 110 AFYVIHELPAIDNFFAELKTIVKPE-GRL 137
                                       3456779999988888888888544.444 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   5.7e-07   0.00035      27      90 ..      32     101 ..      12     142 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 5.7e-07
                                       -GGTTSEEEEES-TTTCCHHHHHCC-...SEEEEE-S-HHHHHHHHCHTT...TCCCEEEE-S-CCGHHH CS
                            RrnaAD  27 nleekltvleigpGkGilTeeLakra...kqvvvlElderLakllqkkls...kdeklkvvhqDflkfet 90 
                                       ++++ +tv++ g G+G  T  +a+++    +v ++   e+++++l+kk +   +++++k+ ++++    +
  gi|298674706|ref|YP_003726456.1|  32 YVKPGQTVMDFGCGPGTYTIDMAQMVgrnGKVIAVDFQEKMLEILEKKCKkegLESRVKIHQNNPESIGV 101
                                       5679**********************98779******************998999999999988866655 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.2e-06   0.00072      63     116 ..      28      81 ..      17      87 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.2e-06
                                       -S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHT CS
                       Fibrillarin  63 lkelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlrelievak 116
                                       + + ++k+g+ v+ +G + Gt    ++ +vg++g+v av+f +++l  l + +k
  gi|298674706|ref|YP_003726456.1|  28 ILDNYVKPGQTVMDFGCGPGTYTIDMAQMVGRNGKVIAVDFQEKMLEILEKKCK 81 
                                       567899*************************************99987777666 PP

>> Rsm22  Mitochondrial small ribosomal subunit Rsm22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0     7e-06    0.0043      36     139 ..      37     140 ..      16     145 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7e-06
                             Rsm22  36 kslldvgegpgtalwaaselweeleevlvidaseelleiskelaadapelkeaalrrsvirealeleea.dLviisy 111
                                       ++++d+g gpgt ++ + ++  +  +v+ +d  e++lei ++  ++     +++ +++   e + + e+ d v   y
  gi|298674706|ref|YP_003726456.1|  37 QTVMDFGCGPGTYTIDMAQMVGRNGKVIAVDFQEKMLEILEKKCKKEGLESRVKIHQNNP-ESIGVSEKvDFVLAFY 112
                                       6899**********************************9888777777666665665555.567776655******* PP

                             Rsm22 112 vLleled.esreklvknlWakaskilviv 139
                                       v++el   ++  + +k +  k +  l++v
  gi|298674706|ref|YP_003726456.1| 113 VIHELPAiDNFFAELKTI-VKPEGRLLVV 140
                                       ****98755554445544.4444455555 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   2.1e-05     0.013       3      55 ..      38      93 ..      36     115 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.1e-05
                   Methyltransf_15  3 vilDlfsGaGGnviqfalv...fekviaieinleklacaqhNaevYgvsdkitlvl 55
                                      +++D  +G G  +i +a++     kvia++ +++ l++ ++ ++  g ++++++ +
  gi|298674706|ref|YP_003726456.1| 38 TVMDFGCGPGTYTIDMAQMvgrNGKVIAVDFQEKMLEILEKKCKKEGLESRVKIHQ 93
                                      799**************99776569***********************99998765 PP

>> NNMT_PNMT_TEMT  NNMT/PNMT/TEMT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   7.3e-05     0.045      55     103 ..      34      84 ..      20      88 .. 0.81
   2 ?    1.3   0.0      0.27   1.6e+02     141     197 ..      89     139 ..      86     142 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.3e-05
                                       S-ECEEEEET-TT--GGGTTGG..GTECEEEEEESSHHHHHHHHHHHTT-T CS
                    NNMT_PNMT_TEMT  55 kkgdtllDiGaGPTvyqllsar..evakeitlsDyldqNrdeLekWlkkee 103
                                       k g+t++D+G GP  y++  a    +  +++  D+ ++ ++ Lek  kke+
  gi|298674706|ref|YP_003726456.1|  34 KPGQTVMDFGCGPGTYTIDMAQmvGRNGKVIAVDFQEKMLEILEKKCKKEG 84 
                                       5689************9755550156667999*************999985 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.27
                                       --TTSSSTTTTSS-SS..EEEEEEESSHHHH-SSHHHHHHHHHHHHTTEEEEEEEEE CS
                    NNMT_PNMT_TEMT 141 vdvhqspvvlagvqlpkkadvvvtifcleaacedleeylralrnlasllkpGGhlvl 197
                                       v +hq+++   g  + +k+d v++++ +    + ++++++ l    + +kp G+l++
  gi|298674706|ref|YP_003726456.1|  89 VKIHQNNPESIG--VSEKVDFVLAFYVIHE-LPAIDNFFAEL---KTIVKPEGRLLV 139
                                       678888887665..8999****99987754.35566666555...566788888765 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   8.4e-06    0.0052      50     107 ..      38      95 ..      29     141 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8.4e-06
                                       EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES- CS
                    Methyltransf_3  50 rvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekieliegd 107
                                        v++ G   G   + +a+ +  +Gk++a+d +++  ei  k  +k g++ ++++++ +
  gi|298674706|ref|YP_003726456.1|  38 TVMDFGCGPGTYTIDMAQMVGRNGKVIAVDFQEKMLEILEKKCKKEGLESRVKIHQNN 95 
                                       68889999999999************************************99998876 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   2.8e-05     0.017     181     230 ..      25      77 ..      17      78 .. 0.91
   2 ?   -1.2   0.0       2.3   1.4e+03      36      62 ..     121     147 ..     117     181 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.8e-05
                                       HHHHHHHHS-TT-EEEETT-TTTH.HHHHHHHTT-E..EEEEESSHHHHHHHH CS
                       N6_N4_Mtase 181 lerlIklstkkgdivlDpFaGSGt.Tavaakelgrk..fiGieieeeyvelae 230
                                       +e +++ + k+g++v+D+ +G Gt T+++a+  gr+   i ++ +e+ +e+ e
  gi|298674706|ref|YP_003726456.1|  25 PEQILDNYVKPGQTVMDFGCGPGTyTIDMAQMVGRNgkVIAVDFQEKMLEILE 77 
                                       7899*******************98**********999999****99999877 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.3
                                       HHHHHHHHHHEEEEEEEEEEE-CCCHH CS
                       N6_N4_Mtase  36 ekvlkevrrvLkddgsifiniddseik 62 
                                        ++++e++ + k+ g +++   +    
  gi|298674706|ref|YP_003726456.1| 121 DNFFAELKTIVKPEGRLLVVEPEVHVR 147
                                       578999999999999998865554444 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.5e-05    0.0094       4      51 ..      38      86 ..      35     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.5e-05
                                      EEEEET-TTSHHHHHHHHHSTTS.EEEEEES-HHHHHHHHHHHHHCTTS CS
                    Methyltransf_4  4 vvleiGcGkGeflvalAkknPdk.nflGiEirvkvvakvlkkiealelk 51
                                      +v++ GcG G+ ++++A++   + ++++++ ++k+++ + kk ++++l+
  gi|298674706|ref|YP_003726456.1| 38 TVMDFGCGPGTYTIDMAQMVGRNgKVIAVDFQEKMLEILEKKCKKEGLE 86
                                      789***************9986548*******************99875 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.6e-05    0.0096     116     217 ..      36     139 ..       7     183 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.6e-05
                                       T-EEEEET-TTSHH...HHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T---EEEEEEE CS
                    Methyltransf_9 116 grtildvGcgnGyh...lwrmvgegaklvvGidPselfliqfeavrkllgedqrahllplgieqlpeleafdtvfsm 189
                                       g+t++d Gcg G +   + +mvg++   v+ +d +e  l  +e   k  g + r+       e +   e  d v++ 
  gi|298674706|ref|YP_003726456.1|  36 GQTVMDFGCGPGTYtidMAQMVGRNG-KVIAVDFQEKMLEILEKKCKKEGLESRVKIHQNNPESIGVSEKVDFVLAF 111
                                       799*********98444567788776.5899*********9999999999999999999999**************9 PP

                                       S-GGG-S-HHHH.HHHHHCTEEEEEEEEE CS
                    Methyltransf_9 190 GvlyhrrsPldh.llqlkdqlvkgGelvl 217
                                        v++     +d+ + +lk  ++ +G l++
  gi|298674706|ref|YP_003726456.1| 112 YVIH-ELPAIDNfFAELKTIVKPEGRLLV 139
                                       9985.555666515679999999999753 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   2.7e-05     0.017      23      88 ..      33      95 ..      16     150 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.7e-05
                   Methyltransf_32 23 esgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfaels 88
                                       ++ +tv+D+G+G g  +  +a+  +  + kv+++d +e++ e  ek  +k g  +++r++ ++++
  gi|298674706|ref|YP_003726456.1| 33 VKPGQTVMDFGCGPGTYTIDMAQ-MVGRNGKVIAVDFQEKMLEILEKKCKKEG--LESRVKIHQNN 95
                                      456799*********99999998.6679*************999998888877..65555544443 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.3   0.00064      0.39      27     126 ..      34     109 ..      31     152 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00064
                                       -TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHHHHHHHTT-GG CS
                           UPF0020  27 kpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvvqgareNaekagvgd 103
                                       kpg++ +D  CG Gt  I  a+++ +                         k++++D+++++++  +++ +k g++ 
  gi|298674706|ref|YP_003726456.1|  34 KPGQTVMDFGCGPGTYTIDMAQMVGRNG-----------------------KVIAVDFQEKMLEILEKKCKKEGLES 87 
                                       6777777777777777777777766655.......................58899999999999999999999999 PP

                                       GEEEEE--GGG--STTS---EEE CS
                           UPF0020 104 liefsqadaakLrlkegevdviv 126
                                       ++++ q +  ++   +++vd ++
  gi|298674706|ref|YP_003726456.1|  88 RVKIHQNNPESIG-VSEKVDFVL 109
                                       9999998888888.555788775 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00031      0.19      95     184 ..      36     137 ..      11     153 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00031
                              DREV  95 dkklldlGaGdGeitkrvaptfee...vyatelsetmrdrlkkk......kynv.lsalelqetdv..kldlilcln 159
                                        ++++d+G G G  t  +a+++ +   v a +  e+m + l+kk      + +v + +++ +  +v  k d +l++ 
  gi|298674706|ref|YP_003726456.1|  36 GQTVMDFGCGPGTYTIDMAQMVGRngkVIAVDFQEKMLEILEKKckkeglESRVkIHQNNPESIGVseKVDFVLAFY 112
                                       579******************987788***********999887221111122212222222223322566666666 PP

                              DREV 160 lldrcfdplklledirsalepngrv 184
                                       ++       +++ +++++ +p+gr 
  gi|298674706|ref|YP_003726456.1| 113 VIHELPAIDNFFAELKTIVKPEGRL 137
                                       6666666666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.50
# Mc/sec: 1137.85
//
Query:       gi|298674707|ref|YP_003726457.1|  [L=407]
Description: HNH endonuclease [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-63  214.3   3.4    1.6e-63  213.7   3.4    1.3  1  RRXRR     RRXRR protein
    7.3e-11   42.1   8.0    1.6e-10   41.0   8.0    1.6  1  HNH       HNH endonuclease
    9.1e-07   28.6   5.3    2.1e-06   27.5   5.3    1.6  1  HNH_5     HNH endonuclease
    0.00022   21.3   0.5    0.00099   19.2   0.5    2.1  1  HNH_2     HNH endonuclease
  ------ inclusion threshold ------
        9.9    5.9   7.4        1.3    8.6   2.8    1.9  2  zf_UBZ    Ubiquitin-Binding Zinc Finger


Domain annotation for each model (and alignments):
>> RRXRR  RRXRR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.7   3.4   4.5e-67   1.6e-63       1     174 []       3     176 ..       3     176 .. 0.99

  Alignments for each domain:
  == domain 1  score: 213.7 bits;  conditional E-value: 4.5e-67
                             RRXRR   1 VfVldkegkplmPtkpkrarklLkqgkAkvvrrkpftiqLkeesseesvqpvelklDpGskvtGiavvsekkvllka 77 
                                       VfVl+k++kplmPt+p++ar+lL++gkAkvvrr pfti+L+++++e++ qpv  ++D+Gsk++G+a+v +++vl+++
  gi|298674707|ref|YP_003726457.1|   3 VFVLSKNKKPLMPTRPAKARRLLESGKAKVVRRSPFTIKLLYDTAEYT-QPVIAGMDSGSKHIGCAAVANDEVLYQS 78 
                                       9***********************************************.**************************** PP

                             RRXRR  78 elelrgkdikkkleeRrelRraRRsrktryrqaRfdnR..kkkegwLapslqhrvqthlrvvkrlakllpitkivve 152
                                       e+elr  d++kk+++R+++Rr+RRsrktryr++Rf+nR  +kk+g++aps++++vq+h r  + ++++lp++k+ ve
  gi|298674707|ref|YP_003726457.1|  79 EVELRD-DVSKKVQQRASYRRNRRSRKTRYRKPRFNNRgnSKKDGRIAPSIKSKVQSHERERRFVESILPVKKWIVE 154
                                       *****9.********************************99************************************ PP

                             RRXRR 153 lvkfDiqklenpeisgaeyqqG 174
                                       +++fDi+k++np++sg++yq+G
  gi|298674707|ref|YP_003726457.1| 155 TASFDIHKITNPNVSGTDYQNG 176
                                       ********************98 PP

>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   8.0   4.6e-14   1.6e-10       1      46 [.     196     240 ..     196     241 .. 0.96

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 4.6e-14
                               HNH   1 CeyCgrkfhksealevdHiipisqggaddieNlqllCksCHnkkhd 46 
                                       C+ C++  ++ + le++Hi+ +s+gg++  +Nl++lC++CH k+h+
  gi|298674707|ref|YP_003726457.1| 196 CQKCKNRSKD-PKLECHHIVFRSKGGTNRPDNLITLCETCHGKLHN 240
                                       *******777.7*********************************8 PP

>> HNH_5  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   5.3   5.9e-10   2.1e-06       1      44 [.     196     239 ..     196     244 .. 0.96

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 5.9e-10
                             HNH_5   1 CiyCgkeiaekelseeHIiPeslGGkltisnlvtlCkkCNqkkg 44 
                                       C+ C+++ ++ +l+  HI+ +s+GG++ ++nl tlC++C+ k+ 
  gi|298674707|ref|YP_003726457.1| 196 CQKCKNRSKDPKLECHHIVFRSKGGTNRPDNLITLCETCHGKLH 239
                                       9***************************************9985 PP

>> HNH_2  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.5   2.8e-07   0.00099      11      72 .]     207     246 ..     196     246 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.8e-07
                             HNH_2  11 lleaAHIiPwslssffndlilnrfeigrillekgstidspsNgllLspdiHklFdqflfafe 72 
                                        le++HI+           ++            ++++++p+N+++L+ ++H   ++++f+++
  gi|298674707|ref|YP_003726457.1| 207 KLECHHIVF----------RS------------KGGTNRPDNLITLCETCHGKLHNGKFTIN 246
                                       566666665..........33............4569**********************996 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   2.8   0.00037       1.3       1      20 [.     192     211 ..     192     212 .. 0.94
   2 ?   -2.1   0.1      0.83     3e+03       4       9 ..     230     235 ..     229     238 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00037
                            zf_UBZ   1 dtylCerCgkeipeselqEH 20 
                                       d+y+C++C+ +  +++l++H
  gi|298674707|ref|YP_003726457.1| 192 DNYTCQKCKNRSKDPKLECH 211
                                       79****************99 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.83
                            zf_UBZ   4 lCerCg 9  
                                       lCe C+
  gi|298674707|ref|YP_003726457.1| 230 LCETCH 235
                                       7****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       953  (0.0531541); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2801.15
//
Query:       gi|298674708|ref|YP_003726458.1|  [L=195]
Description: signal transduction histidine kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-28   98.4   5.1    3.7e-28   97.4   5.1    1.5  1  HisKA_2       Histidine kinase
    1.7e-09   38.2   2.2    2.2e-08   34.6   1.1    2.7  2  HATPase_c     Histidine kinase-, DNA gyrase B-, and HSP90-lik
    4.9e-07   30.3   0.2    7.5e-07   29.8   0.2    1.3  1  HWE_HK        HWE histidine kinase
    0.00062   19.7   0.0     0.0011   18.9   0.0    1.4  1  HATPase_c_2   Histidine kinase-like ATPase domain
     0.0017   18.2   0.4     0.0032   17.3   0.4    1.4  1  HATPase_c_3   Histidine kinase-, DNA gyrase B-, and HSP90-lik
  ------ inclusion threshold ------
       0.16   11.4   0.1        0.2   11.1   0.1    1.1  1  Met_synt_B12  Vitamin B12 dependent methionine synthase, acti


Domain annotation for each model (and alignments):
>> HisKA_2  Histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.4   5.1   1.2e-31   3.7e-28       1      76 []       9      84 ..       9      84 .. 0.98

  Alignments for each domain:
  == domain 1  score: 97.4 bits;  conditional E-value: 1.2e-31
                           HisKA_2  1 EihHRvkNnLqvisslLslqarkakdeevkealresqnRvlsialiheeLyksedletvdfseylekLvenlfksy 76
                                      E+hHR+kNnLq+i sl++lq+++++de+v +a+r++qnRv s++l+h++Ly+s++l++++++ y+++L+enl ++y
  gi|298674708|ref|YP_003726458.1|  9 ELHHRIKNNLQIINSLINLQSENFDDEDVINAFRDTQNRVSSMSLVHQKLYQSQELNNLSLNGYIKDLAENLNDIY 84
                                      99*********************************************************************98765 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.31   9.3e+02      56      90 ..      53      86 ..       7     106 .. 0.61
   2 !   34.6   1.1   7.3e-12   2.2e-08       5     107 ..     107     194 ..     103     195 .] 0.77

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.31
                                      GTCSTTCHHCSTCHTSTSSSHHHHHHHHHHHHTTT CS
                         HATPase_c 56 klfekfsqddstkrggggtGlGlsivkklvelmgG 90
                                      ++++k++q +++ ++ + +G+   ++++l + +gG
  gi|298674708|ref|YP_003726458.1| 53 LVHQKLYQ-SQELNNLSLNGYIKDLAENLNDIYGG 86
                                      55666666.56666666666655555555555554 PP

  == domain 2  score: 34.6 bits;  conditional E-value: 7.3e-12
                                       HHHHHHHHHHHHHHHHHS...TTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHH CS
                         HATPase_c   5 rLrqiisnlvdNavkfat...kageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGl 78 
                                        L  i++++++N++k+a    ++g i +e +++ + +v+ +eDnG+Gip ++     e+  +            lGl
  gi|298674708|ref|YP_003726458.1| 107 PLGMIVNEIISNSLKYAFsddDNGIINIEFNSN-KCYVLIIEDNGKGIPDNIDI---ENPGT------------LGL 167
                                       67789***********55523444555555534.599999*********95544...33333............8** PP

                                       HHHHHHHHHTTTEEEEEEETTTEEEEEEE CS
                         HATPase_c  79 sivkklvelmgGeiwvesepgrGttftft 107
                                        + + lv++++Gei++e ++  Gt+f+++
  gi|298674708|ref|YP_003726458.1| 168 QLINTLVKQLNGEIELERKS--GTKFIIR 194
                                       ****************7777..***9986 PP

>> HWE_HK  HWE histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.2   2.5e-10   7.5e-07       1      53 [.       9      63 ..       9      96 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 2.5e-10
                                      HHHHHHHHHHHHHHHHHHHHSSSXS-HH..HHHHHHHHHHHHHHHHHHHHHHCTT CS
                            HWE_HK  1 ElnHRvKNlLavvqsiarqtlrsaesle..efaeklsgRLqALsaahdllsreew 53
                                      El+HR+KN L +++s+++  +++ ++ +  ++ ++ ++R+ ++s +h+ l +++ 
  gi|298674708|ref|YP_003726458.1|  9 ELHHRIKNNLQIINSLINLQSENFDDEDviNAFRDTQNRVSSMSLVHQKLYQSQE 63
                                      9*****************99888766652245667889*********99888764 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   3.6e-07    0.0011      22     121 ..      98     191 ..      89     195 .] 0.78

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.6e-07
                       HATPase_c_2  22 aglseelldeirlaveEactNavehayleapegpvevrlesdeealtvevaDsGpg.fdpetlpdpteeepkeslke 97 
                                       ++l  +++  + + v+E+++N  ++a  ++ +g +++++  +++  ++ ++D+G+g  d  +            + +
  gi|298674708|ref|YP_003726458.1|  98 FHLGIDTIIPLGMIVNEIISNSLKYAFSDDDNGIINIEFN-SNKCYVLIIEDNGKGiPDNID-----------IENP 162
                                       5566677778899*************************84.44557888*******777764...........4556 PP

                       HATPase_c_2  98 gGrGlalikglvDev..ey...dgegnvv 121
                                       g +Gl li++lv ++  e+   ++ g++ 
  gi|298674708|ref|YP_003726458.1| 163 GTLGLQLINTLVKQLngEIeleRKSGTKF 191
                                       77999999999999866556555556655 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.4   1.1e-06    0.0032       7      52 ..     112     161 ..     108     179 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.1e-06
                       HATPase_c_3   7 laelvdNsld...Adaen..vkievnknrgktgeivieDdGkGmsee.elkn 52 
                                       + e++ Nsl    +d  n  ++ie+n n+     + ieD+GkG++ + +++n
  gi|298674708|ref|YP_003726458.1| 112 VNEIISNSLKyafSDDDNgiINIEFNSNK--CYVLIIEDNGKGIPDNiDIEN 161
                                       679*****997554444477888888875..799**********99988887 PP

>> Met_synt_B12  Vitamin B12 dependent methionine synthase, activation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   6.7e-05       0.2      52     136 ..      14      97 ..       7     126 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.7e-05
                      Met_synt_B12  52 ieekllkakavvglfpAnsegddie.vytdesrsevlatlhtLRqqeekeeeepnlcLaDfvapkesgikdyiGlFa 127
                                       i+++l  ++  ++l   n +++d++  ++d++  + + ++ ++ q+  +++e +nl+L  +++  +++++d  G   
  gi|298674708|ref|YP_003726458.1|  14 IKNNLQIINSLINLQSENFDDEDVInAFRDTQ--NRVSSMSLVHQKLYQSQELNNLSLNGYIKDLAENLNDIYGGNN 88 
                                       55566667777777777777766540443433..45677888889888889999******************99888 PP

                      Met_synt_B12 128 vtagigiee 136
                                       + +++++++
  gi|298674708|ref|YP_003726458.1|  89 TKINVDVQD 97 
                                       777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       809  (0.0451224); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1399.08
//
Query:       gi|298674709|ref|YP_003726459.1|  [L=100]
Description: carboxymuconolactone decarboxylase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.2e-12   45.7   0.0    5.7e-12   45.5   0.0    1.1  1  CMD             Carboxymuconolactone decarboxylase family
  ------ inclusion threshold ------
        0.1   12.4   0.0       0.11   12.2   0.0    1.0  1  DNA_pol3_delta  DNA polymerase III, delta subunit


Domain annotation for each model (and alignments):
>> CMD  Carboxymuconolactone decarboxylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.0   6.4e-16   5.7e-12       9      83 ..      27      99 ..      18     100 .] 0.88

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 6.4e-16
                                      HHHHHHCCGSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHSHHHHHHHHHHH CS
                               CMD  9 alreallareggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaqaaayagwpaaraAlaaa 83
                                      ++ e    ++g+L++k++ Lia+a  a ng  + v+a  + A+eaG+teeei ev+ +  + +g+  + +A +a+
  gi|298674709|ref|YP_003726459.1| 27 NFSETQ--TDGALSAKTKLLIAMALDAGNGDIDGVKALSQHAREAGATEEEILEVIKVIGSVCGTQGLFYATKAF 99
                                      444444..49********************************************************999999987 PP

>> DNA_pol3_delta  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.3e-05      0.11      66     151 ..      10      99 ..       4     100 .] 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.3e-05
                                       -......TT-S-TTHHHHHHHHTT..T--SSEEEEEEES..S--HHHHHHHHHTTTEEEEEE----TTTHHHHHHHH CS
                    DNA_pol3_delta  66 pkllt.kesklnekllkeLeeyls..nlpedtlLiliap.kklderkklvklLkkkatvveaktlkeeelkkwiqkr 138
                                       +++l+ k  k  ++ll++++e+ +   l+++t L++ +  +  +     vk L ++a+   a++ +  e++k i ++
  gi|298674709|ref|YP_003726459.1|  10 LQILKeKDPKYAANLLENFSETQTdgALSAKTKLLIAMAlDAGNGDIDGVKALSQHAREAGATEEEILEVIKVIGSV 86 
                                       345558888999999999998875226899999999999677777777***************************** PP

                                       HHHTT-EE-HHHH CS
                    DNA_pol3_delta 139 aqelglkiekeal 151
                                       + ++gl   ++a+
  gi|298674709|ref|YP_003726459.1|  87 CGTQGLFYATKAF 99 
                                       *****99888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 705.35
//
Query:       gi|298674710|ref|YP_003726460.1|  [L=289]
Description: hypothetical protein Metev_0763 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-05   25.1  15.6     0.0023   18.0   9.8    2.6  2  Rhomboid  Rhomboid family


Domain annotation for each model (and alignments):
>> Rhomboid  Rhomboid family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   9.8   1.3e-07    0.0023       6     116 ..      57     173 ..      52     204 .. 0.75
   2 !   10.1   0.3   3.3e-05      0.59     103     142 ..     231     277 ..     209     284 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.3e-07
                                       -TTHHHHGGG--SSHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHHHHH-S....-EESSHHHH CS
                          Rhomboid   6 elwrlltsmflHagwlHllfNmlallvfGsplerrlGslr..flllyllsglagsllsllfsaeses.plvGaSGai 79 
                                       el  +++s   H ++ H+l N++  +++ s + r +   +  ++ ++l+ g++  l+s+      ++  ++G+SG++
  gi|298674710|ref|YP_003726460.1|  57 ELIPIYFSNYAHSNIQHFLQNLIPYYLLISLIFRFHDNRYqfYIDMFLIFGILPLLISFSNIISFQYkNTLGFSGIV 133
                                       6777889999**********************9999654411445799999998877665444433339******** PP

                                       HHHHHHHHHHHHCCCCGS----HC......CCCCCCCCCC CS
                          Rhomboid  80 fgllgallvlvprnrkllrkliia...llllllfillnlv 116
                                       ++l+ +ll++v++  ++  +l +    +++++ f ++ ++
  gi|298674710|ref|YP_003726460.1| 134 AALVSYLLYTVYTYIQKQCNLYFRniiPVFIFGFTVFIII 173
                                       *********9998887777777773333333333333322 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 3.3e-05
                                       C.........CCCCCCCCCCHHHCTSS.STTTHHHHHHHHHHHHHHH CS
                          Rhomboid 103 a......llllllfillnlvlgllpra.ggvsnlAHlgGllaGlllg 142
                                       +      + + ++++++ ++l+l+p +  + + l H +G ++Gl++ 
  gi|298674710|ref|YP_003726460.1| 231 DiftdlyIFMTIIVFIIVIFLSLFPVNiNNTNILSHYIGYCFGLFAP 277
                                       333345434444445555555666666799*************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1209  (0.0674327); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2148.37
//
Query:       gi|298674711|ref|YP_003726461.1|  [L=270]
Description: hypothetical protein Metev_0764 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.5e-22   77.4   0.1    1.5e-21   76.3   0.1    1.7  1  DUF1724   Domain of unknown function (DUF1724)
  ------ inclusion threshold ------
      0.013   15.4   0.3      0.028   14.3   0.3    1.5  1  HTH_11    HTH domain


Domain annotation for each model (and alignments):
>> DUF1724  Domain of unknown function (DUF1724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.3   0.1   1.7e-25   1.5e-21       2      62 .]     199     259 ..     198     259 .. 0.97

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 1.7e-25
                           DUF1724   2 klyvydeeikplsltvtDkflslslfdkdgkydhkdlisfdesAlkWGeeLFeyYlkrSep 62 
                                       kl + +++ik+ + ++tD+f+ l++fdkd+++d ++++sfdesAlkWG eLF+yY ++S+p
  gi|298674711|ref|YP_003726461.1| 199 KLHISNGNIKLTAAAITDRFVFLCFFDKDQRFDLQYIMSFDESALKWGGELFQYYINQSTP 259
                                       78999******************************************************97 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.3   3.2e-06     0.028       2      42 ..      15      53 ..      14      59 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.2e-06
                            HTH_11  2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeel 42
                                      ++++l lL  +++p ++++++  Lnv+ + +   Ik+L+e+
  gi|298674711|ref|YP_003726461.1| 15 RKKLLLLL--NDNPKNIDYIKTSLNVTSTSIMPQIKILKEK 53
                                      45666666..444458**********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1984.68
//
Query:       gi|298674712|ref|YP_003726462.1|  [L=104]
Description: ArsR family transcriptional regulator [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-11   44.3   0.1    1.7e-11   43.8   0.1    1.3  1  HTH_5        Bacterial regulatory protein, arsR family
      8e-11   41.8   0.0    1.2e-10   41.3   0.0    1.2  1  HTH_20       Helix-turn-helix domain
    3.1e-05   23.8   0.3    0.00011   22.1   0.3    1.8  1  PadR         Transcriptional regulator PadR-like family
    4.1e-05   23.4   0.1    6.5e-05   22.8   0.1    1.3  1  HTH_11       HTH domain
    4.9e-05   23.1   0.1    6.9e-05   22.7   0.1    1.3  1  TrmB         Sugar-specific transcriptional regulator TrmB
     0.0008   19.5   0.3     0.0011   19.1   0.3    1.2  1  HTH_34       Winged helix DNA-binding domain
    0.00096   18.7   0.0     0.0017   17.9   0.0    1.4  1  HTH_24       Winged helix-turn-helix DNA-binding
      0.001   19.2   0.1     0.0014   18.8   0.1    1.2  1  HTH_Tnp_1_2  Helix-turn-helix of insertion element transposas
     0.0013   18.6   0.0     0.0021   18.0   0.0    1.3  1  MarR         MarR family
     0.0029   17.4   0.1     0.0049   16.6   0.1    1.4  1  HTH_23       Homeodomain-like domain
     0.0065   16.3   0.0     0.0086   15.9   0.0    1.2  1  MarR_2       MarR family
     0.0068   17.0   0.2      0.012   16.2   0.2    1.5  1  Mga          Mga helix-turn-helix domain
  ------ inclusion threshold ------
      0.011   16.1   0.0      0.016   15.5   0.0    1.3  1  Rrf2         Transcriptional regulator
       0.02   15.3   0.0      0.053   14.0   0.0    1.7  1  HTH_26       Cro/C1-type HTH DNA-binding domain
      0.037   14.1   0.1      0.066   13.2   0.1    1.3  1  HTH_29       Winged helix-turn helix
      0.044   13.6   0.1       0.06   13.2   0.1    1.3  1  HxlR         HxlR-like helix-turn-helix
      0.065   13.0   0.0       0.11   12.4   0.0    1.3  1  HTH_10       HTH DNA binding domain
      0.074   12.8   0.3       0.12   12.1   0.3    1.4  1  HTH_8        Bacterial regulatory protein, Fis family


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.1   1.7e-14   1.7e-11       1      47 []      17      63 ..      17      63 .. 0.97

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 1.7e-14
                                      SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                      +p Rlk++++Lae+e +v ela+el++s+  +  HLk+L++a++Ve+
  gi|298674712|ref|YP_003726462.1| 17 HPLRLKLIYMLAEREWYVYELAKELKISRQVLYLHLKRLEKADFVES 63
                                      589******************************************96 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.0   1.2e-13   1.2e-10       2      56 ..      10      63 ..       9      65 .. 0.96

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 1.2e-13
                                      HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      +i eA++hP R+++  +L  +++  + ela++l +s++ l+ HL+ Le+a++ve+
  gi|298674712|ref|YP_003726462.1| 10 DIGEAISHPLRLKLIYML-AEREWYVYELAKELKISRQVLYLHLKRLEKADFVES 63
                                      5779**************.**********************************96 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.3   1.1e-07   0.00011       2      65 ..      24      80 ..      23      83 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.1e-07
                                      HHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-S.TSSS-EEEEEE CS
                              PadR  2 LalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglvesewees.gegpprkyYrl 65
                                      +++l+e++ y ye++kel+ +           lY  LkrLek ++ves  + + ++ +++k++rl
  gi|298674712|ref|YP_003726462.1| 24 IYMLAEREWYVYELAKELKIS--------RQVLYLHLKRLEKADFVESDLRLEdEDMRAKKFFRL 80
                                      67899************9988........347****************998887999*****998 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.1   6.6e-08   6.5e-05       3      42 ..      21      58 ..      19      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 6.6e-08
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeel 42
                                      l+++ +L ++r+ +   eLA+eL++Sr++ + ++k+Le++
  gi|298674712|ref|YP_003726462.1| 21 LKLIYML-AERE-WYVYELAKELKISRQVLYLHLKRLEKA 58
                                      6888899.7777.9***********************986 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1   6.9e-08   6.9e-05      15      54 ..      24      63 ..      22      83 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 6.9e-08
                                      HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                              TrmB 15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                                      +++l++ +  ++e+a+el+++r+  Y  L++Le++++Ve 
  gi|298674712|ref|YP_003726462.1| 24 IYMLAEREWYVYELAKELKISRQVLYLHLKRLEKADFVES 63
                                      5688999999****************************97 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.3   1.1e-06    0.0011       1      51 [.      19      68 ..      19      75 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.1e-06
                            HTH_34  1 vRlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefk 51
                                      +Rl+++ +La+ ++    el ++l+++   L+ hlk Leka+++e d+ ++
  gi|298674712|ref|YP_003726462.1| 19 LRLKLIYMLAEREWY-VYELAKELKISRQVLYLHLKRLEKADFVESDLRLE 68
                                      699999999887775.568999***********************998776 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.7e-06    0.0017      22      48 .]      36      62 ..      36      62 .. 0.96

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.7e-06
                            HTH_24 22 eLAerlglSpstvnrrlkrLeeeGlIk 48
                                      eLA++l +S++ +  +lkrLe++ +++
  gi|298674712|ref|YP_003726462.1| 36 ELAKELKISRQVLYLHLKRLEKADFVE 62
                                      8**********************9986 PP

>> HTH_Tnp_1_2  Helix-turn-helix of insertion element transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   1.4e-06    0.0014      13      67 ..      21      75 ..      17      91 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.4e-06
                                      HHHHHHHHHHHH--S-HHHHHHHHTS-HHHHHHHH...H-HHHHHHHHHHHHHHHHTT CS
                       HTH_Tnp_1_2 13 kkaaellvendyekltldeiaeevgvsrsTlykWk...kkkeFieyvnelaeefleee 67
                                      +k++++l+e+++    + e+a+e+ +sr+ ly  +   +k +F+e   +l +e + ++
  gi|298674712|ref|YP_003726462.1| 21 LKLIYMLAEREW---YVYELAKELKISRQVLYLHLkrlEKADFVESDLRLEDEDMRAK 75
                                      699********9...99***************65433489999999888888777665 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.1e-06    0.0021      19      49 ..      33      63 ..      20      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.1e-06
                                      EHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR 19 svseLakklgvskstvtrvldrLekkGlieR 49
                                      +v eLak l++s+  +   l+rLek++++e+
  gi|298674712|ref|YP_003726462.1| 33 YVYELAKELKISRQVLYLHLKRLEKADFVES 63
                                      688**************************97 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   4.9e-06    0.0049       6      41 ..      19      55 ..      15      63 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.9e-06
                            HTH_23  6 eRlrillllae.GlsvreIAreLgvsrrTvyrwlkry 41
                                       Rl+ +++lae  + v e A+eL +sr+ +y  lkr 
  gi|298674712|ref|YP_003726462.1| 19 LRLKLIYMLAErEWYVYELAKELKISRQVLYLHLKRL 55
                                      69********99******************9999996 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   8.7e-06    0.0086      23      53 ..      33      63 ..      17      74 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.7e-06
                                      EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2 23 tvgelarrlglsksavsrilkrLvaaGLver 53
                                       v ela++l++s++ +  +lkrL++a +ve 
  gi|298674712|ref|YP_003726462.1| 33 YVYELAKELKISRQVLYLHLKRLEKADFVES 63
                                      688**************************85 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.2   1.2e-05     0.012      22      65 ..      23      67 ..       3      76 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-05
                                      HHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHHHH.CHCCT-EE CS
                               Mga 22 lkflfeeeevsieelaqelyiSestlkrkikelnkl.Lkefdlel 65
                                      l +++ e+e  ++ela+el iS+  l+ ++k+l+k    e dl+l
  gi|298674712|ref|YP_003726462.1| 23 LIYMLAEREWYVYELAKELKISRQVLYLHLKRLEKAdFVESDLRL 67
                                      457889999************************874244556555 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   1.7e-05     0.016      26      57 ..      32      63 ..      18      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.7e-05
                                      B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2 26 vsseeiaerqnispsylekilakLrkaglvks 57
                                        + e+a++ +is+++l   l++L+ka++v+s
  gi|298674712|ref|YP_003726462.1| 32 WYVYELAKELKISRQVLYLHLKRLEKADFVES 63
                                      5688**************************99 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.3e-05     0.053       1      32 [.      22      53 ..      22      60 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.3e-05
                            HTH_26  1 kLrelmadrgitkseLargtgisaatlsrlvk 32
                                      kL  ++a+r+  ++eLa+ + is++ l+ ++k
  gi|298674712|ref|YP_003726462.1| 22 KLIYMLAEREWYVYELAKELKISRQVLYLHLK 53
                                      56779**********************98877 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   6.7e-05     0.066       2      38 ..      22      57 ..      22      61 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.7e-05
                            HTH_29  2 aqallllaeGvstvsqiAkllglsrrtvyrwlkrfee 38
                                      +++ +l++++++ v ++Ak l +sr+  y +lkr e+
  gi|298674712|ref|YP_003726462.1| 22 KLIYMLAEREWY-VYELAKELKISRQVLYLHLKRLEK 57
                                      67899999***9.*********************886 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   6.1e-05      0.06      10      52 ..      23      64 ..      14      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.1e-05
                                      HHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEE CS
                              HxlR 10 ilvellkgkkRfselkralpkisqkmLaqrLreLeqdgliere 52
                                      +++ l + +    el+++l kis+++L  +L++Le+  ++e +
  gi|298674712|ref|YP_003726462.1| 23 LIYMLAEREWYVYELAKEL-KISRQVLYLHLKRLEKADFVESD 64
                                      5677777777888999**9.******************99876 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00011      0.11      24      49 ..      32      57 ..      28      58 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                            HTH_10 24 vtlkeLAkelGIskstlsehLrkaes 49
                                        + eLAkel Is++ l+ hL++ e+
  gi|298674712|ref|YP_003726462.1| 32 WYVYELAKELKISRQVLYLHLKRLEK 57
                                      55679*****************9886 PP

>> HTH_8  Bacterial regulatory protein, Fis family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   0.00013      0.12      14      42 .]      27      55 ..      23      55 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                                      HHHTTT-HHHHHHHHTS-HHHHHHHHHHT CS
                             HTH_8 14 LertgGnkskAArlLGisRrtLyrKLkkY 42
                                      L++ ++ + + A++L isR+ Ly  Lk++
  gi|298674712|ref|YP_003726462.1| 27 LAEREWYVYELAKELKISRQVLYLHLKRL 55
                                      55666777789*************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 773.41
//
Query:       gi|298674713|ref|YP_003726463.1|  [L=76]
Description: hypothetical protein Metev_0767 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.2e-06   26.2   0.4    8.2e-06   26.0   0.4    1.0  1  TssO            Type VI secretion system, TssO
     0.0013   18.8   0.0     0.0014   18.6   0.0    1.0  1  DUF4577         Domain of unknown function (DUF4577)
     0.0028   15.7   0.0     0.0033   15.5   0.0    1.0  1  Prominin        Prominin
     0.0038   16.8   1.7     0.0045   16.6   1.7    1.1  1  DUF5385         Family of unknown function (DUF5385)
     0.0041   17.2   0.0     0.0053   16.8   0.0    1.1  1  PspB            Phage shock protein B
     0.0049   17.1   0.2     0.0056   17.0   0.2    1.0  1  MscL            Large-conductance mechanosensitive channel, M
     0.0065   16.4   0.0     0.0093   15.9   0.0    1.3  1  FixQ            Cbb3-type cytochrome oxidase component FixQ
  ------ inclusion threshold ------
      0.011   15.6   1.6      0.014   15.4   1.6    1.2  1  Holin_BhlA      BhlA holin family
      0.014   15.6   0.2      0.015   15.4   0.2    1.0  1  UPF0242         Uncharacterised protein family (UPF0242) N-te
      0.015   15.4   0.0      0.018   15.2   0.0    1.1  1  UPF0239         Uncharacterised protein family (UPF0239)
      0.016   15.0   0.3       0.02   14.8   0.3    1.1  1  ODV-E18         Occlusion-derived virus envelope protein ODV-
      0.021   14.9   1.4      0.021   14.9   1.4    1.5  2  DUF1664         Protein of unknown function (DUF1664)
      0.024   14.2   0.1      0.028   14.0   0.1    1.1  1  Trimer_CC       Trimerisation motif
      0.025   14.9   0.2      0.029   14.6   0.2    1.1  1  KxDL            Uncharacterized conserved protein
      0.025   14.8   0.8      0.029   14.6   0.8    1.1  1  BLOC1_2         Biogenesis of lysosome-related organelles com
      0.034   14.4   0.1      0.041   14.1   0.1    1.2  1  Chordopox_A13L  Chordopoxvirus A13L protein
      0.054   13.1   0.4      0.065   12.8   0.4    1.1  1  SLATT_6         SMODS and SLOG-associating 2TM effector domai
      0.054   13.9   3.4      0.078   13.4   3.4    1.3  1  FlaC_arch       Flagella accessory protein C (FlaC)
      0.065   13.2   0.0      0.076   13.0   0.0    1.3  1  CbiN            Cobalt transport protein component CbiN
      0.073   12.8   0.0      0.081   12.6   0.0    1.0  1  Tetraspanin     Tetraspanin family
       0.08   12.8   0.0      0.084   12.7   0.0    1.1  1  Lig_chan        Ligand-gated ion channel
      0.085   11.6   0.3        0.1   11.4   0.3    1.0  1  HN              Haemagglutinin-neuraminidase
      0.098   12.6   0.2       0.13   12.2   0.2    1.2  1  60KD_IMP        60Kd inner membrane protein
       0.17   11.9   2.8       0.22   11.6   2.8    1.1  1  APC_N_CC        Coiled-coil N-terminus of APC, dimerisation d
       0.33   10.6   2.3       0.44   10.2   2.3    1.1  1  SPT_ssu-like    Small subunit of serine palmitoyltransferase-
       0.45    9.3   3.5       0.72    8.6   3.5    1.4  1  PV-1            PV-1 protein (PLVAP)
        3.2    7.0   9.1          3    7.1   0.9    2.0  2  CorA            CorA-like Mg2+ transporter protein
        6.4    6.1   5.5        3.7    6.8   0.3    1.9  2  ThrE            Putative threonine/serine exporter


Domain annotation for each model (and alignments):
>> TssO  Type VI secretion system, TssO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.4   1.3e-08   8.2e-06      11      73 ..      15      75 ..      10      76 .] 0.71

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.3e-08
                              TssO 11 lyflllFlvtvlllflivffffkssplqekeillkelerkkkfeekqkelkkkvdsiykkIds 73
                                      +  +l  ++++++++ iv +f ++s  + +e   +  er++k+e++ +++k++v++i++k+d 
  gi|298674713|ref|YP_003726463.1| 15 FGIFLNIILVLIIIG-IVLYFLNKSNNTGSENK-ESSERISKIEKDVEDIKETVEEIKQKLDE 75
                                      334444445555555.45555554666666666.89************************997 PP

>> DUF4577  Domain of unknown function (DUF4577)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.2e-06    0.0014      63     121 ..      17      74 ..       2      76 .] 0.68

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.2e-06
                           DUF4577  63 ffvgliivlivslalvsfvifliiqtgskmddvsrrltaegkdidelkkinsmivkrln 121
                                       +f+ +i+vli+ + +v + +     tgs+  + s r++   kd++++k   + i ++l+
  gi|298674713|ref|YP_003726463.1|  17 IFLNIILVLII-IGIVLYFLNKSNNTGSENKESSERISKIEKDVEDIKETVEEIKQKLD 74 
                                       24444444443.3444444555678***********************99988888886 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   5.1e-06    0.0033     142     199 ..      15      76 .]      12      76 .] 0.76

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.1e-06
                          Prominin 142 lgvllllltlllliGviiaFv..tNkaldegleesk..etvkrgledlrtflkdvpqhidhv 199
                                       +g++l ++++l++iG+++ F+  +N+  +e+ e+s+  +++++ +ed++  ++++ q++d++
  gi|298674713|ref|YP_003726463.1|  15 FGIFLNIILVLIIIGIVLYFLnkSNNTGSENKESSEriSKIEKDVEDIKETVEEIKQKLDEI 76 
                                       89******************844555555554444322567888999999999999998875 PP

>> DUF5385  Family of unknown function (DUF5385)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   1.7   7.1e-06    0.0045       5      52 ..      18      66 ..      14      76 .] 0.54

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 7.1e-06
                           DUF5385  5 fliiliiiiiiilvivfllrkkkkqkeeekaggkikersdkd..EVWkti 52
                                      fl i++++iii  ++ ++l k  +   e+k++++  ++ +kd  ++  t+
  gi|298674713|ref|YP_003726463.1| 18 FLNIILVLIII-GIVLYFLNKSNNTGSENKESSERISKIEKDveDIKETV 66
                                      56666665555.88999999998866665555444333333311343343 PP

>> PspB  Phage shock protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   8.2e-06    0.0053       8      65 ..      18      74 ..      12      75 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8.2e-06
                              PspB  8 pliifvlfVapiWLiLHYrskkkrskglsaedekrLeellekAekleeRietLEriLd 65
                                       l  ++l++++i+++L++ +k+++  + ++e  +r++++ ++ e ++e +e + + Ld
  gi|298674713|ref|YP_003726463.1| 18 FLN-IILVLIIIGIVLYFLNKSNNTGSENKESSERISKIEKDVEDIKETVEEIKQKLD 74
                                      333.45666789***********************************99998877776 PP

>> MscL  Large-conductance mechanosensitive channel, MscL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.2   8.8e-06    0.0056      68     119 ..      15      72 ..       9      74 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 8.8e-06
                              MscL  68 ygafiqavinFliiafviFlivkaink....kkke..eeeeeeaee....keeellteirdl 119
                                       +g f++ ++ ++ii++v++++ k  n+    k  e  e+ ++   e    + +e ++ei++ 
  gi|298674713|ref|YP_003726463.1|  15 FGIFLNIILVLIIIGIVLYFLNKSNNTgsenK--EssERISKI--EkdveDIKETVEEIKQK 72 
                                       799*****************999999886421..222222211..12332333667777765 PP

>> FixQ  Cbb3-type cytochrome oxidase component FixQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.4e-05    0.0093       7      35 ..      12      40 ..      10      55 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.4e-05
                              FixQ  7 rgfadswgllflvllfygvviyafrpgnr 35
                                      + f  +++ ++lvl+ +g+v+y ++++n+
  gi|298674713|ref|YP_003726463.1| 12 SPFFGIFLNIILVLIIIGIVLYFLNKSNN 40
                                      568889999******************93 PP

>> Holin_BhlA  BhlA holin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   1.6   2.1e-05     0.014      16      68 ..      24      76 .]      16      76 .] 0.87

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.1e-05
                        Holin_BhlA 16 avLfvvllvYilkkqekreekqeerekkyqeiikkltekfeiveeikkdvdei 68
                                      ++  + +++Y+l+k+++  +  +e  ++  +i k++ +  e+veeik+++dei
  gi|298674713|ref|YP_003726463.1| 24 VLIIIGIVLYFLNKSNNTGSENKESSERISKIEKDVEDIKETVEEIKQKLDEI 76
                                      344556789********99999999999999999999999**********998 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.2   2.4e-05     0.015      38      94 ..      15      72 ..      11      76 .] 0.71

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.4e-05
                           UPF0242 38 iGlllaaaGsLlllllllkw.ekalkeklekskleekeaklteldeglktkeealeel 94
                                      +G++l ++  L+++ ++l++ +k  +++ e+++ +e+++k+ +  e++k+  e++++ 
  gi|298674713|ref|YP_003726463.1| 15 FGIFLNIILVLIIIGIVLYFlNKSNNTGSENKESSERISKIEKDVEDIKETVEEIKQK 72
                                      8999999999999988777714445556688888888888887776666666665543 PP

>> UPF0239  Uncharacterised protein family (UPF0239)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   2.8e-05     0.018      23      79 ..      15      72 ..      11      75 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.8e-05
                           UPF0239 23 YGLflGAifqlvCilAiillpsskseesveeeaessee..ksseqvkkpkaaaaqrlkk 79
                                      +G+fl  i+ l+ i  i+l   +ks+++ +e++esse+  k  + v+  k++++++++k
  gi|298674713|ref|YP_003726463.1| 15 FGIFLNIILVLIII-GIVLYFLNKSNNTGSENKESSERisKIEKDVEDIKETVEEIKQK 72
                                      78999989888855.57778899999999999999999767777788888888888887 PP

>> ODV-E18  Occlusion-derived virus envelope protein ODV-E18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.3   3.1e-05      0.02      26      55 ..      17      47 ..       9      55 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.1e-05
                           ODV-E18 26 llltilvvlviiillvllvqsss.tGsdsss 55
                                      ++l i+ vl+ii +++ +++ s  tGs+   
  gi|298674713|ref|YP_003726463.1| 17 IFLNIILVLIIIGIVLYFLNKSNnTGSENKE 47
                                      7999999999999988888877526765543 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       3.7   2.3e+03       7      19 ..      22      34 ..      18      38 .. 0.79
   2 ?   14.9   1.4   3.3e-05     0.021      82     120 ..      38      76 .]      34      76 .] 0.86

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.7
                           DUF1664  7 ivpaavvgavgYg 19
                                      i+  +++g v Y+
  gi|298674713|ref|YP_003726463.1| 22 ILVLIIIGIVLYF 34
                                      5668999999997 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 3.3e-05
                           DUF1664  82 skeikeevtevredlseigedvesvkeavegleskleri 120
                                       s+++ +e +e +e +s+i++dve +ke+ve++++kl++i
  gi|298674713|ref|YP_003726463.1|  38 SNNTGSENKESSERISKIEKDVEDIKETVEEIKQKLDEI 76 
                                       567778888899999999999999999999999999987 PP

>> Trimer_CC  Trimerisation motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   4.3e-05     0.028      15      44 ..      46      75 ..      36      76 .] 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.3e-05
                                      XXXXXX--HHHHHHHHHHHHHHHHHHHHHH CS
                         Trimer_CC 15 tpssdavSRLEEelrkLqatVQelQkRLDr 44
                                        ss+ +S++E ++  ++ tV e  ++LD+
  gi|298674713|ref|YP_003726463.1| 46 KESSERISKIEKDVEDIKETVEEIKQKLDE 75
                                      5799*************************8 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.2   4.6e-05     0.029      36      67 ..      45      76 .]      33      76 .] 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.6e-05
                              KxDL 36 nalsqerlaklrarfkqgtkllkevkkdLesi 67
                                      n++s+er +k+++++++ ++++ e+k+ L+ i
  gi|298674713|ref|YP_003726463.1| 45 NKESSERISKIEKDVEDIKETVEEIKQKLDEI 76
                                      78899999999999999999999999999875 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.8   4.6e-05     0.029      28      56 ..      44      72 ..      30      76 .] 0.47

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.6e-05
                           BLOC1_2 28 lNeaasekykklkdvaaslekkleklnek 56
                                       N+++se++ k+++ ++++++++e++++k
  gi|298674713|ref|YP_003726463.1| 44 ENKESSERISKIEKDVEDIKETVEEIKQK 72
                                      34444444444444444444444444444 PP

>> Chordopox_A13L  Chordopoxvirus A13L protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   6.3e-05     0.041       4      44 ..      17      56 ..      14      72 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.3e-05
                    Chordopox_A13L  4 dlllliiCvaivglivYgiYnrkketqttnpstveeyeeed 44
                                      ++l +i+  +i+g+++Y + n+ ++t  +n+++ e+  + +
  gi|298674713|ref|YP_003726463.1| 17 IFLNIILVLIIIGIVLYFL-NKSNNTGSENKESSERISKIE 56
                                      5666777788899999965.888888888888877766543 PP

>> SLATT_6  SMODS and SLOG-associating 2TM effector domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.4    0.0001     0.065      61     108 ..      22      70 ..      15      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0001
                           SLATT_6  61 salliiigiialyisayekdkekYekagkeltklfneLkelysevks.s 108
                                        ++liiigi+  +++  +++ ++ +++ +++ k+ ++++++  +v++ +
  gi|298674713|ref|YP_003726463.1|  22 ILVLIIIGIVLYFLNKSNNTGSENKESSERISKIEKDVEDIKETVEEiK 70 
                                       46899*****999*****************************9999833 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   3.4   0.00012     0.078      12      38 ..      48      74 ..      37      76 .] 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00012
                         FlaC_arch 12 lsteletvkkeneelsksveelkenVk 38
                                       s +++ ++k+ e+++++vee+k++  
  gi|298674713|ref|YP_003726463.1| 48 SSERISKIEKDVEDIKETVEEIKQKLD 74
                                      445899999999999999999999875 PP

>> CbiN  Cobalt transport protein component CbiN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00012     0.076       5      49 ..      21      66 ..       9      76 .] 0.71

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00012
                              CbiN  5 lllvvllavvplflvkgaeFgGaDd.qaeevIeeiapdyepwfepl 49
                                      ++lv++++ + l++ ++++ +G+ + + +e I++i++d+e++ e +
  gi|298674713|ref|YP_003726463.1| 21 IILVLIIIGIVLYFLNKSNNTGSENkESSERISKIEKDVEDIKETV 66
                                      344444444444444677777877626899**********988876 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00013     0.081      81     140 ..      14      70 ..      11      76 .] 0.54

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                                       XXXXXXXXXXXXXXXXXXXXX--HHH........HHHHHHHHHHHHHHHHHHTHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin  81 tfsllllvlfllelaagilgfvfsdkargkvseiinnaievkyrddldlkkcqnlldslq 140
                                       +f ++l ++++l ++ ++l f +++ ++g  +++  + i++  +d +d+   +++++ ++
  gi|298674713|ref|YP_003726463.1|  14 FFGIFLNIILVLIIIGIVLYFLNKSNNTGSENKESSERISKIEKDVEDI---KETVEEIK 70 
                                       4556666666666666667777777755555555666665544555555...33333333 PP

>> Lig_chan  Ligand-gated ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00013     0.084       6      38 ..      19      51 ..      15      72 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                                      XXXXTXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Lig_chan  6 lsvlvalilvsivlflverfspyewrepeeaae 38
                                      l ++++li+++ivl+++++ +++  +++e++++
  gi|298674713|ref|YP_003726463.1| 19 LNIILVLIIIGIVLYFLNKSNNTGSENKESSER 51
                                      6799********************999865543 PP

>> HN  Haemagglutinin-neuraminidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   0.00016       0.1       4      57 ..      16      67 ..      14      74 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                HN  4 ltvvtLilaIisialnvaaiedaeittqsllssikdkiesiedkikseigpkvk 57
                                       +++ +il+ i+i++  + +++++ t + ++++ +++i++ie+++++ i   v+
  gi|298674713|ref|YP_003726463.1| 16 GIFLNIILVLIIIGIVLYFLNKSNNTGS-ENKESSERISKIEKDVED-IKETVE 67
                                      5788999999999998888888887777.889999999999999876.333444 PP

>> 60KD_IMP  60Kd inner membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2    0.0002      0.13       3      51 ..      19      73 ..      17      76 .] 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0002
                          60KD_IMP  3 laIilltiivrlillpltlkqlkss......akmqelqPelkeiqekykkdkqkl 51
                                      l Iil+ ii+ ++l+ l+++  + s      ++++++++++++i+e  ++ kqkl
  gi|298674713|ref|YP_003726463.1| 19 LNIILVLIIIGIVLYFLNKSNNTGSenkessERISKIEKDVEDIKETVEEIKQKL 73
                                      78*************9998765433222222788888888888888885546665 PP

>> APC_N_CC  Coiled-coil N-terminus of APC, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   2.8   0.00034      0.22      22      52 .]      43      73 ..      35      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00034
                          APC_N_CC 22 rELedNSshLskLEtetsgmKevlkqlqgkl 52
                                       E ++ S ++sk+E++  ++Ke + +++ kl
  gi|298674713|ref|YP_003726463.1| 43 SENKESSERISKIEKDVEDIKETVEEIKQKL 73
                                      677899******************9998876 PP

>> SPT_ssu-like  Small subunit of serine palmitoyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   2.3   0.00068      0.44      28      50 ..      15      37 ..      13      40 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00068
                      SPT_ssu-like 28 fnilifillsllliaaslYlpsh 50
                                      f i++ i+l l++i+ +lY+++ 
  gi|298674713|ref|YP_003726463.1| 15 FGIFLNIILVLIIIGIVLYFLNK 37
                                      7789999*************986 PP

>> PV-1  PV-1 protein (PLVAP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   3.5    0.0011      0.72      24      66 ..      11      51 ..       8      75 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0011
                              PV-1 24 ylryfflfvsliqfliilGlvlfmvyGnvhvstesnlqaterr 66
                                      y  +f +f+ +i  lii+G+vl+ +       t s+ + + +r
  gi|298674713|ref|YP_003726463.1| 11 YSPFFGIFLNIILVLIIIGIVLYFLNKSNN--TGSENKESSER 51
                                      556899****************98754444..44433444444 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   2.8      0.03        19     260     289 ..       3      31 ..       1      38 [. 0.57
   2 ?    7.1   0.9    0.0046         3     180     217 ..      38      75 ..      31      76 .] 0.76

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.03
                              CorA 260 glPelewsygypfvlllglmallailllfw 289
                                        +P+ +++y  +f  +++ ++l+ i++ ++
  gi|298674713|ref|YP_003726463.1|   3 MMPGYGTGYSPFFG-IFLNIILVLIIIGIV 31 
                                       69*99999955555.444444444443333 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0046
                              CorA 180 kaddkllddedkeylrdlldelerllemlealrerles 217
                                       +++++ +++e +e+++ ++ ++e + e++e ++++l+ 
  gi|298674713|ref|YP_003726463.1|  38 SNNTGSENKESSERISKIEKDVEDIKETVEEIKQKLDE 75 
                                       56777788888888888888888888888888888875 PP

>> ThrE  Putative threonine/serine exporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.4      0.11        69     120     148 ..       9      37 ..       3      43 .. 0.84
   2 ?    6.8   0.3    0.0058       3.7      68      99 ..      45      76 .]      36      76 .] 0.85

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.11
                              ThrE 120 aafallfggdwidflvaflagllggllrl 148
                                        + +++fg  ++ +lv  ++g+++++l+ 
  gi|298674713|ref|YP_003726463.1|   9 TGYSPFFGIFLNIILVLIIIGIVLYFLNK 37 
                                       57788999999999999999999999875 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0058
                              ThrE 68 nleklsevnelsreiaageisleeaeerLdeI 99
                                      n e  ++++++ +++++ + ++ee++++LdeI
  gi|298674713|ref|YP_003726463.1| 45 NKESSERISKIEKDVEDIKETVEEIKQKLDEI 76
                                      556678899999999999*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3129  (0.174522); expected 358.6 (0.02)
Passed bias filter:                     1917  (0.106922); expected 358.6 (0.02)
Passed Vit filter:                       322  (0.0179597); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 563.11
//
Query:       gi|298674714|ref|YP_003726464.1|  [L=156]
Description: hypothetical protein Metev_0768 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1141.15
//
Query:       gi|298674715|ref|YP_003726465.1|  [L=312]
Description: nucleoside recognition domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-06   26.8  15.9    5.1e-05   23.5   0.1    3.2  3  Gate      Nucleoside recognition


Domain annotation for each model (and alignments):
>> Gate  Nucleoside recognition
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.1   2.8e-09   5.1e-05       2      96 ..      14      99 ..      13     117 .. 0.89
   2 ?    0.2   0.4     0.048   8.7e+02       4      42 ..     107     145 ..     104     156 .. 0.67
   3 !    8.3   6.2   0.00015       2.6       3      90 ..     181     259 ..     179     309 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.8e-09
                              Gate  2 lkagpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqgfd 80
                                       +++p+++++++l ++  + +++++i++l++p+       l  ++ +s+lt fa+  ++ ++l  l+        ++  
  gi|298674715|ref|YP_003726465.1| 14 STIIPYMIAGVVLAELVVELGWVDKISFLVRPITGFVH--LRKECGISFLTAFASPSAANASLKDLH-------DNELI 83
                                      6799*****************************99999..***********************9998.......99999 PP

                              Gate 81 tpksalafllfvllyt 96
                                      ++k+ +++ +++++ +
  gi|298674715|ref|YP_003726465.1| 84 DEKELIIASVLNSFPS 99
                                      9999999999888866 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.048
                              Gate   4 agpiillasiliwflssssllgrigkllepvfaplg.qel 42 
                                       ++p++++++  i++++  ++l  +g l + ++a +g + l
  gi|298674715|ref|YP_003726465.1| 107 LLPVLVPLLGTIGLIY-VGILTLVGLLKTVIVALIGhFIL 145
                                       6677777777777655.57777777777777777665554 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.00015
                              Gate   3 kagpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqgf 79 
                                       k++ + ++++i++ +l + +++++++++l+ v + l    + +    + + fa+k +++ ++g+l    +ge+l+g+
  gi|298674715|ref|YP_003726465.1| 181 KILVVTVPVTIFVFILMDIGVFDIVSQYLKSVSRLLP--VPVNGLPVIAAQFASKIAGYTIAGNLL---TGEVLSGK 252
                                       788999**************************99988..999999999999999999999999997...44444444 PP

                              Gate  80 dtpksalafll 90 
                                       +  ++    ll
  gi|298674715|ref|YP_003726465.1| 253 EILIT----LL 259
                                       44433....33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       794  (0.0442858); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 2131.45
//
Query:       gi|298674716|ref|YP_003726466.1|  [L=58]
Description: 4Fe-4S ferredoxin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-17   62.3  21.1    7.4e-09   35.1   6.1    2.1  2  Fer4      4Fe-4S binding domain
    9.9e-12   44.8  26.9    7.6e-09   35.6  14.9    1.8  2  Fer4_10   4Fe-4S dicluster domain
    1.2e-11   44.2  21.9    5.9e-06   26.1   6.4    2.1  2  Fer4_6    4Fe-4S binding domain
    2.2e-11   43.7  17.3    7.8e-11   41.9  17.3    1.7  1  Fer4_21   4Fe-4S dicluster domain
    7.2e-11   42.5  12.7    1.2e-10   41.8  12.7    1.3  1  Fer4_7    4Fe-4S dicluster domain
      1e-10   41.0  16.3    1.1e-05   25.3   4.4    2.1  2  Fer4_2    4Fe-4S binding domain
    2.6e-10   40.3  12.2    3.3e-10   40.0  12.2    1.2  1  Fer4_9    4Fe-4S dicluster domain
    8.6e-10   39.4  11.7    5.8e-05   23.9   1.1    2.0  2  Fer4_16   4Fe-4S double cluster binding domain
    1.7e-08   34.3  14.1    0.00046   20.5   4.5    2.1  2  Fer4_4    4Fe-4S binding domain
    7.5e-07   29.7  17.4     0.0017   19.2   5.3    2.1  2  Fer4_3    4Fe-4S binding domain
    8.5e-06   26.4  19.1     0.0027   18.4  19.1    2.9  1  Fer4_15   4Fe-4S single cluster domain
    0.00017   22.0  14.6      0.061   13.8  14.6    2.1  1  Fer4_8    4Fe-4S dicluster domain
    0.00021   21.7  22.7      0.019   15.5   7.7    2.6  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    0.00025   21.5  12.5      0.015   15.8   2.0    2.1  2  Fer4_17   4Fe-4S dicluster domain
     0.0018   19.1   6.9       0.12   13.3   0.9    2.0  2  Fer4_22   4Fe-4S dicluster domain
     0.0031   17.7  16.0     0.0068   16.6   4.5    2.0  2  Fer4_18   4Fe-4S dicluster domain
  ------ inclusion threshold ------
        7.5    7.3  12.2         20    5.9   2.5    2.9  3  AFP       Insect antifreeze protein repeat


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   6.1     7e-12   7.4e-09       2      24 .]       4      26 ..       3      26 .. 0.95
   2 !   33.7   7.0   1.9e-11     2e-08       2      24 .]      34      56 ..      33      56 .. 0.95

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 7e-12
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                      v+d e C+gC aCv+ CPv+AI+
  gi|298674716|ref|YP_003726466.1|  4 VVDSEICTGCEACVDECPVDAIS 26
                                      89********************6 PP

  == domain 2  score: 33.7 bits;  conditional E-value: 1.9e-11
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                      v+dee C+ C aCv++CPv+AI+
  gi|298674716|ref|YP_003726466.1| 34 VVDEEECTDCEACVDICPVEAIS 56
                                      8********************96 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6  14.9   7.2e-12   7.6e-09       3      56 .]       4      51 ..       2      51 .. 0.78
   2 !   20.2   4.0   4.4e-07   0.00046       2      21 ..      33      52 ..      32      58 .] 0.85

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 7.2e-12
                           Fer4_10  3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      v+d++ C++C++Cv+ CP+    +  +  ++++++v  + e+Ct+c+aCv++CP
  gi|298674716|ref|YP_003726466.1|  4 VVDSEICTGCEACVDECPV----DAISMNDDGIAVV--DEEECTDCEACVDICP 51
                                      789****************....3333333333333..469************9 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 4.4e-07
                           Fer4_10  2 vvidddtCirCgkCvkaCPa 21
                                      +v+d++ C+ C++Cv+ CP+
  gi|298674716|ref|YP_003726466.1| 33 AVVDEEECTDCEACVDICPV 52
                                      68899**************9 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   6.4   5.6e-09   5.9e-06       2      24 .]       3      25 ..       2      25 .. 0.95
   2 !   24.5   7.5   1.9e-08     2e-05       1      24 []      32      55 ..      32      55 .. 0.95

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 5.6e-09
                            Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                      +++d + C+gC++Cv+ CP +ai
  gi|298674716|ref|YP_003726466.1|  3 AVVDSEICTGCEACVDECPVDAI 25
                                      79*******************98 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 1.9e-08
                            Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                      ++++d++ C++C++Cv++CP  ai
  gi|298674716|ref|YP_003726466.1| 32 IAVVDEEECTDCEACVDICPVEAI 55
                                      689******************998 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9  17.3   7.4e-14   7.8e-11       1      59 []       3      57 ..       3      57 .. 0.97

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 7.4e-14
                           Fer4_21  1 AridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59
                                      A++d++ C gC+ C+  C+   ++ai+++++ ++ v e+eC+ C+ C+++CPv ++i+m
  gi|298674716|ref|YP_003726466.1|  3 AVVDSEICTGCEACVDECP---VDAISMNDDGIAVVDEEECTDCEACVDICPV-EAISM 57
                                      899****************...8*****************************9.99998 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8  12.7   1.1e-13   1.2e-10       2      52 .]      10      54 ..       9      54 .. 0.94

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 1.1e-13
                            Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      C+gC+aCv+ Cpv+ai+++++    g   +++d+e+C++C+aCv+ CP++a
  gi|298674716|ref|YP_003726466.1| 10 CTGCEACVDECPVDAISMNDD----G--IAVVDEEECTDCEACVDICPVEA 54
                                      ******************997....4..7899****************987 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   4.4     1e-08   1.1e-05       2      21 ..       2      21 ..       1      22 [. 0.93
   2 !   22.1   4.1     1e-07   0.00011       3      21 ..      33      51 ..      31      52 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1e-08
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                      p+vvd+++C+gC+aCv+ CP
  gi|298674716|ref|YP_003726466.1|  2 PAVVDSEICTGCEACVDECP 21
                                      579***************** PP

  == domain 2  score: 22.1 bits;  conditional E-value: 1e-07
                            Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                      +vvd++ C+ C+aCv+ CP
  gi|298674716|ref|YP_003726466.1| 33 AVVDEEECTDCEACVDICP 51
                                      689**************** PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0  12.2   3.1e-13   3.3e-10       2      51 .]      10      55 ..       9      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 3.1e-13
                            Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      CtgC aCv+ Cp +++++ + +  +  ++    +C++C+aCv++Cp +ai
  gi|298674716|ref|YP_003726466.1| 10 CTGCEACVDECPVDAISMNDDGIAVVDEE----ECTDCEACVDICPVEAI 55
                                      ******************99999999765....6************9987 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   1.1   5.5e-08   5.8e-05       2      21 ..      10      29 ..       9      38 .. 0.86
   2 !   21.0   3.6   4.7e-07    0.0005       2      20 ..      40      58 .]      39      58 .] 0.93

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 5.5e-08
                           Fer4_16  2 CgtCgkCaevCPtnaikekk 21
                                      C++C++C++ CP++ai+++ 
  gi|298674716|ref|YP_003726466.1| 10 CTGCEACVDECPVDAISMND 29
                                      ****************9984 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 4.7e-07
                           Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                      C++C++C+++CP++ai++k
  gi|298674716|ref|YP_003726466.1| 40 CTDCEACVDICPVEAISMK 58
                                      ****************976 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   2.1   8.4e-07   0.00088       2      16 ..       8      22 ..       7      29 .. 0.90
   2 !   20.5   4.5   4.4e-07   0.00046       2      16 ..      38      52 ..      37      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 8.4e-07
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      e C+gC +Cv+ CP+
  gi|298674716|ref|YP_003726466.1|  8 EICTGCEACVDECPV 22
                                      66************6 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 4.4e-07
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      e C++C +Cv++CP+
  gi|298674716|ref|YP_003726466.1| 38 EECTDCEACVDICPV 52
                                      78************7 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   5.3   1.6e-06    0.0017       1      15 []      10      24 ..      10      24 .. 0.98
   2 !   16.7   4.3   9.9e-06      0.01       1      15 []      40      54 ..      40      54 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.6e-06
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      CtgC+aCv+ CPv+A
  gi|298674716|ref|YP_003726466.1| 10 CTGCEACVDECPVDA 24
                                      *************98 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 9.9e-06
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      Ct C+aCv+ CPv A
  gi|298674716|ref|YP_003726466.1| 40 CTDCEACVDICPVEA 54
                                      9***********976 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4  19.1   2.6e-06    0.0027       2      65 ..       4      56 ..       3      57 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.6e-06
                           Fer4_15  2 vvDrdaCigcglCvaeap.evfeldedglasvllddgeiaegevpddeeeaaqeAaraCPvdAIr 65
                                      vvD + C+gc++Cv+e+p + + +++dg+a+            v+++e ++ +  ++ CPv+AI+
  gi|298674716|ref|YP_003726466.1|  4 VVDSEICTGCEACVDECPvDAISMNDDGIAV------------VDEEECTDCEACVDICPVEAIS 56
                                      69***************6589*********3............45778899999999******97 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8  14.6   5.7e-05     0.061       3      64 ..       8      53 ..       6      54 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.7e-05
                            Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                      e C++C+aC ++Cpv         + +++ ++ v++e++         Ct c+aC++ Cpv+
  gi|298674716|ref|YP_003726466.1|  8 EICTGCEACVDECPVDAI------SMNDDGIA-VVDEEE---------CTDCEACVDICPVE 53
                                      67************6444......44455556.566555.........************96 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   6.5    0.0002      0.21       1      27 [.       5      32 ..       5      34 .. 0.82
   2 !   15.5   7.7   1.8e-05     0.019       1      17 [.      35      51 ..      35      53 .. 0.97

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0002
                           Fer4_13  1 VDrdtCiacgaCvelaP.dvFeeddegg 27
                                      VD + C++c+aCv+ +P d   ++d+g 
  gi|298674716|ref|YP_003726466.1|  5 VDSEICTGCEACVDECPvDAISMNDDGI 32
                                      899**************66677777665 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.8e-05
                           Fer4_13  1 VDrdtCiacgaCvelaP 17
                                      VD+++C++c+aCv+++P
  gi|298674716|ref|YP_003726466.1| 35 VDEEECTDCEACVDICP 51
                                      9***************9 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   2.0   1.5e-05     0.015       2      17 ..      10      25 ..       9      38 .. 0.79
   2 !   11.3   3.1   0.00037      0.39       1      15 [.      39      53 ..      39      57 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.5e-05
                           Fer4_17  2 CiqCgyClpeCpsyea 17
                                      C++C++C++eCp  ++
  gi|298674716|ref|YP_003726466.1| 10 CTGCEACVDECPVDAI 25
                                      9999999999997555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00037
                           Fer4_17  1 rCiqCgyClpeCpsy 15
                                      +C+ C++C++ Cp  
  gi|298674716|ref|YP_003726466.1| 39 ECTDCEACVDICPVE 53
                                      599999999999875 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.9   0.00011      0.12      77      95 ..       5      23 ..       1      24 [. 0.86
   2 !    9.8   0.6    0.0014       1.4      77      94 ..      35      52 ..      26      54 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                           Fer4_22 77 fgesgCvGCgRCieacpvk 95
                                      ++++ C+GC  C++ cpv+
  gi|298674716|ref|YP_003726466.1|  5 VDSEICTGCEACVDECPVD 23
                                      67899***********985 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0014
                           Fer4_22 77 fgesgCvGCgRCieacpv 94
                                      ++e+ C+ C  C++ cpv
  gi|298674716|ref|YP_003726466.1| 35 VDEEECTDCEACVDICPV 52
                                      567788888888888887 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   3.8    0.0029       3.1      60      74 ..       9      23 ..       3      34 .. 0.82
   2 !   16.6   4.5   6.4e-06    0.0068      53      74 ..      32      53 ..      23      57 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0029
                           Fer4_18 60 dcidcescvkvcPtg 74
                                       c+ ce+cv+ cP++
  gi|298674716|ref|YP_003726466.1|  9 ICTGCEACVDECPVD 23
                                      59***********85 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 6.4e-06
                           Fer4_18 53 rkekgagdcidcescvkvcPtg 74
                                       +  ++ +c+dce+cv++cP++
  gi|298674716|ref|YP_003726466.1| 32 IAVVDEEECTDCEACVDICPVE 53
                                      5567789*************85 PP

>> AFP  Insect antifreeze protein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.3     0.042        45       2      11 ..       4      13 ..       3      14 .. 0.67
   2 ?    5.9   2.5     0.019        20       2       9 ..      10      17 ..       9      20 .. 0.92
   3 ?    5.8   2.2     0.021        22       2       9 ..      40      47 ..      39      48 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.042
                               AFP  2 CTgsknCteA 11
                                      + +s+ Ct +
  gi|298674716|ref|YP_003726466.1|  4 VVDSEICTGC 13
                                      6777777777 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.019
                               AFP  2 CTgsknCt 9 
                                      CTg++ C+
  gi|298674716|ref|YP_003726466.1| 10 CTGCEACV 17
                                      *******8 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.021
                               AFP  2 CTgsknCt 9 
                                      CT+++ C+
  gi|298674716|ref|YP_003726466.1| 40 CTDCEACV 47
                                      *****997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 432.91
//
Query:       gi|298674717|ref|YP_003726467.1|  [L=551]
Description: hypothetical protein Metev_0771 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-72  244.9   5.3    1.6e-72  244.6   5.3    1.0  1  DUF2070       Predicted membrane protein (DUF2070)
  ------ inclusion threshold ------
       0.16   12.3   0.2       0.33   11.3   0.2    1.4  1  Rep_fac-A_3   Replication factor A protein 3
       0.18   11.5   7.2        4.6    7.0   1.1    3.3  2  TCR_zetazeta  T-cell surface glycoprotein CD3 zeta chain


Domain annotation for each model (and alignments):
>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  244.6   5.3   2.7e-76   1.6e-72       6     562 ..      10     548 ..       6     550 .. 0.89

  Alignments for each domain:
  == domain 1  score: 244.6 bits;  conditional E-value: 2.7e-76
                           DUF2070   6 kyifrlPswkvsllliillalligllaflssk.............lfgillfglpalvaflltlpvlrilggrltyk 69 
                                        +if++Ps+k+ + ++i++++++g+l  ls++             ++++++f++palv++ l++++l      ++y 
  gi|298674717|ref|YP_003726467.1|  10 NIIFSVPSLKRVVEALIVTGAIYGVLINLSISylsavplnlyyiiITALFMFIIPALVSGELYYQFL------PEYP 80 
                                       79*************************99999***********************************......7777 PP

                           DUF2070  70 rs..lflalltelivviisllaillsall..qalvllalvlslalvfalrllvlvavsdesllkav.lpaliqplla 141
                                       r+  +fl l++e+++++  ++ ++ +       +  + + ++++ +f  +llvlv + +++++k + ++ ++qpl++
  gi|298674717|ref|YP_003726467.1|  81 RKwgYFLTLFNEFVLFVYGMILTFSA--EsgFISAWNIFWIAIITIFLTSLLVLVGTLGYKYIKRIsILGMVQPLMI 155
                                       7777*************444444433..34666777888999******************9877665********** PP

                           DUF2070 142 illlvly......fspesfllllllslifalavylfivvvdrplkrnlgvsaldllsaFlahilegskelEeffeei 212
                                       + ++ l       ++ ++++  + l+++ +++++l +++ ++ +  n++vsa +l s++l    ++++e+     ++
  gi|298674717|ref|YP_003726467.1| 156 VSAFHLSigksleITVTTYIERIGLLFLAGIMLLLTFFLAEYLISTNVNVSAIKLSSGLL----QKRQEV----LNL 224
                                       ****9999*****99999999***************************************....776665....59* PP

                           DUF2070 213 geeadvpvkvlsfrredgekallvvPniHPGPlgeiGGsnLpkilaerldel..vlvlHgtatHdfNlvsereveki 287
                                       g  ++ +v++l +++e+  +++++vP+iHPGPl ++GG++ ++ l + l+e+   +++H+++tH+ ++v+++++ ki
  gi|298674717|ref|YP_003726467.1| 225 GYSSRPDVQTLEIENEN-SSTTIAVPWIHPGPLEGFGGGRASTDLINHLNENgsGFFFHVPSTHKCDPVNPDDIYKI 300
                                       *************7774.788888******************99999999988************************ PP

                           DUF2070 288 veavkealeeleysskaskpvrvesgd..vkllgqrfgdslllvitrapegiDDiplsvglsimaeakaegfedvll 362
                                       ++a+++ +    +ss+ask+v+ ++ +   +++g+++gd+ l+ +    e   D++ sv+  +++      +e+v++
  gi|298674717|ref|YP_003726467.1| 301 IKALNKPT----KSSTASKLVKESYPEhkLTFYGRKLGDKKLVYME--AENYGDYEISVFRDLID------LENVMI 365
                                       ********....677888888888766458999******6665555..57777******999998......69**** PP

                           DUF2070 363 VDaHNsfseeage..vlpgsedaeeliraaekalekleaaeeselkvgvarsetpkltpeeglGdlgiqvlvlevdg 437
                                       +D HN+++ ++ +   l g+++ae +++ + k+l+kle  ++s+++vg+  +++ +  p+         +l+ +vdg
  gi|298674717|ref|YP_003726467.1| 366 IDLHNHERNKEPDpqLLYGTDEAEIFREKLLKFLDKLEGLKTSDYQVGYCTNTIGT--PK--------FALIENVDG 432
                                       ******9988887999999*******************************888874..33........69******* PP

                           DUF2070 438 qktayvliDgNNmepglreeirealke.vdlevevmTTDtHvvngvslgynpvGekv.skdelielvlelvekAiad 512
                                       qkt+++ + gN++ ++ ++e+r++lk+ +d e+ ++TTDtH++ +     n + +k  ++del     e+++kA ++
  gi|298674717|ref|YP_003726467.1| 433 QKTLLFGTEGNGISEK-MDEVRQNLKDsYD-EILIFTTDTHSSIH-----NMISNKHvETDELY----EVINKASKN 498
                                       *************876.68999****9899.*************9.....55553331355555....55669999* PP

                           DUF2070 513 lepvevgyaterve.vkvfgedrfeelvstvnsvvsvakilaaallllail 562
                                       ++  ++g+++++ e  k++++d +  l+ ++n +v++  +++++l+++ il
  gi|298674717|ref|YP_003726467.1| 499 VSNGSAGFTNNKSEsMKLLKDD-YLGLAYSINILVRLFPLSLLLLYIVLIL 548
                                       *********************9.**********************999887 PP

>> Rep_fac-A_3  Replication factor A protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   5.5e-05      0.33      31      72 ..     458     499 ..     452     514 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.5e-05
                                       TTSSEEEEE-TTS-EEEEEESS--SS---SEEEEEEEE-TTS CS
                       Rep_fac-A_3  31 psgktlilqstdggsvtvrlsedstleiskwvEvvGkvsddl 72 
                                       +s +++++ +td++s   ++ +++++e ++++Ev+ k+s++ 
  gi|298674717|ref|YP_003726467.1| 458 DSYDEILIFTTDTHSSIHNMISNKHVETDELYEVINKASKNV 499
                                       5678899999999999999******************99854 PP

>> TCR_zetazeta  T-cell surface glycoprotein CD3 zeta chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   1.1   0.00077       4.6      12      24 ..      48      60 ..      46      60 .. 0.89
   2 ?    6.0   0.6    0.0016       9.6      11      20 ..      94     103 ..      86     104 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00077
                      TCR_zetazeta 12 LliYgiIiTaLFl 24
                                      L +Y iIiTaLF+
  gi|298674717|ref|YP_003726467.1| 48 LNLYYIIITALFM 60
                                      679*********5 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0016
                      TCR_zetazeta  11 iLliYgiIiT 20 
                                       +L++Yg I+T
  gi|298674717|ref|YP_003726467.1|  94 VLFVYGMILT 103
                                       7********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (551 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       925  (0.0515924); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 3583.63
//
Query:       gi|298674718|ref|YP_003726468.1|  [L=695]
Description: ribonucleoside-diphosphate reductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.2e-172  575.1   1.5   4.6e-171  569.9   1.5    2.2  1  Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
    2.9e-28   97.7   0.1    6.6e-28   96.5   0.1    1.7  1  Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha domain
    5.6e-23   81.3   1.9    1.7e-22   79.8   1.9    1.9  1  ATP-cone         ATP cone domain
  ------ inclusion threshold ------
      0.079   13.6   0.2        1.8    9.3   0.1    2.4  2  RA               Ras association (RalGDS/AF-6) domain


Domain annotation for each model (and alignments):
>> Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  569.9   1.5    1e-174  4.6e-171       1     524 []     190     654 ..     190     654 .. 0.98

  Alignments for each domain:
  == domain 1  score: 569.9 bits;  conditional E-value: 1e-174
                                       EEE.....BSS-EEEE-X..............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC   1 ssCfvlsvedslesIletvkeaallskaggGvGlnlsklRakgslvkgtegaasGpvsfmklidavadvvkqgGkRr 77 
                                       s+Cfvl veds+++I+e+++++ l++k+ggG+G+++sklR++g++vk+t+g asGpvsfm ++d+ ++v+kqgGkRr
  gi|298674718|ref|YP_003726468.1| 190 SACFVLPVEDSMKDIFEALTNMSLIHKSGGGTGFSFSKLRPNGDIVKSTKGVASGPVSFMSIFDQATEVIKQGGKRR 266
                                       79*************************************************************************** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX............ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC  78 GAamvylevwHpDiekfidaKekntgeeenrlsnlnisvgvpdlFmeavkedkdwtLfsPrtvvkleklygeefeee 154
                                       GA+m++l+++HpDi++fi+ Kek     e  l+n+nisvgv+d+Fm+av++d+++ L++Prt +             
  gi|298674718|ref|YP_003726468.1| 267 GANMGILRIDHPDIIEFINSKEK-----EGYLDNFNISVGVTDEFMKAVQSDSKYDLINPRTGK------------- 325
                                       *********************77.....889******************************432............. PP

                                       .............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 155 yeeleekakikkkevkakeLfeeiaesawetgePgvlfkDtiNrrnvlekakggkIratNlCgEiplleyesvavCn 231
                                                 ++++ +a+++f+ i ++aw+tg+Pg++f D+iNrr+++  +++ +I++tN+CgE+pll+yes   Cn
  gi|298674718|ref|YP_003726468.1| 326 ----------TTEKLRARDIFDLITTMAWRTGDPGMIFLDEINRRHPV--SHVRTIESTNPCGEVPLLPYES---CN 387
                                       ..........35699*********************************..999*******************...** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 232 LasinLakfvkkdeegkkefdwdelkkviqlvvraLdnvidvnkyplpeiekntkktRriGlGvmgladalaklgip 308
                                       L+sinL+k+vk     +++++w++lk+ ++  + +Ldnvid+nkypl+ei+++tk++R+iGlGvmgla+++akl+ip
  gi|298674718|ref|YP_003726468.1| 388 LGSINLSKMVK-----NDTINWEKLKNNTHSGIHFLDNVIDANKYPLNEIDRETKNNRKIGLGVMGLAEMFAKLNIP 459
                                       **********5.....56*********************************************************** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......XXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 309 ydseealkfarkitelltyyaykaSvelAkergpfplfekskyskgilpvdefeekekedweeLreeikkyGlrnam 385
                                       y+seea++ a++i+++++ +++k+Svel ++rg+fp+f++s+++k+                        + +rna+
  gi|298674718|ref|YP_003726468.1| 460 YNSEEAIETAENIMKFINEESVKKSVELGEKRGSFPNFKGSQWEKKY-----------------------SSMRNAT 513
                                       *******************************************9994.......................359**** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 386 vtalaPTgsiSliagtssgiePifalvykksvtvgeflevnpvfeeeLkklglwseellkki..lesvqgleeipee 460
                                       v ++aPTg+iS+ia+tssgiePifal ++++v++ ++levnpvfe+  k+++ +s++l  +i  ++s+q+l+++p++
  gi|298674718|ref|YP_003726468.1| 514 VNTIAPTGTISIIANTSSGIEPIFALSFVRNVMATQLLEVNPVFENVAKERNFYSKDLMMDIskTGSIQNLKQVPKD 590
                                       **************************************************************77777********** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 461 ikrvfktaldidqedhikaqaaiqkwidqsiSktinlpneatvedvkelyllAwklGlKgvtyY 524
                                       ++++f+t+ldid+e+h+++qaa qk++d+s+Skt+nlp++at +dvk++y+ A+kl +Kg+t+Y
  gi|298674718|ref|YP_003726468.1| 591 VRDLFVTSLDIDPEWHVRMQAAFQKYVDNSVSKTVNLPEKATLDDVKRIYMMAYKLNCKGITIY 654
                                       **************************************************************99 PP

>> Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.5   0.1   1.5e-31   6.6e-28       2      83 .]     108     187 ..     107     187 .. 0.96

  Alignments for each domain:
  == domain 1  score: 96.5 bits;  conditional E-value: 1.5e-31
                   Ribonuc_red_lgN   2 kltynalkvledrYllkdengeivEspqqmfmRvAlalaiaealydkleedkdlaeefydlmssqkflpasPtlmna 78 
                                       kl++na++vle+rYllk eng++vE+p +mf+RvA  +  +++ y  + +  d   efy++ms+++flp+sPtlmna
  gi|298674718|ref|YP_003726468.1| 108 KLSVNAIRVLERRYLLKGENGNPVETPSEMFERVANSVSSIDKRY--GYNPYDSKAEFYRMMSNLEFLPNSPTLMNA 182
                                       789***************************************976..67**************************** PP

                   Ribonuc_red_lgN  79 Gtelg 83 
                                       Gtelg
  gi|298674718|ref|YP_003726468.1| 183 GTELG 187
                                       **986 PP

>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.8   1.9   3.8e-26   1.7e-22       2      86 .]       3      92 ..       2      92 .. 0.91

  Alignments for each domain:
  == domain 1  score: 79.8 bits;  conditional E-value: 3.8e-26
                                      EEE-TTS-EEE--HHHHHHHHHHHHHH-HHH....HHHHHHHHHHHHHHHHIIT.-BHHHHHHHHHHHHHHSS-HHHHH CS
                          ATP-cone  2 kViKRdGtvepfdvekIkraiekAcegseee....ideiaeeveaevrkrlrdg.isteeIqdlvektliehpdyavaa 75
                                      +++KRdG++++fd +kI++ai kA ++++e+    +++++ +v++++++r++++ +s+e++qd+ve++li++++ +va+
  gi|298674718|ref|YP_003726468.1|  3 YIKKRDGRTVDFDSDKITQAIHKAIHSVNENdgdlARKMSYQVIDNLENRFKNTiPSVEDVQDIVEDVLIKNGYSEVAK 81
                                      79**********************99955553445888888899999***99999************************ PP

                                      HHHHHHHHHHH CS
                          ATP-cone 76 ayilyrnlrke 86
                                      +yilyr++r+e
  gi|298674718|ref|YP_003726468.1| 82 SYILYRRKRSE 92
                                      ********975 PP

>> RA  Ras association (RalGDS/AF-6) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1    0.0004       1.8      23      62 ..      57      94 ..      47     123 .. 0.82
   2 ?    1.6   0.0       0.1   4.5e+02      12      42 ..     616     646 ..     608     657 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0004
                                      EETTSBHHHHHHHHHHHCT-GGGGCCEEEECCCTTTTEEE CS
                                RA 23 vsststaqeViealLekfgledspedyvLveskerggeer 62
                                      ++s + +q+++e++L k+g+ +  ++y L+   ++++e r
  gi|298674718|ref|YP_003726468.1| 57 IPSVEDVQDIVEDVLIKNGYSEVAKSYILY--RRKRSEVR 94
                                      788999***********************5..55544444 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.1
                                       T-TT..EEEEEEETTSBHHHHHHHHHHHCT- CS
                                RA  12 lkpgttyksikvsststaqeViealLekfgl 42 
                                       +  ++ +k+++++++ t ++V +  +  ++l
  gi|298674718|ref|YP_003726468.1| 616 YVDNSVSKTVNLPEKATLDDVKRIYMMAYKL 646
                                       5555679**************9999999888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (695 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 4802.55
//
Query:       gi|298674719|ref|YP_003726469.1|  [L=103]
Description: 30S ribosomal protein S10 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-27   94.9   0.0    2.9e-27   94.8   0.0    1.0  1  Ribosomal_S10  Ribosomal protein S10p/S20e
  ------ inclusion threshold ------
      0.039   14.8   0.0        0.1   13.4   0.0    1.6  2  PriA_C         Primosomal protein N C-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_S10  Ribosomal protein S10p/S20e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.8   0.0   3.2e-31   2.9e-27       1      97 [.       6      99 ..       6     100 .. 0.98

  Alignments for each domain:
  == domain 1  score: 94.8 bits;  conditional E-value: 3.2e-31
                                      EEEEEESSHHHHHHHHHHHHHHTTSSS-EE---EEEEEEEEEEEEE--SS--.S--EEEEEEEEEEEEEEEE.E-HHHH CS
                     Ribosomal_S10  1 rirlkSydsklLekavkkivraakelgikvkgpvplPtkrkrvtvlksphvd.kksreqfeirthkRlidisdatketi 78
                                      ri+l+++d+++L+ ++++++ +a ++g+ ++gpvplPt+++rv+ +ksp++d + +++++e+r+hkRlidis a+++ +
  gi|298674719|ref|YP_003726469.1|  6 RIKLSGTDPENLDGVCDQVKSIADRTGVGMSGPVPLPTRKLRVPARKSPSGDgTATWDHWEMRVHKRLIDIS-ADERAL 83
                                      8**********************************************************************6.****** PP

                                      HHHS-...S---SS-EEEE CS
                     Ribosomal_S10 79 dtllkllqlnlpegVsvev 97
                                      ++l++   +++p+ +++e+
  gi|298674719|ref|YP_003726469.1| 84 RQLMR---IQVPKDINIEI 99
                                      *****...********997 PP

>> PriA_C  Primosomal protein N C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.1e-05       0.1       6      52 ..       5      47 ..       2      52 .. 0.92
   2 ?   -1.6   0.0      0.55   4.9e+03      63      74 ..      77      88 ..      67      99 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.1e-05
                            PriA_C  6 alirvsgkdeekveeaaeelaellkealkleeveilgpapapiakik 52
                                      a+i++sg+d e++  ++++++++  +    ++v + gp+p p  k++
  gi|298674719|ref|YP_003726469.1|  5 ARIKLSGTDPENLDGVCDQVKSIADR----TGVGMSGPVPLPTRKLR 47
                                      89*******************99999....6799*********9987 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.55
                            PriA_C 63 sksrkalqkllk 74
                                      s++++al++l++
  gi|298674719|ref|YP_003726469.1| 77 SADERALRQLMR 88
                                      444555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 822.23
//
Query:       gi|298674720|ref|YP_003726470.1|  [L=421]
Description: translation elongation factor EF-1 subunit alpha [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-56  190.9   0.0    2.3e-56  190.4   0.0    1.2  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    2.4e-37  127.7   0.1    5.6e-37  126.5   0.1    1.7  1  GTP_EFTU_D3  Elongation factor Tu C-terminal domain
    6.5e-16   58.5   1.0    1.7e-15   57.2   1.0    1.8  1  GTP_EFTU_D2  Elongation factor Tu domain 2
    3.6e-06   27.1   0.0    8.6e-05   22.6   0.0    2.4  1  MMR_HSR1     50S ribosome-binding GTPase
    0.00022   20.7   0.0     0.0092   15.3   0.0    2.2  1  Gtr1_RagA    Gtr1/RagA G protein conserved region
    0.00081   19.2   0.5      0.002   18.0   0.5    1.6  1  GTP_EFTU_D4  Elongation factor Tu domain 4
  ------ inclusion threshold ------
      0.017   14.7   0.2       0.47   10.0   0.2    2.6  2  FeoB_N       Ferrous iron transport protein B
      0.032   14.3   0.1         10    6.1   0.0    2.8  3  Dynamin_N    Dynamin family
      0.071   13.3   0.1         12    6.2   0.0    2.4  2  Roc          Ras of Complex, Roc, domain of DAPkinase
       0.14   12.2   0.0       0.39   10.7   0.0    1.7  1  AAA_14       AAA domain


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.4   0.0   1.3e-59   2.3e-56       1     187 [.       5     210 ..       5     217 .. 0.89

  Alignments for each domain:
  == domain 1  score: 190.4 bits;  conditional E-value: 1.3e-59
                                       TCEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHST.............HCHSHHHHHHTSCSSCEEEEEE CS
                          GTP_EFTU   1 krirnigiighvDhGKtTLtdrLlyktgaiskkgekaeeerv.............lDtlkeErergiTiksaaisle 64 
                                       k+++n++iigh+DhGK+TL++rL+y+tgai ++  +++ e++             +D+lkeEr rgiTi++a+  ++
  gi|298674720|ref|YP_003726470.1|   5 KPHMNLAIIGHIDHGKSTLVGRLMYETGAIPQHIIDKNREKAkeqgketfafawiMDSLKEERDRGITIDIAHKRFD 81 
                                       579**************************999877773333345678889*************************** PP

                                       TTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTE.EEEEEESCGST...HH CS
                          GTP_EFTU  65 ketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvp.iivfiNKmDrl...ka 137
                                         t+ky ++++D+PGH+dF+k++i+g++++D avl v+a +Gv+ qt+e++ l +++g++ +iv++NKmD +   ++
  gi|298674720|ref|YP_003726470.1|  82 --TDKYYFTIVDCPGHRDFVKNMITGASQADAAVLSVAAPDGVMDQTKEHVFLSRTLGINdLIVAVNKMDDInydEK 156
                                       ..************************************************************************999 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHH............HHHHH CS
                          GTP_EFTU 138 elkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvk............tllea 187
                                       +++e++++v++ l      l+ +g+k + +v++v++Sa+ g++v             t+lea
  gi|298674720|ref|YP_003726470.1| 157 RYEEVKNQVSE-L------LKMVGFKPD-DVTFVPTSAYLGDNVAklsentpwyngpTILEA 210
                                       99999999995.5......588999996.*************99955555555555555555 PP

>> GTP_EFTU_D3  Elongation factor Tu C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.5   0.1   3.1e-40   5.6e-37       3     111 ..     313     419 ..     311     420 .. 0.97

  Alignments for each domain:
  == domain 1  score: 126.5 bits;  conditional E-value: 3.1e-40
                                       EEECCEEEEEEESSS..SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTTSB-BSS-SSCCSTT-CEEEEEEECCE CS
                       GTP_EFTU_D3   3 kphtkfeAqvyilekerhtpitagYrpvlyirtadvtgkvveLlskldkktekvsekkpefvkpGdnvivevelikp 79 
                                       + +++f+Aq+++l++  +++it gY+pv++++ta++++++++L +k+d+k+++v+e++p f+k+Gd++iv++++++p
  gi|298674720|ref|YP_003726470.1| 313 TVANEFTAQIVVLQH--PSAITVGYTPVFHAHTAQIACTFISLDKKMDPKSGQVKEENPTFLKSGDSAIVTLKPTRP 387
                                       6789***********..************************************************************ PP

                                       EEE--TTTHCCCCEEEEECTTCEEEEEEEEEE CS
                       GTP_EFTU_D3  80 ialekgseypqlGrFaiReggrTvaaGvvtei 111
                                       +++e ++e+p++GrFaiR++g+T+aaG+ +++
  gi|298674720|ref|YP_003726470.1| 388 MIIEPVKEIPHMGRFAIRDMGKTIAAGMCMSV 419
                                       ***************************98877 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   1.0   9.4e-19   1.7e-15       1      72 [.     239     304 ..     239     306 .. 0.96

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 9.4e-19
                                       EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCE CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdt 72 
                                       Gtv  grv++G++kkGd+v +  ++++k+   ++++s+e++he++ +a +g+n+G  v++ g  da ++Gd+
  gi|298674720|ref|YP_003726470.1| 239 GTVPVGRVETGVMKKGDQVTF--MPSGKT---GEVKSIEMHHEEVPQATPGDNIGWSVRGLGKGDA-RRGDV 304
                                       99*******************..777788...*********************************8.****9 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   4.8e-08   8.6e-05       2      92 ..      10     124 ..       9     175 .. 0.59

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 4.8e-08
                                       EEEEESTTSSHHHHHHHHH................T...............STEEESSSTTSSSSEEEEEEEETTEE CS
                          MMR_HSR1   2 vaivGrpNvGKStLinalt................g...............ekaivsdkpgtTrdinegrvklkgke 47 
                                        ai+G+   GKStL+ +l+                +               +  + ++  g T+di ++r+++++  
  gi|298674720|ref|YP_003726470.1|  10 LAIIGHIDHGKSTLVGRLMyetgaipqhiidknreKakeqgketfafawimDSLKEERDRGITIDIAHKRFDTDKYY 86 
                                       69****************96666555555555544044555555555544345677777888888888888888888 PP

                                       EEEEECGGC..SSHHHHHHHHHHHHHHHHCTSEEEEEEETTTTCSHH CS
                          MMR_HSR1  48 ielvDtpGl..iegaseekglgkaflaleeadlillvvdaseeklkp 92 
                                       +++vD+pG   +        +++ +    +ad+++l v a  +++ +
  gi|298674720|ref|YP_003726470.1|  87 FTIVDCPGHrdF--------VKNMITGASQADAAVLSVAAP-DGVMD 124
                                       ********3220........333333333445544444433.22222 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   5.2e-06    0.0092      29     160 ..      67     187 ..      59     190 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.2e-06
                         Gtr1_RagA  29 lrlgatidveksevrflgnltlnlwDcgGqeafveeyls..sqkeeifrnvgvliyVfDvesreleedletlkeile 103
                                       +  g+tid+ ++++  +++ ++ ++Dc+G ++fv+++++  sq++    +v++   V+D +++     +      l+
  gi|298674720|ref|YP_003726470.1|  67 RDRGITIDIAHKRF-DTDKYYFTIVDCPGHRDFVKNMITgaSQADAAVLSVAAPDGVMDQTKE-----H----VFLS 133
                                       55689*********.58999****************654227777777777777777776622.....1....2222 PP

                         Gtr1_RagA 104 alrqyspeakvfvlihKmDliqedereeifeerkeeireeiekleke..eiqffaTSiw 160
                                       +   ++    + v ++KmD i+ d  e+ +ee k++++e ++ ++++  +++f  TS +
  gi|298674720|ref|YP_003726470.1| 134 RTLGIN---DLIVAVNKMDDINYD--EKRYEEVKNQVSELLKMVGFKpdDVTFVPTSAY 187
                                       222222...345667777777433..344566666666666655554447777777765 PP

>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.5   1.1e-06     0.002      21      72 ..     243     293 ..     227     304 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.1e-06
                                       EEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEES CS
                       GTP_EFTU_D4  21 vGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisieg 72 
                                       vG +v +Gv+k g ++      + Ge+++i+ +++++ +a+ G++++ s++g
  gi|298674720|ref|YP_003726470.1| 243 VG-RVETGVMKKGDQVTFMPSGKTGEVKSIEMHHEEVPQATPGDNIGWSVRG 293
                                       88.9*********99976555589*************************998 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.11     2e+02       2      22 ..       9      29 ..       8      56 .. 0.74
   2 ?   10.0   0.2   0.00026      0.47      32     126 ..      70     159 ..      69     199 .. 0.64

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.11
                                      EEEEEESTTSSHHHHHHHHHT CS
                            FeoB_N  2 tvalvGnpnvGkttlfnaltg 22
                                      ++a++G  + Gk+tl+ +l  
  gi|298674720|ref|YP_003726470.1|  9 NLAIIGHIDHGKSTLVGRLMY 29
                                      6799***********998864 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00026
                                       TSSSEEEEEEEEETTEEEEEEE----SSS..SSSSHHHHHHHHHHHCTSSSEEEEEEEGGGHHHHHHHHHHHHHTTS CS
                            FeoB_N  32 GvtvekkegklklkgkeveivDlPGiYsl..sayseeekvardflleeepdvvvnvvdatnlernLyLtlqllelgv 106
                                       G+t++ ++ +++++++ ++ivD PG  ++  + ++   +    +l    pd v+   d t+ +  L  tl +     
  gi|298674720|ref|YP_003726470.1|  70 GITIDIAHKRFDTDKYYFTIVDCPGHRDFvkNMITGASQADAAVLSVAAPDGVM---DQTKEHVFLSRTLGI----N 139
                                       99***********************98774456677777777788888888754...555433333333333....3 PP

                                       SEEEEEETHHHHHHTTEEE- CS
                            FeoB_N 107 pvvlalnmideaekkgieid 126
                                       ++++a+n++d ++ ++ + +
  gi|298674720|ref|YP_003726470.1| 140 DLIVAVNKMDDINYDEKRYE 159
                                       56888888888765544433 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.011        19       1      19 [.      10      28 ..      10      35 .. 0.88
   2 ?    6.1   0.0    0.0058        10      50     114 ..      41      98 ..      30     148 .. 0.68
   3 ?   -2.2   0.0       2.1   3.8e+03      25      41 ..     312     341 ..     307     383 .. 0.59

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.011
                                      EEEEEBTTTTHHHHHHHHH CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLl 19
                                      +a++G+  +GKS+++  L+
  gi|298674720|ref|YP_003726470.1| 10 LAIIGHIDHGKSTLVGRLM 28
                                      589***********98887 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0058
                                       ...SSEEEET-EB--CHHHHHHHHHHHHHHHTSSSS--SS-EEEEEEETTS-SEEEEE---B-SS CS
                         Dynamin_N  50 avkeelkekekkledfsevreeieketekiagankgiskkvillkilsllvkgltlvDlPGldsv 114
                                       +++e+ ke+ k+   f  + + +++e+++         ++ i +k ++ ++   t+vD PG  + 
  gi|298674720|ref|YP_003726470.1|  41 KNREKAKEQGKETFAFAWIMDSLKEERDRGI-------TIDIAHKRFDTDKYYFTIVDCPGHRDF 98 
                                       4455555666666666666666666666644.......34799999***************8773 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.1
                                       ---SSS---S-EEEEE.............C CS
                         Dynamin_N  25 prgpnptTrrplelql.............g 41 
                                       p+ +n  T+ +++lq+              
  gi|298674720|ref|YP_003726470.1| 312 PTVANEFTAQIVVLQHpsaitvgytpvfhA 341
                                       666777888888888844444444444440 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0065        12       2      23 ..      10      31 ..       9      39 .. 0.89
   2 ?    4.7   0.0     0.018        33       9     119 ..      48     149 ..      46     150 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0065
                                      EEEESSTTSSHHHHHHCHCT-C CS
                               Roc  2 vvlvGdsgvGKtsllkrfvedk 23
                                      + ++G    GK++l+ r++ ++
  gi|298674720|ref|YP_003726470.1| 10 LAIIGHIDHGKSTLVGRLMYET 31
                                      679****************876 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.018
                                       TSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCTSCEEEE CS
                               Roc   9 gvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplylreaalail 85 
                                       ++GK +++  ++ d+ +e+++  i +d+++k++           ++k+ + i D  G+ +f + +    ++a++a+l
  gi|298674720|ref|YP_003726470.1|  48 EQGKETFAFAWIMDSLKEERDRGITIDIAHKRFD----------TDKYYFTIVDCPGHRDFVKNMITGASQADAAVL 114
                                       689*************************999873..........135789999**9999999877777777777777 PP

                                       EEE.GHHHHCHHHHHHHHHHHCSSS-EEEEEE-TT CS
                               Roc  86 vyd.srssenlkeWlkelkkvagkspvilvgnkiD 119
                                        +   +   +  +    l++  g + +i+ +nk+D
  gi|298674720|ref|YP_003726470.1| 115 SVAaPDGVMDQTKEHVFLSRTLGINDLIVAVNKMD 149
                                       65523323333333334555556666677777776 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00022      0.39       5     101 ..      10     107 ..       7     125 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00022
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpewek 81 
                                       l+i G    GK+tl+ +l++e  + +++i+  n ++ +++ ++++      i+++lkee+++ + +D +++  +  k
  gi|298674720|ref|YP_003726470.1|  10 LAIIGHIDHGKSTLVGRLMYETGAIPQHIIDKNREKAKEQGKETF--AFAWIMDSLKEERDRGITIDIAHKRFDTDK 84 
                                       678888899**********9999889**********999998888..678888887777888899998888766666 PP

                            AAA_14  82 alkslvd...egknldvivtGSn 101
                                       +   +vd   +++ ++ ++tG +
  gi|298674720|ref|YP_003726470.1|  85 YYFTIVDcpgHRDFVKNMITGAS 107
                                       66666665443334555666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3012.03
//
Query:       gi|298674721|ref|YP_003726471.1|  [L=731]
Description: translation elongation factor aEF-2 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.9e-65  218.0   0.3    1.3e-64  217.3   0.3    1.3  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    4.6e-30  103.9   0.1    2.3e-29  101.6   0.0    2.3  3  EFG_IV       Elongation factor G, domain IV
    5.2e-24   84.1   0.4    5.2e-24   84.1   0.4    2.0  2  EFG_II       Elongation Factor G, domain II
    8.5e-23   80.2   0.0    2.4e-22   78.8   0.0    1.8  1  EFG_C        Elongation factor G C-terminus
    1.2e-15   57.6   0.7      3e-15   56.4   0.7    1.8  1  GTP_EFTU_D2  Elongation factor Tu domain 2
    6.6e-05   23.0   0.1    0.00022   21.3   0.1    1.9  1  MMR_HSR1     50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.017   14.5   0.1       0.32   10.4   0.1    2.7  2  SRPRB        Signal recognition particle receptor beta subuni
      0.031   14.1   0.0      0.073   12.9   0.0    1.7  1  RF3_C        Class II release factor RF3, C-terminal domain
      0.033   13.5   0.2      0.061   12.6   0.2    1.3  1  Septin       Septin
      0.094   12.3   0.1       0.18   11.4   0.1    1.4  1  Ras          Ras family
       0.13   12.8   0.0       0.74   10.4   0.0    2.1  2  DUF4473      Domain of unknown function (DUF4473)
       0.36   10.7   1.8       0.44   10.4   0.3    1.9  3  RsgA_GTPase  RsgA GTPase


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.3   0.3   8.8e-68   1.3e-64       2     193 ..      20     257 ..      19     258 .. 0.89

  Alignments for each domain:
  == domain 1  score: 217.3 bits;  conditional E-value: 8.8e-68
                                       CEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE.T.TCSSEEEEEEE CS
                          GTP_EFTU   2 rirnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle.k.etkkylinliD 76 
                                        irnigi++h+DhGKtTLtd+Ll+ +g+is+  e  +++ ++D+ +eE+ rgiTi+sa++s+  + +++++linliD
  gi|298674721|ref|YP_003726471.1|  20 HIRNIGIVAHIDHGKTTLTDNLLAGAGMISS--ELSGSQLFMDSDEEEQDRGITIDSANVSMVhEyNGEEFLINLID 94 
                                       69*****************************..888889************************6269********** PP

                                       ESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHH CS
                          GTP_EFTU  77 tPGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrk 153
                                       tPGHvdF  +v+r++r++Dgav+v+daveG +pqte+vlr+alke+v++++fiNK+Drl++el+   +e++ +l + 
  gi|298674721|ref|YP_003726471.1|  95 TPGHVDFGGDVTRAMRAVDGAVVVIDAVEGTMPQTETVLRQALKEQVKPVLFINKVDRLINELQVDSQEMQIRLGKL 171
                                       **************************************************************************888 PP

                                       ............HHHHHHHHHTTT..........TTEEEEEEBTTTTBTHH.......................... CS
                          GTP_EFTU 154 ............eeklekygekge..........kevpvvfgSalkgegvk.......................... 182
                                                   e          e          ++ +v+fgSal +++++                          
  gi|298674721|ref|YP_003726471.1| 172 idhvnklikgmnE----------EsynkgwkvsaSDGTVAFGSALYNWAISvpmmdktnigfadvynycqqerqtdl 238
                                       6666555544442..........144555556568899**********99988888888888888888888888888 PP

                                       ........HHHHHHHHHSH CS
                          GTP_EFTU 183 ........tllealvellp 193
                                               ++ ++++++lp
  gi|298674721|ref|YP_003726471.1| 239 aqkcplyeAVNDMVIRHLP 257
                                       8888888778888888887 PP

>> EFG_IV  Elongation factor G, domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       4.3   6.5e+03      68      88 ..     282     301 ..     277     308 .. 0.79
   2 !  101.6   0.0   1.5e-32   2.3e-29       3     120 ..     508     617 ..     506     618 .. 0.96
   3 ?   -3.0   0.0         4     6e+03      22      59 ..     681     715 ..     675     723 .. 0.61

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.3
                                       CCCCCTTS-TTTS--EESEEE CS
                            EFG_IV  68 GfqealkeGplagepvtdvkv 88 
                                        +++a ++G la + vtd++ 
  gi|298674721|ref|YP_003726471.1| 282 QMTKAKENGDLA-FMVTDIRL 301
                                       567888999999.99999986 PP

  == domain 2  score: 101.6 bits;  conditional E-value: 1.5e-32
                                       CESCEE.SS-CCHCCCCCCCHTSSSHCCCCCEEEECCTTTTSSEEEEE--STCCCHCCCCHHHHCCCCCCTTS-TTT CS
                            EFG_IV   3 VayrEtirkpvkereeklkkqsggdgqyakvileiePleegsgnefvdetkggqvpkeyieavekGfqealkeGpla 79 
                                       +++r    +p+ er++kl++ +g+d+++ak  ++i +     +n++ d+tkg+q+++e++e++ +Gf+e+++ Gpla
  gi|298674721|ref|YP_003726471.1| 508 ISMR----MPELERRNKLME-AGMDKEEAKGLVDICE-----SNIYLDQTKGIQHLNETMELILEGFEEVMQAGPLA 574
                                       6666....8999999***99.9***************.....89********************************* PP

                                       S--EESEEEEEEEEE--T..TTC-HHHHHHHHCHHHHHHHHCC CS
                            EFG_IV  80 gepvtdvkvtLldgslhe..vdsseaafkpaarralkeallkA 120
                                       +ep+++vkv+L+d++lhe  +++++a+++pa+r+a+++a+l+A
  gi|298674721|ref|YP_003726471.1| 575 NEPCMGVKVKLIDAKLHEdtIHRGPAQVIPASRQAIQAAMLMA 617
                                       ****************************************998 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 4
                                       CHTSSSHCCCCCEEEECCTTTTSSEEEEE--STCCCHC CS
                            EFG_IV  22 kqsggdgqyakvileiePleegsgnefvdetkggqvpk 59 
                                         ++g+  +++    +eP +   +n + ++++ ++  k
  gi|298674721|ref|YP_003726471.1| 681 SSTEGRAMWSTEFAGFEPIP---SNLIQETISMIRERK 715
                                       56778888888888999998...444444444444333 PP

>> EFG_II  Elongation Factor G, domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.1   0.4   3.5e-27   5.2e-24       1      74 [.     387     460 ..     387     461 .. 0.97
   2 ?   -2.6   0.1         4     6e+03      41      52 ..     554     565 ..     544     567 .. 0.78

  Alignments for each domain:
  == domain 1  score: 84.1 bits;  conditional E-value: 3.5e-27
                            EFG_II   1 fPePvislaiepkskadedklskaLarlleEDptlrverdeeTketilsGmGelHleivverlkreykvevelg 74 
                                       ++ePv+++a+e+k  +d  kl ++L+++ +EDptl+v+ +eeT+e +lsGmGelHle++  r++r+ +ve++++
  gi|298674721|ref|YP_003726471.1| 387 VSEPVVTVAVEAKHMKDLPKLVEVLRQVNKEDPTLNVTLNEETGEHLLSGMGELHLEVIGHRIERDKGVEISTS 460
                                       689*******************************************************************9886 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4
                            EFG_II  41 eeTketilsGmG 52 
                                       +eT e+il+G  
  gi|298674721|ref|YP_003726471.1| 554 NETMELILEGFE 565
                                       79******9975 PP

>> EFG_C  Elongation factor G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8   0.0   1.6e-25   2.4e-22       2      87 ..     621     705 ..     620     707 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 1.6e-25
                                       EEEEEEEEEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EEEEEEEEE CS
                             EFG_C   2 llEPivkveievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegsfsmefsgY 78 
                                       +lEP++kv i vp++ +g ++++++ +rG+i++m+++ ++++ +e ++P+ael+gfa ++rs T+G++++s+ef+g+
  gi|298674721|ref|YP_003726471.1| 621 ILEPYQKVFIYVPQDQMGGATKLIQGKRGIILNMSSE-GDMTAVESKAPVAELFGFAGDIRSSTEGRAMWSTEFAGF 696
                                       8************************************.*************************************** PP

                                       EE--HHHHH CS
                             EFG_C  79 eevpgdkld 87 
                                       e++p+++ +
  gi|298674721|ref|YP_003726471.1| 697 EPIPSNLIQ 705
                                       ****99876 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.4   0.7     2e-18     3e-15       1      74 []     306     373 ..     306     373 .. 0.96

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 2e-18
                                       EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEEE CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtlt 74 
                                       G+va+gr++sGt+k+G+ev i  ++++ k    r++++   ++ e+ +v+  +aG+i+a+ gl+da ivG+t+t
  gi|298674721|ref|YP_003726471.1| 306 GEVATGRLFSGTFKRGMEVNI--SGSPSK---NRVQQVGIYMGSERVEVERIPAGNIAAVTGLKDA-IVGSTVT 373
                                       89*******************..888677...9********************************8.*****86 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.1   1.4e-07   0.00022       2     112 ..      24     147 ..      23     149 .. 0.62

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.4e-07
                                       EEEEESTTSSHHHHHHHHHT................STEEESSSTTSSSSEEEEEEE..ETTEE..EEEEECGGCSS CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg................ekaivsdkpgtTrdinegrvk..lkgke..ielvDtpGlie 58 
                                       ++iv +   GK+tL   l+                 +  + ++  g T+d     +   ++g+e  i+l+DtpG ++
  gi|298674721|ref|YP_003726471.1|  24 IGIVAHIDHGKTTLTDNLLAgagmisselsgsqlfmDSDEEEQDRGITIDSANVSMVheYNGEEflINLIDTPGHVD 100
                                       788888899******9998545555555555544433456677778888885444442433333558*******665 PP

                                       HHHHHHHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEE CS
                          MMR_HSR1  59 gaseekglgkaflaleeadlillvvdaseeklkpldeeleelleeakkplilvl 112
                                           + ++++a++    +d +++v+da e+++ + +  l + l+e+ kp+ l +
  gi|298674721|ref|YP_003726471.1| 101 ---FGGDVTRAMR---AVDGAVVVIDAVEGTMPQTETVLRQALKEQVKPV-LFI 147
                                       ...2223444444...58********996656555555666666666664.444 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00021      0.32       9      84 ..      27     120 ..      20     132 .. 0.70
   2 ?    0.2   0.0       0.3   4.4e+02      63      89 ..     518     544 ..     513     570 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00021
                                       E-STTSSHHHHHHHHHHS......................S---B---SS-EEETTG...GGTT-SEEEETT-GCCS CS
                             SRPRB   9 vGlsdsGKTslftrLttd......................svkktvtSqessaalkvksekgskltliDfPGheklr 63 
                                       v   d GKT+l   L+ +                          t  S + s+++++ + +++ ++liD PGh+ + 
  gi|298674721|ref|YP_003726471.1|  27 VAHIDHGKTTLTDNLLAGagmisselsgsqlfmdsdeeeqDRGITIDSANVSMVHEY-NGEEFLINLIDTPGHVDFG 102
                                       555666777777777776677777777777777666654444557778888888899.88999************99 PP

                                       HHHHHHHHHHGGEEEEEEEEE CS
                             SRPRB  64 qklleklkaksslkglvfvvD 84 
                                        +++  ++    + g v v+D
  gi|298674721|ref|YP_003726471.1| 103 GDVTRAMR---AVDGAVVVID 120
                                       88887744...4444444444 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.3
                                       SHHHHHHHHHHGGEEEEEEEEETTS-H CS
                             SRPRB  63 rqklleklkaksslkglvfvvDStidp 89 
                                       r+kl+e  ++k+++kglv + +S i  
  gi|298674721|ref|YP_003726471.1| 518 RNKLMEAGMDKEEAKGLVDICESNIYL 544
                                       899*****************9999853 PP

>> RF3_C  Class II release factor RF3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.9e-05     0.073      15      81 ..     396     462 ..     381     490 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.9e-05
                                       EEESSGGGHHHHHHHHHHHHHCTSSEEEEET.TSS-EEEEESSTHHHHHHHHHHHHHH---EEEEE- CS
                             RF3_C  15 vrlkdplkrkqlrkgleqLaeEGavqvfkeeeageelilgaVGqLQfeVveeRlknEYgvevrlesl 81 
                                       v++k      +l + l+q+++E  +   + +e++ e +l+ +G+L +eV+ +R+++  gve+++++ 
  gi|298674721|ref|YP_003726471.1| 396 VEAKHMKDLPKLVEVLRQVNKEDPTLNVTLNEETGEHLLSGMGELHLEVIGHRIERDKGVEISTSPP 462
                                       455555555677888999999998877777778899*************************998764 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   4.1e-05     0.061       9     132 ..      26     159 ..      22     176 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.1e-05
                                       EEEBTTSSCCCCCCTTSSSS----.......--------------S-EEEEE.EE.EETTCEEEEEEEE---BSSSS CS
                            Septin   9 vvGesglGkttlintlfetdliee.......ekleeasekkkktveikkkkv.vi.eedgvklnltviDtpgfGdav 76 
                                       +v +   Gkttl + l++   + +         +++ +e++ + ++i++++v ++ e +g ++ +++iDtpg+ d+ 
  gi|298674721|ref|YP_003726471.1|  26 IVAHIDHGKTTLTDNLLAGAGMISselsgsqLFMDSDEEEQDRGITIDSANVsMVhEYNGEEFLINLIDTPGHVDFG 102
                                       66677789****999887554333356665423445556788888888554414415579************75543 PP

                                       .SHHCCCHHH...HHHHHHHHHHHHHHCTSS--SS-----EEEEEEEE-TTSSSS-HHHH CS
                            Septin  77 .dnskswepi...veyideqfeeylreesklkRkkivDkRvHaclyfisPtghglkpldv 132
                                        d +++ +++   v    +  e  + + +++ R+ +++  v  +l fi+ + + +++l+v
  gi|298674721|ref|YP_003726471.1| 103 gDVTRAMRAVdgaVVV-IDAVEGTMPQTETVLRQALKE-QVKPVL-FINKVDRLINELQV 159
                                       1334444443110333.345666777777777766554.466665.46666666666655 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00012      0.18      26     126 ..      66     163 ..      56     174 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                                       SSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEETTBHHHHHTHHHHHHHHHHHST CS
                               Ras  26 eeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvyditsresfenvkkwveeikrvae 102
                                       ++   Ti  ++ +   e++g+e  +++ DT G  +f    +  +r ++g+++v d  +  +  + ++ +++     +
  gi|298674721|ref|YP_003726471.1|  66 QDRGITIDSANVSMVHEYNGEEFLINLIDTPGHVDFGGDVTRAMRAVDGAVVVIDAVEG-TMPQTETVLRQA---LK 138
                                       4455688888888889999**********************************997764.455555444433...33 PP

                                       TTSEEEEEEETTT.GGGG-SS-HHH CS
                               Ras 103 envpivLvGnKvD.leekravstee 126
                                       e+v+ vL  nKvD l ++ +v+ +e
  gi|298674721|ref|YP_003726471.1| 139 EQVKPVLFINKVDrLINELQVDSQE 163
                                       4566788889998445555665555 PP

>> DUF4473  Domain of unknown function (DUF4473)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.8   2.7e+03      49      68 ..     168     187 ..     150     193 .. 0.82
   2 ?   10.4   0.0    0.0005      0.74       6      30 ..     516     540 ..     511     567 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.8
                           DUF4473  49 feklkaevdafiktqseeDq 68 
                                       ++kl+++v++ ik + ee  
  gi|298674721|ref|YP_003726471.1| 168 LGKLIDHVNKLIKGMNEESY 187
                                       5699999******9999875 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0005
                           DUF4473   6 eakaeLvaaGlsekaadglvkiaek 30 
                                       e +++L  aG++++ a+glv+i e 
  gi|298674721|ref|YP_003726471.1| 516 ERRNKLMEAGMDKEEAKGLVDICES 540
                                       7899*****************9775 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       8.1   1.2e+04     111     129 ..      33      51 ..      31      56 .. 0.73
   2 ?   -3.0   0.0         4     6e+03     155     161 ..      92      98 ..      74     103 .. 0.80
   3 ?   10.4   0.3   0.00029      0.44      15      71 ..     111     165 ..     104     184 .. 0.79

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 8.1
                                       SHHHHHHHHCTT-----S- CS
                       RsgA_GTPase 111 GKStLinallpelelktge 129
                                       GK+tL ++ll  + +  +e
  gi|298674721|ref|YP_003726471.1|  33 GKTTLTDNLLAGAGMISSE 51 
                                       9999999998776555555 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4
                                       EESS-SS CS
                       RsgA_GTPase 155 liDtPGf 161
                                       liDtPG 
  gi|298674721|ref|YP_003726471.1|  92 LIDTPGH 98 
                                       89***96 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00029
                                       S--EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHH CS
                       RsgA_GTPase  15 NvdqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkee 71 
                                        vd +++v+ ++  e ++ + + +L +a +++++pv+ +nK+D l +e ++++++ +
  gi|298674721|ref|YP_003726471.1| 111 AVDGAVVVIDAV--EGTMPQTETVLRQALKEQVKPVLFINKVDRLINELQVDSQEMQ 165
                                       588888888887..5566678999*******************87776656555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (731 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.40
# Mc/sec: 5528.05
//
Query:       gi|298674722|ref|YP_003726472.1|  [L=186]
Description: 30S ribosomal protein S7 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-34  118.9   2.6    1.7e-34  118.6   2.6    1.0  1  Ribosomal_S7  Ribosomal protein S7p/S5e
  ------ inclusion threshold ------
       0.13   12.2   0.2       0.89    9.5   0.1    2.3  3  DUF1727       Domain of unknown function (DUF1727)


Domain annotation for each model (and alignments):
>> Ribosomal_S7  Ribosomal protein S7p/S5e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.6   2.6   1.9e-38   1.7e-34      16     149 .]      44     186 .]      34     186 .] 0.93

  Alignments for each domain:
  == domain 1  score: 118.6 bits;  conditional E-value: 1.9e-38
                                       SSTTSBHHHHHHHHHSB....TTBHHHHHHHHHHHHHHHHHHHSS-HHHHHHHHHHHCS-SEEEEEEBSSSSBEEEE CS
                      Ribosomal_S7  16 pkynselveklinklmk....dGkkslAekivygaldiieektkkdplevleeAlenvkPrvevksrrvGGatyqvp 88 
                                       +k + ++ve+l+n+lm+    +Gkk+ A + v++a+dii +kt+++p++vl++A+ n+ Pr+ev ++++GG++++ +
  gi|298674722|ref|YP_003726472.1|  44 NKSEISIVERLVNNLMRkehnTGKKQFALRAVEDAFDIIYSKTERNPVQVLVDAIANTGPREEVVRLKYGGISVPKA 120
                                       457889**************9******************************************************** PP

                                       EEE-HHHHHHHHHHHHHHHH...STSSSS-HHHHHHHHHHHHHTT-..SHHHHHHHHHHHHHHHTG CS
                      Ribosomal_S7  89 vevrpkRrqalAlrwiieaa...rkrkeksmaekLaeElidAaege..gaavkkreethrmAeanr 149
                                       v+ +++Rr+++Alr i  ++   + ++++s+a++La+El+ Aa+++    +v++++  +r+A+++r
  gi|298674722|ref|YP_003726472.1| 121 VDTASQRRVDTALRLISMGVnqaAYKSKRSLADCLASELMGAANRDakYFSVNRKDSKERVAKSAR 186
                                       ****************887766689999******************555699***********987 PP

>> DUF1727  Domain of unknown function (DUF1727)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.27   2.4e+03     100     100 ..      68      68 ..      34     106 .. 0.61
   2 ?    0.0   0.0     0.087   7.8e+02      67      78 ..     106     117 ..      75     123 .. 0.70
   3 ?    9.5   0.1    0.0001      0.89      57      94 ..     121     158 ..     116     172 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.27
                           DUF1727 100 t 100
                                       +
  gi|298674722|ref|YP_003726472.1|  68 K 68 
                                       1 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.087
                           DUF1727  67 malRLkyagvee 78 
                                         +RLky g++ 
  gi|298674722|ref|YP_003726472.1| 106 EVVRLKYGGISV 117
                                       468999999865 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0001
                           DUF1727  57 vvvsGeraeDmalRLkyagveeekieieedleealeae 94 
                                       v ++++r  D+alRL   gv++   + +++l++ l++e
  gi|298674722|ref|YP_003726472.1| 121 VDTASQRRVDTALRLISMGVNQAAYKSKRSLADCLASE 158
                                       557899*********************99999998873 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1404.19
//
Query:       gi|298674723|ref|YP_003726473.1|  [L=142]
Description: 30S ribosomal protein S23 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-44  150.1   0.3    2.1e-44  149.8   0.3    1.1  1  Ribosom_S12_S23  Ribosomal protein S12/S23


Domain annotation for each model (and alignments):
>> Ribosom_S12_S23  Ribosomal protein S12/S23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.8   0.3   1.2e-48   2.1e-44       1     114 []      27     141 ..      27     141 .. 0.97

  Alignments for each domain:
  == domain 1  score: 149.8 bits;  conditional E-value: 1.2e-48
                                       --------S-TSSTTSSEEEEEEEEEEEE---TT--S-EEEEEEEET.TSEEEEEEE-SSS..----TT-EEEEEE- CS
                   Ribosom_S12_S23   1 rkelrkktksdalegapqkrGvvlekvtveakkPnsAlRkvvrvrLikngkevtafipgegalnfldEhdevlvrGi 77 
                                       r++l++  k+d+l+gapq rG+vlekv+veak+PnsA+Rk+vr++Likng++ taf+pg+ga+n++dEhdev+v+ i
  gi|298674723|ref|YP_003726473.1|  27 RRALGLDVKADPLSGAPQGRGIVLEKVGVEAKQPNSAVRKCVRIQLIKNGRQATAFCPGDGAINYIDEHDEVTVERI 103
                                       6788999********************************************************************99 PP

                                       -......BTTSTTEEEEBETS---TSSSTTTTT----T CS
                   Ribosom_S12_S23  78 rrk.gkavkDlpGvrykvvkvagvslkalskykkekpk 114
                                       +++ g +++D+pGvr+kv+ v++vsl+++  +++ekp+
  gi|298674723|ref|YP_003726473.1| 104 GGRmGGSKGDIPGVRFKVIAVNNVSLNEMAIGRREKPR 141
                                       9888*****************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 1072.29
//
Query:       gi|298674724|ref|YP_003726474.1|  [L=141]
Description: NusA family KH domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.3e-19   67.4   2.2    3.2e-14   52.5   0.2    2.1  2  KH_2      KH domain
    2.5e-16   59.5   2.5    7.5e-15   54.8   0.4    2.3  2  KH_5      NusA-like KH domain
    2.1e-05   24.3   0.4      0.035   14.0   0.0    2.2  2  KH_4      KH domain
     0.0013   18.5   2.7        0.3   11.0   0.2    2.7  3  KH_1      KH domain


Domain annotation for each model (and alignments):
>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.5   0.2   7.1e-18   3.2e-14       3      71 ..      13      91 ..      11      99 .. 0.86
   2 !   15.8   0.1   2.1e-06    0.0093      25      55 ..     100     130 ..      77     135 .. 0.77

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 7.1e-18
                                      HHHHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTC............EEEE CS
                              KH_2  3 peslaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkk............Vkln 69
                                      +++ ++++++a+v+++++++  +r+i+v+ ++++g +IGk+G+ i+k+++++ k +e +e+++            V + 
  gi|298674724|ref|YP_003726474.1| 13 YIAMFEQTTGAEVRDCIVDE--DRIIYVVEAGNMGAAIGKNGEHINKVKENVDKHVELVEYSEdpsefiknafgpVAVS 89
                                      78899*************77..***************************************997777777777775555 PP

                                      EE CS
                              KH_2 70 iv 71
                                      +v
  gi|298674724|ref|YP_003726474.1| 90 SV 91
                                      55 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 2.1e-06
                                       CEEEEEEEESCHHHHHTGGGHHHHHHHHHHH CS
                              KH_2  25 nrviiviresqpgivIGkgGsnikkigkelr 55 
                                       + + + + ++ +g++IG +G+ni+k++  ++
  gi|298674724|ref|YP_003726474.1| 100 QYAYVQVSNNSKGLAIGSNGKNIDKVKMIAN 130
                                       45556788999**************997765 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.8   0.4   1.7e-18   7.5e-15       2      68 ..      32      92 ..      31      93 .. 0.97
   2 !    4.7   0.1    0.0069        31      18      34 ..     110     126 ..     100     139 .. 0.78

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 1.7e-18
                              KH_5  2 GertkvaVkshnpnvdpvGaivgkkGsrikavsseLkgekidvvewseDlaefianalsPaevlsVk 68
                                      ++r++ +V+++n     +Ga++gk+G+ i++v++   ++ +++ve+seD++efi+na+ P+ v+sV+
  gi|298674724|ref|YP_003726474.1| 32 EDRIIYVVEAGN-----MGAAIGKNGEHINKVKENV-DKHVELVEYSEDPSEFIKNAFGPVAVSSVN 92
                                      689999******.....*******************.*****************************8 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0069
                              KH_5  18 pvGaivgkkGsrikavs 34 
                                         G ++g +G++i +v+
  gi|298674724|ref|YP_003726474.1| 110 SKGLAIGSNGKNIDKVK 126
                                       47889999999999885 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.1   0.00034       1.5      27      52 ..      31      56 ..      11      59 .. 0.71
   2 !   14.0   0.0   7.8e-06     0.035      18      60 ..      89     131 ..      76     138 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00034
                              KH_4 27 eeveielnvegedlGrvIGkrGrtld 52
                                      +e++i   ve  ++G  IGk+G+ ++
  gi|298674724|ref|YP_003726474.1| 31 DEDRIIYVVEAGNMGAAIGKNGEHIN 56
                                      345666667999**********9875 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 7.8e-06
                              KH_4  18 vevteeeeeeeveielnvegedlGrvIGkrGrtldAlqylvsa 60 
                                        +v++ ++++++   ++v+ + +G+ IG +G+++d  + ++++
  gi|298674724|ref|YP_003726474.1|  89 SSVNLVNKDDKQYAYVQVSNNSKGLAIGSNGKNIDKVKMIANR 131
                                       46888899999999*********************99999887 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.32   1.4e+03      26      50 ..      18      38 ..      13      44 .. 0.64
   2 !   11.0   0.2   6.7e-05       0.3       7      28 ..      40      61 ..      34      82 .. 0.75
   3 !    6.9   0.1    0.0012       5.5       4      25 ..     104     125 ..     102     130 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.32
                                      HHHHT-EEEEES.STT...T.-EEEE CS
                              KH_1 26 reetgakIkvpk.sedegsderevti 50
                                      ++ tga ++  + + d   ++r++ +
  gi|298674724|ref|YP_003726474.1| 18 EQTTGAEVR--DcIVD---EDRIIYV 38
                                      565688877..33444...5677765 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 6.7e-05
                                      GGGHHHHHHTGGGHHHHHHHHH CS
                              KH_1  7 PsslvgriIGkgGsnIkeIree 28
                                       +  +g+ IGk+G++I++ +e 
  gi|298674724|ref|YP_003726474.1| 40 EAGNMGAAIGKNGEHINKVKEN 61
                                      55668999**********9984 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0012
                                       EEEGGGHHHHHHTGGGHHHHHH CS
                              KH_1   4 ilvPsslvgriIGkgGsnIkeI 25 
                                       ++v ++  g+ IG +G+nI + 
  gi|298674724|ref|YP_003726474.1| 104 VQVSNNSKGLAIGSNGKNIDKV 125
                                       68999999***********875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1031.77
//
Query:       gi|298674725|ref|YP_003726475.1|  [L=98]
Description: 50S ribosomal protein L7Ae/L30e/S12e/Gadd45 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.2e-14   51.0   0.0    1.2e-13   50.6   0.0    1.1  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
  ------ inclusion threshold ------
      0.023   14.6   0.1       0.03   14.3   0.1    1.1  1  BRCA-2_OB1      BRCA2, oligonucleotide/oligosaccharide-bindin
      0.028   14.5   0.1      0.032   14.3   0.1    1.1  1  BRCT_3          BRCA1 C Terminus (BRCT) domain


Domain annotation for each model (and alignments):
>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.0     2e-17   1.2e-13       3      94 ..       8      95 ..       7      96 .. 0.92

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 2e-17
                                      HHHHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEESCHHHHHHHTTSSSECS CS
                    Ribosomal_L7Ae  3 ieevlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvkskkeLGelvgkkrpvs 81
                                      i ++l  ++++g +v+G k+++ + e+ ea++++l+++++++ k+k   + +  ++v  ++++s  eLG+ +gk++  +
  gi|298674725|ref|YP_003726475.1|  8 IDKALLSVLRTGSVVIGSKRTIESAEKSEAEMIVLSANCPENVKSK---INSTGIPVLNYSGTS-VELGASCGKPFSIA 82
                                      567788899*********************************9999...566678888899999.************** PP

                                      EEEEEESTTTHHH CS
                    Ribosomal_L7Ae 82 alaikdegdskdl 94
                                      a+ai+d+g+s++l
  gi|298674725|ref|YP_003726475.1| 83 AMAIIDPGESNIL 95
                                      **********997 PP

>> BRCA-2_OB1  BRCA2, oligonucleotide/oligosaccharide-binding, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1     5e-06      0.03      57     110 ..       6      57 ..       4      65 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5e-06
                                       E---HHHHHHHHTT-S-TT-EEEES--EEES--S---GGG--SS-EEE--TTTE CS
                        BRCA-2_OB1  57 avlDaalsrllkrgkikvGqKlvvagaelvgseeavspleaseklllkisaNst 110
                                       +++D+al ++l++g++++G+K  +  ae   se ++ +l+a     +k ++Nst
  gi|298674725|ref|YP_003726475.1|   6 ISIDKALLSVLRTGSVVIGSKRTIESAEK--SEAEMIVLSANCPENVKSKINST 57 
                                       679*************************9..66666667655555666666666 PP

>> BRCT_3  BRCA1 C Terminus (BRCT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   5.4e-06     0.032      24      73 ..      15      62 ..       1      65 [. 0.69

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.4e-06
                            BRCT_3 24 ilklaGaavvkkekseaeeislgkldvvvtdsscpeevlkkaeqlkipvv 73
                                      +l+++   +  ++++  e+++ +  +++v   +cpe+v+ k ++ +ipv+
  gi|298674725|ref|YP_003726475.1| 15 VLRTGSVVI-GSKRT-IESAEKSEAEMIVLSANCPENVKSKINSTGIPVL 62
                                      444433333.33222.23335667799*********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 721.53
//
Query:       gi|298674726|ref|YP_003726476.1|  [L=388]
Description: DNA-directed RNA polymerase subunit A'' [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-57  193.9   1.9    4.6e-57  193.5   1.9    1.1  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
     0.0037   17.0   0.2      0.012   15.3   0.1    1.9  2  Peptidase_M24   Metallopeptidase family M24


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.5   1.9   5.2e-61   4.6e-57      66     265 ..      49     329 ..      15     331 .. 0.92

  Alignments for each domain:
  == domain 1  score: 193.5 bits;  conditional E-value: 5.2e-61
                                       S....B--TT-BHHHHHHHHHHHHHHCCCSSTTSSTCSSTSSSSSSHHHHHHHHTT-SS-SS-EEEEEB-SSSSSCH CS
                                       x....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5  66 g....lvepGeavGiiaaQSiGePgTQltlnTFHfaGvasknvtlGvprlkeilnvskniksksltvllvdeeakel 138
                                       +     vep eavG+++aQSiGePgTQ+t++TFH+aGva+ nvtlG+prl ei+++ k+ +++++tv l + +++++
  gi|298674726|ref|YP_003726476.1|  49 NygyaCVEPCEAVGVVSAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVDARKTPSTPMMTVALEEGYSDSR 125
                                       1444489********************************************************************** PP

                                       HHCHHHHHHHSE................................................................. CS
                                       xxxxxxxxxxxx................................................................. RF
                    RNA_pol_Rpb1_5 139 ekakkvkkaiek................................................................. 150
                                       ++a+k++ +ie                                                                  
  gi|298674726|ref|YP_003726476.1| 126 DEARKLAWQIEAthighlgdvttdlaqmqlvvdlhektltqreisvdeiagilrdklnvlvkisegvdyqiiiqpnq 202
                                       *****999999999*************************************************************** PP

                                       ...................CBTTEEEEEEEEEEEEEEETEEEEEEECS--HHHHTTSTTTBETTTEEESSHHHHHHH CS
                                       ...................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5 151 ...................gikkikrilvkeaekgkeeekelvletegvnlsevlkveevvdageilsndiaeilei 208
                                                          gi++ikr+++++++      +e++l teg +l+evlk+e+ vd++++++n+iaei+e+
  gi|298674726|ref|YP_003726476.1| 203 psyrellqlaknihnvtlkGIEGIKRVVIRKDS------DEYTLYTEGSELNEVLKIEG-VDVTRTYTNNIAEIYEV 272
                                       ******************9999****9999433......456789**************.***************** PP

                                       HCHHHHHHHHHHHHHHHHHHTTS---HHHHHHHHHHHTTTSS---SSTTCHCCSSSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5 209 lgieaarkallkeiqevykvqgvsvndrHlelivdqmtkkgeivavnrsGinkaels 265
                                       +gieaar+al+ke  +++++qg++v+ rH++l++d+mt+ ge+++++r+Gi  ++ s
  gi|298674726|ref|YP_003726476.1| 273 FGIEAARNALVKEAMDTLSEQGLNVDIRHIMLVADIMTCDGEVKQIGRHGISGEKAS 329
                                       ***************************************************987765 PP

>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   1.3e-06     0.012     121     202 ..      28     136 ..      19     149 .. 0.78
   2 ?   -2.6   0.0      0.42   3.8e+03      91     110 ..     257     271 ..     249     306 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.3e-06
                                       HC-STTSBHHHHHHHHHHHHHHTTB....................CCGBSSCSEEEESS.SSSEE..EEEESS.STT CS
                     Peptidase_M24 121 kavkpGvtlseidaaarevlesagl....................akffphglGHgvGl.evhde..gpsvsr.esn 173
                                       +a+k Gv+ +e+ +++++v+ ++g+                    +++++ ++ H  G  e+      p++      
  gi|298674726|ref|YP_003726476.1|  28 DAIKVGVSKKELEEIIHQVMDNYGYacvepceavgvvsaqsigepGTQMTMRTFHYAGVaEINVTlgLPRLIEiVDA 104
                                       699***********************************9999999888899*******6677733334654335334 PP

                                       CSSB--TTBEEEEEEEEEEETTT..E.EEEEB CS
                     Peptidase_M24 174 dgrkleeGmvftiEpgiyfapge..g.gvrie 202
                                       ++++ ++ m++++E g+    +e  + + +ie
  gi|298674726|ref|YP_003726476.1| 105 RKTPSTPMMTVALEEGYSDSRDEarKlAWQIE 136
                                       799************99844322222255555 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.42
                                       EEEEEEECSSGSHHHHHHHH CS
                     Peptidase_M24  91 DitrTvlvGkftpeqrelye 110
                                       D+trT+ +       +e+ye
  gi|298674726|ref|YP_003726476.1| 257 DVTRTYTNN-----IAEIYE 271
                                       555665442.....122222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2938.77
//
Query:       gi|298674727|ref|YP_003726477.1|  [L=881]
Description: DNA-directed RNA polymerase subunit A' [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.9e-104  349.4   0.0   6.2e-104  347.7   0.0    1.8  2  RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
    3.5e-70  235.5   0.2    7.5e-70  234.5   0.2    1.6  1  RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
    2.4e-35  121.8   0.0      8e-35  120.1   0.0    1.9  2  RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
    2.2e-30  104.8   0.0    5.8e-30  103.4   0.0    1.8  1  RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
    3.2e-28   98.9   0.0    6.3e-28   97.9   0.0    1.5  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  347.7   0.0  1.7e-107  6.2e-104       2     312 .]       9     313 ..       8     313 .. 0.93
   2 ?   -1.3   0.0      0.29     1e+03     128     164 ..     561     599 ..     504     680 .. 0.72

  Alignments for each domain:
  == domain 1  score: 347.7 bits;  conditional E-value: 1.7e-107
                                       E---EEEEEE--HHHHHHH-SBB--STTSTCSTSSSSBBSSSSSSSSS-SSSSSTSTTTSSTTTT-----EEEEEEC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1   2 kkikeiqfgiaspeeirkwSvvevtkaetieekslkPeegGllDerlgtidkdleCetCgkkkkeCeghfGhieLak 78 
                                       k++ ei+fg++sp+e+rk+Sv+ + +a+t++++   P ++Gl+D rlg+id  l C+tCg    +C+ghfGhieL +
  gi|298674727|ref|YP_003726477.1|   9 KRVGEIRFGLLSPREVRKMSVTPIITADTYDDDG-YPIDMGLMDMRLGVIDPGLICKTCGSRAGDCPGHFGHIELVA 84 
                                       7999****************************95.9***************************************** PP

                                       EEE-HHHHHHHHHHCTTCETTTTEBSS-TTSH....HHHHHHCSSSCC..CCHHHHHHHHCCS-BE-SSSSB-EEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1  79 Pvfhigffklilkilecvckecskllldeekkkllsklkkrekleelk..krlkaieelckkinlcekCgavqpkle 153
                                       Pv+h+gf+klilk l+++c++cs+ ll++++k+ + ++ ++ k+   +  + ++ + +  +k ++c +C+    ++e
  gi|298674727|ref|YP_003726477.1|  85 PVIHVGFNKLILKSLRSICRNCSNFLLEPQRKNEYLEQLQQLKIMGHStdDLVNDLFKEARKTKVCPHCNE--EQVE 159
                                       *****************************988666666655555433344788889999999999999994..4466 PP

                                       EETTEEEEEESSSSTSCEEEE-HHHHHHHHHCSTHHHHHHTTSBTTTB-GGGCCECCEEE--GGGS-BEESSSSSEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1 154 eegeklkaalkkskeeekeklsaekvkkllkriededvevlgfkssgsrPewliltvlPVpPpeiRPsvqldggrrs 230
                                        ++ek  + +++ ++     l+++++++ +++++d+dv+++g+++s++rPew+iltvlPVpP+++RPs++l++g+rs
  gi|298674727|ref|YP_003726477.1| 160 IKFEKPSDYIENGEK-----LTPTEIRERFENMSDDDVRLMGMDPSNARPEWMILTVLPVPPVTVRPSITLESGQRS 231
                                       677778888877777.....********************************************************* PP

                                       BECCCCHHHHHHHHHHHHHHHHHSSSSSTCHHHHHHHHHHHHHHCC-TTSSSSSEEBSTTSSS--THHHHHTSSSSC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1 231 edDlteklrdiikrNnrLkkaeeegapeliieeekelLQehvatlfdneisglkpatqkskrplkslsqrLkGKeGr 307
                                       edDlt+k++dii++N+r+++++e+gap+li+e+ +elLQ+hv+t+fdne+sg++pa+++s+rplk+l+qrLkGKeGr
  gi|298674727|ref|YP_003726477.1| 232 EDDLTHKMVDIIRINQRFQENREAGAPQLILEDLWELLQYHVTTFFDNEVSGVPPARHRSGRPLKTLTQRLKGKEGR 308
                                       ***************************************************************************** PP

                                       CCCCT CS
                                       xxxxx RF
                    RNA_pol_Rpb1_1 308 fRgnL 312
                                       fRg+L
  gi|298674727|ref|YP_003726477.1| 309 FRGSL 313
                                       ***98 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.29
                                       CHHHHHHHHCCS-BE-..SSSSB-EEEEEETTEEEEEES CS
                                       xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1 128 rlkaieelckkinlce..kCgavqpkleeegeklkaalk 164
                                        l+ ++e+c+k + c+  +C++ +  + e+ge ++ +++
  gi|298674727|ref|YP_003726477.1| 561 NLEYVAEVCSKCDECNreNCENDAYVIIENGELITGTID 599
                                       577788888888888655777755555444444444443 PP

>> RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.5   0.2   2.1e-73   7.5e-70       1     165 [.     315     480 ..     315     481 .. 0.99

  Alignments for each domain:
  == domain 1  score: 234.5 bits;  conditional E-value: 2.1e-73
                                       SEEESSEEEEEEEEESSS-TTEEEEEHHHHTTSEEEEE-STTTHHHHHHHHHHTTTSSSSEEEEESTTSSEEETTTT CS
                    RNA_pol_Rpb1_2   1 GkrvdysaRsvispdpnlkldevgvPisvakkltvpeivtelnikklrklvengpevyPgasyvkredgsekklkak 77 
                                       Gkrv++saR+vispdpnl+++evg+P+ +ak++t+p  v + n +k+r++v++g++v+Pga+yv+r+dg++ k++  
  gi|298674727|ref|YP_003726477.1| 315 GKRVNFSARTVISPDPNLSINEVGLPYAIAKQMTIPVNVISRNLEKMRQYVARGNDVHPGANYVIRADGRRIKVTDV 391
                                       9***************************************************************************9 PP

                                       -S.CHHCCTTTTSEEEEE--TTSEEEEE-SSTTSGGGEEEEEEEEESSSSEEEEGGGHCCCT--SSS-EEEEE--SS CS
                    RNA_pol_Rpb1_2  78 kr.klakelekgdiverhvkdgdvvllNRqPsLhklsimahrvkvlekktlrlnlsvttayNaDFDGDemnlhlpqs 153
                                       +   la++l +g++ver+++dgd+v++NRqPsLhk+simah+vkvl++kt+rln +v+ +yNaDFDGDemnlh+ q+
  gi|298674727|ref|YP_003726477.1| 392 NCtDLAEKLDIGWVVERQLQDGDIVIFNRQPSLHKMSIMAHHVKVLPYKTFRLNPAVCPPYNADFDGDEMNLHVLQT 468
                                       9977************************************************************************* PP

                                       HHHHHHHHHCSB CS
                    RNA_pol_Rpb1_2 154 eearaEaeelll 165
                                       eearaEae l+ 
  gi|298674727|ref|YP_003726477.1| 469 EEARAEAEILMK 480
                                       ********9996 PP

>> RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.99   3.6e+03     105     127 ..     125     146 ..      95     150 .. 0.73
   2 !  120.1   0.0   2.2e-38     8e-35       1     156 [.     484     649 ..     484     650 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.99
                                       SHHHHSSSSTTSHHHHHHHHCHH CS
                    RNA_pol_Rpb1_3 105 dkkvvgkksqgslihvlakeygi 127
                                       + k++g  s  +l++ l+ke   
  gi|298674727|ref|YP_003726477.1| 125 QLKIMG-HSTDDLVNDLFKEARK 146
                                       348999.8999*******99855 PP

  == domain 2  score: 120.1 bits;  conditional E-value: 2.2e-38
                                       CSEETTTTEESSS--THHHHHHHHHSSTTEEEEHHHHHHHHHHSSSCCSSSSSSSSSBESS..SEBEEHHHHHHCCC CS
                    RNA_pol_Rpb1_3   1 nilspqsgkPvigivQDsllGvyllTkedvfidreeaqqllykgvgsdsktvtlrpailkp..kelwtgkqtfsril 75 
                                       nilsp+ g P+ig ++D+++G++llT+ d  i++++a+ ll+k        ++++pa ++   ++ wtgkq+fs +l
  gi|298674727|ref|YP_003726477.1| 484 NILSPRFGGPIIGGIHDHISGMFLLTRTDNDISKNDALDLLRKSHI----RQLPEPAGYRDdgEPYWTGKQIFSQLL 556
                                       9*******************************************55....468888888887556************ PP

                                       HCCCCEEEE.....SSSS........STSEEECSSEEEES--SHHHHSSSSTTSHHHHHHHHCHHHHHHHHHHHHHH CS
                    RNA_pol_Rpb1_3  76 pneinyerk.....neek........dgkvlikngelikGvidkkvvgkksqgslihvlakeygiketvrfldslqr 139
                                       p+++n+e       ++++        d +v+i+ngeli+G+id+k +g + +g +++ ++keyg+++ ++f+d+++r
  gi|298674727|ref|YP_003726477.1| 557 PDDLNLEYVaevcsKCDEcnrencenDAYVIIENGELITGTIDEKGIG-AFKGHIVDKIVKEYGSTKSAEFIDDMTR 632
                                       **888888766555333377777888**********************.999************************* PP

                                       HHHHHHHHHCEB-TGGG CS
                    RNA_pol_Rpb1_3 140 lgfkyllqsgftigigD 156
                                       l+++ +++sg+++gi+D
  gi|298674727|ref|YP_003726477.1| 633 LAIRAIMRSGLSFGISD 649
                                       ***************99 PP

>> RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.4   0.0   1.6e-33   5.8e-30       1     108 []     675     781 ..     675     781 .. 0.97

  Alignments for each domain:
  == domain 1  score: 103.4 bits;  conditional E-value: 1.6e-33
                                       HHHHCTHTCCHHHTTHCHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTTSHHHHHHHCTSSS-HHHHHHHHTB-EEEE CS
                    RNA_pol_Rpb1_4   1 ieeaerygkledlpgksleelfeakinkilnkardkagkiaskslaasNsiliMvksGaKGsiinisqiagclGqqn 77 
                                       ie++e   +le+lpg++l+e+ e+ki++ l  ardk+g++a ++l  +Ns +iM+ksGa+Gs++n++q+a+ +Gqq+
  gi|298674727|ref|YP_003726477.1| 675 IEAYEA-RELEPLPGRTLDETIEMKIMQKLGVARDKTGDVAGNHLGLDNSAVIMAKSGARGSMLNLTQMAASVGQQA 750
                                       567777.89*************************************66***************************** PP

                                       BTTBSS--SSTSCSSTTSSSSESSTTTSSEE CS
                    RNA_pol_Rpb1_4  78 vegkripkgfsgrtlphfkkidespesrGFv 108
                                       v+g+ri +g++grtlphf+k d ++ ++GFv
  gi|298674727|ref|YP_003726477.1| 751 VRGERIRRGYTGRTLPHFSKGDLGADAHGFV 781
                                       ******************************8 PP

>> RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.9   0.0   1.8e-31   6.3e-28       1      66 [.     788     853 ..     788     874 .. 0.95

  Alignments for each domain:
  == domain 1  score: 97.9 bits;  conditional E-value: 1.8e-31
                                       B--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTEEEETTSEEEETTS-EEESSGGGTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5   1 GLkvkefffhtmggReGLiDtAvkTaesGYlqRrlvkaledvvvkyddtvrnsggeivqflygedg 66 
                                       GL+++e+ffh+ ggReGL+DtAv+T++sGYlqRrlv+al+d+ v+yd++vr++ g ivqf+ygedg
  gi|298674727|ref|YP_003726477.1| 788 GLNPTEYFFHAVGGREGLVDTAVRTSQSGYLQRRLVNALQDLEVQYDGSVRETRGVIVQFKYGEDG 853
                                       9****************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (881 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.70u 0.29s 00:00:00.99 Elapsed: 00:00:00.48
# Mc/sec: 5539.11
//
Query:       gi|298674728|ref|YP_003726478.1|  [L=604]
Description: DNA-directed RNA polymerase subunit B [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.1e-123  413.1   0.0   1.5e-123  412.8   0.0    1.1  1  RNA_pol_Rpb2_6   RNA polymerase Rpb2, domain 6
    2.8e-30  104.6   0.4    6.5e-30  103.4   0.4    1.7  1  RNA_pol_Rpb2_7   RNA polymerase Rpb2, domain 7
    4.7e-22   78.0   1.2    9.3e-22   77.1   1.2    1.5  1  RNA_pol_Rpb2_4   RNA polymerase Rpb2, domain 4
    6.5e-11   42.6   1.9    2.4e-10   40.8   1.9    2.0  1  RNA_pol_Rpb2_5   RNA polymerase Rpb2, domain 5
  ------ inclusion threshold ------
       0.02   15.2   0.5       0.32   11.3   0.2    2.6  2  RNA_pol_Rpb2_45  RNA polymerase beta subunit external 1 domai
       0.12   12.6   1.7       0.23   11.6   1.7    1.5  1  Auto_anti-p27    Sjogren's syndrome/scleroderma autoantigen 1
       0.19   11.8   0.7       0.36   10.9   0.7    1.4  1  DUF1451          Zinc-ribbon containing domain
        0.2   11.6   1.1       0.41   10.6   1.1    1.5  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
       0.73   10.4   2.8         49    4.5   0.1    3.3  3  YflT             Heat induced stress protein YflT


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  412.8   0.0  7.4e-127  1.5e-123       3     390 .]     137     507 ..     135     507 .. 0.96

  Alignments for each domain:
  == domain 1  score: 412.8 bits;  conditional E-value: 7.4e-127
                                       HT-SS-TTB-HHHHHHHHHHGGGB-S---TTTTT---SSEEEESS----SSB-S.TTTTTS........GGGS-SEE CS
                    RNA_pol_Rpb2_6   3 klapvvehvqspriiiqaamekqalgiyslnkfkrsnqktyllcinqkPlvktgdkveagqvldgpatekgelalGq 79 
                                         +p++eh+ +pr+++ aam kq +g+ + n+  r +++ ++l+++qk+l kt+  ++ ++        ++e ++Gq
  gi|298674728|ref|YP_003726478.1| 137 GMVPYPEHNAAPRNTMGAAMVKQCVGMSTSNQKLRPDTRAHVLHYPQKALTKTQ-PADSIH--------FDERPAGQ 204
                                       678***************************************************.777777........******** PP

                                       EEEBBBS--TTTTTTT-EEEBCHHHHTTTT-EEEEEE..EEE--SSSS---.-S--..-.....-SS-GGGS-TTSB CS
                    RNA_pol_Rpb2_6  80 navVAvmsyeGYniEDaiilnerlvdrdvftsihikeyeveardtklgeeeitrdipnv.....seealkkLdedGi 151
                                       n+vVAvmsyeGYniEDa+++n+ +++r++++s++++++e e r++ +g+e+ ++ ++++     + ea+++LdedG+
  gi|298674728|ref|YP_003726478.1| 205 NFVVAVMSYEGYNIEDALVFNKGSIERGLARSHFLRTFEGEERRYAGGQEDKFEIPDSDyrgarGAEAYANLDEDGL 281
                                       *************************************************9988888777999999************ PP

                                       --SS-EEETT-EEE---..B-----...-----------..-B---EE--TT-EEEEEEEEE.......EE-TT--E CS
                    RNA_pol_Rpb2_6 152 vrvgaevkegdilvgkvtkgeteltpeekllraifgekarevkdtslrvksgeegvVdkvkvfsrekgdelkagvnk 228
                                       v++++   ++d+l+gk+  ++ ++ +e    ++ fg   ++ +++ ++++s+e+g+Vd+v++       +++ ++++
  gi|298674728|ref|YP_003726478.1| 282 VNPETVAAPNDVLIGKT--SPPRFLEE----QSDFGLAVEQRRESAITMRSNEKGIVDNVIL-------TESINGTR 345
                                       ****************8..88888854....4567777777899******************.......8999**** PP

                                       EEEEEEEEEE---TT-BEEETTS---BBEEEB-TTTSEEETTS---SEEE-GGGCHHH-BTTHHHHHHHHHCCCSSS CS
                    RNA_pol_Rpb2_6 229 lvkvyvaqkRklqvGDKfasrhGqKGvvslilpqeDmPfledGivvDivlNPlgvPSRmtigqllEtllgkaaaleg 305
                                       l+kv+v+++R +++GDKfasrhGqKGv++li+p +DmPf+edG v+D+++NP+++PSRmt+g++lE++ gk++++eg
  gi|298674728|ref|YP_003726478.1| 346 LAKVKVRDQRVPEIGDKFASRHGQKGVIGLIVPYQDMPFTEDGLVPDLIVNPHAIPSRMTVGHVLEMIGGKVGSMEG 422
                                       ***************************************************************************** PP

                                       S--B--TT-...-HHHHHHHHHTTS-TT-EE-EEETTTS-B-SS-EEB-EEEEEEBS--CCCS----SS--B-TTT- CS
                    RNA_pol_Rpb2_6 306 kkvdatvFdgakeeeikelLeeagleasGkevlydGrtGekleaeifvGviYylkLkhlvedKihaRstGpyslltq 382
                                       ++vdat+F+g++eee+++ L+  g++++Gkev++dG+tG+k++a+ f Gvi y+kL+h+v+ K+haRs+Gp+++lt+
  gi|298674728|ref|YP_003726478.1| 423 RRVDATAFSGESEEELRNGLRDYGFSHTGKEVFTDGVTGKKIQADTFSGVILYQKLHHMVASKMHARSRGPVQVLTR 499
                                       ***************************************************************************** PP

                                       -B-SCGGG CS
                    RNA_pol_Rpb2_6 383 QPlgGkaq 390
                                       QP++G+a+
  gi|298674728|ref|YP_003726478.1| 500 QPTEGRAR 507
                                       ******96 PP

>> RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.4   0.4   3.3e-33   6.5e-30       1      84 [.     509     598 ..     509     601 .. 0.98

  Alignments for each domain:
  == domain 1  score: 103.4 bits;  conditional E-value: 3.3e-33
                                       BBEEEEHHHHHHHHHHTBHHHHHHHHTTTTTEEEEEEESSSSSCCCEE......EBTTTTCSSSEEEEEEEHHHHHH CS
                    RNA_pol_Rpb2_7   1 GGlrfGEMErdaliayGaaalLkerltikSDavevdvcgrckllaaan......eCkivkseekiekveipeafklL 71 
                                       GGlrfGEMErd++i++Gaa+ Lkerl+++SD+v   vc++c+++a+++       C++++se++i +ve+++afklL
  gi|298674728|ref|YP_003726478.1| 509 GGLRFGEMERDVMIGHGAAMALKERLMDESDKVVQLVCSNCGMIATYDrkqkmaFCSNCESETDIYPVEMSYAFKLL 585
                                       9**********************************************9*****9*********************** PP

                                       HHHHHHTTBEEEE CS
                    RNA_pol_Rpb2_7  72 lqeLqslgialkl 84 
                                       l+e++slg+++++
  gi|298674728|ref|YP_003726478.1| 586 LDEIKSLGVTPRM 598
                                       **********998 PP

>> RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.1   1.2   4.7e-25   9.3e-22       1      62 []       6      67 ..       6      67 .. 0.99

  Alignments for each domain:
  == domain 1  score: 77.1 bits;  conditional E-value: 4.7e-25
                                      EECTT-BEEE-S-HCCHHHHHHHHCCTTSS-TT-EEEE-TTT--EEEE-SSEEB-EEEEE-S CS
                    RNA_pol_Rpb2_4  1 VfvNGrllGvtrdpkklvetlRelRRkgkiseevsivlnekqkevkiatDgGRvcRPliiVe 62
                                      +f+NG+l+G++++p +lve++Re RR+g is++v+++l+e+ +e+ i++D GR++RPliiV+
  gi|298674728|ref|YP_003726478.1|  6 IFLNGELVGTHNNPVELVEDIREQRRNGLISQQVNVALYEDINEIIINSDIGRARRPLIIVK 67
                                      7************************************************************7 PP

>> RNA_pol_Rpb2_5  RNA polymerase Rpb2, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   1.9   1.2e-13   2.4e-10       2      58 .]      89     128 ..      89     128 .. 0.94

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 1.2e-13
                                       HHHHHTTSEEEEEHHHHTT--EESSTTTCSST-SSTTTSS--TTSSSST-SEEES-G CS
                    RNA_pol_Rpb2_5   2 ddLlregvvEylDaeEEetamIamtpedleksreekealeekenskshtyTHcEIhP 58 
                                       +dL+++g vEylDaeEEe+a+Ia++ +dl+ +                 +TH+EI+P
  gi|298674728|ref|YP_003726478.1|  89 EDLVKQGFVEYLDAEEEENAYIALYASDLTPE-----------------HTHLEIDP 128
                                       69***************************776.................79999999 PP

>> RNA_pol_Rpb2_45  RNA polymerase beta subunit external 1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00016      0.32      11      33 ..      96     118 ..      84     127 .. 0.81
   2 ?    0.6   0.0      0.34   6.7e+02      26      45 ..     270     289 ..     266     300 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                                       EEEEEEHHHHTTSEEE-SSS-BE CS
                   RNA_pol_Rpb2_45  11 evvYLtAdeEekyviAqAnapld 33 
                                        v+YL A+eEe+ +iA   + l 
  gi|298674728|ref|YP_003726478.1|  96 FVEYLDAEEEENAYIALYASDLT 118
                                       599*************7666555 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.34
                                       E-SSS-BETTSCBSSSEEEE CS
                   RNA_pol_Rpb2_45  26 AqAnapldeegrfveerVla 45 
                                       A+A a+lde+g +  e+V+a
  gi|298674728|ref|YP_003726478.1| 270 AEAYANLDEDGLVNPETVAA 289
                                       8999*******998899987 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.7   0.00012      0.23      17      40 .]     545     568 ..     540     568 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                     Auto_anti-p27  17 tCpvCgvPLmrdrkggkvyCvaCd 40 
                                       +C++Cg++   drk++  +C +C+
  gi|298674728|ref|YP_003726478.1| 545 VCSNCGMIATYDRKQKMAFCSNCE 568
                                       7************99********5 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.7   0.00018      0.36     112     141 ..     541     570 ..     534     571 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00018
                           DUF1451 112 lGtlvCekCgkelalkkteeippCpkCgat 141
                                         +lvC +Cg   ++++ +++  C++C+++
  gi|298674728|ref|YP_003726478.1| 541 VVQLVCSNCGMIATYDRKQKMAFCSNCESE 570
                                       568************************986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.1   0.00021      0.41      31      56 ..     546     571 ..     544     572 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00021
                    OrfB_Zn_ribbon  31 CseCgsknkealsgrtfkCpnCgfea 56 
                                       Cs+Cg + +++++++   C+nC  e 
  gi|298674728|ref|YP_003726478.1| 546 CSNCGMIATYDRKQKMAFCSNCESET 571
                                       **********************9775 PP

>> YflT  Heat induced stress protein YflT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.025        49       1      31 [.      13      43 ..      13      55 .. 0.88
   2 ?    1.0   0.1      0.31   6.2e+02      11      28 ..      75      92 ..      72      92 .. 0.89
   3 ?    2.9   0.0     0.079   1.6e+02      64      92 ..     430     459 ..     414     464 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.025
                              YflT  1 igvyeneeellsaieelkaeGyneddiyvva 31
                                      +g+++n  el+++i+e +++G  +++  v+ 
  gi|298674728|ref|YP_003726478.1| 13 VGTHNNPVELVEDIREQRRNGLISQQVNVAL 43
                                      7899*****************9999988865 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.31
                              YflT 11 lsaieelkaeGyneddiy 28
                                       ++ie+lk++++ ++d++
  gi|298674728|ref|YP_003726478.1| 75 DEQIEQLKNNEITSEDLV 92
                                      589************985 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.079
                              YflT  64 frs.kgdelrekleslGltedeaeeyeeel 92 
                                       f++ +++elr+ l+++G++ +  e + + +
  gi|298674728|ref|YP_003726478.1| 430 FSGeSEEELRNGLRDYGFSHTGKEVFTDGV 459
                                       44348899***********98887776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (604 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.61u 0.24s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 4093.99
//
Query:       gi|298674729|ref|YP_003726479.1|  [L=538]
Description: RNA polymerase subunit beta [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-55  186.9   0.3    3.9e-55  186.5   0.3    1.1  1  RNA_pol_Rpb2_1  RNA polymerase beta subunit
    1.4e-26   92.5   0.0    2.3e-26   91.7   0.0    1.4  1  RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
    2.7e-26   92.4   0.0    4.7e-26   91.6   0.0    1.4  1  RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb2_1  RNA polymerase beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.5   0.3   6.5e-59   3.9e-55       2     202 ..      17     384 ..      16     385 .. 0.99

  Alignments for each domain:
  == domain 1  score: 186.5 bits;  conditional E-value: 6.5e-59
                                       TTHHHHHHHHHHHHTHHHHHCTTSSECCHCSSSHCSSSCEEEEEEEEEEESCSSECTTSCEEES.HHHHHHCTSBXE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb2_1   2 LvsqqldSFnkfveqdlekiikeeaaieseeeiqssgeelelkfvsirlgkPvvdesdasereiyPkearlrnltYs 78 
                                       +v+ ++dSFnkf+e  l+k+i+e+  ie++ e       +++k+++ir++kP+v+e+d++ +++yP+earlrn++Y 
  gi|298674729|ref|YP_003726479.1|  17 IVQHHIDSFNKFLESGLQKVIDEQGIIETDLED------IYIKLGNIRVEKPIVKEADGAIENLYPNEARLRNISYT 87 
                                       699**************************9995......9************************************* PP

                                       EEEEEEEEEEECCCCTCCEEEEEEEEEEEEEXBTTSTTSSSTTS.HHHHHHTTS.TTS..SSEEETTCEEEEXEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb2_1  79 aplyvklklvvyekdnkeeikeeevyiGelPlMlrskacvlseaseeelvelkEcpldqGGyFiinGtekvivaqek 155
                                       aply+++  v       +e ++ e +iG+lP+M++s++c+l +++++e+v+ +E+pld+GGyFiinGte+v++ +e+
  gi|298674729|ref|YP_003726479.1|  88 APLYLQMSVVN----GDKETEPMEAKIGQLPIMVKSNYCNLVGINDQEMVQYGEDPLDPGGYFIINGTERVVMTLED 160
                                       ********999....8999********************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                    RNA_pol_Rpb2_1 156 ............................................................................. 155
                                                                                                                    
  gi|298674729|ref|YP_003726479.1| 161 lapnkvmtefserygdpiqvskvfsqrrgyralvvvergrksllevsfpsisgrvnfitlmralgvetdedivkmvs 237
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                    RNA_pol_Rpb2_1 156 ............................................................................. 155
                                                                                                                    
  gi|298674729|ref|YP_003726479.1| 238 tdqeilkymfenleesevetteeaveklgsrvasgqakdyqikranyvidryllphlgndpedrltkahflgrmaes 314
                                       ***************************************************************************** PP

                                       .......................XHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSSSSSHHHHSCSHHHH CS
                                       .......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb2_1 156 .......................laGeLlaslfrvllkklerdvkerlqksleklddlmlqllvnakpit 202
                                                              l G+L+++lfrv++++l+rd+k +l++   ++++l++  lv+a+ +t
  gi|298674729|ref|YP_003726479.1| 315 cfelalgrrnpndkdhysnkrlkLTGDLMEDLFRVAFNRLARDIKYQLERASMRNRELNVVTLVRADVLT 384
                                       *****************************************************************99776 PP

>> RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.7   0.0   3.9e-30   2.3e-26       1      67 [.     405     468 ..     405     469 .. 0.97

  Alignments for each domain:
  == domain 1  score: 91.7 bits;  conditional E-value: 3.9e-30
                    RNA_pol_Rpb2_3   1 qvldrlnplselshlrrvsslrgglskerkttevRdlhpshwGriCpveTPEGencGlvksLallar 67 
                                       q+ldr+ ++s+lshlrrv s+   ls+ + ++e+Rdlhp++wGr+Cp+eTPEG+ncGlvk++a++++
  gi|298674729|ref|YP_003726479.1| 405 QLLDRTDYISTLSHLRRVISP---LSRAQPHFEARDLHPTQWGRLCPSETPEGPNCGLVKNFAQMVE 468
                                       89*******************...***************************************9975 PP

>> RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.6   0.0   7.9e-30   4.7e-26       8     190 .]     170     337 ..     154     337 .. 0.84

  Alignments for each domain:
  == domain 1  score: 91.6 bits;  conditional E-value: 7.9e-30
                                       EE-SSSSSE.SSSCCEECCCEEEEECCCCSTSCEEEEECTTSSSEEEHHHHHHHTT--STTHHHHHHTSSSTTHHHH CS
                    RNA_pol_Rpb2_2   8 ekekdknki.satvtsslisqrgsvlklekdgktliwtriskkrkipivivlkAlglvsdreIlericydsedsqll 83 
                                       ++e++ + i +++v s +  +r++v++++  ++ l ++ +s+  +++++ +++Alg+ +d++I++ ++    ++q +
  gi|298674729|ref|YP_003726479.1| 170 FSERYGDPIqVSKVFSQRRGYRALVVVERGRKSLLEVSFPSISGRVNFITLMRALGVETDEDIVKMVS----TDQEI 242
                                       3555555565556666666777777777777777889******************************9....46777 PP

                                       HHHHHHHHHHCTSSSCHHHHHHHHHCSSTTSSSCCCCCHHHHHHHCHHHHHHHTTTTSSTTTTTSSSTCHH...HHH CS
                    RNA_pol_Rpb2_2  84 eelleeleekeeiqtqeealdyigkvvalrrgeearlqsareilqkrydlgeigreklnkhlglseslenkr.lkaq 159
                                        +++ e+ e++e+ t+eea +++g++va ++ +  ++++a  ++         +r+ l+ hlg + +   +r  ka+
  gi|298674729|ref|YP_003726479.1| 243 LKYMFENLEESEVETTEEAVEKLGSRVASGQAKDYQIKRANYVI---------DRYLLP-HLGNDPE---DRlTKAH 306
                                       7777777788899999*************************995.........8*****.*****99...5667*** PP

                                       HHHHHHHHHHHHHTTSSSS--TTSGGGEEEE CS
                    RNA_pol_Rpb2_2 160 dilymidrLlslklgrrevDDiDhlgnkRvr 190
                                       +++ m++  ++l+lgrr++ D+Dh+ nkR++
  gi|298674729|ref|YP_003726479.1| 307 FLGRMAESCFELALGRRNPNDKDHYSNKRLK 337
                                       *****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (538 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      661  (0.0368676); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 3667.92
//
Query:       gi|298674730|ref|YP_003726480.1|  [L=78]
Description: RNA polymerase Rpb5 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-28   98.9   0.4    1.2e-28   98.7   0.4    1.0  1  RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain
  ------ inclusion threshold ------
      0.068   13.5   0.1      0.076   13.3   0.1    1.2  1  Lzipper-MIP1    Leucine-zipper of ternary complex factor MIP1


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.7   0.4   1.4e-32   1.2e-28       2      73 .]       5      76 ..       4      76 .. 0.98

  Alignments for each domain:
  == domain 1  score: 98.7 bits;  conditional E-value: 1.4e-32
                                      .-TSSSS--EEEEE-HHHHHHHHHHTT--TTCSS-EETTSHHHHCCT--TTSEEEEEEEETTTEEEEEEEEE CS
                    RNA_pol_Rpb5_C  2 nitkHelvPkhevlseeekkellkklkikeeqLPkisksDpvarylglkkGdvvkItrksetageavtYRlV 73
                                      ++++Hel+Pkhe+l  +e +++l++++i++eqLPki+++Dp+++++g+ +GdvvkI rks+ta+e  +YRlV
  gi|298674730|ref|YP_003726480.1|  5 SLLDHELIPKHEILATDELQTVLNHYQIDKEQLPKIKSTDPIIQEIGALEGDVVKISRKSQTAEEGLYYRLV 76
                                      5789*******************************************************************9 PP

>> Lzipper-MIP1  Leucine-zipper of ternary complex factor MIP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   8.5e-06     0.076      28      75 ..      16      65 ..       5      74 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.5e-06
                      Lzipper-MIP1 28 raLe.kalssssdgsllslstllp..kkakellkeiallEeevvkLEqkll 75
                                      ++L  + l++  ++ ++  ++ lp  k++   ++ei  lE +vvk  +k +
  gi|298674730|ref|YP_003726480.1| 16 EILAtDELQTVLNHYQIDKEQ-LPkiKSTDPIIQEIGALEGDVVKISRKSQ 65
                                      555545554444555666666.99667*****************9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:01.12
# Mc/sec: 210.55
//
Query:       gi|298674731|ref|YP_003726481.1|  [L=411]
Description: adenosylhomocysteinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-59  199.8   0.0    7.9e-31  107.3   0.0    2.0  2  AdoHcyase      S-adenosyl-L-homocysteine hydrolase
    2.2e-46  157.9   1.7    2.2e-46  157.9   1.7    1.8  2  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
    2.7e-10   39.9   0.1    6.3e-10   38.7   0.1    1.6  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
      7e-06   25.7   0.1    1.7e-05   24.5   0.1    1.6  1  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
  ------ inclusion threshold ------
      0.029   13.7   1.6       0.06   12.6   1.6    1.6  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
       0.05   13.9   0.1       0.21   11.9   0.1    2.1  1  TrkA_N         TrkA-N domain
      0.051   12.8   0.2       0.12   11.6   0.1    1.7  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> AdoHcyase  S-adenosyl-L-homocysteine hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.3   0.0   3.1e-34   7.9e-31       8     139 ..       5     132 ..       1     139 [. 0.94
   2 !   91.2   0.0   2.4e-29   6.3e-26     175     286 ..     135     405 ..     132     410 .. 0.98

  Alignments for each domain:
  == domain 1  score: 107.3 bits;  conditional E-value: 3.1e-34
                                       GGHHHHHHHHHHHHCC-HHHHHHHHHCTTT-TTTT-EEEEES--SHHHHHHHHHHHHTT-EEEEE-SSTTT--HHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase   8 slaefGrkeielaekempglmalreeyaeekplkgariaGslhmtiqtavLietLvalGaevrWasCnifstqdeaa 84 
                                       +l e G+++ie a + mp l  +r+ +a+ekplkg ria +lh+ ++tavL+etL + Gae+  + Cn  stqd++a
  gi|298674731|ref|YP_003726481.1|   5 TLLESGNQKIEWARNHMPVLSIIRDGFASEKPLKGCRIAMALHVEAKTAVLVETLASGGAEIAITGCNPLSTQDDVA 81 
                                       56789************************************************************************ PP

                                       HHHCCT.TEEEE--TT--HHHHHHHHHHCHS-SSTS-S-SEEEESSSHHHHHHHHH CS
                                       xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase  85 aaiaea.gvpvfawkgetleeywwcieqalkwaedekepnlilDdGGDltllvhkg 139
                                       aa+ ++ +v+ +a    +++ey + i+++l+      epn+i+DdG D+ + +h+ 
  gi|298674731|ref|YP_003726481.1|  82 AALDTRdNVSCYAKNDVSKDEYYEAIDRVLDI-----EPNIIVDDGADIIHKIHTE 132
                                       ***9877***********************66.....7***************983 PP

  == domain 2  score: 91.2 bits;  conditional E-value: 2.4e-29
                                       CCHCC--EEEE-SHHHHHHHHHHHHTT---SEEEESTTSHHHCTTH............................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................... RF
                         AdoHcyase 175 ellkkikGvseetttGvhrLyelakkgkLlvpainvndsvtkskfD............................... 220
                                       +ll ++ G  eetttGvhrL+++++++ L++p+i vnd++tk  fD                               
  gi|298674731|ref|YP_003726481.1| 135 NLLPNVIGGCEETTTGVHRLMSMSENNALKIPTIAVNDALTKFLFDnrygtgqstwdainrttnllvagkdvvvagy 211
                                       5677889999******************************************************************* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                         AdoHcyase 221 ............................................................................. 220
                                                                                                                    
  gi|298674731|ref|YP_003726481.1| 212 gwcgkgvamyaaglganvivtevnpvralearmdgyrvmtmdeaaelgdifvtttgnvsvltrdhfklmkdgvilan 288
                                       ***************************************************************************** PP

                                       .....................................................S-HHHHHHHHHHHHHHHHHHHHTT CS
                                       .....................................................xxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase 221 .....................................................hpsfvmsasftnqvlaqielfkke 244
                                                                                            hp+ vm++sf+nq+l   +l ++ 
  gi|298674731|ref|YP_003726481.1| 289 sghfnvemnleelesmahsirkvksnikeynlkthrinviadqqtvnlaagdgHPAEVMDMSFSNQALCVRHLVDN- 364
                                       *************************************************************************995. PP

                                       SSS-SSEEE--CHHHHHHHHHCCCCCT-------HHHHHCCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase 245 kkyekkvyvlpkklDekvarlhleklgaklteltkeqaeyig 286
                                        + + +v+ +p ++D ++a+l+l+ lg++++elt+eq +y+ 
  gi|298674731|ref|YP_003726481.1| 365 -DLDIDVHAVPPEIDTYIAELKLKVLGIEIDELTTEQEKYMR 405
                                       .56999**********************************85 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.9   7.4e+03      41      59 ..      58      76 ..      55      86 .. 0.73
   2 !  157.9   1.7   8.4e-50   2.2e-46       1     160 [.     181     339 ..     181     341 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.9
                                      HHHHCT-EEEEE-S-HHHH CS
                     AdoHcyase_NAD 41 slkglGarvivtevdPica 59
                                      +l + Ga + +t  +P+++
  gi|298674731|ref|YP_003726481.1| 58 TLASGGAEIAITGCNPLST 76
                                      5677788888888888764 PP

  == domain 2  score: 157.9 bits;  conditional E-value: 8.4e-50
                                       HHHHHCCCCCHHHHHHH-S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTT CS
                     AdoHcyase_NAD   1 nlygcreslvdgikratdvllaGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvk 77 
                                       n yg+ +s  d+i+r+t++l+aGk +vvaGyG  GkG a    glGa vivtev+P+ al a m+G++v+t++e+++
  gi|298674731|ref|YP_003726481.1| 181 NRYGTGQSTWDAINRTTNLLVAGKDVVVAGYGWCGKGVAMYAAGLGANVIVTEVNPVRALEARMDGYRVMTMDEAAE 257
                                       78*************************************************************************** PP

                                       T-SEEEE-SSSSSSB-HHHHCCS-TTEEEEE-SSTTTTBTHHHHHTTT-EEEEEETTEEEEE-TTS-EEEEEGGGSB CS
                     AdoHcyase_NAD  78 kadivvtttGnkdiitlehlkkmkddaivcniGhfdseidvaaleanalkkeevkpqvdrvtlkdgkkiillaeGrl 154
                                        +di+vtttGn  ++t++h+k mkd +i++n Ghf+ e+++++le++a ++ +vk+++++++lk  ++i ++a+ + 
  gi|298674731|ref|YP_003726481.1| 258 LGDIFVTTTGNVSVLTRDHFKLMKDGVILANSGHFNVEMNLEELESMAHSIRKVKSNIKEYNLKT-HRINVIADQQT 333
                                       **************************************************************986.679999***** PP

                                       CHHHTS CS
                     AdoHcyase_NAD 155 lnlgca 160
                                       +nl++ 
  gi|298674731|ref|YP_003726481.1| 334 VNLAAG 339
                                       **9876 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.1   2.5e-13   6.3e-10      20     127 ..     187     290 ..     173     297 .. 0.89

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 2.5e-13
                                       TTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEE CS
                      2-Hacid_dh_C  20 egewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivs 96 
                                       + +w++ ++++   ++gk v + G+G  G+ va +++++g++vi++++++ +  e++  g+++++++e+ +  Di +
  gi|298674731|ref|YP_003726481.1| 187 QSTWDAINRTTNLLVAGKDVVVAGYGWCGKGVAMYAAGLGANVIVTEVNPVRALEARMDGYRVMTMDEAAELGDIFV 263
                                       567877778888899**********************************9998899999****************99 PP

                                       E-S--STTTTTSBSHHHHHCSTTTEEEEESS CS
                      2-Hacid_dh_C  97 lhlpltpetrhlinaeelakmkkgailiNta 127
                                        +      +  +++++++++mk+g+il N +
  gi|298674731|ref|YP_003726481.1| 264 TT----TGNVSVLTRDHFKLMKDGVILANSG 290
                                       75....56999*****************987 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.1   6.5e-09   1.7e-05       2     103 ..     201     298 ..     200     307 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 6.5e-09
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHH CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevye 78 
                                       + gk ++v GyG  G+  a+     g +v+v+  +    + +A+ +g++v+t++ea++  d+ ++ +    + +v++
  gi|298674731|ref|YP_003726481.1| 201 VAGKDVVVAGYGWCGKGVAMYAAGLGANVIVTEVNPV-RALEARMDGYRVMTMDEAAELGDIFVTTT---GNVSVLT 273
                                       5799***************************998887.6778*******************877665...4568899 PP

                                       HHTGGG--TT-EEEESSSHHHHTTS CS
                              IlvN  79 eeiepnlkegkalafahGfnihfgl 103
                                       ++  + +k+g +la +  fn+ ++l
  gi|298674731|ref|YP_003726481.1| 274 RDHFKLMKDGVILANSGHFNVEMNL 298
                                       9999999*******99999998775 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.6   2.3e-05      0.06      29      77 ..     204     251 ..     194     320 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.3e-05
                                       -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEE CS
                       AlaDh_PNT_C  29 akvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvev 77 
                                         v+v G G  G   +  a+glga+V v++v+p r+ + +  g + v +
  gi|298674731|ref|YP_003726481.1| 204 KDVVVAGYGWCGKGVAMYAAGLGANVIVTEVNPVRALEARMDGYR-VMT 251
                                       579******************************988776665555.333 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   8.1e-05      0.21       1      48 [.     206     253 ..     206     258 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.1e-05
                                       EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEEES- CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglevvvgd 48 
                                       ++++G+G  G+ +a +    g  +v+v + ++ r+ e+r +g++v+  d
  gi|298674731|ref|YP_003726481.1| 206 VVVAGYGWCGKGVAMYAAGlGA-NVIVTEVNPVRALEARMDGYRVMTMD 253
                                       79*****************777.6********************99877 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   4.7e-05      0.12     128     176 ..     188     237 ..     134     296 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.7e-05
                                       SECHHHHHHCCSS-T.SEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSS CS
                                       xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 128 rtldsaealklkllp.krivvvGgGyiGvElAaalaklgkevtlveardr 176
                                       +t+d  ++    l+  k++vv G G +G  +A+++a lg++v + e ++ 
  gi|298674731|ref|YP_003726481.1| 188 STWDAINRTTNLLVAgKDVVVAGYGWCGKGVAMYAAGLGANVIVTEVNPV 237
                                       444444444444444799**********************9998888763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       812  (0.0452898); expected 358.6 (0.02)
Passed bias filter:                      626  (0.0349155); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2796.74
//
Query:       gi|298674732|ref|YP_003726482.1|  [L=430]
Description: amidohydrolase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.9e-76  256.6   0.2    4.7e-76  256.3   0.2    1.1  1  Amidohydro_1  Amidohydrolase family
    3.3e-24   86.2   0.3    1.2e-15   58.0   0.0    2.3  2  Amidohydro_3  Amidohydrolase family
     0.0043   16.4   0.0     0.0072   15.7   0.0    1.3  1  A_deaminase   Adenosine/AMP deaminase


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  256.3   0.2   7.9e-80   4.7e-76       1     343 [.      52     398 ..      52     399 .. 0.94

  Alignments for each domain:
  == domain 1  score: 256.3 bits;  conditional E-value: 7.9e-80
                                       EEEE-EEEEEEECETTECSSS....GHHHHH..........STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHH CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrga....tledwl..........vppetaaealesgiktalksGtttvadmgattstgi 63 
                                       +v+PG++++H+H  ++llrg     +l++wl          +++e+a+ +++ ++ +++ksGtt++adm +    +i
  gi|298674732|ref|YP_003726482.1|  52 VVMPGFVNTHTHTGMTLLRGYaddfPLDEWLknyiwpvedrLTDEDAYIGTKLACLEMIKSGTTSFADMFI----HI 124
                                       69*********************************************************************....9* PP

                                       HHHHHHHHTSSSEEEEEEESSEGGS...GCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHH CS
                      Amidohydro_1  64 ealleaaeelplglrilggkvsldr...gsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkea 137
                                       + +++a+++   g+r+ +++ +++    +++++++++ ++++  +    kg+a+g++ +  +ph+++++s+  l+++
  gi|298674732|ref|YP_003726482.1| 125 DKVAQAVKDS--GMRAALSYRMIEAgneEKGKSELDTNKRFINNW----KGEAEGRIITMYGPHAPYTCSEGFLSKV 195
                                       *********9..*************66666666666666666666....**************************** PP

                                       HHHHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHC CS
                      Amidohydro_1 138 lkeakkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeag 214
                                        kea +  + ++iH+let+ e  ++++ +g   ++      ++ lg+l++  +++ah+v+l+++++e+l+ r  ++ 
  gi|298674732|ref|YP_003726482.1| 196 KKEANHDRVGIHIHVLETESELNQMKQHYG---MC--SINLLDRLGFLGP-DVLAAHCVWLSDDDIEILRGR--GVH 264
                                       ******************************...88..9999999******.*****************8888..*** PP

                                       EEHHHHHHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHTH CS
                      Amidohydro_1 215 vahcpfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllyedeegglslkealrmaTi 291
                                       v+h p sn++l+sg++++  +ld+Gv+v+lgtDg+as+n+l+++ee++ a++l+++    d+++ l++ ++l+maT+
  gi|298674732|ref|YP_003726482.1| 265 VSHNPVSNMKLASGVAPVPGMLDRGVNVSLGTDGCASNNNLDMFEEMKTAALLHKVESL-DPTV-LPARQVLEMATT 339
                                       ***************************************************99994433.8888.************ PP

                                       HHHHHTT-TTTSSSS-TTSB--EEEECC.CT........CGGGTTTCTSEEEEEEEETTEE CS
                      Amidohydro_1 292 ngAkalglddkvGsievGkdADlvvvdl.di........laafvglkkdgnvkkvivkGkl 343
                                        gA+alg+  k G + +G+ AD ++vd  ++         +++v++++   v ++iv+G++
  gi|298674732|ref|YP_003726482.1| 340 SGARALGI--KSGVLREGYNADVIIVDMnKPhltpvydiHSHLVYSASGSDVSTTIVDGRI 398
                                       ********..******************93355667777********************98 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.1   8.3e-10     5e-06       1      31 [.      44      72 ..      44      77 .. 0.85
   2 !   58.0   0.0     2e-19   1.2e-15     260     472 ..     187     399 ..     126     400 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 8.3e-10
                      Amidohydro_3  1 eviDakGrlvlPGFvDsHtHlagggvnl.rll 31
                                      ++iDakG +v+PGFv  HtH   +g+ l r++
  gi|298674732|ref|YP_003726482.1| 44 QIIDAKGSVVMPGFVNTHTH---TGMTLlRGY 72
                                      79******************...776665655 PP

  == domain 2  score: 58.0 bits;  conditional E-value: 2e-19
                      Amidohydro_3 260 fedealaelvaaadergldvaihaigdaavd.dvldafeaa....aekngnqdrr.rlehaegvtesqiervaalqv 330
                                       ++++ l ++ ++a++  + ++ih++++++   ++  ++ +      +++g+ +    ++h+ ++++++ie ++  +v
  gi|298674732|ref|YP_003726482.1| 187 CSEGFLSKVKKEANHDRVGIHIHVLETESELnQMKQHYGMCsinlLDRLGFLGPDvLAAHCVWLSDDDIEILRGRGV 263
                                       5555588888999999999999999999988666666666688889999999877899******************* PP

                      Amidohydro_3 331 aagvqpvfnfedelldsrlgperargstpvkellnagvkvalgsD..apvgpfdpwprigaavmrktrrggevlrpd 405
                                         +  pv+n            + a+g++pv  +l+ gv+v+lg+D  a  + +d + ++ +a  + +++      + 
  gi|298674732|ref|YP_003726482.1| 264 HVSHNPVSNM-----------KLASGVAPVPGMLDRGVNVSLGTDgcASNNNLDMFEEMKTAALLHKVES----LDP 325
                                       **********...........899**********************9999***********999999755....477 PP

                      Amidohydro_3 406 eelsleealalyTrgpAkalgledrkGtLevGadADlvvld.adpldvdppelaear........vrltvvdGrvv 472
                                         l+ +++l + T+ +A+alg     G L++G+ AD+++ d ++p   +  ++++ +        v+ t+vdGr++
  gi|298674732|ref|YP_003726482.1| 326 TVLPARQVLEMATTSGARALGIKS--GVLREGYNADVIIVDmNKPHLTPVYDIHSHLvysasgsdVSTTIVDGRIL 399
                                       8***********************..***************755666666666666688889************96 PP

>> A_deaminase  Adenosine/AMP deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.2e-06    0.0072     236     302 ..     260     323 ..     250     342 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.2e-06
                                       HCT-EEEE-HHHHCCCSST-TTTT-CHHHHHHTT-EEEE--BSCCCCT.-SHHHHHHHHHHHHT--HH CS
                       A_deaminase 236 laqiplevcPlSNvalgafleyaenPlkeflerglnvslntDDPlqfg.ttLieeYaiaaqvfklsee 302
                                        + +++   P+SN++l    +    P++  l+rg+nvsl+tD  +  + +++ ee++ aa  +k ++ 
  gi|298674732|ref|YP_003726482.1| 260 GRGVHVSHNPVSNMKL----ASGVAPVPGMLDRGVNVSLGTDGCASNNnLDMFEEMKTAALLHKVESL 323
                                       567888899*******....77889*****************988765156********998887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 3231.18
//
Query:       gi|298674733|ref|YP_003726483.1|  [L=558]
Description: alpha-glucan phosphorylase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-29  101.7   2.5    5.5e-21   74.5   0.0    3.4  4  Phosphorylase   Carbohydrate phosphorylase
    3.6e-05   23.6   0.0    7.2e-05   22.6   0.0    1.4  1  Glyco_transf_5  Starch synthase catalytic domain
  ------ inclusion threshold ------
      0.039   13.4   0.3       0.12   11.8   0.0    1.9  3  Capsule_synth   Capsule polysaccharide biosynthesis protein


Domain annotation for each model (and alignments):
>> Phosphorylase  Carbohydrate phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   1.7e-09     1e-05      22      87 ..      30      95 ..      14     117 .. 0.85
   2 ?   -1.4   0.0     0.087   5.2e+02     250     281 ..     197     228 ..     174     234 .. 0.76
   3 !   74.5   0.0   9.2e-25   5.5e-21     305     581 ..     229     477 ..     212     483 .. 0.84
   4 ?   -0.5   1.2     0.047   2.8e+02     672     707 ..     519     555 ..     500     557 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.7e-09
                                      SSHHHHHHHHHHHHHHHTT-EEEEEEE--SCESEEEEE.ETTEEEEEEEBTTCCG-TT-EE-GGG-E CS
                     Phosphorylase 22 nGGLGRLAacfldslatlelpavGygirYeyGlFkQki.edgaqveepdeWlkkgnpweiereekav 87
                                       GGLG LA   + s a l+lp +  ++  + G+F+Q++ e+g+q+e+ +eW  ++   e+ ++e ++
  gi|298674733|ref|YP_003726483.1| 30 AGGLGVLAGDTIRSSADLNLPIIALTLVSKKGFFNQHFdENGWQIESYEEWDPSK-YAELLEPEINL 95
                                      59************************************889**********8754.34444455555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.087
                                       HHHHCCCEEEEE--SSGGGS-EEEHHHHHHHS CS
                     Phosphorylase 250 weitkktfaytnhtvlpealekwpvellekll 281
                                        e +++ + +t ht ++   +++p +l+e+l+
  gi|298674733|ref|YP_003726483.1| 197 GEKVRNLCVFTTHTPVKAGHDTFPYTLVEELF 228
                                       455789999****************9999986 PP

  == domain 3  score: 74.5 bits;  conditional E-value: 9.2e-25
                                       T-HHHHHHHSSEETSCEEEHHHHHHHCCSEEEESSHHHHHHHHHTTTHHHHHHSGGGEEE----B-CHHHCCCTSHH CS
                     Phosphorylase 305 edeeklerlsiieeekkvrmanlaivgshsvngvaalhsellkkevlkdfyelypekfnnktnGitprrwlllanpe 381
                                       +d+e +e l+  ++++k+ m +la+  s  vngva+ h e+ k +++  +       +n +tnG+ +  w +   ++
  gi|298674733|ref|YP_003726483.1| 229 GDNEDIELLKKYSDSDKLDMTRLALNLSDYVNGVAKRHREISK-QMFPGY------EINTITNGVHTYNWTCSHFKQ 298
                                       45566666666667899***********************875.456654......5899**********8765555 PP

                                       HHHHHHHHCSSGGCCSGGGGGGGGGGCCSHHHHHHHHHHHHHHHHHHHHHHHHHHSS---TTSEEEEEES-SCCCCT CS
                     Phosphorylase 382 laelitekigeewvkdleeLkkLekladdkefleelaeikqenKerlaelikekegvevdpeslfdvqvkRlheYkR 458
                                       l    +e    +w  + e L + +++        ++ e++++ K++l ++++ek+g ++d e+l     +R  eYkR
  gi|298674733|ref|YP_003726483.1| 299 L---YDE-FVPGWAAEPELLVRASNIP-----YGRVWEAHNKAKKDLIDYVNEKTGKDMDYETLTIGFSRRAAEYKR 366
                                       4...444.4589****99887655543.....4566678899999*******************9999********* PP

                                       HHHHHHHHHHHHHHHHHSTTS----EEEEEE----TT-HHHHHHHHHHHHHHHHHCC-TTTCCCEEEEEETT-SHHH CS
                     Phosphorylase 459 qlLnvLhiitlYneikenpekkvvprtvifggkaapgYalAkkiiklinsvaevvnndpevkdklkvvflenynvsl 535
                                         +    i t  +++k+ +     +  +if+gka p     kkii+ i      +   +e+++++k+++le+y++ l
  gi|298674733|ref|YP_003726483.1| 367 HSF----IFTDLERLKKVN--YKGNLQFIFAGKAHPRDEAGKKIIQNIFG---YI---KELEGQIKIAYLEDYDMEL 431
                                       986....666677777764..345788*****************987764...44...57899************** PP

                                       HHHHGGG-SEEEE---TTTSSS-SHHHHHHHTT-EEEEESSTCHHH CS
                     Phosphorylase 536 aekiipaadlseqistagkeASGTgnmkfmlnGaltigtlDGanvE 581
                                       a k++++ d+  +  +   eASGT+ mk + nG +  + lDG  +E
  gi|298674733|ref|YP_003726483.1| 432 ASKMVSGVDIWLNTPMRPYEASGTSGMKAAHNGVINFSVLDGWWIE 477
                                       ******************************************8776 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.047
                                       HHHHCSHHHHHHHHHHHHHCG.GGGBHHHHHHHHHHH CS
                     Phosphorylase 672 eeaYkdkkewakksilniaks.gkFssDrtikeYaee 707
                                        + Y+ +++w k++  +i+ +  +F + r ++ Y +e
  gi|298674733|ref|YP_003726483.1| 519 PTYYERRNDWIKMMSNSISMIaYYFNTHRMMRRYVTE 555
                                       4679999**********998615799********886 PP

>> Glyco_transf_5  Starch synthase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   1.2e-08   7.2e-05      63     233 ..      97     273 ..      73     284 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.2e-08
                    Glyco_transf_5  63 aed.eveve.vekvkvaklkkdgvdvyfldnpeffd....reg...lYgdkgedyednaerfalfsraalelleklg 130
                                       +e+ +v+v+ +  +k+++ +k+ ++++fld +   +    re    lYg    d ++  ++ ++++++ ++++  l 
  gi|298674733|ref|YP_003726483.1|  97 IENrNVKVKaW-LYKYYSFTKEMIPILFLDTDFEENepkdREIthyLYGG---DEKYRLKQEIVLGMGGARMIDAL- 168
                                       44446666644.24677777789999999998844345443335467854...77788888889999999999997. PP

                    Glyco_transf_5 131 wkpdvi..hahDWhtalvpallkelykerglfkkiktvftiHN..layqgrfpkdelaalglpaedfekldglefyg 203
                                        + d+   h++  h++l+ + l + y+ +g   +  +vft H    a + +fp+  +++l  ++ed e l++++ ++
  gi|298674733|ref|YP_003726483.1| 169 -ELDIRkyHMNEGHSSLLTLELLHNYNMDGEKVRNLCVFTTHTpvKAGHDTFPYTLVEELFGDNEDIELLKKYSDSD 244
                                       .4566666*************9999999999999********98777777999999888888889999********* PP

                    Glyco_transf_5 204 kvnflkagivyadavttVSptyakEiltpe 233
                                       k+++ + +++++d v+ V + + +Ei ++ 
  gi|298674733|ref|YP_003726483.1| 245 KLDMTRLALNLSDYVNGVAKRH-REISKQM 273
                                       ******************9887.7777665 PP

>> Capsule_synth  Capsule polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.1       1.3   7.6e+03      96     118 ..     269     293 ..     256     301 .. 0.73
   2 ?   -2.1   0.0      0.35   2.1e+03      73     120 ..     333     381 ..     326     391 .. 0.68
   3 ?   11.8   0.0     2e-05      0.12     193     242 ..     393     441 ..     376     446 .. 0.87

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 1.3
                     Capsule_synth  96 ilqhklpkYkrHrilnalaelk..g 118
                                       i ++ +p+Y+   i+n+ + ++   
  gi|298674733|ref|YP_003726483.1| 269 ISKQMFPGYEINTITNGVHTYNwtC 293
                                       6678899999999999988887433 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.35
                     Capsule_synth  73 pkklaqdvlpqakldiayklialilqhklpkYkrHr.ilnalaelkgsi 120
                                       +k l   v ++   d+ y++  + ++++  +YkrH  i+  l+ lk + 
  gi|298674733|ref|YP_003726483.1| 333 KKDLIDYVNEKTGKDMDYETLTIGFSRRAAEYKRHSfIFTDLERLKKVN 381
                                       5555555666666788889999999999999999973455555555444 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 2e-05
                     Capsule_synth 193 KtHPldeglikyrrvikgyltelaalkkrvllvedvnlpsLldqvdgvvv 242
                                       K HP de+++k  + i gy++el + + +++++ed+++    + v gv +
  gi|298674733|ref|YP_003726483.1| 393 KAHPRDEAGKKIIQNIFGYIKEL-EGQIKIAYLEDYDMELASKMVSGVDI 441
                                       99********************8.6677799*****99888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (558 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 3413.61
//
Query:       gi|298674734|ref|YP_003726484.1|  [L=132]
Description: thioesterase superfamily protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.6e-07   29.3   0.0    1.2e-06   29.0   0.0    1.1  1  4HBT_2       Thioesterase-like superfamily
    6.1e-06   26.5   0.0    9.7e-06   25.9   0.0    1.3  1  4HBT         Thioesterase superfamily
     0.0095   15.2   0.0      0.098   11.9   0.0    2.0  2  Acyl-ACP_TE  Acyl-ACP thioesterase


Domain annotation for each model (and alignments):
>> 4HBT_2  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0     2e-10   1.2e-06       2     121 ..       9     122 ..       8     124 .. 0.93

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 2e-10
                            4HBT_2   2 rpndvDlnghlnnarylryleearvkflertglksrsiarrgiglilssahvryrrplkfpdrltvefrvididakt 78 
                                       r++d+D +gh+nn     ++e+ r   + r+ +  ++++  ++ li+ +++ +++ +l+++  +++ + v  i  ++
  gi|298674734|ref|YP_003726484.1|   9 RFGDMDGLGHINNTVLPVWFEQSRNPIF-RIFT-PDLNP-AKWKLIMVRTEFDFVDELFYGIDVEIKTYVLNIGNTS 82 
                                       689**********************999.6667.67777.57*********************************** PP

                            4HBT_2  79 liiehrflsnadgkkaarveerivvmdygkrskkapvPpellk 121
                                       + + h+  +   gk+ a ++  +v++d g + k+  +P+ +++
  gi|298674734|ref|YP_003726484.1|  83 FTVGHEAWQ--YGKLRAKGKAIMVHYDFGLK-KSIQIPDSIRE 122
                                       *********..9****************888.99999998876 PP

>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   1.6e-09   9.7e-06       2      72 ..      17      91 ..      16      97 .. 0.95

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.6e-09
                                      SSB-HHHHHHHHHHHHHHHHHHTTST....TEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEE CS
                              4HBT  2 GvvhgGvylallDeaagaalrslggr....gilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrd 72
                                      G++++ v+  ++++ +  ++r    +    +  +  v+ + df+    +g ++++++ vl++g+ts++v +e ++
  gi|298674734|ref|YP_003726484.1| 17 GHINNTVLPVWFEQSRNPIFRIFTPDlnpaKWKLIMVRTEFDFVDELFYGIDVEIKTYVLNIGNTSFTVGHEAWQ 91
                                      9****************************999999999***********************************97 PP

>> Acyl-ACP_TE  Acyl-ACP thioesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   1.6e-05     0.098     157     182 ..       4      29 ..       1      94 [. 0.86
   2 ?    2.4   0.0     0.014        81      74     132 ..      68     125 ..      46     130 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.6e-05
                       Acyl-ACP_TE 157 kelkvrysDlDlnqHvNNvkYlewil 182
                                       +  ++r+ D+D  +H+NN++   w +
  gi|298674734|ref|YP_003726484.1|   4 TTVTPRFGDMDGLGHINNTVLPVWFE 29 
                                       5789**************98777765 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.014
                       Acyl-ACP_TE  74 kveietwaesenklfcyrdfkvrdekgekiieaksvfvlmdqetrrlsrvtdeilaeye 132
                                        vei+t++  +++       +  +  g+  ++ k++ v+ d   ++  +++d i++ ++
  gi|298674734|ref|YP_003726484.1|  68 DVEIKTYVLNIGNTSFTVGHEAWQ-YGKLRAKGKAIMVHYDFGLKKSIQIPDSIRESLK 125
                                       566666666666655554444443.6777788899999999999999999999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1011.33
//
Query:       gi|298674735|ref|YP_003726485.1|  [L=152]
Description: DNA ligase D [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.3e-40  135.2   0.0    1.1e-39  134.9   0.0    1.1  1  LigD_N    DNA polymerase Ligase (LigD)


Domain annotation for each model (and alignments):
>> LigD_N  DNA polymerase Ligase (LigD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.9   0.0   6.4e-44   1.1e-39       1     105 []      34     133 ..      34     133 .. 0.98

  Alignments for each domain:
  == domain 1  score: 134.9 bits;  conditional E-value: 6.4e-44
                                       EEEESSSEEEEEEEEETTEEEEEEETT---SSTTSEEEEEEEEEE-GGGGGEEEEE-TTSTT-EEEEEEEEEEEEE. CS
                            LigD_N   1 qeHdaprlHYDlrLeidevlsswavpkglpedpnskrlAvetedhpleyadfegliekgeygaGsvliwDtGtyeve 77 
                                       q+H+a++lHYDlrLe+++vl+swa+pk+++++p+ krlA++tedhpleyadfeg+i++g+ygaG+v iwD+Gt+e+ 
  gi|298674735|ref|YP_003726485.1|  34 QKHNASKLHYDLRLEMNGVLKSWAIPKEPSKNPDVKRLAIQTEDHPLEYADFEGEIPEGQYGAGTVEIWDKGTFEP- 109
                                       89**************************************************************************. PP

                                       .-HHHHHHHTEEEEEEECSSSEEEEEEE CS
                            LigD_N  78 eklaealkkrkiklrLhGeklkgkyvlv 105
                                            ++++++i +rL+G+kl+g+yvl+
  gi|298674735|ref|YP_003726485.1| 110 ----VKTEDEEIIFRLKGNKLEGDYVLI 133
                                       ....6899******************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 1084.62
//
Query:       gi|298674736|ref|YP_003726486.1|  [L=40]
Description: hypothetical protein Metev_0790 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.015   15.4   0.3      0.016   15.3   0.3    1.0  1  zf-CRD           Cysteine rich domain with multizinc binding 
        0.1   13.0   1.3        1.5    9.2   0.1    2.0  2  Lar_restr_allev  Restriction alleviation protein Lar
       0.11   12.4   2.8        1.5    8.8   0.1    2.1  2  zinc_ribbon_4    zinc-ribbon domain
       0.11   13.3   0.5        6.5    7.9   0.1    2.1  2  zf-C2H2_4        C2H2-type zinc finger
       0.13   12.7   0.7        3.8    8.1   0.1    2.1  2  zf-C2H2          Zinc finger, C2H2 type
       0.33   11.3   3.4       0.86   10.0   0.2    2.0  2  C1_2             C1 domain
       0.77    9.6   5.0        2.2    8.1   0.2    2.1  2  zinc_ribbon_5    zinc-ribbon domain
        3.2    7.8   6.9         39    4.3   6.9    2.0  1  ADK_lid          Adenylate kinase, active site lid


Domain annotation for each model (and alignments):
>> zf-CRD  Cysteine rich domain with multizinc binding regions
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.3   7.1e-06     0.016      22      49 ..       3      30 ..       2      38 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7.1e-06
                            zf-CRD 22 tCtaCgqlmPkrpeagvpqqCelCkrpf 49
                                      +C  Cg+  P +p+++++ +C+lC ++f
  gi|298674736|ref|YP_003726486.1|  3 KCGVCGGDAPRQPSVTEDGNCDLCGKKF 30
                                      8************************998 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2     0.031        69      29      37 ..       2      13 ..       1      22 [. 0.55
   2 ?    9.2   0.1   0.00067       1.5       5      22 ..      22      39 ..      18      40 .] 0.88

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.031
                   Lar_restr_allev 29 vyCadCga...s 37
                                      v C  Cg     
  gi|298674736|ref|YP_003726486.1|  2 VKCGVCGGdapR 13
                                      666666664433 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00067
                   Lar_restr_allev  5 pCPfCggravlersqrvv 22
                                       C+ Cg++ vl ++q ++
  gi|298674736|ref|YP_003726486.1| 22 NCDLCGKKFVLAEEQEKS 39
                                      6************99875 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.3     0.016        35      25      32 ..       1       8 [.       1       9 [. 0.90
   2 ?    8.8   0.1   0.00069       1.5       5      18 ..      23      36 ..      22      40 .] 0.89

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.016
                     zinc_ribbon_4 25 kvrCskCg 32
                                      +v+C  Cg
  gi|298674736|ref|YP_003726486.1|  1 MVKCGVCG 8 
                                      79*****8 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00069
                     zinc_ribbon_4  5 CpsCkakyeiddek 18
                                      C  C++k+ +++e+
  gi|298674736|ref|YP_003726486.1| 23 CDLCGKKFVLAEEQ 36
                                      999********997 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.042        94       2       9 ..       3      10 ..       2      17 .. 0.79
   2 ?    7.9   0.1    0.0029       6.5       3      11 ..      23      31 ..      22      35 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.042
                         zf-C2H2_4  2 kCpiCgks 9 
                                      kC +Cg+ 
  gi|298674736|ref|YP_003726486.1|  3 KCGVCGGD 10
                                      8****976 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0029
                         zf-C2H2_4  3 CpiCgksFs 11
                                      C++Cgk F 
  gi|298674736|ref|YP_003726486.1| 23 CDLCGKKFV 31
                                      *******95 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.046     1e+02       2       7 ..       3       8 ..       2      18 .. 0.83
   2 ?    8.1   0.1    0.0017       3.8       3      11 ..      23      31 ..      22      36 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.046
                                     EETTTT CS
                           zf-C2H2 2 kCpdCg 7
                                     kC++Cg
  gi|298674736|ref|YP_003726486.1| 3 KCGVCG 8
                                     8****9 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0017
                                      ETTTTEEES CS
                           zf-C2H2  3 CpdCgksFk 11
                                      C+ Cgk+F 
  gi|298674736|ref|YP_003726486.1| 23 CDLCGKKFV 31
                                      *******95 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.3     0.059   1.3e+02      19      27 ..       2      10 ..       1      14 [. 0.80
   2 ?   10.0   0.2   0.00039      0.86      15      27 ..      17      29 ..      12      36 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.059
                              C1_2 19 fnCsaCgrk 27
                                       +C +Cg +
  gi|298674736|ref|YP_003726486.1|  2 VKCGVCGGD 10
                                      58****965 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00039
                              C1_2 15 ssesfnCsaCgrk 27
                                        e++nC++Cg+k
  gi|298674736|ref|YP_003726486.1| 17 VTEDGNCDLCGKK 29
                                      57899******98 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.9      0.02        45      26      32 ..       2       8 ..       1       9 [. 0.89
   2 ?    8.1   0.2     0.001       2.2       4      19 ..      22      37 ..      21      40 .] 0.85

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.02
                     zinc_ribbon_5 26 VrCakCa 32
                                      V+C+ C+
  gi|298674736|ref|YP_003726486.1|  2 VKCGVCG 8 
                                      9*****7 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.001
                     zinc_ribbon_5  4 rCpdCdtkFklvdskl 19
                                       C+ C+ kF l++++ 
  gi|298674736|ref|YP_003726486.1| 22 NCDLCGKKFVLAEEQE 37
                                      5***********9994 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   6.9     0.017        39      19      32 ..      18      31 ..       3      32 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.017
                                      SSTTB-TTT--.-B CS
                           ADK_lid 19 kveglCDkCGepLv 32
                                       ++g CD CG ++v
  gi|298674736|ref|YP_003726486.1| 18 TEDGNCDLCGKKFV 31
                                      489*******9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 301.44
//
Query:       gi|298674737|ref|YP_003726487.1|  [L=445]
Description: adenylosuccinate lyase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-55  188.6   0.5      3e-55  187.8   0.5    1.3  1  Lyase_1      Lyase
    1.4e-21   76.8   0.2    3.2e-21   75.7   0.2    1.6  1  ADSL_C       Adenylosuccinate lyase C-terminus
      0.004   17.9   0.3      0.027   15.2   0.0    2.4  2  ASL_C2       Argininosuccinate lyase C-terminal
  ------ inclusion threshold ------
      0.012   16.1   0.0      0.012   16.1   0.0    2.3  3  FumaraseC_C  Fumarase C C-terminus


Domain annotation for each model (and alignments):
>> Lyase_1  Lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.8   0.5   6.8e-59     3e-55       8     308 ..      13     292 ..       7     295 .. 0.88

  Alignments for each domain:
  == domain 1  score: 187.8 bits;  conditional E-value: 6.8e-59
                                       CHHHHHHHHHHHHHGGGHHHHHCHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHCHCHHCGGHHHBSSSSSHHHHHH CS
                           Lyase_1   8 dklmgiftersrenfrlseedikalaalkkaaakanvdlkeeaaaiikaldevleegklddqfvlkviqegsgtavn 84 
                                       +++  +++e++r+ + ++     +++al++a a ++++++ +a++i k +d v     l+   ++k i+ ++++++ 
  gi|298674737|ref|YP_003726487.1|  13 EEMKYVWSEENRLYKIMN-----VEVALARAEADVGLIPQDAADKIAKSIDSVK----LE---RVKEIEDEINHDMM 77 
                                       556666777777777777.....99**************888888877777554....45...79999999999987 PP

                                       HHHHHHHHHHTT.HSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-EEEEEETT CS
                           Lyase_1  85 mnlnevigellg.ekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpaleqLidalkekakefkdvvkiGrThl 160
                                       +    v+g +++  + +  ++vh+g++snD+ +Ta  l++k+a+ e L+++l++L++al+++a+++kd v +GrTh+
  gi|298674737|ref|YP_003726487.1|  78 A---VVLG-ISEqCPDDSGKWVHFGATSNDMLDTATGLQIKDAV-EILESKLNNLMQALVNQAEKHKDKVCAGRTHG 149
                                       7...5666.44434568999************************.88****************************** PP

                                       EEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCC.THHHHHHHHHHHHHCSTEESSSHH CS
                           Lyase_1 161 qdAtPvtlgqelsayaealerdrerlkellkrllvellgggtavgtglnadp.efaelvakelakvtglpvkapnsf 236
                                       q  +P+t g  ++ +a ++ r++erl ++++r+lv+++ g++++ ++++ +  e +++ ++ l+ +      + +  
  gi|298674737|ref|YP_003726487.1| 150 QIGVPTTYGLRFAIWASEISRHLERLTQMKPRVLVGQMTGAVGTQAAFGKKGiELQKKAMEYLG-L-----RSVDVS 220
                                       ****************************************999999998887677777777777.4.....457778 PP

                                       HHHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTTSSEEEEGCCTSSC-TTSTTTEBTHHHHHHHHHHH CS
                           Lyase_1 237 eavsdrDavvellgalkllatsLskfaeDlrllssgeaglvelslaesepGSSiMPgKvNPvqlElltgvag 308
                                       +++ +rD+++e++ +++++at L k++ ++r l+ +e+ +ve+s+ +++ GSS+MP+K+NP+++E + g a+
  gi|298674737|ref|YP_003726487.1| 221 NQIIQRDRHAEFVMWMANVATTLDKIGIEIRTLQRSEIAEVEESFGKKQVGSSTMPHKRNPIKSEQICGLAR 292
                                       889***************************************************************998875 PP

>> ADSL_C  Adenylosuccinate lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.7   0.2   7.1e-25   3.2e-21       1      73 []     360     438 ..     360     438 .. 0.96

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 7.1e-25
                                       TGGGHHHHHHHHH.HTH-HHHHHHHHHHHHHHHHHC...HHHHHHT-HHHH.C.HHCHHHHHT-GGGCCTTHHHHHH CS
                            ADSL_C   1 GlifservllaLv.kglgReeAyelVqeaamkawee...llelLaadpevk.k.seeeldalfdpayylgsadeivd 71 
                                       Gl + e+v+++L+ kg gR+ A+e+V+++am+a e+   l+++L++d+ev+ + ++ee+ +l dp +y+g a e+vd
  gi|298674737|ref|YP_003726487.1| 360 GLNMGEAVMIELAkKGAGRQNAHEIVRRNAMEAHESgrhLKDVLLEDSEVSqYlDDEEIVQLVDPYKYIGTAVEQVD 436
                                       899**********66*******************99***************76*999*******************9 PP

                                       HH CS
                            ADSL_C  72 rv 73 
                                        v
  gi|298674737|ref|YP_003726487.1| 437 AV 438
                                       86 PP

>> ASL_C2  Argininosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.82   3.7e+03      36      60 ..      54      78 ..      40      85 .. 0.70
   2 !   15.2   0.0   6.1e-06     0.027      11      66 ..     371     426 ..     370     429 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.82
                                      T--GGG--HHHHHHH-TT--GGGGG CS
                            ASL_C2 36 gkeleeltleelkeisplleedvee 60
                                       k+++ ++le +kei++ ++ d+ +
  gi|298674737|ref|YP_003726487.1| 54 AKSIDSVKLERVKEIEDEINHDMMA 78
                                      5668899999999998888866554 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 6.1e-06
                                       HHHCTS-HHHHHHHHHHHHHHHHHTT--GGG--HHHHHHH-TT--.GGGGGGSSHHH CS
                            ASL_C2  11 LvrkGlpFReAHeivgravrlaeekgkeleeltleelkeisplle.edveeaLdpea 66 
                                       L++kG     AHeiv r + +a e+g++l+++ le+ + +s+ l+ e++ + +dp +
  gi|298674737|ref|YP_003726487.1| 371 LAKKGAGRQNAHEIVRRNAMEAHESGRHLKDVLLEDSE-VSQYLDdEEIVQLVDPYK 426
                                       6777888889****************************.99999999****999976 PP

>> FumaraseC_C  Fumarase C C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.3       2.6   1.1e+04      12      20 ..      48      56 ..      48      57 .. 0.84
   2 ?   -3.1   0.0       2.5   1.1e+04      23      33 ..     108     118 ..     107     124 .. 0.81
   3 ?   16.1   0.0   2.6e-06     0.012      18      51 ..     389     426 ..     379     429 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.6
                                      HHHHHHHHH CS
                       FumaraseC_C 12 ekAakIAke 20
                                      ++A kIAk 
  gi|298674737|ref|YP_003726487.1| 48 DAADKIAKS 56
                                      689****95 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.5
                                       HHT--HHHHHH CS
                       FumaraseC_C  23 kegktlreavl 33 
                                       ++g ++++av 
  gi|298674737|ref|YP_003726487.1| 108 ATGLQIKDAVE 118
                                       68999999985 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 2.6e-06
                                       HHHHHHHT--HHHHHHH....TT-.-HHHHHHHT-HHH CS
                       FumaraseC_C  18 AkeAlkegktlreavle....lgllteeeldelldpek 51 
                                       A eA+++g+ l+++ le     ++l++ee+ +l+dp k
  gi|298674737|ref|YP_003726487.1| 389 AMEAHESGRHLKDVLLEdsevSQYLDDEEIVQLVDPYK 426
                                       789**************9999999************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 3233.44
//
Query:       gi|298674738|ref|YP_003726488.1|  [L=217]
Description: hypothetical protein Metev_0792 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.5e-46  155.9   0.1    9.5e-46  155.5   0.1    1.1  1  DUF2284        Predicted metal-binding protein (DUF2284)
  ------ inclusion threshold ------
       0.01   15.1   0.0      0.014   14.7   0.0    1.2  1  T4_deiodinase  Iodothyronine deiodinase


Domain annotation for each model (and alignments):
>> DUF2284  Predicted metal-binding protein (DUF2284)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.5   0.1   1.1e-49   9.5e-46       1     164 []      23     216 ..      23     216 .. 0.97

  Alignments for each domain:
  == domain 1  score: 155.5 bits;  conditional E-value: 1.1e-49
                           DUF2284   1 klidaedivveervrlkCekgCknYgknlsCPPavptveefrkilkeYkkallvqtkaeledeedd........... 66 
                                       +li+ae+i+ve+r++lkC +gC++Yg+++ CPP++ptv+efrk+l eY++ llv++ +e++ ++++           
  gi|298674738|ref|YP_003726488.1|  23 RLIPAENIIVENRTTLKCIFGCNGYGSHV-CPPFIPTVDEFRKMLDEYDWTLLVDWISENRFSREIsenfvkysvsp 98 
                                       579************************98.*********************************************** PP

                           DUF2284  67 ..............keemkevkeelekillelekeafeagypkalalsagsCtlCet.......CayeegepCrhpe 122
                                                     k+ mke+ke++++ +lelek a++ gy++ala+++g+Ct+C++       Ca  eg +C+hp+
  gi|298674738|ref|YP_003726488.1|  99 pdnedikkqhhqnlKTVMKERKERIQPGSLELEKLAWNLGYNTALATFPGMCTWCANsdysnvcCAGFEG-NCHHPT 174
                                       ********************************************************88899998888886.8***** PP

                           DUF2284 123 karpsmealGidvfktaekaglelevgkeeketvslvglvLl 164
                                        +rp++++lG++++kt+e++g++l+ +++e++ +s+++l+Ll
  gi|298674738|ref|YP_003726488.1| 175 VRRPCLMGLGVRLDKTLEQLGTPLQKFPMENDIPSQYTLILL 216
                                       ****************************************96 PP

>> T4_deiodinase  Iodothyronine deiodinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.5e-06     0.014     109     134 ..      47      72 ..      43     120 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.5e-06
                     T4_deiodinase 109 fGsatcPpflaklsafkrlveefssv 134
                                       +Gs  cPpf+  +++f+++++e+  +
  gi|298674738|ref|YP_003726488.1|  47 YGSHVCPPFIPTVDEFRKMLDEYDWT 72 
                                       8*********************9754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1553.85
//
Query:       gi|298674739|ref|YP_003726489.1|  [L=55]
Description: hypothetical protein Metev_0793 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1106  (0.0616878); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 415.89
//
Query:       gi|298674740|ref|YP_003726490.1|  [L=358]
Description: uroporphyrinogen decarboxylase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-62  211.2   0.0    2.5e-62  211.1   0.0    1.0  1  URO-D     Uroporphyrinogen decarboxylase (URO-D)


Domain annotation for each model (and alignments):
>> URO-D  Uroporphyrinogen decarboxylase (URO-D)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.1   0.0   1.4e-66   2.5e-62       1     344 [.       6     352 ..       6     354 .. 0.92

  Alignments for each domain:
  == domain 1  score: 211.1 bits;  conditional E-value: 1.4e-66
                                       ----HHHHHHTT---SS--B--TT-SSTTSHHHHHHHTSSSHHHHHH-HHHHHHHHHHHHHHH--S-EE-S--TTGG CS
                             URO-D   1 tknerllralrgekvdrvPvwlmRqaGrylpeyraeragvsflelcknpelaaevtlqpvrrfglDaailfsdilve 77 
                                       t+ er+ ++++g+k+drvPv++      ++  y+a ++g+s+ +++++ +++++++++ +r +g++   ++ + ++ 
  gi|298674740|ref|YP_003726490.1|   6 TPPERMAAVMSGQKPDRVPVVP------FILGYAANITGISLGDFYADGDKCFDAQFASMRLHGYEQTPMYGYASCG 76 
                                       5679******************......************************************************* PP

                                       GGGGT-EEEEETTTE...EEEE--S-.....GGGS----GGG.G..HHHHHHHHHHHHH..--SS-EEEEEE-HHHH CS
                             URO-D  78 aealGlevefeegeg...Pvvekpvr.taedveklevpddveegrlpyvleaikllkkel.ggevpligfvgaPftl 149
                                       a+ lG ++ f+  +g   P+ve++++ t+edve+l+vpd    ++lp  ++  + + ++  ++ +p+++ +g+ ft 
  gi|298674740|ref|YP_003726490.1|  77 AWELGGKIGFPYRKGqgaPYVEEHPVnTVEDVENLKVPDFR--NELPGAYKEADKVASKCaERGMPVTVQIGSVFTA 151
                                       ***********9666669****99999***********874..479999988888888775789************* PP

                                       HHHHHCTT-SS-HHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHH.HTT-SEEEEEE....TTGGGS-HHHHHHHTH CS
                             URO-D 150 asylveGgskgfekllkllykdpeevhklldkltdvvieylkaqi.eagAdaiqifD....swagllspedfeefvl 221
                                       as +      +++k++++++++p++vh++ldk++d++i+ ++ ++ + g + +  fD     +++++s ++feef++
  gi|298674740|ref|YP_003726490.1| 152 ASVVA-----ETSKFFNWIVTKPDVVHQILDKVSDMFINAIDYFAdKYGPKTLLPFDggpsESNTMISSKMFEEFAY 223
                                       *****.....***********************************99999**********99*************** PP

                                       HHHHHHHHHHHH.H--S-EEEEESSHH.HHHHHHTT.......S--SEEE--TTS-HHHHHHSS....EEE--B-G. CS
                             URO-D 222 pylkrivdevkaegpkvpvilfikgagaeiledlae.......lgadvlsldwtvdlkeaarevgdkvalqGnldPi 291
                                       py+k+i d+v+++g    v+++++++ ++ +++  +       +   v+ + +++++k ++ ++gd+ +++Gn++P+
  gi|298674740|ref|YP_003726490.1| 224 PYVKKIHDHVNERGI-PAVLMHPCADQNANIPYYVKmreendwSSKYVWLFGPETSIKTQIDAFGDHDIICGNINPP 299
                                       ************986.6899******8774444443244666666669999*************************6 PP

                                       GGGG.S-HHHHHHHHHHHHT.T---SSSEEB-BSS---TTS-HHHHHHHHHHHH CS
                             URO-D 292 alLl.gspeeiekevkeilekgaggkkgyilnlGhgippetppenvkalveavk 344
                                        l   ++ ee  + ++e +e+g++ ++gyil+ G++ pp++ p +v a+v+a++
  gi|298674740|ref|YP_003726490.1| 300 -LFQsSTYEETLEICRENIEEGMNAPNGYILSAGCEFPPNAAPIKVMAMVDAAE 352
                                       .5557***********************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2672.45
//
Query:       gi|298674741|ref|YP_003726491.1|  [L=940]
Description: excinuclease ABC subunit A [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-39  133.5   1.0    6.7e-39  132.3   1.0    1.7  1  UvrA_inter       UvrA interaction domain
    5.9e-35  120.0   0.0    3.9e-33  114.1   0.0    3.0  3  UvrA_DNA-bind    UvrA DNA-binding domain
    5.1e-22   78.9   0.3      3e-10   40.7   0.1    4.3  3  ABC_tran         ABC transporter
    8.7e-12   44.9   0.1     0.0096   15.4   0.0    4.1  3  SMC_N            RecF/RecN/SMC N terminal domain
    7.8e-08   31.9   0.1      0.005   16.6   0.0    2.7  2  AAA_29           P-loop containing region of AAA domain
    1.9e-07   31.6   0.0      0.033   14.6   0.0    3.3  3  AAA_16           AAA ATPase domain
    1.1e-06   28.9   2.0      0.059   13.6   0.0    4.0  3  AAA_22           AAA domain
      2e-06   27.6   2.8      0.011   15.6   0.2    2.5  2  BCA_ABC_TP_C     Branched-chain amino acid ATP-binding casset
    7.8e-06   25.9   7.2      0.012   15.5   0.0    4.2  4  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
      1e-05   25.5   0.1       0.12   12.3   0.0    2.5  2  RsgA_GTPase      RsgA GTPase
    4.4e-05   23.8  10.0      0.041   14.2   0.3    3.9  3  DnaJ_CXXCXGXG    DnaJ central domain
    6.1e-05   23.0   0.7       0.71    9.7   0.0    3.4  3  APS_kinase       Adenylylsulphate kinase
    0.00032   20.3   0.1       0.49    9.9   0.0    3.0  3  AAA_25           AAA domain
    0.00046   20.2   0.1        3.1    7.9   0.1    3.5  3  AAA_14           AAA domain
    0.00061   20.3   0.1        2.2    8.8   0.1    2.8  2  AAA_18           AAA domain
    0.00066   19.4   0.4        1.5    8.5   0.0    3.5  3  AAA_24           AAA domain
    0.00079   19.2   0.1      0.031   14.0   0.1    2.7  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
     0.0013   18.8   0.6       0.17   12.0   0.0    3.2  2  MMR_HSR1         50S ribosome-binding GTPase
     0.0024   17.0   0.1        0.4    9.7   0.0    2.5  2  T2SSE            Type II/IV secretion system protein
     0.0025   17.8   0.0        1.7    8.5   0.0    2.8  2  ATPase_2         ATPase domain predominantly from Archaea
     0.0026   17.4   0.4       0.25   10.9   0.1    2.4  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
     0.0038   17.4   0.1        3.2    7.9   0.1    3.0  2  AAA_33           AAA domain
     0.0046   17.5   3.3        1.2    9.6   0.2    3.0  2  AAA_23           AAA domain
     0.0054   16.0   0.1        1.9    7.7   0.1    2.3  2  DUF2075          Uncharacterized conserved protein (DUF2075)
  ------ inclusion threshold ------
       0.02   14.6   0.1        2.5    7.8   0.0    2.6  2  PRK              Phosphoribulokinase / Uridine kinase family
      0.029   14.1   7.0       0.96    9.1   0.0    4.1  4  AAA_15           AAA ATPase domain
      0.029   14.3   0.1          3    7.8   0.1    2.4  2  NACHT            NACHT domain
      0.034   13.3   0.0        4.4    6.4   0.0    3.1  3  NB-ARC           NB-ARC domain
      0.036   14.4   0.1        2.7    8.4   0.0    2.6  2  RNA_helicase     RNA helicase
      0.046   13.6   2.9        1.9    8.3   0.1    3.6  3  NTPase_1         NTPase
      0.061   12.8   0.1        3.6    7.1   0.1    2.4  2  AAA_7            P-loop containing dynein motor region
      0.064   13.4  14.4       0.11   12.7   1.6    4.3  4  Zn-ribbon_8      Zinc ribbon domain
      0.065   12.6   0.0        7.5    5.8   0.0    2.6  2  ATPase           KaiC
      0.068   12.1   0.0        1.1    8.2   0.0    2.3  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.076   12.7   0.1         10    5.8   0.1    2.9  3  AAA_30           AAA domain
       0.11   12.4   0.3       0.28   11.1   0.3    1.7  1  Pox_E10          E10-like protein conserved region
       0.12   11.6   0.0         20    4.4   0.0    2.7  2  Zeta_toxin       Zeta toxin
       0.17   10.8   0.8       0.96    8.3   0.0    2.0  2  DUF463           YcjX-like family, DUF463
       0.25   11.3   8.3        8.3    6.5   0.0    4.1  3  Anti-TRAP        Tryptophan RNA-binding attenuator protein in
       0.86    9.7   0.0       0.86    9.7   0.0    3.0  3  Zn_Tnp_IS91      Transposase zinc-binding domain
        2.2    8.3   5.4        3.6    7.6   0.0    3.5  4  HypA             Hydrogenase/urease nickel incorporation, met
        7.7    6.6   9.8         26    4.9   0.3    3.7  3  DZR              Double zinc ribbon


Domain annotation for each model (and alignments):
>> UvrA_inter  UvrA interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.3   1.0   1.6e-41   6.7e-39       1     108 [.     132     241 ..     132     242 .. 0.98

  Alignments for each domain:
  == domain 1  score: 132.3 bits;  conditional E-value: 1.6e-41
                        UvrA_inter   1 QsveqIvdqilkleegtkllilaPvvrerkgefkkllenlkkkGfvrvriDgeiydlde..dieldknkkhsievvv 75 
                                       Qs++qIvd+i++l++++k++il+P++rerkge+kkl+++l+++G++rvr+Dg +++lde  ++el +++kh+ie+vv
  gi|298674741|ref|YP_003726491.1| 132 QSIDQIVDNIMNLPHKSKIYILSPIIRERKGEYKKLFTDLQSEGYSRVRVDGDVVSLDEtdELELGRYQKHNIEIVV 208
                                       9*********************************************************988999************* PP

                        UvrA_inter  76 DrlvvkkeersrlaesvetAlklgeglvivsev 108
                                       Drlv+k+  ++rl+e+vetA++ + g+v+++ v
  gi|298674741|ref|YP_003726491.1| 209 DRLVIKEGIEDRLSEAVETAIEKSGGTVMINVV 241
                                       *****************************9876 PP

>> UvrA_DNA-bind  UvrA DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.73   3.1e+02      78     107 ..      37      66 ..      20      68 .. 0.86
   2 !  114.1   0.0   9.1e-36   3.9e-33       1     110 []     291     399 ..     291     399 .. 0.97
   3 ?   -0.9   0.0         5   2.1e+03      27      70 ..     456     499 ..     446     506 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.73
                                       .......---HHHHHHHHHH-------HHH CS
                     UvrA_DNA-bind  78 krsyektfeGvipnlerryreteSeavree 107
                                       + + +  f+ +  + +rry e+ S ++r+ 
  gi|298674741|ref|YP_003726491.1|  37 SGKSSLAFDTIYAEGQRRYVESLSAYARQF 66 
                                       5567778999999***************85 PP

  == domain 2  score: 114.1 bits;  conditional E-value: 9.1e-36
                                       -S----.-----------GGG..TT-HHHHHHHHHHHTTTS------------S-THHHHH----............ CS
                     UvrA_DNA-bind   1 DpdlvvpdpslslaegAiapwsskkssyyrqlleavaehygidldtpfkeLpeeqkdilLyGsgeekikveyksggr 77 
                                       Dp+l+vp+p+l+l +gA++pw sk++ y +q le++a+hyg+++d+p+k+L+ ++k+i++yG++e++   +  ++g+
  gi|298674741|ref|YP_003726491.1| 291 DPELIVPNPNLTLHQGAVEPW-SKRDGYHMQSLESLADHYGFSMDVPYKDLDSNIKKIIMYGTNEKIPLEHVGKRGG 366
                                       9********************.99****************************************9888888888*** PP

                                       .......---HHHHHHHHHH-------HHHHHH CS
                     UvrA_DNA-bind  78 krsyektfeGvipnlerryreteSeavreelek 110
                                       +++++++f+Gv+ +l r y++teSe+++++l+k
  gi|298674741|ref|YP_003726491.1| 367 VWKRRGRFRGVVSYLSRVYNKTESENTKDKLNK 399
                                       *****************************9986 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 5
                                       HHHHHHHHHHHTTTS------------S-THHHHH----..... CS
                     UvrA_DNA-bind  27 syyrqlleavaehygidldtpfkeLpeeqkdilLyGsgeekikv 70 
                                        + r +l++++ ++g+ +d+ +  L+ +     L G + ++i+ 
  gi|298674741|ref|YP_003726491.1| 456 AIARMILKEITSRLGFLMDVGLDYLTLSRSASTLSGGEAQRIRL 499
                                       568899**************999999999999999888877765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   2.3e-05    0.0097       1      28 [.      16      43 ..      16      61 .. 0.92
   2 !   15.2   0.0   5.2e-05     0.022      82     136 ..     462     518 ..     378     519 .. 0.64
   3 !   40.7   0.1   7.1e-13     3e-10       1     136 [.     623     859 ..     623     860 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.3e-05
                                      EEEEEEEEETTSEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  1 lknvslklkegekvaivGenGaGKStLl 28
                                      l+n++++l +++ ++i+G +G+GKS+L+
  gi|298674741|ref|YP_003726491.1| 16 LNNIDVTLPRDKFIVITGLSGSGKSSLA 43
                                      79************************95 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 5.2e-05
                                       HTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHT..SSEEEEESTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx RF
                          ABC_tran  82 deeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkk..pkllllDEpt 136
                                        +ei+  l  l +++l+  ++++s+s+LSgG+ qr+ la  + +     l++lDEp+
  gi|298674741|ref|YP_003726491.1| 462 LKEITSRLGFLMDVGLDYLTLSRSASTLSGGEAQRIRLATQIGSSlmGVLYILDEPS 518
                                       2223333444445557778888889**************9987652257999***95 PP

  == domain 3  score: 40.7 bits;  conditional E-value: 7.1e-13
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       lknv++++  g ++ ++G +G+GKStL++  ++++  ++ + + ++k+ ++++++ l++  +v++ +++   ++  r
  gi|298674741|ref|YP_003726491.1| 623 LKNVDVDIPLGVMLCVTGVSGSGKSTLINDTLHKVLAQKLH-RAKEKPGTYKDIKGLENVDKVITIDQSPIGRT-PR 697
                                       79**************************8766666554333.23455555566666666555555553333333.55 PP

                                       HH........................................................................... CS
                                       xx........................................................................... RF
                          ABC_tran  78 en........................................................................... 79 
                                       +n                                                                           
  gi|298674741|ref|YP_003726491.1| 698 SNpatytnvftpirelfaqtplarargykpgrfsfnirggrcetcsgdgiitiemhflpdvhvqcevcngkrynret 774
                                       55566666777777777777888889*********************************************999999 PP

                                       .........................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTS...S CS
                                       .........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...x RF
                          ABC_tran  80 .........................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkp...k 128
                                                                e   +i+k l++l +++l   ++++s ++LSgG+ qrv+la  l +++   +
  gi|298674741|ref|YP_003726491.1| 775 ldilykgktisdvlemtveealeffENIPKIKKRLQTLYDVGLGYIKLGQSSTTLSGGEAQRVKLASELSRRStgnT 851
                                       99999999999888665555554444444499999999999999*************************98753337 PP

                                       EEEEESTT CS
                                       xxxxxxxx RF
                          ABC_tran 129 llllDEpt 136
                                       l++lDEpt
  gi|298674741|ref|YP_003726491.1| 852 LYILDEPT 859
                                       *******9 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00044      0.19       2      46 ..       3      48 ..       2      62 .. 0.76
   2 !    9.3   0.0    0.0017      0.71     135     211 ..     293     562 ..     145     567 .. 0.66
   3 !   15.4   0.0   2.3e-05    0.0096     135     210 ..     787     902 ..     621     909 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00044
                                      EEEEEEESETTEECEEEEEET.TSSEEEEEESTTSSHHHH.HHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx.xxxxxx RF
                             SMC_N  2 lkrleienFksyagktvilpf.sksftaivGpNGSGKsnl.ldAilF 46
                                      l++++i++ k  + +++++ +  ++f +i+G  GSGKs+l +d i +
  gi|298674741|ref|YP_003726491.1|  3 LNSIIIRGAKEHNLNNIDVTLpRDKFIVITGLSGSGKSSLaFDTI-Y 48
                                      6788899999887777766552567**************834655.5 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0017
                                       T............................................................................ CS
                                       x............................................................................ RF
                             SMC_N 135 e............................................................................ 135
                                       e                                                                            
  gi|298674741|ref|YP_003726491.1| 293 Elivpnpnltlhqgavepwskrdgyhmqslesladhygfsmdvpykdldsnikkiimygtnekiplehvgkrggvwk 369
                                       05555555555555555555555555555555555555555555555555566666666666666666666666666 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|298674741|ref|YP_003726491.1| 370 rrgrfrgvvsylsrvynktesentkdklnkyisnkpcpecngkrlkpevlavtiddnniiditeksvenshhffekl 446
                                       66666666666666666666666666666666666666666666666666666666666666666666666666666 PP

                                       .........................................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS CS
                                       .........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 .........................................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaL 171
                                                                                +LSgGe + + la    i +     ly+lDe    L
  gi|298674741|ref|YP_003726491.1| 447 etkldsreyaiarmilkeitsrlgflmdvgldyltlsrsasTLSGGEAQRIRLATQ--IGSSLMGVLYILDEPSIGL 521
                                       67777777777777777777778888888888888888888999999887766665..66777789*********** PP

                                       -HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEEEE CS
                                       xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 172 Deknvkkvaellkekskn.aQfivislreemlekadklvgv 211
                                        ++   ++ + lk+ ++    ++v+ ++ee++ ++d++v +
  gi|298674741|ref|YP_003726491.1| 522 HQRDNIRLINTLKHLRDLgNTVLVVEHDEETILNSDHVVDM 562
                                       *************999876899**********999998865 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 2.3e-05
                                       T........................................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS CS
                                       x........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 135 e........................................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaL 171
                                                                                +LSgGe + v la  ++  +   + ly+lDe    L
  gi|298674741|ref|YP_003726491.1| 787 VlemtveealeffenipkikkrlqtlydvglgyiklgqsstTLSGGEAQRVKLASELSR-RSTGNTLYILDEPTTGL 862
                                       155555555555555555555566666666666666666669************99985.566789*********** PP

                                       -HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEEE CS
                                       xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 172 Deknvkkvaellkekskn.aQfivislreemlekadklvg 210
                                        ++ vk++ ++l++  +    +ivi ++ ++++ ad l+ 
  gi|298674741|ref|YP_003726491.1| 863 HFEDVKRLLSVLQRLVDAgNTVIVIEHNLDVIKTADWLID 902
                                       *************998876899***********9998876 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00023     0.097      16      38 ..      20      42 ..      11      49 .. 0.76
   2 !   16.6   0.0   1.2e-05     0.005      16      46 ..     627     658 ..     619     665 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00023
                            AAA_29 16 tieidlkgatlltGpsGsGKSTl 38
                                      ++++ ++ ++++tG sGsGKS+l
  gi|298674741|ref|YP_003726491.1| 20 DVTLPRDKFIVITGLSGSGKSSL 42
                                      5666656699***********98 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.2e-05
                            AAA_29  16 tieidlkg.atlltGpsGsGKSTll.DAiqalL 46 
                                       +++i l g +  +tG sGsGKSTl+ D +  +L
  gi|298674741|ref|YP_003726491.1| 627 DVDIPL-GvMLCVTGVSGSGKSTLInDTLHKVL 658
                                       555554.44889************966666665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00036      0.15      25      63 ..      27      66 ..      13      99 .. 0.73
   2 !   14.6   0.0   7.7e-05     0.033      25      53 ..     634     662 ..     621     689 .. 0.81
   3 ?   -0.5   0.0       3.3   1.4e+03     106     142 ..     844     888 ..     770     901 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00036
                            AAA_16 25 elvllsGesGvGKsslv.rellralekdggif..lrgkcdql 63
                                        ++++G sG+GKssl+ ++++   e+++ ++  l++ ++q+
  gi|298674741|ref|YP_003726491.1| 27 KFIVITGLSGSGKSSLAfDTIYA--EGQRRYVesLSAYARQF 66
                                      6899*************666664..44445665688888877 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 7.7e-05
                            AAA_16  25 elvllsGesGvGKsslvrellralekdgg 53 
                                        ++ ++G sG+GKs+l++  l+ + +++ 
  gi|298674741|ref|YP_003726491.1| 634 VMLCVTGVSGSGKSTLINDTLHKVLAQKL 662
                                       5789*************888887777644 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 3.3
                            AAA_16 106 a.............avpelagaeasrllellkrllallsrderplvlvlD 142
                                       +             ++  l+ ++ +rll +l+rl++     +  +v+v++
  gi|298674741|ref|YP_003726491.1| 844 SrrstgntlyildePTTGLHFEDVKRLLSVLQRLVD-----AGNTVIVIE 888
                                       244444444444444555555555888888888882.....333566666 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0    0.0017      0.74       5      26 ..      26      47 ..      24     100 .. 0.78
   2 ?    1.3   0.0      0.86   3.7e+02      40     117 ..     426     538 ..     388     552 .. 0.69
   3 !   13.6   0.0   0.00014     0.059       7      41 ..     635     670 ..     633     705 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0017
                            AAA_22  5 agilvvtGesGtGKTtllrrll 26
                                      ++++v+tG sG+GK+ l+    
  gi|298674741|ref|YP_003726491.1| 26 DKFIVITGLSGSGKSSLAFDTI 47
                                      689************9985555 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.86
                            AAA_22  40 pevvfvtlpsstsskdllrellralglelka................................erlsseellealeq 84 
                                         ++ +t +s ++s  ++++l  +l+++  a                                  + + + +++ +q
  gi|298674741|ref|YP_003726491.1| 426 NNIIDITEKSVENSHHFFEKLETKLDSREYAiarmilkeitsrlgflmdvgldyltlsrsastLSGGEAQRIRLATQ 502
                                       55566666777788888888888888777777777777777777778888888888777777655555555567777 PP

                            AAA_22  85 alraravielliiDEaqh.lr.s..eealeeLrslln 117
                                         ++ +  +l i+DE    l  +   +++++L++l +
  gi|298674741|ref|YP_003726491.1| 503 IGSSLMG-VLYILDEPSIgLHqRdnIRLINTLKHLRD 538
                                       7777777.78888887666644144566666666555 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 0.00014
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee.erpe 41 
                                       +l+vtG sG+GK+tl++  l++  +++ ++  e+p+
  gi|298674741|ref|YP_003726491.1| 635 MLCVTGVSGSGKSTLINDTLHKVLAQKLHRAkEKPG 670
                                       789***************999998888877664443 PP

>> BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2   2.6e-05     0.011       2      15 ..     573     586 ..     572     587 .. 0.93
   2 !   11.9   0.2   0.00038      0.16       1      11 [.     913     923 ..     913     925 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.6e-05
                      BCA_ABC_TP_C   2 vIAeGtPaEvrndP 15 
                                       vI eGtP+E+r d+
  gi|298674741|ref|YP_003726491.1| 573 VISEGTPEEIREDE 586
                                       8***********97 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00038
                      BCA_ABC_TP_C   1 rvIAeGtPaEv 11 
                                       rvIAeGtP+ v
  gi|298674741|ref|YP_003726491.1| 913 RVIAEGTPETV 923
                                       8********98 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.26   1.1e+02       1      15 [.      28      42 ..      28      48 .. 0.93
   2 !    7.3   0.1    0.0086       3.7     112     293 ..     404     544 ..     382     554 .. 0.73
   3 ?    1.8   0.1       0.4   1.7e+02       3      16 ..     637     650 ..     635     652 .. 0.89
   4 !   15.5   0.0   2.7e-05     0.012     237     298 ..     829     890 ..     796     895 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.26
                            AAA_21  1 lnvliGpNgsGKSnL 15
                                      + v++G  gsGKS+L
  gi|298674741|ref|YP_003726491.1| 28 FIVITGLSGSGKSSL 42
                                      689**********98 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0086
                            AAA_21 112 npeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrkerigllnifadyfgfakekrllqrl 188
                                        p+++++ + +++++l+  +  + ++++ +k   ++ ++++            +  +  ++++y+   ++++ ++ +
  gi|298674741|ref|YP_003726491.1| 404 KPCPECNGKRLKPEVLAVTIDDNNIIDITEKSVENSHHFFE------------KLETKLDSREYAIARMILKEITSR 468
                                       56666666666666666666666666666666666666666............777777777788888888888888 PP

                            AAA_21 189 vrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDE 265
                                       ++ l +v++ + +l                             ++a+ lS G  + ++l+t + + l    l+++DE
  gi|298674741|ref|YP_003726491.1| 469 LGFLMDVGLDYLTLS----------------------------RSASTLSGGEAQRIRLATQIGSSLMG-VLYILDE 516
                                       888888888888884............................677788****9999***********9.9****** PP

                            AAA_21 266 pEngLHPkllrrllellkelsrngaQvi 293
                                       p  gLH +   rl+  lk l++ g  v+
  gi|298674741|ref|YP_003726491.1| 517 PSIGLHQRDNIRLINTLKHLRDLGNTVL 544
                                       ******9655566666666666555555 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.4
                            AAA_21   3 vliGpNgsGKSnLL 16 
                                       +++G  gsGKS+L+
  gi|298674741|ref|YP_003726491.1| 637 CVTGVSGSGKSTLI 650
                                       689**********8 PP

  == domain 4  score: 15.5 bits;  conditional E-value: 2.7e-05
                            AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                       lS G  +  +l++ l r+   ++l+++DEp +gLH + ++rll +l +l + g  vi+  H+
  gi|298674741|ref|YP_003726491.1| 829 LSGGEAQRVKLASELSRRSTGNTLYILDEPTTGLHFEDVKRLLSVLQRLVDAGNTVIVIEHN 890
                                       5666655559999**************************99999998877778888876555 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00083      0.36      81     116 ..       7      43 ..       1      61 [. 0.81
   2 !   12.3   0.0   0.00028      0.12     100     122 ..     634     656 ..     592     673 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00083
                                       E--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHH CS
                       RsgA_GTPase  81 lvsaktkegleelkellkd.ktsvlvGqSGvGKStLi 116
                                       +++  ++++l+++   l   k++v+ G SG GKS+L 
  gi|298674741|ref|YP_003726491.1|   7 IIRGAKEHNLNNIDVTLPRdKFIVITGLSGSGKSSLA 43 
                                       55556678899999888766***************95 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00028
                                       SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase 100 ktsvlvGqSGvGKStLinallpe 122
                                        + ++ G SG GKStLin  l +
  gi|298674741|ref|YP_003726491.1| 634 VMLCVTGVSGSGKSTLINDTLHK 656
                                       577899************76554 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.4    0.0052       2.2      15      54 ..     252     288 ..     241     293 .. 0.66
   2 ?    4.8   0.0     0.088        38      41      66 ..     403     412 ..     385     420 .. 0.61
   3 !   14.2   0.3   9.7e-05     0.041      16      51 ..     738     769 ..     724     775 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0052
                     DnaJ_CXXCXGXG  15 ktCktCkGsGvvreeqktlgpfvqqsqstCpeCeGtGkvi 54 
                                         C++C G G ++ e    ++ +++ q  CpeC+G G+++
  gi|298674741|ref|YP_003726491.1| 252 LACSEC-GIGFEELEP--PAFSFNSPQGACPECHGLGTTM 288
                                       468888.778444433..2334456678999999999987 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.088
                     DnaJ_CXXCXGXG  41 qstCpeCeGtGkvikekdkCkkCkGk 66 
                                       ++                +C++C+Gk
  gi|298674741|ref|YP_003726491.1| 403 NK----------------PCPECNGK 412
                                       23................34444443 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 9.7e-05
                     DnaJ_CXXCXGXG  16 tCktCkGsGvvreeqktlgpfvqqsqstCpeCeGtG 51 
                                       +C+tC+G G ++ e++    f   ++ +C+ C+G+ 
  gi|298674741|ref|YP_003726491.1| 738 RCETCSGDGIITIEMH----FLPDVHVQCEVCNGKR 769
                                       6********6555542....45566789*****986 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0031       1.3       4      20 ..      28      44 ..      25      58 .. 0.85
   2 ?   -0.1   0.1       1.8   7.7e+02      22      52 ..     167     197 ..     164     210 .. 0.79
   3 !    9.7   0.0    0.0017      0.71       2      29 ..     633     661 ..     632     670 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0031
                                      EEEEESSTTSSHHHHHH CS
                        APS_kinase  4 vvwltGlsgsGKstian 20
                                       + +tGlsgsGKs++a+
  gi|298674741|ref|YP_003726491.1| 28 FIVITGLSGSGKSSLAF 44
                                      689************97 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.8
                                       HHHHHHHTT--EEEEEHHHHTTTTTTT--SS CS
                        APS_kinase  22 lekkLvekgisvylLdGdnvRhgLnkdLgfs 52 
                                       l + L+++g+s +++dGd+v  + + +L   
  gi|298674741|ref|YP_003726491.1| 167 LFTDLQSEGYSRVRVDGDVVSLDETDELELG 197
                                       557899**************98888877655 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0017
                                       -EEEEEESSTTSSHHHHHHH.HHHHHHHT CS
                        APS_kinase   2 gvvvwltGlsgsGKstiana.lekkLvek 29 
                                       gv++ +tG+sgsGKst+ n  l+k L +k
  gi|298674741|ref|YP_003726491.1| 633 GVMLCVTGVSGSGKSTLINDtLHKVLAQK 661
                                       678999**********8775144444444 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0    0.0011      0.49      26      53 ..      19      46 ..       9      52 .. 0.87
   2 ?   -2.4   0.0       6.7   2.9e+03     167     188 ..     528     548 ..     523     549 .. 0.87
   3 ?    6.7   0.0     0.011       4.9      29      59 ..     629     659 ..     620     672 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0011
                            AAA_25 26 vkgllpagelallaGapgtGKttlaldl 53
                                      ++  lp++++++++G +g+GK+ la d 
  gi|298674741|ref|YP_003726491.1| 19 IDVTLPRDKFIVITGLSGSGKSSLAFDT 46
                                      55579********************986 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.7
                            AAA_25 167 alvealeriarrtgaavllvhH 188
                                       +l++ l+++ r +g +vl+v H
  gi|298674741|ref|YP_003726491.1| 528 RLINTLKHL-RDLGNTVLVVEH 548
                                       789999999.7999*****999 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.011
                            AAA_25  29 llpagelallaGapgtGKttlaldlalavat 59 
                                        +p+g    ++G +g+GK+tl  d  ++v+ 
  gi|298674741|ref|YP_003726491.1| 629 DIPLGVMLCVTGVSGSGKSTLINDTLHKVLA 659
                                       58999*****************999999884 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0     0.011       4.5       2      27 ..      26      51 ..      25      80 .. 0.84
   2 !    7.9   0.1    0.0072       3.1       4      27 ..     635     658 ..     633     687 .. 0.82
   3 ?   -0.1   0.0       2.1   9.1e+02      56      92 ..     843     882 ..     805     894 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.011
                            AAA_14  2 rkilvitGaRrvGKTtllkqlikell 27
                                      +k +vitG+  +GK+ l+++ i+ + 
  gi|298674741|ref|YP_003726491.1| 26 DKFIVITGLSGSGKSSLAFDTIYAEG 51
                                      5899****************998766 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0072
                            AAA_14   4 ilvitGaRrvGKTtllkqlikell 27 
                                       +l++tG+  +GK+tl+++ +++ l
  gi|298674741|ref|YP_003726491.1| 635 MLCVTGVSGSGKSTLINDTLHKVL 658
                                       579***************999888 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 2.1
                            AAA_14  56 ileklkeekktylflDEiqev......pewekalkslvdegkn 92 
                                       + ++ +  ++t+ +lDE          +++ ++l++lvd g n
  gi|298674741|ref|YP_003726491.1| 843 LSRR-S-TGNTLYILDEPTTGlhfedvKRLLSVLQRLVDAG-N 882
                                       3332.2.4789999999665434444488888888888888.4 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0061       2.6       1      15 [.      29      43 ..      29      57 .. 0.95
   2 !    8.8   0.1    0.0053       2.2       2      16 ..     637     651 ..     636     674 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0061
                            AAA_18  1 IlltGtpGvGKttla 15
                                      I++tG +G+GK++la
  gi|298674741|ref|YP_003726491.1| 29 IVITGLSGSGKSSLA 43
                                      99***********98 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0053
                            AAA_18   2 lltGtpGvGKttlak 16 
                                       ++tG++G+GK+tl +
  gi|298674741|ref|YP_003726491.1| 637 CVTGVSGSGKSTLIN 651
                                       89**********975 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.098        42       5      20 ..      29      44 ..      25      53 .. 0.87
   2 ?    3.0   0.0      0.17        71     109     138 ..     524     555 ..     517     564 .. 0.75
   3 !    8.5   0.0    0.0036       1.5       3      25 ..     634     656 ..     632     704 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.098
                            AAA_24  5 iliyGpsgiGKTtlak 20
                                      i+i+G sg+GK++la 
  gi|298674741|ref|YP_003726491.1| 29 IVITGLSGSGKSSLAF 44
                                      89***********996 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.17
                            AAA_24 109 eefrrllkklqelrk..nvifiahektrkded 138
                                       ++ +rl+++l++lr+  n +++ + +++++ +
  gi|298674741|ref|YP_003726491.1| 524 RDNIRLINTLKHLRDlgNTVLVVEHDEETILN 555
                                       56678999999999999777777777777655 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0036
                            AAA_24   3 lkiliyGpsgiGKTtlakelgpk 25 
                                       ++++++G sg+GK+tl++    k
  gi|298674741|ref|YP_003726491.1| 634 VMLCVTGVSGSGKSTLINDTLHK 656
                                       689*************9987444 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.33   1.4e+02       1      15 [.      29      43 ..      29      82 .. 0.83
   2 !   14.0   0.1   7.2e-05     0.031       2      22 ..     637     657 ..     636     693 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.33
                   Viral_helicase1  1 ivvhGvpGcGKStli 15
                                      iv+ G  G+GKS+l 
  gi|298674741|ref|YP_003726491.1| 29 IVITGLSGSGKSSLA 43
                                      79**********975 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 7.2e-05
                   Viral_helicase1   2 vvhGvpGcGKStlirkllrts 22 
                                        v Gv G+GKStli + l++ 
  gi|298674741|ref|YP_003726491.1| 637 CVTGVSGSGKSTLINDTLHKV 657
                                       599***************993 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.18        78       2      15 ..      29      42 ..      28      56 .. 0.91
   2 !   12.0   0.0   0.00039      0.17       3      37 ..     637     676 ..     635     693 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.18
                                      EEEEESTTSSHHHH CS
                          MMR_HSR1  2 vaivGrpNvGKStL 15
                                      ++i G + +GKS+L
  gi|298674741|ref|YP_003726491.1| 29 IVITGLSGSGKSSL 42
                                      89***********9 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00039
                                       EEEESTTSSHHHHHHHHHTS.....TEEESSSTTSSSSEE CS
                          MMR_HSR1   3 aivGrpNvGKStLinaltge.....kaivsdkpgtTrdin 37 
                                       ++ G + +GKStLin  + +       ++++kpgt +di+
  gi|298674741|ref|YP_003726491.1| 637 CVTGVSGSGKSTLINDTLHKvlaqkLHRAKEKPGTYKDIK 676
                                       799************9998543332458899999988875 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.033        14     107     146 ..       5      43 ..       1      53 [. 0.70
   2 !    9.7   0.0   0.00094       0.4     130     156 ..     634     660 ..     600     665 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.033
                             T2SSE 107 dlgaeealkekiaevlrkavrerglilvsGgTgsGKttll 146
                                        +++++a ++++++ +   + + + i+++G  gsGK+ l+
  gi|298674741|ref|YP_003726491.1|   5 SIIIRGAKEHNLNN-IDVTLPRDKFIVITGLSGSGKSSLA 43 
                                       55555555555544.3444468899***********9876 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00094
                             T2SSE 130 glilvsGgTgsGKttllyallkeinks 156
                                        ++ v+G  gsGK+tl++  l+++ ++
  gi|298674741|ref|YP_003726491.1| 634 VMLCVTGVSGSGKSTLINDTLHKVLAQ 660
                                       6889**************999988655 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0041       1.7       6      60 ..      14      62 ..      12     122 .. 0.58
   2 ?    6.1   0.0     0.022       9.4      23      66 ..     636     679 ..     632     716 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0041
                          ATPase_2  6 kelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialree 60
                                        l+++   l r  +++++i+G  gsGK++L    i    +    + y+ +l+ +
  gi|298674741|ref|YP_003726491.1| 14 HNLNNIDVTLPR--DKFIVITGLSGSGKSSLAFDTIYAEGQ----RRYVESLSAY 62
                                      566677766666..89***************9888876644....3344444333 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.022
                          ATPase_2  23 yfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskld 66 
                                       + ++G  gsGK++L++  + + + ++ ++    +   ++i+ l+
  gi|298674741|ref|YP_003726491.1| 636 LCVTGVSGSGKSTLINDTLHKVLAQKLHRAKEKPGTYKDIKGLE 679
                                       6799*************999988777777666666666665555 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.072        31       3      22 ..      29      48 ..      27      56 .. 0.78
   2 !   10.9   0.1   0.00058      0.25       3      23 ..     636     656 ..     634     666 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.072
                                      EEEEESTTCCHHHHHHHHHC CS
                              cobW  3 tvltGflGsGKTtLlnhlle 22
                                      +v+tG  GsGK++L   ++ 
  gi|298674741|ref|YP_003726491.1| 29 IVITGLSGSGKSSLAFDTIY 48
                                      79***********9877774 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00058
                                       EEEEESTTCCHHHHHHHHHCT CS
                              cobW   3 tvltGflGsGKTtLlnhllen 23 
                                       + +tG  GsGK+tL+n +l++
  gi|298674741|ref|YP_003726491.1| 636 LCVTGVSGSGKSTLINDTLHK 656
                                       689**************9965 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.031        13       2      16 ..      29      43 ..      28     102 .. 0.85
   2 !    7.9   0.1    0.0076       3.2       2      19 ..     636     653 ..     635     665 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.031
                            AAA_33  2 vllvGlpGsGKstla 16
                                      +++ Gl+GsGKs la
  gi|298674741|ref|YP_003726491.1| 29 IVITGLSGSGKSSLA 43
                                      6789********998 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0076
                            AAA_33   2 vllvGlpGsGKstlaerl 19 
                                       + + G++GsGKstl+   
  gi|298674741|ref|YP_003726491.1| 636 LCVTGVSGSGKSTLINDT 653
                                       5678**********9764 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.2    0.0028       1.2       2      35 ..       6      42 ..       5      46 .. 0.79
   2 ?    7.4   0.0     0.014       5.8      23      54 ..     637     669 ..     623     708 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0028
                            AAA_23  2 LkienfrsfrdqeidF...skgltlItGpNGaGKTTi 35
                                      + i++ + ++  +id     +++ +ItG  G+GK+++
  gi|298674741|ref|YP_003726491.1|  6 IIIRGAKEHNLNNIDVtlpRDKFIVITGLSGSGKSSL 42
                                      6667777775556666668899*************98 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.014
                            AAA_23  23 lItGpNGaGKTTil.dAiklaLygetprlsrks 54 
                                       ++tG  G+GK+T++ d ++ +L  + +r + k 
  gi|298674741|ref|YP_003726491.1| 637 CVTGVSGSGKSTLInDTLHKVLAQKLHRAKEKP 669
                                       799***********7777777777776666655 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.015       6.2       2      25 ..      27      50 ..      26      74 .. 0.82
   2 !    7.7   0.1    0.0044       1.9       3      26 ..     635     660 ..     633     694 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.015
                           DUF2075  2 avvlVtGvaGtGKtvvllnllael 25
                                      + +++tG +G+GK+ +++  +++ 
  gi|298674741|ref|YP_003726491.1| 27 KFIVITGLSGSGKSSLAFDTIYAE 50
                                      579**************9998875 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0044
                           DUF2075   3 vvlVtGvaGtGKtvvllnllael..e 26 
                                       ++ VtGv+G+GK+ + +  l+++  +
  gi|298674741|ref|YP_003726491.1| 635 MLCVTGVSGSGKSTLINDTLHKVlaQ 660
                                       678**************999998441 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.081        35       1      16 [.      28      43 ..      28      66 .. 0.87
   2 ?    7.8   0.0    0.0058       2.5       3      33 ..     637     668 ..     635     692 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.081
                               PRK  1 vIgvagsSGaGkttva 16
                                      +I ++g SG+Gk+++a
  gi|298674741|ref|YP_003726491.1| 28 FIVITGLSGSGKSSLA 43
                                      599**********986 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0058
                               PRK   3 gvagsSGaGkttv.arklekifgrekvkaaei 33 
                                        v+g SG+Gk+t+   +l+k+++++  +a+e 
  gi|298674741|ref|YP_003726491.1| 637 CVTGVSGSGKSTLiNDTLHKVLAQKLHRAKEK 668
                                       79**********62578999999776665554 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1      0.53   2.3e+02       1      40 [.       1      43 [.       1     174 [. 0.87
   2 ?    3.8   0.6     0.093        40     235     356 ..     415     541 ..     377     551 .. 0.59
   3 ?    0.0   0.0       1.3   5.4e+02      16      41 ..     627     651 ..     621     697 .. 0.68
   4 ?    9.1   0.0    0.0022      0.96     273     365 ..     789     890 ..     766     894 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.53
                            AAA_15  1 MkIkkikikNFRslkdveidlsee...ltvliGkNnsGKSsil 40
                                      M +++i+i+  + +    id+      + v+ G  +sGKSs++
  gi|298674741|ref|YP_003726491.1|  1 MSLNSIIIRGAKEHNLNNIDVTLPrdkFIVITGLSGSGKSSLA 43
                                      778888888888777655555433446**************85 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.093
                            AAA_15 235 eeelteklkeiqeklkeidkklaeelkkilkkkidkik.kfnykgkkneeieik.............ddeelplnkn 297
                                       + e+     + ++ ++ ++k +  e + ++++k+++   + +y ++   ++ei                 + +++  
  gi|298674741|ref|YP_003726491.1| 415 KPEVLAVTIDDNNIIDITEKSV--ENSHHFFEKLETKLdSREYAIARMILKEITsrlgflmdvgldyLTLSRSASTL 489
                                       4344444444444444444444..22233444443333256666666666666677777777766554445556666 PP

                            AAA_15 298 GsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnk 356
                                       + G  + + l+++i +   +       v+++++EP + LH      li++lk l + ++
  gi|298674741|ref|YP_003726491.1| 490 SGGEAQRIRLATQIGSSLMG-------VLYILDEPSIGLHQRDNIRLINTLKHLRDLGN 541
                                       77778888888888888888.......9**********************999876665 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 1.3
                            AAA_15  16 dveidlseeltvliGkNnsGKSsile 41 
                                       dv+i+l   + ++ G  +sGKS++++
  gi|298674741|ref|YP_003726491.1| 627 DVDIPLGV-MLCVTGVSGSGKSTLIN 651
                                       36777777.89999999*****9884 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.0022
                            AAA_15 273 kfnykgkkneeieik..ddeelplnknGsGvqrllllillileaekk........dekeeknvilliEEPEahLHpq 339
                                        + + ++ +++ +i    +  ++l+++G+G+  l   ++ +   e +        +++++ n +++++EP + LH +
  gi|298674741|ref|YP_003726491.1| 789 EMTVEEALEFFENIPkiKKRLQTLYDVGLGYIKLGQSSTTLSGGEAQrvklaselSRRSTGNTLYILDEPTTGLHFE 865
                                       4444445555555556666667777777777666666666655555555667777778888**************** PP

                            AAA_15 340 aqkvlikllkelandnktQviitTHS 365
                                         k l   l++l++ ++  vi+  H+
  gi|298674741|ref|YP_003726491.1| 866 DVKRLLSVLQRLVDAGN-TVIVIEHN 890
                                       ****************9.67766565 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0       0.1        43       3      17 ..      29      43 ..      27      63 .. 0.84
   2 ?    7.8   0.1    0.0069         3       3      23 ..     636     656 ..     634     668 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.1
                                      EEEEC-TTTCHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLl 17
                                      ++++G +GsGK+ L+
  gi|298674741|ref|YP_003726491.1| 29 IVITGLSGSGKSSLA 43
                                      89***********98 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0069
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       ++++G +GsGK+tL+    ++
  gi|298674741|ref|YP_003726491.1| 636 LCVTGVSGSGKSTLINDTLHK 656
                                       79************9765554 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.16        66      21      38 ..      27      44 ..      13      55 .. 0.83
   2 ?    6.4   0.0      0.01       4.4      21      43 ..     634     656 ..     621     664 .. 0.85
   3 ?   -0.8   0.0       1.6   6.8e+02      84     135 ..     862     915 ..     853     935 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.16
                                      EEEEEEESTTSSHHHHHH CS
                            NB-ARC 21 lvvalvGmgGvGKttlak 38
                                       ++ + G  G+GK+ la 
  gi|298674741|ref|YP_003726491.1| 27 KFIVITGLSGSGKSSLAF 44
                                      5899***********984 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.01
                                       EEEEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC  21 lvvalvGmgGvGKttlakqilnk 43 
                                       +++ + G  G+GK+tl+++ l+k
  gi|298674741|ref|YP_003726491.1| 634 VMLCVTGVSGSGKSTLINDTLHK 656
                                       57899************999887 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.6
                                       SSS-STTSHHHHHHHHCCCTTEEEEEE...EE-SHHHH.....HHHHCHTTSEEE CS
                            NB-ARC  84 eekeeveslkrklvrlLltkrfllvlD...DVweeedwdkigvvlparenrlrvl 135
                                        ++e+v+ l   l+rl    ++++v+    DV ++ dw  i +     e++ rv+
  gi|298674741|ref|YP_003726491.1| 862 LHFEDVKRLLSVLQRLVDAGNTVIVIEhnlDVIKTADW-LIDLGPEGGEHGGRVI 915
                                       57888888888999999999******88889******9.8887777777777776 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.26   1.1e+02       1      17 [.      29      45 ..      29      65 .. 0.85
   2 ?    8.4   0.0    0.0062       2.7       2      28 ..     637     664 ..     636     684 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.26
                      RNA_helicase  1 iwlyGpsgeGKStlake 17
                                      i+++G sg GKS+la +
  gi|298674741|ref|YP_003726491.1| 29 IVITGLSGSGKSSLAFD 45
                                      789**********9976 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0062
                      RNA_helicase   2 wlyGpsgeGKStlake.Lakallkklkl 28 
                                       +++G sg GKStl+++ L k l++kl  
  gi|298674741|ref|YP_003726491.1| 637 CVTGVSGSGKSTLINDtLHKVLAQKLHR 664
                                       899************9455555566633 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.56   2.4e+02       2      16 ..      29      43 ..      28      52 .. 0.87
   2 ?    1.4   0.1      0.62   2.7e+02      47      98 ..     183     238 ..     167     252 .. 0.78
   3 ?    8.3   0.1    0.0045       1.9       2      23 ..     636     657 ..     635     664 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.56
                                      EEEE--TTSSHHHHH CS
                          NTPase_1  2 vfiTGppGvGKtTlv 16
                                      ++iTG +G+GK+ l 
  gi|298674741|ref|YP_003726491.1| 29 IVITGLSGSGKSSLA 43
                                      79**********986 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.62
                                       EEEEET.T--EEEEEETT.---SSEETTEEE-HHHHHHHHHHHHHHHHHHH-....E CS
                          NTPase_1  47 FkivdlasgeegiLarve.akreprvgkyvvdvesfeelalealrkalsead....v 98 
                                        ++v+l++ +e +L r + ++ e+ v++ v++ e +e+  +ea+++a+++++    +
  gi|298674741|ref|YP_003726491.1| 183 GDVVSLDETDELELGRYQkHNIEIVVDRLVIK-EGIEDRLSEAVETAIEKSGgtvmI 238
                                       57899988889999888845556678888888.899999999999999888765433 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0045
                                       EEEE--TTSSHHHHHHHHHHHH CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlell 23 
                                       +++TG +G+GK+Tl++  l+++
  gi|298674741|ref|YP_003726491.1| 636 LCVTGVSGSGKSTLINDTLHKV 657
                                       579************9887765 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.15        65      27      55 ..      20      48 ..       2      63 .. 0.78
   2 ?    7.1   0.1    0.0083       3.6      36      61 ..     636     661 ..     630     666 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.15
                             AAA_7 27 elllknkkpvllvGptGtGKtviikdllk 55
                                      +  l ++k ++++G +G+GK++++ d++ 
  gi|298674741|ref|YP_003726491.1| 20 DVTLPRDKFIVITGLSGSGKSSLAFDTIY 48
                                      6667788999************9988544 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0083
                             AAA_7  36 vllvGptGtGKtviikdllkkldkek 61 
                                       ++++G +G+GK+++i+d+l+k+  +k
  gi|298674741|ref|YP_003726491.1| 636 LCVTGVSGSGKSTLINDTLHKVLAQK 661
                                       5689*************988876565 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.55   2.4e+02      27      35 ..     120     128 ..     106     136 .. 0.60
   2 ?   12.7   1.6   0.00025      0.11       7      34 ..     253     283 ..     251     287 .. 0.76
   3 ?    4.1   0.1      0.12        52      26      35 ..     403     413 ..     389     415 .. 0.71
   4 ?    0.3   0.6       1.8   7.8e+02       7      36 ..     738     770 ..     738     773 .. 0.66

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.55
                       Zn-ribbon_8  27 taCPeCgse 35 
                                        +CP Cg +
  gi|298674741|ref|YP_003726491.1| 120 RHCPYCGRR 128
                                       336666653 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00025
                       Zn-ribbon_8   7 rCeeCghefevlqsis...dapltaCPeCgs 34 
                                        C eCg  fe+l + +    +p+ aCPeC++
  gi|298674741|ref|YP_003726491.1| 253 ACSECGIGFEELEPPAfsfNSPQGACPECHG 283
                                       6*********776533325677888****98 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.12
                       Zn-ribbon_8  26 ltaCPeCgs.e 35 
                                       +++CPeC++ +
  gi|298674741|ref|YP_003726491.1| 403 NKPCPECNGkR 413
                                       456****9955 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 1.8
                       Zn-ribbon_8   7 rCeeCghefevlqsis.daplta.CPeCgs.ev 36 
                                       rCe C  +  +  +++  ++  + C  C++ + 
  gi|298674741|ref|YP_003726491.1| 738 RCETCSGDGIITIEMHfLPDVHVqCEVCNGkRY 770
                                       677777766666667755555556999998665 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.017       7.5      16      40 ..      23      47 ..      15      56 .. 0.84
   2 ?    3.7   0.0     0.079        34      16      35 ..     630     649 ..     625     660 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.017
                            ATPase 16 ipegrvvlitGepGtGKtifalqFl 40
                                      +p+++ + itG +G+GK+ +a   +
  gi|298674741|ref|YP_003726491.1| 23 LPRDKFIVITGLSGSGKSSLAFDTI 47
                                      89****************9987655 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.079
                            ATPase  16 ipegrvvlitGepGtGKtif 35 
                                       ip g +  +tG++G+GK+++
  gi|298674741|ref|YP_003726491.1| 630 IPLGVMLCVTGVSGSGKSTL 649
                                       67788899**********98 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.41   1.7e+02      27      45 ..      24      42 ..      10      54 .. 0.79
   2 ?    8.2   0.0    0.0025       1.1      31      54 ..     635     659 ..     622     666 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.41
                                      S-SEEEEEEE-TTSSHHHH CS
                              MeaB 27 GraqvvGltGvPGaGkstl 45
                                       r + + +tG+ G+Gks l
  gi|298674741|ref|YP_003726491.1| 24 PRDKFIVITGLSGSGKSSL 42
                                      5778899**********87 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0025
                                       EEEEEE-TTSSHHHHHHH.HHHHHH CS
                              MeaB  31 vvGltGvPGaGkstlvea.lglelr 54 
                                       ++ +tGv G+Gkstl++  l   l+
  gi|298674741|ref|YP_003726491.1| 635 MLCVTGVSGSGKSTLINDtLHKVLA 659
                                       5789************751444454 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0       0.2        87      17      34 ..      25      42 ..      19      67 .. 0.85
   2 ?    5.8   0.1     0.024        10      20      38 ..     635     653 ..     633     668 .. 0.78
   3 ?   -0.9   0.0       2.6   1.1e+03      85     121 ..     846     886 ..     809     889 .. 0.64

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.2
                            AAA_30 17 gdrvavltGpAGtGKtta 34
                                      +d++ v+tG  G+GK+ +
  gi|298674741|ref|YP_003726491.1| 25 RDKFIVITGLSGSGKSSL 42
                                      56799**********986 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.024
                            AAA_30  20 vavltGpAGtGKttalkal 38 
                                       + ++tG+ G+GK+t+++  
  gi|298674741|ref|YP_003726491.1| 635 MLCVTGVSGSGKSTLINDT 653
                                       5689***********9876 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.6
                            AAA_30  85 rlepgtllivDEagmv....dtkqlaallkaaekagakvil 121
                                       r + +tl+i DE        d k l ++l+++ +ag +vi+
  gi|298674741|ref|YP_003726491.1| 846 RSTGNTLYILDEPTTGlhfeDVKRLLSVLQRLVDAGNTVIV 886
                                       3445599*****66544344555555555555566766665 PP

>> Pox_E10  E10-like protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.3   0.00065      0.28       3      60 ..     391     455 ..     389     464 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00065
                           Pox_E10   3 EacKrklylivetlPCaeCrahAke......aiqknnvm..SskdlNyiyfFfislfNnlasdkky 60 
                                       E+ K kl + +++ PC+eC  + ++       i++nn++   +k +   ++Ff +l  +l s + y
  gi|298674741|ref|YP_003726491.1| 391 ENTKDKLNKYISNKPCPECNGKRLKpevlavTIDDNNIIdiTEKSVENSHHFFEKLETKLDSRE-Y 455
                                       889****************98766533443479*****73368899999999999988877654.5 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.065        28      15      38 ..      25      48 ..      13      86 .. 0.80
   2 ?    4.4   0.0     0.046        20      18      39 ..     635     656 ..     625     662 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.065
                        Zeta_toxin 15 rPklillgGqpGAGKselaellkd 38
                                      r k i++ G +G+GKs+la ++  
  gi|298674741|ref|YP_003726491.1| 25 RDKFIVITGLSGSGKSSLAFDTIY 48
                                      66899************9966554 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.046
                        Zeta_toxin  18 lillgGqpGAGKselaellkde 39 
                                       ++ + G +G+GKs+l++++  +
  gi|298674741|ref|YP_003726491.1| 635 MLCVTGVSGSGKSTLINDTLHK 656
                                       67789***********998776 PP

>> DUF463  YcjX-like family, DUF463
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.2      0.56   2.4e+02       4      15 ..      30      41 ..      29      47 .. 0.86
   2 ?    8.3   0.0    0.0023      0.96       2      28 ..     635     661 ..     634     675 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.56
                            DUF463  4 avTGLsraGKtv 15
                                       +TGLs++GK+ 
  gi|298674741|ref|YP_003726491.1| 30 VITGLSGSGKSS 41
                                      69********96 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0023
                            DUF463   2 rlavTGLsraGKtvfitsLvnqLlaae 28 
                                        l vTG s++GK+++i    +++la++
  gi|298674741|ref|YP_003726491.1| 635 MLCVTGVSGSGKSTLINDTLHKVLAQK 661
                                       689**************9999998554 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.7      0.37   1.6e+02      32      41 ..     277     286 ..     251     293 .. 0.69
   2 ?    6.5   0.0     0.019       8.3      31      43 ..     404     416 ..     390     432 .. 0.87
   3 ?    2.1   0.0      0.43   1.9e+02       6      18 ..     755     767 ..     751     773 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.37
                                       E-TTTTTSSE CS
                         Anti-TRAP  32 eCPkCsGkgl 41 
                                        CP+C G g 
  gi|298674741|ref|YP_003726491.1| 277 ACPECHGLGT 286
                                       5999999775 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.019
                                       .E-TTTTTSSEEE CS
                         Anti-TRAP  31 leCPkCsGkglip 43 
                                        +CP+C+Gk l p
  gi|298674741|ref|YP_003726491.1| 404 KPCPECNGKRLKP 416
                                       59*******9865 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.43
                                       HHHCEEE-TTTTT CS
                         Anti-TRAP   6 lpeLEtkCdaCng 18 
                                       lp+  ++C+ Cng
  gi|298674741|ref|YP_003726491.1| 755 LPDVHVQCEVCNG 767
                                       8999********9 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0     0.002      0.86      55      85 ..     117     147 ..     108     150 .. 0.89
   2 ?   -0.7   0.1       3.5   1.5e+03      39      65 ..     251     283 ..     243     288 .. 0.62
   3 ?   -1.4   0.1       5.8   2.5e+03      56      67 ..     402     413 ..     389     418 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.002
                       Zn_Tnp_IS91  55 CksrhCpsCqkkateewlekqqeellpvpyr 85 
                                        ++rhCp C+++ + + +++  ++++++p+ 
  gi|298674741|ref|YP_003726491.1| 117 IGKRHCPYCGRRIEPQSIDQIVDNIMNLPHK 147
                                       579************************9995 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3.5
                       Zn_Tnp_IS91  39 ryeCeeCg....hekivyfsCksrh..CpsCqk 65 
                                       +++C+eCg    + +  +fs +s    Cp+C+ 
  gi|298674741|ref|YP_003726491.1| 251 KLACSECGigfeELEPPAFSFNSPQgaCPECHG 283
                                       567888865554334445555554444999976 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 5.8
                       Zn_Tnp_IS91  56 ksrhCpsCqkka 67 
                                        ++ Cp+C+ k+
  gi|298674741|ref|YP_003726491.1| 402 SNKPCPECNGKR 413
                                       567799999886 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0         8   3.4e+03      88      94 ..     121     127 ..     104     136 .. 0.72
   2 ?    7.6   0.0    0.0084       3.6      69     105 ..     250     294 ..     215     299 .. 0.79
   3 ?   -0.6   0.1       3.1   1.3e+03      86      98 ..     403     415 ..     385     418 .. 0.65
   4 ?   -0.1   0.2       2.2   9.2e+02      72      96 ..     738     769 ..     731     776 .. 0.61

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 8
                                       S-TTTSS CS
                              HypA  88 rCpkCgs 94 
                                       +Cp Cg+
  gi|298674741|ref|YP_003726491.1| 121 HCPYCGR 127
                                       5777765 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0084
                                       -EEEETTTS-EEECHHH.HH.......S-TTTSSS-EEEEESSSE CS
                              HypA  69 vkvrCreCgkefeleek.al.......rCpkCgsadveivsGeel 105
                                        k+ C+eCg  fe+ e  a+        Cp+C++ ++++    el
  gi|298674741|ref|YP_003726491.1| 250 EKLACSECGIGFEELEPpAFsfnspqgACPECHGLGTTMEFDPEL 294
                                       5789********955533346688899******999888665555 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 3.1
                                       HHS-TTTSSS-EE CS
                              HypA  86 alrCpkCgsadve 98 
                                       +  Cp+C++++++
  gi|298674741|ref|YP_003726491.1| 403 NKPCPECNGKRLK 415
                                       348****998765 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 2.2
                                       EETTTS-EEECHHH.HH......S-TTTSSS- CS
                              HypA  72 rCreCgkefeleek.al......rCpkCgsad 96 
                                       rC++C+ ++ ++ + ++      +C+ C++++
  gi|298674741|ref|YP_003726491.1| 738 RCETCSGDGIITIEmHFlpdvhvQCEVCNGKR 769
                                       67777766654332122344444777777665 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.069        29      12      24 ..     119     131 ..     113     142 .. 0.76
   2 ?    4.9   0.3     0.062        26      11      35 ..     250     282 ..     244     289 .. 0.77
   3 ?    0.7   0.1       1.3   5.6e+02      22      36 ..     397     411 ..     391     418 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.069
                               DZR  12 arfCseCgtklka 24 
                                       +r C++Cg ++++
  gi|298674741|ref|YP_003726491.1| 119 KRHCPYCGRRIEP 131
                                       5677777777764 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.062
                               DZR  11 darfCseCgtklkavaa........edrCpsCg 35 
                                       ++  CseCg   ++ +         + +Cp+C+
  gi|298674741|ref|YP_003726491.1| 250 EKLACSECGIGFEELEPpafsfnspQGACPECH 282
                                       5668*****8865444466899**99******8 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 1.3
                               DZR  22 lkavaaedrCpsCge 36 
                                       l+++ +++ Cp+C+ 
  gi|298674741|ref|YP_003726491.1| 397 LNKYISNKPCPECNG 411
                                       555555677777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (940 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       771  (0.043003); expected 358.6 (0.02)
Passed bias filter:                      725  (0.0404373); expected 358.6 (0.02)
Passed Vit filter:                       127  (0.0070835); expected 17.9 (0.001)
Passed Fwd filter:                        50  (0.00278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              42  [number of targets reported over threshold]
# CPU time: 0.78u 0.27s 00:00:01.05 Elapsed: 00:00:00.45
# Mc/sec: 6259.52
//
Query:       gi|298674742|ref|YP_003726492.1|  [L=79]
Description: hypothetical protein Metev_0796 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0024   18.0   0.0     0.0026   17.9   0.0    1.1  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit
  ------ inclusion threshold ------
       0.02   15.1   0.0      0.021   15.0   0.0    1.2  1  Bac_DNA_binding  Bacterial DNA-binding protein


Domain annotation for each model (and alignments):
>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.9e-07    0.0026       2      47 ..      10      54 ..       9      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.9e-07
                   HicB_lk_antitox  2 piaiekdedsaygvvvPdlpGcfsagdtleeaianakeaielhleg 47
                                      p+++++++ + y v  P ++ c   ++tl+ a++n+++ai++ + +
  gi|298674742|ref|YP_003726492.1| 10 PVTVHEEN-NGYLVKCPFFKDCEVRAETLDKALENIRDAIKTCIRD 54
                                      77888755.59*****************************998865 PP

>> Bac_DNA_binding  Bacterial DNA-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   2.3e-06     0.021      15      51 ..      31      67 ..       5      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.3e-06
                                      ---HHHHHHHHHHHHHHHHHHHHTT-EEEETTTEEEE CS
                   Bac_DNA_binding 15 gltkkdakrvveafldtikeaLkkgekvelsgFGtfk 51
                                      ++  ++  +++e++ d+ik ++  g++ ++++F+t+k
  gi|298674742|ref|YP_003726492.1| 31 EVRAETLDKALENIRDAIKTCIRDGNDYRIQKFCTIK 67
                                      567788999**************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       830  (0.0462937); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 584.31
//
Query:       gi|298674743|ref|YP_003726493.1|  [L=286]
Description: TatD-like deoxyribonuclease [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.5e-24   84.7   0.0    8.2e-24   84.3   0.0    1.1  1  TatD_DNase  TatD related DNase


Domain annotation for each model (and alignments):
>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.3   0.0   4.6e-28   8.2e-24       1     254 [.      12     280 ..      12     281 .. 0.85

  Alignments for each domain:
  == domain 1  score: 84.3 bits;  conditional E-value: 4.6e-28
                                       EEEEE-TTSCCCTTTHHHHHHHHHHTTEEEEEEE-SSG.................GGHHHHHHHHTT.TTTEEEEE- CS
                        TatD_DNase   1 iDaHcHldskefeedreeileraeeagvaavvvvgtss.................kdskavlelakkypnkvyavlG 60 
                                       +D+H+H+d         ++++ +++ag+++++ v+  s                  ++ ++++  +    k ++vlG
  gi|298674743|ref|YP_003726493.1|  12 TDNHMHIDP---RGRGLSAVKDFKNAGGTHIFLVTKPSwtlgvkiskpqdytavfDETIDITRQTEDIGVKSFPVLG 85 
                                       5********...457999*************98887778888888999998765434446777777789999***** PP

                                       --GGGGGC...........C.CCHHHHHHHH.HHCCCTSEEEEEEEEEET-CCCCCGHHHHHHHHHHHHHHHHHTTE CS
                        TatD_DNase  61 iHPnevde...........asedlleelkel.anvkhskvvaiGeiGLDyysreestkeaqeevFeeqlrlAkelkl 125
                                       +HP+e+++           a e +   l+ + ++v++  +v+i ++G+++y+++++ ++a +ev+e+ ++l +e+++
  gi|298674743|ref|YP_003726493.1|  86 VHPAEINNltdnlgmklddAVEVMKGGLDLAaQYVRDGYAVGI-KTGRPHYPVSDEVWRASNEVMEHGFSLGAEIDC 161
                                       *******988898887765455555889999999*********.********************************* PP

                                       EEEEEEES.-HHHHHHHHHHCGGCCS...EEEETT--S-HHHHHHHHHTTEEEEE-GGGGTTTTHHHHHHH..HHS- CS
                        TatD_DNase 126 plviHlrk.aeedlleilkeaaeaka...kvvlHsfsgsaeeakkflklgyyislsglltfknakelrelv..kavp 196
                                       ++++H+++  e +l +i+k+a+ +++   +vv H  s  +  +++   lg++ ++            +e+v  +  +
  gi|298674743|ref|YP_003726493.1| 162 AVQLHTESvGEPELNDITKKAKRSGInlhRVVKHY-SPPMVNICEN--LGIFPGVLS---------GKESVetAFKE 226
                                       ********8999**********9999998888887.5555555555..5*****997.........45555445668 PP

                                       GGGEEE---TTSSEECCCTT.SE--GGGHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHH CS
                        TatD_DNase 197 ldrlLiETDaPyltpkpyrg.krnepanvayvveklaelkaltleelaeitaeNakrlf 254
                                        +r+++ETD  y+++ p r+ ++  p++v++   k+ae    +++ + ++++eN ++++
  gi|298674743|ref|YP_003726493.1| 227 GSRFMMETD--YIDD-PQRPgAVMGPKTVPKRTLKMAEK--YDEDVFWKVHKENPEKVY 280
                                       9********..9999.99999*****************5..568889999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 2106.94
//
Query:       gi|298674744|ref|YP_003726494.1|  [L=344]
Description: 3-isopropylmalate dehydrogenase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.8e-87  291.6   0.0    8.9e-87  291.5   0.0    1.0  1  Iso_dh    Isocitrate/isopropylmalate dehydrogenase


Domain annotation for each model (and alignments):
>> Iso_dh  Isocitrate/isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  291.5   0.0   4.9e-91   8.9e-87       3     345 ..       6     330 ..       4     339 .. 0.93

  Alignments for each domain:
  == domain 1  score: 291.5 bits;  conditional E-value: 4.9e-91
                                       EEEEESTTHHHHHHHHHHHHHHHHHHHT-EEEEEE---THHHHHHHS..SSS-HHHHHHHHHSSEEEEEE---CSSS CS
                            Iso_dh   3 allegdgiGpevveaalkvlkaakekaglelefeevdvGgaaidetg..eplpeetleaikeadvvllgavgtpkek 77 
                                       a+++gdg+Gpe vea++kv++aak    +++ef  +++G+   +e g  + +p+et +++++ad+  +g+++tp + 
  gi|298674744|ref|YP_003726494.1|   6 AVIKGDGVGPELVEAMMKVVNAAK----TNVEFVPCEAGARWWEENGgnTLIPDETWNVLENADACFKGPTTTPGGI 78 
                                       79********************99....5678***********99988899***********************944 PP

                                       SSSHHHHHHHHHHHTTEEEEEEEEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEETTG.GGGEEEEE CS
                            Iso_dh  78 evrpengLlaLrkeldlfanlrpvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkgsifteevavdt 154
                                       +  p++  +++r+  +l+an+rp k f   + + pl      +vd+v+vRe+t+g+Yfgee ++++        + +
  gi|298674744|ref|YP_003726494.1|  79 G-TPKSVAVSIRQRYNLYANVRPTKTF--PNTNAPLG-----DVDFVCVREATEGLYFGEEAKITED-----AHIAI 142
                                       4.45555699*****************..44555555.....59*******************9997.....689** PP

                                       EEEEHHHHHHHHHHHHHHHHHTTTSEEEEEESTTTTHHHH.HHHHHHHHHHCCTTTTSEEEEEEHHHHHHHHHHSGG CS
                            Iso_dh 155 klyseeeieriaraafelAlkrgkkkvtlvdKanvlksse.lwrkiveevaeeeypdielehqlvDsaamqlvkspk 230
                                        ++++++ ++ia+++fe A++r+ ++v++++K+n+lk+++  + ++v++v e +ypdi + +  +D++a+ql+k+p+
  gi|298674744|ref|YP_003726494.1| 143 RKVTRTACRKIAEYSFEEAKRRNYDTVVAIHKSNILKQTDgVFLEEVHKVGE-NYPDIDIWEYHIDNIAQQLIKNPQ 218
                                       ****************************************************.***********************9 PP

                                       GGS..EEEE-HHHHHHHHHHHHHHTTSGCC-EEEEEETSS-EEEEESS---CCCTTSS-S-THHHHHHHHHHHHHTT CS
                            Iso_dh 231 qfd..VivtkNlfGDilSDeaaalvGslGllpSaslgekkvaifEavHGsapdiagkdkaNpiavilSaalmLrysl 305
                                       +f+  +++ +Nlf D++S e++al+Gs+Gl+ Sa++g +++a+fE++HGs p++ g+dk+ p+a+il+ a mL y l
  gi|298674744|ref|YP_003726494.1| 219 NFNnkILLSTNLFMDVISEECSALIGSIGLIYSANIG-DNFAMFEPAHGSSPKYKGQDKVDPVATILAGAWMLDY-L 293
                                       99889********************************.78***********************************.* PP

                                       T-HHHHHHHHHHHHHHHHH.TSCCHHHCTTSTCCCHHHHHH CS
                            Iso_dh 306 gleeaAdkiekAvekvlea.givTkDlageaakevstsefg 345
                                       +++++A++i +Ave+v+e+ +++T+Dl+g+a    + se+ 
  gi|298674744|ref|YP_003726494.1| 294 DEKKQAQAIFNAVENVIEEgKYITYDLGGSA----KLSEMA 330
                                       *******************8899******99....444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2474.78
//
Query:       gi|298674745|ref|YP_003726495.1|  [L=435]
Description: (R)-citramalate synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.8e-35  121.7   0.0    4.7e-35  121.4   0.0    1.1  1  HMGL-like  HMGL-like


Domain annotation for each model (and alignments):
>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.4   0.0   2.6e-39   4.7e-35       2     264 .]      21     289 ..      20     289 .. 0.89

  Alignments for each domain:
  == domain 1  score: 121.4 bits;  conditional E-value: 2.6e-39
                                       -EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT.-B..--EE-SSHHH CS
                         HMGL-like   2 vkivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavk.karilalvrarekd 77 
                                       v i+d+t RDG+q ++  ++ ++kl+i + L e+g++++E+ +    e d+++v +  + +  k++i++++r+ ekd
  gi|298674745|ref|YP_003726495.1|  21 VFISDSTIRDGSQMPGIVMKPSHKLQIYEYLHEIGIEKLETFVFN--ERDRKAVYEMFDRGYeKPEITGWARSSEKD 95 
                                       6799************************************97644..4699999998888751556*********** PP

                                       HHHHHH....TT-SEEEEEEES-HHHHHHHHSS.THHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--.HHHHHHHH CS
                         HMGL-like  78 ikaavealkgagakrvhvfiatselhlkaklkk.dreevakkaeeavkaarslgkdvelsledasrtd.leflaevv 152
                                       i++  +   + g ++  + +++s+ h+  k++  +re + +k  +a+++a ++g ++++ +ed +r+d  +f++ ++
  gi|298674745|ref|YP_003726495.1|  96 IDMVLD---VDGIEETGLLMSVSDSHIFDKMGLpSREAAEEKYLNAIQYAVDHGLRTRVHIEDMTRADnYNFVYPMI 169
                                       ******...89999999**********9999974777788899***********************9835899**** PP

                                       HHHHHHT-.SEEEEEETTS---HH.......HHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEE CS
                         HMGL-like 153 eaaeeaGa.triniaDtvGvltPn.......eaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvd 221
                                       e++ e+ + t++++ Dt+G+  P+           +i+ lk+++   + +++H H+d+Gl +an+la++  Ga++ +
  gi|298674745|ref|YP_003726495.1| 170 EKILEIDPeTTVRVCDTLGYGVPFpdvdepyGLPSMINHLKNELG-AINIETHIHDDFGLSLANSLAGYWYGANWSS 245
                                       ******88478********99765222221156789999999999.9****************************** PP

                                       EBTTS--SSBBB-BHHHHHHHHHHTT.-B----HHHHHHHHHHH CS
                         HMGL-like 222 gtvnGlGeraGnaaleelvaalealg.vdtgldlqklrsiaalv 264
                                        t +G+GeraGna +e+l + l ++     +++l+ + +ia+++
  gi|298674745|ref|YP_003726495.1| 246 LTFLGVGERAGNAEMEKLLLFLSQRVeGFEKYNLEPIADIANFI 289
                                       *********************99887677899999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3109.41
//
Query:       gi|298674746|ref|YP_003726496.1|  [L=167]
Description: amino acid-binding protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00025   20.7   0.3    0.00097   18.9   0.1    2.2  2  ACT       ACT domain
  ------ inclusion threshold ------
      0.028   14.7   0.3      0.054   13.9   0.3    1.4  1  CM_2      Chorismate mutase type II
      0.039   13.7   0.1      0.082   12.7   0.1    1.5  1  ACT_7     ACT domain
      0.067   13.8   0.1       0.33   11.6   0.0    2.0  2  ACT_4     ACT domain


Domain annotation for each model (and alignments):
>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0         1   4.6e+03      16      28 ..      17      29 ..      17      31 .. 0.79
   2 !   18.9   0.1   2.2e-07   0.00097      12      64 ..     107     157 ..     105     160 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1
                                      HHHHHHHHTTSEE CS
                               ACT 16 rvfgaladrgiNi 28
                                      +v+++l +rg+ +
  gi|298674746|ref|YP_003726496.1| 17 KVLRILFERGFQV 29
                                      6999999999755 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 2.2e-07
                                       THHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHT CS
                               ACT  12 GlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkk 64 
                                       G+La+v++++a+++i+i+ + +        ++  ++i++d +++  +++++ k
  gi|298674746|ref|YP_003726496.1| 107 GILAEVATVIANHDISIRQAVSDDPYF--KDEPKLTIITDSKVPGYLVDEILK 157
                                       9*****************998876644..466666666666666555555555 PP

>> CM_2  Chorismate mutase type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.3   1.2e-05     0.054      10      68 ..      17      80 ..      15      82 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.2e-05
                                      HHHHHHHHHHHHHHHHHHHHHHCTS.GSS-HHHHHHHHHHHHHHH.....S-HHHHHHHHHHHHH CS
                              CM_2 10 eileLLaeRaelakevgeyKkeegl.pvydpeReaevlerleega.....ldeeaierifreiis 68
                                      + l++L eR   +++  ++K+ +   p  + +Rea v +r+ + a     l++e++++if++i s
  gi|298674746|ref|YP_003726496.1| 17 KVLRILFERGFQVDNEKKVKSGKIEiPHTQLAREANVDRRVID-AttdtiLKDEMLKEIFQNITS 80
                                      568889999999999999**8555559****************.325668************986 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   1.8e-05     0.082      19      40 ..     104     125 ..      94     130 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.8e-05
                                       SS--HHHHHHHHHHTTT---EE CS
                             ACT_7  19 dvtGivaklaspLaeagIsifq 40 
                                        +tGi+a++a++ a+++Isi q
  gi|298674746|ref|YP_003726496.1| 104 ASTGILAEVATVIANHDISIRQ 125
                                       58*****************976 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.76   3.4e+03      60      78 ..      69      87 ..      64      88 .. 0.72
   2 ?   11.6   0.0   7.3e-05      0.33      17      36 ..     106     125 ..     102     131 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.76
                             ACT_4 60 ehLsrviakLraipgVisV 78
                                      e L+++ +++ +ip   +V
  gi|298674746|ref|YP_003726496.1| 69 EMLKEIFQNITSIPFLRDV 87
                                      5678888888888766555 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 7.3e-05
                             ACT_4  17 kglLaditqviseekanivs 36 
                                       +g+La++++vi++++++i+ 
  gi|298674746|ref|YP_003726496.1| 106 TGILAEVATVIANHDISIRQ 125
                                       79****************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1225.61
//
Query:       gi|298674747|ref|YP_003726497.1|  [L=396]
Description: geranylgeranyl reductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-14   54.5   3.6    5.4e-12   45.6   3.6    3.0  1  FAD_binding_3   FAD binding domain
    5.8e-13   49.0   0.3      8e-13   48.5   0.3    1.2  1  FAD_oxidored    FAD dependent oxidoreductase
    1.5e-11   44.0   0.2      3e-09   36.4   0.1    2.1  2  Lycopene_cycl   Lycopene cyclase protein
    2.5e-10   39.8   0.0    3.5e-06   26.1   0.0    2.1  2  Trp_halogenase  Tryptophan halogenase
      1e-09   38.1   1.8    2.7e-09   36.7   1.8    1.7  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    3.1e-08   33.6   4.3     0.0025   17.5   1.5    2.3  2  DAO             FAD dependent oxidoreductase
    3.1e-07   29.9   2.0    5.1e-07   29.2   2.0    1.3  1  Thi4            Thi4 family
      2e-06   26.8   2.1    2.6e-06   26.4   0.1    2.0  2  HI0933_like     HI0933-like protein
      4e-05   22.9   1.1      6e-05   22.3   0.3    1.7  2  GIDA            Glucose inhibited division protein A
    0.00011   22.4   0.2     0.0003   21.0   0.2    1.8  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
     0.0011   18.2   0.9     0.0011   18.2   0.9    1.9  2  FAD_binding_2   FAD binding domain


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   3.6   3.3e-15   5.4e-12       2     304 ..       3     282 ..       2     287 .. 0.69

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 3.3e-15
                                       EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSS.CCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEE CS
                     FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrstt.vvlpradglnqrtmellrqlGledrilaegapnelmgealy 77 
                                       +dV++VGaGpaG ++++  +  G +v+l+e +++  ++ +  + l++r +   +    +     + + n++ g + y
  gi|298674747|ref|YP_003726497.1|   3 YDVVVVGAGPAGSIASRYAALNGASVLLIEEHQSIgSPVGCTGLLSTRAVSECDLEPSD-----DFVLNNVKGAFIY 74 
                                       79****************************99875144446666666666554433333.....3344566788888 PP

                                       EECCCCCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEE CS
                     FAD_binding_3  78 nelsdtpkaradlelesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvr 154
                                        +        + l+++ + ++ +v++ + ++r L++ a+e g+++   t+ +++e+  +  +  v   ++g ++t++
  gi|298674747|ref|YP_003726497.1|  75 ST------DGIPLQIDGGQTKAYVVSRKTFDRKLAQTAVESGVDILLRTKAVGIENSSSIQKLHV--LKEGVKQTIK 143
                                       88......45566666999*********************************9888777755555..4569****** PP

                                       EEEEEE--GTT-HHHHHHTGGEEEEEEEEEEEEEEEEEEC-SCCCTTCCEEEEECCTTEEEEEECCETEEEEEEEEE CS
                     FAD_binding_3 155 akYlvGaDGgrStvrktlgiefegeetvyeagvldvlfdadlsdiveplvlilsaesrgvmviPlentlerfyvqve 231
                                       a  ++GaDG rS + k +g+     e+++    +d + +++ s++v              ++ P + +   f + v+
  gi|298674747|ref|YP_003726497.1| 144 AHVVIGADGIRSNISKMVGLG--NVEKIVSGIQVDGVYESKNSEFV--------------ELFPGSYAPGFFAWTVP 204
                                       *******************87..33444344444444455444444..............44444444444444444 PP

                                       CCE-GGGSCCCHHHHHHHHHHHHHHTTS.....SCEEEEEEEEEEEEEEEEESSSEETTEEE-GGGTEEE-STTSHH CS
                     FAD_binding_3 232 araekeersekfteeevkarlreivgek.....tldveieevsawtvaqrvaekyrkgrvflaGDAaHihpPtgGqG 303
                                       +++++++    +te ++++ l+ +++++     + + ++ ++ +  +   + +k   + v ++GDAa  + Pt G G
  gi|298674747|ref|YP_003726497.1| 205 LSKSISRIGLGTTEPDAVKYLNHLIKSNpeiseRYQGSMMDFVVGAIPLGTLDKTFTDGVIVVGDAAGQVKPTSGGG 281
                                       44444444444444444444444443321000033445555555556666789999999999999999999999988 PP

                                       H CS
                     FAD_binding_3 304 l 304
                                       +
  gi|298674747|ref|YP_003726497.1| 282 I 282
                                       6 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.3   4.9e-16     8e-13       1     142 [.       4     150 ..       4     153 .. 0.84

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 4.9e-16
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlG......Glltsglvatdignkaeeqvvtgiareflerlrqrg 71 
                                       DvvVvG+gpaG +A   Aa +Ga+vlL+ee++ +G      Gll+  +v+  +   + ++v + + + f+   +   
  gi|298674747|ref|YP_003726497.1|   4 DVVVVGAGPAGSIASRYAALNGASVLLIEEHQSIGspvgctGLLSTRAVSECDLEPSDDFVLNNVKGAFIYSTDG-- 78 
                                       9**********************************9999999999999988888777889999999999999844.. PP

                      FAD_oxidored  72 garlk...krskwntfepevakavleemlaeagvtvllntrlvevekegkriesvtveskeg.rktirAkvfiDA 142
                                         +l+    ++k  ++  +++ + l +   e+gv++ll t++v++e +   i+++ v  keg ++ti+A+v+i A
  gi|298674747|ref|YP_003726497.1|  79 -IPLQidgGQTKAYVVSRKTFDRKLAQTAVESGVDILLRTKAVGIENSS-SIQKLHVL-KEGvKQTIKAHVVIGA 150
                                       .3222211222224688888888888888899***************95.9******6.6777*********976 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.1   1.8e-12     3e-09       1     144 [.       4     156 ..       4     176 .. 0.85
   2 !    5.7   0.0    0.0039       6.4     241     296 ..     249     301 ..     243     327 .. 0.68

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 1.8e-12
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnnyvWsdefedlga.....leecvehsWsgtivylddg 72 
                                       Dvvv+GaGpAg s+A r  +a  g +v+lie  +s+  p   +     +++++      +++v    +g+ +y  dg
  gi|298674747|ref|YP_003726497.1|   4 DVVVVGAGPAG-SIASRY-AALNGASVLLIEEHQSIGSPVGCTGLLSTRAVSEcdlepSDDFVLNNVKGAFIYSTDG 78 
                                       9**********.89***9.8999********9999877766666666666666665558999*************** PP

                     Lycopene_cycl  73 kkillg....raYgrvsskrlkeellerlvengv.klleakvesveeeeageslvvleggr..kirarlvvdargla 142
                                        + +++    +aY  vs+k + ++l++  ve+gv +ll+ k+  +e+++  ++l vl++g+  +i+a +v+ a g+ 
  gi|298674747|ref|YP_003726497.1|  79 IPLQIDggqtKAY-VVSRKTFDRKLAQTAVESGVdILLRTKAVGIENSSSIQKLHVLKEGVkqTIKAHVVIGADGIR 154
                                       ***9999986666.69**************99984578************99999999998799***********55 PP

                     Lycopene_cycl 143 sl 144
                                       s+
  gi|298674747|ref|YP_003726497.1| 155 SN 156
                                       43 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0039
                     Lycopene_cycl 241 gviPvtlggslprleqkvlaiGaaaglvhPaTGYsvarslaeapllasaiaaalre 296
                                       g iP+  g   + +   v+ +G aag v+P+ G  +      a+ +a  +aa  ++
  gi|298674747|ref|YP_003726497.1| 249 GAIPL--GTLDKTFTDGVIVVGDAAGQVKPTSGGGIYPGAVCAK-IAGEVAAKSAL 301
                                       67898..6656666677***************977776666666.44444444333 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.2   5.3e-05     0.086       1      61 [.       4      62 ..       4      78 .. 0.77
   2 !   26.1   0.0   2.2e-09   3.5e-06     147     337 ..      89     283 ..      73     336 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.3e-05
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS---SS-EE--THHHH.THHHHT--HH CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlveseeigtvgvGeatipsirk.llrlLgidee 61
                                      ++v+vG+G+aG++a  + a  +   ++v+l+e  +     vG   + s+r      L+ +++
  gi|298674747|ref|YP_003726497.1|  4 DVVVVGAGPAGSIASRYAALNG---ASVLLIEEHQSIGSPVGCTGLLSTRAvSECDLEPSDD 62
                                      69************99987776...99*****999888889987777777744444555555 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 2.2e-09
                                       -EEEE-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETT...S-EEE-SEEEE-SGGG-IIIIIIT-- CS
                    Trp_halogenase 147 yAyhldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrled...greveadlfiDcsGfrgllieqaLkt 220
                                        Ay + ++ +++ L + a + Gv+++    + v ++++ ++++l++ +    ++++a  +i + G r+ + + +  +
  gi|298674747|ref|YP_003726497.1|  89 KAYVVSRKTFDRKLAQTAVESGVDILLR-TKAVGIENSSSIQKLHVLKegvKQTIKAHVVIGADGIRSNISKMVGLG 164
                                       69**********************9875.56999*********98765466699******************99777 PP

                                       -EEE-TTT----EEEEEEEE--H---SSEEEEE-SSEEEEEEEETTEEEE.EEEE-TTTS-HHHHHHHHHHHCT--T CS
                    Trp_halogenase 221 gfedwsdvLltdrAlavqveseelvepytrataekaGWtWkiPLqhrlgn.GyvyssahadddeAlaellaeldgkl 296
                                       ++e++   + +d   + + +++e ve + ++ a      W +PL+++++  G+       d+ + l++l++  + ++
  gi|298674747|ref|YP_003726497.1| 165 NVEKIVSGIQVDG--VYESKNSEFVELFPGSYAPGF-FAWTVPLSKSISRiGLGTT--EPDAVKYLNHLIKSNPEIS 236
                                       7777777776664..557788889999999998643.68*********99676544..4455777888888888777 PP

                                       TTS-.EEEE---EE.....ES-SEETTEEE-CCCTEE--CCCS-HHH CS
                    Trp_halogenase 297 eaep.rkirfttGr.....rkqawvknvvalGlasgfvePlestsih 337
                                       e+ + +++ f +G        +++  +v+ +G+a+g v P  + +i+
  gi|298674747|ref|YP_003726497.1| 237 ERYQgSMMDFVVGAiplgtLDKTFTDGVIVVGDAAGQVKPTSGGGIY 283
                                       777779*******999998999*******************999998 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   1.8   1.7e-12   2.7e-09       1     142 [.       3     185 ..       3     217 .. 0.80

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 1.7e-12
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................... RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias.................... 57 
                                       +dvvv+G+GpAG  a++++a +ga v+l+  e++   g ++  + ll++++  e  +                    
  gi|298674747|ref|YP_003726497.1|   3 YDVVVVGAGPAGSIASRYAALNGASVLLI--EEHQSIGSPVGCTGLLSTRAVSECDLepsddfvlnnvkgafiystd 77 
                                       69***************************..444555556666666666666655556667789999********** PP

                                       .........................HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---E CS
                                       .........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 .........................evvkklnqgielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGs 109
                                                                   + +++g++ ll++++v+i++ +   kl  +keg +++i+++ ++ A G 
  gi|298674747|ref|YP_003726497.1|  78 giplqidggqtkayvvsrktfdrklA-QTAVESGVDILLRTKAVGIENSSSIQKLHVLKEGVKQTIKAHVVIGADGI 153
                                       **********************9863.3567889*************988555555578899*************** PP

                                       EE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 110 sprdlgipGvaenvgklvrtldsaealklkllp 142
                                       ++++ ++ G+  nv k v+ ++ +  +++k+ +
  gi|298674747|ref|YP_003726497.1| 154 RSNISKMVGL-GNVEKIVSGIQVDGVYESKNSE 185
                                       *****99999.8888888988888888888776 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   1.5   1.5e-06    0.0025       1      38 [.       4      41 ..       4      64 .. 0.85
   2 !   16.6   0.0   2.7e-06    0.0044     146     210 ..      96     161 ..      51     185 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.5e-06
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGG CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSg 38
                                      dvv++G+G +G+ + +++a  g  V+l+e +  +g  +  
  gi|298674747|ref|YP_003726497.1|  4 DVVVVGAGPAGSIASRYAALNGasVLLIEEHQSIG--SPV 41
                                      9********************9*********7776..333 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 2.7e-06
                                       HHHHHHHHHHHHHTT-EEEESECEEEEEEEE..TCEEEEEEECTEEEEEEEE..EEE--GGGHHHHHTT CS
                               DAO 146 akltaalaraaealGveilegtevtgleeed..gkvwgverttpgendaada..vVnaaGawsdllgll 210
                                         + + la++a + Gv+il++t+++g+e+ +   k  +v   ++g +++++a  v+ a G+ s++++++
  gi|298674747|ref|YP_003726497.1|  96 KTFDRKLAQTAVESGVDILLRTKAVGIENSSsiQK-LHV--LKEGVKQTIKAhvVIGADGIRSNISKMV 161
                                       445567*********************88555333.333..3336664445554888999999866544 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   2.0   3.1e-10   5.1e-07      17     176 ..       2     161 ..       1     185 [. 0.80

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 3.1e-10
                                       EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBSEEEEE...TTTHHH.HHHTT---EEESS CS
                              Thi4  17 esDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfsaivvr...kpakel.Ldelgikyedegd 89 
                                       + Dvv+vGaG++G  a++y a + +  v+++e++ s+G  ++  G l ++ v +   +p++++ L+++  ++  + d
  gi|298674747|ref|YP_003726497.1|   2 KYDVVVVGAGPAGSIASRYAALN-GASVLLIEEHQSIGSPVGCTGLLSTRAVSEcdlEPSDDFvLNNVKGAFIYSTD 77 
                                       67*********************.***********************9999987444567665499**999999999 PP

                                       EEEES.EHHHHHHHHHHHHHTSTTEEEEESEEEE...EEEEETBTEEEEEEEEEHHHHTCTTTSS.-B-EEEEEEEE CS
                              Thi4  90 yvvvk.daalftstllskvlqlanvkllnavave...DlivregegvaGvvinwtlvelahdtqscvDPlvirakvv 162
                                       ++  + d  +  + ++s+     + kl   +ave   D+++r  + v G + n++++++ h  +  v  ++i+a+vv
  gi|298674747|ref|YP_003726497.1|  78 GIPLQiDGGQTKAYVVSRKTF--DRKL-AQTAVEsgvDILLRT-KAV-G-IENSSSIQKLHVLKEGVK-QTIKAHVV 147
                                       986653888999999997655..4555.456666556999999.443.4.57999******9999986.79****** PP

                                       EE--GSSSTTTTHH CS
                              Thi4 163 vdatGhdgeivavv 176
                                       + a G  ++i ++v
  gi|298674747|ref|YP_003726497.1| 148 IGADGIRSNISKMV 161
                                       *****999998876 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.1   1.6e-09   2.6e-06       1      43 [.       3      45 ..       3      46 .. 0.95
   2 ?   -1.1   0.2      0.35   5.7e+02     114     163 ..     101     152 ..      86     159 .. 0.72

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 1.6e-09
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHCG CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklgrKilisG 43
                                      +dv+v+G+G+AG  a+  aa +g++Vll+e+ +++g+ +  +G
  gi|298674747|ref|YP_003726497.1|  3 YDVVVVGAGPAGSIASRYAALNGASVLLIEEHQSIGSPVGCTG 45
                                      59**********************************9888887 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.35
                                       HHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE....TTEEEEESEEEE--- CS
                       HI0933_like 114 allkelkeagvklrletevksvekeedgkfrvkt.k..seeeleadklvlAtG 163
                                        l +++ e+gv++ l+t+  ++e++++   ++++ k   +++++a+ ++ A G
  gi|298674747|ref|YP_003726497.1| 101 KLAQTAVESGVDILLRTKAVGIENSSSI-QKLHVlKegVKQTIKAHVVIGADG 152
                                       5778888999999999999999765543.455554322456777777776666 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.3   3.7e-08     6e-05       1     149 [.       4     152 ..       4     196 .. 0.64
   2 ?   -2.5   0.0       1.2     2e+03     223     276 ..     321     373 ..     308     378 .. 0.67

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 3.7e-08
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SSSSEEE-TTHHHHHHH......HHHHT-SHHHHHHHHE CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGakvlLithkldtiaelsCnpsiggiakgllvrE......idalggliikaadkag 71 
                                       dv+V+G+G AG+ A+  aa  Ga+vlLi ++ +    ++C   +   a+++   E      +++++g  i  +d   
  gi|298674747|ref|YP_003726497.1|   4 DVVVVGAGPAGSIASRYAALNGASVLLIEEHQSIGSPVGCTGLLSTRAVSECDLEpsddfvLNNVKGAFIYSTDGIP 80 
                                       79**************************7776666667788766666666655553344445566666666666666 PP

                                       EEEEEESTTS-CCC-EEEEEE-HHHHHHHHHHH.HHTSTTEEEEES-EEEEEECT..TEEEEEEETTS-EEEECEEE CS
                              GIDA  72 iqfrilNrskGpavralraqvdrelyskevtek.lenepnleiieeeveelivee..kkvkgvvtedgetikakavv 145
                                       +q++        + +a    v r+++ +++ ++ +e+  ++ ++  ++  ++ ++  +k+++++   ++tika++v+
  gi|298674747|ref|YP_003726497.1|  81 LQIDG------GQTKAY--VVSRKTFDRKLAQTaVESGVDILLR-TKAVGIENSSsiQKLHVLKEGVKQTIKAHVVI 148
                                       64443......333333..5555555555443313333333333.33333422223445555555556666666666 PP

                                       E--T CS
                              GIDA 146 iatG 149
                                        a G
  gi|298674747|ref|YP_003726497.1| 149 GADG 152
                                       6655 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.2
                                       SSSST.CG----EEEEE--HHHHHHHHCTCCC-T.T----B--S-CCC-SSTCCC CS
                              GIDA 223 lnkpl.nkeqvecfltatneathkiikenlkksaklfegcieelgprycpsiedk 276
                                       + k+l +  ++++f+t++++++ + +   +++ +k+  ++i++ g    psi  k
  gi|298674747|ref|YP_003726497.1| 321 IGKELdTGMKIHEFITNLKDEQLNDLLHSMNN-PKIL-DTITKYGDMDHPSILVK 373
                                       55555345677888888888887777777775.5444.47888888888888765 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.2   1.8e-07    0.0003       1      32 [.       7      38 ..       7      58 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.8e-07
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlG 32
                                      +vGaG +G+ a +++a +g++vll+e ++++G
  gi|298674747|ref|YP_003726497.1|  7 VVGAGPAGSIASRYAALNGASVLLIEEHQSIG 38
                                      8******************************9 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.9   6.5e-07    0.0011       1      36 [.       4      39 ..       4      49 .. 0.93
   2 ?   -0.2   0.1      0.25   4.1e+02     147     227 ..     102     177 ..      90     179 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 6.5e-07
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                                      Dv+V+G+G AG  A+  aa +G++v+++e  q+ g+
  gi|298674747|ref|YP_003726497.1|  4 DVVVVGAGPAGSIASRYAALNGASVLLIEEHQSIGS 39
                                      9*****************************999776 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.25
                                       HHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG..........GSSSBSSGT CS
                     FAD_binding_2 147 lvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgrallkellgaaaeaettnap 223
                                       l+++a + gvd++ rt+a+ +  ++  +    v   ++g +++i+a+ v+ a g  ++  + ++ g ++ +++++  
  gi|298674747|ref|YP_003726497.1| 102 LAQTAVESGVDILLRTKAVGI-ENSSSIQKLHVL--KEGVKQTIKAHVVIGADGIRSN--ISKMVGLGNVEKIVSGI 173
                                       677788888999999999999.335588888888..9999999999888888877776..66666666666666666 PP

                                       T-S- CS
                     FAD_binding_2 224 avtG 227
                                       +v+G
  gi|298674747|ref|YP_003726497.1| 174 QVDG 177
                                       6655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 2623.55
//
Query:       gi|298674748|ref|YP_003726498.1|  [L=411]
Description: adenosylhomocysteinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-57  195.6   0.0      4e-30  105.0   0.0    2.0  2  AdoHcyase      S-adenosyl-L-homocysteine hydrolase
    3.6e-51  173.4   1.7    4.3e-51  173.2   0.6    1.7  2  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
      3e-08   33.2   0.1    5.6e-08   32.3   0.1    1.4  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    5.6e-06   26.0   0.0    9.8e-06   25.2   0.0    1.4  1  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
  ------ inclusion threshold ------
      0.048   13.0   0.5       0.12   11.6   0.5    1.7  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
       0.13   11.7   0.0       0.38   10.1   0.0    1.7  2  GSH-S_ATP      Prokaryotic glutathione synthetase, ATP-grasp 


Domain annotation for each model (and alignments):
>> AdoHcyase  S-adenosyl-L-homocysteine hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.0   0.0   1.3e-33     4e-30       8     140 ..       5     133 ..       1     138 [. 0.94
   2 !   89.6   0.0   6.3e-29   1.9e-25     175     286 ..     135     405 ..     132     410 .. 0.98

  Alignments for each domain:
  == domain 1  score: 105.0 bits;  conditional E-value: 1.3e-33
                                       GGHHHHHHHHHHHHCC-HHHHHHHHHCTTT-TTTT-EEEEES--SHHHHHHHHHHHHTT-EEEEE-SSTTT--HHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase   8 slaefGrkeielaekempglmalreeyaeekplkgariaGslhmtiqtavLietLvalGaevrWasCnifstqdeaa 84 
                                       +l e G+++ie a + mp l  +r+ +a+ekplkg ria +lh+ ++tavL+etL + Gae+  + Cn  stqd++a
  gi|298674748|ref|YP_003726498.1|   5 TLLESGNQKIEWARNHMPVLSIIRDGFASEKPLKGCRIAMALHVEAKTAVLVETLASGGAEIAITGCNPLSTQDDVA 81 
                                       56789************************************************************************ PP

                                       HHHCCT.TEEEE--TT--HHHHHHHHHHCHS-SSTS-S-SEEEESSSHHHHHHHHHH CS
                                       xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase  85 aaiaea.gvpvfawkgetleeywwcieqalkwaedekepnlilDdGGDltllvhkgv 140
                                       aa+ ++ +v+ +a    + +ey + i+++l+      +p++ +DdGGDl  ++hk  
  gi|298674748|ref|YP_003726498.1|  82 AALDTRdNVSCYAKYNASRSEYYESINKVLDI-----NPDITVDDGGDLIFTLHKTR 133
                                       ***9877***********************66.....7****************954 PP

  == domain 2  score: 89.6 bits;  conditional E-value: 6.3e-29
                                       CCHCC--EEEE-SHHHHHHHHHHHHTT---SEEEESTTSHHHCTTH............................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................... RF
                         AdoHcyase 175 ellkkikGvseetttGvhrLyelakkgkLlvpainvndsvtkskfD............................... 220
                                       ell+ ikG +eetttGv rL +++k++ L++p i vn++ tk  fD                               
  gi|298674748|ref|YP_003726498.1| 135 ELLSGIKGGTEETTTGVYRLDSMSKDNALKMPVIAVNNAFTKYLFDnrygtgqstwdainrttnllvagkdvvvagy 211
                                       67899************************************************************************ PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                         AdoHcyase 221 ............................................................................. 220
                                                                                                                    
  gi|298674748|ref|YP_003726498.1| 212 gwcgrgcsmrakglganvivtevnpvralearmdgyrvmtmdeaakigeifitttgnvsvltrdhfklmkdgvilan 288
                                       ***************************************************************************** PP

                                       .....................................................S-HHHHHHHHHHHHHHHHHHHHTT CS
                                       .....................................................xxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase 221 .....................................................hpsfvmsasftnqvlaqielfkke 244
                                                                                            hp+ vm++sf+nq+l   +l ++ 
  gi|298674748|ref|YP_003726498.1| 289 sghfnvemnleelesmsktvrtvrenikeyhlgdrriylladgrlvnlaagdgHPAEVMDMSFSNQALCIRHLVDN- 364
                                       *************************************************************************995. PP

                                       SSS-SSEEE--CHHHHHHHHHCCCCCT-------HHHHHCCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase 245 kkyekkvyvlpkklDekvarlhleklgaklteltkeqaeyig 286
                                        + + +v+ +p ++D ++a+l+l++lg++++elt+eq +y+ 
  gi|298674748|ref|YP_003726498.1| 365 -DLDIDVHAVPPEIDTYIAELKLKALGIEIDELTTEQEKYMR 405
                                       .56999**********************************85 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       2.9   8.7e+03      41      58 ..      58      75 ..      55      84 .. 0.75
   2 !  173.2   0.6   1.4e-54   4.3e-51       1     160 [.     181     339 ..     181     341 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.9
                                      HHHHCT-EEEEE-S-HHH CS
                     AdoHcyase_NAD 41 slkglGarvivtevdPic 58
                                      +l + Ga + +t  +P++
  gi|298674748|ref|YP_003726498.1| 58 TLASGGAEIAITGCNPLS 75
                                      567778888888888876 PP

  == domain 2  score: 173.2 bits;  conditional E-value: 1.4e-54
                                       HHHHHCCCCCHHHHHHH-S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTT CS
                     AdoHcyase_NAD   1 nlygcreslvdgikratdvllaGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvk 77 
                                       n yg+ +s  d+i+r+t++l+aGk +vvaGyG  G+Gc+   kglGa vivtev+P+ al a m+G++v+t++e++k
  gi|298674748|ref|YP_003726498.1| 181 NRYGTGQSTWDAINRTTNLLVAGKDVVVAGYGWCGRGCSMRAKGLGANVIVTEVNPVRALEARMDGYRVMTMDEAAK 257
                                       78*************************************************************************** PP

                                       T-SEEEE-SSSSSSB-HHHHCCS-TTEEEEE-SSTTTTBTHHHHHTTT-EEEEEETTEEEEE-TTS-EEEEEGGGSB CS
                     AdoHcyase_NAD  78 kadivvtttGnkdiitlehlkkmkddaivcniGhfdseidvaaleanalkkeevkpqvdrvtlkdgkkiillaeGrl 154
                                        ++i++tttGn  ++t++h+k mkd +i++n Ghf+ e+++++le++++++ +v+ ++++++l d ++i lla+Grl
  gi|298674748|ref|YP_003726498.1| 258 IGEIFITTTGNVSVLTRDHFKLMKDGVILANSGHFNVEMNLEELESMSKTVRTVRENIKEYHLGD-RRIYLLADGRL 333
                                       ***************************************************************98.6799******* PP

                                       CHHHTS CS
                     AdoHcyase_NAD 155 lnlgca 160
                                       +nl++ 
  gi|298674748|ref|YP_003726498.1| 334 VNLAAG 339
                                       ***976 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.1   1.9e-11   5.6e-08      20     127 ..     187     290 ..     168     297 .. 0.88

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 1.9e-11
                                       TTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEE CS
                      2-Hacid_dh_C  20 egewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivs 96 
                                       + +w++ ++++   ++gk v + G+G  G+    r+k++g++vi++++++ +  e++  g+++++++e+ +  +i +
  gi|298674748|ref|YP_003726498.1| 187 QSTWDAINRTTNLLVAGKDVVVAGYGWCGRGCSMRAKGLGANVIVTEVNPVRALEARMDGYRVMTMDEAAKIGEIFI 263
                                       567777778888899**********************************9998899999**********99888877 PP

                                       E-S--STTTTTSBSHHHHHCSTTTEEEEESS CS
                      2-Hacid_dh_C  97 lhlpltpetrhlinaeelakmkkgailiNta 127
                                            t  +  +++++++++mk+g+il N +
  gi|298674748|ref|YP_003726498.1| 264 T----TTGNVSVLTRDHFKLMKDGVILANSG 290
                                       5....556999*****************987 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   3.3e-09   9.8e-06       2     103 ..     201     298 ..     200     310 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 3.3e-09
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHH CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevye 78 
                                       + gk ++v GyG  G+  ++  +  g +v+v+  +    + +A+ +g++v+t++ea+k  ++ ++ +    + +v++
  gi|298674748|ref|YP_003726498.1| 201 VAGKDVVVAGYGWCGRGCSMRAKGLGANVIVTEVNPV-RALEARMDGYRVMTMDEAAKIGEIFITTT---GNVSVLT 273
                                       5799*************9999999999***9988887.6778****************999876655...5668999 PP

                                       HHTGGG--TT-EEEESSSHHHHTTS CS
                              IlvN  79 eeiepnlkegkalafahGfnihfgl 103
                                       ++  + +k+g +la +  fn+ ++l
  gi|298674748|ref|YP_003726498.1| 274 RDHFKLMKDGVILANSGHFNVEMNL 298
                                       999999**********99**99875 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.5   4.1e-05      0.12      29      75 ..     204     249 ..     196     317 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.1e-05
                                       -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCEC CS
                       AlaDh_PNT_C  29 akvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfv 75 
                                         v+v G G  G      akglga+V v++v+p r+ + +  g + v
  gi|298674748|ref|YP_003726498.1| 204 KDVVVAGYGWCGRGCSMRAKGLGANVIVTEVNPVRALEARMDGYR-V 249
                                       579******************************988776655555.3 PP

>> GSH-S_ATP  Prokaryotic glutathione synthetase, ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.3   3.9e+03      83     121 ..      61      98 ..      54     111 .. 0.74
   2 ?   10.1   0.0   0.00013      0.38      45      97 ..     282     335 ..     270     342 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.3
                                       G-EEEEEEETTEE-SEEEEEE--SS-S---GGGTSCEEE CS
                         GSH-S_ATP  83 eGDkRillvdGepigyalaRvpaegevRsnlaaggraea 121
                                       +G   i +   +p++ +   v+a+ ++R n++  ++ +a
  gi|298674748|ref|YP_003726498.1|  61 SGGAEIAITGCNPLS-TQDDVAAALDTRDNVSCYAKYNA 98 
                                       566666677777777.77788999999999887776655 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00013
                                       TT-EEE-TT-TTHHHHHHHHTTTTTS-EEEEE--GGGGG-EEEEEEE.TTEE-S CS
                         GSH-S_ATP  45 egvfrvkksdpnlksilellteegkepviaqrylpeikeGDkRillv.dGepig 97 
                                       +gv+  ++ + n++  le l +++k+   + + ++e + GD+Ri l+ dG+ ++
  gi|298674748|ref|YP_003726498.1| 282 DGVILANSGHFNVEMNLEELESMSKTVRTVRENIKEYHLGDRRIYLLaDGRLVN 335
                                       5899999999**********************************6543898887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 2536.77
//
Query:       gi|298674749|ref|YP_003726499.1|  [L=431]
Description: amidohydrolase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-75  253.5   0.2      4e-75  253.3   0.2    1.1  1  Amidohydro_1  Amidohydrolase family
    3.8e-24   86.0   0.3    8.9e-16   58.4   0.0    2.3  2  Amidohydro_3  Amidohydrolase family
    0.00086   18.7   0.0     0.0015   17.9   0.0    1.3  1  A_deaminase   Adenosine/AMP deaminase


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  253.3   0.2   6.8e-79     4e-75       1     343 [.      52     399 ..      52     400 .. 0.93

  Alignments for each domain:
  == domain 1  score: 253.3 bits;  conditional E-value: 6.8e-79
                                       EEEE-EEEEEEECETTECSSS....GHHHHH..........STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHH CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrga....tledwl..........vppetaaealesgiktalksGtttvadmgattstgi 63 
                                       +v+PG++++H+H+ ++l+rg     +l++wl          +++e+a+ +++ ++ +++ksGtt++adm++    ++
  gi|298674749|ref|YP_003726499.1|  52 VVMPGFVNTHTHAAMTLFRGYaddiPLDEWLknyiwpaeehLTDEDAYIGTKLACLEMIKSGTTSFADMYI----HM 124
                                       69*********************************************************************....9* PP

                                       HHHHHHHHTSSSEEEEEEESSEGGS...GCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHH CS
                      Amidohydro_1  64 ealleaaeelplglrilggkvsldr...gsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkea 137
                                       +++++a+++   g+r+ ++++ +d    +sa++++ + ++++  +    kg+a+g++ +  +ph+++++s+  l+++
  gi|298674749|ref|YP_003726499.1| 125 NDVAQAVKDS--GMRAALSYGLIDLgenRSADVELSKGKQFVLDW----KGEAEGRIITMYGPHAPYTCSEGFLSKV 195
                                       *********9..*************66666666666666665555....99************************** PP

                                       HHHHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHC CS
                      Amidohydro_1 138 lkeakkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeag 214
                                        kea +  + ++iH+let+ e  ++++++g   ++      ++ lg+l++  +++ah+v+l+++++e+l+ r  ++ 
  gi|298674749|ref|YP_003726499.1| 196 KKEANHDRVGIHIHVLETESELNQMKQQYG---MC--SINLLDRLGFLGP-DVLAAHCVWLSDDDIEILRGR--GVH 264
                                       ******************************...88..9999999******.*****************8888..*** PP

                                       EEHHHHHHHHSEHHHHHHHHHHHHTSCEEEEEECT.TSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHT CS
                      Amidohydro_1 215 vahcpfsnsilrsgrealrkaldeGvkvglgtDga.asgnslnlleelrlalklqrgllyedeegglslkealrmaT 290
                                       v+h p sn++l+sg++++ ++ld+Gv+v+lgtDg+ + +n+l+++ee++ a++l+++    d+++ l++ ++l+maT
  gi|298674749|ref|YP_003726499.1| 265 VSHNPVSNMKLASGVAPVPRMLDRGVNVSLGTDGCaSNNNNLDMFEEMKTAALLHKVESL-DPTV-LPARQVLEMAT 339
                                       ***********************************6667788**********99994433.8888.*********** PP

                                       HHHHHHTT-TTTSSSS-TTSB--EEEECC.CT........CGGGTTTCTSEEEEEEEETTEE CS
                      Amidohydro_1 291 ingAkalglddkvGsievGkdADlvvvdl.di........laafvglkkdgnvkkvivkGkl 343
                                       + gA+alg+  k G + +G+ AD ++vd  ++         +++v++++   v ++iv+G++
  gi|298674749|ref|YP_003726499.1| 340 TSGARALGI--KSGVLREGYNADVIIVDMnKPhltpvydiHSHLVYSASGSDVSTTIVDGRI 399
                                       *********..******************93355667777********************98 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.1   1.3e-09   7.6e-06       1      24 [.      44      67 ..      44      80 .. 0.81
   2 !   58.4   0.0   1.5e-19   8.9e-16     260     472 ..     187     400 ..     122     401 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.3e-09
                      Amidohydro_3  1 eviDakGrlvlPGFvDsHtHlagg 24
                                      ++iDakG +v+PGFv  HtH a +
  gi|298674749|ref|YP_003726499.1| 44 QIIDAKGSVVMPGFVNTHTHAAMT 67
                                      79******************4433 PP

  == domain 2  score: 58.4 bits;  conditional E-value: 1.5e-19
                      Amidohydro_3 260 fedealaelvaaadergldvaihaigdaavd.dvldafeaa....aekngnqdrr.rlehaegvtesqiervaalqv 330
                                       ++++ l ++ ++a++  + ++ih++++++   ++  ++ +      +++g+ +    ++h+ ++++++ie ++  +v
  gi|298674749|ref|YP_003726499.1| 187 CSEGFLSKVKKEANHDRVGIHIHVLETESELnQMKQQYGMCsinlLDRLGFLGPDvLAAHCVWLSDDDIEILRGRGV 263
                                       5555588888999999999999999999999555555555588889999999877899******************* PP

                      Amidohydro_3 331 aagvqpvfnfedelldsrlgperargstpvkellnagvkvalgsD...apvgpfdpwprigaavmrktrrggevlrp 404
                                         +  pv+n            + a+g++pv ++l+ gv+v+lg+D   ++ + +d + ++ +a  + +++      +
  gi|298674749|ref|YP_003726499.1| 264 HVSHNPVSNM-----------KLASGVAPVPRMLDRGVNVSLGTDgcaSNNNNLDMFEEMKTAALLHKVES----LD 325
                                       **********...........899**********************99999***********999999755....47 PP

                      Amidohydro_3 405 deelsleealalyTrgpAkalgledrkGtLevGadADlvvld.adpldvdppelaear........vrltvvdGrvv 472
                                          l+ +++l + T+ +A+alg     G L++G+ AD+++ d ++p   +  ++++ +        v+ t+vdGr++
  gi|298674749|ref|YP_003726499.1| 326 PTVLPARQVLEMATTSGARALGIKS--GVLREGYNADVIIVDmNKPHLTPVYDIHSHLvysasgsdVSTTIVDGRIL 400
                                       78***********************..***************755666666666666688889************96 PP

>> A_deaminase  Adenosine/AMP deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.5e-07    0.0015     236     302 ..     260     324 ..     250     343 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.5e-07
                                       HCT-EEEE-HHHHCCCSST-TTTT-CHHHHHHTT-EEEE--BSCCCCT-S..HHHHHHHHHHHHT--HH CS
                       A_deaminase 236 laqiplevcPlSNvalgafleyaenPlkeflerglnvslntDDPlqfgtt..LieeYaiaaqvfklsee 302
                                        + +++   P+SN++l    +    P+++ l+rg+nvsl+tD  +  + +  + ee++ aa  +k ++ 
  gi|298674749|ref|YP_003726499.1| 260 GRGVHVSHNPVSNMKL----ASGVAPVPRMLDRGVNVSLGTDGCASNNNNldMFEEMKTAALLHKVESL 324
                                       567888899*******....77889*****************999887777799*****9998887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2701.34
//
Query:       gi|298674750|ref|YP_003726500.1|  [L=256]
Description: hypothetical protein Metev_0804 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-75  252.0   3.5    2.8e-75  251.7   3.5    1.1  1  PPS_PS    Phosphopantothenate/pantothenate synthetase
  ------ inclusion threshold ------
      0.066   12.9   0.8       0.13   12.0   0.1    1.8  2  DUF3755   Protein of unknown function (DUF3755)


Domain annotation for each model (and alignments):
>> PPS_PS  Phosphopantothenate/pantothenate synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  251.7   3.5   3.1e-79   2.8e-75       1     176 []      66     240 ..      66     240 .. 0.98

  Alignments for each domain:
  == domain 1  score: 251.7 bits;  conditional E-value: 3.1e-79
                            PPS_PS   1 lllakkpvisvNGNtaaLvaeeiveLaealgaklevNlfyrteeRvekiaellkeagaeevlgleedaripeleseR 77 
                                       lllakkpvis+NGNtaaLv++e+veL++ ++a+levNlf+r+++R+++i e+++++gae+vlg++ d+ + +l+++R
  gi|298674750|ref|YP_003726500.1|  66 LLLAKKPVISINGNTAALVPDEMVELSNIIKASLEVNLFHRSRDRIDRIIEHMESHGAENVLGRKGDS-VLDLSHDR 141
                                       79**************************************************************9876.66****** PP

                            PPS_PS  78 akvskeGiysaDvvlvplEDGDRaeaLvkmgKkviaiDLNPlsRtartatitivdnvvRalpnlteavkelkkkske 154
                                       ++v++eGiysaDvvlvplEDGDR+e+L++m+K viaiDLNPlsRt++ a++tivdn++Ra++n+ ++++e+k+ + +
  gi|298674750|ref|YP_003726500.1| 142 RMVDHEGIYSADVVLVPLEDGDRCEKLSEMDKVVIAIDLNPLSRTSQCADVTIVDNITRAFENMLQYADEMKNLNYD 218
                                       ***************************************************************************** PP

                            PPS_PS 155 eleeivkefdnkkvlkealkei 176
                                       +l+eiv+++dn+++++ a++ei
  gi|298674750|ref|YP_003726500.1| 219 KLREIVDSYDNNRIITLAIDEI 240
                                       ***************9999876 PP

>> DUF3755  Protein of unknown function (DUF3755)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   1.4e-05      0.13       8      26 ..     101     119 ..     101     121 .. 0.93
   2 ?   -2.9   0.1      0.61   5.5e+03      16      27 ..     196     207 ..     196     213 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.4e-05
                           DUF3755   8 idLFcqtRdNImaIlndMs 26 
                                       ++LF++ Rd I+ I ++M 
  gi|298674750|ref|YP_003726500.1| 101 VNLFHRSRDRIDRIIEHME 119
                                       59***************96 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.61
                           DUF3755  16 dNImaIlndMsd 27 
                                       dNI    ++M +
  gi|298674750|ref|YP_003726500.1| 196 DNITRAFENMLQ 207
                                       788877777755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1536.78
//
Query:       gi|298674751|ref|YP_003726501.1|  [L=291]
Description: GHMP kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-09   36.8   2.1    6.4e-09   35.9   2.1    1.5  1  GHMP_kinases_N  GHMP kinases N terminal domain
    2.4e-08   34.2   0.1      6e-07   29.7   0.0    2.9  3  GHMP_kinases_C  GHMP kinases C terminal


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   2.1   7.1e-13   6.4e-09       2      66 .]      84     148 ..      83     148 .. 0.83

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 7.1e-13
                                       EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                    GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglsleeaklaleaerlaqggngsggDvaasvyGg 66 
                                       ++i+++iP+g+GLG S+A a+++++Al+++l+ls    +la   + + + + ++ gD++a +y g
  gi|298674751|ref|YP_003726501.1|  84 VNIRTNIPLGCGLGLSGAGALSVAYALNQALSLSYTSKHLADIVHLAEVNTGSGLGDATAQLYRG 148
                                       789****************************8775336677777765566778999999999976 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.14   1.2e+03      47      60 ..      93     103 ..      60     115 .. 0.83
   2 ?   -0.2   0.0      0.15   1.3e+03      54      65 ..     134     145 ..     119     160 .. 0.84
   3 !   29.7   0.0   6.7e-11     6e-07      15      84 ..     215     278 ..     203     279 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.14
                    GHMP_kinases_C  47 GalgaklsGaGgGp 60 
                                       G +g +lsGa  G+
  gi|298674751|ref|YP_003726501.1|  93 G-CGLGLSGA--GA 103
                                       4.78999999..65 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.15
                    GHMP_kinases_C  54 sGaGgGptvfal 65 
                                       +G+G+G++ + l
  gi|298674751|ref|YP_003726501.1| 134 TGSGLGDATAQL 145
                                       89****997655 PP

  == domain 3  score: 29.7 bits;  conditional E-value: 6.7e-11
                    GHMP_kinases_C  15 ellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvaralreefe 84 
                                       + + +s +     ++g l+++ ++l+ea++  G   +k s+a+ G+tvfa++ dk   ++v+++++e++e
  gi|298674751|ref|YP_003726501.1| 215 NFMEQSKN--FAMETGLLKDRAKDLIEAIELSG---GKASQAMIGDTVFAIT-DKKTKNEVYDSMSEFGE 278
                                       44444444..3449999***********96666...***************9.99999********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.65
# Mc/sec: 1353.41
//
Query:       gi|298674752|ref|YP_003726502.1|  [L=411]
Description: phosphopantothenoylcysteine decarboxylase/phosphopantothenate/cysteine ligase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.6e-49  167.1   0.1    1.5e-48  165.1   0.0    1.8  2  DFP           DNA / pantothenate metabolism flavoprotein
    2.6e-34  118.3   0.3    3.9e-34  117.7   0.3    1.3  1  Flavoprotein  Flavoprotein


Domain annotation for each model (and alignments):
>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.11     1e+03      34      53 ..      42      61 ..      39      82 .. 0.84
   2 !  165.1   0.0   1.7e-52   1.5e-48       1     186 []     199     381 ..     199     381 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.11
                                      HHHHHHHHTT-EEEEEE-S- CS
                               DFP 34 alAeaaaarGaeVtlvsgpv 53
                                       +A+ +++ Ga+V  v+ + 
  gi|298674752|ref|YP_003726502.1| 42 DVARDLIRNGADVYAVTTEA 61
                                      58999*********999874 PP

  == domain 2  score: 165.1 bits;  conditional E-value: 1.7e-52
                                       TTT-EEEEEES-EEEECCTTEEEEE----HHHHHHHHHHHHTT-EEEEEE-S-SS---TT-EEEE--SHHHHHHHHH CS
                               DFP   1 legkkvlvtaGpTrEaiDpVRfisNrSSGkmGyalAeaaaarGaeVtlvsgpvsletpegvevvkvesaeemleave 77 
                                       l+gk+vl+t+G+T E+iDp+R+++NrSSGk+G++lA +a++rGa Vt+v+ +  l+  +g++ + vesa++m ++v+
  gi|298674752|ref|YP_003726502.1| 199 LTGKRVLITGGATAESIDPIRILTNRSSGKTGMELALEAYRRGAYVTIVHRN-YLD-VQGINEIYVESADQMIDSVM 273
                                       689************************************************9.355.55****************** PP

                                       HHHTT-.SEEEE---S--EEES-------------..----EEE---HHHHHHHC-S.S-EEEEEEE-SS....-HH CS
                               DFP  78 ealkea.divimaAAvaDyrpkeaaeeKikkeeeeeeltleleknpdilaelaekkkkkqllvGFaaete....ell 149
                                       ++l++  d++i++AA++Dy+ +  +++Kik   ++++l+l l++++++l+e+ +k+ ++ ++ GF++et     el+
  gi|298674752|ref|YP_003726502.1| 274 DELENGyDAFISSAAISDYTLD-YSSHKIKS--GNDQLSLVLRPTRKLLNEV-RKAYSELVITGFKVETGitedELI 346
                                       9997666**************8.6899**96..7789***************.45566678*******8446779** PP

                                       HHHHHHHHHTT-SEEEEEEGGGTTGGG-SS-EEEEE. CS
                               DFP 150 enareklerkgldlivaNdvskeeagfgsdenevtll 186
                                       +++++  +++gldlivaN+v+ +  g+g+d+nev+++
  gi|298674752|ref|YP_003726502.1| 347 SRSQKLQQEHGLDLIVANNVGYK--GMGDDTNEVYII 381
                                       *********************87..*********986 PP

>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.7   0.3   4.3e-38   3.9e-34       1     154 [.      25     190 ..      25     194 .. 0.90

  Alignments for each domain:
  == domain 1  score: 117.7 bits;  conditional E-value: 4.3e-38
                                       EEEEEEE-SSCGGGCHHHHHHHHHHTTEEEEEEESCHHHHCCHHGGS...........TCSSHHHHHH...CTTESE CS
                      Flavoprotein   1 kkillgiTGsvaaikalellekLkkegievqvvltkaAkkfiskeklklaa.......redpilhiel...rrwadl 67 
                                       k i+lg+TGs+aa+ ++++ + L+++g++v  v t+a++ +i++  l+ a+        +++++h+++   +  adl
  gi|298674752|ref|YP_003726502.1|  25 KTIVLGVTGSIAAVRVVDVARDLIRNGADVYAVTTEASEWIINPCALNYATgnnviteLTGDVEHVKFcglNGCADL 101
                                       679****************************************7766665599999999999***99877788**** PP

                                       EEEEEEEHHHHHHHHTT--SSHHHHHHHT..HCCTTEEEEE.--HHCCTCSTCHHHHHHH.HT.............. CS
                      Flavoprotein  68 lviaPasantlakianGiadnlltlilra..takkpiliaPamnpamyenpqtlknlekl.eegvtvikPsegdigk 141
                                       lvi+Pa+ant++kia Gi d+++t+++    ++++pi+i+Pam+ +my++p +++n++kl + gv +++P   ++g 
  gi|298674752|ref|YP_003726502.1| 102 LVIVPATANTIGKIAGGIDDTPVTTFATTalGSNMPIIIVPAMHESMYNHPGVVENIDKLkSWGVSFVGPY-FEEGV 177
                                       ***********************99994458*****************************55********9.77888 PP

                                       ..GHHHHHHHHHH CS
                      Flavoprotein 142 gkmaeieeivgki 154
                                       +k+a  +++v  +
  gi|298674752|ref|YP_003726502.1| 178 AKIAPNDTVVLNV 190
                                       8888888887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.52
# Mc/sec: 2365.75
//
Query:       gi|298674753|ref|YP_003726503.1|  [L=341]
Description: hypothetical protein Metev_0807 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-18   66.4   0.0    5.3e-18   65.6   0.0    1.4  1  acVLRF1          Actinobacteria/chloroflexi VLRF1 release fac
    7.9e-08   32.6   0.0    1.7e-07   31.6   0.0    1.5  1  baeRF_family10   Bacterial archaeo-eukaryotic release factor 
    8.6e-07   29.3   0.1      2e-06   28.1   0.1    1.6  1  eRF1_2           eRF1 domain 2
      0.001   18.3   9.7      0.001   18.3   9.7    2.0  2  Taxilin          Myosin-like coiled-coil protein
  ------ inclusion threshold ------
       0.01   16.2  12.0      0.018   15.4   9.4    2.3  2  OmpH             Outer membrane protein (OmpH-like)
      0.031   14.0   4.4       0.06   13.1   4.4    1.4  1  DUF745           Protein of unknown function (DUF745)
      0.058   11.6  17.8     0.0094   14.2  13.7    1.6  2  FPP              Filament-like plant protein, long coiled-coi
      0.062   13.5   0.2      0.062   13.5   0.2    2.7  2  FliJ             Flagellar FliJ protein
      0.064   13.2  11.1       0.15   12.0  11.1    1.6  1  YscO             Type III secretion protein YscO
       0.11   10.4   5.5       0.13   10.2   5.5    1.2  1  V_ATPase_I       V-type ATPase 116kDa subunit family
       0.11   11.8   7.2      0.084   12.2   5.0    1.7  2  DUF4407          Domain of unknown function (DUF4407)
       0.12   11.8  21.2       0.62    9.4  16.9    2.6  2  GAS              Growth-arrest specific micro-tubule binding
       0.15   12.4   0.4       0.57   10.5   0.0    2.0  2  Baculo_PEP_N     Baculovirus polyhedron envelope protein, PEP
       0.16   12.2  14.4       0.24   11.6  12.9    2.1  1  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
       0.19   11.4   3.0       0.31   10.7   3.0    1.3  1  DUF789           Protein of unknown function (DUF789)
       0.21   12.4   3.9       0.78   10.5   3.9    2.0  1  CP12             CP12 domain
       0.28   10.8  20.5      0.071   12.8  15.5    2.4  2  Lebercilin       Ciliary protein causing Leber congenital ama
       0.45   10.8  13.3       0.11   12.8   8.0    2.7  2  DUF4164          Domain of unknown function (DUF4164)
       0.46   10.6  14.5      0.043   13.9   9.8    1.7  1  ATF7IP_BD        ATF-interacting protein binding domain
       0.54   10.8  18.2       0.27   11.8  14.5    2.3  2  APG6_N           Apg6 coiled-coil region
       0.54   10.4  15.7       0.25   11.5  11.9    2.3  2  Uds1             Up-regulated During Septation
       0.64   10.8  15.4       0.23   12.2  11.5    2.2  1  DUF4472          Domain of unknown function (DUF4472)
       0.77    9.7   9.0         15    5.5   1.0    4.0  3  GIT_CC           GIT coiled-coil Rho guanine nucleotide excha
       0.88    8.4   4.7        1.9    7.3   4.7    1.6  1  LMBR1            LMBR1-like membrane protein
          1   10.0   8.0        1.3    9.7   5.2    2.3  2  Adaptin_binding  Alpha and gamma adaptin binding protein p34
        1.2    8.2  10.9       0.52    9.3   8.2    1.8  2  Atg14            Vacuolar sorting 38 and autophagy-related su
        1.4    8.1  11.5        2.1    7.6   8.8    2.3  2  DUF3450          Protein of unknown function (DUF3450)
        1.8    9.0   9.0        4.2    7.8   7.7    2.2  2  T3SSipB          Type III cell invasion protein SipB
        2.5    7.6  13.2         17    4.9   0.0    2.5  2  HAUS6_N          HAUS augmin-like complex subunit 6 N-terminu
        2.7    7.8  15.9      0.067   13.0   6.9    2.7  3  Bacillus_HBL     Bacillus haemolytic enterotoxin (HBL)
        3.2    7.9  12.7        4.7    7.3   3.9    3.2  3  DUF1192          Protein of unknown function (DUF1192)
        3.4    8.4   7.5        6.8    7.4   5.2    2.5  2  DUF2203          Uncharacterized conserved protein (DUF2203)
        3.4    6.4  21.0       0.86    8.4  17.0    2.0  2  Spc7             Spc7 kinetochore protein
        3.6    7.1  17.2        2.4    7.7  12.3    2.4  3  HAUS-augmin3     HAUS augmin-like complex subunit 3
        3.6    7.0  19.6        1.8    8.0  13.0    2.4  2  Leu_zip          Leucine zipper
        4.3    6.9  12.0          1    8.9   7.4    2.0  2  LUC7             LUC7 N_terminus
        4.7    7.7  20.7       0.34   11.3   2.1    4.5  4  FlaC_arch        Flagella accessory protein C (FlaC)
        5.8    6.9  24.1       0.79    9.7  11.3    3.2  3  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
          6    6.9  23.7        2.4    8.2  18.7    2.4  2  UPF0242          Uncharacterised protein family (UPF0242) N-t
        7.3    6.8  17.3    1.6e+02    2.4  15.8    3.0  2  CENP-Q           CENP-Q, a CENPA-CAD centromere complex subun
        9.2    6.7  15.1         20    5.6  11.2    2.9  2  Csm1_N           Csm1 N-terminal domain
        9.2    6.6  13.5        1.4    9.2   6.6    2.6  3  DUF641           Plant protein of unknown function (DUF641)


Domain annotation for each model (and alignments):
>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.6   0.0   1.2e-20   5.3e-18       4      94 ..     214     307 ..     212     335 .. 0.88

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 1.2e-20
                           acVLRF1   4 gvllvrrggfavgvveggelvaskvgtrdvqgrtaaGGwSqqRfaRrrenqadalleavaeaaarllaeesae...v 77 
                                        vl +++g   vg+++ +e + ++v ++ v+ ++++GG+Sq+Rf+  r++ +d+++e+v+ + +r+++  +++   +
  gi|298674753|ref|YP_003726503.1| 214 CVLQIHAGESFVGIANPDEFENYSVIKSSVKAKHKKGGFSQKRFEELRNEDIDHHIEKVQSEFDRMMDGIENDidyI 290
                                       67788999999********************************************************655555779* PP

                           acVLRF1  78 vlgGdrslvaevledar 94 
                                       ++gGdr l++ vl++ +
  gi|298674753|ref|YP_003726503.1| 291 ITGGDRGLTQHVLKNIN 307
                                       ************99844 PP

>> baeRF_family10  Bacterial archaeo-eukaryotic release factor family 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0     4e-10   1.7e-07       5     108 ..     202     306 ..     199     321 .. 0.94

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 4e-10
                    baeRF_family10   5 pLlealdeyerygvvlvdreraRlfevylgeleeveevegevpgrtktggwksqdrfqrreeeqaerhlkevAella 81 
                                       +L ++l+++ +++v+ +++++  +     +e+e  +++++ v+ ++k+gg  sq+rf+  + e +++h+++v    +
  gi|298674753|ref|YP_003726503.1| 202 QLNAILEQNFKICVLQIHAGESFVGIANPDEFENYSVIKSSVKAKHKKGGF-SQKRFEELRNEDIDHHIEKVQSEFD 277
                                       6889999********************************************.************************* PP

                    baeRF_family10  82 klle..ergverlvlgGdeeetaalldrl 108
                                       ++++  e++++ +++gGd+  t+++l++ 
  gi|298674753|ref|YP_003726503.1| 278 RMMDgiENDIDYIITGGDRGLTQHVLKNI 306
                                       ***955566************99998875 PP

>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.1   4.7e-09     2e-06       7      90 ..     218     301 ..     212     336 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 4.7e-09
                                       EETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTTESEEEEE CS
                            eRF1_2   7 ldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafllvdkdklkgiila 83 
                                       ++ ge+ +g+ ++   e  + i++sv  Khk+Gg s++rfe lr+e +++ ++kv ++ ++  +   +++++ ii +
  gi|298674753|ref|YP_003726503.1| 218 IHAGESFVGIANPDEFENYSVIKSSVKAKHKKGGFSQKRFEELRNEDIDHHIEKVQSEFDRM-MDGIENDIDYIITG 293
                                       56788889999999999999**************************************9998.86678899999999 PP

                                       ES.STHHH CS
                            eRF1_2  84 gp.gfvke 90 
                                       g  g +++
  gi|298674753|ref|YP_003726503.1| 294 GDrGLTQH 301
                                       84144433 PP

>> Taxilin  Myosin-like coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   9.7   2.4e-06     0.001     244     308 .]      25      89 ..      15     126 .. 0.84
   2 ?   -1.2   0.1       2.1   8.8e+02      56      94 ..     241     280 ..     232     286 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.4e-06
                           Taxilin 244 kEmekmtkktkklEketnlwkskfektnkallemaeertekkkeieklkkkiqkLeklcraLqee 308
                                       k ++++++ + +lE e+++++++ ek +k+   ++ e++e ++++++ + ki++L++ ++ ++ee
  gi|298674753|ref|YP_003726503.1|  25 KRIDELQSYIMELEIESQKLQRRLEKKEKNAKRAISEKQEAEEKLNAANVKIETLQNEIKSIKEE 89 
                                       45778888888999999999999999999999999999999999999999999999988887765 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.1
                           Taxilin  56 eqlqaelskaalaksKLekLcRe.lqkqnkklkeeskqra 94 
                                        +++a+++k+   +++ e+L  e ++++ +k++ e  +++
  gi|298674753|ref|YP_003726503.1| 241 SSVKAKHKKGGFSQKRFEELRNEdIDHHIEKVQSEFDRMM 280
                                       5667777777778888888855326777777777766665 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   9.4   4.2e-05     0.018      22      86 ..      21      96 ..       8     122 .. 0.62
   2 ?    0.6   0.0       1.5   6.4e+02      29      46 ..     263     280 ..     235     325 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.2e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS......-HHHHHH.......HHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH 22 eqlekkfkklqaeleakekelqklqeelqkkakkl.e....keekeqe.......lqkkeqelqqkqqqkaqelqkk 86
                                      ++lek + +lq  + ++e e qklq++l+kk+k++      k+e+e++       ++++++e++   ++++ +lq+ 
  gi|298674753|ref|YP_003726503.1| 21 QKLEKRIDELQSYIMELEIESQKLQRRLEKKEKNAkRaiseKQEAEEKlnaanvkIETLQNEIKS-IKEERDDLQDI 96
                                      67888888888888888888888888888777776447765555555544455555555555555.44444333333 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHHHHHHHHH CS
                              OmpH  29 kklqaeleakekelqklq 46 
                                       ++++  +e+ + e+++++
  gi|298674753|ref|YP_003726503.1| 263 EDIDHHIEKVQSEFDRMM 280
                                       222222222222222222 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   4.4   0.00014      0.06      57     128 ..      17      91 ..      15     106 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00014
                            DUF745  57 LaGKqql...veqleqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaa 128
                                       L+GKq l   +++l++ + e e   q+ ++ l++ e+nak a + +++a+++l+a +  +++ +++++++++  +
  gi|298674753|ref|YP_003726503.1|  17 LSGKQKLekrIDELQSYIMELEIESQKLQRRLEKKEKNAKRAISEKQEAEEKLNAANVKIETLQNEIKSIKEERD 91 
                                       789998766689999999***************************************999999999999987665 PP

>> FPP  Filament-like plant protein, long coiled-coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2  13.7   2.2e-05    0.0094      87     156 ..      20      89 ..      16     102 .. 0.95
   2 ?   -1.9   0.1       1.6   6.9e+02     692     710 ..     252     268 ..     172     328 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.2e-05
                               FPP  87 kaelEeklvelekeLlrlaaendaLsrsLqerenlleklseeksqaeaeieaLksrlesaEkeinsLkYE 156
                                       k++lE++++el+  +++l++e+++L+r L+++e+  ++  +ek++ae +++a + ++e   +ei+s+k E
  gi|298674753|ref|YP_003726503.1|  20 KQKLEKRIDELQSYIMELEIESQKLQRRLEKKEKNAKRAISEKQEAEEKLNAANVKIETLQNEIKSIKEE 89 
                                       678***************************************************************9966 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.6
                               FPP 692 llkeeleelksekenleve 710
                                       ++++ +eel+   e+++++
  gi|298674753|ref|YP_003726503.1| 252 FSQKRFEELRN--EDIDHH 268
                                       33333322221..122222 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   8.2      0.45   1.9e+02      70     112 ..      22      65 ..      18      67 .. 0.75
   2 ?   13.5   0.2   0.00014     0.062       1      59 [.      63     121 ..      63     126 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.45
                              FliJ  70 qaekqvekareewqearqerkkle.kLkerekkeeqkeenrrEq 112
                                       ++ek++++ ++  +e ++e +kl+ +L+++ek++ ++  +++E 
  gi|298674753|ref|YP_003726503.1|  22 KLEKRIDELQSYIMELEIESQKLQrRLEKKEKNAKRAISEKQEA 65 
                                       67888888888889999988888625777777777777777775 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00014
                              FliJ   1 deaareLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisalde 59 
                                       +ea+++L++a+ +++  ++++ +++++r+++q  +  + + l +++++ + + i++l++
  gi|298674753|ref|YP_003726503.1|  63 QEAEEKLNAANVKIETLQNEIKSIKEERDDLQDIKFRNIEVLHPSKFHDLISKIQSLRS 121
                                       689****************************9999999999999999999999999987 PP

>> YscO  Type III secretion protein YscO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0  11.1   0.00036      0.15      53     135 ..      12      94 ..       9      97 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00036
                                       HHHHHHHTTT--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YscO  53 rlyaeiigklvllkelekvkqqvalLrekeaelekqveeakqqleaerealrqarkelqearraveKfaelarlvra 129
                                        l+ ++ gk  l k+++++++ +  L+ ++++l+ ++e+ ++++++++ ++++a+++l +a  + e ++ + +  ++
  gi|298674753|ref|YP_003726503.1|  12 SLFGKLSGKQKLEKRIDELQSYIMELEIESQKLQRRLEKKEKNAKRAISEKQEAEEKLNAANVKIETLQNEIKSIKE 88 
                                       689999999999*******************************************************9999999999 PP

                                       HHHHHH CS
                              YscO 130 easrqq 135
                                       e+  +q
  gi|298674753|ref|YP_003726503.1|  89 ERDDLQ 94 
                                       987766 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   5.5    0.0003      0.13      30     116 ..      25     113 ..      20     290 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0003
                        V_ATPase_I  30 rrcdemerklrfleeeieklekavikeeea...eesleapeekeldeleeelekleeelkelnenleklkkelnelv 103
                                       +r+de++  +  le e +kl+    k+e++   + s++++ e++l+  + ++e+l++e+k+++e+ ++l++ + + +
  gi|298674753|ref|YP_003726503.1|  25 KRIDELQSYIMELEIESQKLQRRLEKKEKNakrAISEKQEAEEKLNAANVKIETLQNEIKSIKEERDDLQDIKFRNI 101
                                       89************999998888877777655444566666777888889999999999999999999998887777 PP

                        V_ATPase_I 104 elkavlekakefl 116
                                       e  +   k ++++
  gi|298674753|ref|YP_003726503.1| 102 EVLHPS-KFHDLI 113
                                       766644.333333 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   5.0    0.0002     0.084     129     226 ..      21     130 ..       3     162 .. 0.61
   2 ?   -1.1   0.0       2.2   9.5e+02     111     144 ..     256     305 ..     253     328 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0002
                           DUF4407 129 aaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelaelkak 205
                                       ++l+++++el++ i +l+ e +++++rl++++++a++ ++ ++          ++   +++ +++++q+e++++k++
  gi|298674753|ref|YP_003726503.1|  21 QKLEKRIDELQSYIMELEIESQKLQRRLEKKEKNAKRAISEKQ--------EAEEKLNAANVKIETLQNEIKSIKEE 89 
                                       4456666666666666666666666666666666666666533........33344444555555555555555555 PP

                           DUF4407 206 ld....................atarlaalraelaeleaer 226
                                       +d                      +++++lr++ ++l +++
  gi|298674753|ref|YP_003726503.1|  90 RDdlqdikfrnievlhpskfhdLISKIQSLRSNTDTLITAY 130
                                       44555555777777766666665555555555555555544 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.2
                           DUF4407 111 elaeeqqeeakelkeqlaaaltaelaeleaqia................a 144
                                       + +e ++e+++++ e+++++++  ++ +e++i+                +
  gi|298674753|ref|YP_003726503.1| 256 RFEELRNEDIDHHIEKVQSEFDRMMDGIENDIDyiitggdrgltqhvlkN 305
                                       56777888889999999988888888888888766665555555554443 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4  16.9    0.0015      0.62      24      95 ..      30     101 ..      24     126 .. 0.89
   2 ?    3.7   0.1     0.078        33      79     134 ..     235     288 ..     230     329 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0015
                               GAS  24 NLelIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlk 95 
                                         ++I +l  e ++l+++ e++ek+ + + +e+++ +e+L++a+ ++e L++++k  ++++ +l+ +k r+ 
  gi|298674753|ref|YP_003726503.1|  30 LQSYIMELEIESQKLQRRLEKKEKNAKRAISEKQEAEEKLNAANVKIETLQNEIKSIKEERDDLQDIKFRNI 101
                                       5678999999999***************************************************99997765 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.078
                               GAS  79 nyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdelykkfeaaiq 134
                                       ny+  k+s k+ +++   ++k +++l+  +e   +++ekv++e+d++ +  e+ i+
  gi|298674753|ref|YP_003726503.1| 235 NYSVIKSSVKAKHKKGGFSQKRFEELR--NEDIDHHIEKVQSEFDRMMDGIENDID 288
                                       555556666666666666666666654..778999***********9998888765 PP

>> Baculo_PEP_N  Baculovirus polyhedron envelope protein, PEP, N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       7.1     3e+03      28      58 ..      29      59 ..      21      64 .. 0.81
   2 ?   10.5   0.0    0.0013      0.57      12      51 ..     127     165 ..     122     177 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 7.1
                                      -.GGGGGGS-GGGEEEHHHHSTTS-TT-EEE CS
                      Baculo_PEP_N 28 pltqalkelPssekkllrqlepcvdanKlfi 58
                                      +l++ + el    +kl r le   ++ K  i
  gi|298674753|ref|YP_003726503.1| 29 ELQSYIMELEIESQKLQRRLEKKEKNAKRAI 59
                                      4688899999999999999999888888766 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0013
                                       -T-EEEHHHHHHHHT--.GGGGGGS-GGGEEEHHHHSTTS CS
                      Baculo_PEP_N  12 vvlwvgadeilsiLkvpltqalkelPssekkllrqlepcv 51 
                                       +++++  d+ ls+Lk p +++l+ + +  k+ll ++e+ +
  gi|298674753|ref|YP_003726503.1| 127 ITAYIKPDDTLSNLKNP-NKLLDSIDDNTKNLLSKIESST 165
                                       689**************.*****************99944 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6  12.9   0.00056      0.24      12      83 ..      25      93 ..      16      97 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00056
                       TMF_TATA_bd 12 qlverlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetl 83
                                      + +++l+s i +lE+E ++l+++   le++ ++a++ i +  +  e+l++++ ++e+l++e+++++e+ + l
  gi|298674753|ref|YP_003726503.1| 25 KRIDELQSYIMELEIESQKLQRR---LEKKEKNAKRAISEKQEAEEKLNAANVKIETLQNEIKSIKEERDDL 93
                                      56899***************986...56778899999****************************9988765 PP

>> DUF789  Protein of unknown function (DUF789)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   3.0   0.00072      0.31      84     175 ..      41     127 ..      17     141 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00072
                            DUF789  84 saksrrkseesesesveesssekssdsesekeslsekseseeesss.sdesessekeskgellfeYfEsesPyeRep 159
                                       s+k +r+ e++e+++ ++ s++++ +++ ++      ++++ e+ + + +s ++e+++ + + f  +E  +P + ++
  gi|298674753|ref|YP_003726503.1|  41 SQKLQRRLEKKEKNAKRAISEKQEAEEKLNA------ANVKIETLQnEIKSIKEERDDLQDIKFRNIEVLHPSKFHD 111
                                       3333444444444433332333333322222......22222222213344445789999***************** PP

                            DUF789 160 LadkiseLaskfpelk 175
                                       L+ ki++L s++ +l 
  gi|298674753|ref|YP_003726503.1| 112 LISKIQSLRSNTDTLI 127
                                       ********99986665 PP

>> CP12  CP12 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   3.9    0.0018      0.78       1      46 [.      44      89 ..      44      98 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0018
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              CP12  1 leekiekaieearevcaekgansaecaaawdeVeeLqaeaahqrak 46
                                      l+ ++ek+ ++a+++ +ek++++++  aa   +e Lq e +  +++
  gi|298674753|ref|YP_003726503.1| 44 LQRRLEKKEKNAKRAISEKQEAEEKLNAANVKIETLQNEIKSIKEE 89
                                      67899**********************************9996653 PP

>> Lebercilin  Ciliary protein causing Leber congenital amaurosis disease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8  15.5   0.00017     0.071     114     185 ..      15      89 ..       2      95 .. 0.78
   2 ?   -0.3   0.0       1.7   7.4e+02      26      54 ..     136     164 ..     107     168 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00017
                        Lebercilin 114 knLaereeLqkkLeeleakleekeekikeLerkleleeksfrrqlaaek...kktkeaqeevkalqeeierlkqk 185
                                        +L  +++L+k+++el++ + e e + ++L+r+le +ek+ +r +  ++   +k ++a+ ++++lq+ei+++k++
  gi|298674753|ref|YP_003726503.1|  15 GKLSGKQKLEKRIDELQSYIMELEIESQKLQRRLEKKEKNAKRAISEKQeaeEKLNAANVKIETLQNEIKSIKEE 89 
                                       578899*************************************88655411155666677778888888877765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.7
                        Lebercilin  26 kleelrkEnklLkrlqkrqekaLskyedt 54 
                                        l++l++ nklL  +    ++ Lsk e++
  gi|298674753|ref|YP_003726503.1| 136 TLSNLKNPNKLLDSIDDNTKNLLSKIESS 164
                                       46677777777777777777777777765 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   8.0   0.00026      0.11      17      86 ..      10      79 ..       7      82 .. 0.92
   2 ?   -1.5   0.0       7.6   3.3e+03      38      47 ..     266     275 ..     253     289 .. 0.49

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00026
                           DUF4164 17 ldsLEkavdrrleaerkrdeleaeiealgedrsRLaeeLdqaearaarleevnrEvsrrLkaaietirav 86
                                      l+sL + +  + + e+  del++ i +l+ + ++L  +L ++e  a+r  + ++E+ ++L+aa+ +i+++
  gi|298674753|ref|YP_003726503.1| 10 LNSLFGKLSGKQKLEKRIDELQSYIMELEIESQKLQRRLEKKEKNAKRAISEKQEAEEKLNAANVKIETL 79
                                      567777788888899999************************************************9876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 7.6
                           DUF4164  38 eaeiealged 47 
                                       +  ie+++++
  gi|298674753|ref|YP_003726503.1| 266 DHHIEKVQSE 275
                                       3333333333 PP

>> ATF7IP_BD  ATF-interacting protein binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   9.8    0.0001     0.043      49     196 ..       5     145 ..       4     165 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.0001
                         ATF7IP_BD  49 kkLkelkervekteCkkkheailteLqaKIarLtkrfkaaledlkkkqeqeclkpvspsksaaskvansksvllern 125
                                       kk  +l+  ++k  +k+k e+ ++eLq+ I  L+ + ++ +  l+kk+++ ++  ++++k+ a+++ n+ +v  e  
  gi|298674753|ref|YP_003726503.1|   5 KKTIHLNSLFGKLSGKQKLEKRIDELQSYIMELEIESQKLQRRLEKKEKN-AK-RAISEKQEAEEKLNAANVKIETL 79 
                                       66778999************************************997544.55.55666666677777888899999 PP

                         ATF7IP_BD 126 agtvrqmleskrsvnesspatfqspekavkkisltspqnevssesknnddVmlisvespnlttpvtsnptd 196
                                       ++++++++e+  ++++    +f +  ++ + ++++   ++ +s  + n+d ++ +   p  t + ++np++
  gi|298674753|ref|YP_003726503.1|  80 QNEIKSIKEERDDLQDI---KFRNI-EVLHPSKFHDLISKIQSLRS-NTDTLITAYIKPDDTLSNLKNPNK 145
                                       99999999998888777...33333.33344444433333333333.444444445555555555555555 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8  14.5   0.00062      0.27      56     128 ..      20      92 ..       3      96 .. 0.90
   2 ?   -1.3   0.1       6.7   2.9e+03      77      90 ..     262     275 ..     231     285 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00062
                            APG6_N  56 leklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlelleleeeldsleaqyeh 128
                                        +klek  +el++ + ele e ++l++ l++ e+ +++   e+++  ++ n+ +++ + l++e +s++ + ++
  gi|298674753|ref|YP_003726503.1|  20 KQKLEKRIDELQSYIMELEIESQKLQRRLEKKEKNAKRAISEKQEAEEKLNAANVKIETLQNEIKSIKEERDD 92 
                                       58999999********************************************************999987665 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 6.7
                            APG6_N  77 reeleaelaaleee 90 
                                       +e+++  +++ ++e
  gi|298674753|ref|YP_003726503.1| 262 NEDIDHHIEKVQSE 275
                                       33333333333333 PP

>> Uds1  Up-regulated During Septation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5  11.9    0.0006      0.25      28     116 ..       5      94 ..       2      96 .. 0.82
   2 ?   -1.9   0.1       8.4   3.6e+03      84     106 ..     255     277 ..     234     284 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0006
                              Uds1  28 kelkaLeerlealrkkLaletklrdaarsLsrlyssskksak.ssaarsnskssreslakaeeelaeserkvdelas 103
                                       k+  +L++   +l+ k +le+++ +    +++l ++s+k ++  +++++n+k+   ++++aee+l++++ k++ l++
  gi|298674753|ref|YP_003726503.1|   5 KKTIHLNSLFGKLSGKQKLEKRIDELQSYIMELEIESQKLQRrLEKKEKNAKRAISEKQEAEEKLNAANVKIETLQN 81 
                                       667788888888888999999999999999999988888766444555667777778999***************** PP

                              Uds1 104 elekleeraaevr 116
                                       e+++++e++ +++
  gi|298674753|ref|YP_003726503.1|  82 EIKSIKEERDDLQ 94 
                                       *******998887 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 8.4
                              Uds1  84 lakaeeelaeserkvdelasele 106
                                       ++ +e   ++ ++ +++++se+ 
  gi|298674753|ref|YP_003726503.1| 255 KRFEELRNEDIDHHIEKVQSEFD 277
                                       22333333455566666666655 PP

>> DUF4472  Domain of unknown function (DUF4472)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2  11.5   0.00053      0.23      33     104 ..      23      94 ..      18      95 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00053
                           DUF4472  33 lknkvlalenrvlelelerekaaeeiqslrerlaeleeekkeleeeyvvlkknyqalekefekekkkqqels 104
                                       l+ ++ +l++ ++ele+e++k+++  ++ +++ + + +ek+e+ee++ + + ++ +l++e ++ k++ + l+
  gi|298674753|ref|YP_003726503.1|  23 LEKRIDELQSYIMELEIESQKLQRRLEKKEKNAKRAISEKQEAEEKLNAANVKIETLQNEIKSIKEERDDLQ 94 
                                       778888999*****************************************************9999988775 PP

>> GIT_CC  GIT coiled-coil Rho guanine nucleotide exchange factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.6     0.042        18      39      65 ..      20      46 ..      17      47 .. 0.89
   2 ?    5.5   1.0     0.036        15      29      64 ..      73      94 ..      48      96 .. 0.67
   3 ?    0.5   0.0       1.3   5.6e+02      39      57 ..     262     280 ..     247     286 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.042
                            GIT_CC 39 NtslsdelrlLQskvqkLqaeNaqlrd 65
                                      +++l++ + +LQs + +L+ e ++l++
  gi|298674753|ref|YP_003726503.1| 20 KQKLEKRIDELQSYIMELEIESQKLQR 46
                                      578999***************999975 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.036
                            GIT_CC 29 eakiqqLlkvNtslsdelrlLQskvqkLqaeNaqlr 64
                                      ++              +++ LQ++++++++e ++l+
  gi|298674753|ref|YP_003726503.1| 73 NV--------------KIETLQNEIKSIKEERDDLQ 94
                                      33..............46667777777777777665 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 1.3
                            GIT_CC  39 NtslsdelrlLQskvqkLq 57 
                                       N+ +   +++ Qs+ ++++
  gi|298674753|ref|YP_003726503.1| 262 NEDIDHHIEKVQSEFDRMM 280
                                       8899999*******99987 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   4.7    0.0044       1.9     197     315 ..      22     144 ..       9     188 .. 0.45

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0044
                             LMBR1 197 dldeelkklyfeaaklntekeeaereledllkevkklrksisesdp.lrkyleeilkkvPeeiaeklks........ 264
                                       +l+++++ l+  +++l+ e ++ +r+le++ k++k++ ++++e ++ l   + +i ++     ++++ks        
  gi|298674753|ref|YP_003726503.1|  22 KLEKRIDELQSYIMELEIESQKLQRRLEKKEKNAKRAISEKQEAEEkLNAANVKI-ETL----QNEIKSikeerddl 93 
                                       5566666666666666666666666666555555555555544442121111111.111....11111122222222 PP

                             LMBR1 265 .................nenkteeslaklekqlikalqkrertekqwkrllekalelediiknksske 315
                                                        +  ++ +sl +++                   l++ +++  d ++n ++ +
  gi|298674753|ref|YP_003726503.1|  94 qdikfrnievlhpskfhDLISKIQSLRSNTDT-----------------LITAYIKPDDTLSNLKNPN 144
                                       22222222222222221112222233333333.................3333333333333333333 PP

>> Adaptin_binding  Alpha and gamma adaptin binding protein p34
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   5.2    0.0029       1.3      39     106 ..      40     126 ..       6     129 .. 0.53
   2 ?    0.4   0.0       2.2   9.6e+02      64      97 ..     240     273 ..     139     285 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0029
                   Adaptin_binding  39 eadeaqlekeeeeqdpsqpastepdksaaesesadaef.............lfggdeaarle.............dl 89 
                                       e++++q++ e+ e++ ++  ++++++  +++e+++a +             +   +e ++l+             ++
  gi|298674753|ref|YP_003726503.1|  40 ESQKLQRRLEKKEKNAKR--AISEKQ--EAEEKLNAANvkietlqneiksiK---EERDDLQdikfrnievlhpsKF 109
                                       222222222222222222..222222..222223233333555555553331...22223334556666788888** PP

                   Adaptin_binding  90 esllsklqqakdnvrnl 106
                                        +l+sk+q++++n+++l
  gi|298674753|ref|YP_003726503.1| 110 HDLISKIQSLRSNTDTL 126
                                       *************9876 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 2.2
                   Adaptin_binding  64 ksaaesesadaeflfggdeaarledlesllsklq 97 
                                       ks+ + + ++ +f+++  e+ r ed++  ++k+q
  gi|298674753|ref|YP_003726503.1| 240 KSSVKAKHKKGGFSQKRFEELRNEDIDHHIEKVQ 273
                                       3444444444444444444444444444444443 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   8.2    0.0012      0.52      22      91 ..      25      91 ..       5     151 .. 0.62
   2 ?   -1.9   0.0       3.2   1.4e+03     109     142 ..     241     275 ..     238     322 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0012
                             Atg14 22 erlyelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdkls 91
                                      +r+ el+  ++ l +e++ l++++ek++++ +   ++ ++ +   +kl+    +i+ l+++++ +k+ ++
  gi|298674753|ref|YP_003726503.1| 25 KRIDELQSYIMELEIESQKLQRRLEKKEKNAK---RAISEKQEAEEKLNAANVKIETLQNEIKSIKEERD 91
                                      34445555555555555555555555555554...33333333333333333333333333333333333 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.2
                             Atg14 109 dklkkRrsdleslqneleerrkkqiaklqdaik.r 142
                                       +++k ++++    q++ ee r++ i+ + ++++ +
  gi|298674753|ref|YP_003726503.1| 241 SSVKAKHKKGGFSQKRFEELRNEDIDHHIEKVQsE 275
                                       55666666666777777777777777777777642 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   8.8    0.0048       2.1      30      99 ..      25      94 ..      14     105 .. 0.69
   2 ?   -0.2   0.0       1.2   5.1e+02      37      87 ..     114     164 ..     110     168 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0048
                           DUF3450 30 aaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelv 99
                                      +   + q+ i +l+ e+q+l++++++ ++ ++++  ++++ e+ +++++ +i+ l+++i++i+e +++l+
  gi|298674753|ref|YP_003726503.1| 25 KRIDELQSYIMELEIESQKLQRRLEKKEKNAKRAISEKQEAEEKLNAANVKIETLQNEIKSIKEERDDLQ 94
                                      4455667777777777777777777777777777777777777777777777777777777777666665 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.2
                           DUF3450  37 kkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeq 87 
                                       +ki++l  ++++l   y +  + l++l+  n+ l+++ ++ ++ ++++e +
  gi|298674753|ref|YP_003726503.1| 114 SKIQSLRSNTDTLITAYIKPDDTLSNLKNPNKLLDSIDDNTKNLLSKIESS 164
                                       588899999999999999999999999999999999888888888887765 PP

>> T3SSipB  Type III cell invasion protein SipB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   7.7    0.0099       4.2      52     111 ..      38      94 ..      16     156 .. 0.71
   2 ?   -0.5   0.0       3.7   1.6e+03      66      97 ..     233     264 ..     228     280 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0099
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---------CHHHHHHHHH CS
                           T3SSipB  52 lseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPdePekakleaaeqQag 111
                                         e +++++ le++ ++a+ a s+ ++a++k+++a  +++ L   + e + +++++  ++
  gi|298674753|ref|YP_003726503.1|  38 EIESQKLQRRLEKKEKNAKRAISEKQEAEEKLNAANVKIETL---QNEIKSIKEERDDLQ 94 
                                       345566677777777777777777777777777777777777...455555555554444 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 3.7
                                       HHHHHHHHHHHHHHHHHHHHHHHHHTT----- CS
                           T3SSipB  66 iekadqaksaadaatkkvdeaqkrlkeLaPde 97 
                                        e++  +ks ++a +kk    qkr +eL  ++
  gi|298674753|ref|YP_003726503.1| 233 FENYSVIKSSVKAKHKKGGFSQKRFEELRNED 264
                                       57778889999999999999999999995544 PP

>> HAUS6_N  HAUS augmin-like complex subunit 6 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1  11.3      0.29   1.2e+02     161     226 ..      18      81 ..       4     124 .. 0.67
   2 ?    4.9   0.0     0.039        17     118     167 ..     238     287 ..     236     329 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.29
                           HAUS6_N 161 rekaaadrarqkyqenaqllekkerelraeleelqaelkaekeaakkekkeasedaeeekikkvrn 226
                                         k++ ++ + ++q++ ++le + ++l+++le+ +++ k  +++++k++ e++ +a + ki++++n
  gi|298674753|ref|YP_003726503.1|  18 SGKQKLEKRIDELQSYIMELEIESQKLQRRLEKKEKNAK--RAISEKQEAEEKLNAANVKIETLQN 81 
                                       455566666666666666666666666666666444444..4444444454555554446665554 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.039
                           HAUS6_N 118 Vlkkvlkekskklalevreaaskkaqdlsklvaahrvslrrflrekaaad 167
                                       V+k  +k+k+kk  ++++++ + +++d+  ++++++ +  r+++ +++++
  gi|298674753|ref|YP_003726503.1| 238 VIKSSVKAKHKKGGFSQKRFEELRNEDIDHHIEKVQSEFDRMMDGIENDI 287
                                       89999**************************************9999864 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   6.9   0.00016     0.067     107     173 ..      20      89 ..       5      92 .. 0.78
   2 ?   -1.1   0.1       3.4   1.5e+03     161     161 ..     138     138 ..     106     166 .. 0.43
   3 ?   -1.1   0.1       3.3   1.4e+03      84     124 ..     233     275 ..     230     285 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00016
                      Bacillus_HBL 107 lekLqeeiqqnqkevkqlikeLkklklklakdsknFktdv...deltsilagdsgvisqlqneiedlqgk 173
                                        +kL++ i + q ++ +l  e +kl+ +l+k++kn k ++   +e+++ l++ + +i++lqnei++++++
  gi|298674753|ref|YP_003726503.1|  20 KQKLEKRIDELQSYIMELEIESQKLQRRLEKKEKNAKRAIsekQEAEEKLNAANVKIETLQNEIKSIKEE 89 
                                       45667777777777777777777788888888888877665559999*******************9975 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3.4
                      Bacillus_HBL 161 s 161
                                       s
  gi|298674753|ref|YP_003726503.1| 138 S 138
                                       2 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 3.3
                      Bacillus_HBL  84 Fqsyyktlveavdkkdkae..llellekLqee.iqqnqkevkql 124
                                       F++y + ++++v++k k++    ++ e+L++e i +  ++v++ 
  gi|298674753|ref|YP_003726503.1| 233 FENY-SVIKSSVKAKHKKGgfSQKRFEELRNEdIDHHIEKVQSE 275
                                       6665.688999954444331145678888877666666666655 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   3.9     0.011       4.7      22      51 ..      27      56 ..      25      62 .. 0.89
   2 ?    3.9   0.7      0.13        56      28      45 ..      75      92 ..      63      97 .. 0.89
   3 ?    0.4   0.0       1.6   6.9e+02      21      41 ..     261     281 ..     245     286 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.011
                           DUF1192 22 veELeerIalLeaEIaRleaaiakkkasra 51
                                      ++EL+ +I +Le E ++l++ ++kk++  +
  gi|298674753|ref|YP_003726503.1| 27 IDELQSYIMELEIESQKLQRRLEKKEKNAK 56
                                      79**********************987654 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.13
                           DUF1192 28 rIalLeaEIaRleaaiak 45
                                       I++L+ EI+ +++++++
  gi|298674753|ref|YP_003726503.1| 75 KIETLQNEIKSIKEERDD 92
                                      69***********99976 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1.6
                           DUF1192  21 SveELeerIalLeaEIaRlea 41 
                                         e+++  I++ ++E +R+ +
  gi|298674753|ref|YP_003726503.1| 261 RNEDIDHHIEKVQSEFDRMMD 281
                                       56899999******9999866 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   5.2     0.016       6.8      14      75 ..      26      89 ..      13     100 .. 0.64
   2 ?   -0.6   0.0       4.9   2.1e+03      48      69 ..     262     283 ..     233     301 .. 0.52

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.016
                           DUF2203 14 llkelleelralrkeleeleeeleeakaeaekse..aaeleaeleeleaeieelveeieelGve 75
                                      +++el + +++l+ e ++l+++le+++++a++    ++e+e++l++++ +ie l +ei++++ e
  gi|298674753|ref|YP_003726503.1| 26 RIDELQSYIMELEIESQKLQRRLEKKEKNAKRAIseKQEAEEKLNAANVKIETLQNEIKSIKEE 89
                                      3444444555666666666666666665544332557777777777777888887777776655 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 4.9
                           DUF2203  48 aaeleaeleeleaeieelveei 69 
                                        +   +++e++++e++++++ i
  gi|298674753|ref|YP_003726503.1| 262 NEDIDHHIEKVQSEFDRMMDGI 283
                                       3333444444444444444444 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4  17.0     0.002      0.86     155     227 ..      20      95 ..      14     125 .. 0.76
   2 ?   -1.8   0.0       2.6   1.1e+03     231     248 ..     264     281 ..     232     326 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.002
                              Spc7 155 kelLekqeeeldellpeleeekaeleeeleklqe.aaeeles..idkeeLeelreelaelkaeieekkkelaelqe 227
                                       k++Lek+ +el+++  ele e ++l+++lek ++ a++ +++    +e+L+++  ++++l++ei++ k+e ++lq+
  gi|298674753|ref|YP_003726503.1|  20 KQKLEKRIDELQSYIMELEIESQKLQRRLEKKEKnAKRAISEkqEAEEKLNAANVKIETLQNEIKSIKEERDDLQD 95 
                                       6889999999999999999999999999988777333333322245788888888888888888888888777775 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.6
                              Spc7 231 eleekieelkeqkselee 248
                                       +++  ie+++++ +++++
  gi|298674753|ref|YP_003726503.1| 264 DIDHHIEKVQSEFDRMMD 281
                                       233333333333333333 PP

>> HAUS-augmin3  HAUS augmin-like complex subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7  12.3    0.0056       2.4      79     144 ..      19      84 ..       2      92 .. 0.88
   2 ?    3.2   0.1      0.13        55      49     138 ..      79     167 ..      77     180 .. 0.78
   3 ?   -2.8   0.1       8.8   3.8e+03     192     212 ..     203     235 ..     195     281 .. 0.46

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0056
                      HAUS-augmin3  79 sleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkklkeaqeelraenaetn 144
                                        +++Le+ ++eLq++   ++ + +kLq    + +++ ++  +e++ea++kl+ a+++++   +e++
  gi|298674753|ref|YP_003726503.1|  19 GKQKLEKRIDELQSYIMELEIESQKLQRRLEKKEKNAKRAISEKQEAEEKLNAANVKIETLQNEIK 84 
                                       57899*************************************************999998887776 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.13
                      HAUS-augmin3  49 LeeaLktiepsdlkqedvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekea 125
                                       L+   k+i++++++ +d +  + i     ++ ++L +++q L++  + ++  + k + + ++l++ ++ l++  +++
  gi|298674753|ref|YP_003726503.1|  79 LQNEIKSIKEERDDLQDIKF-RNIEVLHPSKFHDLISKIQSLRSNTDTLITAYIKPDDTLSNLKNPNKLLDSIDDNT 154
                                       67777777755555555544.333344467889*************************************9999999 PP

                      HAUS-augmin3 126 kkklkeaqeelra 138
                                       k+ l ++++++++
  gi|298674753|ref|YP_003726503.1| 155 KNLLSKIESSTGC 167
                                       9999999988765 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 8.8
                      HAUS-augmin3 192 Lesytkkqff............qGisdlvessd 212
                                       L++  +++f+             Gi + +e+++
  gi|298674753|ref|YP_003726503.1| 203 LNAILEQNFKicvlqihagesfVGIANPDEFEN 235
                                       555555555544444444444433443333332 PP

>> Leu_zip  Leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0  13.0    0.0041       1.8     131     202 ..      30      98 ..      16     141 .. 0.77
   2 ?    2.8   0.3      0.17        72     165     266 ..     238     340 ..     228     341 .] 0.76

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0041
                           Leu_zip 131 LkkeierLkeenekLkerlkelEkqatsaleeksklekalkelqkelgekkdekenskeiskleeklaelkl 202
                                       L+  i +L+ e +kL+ rl++ Ek+a++a++ek++ e++l++++ +++  ++e +   +i++ ++ l+++k 
  gi|298674753|ref|YP_003726503.1|  30 LQSYIMELEIESQKLQRRLEKKEKNAKRAISEKQEAEEKLNAANVKIETLQNEIK---SIKEERDDLQDIKF 98 
                                       888999**********************************999877776665544...45555555544443 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.17
                           Leu_zip 165 klekalkelqkelgekkdekenskeiskleeklaelkldlektleektasaksle..edlastkhelLkvqeqLela 239
                                        +++++k+++k+ g ++++  ++ + ++++++++++++++++ ++  +++ + +    d   t+h l +++ +  + 
  gi|298674753|ref|YP_003726503.1| 238 VIKSSVKAKHKKGGFSQKRF-EELRNEDIDHHIEKVQSEFDRMMDGIENDIDYIItgGDRGLTQHVLKNINTNSPVI 313
                                       55666666655544444333.356778999999**********99999998887522578889999999******** PP

                           Leu_zip 240 ekeLekkfqqtaayknlkemltkkneq 266
                                       ek ++ k+++ +  + lk+ l+ +  q
  gi|298674753|ref|YP_003726503.1| 314 EKSMDSKIEKYNLNNILKNALSYRRYQ 340
                                       *******99998888888888776666 PP

>> LUC7  LUC7 N_terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   7.4    0.0025         1      85     146 ..      26      87 ..      10      96 .. 0.89
   2 ?   -0.4   0.1       1.8   7.5e+02      77     114 ..     248     283 ..     238     326 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0025
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXX CS
                              LUC7  85 flrfleklledvdrkiqkgkqrleltqeekeeeeeakakkqeqlkeleekiekllaeaeelg 146
                                        +++l++++ +++   qk ++rle+++++ +++ ++k++ +e+l+  + kie+l +e+++  
  gi|298674753|ref|YP_003726503.1|  26 RIDELQSYIMELEIESQKLQRRLEKKEKNAKRAISEKQEAEEKLNAANVKIETLQNEIKSIK 87 
                                       57899*************************99999999****************99998765 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.8
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              LUC7  77 kklgyeeeflrfleklledvdrkiqkgkqrleltqeek 114
                                       kk g+ ++ +++l++  ed+d+ i+k ++  + + +  
  gi|298674753|ref|YP_003726503.1| 248 KKGGFSQKRFEELRN--EDIDHHIEKVQSEFDRMMDGI 283
                                       445555555555555..666666666666655554443 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   2.7      0.24     1e+02       4      39 ..      22      57 ..      21      60 .. 0.77
   2 ?   11.3   2.1    0.0008      0.34       4      35 ..      64      95 ..      63     100 .. 0.92
   3 ?   -0.1   0.1       2.9   1.2e+03      27      41 ..     144     158 ..     107     160 .. 0.69
   4 ?    2.1   0.1      0.63   2.7e+02      23      42 ..     262     281 ..     257     286 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.24
                         FlaC_arch  4 elEnklsklsteletvkkeneelsksveelkenVkd 39
                                      +lE+++++l++ +  ++ e ++l+  +e+ ++n k+
  gi|298674753|ref|YP_003726503.1| 22 KLEKRIDELQSYIMELEIESQKLQRRLEKKEKNAKR 57
                                      688888888888888888888888888887777665 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0008
                         FlaC_arch  4 elEnklsklsteletvkkeneelsksveelke 35
                                      e E+kl+   +++et+++e+++++++ ++l++
  gi|298674753|ref|YP_003726503.1| 64 EAEEKLNAANVKIETLQNEIKSIKEERDDLQD 95
                                      679**********************9998875 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 2.9
                         FlaC_arch  27 sksveelkenVkdll 41 
                                       +k ++ +++n k+ll
  gi|298674753|ref|YP_003726503.1| 144 NKLLDSIDDNTKNLL 158
                                       455677777777776 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.63
                         FlaC_arch  23 neelsksveelkenVkdlls 42 
                                       ne++   +e+++ ++ ++++
  gi|298674753|ref|YP_003726503.1| 262 NEDIDHHIEKVQSEFDRMMD 281
                                       78888888888888887775 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7  11.3    0.0018      0.79      80     131 ..      18      69 ..       4      73 .. 0.81
   2 ?    4.3  21.4     0.088        38      15      86 ..      23      94 ..      20     165 .. 0.93
   3 ?   -2.2   0.1       9.1   3.9e+03     105     116 ..     264     275 ..     247     288 .. 0.50

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0018
                    CENP-F_leu_zip  80 sekeeLekelqkkqervseLeslnsslenlleekEqekvqmkeeskaaveeL 131
                                       s k++Lek + + q+ + eLe    +l++ le+kE++ ++   e ++a e+L
  gi|298674753|ref|YP_003726503.1|  18 SGKQKLEKRIDELQSYIMELEIESQKLQRRLEKKEKNAKRAISEKQEAEEKL 69 
                                       679**********************************555555555555555 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.088
                    CENP-F_leu_zip 15 serkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLe 86
                                       e++ d L+  + +Le e + +++ +ek + +a  +  e ++ +e+++  + + + l+ +++++++e+++L+
  gi|298674753|ref|YP_003726503.1| 23 LEKRIDELQSYIMELEIESQKLQRRLEKKEKNAKRAISEKQEAEEKLNAANVKIETLQNEIKSIKEERDDLQ 94
                                      57788999999*******************99999999999********99******************994 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 9.1
                    CENP-F_leu_zip 105 slenlleekEqe 116
                                       ++ + +e+   e
  gi|298674753|ref|YP_003726503.1| 264 DIDHHIEKVQSE 275
                                       222222222222 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2  18.7    0.0057       2.4      97     189 ..      19     119 ..       3     121 .. 0.79
   2 ?    0.9   0.1      0.99   4.2e+02     118     134 ..     261     277 ..     192     328 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0057
                           UPF0242  97 eeeeLkeeldakeeelerlkeenqqLqekleaiaedfee...lkleleeqLaekqellqeyqetieeqrsvlekrqd 170
                                        +++L++++d+ ++ + +l+ e q+Lq +le+  ++ ++    k+e+ee+L+  + +++++q++i++ +++ +  qd
  gi|298674753|ref|YP_003726503.1|  19 GKQKLEKRIDELQSYIMELEIESQKLQRRLEKKEKNAKRaisEKQEAEEKLNAANVKIETLQNEIKSIKEERDDLQD 95 
                                       57899**********************99999877555422269******************999988888776665 PP

                           UPF0242 171 ....qieqLe.skVrDlnyEiktL 189
                                           +ie L  sk +Dl   i+ L
  gi|298674753|ref|YP_003726503.1|  96 ikfrNIEVLHpSKFHDLISKIQSL 119
                                       322267777557888888777765 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.99
                           UPF0242 118 enqqLqekleaiaedfe 134
                                       +n+ +    e+++ +f+
  gi|298674753|ref|YP_003726503.1| 261 RNEDIDHHIEKVQSEFD 277
                                       23333333333333333 PP

>> CENP-Q  CENP-Q, a CENPA-CAD centromere complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4  15.8      0.37   1.6e+02      45     117 ..      24     123 ..      12     165 .. 0.50
   2 ?   -1.2   0.0       4.7     2e+03      34      64 ..     255     285 ..     239     290 .. 0.64

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.37
                            CENP-Q  45 lhslelLeaeiekeeralerdyeaLreLeknakaearerke...klkkehvllqesdseelslleassdevlgea.. 116
                                       ++ +++L+++i ++e + ++ ++ L++ eknak++ +e +e   kl  + v  ++ ++e +s +e+ +d        
  gi|298674753|ref|YP_003726503.1|  24 EKRIDELQSYIMELEIESQKLQRRLEKKEKNAKRAISEKQEaeeKLNAANVKIETLQNEIKSIKEERDD-----Lqd 95 
                                       556666666666666666666666666677777777665552212222222233222222222222222.....122 PP

                            CENP-Q 117 ...........................s 117
                                                                  +
  gi|298674753|ref|YP_003726503.1|  96 ikfrnievlhpskfhdliskiqslrsnT 123
                                       2344444444444444444444444442 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 4.7
                            CENP-Q  34 kaaleaqLspelhslelLeaeiekeeraler 64 
                                       k+ +e   +   h++e+ ++e++++    e+
  gi|298674753|ref|YP_003726503.1| 255 KRFEELRNEDIDHHIEKVQSEFDRMMDGIEN 285
                                       4445555555566777777777766665555 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   6.5       2.8   1.2e+03      40      68 ..      24      52 ..       5      67 .. 0.66
   2 ?    5.6  11.2     0.047        20      11      62 ..      44      95 ..      42     102 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 2.8
                            Csm1_N 40 dqeiesLkeqlaeleekvkeleerrkkqe 68
                                      +++i +L+  + ele ++++l+ r +k+e
  gi|298674753|ref|YP_003726503.1| 24 EKRIDELQSYIMELEIESQKLQRRLEKKE 52
                                      45667777777777777777766666654 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.047
                            Csm1_N 11 VqerldsAdllvsklvhENsvLsqkletkdqeiesLkeqlaeleekvkelee 62
                                      +q rl++ +   ++ + E +  ++kl+  + +ie+L++++++++e++++l++
  gi|298674753|ref|YP_003726503.1| 44 LQRRLEKKEKNAKRAISEKQEAEEKLNAANVKIETLQNEIKSIKEERDDLQD 95
                                      699********************************************99987 PP

>> DUF641  Plant protein of unknown function (DUF641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   6.6    0.0034       1.4      71     119 ..      18      66 ..       2      72 .. 0.77
   2 ?    0.7   2.6       1.4   6.1e+02      78     112 ..      60      94 ..      52     102 .. 0.66
   3 ?   -1.8   0.0       8.9   3.8e+03      85      85 ..     274     274 ..     234     333 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0034
                            DUF641  71 aeeseleaeiqeqrsllktyeitvkkleaelkakdseieeLkekLeeae 119
                                         +++le++i+e++s +  +ei ++kl++ l++k+++ ++  ++ +eae
  gi|298674753|ref|YP_003726503.1|  18 SGKQKLEKRIDELQSYIMELEIESQKLQRRLEKKEKNAKRAISEKQEAE 66 
                                       57899******************************98877655544444 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.4
                            DUF641  78 aeiqeqrsllktyeitvkkleaelkakdseieeLk 112
                                       +e qe  ++l++ ++ ++ l++e+k+ ++e + L+
  gi|298674753|ref|YP_003726503.1|  60 SEKQEAEEKLNAANVKIETLQNEIKSIKEERDDLQ 94 
                                       45566666777777777777777777666666554 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 8.9
                            DUF641  85 s 85 
                                       s
  gi|298674753|ref|YP_003726503.1| 274 S 274
                                       2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2405  (0.13414); expected 358.6 (0.02)
Passed bias filter:                      744  (0.041497); expected 358.6 (0.02)
Passed Vit filter:                       168  (0.00937029); expected 17.9 (0.001)
Passed Fwd filter:                        62  (0.00345808); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              42  [number of targets reported over threshold]
# CPU time: 0.76u 0.30s 00:00:01.06 Elapsed: 00:00:00.48
# Mc/sec: 2128.80
//
Query:       gi|298674754|ref|YP_003726504.1|  [L=64]
Description: hypothetical protein Metev_0808 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.027   14.4   0.0        2.9    7.9   0.0    2.1  2  HTH_1     Bacterial regulatory helix-turn-helix protein, lysR


Domain annotation for each model (and alignments):
>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0   0.00016       2.9      32      47 ..      14      29 ..      13      39 .. 0.89
   2 ?    4.9   0.0    0.0014        26      32      47 ..      45      60 ..      44      64 .] 0.85

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00016
                                      HHHHHHHHHHTS-SEE CS
                             HTH_1 32 rqikrLEeelgvpLfe 47
                                      ++i++LE+ lgv+L+ 
  gi|298674754|ref|YP_003726504.1| 14 KAINDLEKKLGVTLLA 29
                                      79************85 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0014
                                      HHHHHHHHHHTS-SEE CS
                             HTH_1 32 rqikrLEeelgvpLfe 47
                                      + +k+LE+ lg  L+ 
  gi|298674754|ref|YP_003726504.1| 45 KKVKDLEDKLGMSLVA 60
                                      5799*********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 470.56
//
Query:       gi|298674755|ref|YP_003726505.1|  [L=255]
Description: ribosomal RNA methyltransferase RrmJ/FtsJ [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-58  197.1   0.0    2.9e-58  196.9   0.0    1.1  1  FtsJ             FtsJ-like methyltransferase
      6e-09   35.8   1.4    1.5e-08   34.5   1.4    1.7  1  TRAM             TRAM domain
    1.9e-05   24.5   0.3    0.00051   19.9   0.3    2.6  1  Methyltransf_31  Methyltransferase domain
    0.00031   20.6   0.0     0.0024   17.7   0.0    2.2  1  Methyltransf_23  Methyltransferase domain
    0.00048   20.8   0.2      0.035   14.8   0.0    3.0  3  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
      0.034   14.0   0.3      0.073   13.0   0.3    1.7  1  UPF0146          Uncharacterised protein family (UPF0146)
      0.067   13.1   0.1        0.1   12.5   0.1    1.3  1  NAD_binding_10   NAD(P)H-binding
       0.12   13.0   0.1       0.44   11.2   0.0    2.1  2  Methyltransf_11  Methyltransferase domain


Domain annotation for each model (and alignments):
>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.9   0.0   1.3e-61   2.9e-58       1     177 []      17     191 ..      17     191 .. 0.98

  Alignments for each domain:
  == domain 1  score: 196.9 bits;  conditional E-value: 1.3e-61
                                       CCCCHHHHHHHHHHHHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSSHHHTTEEEECS-CCCSSHHH CS
                              FtsJ   1 yrsRsayKLleidekfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpmaplpgvttiqgditdpetie 77 
                                       yrsR+ayKLl+i+++f+++++++t+vDlgaaPGgw qv+ +   +  kvv++Dlq ++ ++gv+t++gd t+ +t +
  gi|298674755|ref|YP_003726505.1|  17 YRSRAAYKLLQINNRFNVIEKNDTIVDLGAAPGGWLQVARKIS-N-NKVVGIDLQRIKSIEGVETVKGDMTSDRTVR 91 
                                       9**************************************9995.3.89***************************** PP

                                       HHCHCHHHSSEEEEEE--S-SS-CHHHHHHHHHCCCCHHHHCCHCCCCECCCEEEECCCHCCCHHHHHHHHHCCEEE CS
                              FtsJ  78 kikealserkvdlvvsDgapdvsgvhdldeylqsqLllaalelalkllkpggtfvlkifrgeeteallkqlkkfFek 154
                                       ki++++++++vd+v+sD ap+ sg+++ld++++++L+++ale+a ++lkp g+fv+k+f+g+ ++++l+++k+ F +
  gi|298674755|ref|YP_003726505.1|  92 KILKTIEDEGVDVVISDAAPNLSGNWNLDHARSIDLVESALEFAKQVLKPSGNFVVKVFQGDMFNDFLEKVKNNFAY 168
                                       ***************************************************************************** PP

                                       EEEEE-SS--CCG-EEEEEEEEC CS
                              FtsJ 155 vsvvkPkssrsesseeflvcrgf 177
                                       v+ ++Pk+srs+s+e++++  +f
  gi|298674755|ref|YP_003726505.1| 169 VKAHEPKASRSQSAEIYVIGMDF 191
                                       ******************99876 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   1.4   6.6e-12   1.5e-08       3      62 .]     197     252 ..     195     252 .. 0.92

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 6.6e-12
                                       XXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEEE CS
                              TRAM   3 yvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGell 62 
                                       +  ++++V+++  + s g+g   ++ g+v+fv++    IGd+V++kI++vk+ ++++ ++
  gi|298674755|ref|YP_003726505.1| 197 KKNEEYDVEITSIG-SGGDGAVTIN-GFVIFVKD--VDIGDRVKIKIEDVKPSFAFANVV 252
                                       6789**********.*****98888.********..459******************986 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.3   2.3e-07   0.00051       2     129 ..      36     169 ..      35     202 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.3e-07
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDise.eaielArenaqklgldnveFeqgdieeleklledekfDl 77 
                                       +k+ +++DlG++ G  + ++    +++ +vvGiD +  ++ie  ++   +  +d        + ++ k++ede +D+
  gi|298674755|ref|YP_003726505.1|  36 EKNDTIVDLGAAPGGWLQVAR--KISNNKVVGIDLQRiKSIEGVETVKGDMTSD------RTVRKILKTIEDEGVDV 104
                                       7999**********9999888..57899******98758999999987777777......44445222356899*** PP

                   Methyltransf_31  78 ilsnevl...........naladpdkileeiervlkpggilliedpr..llaelpakveeeskay 129
                                       ++s+++              +   +++le +++vlkp g +++  ++  +  ++++kv+++  + 
  gi|298674755|ref|YP_003726505.1| 105 VISDAAPnlsgnwnldhaRSIDLVESALEFAKQVLKPSGNFVVKVFQgdMFNDFLEKVKNNFAYV 169
                                       ****88888898888887888889999****************9999665556667777777654 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.1e-06    0.0024      19     124 ..      34     154 ..      14     184 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.1e-06
                   Methyltransf_23  19 klraggrvLdiGcGtGillevlrengf.svtgvDlspeaveiaekakkaqkdqfdeqeaae................ 78 
                                         +++  ++d+G++ G +l+v+r+    +v+g+Dl ++  + +e+  + + d++      +                
  gi|298674755|ref|YP_003726505.1|  34 VIEKNDTIVDLGAAPGGWLQVARKISNnKVVGIDLQRI--KSIEGVETVKGDMTSDRT--Vrkilktiedegvdvvi 106
                                       3678889***************9986669******765..444455555555552222..12244444333334444 PP

                   Methyltransf_23  79 pqgkfdlIvlrevle..hvpdppellrqiatllkpgGylllseplasl 124
                                       +++ ++l  ++++ +  +++ ++++l  +++ lkp G++++ ++  + 
  gi|298674755|ref|YP_003726505.1| 107 SDAAPNLSGNWNLDHarSIDLVESALEFAKQVLKPSGNFVVKVFQGDM 154
                                       444555555555433114445889999999999999999999986554 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.5e-05     0.035       1      97 []      41     143 ..      41     143 .. 0.68
   2 !    6.7   0.0    0.0053        12      25      68 ..     123     169 ..     112     183 .. 0.81
   3 ?   -0.6   0.0         1   2.3e+03      42      67 ..     177     204 ..     153     210 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.5e-05
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEE....... CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvs....... 70 
                                       ++dlG+ +G +++ + k  ++ kv+g+D++     +  e ++ +  + + v++ +++   ed+ +D+v+s       
  gi|298674755|ref|YP_003726505.1|  41 IVDLGAAPGGWLQVARKI-SNNKVVGIDLQRIKSIEGVETVKGDMTSDRTVRKILKT--IEDEGVDVVISdaapnls 114
                                       89*******998877766.68********8755444555554333233333333333..36889*****97777776 PP

                                       .ESTGGG.SSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  71 .sgalhh.lsdedlekalkeiarvLkpgG 97 
                                        + +l h  s + +e al+ +++vLkp G
  gi|298674755|ref|YP_003726505.1| 115 gNWNLDHaRSIDLVESALEFAKQVLKPSG 143
                                       53346674666667889999999999988 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0053
                                       EEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCG..BSSSTTTEEEE CS
                   Methyltransf_25  25 tgvDiseemleaareraeeegl.nvefvqgdaed..lpfedgsfDlv 68 
                                         +D+ e++le a++ ++ +g   v++ qgd+ +  l+  ++ f +v
  gi|298674755|ref|YP_003726505.1| 123 RSIDLVESALEFAKQVLKPSGNfVVKVFQGDMFNdfLEKVKNNFAYV 169
                                       569**************9987789*******9443566777777666 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1
                                       HH.TTTTEEEEESBCCGBSS.STTTEEE CS
                   Methyltransf_25  42 ee.eglnvefvqgdaedlpf.edgsfDl 67 
                                       ++ +++++ ++ +d+ + p  +++++D+
  gi|298674755|ref|YP_003726505.1| 177 SRsQSAEIYVIGMDFLNTPVkKNEEYDV 204
                                       3313347777788888888525557777 PP

>> UPF0146  Uncharacterised protein family (UPF0146)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   3.2e-05     0.073       3      64 ..      27      88 ..      25     112 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.2e-05
                                      HHHHHHHHHS-SSEEEEET-..TT--HHHHHHHHHS-EEEEE-SS-S....STTEE---SSS-- CS
                           UPF0146  3 elakkiaeenargkvvEvGi..GrkldvaealakrgvdlvatDikekkakegvrivrDDvtdPn 64
                                      ++ + + + +++  +v++G+  G  l+va+++++   ++v +D++  k  egv+ v+ D+t+ +
  gi|298674755|ref|YP_003726505.1| 27 QINNRFNVIEKNDTIVDLGAapGGWLQVARKISNN--KVVGIDLQRIKSIEGVETVKGDMTSDR 88
                                      67777888888999*****877899*********9..9***********************865 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   4.6e-05       0.1      34      74 ..      70     120 ..      55     150 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.6e-05
                                       HHHCTTTCEEEE--TT-CCHHHHHHT.....T-SEEEES-....--TCC.H CS
                    NAD_binding_10  34 eleaeeglevvegdvtdvedlaealk.....gadaVvsal....ggggk.d 74 
                                       ++++ eg+e+v+gd+t+  ++++ lk     g+d+V+s +    +g+++ d
  gi|298674755|ref|YP_003726505.1|  70 RIKSIEGVETVKGDMTSDRTVRKILKtiedeGVDVVISDAapnlSGNWNlD 120
                                       3444579******************989999*******9944443333333 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0002      0.44       2      96 .]      43     147 ..      42     147 .. 0.67
   2 ?   -2.8   0.0       4.6     1e+04      45      56 ..     184     195 ..     153     205 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0002
                                       EET-TTSHHHHHHHHTT.SEEEEEES-HHHH.HHHHHHCCHHT-EEEETTEECCC.......T.SS-TT-EEEEEEE CS
                   Methyltransf_11   2 dvGcGtGrlaealakrg.arvvgvDlskeml.klakekaseeglkvefvvadaek.......l.pfednsfDlvvss 68 
                                       d+G+  G  ++   k    +vvg+Dl      +            ve v++d+++       l  +ed+ +D+v+s 
  gi|298674755|ref|YP_003726505.1|  43 DLGAAPGGWLQVARKISnNKVVGIDLQRIKSiEG-----------VETVKGDMTSdrtvrkiLkTIEDEGVDVVISD 108
                                       7777777777777766678888888755443122...........2223333332222222333699*********9 PP

                                       S........-CCC-...CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  69 e........vlhhv...edpekalkeiaRvLkpgGllvi 96 
                                                 l+h    + +e+al+ +++vLkp G +v+
  gi|298674755|ref|YP_003726505.1| 109 AapnlsgnwNLDHArsiDLVESALEFAKQVLKPSGNFVV 147
                                       9777776666666677789****************9986 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.6
                                       EEETTEECCCTS CS
                   Methyltransf_11  45 vefvvadaeklp 56 
                                       + ++ +d+ ++p
  gi|298674755|ref|YP_003726505.1| 184 IYVIGMDFLNTP 195
                                       333333444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       843  (0.0470188); expected 358.6 (0.02)
Passed bias filter:                      639  (0.0356406); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1615.80
//
Query:       gi|298674756|ref|YP_003726506.1|  [L=361]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-25   87.8   3.2    8.6e-25   86.5   1.2    2.5  3  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
    7.6e-10   39.1   1.3    7.6e-10   39.1   1.3    1.7  2  OrfB_IS605       Probable transposase
  ------ inclusion threshold ------
      0.066   12.7   0.1       0.24   10.9   0.1    1.9  2  HTH_OrfB_IS605   Helix-turn-helix domain
       0.07   13.1   0.1       0.12   12.4   0.1    1.4  1  HypA             Hydrogenase/urease nickel incorporation, met
       0.34   11.0   2.8       0.87    9.7   0.1    2.2  2  UPF0547          Uncharacterised protein family UPF0547
          1    9.4   5.0        2.5    8.1   5.0    1.6  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
        1.1    9.4   4.9         12    6.1   2.0    2.9  2  DUF2387          Probable metal-binding protein (DUF2387)
        1.9    8.3   7.0        7.1    6.4   7.0    2.0  1  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
        2.1    8.1   4.5         21    4.9   0.4    2.3  2  Rubredoxin_2     Rubredoxin metal binding domain
        2.2    9.1   6.5        5.2    8.0   6.5    1.6  1  Tnp_zf-ribbon_2  DDE_Tnp_1-like zinc-ribbon


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.6   4.6e+03      12      29 ..     165     182 ..     159     197 .. 0.73
   2 ?   -0.0   0.0      0.47   8.5e+02      15      30 ..     187     202 ..     181     230 .. 0.86
   3 !   86.5   1.2   4.8e-28   8.6e-25       1      69 []     277     346 ..     277     346 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.6
                    OrfB_Zn_ribbon  12 akeyGikveevnpayTSk 29 
                                           G+ + +vn a TS 
  gi|298674756|ref|YP_003726506.1| 165 DDVLGVDLGVVNIATTSD 182
                                       555688888888888886 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.47
                    OrfB_Zn_ribbon  15 yGikveevnpayTSkt 30 
                                       +G k  e+ ++yTS +
  gi|298674756|ref|YP_003726506.1| 187 KGTKADEIRERYTSLK 202
                                       58899999999*9965 PP

  == domain 3  score: 86.5 bits;  conditional E-value: 4.8e-28
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f++l++++ ykak +G++v+ +np yTS++CseCg+++k+ ++++ +fkC++Cg++ ++D+nA+ Ni++r
  gi|298674756|ref|YP_003726506.1| 277 FSELTRFILYKAKLEGVPVVIINPMYTSQQCSECGYIDKNnRQKQSNFKCKRCGHRENADYNASKNIAHR 346
                                       899*************************************99*************************997 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   1.3   4.2e-13   7.6e-10      10     106 ..     159     246 ..     151     256 .. 0.85
   2 ?   -3.4   0.1       6.3   1.1e+04      41      60 ..     314     333 ..     306     346 .. 0.56

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 4.2e-13
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsr 86 
                                        ++  +  ++g+DlG+ n+at+++++    +ykg ++++  ++++  + +lqs    s     a++ l++l++k +r
  gi|298674756|ref|YP_003726506.1| 159 NEVRYNDDVLGVDLGVVNIATTSDNE----VYKGTKADEIRERYTSLKSRLQSAGTWS-----AKKHLRKLSKKERR 226
                                       555566789*****************....***********************96555.....79999999999999 PP

                        OrfB_IS605  87 rrkhllhklathliktlkev 106
                                       + ++l h +a++l+++ k++
  gi|298674756|ref|YP_003726506.1| 227 FKRDLNHRVAKQLVERAKDT 246
                                       9999999***9999987765 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 6.3
                        OrfB_IS605  41 ykgrrlksdykylakeiael 60 
                                        k +r k+ +++ +++  + 
  gi|298674756|ref|YP_003726506.1| 314 DKNNRQKQSNFKCKRCGHRE 333
                                       44445555555555555444 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00013      0.24       1      24 [.       1      23 [.       1      25 [. 0.92
   2 ?   -2.5   0.0         2   3.7e+03      11      24 ..     263     276 ..     256     277 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00013
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartf 24
                                      M l++ k+ l+P+ eQ++kl  t+
  gi|298674756|ref|YP_003726506.1|  1 M-LLTLKVKLNPDREQRNKLLTTM 23
                                      7.8999**************9987 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2
                    HTH_OrfB_IS605  11 yPTpeQeeklartf 24 
                                         T+ Q+  l +++
  gi|298674756|ref|YP_003726506.1| 263 TVTKAQRDRLGKWA 276
                                       56999*99998886 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   6.9e-05      0.12      60      96 ..     288     333 ..     235     343 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.9e-05
                                       -EEE......EEEE--EEEETTTS-EEECHH..H.HHS-TTTSSS- CS
                              HypA  60 aeLe......ieevpvkvrCreCgkefelee..k.alrCpkCgsad 96 
                                       a+Le      i+ +  + +C+eCg+  + ++  + +++C++Cg+++
  gi|298674756|ref|YP_003726506.1| 288 AKLEgvpvviINPMYTSQQCSECGYIDKNNRqkQsNFKCKRCGHRE 333
                                       5555555555777788999*****9888555333788*****9874 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00049      0.87      15      25 ..     305     315 ..     303     316 .. 0.87
   2 ?    1.0   0.6      0.25   4.6e+02      16      22 ..     325     331 ..     324     332 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00049
                           UPF0547  15 qfCphCGyvFq 25 
                                       q C++CGy+++
  gi|298674756|ref|YP_003726506.1| 305 QQCSECGYIDK 315
                                       89******986 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.25
                           UPF0547  16 fCphCGy 22 
                                       +C  CG+
  gi|298674756|ref|YP_003726506.1| 325 KCKRCGH 331
                                       5767777 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   5.0    0.0014       2.5      19      45 ..     305     331 ..     301     332 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0014
                     Zn_Tnp_IS1595  19 fvCPhCgsr.kayriktrglfqCkeCrk 45 
                                       + C  Cg+  k  r k+   f+Ck+C++
  gi|298674756|ref|YP_003726506.1| 305 QQCSECGYIdKNNRQKQ-SNFKCKRCGH 331
                                       57*******77777777.********98 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1     0.099   1.8e+02      38      72 ..     216     250 ..     213     252 .. 0.86
   2 ?    6.1   2.0    0.0068        12      31      49 ..     305     323 ..     299     345 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.099
                           DUF2387  38 ftdelsekgqsvakelktrvnkdeekeasakvqtv 72 
                                       ++ +ls+k++ ++++l+ rv+k+  ++a+++ +++
  gi|298674756|ref|YP_003726506.1| 216 HLRKLSKKERRFKRDLNHRVAKQLVERAKDTFRAI 250
                                       6778999999*************999988887776 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0068
                           DUF2387  31 rECvsCgftdelsekgqsv 49 
                                         C +Cg++d+ + ++qs 
  gi|298674756|ref|YP_003726506.1| 305 QQCSECGYIDKNNRQKQSN 323
                                       5799*******99997664 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   7.0     0.004       7.1       3      26 ..     307     332 ..     305     333 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.004
                                       -SSS-..-B----SSS----SSS--- CS
                    DNA_RNApol_7kD   3 CgeCg..aevslkkgdpiRCkeCGhR 26 
                                       C eCg  +++  +k+   +Ck CGhR
  gi|298674756|ref|YP_003726506.1| 307 CSECGyiDKNNRQKQSNFKCKRCGHR 332
                                       99998666888899999********9 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.3     0.017        31       2       8 ..     306     312 ..     306     315 .. 0.89
   2 ?    4.9   0.4     0.012        21       1      10 [.     324     333 ..     324     335 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.017
                      Rubredoxin_2   2 vCsqCGf 8  
                                       +Cs+CG+
  gi|298674756|ref|YP_003726506.1| 306 QCSECGY 312
                                       7*****9 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.012
                      Rubredoxin_2   1 YvCsqCGfes 10 
                                       + C++CG++ 
  gi|298674756|ref|YP_003726506.1| 324 FKCKRCGHRE 333
                                       78*****986 PP

>> Tnp_zf-ribbon_2  DDE_Tnp_1-like zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   6.5    0.0029       5.2       3      23 ..     307     330 ..     305     335 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0029
                   Tnp_zf-ribbon_2   3 CkvClk...kkikkeTriiCqeCd 23 
                                       C  C +   ++++k++++ C+ C+
  gi|298674756|ref|YP_003726506.1| 307 CSECGYidkNNRQKQSNFKCKRCG 330
                                       999*****8899999********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       947  (0.0528195); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2519.82
//
Query:       gi|298674757|ref|YP_003726507.1|  [L=337]
Description: N-acetyl-gamma-glutamyl-phosphate reductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.3e-35  119.9   0.0    1.3e-34  119.2   0.0    1.3  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
    7.1e-24   84.9   0.0      1e-23   84.4   0.0    1.1  1  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
      0.004   17.7   0.0     0.0083   16.7   0.0    1.6  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
       0.12   13.2   0.0       0.29   12.0   0.0    1.6  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 


Domain annotation for each model (and alignments):
>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.2   0.0   2.9e-38   1.3e-34       2     118 ..       4     135 ..       3     138 .. 0.97

  Alignments for each domain:
  == domain 1  score: 119.2 bits;  conditional E-value: 2.9e-38
                                       EEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGC.TT-SEEEE-SCHH CS
                    Semialdhyde_dh   2 vaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeel.kevdivflalpag 77 
                                       v+i+G +Gy+G el+rlL +h++ ++   +s++  aG+k+++++k+l++  +l++ed+++ +l +++d++fla+p+g
  gi|298674757|ref|YP_003726507.1|   4 VGIIGSSGYTGGELIRLLVNHKYTNIEICTSRKF-AGQKVSDVHKHLKGFINLEFEDISPRDLkNRCDVIFLAVPHG 79 
                                       9********************************9.**********************999999899*********** PP

                                       HHHHHHHHHHHTTSEEEESSSTTTTST...............TSEBE-HHHHGGGG CS
                    Semialdhyde_dh  78 vskelapklaeagvkviDlssdfRlkd...............davyvlpevnreai 118
                                       +s++++p+l+++ +kviDls+d+R+++               ++vy+lpe+++e  
  gi|298674757|ref|YP_003726507.1|  80 TSMNIVPDLLDEYTKVIDLSADYRINSqtfenlygiehsdkrKVVYGLPEIHPEVS 135
                                       ****************************************************9975 PP

>> Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.4   0.0   2.3e-27     1e-23       3     184 .]     156     308 ..     155     308 .. 0.96

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 2.3e-27
                                       HHHHCTT.EEEEEEEEEEEGGGCHHHHHHHHHHHHHHHHHSTTS.CTTTSSHHTTSEESTCSTBTTTTCHCBHHHHH CS
                   Semialdhyde_dhC   3 PLldalgelervivatyqavSGaGkkgvreLlkqvaelqrsdeakpgvfgvpiagNlipyidkeedkgepetreelk 79 
                                       PL++  g ++++i+++++++ GaG +                 +++  ++ + a N+ py+ +  +++  e+ +el+
  gi|298674757|ref|YP_003726507.1| 156 PLANS-GLIDSIIFDSKSGITGAGVN-----------------PTQTSHYPNMAENVQPYKLT-SHRHYAEMFQELS 213
                                       99997.99*****************6.................999*****************.9************ PP

                                       HHHHHHHHCTESCSEEEEEEEESBSSEEEEEEEEEES..SSHHHHHHHHHHHHCSTTEEEEESSHCHHSSHHHHTTC CS
                   Semialdhyde_dhC  80 avaetkkileftekvsatcvrVPvlrGhseavtiklk..lkdveveeveellaaapevkvvvneeedrPtpaavagg 154
                                       +++e+   ++ft+      + +P +rG++++++i ++  ++++ev+ ++++++++ +++v++ +   +P +  v+g 
  gi|298674757|ref|YP_003726507.1| 214 MMDESLININFTP------HVIPSIRGILTTAHIFTNrqVSTEEVKSIYAEYYKD-NPFVRIID--GIPSLSTVRG- 280
                                       *************......78****************999999***********9.*******8..*********9. PP

                                       SSSEEEEEEEEETTCTTEEEEEEEEETTTT CS
                   Semialdhyde_dhC 155 tnsvsVGRirkdemgdeglklvvvgDNllk 184
                                       +n++++G ++ d  +++ +++v+++DNl+k
  gi|298674757|ref|YP_003726507.1| 281 SNFCDIG-FEIDVNNNR-VVVVSAIDNLVK 308
                                       9******.*****8887.**********97 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.9e-06    0.0083       2      93 ..       4      97 ..       3     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.9e-06
                                      EEEE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC....-EEECECHHHHHHH-SEEEE-S-HHHHH CS
                     F420_oxidored  2 igii.GaGnmgealasgllaagaqpheivvansrnpekaeelaeelg....vkvtavdneeaaeeadvvvlavkpedve 75
                                      +gii  +G  g  l++ l+++ +++ ei+   +   +k+   +++l+     + +  +  ++ +++dv++lav+     
  gi|298674757|ref|YP_003726507.1|  4 VGIIgSSGYTGGELIRLLVNHKYTNIEICTSRKFAGQKVSDVHKHLKgfinLEFEDISPRDLKNRCDVIFLAVPHGTSM 82
                                      89**557**************9899999955555578999999999899887778888899*************99888 PP

                                      HHHHHCGHHHHTTSEEEE CS
                     F420_oxidored 76 evlselakdalkgklvis 93
                                      +++ +l   +++ + vi+
  gi|298674757|ref|YP_003726507.1| 83 NIVPDL---LDEYTKVID 97
                                      888888...445555555 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.5e-05      0.29       2      90 ..       3      96 ..       2      96 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.5e-05
                                      EEEEETT.SHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHH.HHHTTHE.....EESS..HHHHHTCTTESEEEE-S- CS
                      GFO_IDH_MocA  2 rvaiiGa.Gkigskhlrplnesqrleevvalldpdaeraeav.aesfgve.....aysd..leelladpeidavivatp 71
                                       v+iiG+ G+ g + +r l ++ + +++  ++ +++ + ++v   + +++      ++d   ++l++  ++d+++ a+p
  gi|298674757|ref|YP_003726507.1|  3 DVGIIGSsGYTGGELIRLLVNH-KYTNIE-ICTSRKFAGQKVsDVHKHLKgfinlEFEDisPRDLKN--RCDVIFLAVP 77
                                      699****788899999666666.555555.6666666666664444444433445555533345555..9********* PP

                                      GGGHHHHHHHHHHTT-EEE CS
                      GFO_IDH_MocA 72 ngtheelakaaleagkhvl 90
                                       gt ++++ ++l    +v+
  gi|298674757|ref|YP_003726507.1| 78 HGTSMNIVPDLLDEYTKVI 96
                                      ***********99988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2294.45
//
Query:       gi|298674758|ref|YP_003726508.1|  [L=155]
Description: hypothetical protein Metev_0814 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-32  110.9   3.0    3.4e-16   59.4   0.2    2.2  2  CBS              CBS domain
  ------ inclusion threshold ------
      0.049   13.1   0.0      0.053   13.0   0.0    1.0  1  Aromatic_hydrox  Homotrimeric ring hydroxylase
      0.068   13.2   0.4       0.16   12.1   0.1    1.8  2  Thioredoxin_3    Thioredoxin domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   0.2   1.1e-17   6.6e-14       1      55 [.       3      57 ..       3      58 .. 0.95
   2 !   59.4   0.2   5.7e-20   3.4e-16       1      55 [.      99     152 ..      99     154 .. 0.95

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 1.1e-17
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55
                                      V+d+m++dv++ + +++++  +++++++g+s++PVVd+ +++vG+++++Dllr+l
  gi|298674758|ref|YP_003726508.1|  3 VKDVMNSDVIYSKSSDSIRSTAQILKKNGISGVPVVDDKNNIVGVISEEDLLRFL 57
                                      89***********************7777*******99999************98 PP

  == domain 2  score: 59.4 bits;  conditional E-value: 5.7e-20
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       V ++m +dv+t++p++t+e a +lm++++++rlPV+ edgkl+Givt+ D+++ l
  gi|298674758|ref|YP_003726508.1|  99 VQQVMKTDVLTITPEDTIEYASQLMTKHKINRLPVI-EDGKLIGIVTRGDIIEGL 152
                                       789**********************9999*******.9*************9865 PP

>> Aromatic_hydrox  Homotrimeric ring hydroxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.9e-06     0.053      94     186 ..      19     127 ..       2     145 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.9e-06
                   Aromatic_hydrox  94 lytehtepvfeatildksaregttyeaavg..............ldvsiWlPgvlkvenfPypdmitye....lyvP 152
                                        + ++ + + ++ i ++ +++++  +++vg               + ++WlP+  +v ++P  +++ +e    ++  
  gi|298674758|ref|YP_003726508.1|  19 SIRSTAQILKKNGISGVPVVDDK--NNIVGviseedllrfleipDHRGLWLPSPFEVIEIPIREFVSWEetkhMLSD 93 
                                       44566666677888888888888..8888888899999998887788******************998755558888 PP

                   Aromatic_hydrox 153 identyeyfellgkeaateeerkefedeyenelk 186
                                         ++  +  +     + t+e+  e+  ++ ++ k
  gi|298674758|ref|YP_003726508.1|  94 FGDKKVQQVMKTDVLTITPEDTIEYASQLMTKHK 127
                                       899999999999999999****999999977665 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   2.6e-05      0.16      37      75 ..      21      57 ..       2      58 .. 0.81
   2 ?   -1.5   0.0      0.46   2.8e+03      21      51 ..     100     132 ..      96     139 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.6e-05
                                      TTHHHH.HHCT-SSSSEEECTTCEEEESS---CCHHHHHH CS
                     Thioredoxin_3 37 tdfeei.ekygVmsvPalvidgkvvvsGkvpseeeirkll 75
                                        + +i +k+g+  vP  v+d+k  ++G v see++ ++l
  gi|298674758|ref|YP_003726508.1| 21 RSTAQIlKKNGISGVP--VVDDKNNIVG-VISEEDLLRFL 57
                                      5667888*********..89********.99999998776 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.46
                                       HHHCHCCTCECEEECC.TTHHHH.HHCT-SSSS CS
                     Thioredoxin_3  21 keaaaekgikaevekv.tdfeei.ekygVmsvP 51 
                                       +++++++ ++++ e++ +  +++  k+++ + P
  gi|298674758|ref|YP_003726508.1| 100 QQVMKTDVLTITPEDTiEYASQLmTKHKINRLP 132
                                       445555544544444433333344666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1080.24
//
Query:       gi|298674759|ref|YP_003726509.1|  [L=394]
Description: arginine biosynthesis bifunctional protein ArgJ [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.2e-139  464.4   6.7   2.5e-139  464.2   6.7    1.0  1  ArgJ      ArgJ family


Domain annotation for each model (and alignments):
>> ArgJ  ArgJ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  464.2   6.7  1.4e-143  2.5e-139       6     376 .]      16     394 .]      10     394 .] 0.95

  Alignments for each domain:
  == domain 1  score: 464.2 bits;  conditional E-value: 1.4e-143
                                       XXSSS..SXXEEEEEEEEEEEEEEEEEXXSSXXHHHHHHHHHHH.HHSEEEEEEEEEEXXXSXHHHHHHHHHHHHHH CS
                              ArgJ   6 aagikkkkkdlalivseepasaaavfTknkvkAapvkvsrevlkkkkgaravvvnsgnANavtgeqGledaeemaea 82 
                                       a gik  k+ l +i++  + + a+vfT+nkv Aap+ v+re++++k +++av++nsgnANa+tge+G++d+  ma++
  gi|298674759|ref|YP_003726509.1|  16 AGGIKPGKNGLGVITA--SGNSAGVFTRNKVIAAPLIVTRERITEKGHLSAVIMNSGNANAFTGEEGIDDSVYMAKL 90 
                                       34799889*****998..5788*********************99888***************************** PP

                                       HHHHHTSXGGGEEEEEEEESSXXXXHHHHHHHHHHX....X......HHHHHHHXSSXSSXXEEEEEEEETEEEEEE CS
                              ArgJ  83 vaealgikeeevlvasTGviGerlpmekieagieklvekle......eeaaeAimTTDtvpKlaavevelgkevtia 153
                                       +a++l+i+ ++v vasTGviG++l+++ + ++i+++ ++l+      ++aa++imTTDt++K+ a+e++  + ++i+
  gi|298674759|ref|YP_003726509.1|  91 LADKLDIPDKQVGVASTGVIGKKLDTDWLDENIDEVLNSLSnspdgsQSAARSIMTTDTFAKESAIELN--NGIRIG 165
                                       **************************************9977888889******************985..9***** PP

                                       EEEEXSSSXXXXEE--EEEEEE-----HHHHHHHHHHHHHHTGGGB-SSS---SS-EEEEEE--TTTT.STTHHHHH CS
                              ArgJ 154 giaKGaGmihPnmaTmLafittDaavsaealqellkeavdksFnsisvDgdtSTnDtvlllAngaaeeeeedleefe 230
                                       giaKG+Gmi+Pnm+TmLafi+tDa +++++l++ lk+ vdksFn+i vDgdtSTnD+vll A+g++   e+d+++f+
  gi|298674759|ref|YP_003726509.1| 166 GIAKGSGMIEPNMGTMLAFIYTDAVLDSKSLNKSLKAGVDKSFNMIVVDGDTSTNDMVLLTATGES-GVETDINDFQ 241
                                       *****************************************************************8.3488****** PP

                                       HHHHHHHHHHHHHHHHTSTT-S-EEEEEEEEESSHHHHHHHHHHHHT-HHHHHHHHTT---HHHHHHHHHHSSS--- CS
                              ArgJ 231 ealtevlqeLakqivrDGEGatklveveVkgakseeeAkkvaksvanssLvKtAlfGeDanwGRilaavGyagaeld 307
                                       e l+ vl++Lak+i+rDGEGatkl+ev+V+ga ++++A+ vaks+++s+LvKtA+fG+D+nwGRi+aa+Gy+ga+++
  gi|298674759|ref|YP_003726509.1| 242 EGLDFVLTDLAKMIARDGEGATKLIEVNVDGAFTYDDARLVAKSIVRSPLVKTAIFGHDPNWGRIIAAIGYSGANIR 318
                                       ***************************************************************************** PP

                                       TTS-EE..TT....EEEEETTE...E----HHHHHHHHH-SSEEEEEE--SSSEEEEEEEE---HHHHHHHTT-XX CS
                              ArgJ 308 pekvsvllge....vkvlekge...peevdeerakeilkeeeveievdlgegeeeatvwtcDLsyeYvkiNadYrt 376
                                       ++k+s+++++    v+++++g+   +++ ++++ k+i+++++++i ++lg+++++at+w+cDL+y+Y+kiNa+Y+t
  gi|298674759|ref|YP_003726509.1| 319 QDKISLAFSDgkntVELVKNGRivtNDRNSQDALKNIMEKKDIKILINLGMDNKSATAWGCDLTYDYIKINAEYTT 394
                                       ******55544455*******97645556888999***************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 3166.50
//
Query:       gi|298674760|ref|YP_003726510.1|  [L=486]
Description: ADP-specific phosphofructokinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   2.5e-116  388.7   0.3   2.9e-116  388.5   0.3    1.0  1  ADP_PFK_GK  ADP-specific Phosphofructokinase/Glucokinase cons
     0.0039   16.7   0.0      0.009   15.5   0.0    1.5  1  DUF2290     Uncharacterized conserved protein (DUF2290)


Domain annotation for each model (and alignments):
>> ADP_PFK_GK  ADP-specific Phosphofructokinase/Glucokinase conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  388.5   0.3  3.2e-120  2.9e-116       2     423 ..      26     479 ..      25     480 .. 0.94

  Alignments for each domain:
  == domain 1  score: 388.5 bits;  conditional E-value: 3.2e-120
                                       EEEEES--EEEEE.....HHHHHHHHCC-HH.HHHHHHC--SSBSSHHHHHHHHHHHHHHT--EEEEB--HHHHHHH CS
                        ADP_PFK_GK   2 kvavGynanvDai.....vdavelleklgleevkekseedhdeikskedlletfayffkkGaaaErfvenkelfeel 73 
                                        ++v+yn+n+Dai     +d+ +ll++++l++vk++s++ +++ik+++dl++++++++++G+aaE+++++++++e+l
  gi|298674760|ref|YP_003726510.1|  26 GIFVAYNSNIDAIkhiekDDFDKLLKHVNLKNVKHRSMSFPRVIKDPDDLMARLVIAMRDGKAAEVPTYSTDVHEWL 102
                                       69*************************************************************************** PP

                                       H....CC--SEEEEESHHHHHHHHHCCTT-.EEEEE-.---HHHHTTS-SS.......EE....EEEEGGG-S-... CS
                        ADP_PFK_GK  74 vkaakklkkaelrmGGnagimanrlakega.kvllga.klskklkellsek.......iv....vlgkpseaske.. 135
                                       ++   ++++++++mGG+agi++n la+ ++ +v++++ +lsk+++e+++++       ++      ++p++a++   
  gi|298674760|ref|YP_003726510.1| 103 TN---HIDFDNAYMGGQAGIISNFLANIDIkNVVTYVpWLSKEQAEYFTNSknllypvVEnsklSFKHPINAYNPey 176
                                       *9...**********************************************88877751166678899999999899 PP

                                       ---EEEEEEE-TT-EE....TEEE-SS-EEEEEE--STCGGTS--HHHCTTHHHHH..-SEEEE--GGG--TB-TTS CS
                        ADP_PFK_GK 136 kdeiHlIlEykkgekw....geieapraNRfIissdpenlrlsileefkealkefk..pdllvlsGlqmleeqykeg 206
                                       ++++++I+E++kg ++    +e+++pr+NR+I+ss+p++lr+++++e++e+l+e++  +d+++lsG+qm++e+y++g
  gi|298674760|ref|YP_003726510.1| 177 EPKVNWIMEFSKGLEVqcgeEEFVVPRDNRLILSSRPTWLRIDMSKELYEQLPELGknVDGAILSGYQMIKENYEDG 253
                                       99****************8555********************************8889******************* PP

                                       TCHHHHHHHHHHHHHHHC..C.T-EEEEE----S-HHHHHHHHHHCGGG.-SEEEE-HHHHHHHHHHTT-HHHCCSS CS
                        ADP_PFK_GK 207 kereerlekvkeqlkslk..n.kikiHlElAsfqdeellkeilekilpy.vdslGlnEqElanllsvlggeekelte 279
                                       ++++++++k ++ +k+lk  n +i+iH+E++s+qd+ ++++il++i+++ v+slGl++ E+an l+vl++ee     
  gi|298674760|ref|YP_003726510.1| 254 STYHNYVKKSVDAIKRLKngNpDIRIHVEFTSIQDKFIRERILKDIVSQhVHSLGLDTIEVANALNVLDYEELAYAV 330
                                       ******************9978***********************88766********************8888888 PP

                                       ...CC--HHHHHHHHHHHHH.....HHTT-SEEEEEETTEEEEEEETTSSS-HHHHHHHHHHHHHHHHHHHHH...- CS
                        ADP_PFK_GK 280 vsdkepriakvlealrkllkllkkskkrkltrihvHtlayqiiltkkesewkneaakkalakaallAarkacn...s 353
                                       + ++e+ i +++e++++ll      +  +l+r+hvH+l+y i+++k++++++ e++++al +a++++a+ka+    +
  gi|298674760|ref|YP_003726510.1| 331 INKTEKGISALYEGAVRLLY-----EL-ELERVHVHSLGYFICVVKNTHPVDIEDHRNALLFASTASAAKAKIgniK 401
                                       8999****************.....88.********************************************97655 PP

                                       SHHHHHHHH..........HS-B-TT..HHHHHHHHCC................EETTEEEEEEE-B--SS-S--TT CS
                        ADP_PFK_GK 354 dleklelklddsfsvskskkiplnek..epvscweeei................eleevevclaPvlvckkpkkTvG 412
                                       ++++++ +l           +p++ek  +++++++++                 ++  ++v+++P++v++kp++TvG
  gi|298674760|ref|YP_003726510.1| 402 SIDDIKKGL----------GTPVSEKgyNHLQELAKYLekegiclteefekgyiRTPYHDVIIIPTKVVEKPVATVG 468
                                       *********..........8888888887777777777777888888889****999******************** PP

                                       HHHHHHHHHHH CS
                        ADP_PFK_GK 413 lGDtISaaglv 423
                                       +GD ISa++++
  gi|298674760|ref|YP_003726510.1| 469 IGDIISASAFA 479
                                       *********96 PP

>> DUF2290  Uncharacterized conserved protein (DUF2290)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0     1e-06     0.009      26      84 ..     313     371 ..     300     388 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1e-06
                           DUF2290  26 klsialknvdyae.iYsallekkkynikliDGaliqllYtlkegkllkHrllyfpsPlle 84 
                                       +++ al+ +dy+e  Y  +++ +k    l +Ga ++llY+l+ +++  H+l yf + +++
  gi|298674760|ref|YP_003726510.1| 313 EVANALNVLDYEElAYAVINKTEKGISALYEGA-VRLLYELELERVHVHSLGYFICVVKN 371
                                       567788899***999*********999*****9.8*********************8883 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (486 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3437.32
//
Query:       gi|298674761|ref|YP_003726511.1|  [L=446]
Description: ADP-specific phosphofructokinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-98  330.6   0.1    1.3e-98  330.4   0.1    1.0  1  ADP_PFK_GK  ADP-specific Phosphofructokinase/Glucokinase cons
  ------ inclusion threshold ------
       0.01   15.2   0.0        0.4   10.0   0.0    2.5  2  PfkB        pfkB family carbohydrate kinase
      0.039   13.9   0.0       0.12   12.3   0.0    1.8  1  DUF771      Domain of unknown function (DUF771)


Domain annotation for each model (and alignments):
>> ADP_PFK_GK  ADP-specific Phosphofructokinase/Glucokinase conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  330.4   0.1  2.1e-102   1.3e-98       2     422 ..       2     435 ..       1     437 [. 0.91

  Alignments for each domain:
  == domain 1  score: 330.4 bits;  conditional E-value: 2.1e-102
                                       EEEEES--EEEEE.....HHHHHHHHCC-HH.HHHHHHC--SSBSSHHHHHHHHHHHHHHT--EEEEB--HHHHHHH CS
                        ADP_PFK_GK   2 kvavGynanvDai.....vdavelleklgleevkekseedhdeikskedlletfayffkkGaaaErfvenkelfeel 73 
                                       ++++Gynan+D +     +++++lle+ +++++++k e++++ i+s +d+++++++++++G++aE++v+++ +fe l
  gi|298674761|ref|YP_003726511.1|   2 NILCGYNANIDSVyritgDEINRLLEHQNQDNIIKKIENPPNRIDSIDDFIAGLIICIRNGSGAEWLVHDDSVFEFL 78 
                                       79*************************************************************************** PP

                                       H....CC--SEEEEESHHHHHHHHHCCTT-.EEEEE-.---HHHHTTS-SS..EEEEEEGGG-S-...---EEEEEE CS
                        ADP_PFK_GK  74 vkaakklkkaelrmGGnagimanrlakega.kvllga.klskklkellsek..ivvlgkpseaske..kdeiHlIlE 144
                                       ++   +++++ +rmGGn+gim+n+l+ +ga +v+ ++ k sk++ + ++++  i + g++++++++  k+ iH++++
  gi|298674761|ref|YP_003726511.1|  79 KN--YFFDNSIIRMGGNCGIMSNVLSLMGAgEVVPNIaKPSKTQLDAFTDNesIIIPGYNNQNDINedKELIHFVFD 153
                                       *9..**********************************************977445566666555555889****** PP

                                       E-TT-EE...TE.EE-SS-EEEEEE--STCGGTS--HHHCTTHHHHH..-SEEEE--GGG--TB-TTSTCHHHHHHH CS
                        ADP_PFK_GK 145 ykkgekw...ge.ieapraNRfIissdpenlrlsileefkealkefk..pdllvlsGlqmleeqykegkereerlek 215
                                       +kkgek+   g  ++apr+NRfI+++d  n++l+i+ +fk++++e+   +d++++sG++ml+e+y +g+++ ++++k
  gi|298674761|ref|YP_003726511.1| 154 FKKGEKVtlnGYsMVAPRENRFIATYDCLNIELTINPDFKHYADEHIdeMDGALISGYHMLQEYYPDGSSYVDKFQK 230
                                       *********9667********************************999***************************** PP

                                       HHHHHHHHC..C.T-EEEEE----S-HHHHHHHHHHCGGG-SEEEE-HHHHHHHHHHTT-HHHCCSS...CC--HHH CS
                        ADP_PFK_GK 216 vkeqlkslk..n.kikiHlElAsfqdeellkeilekilpyvdslGlnEqElanllsvlggeekeltevsdkepriak 289
                                         +q+k++k  n ++  H El++f++ e+++ +++++  +vd +G+nE+Ela+l+ + + + +++ +      +  +
  gi|298674761|ref|YP_003726511.1| 231 SLDQIKNWKqlNkQLLLHAELGHFSNVEIAQYVFTSLTDHVDGMGMNEDELAMLHGIHNIPVNDILQ-----MNAIS 302
                                       ***********66********************************************9887777744.....56788 PP

                                       HHHHHHHHHH.....HHTT-SEEEEEETTEEEEEEETTSSS-HHHHHHHHHHHHHHHHHHHHH...-SHHHHHHHH. CS
                        ADP_PFK_GK 290 vlealrkllkllkkskkrkltrihvHtlayqiiltkkesewkneaakkalakaallAarkacn...sdleklelkld 363
                                       +lea+++++      k+ +l++  +Ht+++ ++++k  +  +   +++++++++++Aa  a +   ++++ +e ++ 
  gi|298674761|ref|YP_003726511.1| 303 ILEASLQCVL-----KS-GLQKFIIHTREFTLCVCK-PDVFDAVCELESMKFGVKCAAVFADTgilKNRNYVEKTA- 371
                                       9999999999.....67.*****************6.6669**********************7666999999998. PP

                                       .........HS-B-TT..HHHHHHHHCC...........EETTEEEEEEE-B--SS-S--TTHHHHHHHHHH CS
                        ADP_PFK_GK 364 dsfsvskskkiplnek..epvscweeei...........eleevevclaPvlvckkpkkTvGlGDtISaagl 422
                                               +k++ ++   ++v++++e i           ++++++v ++P+l+ k+p +TvGlGDt++a++ 
  gi|298674761|ref|YP_003726511.1| 372 --------SKLEESDFglNEVEKIKEFIngksynngtygSRSGLSVGIIPTLISKNPISTVGLGDTFCAGTY 435
                                       ........444444445555555555555559999999999****************************986 PP

>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.014        87     175     211 ..     262     298 ..     228     323 .. 0.77
   2 ?   10.0   0.0   6.6e-05       0.4     231     264 ..     399     433 ..     396     440 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.014
                                       HHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHH CS
                              PfkB 175 eallellaladllkpneeElealtgekledieealaa 211
                                        ++ +l  ++d + +ne+El+ l g ++  ++++l++
  gi|298674761|ref|YP_003726511.1| 262 YVFTSLTDHVDGMGMNEDELAMLHGIHNIPVNDILQM 298
                                       556677899****************999555555554 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 6.6e-05
                                       EEEEEE.TTEEEEEEE.SSSS-SBGTTHHHHHHHH CS
                              PfkB 231 Galvve.kdgelkvpavpkvkvvDttGAGDsfvgg 264
                                       G++ +  +  + ++p+++++++++t+G GD+f++g
  gi|298674761|ref|YP_003726511.1| 399 GTYGSRsGLSVGIIPTLISKNPISTVGLGDTFCAG 433
                                       55555556677899********************9 PP

>> DUF771  Domain of unknown function (DUF771)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     2e-05      0.12      24      87 ..      17      82 ..       9      84 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2e-05
                            DUF771 24 wtlkdlekkls.kssewikeniLenprfrkeldi.ekggfvlypkgkgkkwlfkakkmakFldenf 87
                                      +t ++++  l+ ++++ i+++i ++p+    +d    g ++  ++g g +wl++  ++ +Fl + f
  gi|298674761|ref|YP_003726511.1| 17 ITGDEINRLLEhQNQDNIIKKIENPPNRIDSIDDfIAGLIICIRNGSGAEWLVHDDSVFEFLKNYF 82
                                      56778888888899999*********9999999889**************************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 3027.27
//
Query:       gi|298674762|ref|YP_003726512.1|  [L=454]
Description: CCA-adding enzyme [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-43  147.8   0.0    3.2e-43  146.6   0.0    1.7  1  tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
    3.3e-16   59.4   0.0    9.2e-16   57.9   0.0    1.8  1  NTP_transf_2     Nucleotidyltransferase domain
    1.4e-07   31.8   0.1    3.2e-07   30.6   0.1    1.5  1  SMODS            Second Messenger Oligonucleotide or Dinucleo
  ------ inclusion threshold ------
      0.062   13.4   0.0        0.2   11.8   0.0    1.9  1  Polbeta          Polymerase beta, Nucleotidyltransferase
       0.19   11.4   0.1       0.32   10.7   0.1    1.3  1  Raco_middle      RACo middle region


Domain annotation for each model (and alignments):
>> tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.6   0.0     9e-47   3.2e-43       1     113 []     162     272 ..     162     272 .. 0.99

  Alignments for each domain:
  == domain 1  score: 146.6 bits;  conditional E-value: 9e-47
                                       HHHHHHHHHHHHTT-BSSSTTT-SB-HHHHHHHHHHHSSHHHHHHHHTT--TTEEEE......EEE..-SS-EEEET CS
                   tRNA_NucTransf2   1 devrllKkflkgigvYGselkvkGfsGYlaEllvleygsfeevleaaakwkpkvvidleekeallkkfdeplvviDP 77 
                                       dev +lK+f++gigvYGselk++GfsGY aEll++++gsf+++l++a +w+p++vid++++ +  +++dep+v+iDP
  gi|298674762|ref|YP_003726512.1| 162 DEVLILKQFMHGIGVYGSELKTRGFSGYFAELLIIHFGSFDNLLKSACNWSPGMVIDMMNHGQ--SEHDEPFVMIDP 236
                                       89**********************************************************999..99********** PP

                                       TEEEEETTTTS-HHHHHHHHHHHHHHHHS--GGGGS CS
                   tRNA_NucTransf2  78 vDpkRNvaaalsleklaefilaareflkkpseefff 113
                                       +Dp RNvaaals +klaef+ ++r+f ++ps++fff
  gi|298674762|ref|YP_003726512.1| 237 TDPGRNVAAALSINKLAEFVDKSRSFFESPSLDFFF 272
                                       **********************************96 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.9   0.0   2.6e-19   9.2e-16       1      94 [.      38     148 ..      38     149 .. 0.96

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 2.6e-19
                                       HHHHHHHHHHHTT.TSEEEEEHHHHCTTSCTT.SSEEEEEEESTTCHHH...............HHHEHHHHHHHHC CS
                      NTP_transf_2   1 lkklleelkelep.vakvvlfGSyarGtalkg.SDiDllvvlpeevsre...............kkeegleklaeii 60 
                                       +kk++  ++e+++ ++++ l+GS+arGt+l+g +D+D+++++pe+++                 + e+ +e +ae++
  gi|298674762|ref|YP_003726512.1|  38 IKKINSNVSEMDLsGVSAQLVGSAARGTWLSGtHDLDIFILFPENTDVKyleyyglkiarkvaeEAENWQEQYAEHP 114
                                       799999***************************************8887***************99999******** PP

                                       CCEEECTTEEEEEECEEECCCCTEEEEEECEEEH CS
                      NTP_transf_2  61 kfleellglevdlvtrekledpllvksileerpl 94 
                                       +   +++g+ vd+v++  +++ ++++s+++++p+
  gi|298674762|ref|YP_003726512.1| 115 YISLKFRGYDVDIVPCFRVQSASNIRSAVDRTPF 148
                                       *******************************997 PP

>> SMODS  Second Messenger Oligonucleotide or Dinucleotide Synthetase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.1     9e-11   3.2e-07       9     135 ..      15     135 ..      10     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 9e-11
                             SMODS   9 eflsnielsqttkdsissrvkaitkrLnkdfrelkskiaesllvGSyardTaikpvsdkdmlfeldvdllvvvneve 85 
                                       + l+ +++ +++++++ + v+ + k++n++ +e++ + ++  lvGS ar+T + ++ d+d+   ++ +  v++ e+ 
  gi|298674762|ref|YP_003726512.1|  15 DVLTRVKPTSDEQKHLFDVVDYLIKKINSNVSEMDLSGVSAQLVGSAARGTWLSGTHDLDIFILFPENTDVKYLEYY 91 
                                       678999*****************************9999999*********************************99 PP

                             SMODS  86 gdepsdlleklkkalkktyksseirqdrqvvvvelneikidvvPavenkd 135
                                       g + ++ + +  +  +++        +++ + +++ ++++d+vP+++ ++
  gi|298674762|ref|YP_003726512.1|  92 GLKIARKVAEEAENWQEQ------YAEHPYISLKFRGYDVDIVPCFRVQS 135
                                       875555555444444555......555*******************9876 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.5e-05       0.2      16      51 ..      55      91 ..      39     130 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.5e-05
                                      TTEEEEEE-S----.--EEEEEEEESS---HHHHHHH CS
                           Polbeta 16 aylFGSrakgkare.eSDiDlavllkekldleeelel 51
                                      a l GS a+g+  +  +D+D+++l+ e+ d+++   +
  gi|298674762|ref|YP_003726512.1| 55 AQLVGSAARGTWLSgTHDLDIFILFPENTDVKYLEYY 91
                                      5578******987549************444443222 PP

>> Raco_middle  RACo middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   8.9e-05      0.32      29      73 ..       4      48 ..       1      61 [. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8.9e-05
                       Raco_middle 29 salNpQikyGeDvlsRiayakeeeegleklqkavveeinelieel 73
                                      ++ N  +++ +Dvl+R++ +++e+++l ++ + ++++in+ ++e+
  gi|298674762|ref|YP_003726512.1|  4 NMSNIPKNIKKDVLTRVKPTSDEQKHLFDVVDYLIKKINSNVSEM 48
                                      56677788899*****************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3333.15
//
Query:       gi|298674763|ref|YP_003726513.1|  [L=400]
Description: glycine betaine/L-proline ABC transporter ATPase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-33  116.7   0.0    2.6e-33  115.4   0.0    1.7  1  ABC_tran       ABC transporter
    7.4e-15   55.1   1.0    2.8e-07   30.9   0.0    2.6  2  CBS            CBS domain
    2.5e-05   24.2   1.0       0.07   12.9   0.1    2.2  2  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
    5.8e-05   22.1   0.8       0.11   11.3   0.1    3.1  3  ABC_ATPase     Predicted ATPase of the ABC class
    0.00011   22.2   0.1    0.00037   20.4   0.0    2.0  2  RsgA_GTPase    RsgA GTPase
    0.00012   21.8   0.0    0.00035   20.3   0.0    1.8  1  AAA_29         P-loop containing region of AAA domain
     0.0006   20.2   0.1     0.0012   19.2   0.1    1.7  1  AAA_16         AAA ATPase domain
     0.0012   19.2   0.1     0.0049   17.1   0.1    2.0  1  AAA_22         AAA domain
     0.0013   19.2   0.1     0.0041   17.6   0.1    1.7  1  AAA_23         AAA domain
      0.004   16.3   0.2       0.46    9.5   0.0    2.4  2  T2SSE          Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.012   15.1   0.3       0.61    9.5   0.3    2.3  1  SMC_N          RecF/RecN/SMC N terminal domain
      0.012   15.3   0.0       0.47   10.1   0.0    2.4  2  AAA_30         AAA domain
      0.014   14.8   0.0      0.024   14.0   0.0    1.3  1  Mg_chelatase   Magnesium chelatase, subunit ChlI
      0.044   13.8   0.0       0.11   12.5   0.0    1.7  1  AAA_14         AAA domain
        0.1   12.8   0.0       0.29   11.3   0.0    1.8  1  AAA_33         AAA domain
        0.1   12.6   0.0       0.25   11.3   0.0    1.7  1  AAA_5          AAA domain (dynein-related subfamily)
       0.12   12.5   0.1        3.6    7.7   0.0    2.9  3  MMR_HSR1       50S ribosome-binding GTPase
       0.12   12.2   0.0       0.21   11.4   0.0    1.5  1  CPT            Chloramphenicol phosphotransferase-like protei
       0.13   12.4   0.1       0.28   11.3   0.1    1.5  1  RTT107_BRCT_6  Regulator of Ty1 transposition protein 107 BRC
       0.13   12.5   1.2       0.73   10.1   1.2    2.2  1  SbcCD_C        Putative exonuclease SbcCD, C subunit
       0.18   10.9   0.0       0.21   10.7   0.0    1.3  1  G-alpha        G-protein alpha subunit


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.4   0.0   3.1e-36   2.6e-33       1     136 [.      48     196 ..      48     197 .. 0.94

  Alignments for each domain:
  == domain 1  score: 115.4 bits;  conditional E-value: 3.1e-36
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpe 73 
                                       l+++++k+++ge+ +++G +G+GKStLl+++ +l  pt Ge+ ++g+d+ +    q +++ r+++++++q+  l p+
  gi|298674763|ref|YP_003726513.1|  48 LHDINFKVQKGEIFVLMGLSGSGKSTLLRCINRLIPPTYGEVYIEGEDIAKmdmeQLRKIRREKLSMVFQNFALLPH 124
                                       789***********************************************9999888999999************** PP

                                       SBHHHH..........HHHTC...HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxx..........xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren..........esdee...iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                        tv +n          e++e+     +a++++glk+ +++++    ++LSgG++qrv laral+++p +ll+DE++
  gi|298674763|ref|YP_003726513.1| 125 RTVLDNvayglevygvEKEERykaSREAIETVGLKGYEESRI----TQLSGGMQQRVGLARALATDPHFLLMDEAF 196
                                       ***************944444455889999999999999999....****************************97 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   3.2e-10   2.8e-07       2      54 ..     281     333 ..     280     336 .. 0.90
   2 !   22.5   0.2   1.4e-07   0.00012       2      56 ..     341     394 ..     340     395 .. 0.90

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 3.2e-10
                                       HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                       +++m ++ ++v+ ++  + al+lmre+g+s+++VV++ + l G+vt +D ++a
  gi|298674763|ref|YP_003726513.1| 281 ESVMMDPEPVVSINSGPSVALQLMREHGISSIFVVNKHKGLEGVVTVEDAAEA 333
                                       578888888**************************98888*********9887 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 1.4e-07
                                       HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEE.E.ETTTBEEEEEEHHHHHHHHH CS
                               CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPV.V.dedgklvGivtlrDllrall 56 
                                       +d+  r+++t + dt l++++ +++e   s++PV V d+++kl+G++ +  +l a++
  gi|298674763|ref|YP_003726513.1| 341 EDVIIREYPTTTKDTQLKDIIPMIAE---SSYPVaVvDDNNKLHGVLVRGGILGAIA 394
                                       58889999****************88...89998888**********9999999886 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.1   8.2e-05      0.07       1      22 [.      60      81 ..      60     137 .. 0.83
   2 !   10.5   0.1   0.00044      0.38     219     299 ..     144     229 ..      84     232 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.2e-05
                            AAA_21  1 lnvliGpNgsGKSnLLdaldll 22
                                      + vl G  gsGKS+LL+++  l
  gi|298674763|ref|YP_003726513.1| 60 IFVLMGLSGSGKSTLLRCINRL 81
                                      67999**************988 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00044
                            AAA_21 219 r.......gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll.ellkelsr 287
                                       +        + ++  +++ e  +++lS G+++  +l+ al+ ++    +ll DE  + L+P + ++   ell + ++
  gi|298674763|ref|YP_003726513.1| 144 ErykasreAIETVGLKGYEESRITQLSGGMQQRVGLARALATDP---HFLLMDEAFSALDPLIRSEMQdELLALQEQ 217
                                       044444446677777778888899*********9********99...89************6666666666644444 PP

                            AAA_21 288 ngaQviltTHSp 299
                                           +i++TH+ 
  gi|298674763|ref|YP_003726513.1| 218 VHKTIIFVTHDL 229
                                       445*******95 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0017       1.4     242     306 ..      55     116 ..      41     126 .. 0.74
   2 !   11.3   0.1   0.00013      0.11     321     386 ..     167     232 ..     159     268 .. 0.83
   3 ?   -0.9   0.0      0.63   5.4e+02     379     395 ..     299     315 ..     278     330 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0017
                                       E-SS.EEEEEE-TTSSHHHHHHHHHHCCSEE-TTSS-TTEEE-TT-EEE---TT--EEEE--TTTB CS
                        ABC_ATPase 242 ipkG.vtlIvGggfhGKsTLLeAlekGvynhvpgDGRefvvtdktavkiraEdgrsvkgvDispFi 306
                                       ++kG +++++G    GKsTLL+ +++ + +       e+ +  ++++k++ E+ r++++  +s+ +
  gi|298674763|ref|YP_003726513.1|  55 VQKGeIFVLMGLSGSGKSTLLRCINRLIPPTY----GEVYIEGEDIAKMDMEQLRKIRREKLSMVF 116
                                       68899******************998653322....255566666666666666666666666555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00013
                                       SS--HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG--B--HHHCHHHHHHH CS
                        ABC_ATPase 321 edASGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekepitplvdrvrelykk 386
                                       ++ SG + q + +++al  + + lL+DE  sA   +ir e+ +el++ +++  ++++   ++l + 
  gi|298674763|ref|YP_003726513.1| 167 TQLSGGMQQRVGLARALATDPHFLLMDEAFSALDPLIRSEMQDELLALQEQVHKTIIFVTHDLDEA 232
                                       6779******************************************87776666776666666554 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.63
                                       CHHHHHHHH--EEEEEE CS
                        ABC_ATPase 379 rvrelykklgvstilvv 395
                                        + +l++++g+s+i vv
  gi|298674763|ref|YP_003726513.1| 299 VALQLMREHGISSIFVV 315
                                       56799**********98 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   4.4e-07   0.00037      76     120 ..      32      79 ..       4     102 .. 0.77
   2 ?   -2.2   0.0         4   3.4e+03      39      67 ..     301     329 ..     298     368 .. 0.61

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 4.4e-07
                                       TSEEEE--TTTH..TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  76 gyevllvsaktk..egleelkellkd.ktsvlvGqSGvGKStLinall 120
                                       gy+   +++kt+   gl++++ ++++ ++ vl+G SG GKStL+  ++
  gi|298674763|ref|YP_003726513.1|  32 GYTKNEIHEKTGqtVGLHDINFKVQKgEIFVLMGLSGSGKSTLLRCIN 79 
                                       5555555555541157899*9999998****************86654 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4
                                       HHHHHHTT-EEEEEEE-GGG--HHHHHHH CS
                       RsgA_GTPase  39 LvlaeekgiepvivlnKiDlleeeeelee 67 
                                       L l+ e+gi+ + v+nK   le   ++e+
  gi|298674763|ref|YP_003726513.1| 301 LQLMREHGISSIFVVNKHKGLEGVVTVED 329
                                       55667778888888888766555543333 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   4.1e-07   0.00035      15      49 ..      49      85 ..      43      90 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.1e-07
                            AAA_29 15 htieidlkg..atlltGpsGsGKSTllDAiqalLvpa 49
                                      h+i+++++   +++l+G sGsGKSTll  i+ l+ p+
  gi|298674763|ref|YP_003726513.1| 49 HDINFKVQKgeIFVLMGLSGSGKSTLLRCINRLIPPT 85
                                      555555544479***************8888887665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   1.4e-06    0.0012      22      59 ..      58      94 ..      48     234 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.4e-06
                            AAA_16 22 grpelvllsGesGvGKsslvrellralekdggif.lrgk 59
                                      g  e+ +l G sG+GKs+l+r++ r +  ++g + ++g+
  gi|298674763|ref|YP_003726513.1| 58 G--EIFVLMGLSGSGKSTLLRCINRLIPPTYGEVyIEGE 94
                                      3..899******************998888544434443 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   5.8e-06    0.0049       5     134 ..      58     230 ..      54     233 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.8e-06
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee.....erpevvfvtlpsstsskdl.lrellralglelka..... 70 
                                         i v++G sG+GK+tllr + +  +      +     e+ +++++++ ++ + +   l+++++++ l  ++     
  gi|298674763|ref|YP_003726513.1|  58 GEIFVLMGLSGSGKSTLLRCINRLIPPT----YgevyiEGEDIAKMDMEQLRKIRREkLSMVFQNFALLPHRtvldn 130
                                       6789*******************98643....244568888888999988885544448888888888777789999 PP

                            AAA_22  71 ...............................erlsseellealeqalrarav....ielliiDEaqh.lr...seea 108
                                                                      e+ +  +l   ++q +  +++    +++l+ DEa   l+   + e+
  gi|298674763|ref|YP_003726513.1| 131 vayglevygvekeerykasreaietvglkgyEESRITQLSGGMQQRVGLARAlatdPHFLLMDEAFSaLDpliRSEM 207
                                       99999999999999999999999999998987888888886666655555555889999999999988877766888 PP

                            AAA_22 109 leeLrsllnlsrkgvqliLvGtpelr 134
                                         eL  l++  +   + i++ t++l+
  gi|298674763|ref|YP_003726513.1| 208 QDELLALQE--Q-VHKTIIFVTHDLD 230
                                       888877777..4.4444445555555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   4.8e-06    0.0041      14      40 ..      50      79 ..      43      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.8e-06
                            AAA_23 14 eidF...skgltlItGpNGaGKTTildAik 40
                                      +i+F   +  ++++ G  G+GK+T+l++i 
  gi|298674763|ref|YP_003726513.1| 50 DINFkvqKGEIFVLMGLSGSGKSTLLRCIN 79
                                      5899987778******************96 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00054      0.46     122     176 ..      51     106 ..      31     122 .. 0.79
   2 ?    4.4   0.1     0.019        16     157     186 ..     321     350 ..     309     362 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00054
                             T2SSE 122 lrkavrerglilvsGgTgsGKttllyallkeinks.derivtvEDpvEiqleganq 176
                                       ++  v++  ++++ G  gsGK+tll  +   i+ +  e  +  ED + +++e+  +
  gi|298674763|ref|YP_003726513.1|  51 INFKVQKGEIFVLMGLSGSGKSTLLRCINRLIPPTyGEVYIEGEDIAKMDMEQLRK 106
                                       5667888999*****************99999887455556677777777766655 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.019
                             T2SSE 157 derivtvEDpvEiqleganqvqlnakkakv 186
                                        e +vtvED++E + +++n   +  ++   
  gi|298674763|ref|YP_003726513.1| 321 LEGVVTVEDAAEARRNKKNLEDVIIREYPT 350
                                       4789***********999988887774444 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.3   0.00071      0.61      56     197 ..      91     227 ..      49     246 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00071
                                       TTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  56 lrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvkrkgeseykingkevtkkevsellesagi 132
                                       +  e++ ++    ++ +++ + ++++                                                   
  gi|298674763|ref|YP_003726513.1|  91 IEGEDIAKMDM--EQLRKIRREKLSM--------------------------------------------------- 114
                                       22233332222..2333333333333................................................... PP

                                       STT....................................................CS-HHHHHHHHHHHHHHHHCCS CS
                                       xxx....................................................xxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 133 ske....................................................lLSgGektLvalaLlfAiqkvk 157
                                                                                              +LSgG ++ v la  +A+    
  gi|298674763|ref|YP_003726513.1| 115 --VfqnfallphrtvldnvayglevygvekeerykasreaietvglkgyeesritQLSGGMQQRVGLARALATD--- 186
                                       ..233344444444444444444444444444444444444444444444555558999999999999998864... PP

                                       --SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                             SMC_N 158 paplyllDeidaaLDeknvkkvaellkekskn..aQfivisl 197
                                       p  + l+De  +aLD   ++++ + l + +++    +i +++
  gi|298674763|ref|YP_003726513.1| 187 P-HFLLMDEAFSALDPLIRSEMQDELLALQEQvhKTIIFVTH 227
                                       4.48999********999988887766555552133333444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00055      0.47      18      43 ..      58      83 ..      52     109 .. 0.85
   2 ?    2.7   0.1      0.11        93       6     141 ..     249     394 ..     246     400 .] 0.72

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00055
                            AAA_30 18 drvavltGpAGtGKttalkalreawe 43
                                        + vl G  G+GK+t+l+ +++++ 
  gi|298674763|ref|YP_003726513.1| 58 GEIFVLMGLSGSGKSTLLRCINRLIP 83
                                      35899**************9998875 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.11
                            AAA_30   6 QaaavealltsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlk. 81 
                                       Q   +e++lt+++   v +  AG  K+ +l+a   +++   ++v+ + +   +A +L +e gi +  + +  k l+ 
  gi|298674763|ref|YP_003726513.1| 249 QVGTAEEILTKPANQYVSQFIAGVDKSKVLTAESVMMD--PEPVVSINSGPSVALQLMREHGISSIFVVNKHKGLEg 323
                                       6777899999999999999999999*999988666666..5569999999999999999999865544433333334 PP

                            AAA_30  82 ........grarlepg.tllivDEagmv.dtkqlaallkaaekagakvilvGDerQlasVea.Ggvlrdlv 141
                                               ++ r +++ + +i+ E   +   +ql++++  +++++  v +v D++ l  V   Gg+l  ++
  gi|298674763|ref|YP_003726513.1| 324 vvtvedaaEARRNKKNlEDVIIREYPTTtKDTQLKDIIPMIAESSYPVAVVDDNNKLHGVLVrGGILGAIA 394
                                       66777786333333445678888876553667888888888888999999999998888853388877775 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.8e-05     0.024      24      65 ..      60     101 ..      38     128 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.8e-05
                      Mg_chelatase  24 nlllvGppGsGKtmlakrlpsllpplseeealevakiasvag 65 
                                        ++l+G +GsGK+ l ++++ l+pp   e  +e + ia +  
  gi|298674763|ref|YP_003726513.1|  60 IFVLMGLSGSGKSTLLRCINRLIPPTYGEVYIEGEDIAKMDM 101
                                       57899*********************9999999988876655 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00013      0.11       2      50 ..      58     113 ..      57     140 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                            AAA_14   2 rkilvitGaRrvGKTtllkqlikell........vkkesilyinldderdkkladpe 50 
                                       ++i v++G+  +GK+tll ++i++l+        ++ e+i  +++++ r+ ++++ +
  gi|298674763|ref|YP_003726513.1|  58 GEIFVLMGLSGSGKSTLL-RCINRLIpptygevyIEGEDIAKMDMEQLRKIRREKLS 113
                                       5799*************8.55666666777888888888888888887776544432 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00034      0.29       2      17 ..      61      76 ..      60     126 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00034
                            AAA_33  2 vllvGlpGsGKstlae 17
                                      ++l Gl+GsGKstl++
  gi|298674763|ref|YP_003726513.1| 61 FVLMGLSGSGKSTLLR 76
                                      6799**********97 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00029      0.25       2      55 ..      61     115 ..      60     131 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00029
                                       EEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--HHHHH--B--........ CS
                             AAA_5   2 vlLvGppGtgKselaerlaaal.nreveyvqltrdtteedlkgrreikngttslv 55 
                                       ++L G +G+gKs+l + + +++  +  e++   +d+ + d+ + r+i+ ++ s+v
  gi|298674763|ref|YP_003726513.1|  61 FVLMGLSGSGKSTLLRCINRLIpPTYGEVYIEGEDIAKMDMEQLRKIRREKLSMV 115
                                       689*******************755556666678899999999999876665554 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0042       3.6       3      19 ..      62      78 ..      60     118 .. 0.90
   2 ?   -1.3   0.0       2.6   2.2e+03      66     110 ..     179     224 ..     125     229 .. 0.49
   3 ?    1.0   0.0      0.51   4.3e+02      23      42 ..     342     361 ..     322     376 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0042
                                      EEEESTTSSHHHHHHHH CS
                          MMR_HSR1  3 aivGrpNvGKStLinal 19
                                      +++G + +GKStL++ +
  gi|298674763|ref|YP_003726513.1| 62 VLMGLSGSGKSTLLRCI 78
                                      799**********9865 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.6
                                       HHHHHHHHHCTSEEEEEEETT........TTCSHHHHHHHHHHHHHTTSEEEE CS
                          MMR_HSR1  66 lgkaflaleeadlillvvdas........eeklkpldeeleelleeakkplil 110
                                       l++a++    +d  +l++d +        +   ++++ el +l+e+ +k +i+
  gi|298674763|ref|YP_003726513.1| 179 LARALA----TDPHFLLMDEAfsaldpliR---SEMQDELLALQEQVHKTIIF 224
                                       222222....45556666633433322221...22344455554445555554 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.51
                                       TEEESSSTTSSSSEEEEEEE CS
                          MMR_HSR1  23 kaivsdkpgtTrdinegrvk 42 
                                        +i+ ++p tT+d++ + + 
  gi|298674763|ref|YP_003726513.1| 342 DVIIREYPTTTKDTQLKDII 361
                                       578999*******9988765 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00024      0.21       1      32 [.      58      89 ..      58     160 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00024
                                      --EEEEEE-TTSSHHHHHHHHHHHSSS-EEEE CS
                               CPT  1 ariilLnGgsssGKsslaralqevldepwlhl 32
                                      ++i +L G s sGKs+l r++  +++ ++ ++
  gi|298674763|ref|YP_003726513.1| 58 GEIFVLMGLSGSGKSTLLRCINRLIPPTYGEV 89
                                      6799******************9999888665 PP

>> RTT107_BRCT_6  Regulator of Ty1 transposition protein 107 BRCT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00033      0.28      16      93 ..     292     373 ..     289     378 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00033
                     RTT107_BRCT_6  16 dipggtevissiLkahGikevkvlskklkiedlvkn.ekkkkkekkkspeyvliatkasqvk..kfkkllkee.ken 88 
                                       +i++g  v  +++++hGi+++ v++k+   e +v+  ++++++++kk+ e v+i + ++++k  ++k ++    +++
  gi|298674763|ref|YP_003726513.1| 292 SINSGPSVALQLMREHGISSIFVVNKHKGLEGVVTVeDAAEARRNKKNLEDVIIREYPTTTKdtQLKDIIPMIaESS 368
                                       57888999999***************999999988734556667777888899988777777556666665443445 PP

                     RTT107_BRCT_6  89 kkvlv 93 
                                         v v
  gi|298674763|ref|YP_003726513.1| 369 YPVAV 373
                                       55555 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.2   0.00086      0.73      50      83 ..     173     206 ..     141     213 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00086
                           SbcCD_C  50 laalyssaegrepalrlvfLDEAFsklDeesiat 83 
                                       + + ++ a++  +++ ++++DEAFs lD+  +++
  gi|298674763|ref|YP_003726513.1| 173 MQQRVGLARALATDPHFLLMDEAFSALDPLIRSE 206
                                       4555555544567899************866655 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00025      0.21      26      52 ..      61      87 ..      34     267 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00025
                                      EEEEESTTSSHHHHHHHHHHHCS---- CS
                           G-alpha 26 llllGqseSGKsTilkqlkllykkgfs 52
                                      ++l+G s+SGKsT+l+ + +l  +++ 
  gi|298674763|ref|YP_003726513.1| 61 FVLMGLSGSGKSTLLRCINRLIPPTYG 87
                                      7899***************99999844 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       747  (0.0416643); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2572.94
//
Query:       gi|298674764|ref|YP_003726514.1|  [L=278]
Description: binding-protein-dependent transporter inner membrane component [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-22   79.0  13.6    3.5e-22   79.0  13.6    2.1  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.6  17.1      0.87   1.6e+04       4      71 ..      25     109 ..      23     110 .. 0.78
   2 !   79.0  13.6   1.9e-26   3.5e-22       1     168 [.     111     268 ..     107     276 .. 0.92

  Alignments for each domain:
  == domain 1  score: -4.6 bits;  conditional E-value: 0.87
                      BPD_transp_1   4 lGilaalnrnkkldkllrpliivllslPsfvlaillvlvf..................vilsilghlilpviillll 62 
                                       +G+++    + +l+ ll+ + ++ll lP+ ++++l+++++                  ++l+ l+ + l++ +++l+
  gi|298674764|ref|YP_003726514.1|  25 FGFILD-GISAILSFLLDLFLDILLFLPHWLFIVLFIVAAyfltgrnwhiaaiggigfFVLDNLQLWSLGMQTIALV 100
                                       677777.778899999************9997777776667899999999999999998888888888886666666 PP

                      BPD_transp_1  63 saapyvrli 71 
                                        + +++ li
  gi|298674764|ref|YP_003726514.1| 101 ISSAVIALI 109
                                       666666554 PP

  == domain 2  score: 79.0 bits;  conditional E-value: 1.9e-26
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalr 77 
                                       gi++Gil+   +n  ++ ++ pl ++++++P+fv +i+ v        +g ++ p++i+++++a+p+ ++++  ++r
  gi|298674764|ref|YP_003726514.1| 111 GIPVGILSS--KNDNFKAAIKPLLDLMQTMPPFVYLIPAV------IFFGLGNVPGLIATIVFAMPPGIRLTDLGIR 179
                                       678888888..***********************999999......88***************************** PP

                      BPD_transp_1  78 slpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis 154
                                       ++p++lve+a a G ++ q ++kv lP al +i+tg+  +++++l   v++ ++g+  Glg+++l  i+  d+ ++ 
  gi|298674764|ref|YP_003726514.1| 180 QVPTELVEVADAFGSTPMQKLVKVQLPVALQTIMTGINQVIMLSLSMVVIAAMIGAR-GLGYQVLIGIQRVDIGLGF 255
                                       *******************************************************66.7***************999 PP

                      BPD_transp_1 155 nggvlalviavlll 168
                                         + l +vi+ ++l
  gi|298674764|ref|YP_003726514.1| 256 -EAGLGIVIIAIIL 268
                                       .5555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       747  (0.0416643); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2073.15
//
Query:       gi|298674765|ref|YP_003726515.1|  [L=304]
Description: glycine betaine ABC transporter substrate-binding protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-61  206.1   5.2    7.9e-61  205.9   5.2    1.0  1  OpuAC     Substrate binding domain of ABC-type glycine betain
  ------ inclusion threshold ------
      0.025   15.2   1.2        5.4    7.7   0.0    2.8  2  MucBP_2   Mucin binding domain
      0.035   14.3   0.3      0.088   13.0   0.3    1.7  1  DUF4912   Domain of unknown function (DUF4912)


Domain annotation for each model (and alignments):
>> OpuAC  Substrate binding domain of ABC-type glycine betaine transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.9   5.2   1.3e-64   7.9e-61       1     257 []      48     291 ..      48     291 .. 0.98

  Alignments for each domain:
  == domain 1  score: 205.9 bits;  conditional E-value: 1.3e-64
                                       CEEEEEEESSHHHHHHHHHHHHHHHHTTEEEEEEEEESHHHHHHHHHTTSSSEEEEEEHHHHHHHHHHHHHHHHEEE CS
                             OpuAC   1 ktivigsknwteqevlaeilkqllekkGykveltnlgstavlfaalasGdiDvypeewtgtayeaykkaveekkgle 77 
                                       k+++i++ +w+++e++++++k++ e++Gy+v+l+n ++ +++++++a+Gd+D+ +  w++ +++ y++++ ++ + +
  gi|298674765|ref|YP_003726515.1|  48 KSVTIAYVQWASAEATTNVVKEVYEQAGYEVNLQNTAA-GIMYQGIANGDADFSVCSWLPDTQANYWDQYGDQIDRV 123
                                       68************************************.********************************888877 PP

                                       EEEEESEEECEEEEEEHHHHHHHTTTBHHHHCTHHGGTEEEEEHHCCHSTTSHHCCHHHHHHHHHHT-TTCEEEGSC CS
                             OpuAC  78 vlgplgagnteglavpkyvaekygiksisDLkkpaedlelgakgeflgrpdgwgcekvtegllkaYgldkvelvegs 154
                                           +  + + gl+vp+yv    ++++i +Lk +++    +++g ++g+++g+g++  te++l++Y+ld++el ++s
  gi|298674765|ref|YP_003726515.1| 124 --RVNTPEVKTGLVVPEYV----DVDTIPELKGNES----QFDGTITGIDPGAGIMSQTETALEEYELDGYELESSS 190
                                       ..899**************....*************....9************************************ PP

                                       EEEEHHHHHHHHHTTCSSEEEEETTSTHHHHTTEEE-B-TTSTS-SSEEEEEEEEHHHHHHSCTHHHHHHHHC--HH CS
                             OpuAC 155 eaamdaelyaaykrgepvvvyawtPdwaikkydlvvLedpkglfppaynvvpvvrkefaekaPevaafLeklsldte 231
                                       ++am+++l + + +++ +vv++w P+wa++++dl++L+dp+++++  +++v+++r++++e++P+++++Le+l+++ +
  gi|298674765|ref|YP_003726515.1| 191 GPAMTSALRSVISNEDSIVVTLWNPHWAFARWDLKYLDDPQDVYGS-DDIVTIARQGLEEDKPNAYTILENLNWTVA 266
                                       **********************************************.****************************** PP

                                       HHHHHHHHHHTTTT-HHHHHHHHHHH CS
                             OpuAC 232 tlnelnaqvdvegkdpeevAkawlae 257
                                       + ++++a++d+ g++ ee+A++w++e
  gi|298674765|ref|YP_003726515.1| 267 DNEQVMAYIDQ-GMSGEEAAEKWVEE 291
                                       **********7.***********986 PP

>> MucBP_2  Mucin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.7    0.0063        38      33      71 ..      63     101 ..      30     102 .. 0.69
   2 ?    7.7   0.0    0.0009       5.4       7      58 ..     139     201 ..     136     213 .. 0.59

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0063
                           MucBP_2  33 tadtik.aleaqgYvlvssdgfpagttFdnddatdqtftv 71 
                                       t++ +k  +e++gY++   +++ ag+ ++   + d +f v
  gi|298674765|ref|YP_003726515.1|  63 TTNVVKeVYEQAGYEVN-LQNTAAGIMYQGIANGDADFSV 101
                                       344566679******74.8999999888888888887766 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0009
                           MucBP_2   7 yiDdttnktltd......dtltG.ktgetisYstadtikaleaqgYvlvssdgfpagt.....t 58 
                                       y+D +t  +l+        t+tG + g+ i  +t+++++++e  gY+l  s++ pa t     +
  gi|298674765|ref|YP_003726515.1| 139 YVDVDTIPELKGnesqfdGTITGiDPGAGIMSQTETALEEYELDGYELE-SSSGPAMTsalrsV 201
                                       5566655555554444445555533445555478889***********6.77776666444433 PP

>> DUF4912  Domain of unknown function (DUF4912)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   1.5e-05     0.088       2      23 ..     204     225 ..     204     241 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.5e-05
                           DUF4912   2 nedrivllprdpewlyayWeis 23 
                                       ned+iv+++ +p+w++a W+++
  gi|298674765|ref|YP_003726515.1| 204 NEDSIVVTLWNPHWAFARWDLK 225
                                       799*****************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2157.16
//
Query:       gi|298674766|ref|YP_003726516.1|  [L=308]
Description: glycine betaine ABC transporter substrate-binding protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-67  228.3   7.0    1.4e-67  228.0   7.0    1.0  1  OpuAC     Substrate binding domain of ABC-type glycine betain


Domain annotation for each model (and alignments):
>> OpuAC  Substrate binding domain of ABC-type glycine betaine transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  228.0   7.0   7.6e-72   1.4e-67       1     256 [.      53     294 ..      53     295 .. 0.98

  Alignments for each domain:
  == domain 1  score: 228.0 bits;  conditional E-value: 7.6e-72
                                       CEEEEEEESSHHHHHHHHHHHHHHHHTTEEEEEEEEESHHHHHHHHHTTSSSEEEEEEHHHHHHHHHHHHHHHHEEE CS
                             OpuAC   1 ktivigsknwteqevlaeilkqllekkGykveltnlgstavlfaalasGdiDvypeewtgtayeaykkaveekkgle 77 
                                       k++ i++ +w++++++++++kq+ ek+Gy+v++ ++++ +++++a+asGd+D+ + +w++++++ y++++ ++ +++
  gi|298674766|ref|YP_003726516.1|  53 KEVSIAYVQWDDAIATTNVVKQVYEKAGYDVKMNSVAA-GAMYQAIASGDVDFSACGWLPNTQANYWEEYGDQIDKV 128
                                       689***********************************.99******************************999999 PP

                                       EEEEESEEECEEEEEEHHHHHHHTTTBHHHHCTHHGGTEEEEEHHCCHSTTSHHCCHHHHHHHHHHT-TTCEEEGSC CS
                             OpuAC  78 vlgplgagnteglavpkyvaekygiksisDLkkpaedlelgakgeflgrpdgwgcekvtegllkaYgldkvelvegs 154
                                         gp+ +g+  gl+vp+y+    +i+si++L+ ++e    +++g+++g+++g+g++  t++++++Y+l ++el+++s
  gi|298674766|ref|YP_003726516.1| 129 --GPNLEGASTGLVVPTYM----DIDSIEELNENKE----KLDGKITGIDPGAGIMSQTDTAIQEYNL-DYELMSSS 194
                                       ..9****************....********99999....9***************************.8******* PP

                                       EEEEHHHHHHHHHTTCSSEEEEETTSTHHHHTTEEE-B-TTSTS-SSEEEEEEEEHHHHHHSCTHHHHHHHHC--HH CS
                             OpuAC 155 eaamdaelyaaykrgepvvvyawtPdwaikkydlvvLedpkglfppaynvvpvvrkefaekaPevaafLeklsldte 231
                                        a+m ++l+aay+++ep+vv++w P+wa++++dl++L+dpkg+++  +++v ++r+++ e++Pe++++L++++++ e
  gi|298674766|ref|YP_003726516.1| 195 SAGMASALKAAYDKKEPIVVTLWNPHWAFARWDLKYLDDPKGVYGE-DQIVNLARQGMSEDKPEAYEILNRFEWSME 270
                                       **********************************************.****************************** PP

                                       HHHHHHHHHHTTTT-HHHHHHHHHH CS
                             OpuAC 232 tlnelnaqvdvegkdpeevAkawla 256
                                       ++++++a+++  g  +ee+A +w++
  gi|298674766|ref|YP_003726516.1| 271 DVESVMADIQS-GTPAEEAASKWIE 294
                                       **********8.***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2279.00
//
Query:       gi|298674767|ref|YP_003726517.1|  [L=350]
Description: radical SAM domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-06   28.4   0.0    2.4e-05   24.5   0.0    2.3  2  Fer4_14      4Fe-4S single cluster domain
      2e-05   25.1   0.0    4.9e-05   23.8   0.0    1.8  1  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   2.6e-09   2.4e-05       1      95 [.      31     123 ..      31     132 .. 0.71
   2 ?    1.2   0.0     0.044   3.9e+02      68      96 ..     224     253 ..     217     271 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2.6e-09
                           Fer4_14   1 lfvrlsgCnlsCkgCdnketwks...elgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrl 74 
                                       lfv ++ C  +C  C  +e+ k+    +++  ++ ++ ++++++   ++++ g  +tGGeP+  ++ +  +  ++ l
  gi|298674767|ref|YP_003726517.1|  31 LFV-TGVCGRNCYYCPLSEERKEdtvYANETIVYSDM-DVINEV--LQMNALGTGITGGEPF--YKPERTIYYISLL 101
                                       588.999********9555333312233444444555.334333..334446789*******..5788888899*** PP

                           Fer4_14  75 keey.pekkiwletngtleiel 95 
                                       k e+ ++++i+l+t+  l+++ 
  gi|298674767|ref|YP_003726517.1| 102 KSEFgESHHIHLYTSIALDKDT 123
                                       ***9777********9998765 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.044
                           Fer4_14  68 lklvkrlkeeypekkiwl.etngtleiele 96 
                                        +l ++l e+y++ +i++  ++++ +++++
  gi|298674767|ref|YP_003726517.1| 224 RELAENLAENYQNASIHFcSSSYKDAVQFK 253
                                       5789999*********96256788888887 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   5.5e-09   4.9e-05       3     106 ..      33     136 ..      31     182 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 5.5e-09
                                       EESEESS--TTTSCCTT.....HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC CS
                                       xxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpet.....vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla 74 
                                       vt  C ++C +C+ +e      v+ +++  + +++ i e ++ +     + +  ++ggep++ p+ + ++  l k +
  gi|298674767|ref|YP_003726517.1|  33 VTGVCGRNCYYCPLSEErkedtVYANETIVYSDMDVINEVLQMN-----ALGTGITGGEPFYKPERTIYYISLLKSE 104
                                       6788************9977766666666666666666666666.....788999********************** PP

                                       .CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEE CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  75 .vpgiritvetngtlpdeeklerllelgvdrvs 106
                                         +  +i++ t+  l+ ++ l  l++ g+d + 
  gi|298674767|ref|YP_003726517.1| 105 fGESHHIHLYTSIALD-KDTLTILKNVGLDEIR 136
                                       9999999999999996.8888888888877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 2038.08
//
Query:       gi|298674768|ref|YP_003726518.1|  [L=103]
Description: hypothetical protein Metev_0824 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-32  112.2   0.8    1.2e-32  111.9   0.8    1.1  1  DUF2551   Protein of unknown function (DUF2551)
     0.0074   16.4   0.1       0.01   16.0   0.1    1.2  1  FUR       Ferric uptake regulator family


Domain annotation for each model (and alignments):
>> DUF2551  Protein of unknown function (DUF2551)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.9   0.8   1.4e-36   1.2e-32       1      83 []      15      96 ..      15      96 .. 0.99

  Alignments for each domain:
  == domain 1  score: 111.9 bits;  conditional E-value: 1.4e-36
                           DUF2551  1 LkkylerDksGiRrevLklfleakkltveeiyeklkek.fdvsykgvasmvGliasrlGIlkvkkeskgeknvYsLkee 78
                                      L+kyl+rD++GiR++vLklfle + +t++++ye l+++ fdvsy+gv++mvGl+++rlGIl++  +++g++nvY+Lke+
  gi|298674768|ref|YP_003726518.1| 15 LTKYLSRDSTGIRKAVLKLFLEDDAYTTSDVYEYLRNHnFDVSYRGVSAMVGLMNTRLGILSI--DVTGDHNVYMLKED 91
                                      78***********************************99************************..************** PP

                           DUF2551 79 yadlv 83
                                      y+++v
  gi|298674768|ref|YP_003726518.1| 92 YRQIV 96
                                      **998 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   1.1e-06      0.01       7      74 ..      24      90 ..      21     100 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.1e-06
                                      HHHHHHHHHHHHHHSSSBEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEESS CS
                               FUR  7 TkqRekilevlekseehlsaeevykelkeedpeislaTVYrtLklleeaglvkelefedgesryelak 74
                                      T  R+++l+++ + +++ +  +vy+ l++++ ++s   V  ++ l++ +  + ++++++++++y l++
  gi|298674768|ref|YP_003726518.1| 24 TGIRKAVLKLFLEDDAYTT-SDVYEYLRNHNFDVSYRGVSAMVGLMNTRLGILSIDVTGDHNVYMLKE 90
                                      778**********999865.79**************************99999***********9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 636.79
//
Query:       gi|298674769|ref|YP_003726519.1|  [L=282]
Description: undecaprenyl diphosphate synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-67  227.6   0.0    1.6e-67  227.3   0.0    1.0  1  Prenyltransf  Putative undecaprenyl diphosphate synthase


Domain annotation for each model (and alignments):
>> Prenyltransf  Putative undecaprenyl diphosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.3   0.0     9e-72   1.6e-67       1     220 [.      29     252 ..      29     256 .. 0.93

  Alignments for each domain:
  == domain 1  score: 227.3 bits;  conditional E-value: 9e-72
                                       EE--HHHHHHHTT.S-HHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEEGGGGGS-HHHHHHHHHHHH...HHHHHH CS
                      Prenyltransf   1 imDGNrRwAkkrgleereeGhkaGaealkeilelclelgvkvvtvYafSteNfkRskeevdalmellk...eellke 74 
                                       imDGNrR+A++ g +++ +Gh++G +  ++++e++ e+gvk +t+YafSteNf+R+k+e ++l+el++   +e++++
  gi|298674769|ref|YP_003726519.1|  29 IMDGNRRFAQHIG-KHSYYGHRKGSDITEKVIEWSCEIGVKELTIYAFSTENFNRPKHETEKLFELISlkfNEITDD 104
                                       9************.88888************************************************8766666666 PP

                                       HHHHHHHTTEEEEEESSGGGS-HHHHHHHHHHHHHHT.TTTSEEEEEEEEE-HHHHHHHHHHHHHHTT..SSSG.GG CS
                      Prenyltransf  75 elkellkegvrvrviGdlellpedvlealekaeeatkknnkklvlniavnYgsrdeiveavrelvkekseekkk.ee 150
                                       e  +++++++++r+iGd+e+lp +++e++ekae+at  n ++++ln+a+ Yg+r++iv+av+e++++ s+   + ++
  gi|298674769|ref|YP_003726519.1| 105 E--RTHERRMKIRAIGDIERLPIHLQESIEKAETATC-NYENFKLNVALTYGGRQDIVQAVQEMARKISNGYLElDD 178
                                       6..99999*****************************.6666**********************9998766665567 PP

                                       HSHHHHHCTSTT..T..SSS-SEEEEESS--S-TTSSTTTTTT-E..EEEESSSGGG--HHHHHHHHHHHHHCH CS
                      Prenyltransf 151 ideetlekhlytaka..lpdpDlliRtsGeeRlSnFllwqlayse..lyfldvlWPdfskedllealleyqkre 220
                                       i+e+t++++ly a    + ++Dl+iRt+G+eR+SnFl wq+  +e   yf+  +WP f+k d+l+ ++ yq+r 
  gi|298674769|ref|YP_003726519.1| 179 INESTISEYLYPACGpsVSNVDLIIRTGGNERISNFLPWQTNGNEcaTYFCAPFWPSFRKIDFLRSIRLYQSRL 252
                                       89*********75447899*********************99999999***********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1704.00
//
Query:       gi|298674770|ref|YP_003726520.1|  [L=299]
Description: ADP-ribosylation/Crystallin J1 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-63  215.4   0.0    1.6e-63  215.1   0.0    1.1  1  ADP_ribosyl_GH  ADP-ribosylglycohydrolase
  ------ inclusion threshold ------
       0.25   11.4   2.3        1.2    9.3   0.1    2.8  3  STb_secrete     Heat-stable enterotoxin B, secretory


Domain annotation for each model (and alignments):
>> ADP_ribosyl_GH  ADP-ribosylglycohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.1   0.0   1.8e-67   1.6e-63       1     290 [.       9     275 ..       9     276 .. 0.94

  Alignments for each domain:
  == domain 1  score: 215.1 bits;  conditional E-value: 1.8e-67
                                       HHHHHHHHHHHHHGGGTT--HHHHHHHTSS--S-----STTTTTS-TT---HHHHHHHHHHHTEET.TEE-HHHHHH CS
                    ADP_ribosyl_GH   1 GallGaavGDAlGlpvefwsydeirrrygelgetpdktgfghfglkpgewtddtqmalllleslleaggldpedlar 77 
                                       G+llG+avGDAlG+p+e +++++++                +   +pgewtddt++al+l+esl+ ++++dp+d ++
  gi|298674770|ref|YP_003726520.1|   9 GSLLGLAVGDALGAPLESKPPHSFE--------------PINDMVEPGEWTDDTSQALCLAESLIMRKRFDPTDQLE 71 
                                       89***************99888886..............345889******************************** PP

                                       HHHH.HHT.......T--SS--HHHHHHHHHTTTT-...-S-B...---BTTTGGG-HHHHHHTSS-HHHHHHHHHH CS
                    ADP_ribosyl_GH  78 rflaeWlee.p..gdteprgignttrealrnlksgepppeaganangsagngalmRaaplgllyagdpeeaaelaee 151
                                       r+l+ W+++ +  +  + + ig+tt ++l++++   +p +++    +s +ng+lmR+ap++l++a++pe+a++++ e
  gi|298674770|ref|YP_003726520.1|  72 RYLK-WFKTgYlsSRNQSFNIGPTTTKSLQEFEISLEPIRERNE--NSVTNGSLMRIAPVPLAFADKPETAIDWSGE 145
                                       *999.***988*9999****************998777776665..8****************************** PP

                                       HHHTTB--HHHHHHHHHHHHHHHHHHTT--STHHHHHH..HHHHTTT-HHHHHHHGGGGG---HHH........HHH CS
                    ADP_ribosyl_GH 152 aarlTHnhpeavagaaayaaliaaalrgksleealdaaeeelavapaeeelaaalrkalaladsdkdvdvdaeeavd 228
                                       ++++THn+  av+++ ++ ali  a+++ ++e+ l ++    + ++++++l++ ++++++ + ++k        +  
  gi|298674770|ref|YP_003726520.1| 146 SSKTTHNSTIAVDACRYMGALIVGAVNNFPKEDLLSNLFTPIRGYWDKKPLCDPIKEIAKESFKNK--------EPP 214
                                       **************************************9999999999999999999988666665........777 PP

                                       HH--SSBHHHHHHHHHHHHHH.-SSHHHHHHHHHTS-SSHHHHHHHHHHHHHHHH-GGGS-H CS
                    ADP_ribosyl_GH 229 elgsggyavealaaalyallhaaddfeeallaavnlGgDtdttgaiaGallGalyGleaiPe 290
                                       e++s  y++++l+aal+a+++ +++f+e++l+avnlG D+dt+ga++G+++Ga+yG + iP+
  gi|298674770|ref|YP_003726520.1| 215 EIKSELYTPKTLEAALWAFYK-SSSFKEGCLKAVNLGDDADTVGAVYGQIAGAYYGKKDIPA 275
                                       88899****************.99*************************************7 PP

>> STb_secrete  Heat-stable enterotoxin B, secretory
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0         1   9.1e+03       8      14 ..       2       8 ..       2       9 .. 0.91
   2 ?    9.3   0.1   0.00013       1.2       5      22 ..     192     209 ..     190     211 .. 0.92
   3 ?    0.4   0.1      0.08   7.2e+02      18      40 ..     240     262 ..     234     269 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1
                       STb_secrete  8 DLCenyr 14
                                      DL e+yr
  gi|298674770|ref|YP_003726520.1|  2 DLIEKYR 8 
                                      89****9 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00013
                       STb_secrete   5 nkkDLCenyrqiakesCk 22 
                                       +kk LC+  + iakes k
  gi|298674770|ref|YP_003726520.1| 192 DKKPLCDPIKEIAKESFK 209
                                       69**************88 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.08
                       STb_secrete  18 kesC.kkGfLGvrDGtaGaCfGaq 40 
                                       ke C k   LG    t Ga +G q
  gi|298674770|ref|YP_003726520.1| 240 KEGClKAVNLGDDADTVGAVYG-Q 262
                                       7888344468888899999998.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1786.60
//
Query:       gi|298674771|ref|YP_003726521.1|  [L=265]
Description: DNA-directed RNA polymerase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.6e-28   97.6   0.0    1.5e-27   96.1   0.0    1.7  2  RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
    7.9e-15   54.1   0.0      1e-14   53.7   0.0    1.2  1  RNA_pol_L      RNA polymerase Rpb3/Rpb11 dimerisation domain
    3.4e-07   29.8  12.4    9.3e-05   22.1   3.0    3.3  3  Fer4           4Fe-4S binding domain
    4.5e-07   30.4   7.5    4.5e-07   30.4   7.5    2.6  2  Fer4_7         4Fe-4S dicluster domain
    2.4e-06   27.6   9.6    2.4e-06   27.6   9.6    2.7  3  Fer4_9         4Fe-4S dicluster domain
      7e-06   26.1   7.9      7e-06   26.1   7.9    2.3  2  Fer4_10        4Fe-4S dicluster domain
    0.00013   22.9  12.4     0.0077   17.2   0.6    3.1  3  Fer4_16        4Fe-4S double cluster binding domain
    0.00028   21.2  13.8      0.065   13.7   0.1    2.9  2  Fer4_8         4Fe-4S dicluster domain
    0.00054   19.9   2.8    0.00054   19.9   2.8    3.1  3  Fer4_6         4Fe-4S binding domain
    0.00094   19.7  17.7      0.089   13.4   3.0    3.3  3  Fer4_17        4Fe-4S dicluster domain
     0.0044   17.4  19.4       0.15   12.6   1.6    3.3  3  Fer4_4         4Fe-4S binding domain
     0.0051   16.9  12.2     0.0051   16.9  12.2    2.5  2  Fer4_21        4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.017   15.2   5.2      0.082   13.1   1.9    2.2  2  Furin-like_2   Furin-like repeat, cysteine-rich
       0.05   14.6   3.5       0.05   14.6   3.5    3.4  3  Fer4_3         4Fe-4S binding domain
       0.48   10.6  13.5       0.15   12.2   9.8    2.1  2  Fer4_18        4Fe-4S dicluster domain
        3.5    7.9  22.5       0.11   12.7   2.4    3.4  3  Fer4_2         4Fe-4S binding domain
        4.2    8.2  11.1       0.28   12.0   1.3    2.6  2  Fer4_15        4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.1   0.0   1.5e-30   1.5e-27       2     112 .]      47     154 ..      46     154 .. 0.97
   2 ?   -1.8   0.0       3.8     4e+03      35      51 ..     200     218 ..     187     254 .. 0.65

  Alignments for each domain:
  == domain 1  score: 96.1 bits;  conditional E-value: 1.5e-30
                                       EEEECTSSS.HHHHHCHHHCSTCBSSCHHHHHHHHCTT-ETSSSSTTCSEEEEEEEEESSECEEGGGCBESSSSCEE CS
                     RNA_pol_A_bac   2 eieentsvlqDEvvaHrlgliplvsedvleillnlkelveeeeegeeeksvelkLnvkgpgevtagdlkledadvei 78 
                                       +i++ntsvl+DE +  rl+lipl +e++++ +    e+  ++eeg+++++v+++L+++gp+ v++gdl ++d+ +++
  gi|298674771|ref|YP_003726521.1|  47 NIYNNTSVLYDEQLGLRLALIPLATENIDD-YTTQDEC--TCEEGCPSCEVSITLSAEGPKMVYSGDLISSDPGIQP 120
                                       69****************************.7777888..8************************************ PP

                                       SSTTSEEEEEETT-EEEEEEEEEEESSEECTTT- CS
                     RNA_pol_A_bac  79 vnpdilIakLrkgqeleleakvkkGiGkehakfs 112
                                       ++ +i+I++L+++q++ lea + kG Gk+ ak++
  gi|298674771|ref|YP_003726521.1| 121 ADTNIPIIELKEDQRVVLEALAHKGLGKDNAKWQ 154
                                       *********************************6 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.8
                                       HHCTT-..ETSSSSTTCSE CS
                     RNA_pol_A_bac  35 nlkelv..eeeeegeeeks 51 
                                       nl ++   + +ee++e + 
  gi|298674771|ref|YP_003726521.1| 200 NLMDCIlcKLCEEACEIDA 218
                                       4444533213555555443 PP

>> RNA_pol_L  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.7   0.0   9.7e-18     1e-14       1      68 [.      16     254 ..      16     255 .. 0.80

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 9.7e-18
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................... RF
                         RNA_pol_L   1 efllrgvdhtlgNaLRrillsevpgvaiea............................................... 30 
                                       +f+l++++++++N++Rr +l++vp++ai+                                                
  gi|298674771|ref|YP_003726521.1|  16 RFVLSNTTPAFANSIRRAMLADVPTFAIDDlniynntsvlydeqlglrlaliplateniddyttqdectceegcpsc 92 
                                       599***************************************************99999999999999999999999 PP

                                       ............................................................................. RF
                         RNA_pol_L  31 ............................................................................. 30 
                                                                                                                    
  gi|298674771|ref|YP_003726521.1|  93 evsitlsaegpkmvysgdlissdpgiqpadtnipiielkedqrvvlealahkglgkdnakwqagvacgyknlplirv 169
                                       99999999998888888888888888888888877777777777666666666666666666666666666655555 PP

                                       .............xx..................................xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         RNA_pol_L  31 .............pv..................................vkvntdkdklilevetdgslkPeealke 60 
                                                    p+                                  ++v++d++ + ++ve+dgs++ ++++ +
  gi|298674771|ref|YP_003726521.1| 170 nncdkcglcvsecPKgiiyldeegakvadenlmdcilcklceeaceidaISVKEDESSFLFTVESDGSYSSQQLIIN 246
                                       55555555555551166666666666666666666666666666677778999************************ PP

                                       xxxxxxxx RF
                         RNA_pol_L  61 AlkiLkek 68 
                                       A + +k+k
  gi|298674771|ref|YP_003726521.1| 247 AGNTIKAK 254
                                       *9999987 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   2.6       3.7   3.9e+03      13      19 ..      84      90 ..      83      91 .. 0.87
   2 !   22.1   3.0   8.8e-08   9.3e-05       5      24 .]     169     188 ..     165     188 .. 0.88
   3 !   20.3   2.1   3.2e-07   0.00033       7      24 .]     203     220 ..     199     220 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3.7
                                      HHHHHST CS
                              Fer4 13 aCvevCP 19
                                      +C+e CP
  gi|298674771|ref|YP_003726521.1| 84 TCEEGCP 90
                                      6*****9 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 8.8e-08
                                       TTTSSS-THHHHHSTTTEEE CS
                              Fer4   5 eekCigCGaCvevCPvgAIt 24 
                                        + C +CG+Cv+ CP g I+
  gi|298674771|ref|YP_003726521.1| 169 VNNCDKCGLCVSECPKGIIY 188
                                       578**************996 PP

  == domain 3  score: 20.3 bits;  conditional E-value: 3.2e-07
                                       TSSS-THHHHHSTTTEEE CS
                              Fer4   7 kCigCGaCvevCPvgAIt 24 
                                       +Ci C++C+e+C  +AI+
  gi|298674771|ref|YP_003726521.1| 203 DCILCKLCEEACEIDAIS 220
                                       7***************96 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.6      0.67   7.1e+02      44      50 ..      85      91 ..      70     105 .. 0.75
   2 !   30.4   7.5   4.2e-10   4.5e-07       2      51 ..     172     217 ..     171     218 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.67
                            Fer4_7 44 CvavCPt 50
                                      C++ CP+
  gi|298674771|ref|YP_003726521.1| 85 CEEGCPS 91
                                      5555553 PP

  == domain 2  score: 30.4 bits;  conditional E-value: 4.2e-10
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51 
                                       C +Cg Cv+ Cp + i+ldee    g + ++ + ++C+ C+ C+++C  +
  gi|298674771|ref|YP_003726521.1| 172 CDKCGLCVSECPKGIIYLDEE----GAKVADENLMDCILCKLCEEACEID 217
                                       ******************998....88899*****************765 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2  11.4   3.5e-05     0.037       4      51 .]      82     187 ..      80     187 .. 0.92
   2 !   27.6   9.6   2.3e-09   2.4e-06       1      51 []     171     219 ..     171     219 .. 0.92
   3 !   12.3   2.2   0.00014      0.15       1      23 [.     203     225 ..     203     232 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.5e-05
                            Fer4_9   4 gCgaCveaCpagvvvedaaerkarlraase............................................... 33 
                                       +C+ C+e Cp++ v+   +++  ++   ++                                               
  gi|298674771|ref|YP_003726521.1|  82 ECT-CEEGCPSCEVSITLSAEGPKMVYSGDlissdpgiqpadtnipiielkedqrvvlealahkglgkdnakwqagv 157
                                       577.*****9999999888888888888889999999999999********************************** PP

                            Fer4_9  34 ............eaCigCgaCveaCpkgai 51 
                                                   ++C +Cg Cv  Cpkg+i
  gi|298674771|ref|YP_003726521.1| 158 acgyknlplirvNNCDKCGLCVSECPKGII 187
                                       ************9**************976 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 2.3e-09
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       +C +Cg Cv+ Cp+g++  d+ + k++ ++  +  Ci C+ C+eaC+ +ai
  gi|298674771|ref|YP_003726521.1| 171 NCDKCGLCVSECPKGIIYLDEEGAKVADENLMD--CILCKLCEEACEIDAI 219
                                       6************************99988765..***********98876 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00014
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaae 23 
                                       +C+ C+ C+eaC+ ++++ ++ e
  gi|298674771|ref|YP_003726521.1| 203 DCILCKLCEEACEIDAISVKEDE 225
                                       59999999999999999887765 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.25   2.7e+02      14      22 ..      84      92 ..      75     139 .. 0.75
   2 !   26.1   7.9   6.7e-09     7e-06       4      55 ..     167     214 ..     164     215 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.25
                           Fer4_10 14 kCvkaCPad 22
                                      +C + CP++
  gi|298674771|ref|YP_003726521.1| 84 TCEEGCPSC 92
                                      477777774 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 6.7e-09
                           Fer4_10   4 idddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                       i  + C +Cg Cv+ CP        +  +++ ++ ++++ +C+ c  C eaC
  gi|298674771|ref|YP_003726521.1| 167 IRVNNCDKCGLCVSECPK----GIIYLDEEGAKVADENLMDCILCKLCEEAC 214
                                       66789*************....555555556666666*************** PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   1.0       3.8     4e+03       8      59 ..      85      91 ..      69      96 .. 0.60
   2 !   17.2   0.6   7.3e-06    0.0077       1      23 [.     171     193 ..     171     201 .. 0.82
   3 !   13.0   0.2   0.00014      0.15       2      24 ..     204     226 ..     203     261 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3.8
                           Fer4_16  8 CaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdi 59
                                      C                                               gC  
  gi|298674771|ref|YP_003726521.1| 85 CE---------------------------------------------EGCPS 91
                                      33.............................................34444 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 7.3e-06
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkek 23 
                                       +C +Cg C++ CP + i  ++e 
  gi|298674771|ref|YP_003726521.1| 171 NCDKCGLCVSECPKGIIYLDEEG 193
                                       6****************988554 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 0.00014
                           Fer4_16   2 CgtCgkCaevCPtnaikekkeke 24 
                                       C+ C+ C e+C  +ai+ k++++
  gi|298674771|ref|YP_003726521.1| 204 CILCKLCEEACEIDAISVKEDES 226
                                       *****************985543 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   9.9    0.0038         4      11      65 .]      85     186 ..      70     186 .. 0.52
   2 !   13.7   0.1   6.1e-05     0.065      45      63 ..     198     216 ..     188     249 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0038
                            Fer4_8  11 CqsaCpvlrr.........................................tkkhlldargeaae...........d 35 
                                       C++ Cp+++                                                                   d
  gi|298674771|ref|YP_003726521.1|  85 CEEGCPSCEVsitlsaegpkmvysgdlissdpgiqpadtnipiielkedqrV------------VlealahkglgkD 149
                                       7777775555333433444444433333333333333333333322222220............0222222222222 PP

                            Fer4_8  36 vqeeqvlee.......eealwsCttcgaCtevCpvgi 65 
                                       + ++q+  +          +++C  cg C+++Cp+gi
  gi|298674771|ref|YP_003726521.1| 150 NAKWQAGVAcgyknlpLIRVNNCDKCGLCVSECPKGI 186
                                       33333333366666777789**************997 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 6.1e-05
                            Fer4_8  45 eealwsCttcgaCtevCpv 63 
                                       +e+l  C  c+ C+e+C +
  gi|298674771|ref|YP_003726521.1| 198 DENLMDCILCKLCEEACEI 216
                                       5566777777777777754 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   2.2       7.7   8.2e+03      15      20 ..      85      90 ..      84      94 .. 0.77
   2 !   19.9   2.8   5.1e-07   0.00054       6      24 .]     169     187 ..     165     187 .. 0.89
   3 !    8.5   4.3     0.002       2.1       9      24 .]     204     219 ..     203     219 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 7.7
                            Fer4_6 15 CvrvCP 20
                                      C+  CP
  gi|298674771|ref|YP_003726521.1| 85 CEEGCP 90
                                      888888 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 5.1e-07
                            Fer4_6   6 pdkCigCgdCvrvCPegai 24 
                                        ++C+ Cg Cv+ CP g+i
  gi|298674771|ref|YP_003726521.1| 169 VNNCDKCGLCVSECPKGII 187
                                       589************9987 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.002
                            Fer4_6   9 CigCgdCvrvCPegai 24 
                                       Ci C  C+ +C  +ai
  gi|298674771|ref|YP_003726521.1| 204 CILCKLCEEACEIDAI 219
                                       ***********98876 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.21   2.3e+02       8      17 ..      85      94 ..      57     114 .. 0.79
   2 !   13.4   3.0   8.4e-05     0.089      42      60 ..     168     186 ..     131     187 .. 0.81
   3 !   12.4  13.4   0.00016      0.17       1      57 [.     171     215 ..     171     218 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.21
                           Fer4_17  8 ClpeCpsyea 17
                                      C++ Cps+e 
  gi|298674771|ref|YP_003726521.1| 85 CEEGCPSCEV 94
                                      6666776665 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 8.4e-05
                           Fer4_17  42 kaslCieCgeCerkCPqgl 60 
                                       ++++C +Cg+C+++CP+g+
  gi|298674771|ref|YP_003726521.1| 168 RVNNCDKCGLCVSECPKGI 186
                                       6799************986 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00016
                           Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCP 57 
                                       +C +Cg C+ eCp +++y +e+   +            ++e+  +Ci C++Ce++C 
  gi|298674771|ref|YP_003726521.1| 171 NCDKCGLCVSECPKGIIYLDEEGAKV------------ADENLMDCILCKLCEEACE 215
                                       6*****************99655322............246789************6 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   4.3      0.15   1.6e+02       1      11 [.      80      93 ..      80      95 .. 0.86
   2 !   12.6   1.6   0.00014      0.15       2      16 ..     170     184 ..     170     191 .. 0.91
   3 !   10.9   0.3   0.00051      0.53       4      15 ..     204     215 ..     198     232 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.15
                            Fer4_4  1 qerCi...gCgsCv 11
                                      q+ C+   gC+sC+
  gi|298674771|ref|YP_003726521.1| 80 QDECTceeGCPSCE 93
                                      78999999*****8 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00014
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       ++C  Cg Cv+ CP 
  gi|298674771|ref|YP_003726521.1| 170 NNCDKCGLCVSECPK 184
                                       68************6 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00051
                            Fer4_4   4 CigCgsCvaaCP 15 
                                       Ci C+ C+ aC+
  gi|298674771|ref|YP_003726521.1| 204 CILCKLCEEACE 215
                                       ***********7 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.9         1   1.1e+03      38      47 ..      80      92 ..      67      98 .. 0.57
   2 !   16.9  12.2   4.8e-06    0.0051       3      58 ..     167     220 ..     165     221 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1
                           Fer4_21 38 edeCv...GCnlC 47
                                      +deC+   GC  C
  gi|298674771|ref|YP_003726521.1| 80 QDECTceeGCPSC 92
                                      4555422233333 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 4.8e-06
                           Fer4_21   3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                       i  ++C +Cg+C+  C++ ++  ++ ++++v+     +C+ C+lC + C + d+i+
  gi|298674771|ref|YP_003726521.1| 167 IRVNNCDKCGLCVSECPK-GIIYLDEEGAKVADENLMDCILCKLCEEACEI-DAIS 220
                                       77899************4.4444444555555555679************8.8886 PP

>> Furin-like_2  Furin-like repeat, cysteine-rich
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.092        98       4      37 ..      80     113 ..      77     118 .. 0.77
   2 ?   13.1   1.9   7.8e-05     0.082      13      66 ..     156     215 ..     148     244 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.092
                      Furin-like_2   4 calcseenGclkckkklfllleregirqiGvcla 37 
                                       ++ c+ e+Gc +c+  + l  e  ++   G  ++
  gi|298674771|ref|YP_003726521.1|  80 QDECTCEEGCPSCEVSITLSAEGPKMVYSGDLIS 113
                                       678999*******999988887777777776655 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 7.8e-05
                      Furin-like_2  13 clkckkklfllleregirqiGvclascpaG..yf...gvrnkevn..rctkckaeeces.cf 66 
                                        ++c  k + l++ ++  + G c+++cp+G  y    g +  + n   c+ ck   ce+ c 
  gi|298674771|ref|YP_003726521.1| 156 GVACGYKNLPLIRVNNCDKCGLCVSECPKGiiYLdeeGAKVADENlmDCILCKL--CEEaCE 215
                                       57888888899999****************444333334444433227999998..654154 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   4.0      0.82   8.6e+02       3      13 ..      82      91 ..      81      93 .. 0.84
   2 ?   14.6   3.5   4.7e-05      0.05       1      15 []     172     186 ..     172     186 .. 0.95
   3 ?    9.4   2.3    0.0021       2.2       1      11 [.     204     214 ..     204     218 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.82
                            Fer4_3  3 gCgaCvevCPv 13
                                       C +C+e CP+
  gi|298674771|ref|YP_003726521.1| 82 EC-TCEEGCPS 91
                                      69.6******6 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 4.7e-05
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+ Cg+Cv  CP+g+
  gi|298674771|ref|YP_003726521.1| 172 CDKCGLCVSECPKGI 186
                                       *************95 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0021
                            Fer4_3   1 CtgCgaCvevC 11 
                                       C+ C +C+e+C
  gi|298674771|ref|YP_003726521.1| 204 CILCKLCEEAC 214
                                       *********** PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       2.4   2.5e+03      58      71 ..      80      92 ..      49     102 .. 0.51
   2 ?   12.2   9.8   0.00014      0.15      58      97 ..     169     216 ..     132     232 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.4
                           Fer4_18 58 agdcidcescvkvc 71
                                      + +c+ ce     c
  gi|298674771|ref|YP_003726521.1| 80 QDECT-CEEGCPSC 92
                                      22222.32222223 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00014
                           Fer4_18  58 agdcidcescvkvcPtgi........dirkGlqleciscllcidacdk 97 
                                       +++c +c+ cv+ cP gi         + +   ++ci c lc +ac+ 
  gi|298674771|ref|YP_003726521.1| 169 VNNCDKCGLCVSECPKGIiyldeegaKVADENLMDCILCKLCEEACEI 216
                                       689*************9844433222355666799***********84 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   3.7       3.7   3.9e+03       8      21 ..      83      90 ..      78      95 .. 0.56
   2 ?   12.7   2.4    0.0001      0.11       7      21 ..     169     183 ..     164     184 .. 0.88
   3 ?    7.7   1.4    0.0039       4.1       9      20 ..     203     214 ..     194     215 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.7
                            Fer4_2  8 drCigCgaCvsaCP 21
                                       +C         CP
  gi|298674771|ref|YP_003726521.1| 83 CTC------EEGCP 90
                                      345......44454 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.0001
                            Fer4_2   7 tdrCigCgaCvsaCP 21 
                                        ++C  Cg Cvs CP
  gi|298674771|ref|YP_003726521.1| 169 VNNCDKCGLCVSECP 183
                                       578***********9 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0039
                            Fer4_2   9 rCigCgaCvsaC 20 
                                        Ci C+ C  aC
  gi|298674771|ref|YP_003726521.1| 203 DCILCKLCEEAC 214
                                       5*********** PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.3   0.00026      0.28       7      30 ..     171     195 ..     168     203 .. 0.75
   2 ?    0.3   2.8       1.2   1.2e+03       7      19 ..     203     215 ..     200     237 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00026
                           Fer4_15   7 aCigcglCvaeape.vfeldedgla 30 
                                       +C+ cglCv e+p+ ++ lde+g +
  gi|298674771|ref|YP_003726521.1| 171 NCDKCGLCVSECPKgIIYLDEEGAK 195
                                       8***********7626677777766 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.2
                           Fer4_15   7 aCigcglCvaeap 19 
                                        Ci c lC ++++
  gi|298674771|ref|YP_003726521.1| 203 DCILCKLCEEACE 215
                                       5999999999983 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       829  (0.0462379); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1624.39
//
Query:       gi|298674772|ref|YP_003726522.1|  [L=126]
Description: 30S ribosomal protein S11 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-47  159.7   2.7    3.7e-47  159.3   2.7    1.2  1  Ribosomal_S11  Ribosomal protein S11
    0.00017   21.4   0.2    0.00021   21.1   0.2    1.2  1  Pilus_CpaD     Pilus biogenesis CpaD protein (pilus_cpaD)
  ------ inclusion threshold ------
       0.12   12.7   0.2       0.24   11.7   0.0    1.6  2  CBM_25         Carbohydrate binding domain (family 25)


Domain annotation for each model (and alignments):
>> Ribosomal_S11  Ribosomal protein S11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.3   2.7   6.1e-51   3.7e-47       1     110 []       7     125 ..       7     125 .. 0.99

  Alignments for each domain:
  == domain 1  score: 159.3 bits;  conditional E-value: 6.1e-51
                     Ribosomal_S11   1 GvahiqasfnntiititdlkGaevlvksaGglgvkasr.kssPyaaqlaaekaaekvldkGikavevkvkg...... 70 
                                       Gvahi++sfnntiit+tdl+Gae+l+ks+Gg++ ka+r +ssPy+a+++a+++a+ ++dkG++ v++kv++      
  gi|298674772|ref|YP_003726522.1|   7 GVAHIKSSFNNTIITVTDLTGAETLAKSSGGMVTKAARdESSPYTAMQMARQVADMLKDKGVQGVHIKVRApggnkh 83 
                                       9**************************************************************************** PP

                     Ribosomal_S11  71 ..pGpGreaalralaraGlkigriedvtPiPhdgirrpkkrr 110
                                         pGpG++aa+ra+araG++igriedvtP+Phdg+r++++rr
  gi|298674772|ref|YP_003726522.1|  84 rsPGPGAQAAIRAFARAGIRIGRIEDVTPVPHDGTRPEGGRR 125
                                       ***************************************998 PP

>> Pilus_CpaD  Pilus biogenesis CpaD protein (pilus_cpaD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.2   3.5e-08   0.00021      68     122 ..      30      84 ..      21     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.5e-08
                        Pilus_CpaD  68 yrregagaivisvpsgssneaaaaaaaaeiravlaaaGvpaseisvrayqaaape 122
                                         ++++g +v ++ +++s++ +a+++a++++++l+++Gv++ +i+vra  +++ +
  gi|298674772|ref|YP_003726522.1|  30 TLAKSSGGMVTKAARDESSPYTAMQMARQVADMLKDKGVQGVHIKVRAPGGNKHR 84 
                                       567788889999999999999*************************998777654 PP

>> CBM_25  Carbohydrate binding domain (family 25)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.76   4.6e+03      89      89 ..      24      24 ..       7      48 .. 0.55
   2 ?   11.7   0.0     4e-05      0.24      13      65 ..      64     116 ..      55     120 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.76
                            CBM_25 89 d 89
                                      d
  gi|298674772|ref|YP_003726522.1| 24 D 24
                                      2 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 4e-05
                            CBM_25  13 rkkGftsayihyrpaGGswtavpGvkmrdaeaGyakkdvdlGaassleaafnd 65 
                                       + kG +  +i+ r  GG     pG + ++a   +a+  + +G   +++    d
  gi|298674772|ref|YP_003726522.1|  64 KDKGVQGVHIKVRAPGGNKHRSPGPGAQAAIRAFARAGIRIGRIEDVTPVPHD 116
                                       6799999***********************************98887766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 799.49
//
Query:       gi|298674773|ref|YP_003726523.1|  [L=184]
Description: 30S ribosomal protein S4 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-13   48.7   0.0      1e-12   47.5   0.0    1.6  1  S4        S4 domain


Domain annotation for each model (and alignments):
>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   0.0   5.8e-17     1e-12       1      46 [.     108     153 ..     108     155 .. 0.95

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 5.8e-17
                                       EEHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTC CS
                                S4   1 rRLdkvlarlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgD 46 
                                       rRL++ +++lgla +  +Arq+I hG++ VNG++v+ ps +++  +
  gi|298674773|ref|YP_003726523.1| 108 RRLQTQVHKLGLARTLLQARQFITHGHIAVNGRKVTVPSKMITKDE 153
                                       8***************************************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       835  (0.0465726); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1429.93
//
Query:       gi|298674774|ref|YP_003726524.1|  [L=149]
Description: 30S ribosomal protein S13 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.6e-42  143.2   0.1    6.4e-42  143.0   0.1    1.0  1  Ribosomal_S13  Ribosomal protein S13/S18
      0.006   15.4   0.0     0.0063   15.3   0.0    1.1  1  FbpA           Fibronectin-binding protein A N-terminus (FbpA
  ------ inclusion threshold ------
      0.081   13.2   0.0       0.16   12.3   0.0    1.4  1  HHH_6          Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.0   0.1   1.1e-45   6.4e-42       1     127 [.      11     137 ..      11     138 .. 0.96

  Alignments for each domain:
  == domain 1  score: 143.0 bits;  conditional E-value: 1.1e-45
                     Ribosomal_S13   1 RilgtdidgkkkveialtaikGiGrrkakiilkkadvdedkrigelteeeiekieeivenkaqykipnwi.nrqkdi 76 
                                       R+++td++g++ v++alt ikGiGrr+a+i+++  ++d d++ig l++eei++++ +++n+ + + p+w+ nrq+d 
  gi|298674774|ref|YP_003726524.1|  11 RVMNTDLPGDQPVRLALTGIKGIGRRTANIVVEGSGIDPDTKIGYLSDEEIDTLNSTINNFES-HLPSWMlNRQNDP 86 
                                       9***********************************************************555.5555555****** PP

                     Ribosomal_S13  77 kdGkdshvvendlrrklredieRlkkirsyrGlRHkrGlkvRGQrTkttgR 127
                                        +G+++h++ +d+ ++lred++ lkk r+yrG+RH+rGlkvRGQrTk+tgR
  gi|298674774|ref|YP_003726524.1|  87 YSGENKHLLGQDIFMSLREDVNTLKKTRAYRGVRHERGLKVRGQRTKSTGR 137
                                       **************************************************9 PP

>> FbpA  Fibronectin-binding protein A N-terminus (FbpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0     1e-06    0.0063     184     243 ..      15      76 ..       2     113 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1e-06
                                       H..S.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH...............HHHHHHHHTXXX CS
                              FbpA 184 k..kekdlvkaLvkafqGlspllaeelleragldketsakelseedlerlyealqelleele 243
                                       +  + ++ v+  ++ ++G+++ +a+ ++e  g+d++t++  ls+e++++l+++++++ ++l 
  gi|298674774|ref|YP_003726524.1|  15 TdlPGDQPVRLALTGIKGIGRRTANIVVEGSGIDPDTKIGYLSDEEIDTLNSTINNFESHLP 76 
                                       356778888999999***************************************99988775 PP

>> HHH_6  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.6e-05      0.16      23      45 ..      20      43 ..       6      48 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.6e-05
                             HHH_6 23 ga.irlGLaaikglgeaaaeriva 45
                                      ++ +rl+L+ ikg+g+++a+ +v+
  gi|298674774|ref|YP_003726524.1| 20 DQpVRLALTGIKGIGRRTANIVVE 43
                                      345****************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 1016.32
//
Query:       gi|298674775|ref|YP_003726525.1|  [L=340]
Description: rRNA pseudouridine synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.1e-26   90.6   0.0    9.6e-26   89.7   0.0    1.5  1  TruB_C_2      tRNA pseudouridylate synthase B C-terminal doma
    4.4e-24   85.5   0.1    1.8e-20   73.8   0.1    3.5  2  TruB_N        TruB family pseudouridylate synthase (N termina
    7.7e-17   61.1   0.5    1.9e-16   59.9   0.5    1.6  1  DKCLD         DKCLD (NUC011) domain
    6.7e-15   54.8   0.8    1.3e-14   53.9   0.1    1.9  2  PUA           PUA domain
  ------ inclusion threshold ------
       0.11   12.4   0.0       0.42   10.5   0.0    2.1  2  RRM_occluded  Occluded RNA-recognition motif


Domain annotation for each model (and alignments):
>> TruB_C_2  tRNA pseudouridylate synthase B C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.7   0.0   2.7e-29   9.6e-26       1      63 [.     183     248 ..     183     249 .. 0.95

  Alignments for each domain:
  == domain 1  score: 89.7 bits;  conditional E-value: 2.7e-29
                                       HHHHHHHHHHTTS-EEEEEEEEEEETTEGG-..B-HHHHHHHHHHHHT..--H.HHHHEEEGGGGG CS
                          TruB_C_2   1 RtLcdDiGeaLgcgAhveeLRRtrvgpfdeedmvtledLedavllyke..dee.LdrlllPlesal 63 
                                       R+Lc+DiGea+gcgAh++eL+Rt++gpf e++m tl+dL+da+ ++ke   e+ L+++++P+e al
  gi|298674775|ref|YP_003726525.1| 183 RKLCTDIGEAIGCGAHMQELKRTKTGPFCEDNMTTLHDLKDAYVFWKEygTESeLRKFVQPVELAL 248
                                       9***********************************************985557*********997 PP

>> TruB_N  TruB family pseudouridylate synthase (N terminal domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.8   0.1     5e-24   1.8e-20       1     148 [.      69     181 ..      69     182 .. 0.94
   2 ?   -2.3   0.0       1.4     5e+03      97     148 ..     280     331 ..     260     331 .. 0.70

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 5e-24
                                       HHHTT-S-EEESS---TT-EEEEEEEEGGGGGGHHHCTTS-EEEEEEEEETEEETTSBTTS-EEE-.--TT--HHHH CS
                            TruB_N   1 krllkakkvGhtGtLDplatGvLvvavgeaTklleylleadKeYeatirlgaetdteDaegeileeekveklteekl 77 
                                       k +l+++k+Gh+G+LDp++tGvL++++ +aTk++ +l  ++KeY++ ++l+ + +  D                 ++
  gi|298674775|ref|YP_003726525.1|  69 KDILNINKAGHSGSLDPKVTGVLPIMLQKATKAIGSLRLSNKEYVCLMQLHDTVTA-D-----------------EI 127
                                       7899**********************************************865443.3.................47 PP

                                       HHHHHHC-EEE---------------------------------EEEEEEEEEEEEEEEEEEEEEESTTTT CS
                            TruB_N  78 eevlkkftGeieqvppmySAvkvnGkrlyelaregeeverkkrkvtiyelelleveepevelevecskGtY 148
                                        +v+k+f+G i q pp+ SAvk                 rk r  ti+ l++le++ ++v l+v c++GtY
  gi|298674775|ref|YP_003726525.1| 128 IRVCKEFEGPIFQKPPIKSAVK-----------------RKLRIRTIDYLNILEIKGSSVLLKVGCEAGTY 181
                                       899*******************.................999***************************** PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.4
                                       -------------------------EEEEEEEEEEEEEEEEEEEEEESTTTT CS
                            TruB_N  97 AvkvnGkrlyelaregeeverkkrkvtiyelelleveepevelevecskGtY 148
                                       A   nG+ +  ++++ge v + k ++  +e+  +e     ++ +v +++GtY
  gi|298674775|ref|YP_003726525.1| 280 ANIFNGNTVCLFTQKGEIVALCKASMDADEILETENGLAAITENVIMNAGTY 331
                                       4456777788888888888877777777776666666667777888888887 PP

>> DKCLD  DKCLD (NUC011) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9   0.5   5.2e-20   1.9e-16      17      57 ..      24      64 ..      13      65 .. 0.92

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 5.2e-20
                                      SS-----TTSS--GGG--HHHHHHTEEEEEEE-SSS-HHHH CS
                             DKCLD 17 rtehytplpaGssPlkRpieeyikyGvinLDKPsnPsSHEV 57
                                      + + +t+ ++G+ P +Rpi ++i++Gv+nLDKP++P+SHE+
  gi|298674775|ref|YP_003726525.1| 24 KFKPFTNPNYGCPPENRPIYDHINMGVVNLDKPKGPTSHEI 64
                                      55679***********************************8 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.0       4.5   1.6e+04      42      50 ..     188     196 ..     185     198 .. 0.76
   2 !   53.9   0.1   3.7e-18   1.3e-14       1      72 [.     252     323 ..     252     325 .. 0.94

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 4.5
                                       TTSCEEEEE CS
                               PUA  42 edgelvavG 50 
                                         ge++++G
  gi|298674775|ref|YP_003726525.1| 188 DIGEAIGCG 196
                                       449999999 PP

  == domain 2  score: 53.9 bits;  conditional E-value: 3.7e-18
                                       CEEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEE CS
                               PUA   1 grvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveier 72 
                                       + +v+ d+Av+a+++gasL +pG+v+ + ++  g +V +++++ge+va+ +a ++++e+ + + g ++ +e+
  gi|298674775|ref|YP_003726525.1| 252 PSIVIRDSAVDAICRGASLAIPGIVSLNANIFNGNTVCLFTQKGEIVALCKASMDADEILETENGLAAITEN 323
                                       579***********************************************************9998876665 PP

>> RRM_occluded  Occluded RNA-recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00012      0.42       3      29 ..     112     138 ..     110     146 .. 0.90
   2 ?   -2.5   0.0       1.3   4.7e+03      17      43 ..     236     265 ..     233     288 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00012
                      RRM_occluded   3 tisllplsDtvnkariralveekegei 29 
                                        ++l++l Dtv+ ++i ++++e eg+i
  gi|298674775|ref|YP_003726525.1| 112 YVCLMQLHDTVTADEIIRVCKEFEGPI 138
                                       689*******************98876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.3
                      RRM_occluded  17 riralveek...egeikkivLvpdheGAiv 43 
                                       ++r++v++      ++  iv++ +   Ai 
  gi|298674775|ref|YP_003726525.1| 236 ELRKFVQPVelaLTHLPSIVIRDSAVDAIC 265
                                       566666665332244444454444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2522.83
//
Query:       gi|298674776|ref|YP_003726526.1|  [L=178]
Description: cytidylate kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.8e-26   91.0   0.0    3.8e-24   85.8   0.0    2.0  1  Cytidylate_kin2  Cytidylate kinase-like family
    4.3e-13   49.9   0.0    5.7e-13   49.5   0.0    1.2  1  AAA_18           AAA domain
    1.8e-11   44.6   0.0    3.1e-11   43.9   0.0    1.5  1  AAA_17           AAA domain
    7.2e-11   42.2   0.1    2.4e-06   27.4   0.0    2.1  2  Cytidylate_kin   Cytidylate kinase
    0.00011   22.3   0.0    0.00048   20.3   0.0    2.0  1  ADK              Adenylate kinase
    0.00081   19.6   0.0     0.0086   16.2   0.0    2.0  1  AAA_33           AAA domain
      0.001   18.8   0.0       0.43   10.2   0.0    2.1  2  CoaE             Dephospho-CoA kinase
     0.0011   19.2   0.0      0.002   18.4   0.0    1.4  1  AAA_28           AAA domain
     0.0042   17.5   0.0     0.0061   17.0   0.0    1.3  1  Sulfotransfer_3  Sulfotransferase family
  ------ inclusion threshold ------
      0.012   15.8   0.1      0.022   14.9   0.1    1.4  1  SKI              Shikimate kinase
       0.08   12.8   0.1       0.65    9.8   0.0    2.1  2  dNK              Deoxynucleoside kinase


Domain annotation for each model (and alignments):
>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.8   0.0   2.3e-27   3.8e-24       3     179 .]       4     157 ..       2     157 .. 0.94

  Alignments for each domain:
  == domain 1  score: 85.8 bits;  conditional E-value: 2.3e-27
                   Cytidylate_kin2   3 TIsreyGsgGetigeaLAekLglpfydr.eiieevakelglseeeveevdersrlssflskllaarvagdtldekld 78 
                                       TIs+  Gsg +t+   L++++++++++  e+++++a+e g++ ee+ ++ e++                     ++d
  gi|298674776|ref|YP_003726526.1|   4 TISGLPGSGTTTVSNLLSKHYNVDLISAgEVFRKLADEYGMTLEEFGNFAESE--------------------PSID 60 
                                       9**************************************************44....................4678 PP

                   Cytidylate_kin2  79 delfeaqervirelaaeesvVivGRgadliLkdrpnvlrvfltapledrvkrvaereglseeearekiketDkrrak 155
                                        e+ ++q+++  e    +++++ GR a ++ +  +nvl+++l apl++rv+r+ ereg s +e+ e  k+++  + +
  gi|298674776|ref|YP_003726526.1|  61 LEIDRRQQEIASEK---NNCILEGRLAGYMAET-DNVLKIWLKAPLDVRVERLIEREGGSFDEVFESTKKRETSENA 133
                                       88888899888887...4**********99988.88***************************************** PP

                   Cytidylate_kin2 156 yykkytgqdwgdaenYdlvlntsk 179
                                       +y  ++g d++d++ Ydlv++ts+
  gi|298674776|ref|YP_003726526.1| 134 RYWDIHGIDLTDMSIYDLVIDTSR 157
                                       **********************95 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   0.0   3.5e-16   5.7e-13       3     117 ..       5     116 ..       3     136 .. 0.86

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 3.5e-16
                            AAA_18   3 ltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleeg 74 
                                       ++G pG+G tt+++ Lsk+ ++     g++ r++a e g+ le++ +    + +  +d   ++ +  +e++s   e 
  gi|298674776|ref|YP_003726526.1|   5 ISGLPGSGTTTVSNLLSKHYNVdlisaGEVFRKLADEYGMTLEEFGN--FAESEPSIDL--EIDRRQQEIAS---EK 74 
                                       89*****************877*************************..5555555555..67777777765...77 PP

                            AAA_18  75 knlvidghlaeleseaakdikkvvLtaspeelleRlekRgyee 117
                                       +n++++g+la +  e +  +k ++L+a+ +++ eRl +R+  +
  gi|298674776|ref|YP_003726526.1|  75 NNCILEGRLAGYMAETDNVLK-IWLKAPLDVRVERLIEREGGS 116
                                       899************999999.*****************9665 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   1.9e-14   3.1e-11       2     123 ..       7     113 ..       6     133 .. 0.79

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 1.9e-14
                                       E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTS.HSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEE CS
                            AAA_17   2 GgPGsGKgtqceklvekygfthlsaGdllreeakrggl.akardemrklpleekkelqkeaaekiaeeakkkgvlvd 77 
                                       G+PGsG +t+++ l ++y++  +saG+++r+ a + g+  ++++++++ + +++ e++++ + +ia e  k++ +++
  gi|298674776|ref|YP_003726526.1|   7 GLPGSGTTTVSNLLSKHYNVDLISAGEVFRKLADEYGMtLEEFGNFAESEPSIDLEIDRRQQ-EIASE--KNNCILE 80 
                                       9***********************************98788899999999999999998886.57765..7899**9 PP

                                       E-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHT CS
                            AAA_17  78 ghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdr 123
                                       g        g+     +e+ + l     i l+a+ ++ +er+++++
  gi|298674776|ref|YP_003726526.1|  81 GRLA-----GY----MAETDNVL----KIWLKAPLDVRVERLIERE 113
                                       9974.....33....33333333....5556666666666666654 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   3.5e-05     0.058       2      37 ..       4      39 ..       3      44 .. 0.94
   2 !   27.4   0.0   1.5e-09   2.4e-06      94     180 ..      55     137 ..      45     170 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.5e-05
                                      EEE-STTSSHHHHHHHHHHHHT-EEEEHHHHHHHHH CS
                    Cytidylate_kin  2 aiDGPagsGKssvaralaeklglkyldtgalYRala 37
                                      +i G  gsG  +v+ +l+++ ++ ++++g+++R la
  gi|298674776|ref|YP_003726526.1|  4 TISGLPGSGTTTVSNLLSKHYNVDLISAGEVFRKLA 39
                                      788999***************************987 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 1.5e-09
                                       TSHHHHHHHHHHHHTT-B.SSBEEEEESSIIIIISTT-SEEEEEE--HHHHHHHHHHHHHHTT----HHHHHHHHHH CS
                    Cytidylate_kin  94 aipavRailvkklrelvk.karvvveGRDigtvvfpdaelKifldAsveeRakRRlkqlkakgtsvsleellaeike 169
                                       + p++  ++ ++++e+++ k+++++eGR  g +   d  lKi+l+A  ++R++R ++    +g   s++e+ ++ k+
  gi|298674776|ref|YP_003726526.1|  55 SEPSIDLEIDRRQQEIASeKNNCILEGRLAGYMAETDNVLKIWLKAPLDVRVERLIER---EG--GSFDEVFESTKK 126
                                       56788889999****998799*********************************9988...33..4699******** PP

                                       HHHHHHCTSSS CS
                    Cytidylate_kin 170 RDklDkerevg 180
                                       R +  ++r  +
  gi|298674776|ref|YP_003726526.1| 127 RETSENARYWD 137
                                       **999999643 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   2.9e-07   0.00048       1      36 [.       5      40 ..       5     136 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.9e-07
                                      EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK  1 llGaPgaGKGtqaeklvkkyglahlstGdllRaevk 36
                                      + G Pg+G  t+++ l k+y++  +s+G+++R+   
  gi|298674776|ref|YP_003726526.1|  5 ISGLPGSGTTTVSNLLSKHYNVDLISAGEVFRKLAD 40
                                      579*****************************8654 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   5.3e-06    0.0086       2     118 ..       3     112 ..       2     135 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.3e-06
                            AAA_33   2 vllvGlpGsGKstlaerllkklgavllssdtlrrrlfgtdqqskt...dytrvldrlyqilnelarkalsagrnvil 75 
                                       + + GlpGsG +t++  l k+  + l+s  +++r+l+ +   +++   + ++ ++++   + ++ ++ +s+++n+il
  gi|298674776|ref|YP_003726526.1|   3 LTISGLPGSGTTTVSNLLSKHYNVDLISAGEVFRKLADEYGMTLEefgNFAESEPSIDLEIDRRQQEIASEKNNCIL 79 
                                       5678******9999999999999***************8888888333444455558889999999**********9 PP

                            AAA_33  76 datnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakR 118
                                          ++    +a+ +++++        ++++++ ++  eRl +R
  gi|298674776|ref|YP_003726526.1|  80 EGRLAG--YMAETDNVLK--------IWLKAPLDVRVERLIER 112
                                       865443..3333333333........55555555555555555 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   0.00026      0.43       2      47 ..       2      48 ..       1      66 [. 0.86
   2 !    6.9   0.0    0.0029       4.6     122     156 ..      90     126 ..      56     137 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00026
                                      EEEEEESTTSSHHHHHHHHHH.TT-EEEEHHHHHHHTTCCTHHHHHH CS
                              CoaE  2 ivgltGgiasGKstvanlfad.lgvpivDaDlvArqvvepgsealkk 47
                                      ++ ++G  +sG +tv+nl+++ ++v+++ a  v r++  +   +l++
  gi|298674776|ref|YP_003726526.1|  2 LLTISGLPGSGTTTVSNLLSKhYNVDLISAGEVFRKLADEYGMTLEE 48
                                      56789999************99*********9999998877777665 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0029
                                       SSEEEEE..E--HHHHHHHHHHCCTSTHHHHHHHHHH CS
                              CoaE 122 iervlvv..dvelelqveRlvardgvseeevkaiiaa 156
                                       +++vl +  +++l+ +veRl++r+g s +ev +  + 
  gi|298674776|ref|YP_003726526.1|  90 TDNVLKIwlKAPLDVRVERLIEREGGSFDEVFESTKK 126
                                       55565551157899***********999998766554 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.2e-06     0.002       4      69 ..       5      75 ..       2      84 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.2e-06
                            AAA_28  4 itGgestGKTtlleaLaar.gypvv..pEaareileekl...akgedalpwvedllafaervleeqleeeaa 69
                                      i+G +++G+Tt+++ L+++ ++  +   E++r++ +e +   ++ ++ +++ e  +++++ + +++++ e++
  gi|298674776|ref|YP_003726526.1|  5 ISGLPGSGTTTVSNLLSKHyNVDLIsaGEVFRKLADEYGmtlEEFGNFAES-EPSIDLEIDRRQQEIASEKN 75
                                      89****************998887778********9998554444444444.68899999888888776654 PP

>> Sulfotransfer_3  Sulfotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   3.7e-06    0.0061       4      48 ..       5      52 ..       3     105 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.7e-06
                                      EE--TTSSHHHHHHHHHTSTT...EE--S--..--TT.-SBHHHHHHHH CS
                   Sulfotransfer_3  4 ivGlpRSGTTlLhrlLaahpd...vripeet.lfvaprllalleawskd 48
                                      i Glp SGTT +++lL++h     + +++e   ++a+++   le+++ +
  gi|298674776|ref|YP_003726526.1|  5 ISGLPGSGTTTVSNLLSKHYNvdlI-SAGEVfRKLADEYGMTLEEFGNF 52
                                      88****************9996633.44444034455555545544443 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   1.4e-05     0.022       1     107 [.       9     114 ..       9     141 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.4e-05
                                       TTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHTS-HHHHHHHHHHHHHHHHHHHHHHHHCCCSSEEEEE-TTGGGSHH CS
                               SKI   1 mGaGKstvGkllAkklglefiDlDeliekrtgksiaeifeeegeegFrelEsevlkelleeeglViatGGGavlsee 77 
                                       +G+G +tv +ll+k++++++i + e++ k +  +    +ee    +F e E  +  e+ ++++ + +    ++l+ +
  gi|298674776|ref|YP_003726526.1|   9 PGSGTTTVSNLLSKHYNVDLISAGEVFRKLAD-EYGMTLEEF--GNFAESEPSIDLEIDRRQQEIASEKNNCILEGR 82 
                                       69***********************9988776.666666655..458888888888888888888888888888888 PP

                                       HHHHHH..HHSEEEEEE--HHHHHHHHHHTTS CS
                               SKI  78 nrellk..ekgiviyLdvsleellerlkadke 107
                                          +++  ++ + i+L+++l++ +erl +++ 
  gi|298674776|ref|YP_003726526.1|  83 LAGYMAetDNVLKIWLKAPLDVRVERLIEREG 114
                                       88888844444459************987776 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0    0.0004      0.65       1      28 [.       3      30 ..       3      52 .. 0.84
   2 ?    0.4   0.0      0.31   5.1e+02     120     144 ..      90     113 ..      65     123 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0004
                                      EEEEESTTSSHHHHHHHHHCCSTCEEEE CS
                               dNK  1 ivveGnIgaGKstlvklLskklgvkvfe 28
                                      ++++G  g+G +t+ +lLsk+++v  ++
  gi|298674776|ref|YP_003726526.1|  3 LTISGLPGSGTTTVSNLLSKHYNVDLIS 30
                                      589*******************987654 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.31
                                       CCH-SEEEEEE--HHHHHHHHHHCT CS
                               dNK 120 lakpdlliYLkasletclerikkRg 144
                                        +   l i+Lka+l++ +er+ +R+
  gi|298674776|ref|YP_003726526.1|  90 TD-NVLKIWLKAPLDVRVERLIERE 113
                                       44.4466999999999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1277.56
//
Query:       gi|298674777|ref|YP_003726527.1|  [L=208]
Description: hypothetical protein Metev_0833 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      2e-49  167.6  10.0      3e-49  167.0  10.0    1.2  1  EMC3_TMCO1  Integral membrane protein EMC3/TMCO1-like
  ------ inclusion threshold ------
      0.035   14.0   0.3      0.062   13.1   0.0    1.5  2  HPIH        N-terminal domain with HPIH motif


Domain annotation for each model (and alignments):
>> EMC3_TMCO1  Integral membrane protein EMC3/TMCO1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.0  10.0   3.3e-53     3e-49       2     169 ..      44     206 ..      43     207 .. 0.97

  Alignments for each domain:
  == domain 1  score: 167.0 bits;  conditional E-value: 3.3e-53
                        EMC3_TMCO1   2 lvldplirdwvllPivivillvgiltgllsellqkllidkkkmekeqkrekelqkrarelqkngdklklkklekrqe 78 
                                       ++++pl+    +  ++iv+++++++t+l+++l+qk++id++ m+k+q+r+k++qk++re+q ++++ k k+le+++ 
  gi|298674777|ref|YP_003726527.1|  44 ILMNPLVMLVGQENFHIVLFVMAAITALYASLIQKYTIDWELMRKTQERMKAFQKEFREAQLSQNNYKIKQLEEQRS 120
                                       6788999999999**************************************************************** PP

                        EMC3_TMCO1  79 elmedqsemmmdqmkpmivtmipqiliffwlnsffsgfvvaklpfpltgrfksllqrglesldvrfvssiswYflcs 155
                                       e+m+dq+em+++q+kpm+++ i+++++f+w ++++sg++ a ++fp++g+++ l     ++  ++++ +i wYf++s
  gi|298674777|ref|YP_003726527.1| 121 EMMGDQMEMSKQQFKPMAYISIISLPLFMWAYYYISGHTGASMVFPFIGEME-LV----STIIGPIQFWILWYFITS 192
                                       ****************************************************.44....6***************** PP

                        EMC3_TMCO1 156 fglsqiirklLgea 169
                                       +++sq+irk+L+++
  gi|298674777|ref|YP_003726527.1| 193 LAISQLIRKALNIG 206
                                       ***********986 PP

>> HPIH  N-terminal domain with HPIH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.9e-06     0.062      19      54 ..      59      94 ..      56     132 .. 0.82
   2 ?   -3.2   0.1      0.72   6.5e+03      30      44 ..     137     151 ..     134     154 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.9e-06
                              HPIH 19 htIvvvallasttYlsvleeslfdwkldsksissag 54
                                      h++++v+   ++ Y s+++++  dw+l +k++   +
  gi|298674777|ref|YP_003726527.1| 59 HIVLFVMAAITALYASLIQKYTIDWELMRKTQERMK 94
                                      999999999999***************998876543 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.72
                              HPIH  30 ttYlsvleeslfdwk 44 
                                       ++Y+s++   lf w 
  gi|298674777|ref|YP_003726527.1| 137 MAYISIISLPLFMWA 151
                                       689999999888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2114  (0.11791); expected 358.6 (0.02)
Passed bias filter:                      882  (0.049194); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1559.03
//
Query:       gi|298674778|ref|YP_003726528.1|  [L=215]
Description: adenylate kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-60  201.7   0.0    7.2e-60  201.5   0.0    1.0  1  ADK              Adenylate kinase
    1.3e-29  103.3   0.0    5.5e-29  101.3   0.0    1.8  2  AAA_17           AAA domain
    2.3e-17   62.7   3.3    4.3e-17   61.8   2.5    2.0  3  ADK_lid          Adenylate kinase, active site lid
    1.5e-06   28.8   0.0    3.3e-06   27.7   0.0    1.5  1  AAA_18           AAA domain
    2.1e-06   28.2   0.0      0.096   13.0   0.1    2.4  2  Hydin_ADK        Hydin Adenylate kinase-like domain
    6.2e-05   23.2   0.0     0.0003   21.0   0.0    1.8  2  AAA_33           AAA domain
      0.003   17.2   2.4       0.22   11.2   0.3    2.3  2  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
     0.0092   16.2   0.0       0.02   15.1   0.0    1.6  2  AAA_28           AAA domain
  ------ inclusion threshold ------
      0.011   15.4   0.2       0.22   11.2   0.1    2.5  2  Thymidylate_kin  Thymidylate kinase
      0.018   14.7   0.0       0.03   14.1   0.0    1.5  1  AAA_24           AAA domain
       0.02   14.8   0.0      0.039   13.9   0.0    1.4  1  DUF5402          Family of unknown function (DUF5402)
      0.043   13.5   0.0      0.065   13.0   0.0    1.3  1  Cytidylate_kin   Cytidylate kinase
      0.048   13.0   0.0        0.2   11.0   0.0    1.9  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.067   13.5   0.0       0.18   12.1   0.0    2.0  2  AAA_22           AAA domain
       0.12   12.7   0.9        4.6    7.6   0.1    2.3  2  Prim_Zn_Ribbon   Zinc-binding domain of primase-helicase
       0.15   12.0   2.7          4    7.5   0.1    2.3  2  Prok-RING_1      Prokaryotic RING finger family 1
       0.19   11.9   0.0       0.67   10.1   0.0    1.8  2  PknG_rubred      Protein kinase G rubredoxin domain
       0.32   11.6   3.3        3.9    8.1   0.4    2.5  2  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
       0.41   10.5   2.3        5.7    6.8   0.1    2.7  3  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger


Domain annotation for each model (and alignments):
>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.5   0.0   7.6e-63   7.2e-60       1     150 [.       5     190 ..       5     191 .. 0.99

  Alignments for each domain:
  == domain 1  score: 201.5 bits;  conditional E-value: 7.6e-63
                                       EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHCT-HHHHHHHHHHHTTSS--HHHHHHHHHHHHHCHGTTTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK   1 llGaPgaGKGtqaeklvkkyglahlstGdllRaevksgtelGkeakevmdkgelvpdevvvklvkeelekedkkkgf 77 
                                       l G+PgaGKGtqa++l + y+++h+stGd+lR++vk++telG +ake+mdkgelvpdev+++++k++l ++d+++g+
  gi|298674778|ref|YP_003726528.1|   5 LFGPPGAGKGTQAKELSEFYTIPHISTGDILRENVKNETELGSKAKEYMDKGELVPDEVLIGIIKNRLVEPDCENGY 81 
                                       68*************************************************************************** PP

                                       EEESB-SSHHHHHHHHHHHHHHTSEESEEEEEE--HHHHHHHHHT................................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................ RF
                               ADK  78 llDGfPRtveqaealeelleeekvkldlvleldvpeevlveRltg................................ 122
                                       +lDG+PRtv+qa+ale++l++ ++ l++vl+++vpee l++Rl+g                                
  gi|298674778|ref|YP_003726528.1|  82 ILDGYPRTVNQADALEDILNKLEKPLEVVLNIEVPEEELITRLSGrricsncganyhlkfsppekdgicdvcggkly 158
                                       ***************************************************************************** PP

                                       ....GSHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                                       ....xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK 123 ....DneetvkkRletykkqtkplidyykkkg 150
                                           D+ee +k+Rl+ty++qt+plidyyk+k+
  gi|298674778|ref|YP_003726528.1| 159 qrddDKEEVIKQRLDTYNNQTAPLIDYYKRKD 190
                                       *****************************986 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.3   0.0   5.9e-32   5.5e-29       1     123 [.       6     128 ..       6     132 .. 0.95
   2 ?   -0.7   0.0       1.8   1.7e+03     127     136 .]     160     169 ..     154     179 .. 0.69

  Alignments for each domain:
  == domain 1  score: 101.3 bits;  conditional E-value: 5.9e-32
                                       EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTT.TS.HSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEE CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrg.gl.akardemrklpleekkelqkeaaekiaeeakkkgvl 75 
                                       +G+PG+GKgtq+++l e y ++h+s+Gd+lre++k++ +l +ka+++m+k++l++++ l  ++++++ e ++++g++
  gi|298674778|ref|YP_003726528.1|   6 FGPPGAGKGTQAKELSEFYTIPHISTGDILRENVKNEtELgSKAKEYMDKGELVPDEVLIGIIKNRLVEPDCENGYI 82 
                                       6*********************************999666799********************************** PP

                                       EEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHT CS
                            AAA_17  76 vdghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdr 123
                                       +dg+pr+ +qa++l+++  + ++ l  ++++ +e+++ee++ r+  +r
  gi|298674778|ref|YP_003726528.1|  83 LDGYPRTVNQADALEDILNKLEKPL--EVVLNIEVPEEELITRLSGRR 128
                                       ******************9999888..99999***********98775 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.8
                                       -TS-SHHHHH CS
                            AAA_17 127 rdddneesik 136
                                       rddd ee+ik
  gi|298674778|ref|YP_003726528.1| 160 RDDDKEEVIK 169
                                       5556655554 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       8.8   8.3e+03       1      11 [.      71      81 ..      71      84 .. 0.82
   2 ?   -3.3   0.0       9.9   9.4e+03      28      34 ..     117     123 ..     115     123 .. 0.81
   3 !   61.8   2.5   4.5e-20   4.3e-17       1      36 []     127     162 ..     127     162 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 8.8
                                      EEE-TTT--EE CS
                           ADK_lid  1 RrvCpkCGrsY 11
                                      R+v p+C   Y
  gi|298674778|ref|YP_003726528.1| 71 RLVEPDCENGY 81
                                      78889998877 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 9.9
                                       --.-B-- CS
                           ADK_lid  28 GepLvqR 34 
                                        e+L++R
  gi|298674778|ref|YP_003726528.1| 117 EEELITR 123
                                       689**99 PP

  == domain 3  score: 61.8 bits;  conditional E-value: 4.5e-20
                                       EEE-TTT--EEETTTB--SSTTB-TTT--.-B--GG CS
                           ADK_lid   1 RrvCpkCGrsYhvvfnpPkveglCDkCGepLvqRsD 36 
                                       Rr+C++CG+ Yh++f pP ++g+CD+CG++L+qR+D
  gi|298674778|ref|YP_003726528.1| 127 RRICSNCGANYHLKFSPPEKDGICDVCGGKLYQRDD 162
                                       9**********************************9 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   3.5e-09   3.3e-06       1     114 [.       3     128 ..       3     133 .. 0.72

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 3.5e-09
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpe.aldeskrldedkldklldaleenssal 71 
                                       I+l G+pG+GK t akeLs+   +     g++lr+++k++  l +  +e + + +++ de     + + l e +   
  gi|298674778|ref|YP_003726528.1|   3 IVLFGPPGAGKGTQAKELSEFYTIphistGDILRENVKNETELGSKAKEyMDKGELVPDEVLIGIIKNRLVEPD--- 76 
                                       89****************99634498899999999999988888888884444444444444455555555532... PP

                            AAA_18  72 eegknlvidghlaeleseaakdikk..........vvLtaspeelleRlekRg 114
                                         ++ +++dg +    +++a +               +++++eel+ Rl+ R+
  gi|298674778|ref|YP_003726528.1|  77 -CENGYILDGYPRTVNQADALEDILnklekplevvLNIEVPEEELITRLSGRR 128
                                       .244457777777777666555444567777775577899**********996 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   0.00011       0.1       2      51 ..       3      51 ..       2      56 .. 0.90
   2 !   13.0   0.1    0.0001     0.096     170     197 ..      58      85 ..      54      86 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                         Hydin_ADK  2 iivhGaPlsGKtatavtLakkYeaAlltiDsvvleAisdgnssaGlrAre 51
                                      i++ G+P +GK + a  L+  Y +  ++  +++ e + ++ ++ G +A+e
  gi|298674778|ref|YP_003726528.1|  3 IVLFGPPGAGKGTQAKELSEFYTIPHISTGDILRENVKNE-TELGSKAKE 51
                                      8999*******************************99875.677888887 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.0001
                         Hydin_ADK 170 vLPedllveIlsERlqlndCyrGvvfDg 197
                                       + P+++l+ I+  Rl   dC  G ++Dg
  gi|298674778|ref|YP_003726528.1|  58 LVPDEVLIGIIKNRLVEPDCENGYILDG 85 
                                       57*************************9 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   3.2e-07    0.0003       2     119 ..       3     128 ..       3     138 .. 0.75
   2 ?   -0.3   0.0       1.2   1.1e+03      37      78 ..     157     198 ..     151     214 .. 0.65

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.2e-07
                            AAA_33   2 vllvGlpGsGKstlaerllkklgavllss.dtlrrrlfg..tdqqsktdytrvldr.....lyqilnelarkalsag 70 
                                       ++l G+pG+GK t a++l +  +  ++s+ d+lr+++++  +   + ++y +  +      l++i+++++      +
  gi|298674778|ref|YP_003726528.1|   3 IVLFGPPGAGKGTQAKELSEFYTIPHISTgDILRENVKNetELGSKAKEYMDKGELvpdevLIGIIKNRLV-EPDCE 78 
                                       6789***************9999999998355555888775333344444443333211245555555553.34666 PP

                            AAA_33  71 rnvildatnlsrrerarflklarrlgvpvri.vvvetdeetlkeRlakRa 119
                                       +++ild   ++ ++ +++  ++++l+ p ++ + +e++ee+l  Rl  R 
  gi|298674778|ref|YP_003726528.1|  79 NGYILDGYPRTVNQADALEDILNKLEKPLEVvLNIEVPEEELITRLSGRR 128
                                       99*********************999998772569***********9996 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.2
                            AAA_33  37 lfgtdqqsktdytrvldrlyqilnelarkalsagrnvildat 78 
                                       l+ +d+++++  ++ ld  +++++ l++ + ++ + v +d t
  gi|298674778|ref|YP_003726528.1| 157 LYQRDDDKEEVIKQRLDTYNNQTAPLIDYYKRKDILVNIDGT 198
                                       455555555555566677777777777777777777777777 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.013        12      20      29 ..     126     135 ..     124     137 .. 0.85
   2 !   11.2   0.3   0.00024      0.22       3      18 ..     146     162 ..     144     163 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.013
                           zf-RRN7  20 GfyyCrrCht 29 
                                       G+++C +C+ 
  gi|298674778|ref|YP_003726528.1| 126 GRRICSNCGA 135
                                       9999999995 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00024
                           zf-RRN7   3 kgppCgvCgcrsftl.d 18 
                                       k  +C+vCg+++++  d
  gi|298674778|ref|YP_003726528.1| 146 KDGICDVCGGKLYQRdD 162
                                       6679**********955 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.1e-05      0.02       1      47 [.       2      51 ..       2      84 .. 0.85
   2 ?   -2.5   0.0       5.6   5.2e+03     131     161 ..     172     202 ..     155     203 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.1e-05
                            AAA_28  1 kivitGgestGKTtlleaLaar.gypvv..pEaareileeklakgedalp 47
                                      +iv++G++++GK t +++L++   +p++   ++ re ++++++ g +a +
  gi|298674778|ref|YP_003726528.1|  2 NIVLFGPPGAGKGTQAKELSEFyTIPHIstGDILRENVKNETELGSKAKE 51
                                      69******************975899888899999999999988776544 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.6
                            AAA_28 131 leereaiderlrealrelgipviivpsgdve 161
                                       l+  ++ ++ l++ +++ +i v i+ +g+ve
  gi|298674778|ref|YP_003726528.1| 172 LDTYNNQTAPLIDYYKRKDILVNIDGTGNVE 202
                                       3334444455677777777777777777776 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00023      0.22       3      65 ..       7      71 ..       7     138 .. 0.89
   2 ?    1.7   0.0      0.19   1.8e+02     137     185 .]     159     208 ..     151     208 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                                      ESTTSSHHHHHHHHHHHHHHTTE....EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHHHHH CS
                   Thymidylate_kin  3 GlDGaGKttqaellkerlkeegik...vvltrepggteiGekirelllkeeeleeqteallfaadr 65
                                      G  GaGK tqa+ l e ++  +i+   +++   + +te+G+k++e++  + el +  +++ + ++r
  gi|298674778|ref|YP_003726528.1|  7 GPPGAGKGTQAKELSEFYTIPHIStgdILRENVKNETELGSKAKEYMD-KGELVPDEVLIGIIKNR 71
                                      5669**************999998866777777899**********98.77777777776666666 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.19
                                       TTSS.TTTSHHHHHHHHHHHHHHHHHHHHTTSTEEEEETTS-HHHHHHHH CS
                   Thymidylate_kin 137 krde.ldeeeeeqldflrkvrerylelakederiliidasksieevheeI 185
                                       +rd  ++e ++++ld++++ ++ + + +k ++ ++ id + ++e+v eeI
  gi|298674778|ref|YP_003726528.1| 159 QRDDdKEEVIKQRLDTYNNQTAPLIDYYKRKDILVNIDGTGNVEDVFEEI 208
                                       445435677888899999999999999*988888899*********9998 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.2e-05      0.03       4      30 ..       2      42 ..       1     105 [. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.2e-05
                            AAA_24  4 kiliyGpsgiGKTtlakelgpkplfi...............d 30
                                      +i+++Gp+g+GK t+akel  ++  i                
  gi|298674778|ref|YP_003726528.1|  2 NIVLFGPPGAGKGTQAKEL-SEFYTIphistgdilrenvknE 42
                                      79*****************.7776665555555555555554 PP

>> DUF5402  Family of unknown function (DUF5402)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.2e-05     0.039      62     111 ..      94     143 ..      89     150 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.2e-05
                           DUF5402  62 eklkelakdleikadvvyarvvPGtaevidlavrklcnrcrkefsgkkPr 111
                                       + l++++ +le   +vv    vP  + +  l+ r++c+ c  ++  k   
  gi|298674778|ref|YP_003726528.1|  94 DALEDILNKLEKPLEVVLNIEVPEEELITRLSGRRICSNCGANYHLKFSP 143
                                       789999999999999*****************************776544 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.9e-05     0.065       2      34 ..       4      36 ..       3      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.9e-05
                                      EEE-STTSSHHHHHHHHHHHHT-EEEEHHHHHH CS
                    Cytidylate_kin  2 aiDGPagsGKssvaralaeklglkyldtgalYR 34
                                       + GP g+GK++ a++l+e   +  ++tg + R
  gi|298674778|ref|YP_003726528.1|  4 VLFGPPGAGKGTQAKELSEFYTIPHISTGDILR 36
                                      567**************************9988 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00021       0.2      24      55 ..       2      35 ..       1      58 [. 0.76
   2 ?   -0.9   0.0      0.95   8.9e+02     159     196 ..      77     114 ..      74     121 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00021
                      Mg_chelatase 24 nlllvGppGsGKtmlakrlpsl..lpplseeeal 55
                                      n++l+GppG+GK   ak l++   +p++s+ ++l
  gi|298674778|ref|YP_003726528.1|  2 NIVLFGPPGAGKGTQAKELSEFytIPHISTGDIL 35
                                      899***************9875226666666665 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.95
                      Mg_chelatase 159 cpcgklkdkekectcsekeierYlsklsgplldRidlq 196
                                       c  g++ d   +++ ++++ e+ l+kl +pl   ++++
  gi|298674778|ref|YP_003726528.1|  77 CENGYILDGYPRTVNQADALEDILNKLEKPLEVVLNIE 114
                                       67777777777788888888888888888886555554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00019      0.18       8      30 ..       3      25 ..       1     128 [. 0.90
   2 ?   -2.7   0.0       7.2   6.8e+03      38      60 ..     186     208 ..     162     213 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                            AAA_22  8 lvvtGesGtGKTtllrrlleqld 30
                                      +v++G++G+GK t +++l e ++
  gi|298674778|ref|YP_003726528.1|  3 IVLFGPPGAGKGTQAKELSEFYT 25
                                      89****************99885 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.2
                            AAA_22  38 erpevvfvtlpsstsskdllrel 60 
                                        +++ ++v++ + ++ +d+++e+
  gi|298674778|ref|YP_003726528.1| 186 YKRKDILVNIDGTGNVEDVFEEI 208
                                       44444555555555556655555 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1       0.1        95      24      33 ..     126     134 ..     119     138 .. 0.80
   2 ?    7.6   0.1    0.0049       4.6       2      12 ..     146     156 ..     145     165 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.1
                                       S-EEETTTTB CS
                    Prim_Zn_Ribbon  24 GtwfCrqCgg 33 
                                       G  +C+ C g
  gi|298674778|ref|YP_003726528.1| 126 GRRICSNC-G 134
                                       8889**99.5 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0049
                                       EEE--TTTT-T CS
                    Prim_Zn_Ribbon   2 khspCPvCGGr 12 
                                       k + C+vCGG+
  gi|298674778|ref|YP_003726528.1| 146 KDGICDVCGGK 156
                                       6677*****98 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1    0.0042         4      22      32 ..     129     139 ..     128     141 .. 0.91
   2 ?    4.1   0.6     0.047        44       5      19 ..     148     162 ..     145     163 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0042
                       Prok-RING_1  22 vCpeCgtpyHr 32 
                                       +C +Cg+ yH 
  gi|298674778|ref|YP_003726528.1| 129 ICSNCGANYHL 139
                                       7*********6 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.047
                       Prok-RING_1   5 kkCpvCgkelkeedD 19 
                                        +C vCg +l + dD
  gi|298674778|ref|YP_003726528.1| 148 GICDVCGGKLYQRDD 162
                                       57*******999887 PP

>> PknG_rubred  Protein kinase G rubredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       2.7   2.5e+03     121     137 ..      20      36 ..       9      52 .. 0.68
   2 ?   10.1   0.0   0.00071      0.67      91     122 ..     126     155 ..     103     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.7
                                       --EEE-S-SS-TT-EET CS
                       PknG_rubred 121 gspysFlPqLspGdvva 137
                                        s +  +P++s+Gd++ 
  gi|298674778|ref|YP_003726528.1|  20 LSEFYTIPHISTGDILR 36 
                                       45566677777777764 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00071
                                       GG-B-TTT--B-S---SS----SEEE-TTT-- CS
                       PknG_rubred  91 skRfCwrCGrpvGRsekerkgaseGtCpkCgs 122
                                       ++R C++CG++     k ++ +++G+C  Cg 
  gi|298674778|ref|YP_003726528.1| 126 GRRICSNCGANY--HLKFSPPEKDGICDVCGG 155
                                       69*******986..56778999********95 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.4    0.0041       3.9       2      17 ..     124     139 ..     123     148 .. 0.88
   2 ?    3.6   0.2       0.1        95       7      21 ..     149     163 ..     148     187 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0041
                   Zn_ribbon_recom   2 LsGllrCgeCGspmtr 17 
                                       LsG  +C +CG++++ 
  gi|298674778|ref|YP_003726528.1| 124 LSGRRICSNCGANYHL 139
                                       89999********986 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.1
                   Zn_ribbon_recom   7 rCgeCGspmtrrkrk 21 
                                       +C  CG+++++r   
  gi|298674778|ref|YP_003726528.1| 149 ICDVCGGKLYQRDDD 163
                                       699******998654 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       3.8   3.6e+03      28      32 ..      75      79 ..      74      83 .. 0.79
   2 ?    2.7   0.1      0.11   1.1e+02       2      16 ..     128     142 ..     127     145 .. 0.86
   3 ?    6.8   0.1    0.0061       5.7       2      15 ..     148     161 ..     147     166 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.8
                                      .T--- CS
                    zf-C4_Topoisom 28 PeCkf 32
                                      P+C++
  gi|298674778|ref|YP_003726528.1| 75 PDCEN 79
                                      99987 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.11
                                       EE-SSS--EEEEEE- CS
                    zf-C4_Topoisom   2 ekCPkCggdLvlkrg 16 
                                       + C  Cg++ +lk +
  gi|298674778|ref|YP_003726528.1| 128 RICSNCGANYHLKFS 142
                                       67*******999976 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0061
                                       EE-SSS--EEEEEE CS
                    zf-C4_Topoisom   2 ekCPkCggdLvlkr 15 
                                       + C+ Cgg+L ++ 
  gi|298674778|ref|YP_003726528.1| 148 GICDVCGGKLYQRD 161
                                       78********9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1509.21
//
Query:       gi|298674779|ref|YP_003726529.1|  [L=490]
Description: preprotein translocase subunit SecY [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-68  230.1  23.4    4.3e-68  229.8  23.4    1.1  1  SecY             SecY translocase
    1.4e-11   44.1   0.6    3.8e-11   42.6   0.6    1.8  1  Plug_translocon  Plug domain of Sec61p


Domain annotation for each model (and alignments):
>> SecY  SecY translocase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  229.8  23.4   4.8e-72   4.3e-68       1     306 []      72     468 ..      72     468 .. 0.82

  Alignments for each domain:
  == domain 1  score: 229.8 bits;  conditional E-value: 4.8e-72
                                       BTTSSTCHHHHHHHHHHHHH.HHHSSSSSSTS-SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC........... CS
                              SecY   1 sifaLGImPyitasIilqLl.tvvipkleelkkegeegrkkinqitryltvvlalvqalgialslg........... 65 
                                       s++ LGI+P++tasI+lqLl ++    + +l+  ++++++++++++++l+++++++q l  +++ g           
  gi|298674779|ref|YP_003726529.1|  72 SLMMLGIGPIVTASIVLQLLvGA---DVVKLDLSDPNDQALFQGAQKFLVIIMIILQTLPQMFG-Gfiqpsgsvaaa 144
                                       89******************999...6677776699**********************997754.468899999999 PP

                                       ......HH.HHHHHHHHHHHHHHHHHHHHHHHHSSTTHHHHHHHHHHHHHHCCHSS...........-HHHH..... CS
                              SecY  66 ......lalllivlqltagtvllmwLgEqitekGiGnGisllifagivarlpkals...........gliel..... 120
                                             ++ +++++q+++g++l+++++E i+++GiG+G+ l+i+ag+++++++ +            g   +     
  gi|298674779|ref|YP_003726529.1| 145 lgvstgVMSAILFVQIFIGGILILFMDEIISKWGIGSGVGLFIVAGVSQQIVTGIVnwvpgedglpvG---Iipkwi 218
                                       9999998899******************************************8888455555555552...033335 PP

                                       .........SS...........THHHHHHHHHHHHHHHHHCHHHHBEEEECBBBS.TT....S.S-EEEEETTCCCS CS
                              SecY 121 .........ale.........gilallllllvtllvillvvyveeaerripvqya.krgrkggqssylPlklnyagv 178
                                                a           +  a +l+l++t++++llvvyve+++++ip+ ++  r    g+++++P+kl+ya+v
  gi|298674779|ref|YP_003726529.1| 219 yiiqnfgseA-IstdpmflllN--AGILALITTVIIFLLVVYVESTRIEIPLAHSsVR----GARGRYPVKLIYASV 288
                                       5444455441.04566544222..8899***************************777....9************** PP

                                       CHHHHHHHHHH..........................................HHHCCCCS............TCCC CS
                              SecY 179 iPiIfasslla..........................................lpstiaqfl...........lall 202
                                       +P+I++++l+a                                          +ps     l               
  gi|298674779|ref|YP_003726529.1| 289 LPMILVRALQAnlqliglvlhrsglgflgeysgstpisgfmyylspirspqdwIPS-----LvreaytqypvaP--- 357
                                       ***********777777777777777777777766666665555555533333233.....2443334444431... PP

                                       S...THHHHHHHHHHHHHH....HHHHHHTCT.THHHHHHHCCHHTBSSSCTTT.TCHHHHHHHHHHHHHHHHHHHH CS
                              SecY 203 s...psvlyvvlyvlliif....Fayfyteit.fnpkevaenlkksggfipgir.pgketakyLekvlsritliGal 270
                                           +  l+v++ ++++i+    Fa+f++e+t + pk +a+++ +sg++ipg+r +  +++k++e++++++t+iG++
  gi|298674779|ref|YP_003726529.1| 358 PatwQIGLHVLVDAIMLIGggiiFAIFWIETTgMGPKPTAKKIFNSGMQIPGFRrNIGSIEKVMERYIPKVTVIGGA 434
                                       03335556999999999999999*******************************99********************* PP

                                       HHHHHHHHHHHHTTS.TT.TTHHHHHHHHHHHHHHH CS
                              SecY 271 flaliavlpdllgasligafggtslLivVgvaletv 306
                                       f+++++++++llg+  ig  +gt+lL++V+++++++
  gi|298674779|ref|YP_003726529.1| 435 FIGFLTLVASLLGT--IGGASGTGLLLAVSIVYRLY 468
                                       **************..999*************9875 PP

>> Plug_translocon  Plug domain of Sec61p
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.6   4.2e-15   3.8e-11       2      35 .]      39      71 ..      38      71 .. 0.97

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 4.2e-15
                                      HHHHHCCSB-TT--SSS-TCCHTTTCCCCTSSTT CS
                   Plug_translocon  2 lYlvlsqiPLyGissssssDpfywlRaifAsnrG 35
                                      lY++l+++PL+G+s ++s+D+f+ +Ra fA+++G
  gi|298674779|ref|YP_003726529.1| 39 LYFILTNVPLFGLS-AESIDLFESYRAFFAGASG 71
                                      8************9.****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 3448.91
//
Query:       gi|298674780|ref|YP_003726530.1|  [L=143]
Description: 50S ribosomal protein L15 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-22   80.1   2.0    2.7e-22   79.8   2.0    1.1  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27
  ------ inclusion threshold ------
       0.12   12.7   0.0       0.14   12.5   0.0    1.1  1  FAM153          FAM153 family


Domain annotation for each model (and alignments):
>> Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.8   2.0     3e-26   2.7e-22       2     127 ..      27     140 ..      26     141 .. 0.86

  Alignments for each domain:
  == domain 1  score: 79.8 bits;  conditional E-value: 3e-26
                                       GGGTSSTTTTTTTTT-..S--........S--.........---.GGG..---EEEEHHHHHHTTTTGTTS.--... CS
                    Ribosomal_L27A   2 GktgGrGhkGqkkrsg..vkkkpg..feGGqmplyrrlpkrGfk.nskfkkeykvvnlkdLdelideerle.la... 69 
                                       G++gGrG+ G++k++   ++k +g  f  G++         Gf+  +k+  ++++vn+++Ldeli++++ +  a   
  gi|298674780|ref|YP_003726530.1|  27 GNRGGRGNSGTRKHNVtrSMK-RGqtF--GKY---------GFEvPKKNIYKESIVNVGELDELIEQLVDDgIAeek 91 
                                       9*************8743332.22236..666.........**97555557779***************99877898 PP

                                       ----EEEGGGTTTTSSS....SE.EEE--S---.--EEEESEE-HHHHHHHHHTT-EEE CS
                    Ribosomal_L27A  70 deaeeidleelaeaglikkkdgv.KvlgkgeltkklkvkaskfSkkAkekIeaaGGkve 127
                                       d+a+ idl++l           + Kvlg g++tk l v+a++fS++Ak kIe+  G+++
  gi|298674780|ref|YP_003726530.1|  92 DGAYHIDLNSL----------DInKVLGAGKVTKSLVVTARNFSNAAKDKIEKSNGTCI 140
                                       89*********..........788*********************************96 PP

>> FAM153  FAM153 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.6e-05      0.14      11     107 ..      41     134 ..      34     143 .] 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.6e-05
                            FAM153  11 emkrqlrrlrelhlystwkkyqealktslgvpqrgdledleehvpgqtvseeatgvhmmqvdpatpakkledstitg 87 
                                       ++ r ++r + +  y  +   ++  k s  + + g+l++l e + ++ ++ee  g + ++++     k l    +t 
  gi|298674780|ref|YP_003726530.1|  41 NVTRSMKRGQTFGKYGFEVPKKNIYKES--IVNVGELDELIEQLVDDGIAEEKDGAYHIDLNSLDINKVLGAGKVTK 115
                                       5667777777777777777777777765..5689**********************************999999999 PP

                            FAM153  88 shqqmsaspssapaeeatek 107
                                       s   ++a   s  a++  ek
  gi|298674780|ref|YP_003726530.1| 116 SLV-VTARNFSNAAKDKIEK 134
                                       875.4555555556666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1059.37
//
Query:       gi|298674781|ref|YP_003726531.1|  [L=153]
Description: 50S ribosomal protein L30 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.7e-14   51.5   0.2    1.6e-13   50.3   0.2    1.7  1  Ribosomal_L30  Ribosomal protein L30p/L7e


Domain annotation for each model (and alignments):
>> Ribosomal_L30  Ribosomal protein L30p/L7e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3   0.2     9e-18   1.6e-13       1      51 []       2      52 ..       2      52 .. 0.95

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 9e-18
                                      EEEEE-S-STTS-HHHHHHHHHTT-SSTTEEEE--SSHHHHHHHHHCCCGE CS
                     Ribosomal_L30  1 lfVtrirsiigvppkvrktLqlLgLrkingtvvklntpsirGmLkkVkhlV 51
                                      ++V+r r+ ++v   + +tL++L+L+k+n+ vv+  +ps  Gm++kVk++V
  gi|298674781|ref|YP_003726531.1|  2 YAVVRLRGNVNVMYTIEDTLKMLRLNKVNHCVVLDENPSNLGMVQKVKDYV 52
                                      57***************************88888888*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1102.13
//
Query:       gi|298674782|ref|YP_003726532.1|  [L=220]
Description: 30S ribosomal protein S5 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-23   81.7   0.2      3e-23   81.1   0.2    1.3  1  Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain
    2.3e-23   81.9   0.8    2.3e-23   81.9   0.8    1.8  2  Ribosomal_S5    Ribosomal protein S5, N-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.1   0.2   3.3e-27     3e-23       1      66 [.     134     200 ..     134     202 .. 0.97

  Alignments for each domain:
  == domain 1  score: 81.1 bits;  conditional E-value: 3.3e-27
                                       EEEETTEEEEEEE--TT--EES-HHHHHHHHHHT--SEE---BS.-SSHHHHHHHHHHHHHHTTTT- CS
                    Ribosomal_S5_C   1 tgkfgavkvllkpaprGtGiiaggavravlelaGikDvlakslg.srnpinvvkAtfeALkklrspe 66 
                                       +gk g+vkv lkpaprG G+ ag+++ +vle aGikDv+++++g +r+++n++kAt++AL+++++++
  gi|298674782|ref|YP_003726532.1| 134 EGKAGSVKVVLKPAPRGLGLAAGDTAVKVLEKAGIKDVWTRTEGkTRTTLNFAKATYNALTRTSTIK 200
                                       59*************************************************************9986 PP

>> Ribosomal_S5  Ribosomal protein S5, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       1.3   1.2e+04      13      20 ..      16      23 ..      11      26 .. 0.61
   2 !   81.9   0.8   2.6e-27   2.3e-23       1      64 [.      49     112 ..      49     113 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.3
                                      EEETTEEE CS
                      Ribosomal_S5 13 kvtkgGrr 20
                                      k+++ G++
  gi|298674782|ref|YP_003726532.1| 16 KMVQDGQI 23
                                      66666666 PP

  == domain 2  score: 81.9 bits;  conditional E-value: 2.6e-27
                                       XEEEEEEEEEEEEEETTEEEEEEEEEEEEEETTTEEEEEEEEESSHHHHHHHHHHHHHHTEEE- CS
                      Ribosomal_S5   1 lkekvlkikrvqkvtkgGrrtsfsalvvvGdgnGlvGlGvgkakevatAirkAiekAkknlvpv 64 
                                       l+++vl+i++vq++t++Grr +f+a+v+vG+gnG+vG+G +k  +v  AirkAi+ Ak n++++
  gi|298674782|ref|YP_003726532.1|  49 LDDEVLDINMVQRMTDSGRRVKFRATVIVGNGNGYVGFGQAKDGQVGPAIRKAIDTAKINVTRI 112
                                       689*********************************************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1682.13
//
Query:       gi|298674783|ref|YP_003726533.1|  [L=173]
Description: 50S ribosomal protein L18 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-30  106.6   0.1    2.4e-21   76.4   0.0    2.2  2  Ribosomal_L5e   Ribosomal large subunit proteins 60S L5, and 
     0.0004   20.7   0.0    0.00052   20.4   0.0    1.2  1  Ribosomal_L18p  Ribosomal L18 of archaea, bacteria, mitoch. a


Domain annotation for each model (and alignments):
>> Ribosomal_L5e  Ribosomal large subunit proteins 60S L5, and 50S L18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.4   0.0   2.7e-25   2.4e-21       2      98 ..       6      95 ..       5      99 .. 0.96
   2 !   28.5   0.0   1.5e-10   1.3e-06     131     163 .]     101     133 ..      95     133 .. 0.94

  Alignments for each domain:
  == domain 1  score: 76.4 bits;  conditional E-value: 2.7e-25
                     Ribosomal_L5e  2 rfqvkfrrrregktdYyarkrliiqdknkyntpkyRlvVrvtnkdiicqiayakiegdkvlaaayskelpkygvkvglt 80
                                      r+ v frrrreg+tdY++r rl+  d++       R+vVr + ++i +q+++ + +gd vl +a+s+el+kyg++ +  
  gi|298674783|ref|YP_003726533.1|  6 RYNVPFRRRREGRTDYHQRLRLLLSDED-------RVVVRKSLNNIQIQLITPESDGDDVLLSATSTELKKYGYEESTG 77
                                      9************************997.......9******************************************* PP

                     Ribosomal_L5e 81 nyaaaYatglllarrllk 98
                                      n +aaY+tgll++ ++l 
  gi|298674783|ref|YP_003726533.1| 78 NITAAYLTGLLFGLKALD 95
                                      ************988875 PP

  == domain 2  score: 28.5 bits;  conditional E-value: 1.5e-10
                     Ribosomal_L5e 131 aiLdvGLartttgakvfgalkgavdgglsiphs 163
                                        +Ld+GL+ ++ g++++++l g+vd+g+++ph+
  gi|298674783|ref|YP_003726533.1| 101 GVLDIGLHSSSAGSRIYASLNGIVDAGMDVPHN 133
                                       58******************************7 PP

>> Ribosomal_L18p  Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   5.8e-08   0.00052       3      94 ..      14     106 ..      12     128 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 5.8e-08
                                       CCHHHCHHHHHHTTT--TTSSS-EEEEEE-SS-EEEEEE-TTT..--EEEEECS-SCCCT..S-SSSCHHHHHHHHH CS
                    Ribosomal_L18p   3 kkearkrRhkRirkklsgtaerprlvvfrsnrhiyaQviddvk..gktlasastlekelk..lkstknkeaakkvge 75 
                                       ++e r+  h+R+r  ls  +   r+vv +s ++i +Q+i   +  + +l sa + e +     +st+n+ aa   g 
  gi|298674783|ref|YP_003726533.1|  14 RREGRTDYHQRLRLLLSDED---RVVVRKSLNNIQIQLITPESdgDDVLLSATSTELKKYgyEESTGNITAAYLTGL 87 
                                       77888999999999999988...****************865411456666655554433578999*********** PP

                                       HHHHHHCHHCHTC-EE--T CS
                    Ribosomal_L18p  76 liAerakekgiekvvfDrg 94 
                                       l+  +a++ g e+ v D g
  gi|298674783|ref|YP_003726533.1|  88 LFGLKALDEGYETGVLDIG 106
                                       *******999999998866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1298.68
//
Query:       gi|298674784|ref|YP_003726534.1|  [L=148]
Description: 50S ribosomal protein L19e [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-57  192.7   7.0    3.5e-57  192.5   7.0    1.0  1  Ribosomal_L19e  Ribosomal protein L19e


Domain annotation for each model (and alignments):
>> Ribosomal_L19e  Ribosomal protein L19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.5   7.0     2e-61   3.5e-57       2     140 ..       4     142 ..       3     146 .. 0.98

  Alignments for each domain:
  == domain 1  score: 192.5 bits;  conditional E-value: 2e-61
                                       THHHHHHHHHHTTS-GGGEEE-GGGHHHHHH--SHHHHHHHHHTTSEEE-------THHHHHHHHHHHTT-S-SGGG CS
                    Ribosomal_L19e   2 lklqkrlaasvlkvGknrvwldpeeleeiaeAitredirklikdglIikkpkkgnsrararerkekkrkgrrrgsGk 78 
                                       +++qk+laa++l++G+nrvw++pe+++++a+Aitredir+ i++g I+++p kg sr+rarer++k+++g+r+g+G+
  gi|298674784|ref|YP_003726534.1|   4 VSNQKKLAAKILGCGVNRVWVNPEASDDVAAAITREDIREQIENGNIKAQPIKGVSRSRARERDAKRKYGHRKGHGS 80 
                                       789************************************************************************** PP

                                       --S-HHHHS-HHHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHTT--SSHHHHHHHH CS
                    Ribosomal_L19e  79 rkGtkeaRlpekelWikriRalRrlLkelrekkkidkktYrelYrkakGgefknkavLkeyi 140
                                       rkG+k+aR peke+W+k+iRalR+ Lkelr+++++d+ tY +lYr+akGg+f+++a+L++++
  gi|298674784|ref|YP_003726534.1|  81 RKGKKGARNPEKEQWMKKIRALRKRLKELRDDGTLDRPTYCKLYRQAKGGQFRSTAHLEAHL 142
                                       ***********************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       973  (0.0542696); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1024.55
//
Query:       gi|298674785|ref|YP_003726535.1|  [L=144]
Description: 50S ribosomal protein L32e [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-37  126.9   0.1    6.2e-37  126.3   0.1    1.3  1  Ribosomal_L32e  Ribosomal protein L32


Domain annotation for each model (and alignments):
>> Ribosomal_L32e  Ribosomal protein L32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.3   0.1   3.4e-41   6.2e-37       1     108 []      32     138 ..      32     138 .. 0.96

  Alignments for each domain:
  == domain 1  score: 126.3 bits;  conditional E-value: 3.4e-41
                                       ------TTTTT-TTS-SS------TT-TTTTT-TTS-----GGG---TTTTT--TTS-EEEEESSGGGGTT--TTTE CS
                    Ribosomal_L32e   1 tkkFirhqsdryvklkeswrkprGidnrvrrrfkgqilmpkiGYgspkktrgllpsGfkkvlVhnvkeLevllmenk 77 
                                       +++F+r +s+r +++ +swr+p+G+++++r+ +k++ +++k+GYgsp++++gl+psG++++lV+nvk++e++   + 
  gi|298674785|ref|YP_003726535.1|  32 KPSFNRVDSHRLKRVPSSWRRPKGVNSKLRKGIKAKGSLVKVGYGSPEAVKGLHPSGYTEILVYNVKDVENISNPSS 108
                                       589*********************************************************************76644 PP

                                       ..EEEE-TTS-HHHHHHHHHHHHHTT-EBSS CS
                    Ribosomal_L32e  78 syaaeiahsVsskkrkeiverAaelgikVtN 108
                                         a++i+++V++kkr++i+e+AaelgikV+N
  gi|298674785|ref|YP_003726535.1| 109 -EAIRIGRTVGAKKRTMIEEKAAELGIKVLN 138
                                       .7****************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1043.34
//
Query:       gi|298674786|ref|YP_003726536.1|  [L=176]
Description: 50S ribosomal protein L6 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-25   88.6   0.3    8.8e-12   45.5   0.0    2.1  2  Ribosomal_L6  Ribosomal protein L6


Domain annotation for each model (and alignments):
>> Ribosomal_L6  Ribosomal protein L6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.0   4.9e-16   8.8e-12       1      76 []      11      83 ..      11      83 .. 0.94
   2 !   41.5   0.1   8.7e-15   1.6e-10       1      76 []      95     169 ..      95     169 .. 0.98

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 4.9e-16
                                      CSTTEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHHHHHHHHHHHHHHHHHHHHTC CS
                      Ribosomal_L6  1 iPvgvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekvAligtvrslinnmikGVteg 76
                                      iP++ +vs++g + ++v+Gpkg+ +  +++   v++   + +vt + +s  + +k+  igt+ ++ +nm++GVteg
  gi|298674786|ref|YP_003726536.1| 11 IPEDITVSLDG-KYLTVTGPKGTNKKFMWYP-GVAITPTDSEVTIEALSTRRDKKA-IIGTFAAHLRNMMTGVTEG 83
                                      8*********8.*****************99.5555589*****************.*****************98 PP

  == domain 2  score: 41.5 bits;  conditional E-value: 8.7e-15
                                       CSTTEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHH....HHHHHHHHHHHHHHHHH CS
                      Ribosomal_L6   1 iPvgvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekv....AligtvrslinnmikGV 73 
                                       +P+  +v +++  + ++lG+k+++ ++i  ++ ve+      +++i+++gi+ke+v    A+i++++++++ + + +
  gi|298674786|ref|YP_003726536.1|  95 FPMQLKVDGNKFMISNFLGEKKPRVADIIGDTSVEIN-----GDEIIITGINKEDVgqtaANIEQTTKINRFDPRIF 166
                                       79999******************************99.....*********************************** PP

                                       HTC CS
                      Ribosomal_L6  74 teg 76 
                                       ++g
  gi|298674786|ref|YP_003726536.1| 167 QDG 169
                                       *98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1332.67
//
Query:       gi|298674787|ref|YP_003726537.1|  [L=130]
Description: 30S ribosomal protein S8 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-27   95.6   0.0    2.4e-27   95.4   0.0    1.1  1  Ribosomal_S8  Ribosomal protein S8


Domain annotation for each model (and alignments):
>> Ribosomal_S8  Ribosomal protein S8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.4   0.0   1.4e-31   2.4e-27       1     127 []       5     130 .]       5     130 .] 0.89

  Alignments for each domain:
  == domain 1  score: 95.4 bits;  conditional E-value: 1.4e-31
                                       -HHHHHHHHHHHHHHTT-SEEEE.E--HHHHHHHHHHHHCTSEEEEEEE.CCCCCC..EEEEE-BSSS-SBSSSEEE CS
                      Ribosomal_S8   1 DpiadmltrirNaekakkeevev.pasklkeeilkvLkeeGyikdfeve.eekkkk..ikielkynkkkksvikklk 73 
                                       Dp+a++l++i+Nae+++ke++++ paskl+ ++l+v+k+ Gyi +fe + + k  +  +k+++++n+  +++ik   
  gi|298674787|ref|YP_003726537.1|   5 DPLANALSTIKNAENVGKESCTIqPASKLIGNVLSVMKDYGYIGEFELVeDGKAGIynVKLAGRINN--CGAIKPRY 79 
                                       9***********************************************8444444456888888888..*****999 PP

                                       E-SBTTC--EE-CCC---CGGGTSEEEEEETTEEEEHHHHHHCT--EEEEEEEE CS
                      Ribosomal_S8  74 rvskpgrrvYakvkelpkvlnglGiaivsTskGvmtdkeArkkkvGGevlayvw 127
                                        vs++  +   + ++     +++G++i++Ts Gv ++ eAr+++vGG++layv+
  gi|298674787|ref|YP_003726537.1|  80 SVSTANFE---GWEKQFLPGKNFGTLILTTSMGVKSQYEARDENVGGQLLAYVY 130
                                       99998777...55555555689*******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 1004.84
//
Query:       gi|298674788|ref|YP_003726538.1|  [L=51]
Description: 30S ribosomal protein S14 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-14   52.6   4.2    2.9e-14   52.5   4.2    1.0  1  Ribosomal_S14    Ribosomal protein S14p/S29e
     0.0015   19.2   1.0     0.0015   19.2   1.0    1.1  1  MRNIP            MRN-interacting protein
     0.0041   16.8   1.1     0.0051   16.5   1.1    1.1  1  zf-P11           P-11 zinc finger
  ------ inclusion threshold ------
      0.013   15.5   0.9      0.014   15.5   0.9    1.1  1  DUF1451          Zinc-ribbon containing domain
      0.015   15.4   2.4      0.016   15.3   2.4    1.1  1  Ribosomal_L37ae  Ribosomal L37ae protein family
        1.1    9.3   8.7        5.4    7.1   8.5    1.9  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Ribosomal_S14  Ribosomal protein S14p/S29e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.5   4.2   9.8e-18   2.9e-14       8      53 ..       6      50 ..       2      51 .] 0.93

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 9.8e-18
                                      SS..CTTT---SSS--SSSEE-GGG-..EHHHHHHHTTT...TT-EE- CS
                     Ribosomal_S14  8 nssptrirnrCrvtGrprGvirkfgL..sRicfRelAlkgelpGvkKa 53
                                       +s +r+  +C+ +Gr ++++rk+g+  +R+cfRe+A++   +G++K+
  gi|298674788|ref|YP_003726538.1|  6 TKSFGRGASQCKRCGRKQSLVRKYGIymCRHCFREMAHE---MGFEKY 50
                                      46789**********************************...*****8 PP

>> MRNIP  MRN-interacting protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   1.0   5.1e-07    0.0015      20      45 ..      13      39 ..       1      50 [. 0.78

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 5.1e-07
                             MRNIP 20 kwkCkvCnekqslkkvygsgsgkdc.r 45
                                        +Ck C+ kqsl + yg ++ + c r
  gi|298674788|ref|YP_003726538.1| 13 ASQCKRCGRKQSLVRKYGIYMCRHCfR 39
                                      569***************999988834 PP

>> zf-P11  P-11 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   1.1   1.7e-06    0.0051       1      29 [.      12      39 ..      12      44 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.7e-06
                                      -SSSBTTTSS--SSEEE-SSSEEEHHHHH CS
                            zf-P11  1 GplsCksCWfkdksLveCsdHYLClrClq 29
                                      G  +Ck C   ++sLv+    Y+C++C++
  gi|298674788|ref|YP_003726538.1| 12 GASQCKRCGR-KQSLVRKYGIYMCRHCFR 39
                                      6789****86.579*************86 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.9   4.6e-06     0.014     109     139 ..       8      38 ..       1      43 [. 0.88

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.6e-06
                           DUF1451 109 vvglGtlvCekCgkelalkkteeippCpkCg 139
                                         g G  +C++Cg++ +l +   i  C +C 
  gi|298674788|ref|YP_003726538.1|   8 SFGRGASQCKRCGRKQSLVRKYGIYMCRHCF 38 
                                       67899*************************5 PP

>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   2.4   5.3e-06     0.016      24      62 ..       4      42 ..       1      46 [. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.3e-06
                                      HHHHHHHHS-BEESSSSSSEEEEEETTEEEETTTTEEEE CS
                   Ribosomal_L37ae 24 kkieisqhakytCpfcgktkvkRkavgiwkCkkcgktva 62
                                      k ++   + + +C++cg+++   +  gi+ C++c +++a
  gi|298674788|ref|YP_003726538.1|  4 KTTKSFGRGASQCKRCGRKQSLVRKYGIYMCRHCFREMA 42
                                      555555667789*******8888889********99998 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   8.5    0.0018       5.4      19      44 ..      14      38 ..       6      40 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0018
                     Zn_Tnp_IS1595 19 fvCPhCgsrkayriktrglfqCkeCr 44
                                        C +Cg rk   +++ g ++C++C 
  gi|298674788|ref|YP_003726538.1| 14 SQCKRCG-RKQSLVRKYGIYMCRHCF 38
                                      46*****.6666666679*******5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 357.95
//
Query:       gi|298674789|ref|YP_003726539.1|  [L=172]
Description: 50S ribosomal protein L5 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-28   98.6   0.0    2.5e-28   98.1   0.0    1.3  1  Ribosomal_L5_C  ribosomal L5P family C-terminus
    3.6e-21   75.3   0.1    6.2e-21   74.5   0.1    1.4  1  Ribosomal_L5    Ribosomal protein L5


Domain annotation for each model (and alignments):
>> Ribosomal_L5_C  ribosomal L5P family C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.1   0.0   2.8e-32   2.5e-28       1      94 []      63     162 ..      63     162 .. 0.89

  Alignments for each domain:
  == domain 1  score: 98.1 bits;  conditional E-value: 2.8e-32
                    Ribosomal_L5_C   1 piGvkvtLrgekmyefldkllevvlprlrdFkGiskssfdgrGnvsfGikeqiifpeieydkdkgifGmditivtta 77 
                                       piG+kvtLrg+++ efl++ l++v++rl       +s+fd++Gnv+fGi+e+++fp+++yd+++gifGmdi++v+t+
  gi|298674789|ref|YP_003726539.1|  63 PIGCKVTLRGKRAQEFLETSLSIVENRLD------ESQFDESGNVAFGIDEHTDFPGMKYDPNIGIFGMDIMVVVTR 133
                                       8****************************......****************************************** PP

                    Ribosomal_L5_C  78 k....tde.........earallkelgipf 94 
                                       +     d+         +++ ++ke++i+f
  gi|298674789|ref|YP_003726539.1| 134 PgyriKDRkvesrkipgSHK-IVKEDSIEF 162
                                       *8775333677777776666.777777776 PP

>> Ribosomal_L5  Ribosomal protein L5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.5   0.1   6.9e-25   6.2e-21       1      57 []       6      59 ..       6      59 .. 0.99

  Alignments for each domain:
  == domain 1  score: 74.5 bits;  conditional E-value: 6.9e-25
                                      SCTTS-EEEEEEEEEE-SSSSSCHHHHHCCHHHHCCCHSS--EECC--TTCTTTCSC CS
                      Ribosomal_L5  1 NvMqvPrleKivinmgvGeagedkkllekaakeLaeItGQkPvvtkakksianFkiR 57
                                      N+M+ P+++K+v++mgvGe+g++   l +a+++L++ItGQ  v+t+ak++ ++F+iR
  gi|298674789|ref|YP_003726539.1|  6 NPMRTPKIDKVVVHMGVGESGQT---LVNAEQILQTITGQSGVRTYAKRTQPAFGIR 59
                                      9**********************...******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 976.54
//
Query:       gi|298674790|ref|YP_003726540.1|  [L=240]
Description: 30S ribosomal protein S4e [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.2e-21   74.1   0.9      1e-20   73.4   0.9    1.4  1  Ribosomal_S4e  Ribosomal family S4e
    7.1e-11   41.7   0.1    1.5e-10   40.6   0.1    1.6  1  S4             S4 domain
    1.7e-09   37.7   2.9    2.6e-09   37.0   2.9    1.3  1  RS4NT          RS4NT (NUC023) domain
    0.00012   21.9   0.1    0.00035   20.4   0.1    1.8  1  KOW            KOW motif
     0.0019   18.7   0.2     0.0033   17.9   0.2    1.4  1  DUF3994        Domain of unknown function (DUF3994)
  ------ inclusion threshold ------
      0.031   14.1   0.0       0.11   12.3   0.0    1.9  2  S4_2           S4 domain
      0.061   13.6   0.6       0.18   12.1   0.3    2.0  1  DUF3912        Protein of unknown function (DUF3912)


Domain annotation for each model (and alignments):
>> Ribosomal_S4e  Ribosomal family S4e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.4   0.9   4.1e-24     1e-20       1      75 []      91     163 ..      91     163 .. 0.95

  Alignments for each domain:
  == domain 1  score: 73.4 bits;  conditional E-value: 4.1e-24
                                       TTEEEEEEE-TTSSEEEEEE-TTCCCEEEEEECEEEEECCCEEEEEETTS-EEEESSTT-STTEEEEEETTTTEE CS
                     Ribosomal_S4e   1 tgenyrllydtkgrfalhkItseeakyKLcKikkkttvkkgipqlvthdGrtirypdpdikvnDtvkidleenkI 75 
                                       ++e+yrll+++k ++ l+k ++++ + KLcKi++kttvk g +ql+++dG++++ +++ +k++D++ i++++++I
  gi|298674790|ref|YP_003726540.1|  91 MNESYRLLINQKSKLILQKLEESDTN-KLCKINDKTTVKSGAIQLNLSDGTNLIGSND-YKAKDSIIITVPDKNI 163
                                       59******************766655.******************************9.*************998 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.1   5.8e-14   1.5e-10       5      48 .]      42      86 ..      38      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 5.8e-14
                                      HHH.HHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTCEE CS
                                S4  5 kvl.arlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgDvi 48
                                      ++l   lgl+  r+eA++  ++G+VlV+Gk++kd +++V+  D+i
  gi|298674790|ref|YP_003726540.1| 42 VILrDMLGLVDNRSEAKRVLSQGKVLVDGKPRKDLKFPVGLFDII 86
                                      5666679*********************************99987 PP

>> RS4NT  RS4NT (NUC023) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   2.9     1e-12   2.6e-09       5      37 .]       3      35 ..       1      35 [. 0.96

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 1e-12
                                      --EETTTS-TTS---SSSSSEE----SSSS-TT CS
                             RS4NT  5 kHLKrlaAPkhWpldkkegvfavkPspGPHklr 37
                                      kH Kr++ P +W ++kk++++++++spGPH ++
  gi|298674790|ref|YP_003726540.1|  3 KHQKRISIPNSWRVAKKSNKWVTTTSPGPHHKE 35
                                      9*****************************985 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   1.4e-07   0.00035       2      31 ..     172     205 ..     171     206 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.4e-07
                                       TSEEEESSSTTTTCEEEEEEEETTT....TEEEE CS
                               KOW   2 GdhVkVvsGphkGktGkVvkvdqhk....vrVfv 31 
                                       G+  ++v+G+h G++G+++ + + +    ++V +
  gi|298674790|ref|YP_003726540.1| 172 GNLAMIVGGKHTGEIGTIKTITKTRgseaNTVEI 205
                                       9*******************99999888877765 PP

>> DUF3994  Domain of unknown function (DUF3994)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.2   1.3e-06    0.0033      37      82 ..     113     158 ..      95     173 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.3e-06
                           DUF3994  37 vssddlksldkkaGikienvinnvkdGtelvGnwGidyddgvkvsl 82 
                                       + +++l ++++k+ +k  +++ n+ dGt+l+G   ++ +d++ +++
  gi|298674790|ref|YP_003726540.1| 113 SDTNKLCKINDKTTVKSGAIQLNLSDGTNLIGSNDYKAKDSIIITV 158
                                       56899***********************************998876 PP

>> S4_2  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.3e-05      0.11      17      41 ..      48      72 ..      43      95 .. 0.89
   2 ?   -2.1   0.0       1.4   3.5e+03      42      56 ..     114     128 ..     111     135 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.3e-05
                              S4_2 17 aglvesGgeaKafiaegeVkvNGev 41
                                      +glv++  eaK ++++g+V+v+G+ 
  gi|298674790|ref|YP_003726540.1| 48 LGLVDNRSEAKRVLSQGKVLVDGKP 72
                                      68899999***************86 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.4
                              S4_2  42 etrRgkKlraGdvVe 56 
                                       +t + +K+ +  +V+
  gi|298674790|ref|YP_003726540.1| 114 DTNKLCKINDKTTVK 128
                                       566666666555554 PP

>> DUF3912  Protein of unknown function (DUF3912)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   7.2e-05      0.18       7      54 ..     172     221 ..     170     232 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.2e-05
                           DUF3912   7 GqkvyvkdGPyrnklGvvkkkeqedddh.ftvviddqdidvel.kdillv 54 
                                       G  + +  G + + +G +k + +   ++  tv i +q+ d+e  +d+++v
  gi|298674790|ref|YP_003726540.1| 172 GNLAMIVGGKHTGEIGTIKTITKTRGSEaNTVEISGQNYDFETiEDYVVV 221
                                       66678899************9988766515666*********72455543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 1349.34
//
Query:       gi|298674791|ref|YP_003726541.1|  [L=117]
Description: 50S ribosomal protein L24 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      5e-31  107.0   0.4      6e-31  106.7   0.4    1.1  1  Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archae
    1.9e-05   24.5   3.5    4.1e-05   23.4   3.5    1.6  1  KOW            KOW motif


Domain annotation for each model (and alignments):
>> Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archaeal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.7   0.4   6.7e-35     6e-31       1      82 []       3     117 .]       3     117 .] 0.99

  Alignments for each domain:
  == domain 1  score: 106.7 bits;  conditional E-value: 6.7e-35
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................xx RF
                     Ribosomal_L26   1 sssrrkqrKahfnapshirrklmsapLskeLrekygvrslpir................................gv 45 
                                       s+++rkq K ++nap+h+++k+m apLskeLrekyg+rs+ +                                 gv
  gi|298674791|ref|YP_003726541.1|   3 SKQPRKQIKSRYNAPLHKKQKFMAAPLSKELREKYGTRSVSVIvgdtvkvlrgdhatttgkvenvslkdgviyieGV 79 
                                       89*************************************************************************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                     Ribosomal_L26  46 trekangttvpvgihpSkvvItklkl.DkdrkkiLerk 82 
                                       t+ ka+gt++ ++++pS+v+It+l++ D++rk+++++k
  gi|298674791|ref|YP_003726541.1|  80 TVPKADGTEMARPVDPSNVMITSLNMeDEHRKTVISKK 117
                                       ***********************************998 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   3.5   4.5e-09   4.1e-05       1      32 []      46      77 ..      46      81 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 4.5e-09
                                      TTSEEEESSSTTTTCEEEEEEEETTTTEEEEE CS
                               KOW  1 pGdhVkVvsGphkGktGkVvkvdqhkvrVfvd 32
                                      +Gd+VkV++G h+  tGkV+ v  +   ++++
  gi|298674791|ref|YP_003726541.1| 46 VGDTVKVLRGDHATTTGKVENVSLKDGVIYIE 77
                                      7*********************9999777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 718.73
//
Query:       gi|298674792|ref|YP_003726542.1|  [L=132]
Description: 50S ribosomal protein L14 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-36  125.1   0.5    1.7e-36  125.0   0.5    1.0  1  Ribosomal_L14  Ribosomal protein L14p/L23e


Domain annotation for each model (and alignments):
>> Ribosomal_L14  Ribosomal protein L14p/L23e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.0   0.5   9.6e-41   1.7e-36       3     122 .]      13     132 .]      11     132 .] 0.95

  Alignments for each domain:
  == domain 1  score: 125.0 bits;  conditional E-value: 9.6e-41
                                       CSS-EEE--SSSSBSEEEEEEETT-.....---EE-SSSEEEEEESSS-T...TTSSCEEEEEEEE-SS-EE-TTS- CS
                     Ribosomal_L14   3 qlktrlkvaDNsgakevecikvlggk....krkaasvGdiivvsvkkakpkgkvkkgdvvkavvvrtkkevrrkdGs 75 
                                       +++++l+++DN+gak ve+i+v +++    ++++a +Gd++vvsvkk++p   ++++++++av+vr+kke++r+dG 
  gi|298674792|ref|YP_003726542.1|  13 NTGANLNCVDNTGAKVVEIISVKNYRgvksRHPKAGIGDMCVVSVKKGTP---EMRKQILYAVIVRQKKEYKRPDGL 86 
                                       57899*****************9877666677******************...99********************** PP

                                       EEEESS-EEEEB-TTS-BSS-.B-SBEEHHHHHH.-HHHHHTBSBE. CS
                     Ribosomal_L14  76 virfddnaaVllnkkgeplGtrifgpvarelrekkflkivslApevl 122
                                       +++f+dna+V+ + +g p+Gt i+gp+are++e+ f+k+ ++A++++
  gi|298674792|ref|YP_003726542.1|  87 HVSFEDNAVVITDISGFPKGTDIKGPIAREAAER-FPKVGTTASMIV 132
                                       *********************************9.********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 795.50
//
Query:       gi|298674793|ref|YP_003726543.1|  [L=109]
Description: 30S ribosomal protein S17 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.8e-28   96.4   1.1    9.6e-28   96.1   1.1    1.1  1  Ribosomal_S17    Ribosomal protein S17
     0.0003   21.1   0.0     0.0013   19.0   0.0    2.0  2  Ribosomal_S17_N  Ribosomal_S17 N-terminal


Domain annotation for each model (and alignments):
>> Ribosomal_S17  Ribosomal protein S17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.1   1.1   1.1e-31   9.6e-28       1      68 []      36     104 ..      36     104 .. 0.99

  Alignments for each domain:
  == domain 1  score: 96.1 bits;  conditional E-value: 1.1e-31
                                       EEEEE--STTEEEEEEEEEEEETTTTEEEEEEEEEEEE-TTTS.--TT-EEEEEEECECSSSEEEEEEE CS
                     Ribosomal_S17   1 GvVvsdkmdkTvvVrverlvkhpkykkyvkrrkkylahdenns.vkvGDiVrieecrPlSktkrfvvve 68 
                                       G+V+sd  dkTv++++++   ++ky++y+kr++k++ah+++++ +k+GD+V+i+ecrPlSktk+fvvve
  gi|298674793|ref|YP_003726543.1|  36 GTVISDDRDKTVTIQRNYERLIKKYQRYEKRHSKISAHNPPCIdAKEGDVVKIAECRPLSKTKSFVVVE 104
                                       99*****************************************************************97 PP

>> Ribosomal_S17_N  Ribosomal_S17 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.5e-07    0.0013      33      69 .]       2      34 ..       1      34 [. 0.87
   2 ?   -0.5   0.0      0.18   1.6e+03      22      31 ..      57      66 ..      42      85 .. 0.54

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.5e-07
                                      -----TT----GGGGS-----TTSSSSSS----S-EE CS
                   Ribosomal_S17_N 33 vknvglgfktPkeAiegtYiDkKCPFtGnvsirGriL 69
                                       k++gl  + P++  +    D  CPF Gn s+rG++L
  gi|298674793|ref|YP_003726543.1|  2 TKDIGLDVQSPSKECD----DTNCPFHGNLSVRGQVL 34
                                      5889999999988777....899************98 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.18
                                      ----....-- CS
                   Ribosomal_S17_N 22 ekkkkkkkkr 31
                                       kk ++ +kr
  gi|298674793|ref|YP_003726543.1| 57 IKKYQRYEKR 66
                                      2222222233 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 669.30
//
Query:       gi|298674794|ref|YP_003726544.1|  [L=100]
Description: ribonuclease P [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-23   80.8   0.0    5.6e-23   80.7   0.0    1.0  1  UPF0086   Domain of unknown function UPF0086


Domain annotation for each model (and alignments):
>> UPF0086  Domain of unknown function UPF0086
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.7   0.0   3.1e-27   5.6e-23       2      83 ..       7      94 ..       6      95 .. 0.95

  Alignments for each domain:
  == domain 1  score: 80.7 bits;  conditional E-value: 3.1e-27
                                      HHCCSXXSS-EEEEEECSSTTTTTEEEEEEEEETTEEEEEECTTEEEEEESTTCEEEEEE..........TTEEEEEEC CS
                           UPF0086  2 kLlkadlhGaeveVvrsknpslvgikGiVvkEtkntlkivtkksrvktvpKegsvFefev.........kdvlevevdG 71
                                      +L+ ++l+G++v Vv+s+np l +i+G+V +Etkntl ivt +++ k+vpK+++ F f+v         +   +v+v+G
  gi|298674794|ref|YP_003726544.1|  7 NLIYHELIGLPVDVVESTNPLLDNINGVVRDETKNTLIIVT-DNNNKMVPKANANFVFKVpvefgdkylV--KHVKVNG 82
                                      89***************************************.99*********************99652..68***** PP

                                      CCCSSXHHHHHC CS
                           UPF0086 72 sqlryrpadRae 83
                                      + l+++p++R++
  gi|298674794|ref|YP_003726544.1| 83 KLLLSQPESRTK 94
                                      **********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 619.04
//
Query:       gi|298674795|ref|YP_003726545.1|  [L=67]
Description: 50S ribosomal protein L29 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-17   62.2   0.2      4e-17   61.9   0.2    1.1  1  Ribosomal_L29  Ribosomal L29 protein


Domain annotation for each model (and alignments):
>> Ribosomal_L29  Ribosomal L29 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.9   0.2   2.2e-21     4e-17       1      56 [.       7      63 ..       7      63 .. 0.98

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 2.2e-21
                                      HHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHT.SSS-CHHHHHHHHHHHHHHHHHHH CS
                     Ribosomal_L29  1 kelrelsdeeLkeklkelkkeLfnLrfqkatg.qlenpsrirkvRkdIARikTvlre 56
                                      +e+r++s +e k+++++ ++eL n +   ++g ++enp+ri ++++++ARikT++re
  gi|298674795|ref|YP_003726545.1|  7 NEIRNMSPQERKDEIEKFQTELSNEKALTSAGgSPENPGRIGELKRTVARIKTIQRE 63
                                      69****************************999***********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 432.50
//
Query:       gi|298674796|ref|YP_003726546.1|  [L=307]
Description: 30S ribosomal protein S3 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      5e-22   78.2   0.5    1.1e-21   77.1   0.5    1.6  1  Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
    4.5e-16   58.4   0.0    1.2e-15   57.1   0.0    1.8  1  KH_2            KH domain
  ------ inclusion threshold ------
      0.015   15.1   0.7       0.11   12.4   0.2    2.5  2  KH_1            KH domain
       0.36   10.7   0.1       0.36   10.7   0.1    2.4  3  KH_4            KH domain


Domain annotation for each model (and alignments):
>> Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.1   0.5   2.5e-25   1.1e-21       1      83 []      99     182 ..      99     182 .. 0.98

  Alignments for each domain:
  == domain 1  score: 77.1 bits;  conditional E-value: 2.5e-25
                                       HHHHHHTT--HHHHHHHHHHHHHHCC-SEEEEEEEC-SS.TTT--EEEEEEC----..TCHHHH-EEEEEEEEETTE CS
                    Ribosomal_S3_C   1 iaeqlekrvsfRramkkairramkagakGikiqvsGrLggaeiarsekykeGrvpl..htlradidyavaeaktkyG 75 
                                       +a ++e+++ fR+a ++air++m aga G++i++sG+L+ + +ar ek+ +G++++  +++++ +d+++a+a  k G
  gi|298674796|ref|YP_003726546.1|  99 LAASIERGWYFRKAGHNAIRAIMGAGALGCEIIMSGKLT-GPRARVEKLVRGYIKHagKPVDDIVDEGFATAVKKLG 174
                                       5889***********************************.9************************************ PP

                                       EEEEEEEE CS
                    Ribosomal_S3_C  76 iiGvkVwI 83 
                                       +iG+kV+I
  gi|298674796|ref|YP_003726546.1| 175 TIGCKVRI 182
                                       ******98 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.1   0.0   2.7e-19   1.2e-15       2      78 .]      17      90 ..      16      90 .. 0.93

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 2.7e-19
                                      HHHHHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEEEEEETTTGG CS
                              KH_2  2 ipeslaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVklnivkVkkpel 78
                                      ++e++a+++  ag++++eI+rt+ ++ i+i++++pg+vIGkgG+ i+k++ ++ k    + + ++     +Vk pel
  gi|298674796|ref|YP_003726546.1| 17 LDEYFAKQLNRAGYGGMEINRTPMGTQITIYAEKPGMVIGKGGKVIRKLTRDVDKLYN-MDNPQID--AQEVKTPEL 90
                                      5799*****************************************************5.8888887..889999885 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   2.4e-05      0.11       6      27 ..      46      67 ..      41      71 .. 0.81
   2 ?   -0.3   0.0      0.21   9.6e+02      29      40 ..     175     186 ..     173     223 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.4e-05
                                      EGGGHHHHHHTGGGHHHHHHHH CS
                              KH_1  6 vPsslvgriIGkgGsnIkeIre 27
                                      + +++ g +IGkgG++I+++ +
  gi|298674796|ref|YP_003726546.1| 46 IYAEKPGMVIGKGGKVIRKLTR 67
                                      55566699***********987 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.21
                                       H.T-EEEEESSTT CS
                              KH_1  29 t.gakIkvpksed 40 
                                       t g+k++++  +d
  gi|298674796|ref|YP_003726546.1| 175 TiGCKVRII-HPD 186
                                       669999998.443 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   8.1e-05      0.36      32      52 ..      43      63 ..      20      65 .. 0.85
   2 ?   -2.3   0.1      0.93   4.2e+03      16      39 ..     205     227 ..     200     232 .. 0.53
   3 ?   -1.8   0.5      0.64   2.9e+03       8      29 ..     219     240 ..     212     253 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8.1e-05
                              KH_4 32 elnvegedlGrvIGkrGrtld 52
                                      ++++  e+ G vIGk G++++
  gi|298674796|ref|YP_003726546.1| 43 QITIYAEKPGMVIGKGGKVIR 63
                                      67788999**********985 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.93
                              KH_4  16 eevevteeeeeeeveielnveged 39 
                                       ee ev eee+ ee  i+  ve+e 
  gi|298674796|ref|YP_003726546.1| 205 EEFEVVEEES-EESGIQELVEEES 227
                                       4666666633.3444444455555 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.64
                              KH_4   8 lkalvddpeevevteeeeeeev 29 
                                       +++lv+++ + ev e e+e+e+
  gi|298674796|ref|YP_003726546.1| 219 IQELVEEESTGEVAEAESETEE 240
                                       5778888888888888666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1132  (0.0631379); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:01.01
# Mc/sec: 921.04
//
Query:       gi|298674797|ref|YP_003726547.1|  [L=150]
Description: 50S ribosomal protein L22 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.3e-30  103.5   0.4    7.5e-30  103.2   0.4    1.1  1  Ribosomal_L22  Ribosomal protein L22p/L17e
  ------ inclusion threshold ------
       0.11   13.1   0.4       0.26   11.8   0.1    1.8  2  Acyl-thio_N    Acyl-ATP thioesterase


Domain annotation for each model (and alignments):
>> Ribosomal_L22  Ribosomal protein L22p/L17e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.2   0.4   8.4e-34   7.5e-30       1     103 []      18     148 ..      18     148 .. 0.97

  Alignments for each domain:
  == domain 1  score: 103.2 bits;  conditional E-value: 8.4e-34
                                       EEEEEESS-HHHHHHHHHHHTTSBHHHHHHHHHT..-SST..........................THHHHHHHHHH CS
                     Ribosomal_L22   1 akgsnlrvsfkklrevarlIrgmkveeAlkyLkf..skkk..........................aakfvlklLkn 49 
                                       a+gs+l++s+k  re+ r I+gmk++ A++yL++  + k+                          +a+++lk+++n
  gi|298674797|ref|YP_003726547.1|  18 AMGSELHISPKTSRELSREIKGMKASAAKQYLENviQFKQavpmkshndscghrkgsmaegrfpvkVAQEFLKVIQN 94 
                                       6899*******************************866779************************************ PP

                                       HHHHHH..HT-GGGEEEEEEEEEEEEEEEEEEEESTTEEEEEEEEEEEEEEEEE CS
                     Ribosomal_L22  50 aeanaelkgldvdslvIeeiqvnkgpklkrrtyrArGrinpirkspchievvlk 103
                                       ae+nae+kgl+++++ I++i ++kg+ ++++++rArGr++p + +++++e++l+
  gi|298674797|ref|YP_003726547.1|  95 AENNAEYKGLEPENMKIAHISAKKGRVIQGMRPRARGRATPENTETVNLEMILS 148
                                       ****************************************************95 PP

>> Acyl-thio_N  Acyl-ATP thioesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.22     2e+03      31      47 ..      31      47 ..       7      76 .. 0.58
   2 ?   11.8   0.1   2.9e-05      0.26      21      71 ..      94     144 ..      72     150 .] 0.79

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.22
                       Acyl-thio_N 31 gkesldlrGikakpass 47
                                      ++ s +++G+ka  a  
  gi|298674797|ref|YP_003726547.1| 31 RELSREIKGMKASAAKQ 47
                                      44455555555544442 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 2.9e-05
                       Acyl-thio_N  21 eakaskkl.gegkesldlrGikakpasssgalkvkanaqavpkvngtkvgla 71 
                                       +a+++ +  g ++e++++  i+ak++ + ++++ +a+ +a p  n+++v+l+
  gi|298674797|ref|YP_003726547.1|  94 NAENNAEYkGLEPENMKIAHISAKKGRVIQGMRPRARGRATPE-NTETVNLE 144
                                       33333333599*******************************9.99998885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 919.80
//
Query:       gi|298674798|ref|YP_003726548.1|  [L=137]
Description: 30S ribosomal protein S19 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.9e-23   80.3   0.3      1e-22   79.8   0.3    1.3  1  Ribosomal_S19  Ribosomal protein S19
  ------ inclusion threshold ------
       0.14   11.2   0.0       0.14   11.2   0.0    1.1  1  Citrate_synt   Citrate synthase, C-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_S19  Ribosomal protein S19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.8   0.3   1.2e-26     1e-22       1      81 []      44     120 ..      44     120 .. 0.96

  Alignments for each domain:
  == domain 1  score: 79.8 bits;  conditional E-value: 1.2e-26
                                       .HHHSS.TTCCCHHHHHHHHHHTS-----EEES-TT-B--GGGTT-EEEEE-SSSEEEEE--CCCTTSBCGGGT-SS CS
                     Ribosomal_S19   1 rslkkg.pfvqesllkkvrkakaekkkevikthsRdstIlPemvgltvgVynGktfvpveikeemvGhkLgEFspTr 76 
                                       rs+++g +  q+++l+++r+ +     e ++th R+++IlPemvg  ++VynG  fv++++ +em Gh+ gE++++r
  gi|298674798|ref|YP_003726548.1|  44 RSIRRGfTENQKKVLQQFRDGE-----ESVRTHDRAMVILPEMVGKSIEVYNGTRFVKIDVAPEMLGHRVGEYAMSR 115
                                       799999999999****999887.....689*********************************************** PP

                                       ----S CS
                     Ribosomal_S19  77 kpvkh 81 
                                        +vkh
  gi|298674798|ref|YP_003726548.1| 116 GVVKH 120
                                       ****9 PP

>> Citrate_synt  Citrate synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   1.6e-05      0.14      12      82 ..       6      69 ..       1      98 [. 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.6e-05
                                      SEEEETTTTEEEETTEEHHHHHHHHS-HHHHHHHHHHSS---HHHHHHHHHHHHCTT.S--HHHHHHHHCSS CS
                      Citrate_synt 12 isevdgekgelrYRGydieeLaeekssfeevaylLltgelPtkeelkefkeelaear.klpekvlealealp 82
                                       ++v ++kge  +RG ++eeL   + ++ee a lL     P+ ++ +++++ ++e++ k+ +++++  e+++
  gi|298674798|ref|YP_003726548.1|  6 STRVPKRKGEFKFRGKTLEELK--ELTIEEFAELL-----PS-SQRRSIRRGFTENQkKVLQQFRDGEESVR 69
                                      5777788999**********77..79*********.....85.88888888888854255555544333555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.34s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 797.37
//
Query:       gi|298674799|ref|YP_003726549.1|  [L=237]
Description: 50S ribosomal protein L2 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-44  150.5   0.5      4e-44  149.8   0.5    1.3  1  Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
    9.7e-15   54.3   0.3    3.4e-14   52.5   0.0    2.1  2  Ribosomal_L2    Ribosomal Proteins L2, RNA binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.8   0.5   4.5e-48     4e-44       1     120 [.      90     220 ..      90     225 .. 0.94

  Alignments for each domain:
  == domain 1  score: 149.8 bits;  conditional E-value: 4.5e-48
                                       SSSS-EBSSSS-TTB-BBSE-SSTTS--SSS-SSSB-EEBB-B.SSEEEEEETTS-EEEEETTSBEBES-BS-TTCT CS
                    Ribosomal_L2_C   1 kvGnvlplknipeGtivhnielkpgkggklarsaGtyaqvvakegkkvtvklpSgevrkvssecrAtiGvvsngehk 77 
                                       k+Gn+lpl++ipeG+ ++n+e+kp++gg + rs+Gtya++v++e+ k++v +pSge ++++ +c AtiG+v++g++ 
  gi|298674799|ref|YP_003726549.1|  90 KPGNTLPLSDIPEGVPICNVESKPNDGGCFGRSSGTYATLVSHERGKAIVEMPSGELKWFNPKCKATIGIVAGGGRV 166
                                       68*************************************************************************** PP

                                       T----STTHHHHT.....TBS----SSSS-TTTSSS--SS....SS..--SSSS CS
                    Ribosomal_L2_C  78 ekklgkAgrkrwl.....grrpkvrGvamnpvdHphGGGe....Gk..tksrka 120
                                       +k+++kAg+k+ +     +++p+v Gvamn+vdHp+GGG+    Gk  t++r+ 
  gi|298674799|ref|YP_003726549.1| 167 DKPFLKAGKKYNKlkssaQKYPRVSGVAMNSVDHPFGGGNrkhpGKptTVGRNR 220
                                       ****************************************77776665555655 PP

>> Ribosomal_L2  Ribosomal Proteins L2, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.5   0.0   3.8e-18   3.4e-14       1      75 [.      11      81 ..      11      83 .. 0.92
   2 ?   -3.1   0.3      0.88   7.9e+03       1      11 [.     217     228 ..     217     235 .. 0.65

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 3.8e-18
                                      TB-TT.--BSSTT--------EE-B--S---SS--EEEEEEE--TT-SS-EEEEEETTTEEEEEE--SS--SS-EE CS
                      Ribosomal_L2  1 Grnns.gritvrhrggGhkkkyrlidfkrnkekvkgkVveieyDpgRsApiAlvkyedgekryiiapeglkvGdtv 75
                                      Gr+ + +r+++++++     k + i     +e++ g+V ei +Dp RsApiA v++e+g++r+++ peg++vG+++
  gi|298674799|ref|YP_003726549.1| 11 GRGGPnYRAPSHKYKA--SLKHPNIGE---NETLYGTVTEITHDPSRSAPIAKVEFENGDERLVLVPEGISVGEKL 81
                                      999999**********..778888888...56788**************************************986 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.88
                                       TB-TT.--BSST CS
                      Ribosomal_L2   1 Grnns.gritvr 11 
                                       Grn++ gr   +
  gi|298674799|ref|YP_003726549.1| 217 GRNRPaGRKVGH 228
                                       777777776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1457.42
//
Query:       gi|298674800|ref|YP_003726550.1|  [L=82]
Description: 50S ribosomal protein L23 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-17   63.2   2.9    5.4e-17   61.9   2.9    1.5  1  Ribosomal_L23    Ribosomal protein L23
  ------ inclusion threshold ------
      0.018   15.7   0.0      0.021   15.5   0.0    1.1  1  Asp_protease_2   Aspartyl protease
      0.045   13.9   0.1      0.061   13.5   0.1    1.2  1  PRE_C2HC         Associated with zinc fingers
      0.047   14.2   0.1      0.053   14.1   0.1    1.2  1  gag-asp_proteas  gag-polyprotein putative aspartyl protease


Domain annotation for each model (and alignments):
>> Ribosomal_L23  Ribosomal protein L23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.9   2.9   1.2e-20   5.4e-17       2      65 ..       3      67 ..       2      75 .. 0.86

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 1.2e-20
                                      SEEEE--SHHHHHHHTTE.EEEEE-SS-THHHHHHHHHHHHT--EEEEEEEEE--EBE.SSSSSE CS
                     Ribosomal_L23  2 vilkPvitEkstklaeknkyvFeVakdanKleikkaveklFgVkVekVntlnvkgkkk.rvgrkv 65
                                      vi +P +tEk+++l+e+nk+ F V+ +anK++ikk +e+++g  V+kV+t+   + +k  v +++
  gi|298674800|ref|YP_003726550.1|  3 VIENPFVTEKAMMLMEDNKLQFIVDTRANKHQIKKELEEMYGFSVNKVHTMTTMKGTKkAVVKFE 67
                                      7899***********************************************87665551444444 PP

>> Asp_protease_2  Aspartyl protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   4.6e-06     0.021       6      50 ..      18      62 ..      13      77 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.6e-06
                    Asp_protease_2  6 nGkpvrfllDTGasttlispelaeklglkvreseltvrvsgagge 50
                                      ++ +++f++DT a+   i +el e  g +v + ++ ++++g  ++
  gi|298674800|ref|YP_003726550.1| 18 EDNKLQFIVDTRANKHQIKKELEEMYGFSVNKVHTMTTMKGTKKA 62
                                      57899***************************9754555544444 PP

>> PRE_C2HC  Associated with zinc fingers
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   1.4e-05     0.061       1      24 [.      32      56 ..      32      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.4e-05
                          PRE_C2HC  1 kaqIeeaLkkh.gfevknihnmrkr 24
                                      k+qI+++L++  gf+v+++h+m++ 
  gi|298674800|ref|YP_003726550.1| 32 KHQIKKELEEMyGFSVNKVHTMTTM 56
                                      69******9855**********987 PP

>> gag-asp_proteas  gag-polyprotein putative aspartyl protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   1.2e-05     0.053       6      53 ..      18      62 ..      13      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.2e-05
                                      TTEEEEEEEETT-SS-EEEHHHHHHTTGGGGEB..TT--EE-TTSTT- CS
                   gag-asp_proteas  6 ngkpvkflvDTGAsstiiseelaerlglsrkedkgkvevktangevea 53
                                       +++++f+vDT A++  i++el e  g s ++     +++t++g+++a
  gi|298674800|ref|YP_003726550.1| 18 EDNKLQFIVDTRANKHQIKKELEEMYGFSVNKV---HTMTTMKGTKKA 62
                                      6789**************************996...567777776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1396  (0.0778627); expected 358.6 (0.02)
Passed bias filter:                      733  (0.0408835); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 509.08
//
Query:       gi|298674801|ref|YP_003726551.1|  [L=253]
Description: 50S ribosomal protein L4P [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-47  160.2   1.2    5.4e-47  160.0   1.2    1.0  1  Ribosomal_L4    Ribosomal protein L4/L1 family
  ------ inclusion threshold ------
      0.088   11.7   0.0       0.12   11.4   0.0    1.1  1  Glyco_hydro_52  Glycosyl hydrolase family 52
       0.11   12.6   0.1       0.19   11.8   0.1    1.3  1  GutM            Glucitol operon activator protein (GutM)


Domain annotation for each model (and alignments):
>> Ribosomal_L4  Ribosomal protein L4/L1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.0   1.2   9.1e-51   5.4e-47       1     190 [.      17     249 ..      17     251 .. 0.93

  Alignments for each domain:
  == domain 1  score: 160.0 bits;  conditional E-value: 9.1e-51
                                       EEE-HHHHSS---HHHHHHHHHHHHHSS-EE-----.-TTTSS---S-SS-SSSSSS---S-TT.......STTSTT CS
                      Ribosomal_L4   1 veLspkvFaapirrdlihravvaylanrrqgtastk.arsevsgsgrklwkQKGtGrARvgsir.......spiarg 69 
                                       ++L p+vF++ +r+dli++av++ +anr q+++    a+  +s+   ++++  G+G A v+++        +p+ +g
  gi|298674801|ref|YP_003726551.1|  17 IDL-PQVFNESLRPDLIKKAVLSSQANRLQPYGPYArAGLNTSA--VSWGS--GRGVAMVPRLAnssraarVPQSVG 88 
                                       578.9****************************98878888888..6****..**********99************ PP

                                       ---SS---S.EEHHHHHHHHHHHHHHHHHHHHHHHTT-EEEES--.-..-S.........S--HHHHHHHHHHTT-. CS
                      Ribosomal_L4  70 GgvahgpkperdystklnkKvrrlAlrsaLsakakqglllvvdnl.e.ple.........esktkelvellkklgl. 134
                                       G++ah+pkpe d ++k+nkK+++lA+rsa++a+++ +l + ++++ + +l+           ktk++v+++k  gl 
  gi|298674801|ref|YP_003726551.1|  89 GRRAHPPKPETDRTEKINKKEKKLAIRSAIAATTNPELAKKRGHVfDvELPvvaddelenLTKTKDVVNFFKTAGLy 165
                                       *******************************************5545445577999999999***********8888 PP

                                       .........................TTSSEEEEESSSSCHHHHHHTT-TTEEEEESTT--CHHHHHSSE....EEEE CS
                      Ribosomal_L4 135 .........................ksksvLivvsekdenlvlaarnlpgvevieveslnvydllkadk....vvit 182
                                                                ++ksvLivvs+ ++ +++aarnlpgvev+++ sln++ l+++++    +v+t
  gi|298674801|ref|YP_003726551.1| 166 kdvlrakegkhvragkgksrgrkyrQKKSVLIVVSD-NNSVIKAARNLPGVEVATIGSLNAELLAPGTHagrlTVWT 241
                                       88888899999999999999999999********98.99************************************** PP

                                       HHHHHHHH CS
                      Ribosomal_L4 183 ksavekle 190
                                       +sa+++le
  gi|298674801|ref|YP_003726551.1| 242 ESAISSLE 249
                                       *****998 PP

>> Glyco_hydro_52  Glycosyl hydrolase family 52
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   1.9e-05      0.12      83     206 ..     102     226 ..      97     241 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.9e-05
                    Glyco_hydro_52  83 tdtwragdltfrilspfesvpdPaaadeeelkaalvPavlaeltldNtegdeerealFgleg.sdplsdlregkllg 158
                                       t++++ ++ ++ i s++ +  +P+ a++    + +   v+a+ +l+N ++++++  +F   g  + +  ++egk + 
  gi|298674801|ref|YP_003726551.1| 102 TEKINKKEKKLAIRSAIAATTNPELAKKRGHVFDVELPVVADDELENLTKTKDVVNFFKTAGlYKDVLRAKEGKHVR 178
                                       688899999***************9999999999988888999*******************978888889999999 PP

                    Glyco_hydro_52 159 vaqgrktgiavteeegveealdfd..vleaafeeenkefllgktgallle 206
                                       +++g++ g    ++++v  +++ +  v++aa   + +   +++ g+l  e
  gi|298674801|ref|YP_003726551.1| 179 AGKGKSRGRKYRQKKSVLIVVSDNnsVIKAAR--NLPGVEVATIGSLNAE 226
                                       99999999998888877655443334666665..6666777777777665 PP

>> GutM  Glucitol operon activator protein (GutM)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   3.2e-05      0.19      35      74 ..     177     218 ..     158     222 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.2e-05
                              GutM  35 gkvaiGrkkgrf..ragvivllavdedgiivearvmkGvTvf 74 
                                        + + G+++gr   +++++++++ d++  i++ar + Gv v 
  gi|298674801|ref|YP_003726551.1| 177 VRAGKGKSRGRKyrQKKSVLIVVSDNNSVIKAARNLPGVEVA 218
                                       355667777755557889999999999***********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1513.78
//
Query:       gi|298674802|ref|YP_003726552.1|  [L=337]
Description: 50S ribosomal protein L3 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.7e-88  294.8   0.4    1.2e-87  294.3   0.4    1.2  1  Ribosomal_L3  Ribosomal protein L3


Domain annotation for each model (and alignments):
>> Ribosomal_L3  Ribosomal protein L3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  294.3   0.4   6.5e-92   1.2e-87       2     369 .]       2     337 .]       1     337 [] 0.94

  Alignments for each domain:
  == domain 1  score: 294.3 bits;  conditional E-value: 6.5e-92
                                       X.S.SXXXXSSXCCCTTXSBXSXSSXXXSX.XXSBTTTTTXBSEEEEEEEEEEEEEEECHHTTSCCCCCEEEEEEEE CS
                      Ribosomal_L3   2 shrkfeaprhgslGflprkRaerergkvksfPkddtskpvkltaflGyKaGmthiVrevdkpgskldkkevveavtv 78 
                                       +    ++p +gsl ++prkRa+++ +k++s+P+ d +   kl+ f+GyK Gmth++  +d  +s ++++e+ ++ tv
  gi|298674802|ref|YP_003726552.1|   2 P--DVGRPNRGSLAYSPRKRAKSHIPKFRSWPNLDGN--PKLQDFAGYKVGMTHVIMIDDTKNSVTEGAEISVPATV 74 
                                       5..4589****************************99..789*********************************** PP

                                       EEC--EEEEEEEEEEEETTEEEEEEEEESSS.SHHHHCCCSTSTTTSSSSSSHCCCCHCSSCCCCCCHHHHHHHHHH CS
                      Ribosomal_L3  79 vetppmvivgvvgyvetprGlrslktvwaehlseevkrrlyknwykskkkaftkyskkyeskdvkklieadleeikk 155
                                       vetp + ++++++y + ++G++++ + wa +l  +v r++                k  +++d++k++e+  + i +
  gi|298674802|ref|YP_003726552.1|  75 VETPDIGVASIRAYKDSEYGKKPVAEAWATDLDADVLRKV----------------KSPDNHDTEKSLEKMESLIDD 135
                                       **************************************99................445677888888875444544 PP

                                       .SCSCEEEEEEEECCCSS-SCCSSHHEEEEECHCSCHHHHHHHHHHCCTCEEECCCCS-TTSEEEEEEEE---EEE- CS
                      Ribosomal_L3 156 .easvvrviahtvirktkslaqKkahllEiqvngGtiaekldfarealektvavaavFrqgeliDvigvtkGkGfeG 231
                                             rv+++t   +++++ +Kk++++E+ v g  + ek+++a++ l  ++ +++vF++g ++D++++t GkG++G
  gi|298674802|ref|YP_003726552.1| 136 gTVKDLRVVTYTLPSNLTGVPKKKSDIMETGVSGSDMKEKFEYAKSILGTKISITDVFNPGGIVDIAAITTGKGTQG 212
                                       134569*********************************************************************** PP

                                       HHHHCT----STTTSSS..SSS-S-SS-SSSSS--TTS--SEEESCCEEEEEEEEEEEEETTTSSTTTSSTTT.SS. CS
                      Ribosomal_L3 232 vvkRWgvkklprkthrg..lRkvaaigawdparVsstvaraGqkGyhhRtelnkkiyrigkgedaknastefdltek 306
                                       +vkRWg++  + k++r    R+v+++g+w+pa++s+ v++ Gq+Gyh+Rte+nk+i+++ +              + 
  gi|298674802|ref|YP_003726552.1| 213 PVKRWGIQIAKHKHNRAgsARQVGTLGPWHPAHISWRVPQMGQMGYHQRTEYNKRIIKVSN-------------EGS 276
                                       ****************999****************************************99.............578 PP

                                       .SS.TTTCTTCB..TSCEEEEES--SSSTTEEEEEEE-SSGGGSCCCSS-EEEEEE-TTCTSS CS
                      Ribosomal_L3 307 eitPmGGfvhyGevkndfilvkGsvpGpkkrlvklrkslltqtsrkaeeevslkfidtaskfg 369
                                       ei+P+GGf +yG v+++++l+kGsvpGp krlv++r+ ++++ s  +e+++   +++t+sk+g
  gi|298674802|ref|YP_003726552.1| 277 EINPDGGFLNYGLVRGNYVLIKGSVPGPSKRLVRFRDPIRSKVSSTKEPQI--VHLNTQSKQG 337
                                       9************************************************99..7889999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 2005.34
//
Query:       gi|298674803|ref|YP_003726553.1|  [L=204]
Description: indolepyruvate ferredoxin oxidoreductase subunit beta [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.2e-38  130.1   0.0    1.1e-37  129.8   0.0    1.0  1  POR       Pyruvate ferredoxin/flavodoxin oxidoreductase


Domain annotation for each model (and alignments):
>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.8   0.0   6.1e-42   1.1e-37       1     177 []      15     191 ..      15     191 .. 0.95

  Alignments for each domain:
  == domain 1  score: 129.8 bits;  conditional E-value: 6.1e-42
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEE CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglk 77 
                                       GGqG+++a+ i++k+ + +G+ v a++++g+++rGg+++ hvri+ +   ++i+ ++ad+l+al++ ++ +++++l 
  gi|298674803|ref|YP_003726553.1|  15 GGQGTILASDIIGKSSVLEGLPVRAAETHGMAQRGGSVINHVRIGTD-LGSMIPDQGADVLLALEPVEAIRYINHLS 90 
                                       9**********************************************.8999999***********9999******* PP

                                       EEEEEEEECTCGTT-CCHHHCTS-HHHHHHH.....T-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHTS-HHH CS
                               POR  78 pggiiiynseelkpdelkkakeeerelkerl.....gvrvygvdatkiakeiggneraaNtvmlGalaallglplea 149
                                       ++gi+++n++ + p +++ ++  ++++ e       +++vy++da+++a ++g  +  +N+vm+Ga++  l ++ + 
  gi|298674803|ref|YP_003726553.1|  91 ENGIVVLNTKPVYPVTVTSSDQ-YPDVSEIIntlkkKYEVYPLDASELAIKAGH-PQSMNVVMVGAVSSYLPISKNR 165
                                       *********9999999988775.77777666899***************99887.********************** PP

                                       HHHHHHCCS-CH.HHHHHHHHHHHHHHH CS
                               POR 150 leeaikkrfpkkkeviekNlkafragye 177
                                       lee ik+ +p k   ++ Nlkaf++g+e
  gi|298674803|ref|YP_003726553.1| 166 LEECIKELVPPK--TVDINLKAFELGRE 191
                                       **********95..9***********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1223.15
//
Query:       gi|298674804|ref|YP_003726554.1|  [L=605]
Description: indolepyruvate ferredoxin oxidoreductase subunit alpha [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.4e-28   98.0   0.1    9.5e-28   96.9   0.1    1.6  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    9.3e-12   45.2   0.0    1.6e-11   44.4   0.0    1.3  1  POR_N         Pyruvate flavodoxin/ferredoxin oxidoreductase, 
    2.9e-09   36.3  11.7    0.00012   21.7   2.2    3.2  3  Fer4          4Fe-4S binding domain
    2.9e-06   27.3   7.9    8.6e-06   25.8   7.9    1.9  1  Fer4_21       4Fe-4S dicluster domain
    1.4e-05   25.2  10.6    3.8e-05   23.8  10.6    1.8  1  Fer4_9        4Fe-4S dicluster domain
    2.1e-05   24.3  15.8    0.00047   20.1   2.5    3.4  3  Fer4_2        4Fe-4S binding domain
    5.8e-05   23.1  10.4    0.00018   21.6  10.4    1.8  1  Fer4_10       4Fe-4S dicluster domain
    0.00024   21.4  12.6     0.0068   16.8   2.6    2.8  2  Fer4_4        4Fe-4S binding domain
     0.0023   18.5  13.6      0.051   14.2  12.9    2.8  2  Fer4_7        4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.011   15.8  17.2      0.016   15.3   2.2    3.5  3  Fer4_6        4Fe-4S binding domain
        0.1   13.2   8.5        2.4    8.7   0.9    2.6  2  Fer4_17       4Fe-4S dicluster domain
       0.42   11.5   7.5       0.91   10.4   0.9    2.7  2  Fer4_22       4Fe-4S dicluster domain
       0.55   11.0  14.6       0.61   10.9   1.8    3.4  3  Fer4_15       4Fe-4S single cluster domain
          5    8.1  12.9        2.2    9.3   2.0    2.7  4  Fer4_16       4Fe-4S double cluster binding domain
        8.1    7.6  13.9         13    7.0   4.5    3.1  2  Fer4_3        4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.9   0.1   7.9e-31   9.5e-28       1     151 [.     390     529 ..     390     531 .. 0.94

  Alignments for each domain:
  == domain 1  score: 96.9 bits;  conditional E-value: 7.9e-31
                                       ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEE CS
                      TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpit 76 
                                       diGc+tl      +v  ++ +++  ++ +mG ++++A+G+    ++r+v + +GD++fl++ ++ l +av+++++it
  gi|298674804|ref|YP_003726554.1| 390 DIGCYTL------GV--QGGTVD--TTLCMGASISVASGIYQSGEKRPVCCAIGDSTFLHTgINSLLNAVYNKADIT 456
                                       7999999......33..667777..89***************77899****************************** PP

                                       EEEEE-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEEE CS
                      TPP_enzyme_C  77 vvvlnNegygmtggqqepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpali 151
                                       v +l+N++++mtg+q++p  gk+ + ++   + +v+f +l+++lGa+ + +v+++d +   +++k+a e +g++++
  gi|298674804|ref|YP_003726554.1| 457 VTILDNRVTAMTGHQPNPGMGKTATYED---TLEVSFDQLCRGLGAEfVEVVDPYDYDSAVDVFKRAKEFDGTSVV 529
                                       **********************999988...9***************888************************98 PP

>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.0   1.3e-14   1.6e-11       2     180 ..      16     189 ..      15     228 .. 0.76

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 1.3e-14
                                       HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCC CS
                             POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmien 78 
                                       + i++g +vi++YP TPssei+++l+++  + +    +v    +E  a+++++GA+++G+ ++++    Gl  + + 
  gi|298674804|ref|YP_003726554.1|  16 GIIEGGGQVITGYPGTPSSEIVDTLSSMD-DRD---FYVEWSVNEKVAMEVAAGASMSGVNSVVTMKHVGLNVAADP 88 
                                       67888889**************9999875.444...37888889***************************999877 PP

                                       HHHHHHTT-.-EEEEEEEEE-STTBEEEEE--TTCHHHHS---E.EEE-SSHHHHHHHHHHHHHHHHHCTSEEEEEE CS
                             POR_N  79 lglaageel.PvvivvvaRalpstglsirtdqsDlmaardtgli.vlasenvqeafdlalvAfnlAekvrvPvivlf 153
                                       l+  a + +   +iv+va   ++++    +  +D     ++ li  l +++ qea d++  Af  + k  +Pvi   
  gi|298674804|ref|YP_003726554.1|  89 LMTLAYMGVkGGMIVIVA---DDPACHSSQNEQDTRRYSQFSLIpCLDPSTPQEAKDMIPYAFEFSSKHGIPVIF-R 161
                                       665555554155555554...566666677778888888888774799************************985.6 PP

                                       EHHHH.HEEEEEEC-SGG..GS-----S CS
                             POR_N 154 Dgfllshevekvelpdee.delklikek 180
                                         +++sh  +++el++++ ++ + + ek
  gi|298674804|ref|YP_003726554.1| 162 STTRISHGKSDIELLPVNkEKPQPEFEK 189
                                       688889***********92222222222 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       4.3   5.2e+03       3      10 ..     403     410 ..     402     410 .. 0.85
   2 !   19.2   1.3   6.3e-07   0.00076       1      15 [.     549     563 ..     549     565 .. 0.92
   3 !   21.7   2.2     1e-07   0.00012       5      23 ..     582     600 ..     580     601 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.3
                                       EETTTSSS CS
                              Fer4   3 ideekCig 10 
                                       +d+ +C+g
  gi|298674804|ref|YP_003726554.1| 403 VDTTLCMG 410
                                       899***97 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 6.3e-07
                                       EEEETTTSSS-THHH CS
                              Fer4   1 vvideekCigCGaCv 15 
                                       ++ideekC+gC++Cv
  gi|298674804|ref|YP_003726554.1| 549 YTIDEEKCTGCKQCV 563
                                       58************9 PP

  == domain 3  score: 21.7 bits;  conditional E-value: 1e-07
                                       TTTSSS-THHHHHSTTTEE CS
                              Fer4   5 eekCigCGaCvevCPvgAI 23 
                                        ++C+gCG C++ C ++AI
  gi|298674804|ref|YP_003726554.1| 582 NSMCTGCGVCAQLCKFDAI 600
                                       579***************9 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   7.9   7.2e-09   8.6e-06       2      56 ..     550     599 ..     543     603 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 7.2e-09
                           Fer4_21   2 ridedkCigCgkCli.aCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedc 56 
                                       +ide+kC gC++C+   C+     aie+da+ + + +++ C+GC +C++ C   d+
  gi|298674804|ref|YP_003726554.1| 550 TIDEEKCTGCKQCVYfGCP-----AIEFDASLKKARINSMCTGCGVCAQLCKF-DA 599
                                       59***********761688.....9******99999***************86.44 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8  10.6   3.1e-08   3.8e-05       1      51 []     555     600 ..     555     600 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 3.1e-08
                            Fer4_9   1 kCtgCgaCvea.CpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       kCtgC++Cv+  Cpa  +  + ++  ++        C+gCg C++ C+ +ai
  gi|298674804|ref|YP_003726554.1| 555 KCTGCKQCVYFgCPAIEFDASLKKARINS------MCTGCGVCAQLCKFDAI 600
                                       7*******9988******99999888886......5***********99887 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       1.7     2e+03       7      14 ..     362     369 ..     358     370 .. 0.82
   2 !   20.1   2.5   3.9e-07   0.00047       2      22 .]     548     569 ..     547     569 .. 0.92
   3 !   10.5   2.5   0.00043      0.51       9      20 ..     584     595 ..     578     597 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.7
                            Fer4_2   7 tdrCigCg 14 
                                       +++C gC+
  gi|298674804|ref|YP_003726554.1| 362 PAMCPGCS 369
                                       789****5 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 3.9e-07
                            Fer4_2   2 pvvvdtdrCigCgaCvsa.CPa 22 
                                       p+ +d+++C+gC+ Cv   CPa
  gi|298674804|ref|YP_003726554.1| 548 PYTIDEEKCTGCKQCVYFgCPA 569
                                       5789************999**8 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00043
                            Fer4_2   9 rCigCgaCvsaC 20 
                                       +C+gCg C + C
  gi|298674804|ref|YP_003726554.1| 584 MCTGCGVCAQLC 595
                                       8*********99 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6  10.4   1.5e-07   0.00018       3      55 ..     550     595 ..     549     596 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.5e-07
                           Fer4_10   3 vidddtCirCgkCvka.CPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                        id+++C++C++Cv + CPa       ++++   ++ r+  + Ctgcg C++ C
  gi|298674804|ref|YP_003726554.1| 550 TIDEEKCTGCKQCVYFgCPA-------IEFDASLKKARI-NSMCTGCGVCAQLC 595
                                       599************99***.......777777777777.789*********99 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   2.6   5.7e-06    0.0068       2      15 ..     554     568 ..     553     574 .. 0.92
   2 !    8.8   2.5    0.0021       2.5       3      16 ..     584     597 ..     581     598 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.7e-06
                            Fer4_4   2 erCigCgsCvaa.CP 15 
                                       e+C+gC++Cv++ CP
  gi|298674804|ref|YP_003726554.1| 554 EKCTGCKQCVYFgCP 568
                                       89**********999 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0021
                            Fer4_4   3 rCigCgsCvaaCPq 16 
                                        C+gCg+C   C++
  gi|298674804|ref|YP_003726554.1| 584 MCTGCGVCAQLCKF 597
                                       6*******999976 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   3.3   0.00052      0.62      29      49 ..     547     568 ..     515     570 .. 0.77
   2 !   14.2  12.9   4.3e-05     0.051       1      52 []     555     599 ..     555     599 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00052
                            Fer4_7  29 ekveidpekClgCgaCva.vCP 49 
                                         ++id+ekC+gC++Cv   CP
  gi|298674804|ref|YP_003726554.1| 547 NPYTIDEEKCTGCKQCVYfGCP 568
                                       44799***********985676 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 4.3e-05
                            Fer4_7   1 rCigCgaCvaa.CpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       +C+gC++Cv   Cp  aie+d + ++     ++i  ++C+gCg+C++ C ++a
  gi|298674804|ref|YP_003726554.1| 555 KCTGCKQCVYFgCP--AIEFDASLKK-----ARI-NSMCTGCGVCAQLCKFDA 599
                                       7********755**..9999998544.....444.589***********9987 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.2       3.4   4.1e+03       7      12 ..     363     368 ..     362     370 .. 0.78
   2 ?   15.3   2.2   1.3e-05     0.016       3      21 ..     550     569 ..     550     574 .. 0.85
   3 ?    8.9   2.3    0.0013       1.6       7      24 .]     583     600 ..     579     600 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.4
                            Fer4_6   7 dkCigC 12 
                                         C gC
  gi|298674804|ref|YP_003726554.1| 363 AMCPGC 368
                                       68**** PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.3e-05
                            Fer4_6   3 eidpdkCigCgdC.vrvCPe 21 
                                       +id++kC+gC  C +  CP+
  gi|298674804|ref|YP_003726554.1| 550 TIDEEKCTGCKQCvYFGCPA 569
                                       79***********6666996 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0013
                            Fer4_6   7 dkCigCgdCvrvCPegai 24 
                                       + C+gCg C+  C ++ai
  gi|298674804|ref|YP_003726554.1| 583 SMCTGCGVCAQLCKFDAI 600
                                       78***********99998 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   1.4    0.0045       5.3      44      57 ..     554     568 ..     528     570 .. 0.78
   2 ?    8.7   0.9     0.002       2.4       2      14 ..     585     597 ..     575     604 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0045
                           Fer4_17  44 slCieCgeCe.rkCP 57 
                                       ++C++C++C+   CP
  gi|298674804|ref|YP_003726554.1| 554 EKCTGCKQCVyFGCP 568
                                       79*******988898 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.002
                           Fer4_17   2 CiqCgyClpeCps 14 
                                       C++Cg C++ C +
  gi|298674804|ref|YP_003726554.1| 585 CTGCGVCAQLCKF 597
                                       7888888887765 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.9     0.079        94      75      90 ..     549     564 ..     522     570 .. 0.80
   2 ?   10.4   0.9   0.00076      0.91      77      93 ..     580     596 ..     571     599 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.079
                           Fer4_22  75 ekfgesgCvGCgRCie 90 
                                        +++e++C+GC  C+ 
  gi|298674804|ref|YP_003726554.1| 549 YTIDEEKCTGCKQCVY 564
                                       4568999*******86 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00076
                           Fer4_22  77 fgesgCvGCgRCieacp 93 
                                         +s+C+GCg C + c+
  gi|298674804|ref|YP_003726554.1| 580 RINSMCTGCGVCAQLCK 596
                                       45789***********7 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       7.2   8.6e+03       2      12 ..     402     412 ..     402     416 .. 0.81
   2 ?   10.9   1.8   0.00051      0.61       2      17 ..     550     565 ..     550     583 .. 0.78
   3 ?    5.3   3.5     0.027        33       7      19 ..     584     596 ..     581     604 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 7.2
                           Fer4_15   2 vvDrdaCigcg 12 
                                       +vD ++C+g  
  gi|298674804|ref|YP_003726554.1| 402 TVDTTLCMGAS 412
                                       69*****9965 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00051
                           Fer4_15   2 vvDrdaCigcglCvae 17 
                                       ++D+++C+gc +Cv  
  gi|298674804|ref|YP_003726554.1| 550 TIDEEKCTGCKQCVYF 565
                                       69***********975 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.027
                           Fer4_15   7 aCigcglCvaeap 19 
                                        C+gcg+C+++++
  gi|298674804|ref|YP_003726554.1| 584 MCTGCGVCAQLCK 596
                                       6**********95 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   3.9      0.27   3.2e+02      51      65 ..     553     568 ..     526     570 .. 0.66
   2 ?    2.2   2.9       0.3   3.5e+02       1      14 [.     555     569 ..     555     584 .. 0.71
   3 ?    8.4   1.9    0.0035       4.2      46      66 ..     577     597 ..     570     598 .. 0.74
   4 ?    9.3   2.0    0.0019       2.2       2      20 ..     585     603 ..     584     605 .] 0.87

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.27
                           Fer4_16  51 qeaitgCdiCqdv.CP 65 
                                       +e++tgC+ C+   CP
  gi|298674804|ref|YP_003726554.1| 553 EEKCTGCKQCVYFgCP 568
                                       5667788888754355 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.3
                           Fer4_16   1 rCgtCgkCa.evCPt 14 
                                       +C++C++C+   CP+
  gi|298674804|ref|YP_003726554.1| 555 KCTGCKQCVyFGCPA 569
                                       599999997345886 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0035
                           Fer4_16  46 ekckkqeaitgCdiCqdvCPa 66 
                                       +k  ++  +tgC++C++ C +
  gi|298674804|ref|YP_003726554.1| 577 KKARINSMCTGCGVCAQLCKF 597
                                       445556789999999999966 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.0019
                           Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                       C++Cg Ca+ C  +ai e 
  gi|298674804|ref|YP_003726554.1| 585 CTGCGVCAQLCKFDAIVEV 603
                                       99*********99999876 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   1.9     0.056        67       1       9 [.     556     564 ..     556     565 .. 0.92
   2 ?    7.0   4.5     0.011        13       1      15 []     585     599 ..     585     599 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.056
                            Fer4_3   1 CtgCgaCve 9  
                                       CtgC +Cv 
  gi|298674804|ref|YP_003726554.1| 556 CTGCKQCVY 564
                                       *******95 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.011
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       CtgCg C + C  +A
  gi|298674804|ref|YP_003726554.1| 585 CTGCGVCAQLCKFDA 599
                                       ***********8876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (605 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.72u 0.32s 00:00:01.04 Elapsed: 00:00:00.51
# Mc/sec: 3539.88
//
Query:       gi|298674805|ref|YP_003726555.1|  [L=448]
Description: gamma-glutamyl phosphate reductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.4e-15   54.2   0.0      1e-12   47.4   0.0    2.2  2  Aldedh    Aldehyde dehydrogenase family


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4   0.0   5.7e-17     1e-12      16     296 ..      12     286 ..       2     297 .. 0.82
   2 !    4.7   0.0   0.00049       8.7     374     429 ..     325     380 ..     305     389 .. 0.89

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 5.7e-17
                                       TCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HHHHHHHHHH CS
                            Aldedh  16 tgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletGkplaearaevee 92 
                                        ++   k ++ ++++ ++a++a +ea +  ++  ++e ++  + a +l+ee k  l+++++       ++ ++ +e 
  gi|298674805|ref|YP_003726555.1|  12 AKKSSVKLASIDTDTKNRALEAMAEALDIHRSFIIQENSKDQEDAKKLMEEGK--LSKALVERLKVDNNKIDGMIEG 86 
                                       45556677777888888888888888888888888888888888888888844..4444444444444444444555 PP

                                       HHHHHHHHHHHHHHHSEEEEEECTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEEE-TTSHHHH CS
                            Aldedh  93 aidvlryyaelaeklegevlpssegklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlKPaeetplsa 169
                                       + dv+++     ++l+   ++ +eg + + +  P+Gv+g+I  ++    ++ + +  +l  GN++++K  +e+++s 
  gi|298674805|ref|YP_003726555.1|  87 IKDVIQLNDPVGDTLNS--IELDEGLELYQVSCPIGVIGVI--FESRPDVVPQVMSLCLKSGNATIFKGGSEASHSN 159
                                       55555555555555543..566789999*************..88888888899999******************** PP

                                       HHHHHHHHHT.....TS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE---EE CS
                            Aldedh 170 lllaelfeea.....glPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElGGknp 241
                                        +++ ++ +a      +P+++++++ +  +ev + l +++ +d++   Gs++  + i+ +      +v+    G  +
  gi|298674805|ref|YP_003726555.1| 160 RAIFDVLTDAikhteTVPEDAFQLMET-REEVMDVLKQDQYIDLLIPRGSNTFVKFIQDNTR---IPVLGHSDGICH 232
                                       ************************988.999**************************99988...9*********** PP

                                       EEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT- CS
                            Aldedh 242 livledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakkl 296
                                       ++v ++a+ld a + +  + + +   vC a++ llv+ +i+d+f+  +++ ++k 
  gi|298674805|ref|YP_003726555.1| 233 AFVDSKANLDTAYDVCYDSKVQYP-AVCNAIETLLVHTDIADDFLPYMADMYNKA 286
                                       ******************999886.8*******************9999988776 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.00049
                                       EEEEEEESSHHHHHHHHHSSSEESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST- CS
                            Aldedh 374 VlsvikfkdeeeaieiaNdteyGLaagvftkdleraervaerleaGnvyiNdsttg 429
                                       +ls+  +++++ a++  N+     +  ++t+d ++ + +++ ++  +v+i  st++
  gi|298674805|ref|YP_003726555.1| 325 ILSIKVVDSIDNAVDHINNYGSHHTDVIITNDKDNKKLFSSLVDSSSVMIDASTRF 380
                                       899**************************************99*****99888665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 2758.08
//
Query:       gi|298674806|ref|YP_003726556.1|  [L=374]
Description: glutamate 5-kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.9e-41  141.2   0.3    5.3e-41  140.8   0.3    1.2  1  AA_kinase  Amino acid kinase family
    2.4e-17   62.7   0.4    1.3e-16   60.3   0.1    2.2  2  PUA        PUA domain


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.8   0.3   5.9e-45   5.3e-41       2     241 .]      13     244 ..      12     244 .. 0.94

  Alignments for each domain:
  == domain 1  score: 140.8 bits;  conditional E-value: 5.9e-45
                                       EEEEEE-TTCCCCTCC....HHHHHHHHHHHHHHHHTTEEEEEE--H.HHHHHHHHHTCCCCCHHHC....E..HHH CS
                         AA_kinase   2 rvVvKlGGssltdkee....aslrrlaeqiaalkesgnklvvVhGgg.sftdgllalksglssgelaaglrstleea 73 
                                       +vVvK+G ss+++ ++    + ++r+  q+++l++ g+++++V++g+ +++ g+l+l  g +++e+           
  gi|298674806|ref|YP_003726556.1|  13 KVVVKIGTSSISNDDGtlnhDLMDRISYQVSELHNMGKEVIIVSSGSiGVGVGQLNL--GSKPREIP---------- 77 
                                       79**********77777*****************************55888888888..88888887.......... PP

                                       HHHHHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEE CS
                         AA_kinase  74 gevatrdalaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigld 150
                                            r+a+a++g++++++ + + +++++l++a++++t + +   s++  + + ++ i +ll+ gv+p++++++  +
  gi|298674806|ref|YP_003726556.1|  78 ----VRQAAAAVGQSVLMQEWIKTFQKYNLNVAQILITYESF---SNRLTYLNLRNSISTLLNYGVIPIINENDSTS 147
                                       ....46************************************...*****************************999 PP

                                       TTTE.EEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH......CSSS.TTTHHH CS
                         AA_kinase 151 eege.lgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee......saselatgGmk 220
                                       +++   ++g++D ++a++A +++Ad li l+d+dG+yd++pk + +arl +++++ + e        +s  + gGm+
  gi|298674806|ref|YP_003726556.1| 148 VHEIeATFGDNDKLSAMVASKMEADLLIMLSDIDGLYDKNPKRNHNARLMKTVEAITPEIesyggdPTSLKGVGGMR 224
                                       99999************************************************88877777799998888899**** PP

                                       HCHHHHHHHHHCTT-EEEEEE CS
                         AA_kinase 221 vkhpaalaaarrggipvvItn 241
                                       +k++aa  + ++g + +vI+n
  gi|298674806|ref|YP_003726556.1| 225 TKIEAAKICSMSG-CYMVIAN 244
                                       *****99999999.*****98 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.14   1.2e+03      34      57 ..      49      72 ..      43      76 .. 0.86
   2 !   60.3   0.1   1.4e-20   1.3e-16       1      74 []     285     357 ..     285     357 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.14
                                      TSEEEEEETTSCEEEEEEESS-HH CS
                               PUA 34 gdvVaivdedgelvavGlanysse 57
                                      g +V iv+ +   v+vG  n+ s+
  gi|298674806|ref|YP_003726556.1| 49 GKEVIIVSSGSIGVGVGQLNLGSK 72
                                      778999999888899999998875 PP

  == domain 2  score: 60.3 bits;  conditional E-value: 1.4e-20
                                       CEEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEEEE CS
                               PUA   1 grvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveiervl 74 
                                       g++ +d gA ka+ +  sLl+ Gvv++ g+f +gd+V+++   ge+ a+G++ y+s+el++ikg++++ i ++l
  gi|298674806|ref|YP_003726556.1| 285 GTIDIDSGAKKAIENHMSLLPSGVVDITGEFDRGDIVELKCD-GEVFAKGITDYTSDELKQIKGKHTDMIADIL 357
                                       5788*************************************9.************************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2216.07
//
Query:       gi|298674807|ref|YP_003726557.1|  [L=705]
Description: Cache sensor-containing methyl-accepting chemotaxis sensory transducer [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-53  180.4  67.6    8.3e-52  175.5  24.7    5.2  6  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
    6.6e-31  108.0   5.0    6.6e-31  108.0   5.0    4.3  4  dCache_1         Cache domain
    2.6e-13   50.1   0.2    8.7e-11   42.0   0.0    4.5  3  HAMP             HAMP domain
    3.5e-09   36.8  49.3      0.028   14.6   6.5    6.8  5  DUF948           Bacterial protein of unknown function (DUF94
    1.5e-06   28.2  35.6     0.0045   16.9  14.1    2.6  2  PhageMin_Tail    Phage-related minor tail protein
    0.00023   20.3  10.9    0.00023   20.3  10.9    3.7  3  IFT57            Intra-flagellar transport protein 57
    0.00053   20.0   6.1    0.00053   20.0   6.1    4.8  4  DUF1664          Protein of unknown function (DUF1664)
    0.00058   19.1   0.0    0.00058   19.1   0.0    4.8  5  dCache_2         Cache domain
      0.004   17.0   0.1      0.004   17.0   0.1    4.6  4  sCache_2         Single Cache domain 2
     0.0049   16.6   9.2     0.0068   16.2   0.1    3.4  3  DUF1848          Domain of unknown function (DUF1848)
  ------ inclusion threshold ------
      0.011   15.4  34.3      0.039   13.6   9.8    3.3  3  TMP_2            Prophage tail length tape measure protein
      0.059   13.3   1.6       0.16   11.9   0.3    2.5  1  GnsAB_toxin      GnsA/GnsB toxin of bacterial toxin-antitoxin
      0.066   13.2  54.8       0.56   10.2   9.5    5.5  5  Laminin_II       Laminin Domain II
      0.073   12.9   0.0       0.19   11.6   0.0    1.7  1  Maff2            Maff2 family
      0.076   11.2  40.2      0.044   12.0  10.8    3.9  3  EzrA             Septation ring formation regulator, EzrA
      0.098   13.2  43.0       0.45   11.1   5.6    5.6  6  Syntaxin-6_N     Syntaxin 6, N-terminal
       0.18    9.8  34.2      0.029   12.4  10.5    3.6  4  Prominin         Prominin
       0.18   10.5  26.6       0.12   11.1   9.5    3.2  3  DUF773           CDK5 regulatory subunit-associated protein 3
        0.2   11.5  42.7        0.4   10.5   1.3    5.4  6  Sec34            Sec34-like family
       0.39   11.0  44.4       0.14   12.4   1.6    6.3  6  WXG100           Proteins of 100 residues with WXG
       0.83    8.7  49.6      0.023   13.8  15.9    2.7  3  AIP3             Actin interacting protein 3
        1.5    9.3  45.1        0.3   11.6   3.8    6.6  4  NPV_P10          Nucleopolyhedrovirus P10 protein
        1.8    6.8  45.5       0.14   10.5  17.5    2.5  3  MAD              Mitotic checkpoint protein
        2.4    6.3  44.2       0.01   14.1  34.8    1.7  2  FPP              Filament-like plant protein, long coiled-coi
        2.9    8.1  49.4       0.27   11.4   8.5    5.3  5  Fib_alpha        Fibrinogen alpha/beta chain family
        4.3    7.3  25.8        2.9    7.9  10.1    3.5  3  Serine_rich      Serine rich protein interaction domain
        5.7    5.7  51.5       0.16   10.8  25.7    2.9  3  DUF812           Protein of unknown function (DUF812)
          6    5.7  43.8       0.27   10.1   8.9    4.3  5  Vps53_N          Vps53-like, N-terminal
        9.5    6.4  18.5       0.77    9.9   0.7    4.9  4  Med9             RNA polymerase II transcription mediator com


Domain annotation for each model (and alignments):
>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.2       1.1   6.7e+02     133     160 ..      51      78 ..      33      91 .. 0.69
   2 !    9.0   5.5    0.0018       1.1      99     169 ..     352     423 ..     325     426 .. 0.56
   3 !   14.5   9.8   3.8e-05     0.023      88     170 ..     363     445 ..     354     447 .. 0.89
   4 !   11.2   9.4   0.00038      0.23      88     160 ..     426     498 ..     421     500 .. 0.91
   5 !  175.5  24.7   1.3e-54   8.3e-52      17     171 ..     488     642 ..     486     643 .. 0.97
   6 !    7.9   4.6    0.0039       2.4     116     166 ..     636     686 ..     636     692 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 133 iveavaevadlvqeiaaaseeqsasiee 160
                                        +++++ev++ ++e  ++s+++s+ ++e
  gi|298674807|ref|YP_003726557.1|  51 AADHANEVEADMREYLTTSKQLSNVLSE 78 
                                       4567777778888888888877776655 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0018
                                       ...........HHHHHHHHHHHHHHHHHC.CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  99 qkeindsvesleetrqrveegselveetg.ealkeiveavaevadlvqeiaaaseeqsasieevnqaveeva 169
                                       +++i+ds++  ++     +++ +++++   + +++i+ a+++ a+  qe++a+se++++++++++++v+e++
  gi|298674807|ref|YP_003726557.1| 352 TAKIDDSLTQNDDEIGSLAKSFDKMSSNLaDLVNRITIAADNTASKAQELSASSEQMTSTSNQIADTVTEIS 423
                                       333333333333333333333333333330233555556666777788888888888888999988888876 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 3.8e-05
                                       HHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  88 akeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqa 164
                                         ei +l +   k + + ++ ++  +  +++++++++e   + ++++++ +++ad+v+ei+  +++qs+ i+ev++a
  gi|298674807|ref|YP_003726557.1| 363 DDEIGSLAKSFDKMSSNLADLVNRITIAADNTASKAQELSASSEQMTSTSNQIADTVTEISNGAQNQSTKIQEVSRA 439
                                       56788888888888888888999999999999999999999999********************************* PP

                                       HHHHHH CS
                         MCPsignal 165 veevak 170
                                       ++ +++
  gi|298674807|ref|YP_003726557.1| 440 MNDMNQ 445
                                       ***997 PP

  == domain 4  score: 11.2 bits;  conditional E-value: 0.00038
                                       HHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  88 akeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasiee 160
                                       a++ ++ i+e+ + +nd  +s++++ ++++++se v +  e+ +++ e+ +e++  ++e+++a ++ s+ i++
  gi|298674807|ref|YP_003726557.1| 426 AQNQSTKIQEVSRAMNDMNQSVQDVASNAQKASEDVTDVSEKSQNVGEKSHELSVKMNEVQSAMNDSSQVIQD 498
                                       6666778999*********************************************************999886 PP

  == domain 5  score: 175.5 bits;  conditional E-value: 1.3e-54
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  17 evanvvkqmeeieksskeisdiieVideiadQTNlLALNAaiEAARAGeqGrGFaVVAdEVrkLAersaqaakeiea 93 
                                        +++  + +++++++sk+i +i++ i++iadQTNlLALNAaiEAARAGe+GrGFaVVAdEVrkLAe+s ++a++ie+
  gi|298674807|ref|YP_003726557.1| 488 AMNDSSQVIQDLDEKSKKIGEIVSMITNIADQTNLLALNAAIEAARAGEHGRGFAVVADEVRKLAEESSNSAQQIED 564
                                       5778888999******************************************************************* PP

                                       HH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  94 liieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqaveevak 170
                                       li+eiq  + ++v+s+++ +q+ve+g+e+ +et e+++++ve+v+ va++vq+iaa+++eqsasieev+++veev++
  gi|298674807|ref|YP_003726557.1| 565 LIQEIQDSTGQAVTSIQNGTQEVETGTETLNETVESISTVVENVNGVAKMVQDIAASAQEQSASIEEVTSSVEEVSS 641
                                       **************************************************************************998 PP

                                       H CS
                         MCPsignal 171 v 171
                                       +
  gi|298674807|ref|YP_003726557.1| 642 I 642
                                       6 PP

  == domain 6  score: 7.9 bits;  conditional E-value: 0.0039
                                       HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 116 veegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqave 166
                                       vee s+++ee++++ +e +++v+e ++++qe+++a++e+++++++  ++ve
  gi|298674807|ref|YP_003726557.1| 636 VEEVSSIAEESASSTEEASASVEEQTSSMQELSKAAQELTETADNLKKSVE 686
                                       567788888999999999999999999999999999999999999988886 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.0   5.0   1.1e-33   6.6e-31       7     248 ..      43     292 ..      38     293 .. 0.80
   2 ?    1.7   6.8      0.29   1.8e+02       8      78 ..     401     465 ..     390     529 .. 0.63
   3 ?    1.6   2.2      0.31   1.9e+02       4      50 ..     562     609 ..     544     643 .. 0.50
   4 ?   -1.6   0.6         3   1.8e+03      10      35 ..     645     670 ..     618     698 .. 0.52

  Alignments for each domain:
  == domain 1  score: 108.0 bits;  conditional E-value: 1.1e-33
                          dCache_1   7 aeeqllglaeqlanniedvldslenlaetlasnpslqdlleepnraneasreslqallksilksnpdisgvylvd.. 81 
                                       a+++++++a   an++e++++++ +++++l       + l+e++     +re+++++l+++l+ n+++ g y+++  
  gi|298674807|ref|YP_003726557.1|  43 AYKESSEMAADHANEVEADMREYLTTSKQL------SNVLSEYE---SGNREEVNNMLENTLNDNSKLLGTYVAYen 110
                                       678999****************98766666......55699988...699************************955 PP

                          dCache_1  82 .............adGqviassdpssppnleg....................tddpadrdwykealaggggkpvisd 125
                                                                                           ++++ +++wy+ +++++   +++s+
  gi|298674807|ref|YP_003726557.1| 111 nafdnngnldakgT-----------------TdngrfapywnrfggsvsvepLQNIDSSNWYTVPKNTE--STFVSE 168
                                       55543333333330.................134444444445556668888*****************..9***** PP

                          dCache_1 126 pyvdqtggkpvitiavpiyddsgkfiGvlaadldldnlqdllsniklgetgyvfivdsdGniiahpd.kdllgknlr 201
                                       p ++ + gk+++++a+pi++ +g f+G+ ++d++l++l+  +s+ik+ ++gy+f+v+++G + +hp+ kd++g++ +
  gi|298674807|ref|YP_003726557.1| 169 PLMY-N-GKLMVSFASPIMK-NGDFVGISGVDVSLNYLDGVISDIKVFDSGYAFLVSQEGVVMTHPEnKDWIGEKNI 242
                                       *995.7.8***********9.6*********************************************9999875444 PP

                          dCache_1 202 delkaq...ealekalakiesgvssvklngeeylva.yapiptglgWylvv 248
                                       +   a    + ++++++++e+ + +v+ +++e+    y+p++t  +  +vv
  gi|298674807|ref|YP_003726557.1| 243 KDIDADgfdQMAKDISNGNEGRIETVDPTNDERSTLfYRPVET-GNLAVVV 292
                                       4444446966666666666777777776665554445*****8.8888887 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.29
                          dCache_1   8 eeqllglaeqlanniedvlds....lenlaetlasnpslqdlleepnraneasreslqallksilksnpdisgvy 78 
                                          +++++++++n+i d++++    ++n+++ + +   + +++       +++ +s+q+   + +k+ +d+ +v+
  gi|298674807|ref|YP_003726557.1| 401 LSASSEQMTSTSNQIADTVTEisngAQNQSTKIQE---VSRAM-------NDMNQSVQDVASNAQKASEDVTDVS 465
                                       44555555555555555555511115566666633...44444.......6788899999888888888776654 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.31
                          dCache_1   4 eeqaeeqllglaeqlanniedvldslenlaetlasn.pslqdlleepn 50 
                                       +e+ +++ +++ +q+  +i++  +++e+ +etl+++ +s+   +e+ n
  gi|298674807|ref|YP_003726557.1| 562 IEDLIQEIQDSTGQAVTSIQNGTQEVETGTETLNETvESISTVVENVN 609
                                       333344444444444444444444444444444333223333333322 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 3
                          dCache_1  10 qllglaeqlanniedvldslenlaet 35 
                                       ++ ++ e++++++e++  s++ l++ 
  gi|298674807|ref|YP_003726557.1| 645 ESASSTEEASASVEEQTSSMQELSKA 670
                                       34444444444444444333322221 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.0   1.4e-13   8.7e-11       1      52 [.     327     381 ..     327     382 .. 0.93
   2 ?    1.0   0.1      0.95   5.9e+02      12      47 ..     414     443 ..     406     453 .. 0.72
   3 ?    0.5   0.0       1.3   7.9e+02       9      28 ..     663     684 ..     660     691 .. 0.75

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 1.4e-13
                                       HHHHTTHHHHHHHHHHHHHHTTTBTSST...CCTTSSSHHHHHHHHHHHHHHHHH CS
                              HAMP   1 llarrilrPLrrLaraarriaaGdldtr...lpvsgrDEiGeLarafNaMldrLr 52 
                                       l+ar+i +P+++++ +a++i++Gdl++      +  +DEiG La++f+ M+ +L 
  gi|298674807|ref|YP_003726557.1| 327 LIARSIANPIEKIEGVADKISNGDLTAKiddSLTQNDDEIGSLAKSFDKMSSNLA 381
                                       69**************************88666689***************9995 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.95
                                       HHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHH CS
                              HAMP  12 rLaraarriaaGdldtrlpvsgrDEiGeLarafNaM 47 
                                       ++a+++ +i++G  +++        i e+ ra+N+M
  gi|298674807|ref|YP_003726557.1| 414 QIADTVTEISNGAQNQS------TKIQEVSRAMNDM 443
                                       67777777777744444......4477777788777 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHHTTT..BTSST CS
                              HAMP   9 PLrrLaraarriaaG..dldtr 28 
                                       ++++L++aa+++ +   +l+++
  gi|298674807|ref|YP_003726557.1| 663 SMQELSKAAQELTETadNLKKS 684
                                       6789999999999755566665 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.032        20       3      56 ..      23      76 ..      22      97 .. 0.85
   2 ?    4.6  15.4     0.062        38      23      88 ..     386     451 ..     311     480 .. 0.79
   3 !    8.9   8.6    0.0028       1.7      23      88 ..     435     500 ..     432     524 .. 0.85
   4 !   14.6   6.5   4.6e-05     0.028      20      87 ..     544     611 ..     540     623 .. 0.71
   5 !   12.9   4.7   0.00016     0.098      19      88 ..     613     682 ..     611     683 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.032
                            DUF948  3 glIaAiAFvvLviflivvllklkktldeaaatieelekqvdpilkevedllakv 56
                                      +l+a +AF+v  ++     +  k+  + aa++ +e+e +++++l+ +++l +  
  gi|298674807|ref|YP_003726557.1| 23 VLVASGAFIVSEVYSQQEHMAYKESSEMAADHANEVEADMREYLTTSKQLSNVL 76
                                      699*************************************99999988886654 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.062
                            DUF948  23 klkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                       +++  +d++a+  +el    ++++  ++++ ++v e+ ++ ++++ k++++  a++d+ +sv+++ 
  gi|298674807|ref|YP_003726557.1| 386 RITIAADNTASKAQELSASSEQMTSTSNQIADTVTEISNGAQNQSTKIQEVSRAMNDMNQSVQDVA 451
                                       333344555555555555555555555555555555666666688888888888888888888765 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0028
                            DUF948  23 klkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                       ++++ ++ ++++++++ +++++ +++v+d+ +k++++ e  +e + k++++ +a++d ++ +++l 
  gi|298674807|ref|YP_003726557.1| 435 EVSRAMNDMNQSVQDVASNAQKASEDVTDVSEKSQNVGEKSHELSVKMNEVQSAMNDSSQVIQDLD 500
                                       688999999999999999999999999999999999888888888888888888888888888874 PP

  == domain 4  score: 14.6 bits;  conditional E-value: 4.6e-05
                            DUF948  20 vllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                       v  +++k+++e +++ +++e+ +++i + + ++++ +++ +++v+  +e++++ +e++ ++ e+v+ +
  gi|298674807|ref|YP_003726557.1| 544 VADEVRKLAEESSNSAQQIEDLIQEIQDSTGQAVTSIQNGTQEVETGTETLNETVESISTVVENVNGV 611
                                       55667788888888888888777777777777777777777777777777777777777777776544 PP

  == domain 5  score: 12.9 bits;  conditional E-value: 0.00016
                            DUF948  19 vvllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                       +++  ++  ++e +a+iee+++ v++++  +e+  + ++e  + v+e++ ++++l +a+++l+e+  +l+
  gi|298674807|ref|YP_003726557.1| 613 KMVQDIAASAQEQSASIEEVTSSVEEVSSIAEESASSTEEASASVEEQTSSMQELSKAAQELTETADNLK 682
                                       56677788899999*************************************************9998885 PP

>> PhageMin_Tail  Phage-related minor tail protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9  14.1   7.3e-06    0.0045      49     184 ..     353     506 ..     323     522 .. 0.72
   2 !   16.7  13.6   8.4e-06    0.0052       3     153 ..     547     688 ..     545     702 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7.3e-06
                     PhageMin_Tail  49 ggadd.leeaaeilstalnafglsaadaeeaaDvlaaaanngatsvedlaealkevgavakaaGlsfeetaaalall 124
                                       ++ dd l++  + ++++++ f + +++++++++ ++ aa+n+a+++++l+ +  ++ ++ +++    ++t + ++++
  gi|298674807|ref|YP_003726557.1| 353 AKIDDsLTQNDDEIGSLAKSFDKMSSNLADLVNRITIAADNTASKAQELSASSEQMTSTSNQI----ADTVTEISNG 425
                                       44444477777888999999988878***********************99999999999995....5555555555 PP

                     PhageMin_Tail 125 aaag.ikgseAgtalknllsrl...tkeaaealkkl.................Gistkdaqgkmksldeiledlsea 180
                                       a++   k  e+  a++ + ++      +a++a +++                  +++ ++q  m + +++++dl e+
  gi|298674807|ref|YP_003726557.1| 426 AQNQsTKIQEVSRAMNDMNQSVqdvASNAQKASEDVtdvseksqnvgekshelSVKMNEVQSAMNDSSQVIQDLDEK 502
                                       55444555555555555555553334456666666555555555553333333588888888888888888888888 PP

                     PhageMin_Tail 181 lkkl 184
                                        kk+
  gi|298674807|ref|YP_003726557.1| 503 SKKI 506
                                       8877 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 8.4e-06
                     PhageMin_Tail   3 lakelgektkysatelaealeelas..aGvsteeilnll.egaaklataggaddleeaaeilstalnafglsaadae 76 
                                       ++++l+e     ++  a+ +e+l++  +  st+++ + + +g+  + t ++ + l+e++e++st+ ++ +  a    
  gi|298674807|ref|YP_003726557.1| 547 EVRKLAE----ESSNSAQQIEDLIQeiQ-DSTGQAVTSIqNGTQEVETGTE-T-LNETVESISTVVENVNGVA---- 612
                                       5677888....66666777777777432.3444444444477777999999.8.9***********9888885.... PP

                     PhageMin_Tail  77 eaaDvlaaaanngatsvedlaealkevgavakaaGlsfeetaaalallaaagikgseAgtalknllsrltkeaaeal 153
                                       +++  +aa a++ ++s+e+  ++  ev++ a  +  s ee++a++  ++++ ++ s+A++ l +   +l k++ e +
  gi|298674807|ref|YP_003726557.1| 613 KMVQDIAASAQEQSASIEEVTSSVEEVSSIAEESASSTEEASASVEEQTSSMQELSKAAQELTETADNL-KKSVEFF 688
                                       777777778888889999999999999999999999999999999999999999999999999999999.6665555 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   1.0      0.59   3.7e+02     270     299 ..      56      85 ..      34     104 .. 0.72
   2 !   20.3  10.9   3.7e-07   0.00023     230     336 ..     391     497 ..     343     517 .. 0.89
   3 ?    2.0  13.9      0.13        81     226     337 ..     552     667 ..     542     682 .. 0.62

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.59
                             IFT57 270 sqleellqeyreaqeelsevkekykqlseg 299
                                       +++e  ++ey +++++ls+v  +y+  +++
  gi|298674807|ref|YP_003726557.1|  56 NEVEADMREYLTTSKQLSNVLSEYESGNRE 85 
                                       566777888888888888888888776543 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 3.7e-07
                             IFT57 230 kkhkksieeslpetksqlkklhedisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltre 306
                                        ++  s +++l+ +++q++  +++i+ t+++i++  ++  ++++e  +  +++++++++v  + +++se v++ +++
  gi|298674807|ref|YP_003726557.1| 391 ADNTASKAQELSASSEQMTSTSNQIADTVTEISNGAQNQSTKIQEVSRAMNDMNQSVQDVASNAQKASEDVTDVSEK 467
                                       555556678899999************************************************************** PP

                             IFT57 307 laeiseelekvkqemeergssmtDgsplvk 336
                                        +++ e+ ++++ +m+e +s m+D+s++++
  gi|298674807|ref|YP_003726557.1| 468 SQNVGEKSHELSVKMNEVQSAMNDSSQVIQ 497
                                       **************************9986 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.13
                             IFT57 226 leqmkkhkksieeslpetksqlkklhedisktlekiesrEkylnsqleellqe...yreaqeelsevkekykqlseg 299
                                        e+ ++  ++ie+ ++e++ +  +  + i++  +++e+  + ln+ +e+  +     + + + ++++  + ++ s++
  gi|298674807|ref|YP_003726557.1| 552 AEESSNSAQQIEDLIQEIQDSTGQAVTSIQNGTQEVETGTETLNETVESISTVvenVNGVAKMVQDIAASAQEQSAS 628
                                       45666777889999999999999999999999999999999999888776543001344444555555555666666 PP

                             IFT57 300 vseltrelaeiseelekvkqemeergssmtDg.splvki 337
                                       ++e t   +e+s   e+  +  ee ++s+ ++ s+++++
  gi|298674807|ref|YP_003726557.1| 629 IEEVTSSVEEVSSIAEESASSTEEASASVEEQtSSMQEL 667
                                       666666665555555555555555555554431333334 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   6.1   8.7e-07   0.00053      38     122 ..     368     452 ..     367     455 .. 0.96
   2 ?    4.6   3.9     0.052        32      75     120 ..     461     506 ..     452     526 .. 0.50
   3 !    9.9   2.2    0.0011       0.7      62     120 ..     549     608 ..     541     611 .. 0.76
   4 ?    6.0   6.1     0.019        12      50     121 ..     611     682 ..     602     687 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 8.7e-07
                           DUF1664  38 slsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                       sl++  +++s++l ++ + ++ + ++ +s+ +++ ++ ++++ +s++i++ vte++++ ++ ++++++v++a+++++
  gi|298674807|ref|YP_003726557.1| 368 SLAKSFDKMSSNLADLVNRITIAADNTASKAQELSASSEQMTSTSNQIADTVTEISNGAQNQSTKIQEVSRAMNDMN 444
                                       789999*********************************************************************** PP

                           DUF1664 115 skleriee 122
                                       ++++++ +
  gi|298674807|ref|YP_003726557.1| 445 QSVQDVAS 452
                                       ***99876 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.052
                           DUF1664  75 ldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                       + +++e s+++ e+ +e++ +++e+++ ++  ++++++l++k ++i
  gi|298674807|ref|YP_003726557.1| 461 VTDVSEKSQNVGEKSHELSVKMNEVQSAMNDSSQVIQDLDEKSKKI 506
                                       3344444444444444444444444444444444444444444433 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0011
                           DUF1664  62 rhLssridrvdkklde.qkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                       r+L+++  +  +++++  +ei+ ++ + vt+++++++e+++  e+++e+ve++ + +e++
  gi|298674807|ref|YP_003726557.1| 549 RKLAEESSNSAQQIEDlIQEIQDSTGQAVTSIQNGTQEVETGTETLNETVESISTVVENV 608
                                       566666666666666525789999999999999999999999999999999998888776 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.019
                           DUF1664  50 leqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                       + ++ +++aa  ++ s+ i++v ++++e++ i++e ++  +e++  ++e  + ++++++a ++l ++ ++++
  gi|298674807|ref|YP_003726557.1| 611 VAKMVQDIAASAQEQSASIEEVTSSVEEVSSIAEESASSTEEASASVEEQTSSMQELSKAAQELTETADNLK 682
                                       455667788888888999999999999999999999999999999999999999999999999988776664 PP

>> dCache_2  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   1.7       4.9     3e+03      14      61 ..      52     102 ..      34     114 .. 0.56
   2 !   19.1   0.0   9.4e-07   0.00058      87     185 ..     209     299 ..     202     329 .. 0.65
   3 ?   -3.6   6.5       7.8   4.8e+03      17      78 ..     443     510 ..     426     523 .. 0.52
   4 ?    2.6   2.6       0.1        65      14      78 ..     559     633 ..     547     641 .. 0.63
   5 ?   -1.2   2.4       1.5   9.3e+02      21      67 ..     629     674 ..     611     691 .. 0.47

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.9
                          dCache_2  14 eetikerkellksevdsaielie...yeknsleeslkesLksrveeaysia 61 
                                        ++++e +  ++++    ++l +    +++ ++e++++ L +  ++  ++ 
  gi|298674807|ref|YP_003726557.1|  52 ADHANEVEADMREYLTTSKQLSNvlsEYESGNREEVNNMLENTLNDNSKLL 102
                                       333334444444443333333333326666677777777777777666655 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 9.4e-07
                          dCache_2  87 sirydggegyyfiidskgtlilhpdspsleG.knlldlkdkdGryiiremiklakkkgeGfveytwpkpdekkprkk 162
                                       +i  ++++gy f ++++g+++ hp++++  G kn+ d+  +     + +m+k +++ +eG +e      d++++++ 
  gi|298674807|ref|YP_003726557.1| 209 DIK-VFDSGYAFLVSQEGVVMTHPENKDWIGeKNIKDIDADG----FDQMAKDISNGNEGRIETV----DPTNDERS 276
                                       444.56666667666677777777666666655555553333....6666666666666666665....55666666 PP

                          dCache_2 163 isyvkyfepldwiIGtgaylddi 185
                                       ++++++ e+ ++ ++++a  d+ 
  gi|298674807|ref|YP_003726557.1| 277 TLFYRPVETGNLAVVVSAPEDEM 299
                                       66666666666666666665554 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 7.8
                          dCache_2  17 ikerkellksevdsaielie..yekns.......leeslkesLksrveeaysiaeeiyekyknelseeeak 78 
                                       ++++ + + s+ ++a e ++  +ek++         +   ++++s +++  ++++++ ek k+     e+ 
  gi|298674807|ref|YP_003726557.1| 443 MNQSVQDVASNAQKASEDVTdvSEKSQnvgekshELSVKMNEVQSAMNDSSQVIQDLDEKSKK---IGEIV 510
                                       344444444444444444445444444222222255555566666666666777777777443...44444 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.1
                          dCache_2  14 eetikerkellksevdsaielieyeknsleeslkesLksrveeay..........siaeeiyekykn.elseeeak 78 
                                        ++i+   +++++++ +a+++i+ + ++  e+ +e+L++ ve++           +++++i +  ++   s ee++
  gi|298674807|ref|YP_003726557.1| 559 AQQIEDLIQEIQDSTGQAVTSIQ-NGTQEVETGTETLNETVESIStvvenvngvaKMVQDIAASAQEqSASIEEVT 633
                                       45788888888889999999997.6666777788888888888883333333444444444444444455555544 PP

  == domain 5  score: -1.2 bits;  conditional E-value: 1.5
                          dCache_2  21 kellksevdsaielieyeknsleeslkesLksrveeaysiaeeiyek 67 
                                        e++ s+v+++ ++i+ e  s  e++  s+ +++ +++++ +  +e 
  gi|298674807|ref|YP_003726557.1| 629 IEEVTSSVEEV-SSIAEESASSTEEASASVEEQTSSMQELSKAAQEL 674
                                       44444444444.33333444444444444444444444444443333 PP

>> sCache_2  Single Cache domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   6.4e-06     0.004      45     108 ..     207     267 ..     199     281 .. 0.78
   2 ?    1.7   1.7      0.34   2.1e+02       8      51 ..     403     446 ..     396     449 .. 0.89
   3 ?    0.4   0.2      0.82   5.1e+02       7      48 ..     567     608 ..     561     613 .. 0.81
   4 ?    0.4   0.7      0.84   5.2e+02       8      48 ..     624     664 ..     617     669 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.4e-06
                          sCache_2  45 vnglkfgdGkgYffvldedgtllvhPfnpqleGknasnlkDanGkyiirelvkeakkkgggfvt 108
                                       ++++k  d +gY f++ ++g ++ hP n++++G++ ++  Da+G   + + +++++  +g++ t
  gi|298674807|ref|YP_003726557.1| 207 ISDIKVFD-SGYAFLVSQEGVVMTHPENKDWIGEKNIKDIDADGFDQMAKDISNGN--EGRIET 267
                                       56667777.*************************9999999998666666666665..555555 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.34
                          sCache_2   8 elknqvetaislieavykqvesgkiteeeaqeevkelvnglkfg 51 
                                       + ++q++++ ++i+   ++  +g+  +    +ev  ++n+++++
  gi|298674807|ref|YP_003726557.1| 403 ASSEQMTSTSNQIADTVTEISNGAQNQSTKIQEVSRAMNDMNQS 446
                                       56789************************************986 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.82
                          sCache_2   7 aelknqvetaislieavykqvesgkiteeeaqeevkelvngl 48 
                                       +e++  +  a++ i+   ++ve+g  t++e  e + + v++ 
  gi|298674807|ref|YP_003726557.1| 567 QEIQDSTGQAVTSIQNGTQEVETGTETLNETVESISTVVENV 608
                                       566777778899999999999999999999999999888875 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.84
                          sCache_2   8 elknqvetaislieavykqvesgkiteeeaqeevkelvngl 48 
                                       e ++ +e++ s +e+v + +e+++ + eea + v+e  +++
  gi|298674807|ref|YP_003726557.1| 624 EQSASIEEVTSSVEEVSSIAEESASSTEEASASVEEQTSSM 664
                                       556789999**********************9999877666 PP

>> DUF1848  Domain of unknown function (DUF1848)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       0.9   5.6e+02      48      98 ..      62     112 ..      39     126 .. 0.81
   2 !   16.2   0.1   1.1e-05    0.0068      23     211 ..     261     447 ..     256     479 .. 0.81
   3 ?    2.8   1.5      0.13        82     132     198 ..     558     630 ..     548     686 .. 0.61

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.9
                           DUF1848  48 vdlivFwtknpkpllkkleelkergiklyfqfTltdyekelepnvpsleer 98 
                                       ++  +  +k+ +++l++ e+ ++++++ +++ Tl+d +k l + v   +++
  gi|298674807|ref|YP_003726557.1|  62 MREYLTTSKQLSNVLSEYESGNREEVNNMLENTLNDNSKLLGTYVAYENNA 112
                                       5555667999999***99999999************999998888766665 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.1e-05
                           DUF1848  23 kegyvlvrnPfnkkqvsrvslspedvdlivFwtknpkpllkkleelkergiklyfqfTltdyekelepnvpsleeri 99 
                                       +eg +++ +P n ++ +      e+ +l v ++   +++l+++ ++k+ +i ++f  ++   +        s+++ i
  gi|298674807|ref|YP_003726557.1| 261 NEGRIETVDPTNDERSTLFYRPVETGNLAVVVSAPEDEMLSSAITVKN-EIIMIFAASIAILGGVAFLIARSIANPI 336
                                       578888888999888555555556667788888888899999988876.799999999999999888889999**** PP

                           DUF1848 100 etfkelseklgkerviwRyDPilltekltvelhlekfeklaeelkgytekvviSfvdlykkvkrnlkkklelrelse 176
                                       e+++ +++k+++  ++ + D  l++++ ++  + ++f+k++++l++ +++++i+  ++ +k+++  ++  e  + ++
  gi|298674807|ref|YP_003726557.1| 337 EKIEGVADKISNGDLTAKIDDSLTQNDDEIGSLAKSFDKMSSNLADLVNRITIAADNTASKAQELSAS-SEQMTSTS 412
                                       *****************************************************988888887766644.67777788 PP

                           DUF1848 177 eekeelaeelaeiakklglelatCaekedlselgi 211
                                       ++ +++++e+++ a++++ +++  + + +  +  +
  gi|298674807|ref|YP_003726557.1| 413 NQIADTVTEISNGAQNQSTKIQEVSRAMNDMNQSV 447
                                       88899999999999999999988776665444444 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.13
                           DUF1848 132 hlekfeklaeelkgytekvviSfvdlykkvkrnlkk..k.lelrelseeeke...elaeelaeiakklglela 198
                                         +++e+l +e+++ t + v+S+ +  ++v++ +++  + +e  ++  e+ +   ++++++a+ a++++ +++
  gi|298674807|ref|YP_003726557.1| 558 SAQQIEDLIQEIQDSTGQAVTSIQNGTQEVETGTETlnEtVESISTVVENVNgvaKMVQDIAASAQEQSASIE 630
                                       4678889999999999999999988888888877543212222222233333111444444444444444443 PP

>> TMP_2  Prophage tail length tape measure protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   9.8   6.4e-05     0.039      98     189 ..     381     468 ..     365     484 .. 0.80
   2 ?    1.3   1.2      0.39   2.4e+02     117     170 ..     526     579 ..     488     589 .. 0.55
   3 ?    8.2  12.2    0.0029       1.8      91     197 ..     570     682 ..     566     689 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.4e-05
                             TMP_2  98 nkaliltGnaaGlTasqLeamaesiaeaggtqaaaaealaalastGkiggeqlervakaaaelekatGqsvdetake 174
                                          ++ +  aa+ Tas+ +++++s +++++t +++a++++++ + ++  ++++++v++a  ++++    sv+++a++
  gi|298674807|ref|YP_003726557.1| 381 ADLVNRITIAADNTASKAQELSASSEQMTSTSNQIADTVTEISNGAQNQSTKIQEVSRAMNDMNQ----SVQDVASN 453
                                       44455566689************************************************999886....77777888 PP

                             TMP_2 175 laklakdPvkaaekl 189
                                        +k+++d ++ +ek 
  gi|298674807|ref|YP_003726557.1| 454 AQKASEDVTDVSEKS 468
                                       888887777666554 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.39
                             TMP_2 117 amaesiaeaggtqaaaaealaalastGkiggeqlervakaaaelekatGqsvde 170
                                       ++a ++a+ag+  +  a ++ ++ + ++ ++++ +++     e+++ tGq+v  
  gi|298674807|ref|YP_003726557.1| 526 NAAIEAARAGEHGRGFAVVADEVRKLAEESSNSAQQIEDLIQEIQDSTGQAVTS 579
                                       444444444444444444444444444444444444444445666677776654 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0029
                             TMP_2  91 akearefnkaliltGnaaGlTasqLeamaesiaeaggtqaaaaealaalastGkiggeqlervakaaaelekatGqs 167
                                       ++++ +  +++++  + + + ++ L++  esi+++ ++++ +a++++ +a++++  ++++e+v++ + e+++   +s
  gi|298674807|ref|YP_003726557.1| 570 QDSTGQAVTSIQNGTQEVETGTETLNETVESISTVVENVNGVAKMVQDIAASAQEQSASIEEVTSSVEEVSSIAEES 646
                                       677778888999999999999*************************************9*99999998888777666 PP

                             TMP_2 168 vdetakelakl......akdPvkaaeklneqlhfLt 197
                                       ++ t ++ a++      +++  kaa++l+e+  +L 
  gi|298674807|ref|YP_003726557.1| 647 ASSTEEASASVeeqtssMQELSKAAQELTETADNLK 682
                                       665555444440000005555677777777666665 PP

>> GnsAB_toxin  GnsA/GnsB toxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   0.00026      0.16       5      49 ..     547     593 ..     544     596 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00026
                                       HHHHHHHH..HHHHHHHHHHHHHHHHHSSEEEEEEEEEEEETTEEEE CS
                       GnsAB_toxin   5 eLkkkAEe..eiaeliakKiaELkKkTGkEVseieFtaREkmtGLEs 49 
                                       e++k AEe  + a+ i   i E++  TG+ V++i+  + E  tG E+
  gi|298674807|ref|YP_003726557.1| 547 EVRKLAEEssNSAQQIEDLIQEIQDSTGQAVTSIQNGTQEVETGTET 593
                                       5666676522468889999*********************9999886 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.5       1.3   7.9e+02       7      49 ..      50      93 ..      45     106 .. 0.66
   2 ?    9.3   8.2    0.0018       1.1       9      71 ..     388     450 ..     377     455 .. 0.90
   3 ?    9.8   7.0    0.0012      0.77       4      70 ..     446     512 ..     444     529 .. 0.88
   4 ?    7.1   3.0    0.0083       5.1       2      73 ..     549     603 ..     542     611 .. 0.48
   5 ?   10.2   9.5   0.00091      0.56       6      93 ..     602     686 ..     599     695 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.3
                                      XXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II  7 eanetakevleqlap...lsqnlentkeklseinrsveetnekvkd 49
                                       a + a+ev++++ +    s++l+n+ +++++ nr+  e+n+ +++
  gi|298674807|ref|YP_003726557.1| 50 MAADHANEVEADMREyltTSKQLSNVLSEYESGNRE--EVNNMLEN 93
                                      455555666655554222588999999999999888..77776663 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0018
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTT CS
                        Laminin_II   9 netakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqL 71 
                                          a ++ ++ ++ls+  e++ +  ++i+++v e+ + +++ ++ i++++r++ ++++ ++++
  gi|298674807|ref|YP_003726557.1| 388 TIAADNTASKAQELSASSEQMTSTSNQIADTVTEISNGAQNQSTKIQEVSRAMNDMNQSVQDV 450
                                       55678899999***********************************************99987 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0012
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTT CS
                        Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapq 70 
                                        ++++ + a++  e+++++s++ +n+ ek +e+  +++e++  ++d++++i+d  +++kk+ + +  
  gi|298674807|ref|YP_003726557.1| 446 SVQDVASNAQKASEDVTDVSEKSQNVGEKSHELSVKMNEVQSAMNDSSQVIQDLDEKSKKIGEIVSM 512
                                       6788899999999********************************************9998876655 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.0083
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGG CS
                        Laminin_II   2 kelaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLld 73 
                                       ++la+e +++a+++++ +++++  +                  + v + +++++++++   +L+++++ +  
  gi|298674807|ref|YP_003726557.1| 549 RKLAEESSNSAQQIEDLIQEIQDSTG-----------------QAVTSIQNGTQEVETGTETLNETVESIST 603
                                       34455555555555555555555444.................44445555555555555555554444433 PP

  == domain 5  score: 10.2 bits;  conditional E-value: 0.00091
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHH CS
                        Laminin_II   6 aeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqle 82 
                                       + + e ++ v + ++++++  ++ +++++e+ +svee+   ++++   +++A+ sv + +  +++L +  +el +  
  gi|298674807|ref|YP_003726557.1| 602 STVVENVNGVAKMVQDIAASAQEQSASIEEVTSSVEEVSSIAEESASSTEEASASVEEQTSSMQELSKAAQELTETA 678
                                       5566788899999******************************9999999***999999999999999988888888 PP

                                       HH...HHHHHH CS
                        Laminin_II  83 eassslsdnis 93 
                                       ++   l+++++
  gi|298674807|ref|YP_003726557.1| 679 DN---LKKSVE 686
                                       88...888776 PP

>> Maff2  Maff2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00031      0.19       3      53 ..     299     349 ..     297     353 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00031
                             Maff2   3 fftsavdvlktlvvalGaglgvWGvvnlleGyGndnPGaksqGikqlmaGg 53 
                                       +++sa++v + +++   a++++ G+v +l      nP  k  G+   ++ g
  gi|298674807|ref|YP_003726557.1| 299 MLSSAITVKNEIIMIFAASIAILGGVAFLIARSIANPIEKIEGVADKISNG 349
                                       689***************************************998877765 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   1.3      0.68   4.2e+02      97     141 ..      49      90 ..      32     111 .. 0.51
   2 ?    3.4  19.3     0.028        18      59     497 ..     370     512 ..     310     597 .. 0.60
   3 ?   12.0  10.8   7.1e-05     0.044      68     190 ..     558     681 ..     543     696 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.68
                                       HHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHH CS
                              EzrA  97 kkakkklaeleeeldeveekikkileelkelteseeknreeiekl 141
                                         a    +e+e+++ e+ +++k++ + l+   e e+ nree++ +
  gi|298674807|ref|YP_003726557.1|  49 EMAADHANEVEADMREYLTTSKQLSNVLS---EYESGNREEVNNM 90 
                                       33444445555555555555555554333...3444455555444 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.028
                                       HHHHHHHHHHHHHHHHHHTHHHHHT-GGGT--S-SHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTH CS
                              EzrA  59 eekfeewkkkwdeiktkklpeieellfeaeelldkykfkkakkklaeleeeldeveekikkileelkelteseeknr 135
                                        ++f+++ ++                                                                   
  gi|298674807|ref|YP_003726557.1| 370 AKSFDKMSSNL------------------------------------------------------------------ 380
                                       22222222222.................................................................. PP

                                       HHHHHHHHHHHHHHHT--TTTTHHHHHHHHHHHHHHHH----------------HHHHHHHHHHHHHHHHHHHHHHH CS
                              EzrA 136 eeieklkekYrelrkkllanrfsygealeelekqleniekefsefeeltengdyveakeilkkleeeideleeviee 212
                                                                                                                    
  gi|298674807|ref|YP_003726557.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       HHHHHTTTTTTSHHHHHHHHHHHHHSTTS--SGGGSSSSSHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHH CS
                              EzrA 213 iPelleelkkelpkqleelkegykemkeegYaleelniekeieelekkieeilerlkeleledveeelktieeeids 289
                                                                                                                    
  gi|298674807|ref|YP_003726557.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       HHHHHHHHHHHHHHHTTTSSSSSHHHHT--HHHHTTGGG-TTTS-GGGSSTTTSTTHHHHHHHHHHHHHHHHHHHHH CS
                              EzrA 290 LyddlekEveAkkeveknlkelkeklehlekqnkelkeeldrlkqsYeLseeeleklrelekelkelekdyeeleek 366
                                                                                                                  + 
  gi|298674807|ref|YP_003726557.1| 381 --------------------------------------------------------------------------ADL 383
                                       ..........................................................................233 PP

                                       HS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSS-SS-S-TTTHH CS
                              EzrA 367 leekkvaYSelqeeleeleekleeieekqeeileslkslrkdEkrAreqldeikkelkeikrkieksnLPgiPesyl 443
                                       ++  ++a  + +++ +el+ + e++ +  ++i ++++++ +  ++   +++e+++ ++++++++++    +  ++  
  gi|298674807|ref|YP_003726557.1| 384 VNRITIAADNTASKAQELSASSEQMTSTSNQIADTVTEISNGAQNQSTKIQEVSRAMNDMNQSVQD--VASNAQKAS 458
                                       333344444444455555555555555555555555555555555555555555555555555543..345555555 PP

                                       HHSTTTSTTTHHHHHHHT-TT--HHHHHHHHHTTTTTSGGGTHHHHHHHHHHHH CS
                              EzrA 444 eelkeasdeieelakeLekkpinikevnkrldeardlveklyektneliktAtl 497
                                       e+++++s++ +++ ++  +  ++++ev++ +++ +++++ l+ek++++ + + +
  gi|298674807|ref|YP_003726557.1| 459 EDVTDVSEKSQNVGEKSHELSVKMNEVQSAMNDSSQVIQDLDEKSKKIGEIVSM 512
                                       555555555555555555555555555555555555555555555555544444 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 7.1e-05
                                       HHHHHHHHHTHHHHHT-GGGT--..S-SHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHH CS
                              EzrA  68 kwdeiktkklpeieellfeaeel..ldkykfkkakkklaeleeeldeveekikkileelkelteseeknreeieklk 142
                                       + ++i++  ++ei++   +a  +  + + ++ + +++l+e+ e +++v e+++ + + ++++  s +++++ ie++ 
  gi|298674807|ref|YP_003726557.1| 558 SAQQIED-LIQEIQDSTGQAVTSiqNGTQEVETGTETLNETVESISTVVENVNGVAKMVQDIAASAQEQSASIEEVT 633
                                       3334433.44455555444444311345677788899999999999999**************************** PP

                                       HHHHHHHHT--TTTTHHHHHHHHHHHHHHHH----------------H CS
                              EzrA 143 ekYrelrkkllanrfsygealeelekqleniekefsefeeltengdyv 190
                                       +  +e++   ++   s +ea +++e+q + +++  ++ +elte  d +
  gi|298674807|ref|YP_003726557.1| 634 SSVEEVSSIAEESASSTEEASASVEEQTSSMQELSKAAQELTETADNL 681
                                       ******************************************998865 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.3      0.93   5.8e+02      10      60 ..      51     101 ..      40     125 .. 0.58
   2 ?    5.4   0.9     0.044        27       8      90 ..     330     417 ..     326     424 .. 0.57
   3 ?    6.9   6.4     0.015       9.1      12      93 ..     393     476 ..     386     479 .. 0.85
   4 ?    7.0   3.5     0.014       8.4       7      62 ..     444     501 ..     433     522 .. 0.69
   5 ?   11.1   5.6   0.00072      0.45       3      98 ..     541     639 ..     540     642 .. 0.73
   6 ?    9.6   6.4    0.0022       1.3       8      73 ..     630     694 ..     626     701 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.93
                      Syntaxin-6_N  10 VqkslnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledL 60 
                                         + +n++e+ +r++  + ++ s+  se  +  r+e+++ l++  +d + L
  gi|298674807|ref|YP_003726557.1|  51 AADHANEVEADMREYLTTSKQLSNVLSEYESGNREEVNNMLENTLNDNSKL 101
                                       555666667777777443333333334444445555555555555555554 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.044
                      Syntaxin-6_N   8 eeVqkslnkaeslyrrwe.rlledtssstseeldetrteLrkalrsiewdledLeetvriveknp....skfkidek 79 
                                       + + + ++k+e++ ++ +   l+ +++++  + d+    L k+ ++++ +l dL + + i+  n     ++ + +++
  gi|298674807|ref|YP_003726557.1| 330 RSIANPIEKIEGVADKISnGDLTAKIDDSLTQNDDEIGSLAKSFDKMSSNLADLVNRITIAADNTaskaQELSASSE 406
                                       55666677777777777422233333344666666677788899999999999999998887764211122334444 PP

                      Syntaxin-6_N  80 elsrrrafvee 90 
                                       ++++  + +++
  gi|298674807|ref|YP_003726557.1| 407 QMTSTSNQIAD 417
                                       44444444444 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.015
                      Syntaxin-6_N  12 kslnkaeslyrrwerlledtss..stseeldetrteLrkalrsiewdledLeetvriveknpskfkidekelsrrra 86 
                                       ++++ka++l ++ e++ +++++  +t  e+++  ++  +++++++  ++d++++v+ v +n +k + d +++s++ +
  gi|298674807|ref|YP_003726557.1| 393 NTASKAQELSASSEQMTSTSNQiaDTVTEISNGAQNQSTKIQEVSRAMNDMNQSVQDVASNAQKASEDVTDVSEKSQ 469
                                       567788888888888777777766689999999999999**********************************9999 PP

                      Syntaxin-6_N  87 fveevre 93 
                                        v e  +
  gi|298674807|ref|YP_003726557.1| 470 NVGEKSH 476
                                       9877655 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.014
                      Syntaxin-6_N   7 keeVqkslnkaeslyrrwerlledtss..stseeldetrteLrkalrsiewdledLee 62 
                                       ++ Vq+ +++a++  +  +++ e++++  ++s+el+  ++e+++a+++ ++ ++dL+e
  gi|298674807|ref|YP_003726557.1| 444 NQSVQDVASNAQKASEDVTDVSEKSQNvgEKSHELSVKMNEVQSAMNDSSQVIQDLDE 501
                                       3444444444444444444444444333337999999999999999999999999997 PP

  == domain 5  score: 11.1 bits;  conditional E-value: 0.00072
                      Syntaxin-6_N   3 FfevkeeVqkslnkaeslyrrwerlledtss...stseeldetrteLrkalrsiewdledLeetvriveknpskfki 76 
                                       F +v++eV+k +++  +  ++ e+l ++ ++   +   ++++ ++e+++  +++++++e +  +v+ v+   + ++ 
  gi|298674807|ref|YP_003726557.1| 541 FAVVADEVRKLAEESSNSAQQIEDLIQEIQDstgQAVTSIQNGTQEVETGTETLNETVESISTVVENVNGVAKMVQD 617
                                       78899999999888888888885544443332223578888888999999999999999999999888776555666 PP

                      Syntaxin-6_N  77 dekelsrrrafveevreevkem 98 
                                        ++  +++ a +eev + v+e+
  gi|298674807|ref|YP_003726557.1| 618 IAASAQEQSASIEEVTSSVEEV 639
                                       6777788888888888888775 PP

  == domain 6  score: 9.6 bits;  conditional E-value: 0.0022
                      Syntaxin-6_N   8 eeVqkslnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLeetvriveknpsk 73 
                                       eeV +s++++ s+ ++  +  e++s ++ ee  + ++eL ka +++ ++ ++L+++v+  + + s+
  gi|298674807|ref|YP_003726557.1| 630 EEVTSSVEEVSSIAEESASSTEEAS-ASVEEQTSSMQELSKAAQELTETADNLKKSVEFFKLDSSQ 694
                                       7999999999999999876444444.45999999***********************877766554 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1     0.031        19     141     226 ..      13     106 ..       5     113 .. 0.62
   2 ?   12.4  10.5   4.7e-05     0.029     299     439 ..     394     527 ..     327     543 .. 0.67
   3 ?    4.1   3.8     0.015       9.3     644     705 ..     540     609 ..     513     630 .. 0.69
   4 ?    1.6  11.6     0.084        52     281     403 ..     560     683 ..     542     697 .. 0.49

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.031
                          Prominin 141 tlgvllllltlllliGviia.FvtNkaldegl....eesketvkrgledlrtflkdvpqhidhvlvqnye.....el 207
                                       t++++l ll++l+  G +i   v  ++ +       e +   +++   d+r +l+ +++++ +vl + ye     e+
  gi|298674807|ref|YP_003726557.1|  13 TVYIILPLLLVLVASGAFIVsEVYSQQEHMAYkessEMAADHANEVEADMREYLT-TSKQLSNVLSE-YEsgnreEV 87 
                                       5566666666666666544313333333333300003344455666679999995.899******99.853222277 PP

                          Prominin 208 ekhvsddLddagkhlgldl 226
                                       ++ ++++L+d +k lg+ +
  gi|298674807|ref|YP_003726557.1|  88 NNMLENTLNDNSKLLGTYV 106
                                       8888888888888888765 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 4.7e-05
                          Prominin 299 ilssleiekldtskcldqlpnvdevlealeevletnlssivkeglarlneipekvknqtaevvpdlkkalakgreqi 375
                                       + s+      ++s++ +q+ ++++++    +   t++s+ ++++ ++++e+++ + n++++ v+d+ ++ +k++e +
  gi|298674807|ref|YP_003726557.1| 394 TASK----AQELSASSEQMTSTSNQIA---DT-VTEISNGAQNQSTKIQEVSR-AMNDMNQSVQDVASNAQKASEDV 461
                                       1222....2345556655555544432...22.24556777778888888875.45789999999999999999888 PP

                          Prominin 376 kklakkip..realdavisdlenterssktfddvvekyekyrwliglivcsllllivvililgLlc 439
                                        ++++k     e+  +++ +++++++ ++  ++v++ ++++ + ig iv+++  +    ++l+L+ 
  gi|298674807|ref|YP_003726557.1| 462 TDVSEKSQnvGEKSHELSVKMNEVQSAMNDSSQVIQDLDEKSKKIGEIVSMITNIADQTNLLALNA 527
                                       88887774446778889999999999999999******9999999999999998888888888875 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.015
                          Prominin 644 k........knlkqslkneaqdlraiqqelvlplessvkklkksvkkldeensdlqesikkllaaverae 705
                                                ++l ++  n+aq+++++ qe+ +   ++v ++++ ++++++ +++l+e+++ + + ve+ +
  gi|298674807|ref|YP_003726557.1| 540 GfavvadevRKLAEESSNSAQQIEDLIQEIQDSTGQAVTSIQNGTQEVETGTETLNETVESISTVVENVN 609
                                       1455555556778888888888888888888888888888888888888888888888887777776654 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.084
                          Prominin 281 rdlnqalsnlCq..s.eeCskilssleiekldtskcl..dqlpnvdevlealeevle..tnlssivkeglarlneip 350
                                       +++++++++ +q  + +  ++i++ ++   ++t+++   ++++++++v+e++++v +  ++++  ++e+ a+++e+ 
  gi|298674807|ref|YP_003726557.1| 560 QQIEDLIQE-IQdsTgQAVTSIQNGTQE--VETGTETlnETVESISTVVENVNGVAKmvQDIAASAQEQSASIEEVT 633
                                       233333333.221111333333333333..33333333455555555555555554322455555666666666666 PP

                          Prominin 351 ekvknqtaevvpdlkkalakgreqikklakkiprealdavisdlentersskt 403
                                       + v+ +++++ ++  ++ +++++ ++++++++  + l++ +++l +t +++k+
  gi|298674807|ref|YP_003726557.1| 634 SSVE-EVSSIAEESASSTEEASASVEEQTSSM--QELSKAAQELTETADNLKK 683
                                       6664.456666666666666666666666665..4455555555555555444 PP

>> DUF773  CDK5 regulatory subunit-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   9.5   0.00019      0.12     387     485 ..     394     490 ..     371     507 .. 0.87
   2 ?    8.5   3.0    0.0012      0.72     401     496 ..     553     648 ..     539     651 .. 0.89
   3 ?    3.1   5.7     0.052        32     400     492 ..     591     686 ..     568     688 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00019
                            DUF773 387 qfqsapevlqsqtkeeiekmlsaveealslltnkklqqLiliktspryvdrlvasLeqklkqeeklkeklkdleekr 463
                                       ++++a+e   s ++e++++ ++++ + +++++n   +q  +i++ +r ++ + +s ++ +++++k  e ++d++ek+
  gi|298674807|ref|YP_003726557.1| 394 TASKAQE--LSASSEQMTSTSNQIADTVTEISNGAQNQSTKIQEVSRAMNDMNQSVQDVASNAQKASEDVTDVSEKS 468
                                       4444444..578999************************************************************** PP

                            DUF773 464 eelqeelselepkleklvkktr 485
                                       +++ e+  el+ k++++ +   
  gi|298674807|ref|YP_003726557.1| 469 QNVGEKSHELSVKMNEVQSAMN 490
                                       **************99876655 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0012
                            DUF773 401 eeiekmlsaveealslltnkklqqLiliktspryvdrlvasLeqklkqeeklkeklkdleekreelqeelselepkl 477
                                       ee  +  +++e++++++++++ q    i++  + v+  +++L++  ++++ + e+++ +++  +++  + +e+++ +
  gi|298674807|ref|YP_003726557.1| 553 EESSNSAQQIEDLIQEIQDSTGQAVTSIQNGTQEVETGTETLNETVESISTVVENVNGVAKMVQDIAASAQEQSASI 629
                                       455667899******************************************************************** PP

                            DUF773 478 eklvkktrelkkliekelS 496
                                       e+++++  e+ +  e++ S
  gi|298674807|ref|YP_003726557.1| 630 EEVTSSVEEVSSIAEESAS 648
                                       **99999888887777655 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.052
                            DUF773 400 keeiekmlsaveealslltn..kklqqLil.iktspryvdrlvasLeqklkqeeklkeklkdleekreelqeelsel 473
                                       +e++++ ++++++++++++   k +q++    ++++  ++ +++s e+  + +e + ++ +++++  ee +++++el
  gi|298674807|ref|YP_003726557.1| 591 TETLNETVESISTVVENVNGvaKMVQDIAAsAQEQSASIEEVTSSVEEVSSIAEESASSTEEASASVEEQTSSMQEL 667
                                       34555566666666666653213455554315677789999999999999999999999999999999999999999 PP

                            DUF773 474 epkleklvkktrelkklie 492
                                       ++  ++l++++ +lkk +e
  gi|298674807|ref|YP_003726557.1| 668 SKAAQELTETADNLKKSVE 686
                                       9999999999999999998 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.3       4.3   2.7e+03      20      82 ..      63      77 ..      38     104 .. 0.43
   2 ?    6.5   3.6     0.012       7.2       3      66 ..     357     424 ..     355     441 .. 0.83
   3 ?    7.0   5.1    0.0083       5.1      10      68 ..     431     489 ..     423     504 .. 0.61
   4 ?    2.6   0.2      0.18   1.1e+02       3      43 ..     483     523 ..     481     529 .. 0.82
   5 ?   10.5   1.3   0.00065       0.4       6      65 ..     556     616 ..     551     623 .. 0.83
   6 ?    7.4   5.1    0.0059       3.6       6      72 ..     623     689 ..     618     697 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4.3
                             Sec34 20 dealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFeeldpitrkLn 82
                                      +e l++ +                                                ++++ L+
  gi|298674807|ref|YP_003726557.1| 63 REYLTTSK------------------------------------------------QLSNVLS 77
                                      22222222................................................2222222 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.012
                             Sec34   3 dqLeskeeecdelleqtdealeqLeeleekfk....svsektsslheaceqlleeqkrleelaeeiee 66 
                                       d L+++ +e+ +l ++ d++ ++L++l ++ +    + ++k ++l++++eq+++  +++ +++ ei++
  gi|298674807|ref|YP_003726557.1| 357 DSLTQNDDEIGSLAKSFDKMSSNLADLVNRITiaadNTASKAQELSASSEQMTSTSNQIADTVTEISN 424
                                       67999999**********9999999998887511115666778999999***9999999999999987 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0083
                             Sec34  10 eecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekL 68 
                                        +++e+ + +++++++++++ ++ ++ se+ ++++e+++++ e+ ++l+   +e+++ +
  gi|298674807|ref|YP_003726557.1| 431 TKIQEVSRAMNDMNQSVQDVASNAQKASEDVTDVSEKSQNVGEKSHELSVKMNEVQSAM 489
                                       55566666666666666666666666666666666666666666666666666665544 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.18
                             Sec34   3 dqLeskeeecdelleqtdealeqLeeleekfksvsektssl 43 
                                       ++++s  +   ++++++de  +++ e+ +  ++++++t+ l
  gi|298674807|ref|YP_003726557.1| 483 NEVQSAMNDSSQVIQDLDEKSKKIGEIVSMITNIADQTNLL 523
                                       67788888889999999999999999999999999999876 PP

  == domain 5  score: 10.5 bits;  conditional E-value: 0.00065
                             Sec34   6 eskeeecdelleqtd.ealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeie 65 
                                       +++ +++++l+++++ ++ + ++++++  ++v++ t++l+e+ e++ +  ++++ +a+ ++
  gi|298674807|ref|YP_003726557.1| 556 SNSAQQIEDLIQEIQdSTGQAVTSIQNGTQEVETGTETLNETVESISTVVENVNGVAKMVQ 616
                                       567889999**99962567889**********************99988888887777665 PP

  == domain 6  score: 7.4 bits;  conditional E-value: 0.0059
                             Sec34   6 eskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFe 72 
                                       ++++++++e+ ++++e+ +  ee  ++ ++ s++ ++  +++++l +  ++l+e+a+++++ +++F+
  gi|298674807|ref|YP_003726557.1| 623 QEQSASIEEVTSSVEEVSSIAEESASSTEEASASVEEQTSSMQELSKAAQELTETADNLKKSVEFFK 689
                                       5677788888888888888888888888888888888888888999999***********9999996 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       5.9   3.7e+03       4      20 ..     245     261 ..     244     264 .. 0.84
   2 ?    1.2   0.0      0.72   4.4e+02       7      30 ..     364     387 ..     358     392 .. 0.78
   3 ?    7.8   9.9     0.006       3.7       9      83 ..     387     463 ..     384     467 .. 0.76
   4 ?   -0.1   0.1       1.8   1.1e+03      56      76 ..     478     498 ..     466     505 .. 0.57
   5 ?   12.4   1.6   0.00023      0.14      12      77 ..     544     608 ..     541     611 .. 0.93
   6 ?    5.5   7.5     0.032        20       7      78 ..     613     685 ..     607     689 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 5.9
                                       SHHHHHHHHHHHHHHHH CS
                            WXG100   4 vdpeelrqaaarfqkqa 20 
                                       +d++  +q+a+++++ +
  gi|298674807|ref|YP_003726557.1| 245 IDADGFDQMAKDISNGN 261
                                       7899999****999876 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.72
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100   7 eelrqaaarfqkqaeeledelqrl 30 
                                       +e+ + a++f+k +++l d+++r+
  gi|298674807|ref|YP_003726557.1| 364 DEIGSLAKSFDKMSSNLADLVNRI 387
                                       677788888888888888888876 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.006
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHCGCGCT..HHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100   9 lrqaaarfqkqaeeledelqrlkaevdalqsgWs..GaaadafqaefeewkqaaqklvdaLeeisealkqaanafed 83 
                                       ++ aa + +++a+el++  +++ ++ ++++++     + a+     ++e+ +a++++++  ++++++ ++a++ ++d
  gi|298674807|ref|YP_003726557.1| 387 ITIAADNTASKAQELSASSEQMTSTSNQIADTVTeiSNGAQNQSTKIQEVSRAMNDMNQSVQDVASNAQKASEDVTD 463
                                       455666667777777777777777777775555535567888899999*********************99998876 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  56 wkqaaqklvdaLeeisealkq 76 
                                       +  ++++++ a+++ s+ ++ 
  gi|298674807|ref|YP_003726557.1| 478 LSVKMNEVQSAMNDSSQVIQD 498
                                       444455555555555555443 PP

  == domain 5  score: 12.4 bits;  conditional E-value: 0.00023
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCGCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  12 aaarfqkqaeeledelqrlkaevdalqsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqa 77 
                                       +a +++k aee ++  q+++  ++++q++  G+a ++ q+  +e+  + ++l++  e+is  ++++
  gi|298674807|ref|YP_003726557.1| 544 VADEVRKLAEESSNSAQQIEDLIQEIQDS-TGQAVTSIQNGTQEVETGTETLNETVESISTVVENV 608
                                       68999*********************887.8*****************************998875 PP

  == domain 6  score: 5.5 bits;  conditional E-value: 0.032
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC.GCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100   7 eelrqaaarfqkqaeeledelqrlkaevdal.qsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaa 78 
                                       +++++ aa++q+q++++e++ ++++   +   +s+ s + a+a  +e++  +q++ k +++L+e++++lk++ 
  gi|298674807|ref|YP_003726557.1| 613 KMVQDIAASAQEQSASIEEVTSSVEEVSSIAeESASSTEEASASVEEQTSSMQELSKAAQELTETADNLKKSV 685
                                       567888999999999999999998888888888888899999999***********************99875 PP

>> AIP3  Actin interacting protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.3       2.4   1.5e+03     152     191 ..      52      89 ..      32     106 .. 0.47
   2 ?    4.7  20.4     0.021        13      72     202 ..     364     505 ..     339     519 .. 0.56
   3 ?   13.8  15.9   3.8e-05     0.023      66     221 ..     522     692 ..     513     696 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.4
                                       XXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXHHHHHHH CS
                              AIP3 152 sefkseikeslselrekakkvkeaslastkkssnrayiek 191
                                       +++ +e+++ + e  ++ k++   ++ s  +s+nr+ +++
  gi|298674807|ref|YP_003726557.1|  52 ADHANEVEADMREYLTTSKQLS--NVLSEYESGNREEVNN 89 
                                       3333444444444444444444..3333334444444433 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.021
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXX..................XXXX CS
                              AIP3  72 epldevkkhideslaslskelkelkssiesqkaslqevserqeeaakekasesla.........kkelkaqlkevqs 139
                                       +++ ++ k +d++ ++l++ +++++ + +++++++qe+s+++e+ ++++++  +a         +++++++++ev++
  gi|298674807|ref|YP_003726557.1| 364 DEIGSLAKSFDKMSSNLADLVNRITIAADNTASKAQELSASSEQMTSTSNQ--IAdtvteisngAQNQSTKIQEVSR 438
                                       345556666666666666666666666666666666666555555544444..223455664444444444444444 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXX.XXXXXXHHHHHHHHH...HHHHHHHHH CS
                              AIP3 140 lrrdLavlrqlysefkseikeslselrekakkvk..easlastkkssnrayiekgk...kkLseesdk 202
                                         +d++   q  +++ ++ +e +++++ek ++v   + +l s+k+++ ++ ++++    + L+e+s+k
  gi|298674807|ref|YP_003726557.1| 439 AMNDMNQSVQDVASNAQKASEDVTDVSEKSQNVGekSHEL-SVKMNEVQSAMNDSSqviQDLDEKSKK 505
                                       4444444444445555566667777777777776432222.555555566666555111345555554 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 3.8e-05
                                       XXXXX..................XXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXX CS
                              AIP3  66 vLsLn..................iepldevkkhideslaslskelkelkssiesqkaslqevserqeeaakekases 124
                                       +L Ln                   +++ ++ ++ ++s +++++ ++e+++s+ +  +s+q+ +++ e+ +++ ++++
  gi|298674807|ref|YP_003726557.1| 522 LLALNaaieaaragehgrgfavvADEVRKLAEESSNSAQQIEDLIQEIQDSTGQAVTSIQNGTQEVETGTETLNETV 598
                                       56666666666666555555433335555555666666666777777777777777777776666666666666767 PP

                                       XX.........XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXHHHHHHHHHHHHHHHHH CS
                              AIP3 125 lakkelkaqlkevqslrrdLavlrqlysefkseikeslselrekakkvkeaslastkkssnrayiekgkkkLseesd 201
                                        + ++  ++++ v ++ +d+a+  q +s++ +e+++s++e+++ a++   +s  + + s++ +  +++ ++Ls+ ++
  gi|298674807|ref|YP_003726557.1| 599 ESISTVVENVNGVAKMVQDIAASAQEQSASIEEVTSSVEEVSSIAEESA-SS--TEEASASVEEQTSSMQELSKAAQ 672
                                       7788899999999999999999999999999999999999999888777.22..34445555666789999****** PP

                                       HHHHHHHHHHHHHHHHHHHH CS
                              AIP3 202 klvtkvddLqDlvedlrkDV 221
                                       +l +  d+L+  ve  + D 
  gi|298674807|ref|YP_003726557.1| 673 ELTETADNLKKSVEFFKLDS 692
                                       **************999885 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   3.9    0.0011      0.67      14      63 ..     469     518 ..     458     529 .. 0.85
   2 ?    0.0   0.9       1.9   1.2e+03      37      56 ..     562     582 ..     542     596 .. 0.39
   3 ?   11.6   3.8   0.00048       0.3      14      65 ..     592     643 ..     579     652 .. 0.91
   4 ?    1.1   0.5      0.88   5.5e+02      29      58 ..     656     685 ..     643     697 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0011
                           NPV_P10  14 kavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqd 63 
                                       ++v +k   l+ ++++vq+ ++d +++ + Ld+ s+++ e+ + ++nI d
  gi|298674807|ref|YP_003726557.1| 469 QNVGEKSHELSVKMNEVQSAMNDSSQVIQDLDEKSKKIGEIVSMITNIAD 518
                                       567777788889999999999999999999******99999999999987 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.9
                           NPV_P10  37 vtelnekL.daqsaqLaelet 56 
                                       +++l +++ d+  ++++++++
  gi|298674807|ref|YP_003726557.1| 562 IEDLIQEIqDSTGQAVTSIQN 582
                                       222222220222233333333 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00048
                           NPV_P10  14 kavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiL 65 
                                       + +++ V+++++ v++v+   + v+++ +  ++qsa+++e+ ++ve++++i 
  gi|298674807|ref|YP_003726557.1| 592 ETLNETVESISTVVENVNGVAKMVQDIAASAQEQSASIEEVTSSVEEVSSIA 643
                                       568999******************************************9995 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.88
                           NPV_P10  29 dvqenlpdvtelnekLdaqsaqLaeletkv 58 
                                       +v+e+   ++el++  ++++++ ++l+++v
  gi|298674807|ref|YP_003726557.1| 656 SVEEQTSSMQELSKAAQELTETADNLKKSV 685
                                       455555555555555555555555555554 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   1.1         4   2.5e+03     306     322 ..      55      71 ..      33     105 .. 0.35
   2 ?    8.8  14.9   0.00073      0.45      38     182 ..     368     516 ..     352     526 .. 0.74
   3 ?   10.5  17.5   0.00022      0.14      41     221 ..     497     686 ..     493     700 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4
                               MAD 306 lkqlekaqreleqelaq 322
                                       + ++e+  re  +  +q
  gi|298674807|ref|YP_003726557.1|  55 ANEVEADMREYLTTSKQ 71 
                                       11111111111111111 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00073
                               MAD  38 alkrqleeesdrnqelqkrikllekreeekeealreqiElarlk.kknlealnkkekekesklaearevisal...k 110
                                       +l++ +++ s    +l +ri+   ++ + k+++l++  E+  ++ ++  +++++  +  +++ ++++ev++a+   +
  gi|298674807|ref|YP_003726557.1| 368 SLAKSFDKMSSNLADLVNRITIAADNTASKAQELSASSEQMTSTsNQIADTVTEISNGAQNQSTKIQEVSRAMndmN 444
                                       67788888888888999999999888888888888888876654156667777777777777777777766541115 PP

                               MAD 111 nelaelkrqiekqelelsekeseleelqerldllkkklseleqliqqlekkqkelaeaeqrikeLefeiqsq 182
                                       + +++ + +++k+  +++  +++ +++ e+  +l  k++e++  +++  +  + l e+ ++i e+   i + 
  gi|298674807|ref|YP_003726557.1| 445 QSVQDVASNAQKASEDVTDVSEKSQNVGEKSHELSVKMNEVQSAMNDSSQVIQDLDEKSKKIGEIVSMITNI 516
                                       678888888888888899999999999999999999999998888888888888888888888877666554 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00022
                               MAD  41 rqleeesdrnqelqkrikllekreeekeealreqi......Elarlkkknlealnkkekekesklaearevisalkn 111
                                       ++l+e+s++  e+   i+++ ++ +    al++ i      E  r      +++ k+++e +++ ++++++i+++++
  gi|298674807|ref|YP_003726557.1| 497 QDLDEKSKKIGEIVSMITNIADQTNL--LALNAAIeaaragEHGRGFAVVADEVRKLAEESSNSAQQIEDLIQEIQD 571
                                       67888888888888888887777632..223333300011255566667899************************* PP

                               MAD 112 elaelkrqiekqelelsekeseleelqerldllkkklseleqliqqlekkqkelaeaeqrikeLefeiqs....qed 184
                                        + +  ++i++  +e+++ ++ l+e  e      ++++++ + +q+  ++ +e +++ + +     e++s     ++
  gi|298674807|ref|YP_003726557.1| 572 STGQAVTSIQNGTQEVETGTETLNETVESISTVVENVNGVAKMVQDIAASAQEQSASIEEVTSSVEEVSSiaeeSAS 648
                                       *****************************************999888888887777777666655555554433666 PP

                               MAD 185 dslivknsksel.aripelekelerlreenkklnelke 221
                                       + ++  +s +e+  ++ el k  ++l e   +l+++ e
  gi|298674807|ref|YP_003726557.1| 649 STEEASASVEEQtSSMQELSKAAQELTETADNLKKSVE 686
                                       66666666666667788888888888888777776654 PP

>> FPP  Filament-like plant protein, long coiled-coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   1.8       3.8   2.4e+03     764     798 ..      52      86 ..      32     104 .. 0.37
   2 ?   14.1  34.8   1.7e-05      0.01     457     820 ..     359     675 ..     288     699 .. 0.48

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3.8
                               FPP 764 etrateleaelnelkqkieaLeveLeeekksheel 798
                                         +a+e+ea+++e  +  ++L++ L+e ++  +e 
  gi|298674807|ref|YP_003726557.1|  52 ADHANEVEADMREYLTTSKQLSNVLSEYESGNREE 86 
                                       22222222222222222222222222222222222 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1.7e-05
                               FPP 457 lskLqsrlkvilesrvkekslekiledirvalkevneesaeasdslasseeeeedassdektlkedslevekeeevs 533
                                       l++ ++ + ++ +s                                               +++++ +++ + ++ +
  gi|298674807|ref|YP_003726557.1| 359 LTQNDDEIGSLAKS---------------------------------------------FDKMSSNLADLVNRITIA 390
                                       33333333333333.............................................333344444444444445 PP

                               FPP 534 eeeksseeeskqkiqqelskaiskiielveslskealklqdkssksselsevleqFsavvndllsgkadledfvleL 610
                                        +++ s+ ++ +++++++++  ++i + v+ +s+ a +    s+k +e+s+ +++  ++v+d+ s+ ++ ++ v+++
  gi|298674807|ref|YP_003726557.1| 391 ADNTASKAQELSASSEQMTSTSNQIADTVTEISNGAQNQ---STKIQEVSRAMNDMNQSVQDVASNAQKASEDVTDV 464
                                       555555555555555566666666666666665554333...55556666666666666666666655555555555 PP

                               FPP 611 ssvldeise....lkfslldv.ssmeeeikksddidkvalsenkvaqkgessnecaeisklssekeipselplvsgs 682
                                       s+  +++ e    l +++ +v s+m++ ++  +d+d+ + +  +++++  +  + +++  l+   e    +   +g 
  gi|298674807|ref|YP_003726557.1| 465 SEKSQNVGEksheLSVKMNEVqSAMNDSSQVIQDLDEKSKKIGEIVSMITNIADQTNLLALNAAIEAARAGEHGRG- 540
                                       5544444331100233333321223333344444444444444443331111111112222222222222222222. PP

                               FPP 683 neskkeenkllkeeleelksekenlevelksatenleslkaqlqesEqllaelkseLeslkeskslaetqlkcmkes 759
                                       +   ++e ++l ee  +   +   +e  +++ +++  ++++ +q+  q ++  ++ L+++ es s + + ++  + +
  gi|298674807|ref|YP_003726557.1| 541 FAVVADEVRKLAEESSNSAQQ---IEDLIQEIQDSTGQAVTSIQNGTQEVETGTETLNETVESISTVVENVNGVAKM 614
                                       222233333333333222222...22223333333334444444444444444445555555555555555555555 PP

                               FPP 760 yesletrateleaelnelkqkieaLeveLeeekksheeleakckelqeqlervekkevsks 820
                                        +++   a+e  a ++e+ + +e++++  ee  +s ee+ a+++e    ++  +k      
  gi|298674807|ref|YP_003726557.1| 615 VQDIAASAQEQSASIEEVTSSVEEVSSIAEESASSTEEASASVEEQTSSMQELSKAAQELT 675
                                       5555555555555555555555555555555555555555555555555554443322211 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.9      0.28   1.7e+02      47      91 ..      44      88 ..      33     109 .. 0.58
   2 ?    5.5   8.6     0.028        18      26     126 ..     355     455 ..     347     460 .. 0.74
   3 ?    6.1   9.6     0.019        12      32     117 ..     435     519 ..     432     533 .. 0.75
   4 ?    8.2   2.2    0.0043       2.7      39      97 ..     547     605 ..     540     607 .. 0.80
   5 ?   11.4   8.5   0.00044      0.27      26     125 ..     580     685 ..     577     691 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.28
                                      CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC CS
                         Fib_alpha 47 isnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeil 91
                                      +++s++ a ++ +e++  +re  +++k+ +nv++++++  +ee++
  gi|298674807|ref|YP_003726557.1| 44 YKESSEMAADHANEVEADMREYLTTSKQLSNVLSEYESGNREEVN 88
                                      344455555555555555555555555555555555555555544 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.028
                                       CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHCCCHHHHHHHCCH CS
                         Fib_alpha  26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn.dnvikksskeleeeilrlketidaqe 101
                                       +++  ++ ++++ +l ++++++s++  +  + ++   d +++k ++ + + +++++ s++  +  ++++ +  ++q 
  gi|298674807|ref|YP_003726557.1| 355 IDDSLTQNDDEIGSLAKSFDKMSSNLADLVNRITIAADNTASKAQELSASsEQMTSTSNQIAD-TVTEISNGAQNQS 430
                                       556667778889999999999988888887777776666655555555451555555555555.9************ PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 102 snirvLqnvlesneqkiqkLeqdid 126
                                       ++i++    +++ +q++q+  ++ +
  gi|298674807|ref|YP_003726557.1| 431 TKIQEVSRAMNDMNQSVQDVASNAQ 455
                                       *************999999876655 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.019
                                       CCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHH CS
                         Fib_alpha  32 dvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLq 108
                                       +v++ ++++++++++++++ ++a+e v++++++ ++  +++++ +  ++++++ ++ + +++ + +d++ ++i ++ 
  gi|298674807|ref|YP_003726557.1| 435 EVSRAMNDMNQSVQDVASNAQKASEDVTDVSEKSQNVGEKSHELSVKMNEVQSAMN-DSSQVIQDLDEKSKKIGEIV 510
                                       67788888888888888888888888888888888888888877888888888888.77777778888888888777 PP

                                       HHHHHHHHH CS
                         Fib_alpha 109 nvlesneqk 117
                                       +++ +   +
  gi|298674807|ref|YP_003726557.1| 511 SMITNIADQ 519
                                       777766544 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.0043
                                       CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHH CS
                         Fib_alpha  39 kleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketi 97 
                                       ++++  ee sns +++e+l++ei+ds+ ++ +s ++ ++ ++  +++l+e ++ +   +
  gi|298674807|ref|YP_003726557.1| 547 EVRKLAEESSNSAQQIEDLIQEIQDSTGQAVTSIQNGTQEVETGTETLNETVESISTVV 605
                                       56677788899999999999999999999999999778888888888887777776655 PP

  == domain 5  score: 11.4 bits;  conditional E-value: 0.00044
                                       CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHCCC...HHHHH CS
                         Fib_alpha  26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn...dnvikksskeleeeil...rlket 96 
                                       +++  ++v++  e+l++++e+is   ++++ + k ++d+ +++q++++     ++ ++++s+  ee  +   +  ++
  gi|298674807|ref|YP_003726557.1| 580 IQNGTQEVETGTETLNETVESISTVVENVNGVAKMVQDIAASAQEQSASIeevTSSVEEVSSIAEESASsteEASAS 656
                                       677889999*****************************999999999864233455556666666554400044457 PP

                                       HHCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  97 idaqesnirvLqnvlesneqkiqkLeqdi 125
                                       + +q s++++L +  +++ +   +L++ +
  gi|298674807|ref|YP_003726557.1| 657 VEEQTSSMQELSKAAQELTETADNLKKSV 685
                                       88888888888888888888888888766 PP

>> Serine_rich  Serine rich protein interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9  10.1    0.0047       2.9       9     102 ..     400     502 ..     393     534 .. 0.79
   2 ?    3.3   0.5      0.12        72      66     147 ..     527     616 ..     499     621 .. 0.59
   3 ?    3.7   7.0     0.092        57       7     120 ..     591     674 ..     544     697 .. 0.44

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0047
                       Serine_rich   9 tlarlqqevesavskLlsfvsskWRskenleanlqeirlavdrlrtslrefleFargalanaaklsd.........k 76 
                                       +l+   ++++s+ +++ + v++     +n++ ++qe+ +a++++++s+++++  a++a    + +s+         +
  gi|298674807|ref|YP_003726557.1| 400 ELSASSEQMTSTSNQIADTVTEISNGAQNQSTKIQEVSRAMNDMNQSVQDVASNAQKASEDVTDVSEksqnvgeksH 476
                                       56666777778888888888888888999*******************************99999988867777777 PP

                       Serine_rich  77 nlqtkLrkqlqkledsdqilqetsqe 102
                                       +l+ k+++  ++++ds q++q+  ++
  gi|298674807|ref|YP_003726557.1| 477 ELSVKMNEVQSAMNDSSQVIQDLDEK 502
                                       77777777777777777777765554 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.12
                       Serine_rich  66 alanaaklsd.....knlqtkLrkqlqkledsdqilqetsqeLdsceWslealasdkkqek...pddlDrlvmvart 134
                                       a+  aa++ +       ++   rk+ ++ ++s+q +++  qe++++  ++ +  ++  qe    +++l+  v   +t
  gi|298674807|ref|YP_003726557.1| 527 AAIEAARAGEhgrgfAVVADEVRKLAEESSNSAQQIEDLIQEIQDSTGQAVTSIQNGTQEVetgTETLNETVESIST 603
                                       55555555554444445666667777777777777777777765554444444444444334667777777777777 PP

                       Serine_rich 135 vpdDvkqlasfiq 147
                                       v + v+ +a ++q
  gi|298674807|ref|YP_003726557.1| 604 VVENVNGVAKMVQ 616
                                       7777777777776 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.092
                       Serine_rich   7 letlarlqqevesavskLlsfvsskWRskenleanlqeirlavdrlrtslrefleFargalanaaklsdknlqtkLr 83 
                                        etl+++     +++s  ++ v+   +  + + a +qe  ++++++ +s++e+   a+++                 
  gi|298674807|ref|YP_003726557.1| 591 TETLNET----VESISTVVENVNGVAKMVQDIAASAQEQSASIEEVTSSVEEVSSIAEES----------------- 646
                                       2222222....2222222222222223334444444444444444444444444444443................. PP

                       Serine_rich  84 kqlqkledsdqilqetsqeLdsceWslealasdkkqe 120
                                                ++  +e+s + +++  s++ l++  ++ 
  gi|298674807|ref|YP_003726557.1| 647 ---------ASSTEEASASVEEQTSSMQELSKAAQEL 674
                                       .........3333333333333333333333332222 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.9      0.69   4.3e+02     334     381 ..      43      90 ..      32     119 .. 0.63
   2 ?   10.8  25.7   0.00027      0.16     255     482 ..     353     601 ..     328     609 .. 0.69
   3 ?    4.6  20.0     0.019        12     269     397 ..     553     694 ..     542     698 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.69
                            DUF812 334 elqeqieeleskieeleeeikklessikqveeeleeekeeneelekev 381
                                       + +e  e +   ++e+e++++++ ++ kq+++ l e ++ n e+ +++
  gi|298674807|ref|YP_003726557.1|  43 AYKESSEMAADHANEVEADMREYLTTSKQLSNVLSEYESGNREEVNNM 90 
                                       444444555555566666666666666666666666666665555443 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00027
                            DUF812 255 eqlrkaalkseeae....ssasksksdlaellsefseksetdslktkgsrfthaeklqftke.......elakkaet 320
                                       +++  ++++++ ++    +s  k +s+la+l+++++ ++ +++  + ++  +++e+++ t++       e ++ a++
  gi|298674807|ref|YP_003726557.1| 353 AKIDDSLTQNDDEIgslaKSFDKMSSNLADLVNRITIAA-DNTASKAQELSASSEQMTSTSNqiadtvtEISNGAQN 428
                                       444444444433332001333345556666666662222.2222222222333333322222233334344588888 PP

                            DUF812 321 eeelkkkreeeleelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlellpdaeen 397
                                       +    ++ ++ ++++++ ++++ s++++ +e++ +++++ + v e+  e+  + +e ++ ++   ++++ l++  + 
  gi|298674807|ref|YP_003726557.1| 429 QSTKIQEVSRAMNDMNQSVQDVASNAQKASEDVTDVSEKSQNVGEKSHELSVKMNEVQSAMNDSSQVIQDLDEKSKK 505
                                       88888999999****************************************************************** PP

                            DUF812 398 iekLqalveasa..qrlvelakqWekhRv........plieeyrelkesksekekeaerkleeikklr.ekmkevae 463
                                       i +  +++ + a   +l+ l +  e++R+         + +e r+l e+ s+ ++++e+ ++ei+    + +  +++
  gi|298674807|ref|YP_003726557.1| 506 IGEIVSMITNIAdqTNLLALNAAIEAARAgehgrgfaVVADEVRKLAEESSNSAQQIEDLIQEIQDSTgQAVTSIQN 582
                                       ********97651167999********96333333325778999999999999999999999998654145566666 PP

                            DUF812 464 elrqkeellkqLvaelekl 482
                                        +++ e  ++ L++ +e++
  gi|298674807|ref|YP_003726557.1| 583 GTQEVETGTETLNETVESI 601
                                       6666666666666666655 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.019
                            DUF812 269 ssasksksdlaellsefseksetd.slktkgsrfthaeklqftke............elakkaeteeelkkkreeel 332
                                       +++s+s++++++l++e+++++ +  ++ ++g++  ++ + ++++              +ak +++     +++++++
  gi|298674807|ref|YP_003726557.1| 553 EESSNSAQQIEDLIQEIQDSTGQAvTSIQNGTQEVETGTETLNETvesistvvenvnGVAKMVQDIAASAQEQSASI 629
                                       44556677777777777333322212233444444444444433333444444433333378888888899999999 PP

                            DUF812 333 eelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlellpdaeen 397
                                       ee+ + +ee++s +ee ++  ++ ++s+++ +++++e+ +  +el+++ ++ kk +e  + + ++
  gi|298674807|ref|YP_003726557.1| 630 EEVTSSVEEVSSIAEESASSTEEASASVEEQTSSMQELSKAAQELTETADNLKKSVEFFKLDSSQ 694
                                       99999999999999999999999999999999999999999999999999999988877665555 PP

>> Vps53_N  Vps53-like, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   3.0       0.5   3.1e+02      20      92 ..     359     438 ..     349     441 .. 0.66
   2 ?    3.7   7.4      0.04        25      32      91 ..     406     465 ..     377     467 .. 0.85
   3 ?    9.8   8.5   0.00055      0.34      19      92 ..     439     515 ..     436     522 .. 0.89
   4 ?    2.3   2.8      0.11        65      38      94 ..     545     601 ..     535     604 .. 0.74
   5 ?   10.1   8.9   0.00044      0.27      21     112 ..     592     682 ..     588     685 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.5
                           Vps53_N  20 lanideli.......kklqeeikklddeiksvvraqanvgekgkealeeaqkaieelfqkikeikdkaekseemvke 89 
                                       l++ d+ i       +k+  ++  l + i  + ++ a+ +++   + e+++++ +++ + ++ei + a++  + ++e
  gi|298674807|ref|YP_003726557.1| 359 LTQNDDEIgslaksfDKMSSNLADLVNRITIAADNTASKAQELSASSEQMTSTSNQIADTVTEISNGAQNQSTKIQE 435
                                       44444444222244466666666677777777777777777766777777777788888888888888888888888 PP

                           Vps53_N  90 itr 92 
                                       ++r
  gi|298674807|ref|YP_003726557.1| 436 VSR 438
                                       876 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.04
                           Vps53_N  32 eeikklddeiksvvraqanvgekgkealeeaqkaieelfqkikeikdkaekseemvkeit 91 
                                       e++    ++i+ +v + +n +++   +++e+ +a++++ q+++++ + a+k+ e v +++
  gi|298674807|ref|YP_003726557.1| 406 EQMTSTSNQIADTVTEISNGAQNQSTKIQEVSRAMNDMNQSVQDVASNAQKASEDVTDVS 465
                                       455667788999999999999999999************************999998876 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00055
                           Vps53_N  19 slanidelikklqeeikklddeiksvvraqanvgekgke...aleeaqkaieelfqkikeikdkaekseemvkeitr 92 
                                       +++++++ ++ +  + +k  +++  v +++ nvgek++e   +++e+q+a+++ +q i+++ +k++k  e+v+ it+
  gi|298674807|ref|YP_003726557.1| 439 AMNDMNQSVQDVASNAQKASEDVTDVSEKSQNVGEKSHElsvKMNEVQSAMNDSSQVIQDLDEKSKKIGEIVSMITN 515
                                       578889999999999999999999999999****999875557*****************************99995 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.11
                           Vps53_N  38 ddeiksvvraqanvgekgkealeeaqkaieelfqkikeikdkaekseemvkeitrdI 94 
                                        de++++ ++++n++++ ++ ++e+q++  + + +i++  +  e   e+++e  + I
  gi|298674807|ref|YP_003726557.1| 545 ADEVRKLAEESSNSAQQIEDLIQEIQDSTGQAVTSIQNGTQEVETGTETLNETVESI 601
                                       678889999999999999988999998887777777766666666666666655555 PP

  == domain 5  score: 10.1 bits;  conditional E-value: 0.00044
                           Vps53_N  21 anidelikklqeeikklddeiksvvraqanvgekgkealeeaqkaieelfqkikeikdkaekseemvkeitrdIkqL 97 
                                       + ++e+++++ + +++++   k +v++ a ++++   ++ee+++++ee+++  +e  + +e++ ++v+e t+ +++L
  gi|298674807|ref|YP_003726557.1| 592 ETLNETVESISTVVENVNGVAK-MVQDIAASAQEQSASIEEVTSSVEEVSSIAEESASSTEEASASVEEQTSSMQEL 667
                                       5678899999998888866555.555555577887999*************************************** PP

                           Vps53_N  98 DiAKknlttsiTtlk 112
                                         A ++lt +   lk
  gi|298674807|ref|YP_003726557.1| 668 SKAAQELTETADNLK 682
                                       ********9877665 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0         2   1.2e+03      48      79 ..     355     386 ..     336     387 .. 0.76
   2 ?   -0.7   2.3       2.5   1.5e+03      44      44 ..     463     463 ..     414     520 .. 0.51
   3 ?    9.9   0.7    0.0012      0.77       5      64 ..     561     634 ..     551     640 .. 0.90
   4 ?    4.6   0.6     0.057        35      44      78 ..     649     683 ..     643     685 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2
                              Med9  48 idrsveeqeaeieeleeqlakKrelLkkyknr 79 
                                       id s  + ++ei +l ++ +k  + L+++ nr
  gi|298674807|ref|YP_003726557.1| 355 IDDSLTQNDDEIGSLAKSFDKMSSNLADLVNR 386
                                       99999999999999999999888888887776 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.5
                              Med9  44 e 44 
                                        
  gi|298674807|ref|YP_003726557.1| 463 D 463
                                       1 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0012
                              Med9   5 liydilksiekdp.......nlsskdletktgelrhkLkkarelirelpg.......idrsveeqeaeieelee 64 
                                       +i d++++i++ +       ++ ++++et t  l+   +++ ++++++ g       i  s +eq a iee   
  gi|298674807|ref|YP_003726557.1| 561 QIEDLIQEIQDSTgqavtsiQNGTQEVETGTETLNETVESISTVVENVNGvakmvqdIAASAQEQSASIEEVTS 634
                                       577889999888888999999999**************************9999999999*****999998765 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.057
                              Med9  44 elpgidrsveeqeaeieeleeqlakKrelLkkykn 78 
                                       + ++ + sveeq   ++el++  +   e   ++k+
  gi|298674807|ref|YP_003726557.1| 649 STEEASASVEEQTSSMQELSKAAQELTETADNLKK 683
                                       5677899*************999998887777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (705 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3043  (0.169725); expected 358.6 (0.02)
Passed bias filter:                      762  (0.042501); expected 358.6 (0.02)
Passed Vit filter:                       197  (0.0109878); expected 17.9 (0.001)
Passed Fwd filter:                       147  (0.00819901); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 2.23u 0.40s 00:00:02.63 Elapsed: 00:00:00.66
# Mc/sec: 3222.25
//
Query:       gi|298674808|ref|YP_003726558.1|  [L=167]
Description: CheW protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-42  144.3   3.2    2.1e-42  144.1   3.2    1.1  1  CheW      CheW-like domain


Domain annotation for each model (and alignments):
>> CheW  CheW-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.1   3.2   1.1e-46   2.1e-42       1     137 [.      17     154 ..      17     155 .. 0.97

  Alignments for each domain:
  == domain 1  score: 144.1 bits;  conditional E-value: 1.1e-46
                                       EEEEEEETTEEEEEEGGGEEEEEECCT.BTTTTSSTTEEEEEEETTEEEEEEEHHHHCTSSSSTTSTCEEEEEEEET CS
                              CheW   1 qlllfrlgeetyaiplakvreilevppitpipgapgavlgvinlrGevipvidLrellglgpeesrentrvivvelg 77 
                                       ql+ f lg+e++++++++v+ei++++++t+ip+ap++v+gvin+rG++i v++L + lgl+++e +e++r+ivve+g
  gi|298674808|ref|YP_003726558.1|  17 QLVAFNLGDEEFGVDIMQVQEIIRMQEVTRIPQAPDFVKGVINIRGKIIVVVSLDKCLGLESKETDEHSRIIVVEVG 93 
                                       7899************************************************************************* PP

                                       TEEEEEEESEEEEEEEEECCGEETT..TSSTSSTCCCEEEEEECTTSEEEEEE-CCCHHHHH CS
                              CheW  78 nqvvGllVdevkgiqeivikqiepp..lglssdlagyisGatklgdgrlvliLDveallrsl 137
                                       ++vvG++Vd+v++i++i++++iep+  +  s+++a+y++G+ kl ++rl+++LD+e++l+++
  gi|298674808|ref|YP_003726558.1|  94 GSVVGMVVDSVSEILSIQESSIEPApdIIASKINADYLKGVGKL-ENRLLILLDLEKILTEE 154
                                       ***************************55599************.999**********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 988.81
//
Query:       gi|298674809|ref|YP_003726559.1|  [L=118]
Description: response regulator receiver protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-30  104.8   3.5      3e-30  104.7   3.5    1.0  1  Response_reg  Response regulator receiver domain
  ------ inclusion threshold ------
      0.085   12.0   0.0       0.27   10.4   0.0    1.6  2  2-ph_phosp    2-phosphosulpholactate phosphatase


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.7   3.5   3.3e-34     3e-30       1     111 [.       4     114 ..       4     115 .. 0.98

  Alignments for each domain:
  == domain 1  score: 104.7 bits;  conditional E-value: 3.3e-34
                                       EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEE CS
                      Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviil 77 
                                       v+ivdD   +r++++++l+++g e+vaea+dg+e +e++   k+dl+++D+ mp+m+G e+lk+i + dpe +vi++
  gi|298674809|ref|YP_003726559.1|   4 VMIVDDAAFMRMVIKDILTKNGHEVVAEASDGTESVEKYPDLKPDLVFMDVVMPTMEGTEALKKIMDMDPEAKVIMC 80 
                                       89*************************************************************************** PP

                                       ESSTSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                      Response_reg  78 tahseeedavealkagaddflsKpfdpeeLlkal 111
                                       ++ +++++++ea+++ga+df++Kpfd +++++ +
  gi|298674809|ref|YP_003726559.1|  81 SSIGQQSVVKEAIDIGAQDFIVKPFDADKVMEVV 114
                                       *****************************99987 PP

>> 2-ph_phosp  2-phosphosulpholactate phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0     0.091   8.1e+02      89     107 ..      24      42 ..      13      52 .. 0.76
   2 ?   10.4   0.0     3e-05      0.27      92     130 ..      53      94 ..      45     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.091
                                       TTSEEEEE-CCHHHHHHHC CS
                        2-ph_phosp  89 kgktvvltTtNGTraleka 107
                                       +g++vv  ++ GT+++ek 
  gi|298674809|ref|YP_003726559.1|  24 NGHEVVAEASDGTESVEKY 42 
                                       4778888888888877765 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 3e-05
                                       EEEEE-CCHHHHHHHCCTS...SEEEEE-STTHHHHHHHHHH CS
                        2-ph_phosp  92 tvvltTtNGTralekaasa...krvligsllNakavaeklke 130
                                       +vv+ T  GT+al+k+ +     +v+++s +  ++v++++ +
  gi|298674809|ref|YP_003726559.1|  53 DVVMPTMEGTEALKKIMDMdpeAKVIMCSSIGQQSVVKEAID 94 
                                       69**************98435589***********9988654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 738.45
//
Query:       gi|298674810|ref|YP_003726560.1|  [L=363]
Description: response regulator receiver modulated CheB methylesterase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.7e-60  201.9   0.1    1.4e-59  200.6   0.1    1.7  1  CheB_methylest  CheB methylesterase
    9.1e-22   77.4   0.1    2.6e-21   75.9   0.1    1.8  1  Response_reg    Response regulator receiver domain
  ------ inclusion threshold ------
      0.027   14.1   0.0      0.053   13.2   0.0    1.4  1  ATP-synt_ab     ATP synthase alpha/beta family, nucleotide-bi


Domain annotation for each model (and alignments):
>> CheB_methylest  CheB methylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.6   0.1   2.3e-63   1.4e-59       1     169 [.     175     357 ..     175     358 .. 0.95

  Alignments for each domain:
  == domain 1  score: 200.6 bits;  conditional E-value: 2.3e-63
                                       EEEEE-TTHHHHHTTTGGGS-TT-SS-EEEEE---TT-HHHHHHHHHHH-SSEEEE--TT-B--TTEEEE--TTSEE CS
                    CheB_methylest   1 vvigaStGGlealkellaalpedfpaavvvvqhmppsftsslaelLnresslkVkeaedgeelepgrvyvapgdkhl 77 
                                       v+ig+StGG++al++l+++lp ++p++v+vvqhmp++ft s+a++Ln++ssl+V+ea++g+ +e+g vy+apgd+h+
  gi|298674810|ref|YP_003726560.1| 175 VAIGSSTGGPRALEKLIPKLPGNLPVPVLVVQHMPAGFTDSFAKRLNQKSSLEVREAKEGDVIEKGIVYLAPGDYHM 251
                                       89*************************************************************************** PP

                                       EEE................E.E.-.-SS-HHHHHHHHHHHH.GGEEEEE-SBSS-TTHHHHHHHHHTT-EEEEE-GG CS
                    CheB_methylest  78 lie...........lals.a.k.kgerpsiDvlfesaaeaygeraigviLtGmgsDGaeGlkaikeaggltiaqdpe 140
                                       +i+           ++l+ + + +g rps++vl++s+  +yg+ ++ viLtGmgsDG+eG+++++++g+ +ia+ ++
  gi|298674810|ref|YP_003726560.1| 252 EITkknirgiskevISLNqKpReHGVRPSVNVLLRSLKPVYGSGVLSVILTGMGSDGSEGVAELNKQGAQCIAEAES 328
                                       ***99999988877656642333556*************************************************** PP

                                       G-SSBSHHHHHHHTT--SEEE-GGGHHHH CS
                    CheB_methylest 141 savvpgmPkaaieagavdevlpleeiaee 169
                                       s++++gmPka++++g++d v+++++ia++
  gi|298674810|ref|YP_003726560.1| 329 SCIIYGMPKAIVNSGLADTVATIDNIAKK 357
                                       **************************987 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.9   0.1   4.3e-25   2.6e-21       2     103 ..       6     109 ..       5     115 .. 0.93

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 4.3e-25
                                       EEESSSHHHHHHHHHHHH.HTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEE CS
                      Response_reg   2 livdDdplvrellrqlle.eegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviil 77 
                                       l+vdD+  +r++++++l+ + +++++a+ ++g+ea+e++++ k+d+i+lD  mp +dGl++l  i  e   +pv++l
  gi|298674810|ref|YP_003726560.1|   6 LVVDDSAFMRKVITDILNnDPEITVIATSRNGQEAIEKTEKLKPDVITLDNHMPVLDGLHALGYIMSEC-PTPVVML 81 
                                       8*****************999999*****************************************8877.79***** PP

                                       ESSTS..HHHHHHHHHCTESEEEESSG- CS
                      Response_reg  78 tahse..eedavealkagaddflsKpfd 103
                                       +a +e   e++  a+++ga+df++Kp  
  gi|298674810|ref|YP_003726560.1|  82 SAVDEkaAETTLTAFEYGAVDFIQKPSG 109
                                       *776645789999*************76 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   8.9e-06     0.053     155     209 ..     226     284 ..     203     287 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.9e-06
                                       E...TSSEEEEEEEEEEE-GGCSTTSHHHH.HHHHHSSEEEEB-HHHHHTTBSSSBCTT CS
                                       x...xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 155 a...pdrtGsvtivaavspaggDfsdpvtt.atlgitdgfivLdkklaqrkhfPainvl 209
                                       +   + ++G v    +v+ a gD++  +t+ +++gi +  i L++k  +++++P++nvl
  gi|298674810|ref|YP_003726560.1| 226 LevrEAKEGDVIEKGIVYLAPGDYHMEITKkNIRGISKEVISLNQKPREHGVRPSVNVL 284
                                       24455578999999**********9999853799***********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       936  (0.0522059); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 2175.11
//
Query:       gi|298674811|ref|YP_003726561.1|  [L=690]
Description: signal transduction histidine kinase CheA [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-22   78.8   1.6    6.1e-22   77.8   1.6    1.6  1  CheW          CheW-like domain
    7.3e-22   77.2   3.8    7.3e-22   77.2   3.8    3.1  2  P2            P2 response regulator binding domain
      1e-19   70.5   0.6    3.5e-19   68.9   0.6    2.0  1  Hpt           Hpt domain
      5e-19   68.9   0.2    2.3e-18   66.7   0.2    2.2  1  HATPase_c     Histidine kinase-, DNA gyrase B-, and HSP90-lik
    1.1e-13   51.4   3.2    1.1e-13   51.4   3.2    3.3  3  H-kinase_dim  Signal transducing histidine kinase, homodimeri
    0.00062   19.6   0.2    0.00062   19.6   0.2    2.7  3  HATPase_c_3   Histidine kinase-, DNA gyrase B-, and HSP90-lik
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.082   12.9   0.0    2.3  2  HATPase_c_2   Histidine kinase-like ATPase domain
          2    8.2   8.6        5.1    6.8   4.6    2.4  2  ATP11         ATP11 protein
        4.2    7.2   8.9        1.8    8.5   1.3    3.5  3  DASH_Dam1     DASH complex subunit Dam1
          6    7.0  10.6         22    5.2   4.4    2.6  2  CPSF100_C     Cleavage and polyadenylation factor 2 C-termina


Domain annotation for each model (and alignments):
>> CheW  CheW-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.8   1.6   3.4e-25   6.1e-22       3     133 ..     561     689 ..     559     690 .] 0.95

  Alignments for each domain:
  == domain 1  score: 77.8 bits;  conditional E-value: 3.4e-25
                                       EEEEETTEEEEEEGGGEEEEEECCT.BTTTTSSTTEEEEEEETTEEEEEEEHHHHCTSSSSTT....STCEEEEEEE CS
                              CheW   3 llfrlgeetyaiplakvreilevppitpipgapgavlgvinlrGevipvidLrellglgpees....rentrvivve 75 
                                       +l ++ +ety+ipl +v   +++++ ++i++ +g   + i lrGev+p+++L+ +l+ +++++    + + +v++ve
  gi|298674811|ref|YP_003726561.1| 561 ILAKVSDETYVIPLTNVVRNVSIKE-SDIKTIKGE--EAILLRGEVLPIVRLHDVLNTSKNNQqqddDGELIVVIVE 634
                                       678999*******************.*********..*****************************99********* PP

                                       ETTEEEEEEESEEEEEEEEECCGEETT.TSSTSSTCCCEEEEEECTTSEEEEEE-CCCH CS
                              CheW  76 lgnqvvGllVdevkgiqeivikqiepp.lglssdlagyisGatklgdgrlvliLDveal 133
                                       + +++vGl+Vd ++g qe+ ik +++  l+   + +g ++Gat+lgdg+++liLD+  l
  gi|298674811|ref|YP_003726561.1| 635 RMGKKVGLIVDDLIGKQEVMIKTLDNKlLK---NTKG-FAGATILGDGNVALILDISTL 689
                                       ***************************444...7777.******************988 PP

>> P2  P2 response regulator binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   2.8       2.8   5.1e+03      45      68 ..     146     171 ..      88     178 .. 0.76
   2 !   77.2   3.8   4.1e-25   7.3e-22       3      81 .]     179     257 ..     177     257 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.8
                                       T-S.SSEEEEEEE.ESS-HHHHHHHH CS
                                P2  45 ekf.degfevvll.tkeskeeikeal 68 
                                       e+  +++fe+ +  ++e+ ++i++a 
  gi|298674811|ref|YP_003726561.1| 146 ETTsETDFELNIDfSDEEIQQIQDAN 171
                                       44457788888844788777777765 PP

  == domain 2  score: 77.2 bits;  conditional E-value: 4.1e-25
                                       EEEEE--TT-SSHHHHHHHHHHHHHHTTEEEEEES-HHHHHTT-SSSEEEEEEEESS-HHHHHHHHHTSSS-SEEEE CS
                                P2   3 kikvkldedclmksvRaflvfkaLeelgeiiksiPsvedieeekfdegfevvlltkeskeeikealasiseiesvev 79 
                                        +k++ld++c++ks+R+ +v+k+++e+g+iik++Ps++d++ee+f+++f vv++t+++++ ike++++isei++v++
  gi|298674811|ref|YP_003726561.1| 179 GAKITLDDSCMLKSARSSIVLKKISEYGTIIKTVPSMDDLDEENFETEFNVVFSTENNQDIIKEEVQKISEIQNVTL 255
                                       589************************************************************************98 PP

                                       EE CS
                                P2  80 ee 81 
                                       +e
  gi|298674811|ref|YP_003726561.1| 256 SE 257
                                       75 PP

>> Hpt  Hpt domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.9   0.6   1.9e-22   3.5e-19       2      83 ..       6      97 ..       5     106 .. 0.86

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 1.9e-22
                                      HHHHHHHHHHHHHHHHHHHH........SCCHHHHHHHHHHHHHHHHHHTTBHHHHHHHHHHHHHHH..HCTSCHHHHH CS
                               Hpt  2 llelfleeaeelleqleqal........dqedlqelaraaHtLKGsagmlGltelaelahelEdlld..ragelelepe 70
                                      + ++f +e++e+l+ql+++l        d e+++ ++r aHtLKG+a+++G++ +ael+he+E+l+d  r+++ +l+++
  gi|298674811|ref|YP_003726561.1|  6 YKQVFQAESDEHLQQLNDSLlkleqnheDLEQINIMFRSAHTLKGMASTMGFSSIAELTHEMENLMDgiRNKQIKLDDS 84
                                      679********************986555556666******************************************** PP

                                      HHHHHHHHHHHHH CS
                               Hpt 71 llealkallealr 83
                                       ++ l ++l+ ++
  gi|298674811|ref|YP_003726561.1| 85 IIDILFECLDTIE 97
                                      ***5555555444 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.7   0.2   1.3e-21   2.3e-18       4     111 ..     415     554 ..     412     555 .. 0.89

  Alignments for each domain:
  == domain 1  score: 66.7 bits;  conditional E-value: 1.3e-21
                                       HHHHHHHHHHHHHHHHH......HSTTTEEEEEEEEEE..TEEEEEEEESSSSSTTHHHT................. CS
                         HATPase_c   4 krLrqiisnlvdNavkf......atkageieveikase..ddlvisveDnGiGipkedlk................. 55 
                                       + L ++++n vd+ +++      ++k+++++++++as   + + i+veD+G+G+++++l                  
  gi|298674811|ref|YP_003726561.1| 415 DPLVHLLRNSVDHGIEEpekrreTGKSETGHIRLSASRqrNSILIEVEDDGKGMNPDKLRetavkkglmsqsevdrm 491
                                       6799*************9999873344455555555233589999******************************** PP

                                       .......GTCS.TTCHHCSTCHTSTSSSHHHHHHHH.HHHHTTTEEEEEEETTTEEEEEEEEESS CS
                         HATPase_c  56 .......klfe.kfsqddstkrggggtGlGlsivkk.lvelmgGeiwvesepgrGttftftlple 111
                                              ++f+  fs  +++ ++ +g+G+G+  vk+ + e +gG+++ es +g+Gt+++++lpl+
  gi|298674811|ref|YP_003726561.1| 492 sdeeamnLIFTpGFSG-AEKVTDVSGRGVGMDAVKAkIEE-LGGSVKTESFEGEGTKIQLQLPLT 554
                                       ***********99999.9999999************6666.**********************97 PP

>> H-kinase_dim  Signal transducing histidine kinase, homodimeric domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.5      0.48   8.6e+02      37      63 ..      10      36 ..       3      41 .. 0.84
   2 ?   -3.0   0.2       5.6     1e+04      27      27 ..     277     277 ..     237     305 .. 0.52
   3 !   51.4   3.2   6.1e-17   1.1e-13       2      68 ..     308     366 ..     307     367 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.48
                      H-kinase_dim 37 fenglkasvtelksslqnlgrisgeLQ 63
                                      f++++++  ++l++sl +l++  ++L 
  gi|298674811|ref|YP_003726561.1| 10 FQAESDEHLQQLNDSLLKLEQNHEDLE 36
                                      57889999999*********9999995 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.6
                      H-kinase_dim  27 r 27 
                                       +
  gi|298674811|ref|YP_003726561.1| 277 E 277
                                       1 PP

  == domain 3  score: 51.4 bits;  conditional E-value: 6.1e-17
                      H-kinase_dim   2 stlRVdakrlDyLlnlvGElVitkarLnqsleefrfenglkasvtelksslqnlgrisgeLQegvmk 68 
                                       +++R+d++rlD+++nlvGEl+i+k r+nq++++           ++l ++l+ l+r+++++Q +vm+
  gi|298674811|ref|YP_003726561.1| 308 QSVRIDIDRLDNMMNLVGELIINKIRINQLTSDYD--------IKDLDDTLADLDRLTNDIQTEVME 366
                                       68*********************************........9**********************6 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.4       3.1   5.5e+03      93     125 ..     232     264 ..     222     277 .. 0.61
   2 ?   -2.9   0.1       3.1   5.5e+03      92     124 ..     298     332 ..     287     340 .. 0.60
   3 !   19.6   0.2   3.4e-07   0.00062       7      61 ..     417     487 ..     414     551 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.1
                       HATPase_c_3  93 kkegesstltldvdkidkenekvleeltveeie 125
                                       ++e+++  ++ +v+ki++ ++ +l+e++ e+ e
  gi|298674811|ref|YP_003726561.1| 232 STENNQDIIKEEVQKISEIQNVTLSEISLENKE 264
                                       445555556666666666666666666666554 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.1
                       HATPase_c_3  92 tkkegess...tltldvdkidkenekvleeltveei 124
                                       +k ++e+     +++d+d +d+  ++ + el +++i
  gi|298674811|ref|YP_003726561.1| 298 SKRSNEMKsvqSVRIDIDRLDN-MMNLVGELIINKI 332
                                       4444444434478888888876.4455655555555 PP

  == domain 3  score: 19.6 bits;  conditional E-value: 3.4e-07
                       HATPase_c_3   7 laelvdNsldAdaen..............vkievnknrgktgeivieDdGkGmseeelkn.alr..latssk 61 
                                       l+ l++Ns+d   e+              + ++++++r ++  i +eDdGkGm++++l++ a +  l+++s+
  gi|298674811|ref|YP_003726561.1| 417 LVHLLRNSVDHGIEEpekrretgksetghIRLSASRQR-NSILIEVEDDGKGMNPDKLREtAVKkgLMSQSE 487
                                       67899999999999899999999999988999999988.6899****************9877623444443 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.65   1.2e+03      21      50 ..     309     338 ..     301     365 .. 0.84
   2 ?   12.9   0.0   4.6e-05     0.082      51     101 ..     441     518 ..     420     550 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.65
                       HATPase_c_2  21 raglseelldeirlaveEactNavehayle 50 
                                        ++++ ++ld++   v+E+++N ++ ++l 
  gi|298674811|ref|YP_003726561.1| 309 SVRIDIDRLDNMMNLVGELIINKIRINQLT 338
                                       567888999999999*********999875 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 4.6e-05
                       HATPase_c_2  51 apegpvevrlesdeealtvevaDsGpgfdpetlpdpteeep...........................keslkegGr 100
                                        ++g+++++++++ +++ +ev+D+G+g +p +l++ ++++                            +   + +Gr
  gi|298674811|ref|YP_003726561.1| 441 SETGHIRLSASRQRNSILIEVEDDGKGMNPDKLRETAVKKGlmsqsevdrmsdeeamnliftpgfsgaEKVTDVSGR 517
                                       336999*************************9999988766666666666666666666666666665444455555 PP

                       HATPase_c_2 101 G 101
                                       G
  gi|298674811|ref|YP_003726561.1| 518 G 518
                                       5 PP

>> ATP11  ATP11 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.049        88       8      71 ..      46     137 ..      39     177 .. 0.65
   2 ?    6.8   4.6    0.0028       5.1      16      94 ..     241     323 ..     233     364 .. 0.66

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.049
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX........................................ CS
                             ATP11   8 eKLeqkakeeglesieeLkeaykdkieekrkeaaaid........................................ 44 
                                       + L+  a   g++si eL +++++ ++  r+++ + d                                        
  gi|298674811|ref|YP_003726561.1|  46 HTLKGMASTMGFSSIAELTHEMENLMDGIRNKQIKLDdsiidilfecldtieslvetidseddvdishlknnlnsii 122
                                       56778888899999999999999999888888866668888888888888888888888888888777666555544 PP

                                       ......XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             ATP11  45 ......leesksesekekeakasssektekkes 71 
                                             +                  e++e++e+
  gi|298674811|ref|YP_003726561.1| 123 enggsgQ------------------ETQEESEQ 137
                                       3332211..................11111111 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0028
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX---...........SS--H CS
                             ATP11  16 eeglesieeLkeaykdkieekrkeaaaidleesksesekekeakasssektekkesaaksk....kkskskspvkpL 88 
                                       +e +++i+e+++   ++i+ ++ke +++++e+ ++++ ++++++++++e+t++ ++++k++    + ++ +  +  L
  gi|298674811|ref|YP_003726561.1| 241 KEEVQKISEIQNVTLSEISLENKEPSEPSSETDNKNELETETQPSNTQEQTQSGQDTSKRSnemkSVQSVRIDIDRL 317
                                       57788999999999999999999987777544444444443333333333333333333333343444445556666 PP

                                       HHHS-H CS
                             ATP11  89 ssildl 94 
                                       +++++l
  gi|298674811|ref|YP_003726561.1| 318 DNMMNL 323
                                       666665 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   1.3   0.00098       1.8       4      26 ..      17      39 ..      15      43 .. 0.92
   2 ?   -0.9   0.1      0.82   1.5e+03       4      18 ..      59      73 ..      58      84 .. 0.78
   3 ?    1.0   0.1      0.21   3.8e+02       5      23 ..     343     361 ..     340     367 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00098
                         DASH_Dam1  4 afaeLaDsletLdknledLqqih 26
                                       +++L+Dsl +L++n edL+qi+
  gi|298674811|ref|YP_003726561.1| 17 HLQQLNDSLLKLEQNHEDLEQIN 39
                                      799*****************996 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.82
                         DASH_Dam1  4 afaeLaDsletLdkn 18
                                      ++aeL+ ++e+L++ 
  gi|298674811|ref|YP_003726561.1| 59 SIAELTHEMENLMDG 73
                                      578888888888765 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.21
                         DASH_Dam1   5 faeLaDsletLdknledLq 23 
                                       +++L D l++Ld+ ++d+q
  gi|298674811|ref|YP_003726561.1| 343 IKDLDDTLADLDRLTNDIQ 361
                                       5666666666666666555 PP

>> CPSF100_C  Cleavage and polyadenylation factor 2 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.4     0.014        25      17      64 ..     107     155 ..      79     196 .. 0.55
   2 ?    5.2   4.4     0.012        22      35     114 ..     262     337 ..     232     341 .. 0.49

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.014
                         CPSF100_C  17 eglevatvtgeleieeea.eeaeeeekeeeeeeeeeeeeeeeaskkqkl 64 
                                       +++++++++ +l+   e+  + +e+++e+e+ e+e+e+ee +++ + +l
  gi|298674811|ref|YP_003726561.1| 107 DDVDISHLKNNLNSIIENgGSGQETQEESEQVENESEDEETTSETDFEL 155
                                       3588888888888444333222222222222222222223333333333 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.012
                         CPSF100_C  35 eeaeeeekeeeeeeeeeeeeeeeaskkqklaeksekeaseeeseekkeslp.tldvlpankasvrsaaqplfvGdlr 110
                                       +++ +e ++e+++++e e+e ++++ ++++ ++ +++++++++ ++ +s++  +d l +    + +   +l ++ +r
  gi|298674811|ref|YP_003726561.1| 262 NKEPSEPSSETDNKNELETETQPSNTQEQT-QSGQDTSKRSNEMKSVQSVRiDIDRLDN----MMNLVGELIINKIR 333
                                       333344444444445555544444444444.2222222222222222222213333332....22467788888888 PP

                         CPSF100_C 111 LadL 114
                                       +++L
  gi|298674811|ref|YP_003726561.1| 334 INQL 337
                                       8776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (690 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1746  (0.0973841); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.77u 0.36s 00:00:01.12 Elapsed: 00:00:00.51
# Mc/sec: 4053.77
//
Query:       gi|298674812|ref|YP_003726562.1|  [L=204]
Description: inhibitor of MCP methylation CheC [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-11   42.1   0.9    1.3e-09   37.8   0.5    2.4  2  CheC      CheC-like family
    0.00073   19.7   0.8     0.0042   17.2   0.3    2.4  2  CheX      Chemotaxis phosphatase CheX


Domain annotation for each model (and alignments):
>> CheC  CheC-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.5   1.5e-13   1.3e-09       1      37 [.       7      43 ..       7      44 .. 0.94
   2 ?    2.4   0.0     0.017   1.5e+02      13      37 ..     119     143 ..     119     144 .. 0.87

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 1.5e-13
                                      HHHHHHHHHHHHHHHHHHHHHHTCCTS-EEE---EEE CS
                              CheC  1 melSAlgEigNIlaGsaatalatllnfkidisPPtvv 37
                                      m +SAl+E+gNI++G+ atal+++  +++ i  Ptv 
  gi|298674812|ref|YP_003726562.1|  7 MTKSALQEAGNIGMGNLATALSKMVSREVKINIPTVE 43
                                      679****************************999986 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.017
                                       HHHHHHHHHHTCCTS-EEE---EEE CS
                              CheC  13 laGsaatalatllnfkidisPPtvv 37 
                                       +++ ++++ +++l+ +++ s P++v
  gi|298674812|ref|YP_003726562.1| 119 MCSTYMSSVNEFLGTNLEVSKPEIV 143
                                       899***********99999877765 PP

>> CheX  Chemotaxis phosphatase CheX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.3   4.7e-07    0.0042      36      73 ..       2      43 ..       1      67 [. 0.81
   2 ?    0.5   0.0     0.077   6.9e+02       6      30 ..      68      92 ..      61     161 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.7e-07
                              CheX 36 eeieedvndavgEltNmiaGnaksklge....evklspPlvi 73
                                      eei+e+ ++a++E  N+ +Gn+ + l++    evk+++P+v 
  gi|298674812|ref|YP_003726562.1|  2 EEIDEMTKSALQEAGNIGMGNLATALSKmvsrEVKINIPTVE 43
                                      5679*******************8884445559******984 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.077
                              CheX  6 glaGdisGliilsadeelalkiasa 30
                                      +++Gd+ G  ++ +++ +a  +   
  gi|298674812|ref|YP_003726562.1| 68 KITGDVTGGTVILLPKYSAFSFSDL 92
                                      5677777777777777776666443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1219.46
//
Query:       gi|298674813|ref|YP_003726563.1|  [L=273]
Description: MCP methyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-55  187.2   0.2    2.7e-55  186.9   0.2    1.1  1  CheR             CheR methyltransferase, SAM binding domain
    8.7e-13   47.8   0.3    1.6e-12   47.0   0.3    1.5  1  CheR_N           CheR methyltransferase, all-alpha domain
    4.4e-06   27.3   0.1    1.8e-05   25.4   0.1    1.9  1  Methyltransf_12  Methyltransferase domain
    1.7e-05   24.6   0.1    0.00048   20.0   0.1    2.4  2  Methyltransf_31  Methyltransferase domain
     0.0022   18.6   0.0       0.68   10.6   0.0    2.4  2  Methyltransf_11  Methyltransferase domain
     0.0052   17.4   0.0        1.4    9.7   0.0    2.4  2  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
      0.039   13.8   0.0      0.056   13.3   0.0    1.2  1  Methyltransf_23  Methyltransferase domain


Domain annotation for each model (and alignments):
>> CheR  CheR methyltransferase, SAM binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.9   0.2   1.1e-58   2.7e-55       1     192 [.      74     267 ..      74     270 .. 0.92

  Alignments for each domain:
  == domain 1  score: 186.9 bits;  conditional E-value: 1.1e-58
                                       SS--TTTTCHHHHHHHHCCH.HHHHHHHTS..SSEEEEEES-TTTHHHHHHHHHHHCHSTTTSSS.-EEEEEEESSC CS
                              CheR   1 neTeffreakhfeelekevlepllakakne..krvriwsagcssGeEpYslAmllketlpkaakl.kvkilAtDidl 74 
                                       n+T+ffr++++++ +e+ vl++ +++++n+  k++riwsagcs G E+YslA++l++ l+++ k  +++i++tDid+
  gi|298674813|ref|YP_003726563.1|  74 NVTNFFRNPDSYQIVENDVLPDIIKSKSNSsnKSIRIWSAGCSIGVEAYSLAIILHQLLKNEFKKyRINIIGTDIDN 150
                                       79******************87777666667788***********************888776544*********** PP

                                       HHHHHHHHTEEECCHHTTS-HHHHHHHEEEEETTCEEE-HHHHTTEEEEE--TTT-SGGG--EEEEEE-SSGGGC-C CS
                              CheR  75 kvlekAkagvykeeeleglseelleryfekseddsykvkkeikelvkFeklnllekksvlgklDvifcrnvliYfde 151
                                       ++l++Ak+g y+e+el+g+ ++++++yf +++d+ y +++e+k+  +F+ ++l++  +  + +D+ifcrnv iYf++
  gi|298674813|ref|YP_003726563.1| 151 EALSRAKEGKYTETELKGVDDKIIDKYF-EKKDGWYFISDELKKVANFKWHDLIA-GKKMSGFDLIFCRNVTIYFEK 225
                                       ****************************.66777999******************.888899*************** PP

                                       HHHHHHHHHHHCCEEEEEEEEE-TTB--S.SSCCCCCEEEEC CS
                              CheR 152 etqekvlerfaeklkpgglLllGhsEslk.klkdkfevvkst 192
                                       + qek++ +f+++l++gg+ ++G++E+l  ++++ f+  +s+
  gi|298674813|ref|YP_003726563.1| 226 DLQEKLYMNFYNALNQGGYFVMGKTETLVgESQNLFKPYNSR 267
                                       *****************************7888888877765 PP

>> CheR_N  CheR methyltransferase, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.3   6.1e-16   1.6e-12       3      53 .]      11      61 ..       9      61 .. 0.96

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 6.1e-16
                                      HHHHHHHHHHTT-EE--SSTHHHHHTHHHHHHHTTT-SSSHHHHHHTSHSS CS
                            CheR_N  3 ferlleliyertGidlsdyKrallkrRlsrRmralglksfeeYldlLrsdp 53
                                      ++ l++li ++ G++  +yK +  krR++ Rmra++ ++++eY++ L+++p
  gi|298674813|ref|YP_003726563.1| 11 YSSLKSLINKNLGFHCDQYKDTHFKRRIAVRMRATNSRDYSEYIKVLKDNP 61
                                      8899********************************************997 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.1     7e-09   1.8e-05      16      99 .]     133     245 ..     114     245 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 7e-09
                   Methyltransf_12  16 ekl...pdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg......................... 64 
                                       ++     +i+++g+Di+ +a+ +ake    +      +++  ++ ++d+  +                         
  gi|298674813|ref|YP_003726563.1| 133 KNEfkkYRINIIGTDIDNEALSRAKEGKYTET-----ELKGVDDKIIDKYFEkkdgwyfisdelkkvanfkwhdlia 204
                                       33357789*************44444433333.....34444444433333345678******************** PP

                   Methyltransf_12  65 ....ssfDlvvasnvlhhl.kdir.evldnirklLkpgGrl 99 
                                           s fDl+++ nv  ++ kd++ ++  n++++L++gG++
  gi|298674813|ref|YP_003726563.1| 205 gkkmSGFDLIFCRNVTIYFeKDLQeKLYMNFYNALNQGGYF 245
                                       ********************999988889**********85 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       3.3   8.5e+03     109     127 ..      51      69 ..      40      91 .. 0.63
   2 !   20.0   0.1   1.9e-07   0.00048       4     113 ..     107     251 ..     104     269 .. 0.67

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3.3
                   Methyltransf_31 109 iedprllaelpakveeesk 127
                                       +e++++l+++p++ ++ +k
  gi|298674813|ref|YP_003726563.1|  51 SEYIKVLKDNPDEYRNLMK 69 
                                       4556666666655555555 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 1.9e-07
                   Methyltransf_31   4 glrvlDlGCGtGeltfelae........elgp..kaevvGiDiseeaielAre....naqklgld....nveFeqgd 62 
                                        +r+  +GC  G  ++ la         e ++  +++++G Di+ ea+++A+e    +++ +g+d       Fe+  
  gi|298674813|ref|YP_003726563.1| 107 SIRIWSAGCSIGVEAYSLAIilhqllknE-FKkyRINIIGTDIDNEALSRAKEgkytETELKGVDdkiiDKYFEKK- 181
                                       56666677888877777777666554322.2235566****************87774444444433223333332. PP

                   Methyltransf_31  63 ieeleklled..........................ekfDlilsnevlnala..dpdkileeiervlkpggillied 111
                                                d                          + fDli++++v  ++    ++k +++  ++l++gg++++  
  gi|298674813|ref|YP_003726563.1| 182 ---------DgwyfisdelkkvanfkwhdliagkkmSGFDLIFCRNVTIYFEkdLQEKLYMNFYNALNQGGYFVMGK 249
                                       .........12222233333344455566*****************995554115778999*************987 PP

                   Methyltransf_31 112 pr 113
                                         
  gi|298674813|ref|YP_003726563.1| 250 TE 251
                                       66 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.0    0.0083        21       4      40 ..     114     162 ..     111     181 .. 0.73
   2 !   10.6   0.0   0.00027      0.68      61      96 .]     210     247 ..     191     247 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0083
                                       T-TTSHHHHHHH...........HTT.SEEEEEES-HHHHHHHHHHCCH CS
                   Methyltransf_11   4 GcGtGrlaeala...........krg.arvvgvDlskemlklakekase 40 
                                       Gc  G  a  la           k++  +++g+D+++e+l +ake + +
  gi|298674813|ref|YP_003726563.1| 114 GCSIGVEAYSLAiilhqllknefKKYrINIIGTDIDNEALSRAKEGKYT 162
                                       6666666666666666666655544469************999876554 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00027
                                       -EEEEEEES-CCC-..CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  61 sfDlvvssevlhhv..edpekalkeiaRvLkpgGllvi 96 
                                        fDl+++++v  ++  + +ek+  +++  L +gG++v+
  gi|298674813|ref|YP_003726563.1| 210 GFDLIFCRNVTIYFekDLQEKLYMNFYNALNQGGYFVM 247
                                       5*************9778999**************985 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.011        29      17      39 ..     134     158 ..     112     182 .. 0.79
   2 !    9.7   0.0   0.00054       1.4      63      97 .]     209     243 ..     189     243 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.011
                                       CTS.T.SSEEEEEESSHHHHHHHHH CS
                   Methyltransf_25  17 krl.g.kakvtgvDiseemleaare 39 
                                       +++ + + +++g+Di+ e+l +a+e
  gi|298674813|ref|YP_003726563.1| 134 NEFkKyRINIIGTDIDNEALSRAKE 158
                                       444324689**************96 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00054
                                       TTEEEEEEESTGGGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  63 gsfDlvvssgalhhlsdedlekalkeiarvLkpgG 97 
                                       + fDl++++++  +++++ +ek++ +++++L++gG
  gi|298674813|ref|YP_003726563.1| 209 SGFDLIFCRNVTIYFEKDLQEKLYMNFYNALNQGG 243
                                       57******988999999999**************9 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.2e-05     0.056      38     116 ..     134     246 ..      90     259 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.2e-05
                   Methyltransf_23  38 evlrengfsvtgvDlspeaveiae...........kakkaqkdqfdeqeaaepqg...................... 81 
                                       +++++++ +++g D++ ea ++a+            ++k +++ f         +                      
  gi|298674813|ref|YP_003726563.1| 134 NEFKKYRINIIGTDIDNEALSRAKegkytetelkgVDDKIIDKYFEKK------Dgwyfisdelkkvanfkwhdlia 204
                                       34566888**************99999999999984444444444111......12344444444455555556666 PP

                   Methyltransf_23  82 .....kfdlIvlrevlehvp.d.ppellrqiatllkpgGyll 116
                                             fdlI +r+v+  ++ d  ++l  ++++ l+ gGy++
  gi|298674813|ref|YP_003726563.1| 205 gkkmsGFDLIFCRNVTIYFEkDlQEKLYMNFYNALNQGGYFV 246
                                       66677***************658999999***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1633.92
//
Query:       gi|298674814|ref|YP_003726564.1|  [L=209]
Description: inhibitor of MCP methylation CheC [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-16   59.8   2.5    2.1e-07   30.7   0.2    2.5  2  CheC      CheC-like family
    7.6e-10   38.8   1.7    4.2e-06   26.8   0.2    2.2  2  CheX      Chemotaxis phosphatase CheX


Domain annotation for each model (and alignments):
>> CheC  CheC-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.2   2.4e-11   2.1e-07       2      29 ..      10      37 ..       9      40 .. 0.91
   2 !   28.9   0.1   8.8e-11   7.9e-07       1      37 [.     105     141 ..     105     142 .. 0.94

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 2.4e-11
                                      HHHHHHHHHHHHHHHHHHHHHTCCTS-E CS
                              CheC  2 elSAlgEigNIlaGsaatalatllnfki 29
                                      + +A +EigNI++G+a t+l++l+++++
  gi|298674814|ref|YP_003726564.1| 10 QIDAMKEIGNIGMGNATTSLSELTGKRV 37
                                      6799********************9876 PP

  == domain 2  score: 28.9 bits;  conditional E-value: 8.8e-11
                                       HHHHHHHHHHHHHHHHHHHHHHTCCTS-EEE---EEE CS
                              CheC   1 melSAlgEigNIlaGsaatalatllnfkidisPPtvv 37 
                                       m +SAl Ei NIl+Gs++t+++ +l+++  +s+P++v
  gi|298674814|ref|YP_003726564.1| 105 MNESALNEISNILTGSYLTSISSFLQVNGLHSVPQTV 141
                                       779***********************99999999876 PP

>> CheX  Chemotaxis phosphatase CheX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.1   3.1e-05      0.28      44      69 ..      12      41 ..       4      54 .. 0.83
   2 !   26.8   0.2   4.7e-10   4.2e-06       4      82 ..      66     150 ..      62     160 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.1e-05
                              CheX 44 davgEltNmiaGnakskl....geevklsp 69
                                      da+ E+ N+ +Gna++ l    g++v+l++
  gi|298674814|ref|YP_003726564.1| 12 DAMKEIGNIGMGNATTSLseltGKRVQLNL 41
                                      9**************888555777888876 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 4.7e-10
                              CheX   4 iiglaGdisGliilsadeelalkiasa.lgedeee.ieedvndavgEltNmiaGnakskl....geevklspPlvis 74 
                                       +  ++Gdi+G+i+  ++ + a+ +++  l e+e e + e+ ++a+ E+ N+++G++ + +    + +   s+P++++
  gi|298674814|ref|YP_003726564.1|  66 MHTIKGDIQGVILNLFEISNAMVLTNLlLSETEYEyDPEMNESALNEISNILTGSYLTSIssflQVNGLHSVPQTVT 142
                                       5578*********************984699977757889999**************9995545558889******* PP

                              CheX  75 gkeltise 82 
                                       g+   i +
  gi|298674814|ref|YP_003726564.1| 143 GSMEDILD 150
                                       *9888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 1246.43
//
Query:       gi|298674815|ref|YP_003726565.1|  [L=175]
Description: hypothetical protein Metev_0871 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       909  (0.0507); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1054.41
//
Query:       gi|298674816|ref|YP_003726566.1|  [L=207]
Description: hypothetical protein Metev_0872 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1293.15
//
Query:       gi|298674817|ref|YP_003726567.1|  [L=201]
Description: hypothetical protein Metev_0873 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   12.3   0.0        6.9    6.8   0.0    2.3  2  DUF5415   Family of unknown function (DUF5415)


Domain annotation for each model (and alignments):
>> DUF5415  Family of unknown function (DUF5415)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0    0.0056     1e+02       6      23 ..      87     104 ..      83     111 .. 0.86
   2 ?    6.8   0.0   0.00039       6.9       6      34 ..     164     192 ..     159     198 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.0056
                           DUF5415   6 tPfekaaskilerrGvse 23 
                                        Pf ka s  ++r G+ +
  gi|298674817|ref|YP_003726567.1|  87 CPFSKAISEYIKRLGIMN 104
                                       7************99865 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.00039
                           DUF5415   6 tPfekaaskilerrGvseaqwkkevlekv 34 
                                       tP e     +le+ G+se+q   e+ e +
  gi|298674817|ref|YP_003726567.1| 164 TPPESWKKVLLEKAGISETQGFMEMRENA 192
                                       66677777789*********988887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1276.31
//
Query:       gi|298674818|ref|YP_003726568.1|  [L=350]
Description: cytochrome c assembly protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-34  118.4  25.0    3.5e-34  118.4  25.0    2.4  2  Cytochrom_C_asm  Cytochrome C assembly protein
  ------ inclusion threshold ------
       0.01   15.5   1.5       0.01   15.5   1.5    2.6  2  DUF4051          Protein of unknown function (DUF4051)


Domain annotation for each model (and alignments):
>> Cytochrom_C_asm  Cytochrome C assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.3     0.058   5.2e+02      28      52 ..      37      66 ..       6      80 .. 0.62
   2 !  118.4  25.0   3.9e-38   3.5e-34       1     208 [.      87     310 ..      87     317 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.058
                   Cytochrom_C_asm 28 klnlsllaavaliaalillgfalf.....l 52
                                      ++ l++ aa+a+++a++ll + lf      
  gi|298674818|ref|YP_003726568.1| 37 SCRLEIGAAGAVTVAVFLLSYYLFhvqtaY 66
                                      355667777777777777777777333332 PP

  == domain 2  score: 118.4 bits;  conditional E-value: 3.9e-38
                   Cytochrom_C_asm   1 lsnleesllllawilsllgllleylarklnlsllaavaliaalillgfalf.......................... 51 
                                       +   e+s+ll+ w+++++ l+l+y + k ++s      l++++ +++ ++f                          
  gi|298674818|ref|YP_003726568.1|  87 WAGQEGSFLLWGWLILVILLVLKYTMHKKQFSGTRLYELTVTISIFIASVFllllvlknpfsmyyavpsgtieltnw 163
                                       66779******************99998777655544444444444444445569********************** PP

                   Cytochrom_C_asm  52 ...lllaelqesadlnpalqspilmiHvplallsYatliigallsialliierqlkkkkklklsanlkllkqldrls 125
                                          +   +   ++ +np+l++p+++iH+p+++++Ya+ +i ++ ++a l                 +   +++ +++
  gi|298674818|ref|YP_003726568.1| 164 npfVTAFQAPYGQGMNPLLRNPWMAIHPPVLFIGYAAITIPFASAFASL-----------------ILDDNRWTEIA 223
                                       99866777778899***********************************.................6666788889* PP

                   Cytochrom_C_asm 126 yriiliGfvlltigiilGsvWa..eeaWGsy.wsWDpketaslitWlvfaallhsriek.gwrgkkaailailgfll 198
                                        +++ +++++lt+gi lG +Wa   ++WG + wsWDp+et+sli+W++ +a+lh+ i++ ++  k a  lai+ f+l
  gi|298674818|ref|YP_003726568.1| 224 THWMRVSWLFLTLGIGLGGFWAyeVLGWGAWyWSWDPVETSSLIPWITSTAYLHTQIHNgNKFRKLAPALAIFSFVL 300
                                       **********************8778999866*************************8889999************* PP

                   Cytochrom_C_asm 199 lllayfgvrl 208
                                       +++a+f+ r+
  gi|298674818|ref|YP_003726568.1| 301 VVFATFVTRS 310
                                       *******998 PP

>> DUF4051  Protein of unknown function (DUF4051)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   1.5   1.2e-06      0.01       2      23 ..      94     115 ..      93     118 .. 0.91
   2 ?   -4.8   2.3         2   1.8e+04       4       7 ..     253     256 ..     253     257 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.2e-06
                           DUF4051   2 fIaWywlllvvlvvvgyichlk 23 
                                       f+ W wl+lv+l+v+ y +h k
  gi|298674818|ref|YP_003726568.1|  94 FLLWGWLILVILLVLKYTMHKK 115
                                       889****************976 PP

  == domain 2  score: -4.8 bits;  conditional E-value: 2
                           DUF4051   4 aWyw 7  
                                       aWyw
  gi|298674818|ref|YP_003726568.1| 253 AWYW 256
                                       7*** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       851  (0.047465); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2132.39
//
Query:       gi|298674819|ref|YP_003726569.1|  [L=312]
Description: hypothetical protein Metev_0875 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-15   57.9   4.3    1.6e-15   57.2   4.3    1.2  1  CcmF_C    Cytochrome c-type biogenesis protein CcmF C-termina
     0.0013   17.5   1.1      0.015   14.1   0.1    2.1  2  ResB      ResB-like family


Domain annotation for each model (and alignments):
>> CcmF_C  Cytochrome c-type biogenesis protein CcmF C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   4.3   1.8e-19   1.6e-15      30     317 ..       7     294 ..       2     300 .. 0.72

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 1.8e-19
                            CcmF_C  30 lvSREsaLllnNllLvvaaavVllGTLyPlvldalglgkiSVGaPyFnavfvplmvplllllgvGpllrWkraklae 106
                                       ++ + +++l+  l++v  aa++ +G L Pl++d l+++++   a yFn   ++ + +l++ll +  ll   + + ++
  gi|298674819|ref|YP_003726569.1|   7 ILTKSNVMLAALLVFVLLAALITVGMLTPLLVDFLTGNSMNLDAYYFNIRAALPTGVLIILLSIYLLLG--KLSEKK 81 
                                       455666677777777777788889*************************99999999999998877664..455567 PP

                            CcmF_C 107 llkrllvalvlalvlalllal.llgelkvlaalglalavwvvlaalaelaerlrakakellarlrklprsawGmvlA 182
                                       l+ ++ v++vl++++a++l++  l+ +++++ +++      ++a l+++++ ++      ++     ++  ++ ++ 
  gi|298674819|ref|YP_003726569.1|  82 LFVTVSVVVVLSAIFAVILPFnSLP-VDFIIPFSV----LAIIAILYNILHSVT-----GWKYNPYKNARSISAHII 148
                                       7778888888999999999984443.555555544....444444555555542.....233333334455677889 PP

                            CcmF_C 183 HlGvavtvlGvalvsayeverdvrlkpges..vevagyefefegv.eeveGpNYtaera.......elevsrdgkev 249
                                       HlG+ +++lGv+l++ ++ve+++ +++ ++  +e ++y+++ +++ ++ eG+ ++++ +       +++v+++g+ +
  gi|298674819|ref|YP_003726569.1| 149 HLGLVLIILGVVLSTGLTVEDSTVVSTESRgfFEGQDYSVSVTKIsSQFEGEPFKSHPGssyvtnvSFDVYKNGEYF 225
                                       *******************9998887766533666777777777633567777776655222222268899999998 PP

                            CcmF_C 250 atlepek.RlYtvqempmteaaidagllrdlYval.GeeledeawavrlyvkpfvrwiWlGallmalGGl 317
                                        + + +  R  +  +++ t + i+++ll++ ++a  G ++e +++++     pf++++W G +lma+G l
  gi|298674819|ref|YP_003726569.1| 226 DSGNVKSiRDLKW-DQSYTTTYIHRNLLEEYFIAPkGVDMETGKVNLYSRTVPFITFVWGGLCLMAFGVL 294
                                       8776654166655.67778899***********9746667777777777788***************854 PP

>> ResB  ResB-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.1   1.7e-06     0.015     151     222 ..     143     222 ..     139     234 .. 0.82
   2 !    2.4   0.1    0.0058        52     416     460 ..     255     300 ..     225     303 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.7e-06
                              ResB 151 lGnlvfHialvliligallgslfgfrgnvivpe.......Gqsfnnail..dsfrdGslvqelpfslrldkFtveyy 218
                                       +   ++H++lvli++g++l + ++++ + +v++       Gq  +++++  +s+ +G++++++p s  + + + ++y
  gi|298674819|ref|YP_003726569.1| 143 ISAHIIHLGLVLIILGVVLSTGLTVEDSTVVSTesrgffeGQDYSVSVTkiSSQFEGEPFKSHPGSSYVTNVSFDVY 219
                                       567899********************999999999999998888888778899999******997767777777777 PP

                              ResB 219 dtkg 222
                                       ++ g
  gi|298674819|ref|YP_003726569.1| 220 KN-G 222
                                       76.3 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.0058
                              ResB 416 lllqlddfe.qrqasgLqvsrdpgknlvllgalllvlGlvlslyvr 460
                                       +++  ++++ +   ++L  +  p+ ++v+ g  l+  G++  l v+
  gi|298674819|ref|YP_003726569.1| 255 YFIAPKGVDmETGKVNLYSRTVPFITFVWGGLCLMAFGVLSLLAVS 300
                                       4444555666666678888999*****************9988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1128  (0.0629148); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 1855.34
//
Query:       gi|298674820|ref|YP_003726570.1|  [L=175]
Description: hypothetical protein Metev_0876 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-47  161.7   3.9    1.9e-47  161.5   3.9    1.0  1  CarS-like     CDP-archaeol synthase
    2.6e-05   24.1   6.7    2.6e-05   24.1   6.7    2.0  2  CTP_transf_1  Cytidylyltransferase family


Domain annotation for each model (and alignments):
>> CarS-like  CDP-archaeol synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.5   3.9   2.1e-51   1.9e-47      12     175 .]       1     175 []       1     175 [] 0.91

  Alignments for each domain:
  == domain 1  score: 161.5 bits;  conditional E-value: 2.1e-51
                         CarS-like  12 llpayvanasavlvGGGtpvdlGktlvdGrrliGdGvtyrGtvaGvlvGvlvgliqgllek.....lsilaldssgs 83 
                                       +lpay++   a l+GGG+p+d+  tl dG r+ GdG+t+rG+ aG+++G+++g+ q +l+      ++i+  ++  s
  gi|298674820|ref|YP_003726570.1|   1 MLPAYIPSPAASLFGGGKPLDFNVTLKDGERVFGDGKTFRGLFAGTIIGLFIGIAQMVLVSggyspFDIQLPKFGSS 77 
                                       8**********************************************************863322244555567788 PP

                         CarS-like  84 vlefvilalllafGallGdavGsfikrrlkierGkpalildqldfvlgalllayp......vkllpieliilivlit 154
                                       ++  +++ + l+fG+llGd+  sf+krrlk++rG p +++dqldfvlga ll+y       +  +++++i++i+++t
  gi|298674820|ref|YP_003726570.1|  78 FIGSILVIFSLSFGSLLGDLFMSFLKRRLKLKRGAPLPVIDQLDFVLGAWLLVYLaspvwfISNFTYKIILIILILT 154
                                       999999999*****************************************999765557667899************ PP

                         CarS-like 155 lvlhlsaniiayklglkdvwy 175
                                       ++lh+ +n+i y +g+k+ ++
  gi|298674820|ref|YP_003726570.1| 155 PLLHIVTNVIGYLIGVKKEPW 175
                                       *****************9887 PP

>> CTP_transf_1  Cytidylyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   6.7   2.9e-09   2.6e-05     170     233 ..      36     109 ..      35     133 .. 0.90
   2 ?    0.4   2.5      0.05   4.5e+02     113     155 ..     125     169 ..     114     172 .. 0.44

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2.9e-09
                                       --BHHHHHHHHHHHHHHHHHHHHHHHCTS..........---TTSHHHHHHHHHHHHHHHHHHHHHHHHHHT-S CS
                      CTP_transf_1 170 kKTveGfigGlvaavvvglllalvlskal..........alsllhllllslllslvavfGDLveSglKRafgiK 233
                                       +KT  G+++G+++ + +g++ + ++s               s++ ++l+ + ls+ + +GDL++S lKR+++ K
  gi|298674820|ref|YP_003726570.1|  36 GKTFRGLFAGTIIGLFIGIAQMVLVSGGYspfdiqlpkfGSSFIGSILVIFSLSFGSLLGDLFMSFLKRRLKLK 109
                                       69****************99998888777899*****99999999***************************99 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.05
                                       HHHHTHHHH.TTHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHH CS
                      CTP_transf_1 113 allyvvlllqslllienikeglllvllll..alvvaaDigaYffG 155
                                        ++ +v+l + + +i+n +  ++l++l+l  +l +++ +++Y++G
  gi|298674820|ref|YP_003726570.1| 125 GAWLLVYLASPVWFISNFTYKIILIILILtpLLHIVTNVIGYLIG 169
                                       333333333333333443333333333221123334446666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1069.03
//
Query:       gi|298674821|ref|YP_003726571.1|  [L=174]
Description: orotate phosphoribosyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-13   50.1   0.7    2.9e-13   49.6   0.7    1.1  1  Pribosyltran   Phosphoribosyl transferase domain
  ------ inclusion threshold ------
      0.027   13.9   0.0      0.038   13.4   0.0    1.2  1  UPRTase        Uracil phosphoribosyltransferase
      0.069   12.9   0.1       0.14   12.0   0.1    1.6  1  Flagellar_put  Putative flagellar
      0.074   13.3   0.1        0.2   12.0   0.1    1.7  1  SH3_3          Bacterial SH3 domain


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.7   6.5e-17   2.9e-13       8     136 ..      42     159 ..      36     168 .. 0.93

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 6.5e-17
                                       ---EEEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE--- CS
                      Pribosyltran   8 npaildavarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlled 84 
                                        p +l+ + ++aaei+++     d v g++ gGvp+a++++ e ++p+ ++rk++++ ++++  +           +
  gi|298674821|ref|YP_003726571.1|  42 RPDTLKLIGKKAAEIIKS--IDVDNVGGVELGGVPIATAVSLESGLPMIIIRKSSKEYGTGGRLV---------GQL 107
                                       578899************..9*******************************************6.........678 PP

                                       -TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHHHHH CS
                      Pribosyltran  85 pagkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpateeevdkn 136
                                        +g++V++ +D+ ++Gg++++a+  + ++g  +  ++++vd+ +++ee  k+
  gi|298674821|ref|YP_003726571.1| 108 EKGERVILLEDVTTSGGSVKEAVSNIQNEGGYIDTVITVVDREEGAEENLKS 159
                                       9******************************998999999999999987765 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   8.5e-06     0.038     118     170 ..     106     157 ..      87     170 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.5e-06
                           UPRTase 118 ki.aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrla 170
                                       ++ + ++v+ll+ v  +Ggs+ +a++ ++++g   +  +v++v+  eeg+++ +
  gi|298674821|ref|YP_003726571.1| 106 QLeKGERVILLEDVTTSGGSVKEAVSNIQNEGGYID--TVITVVDREEGAEENL 157
                                       5545678***********************998766..5678888888887655 PP

>> Flagellar_put  Putative flagellar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   3.1e-05      0.14       1      13 [.     142     154 ..     142     157 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.1e-05
                     Flagellar_put   1 TVITAmdkeemke 13 
                                       TVIT++d+ee +e
  gi|298674821|ref|YP_003726571.1| 142 TVITVVDREEGAE 154
                                       9********9874 PP

>> SH3_3  Bacterial SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   4.4e-05       0.2      10      32 ..      98     120 ..      86     123 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.4e-05
                             SH3_3  10 stssevigtlpyGekVevleetg 32 
                                       +t+++ +g+l +Ge+V++le++ 
  gi|298674821|ref|YP_003726571.1|  98 GTGGRLVGQLEKGERVILLEDVT 120
                                       79999***************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1097.30
//
Query:       gi|298674822|ref|YP_003726572.1|  [L=434]
Description: phosphoribosylamine/glycine ligase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-57  194.8   0.8    1.7e-57  194.3   0.1    1.6  2  GARS_A         Phosphoribosylglycinamide synthetase, ATP-gras
    6.4e-26   91.0   0.1    1.5e-25   89.8   0.1    1.7  1  GARS_N         Phosphoribosylglycinamide synthetase, N domain
      8e-14   51.7   0.4    3.9e-13   49.5   0.1    2.3  3  GARS_C         Phosphoribosylglycinamide synthetase, C domain
     0.0003   20.4   0.0     0.0017   18.0   0.0    2.1  2  ATP-grasp_4    ATP-grasp domain
     0.0013   18.1   0.0     0.0029   17.0   0.0    1.5  1  GSH-S_ATP      Prokaryotic glutathione synthetase, ATP-grasp 
  ------ inclusion threshold ------
      0.012   15.7   0.0      0.024   14.7   0.0    1.6  1  ATP-grasp_3    ATP-grasp domain
      0.037   14.8   0.0       0.13   13.1   0.0    2.0  1  GFO_IDH_MocA   Oxidoreductase family, NAD-binding Rossmann fo
       0.14   11.7   0.0       0.38   10.3   0.0    1.7  2  ATP-grasp      ATP-grasp domain
       0.15   12.1   0.0       0.26   11.3   0.0    1.4  1  CoA_binding_3  CoA-binding domain


Domain annotation for each model (and alignments):
>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.3   0.1   8.5e-61   1.7e-57       2     194 .]     105     297 ..     104     297 .. 0.92
   2 ?   -3.6   0.0         4   7.9e+03      54      88 ..     385     420 ..     366     422 .. 0.69

  Alignments for each domain:
  == domain 1  score: 194.3 bits;  conditional E-value: 8.5e-61
                                       BHHHHHHHHHHTT--B-.-EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEE....SSHHHHHHHHHHHCTS CS
                            GARS_A   2 sKsfakdllkkagipta.eyeaftdpeeakeyieeatakalVvKadglaagKgviva....kseeealkavkeilek 73 
                                       +K++a++++kk++i++  e++ f++ ++++e+ie++++ a  vK+ gl++gKgv+v+     + + a ++++ +l+ 
  gi|298674822|ref|YP_003726572.1| 105 NKAWARNFMKKYNIEGCpEFNIFDNEKDVNEFIEKLGNVA--VKPIGLTGGKGVKVMgdqlPDIDSAKEYARTLLK- 178
                                       79*************977*******************988..***************5555556777777777776. PP

                                       -TTCCCCSSEEEEE---SEEEEEEEEECTTEEEE---BEEEEEEECCCEEEEECECEEEE....S-TTS-HHHHHHH CS
                            GARS_A  74 kkfGeagekvviEelleGeEvsllalvdgktvkplplaqdhkrvlegDkgpnTGGmGays....papvvteelleki 146
                                               kvviEe l GeE++++a+vdg++++ +p+ qdhkr++e+D+gpnTGGmG+ys     +p++ +e+lek+
  gi|298674822|ref|YP_003726572.1| 179 ------DGKVVIEENLVGEEFTVQAFVDGNNLAFTPPIQDHKRAFENDRGPNTGGMGSYSsaddVLPFMNKEDLEKA 249
                                       ......459***************************************************888889*********** PP

                                       HHHTHHHHHHHHHCT.T---EEEEEEEEEEETTEEEEEEEESS--TTCH CS
                            GARS_A 147 keeileptveglkke.gipfkGvLyaglmlvedgpkvlefnvRfgDpet 194
                                       ++ il+ tv+ l ke gi++kG++y+++ml++dgpkv+e+n+RfgDpe+
  gi|298674822|ref|YP_003726572.1| 250 QK-ILKDTVDSLYKEtGIHYKGIIYGQFMLTKDGPKVIEYNARFGDPEA 297
                                       99.*********8873689****************************97 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4
                                       EEEESSHHHHHHHHHHHCTS-TTC.CCCSSEEEEE- CS
                            GARS_A  54 vivakseeealkavkeilekkkfG.eagekvviEel 88 
                                       v va++ +ea ++++  l++ k+  +a + +  Ee+
  gi|298674822|ref|YP_003726572.1| 385 VGVANTISEAENIAQTSLDNVKGKiQARRDIGTEEF 420
                                       567777788888877777644433466666666665 PP

>> GARS_N  Phosphoribosylglycinamide synthetase, N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.8   0.1   7.4e-29   1.5e-25       1      90 []       1     103 [.       1     103 [. 0.96

  Alignments for each domain:
  == domain 1  score: 89.8 bits;  conditional E-value: 7.4e-29
                                       EEEEEEESSHHHHHHHHHHTTSTTESEEEEEE..--CGG............TTHHHHHHHHHHCTESEEEE-SHHHH CS
                            GARS_N   1 mkvLvvGsGGRehalawklaqspkvekvyvap..gNagt............edlealvefakeekidlvvvGpeapL 63 
                                       m++LvvG+GGReh +a+++a+s++  ++y+++  +N+g+            ++++++v++ak++k+d+vv+Gpe+pL
  gi|298674822|ref|YP_003726572.1|   1 MNILVVGGGGREHVIAQTIANSKHNPSLYAVMskKNPGIaslcndyliddeNNIDRIVAYAKSKKVDIVVIGPEKPL 77 
                                       9****************************998889********9999998877899********************* PP

                                       HTTHHHHHHHHHT-EEES--CCCCHHH CS
                            GARS_N  64 vaGvadaleeekgikvfGpskeaAqlE 90 
                                       ++G+adale++ +i v+Gp+k+a ++E
  gi|298674822|ref|YP_003726572.1|  78 ASGLADALERA-KIGVVGPKKDAGKIE 103
                                       ********666.************999 PP

>> GARS_C  Phosphoribosylglycinamide synthetase, C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.7   5.5e+03      52      74 ..      81     110 ..      77     111 .. 0.62
   2 ?   -2.9   0.0       4.4   8.7e+03      50      66 ..     244     260 ..     241     271 .. 0.69
   3 !   49.5   0.1     2e-16   3.9e-13       1      79 [.     332     417 ..     332     418 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.7
                                       HHHHHHHHH.......HHHTTCB-TTEE-- CS
                            GARS_C  52 leeArakay.......eavkkikfeglfyR 74 
                                       l++A ++a        + + ki+f++++ R
  gi|298674822|ref|YP_003726572.1|  81 LADALERAKigvvgpkKDAGKIEFNKAWAR 110
                                       556666666444455566668999998888 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.4
                                       SSHHHHHHHHHHHHTTC CS
                            GARS_C  50 etleeArakayeavkki 66 
                                       e+le+A++   + v+++
  gi|298674822|ref|YP_003726572.1| 244 EDLEKAQKILKDTVDSL 260
                                       78999999888888863 PP

  == domain 3  score: 49.5 bits;  conditional E-value: 2e-16
                                       EEEEEEEETTTTSS--ST-EEBS...TTEEEEESSEE.....EEE-SSEEEEEEEEESSHHHHHHHHHHHHTTCB-T CS
                            GARS_C   1 avgvvlaskGYPgsyekgkeitg...egvkvfhagtk.....lvtsGGRvlavvavgetleeArakayeavkkikfe 69 
                                       +v+ +++++GYP ++ k++ei     +++ +++a++      ++tsG+R la v+v++t++eA++ a   ++++k  
  gi|298674822|ref|YP_003726572.1| 332 TVCKYAVPEGYPYEPVKDSEIIIddiGDALLYYASVYeengkIYTSGSRALAFVGVANTISEAENIAQTSLDNVKG- 407
                                       69*******************5599977889999876677779*******************************75. PP

                                       TEE--STTTH CS
                            GARS_C  70 glfyRkDIGa 79 
                                       +++ R+DIG+
  gi|298674822|ref|YP_003726572.1| 408 KIQARRDIGT 417
                                       7********7 PP

>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   8.5e-07    0.0017      42      88 ..     169     215 ..     145     224 .. 0.83
   2 ?   -0.6   0.0      0.45     9e+02     106     153 ..     246     292 ..     229     296 .. 0.60

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 8.5e-07
                       ATP-grasp_4  42 keeykeevveeesflvEeyieGeEfavdayfdeeGepvilnilkkef 88 
                                       ++ey+++ ++++++++Ee + GeEf v a++d +  +    i +++ 
  gi|298674822|ref|YP_003726572.1| 169 AKEYARTLLKDGKVVIEENLVGEEFTVQAFVDGNNLAFTPPIQDHKR 215
                                       45699**************************9886666666666665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.45
                       ATP-grasp_4 106 ieetlealeellkevnallglk.nfpvHiElrvsedgkiipiEvnplrf 153
                                       +e+ ++ l+++++++ +++g++ ++ +   + +++dg+ + iE n+ rf
  gi|298674822|ref|YP_003726572.1| 246 LEKAQKILKDTVDSLYKETGIHyKGIIYGQFMLTKDGPKV-IEYNA-RF 292
                                       4556666677777777777766235556666666666444.66666.55 PP

>> GSH-S_ATP  Prokaryotic glutathione synthetase, ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.5e-06    0.0029      12      63 ..     121     172 ..     109     190 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.5e-06
                                       S--EEEES-HHHHHHHHHHHSSEEEEESS--TTTT-EEE-TT-TTHHHHHHH CS
                         GSH-S_ATP  12 ipktlvskdkeeirafleeqgdvilKPldgkgGegvfrvkksdpnlksilel 63 
                                       +p+  +  +++++++f+e+ g+v +KP++ +gG+gv  + ++ p+++s  e 
  gi|298674822|ref|YP_003726572.1| 121 CPEFNIFDNEKDVNEFIEKLGNVAVKPIGLTGGKGVKVMGDQLPDIDSAKEY 172
                                       67888999*****************************999999999887775 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.2e-05     0.024      24     159 ..     133     293 ..      98     295 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-05
                                       -EESS--SSSEEEEESS-------B--SS--TTE................EEEE---SEEEEEEEEE.SSSEEEEEE CS
                       ATP-grasp_3  24 aeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve.........lvqefieGkplSvsllsdgekvlvlav 91 
                                        +e+ e+  ++ vKp+   gg++v v+ ++  +  + +e +         ++ e + G++++v++ +dg ++l ++ 
  gi|298674822|ref|YP_003726572.1| 133 VNEFIEKLGNVAVKPIGLTGGKGVKVMGDQLPDIDSAKEYArtllkdgkvVIEENLVGEEFTVQAFVDG-NNLAFTP 208
                                       5566666778899**********998887755554444444699999********************98.5555555 PP

                                       EEEEEET...............TEEEEEEES----H.HHHHHHHHHHHHTTSTT--E..EEEE...EEEESS.SEEE CS
                       ATP-grasp_3  92 nrqliekaeke...........fvyaGnvtpietel.keevvelaeevvekleglaG..yvGv...Dlvlkdeepyv 151
                                       + q  ++a ++           ++ a  v p+  ++  e+++++ +++v +l +  G  y G+    ++l++++p v
  gi|298674822|ref|YP_003726572.1| 209 PIQDHKRAFENdrgpntggmgsYSSADDVLPFMNKEdLEKAQKILKDTVDSLYKETGihYKGIiygQFMLTKDGPKV 285
                                       5555544444489999999976666778899877665899************95555335676555899******** PP

                                       EEEESS-- CS
                       ATP-grasp_3 152 iEvNPRlt 159
                                       iE N+R+ 
  gi|298674822|ref|YP_003726572.1| 286 IEYNARFG 293
                                       ******95 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.6e-05      0.13       1      85 [.       1      88 [.       1      94 [. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.6e-05
                                      EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCT...TESEEEE-S-GGGHH CS
                      GFO_IDH_MocA  1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladp...eidavivatpngthe 76
                                      ++++++G+G      ++ + +s+++  + a+++++++    +++ + ++  +++++++a     ++d+v+++    +  
  gi|298674822|ref|YP_003726572.1|  1 MNILVVGGGGREHVIAQTIANSKHNPSLYAVMSKKNPGIASLCNDYLIDDENNIDRIVAYAkskKVDIVVIGPEKPLAS 79
                                      6899****888888899999999999***********************8888776655444449*****997776666 PP

                                      HHHHHHHHT CS
                      GFO_IDH_MocA 77 elakaalea 85
                                       la a+ +a
  gi|298674822|ref|YP_003726572.1| 80 GLADALERA 88
                                      666665555 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00019      0.38       8      71 ..     121     187 ..     113     216 .. 0.80
   2 ?   -2.6   0.0       1.7   3.4e+03     114     133 ..     241     260 ..     236     267 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00019
                                       B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTC.CGHHCHHHHC....GTTCEEEEE- CS
                         ATP-grasp   8 vprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrse.edleqaleal....keekvivEef 71 
                                        p+f + +++++++e++e+lg ++ vK +++   GkG +v+ ++  d+++a e++    k++kv++Ee 
  gi|298674822|ref|YP_003726572.1| 121 CPEFNIFDNEKDVNEFIEKLGNVA-VK-PIGLTGGKGVKVMGDQlPDIDSAKEYArtllKDGKVVIEEN 187
                                       589******************865.68.9999*******998762577777777688899999999986 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.7
                                       -SCHHHHHHHHHHHHHHHHH CS
                         ATP-grasp 114 vsekaqkkaeeiakkiveeL 133
                                       +++++++ka++i+k+ v++L
  gi|298674822|ref|YP_003726572.1| 241 MNKEDLEKAQKILKDTVDSL 260
                                       56788999999999988887 PP

>> CoA_binding_3  CoA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00013      0.26      79     147 ..       1      71 [.       1      72 [. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                     CoA_binding_3  79 nerrvvavgggeelakqiranpelgfrvvgvfddrddarseeva..gvpvlgnladlveyvretrvdevyl 147
                                       +++ vv++gg e++++q  an + + +  +v+ +++++  + ++   ++ + n++++v+y+++++vd v++
  gi|298674822|ref|YP_003726572.1|   1 MNILVVGGGGREHVIAQTIANSKHNPSLYAVMSKKNPGIASLCNdyLIDDENNIDRIVAYAKSKKVDIVVI 71 
                                       67789999999999999999999****************99996568899*****************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 2572.77
//
Query:       gi|298674823|ref|YP_003726573.1|  [L=303]
Description: ornithine carbamoyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.5e-59  198.3   0.0    1.2e-58  197.7   0.0    1.3  1  OTCace    Aspartate/ornithine carbamoyltransferase, Asp/Orn b
    2.1e-54  183.6   0.1    3.3e-54  182.9   0.1    1.3  1  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl
  ------ inclusion threshold ------
       0.16   12.7   0.1        0.5   11.1   0.1    1.8  2  DUF2281   Protein of unknown function (DUF2281)


Domain annotation for each model (and alignments):
>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.7   0.0     2e-62   1.2e-58       1     155 [.     148     297 ..     148     299 .. 0.96

  Alignments for each domain:
  == domain 1  score: 197.7 bits;  conditional E-value: 2e-62
                                       CC.EEEEESSTTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE CS
                            OTCace   1 kglkiafvGdkknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvyt 77 
                                       k+lk+a+vGd+ nnv+ns i ++a++gmd+v+++P+g+ep+  ++e+     kk gg++tit+d++ea+++aD++yt
  gi|298674823|ref|YP_003726573.1| 148 KNLKFAWVGDG-NNVCNSAILGCAIVGMDIVVACPEGYEPNSYIVEQG----KKIGGNVTITHDPAEAAENADILYT 219
                                       689********.****************************99999555....556********************** PP

                                       --SSETTCCGGHHHHHHHHCCCSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHHHHHH CS
                            OTCace  78 dvwvsmgeekereerlkklkdyqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhtikAll 154
                                       dvw+smg+e+ere+rl++l +yq++++l++lak d+iv+HcLPa+rgeE+t++V ++ +sv+f+qaeNrlh++kAl+
  gi|298674823|ref|YP_003726573.1| 220 DVWISMGDEEEREKRLNDLGGYQINSNLVNLAKRDVIVMHCLPAHRGEEITEDVLNGSHSVIFDQAENRLHAQKALI 296
                                       ****************************************************************************9 PP

                                       H CS
                            OTCace 155 v 155
                                       +
  gi|298674823|ref|YP_003726573.1| 297 L 297
                                       7 PP

>> OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.9   0.1   5.5e-58   3.3e-54       1     148 []       2     142 ..       2     142 .. 0.98

  Alignments for each domain:
  == domain 1  score: 182.9 bits;  conditional E-value: 5.5e-58
                                       S-BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTS CS
                          OTCace_N   1 rhllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaedi 77 
                                       +hl+s++dls+e i+elld a++lkek++++k ++llk+k+la++Fe+pStRTrvSfevA+++lGg+ l+l+  +di
  gi|298674823|ref|YP_003726573.1|   2 KHLISMADLSDEVIHELLDSAQDLKEKRARDKVTELLKNKSLAMIFEKPSTRTRVSFEVAMSDLGGHGLYLN-YKDI 77 
                                       8***********************************************************************.779* PP

                                       CTTTGGSTTSSCHHHHHHHHHHHTSEEEEEESSHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHHH CS
                          OTCace_N  78 qlssvskgrkEsleDtarvlsryvdaiviRhpgaeeleelakyasvpviNagdgdgeHPtQaLaDlltire 148
                                       ql      r+E+++Dta vlsryv++i+ R++++++++++aky++vpviNa+ +d+eHP+Q+LaDllti+e
  gi|298674823|ref|YP_003726573.1|  78 QLD-----RGEPISDTAAVLSRYVHGIAGRVNSHDTIKQMAKYSTVPVINAL-SDMEHPCQILADLLTIQE 142
                                       **9.....77******************************************.****************98 PP

>> DUF2281  Protein of unknown function (DUF2281)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   8.3e-05       0.5       8      35 ..       9      36 ..       6      45 .. 0.85
   2 ?   -2.3   0.0       1.2   7.4e+03      29      42 ..     143     156 ..     135     160 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.3e-05
                           DUF2281  8 eLPedlkqEvldFaefLleKyaakkkkt 35
                                       L++++++E+ld a+ L+eK+a +k ++
  gi|298674823|ref|YP_003726573.1|  9 DLSDEVIHELLDSAQDLKEKRARDKVTE 36
                                      599******************7766554 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.2
                           DUF2281  29 aakkkktlklrlaG 42 
                                        ++ +k+lk+ ++G
  gi|298674823|ref|YP_003726573.1| 143 YKNRTKNLKFAWVG 156
                                       36678888899998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1907.19
//
Query:       gi|298674824|ref|YP_003726574.1|  [L=386]
Description: sulfate adenylyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-88  294.9   0.0    3.7e-88  294.5   0.0    1.1  1  ATP-sulfurylase  ATP-sulfurylase
    9.1e-51  171.7   0.0    1.4e-50  171.1   0.0    1.3  1  PUA_2            PUA-like domain


Domain annotation for each model (and alignments):
>> ATP-sulfurylase  ATP-sulfurylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  294.5   0.0   4.2e-92   3.7e-88       2     211 ..     169     379 ..     168     380 .. 0.98

  Alignments for each domain:
  == domain 1  score: 294.5 bits;  conditional E-value: 4.2e-92
                                       CCB.-HHHHHHHHHHTT-SSEEEEEESS---HHHHHHHHHHHHHTSEEEEEEEB-SB-STTSTTHHHHHHHHHHHHH CS
                   ATP-sulfurylase   2 eyrltPaevreefkekgwdkVvAfqtrnplHraHeellkraleeeadglllhplvgptkpgdvpaevrvrayealie 78 
                                       ey l+Pae+r +fkek+w+kVv+fqtrn++H +He ++k+al   +dgl+++p++g++k+gd++++v++ +ye lie
  gi|298674824|ref|YP_003726574.1| 169 EYALKPAETRSMFKEKDWEKVVGFQTRNVPHLGHEFIQKTALS-LVDGLFINPVIGRKKSGDFKDNVILDSYESLIE 244
                                       699****************************************.8******************************** PP

                                       HHS-GGGEEE-BB-SB---SCHHHHHHHHHHHHHTT-SEEEE-TTTT-STCSS-TTHHHHHHHHCHHH.CTSEEEE- CS
                   ATP-sulfurylase  79 eylpkdrvvlallplamryaGprEallhaiirknyGcthfivGrdhagvgdfYgpydaqellakvage.lgiepvkf 154
                                       +y+p+dr++l +++++mryaGprEa++hai+rkn+GcthfivGrdhagvg+fY+p++a+e+++++++e lgi+p++f
  gi|298674824|ref|YP_003726574.1| 245 NYFPQDRATLGIFQTEMRYAGPREAIFHAIVRKNFGCTHFIVGRDHAGVGSFYHPFAAHEIFSEFDEEeLGITPIFF 321
                                       ****************************************************************99888******** PP

                                       --EEEETTTTEEEECCCC.GCCGGEEE--HHHHHCCHHTT----TTTS-HHHHHHHHH CS
                   ATP-sulfurylase 155 eeavYckkegevasektc.hkkeevesisgtelrkllregeeipewfsrpevlkvLre 211
                                       + ++Yckk++++a+ ktc h++e+++++sgt++r++l++ge++p+  +rpev++ + +
  gi|298674824|ref|YP_003726574.1| 322 KSFFYCKKCRGIANDKTCpHSEEQIVNFSGTRMREMLTNGERPPADSMRPEVADSILK 379
                                       *****************************************************99876 PP

>> PUA_2  PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.1   0.0   1.5e-54   1.4e-50       2     158 ..       6     161 ..       5     162 .. 0.99

  Alignments for each domain:
  == domain 1  score: 171.1 bits;  conditional E-value: 1.5e-54
                                       S-TTSS----B--CHHHHHHHHHHHTS-EEE--HHHHHHHHHHHTTTTTT-SCC--HHHHHHHHHHSEETTS-E-SS CS
                             PUA_2   2 kphggkLvelvvedeekeellkeakelpsielskrelqdlellaeGgfsPLegFmreedyesvleemrLadgllwsi 78 
                                       kphggkL+++ +++ e e+  ++a++++sie+ ++ ++d+e +a G+fsPLegF++++dye+vl + rL++g  w+i
  gi|298674824|ref|YP_003726574.1|   6 KPHGGKLIDRTLSNGEAEDIINRANDFQSIEIGPELVKDVENIASGLFSPLEGFLTSDDYERVLYDKRLSSGIPWTI 82 
                                       7**************************************************************************** PP

                                       ---EEEECCHCHHHTT-SEEEEEETTTEEEEEEEEEEEEE-HHHHHHHHHHS---TTSHHHHHHCTS-SEEEEEEEE CS
                             PUA_2  79 PivLdvseedakklkegdrvaLkdkegellAileveeiyeldkeeeaekvfgttdeaHPgvkkvleqgevlvgGkve 155
                                       PivLd s+e+a++l+ gd+v+L+++ ++++A+l+v+++y+++k+ ++e+vfgttd aHPgv+k+++ ++ lvgGk++
  gi|298674824|ref|YP_003726574.1|  83 PIVLDLSKEKASNLNPGDEVLLRHN-NQPVALLNVDDVYKFNKRVHCEQVFGTTDDAHPGVAKIYQLNDRLVGGKIN 158
                                       *************************.*************************************************** PP

                                       E-S CS
                             PUA_2 156 vle 158
                                       +l+
  gi|298674824|ref|YP_003726574.1| 159 LLN 161
                                       998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 2291.86
//
Query:       gi|298674825|ref|YP_003726575.1|  [L=236]
Description: adenylylsulfate reductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.6e-52  177.4   0.0    3.2e-52  177.1   0.0    1.1  1  PAPS_reduct  Phosphoadenosine phosphosulfate reductase family


Domain annotation for each model (and alignments):
>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.1   0.0   1.8e-56   3.2e-52       2     174 .]      32     206 ..      31     206 .. 0.98

  Alignments for each domain:
  == domain 1  score: 177.1 bits;  conditional E-value: 1.8e-56
                                       EEEE--SSCTCHHHHHHHHHHCTTHEEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-THH CS
                       PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpvpvvfvdtghefpetiefvdeleeryglrlkvyepeeevaekinaekhgssly 78 
                                       + +s+s G++++Vl+++a k+ +++ v+ +dtg+ +pet++f++e+++ y++++ vy p++e++ek+++ek  +s+y
  gi|298674825|ref|YP_003726575.1|  32 ISISFS-GAEDVVLIDMAKKIRDDISVFTLDTGRLYPETYRFIEEIRDYYNIDIDVYMPDRESTEKLVKEKGLFSFY 107
                                       778999.********************************************************************** PP

                                       HC...HHHHHHTHHHHHHHHHCTTECEEE----CCCTTTTTTSSSEEECTTT-S..CEEE-CCCT--HHHHHHHHHH CS
                       PAPS_reduct  79 ee...aaeriaKveplkkaLekldedalltGaRrdesksraklpiveidedfek..slrvfPllnWteedvwqyilr 150
                                       ++   ++++++K+ plk+aL++ld  a++tG+R+d+s+sr+ lp+v+id +f     ++++Pl+nWt ++vwqyi +
  gi|298674825|ref|YP_003726575.1| 108 NDghnECCSVRKIAPLKRALDGLD--AWVTGQRKDQSPSRSDLPVVQIDPAFGGgeLVKFNPLANWTLKQVWQYIFE 182
                                       ************************..**************************97779******************** PP

                                       CT--B-CCCCTT-SS--BCTTB-S CS
                       PAPS_reduct 151 enipynpLydqgfrsiGcvpctga 174
                                       +++pyn+L+++g+ siGc pct++
  gi|298674825|ref|YP_003726575.1| 183 NDVPYNKLHEKGYISIGCEPCTRP 206
                                       **********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1402.80
//
Query:       gi|298674826|ref|YP_003726576.1|  [L=431]
Description: methanogenesis marker 16 metalloprotein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   5.9e-110  367.4   0.0   6.7e-110  367.2   0.0    1.0  1  HcyBio    Homocysteine biosynthesis enzyme, sulfur-incorporat
    0.00017   21.7  10.7    0.00034   20.7  10.7    1.5  1  Fer4_9    4Fe-4S dicluster domain
    0.00075   19.9   3.7       0.45   11.0   0.0    2.4  2  Fer4_8    4Fe-4S dicluster domain
     0.0023   17.9  11.0      0.016   15.3   3.1    2.6  2  Fer4_6    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.017   15.7  14.7       0.11   13.1  13.4    2.4  3  Fer4_7    4Fe-4S dicluster domain
       0.12   12.6   3.6       0.23   11.7   3.6    1.4  1  Fer4_18   4Fe-4S dicluster domain
       0.16   12.1  12.1        0.3   11.2  11.6    1.8  1  Fer4_10   4Fe-4S dicluster domain
       0.22   11.7  12.8       0.86    9.8   2.5    2.7  2  Fer4_2    4Fe-4S binding domain
       0.48   11.4   8.8        2.7    9.0   0.6    2.6  2  Fer4_16   4Fe-4S double cluster binding domain
        0.5   11.0  12.7        5.2    7.8   3.7    2.7  2  Fer4_4    4Fe-4S binding domain
       0.61   10.7  12.9        3.4    8.3   3.1    2.4  2  Fer4_17   4Fe-4S dicluster domain
        0.7    9.8  12.8        3.4    7.6   1.1    3.3  2  Fer4      4Fe-4S binding domain
        3.7    7.8  13.7        4.7    7.4   2.8    2.4  2  Fer4_21   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> HcyBio  Homocysteine biosynthesis enzyme, sulfur-incorporation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  367.2   0.0  4.9e-113  6.7e-110       1     347 []      20     422 ..      20     422 .. 0.97

  Alignments for each domain:
  == domain 1  score: 367.2 bits;  conditional E-value: 4.9e-113
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx......xx RF
                            HcyBio   1 avVltaeelkklvrekgekkaaeevDVVttgTfgvmsssgallnlgvaepkiki..ekvwLngvpayag......la 69 
                                       avVlta+e++++vr+ gek ++e+vDVVtt+T+g+ms+++a+++++vaep+++i  ++vwLn+vpa++g      l+
  gi|298674826|ref|YP_003726576.1|  20 AVVLTADEICNRVRS-GEKINFEDVDVVTTATRGIMSGTYAVFSFKVAEPNSFIkaSRVWLNNVPAQVGpcpnerLG 95 
                                       8**************.***********************************999889******************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            HcyBio  70 avdlylgataeseddkeeeeyGGghviedLvagkeveleaeaketdcyprkeieteitlddlneailvnpRnayqnY 146
                                       ++dl++++ta+s+   ++ +yGGgh+++++v+gk +++e+e+ e+     + ++t+++++d+++a+l+++R+a++nY
  gi|298674826|ref|YP_003726576.1|  96 VLDLIVHGTAHSK---TNPNYGGGHLFREIVEGKPITVEIETVEG-----HWFSTHTNIKDMQYAKLFGTRHAFRNY 164
                                       *************...4559*************************.....*************************** PP

                                       xxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            HcyBio 147 naavNssee...tiytymgelkpnlgnatysgaGelsPllnDpelktigiGtrilLgGaeGyvigeGTqsspekkre 220
                                        a+vN+ +e   +i++ + e+++nl++at++g+Gel+P++nDp+l+tigiGtr++++G  Gyv g GT+ssp k+  
  gi|298674826|ref|YP_003726576.1| 165 LAFVNPVNEslpSIFH-AAEFRGNLSEATFCGCGELNPIENDPDLQTIGIGTRVMINGNYGYVSGLGTRSSPGKP-- 238
                                       ********9999****.**********************************************************.. PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            HcyBio 221 ngvplgpagtLavigdlkeMspeylrgafltsyGpelivgvgipiPvldeevleelavkdedielpvvDvserrrer 297
                                                +L  ++d++eM pey+ g+f+ts+Gpe+i+++++piPv+++++l+++   ++diel+vvDvs r    
  gi|298674826|ref|YP_003726576.1| 239 ---------NLGGFSDMHEMIPEYM-GGFVTSAGPEIINTWAVPIPVINQDILDNIVKINSDIELKVVDVSGR---- 301
                                       .........****************.***********************************************.... PP

                                       xxxxxxxxxxx.................................................................. RF
                            HcyBio 298 ktlgevsYael.................................................................. 308
                                        +l++++Ya++                                                                  
  gi|298674826|ref|YP_003726576.1| 302 LPLCKTNYADVwsnvdeevtyqpsecidcrvcevertcpmgavthkrgesaahnpilcfncglcttncagnafsaal 378
                                       89*************************************************************************** PP

                                       xxxxxxxx....xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            HcyBio 309 Gkieiegk....ev.ktarlsslkrareiaeeLkewiekgeflL 347
                                       G+i++ +      + +++r+s++ ra ++a+eLk++i +g+f++
  gi|298674826|ref|YP_003726576.1| 379 GNIDYCTAetekGIpVVVRQSDRLRALKAADELKTKIISGKFKI 422
                                       ***87554344478999*************************85 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7  10.7   2.5e-07   0.00034       1      49 [.     326     372 ..     326     374 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.5e-07
                            Fer4_9   1 kCtgCgaC..veaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                       +C++C+ C  ++ Cp+g+v+ +++e  a + +     C+ Cg C+  C  +
  gi|298674826|ref|YP_003726576.1| 326 ECIDCRVCevERTCPMGAVTHKRGESAAHNPI----LCFNCGLCTTNCAGN 372
                                       5*******76677**************99987....6***********876 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8  12.0      0.24   3.4e+02       3      61 ..     325     369 ..     323     369 .. 0.73
   2 !   11.0   0.0   0.00033      0.45       5      17 ..     359     383 ..     357     419 .. 0.58

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.24
                            Fer4_8   3 ekCieCgaCq..saCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevC 61 
                                       ++Ci C  C+   +Cp+   t k     rge a+      +         C +cg Ct++C
  gi|298674826|ref|YP_003726576.1| 325 SECIDCRVCEveRTCPMGAVTHK-----RGESAA---H--N------PILCFNCGLCTTNC 369
                                       58*******97777**9999944.....455444...1..1......34699999999998 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00033
                            Fer4_8   5 CieCgaCqsaCp............v 17 
                                       C +Cg+C+++C              
  gi|298674826|ref|YP_003726576.1| 359 CFNCGLCTTNCAgnafsaalgnidY 383
                                       999********54433333333330 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   3.1   1.2e-05     0.016       2      23 ..     320     343 ..     319     344 .. 0.87
   2 !    6.8   1.0    0.0054       7.5       8      20 ..     358     370 ..     351     376 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-05
                            Fer4_6   2 veidpdkCigCgdC..vrvCPega 23 
                                       v+++p+ Ci+C+ C  +r CP+ga
  gi|298674826|ref|YP_003726576.1| 320 VTYQPSECIDCRVCevERTCPMGA 343
                                       8999**********76677***98 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0054
                            Fer4_6   8 kCigCgdCvrvCP 20 
                                       +C  Cg C+++C 
  gi|298674826|ref|YP_003726576.1| 358 LCFNCGLCTTNCA 370
                                       6779********7 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   4.3    0.0006      0.83      29      52 .]     318     343 ..     302     343 .. 0.73
   2 ?   13.1  13.4     8e-05      0.11       2      49 ..     327     370 ..     326     373 .. 0.87
   3 ?    8.8   3.3    0.0017       2.4       2      20 ..     359     377 ..     358     401 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0006
                            Fer4_7  29 ekveidpekClgCgaCva..vCPtga 52 
                                       e+v+++p++C++C++C+   +CP ga
  gi|298674826|ref|YP_003726576.1| 318 EEVTYQPSECIDCRVCEVerTCPMGA 343
                                       679*************85449**997 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 8e-05
                            Fer4_7   2 CigCgaCv..aaCpvkaieldeeenekgtekveidpekClgCgaCvavCP 49 
                                       Ci C+ C+  ++Cp++a++ +        e+++++p  C +Cg C + C 
  gi|298674826|ref|YP_003726576.1| 327 CIDCRVCEveRTCPMGAVTHKRG------ESAAHNPILCFNCGLCTTNCA 370
                                       *******86679*******9653......78899***************6 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0017
                            Fer4_7   2 CigCgaCvaaCpvkaield 20 
                                       C +Cg C+ +C  +a++  
  gi|298674826|ref|YP_003726576.1| 359 CFNCGLCTTNCAGNAFSAA 377
                                       9**********99998865 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   3.6   0.00017      0.23      46      96 ..     312     370 ..     297     383 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                           Fer4_18  46 alkekeerkekgagdcidcesc.v.kvcPtg.idirkGlq.....leciscllcidacd 96 
                                       + ++++e+ + + ++cidc++c v + cP+g +  + G       + c +c+lc   c 
  gi|298674826|ref|YP_003726576.1| 312 VWSNVDEEVTYQPSECIDCRVCeVeRTCPMGaVTHKRGESaahnpILCFNCGLCTTNCA 370
                                       55667777788899********53368***93455566542223377*******99995 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2  11.6   0.00022       0.3       2      55 ..     320     369 ..     319     370 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                           Fer4_10   2 vvidddtCirCgkCvk..aCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                       v ++++ Ci C+ C     CP+      +    +++e   +++  C +cg C+  C
  gi|298674826|ref|YP_003726576.1| 320 VTYQPSECIDCRVCEVerTCPM------GAVTHKRGESAAHNPILCFNCGLCTTNC 369
                                       578999********87446***......7777777777778888888888888888 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   2.8    0.0068       9.4       7      21 ..     324     340 ..     318     341 .. 0.72
   2 ?    9.8   2.5   0.00063      0.86       6      20 ..     355     369 ..     350     370 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0068
                            Fer4_2   7 tdrCigCgaCv..saCP 21 
                                       +  Ci C+ C     CP
  gi|298674826|ref|YP_003726576.1| 324 PSECIDCRVCEveRTCP 340
                                       455*******5347799 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00063
                            Fer4_2   6 dtdrCigCgaCvsaC 20 
                                       ++  C +Cg C+++C
  gi|298674826|ref|YP_003726576.1| 355 NPILCFNCGLCTTNC 369
                                       5557*********** PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   2.0     0.018        25       2      23 ..     327     350 ..     326     357 .. 0.76
   2 ?    9.0   0.6    0.0019       2.7       2      27 ..     359     383 ..     358     415 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.018
                           Fer4_16   2 CgtCgkCa..evCPtnaikekkek 23 
                                       C++C+ C    +CP +a+++k+ +
  gi|298674826|ref|YP_003726576.1| 327 CIDCRVCEveRTCPMGAVTHKRGE 350
                                       *******63379******999443 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0019
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeiea 27 
                                       C +Cg C+  C  na+++    +i++
  gi|298674826|ref|YP_003726576.1| 359 CFNCGLCTTNCAGNAFSAA-LGNIDY 383
                                       99*************9987.344444 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   3.7    0.0038       5.2       2      16 ..     325     341 ..     324     342 .. 0.79
   2 ?    7.4   1.7     0.005         7       4      14 ..     359     369 ..     353     372 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0038
                            Fer4_4   2 erCigCgsCvaa..CPq 16 
                                       + Ci+C++C+    CP+
  gi|298674826|ref|YP_003726576.1| 325 SECIDCRVCEVErtCPM 341
                                       67*******97666886 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.005
                            Fer4_4   4 CigCgsCvaaC 14 
                                       C++Cg C+  C
  gi|298674826|ref|YP_003726576.1| 359 CFNCGLCTTNC 369
                                       ********998 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   3.1    0.0025       3.4      41      59 ..     322     342 ..     301     344 .. 0.78
   2 ?    7.8   2.0    0.0035       4.8      39      57 ..     352     370 ..     342     373 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0025
                           Fer4_17  41 ekaslCieCgeCe..rkCPqg 59 
                                        + s+Ci C+ Ce  r CP+g
  gi|298674826|ref|YP_003726576.1| 322 YQPSECIDCRVCEveRTCPMG 342
                                       56799*******98899**97 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0035
                           Fer4_17  39 keekaslCieCgeCerkCP 57 
                                       + ++  lC +Cg+C++ C 
  gi|298674826|ref|YP_003726576.1| 352 AAHNPILCFNCGLCTTNCA 370
                                       4566778999999999996 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   4.6     0.015        21       2      16 ..     321     335 ..     320     345 .. 0.74
   2 ?    7.6   1.1    0.0025       3.4       4      18 ..     355     369 ..     352     374 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.015
                                       EEETTTSSS-THHHH CS
                              Fer4   2 videekCigCGaCve 16 
                                       ++ ++ Ci C  C+ 
  gi|298674826|ref|YP_003726576.1| 321 TYQPSECIDCRVCEV 335
                                       56799********85 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0025
                                       ETTTSSS-THHHHHS CS
                              Fer4   4 deekCigCGaCvevC 18 
                                       ++ +C +CG+C   C
  gi|298674826|ref|YP_003726576.1| 355 NPILCFNCGLCTTNC 369
                                       6678*******9999 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   3.5     0.018        25      32      57 ..     318     344 ..     304     347 .. 0.68
   2 ?    7.4   2.8    0.0034       4.7       7      26 ..     358     377 ..     352     395 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.018
                           Fer4_21  32 tvlkvvedeCvGCnlCs..svCPvedci 57 
                                       + ++++ +eC+ C +C     CP+ +++
  gi|298674826|ref|YP_003726576.1| 318 EEVTYQPSECIDCRVCEveRTCPM-GAV 344
                                       555777889999999963357986.665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0034
                           Fer4_21   7 kCigCgkCliaCedtshqai 26 
                                        C +Cg+C++ C  ++  a 
  gi|298674826|ref|YP_003726576.1| 358 LCFNCGLCTTNCAGNAFSAA 377
                                       6***********99988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2587.19
//
Query:       gi|298674827|ref|YP_003726577.1|  [L=384]
Description: thiamine pyrophosphate domain-containing TPP-binding protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.2e-19   68.5   0.0    1.6e-18   67.0   0.0    1.8  2  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    2.9e-11   43.3   0.0    1.1e-10   41.4   0.0    1.8  2  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.48   4.3e+03     112     151 ..     120     160 ..     108     160 .. 0.69
   2 !   67.0   0.0   1.8e-22   1.6e-18      20     153 .]     236     356 ..     223     356 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.48
                                       -HHHHHHHTTSE.EE..EESSH.HHHHHHHHHHHHCSSSEEEE CS
                      TPP_enzyme_C 112 dfaklaealGak.ga..rvekadveeleealkealekkgpali 151
                                       ++  + e++G++  +   vek     +++a+ + +++++p +i
  gi|298674827|ref|YP_003726577.1| 120 SLPSILEGAGIEyTIidEVEKL--YLVDRAISDSFKNRRPHII 160
                                       6677899999996554444443..7778888888888888765 PP

  == domain 2  score: 67.0 bits;  conditional E-value: 1.8e-22
                                       EEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-.SEEEEEEE-SBCCCHHHHHHHH CS
                      TPP_enzyme_C  20 syltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnl.pitvvvlnNegygmtggqqepf 95 
                                       + l+ ++lg++G + ++++G++l+  +r+vv++ GDG++lm+ ++l+ ++r +  +++vv l+N++yg tg q++ +
  gi|298674827|ref|YP_003726577.1| 236 RELNYYMLGSLGLASSIGMGIALK-SERDVVVLDGDGSILMNPNALIEIARAKPsNLIVVALDNGAYGSTGSQETLT 311
                                       5567889****************6.689*************************99******************9988 PP

                                       TCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                      TPP_enzyme_C  96 ggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpaliev 153
                                        +             +d++ +a+a G     +v+++  +ele+a+ +a ++++ a+i+v
  gi|298674827|ref|YP_003726577.1| 312 AK------------FFDLELFARASGFInTTKVHTK--DELEDAFVKAKNSGELAFIHV 356
                                       64............489*********9967798888..*******************97 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.0   1.3e-14   1.1e-10       6     165 ..      13     168 ..      10     173 .. 0.79
   2 ?   -0.8   0.0      0.11     1e+03      83     143 ..     281     345 ..     220     348 .. 0.66

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 1.3e-14
                                       HHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHH CS
                      TPP_enzyme_N   6 alvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnalta 82 
                                       ++v+++ ++g++++ ++p++ri++ll  +s++  +++ l+r E+g+++ A g+++a  kp++++ +s  G+ n+++a
  gi|298674827|ref|YP_003726577.1|  13 IVVQMMLDNGIDYLATLPCDRIKNLLPLISKN-FVEIPLTREENGVGICA-GLYMAGAKPMMAIQSS--GLGNMINA 85 
                                       799*****************************.79999999999988888.5569999*********..57788888 PP

                                       HHHHHHH.T--EEEEEEE--CCCHHS..TC--T..-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEE CS
                      TPP_enzyme_N  83 laeAkvd.riPllvlsgdrptslrgqgvlqqel..dqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPvy 156
                                       l + + +  iPl vl+ +r+++++g + ++  l  +  ++++      +++ +  e   +++rAi  +  ++++P  
  gi|298674827|ref|YP_003726577.1|  86 LESLNIAcDIPLPVLASWRGVYKEGIESQK-PLgkSLPSILEGAG-IEYTIIDEVEKLYLVDRAISDS-FKNRRPHI 159
                                       888887769****************66655.44444445555444.5666666666688888888888.66666777 PP

                                       EEEEHHHCC CS
                      TPP_enzyme_N 157 lelpkdvll 165
                                       +  +  v++
  gi|298674827|ref|YP_003726577.1| 160 ILMSPRVWE 168
                                       776666665 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.11
                                       HHHHHHHT--EEEEEEE--CCCHH..S..TC--T-CCHHHCCCSSE..EEE-SSGGGHHHHHHHH CS
                      TPP_enzyme_N  83 laeAkvdriPllvlsgdrptslrg..qgvlqqeldqlalfrpvtky..aervtspeelpealrrA 143
                                       +  A+   + l+v++ d++++     q++l   +  l+lf+    +  +++v++++el+ a+ +A
  gi|298674827|ref|YP_003726577.1| 281 IEIARAKPSNLIVVALDNGAYGSTgsQETLTAKFFDLELFARASGFinTTKVHTKDELEDAFVKA 345
                                       33455556667777777777766645566665555566655444443366777777777666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2380.90
//
Query:       gi|298674828|ref|YP_003726578.1|  [L=174]
Description: hypothetical protein Metev_0885 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0033   17.8   0.0      0.041   14.4   0.1    2.1  2  DUF4179   Domain of unknown function (DUF4179)
  ------ inclusion threshold ------
      0.084   12.6   0.0       0.15   11.8   0.0    1.4  1  COXG      Carbon monoxide dehydrogenase subunit G (CoxG)


Domain annotation for each model (and alignments):
>> DUF4179  Domain of unknown function (DUF4179)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   4.6e-06     0.041       5      43 ..      22      55 ..      19      84 .. 0.69
   2 ?    1.5   0.0     0.046   4.2e+02      19      37 ..      88     105 ..      79     147 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.6e-06
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...--SS-HHH CS
                           DUF4179  5 rikkvaaaaaalvllllssrllspalAsal..npvigslfe 43
                                       ++k ++ a+ ++ll ++++l+ pa+A+++  +       +
  gi|298674828|ref|YP_003726578.1| 22 MVMKSIILAIFIILL-SCTTLGYPAFAQTVdnK------HQ 55
                                      456677777777777.9**********888432......22 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.046
                                       XXXXXXXXXXXXXXXX.-- CS
                           DUF4179  19 lllssrllspalAsalnpv 37 
                                        +l+sr+l p++  ++ + 
  gi|298674828|ref|YP_003726578.1|  88 FVLGSRNLEPTFNDMF-SE 105
                                       2469999999998776.33 PP

>> COXG  Carbon monoxide dehydrogenase subunit G (CoxG)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.7e-05      0.15      88     131 ..      63     106 ..      53     110 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.7e-05
                                       EEEEEEEETTEEEEEEEEEEEEEHHHHS-HHHHHHHHHHHHHHH CS
                              COXG  88 lvvlveegggtrlswsakvnvggllaslGsrlidsaarklinel 131
                                       ++  ++++++ r++++ +  +++ +  lGsr+++ + + +  e+
  gi|298674828|ref|YP_003726578.1|  63 VIEFDDNDAQARINYELDLFAQMYVFVLGSRNLEPTFNDMFSEF 106
                                       4455667899***************************9998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1037.80
//
Query:       gi|298674829|ref|YP_003726579.1|  [L=649]
Description: peptidase S16, Lon-like protease [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-33  116.2   5.8    2.3e-33  115.5   5.8    1.4  1  Lon_C            Lon protease (S16) C-terminal proteolytic do
    5.5e-28   98.0   0.0    3.5e-19   69.0   0.0    2.3  2  AAA_32           AAA domain
    8.5e-16   58.0   0.1    1.4e-09   37.7   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    3.7e-15   56.0   0.0    5.5e-08   32.7   0.0    2.7  2  Sigma54_activat  Sigma-54 interaction domain
    7.2e-12   45.5   0.0    4.8e-05   23.4   0.0    2.7  2  AAA_5            AAA domain (dynein-related subfamily)
    7.2e-11   42.0   1.0    1.6e-10   40.9   1.0    1.6  1  ChlI             Subunit ChlI of Mg-chelatase
    1.1e-07   32.3   0.0      0.012   16.0   0.0    2.8  2  AAA              ATPase family associated with various cellul
    2.2e-06   27.0   0.3        0.1   11.6   0.0    3.2  3  MCM              MCM P-loop domain
    1.5e-05   24.8   0.1      0.015   15.1   0.0    2.4  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    3.8e-05   24.0   0.0     0.0044   17.3   0.0    2.7  2  AAA_22           AAA domain
    7.6e-05   22.3   0.0     0.0008   19.0   0.0    2.3  2  AAA_7            P-loop containing dynein motor region
    0.00014   21.7   0.0       0.45   10.4   0.0    2.7  2  AAA_3            ATPase family associated with various cellul
    0.00027   21.1   0.0       0.97    9.6   0.0    2.6  2  Sigma54_activ_2  Sigma-54 interaction domain
    0.00029   20.2   0.0       0.75    8.9   0.0    2.4  2  TIP49            TIP49 P-loop domain
    0.00052   20.4   0.4     0.0056   17.0   0.4    2.4  1  AAA_19           AAA domain
    0.00084   19.7   0.1     0.0022   18.4   0.1    1.6  1  MCM_lid          MCM AAA-lid domain
      0.003   16.5   0.4        1.8    7.4   0.0    2.6  3  AAA_PrkA         PrkA AAA domain
     0.0036   16.8   0.0     0.0089   15.5   0.0    1.6  1  PhoH             PhoH-like protein
     0.0037   17.0   0.0      0.022   14.5   0.0    2.1  2  AAA_30           AAA domain
     0.0091   15.7   0.0      0.032   14.0   0.0    1.8  2  IstB_IS21        IstB-like ATP binding protein
  ------ inclusion threshold ------
      0.011   15.9   0.0      0.024   14.8   0.0    1.6  1  AAA_33           AAA domain
      0.016   13.9   0.7      0.031   13.0   0.7    1.4  1  SepSecS          O-phosphoseryl-tRNA(Sec) selenium transferas
      0.019   14.0   0.0      0.033   13.3   0.0    1.3  1  Parvo_NS1        Parvovirus non-structural protein NS1
      0.024   13.8   0.0      0.051   12.7   0.0    1.5  1  DUF815           Protein of unknown function (DUF815)
      0.026   14.8   1.2       0.05   13.8   1.2    1.4  1  VirB3            Type IV secretory pathway, VirB3-like protei
      0.026   13.4   0.0      0.056   12.4   0.0    1.5  1  AAA_10           AAA-like domain
      0.033   14.6   0.0        0.1   13.0   0.0    1.8  1  AAA_16           AAA ATPase domain
      0.039   14.5   0.0       0.13   12.8   0.0    1.8  1  ABC_tran         ABC transporter
      0.084   13.4   0.0        1.1    9.9   0.0    2.5  2  AAA_18           AAA domain
       0.11   12.8   0.0       0.39   11.1   0.0    1.9  1  Styelin          Styelin
       0.12   12.2   0.5       0.51   10.2   0.2    2.0  2  DUF4118          Domain of unknown function (DUF4118)


Domain annotation for each model (and alignments):
>> Lon_C  Lon protease (S16) C-terminal proteolytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.5   5.8     4e-36   2.3e-33       2     204 ..     405     605 ..     404     606 .. 0.87

  Alignments for each domain:
  == domain 1  score: 115.5 bits;  conditional E-value: 4e-36
                                       E-TTTTHHHH-S-SS--SSSSS--BSSEEEEEEEET.TEEEEEEEEEEEES....S-S-EEEEES--HHHHHHHHHH CS
                             Lon_C   2 vtakeleellGkkrfrseeaekedqvGvvtGlawte.vGGdlltieavllp....gkgklkltGklgdvmkesaqaa 73 
                                       ++++  +++l +k+  +   ++ +qvG v Gla      G +l i a ++p     +g+++ tG l+d+ ke++q  
  gi|298674829|ref|YP_003726579.1| 405 IEQQVADNYLEQKKQYQLFSKEGEQVGRVNGLAVMGgDSGVVLPIIAEVTPslsnSEGSVIATGMLKDIAKEAVQNV 481
                                       566667788888877777788899********97531456689998877653333789*****************99 PP

                                       HHHHTSS-GGGSS-SS-TTT-EEEEEE-S-B-GGGGGGGHHHHHHHHHHHHTS--B-TTBEE--EE-TT-BEE--S- CS
                             Lon_C  74 lsyvrsraeelgidkevfekkdihihvPeGavPkdGPsaGvtlatalvslltgkkvrkdvamtGeitLrGrvlpiGG 150
                                        +++++ +       +   ++dihi +       +G sa +++ata++s++ +++v++ vamtG +++rG vlp+GG
  gi|298674829|ref|YP_003726579.1| 482 SAVIKNITG------KDIANRDIHIQFVGTYEGVEGDSASISVATAVISAIEQVPVNQTVAMTGSLSVRGDVLPVGG 552
                                       888875433......335689******9999999******************************************* PP

                                       HHHHHHHHHHTT-SBEEEEGGGGGGTTTS-HHHHTS-B--EESBHHHHHHHHB- CS
                             Lon_C 151 lkekllaakragikkvilPkenekdlediPeevreeleiilveevdevlkaalv 204
                                       +  k+ aa +agi+k+i+Pk+ne d+  i ++ ++++eii+v+++ ev+++ lv
  gi|298674829|ref|YP_003726579.1| 553 VTYKIEAAAQAGIQKIIIPKANEADVL-IEDQYKDQVEIIPVSTITEVIEHSLV 605
                                       *************************95.99*********************996 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   4.3e-09   2.5e-06       7      91 ..      33     112 ..      29     123 .. 0.84
   2 !   69.0   0.0     6e-22   3.5e-19     281     509 ..     173     400 ..     170     404 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 4.3e-09
                            AAA_32   7 leeiigqeRAvealefglkikkkgYNifvlGesgtGrttlvkrlleeiakkeptpdDwcYvnnfdnpeePkalsLpa 83 
                                       ++++igq+ Ave ++ + +      ++ ++G++gtG++ l+k + e   k e   +D++   n ++p++Pk+ ++pa
  gi|298674829|ref|YP_003726579.1|  33 IDQVIGQDHAVEVVKKAAEQ---RRHVMMIGSPGTGKSLLAKAMAELLPK-E-ELKDVLVYPNTEDPNNPKVREVPA 104
                                       5899*********9988765...559************999999877644.3.456777778*************** PP

                            AAA_32  84 GkGkelkk 91 
                                       GkG+e  +
  gi|298674829|ref|YP_003726579.1| 105 GKGREIVQ 112
                                       ****9876 PP

  == domain 2  score: 69.0 bits;  conditional E-value: 6e-22
                            AAA_32 281 nvlvdnsetegaPVvvednptyanLfGkieyesemg..alvtdftlIkaGaLhkAnGGyLildaedlLeeplaWeaL 355
                                       +++v+n e+e+aP +  +  +   L+G + ++  +   + +  + ++++G +hk + G+L +d  + L+ + + +++
  gi|298674829|ref|YP_003726579.1| 173 KLIVSNYEKEHAPYIDATGTHAGALLGDVRHDPFQSggMETPAHDRVESGDIHKSHKGVLFIDEINTLNIE-TQQNM 248
                                       79****************************9975433488889**********************999765.56777 PP

                            AAA_32 356 kraLrskeikiesleeqlglistvsLkPepipldvKViLiGsrelYylLseyDpdfkklFkvkadFddemerteene 432
                                         aL++ke  i       + +s    k +p+p+d   +  G+ +  + ++ +     k +  +  + d+me t+en 
  gi|298674829|ref|YP_003726579.1| 249 LTALQEKEYPITGQ---SERSSGALVKSDPVPCDFIMVAAGNLDAVENMHPALRSRLKGYGYELYMRDTMEDTPENR 322
                                       78**********53...446788999*********99999998887777777777777788999************* PP

                            AAA_32 433 kkyarfiasivkke.kllpfdrsavarlieyssrlaedqeklstrfseiadllrEAdywakkegaevveaehVekAl 508
                                       k+++rf+a+ vk++ ++++f++sav ++i++s r a+++ +l+++++++  l+r A  +ak eg+e+ ++ehV  A 
  gi|298674829|ref|YP_003726579.1| 323 KDLVRFVAQEVKRDgHIPHFNKSAVDEIIRESRRRAGRKGHLTLKLRDLGGLIRVAGDIAKAEGSEYATEEHVISAK 399
                                       ********9998772589*******************************************************9986 PP

                            AAA_32 509 e 509
                                       +
  gi|298674829|ref|YP_003726579.1| 400 R 400
                                       5 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.0   2.4e-12   1.4e-09       3      55 ..      34      86 ..      32     117 .. 0.91
   2 !   17.8   0.0   2.8e-06    0.0016      96     158 ..     218     288 ..     209     313 .. 0.75

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 2.4e-12
                      Mg_chelatase  3 kdvkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeeal 55
                                       +v+Gq++a ++++ aa  + +++++G+pG+GK++lak++++llp+ + +++l
  gi|298674829|ref|YP_003726579.1| 34 DQVIGQDHAVEVVKKAAEQRRHVMMIGSPGTGKSLLAKAMAELLPKEELKDVL 86
                                      689******************************************99888876 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 2.8e-06
                      Mg_chelatase  96 kpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakv........efparfqlvaamNp 158
                                       +++ G+i ++h+GvLf+DE+  ++ ++ + + + l+++e  i+ ++++           p++f +vaa N+
  gi|298674829|ref|YP_003726579.1| 218 RVESGDIHKSHKGVLFIDEINTLNIETQQNMLTALQEKEYPITGQSERSsgalvksdPVPCDFIMVAAGNL 288
                                       6789*******************999999999999999888764433220111221235777777777775 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0     6e-07   0.00035      10      49 ..      41      80 ..      33      96 .. 0.85
   2 !   32.7   0.0   9.5e-11   5.5e-08      82     130 ..     216     265 ..     207     295 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 6e-07
                                      HHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTT CS
                   Sigma54_activat 10 elleqikkvaktdlsvlitGesGtGKellaraiheaskrk 49
                                      +++e +kk+a+++ +v++ G  GtGK+lla+a+ e  +++
  gi|298674829|ref|YP_003726579.1| 41 HAVEVVKKAAEQRRHVMMIGSPGTGKSLLAKAMAELLPKE 80
                                      67899****************************9876654 PP

  == domain 2  score: 32.7 bits;  conditional E-value: 9.5e-11
                                       SS-BE.HHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSE CS
                   Sigma54_activat  82 ekekk.GlfekadgGtlfLDeigelplelQekLlrvlqegevervGsske 130
                                       +++ + G ++k+++G+lf+Dei++l++e+Q+++l++lqe+e+   G+s+ 
  gi|298674829|ref|YP_003726579.1| 216 HDRVEsGDIHKSHKGVLFIDEINTLNIETQQNMLTALQEKEYPITGQSER 265
                                       444444************************************99998765 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.5e-06   0.00085       1      36 [.      55      91 ..      55     114 .. 0.86
   2 !   23.4   0.0   8.3e-08   4.8e-05      64     138 .]     213     302 ..     145     302 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.5e-06
                                      EEEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT- CS
                             AAA_5  1 dvlLvGppGtgKselaerlaaal.nreveyvqltrdt 36
                                      +v+++G pGtgKs la+ +a++l + e+  v+ + +t
  gi|298674829|ref|YP_003726579.1| 55 HVMMIGSPGTGKSLLAKAMAELLpKEELKDVLVYPNT 91
                                      79*********************86666665555555 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 8.3e-08
                                       -..............G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---............-EEEEEE CS
                             AAA_5  64 r..............egeilvlDEveraesevlnsLlslleerrllleeggelvkaknddller......frviata 120
                                       +              ++ +l++DE+++++ e+++ +l+ l e+++++    e+ + +     +       f  +a++
  gi|298674829|ref|YP_003726579.1| 213 TpahdrvesgdihksHKGVLFIDEINTLNIETQQNMLTALQEKEYPITGQSERSSGALV---KSdpvpcdFIMVAAG 286
                                       055555556666666899****************************8877777777763...234779999999999 PP

                                       SS--.-TT-TTHHHHTT- CS
                             AAA_5 121 npldrslnelspalrsRf 138
                                       n     ++++ palrsR+
  gi|298674829|ref|YP_003726579.1| 287 NLDA--VENMHPALRSRL 302
                                       9888..9999******96 PP

>> ChlI  Subunit ChlI of Mg-chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   1.0   2.7e-13   1.6e-10      11     121 .]     463     574 ..     453     574 .. 0.94

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 2.7e-13
                              ChlI  11 kftivGlpdtavkeskervrsalkn.sgfefpakkitvnLaPadlkkeGsafDLpiAigilaaleqieaeeetlflG 86 
                                       ++  +G+++   ke+ + v + +kn +g ++ ++ i +         eG + ++++A ++++a+eq+++++++ + G
  gi|298674829|ref|YP_003726579.1| 463 SVIATGMLKDIAKEAVQNVSAVIKNiTGKDIANRDIHIQFVGTYEGVEGDSASISVATAVISAIEQVPVNQTVAMTG 539
                                       55668999999**************889************************************************* PP

                              ChlI  87 eLsldGslrpvkgvlpialaakkegikkvivpken 121
                                        Ls  G++ pv gv+  + aa+++gi+k+i+pk+n
  gi|298674829|ref|YP_003726579.1| 540 SLSVRGDVLPVGGVTYKIEAAAQAGIQKIIIPKAN 574
                                       *********************************98 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.1e-05     0.012       1      22 [.      56      77 ..      56     130 .. 0.80
   2 !   13.2   0.0   0.00016     0.091      56     125 ..     227     303 ..     211     306 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.1e-05
                                      EEEESSTTSSHHHHHHHHHHHH CS
                               AAA  1 vllyGppGtGKTllakavakel 22
                                      v+++G pGtGK+llaka+a+ l
  gi|298674829|ref|YP_003726579.1| 56 VMMIGSPGTGKSLLAKAMAELL 77
                                      6899**************9876 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00016
                                       TSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS..................SSTEEEEEEESS..G CS
                               AAA  56 kakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk..................eskvivigatnr..p 112
                                       + ++ +lfiDEi  l+ +            ++ +lt+l++ +                      ++i+++a+n   +
  gi|298674829|ref|YP_003726579.1| 227 S-HKGVLFIDEINTLNIET-----------QQNMLTALQEKEYPitgqserssgalvksdpvPCDFIMVAAGNLdaV 291
                                       2.359**********7777...........9999999999999999999999*********9667*********99* PP

                                       GGSTHHHHSTTSS CS
                               AAA 113 dkldpallrgRfd 125
                                       +++ pal+ +R++
  gi|298674829|ref|YP_003726579.1| 292 ENMHPALR-SRLK 303
                                       ********.9975 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00018       0.1      51      84 ..      47      80 ..       9      85 .. 0.81
   2 !   11.2   0.0   0.00025      0.14      86     148 ..     186     255 ..     169     261 .. 0.75
   3 ?   -0.8   0.1       1.1   6.4e+02      19      52 ..     481     514 ..     469     525 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                                      SSBBCSS-EEEEEESSTSTHHHHHHHHHHHSSSE CS
                               MCM 51 ktklrgdinvllvgdpgtaKsqlLkyveklapra 84
                                      k+    + +v+++g pgt+Ks l k++++l+p+ 
  gi|298674829|ref|YP_003726579.1| 47 KKAAEQRRHVMMIGSPGTGKSLLAKAMAELLPKE 80
                                      44466778********************999975 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00025
                                       EEESSSSSSSHSSSEEEEESSSSS.......EEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHS CS
                               MCM  86 ytsgkgssaagLtaavvrdeetge.......fvleaGalvladkGvcciDefdkmkeedrsalhEamEqq 148
                                       y+ ++g+ a  L   v++d+ ++          +e+G +  ++kGv+ iDe++  + e+++ ++ a+ ++
  gi|298674829|ref|YP_003726579.1| 186 YIDATGTHAGALLGDVRHDPFQSGgmetpahDRVESGDIHKSHKGVLFIDEINTLNIETQQNMLTALQEK 255
                                       66666666666666666666554433333324589*************************9999998765 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.1
                                       HHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSS CS
                               MCM  19 vksiapsiyghedvkkaillqlfggvkkkledkt 52 
                                       v++++++i+g++   + i +q +g+++  + d++
  gi|298674829|ref|YP_003726579.1| 481 VSAVIKNITGKDIANRDIHIQFVGTYEGVEGDSA 514
                                       4567888999999999999999998887766655 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.5e-05     0.015       7      56 ..      34      76 ..      28      85 .. 0.74
   2 !    7.1   0.0    0.0071       4.1      84     115 ..     228     259 ..     223     301 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.5e-05
                            RuvB_N  7 eeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiake 56
                                      ++ igq++    ++++ +aa++r     hv+++G+PG Gk+ lak +a+ 
  gi|298674829|ref|YP_003726579.1| 34 DQVIGQDHA---VEVVKKAAEQR----RHVMMIGSPGTGKSLLAKAMAEL 76
                                      556666654...44555666666....6*****************99975 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0071
                            RuvB_N  84 ekdvlfideihrlsraveevlysamedfrldi 115
                                       +k vlfidei  l+ ++++ + +a+++ +  i
  gi|298674829|ref|YP_003726579.1| 228 HKGVLFIDEINTLNIETQQNMLTALQEKEYPI 259
                                       578***************99999998876655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   7.6e-06    0.0044       4      36 ..      52      84 ..      48     130 .. 0.77
   2 ?    3.5   0.0      0.14        82      86     112 ..     224     252 ..     216     264 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 7.6e-06
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakae 36
                                      ++++++ +G +GtGK++l++ ++e l++e+  +
  gi|298674829|ref|YP_003726579.1| 52 QRRHVMMIGSPGTGKSLLAKAMAELLPKEELKD 84
                                      8999**********************9776543 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.14
                            AAA_22  86 lraravielliiDEaqhlr...seealeeL 112
                                       +++ ++ ++l iDE+  l+   ++++l+ L
  gi|298674829|ref|YP_003726579.1| 224 IHKSHK-GVLFIDEINTLNietQQNMLTAL 252
                                       566667.9**********886558888777 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.4e-06    0.0008      25      63 ..      45      83 ..      30      91 .. 0.91
   2 ?    0.2   0.0      0.81   4.7e+02     100     116 ..     228     244 ..     225     251 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.4e-06
                             AAA_7 25 llelllknkkpvllvGptGtGKtviikdllkkldkekyl 63
                                      ++++  +++++v+++G+ GtGK++++k + + l+ke+++
  gi|298674829|ref|YP_003726579.1| 45 VVKKAAEQRRHVMMIGSPGTGKSLLAKAMAELLPKEELK 83
                                      5788999**************************999876 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.81
                             AAA_7 100 kklvvFvDDlnmpakek 116
                                       +k v+F+D++n  + e+
  gi|298674829|ref|YP_003726579.1| 228 HKGVLFIDEINTLNIET 244
                                       6889*******998886 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0033       1.9       1      24 [.      55      78 ..      55      90 .. 0.90
   2 !   10.4   0.0   0.00078      0.45      64      98 ..     230     264 ..     213     284 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0033
                             AAA_3  1 hvllegvPGlaktllvkalakald 24
                                      hv++ g PG++k ll+ka+a+ l 
  gi|298674829|ref|YP_003726579.1| 55 HVMMIGSPGTGKSLLAKAMAELLP 78
                                      9*******************9885 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00078
                             AAA_3  64 nllladeinrappktqsalleameerqvtvegeth 98 
                                        +l+ dein  +  tq  +l a++e++  ++g++ 
  gi|298674829|ref|YP_003726579.1| 230 GVLFIDEINTLNIETQQNMLTALQEKEYPITGQSE 264
                                       5899**********************998888765 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0032       1.8      14      43 ..      46      75 ..      42      91 .. 0.88
   2 !    9.6   0.0    0.0017      0.97      66      97 ..     225     256 ..     202     293 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0032
                                      HHHHHT-SS-EEEEEETT--HHHHHHCC-- CS
                   Sigma54_activ_2 14 LeqaaqsklpvfltGekGsgkelvArlLhk 43
                                      +++aa++   v ++G +G+gk+l A+++++
  gi|298674829|ref|YP_003726579.1| 46 VKKAAEQRRHVMMIGSPGTGKSLLAKAMAE 75
                                      78999*********************9987 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0017
                                       HHTTTSEEEEEE-TT--HHHHHHHHHHHHHHT CS
                   Sigma54_activ_2  66 eqakggtLylkdiadlskaeqkeLlellakae 97 
                                        +++ g+L++ +i+ l+ + q+++l +l+++e
  gi|298674829|ref|YP_003726579.1| 225 HKSHKGVLFIDEINTLNIETQQNMLTALQEKE 256
                                       45789************************965 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0017      0.99      40      75 ..      43      78 ..      14      86 .. 0.76
   2 !    8.9   0.0    0.0013      0.75     279     309 ..     229     259 ..     218     266 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0017
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 40 velikekklaGravLlaGpsgtGktalaiaiskelg 75
                                      ve++k+     r v++ G +gtGk+ la a+++ l 
  gi|298674829|ref|YP_003726579.1| 43 VEVVKKAAEQRRHVMMIGSPGTGKSLLAKAMAELLP 78
                                      5667776667799*****************998775 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0013
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 279 pGvlfiDevhmlDiecfsylnraleselaPi 309
                                       +GvlfiDe++ l+ie+   +  al ++  Pi
  gi|298674829|ref|YP_003726579.1| 229 KGVLFIDEINTLNIETQQNMLTALQEKEYPI 259
                                       7***************999999998887776 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.4   9.7e-06    0.0056       7     128 ..      50     255 ..      42     261 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 9.7e-06
                            AAA_19   7 alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrA.akelrerlaalgaeatTiHrlal..... 77 
                                       a +++++++++ pGtGK+ + k++ +ll +++   ++++l+   t+     ++re  a+ g+e+   H++       
  gi|298674829|ref|YP_003726579.1|  50 AEQRRHVMMIGSPGTGKSLLAKAMAELLPKEE---LKDVLVYPNTEDPnNPKVREVPAGKGREIVQAHKMEArkrsq 123
                                       5678999**********998888888887777...467888887776514589999989999999999986689999 PP

                            AAA_19  78 ............................................................................. 77 
                                                                                                                    
  gi|298674829|ref|YP_003726579.1| 124 srnmlmlllifgivmysfyvgqllwgiiaailllvltrqfmpkddlmvpklivsnyekehapyidatgthagallgd 200
                                       99999999999999999999999999999999999999999999999999999999999998877766666666666 PP

                            AAA_19  78 .....ldfddlltealelle..........eaeeekklqeee.llivDEfqdvd.elqyrLlkallge 128
                                                          +          + e+ +  ++++ +l++DE+  ++ e+q+++l al ++
  gi|298674829|ref|YP_003726579.1| 201 vrhdpF-------------QsggmetpahdRVESGDIHKSHKgVLFIDEINTLNiETQQNMLTALQEK 255
                                       444331.............033333555532223333344557********************99854 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   3.8e-06    0.0022      32      84 ..     353     403 ..     331     405 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.8e-06
                                       HHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHHHHHHHHH CS
                           MCM_lid  32 elRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedveeairllk 84 
                                       e R+++   ++ +++   R L  liR++  +Ak + se++tee+v +a r+ +
  gi|298674829|ref|YP_003726579.1| 353 ESRRRAG--RKGHLTLKLRDLGGLIRVAGDIAKAEGSEYATEEHVISAKRMAR 403
                                       4555552..4789999******************************9998865 PP

>> AAA_PrkA  PrkA AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.0    0.0057       3.3      67     129 ..      30      94 ..       5     103 .. 0.72
   2 !    7.4   0.0    0.0031       1.8     226     267 ..     221     262 ..     197     271 .. 0.93
   3 ?   -3.0   0.2       4.5   2.6e+03     274     330 ..     566     623 ..     557     634 .. 0.56

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0057
                          AAA_PrkA  67 eetiekive..yfraaaqrleerkqilyllGPvggGksslverlkklleaapiyalegsPvfeeP 129
                                       e+ i+++++  +  +  ++  e+++ ++++G  g+Gks l++++ +ll ++ +  +   P +e+P
  gi|298674829|ref|YP_003726579.1|  30 EQLIDQVIGqdHAVEVVKKAAEQRRHVMMIGSPGTGKSLLAKAMAELLPKEELKDVLVYPNTEDP 94 
                                       566777776334445567777888888899**************999988876666666666665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0031
                          AAA_PrkA 226 sGalnranrGllefvemfkadikvlhplltatqegnykstek 267
                                       sG++ ++ +G+l   e+   +i+   ++lta qe++y+ t++
  gi|298674829|ref|YP_003726579.1| 221 SGDIHKSHKGVLFIDEINTLNIETQQNMLTALQEKEYPITGQ 262
                                       7999********99***********************99886 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 4.5
                          AAA_PrkA 274 dgiilahsnesewkkfksnkknealldrivvvkv.Pyclrvseekkiyekllkesela 330
                                       + ii+  +ne++     + k+   ++   ++ +v  ++l  +e k+i +kl k s++ 
  gi|298674829|ref|YP_003726579.1| 566 QKIIIPKANEADVLIEDQYKDQVEIIPVSTITEViEHSLVGNEKKNIVDKLKKVSNVK 623
                                       5666666777665544444444334433333333144555556666777777777764 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.5e-05    0.0089       9      51 ..      39      84 ..      34      94 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.5e-05
                                      HHHHHHHHH....H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SE CS
                              PhoH  9 Qkeylealk....kndivfaiGpaGtGKtylavalavealkkkkvkr 51
                                      Q++++e++k    +   v++iG+ GtGK++la a+a e+l k+++k 
  gi|298674829|ref|YP_003726579.1| 39 QDHAVEVVKkaaeQRRHVMMIGSPGTGKSLLAKAMA-ELLPKEELKD 84
                                      66677776655446779*****************98.4555555554 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   3.8e-05     0.022       9      52 ..      45      88 ..      38     113 .. 0.81
   2 ?   -0.9   0.0         2   1.2e+03      88     115 ..     228     255 ..     196     259 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.8e-05
                            AAA_30  9 avealltsgdrvavltGpAGtGKttalkalreaweaa.ggrvigl 52
                                      +v+++++++ r +++ G +GtGK+ + ka++e++ ++  ++v+++
  gi|298674829|ref|YP_003726579.1| 45 VVKKAAEQR-RHVMMIGSPGTGKSLLAKAMAELLPKEeLKDVLVY 88
                                      455555555.69999******************999844666655 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2
                            AAA_30  88 pgtllivDEagmvdtkqlaallkaaeka 115
                                       ++ +l +DE+  +++++ +++l+a++++
  gi|298674829|ref|YP_003726579.1| 228 HKGVLFIDEINTLNIETQQNMLTALQEK 255
                                       457999*******999999999998875 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   5.5e-05     0.032      45      69 ..      51      75 ..       6      89 .. 0.70
   2 ?   -2.7   0.0       7.3   4.2e+03     110     127 ..     230     247 ..     220     257 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.5e-05
                         IstB_IS21 45 ekkenivllGpsGvGKshlaialgv 69
                                      e++  ++++G +G+GKs la a++ 
  gi|298674829|ref|YP_003726579.1| 51 EQRRHVMMIGSPGTGKSLLAKAMAE 75
                                      567789*****************96 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.3
                         IstB_IS21 110 dllilDdlgllpldqaea 127
                                        +l +D++ +l+++ +++
  gi|298674829|ref|YP_003726579.1| 230 GVLFIDEINTLNIETQQN 247
                                       689999999999988764 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   4.1e-05     0.024       2      24 ..      56      78 ..      56     130 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.1e-05
                            AAA_33  2 vllvGlpGsGKstlaerllkklg 24
                                      v+++G pG+GKs la+ +++ l+
  gi|298674829|ref|YP_003726579.1| 56 VMMIGSPGTGKSLLAKAMAELLP 78
                                      89***************996665 PP

>> SepSecS  O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.7   5.4e-05     0.031     115     191 ..     557     633 ..     546     640 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.4e-05
                                       HHHHHCTT-EEEEE-EEECTTEEEEHHHHHHHHH..HCCTCCCEEEEEECSSTTTTB----HHHHHHHHHCCT--EE CS
                           SepSecS 115 lkavelaGleialvekvlegDelitdvedveeii..ekkreevilavlstlsffaprspDdvkeiakiCaeydvPhl 189
                                       + a+ +aG++ ++++k +e D li d+ + +  i       e  ++ +s +     +  D++k+++++  ++d+P +
  gi|298674829|ref|YP_003726579.1| 557 IEAAAQAGIQKIIIPKANEADVLIEDQYKDQVEIipVSTITE--VIEHSLVGNEKKNIVDKLKKVSNVKWNFDMPEV 631
                                       68999*******************998654443312444444..44467777778899******************9 PP

                                       EE CS
                           SepSecS 190 vN 191
                                       v 
  gi|298674829|ref|YP_003726579.1| 632 VP 633
                                       96 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.8e-05     0.033     104     140 ..      43      79 ..       7      97 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.8e-05
                         Parvo_NS1 104 lawlskqlgkrntvwfyGpantGktnlaeaIakavpl 140
                                       + +++k   +r  v+++G++ tGk+ la+a+a+ +p+
  gi|298674829|ref|YP_003726579.1|  43 VEVVKKAAEQRRHVMMIGSPGTGKSLLAKAMAELLPK 79 
                                       5678899999***********************9985 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   8.8e-05     0.051      52      83 ..      52      83 ..      16      92 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.8e-05
                            DUF815 52 pannvLLwGarGtGKSslvkallneyaeegLr 83
                                      + ++v+++G+ GtGKS l ka+ + + +e+L+
  gi|298674829|ref|YP_003726579.1| 52 QRRHVMMIGSPGTGKSLLAKAMAELLPKEELK 83
                                      4579******************9999998887 PP

>> VirB3  Type IV secretory pathway, VirB3-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.2   8.7e-05      0.05      21      65 ..     128     172 ..     126     183 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.7e-05
                             VirB3  21 elvllnllvsvilflvglslwillllvplhlvlrliakrDpqmfr 65 
                                        ++ll+++++++ f vg+ lw ++++++l+++ r+   +D+ m+ 
  gi|298674829|ref|YP_003726579.1| 128 LMLLLIFGIVMYSFYVGQLLWGIIAAILLLVLTRQFMPKDDLMVP 172
                                       567889999999999*******************99999999975 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   9.7e-05     0.056      12      60 ..      44      92 ..      37     124 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.7e-05
                            AAA_10 12 qevkgsktnasasliiGdlGnGKSvlakllvlyisllggkaliiDpkke 60
                                      + vk + ++  ++++iG++G GKS+lak +   +   + k +++ p  e
  gi|298674829|ref|YP_003726579.1| 44 EVVKKAAEQRRHVMMIGSPGTGKSLLAKAMAELLPKEELKDVLVYPNTE 92
                                      66888889999*******************9988888888888877777 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00017       0.1      16      55 ..      46      87 ..      35     125 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00017
                            AAA_16 16 lervrsgrpelvllsGesGvGKsslvrellralekd...ggif 55
                                      +++++++r + v+ +G +G+GKs l+++ ++ l k+   ++++
  gi|298674829|ref|YP_003726579.1| 46 VKKAAEQR-RHVMMIGSPGTGKSLLAKAMAELLPKEelkDVLV 87
                                      44444444.99******************99888875544555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00022      0.13       9      39 ..      51      81 ..      44     127 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00022
                                      ETTSEEEEEESTTSSHHHHHHHHTTSS--SE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  9 kegekvaivGenGaGKStLlkllagllkpte 39
                                      ++ + v ++G+ G+GKS L+k++a+ll ++e
  gi|298674829|ref|YP_003726579.1| 51 EQRRHVMMIGSPGTGKSLLAKAMAELLPKEE 81
                                      5667899*****************9987654 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0    0.0018       1.1       2      51 ..      57     101 ..      56     145 .. 0.72
   2 ?    0.1   0.0       1.9   1.1e+03      17      68 ..     367     418 ..     357     445 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0018
                            AAA_18   2 lltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskr 51 
                                       +  G pG+GK+ lak+ +++l   ++l+dv+   +++++++p+     ++
  gi|298674829|ref|YP_003726579.1|  57 MMIGSPGTGKSLLAKAMAELL-PKEELKDVLVYPNTEDPNNPK----VRE 101
                                       6689*************9995.367777777777777777777....333 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.9
                            AAA_18  17 eLskrlgfgvnlrdvakenglllevdpealdeskrldedk.ldklldaleens 68 
                                        L++++g+ ++ +d+ak +g+++  +++ + + kr+ +   ++++ + le+  
  gi|298674829|ref|YP_003726579.1| 367 KLRDLGGLIRVAGDIAKAEGSEYATEEH-VISAKRMARSIeQQVADNYLEQKK 418
                                       5656556677889999999999999999.444444444440444444444443 PP

>> Styelin  Styelin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00068      0.39      10      42 ..     176     208 ..     173     213 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00068
                           Styelin  10 vskfYkkhktYikaalsiakhlLGDmtDeefqe 42 
                                       vs++ k h  Yi a+   a  lLGD+  + fq 
  gi|298674829|ref|YP_003726579.1| 176 VSNYEKEHAPYIDATGTHAGALLGDVRHDPFQS 208
                                       89************8877777******999995 PP

>> DUF4118  Domain of unknown function (DUF4118)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.2   0.00088      0.51      25      58 ..     126     160 ..     114     165 .. 0.79
   2 ?   -1.5   0.0       3.6   2.1e+03      61      80 ..     232     251 ..     231     252 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00088
                           DUF4118  25 anivllfllavllvallg.glgpgllaallsvllf 58 
                                       + ++ll+++++++ +++   l++g++aa+l  +l 
  gi|298674829|ref|YP_003726579.1| 126 NMLMLLLIFGIVMYSFYVgQLLWGIIAAILLLVLT 160
                                       44566888999999999889*********988876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.6
                           DUF4118  61 fftpPyftltiadpeylltl 80 
                                       +f+  + tl+i+ ++++lt 
  gi|298674829|ref|YP_003726579.1| 232 LFIDEINTLNIETQQNMLTA 251
                                       6999999**********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (649 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1172  (0.065369); expected 358.6 (0.02)
Passed bias filter:                      784  (0.043728); expected 358.6 (0.02)
Passed Vit filter:                       141  (0.00786435); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.84u 0.37s 00:00:01.21 Elapsed: 00:00:00.54
# Mc/sec: 3650.15
//
Query:       gi|298674830|ref|YP_003726580.1|  [L=443]
Description: peptidase U62 modulator of DNA gyrase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.1e-70  235.7   0.7    1.3e-69  235.2   0.7    1.2  1  PmbA_TldD  Putative modulator of DNA gyrase


Domain annotation for each model (and alignments):
>> PmbA_TldD  Putative modulator of DNA gyrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.2   0.7     7e-74   1.3e-69       2     279 .]       7     299 ..       6     299 .. 0.92

  Alignments for each domain:
  == domain 1  score: 235.2 bits;  conditional E-value: 7e-74
                                       EEEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE...ESSHHHHHHHHHHHHHHCCS---TT-... CS
                         PmbA_TldD   2 aevrleesestsvrfengevetnsssedsglgvrvikggrlgfastldtsdealeeaveraveiaklapedpea... 75 
                                       +++r++e+++ts++++ng+ve +s   ++g+gvr+++gg++gf+s +     +l+++++ a ++ak  +++  +   
  gi|298674830|ref|YP_003726580.1|   7 YDARVVEGTTTSIFLDNGKVEDISVDFSRGAGVRALCGGSWGFTSVDGNF--DLDKTIDSAAKLAKTMDNKTPKeki 81 
                                       799****************************************9966555..8************999888888999 PP

                                       ....................GGS-HHHHHHHHHHHHHH.CHCSTTEEEEEEEEEE......EEE.EEEEEEETTSEE CS
                         PmbA_TldD  76 ....................eevsaeekielleelekalrsadpkienskgarisgvsaslsaskeeklianSeGld 132
                                                           +++++eek+++l+++++         +n +  ++s+++a++++s  +  + nSeGld
  gi|298674830|ref|YP_003726580.1|  82 nlksspepevkntpnvkkdpRDIPIEEKVQILKDIDES--------ANIE--GVSNTTAIYTESIVKFEYTNSEGLD 148
                                       *****************************999999954........2333..99*********************** PP

                                       EEEEEEEEEEEEEEEE..STCS..ET.EEEEEEEESSHHHS..SSHHHHHHHHHHCTTT-B---SEEEEEEE-HHHH CS
                         PmbA_TldD 133 veqtrtrvslslsviad.dggs..gd.gmgggsgyedleeedleeiaeeaaekalasleakplppgkypVvlspeav 205
                                       +e++ tr+++ +s++a+ +g++  g+ ++   sg+e ++e+d+ +++e a  +a+++l ak+++ g++pV+l pe +
  gi|298674830|ref|YP_003726580.1| 149 CEHELTRTGFAVSAVASgNGEYqvGReSRFDVSGFELFDENDALALGESAGHTAVDLLSAKKPKGGNMPVILNPELA 225
                                       ****************536666565555555555689999************************************* PP

                                       HHHHHGHHHHHTBHHHHHTT--TTTT-TTSB-S-TT--EEEETT-.....-SB-TTSBB---EEEEETTEE--- CS
                         PmbA_TldD 206 gsllheavghaleadavlegrSflkdklGekvaselltivddptsgglgsypfDdEGvptqrtvlIenGvLkny 279
                                       g+++heavgha ead vleg S++++++Ge++as+l+ ++ddpt +++g+ypfD+EGv++++t++I++GvL++y
  gi|298674830|ref|YP_003726580.1| 226 GVFVHEAVGHASEADLVLEGNSVFENHIGEQIASSLVDVIDDPTLHKYGYYPFDAEGVQSSKTEIIKDGVLNSY 299
                                       ************************889****************99***************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 2621.56
//
Query:       gi|298674831|ref|YP_003726581.1|  [L=436]
Description: peptidase U62 modulator of DNA gyrase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.6e-53  181.2   1.0    4.9e-53  180.8   1.0    1.2  1  PmbA_TldD  Putative modulator of DNA gyrase


Domain annotation for each model (and alignments):
>> PmbA_TldD  Putative modulator of DNA gyrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.8   1.0   2.7e-57   4.9e-53       1     279 []      19     305 ..      19     305 .. 0.84

  Alignments for each domain:
  == domain 1  score: 180.8 bits;  conditional E-value: 2.7e-57
                                       EEEEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE...ESSHHHHHHHHHHHHHHCCS---TT-.. CS
                         PmbA_TldD   1 eaevrleesestsvrfengevetnsssedsglgvrvikggrlgfastldtsdealeeaveraveiaklapedpea.. 75 
                                       e+ev++ ++ sts  ++++ v++++++ ++g+g+r i +g++gfast+  +   le++v+ a+++a++ ++dpe+  
  gi|298674831|ref|YP_003726581.1|  19 EVEVYVLDNHSTSADVRKNIVDSSNENYTKGIGIRTIINGAVGFASTNLYN--RLEDTVNIAISSARVREKDPEWvs 93 
                                       68*********************************888********88888..***********************9 PP

                                       ..........GGS-HHHHHH....H.HHHHHHH.CHCSTTEEEEE.EEEEE......EEE.EEEEEEETTSEEEEEE CS
                         PmbA_TldD  76 ..........eevsaeekie....l.leelekalrsadpkiensk.garisgvsaslsaskeeklianSeGldveqt 136
                                                 +       ++    l l+ele+ +    ++ie +    ++  +s+s s  + ++li+nS+G++ e++
  gi|298674831|ref|YP_003726581.1|  94 lpsntqyptiR-------NTfddkLmLLELEDCIDLTTQMIEGVTsISDVMATSGSFSRFHDKRLIMNSNGIETEEE 163
                                       98765554321.......221112236666644333333444444222444556666666777************** PP

                                       EEEEEEEEEEEE..STCSETEEEEEEEE..SSHHHS..SSHHHHHHHHHHCTTT-B---SEEEEEEE-HHHHHHHHH CS
                         PmbA_TldD 137 rtrvslslsvia.ddggsgdgmgggsgy..edleeedleeiaeeaaekalasleakplppgkypVvlspeavgsllh 210
                                        t vs ++ vi+  d+     + + +++   +  ++d++ei++ aae a +s +   ++p k++V+l+p a++++l+
  gi|298674831|ref|YP_003726581.1| 164 GTGVSGFIDVITtTDN-----KATAYDFkiSRNLDIDFYEIGKNAAELAQKSRNGITIEPHKTDVILHPFAFADILE 235
                                       ************5452.....33455555444455899*************************************** PP

                                       GHHHHHTBHHHHHTT--TTTT-TTSB-S-TT--EEEETT-......-SB-TTSBB---EEEEETTEE--- CS
                         PmbA_TldD 211 eavghaleadavlegrSflkdklGekvaselltivddpts.gglgsypfDdEGvptqrtvlIenGvLkny 279
                                        ++++a++ad+v++grS lk+kl+e +a + l+ivdd+t  gg+ ++  DdEG+p+q++++I++Gv+k+y
  gi|298674831|ref|YP_003726581.1| 236 STLASAIDADNVHKGRSSLKGKLNEDIATPDLSIVDDGTLdGGIETALTDDEGMPSQKNTVIDKGVFKSY 305
                                       *******************99******************99***************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.62
# Mc/sec: 2123.59
//
Query:       gi|298674832|ref|YP_003726582.1|  [L=345]
Description: radical SAM domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-08   35.1   0.6    3.1e-07   30.9   0.5    2.3  2  Radical_SAM  Radical SAM superfamily
    5.7e-05   23.4   0.2    0.00018   21.8   0.1    1.8  2  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.5   3.5e-11   3.1e-07       2     155 ..     137     280 ..     136     291 .. 0.89
   2 ?    2.1   0.0     0.025   2.2e+02     121     144 ..     319     342 ..     300     345 .] 0.86

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 3.5e-11
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgi 78 
                                       +++ gC + C++C++   + r + g ++ +  +++++++ + + g k+v ++  +p l+   v ++ + + +   ++
  gi|298674832|ref|YP_003726582.1| 137 IFFTGCVFSCVYCQNCDISTRPESGIEINPLHLAKIIDARR-REGSKNVNFVTPTPHLHT--VLKTINNISE---NL 207
                                       6899*************988999999999999999999995.889******999888865..6666666665...9* PP

                                       EEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  79 ritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGe 155
                                        +   +n ++   e + +lle  +d +  +   +++++ +k+ n ++  e v+++++k+ ++  + +++r+++lpG 
  gi|298674832|ref|YP_003726582.1| 208 PVIWNSNMYH--SEEASELLEGIIDMFLADFRYGNNRCAKKYSNINNYTEIVKRNFKKAYQH-SD-IIIRHLVLPGH 280
                                       **********..69999999988**************88899989999*********99999.77.9********96 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.025
                                       HTCTSHHHHHHHHHHHHHHTTSET CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 121 mnrghtfeevlealeklreagikr 144
                                       +nr+ +++e+ +a+e+++++gi++
  gi|298674832|ref|YP_003726582.1| 319 INRKLGLDEQEKAIEIAKNYGIED 342
                                       569999***************985 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1     2e-08   0.00018       9     101 ..     136     223 ..     126     246 .. 0.88
   2 ?   -2.3   0.0      0.53   4.8e+03      81     112 ..     281     315 ..     264     333 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2e-08
                           Fer4_12   9 slfvsgCnlsCkgCfnketw.sfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekp 84 
                                       ++f++gC +sC +C n+++  +++sg e++   l++ii+    e  + + ++   P l     ++l+ ++++ e+ p
  gi|298674832|ref|YP_003726582.1| 136 TIFFTGCVFSCVYCQNCDIStRPESGIEINPLHLAKIIDARRREGSKNVNFVTPTPHL----HTVLKTINNISENLP 208
                                       79***************9864899****************999999******888888....9999999***99999 PP

                           Fer4_12  85 ekdiwlytgytleelsk 101
                                         +iw ++ y  ee s+
  gi|298674832|ref|YP_003726582.1| 209 --VIWNSNMYHSEEASE 223
                                       ..89****999999873 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.53
                           Fer4_12  81 eekpekdiwlytgytleelskk...ekeellkeid 112
                                        e+ +k ++++t+  + +++ +   ++ +++k ++
  gi|298674832|ref|YP_003726582.1| 281 IECCTKPVIEWTVENITHVRFNlmfQYTPFYKSCE 315
                                       56677788899988887776556667777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 2020.79
//
Query:       gi|298674833|ref|YP_003726583.1|  [L=569]
Description: ATP-dependent DNA ligase I [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-61  207.7   0.1    2.8e-61  206.7   0.1    1.5  1  DNA_ligase_A_M   ATP dependent DNA ligase domain
    3.2e-37  128.5   0.1    2.6e-36  125.6   0.0    2.2  2  DNA_ligase_A_N   DNA ligase N terminus
      3e-17   63.0   0.0    8.1e-17   61.6   0.0    1.8  1  DNA_ligase_A_C   ATP dependent DNA ligase C terminal region
    3.7e-06   27.4   0.0      1e-05   25.9   0.0    1.8  1  RNA_ligase       RNA ligase
      0.006   16.4   0.2        3.6    7.4   0.0    2.8  3  mRNA_cap_enzyme  mRNA capping enzyme, catalytic domain


Domain annotation for each model (and alignments):
>> DNA_ligase_A_M  ATP dependent DNA ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.7   0.1   7.7e-65   2.8e-61       2     204 .]     234     430 ..     233     430 .. 0.98

  Alignments for each domain:
  == domain 1  score: 206.7 bits;  conditional E-value: 7.7e-65
                                       EEEEEESCHHHHHHHTTTSEEEEEEEESSEEEEEEEETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEEEEE CS
                    DNA_ligase_A_M   2 mLAeslksiekalkkleekafivEiKyDGeRaqvhkegdkvklfSRrlkditaakpelvkalkeafkkdeksvilDG 78 
                                       mLA+ + sie+a++++ ++a+ +E+K+DG+R+q+hk++++v++fSR+l+++t+++p++v+ +k+++ +d   +i+DG
  gi|298674833|ref|YP_003726583.1| 234 MLAQVTPSIETAFNEM-GTAA-IEWKFDGARVQIHKDKEEVNIFSRKLENVTNSLPDIVESVKNQLNAD--TAIIDG 306
                                       9**************9.6666.9*******************************************998..7***** PP

                                       EEEEEETTTTCBEHHHHHCHHHHCHCCTHHHHHHSEEEEEEEEEEEETTEEHTTSCHHHHHHHHHHHB--BTTTEEE CS
                    DNA_ligase_A_M  79 ElvavdketgeilpfqklasrkkkkkkveeklkeaelclfvFDiLyldgesltdeplkeRrklLeeilkesedrvel 155
                                       E+va+d++ g+++ fq++ +r+++k++v ++ ke+++ l +FD++yldges++d+plk Rr++L +i+ e+++ +++
  gi|298674833|ref|YP_003726583.1| 307 EAVAIDED-GRPRAFQDILRRFRRKYDVLSTSKEIPIILNMFDLMYLDGESYIDLPLKYRREILGNIV-ENTKSIKV 381
                                       *****988.***********************************************************.******** PP

                                       --EEEESSHHHHHHHHHHHHHTTECEEEEEETT-CC-TTCEEEEEEEEE CS
                    DNA_ligase_A_M 156 aeslevkdveeleelleeaiseglEGlvvKnpdskYepgkrsknwlKvK 204
                                        +++ ++dvee+++++++a+s+g+EG+++Knp+s+Y pgkr+knwlK K
  gi|298674833|ref|YP_003726583.1| 382 DKQILTSDVEEANRVYNNALSAGHEGIMIKNPESPYSPGKRGKNWLKKK 430
                                       ***********************************************87 PP

>> DNA_ligase_A_N  DNA ligase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.6   0.0   7.2e-40   2.6e-36       1     172 [.       3     184 ..       3     185 .. 0.95
   2 ?    4.0   0.0     0.015        55      65     112 ..     181     229 ..     180     306 .. 0.67

  Alignments for each domain:
  == domain 1  score: 125.6 bits;  conditional E-value: 7.2e-40
                                       BCHHHHHHHHHHCC.---HHHHHHHHHHHHHTS-..SHHHHHHHHHH....SS-CCCS------HHHHHHHHHHHHT CS
                    DNA_ligase_A_N   1 pFaelaelfekieestkkrlekrailanffrkvesagpedlypalrL....llPdydgreygigesllakalaealg 73 
                                       +F+++a++++ ie+  ++ le+++ +a+++ kv+    ++l  ++ +    ++P++ + e+gigesll+ al++a+g
  gi|298674833|ref|YP_003726583.1|   3 SFKQFADACKNIEK-ITSSLEMTDQVADLLAKVD---TDELPVVTHFimgqIFPSWSSQELGIGESLLYTALSKASG 75 
                                       69************.7788***********9987...4589999999****************************** PP

                                       --HHHHHHHHHHHS-HHHHHHHHHCCHHHH.........------BHHHHHHHHHHHHH-.STTHHHHHHHHHHHHH CS
                    DNA_ligase_A_N  74 lskkkikdalakvgDlgevaeevlskrstl.........akkspltieevnelLdklaaa.gkgsedekkkilkkll 140
                                       ls ++i++  +++gD+ge+a ++lsk s +         ++ +++ti ev + L+++a+  gkgs+++k+k l+ l+
  gi|298674833|ref|YP_003726583.1|  76 LSVDDIENIIRDTGDIGETAVRALSKLSRNqvtfssfveEPTPQITILEVSDRLKRIANVsGKGSQNQKVKNLQYLF 152
                                       *********999************9998889999**99888899**************999**************** PP

                                       HHS-HHHHHHHHHHHCT---SS--HHHHHHHH CS
                    DNA_ligase_A_N 141 kraspeEakyliriilkdlriglsektvldal 172
                                       +++speEa+yl r+  ++lrig++e+ v+da+
  gi|298674833|ref|YP_003726583.1| 153 NASSPEEARYLSRLAVEELRIGVGEGIVRDAI 184
                                       ******************************98 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.015
                                       HHHHHHHHT--HHHHHHHHHHHS-HHHHHHHHHCCHHHH------BH...H CS
                    DNA_ligase_A_N  65 akalaealglskkkikdalakvgDlgevaeevlskrstlakksplti...e 112
                                       + a+++a++++ +k++     ++Dlg va ++ +   +  + s+l i   +
  gi|298674833|ref|YP_003726583.1| 181 RDAISKAFNVPVEKLERSFMLTNDLGAVAVAAQQGGEE--EVSKLDIqvnR 229
                                       5799*******77677764348******8886655554..66777663341 PP

>> DNA_ligase_A_C  ATP dependent DNA ligase C terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.6   0.0   2.3e-20   8.1e-17       2      99 .]     451     542 ..     450     542 .. 0.92

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 2.3e-20
                                       GGSEEEEEEEEEE..TTEEEEEEEE-SS--HHHHHHHHHHHGGGEECTTCESS---HHHHTTEEE-TT-EEEEEESE CS
                    DNA_ligase_A_C   2 gglvgslllgvyd..dgkleyvgkvgtGfsdaeleelrkklkelerkkppfaekvpeeekrdvWvePelvveVkfae 76 
                                       ++l+gs+ +++yd  +g++  +gkv+tG++d++leel+  +++l  +++      + e      ++Pe+v+e+ f+e
  gi|298674833|ref|YP_003726583.1| 451 ANLIGSYAIACYDrdRGQYLPIGKVATGITDEKLEELTSLFSDLIVSEKGR----KIE------FKPEIVFEIGFEE 517
                                       6789*********98899***********************9888887777....222......89*********** PP

                                       EECTSSSTT..EECT-EEEEE-TTS CS
                    DNA_ligase_A_C  77 itasgkyka..slRfPrfkrlReDk 99 
                                       i++s++y++  +lRfPr++++R+Dk
  gi|298674833|ref|YP_003726583.1| 518 IQKSNNYESgyALRFPRLVNVRDDK 542
                                       ************************8 PP

>> RNA_ligase  RNA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   2.9e-09     1e-05       5     161 .]     254     430 ..     250     430 .. 0.63

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 2.9e-09
                                       EEEE-SSEEEEEEEETT.EEEEETTCEBCTTTHHHHHHTHHHHHHHHHHHHH..ECCEEEEEEEES.SS..TTSS.. CS
                        RNA_ligase   5 vtEKlDGtnfriylvke.vgvasRsqilpfgeekfkefkrwaaalrkklkeklaneelilyGElighsikygglpk. 79 
                                       ++ K DG++++i+++ke v+++sR+ +           ++   +  + +k++l+  + i+ GE +   i  +g+p  
  gi|298674833|ref|YP_003726583.1| 254 IEWKFDGARVQIHKDKEeVNIFSRKLEN---------VTNSLPDIVESVKNQLNADTAIIDGEAVA--IDEDGRPRa 319
                                       778************777*******999.........234445566688889997789********..544443322 PP

                                       .......................EEEEEEEEEEECTTBECE--HHHHHHHHHCCTB..EEEEE.SSHHHHHCCC... CS
                        RNA_ligase  80 .......................efyvFdifdirdkeeqrylspdevealakglgtvpvlyegkflaaeellel... 130
                                                               + +Fd++ ++  e+   l+ + +++++ ++  v   ++ k    +++l+    
  gi|298674833|ref|YP_003726583.1| 320 fqdilrrfrrkydvlstskeipiILNMFDLMYLD-GESYIDLPLKYRREILGNI--VENTKSIK--VDKQILTSdve 391
                                       3333333333333344455665555557777666.2355556666664444433..22222222..23333333555 PP

                                       ......H.HHHTC--EEEEEESSSSBE.TTE.BSEEEEE CS
                        RNA_ligase 131 .....ll.skgnkrEGlVikpeselyk.nkg.raifKvk 161
                                            ++   +   EG+ ik++++ y+  k+ ++++K k
  gi|298674833|ref|YP_003726583.1| 392 eanrvYNnALSAGHEGIMIKNPESPYSpGKRgKNWLKKK 430
                                       5577533445569***************9999*****76 PP

>> mRNA_cap_enzyme  mRNA capping enzyme, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0     0.001       3.6      20      80 ..     254     309 ..     249     328 .. 0.79
   2 !    5.5   0.0    0.0039        14      95     139 ..     346     390 ..     332     401 .. 0.84
   3 ?   -1.0   0.0      0.36   1.3e+03     166     195 .]     400     430 ..     390     430 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.001
                                       EEEEESSEEEEEEEEECTEEEEEEETTS-EEEESSST-BTTSSSSTCTSBGGSEEEEEEEE CS
                   mRNA_cap_enzyme  20 vseKaDGiRylmllteeeegvylidRenevyrvenlrfprekdkeklekvldetllDgElv 80 
                                       + +K DG R+ +  ++e  +v ++ R+ e    +  +++++    k++   d++++DgE v
  gi|298674833|ref|YP_003726583.1| 254 IEWKFDGARVQIHKDKE--EVNIFSRKLENVTNSLPDIVESV---KNQLNADTAIIDGEAV 309
                                       57*******98776666..8******9998777766777666...345678899*****76 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0039
                                       EEEEEEETTEEGTTSBHHHHHHHHHHHTHHHHHHHHHTTCCCCTT CS
                   mRNA_cap_enzyme  95 iyDivaingvtvaeeplskRleilkkelikprneekktglletdk 139
                                       ++D++ ++g ++ + pl+ R eil   + + +  +  +++l+ d 
  gi|298674833|ref|YP_003726583.1| 346 MFDLMYLDGESYIDLPLKYRREILGNIVENTKSIKVDKQILTSDV 390
                                       8************************99999888887777766665 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.36
                                       CTTSTEEEEEEEESSSB--SE.EEEEEEEE- CS
                   mRNA_cap_enzyme 166 klshesDGLIfqpvkepyvag.rdsdllKwK 195
                                        ls    G++++  ++py +g r ++ lK K
  gi|298674833|ref|YP_003726583.1| 400 ALSAGHEGIMIKNPESPYSPGkRGKNWLKKK 430
                                       5677889**************6677888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (569 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.51
# Mc/sec: 3349.29
//
Query:       gi|298674834|ref|YP_003726584.1|  [L=331]
Description: homoserine dehydrogenase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-57  194.3   0.5    2.3e-57  193.7   0.2    1.5  2  Homoserine_dh    Homoserine dehydrogenase
      2e-11   44.6   0.0    3.8e-11   43.7   0.0    1.5  1  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain
    4.9e-06   26.5   0.4    1.1e-05   25.3   0.4    1.6  1  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
  ------ inclusion threshold ------
       0.01   16.1   0.1      0.021   15.1   0.1    1.6  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
       0.02   15.6   0.1      0.043   14.5   0.1    1.6  1  DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomer


Domain annotation for each model (and alignments):
>> Homoserine_dh  Homoserine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.4   5.1e+03     107     117 ..      33      45 ..      16      83 .. 0.54
   2 !  193.7   0.2   6.6e-61   2.3e-57       1     173 []     153     326 ..     153     326 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.4
                                       TEEEEEEEEE..C CS
                     Homoserine_dh 107 gkvlklvasa..v 117
                                       g  +k++a++   
  gi|298674834|ref|YP_003726584.1|  33 GLDIKIIAISdsK 45 
                                       5555555544331 PP

  == domain 2  score: 193.7 bits;  conditional E-value: 6.6e-61
                                       --HHHHHHTCTTSEEEEEEEE--HHHHHHHHHHHCHTT-HHHHHHHHHHTTSS-SSTHHHHTTHHHHHHHHHHHHHH CS
                     Homoserine_dh   1 PiiktlkeilsgdritrieGilngtlnyiltemeeegasfsevlkeaqelGyaeaDptdDveGlDaarKlailarla 77 
                                       Pii+ +k++l+g+++ ++eGilngt+nyilt+m ee+a ++++l+e qelG+ae+Dp+ Dv+G+D+a Kl+ila+ +
  gi|298674834|ref|YP_003726584.1| 153 PIINLIKDVLAGNDVISVEGILNGTCNYILTRMMEENAPYEQMLAESQELGIAETDPSYDVDGIDSACKLVILANSV 229
                                       9**********************************9999************************************** PP

                                       CTTT--GGGSEE--STTS-HHHHHHHHCTTEEEEEEEEE..CEEEEEEEEEETTSGGGHSSST-EEEEEEESSSEEE CS
                     Homoserine_dh  78 fgleveledvevegiskltaedikeakeegkvlklvasa..vearVkpelvpkshplasvkgsenavlvetdrlgel 152
                                       fg+ ++++dv+v+gi+k+t+e +  a+++g+v+kl++++    +rV+p+lvp+++pla v g+ n+ +++td  g++
  gi|298674834|ref|YP_003726584.1| 230 FGMCLSYKDVDVTGITKITPESLLLAQNNGYVIKLIGEVkdNLIRVAPRLVPEDSPLA-VGGTLNVASIQTDLSGTV 305
                                       **************************************766359**************.****************** PP

                                       EEEES-SSHHHHHHHHHHHHH CS
                     Homoserine_dh 153 viqGpgaGaepTAsavlsDll 173
                                       +++G+gaG+ +TAsavlsD++
  gi|298674834|ref|YP_003726584.1| 306 TVTGRGAGSIETASAVLSDIV 326
                                       *******************96 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.0   1.1e-14   3.8e-11       1     117 []      10     145 ..      10     145 .. 0.82

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 1.1e-14
                                       --SHHHHHHHHHHHH---S.....SEEEEEEEEESS.EEE-TT.........HHHHHT--CB--.-HHHHHHHHS-E CS
                     NAD_binding_3   1 GlGaiGsavleqlkrqqse.....ielelvavadrd.sllskd.........rkallasealtl.dlddliahldpd 61 
                                       G+Ga+G++v+e l+++q++     +++++ a+ d++ s+++ d         rk++ ++ al + +  ++i+ +d d
  gi|298674834|ref|YP_003726584.1|  10 GFGAVGQGVAEVLLKKQDYlknvgLDIKIIAISDSKgSEINTDgidlssalaRKREKGTVALEDkSSLEIIESVDHD 86 
                                       99********************999999999999999999999****988664444444444331344567767*** PP

                                       EEEE-S--HHHH.....TTHHHHHHTTEEEE-S--CGGG-HHHHHHHTSSSTTS--.EE-G CS
                     NAD_binding_3  62 vvVEcasseava.....elvlkaLkagkdvvtankgaladealyeeLreaaeangakiyve 117
                                       +v+E +s +        + +l+a ++gkdvvt nkg la   +y+eL+ea++ +g ++++e
  gi|298674834|ref|YP_003726584.1|  87 LVIETTSTDINTggiglKNMLSAFNSGKDVVTSNKGPLA--LKYNELMEASRNSGSNFRFE 145
                                       *******998762222246799*****************..**************999886 PP

>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.4     3e-09   1.1e-05      33     116 ..       4      96 ..       1     124 [. 0.73

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 3e-09
                                       EEEEEE--SHHHHHHHHHHHH.........CT-EEEEEEESSEEEEETTEE-HHHHHHHHHCSSSSTTHSHHSTSTS CS
                     ELFV_dehydrog  33 krvaisGsGnvgsyaalllte.........lgakvvavsDssGviydpeGldieellelkeerksvkeykkssekka 100
                                        r  isG+G vg+ +a+ l +         l  k++a+sDs+G  ++++G+d+ + l+ k+e+++v+  +kss + +
  gi|298674834|ref|YP_003726584.1|   4 IRASISGFGAVGQGVAEVLLKkqdylknvgLDIKIIAISDSKGSEINTDGIDLSSALARKREKGTVALEDKSSLEII 80 
                                       5789**********99988662222222224579*******************************887776655455 PP

                                       EEESHHSHHHHSS-SE CS
                     ELFV_dehydrog 101 eyieneeellelkvdi 116
                                       e ++ +  + ++ +di
  gi|298674834|ref|YP_003726584.1|  81 ESVDHDLVIETTSTDI 96 
                                       5555553333345555 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1   5.9e-06     0.021       5      40 ..      10      49 ..       7      96 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.9e-06
                                      --SHHHHHHHHHHHCTCCT-G....EEEEEESSHHHHHHH CS
                   Sacchrp_dh_NADP  5 GaGsvGqavaellarhfdvda....eitvadrskekleal 40
                                      G+G+vGq+vae+l++++d+ +    +i ++  s++k  ++
  gi|298674834|ref|YP_003726584.1| 10 GFGAVGQGVAEVLLKKQDYLKnvglDIKIIAISDSKGSEI 49
                                      9******************998888888888888876666 PP

>> DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   1.2e-05     0.043      60     123 ..      54     122 ..      13     126 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.2e-05
                                       HHHHHHHHHTTSSSEEEESHHHHHHHHCHTT-SEEEE--.....SSGGGHHHHHHHHHTTSEEEE--SH CS
                   DXP_reductoisom  60 eelkealkekelktevlvGeealkelaeeeeadvvvaai.....vGaaGLkptlaaikagkriaLANKE 123
                                        +l++al++k  k +v+  +++  e++e+ + d+v+        +G +GLk  l+a ++gk+++ +NK 
  gi|298674834|ref|YP_003726584.1|  54 IDLSSALARKREKGTVALEDKSSLEIIESVDHDLVIETTstdinTGGIGLKNMLSAFNSGKDVVTSNKG 122
                                       468889999999999*********************98633334699*********************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 1963.71
//
Query:       gi|298674835|ref|YP_003726585.1|  [L=166]
Description: amino acid-binding ACT domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-06   26.3   0.2    1.3e-05   24.8   0.0    1.8  2  ACT       ACT domain


Domain annotation for each model (and alignments):
>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   7.4e-10   1.3e-05       5      64 ..       7      69 ..       3      71 .. 0.95
   2 ?   -1.8   0.1      0.16   2.9e+03      41      59 ..      97     115 ..      89     117 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 7.4e-10
                                      EEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTT...ECEEEEEEEEEEHHHHHHHHHHHHT CS
                               ACT  5 vgvpDrPGlLarvfgaladrgiNidsieqrssedk...vagivfvvivvdeedleevlealkk 64
                                      ++++DrPG L + ++ ++d+  N++s+ ++  ++k       v +vi +d+e l+e++ +lk+
  gi|298674835|ref|YP_003726585.1|  7 IELQDRPGQLLQALQPISDLKGNLISVVHHHEKEKnrrSKIPVQCVIDIDPEKLDELKSQLKE 69
                                      789*********************************************************997 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.16
                                       CEEEEEEEEEEHHHHHHHH CS
                               ACT  41 agivfvvivvdeedleevl 59 
                                       ++i +++++vd  + +ev+
  gi|298674835|ref|YP_003726585.1|  97 NDIQDTIDTVDRTGYAEVV 115
                                       4577777888877777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      632  (0.0352502); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1022.74
//
Query:       gi|298674836|ref|YP_003726586.1|  [L=268]
Description: hypothetical protein Metev_0893 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-06   27.0   0.3    6.6e-06   26.3   0.3    1.3  1  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    0.00012   21.5   0.0    0.00026   20.5   0.0    1.5  1  HTH_24           Winged helix-turn-helix DNA-binding
    0.00031   20.7   0.4    0.00056   19.9   0.4    1.5  1  CarbopepD_reg_2  CarboxypepD_reg-like domain
    0.00048   20.6   0.1     0.0011   19.4   0.1    1.6  1  HTH_27           Winged helix DNA-binding domain
    0.00051   19.9   0.0     0.0011   18.8   0.0    1.5  1  MarR_2           MarR family
     0.0016   18.4   0.0      0.007   16.3   0.0    1.9  2  MarR             MarR family
      0.002   18.3   0.0     0.0034   17.5   0.0    1.3  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
     0.0077   16.1   0.1      0.013   15.4   0.1    1.4  1  TrmB             Sugar-specific transcriptional regulator Trm
     0.0084   16.3   0.0      0.015   15.4   0.0    1.4  1  HTH_34           Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.016   15.2   0.0      0.031   14.3   0.0    1.5  1  HTH_Crp_2        Crp-like helix-turn-helix domain
       0.14   11.9   0.5        5.3    6.8   0.2    2.2  2  RSN1_TM          Late exocytosis, associated with Golgi trans
        1.7    8.5   4.7        0.3   11.0   0.3    2.0  2  TMEM154          TMEM154 protein family


Domain annotation for each model (and alignments):
>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.3   4.4e-09   6.6e-06       1      81 [.      30     109 ..      30     110 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 4.4e-09
                   CarboxypepD_reg   1 tisGrVtd.asgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatr...eevtltagq 73 
                                       t++G + + ++ +p+++a Vtv     +t ++   ++ G ++++ l pg+y++t+ +    t ++   e++t+  g+
  gi|298674836|ref|YP_003726586.1|  30 TVHGEIYNwETFEPVENAIVTVN----STPKQSIVAEYGVYTFS-LSPGDYQITAKSYQNGTISYrtqENITIKSGG 101
                                       6888888866899**********....89**************7.**********443333322234479******9 PP

                   CarboxypepD_reg  74 tttlditL 81 
                                       +  ld+ L
  gi|298674836|ref|YP_003726586.1| 102 NYSLDLLL 109
                                       99999876 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.7e-07   0.00026      16      48 .]     215     247 ..     205     247 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.7e-07
                            HTH_24  16 prisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                       +ri+q++L  rl  S + ++  +  Lee G+++
  gi|298674836|ref|YP_003726586.1| 215 GRITQKDLRNRLKYSEAKISLMISDLEERGYVE 247
                                       89*****************************96 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.4   3.8e-07   0.00056       1      77 [.      31     110 ..      31     121 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.8e-07
                   CarbopepD_reg_2   1 isGtVvdketkeplpgatVyvkgtkkgtvTdenGnFelknlpagkytLvvsy.....vGyktqekkvtvskektldv 72 
                                       ++G++++ et ep++ a V+v++t k+ +  e G ++++ l +g+y++++++     ++y+tqe ++t++++ + ++
  gi|298674836|ref|YP_003726586.1|  31 VHGEIYNWETFEPVENAIVTVNSTPKQSIVAEYGVYTFS-LSPGDYQITAKSyqngtISYRTQE-NITIKSGGNYSL 105
                                       6799**********************************6.999*****9986455557899975.788888777777 PP

                   CarbopepD_reg_2  73 nillk 77 
                                       ++ll+
  gi|298674836|ref|YP_003726586.1| 106 DLLLT 110
                                       66664 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   7.3e-07    0.0011      14      60 ..     212     255 ..     204     262 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 7.3e-07
                            HTH_27  14 hrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrek 60 
                                         ++r +++dl+ rl+++ + is +++ L+e+G+ve+ ++    r  
  gi|298674836|ref|YP_003726586.1| 212 KSGGRITQKDLRNRLKYSEAKISLMISDLEERGYVEKFKKG---RGN 255
                                       56777888***************************999775...544 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   7.3e-07    0.0011      14      53 ..     210     248 ..     205     255 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 7.3e-07
                                       HHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2  14 LgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53 
                                       +  ++gr +t+++l  rl++s + +s ++ +L+++G+ve+
  gi|298674836|ref|YP_003726586.1| 210 VKKSGGR-ITQKDLRNRLKYSEAKISLMISDLEERGYVEK 248
                                       5567775.9*****************************97 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   4.7e-06     0.007      16      52 ..     215     251 ..     210     254 .. 0.92
   2 ?   -0.9   0.0         1   1.6e+03      31      44 ..     253     266 ..     252     267 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.7e-06
                                       TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                              MarR  16 gplsvseLakklgvskstvtrvldrLekkGlieRsks 52 
                                       g +++++L ++l+ s + ++ ++  Le++G++e+ k+
  gi|298674836|ref|YP_003726586.1| 215 GRITQKDLRNRLKYSEAKISLMISDLEERGYVEKFKK 251
                                       679******************************9875 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1
                                       HHHHHHHHHHHHHT CS
                              MarR  31 kstvtrvldrLekk 44 
                                       +++v r++d+L ++
  gi|298674836|ref|YP_003726586.1| 253 RGNVVRIVDELNDN 266
                                       689*******9776 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.3e-06    0.0034      10      56 ..     203     250 ..     197     254 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.3e-06
                                       HHHHHHHHH.HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                    Fe_dep_repress  10 LetIYtlse.ekkvvktkdlaerLnvspssVsemlkkLekdGyveyek 56 
                                       L+ ++++ + +++ +++kdl  rL+ s + +s m++ Le+ Gyve  k
  gi|298674836|ref|YP_003726586.1| 203 LQKVFDVVKkSGGRITQKDLRNRLKYSEAKISLMISDLEERGYVEKFK 250
                                       677888888899********************************9655 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   8.5e-06     0.013      21      58 ..     215     252 ..     205     262 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.5e-06
                                       CCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB  21 gpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58 
                                       g+ t +++ ++l+ +++k+  +++ Le++G+Ve+ k+ 
  gi|298674836|ref|YP_003726586.1| 215 GRITQKDLRNRLKYSEAKISLMISDLEERGYVEKFKKG 252
                                       667899***************************98844 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0     1e-05     0.015      15      51 ..     217     253 ..     210     262 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1e-05
                            HTH_34  15 adfvelkealeatdgnLsvhlkkLekagYievdkefk 51 
                                       ++ ++l++ l+ +++++s  ++ Le+ gY+e  k+ +
  gi|298674836|ref|YP_003726586.1| 217 ITQKDLRNRLKYSEAKISLMISDLEERGYVEKFKKGR 253
                                       67899*************************9776655 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.1e-05     0.031      21      61 ..     216     261 ..     191     265 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.1e-05
                                       EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE..E.TEE..EEES- CS
                         HTH_Crp_2  21 pltqeelAsmlGltretvsrilseLkreglis..r.grr..irild 61 
                                       ++tq++l ++l  +   +s ++s+L+++g+++  + gr+  +ri d
  gi|298674836|ref|YP_003726586.1| 216 RITQKDLRNRLKYSEAKISLMISDLEERGYVEkfKkGRGnvVRIVD 261
                                       79******************************76335555777776 PP

>> RSN1_TM  Late exocytosis, associated with Golgi transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2    0.0035       5.3      87     111 ..       7      31 ..       1      68 [. 0.74
   2 ?    3.4   0.0      0.04        59      99     154 ..     108     165 ..     104     167 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0035
                           RSN1_TM  87 kiflvlavlalivLlPvnatggege 111
                                         ++++++l+li ++Pvna  ++  
  gi|298674836|ref|YP_003726586.1|   7 FKLTFCIILVLILIIPVNAETTATV 31 
                                       34566778888899****9876655 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.04
                           RSN1_TM  99 vLlPvnatggegedskesk.sgl.dklsisnvsegsnrlwahvvvayiftglvlylly 154
                                        L Pv+ t+  +++++++  +++ +  ++ + +e+ n l+++++ +++f++ +l +++
  gi|298674836|ref|YP_003726586.1| 108 LLTPVYDTNLLNDTESSQIsESFeNDSKLIDGKEDDNHLIIYLIPVIVFSLAALSFIV 165
                                       6889999988777666555445534444444448999*************99998886 PP

>> TMEM154  TMEM154 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.5       2.3   3.4e+03      58      65 ..      15      22 ..       8      28 .. 0.55
   2 ?   11.0   0.3    0.0002       0.3      40      79 ..     127     166 ..      57     174 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.3
                           TMEM154 58 lvlmiiiP 65
                                      lvl++iiP
  gi|298674836|ref|YP_003726586.1| 15 LVLILIIP 22
                                      23333443 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0002
                           TMEM154  40 akeslssaelsnesdqlelvlmiiiPlvllillllvviil 79 
                                       ++  ++  +l + +++ + +++++iP +++ l  l+ i++
  gi|298674836|ref|YP_003726586.1| 127 SESFENDSKLIDGKEDDNHLIIYLIPVIVFSLAALSFIVF 166
                                       2223344455555556677899*******99999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1056  (0.058899); expected 358.6 (0.02)
Passed bias filter:                      788  (0.0439511); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.59u 0.35s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 1604.56
//
Query:       gi|298674837|ref|YP_003726587.1|  [L=516]
Description: hypothetical protein Metev_0894 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.015   15.2  40.1       0.18   11.7   9.6    2.3  2  Apolipoprotein  Apolipoprotein A1/A4/E domain
        2.6    8.1  42.5      0.091   12.8   2.1    5.0  5  DUF1664         Protein of unknown function (DUF1664)


Domain annotation for each model (and alignments):
>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7  23.2     8e-05      0.71      85     169 ..      56     143 ..      44     153 .. 0.90
   2 ?   11.7   9.6     2e-05      0.18       8     183 ..     142     341 ..     137     344 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 8e-05
                                       HHHHCHHCCHHCHCCHCHHHHHHHHHHHHHHHHHHCHHHHHHHH...HHHHHHHHHHH-----..-----SSSHHHH CS
                    Apolipoprotein  85 rlaadaeelqeqlavyaeelrerlerhvealkarlapyveelrq...klaerleelkeslaphaeeveerlssrvee 158
                                         ++++ee +e+++ ++e ++e++e ++e+  ++l+  +e++ +   kl+e+lee ke+++ + e+veer+ +r e+
  gi|298674837|ref|YP_003726587.1|  56 NQEEELEEREEKIERKQERIEEKIENKTEKREEKLEKKRERIENkneKLEEKLEERKEKIERKHERVEERIKKRKEQ 132
                                       456789999*********************************95555****************************** PP

                                       HHHTS-TTSHH CS
                    Apolipoprotein 159 lrekleeqaee 169
                                       l+ + + +a++
  gi|298674837|ref|YP_003726587.1| 133 LENARNNYAKA 143
                                       **999999876 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 2e-05
                                       CHHHHHCCHHHCHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHCCCHHHHHHHHHCCHHHHHHHH CS
                    Apolipoprotein   8 elkayaeeleeqlaplaqelrdrlskeleelrarlraeleevrarlepyrdevqeqlgqnleelrqrlapyteelre 84 
                                       ++k+++  ++++++    +l ++ +k  ++ ++ l++ l+   + le++  ++++  +  +++  ++l++y++el++
  gi|298674837|ref|YP_003726587.1| 142 KAKSNFHSINKKVSGN--KLNPNSEKVINATKNYLNSTLDYMIEHLENKKTNINASNANFTDKSIEDLNEYINELKQ 216
                                       5566666666666665..78899999999999999****************************************87 PP

                                       .HHHHCHHCCHHCHCCHCHH...................HHHHHHHHHHHHHHHHCHHHHHHHH..HHHHHHHHHHH CS
                    Apolipoprotein  85 .rlaadaeelqeqlavyaee...................lrerlerhvealkarlapyveelrq..klaerleelke 139
                                        r+++++ e +e +++ ++e                   ++er+ +h+e+ k+    +  e++q    ++++ ++++
  gi|298674837|ref|YP_003726587.1| 217 kRVELKSAETREEISEISDEireiwrdaqtnsnsiaiktVNERINEHLEKSKSISLRIEKEIKQleAEGKNVSDVEK 293
                                       79******************666666666666666666666666666666666555555555544467788888888 PP

                                       -----..-----SSSHHHHHHHTS-T.....TSHHHHHS--XXXXXXXX CS
                    Apolipoprotein 140 slaphaeeveerlssrveelreklee.....qaeelrerleanleelka 183
                                        l+ ++e++  ++ ++ +++++ ++       +++ + +l+++++elk+
  gi|298674837|ref|YP_003726587.1| 294 LLNGYKEKIS-NIKEHQSNAEKIYSNatdekSIKDAKLKLQKAISELKE 341
                                       8888888777.66677777666666677788999999999999999997 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   9.0      0.16   1.4e+03      61     117 ..      58     115 ..      43     117 .. 0.46
   2 ?    6.2   9.1    0.0011        10      39     103 ..      90     154 ..      77     160 .. 0.56
   3 ?   12.8   2.1     1e-05     0.091      31     104 ..     166     245 ..     162     252 .. 0.78
   4 ?    7.5   3.3   0.00044         4      68     124 .]     253     309 ..     244     309 .. 0.91
   5 ?    0.8   0.5     0.052   4.7e+02      55      87 ..     323     355 ..     313     368 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.16
                           DUF1664  61 krhLssridrvdkkldeqke.iskeikeevtevredlseigedvesvkeavegleskl 117
                                        ++L++r +++++k++  +e i +++++  ++++++ ++i+++ e+++e  e+ ++k+
  gi|298674837|ref|YP_003726587.1|  58 EEELEEREEKIERKQERIEEkIENKTEKREEKLEKKRERIENKNEKLEEKLEERKEKI 115
                                       3444444444444444443313333444444444444444444444444444444444 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0011
                           DUF1664  39 lsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedv 103
                                       l++  e++ ++ e++ e+l++ k++++++ +rv++++++ ke  ++ +++ ++++++ ++i+++v
  gi|298674837|ref|YP_003726587.1|  90 LEKKRERIENKNEKLEEKLEERKEKIERKHERVEERIKKRKEQLENARNNYAKAKSNFHSINKKV 154
                                       44444555555555555555555555555555555555555555555555555555555555544 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 1e-05
                           DUF1664  31 lmfvTkrslsdavesvskqleqvseslaatkrhLssr.idrvdkkldeqkei.....skeikeevtevredlseige 101
                                       ++ +Tk  l++ ++ + ++le+ +++++a   +++++ i+ +++ ++e k+      s+e++ee++e++++++ei +
  gi|298674837|ref|YP_003726587.1| 166 VINATKNYLNSTLDYMIEHLENKKTNINASNANFTDKsIEDLNEYINELKQKrvelkSAETREEISEISDEIREIWR 242
                                       6779******************************9644*****9999877541122256777777777777777776 PP

                           DUF1664 102 dve 104
                                       d +
  gi|298674837|ref|YP_003726587.1| 243 DAQ 245
                                       665 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.00044
                           DUF1664  68 idrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerieekQ 124
                                       i++v+++++e  e sk+i+  +++  ++l++ g++v+ v+++ +g ++k+++i+e+Q
  gi|298674837|ref|YP_003726587.1| 253 IKTVNERINEHLEKSKSISLRIEKEIKQLEAEGKNVSDVEKLLNGYKEKISNIKEHQ 309
                                       889999999999999999999999999999999********************9988 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 0.052
                           DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeike 87 
                                       +s++++k +L++ i ++ +     kei k+ik+
  gi|298674837|ref|YP_003726587.1| 323 KSIKDAKLKLQKAISELKEANIILKEIFKQIKD 355
                                       688999999999998887776666666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (516 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      4644  (0.259022); expected 358.6 (0.02)
Passed bias filter:                      844  (0.0470746); expected 358.6 (0.02)
Passed Vit filter:                       343  (0.019131); expected 17.9 (0.001)
Passed Fwd filter:                       120  (0.00669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 2.09u 0.42s 00:00:02.50 Elapsed: 00:00:00.61
# Mc/sec: 2539.25
//
Query:       gi|298674838|ref|YP_003726588.1|  [L=85]
Description: hypothetical protein Metev_0895 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.024   13.8   0.6      0.028   13.6   0.6    1.0  1  M16C_assoc  Peptidase M16C associated


Domain annotation for each model (and alignments):
>> M16C_assoc  Peptidase M16C associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.6   1.5e-06     0.028       2      53 ..      28      80 ..      28      82 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.5e-06
                        M16C_assoc  2 kPdeeleeekekeekerLaakkaslseeekekiveetkeLkerQekpds.edl 53
                                      +Pd++ ++  +++++  La+  a l++ e+e + +etkeL +  e+ d+ e++
  gi|298674838|ref|YP_003726588.1| 28 SPDSDNQQTTTDNTSSILAKNNAILTDTEIESLENETKELDRLIESMDTdENI 80
                                      5999999**************************************99998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1118  (0.0623571); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 527.53
//
Query:       gi|298674839|ref|YP_003726589.1|  [L=320]
Description: hypothetical protein Metev_0896 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.01   16.0   0.0       0.01   16.0   0.0    3.3  3  SMBP      Small metal-binding protein
         10    6.6   8.7        1.7    9.1   0.2    3.6  4  FlgM      Anti-sigma-28 factor, FlgM


Domain annotation for each model (and alignments):
>> SMBP  Small metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.0   0.0   1.2e-06      0.01       4      90 ..       6     108 ..       3     119 .. 0.82
   2 ?    0.4   1.0     0.082   7.3e+02      26      77 ..     144     202 ..     116     245 .. 0.60
   3 ?    0.7   2.8     0.067     6e+02      26      61 ..     256     291 ..     223     312 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.2e-06
                                       XXXXXXXXXXXXXXXXXXXX--...............HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH.. CS
                              SMBP   4 isallaalvlalfsssavaaee...............hlaeAiehaeaAvahgkaghakalveHaeealkhakaaae 65 
                                        +al++a++++l++++++ a++                +++A+e  + + ++g+++++   ++ aee + +aka ae
  gi|298674839|ref|YP_003726589.1|   6 AKALTIASIMILMFTMSATAQDedlpdpgitpdspfyGIDKAMESIQGVFNSGNEQKSRYGLNIAEERIAEAKAMAE 82 
                                       5677888888888898888886667778888889999**************************************88 PP

                                       .-------HH.HHHHHHHHHHHHHHH CS
                              SMBP  66 kakeeekehl.degikhLeeAIkhgk 90 
                                       k++ +  e + +e  k++e+ I+ g+
  gi|298674839|ref|YP_003726589.1|  83 KGNYQLSEEMsNEYEKQIENTIETGN 108
                                       88877665551455577888888776 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.082
                                       HHHHHHHHHHHHHHHHHTT-HHHH..HHHHHHHHHHHHHH........-------HHHH CS
                              SMBP  26 hlaeAiehaeaAvahgkaghakal..veHaeealkhakaa.....aekakeeekehlde 77 
                                        ++eAi+   +A + g ++  k l  ++ a++a+   + a     ++k+++++++ ++e
  gi|298674839|ref|YP_003726589.1| 144 TAQEAINNSLKASSRGREKSLKSLgdTNPAKAAKIRFEFAnnrinSIKGNASKEKLVNE 202
                                       56677777777777776666555533333444443333334445544444444444443 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.067
                                       HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                              SMBP  26 hlaeAiehaeaAvahgkaghakalveHaeealkhak 61 
                                        +++Ai+ha ++   g ++  ++l +   e  + +k
  gi|298674839|ref|YP_003726589.1| 256 PAKDAIKHAMNVSVRGHKKALENLQDKNPEKAEMIK 291
                                       345666666666666665555555444444444444 PP

>> FlgM  Anti-sigma-28 factor, FlgM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.2   0.00019       1.7      24      45 ..      68      89 ..      44      92 .. 0.78
   2 ?    0.9   0.1     0.067     6e+02      20      34 ..     174     191 ..     109     213 .. 0.74
   3 ?   -2.1   0.0      0.59   5.3e+03      27      39 ..     225     237 ..     202     239 .. 0.51
   4 ?   -0.8   0.2      0.23   2.1e+03      15      37 ..     272     294 ..     257     296 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00019
                              FlgM 24 evreekVaelKeaIasGtYqvd 45
                                      ++ ee++ae K+  + G+Yq +
  gi|298674839|ref|YP_003726589.1| 68 NIAEERIAEAKAMAEKGNYQLS 89
                                      799****************976 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.067
                              FlgM  20 aaap...evreekVaelK 34 
                                       +aa    e+ +++++++K
  gi|298674839|ref|YP_003726589.1| 174 KAAKirfEFANNRINSIK 191
                                       333333567777777776 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.59
                              FlgM  27 eekVaelKeaIas 39 
                                       +  V +l e++a+
  gi|298674839|ref|YP_003726589.1| 225 NMNVTALEEKVAN 237
                                       3356666666665 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 0.23
                              FlgM  15 akqaaaaapevreekVaelKeaI 37 
                                        k+a+++  + + ek + +K+ I
  gi|298674839|ref|YP_003726589.1| 272 HKKALENLQDKNPEKAEMIKKNI 294
                                       45566666778888888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2224  (0.124045); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.51
# Mc/sec: 1887.31
//
Query:       gi|298674840|ref|YP_003726590.1|  [L=286]
Description: peptidase M48 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-38  133.0   0.1    1.5e-38  132.5   0.1    1.2  1  Peptidase_M48  Peptidase family M48
    7.4e-05   22.1   0.0    0.00015   21.1   0.0    1.4  1  Peptidase_M56  BlaR1 peptidase M56
  ------ inclusion threshold ------
      0.067   12.9   6.8       0.31   10.7   1.1    2.2  2  Yip1           Yip1 domain


Domain annotation for each model (and alignments):
>> Peptidase_M48  Peptidase family M48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.5   0.1   2.5e-42   1.5e-38       3     195 ..      67     285 ..      65     286 .] 0.81

  Alignments for each domain:
  == domain 1  score: 132.5 bits;  conditional E-value: 2.5e-42
                                       -SSHHHHHHHHHHHHTT-..-EEEEEEE-GGGT-EEEEESSS-E.EEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48   3 reaelkevveelakeaglpkpltkvyvvnspkrNAFalgggknk.rivltdgLlkqllseeelaaVlGHElGHikhr 78 
                                       + ++l ++v++la +a+l  p++kvyvv+ +  NAFa+g++ ++  ++ t+g++ +ll++eel++V++HE++H+khr
  gi|298674840|ref|YP_003726590.1|  67 EYPQLYSIVRNLATKANL--PMPKVYVVETSMPNAFATGRNPENsAVAATTGIM-NLLTPEELEGVFAHEMAHVKHR 140
                                       6689999***********..********************98888*********.********************** PP

                                       HHHHHHHHHHHHHHHHHHHHHH....HTT-....SHHHHHTT--S---HHHHHHHHHHTTHHHHHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxx....xxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48  79 hsvvslivsllasillllglal....lisr....aeedaagafldalavliglliillflalSRkrEyqADeagvel 147
                                       +++vs+i +++a  + +l++++    +++      e+ ++ + + ala+l+ +   + +la+SR+rE+ AD+ g+++
  gi|298674840|ref|YP_003726590.1| 141 DTLVSTIAATIAGAITMLAYMAqwaaIFGGlgrdDEGGNNIIGYLALAILAPIAATIIQLAISRSREFAADAEGAKI 217
                                       *****8877777666665554311112222000022223333345555555555556666***************** PP

                                       TT.HHHHHHHHHHHHHHTT--S---HHHH....................HHS-SS--HHHHHHHHHH- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................xxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48 148 lkrakdlvraliklakdlerqdvsaslrs....................ellstHPplleRiqalkel 195
                                       ++++ +l++al kl +++++++  +++ +                     l++tHP ++eRi++lk++
  gi|298674840|ref|YP_003726590.1| 218 TNKPWALANALSKLEQGAANYKPRKDEVKasentahmfivnplkgktlaSLFRTHPVTEERIKRLKSM 285
                                       ******************9966666666567777999999999999999****************987 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   2.5e-08   0.00015     114     220 ..      37     150 ..      31     157 .. 0.67

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.5e-08
                     Peptidase_M56 114 lilllyliaallvlkkrfvr..klgklraeelkeaLkeakeemqlkrnikirlsssid..sPavlgllkp....rIv 182
                                        i +++  a++ + +k +++  +++++ +e+++ +L ++ ++ + k n+ + +  +++   P  ++  ++     + 
  gi|298674840|ref|YP_003726590.1|  37 FIAVIMNFASYWYSDKIVLKmyRAKEV-NESEYPQLYSIVRNLATKANLPMPKVYVVEtsMPNAFATGRNpensAVA 112
                                       333344455555444443331122233.4467888888888888888888777666641158888877643333688 PP

                     Peptidase_M56 183 lPadflkklsdeeleyillHElaHlkrkDllvnllvav 220
                                         + +++ l+ eele +++HE aH+k++D+lv  ++a 
  gi|298674840|ref|YP_003726590.1| 113 ATTGIMNLLTPEELEGVFAHEMAHVKHRDTLVSTIAAT 150
                                       88889999************************999875 PP

>> Yip1  Yip1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.5    0.0022        13      59      91 ..      14      49 ..       3      75 .. 0.66
   2 ?   10.7   1.1   5.2e-05      0.31      54     117 ..     138     201 ..     109     205 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0022
                              Yip1 59 lssllgaiiggylgl...llgllllalllhliakll 91
                                      +++ l ++igg++g+   l+ ++++a+++++++ ++
  gi|298674840|ref|YP_003726590.1| 14 SLTGLLIVIGGAIGGrggLIFAFFIAVIMNFASYWY 49
                                      444455566666666666888888888888876665 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 5.2e-05
                              Yip1  54 vqgltlssllgaiiggylglllgllllalllhliakllggkgsfkqtlsvvgyallPlilgali 117
                                         + tl+s ++a i+g++++l+  + +a+++  +++   g  ++  +l+++ +a ++  + +l+
  gi|298674840|ref|YP_003726590.1| 138 KHRDTLVSTIAATIAGAITMLAYMAQWAAIFGGLGRDDEGGNNIIGYLALAILAPIAATIIQLA 201
                                       45677889999999999999****************999**9*999999999998888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1775.35
//
Query:       gi|298674841|ref|YP_003726591.1|  [L=233]
Description: hypothetical protein Metev_0899 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-67  225.7   0.0    5.1e-67  225.6   0.0    1.0  1  AIM24     Mitochondrial biogenesis AIM24


Domain annotation for each model (and alignments):
>> AIM24  Mitochondrial biogenesis AIM24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.6   0.0   2.9e-71   5.1e-67       1     200 [.       4     211 ..       4     212 .. 0.97

  Alignments for each domain:
  == domain 1  score: 225.6 bits;  conditional E-value: 2.9e-71
                                       EEEESSSS-EEEEEE-TT-EEEE-CCGEEEEETTEEEEE....--------------EEEEEEE.S.SS-EEEEE-- CS
                             AIM24   1 fevlgepssllsvtLspgeelyaerGalvamsgkvemet....gllkalkrlltgeslfllkft.akissgtvllap 72 
                                       ++++g+++++++v+L+p e++ ae Ga+ +m ++++m+t    gl+++lkr+ltges+f+++f  + +++g v++++
  gi|298674841|ref|YP_003726591.1|   4 YNIIGDDMQIVEVELDPEESVRAEVGAMAYMGPGIKMQTstggGLFSGLKRMLTGESFFITSFVyEGKDKGFVAFGA 80 
                                       789*************************************************************644466******* PP

                                       SSSEEEEEEEG.GTT.EEEEEGGGEEEEETT-EEEEEEEE--.SSGGGTS-EEEEEEESSSEEEEEEECSEEEEEEE CS
                             AIM24  73 klpgtivtlel.gggdwlivqkdafLAatgnveldikfqkgl.kglfggeglflqkltGrGlvalsgyGaiyeielk 147
                                       ++pg+i++++l + + ++++qkdafL+a++++++d++ +k+l +g+fggeg++lqkl+G+G+++++++G+i+++el+
  gi|298674841|ref|YP_003726591.1|  81 PYPGKIIPIDLaKFDGNILCQKDAFLCAAKGIDIDVALTKRLgSGFFGGEGFILQKLSGDGMAFVHAGGTIIKKELA 157
                                       ***********676779***********************99*********************************** PP

                                       .EEEEEEEGGGEEEEETTEEEEEEEETT---STTTTS-E.EEEEEEEEEEEEES CS
                             AIM24 148 ageelvvdpghlvafsgslkfdiervgglkrrligGegl.flkltGpgtvllqs 200
                                       +ge l+vd+g+l af++s++++i+ +gg+k++l+gGeg+ ++ l+Gpgtv+lqs
  gi|298674841|ref|YP_003726591.1| 158 DGEHLRVDTGCLAAFTDSIDYNIQFIGGFKNALFGGEGVfLASLKGPGTVYLQS 211
                                       ***************************************999***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       189  (0.0105416); expected 358.6 (0.02)
Passed bias filter:                      181  (0.0100954); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1448.58
//
Query:       gi|298674842|ref|YP_003726592.1|  [L=217]
Description: thymidylate synthase, methanogen type [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-19   70.7   0.1    1.3e-19   70.4   0.1    1.1  1  Thymidylat_synt  Thymidylate synthase


Domain annotation for each model (and alignments):
>> Thymidylat_synt  Thymidylate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.4   0.1   7.2e-24   1.3e-19      83     223 ..      66     213 ..      12     215 .. 0.77

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 7.2e-24
                                       H..............HHHTTB-SSSHHHHHHHBTSTTTSSB-HHHHHHHHHHHSTT-ST-EEE---GGGGGGSSS-- CS
                   Thymidylat_synt  83 w..............adeegdlgpvYGkqwrkfkaeegkkidqlakvidqlkenpdsRriivsawnpaeldkmaLpp 145
                                       w               d++++ +  YG+ +r+++    ++idq+++vid+l e+ + Rr     w p    k+   p
  gi|298674842|ref|YP_003726592.1|  66 WnrerldeyskqlisGDNTQNFEYTYGQRLRNWN----DEIDQISYVIDKLTESSSTRRATAVTWVPPIDTKVDEVP 138
                                       1333333333333322445899***********8....69*************************9765445999** PP

                                       SEEEEEEEE..SEETEEEEEEEEEEEETTTHHHHHHHHHHHHHHHHHHHHT-EEEEEEEEEEEEEEEGGGHHHHHHH CS
                   Thymidylat_synt 146 ChvlfqfyvkdkkegkLslqlyqRSaDvflGvpFNiasyalLthmlaqvtglkpgelihtigdaHiYsnhveqvkeq 222
                                       C+++  f+++   +gkL+l+   RS D++ + p N+   + L+  +a+  g+++g+++     aHiY+   ++++  
  gi|298674842|ref|YP_003726592.1| 139 CMIIDDFKIR---NGKLHLTTLFRSHDFAGAYPANLYGLSGLLRYVAEKSGVSTGKITTISVSAHIYEHDWDKIEDI 212
                                       *********4...457******************************************************9999876 PP

                                       H CS
                   Thymidylat_synt 223 l 223
                                       +
  gi|298674842|ref|YP_003726592.1| 213 I 213
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1547.14
//
Query:       gi|298674843|ref|YP_003726593.1|  [L=427]
Description: 3-phosphoshikimate 1-carboxyvinyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     3e-112  375.4   0.1   3.5e-112  375.2   0.1    1.0  1  EPSP_synthase    EPSP synthase (3-phosphoshikimate 1-carboxyv
  ------ inclusion threshold ------
      0.035   14.6   0.1       0.32   11.5   0.0    2.6  2  Cu_amine_oxidN1  Copper amine oxidase N-terminal domain
       0.11   12.2   0.1        4.2    7.0   0.0    2.5  3  YscJ_FliF        Secretory protein of YscJ/FliF family
       0.15   12.1   0.1         15    5.7   0.0    3.1  3  Sigma70_r1_1     Sigma-70 factor, region 1.1
       0.16   12.0   0.0       0.32   11.0   0.0    1.5  1  Lig_C            Ligase Pab1020 C-terminal region


Domain annotation for each model (and alignments):
>> EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  375.2   0.1  9.7e-116  3.5e-112       5     417 .]       8     415 ..       5     415 .. 0.92

  Alignments for each domain:
  == domain 1  score: 375.2 bits;  conditional E-value: 9.7e-116
                                       S--EEEEE--B-HHHHHHHHHHHGGGBSSEEEES---SHHHHHHHHHHHHTT.EEEEEECTSEEEEEGTT..--EE- CS
                     EPSP_synthase   5 krlegevkvpGsksisnralllAaLaegestitnlLdseDvrsmlealreLgaeiikldeekevviveglggsfeap 81 
                                       ++l ge+ +p+sks+++ra+ +++L+  +sti  +L s+D+++++ a+ ++ga+i   +++++ + ++g  g+  +p
  gi|298674843|ref|YP_003726593.1|   8 SKLHGELYAPPSKSYTHRAITIGSLS-HQSTIHRPLLSADTEATIRACEMFGANI---EKKNNKLEINGIDGAPHVP 80 
                                       799*********************97.589**********************755...4567788888888999999 PP

                                       HHHHTT-GGGGGGHHHHHHHHSEESSEEEEE-SBTTCGS--HHHHHHHHHTT-EEEEETTEEEEEESEET.SS-BEE CS
                     EPSP_synthase  82 eelvldlgnsgtalrlLtallalasgevvLtGdesirkRPidrlldaLrqlGaeieveegenkaplkvkg.lklkgv 157
                                        e+v+d+ nsgt+lr++tal++l +g +vLtGd s+r+RP  +ll+ L++lG+++ + ++++ apl vkg lk+  +
  gi|298674843|ref|YP_003726593.1|  81 -EDVIDVENSGTTLRFMTALATLTDGVTVLTGDRSVRTRPNGPLLEVLQNLGVDVFSTRNNGRAPLVVKGgLKGAIT 156
                                       .7********************************************************************9****** PP

                                       EEETSSTTHHHHHHHHHHHTTSBS.EEEEES.-TTHHHHHHHHHHHHHTT-EEEETTSSE.EEEEE--SSB--EEEE CS
                     EPSP_synthase 158 eikaevsSqqvtsllllaallaeg.ttelee.lasepsiddtlkmlkkfgikietsgtee.sitvkGkeklpgteyv 231
                                       +i++++sSq+v++ll++ +l+ +  t+ +++ l+s+p++d+t ++++k+g +i  +++ + ++ +  k+k +  ey+
  gi|298674843|ref|YP_003726593.1| 157 KIDGSISSQFVSALLIACPLTNNStTLSIKGeLKSKPYVDITTEIIEKAGCEIFVDKNHNtKFIIPAKQKYDLKEYT 233
                                       *******************887779999999********************998877776245555566655558** PP

                                       --B-HHHHHHHHHHHHHTT-EEEEES--GGGGHHH..HHHHHHHHTTEEEEEESTS.EEEEEETTS--BEEEEEBGS CS
                     EPSP_synthase 232 vegDassAayflvaAaitggevtvenvginslqGdiealdeilekmgaeitqeeda.sivvgpsglklkdvdietlp 307
                                       v+gD ssA+y+l+aAa+tg++vtv+n+++ s qGd++++d ile+mga+i + +d+ + +v+   l+++ vd+   p
  gi|298674843|ref|YP_003726593.1| 234 VPGDFSSASYLLAAAAMTGSKVTVKNLFP-SKQGDVKIID-ILEQMGANIHWDKDKgDVSVNGGDLNGITVDLGASP 308
                                       **************************987.6799*****9.**********9876614455555************* PP

                                       TTSBHGGGHHHHHHHHHTSBSEEEEEGSSSTTCCHHHHHHHTTT-EEEEETTEEEEEEEEE.EB-EEEE-TTSTTTT CS
                     EPSP_synthase 308 deaptlavlaafaegttviegiaelrvketdrlaamateLrklGaeveeeedgliiipaekqlkgaevesydDhRia 384
                                       d++pt+avl ++a+gttvi++++++r+ketdr++ama+eL+k+G +v+ee+d l+++++  +lk+a+v   +DhRi 
  gi|298674843|ref|YP_003726593.1| 309 DLFPTIAVLGTVAKGTTVIRNAEHVRYKETDRIHAMANELQKMGIKVKEEKDRLTVNGG--NLKKANVYGWHDHRIV 383
                                       *******************************************************8887..49************** PP

                                       HHHHHHHHHSBSEEEEETTHHHHHHSSSHHHHH CS
                     EPSP_synthase 385 malalaglvaegeveiddiectdksfpefeekL 417
                                       mal++agl+a g++++d +e + +s+p+f+e++
  gi|298674843|ref|YP_003726593.1| 384 MALTIAGLIA-GDTTVDTAESVFISYPNFFEDM 415
                                       *******665.55*****************976 PP

>> Cu_amine_oxidN1  Copper amine oxidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   8.8e-05      0.32      11      35 ..     272     296 ..     268     311 .. 0.84
   2 ?   -1.7   0.1       1.2   4.4e+03      16      50 ..     351     365 ..     319     376 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.8e-05
                   Cu_amine_oxidN1  11 aiaealGakvewdeetktVtikkgd 35 
                                        i e++Ga+++wd++++ V ++ gd
  gi|298674843|ref|YP_003726593.1| 272 DILEQMGANIHWDKDKGDVSVNGGD 296
                                       689*****************98766 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.2
                   Cu_amine_oxidN1  16 lGakvewdeetktVtikkgdktiklkigsneatvn 50 
                                       +G                    ik+k +++++tvn
  gi|298674843|ref|YP_003726593.1| 351 MG--------------------IKVKEEKDRLTVN 365
                                       23....................3333333333443 PP

>> YscJ_FliF  Secretory protein of YscJ/FliF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.1     4e+03      40      66 ..     202     229 ..     167     232 .. 0.60
   2 ?    7.0   0.0    0.0012       4.2      10      72 ..     246     306 ..     239     312 .. 0.78
   3 ?    2.3   0.0     0.032   1.1e+02      30      60 ..     338     366 ..     313     376 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.1
                         YscJ_FliF  40 Ldeegipyklsdd.ggtilVpedqvsea 66 
                                       ++++g +  ++++ ++++ +p++q +++
  gi|298674843|ref|YP_003726593.1| 202 IEKAGCEIFVDKNhNTKFIIPAKQKYDL 229
                                       3566666666664366677777777765 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0012
                         YscJ_FliF  10 vvlvlwlsrpeyevLysnlsekdaaeivekLdeegipyklsddggtilVpedqvsearlklas 72 
                                       +++++  s+ + + L+ + + +   +i++ L+++g + + ++d+g ++V+  +++ + ++l++
  gi|298674843|ref|YP_003726593.1| 246 AAAAMTGSKVTVKNLFPSKQGD--VKIIDILEQMGANIHWDKDKGDVSVNGGDLNGITVDLGA 306
                                       5555666666666666544443..48************************9999998888865 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.032
                         YscJ_FliF  30 ekdaaeivekLdeegipyklsddggtilVpe 60 
                                       ++   +++++L+++gi++k ++d   ++V+ 
  gi|298674843|ref|YP_003726593.1| 338 TDRIHAMANELQKMGIKVKEEKDR--LTVNG 366
                                       55677899***********99865..45555 PP

>> Sigma70_r1_1  Sigma-70 factor, region 1.1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.37   1.3e+03      42      56 ..     123     137 ..     122     143 .. 0.83
   2 ?    1.6   0.1     0.079   2.8e+02      41      61 ..     269     289 ..     266     296 .. 0.85
   3 ?    5.7   0.0    0.0043        15      36      58 ..     338     360 ..     334     372 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.37
                                       HHHHHHCCT-EEE-S CS
                      Sigma70_r1_1  42 iiemLedmgIdvvee 56 
                                       ++e L+++g+dv+ +
  gi|298674843|ref|YP_003726593.1| 123 LLEVLQNLGVDVFST 137
                                       5789********976 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.079
                                       HHHHHHHCCT-EEE-SS-... CS
                      Sigma70_r1_1  41 diiemLedmgIdvveeaeded 61 
                                       +ii++Le+mg +++ ++++ d
  gi|298674843|ref|YP_003726593.1| 269 KIIDILEQMGANIHWDKDKGD 289
                                       69***********98887554 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0043
                                       HHHHHHHHHHHHCCT-EEE-SS- CS
                      Sigma70_r1_1  36 seqiediiemLedmgIdvveeae 58 
                                       ++ i  +   L++mgI+v ee++
  gi|298674843|ref|YP_003726593.1| 338 TDRIHAMANELQKMGIKVKEEKD 360
                                       6888889999**********987 PP

>> Lig_C  Ligase Pab1020 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0     9e-05      0.32      47      98 ..     310     362 ..     296     373 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9e-05
                                       HHHHHHHHHHHHTT---EE.EEEEE-SSHHHHHHHHHHHHCTT--EEEEEEE. CS
                             Lig_C  47 Lepmvetikkvkeeekvke.efrvrfkdeenieellehLrrlgvkaeveekek 98 
                                       L p +  +  v+++ +v +   +vr k+ + i+++ + L+++g+k++ e+++ 
  gi|298674843|ref|YP_003726593.1| 310 LFPTIAVLGTVAKGTTVIRnAEHVRYKETDRIHAMANELQKMGIKVKEEKDRL 362
                                       66777777888888776550567***********************9888874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      634  (0.0353617); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3080.44
//
Query:       gi|298674844|ref|YP_003726594.1|  [L=573]
Description: methyl-coenzyme M reductase subunit alpha [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   8.9e-147  487.6   0.5   1.2e-146  487.3   0.5    1.1  1  MCR_alpha_N  Methyl-coenzyme M reductase alpha subunit, N-ter
    2.1e-66  222.2   4.5    3.4e-66  221.5   3.6    1.9  2  MCR_alpha    Methyl-coenzyme M reductase alpha subunit, C-ter
  ------ inclusion threshold ------
      0.015   15.4   0.0       0.11   12.6   0.0    2.1  2  BofC_C       BofC C-terminal domain


Domain annotation for each model (and alignments):
>> MCR_alpha_N  Methyl-coenzyme M reductase alpha subunit, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  487.3   0.5  1.9e-150  1.2e-146       1     270 []      15     284 ..      15     284 .. 0.99

  Alignments for each domain:
  == domain 1  score: 487.3 bits;  conditional E-value: 1.9e-150
                                       XX--HHHHHHH-S.S.-TT--B---S-S-GGGG-HHHHHHHHHHHHHHHHH-S----TTS....S--S-SS---EEE CS
                       MCR_alpha_N   1 eklflkalkkkfkke.dpeekktkfykfeGlkqserkrefveaakkiakkrgislynpdilhl.GvplGqrklmpyk 75 
                                       e++f++++ ++++++ ++++kkt++ +++G+ qs+rk+e+ +a+++++kkrg++ ynpd  h+ Gv+lGqr+l+p+ 
  gi|298674844|ref|YP_003726594.1|  15 ERKFTQEFGDNKQSGgEITDKKTEY-QRMGVAQSPRKMEMLKAGQELSKKRGLVGYNPDL-HAgGVQLGQRALTPSY 89 
                                       589******99998779*******9.********************************88.887************* PP

                                       BTTS--EEEGGGSSGGG-HHHHHHHHHHHTEEEEE-HHHHHHHHHTT-----HHHHHHHHHHHHHHTTT--SS-TT- CS
                       MCR_alpha_N  76 vsgtdvlvegddlhfvnnaalqqlwddirrtvivgldtahevlekrlGkevtPetineylevlnhalPGgavvqehm 152
                                       +sgtd+l+e+ddlh+vnnaa+qq+wddirrt+ivg+d+ahe+lekrlG+evtPetin+ylevlnha+PGgavvqehm
  gi|298674844|ref|YP_003726594.1|  90 LSGTDMLTEMDDLHYVNNAAMQQMWDDIRRTCIVGMDSAHETLEKRLGIEVTPETINHYLEVLNHAIPGGAVVQEHM 166
                                       ***************************************************************************** PP

                                       ----TTT-TT-EEEEEES-HHHHTTS-GGGB--HHHHS-HHHHHHHHHHH-S-EEEEEE--HHHHHHS-HHHHHHHH CS
                       MCR_alpha_N 153 vethPalvedcyvkvftGddeladeidkqflidinkefpeeqaeqlkkaiGkklyqvvriPtivsrtcdGgttsrws 229
                                       vethP+l+edcyvk+ftGdd+ladeid+qflidi+kefpe+qa+qlk++iGk+++qv++iPt+vsrt+dGg+t+rw+
  gi|298674844|ref|YP_003726594.1| 167 VETHPGLTEDCYVKIFTGDDDLADEIDDQFLIDIDKEFPEDQAQQLKESIGKTTWQVAHIPTVVSRTTDGGQTRRWM 243
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHT--SS-TTHHHHHHHHHTTSEEES---B- CS
                       MCR_alpha_N 230 amqigmsfisayklcaGeaavadlayaakhaeviemgellP 270
                                       amq+gmsfi+ay++caGeaavadl+yaakha+vi+mge+lP
  gi|298674844|ref|YP_003726594.1| 244 AMQLGMSFINAYHMCAGEAAVADLSYAAKHASVINMGEMLP 284
                                       ****************************************9 PP

>> MCR_alpha  Methyl-coenzyme M reductase alpha subunit, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.1   6.7e+03      28      43 ..      99     114 ..      74     151 .. 0.47
   2 !  221.5   3.6   5.7e-70   3.4e-66       1     127 []     332     464 ..     332     464 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.1
                         MCR_alpha  28 lddfvyygvdyvkdky 43 
                                       +dd  y +   +++ +
  gi|298674844|ref|YP_003726594.1|  99 MDDLHYVNNAAMQQMW 114
                                       3455555444444444 PP

  == domain 2  score: 221.5 bits;  conditional E-value: 5.7e-70
                         MCR_alpha   1 dqiwlGsymsGGvGftqyataaytdnilddfvyygvdyvkdky......gglakvkatlevvkdiatevtlyaleqy 71 
                                       dqiwlGsymsGGvGftqyataayt+nildd +yy ++y++dky      g+ +k++at++vvkdiate tly+le+y
  gi|298674844|ref|YP_003726594.1| 332 DQIWLGSYMSGGVGFTQYATAAYTNNILDDNLYYDIEYINDKYnnagkpGADNKAPATMDVVKDIATESTLYGLENY 408
                                       9******************************************999999999************************* PP

                         MCR_alpha  72 ekyptlledhfGGsqraavlaaaagistalatgnsnaGlngwylsmllhkeahsrl 127
                                       ekypt+ledhfGGsqra+vl+aaag +t++atgnsnaGl++wylsm+lhkeah+rl
  gi|298674844|ref|YP_003726594.1| 409 EKYPTALEDHFGGSQRATVLSAAAGSATSIATGNSNAGLSAWYLSMYLHKEAHGRL 464
                                       *******************************************************8 PP

>> BofC_C  BofC C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.21   1.2e+03      51      71 ..     134     154 ..     116     155 .. 0.68
   2 ?   12.6   0.0   1.8e-05      0.11      12      57 ..     170     216 ..     162     222 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.21
                                       HHHHH--S-..--HHHHHHHHHH CS
                            BofC_C  51 eqLkkGIrv..eskeeyesvlet 71 
                                       ++L  GI+v  e+ ++y +vl++
  gi|298674844|ref|YP_003726594.1| 134 KRL--GIEVtpETINHYLEVLNH 154
                                       333..7776336899*****975 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 1.8e-05
                                       -EEEETTTEEEEBSSS-STT-BS-------TTT.S-HHHHHHHHH-- CS
                            BofC_C  12 YfGldedgtlslfeGepeeekviksffqidvek.lesslkeqLkkGI 57 
                                       + Gl+ed  + +f+G  +  + i + f id++k  ++ + +qLk+ I
  gi|298674844|ref|YP_003726594.1| 170 HPGLTEDCYVKIFTGDDDLADEIDDQFLIDIDKeFPEDQAQQLKESI 216
                                       669****************************7637888889999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (573 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 3898.59
//
Query:       gi|298674845|ref|YP_003726595.1|  [L=249]
Description: methyl-coenzyme M reductase subunit gamma [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   1.5e-116  387.9   0.3   1.7e-116  387.7   0.3    1.0  1  MCR_gamma  Methyl-coenzyme M reductase gamma subunit


Domain annotation for each model (and alignments):
>> MCR_gamma  Methyl-coenzyme M reductase gamma subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  387.7   0.3  9.7e-121  1.7e-116       1     246 []       6     247 ..       6     247 .. 0.99

  Alignments for each domain:
  == domain 1  score: 387.7 bits;  conditional E-value: 9.7e-121
                         MCR_gamma   1 aqyyPGeskvaenrrkfmdpeaeleklreisdedvvkilghraPGeeyksvhPPleemdepedpirelvePieGaka 77 
                                       +qy PG+++va+nr k+m  +++leklreisded+  ilghr+PG++y+s+hPPleem epe++ire+veP+eGaka
  gi|298674845|ref|YP_003726595.1|   6 KQYHPGKTSVAKNRSKHM--SNDLEKLREISDEDLTLILGHRSPGSDYPSTHPPLEEMGEPECSIREIVEPTEGAKA 80 
                                       59****************..899****************************************************** PP

                         MCR_gamma  78 GdrvryiqfadsmyfaPaqPyqrarlellryrgvdtGtlsGrqiievrerdlekiskelletelfdpartgirGatv 154
                                       Gdr+ry q++dsmy+aPa+Py r++ +++++r+vd+GtlsGrq++e+rerd+ek++k  lete+++p  +g+rGatv
  gi|298674845|ref|YP_003726595.1|  81 GDRIRYAQWVDSMYNAPATPYFRTYHAAINFRAVDPGTLSGRQLVEARERDMEKMTKVQLETEMTCPGLAGLRGATV 157
                                       ***************************************************************************** PP

                         MCR_gamma 155 hGhslrldenGlmfdalqrlvldeedgevkyvkdqvgvpldkkvdvGkpldedelkkkttiyrldgvalrddkevve 231
                                       hGhslrl+e+G+mfd+l+r+ l+  +g++++ kdq ++p+dkkvd+Gkp++ede  k+ttiyr+d+v +rdd+evve
  gi|298674845|ref|YP_003726595.1| 158 HGHSLRLQEDGVMFDMLDRRRLE--NGTIVMDKDQQARPIDKKVDLGKPMSEDEAAKRTTIYRADNVPFRDDDEVVE 232
                                       **********************5..9*************************************************** PP

                         MCR_gamma 232 vvkrihelrtklgfk 246
                                       +v+ri+e+rt++gf+
  gi|298674845|ref|YP_003726595.1| 233 WVHRIWEQRTEYGFQ 247
                                       *************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1699.36
//
Query:       gi|298674846|ref|YP_003726596.1|  [L=201]
Description: methyl-coenzyme M reductase I operon protein C [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-09   36.4   0.5    4.3e-09   35.9   0.5    1.4  1  MCR_C     Methyl-coenzyme M reductase operon protein C


Domain annotation for each model (and alignments):
>> MCR_C  Methyl-coenzyme M reductase operon protein C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.5   2.4e-13   4.3e-09      72     172 ..      39     145 ..      27     199 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 2.4e-13
                             MCR_C  72 iavvsptLarhhlPhsaCDvaeylrraGaktnmiGlarGvgkriaq.......ikeeekrlinehDlavfvlGnfkd 141
                                       +  v++   r+h+  ++C+++  +r+aG +  ++ l+ G+g+  +        i+ ee++ i  h lav  +Gn ++
  gi|298674846|ref|YP_003726596.1|  39 VIAVAMGPGRRHITKPVCELTYGMRQAGIQVSVLVLSGGTGQPESGlisgsfgIEPEETDQIARHKLAVIHVGNVAQ 115
                                       5567888899*******************************9765422222336889******************** PP

                             MCR_C 142 CikkkkeklfedievPvvvtggPeelkleev 172
                                        i kk +k++e++e+P +v++    ++ e++
  gi|298674846|ref|YP_003726596.1| 116 HIIKKIRKILENVEIPAIVVSQA-LVDFEDL 145
                                       ******************99876.5555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1398.17
//
Query:       gi|298674847|ref|YP_003726597.1|  [L=168]
Description: methyl-coenzyme M reductase operon protein D [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.8e-55  184.3   0.0    1.1e-54  184.1   0.0    1.0  1  MCR_D     Methyl-coenzyme M reductase operon protein D


Domain annotation for each model (and alignments):
>> MCR_D  Methyl-coenzyme M reductase operon protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.1   0.0   6.3e-59   1.1e-54       1     142 [.      14     154 ..      14     155 .. 0.98

  Alignments for each domain:
  == domain 1  score: 184.1 bits;  conditional E-value: 6.3e-59
                             MCR_D   1 dveifpeRlLkpetteklLnelvelegikrvvihGprLPkkvpygpakGkevehkerkvievkgeeveLkvkvGril 77 
                                       ++e+fp+RlLkpett++lL+el+e++gi r++ihGprLP +vp gpa+G++veh++rkvi+++++++eL+++vGri+
  gi|298674847|ref|YP_003726597.1|  14 QIELFPTRLLKPETTQNLLEELSEVDGIIRAFIHGPRLPLTVPSGPATGQDVEHPHRKVIQIGDTAIELSISVGRIR 90 
                                       89*************************************************************************** PP

                             MCR_D  78 leledeeviekieeiceevlpfsyeikegkfirkkktvsDyakyGeeeadkrllGlvDpksklee 142
                                       le++de+v e+ie+i e+vlp++ye++eg fi k++tv+Dyak+G++ ad++  Gl Dpk+  e+
  gi|298674847|ref|YP_003726597.1|  91 LEITDEDVEEEIETIAEKVLPCKYELREGYFIPKESTVTDYAKRGPN-ADPKRRGLSDPKASEES 154
                                       ***********************************************.************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1235.63
//
Query:       gi|298674848|ref|YP_003726598.1|  [L=434]
Description: methyl-coenzyme M reductase subunit beta [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   7.3e-138  458.2   3.1   7.3e-138  458.2   3.1    1.4  2  MCR_beta    Methyl-coenzyme M reductase beta subunit, C-termi
    1.2e-82  276.0   1.3      2e-82  275.2   1.3    1.4  1  MCR_beta_N  Methyl-coenzyme M reductase beta subunit, N-termi
  ------ inclusion threshold ------
      0.097   12.0   0.0       0.16   11.3   0.0    1.3  1  IL12        Interleukin-12 alpha subunit


Domain annotation for each model (and alignments):
>> MCR_beta  Methyl-coenzyme M reductase beta subunit, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.1   6.3e+03      75     236 ..     128     141 ..     118     152 .. 0.44
   2 !  458.2   3.1  1.2e-141  7.3e-138       1     248 [.     186     433 ..     186     434 .] 1.00

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.1
                          MCR_beta  75 gtvGtvveslveraiedkvikvekklpsgyklyetkdvalwnayaaaGllaavivnvgaaraaqavsstllyyndll 151
                                       +tvG                                                                         
  gi|298674848|ref|YP_003726598.1| 128 TTVG------------------------------------------------------------------------- 131
                                       2333......................................................................... PP

                          MCR_beta 152 eketglpGvdfGrveGtavGfsffshsiyGGGGpGifnGnhvvtrhskGfaipcvaaavaldaGtqlfspeatsglv 228
                                                                                                                    
  gi|298674848|ref|YP_003726598.1| 132 ---------------------------------------------------------------------------AA 133
                                       ...........................................................................22 PP

                          MCR_beta 229 gevfgeid 236
                                        +v + id
  gi|298674848|ref|YP_003726598.1| 134 ATVQSIID 141
                                       22333333 PP

  == domain 2  score: 458.2 bits;  conditional E-value: 1.2e-141
                          MCR_beta   1 GyalrnikanhvvaitkknalnaaalssileqtavfemGdavGaferahllglayqGlnannlvydlvkengkegtv 77 
                                       Gy+lrni++nh+vait+k+a+naa+lssi+eq+a++emG+avG+fer++llglayqGlnannlvyd++k+ngk+gt+
  gi|298674848|ref|YP_003726598.1| 186 GYSLRNIMTNHIVAITNKKAMNAACLSSIYEQVAMYEMGNAVGEFERQQLLGLAYQGLNANNLVYDIIKDNGKDGTI 262
                                       9**************************************************************************** PP

                          MCR_beta  78 GtvveslveraiedkvikvekklpsgyklyetkdvalwnayaaaGllaavivnvgaaraaqavsstllyyndlleke 154
                                       Gtv++s v+ra+ed+vi+v+k+ psgy++y+++dv++wnayaaaG+laa++vn+ga+r  q+vsstlly+nd++eke
  gi|298674848|ref|YP_003726598.1| 263 GTVIDSTVNRALEDNVISVDKTAPSGYSFYKANDVPMWNAYAAAGQLAASMVNCGAGRSPQNVSSTLLYFNDIIEKE 339
                                       ***************************************************************************** PP

                          MCR_beta 155 tglpGvdfGrveGtavGfsffshsiyGGGGpGifnGnhvvtrhskGfaipcvaaavaldaGtqlfspeatsglvgev 231
                                       tglpG+d+Grv+Gt+vGfsffshsiyGGGGpGifnGnh+vtrhs+Gfaipcvaa+++ldaGtq+f+peats+l+g+v
  gi|298674848|ref|YP_003726598.1| 340 TGLPGCDYGRVQGTSVGFSFFSHSIYGGGGPGIFNGNHIVTRHSRGFAIPCVAASASLDAGTQMFTPEATSSLIGDV 416
                                       ***************************************************************************** PP

                          MCR_beta 232 fgeidefreplkavaea 248
                                       fg+i++frep+ ava+a
  gi|298674848|ref|YP_003726598.1| 417 FGSIETFREPIDAVAKA 433
                                       **************985 PP

>> MCR_beta_N  Methyl-coenzyme M reductase beta subunit, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  275.2   1.3   3.4e-86     2e-82       1     182 []       3     184 ..       3     184 .. 1.00

  Alignments for each domain:
  == domain 1  score: 275.2 bits;  conditional E-value: 3.4e-86
                        MCR_beta_N   1 DkidlyddkGkllesdvpleaisPlknpaikkivkdvkrtvavnlagiekalktgkvggkaskilGreldldivena 77 
                                       D+idly+d+Gklles+v+l++i+P+kn+aikki++d+k++va+nl+gi+kal+tgk+ggk+++i+G eld+d+v na
  gi|298674848|ref|YP_003726598.1|   3 DNIDLYNDRGKLLESNVDLMDIAPTKNDAIKKIIDDTKKSVAINLNGIQKALSTGKMGGKGRHIPGYELDYDLVGNA 79 
                                       89*************************************************************************** PP

                        MCR_beta_N  78 daiaekikelvqveedddtkvkllngGkqllvqvPskRleaaaeysvallataaavveaiidefdvdmfdasvvkaa 154
                                       d+i ++++elv+v+ +ddt+v++l gGkqll+qvP++Rl+a+a+y++a+++ aaa+v++iid+f++dmf a++vkaa
  gi|298674848|ref|YP_003726598.1|  80 DSIRDSVEELVRVDPNDDTNVESLYGGKQLLIQVPDERLQAGADYASATTVGAAATVQSIIDKFNTDMFVAPIVKAA 156
                                       ***************************************************************************** PP

                        MCR_beta_N 155 vlGryPqtvdlaggnvasilsipqkneG 182
                                       v+G+yPqtvdl+ggn+asil+ipq+neG
  gi|298674848|ref|YP_003726598.1| 157 VWGSYPQTVDLSGGNIASILKIPQQNEG 184
                                       ***************************9 PP

>> IL12  Interleukin-12 alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.7e-05      0.16     106     131 ..     198     223 ..     181     234 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.7e-05
                              IL12 106 laskktsflktLClssiyedLklykv 131
                                       +a +++  + + Clssiye + +y++
  gi|298674848|ref|YP_003726598.1| 198 VAITNKKAMNAACLSSIYEQVAMYEM 223
                                       56677889****************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 3125.67
//
Query:       gi|298674849|ref|YP_003726599.1|  [L=37]
Description: hypothetical protein Metev_0907 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       200  (0.0111551); expected 358.6 (0.02)
Passed bias filter:                      138  (0.00769703); expected 358.6 (0.02)
Passed Vit filter:                         3  (0.000167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 279.88
//
Query:       gi|298674850|ref|YP_003726600.1|  [L=408]
Description: methanogenesis marker protein 10 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      4e-18   66.4   7.0    2.3e-15   57.4   5.9    3.4  2  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
      0.084   12.9   0.0       0.18   11.9   0.0    1.5  1  Limkain-b1   Limkain b1
       0.15   11.7   0.0       0.39   10.4   0.0    1.7  1  MIX          Mitochondrial membrane-anchored proteins
        1.6    9.0   4.8         11    6.3   4.8    2.3  1  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   5.9   5.2e-19   2.3e-15       7     160 ..      15     191 ..      10     199 .. 0.91
   2 ?    2.0   0.0     0.052   2.4e+02      29     108 ..     234     316 ..     224     320 .. 0.66

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 5.2e-19
                                       ESS--TTTSCCTT.........................HHHHHHHHHHHHHHHHHHHHHHH.HHTT.SEEEEEESST CS
                                       xxxxxxxxxxxxx.........................xxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxx RF
                       Radical_SAM   7 CnlrCsfCarpet.........................vrregrgrslsveeileevkelk.aekg.vkevilggge 56 
                                       Cn+ C++C++++                          + +e ++ +++v+ +l+ev ++  +++   k  i+ggg+
  gi|298674850|ref|YP_003726600.1|  15 CNGFCKYCYFNKVkdenipvfgckhcfpfkkgcdycirSVKESYPGFKPVQIVLQEVSQNLyFNPYtDKITISGGGD 91 
                                       88999999999888999999999999999999999999889****************99998999977777788*** PP

                                       GGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  57 pllypdfvellerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlea 133
                                       ++ yp++ el+  l+k + + i++ +++  +  +++ ++ l + gv+ v++++ a+d++  ++  +r +++e  le+
  gi|298674850|ref|YP_003726600.1|  92 VSCYPELKELVNSLSKFE-KPIHLGYTSGKGFNNKDDADFLIDKGVNEVTFTVFATDPK-LRNEYMRDPEPEVSLEV 166
                                       ****************97.**********99999*************************.777777*********** PP

                                       HHHHHHTTSETEEEEEEEBTTTSHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 134 leklreagikrvvdrivglpGendeel 160
                                       lek+ +  ++ v+  +v++pG nd ++
  gi|298674850|ref|YP_003726600.1| 167 LEKFCKD-CE-VYAALVLIPGINDGDV 191
                                       *******.**.*************876 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.052
                                       HHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC......CCTEEEEEEECSSCHGHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  29 lsveeileevkelkaekgvkevilgggepllypdfvellerlakla......vpgiritvetngtlpdeeklerlle 99 
                                        s++e +e+v+ ++ +  ++++ ++g  pl +p +    + +  ++      + + + tv+t+     ++  e +++
  gi|298674850|ref|YP_003726600.1| 234 HSIDEFKEIVRDAA-S--KHNLKITGT-PLEDPYIGSPFAIRNSEKfmsnlpEVKKEATVITSSAAA-PRLQEIFDN 305
                                       57788888888884.4..666666665.888777777777777777888888455555555555554.566666666 PP

                                       TT..-SEEEEE CS
                                       xx..xxxxxxx RF
                       Radical_SAM 100 lg..vdrvslg 108
                                       lg  v++v+++
  gi|298674850|ref|YP_003726600.1| 306 LGgkVNVVNVD 316
                                       66667777765 PP

>> Limkain-b1  Limkain b1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.1e-05      0.18       6      39 ..     276     313 ..     272     320 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.1e-05
                        Limkain-b1   6 vvsnLPtnrdk....lkkaiknrLrrLsdncGGkvlsi 39 
                                       ++snLP  ++       +a   rL+ ++dn GGkv  +
  gi|298674850|ref|YP_003726600.1| 276 FMSNLPEVKKEatviTSSAAAPRLQEIFDNLGGKVNVV 313
                                       6789996554323345788999*************877 PP

>> MIX  Mitochondrial membrane-anchored proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   8.6e-05      0.39     112     150 ..     303     344 ..     275     346 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 8.6e-05
                               MIX 112 kdpnggrvnr.dveeii..smavddleamdlspsadavlvpt 150
                                        d  gg+vn  +v++ i   m+++dl+++dls   ++vl+p 
  gi|298674850|ref|YP_003726600.1| 303 FDNLGGKVNVvNVDKDIgcLMTINDLQNLDLSQIKETVLIPG 344
                                       567788877434554441169*******************96 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   4.8    0.0024        11      14      83 ..      14     109 ..      13     154 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0024
                           Fer4_12  14 gCnlsCkgCfnketwsfk...........................sgkeftkelleeiiedlk.kesiegltllGGE 62 
                                       +Cn  Ck+C+ +++++ +                            g +  + +l+e+ ++l  +++ +++t++GG 
  gi|298674850|ref|YP_003726600.1|  14 DCNGFCKYCYFNKVKDENipvfgckhcfpfkkgcdycirsvkesyPGFKPVQIVLQEVSQNLYfNPYTDKITISGGG 90 
                                       69999999999999966666666777777777777777765544433333355666666666547999******998 PP

                           Fer4_12  63 Pllpenaeallelvkevkeek 83 
                                        +    +++l elv+++ +  
  gi|298674850|ref|YP_003726600.1|  91 DVS--CYPELKELVNSLSKFE 109
                                       888..7899999998876644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2767.32
//
Query:       gi|298674851|ref|YP_003726601.1|  [L=1152]
Description: DNA polymerase II large subunit DP2 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
          0 1309.9   0.0          0 1309.1   0.0    1.4  2  PolC_DP2        DNA polymerase II large subunit DP2
  ------ inclusion threshold ------
        2.6    8.0  12.0        3.3    7.7   3.2    3.3  3  Zn_ribbon_SprT  SprT-like zinc ribbon domain


Domain annotation for each model (and alignments):
>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1309.1   0.0         0         0       1     864 []      12     902 ..      12     902 .. 0.96
   2 ?   -3.5   0.1      0.18   1.6e+03     620     673 ..    1070    1127 ..    1066    1138 .. 0.48

  Alignments for each domain:
  == domain 1  score: 1309.1 bits;  conditional E-value: 0
                          PolC_DP2   1 eYfeklekeleeayeiaekarskgldpkeevEiplAkdladRvekllgikgvaerirelekelsreevalkiakeia 77 
                                       eYf++le++l+  ++ia kars+g+dp+++vEip+AkdladRve+l+g++gvaerirele++ sree+al+++ke+a
  gi|298674851|ref|YP_003726601.1|  12 EYFNNLENKLNYEIQIAGKARSHGKDPSSNVEIPVAKDLADRVENLIGVSGVAERIRELENDKSREEAALSLGKEVA 88 
                                       6**************************************************************************** PP

                          PolC_DP2  78 egkvgeaeskeeavdkavrtalalltegvvaAPleGiakvkikknddgteylkvyyaGPiRsaGGtaqalsvLvaDy 154
                                       eg vg++esk+++v++a+r+a+a+ltegvvaAP+eGi++v++ knddgtey++++yaGP+RsaGGtaqalsvLv+Dy
  gi|298674851|ref|YP_003726601.1|  89 EGYVGNFESKKDSVESAIRVAVAMLTEGVVAAPIEGIDSVNLAKNDDGTEYISIFYAGPVRSAGGTAQALSVLVGDY 165
                                       ***************************************************************************** PP

                          PolC_DP2 155 vrkklgldrykpreeeieRyveEielYervaslqyspsdeeirlivknipveidGeatedeevsgyrdlervetnrv 231
                                       vr+ l++drykpr+ee+eRyveEi+lY+rva+lqy+ps+eeirliv+n+p+++dGe+te++ev+gyrdlerv tnr+
  gi|298674851|ref|YP_003726601.1| 166 VRRGLNIDRYKPRKEEVERYVEEITLYRRVAGLQYMPSEEEIRLIVENCPICLDGEPTEQAEVEGYRDLERVGTNRI 242
                                       ***************************************************************************** PP

                          PolC_DP2 232 RGGmllvlaeGialkakKikkkvkklklegWewleelika..........ekeekkeeeeekkevkpkekylrdlia 298
                                       RGG+ lvlaeGialka+Ki+k+vkk++++gWewl++l+++           +ee+ ++++++k+ kpk+kylrdlia
  gi|298674851|ref|YP_003726601.1| 243 RGGVGLVLAEGIALKAPKIQKYVKKYDIDGWEWLDTLMSGeksekkddggGTEESGDNKKSEKKPKPKDKYLRDLIA 319
                                       ****************************************66666555554455555555559************** PP

                          PolC_DP2 299 GRpvlshpsrkGGfRLrYGRsrntglatagihPatmelldeflavGtqlkverPgKaaavvpvdsiegPtvklknGd 375
                                       GRpv+shpsr+GGfRLrYGRsrnt++a+agi+Pa+m+++d+f+++Gtqlkve PgKa++++pvd iegPtv+lk+Gd
  gi|298674851|ref|YP_003726601.1| 320 GRPVFSHPSRPGGFRLRYGRSRNTSFASAGINPASMVIMDKFIVAGTQLKVEIPGKAMGMAPVDFIEGPTVRLKSGD 396
                                       ***************************************************************************** PP

                          PolC_DP2 376 vvriddveealeikkeveeildlGeiLvayGeflennhpLvpasyveewwiqelekaaakkeaee...kpsaeeale 449
                                       v+riddv++a e+  +ve+i+d+Ge+L++yG+flennhpLvp++y++ewwiqe++++++++ ++e   + ++++al+
  gi|298674851|ref|YP_003726601.1| 397 VLRIDDVNDAYELYPQVEHIIDIGEMLINYGDFLENNHPLVPSPYCFEWWIQEYRNTVSDTCTDEeleDLTQDDALR 473
                                       *******************************************************999988766666699******* PP

                          PolC_DP2 450 lseeldvpLhPkytylwhdisveelekLaeavaekkkl..eeeklvleleee....vkeiLekllvehkvkeekivi 520
                                       ++++++vpLhPk+tylwhdi+ +e+e+La++v+e+++l  ++++l+++++++    +k iLekll+ hkv++++i i
  gi|298674851|ref|YP_003726601.1| 474 VCDQYNVPLHPKFTYLWHDITPQEFENLARFVSEHGNLsdDNSVLQIPYNNAddngIKLILEKLLLFHKVRDGMILI 550
                                       ************************************88665666777776657788********************* PP

                          PolC_DP2 521 eealallkslgldleeekleke...eekdalelvnelsglevrekaptrigaRmGRPeKskeRkmkpavhvLfpige 594
                                       +e l+++++lgl+++ e + ++   +++da  +vn++sg+ vr+++ tr+gaRmGRPeKs++Rkm+p ++vLfpig+
  gi|298674851|ref|YP_003726601.1| 551 SEPLPFIRCLGLNSNLELKWDDidfDDEDAQYAVNNVSGVVVRDRSLTRVGARMGRPEKSNRRKMSPVPNVLFPIGD 627
                                       ************9986654333677778************************************************* PP

                          PolC_DP2 595 aggkrrsvkeaak.k......kgeieveiarrkCkkCgketlearCeeCgekteeklvCkkceeeveeekcekceke 664
                                       +gg++r++++a++ k       gei+vei+ r+C++Cg et+e+rC+ Cge t +k++C+ c+ ++++  c+kc+++
  gi|298674851|ref|YP_003726601.1| 628 SGGNTRQLDDASNyKatmnskVGEIKVEIGIRECQSCGIETYECRCD-CGEFTFPKMSCPWCDIKANDGVCPKCGAK 703
                                       ************96478999999***********************9.***************************** PP

                          PolC_DP2 665 akavkkkkidlkellekaleklgereekleelkgvkgltskekipEpleKgilRakhdvsvfkdgtvRyDmtdlplt 741
                                       a++vk+k+id+k++++ka+e+lger+ ++e++kgvk+l+sk+++pEp+eKg+lRak ++++fkd+tvRyDm+d+plt
  gi|298674851|ref|YP_003726601.1| 704 ASSVKTKNIDFKSIYQKAFENLGERD-NFESFKGVKRLMSKNMTPEPIEKGVLRAKYNLYTFKDATVRYDMSDIPLT 779
                                       ************************66.9************************************************* PP

                          PolC_DP2 742 hfrpkeigvsveklrelGYteDieGkplesedqivelkvqDivlsedaaeyllkvakfvDdlLeklyglerfYnvek 818
                                       h+rp+e+gv++ +lrelGYteDi+Gkp++++dqiv+lkvqD+v++ daa+yllk+a+++DdlL+k+ygle++Yn+++
  gi|298674851|ref|YP_003726601.1| 780 HIRPDELGVTAYQLRELGYTEDIYGKPFTKDDQIVCLKVQDLVVPYDAADYLLKTAQYIDDLLVKYYGLEPYYNAKT 856
                                       ***************************************************************************** PP

                          PolC_DP2 819 kedLiGklviglaPHtsagvlgRiiGftkasvgyahPyfHaakRRn 864
                                        +d++G l++glaPHtsagvlgR++Gftkasvg+ahP+fHaakRRn
  gi|298674851|ref|YP_003726601.1| 857 IDDIVGVLLMGLAPHTSAGVLGRLVGFTKASVGFAHPFFHAAKRRN 902
                                       *********************************************9 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 0.18
                          PolC_DP2  620 kCkkCgke....tlearCeeCgekteeklvCkkceeeveeekcekcekeakavkkkki 673 
                                        +C kCg++     l+ +C++Cg k+  +++   +++  + ++   ++ ++++++k++i
  gi|298674851|ref|YP_003726601.1| 1070 RCVKCGEKfrrpPLSGNCTRCGGKVILTVHEGAVKKYLDISSKVANDYNVSEYTKQRI 1127
                                        5666665411113445666666666665544444443333222333333444444444 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.8      0.12     1e+03       2      15 ..     668     677 ..     667     681 .. 0.66
   2 ?    4.1   0.0    0.0048        43       6      24 ..     696     711 ..     694     718 .. 0.86
   3 ?    7.7   3.2   0.00037       3.3       6      36 ..    1070    1096 ..    1070    1098 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.12
                    Zn_ribbon_SprT   2 kyvYrCtgCgreyt 15 
                                       +y+ rC +Cg   +
  gi|298674851|ref|YP_003726601.1| 668 TYECRC-DCG---E 677
                                       566688.888...4 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0048
                    Zn_ribbon_SprT   6 rCtgCgreythhlsirrhn 24 
                                       +C+ Cg      +s+++ n
  gi|298674851|ref|YP_003726601.1| 696 VCPKCG---AKASSVKTKN 711
                                       8*****...9999999987 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.00037
                    Zn_ribbon_SprT    6 rCtgCgreythhlsirrhnYrCrrCkgtLrg 36  
                                        rC+ Cg+++ ++  + +    C rC+g+  +
  gi|298674851|ref|YP_003726601.1| 1070 RCVKCGEKFRRPPLSGN----CTRCGGKVIL 1096
                                        8****************....*****98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.71u 0.27s 00:00:00.98 Elapsed: 00:00:00.43
# Mc/sec: 8017.50
//
Query:       gi|298674852|ref|YP_003726602.1|  [L=209]
Description: type 11 methyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-23   82.2   0.0    4.8e-23   81.6   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    9.7e-22   77.4   0.0    1.2e-21   77.1   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    4.8e-21   75.3   0.0      1e-20   74.2   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    3.6e-15   56.2   0.0    4.6e-15   55.8   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
      6e-15   55.2   0.0    2.1e-14   53.4   0.0    1.6  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    2.2e-14   54.0   0.0    3.4e-14   53.4   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    7.3e-06   25.5   0.1    3.4e-05   23.3   0.0    1.8  2  CMAS             Mycolic acid cyclopropane synthetase
    4.7e-05   22.8   0.0    5.8e-05   22.5   0.0    1.1  1  Methyltransf_2   O-methyltransferase domain
    0.00041   20.2   0.0     0.0006   19.6   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    0.00056   19.5   0.0     0.0038   16.8   0.0    2.0  2  MTS              Methyltransferase small domain
     0.0012   18.7   0.0     0.0048   16.8   0.0    1.9  1  Methyltransf_8   Hypothetical methyltransferase
     0.0013   18.8   0.0     0.0015   18.5   0.0    1.3  1  Methyltransf_32  Methyltransferase domain
     0.0015   17.5   0.0     0.0017   17.3   0.0    1.2  1  Methyltransf_9   Protein of unknown function (DUF1698)
     0.0029   17.2   0.0     0.0045   16.6   0.0    1.3  1  MetW             Methionine biosynthesis protein MetW
     0.0047   16.4   0.3        0.1   12.1   0.0    2.1  2  Methyltransf_4   Putative methyltransferase
      0.006   16.0   0.0      0.016   14.6   0.0    1.7  2  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0068   16.0   0.1      0.013   15.0   0.1    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
     0.0089   15.6   0.0      0.035   13.6   0.0    1.9  1  DOT1             Histone methylation protein DOT1
  ------ inclusion threshold ------
      0.013   15.2   0.0      0.017   14.8   0.0    1.1  1  NodS             Nodulation protein S (NodS)
      0.041   13.0   0.0      0.078   12.1   0.0    1.4  1  Fibrillarin      Fibrillarin
      0.057   13.1   0.7       0.59    9.8   0.4    2.5  2  N6_N4_Mtase      DNA methylase
      0.058   14.0   0.0       0.12   13.0   0.0    1.5  1  Bin3             Bicoid-interacting protein 3 (Bin3)


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.6   0.0   5.9e-26   4.8e-23       1      96 []      49     148 ..      49     148 .. 0.93

  Alignments for each domain:
  == domain 1  score: 81.6 bits;  conditional E-value: 5.9e-26
                                       EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CCC CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlhh 73 
                                       LdvGcG+G+  + la+ +  ++v g+D+s+em+ +a+e ++e     +ve+  ++++++p+ dn+fDlv+++e+  +
  gi|298674852|ref|YP_003726602.1|  49 LDVGCGGGKAIQILADFCpyGKVHGIDYSEEMVSMAQEVNNELVKnnHVEIKYGTVSSIPYSDNTFDLVTAFETYYF 125
                                       8**************99999*************999766666555778***************************** PP

                                       -CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  74 vedpekalkeiaRvLkpgGllvi 96 
                                       ++d+e  lkei+RvLkp+G+l+i
  gi|298674852|ref|YP_003726602.1| 126 WPDLENDLKEIYRVLKPEGVLLI 148
                                       ********************986 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.1   0.0   1.5e-24   1.2e-21       3     113 ..      44     152 ..      42     198 .. 0.82

  Alignments for each domain:
  == domain 1  score: 77.1 bits;  conditional E-value: 1.5e-24
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielAre.naqklgldnveFeqgdieeleklledekfDli 78 
                                        ++ vlD+GCG G+ +  la   +p ++v+GiD+see+++ A+e n +  + + ve + g + +++  ++d++fDl+
  gi|298674852|ref|YP_003726602.1|  44 PDYLVLDVGCGGGKAIQILA-DFCPYGKVHGIDYSEEMVSMAQEvNNELVKNNHVEIKYGTVSSIP--YSDNTFDLV 117
                                       56779***************.9**********************444444444788888*******..********* PP

                   Methyltransf_31  79 lsnevlnaladpdkileeiervlkpggilliedpr 113
                                       +++e+ +  +d+++ l+ei rvlkp+g+lli +  
  gi|298674852|ref|YP_003726602.1| 118 TAFETYYFWPDLENDLKEIYRVLKPEGVLLIVNEV 152
                                       *****************************987766 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.2   0.0   1.2e-23     1e-20       1      97 []      48     144 ..      48     144 .. 0.93

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 1.2e-23
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHH..TTTTEEEEESBCCGBSSSTTTEEEEEEESTGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraee..eglnvefvqgdaedlpfedgsfDlvvssgalh 75 
                                       vLd+GcG G+ ++ la+ ++ +kv+g+D+seem+  a+e ++e  ++ +ve+  g ++++p+ d++fDlv+++ +  
  gi|298674852|ref|YP_003726602.1|  48 VLDVGCGGGKAIQILADFCPYGKVHGIDYSEEMVSMAQEVNNElvKNNHVEIKYGTVSSIPYSDNTFDLVTAF-ETY 123
                                       9****************9999*****************9998866556************************5.657 PP

                                       GSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  76 hlsdedlekalkeiarvLkpgG 97 
                                       +++ +dle+ lkei+rvLkp+G
  gi|298674852|ref|YP_003726602.1| 124 YFW-PDLENDLKEIYRVLKPEG 144
                                       787.79**************99 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   0.0   5.7e-18   4.6e-15      25     164 ..      47     192 ..      18     193 .. 0.77

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 5.7e-18
                   Methyltransf_23  25 rvLdiGcGtGillevlren.gf.svtgvDlspeaveiae........kakkaqkdqfdeq......eaaepqgkfdl 85 
                                        vLd+GcG G   ++l+++ ++ +v g+D s+e+v++a+        + +         +      ++++++++fdl
  gi|298674852|ref|YP_003726602.1|  47 LVLDVGCGGGKAIQILADFcPYgKVHGIDYSEEMVSMAQevnnelvkNNHVE-------IkygtvsSIPYSDNTFDL 116
                                       59**************9984559***************97666555533333.......13333338888******* PP

                   Methyltransf_23  86 IvlrevlehvpdppellrqiatllkpgGylllseplaslkedrllldwlylvpagrhisffsarslkelleeaGlev 162
                                       ++++e+ +  pd++  l+ i++ lkp+G+ll+       + +  +++  ++  +   +++++ ++ ke+l + G++ 
  gi|298674852|ref|YP_003726602.1| 117 VTAFETYYFWPDLENDLKEIYRVLKPEGVLLIVNE---VYKNGNFDERNMEYVNTLDMHYHNPKEHKEILVKTGFTS 190
                                       ***************************99988764...355555555555555534457788888888888888877 PP

                   Methyltransf_23 163 ve 164
                                       ve
  gi|298674852|ref|YP_003726602.1| 191 VE 192
                                       65 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.0   2.6e-17   2.1e-14      33     152 ..      31     149 ..      25     158 .. 0.86
   2 ?   -1.1   0.0       1.2     1e+03     197     218 ..     172     193 ..     157     198 .. 0.74

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 2.6e-17
                                       HHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TT CS
                   Ubie_methyltran  33 rlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqanae 108
                                       +lWk  +e+++   +   vlDv +G g  a++++      gkv+++D++e+m++++++  +e  k  ++e   +   
  gi|298674852|ref|YP_003726602.1|  31 DLWKWGLEHISI-NPDYLVLDVGCGGGK-AIQILADFCPYGKVHGIDYSEEMVSMAQEVNNELVKNnHVEIKYGTVS 105
                                       677776666554.456789******886.889999999******************99888877777899999**** PP

                                       T-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEE CS
                   Ubie_methyltran 109 eLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvl 152
                                        +p++d++fD+vt        +D ++ Lke+yrvlkp G l+++
  gi|298674852|ref|YP_003726602.1| 106 SIPYSDNTFDLVTAFETYYFWPDLENDLKEIYRVLKPEGVLLIV 149
                                       *************87788889******************99876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.2
                                       HS--HHHHHHHHHHTTEEEEEE CS
                   Ubie_methyltran 197 afPdqetlkeliedaGfksvey 218
                                       ++ + ++ ke++ + Gf+sve 
  gi|298674852|ref|YP_003726602.1| 172 HYHNPKEHKEILVKTGFTSVET 193
                                       5667788999999999999974 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.0   4.2e-17   3.4e-14       1      99 []      49     146 ..      49     146 .. 0.91

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 4.2e-17
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       L++GcG G  ++ l++  p  +++g+D+s++++  a+e  ++  +nn+ ++++ + +++  ++ ++fDlv+a+++  
  gi|298674852|ref|YP_003726602.1|  49 LDVGCGGGKAIQILADFCPYGKVHGIDYSEEMVSMAQEVNNELVKNNHVEIKYGTVSSIPYSD-NTFDLVTAFETYY 124
                                       8********************************999999999998888888888877665544.6************ PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgGrl 99 
                                        ++d++  l++i+++Lkp+G+l
  gi|298674852|ref|YP_003726602.1| 125 FWPDLENDLKEIYRVLKPEGVL 146
                                       ********************97 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   4.2e-08   3.4e-05      53     166 ..      35     150 ..      20     168 .. 0.79
   2 ?    1.0   0.0      0.25   2.1e+02     216     242 ..     159     185 ..     142     196 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 4.2e-08
                                       HHHTTTT--TT-EEEEES-TTSHHHHHHHH..HH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---- CS
                              CMAS  53 lileklelkpGmtlLdiGcGWGslvrrave..rydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldek 127
                                         le ++++p   +Ld+GcG G+ ++  ++   y  kv g+  S+e   +a+++ +el  +++ve+k+     ++  
  gi|298674852|ref|YP_003726602.1|  35 WGLEHISINPDYLVLDVGCGGGKAIQILADfcPY-GKVHGIDYSEEMVSMAQEVNNELVKNNHVEIKYGTVSSIPYS 110
                                       568899999999**********999887762235.49*******************************999999875 PP

                                       -SEEEEES-GGGTS.GGGHHHHHHHHHHHS-TT-EEEEEE CS
                              CMAS 128 vdrvvsvgafehvg.kenydtffkklkkllkedGllllht 166
                                        +    v afe       +++  k+++++lk++G+ll+  
  gi|298674852|ref|YP_003726602.1| 111 DNTFDLVTAFETYYfWPDLENDLKEIYRVLKPEGVLLIVN 150
                                       4555555556655314678888999*********999754 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.25
                                       EE-HHHHHHHHHHHHHHHHHTHHHHHH CS
                              CMAS 216 eslrahYakTLkaWaealqenkdeaia 242
                                       ++ +++Y++TL++ +++ +e+k+ +++
  gi|298674852|ref|YP_003726602.1| 159 DERNMEYVNTLDMHYHNPKEHKEILVK 185
                                       445678888888888888888876665 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   7.2e-08   5.8e-05      61     209 ..      43     188 ..      17     189 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 7.2e-08
                                       GG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-H.HHHHHHHHHS.-----TTEEEEES-TTTS-----S....EE CS
                    Methyltransf_2  61 eglkslvDvGGGtGalakaivsayPtikvivfDlp.eVveaAkehl.sageeervefvgGdffkdslPeaD....ai 131
                                       ++   ++DvG G G +++  +   P  kv   D + e v+ A+e   +  ++++ve   G +   s+P +D    ++
  gi|298674852|ref|YP_003726602.1|  43 NPDYLVLDVGCGGGKAIQILADFCPYGKVHGIDYSeEMVSMAQEVNnELVKNNHVEIKYGTVS--SIPYSDntfdLV 117
                                       5556789**************************973589999988777889999******998..9**776211145 PP

                                       EEESSGGGS-HHHHHHHHHHHHHH--TT-EEEEEE----TTS---HHHHHH.HHHHHHCSS-----HHHHHHHHHHC CS
                    Methyltransf_2 132 llkrvlhDwsdekcvklLkrvkkalpagGkvivveavlgadpsgeletelv.dlimlvqteGkeRteaeyeellsea 207
                                             + w d    + Lk++++ l+++G +++v+ v ++++ +e + e v  l m         +++e++e+l + 
  gi|298674852|ref|YP_003726602.1| 118 TAFETYYFWPD--LENDLKEIYRVLKPEGVLLIVNEVYKNGNFDERNMEYVnTLDMHY------HNPKEHKEILVKT 186
                                       55556677776..5677********************999998888877753444444......4677777777777 PP

                                       T- CS
                    Methyltransf_2 208 Gf 209
                                       Gf
  gi|298674852|ref|YP_003726602.1| 187 GF 188
                                       77 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   7.3e-07    0.0006      66     125 ..      37      94 ..      21     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 7.3e-07
                                       HHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCS CS
                              PCMT  66 lellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlen 125
                                       le++++++   vL+vG+G G    +la +  + g+v +i++++e+v+ a++  +++ ++n
  gi|298674852|ref|YP_003726602.1|  37 LEHISINPDYLVLDVGCGGGKAIQILADFC-PYGKVHGIDYSEEMVSMAQEV-NNELVKN 94 
                                       78899*****************99999975.7899***********999764.4433333 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   4.6e-06    0.0038      25      86 ..      38     101 ..      36     119 .. 0.70
   2 ?    0.3   0.0      0.55   4.4e+02     126     140 ..     137     151 ..     130     175 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.6e-06
                                       HHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHH....HHHTTGCEEEEE CS
                               MTS  25 etlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesaken....leanklevevva 86 
                                       e+++ + +  vlD+GcG G     la+++p  +v+ +d + + + +a+e     +++n+  ve+  
  gi|298674852|ref|YP_003726602.1|  38 EHISINPDYLVLDVGCGGGKAIQILADFCPYGKVHGIDYSEEMVSMAQEVnnelVKNNH--VEIKY 101
                                       56666667779******************************999999874111133333..33333 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.55
                                       HHHEEEEEEEEEEEE CS
                               MTS 126 keaLkegGeLliVan 140
                                        ++Lk++G LliV +
  gi|298674852|ref|YP_003726602.1| 137 YRVLKPEGVLLIVNE 151
                                       579********9965 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   5.9e-06    0.0048     107     161 ..      98     154 ..      37     206 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.9e-06
                                       TEEES-TTS-S--TT-EEEEE.EES---SS-HHHHHHHHHHHEEEEEEE.EEEEEGG CS
                    Methyltransf_8 107 rvvacdlakvPledesvdvav.fclslmgtnladflkeanrvlkvGGll.kvaevks 161
                                       ++    ++ +P  d++ d++  f       +l++ lke++rvlk+ G+l  v ev  
  gi|298674852|ref|YP_003726602.1|  98 EIKYGTVSSIPYSDNTFDLVTaFETYYFWPDLENDLKEIYRVLKPEGVLlIVNEVYK 154
                                       233456799*********775266778899**************9887615667754 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.8e-06    0.0015      25      92 ..      44     107 ..      36     188 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.8e-06
                   Methyltransf_32  25 galtvvDvGaGkgYLsfvlalkeke.yklkvvgidakeelvekaekraeklgkkfnkrlsfaelsieea 92 
                                       ++  v+DvG+G g   ++la+        kv+gid +ee+v+ a++++++l    n++++ + ++++++
  gi|298674852|ref|YP_003726602.1|  44 PDYLVLDVGCGGGKAIQILAD---FcPYGKVHGIDYSEEMVSMAQEVNNELV--KNNHVEIKYGTVSSI 107
                                       567799***************...44678**********************9..556777776666655 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.1e-06    0.0017     102     220 ..      33     151 ..      13     198 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.1e-06
                                       HHHHHHGGGS.--TT-EEEEET-TTSHHHHHHHHCT-.SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS CS
                    Methyltransf_9 102 wkWdrvlphlsdlkgrtildvGcgnGyhlwrmvgega.klvvGidPselfliqfeavrkllgedqrahllplgieql 177
                                       wkW   l+h+s   +  +ldvGcg G  +  ++   +   v Gid se  +   + v++ l +++++     ++  +
  gi|298674852|ref|YP_003726602.1|  33 WKW--GLEHISINPDYLVLDVGCGGGKAIQILADFCPyGKVHGIDYSEEMVSMAQEVNNELVKNNHVEIKYGTVSSI 107
                                       555..589****************998765555444425799*****99998888887766555555544467999* PP

                                       -T.---EEEEEEES-GGG-S-HHHHHHHHHCTEEEEEEEEEEEE CS
                    Methyltransf_9 178 pe.leafdtvfsmGvlyhrrsPldhllqlkdqlvkgGelvletl 220
                                       p   ++fd v +    y      + l ++   l+ +G l++   
  gi|298674852|ref|YP_003726602.1| 108 PYsDNTFDLVTAFETYYFWPDLENDLKEIYRVLKPEGVLLIVNE 151
                                       996789*******9999998888899999999999998866544 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   5.5e-06    0.0045      11      98 ..      42     136 ..      37     148 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.5e-06
                              MetW  11 ikpgsrvldlGcGdGellellkeekqv.dgrGleldeegvaecvakGlsvi...qgdldkdlen...fedksfdyvv 80 
                                       i+p   vld+GcG G+ +++l++     + +G++ +ee v  + +   +++   + ++  +      ++d++fd+v 
  gi|298674852|ref|YP_003726602.1|  42 INPDYLVLDVGCGGGKAIQILADFCPYgKVHGIDYSEEMVSMAQEVNNELVknnHVEIKYGTVSsipYSDNTFDLVT 118
                                       778889****************9765426789999999997665444333300033444443323448899999987 PP

                              MetW  81 lsqtlqatrnpkevldel 98 
                                          t     + ++ l+e+
  gi|298674852|ref|YP_003726602.1| 119 AFETYYFWPDLENDLKEI 136
                                       766665555555555555 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00012       0.1       4      52 ..      47      94 ..      44     104 .. 0.84
   2 ?    2.4   0.1      0.12        97     100     131 ..     133     167 ..     130     206 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                                      EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSS CS
                    Methyltransf_4  4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkN 52
                                      +vl++GcG G+++  lA   P  ++ Gi+ ++++v  + + ++++ +kN
  gi|298674852|ref|YP_003726602.1| 47 LVLDVGCGGGKAIQILADFCPYGKVHGIDYSEEMVSMAQE-VNNELVKN 94
                                      79*****************************999987655.55554555 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.12
                                       HHHHHHHEEEEEEEEEEES...HHHHHHHHHHHHH CS
                    Methyltransf_4 100 lkelarvLkkgGvlelaTD...veeyaeemlkvle 131
                                       lke+ rvLk++Gvl ++       ++ e+ ++ ++
  gi|298674852|ref|YP_003726602.1| 133 LKEIYRVLKPEGVLLIVNEvykNGNFDERNMEYVN 167
                                       7899999*****99999883332234443333333 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0     2e-05     0.016     159     232 ..      42     119 ..      35     149 .. 0.69
   2 ?   -1.5   0.0       1.6   1.3e+03     275     295 ..     186     208 ..     174     209 .] 0.65

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2e-05
                              PrmA 159 vkegeevlDvGtGSG.iLaiaaakLgakkvvavDiDevAvkvake.Nael...Nkveaklevalseell.keekadv 229
                                       ++++  vlDvG+G G  + i a      kv+++D+ e  v++a+e N el   N+ve k    + ++++ +++++d+
  gi|298674852|ref|YP_003726602.1|  42 INPDYLVLDVGCGGGkAIQILADFCPYGKVHGIDYSEEMVSMAQEvNNELvknNHVEIKY--GTVSSIPySDNTFDL 116
                                       566778*******99668999999*****************9997444331114444333..233444433688888 PP

                              PrmA 230 iva 232
                                       + a
  gi|298674852|ref|YP_003726602.1| 117 VTA 119
                                       877 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.6
                              PrmA 275 qgfeleevle..reeWvaivakk 295
                                        gf+ +e+ +  +++W++i+akk
  gi|298674852|ref|YP_003726602.1| 186 TGFTSVETYTkpENNWITIIAKK 208
                                       46666555431267899999887 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   1.6e-05     0.013       4      60 ..      48     106 ..      46     129 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.6e-05
                   Methyltransf_15   4 ilDlfsGaGGnviqfalv...fekviaieinleklacaqh.NaevYgvsdkitlvlgdvfe 60 
                                       +lD+ +G GG++iq+      + kv++i++++e + +aq+ N e+   ++++ +++g v +
  gi|298674852|ref|YP_003726602.1|  48 VLDVGCG-GGKAIQILADfcpYGKVHGIDYSEEMVSMAQEvNNELV-KNNHVEIKYGTVSS 106
                                       8999998.5677776666367789***********99997344443.58888888887766 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   4.3e-05     0.035      29      92 ..      31      94 ..      22     181 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.3e-05
                                      HHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHHHHHHHHHHHH CS
                              DOT1 29 eflsevldkvnlkkedvFvDLGSGvGnvvlqaalevgcklsvGvEimdnaselaekqkeelkkr 92
                                      ++ +  l+++ ++++ + +D G G G+ +   a  +   +  G++ +++  ++a++ ++el k 
  gi|298674852|ref|YP_003726602.1| 31 DLWKWGLEHISINPDYLVLDVGCGGGKAIQILADFCPYGKVHGIDYSEEMVSMAQEVNNELVKN 94
                                      555566899**********************************************999988664 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.1e-05     0.017      47     143 ..      48     147 ..      17     155 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.1e-05
                              NodS  47 alevGcaaGalterlapyck..rltvvdvveeaiararervke...sshiswivsdvqqfs.tdekfdlivvaevly 117
                                       +l+vGc  G   + la +c   ++  +d  ee ++ a+e  +e    +h+      v  +  +d+ fdl+   e  y
  gi|298674852|ref|YP_003726602.1|  48 VLDVGCGGGKAIQILADFCPygKVHGIDYSEEMVSMAQEVNNElvkNNHVEIKYGTVSSIPySDNTFDLVTAFETYY 124
                                       89*****************72256669999998888887655411147777777788877536899*********99 PP

                              NodS 118 yiedvaelraavrnlvsllapdgqlv 143
                                       +  d++     ++++ ++l+p+g l+
  gi|298674852|ref|YP_003726602.1| 125 FWPDLE---NDLKEIYRVLKPEGVLL 147
                                       998865...68999999999999876 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   9.5e-05     0.078      62     109 ..      36      82 ..      31      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.5e-05
                                       T-S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHH CS
                       Fibrillarin  62 glkelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlr 109
                                       gl+++ i+++  vL +G + G+++  ++D +   g+v+++++s+ ++ 
  gi|298674852|ref|YP_003726602.1|  36 GLEHISINPDYLVLDVGCGGGKAIQILADFCP-YGKVHGIDYSEEMVS 82 
                                       899***************************98.9*********97764 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.1   1.7e+03     188     229 ..      41      84 ..      37      86 .. 0.63
   2 ?    9.8   0.4   0.00073      0.59      26      56 ..     118     150 ..     101     209 .] 0.70

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.1
                                       HS-TT-EEEETT-TTTHHHHHHHHT..T-EEEEEESSHHHHHHH CS
                       N6_N4_Mtase 188 stkkgdivlDpFaGSGtTavaakel..grkfiGieieeeyvela 229
                                       s +++ +vlD  +G G  +++ +      k  Gi+++ee v +a
  gi|298674852|ref|YP_003726602.1|  41 SINPDYLVLDVGCGGGKAIQILADFcpYGKVHGIDYSEEMVSMA 84 
                                       66778888888888777666655441124566777777777666 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00073
                                       CHHHHHHHH..HHHHHHHHHHHEEEEEEEEEEE CS
                       N6_N4_Mtase  26 dsyeeylef..lekvlkevrrvLkddgsifini 56 
                                         +e+y  +  le+ lke++rvLk+ g+++i  
  gi|298674852|ref|YP_003726602.1| 118 TAFETYYFWpdLENDLKEIYRVLKPEGVLLIVN 150
                                       445555555559999**************9973 PP

>> Bin3  Bicoid-interacting protein 3 (Bin3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00015      0.12      22      94 ..     129     199 ..     127     207 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00015
                              Bin3  22 lkrlfkkiyellkpgGvlilEpqewksYkkkkklseelkenykelkl...rpedfeevLleevgfesveeleekee 94 
                                       l + +k+iy++lkp+Gvl++  + +k+ +     +e+  e +++l +   +p++ +e+L + +gf+sve+ ++ e+
  gi|298674852|ref|YP_003726602.1| 129 LENDLKEIYRVLKPEGVLLIVNEVYKNGN----FDERNMEYVNTLDMhyhNPKEHKEILVK-TGFTSVETYTKPEN 199
                                       556689***********988654443332....2333333344444400156688888888.*******9996654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1328.64
//
Query:       gi|298674853|ref|YP_003726603.1|  [L=278]
Description: rhodanese domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-20   74.2   0.0    2.2e-20   73.2   0.0    1.6  1  Rhodanese     Rhodanese-like domain
    1.6e-10   41.5   7.3    4.9e-05   23.7   1.5    2.5  2  Rubrerythrin  Rubrerythrin
    1.3e-09   38.4   1.6    3.7e-05   23.9   0.3    2.2  2  Ferritin_2    Ferritin-like domain
     0.0038   17.6   4.4     0.0083   16.5   0.6    2.5  3  DUF2383       Domain of unknown function (DUF2383)
  ------ inclusion threshold ------
      0.022   14.7   6.2        0.3   11.0   6.2    2.4  1  Ferritin      Ferritin-like domain
      0.023   14.5   2.3        0.4   10.5   0.0    2.2  2  Exo84_C       Exocyst component 84 C-terminal


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.2   0.0   7.4e-24   2.2e-20       1     105 [.      14     106 ..      14     108 .. 0.91

  Alignments for each domain:
  == domain 1  score: 73.2 bits;  conditional E-value: 7.4e-24
                         Rhodanese   1 sakelkellekgkva...llDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycd 74 
                                       s+++lk++l++++     l+DvR+peeYe++hIpg+  v             pl+el +++ el  d++k +++yc+
  gi|298674853|ref|YP_003726603.1|  14 SPEKLKQMLDNDREGiniLVDVRQPEEYEQSHIPGSKLV-------------PLDELDARYDEL--DKNKNIITYCR 75 
                                       689******55543459**********************.............************..*********** PP

                         Rhodanese  75 gggraaaaaallkklGyknvsvldGGfkawk 105
                                        g r+  aa+ l  lG++nv+ +dGG+ +w+
  gi|298674853|ref|YP_003726603.1|  76 AGRRSLGAATYLCNLGFQNVYTMDGGILEWN 106
                                       ****8888777777****************7 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   2.4e-07   0.00071      68     134 ..     110     176 ..     101     179 .. 0.93
   2 !   23.7   1.5   1.6e-08   4.9e-05       1      55 [.     224     276 ..     224     277 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.4e-07
                                       BS-------TTGGHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  68 vreyaeakpkflttaknLeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlr 134
                                         +y e kp+f+t ++++++++  a + e+ +  fy +++++e  ++++++++kl++ E  H +rl 
  gi|298674853|ref|YP_003726603.1| 110 LSGYPEEKPEFITGNEQIKDILLTALKLEKGAQDFYLRAKNNEISSNIRQTLDKLSQFEDAHMNRLY 176
                                       568999********************************************************99985 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 1.6e-08
                                       HHHHHHHHHHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin   1 eiLekAiagEssarrlYkelaekakegypqiaelFeelAeeEreHakilnkllek 55 
                                       ++Le+Ai  E+  + +Yk +ae +    +++++l++elA eE+ H   l + l+k
  gi|298674853|ref|YP_003726603.1| 224 DVLETAIEKEYLSFDFYKRMAEIMS--DKNTRKLLHELASEEKNHITYLTNNLKK 276
                                       68999******************99..56669************99888776665 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.1   1.9e-05     0.056       4      58 ..     129     176 ..     126     219 .. 0.87
   2 !   23.9   0.3   1.2e-08   3.7e-05       2      61 ..     222     274 ..     221     277 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.9e-05
                        Ferritin_2   4 diLnfAlnlEyleaafYtaalegaslddkalldaevrevaeeiakheeaHveflk 58 
                                       diL  Al lE  +++fY +a +       + +++++r+ + ++ + e aH++ l 
  gi|298674853|ref|YP_003726603.1| 129 DILLTALKLEKGAQDFYLRAKN-------NEISSNIRQTLDKLSQFEDAHMNRLY 176
                                       89*****************997.......7899*****************98775 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 1.2e-08
                        Ferritin_2   2 dvdiLnfAlnlEyleaafYtaalegaslddkalldaevrevaeeiakheeaHveflkaal 61 
                                       ++d+L+ A+  Eyl  +fY++++e         +d+++r+++ e+a++e++H+++l++ l
  gi|298674853|ref|YP_003726603.1| 222 EIDVLETAIEKEYLSFDFYKRMAE-------IMSDKNTRKLLHELASEEKNHITYLTNNL 274
                                       79*********************9.......789***********************988 PP

>> DUF2383  Domain of unknown function (DUF2383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.2       0.1     3e+02       9      50 ..     134     175 ..     126     186 .. 0.79
   2 ?   -0.0   0.1      0.37   1.1e+03      27      53 ..     167     193 ..     151     205 .. 0.79
   3 !   16.5   0.6   2.8e-06    0.0083       2      55 ..     222     275 ..     221     277 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.1
                                       HHHHHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHH CS
                           DUF2383   9 LietlkdgeegykeaaekvkdpqlktlleriaeereeaaeeL 50 
                                        ++ +k ++++y +a+ +  +++++++l++ ++   +++ +L
  gi|298674853|ref|YP_003726603.1| 134 ALKLEKGAQDFYLRAKNNEISSNIRQTLDKLSQFEDAHMNRL 175
                                       577889999999999999999999999998888777766666 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.37
                                       --SHHHHHHHHHHHHHHHHHHHHHHHH CS
                           DUF2383  27 vkdpqlktlleriaeereeaaeeLqse 53 
                                        +d++++ l++r+a+  ee + eL+  
  gi|298674853|ref|YP_003726603.1| 167 FEDAHMNRLYRRYANTVEEDIPELEVL 193
                                       678888899999999999988888765 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 2.8e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           DUF2383   2 vieaLndLietlkdgeegykeaaekvkdpqlktlleriaeereeaaeeLqseir 55 
                                        i+ L++ ie+++ + ++yk++ae   d++ ++ll + a e +++++ L + ++
  gi|298674853|ref|YP_003726603.1| 222 EIDVLETAIEKEYLSFDFYKRMAEIMSDKNTRKLLHELASEEKNHITYLTNNLK 275
                                       6899*******************************************9998776 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   6.2    0.0001       0.3      71     139 ..     199     277 ..     124     277 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0001
                                       H.............C-SSSSCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin  71 e.............ieapkefgsveevleaalehekkvteslrelielaeeegDpatadfledfleeqeehewelea 134
                                                     ++++++f++  +vle a+e e+   + +++++e+     D  t+ +l ++  e+  h+  l +
  gi|298674853|ref|YP_003726603.1| 199 FeymeggiklskelLKSDEKFKDEIDVLETAIEKEYLSFDFYKRMAEIMS---DKNTRKLLHELASEEKNHITYLTN 272
                                       0444455555556555556699**************************99...66********************99 PP

                                       HHHHH CS
                          Ferritin 135 llekl 139
                                        l+k+
  gi|298674853|ref|YP_003726603.1| 273 NLKKI 277
                                       99875 PP

>> Exo84_C  Exocyst component 84 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00013       0.4      85     113 ..     131     159 ..     108     167 .. 0.86
   2 ?    3.2   1.0     0.023        68       3      87 ..     183     271 ..     181     277 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00013
                           Exo84_C  85 lLirLgledkArelfLenrsnliqkrirq 113
                                       lL+ L le+ A + +L +++n i++ irq
  gi|298674853|ref|YP_003726603.1| 131 LLTALKLEKGAQDFYLRAKNNEISSNIRQ 159
                                       599*************************9 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.023
                           Exo84_C   3 vedlldeldieiarrkFeeAVdlleklesklkklskklkd.....eeavlqdlislkveqrreelasklsrellskn 74 
                                       ve+ + el++    ++Fe     ++  +++l k  +k kd     e a+ ++ +s+   +r++e++s+ +++ l ++
  gi|298674853|ref|YP_003726603.1| 183 VEEDIPELEVLKKELDFEYMEGGIKL-SKELLKSDEKFKDeidvlETAIEKEYLSFDFYKRMAEIMSDKNTRKLLHE 258
                                       78888888888888888887777754.4444444444443233347788999999********99998887777777 PP

                           Exo84_C  75 evkklksnvslLi 87 
                                         ++ k++++ L+
  gi|298674853|ref|YP_003726603.1| 259 LASEEKNHITYLT 271
                                       6666777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       956  (0.0533214); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1883.90
//
Query:       gi|298674854|ref|YP_003726604.1|  [L=454]
Description: rhodanese domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.8e-25   88.9   0.1    8.2e-14   52.0   0.1    3.1  3  Rhodanese    Rhodanese-like domain
    3.2e-09   37.1   0.5    1.1e-07   32.1   0.5    2.6  1  Lactamase_B  Metallo-beta-lactamase superfamily


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.27   2.4e+03      44      78 ..     149     183 ..     142     196 .. 0.75
   2 !   33.1   0.0   7.1e-12   6.4e-08       2     106 ..     255     345 ..     254     346 .. 0.85
   3 !   52.0   0.1   9.2e-18   8.2e-14       3     106 ..     359     447 ..     357     448 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.27
                         Rhodanese  44 akkseapllelpeellelgidnkktvvvycdgggr 78 
                                       ++  ++  ++++e++ e+ +  +++v++  ++g++
  gi|298674854|ref|YP_003726604.1| 149 PDDAPRLADNMYESIFEKIVPLGDHVILCPAHGSG 183
                                       55556666677777777767779*****9999988 PP

  == domain 2  score: 33.1 bits;  conditional E-value: 7.1e-12
                         Rhodanese   2 akelkellekgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggr 78 
                                       ++e+++ +++g+  +lD+R+p+ ++ +hI+ + n+             +    ++ ++     +kk+v ++ +++++
  gi|298674854|ref|YP_003726604.1| 255 PHEFRKQIHNGA-LILDTREPVSFAGCHIKDSYNI-----------WLDGVPSYAGWILS---YKKPVLLVMEEKKH 316
                                       578889998887.5*********************...........77777777777775...8************* PP

                         Rhodanese  79 aaaa.aallkklGykn.vsvldGGfkawke 106
                                          +  +ll+ lG+ n   +l+GG+++w++
  gi|298674854|ref|YP_003726604.1| 317 LDTVlRYLLR-LGFDNiAGYLRGGIESWYN 345
                                       5555255666.*****************97 PP

  == domain 3  score: 52.0 bits;  conditional E-value: 9.2e-18
                         Rhodanese   3 kelkellekgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggra 79 
                                       ++l+e +++++  +lDvR  +e++ ghI+ Av++                el  ++ e    + k++ v+c+ g+ra
  gi|298674854|ref|YP_003726604.1| 359 HKLREEIKNNNLNVLDVRRNDEWNSGHIKSAVHI-------------YVGELENRIDEV--PDSKPIAVVCNVGKRA 420
                                       5788899888888*********************.............899999999998..99*************8 PP

                         Rhodanese  80 aaaaallkklGyknvsvldGGfkawke 106
                                       + a+ +lkk G+ +v+++ G+++aw++
  gi|298674854|ref|YP_003726604.1| 421 SLATSILKKNGFDDVYNVMGSMTAWNN 447
                                       88899******989***********97 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.5   1.2e-11   1.1e-07       5     197 .]      12     180 ..       9     180 .. 0.80

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 1.2e-11
                                       SSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHC CS
                       Lactamase_B   5 pvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapa 81 
                                        + sy+i  ++++i+iD+  + +   +      +  +  ++++++ TH   D + g  +l++ t++ +++ +  +++
  gi|298674854|ref|YP_003726604.1|  12 AHLSYFIGSENEAIVIDPRRDCRIYTEI-----AFEQNMNIRYIFETHRNEDYVIGSVELANLTGAEIYHGKYLDFK 83 
                                       5679***********************8.....89****************************************** PP

                                       CHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCC......EEEECTTT CS
                       Lactamase_B  82 lfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggk......vlftGDal 152
                                       + +  +                        ++ ++ +g +   ++++pgh+  ++++ + + +      ++ftGD+l
  gi|298674854|ref|YP_003726604.1|  84 YGNSVE------------------------DGSEFYFGSLKITAIHTPGHTDESVSYLLSDTDtgkekiMVFTGDTL 136
                                       **9999........................5566666666666666666666666664444332222338******* PP

                                       SSHHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEE.SS CS
                       Lactamase_B 153 lagetgridltlrgaevrdpsdaekyldsllklaglkaevlvp.gH 197
                                       ++g+tgr+dl + + ++r ++   +++  ++k++ l + v+++ +H
  gi|298674854|ref|YP_003726604.1| 137 FVGDTGRTDLYGPDDAPRLADNMYESI--FEKIVPLGDHVILCpAH 180
                                       **********66666666666666655..99999999999888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 3200.37
//
Query:       gi|298674855|ref|YP_003726605.1|  [L=75]
Description: hypothetical protein Metev_0913 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.01   15.8   0.0      0.011   15.6   0.0    1.0  1  SLATT_1   SMODS and SLOG-associating 2TM effector domain 1
      0.032   14.0   2.7      0.036   13.9   2.7    1.2  1  DUF443    Protein of unknown function (DUF443)
       0.21   11.8   1.1       0.35   11.0   1.1    1.4  1  DUF872    Eukaryotic protein of unknown function (DUF872)


Domain annotation for each model (and alignments):
>> SLATT_1  SMODS and SLOG-associating 2TM effector domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.0   1.9e-06     0.011      15      74 ..      13      73 ..       6      75 .] 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.9e-06
                           SLATT_1 15 kkaeeneraakrwrlllillellalllaalrafgelsv.dlvgvlaavaaallaWlelkqy 74
                                      +k++e  r++k+++l+ i++  ++l+l++l   + ++   ++g+++ + +a++++++ ++ 
  gi|298674855|ref|YP_003726605.1| 13 QKSSEIIRRNKKINLINIAVISIGLILMLLDYRNIAEHfIWLGFIIFLYTAGTTFIARREA 73
                                      68888999***********************55555557****************998776 PP

>> DUF443  Protein of unknown function (DUF443)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   2.7     6e-06     0.036     154     196 ..      29      71 ..       4      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6e-06
                            DUF443 154 fflglvilalvalietqniiilivlllllfllfllnvltisdg 196
                                        +++++i ++++l++++ni  ++++l+++++l ++  ++i  +
  gi|298674855|ref|YP_003726605.1|  29 NIAVISIGLILMLLDYRNIAEHFIWLGFIIFLYTAGTTFIARR 71 
                                       567899999********************99999998888765 PP

>> DUF872  Eukaryotic protein of unknown function (DUF872)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.1   5.9e-05      0.35      33      79 ..      13      59 ..       2      70 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.9e-05
                            DUF872 33 wlkhPkvkknrkvvlaallLlllGlvLlllgvvilvepseGvssavf 79
                                        ++  +++n+k  l  ++++ +Gl+L+ll +   +e+       +f
  gi|298674855|ref|YP_003726605.1| 13 QKSSEIIRRNKKINLINIAVISIGLILMLLDYRNIAEHFIWLGFIIF 59
                                      5566789***********************99888877655555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1089  (0.0607396); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 533.14
//
Query:       gi|298674856|ref|YP_003726606.1|  [L=358]
Description: Sua5/YciO/YrdC/YwlC family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.2e-55  185.3   0.0    1.2e-54  184.5   0.0    1.4  1  Sua5_yciO_yrdC  Telomere recombination
    4.8e-29  101.6   0.0    7.1e-29  101.1   0.0    1.3  1  SUA5            Putative GTP-binding controlling metal-bindin


Domain annotation for each model (and alignments):
>> Sua5_yciO_yrdC  Telomere recombination
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.5   0.0   1.4e-58   1.2e-54       2     179 .]      25     200 ..      24     200 .. 0.98

  Alignments for each domain:
  == domain 1  score: 184.5 bits;  conditional E-value: 1.4e-58
                                       HHHTTSEEEEE-SSSEEEEEETTSHHHHHHHHHHHTSHCCC--EEEESSCCCCCCCC-TC--HHHHHHHHCT-SSSC CS
                    Sua5_yciO_yrdC   2 alrkGgivaiptetvYgLacdatneeaverlreiKgrpsdkplavlvasledlkklaeseveeealkllerfwPGpi 78 
                                       +l++ g va+ptetvYgL+++a ++ +v++++ +Kgrp d+pl+v++as e++ ++ e +++++a+ l+++fwPGp+
  gi|298674856|ref|YP_003726606.1|  25 ILKNRGTVAFPTETVYGLGANALDSVSVRKIFSAKGRPPDNPLIVHIASKEQAIDISE-DIPDNAFLLMDAFWPGPL 100
                                       789999***************************************************9.****************** PP

                                       EEEEE..E-TS-HHHHTTTTEEEEEE-SSHHHHHHHHHCTS-EEEEES-STTS-S-SSHHHHHHHC-TTSECB-SS- CS
                    Sua5_yciO_yrdC  79 tlllkrskeklpkevapglktvGvrlPdtplarlLlealgeplvaTSanlsgepsitdaeeveeelgeivdlildgg 155
                                       tl+lkr k+ +p++ ++gl+tv++r+Pd+++a +L++++g p++a+San+sg+ps+t+ae+v ++l +++d+i+d+g
  gi|298674856|ref|YP_003726606.1| 101 TLILKR-KNFVPDVTTGGLNTVAIRMPDNETAIELIKKAGVPIAAPSANISGKPSPTTAEHVISDLYGKIDAIVDNG 176
                                       *****8.555******************************************************************* PP

                                       --SSS---EEEETTSSTSSECEXX CS
                    Sua5_yciO_yrdC 156 eiavgvdstVvdltegkpkilRrG 179
                                        + +gv+stVvd+t++kp +lR+G
  gi|298674856|ref|YP_003726606.1| 177 AVDIGVESTVVDMTSDKPLLLRPG 200
                                       **********************98 PP

>> SUA5  Putative GTP-binding controlling metal-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.1   0.0   7.9e-33   7.1e-29       3     133 ..     204     344 ..     202     345 .. 0.86

  Alignments for each domain:
  == domain 1  score: 101.1 bits;  conditional E-value: 7.9e-33
                                       HHHHHHHS...--...-......-------------S-SSEEEEE--GGGHHHH.....HHHHHTTS-EEEEEEGGG CS
                              SUA5   3 leeleevl...da...vek..keekpraPGmkyrHYaPkapvvlveaeeeeeaakeekleekkksgkkvgvlatses 71 
                                       +e+l+e +   ++   + +   ++k+++PGmky HY+P+ +vvlve+    +++ ++ +++++k++ +vg+l t+e+
  gi|298674856|ref|YP_003726606.1| 204 IEDLKEYIpdiEIgynS-EnlIDKKVKSPGMKYIHYSPSSKVVLVEGFYRVSEKINQVISDYHKNDLNVGLLVTNET 279
                                       67888887543112222.14678999***********************9999999******************999 PP

                                       TGG.TSEEEEE...E-TT-HHHHHHHHHHHHHHHHHS--SEEEEE.----STTHHHHHHHHHHHT CS
                              SUA5  72 kea.assvlsl.slgsrsdleeaarnLFaaLrelDeegvdlilve.gvpeeglglAvmnRLrkAA 133
                                        ++ +++++++  lg+r++ +++a+nLF++Lr+lD++++d+i+v+ ++++eg+g Av nRL+kAA
  gi|298674856|ref|YP_003726606.1| 280 GNQiTDKNINIfLLGNRDNIKKVANNLFKGLRTLDDMNLDVIIVDgSIKHEGIGSAVINRLQKAA 344
                                       99985555555459*********************99********666788*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2553.10
//
Query:       gi|298674857|ref|YP_003726607.1|  [L=426]
Description: ribulose bisphosphate carboxylase I [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.2e-101  339.9   0.6   1.5e-101  339.6   0.6    1.1  1  RuBisCO_large    Ribulose bisphosphate carboxylase large chai
    6.3e-44  149.0   0.0    1.8e-43  147.5   0.0    1.8  2  RuBisCO_large_N  Ribulose bisphosphate carboxylase large chai


Domain annotation for each model (and alignments):
>> RuBisCO_large  Ribulose bisphosphate carboxylase large chain, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  339.6   0.6  1.6e-105  1.5e-101       2     299 .]     131     425 ..     130     425 .. 0.97

  Alignments for each domain:
  == domain 1  score: 339.6 bits;  conditional E-value: 1.6e-105
                                       HHHHHHHH...T--EEEEE-SSSS---HHHHHHHHHHHHTT-.SEEE--TT-SSBTTB-HHHHHHHHHHHHHHHHHH CS
                     RuBisCO_large   2 iaverevlnkegrpilGtiiKPklGLspknyarvvyelllgglDfiKdDEnlnsqpfarlkdrieavaeaikraqde 78 
                                       +++ r++ ++++rp++Gti+KPk+GLs++++a+v+y+ + gg D++KdDEnl++q f+ + +r++  ++a ++a++e
  gi|298674857|ref|YP_003726607.1| 131 LNGVRDLFGVYDRPLVGTIVKPKVGLSSEKHADVAYKSFVGGCDIVKDDENLTNQKFNAFDKRVKITLDAKEKAEKE 207
                                       5678999********************************************************************** PP

                                       HSS--EEEEE---SSHHHHHHHHHHHHHHHGGEEEEEHHHH-HHHHHHHHHHSTTS..EEEEE-TTTHHHHST--SE CS
                     RuBisCO_large  79 tGekklyalnitaddleemlrraefvketggeivlvdvlviGfaaitslrkafrknelllHlHraghgaltrqskhG 155
                                       tGe+k+y +nita ++eemlrrae + ++gg+ v++d++++G++a++slr+a+++ ++++H+Hr +h+++tr+++hG
  gi|298674857|ref|YP_003726607.1| 208 TGERKMYLCNITAPTCEEMLRRAEVINDLGGKYVMIDIITAGWSALQSLREATEDMDIAIHAHRCMHSVMTRNPRHG 284
                                       ***************************************************************************** PP

                                       E-HHHHHHHHHHHT-SEEE---TTSSSBS--GG......GHHHHHHHHSSEEE-SS-EEE-TT----EEEEESS--T CS
                     RuBisCO_large 156 isfrvlakllRLlGvdhlhtgtvgvgklegdesvvkgfkdtlrekmleedeaegiffeqdlaslkavlpvasgGiha 232
                                       +++  lakl+RL+G d+lh+gtv vgk+ gd++ v + +d++  +++ ++ +   ++eqd++++k+++pvasgG+  
  gi|298674857|ref|YP_003726607.1| 285 VNMVALAKLTRLIGHDQLHIGTV-VGKMHGDKDEVLSLRDECALDYMPANDQ-LHILEQDWGNIKPMMPVASGGLEP 359
                                       ***********************.****************998877776654.4589******************** PP

                                       TTHHHHHHHHS---SEEE-HHHHHTSTT-HHHHHHHHHHHHHHHHHT--HHHHHTT-HHHHHHHHHX CS
                     RuBisCO_large 233 gqlpellenlgesdvilqaGGGilgHpdgaaaGakalrqaleaaveGadleeyAkehkeLarAlesw 299
                                       g +p+l++++g+ dvi+q+G Gi++Hp+g++aGa+a rq++eaa+e + leeyA +hkeL+ Ale+w
  gi|298674857|ref|YP_003726607.1| 360 GMIPDLYNMFGK-DVIMQFGAGIHAHPMGTEAGATACRQSVEAALENITLEEYASNHKELQSALEKW 425
                                       ************.*****************************************************9 PP

>> RuBisCO_large_N  Ribulose bisphosphate carboxylase large chain, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.5   0.0   2.1e-47   1.8e-43       1     119 [.       4     119 ..       4     120 .. 0.98
   2 ?   -2.6   0.0      0.65   5.8e+03      20      44 ..     150     173 ..     145     191 .. 0.65

  Alignments for each domain:
  == domain 1  score: 147.5 bits;  conditional E-value: 2.1e-47
                   RuBisCO_large_N   1 dyvdedyepketdllaafrvePaegvsveeaaaavAaeSStgtwtevsttkdellkklkakvyeieeveeekelvki 77 
                                       dy++++y+pk ++l++++++ePa+gvs+e+a++++A+eSS++tw+++st ++e++++lk++v++i++   e+ +vk+
  gi|298674857|ref|YP_003726607.1|   4 DYIETEYKPKPDELVCEYYMEPADGVSFEKACNHMAGESSIDTWSDISTLSPEKAQELKPHVFSIDK---ERGVVKV 77 
                                       69***************************************************************99...79***** PP

                   RuBisCO_large_N  78 AYplelFeegsipqllssiaGnifgmkavkalrleDirlPka 119
                                       AY+++lFe +s+pq+ls+iaGni++mk vk+lrleDi++Pk+
  gi|298674857|ref|YP_003726607.1|  78 AYKQDLFEIDSVPQILSAIAGNIMSMKLVKNLRLEDIAFPKD 119
                                       ****************************************85 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.65
                   RuBisCO_large_N  20 vePaegvsveeaaaavAaeSStgtw 44 
                                       v+P+ g+s e+ a  vA +S +g  
  gi|298674857|ref|YP_003726607.1| 150 VKPKVGLSSEKHA-DVAYKSFVGGC 173
                                       7888888887765.57777776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2910.79
//
Query:       gi|298674858|ref|YP_003726608.1|  [L=234]
Description: hypothetical protein Metev_0916 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-21   77.9   0.0    1.2e-21   77.6   0.0    1.1  1  Lactamase_B    Metallo-beta-lactamase superfamily
      2e-06   27.4   0.0    2.7e-06   27.1   0.0    1.2  1  Lactamase_B_2  Beta-lactamase superfamily domain
     0.0037   16.7   0.2      0.012   15.1   0.1    1.7  2  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
     0.0041   17.0   0.1      0.042   13.8   0.0    2.2  3  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.6   0.0   2.8e-25   1.2e-21       4     197 .]      14     211 ..      11     211 .. 0.84

  Alignments for each domain:
  == domain 1  score: 77.6 bits;  conditional E-value: 2.8e-25
                                       CSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHH CS
                       Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeap 80 
                                       +++n+yl+ g + ++L+D+G+ +    +  +l+ +gl+  d+d +i+TH+H+DH+G+l +++e+  + v a+  e  
  gi|298674858|ref|YP_003726608.1|  14 GNSNAYLVIGADITFLVDAGVYGHIHNLETILFNNGLDFQDIDLIIITHSHYDHVGNLCEIKEKSFARVLAHVNESG 90 
                                       689************************************************************************** PP

                                       CCHCHHHHHHHHHCCHH............TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEE.TTCC CS
                       Lactamase_B  81 alfmeeaddaasrkgll............lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvvey.gggk 144
                                        l++ ++    +  +                   + +p++++   dg+     +++v+   ++gh++g+++   + k
  gi|298674858|ref|YP_003726608.1|  91 FLKEGYMPIPKGTSPFSnviswmsnsfssS--KIRYNPVTPDILVDGDCELLTGGEVIILTAPGHTSGSICViVNNK 165
                                       *******6666555555**********554..55555555555555555555555555555555555555555899* PP

                                       EEEECTTTSSHHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 145 vlftGDallagetgridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                       ++++GD+l++  + ++ +       ++++d + ++++++kl     ++ +pgH
  gi|298674858|ref|YP_003726608.1| 166 YAIVGDTLFNVFENCFYP-------LFADDEKTLIKTWDKLLSTGCKIFYPGH 211
                                       *********999999888.......***************************9 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   5.9e-10   2.7e-06      25      65 ..      49      87 ..      27     127 .. 0.72

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 5.9e-10
                                      S--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHH CS
                     Lactamase_B_2 25 rdelppidaVllthaHyDHlaglltlrelrpkklplyapkg 65
                                        ++++id++++th+HyDH+ +l  ++e +   ++++a+  
  gi|298674858|ref|YP_003726608.1| 49 GLDFQDIDLIIITHSHYDHVGNLCEIKEKSF--ARVLAHVN 87
                                      45789***************99999999544..44666654 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   2.6e-06     0.012       6      53 ..      25      72 ..      20      86 .. 0.79
   2 ?   -1.9   0.0      0.41   1.8e+03      97     118 ..     211     232 ..     193     233 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.6e-06
                     Lactamase_B_6  6 nvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGaya 53
                                      ++++L+D G+ ++  +le++l +     +++dli+++h+  +h+G + 
  gi|298674858|ref|YP_003726608.1| 25 DITFLVDAGVYGHIHNLETILFNNGLDFQDIDLIIITHSHYDHVGNLC 72
                                      799********99888877777666678*****************753 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.41
                     Lactamase_B_6  97 dseeleledideafdkiktlkY 118
                                       + + + le+++e+f ki++l Y
  gi|298674858|ref|YP_003726608.1| 211 HGKPVLLENFNECFYKISKLYY 232
                                       4556789999999999999988 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   9.3e-06     0.042       7      50 ..      16      68 ..      11     126 .. 0.76
   2 ?   -3.6   0.0         2     9e+03       8      25 ..     136     153 ..     133     158 .. 0.76
   3 ?    0.8   0.0      0.09     4e+02     103     115 ..     201     213 ..     193     223 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.3e-06
                     Lactamase_B_3  7 hnsflletagarilvDPf........kanlgyeppa.........eeaDlvlisqaledHa 50
                                      +n++l+ +a+ + lvD +        +        +         +++Dl++i++++ dH 
  gi|298674858|ref|YP_003726608.1| 16 SNAYLVIGADITFLVDAGvyghihnlE--------TilfnngldfQDIDLIIITHSHYDHV 68
                                      688888888999999988444443331........13444555669**************6 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2
                     Lactamase_B_3   8 nsflletagarilvDPfk 25 
                                        + ll+++++ il+ P++
  gi|298674858|ref|YP_003726608.1| 136 DCELLTGGEVIILTAPGH 153
                                       577888889999998876 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.09
                     Lactamase_B_3 103 qdgltiyhlGhla 115
                                       ++g +i+++Gh+ 
  gi|298674858|ref|YP_003726608.1| 201 STGCKIFYPGHGK 213
                                       4799*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1709.59
//
Query:       gi|298674859|ref|YP_003726609.1|  [L=343]
Description: phosphoesterase PA-phosphatase-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.9e-10   40.8  21.8    1.2e-09   38.1  21.8    2.2  1  PAP2_3     PAP2 superfamily
    2.1e-10   40.5   1.8    2.1e-10   40.5   1.8    2.6  3  PAP2       PAP2 superfamily
  ------ inclusion threshold ------
      0.032   14.8   7.8      0.032   14.8   7.8    3.0  3  PAP2_C     PAP2 superfamily C-terminal
       0.12   12.4   1.3        0.2   11.7   1.3    1.2  1  Elf1       Transcription elongation factor Elf1 like
        7.4    6.7   5.9         46    4.1   2.0    2.9  3  P5-ATPase  P5-type ATPase cation transporter


Domain annotation for each model (and alignments):
>> PAP2_3  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1  21.8   3.4e-13   1.2e-09      25     188 ..     100     255 ..      87     257 .. 0.76

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 3.4e-13
                            PAP2_3  25 hpalavilalaYaslhf.qvtllvlvllflrrrerlreflttlllatllgllvyalfPaagPrlleeagfvdtvaaa 100
                                       +p l+++ + +Y + ++ ++++++++l+++r++++l+e+ ++++l+ ++++ ++++fP+    +        ++++ 
  gi|298674859|ref|YP_003726609.1| 100 TPLLTYVNSAIYLFGFPfLLVFTFFILVYTRKFRALQEYTIAFVLVYVIAYPFFVFFPVEVTGYT-------LHSVD 169
                                       57799999999998765155666777777******************************999444.......12222 PP

                            PAP2_3 101 slagalrdgasravllrgtienglaafPSlHvawallvalalwrlrrkrllrvlalllnvlmivatvatgnHYlvDv 177
                                        l  +l+   +  + l++   +   ++PSlH+a+++  +l+++   +  +++++ + +   ++++++++g H ++D+
  gi|298674859|ref|YP_003726609.1| 170 PLLYNLSPIIVEGIKLSDP--GLDNCLPSLHTALSITAMLIVVFRTNFIRFKMFSIGITTSILFTILYLGIHWMTDM 244
                                       2222333333444444444..44566*********998887443333336999************************ PP

                            PAP2_3 178 iaGvalalvai 188
                                       iaG++lal+a+
  gi|298674859|ref|YP_003726609.1| 245 IAGIVLALAAY 255
                                       ********998 PP

>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.2       1.4   5.2e+03      72      78 ..      17      23 ..       7      59 .. 0.51
   2 ?    0.0   2.4      0.19   6.6e+02      66      95 ..     119     157 ..     115     167 .. 0.67
   3 !   40.5   1.8   5.8e-14   2.1e-10      53     133 ..     191     264 ..     171     267 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.4
                              PAP2 72 alllrrk 78
                                      al+++  
  gi|298674859|ref|YP_003726609.1| 17 ALMIWAG 23
                                      3332222 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.19
                              PAP2  66 alalllalllrrkrkkig.........lvllalilllla 95 
                                       +++++++l+++rk++  +         +v+++ +++++ 
  gi|298674859|ref|YP_003726609.1| 119 LVFTFFILVYTRKFRALQeytiafvlvYVIAYPFFVFFP 157
                                       567788888888888877877666555555555555555 PP

  == domain 3  score: 40.5 bits;  conditional E-value: 5.8e-14
                              PAP2  53 kesfPSgHsafafalalllalllrrkrkkiglvllalillllavlvalsRlylgvHflsDvlaGlliGialaalayr 129
                                       ++++PS H+a + +++l++++  +  r+k       ++ +  ++ + ++ lylg+H+ +D +aG+++++a  +++++
  gi|298674859|ref|YP_003726609.1| 191 DNCLPSLHTALSITAMLIVVFRTNFIRFK-------MFSIGITTSILFTILYLGIHWMTDMIAGIVLALAAYFITTK 260
                                       5789****************999999999.......899999*****************************999998 PP

                              PAP2 130 lvqk 133
                                       ++++
  gi|298674859|ref|YP_003726609.1| 261 YRET 264
                                       8776 PP

>> PAP2_C  PAP2 superfamily C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.4       1.9   6.7e+03      26      26 ..      39      39 ..      10      63 .. 0.55
   2 ?    0.3   2.0       0.3   1.1e+03      14      65 ..     118     149 ..      94     158 .. 0.57
   3 ?   14.8   7.8   8.9e-06     0.032       8      71 ..     196     257 ..     192     261 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.9
                            PAP2_C 26 p 26
                                      +
  gi|298674859|ref|YP_003726609.1| 39 S 39
                                      2 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.3
                            PAP2_C  14 ltlavlfileyspkklailkvillllallglfliiasrkHYtvDVllglyit 65 
                                       l+++++fil y++k  a+ +                    Yt+  +l ++i+
  gi|298674859|ref|YP_003726609.1| 118 LLVFTFFILVYTRKFRALQE--------------------YTIAFVLVYVIA 149
                                       34444444444444443322....................333333333333 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 8.9e-06
                            PAP2_C   8 SGHtvvltlavlfileyspkklailkvillllallglfliiasrkHYtvDVllglyittlvfll 71 
                                       S Ht+  ++a+l+++  ++     +k++++ ++ ++lf i++   H+  D++ g++++ + +++
  gi|298674859|ref|YP_003726609.1| 196 SLHTALSITAMLIVVFRTNFIR--FKMFSIGITTSILFTILYLGIHWMTDMIAGIVLALAAYFI 257
                                       66*******************9..**********************************999865 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.3   5.6e-05       0.2      24      63 ..     291     330 ..     278     337 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.6e-05
                              Elf1  24 CpfCnheksvevkldkkekiaevsCkvCge..sfetkvnals 63 
                                       C +C  e  ++v+ ++++++++v+C +C +  ++++  + l+
  gi|298674859|ref|YP_003726609.1| 291 CINCACE--ISVNPSTSSSVGSVQCPYCDTvqEYHLLTHLLE 330
                                       99*****..*******************98334444455555 PP

>> P5-ATPase  P5-type ATPase cation transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.2     0.039   1.4e+02      14      35 ..      41      62 ..      37      63 .. 0.86
   2 ?   -2.1   0.0       1.1   3.9e+03       5      29 ..     158     182 ..     157     184 .. 0.82
   3 ?    4.1   2.0     0.013        46       5      39 ..     206     242 ..     203     250 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.039
                         P5-ATPase 14 rwrlalyilgciltlGlllLlf 35
                                      +  l++++l++il lG++++l+
  gi|298674859|ref|YP_003726609.1| 41 MHELLIVTLMYILPLGFIYVLV 62
                                      5578999************985 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.1
                         P5-ATPase   5 ieiaGyrtsrwrlalyilgciltlG 29 
                                       +e++Gy  + +  +ly l  i+  G
  gi|298674859|ref|YP_003726609.1| 158 VEVTGYTLHSVDPLLYNLSPIIVEG 182
                                       6899*****9999999987776555 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.013
                         P5-ATPase   5 ieiaGyrtsrwrlalyilgcilt..lGlllLlfrWlP 39 
                                       + i+ +rt+ +r+ ++++g+  +  + +l+L ++W+ 
  gi|298674859|ref|YP_003726609.1| 206 MLIVVFRTNFIRFKMFSIGITTSilFTILYLGIHWMT 242
                                       78999****99999999999876337999******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       984  (0.0548832); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.55
# Mc/sec: 1862.83
//
Query:       gi|298674860|ref|YP_003726610.1|  [L=115]
Description: monovalent cation/proton antiporter subunit MnhG/PhaG [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.6e-26   90.2  12.9    8.9e-26   89.9  12.9    1.1  1  PhaG_MnhG_YufB  Na+/H+ antiporter subunit
  ------ inclusion threshold ------
       0.44   10.5   2.9        2.1    8.4   0.1    2.1  2  DUF5345         Family of unknown function (DUF5345)


Domain annotation for each model (and alignments):
>> PhaG_MnhG_YufB  Na+/H+ antiporter subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.9  12.9   9.9e-30   8.9e-26       1      79 []      15      94 ..      15      94 .. 0.98

  Alignments for each domain:
  == domain 1  score: 89.9 bits;  conditional E-value: 9.9e-30
                    PhaG_MnhG_YufB  1 llllGalfvllgaigllrlpdvytRlhaatkadtlGlllillGlllrf.slaaslkllliilfllltaPvaahliaraa 78
                                      +l++G++fv+lg++gl+rlpdvy+Rlh++tk+ tlG++ ++l++ll++  +a+ lk++ i lfllltaPvaah+iaraa
  gi|298674860|ref|YP_003726610.1| 15 FLIVGLFFVFLGMLGLIRLPDVYNRLHTTTKIGTLGAFGVMLSILLKVgFSAMGLKAVTIGLFLLLTAPVAAHMIARAA 93
                                      79**********************************************99999*************************9 PP

                    PhaG_MnhG_YufB 79 y 79
                                      +
  gi|298674860|ref|YP_003726610.1| 94 H 94
                                      7 PP

>> DUF5345  Family of unknown function (DUF5345)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1   0.00024       2.1      43      67 ..      14      38 ..      12      46 .. 0.90
   2 ?    2.5   0.3     0.015   1.4e+02      43      65 ..      63      85 ..      61      93 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00024
                           DUF5345 43 lFlliAllilsllllalvqapalfi 67
                                      +Fl++ l+++ l++l l + p ++ 
  gi|298674860|ref|YP_003726610.1| 14 IFLIVGLFFVFLGMLGLIRLPDVYN 38
                                      8********************9995 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.015
                           DUF5345 43 lFlliAllilsllllalvqapal 65
                                       F  + l  ++++l++l++ap++
  gi|298674860|ref|YP_003726610.1| 63 GFSAMGLKAVTIGLFLLLTAPVA 85
                                      588888999************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 686.81
//
Query:       gi|298674861|ref|YP_003726611.1|  [L=88]
Description: multiple resistance and pH regulation protein F [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.5e-19   68.3   6.1    5.5e-19   68.3   6.1    2.0  2  MrpF_PhaF      Multiple resistance and pH regulation protein 
  ------ inclusion threshold ------
        1.5    8.8   5.1       0.84    9.6   1.2    1.9  2  DUF2393        Protein of unknown function (DUF2393)
        5.3    7.0   5.6        1.5    8.7   0.2    2.4  3  Deltameth_res  Deltamethrin resistance


Domain annotation for each model (and alignments):
>> MrpF_PhaF  Multiple resistance and pH regulation protein F (MrpF / PhaF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.3     0.076   4.5e+02       8      23 ..       2      17 ..       1      19 [. 0.69
   2 !   68.3   6.1   9.3e-23   5.5e-19       1      52 [.      31      82 ..      31      83 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.076
                         MrpF_PhaF  8 Dllgtllvallallai 23
                                      +++ +  v+ +++++i
  gi|298674861|ref|YP_003726611.1|  2 NTILFDFVLTFLVFSI 17
                                      6777777777777776 PP

  == domain 2  score: 68.3 bits;  conditional E-value: 9.3e-23
                         MrpF_PhaF  1 aDRvvAlDllgtllvallallailtgrpayldvalvlAllgFvgtvafarfl 52
                                      +DRvvAlD+++ ++va l+++++++++ +++dvalvl++++Fvgtv ++++l
  gi|298674861|ref|YP_003726611.1| 31 PDRVVALDAMTLVIVATLGVYSFIQESVFFMDVALVLSIIAFVGTVTISKYL 82
                                      8**************************************************9 PP

>> DUF2393  Protein of unknown function (DUF2393)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1     0.065   3.9e+02      19      38 ..       5      24 ..       2      39 .. 0.70
   2 ?    9.6   1.2   0.00014      0.84       2      44 ..      43      82 ..      42      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.065
                           DUF2393 19 lfliflsllilflapfvvhl 38
                                      lf ++l +l++++ p v+ +
  gi|298674861|ref|YP_003726611.1|  5 LFDFVLTFLVFSIIPCVYRI 24
                                      34456667777777766654 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00014
                           DUF2393  2 llllllglllkkrsavalfliflsllilflapfvvhliidkyl 44
                                      +++  lg++ + ++ v   +++   l+l++ +fv+ ++i+kyl
  gi|298674861|ref|YP_003726611.1| 43 VIVATLGVYSFIQESV---FFMDVALVLSIIAFVGTVTISKYL 82
                                      7899999999999965...5566678888889**********8 PP

>> Deltameth_res  Deltamethrin resistance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.35   2.1e+03      29      37 ..      10      18 ..       2      25 .. 0.64
   2 ?    0.2   0.1      0.12   7.2e+02      33      47 ..      39      53 ..      34      56 .. 0.75
   3 ?    8.7   0.2   0.00025       1.5      24      42 ..      64      82 ..      59      84 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.35
                     Deltameth_res 29 iviligTia 37
                                      +++l+++i+
  gi|298674861|ref|YP_003726611.1| 10 LTFLVFSII 18
                                      456666665 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.12
                     Deltameth_res 33 igTialakesglinl 47
                                      ++T++++ + g++ +
  gi|298674861|ref|YP_003726611.1| 39 AMTLVIVATLGVYSF 53
                                      678888888888877 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00025
                     Deltameth_res 24 vLaaGiviligTialakes 42
                                       L+++i++++gT+++ k+ 
  gi|298674861|ref|YP_003726611.1| 64 ALVLSIIAFVGTVTISKYL 82
                                      599************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 544.05
//
Query:       gi|298674862|ref|YP_003726612.1|  [L=164]
Description: cation antiporter [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-43  145.9   0.3    7.8e-43  145.7   0.3    1.0  1  MNHE      Na+/H+ ion antiporter subunit


Domain annotation for each model (and alignments):
>> MNHE  Na+/H+ ion antiporter subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.7   0.3   4.4e-47   7.8e-43       3     145 ..      10     161 ..       8     162 .. 0.96

  Alignments for each domain:
  == domain 1  score: 145.7 bits;  conditional E-value: 4.4e-47
                              MNHE   3 llflvWllltgs..lgelllGlllallvalllrrll.........lplrrvllrllayllvflweivkanldVakrv 68 
                                        l+++W++++g+  + +++lGl+l+ +v+  +++l+          ++rr+++  l+yl+v+++ei+kan+ Vak+v
  gi|298674862|ref|YP_003726612.1|  10 PLAILWCFVNGDisIVNFMLGLVLSPVVIKPFKSLYnfeaevsirDNIRRIPK-QLKYLAVLAIEITKANIMVAKIV 85 
                                       699*****************************999999999888777778888.9********************** PP

                              MNHE  69 lrpklpirpgivkvplrlksdlaltllansitltPGTltvdvdedrrvlyvHvldvedeeeeareeikgrlErrlle 145
                                       lrp+++i+pgi++vp+r k+d+++t++an+i+ltPGTlt+dv +d++vlyvH +d++d +ee+r++i+++lE+++le
  gi|298674862|ref|YP_003726612.1|  86 LRPRININPGIITVPIRAKTDAGITAIANTISLTPGTLTIDVADDKSVLYVHLIDIHD-REEIRASIRDDLEEYVLE 161
                                       **********************************************************.9**************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 994.16
//
Query:       gi|298674863|ref|YP_003726613.1|  [L=514]
Description: proton-translocating NADH-quinone oxidoreductase subunit M [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-70  236.7  28.3      3e-70  236.7  28.3    2.8  3  Proton_antipo_M  Proton-conducting membrane transporter
    1.6e-06   27.7   4.4    1.6e-06   27.7   4.4    2.7  3  NADHdeh_related  NADH dehydrogenase I, subunit N related prot
    1.5e-05   25.0   0.6    1.5e-05   25.0   0.6    4.5  7  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1      0.45   2.7e+03      34      56 ..      84     105 ..      78     120 .. 0.77
   2 !  236.7  28.3     5e-74     3e-70       3     293 .]     133     433 ..     131     433 .. 0.94
   3 ?    0.5   0.0     0.046   2.8e+02     237     262 ..     461     488 ..     444     496 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.45
                   Proton_antipo_M  34 AslklflltllgsliLLlgilll 56 
                                       A++ +fl + ++ l+LL+++ ++
  gi|298674863|ref|YP_003726613.1|  84 AGM-VFLSSGISFLALLYSMDYM 105
                                       444.6888889999999998777 PP

  == domain 2  score: 236.7 bits;  conditional E-value: 5e-74
                   Proton_antipo_M   3 dLlllylglElvllplylLiglwk.....kkpksleAslklflltllgsliLLlgilllynltgtlefeelskal.. 72 
                                       d++ l++++E+ ll++  L+  ++     k+  ++eA++k+++l++++s+i+L++i+ ly+  gtl++ +++  +  
  gi|298674863|ref|YP_003726613.1| 133 DIFNLFVFFEILLLSSCGLVVAYGkggftKSDHKMEATFKYLVLNMISSFIMLVAIASLYATVGTLNMADMAAKInv 209
                                       8899*************9996654122226889**************************************998878 PP

                   Proton_antipo_M  73 ..elglnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla.vssnei 146
                                         e+g   + ++ ++ll++v +  K+a +plh Wlpd++  aP p+sa+l+++l k+g+++++r+++l++       
  gi|298674863|ref|YP_003726613.1| 210 msETGNLPWHIFPAALLFIVVFGNKAAIFPLHYWLPDVHPSAPSPISAMLSGVLIKVGAYGILRMFFLIFdGTLYMF 286
                                       8888888999999********************************************************98999999 PP

                   Proton_antipo_M 147 sqlllilaiismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsvi 223
                                       + ++++la+++++lgs+ a+ q+diKrllAySsis++Gy++++++++t+  ++a++++l+ ha+ k++lF+++gs+i
  gi|298674863|ref|YP_003726613.1| 287 QPIIIFLALVTIILGSISAVGQNDIKRLLAYSSISQIGYVFLGIGMGTVTTIAASLVYLVNHAVAKSMLFMASGSII 363
                                       ****************************************************************************9 PP

                   Proton_antipo_M 224 yerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvla.vvasvlt 293
                                       +e   trd+r++gg++++ P+l+ ++l++++s+aG+Pp+ gF++kf ++ + +  + ++ +l+ +v +v+t
  gi|298674863|ref|YP_003726613.1| 364 HEA-GTRDMRKMGGMVNSAPFLSGMFLIGAMSVAGIPPMGGFIAKFVLFDSGITSKYYIPILIaLVFAVFT 433
                                       998.9***********************************************9999999888877777775 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.046
                   Proton_antipo_M 237 gLak..kmPilalvllvlllslaGlPpt 262
                                       gL++  ++Pil l +lv++++l + P++
  gi|298674863|ref|YP_003726613.1| 461 GLSWkmSVPILVLSVLVVVFGLYAEPLL 488
                                       66663467**************999987 PP

>> NADHdeh_related  NADH dehydrogenase I, subunit N related protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.6      0.77   4.6e+03     135     175 ..      20      59 ..      12      71 .. 0.46
   2 !   27.7   4.4   2.7e-10   1.6e-06      80     157 ..     125     206 ..     103     242 .. 0.81
   3 ?    0.8  11.9     0.043   2.6e+02      73     191 ..     292     412 ..     281     439 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.77
                   NADHdeh_related 135 lfggaalilastGtlsifelaklagd.vlliaklllvlGvvG 175
                                       lf++  + l s+   s+  + +l+++  lli  +ll++ v+ 
  gi|298674863|ref|YP_003726613.1|  20 LFSALMMFLRSAP--SVQKVINLTVSfGLLILSILLLINVLN 59 
                                       4444444444332..333333333332244555555555554 PP

  == domain 2  score: 27.7 bits;  conditional E-value: 2.7e-10
                   NADHdeh_related  80 latlgavvtgdvfnftlflaliGianiGivaav......kkefvleaafnyGlvaliatlplfggaalilastGtls 150
                                       +   g+ +tgd+fn  +f  ++ ++  G+v a+      k+ + +ea+f+y ++ +i++  ++ + a + a+ Gtl 
  gi|298674863|ref|YP_003726613.1| 125 I--NGTFLTGDIFNLFVFFEILLLSSCGLVVAYgkggftKSDHKMEATFKYLVLNMISSFIMLVAIASLYATVGTLN 199
                                       4..47889**********************9874444447799********************************** PP

                   NADHdeh_related 151 ifelakl 157
                                       + ++a+ 
  gi|298674863|ref|YP_003726613.1| 200 MADMAAK 206
                                       *998765 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.043
                   NADHdeh_related  73 llaivcg.latlgavvtgdvfnftlflal..iGianiGivaavkkefvleaafnyGlvaliatlplfggaalilast 146
                                       +la+v+  l ++ av   d+     + ++  iG + +Gi  ++     + a+  y +   +a   lf +++ i+ ++
  gi|298674863|ref|YP_003726613.1| 292 FLALVTIiLGSISAVGQNDIKRLLAYSSIsqIGYVFLGI--GMGTVTTIAASLVYLVNHAVAKSMLFMASGSIIHEA 366
                                       566665414566777777776655554432255555555..556677889999**999******************* PP

                   NADHdeh_related 147 GtlsifelaklagdvlliaklllvlGvvGetGvaPf..yaakaeifr 191
                                       Gt  +  + ++  + ++++ ++ ++G +  +G+ P+  ++ak  +f 
  gi|298674863|ref|YP_003726613.1| 367 GTRDMRKMGGMVNSAPFLSGMF-LIGAMSVAGIPPMggFIAKFVLFD 412
                                       ***********99988887765.579999999999755777776664 PP

>> Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.4       1.9   1.1e+04      17      34 ..       6      23 ..       2      27 .. 0.61
   2 ?   -4.2   0.9         3   1.8e+04      21      36 ..      40      55 ..      37      58 .. 0.58
   3 !   25.0   0.6   2.5e-09   1.5e-05      15      47 ..      76     108 ..      67     121 .. 0.85
   4 ?   -2.7   0.2       1.1   6.7e+03      27      39 ..     174     186 ..     164     192 .. 0.62
   5 ?   -3.3   0.3       1.7     1e+04      23      32 ..     290     299 ..     284     303 .. 0.81
   6 ?   -1.2   0.1      0.36   2.2e+03      31      46 ..     424     439 ..     419     460 .. 0.76
   7 ?   -0.4   0.9       0.2   1.2e+03      20      39 ..     461     480 ..     456     483 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.9
                   Proton_antipo_N 17 llDklsalmllvvtfvsl 34
                                        D l +lm+++  + s+
  gi|298674863|ref|YP_003726613.1|  6 ITDHLPILMVAIPILFSA 23
                                      567777888776555444 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 3
                   Proton_antipo_N 21 lsalmllvvtfvsllv 36
                                      l++ + l++  + ll+
  gi|298674863|ref|YP_003726613.1| 40 LTVSFGLLILSILLLI 55
                                      5555556666555555 PP

  == domain 3  score: 25.0 bits;  conditional E-value: 2.5e-09
                   Proton_antipo_N  15 gfllDklsalmllvvtfvsllvhlYSigYMadd 47 
                                        +  D lsa m+++ +++s+l +lYS+ YM++ 
  gi|298674863|ref|YP_003726613.1|  76 VLVADLLSAGMVFLSSGISFLALLYSMDYMEEK 108
                                       57789*************************964 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 1.1
                   Proton_antipo_N  27 lvvtfvsllvhlY 39 
                                       lv  ++s++++l 
  gi|298674863|ref|YP_003726613.1| 174 LVLNMISSFIMLV 186
                                       4445555555553 PP

  == domain 5  score: -3.3 bits;  conditional E-value: 1.7
                   Proton_antipo_N  23 almllvvtfv 32 
                                       +++l++vt++
  gi|298674863|ref|YP_003726613.1| 290 IIFLALVTII 299
                                       6889999987 PP

  == domain 6  score: -1.2 bits;  conditional E-value: 0.36
                   Proton_antipo_N  31 fvsllvhlYSigYMad 46 
                                       +++l+  ++++ YM +
  gi|298674863|ref|YP_003726613.1| 424 LIALVFAVFTVFYMIR 439
                                       5777888999999954 PP

  == domain 7  score: -0.4 bits;  conditional E-value: 0.2
                   Proton_antipo_N  20 klsalmllvvtfvsllvhlY 39 
                                       +ls  m + + ++s+lv ++
  gi|298674863|ref|YP_003726613.1| 461 GLSWKMSVPILVLSVLVVVF 480
                                       68999999*********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (514 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1039  (0.0579508); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 3169.99
//
Query:       gi|298674864|ref|YP_003726614.1|  [L=139]
Description: NADH-ubiquinone oxidoreductase subunit 4L [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.4e-35  119.8   3.3    4.4e-35  119.5   3.3    1.1  1  Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase cha


Domain annotation for each model (and alignments):
>> Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.5   3.3   2.4e-39   4.4e-35       1     104 [.       5     135 ..       5     136 .. 0.98

  Alignments for each domain:
  == domain 1  score: 119.5 bits;  conditional E-value: 2.4e-39
                                       HHHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC............................. CS
                       Oxidored_q2   1 flllliallfliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvi....................... 54 
                                       fl+l+ia+lf++G++++l r++++kv+igl++is+avn+++v +gvf ++ ++i                       
  gi|298674864|ref|YP_003726614.1|   5 FLSLTIAILFGLGTFLIL-RKDVIKVIIGLSIISHAVNVFIVSSGVFNGDNAPIinghgsdsssniifndvldndvl 80 
                                       689***************.******************************999999********************** PP

                                       ............TTSCGGHHHHHHHHHHHHHHHHHHHHHHHHHHHSSS-BCCG-- CS
                       Oxidored_q2  55 .....tnpatefadplpqalvLtaivigaaetavgLallvrlyreygtddvqelr 104
                                            ++++  ++dpl+qalvLtaivig+++ta++L l++r+y+eygt+d+ el+
  gi|298674864|ref|YP_003726614.1|  81 apvvaNTKEVVYVDPLVQALVLTAIVIGFSITAFILILAYRIYEEYGTTDITELK 135
                                       ****9999999******************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 920.62
//
Query:       gi|298674865|ref|YP_003726615.1|  [L=138]
Description: Na+/H+ antiporter MnhB subunit-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-34  117.1  11.3    6.5e-34  116.9  11.3    1.0  1  MnhB      Domain related to MnhB subunit of Na+/H+ antiporter


Domain annotation for each model (and alignments):
>> MnhB  Domain related to MnhB subunit of Na+/H+ antiporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.9  11.3   3.6e-38   6.5e-34       1     123 [.       5     128 ..       5     129 .. 0.97

  Alignments for each domain:
  == domain 1  score: 116.9 bits;  conditional E-value: 3.6e-38
                              MnhB   1 ilrtvarllvplillvslylllrGhnsPGGGFqgGlilaaalillylafgleelekllrvklaprileglglllavl 77 
                                       i++tv++  vpli+l+s++ll++GhnsPGGGF+gG+++aa+l lly++fgl++ +++l+ +  + +++g+glll vl
  gi|298674865|ref|YP_003726615.1|   5 ITKTVSKASVPLIILFSISLLIAGHNSPGGGFIGGVMFAASLSLLYVVFGLDHIKSVLNPD--WGKWFGFGLLLSVL 79 
                                       789***************************************************9**9999..77************ PP

                              MnhB  78 tgllglllg..fltslflelel.llgevelgtallfdlgVylvVvggll 123
                                       t++ ++++g  f++s++ +++l l+ge el + +lfd+gVy+vV+g+ll
  gi|298674865|ref|YP_003726615.1|  80 TAFGAIFFGynFFRSSIKFIHLpLVGEIELVSSILFDIGVYFVVIGSLL 128
                                       ***************9999999999*********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 825.55
//
Query:       gi|298674866|ref|YP_003726616.1|  [L=788]
Description: NADH/ubiquinone/plastoquinone complex I [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.3e-69  232.2  20.0    7.3e-69  232.2  20.0    3.0  3  Proton_antipo_M  Proton-conducting membrane transporter
    2.9e-19   69.0  10.2    2.9e-19   69.0  10.2    4.5  5  DUF4040          Domain of unknown function (DUF4040)
      3e-11   43.2   0.7      3e-11   43.2   0.7    4.7  5  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   1.6      0.22   1.3e+03     102     153 ..      64     121 ..       3     133 .. 0.51
   2 !  232.2  20.0   1.2e-72   7.3e-69       1     283 [.     130     417 ..     130     427 .. 0.94
   3 ?   -0.0   7.7     0.067     4e+02     154     276 ..     624     749 ..     577     761 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.22
                   Proton_antipo_M 102 hlWlpdayveaPtpv...sallAatlvkagvlllirllllla...vssneisqlllil 153
                                         Wlp + ve ++ +   s+l+  +++ +g++++   +  ++     s  +++lll++
  gi|298674866|ref|YP_003726616.1|  64 VSWLPSVGVEFSVYIdglSLLIGLIASGIGIIIMSYSNGYMShkeDLSRYYQYLLLFM 121
                                       4677777777776543336777777777777777666666664332333344443333 PP

  == domain 2  score: 232.2 bits;  conditional E-value: 1.2e-72
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskal...el 74 
                                       + + ++l++++El+++ ++lLig+w+++p s++ + k++++t++g li+++g+l+l+++tgt ++++++      e+
  gi|298674866|ref|YP_003726616.1| 130 SANTIQLFIFWELTSITSFLLIGFWRHRPLSIYGATKSLIITAAGGLIMFIGFLILHSITGTFDIPTILHDSsmiEN 206
                                       56889***************************************************************877666799 PP

                   Proton_antipo_M  75 glnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsall.Aatlvkagvlllirlllllavssneisqll 150
                                        +n   +l+ l+++++g+++Ksaq p+  Wlp+a +eaPtpvsa+l +at+vkagv+l++r++++++  ++++  l+
  gi|298674866|ref|YP_003726616.1| 207 IKNHDLFLVTLIFIFIGAAAKSAQGPFYIWLPNA-MEAPTPVSAFLhSATMVKAGVFLIARIHPIFS-GTEAWFLLV 281
                                       99********************************.********************************.9999999** PP

                   Proton_antipo_M 151 lilaiismllgslvalaqtdiKrllAySsishlGymlialavatq....ygveaaiihllthalfkallFllagsvi 223
                                          ++++m+l++++a +q+diK +lA+S+is+l+y++   + +t+    +gv+aa +hll ha fka lFl+ag v 
  gi|298674866|ref|YP_003726616.1| 282 SGTGMATMVLAGFLAFRQNDIKGILAFSTISQLAYLVTMYGYTTYhepgIGVAAATFHLLNHATFKACLFLVAGIVA 358
                                       ************************************999999665333369**********************7775 PP

                   Proton_antipo_M 224 yerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslill 283
                                       +e   trdir++ggL+  mP++++v  +++l++aG+Pp+ gFlsk +  +++v++++ l 
  gi|298674866|ref|YP_003726616.1| 359 HE-AATRDIRKLGGLRHEMPLTFIVASIGALAMAGIPPLNGFLSKEMFYKSSVEMGAALG 417
                                       55.59*******************************************999999988765 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.067
                   Proton_antipo_M 154 aiismllgslvala.qtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsviye.rek 228
                                        ++ m++++++a +    i  ++A Ss   lGym++ l++   ++ ++a++++l+  l+++   l+++ + +  rek
  gi|298674866|ref|YP_003726616.1| 624 LMLLMVVAAIAATVlPKYIPAIIALSS---LGYMVSLLFI-YLKAPDLALTQILVETLTTIIFLLVIVRIPQTfREK 696
                                       333333333333331445667778777...6888888888.77789**************99999999998888999 PP

                   Proton_antipo_M 229 trdirayggLakkmPilalvllvlllslaGl.Ppt....agFlskfliLeaav 276
                                         + + ++  + +  +   v++vl+ ++ G+ Pp+     +F+ k   L++  
  gi|298674866|ref|YP_003726616.1| 697 LSKANLTRDVFISGLVSVGVFIVLINATQGIvPPFeslsHYFIEKSVSLTGGH 749
                                       99999999999999999999999999999865888777777888877777655 PP

>> DUF4040  Domain of unknown function (DUF4040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.8      0.34     2e+03      18      38 ..     166     186 ..     163     188 .. 0.89
   2 ?   -2.9   0.6       1.3     8e+03      28      39 ..     213     224 ..     213     225 .. 0.86
   3 ?   -2.4   0.4      0.92   5.5e+03       4      30 ..     289     315 ..     286     320 .. 0.70
   4 !   69.0  10.2   4.9e-23   2.9e-19       1      67 []     626     691 ..     626     691 .. 0.98
   5 ?   -3.6   0.2       2.3   1.3e+04      21      32 ..     707     718 ..     701     721 .. 0.50

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.34
                           DUF4040  18 aavillgvvGllvallfvllg 38 
                                       +++i++++ Gl++ + f++l+
  gi|298674866|ref|YP_003726616.1| 166 KSLIITAAGGLIMFIGFLILH 186
                                       78999************9986 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.3
                           DUF4040  28 llvallfvllgA 39 
                                       +lv+l+f++ gA
  gi|298674866|ref|YP_003726616.1| 213 FLVTLIFIFIGA 224
                                       689999999998 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.92
                           DUF4040   4 vlaalaavlardrlaavillgvvGllv 30 
                                       +++a ++++ ++ ++ +++++ ++ l+
  gi|298674866|ref|YP_003726616.1| 289 MVLAGFLAFRQNDIKGILAFSTISQLA 315
                                       566777777777788888888877655 PP

  == domain 4  score: 69.0 bits;  conditional E-value: 4.9e-23
                           DUF4040   1 lllvlaalaavlardrlaavillgvvGllvallfvllgAPDvAlTqaavveglttvllllalrrlpr 67 
                                       ll+v+aa+aa++ ++ + a+i+l+ +G++v+llf++l+APD+AlTq+ +ve+ltt+++ll++ r+p+
  gi|298674866|ref|YP_003726616.1| 626 LLMVVAAIAATVLPKYIPAIIALSSLGYMVSLLFIYLKAPDLALTQI-LVETLTTIIFLLVIVRIPQ 691
                                       69*********************************************.***************9985 PP

  == domain 5  score: -3.6 bits;  conditional E-value: 2.3
                           DUF4040  21 illgvvGllval 32 
                                        ++g+v+++v +
  gi|298674866|ref|YP_003726616.1| 707 FISGLVSVGVFI 718
                                       444444444433 PP

>> Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.7   4.9e-15     3e-11       3      57 ..      65     117 ..      63     118 .. 0.93
   2 ?   -3.7   0.7       2.2   1.3e+04      24      39 ..     466     481 ..     465     482 .. 0.88
   3 ?   -0.2   1.0      0.18   1.1e+03      23      33 ..     518     528 ..     515     534 .. 0.76
   4 ?   -2.9   1.6       1.3   7.6e+03      32      44 ..     642     654 ..     610     656 .. 0.59
   5 ?   -4.0   0.5       2.9   1.7e+04      17      29 ..     673     685 ..     670     687 .. 0.56

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 4.9e-15
                   Proton_antipo_N   3 tWlsvgglsieigfllDklsalmllvvtfvsllvhlYSigYMaddegyqRFfayl 57 
                                       +Wl++    +e+++++D+ls+l  l+ ++++ +++ YS gYM++ e  +R++ yl
  gi|298674866|ref|YP_003726616.1|  65 SWLPSV--GVEFSVYIDGLSLLIGLIASGIGIIIMSYSNGYMSHKEDLSRYYQYL 117
                                       799944..49********************************************9 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.2
                   Proton_antipo_N  24 lmllvvtfvsllvhlY 39 
                                       +ml+   ++s+lv+l+
  gi|298674866|ref|YP_003726616.1| 466 VMLIPAGLLSVLVILF 481
                                       7999999999999998 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.18
                   Proton_antipo_N  23 almllvvtfvs 33 
                                       a m++++tfv 
  gi|298674866|ref|YP_003726616.1| 518 AFMMTIITFVL 528
                                       68999999994 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 1.3
                   Proton_antipo_N  32 vsllvhlYSigYM 44 
                                       + +++ l S+gYM
  gi|298674866|ref|YP_003726616.1| 642 IPAIIALSSLGYM 654
                                       3345555566666 PP

  == domain 5  score: -4.0 bits;  conditional E-value: 2.9
                   Proton_antipo_N  17 llDklsalmllvv 29 
                                       l+ +l+ +  l+v
  gi|298674866|ref|YP_003726616.1| 673 LVETLTTIIFLLV 685
                                       5666666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (788 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       974  (0.0543254); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.80u 0.33s 00:00:01.13 Elapsed: 00:00:00.52
# Mc/sec: 4555.50
//
Query:       gi|298674867|ref|YP_003726617.1|  [L=184]
Description: heat shock protein Hsp20 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.4e-09   36.1   0.0    4.8e-09   35.6   0.0    1.2  1  ArsA_HSP20  HSP20-like domain found in ArsA
    5.1e-07   29.8   0.7    1.8e-05   24.8   0.7    2.2  1  HSP20       Hsp20/alpha crystallin family
     0.0024   18.8   0.2     0.0043   18.0   0.2    1.4  1  CS          CS domain
  ------ inclusion threshold ------
      0.046   13.8   0.4      0.064   13.3   0.4    1.3  1  GvpH        GvpH


Domain annotation for each model (and alignments):
>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0   1.1e-12   4.8e-09       1      63 []     105     170 ..     105     170 .. 0.96

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 1.1e-12
                        ArsA_HSP20   1 ddeyvlkldLPfvdkeeidlsrsgdeLtIkig....nfrRqitLPsvlarkevtsAkfedgvLeIrF 63 
                                       dd++ +++++P+v+ke+i+l+ ++ +  I++     n++  +  P +++   + sA+f++gvLeI F
  gi|298674867|ref|YP_003726617.1| 105 DDHVYVVAEMPGVEKEDINLHSTEWTVEITATkgesNYSEIVEFPVKVDPNSA-SATFKNGVLEIIF 170
                                       799***************************99999999999**********77.***********88 PP

>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.7     4e-09   1.8e-05       1      97 [.     100     179 ..     100     184 .] 0.88

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 4e-09
                                       E--SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--..---TT----SS---EEEEEE--STTB-TTT-EEEEE CS
                             HSP20   1 dikeeeeefevkldvpglkkeelkvkvednrvlvkgeheeeeedekglikerssrkFsrkftLPenvdadkvkaslk 77 
                                       d++e++++  v +++pg++ke+++++ ++ +v +++++               ++++s  ++ P  vd+++ +a++k
  gi|298674867|ref|YP_003726617.1| 100 DVMESDDHVYVVAEMPGVEKEDINLHSTEWTVEITATKG--------------ESNYSEIVEFPVKVDPNSASATFK 162
                                       68999******************************9998..............2567788899************** PP

                                       TTEEEEEEEBSS--..---- CS
                             HSP20  78 dGvLtvtvpkkepekkkker 97 
                                       +GvL++  +k+ +++k    
  gi|298674867|ref|YP_003726617.1| 163 NGVLEIIFDKTDTDQK---V 179
                                       *********9998843...3 PP

>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.2   9.6e-07    0.0043       7      76 .]     103     172 ..      99     172 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 9.6e-07
                                       EETTEEEEEEE-TTCTTTTTCEEEEEETTEEEEEE..TS.CEEEEECEBSS-BETTTEEEEEETTEEEEEEEB CS
                                CS   7 QtldeVvvtiyvkkvnikkkdvkvefkerslkvki..gk.eklliegeLfgpIdpeesswtieskkveitLkK 76 
                                       +++d+V+v  ++++v  +k+d++++ +e ++++    g+ ++  i + +  ++dp+++s t+++  +ei+ +K
  gi|298674867|ref|YP_003726617.1| 103 ESDDHVYVVAEMPGV--EKEDINLHSTEWTVEITAtkGEsNYSEIVE-FPVKVDPNSASATFKNGVLEIIFDK 172
                                       789***********9..********8888888888765544444444.*********************9988 PP

>> GvpH  GvpH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.4   1.4e-05     0.064      98     167 ..     103     174 ..      58     180 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.4e-05
                              GvpH  98 ddsdelvvvadlpGvtdedvdvaletdeqaltlrvdd....dvverlvlddpdvaitdltlrnqvlelrlarse 167
                                       ++ d++ vva++pGv  ed++      +  +t + ++    ++ve  v  dp+ a  + t +n vle+   +++
  gi|298674867|ref|YP_003726617.1| 103 ESDDHVYVVAEMPGVEKEDINLHSTEWTVEITATKGEsnysEIVEFPVKVDPNSA--SATFKNGVLEIIFDKTD 174
                                       5667788***********9988766566666665554222267887777788765..7899******9887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 1095.63
//
Query:       gi|298674868|ref|YP_003726618.1|  [L=91]
Description: hypothetical protein Metev_0928 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-12   45.9   0.5    5.6e-12   45.5   0.5    1.1  1  DUF2892   Protein of unknown function (DUF2892)
     0.0034   17.6   0.1     0.0045   17.2   0.1    1.2  1  DUF3017   Protein of unknown function (DUF3017)


Domain annotation for each model (and alignments):
>> DUF2892  Protein of unknown function (DUF2892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.5   6.2e-16   5.6e-12       2      63 ..      26      89 ..      25      91 .] 0.92

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 6.2e-16
                           DUF2892  2 kkNvgtldRilrivvGlvllllallglsggw..gwllglvGavllltgltgfCplyallgintc 63
                                      ++Nvg++d  +r+++G+++ +++++ l       w+++l++++ l+t++t++C  y+++g++t 
  gi|298674868|ref|YP_003726618.1| 26 QENVGGVDLYARALIGSIATIALAMDLVETYpwNWVTALIALAGLFTAMTRHCTPYSFIGFSTV 89
                                      78********************99999776688***************************9994 PP

>> DUF3017  Protein of unknown function (DUF3017)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1     5e-07    0.0045       5      52 ..      43      90 ..      39      91 .] 0.92

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5e-07
                           DUF3017  5 llvvavglllvaldhwRrGalllGvalllaAvlRlvlpsrrvGlLaVR 52
                                      ++++a+++ lv ++ w + ++l+++a l+ A+ R ++p + +G+  VR
  gi|298674868|ref|YP_003726618.1| 43 IATIALAMDLVETYPWNWVTALIALAGLFTAMTRHCTPYSFIGFSTVR 90
                                      6789999999******************************99999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 558.50
//
Query:       gi|298674869|ref|YP_003726619.1|  [L=435]
Description: major facilitator superfamily protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-50  171.0  69.3    4.8e-45  154.0  35.5    2.0  2  MFS_1          Major Facilitator Superfamily
  ------ inclusion threshold ------
       0.13   11.6   0.3       0.24   10.7   0.3    1.4  1  Sarcoglycan_1  Sarcoglycan complex subunit protein


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.0  35.5   5.4e-49   4.8e-45       1     350 [.      14     394 ..      14     394 .. 0.84
   2 !   30.9  25.8   1.4e-11   1.3e-07      65     170 ..     323     428 ..     318     434 .. 0.88

  Alignments for each domain:
  == domain 1  score: 154.0 bits;  conditional E-value: 5.4e-49
                             MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgll 77 
                                       ll++ f+ +l++si++p+l  +l + +g +   +g++ ++y ++++v++++lGr+sd +Gr+++l+l+ l+++l+ +
  gi|298674869|ref|YP_003726619.1|  14 LLMVNFIGTLGFSIVLPFLV-FLVDRFGGNSIIYGIIGATYPVFQLVGAPVLGRWSDIYGRKKILFLSQLGTLLS-W 88 
                                       57899***************.******************************************************.6 PP

                             MFS_1  78 lll.fa.....ss.................lwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfs 131
                                       +++ +a     ++                 l +l+v+r+l G++ g+ +++++a++ad++++e+r++ +g++s++++
  gi|298674869|ref|YP_003726619.1|  89 FIFlIAllipiTTlmeidnnilgsfnltvpLLILFVARALDGIT-GGNVSVANAYLADITSEEDRSKNYGWMSVTTN 164
                                       666322343442255555667777777764557**********9.89****************************** PP

                             MFS_1 132 lGailgpllgglla.sslgWravfyilaivsllafvlfllllpeepperkrkspkeee..................k 189
                                       lG i+gp+l+++l+  s+ + ++ +++ i+s+++ +   + l+  p +rk + + e++                  +
  gi|298674869|ref|YP_003726619.1| 165 LGLIVGPALASILSaISYQYLSPVFAAIIISFIGTL---VILFIVPESRKCVYQFEDKtnlkdvfgyeqrecgvysS 238
                                       **************777778888999999****999...5555555555555556666666999999999***9988 PP

                             MFS_1 190 gtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgail.allag 265
                                       g ++ + +  +k +lk +++ ++l+  +l+f+gf++++t +pl +   l +  +  +gl++ +l+ +++++ +++++
  gi|298674869|ref|YP_003726619.1| 239 GGEKVEKIG-FKRILKINHIPYVLLLYFLIFLGFNIFYTAFPLHALNLLEWQ-VSDMGLYFTVLSSMMMFVeGPVFS 313
                                       888888888.**********878888888889********************.9****9999999999888888888 PP

                             MFS_1 266 rlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfpsllalasdlappeeagtasglfn 342
                                         ++ ++     l+ +++++l+  +l+l+    s +l++++ +++ +g g+++ps+l+++s++a+p+++g+++g+++
  gi|298674869|ref|YP_003726619.1| 314 NAAKVYSD--SFLVVIGSFVLGINFLLLVTG--SEILTYIAAIFFAVGNGLMWPSVLSILSKFAGPKYQGAVQGFAG 386
                                       87777665..344444444444333333333..47999999************************************ PP

                             MFS_1 343 tagslgga 350
                                       ++ sl+++
  gi|298674869|ref|YP_003726619.1| 387 SFMSLASI 394
                                       ***99975 PP

  == domain 2  score: 30.9 bits;  conditional E-value: 1.4e-11
                             MFS_1  65 lllglllfalglllllfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpll 140
                                       +l+ + +f+lg+ +ll+++++  l +++ ++ ++g g+++p++++++++ + ++ +g + g++++++sl++i g ++
  gi|298674869|ref|YP_003726619.1| 323 FLVVIGSFVLGINFLLLVTGSEiLTYIAAIFFAVGNGLMWPSVLSILSKFAGPKYQGAVQGFAGSFMSLASIAGLIF 399
                                       778888899994444445899999***************************************************** PP

                             MFS_1 141 ggllasslgWravfyilaivsllafvlfll 170
                                       gg+l+ +l+ +++f+i a++  ++fvl + 
  gi|298674869|ref|YP_003726619.1| 400 GGFLYGYLS-TGTFFISAVIIYIVFVLSFR 428
                                       *****8887.79999999999999997444 PP

>> Sarcoglycan_1  Sarcoglycan complex subunit protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   2.7e-05      0.24       4      52 ..      70     118 ..      69     156 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.7e-05
                     Sarcoglycan_1   4 lrgrrkrclyllvllLlllaivnLaltiwilkvLrissnGmgsleiipd 52 
                                       ++gr+k++++  + +Ll   i  +al i i + ++i++n +gs +++  
  gi|298674869|ref|YP_003726619.1|  70 IYGRKKILFLSQLGTLLSWFIFLIALLIPITTLMEIDNNILGSFNLTVP 118
                                       79***********************************999888877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.51
# Mc/sec: 2578.70
//
Query:       gi|298674870|ref|YP_003726620.1|  [L=311]
Description: adenosine kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-38  131.0   0.0    7.3e-38  130.6   0.0    1.1  1  PfkB      pfkB family carbohydrate kinase


Domain annotation for each model (and alignments):
>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.6   0.0   4.1e-42   7.3e-38      26     297 ..      37     291 ..      14     295 .. 0.92

  Alignments for each domain:
  == domain 1  score: 130.6 bits;  conditional E-value: 4.1e-42
                                       E.EESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTEEETTEEEESSSEEEEEEEEETTTS CS
                              PfkB  26 v.evktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegvdtdyvkidedtrtglalivvdedg 101
                                       +  v+++++ +GG++ N+A +l+ lg+d   +g vG D+  + + +++++ ++  ++v + ++t t+ a+i++d d 
  gi|298674870|ref|YP_003726620.1|  37 SfLVPELRREFGGCAGNIAYNLKLLGGDPLPMGTVGADF--DPYSQWMDDQNISREHVTVLNETFTAQAFITTDMD- 110
                                       45789999*******************************..*********************************98. PP

                                       EEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEESEECTTSHHHHHHHHHHHHHHTTE..EEEEECESSSHHHHHH CS
                              PfkB 102 ertivfnrgaaadltkeeleededlleeadllyisgllsselpeavleelaeaaknggt..fdpnlldplgaqfkea 176
                                       +++i+++ + a +++ +      + l ++d  +  g++ ++ ++ ++++++e  ++g    fdp +  p      e+
  gi|298674870|ref|YP_003726620.1| 111 DNQITAFHPGAMNYSHH-----NSVLDANDPTV--GIVAPDGRDGMVQHASEFVHAGIPfiFDPGQGLPMFN--GEE 178
                                       66666666667777774.....45666777655..5778899***************************997..5** PP

                                       HHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGGGEEEEEETTEEEEEEE.SSSS-SB CS
                              PfkB 177 llellaladllkpneeElealtgekledieealaalhklkakgaktvvvtlGkeGalvvekdgelkvpavpkvkvvD 253
                                       l++++ +a++l++n++E++ ++++++++ ee++ +l +        +++t+G eG+l+++ d++++vpa+ +++  D
  gi|298674870|ref|YP_003726620.1| 179 LMDFIDKATWLTVNDYEWQLISDRTGKNKEEIATYLDA--------LIITKGPEGSLIYTDDEVIHVPAAEPKELKD 247
                                       ***********************************976........9****************************** PP

                                       GTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTSSSSST CS
                              PfkB 254 ttGAGDsfvggflaallegksleealrfanavAalvvqkkgaia 297
                                       +tG GD++ +g+l++l++  ++e+  r+a+  +a+ ++++g+++
  gi|298674870|ref|YP_003726620.1| 248 PTGCGDAYRAGLLYGLTNDLDWETTGRIASLMGAIKIEHQGTQN 291
                                       ******************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1890.09
//
Query:       gi|298674871|ref|YP_003726621.1|  [L=278]
Description: type 11 methyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.5e-22   77.6   0.0    1.5e-21   76.8   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    2.1e-17   63.6   0.0    5.6e-17   62.2   0.0    1.8  1  Methyltransf_25  Methyltransferase domain
    1.6e-14   54.0   0.0    3.8e-14   52.8   0.0    1.7  2  Methyltransf_31  Methyltransferase domain
    5.9e-12   45.7   0.0    7.4e-12   45.4   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    1.5e-11   44.1   0.2    2.4e-11   43.4   0.0    1.3  2  CMAS             Mycolic acid cyclopropane synthetase
    2.1e-09   37.0   0.0    3.9e-09   36.2   0.0    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    1.1e-08   35.7   0.0    2.4e-08   34.6   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
    5.6e-06   25.2   0.0      1e-05   24.3   0.0    1.3  2  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m
    0.00017   20.9   0.0    0.00029   20.2   0.0    1.3  1  Methyltransf_2   O-methyltransferase domain
    0.00022   21.2   0.0     0.0025   17.7   0.0    2.1  1  Methyltransf_8   Hypothetical methyltransferase
    0.00029   20.3   0.0    0.00048   19.6   0.0    1.3  1  TehB             Tellurite resistance protein TehB
    0.00046   19.2   0.0     0.0017   17.3   0.0    1.7  2  Methyltransf_9   Protein of unknown function (DUF1698)
    0.00074   19.2   0.0     0.0012   18.4   0.0    1.3  1  MetW             Methionine biosynthesis protein MetW
     0.0015   18.1   0.0     0.0031   17.0   0.0    1.5  2  Methyltransf_PK  AdoMet dependent proline di-methyltransferas
     0.0025   17.4   0.0     0.0046   16.5   0.0    1.4  1  MTS              Methyltransferase small domain
     0.0067   16.4   0.1      0.014   15.4   0.0    1.5  2  Methyltransf_32  Methyltransferase domain
  ------ inclusion threshold ------
      0.039   13.9   0.0      0.073   13.0   0.0    1.5  1  Methyltransf_18  Methyltransferase domain
      0.039   13.3   0.0      0.061   12.7   0.0    1.3  1  Orn_Arg_deC_N    Pyridoxal-dependent decarboxylase, pyridoxal
      0.054   13.2   0.0        0.1   12.3   0.0    1.5  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.061   13.4   0.0        0.1   12.7   0.0    1.5  1  FtsJ             FtsJ-like methyltransferase
       0.07   13.5   0.0         20    5.5   0.0    2.4  2  CPL              CPL (NUC119) domain
        0.1   12.5   0.0       0.17   11.8   0.0    1.3  1  UPF0146          Uncharacterised protein family (UPF0146)
       0.12   13.4   0.0       0.22   12.6   0.0    1.4  1  Methyltransf_24  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.8   0.0     2e-24   1.5e-21       1      96 []      71     169 ..      71     169 .. 0.95

  Alignments for each domain:
  == domain 1  score: 76.8 bits;  conditional E-value: 2e-24
                                       EEET-TTSHHHHHHH.HTTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CCC- CS
                   Methyltransf_11   1 LdvGcGtGrlaeala.krgarvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlhhv 74 
                                       Ld+G+G G  a++la ++g++vv+++ls+   ++ ++ ++e+ l   +++v +++e+lp++d+sfD+v+s+ ++ h 
  gi|298674871|ref|YP_003726621.1|  71 LDIGAGYGGAARYLArNNGCQVVALNLSEVENERDRKMNEEQALdhLITVVDGSFENLPYPDDSFDVVWSQDSILHS 147
                                       8**************5555*************99999999999999999**************************** PP

                                       CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  75 edpekalkeiaRvLkpgGllvi 96 
                                        ++e+++ke+aRvLk gG +++
  gi|298674871|ref|YP_003726621.1| 148 GEREQVIKEVARVLKSGGDFIF 169
                                       ******************9987 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2   0.0   7.2e-20   5.6e-17       1      97 []      70     165 ..      70     165 .. 0.93

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 7.2e-20
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgalh 75 
                                       +Ld+G+G G  +++la++ g ++v+++ +se   e+ r+ +ee+ l   +++v g++e+lp++d+sfD+v+s+ ++ 
  gi|298674871|ref|YP_003726621.1|  70 ILDIGAGYGGAARYLARNNG-CQVVALNLSEVENERDRKMNEEQALdhLITVVDGSFENLPYPDDSFDVVWSQDSIL 145
                                       8*****************76.*****************99999888989999********************88855 PP

                                       GSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  76 hlsdedlekalkeiarvLkpgG 97 
                                       h    ++e+++ke+arvLk gG
  gi|298674871|ref|YP_003726621.1| 146 H--SGEREQVIKEVARVLKSGG 165
                                       5..35789*************9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       9.9   7.8e+03      39      60 ..       7      28 ..       5      42 .. 0.76
   2 !   52.8   0.0   4.9e-17   3.8e-14       2     119 ..      65     179 ..      64     233 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 9.9
                   Methyltransf_31 39 eaielArenaqklgldnveFeq 60
                                      +a+ +A+e   ++  dn+ F +
  gi|298674871|ref|YP_003726621.1|  7 TAVDKAQEYYNSNDADNFYFTI 28
                                      6888888888888888888765 PP

  == domain 2  score: 52.8 bits;  conditional E-value: 4.9e-17
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDl 77 
                                       +k+ ++lD+G+G G  +  la   + +++vv +  se   e+ r++ +++ ld  +++  g++e+l+  + d++fD+
  gi|298674871|ref|YP_003726621.1|  65 NKNSKILDIGAGYGGAARYLA--RNNGCQVVALNLSEVENERDRKMNEEQALDhLITVVDGSFENLP--YPDDSFDV 137
                                       7999*****************..35689*************************8899999*******..******** PP

                   Methyltransf_31  78 ilsnevlnaladpdkileeiervlkpggilliedprllaelp 119
                                       + s++ + +  + +++++e+ rvlk+gg ++ +dp   ++ p
  gi|298674871|ref|YP_003726621.1| 138 VWSQDSILHSGEREQVIKEVARVLKSGGDFIFTDPMQTDDCP 179
                                       **********************************98555555 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.0   9.5e-15   7.4e-12      10     125 ..      51     200 ..      41     252 .. 0.75

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 9.5e-15
                   Methyltransf_23  10 sdklerllpk...lraggrvLdiGcGtGillevl.rengfsvtgvDlspeaveiaekakkaqkdqfdeqeaae.... 78 
                                       ++ +er++ k   l++++++LdiG+G+G  +++l r ng++v++  ls++ +e+   ++k++ +q+  + +++    
  gi|298674871|ref|YP_003726621.1|  51 RRTVERMASKinnLNKNSKILDIGAGYGGAARYLaRNNGCQVVALNLSEVENER---DRKMNEEQALDHLITVvdgs 124
                                       45667777444447999*****************6666**********998887...56666666655533334444 PP

                   Methyltransf_23  79 ......pqgkfdlIvlrevlehvpdppellrqiatllkpgGylllseplasl.......................k 125
                                             p+++fd++ + +++ h    + +++ +a+ lk gG +++++p + +                        
  gi|298674871|ref|YP_003726621.1| 125 fenlpyPDDSFDVVWSQDSILHSGEREQVIKEVARVLKSGGDFIFTDPMQTDdcpegvlqpildrihleslgspgF 200
                                       444444999**************************************96655456666555555555555555443 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.0   3.1e-14   2.4e-11       8     164 ..      10     169 ..       3     185 .. 0.85
   2 ?   -2.7   0.0       3.8   2.9e+03     214     249 ..     218     249 ..     199     262 .. 0.58

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 3.1e-14
                                       HHHHHHH...TS-HHHHCTTS-TT---S----SSTT--HHHHHHHHHHHHHTTT.T--TT-EEEEES-TTSHHHHHH CS
                              CMAS   8 enikahY...DlsndffalfldptmtYsCAyferddmtLeeAqlaKldlilekl.elkpGmtlLdiGcGWGslvrra 80 
                                       ++ ++ Y   D  n +f+++ ++++      ++++d+ + +A ++ ++++  k+ +l++ +++LdiG+G+G+ +r+ 
  gi|298674871|ref|YP_003726621.1|  10 DKAQEYYnsnDADNFYFTIWGGEDIH--VGLYQSEDEPIFDASRRTVERMASKInNLNKNSKILDIGAGYGGAARYL 84 
                                       45555552225556677888888776..4689999999999999999988888736********************* PP

                                       HHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---...--SEEEEES-GGGTSGGGHHHHHHHHHH CS
                              CMAS  81 verydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde...kvdrvvsvgafehvgkenydtffkklkk 154
                                       +++ + +vv+l lS+ ++++ +k+ +e+ l++  +v    +e+l+     +d v s + + h g++  ++ +k++ +
  gi|298674871|ref|YP_003726621.1|  85 ARNNGCQVVALNLSEVENERDRKMNEEQALDHLITVVDGSFENLPYpddSFDVVWSQDSILHSGER--EQVIKEVAR 159
                                       ********************************************765569************9987..57899999* PP

                                       HS-TT-EEEE CS
                              CMAS 155 llkedGllll 164
                                       +lk++G ++ 
  gi|298674871|ref|YP_003726621.1| 160 VLKSGGDFIF 169
                                       **99998875 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.8
                                       EEEE-HHHHHHHHHHHHHHHHHTHHHHHHHSHHHHH CS
                              CMAS 214 dveslrahYakTLkaWaealqenkdeaialvseeva 249
                                       ++++l +hY + Lk+     +++ de+ ++vs+e +
  gi|298674871|ref|YP_003726621.1| 218 HTSQLPTHYGRVLKET----KRREDELSNVVSQEYI 249
                                       4455666666666543....2334444444444444 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.0     5e-12   3.9e-09      38     150 ..      57     168 ..      47     176 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 5e-12
                                       HHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT-TTS CS
                   Ubie_methyltran  38 fveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqanaeeLpfe 113
                                       +  k+++  + +k+lD+ +G g  a  l+++ g   +vv l+++e   +  +k  +e++    i  + ++ e+Lp+ 
  gi|298674871|ref|YP_003726621.1|  57 MASKINNLNKNSKILDIGAGYGGAARYLARNNG--CQVVALNLSEVENERDRKMNEEQALDhLITVVDGSFENLPYP 131
                                       566788888999*************99988654..5899999999888888877778887667999*********** PP

                                       -T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEE CS
                   Ubie_methyltran 114 ddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlv 150
                                       ddsfDvv     +    ++++++ke+ rvlk GG ++
  gi|298674871|ref|YP_003726621.1| 132 DDSFDVVWSQDSILHSGEREQVIKEVARVLKSGGDFI 168
                                       **********************************986 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   3.1e-11   2.4e-08       1      98 [.      71     166 ..      71     167 .. 0.79

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 3.1e-11
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakre..nnnnnnvelealdlldldggssfDlvvasnv 75 
                                       L+iG+G G  +r+l+++  +++++++ +s+     + +k+++++  ++  ++v+   ++l   d  +sfD+v++ + 
  gi|298674871|ref|YP_003726621.1|  71 LDIGAGYGGAARYLARN-NGCQVVALNLSEVEN-ERDRKMNEEQalDHLITVVDGSFENLPYPD--DSFDVVWSQDS 143
                                       8*************999.9***********999.444444444400344455555555554444..6********** PP

                   Methyltransf_12  76 lhhlkdirevldnirklLkpgGr 98 
                                       + h  ++++v+++++++Lk gG 
  gi|298674871|ref|YP_003726621.1| 144 ILHSGEREQVIKEVARVLKSGGD 166
                                       **********************7 PP

>> Methyltransf_29  Putative S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   1.3e-08     1e-05     105     220 ..      54     172 ..      46     184 .. 0.74
   2 ?   -3.9   0.0       4.8   3.7e+03      42      79 ..     223     261 ..     220     264 .. 0.58

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.3e-08
                   Methyltransf_29 105 laelipliaaggkvrtvlDvGCgvasfgayllsrd...vltlslapkDeheaqvqfaLeRgvpailavl..gtkrlp 176
                                       ++++ ++i++ +k  ++lD+G g    + yl  ++   v++l l+  ++ +   ++  e+ +  +++v+  + + lp
  gi|298674871|ref|YP_003726621.1|  54 VERMASKINNLNKNSKILDIGAGYGGAARYLARNNgcqVVALNLSEVENER-DRKMNEEQALDHLITVVdgSFENLP 129
                                       45566666666777789*****99988888887654448888887655443.34666777777777777334579** PP

                   Methyltransf_29 177 yPsrsfdlihCsrCridwteedgilllevdRvlRpgGyfvlsap 220
                                       yP  sfd++      i ++ e   ++ ev Rvl++gG f+++ p
  gi|298674871|ref|YP_003726621.1| 130 YPDDSFDVVWSQD-SILHSGEREQVIKEVARVLKSGGDFIFTDP 172
                                       ********98655.566666667889**************9866 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 4.8
                   Methyltransf_29  42 PkgYktpikWPksrdkvwyanvphtklaeekk.kqnWvk 79 
                                       P+ Y + +k  k r+    + v+ + +++ k+  q+Wv+
  gi|298674871|ref|YP_003726621.1| 223 PTHYGRVLKETKRREDELSNVVSQEYINNMKQgLQHWVN 261
                                       556666666666666666666666666655431466665 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   3.7e-07   0.00029      54     169 ..      57     174 ..      43     196 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.7e-07
                                       HHHSS-.GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-HHHHHHHHHHS..-----TTEEEEES-TTTS---. CS
                    Methyltransf_2  54 vleafd.leglkslvDvGGGtGalakaivsayPtikvivfDlpeVveaAkehl..sageeervefvgGdffkdslP. 126
                                       +  +++ l++ ++++D+G G G +a+  +++  +++v+ + l+eV ++  +++  ++++++ +++v+G+f + + P 
  gi|298674871|ref|YP_003726621.1|  57 MASKINnLNKNSKILDIGAGYGGAARYLARN-NGCQVVALNLSEVENERDRKMneEQALDHLITVVDGSFENLPYPd 132
                                       444444599999***********99998876.69************9999998656677899*******98555553 PP

                                       .--SEE.EEESSGGGS-HHHHHHHHHHHHHH--TT-EEEEEE--- CS
                    Methyltransf_2 127 .eaDai.llkrvlhDwsdekcvklLkrvkkalpagGkvivveavl 169
                                        + D++ +  ++lh  +     +++k+v + l++gG  i  + + 
  gi|298674871|ref|YP_003726621.1| 133 dSFDVVwSQDSILHSGE---REQVIKEVARVLKSGGDFIFTDPMQ 174
                                       33344413456888654...5567899999999***999888774 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   3.3e-06    0.0025      59     154 ..      53     167 ..      39     172 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.3e-06
                                       HHHHHHHHHCTS-TTS-EEEES-TT-HHH..HH--S-..EEEEESS-SSTT..............EEES-..TTS-S CS
                    Methyltransf_8  59 PldviirklkkkkdnlvvadlGcGeakia..eavrekekvrsfdlvavner..............vvacd..lakvP 117
                                        +++++ k+++ ++n  + d+G G    a   a ++  +v +++l  v+++              +++ d  + ++P
  gi|298674871|ref|YP_003726621.1|  53 TVERMASKINNLNKNSKILDIGAGYGGAAryLARNNGCQVVALNLSEVENErdrkmneeqaldhlITVVDgsFENLP 129
                                       57778888888888888888888766666333455556777777766543212222222233333555552269*** PP

                                       --TT-EEEEEEES---SS.-HHHHHHHHHHHEEEEEEE CS
                    Methyltransf_8 118 ledesvdvavfclslmgt.nladflkeanrvlkvGGll 154
                                         d+s dv+    s++   + ++ +ke+ rvlk GG +
  gi|298674871|ref|YP_003726621.1| 130 YPDDSFDVVWSQDSILHSgEREQVIKEVARVLKSGGDF 167
                                       ***********9998865267889************76 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   6.2e-07   0.00048      29     144 ..      65     181 ..      48     187 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 6.2e-07
                                       S-S-EEEEES-TTSHHHHHHHH.TT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--.GGG---.-S-EEEEEEE CS
                              TehB  29 vkpgkvldlgcgqgrnslylsl.lgydvtawdknensiafleeikekenlknistalyd.ineakl.derydfilst 102
                                        k +k+ld+g g g  + yl+  +g +v a++  e   +  ++++e ++l+ + t +    +++   d+ +d + s 
  gi|298674871|ref|YP_003726621.1|  65 NKNSKILDIGAGYGGAARYLARnNGCQVVALNLSEVENERDRKMNEEQALDHLITVVDGsFENLPYpDDSFDVVWSQ 141
                                       5789****************9637********99999999999999*****9888664324555434899***9999 PP

                                       SSGGGS-GGGHHHHHHHHHHTEEEEEEEEEEEEB--SSS--S CS
                              TehB 103 vvlmfleaeripsiienmqectkvggynlivaamstddvpct 144
                                         +  l++    ++i+++ +  k gg  +    m+tdd p  
  gi|298674871|ref|YP_003726621.1| 142 DSI--LHSGEREQVIKEVARVLKSGGDFIFTDPMQTDDCPEG 181
                                       876..455666899************************9965 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.2e-06    0.0017     103     218 ..      53     170 ..      48     186 .. 0.87
   2 ?   -0.9   0.0      0.78   6.1e+02       5      35 ..     240     270 ..     237     273 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.2e-06
                                       HHHHHGGGS.--.TT-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS- CS
                    Methyltransf_9 103 kWdrvlphlsdl.kgrtildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllgedqrahllplgieqlp 178
                                         +r+   +++l k+ +ild+G g G     ++ ++  +vv ++ se+     + +++  + d+  +++  + e+lp
  gi|298674871|ref|YP_003726621.1|  53 TVERMASKINNLnKNSKILDIGAGYGGAARYLARNNGCQVVALNLSEVENERDRKMNEEQALDHLITVVDGSFENLP 129
                                       56899999999956789*********9888888888999****99999998888888888889999999999***** PP

                                       T.---EEEEEEES-GGG-S-HHHHHHHHHCTEEEEEEEEEE CS
                    Methyltransf_9 179 e.leafdtvfsmGvlyhrrsPldhllqlkdqlvkgGelvle 218
                                          ++fd+v+s   + h     + + ++   l++gG++++ 
  gi|298674871|ref|YP_003726621.1| 130 YpDDSFDVVWSQDSILHSGEREQVIKEVARVLKSGGDFIFT 170
                                       9899*************99999999************9974 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.78
                                       HCTSTTHHHHHCHHHHHHHHHHCTCCHHHCC CS
                    Methyltransf_9   5 iakaklsewletlpaqlkewqekehgdlkrw 35 
                                       +++   +e+++ +++ l++w++  ++ +  w
  gi|298674871|ref|YP_003726621.1| 240 LSNVVSQEYINNMKQGLQHWVNGGNSGYLTW 270
                                       5666778999999999999999988888877 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.6e-06    0.0012      10     102 ..      63     161 ..      55     170 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.6e-06
                              MetW  10 likpgsrvldlGcGdGellellkeekqvdgrGlelde.....e...gvaecvakGlsviqgdldkdlenfedksfdy 78 
                                        ++++s++ld+G+G G   ++l+ +++ +   l+l+e     +   +  +++ + ++v++g  ++    ++d+sfd+
  gi|298674871|ref|YP_003726621.1|  63 NLNKNSKILDIGAGYGGAARYLARNNGCQVVALNLSEvenerDrkmNEEQALDHLITVVDGSFEN--LPYPDDSFDV 137
                                       46789****************99887666555544321111121112345677778888887765..469******* PP

                              MetW  79 vvlsqtlqatrnpkevldellrig 102
                                       v  + ++    + ++v++e+ r+ 
  gi|298674871|ref|YP_003726621.1| 138 VWSQDSILHSGEREQVIKEVARVL 161
                                       99999***************9995 PP

>> Methyltransf_PK  AdoMet dependent proline di-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0     4e-06    0.0031      20     162 ..      32     172 ..       6     180 .. 0.67
   2 ?   -2.8   0.0       4.6   3.6e+03     103     125 ..     246     268 ..     228     271 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4e-06
                   Methyltransf_PK  20 vdGvLGGygavskiDvkgsrkflkklkkeslpgkrevkvaldcGaGiGrvtknlLlkllskv...Dlvepvekflek 93 
                                       +d  +G y++ ++    +sr+ ++++ ++   + ++++ +ld+GaG G  ++ l  +   +v   +l e+ ++   k
  gi|298674871|ref|YP_003726621.1|  32 EDIHVGLYQSEDEPIFDASRRTVERMASK-INNLNKNSKILDIGAGYGGAARYLARNNGCQVvalNLSEVENERDRK 107
                                       444444455556666789********999.779****************9999988776555111344444444444 PP

                   Methyltransf_PK  94 akeelaeekkkvgkvyvvglqeftPeegrYdliWiqWcvghLtDedlvaflkrckkalkpnGlivvken 162
                                       ++ee a   ++   v   ++++    ++++d++W q  + h  + + v  +k +++ lk +G ++  + 
  gi|298674871|ref|YP_003726621.1| 108 MNEEQAL--DHLITVVDGSFENLPYPDDSFDVVWSQDSILHSGEREQV--IKEVARVLKSGGDFIFTDP 172
                                       4444333..4455666667888888899*********99998876644..6777777777777776665 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.6
                   Methyltransf_PK 103 kkvgkvyvvglqeftPeegrYdl 125
                                       ++  + +  glq+++   ++  l
  gi|298674871|ref|YP_003726621.1| 246 QEYINNMKQGLQHWVNGGNSGYL 268
                                       44556667788888766665555 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   5.9e-06    0.0046      28     136 ..      62     168 ..      48     175 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.9e-06
                                       HCC.TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTST..TS-EE CS
                               MTS  28 pke.lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvleeve..ekkfd 99 
                                       ++  ++ k+lD+G+G+G  +  la+++   +v++++ +    e  ++  e+++l+  ++vv    +e+++  +++fd
  gi|298674871|ref|YP_003726621.1|  62 NNLnKNSKILDIGAGYGGAARYLARNNGC-QVVALNLSEVENERDRKMNEEQALDhlITVVDG-SFENLPypDDSFD 136
                                       33345778**********99999986665.777887777777778888888888863444433.4455444599*** PP

                                       EEEE---STTTCHCHHHHHHHHHHHHHHHEEEEEEEE CS
                               MTS 100 livsNPPfhagkatelavaeeliaeAkeaLkegGeLl 136
                                       ++ s   + ++ +      e++i+e +++Lk+gG+++
  gi|298674871|ref|YP_003726621.1| 137 VVWSQDSILHSGE-----REQVIKEVARVLKSGGDFI 168
                                       **99877644444.....4899999999999999876 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.8e-05     0.014      13      74 ..      54     112 ..      50     135 .. 0.81
   2 ?   -3.1   0.1       8.5   6.6e+03      80      94 ..     211     225 ..     202     250 .. 0.49

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.8e-05
                   Methyltransf_32  13 vakllkelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraekl 74 
                                       v++++ ++++ +++ +++D+GaG g  ++ la    +++++vv+++++e  +e+ +k++e+ 
  gi|298674871|ref|YP_003726621.1|  54 VERMASKINNLNKNSKILDIGAGYGGAARYLAR---NNGCQVVALNLSEVENERDRKMNEEQ 112
                                       4555555555566789*****************...889*********99999999998875 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 8.5
                   Methyltransf_32  80 krlsfaelsieeats 94 
                                       k+++f+e++++  t+
  gi|298674871|ref|YP_003726621.1| 211 KEIEFEEHTSQLPTH 225
                                       555555555443333 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   9.4e-05     0.073       3      70 ..      55     121 ..      53     139 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.4e-05
                   Methyltransf_18   3 kRLkaiaslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievr 70 
                                       +R+++ ++ ++k+s+++DiG+  g  + yl++++ + +v+a +++e   e+ ++  e++ l++ i+v+
  gi|298674871|ref|YP_003726621.1|  55 ERMASKINNLNKNSKILDIGAGYGGAARYLARNNGC-QVVALNLSEVENERDRKMNEEQALDHLITVV 121
                                       68888889999*********************9999.7999999999999999888888887766654 PP

>> Orn_Arg_deC_N  Pyridoxal-dependent decarboxylase, pyridoxal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   7.9e-05     0.061     156     204 ..      31      80 ..      10     114 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.9e-05
                                       EEE---BSSC-SCHHHHHHHHH.HHHHHHHHHHHT---SEEE--S-BS-H CS
                     Orn_Arg_deC_N 156 GvsfHvGSgvsdleafvkavek.alklfdelaelGvklkiLdvGGGfgve 204
                                       G ++HvG   s+ e++ +a ++ + ++ +++++l  + kiLd+G G+g +
  gi|298674871|ref|YP_003726621.1|  31 GEDIHVGLYQSEDEPIFDASRRtVERMASKINNLNKNSKILDIGAGYGGA 80 
                                       5689***8777777777776651667778888***************533 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00013       0.1      67     134 ..      59     124 ..      45     175 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                                       HHTT.--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GG CS
                              PCMT  67 elle.lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGr 134
                                         ++ l+k +++L++G+G G  +  lar   + ++vv+++   e+ +e  r+++++++ +  ++v DG 
  gi|298674871|ref|YP_003726621.1|  59 SKINnLNKNSKILDIGAGYGGAARYLARN--NGCQVVALNL-SEVENERDRKMNEEQALDHLITVVDGS 124
                                       334449***********999988888874..5567788875.456666666666666665566666775 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00013       0.1      14      58 ..      59     104 ..      53     177 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                                       HHHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS...H CS
                              FtsJ  14 ekfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm...a 58 
                                       +k + ++++ +++D+ga+ Gg + +l+++ g  ++vva+ l ++   +
  gi|298674871|ref|YP_003726621.1|  59 SKINNLNKNSKILDIGAGYGGAARYLARNNG--CQVVALNLSEVeneR 104
                                       55666788899******************54..9*******9984441 PP

>> CPL  CPL (NUC119) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0      0.03        24      69     111 ..      82     131 ..      78     147 .. 0.80
   2 ?    5.5   0.0     0.025        20      42      72 ..     231     261 ..     225     270 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.03
                               CPL  69 ellsdnlgsqfvaevLlsaegdkq......eaieaiaklakgdlvaee.k 111
                                         l+ n g+q+va  L   e+++       +a++ +++++ g++ + +  
  gi|298674871|ref|YP_003726621.1|  82 RYLARNNGCQVVALNLSEVENERDrkmneeQALDHLITVVDGSFENLPyP 131
                                       568899*******99999988666778888*********99998766654 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.025
                               CPL  42 KdaevRrkELleaispallsaiaknaeells 72 
                                       K+++ R+ EL++ +s+++++ +++ ++ +++
  gi|298674871|ref|YP_003726621.1| 231 KETKRREDELSNVVSQEYINNMKQGLQHWVN 261
                                       8999******************999999886 PP

>> UPF0146  Uncharacterised protein family (UPF0146)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00022      0.17       4      48 ..      57     101 ..      54     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00022
                                       HHHHHHHHS-SSEEEEET-TT--HHHHHHHHHS.-EEEEE-SS-S. CS
                           UPF0146   4 lakkiaeenargkvvEvGiGrkldvaealakrg.vdlvatDikekk 48 
                                       +a+ki ++n+++k+ ++G+G     a++la+   +++va ++ e +
  gi|298674871|ref|YP_003726621.1|  57 MASKINNLNKNSKILDIGAGYGG-AARYLARNNgCQVVALNLSEVE 101
                                       7889999*************976.5888887655*****9988764 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00028      0.22       3     104 ..      73     170 ..      71     171 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00028
                   Methyltransf_24   3 iGvysGvstlwllralrrngagrlvavdhdpgaee.aaalareaglddrvrlikadseealaslaagsiDllfi.Dg 77 
                                       iG+ +G  + +l+    rn+  ++va+   + ++e  +++ +e+ ld+ ++++ + +e++ +  + +s+D+++  D 
  gi|298674871|ref|YP_003726621.1|  73 IGAGYGGAARYLA----RNNGCQVVALNLSEVENErDRKMNEEQALDHLITVVDGSFENL-PYPD-DSFDVVWSqDS 143
                                       7755666555555....6666688888888874441455556699999999999977776.5444.79*****7355 PP

                   Methyltransf_24  78 ghaaeavledleallprlapggvvlfd 104
                                            ++ + ++ + ++l++gg ++f 
  gi|298674871|ref|YP_003726621.1| 144 ILHSGEREQVIKEVARVLKSGGDFIFT 170
                                       555566777789999999999987775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 1690.23
//
Query:       gi|298674872|ref|YP_003726622.1|  [L=275]
Description: type 12 methyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.2e-16   59.1   0.0    9.5e-16   58.3   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
      2e-10   41.2   0.0    3.4e-10   40.4   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    9.3e-10   38.5   0.0    1.2e-09   38.2   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    1.2e-09   38.8   0.0    2.1e-09   38.0   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
      5e-07   29.3   0.1    8.1e-07   28.6   0.1    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      1e-06   28.7   0.0    1.5e-06   28.2   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
     0.0026   17.3   0.0     0.0039   16.8   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
     0.0046   16.4   0.0     0.0079   15.6   0.0    1.3  1  TehB             Tellurite resistance protein TehB
  ------ inclusion threshold ------
      0.017   15.7   0.1        0.2   12.3   0.1    2.4  1  Bin3             Bicoid-interacting protein 3 (Bin3)
      0.024   14.4   0.0      0.036   13.8   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.043   13.8   0.1       0.19   11.8   0.0    2.0  2  DUF1414          Protein of unknown function (DUF1414)
      0.046   13.3   0.0      0.069   12.7   0.0    1.3  1  MTS              Methyltransferase small domain
      0.053   13.0   0.0       0.12   11.8   0.0    1.5  2  CheR             CheR methyltransferase, SAM binding domain


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   0.0   6.9e-19   9.5e-16       1      97 []      68     165 ..      68     165 .. 0.95

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 6.9e-19
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBS.SSTTTEEEEEEEST.GG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlp.fedgsfDlvvssga.lh 75 
                                       vLd+++GtG ++ +l++++   +v+  D s+eml +a e+a++ g+ ++ vq+d + ++   +++fD++++ g+ + 
  gi|298674872|ref|YP_003726622.1|  68 VLDVATGTGFNSVRLLQAG--FEVVSADGSPEMLVKAFENARQYGYLMRTVQADWRWMNkDIHEEFDAILCLGNsFT 142
                                       9*****************5..**********************************999735788*********9999 PP

                                       G.SSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  76 h.lsdedlekalkeiarvLkpgG 97 
                                       h ++++d++kal+e++ +Lk +G
  gi|298674872|ref|YP_003726622.1| 143 HlFNERDRRKALAEFYALLKHDG 165
                                       999*****************998 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.0   2.5e-13   3.4e-10       1      95 [.      69     168 ..      69     169 .. 0.91

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 2.5e-13
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCT.SS-TT-EEEEEEES.-CCC-. CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaekl.pfednsfDlvvsse.vlhhv. 74 
                                       Ldv++GtG ++  l ++g +vv  D s+eml  a e+a++ g  ++ v+ad + + +   + fD++++   +++h+ 
  gi|298674872|ref|YP_003726622.1|  69 LDVATGTGFNSVRLLQAGFEVVSADGSPEMLVKAFENARQYGYLMRTVQADWRWMnKDIHEEFDAILCLGnSFTHLf 145
                                       8******************************9999999999998999******88444558******9877888888 PP

                                       ..CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  75 ..edpekalkeiaRvLkpgGllv 95 
                                          d++kal+e++ +Lk +G+l+
  gi|298674872|ref|YP_003726622.1| 146 neRDRRKALAEFYALLKHDGVLL 168
                                       988*****************997 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.0   8.6e-13   1.2e-09       5     116 ..      66     176 ..      62     239 .. 0.80

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 8.6e-13
                   Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsn 81 
                                       ++vlD+++GtG+ + +l  ++g   evv+ D s+e++ +A ena++ g+  ++  q+d+  ++k+++ e fD il+ 
  gi|298674872|ref|YP_003726622.1|  66 KKVLDVATGTGFNSVRLL-QAG--FEVVSADGSPEMLVKAFENARQYGYL-MRTVQADWRWMNKDIH-EEFDAILCL 137
                                       68****************.655..48***********************6.************8877.79******6 PP

                   Methyltransf_31  82 evl....naladpdkileeiervlkpggilliedprlla 116
                                       +          d  k+l e   +lk +g+ll+++ +  +
  gi|298674872|ref|YP_003726622.1| 138 GNSfthlFNERDRRKALAEFYALLKHDGVLLLDQRNYDS 176
                                       333443355678899****************99888333 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.0   1.5e-12   2.1e-09       1      99 []      69     167 ..      69     167 .. 0.83

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 1.5e-12
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvas.nvl 76 
                                       L++ +GtG ++ +ll++  + e++  D sp+++++a e  ++++ +    v+ + +   ++d  + fD+++++ n +
  gi|298674872|ref|YP_003726622.1|  69 LDVATGTGFNSVRLLQA--GFEVVSADGSPEMLVKAFENARQYGYL-MRTVQADWRW-MNKDIHEEFDAILCLgNSF 141
                                       89***************..**************8877777777754.3333333222.34444469*******9*** PP

                   Methyltransf_12  77 hhl...kdirevldnirklLkpgGrl 99 
                                        hl   +d+r++l+++++lLk +G+l
  gi|298674872|ref|YP_003726622.1| 142 THLfneRDRRKALAEFYALLKHDGVL 167
                                       ************************87 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.1   5.8e-10   8.1e-07      39     216 ..      56     243 ..      36     247 .. 0.67

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 5.8e-10
                                       HHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS....TEEEEE--TTT-T CS
                   Ubie_methyltran  39 veklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki....nieflqanaeeLp 111
                                       ++++  ++  +kvlDva+Gtg  +++l+   ++ ++vv +D +++mL  + + +++ g+     + ++   n +++ 
  gi|298674872|ref|YP_003726622.1|  56 IINILKERGVKKVLDVATGTGFNSVRLL---QAGFEVVSADGSPEMLVKAFENARQYGYLmrtvQADWRWMN-KDIH 128
                                       56666777778**********7777775...6789***********************98554444554444.4455 PP

                                       TS-T-EEEEEEES-.GGG-S-HHHHHHHHHHHEEEEEEEEEEEE----SHHHHHHHHH.HHH.HHHHHHHHHHS-HH CS
                   Ubie_methyltran 112 feddsfDvvtvsfG.lrnvtDklkaLkeayrvlkpGGrlvvlefskvelpllsqayel.yskevlPvlGkllakdld 186
                                       +e d+  ++  sf  l n  D+ kaL e y  lk  G l+  +  +    +l+q y+  ++++      ++  +++d
  gi|298674872|ref|YP_003726622.1| 129 EEFDAILCLGNSFThLFNERDRRKALAEFYALLKHDGVLLL-DQ-RNYDSILDQGYSSkHAHYYCGDSVSVYPEHVD 203
                                       56667777788996599********************8764.32.33334455555321222222222233333332 PP

                                       H......HHHHHHHH...HHS--HHHH.HHHHHHTTEEEE CS
                   Ubie_methyltran 187 s......yryLvesi...rafPdqetl.keliedaGfksv 216
                                       +      y++L +s+   ++fP ++++ + l+++ Gf+++
  gi|298674872|ref|YP_003726622.1| 204 EglarfrYEFLDNSVyylNMFPLRKDYtRRLLHEVGFQEI 243
                                       2222222777888864446788776652467888888776 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   1.1e-09   1.5e-06      20     161 ..      62     241 ..      25     245 .. 0.71

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.1e-09
                   Methyltransf_23  20 lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.....kakkaqkdqfdeqeaaepqg.......... 81 
                                       +r  ++vLd+++GtG ++  l + gf+v+  D spe+  +a                         g          
  gi|298674872|ref|YP_003726622.1|  62 ERGVKKVLDVATGTGFNSVRLLQAGFEVVSADGSPEMLVKAFenarqY------------------Gylmrtvqadw 120
                                       34456**********9999999*************9988873322220..................12222222234 PP

                   Methyltransf_23  82 .........kfdlIvlr.evlehvp...dppellrqiatllkpgGylllseplasl..................... 124
                                                 fd I +  +++ h+    d  ++l+ +++llk +G+lll   + ++                     
  gi|298674872|ref|YP_003726622.1| 121 rwmnkdiheEFDAILCLgNSFTHLFnerDRRKALAEFYALLKHDGVLLLDQRNYDSildqgysskhahyycgdsvsv 197
                                       444456777*****98523455554266799*******************999887888888888888888888888 PP

                   Methyltransf_23 125 ...kedrllldwlylvpagrhi..sff..sarslkelleeaGle 161
                                          + d+ l   +y++ ++ +   ++f  + +  ++ll+e G++
  gi|298674872|ref|YP_003726622.1| 198 ypeHVDEGLARFRYEFLDNSVYylNMFplRKDYTRRLLHEVGFQ 241
                                       88777888888888877773333344422445667777777776 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.8e-06    0.0039       2      61 ..      66     123 ..      65     148 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.8e-06
                   Methyltransf_15   2 rvilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfel 61 
                                       + +lD+ +G+G n++ + + + +v++ + ++e l  a +Na+ Yg    + +v++d+  +
  gi|298674872|ref|YP_003726622.1|  66 KKVLDVATGTGFNSVRLLQAGFEVVSADGSPEMLVKAFENARQYGYL--MRTVQADWRWM 123
                                       679*****************88**********************765..55677777654 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   5.7e-06    0.0079      31     101 ..      65     136 ..      46     156 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.7e-06
                                       S-EEEEES-TTSHHHHHHHHTT-EEEEEES-.HHHHHHHHHHHHHTT-TTEEEEE--GGG----S-EEEEEE CS
                              TehB  31 pgkvldlgcgqgrnslylsllgydvtawdkn.ensiafleeikekenlknistalydineaklderydfils 101
                                         kvld+  g g ns+ l   g++v + d   e+ ++ +e+ ++   l     a +   + +++e++d il 
  gi|298674872|ref|YP_003726622.1|  65 VKKVLDVATGTGFNSVRLLQAGFEVVSADGSpEMLVKAFENARQYGYLMRTVQADWRWMNKDIHEEFDAILC 136
                                       469**********************99996537889999999999999877777777778899999999985 PP

>> Bin3  Bicoid-interacting protein 3 (Bin3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00014       0.2       1      79 [.     131     208 ..     131     261 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                              Bin3   1 ydvilalSvtkwihLnkgDeglkrlfkkiyellkpgGvlilEpqewksYkkkkklseelkeny.kelklrpedfeev 76 
                                       +d il+l    + hL +  +  ++ ++++y+llk++Gvl+l++++++s  ++   s++++    +++++ pe+++e 
  gi|298674872|ref|YP_003726622.1| 131 FDAILCLG-NSFTHLFNE-RDRRKALAEFYALLKHDGVLLLDQRNYDSILDQGYSSKHAHYYCgDSVSVYPEHVDEG 205
                                       89999998.569999654.445899********************99987666655544433225677777766665 PP

                              Bin3  77 Lle 79 
                                       L +
  gi|298674872|ref|YP_003726622.1| 206 LAR 208
                                       555 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.6e-05     0.036      68     123 ..      59     111 ..      53     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.6e-05
                                       HTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTT CS
                              PCMT  68 llelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldl 123
                                        l+ + +++vL+v +G+G++++   rl+++ + vvs + ++e+  +a +n ++ ++
  gi|298674872|ref|YP_003726622.1|  59 ILKERGVKKVLDVATGTGFNSV---RLLQAGFEVVSADGSPEMLVKAFENARQYGY 111
                                       55556689************96...88999*****************999988765 PP

>> DUF1414  Protein of unknown function (DUF1414)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1         2   2.7e+03      13      22 ..      53      62 ..      53      63 .. 0.89
   2 ?   11.8   0.0   0.00014      0.19       9      37 ..     134     159 ..     133     161 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2
                                      HHHHHHHHTT CS
                           DUF1414 13 GNmvTnilns 22
                                      GN + nil++
  gi|298674872|ref|YP_003726622.1| 53 GNTIINILKE 62
                                      9*******86 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00014
                                       HHHHHHHHHHHHTTTS-CCCHHHHHHHHH CS
                           DUF1414   9 LmvLGNmvTnilnssVpeaqRealAekFa 37 
                                       +++LGN  T+++n++   + R+alAe +a
  gi|298674872|ref|YP_003726622.1| 134 ILCLGNSFTHLFNER---DRRKALAEFYA 159
                                       79**********985...77999998765 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     5e-05     0.069      23     103 ..      56     136 ..      52     169 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5e-05
                                       HHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-S...TTTTSTTS CS
                               MTS  23 LletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasd...vleeveek 96 
                                       +++ l+++  +kvlD+++G+G+ ++ l+++  e  v+  d + + l  a en+++ +  +++v+ d   + ++++ +
  gi|298674872|ref|YP_003726622.1|  56 IINILKERGVKKVLDVATGTGFNSVRLLQAGFE--VVSADGSPEMLVKAFENARQYGYLMRTVQADwrwMNKDIH-E 129
                                       577889988889***************997766..9*****************9999886666555211566666.9 PP

                                       -EEEEEE CS
                               MTS  97 kfdlivs 103
                                       +fd+i++
  gi|298674872|ref|YP_003726622.1| 130 EFDAILC 136
                                       9999987 PP

>> CheR  CheR methyltransferase, SAM binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.7   3.7e+03      64      81 ..      86     103 ..      81     121 .. 0.76
   2 ?   11.8   0.0   8.8e-05      0.12     131     173 ..     125     169 ..     114     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.7
                                       -EEEEEEESSCHHHHHHH CS
                              CheR  64 kvkilAtDidlkvlekAk 81 
                                        ++++  D + ++l kA 
  gi|298674872|ref|YP_003726622.1|  86 GFEVVSADGSPEMLVKAF 103
                                       578888999999888774 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 8.8e-05
                                       SGGG--EEEEEE-.S.SGGGC-CHHHHHHHHHHHCCEEEEEEEEE CS
                              CheR 131 ksvlgklDvifcr.n.vliYfdeetqekvlerfaeklkpgglLll 173
                                       k++++++D i+c  n     f+e +++k l +f+  lk++g+Lll
  gi|298674872|ref|YP_003726622.1| 125 KDIHEEFDAILCLgNsFTHLFNERDRRKALAEFYALLKHDGVLLL 169
                                       78899******9535145679**********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 1642.90
//
Query:       gi|298674873|ref|YP_003726623.1|  [L=467]
Description: adenosylhomocysteinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   6.4e-147  488.5   0.1   7.2e-147  488.3   0.1    1.0  1  AdoHcyase      S-adenosyl-L-homocysteine hydrolase
      6e-78  260.5   2.2    8.8e-78  260.0   2.2    1.2  1  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
    4.3e-06   26.2   0.1    7.9e-06   25.4   0.1    1.3  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    0.00043   19.9   0.2     0.0008   19.0   0.2    1.4  1  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
      0.001   19.3   0.0     0.0029   17.8   0.0    1.8  1  TrkA_N         TrkA-N domain
  ------ inclusion threshold ------
      0.039   14.4   0.4        0.1   13.1   0.2    1.8  2  NAD_binding_7  Putative NAD(P)-binding
       0.05   14.2   0.0       0.14   12.8   0.0    1.8  1  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
       0.13   12.1   0.1       0.27   11.1   0.1    1.6  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d


Domain annotation for each model (and alignments):
>> AdoHcyase  S-adenosyl-L-homocysteine hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  488.3   0.1  3.2e-150  7.2e-147       1     299 []       5     466 ..       5     466 .. 0.99

  Alignments for each domain:
  == domain 1  score: 488.3 bits;  conditional E-value: 3.2e-150
                                       --B-S-GGGHHHHHHHHHHHHCC-HHHHHHHHHCTTT-TTTT-EEEEES--SHHHHHHHHHHHHTT-EEEEE-SSTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase   1 dykvkdislaefGrkeielaekempglmalreeyaeekplkgariaGslhmtiqtavLietLvalGaevrWasCnif 77 
                                       dyk+kdi lae+Grk+i++aekempgl+a+re+y+ +kplkgar++Gslhmt+qtavLietLv+lGa+vrWasCnif
  gi|298674873|ref|YP_003726623.1|   5 DYKIKDIGLAELGRKQINMAEKEMPGLIATREKYGPQKPLKGARVSGSLHMTVQTAVLIETLVELGADVRWASCNIF 81 
                                       8**************************************************************************** PP

                                       T--HHHHHHHCCTTEEEE--TT--HHHHHHHHHHCHS-SSTS-S-SEEEESSSHHHHHHHHHHHHH.H......S.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x.xxxxxxxx RF
                         AdoHcyase  78 stqdeaaaaiaeagvpvfawkgetleeywwcieqalkwaedekepnlilDdGGDltllvhkgvkee.e.svlekeed 152
                                       stqdeaaaaia++g+pvfawkget +eywwc++qal+w  d+k+p+li+DdGGD+tl++h+g+++e + s+l+++++
  gi|298674873|ref|YP_003726623.1|  82 STQDEAAAAIAAEGIPVFAWKGETVDEYWWCTKQALTWS-DGKGPHLIVDDGGDATLMMHRGYEAEdNpSILDEPTE 157
                                       ************************************995.788*********************775679******* PP

                                       SHHHHHHHHHHHHHHTT..THHCCCHCC--EEEE-SHHHHHHHHHHHHTT---SEEEESTTSHHHCTTH........ CS
                                       xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........ RF
                         AdoHcyase 153 eeeekvvlellkksleed.kkytellkkikGvseetttGvhrLyelakkgkLlvpainvndsvtkskfD........ 220
                                       +++ ++ +++lk+s++ed + ++++++++kGvseetttGvhrLy+ +k+g+LlvpainvndsvtkskfD        
  gi|298674873|ref|YP_003726623.1| 158 NKDLMAQNKILKDSQAEDpQFWHKAVAEWKGVSEETTTGVHRLYHWEKDGELLVPAINVNDSVTKSKFDniygcres 234
                                       ***************9999********************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                         AdoHcyase 221 ............................................................................. 220
                                                                                                                    
  gi|298674873|ref|YP_003726623.1| 235 lvdaikrgtdvmvagkvavvcgygdvgkgsaealanhkarvivtesdpicalqalmegysvmtvedalpygdiyvtt 311
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                         AdoHcyase 221 ............................................................................. 220
                                                                                                                    
  gi|298674873|ref|YP_003726623.1| 312 tgnrdvittdhmskmkdqaivcnighfdneiqvdelnkmnnvekveikpqvdkyefpdghsiymlaegrlvnlglat 388
                                       ***************************************************************************** PP

                                       .S-HHHHHHHHHHHHHHHHHHHHTTSSS-SSEEE--CHHHHHHHHHCCCCCT-------HHHHHCCTSXTTSXXSXT CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase 221 .hpsfvmsasftnqvlaqielfkkekkyekkvyvlpkklDekvarlhleklgaklteltkeqaeyigveveGPfkpd 296
                                        hpsfvms+sftnq+laqi+l+++ k  + +vy+lpk lDe+varlhl+klgaklt++t+eqaeyig +v+GP+kpd
  gi|298674873|ref|YP_003726623.1| 389 gHPSFVMSNSFTNQTLAQIDLWENPK--DIGVYRLPKVLDEEVARLHLDKLGAKLTKMTQEQAEYIGFPVDGPHKPD 463
                                       ***********************655..899********************************************** PP

                                       TXX CS
                                       xxx RF
                         AdoHcyase 297 hYr 299
                                       hYr
  gi|298674873|ref|YP_003726623.1| 464 HYR 466
                                       **9 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  260.0   2.2   3.9e-81   8.8e-78       1     162 []     227     389 ..     227     389 .. 0.99

  Alignments for each domain:
  == domain 1  score: 260.0 bits;  conditional E-value: 3.9e-81
                                       HHHHHCCCCCHHHHHHH-S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTT CS
                     AdoHcyase_NAD   1 nlygcreslvdgikratdvllaGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvk 77 
                                       n+ygcreslvd+ikr+tdv++aGkvavv+GyGdvGkG+a++l ++ arvivte dPicalqa+meG++v+t+e+++ 
  gi|298674873|ref|YP_003726623.1| 227 NIYGCRESLVDAIKRGTDVMVAGKVAVVCGYGDVGKGSAEALANHKARVIVTESDPICALQALMEGYSVMTVEDALP 303
                                       89*************************************************************************** PP

                                       T-SEEEE-SSSSSSB-HHHHCCS-TTEEEEE-SSTTTTBTHHHHHTT.T-EEEEEETTEEEEE-TTS-EEEEEGGGS CS
                     AdoHcyase_NAD  78 kadivvtttGnkdiitlehlkkmkddaivcniGhfdseidvaalean.alkkeevkpqvdrvtlkdgkkiillaeGr 153
                                        +di+vtttGn+d+it++h++kmkd+aivcniGhfd+ei+v++l+++ +++k+e+kpqvd+++++dg++i +laeGr
  gi|298674873|ref|YP_003726623.1| 304 YGDIYVTTTGNRDVITTDHMSKMKDQAIVCNIGHFDNEIQVDELNKMnNVEKVEIKPQVDKYEFPDGHSIYMLAEGR 380
                                       ********************************************998799*************************** PP

                                       BCHHHTS-- CS
                     AdoHcyase_NAD 154 llnlgcatg 162
                                       l+nlg atg
  gi|298674873|ref|YP_003726623.1| 381 LVNLGLATG 389
                                       ******997 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.1   3.5e-09   7.9e-06      33     127 ..     246     336 ..     231     342 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 3.5e-09
                                       -GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S--STTTTTSB CS
                      2-Hacid_dh_C  33 elsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivslhlpltpetrhli 109
                                        ++gk   + G+G++G+  a+ l+  +++vi+++  +    ++  +g++++++e++l   Di +     t  +r++i
  gi|298674873|ref|YP_003726623.1| 246 MVAGKVAVVCGYGDVGKGSAEALANHKARVIVTESDPICALQALMEGYSVMTVEDALPYGDIYVT----TTGNRDVI 318
                                       578999*****************************999777899999**************9876....5679**** PP

                                       SHHHHHCSTTTEEEEESS CS
                      2-Hacid_dh_C 110 naeelakmkkgailiNta 127
                                       + ++++kmk++ai+ N++
  gi|298674873|ref|YP_003726623.1| 319 TTDHMSKMKDQAIVCNIG 336
                                       ****************98 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.2   3.6e-07    0.0008       3      92 ..     248     333 ..     246     373 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 3.6e-07
                                       HTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHHH CS
                              IlvN   3 kgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevyee 79 
                                        gk  +v GyG  G+  a+ l + +  v+v+  +    + +A  eg++v+tv++a    d+ ++ +    +++v+++
  gi|298674873|ref|YP_003726623.1| 248 AGKVAVVCGYGDVGKGSAEALANHKARVIVTESDPI-CALQALMEGYSVMTVEDALPYGDIYVTTT---GNRDVITT 320
                                       56667788*********************9877766.8899*******************876654...45677777 PP

                                       HTGGG--TT-EEE CS
                              IlvN  80 eiepnlkegkala 92 
                                       + + ++k+++++ 
  gi|298674873|ref|YP_003726623.1| 321 DHMSKMKDQAIVC 333
                                       7777777776554 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.3e-06    0.0029       2      45 ..     253     296 ..     252     302 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.3e-06
                                       EEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEE CS
                            TrkA_N   2 iiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevv 45 
                                       +++G+G+vG+  ae L +++ +v+v ++d+  + ++  eg+ v+
  gi|298674873|ref|YP_003726623.1| 253 VVCGYGDVGKGSAEALANHKARVIVTESDPICALQALMEGYSVM 296
                                       8*****************7767*******988888888887765 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       7.2   1.6e+04      25      41 ..      65      81 ..      63     101 .. 0.55
   2 ?   13.1   0.2   4.5e-05       0.1       5      91 ..     247     335 ..     245     344 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 7.2
                     NAD_binding_7 25 klleagakvtvvapevk 41
                                      +l+e ga+v   + +++
  gi|298674873|ref|YP_003726623.1| 65 TLVELGADVRWASCNIF 81
                                      56666666655554442 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 4.5e-05
                     NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvk.laeeelekdlegadlviaatddrelner.ia 79 
                                       + gk  +v G G+v+   ++ l++ +a+v+v   +   +l+ l++ ++  ++e+ l   d+ +++t +r++ +   +
  gi|298674873|ref|YP_003726623.1| 247 VAGKVAVVCGYGDVGKGSAEALANHKARVIVTESDPICALQALMEgYSVMTVEDALPYGDIYVTTTGNRDVITTdHM 323
                                       578999*************************9999655555555545556668888888888888888776443266 PP

                     NAD_binding_7  80 eaakarrilvnv 91 
                                        ++k++ i++n+
  gi|298674873|ref|YP_003726623.1| 324 SKMKDQAIVCNI 335
                                       677778888876 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.1e-05      0.14       1      71 [.     250     314 ..     250     332 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.1e-05
                                       EEEEE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-H CS
                     F420_oxidored   1 kigii.GaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkp 71 
                                       k++++ G+G++g++ a+ l+++      ++v+ s     +++l e ++     ++ e+a+   d++v +   
  gi|298674873|ref|YP_003726623.1| 250 KVAVVcGYGDVGKGSAEALANHK---ARVIVTESDPICALQALMEGYS----VMTVEDALPYGDIYVTTTGN 314
                                       689999****************9...9999886666666666666665....34477888888887776555 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00012      0.27       3      36 ..     253     286 ..     250     334 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                                       EEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHH CS
                           3HCDH_N   3 aviGaGtmGagiaavfasagleVvlvdiseeale 36 
                                        v+G G +G+g a+++a+++ +V +++ ++  + 
  gi|298674873|ref|YP_003726623.1| 253 VVCGYGDVGKGSAEALANHKARVIVTESDPICAL 286
                                       367**********************999876554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 2835.62
//
Query:       gi|298674874|ref|YP_003726624.1|  [L=399]
Description: S-adenosylmethionine synthetase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-62  210.0   0.1    1.2e-61  206.7   0.0    2.1  2  S-AdoMet_synt_C  S-adenosylmethionine synthetase, C-terminal 
    4.2e-40  136.7   0.0    9.3e-40  135.6   0.0    1.6  1  S-AdoMet_synt_M  S-adenosylmethionine synthetase, central dom
    1.2e-32  112.6   1.5    1.2e-32  112.5   0.3    1.7  2  S-AdoMet_synt_N  S-adenosylmethionine synthetase, N-terminal 
  ------ inclusion threshold ------
       0.05   12.4   0.0      0.083   11.7   0.0    1.5  1  AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synt


Domain annotation for each model (and alignments):
>> S-AdoMet_synt_C  S-adenosylmethionine synthetase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.096   4.3e+02      62     103 ..     174     215 ..     171     227 .. 0.79
   2 !  206.7   0.0   2.6e-65   1.2e-61       1     138 []     240     382 ..     240     382 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.096
                                       EEEEEEEE-TT-SS-SEEEEEE-S-BSS-HHHHHHHHHHH-- CS
                   S-AdoMet_synt_C  62 kvevqlsYaigvaepvsisvetfgtekvseeeiaeivkevfd 103
                                       k +v + Y+ g  + ++  v +++t+ v+ e++ + + + ++
  gi|298674874|ref|YP_003726624.1| 174 KSQVSIKYVNGKPDHITTVVVSQQTDDVPLEKVRNDIVDLVN 215
                                       668999************9*999**99988888776655544 PP

  == domain 2  score: 206.7 bits;  conditional E-value: 2.6e-65
                                       S-TTTTS-EETTS-TTTTTTTTSS---S---TTB-TTSHHHHHHHHHHHHHHHHHHTTSBSEEEEEEEE-TT-SS-S CS
                   S-AdoMet_synt_C   1 iGgpkgdaGltgrkiivdtYgglaahgggafsgKdptkvDrsaayaaryvaknlvaaglakkvevqlsYaigvaepv 77 
                                       +Ggp +daGltgrkiivdtYgg+++hgggafsgKdp+kvDrsaay+ar+ akn+vaagla+k+e+q++Yaigva+p+
  gi|298674874|ref|YP_003726624.1| 240 LGGPYADAGLTGRKIIVDTYGGVGSHGGGAFSGKDPSKVDRSAAYYARHAAKNIVAAGLADKCEIQVAYAIGVAKPL 316
                                       59*************************************************************************** PP

                                       EEEEEE-S-BSS-HHHHHHHHH..HH----HHHHHHHHTTTSS...--TGGGSS-SSS--T-TTS. CS
                   S-AdoMet_synt_C  78 sisvetfgtekvseeeiaeivk..evfdlrpaaiieeldLkkp...iykktaayghfgreelpwek 138
                                       si+v+t+gt+ v+++ei+++++  e+fd+rpaa+i++l+L +p    y++ ++yghfgr+ +pwe+
  gi|298674874|ref|YP_003726624.1| 317 SINVDTYGTGVVEDQEIQDVLEsgEIFDFRPAALIDDLELLNPkgwSYREASTYGHFGRDIFPWEQ 382
                                       *********************85579**************9987779*****************97 PP

>> S-AdoMet_synt_M  S-adenosylmethionine synthetase, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.6   0.0   2.1e-43   9.3e-40       1     120 []     122     238 ..     122     238 .. 0.92

  Alignments for each domain:
  == domain 1  score: 135.6 bits;  conditional E-value: 2.1e-43
                   S-AdoMet_synt_M   1 eigAgDqGimfGYAtdeteelmPlpillahklaerlaelrkegeleylrpDaKsqvtveYeeelkpvrvdtvvistq 77 
                                       ++gAgDqG+mfGYAt+et+e+mP+pi+++h+l++ l+++rkeg+l+ylrpD+Ksqv+++Y  ++kp +++tvv+s q
  gi|298674874|ref|YP_003726624.1| 122 DQGAGDQGMMFGYATNETPEFMPAPIAYSHRLLQYLDTVRKEGKLSYLRPDSKSQVSIKYV-NGKPDHITTVVVSQQ 197
                                       58**********************************************************5.99***********99 PP

                   S-AdoMet_synt_M  78 hdeevsqeklredlkekvikkvl.keelldekktkllinptGkF 120
                                        d +v  ek+r+d+ + v + vl ++ ll++ +t+++inptG+F
  gi|298674874|ref|YP_003726624.1| 198 TD-DVPLEKVRNDIVDLVND-VLePTGLLRS-DTEYFINPTGSF 238
                                       99.5899********98866.6615557655.7*********99 PP

>> S-AdoMet_synt_N  S-adenosylmethionine synthetase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.5   0.3   2.7e-36   1.2e-32       2      99 .]       8     107 ..       7     107 .. 0.95
   2 ?   -3.0   0.1       2.8   1.2e+04      11      22 ..     183     194 ..     169     217 .. 0.65

  Alignments for each domain:
  == domain 1  score: 112.5 bits;  conditional E-value: 2.7e-36
                   S-AdoMet_synt_N   2 ylftsesVseGHPDkvadqisdaildailkedpkarvacetlvttglvvvageittk..akvdiekivrevikeigY 76 
                                       ++ftse+V +GHPDkv+dq+sda+lda+l++d+++rvacetlv+++l++ ageit k   ++++e+i+r+ +++igY
  gi|298674874|ref|YP_003726624.1|   8 HVFTSEAVGSGHPDKVCDQVSDAVLDACLAADKDSRVACETLVAHDLLINAGEITCKgmDQINTENIARDIVRDIGY 84 
                                       68****************************************************98733568*************** PP

                   S-AdoMet_synt_N  77 ekeelgfdaktcevlvaleeqsp 99 
                                       + e+l f  +++e +++++eqsp
  gi|298674874|ref|YP_003726624.1|  85 DCEDLLFWDQSFEYMSKIHEQSP 107
                                       *99*******************7 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.8
                   S-AdoMet_synt_N  11 eGHPDkvadqis 22 
                                       +G PD+++  + 
  gi|298674874|ref|YP_003726624.1| 183 NGKPDHITTVVV 194
                                       466666655433 PP

>> AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synthetase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.8e-05     0.083      21      42 ..      12      33 ..       2     135 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.8e-05
                                      EEEE-TTSHHHHHHHHHHHHHH CS
                   AdoMet_Synthase 21 vErKGiGHPDsiaDgiaeavsr 42
                                       E  G GHPD+++D++++av  
  gi|298674874|ref|YP_003726624.1| 12 SEAVGSGHPDKVCDQVSDAVLD 33
                                      57889*************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2406.50
//
Query:       gi|298674875|ref|YP_003726625.1|  [L=260]
Description: 6-phosphogluconate dehydrogenase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-05   25.4   0.0      3e-05   24.4   0.0    1.5  1  NAD_binding_7  Putative NAD(P)-binding
    8.1e-05   22.8   0.0    0.00015   22.0   0.0    1.4  1  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
    0.00052   19.9   0.0     0.0009   19.2   0.0    1.4  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
     0.0014   18.0   0.0     0.0023   17.3   0.0    1.4  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
      0.006   17.1   0.0      0.014   15.9   0.0    1.7  1  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.011   15.0   0.0      0.018   14.3   0.0    1.3  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
      0.013   15.0   0.0       0.11   12.0   0.0    2.0  2  adh_short      short chain dehydrogenase
      0.069   13.2   0.0       0.18   11.9   0.0    1.8  2  Shikimate_DH   Shikimate / quinate 5-dehydrogenase
      0.069   13.4   0.0       0.15   12.4   0.0    1.5  1  TrkA_N         TrkA-N domain
      0.096   12.3   0.0       0.16   11.6   0.0    1.4  1  ApbA           Ketopantoate reductase PanE/ApbA


Domain annotation for each model (and alignments):
>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   1.7e-08     3e-05       6      74 ..     140     210 ..     138     230 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.7e-08
                     NAD_binding_7   6 kgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvk...laeeelekdlegadlviaatddrel 74 
                                       ++k +lv+G G+v++  +++l+++g +v  ++p+ +e+l++ v+   +++ ++++d +++ +v+ at++++ 
  gi|298674875|ref|YP_003726625.1| 140 DTKDILVIGLGKVGYAGASHLIRKGFNVYAYDPD-NEALNSAVQelgVHPYDIHRDGKKFCMVFEATPNENT 210
                                       5799******************************.55556444444489999***************99865 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   8.1e-08   0.00015       2      44 ..     144     187 ..     143     220 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 8.1e-08
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHT.TEE CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvae.gak 44 
                                       i +iGlG+ G   a++l+++g++v++y+ ++e+++++v+e g++
  gi|298674875|ref|YP_003726625.1| 144 ILVIGLGKVGYAGASHLIRKGFNVYAYDPDNEALNSAVQElGVH 187
                                       779*********************************99983343 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0     5e-07    0.0009       2      44 ..     144     186 ..     143     217 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 5e-07
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekiek 44 
                                       + viG G +G   a+ ++++g++V  +d ++eal++a +++  
  gi|298674875|ref|YP_003726625.1| 144 ILVIGLGKVGYAGASHLIRKGFNVYAYDPDNEALNSAVQELGV 186
                                       679**********************************998865 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.3e-06    0.0023      16      85 ..     121     191 ..      99     223 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.3e-06
                                       HHHHTTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.CHHHHTCEECSH CS
                      2-Hacid_dh_C  16 eevregewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee.eeeelgvelvsl 85 
                                       + v +g   +e a + k    k + +iGlG++G a a  l   g++v+ayd+ +++ + +++elgv+  ++
  gi|298674875|ref|YP_003726625.1| 121 NHVCTGVIYAEIASRCKYADTKDILVIGLGKVGYAGASHLIRKGFNVYAYDPDNEALNsAVQELGVHPYDI 191
                                       45555544556666777788999*****************************9876555666666655555 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     8e-06     0.014       2      49 ..     144     187 ..     143     213 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8e-06
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-E CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvk 49 
                                       i +iG G++g a as l+++g    +++ a ++++e ++++ +elgv 
  gi|298674875|ref|YP_003726625.1| 144 ILVIGLGKVGYAGASHLIRKG---FNVY-AYDPDNEALNSAVQELGVH 187
                                       669******************...****.99*************9964 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     1e-05     0.018      28     111 ..     141     237 ..     126     247 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1e-05
                                       --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHH.HHHTTTCECEE............HCHHHHHHHHHHHH CS
                       AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgakVtvlDvrparleq.leslgakfvev............lksqeellaeavke 91 
                                          +lviG G +G + ++   + g +V+++D + ++l+  +++lg +  ++             + +e+++++ + +
  gi|298674875|ref|YP_003726625.1| 141 TKDILVIGLGKVGYAGASHLIRKGFNVYAYDPDNEALNSaVQELGVHPYDIhrdgkkfcmvfeATPNENTITKDMIS 217
                                       5679***************************9988877515668887777777999999998888889999999999 PP

                                       -SEEEE---BTTSS---SC- CS
                       AlaDh_PNT_C  92 advvigtvlipGkkaPkLvt 111
                                          +++t  ip   +P L +
  gi|298674875|ref|YP_003726625.1| 218 ERCLVSTPGIPCGLSPELGN 237
                                       99999999999888888865 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.21   3.8e+02     163     188 ..     109     134 ..     108     139 .. 0.86
   2 ?   12.0   0.0   5.9e-05      0.11       3      46 ..     144     186 ..     142     199 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.21
                                       HHHHHGGGTEEEEEEEESSBSSHHHH CS
                         adh_short 163 lakelaptgirvnavaPGlvdTdmak 188
                                       +a+ l++ +i  n v++G++  ++a 
  gi|298674875|ref|YP_003726625.1| 109 IAHNLRNGKIATNHVCTGVIYAEIAS 134
                                       578899999**********9988765 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 5.9e-05
                                       EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHH CS
                         adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelke 46 
                                       +lv+G ++ +G+a a +l+++G++v+++d  +e+l+ +++el+ 
  gi|298674875|ref|YP_003726625.1| 144 ILVIGLGK-VGYAGASHLIRKGFNVYAYDPDNEALNSAVQELGV 186
                                       77888775.8*******************************985 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       3.5   6.2e+03      43      67 ..      13      37 ..       8      62 .. 0.59
   2 ?   11.9   0.0   9.9e-05      0.18       9      39 ..     138     167 ..     131     222 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.5
                                      ESSHHHHHHHHHHHT.ET-EEEEGC CS
                      Shikimate_DH 43 NRtlerakelaeelkgeeiealkle 67
                                       R++e+ +++ ++  g+ i+ +  +
  gi|298674875|ref|YP_003726625.1| 13 SRQFEKNNDIIKRATGQGIRDICES 37
                                      5677777777777666655544444 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 9.9e-05
                                       ..TT-EEEEES-SHHHHHHHHHHHCCT-CEE CS
                      Shikimate_DH   9 slkekkvlliGaGemaelvakhLlakgvkkv 39 
                                         ++k +l+iG G+++   a+hL++kg++ v
  gi|298674875|ref|YP_003726625.1| 138 YADTKDILVIGLGKVGYAGASHLIRKGFN-V 167
                                       467899********************987.4 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   8.2e-05      0.15       1      41 [.     144     184 ..     144     196 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.2e-05
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTT CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeg 41 
                                       i++iGlG+vG++ a  L ++g +v++ d d e+++++ +e 
  gi|298674875|ref|YP_003726625.1| 144 ILVIGLGKVGYAGASHLIRKGFNVYAYDPDNEALNSAVQEL 184
                                       79*****************6646***********9987665 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   8.8e-05      0.16       1      47 [.     144     192 ..     144     227 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.8e-05
                                       EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHH.HHHHCEEEEETT CS
                              ApbA   1 iailGaGaiGsllaakLakagadvtlilrsr.rlea.lkknGlrltseg 47 
                                       i+++G+G +G   a +L ++g +v+ ++ ++  l++ +++ G++ ++ +
  gi|298674875|ref|YP_003726625.1| 144 ILVIGLGKVGYAGASHLIRKGFNVYAYDPDNeALNSaVQELGVHPYDIH 192
                                       89*****************************999888888887765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.56u 0.34s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 1521.44
//
Query:       gi|298674876|ref|YP_003726626.1|  [L=370]
Description: hypothetical protein Metev_0936 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.2e-15   55.4   0.1    1.2e-14   54.7   0.1    1.3  1  ATP-grasp_3      ATP-grasp domain
    1.3e-05   24.8   0.1    2.3e-05   24.0   0.1    1.5  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    0.00013   21.7   0.0    0.00025   20.8   0.0    1.4  1  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
    0.00063   19.4   4.3     0.0068   16.0   0.1    2.8  3  ATP-grasp_4      ATP-grasp domain
     0.0029   17.2   0.0      0.005   16.4   0.0    1.3  1  ATP-grasp        ATP-grasp domain
  ------ inclusion threshold ------
      0.035   14.7   0.0       0.11   13.1   0.0    1.9  1  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
       0.16   11.7   1.2        1.9    8.2   0.2    2.9  4  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr


Domain annotation for each model (and alignments):
>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.7   0.1   4.7e-18   1.2e-14       2     158 ..     102     245 ..     101     248 .. 0.86

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 4.7e-18
                                       TSHHHHHHHHTTT.S---....-EESS--SSSEEEEESS-------B--SS--TTE.......EEEE---SEEEEEE CS
                       ATP-grasp_3   2 sdKlktykkLkeagvkvPtkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieevelvqefieGkplSvs 78 
                                       sdK k+ + +k  ++++P      +  + + ++++Kp + + + +v+++++++ ++++ +e++++ efieG+ +S++
  gi|298674876|ref|YP_003726626.1| 102 SDKQKSKQYFKSINIPTP------KDYPCKLPCIIKPLSESSSIGVSIIHDNKYLDSKTDELKIIEEFIEGDVVSLE 172
                                       89***********99999......44556779********************************************* PP

                                       EEE.SSSEEEEEEEEEEEET....TEEEEEE.ES----HHHHHHHHHHHHHTTSTT--EEEEEEEEESS.SEEEEEE CS
                       ATP-grasp_3  79 llsdgekvlvlavnrqliekaekefvyaGnv.tpietelkeevvelaeevvekleglaGyvGvDlvlkdeepyviEv 154
                                       +++dg +   +av ++ i +   +++y   + tp   e++ e++++a ++ ++l gl+G++ v+ + + +++ viE+
  gi|298674876|ref|YP_003726626.1| 173 VVGDGTN---FAVVKETIVHI--DEKYDCHMvTPL--EHDIEFRKIAYKLASNL-GLKGIMDVEAIKNPDDLRVIEI 241
                                       ***9944...44555555442..346665550555..5899*************.********************** PP

                                       ESS- CS
                       ATP-grasp_3 155 NPRl 158
                                        +R+
  gi|298674876|ref|YP_003726626.1| 242 DARF 245
                                       ***8 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.1   9.1e-09   2.3e-05      35     114 ..     124     197 ..      94     255 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 9.1e-09
                                       C-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT-SCEEEEE--ESEEEEEEEEETSSCEEEEEEEEE-SSSSS CS
                   Dala_Dala_lig_C  35 lgypvfVKpareGSSvGvskveseeelkeaieeafkydekvlvEeaiegreievavlgneklevsevgeivvkkgfy 111
                                        ++p+++Kp  e SS+Gvs ++ ++ l +      k de  ++Ee+ieg+ +   v+g++++ + + + iv  ++ y
  gi|298674876|ref|YP_003726626.1| 124 CKLPCIIKPLSESSSIGVSIIHDNKYLDS------KTDELKIIEEFIEGDVVSLEVVGDGTNFAVVKETIVHIDEKY 194
                                       579*******************9998876......6788889****************8887777666666666666 PP

                                       -HH CS
                   Dala_Dala_lig_C 112 dye 114
                                       d +
  gi|298674876|ref|YP_003726626.1| 195 DCH 197
                                       644 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   9.9e-08   0.00025       7     111 ..     160     272 ..     155     290 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 9.9e-08
                      ATPgrasp_Ter   7 vmeyLegpEySvDvlaek......gevlaavpRrKekgglqelekdeelielaerlaeefgldglvnvQvrededgp 77 
                                       + e++eg+ +S  v+ +        e+++ +  + + + ++ le+d e  ++a +la ++gl+g++ v   ++ d +
  gi|298674876|ref|YP_003726626.1| 160 IEEFIEGDVVSLEVVGDGtnfavvKETIVHIDEKYDCHMVTPLEHDIEFRKIAYKLASNLGLKGIMDVEAIKNPDDL 236
                                       667777777777777762233333333444444444566679*********************************** PP

                      ATPgrasp_Ter  78 kLLEiNpRasGGlgy..salaGvnlpylalklllgl 111
                                       +++Ei +R+ + + +     +G+nl +l ++++ g 
  gi|298674876|ref|YP_003726626.1| 237 RVIEIDARFPSQTPIvvYHSTGINLLNLLMQAFYGD 272
                                       ********9887655105567**********99995 PP

>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.2   3.1e+03      70     100 ..      18      47 ..       5      72 .. 0.68
   2 !   16.0   0.1   2.6e-06    0.0068       2      31 ..     125     154 ..     124     158 .. 0.85
   3 !    4.9   0.6    0.0071        18      54      98 ..     157     197 ..     147     248 .. 0.57

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.2
                       ATP-grasp_4  70 ayfdeeGepvilnilkkefaseedvsdrlyv 100
                                        + ++ G + +l i ++e    +d++d+ y 
  gi|298674876|ref|YP_003726626.1|  18 YLAKKSGMK-VLLIDRHEKPLIRDLVDEFYN 47 
                                       344445544.556888888888888888885 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 2.6e-06
                       ATP-grasp_4   2 slPvviKPsvgffSlGVykinneeewkaav 31 
                                       +lP++iKP ++++S+GV++i++++ +++  
  gi|298674876|ref|YP_003726626.1| 125 KLPCIIKPLSESSSIGVSIIHDNKYLDSKT 154
                                       68*******************998777655 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.0071
                       ATP-grasp_4  54 sflvEeyieGeEfavdayfdeeGepvilnilkkefaseedvsdrl 98 
                                         ++Ee+ieG+ +++++  d        +++k +  + ++  d+ 
  gi|298674876|ref|YP_003726626.1| 157 LKIIEEFIEGDVVSLEVVGDGTNF----AVVKETIVHIDEKYDCH 197
                                       459************998744322....33334444444444444 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0     2e-06     0.005      28     158 ..     125     243 ..      95     247 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2e-06
                                       -SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHCGTTCEEEEE----SEEEEEEEEEETTC-EEE--EEEEEEETTE CS
                         ATP-grasp  28 glpvvvKarrlgydGkGqsvvrseedleqalealkeekvivEefvpfekElsvlvvrsaeGetafypvvetvqedgi 104
                                       +lp+++K +   ++  G s++++++ l++ +++l     i+Eef++ ++ +s+ vv +     ++ +++ ++ e+ +
  gi|298674876|ref|YP_003726626.1| 125 KLPCIIK-PLSESSSIGVSIIHDNKYLDSKTDEL----KIIEEFIEGDV-VSLEVVGDGTNFAVVKETIVHIDEKYD 195
                                       789****.8888999*********9999999988....79*****9775.777777766666777788888888888 PP

                                       EEEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEEEEES CS
                         ATP-grasp 105 lrlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvledgellvnElap 158
                                       ++++  p e    +  + ++ia k++++Lg  G++ vE      ++l v E+  
  gi|298674876|ref|YP_003726626.1| 196 CHMVT-PLE----HDIEFRKIAYKLASNLGLKGIMDVEAIKN-PDDLRVIEIDA 243
                                       88764.454....55778999*****************9887.44477777655 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.3e-05      0.11       2      44 ..       4      40 ..       3      47 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.3e-05
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TTSSHHHHH CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll.rllDeeask 44
                                      ++++Gg + g E+   +++ g kV +++r++k+l r       +
  gi|298674876|ref|YP_003726626.1|  4 IAIIGGKLQGFEVTYLAKKSGMKVLLIDRHEKPLiR-------D 40
                                      89*******************************953.......3 PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.55   1.4e+03      84     106 ..       6      28 ..       2      33 .. 0.83
   2 ?   -0.8   0.0      0.42   1.1e+03       2      19 ..     103     120 ..     102     125 .. 0.86
   3 ?    8.2   0.2   0.00074       1.9      62     108 ..     135     183 ..     124     190 .. 0.74
   4 ?   -1.6   0.0      0.78     2e+03     163     189 ..     219     245 ..     204     247 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.55
                                       EEEE---SEEEEEEEEECTTEEE CS
                            GARS_A  84 viEelleGeEvsllalvdgktvk 106
                                       +i  +l+G Ev+ la   g +v 
  gi|298674876|ref|YP_003726626.1|   6 IIGGKLQGFEVTYLAKKSGMKVL 28 
                                       77889********9998888775 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.42
                                       BHHHHHHHHHHTT--B-- CS
                            GARS_A   2 sKsfakdllkkagiptae 19 
                                       +K+ +k+++k ++ipt++
  gi|298674876|ref|YP_003726626.1| 103 DKQKSKQYFKSINIPTPK 120
                                       78999**********984 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00074
                                       HHHHHHHHHCTS-TTCCC..CSSEEEEE---SEEEEEEEEECTTEEEE- CS
                            GARS_A  62 ealkavkeilekkkfGea..gekvviEelleGeEvsllalvdgktvkpl 108
                                       e+ ++  +i++++k+ ++   e  +iEe++eG+ vsl ++ dg++++ +
  gi|298674876|ref|YP_003726626.1| 135 ESSSIGVSIIHDNKYLDSktDELKIIEEFIEGDVVSLEVVGDGTNFAVV 183
                                       5555556777777776441145569******************998765 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 0.78
                                       ---EEEEEEEEEEETTEEEEEEEESS- CS
                            GARS_A 163 ipfkGvLyaglmlvedgpkvlefnvRf 189
                                          kG++ ++ +  +d  +v+e+++Rf
  gi|298674876|ref|YP_003726626.1| 219 LGLKGIMDVEAIKNPDDLRVIEIDARF 245
                                       6677888888777788899*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 2198.75
//
Query:       gi|298674877|ref|YP_003726627.1|  [L=346]
Description: radical SAM domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.2e-12   47.1   0.0    7.2e-12   46.0   0.0    1.6  1  Radical_SAM   Radical SAM superfamily
    4.5e-06   26.8   0.1    1.5e-05   25.1   0.1    1.9  1  Fer4_14       4Fe-4S single cluster domain
    1.6e-05   25.2   0.0      3e-05   24.3   0.0    1.5  1  Fer4_12       4Fe-4S single cluster domain
     0.0027   17.2   0.0     0.0055   16.2   0.0    1.5  1  His_biosynth  Histidine biosynthesis protein
  ------ inclusion threshold ------
      0.037   14.2   0.0       0.15   12.2   0.0    2.0  1  BATS          Biotin and Thiamin Synthesis associated domain
      0.079   12.7   0.2        1.6    8.5   0.0    2.8  3  CUE           CUE domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.0   0.0   2.4e-15   7.2e-12       3     150 ..      63     205 ..      61     220 .. 0.91

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 2.4e-15
                                       EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgir 79 
                                       ++  C + CsfC+ ++   ++   + ls++eil++  ++ + k+++ v l++ge  +y +   ll  ++k+ ++++ 
  gi|298674877|ref|YP_003726627.1|  63 FSTYCKNECSFCYYNKL--NNISRYRLSTDEILRICSSF-KGKQIHMVDLTMGEDPYYHNNPHLLVDIVKNVKNELD 136
                                       7889***********97..********************.5888**************************9977777 PP

                                       EEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  80 itvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdriv 150
                                       + + ++++++d + le l + g d ++l  e++d++   ++++ g++f ++++a + +++ g+  v d+i+
  gi|298674877|ref|YP_003726627.1| 137 LPIMVSPGVVDNDTLENLYNSGADFLALYQETYDKD-LYERIRVGQSFRDRINARKFAKKIGFC-VEDGIL 205
                                       77777777777*************************.******99*****************99.888876 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.1   4.9e-09   1.5e-05       6      95 ..      65     151 ..      60     168 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 4.9e-09
                           Fer4_14   6 sgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvlt.GGePLhyenkkellklvkrlkeeypek 81 
                                         C+ +C +C+ ++  + +    +t+e+l +i +++k ++i  + + lt G +P  + n + l+++vk++k+e  ++
  gi|298674877|ref|YP_003726627.1|  65 TYCKNECSFCYYNKLNNISRYRLSTDEIL-RICSSFKGKQI--HMVDLTmGEDPYYHNNPHLLVDIVKNVKNEL-DL 137
                                       57*********999999999999999999.99999999999..5555651667**99999999**********9.99 PP

                           Fer4_14  82 kiwletngtleiel 95 
                                       +i +  + + +  l
  gi|298674877|ref|YP_003726627.1| 138 PIMVSPGVVDNDTL 151
                                       99998888877444 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0     1e-08     3e-05       9      93 ..      61     144 ..      50     173 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1e-08
                           Fer4_12   9 slfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGE.Pllpenaeallelvkevkeekp 84 
                                       + f + C+ +C++C+ +++ + ++ +  t+e+l +i+ ++k ++i  + l+ GE P  ++n   l+++vk+vk+e  
  gi|298674877|ref|YP_003726627.1|  61 IYFSTYCKNECSFCYYNKLNNISRYRLSTDEIL-RICSSFKGKQIHMVDLTMGEdPYYHNNPHLLVDIVKNVKNELD 136
                                       456789*********************999987.9***************9776366666668899*******9976 PP

                           Fer4_12  85 ekdiwlytg 93 
                                          i+++ g
  gi|298674877|ref|YP_003726627.1| 137 -LPIMVSPG 144
                                       .34555555 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.8e-06    0.0055      44     100 ..     102     163 ..      81     178 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.8e-06
                                       SEEEEEEHHHHC.....TTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEE CS
                      His_biosynth  44 delhvvDldaak.....egreanldlveeiaeevfipvqvGGGIrsledveelleagadkvi 100
                                       +++h+vDl+  +     ++     d+v+++ +e+++p++v  G+ + +++e+l ++gad + 
  gi|298674877|ref|YP_003726627.1| 102 KQIHMVDLTMGEdpyyhNNPHLLVDIVKNVKNELDLPIMVSPGVVDNDTLENLYNSGADFLA 163
                                       789*****9887666645566667**********************************9765 PP

>> BATS  Biotin and Thiamin Synthesis associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   5.2e-05      0.15       4      85 ..     234     332 ..     231     333 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.2e-05
                                       B----TCCCC...........HHHHHHHHHHSTTSECCCT....CHH-HHHHHHHHHCCT--EEE-C---TTTGGGS CS
                              BATS   4 rlrpikdtpl...........lkiiaalRlllPkagills....gResaefrdqlllklGansisagsktevggyaf 65 
                                        + p ++tpl           lkii +lRl++P+  i +s    g   + +r +      ++si+  ++t  g  ++
  gi|298674877|ref|YP_003726627.1| 234 TFTPQEGTPLenqrqssseqeLKIISILRLMFPDKLIPASldieGIDGMVKRLNSG-ANVVTSIIPSNTTLEGVVNY 309
                                       57899*****************************9854441111555555555544.44556666666554443333 PP

                                       ES...STT-TCCCCHHHHHHTT- CS
                              BATS  66 lt...tdgrsleedvkmleelGl 85 
                                       +    + +r++e++v+ l+++G+
  gi|298674877|ref|YP_003726627.1| 310 DRdleKRNRNVENVVSRLKTMGM 332
                                       22111455667777777777776 PP

>> CUE  CUE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.72   2.2e+03      15      28 ..      19      32 ..      18      35 .. 0.78
   2 ?    0.6   0.0      0.16   4.7e+02       5      14 ..     258     267 ..     256     267 .. 0.86
   3 ?    8.5   0.0   0.00054       1.6      22      41 ..     311     330 ..     310     331 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.72
                                      S-HHHHHHHHHHCT CS
                               CUE 15 ldeevIravLrasn 28
                                      l+++ I++ L+ +n
  gi|298674877|ref|YP_003726627.1| 19 LSDSEIKHLLSTEN 32
                                      78999**9996655 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.16
                                       HHHHHHHSTT CS
                               CUE   5 letLkemFPd 14 
                                       ++ L+ mFPd
  gi|298674877|ref|YP_003726627.1| 258 ISILRLMFPD 267
                                       788999***8 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.00054
                                       HHHHHCTTTHHHHHHHHHHC CS
                               CUE  22 avLrasngnvEatinaLLeg 41 
                                       ++L+ +n nvE+++++L  +
  gi|298674877|ref|YP_003726627.1| 311 RDLEKRNRNVENVVSRLKTM 330
                                       69**************9655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.35s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2073.30
//
Query:       gi|298674878|ref|YP_003726628.1|  [L=486]
Description: cysteinyl-tRNA synthetase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.8e-98  328.2   2.5      1e-97  327.2   2.5    1.5  1  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
    3.6e-19   68.8   2.2    2.1e-09   36.6   0.0    2.6  3  tRNA-synt_1g  tRNA synthetases class I (M)
    1.1e-11   45.0   0.6    3.6e-11   43.4   0.6    1.9  1  DALR_2        DALR domain
    3.6e-07   28.8   0.0     0.0033   15.7   0.0    2.3  2  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
    6.5e-07   28.6   0.1      0.011   14.7   0.0    2.4  2  tRNA-synt_1f  tRNA synthetases class I (K)
     0.0016   17.4   1.1     0.0046   15.9   0.2    2.2  3  tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic d
  ------ inclusion threshold ------
      0.014   14.4   0.8       0.17   10.8   0.0    2.5  3  tRNA-synt_1d  tRNA synthetases class I (R)


Domain annotation for each model (and alignments):
>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  327.2   2.5  3.9e-101     1e-97       4     300 ..      18     339 ..      15     340 .. 0.95

  Alignments for each domain:
  == domain 1  score: 327.2 bits;  conditional E-value: 3.9e-101
                                       -SBTTEEEEEEEEEBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--..........SHHHHHHHHHTTS CS
                      tRNA-synt_1e   4 pleekkvtlYvCGptvydashlGhaRslvafDilrrilqalgYdvqfvqnvtDi..........dDkiikrareeek 70 
                                       p+++k v +Y CGptvy  +h+G+ Rs+++ D+l+r+l+  gY+v+   n+tD+          +Dk+   a +e++
  gi|298674878|ref|YP_003726628.1|  18 PVDDKFVRMYNCGPTVYGRVHIGNIRSFLMADLLKRFLNLEGYQVRQAMNITDVghmtsdsdegEDKLQVAADKEKL 94 
                                       678899***********************************************9777777766679*********** PP

                                       -HHHHHHHHHHHHHHHHHHTT----SB--BGGGGHHHHHHHHHHHHHTTSEEE-TTS-EEE-GGG-TTTTTTTT--H CS
                      tRNA-synt_1e  71 svkelaekfieefkkdleaLnvlkptleprvsekvdeiielvekliekgyaYavsdgdvyfdvskkeeYgklskqnl 147
                                         +++a+k+ + f +dl++Ln+  +++ pr++++++e+ie+++kli++gyaY++  g+vyfd +k++eYgkls + l
  gi|298674878|ref|YP_003726628.1|  95 DPWKIADKYKQLFIDDLNKLNIDDADVYPRATQHINEMIEVIKKLIDNGYAYVSG-GNVYFDITKFPEYGKLSGNVL 170
                                       ******************************************************9.********************* PP

                                       HHHHHT----S--S-SSTT-EEEEEE-.-TTS..--B--TTSSEEE-SSHHHHHHHHHHH-............SSEE CS
                      tRNA-synt_1e 148 eelelgaegevseekkdkkDfaLWkas.kege..pswdsPwgkGRPGWhieCsvmaskllg............seid 209
                                       e+l+++++      k++++Df+LW ++ k  +  ++wdsPwg+G PGWhieCs+ma k+l             ++id
  gi|298674878|ref|YP_003726628.1| 171 EKLQSQERAVYDPYKRNPQDFVLWFSHsKYKNhiMNWDSPWGEGYPGWHIECSAMALKYLTdafnkhfdseksTTID 247
                                       *********999************76413333559*************************999999999999889** PP

                                       EEEEEGGGTTTHHHHHHHHHHHHSSS--EEEEEEE--EEETTBE--TTTT---BHHHHHTT.S-HHHHHHHHHSS-T CS
                      tRNA-synt_1e 210 ihsGGiDLafPhhenelaqseaafdkqlvkyflhnghlkiegekmsksLknfitikdvlkk.fdprqlRllllsahy 285
                                       ih+GG D +fPhhe e+aqse a+++++v+y++h  hl +eg+kmsksL+n+ t+ d+l++ ++p+++R++ll++hy
  gi|298674878|ref|YP_003726628.1| 248 IHTGGEDNKFPHHECEIAQSEGATGQKFVNYWMHVTHLLVEGDKMSKSLNNIYTLPDILNQgYKPEAVRYVLLTTHY 324
                                       ***********************************************************866*************** PP

                                       TS-EEE-HHHHHHHH CS
                      tRNA-synt_1e 286 rsqldfkeelleeak 300
                                       r++l+f+ ++l++++
  gi|298674878|ref|YP_003726628.1| 325 RQKLNFTFKNLQASQ 339
                                       *******99999876 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   8.2e-13   2.1e-09      11     123 ..      34     155 ..      29     161 .. 0.82
   2 !   31.0   0.3   4.3e-11   1.1e-07     270     377 ..     232     341 ..     221     354 .. 0.83
   3 ?   -2.1   0.0      0.47   1.2e+03     361     386 ..     357     382 ..     343     384 .. 0.83

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 8.2e-13
                                       SS---HHHHHHHHHHHHHHHHHHHTT-EEE..........EEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHH CS
                      tRNA-synt_1g  11 ngklHlGhllevisaDifaRykrlrgeevl..........fvcgtDehGtpielkAekegvtpeelvekvheeikel 77 
                                        g++H+G++++ + aD + R+  l+g++v           + + +De   + +++A+ke+++p ++++k+++ + ++
  gi|298674878|ref|YP_003726628.1|  34 YGRVHIGNIRSFLMADLLKRFLNLEGYQVRqamnitdvghMTSDSDEGEDKLQVAADKEKLDPWKIADKYKQLFIDD 110
                                       5899*********************99874222333333244567887789************************** PP

                                       HHHTT--.-SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEE CS
                      tRNA-synt_1g  78 fkklnis.fdkygrttseehkelvqeifkklkekgliyekeieqlyc 123
                                       ++klni   d y r+t++ ++ +  e++kkl ++g+ y +  +++++
  gi|298674878|ref|YP_003726628.1| 111 LNKLNIDdADVYPRATQHINEMI--EVIKKLIDNGYAYVSGGNVYFD 155
                                       ******63799***998877765..899*******999887777776 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 4.3e-11
                                       GGGG.G--S.......EEEEEGGG.HHHHHTHHHHHHHHTT----S-EEEE--EEE--------------HHHHHHH CS
                      tRNA-synt_1g 270 ekwkeyWakdkevel.vhfigkdi.ikFHtifwPaillgaelklpkkvvaheyltvegkKlSkSrgvvvkakealer 344
                                       + ++++++++k + + +h  g d+  ++H         +++ k+++  +   +l veg+K+SkS +++ +  ++l++
  gi|298674878|ref|YP_003726628.1| 232 DAFNKHFDSEKSTTIdIHTGGEDNkFPHHECEIAQSEGATGQKFVNYWMHVTHLLVEGDKMSKSLNNIYTLPDILNQ 308
                                       6799999666665553788888874688999999999999***********************************99 PP

                                       .H-HHHHHHHHHHHS-TTS-EEE-HHHHHHHHHH CS
                      tRNA-synt_1g 345 .ldadllRYylaaeapekkDldfswedfvervNs 377
                                        ++++++RY+l++++   + l+f+++++++  N+
  gi|298674878|ref|YP_003726628.1| 309 gYKPEAVRYVLLTTHY-RQKLNFTFKNLQASQNA 341
                                       9**********98655.56699999999999885 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.47
                                       TS-EEE-HHHHHHHHHHHCCCHHHHH CS
                      tRNA-synt_1g 361 kkDldfswedfvervNseLadklgnl 386
                                       ++  df+ e+f e+v ++ +++l n 
  gi|298674878|ref|YP_003726628.1| 357 NESGDFEAEKFAEKVKDDFIKELEND 382
                                       56679999*********999999885 PP

>> DALR_2  DALR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.6   1.4e-14   3.6e-11       2      56 ..     375     429 ..     367     436 .. 0.94

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 1.4e-14
                                       HHHHHTBT--HHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHGGGT-S- CS
                            DALR_2   2 FeeaMdDDFNTaeAiavlFelakeiNralkeedkaaasalkallrelaevLGllq 56 
                                       F++++++D+N a Ai+vlFe +k+iN+ l++  +++a+ l ++l+++ +vLG+l 
  gi|298674878|ref|YP_003726628.1| 375 FIKELENDLNIAGAIGVLFEAVKTINKSLTNIGQQEADILLDMLKDVDKVLGVLD 429
                                       99***************************************************86 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   4.1e-05      0.11      27     166 ..      26     155 ..      14     160 .. 0.78
   2 !   15.7   0.0   1.3e-06    0.0033     547     601 ..     275     330 ..     222     331 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.1e-05
                       tRNA-synt_1  27 lvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakvekklgakekkerkklgreefrek 103
                                       ++   P v G++HiG++    + d++ r+ +++G++v+  + +   G  +          +e++++ ++++++ +  
  gi|298674878|ref|YP_003726628.1|  26 MYNCGPTVYGRVHIGNIRSFLMADLLKRFLNLEGYQVRQAMNITDVGHMTSD-------SDEGEDKLQVAADKEKLD 95 
                                       5667799******************************998877666644432.......355566778888888888 PP

                       tRNA-synt_1 104 vrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliyrgkklvnws 166
                                        ++++++y++   +++++l +  D d +     ++  + ++ev+++l+d+g  y +   v+++
  gi|298674878|ref|YP_003726628.1|  96 PWKIADKYKQLFIDDLNKLNI--D-DADVYPRATQHINEMIEVIKKLIDNGYAYVSGGNVYFD 155
                                       899999999999999999854..4.45555555667777888999999999888777666665 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.3e-06
                       tRNA-synt_1 547 fkevlvhglvrdeeGrKmSKslgNvidpldvikk.ygadalRltlilsdvgrdinl 601
                                       f +  +h   +  eG KmSKsl N+    d++++ y  +a+R++l+++++ + +n+
  gi|298674878|ref|YP_003726628.1| 275 FVNYWMHVTHLLVEGDKMSKSLNNIYTLPDILNQgYKPEAVRYVLLTTHYRQKLNF 330
                                       55555666666679**********9886666665499*************999886 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   4.5e-05      0.11      27      71 ..      27      71 ..       9      86 .. 0.88
   2 !   14.7   0.0   4.1e-06     0.011     276     340 ..     286     350 ..     276     374 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.5e-05
                      tRNA-synt_1f 27 vesGispSGliHiGnlrevltadlvaralrkrgeevrlilisDdm 71
                                       + G ++ G++HiGn+r  l adl+ r l+  g +vr+ + + d+
  gi|298674878|ref|YP_003726628.1| 27 YNCGPTVYGRVHIGNIRSFLMADLLKRFLNLEGYQVRQAMNITDV 71
                                      57899999**********************999999987776665 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 4.1e-06
                      tRNA-synt_1f 276 lkggekmssSkGnvltledwlev.aepevlrflilrrkPkkakkldldleilrlvdeYdklerkyf 340
                                       l +g+kms+S  n+ tl d+l+  ++pe +r+++l ++ +++++++++ ++++  +  d+l++ +f
  gi|298674878|ref|YP_003726628.1| 286 LVEGDKMSKSLNNIYTLPDILNQgYKPEAVRYVLLTTHYRQKLNFTFK-NLQASQNAIDRLQELIF 350
                                       45677***************976379**********************.99999999999998887 PP

>> tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.71   1.8e+03       8      25 ..      31      48 ..      30      60 .. 0.81
   2 !   15.9   0.2   1.8e-06    0.0046      44      97 ..      95     148 ..      86     151 .. 0.91
   3 ?   -1.9   0.0      0.48   1.2e+03     237     273 ..     285     320 ..     274     348 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.71
                                      --SSSS-BHHHHHHHHHH CS
                      tRNA-synt_1c  8 PePtGyLHiGhakaalln 25
                                      P   G  HiG+ ++ l+ 
  gi|298674878|ref|YP_003726628.1| 31 PTVYGRVHIGNIRSFLMA 48
                                      5566999*****998875 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.8e-06
                                       SCCC--HHHHHHHHHHHHHTT---SSEEEEGGGGHHHHHHHHHHHHHTTSEEEE CS
                      tRNA-synt_1c  44 dperekeeaeesiledlkwlgikwdekptyqsdrfdelkkyaeeLikkGkAYvc 97 
                                       dp + + ++++  ++dl+ l+i+  +   +++++ +e+ +++++Li +G+AYv 
  gi|298674878|ref|YP_003726628.1|  95 DPWKIADKYKQLFIDDLNKLNIDDADVYPRATQHINEMIEVIKKLIDNGYAYVS 148
                                       6677788999999**********988888***********************85 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.48
                                       EEETTSB-SHHHHHHHHHTTSSSSTT-TTSCBHHHHH CS
                      tRNA-synt_1c 237 lnlekkklSKRklsllvdekqvkewddlreallnflr 273
                                       l +e+ k+SK  +++  +  ++ ++++ +ea+  +l 
  gi|298674878|ref|YP_003726628.1| 285 LLVEGDKMSKSLNNIY-TLPDILNQGYKPEAVRYVLL 320
                                       3467788888777776.77888888888888755544 PP

>> tRNA-synt_1d  tRNA synthetases class I (R)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   6.7e-05      0.17      25      70 ..      27      72 ..       4      75 .. 0.81
   2 ?    1.1   0.0     0.058   1.5e+02     168     207 ..     130     172 ..      89     185 .. 0.80
   3 ?   -2.5   0.1      0.73   1.9e+03     111     126 ..     364     380 ..     321     419 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.7e-05
                                      E----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEEEEE--B-SS CS
                      tRNA-synt_1d 25 dfssPniakemhvGhLrstiiGdavsrlleflGydvirlnhvGDWG 70
                                          P +   +h+G +rs ++ d + r l++ Gy+v ++  + D G
  gi|298674878|ref|YP_003726628.1| 27 YNCGPTVYGRVHIGNIRSFLMADLLKRFLNLEGYQVRQAMNITDVG 72
                                      4467999999**************************9999898887 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.058
                                       CCHHHHHHHHHCTT-EEECTTCEEEEECCC...TSSCCEECC- CS
                      tRNA-synt_1d 168 eslneivkelkkkglvkesdGalvvfldef...gkrlgvvvqk 207
                                       + + e++k+l ++g++ +s G    ++++f   gk  g v+ k
  gi|298674878|ref|YP_003726628.1| 130 NEMIEVIKKLIDNGYAYVSGGNVYFDITKFpeyGKLSGNVLEK 172
                                       4677999***************999998886667777777666 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.73
                                       SHCCCHHHH.HHHHHHH CS
                      tRNA-synt_1d 111 eeifaerar.nyvvkLq 126
                                        e fae+ + +++++L+
  gi|298674878|ref|YP_003726628.1| 364 AEKFAEKVKdDFIKELE 380
                                       23344433312333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (486 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       942  (0.0525406); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.70u 0.34s 00:00:01.04 Elapsed: 00:00:00.53
# Mc/sec: 2757.75
//
Query:       gi|298674879|ref|YP_003726629.1|  [L=400]
Description: nicotinate phosphoribosyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-29  101.4   0.0      6e-29  101.0   0.0    1.2  1  QRPTase_C       Quinolinate phosphoribosyl transferase, C-ter
     0.0094   16.4   0.0      0.019   15.4   0.0    1.5  1  NAPRTase_C      Nicotinate phosphoribosyltransferase C-termin
  ------ inclusion threshold ------
      0.019   15.3   0.0        3.8    7.9   0.0    2.3  2  NAPRTase_N      Nicotinate phosphoribosyltransferase (NAPRTas
      0.037   13.4   0.0      0.057   12.8   0.0    1.3  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
       0.04   13.2   0.0      0.063   12.6   0.0    1.3  1  TMP-TENI        Thiamine monophosphate synthase
       0.12   12.4   0.0       0.31   11.1   0.0    1.7  1  QRPTase_N       Quinolinate phosphoribosyl transferase, N-ter
       0.16   11.1   0.0       0.28   10.3   0.0    1.3  1  DUF561          Protein of unknown function (DUF561)


Domain annotation for each model (and alignments):
>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.0   0.0   2.3e-32     6e-29       1     169 []     122     310 ..     122     310 .. 0.95

  Alignments for each domain:
  == domain 1  score: 101.0 bits;  conditional E-value: 2.3e-32
                                       HHHHHHHHHHHHHCTSSEEEE-S---TTTHHHHHHHHHHTTSB.......--TSSTTTSEEE-HHHHHHHSSHHHHH CS
                         QRPTase_C   1 iAtltarmveaaksakvrildTRkttPglrllekyAvliGGgd.......nhrlgLsdmvlikdnhiaaagsiveav 70 
                                       +At++ar+++aaks  v +++ R+++Pg++++  +A++iGG+d          +g++   +++++  +++g+ ++a 
  gi|298674879|ref|YP_003726629.1| 122 VATKSARVKKAAKSCDVMSFGIRRMHPGIAPVIDRAAYIGGCDsvsciagAEEVGIEPKGTMPHALSIIFGDPKKAY 198
                                       8*************************************************9************************** PP

                                       HHHHHHHTTTSE..EEEEESSHHHHHHHHHHT.....-SEEEEES--H..HHHHHHHHHH.HHHSTT...SEEEEES CS
                         QRPTase_C  71 ksvreavdkevk..ievevesleeleevleae.....adiimLDnfsv..eelkkaveel.keknkr...vlievSG 134
                                       k+++++++k ++    v+++ +e +e  ++ae       +i+LD++++   +lkk+++e+ +e + r    +i +SG
  gi|298674879|ref|YP_003726629.1| 199 KAFDDVLSKDIAriALVDTYYDETIESFMAAEamgenLYGIRLDTPTSrrGNLKKIAQEIkWELKCRgvdARIIASG 275
                                       *******999988889*************98866555679******887799*******988988889999****** PP

                                       S--TTTHHHHHCTT-SEEEECHHCHTB----EEEE CS
                         QRPTase_C 135 gvtlenveeyaksgvdvisvgalthsvkalDislk 169
                                       g+++ ++ e++k gvd ++vg+ ++++ ++D+s++
  gi|298674879|ref|YP_003726629.1| 276 GINEYTIPELRKAGVDGFGVGTTISNADTIDFSMD 310
                                       *********************************97 PP

>> NAPRTase_C  Nicotinate phosphoribosyltransferase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   7.4e-06     0.019      50      89 ..     357     396 ..     309     398 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.4e-06
                        NAPRTase_C  50 srvekLlkkvfkdGklvyelpsleeireyvkeqlaelrpe 89 
                                        ++ ++l+k++++Gk++++ ps  + +  v +ql++l+ +
  gi|298674879|ref|YP_003726629.1| 357 NKMVPMLQKFMENGKILDDYPSALDLKTNVTNQLQKLEAD 396
                                       57899*******************************9876 PP

>> NAPRTase_N  Nicotinate phosphoribosyltransferase (NAPRTase) N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0015       3.8       3      52 ..      18      68 ..      17      74 .. 0.94
   2 ?    5.2   0.0      0.01        26      97     124 ..      89     116 ..      70     117 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0015
                        NAPRTase_N  3 tDlYkltmaqavfkkgp.dvevvfelffRkkpfkgeyaivagleevieyle 52
                                      tD Y  ++++++ kkg  +++vv e++  + p + + +++agl+ev+  le
  gi|298674879|ref|YP_003726629.1| 18 TDIYFENIMEIFNKKGVgNENVVAEFTASSLPDEWRWGVFAGLDEVLCLLE 68
                                      9********************************************998776 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.01
                        NAPRTase_N  97 vfpgepeirveGpwieaillEtplLaiv 124
                                          ++p + +eG   +  ++Etp+L ++
  gi|298674879|ref|YP_003726629.1|  89 EGVNTPVMFIEGSYKKFCIYETPILGLI 116
                                       456899*******************876 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.2e-05     0.057     151     197 ..     252     299 ..     248     300 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.2e-05
                                       HHH.HHHHHHHHHHT---EEEEESS--TTTCHHHHHHT--EEEESHHH CS
                    Ribul_P_3_epim 151 eki.kkvrklidekeldlkievDGGvkldnieqiaeagadvlVagsav 197
                                       +ki ++++  ++ +++d +i + GG+++ +i ++ +ag+d + +g+++
  gi|298674879|ref|YP_003726629.1| 252 KKIaQEIKWELKCRGVDARIIASGGINEYTIPELRKAGVDGFGVGTTI 299
                                       555256788888899*************************99999875 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.4e-05     0.063     146     178 ..     255     296 ..     241     299 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.4e-05
                          TMP-TENI 146 aeale.........iPvvaiGGitlenvaevleagadgvavv 178
                                       a++++           ++a GGi++ +++e+++ag+dg  v 
  gi|298674879|ref|YP_003726629.1| 255 AQEIKwelkcrgvdARIIASGGINEYTIPELRKAGVDGFGVG 296
                                       4444444334444479*********************98775 PP

>> QRPTase_N  Quinolinate phosphoribosyl transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00012      0.31      27      88 ..      54     119 ..      36     120 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                                       SEEE-SHHHHHHHHHHHTTTEEEESS-TT-EEETTEE......EEEEEEEHHHHHHHHHHHHHHHHHH CS
                         QRPTase_N  27 egvvaGlevaeevfellpglevellvkDGervekgdv......lleieGnarallsaERvaLnllqrl 88 
                                       +gv+aGl+++  ++e   ++ + +  ++G+ ++ +d+      ++ ieG+++++  +E  +L l+ + 
  gi|298674879|ref|YP_003726629.1|  54 WGVFAGLDEVLCLLEGK-NVDI-YALPEGTVFRHQDTegvntpVMFIEGSYKKFCIYETPILGLICHP 119
                                       79*******99999966.5554.45599999987654333333**********************986 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00011      0.28     184     233 ..     266     314 ..     246     323 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00011
                            DUF561 184 kvslPvicasGlsdvtvplalslgasGiGigsavsklndeeemvallsei 233
                                        v+  +i++ G+++ t+p   ++g  G G+g ++s+  d+++++  + e+
  gi|298674879|ref|YP_003726629.1| 266 GVDARIIASGGINEYTIPELRKAGVDGFGVGTTISNA-DTIDFSMDIVEM 314
                                       577789****************************985.555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2391.82
//
Query:       gi|298674880|ref|YP_003726630.1|  [L=91]
Description: hypothetical protein Metev_0940 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.003   17.7   0.0     0.0038   17.3   0.0    1.1  1  ZT_dimer  Dimerisation domain of Zinc Transporter


Domain annotation for each model (and alignments):
>> ZT_dimer  Dimerisation domain of Zinc Transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.1e-07    0.0038       9      76 ..      21      88 ..      17      89 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.1e-07
                                      HHHHHTT-SS-EEEEEEEEE-S----EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-TT--EEEEEE CS
                          ZT_dimer  9 ireiiksvpgvkgvhdlrtrksGskifvdlhievdgdlsvkeaHeiadevekrikeefpgvadvliHv 76
                                      i  +++s + v+++ ++ + +s + + ++l ++++ dl +++   ia+ +++ +++ f+g+++v++H+
  gi|298674880|ref|YP_003726630.1| 21 ICYVVNSLDFVSDCYKVNITESLEGVSIELGVKIKSDLLIEDRNFIANSIKQYLMNYFDGISNVTTHI 88
                                      6667888888999999999999999******************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 566.60
//
Query:       gi|298674881|ref|YP_003726631.1|  [L=474]
Description: putative PAS/PAC sensor protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-39  132.0   1.9    1.5e-19   70.1   0.2    2.4  2  PAS_3     PAS fold
    1.6e-13   51.1   0.0    2.4e-13   50.6   0.0    1.2  1  GAF_2     GAF domain
      2e-11   44.0   0.3    4.4e-05   23.7   0.1    2.5  2  PAS_9     PAS domain
    3.9e-09   36.5   0.0     0.0068   16.4   0.0    3.3  3  PAS       PAS fold
    6.8e-08   32.9   0.0      1e-07   32.4   0.0    1.3  1  GAF_3     GAF domain
    4.1e-05   23.8   0.0       0.29   11.4   0.0    2.5  2  PAS_4     PAS fold
    0.00059   20.5   0.0      0.001   19.7   0.0    1.4  1  GAF       GAF domain
    0.00064   19.8   0.0      0.035   14.2   0.0    2.3  2  PAS_11    PAS domain
     0.0018   18.1   0.1        2.2    8.2   0.0    2.4  2  PAS_6     YheO-like PAS domain
     0.0061   16.4   0.1      0.025   14.4   0.0    2.0  2  VanY      D-alanyl-D-alanine carboxypeptidase
  ------ inclusion threshold ------
      0.043   13.9   0.1       0.27   11.3   0.0    2.1  2  SpoVT_C   Stage V sporulation protein T C-terminal, transcrip
       0.19   12.3   0.1        1.3    9.6   0.0    2.1  2  DUF2385   Protein of unknown function (DUF2385)


Domain annotation for each model (and alignments):
>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.3   0.1   5.3e-20     8e-17       3      89 .]      56     142 ..      54     142 .. 0.96
   2 !   70.1   0.2   9.9e-23   1.5e-19       3      89 .]     193     279 ..     191     279 .. 0.94

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 5.3e-20
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvirde 78 
                                       yvse++ +  Gy++e++++   +++d++hpeD  +vr+++ +  + g   ++ +yRi++k+  +rwv  ++ v +de
  gi|298674881|ref|YP_003726631.1|  56 YVSENILQF-GYTKEDFISGRMNYIDIIHPEDAGKVRKKFSRNYNYGYkNISLQYRILTKSKNIRWVNGKTLVQFDE 131
                                       888888887.*************************************999*************************** PP

                             PAS_3  79 ngkpvrvigva 89 
                                       +gkp +++g++
  gi|298674881|ref|YP_003726631.1| 132 KGKPSHFLGII 142
                                       *********85 PP

  == domain 2  score: 70.1 bits;  conditional E-value: 9.9e-23
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvirde 78 
                                       +vs+++ + +Gy+p+e+   + ++ d+++p+D+e+v+ +l +  +kg+ ++++eyRi++k+Ge+rwv++r+++ rd+
  gi|298674881|ref|YP_003726631.1| 193 FVSDNINR-FGYTPDEFVTGKLQYGDIIYPDDLEHVQYELCKRREKGHnDFSQEYRIVTKSGEIRWVDERTFIQRDK 268
                                       67777755.5************************************999**************************** PP

                             PAS_3  79 ngkpvrvigva 89 
                                       +g+pv ++g++
  gi|298674881|ref|YP_003726631.1| 269 DGNPVSYQGII 279
                                       *********96 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.0   1.6e-16   2.4e-13       4     136 ..     308     441 ..     306     443 .. 0.89

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 1.6e-16
                                       HHHHHHHHHHHHHHSS...EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B---TT.HHHHHHHHTS-EEES-GGG-S CS
                             GAF_2   4 leelldlvldelvelg.aalgyillvdddgglrlaawgeaeeefgaaldrplgeg.lvgealrtgrpvilndleedp 78 
                                       +e +l++vl+ ++++g +++g+i+l d++++l l  + +    f  ++ + lg+  ++ ++++tg+pv+  d+ e p
  gi|298674881|ref|YP_003726631.1| 308 PEVILNQVLELILDIGvVDCGCIHLADENNDLNLIISVGLSNDFVTSI-SYLGSNsILNRIIMTGQPVY-KDYSEIP 382
                                       6789************9**************99998888888888888.36688879************.9999999 PP

                                       -HHHHH.HHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHH CS
                             GAF_2  79 dkkglp.aghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaia 136
                                        k+ +     ++lr+ + +Pl+ +g+v+G+lnly++  ++   + ++ +e++a+q++  
  gi|298674881|ref|YP_003726631.1| 383 FKSDESaKNSEKLRAVALIPLVFNGEVLGALNLYSHLYDEIPSDVRTAIETIAAQLGGF 441
                                       9999988999999999*****************999999998888899*******9865 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.5e-06    0.0023      12     104 .]      53     147 ..      40     147 .. 0.78
   2 !   23.7   0.1     3e-08   4.4e-05      13     104 .]     191     284 ..     183     284 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.5e-06
                             PAS_9  12 rilyaNeaalrllGyspeevlgks..itdlfvtdpeanerlraaleqgrk...kerevevvlirkngetfwvlltas 83 
                                       +++y++e  l++ Gy++e+++  +  + d++  +pe++ ++r+ + +  +   k  + ++ + +k+ +  wv+    
  gi|298674881|ref|YP_003726631.1|  53 PVEYVSENILQF-GYTKEDFISGRmnYIDII--HPEDAGKVRKKFSRNYNygyKNISLQYRILTKSKNIRWVN--GK 124
                                       5679******99.*********996655666..56666666666666656699******************55..54 PP

                             PAS_9  84 pv..kdddgelvgiivilrDite 104
                                       ++  +d++g+  ++++i++Dit+
  gi|298674881|ref|YP_003726631.1| 125 TLvqFDEKGKPSHFLGIIVDITD 147
                                       4445799***************6 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 3e-08
                             PAS_9  13 ilyaNeaalrllGyspeevlgks..itdlfvtdpeanerlraaleqgrk..kerevevvlirkngetfwvlltaspv 85 
                                       ++++++  +r+ Gy+p+e++  +  + d++  +++ ++   ++ ++ +k  + +++e+ +++k+ge  wv+ + +  
  gi|298674881|ref|YP_003726631.1| 191 VEFVSDNINRF-GYTPDEFVTGKlqYGDII-YPDDLEHVQYELCKRREKghNDFSQEYRIVTKSGEIRWVDERTFIQ 265
                                       56888888888.******887776788888.44444444444444444478********************777666 PP

                             PAS_9  86 kdddgelvgiivilrDite 104
                                       +d+dg+ v++ +i++Dit+
  gi|298674881|ref|YP_003726631.1| 266 RDKDGNPVSYQGIIVDITD 284
                                       799***************6 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   4.5e-06    0.0068       6     113 .]      35     145 ..      30     145 .. 0.86
   2 !   15.8   0.1   7.1e-06     0.011      34     113 .]     201     282 ..     163     282 .. 0.85
   3 ?   -3.5   0.0         7     1e+04      45      69 ..     418     438 ..     417     446 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.5e-06
                                       HHHHSSSEEEEEE.TTSBEEEECHHHHHHHSSTH.HHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEE CS
                               PAS   6 ileslpdpifvvD.edgrilyvNaaaeellGlsr.eevlgkslldliheedda.elaelleqlleqgeesrageisf 79 
                                       ++ ++p+ +f++  e  + ++  ++   ++G++  + ++g++ +++i++++da +++++++++++ g ++ + + ++
  gi|298674881|ref|YP_003726631.1|  35 LVAHTPVYVFLWKpEYNWPVEYVSENILQFGYTKeDFISGRMNYIDIIHPEDAgKVRKKFSRNYNYGYKNISLQYRI 111
                                       55666666666666666666666666789****977799************************************** PP

                                       ECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  80 klrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                        ++ + ++++   +   +d++g++ +flg++ di
  gi|298674881|ref|YP_003726631.1| 112 LTKSKNIRWVNGKTLVQFDEKGKPSHFLGIIVDI 145
                                       ******************************9887 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 7.1e-06
                                       HSSTH.HHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEEEEEEEEETTEEEEEEEE CS
                               PAS  34 lGlsr.eevlgkslldliheedda.elaelleqlleqgeesrageisfklrdgrpihlevraspvrdaggeilgflg 108
                                       +G+++ e v gk  +++i+ +dd   ++ +l +++e g++  ++e ++ ++ g++++++ r+   rd++g++  + g
  gi|298674881|ref|YP_003726631.1| 201 FGYTPdEFVTGKLQYGDIIYPDDLeHVQYELCKRREKGHNDFSQEYRIVTKSGEIRWVDERTFIQRDKDGNPVSYQG 277
                                       89999899***************988888999999999999******************************999999 PP

                                       EEEES CS
                               PAS 109 vlrdi 113
                                       ++ di
  gi|298674881|ref|YP_003726631.1| 278 IIVDI 282
                                       98776 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 7
                                       BGGGGBSTTHHHHHHHHHHHHHHHT CS
                               PAS  45 slldliheeddaelaelleqlleqg 69 
                                       +l+d+i+ +    ++ ++e+ ++q 
  gi|298674881|ref|YP_003726631.1| 418 HLYDEIPSD----VRTAIETIAAQL 438
                                       688899887....888888877765 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0   6.7e-11     1e-07       1     129 []     307     444 ..     307     444 .. 0.86

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 6.7e-11
                             GAF_3   1 sldellekllkllvkllgaevgalllldedgnklqvaagwdgkpalsesld..edsalarralssgevvse...... 69 
                                       +++ +l+++l+l+ ++  ++ g ++l d + n+l+ +++ + ++++++s+     ++   r +++g++v++      
  gi|298674881|ref|YP_003726631.1| 307 EPEVILNQVLELILDIGVVDCGCIHLAD-ENNDLNLIISVGLSNDFVTSISylGSNSILNRIIMTGQPVYKdyseip 382
                                       5899************************.779**99999999*******9997666666688888999988777776 PP

                             GAF_3  70 ...psfaeedglpdraalavPLvagrqviGvlalastkprafdaedlelleslArqiataier 129
                                           +  ++++  +ra+ ++PLv   +v+G l l+s+ + ++ ++ +  +e++A+q++  i+r
  gi|298674881|ref|YP_003726631.1| 383 fksDE-SAKNSEKLRAVALIPLVFNGEVLGALNLYSHLYDEIPSDVRTAIETIAAQLGGFIAR 444
                                       64322.2346677899999*****66*********************************9987 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00048      0.71       3     109 ..      38     149 ..      36     150 .. 0.80
   2 !   11.4   0.0   0.00019      0.29      68     109 ..     244     286 ..     191     287 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00048
                             PAS_4   3 slpdalavldpdgr..vlyaNaaaaelfgappeellGktla..ellpeedaarleralrrvle.geepiefleelll 74 
                                       ++p++++ + p+++  v+y+++++ + fg++ e+++  ++   ++  +eda+ ++    r    g + i+ +   l+
  gi|298674881|ref|YP_003726631.1|  38 HTPVYVFLWKPEYNwpVEYVSENILQ-FGYTKEDFISGRMNyiDIIHPEDAGKVRKKFSRNYNyGYKNISLQYRILT 113
                                       77888888866666336999999999.99999999988888898877788888888877765416677777777777 PP

                             PAS_4  75 .pgeerhyelrllPlrdesGevigvlvisrDiTerr 109
                                        ++  r+++   l  +de+G++ ++l+i++DiT+++
  gi|298674881|ref|YP_003726631.1| 114 kSKNIRWVNGKTLVQFDEKGKPSHFLGIIVDITDQK 149
                                       99*******9998888*****************986 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00019
                             PAS_4  68 fleelll.pgeerhyelrllPlrdesGevigvlvisrDiTerr 109
                                       ++   ++ +ge r+++ r +  rd +G ++ + +i++DiT+r+
  gi|298674881|ref|YP_003726631.1| 244 QEYRIVTkSGEIRWVDERTFIQRDKDGNPVSYQGIIVDITDRK 286
                                       334444469**********999*******************97 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   6.7e-07     0.001       2     130 ..     308     439 ..     307     442 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 6.7e-07
                                       HHHHHHHHHHHHHHHHTESEEEEEEEEETT.EEECEEEEECC.....EEEETTSHHHHHHHHHSSSEEESTGGTSTT CS
                               GAF   2 leelldtvveelrellgadrvalylpdydG.lhydipqasrw.....lfmkngrgicgqvlatgqplvipdstpdpr 72 
                                       +e +l++v+e + ++  +d ++++l+d++  l+  i+ +++      +      +i ++++ tgqp+  + s  +  
  gi|298674881|ref|YP_003726631.1| 308 PEVILNQVLELILDIGVVDCGCIHLADENNdLNLIISVGLSNdfvtsISYLGSNSILNRIIMTGQPVYKDYS--EIP 382
                                       6899********************9545552344677777775564333333555899*********99963..333 PP

                                       HHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEE..SSSCSHHHHHHHH.HHHHHHHH CS
                               GAF  73 faqynrrdllenmgirsslvvPlvndgelwGllvlhn..psppftreelell.qvladqva 130
                                       f    + +  +    r+++ +Plv +ge++G+l l++   ++   +++++ + +++a+q++
  gi|298674881|ref|YP_003726631.1| 383 FKS--DESAKNSEKLRAVALIPLVFNGEVLGALNLYShlYDE--IPSDVRTAiETIAAQLG 439
                                       444..34455689999*********************64322..55666666699998886 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   2.3e-05     0.035      37     100 ..      75     138 ..      57     149 .. 0.78
   2 ?    3.1   0.0     0.065        97      40      91 ..     215     266 ..     200     281 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.3e-05
                            PAS_11  37 grsiydLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvkvktksklfknqksneqdf 100
                                       ++ + d++hp+d  +++++++  ++   ++ s+ yR+ ++++++ +v+ k+ +  ++k + ++f
  gi|298674881|ref|YP_003726631.1|  75 RMNYIDIIHPEDAGKVRKKFSRNYNYGYKNISLQYRILTKSKNIRWVNGKTLVQFDEKGKPSHF 138
                                       345779******************9999999999*****9998888888887777776666666 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.065
                            PAS_11  40 iydLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvkvktksklfk 91 
                                       + d++ p+dl+++++ l +  ++  +  s+ yR+ ++++++ +v  ++ + +
  gi|298674881|ref|YP_003726631.1| 215 YGDIIYPDDLEHVQYELCKRREKGHNDFSQEYRIVTKSGEIRWVDERTFIQR 266
                                       448999**************97777778889*****9998777655554444 PP

>> PAS_6  YheO-like PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0025       3.7      71     110 ..     110     149 ..      88     153 .. 0.80
   2 !    8.2   0.0    0.0014       2.2      49     113 ..     223     289 ..     219     291 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0025
                             PAS_6  71 nyktktkdgkilksstifirdekgkliglLCiNldlskle 110
                                         +tk+k+ + +   t++  dekgk+  +L+i +d+++ +
  gi|298674881|ref|YP_003726631.1| 110 RILTKSKNIRWVNGKTLVQFDEKGKPSHFLGIIVDITDQK 149
                                       34578888999*************************9866 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0014
                             PAS_6  49 pltdlvlellkeeeeeeedvlvnyktktkdgki..lksstifirdekgkliglLCiNldlskleaae 113
                                        l+++  el k++e+ ++d  ++y+  tk+g+i  +   t++ rd++g+++   +i +d+++ +++e
  gi|298674881|ref|YP_003726631.1| 223 DLEHVQYELCKRREKGHNDFSQEYRIVTKSGEIrwVDERTFIQRDKDGNPVSYQGIIVDITDRKHTE 289
                                       56778889999999999************9976448999*********************9977665 PP

>> VanY  D-alanyl-D-alanine carboxypeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.5   2.2e+03      85     110 ..      22      47 ..       9      70 .. 0.63
   2 !   14.4   0.0   1.7e-05     0.025      25     110 ..      95     180 ..      87     196 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.5
                                       -SCGGGHCHHHHHHHHHGGGGTEEES CS
                              VanY  85 leesfeetkafkwlqknaakygFvlr 110
                                       ++++ e+++  k+l ++ + y F ++
  gi|298674881|ref|YP_003726631.1|  22 MKSTTENSSNLKKLVAHTPVYVFLWK 47 
                                       45666666677777777777666654 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 1.7e-05
                                       -EEEEE----HHHHHHHH..HHHHHHHHHHHHHHHS--TTT-GGGGTSEEEEEEGGGTT.--SCGGGHCHHHHHHHH CS
                              VanY  25 elalvsgfRsverQeelf.ekksvkeeklkeilrvsalpGaSeHhtGlaiDisdkeaeetkleesfeetkafkwlqk 100
                                       + +   g+ +++ Q ++  ++k+ ++ + k+  +++   G+  H +G+ +Di+d++++e+kl+e+++ +++ + + +
  gi|298674881|ref|YP_003726631.1|  95 SRNYNYGYKNISLQYRILtKSKNIRWVNGKTLVQFD-EKGKPSHFLGIIVDITDQKMKEEKLQETLAIKDELESIIN 170
                                       5556679***********777777777777766666.569999***********************99999999999 PP

                                       HGGGGTEEES CS
                              VanY 101 naakygFvlr 110
                                       n++   F ++
  gi|298674881|ref|YP_003726631.1| 171 NSPAIVFQWK 180
                                       9988888765 PP

>> SpoVT_C  Stage V sporulation protein T C-terminal, transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.87   1.3e+03      43      64 ..     159     180 ..     141     196 .. 0.72
   2 ?   11.3   0.0   0.00018      0.27      69     119 ..     384     437 ..     360     444 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.87
                           SpoVT_C  43 keiskeleklmeerktvlakke 64 
                                         i++ele+++++   ++++ +
  gi|298674881|ref|YP_003726631.1| 159 LAIKDELESIINNSPAIVFQWK 180
                                       3799999999999888777654 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00018
                           SpoVT_C  69 v...veeekeeysaqviaPIiaeGdviGaVillskeekkklgelekklaetaAs 119
                                             +++e+++a +++P++ +G+v+Ga  l s+  ++  +++ + +  +aA+
  gi|298674881|ref|YP_003726631.1| 384 KsdeSAKNSEKLRAVALIPLVFNGEVLGALNLYSHLYDEIPSDVRTAIETIAAQ 437
                                       2332255668999*********************99999999998888777775 PP

>> DUF2385  Protein of unknown function (DUF2385)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00089       1.3      45      73 ..      87     115 ..      66     123 .. 0.79
   2 ?   -0.5   0.0       1.2   1.9e+03      49      75 ..     228     254 ..     222     263 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00089
                           DUF2385  45 searrarlveaFNrgyrsyasvyrtCtea 73 
                                         + r+++ + +N gy++++ +yr  t++
  gi|298674881|ref|YP_003726631.1|  87 AGKVRKKFSRNYNYGYKNISLQYRILTKS 115
                                       347899******************98876 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.2
                           DUF2385  49 rarlveaFNrgyrsyasvyrtCteaaa 75 
                                       + +l ++  +g+++++++yr  t++ +
  gi|298674881|ref|YP_003726631.1| 228 QYELCKRREKGHNDFSQEYRIVTKSGE 254
                                       557788888999999999999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 2926.31
//
Query:       gi|298674882|ref|YP_003726632.1|  [L=337]
Description: MtaA/CmuA family methyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.1e-89  299.5   0.0    3.6e-89  299.3   0.0    1.0  1  URO-D        Uroporphyrinogen decarboxylase (URO-D)
  ------ inclusion threshold ------
       0.13   11.9   0.0        0.5   10.0   0.0    1.9  2  Pterin_bind  Pterin binding enzyme


Domain annotation for each model (and alignments):
>> URO-D  Uroporphyrinogen decarboxylase (URO-D)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  299.3   0.0     4e-93   3.6e-89       3     346 .]       5     335 ..       3     335 .. 0.98

  Alignments for each domain:
  == domain 1  score: 299.3 bits;  conditional E-value: 4e-93
                                       --HHHHHHTT---SS--B--TT-SSTTSHHHHHHHTSSSHHHHHH-HHHHHHHHHHHHHHH--S-EE-S--TTGGGG CS
                             URO-D   3 nerllralrgekvdrvPvwlmRqaGrylpeyraeragvsflelcknpelaaevtlqpvrrfglDaailfsdilveae 79 
                                       nerl++al+ge+vd+ P +    +++++  + + ++g+ +++++++pe++a ++++ +++ +l+a+  +++++v ae
  gi|298674882|ref|YP_003726632.1|   5 NERLINALKGEEVDKKPAVS---VTQTAIVELMDITGAEWPDAHSDPEKMATLSMASHEQGNLEAIRNPFCLTVLAE 78 
                                       9*******************...999*************************************************** PP

                                       GGT-EEEEETTTE.EEEE--S-....GGGS----GGG..G..HHHHHHHHHHHHH.--SS-EEEEEE-HHHHHHHHH CS
                             URO-D  80 alGlevefeegeg.Pvvekpvrtaedveklevpddvee.grlpyvleaikllkkelggevpligfvgaPftlasylv 154
                                       alG++v++++++  P++++++  ++d+ +l+ pdd+ + gr+p v+e+ k++k+++g+evpli ++ +P tlas lv
  gi|298674882|ref|YP_003726632.1|  79 ALGCGVNMGTKNRqPSITDHPY-PKDISDLKMPDDLYNtGRIPAVFESSKIIKDKYGDEVPLISGLEGPATLASDLV 154
                                       **********6666********.************87689************************************* PP

                                       CTT-SS-HHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEE..TTGGGS-HHHHHHHTHHHHHHHHH CS
                             URO-D 155 eGgskgfekllkllykdpeevhklldkltdvvieylkaqieagAdaiqifD..swagllspedfeefvlpylkrivd 229
                                              ++++k+ +k+p+++++++d++td++iey++ ++ +gAd+++++D  ++++llsp+df+  + p l+r ++
  gi|298674882|ref|YP_003726632.1| 155 -----SPKSFMKWSIKKPDNFDAIMDFATDACIEYANGMVNNGADVVCVADpvASPDLLSPNDFDNRIKPRLQRFAE 226
                                       .....************************************************************************ PP

                                       HHHH.H--S-EEEEESSHH.HHHHHHTTS--SEEE--TTS.-HHHHHHSS....EEE--B-G.GGGG.S-HHHHHHH CS
                             URO-D 230 evkaegpkvpvilfikgagaeiledlaelgadvlsldwtv.dlkeaarevgdkvalqGnldPialLl.gspeeieke 304
                                       evka     p +l+i+g+ ++i++ +a++g+d+lsl+++v dlk a+++vgd++ ++Gn++ + ++l g+p+++++ 
  gi|298674882|ref|YP_003726632.1| 227 EVKA-----PTVLHICGNVTPIIDMMADTGFDGLSLEEKVkDLKGAKETVGDRASIVGNVSSPFTILgGTPDKVKED 298
                                       ****.....*******************************889888889***********98889999********* PP

                                       HHHHHT.T---SSSEEB-BSS---TTS-HHHHHHHHHHHHT- CS
                             URO-D 305 vkeilekgaggkkgyilnlGhgippetppenvkalveavkey 346
                                       +k+++++g++     +l++G+gi+p++p++nv+alv+a++ey
  gi|298674882|ref|YP_003726632.1| 299 AKKAMDDGVD-----VLAPGCGIAPNSPLANVQALVDARNEY 335
                                       **********.....***********************9987 PP

>> Pterin_bind  Pterin binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   5.6e-05       0.5      12      74 ..     170     230 ..     165     234 .. 0.81
   2 ?   -3.0   0.0      0.53   4.8e+03      20      38 ..     292     310 ..     288     314 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 5.6e-05
                                       HCCHHCTHHHHHHHHHHHHHHTT-SEEEEESS-TSTT--CCHHHHHHHHHHHHHHHHHHHCTS CS
                       Pterin_bind  12 sdggkfedldkalaqarkmveeGAdilDiggestrPgaervdeeeelervvpvlealrdeadv 74 
                                       +d ++ ++ d++++ a+ mv++GAd++ +    + P+   +++++  +r+ p l++ ++e++ 
  gi|298674882|ref|YP_003726632.1| 170 FDAIMDFATDACIEYANGMVNNGADVVCVADPVASPD--LLSPNDFDNRIKPRLQRFAEEVKA 230
                                       46566689******************99988888666..889988889999999988887754 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.53
                                       HHHHHHHHHHHHHTT-SEE CS
                       Pterin_bind  20 ldkalaqarkmveeGAdil 38 
                                       +dk+ + a+k +++G d+l
  gi|298674882|ref|YP_003726632.1| 292 PDKVKEDAKKAMDDGVDVL 310
                                       5778888999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1988.06
//
Query:       gi|298674883|ref|YP_003726633.1|  [L=214]
Description: GPR1/FUN34/yaaH family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-22   79.3  25.3    3.7e-22   79.0  25.3    1.1  1  Gpr1_Fun34_YaaH  GPR1/FUN34/yaaH family
  ------ inclusion threshold ------
        3.4    5.4   7.0        4.6    5.0   7.0    1.2  1  DUF3367          Alpha-(1->3)-arabinofuranosyltransferase


Domain annotation for each model (and alignments):
>> Gpr1_Fun34_YaaH  GPR1/FUN34/yaaH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.0  25.3   4.1e-26   3.7e-22      17     193 ..      36     205 ..      26     213 .. 0.90

  Alignments for each domain:
  == domain 1  score: 79.0 bits;  conditional E-value: 4.1e-26
                   Gpr1_Fun34_YaaH  17 faNPaPlgllafalttfvlslvnlgargitepnvvvglalfyGGlvqllaGiwefavgntFgatalssYGgFwlsya 93 
                                        aNPaPlg++++++ +f+lsl  +g+  + +  ++v+la+f+GG++++laG+  +  g+ F+ ta+  YG Fw ++a
  gi|298674883|ref|YP_003726633.1|  36 TANPAPLGFTGYGIAAFLLSLTFIGVYPVGS--MIVSLAIFIGGIAEILAGLQAWRRGDVFAGTAFAAYGLFWPTFA 110
                                       79**************************987..9******************************************* PP

                   Gpr1_Fun34_YaaH  94 ailipgfgilaaYeedeeelnnalglyllgwfiftfllllatlrs.tvalfllfffldltflllaigeltgsakvlk 169
                                       +++i +   + a          a+  +l ++ i+t+ l++atl   + a+ +++ +l+l f+ laig+  g a +++
  gi|298674883|ref|YP_003726633.1| 111 FLVIFESTAMVAG-----PTPMAMVAFLGIFGIYTLGLFIATLGIgSRAIQFVIGTLFLLFITLAIGNA-GVAMMTT 181
                                       **99655555554.....3456777788889999999999999753788999999************96.8899*** PP

                   Gpr1_Fun34_YaaH 170 AggvfgiiaaflawYnalaglatk 193
                                        gg++g i+++++ Y+ala ++++
  gi|298674883|ref|YP_003726633.1| 182 IGGYIGAISGLAGIYTALAMILNE 205
                                       ********************9975 PP

>> DUF3367  Alpha-(1->3)-arabinofuranosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   7.0   0.00051       4.6      35     114 ..      86     165 ..      81     182 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.00051
                           DUF3367  35 hlWtdtaplGqlqnQayGYlfPhglFfalldllglpaWvtqRlWwalllvvaflGvvrl...aealgigspasrvla 108
                                       ++W     +      ayG ++P  +F ++++     a v+    +a++ +++ +G++ l     +lgigs+a +++ 
  gi|298674883|ref|YP_003726633.1|  86 QAWRRGDVFAGTAFAAYGLFWPTFAFLVIFEST---AMVAGPTPMAMVAFLGIFGIYTLglfIATLGIGSRAIQFVI 159
                                       6666666666667789***************99...77999999***********9988444689************ PP

                           DUF3367 109 alayaL 114
                                       ++++ L
  gi|298674883|ref|YP_003726633.1| 160 GTLFLL 165
                                       ****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1292.26
//
Query:       gi|298674884|ref|YP_003726634.1|  [L=461]
Description: methanol-5-hydroxybenzimidazolylcobamide co-methyltransferase 3 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.1e-232  771.9   4.6   2.4e-232  771.7   4.6    1.0  1  MtaB      Methanol-cobalamin methyltransferase B subunit


Domain annotation for each model (and alignments):
>> MtaB  Methanol-cobalamin methyltransferase B subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  771.7   4.6  1.3e-236  2.4e-232       2     460 .]       4     460 ..       3     460 .. 1.00

  Alignments for each domain:
  == domain 1  score: 771.7 bits;  conditional E-value: 1.3e-236
                              MtaB   2 kkftklayksaddlvfGkakkPvkaklgleiGaGtvvpeinvapreeseeskeklvkeyekittdileravelglPa 78 
                                       ++++k+ay++add+vfGk+k+Pvka+l+leiG+G+++ e+n+apr+e+++skeklvkey+kit+di+ r+v++g+P+
  gi|298674884|ref|YP_003726634.1|   4 NRCKKMAYDKADDMVFGKSKHPVKAGLDLEIGGGYTTGEVNYAPRPEAGTSKEKLVKEYQKITRDIMGRMVAVGAPS 80 
                                       7899************************************************************************* PP

                              MtaB  79 vvlEtEhvqqmtenpewgaevakaqkeileeyedkyglksalratiaDiReeeealelrgdkllekllesfeevaen 155
                                       vvlEtEhvqqmt+npewg+eva+aqk+i+eey+d+yg+k+alr+t++DiRee+++l+lrg+k+ ++l+esfeeva+n
  gi|298674884|ref|YP_003726634.1|  81 VVLETEHVQQMTNNPEWGGEVANAQKAIMEEYHDEYGIKCALRHTPGDIREERDYLQLRGEKY-NTLMESFEEVASN 156
                                       ***************************************************************.************* PP

                              MtaB 156 GadllsiEsvGGKevsDeaivrndirgvlfaigvlGsiDmeylWkeivkiakkkgvvaaGDtdCaqantamflaggl 232
                                       GadllsiE++GGKe+ D+a++r+d+ gvl+aig+lG+iDmey+W++i+kia+k++vv+aGDtdCaqantamf+aggl
  gi|298674884|ref|YP_003726634.1| 157 GADLLSIETMGGKEILDYALIRDDTPGVLYAIGCLGAIDMEYIWQDIAKIADKHNVVPAGDTDCAQANTAMFIAGGL 233
                                       ***************************************************************************** PP

                              MtaB 233 ldkdvpktlaavaRaiaaarsLvayEaGavGPdKDCgYEnpiiKaiagvPisqEGktaacAHsdlvGnlaaavcDlW 309
                                       ldk++++t a++aRai+a+r+Lv+yEaGa+GP+KDCgYEn+i+K++agvPisqEGkt++cAHsd++Gnl++++cDlW
  gi|298674884|ref|YP_003726634.1| 234 LDKNLAHTDATIARAISASRTLVGYEAGAKGPGKDCGYENTIVKSVAGVPISQEGKTSTCAHSDVLGNLVMQCCDLW 310
                                       ***************************************************************************** PP

                              MtaB 310 snEsveyhkelggttvqvwleqlgydcalmntalekgqekelrdllvesDkyrdpqayiLaydnaykigeaivkegd 386
                                       snEsveyh e+ggttv++w+e+l+ydcalmn+al++g+ek+lrd++++sDkyrdpq+y+L+ydna+k+g+ai+++gd
  gi|298674884|ref|YP_003726634.1| 311 SNESVEYHGEFGGTTVECWSETLMYDCALMNVALQSGNEKVLRDMFAASDKYRDPQGYMLSYDNAWKVGKAIADNGD 387
                                       ***************************************************************************** PP

                              MtaB 387 dlylrakaaalkaielleeaveekklklskfekkaLdkakkelealpddedkFikeclkkykkevkkfkpenYg 460
                                       dlylrak+aal+a++l++e++ ++kl+ls+fe++aL++ak++le+l+dd+dkF+++c+kky+kevk f+penYg
  gi|298674884|ref|YP_003726634.1| 388 DLYLRAKKAALTACDLMDEGA-KGKLQLSRFETNALKRAKESLENLTDDKDKFMEDCQKKYEKEVKVFRPENYG 460
                                       *******************98.9**************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.52
# Mc/sec: 2684.43
//
Query:       gi|298674885|ref|YP_003726635.1|  [L=256]
Description: methyltransferase cognate corrinoid protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-18   67.3   0.1    1.7e-18   66.8   0.1    1.3  1  B12-binding    B12 binding domain
    2.7e-15   56.6   0.0      6e-15   55.4   0.0    1.6  1  B12-binding_2  B12 binding domain
     0.0088   16.2   0.0      0.017   15.2   0.0    1.4  1  Ocnus          Janus/Ocnus family (Ocnus)
  ------ inclusion threshold ------
      0.063   13.1   0.2       0.12   12.2   0.2    1.4  1  DUF4909        Domain of unknown function (DUF4909)


Domain annotation for each model (and alignments):
>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.8   0.1   3.9e-22   1.7e-18       2     112 ..     124     228 ..     123     237 .. 0.91

  Alignments for each domain:
  == domain 1  score: 66.8 bits;  conditional E-value: 3.9e-22
                       B12-binding   2 kvllatvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvellkri 78 
                                       k++  +++gd+h++G++++   l+++gf+V++lg +v++e++v+++ +ekp +v  +al+t+++  +k++ e+l r 
  gi|298674885|ref|YP_003726635.1| 124 KIVCFVAEGDIHDIGKNIVSVLLKAKGFDVVDLGRDVPVEEVVESVLDEKPIMVSGTALMTTTMYSFKKIKEELTRF 200
                                       788999*********************************************************************** PP

                       B12-binding  79 rprvkvvvGGahpsldpeetleaklgiddvvvge 112
                                       + ++++v+GG +  ++++++ ++klg  +   ge
  gi|298674885|ref|YP_003726635.1| 201 DMETPLVCGGGA--VTQDFVTKYKLG-IY---GE 228
                                       **********88..888888888888.44...44 PP

>> B12-binding_2  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.4   0.0   1.3e-18     6e-15       5      74 ..      42     111 ..      40     112 .. 0.95

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 1.3e-18
                     B12-binding_2   5 lhwaivhgdkegieelidealaqgsaavdvlndvllpamkeVGdlfgagelflpqvllsaevmkkavahL 74 
                                       ++++i +gd++++++ ++ a+++g  + d++n++l+++m +V +l++ g l+lp+v+ sa++m  +v+++
  gi|298674885|ref|YP_003726635.1|  42 IAKSIFEGDEDDVVAHLQNAIDAGRHPIDLINNALIKGMSIVSKLYDDGDLYLPDVIISAQAMVVGVNYC 111
                                       67899**********************************************************8888776 PP

>> Ocnus  Janus/Ocnus family (Ocnus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   3.9e-06     0.017      28      83 ..     171     228 ..     162     231 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.9e-06
                             Ocnus  28 eeekeivrglkkaeyhadifekveeeleklglev.kclGGGriehdeekkk.ikvYGy 83 
                                       +e+  +v g++ ++  +  f+k++eel+++++e+  ++GGG +++d  +k+ + +YG 
  gi|298674885|ref|YP_003726635.1| 171 DEKPIMVSGTALMTTTMYSFKKIKEELTRFDMETpLVCGGGAVTQDFVTKYkLGIYGE 228
                                       56678999*9**********************995578********9887559***96 PP

>> DUF4909  Domain of unknown function (DUF4909)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   2.8e-05      0.12      42     111 ..       8      80 ..       3      88 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.8e-05
                           DUF4909  42 krylfieyipdnvlnckpdfwktlkykkdkvtyyvy..lie.nlddevfhlsalqdmnripidiaddvatmgk 111
                                       k  +f+ y  +   +  pd    + y kd++ y +   + e + dd v hl    d  r pid+ ++    g 
  gi|298674885|ref|YP_003726635.1|   8 KTNVFVRYNVNVENDMTPDELAEVLYPKDELVYPIAksIFEgDEDDVVAHLQNAIDAGRHPIDLINNALIKGM 80 
                                       56788898877777799****************8742245525677889**************9998766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1544.63
//
Query:       gi|298674886|ref|YP_003726636.1|  [L=980]
Description: putative PAS/PAC sensor protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-54  180.8   1.6    1.9e-16   60.1   0.2    5.5  5  PAS_3     PAS fold
    9.9e-36  122.2   0.1    2.5e-07   30.7   0.0    5.4  5  PAS       PAS fold
      8e-34  116.0  10.3    2.4e-10   40.6   0.1    5.8  5  PAS_9     PAS domain
    1.8e-23   83.4   0.0    2.1e-12   47.5   0.0    2.4  2  GAF_2     GAF domain
    1.1e-19   70.7   0.0    0.00036   20.8   0.0    4.8  5  PAS_4     PAS fold
      2e-19   69.2   0.0    4.9e-06   26.4   0.0    4.0  4  PAS_8     PAS domain
    3.1e-09   37.3   0.0    3.1e-06   27.6   0.0    2.4  2  GAF_3     GAF domain
    2.5e-05   24.3   0.0       0.69   10.1   0.0    3.9  4  PAS_11    PAS domain
     0.0016   19.1   0.0       0.86   10.2   0.0    2.5  2  GAF       GAF domain


Domain annotation for each model (and alignments):
>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.0   4.6e-15   9.2e-12      10      85 ..      56     132 ..      50     136 .. 0.93
   2 !   28.0   0.0   9.7e-10   1.9e-06       3      78 ..     177     252 ..     175     260 .. 0.88
   3 !   21.3   0.0   1.3e-07   0.00025       3      77 ..     468     541 ..     466     552 .. 0.77
   4 !   60.1   0.2   9.4e-20   1.9e-16       4      89 .]     600     685 ..     597     685 .. 0.92
   5 !   20.5   0.0   2.1e-07   0.00042       2      71 ..     886     952 ..     885     967 .. 0.90

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 4.6e-15
                             PAS_3  10 eilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvirdengkpvrv 85 
                                        +lGy pe+++  +  + d++h  Dre+v++++ ++++k++  y+ +yR+++  G +rwv++r++v++  +g ++r 
  gi|298674886|ref|YP_003726636.1|  56 TLLGYKPEQFKPGKLYYNDIIHSVDREYVESEISNCFEKRCsGYNLQYRVLTGEGNIRWVDERTVVLYGGDGSVDRQ 132
                                       579**********999*************************9******************************99885 PP

  == domain 2  score: 28.0 bits;  conditional E-value: 9.7e-10
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge..pyegeyRirrkdGeyrwveararvird 77 
                                       ++++++e+i+Gy ++e++++  ++ld++  e +  v+++++++lk+    py+ e+ i+ k+ + + ve   ++i+ 
  gi|298674886|ref|YP_003726636.1| 177 FANRAFENITGYKRDEIIET--TFLDYIPVEYQRMVNKKYEKLLKTEPkyPYTYEVYIQSKSEGLIPVEINLSAINF 251
                                       89******************..**********************55443799***************9999999844 PP

                             PAS_3  78 e 78 
                                       e
  gi|298674886|ref|YP_003726636.1| 252 E 252
                                       3 PP

  == domain 3  score: 21.3 bits;  conditional E-value: 1.3e-07
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge..pyegeyRirrkdGeyrwveararvird 77 
                                       ++++++e+i+Gy ++e++++  s+l ++  e +  v +++++ lk ++  +   e+ ++     ++  e   ++i  
  gi|298674886|ref|YP_003726636.1| 468 FANKAFENITGYKRDEITET--SFLAYIPVEYQRMVLKKYNKTLKANQdnSRIYEVNFLSSTKNTVPTEINFSPI-H 541
                                       89******************..**********************8877323344455666666666666666666.4 PP

  == domain 4  score: 60.1 bits;  conditional E-value: 9.4e-20
                             PAS_3   4 vserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvirden 79 
                                       vse++ + +Gy pe++++    + d++hp+D+++vr++++   ++++ +++ eyRi++ + e+rwv++r+++++den
  gi|298674886|ref|YP_003726636.1| 600 VSENIMQ-FGYIPEDFTSERIIYGDIIHPDDLQKVRNKMAGRYEDKSgEFNLEYRILTSNDEVRWVDERTTIHYDEN 675
                                       5666644.5*******************************99988777***************************** PP

                             PAS_3  80 gkpvrvigva 89 
                                       g++ +++g++
  gi|298674886|ref|YP_003726636.1| 676 GNVNYLQGII 685
                                       *******985 PP

  == domain 5  score: 20.5 bits;  conditional E-value: 2.1e-07
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwvear 71 
                                       +y++++ ++ lGy+++el++   ++++l +     ++ +++ +++ +g ++++++ ++ kdG++++ +++
  gi|298674886|ref|YP_003726636.1| 886 LYANKATQDRLGYTEQELQEM--NIINLHYSKQALKAASNISDVV-SGNRFSCDIPLIAKDGTIIYKDTK 952
                                       89*******************..**********************.5556**************987666 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.052     1e+02      32     102 ..      56     128 ..      29     131 .. 0.86
   2 !   26.8   0.0   2.1e-09   4.2e-06       2      70 ..     155     222 ..     154     264 .. 0.79
   3 !   29.1   0.0   3.8e-10   7.5e-07       2     113 .]     446     555 ..     445     555 .. 0.90
   4 !   25.6   0.1   4.7e-09   9.4e-06       3     113 .]     575     688 ..     573     688 .. 0.92
   5 !   30.7   0.0   1.3e-10   2.5e-07       5      55 ..     867     916 ..     864     970 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.052
                                       HHHSSTH.HHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEEEEEEEEETTEE CS
                               PAS  32 ellGlsr.eevlgkslldliheedda.elaelleqlleqgeesrageisfklrdgrpihlevraspvrdagge 102
                                       +llG+++ +   gk ++ +i++  d+ ++ ++++++ e + ++ + + ++ +  g +++++ r++ ++ ++g 
  gi|298674886|ref|YP_003726636.1|  56 TLLGYKPeQFKPGKLYYNDIIHSVDReYVESEISNCFEKRCSGYNLQYRVLTGEGNIRWVDERTVVLYGGDGS 128
                                       588999956668********99988889*********99999999999999999******9999999999885 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 2.1e-09
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqge 70 
                                       ++++++e  +d+i++v  dg i ++N+a+e ++G++r+e++  ++ld+i+ e+++ +++++e+ll++  
  gi|298674886|ref|YP_003726636.1| 155 KYSTLIECGIDGILIV-QDGYIKFANRAFENITGYKRDEIIETTFLDYIPVEYQRMVNKKYEKLLKTEP 222
                                       5778888889******.**************************************99999988888765 PP

  == domain 3  score: 29.1 bits;  conditional E-value: 3.8e-10
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT.-ECCCCE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqge.esragei 77 
                                       ++++++e  +d++++v  d  i ++N+a+e ++G++r+e+   s+l +i+ e+++ + +++ + l++++ +sr++e+
  gi|298674886|ref|YP_003726636.1| 446 KYSTLVEKGIDGTLIV-QDEAIKFANKAFENITGYKRDEITETSFLAYIPVEYQRMVLKKYNKTLKANQdNSRIYEV 521
                                       6889999999******.**************************************77777777776655278999** PP

                                       EEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  78 sfklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       +f    + +++ e++ sp+  +g+    +++ +rdi
  gi|298674886|ref|YP_003726636.1| 522 NFLSSTKNTVPTEINFSPIHYEGKP--AVMLNVRDI 555
                                       **********************887..999999997 PP

  == domain 4  score: 25.6 bits;  conditional E-value: 4.7e-09
                                       HHHHHHHSSSEEEEEE.TTSBEEEECHHHHHHHSSTH.HHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCC CS
                               PAS   3 lraileslpdpifvvD.edgrilyvNaaaeellGlsr.eevlgkslldliheedda.elaelleqlleqgeesrage 76 
                                       l+ i++++p+ +f+++ e+ + +++ ++   ++G+ + +  + + ++++i+++dd  +++ ++  ++e+++ + + e
  gi|298674886|ref|YP_003726636.1| 575 LEDIINNSPAIVFIWRaEKDWPVEFVSENIMQFGYIPeDFTSERIIYGDIIHPDDLqKVRNKMAGRYEDKSGEFNLE 651
                                       6789************9999999999999999999885778899**********99999999999999999999999 PP

                                       EEEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  77 isfklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                        ++ + + ++++++ r++  +d+ g++ ++ g++ di
  gi|298674886|ref|YP_003726636.1| 652 YRILTSNDEVRWVDERTTIHYDENGNVNYLQGIIIDI 688
                                       99999******************************98 PP

  == domain 5  score: 30.7 bits;  conditional E-value: 1.3e-10
                                       HHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHH CS
                               PAS   5 aileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedd 55 
                                        +l++ +d+ifv+D  g ily+N+a+++ lG++++e+   +++  +h  ++
  gi|298674886|ref|YP_003726636.1| 867 KLLDNVDDFIFVIDSEGHILYANKATQDRLGYTEQELQEMNII-NLHYSKQ 916
                                       689************************************9999.4554444 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.011        21      22     103 ..      56     140 ..      37     141 .. 0.82
   2 !   40.6   0.1   1.2e-13   2.4e-10       2     104 .]     165     266 ..     164     266 .. 0.85
   3 !   39.0   0.1   3.7e-13   7.4e-10       2     104 .]     456     557 ..     455     557 .. 0.89
   4 !   14.4   0.2   1.8e-05     0.035       5     104 .]     587     690 ..     583     690 .. 0.76
   5 !   19.1   0.0   5.8e-07    0.0012       2      76 ..     874     947 ..     873     971 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.011
                             PAS_9  22 rllGyspeevlgks.itdlf...vtdpeanerlraaleqgrkkerevevvlirkngetfwvlltaspvkdddgelvg 94 
                                       +llGy+pe++   + + + +   v+ ++ ++++++++e    + ++ ++   + +g+  wv+ + + ++ +dg + +
  gi|298674886|ref|YP_003726636.1|  56 TLLGYKPEQFKPGKlYYNDIihsVDREYVESEISNCFEKRC-SGYNLQYRVLTGEGNIRWVDERTVVLYGGDGSVDR 131
                                       689*****9874444555555**99**********999999.9******************9777777777777666 PP

                             PAS_9  95 iivilrDit 103
                                         +++ Dit
  gi|298674886|ref|YP_003726636.1| 132 QESVVFDIT 140
                                       557777777 PP

  == domain 2  score: 40.6 bits;  conditional E-value: 1.2e-13
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk...kerevevvlirknget 75 
                                       dgili+  dg i +aN+a+++++Gy+++e++ + + d + + ++ +   +++ + +++    ++++ev ++ k+++ 
  gi|298674886|ref|YP_003726636.1| 165 DGILIV-QDGYIKFANRAFENITGYKRDEIIETTFLDYI-PVEYQRMVNKKYEKLLKTepkYPYTYEVYIQSKSEGL 239
                                       89**99.***777**************************.444444444444444444888**************** PP

                             PAS_9  76 fwvlltaspvkdddgelvgiivilrDite 104
                                       ++v++++s++  + +  v+  + +rDite
  gi|298674886|ref|YP_003726636.1| 240 IPVEINLSAINFEANPAVM--FNIRDITE 266
                                       **********888777777..9******8 PP

  == domain 3  score: 39.0 bits;  conditional E-value: 3.7e-13
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk...kerevevvlirknget 75 
                                       dg+li+  d  i +aN+a+++++Gy+++e+  +s+   + + ++ +  l+++ ++++    + r +ev +  ++ +t
  gi|298674886|ref|YP_003726636.1| 456 DGTLIV-QDEAIKFANKAFENITGYKRDEITETSFLAYI-PVEYQRMVLKKYNKTLKAnqdNSRIYEVNFLSSTKNT 530
                                       788887.566466*********************99999.777777777777777777888**************** PP

                             PAS_9  76 fwvlltaspvkdddgelvgiivilrDite 104
                                       +++++++sp++ +++  v+  + +rDit+
  gi|298674886|ref|YP_003726636.1| 531 VPTEINFSPIHYEGKPAVM--LNVRDITK 557
                                       ******************9..******95 PP

  == domain 4  score: 14.4 bits;  conditional E-value: 1.8e-05
                             PAS_9   5 li..dnpdgrilyaNeaalrllGyspeevlgks..itdlfvtdpeanerlraaleqgrk...kerevevvlirknge 74 
                                       +i    +d ++++++e  +++ Gy pe++   +  + d++  +p++ +++r+ +    +    e++ e+ + ++n+e
  gi|298674886|ref|YP_003726636.1| 587 FIwrAEKDWPVEFVSENIMQF-GYIPEDFTSERiiYGDII--HPDDLQKVRNKMAGRYEdksGEFNLEYRILTSNDE 660
                                       455444455677999999999.999***999988778888..444444444444444335668************** PP

                             PAS_9  75 tfwvlltaspvkdddgelvgiivilrDite 104
                                         wv+ + +  +d++g++  + +i++Dit+
  gi|298674886|ref|YP_003726636.1| 661 VRWVDERTTIHYDENGNVNYLQGIIIDITK 690
                                       *****7777777899****9********95 PP

  == domain 5  score: 19.1 bits;  conditional E-value: 5.8e-07
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetf 76 
                                       d i++++++g+ilyaN+a  + lGy+++e+   +i +l   +++ +a++++++++     + ++ ++ li k+g+ +
  gi|298674886|ref|YP_003726636.1| 874 DFIFVIDSEGHILYANKATQDRLGYTEQELQEMNIINLHysKQALKAASNISDVVSG---NRFSCDIPLIAKDGTII 947
                                       6788888**********************9999999999443333333333333333...33666666666666555 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   0.0   1.1e-15   2.1e-12       5     134 ..     296     428 ..     294     432 .. 0.79
   2 !   33.4   0.0   2.3e-11   4.6e-08       3     137 ..     714     849 ..     712     849 .. 0.85

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 1.1e-15
                                       HHHHHHHHHHHHHSS...EEEEEEE-.TTS-..EEEEEEEES-TTSTT-S-B.--.-TTHHHHHHHHTS-EEES-GG CS
                             GAF_2   5 eelldlvldelvelg.aalgyillvd.ddgg..lrlaawgeaeeefgaaldr.pl.geglvgealrtgrpvilndle 75 
                                       ee+ +lvlde+++l+ ++ gyi++ + +d++  +++++   ++ ++++++ + +l + gl+ ++++++ pvi n++ 
  gi|298674886|ref|YP_003726636.1| 296 EEITNLVLDEMIRLTqSDSGYIVFFNnEDESssIYVLSK-DETNSVSDKQFKnSLkNTGLWNRVIKQKHPVISNNIS 371
                                       7999*********955****9999552333333433333.3333333333332446888****************** PP

                                       G-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHH CS
                             GAF_2  76 edpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqia 134
                                        d +      g  ++++ l +P+++++ vv+v ++ +nk  ++d +++++L++l + + 
  gi|298674886|ref|YP_003726636.1| 372 VDFYDEDFY-GNLNIKRLLNIPIFDDDSVVAVGGV-FNKNKDYDKSNIRQLTLLLNIML 428
                                       *99999998.***************999******8.899999***********988765 PP

  == domain 2  score: 33.4 bits;  conditional E-value: 2.3e-11
                                       HHHHHHHHHHHHHHHSS...EE.EEEEE-TTS-EEEEEEEES-TTSTT-S-B---TTHHHHHHHHTS-EE.ES-GGG CS
                             GAF_2   3 dleelldlvldelvelg.aalg.yillvdddgglrlaawgeaeeefgaaldrplgeglvgealrtgrpvi.lndlee 76 
                                       +l+e++++ ld ++ ++ +++g  +l+++  ++l l+++ +   e+ ++ ++   +++  + + tg p++ l  + e
  gi|298674886|ref|YP_003726636.1| 714 NLQEIFEQYLDFCISMDpIDCGgLYLIDEVTNDLNLVSSEGLSSELMQKMSHFTPNSIQHRLFTTGHPIYkL--YSE 788
                                       79**************8899772555555778899999999999999999775567799***********44..99* PP

                                       -S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  77 dpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                         +  g  + ++ lr+++++P+++++ vv+v++l++++ ++ +++ +  Le++a+qi+  i
  gi|298674886|ref|YP_003726636.1| 789 IISITGNDLPYESLRATAIIPVRYQDDVVAVMFLASKNNYEISQDVRISLETVADQIGETI 849
                                       **********************99777*******877777776666666********9765 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0         3     6e+03      42      96 ..      74     130 ..      45     142 .. 0.71
   2 !   15.9   0.0     6e-06     0.012      13     110 .]     171     269 ..     165     269 .. 0.87
   3 !   15.1   0.0     1e-05      0.02      15     110 .]     464     560 ..     456     560 .. 0.94
   4 !   12.7   0.0   5.6e-05      0.11       2     109 ..     580     692 ..     579     693 .. 0.93
   5 !   20.8   0.0   1.8e-07   0.00036       1      36 [.     869     904 ..     869     934 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3
                             PAS_4  42 ellpeedaarleralrrvlegeepiefleelll..pgeerhyelrllPlrdesGevi 96 
                                       ++    d++ +e+ +  + e + + + l++++l  +g  r+++ r + l   +G v+
  gi|298674886|ref|YP_003726636.1|  74 DIIHSVDREYVESEISNCFEKRCSGYNLQYRVLtgEGNIRWVDERTVVLYGGDGSVD 130
                                       566666777777777777777777777777777788888998888888888777766 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 6e-06
                             PAS_4  13 pdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll...pgeerhyelrll 86 
                                        dg + +aN+a++ + g+ ++e++  t+ ++ p e ++ +   ++++l++e  +  + e+     + +  ++e++l+
  gi|298674886|ref|YP_003726636.1| 171 QDGYIKFANRAFENITGYKRDEIIETTFLDYIPVEYQRMVNKKYEKLLKTEPKYPYTYEVYIqskSEGLIPVEINLS 247
                                       5999**********************************************987766666555678999999999999 PP

                             PAS_4  87 PlrdesGevigvlvisrDiTerrr 110
                                        +  e     +v++ +rDiTer++
  gi|298674886|ref|YP_003726636.1| 248 AINFEAN--PAVMFNIRDITERKE 269
                                       9955444..599999*****9985 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 1e-05
                             PAS_4  15 grvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll...pgeerhyelrllPl 88 
                                         + +aN+a++ + g+ ++e++  ++  + p e ++ +   +++ l+ ++  ++  e+++    + +++ e++++P+
  gi|298674886|ref|YP_003726636.1| 464 EAIKFANKAFENITGYKRDEITETSFLAYIPVEYQRMVLKKYNKTLKANQDNSRIYEVNFlssTKNTVPTEINFSPI 540
                                       56789********************************************99999999999999************** PP

                             PAS_4  89 rdesGevigvlvisrDiTerrr 110
                                       +  +G+  +v++ +rDiT +r+
  gi|298674886|ref|YP_003726636.1| 541 H-YEGK-PAVMLNVRDITKQRQ 560
                                       5.7***.9**********9985 PP

  == domain 4  score: 12.7 bits;  conditional E-value: 5.6e-05
                             PAS_4   2 dslpdalavl..dpdgrvlyaNaaaaelfgappeellGktla..ellpeedaarleralrrvlegeepiefleelll 74 
                                       +++p++++++   +d  v+++++++++ fg+ pe+++ ++    ++  ++d + +++ ++   e +   + le++ l
  gi|298674886|ref|YP_003726636.1| 580 NNSPAIVFIWraEKDWPVEFVSENIMQ-FGYIPEDFTSERIIygDIIHPDDLQKVRNKMAGRYEDKSGEFNLEYRIL 655
                                       799********9***************.8888888888887779999999***********************9999 PP

                             PAS_4  75 ..pgeerhyelrllPlrdesGevigvlvisrDiTerr 109
                                         ++e r+++ r +   de+G v  + +i++DiT  +
  gi|298674886|ref|YP_003726636.1| 656 tsNDEVRWVDERTTIHYDENGNVNYLQGIIIDITKKK 692
                                       9*********************************876 PP

  == domain 5  score: 20.8 bits;  conditional E-value: 1.8e-07
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeell 36 
                                       ld++ d ++v+d++g++lyaN+a ++ +g++ +el 
  gi|298674886|ref|YP_003726636.1| 869 LDNVDDFIFVIDSEGHILYANKATQDRLGYTEQELQ 904
                                       799************************999999986 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   2.4e-09   4.9e-06       2      61 ..     155     216 ..     154     222 .. 0.88
   2 !   15.2   0.0   8.3e-06     0.016       3      56 ..     447     500 ..     445     512 .. 0.76
   3 ?   -3.5   0.0         6   1.2e+04       3      17 ..     575     589 ..     574     595 .. 0.82
   4 !   22.5   0.0   4.1e-08   8.2e-05       5      45 ..     867     908 ..     865     919 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 2.4e-09
                             PAS_8   2 rlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpvlrplle..daeq 61 
                                       ++ +l+e+  dgi++v +g  i ++N+a++ ++Gy+ +++++ ++ +++pv +  ++   +e 
  gi|298674886|ref|YP_003726636.1| 155 KYSTLIECGIDGILIVQDGY-IKFANRAFENITGYKrDEIIETTFLDYIPVEYQRMVnkKYEK 216
                                       799999*********99899.*****************************9999888655555 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 8.3e-06
                             PAS_8   3 lralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpvlrpll 56 
                                       + +l+e   dg ++v + + i ++N+a++ ++Gy+ +++ +  +  ++pv +  +
  gi|298674886|ref|YP_003726636.1| 447 YSTLVEKGIDGTLIVQD-EAIKFANKAFENITGYKrDEITETSFLAYIPVEYQRM 500
                                       66666655666666643.46***************99999998888887776666 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 6
                             PAS_8   3 lralfesspdgiavv 17 
                                       l+ ++++sp  ++++
  gi|298674886|ref|YP_003726636.1| 575 LEDIINNSPAIVFIW 589
                                       78899****999986 PP

  == domain 4  score: 22.5 bits;  conditional E-value: 4.1e-08
                             PAS_8   5 alfesspdgiavvd.lgdrivdvNqaalellGys.adlkgell 45 
                                        l+++++d i+v+d +g  i+++N+a+++ lGy+ ++l ++ +
  gi|298674886|ref|YP_003726636.1| 867 KLLDNVDDFIFVIDsEGH-ILYANKATQDRLGYTeQELQEMNI 908
                                       699***********6666.*************99877777654 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0032       6.4       4     102 ..     297     407 ..     295     425 .. 0.72
   2 !   27.6   0.0   1.6e-09   3.1e-06       1     127 [.     714     849 ..     714     850 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0032
                             GAF_3   4 ellekllkllvkllgaevgalllldedgn.klqvaagwdgkpalse....sld.edsalarralssgevvse....p 70 
                                       e+ + +l+++ +l+++++g ++ ++++ + +   + ++d+ +++s     +   +++ l+ r+++++ +v+      
  gi|298674886|ref|YP_003726636.1| 297 EITNLVLDEMIRLTQSDSGYIVFFNNEDEsSSIYVLSKDETNSVSDkqfkN-SlKNTGLWNRVIKQKHPVISnnisV 372
                                       666668999999*****9999998888883557778888888887775553.1589*************99966663 PP

                             GAF_3  71 sf...aeedglpdraalavPLvagrqviGvlalas 102
                                       +f   +   +l+   +l +P+ + + v+ v ++  
  gi|298674886|ref|YP_003726636.1| 373 DFydeDFYGNLNIKRLLNIPIFDDDSVVAVGGVFN 407
                                       33222234668888889999999888888766544 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 1.6e-09
                             GAF_3   1 sldellekllkllvkllgaevgalllldedgnklqvaagwdgkpalse..sldedsalarralssgevvse...... 69 
                                       +l+e++e+ l++  ++   + g l+l de  n+l+ +++++ +  l +  s  ++++  +r++++g ++++      
  gi|298674886|ref|YP_003726636.1| 714 NLQEIFEQYLDFCISMDPIDCGGLYLIDEVTNDLNLVSSEGLSSELMQkmSHFTPNSIQHRLFTTGHPIYKlyseii 790
                                       689**********************************999666666552355599999**********999665565 PP

                             GAF_3  70 .psfaeedglpdraalavPLvagrqviGvlalastkprafdaedlelleslArqiatai 127
                                         ++ + ++  +ra  ++P++ ++ v+ v++las+++ +++++ +  le++A+qi+  i
  gi|298674886|ref|YP_003726636.1| 791 sITGNDLPYESLRATAIIPVRYQDDVVAVMFLASKNNYEISQDVRISLETVADQIGETI 849
                                       533366788999********************************************876 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.61   1.2e+03      38      80 ..      70     112 ..      58     122 .. 0.82
   2 ?   -2.2   0.0       2.2   4.3e+03      28      71 ..     477     519 ..     460     535 .. 0.71
   3 !    8.4   0.0    0.0011       2.2      37      92 ..     618     675 ..     603     688 .. 0.71
   4 !   10.1   0.0   0.00035      0.69       3      86 ..     874     952 ..     872     957 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.61
                            PAS_11  38 rsiydLchpqdlstlkshlrevissngeatsslyRLrlsqdkf 80 
                                       +++ d++h  d++ ++s  ++ ++++  +  + yR  ++++++
  gi|298674886|ref|YP_003726636.1|  70 LYYNDIIHSVDREYVESEISNCFEKRCSGYNLQYRVLTGEGNI 112
                                       678899*************999977777777889998877765 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.2
                            PAS_11  28 lglekeelvgrsiydLchpqdlstlkshlrevissngeatssly 71 
                                       +g++++e++++s+ + +  +  + + +++ +++ + ++  s +y
  gi|298674886|ref|YP_003726636.1| 477 TGYKRDEITETSFLAYIPVEYQRMVLKKYNKTL-KANQDNSRIY 519
                                       677888888888877777777777777777777.4444455444 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0011
                            PAS_11  37 grsiydLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvkv..ktksklfkn 92 
                                       ++++ d++hp+dl++++++    ++ +     + yR+ +s+d++ +v  +t+ +  +n
  gi|298674886|ref|YP_003726636.1| 618 RIIYGDIIHPDDLQKVRNKMAGRYEDKSGEFNLEYRILTSNDEVRWVdeRTTIHYDEN 675
                                       345559******************4444447788*****9997655511455554444 PP

  == domain 4  score: 10.1 bits;  conditional E-value: 0.00035
                            PAS_11   3 qfttrldidgkIisvDtsaLrasfslglekeelvgrsiydLchpqdlstlkshlrevissngeatsslyRLrlsqdk 79 
                                        f++ +d +g I+  ++     + +lg++++el+++ i +L+  ++  +++s  ++v+  +g+  s    L++++++
  gi|298674886|ref|YP_003726636.1| 874 DFIFVIDSEGHILYANK---ATQDRLGYTEQELQEMNIINLHYSKQALKAASNISDVV--SGNRFSCDIPLIAKDGT 945
                                       69999************...**************************************..55555555667777777 PP

                            PAS_11  80 fvkvktk 86 
                                       +++  tk
  gi|298674886|ref|YP_003726636.1| 946 IIYKDTK 952
                                       7776666 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   0.00043      0.86       3     112 ..     296     410 ..     295     426 .. 0.67
   2 !    6.3   0.0    0.0073        15      87     131 ..     802     847 ..     733     849 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00043
                                       HHHHHHHHHHHHHHHTESEEEEEE...EEETTEEE.......CEEEEECCEEEET..TSHHHHHHHHHSSSEEESTG CS
                               GAF   3 eelldtvveelrellgadrvalyl...pdydGlhy.......dipqasrwlfmkn..grgicgqvlatgqplvipds 67 
                                       ee+ + v++e+ +l++ d + +     +d++ + y       +     ++       ++g+ ++v++++ p++ +++
  gi|298674886|ref|YP_003726636.1| 296 EEITNLVLDEMIRLTQSDSGYIVFfnnEDESSSIYvlskdetNSVSDKQFKN--SlkNTGLWNRVIKQKHPVISNNI 370
                                       67888899***********999554553333334455553222333333333..343677677************73 PP

                                       GTSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS CS
                               GAF  68 tpdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp 112
                                         + +f +    d+ +n +i+ +l +P+++d+ ++++  + n+ +
  gi|298674886|ref|YP_003726636.1| 371 --SVDFYD---EDFYGNLNIKRLLNIPIFDDDSVVAVGGVFNKNK 410
                                       ..333444...466679*****************99977777544 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0073
                                       ESEEEEEEEEETTEEEEEEEEEESSS.CSHHHHHHHHHHHHHHHHH CS
                               GAF  87 irsslvvPlvndgelwGllvlhnpsp.pftreelellqvladqvav 131
                                        r+ + +P++ ++++++++ l ++ + + +++ +  l+++adq++ 
  gi|298674886|ref|YP_003726636.1| 802 LRATAIIPVRYQDDVVAVMFLASKNNyEISQDVRISLETVADQIGE 847
                                       568999*****************88844455555556******985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (980 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       825  (0.0460148); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.77u 0.34s 00:00:01.11 Elapsed: 00:00:00.51
# Mc/sec: 5806.35
//
Query:       gi|298674887|ref|YP_003726637.1|  [L=352]
Description: cobalamin synthesis protein P47K [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.7e-39  135.2   0.0    3.3e-39  134.3   0.0    1.5  1  cobW        CobW/HypB/UreG, nucleotide-binding domain
    0.00036   20.6   0.5      0.001   19.1   0.5    2.1  1  CbiA        CobQ/CobB/MinD/ParA nucleotide binding domain
     0.0017   18.1   0.3     0.0098   15.5   0.1    2.1  2  SRP54       SRP54-type protein, GTPase domain
  ------ inclusion threshold ------
      0.011   15.6   0.1          6    6.6   0.0    3.1  3  CLP1_P      mRNA cleavage and polyadenylation factor CLP1 P-l
      0.015   14.3   0.2       0.11   11.5   0.1    2.1  2  MeaB        Methylmalonyl Co-A mutase-associated GTPase MeaB
      0.015   15.2   0.0       0.04   13.8   0.0    1.8  1  MobB        Molybdopterin guanine dinucleotide synthesis prot
      0.019   14.5   0.0       0.05   13.1   0.0    1.7  1  KTI12       Chromatin associated protein KTI12
      0.049   13.5   0.0       0.15   11.9   0.0    1.9  2  NTPase_1    NTPase
      0.053   13.3   1.6       0.52   10.1   0.0    2.7  3  ATP_bind_1  Conserved hypothetical ATP binding protein
      0.053   13.6   0.4         12    6.0   0.0    2.5  2  DUF520      Protein of unknown function (DUF520)


Domain annotation for each model (and alignments):
>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.3   0.0   1.9e-42   3.3e-39       2     176 ..       3     178 ..       2     179 .. 0.94

  Alignments for each domain:
  == domain 1  score: 134.3 bits;  conditional E-value: 1.9e-42
                                       EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT.EEEETTTTECCHCTT-HHHHHHHH CS
                              cobW   2 vtvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgveivelenGciCctlredllkeleal 76 
                                       v+v++GflGsGKTt + +l     ++++++a+ivNe+ge+++D++++++ g  ++el+ GciCc+l++dl  +++ l
  gi|298674887|ref|YP_003726637.1|   3 VLVIGGFLGSGKTTAILNLGkyLSENNYRVAIIVNEIGEIGLDGDVISKYGFDTTELTSGCICCSLKTDLRYTVTTL 79 
                                       79****************99888899*************************************************** PP

                                       HHHHTT-SEEEEEECTTTTHHHHHTT.SHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHH CS
                              cobW  77 eereerldviliEttGlaePapvaft.eeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDl 152
                                        +++ ++d+++iE tG+a P+ +  + +    +d++   +v+ +D++++++  ++i++  ++q+  a++lv+nKtDl
  gi|298674887|ref|YP_003726637.1|  80 YNNY-NPDILIIEPTGIAFPNVIRNEvNLMNLDDIEFAPLVTFIDGSRFKQLMKEIRHFSQRQIIDAEILVINKTDL 155
                                       ****.9*****************333355556799**************999************************* PP

                                       HCHC..HHHHHHHHHHHHTTS-EE CS
                              cobW 153 ldeeallekleerlrqlnpeakvl 176
                                       +++++l   +e+ ++qlnp+a+++
  gi|298674887|ref|YP_003726637.1| 156 IESRQL-PIIEDAVHQLNPDADII 178
                                       ****76.*************9987 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.5   5.8e-07     0.001       3      33 ..       5      35 ..       3     269 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 5.8e-07
                                      EEESSTTSSHHHHHHHHHHHHHHTT--EEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  3 iastkGGvGKTtlaanLaralarrglrVllv 33
                                      ++++  G+GKTt  +nL+++l+++++rV+ +
  gi|298674887|ref|YP_003726637.1|  5 VIGGFLGSGKTTAILNLGKYLSENNYRVAII 35
                                      5566669*********************998 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   5.5e-06    0.0098       2      35 ..       2      35 ..       1      39 [. 0.91
   2 ?   -0.1   0.0      0.34   6.1e+02      99     123 ..     128     152 ..     115     179 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.5e-06
                                      EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEE CS
                             SRP54  2 nvillvGlqGaGKTttlaKLaallkkegkkvllv 35
                                      +v+++ G+ G+GKTt++  L ++l++++++v+++
  gi|298674887|ref|YP_003726637.1|  2 KVLVIGGFLGSGKTTAILNLGKYLSENNYRVAII 35
                                      5788999************************998 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.34
                                       HHHHHHHHHHHHHHSSSEEEEEEET CS
                             SRP54  99 kelmeelkkikkvvkpdevllvlda 123
                                       k+lm+e++++++    d  +lv++ 
  gi|298674887|ref|YP_003726637.1| 128 KQLMKEIRHFSQRQIIDAEILVINK 152
                                       4566666666666666666666654 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.018        32       4      28 ..      11      35 ..       8      42 .. 0.89
   2 ?    6.6   0.0    0.0033         6      84     145 ..     127     188 ..     124     226 .. 0.78
   3 ?    2.8   0.0     0.051        91      92     140 ..     181     229 ..     175     247 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.018
                            CLP1_P  4 dsGKSTlarlLlNyalrkgrkpvyv 28
                                       sGK+T + +L  y+ +++++++++
  gi|298674887|ref|YP_003726637.1| 11 GSGKTTAILNLGKYLSENNYRVAII 35
                                      69*******************9954 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0033
                            CLP1_P  84 vkelareveekleenkkakasgliIntpGwvkglgaellleliealepdvvvvldq.eellne 145
                                       +k+l++e++ ++++++   a++l+In + ++++  + +++++++ l+pd+ ++  + + ++n+
  gi|298674887|ref|YP_003726637.1| 127 FKQLMKEIR-HFSQRQIIDAEILVINKTDLIESRQLPIIEDAVHQLNPDADIIRLSaKMDDNK 188
                                       577888888.788889999*****************************875554442444444 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.051
                            CLP1_P  92 eekleenkkakasgliIntpGwvkglgaellleliealepdvvvvldqe 140
                                       + k++ nk +k   liI  pG+  ++  +l +e i+ +++++v+  ++e
  gi|298674887|ref|YP_003726637.1| 181 SAKMDDNKFRKFAKLIIEKPGLTPEIIQDLSEEEIDSIQCSNVATYSKE 229
                                       5688999999999****************************99988875 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   5.9e-05      0.11      31      63 ..       3      35 ..       1      41 [. 0.92
   2 ?    0.6   0.0      0.12   2.2e+02     169     183 ..     145     159 ..      76     207 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.9e-05
                                      EEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEE CS
                              MeaB 31 vvGltGvPGaGkstlvealglelrrrGkrvavl 63
                                      v+ + G+ G+Gk t++ +lg  l ++ +rva++
  gi|298674887|ref|YP_003726637.1|  3 VLVIGGFLGSGKTTAILNLGKYLSENNYRVAII 35
                                      67788***************************8 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.12
                                       -SEEEEE---HHHHH CS
                              MeaB 169 aDiivvnkaDkkeae 183
                                       a+i+v+nk+D+ e++
  gi|298674887|ref|YP_003726637.1| 145 AEILVINKTDLIESR 159
                                       789999999976654 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.2e-05      0.04       1      40 [.       3      42 ..       3      84 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.2e-05
                              MobB  1 vlgivgksgsGKTtLleklipelkarglrvgtiKhahhgf 40
                                      vl i g+ gsGKTt + +l + l+++++rv++i  +  ++
  gi|298674887|ref|YP_003726637.1|  3 VLVIGGFLGSGKTTAILNLGKYLSENNYRVAIIVNEIGEI 42
                                      5788899************************997766554 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.8e-05      0.05       1      38 [.       1      38 [.       1      52 [. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.8e-05
                                      E.EEEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-TH CS
                             KTI12  1 MpLvvltGlPssGKstrakeLakaleeekrsvvvidde 38
                                      M  +v+ G+  sGK+t+  +L k+l+e++++v +i +e
  gi|298674887|ref|YP_003726637.1|  1 MKVLVIGGFLGSGKTTAILNLGKYLSENNYRVAIIVNE 38
                                      778999****************************9887 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   8.5e-05      0.15       2      39 ..       4      40 ..       3     113 .. 0.78
   2 ?   -2.2   0.0       1.9   3.4e+03       3      19 ..     308     324 ..     272     333 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.5e-05
                                      EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE- CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevr 39
                                      ++i G  G+GKtT + ++ + l++++++v+ ++++e+ 
  gi|298674887|ref|YP_003726637.1|  4 LVIGGFLGSGKTTAILNLGKYLSENNYRVA-IIVNEIG 40
                                      578999**********************98.4555544 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.9
                                       EEE--TTSSHHHHHHHH CS
                          NTPase_1   3 fiTGppGvGKtTlvkkv 19 
                                       ++T+ + v K+ lv+ v
  gi|298674887|ref|YP_003726637.1| 308 ILTAVSNVEKSELVNTV 324
                                       34444444444444444 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00029      0.52       3      30 ..       8      35 ..       5      37 .. 0.85
   2 ?    1.3   0.0      0.14   2.5e+02     159     219 ..     146     208 ..     107     223 .. 0.65
   3 ?   -1.4   0.0       0.9   1.6e+03      26      48 ..     317     340 ..     268     346 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00029
                        ATP_bind_1  3 GpaGsGKttfvgalseilelrgrsvavv 30
                                      G  GsGKtt + +l ++l++++++va++
  gi|298674887|ref|YP_003726637.1|  8 GFLGSGKTTAILNLGKYLSENNYRVAII 35
                                      567******************9999865 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.14
                        ATP_bind_1 159 hvvvlnkfDllkek.....lekeleffedvealslllekeeekykklaeaiaelleefalvlrflp 219
                                        + v+nk+Dl++++     ++   +  +d + ++l ++ +++k++k a+    ++e+++l++++++
  gi|298674887|ref|YP_003726637.1| 146 EILVINKTDLIESRqlpiiEDAVHQLNPDADIIRLSAKMDDNKFRKFAKL---IIEKPGLTPEIIQ 208
                                       58999*****9966655543344444445555555555555554444433...3455555555554 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.9
                        ATP_bind_1  26 svavvN.LDPAaeelpYeaavdir 48 
                                       ++++vN  D  +e++ Ye +++i+
  gi|298674887|ref|YP_003726637.1| 317 KSELVNtVDRCVENIFYEYDIEIE 340
                                       334555456666666666666665 PP

>> DUF520  Protein of unknown function (DUF520)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0    0.0067        12      76     123 ..     216     263 ..     204     268 .. 0.86
   2 ?    5.3   0.1     0.011        19       6      39 ..     312     345 ..     308     352 .] 0.85

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0067
                            DUF520  76 kaldlgkvekasgkkvkqevklkegidkekakkivklikdsklkvqas 123
                                        +++ ++v + s++ v  + +l++ + +  a++iv ++kd+ +k + +
  gi|298674887|ref|YP_003726637.1| 216 DSIQCSNVATYSKEFVVSRKNLESDVASSIARDIVYTLKDEVIKLNPE 263
                                       56777888889999999999***********************98865 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.011
                            DUF520   6 vsevdlqevknAvdqakkeistRfDfkgskaeie 39 
                                       vs+v+++e+ n+vd++  +i   +D+   k++ +
  gi|298674887|ref|YP_003726637.1| 312 VSNVEKSELVNTVDRCVENIFYEYDIEIEKSDTH 345
                                       9************************987776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2112.47
//
Query:       gi|298674888|ref|YP_003726638.1|  [L=539]
Description: putative flavoprotein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.1e-71  239.1   0.3    8.1e-71  238.1   0.2    1.6  2  RACo_C_ter   C-terminal domain of RACo the ASKHA domain
    1.4e-10   41.1   0.1    3.8e-10   39.7   0.1    1.8  1  Raco_middle  RACo middle region
    0.00018   22.0   4.1     0.0007   20.1   4.4    1.8  1  Fer4_7       4Fe-4S dicluster domain
    0.00027   21.1   3.4    0.00053   20.1   3.4    1.5  1  Fer4_9       4Fe-4S dicluster domain
    0.00088   20.2   5.2       0.62   11.0   1.7    2.7  2  Fer4_16      4Fe-4S double cluster binding domain
     0.0023   17.7   5.0       0.12   12.2   1.6    2.7  2  Fer4         4Fe-4S binding domain
     0.0037   17.3   5.1       0.01   15.8   0.9    2.4  2  Fer4_6       4Fe-4S binding domain
  ------ inclusion threshold ------
       0.01   15.9   7.1      0.034   14.3   7.2    1.8  1  Fer4_21      4Fe-4S dicluster domain
      0.026   14.6   0.3      0.075   13.2   0.3    1.7  1  Fer4_11      4Fe-4S dicluster domain
      0.047   13.8   6.4      0.058   13.5   2.3    2.3  2  Fer4_10      4Fe-4S dicluster domain
       0.19   11.9   9.4        3.2    8.0   7.3    3.1  3  Fer4_18      4Fe-4S dicluster domain
       0.62   11.1  10.9       0.33   12.0   4.8    2.4  2  Fer4_3       4Fe-4S binding domain
        1.1    9.5   7.3      0.079   13.1   1.6    2.1  2  Fer4_2       4Fe-4S binding domain
        1.2    9.8   9.0      0.049   14.2   3.0    1.8  1  Fer4_4       4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> RACo_C_ter  C-terminal domain of RACo the ASKHA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0         4   5.1e+03     150     171 ..      65      86 ..      62      87 .. 0.80
   2 !  238.1   0.2   6.3e-74   8.1e-71       1     259 [.     169     428 ..     169     429 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 4
                                       HHHHHHHTT--GGG--EEEEES CS
                        RACo_C_ter 150 iktLleevglevediekvylAG 171
                                       +k ++++++++++++e++ ++G
  gi|298674888|ref|YP_003726638.1|  65 VKNIISKLEVDIDNLERISVCG 86 
                                       5677889999999999999888 PP

  == domain 2  score: 238.1 bits;  conditional E-value: 6.3e-74
                                       S-EEEEEESSSEEEEEE-SS-EEEEEEE--SCCCTTTSTTBE-SSTTEEEEEEEEGGGSSEEEEECTSS-....... CS
                        RACo_C_ter   1 elslliDiGTNaEivlgnkdellaasaaaGPAlEGaeikcGmrAapgAIedveidpetlevelkvigdek....... 70 
                                       e+++ +D+GTNaE++l+++d ++++saaaGPAlEG++ik+G++A+p++I+d+e+++    ++  v+++e        
  gi|298674888|ref|YP_003726638.1| 169 EVAIATDYGTNAEMALKVDDVIYTGSAAAGPALEGQQIKHGVLASPYTISDIEFEDGY--LRNYVLNEEMipvkgdl 243
                                       67899*************************************************9998..33334433323344445 PP

                                       ...............-SEEEHHHHHHHHHHHHHTTSB-TTS-B-GGG-TTTEEEETTCEEEEEE-GGGSSSS-EEEE CS
                        RACo_C_ter  71 ...............akGicGsGiidliaelleagiidkkgklnkelkserireeeetleyvlakaeetetkdivit 132
                                                      akGi+G+G+i+li e++e+g+i k +k+             +t + +l  ++     ++ ++
  gi|298674888|ref|YP_003726638.1| 244 vdpktgevkeegnirAKGITGTGVIALIDECIENGLI-KLPKI-------------QTSDGILRLQD-----NVLFS 301
                                       666677777777777**********************.55688.............67889999987.....9**** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHTT--GGG--EEEEESSGGGCEEHHHHHHHTSS-SS-GGGEEEECSHHHHHHHH CS
                        RACo_C_ter 133 ekDieelikakaAiyagiktLleevglevediekvylAGafGsyidaekAitiGllPdlelekvvqvGNtslagAre 209
                                       +kD++e++ka +A++ag+ tL++++g+e+ d++++y++Ga+G+y+da k+ +iG+ P  ++++++q+GNtsl +Are
  gi|298674888|ref|YP_003726638.1| 302 DKDLSEAGKALGALRAGHITLCNAAGIEMGDVTRAYMSGASGTYVDALKSYRIGMSPY-NVDHISQIGNTSLVVARE 377
                                       **********************************************************.****************** PP

                                       HHCBHHHHHHHHHHHHHE..EE--TTSSSHHHHHHHHHSSSS-SSGGG-ST- CS
                        RACo_C_ter 210 allseealeeleeiarki..tyielateeeFqeeyvaalflphtdlelfpsv 259
                                       +llse++l+el++ia+ki  ++ ++ate++F ++yv +++++++++ +f+++
  gi|298674888|ref|YP_003726638.1| 378 ILLSEDRLWELQDIANKIvgHHTMFATEPAFRDTYVLEIAYWDEGM-PFKML 428
                                       **********************************************.99987 PP

>> Raco_middle  RACo middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.1     3e-13   3.8e-10       2     161 ..       4     165 ..       3     167 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 3e-13
                       Raco_middle   2 GlavDiGtTtvvaaLvdletgkelaeasalNpQikyGeDvlsRiayakeeeegleklqkavveeinelieelleeag 78 
                                       G+a+D+Gt+   a+ +dletg++  +  +l +    G++v+  + +a +   g +  + +v+++++++i++l    +
  gi|298674888|ref|YP_003726638.1|   4 GVAFDLGTSGFRAHKMDLETGEIKRTVITLRNP-IPGTNVMDHMDFAIH--YGQDLTHYLVIDAVKNIISKL----E 73 
                                       9********************988887777554.56*************..777778899999999999887....7 PP

                       Raco_middle  79 iekeeiyevvvagNttMlhlllgldpksla......kapyv..pvvseavelkakel.glkinpeakvyvlpnvssy 146
                                       ++ ++++++ v+gN + l l+ g++ + la      k+ y+   + ++a +l+++e+ gl+  +++kv++ p++ + 
  gi|298674888|ref|YP_003726638.1|  74 VDIDNLERISVCGNPIQLSLFQGMTIEDLAyagerkKEKYNikDQERKANILDSSEInGLEDFKDCKVVIPPAIRHE 150
                                       8889*************************83222222344411556677788888884689999************* PP

                       Raco_middle 147 vGgDivagilasglh 161
                                       vG+D++a +++sg+ 
  gi|298674888|ref|YP_003726638.1| 151 VGADALALMVVSGML 165
                                       ************995 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   4.4   5.5e-07    0.0007       4      51 ..     484     527 ..     483     528 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.5e-07
                            Fer4_7   4 gCgaCvaaCpvkaieldeeenekgtekveidpekC..lgCgaCvavCPtg 51 
                                        C++ v++Cp++ai++d+        kv i+ + C  ++C++Cv++CPtg
  gi|298674888|ref|YP_003726638.1| 484 SCEKSVEVCPTSAISIDDN------GKVLIRTDLCegIHCQKCVRACPTG 527
                                       6888899*********996......58999999995569*********98 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   3.4   4.2e-07   0.00053       4      49 ..     484     527 ..     483     529 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.2e-07
                            Fer4_9   4 gCgaCveaCpagvvvedaaerkarlraaseeaC..igCgaCveaCpkg 49 
                                       +C + ve+Cp+ +++ d++++    +      C  i+C++Cv aCp+g
  gi|298674888|ref|YP_003726638.1| 484 SCEKSVEVCPTSAISIDDNGKVLIRTD----LCegIHCQKCVRACPTG 527
                                       688889********9999999988755....598899*********97 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.1    0.0013       1.6       4      25 ..     484     505 ..     482     514 .. 0.82
   2 !   11.0   1.7   0.00049      0.62       3      18 ..     515     530 ..     511     537 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0013
                           Fer4_16   4 tCgkCaevCPtnaikekkekei 25 
                                       +C+k +evCPt+ai+ + + ++
  gi|298674888|ref|YP_003726638.1| 484 SCEKSVEVCPTSAISIDDNGKV 505
                                       8*************98866665 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00049
                           Fer4_16   3 gtCgkCaevCPtnaik 18 
                                       + C+kC+ +CPt+ ++
  gi|298674888|ref|YP_003726638.1| 515 IHCQKCVRACPTGELN 530
                                       47**********9886 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.1    0.0082        11      15      24 .]     489     498 ..     489     498 .. 0.91
   2 !   12.2   1.6   9.6e-05      0.12       9      21 ..     515     527 ..     515     527 .. 0.94

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0082
                                       HHHSTTTEEE CS
                              Fer4  15 vevCPvgAIt 24 
                                       vevCP+ AI+
  gi|298674888|ref|YP_003726638.1| 489 VEVCPTSAIS 498
                                       89******95 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 9.6e-05
                                       SS-THHHHHSTTT CS
                              Fer4   9 igCGaCvevCPvg 21 
                                       i+C +Cv +CP+g
  gi|298674888|ref|YP_003726638.1| 515 IHCQKCVRACPTG 527
                                       79*********97 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.2       0.1   1.3e+02      16      24 .]     489     497 ..     484     497 .. 0.86
   2 !   15.8   0.9   8.2e-06      0.01       2      22 ..     505     527 ..     504     529 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.1
                            Fer4_6  16 vrvCPegai 24 
                                       v vCP+ ai
  gi|298674888|ref|YP_003726638.1| 489 VEVCPTSAI 497
                                       789***998 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 8.2e-06
                            Fer4_6   2 veidpdkCi..gCgdCvrvCPeg 22 
                                       v i  d+C   +C +Cvr+CP+g
  gi|298674888|ref|YP_003726638.1| 505 VLIRTDLCEgiHCQKCVRACPTG 527
                                       567789997447*********97 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   7.2   2.6e-05     0.034       9      53 ..     483     526 ..     476     530 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.6e-05
                           Fer4_21   9 igCgkCliaCedtshqaieidaktvlkvvedeCvG..CnlCssvCPv 53 
                                       ++C+k + +C+   + ai+id++ ++ +++d C G  C+ C+  CP+
  gi|298674888|ref|YP_003726638.1| 483 VSCEKSVEVCP---TSAISIDDNGKVLIRTDLCEGihCQKCVRACPT 526
                                       79*********...699****************8888*********7 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   5.8e-05     0.075      19      63 ..     489     533 ..     481     537 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.8e-05
                           Fer4_11  19 vasapseaivkdeetGaVlldektkk.eevrevveacPykivrkne 63 
                                       v+++p++ai  d+ +G Vl+  + ++  +++++v+acP     ++e
  gi|298674888|ref|YP_003726638.1| 489 VEVCPTSAISIDD-NGKVLIRTDLCEgIHCQKCVRACPTGELNWDE 533
                                       6788888999988.9***********999*********87776665 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   7.1     0.001       1.3      11      56 .]     484     525 ..     482     525 .. 0.77
   2 ?   13.5   2.3   4.5e-05     0.058       2      21 ..     505     526 ..     504     535 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.001
                           Fer4_10  11 rCgkCvkaCPadltsvgakgeaseeeavrkkvekCtg..cgaCveaCP 56 
                                        C+k v++CP+          ++++++v +  + C+g  c +Cv+aCP
  gi|298674888|ref|YP_003726638.1| 484 SCEKSVEVCPT------SAISIDDNGKVLIRTDLCEGihCQKCVRACP 525
                                       58888899999......5566667777777888888777899999999 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 4.5e-05
                           Fer4_10   2 vvidddtC..irCgkCvkaCPa 21 
                                       v i +d C  i+C+kCv+aCP+
  gi|298674888|ref|YP_003726638.1| 505 VLIRTDLCegIHCQKCVRACPT 526
                                       67889999888**********9 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.45   5.7e+02      27      67 ..     102     142 ..      82     153 .. 0.70
   2 ?    8.0   7.3    0.0025       3.2      56      96 ..     477     525 ..     464     526 .. 0.69
   3 ?    6.1   2.0    0.0096        12      59      74 ..     512     527 ..     504     532 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.45
                           Fer4_18  27 vvydakrGekiagrkkekkalkekeerkekgagdcidcesc 67 
                                        +y  +r +++++ k ++++ +  ++ + +g  d  dc++ 
  gi|298674888|ref|YP_003726638.1| 102 LAYAGERKKEKYNIKDQERKANILDSSEINGLEDFKDCKVV 142
                                       56777788888888888888888888888888888888764 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0025
                           Fer4_18  56 kgagdcidcescvkvcPtg.idirk.Glql......eciscllcidacd 96 
                                        +  d ++ce+ v+vcPt  i i + G  l      e i c++c+ ac 
  gi|298674888|ref|YP_003726638.1| 477 MTLEDPVSCEKSVEVCPTSaISIDDnGKVLirtdlcEGIHCQKCVRACP 525
                                       5567899**********954666541222122222278**********5 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0096
                           Fer4_18  59 gdcidcescvkvcPtg 74 
                                        + i+c++cv+ cPtg
  gi|298674888|ref|YP_003726638.1| 512 CEGIHCQKCVRACPTG 527
                                       67899*********97 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.3      0.36   4.6e+02       8      15 .]     489     496 ..     485     496 .. 0.88
   2 ?   12.0   4.8   0.00025      0.33       2      14 ..     515     527 ..     512     527 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.36
                            Fer4_3   8 vevCPvgA 15 
                                       vevCP+ A
  gi|298674888|ref|YP_003726638.1| 489 VEVCPTSA 496
                                       89***976 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00025
                            Fer4_3   2 tgCgaCvevCPvg 14 
                                       ++C+ Cv++CP+g
  gi|298674888|ref|YP_003726638.1| 515 IHCQKCVRACPTG 527
                                       69*********97 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.4       2.5   3.1e+03      17      22 .]     489     494 ..     484     494 .. 0.72
   2 ?   13.1   1.6   6.2e-05     0.079       5      22 .]     507     526 ..     503     526 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.5
                            Fer4_2  17 vsaCPa 22 
                                       v +CP+
  gi|298674888|ref|YP_003726638.1| 489 VEVCPT 494
                                       689**7 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 6.2e-05
                            Fer4_2   5 vdtdrCig..CgaCvsaCPa 22 
                                       + td C g  C +Cv aCP+
  gi|298674888|ref|YP_003726638.1| 507 IRTDLCEGihCQKCVRACPT 526
                                       5688897777*********7 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   3.0   3.8e-05     0.049       2      17 .]     510     527 ..     509     527 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.8e-05
                            Fer4_4   2 erC..igCgsCvaaCPqg 17 
                                       + C  i+C +Cv+aCP+g
  gi|298674888|ref|YP_003726638.1| 510 DLCegIHCQKCVRACPTG 527
                                       567779**********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (539 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.72u 0.32s 00:00:01.04 Elapsed: 00:00:00.51
# Mc/sec: 3168.46
//
Query:       gi|298674889|ref|YP_003726639.1|  [L=85]
Description: hypothetical protein Metev_0949 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.06   13.4   0.0      0.085   12.9   0.0    1.4  1  HisKA     His Kinase A (phospho-acceptor) domain
      0.086   12.7   0.1        0.1   12.5   0.1    1.1  1  PRP38     PRP38 family


Domain annotation for each model (and alignments):
>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   9.4e-06     0.085      42      66 ..      23      47 ..       6      48 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.4e-06
                                      HHHHHHHHHHHHHHHHHHHHCCHHH CS
                             HisKA 42 etiesearrldhlvedlLdlsriea 66
                                      ++i ++++ l +l+++lLdls+ e+
  gi|298674889|ref|YP_003726639.1| 23 KIINKGGQNLFDLIDNLLDLSKVES 47
                                      78999*****************986 PP

>> PRP38  PRP38 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   1.1e-05       0.1      95     156 ..       3      72 ..       1      76 [. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.1e-05
                             PRP38  95 algllYlRlvle..............pkelykllepllnDyrklkrrekdgevdpkgvklitidelvddLltkdri 156
                                        l+l+Y+R++ +               ++l++l+++ll+   k+ + +        +++ i i e++ddL tk ++
  gi|298674889|ref|YP_003726639.1|   3 YLILFYIRFASKrllhiklskiinkgGQNLFDLIDNLLD-LSKVESSDFAI-----HCEKIPIHEFIDDLKTKIHL 72 
                                       699****************99999999999999999875.55666666666.....9*************999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 524.71
//
Query:       gi|298674890|ref|YP_003726640.1|  [L=142]
Description: phosphoesterase PA-phosphatase-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-19   68.3   9.8    5.4e-19   68.3   9.8    1.8  2  PAP2      PAP2 superfamily
    1.7e-09   37.7   4.1    1.7e-09   37.7   4.1    2.0  2  PAP2_3    PAP2 superfamily
    0.00058   20.3   1.1    0.00058   20.3   1.1    2.2  2  PAP2_C    PAP2 superfamily C-terminal
  ------ inclusion threshold ------
       0.54   10.8   6.9        2.7    8.6   0.8    2.7  2  DUF1279   Protein of unknown function (DUF1279)


Domain annotation for each model (and alignments):
>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.2       2.1   9.5e+03      89      89 ..      16      16 ..       5      25 .. 0.49
   2 !   68.3   9.8   1.2e-22   5.4e-19       2     132 ..      29     136 ..      28     139 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.1
                              PAP2 89 l 89
                                      l
  gi|298674890|ref|YP_003726640.1| 16 L 16
                                      1 PP

  == domain 2  score: 68.3 bits;  conditional E-value: 1.2e-22
                              PAP2   2 llalllalalaalltsvlKdlvgrpRPfflaeetkldtqvstletseskeakesfPSgHsafafalalllalllrrk 78 
                                       +++++l+l++  +++  lK ++  pRP  +    + ++               s+PS H++ +fa+a++l+ + +r+
  gi|298674890|ref|YP_003726640.1|  29 AIRYILVLLSVSFIVFSLKAYLMVPRPQDVRIVLEAYGY--------------SMPSAHASLSFASAVFLHPIAGRL 91 
                                       6789***********************999999998887..............9*********************** PP

                              PAP2  79 rkkiglvllalillllavlvalsRlylgvHflsDvlaGlliGialaalayrlvq 132
                                       ++          l+lla+l+++sR++lgvH++ D+++G++iG+++++l y+l++
  gi|298674890|ref|YP_003726640.1|  92 KYG---------LWLLAILISISRISLGVHYPVDIVVGAFIGGFIGYLGYHLRP 136
                                       ***.........************************************998875 PP

>> PAP2_3  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   5.9      0.19   8.4e+02      41      79 ..      11      50 ..       1      56 [. 0.61
   2 !   37.7   4.1   3.8e-13   1.7e-09     125     187 ..      67     127 ..      56     130 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.19
                            PAP2_3 41 fqvtllvlvllf.lrrrerlreflttlllatllgllvyal 79
                                      +++++l+l+l + + ++++ r +l++l +++++ +l ++l
  gi|298674890|ref|YP_003726640.1| 11 PLWIILILFLYYqWGKTTAIRYILVLLSVSFIVFSLKAYL 50
                                      4455555555556777777777777777777774444443 PP

  == domain 2  score: 37.7 bits;  conditional E-value: 3.8e-13
                            PAP2_3 125 aafPSlHvawallvalalwrlrrkrllrvlalllnvlmivatvatgnHYlvDviaGvalalva 187
                                       +++PS H+ +++  a++l  ++ +   ++ ++ll++l+ ++ + +g HY vD+++G++++  +
  gi|298674890|ref|YP_003726640.1|  67 YSMPSAHASLSFASAVFLHPIAGRL--KYGLWLLAILISISRISLGVHYPVDIVVGAFIGGFI 127
                                       79***************77777666..******************************998765 PP

>> PAP2_C  PAP2 superfamily C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   2.8     0.052   2.3e+02      15      46 ..      13      44 ..       3      49 .. 0.73
   2 !   20.3   1.1   1.3e-07   0.00058      10      69 ..      73     128 ..      67     134 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.052
                            PAP2_C 15 tlavlfileyspkklailkvillllallglfl 46
                                      +++++++l+y   k +++++il+ll+++++++
  gi|298674890|ref|YP_003726640.1| 13 WIILILFLYYQWGKTTAIRYILVLLSVSFIVF 44
                                      55666666666666667999999999887766 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 1.3e-07
                            PAP2_C  10 HtvvltlavlfileyspkklailkvillllallglfliiasrkHYtvDVllglyittlvf 69 
                                       H+   + +++f++  + +    lk+ l+lla+l++++ i    HY vD+++g++i  ++ 
  gi|298674890|ref|YP_003726640.1|  73 HASLSFASAVFLHPIAGR----LKYGLWLLAILISISRISLGVHYPVDIVVGAFIGGFIG 128
                                       554444444444444433....599*****************************987765 PP

>> DUF1279  Protein of unknown function (DUF1279)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.5     0.013        57      17      50 ..      35      69 ..      20      81 .. 0.60
   2 ?    8.6   0.8   0.00059       2.7       9      30 ..      92     113 ..      90     134 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.013
                           DUF1279 17 vylsislidlgi.cYllvksgvdveelleklklsv 50
                                      v ls+s+i +++  Yl+v    dv  +le ++ s+
  gi|298674890|ref|YP_003726640.1| 35 VLLSVSFIVFSLkAYLMVPRPQDVRIVLEAYGYSM 69
                                      55566666666534666666666666666655553 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00059
                           DUF1279   9 kYGkvalgvylsislidlgicY 30 
                                       kYG + l++ +sis i+lg+ Y
  gi|298674890|ref|YP_003726640.1|  92 KYGLWLLAILISISRISLGVHY 113
                                       8******************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 870.87
//
Query:       gi|298674891|ref|YP_003726641.1|  [L=179]
Description: inorganic diphosphatase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.2e-55  185.6   0.1      6e-55  185.4   0.1    1.0  1  Pyrophosphatase  Inorganic pyrophosphatase


Domain annotation for each model (and alignments):
>> Pyrophosphatase  Inorganic pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.4   0.1   3.3e-59     6e-55       1     160 []      21     174 ..      21     174 .. 0.98

  Alignments for each domain:
  == domain 1  score: 185.4 bits;  conditional E-value: 3.3e-59
                                       EEEEE-TTCSEEEEEETTTTEEEEEEE-SSSB-BSSEEEEETT--BTCCBEETSSSEEEEEESSS---TTEEEEEEE CS
                   Pyrophosphatase   1 vvvEiprgsnaKyeidkeegklrldrvlftskgypanYGfipqTledtelkGDgDPlDvlvlgeeplspgevvevkv 77 
                                       +v+Eip+gs++K+e++ke g+  ldrvl++ + yp +YGfip+T+ d     DgDP+D++vl++e+++pg+++e+++
  gi|298674891|ref|YP_003726641.1|  21 AVIEIPKGSRNKFEYSKEFGTYILDRVLHSPQYYPGEYGFIPKTMYD-----DGDPMDIIVLMDERTFPGCMLEARP 92 
                                       69*********************************************.....************************* PP

                                       EEEEEEEETTEEEEEEEEEETTSGGGTT-SSGGGSTHHHHHHHHHHHHHTTTTSCCT-SEEEEEEEEHHHHHHHHHH CS
                   Pyrophosphatase  78 lGvlamiDegetDdKiiavpvkdprlkkindiedlpgllleeiehfFetykdlegkkknvkveewkdkeeAekviee 154
                                       +G++ m+D+getDdKi+avp+kdpr+++i+di+d+ +++++ei++fF+tykdle + k+v+v++w +ke+A+k i++
  gi|298674891|ref|YP_003726641.1|  93 VGLMLMTDSGETDDKILAVPNKDPRYSHIKDISDVTPHVMAEISQFFNTYKDLEYE-KDVAVHGWDNKEAAIKAINH 168
                                       ******************************************************65.899***************** PP

                                       HHHHHH CS
                   Pyrophosphatase 155 aheryk 160
                                       +++ yk
  gi|298674891|ref|YP_003726641.1| 169 SVQLYK 174
                                       *99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1132.76
//
Query:       gi|298674892|ref|YP_003726642.1|  [L=361]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-25   89.0   1.7    8.6e-25   86.5   1.0    2.5  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    2.2e-09   37.6   1.3    2.2e-09   37.6   1.3    1.6  2  OrfB_IS605      Probable transposase
  ------ inclusion threshold ------
      0.018   15.1   0.1      0.033   14.2   0.1    1.5  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.042   13.5   6.1       0.15   11.8   6.1    1.9  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
       0.14   11.7   0.2        0.3   10.6   0.2    1.5  1  TF_Zn_Ribbon    TFIIB zinc-binding
       0.69    9.9   4.1        9.9    6.2   1.2    2.4  2  zinc_ribbon_4   zinc-ribbon domain
        1.6    8.8   5.3        3.5    7.7   5.3    1.5  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
        2.5    7.9   5.6        8.9    6.1   0.4    2.5  2  Rubredoxin_2    Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.53   1.2e+03      15      29 ..     187     201 ..     184     209 .. 0.87
   2 !   86.5   1.0   3.8e-28   8.6e-25       1      69 []     277     346 ..     277     346 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.53
                    OrfB_Zn_ribbon  15 yGikveevnpayTSk 29 
                                       +G k  e+ ++yTS 
  gi|298674892|ref|YP_003726642.1| 187 KGTKADEIRERYTSL 201
                                       5889999******96 PP

  == domain 2  score: 86.5 bits;  conditional E-value: 3.8e-28
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f++l+ ++ ykak +G++v+ +np yTS++CseCg++nk  ++++ +f+C+ Cg++ ++D+nA+ Ni++r
  gi|298674892|ref|YP_003726642.1| 277 FSELTDFILYKAKLEGVPVVIINPMYTSQQCSECGHINKSnRQKQANFRCKTCGHRENADYNASKNIAHR 346
                                       899*************************************9**************************997 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   1.3   9.6e-13   2.2e-09      16     106 ..     165     246 ..     152     256 .. 0.87
   2 ?   -4.0   0.1       7.2   1.6e+04      41      60 ..     314     333 ..     309     345 .. 0.59

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 9.6e-13
                        OrfB_IS605  16 nkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsrrrkhll 92 
                                         + g+DlG+ n+at+++++    +ykg ++++  ++++  + +lqs    s     a++ l++l++k +r+ ++l 
  gi|298674892|ref|YP_003726642.1| 165 DDVMGVDLGVVNIATTSDNE----IYKGTKADEIRERYTSLKSRLQSAGTWS-----AKKHLKKLSKKERRFKRDLN 232
                                       5689****************....***********************95555.....79999*************** PP

                        OrfB_IS605  93 hklathliktlkev 106
                                       h +a++l+k+ k++
  gi|298674892|ref|YP_003726642.1| 233 HRVAKQLVKRAKDT 246
                                       ********998765 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 7.2
                        OrfB_IS605  41 ykgrrlksdykylakeiael 60 
                                       +k++r k+++++ + +  + 
  gi|298674892|ref|YP_003726642.1| 314 NKSNRQKQANFRCKTCGHRE 333
                                       55666666666665555544 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.5e-05     0.033      60      96 ..     288     333 ..     236     343 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.5e-05
                                       -EEE......EEEE--EEEETTTS-EEECHH..H.HHS-TTTSSS- CS
                              HypA  60 aeLe......ieevpvkvrCreCgkefelee..k.alrCpkCgsad 96 
                                       a+Le      i+ +  + +C+eCg+  ++++  + ++rC++Cg+++
  gi|298674892|ref|YP_003726642.1| 288 AKLEgvpvviINPMYTSQQCSECGHINKSNRqkQaNFRCKTCGHRE 333
                                       5555555545777788999*****9988665333788******874 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   6.1   6.5e-05      0.15       3      26 ..     307     332 ..     306     333 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.5e-05
                                       -SSS--B--..--SSS----SSS--- CS
                    DNA_RNApol_7kD   3 CgeCgaevs..lkkgdpiRCkeCGhR 26 
                                       C eCg+ ++   +k++  RCk+CGhR
  gi|298674892|ref|YP_003726642.1| 307 CSECGHINKsnRQKQANFRCKTCGHR 332
                                       99**9977755788899********9 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   0.00013       0.3       2      27 ..     306     331 ..     305     344 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00013
                                       EETTTTCEECHEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon   2 kCPnCgstnlveDpergelvCtdCGl 27 
                                       +C +Cg+ n  +  ++++++C+ CG 
  gi|298674892|ref|YP_003726642.1| 306 QCSECGHINKSNRQKQANFRCKTCGH 331
                                       8******776899************7 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.021        47      27      34 ..     306     313 ..     298     313 .. 0.85
   2 ?    6.2   1.2    0.0044       9.9      20      33 ..     318     331 ..     314     332 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.021
                     zinc_ribbon_4  27 rCskCghv 34 
                                       +Cs Cgh+
  gi|298674892|ref|YP_003726642.1| 306 QCSECGHI 313
                                       8******6 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0044
                     zinc_ribbon_4  20 pakgvkvrCskCgh 33 
                                       ++k ++ rC+ Cgh
  gi|298674892|ref|YP_003726642.1| 318 RQKQANFRCKTCGH 331
                                       5788999******9 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   5.3    0.0015       3.5      19      45 ..     305     331 ..     301     332 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0015
                     Zn_Tnp_IS1595  19 fvCPhCgsr.kayriktrglfqCkeCrk 45 
                                       + C  Cg+  k+ r k+   f+Ck C++
  gi|298674892|ref|YP_003726642.1| 305 QQCSECGHInKSNRQKQ-ANFRCKTCGH 331
                                       57*****9999999998.********98 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.7     0.025        56       2       8 ..     306     312 ..     306     316 .. 0.82
   2 ?    6.1   0.4     0.004       8.9       1      10 [.     324     333 ..     324     335 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.025
                      Rubredoxin_2   2 vCsqCGf 8  
                                       +Cs+CG+
  gi|298674892|ref|YP_003726642.1| 306 QCSECGH 312
                                       6999998 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.004
                      Rubredoxin_2   1 YvCsqCGfes 10 
                                       ++C+ CG++ 
  gi|298674892|ref|YP_003726642.1| 324 FRCKTCGHRE 333
                                       8******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1029  (0.0573931); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2209.64
//
Query:       gi|298674893|ref|YP_003726643.1|  [L=168]
Description: heat shock protein DnaJ domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.5e-23   80.6   0.5    1.2e-22   79.8   0.5    1.4  1  DnaJ           DnaJ domain
  ------ inclusion threshold ------
      0.042   13.5   2.0       0.52   10.0   0.0    2.1  2  DDE_1          DDE superfamily endonuclease
       0.05   13.9   1.0       0.96    9.8   1.0    2.2  1  Orf78          Orf78 (ac78)
      0.051   13.5   0.0       0.12   12.4   0.0    1.6  1  RPT            A repeated domain in UCH-protein
      0.058   13.7   1.6        7.1    7.0   0.2    2.2  2  Thioredoxin_8  Thioredoxin-like
      0.098   12.4   0.0       0.14   11.8   0.0    1.2  1  DotU           Type VI secretion system protein DotU


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.8   0.5   3.9e-26   1.2e-22       1      63 []      11      72 ..      11      72 .. 0.98

  Alignments for each domain:
  == domain 1  score: 79.8 bits;  conditional E-value: 3.9e-26
                                      HHHHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHTSHHHHHHHH CS
                              DnaJ  1 dyYeiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLsdpekRkqYD 63
                                      d+Ye+Lgv+ das++eIk+aYrk++l +HPDkn + +ea +k +++n+A+evL d++kR++YD
  gi|298674893|ref|YP_003726643.1| 11 DPYEVLGVTDDASHEEIKRAYRKQILFWHPDKN-STQEAINKAQNVNKAFEVLGDEKKREIYD 72
                                      78*******************************.8889************************9 PP

>> DDE_1  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00017      0.52     121     159 ..      24      62 ..      13      72 .. 0.89
   2 ?    3.1   0.5     0.021        64      34      65 ..     104     140 ..      86     153 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00017
                             DDE_1 121 vselKarYrrqllqalleeqnrlskeqkkltlldalkfi 159
                                        +e+K+ Yr+q+l +  +++++++   k+ ++++a++++
  gi|298674893|ref|YP_003726643.1|  24 HEEIKRAYRKQILFWHPDKNSTQEAINKAQNVNKAFEVL 62 
                                       5799********************************986 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.021
                             DDE_1  34 n.....gektkkkldveyksnrkawltssifeeWLkv 65 
                                             + k k+++  +y++++ka++ +++   W k+
  gi|298674893|ref|YP_003726643.1| 104 VyrysySPKRKNTFSRHYNASKKAKTNNKTPWIWVKW 140
                                       0333444566679999*********999987777766 PP

>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.0   0.00032      0.96      40      86 ..     101     152 ..       8     163 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00032
                             Orf78  40 kksaaeknditekesn.........aaekaqalnillisllavvcvlvllyviyYf 86 
                                       +++++ ++ + + +++         +a++++++  ++++ +a+++vl++ y     
  gi|298674893|ref|YP_003726643.1| 101 RRTVYRYSYSPKRKNTfsrhynaskKAKTNNKTPWIWVKWIALLIVLIISY----S 152
                                       222222222222222244566543344444555566666666655555544....3 PP

>> RPT  A repeated domain in UCH-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.9e-05      0.12       6      50 ..      13      67 ..      11      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.9e-05
                               RPT  6 yklLgidentdDdviitayqvkl.....ed....dp.sqkdklrrALkvIAeeRk 50
                                      y++Lg++++++ ++i  ay+ ++     ++    ++ + + + ++A++v ++e+k
  gi|298674893|ref|YP_003726643.1| 13 YEVLGVTDDASHEEIKRAYRKQIlfwhpDKnstqEAiNKAQNVNKAFEVLGDEKK 67
                                      99********************999976226677566999999999999999987 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.2    0.0024       7.1      25      83 ..       3      58 ..       1      70 [. 0.80
   2 ?    6.2   0.1    0.0043        13      53      82 ..      96     125 ..      84     150 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0024
                                      HHHHHHHHTTSEEEEEEE-SS-HHHHHHHGGGS-TTSEE.EE-TT-..HHHHTT-S--TT- CS
                     Thioredoxin_8 25 elyeklkkkkkveivyvsldkkeeefekylkknkkpwlsvpfddkk..rnklkkkynvkai 83
                                      ++ye+++  + +e++ v  d + ee ++  +k+    + +  +dk+  +++++k  nv++ 
  gi|298674893|ref|YP_003726643.1|  3 DVYENME-IDPYEVLGVTDDASHEEIKRAYRKQ----ILFWHPDKNstQEAINKAQNVNKA 58
                                      6788887.89***********************....555666665547788888888865 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0043
                                       HGGGS-TTSEE.EE-TT-HHHHTT-S--TT CS
                     Thioredoxin_8  53 ylkknkkpwlsvpfddkkrnklkkkynvka 82 
                                        +k+ +++ +++ ++ k++n++ ++yn ++
  gi|298674893|ref|YP_003726643.1|  96 ARKNSRRTVYRYSYSPKRKNTFSRHYNASK 125
                                       45666789*******************886 PP

>> DotU  Type VI secretion system protein DotU
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.7e-05      0.14     129     201 ..      78     153 ..      65     156 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.7e-05
                              DotU 129 Gryrleadgee.......elealrqrlyeeirrlrgeaeealsphwqagdeaarrllrrelp.lwvilalallvlll 197
                                       G+yr ++   +        +++ r+++y+      +++++++s h +a+++a+     ++ p +wv ++++l+vl++
  gi|298674893|ref|YP_003726643.1|  78 GKYRDNKASYDrakkpssARKNSRRTVYRYSY--SPKRKNTFSRHYNASKKAKTN---NKTPwIWVKWIALLIVLII 149
                                       68887766555666344455555555555544..5888888****9944444444...3678679999999999988 PP

                              DotU 198 lflg 201
                                        +++
  gi|298674893|ref|YP_003726643.1| 150 SYSF 153
                                       8876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1747  (0.0974399); expected 358.6 (0.02)
Passed bias filter:                      677  (0.0377601); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1028.37
//
Query:       gi|298674894|ref|YP_003726644.1|  [L=321]
Description: hypothetical protein Metev_0955 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.064   13.2   0.1       0.28   11.2   0.0    2.1  2  DUF2150   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2150  Uncharacterized protein conserved in archaea (DUF2150)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   1.5e-05      0.28     103     177 ..      39     111 ..       5     121 .. 0.82
   2 ?   -1.6   0.1      0.13   2.3e+03     161     186 ..     149     174 ..     140     176 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.5e-05
                           DUF2150 103 eeyieggvakekdieelvkaaaeaeaeedleaaleivaqiGakvidgeklpekvledleyglvaewldgidslaa 177
                                         y+ ++   + di++ + + +++  ++++e++ e+ a +  ++ +g +   + + + ++g + e+l+++d+ ++
  gi|298674894|ref|YP_003726644.1|  39 SMYVFEKS--KVDIKNKLIESRKKYLQGEFEKSVELFAYAACHICNGMNTVYNYYPQNDEGYILEYLNNLDDFSR 111
                                       45666666..4688888888888888************************99999****************9875 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.13
                           DUF2150 161 eyglvaewldgidslaaamsssesve 186
                                       +++++ e  ++id++ +am++  +v+
  gi|298674894|ref|YP_003726644.1| 149 DESFLVEGEIDIDKVVSAMETRRHVD 174
                                       66777788889999999999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1991.54
//
Query:       gi|298674895|ref|YP_003726645.1|  [L=107]
Description: small multidrug resistance protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-29  102.1  10.8    2.6e-29  101.7  10.8    1.1  1  Multi_Drug_Res  Small Multidrug Resistance protein
    0.00028   21.0  15.7    0.00073   19.7  15.7    1.6  1  EamA            EamA-like transporter family
     0.0018   18.1   3.2     0.0018   18.1   3.2    2.1  2  DUF5381         Family of unknown function (DUF5381)
  ------ inclusion threshold ------
       0.18   10.8  10.5       0.32    9.9  10.5    1.5  1  TMEM144         Transmembrane family, TMEM144 of transporters
       0.59   10.2  10.3        4.9    7.2  10.3    1.9  1  CD20            CD20-like family
        2.1    7.9   7.9       0.58    9.7   4.7    1.6  2  SLATT_6         SMODS and SLOG-associating 2TM effector domai
        2.5    8.4  10.4         24    5.2  10.6    2.5  1  DUF4383         Domain of unknown function (DUF4383)


Domain annotation for each model (and alignments):
>> Multi_Drug_Res  Small Multidrug Resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.7  10.8     1e-32   2.6e-29       1      93 []       1      93 [.       1      93 [. 0.98

  Alignments for each domain:
  == domain 1  score: 101.7 bits;  conditional E-value: 1e-32
                                      XX-HHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHH- CS
                    Multi_Drug_Res  1 mnwvllvlAillevvgailLklsegftkltpsllvivgygisfllLskalkslpvsvAYavwsGiGtvlivlvgillfg 79
                                      m++++l+l i++ev+g++ +klsegf++++ps+l+ v+y+isf++ ++alk+++vsvAYa+w+G+Gt+li+++gi +f+
  gi|298674895|ref|YP_003726645.1|  1 MSYIMLLLGIIFEVFGTTCMKLSEGFARTIPSILIFVFYAISFTFVTFALKKIDVSVAYAIWAGFGTALITIIGIFWFK 79
                                      89***************************************************************************** PP

                                      -------HHHHHHH CS
                    Multi_Drug_Res 80 eslslkkliglali 93
                                      e+++l k+++l ++
  gi|298674895|ref|YP_003726645.1| 80 EPMNLLKMVSLLVV 93
                                      **********9876 PP

>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7  15.7   2.9e-07   0.00073      57     134 ..      20      99 ..       1     102 [. 0.81

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.9e-07
                              EamA  57 aklslkdwlll.lllgllgtvlafllffyalkktsasnasli.tslePvftlilsvlllgekltlkqllgivlillG 131
                                        kls      +  +l ++  ++ f + + alkk+++s+a  i   +  ++++i+++++++e+++l+++++++++++G
  gi|298674895|ref|YP_003726645.1|  20 MKLSEGFARTIpSILIFVFYAISFTFVTFALKKIDVSVAYAIwAGFGTALITIIGIFWFKEPMNLLKMVSLLVVVIG 96 
                                       45666666666688999999*******************999899******************************** PP

                              EamA 132 vll 134
                                       ++ 
  gi|298674895|ref|YP_003726645.1|  97 IMG 99 
                                       *86 PP

>> DUF5381  Family of unknown function (DUF5381)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   4.1      0.93   2.4e+03      22      60 ..       5      44 ..       1      55 [. 0.45
   2 !   18.1   3.2     7e-07    0.0018       5      52 ..      53     100 ..      49     105 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.93
                           DUF5381 22 lglaglfl.lfeglkfeskysllyiiigiigtifgliill 60
                                      ++l g+   +f +  ++ +  +   i +i+  +f++i++ 
  gi|298674895|ref|YP_003726645.1|  5 MLLLGIIFeVFGTTCMKLSEGFARTIPSILIFVFYAISFT 44
                                      3333332202222222334445555555555555555555 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 7e-07
                           DUF5381   5 vksrkflrvllflatvglglaglfllfeglkfeskysllyiiigiigt 52 
                                       + ++  +++++ ++t++++++g+f ++e +++    sll+++igi+g+
  gi|298674895|ref|YP_003726645.1|  53 IDVSVAYAIWAGFGTALITIIGIFWFKEPMNLLKMVSLLVVVIGIMGL 100
                                       56778899*************************************986 PP

>> TMEM144  Transmembrane family, TMEM144 of transporters
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9  10.5   0.00013      0.32     257     330 ..      29      98 ..       1     104 [. 0.79

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00013
                           TMEM144 257 vlPsllaGilwaiavtsffvanqkLsqvvsyPiiskaPgliaalwsvflfkeikGkrnlillaiavaitligvi 330
                                        +Ps+l  +++ai+ t    a +k++  v+y i +     + ++ ++f fke     +++ l     +++ig++
  gi|298674895|ref|YP_003726645.1|  29 TIPSILIFVFYAISFTFVTFALKKIDVSVAYAIWAGFGTALITIIGIFWFKEPMNLLKMVSL----LVVVIGIM 98 
                                       69*************************************************97654444444....44444443 PP

>> CD20  CD20-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2  10.3    0.0019       4.9       8      72 ..       7      98 ..       2     103 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0019
                              CD20  8 llGllslvlGilllsvsss...........................tllasgypfWgGivfiisGvlgiaaekrstkll 59
                                      llG++  v+G+ ++ +s+                            + + + y++W+G+  ++  ++gi+  k ++ ll
  gi|298674895|ref|YP_003726645.1|  7 LLGIIFEVFGTTCMKLSEGfartipsilifvfyaisftfvtfalkkIDVSVAYAIWAGFGTALITIIGIFWFKEPMNLL 85
                                      566666666666666666666666666666666666666666666679999**************************99 PP

                              CD20 60 vklslllnlvslv 72
                                       ++sll  +++++
  gi|298674895|ref|YP_003726645.1| 86 KMVSLLVVVIGIM 98
                                      9999999998877 PP

>> SLATT_6  SMODS and SLOG-associating 2TM effector domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.4      0.32   8.2e+02      43      72 ..      13      43 ..       1      55 [. 0.48
   2 ?    9.7   4.7   0.00023      0.58      29      75 ..      54     103 ..      36     106 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.32
                           SLATT_6 43 lavGilalv.ieelstkllsalliiigiial 72
                                       ++G   +   e+++  + s+l+ ++  i++
  gi|298674895|ref|YP_003726645.1| 13 EVFGTTCMKlSEGFARTIPSILIFVFYAISF 43
                                      3333333332344445555555555555544 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00023
                           SLATT_6  29 diveKlpglislislavGilalv..ieels.tkllsalliiigiialyis 75 
                                       d+      + ++ +  + i++++   e ++  k++s+l+++igi++l is
  gi|298674895|ref|YP_003726645.1|  54 DVSVAYAIWAGFGTALITIIGIFwfKEPMNlLKMVSLLVVVIGIMGLHIS 103
                                       44555566777878777777777545667789***************997 PP

>> DUF4383  Domain of unknown function (DUF4383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2  10.6    0.0094        24      57     115 ..      40      99 ..       2     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0094
                           DUF4383  57 lvGvlglaaa.rsasgarlyllllgvvylllailgllvldktanllplngadnwlhllla 115
                                       ++ ++ +++a ++   + +y++++g   +l++i+g++ +++++nll +    +++ ++++
  gi|298674895|ref|YP_003726645.1|  40 AISFTFVTFAlKKIDVSVAYAIWAGFGTALITIIGIFWFKEPMNLLKMVSLLVVVIGIMG 99 
                                       445555556659999**************************9999988665555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       848  (0.0472977); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 687.84
//
Query:       gi|298674896|ref|YP_003726646.1|  [L=125]
Description: hypothetical protein Metev_0957 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.9e-27   93.3   5.6      1e-26   93.2   5.6    1.0  1  DUF2178          Predicted membrane protein (DUF2178)
    0.00084   19.3   1.2     0.0011   18.9   1.2    1.2  1  7TMR-DISM_7TM    7TM diverse intracellular signalling
  ------ inclusion threshold ------
      0.021   15.3   0.2      0.021   15.3   0.2    1.8  2  DUF3796          Protein of unknown function (DUF3796)
        8.5    6.5   8.6       0.28   11.2   0.5    2.2  2  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe


Domain annotation for each model (and alignments):
>> DUF2178  Predicted membrane protein (DUF2178)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.2   5.6   2.2e-30     1e-26       1     101 [.       3     113 ..       3     118 .. 0.96

  Alignments for each domain:
  == domain 1  score: 93.2 bits;  conditional E-value: 2.2e-30
                           DUF2178   1 lliivavialvglgiwa.....aignvllaviavaaGvllaillkkkve.....evveDERlariaekAsrktlqil 67 
                                       +lii++v++l+g+g+++     ++++v++++++++aGv+++++++++++     +v+eDER++riaekAs+k+l+i+
  gi|298674896|ref|YP_003726646.1|   3 MLIIGIVLSLIGIGFYVfepawIASSVGAGGAFIGAGVAMIAIILRSLQirkkrGVIEDERDYRIAEKASHKALTII 79 
                                       79*************888999999************************999************************** PP

                           DUF2178  68 lfliallgvvlivlksdfpeytrvgfllafsall 101
                                       ++l+++l + ++v++s+++++++v++l+a+++l 
  gi|298674896|ref|YP_003726646.1|  80 IILEGVLLAGIGVTESNIQAQPVVSLLFAVTMLT 113
                                       ******************************9654 PP

>> 7TMR-DISM_7TM  7TM diverse intracellular signalling
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   1.2   2.4e-07    0.0011      41     149 ..       5     124 ..       1     125 [] 0.73

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.4e-07
                     7TMR-DISM_7TM  41 fllyllslngllfqylwpnappalnnkllyltlllllilfll.Farsflelkkkp..............rllkllll 102
                                       ++ ++lsl g++f+++ p   +++++ +     +++++++++  + + l+++kk+                 k+l +
  gi|298674896|ref|YP_003726646.1|   5 IIGIVLSLIGIGFYVFEP---AWIASSVGAGGAFIGAGVAMIaIILRSLQIRKKRgviederdyriaekASHKALTI 78 
                                       566677789*******44...4666666666666666666666777779997777899******9999877777888 PP

                     7TMR-DISM_7TM 103 lavllsllllllpllpyteslslaqllallvillllligikawrkgn 149
                                       + +l ++ll+ + ++  + + + + + +l+++ +l+++g++ w+k++
  gi|298674896|ref|YP_003726646.1|  79 IIILEGVLLAGIGVTESNIQAQPV-VSLLFAVTMLTYVGFYYWYKRQ 124
                                       887777777775555444444444.88888899999*******9975 PP

>> DUF3796  Protein of unknown function (DUF3796)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.2      0.53   2.4e+03      95     112 ..       4      21 ..       1      26 [. 0.71
   2 ?   15.3   0.2   4.6e-06     0.021      43     108 ..      53     118 ..      38     125 .] 0.79

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.53
                           DUF3796  95 lllaslilafGlslflle 112
                                       l++++++   G+  +++e
  gi|298674896|ref|YP_003726646.1|   4 LIIGIVLSLIGIGFYVFE 21 
                                       556666667788888877 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 4.6e-06
                           DUF3796  43 aklstvllDErfeenvkraaaiafk.vaileiiiavlislilsrvelsevllalllaslilafGlsl 108
                                        k ++v+ DEr +  +++a   a + + ile ++++ i +  s++ + + +++ll+a+++l++    
  gi|298674896|ref|YP_003726646.1|  53 RKKRGVIEDERDYRIAEKASHKALTiIIILEGVLLAGIGVTESNI-QAQPVVSLLFAVTMLTYVGFY 118
                                       566899*****8888777777776515667899999****99999.788999**********95444 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.5   6.3e-05      0.28      47      93 ..       4      54 ..       1      64 [. 0.57
   2 ?   -1.0   2.2      0.38   1.7e+03      71      71 ..     102     102 ..      67     124 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.3e-05
                   Phage_holin_3_6 47 allalllllvalalalaa....lwlaali.vaavllvlagvlalvglk..klkk 93
                                      ++++++l l+++ +        +w+a  +  +++++ +++++++++l+  +++k
  gi|298674896|ref|YP_003726646.1|  4 LIIGIVLSLIGIGF---YvfepAWIASSVgAGGAFIGAGVAMIAIILRslQIRK 54
                                      33333333333322...1235789999996677777777778888877444444 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.38
                   Phage_holin_3_6  71 i 71 
                                       +
  gi|298674896|ref|YP_003726646.1| 102 V 102
                                       1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       934  (0.0520944); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 771.52
//
Query:       gi|298674897|ref|YP_003726647.1|  [L=68]
Description: transcriptional regulator, XRE family [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-18   66.5   0.0    1.8e-18   66.3   0.0    1.0  1  HTH_3           Helix-turn-helix
      1e-08   35.5   0.0    1.2e-08   35.2   0.0    1.1  1  HTH_26          Cro/C1-type HTH DNA-binding domain
    4.8e-08   32.9   0.1    5.4e-08   32.8   0.1    1.0  1  HTH_19          Helix-turn-helix domain
    1.6e-06   28.4   0.0    1.9e-06   28.1   0.0    1.1  1  HTH_31          Helix-turn-helix domain
    0.00031   20.6   0.0    0.00051   19.9   0.0    1.3  1  HTH_11          HTH domain
     0.0023   17.8   0.0     0.0027   17.5   0.0    1.2  1  HTH_25          Helix-turn-helix domain
     0.0065   16.0   0.0     0.0099   15.4   0.0    1.3  1  Sigma70_r4      Sigma-70, region 4
     0.0093   15.9   0.0      0.012   15.5   0.0    1.2  1  HTH_Crp_2       Crp-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.044   13.6   0.0       0.05   13.5   0.0    1.2  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.079   12.8   0.0       0.12   12.1   0.0    1.4  1  HTH_10          HTH DNA binding domain
       0.11   12.4   0.0       0.15   12.0   0.0    1.2  1  MarR_2          MarR family
       0.13   12.0   0.0       0.18   11.6   0.0    1.3  1  HTH_38          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   0.0   1.2e-21   1.8e-18       1      55 []       5      59 ..       5      59 .. 0.96

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 1.2e-21
                                      HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHHHH CS
                             HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvsldel 55
                                      lk +R +++++qe+LA+++Gv+r+ti++iE+G+  Ps++ ++kl++++ +s+++l
  gi|298674897|ref|YP_003726647.1|  5 LKVWRAKKDITQEYLAKEMGVTRQTINAIERGKYDPSIQLAFKLSRFFECSIEDL 59
                                      56689***********************************************987 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.0   8.1e-12   1.2e-08       1      62 [.       4      64 ..       4      65 .. 0.97

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 8.1e-12
                            HTH_26  1 kLrelmadrgitkseLargtgisaatlsrlvkgkpervsldtLdkiCdaLgctpgDLleyep 62
                                      +L+++ a+++it+  La+  g++++t++ +  gk   +s++   k+ + ++c+++DL+++e 
  gi|298674897|ref|YP_003726647.1|  4 NLKVWRAKKDITQEYLAKEMGVTRQTINAIERGK-YDPSIQLAFKLSRFFECSIEDLFIFEE 64
                                      799******************************9.6***********************985 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.1   3.6e-11   5.4e-08       3      60 ..       4      60 ..       3      64 .. 0.93

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 3.6e-11
                            HTH_19  3 rLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidleyll 60
                                      +Lk  R ++ +tqe la++ g++r  i+aiE gk+ +ps+ l  k++++++ ++e l+
  gi|298674897|ref|YP_003726647.1|  4 NLKVWRAKKDITQEYLAKEMGVTRQTINAIERGKY-DPSIQLAFKLSRFFECSIEDLF 60
                                      6777799999************************9.*****************99987 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   1.3e-09   1.9e-06       6      55 ..       5      53 ..       4      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1.3e-09
                            HTH_31  6 LralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralg 55
                                      L+ +R++  ++qe +A+  gv++ t++ +E+G+ + ps +   +l r + 
  gi|298674897|ref|YP_003726647.1|  5 LKVWRAKKDITQEYLAKEMGVTRQTINAIERGKYD-PSIQLAFKLSRFFE 53
                                      789*******************************7.***99999988765 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   3.4e-07   0.00051      11      32 ..       9      30 ..       5      32 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.4e-07
                            HTH_11 11 eargpisgeeLAeeLnvSrrtv 32
                                      +a+++i+ e+LA+e++v+r+t+
  gi|298674897|ref|YP_003726647.1|  9 RAKKDITQEYLAKEMGVTRQTI 30
                                      57889****************9 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.8e-06    0.0027       3      36 ..       6      39 ..       4      46 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.8e-06
                                      HHHHHTTT--HHHHHHHSS--HHHHHHHHCT--T CS
                            HTH_25  3 raaRearglsleevaketkIrkdylealEeddfd 36
                                      +  R ++ ++ e +ake  +  +++ a+E++++d
  gi|298674897|ref|YP_003726647.1|  6 KVWRAKKDITQEYLAKEMGVTRQTINAIERGKYD 39
                                      55699***************************98 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   6.6e-06    0.0099      19      42 ..      12      35 ..       7      36 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.6e-06
                                      TT--HHHHHHHHTS-HHHHHHHHH CS
                        Sigma70_r4 19 eglTleEIgerlgiSrerVrqiek 42
                                      ++ T+e +++++g++r ++  ie+
  gi|298674897|ref|YP_003726647.1| 12 KDITQEYLAKEMGVTRQTINAIER 35
                                      788*******************97 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   8.3e-06     0.012      21      40 ..      13      32 ..       3      35 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.3e-06
                                      EHHHHHHHHHTTSSHHHHHH CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsr 40
                                      ++tqe lA  +G+tr+t++ 
  gi|298674897|ref|YP_003726647.1| 13 DITQEYLAKEMGVTRQTINA 32
                                      69****************96 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.3e-05      0.05      10      32 ..      15      37 ..       9      58 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.3e-05
                    YdaS_antitoxin 10 gqkaLAealgvsqqaVsqWlkgk 32
                                      +q  LA++ gv++q+++   +gk
  gi|298674897|ref|YP_003726647.1| 15 TQEYLAKEMGVTRQTINAIERGK 37
                                      7999*************987776 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   8.3e-05      0.12      22      41 ..      12      31 ..       9      40 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.3e-05
                            HTH_10 22 RrvtlkeLAkelGIskstls 41
                                      +++t + LAke+G++++t+ 
  gi|298674897|ref|YP_003726647.1| 12 KDITQEYLAKEMGVTRQTIN 31
                                      89999*************86 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0001      0.15      20      41 ..      12      33 ..       6      35 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0001
                                      SEEEHHHHHHHHTSSHHHHHHH CS
                            MarR_2 20 rdltvgelarrlglsksavsri 41
                                      +d+t+  la+++g+++++++ i
  gi|298674897|ref|YP_003726647.1| 12 KDITQEYLAKEMGVTRQTINAI 33
                                      479***************9876 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00012      0.18      13      38 ..       5      31 ..       2      35 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                            HTH_38 13 IerllaeG.lslreIArrLgrspsTIs 38
                                      +  ++a++  ++   A+++g+ ++TI+
  gi|298674897|ref|YP_003726647.1|  5 LKVWRAKKdITQEYLAKEMGVTRQTIN 31
                                      6678865559****************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.47u 0.33s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 413.04
//
Query:       gi|298674898|ref|YP_003726648.1|  [L=256]
Description: NADPH-dependent FMN reductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.8e-23   81.6   0.0    7.3e-23   81.0   0.0    1.2  1  FMN_red       NADPH-dependent FMN reductase
    1.9e-12   47.3   0.0    2.7e-12   46.8   0.0    1.2  1  Flavodoxin_2  Flavodoxin-like fold
  ------ inclusion threshold ------
      0.041   13.6   0.0      0.061   13.0   0.0    1.1  1  PlyB_C        Pleurotolysin B C-terminal domain


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.0   0.0   1.2e-26   7.3e-23       1     136 [.       1     140 [.       1     153 [. 0.87

  Alignments for each domain:
  == domain 1  score: 81.0 bits;  conditional E-value: 1.2e-26
                                       -EEEEEES--STT-HHHHHHHHHHCCT-T..T-CEEEEETTTS..--.....---HCHGHTCGGSHHHHHHHHHHHH CS
                           FMN_red   1 mkilvisGSlrkgsntrklaewaaealkea.gaevelidladl.ilpc...alcdkdlesegqtsddvaellekiaa 72 
                                       m +l+i+GS+r +snt+k+++ +++++k+  ++++e+i l+++  + c   + c+   e++++ +d+  e+ ek+ +
  gi|298674898|ref|YP_003726648.1|   1 MEVLAIIGSPRGKSNTYKAVRLVEKEMKNFgDVNLEYILLNEIdLKTCkgcFNCLRIGEERCPLKDAQIEIEEKMIS 77 
                                       89*************************99965***99999999888888776666666667**************** PP

                                       -SCEEEEEEECTTCE-HHHHHHHHCHT-.SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHH CS
                           FMN_red  73 adaliivtPeYngsysgllKnalDrlsrtrgkkelrgKpvalvavgggrrgglraeeqlrqvla 136
                                       +d++i+++P+Y  ++s l+Kn+lDr+ ++ ++  l +  +++++++g+  g+  + e + ++ +
  gi|298674898|ref|YP_003726648.1|  78 SDGIIFASPTYVMNVSWLFKNFLDRFAYICHRPRLFNQSALVLTTVGS-YGAKTTLEYMANAVT 140
                                       ****************************99999999999999999977.888777776666655 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.0   4.4e-16   2.7e-12       1     140 [.       1     129 [.       1     148 [. 0.80

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 4.4e-16
                                       -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCCT-----CCCCHCC.HHHHTTC.HHHHHHHHHHH CS
                      Flavodoxin_2   1 mkiLiinahprpeksfssalaqafvealekagphevtvrdLyadflpvlttrdlaak.layeekp.adveseqiekl 75 
                                       m +L i ++pr+ ks+++++ + + +++++ g  + +++ L+++ +   ++ ++++    +e+ p  d++ e  ek+
  gi|298674898|ref|YP_003726648.1|   1 MEVLAIIGSPRG-KSNTYKAVRLVEKEMKNFGDVNLEYILLNEI-DLKTCKGCFNCLrIGEERCPlKDAQIEIEEKM 75 
                                       89**********.8******************855888888886.555556699985333333366788888888** PP

                                       HCSSEEEEEEE-BTTB--HHHHHHHHHHS-TTTSC.EETTCSSCCCCTTTTSEEEEEEEESS-GGG CS
                      Flavodoxin_2  76 laadaivlqfPlwwfgvPailKgwiDrvltagfaf.yteeggegrgggLkgkkalvivttGgpees 140
                                        ++d i++++P + ++v++++K+++Dr      a+         ++ +L + +alv++t+G+ ++ 
  gi|298674898|ref|YP_003726648.1|  76 ISSDGIIFASPTYVMNVSWLFKNFLDRF-----AYiC-------HRPRLFNQSALVLTTVGSYGAK 129
                                       ***************************6.....5511.......2358999999999999998554 PP

>> PlyB_C  Pleurotolysin B C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     1e-05     0.061      51     136 ..     153     239 ..     139     245 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1e-05
                            PlyB_C  51 tlPakaGrnpaltgahe.gegvseqplvdlakyqflstyfgqlvietapGsllralrPdlallgryelyGdsistav 126
                                       t+P  +G++ ++++  e  e +s+q + dl + ++ls  f +lv+ +   +++      + ++  ye y  +is+  
  gi|298674898|ref|YP_003726648.1| 153 TVPPVGGKEEIVDQDIEtLEKTSKQFYNDLVNKDILSPKFSSLVQFRLQKAIFTEAGAKIDFPKDYEYYTTKISSNY 229
                                       899999**99999998846788899999************************************************* PP

                            PlyB_C 127 yvtrPvsavd 136
                                       yv   v++++
  gi|298674898|ref|YP_003726648.1| 230 YVNANVNPIK 239
                                       ***9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1566.67
//
Query:       gi|298674899|ref|YP_003726649.1|  [L=267]
Description: hypothetical protein Metev_0960 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1286  (0.0717274); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1706.70
//
Query:       gi|298674900|ref|YP_003726650.1|  [L=299]
Description: hypothetical protein Metev_0962 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.12   13.3   0.2       0.12   13.3   0.2    3.4  5  Pilin_N       Archaeal Type IV pilin, N-terminal
        3.7    7.8  40.6      0.034   14.4   4.7    3.8  3  DUF996        Protein of unknown function (DUF996)


Domain annotation for each model (and alignments):
>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.4       0.6   5.4e+03      16      28 ..      31      43 ..      26      67 .. 0.59
   2 ?   13.3   0.2   1.4e-05      0.12       6      53 ..      84     131 ..      81     149 .. 0.87
   3 ?   -3.3   0.4         2   1.8e+04      18      30 ..     183     195 ..     175     198 .. 0.72
   4 ?   -1.9   2.8      0.76   6.8e+03       9      21 ..     226     238 ..     223     248 .. 0.60
   5 ?   -5.8   3.2         2   1.8e+04       4      18 ..     260     274 ..     259     279 .. 0.59

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.6
                           Pilin_N 16 tvIlaAviaafvl 28
                                      ++I +A +a  v+
  gi|298674900|ref|YP_003726650.1| 31 IIIGIAWVAYAVI 43
                                      4444555544332 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.4e-05
                           Pilin_N   6 ViGviLmvaitvIlaAviaafvlglasneekapqasievkidssastg 53 
                                       Vi  i+m  it+++ A++ + ++g+++++    ++s+e+ i+s+++  
  gi|298674900|ref|YP_003726650.1|  84 VISLIIMWIITLLIQAFFTTGAIGMSKDAAINGRTSFEEMINSGKKHF 131
                                       99***********************99999999999988888887764 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 2
                           Pilin_N  18 IlaAviaafvlgl 30 
                                       I+ ++i + vl+l
  gi|298674900|ref|YP_003726650.1| 183 IIYSIIVTLVLSL 195
                                       7788888888876 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 0.76
                           Pilin_N   9 viLmvaitvIlaA 21 
                                       v+L ++i+ I++A
  gi|298674900|ref|YP_003726650.1| 226 VVLWLVIIAIVVA 238
                                       4555555555554 PP

  == domain 5  score: -5.8 bits;  conditional E-value: 2
                           Pilin_N   4 SpViGviLmvaitvI 18 
                                       S +i v+   a++ I
  gi|298674900|ref|YP_003726650.1| 260 STIISVVVVPAVITI 274
                                       556666665555544 PP

>> DUF996  Protein of unknown function (DUF996)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9  11.4     0.014   1.2e+02      30      92 ..      28     102 ..      12     113 .. 0.60
   2 ?   14.4   4.7   3.8e-06     0.034      26      97 ..     128     204 ..     121     218 .. 0.75
   3 ?    1.9   7.7     0.029   2.6e+02       6      56 ..     232     284 ..     228     294 .. 0.63

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.014
                            DUF996  30 liafilsiialvvailalllvlgalatalelpgleeaas............lilllllvliiayvlliisavflk 92 
                                       l  +i++i++++ a+++ +  + al    +l    ++ +            +i+ l+++lii+++++++  +f+ 
  gi|298674900|ref|YP_003726650.1|  28 LSTIIIGIAWVAYAVIIAVSMIPALSQTSQLSFGPQMNQeefmellsmispYIVPLVISLIIMWIITLLIQAFFT 102
                                       334455555554443333333333332222222222222456889999999888999999999988777766654 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 3.8e-06
                            DUF996  26 fsnaliafilsiialvvailalllvlgalatalelpgleeaas...lilllllvliiay..vlliisavflkksyel 97 
                                       ++ ++ +f+l+ii ++++ + +++vl  ++ + +++++e +++   ++l+ + ++ii    v+l++s +++  ++++
  gi|298674900|ref|YP_003726650.1| 128 KKHFFNYFLLQIIYYLITLAGVVFVLPGILQINNFTDPESILPalpALLVGIGLWIIYSiiVTLVLSLTYYALVVDT 204
                                       5789999*******************************999887774444444444433115566666666655555 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.029
                            DUF996   6 liLvlvalkeiskavndekifsnaliafilsiialvva...ilalllvlgalat 56 
                                       +i ++val+ +  ++   +   ++l++fi +ii++vv+   i +  ++l++  t
  gi|298674900|ref|YP_003726650.1| 232 IIAIVVALNVMGGIFTPFE-TLSVLWSFISTIISVVVVpavITIWWTILYMGNT 284
                                       5667777777777777666.4568999999999998884433333333444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1260  (0.0702772); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.72u 0.32s 00:00:01.04 Elapsed: 00:00:00.49
# Mc/sec: 1836.55
//
Query:       gi|298674901|ref|YP_003726651.1|  [L=236]
Description: iron-sulfur flavoprotein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.4e-15   54.8   0.0    1.5e-14   54.1   0.0    1.4  1  FMN_red          NADPH-dependent FMN reductase
    6.3e-08   32.6   0.0    8.9e-08   32.1   0.0    1.3  1  Flavodoxin_2     Flavodoxin-like fold
  ------ inclusion threshold ------
      0.018   15.2   0.0      0.028   14.6   0.0    1.3  1  PEP-utilisers_N  PEP-utilising enzyme, N-terminal
       0.14   11.4   0.0       0.22   10.8   0.0    1.3  1  Methyltransf_2   O-methyltransferase domain


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   0.0   3.3e-18   1.5e-14       1     100 [.       1     105 [.       1     121 [. 0.91

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 3.3e-18
                                       -EEEEEES--S.TT-HHHHHHHHHHCCT-T.T-CEEEEETTTS..--.....---HCHGHTCGGSHHHHHHHHHHHH CS
                           FMN_red   1 mkilvisGSlr.kgsntrklaewaaealkeagaevelidladl.ilpc...alcdkdlesegqtsddvaellekiaa 72 
                                       mki v++GS++ k+snt ++++ ++e + +aga++e i la++ i +c   + c+ +++ +++ +dd+  l++   +
  gi|298674901|ref|YP_003726651.1|   1 MKITVFNGSPKgKKSNTHRIVNPLLEGAIQAGAQTEEIFLAEYnINHCygcFSCWTKTPGKCVINDDMSNLINLFFE 77 
                                       9*********9899**********************************9776666666677**************** PP

                                       -SCEEEEEEECTTCE-HHHHHHHHCHT- CS
                           FMN_red  73 adaliivtPeYngsysgllKnalDrlsr 100
                                       +d + ++tP+Y   ++++lK + +rl +
  gi|298674901|ref|YP_003726651.1|  78 SDYVGMATPVYGLFMTSILKKFNERLLP 105
                                       **********************999954 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0     2e-11   8.9e-08       1     137 [.       1     139 [.       1     158 [. 0.80

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 2e-11
                                       -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCCT-----CCCCHCCHHHHTTC.HHHHHHH.HHHH CS
                      Flavodoxin_2   1 mkiLiinahprpeksfssalaqafvealekagphevtvrdLyadflpvlttrdlaaklayeekp.adveseq.iekl 75 
                                       mki++ n++p+++ks+++++ + ++e++ +ag ++ +++ L++  + + +  ++++   ++ k+ ++ ++ + i  +
  gi|298674901|ref|YP_003726651.1|   1 MKITVFNGSPKGKKSNTHRIVNPLLEGAIQAG-AQTEEIFLAEY-NINHCYGCFSCWTKTPGKCvINDDMSNlINLF 75 
                                       9*******************************.9*********6.4455556888764444447799999999**** PP

                                       HCSSEEEEEEE-BTTB--HHHHHHHHHHS-TTTSC.E.ETTCS.SCCCCTTTTSEEEEEEEESS- CS
                      Flavodoxin_2  76 laadaivlqfPlwwfgvPailKgwiDrvltagfaf.y.teegg.egrgggLkgkkalvivttGgp 137
                                        ++d + +++P++ + + +ilK++ +r l     +   +e+g  + ++++++  + + i+ +G+p
  gi|298674901|ref|YP_003726651.1|  76 FESDYVGMATPVYGLFMTSILKKFNERLLPTATPHiHkNEDGScY-HEERMHYPRFFMIANAGFP 139
                                       **************************9986666554424444433.5666666666666666666 PP

>> PEP-utilisers_N  PEP-utilising enzyme, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   6.2e-06     0.028      20      82 ..     169     227 ..     149     233 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.2e-06
                                       -----G.GGHHHHHHHHHHHHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHT-HHHHHHHHHH CS
                   PEP-utilisers_N  20 eeeeveaedveaelerleeAlekvreelealaekalgeeeaaifeahlmlleDpelleeveer 82 
                                       eee+ ++e+v++ ++ + +Al+k+ +e+ +   ++   +e  i + h++l++D+e+++ v+++
  gi|298674901|ref|YP_003726651.1| 169 EEEDWPDENVKKRINEFYDALRKAGKEMVTNG-QV---SENIIKTIHAELISDDEFMAGVNQH 227
                                       567889999*******************8743.22...23448899************99986 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   4.9e-05      0.22     139     182 ..     172     215 ..     167     229 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.9e-05
                                       GS-HHHHHHHHHHHHHH--TT-EEEEEE----TTS---HHHHHH CS
                    Methyltransf_2 139 DwsdekcvklLkrvkkalpagGkvivveavlgadpsgeletelv 182
                                       Dw de+++k +++ ++al++ Gk +v +  ++++  ++ ++el+
  gi|298674901|ref|YP_003726651.1| 172 DWPDENVKKRINEFYDALRKAGKEMVTNGQVSENIIKTIHAELI 215
                                       9**************************99999988888877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1499.54
//
Query:       gi|298674902|ref|YP_003726652.1|  [L=334]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.3e-25   86.4   0.3    3.5e-24   84.5   0.0    2.2  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    0.00027   21.1   0.4    0.00061   20.0   0.4    1.5  1  OrfB_IS605      Probable transposase
     0.0015   18.5   1.7      0.094   12.7   0.1    2.8  2  HypA            Hydrogenase/urease nickel incorporation, meta
  ------ inclusion threshold ------
       0.02   14.5   0.8      0.042   13.5   0.8    1.5  1  Zn_ribbon_17    Zinc-ribbon, C4HC2 type
      0.032   14.3   4.7       0.16   12.1   0.9    2.5  2  UPF0547         Uncharacterised protein family UPF0547
       0.48   10.5   3.1       0.53   10.3   1.7    1.9  2  DZR             Double zinc ribbon
       0.76    9.8   3.3        2.4    8.1   0.2    3.0  3  zinc_ribbon_4   zinc-ribbon domain
        1.4    8.8   8.2        1.5    8.6   5.4    2.6  3  zinc_ribbon_2   zinc-ribbon domain
        1.5    8.6   6.9       0.62    9.8   2.6    2.6  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
        1.5    8.8   5.0       0.63   10.1   0.6    2.3  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
        6.8    6.2   9.7       0.48    9.9   3.4    2.4  3  zf-ribbon_3     zinc-ribbon domain


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       3.5   5.7e+03      33      49 ..     214     231 ..     210     235 .. 0.56
   2 !   84.5   0.0   2.2e-27   3.5e-24       1      68 [.     244     309 ..     244     310 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.5
                    OrfB_Zn_ribbon  33 eCgsknke.alsgrtfkC 49 
                                       +Cg ++++ +  ++  kC
  gi|298674902|ref|YP_003726652.1| 214 NCGIRMENlKGIRDSAKC 231
                                       666666664444444444 PP

  == domain 2  score: 84.5 bits;  conditional E-value: 2.2e-27
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       f++l+ +leyka+  G+k+e v+p+yTS++Cs+Cg+ + +  +g+ fkCp+Cg++ ++D nAa+Ni+ 
  gi|298674902|ref|YP_003726652.1| 244 FYQLQFMLEYKARLLGVKIEFVEPEYTSQDCSRCGYLGIR--NGDSFKCPHCGHVDHADANAAFNIAM 309
                                       899*************************************..************************96 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.4   3.7e-07   0.00061       3     107 ..     118     214 ..     114     225 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3.7e-07
                        OrfB_IS605   3 pvevevelpkpkgnkaagiDlGin.nLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrkla 78 
                                        v+v++ +++ +++  +g+Dl+   ++a++++ ++  + + g++++    ++++ +++lq k k         +k++
  gi|298674902|ref|YP_003726652.1| 118 SVTVPE-KEQIEPEDYLGVDLNTTgHIAVMSNPKTGKIWKLGKKAQHIHLKYKNDRRKLQVKGKY--------KKVK 185
                                       344444.88999**********87367777777766677889******************98433........5799 PP

                        OrfB_IS605  79 rlhrkrsrrrkhllhklathliktlkevg 107
                                        + ++ sr++++l hk+++++++t  +++
  gi|298674902|ref|YP_003726652.1| 186 QVNDRESRIVRDLNHKISSRIVDTAAANN 214
                                       9**********************988775 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0      0.03        49       9      35 ..      46      73 ..      40      79 .. 0.75
   2 !   12.7   0.1   5.8e-05     0.094      59      96 ..     259     297 ..     236     308 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.03
                                      HHHHHHHHHH.CCTT..EEEEEEEEEET CS
                              HypA  9 sivevveeea.keaaarkvtkvkvevGe 35
                                      +i +++ ++  k+++a+kvt+vk+++ +
  gi|298674902|ref|YP_003726652.1| 46 AISNQILKKYaKDKSAKKVTSVKLTIPN 73
                                      5666666666377999********9865 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 5.8e-05
                                       T-EEE.EEEE--EEEETTTS-EEECHHHHHS-TTTSSS- CS
                              HypA  59 gaeLe.ieevpvkvrCreCgkefeleekalrCpkCgsad 96 
                                       g ++e +e +  +  C++Cg+ +  + ++++Cp+Cg+ d
  gi|298674902|ref|YP_003726652.1| 259 GVKIEfVEPEYTSQDCSRCGYLGIRNGDSFKCPHCGHVD 297
                                       455553455556778*****9998777799******876 PP

>> Zn_ribbon_17  Zinc-ribbon, C4HC2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.8   2.6e-05     0.042       6      34 ..     273     303 ..     269     317 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.6e-05
                      Zn_ribbon_17   6 sCayCe.lav.kgrvvlcgvCeHvlHasCar 34 
                                        C+ C  l + +g  + c+ C+Hv Ha+  +
  gi|298674902|ref|YP_003726652.1| 273 DCSRCGyLGIrNGDSFKCPHCGHVDHADANA 303
                                       566664244415889************9765 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2     0.056        91      15      22 ..     272     279 ..     271     280 .. 0.88
   2 ?   12.1   0.9   9.9e-05      0.16      16      25 ..     289     298 ..     286     299 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.056
                           UPF0547  15 qfCphCGy 22 
                                       q C+ CGy
  gi|298674902|ref|YP_003726652.1| 272 QDCSRCGY 279
                                       78*****9 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 9.9e-05
                           UPF0547  16 fCphCGyvFq 25 
                                       +CphCG+v+ 
  gi|298674902|ref|YP_003726652.1| 289 KCPHCGHVDH 298
                                       7******985 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.7   0.00033      0.53      27      49 .]     267     294 ..     213     294 .. 0.80
   2 ?   -3.7   0.0         8   1.3e+04      17      20 ..     314     317 ..     309     321 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00033
                               DZR  27 a...edrCpsCgek.vdpearf.CpeCG 49 
                                           ++ C++Cg+  + ++++f Cp+CG
  gi|298674902|ref|YP_003726652.1| 267 PeytSQDCSRCGYLgIRNGDSFkCPHCG 294
                                       0444899*******999**********9 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 8
                               DZR  17 eCgt 20 
                                       +Cg+
  gi|298674902|ref|YP_003726652.1| 314 QCGA 317
                                       3443 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       2.5     4e+03      30      35 ..     230     235 ..     224     236 .. 0.65
   2 ?    0.5   0.0      0.36   5.9e+02      28      33 ..     274     279 ..     265     280 .. 0.83
   3 ?    8.1   0.2    0.0015       2.4      22      34 ..     284     296 ..     283     296 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.5
                     zinc_ribbon_4  30 kCghvF 35 
                                       kC+++F
  gi|298674902|ref|YP_003726652.1| 230 KCKKSF 235
                                       455544 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.36
                     zinc_ribbon_4  28 CskCgh 33 
                                       Cs+Cg 
  gi|298674902|ref|YP_003726652.1| 274 CSRCGY 279
                                       999985 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0015
                     zinc_ribbon_4  22 kgvkvrCskCghv 34 
                                       +g + +C++Cghv
  gi|298674902|ref|YP_003726652.1| 284 NGDSFKCPHCGHV 296
                                       56789*******8 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.2     0.075   1.2e+02      16      21 ..     274     279 ..     270     281 .. 0.73
   2 ?    8.6   5.4   0.00094       1.5       2      21 ..     274     295 ..     274     296 .. 0.93
   3 ?   -3.0   0.0       4.3   7.1e+03      19      21 ..     315     317 ..     314     318 .. 0.52

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.075
                     zinc_ribbon_2  16 CpyCGt 21 
                                       C++CG+
  gi|298674902|ref|YP_003726652.1| 274 CSRCGY 279
                                       777775 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00094
                     zinc_ribbon_2   2 CpnCGael.qdnakF.CpyCGt 21 
                                       C++CG+    +++ F Cp+CG+
  gi|298674902|ref|YP_003726652.1| 274 CSRCGYLGiRNGDSFkCPHCGH 295
                                       9999999879***********8 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 4.3
                     zinc_ribbon_2  19 CGt 21 
                                       CG+
  gi|298674902|ref|YP_003726652.1| 315 CGA 317
                                       554 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1         1   1.7e+03      22      26 ..     214     218 ..     213     233 .. 0.66
   2 ?    9.8   2.6   0.00038      0.62       2      25 ..     273     295 ..     273     296 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1
                                       SS--- CS
                    DNA_RNApol_7kD  22 eCGhR 26 
                                       +CG R
  gi|298674902|ref|YP_003726652.1| 214 NCGIR 218
                                       56666 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00038
                                       B-SSS--B----SSS----SSS-- CS
                    DNA_RNApol_7kD   2 iCgeCgaevslkkgdpiRCkeCGh 25 
                                       +C +Cg    +++gd+ +C +CGh
  gi|298674902|ref|YP_003726652.1| 273 DCSRCGY-LGIRNGDSFKCPHCGH 295
                                       5889985.78*************9 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   5.4     0.026        43      14      25 ..     283     294 ..     270     295 .. 0.56
   2 ?   10.1   0.6   0.00039      0.63      15      27 ..     284     296 ..     279     305 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.026
                     Zn_Tnp_IS1595  14 rWpngfvCPhCg 25 
                                       r ++ f CPhCg
  gi|298674902|ref|YP_003726652.1| 283 RNGDSFKCPHCG 294
                                       334446666666 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00039
                     Zn_Tnp_IS1595  15 WpngfvCPhCgsr 27 
                                        ++ f CPhCg+ 
  gi|298674902|ref|YP_003726652.1| 284 NGDSFKCPHCGHV 296
                                       4677*******87 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0         2   3.2e+03      21      25 ..     214     218 ..     213     219 .. 0.66
   2 ?    9.9   3.4   0.00029      0.48       5      25 ..     274     296 ..     272     296 .. 0.87
   3 ?   -3.5   0.1       4.9     8e+03       7      10 ..     314     317 ..     313     317 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2
                       zf-ribbon_3  21 yCGtk 25 
                                       +CG +
  gi|298674902|ref|YP_003726652.1| 214 NCGIR 218
                                       67765 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00029
                       zf-ribbon_3   5 CPnCGap.lssddnv.CpyCGtk 25 
                                       C++CG + ++ +d++ Cp+CG++
  gi|298674902|ref|YP_003726652.1| 274 CSRCGYLgIRNGDSFkCPHCGHV 296
                                       99****7799999966*****86 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 4.9
                       zf-ribbon_3   7 nCGa 10 
                                       +CGa
  gi|298674902|ref|YP_003726652.1| 314 QCGA 317
                                       7886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1363  (0.0760221); expected 358.6 (0.02)
Passed bias filter:                      670  (0.0373696); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2249.66
//
Query:       gi|298674903|ref|YP_003726653.1|  [L=88]
Description: hypothetical protein Metev_0965 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.012   15.7   0.2      0.013   15.7   0.2    1.2  1  Sld3_N    Sld3 N-terminal domain


Domain annotation for each model (and alignments):
>> Sld3_N  Sld3 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   0.2     7e-07     0.013      34      74 ..      29      73 ..       4      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7e-07
                                      -STTTS-TT-EEEEE....-SS-EEEEEE-STTEEE.EEEBSS-- CS
                            Sld3_N 34 selenspislKHllk...daddkyflLErYgkeywv.lWevvsvd 74
                                      + le+++i  +H+ k   + +d+y++L  Y ++ w+ +W v s++
  gi|298674903|ref|YP_003726653.1| 29 DYLEQNNIEFNHISKvlnEINDEYLMLDSYRQGVWIpKWVVESEK 73
                                      457999999***988774699***************779985554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 593.84
//
Query:       gi|298674904|ref|YP_003726654.1|  [L=82]
Description: hypothetical protein Metev_0966 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.089   12.9   0.0      0.089   12.9   0.0    1.4  1  Sld3_N    Sld3 N-terminal domain


Domain annotation for each model (and alignments):
>> Sld3_N  Sld3 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     5e-06     0.089      45      70 ..      50      75 ..       4      81 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5e-06
                                      EEEE.-SS-EEEEEE-STTEEEEEEB CS
                            Sld3_N 45 HllkdaddkyflLErYgkeywvlWev 70
                                      Hll++ +d+++lL  +++++w+  +v
  gi|298674904|ref|YP_003726654.1| 50 HLLHETSDSFLLLDSFNNSTWIPKDV 75
                                      *********************97666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 562.96
//
Query:       gi|298674905|ref|YP_003726655.1|  [L=169]
Description: ISA1083-3 transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.5e-17   61.4   0.4    1.6e-16   60.6   0.4    1.4  1  HTH_32         Homeodomain-like domain
    8.1e-10   38.2   0.0    1.9e-09   37.1   0.0    1.7  2  HTH_33         Winged helix-turn helix
    7.6e-09   35.5   0.1    2.3e-08   33.9   0.0    1.7  2  HTH_29         Winged helix-turn helix
    4.1e-05   23.2   0.4    0.00041   20.0   0.1    2.5  3  HTH_23         Homeodomain-like domain
    0.00062   19.8   0.4     0.0014   18.7   0.2    1.7  2  HTH_28         Helix-turn-helix domain
     0.0026   18.3   0.1     0.0038   17.7   0.1    1.3  1  LZ_Tnp_IS481   leucine-zipper of insertion element IS481
  ------ inclusion threshold ------
      0.059   13.6   0.0       0.11   12.7   0.0    1.5  1  HTH_Tnp_Tc3_2  Transposase


Domain annotation for each model (and alignments):
>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.6   0.4   6.3e-20   1.6e-16       3      73 .]      70     140 ..      68     140 .. 0.97

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 6.3e-20
                            HTH_32   3 srwlkRyneeGlegLkdrprrgrprklsdevrariiallreeprWsprqlaarlaeregvkvShstvyriL 73 
                                       +rw kR+ne+G+egL +r  +grp+kl+++++++++++l+++  W++ q+++ +  ++gv++   +++riL
  gi|298674905|ref|YP_003726655.1|  70 HRWQKRWNESGYEGLIPRYTGGRPPKLTQQQKDQLKQILKSRNGWTTNQVRELIINEFGVEYCLMQIRRIL 140
                                       8**************************************8888***********9999************8 PP

>> HTH_33  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       3.2   8.1e+03      28      34 ..      70      76 ..      64      77 .. 0.64
   2 !   37.1   0.0   7.2e-13   1.9e-09       4      47 ..     113     156 ..     110     169 .] 0.86

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.2
                            HTH_33 28 yrlLkrl 34
                                      +r+ kr+
  gi|298674905|ref|YP_003726655.1| 70 HRWQKRW 76
                                      5666666 PP

  == domain 2  score: 37.1 bits;  conditional E-value: 7.2e-13
                            HTH_33   4 rWtlarlaqlieerfgvsysvsgvyrlLkrlGfsyqkPrprapk 47 
                                        Wt+ ++++li  +fgv+y   +++r+Lk+ G+ y kP p+ ++
  gi|298674905|ref|YP_003726655.1| 113 GWTTNQVRELIINEFGVEYCLMQIRRILKEFGMKYAKPYPHDYR 156
                                       6*************************************998754 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   8.9e-12   2.3e-08       9      62 ..      50     101 ..      46     102 .. 0.94
   2 ?   -2.1   0.0       1.6   4.1e+03      28      36 ..     135     143 ..     130     147 .. 0.75

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 8.9e-12
                            HTH_29   9 aeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsgrprnrlseeqe 62 
                                       +eG s v    +++g+s +   rw+kr++e G ++l++r+ +grp + l+++q+
  gi|298674905|ref|YP_003726655.1|  50 YEGNS-VIISSERVGISSPVGHRWQKRWNESGYEGLIPRYTGGRPPK-LTQQQK 101
                                       58997.999*************************************6.9*9997 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.6
                            HTH_29  28 tvyrwlkrf 36 
                                       +++r+lk f
  gi|298674905|ref|YP_003726655.1| 135 QIRRILKEF 143
                                       688888877 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   1.6e-07   0.00041       2      50 .]      37      85 ..      36      85 .. 0.93
   2 ?   -1.7   0.0       1.1   2.7e+03      11      23 ..     107     119 ..      99     123 .. 0.69
   3 ?   -0.2   0.0      0.37   9.4e+02      32      41 ..     134     143 ..     131     146 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.6e-07
                            HTH_23  2 asereRlrillllaeGlsvreIAreLgvsrrTvyrwlkryreeGlegll 50
                                      a+++ Rl  ++   eG sv   +++ g+s     rw kr++e+G egl+
  gi|298674905|ref|YP_003726655.1| 37 ARVLTRLYFIKYRYEGNSVIISSERVGISSPVGHRWQKRWNESGYEGLI 85
                                      6888999999999999999999*************************95 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.1
                            HTH_23  11 llllaeGlsvreI 23 
                                       +l  ++G+++ ++
  gi|298674905|ref|YP_003726655.1| 107 ILKSRNGWTTNQV 119
                                       5556668887665 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.37
                            HTH_23  32 rTvyrwlkry 41 
                                       ++++r+lk +
  gi|298674905|ref|YP_003726655.1| 134 MQIRRILKEF 143
                                       6889999987 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.2   5.6e-07    0.0014      20      52 .]      60      92 ..      46      94 .. 0.87
   2 ?   -2.8   0.0       2.8   7.2e+03      22      35 ..     127     142 ..     119     144 .. 0.58

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 5.6e-07
                            HTH_28 20 relgisrrtvyrWikryeegGiagLvprrrrpr 52
                                      +++gis+    rW kr++e G +gL pr  ++r
  gi|298674905|ref|YP_003726655.1| 60 ERVGISSPVGHRWQKRWNESGYEGLIPRYTGGR 92
                                      78888888889*****************76554 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.8
                            HTH_28  22 lgi..srrtvyrWikr 35 
                                       +g+  +  +++r +k 
  gi|298674905|ref|YP_003726655.1| 127 FGVeyCLMQIRRILKE 142
                                       5554444466776665 PP

>> LZ_Tnp_IS481  leucine-zipper of insertion element IS481
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   1.5e-06    0.0038      27      71 ..      54      97 ..      32     113 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.5e-06
                      LZ_Tnp_IS481 27 tvaqvarelGvslrtaykwlarfraeGldGlldrssrPrrvPkat 71
                                      +v   ++ +G+s  ++++w  r+   G +Gl+ r +   r Pk t
  gi|298674905|ref|YP_003726655.1| 54 SVIISSERVGISSPVGHRWQKRWNESGYEGLIPRYTGG-RPPKLT 97
                                      45557889************************997533.234444 PP

>> HTH_Tnp_Tc3_2  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.4e-05      0.11      23      49 ..     123     150 ..     101     153 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.4e-05
                     HTH_Tnp_Tc3_2  23 lkee.GksvsreTirrrLrkaglkkrkp 49 
                                       + +e G++ + + irr+L+++g+k  kp
  gi|298674905|ref|YP_003726655.1| 123 IINEfGVEYCLMQIRRILKEFGMKYAKP 150
                                       34445*******************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1380.29
//
Query:       gi|298674906|ref|YP_003726656.1|  [L=179]
Description: ISA1083-3 transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-23   83.4   0.1    1.9e-23   82.9   0.1    1.2  1  DDE_3     DDE superfamily endonuclease
    4.7e-05   23.1   0.0    7.5e-05   22.4   0.0    1.3  1  DDE_1     DDE superfamily endonuclease
     0.0089   16.2   0.0      0.033   14.4   0.0    1.8  2  rve       Integrase core domain


Domain annotation for each model (and alignments):
>> DDE_3  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.9   0.1   3.1e-27   1.9e-23       4     135 ..       9     133 ..       7     143 .. 0.90

  Alignments for each domain:
  == domain 1  score: 82.9 bits;  conditional E-value: 3.1e-27
                             DDE_3   4 fiDEsgfqlgtvrrrawakkGkrerleeygrrgrvnligaldekgglafvtfeetlnaedfaeflerlletalqakk 80 
                                       f+DE+  q++++  r w+    +     ++ + +vn +g++  +g + ++ f+   ++ed+ efl  + ++ +++ +
  gi|298674906|ref|YP_003726656.1|   9 FLDETSPQNNANTLRFWSFNKPQI---YRNTWIKVNTLGFYALNG-KSVIEFSPHSKKEDVCEFLMNIRKNNPDK-R 80 
                                       99*********9999999987765...789999***********9.6677889999******************8.* PP

                             DDE_3  81 ivlilDnasiHkseslrelveeeadrlellylPpySPelNpiEivwsklkrellk 135
                                       iv+ilDn + H++++++e +++   ++el+ylPpySPelNpiE +w+++ r +  
  gi|298674906|ref|YP_003726656.1|  81 IVIILDNFRSHHAKTVVECAAN--NGIELVYLPPYSPELNPIEFIWKSIRRVISG 133
                                       **********************..************************9998876 PP

>> DDE_1  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.3e-08   7.5e-05      72     111 ..      76     116 ..      63     129 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.3e-08
                             DDE_1  72 aekrkilLlldssrshetvelleselqn.iklvflPassas 111
                                       +++++i+++ld++rsh++ ++ e++ +n i+lv+lP+ s +
  gi|298674906|ref|YP_003726656.1|  76 NPDKRIVIILDNFRSHHAKTVVECAANNgIELVYLPPYSPE 116
                                       7899*************999978877666*******98765 PP

>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   5.5e-06     0.033      40     106 ..      55     119 ..      47     130 .. 0.83
   2 ?   -0.6   0.0      0.24   1.5e+03      69      90 ..     136     157 ..     121     165 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.5e-06
                               rve  40 ealsdemdastvlalleravarfggvepervlsDngseytskafrefladlgirvsftrpgrpqdnG 106
                                       e+ +++ ++++v+++l +  ++    +  +++ Dn ++  +k++ e +a++gi++ + +p++p+ n 
  gi|298674906|ref|YP_003726656.1|  55 EFSPHS-KKEDVCEFLMNIRKNNPD-KRIVIILDNFRSHHAKTVVECAANNGIELVYLPPYSPELNP 119
                                       555566.889999999965555555.5899*********************************9997 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.24
                               rve  69 rvlsDngseytskafrefladl 90 
                                       ++ +D++++ + +af ++ a+ 
  gi|298674906|ref|YP_003726656.1| 136 AIDTDHMKQLIYEAFMQLSANI 157
                                       5789999999999998887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.53
# Mc/sec: 1011.80
//
Query:       gi|298674907|ref|YP_003726657.1|  [L=385]
Description: glucose/sorbosone dehydrogenase-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-34  117.7   0.5    1.5e-32  113.2   0.8    2.3  2  GSDH      Glucose / Sorbosone dehydrogenase


Domain annotation for each model (and alignments):
>> GSDH  Glucose / Sorbosone dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.2   0.8   8.5e-37   1.5e-32       2     223 ..      26     248 ..      25     315 .. 0.85
   2 ?   -1.0   0.0     0.047   8.5e+02      77     128 ..     294     342 ..     277     353 .. 0.70

  Alignments for each domain:
  == domain 1  score: 113.2 bits;  conditional E-value: 8.5e-37
                                       S-EEEEEE-TT.S-......EEEEETTTEEEEEE.TTEE.EEEEE-.......----STT-SEEEEEE-TTTTTS-E CS
                              GSDH   2 ehPwslaflpd.gr......lLvtersGrlrlvkadgklkepiagv......pevvakgqgGlldvalhpdfaenrl 65 
                                       + P ++af+p+ g+      l +te  G++++v++d ++ +  +++       +   +g++Gl +++++p+   ++ 
  gi|298674907|ref|YP_003726657.1|  26 DLPVNIAFVPKhGDnpksplLYITELYGQVKVVTNDYSVYTYAKNLlnyepsHQFPGNGESGLTGICVEPE---SGD 99 
                                       56777777764322222232469***********9999977777775556433558899***********6...999 PP

                                       EEEEEEE-...TTSSEEEEEEEEE-SS..-EEEEEEEEEEE---TT-------EEE-TTS-EEEE---TT-GGGGG- CS
                              GSDH  66 vYltyaeaeeekggagtavararlsedeaaledlevifrqepkvesgahfGsrlafgpdgtLfvtvGdrskreeaqd 142
                                       +Yl++    eekg+ + +++r r ++   +++d++ +++++p+ +++ah    + +g d++++v  Gd +   ++qd
  gi|298674907|ref|YP_003726657.1| 100 LYLSMIY--EEKGEVKSKLVRTRSDN-GLSMKDQKIVLDDIPS-TRRAHQIQAVSIGFDNKIYVNFGDGGAWYKSQD 172
                                       ******4..5999999*******955.59**************.666999999************************ PP

                                       TT-SSSEEEEE-TTSSB-TT-TTTT-TTS-TTEEEE--SCE---EE-TTT--EEEEEE--SSSEEEEEE-TT-B--T CS
                              GSDH 143 lsselGkilrlnkdGsvpadnpfvgkagakpeiwsyGhRnpqGlaldpdtgeLwesEhGprggDelnlieaGknYGW 219
                                        ++  Gk++rln+dG++p dnp+      ++ +++ G Rnp G+a++++ ++L+    Gp ++D + ++++ +nYGW
  gi|298674907|ref|YP_003726657.1| 173 ENDFRGKVVRLNHDGTIPWDNPIS-----ENPVYAKGFRNPFGAAWRKSDQHLYIAGNGPDQDDRIVRVKPYENYGW 244
                                       ***********************5.....789********************************************* PP

                                       TT-S CS
                              GSDH 220 plvs 223
                                       p + 
  gi|298674907|ref|YP_003726657.1| 245 PNTM 248
                                       *876 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.047
                                       TTSSEEEEEEEEE-SS..-EEEEEEEEEEE---TT-------EEE-TTS-EE CS
                              GSDH  77 kggagtavararlsedeaaledlevifrqepkvesgahfGsrlafgpdgtLf 128
                                       +g +g+++a+ +l+++ +a++++++ +  + +   g    + lafgpdg  f
  gi|298674907|ref|YP_003726657.1| 294 TGVKGKRIAKLQLNDEGTAVKSYDDFVVYKGE---GPASTCGLAFGPDGLYF 342
                                       45667899999999988888877776655544...55667778888888444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2744.83
//
Query:       gi|298674908|ref|YP_003726658.1|  [L=321]
Description: aldo/keto reductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.4e-62  210.3   0.0    3.8e-62  210.1   0.0    1.0  1  Aldo_ket_red  Aldo/keto reductase family


Domain annotation for each model (and alignments):
>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.1   0.0   2.1e-66   3.8e-62       2     292 ..      16     302 ..      15     304 .. 0.94

  Alignments for each domain:
  == domain 1  score: 210.1 bits;  conditional E-value: 2.1e-66
                                       EEEE-SSS-ST.TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE..--SSST CS
                      Aldo_ket_red   2 lglGtwqlgskeeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKv..dlrdae 76 
                                       +g+G    g   + ++++ l+++++a+e+G+n++Dt++vYg+g++e+++G+al +   +r++v+ia+K   ++    
  gi|298674908|ref|YP_003726658.1|  16 IGFGSQPTG---YHDESYGLQAIHTAFEHGVNLIDTSPVYGNGRAEQIVGKALRN--YDRDDVVIASKTglEKTGRG 87 
                                       778877777...89*****************************************..************88788888 PP

                                       TSSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--HHHHHHHHHTT CS
                      Aldo_ket_red  77 iksglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfsveqlekakkkk 153
                                         ++ s+e i + +e sl+rLgtdy+D++++H+pdp  p   e+++++e l++e  i+aiGvSnfsveq++     +
  gi|298674908|ref|YP_003726658.1|  88 AVRNSSPEFILKDIEGSLQRLGTDYIDIYQIHWPDPVQP-FHETAEVMESLREEDRIKAIGVSNFSVEQMKCF--SE 161
                                       999************************************.*******************************88..** PP

                                       T--EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------.....TS-HHH CS
                      Aldo_ket_red 154 kvkivavqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrd.....ertskn 225
                                       +v+i + q  yn++++l e g++++c  +++ l +y  l +G+ltg  + ++d+ +   +kd   d      r+++ 
  gi|298674908|ref|YP_003726658.1| 162 YVDINTCQSPYNIFERLIEGGVIPYCIRNNITLLTYRSLCQGILTGALEYNTDYSKHPVKKD---DpkfksPRYEQY 235
                                       *************************************************9999975433443...3446999***** PP

                                       HHHHHHHHHHHHH.TT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHHHH CS
                      Aldo_ket_red 226 ldaaeelselake.hgvslaqlalryalsqpavgivipgasnieqlednldalelklseeevaeldel 292
                                       lda+++l +++++ h++s+  la++++l  +a+++++ ga ++e+++d+    ++  ++e+  +++++
  gi|298674908|ref|YP_003726658.1| 236 LDAVKNLANFVQNeHNKSMIDLAIQWIL-DKANTVALWGAWKPEHIDDVNLLSNWSVDKETRYRIEKI 302
                                       ********999998**************.79*****************99999999999998888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2238.47
//
Query:       gi|298674909|ref|YP_003726659.1|  [L=174]
Description: hypothetical protein Metev_0972 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.081   13.7   0.0       0.19   12.5   0.0    1.6  1  Big_7     Bacterial Ig domain
       0.58   10.2   0.1       0.58   10.2   0.1    2.8  3  Y_Y_Y     Y_Y_Y domain


Domain annotation for each model (and alignments):
>> Big_7  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.1e-05      0.19      18      65 ..     111     156 ..     103     161 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.1e-05
                                       EEEEEEEEE-SS-EEEEEEEET.TEE.EEEE-SSSEEEEEE--...SEE CS
                             Big_7  18 tvtisasAsddggvskVefyvd.gtlglgtdtsapysltwtttaltagt 65 
                                       +++i + A d+  vskV + +   ++ l +d+++++++ ++t++l++g 
  gi|298674909|ref|YP_003726659.1| 111 DIKIYGKAKDN--VSKVNINIKvLQS-LKADNQGNFRYDYDTSSLPEGK 156
                                       78999999999..******9984455.9*****************9995 PP

>> Y_Y_Y  Y_Y_Y domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1      0.42   3.8e+03      10      16 ..      51      57 ..      46      72 .. 0.67
   2 ?   10.2   0.1   6.5e-05      0.58      36      59 ..     105     129 ..      92     132 .. 0.85
   3 ?    0.5   0.2     0.065   5.9e+02      34      46 ..     150     162 ..     136     173 .. 0.59

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.42
                                      EEEEEET CS
                             Y_Y_Y 10 YrYrleg 16
                                      Y+Y le+
  gi|298674909|ref|YP_003726659.1| 51 YEYYLEK 57
                                      5555554 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 6.5e-05
                                       --SEEEEEEEEEEETTS-B-SS-.E CS
                             Y_Y_Y  36 lppGdYtlkVkakdndgqwnydi.t 59 
                                        p+G+Y +k+++k +d+ ++ +i  
  gi|298674909|ref|YP_003726659.1| 105 IPSGSYDIKIYGKAKDNVSKVNInI 129
                                       69************99999888533 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.065
                                       ES--SEEEEEEEE CS
                             Y_Y_Y  34 tnlppGdYtlkVk 46 
                                       + lp+G++ + V+
  gi|298674909|ref|YP_003726659.1| 150 SSLPEGKFLIGVE 162
                                       5566666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1326.60
//
Query:       gi|298674910|ref|YP_003726660.1|  [L=228]
Description: hypothetical protein Metev_0973 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.027   14.2   0.0      0.033   13.9   0.0    1.1  1  Cactin_mid  Conserved mid region of cactin
       0.24   11.4   0.2       0.24   11.4   0.2    1.9  2  TNFR_16_TM  Tumor necrosis factor receptor member 16 trans-me


Domain annotation for each model (and alignments):
>> Cactin_mid  Conserved mid region of cactin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.7e-06     0.033      60     104 ..      51      95 ..      12     105 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.7e-06
                        Cactin_mid  60 adleieleePykileglsleeleeleediksylelekseknaefW 104
                                       +  +i+ eePyk++ +ls+ +++++ +d+++ ++ ++++++ +f 
  gi|298674910|ref|YP_003726660.1|  51 HYYNINSEEPYKLYVSLSVPDIKDIDKDVSAKITRKHEGEHNDFH 95 
                                       5678999**************************999999999985 PP

>> TNFR_16_TM  Tumor necrosis factor receptor member 16 trans-membrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.7      0.35   3.2e+03      17      25 ..       4      12 ..       1      14 [. 0.78
   2 ?   11.4   0.2   2.7e-05      0.24      17      35 ..     207     225 ..     203     228 .] 0.84

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.35
                        TNFR_16_TM 17 VvvgLlaYv 25
                                      +++ ++a++
  gi|298674910|ref|YP_003726660.1|  4 IILIIVAFL 12
                                      788999986 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 2.7e-05
                        TNFR_16_TM  17 VvvgLlaYvifKrwksckq 35 
                                       Vvv LlaYv fK+ k  ++
  gi|298674910|ref|YP_003726660.1| 207 VVVALLAYVGFKLNKYLNK 225
                                       9***********9875555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1682.40
//
Query:       gi|298674911|ref|YP_003726661.1|  [L=324]
Description: hypothetical protein Metev_0974 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-33  116.2   0.0      2e-33  115.3   0.0    1.5  1  DUF523         Protein of unknown function (DUF523)
    3.4e-24   85.4   3.0    3.4e-24   85.4   3.0    1.6  2  DUF1722        Protein of unknown function (DUF1722)
  ------ inclusion threshold ------
       0.02   15.3   5.7      0.033   14.6   2.9    2.3  2  DUF5598        Domain of unknown function (DUF5598)
       0.11   11.4   0.0        0.2   10.5   0.0    1.4  1  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-


Domain annotation for each model (and alignments):
>> DUF523  Protein of unknown function (DUF523)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.3   0.0   4.5e-37     2e-33       1     136 [.       9     148 ..       9     149 .. 0.95

  Alignments for each domain:
  == domain 1  score: 115.3 bits;  conditional E-value: 4.5e-37
                            DUF523   1 ilvSaCLlgekvrydgkakksevleeelkelvkeelvpvCPEvaggLptPRepael.....akr.vlkkegedvtea 71 
                                       +lvS+CL +e+vrydg+  +s+++++ l+ +v  ++++vCPEv++gL++PR+p+++     + r +++++++d+te+
  gi|298674911|ref|YP_003726661.1|   9 VLVSRCLEFENVRYDGHVISSQIVKD-LEPYV--DYIKVCPEVEIGLGVPRDPIRIvkingRYRlIQHRTNRDITEE 82 
                                       79*****************9877766.*****..**************************9778899999******* PP

                            DUF523  72 lekgaeealeelkeeeikgailkekSPSCGveki..Ydgtfskkl.vegeGvfaallkeegievpsee 136
                                       + k+++++l++l+  +++g+i+k++SP+ G+++i  Y+g  s +  ++g+G+faa + e++  +p+ee
  gi|298674911|ref|YP_003726661.1|  83 MDKFTDDFLDKLQ--DVDGFIFKSGSPTIGYRNIkvYSGMESATViEKGSGFFAAKILEKYNGYPVEE 148
                                       ***********99..6*******************9**999999989*************99999987 PP

>> DUF1722  Protein of unknown function (DUF1722)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       2.5   1.1e+04      17      39 ..      69      91 ..      68      95 .. 0.69
   2 !   85.4   3.0   7.6e-28   3.4e-24       2     117 .]     192     307 ..     191     307 .. 1.00

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.5
                           DUF1722 17 rlvanakkepleelaeeYeellm 39
                                      rl+++++++++ e ++++ + + 
  gi|298674911|ref|YP_003726661.1| 69 RLIQHRTNRDITEEMDKFTDDFL 91
                                      56777777778887777777665 PP

  == domain 2  score: 85.4 bits;  conditional E-value: 7.6e-28
                           DUF1722   2 yllmahsqkeyrelgrlvanakkepleelaeeYeellmealskpatrkkhinvlqhilgyfkkklsaeekqelleli 78 
                                       yl++ ++ k+y+e++ l++n  + p+++l+++Ye +l+e++skp+  + ++++++ ++ +f++k+ ++e +++++++
  gi|298674911|ref|YP_003726661.1| 192 YLFLTYNIKIYNEMESLIKNCFDIPIKTLFDNYEYHLKELFSKPPVSEYYLQTANTVFSQFSSKVPQNEIEYFNQVL 268
                                       9**************************************************************************** PP

                           DUF1722  79 ekYregkvplsvpltlLkhyarkydneylleqtylnpyP 117
                                       ekY++++++l+ +l++Lk y+ ++dn+ +++ ++++pyP
  gi|298674911|ref|YP_003726661.1| 269 EKYKQNLITLHGLLEILKLYVLRFDNTGIKDDRLFQPYP 307
                                       **************************************9 PP

>> DUF5598  Domain of unknown function (DUF5598)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.17   7.7e+02      43      89 ..     133     177 ..     111     180 .. 0.61
   2 ?   14.6   2.9   7.3e-06     0.033       9      92 ..     186     273 ..     184     277 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.17
                           DUF5598  43 GLqyllkeylegqvvteekveeakevvkehfkkevfnekgwekildk 89 
                                         + +l++y     v e++  +  + +++hf +++f  +++++i +k
  gi|298674911|ref|YP_003726661.1| 133 FAAKILEKYNGY-PVEENDRLRNSR-IRHHFLTNLFAFTEFRRIKSK 177
                                       445566665444.455555555555.467788999999999888765 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 7.3e-06
                           DUF5598   9 YKlsHkkqypkgtekvysylesRkggkyd...evvffGLqyllkeylegqvvteekveeakevvkehfkkevfne.k 81 
                                       Y   H+ ++ +   k+y  +es  ++ +d   +++f   +y lke+++++ v+e  ++ a++v+++   k   ne +
  gi|298674911|ref|YP_003726661.1| 186 YHKKHHYLFLTYNIKIYNEMESLIKNCFDipiKTLFDNYEYHLKELFSKPPVSEYYLQTANTVFSQFSSKVPQNEiE 262
                                       788999*****************99888766789*******************************966655555436 PP

                           DUF5598  82 gwekildkhdG 92 
                                        ++++l+k++ 
  gi|298674911|ref|YP_003726661.1| 263 YFNQVLEKYKQ 273
                                       78999999975 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   4.5e-05       0.2     162     236 ..     147     222 ..     132     232 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.5e-05
                     TrwB_AAD_bind 162 eeaer.taasiratlatnlevlelLaekgerFSireWleeedesgwlfltskaeqrallrpllsawldlaikalls 236
                                       ee++r   + ir  + tnl ++   +  +++ Si e ++ ++++  lflt++ +  + +  l+    d+ ik+l +
  gi|298674911|ref|YP_003726661.1| 147 EENDRlRNSRIRHHFLTNLFAFTEFRRIKSKKSIDELIKYHKKHHYLFLTYNIKIYNEMESLIKNCFDIPIKTLFD 222
                                       4455534567***************9777777*************************************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       934  (0.0520944); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2342.17
//
Query:       gi|298674912|ref|YP_003726662.1|  [L=299]
Description: beta-Ig-H3/fasciclin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.2e-79  263.0   1.7    4.9e-39  133.5   0.1    2.1  2  Fasciclin  Fasciclin domain
     0.0014   18.7  11.8     0.0091   16.1   1.1    2.9  2  DUF211     Uncharacterized ArCR, COG1888
  ------ inclusion threshold ------
       0.17   12.2   0.1          7    7.0   0.0    2.4  2  SbcCD_C    Putative exonuclease SbcCD, C subunit


Domain annotation for each model (and alignments):
>> Fasciclin  Fasciclin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.1   0.2   1.8e-41   1.1e-37       2     128 .]      40     159 ..      39     159 .. 0.97
   2 !  133.5   0.1   8.2e-43   4.9e-39       2     128 .]     179     299 .]     178     299 .] 0.98

  Alignments for each domain:
  == domain 1  score: 129.1 bits;  conditional E-value: 1.8e-41
                                       GGHHHHHHHHTTTCCCCCTCSSSSEEEEEE-HHHHCCCHHHHHHHHHTCHHHHHHHHHTTEEESSS-HHHHHHHHEE CS
                         Fasciclin   2 dlstfvsllekaglaeeLnkkdgglTvFaPtneAfaklppellakllndkkklkeiLkyHvvpetvsssalkkaset 78 
                                        ++t+v+++++a+l+e+L +++g++TvFaPt+eAf+klp+++l++llndk+kl+++L+yHvv++++++++++++  +
  gi|298674912|ref|YP_003726662.1|  40 SFNTLVQAVQEAELVETL-SGEGPFTVFAPTDEAFDKLPEGTLEELLNDKEKLRKVLTYHVVSGKYMANEVVEM-DS 114
                                       699***************.888***************************************************9.** PP

                                       EECCTTSSEEEEEEEGGTTEEEETTEEEEEEEEEEESSEEEEEESS-TSX CS
                         Fasciclin  79 latllegaklrvniekgngtvtvngkarvvrsdieatngvihvidkvLlp 128
                                       ++t ++g++l+++ +   g v+vn+ a+v+++die++ngvih idkv+lp
  gi|298674912|ref|YP_003726662.1| 115 IKT-VQGENLSITAN---GGVMVND-ANVTQTDIESSNGVIHAIDKVILP 159
                                       ***.**********9...67*****.**********************98 PP

  == domain 2  score: 133.5 bits;  conditional E-value: 8.2e-43
                                       GGHHHHHHHHTTTCCCCCTCSSSSEEEEEE-HHHHCCCHHHHHHHHHTCHHHHHHHHHTTEEESSS-HHHHHHHHEE CS
                         Fasciclin   2 dlstfvsllekaglaeeLnkkdgglTvFaPtneAfaklppellakllndkkklkeiLkyHvvpetvsssalkkaset 78 
                                        ++t+v+++++agl+++L ++dg++TvFaPt+eAf+klp+++ ++ll+d+++l+++L+yHvv++++++++++++ e+
  gi|298674912|ref|YP_003726662.1| 179 SFNTLVQAVQAAGLENTL-RGDGPYTVFAPTDEAFEKLPEGTIENLLADEEQLTNVLTYHVVSGEYMANEVVEM-ES 253
                                       699***************.777***************************************************9.** PP

                                       EECCTTSSEEEEEEEGGTTEEEETTEEEEEEEEEEESSEEEEEESS-TSX CS
                         Fasciclin  79 latllegaklrvniekgngtvtvngkarvvrsdieatngvihvidkvLlp 128
                                       ++t l+g++l+++++  + +v + + a+vv++di+++ngvihvid+vL+p
  gi|298674912|ref|YP_003726662.1| 254 IET-LQGSTLEITTT--DSEVNIGN-ATVVQTDIKCSNGVIHVIDEVLIP 299
                                       ***.***********..99******.**********************98 PP

>> DUF211  Uncharacterized ArCR, COG1888
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   1.1   1.5e-06    0.0091      37      87 ..     109     165 ..      92     167 .. 0.76
   2 !    6.4   3.8    0.0017        10      20      79 ..     244     297 ..     230     298 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.5e-06
                                       EEEE-....SSEEEEEEEEEESSE..-HHHHHHHHHCTT-EEEEEEEEEEESS---- CS
                            DUF211  37 vkevD....ketenlkitieGeni..dyeeieeaieelggvihSiDevvaGkkivee 87 
                                       v+e+D    ++ enl+it +G  +  d +  ++ ie+ +gvih iD+v+   ++ e+
  gi|298674912|ref|YP_003726662.1| 109 VVEMDsiktVQGENLSITANGGVMvnDANVTQTDIESSNGVIHAIDKVILPPSMTET 165
                                       6677733223668999999987765466667788**************987777765 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0017
                                       HHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHCTT-EEEEEEEEE CS
                            DUF211  20 lakklaelegvdgvnitvkevDketenlkitieGenidyeeieeaieelggvihSiDevv 79 
                                       +a+++ e+e+++  + +  e+ ++   ++i       +   +++ i+  +gvih iDev 
  gi|298674912|ref|YP_003726662.1| 244 MANEVVEMESIETLQGSTLEITTTDSEVNIG------NATVVQTDIKCSNGVIHVIDEVL 297
                                       5555555555555555555554433333332......45679999*************96 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.023   1.4e+02      70      85 ..      70      85 ..      22      87 .. 0.87
   2 ?    7.0   0.0    0.0012         7      32      85 ..     174     224 ..     161     226 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.023
                           SbcCD_C 70 DEAFsklDeesiatll 85
                                      DEAF+kl e ++++ll
  gi|298674912|ref|YP_003726662.1| 70 DEAFDKLPEGTLEELL 85
                                      *******999998887 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0012
                           SbcCD_C  32 tlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatll 85 
                                       + S G   +l++ + aa+l   ++ +    p   +   DEAF+kl e +i++ll
  gi|298674912|ref|YP_003726662.1| 174 AISEGSFNTLVQAVQAAGLENTLRGD---GPYTVFAPTDEAFEKLPEGTIENLL 224
                                       56778888999999999999999995...677788889*******999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       796  (0.0443973); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2166.67
//
Query:       gi|298674913|ref|YP_003726663.1|  [L=91]
Description: hypothetical protein Metev_0976 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00089   19.1   1.3    0.00089   19.1   1.3    1.3  1  DUF5381      Family of unknown function (DUF5381)
  ------ inclusion threshold ------
      0.047   13.8   7.1      0.053   13.6   7.1    1.2  1  ECF_trnsprt  ECF transporter, substrate-specific component


Domain annotation for each model (and alignments):
>> DUF5381  Family of unknown function (DUF5381)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   1.3   9.9e-08   0.00089      29      80 ..       2      52 ..       1      59 [. 0.92

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 9.9e-08
                           DUF5381 29 llfeglkfeskysllyiiigiigtifgliillmvlpallkkGkvlftikeGe 80
                                      ++++ + +++   +l+i+ g+ g i+g+ +++  ++++l+ G+ +f+i  G+
  gi|298674913|ref|YP_003726663.1|  2 VIIKEIDISGLAKILAIANGTAGFIYGMFTTMAAFSGYLP-GEGIFSILLGQ 52
                                      577889999999****************************.*******9886 PP

>> ECF_trnsprt  ECF transporter, substrate-specific component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   7.1   5.9e-06     0.053      41     100 ..      21      84 ..       1      90 [. 0.63

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.9e-06
                                       HCTTCHHHHHHHHHHHHHHHHCHT-SSTTHHHH.........HHHHHHHHCHHHHHHHHHHCCCHTTHH CS
                       ECF_trnsprt  41 llfGpikGailgiitsvlkailtggtgalssfv.........piaflsriligliagllykkgkkknlk 100
                                          G i+G++  +    ++  l +g g++s+++         +++ +s+ ligliag++y+k   +  k
  gi|298674913|ref|YP_003726663.1|  21 GTAGFIYGMFTTM--AAFSGYL-PGEGIFSILLgqwsivmlpVFYGVSGYLIGLIAGYIYNK--TVGSK 84 
                                       3444444444444..4445555.5666666555677777899******************55..44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 628.45
//
Query:       gi|298674914|ref|YP_003726664.1|  [L=208]
Description: hypothetical protein Metev_0977 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0031   17.5   0.2     0.0055   16.7   0.2    1.4  1  YyzF      YyzF-like protein


Domain annotation for each model (and alignments):
>> YyzF  YyzF-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   3.1e-07    0.0055       9      43 ..      81     121 ..      77     125 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.1e-07
                              YyzF   9 AlDefVdeyeqaPdiekleeve......klsktCefCekpA 43 
                                        +D+f +  e++P+++kl++ e       ++++C fCe++ 
  gi|298674914|ref|YP_003726664.1|  81 FIDTFNQSLEDYPELNKLDDMEqnavfqIEPVSCVFCENQN 121
                                       589999999*************99999989********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       809  (0.0451224); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1601.72
//
Query:       gi|298674915|ref|YP_003726665.1|  [L=39]
Description: hypothetical protein Metev_0978 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.21s 00:00:00.53 Elapsed: 00:00:00.34
# Mc/sec: 338.59
//
Query:       gi|298674916|ref|YP_003726666.1|  [L=1220]
Description: 5-oxoprolinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.8e-207  689.8   0.2   3.5e-207  688.9   0.2    1.5  1  Hydantoinase_B  Hydantoinase B/oxoprolinase
   1.4e-119  398.7   0.0     3e-119  397.6   0.0    1.6  1  Hydantoinase_A  Hydantoinase/oxoprolinase
    4.1e-66  222.1   0.1    1.2e-64  217.3   0.0    2.4  2  Hydant_A_N      Hydantoinase/oxoprolinase N-terminal region
  ------ inclusion threshold ------
        0.1   12.0   0.8       0.35   10.3   0.1    2.0  2  F-actin_cap_A   F-actin capping protein alpha subunit


Domain annotation for each model (and alignments):
>> Hydantoinase_B  Hydantoinase B/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  688.9   0.2  7.8e-211  3.5e-207       1     514 [.     707    1211 ..     707    1213 .. 0.98

  Alignments for each domain:
  == domain 1  score: 688.9 bits;  conditional E-value: 7.8e-211
                    Hydantoinase_B    1 DpitlevfrnrlmsiaeemgrtlqrtaiSpnikerlDfscalfdadgelvaqaphipvhlgsmseavkavlekfe 75  
                                        Dp+ le+f+nr+ms+ae+mg tlq+ta+S+niker+Dfscalfd++g+lva+aphipvh+gsmse+vk+++++  
  gi|298674916|ref|YP_003726666.1|  707 DPVILEIFNNRFMSVAEQMGYTLQNTAHSVNIKERRDFSCALFDKKGNLVANAPHIPVHIGSMSECVKSLINNKG 781 
                                        9**********************************************************************9886 PP

                    Hydantoinase_B   76 gelkpGDvlltNdPyaggtHlpDitvitPvfhege.lvffvasraHhaDiGGitpGsmppdateifeEGlrippv 149 
                                         ++k+GDv+++N+Py+ggtHlpDitv+tPvf +++ +  ++asr+HhaDiGGitpGsmppd+++i+eEG+  + +
  gi|298674916|ref|YP_003726666.1|  782 TDMKKGDVYMLNSPYHGGTHLPDITVVTPVFDNDNnIYSYIASRGHHADIGGITPGSMPPDSKNIHEEGVFTDGI 856 
                                        79*****************************87779*************************************** PP

                    Hydantoinase_B  150 klveege.leedvlelllanv...RtpednlgDlkAqiaanqvgerrlkelieeyGldtveaamdeildnaerav 220 
                                        klv+ g+ +e++++++l +     R+pe+n++Dl+Aqiaan++g ++lk+l ++y+l+t++a+m++++dnae  v
  gi|298674916|ref|YP_003726666.1|  857 KLVDSGHfQENELFKWLNSGDypaRNPEQNVSDLHAQIAANEKGSQELKNLKDQYSLETIKAYMEYVQDNAESEV 931 
                                        ******************88899**************************************************** PP

                    Hydantoinase_B  221 raalaelpdgtyeaedylddgipikvtvtidgde..atvDftgtspqvkgniNaplavtlsaviyvlrclvdedi 293 
                                         +++ +l++g   +++ +ddg+ ikv+++id+++  a +Dftgts q+ +n+Nap +v+++a++yv+r+++++di
  gi|298674916|ref|YP_003726666.1|  932 CKVIGKLNNGI--FSYQMDDGSIIKVQIKIDNENksACIDFTGTSAQLFNNFNAPVSVCKAAILYVFRTMIESDI 1004
                                        **********5..5566****999999999888888*************************************** PP

                    Hydantoinase_B  294 plNeGclrpievklpegsllnpsepaavvggnvetsqrvvdvvlkalaqalpervaAasqgtmnnltfggvderg 368 
                                        plN+Gclrpi++++p+gs+lnp +paavv+gnvetsq +vd++++al+      v+Aasqgtmnn+tfg      
  gi|298674916|ref|YP_003726666.1| 1005 PLNDGCLRPIDIIVPKGSMLNPVYPAAVVAGNVETSQYIVDTLFGALG------VMAASQGTMNNFTFG------ 1067
                                        ************************************************......***************...... PP

                    Hydantoinase_B  369 geffgyyetiagGaGArpgkdGasavhvhmtntrntdvEilErryPvlverfelrpdsgGaGkyrGGdGvvreie 443 
                                        ++f +yyeti+gG+GA++g++G++avh+hmtn+++td+E+lE+ryPv++e+f++r++sgG G y+GG+G++r+i+
  gi|298674916|ref|YP_003726666.1| 1068 NKFHQYYETICGGSGAGAGFHGTDAVHTHMTNSKITDPEVLESRYPVILEEFSIRKNSGGCGMYKGGNGIIRKIR 1142
                                        5788*********************************************************************** PP

                    Hydantoinase_B  444 flepevtvsilserrvfapwGlaGGepGargrvvlnllvr..geeenlggkatvelkagdvlvietpGGGGyG 514 
                                        fle+ + ++ils++r+++p+Gl GG pG++g+   n+++r  g+++++ggka++++ ++dv++ietpGGGGyG
  gi|298674916|ref|YP_003726666.1| 1143 FLEE-MDAAILSSHRKYPPFGLYGGIPGKCGS---NRVIRkdGSVIEMGGKAKFRVYKDDVFTIETPGGGGYG 1211
                                        ***7.***************************...9999999******************************* PP

>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  397.6   0.0  6.7e-123    3e-119       1     289 [.     206     505 ..     206     507 .. 0.99

  Alignments for each domain:
  == domain 1  score: 397.6 bits;  conditional E-value: 6.7e-123
                    Hydantoinase_A   1 rtetavvnAylspilreylesvekslekrgak........arlmvmqsdGglvsadearkkpvetilSGPaaGvvga 69 
                                       r+et++v+Aylsp+l +y++ + + l++++ +        +rlm+mqs+Gglv+ad +++k  ++ilSGPa+Gvvga
  gi|298674916|ref|YP_003726666.1| 206 RAETTIVDAYLSPVLGRYINDIISMLKNNQTHekddetekTRLMFMQSNGGLVNADSFQGK--DCILSGPAGGVVGA 280
                                       899*************************998899***************************..************** PP

                    Hydantoinase_A  70 aatsklagekkvItfDmGGTstDvslikdgevevsleteiagvkvrlpaldirtvgagGgsilvvdeggklrvgpes 146
                                       + ts +ag++kvI fDmGGTstDv++++ ge+e+s+e +i+g+ +r+p+++i+t++ gGgsil +++g+++rvgp+s
  gi|298674916|ref|YP_003726666.1| 281 VTTSSMAGFDKVISFDMGGTSTDVAHYR-GEYERSFENIIGGIHLRSPMMQIHTIASGGGSIL-HFDGERFRVGPDS 355
                                       ****************************.**********************************.************* PP

                    Hydantoinase_A 147 agadpgpacyrkGgteltvTDanlvLGrlqpedfls..gpdgdqkldvelarrafeelakelnlk......veevAe 215
                                       ag+dpgpacyr+Gg +ltvTD+nl+L++++pe+f+   gpd + +ld++l+ ++f+el +++         +eevAe
  gi|298674916|ref|YP_003726666.1| 356 AGSDPGPACYRRGG-PLTVTDCNLMLNKINPEYFPHvfGPDANLPLDNQLVFEKFDELVDKITSYtgknhtIEEVAE 431
                                       **************.***********************************************98899********** PP

                    Hydantoinase_A 216 gilsvavenmanavrklsvergldpkeltlvvfGGaGaqhaaalaeelgvkkvivppyagvlsalGmalAdvre 289
                                       g+l+vavenmana++k++ +rg+d+ke++l++fGGaG+qha+ +a++lg++k++++pyagvlsa+G++lAd++e
  gi|298674916|ref|YP_003726666.1| 432 GFLDVAVENMANAIKKITTQRGYDIKEYALCCFGGAGGQHACKVADKLGINKIFIHPYAGVLSAYGIGLADQKE 505
                                       ***********************************************************************987 PP

>> Hydant_A_N  Hydantoinase/oxoprolinase N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.3   0.0   2.7e-68   1.2e-64       2     178 .]       8     187 ..       7     187 .. 0.99
   2 ?    2.3   0.0     0.027   1.2e+02       3      18 ..     294     309 ..     292     321 .. 0.82

  Alignments for each domain:
  == domain 1  score: 217.3 bits;  conditional E-value: 2.7e-68
                        Hydant_A_N   2 igIDvGGTfTDavaldekeeevavlKllst.....pdavaegirealeevleesiprtskidvvrmGTTvatNalle 73 
                                       ++ID+GGTfTD+va +++ ++++++Kllst      da+++gi+++l+++ +++ p  +kidv++mGTTv tNalle
  gi|298674916|ref|YP_003726666.1|   8 FWIDRGGTFTDIVAKKPN-GKLVTHKLLSTnpeqyHDAAIQGIKDILNSSNDAPVP-ADKIDVIKMGTTVGTNALLE 82 
                                       8***************99.99********************************999.******************** PP

                        Hydant_A_N  74 rkgervaLittkgfrdlleigrqnrpdlfelrikkplvlyeevvevderveadgevlkpldeeevrealkalkaagv 150
                                       rkge+++L++tkgf+d+l+ig+qnrpd+f+l+i kp  ly+ v+ev++r++adg+v++pl+ e+vre+lk+++++g 
  gi|298674916|ref|YP_003726666.1|  83 RKGEKTVLVITKGFKDALRIGYQNRPDIFALEIIKPQQLYDCVIEVSGRYNADGQVINPLEFESVREKLKSAYDSGL 159
                                       ***************************************************************************** PP

                        Hydant_A_N 151 esiavvllhSylnpehElrvaeiareig 178
                                       +sia++++h+y++p+hE+++aeia+eig
  gi|298674916|ref|YP_003726666.1| 160 NSIAIAFMHAYRYPSHEIKIAEIAKEIG 187
                                       *************************986 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.027
                        Hydant_A_N   3 gIDvGGTfTDavalde 18 
                                         D+GGT TD+  +++
  gi|298674916|ref|YP_003726666.1| 294 SFDMGGTSTDVAHYRG 309
                                       56********987765 PP

>> F-actin_cap_A  F-actin capping protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   7.7e-05      0.35      46     123 ..     564     645 ..     504     694 .. 0.74
   2 ?   -0.7   0.1      0.17   7.8e+02      93     129 ..     900     943 ..     876     984 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 7.7e-05
                                       T-EEE.ETTE..EEE--STTEEETTEEEEGGGTEEEEEETTTTEEEEEEE--S-...GGGHHHHHHHHHHHHHHHHH CS
                     F-actin_cap_A  46 lvtve.lpgssekvliseanklgeeryvdpkskksfkfdhlkqkasdvesvele...seleelrkalekalekYvke 118
                                       + +v+ ++g +++++is+ nk +++r+   + +k++ ++ ++ +++ +++++ e   + +++    l  ++e ++++
  gi|298674916|ref|YP_003726666.1| 564 TLMVDfVEGMDKESIISNFNKKHKQRFGFMSPEKTVVVEAVSMEVIGASDMKSEpvqKISKNNECVLTGNIEMFTDN 640
                                       33444268999*********************************999998844432134445556678899999999 PP

                                       H-TT- CS
                     F-actin_cap_A 119 hYpsg 123
                                       +Y++ 
  gi|298674916|ref|YP_003726666.1| 641 KYHDT 645
                                       99974 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.17
                                       EE--S-GGGHHHHHHHHHHHHHHHHHH-TT-EEEEE.......E CS
                     F-actin_cap_A  93 esveleseleelrkalekalekYvkehYpsgvasvy.......p 129
                                        s el++ + ++  +  ka  +Yv+++ +s v++v+        
  gi|298674916|ref|YP_003726666.1| 900 GSQELKNLKDQYSLETIKAYMEYVQDNAESEVCKVIgklnngiF 943
                                       33345556667777788888889999988888888844444440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.73u 0.32s 00:00:01.05 Elapsed: 00:00:00.45
# Mc/sec: 8086.41
//
Query:       gi|298674917|ref|YP_003726667.1|  [L=139]
Description: hypothetical protein Metev_0980 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1189.54
//
Query:       gi|298674918|ref|YP_003726668.1|  [L=346]
Description: hypothetical protein Metev_0981 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-09   38.1   5.7    1.7e-09   38.1   5.7    3.3  4  DUF4367    Domain of unknown function (DUF4367)
    6.5e-09   35.8   1.6    6.3e-06   26.0   0.0    2.5  2  LolA_like  Outer membrane lipoprotein-sorting protein
    0.00073   18.9   0.3     0.0035   16.7   0.0    2.1  2  DUF2092    Predicted periplasmic protein (DUF2092)
     0.0029   17.3   2.3       0.05   13.3   0.3    2.3  2  LolA       Outer membrane lipoprotein carrier protein LolA
  ------ inclusion threshold ------
      0.038   13.4   0.6       0.15   11.5   0.0    2.1  3  DUF1571    Protein of unknown function (DUF1571)


Domain annotation for each model (and alignments):
>> DUF4367  Domain of unknown function (DUF4367)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   1.2      0.45   1.6e+03      21      52 ..      41      73 ..      25     128 .. 0.53
   2 ?   -3.4   0.0       3.8   1.4e+04      22      35 ..     142     155 ..     137     166 .. 0.57
   3 ?   -1.3   0.1      0.81   2.9e+03      15      38 ..     193     216 ..     180     236 .. 0.68
   4 !   38.1   5.7   4.8e-13   1.7e-09       3     110 .]     241     342 ..     239     342 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.45
                           DUF4367 21 dsesalleYkdengelisfs.iskqskeesqkl 52
                                        +++ ++  +++ ++i+    +k+ ++e+  l
  gi|298674918|ref|YP_003726668.1| 41 YTYTMNITLPNNSTNYIVSEvSYKEPGKEKMTL 73
                                      444444444333333333332222222333333 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.8
                           DUF4367  22 sesalleYkdenge 35 
                                       ++s+++++k + ++
  gi|298674918|ref|YP_003726668.1| 142 KQSYIMQFKLNTQQ 155
                                       45556666544433 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.81
                           DUF4367  15 ktnisedsesalleYkdengelis 38 
                                       + +i+e+ ++ ++eY+  ++  i+
  gi|298674918|ref|YP_003726668.1| 193 DFKINENVSDSVFEYTPPENAIIM 216
                                       557888888888888766666655 PP

  == domain 4  score: 38.1 bits;  conditional E-value: 4.8e-13
                           DUF4367   3 eptylPeGykfkktnisedsesalleYkdengelisfsiskqskeesqklsidtedaevekieingikatyyekedg 79 
                                        ptylP++y+    + + +++s++++Y+++    i ++ +  +++  ++  i       e+++i+  ++ y      
  gi|298674918|ref|YP_003726668.1| 241 IPTYLPKNYEMDYIQYVPEDSSVVIYYENDRYRDILVVLQRPYMKPEKEPRIF----GQENVTIGDDEGIYSNRTR- 312
                                       69*************************99555555555344455444444444....45899******99998666. PP

                           DUF4367  80 eyvlvwedegvvytlsg.niskeelikiaesi 110
                                         +l w+++ v y l++ +++k+elikiaes+
  gi|298674918|ref|YP_003726668.1| 313 --TLEWNNKSVEYILQSeKLDKDELIKIAESM 342
                                       ..5****************************8 PP

>> LolA_like  Outer membrane lipoprotein-sorting protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.7   0.00052       1.8     125     174 ..      25      70 ..      17      76 .. 0.88
   2 !   26.0   0.0   1.8e-09   6.3e-06      67     136 ..     126     195 ..      80     241 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00052
                                       -EEEEEEEEEEEEETTEEEEEEEEEEETTT--EEEEEEEEEEE--.--GG CS
                         LolA_like 125 kllKtltvsdiekidgrwtptkmtmedlkkghkTvleisevefdkglpdk 174
                                       +++K++t++++e+id++ + +++t+ +    ++T   +sev+++++ ++k
  gi|298674918|ref|YP_003726668.1|  25 DQIKQTTIEKFETIDDYTYTMNITLPN----NSTNYIVSEVSYKEPGKEK 70 
                                       689*********************998....9999999999999877666 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 1.8e-09
                                       CCCEEEEEEEEEEETTEEEEEEEEEESS..TTSSECEEEEEEETTT--EEEEEEEETTS-EEEEEEEEEEE CS
                         LolA_like  67 vedythellgeeevggkdcyvleltpkd.aadvsYskivlwvdketylplkvefydksgkllKtltvsdie 136
                                       +++ + ellg+e+++gk+ y+++ + ++ ++    sk+++w+ ke+ylp+k+e+y   ++l+ t+ ++d++
  gi|298674918|ref|YP_003726668.1| 126 INNSSPELLGSETLNGKQSYIMQFKLNTqQSIIPLSKTKTWIGKENYLPVKSELYIN-DTLIITAFFRDFK 195
                                       5677889****************99999344556*********************85.5677777776665 PP

>> DUF2092  Predicted periplasmic protein (DUF2092)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.14     5e+02      50      82 ..      69     101 ..      24     110 .. 0.67
   2 !   16.7   0.0   9.8e-07    0.0035     153     207 ..     164     214 ..     117     217 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.14
                           DUF2092  50 dklrvdtsgdekdrefyyDGktftlydkaenvY 82 
                                        k+  ++  +++d  ++ +G t+ +y++++n+ 
  gi|298674918|ref|YP_003726668.1|  69 EKMTLHRYPENTDFTAVNNGSTIWIYNSEDNIA 101
                                       456666667788888899999999999999875 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 9.8e-07
                           DUF2092 153 qlWIsqgdkpLprkivityktdpgapqytaefsdWnldpeipedtFrftpPkgAr 207
                                         WI+++++ Lp k      +d   + +ta f+d+++++++++++F++tpP++A 
  gi|298674918|ref|YP_003726668.1| 164 KTWIGKENY-LPVKSELY-IND--TLIITAFFRDFKINENVSDSVFEYTPPENAI 214
                                       558888888.88776543.333..367899***********************95 PP

>> LolA  Outer membrane lipoprotein carrier protein LolA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.011        41     127     158 ..      28      59 ..      16      66 .. 0.83
   2 !   13.3   0.3   1.4e-05      0.05      48     165 .]      83     208 ..      60     208 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.011
                                       ETTEEEEEEEEETT--EEEEEEEEEEES---- CS
                              LolA 127 kkgllkqlkvvdaqGqrttitfsnvkenakla 158
                                       k++++++++++d++ ++ +it+ n  +n+ ++
  gi|298674918|ref|YP_003726668.1|  28 KQTTIEKFETIDDYTYTMNITLPNNSTNYIVS 59 
                                       4555******************9999887665 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.4e-05
                                       EEEEETTEEEEEETTTTEEEEEE.......HHHHTTT-GGGGGGS-HH.HHTTTEEEEEEEETTEEEEEEEESSS-S CS
                              LolA  48 livsdgktvwlydpdleqvties.......lkqalsktplvlLledka.klskdynvsvkkeqdldtltlkpkakda 116
                                       + v +g t+w+y+++ + +t+++         ++l+   ++ L+++ + +l  + +++  k+  + +++l+ +++  
  gi|298674918|ref|YP_003726668.1|  83 TAVNNGSTIWIYNSEDNIATRNPsgvtsllELNPLNYRSFIKLINNSSpELLGSETLN-GKQSYIMQFKLNTQQSII 158
                                       5699***************999877666667789999999999955441555665666.99**************** PP

                                       SECEEEEEE.ETTE.EEEEEEEETT--EEEEEEEEEEES----GGGG--- CS
                              LolA 117 nlsritigfdkkgl.lkqlkvvdaqGqrttitfsnvkenakladdlFkft 165
                                        ls+ + ++ k+++ + + +++ ++   +t  f+++k n++++d++F++t
  gi|298674918|ref|YP_003726668.1| 159 PLSKTKTWIGKENYlPVKSELYINDTLIITAFFRDFKINENVSDSVFEYT 208
                                       **************99*******************************986 PP

>> DUF1571  Protein of unknown function (DUF1571)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.27   9.8e+02     129     173 ..      25      69 ..      13      87 .. 0.72
   2 ?   11.5   0.0   4.1e-05      0.15     115     204 ..     128     210 ..     107     214 .. 0.85
   3 ?   -2.6   0.1      0.85     3e+03     116     131 ..     262     277 ..     247     335 .. 0.52

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.27
                           DUF1571 129 rrvtalevehpskeeqvefskaelllDeelklpirveaydwPaae 173
                                        ++ + ++e+ +  +++++ +  +l  + ++++++  +y+ P +e
  gi|298674918|ref|YP_003726668.1|  25 DQIKQTTIEKFETIDDYTYTMNITLPNNSTNYIVSEVSYKEPGKE 69 
                                       556667777777788888888888888888888888888777444 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 4.1e-05
                           DUF1571 115 eaevelkreerldgrrvtalevehpskeeqvefskaelllDeelklpirveaydwPaaeddseelvEeyeyadlkln 191
                                       +++ el   e+l+g++  +++ +  +++   + sk+++++ +e+ lp++ e y        + +l+    ++d k+n
  gi|298674918|ref|YP_003726668.1| 128 NSSPELLGSETLNGKQSYIMQFKLNTQQSIIPLSKTKTWIGKENYLPVKSELY-------INDTLIITAFFRDFKIN 197
                                       566667778999*****************************************.......56778888889999999 PP

                           DUF1571 192 vgltdadFdpanp 204
                                       ++++d+ F+ + p
  gi|298674918|ref|YP_003726668.1| 198 ENVSDSVFEYTPP 210
                                       9999999987766 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.85
                           DUF1571 116 aevelkreerldgrrv 131
                                       + v +++++r  +  v
  gi|298674918|ref|YP_003726668.1| 262 SVVIYYENDRYRDILV 277
                                       3344444444433333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2413.57
//
Query:       gi|298674919|ref|YP_003726669.1|  [L=82]
Description: hypothetical protein Metev_0982 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-09   35.8  23.5    7.8e-09   35.6  23.5    1.0  1  BofA      SigmaK-factor processing regulatory protein BofA


Domain annotation for each model (and alignments):
>> BofA  SigmaK-factor processing regulatory protein BofA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6  23.5   4.4e-13   7.8e-09       3      75 .]       9      78 ..       7      78 .. 0.96

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 4.4e-13
                              BofA  3 illlllvikllkkplkillkllinavlGlvlLflvNllgavfglhipiNlitaliagflGipGvilLillklf 75
                                      i+++l+++ +++  +k++ +l++na++Glv+Lf +N    +fgl i++ ++ +li++++G  G++l+i+l++f
  gi|298674919|ref|YP_003726669.1|  9 IIIALIALAVIYFFFKTFKSLIVNAIVGLVILFGAN---MLFGLGIAYTWLVILISAIGGALGALLIIVLHVF 78
                                      89999*******************************...88*****************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1408  (0.078532); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 634.73
//
Query:       gi|298674920|ref|YP_003726670.1|  [L=570]
Description: signal transduction histidine kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-29  101.7   4.6    1.8e-29  101.7   4.6    2.5  2  HisKA_2          Histidine kinase
    5.2e-24   84.5  11.7    7.8e-11   42.2   0.0    4.4  5  PAS_9            PAS domain
    4.7e-22   78.1   0.0    4.4e-17   62.2   0.0    3.8  3  PAS_3            PAS fold
    1.9e-16   60.1   0.1    1.1e-05   25.4   0.0    4.3  3  PAS              PAS fold
    7.3e-16   58.4   0.0    1.6e-05   25.1   0.0    3.8  3  PAS_4            PAS fold
    1.9e-11   43.7   0.0    2.5e-05   24.2   0.0    2.6  2  PAS_8            PAS domain
    3.3e-11   43.7   0.4      1e-09   38.9   0.2    2.9  2  HATPase_c        Histidine kinase-, DNA gyrase B-, and HSP90-
      1e-07   32.5   0.1    2.9e-07   31.1   0.1    1.9  1  HWE_HK           HWE histidine kinase
    1.3e-07   31.8   0.2       0.32   11.1   0.0    3.8  3  PAS_11           PAS domain
     0.0019   18.2   0.0     0.0044   17.0   0.0    1.6  1  HATPase_c_2      Histidine kinase-like ATPase domain
     0.0045   16.8   0.1     0.0045   16.8   0.1    2.3  3  HATPase_c_3      Histidine kinase-, DNA gyrase B-, and HSP90-
  ------ inclusion threshold ------
       0.06   13.9   5.3       0.14   12.8   0.0    3.7  3  PAS_10           PAS domain
        0.1   12.7   3.0         15    5.8   0.2    3.8  3  PAS_7            PAS fold
       0.16   11.8   0.1        0.3   10.9   0.1    1.4  1  FdhE             Protein involved in formate dehydrogenase fo
       0.53    9.5   7.0        1.5    8.0   0.1    2.4  2  Cache_3-Cache_2  Cache 3/Cache 2 fusion domain
        3.5    7.5   8.3        7.4    6.4   0.1    2.6  2  ACCA             Acetyl co-enzyme A carboxylase carboxyltrans
        5.6    6.9  10.6        3.8    7.4   4.0    3.3  4  EMP24_GP25L      emp24/gp25L/p24 family/GOLD


Domain annotation for each model (and alignments):
>> HisKA_2  Histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       2.9   3.1e+03      13      43 ..     324     354 ..     323     377 .. 0.68
   2 !  101.7   4.6   1.7e-32   1.8e-29       1      76 []     379     454 ..     379     454 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.9
                           HisKA_2  13 isslLslqarkakdeevkealresqnRvlsi 43 
                                       i++++s+ ++ +++ +++e ++e+ n+ + i
  gi|298674920|ref|YP_003726670.1| 324 IIGIISVSSDITDKVRAEEKIKEYTNKLEEI 354
                                       5666777777777777777777777766544 PP

  == domain 2  score: 101.7 bits;  conditional E-value: 1.7e-32
                           HisKA_2   1 EihHRvkNnLqvisslLslqarkakdeevkealresqnRvlsialiheeLyksedletvdfseylekLvenlfksy 76 
                                       E+hHR+kNnLqvissl++lq++k++deev ea+ ++qnR+ s++l+h++Ly++++l++++f++y+++L+++l ++y
  gi|298674920|ref|YP_003726670.1| 379 ELHHRIKNNLQVISSLINLQSEKFDDEEVYEAFIDTQNRIVSMSLVHQKLYQTSNLNSINFKDYIQDLLTHLTRLY 454
                                       99**********************************************************************9876 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.2    0.0031       3.3      40     104 .]      34      99 ..       4      99 .. 0.78
   2 !   42.2   0.0   7.4e-14   7.8e-11       2     104 .]     123     222 ..     122     222 .. 0.95
   3 !   40.0   0.2   3.5e-13   3.7e-10       2     104 .]     239     336 ..     238     336 .. 0.89
   4 ?   -1.7   0.2       3.3   3.5e+03      48      83 ..     360     398 ..     345     416 .. 0.50
   5 ?   -1.9   0.0       3.7   3.9e+03      82      82 ..     532     532 ..     481     568 .. 0.53

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0031
                             PAS_9  40 f..vtdpeanerlraaleqgrkkerevevvlirkngetfw.vlltaspvkdddgelvgiivilrDite 104
                                       +  ++ p+ +++l+++l++ +   +e e+ +irk+ +++  v+ + + + d+d++ + + +  +Dite
  gi|298674920|ref|YP_003726670.1|  34 VhpEDIPYMENKLQDCLNNSS--SYEIELRIIRKDTGEIRnVKTHGRIISDNDNNPIKMYGATQDITE 99 
                                       445555777889999999999..***********99777735599999999999999999******98 PP

  == domain 2  score: 42.2 bits;  conditional E-value: 7.4e-14
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetf 76 
                                       d+i++ n +g+ l +Ne+a + lGys++e+l     d+   ++++  +e+++++le+g      +e v+i++ng+++
  gi|298674920|ref|YP_003726670.1| 123 DAIFVQNLQGNFLNVNETAVKRLGYSRDELLSMAAQDVDykYPSSGVKEKIDEILETGL---LKFESVHITNNGTKI 196
                                       899**99**********************9998877766888****************9...*************** PP

                             PAS_9  77 wvlltaspvkdddgelvgiivilrDite 104
                                       +v+++ + ++  d+  v+  +i rDite
  gi|298674920|ref|YP_003726670.1| 197 PVEVNSTLIHYRDKPAVL--SIARDITE 222
                                       *************99999..*******8 PP

  == domain 3  score: 40.0 bits;  conditional E-value: 3.5e-13
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetf 76 
                                       ++i++ n++g+i ++N+a+ +++G++ +e++g ++  l+  ++d  + + ++ ++++g+   +e+ +++ ++     
  gi|298674920|ref|YP_003726670.1| 239 EMIVFHNTEGKIKWCNKAFSKFTGFKQDELIGAYCYKLLhnKSDICDCCPISYIVKTGK--HHEKITTFPNN----- 308
                                       6788888***999**************************88888888888888888888..66666666666..... PP

                             PAS_9  77 wvlltaspvkdddgelvgiivilrDite 104
                                        ++++  pv+d +g+++gii+++ Dit+
  gi|298674920|ref|YP_003726670.1| 309 VFNIKRDPVRDINGNIIGIISVSSDITD 336
                                       788************************6 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 3.3
                             PAS_9  48 erlraaleqgrk..kerevevvlirkngetfwvl.ltas 83 
                                       +r++++ eq+r+    re e++++ kn+ ++    +++ 
  gi|298674920|ref|YP_003726670.1| 360 NRVEEQTEQIRNaeRMRELELHHRIKNNLQVISSlINLQ 398
                                       444444444444333445555555555533332224444 PP

  == domain 5  score: -1.9 bits;  conditional E-value: 3.7
                             PAS_9  82 a 82 
                                       +
  gi|298674920|ref|YP_003726670.1| 532 I 532
                                       1 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2   0.0   4.1e-20   4.4e-17       2      88 ..       8      93 ..       7      94 .. 0.96
   2 !    6.7   0.0    0.0082       8.6       2      79 ..     135     209 ..     134     216 .. 0.81
   3 ?    4.5   0.0      0.04        42       3      31 ..     252     278 ..     250     281 .. 0.90

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 4.1e-20
                             PAS_3  2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrk.dGeyrwveararvirden 79
                                      i vs+++++i G     l+ +  ++l++vhpeD+++++++lq++l++ ++ye+e Ri+rk  Ge+r v++++r+i d++
  gi|298674920|ref|YP_003726670.1|  8 IIVSNEWRKIHGCNNKVLTYN--KLLQIVHPEDIPYMENKLQDCLNNSSSYEIELRIIRKdTGEIRNVKTHGRIISDND 84
                                      6799**********9999999..*************************************88***************** PP

                             PAS_3 80 gkpvrvigv 88
                                      ++p+++ g 
  gi|298674920|ref|YP_003726670.1| 85 NNPIKMYGA 93
                                      ******995 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0082
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       + v+e+  + lGys++ell+      d+ +    + v+e+++e+l++g  +++e   ++ +G+ + ve   + i+++
  gi|298674920|ref|YP_003726670.1| 135 LNVNETAVKRLGYSRDELLSM--AAQDVDYKYPSSGVKEKIDEILETGL-LKFESVHITNNGTKIPVEVNSTLIHYR 208
                                       67999999*************..66666666667799999999999998.666666699999999999998888666 PP

                             PAS_3  79 n 79 
                                       +
  gi|298674920|ref|YP_003726670.1| 209 D 209
                                       5 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.04
                             PAS_3   3 yvserveeilGyspeellgkveswldlvh 31 
                                        +++++++ +G+ ++el+g    +++l+h
  gi|298674920|ref|YP_003726670.1| 252 WCNKAFSKFTGFKQDELIGA--YCYKLLH 278
                                       599****************9..8999988 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.056        59      30     110 ..      14      94 ..       8      97 .. 0.76
   2 !   25.4   0.0     1e-08   1.1e-05       6     113 .]     117     220 ..     112     220 .. 0.79
   3 !   25.3   0.0   1.1e-08   1.2e-05       2     110 ..     229     331 ..     228     334 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.056
                                       HHHHHSSTHHHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEEEEEEEEETTEEEEE CS
                               PAS  30 aeellGlsreevlgkslldliheedda.elaelleqlleqgeesrageisfklrdgrpihlevraspvrdaggeilg 105
                                       ++++ G + + +   +ll  +h+ed   ++  +l+ +l+++++ +++ + +++  g+++ + ++ + + d + +++ 
  gi|298674920|ref|YP_003726670.1|  14 WRKIHGCNNKVLTYNKLLQIVHPED-IpYMENKLQDCLNNSSSYEIELRIIRKDTGEIRNVKTHGRIISDNDNNPIK 89 
                                       5555555666666666665555555.459********************9999999999999999999999988775 PP

                                       EEEEE CS
                               PAS 106 flgvl 110
                                         g  
  gi|298674920|ref|YP_003726670.1|  90 MYGAT 94 
                                       55555 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 1e-08
                                       HHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEEEC CS
                               PAS   6 ileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda.elaelleqlleqgeesrageisfkl 81 
                                       +++++ d+ifv + +g++l vN++a + lG+sr+e+l+     ++  ++++  ++e++ + le+g   + + + ++ 
  gi|298674920|ref|YP_003726670.1| 117 LFNNMNDAIFVQNLQGNFLNVNETAVKRLGYSRDELLSMA-AQDVDYKYPSsGVKEKIDEILETG-LLKFESVHITN 191
                                       789*********************************9765.557778888855555555555544.44444666677 PP

                                       TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  82 rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                        +g++i++ev+ + +  +++    +l ++rdi
  gi|298674920|ref|YP_003726670.1| 192 -NGTKIPVEVNSTLIHYRDKP--AVLSIARDI 220
                                       .99999999999999999887..888888887 PP

  == domain 3  score: 25.3 bits;  conditional E-value: 1.1e-08
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       + + il+s+ ++i+  +  g+i ++N+a+ +++G++++e++g   + l+h+++d    ++    + +++ +++++i+
  gi|298674920|ref|YP_003726670.1| 229 EKSVILNSTSEMIVFHNTEGKIKWCNKAFSKFTGFKQDELIGAYCYKLLHNKSD--ICDCCPISYIVKTGKHHEKIT 303
                                       56789*********************************************8765..333333333333333333333 PP

                                       EECTTSSEEEEEEEEEEEEETTEEEEEEEEEE CS
                               PAS  79 fklrdgrpihlevraspvrdaggeilgflgvl 110
                                                 + + + pvrd+ g+i+g++ v 
  gi|298674920|ref|YP_003726670.1| 304 TFP----NNVFNIKRDPVRDINGNIIGIISVS 331
                                       333....4556666667777777777766665 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.035        36      45     107 ..      35      99 ..      10     102 .. 0.81
   2 !   25.1   0.0   1.5e-08   1.6e-05       1     109 [.     118     224 ..     118     225 .. 0.90
   3 !   24.0   0.0   3.4e-08   3.6e-05       1     110 []     234     339 ..     234     339 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.035
                             PAS_4  45 peedaarleralrrvlegeepiefleelll..pgeerhyelrllPlrdesGevigvlvisrDiTe 107
                                        +ed +  e+ l+ +l    ++e +    +   ge r + ++ + + d +  +i  ++ ++DiTe
  gi|298674920|ref|YP_003726670.1|  35 HPEDIPYMENKLQDCLNNSSSYEIELRIIRkdTGEIRNVKTHGRIISDNDNNPIKMYGATQDITE 99 
                                       444777777778888888888888887777889*******************************9 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 1.5e-08
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pg 76 
                                       +++++da++v + +g++l +N++a + +g++++ell +  +++  +    ++ + +++ le++  ++f+ ++ + +g
  gi|298674920|ref|YP_003726670.1| 118 FNNMNDAIFVQNLQGNFLNVNETAVKRLGYSRDELLSMAAQDVDYKYPSSGVKEKIDEILETG-LLKFESVHITnNG 193
                                       7899*************************************875555789************9.88888888888** PP

                             PAS_4  77 eerhyelrllPlrdesGevigvlvisrDiTerr 109
                                          ++e++ + ++ ++    +vl i+rDiTer+
  gi|298674920|ref|YP_003726670.1| 194 TKIPVEVNSTLIHYRD--KPAVLSIARDITERK 224
                                       *********9996644..46************8 PP

  == domain 3  score: 24.0 bits;  conditional E-value: 3.4e-08
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       l+s+++++++ +++g++ ++N+a+ +  g+ ++el+G  ++ ll   +    ++++   +++++++e  ++      
  gi|298674920|ref|YP_003726670.1| 234 LNSTSEMIVFHNTEGKIKWCNKAFSKFTGFKQDELIGAYCYKLLHNKSDICDCCPISYIVKTGKHHEKITTFPN--- 307
                                       6889999999*******************************988876555567888999999988888885555... PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerrr 110
                                         ++++   P+rd +G +ig++ +s DiT+ +r
  gi|298674920|ref|YP_003726670.1| 308 -NVFNIKRDPVRDINGNIIGIISVSSDITDKVR 339
                                       .8***************************9865 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   2.4e-08   2.5e-05       4      46 ..     115     158 ..     113     178 .. 0.84
   2 !   16.6   0.0   5.6e-06     0.006       6      50 ..     233     278 ..     228     288 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2.4e-08
                             PAS_8   4 ralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellg 46 
                                         lf++++d+i+v +l+++++ vN++a + lGys ++l+ +  +
  gi|298674920|ref|YP_003726670.1| 115 NYLFNNMNDAIFVQNLQGNFLNVNETAVKRLGYSrDELLSMAAQ 158
                                       579**********995556***************9998887774 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 5.6e-06
                             PAS_8   6 lfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellgqllp 50 
                                       +++s ++ i+  + +g +i ++N+a+ +++G++ ++l+g+ + +ll+
  gi|298674920|ref|YP_003726670.1| 233 ILNSTSEMIVFHNtEG-KIKWCNKAFSKFTGFKqDELIGAYCYKLLH 278
                                       799999****767455.5***************99999999876665 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.55   5.8e+02      37      53 ..     184     200 ..     140     236 .. 0.79
   2 !   38.9   0.2   9.6e-13     1e-09       5     107 ..     478     567 ..     475     569 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.55
                                       EEEEEEEESSSSSTTHH CS
                         HATPase_c  37 dlvisveDnGiGipked 53 
                                         ++ +++nG  ip+e 
  gi|298674920|ref|YP_003726670.1| 184 FESVHITNNGTKIPVEV 200
                                       56789*********985 PP

  == domain 2  score: 38.9 bits;  conditional E-value: 9.6e-13
                                       HHHHHHHHHHHHHHHH...HSTTTEEEEEEEE.EETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHH CS
                         HATPase_c   5 rLrqiisnlvdNavkf...atkageieveika.seddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlG 77 
                                        L  +i++lv+N++k+   ++++gei++ +++ +++++++ v DnG+Gip+++       +++            lG
  gi|298674920|ref|YP_003726670.1| 478 PLAMLINELVSNSLKYafsENESGEIKIMLHQiDNENYTLIVADNGRGIPEDIDI-----HDT----------DSLG 539
                                       67889***********66544999999999975337**************96555.....223..........569* PP

                                       HHHHHHHHHHTTTEEEEEEETTTEEEEEEE CS
                         HATPase_c  78 lsivkklvelmgGeiwvesepgrGttftft 107
                                       l +v+ lv+++gG +++e ++  G++f+++
  gi|298674920|ref|YP_003726670.1| 540 LRLVNTLVDQIGGCLELERRK--GSKFIIE 567
                                       *****************6666..9999875 PP

>> HWE_HK  HWE histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.1   2.8e-10   2.9e-07       1      72 [.     379     453 ..     379     465 .. 0.73

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 2.8e-10
                                       HHHHHHHHHHHHHHHHHHHHSSSXS-HHHHHHHH..HHHHHHHHHHHHHHHHC.TTS-EEHHHHHHHHHHHHHHH CS
                            HWE_HK   1 ElnHRvKNlLavvqsiarqtlrsaesleefaekl..sgRLqALsaahdllsre.ewagaeLaelleeelapyede 72 
                                       El+HR+KN L v++s+++  +++ ++ e +++ +  ++R+ ++s +h+ l ++ + +++++++ +++ l +  + 
  gi|298674920|ref|YP_003726670.1| 379 ELHHRIKNNLQVISSLINLQSEKFDDEEVYEAFIdtQNRIVSMSLVHQKLYQTsNLNSINFKDYIQDLLTHLTRL 453
                                       9*****************99887776665555433368*********9877651567788887777777666554 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0    0.0003      0.32      40     107 ..      30      97 ..       8     101 .. 0.84
   2 ?    5.9   0.0     0.013        13       6      94 ..     126     209 ..     122     225 .. 0.88
   3 !   10.0   0.0   0.00068      0.72       2      47 ..     238     280 ..     237     288 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0003
                            PAS_11  40 iydLchpqdlstlkshlrevissngeatsslyRLrl.sqdkfvkvktksklfknqksneqdfimathtl 107
                                       + +++hp+d   ++++l++ + +n  + +   R++   ++++ +vkt +++  ++++n  +++ at+ +
  gi|298674920|ref|YP_003726670.1|  30 LLQIVHPEDIPYMENKLQDCL-NNSSSYEIELRIIRkDTGEIRNVKTHGRIISDNDNNPIKMYGATQDI 97 
                                       5689*****************.777778888888876899999***********999988888777765 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.013
                            PAS_11   6 trldidgkIisvDtsaLrasfslglekeelvgrsiydLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvk 82 
                                       + + ++g++++v++    a  +lg++++el+ + ++d   +   s +k++  e++ ++g  +  +++++  +++ + 
  gi|298674920|ref|YP_003726670.1| 126 FVQNLQGNFLNVNE---TAVKRLGYSRDELLSMAAQDVDYKYPSSGVKEKIDEIL-ETGLLKFESVHITN-NGTKIP 197
                                       667899********...9999*****************99999************.99999999999877.889999 PP

                            PAS_11  83 vktksklfknqk 94 
                                       v  +s l   ++
  gi|298674920|ref|YP_003726670.1| 198 VEVNSTLIHYRD 209
                                       998888877655 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00068
                            PAS_11   2 eqfttrldidgkIisvDtsaLrasfslglekeelvgrsiydLchpq 47 
                                       +++++ + ++gkI  +++     s  +g++++el+g + y+L+h +
  gi|298674920|ref|YP_003726670.1| 238 SEMIVFHNTEGKIKWCNK---AFSKFTGFKQDELIGAYCYKLLHNK 280
                                       789999************...888899*****************76 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   4.2e-06    0.0044      30     112 ..     477     550 ..     465     566 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.2e-06
                       HATPase_c_2  30 deirlaveEactNavehayleapegpvevr.lesdeealtvevaDsGpgfdpetlpdpteeepkeslkegGrGlali 105
                                         + + ++E+++N  ++a  e+++g++++   ++d+e  t+ vaD+G+g +             +  ++  +Gl l+
  gi|298674920|ref|YP_003726670.1| 477 IPLAMLINELVSNSLKYAFSENESGEIKIMlHQIDNENYTLIVADNGRGIPEDI----------DIHDTDSLGLRLV 543
                                       5567889*********************9966789999***********76653..........5666778999999 PP

                       HATPase_c_2 106 kglvDev 112
                                       ++lvD++
  gi|298674920|ref|YP_003726670.1| 544 NTLVDQI 550
                                       9999987 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       3.3   3.5e+03      78     112 ..     210     245 ..     208     261 .. 0.73
   2 ?   -2.5   0.2         4   4.3e+03      86     122 ..     332     368 ..     325     378 .. 0.59
   3 !   16.8   0.1   4.3e-06    0.0045       7      50 ..     483     532 ..     478     545 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.3
                       HATPase_c_3  78 klAslslgkkltvitkkegess.tltldvdkidken 112
                                       k A+ls+++++t   k+e+e+s  l  + + i ++n
  gi|298674920|ref|YP_003726670.1| 210 KPAVLSIARDITERKKAEEEKSvILNSTSEMIVFHN 245
                                       568888999988888888877745666666666665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4
                       HATPase_c_3  86 kkltvitkkegesstltldvdkidkenekvleeltve 122
                                       +++t   ++e++  ++t +++ i+ e e+ +ee t++
  gi|298674920|ref|YP_003726670.1| 332 SDITDKVRAEEKIKEYTNKLEEINTELENRVEEQTEQ 368
                                       4444445566666667777777766666666655554 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 4.3e-06
                       HATPase_c_3   7 laelvdNsld.Adaen....vkievnknrgktgeivieDdGkGmsee.el 50 
                                       + elv Nsl  A +en    +ki +++ ++++ ++ + D+G G++e+ ++
  gi|298674920|ref|YP_003726670.1| 483 INELVSNSLKyAFSENesgeIKIMLHQIDNENYTLIVADNGRGIPEDiDI 532
                                       569******98777767788************************998666 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.57     6e+02      34      84 ..      79     129 ..      21     133 .. 0.80
   2 ?   12.8   0.0   0.00013      0.14       4     106 .]     233     335 ..     231     335 .. 0.86
   3 ?   -0.8   0.4       2.2   2.4e+03      33      67 ..     356     374 ..     338     419 .. 0.52

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.57
                            PAS_10  34 lipadvGrpladihpkkavknveeviealrtgekdevevvvpkngkwvlvr 84 
                                       +i++   +p++    ++ +++ ++v ++lr++ ++      ++n+ +++++
  gi|298674920|ref|YP_003726670.1|  79 IISDNDNNPIKMYGATQDITEWKKVHDELRKTADEFNYLFNNMNDAIFVQN 129
                                       455555567777777888888999999999998888777777777777665 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00013
                            PAS_10   4 lLnstpieltflDdnlqirrFtpaakklfklipad.vGrpladi.hpkkavknveeviealrtgekdevevvvpkng 78 
                                       +Lnst   ++f +++ +i++ ++a +k+  +++++ +G    ++ h+k+ + +   +   ++tg+ +  e+  + ++
  gi|298674920|ref|YP_003726670.1| 233 ILNSTSEMIVFHNTEGKIKWCNKAFSKFTGFKQDElIGAYCYKLlHNKSDICDCCPISYIVKTGKHH--EKITTFPN 307
                                       7999999999999999999999999999988876637999888768889999999998888888854..55677899 PP

                            PAS_10  79 kwvlvrylpyrdedgeiaGvvetfvDit 106
                                       +++ ++  p+rd +g+i G++ +  Dit
  gi|298674920|ref|YP_003726670.1| 308 NVFNIKRDPVRDINGNIIGIISVSSDIT 335
                                       **************************97 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 2.2
                            PAS_10  33 klipadvGrpladihpkkavknveeviealrtgek 67 
                                                          +++vee +e++r+ e+
  gi|298674920|ref|YP_003726670.1| 356 TEL----------------ENRVEEQTEQIRNAER 374
                                       222................3333333333333333 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.2     0.014        15      17     115 .]     134     228 ..     118     228 .. 0.58
   2 ?    4.8   0.0     0.029        30      87     115 .]     309     342 ..     234     342 .. 0.74
   3 ?    3.2   0.3     0.091        96      99     115 .]     326     342 ..     320     394 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.014
                             PAS_7  17 LvawNrrylelldlpeelvqvgvpleellrynaergefg..agdveaeverrlaaaragkphsfererpdgrvievr 91 
                                        + +N+  ++         + g + +ell + a+  +++  ++ v+++++++l+     k +s++  +++g+ i v+
  gi|298674920|ref|YP_003726670.1| 134 FLNVNETAVK---------RLGYSRDELLSMAAQDVDYKypSSGVKEKIDEILETGLL-KFESVHI-TNNGTKIPVE 199
                                       4444444433.........556666677777777777776555577778888854333.2222222.3566666665 PP

                             PAS_7  92 gnpl.....pdgGfVttytDiTerrraee 115
                                        n +     ++  ++++  DiTer++aee
  gi|298674920|ref|YP_003726670.1| 200 VNSTlihyrDKPAVLSIARDITERKKAEE 228
                                       55555577556677778899999999986 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.029
                             PAS_7  87 vievrgnplpd.....gGfVttytDiTerrraee 115
                                       v ++++ p+ d      G++++ +DiT+++raee
  gi|298674920|ref|YP_003726670.1| 309 VFNIKRDPVRDingniIGIISVSSDITDKVRAEE 342
                                       5555555553322222599************996 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.091
                             PAS_7  99 GfVttytDiTerrraee 115
                                       G++++ +DiT+++raee
  gi|298674920|ref|YP_003726670.1| 326 GIISVSSDITDKVRAEE 342
                                       77778888888888875 PP

>> FdhE  Protein involved in formate dehydrogenase formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00028       0.3      17      95 ..     370     450 ..     359     469 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00028
                                       HHHHHHHHHHTT-TTHHHHHHHHHHHHHHHHHHCS---....--HHHHHHHHHTT--TT-HHHHHHH-TTHHHHHHH CS
                              FdhE  17 rraeRLrqLaeehpladYLrflaalaeaqqkvlaaekpla..ldaeaieraqehgmpplaakalerdeawqelLqal 91 
                                       r aeR+r+L  +h +++ L+++++l++ q++ +++e+  +  +d+++   + +   + l +++  ++ ++++++q l
  gi|298674920|ref|YP_003726670.1| 370 RNAERMRELELHHRIKNNLQVISSLINLQSEKFDDEEVYEafIDTQNRIVSMSLVHQKLYQTSNLNSINFKDYIQDL 446
                                       789******************************77777665655554444444445555555555557777777777 PP

                                       HHT- CS
                              FdhE  92 leal 95 
                                       l +l
  gi|298674920|ref|YP_003726670.1| 447 LTHL 450
                                       7754 PP

>> Cache_3-Cache_2  Cache 3/Cache 2 fusion domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1    0.0015       1.5     158     182 ..     315     339 ..     307     349 .. 0.86
   2 ?    2.9   2.9     0.052        55       6      52 ..     352     409 ..     348     466 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0015
                   Cache_3-Cache_2 158 ePikdadgkViGilyVgvdqsealk 182
                                       +P++d +g++iGi+ V  d+++ ++
  gi|298674920|ref|YP_003726670.1| 315 DPVRDINGNIIGIISVSSDITDKVR 339
                                       6******************988874 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.052
                   Cache_3-Cache_2   6 eevnklieeelekevedlaetletqdellrekverdlnvfakllsn...........e 52 
                                       ee+n + e+++e+++e++++  ++++  l+ +++++l+v+++l++            e
  gi|298674920|ref|YP_003726670.1| 352 EEINTELENRVEEQTEQIRNAERMRELELHHRIKNNLQVISSLINLqsekfddeevyE 409
                                       689999************************************9998666666666662 PP

>> ACCA  Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   4.7      0.24   2.5e+02       4      52 ..     340     389 ..     337     400 .. 0.78
   2 ?    6.4   0.1     0.007       7.4      63      90 ..     434     461 ..     398     464 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.24
                              ACCA   4 fekpiaeleekieelkklaeesevdlseeieklekkle.klkkeiyknlt 52 
                                        e++i+e ++k+ee+++  e++  + +e+i++ e+  e +l+++i++nl+
  gi|298674920|ref|YP_003726670.1| 340 AEEKIKEYTNKLEEINTELENRVEEQTEQIRNAERMRElELHHRIKNNLQ 389
                                       68999999999999999988888888999988887655256667777776 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.007
                              ACCA  63 peRpktldyiealfedfvelhGDrafad 90 
                                        + ++++dyi+ l+++ + l GD++++ 
  gi|298674920|ref|YP_003726670.1| 434 LNSINFKDYIQDLLTHLTRLYGDNNITL 461
                                       5567899****************99865 PP

>> EMP24_GP25L  emp24/gp25L/p24 family/GOLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       2.3   2.4e+03     118     137 ..      90     117 ..      42     128 .. 0.43
   2 ?    7.4   4.0    0.0036       3.8     102     147 ..     332     378 ..     307     388 .. 0.84
   3 ?   -2.3   0.0       3.5   3.7e+03     121     161 ..     382     424 ..     379     425 .. 0.72
   4 ?    1.0   0.0      0.34   3.6e+02      54      88 ..     483     516 ..     453     549 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.3
                       EMP24_GP25L 118 s........elkkleekldsikreqkyl 137
                                                e kk+++ l++  +e++yl
  gi|298674920|ref|YP_003726670.1|  90 MygatqditEWKKVHDELRKTADEFNYL 117
                                       1222223334455555555555555554 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0036
                       EMP24_GP25L 102 sd.ykdsakkekletleselkkleekldsikreqkylrereerlrdt 147
                                       sd  +++  +ek+++++++l+++++ l++  +eq+ + ++ er+r++
  gi|298674920|ref|YP_003726670.1| 332 SDiTDKVRAEEKIKEYTNKLEEINTELENRVEEQTEQIRNAERMREL 378
                                       332345677************************************86 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 3.5
                       EMP24_GP25L 121 kkleekldsikreqkylrer..eerlrdtnestnsrvvwwsil 161
                                       ++++++l+ i + ++++ e+   e+ +++  +t++r+v  s++
  gi|298674920|ref|YP_003726670.1| 382 HRIKNNLQVISSLINLQSEKfdDEEVYEAFIDTQNRIVSMSLV 424
                                       5677788877776666655422678889999999999998875 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.34
                       EMP24_GP25L  54 vkkkdresegdfsftakesgeykvCfdnsfstkss 88 
                                       +++  ++++ +++f+ +esge+k+ ++ +++  ++
  gi|298674920|ref|YP_003726670.1| 483 INE-LVSNSLKYAFSENESGEIKIMLHQIDNENYT 516
                                       555.5555669999999*****9999988876554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (570 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1711  (0.095432); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.67u 0.27s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 3631.42
//
Query:       gi|298674921|ref|YP_003726671.1|  [L=49]
Description: hypothetical protein Metev_0984 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0052   17.1   0.0     0.0059   16.9   0.0    1.1  1  ECSIT_C    C-terminal domain of the ECSIT protein
  ------ inclusion threshold ------
      0.015   15.2   1.8       0.02   14.8   1.8    1.2  1  RBD-FIP    FIP domain
      0.045   13.8   3.0      0.056   13.5   3.0    1.1  1  bZIP_1     bZIP transcription factor
      0.078   13.1   0.8       0.18   11.9   0.1    1.9  3  Hormone_3  Pancreatic hormone peptide
       0.18   11.8   2.6       0.32   11.0   2.6    1.6  1  DUF2205    Short coiled-coil protein
       0.25   11.7   3.2       0.27   11.6   3.2    1.0  1  DUF737     Protein of unknown function (DUF737)


Domain annotation for each model (and alignments):
>> ECSIT_C  C-terminal domain of the ECSIT protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     2e-06    0.0059     100     130 ..       5      35 ..       3      36 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2e-06
                           ECSIT_C 100 tgtsskdsllsWirlLqktnpiLkeipvlfr 130
                                       t + s d l+++i+ L+++n+ L++ ++lf+
  gi|298674921|ref|YP_003726671.1|   5 TEKASSDELQRYIEKLENENKELQKYKTLFK 35 
                                       778899************************7 PP

>> RBD-FIP  FIP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   1.8   6.7e-06      0.02       1      22 [.       9      30 ..       9      31 .. 0.96

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.7e-06
                                      THHHHHHHHHHHHHHHHHHHHH CS
                           RBD-FIP  1 srdeLiqalqkqEeenrrLedY 22
                                      s deL+  ++k E+en +L+ Y
  gi|298674921|ref|YP_003726671.1|  9 SSDELQRYIEKLENENKELQKY 30
                                      67******************99 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   3.0   1.9e-05     0.056      25      59 ..       7      40 ..       6      43 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.9e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1 25 qaeieeLerrvkaLekeNksLkseleelkkevekL 59
                                      +a+ +eL+r  ++Le+eNk+L++  ++l ke e+L
  gi|298674921|ref|YP_003726671.1|  7 KASSDELQRYIEKLENENKELQK-YKTLFKEAEYL 40
                                      67889**************9975.67777777766 PP

>> Hormone_3  Pancreatic hormone peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   5.9e-05      0.18       9      24 ..       6      21 ..       5      22 .. 0.91
   2 ?   -1.5   0.0      0.95   2.9e+03      15      19 ..      26      30 ..      25      33 .. 0.62
   3 ?   -3.2   0.0       3.1   9.3e+03      18      22 ..      38      42 ..      37      44 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.9e-05
                                      TTS-HHHHHHHHHHHH CS
                         Hormone_3  9 edaspEeLakYyaaLr 24
                                      e+as +eL +Y+ +L+
  gi|298674921|ref|YP_003726671.1|  6 EKASSDELQRYIEKLE 21
                                      78************97 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.95
                                      HHHHH CS
                         Hormone_3 15 eLakY 19
                                      eL kY
  gi|298674921|ref|YP_003726671.1| 26 ELQKY 30
                                      55565 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 3.1
                                      HHHHH CS
                         Hormone_3 18 kYyaa 22
                                       Y+++
  gi|298674921|ref|YP_003726671.1| 38 EYLSS 42
                                      56655 PP

>> DUF2205  Short coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.6   0.00011      0.32      46      59 ..      17      30 ..       7      44 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                           DUF2205 46 hdKLesenrfLqqY 59
                                       +KLe+en+ Lq+Y
  gi|298674921|ref|YP_003726671.1| 17 IEKLENENKELQKY 30
                                      58************ PP

>> DUF737  Protein of unknown function (DUF737)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   3.2   9.1e-05      0.27     139     169 ..       6      36 ..       1      39 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.1e-05
                            DUF737 139 lkaqllelerkarqLeekekeLkkqdafYke 169
                                       +ka   el+r++ +Le+ +keL+k  +++ke
  gi|298674921|ref|YP_003726671.1|   6 EKASSDELQRYIEKLENENKELQKYKTLFKE 36 
                                       45555566**********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2238  (0.124826); expected 358.6 (0.02)
Passed bias filter:                     1175  (0.0655363); expected 358.6 (0.02)
Passed Vit filter:                       121  (0.00674884); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 352.45
//
Query:       gi|298674922|ref|YP_003726672.1|  [L=134]
Description: hypothetical protein Metev_0985 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-57  193.0   1.5    1.5e-57  192.8   1.5    1.0  1  DUF1699   Protein of unknown function (DUF1699)


Domain annotation for each model (and alignments):
>> DUF1699  Protein of unknown function (DUF1699)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.8   1.5   8.6e-62   1.5e-57       1     129 [.       1     129 [.       1     130 [. 0.99

  Alignments for each domain:
  == domain 1  score: 192.8 bits;  conditional E-value: 8.6e-62
                           DUF1699   1 mkirvvsskeeietlnenekivHlafrpsntdilslvkkcpklkaiqvpeSykktlsksakmfleiqgiellegdvw 77 
                                       mk+rv+s+k++ie++++n++++H+afrpsntdi++ +++ p++kaiq+p+Sy+ktlsks+kmf++i++++l+egd+w
  gi|298674922|ref|YP_003726672.1|   1 MKFRVISTKSDIENIDKNDEYIHFAFRPSNTDIFNAISNNPDIKAIQIPSSYMKTLSKSMKMFFDIHNVSLIEGDIW 77 
                                       9**************************************************************************** PP

                           DUF1699  78 ghrkdineyyevseevierikelkseglseeeiaeklsketklspdlikfll 129
                                       ghrkdineyyev+++v+++++e+ +eglse++i+ek+sket+l+pd+i+fll
  gi|298674922|ref|YP_003726672.1|  78 GHRKDINEYYEVPDSVYKKLREMVNEGLSEDNIIEKMSKETRLDPDFIRFLL 129
                                       **************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1043.41
//
Query:       gi|298674923|ref|YP_003726673.1|  [L=241]
Description: UBA/THIF-type NAD/FAD-binding protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-65  220.3   0.0      3e-65  220.0   0.0    1.0  1  ThiF             ThiF family
     0.0059   16.9   0.1      0.013   15.8   0.1    1.6  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
      0.029   14.2   0.0      0.041   13.8   0.0    1.3  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
      0.032   13.8   0.2      0.065   12.8   0.2    1.6  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
      0.063   13.3   0.1        0.2   11.7   0.0    1.8  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase


Domain annotation for each model (and alignments):
>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  220.0   0.0   8.2e-69     3e-65       1     240 [.      10     235 ..      10     239 .. 0.96

  Alignments for each domain:
  == domain 1  score: 220.0 bits;  conditional E-value: 8.2e-69
                                       THHHHHHHHHHHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSBHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF   1 ysrqlallgedgqekLrdskvllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqflfreediGkpKaeva 77 
                                       ysrq++++ge+gqekL++s+v + G GglGs+++ +La++Gvgk++++D+D++ lsNlnRq+l+ ++diG  K+++a
  gi|298674923|ref|YP_003726673.1|  10 YSRQIMMFGEEGQEKLKNSSVTITGSGGLGSPIAIYLAAAGVGKIRIIDHDTVALSNLNRQILHHHKDIGVLKVDSA 86 
                                       89*************************************************************************** PP

                                       HHHHHHT-TTSEEEEEES-CCGCCS-HHHHTT-SEEEEESSSHHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  78 aealqeinpdveveavteritdetvleellesvDlVvdalDniearrlvnracvkkgiplieagtlgfegqvvviip 154
                                       + +l+++np++++e+++e +++++  ++l+ +  +VvdalDn+ +r+ +n+a+v+++ipl++++++gf+gqv++iip
  gi|298674923|ref|YP_003726673.1|  87 KGKLNDLNPNIDIETFNETLSPDN-IKNLIGKSHIVVDALDNYHTRFSLNEAAVQEQIPLVHGAVEGFHGQVTTIIP 162
                                       **********************98.57************************************************** PP

                                       CCS-ECTSS-TGGS.EECCCCEEHHHHHHCTE-B-HHHHHHHHHHHHHHHHHHHTTBCGGGCCEEEECCTTTTEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 155 gktgcyeCldpsstedptekkvplctsiagnipaiatttavvaglaalellkllsgkeklenslltqvdllesrfen 231
                                       g+t+c++C     +++p++k++p++          +tt ++++ ++a+e++k+l g  kl   +l   d+++s++e+
  gi|298674923|ref|YP_003726673.1| 163 GETPCMRCFI---SKTPPKKTFPIL----------GTTAGIIGTMQANEVIKYLTGSGKLLTGRLLLWDGFNSKTEE 226
                                       *********8...599999999888..........9******************888888888888*********** PP

                                       ECCEEEEEE CS
                                       xxxxxxxxx RF
                              ThiF 232 velerakks 240
                                       v++++++ +
  gi|298674923|ref|YP_003726673.1| 227 VPVNKNQYC 235
                                       **9887644 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   3.5e-06     0.013       2      98 ..      31     147 ..      30     178 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.5e-06
                                       EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH.....................TTTCEEEEE--TT CS
                   Sacchrp_dh_NADP   2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka.....................lgvrfeaialdae 57 
                                        i G+G+ G+++a +la+ +    +i ++d +   l +l  ++                     l++++++++++  
  gi|298674923|ref|YP_003726673.1|  31 TITGSGGLGSPIAIYLAAAGVG--KIRIIDHDTVALSNLNRQIlhhhkdigvlkvdsakgklndLNPNIDIETFNET 105
                                       688***************9976..9*********999999999999******************************* PP

                                       THHHHHHHHHTTSSEEEE-SSGG.GHHHHHHHHHHHT-EEEE CS
                   Sacchrp_dh_NADP  58 nyeavLaallkegdlvvnlsppi.ssldvlkaCietgvhyvd 98 
                                         ++ ++ l+ +  +vv+++ ++    ++ +a+++ ++  v 
  gi|298674923|ref|YP_003726673.1| 106 LSPDNIKNLIGKSHIVVDALDNYhTRFSLNEAAVQEQIPLVH 147
                                       ***********************5555999999998887765 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.1e-05     0.041       2      74 ..      30     100 ..      29     125 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.1e-05
                                       EEEE--SCCHHHHHHHHHHTT-.EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HH CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagl.eVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdle 74 
                                       v++ G+G +G+ ia  +a+ag+ +++++d ++ al + +++i +  +     g lk ++++  l+ ++++ d+e
  gi|298674923|ref|YP_003726673.1|  30 VTITGSGGLGSPIAIYLAAAGVgKIRIIDHDTVALSNLNRQILHHHKD---IGVLKVDSAKGKLNDLNPNIDIE 100
                                       9*******************9868***********9999998764333...35555555555555555555554 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   1.8e-05     0.065       2      45 ..      29      73 ..      28     101 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.8e-05
                                      EEEEE--STTHHHHHHHHHHCT.SEEEEE-S-HHHHHHHCTTS-S CS
                    UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeig.hevigvDideekvdklnsgkip 45
                                       +++ G+G +G + a+ la++g  ++ ++D d+ + ++ln++ ++
  gi|298674923|ref|YP_003726673.1| 29 SVTITGSGGLGSPIAIYLAAAGvGKIRIIDHDTVALSNLNRQILH 73
                                      589*******************77999*************98765 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.6e-05       0.2       8      71 ..      23      88 ..      17      98 .. 0.81
   2 ?   -2.1   0.0      0.99   3.6e+03      66      84 ..     108     126 ..      89     141 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.6e-05
                                      S..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHH..T.ET-EEEEGCGHHH CS
                      Shikimate_DH  8 eslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeel..kgeeiealkleelke 71
                                      e+lk++ v++ G G +++ +a +L+a+gv k+ ++  +    ++l +++  ++++i +lk+++ k 
  gi|298674923|ref|YP_003726673.1| 23 EKLKNSSVTITGSGGLGSPIAIYLAAAGVGKIRIIDHDTVALSNLNRQIlhHHKDIGVLKVDSAKG 88
                                      6899*******************************9999988888888754455566666666655 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.99
                                       GCGHHHHHHT-SEEEE-SS CS
                      Shikimate_DH  66 leelkellaeadvvisata 84 
                                        +++k+l+ ++++v+ a  
  gi|298674923|ref|YP_003726673.1| 108 PDNIKNLIGKSHIVVDALD 126
                                       5677778888888877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.21s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 1848.06
//
Query:       gi|298674924|ref|YP_003726674.1|  [L=386]
Description: HtrA2 peptidase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.8e-34  117.4   0.2    1.6e-33  116.7   0.2    1.3  1  Trypsin_2      Trypsin-like peptidase domain
    6.4e-18   64.9   0.1    1.6e-17   63.6   0.1    1.7  1  PDZ_2          PDZ domain
    2.4e-12   47.2   0.0    5.7e-12   45.9   0.0    1.6  1  Trypsin        Trypsin
    6.9e-08   32.2   1.8    6.1e-05   22.8   0.3    2.5  2  PDZ_6          PDZ domain
    4.2e-06   27.0   0.4     0.0029   17.9   0.0    3.1  2  PDZ            PDZ domain
      8e-05   23.0   1.1    0.00096   19.5   0.1    2.8  2  GRASP55_65     GRASP55/65 PDZ-like domain
  ------ inclusion threshold ------
      0.012   15.2   0.1      0.027   14.0   0.2    1.5  2  DUF316         Chymotrypsin family Peptidase-S1
      0.051   12.8   0.2          4    6.5   0.0    2.2  2  Peptidase_S32  Equine arteritis virus serine endopeptidase S3
      0.062   12.6   0.0       0.12   11.7   0.0    1.4  1  CPSF_A         CPSF A subunit region


Domain annotation for each model (and alignments):
>> Trypsin_2  Trypsin-like peptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.7   0.2     8e-37   1.6e-33       1     150 []      94     236 ..      94     236 .. 0.98

  Alignments for each domain:
  == domain 1  score: 116.7 bits;  conditional E-value: 8e-37
                         Trypsin_2   1 GsGflvgsdglilTnaHvvdsadgaavkaikkkveeagadgrevpakvvaadpelDlAllkv...ssderaglpplp 74 
                                       GsGf+++s+ +ilTn+Hv+d+a++++v         ++++g +++a++v++d  +D+A+l+v   +++e+++  pl+
  gi|298674924|ref|YP_003726674.1|  94 GSGFIYDSNRHILTNQHVIDGAENVEV---------VFSNGATQRANIVGSDKYSDIAVLRVdniPEEENYSPSPLK 161
                                       9**************************.........****************777********************** PP

                         Trypsin_2  75 lgpsealkggepvyvvGyplggeksgsvssGivsgvve.sesaasgegesflqtdaatspGsSGGplfdsdGrvvGl 150
                                       lg+s++++ ge v ++G+p g e+  s++ Givs++ +  ++ ++++ ++++qtda+++pG+SGGpl+d  G+++G+
  gi|298674924|ref|YP_003726674.1| 162 LGNSSNIESGEFVMAIGNPFGLEG--SITHGIVSATGRvLPTEEGFSIPNVIQTDAPLNPGNSGGPLLDLSGQIIGV 236
                                       ************************..9*************************************************8 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.6   0.1   8.1e-21   1.6e-17       1      82 []     270     377 ..     270     377 .. 0.98

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 8.1e-21
                                       ....XX------..............-EEEEEE-TTSGGGGT.--T..............T-EEEEETTB--SSHHH CS
                             PDZ_2   1 pylGvsvsdeed............tggvlvvsVkeggPaakaglka..............gDvilkvdgkkvksled 51 
                                       +++G+s+++++             ++gv +v V +ggPa+kagl++              gD+il  d++++ ++++
  gi|298674924|ref|YP_003726674.1| 270 AWIGISMVPVSYnaanymdlndtvSEGVMIVRVIDGGPAEKAGLEPgkqivvngeptwvnGDIILGMDNREIRNSDQ 346
                                       579********9***************************************************************** PP

                                       HHHHHHTS-TT-EEEEEEEETTEEEEEEEE- CS
                             PDZ_2  52 lislllkkkpGdtVkltvlRdgkkktvevkl 82 
                                       li++l +k pGd +kl+++R+ + ktv+v+l
  gi|298674924|ref|YP_003726674.1| 347 LITYLDTKLPGDRIKLKIYRNENIKTVNVTL 377
                                       *****************************97 PP

>> Trypsin  Trypsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   0.0   2.9e-15   5.7e-12      26     215 ..      93     252 ..      66     258 .. 0.77

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 2.9e-15
                                       EEEEEEEETT.EEEEEGGGTTTGGGEEEEESESBTTSCTTTEEEEEEEEEEEETTEBTTTTTTTEEEEEESSSSTSB CS
                           Trypsin  26 lCgGslisen.wvlTAaHCvsnasdvkvvlgehnlkksegkeqklkvekvivhpnynpstldnDiallklkepvklg 101
                                         +G+++++n  +lT++H++++a++v+vv+++       g  q++++          +++   Dia+l++++     
  gi|298674924|ref|YP_003726674.1|  93 QGSGFIYDSNrHILTNQHVIDGAENVEVVFSN-------GATQRANIVG--------SDK-YSDIAVLRVDNI-PEE 152
                                       45799999999***********9999996664.......4445555555........454.57********96.778 PP

                                       SSBHCCBBCSTTHTTSTTTEEEEEESSBSSTSS..BSSBEEEEEEEEEEHHHHHHHTTTTSTTTEEEEESTTSSSBC CS
                           Trypsin 102 dtvrpiclpaassslpvgttclvsGwgrtkekg..ksdtlqevevpvvsretcksaykgkvtenmlcagakeggkda 176
                                       ++ +p  l   ++s++++++ +v+++g+++  +   ++ + +++ +v+++e+  s       +n ++++a       
  gi|298674924|ref|YP_003726674.1| 153 ENYSPSPLKL-GNSSNIESGEFVMAIGNPFGLEgsITHGIVSATGRVLPTEEGFS------IPNVIQTDA-----PL 217
                                       8888888888.66679************998886666666667777777777777......59*******.....7* PP

                                       TTTTTTSEEEETTTEEEEEEEEESSSSCTTSEEEEEEGG CS
                           Trypsin 177 cqGDSGGPlvcsdgelvGivswgkgcakgnrpgvytkvs 215
                                       ++G+SGGPl+  +g+++G++ ++ g +     g++++ +
  gi|298674924|ref|YP_003726674.1| 218 NPGNSGGPLLDLSGQIIGVNRAKSGDNV----GFAIPAN 252
                                       ********************99755444....4666665 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.3     3e-08   6.1e-05       2      33 ..     299     327 ..     298     328 .. 0.94
   2 !    8.7   0.0   0.00078       1.6      19      56 .]     330     366 ..     327     366 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 3e-08
                             PDZ_6   2 VtaVdpgsPAdrAGlrvGDiilsvNGqpvegl 33 
                                       +  V+ g+PA++AGl++G +i+ vNG+p+  +
  gi|298674924|ref|YP_003726674.1| 299 IVRVIDGGPAEKAGLEPGKQIV-VNGEPT--W 327
                                       678*******************.*****9..6 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00078
                             PDZ_6  19 GDiilsvNGqpveglsladvaallr.gsagesvvlvvrr 56 
                                       GDiil  +++++  ++ ++++ +l    +g ++ l++ r
  gi|298674924|ref|YP_003726674.1| 330 GDIILGMDNREI--RNSDQLITYLDtKLPGDRIKLKIYR 366
                                       9***********..*********9988888888888876 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.4e-06    0.0029       6      57 ..     265     325 ..     260     327 .. 0.83
   2 !    5.9   0.1    0.0085        17      47      81 ..     330     364 ..     328     365 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.4e-06
                                       TS.TTSESSEEEEEETTSS.........SSSSEEEEEECTTSHHHHHTSSTTEEEEEETTEE CS
                               PDZ   6 ke.grgglGfslkggsdqr.........gdkgifvsevlpggaaeadglkvGDkIlsvNgvd 57 
                                        e ++ ++G+s +  s +           ++g+ + +v  gg+ae++gl++G +I+ vNg++
  gi|298674924|ref|YP_003726674.1| 265 GEyEHAWIGISMVPVSYNAanymdlndtVSEGVMIVRVIDGGPAEKAGLEPGKQIV-VNGEP 325
                                       4468888888888888777888999898999***********************98.88876 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0085
                                       TEEEEEETTEETTTSHHHHHHHHHHTTTSEEEEEE CS
                               PDZ  47 GDkIlsvNgvdvenvsheeavqaikgskgkvtLti 81 
                                       GD+Il+++++ ++n  ++   + +k +++ ++L+i
  gi|298674924|ref|YP_003726674.1| 330 GDIILGMDNREIRNSDQLITYLDTKLPGDRIKLKI 364
                                       9*************988877777777777777776 PP

>> GRASP55_65  GRASP55/65 PDZ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       2.1   4.3e+03      98     111 ..      68      81 ..      41      94 .. 0.64
   2 !   19.5   0.1   4.8e-07   0.00096      34     112 ..     286     378 ..     247     382 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.1
                                       EEETTTTEEEEEEE CS
                        GRASP55_65  98 vYnsesdevrevtv 111
                                       +Yn++sd+v ++ +
  gi|298674924|ref|YP_003726674.1|  68 LYNQVSDSVVSINI 81 
                                       57888887777777 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 4.8e-07
                                       EEE-TTTTTS-EEEEEEBTTSHHHHHT--TTTEEEEEEE..............SSSSSTSCSHHHHTTTS.SS-EEE CS
                        GRASP55_65  34 laslekaaeevwhvldvlegsPaakagLvpksDYiiGldk.............gllkgeedlselveahe.ekelkL 96 
                                       + +l+++++e + ++ v++g+Pa+kagL p +  ++  +                ++++++l++ + ++     +kL
  gi|298674924|ref|YP_003726674.1| 286 YMDLNDTVSEGVMIVRVIDGGPAEKAGLEPGKQIVVNGEPtwvngdiilgmdnREIRNSDQLITYLDTKLpGDRIKL 362
                                       556788999999****************9976544433332333333333333888888888888887652569*** PP

                                       EEEETTTTEEEEEEE- CS
                        GRASP55_65  97 lvYnsesdevrevtvk 112
                                        +Y +e+ ++ +vt++
  gi|298674924|ref|YP_003726674.1| 363 KIYRNENIKTVNVTLQ 378
                                       ***9988888777764 PP

>> DUF316  Chymotrypsin family Peptidase-S1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   1.4e-05     0.027       4      93 ..      20     117 ..      17     158 .. 0.67
   2 ?   -3.1   0.0       2.3   4.5e+03     217     251 ..     206     237 ..     190     245 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.4e-05
                            DUF316   4 llisiiiiilvs.sqklsekEneerlksCGnktlpkkskknngtyaekseneWlvlvafkngnekkela......pa 73 
                                        +i+ + +++vs +  l  +En++  ++ +n ++  ++  n +++ +   n+   +v   n+ e    +      ++
  gi|298674924|ref|YP_003726674.1|  20 FFIAGLLVGGVSlALSLNPDENQNQNQTQKNVHININKTINYSETYKELYNQVSDSVVSINIRESGLGSrisgqgSG 96 
                                       5666666655552689******************9999885555555545555555555554443333344476444 PP

                            DUF316  74 tvI..SsrHiltssrviltsks 93 
                                        +I  S+rHilt+ +vi  +++
  gi|298674924|ref|YP_003726674.1|  97 -FIydSNRHILTNQHVIDGAEN 117
                                       .5557**********9976555 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.3
                            DUF316 217 saeasiktsqylskkddggslikkvsgkntvlGfg 251
                                       s    i+t+ +l+ +++gg+l    s    ++G++
  gi|298674924|ref|YP_003726674.1| 206 SIPNVIQTDAPLNPGNSGGPLL-DLS--GQIIGVN 237
                                       5566789999999999999998.334..4455655 PP

>> Peptidase_S32  Equine arteritis virus serine endopeptidase S32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.002         4     113     164 ..      91     147 ..      77     155 .. 0.70
   2 ?    4.3   0.0    0.0096        19     206     227 ..     218     239 ..     193     301 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.002
                                       EEEEEEEECTTEEEEEEEHHHH-..TSEEEEEETTEEEEEEE...EEETTEEEEEET CS
                     Peptidase_S32 113 lGsGgvftidgevvvvtashvlg..dnkarvsivgasqtltf...ktkGDyalavva 164
                                       +G G+ f  d ++ ++t  hv+   +n  +v  +ga+q ++    ++  D a+ +v+
  gi|298674924|ref|YP_003726674.1|  91 SGQGSGFIYDSNRHILTNQHVIDgaENVEVVFSNGATQRANIvgsDKYSDIAVLRVD 147
                                       689999999*************86456666767777766554121444555555555 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0096
                                       -GGGTT-EEEETTE.EEEEEEE CS
                     Peptidase_S32 206 kcGDsGspvvdedgelvGvhtG 227
                                       ++G+sG p++d +g+++Gv   
  gi|298674924|ref|YP_003726674.1| 218 NPGNSGGPLLDLSGQIIGVNRA 239
                                       68*****************754 PP

>> CPSF_A  CPSF A subunit region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0     6e-05      0.12     186     233 ..     128     177 ..     110     195 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6e-05
                                       SSSEEEEEETTSEEEEEE--TTSGGGTTTT....EEEEEEEEE-SS----E CS
                            CPSF_A 186 gedtvlvaDkfgnlfvlrydpeasessdgdp...rleeraefhlgeivtsl 233
                                       ++ +++++Dk   + vlr+d + +e+++  p   +l +++++  ge+v  +
  gi|298674924|ref|YP_003726674.1| 128 QRANIVGSDKYSDIAVLRVD-NIPEEENYSPsplKLGNSSNIESGEFVMAI 177
                                       4359****************.89999999999***************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       904  (0.0504211); expected 358.6 (0.02)
Passed bias filter:                      671  (0.0374254); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.39
# Mc/sec: 2945.26
//
Query:       gi|298674925|ref|YP_003726675.1|  [L=79]
Description: redox-active disulfide protein 2 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-21   76.0   1.8    1.8e-21   75.9   1.8    1.0  1  Thioredoxin_3  Thioredoxin domain
     0.0017   18.7   0.1     0.0018   18.7   0.1    1.1  1  DUF836         Glutaredoxin-like domain (DUF836)
     0.0021   17.1   0.0     0.0021   17.1   0.0    1.0  1  T2SSE          Type II/IV secretion system protein
     0.0048   17.1   0.3        2.9    8.0   0.1    2.0  2  Thioredoxin_4  Thioredoxin
     0.0078   16.6   0.0      0.013   15.8   0.0    1.4  1  ArsD           Arsenical resistance operon trans-acting repre
  ------ inclusion threshold ------
      0.046   14.2   0.1       0.15   12.5   0.1    1.7  1  Thioredoxin_2  Thioredoxin-like domain
      0.066   13.4   0.1       0.16   12.2   0.1    1.6  1  Glutaredoxin   Glutaredoxin
      0.082   13.2   0.0          1    9.7   0.0    2.0  2  BON            BON domain


Domain annotation for each model (and alignments):
>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.9   1.8   8.2e-25   1.8e-21       1      75 [.       1      78 [.       1      79 [] 0.91

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 8.2e-25
                                      EEEEEE.SSSSTTCHHHHHHHHHHCHCCT..CECEEECCTTHHHHHHCT-SSSSEEECTTCEEEESS---CCHHHHHH CS
                     Thioredoxin_3  1 meikvl.gpgCakCpklekavkeaaaekg..ikaevekvtdfeeiekygVmsvPalvidgkvvvsGkvpseeeirkll 75
                                      m+i+vl  +gC +C kl++++++++ e+g   ++e++k++d+ ei+k+g+m++P +v dg+v+++Gkvps +ei+++l
  gi|298674925|ref|YP_003726675.1|  1 MKIEVLgASGCSTCSKLKENIEKIVSEMGksSEVEIVKIEDPVEIAKRGIMKTPVVVADGEVKFKGKVPSDDEIKEFL 78
                                      89***93456******************83455588899*************************************98 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   7.9e-07    0.0018       1      60 [.       2      63 ..       2      79 .] 0.78

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 7.9e-07
                                      -EEEEE-TT-HHHHHHHHHHHH.HCCCTT..EEEEEEETTT-CCCHCCCCTTTTEEEECTTCG CS
                            DUF836  1 kltLyskpgChlCeqakekLke.lkleeg..leleviDIakdeeleakYgleipvlalegvkk 60
                                      k+  ++  gC+ C ++ke +++ +  e g   e+e + I++  e  ++   ++pv++ +g  k
  gi|298674925|ref|YP_003726675.1|  2 KIEVLGASGCSTCSKLKENIEKiV-SEMGksSEVEIVKIEDPVEIAKRGIMKTPVVVADGEVK 63
                                      57889999*************953.44334689999999999999999999999999998443 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   9.6e-07    0.0021     149     190 ..      24      66 ..       7      79 .] 0.76

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 9.6e-07
                             T2SSE 149 llkeinks.derivtvEDpvEiqleganqvqlnakkakvtfad 190
                                       +++e+ ks + +iv +EDpvEi  +g+ ++ ++ ++++v f+ 
  gi|298674925|ref|YP_003726675.1|  24 IVSEMGKSsEVEIVKIEDPVEIAKRGIMKTPVVVADGEVKFKG 66 
                                       56666666589*********************99956665543 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.1    0.0013       2.9      23      50 ..       9      36 ..       2      44 .. 0.80
   2 !    7.9   0.0    0.0015       3.3     134     165 ..      46      79 .]      38      79 .] 0.80

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0013
                                      TT-HHHHHHHHHHHHHHHHHHHTTSEEE CS
                     Thioredoxin_4 23 lrCphCakfeeeveklleeyidtGkvkf 50
                                        C++C k++e++ek+++e  ++ +v++
  gi|298674925|ref|YP_003726675.1|  9 SGCSTCSKLKENIEKIVSEMGKSSEVEI 36
                                      67****************9766666655 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0015
                                       HHHT--SS-EEEETTEE..E-TT--HHHHHHHHT CS
                     Thioredoxin_4 134 kkagiestPtfiingek..veepqtyeelkalid 165
                                        k+gi  tP ++ +ge+    + ++ +e+k++++
  gi|298674925|ref|YP_003726675.1|  46 AKRGIMKTPVVVADGEVkfKGKVPSDDEIKEFLQ 79 
                                       689*************973356777888888875 PP

>> ArsD  Arsenical resistance operon trans-acting repressor ArsD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   5.8e-06     0.013      65      98 ..      45      78 ..      30      79 .] 0.90

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.8e-06
                              ArsD 65 lekkgaeaLPlvlvdgeivktgrYptreelaewl 98
                                      ++k+g  + P+v+ dge+  +g+ p+++e++e+l
  gi|298674925|ref|YP_003726675.1| 45 IAKRGIMKTPVVVADGEVKFKGKVPSDDEIKEFL 78
                                      6789999**********************99876 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   6.7e-05      0.15      11     102 ..       5      70 ..       2      78 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.7e-05
                     Thioredoxin_2  11 vftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPtivfl 87 
                                       v  +++C  C klk++++++  v +      +++s+e   v+i + ++++          e a++ g+  tP +v  
  gi|298674925|ref|YP_003726675.1|   5 VLGASGCSTCSKLKENIEKI--VSE------MGKSSE---VEIVKIEDPV----------EIAKR-GIMKTPVVVAD 59 
                                       567899**************..222......355544...4444445553..........45555.77777766554 PP

                     Thioredoxin_2  88 dgkeivarlpGyvpa 102
                                        +     + +G vp+
  gi|298674925|ref|YP_003726675.1|  60 GEV----KFKGKVPS 70 
                                       444....66777766 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   6.9e-05      0.16       2      59 ..       4      62 ..       3      63 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.9e-05
                                      EEEESTSSHHHHHHHHHH....HHTTGGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEETTEE CS
                      Glutaredoxin  2 vlftkptCpyCkkakrlL....kelgvkfeeidvdkdeeireelkelsgvrtvPqvfidgkh 59
                                      ++ + ++C  C+k k+       e+g k  e+++ k  e   e+ ++ g+++ P+v+ dg++
  gi|298674925|ref|YP_003726675.1|  4 EVLGASGCSTCSKLKENIekivSEMG-KSSEVEIVKI-EDPVEIAKR-GIMKTPVVVADGEV 62
                                      5667789*****99998833335555.3556777776.778899888.************96 PP

>> BON  BON domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.19   4.2e+02      37      61 ..      10      34 ..       9      40 .. 0.72
   2 ?    9.7   0.0   0.00045         1      26      45 ..      55      74 ..      52      77 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.19
                                      CEEECHHHHHHHHHHHHCCTTEEEE CS
                               BON 37 GtVdseaekekAveiarnvaGVkkV 61
                                      G+ +  + ke +++i+ +     +V
  gi|298674925|ref|YP_003726675.1| 10 GCSTCSKLKENIEKIVSEMGKSSEV 34
                                      6677778899999999887666666 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00045
                                      EEEETTCEEEECEEECHHHH CS
                               BON 26 VevenGvVtLsGtVdseaek 45
                                      V+v +G+V  +G V+s++e+
  gi|298674925|ref|YP_003726675.1| 55 VVVADGEVKFKGKVPSDDEI 74
                                      89**************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1029  (0.0573931); expected 358.6 (0.02)
Passed bias filter:                      754  (0.0420548); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 571.91
//
Query:       gi|298674926|ref|YP_003726676.1|  [L=204]
Description: 4Fe-4S ferredoxin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.7e-14   51.1  19.0      1e-11   44.6   0.9    3.9  4  Fer4_5           4Fe-4S binding domain
    1.8e-08   34.4  16.2    5.9e-06   26.3  15.6    3.0  3  Fer4_9           4Fe-4S dicluster domain
    2.4e-08   34.4  14.6    0.00023   21.7   2.5    3.2  3  Fer4_7           4Fe-4S dicluster domain
    1.4e-07   31.0  24.8    5.4e-05   22.8   5.5    3.4  3  Fer4             4Fe-4S binding domain
    2.9e-07   31.3  10.1     0.0013   19.6   2.6    3.3  3  Fer4_16          4Fe-4S double cluster binding domain
    9.6e-07   28.8  21.6      3e-05   24.0  17.7    3.2  4  Fer4_10          4Fe-4S dicluster domain
    2.7e-06   27.4  16.5    0.00038   20.5   2.7    2.6  3  Fer4_21          4Fe-4S dicluster domain
    1.8e-05   24.9  11.0    3.4e-05   24.0  10.5    1.8  1  Fer4_18          4Fe-4S dicluster domain
    2.8e-05   24.0  21.1     0.0011   18.9   5.0    2.7  2  Fer4_6           4Fe-4S binding domain
     0.0002   21.3  12.3    0.00063   19.7   1.9    3.1  3  Fer4_2           4Fe-4S binding domain
    0.00026   21.5  20.2       0.03   14.9   6.7    3.1  3  Fer4_17          4Fe-4S dicluster domain
     0.0038   18.1   5.2     0.0038   18.1   5.2    3.7  3  Fer4_3           4Fe-4S binding domain
     0.0073   16.8  18.4     0.0094   16.5   2.4    2.7  3  Fer4_13          4Fe-4S single cluster domain of Ferredoxin I
      0.008   16.6  22.5      0.023   15.2   2.5    3.3  3  Fer4_4           4Fe-4S binding domain
  ------ inclusion threshold ------
      0.062   13.8  20.0       0.19   12.2   3.8    2.6  3  Fer4_8           4Fe-4S dicluster domain
      0.075   13.9  10.8        1.3    9.9   2.0    2.4  2  Fer4_22          4Fe-4S dicluster domain
       0.59    9.4   3.5        1.2    8.4   3.5    1.5  1  DUF4407          Domain of unknown function (DUF4407)
        1.4    8.1   7.4        1.6    7.8   7.4    1.1  1  CitMHS           Citrate transporter
        2.7    8.2   8.9        0.2   11.8   1.2    2.2  2  ETF_QO           Electron transfer flavoprotein-ubiquinone ox
        6.2    7.6  13.0        4.6    8.1   2.8    2.3  2  Fer4_15          4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Fer4_5  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.5       5.7   5.1e+03       8      18 ..      10      20 ..       6      23 .. 0.50
   2 !   44.6   0.9   1.1e-14     1e-11       2      48 .]      26      72 ..      25      72 .. 0.90
   3 !   16.5   2.2   6.9e-06    0.0061       9      38 ..     119     147 ..     106     152 .. 0.83
   4 ?    0.5   0.0      0.69   6.2e+02      24      33 ..     191     200 ..     191     201 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.7
                            Fer4_5  8 lflaivlvtll 18
                                      ++++iv +++l
  gi|298674926|ref|YP_003726676.1| 10 ILVLIVSIAGL 20
                                      33444444444 PP

  == domain 2  score: 44.6 bits;  conditional E-value: 1.1e-14
                            Fer4_5  2 allllilflaivlvtllfGRafCgWiCPfGalqellakllrrklgkp 48
                                      ++++l+ f+a++l++ + GR+fCg++CP+G+l +++   + +++++p
  gi|298674926|ref|YP_003726676.1| 26 GYFMLVVFAALLLISPFRGRWFCGNLCPRGSLNDFVVGKITKNKKIP 72
                                      789********************************988777777765 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 6.9e-06
                            Fer4_5   9 flaivlvtllfGRafCgWiCPfGalqella 38 
                                        +a+vl   +  R +C+ +CP G+ q +l+
  gi|298674926|ref|YP_003726676.1| 119 SIAVVLGISISPRTWCS-FCPMGTAQRILG 147
                                       46777777779******.********9986 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.69
                            Fer4_5  24 CgWiCPfGal 33 
                                       C ++CP Ga+
  gi|298674926|ref|YP_003726676.1| 191 CVNACPKGAI 200
                                       999***9986 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.99   8.9e+02       8      27 ..      48      67 ..      45      77 .. 0.72
   2 !   20.2   3.3   5.4e-07   0.00049      11      49 ..     136     173 ..     132     175 .. 0.91
   3 !   26.3  15.6   6.6e-09   5.9e-06       1      51 []     159     200 ..     159     200 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.99
                            Fer4_9  8 CveaCpagvvvedaaerkar 27
                                      C + Cp g  ++  ++++ +
  gi|298674926|ref|YP_003726676.1| 48 CGNLCPRGSLNDFVVGKITK 67
                                      67778877777766666655 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 5.4e-07
                            Fer4_9  11 aCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                        Cp+g++++  +++k +l+++++ +Ci+C++C + Cp +
  gi|298674926|ref|YP_003726676.1| 136 FCPMGTAQRILGGNKYQLDIDED-RCISCKKCDKSCPMH 173
                                       4*****************99887.9************86 PP

  == domain 3  score: 26.3 bits;  conditional E-value: 6.6e-09
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       +C++C++C ++Cp+++ v ++ ++          +Ci+C++Cv+aCpkgai
  gi|298674926|ref|YP_003726676.1| 159 RCISCKKCDKSCPMHLKVHKNETKP---------DCIKCERCVNACPKGAI 200
                                       6****************99988877.........5**************98 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0       0.7   6.2e+02       7      17 ..      47      57 ..      45      96 .. 0.81
   2 !   15.6   4.2   2.1e-05     0.019      29      50 ..     151     172 ..     132     174 .. 0.74
   3 !   21.7   2.5   2.6e-07   0.00023       2      20 ..     185     203 ..     184     204 .] 0.93

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.7
                            Fer4_7  7 aCvaaCpvkai 17
                                      +C + Cp + +
  gi|298674926|ref|YP_003726676.1| 47 FCGNLCPRGSL 57
                                      68888887655 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 2.1e-05
                            Fer4_7  29 ekveidpekClgCgaCvavCPt 50 
                                        +++id+++C++C++C + CP 
  gi|298674926|ref|YP_003726676.1| 151 YQLDIDEDRCISCKKCDKSCPM 172
                                       3578999*************95 PP

  == domain 3  score: 21.7 bits;  conditional E-value: 2.6e-07
                            Fer4_7   2 CigCgaCvaaCpvkaield 20 
                                       Ci+C++Cv+aCp +ai+++
  gi|298674926|ref|YP_003726676.1| 185 CIKCERCVNACPKGAIDFQ 203
                                       ****************997 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       1.2     1e+03      14      21 ..      48      55 ..      47      57 .. 0.79
   2 !   20.1   2.6   4.4e-07    0.0004       3      20 ..     155     172 ..     153     173 .. 0.92
   3 !   22.8   5.5   6.1e-08   5.4e-05       7      24 .]     184     201 ..     183     201 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.2
                                      HHHHSTTT CS
                              Fer4 14 CvevCPvg 21
                                      C + CP g
  gi|298674926|ref|YP_003726676.1| 48 CGNLCPRG 55
                                      8889*987 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 4.4e-07
                                       EETTTSSS-THHHHHSTT CS
                              Fer4   3 ideekCigCGaCvevCPv 20 
                                       ide++Ci C++C + CP 
  gi|298674926|ref|YP_003726676.1| 155 IDEDRCISCKKCDKSCPM 172
                                       9****************5 PP

  == domain 3  score: 22.8 bits;  conditional E-value: 6.1e-08
                                       TSSS-THHHHHSTTTEEE CS
                              Fer4   7 kCigCGaCvevCPvgAIt 24 
                                       +Ci+C +Cv++CP gAI+
  gi|298674926|ref|YP_003726676.1| 184 DCIKCERCVNACPKGAID 201
                                       5***************95 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.92   8.2e+02       8      31 ..      48      71 ..      46      81 .. 0.76
   2 !   13.0   1.0   0.00017      0.15       1      15 [.     159     173 ..     149     183 .. 0.83
   3 !   19.6   2.6   1.4e-06    0.0013       2      19 ..     185     202 ..     184     204 .] 0.92

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.92
                           Fer4_16  8 CaevCPtnaikekkekeieareci 31
                                      C + CP + ++     +i ++++i
  gi|298674926|ref|YP_003726676.1| 48 CGNLCPRGSLNDFVVGKITKNKKI 71
                                      888999999998876777666655 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00017
                           Fer4_16   1 rCgtCgkCaevCPtn 15 
                                       rC++C+kC ++CP +
  gi|298674926|ref|YP_003726676.1| 159 RCISCKKCDKSCPMH 173
                                       599999999999975 PP

  == domain 3  score: 19.6 bits;  conditional E-value: 1.4e-06
                           Fer4_16   2 CgtCgkCaevCPtnaike 19 
                                       C++C++C+++CP +ai+ 
  gi|298674926|ref|YP_003726676.1| 185 CIKCERCVNACPKGAIDF 202
                                       ****************86 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       3.7   3.4e+03      15      21 ..      48      54 ..      47      75 .. 0.58
   2 ?   -1.9   0.0       4.1   3.7e+03      18      21 ..     136     139 ..     134     150 .. 0.66
   3 !   24.0  17.7   3.3e-08     3e-05       4      56 .]     155     196 ..     152     196 .. 0.82
   4 !   14.4   5.1   3.5e-05     0.032       8      21 ..     184     197 ..     177     204 .] 0.80

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.7
                           Fer4_10 15 CvkaCPa 21
                                      C + CP 
  gi|298674926|ref|YP_003726676.1| 48 CGNLCPR 54
                                      7778887 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.1
                           Fer4_10  18 aCPa 21 
                                       +CP+
  gi|298674926|ref|YP_003726676.1| 136 FCPM 139
                                       6999 PP

  == domain 3  score: 24.0 bits;  conditional E-value: 3.3e-08
                           Fer4_10   4 idddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       id+d+Ci C+kC k+CP+             + ++++   +C++c+ Cv aCP
  gi|298674926|ref|YP_003726676.1| 155 IDEDRCISCKKCDKSCPM-----------HLKVHKNETKPDCIKCERCVNACP 196
                                       89****************...........344444444468***********9 PP

  == domain 4  score: 14.4 bits;  conditional E-value: 3.5e-05
                           Fer4_10   8 tCirCgkCvkaCPa 21 
                                        Ci+C++Cv+aCP 
  gi|298674926|ref|YP_003726676.1| 184 DCIKCERCVNACPK 197
                                       6************8 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       7.2   6.5e+03      47      52 ..      48      53 ..      46      58 .. 0.73
   2 !   20.5   2.7   4.3e-07   0.00038      17      53 ..     136     172 ..     131     178 .. 0.87
   3 !   14.1   3.3   4.3e-05     0.038       7      23 ..     184     200 ..     179     203 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 7.2
                           Fer4_21 47 CssvCP 52
                                      C + CP
  gi|298674926|ref|YP_003726676.1| 48 CGNLCP 53
                                      778888 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 4.3e-07
                           Fer4_21  17 aCedtshqaieidaktvlkvvedeCvGCnlCssvCPv 53 
                                        C+ ++ q i + +k +l + ed+C+ C+ C + CP+
  gi|298674926|ref|YP_003726676.1| 136 FCPMGTAQRILGGNKYQLDIDEDRCISCKKCDKSCPM 172
                                       6999999999999999999999999999999999997 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 4.3e-05
                           Fer4_21   7 kCigCgkCliaCedtsh 23 
                                       +Ci+C++C+ aC+++++
  gi|298674926|ref|YP_003726676.1| 184 DCIKCERCVNACPKGAI 200
                                       68888888888887665 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0  10.5   3.8e-08   3.4e-05      57      97 ..     156     197 ..     139     203 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 3.8e-08
                           Fer4_18  57 gagdcidcescvkvcPtgidirk.Glqleciscllcidacdk 97 
                                       ++  ci+c++c k cP+++ + k   + +ci+c +c++ac k
  gi|298674926|ref|YP_003726676.1| 156 DEDRCISCKKCDKSCPMHLKVHKnETKPDCIKCERCVNACPK 197
                                       5678****************97625789************65 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   4.2   4.6e-05     0.041       4      21 ..     155     172 ..     154     174 .. 0.93
   2 !   18.9   5.0   1.2e-06    0.0011       9      24 .]     185     200 ..     182     200 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.6e-05
                            Fer4_6   4 idpdkCigCgdCvrvCPe 21 
                                       id+d+Ci+C +C + CP+
  gi|298674926|ref|YP_003726676.1| 155 IDEDRCISCKKCDKSCPM 172
                                       8***************96 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 1.2e-06
                            Fer4_6   9 CigCgdCvrvCPegai 24 
                                       Ci C++Cv++CP gai
  gi|298674926|ref|YP_003726676.1| 185 CIKCERCVNACPKGAI 200
                                       **************98 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.7       7.6   6.8e+03      16      21 ..     134     138 ..     134     139 .. 0.78
   2 !   19.7   1.9     7e-07   0.00063       5      21 ..     155     171 ..     152     172 .. 0.94
   3 !   13.8   3.1   5.4e-05     0.048       7      21 ..     183     196 ..     177     197 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 7.6
                            Fer4_2  16 CvsaCP 21 
                                       C s CP
  gi|298674926|ref|YP_003726676.1| 134 C-SFCP 138
                                       7.8898 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 7e-07
                            Fer4_2   5 vdtdrCigCgaCvsaCP 21 
                                       +d+drCi+C++C ++CP
  gi|298674926|ref|YP_003726676.1| 155 IDEDRCISCKKCDKSCP 171
                                       79*************** PP

  == domain 3  score: 13.8 bits;  conditional E-value: 5.4e-05
                            Fer4_2   7 tdrCigCgaCvsaCP 21 
                                       +d Ci C+ Cv+aCP
  gi|298674926|ref|YP_003726676.1| 183 PD-CIKCERCVNACP 196
                                       45.***********9 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.9   1.7e+03       8      20 ..      48      60 ..      46      78 .. 0.70
   2 !   14.9   6.7   3.4e-05      0.03      44      60 ..     158     174 ..     133     175 .. 0.82
   3 !   11.2   4.8   0.00046      0.41      39      59 ..     178     198 ..     175     199 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.9
                           Fer4_17  8 ClpeCpsyeaydn 20
                                      C + Cp++  +d+
  gi|298674926|ref|YP_003726676.1| 48 CGNLCPRGSLNDF 60
                                      7888888777665 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 3.4e-05
                           Fer4_17  44 slCieCgeCerkCPqgl 60 
                                       ++Ci+C++C+++CP++l
  gi|298674926|ref|YP_003726676.1| 158 DRCISCKKCDKSCPMHL 174
                                       79**************9 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00046
                           Fer4_17  39 keekaslCieCgeCerkCPqg 59 
                                       k+e+  +Ci+C++C+ +CP+g
  gi|298674926|ref|YP_003726676.1| 178 KNETKPDCIKCERCVNACPKG 198
                                       5666779************86 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1       1.2     1e+03       7      14 ..      48      55 ..      46      56 .. 0.80
   2 ?    5.1   3.9     0.057        51       1      12 [.     160     171 ..     160     173 .. 0.93
   3 !   18.1   5.2   4.3e-06    0.0038       1      15 []     185     199 ..     185     199 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 1.2
                            Fer4_3  7 CvevCPvg 14
                                      C + CP g
  gi|298674926|ref|YP_003726676.1| 48 CGNLCPRG 55
                                      77889987 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.057
                            Fer4_3   1 CtgCgaCvevCP 12 
                                       C+ C  C ++CP
  gi|298674926|ref|YP_003726676.1| 160 CISCKKCDKSCP 171
                                       ************ PP

  == domain 3  score: 18.1 bits;  conditional E-value: 4.3e-06
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+ C++Cv++CP+gA
  gi|298674926|ref|YP_003726676.1| 185 CIKCERCVNACPKGA 199
                                       **************9 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       7.7   6.9e+03      12      17 ..      48      53 ..      47      54 .. 0.87
   2 !   16.5   2.4   1.1e-05    0.0094       1      24 [.     155     178 ..     155     182 .. 0.87
   3 !    9.4   4.3    0.0018       1.6       5      18 ..     184     197 ..     180     198 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 7.7
                           Fer4_13 12 CvelaP 17
                                      C++l+P
  gi|298674926|ref|YP_003726676.1| 48 CGNLCP 53
                                      99***9 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.1e-05
                           Fer4_13   1 VDrdtCiacgaCvelaPdvFeedd 24 
                                       +D+d+Ci+c++C + +P + +  +
  gi|298674926|ref|YP_003726676.1| 155 IDEDRCISCKKCDKSCPMHLKVHK 178
                                       89***************9987665 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0018
                           Fer4_13   5 tCiacgaCvelaPd 18 
                                        Ci c+ Cv+++P+
  gi|298674926|ref|YP_003726676.1| 184 DCIKCERCVNACPK 197
                                       6************6 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1       2.3     2e+03      12      17 .]     135     140 ..     135     140 .. 0.81
   2 !   13.2   3.5   0.00011     0.099       2      16 ..     158     172 ..     157     175 .. 0.94
   3 !   15.2   2.5   2.6e-05     0.023       4      16 ..     185     197 ..     178     201 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2.3
                            Fer4_4  12 aaCPqg 17 
                                       ++CP+g
  gi|298674926|ref|YP_003726676.1| 135 SFCPMG 140
                                       69**86 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00011
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       +rCi C++C  +CP+
  gi|298674926|ref|YP_003726676.1| 158 DRCISCKKCDKSCPM 172
                                       8*************5 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 2.6e-05
                            Fer4_4   4 CigCgsCvaaCPq 16 
                                       Ci C +Cv+aCP 
  gi|298674926|ref|YP_003726676.1| 185 CIKCERCVNACPK 197
                                       ************6 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   3.8   0.00021      0.19      49      64 ..     158     173 ..     141     176 .. 0.79
   2 ?   12.0   4.1   0.00025      0.22       4      19 ..     159     174 ..     156     184 .. 0.61
   3 ?    9.5   4.7    0.0015       1.3       5      16 ..     185     196 ..     182     199 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00021
                            Fer4_8  49 wsCttcgaCtevCpvg 64 
                                       ++C +c++C++ Cp++
  gi|298674926|ref|YP_003726676.1| 158 DRCISCKKCDKSCPMH 173
                                       5788888888888876 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00025
                            Fer4_8   4 kCieCgaCqsaCpvlr 19 
                                       +Ci C  C ++Cp+  
  gi|298674926|ref|YP_003726676.1| 159 RCISCKKCDKSCPMHL 174
                                       5666666666665443 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0015
                            Fer4_8   5 CieCgaCqsaCp 16 
                                       Ci+C++C +aCp
  gi|298674926|ref|YP_003726676.1| 185 CIKCERCVNACP 196
                                       777777777776 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.5    0.0024       2.2      74      95 ..     152     173 ..     143     174 .. 0.76
   2 ?    9.9   2.0    0.0015       1.3      73      94 ..     176     197 ..     172     199 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0024
                           Fer4_22  74 kekfgesgCvGCgRCieacpvk 95 
                                       +  ++e  C+ C +C+++cp++
  gi|298674926|ref|YP_003726676.1| 152 QLDIDEDRCISCKKCDKSCPMH 173
                                       5556788888888888888875 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0015
                           Fer4_22  73 fkekfgesgCvGCgRCieacpv 94 
                                       ++++  +  C+ C RC++acp+
  gi|298674926|ref|YP_003726676.1| 176 VHKNETKPDCIKCERCVNACPK 197
                                       556677889***********97 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   3.5    0.0013       1.2      13      95 ..       7      93 ..       4     100 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0013
                           DUF4407 13 yagiGavvlltallAalsgayAlytvlkspll.....lallvGllwgllIfnlDRfivssikkrakkrrelalalpRl. 85
                                      y gi ++++++a l++ +++y++  v+ + ll     + +++G l      +l  f+v  i+k++k   +l++++ R+ 
  gi|298674926|ref|YP_003726676.1|  7 YLGILVLIVSIAGLWFPILGYFMLVVFAALLLispfrGRWFCGNLCPR--GSLNDFVVGKITKNKKIPETLKTLWLRVp 83
                                      8999**************************985555555555555544..6899***********************98 PP

                           DUF4407 86 llAvligvvi 95
                                      ++A+l+g++ 
  gi|298674926|ref|YP_003726676.1| 84 VFAALMGFMG 93
                                      89*****985 PP

>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   7.4    0.0018       1.6     148     267 ..       8     130 ..       1     145 [. 0.78

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0018
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................xxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 148 lpnllllalllvgllplvllfmfgvalalpvnap......................kvkkqkaiieaiarsllpvat 202
                                       l  l+l++ ++ + +p++ +fm  v+ al+   p                      k +k+k+i e++++ l+  + 
  gi|298674926|ref|YP_003726676.1|   8 LGILVLIVSIAGLWFPILGYFMLVVFAALLLISPfrgrwfcgnlcprgslndfvvgKITKNKKIPETLKT-LWLRVP 83 
                                       334444555555559999999999999999999999**********************************.554666 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                            CitMHS 203 illlaykkveWsvlllfaGvfllvgaleqtGilealadllgaggplvalalvlglial.lsafisn 267
                                       ++              +   f++  +++  G++++++ ++      v++ lv+  ia+ l + is+
  gi|298674926|ref|YP_003726676.1|  84 VF-------------AALMGFMGFRIMQTQGLINQIGMVF------VVMCLVTTSIAVvLGISISP 130
                                       66.............56667777899**********9888......65666666666557776665 PP

>> ETF_QO  Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.2   0.00022       0.2      48      86 ..     135     171 ..     126     181 .. 0.84
   2 ?    0.0   1.9         1   9.1e+02      74      92 ..     184     202 ..     173     204 .] 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00022
                                       HH-TTS-EEEEETTTTSSEEEEE-CCC--S--HHHHH-T CS
                            ETF_QO  48 ryCPagvyeivedeeakekklqinaqnCvhCktCdikdp 86 
                                        +CP g  + +     ++ +l i+   C+ Ck Cd   p
  gi|298674926|ref|YP_003726676.1| 135 SFCPMGTAQRILGG--NKYQLDIDEDRCISCKKCDKSCP 171
                                       58999988877666..6899***************7655 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1
                                       C--S--HHHHH-TT--EEE CS
                            ETF_QO  74 nCvhCktCdikdpsqniew 92 
                                       +C+ C  C    p+  i++
  gi|298674926|ref|YP_003726676.1| 184 DCIKCERCVNACPKGAIDF 202
                                       7*******99999988887 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   2.8    0.0051       4.6       3      20 ..     155     172 ..     153     182 .. 0.84
   2 ?    5.0   2.7     0.046        41       7      20 ..     184     197 ..     180     202 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0051
                           Fer4_15   3 vDrdaCigcglCvaeape 20 
                                       +D+d+Ci+c  C + +p 
  gi|298674926|ref|YP_003726676.1| 155 IDEDRCISCKKCDKSCPM 172
                                       9***********999985 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.046
                           Fer4_15   7 aCigcglCvaeape 20 
                                        Ci c++Cv ++p+
  gi|298674926|ref|YP_003726676.1| 184 DCIKCERCVNACPK 197
                                       7**********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1387  (0.0773607); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 1558.00
//
Query:       gi|298674927|ref|YP_003726677.1|  [L=132]
Description: transcriptional regulator TrmB [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-05   23.1   0.0    6.9e-05   22.7   0.0    1.2  1  MarR_2           MarR family
      5e-05   23.4   0.3    0.00012   22.2   0.0    1.8  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
    7.2e-05   22.6   0.1     0.0001   22.1   0.1    1.3  1  TrmB             Sugar-specific transcriptional regulator Trm
    0.00079   18.4   0.7    0.00083   18.3   0.7    1.1  1  HTH_micro        HTH-like
    0.00096   18.7   0.0     0.0015   18.0   0.0    1.4  1  HTH_24           Winged helix-turn-helix DNA-binding
     0.0028   17.5   0.1     0.0063   16.4   0.1    1.6  1  MarR             MarR family
     0.0032   17.4   0.1     0.0054   16.6   0.1    1.5  1  HTH_11           HTH domain
      0.005   16.7   2.2     0.0076   16.1   2.1    1.3  1  TFIIE_alpha      TFIIE alpha subunit
     0.0058   16.6   0.0      0.012   15.5   0.0    1.5  1  HTH_36           Helix-turn-helix domain
  ------ inclusion threshold ------
      0.017   14.8   0.1      0.049   13.3   0.0    1.7  2  HTH_41           Helix-turn-helix domain
      0.019   15.1   0.2      0.053   13.6   0.1    1.9  2  Trans_reg_C      Transcriptional regulatory protein, C termin
      0.019   14.7   2.3      0.037   13.8   2.3    1.5  1  Stealth_CR1      Stealth protein CR1, conserved region 1
       0.02   15.3   0.2      0.025   14.9   0.2    1.3  1  Penicillinase_R  Penicillinase repressor
      0.022   15.0   0.1      0.029   14.6   0.1    1.3  1  Rio2_N           Rio2, N-terminal
      0.031   14.8   0.1      0.059   13.9   0.1    1.5  1  HTH_27           Winged helix DNA-binding domain
      0.035   14.4   0.1      0.054   13.8   0.1    1.3  1  TFIIE_beta       TFIIE beta subunit core domain
      0.043   14.2   0.0      0.066   13.6   0.0    1.3  1  Rrf2             Transcriptional regulator
      0.067   13.2   0.0       0.19   11.7   0.0    1.8  1  Dimerisation     Dimerisation domain
      0.099   12.3   0.1        0.3   10.8   0.1    1.7  2  GntR             Bacterial regulatory proteins, gntR family


Domain annotation for each model (and alignments):
>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   7.3e-08   6.9e-05       2      56 ..      20      74 ..      19      78 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 7.3e-08
                                      T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                       lt ++++++++  r  +r +t   +a +l+l+ s+v++++k+L +   + r+ +
  gi|298674927|ref|YP_003726677.1| 20 NLTKSELDIMNYFLRDTDRWVTTENIATELKLDLSTVQKAVKKLHSNEVLKRSQN 74
                                      5788999999998888889***************************999999977 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   1.3e-07   0.00012      14      53 ..      31      70 ..      30      76 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.3e-07
                                      HHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress 14 YtlseekkvvktkdlaerLnvspssVsemlkkLekdGyve 53
                                      Y l ++   v+t ++a +L+   s+V++ +kkL++++ ++
  gi|298674927|ref|YP_003726677.1| 31 YFLRDTDRWVTTENIATELKLDLSTVQKAVKKLHSNEVLK 70
                                      667788899**************************98776 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   1.1e-07    0.0001       1      65 [.      15      88 ..      15      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.1e-07
                                      HH.HCHHHHHCCCHCHHHH..HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST......TTEEEE- CS
                              TrmB  1 Lq.klGLseyEakvYlaLl..klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr......pklYrav 65
                                      L+ +l+L++ E ++  + l  +    t++ ia el+++ s+v++++++L +  + +r++ +       ++Yr  
  gi|298674927|ref|YP_003726677.1| 15 LKcALNLTKSELDIMNYFLrdTDRWVTTENIATELKLDLSTVQKAVKKLHSNEVLKRSQNNldnggyVYIYRIY 88
                                      67789999999999999998778889*********************************999999986677754 PP

>> HTH_micro  HTH-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.7   8.8e-07   0.00083      93     152 ..      25      89 ..      12     125 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 8.8e-07
                         HTH_micro  93 yykivdflvkak.dyvkaaelraklnidpKklfYvikkLakkglieqktkeeak.....ivikink 152
                                         +i+++ ++   + v++ ++ ++l++d  ++  ++kkL+++++++  +++        ++++i +
  gi|298674927|ref|YP_003726677.1|  25 ELDIMNYFLRDTdRWVTTENIATELKLDLSTVQKAVKKLHSNEVLKRSQNNL-DnggyvYIYRIYS 89 
                                       469******988689*******************************554443.3477445555544 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.6e-06    0.0015       2      48 .]      22      70 ..      21      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.6e-06
                            HTH_24  2 detdrkILelLqk.npr.isqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                       + +++I+++  +   r  +   +A +l l +stv + +k+L +++++k
  gi|298674927|ref|YP_003726677.1| 22 TKSELDIMNYFLRdTDRwVTTENIATELKLDLSTVQKAVKKLHSNEVLK 70
                                      577889997766668889************************9999875 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   6.7e-06    0.0063      20      55 ..      42      77 ..      32      78 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.7e-06
                                      HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTS CS
                              MarR 20 vseLakklgvskstvtrvldrLekkGlieRskspeD 55
                                         +a  l+++ stv +++++L  ++ ++Rs++  D
  gi|298674927|ref|YP_003726677.1| 42 TENIATELKLDLSTVQKAVKKLHSNEVLKRSQNNLD 77
                                      5689****************************9765 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   5.8e-06    0.0054       3      42 ..      26      66 ..      24      92 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.8e-06
                            HTH_11  3 lqilelLleargp.isgeeLAeeLnvSrrtvrrdIkaLeel 42
                                      l+i+  +l+ ++  ++ e +A eL++  +tv++ +k+L + 
  gi|298674927|ref|YP_003726677.1| 26 LDIMNYFLRDTDRwVTTENIATELKLDLSTVQKAVKKLHSN 66
                                      67888877888888************************765 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   2.1   8.1e-06    0.0076      27     100 ..      39     112 ..      21     115 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.1e-06
                                       SEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEE.CCCHCCCHHHHHHHHHHHHHHHH CS
                       TFIIE_alpha  27 evteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrin.yeklvdvvkrkleevvkkLeekl 100
                                        vt e++a elk+dl  + k++ +L +  + k  +  + + + y y +ri   +++ + + + +   v ++ ++l
  gi|298674927|ref|YP_003726677.1|  39 WVTTENIATELKLDLSTVQKAVKKLHSNEVLKRSQ-NNLDNGGYVYIYRIYsRREIKNLIMDIVYTWVNRVDNEL 112
                                       4899*************************997444.445566777888875145677777777766666666665 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.3e-05     0.012      25      50 ..      39      64 ..      32      68 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.3e-05
                            HTH_36 25 fpsqetlakrlglsknTvsraikeLe 50
                                      + + e +a+ l+l+ +Tv++a+k+L 
  gi|298674927|ref|YP_003726677.1| 39 WVTTENIATELKLDLSTVQKAVKKLH 64
                                      8899*********************7 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       4.4   4.1e+03      11      18 ..       4      11 ..       2      12 .. 0.77
   2 ?   13.3   0.0   5.2e-05     0.049       4      35 ..      37      68 ..      36      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.4
                            HTH_41 11 elakeleL 18
                                        +ke+eL
  gi|298674927|ref|YP_003726677.1|  4 FACKEFEL 11
                                      5699**98 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 5.2e-05
                            HTH_41  4 dRlktIeelakeleLSvGlvQkALklLeddka 35
                                      dR  t e++a el L   +vQkA+k+L ++ +
  gi|298674927|ref|YP_003726677.1| 37 DRWVTTENIATELKLDLSTVQKAVKKLHSNEV 68
                                      677788999******************99876 PP

>> Trans_reg_C  Transcriptional regulatory protein, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   5.6e-05     0.053       4      35 ..      19      50 ..      16      83 .. 0.89
   2 ?   -1.8   0.0       3.6   3.4e+03      24      48 ..      87     114 ..      83     117 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.6e-05
                                      EE-SHHHHHHHHHHHHTTTSEEEHHHHHHHHT CS
                       Trans_reg_C  4 veltpkefklLelLlenpgrvvsreeLleevw 35
                                      ++lt+ e +++ ++l++ +r v+ e++  e+ 
  gi|298674927|ref|YP_003726677.1| 19 LNLTKSELDIMNYFLRDTDRWVTTENIATELK 50
                                      78*************************99875 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.6
                                       EEEHHHHHHHHTTTTS...TSHTHHHHH CS
                       Trans_reg_C  24 vvsreeLleevwgede...dvddrtvdv 48 
                                       ++sr e+ + + +  +   +  d+ +d+
  gi|298674927|ref|YP_003726677.1|  87 IYSRREIKNLIMDIVYtwvNRVDNELDQ 114
                                       5666666655555555444466666666 PP

>> Stealth_CR1  Stealth protein CR1, conserved region 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   2.3   3.9e-05     0.037       3      11 ..      98     106 ..      97     106 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.9e-05
                       Stealth_CR1   3 IDvVYTWVN 11 
                                       +D+VYTWVN
  gi|298674927|ref|YP_003726677.1|  98 MDIVYTWVN 106
                                       6*******9 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.2   2.6e-05     0.025       1      62 [.      21      83 ..      21     120 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.6e-05
                                      ---S-SHHHHHHHHHS-..EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEE...TTEEEE CS
                   Penicillinase_R  1 lgelEaevmeilwekge..atvkevveeleeekelaysTVktllrrLvkKgllsreke...grafiY 62
                                      l+++E+ +m+++ +  +  +t++++ +el+ +     sTV+  +++L+  ++l+r ++   +  ++Y
  gi|298674927|ref|YP_003726677.1| 21 LTKSELDIMNYFLRDTDrwVTTENIATELKLD----LSTVQKAVKKLHSNEVLKRSQNnldNGGYVY 83
                                      699*******9877766588888898888877....9*****************9986333344555 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   3.1e-05     0.029      23      69 ..      38      86 ..      21      96 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.1e-05
                            Rio2_N 23 evVptelieeisrlkeeevkkrlsrllkaklisr..ktakydGYkLtye 69
                                      ++V te i++  +l+ + v+k++++l+ ++ ++r  ++    GY  +y 
  gi|298674927|ref|YP_003726677.1| 38 RWVTTENIATELKLDLSTVQKAVKKLHSNEVLKRsqNNLDNGGYVYIYR 86
                                      69********************************544444558877776 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   6.2e-05     0.059      14      58 ..      35      79 ..      21      87 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.2e-05
                            HTH_27 14 hrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrr 58
                                       ++r ++ + ++  l+++ s++ +++kkL+ +++++r++   d +
  gi|298674927|ref|YP_003726677.1| 35 DTDRWVTTENIATELKLDLSTVQKAVKKLHSNEVLKRSQNNLDNG 79
                                      5678889999*************************9988766655 PP

>> TFIIE_beta  TFIIE beta subunit core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   5.8e-05     0.054      11      50 ..      32      68 ..      24      84 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.8e-05
                        TFIIE_beta 11 ylKkkdgplsleeIlsylslqldlsdknwllleaLknnpk 50
                                      +l+ +d++++ e+I+ +l+l  dls+  ++ ++ L +n+ 
  gi|298674927|ref|YP_003726677.1| 32 FLRDTDRWVTTENIATELKL--DLST-VQKAVKKLHSNEV 68
                                      7999****************..9964.5667888888874 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     7e-05     0.066      13      56 ..      28      70 ..      20      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7e-05
                                      HHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 13 allyLakeeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      ++ y  +  ++  v++e+ia++ ++  s ++k ++kL  ++++k
  gi|298674927|ref|YP_003726677.1| 28 IMNYFLRDTDR-WVTTENIATELKLDLSTVQKAVKKLHSNEVLK 70
                                      56666666665.5*************************999887 PP

>> Dimerisation  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0    0.0002      0.19       2      34 ..      14      51 ..      14      64 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0002
                      Dimerisation  2 vLKaAi.....ELglldiiakaggkplspsEiaskLpt 34
                                      vLK+A+     EL++++     +++++++++ia+ L+ 
  gi|298674927|ref|YP_003726677.1| 14 VLKCALnltksELDIMNYFLRDTDRWVTTENIATELKL 51
                                      7888876666699***********************94 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00031       0.3      28      59 ..      43      74 ..      40      75 .. 0.91
   2 ?   -2.3   0.0       3.8   3.6e+03       4      14 ..     107     117 ..     105     120 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00031
                                      HHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                              GntR 28 reLaaefgVsrttvReALrrLeaeglverrqg 59
                                      + +a+e++ + +tv++A ++L +  ++ r q+
  gi|298674927|ref|YP_003726677.1| 43 ENIATELKLDLSTVQKAVKKLHSNEVLKRSQN 74
                                      679************************99875 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.8
                                       HHHHHHHHHHH CS
                              GntR   4 qvyerLredIl 14 
                                       +v  +L+++I+
  gi|298674927|ref|YP_003726677.1| 107 RVDNELDQWIM 117
                                       78889999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1173  (0.0654247); expected 358.6 (0.02)
Passed bias filter:                      630  (0.0351386); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 965.04
//
Query:       gi|298674928|ref|YP_003726678.1|  [L=389]
Description: major facilitator superfamily protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-44  151.1  38.1    3.8e-44  151.1  38.1    2.0  2  MFS_1     Major Facilitator Superfamily
      2e-10   39.7  16.3    2.3e-10   39.5  16.3    1.0  1  MFS_3     Transmembrane secretion effector


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.1  38.1   4.2e-48   3.8e-44       1     353 []      11     347 ..      11     347 .. 0.91
   2 !    3.1   4.0     0.004        36     132     172 ..     341     379 ..     340     388 .. 0.86

  Alignments for each domain:
  == domain 1  score: 151.1 bits;  conditional E-value: 4.2e-48
                             MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgll 77 
                                       l+l++f+ + ++++lgp+lp ++ e l+ s  ++gl+l++y+l +a+++l +G+++dr+ ++++l+ +l++ +l+++
  gi|298674928|ref|YP_003726678.1|  11 LCLITFFGMSGSTLLGPVLP-TIVEPLNTSREAVGLILAVYTLSTALFTLAIGSITDRINHKKILIPCLIVNGLSGM 86 
                                       68999***************.9*****************************************************77 PP

                             MFS_1  78 lllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravf 154
                                       +++fa+ l+lll+ r++qG + ++++p+++++i  ++++++r  a+g  s+++++Ga+  p +gg +   +gW  +f
  gi|298674928|ref|YP_003726678.1|  87 AAFFATDLTLLLFIRFIQGSAVAGMTPLAMTIIGGLYSGKQRIHAMGRRSMSIAIGAVSLPFIGGSMG-IFGWNFPF 162
                                       777866666***********************************************************.*******9 PP

                             MFS_1 155 yilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllp 231
                                       ++ ++   +a+v   +++  ++++++ +++k      + + +++a+k ++ +      ++ ++ ++f ++++ +++p
  gi|298674928|ref|YP_003726678.1| 163 LFYCLTIPIAIV---AVFALPETNPEEFTGKAT---IELTDIKEALKDFRVSY----TIFLSFAIAFLLYSVIIYVP 229
                                       999999999999...777777777777777777...35566666677777777....77777777789999****** PP

                             MFS_1 232 lylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlv 308
                                       ++l + ++++    ag++l+l ++ ++++a  a +ls  ++ ++ +  +++ll++a +g+ ++++    + + l+l+
  gi|298674928|ref|YP_003726678.1| 230 FILEDSFDFT-SQGAGIALSLRGASVIVVASQARKLSEIYSEHIVMSAGFGLLSAAIAGFPFVNTV---SSTFLLLL 302
                                       **********.688999999999999999*************************************...44445788 PP

                             MFS_1 309 liGfglgfvfpsllalasdlappeeagtasglfntagslggalgp 353
                                       l+G g+g+++p l++l+ ++ p + +g ++++fnt+ ++g   +p
  gi|298674928|ref|YP_003726678.1| 303 LFGAGFGMIQPFLTTLIIQVSPSNIMGGIVSIFNTMKYIGQTAAP 347
                                       9***************************************99887 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.004
                             MFS_1 132 lGailgpllggllasslgWravfyilaivsllafvlfllll 172
                                       +G   +p + g+++ +++   +f++  i++++ ++   ++l
  gi|298674928|ref|YP_003726678.1| 341 IGQTAAPSVLGIILFYFNMDMIFIVSSIFGFIIALS--VYL 379
                                       79999****************************884..333 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5  16.3   2.6e-14   2.3e-10      38     394 ..      34     381 ..      13     389 .] 0.87

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 2.6e-14
                             MFS_3  38 tdisasplmvAlvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltllig 114
                                         +++s  +v l+ a  tL + l+++  G ++D ++++k+l+   ++  l+ + +     +  ++  lll + ++ g
  gi|298674928|ref|YP_003726678.1|  34 EPLNTSREAVGLILAVYTLSTALFTLAIGSITDRINHKKILIPCLIVNGLSGMAA-----FFATDLTLLLFIRFIQG 105
                                       56899************************************98766655554433.....334566789999***** PP

                             MFS_3 115 iGaalndPaWqAsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafavnalsylalivallrwkr 191
                                          a ++P    ++g l + ++   A+   s+ i i     P +gG  + ++G  + f +  l+  + iva+ +   
  gi|298674928|ref|YP_003726678.1| 106 SAVAGMTPLAMTIIGGLYSGKQRIHAMGRRSMSIAIGAVSLPFIGGS-MGIFGWNFPFLFYCLTIPIAIVAVFALPE 181
                                       ******************9999999*********************8.599**********************9999 PP

                             MFS_3 192 evrksslprEkl.lealraglRftaasreikavlvRaalFglsasavlaLLPlvardqldgdalvyGillgalGvGA 267
                                       + +++   + ++ l+ ++++l+  ++s  i  ++  a++F l +  v+  +P++  d  d  +   Gi l+  G+  
  gi|298674928|ref|YP_003726678.1| 182 TNPEEFTGKATIeLTDIKEALKDFRVSYTIFLSF--AIAFLLYS--VIIYVPFILEDSFDFTSQGAGIALSLRGASV 254
                                       9999999999884578******99**99987665..56676665..66679************************** PP

                             MFS_3 268 ilgalllsrLRerlsserlvllaavalAlvllslalasslwvavlvlllgGaaWitalstlnvavqlavPrWvvgRa 344
                                       i+ a +  +L e+ s++ +++  +  l + ++   +++++  ++l lll Ga++ +    l + +  ++P+ + g  
  gi|298674928|ref|YP_003726678.1| 255 IVVASQARKLSEIYSEHIVMSAGFGLLSAAIAGFPFVNTVSSTFLLLLLFGAGFGMIQPFLTTLIIQVSPSNIMGGI 331
                                       **********99877776666667778999999**********************9999999999999********* PP

                             MFS_3 345 lavYltvlaGglaaGsllWGavaealsvtlaLlaaaaalllaaaillllk 394
                                       ++++ t+ + g +a   + G +    ++ +  +++++  ++ a+ ++l+k
  gi|298674928|ref|YP_003726678.1| 332 VSIFNTMKYIGQTAAPSVLGIILFYFNMDMIFIVSSIFGFIIALSVYLTK 381
                                       *******9988888888889999999999999998887666666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2877.41
//
Query:       gi|298674929|ref|YP_003726679.1|  [L=275]
Description: phosphoesterase PA-phosphatase-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-13   50.4  16.4    2.1e-13   50.4  16.4    2.3  2  PAP2_3    PAP2 superfamily
    9.8e-09   35.1   2.8    9.8e-09   35.1   2.8    2.8  3  PAP2      PAP2 superfamily
  ------ inclusion threshold ------
      0.015   15.8   4.1      0.015   15.8   4.1    3.4  4  PAP2_C    PAP2 superfamily C-terminal
        1.3    9.1   0.0        1.3    9.1   0.0    4.1  4  FixQ      Cbb3-type cytochrome oxidase component FixQ


Domain annotation for each model (and alignments):
>> PAP2_3  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.2      0.21   9.3e+02      59      81 ..       6      28 ..       3      30 .. 0.59
   2 !   50.4  16.4   4.6e-17   2.1e-13      24     190 .]      98     255 ..      86     255 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.21
                            PAP2_3 59 lreflttlllatllgllvyalfP 81
                                      l++++t++++++l  +  y+++P
  gi|298674929|ref|YP_003726679.1|  6 LLSIITLFVVIFLSIIGYYVFIP 28
                                      55666666666666666666655 PP

  == domain 2  score: 50.4 bits;  conditional E-value: 4.6e-17
                            PAP2_3  24 ahpalavilalaYaslh.fqvtllvlvllflrrrerlreflttlllatllgllvyalfPaagPrlleeagfvdtvaa 99 
                                       a+p l++i + +Y + + f++++++++l+++++ + l++f ++++l+ l+++ +y+l+P+    +     +++   +
  gi|298674929|ref|YP_003726679.1|  98 ANPLLTYISSAVYLFAFpFLLVFTFFILVYTQKLKLLKQFTIAFILIYLIAYPFYVLLPVEVTGYT----LKN---V 167
                                       678899999999997661556667777777*******************************99444....233...3 PP

                            PAP2_3 100 aslagalrdgasravllrgtienglaafPSlHvawallvalalwrlrrkrllrvlalllnvlmivatvatgnHYlvD 176
                                         l  +l+   s+ +++++   n   ++PSlH+a++++ +l++++   +r ++++a  + ++++++t+++g H ++D
  gi|298674929|ref|YP_003726679.1| 168 EPLLYELNPIISQGIRMSDP--NLDNCLPSLHTALSVMSILIVFKSGLRR-YKMFATSVTAAILFTTLYLGIHWIID 241
                                       33333334444555666666..77778***************99998888.************************** PP

                            PAP2_3 177 viaGvalalvaial 190
                                       +i G++lal+++++
  gi|298674929|ref|YP_003726679.1| 242 LITGFILALGVFYI 255
                                       **********9985 PP

>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1       0.2   9.1e+02      63      93 ..       8      55 ..       1      63 [. 0.49
   2 ?   -0.7   2.8      0.25   1.1e+03      67     100 ..     119     149 ..     103     164 .. 0.57
   3 !   35.1   2.8   2.2e-12   9.8e-09      51     126 ..     188     255 ..     157     261 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.2
                              PAP2 63 fafalalllalllrrkrkkig.................lvllalilll 93
                                         +l+++++l +   + +i                   +l+++i+++
  gi|298674929|ref|YP_003726679.1|  8 SIITLFVVIFLSIIGYYVFIPsefknehnkpqkqklviDTLIYFIPII 55
                                      444444444444444444433445556677776666664444444444 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.25
                              PAP2  67 lalllalllrrkrkkiglvllalillllavlval 100
                                       ++++++l++++k k    +  ++i+++l+ l+a+
  gi|298674929|ref|YP_003726679.1| 119 VFTFFILVYTQKLKL---LKQFTIAFILIYLIAY 149
                                       233333333333333...3344444444444444 PP

  == domain 3  score: 35.1 bits;  conditional E-value: 2.2e-12
                              PAP2  51 eakesfPSgHsafafalalllalllrrkrkkiglvllalillllavlvalsRlylgvHflsDvlaGlliGialaal 126
                                       + ++++PS H+a ++++ l+++   + +r+k       ++++ +++ + ++ lylg+H+  D+++G+++++ ++++
  gi|298674929|ref|YP_003726679.1| 188 NLDNCLPSLHTALSVMSILIVF-KSGLRRYK-------MFATSVTAAILFTTLYLGIHWIIDLITGFILALGVFYI 255
                                       567899*******998776665.55666666.......69******************************999886 PP

>> PAP2_C  PAP2 superfamily C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.3      0.21   9.3e+02      14      46 ..       9      25 ..       1      33 [. 0.49
   2 ?   -3.5   0.1       3.6   1.6e+04      40      42 ..      53      55 ..      39      63 .. 0.44
   3 ?    0.3   1.8      0.24   1.1e+03      13      38 ..     116     140 ..     102     156 .. 0.63
   4 ?   15.8   4.1   3.3e-06     0.015       8      71 ..     195     255 ..     191     258 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.21
                            PAP2_C 14 ltlavlfileyspkklailkvillllallglfl 46
                                      ++++                +++++l+++g+++
  gi|298674929|ref|YP_003726679.1|  9 IITL----------------FVVIFLSIIGYYV 25
                                      3333................3344455555555 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.6
                            PAP2_C 40 all 42
                                       ++
  gi|298674929|ref|YP_003726679.1| 53 PII 55
                                      222 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.24
                            PAP2_C  13 vltlavlfileyspkklailkvilll 38 
                                       +l+++++fil y++k   +lk +++ 
  gi|298674929|ref|YP_003726679.1| 116 FLLVFTFFILVYTQKLK-LLKQFTIA 140
                                       46677777777777764.33332222 PP

  == domain 4  score: 15.8 bits;  conditional E-value: 3.3e-06
                            PAP2_C   8 SGHtvvltlavlfileyspkklailkvillllallglfliiasrkHYtvDVllglyittlvfll 71 
                                       S Ht+  ++++l++++   +++   k++++ +++ +lf  ++   H+ +D + g++++  vf++
  gi|298674929|ref|YP_003726679.1| 195 SLHTALSVMSILIVFKSGLRRY---KMFATSVTAAILFTTLYLGIHWIIDLITGFILALGVFYI 255
                                       66**************999996...************************************975 PP

>> FixQ  Cbb3-type cytochrome oxidase component FixQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00029       1.3      12      35 ..       8      32 ..       1      38 [. 0.83
   2 ?   -1.9   4.0      0.75   3.3e+03       8      29 ..     107     128 ..     102     130 .. 0.79
   3 ?   -0.5   1.3      0.28   1.3e+03      12      31 ..     136     155 ..     132     156 .. 0.63
   4 ?   -1.9   0.6      0.78   3.5e+03       9      27 ..     219     237 ..     217     239 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00029
                              FixQ 12 swgllflvllfygvviyafrpgn.r 35
                                      s+ +lf v+++ ++ +y+f p+  +
  gi|298674929|ref|YP_003726679.1|  8 SIITLFVVIFLSIIGYYVFIPSEfK 32
                                      889****************999765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.75
                              FixQ   8 gfadswgllflvllfygvviya 29 
                                          + +   fl+++   +++y+
  gi|298674929|ref|YP_003726679.1| 107 SAVYLFAFPFLLVFTFFILVYT 128
                                       5667888889999999999986 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.28
                              FixQ  12 swgllflvllfygvviyafr 31 
                                        + + f ++ ++++ +y++ 
  gi|298674929|ref|YP_003726679.1| 136 QFTIAFILIYLIAYPFYVLL 155
                                       45566666667777777765 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 0.78
                              FixQ   9 fadswgllflvllfygvvi 27 
                                       fa s+   +l+ ++y  + 
  gi|298674929|ref|YP_003726679.1| 219 FATSVTAAILFTTLYLGIH 237
                                       5666666667777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1011  (0.0563891); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1978.46
//
Query:       gi|298674930|ref|YP_003726680.1|  [L=523]
Description: radical SAM domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.7e-08   33.9   0.0    8.4e-08   32.8   0.0    1.6  1  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
       0.19   11.9   0.0       0.47   10.7   0.0    1.6  1  DUF5069      Domain of unknown function (DUF5069)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0   9.3e-12   8.4e-08       1     166 [.     226     410 ..     226     411 .. 0.79

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 9.3e-12
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS........TTHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly........pdfveller 69 
                                       v+v+rgC ++CsfC+ +       + +++++e il+ v+ + ++ g + +il++ + l y        ++ v +l++
  gi|298674930|ref|YP_003726680.1| 226 VEVFRGCGRGCSFCTPT-----MQKLHFKPIEHILQDVQTN-VNFGQHSIILHSEDILRYgakgikpnSEQVLDLFK 296
                                       6899*************.....69*****************.9**********999999988888766555555555 PP

                                       HHHTC.....CCTEEEEEEECSSCHG......HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHH........ CS
                                       xxxxx.....xxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........ RF
                       Radical_SAM  70 lakla.....vpgiritvetngtlpd......eeklerllelgvdrvslgleaaddekvlklmnrghtf........ 127
                                        +            ++++ t +  p+      +    +l +      + g+e+++ + + ++m+++  +        
  gi|298674930|ref|YP_003726680.1| 297 QVVSTegvdkIGTSHLALATVYSNPElvesvtDTCYSELEQNS-LGAQTGIETGSTRLIARYMEGKS-Lpespekwq 371
                                       5555578777455555555555555555589888888888866.99999999999999999996444.448887777 PP

                                       HHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 128 eevlealeklreagikrvvdrivglpGendeeleellel 166
                                       e v++a  +l ++++    + i glp e+ ++++  +el
  gi|298674930|ref|YP_003726680.1| 372 EVVKQAYGILDDNNWITAATLINGLPSETTDDINTSIEL 410
                                       77778888888888777***************9998887 PP

>> DUF5069  Domain of unknown function (DUF5069)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   5.2e-05      0.47      59     101 ..     467     509 ..     455     515 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.2e-05
                           DUF5069  59 avlsgksDeeilawvkenakprsaeeieeWnkslekrgpkdae 101
                                        +++ k+D++i +w+ e++  ++ + i+++ +++++  p +++
  gi|298674930|ref|YP_003726680.1| 467 LLKNYKNDTSIKSWILEHSLKKTGKRINKYVNRMKRGEPPTDN 509
                                       567889*****************************98875554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (523 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.21s 00:00:00.74 Elapsed: 00:00:00.68
# Mc/sec: 2310.32
//
Query:       gi|298674931|ref|YP_003726681.1|  [L=169]
Description: peptidase zinc-dependent [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.1e-27   94.9   0.1    7.1e-27   94.7   0.1    1.1  1  Peptidase_M54  Peptidase family M54
    0.00058   19.7   0.1    0.00085   19.2   0.1    1.4  1  Peptidase_M10  Matrixin
      0.005   16.5   0.1      0.009   15.7   0.1    1.4  1  Reprolysin_4   Metallo-peptidase family M12B Reprolysin-like
  ------ inclusion threshold ------
      0.031   14.4   0.0        1.4    9.1   0.0    2.4  2  Zincin_1       Zincin-like metallopeptidase
      0.055   14.0   0.2      0.065   13.8   0.2    1.4  1  Reprolysin_3   Metallo-peptidase family M12B Reprolysin-like
      0.074   11.6   0.2        0.1   11.2   0.2    1.1  1  Metallopep     Putative peptidase family
        0.1   12.5   0.1       0.15   12.0   0.1    1.3  1  Peptidase_M43  Pregnancy-associated plasma protein-A
       0.11   12.7   0.0       0.11   12.6   0.0    1.2  1  Reprolysin_5   Metallo-peptidase family M12
       0.21   10.8   0.0       0.37   10.0   0.0    1.3  1  DUF4953        Met-zincin


Domain annotation for each model (and alignments):
>> Peptidase_M54  Peptidase family M54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.7   0.1   3.5e-30   7.1e-27      55     189 ..      38     166 ..      12     169 .] 0.85

  Alignments for each domain:
  == domain 1  score: 94.7 bits;  conditional E-value: 3.5e-30
                                       ...GGGEETTTTEEEHHHHHHHHHT--S--..SEE........EEEESS-EE-TT-S-BSEEE-SSSSEEEEE-T.. CS
                     Peptidase_M54  55 eteegavkmyrleavveallgkLkemkddvndDsitkifgittlplgsrdqyidiykkvlGievsiGnyavlals.. 129
                                       ++ e+a++  r+++   ++l+   em + + +D+         l++++ d y++ +++v+G + +  + av++++  
  gi|298674931|ref|YP_003726681.1|  38 DVPENAYDPGRGQYHSSKILE---EMSETIPEDAS------HVLGITDVDLYVPQLNFVFGEASN--KVAVISITrl 103
                                       455677777888888887754...66666667766......56889999*************999..99****9998 PP

                                       --.......SHHHHHHHHHHHHHHHHHHHTT----S-.TSTTS--SSHHHHHHS-SS--HHHH CS
                     Peptidase_M54 130 ikefyte..dkeLflervvkevlhelGhlyGLshCke.dCvmnfsndlkdvDrkapkyCksCl 189
                                       ++e+y    d eLf +r++ke +he+Gh++G+ hC++ +Cvm fsn+l+d D k+ + C +C 
  gi|298674931|ref|YP_003726681.1| 104 RNEYYGLpkDYELFKNRIIKEAIHEIGHMFGFKHCPKkECVMHFSNSLEDTDTKSYRLCSKCQ 166
                                       899997545**************************999************************7 PP

>> Peptidase_M10  Matrixin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   4.3e-07   0.00085     111     137 ..     123     149 ..      70     162 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.3e-07
                                       HHHHHHHHHHTTBESXSSTTSTTSSSC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M10 111 lVaaHEiGHalGLeHssdkdalmyply 137
                                         a+HEiGH+ G +H  +k+ +m+   
  gi|298674931|ref|YP_003726681.1| 123 KEAIHEIGHMFGFKHCPKKECVMHFSN 149
                                       5589*******************8654 PP

>> Reprolysin_4  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   4.5e-06     0.009     141     166 ..     127     153 ..     118     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.5e-06
                      Reprolysin_4 141 HEiGHtfGaaHdlsdegegl.ssktee 166
                                       HEiGH+fG +H  ++e+    s + e+
  gi|298674931|ref|YP_003726681.1| 127 HEIGHMFGFKHCPKKECVMHfSNSLED 153
                                       ************999998655666554 PP

>> Zincin_1  Zincin-like metallopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.071   1.4e+02      67      91 ..      55      79 ..      49      82 .. 0.86
   2 ?    9.1   0.0   0.00068       1.4      69      87 ..     118     136 ..     104     139 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.071
                                      -HHHHHHHHHHHHHHHHHTT-HHHH CS
                          Zincin_1 67 eleeevretllHEighhfGlddedl 91
                                      ++ ee  et+ ++  h +G+ d dl
  gi|298674931|ref|YP_003726681.1| 55 KILEEMSETIPEDASHVLGITDVDL 79
                                      56789999999***********998 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00068
                                       HHHHHHHHHHHHHHHHTT- CS
                          Zincin_1  69 eeevretllHEighhfGld 87 
                                       ++ + +  +HEigh+fG++
  gi|298674931|ref|YP_003726681.1| 118 KNRIIKEAIHEIGHMFGFK 136
                                       566677789********85 PP

>> Reprolysin_3  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   3.2e-05     0.065     108     123 ..     119     137 ..      23     138 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.2e-05
                      Reprolysin_3 108 a...dtvaHEiGHnfganH 123
                                       +   + ++HEiGH fg +H
  gi|298674931|ref|YP_003726681.1| 119 NriiKEAIHEIGHMFGFKH 137
                                       1334889*********999 PP

>> Metallopep  Putative peptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   5.1e-05       0.1     319     336 ..     126     145 ..     124     160 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.1e-05
                        Metallopep 319 lHEiGHllglpHqed..Gvm 336
                                       +HEiGH++g  H+++   vm
  gi|298674931|ref|YP_003726681.1| 126 IHEIGHMFGFKHCPKkeCVM 145
                                       8***********98755777 PP

>> Peptidase_M43  Pregnancy-associated plasma protein-A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   7.4e-05      0.15      73     105 ..     126     158 ..     105     169 .] 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.4e-05
                     Peptidase_M43  73 thelGhfLgLihtfeggCerGegDkvsDtpsed 105
                                        he+Gh++g++h  + +C    ++ ++Dt++++
  gi|298674931|ref|YP_003726681.1| 126 IHEIGHMFGFKHCPKKECVMHFSNSLEDTDTKS 158
                                       6*****************999999999999874 PP

>> Reprolysin_5  Metallo-peptidase family M12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.5e-05      0.11     146     164 ..     125     143 ..      67     167 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.5e-05
                      Reprolysin_5 146 vaHElGHnfGavHDcdsss 164
                                         HE+GH+fG +H +++++
  gi|298674931|ref|YP_003726681.1| 125 AIHEIGHMFGFKHCPKKEC 143
                                       57***********877654 PP

>> DUF4953  Met-zincin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00018      0.37       5      29 ..     113     137 ..     110     140 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00018
                           DUF4953   5 pdelmgallrfvvaHEvGhtLGLrh 29 
                                       + el+++++   + HE+Gh +G++h
  gi|298674931|ref|YP_003726681.1| 113 DYELFKNRIIKEAIHEIGHMFGFKH 137
                                       5688999999999***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1149.07
//
Query:       gi|298674932|ref|YP_003726682.1|  [L=128]
Description: hypothetical protein Metev_0997 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.7e-14   51.0   4.6    1.2e-13   50.7   2.0    2.3  2  DUF1641   Protein of unknown function (DUF1641)


Domain annotation for each model (and alignments):
>> DUF1641  Protein of unknown function (DUF1641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0     0.054   9.7e+02      10      18 ..      50      58 ..      49      58 .. 0.90
   2 !   50.7   2.0   6.7e-18   1.2e-13       4      39 .]      81     116 ..      78     116 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.054
                           DUF1641 10 GlfgLlraL 18
                                      ++f+Ll a+
  gi|298674932|ref|YP_003726682.1| 50 SMFKLLNAM 58
                                      79****998 PP

  == domain 2  score: 50.7 bits;  conditional E-value: 6.7e-18
                           DUF1641   4 eepkpvGlfgLlraLrDPDVqrGLGfllalLKalGk 39 
                                        +p+ +G++g++r+L+D+DVq+G+G++++lLKa+Gk
  gi|298674932|ref|YP_003726682.1|  81 LDPPQLGMMGIIRELKDEDVQKGVGVMMELLKAIGK 116
                                       579999*****************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1044.60
//
Query:       gi|298674933|ref|YP_003726683.1|  [L=398]
Description: FAD-dependent pyridine nucleotide-disulfide oxidoreductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-20   73.3   0.0    1.9e-19   70.0   0.0    2.0  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
     0.0012   18.5   0.0      0.068   12.8   0.0    2.3  3  DAO              FAD dependent oxidoreductase
     0.0021   18.6   0.0        2.7    8.6   0.0    2.4  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
  ------ inclusion threshold ------
      0.017   15.3   0.0      0.037   14.3   0.0    1.5  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.019   14.9   0.0        2.3    8.2   0.0    2.3  2  NAD_binding_9    FAD-NAD(P)-binding
      0.057   13.7   0.0       0.14   12.4   0.0    1.6  1  NAD_binding_8    NAD(P)-binding Rossmann-like domain


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.0   0.0   6.3e-23   1.9e-19       2     290 ..       4     313 ..       3     317 .. 0.78

  Alignments for each domain:
  == domain 1  score: 70.0 bits;  conditional E-value: 6.3e-23
                                       SEEEE--SHHHHHHHHHHHH........HTS-EEEEETTHCHHHCSHHH.HCHHHHHHHHHHHHH.HHHHCHHHH.C CS
                                       xxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx.xxxxxxxxx.x RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq........agakvtlvelegtclnggcll.skallgvaedaeias.evvkklnqg.i 67 
                                       +v+++G+G AG+ +a +la+          ++vt+++++++  n+g +   +  l ++ed e  + ev  + + + +
  gi|298674933|ref|YP_003726683.1|   4 NVLILGAGYAGTVVANKLARefrreiarGDLNVTILDKDDMNINQGGFTfLPFGLYTPEDLERPRkEV-LSPRINcV 79 
                                       79*******************99999877999****85555555555443555555666555444444.44444426 PP

                                       CCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                       Pyr_redox_2  68 elllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp.. 142
                                          +g e++++d +++kv++     +++ ++ yd+lv+AtGs++ + +ipG+ e++ ++  ++d+a +lk+k  +  
  gi|298674933|ref|YP_003726683.1|  80 FGEKG-EITGVDLENRKVQV-----KSGDTFNYDYLVIATGSTTDISNIPGLSEDYNTFYTSMDDAFKLKEKIDNfe 150
                                       66666.9*************.....45569**********************8877777789999999999888898 PP

                                       ........SEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSS........TTS-HHHHHHHHHHHHHTTEEEEES CS
                                       ........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 143 ........krivvvGgGyiGvElAaalaklgkevtlveardrll........raldkelsaaleealekeGvevklg 203
                                               +++ v   G++ v +A +l+++ k     e ++++         +  ++e+ + +++++e++++ev  +
  gi|298674933|ref|YP_003726683.1| 151 qgriaisvAQMPVSCPGAT-VKFAVMLNDYIKFMKTEEMCKNIQisffwpmePIGPPEFNKVATKVFEDDNIEVNRN 226
                                       8777776655555555555.8999999999886666666666554334333333469******************** PP

                                       CEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTS......BESSTTEEE- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxx RF
                       Pyr_redox_2 204 tsvkeidgngeklevvledgeeidadlvvvavGvrpstelleeklglelderggivvdefl......rtnvpgiyai 274
                                        +  e+d++++  e v ++g+++++dl+++    +  ++++  ++gl +de+g+i vd+f       + n+ ++y++
  gi|298674933|ref|YP_003726683.1| 227 FKLAEVDSKNR--EIVSQNGDREKYDLLITTPPHKSPQPII--DSGL-TDETGWIPVDKFTlqyrgpAGNHNEVYVA 298
                                       *******9998..9****************99777777776..8899.58**********9877665569******* PP

                                       GGGCTECCSS--HHHH CS
                                       xxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 275 GDvaggkggpelaqaA 290
                                       GD ag+ +++++   A
  gi|298674933|ref|YP_003726683.1| 299 GD-AGPASVIKSGIGA 313
                                       **.5466666665555 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   2.3e-05     0.068       2      30 ..       5      43 ..       4      61 .. 0.83
   2 ?    3.5   0.0     0.014        43     168     207 ..      85     120 ..      77     226 .. 0.80
   3 ?   -3.7   0.0       2.3   6.8e+03     130     152 ..     263     285 ..     228     290 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.3e-05
                                      EEEECTSHHHHHHHHHHHH.......TT...EEEEESSS CS
                               DAO  2 vviiGGGiiGlstAyeLar.......rg...Vtllekgd 30
                                      v+i G+G++G  +A  Lar       rg   Vt+l+k+d
  gi|298674933|ref|YP_003726683.1|  5 VLILGAGYAGTVVANKLARefrreiaRGdlnVTILDKDD 43
                                      99***************884544333459********94 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.014
                                       CEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GGGHHHH CS
                               DAO 168 evtgleeedgkvwgverttpgendaadavVnaaGawsdll 207
                                       e+tg++ e+ k ++v   ++g ++ +d++V+a+G  +d++
  gi|298674933|ref|YP_003726683.1|  85 EITGVDLENRK-VQV---KSGDTFNYDYLVIATGSTTDIS 120
                                       67777665323.444...3477767899******999955 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 2.3
                                       TTSEEEEETTEEEEEHHHHHHHH CS
                               DAO 130 gllgalfypdtgqvdpakltaal 152
                                       ++  + ++++tg++   k+t  +
  gi|298674933|ref|YP_003726683.1| 263 PIIDSGLTDETGWIPVDKFTLQY 285
                                       34444466777999988888766 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0    0.0021       6.2       1      20 [.       4      23 ..       4      46 .. 0.75
   2 !    8.6   0.0   0.00092       2.7      38      73 ..     204     240 ..     197     244 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0021
                                      EEEEECSSHHHHHHHHHHHH CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalae 20
                                      +v+++G+Gy g  +A+ la+
  gi|298674933|ref|YP_003726683.1|  4 NVLILGAGYAGTVVANKLAR 23
                                      599**************955 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00092
                                       SSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTS.E CS
                         Pyr_redox  38 lDeeaskilqeklekngievllntkveeiegsedg.v 73 
                                        ++e+ k+ ++ +e+ +iev  n k++e++ ++++ v
  gi|298674933|ref|YP_003726683.1| 204 GPPEFNKVATKVFEDDNIEVNRNFKLAEVDSKNREiV 240
                                       578999************************9988744 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.2e-05     0.037       1      35 [.       5      44 ..       5      55 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.2e-05
                                      EEEE--SHHHHHHHHHHHCTCCT-G.....EEEEEESSHH CS
                   Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvda.....eitvadrske 35
                                      vli+GaG+ G +va +lar+f  +      ++t+ d+++ 
  gi|298674933|ref|YP_003726683.1|  5 VLILGAGYAGTVVANKLAREFRREIargdlNVTILDKDDM 44
                                      89*****************998755668889999998875 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0   0.00076       2.3       2      35 ..       7      43 ..       6      51 .. 0.84
   2 ?    4.5   0.0      0.01        31     121     155 ..      83     115 ..      55     116 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00076
                     NAD_binding_9  2 ivGaGprGlavlerLlara...kkkspleitlfdpse 35
                                      i GaG +G+ v+++L+++      + +l++t+ d++ 
  gi|298674933|ref|YP_003726683.1|  7 ILGAGYAGTVVANKLAREFrreIARGDLNVTILDKDD 43
                                      89***************98765566789999999865 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.01
                     NAD_binding_9 121 raevvdleeradgqavlladgaslaadaVvLAlGh 155
                                       ++e++ ++ ++++  v  ++g+++ +d++v+A+G 
  gi|298674933|ref|YP_003726683.1|  83 KGEITGVDLENRK--VQVKSGDTFNYDYLVIATGS 115
                                       5577777777666..5559***************6 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.6e-05      0.14       1      29 [.       7      43 ..       7      44 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.6e-05
                                      EE--SHHHHHHHHHHHCC........TEEEEEE-SSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLaka........gfdvlllekrd 29
                                      I+GaG +G v A  La++        +++v++l+k d
  gi|298674933|ref|YP_003726683.1|  7 ILGAGYAGTVVANKLAREfrreiargDLNVTILDKDD 43
                                      89**************8443445567889****9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.22s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3002.51
//
Query:       gi|298674934|ref|YP_003726684.1|  [L=126]
Description: hypothetical protein Metev_0999 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.27   11.3   3.9        1.6    8.8   3.9    2.5  1  ORF6C     ORF6C domain
       0.46   10.3   6.2      0.098   12.5   2.0    1.9  2  DUF5100   Domain of unknown function (DUF5100)
        2.6    8.0   9.1        4.1    7.3   2.5    3.0  4  HSBP1     Heat shock factor binding protein 1


Domain annotation for each model (and alignments):
>> ORF6C  ORF6C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   3.9   0.00027       1.6      11      93 ..       3      97 ..       1     117 [. 0.64

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00027
                             ORF6C 11 ehdekieeiderv.kkLe....enmplde...sekeeiqkkvkkkvvellggkkspaykdkslrkkvfsdiyrdlkref 81
                                      e+d++i+e+++++ ++L+    +   +++   +  + ++++ ++  ++l   k  + y++++l k+++ diyr+  + f
  gi|298674934|ref|YP_003726684.1|  3 ETDKRIDEMETKMlNELKdcfsRIRHIKNnytNVDNLLDELENEFGIKLSSKKRENKYSKNELVKSIYLDIYRETGEDF 81
                                      6777788777764366775554333333300033455888889999999999****************99999876666 PP

                             ORF6C 82 ....gVasYkdikkkd 93
                                          ++ ++ ++   d
  gi|298674934|ref|YP_003726684.1| 82 vpieDIIERAQVEGAD 97
                                      2222444444444444 PP

>> DUF5100  Domain of unknown function (DUF5100)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   2.0   1.6e-05     0.098      60     111 ..      12      61 ..       6      74 .. 0.70
   2 ?   -0.4   0.1      0.17   9.9e+02      88     108 ..      99     119 ..      85     125 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.6e-05
                           DUF5100  60 rtkqlpecekfikskakkisveewneaidevldiLee.ieleevefeeskkki 111
                                       +tk l+e++  ++  ++   ++++++++d+ ld Le+ + ++    + ++k++
  gi|298674934|ref|YP_003726684.1|  12 ETKMLNELKDCFSRIRH---IKNNYTNVDNLLDELENeFGIKLSSKKRENKYS 61 
                                       78899999999998888...89*************843444433333333333 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.17
                           DUF5100  88 devldiLeeieleevefeesk 108
                                       +++l+ ++++ l++  ++ ++
  gi|298674934|ref|YP_003726684.1|  99 EDILELIDDLRLQDYLIQLND 119
                                       578888888888877666665 PP

>> HSBP1  Heat shock factor binding protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   2.5   0.00069       4.1      29      43 ..       1      15 [.       1      21 [. 0.89
   2 ?    0.1   0.0      0.12   7.2e+02       9      21 ..      14      26 ..      13      28 .. 0.83
   3 ?    3.7   0.0    0.0095        57       7      18 ..      36      47 ..      33      50 .. 0.88
   4 ?   -2.8   0.4         1     6e+03      25      39 ..     101     108 ..      99     109 .. 0.48

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00069
                             HSBP1 29 iDdMssriDdLEksi 43
                                      +D+  +riD++E+ +
  gi|298674934|ref|YP_003726684.1|  1 MDETDKRIDEMETKM 15
                                      9***********988 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.12
                             HSBP1  9 nlLqqlqdkFqtm 21
                                      ++L++l+d F+++
  gi|298674934|ref|YP_003726684.1| 14 KMLNELKDCFSRI 26
                                      599***9999876 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.0095
                             HSBP1  7 VenlLqqlqdkF 18
                                      V+nlL++l++ F
  gi|298674934|ref|YP_003726684.1| 36 VDNLLDELENEF 47
                                      999****99988 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 1
                             HSBP1  25 ilsriDdMssriDdL 39 
                                       il+        iDdL
  gi|298674934|ref|YP_003726684.1| 101 ILEL-------IDDL 108
                                       4444.......5554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1533  (0.0855039); expected 358.6 (0.02)
Passed bias filter:                      750  (0.0418317); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 972.03
//
Query:       gi|298674935|ref|YP_003726685.1|  [L=383]
Description: eRF1 domain 2 protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-25   88.8   0.0    5.7e-25   88.2   0.0    1.2  1  baeRF_family10  Bacterial archaeo-eukaryotic release factor f
    4.9e-21   75.4   0.1    2.5e-20   73.2   0.0    2.1  3  eRF1_2          eRF1 domain 2
    1.1e-13   51.5   0.0    1.7e-13   51.0   0.0    1.2  1  acVLRF1         Actinobacteria/chloroflexi VLRF1 release fact
    3.4e-09   37.2   0.0    9.1e-09   35.8   0.0    1.7  1  eRF1_3          eRF1 domain 3
    4.3e-08   33.3   0.0    5.9e-08   32.9   0.0    1.2  1  baeRF_family2   Bacterial archaeo-eukaryotic release factor f
    9.3e-06   26.3   0.0    2.4e-05   24.9   0.0    1.8  1  baeRF_family12  Bacterial archaeo-eukaryotic release factor f
      0.002   18.7   0.0     0.0037   17.8   0.0    1.4  1  Host_attach     Protein required for attachment to host cells
     0.0044   17.2   0.1      0.022   14.9   0.1    2.1  1  baeRF_family5   Bacterial archaeo-eukaryotic release factor f
  ------ inclusion threshold ------
      0.011   16.0   0.0      0.019   15.2   0.0    1.4  1  baeRF_family3   Bacterial archaeo-eukaryotic release factor f
      0.062   13.6   0.2       0.14   12.5   0.2    1.5  1  zf-Di19         Drought induced 19 protein (Di19), zinc-bindi


Domain annotation for each model (and alignments):
>> baeRF_family10  Bacterial archaeo-eukaryotic release factor family 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.2   0.0   3.2e-28   5.7e-25       1     131 [.     125     254 ..     125     259 .. 0.97

  Alignments for each domain:
  == domain 1  score: 88.2 bits;  conditional E-value: 3.2e-28
                    baeRF_family10   1 PylapLlealdeyerygvvlvdreraRlfevylgeleeveevegevpgrtktggwksqdrfqrreeeqaerhlkevA 77 
                                       P+l pL+++ d+y  yg+vl+d ++ Rlf+++ + ++++++++ +  +++k+ggw sq+rf r ++e ++ +l  vA
  gi|298674935|ref|YP_003726685.1| 125 PFLLPLARLRDDYSDYGIVLLDSHESRLFNIRSDAVKQTSHLSTDLMNKHKKGGW-SQMRFNRLRKEAIKSFLSSVA 200
                                       9******************************************************.********************* PP

                    baeRF_family10  78 ellaklleergverlvlgGdeeetaalldrlpkalrarvvgtlplpvdasaaaV 131
                                       e +++++++++v+ l+++G+ +++++l+d lp+ +r +v++ ++ p+d s++++
  gi|298674935|ref|YP_003726685.1| 201 ESIEEYCKNHQVKGLIIAGPGDAKKELRDILPEWIRNKVMDIVDTPIDVSEKEL 254
                                       *****************************************9988887788776 PP

>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       4.9   8.8e+03      24      37 ..      59      72 ..      50      82 .. 0.54
   2 !   73.2   0.0   1.4e-23   2.5e-20       1     112 [.     139     245 ..     139     268 .. 0.86
   3 ?   -1.6   0.0       1.7   3.1e+03      82     111 ..     337     366 ..     334     369 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.9
                                      EEEEEE------BS CS
                            eRF1_2 24 vlkkievsvPkKhk 37
                                       +k+i   +P K k
  gi|298674935|ref|YP_003726685.1| 59 RIKNIRKALPEKFK 72
                                      34445555555543 PP

  == domain 2  score: 73.2 bits;  conditional E-value: 1.4e-23
                                       EEEEEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTTE CS
                            eRF1_2   1 kvglivldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafllvdkdkl 77 
                                       ++g+++ld +e+ ++ +++  ++  +++++++  Khk+Gg s+ rf+Rlr+e++++fl +vae+++++    +++++
  gi|298674935|ref|YP_003726685.1| 139 DYGIVLLDSHESRLFNIRSDAVKQTSHLSTDLMNKHKKGGWSQMRFNRLRKEAIKSFLSSVAESIEEY---CKNHQV 212
                                       69******************************************************************...99**** PP

                                       SEEEEEESSTHHHHHHHHHHHHHHHHTCCEEEEE- CS
                            eRF1_2  78 kgiilagpgfvkeefldkdlldaelkkkviklvdv 112
                                       kg+i+agpg++k+e+ d  +l +  ++kv+++vd+
  gi|298674935|ref|YP_003726685.1| 213 KGLIIAGPGDAKKELRD--ILPEWIRNKVMDIVDT 245
                                       ***************76..4445555555555543 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.7
                                       EEESSTHHHHHHHHHHHHHHHHTCCEEEEE CS
                            eRF1_2  82 lagpgfvkeefldkdlldaelkkkviklvd 111
                                       ++g    k+e+++k++ +a+ +++ +  vd
  gi|298674935|ref|YP_003726685.1| 337 ICGGTTSKTEIIEKLYEMAQYTDAEVEFVD 366
                                       678888899999999999998887777665 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.0   9.2e-17   1.7e-13       5      92 ..     142     230 ..     138     256 .. 0.83

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 9.2e-17
                           acVLRF1   5 vllvrrggfavgvveggelvaskvgtrdvqgrtaaGGwSqqRfaRrrenqadalleavaeaaarllaeesae.vvlg 80 
                                       ++l  +    +  ++++++ ++++ ++d ++++++GGwSq Rf R r + +++ l+ vae +++ +++++ + ++++
  gi|298674935|ref|YP_003726685.1| 142 IVLLDSHESRLFNIRSDAVKQTSHLSTDLMNKHKKGGWSQMRFNRLRKEAIKSFLSSVAESIEEYCKNHQVKgLIIA 218
                                       5555555556666778999999********************************************8777778**** PP

                           acVLRF1  81 Gdrslvaevled 92 
                                       G+  + +e+++ 
  gi|298674935|ref|YP_003726685.1| 219 GPGDAKKELRDI 230
                                       ********9986 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.0   5.1e-12   9.1e-09      17     111 ..     283     383 .]     270     383 .] 0.90

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 5.1e-12
                                       CTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSH.HHHHS...........-HHH-HHHHHHHHHHHHHHHHHT CS
                            eRF1_3  17 kdtgkavYGveevlkalemgAvetLLvseelersrdt.lkekv...........ketgeelelvelieelvenvees 81 
                                        + g+a YG++ +++ l  g v+ LL+++++     + +k+++           + +g ++++ e+ie+l+e+++ +
  gi|298674935|ref|YP_003726685.1| 283 SG-GLAEYGIDAIKNDLYQGRVSVLLILNNIAVPGSKcEKCQElhvtgnsypacPICGGTTSKTEIIEKLYEMAQYT 358
                                       44.8999************************9998776777669**********9********************** PP

                                       T-EEEEE-TTSHHHHHHHHHTTTEEEEESS CS
                            eRF1_3  82 gakveiisseseeGeqlvkafgGiaaiLRy 111
                                        a+ve++ ++     +++++ gG++aiLRy
  gi|298674935|ref|YP_003726685.1| 359 DAEVEFVDDD-----KFLESIGGVGAILRY 383
                                       *******886.....577***********9 PP

>> baeRF_family2  Bacterial archaeo-eukaryotic release factor family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   3.3e-11   5.9e-08      23     105 ..     159     241 ..     139     280 .. 0.87

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 3.3e-11
                     baeRF_family2  23 eeeetveGghdpvhkvraggwshrryqrraeeswerNaeavAeevdrlvresgaelVvlaGDvrarsllrdeLperv 99 
                                       + ++t + ++d ++k ++ggws+ r+ r  +e+++     vAe ++++++ ++++ +++aG   a + lrd Lpe +
  gi|298674935|ref|YP_003726685.1| 159 AVKQTSHLSTDLMNKHKKGGWSQMRFNRLRKEAIKSFLSSVAESIEEYCKNHQVKGLIIAGPGDAKKELRDILPEWI 235
                                       66777778889999*************************************************************** PP

                     baeRF_family2 100 relvve 105
                                       r+ v +
  gi|298674935|ref|YP_003726685.1| 236 RNKVMD 241
                                       998876 PP

>> baeRF_family12  Bacterial archaeo-eukaryotic release factor family 12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   1.3e-08   2.4e-05      53     134 ..     176     254 ..     140     257 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.3e-08
                    baeRF_family12  53 sggagrsameetdfkeqeeerFakeladeLkkrakegkferlvlvappetlgelrkhlhkevkkrlvgeiaknltkh 129
                                        gg +  +m     ++++ + F+ ++a+ +++ +k+++++ l++ +p ++ +elr+ l++ +++++   i  ++++ 
  gi|298674935|ref|YP_003726685.1| 176 KGGWS--QMRFNRLRKEAIKSFLSSVAESIEEYCKNHQVKGLIIAGPGDAKKELRDILPEWIRNKVMD-IVDTPIDV 249
                                       33333..55555566668899********************************************654.44455555 PP

                    baeRF_family12 130 ppaei 134
                                       +++e+
  gi|298674935|ref|YP_003726685.1| 250 SEKEL 254
                                       55555 PP

>> Host_attach  Protein required for attachment to host cells
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.1e-06    0.0037      33     120 ..     159     241 ..     146     248 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.1e-06
                       Host_attach  33 srlkerelgsdrpgrsnesaggggrsavdeetdpkeeeeerfarevadrLekaraagkferlvlvApPrflGlLrea 109
                                       + ++++ l +d   ++++    gg s++   +  ++e+ ++f+  va+ +e+++++++++ l+++ p  + ++Lr+ 
  gi|298674935|ref|YP_003726685.1| 159 AVKQTSHLSTDLMNKHKK----GGWSQM-RFNRLRKEAIKSFLSSVAESIEEYCKNHQVKGLIIAGPGDAKKELRDI 230
                                       566777777777777766....557788.6777777789************************************99 PP

                       Host_attach 110 lskelkklvvk 120
                                       l + ++++v  
  gi|298674935|ref|YP_003726685.1| 231 LPEWIRNKVMD 241
                                       99988888765 PP

>> baeRF_family5  Bacterial archaeo-eukaryotic release factor family 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   1.2e-05     0.022      48     113 ..     173     238 ..     139     245 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.2e-05
                     baeRF_family5  48 erssgsgskdefeerfeenqqRwyKslaskleklakereweeiylvGekeeakeleeelnkkvkev 113
                                       ++++g+ s+ +f++  +e  + ++ s+a+++e+  k+++ + ++++G  ++ kel++ l + +++ 
  gi|298674935|ref|YP_003726685.1| 173 KHKKGGWSQMRFNRLRKEAIKSFLSSVAESIEEYCKNHQVKGLIIAGPGDAKKELRDILPEWIRNK 238
                                       3355666688999999999************************************99997766655 PP

>> baeRF_family3  Bacterial archaeo-eukaryotic release factor family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   1.1e-05     0.019       2     168 .]     140     302 ..     139     302 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.1e-05
                     baeRF_family3   2 YwVLaLsqdkvrLfegtrdsleeveadgfPltleealgeedperqeghgdkkseyrdedtrrFlreVdkalqevls. 77 
                                       Y + +L+ ++ rLf+ + d +++ ++  + ++l ++ + +   +q     + +  r+e ++ Fl +V ++++e+++ 
  gi|298674935|ref|YP_003726685.1| 140 YGIVLLDSHESRLFNIRSDAVKQTSH--LSTDLMNKHK-KGGWSQM----RFNRLRKEAIKSFLSSVAESIEEYCKn 209
                                       66777888888888888888888774..2222211111.2222333....33556899******************5 PP

                     baeRF_family3  78 esplplvlaGveenlslfrevsknp..sliegglegnpaelsaeeLreaawplveayaeeeraealeeldear.grg 151
                                       ++   l++aG  ++ + +r++      + + + +   p ++s++eL+     +++ + +    e+++++++a+ + g
  gi|298674935|ref|YP_003726685.1| 210 HQVKGLIIAGPGDAKKELRDILPEWirNKVMDIV-DTPIDVSEKELVNTGDIILKTNEKSYSREKANNFRAAVlSGG 285
                                       56668*****999998888887766554444444.566799999999999999999999999999999999983556 PP

                     baeRF_family3 152 kfaagldevwqaareGR 168
                                       ++  g+d + +  ++GR
  gi|298674935|ref|YP_003726685.1| 286 LAEYGIDAIKNDLYQGR 302
                                       77779999999999998 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   7.9e-05      0.14      18      48 ..     319     350 ..     317     356 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.9e-05
                           zf-Di19  18 veHvedeHrveskevvCPvCaekvtk.dlvaH 48 
                                       +e +++ H   + +  CP+C  +++k ++++ 
  gi|298674935|ref|YP_003726685.1| 319 CEKCQELHVTGNSYPACPICGGTTSKtEIIEK 350
                                       899*****************976655366665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       978  (0.0545485); expected 358.6 (0.02)
Passed bias filter:                      731  (0.0407719); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2535.44
//
Query:       gi|298674936|ref|YP_003726686.1|  [L=498]
Description: class I/II aminotransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-47  161.3   0.0    5.2e-47  160.8   0.0    1.2  1  Aminotran_1_2    Aminotransferase class I and II
    4.2e-28   97.1   7.4    9.7e-28   95.9   7.4    1.6  1  zf-like          Cysteine-rich small domain
     0.0085   15.1   0.0          1    8.2   0.0    3.2  3  Aminotran_5      Aminotransferase class-V
  ------ inclusion threshold ------
       0.14   12.1   0.0       0.32   11.0   0.0    1.5  1  Prefoldin_2      Prefoldin subunit
       0.18   11.1   0.0       0.39   10.0   0.0    1.5  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.8   0.0   1.5e-50   5.2e-47      32     362 ..      67     375 ..      34     376 .. 0.89

  Alignments for each domain:
  == domain 1  score: 160.8 bits;  conditional E-value: 1.5e-50
                                       HHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHH CS
                     Aminotran_1_2  32 laggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasykn 108
                                       + +++l++y++++ + e++ a a f+g     +l+re +++ g+G+++li +++ +  +++gd++++p+pt+++y+ 
  gi|298674936|ref|YP_003726686.1|  67 NNTEKLTRYPDNR-YLEFRDAAAGFIG-----NLDRE-NIIPGNGSCELIRLVAECV-VEKGDQVIIPQPTFDEYEL 135
                                       677899*******.*************.....9****.*******************.9****************** PP

                                       HHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEE CS
                     Aminotran_1_2 109 ilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllf 185
                                        +r+ g+  v+++++        + ++ + l +        k+++v++p+NPtG ++++ +l++l+d + +   llf
  gi|298674936|ref|YP_003726686.1| 136 QCRIFGARPVYINYS-------EIPQISDELLN------SSKILFVCNPNNPTGELLSRSTLKDLADRCAETSTLLF 199
                                       *************77.......89999998888......679*********************************** PP

                                       EEETTTTCBSSSSHTHHHHGGSTTSTT.EEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTS...SHHHHH CS
                     Aminotran_1_2 186 vDeaYagfvfgsldavatranveeepn.llivgslsKafGlaGeRvGyilgnaavvsqlrklsrpfls...ssllqa 258
                                       vDea+ ++   +++    +a++ ++ n +++++sl K+f+++G+RvG+ ++++++++ l ++  +++    s ++  
  gi|298674936|ref|YP_003726686.1| 200 VDEAFIELSDPEQS----VAELVKDNNfVFVMRSLTKSFAIPGIRVGFGVASQKLANVLDNARLSWNMgfvSDVVGT 272
                                       *********99664....7777777788*************************888888777777666334555555 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.TEEEECCSCSSEEEEEETHH.CHHHHHHHHHHTCTEEEE CS
                     Aminotran_1_2 259 avaaalsdallkqseleemrqrlqkrrkelrdeLael.glkvlasqsgmflltdlsae.takelskkLleevgvyvt 333
                                        ++++   +    s++ ++r+ + ++rk+l d++ ++ g++ l+s  +++l+ + +   + kel + L+ + g++v+
  gi|298674936|ref|YP_003726686.1| 273 ELLKMKGGVY--SSYFRDSRKMIDRERKYLIDRISRIhGFTLLDSSVNYILVDVSESVmDSKELTQRLAAR-GILVR 346
                                       5555555554..34********************999********9999999666666999**********.***** PP

                                       EGGGGTS..TTEEEEECTTS-HHHHHHHHHH CS
                     Aminotran_1_2 334 pgtsftv..pgrlRitvAglteeeleelvea 362
                                        ++sf     +++R+ v   ++e+ ++l++ 
  gi|298674936|ref|YP_003726686.1| 347 DCSSFCSlgDEFIRVAV--RNSEDTNKLAKN 375
                                       *****999*********..888888887765 PP

>> zf-like  Cysteine-rich small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.9   7.4   2.7e-31   9.7e-28       4      80 ..     405     482 ..     402     484 .. 0.93

  Alignments for each domain:
  == domain 1  score: 95.9 bits;  conditional E-value: 2.7e-31
                           zf-like   4 ffsnkeCeyyPCHktedenClfCyCPlYaledeel.Gefveteng.kvkdCskCllvHkkevadellkklkeileel 78 
                                       + sn++C+yyPCH+ e+++C+fC+CP+Y++ede++ G+++e+++g kv++C+kC++vH++eva+e+l+ l+e+ e+ 
  gi|298674936|ref|YP_003726686.1| 405 VGSNTACPYYPCHY-EGQDCTFCFCPFYPCEDERTgGKCIERSSGgKVWSCMKCYIVHDPEVAQEILDVLRENGEMD 480
                                       5789**********.99***************98769*******99**************************99988 PP

                           zf-like  79 kk 80 
                                       +k
  gi|298674936|ref|YP_003726686.1| 481 NK 482
                                       76 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0   0.00029         1      29      95 ..      64     127 ..      54     205 .. 0.83
   2 ?    2.3   0.0     0.019        67     276     337 ..     289     347 ..     282     374 .. 0.86
   3 ?   -1.3   0.0      0.23   8.2e+02     267     306 ..     372     411 ..     365     415 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00029
                                       SSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEET CS
                       Aminotran_5  29 nvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvte 95 
                                        v +++ +l+    + + e r+  a +i+  ++e+ii   G+ e i lva ++   +++gd++++ +
  gi|298674936|ref|YP_003726686.1|  64 LVSNNTEKLTRYPDNRYLEFRDAAAGFIGNLDRENIIPGNGSCELIRLVAECV---VEKGDQVIIPQ 127
                                       466678888888899999***********************************...********975 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.019
                                       HHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTCSHHHHHHHHHHTTEEEEE CS
                       Aminotran_5 276 iekhekelaeyllerlkslpgvrlygpdkaerrasivsfnfkgvhaedvatlLdeegIavrs 337
                                       ++k  ++ ++yl +r++ + g++l+++     +  +v ++   ++++++ + L+ +gI vr 
  gi|298674936|ref|YP_003726686.1| 289 SRKMIDRERKYLIDRISRIHGFTLLDS---SVNYILVDVSESVMDSKELTQRLAARGILVRD 347
                                       667788999***************775...88999999999*******************96 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.23
                                       HHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-C CS
                       Aminotran_5 267 yleeigleaiekhekelaeyllerlkslpgvrlygpdkae 306
                                       + ++ig +  ++  ++++e+l+ r++s++g  l+g+++a+
  gi|298674936|ref|YP_003726686.1| 372 LAKNIGRAMTDRSRDSAKEKLEHRINSSKGRSLVGSNTAC 411
                                       568999999999999****************999976665 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0     9e-05      0.32      40      75 ..     365     400 ..     359     404 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9e-05
                                       HS-TT--EEEEETTEEEEE-HHHHHHHHHHHHHHHH CS
                       Prefoldin_2  40 lldedtkvyklvGdvlvkqdkeevkeeLeerketle 75 
                                       + ++++k  k++G+++  ++++++ke+Le r+++ +
  gi|298674936|ref|YP_003726686.1| 365 NSEDTNKLAKNIGRAMTDRSRDSAKEKLEHRINSSK 400
                                       67889**************************98876 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00011      0.39      18      91 ..      71     148 ..      59     155 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00011
                                       -SSS..SHHHHHHHHHHHHHHT..-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE CS
                   DegT_DnrJ_EryC1  18 wlts..gpeveeFEkafaaylg..vkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfv 90 
                                       +lt+  +++  eF  a a ++g  ++  i   +G+  l  +   + v++gd+VI+p+ tF       +  ga+pv++
  gi|298674936|ref|YP_003726686.1|  71 KLTRypDNRYLEFRDAAAGFIGnlDRENIIPGNGSCELIRLVAECVVEKGDQVIIPQPTFDEYELQCRIFGARPVYI 147
                                       45555677778899999999996667788888888777666666*******************************98 PP

                                       - CS
                   DegT_DnrJ_EryC1  91 D 91 
                                       +
  gi|298674936|ref|YP_003726686.1| 148 N 148
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (498 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 3630.06
//
Query:       gi|298674937|ref|YP_003726687.1|  [L=387]
Description: major facilitator superfamily protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-47  161.1  47.1    3.4e-47  161.1  47.1    2.0  2  MFS_1          Major Facilitator Superfamily
    2.6e-14   52.5  22.4    3.5e-14   52.1  22.4    1.1  1  MFS_3          Transmembrane secretion effector
    0.00032   19.7   9.7    0.00032   19.7   9.7    2.9  3  Sugar_tr       Sugar (and other) transporter
  ------ inclusion threshold ------
       0.13   12.0   0.3       0.13   12.0   0.3    3.5  3  PMP1_2         ATPase proteolipid family


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.1  47.1   7.6e-51   3.4e-47       1     352 [.      12     345 ..      12     346 .. 0.88
   2 !    7.5   6.6   0.00037       1.7     123     172 ..     331     380 ..     331     385 .. 0.91

  Alignments for each domain:
  == domain 1  score: 161.1 bits;  conditional E-value: 7.6e-51
                             MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgll 77 
                                       l+l+af+ ++++++ gp+lp  + + l+++p ++g+++++y+l  a+++l+lG  +d++ r++vl+++l++ +l+++
  gi|298674937|ref|YP_003726687.1|  12 LCLVAFFGMTGSALMGPVLP-DMVDPLNSTPEAVGWVMGVYTLSNALFMLLLGTRIDNLARKKVLITCLIINGLSGF 87 
                                       6899****************.**************************************9999************89 PP

                             MFS_1  78 lllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravf 154
                                       +++fa++l++llv+r++qG+g+++++p+++++i ++++  er  a+g +s+++s+G + +pl+gg la  +gW ++f
  gi|298674937|ref|YP_003726687.1|  88 AGFFAPNLPVLLVFRFIQGIGTAGMMPLVMTMIGELYKNIERIHAMGRVSLTTSIGEVTAPLIGGSLA-IFGWNYPF 163
                                       999999999***********************************************************.*******9 PP

                             MFS_1 155 yilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllp 231
                                       ++ ++   la+v    +++ ++++   +++k+         + ++ +al++ +v + ++++++lf f+++++ +++p
  gi|298674937|ref|YP_003726687.1| 164 LFYGLTIPLAIV---SVFVLPETNVVLPKQKTG--------IYEIVTALKNFNVAYTMFLVSALF-FFLFTIIIYVP 228
                                       999999999988...555555555555554444........334333444444444355555555.48889****** PP

                             MFS_1 232 lylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlv 308
                                       ++l++ +g++ +  ag++l++ ++ +a++a  + rls  ++++++++ +++++ +a  g+ ++ +    + + l+l+
  gi|298674937|ref|YP_003726687.1| 229 FLLKDNFGFT-AQGAGIALGIQGASMAVVASQTKRLSLIFSNQTITIAGFVIVGIAITGMSYAYNL---TSVFLLLL 301
                                       **********.8999999*********************999888888888888888888888888...55555789 PP

                             MFS_1 309 liGfglgfvfpsllalasdlappeeagtasglfntagslggalg 352
                                       ++G g+g+  p l++l++++ap++ +g ++++fnt+  +g+ l+
  gi|298674937|ref|YP_003726687.1| 302 IFGAGFGILIPFLNTLITQVAPTRVMGGIISIFNTMKFVGMTLA 345
                                       9***************************************9997 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00037
                             MFS_1 123 igllsagfslGailgpllggllasslgWravfyilaivsllafvlfllll 172
                                       i++++++  +G+ l+ ++ g+++   g ++vf++ +++++ ++++  +++
  gi|298674937|ref|YP_003726687.1| 331 ISIFNTMKFVGMTLASGILGFILLKSGLEYVFIVSGLIAFGVVIINSFVY 380
                                       799********************9******************99766665 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1  22.4   7.9e-18   3.5e-14      37     390 ..      34     376 ..       6     386 .. 0.85

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 7.9e-18
                             MFS_3  37 mtdisasplmvAlvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspw..lllaltl 111
                                       +  ++++p +v  v    tL   l+ +l G   Dn+ r+kvl++  ++         ++ + g+++p   +ll++ +
  gi|298674937|ref|YP_003726687.1|  34 VDPLNSTPEAVGWVMGVYTLSNALFMLLLGTRIDNLARKKVLITCLIING-------LSGFAGFFAPNlpVLLVFRF 103
                                       556778899999999999***********************997544332.......3444555555422799**** PP

                             MFS_3 112 ligiGaalndPaWqAsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafavnalsylalivallr 188
                                       + giG+a ++P    ++gel k+ +   A+   s+   i     P +gG  +a++G  + f +  l+    iv +  
  gi|298674937|ref|YP_003726687.1| 104 IQGIGTAGMMPLVMTMIGELYKNIERIHAMGRVSLTTSIGEVTAPLIGGS-LAIFGWNYPFLFYGLTIPLAIVSVFV 179
                                       ***********************99999*********************7.699**999999999998777777766 PP

                             MFS_3 189 wkrevrksslprEkllealraglRftaasreikavlvRaalFglsasavlaLLPlvardqldgdalvyGillgalGv 265
                                          +    +  +  + e ++a   f        + lv a  F+l+++ +   +P++ +d+ +  a   Gi lg  G+
  gi|298674937|ref|YP_003726687.1| 180 LPETNVVLPKQKTGIYEIVTALKNFNV---AYTMFLVSALFFFLFTIII--YVPFLLKDNFGFTAQGAGIALGIQGA 251
                                       666655555555666666666555543...4556799999999998766..68************************ PP

                             MFS_3 266 GAilgalllsrLRerlsserlvllaavalAlvllslalasslwvavlvlllgGaaWitalstlnvavqlavPrWvvg 342
                                          + a +++rL  ++s+++++   +v + + +  ++ a +l  ++l ll+ Ga++ + +  ln+ +  + P  v g
  gi|298674937|ref|YP_003726687.1| 252 SMAVVASQTKRLSLIFSNQTITIAGFVIVGIAITGMSYAYNLTSVFLLLLIFGAGFGILIPFLNTLITQVAPTRVMG 328
                                       99999999********************************************************************* PP

                             MFS_3 343 RalavYltvlaGglaaGsllWGavaealsvtlaLlaaaaalllaaail 390
                                         ++++ t+ + g+++ s + G +  + +++   +++++  + +++i 
  gi|298674937|ref|YP_003726687.1| 329 GIISIFNTMKFVGMTLASGILGFILLKSGLEYVFIVSGLIAFGVVIIN 376
                                       ********************************9999987655554443 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   9.7   7.1e-08   0.00032      47     194 ..      43     183 ..      18     193 .. 0.87
   2 ?   -1.8   1.4      0.24   1.1e+03     417     438 ..     206     227 ..     192     237 .. 0.65
   3 !    4.6  16.1    0.0028        12      80     158 ..     272     349 ..     242     380 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 7.1e-08
                                       HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHH CS
                          Sugar_tr  47 lsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlv 123
                                        +g++++++ +  ++  l++g+ +d + Rkk+l+++ ++   +++  ++a+   ++ vl+v R++ Gig  +   lv
  gi|298674937|ref|YP_003726687.1|  43 AVGWVMGVYTLSNALFMLLLGTRIDNLARKKVLITCLIINGLSGFAGFFAP---NLPVLLVFRFIQGIGTAGMMPLV 116
                                       4799***********************************************...9********************** PP

                                       HHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS--- CS
                          Sugar_tr 124 PmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllflPES 194
                                        + i+E+ +   R   ++   l +++G + a  +g  l+ ++    +++l++   +   l ++ +++lPE+
  gi|298674937|ref|YP_003726687.1| 117 MTMIGELYKNIERIHAMGRVSLTTSIGEVTAPLIGGSLAIFGW--NYPFLFY--GLTIPLAIVSVFVLPET 183
                                       *************99999999**************99987754..4555443..33333457778888998 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.24
                                       HHHHHHHHHHHHHHHHHHHHS- CS
                          Sugar_tr 417 yvflvfaglavlfiifvfffvp 438
                                       + + +f + a++f++f+ + ++
  gi|298674937|ref|YP_003726687.1| 206 VAYTMFLVSALFFFLFTIIIYV 227
                                       4456667777777777776655 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.0028
                                       HHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr  80 liaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaai 156
                                       +++a ++++g+++++++ ++ ++  +++  ++ G g G+   +  ++i  +Ap+++ g ++s+++++  +G+ +a++
  gi|298674937|ref|YP_003726687.1| 272 ITIAGFVIVGIAITGMSYAY-NLTSVFLLLLIFGAGFGILIPFLNTLITQVAPTRVMGGIISIFNTMKFVGMTLASG 347
                                       33344556666777777655.888899999*********************************************98 PP

                                       HH CS
                          Sugar_tr 157 fg 158
                                       + 
  gi|298674937|ref|YP_003726687.1| 348 IL 349
                                       73 PP

>> PMP1_2  ATPase proteolipid family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.6       1.2   5.2e+03       5      16 ..     169     180 ..     167     181 .. 0.81
   2 ?   -1.0   0.3      0.34   1.5e+03      13      20 ..     276     283 ..     273     287 .. 0.79
   3 ?   12.0   0.3     3e-05      0.13       8      36 ..     356     386 ..     342     387 .] 0.85

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.2
                            PMP1_2   5 tLPGGviLvFvL 16 
                                       t+P  ++ vFvL
  gi|298674937|ref|YP_003726687.1| 169 TIPLAIVSVFVL 180
                                       778888889997 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.34
                            PMP1_2  13 vFvLvGLA 20 
                                        Fv+vG+A
  gi|298674937|ref|YP_003726687.1| 276 GFVIVGIA 283
                                       699***98 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 3e-05
                            PMP1_2   8 GGviLvFvLvGLAC..vAivltilYRkWqeR 36 
                                        G   vF++ GL    v i+   +YRk+q++
  gi|298674937|ref|YP_003726687.1| 356 SGLEYVFIVSGLIAfgVVIINSFVYRKFQNK 386
                                       56778******97534899**********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       968  (0.0539907); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.41
# Mc/sec: 2847.00
//
Query:       gi|298674938|ref|YP_003726688.1|  [L=383]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-26   92.0   1.6    7.1e-26   90.8   1.6    1.5  1  OrfB_IS605      Probable transposase
    8.9e-23   80.0   0.3    1.9e-22   79.0   0.3    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    4.2e-20   71.0   1.4    9.3e-20   69.8   1.4    1.6  1  HTH_OrfB_IS605  Helix-turn-helix domain
  ------ inclusion threshold ------
      0.013   15.7   0.2      0.034   14.3   0.2    1.7  1  zf-piccolo      Piccolo Zn-finger
      0.022   14.5   5.1       0.48   10.2   2.4    2.4  2  Phage_GP20      Phage minor structural protein GP20
      0.073   12.9   2.0       0.52   10.2   0.3    2.4  2  LemA            LemA family
       0.24   11.5   0.6       0.64   10.1   0.4    1.8  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.79   10.0   6.6        0.3   11.4   1.3    2.3  2  MapZ_EC1        MapZ extracellular domain 1
        1.2    8.9   7.2      0.083   12.7   1.5    1.9  3  DASH_Spc34      DASH complex subunit Spc34


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.8   1.6   3.6e-29   7.1e-26      10     117 ..     180     284 ..     167     286 .. 0.91

  Alignments for each domain:
  == domain 1  score: 90.8 bits;  conditional E-value: 3.6e-29
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsr 86 
                                       +++  + +++g+D+Gi+++a++++++   ++ ++r lk+  ++l+  +++l++k+k+s+ny+k + ++a++h+k+++
  gi|298674938|ref|YP_003726688.1| 180 KQTFYEVNTIGVDVGIKDFAVTSDGE---KIGNPRYLKNSIERLKVLQKRLSRKKKGSNNYRKLKHQIAKYHEKIAN 253
                                       44555689******************...************************************************ PP

                        OrfB_IS605  87 rrkhllhklathliktlkevgvetLnvgnmk 117
                                       +r +++hkl+++li ++++v++e Lnv+++ 
  gi|298674938|ref|YP_003726688.1| 254 QREDFQHKLSNKLISENQAVALECLNVKGLL 284
                                       ****************************986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.0   0.3   9.4e-26   1.9e-22       1      68 [.     298     367 ..     298     368 .. 0.98

  Alignments for each domain:
  == domain 1  score: 79.0 bits;  conditional E-value: 9.4e-26
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpay.TSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       ++++ ++leyka++yG++++++ ++  +Sk C++Cg+  ++ +l++r+++Cp+C++ +drD+nA++Ni k
  gi|298674938|ref|YP_003726688.1| 298 WSSFVQKLEYKAEWYGKNIIKIGRFDpSSKICHVCGYYYQDlELKDREWECPDCKTIHDRDINASVNIKK 367
                                       99******************************************************************87 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.8   1.4   4.7e-23   9.3e-20       1      47 []       9      54 ..       9      54 .. 0.98

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 4.7e-23
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeegk 47
                                      M lkaykyr yP++ Q+e++a+++G++Rf+YN+aL+ +++ ye+ gk
  gi|298674938|ref|YP_003726688.1|  9 M-LKAYKYRMYPNQIQQELIAKHIGACRFIYNWALENKIKSYEQDGK 54
                                      8.******************************************997 PP

>> zf-piccolo  Piccolo Zn-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   1.7e-05     0.034      28      55 ..     326     353 ..     322     356 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.7e-05
                        zf-piccolo  28 kqvCnlCGFnptphltekkeWlclnCQt 55 
                                       +++C +CG+  ++   + +eW c  C t
  gi|298674938|ref|YP_003726688.1| 326 SKICHVCGYYYQDLELKDREWECPDCKT 353
                                       79************************86 PP

>> Phage_GP20  Phage minor structural protein GP20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.014        27     113     137 ..      51      78 ..      22      87 .. 0.77
   2 ?   10.2   2.4   0.00024      0.48      32      90 ..     218     276 ..     211     286 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.014
                        Phage_GP20 113 edgelkg...LdeqikkLkesdkyLFee 137
                                       +dg+ +    L++qi  Lke++++L e 
  gi|298674938|ref|YP_003726688.1|  51 QDGKAISrfeLNKQIRVLKEDHEWLNEI 78 
                                       566665444499**********999873 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00024
                        Phage_GP20  32 eqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeyeakiadlkldnaielaLk 90 
                                       e+lk  +k L+  kk +++  +L+ qi+++ +k++++ ++ + k+++  +++    aL+
  gi|298674938|ref|YP_003726688.1| 218 ERLKVLQKRLSRKKKGSNNYRKLKHQIAKYHEKIANQREDFQHKLSNKLISENQAVALE 276
                                       67888899999999*******************************99877766666655 PP

>> LemA  LemA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1      0.11   2.1e+02      35      82 ..      65     112 ..      42     116 .. 0.81
   2 ?   10.2   0.3   0.00026      0.52      60     108 ..     213     262 ..     197     271 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.11
                              LemA  35 eevteaRakaaeaesveekaeaenqlssalsrllavaEnYPdLkanen 82 
                                        +v +  ++  ++ + ++ + a  +l++a+ +++     +P++k+++n
  gi|298674938|ref|YP_003726688.1|  65 IRVLKEDHEWLNEINSQSLQGATLNLENAFTKFFREKSGFPKFKSKKN 112
                                       4555555666788889999999***********************987 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00026
                              LemA  60 lssalsrllavaEnY.PdLkanenfleLqeelegtEnriavaRrrYneav 108
                                       l+++++rl +++ +   + k ++n+++L++++++  ++ia++R++++++ 
  gi|298674938|ref|YP_003726688.1| 213 LKNSIERLKVLQKRLsRKKKGSNNYRKLKHQIAKYHEKIANQREDFQHKL 262
                                       55666666666655414457899**********************98765 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.4   0.00032      0.64      68      95 ..     324     354 ..     301     369 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00032
                                       --EEEETTTS-EEE.CHH.H.HHS-TTTSSS CS
                              HypA  68 pvkvrCreCgkefe.lee.k.alrCpkCgsa 95 
                                       p +  C++Cg+ ++ le  + + +Cp+C++ 
  gi|298674938|ref|YP_003726688.1| 324 PSSKICHVCGYYYQdLELkDrEWECPDCKTI 354
                                       56678******999544443688*****975 PP

>> MapZ_EC1  MapZ extracellular domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.3      0.23   4.6e+02      48      84 ..      42      81 ..      39      93 .. 0.74
   2 ?   11.4   1.3   0.00015       0.3      37      78 ..     213     254 ..     174     277 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.23
                          MapZ_EC1 48 LekkLeklk.gskeYk..klkkkldslkkqisaieavNsq 84
                                      Le+k++ ++ + k  +  +l+k++  lk+  + ++++Nsq
  gi|298674938|ref|YP_003726688.1| 42 LENKIKSYEqDGKAISrfELNKQIRVLKEDHEWLNEINSQ 81
                                      5666666664333332227999999999999999999997 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00015
                          MapZ_EC1  37 lknsefaklseLekkLeklk.gskeYkklkkkldslkkqisai 78 
                                       lkns ++ l+ L+k L   k gs++Y+klk+++++  ++i+ +
  gi|298674938|ref|YP_003726688.1| 213 LKNS-IERLKVLQKRLSRKKkGSNNYRKLKHQIAKYHEKIANQ 254
                                       4443.688999*****98777*****************99865 PP

>> DASH_Spc34  DASH complex subunit Spc34
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       1.8   3.5e+03     170     199 ..      17      51 ..      15      83 .. 0.59
   2 ?   -2.9   0.0       2.4   4.8e+03      55      68 ..     134     153 ..     117     163 .. 0.70
   3 ?   12.7   1.5   4.2e-05     0.083     182     219 ..     232     269 ..     218     288 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.8
                        DASH_Spc34 170 kyplleake....kieelreeYe.elseeieelea 199
                                       +yp+++++e    +i + r  Y+  l+++i+++e+
  gi|298674938|ref|YP_003726688.1|  17 MYPNQIQQEliakHIGACRFIYNwALENKIKSYEQ 51 
                                       67777777755553333344444234444444443 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.4
                        DASH_Spc34  55 k......vekkpeRkDGkkg 68 
                                              +++ ++R DGk+ 
  gi|298674938|ref|YP_003726688.1| 134 IpkigwiKTRLHRRFDGKQR 153
                                       05566656778899999985 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 4.2e-05
                        DASH_Spc34 182 elreeYeelseeieeleaeiaeQkkqLeaqnknesess 219
                                       + +++Y++l+++i++++++ia Q+++++++ +n+  s+
  gi|298674938|ref|YP_003726688.1| 232 KGSNNYRKLKHQIAKYHEKIANQREDFQHKLSNKLISE 269
                                       55789************************998876554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1546  (0.086229); expected 358.6 (0.02)
Passed bias filter:                      689  (0.0384294); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2748.44
//
Query:       gi|298674939|ref|YP_003726689.1|  [L=170]
Description: hypothetical protein Metev_1004 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.9e-24   84.1   0.0    1.1e-23   83.8   0.0    1.0  1  DUF98       p-hydroxybenzoic acid synthase
     0.0019   17.9   0.0     0.0021   17.7   0.0    1.1  1  Chor_lyase  Chorismate lyase
      0.004   17.0   0.0     0.0055   16.6   0.0    1.3  1  UTRA        UTRA domain


Domain annotation for each model (and alignments):
>> DUF98  p-hydroxybenzoic acid synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.8   0.0   1.9e-27   1.1e-23       3     144 ..      24     165 ..      23     170 .] 0.92

  Alignments for each domain:
  == domain 1  score: 83.8 bits;  conditional E-value: 1.9e-27
                                       --S-HHHHHHHHHSS-EEEEEEEEEEEE--HHHHHHHTS-TT-EEEEEEEEEEETTEEEEEEEEEEEGGGS-HHHHH CS
                             DUF98   3 gDGsvTrhlelltqekveveliemeaeeseeeeapkeveelkkpllrRqVwlrangqklayAeSwwneeelekylke 79 
                                       +DGs+T  le++t+e+v+v + ++  +++++++a   + ++++++++R V l a++++++yA S  +++++   +k+
  gi|298674939|ref|YP_003726689.1|  24 TDGSITFLLEIMTKEDVSVITKNQYLIPADKDTASLFNIDIGDEINYRTVALVAGNKPYVYARSLSPIKRMPPEVKQ 100
                                       8*******************************************************************987666665 PP

                                       ....SSS-HHHHHHHTT--BEEEEEEEEEEE--HHHHHHTSS-EEEEEEEEEEETTEEEEEEEEEEEG. CS
                             DUF98  80 ....kdqpiwksLtkerlelfReirglalgeadeLeeafgekgpfwsRhYrlfhkgkpltvirEvFspa 144
                                           +d+pi+k+L+++++e++R+ + l+++e++   e f+++  ++sR Y+++h++++l+ i E+F++ 
  gi|298674939|ref|YP_003726689.1| 101 dmmrADIPIGKILRNHDIETRRDFENLEVEENH---EYFECN-QVLSRSYKIIHHNHVLMWINELFPVD 165
                                       5665*************************9986...567665.799********************985 PP

>> Chor_lyase  Chorismate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   3.6e-07    0.0021      28     157 ..      26     162 ..      15     169 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.6e-07
                        Chor_lyase  28 gsLtrrlkalae.elrvelLaeswitlrddeeqllaseealsgwvRevilkgddrPlvfartliprssletqgfdla 103
                                       gs+t  l+ +++ ++ v    + +i   +d   l++ + +     R v l + ++P+v+ar+l p   +  +  +  
  gi|298674939|ref|YP_003726689.1|  26 GSITFLLEIMTKeDVSVITKNQYLIPADKDTASLFNIDIGDEINYRTVALVAGNKPYVYARSLSPIKRMPPEVKQDM 102
                                       666666666555356665555555566777777788888888999********************888887777767 PP

                        Chor_lyase 104 qlGkraLGellfsdsdvkRdklevtrveae.....leaLyaRRsrlsigakn.vlvaelf 157
                                       +  ++++G++l  ++   R  +e   ve +      +++++R  ++   ++  + + elf
  gi|298674939|ref|YP_003726689.1| 103 MRADIPIGKILRNHDIETRRDFENLEVEENheyfeCNQVLSRSYKIIHHNHVlMWINELF 162
                                       78999******9998777766554444443345557788888777766555414577777 PP

>> UTRA  UTRA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   9.2e-07    0.0055      14      93 ..      48     128 ..      38     138 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9.2e-07
                                       EEEE--HHHHHHHTS-TTSEEEEEEEEEEETTEEEEEEEEEEEGGGTTTCHHHHHH..CS-HHHHHHHHHTTSEEEE CS
                              UTRA  14 eevpasaeiaeaLglpagepvlrieRlrladgepvaleesylpaslvpdlleedle..egslyayleerlgvpitra 88 
                                         +pa+++ a +++++ g+++ + +    a+++p+++++s  p ++ p+  ++d+   + ++ ++l++ + ++ +r 
  gi|298674939|ref|YP_003726689.1|  48 YLIPADKDTASLFNIDIGDEINYRTVALVAGNKPYVYARSLSPIKRMPPEVKQDMMraDIPIGKILRN-HDIETRRD 123
                                       579********************************************999999985568889999998.77777766 PP

                                       EEEEE CS
                              UTRA  89 eetie 93 
                                        e +e
  gi|298674939|ref|YP_003726689.1| 124 FENLE 128
                                       66655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1191.88
//
Query:       gi|298674940|ref|YP_003726690.1|  [L=104]
Description: hypothetical protein Metev_1005 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-35  122.6   1.0    1.2e-35  122.4   1.0    1.0  1  DUF5611     Domain of unknown function (DUF5611)
  ------ inclusion threshold ------
      0.041   13.8   0.2      0.082   12.8   0.2    1.6  1  Imm6        Immunity protein Imm6
       0.27   10.6   0.1       0.41   10.0   0.1    1.2  1  UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit T


Domain annotation for each model (and alignments):
>> DUF5611  Domain of unknown function (DUF5611)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.4   1.0   2.1e-39   1.2e-35       1     103 []       1     100 [.       1     100 [. 0.99

  Alignments for each domain:
  == domain 1  score: 122.4 bits;  conditional E-value: 2.1e-39
                                       -EEE---SSS--SH.HHHHHHHHHHT.-EEEEETTEEEEE-TTBS-EEEEE..-SS-EEEEE--.B...-TTS-HHH CS
                           DUF5611   1 mreYkiKrGfkkeeeerlkelleeyfggeveeegdllvvsfgaikklevkisskkkklvvdteerdaeeeddeaald 77 
                                       m+ Yk+KrG+k++  +r++++l e+f++e++ e+d++++s+ga+ k+ev++  ++kk++v+te+ d++e dde +ld
  gi|298674940|ref|YP_003726690.1|   1 MQLYKLKRGYKPDS-DRIYSILDECFPTEIKCEDDKFITSYGALDKVEVWL--EGKKMAVETESADETELDDELILD 74 
                                       99************.************************************..************************ PP

                                       HHHHHHHHHHHHH---GGGHHHHH-- CS
                           DUF5611  78 tvkkfndFLeeaTGydaKeRkkkakk 103
                                       t+k+f+dFL++aTGy+aKeR+k+akk
  gi|298674940|ref|YP_003726690.1|  75 TNKRFRDFLYQATGYTAKERVKMAKK 100
                                       ************************97 PP

>> Imm6  Immunity protein Imm6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   1.4e-05     0.082       5      46 ..      17      58 ..      14     102 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.4e-05
                              Imm6  5 illaiaekllslikkkddevevveeaLdvckkwlegenvtad 46
                                      i+ ++ e+   +ik +dd++     aLd+++ wleg+++ ++
  gi|298674940|ref|YP_003726690.1| 17 IYSILDECFPTEIKCEDDKFITSYGALDKVEVWLEGKKMAVE 58
                                      677899************99999*************998765 PP

>> UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   6.8e-05      0.41      12      22 ..      80      90 ..      73      92 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 6.8e-05
                        UCR_Fe-S_N 12 RDFLyiATgav 22
                                      RDFLy ATg +
  gi|298674940|ref|YP_003726690.1| 80 RDFLYQATGYT 90
                                      ********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 774.50
//
Query:       gi|298674941|ref|YP_003726691.1|  [L=144]
Description: flavodoxin/nitric oxide synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.9e-14   51.9   0.0    1.3e-13   51.4   0.0    1.2  1  Flavodoxin_1   Flavodoxin
    1.2e-10   41.8   0.0    1.4e-10   41.6   0.0    1.2  1  Flavodoxin_5   Flavodoxin domain
      6e-06   26.1   0.4     0.0015   18.3   0.1    2.1  2  FMN_red        NADPH-dependent FMN reductase
    8.1e-05   22.4   0.0    0.00011   21.9   0.0    1.3  1  Flavodoxin_3   Flavodoxin domain
     0.0063   16.2   0.0     0.0081   15.9   0.0    1.1  1  Peptidase_U40  Peptidase U40
  ------ inclusion threshold ------
       0.14   11.8   0.0       0.46   10.2   0.0    1.9  1  Flavodoxin_2   Flavodoxin-like fold


Domain annotation for each model (and alignments):
>> Flavodoxin_1  Flavodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.4   0.0   4.2e-17   1.3e-13       1     140 [.       6     131 ..       6     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 4.2e-17
                                       EEEETSSSHHHHHHHHHHHHHHHTTTEEEEEEEEGTTSCGGGGGTHSEEEEEEEEETTTBEEGGGHHHHHHHHHHHC CS
                      Flavodoxin_1   1 ilYgSetGnteklAkqlaeelgehgfnadvvslsdydeslseieeealllvvtsTfgnGdppengesffqdllelkg 77 
                                       ++Y S++Gnt+++A+++a +++++ +++dv s++d    ++e+ + + ++++ sTf+ G +    e +f+d+l  k 
  gi|298674941|ref|YP_003726691.1|   6 VVYLSTQGNTKTMAESIANGAKSRHVDVDVSSFYDTT--VDEVAAADAIAIGSSTFYYGMLA-PIE-KFVDELVQK- 77 
                                       89***********************999999999999..67******************887.333.344444444. PP

                                       HHGCCSTTTTEEEEEEEEECTTSSSTTHHHHHHHHHHHHTTCEEESSSEEEETTST.HGHHHHH CS
                      Flavodoxin_1  78 deledgdlsgvrfavfglGdsayenFcaagkkldekleelGaerllkllegdednq.egqeeaf 140
                                             d  g+     ++G++++++  +a +++ +k+ ++G++++ ++l+++  ++ ++  e+ 
  gi|298674941|ref|YP_003726691.1|  78 ------DVDGK--IGAAFGSYGWSG--EAPHMIADKMRKAGMNVVDPVLRIQHIPNdKDISECE 131
                                       ......23344..4689999*****..*************************999877776665 PP

>> Flavodoxin_5  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.0   4.7e-14   1.4e-10       2      92 ..       6      98 ..       5     125 .. 0.85

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 4.7e-14
                      Flavodoxin_5  2 ilYsSrdGqTkkiaeriaeelreegelvdved.vekesedlesydavvigasvyygkllpelakFvekh.reaLstkpv 78
                                      ++Y S++G+Tk+ ae+ia+  +++  +vdv++  ++  ++++ +da+ ig+s +y ++l  ++kFv++  +++++ k  
  gi|298674941|ref|YP_003726691.1|  6 VVYLSTQGNTKTMAESIANGAKSRHVDVDVSSfYDTTVDEVAAADAIAIGSSTFYYGMLAPIEKFVDELvQKDVDGKIG 84
                                      89**********************999*****7778999**************99999999*****9977999999999 PP

                      Flavodoxin_5 79 alfsvsltarkpek 92
                                      a+f    ++ ++  
  gi|298674941|ref|YP_003726691.1| 85 AAFGSYGWSGEAPH 98
                                      99887777554444 PP

>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0    0.0022       6.7       8      37 ..       9      36 ..       2      42 .. 0.80
   2 !   18.3   0.1     5e-07    0.0015      67     136 ..      43     109 ..      39     124 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0022
                                      S--STT-HHHHHHHHHHCCT-T.T-CEEEE CS
                           FMN_red  8 GSlrkgsntrklaewaaealkeagaeveli 37
                                       S   ++nt+++ae +a+ +k + ++v++ 
  gi|298674941|ref|YP_003726691.1|  9 LS--TQGNTKTMAESIANGAKSRHVDVDVS 36
                                      44..57**************9999998875 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 5e-07
                                       HHHHHH-SCEEEEEEECTTCE-HHHHHHHHCHT-.SSCHCCTT-EEEEE.EE-SSTTTTHHHHHHHHHHHH CS
                           FMN_red  67 lekiaaadaliivtPeYngsysgllKnalDrlsrtrgkkelrgKpvalv.avgggrrgglraeeqlrqvla 136
                                       ++ +aaada+ i++ ++ +++ +++  + D l+    +k + gK++a++ ++g +    + ++ ++r++ +
  gi|298674941|ref|YP_003726691.1|  43 VDEVAAADAIAIGSSTFYYGMLAPIEKFVDELV----QKDVDGKIGAAFgSYGWSGEAPHMIADKMRKAGM 109
                                       5789****************************9....********97764888777777777777777666 PP

>> Flavodoxin_3  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   3.8e-08   0.00011       2      86 ..       6      99 ..       5     117 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 3.8e-08
                      Flavodoxin_3  2 ilysSltGNTkkvAeaikealeeekeivsikeakek....veeadvvfvGfwvdkgtadeealkfletlknkki..... 71
                                      ++y S  GNTk +Ae+i++ +++ +  v++++  ++    v++ad +++G  +    + + ++kf+ +l  k++     
  gi|298674941|ref|YP_003726691.1|  6 VVYLSTQGNTKTMAESIANGAKSRHVDVDVSSFYDTtvdeVAAADAIAIGSSTFYYGMLAPIEKFVDELVQKDVdgkig 84
                                      9*******************999665566655544455678999*******9998888888888888888887744444 PP

                      Flavodoxin_3 72 llfgTlGagkdseya 86
                                      ++fg  G +++  ++
  gi|298674941|ref|YP_003726691.1| 85 AAFGSYGWSGEAPHM 99
                                      678888888777774 PP

>> Peptidase_U40  Peptidase U40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.7e-06    0.0081      34     124 ..      15     111 ..       4     115 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.7e-06
                     Peptidase_U40  34 kkaivelqallpkaqsvgnnrvrfttaevdsavarisqkigvpasyyqflipienfv...vaggfettvs...gsfr 104
                                        k++ e  a   k++ v  +   f  + vd   a  +  ig  + yy +l pie+fv   v   ++  +    gs+ 
  gi|298674941|ref|YP_003726691.1|  15 TKTMAESIANGAKSRHVDVDVSSFYDTTVDEVAAADAIAIGSSTFYYGMLAPIEKFVdelVQKDVDGKIGaafGSYG 91 
                                       57778888888899999999999*99********99********************855544445544441115555 PP

                     Peptidase_U40 105 glgqfnrqtwdrlrrlgrnl 124
                                         g+  +   d++r+ g n+
  gi|298674941|ref|YP_003726691.1|  92 WSGEAPHMIADKMRKAGMNV 111
                                       56667777778888888775 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00015      0.46      70     110 ..      40      87 ..       2     112 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00015
                                       HH.HHHHHCSSEEEEEEE-BTTB--HHHHHHHHHHS-TTT......SC CS
                      Flavodoxin_2  70 eq.iekllaadaivlqfPlwwfgvPailKgwiDrvltagf......af 110
                                       +  +++++aadai +++   ++g+ a   +++D+ +++        af
  gi|298674941|ref|YP_003726691.1|  40 DTtVDEVAAADAIAIGSSTFYYGMLAPIEKFVDELVQKDVdgkigaAF 87 
                                       333589999999999999999999999999999999987755565555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 962.46
//
Query:       gi|298674942|ref|YP_003726692.1|  [L=689]
Description: signal transduction histidine kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      3e-31  107.3   2.5    5.4e-31  106.5   0.7    2.4  2  HisKA_2      Histidine kinase
    1.2e-28  100.5   4.6    1.2e-28  100.5   4.6    2.4  2  dCache_1     Cache domain
      2e-10   41.1   2.1    3.8e-10   40.3   0.5    2.4  2  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    3.9e-06   27.5   0.1    1.2e-05   26.0   0.1    1.8  1  HWE_HK       HWE histidine kinase
      0.001   19.4   0.0      0.023   15.1   0.0    2.8  2  HAMP         HAMP domain
     0.0025   17.7   0.0     0.0056   16.6   0.0    1.6  1  HATPase_c_2  Histidine kinase-like ATPase domain
     0.0047   16.2   0.0     0.0047   16.2   0.0    3.1  3  dCache_2     Cache domain
     0.0053   16.6   0.7      0.017   15.0   0.0    2.1  2  sCache_2     Single Cache domain 2
  ------ inclusion threshold ------
      0.014   15.3   0.4      0.042   13.7   0.4    1.8  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
      0.064   13.3   0.0       0.52   10.3   0.0    2.3  1  Phage_coat   Phage PP7 coat protein
       0.52   10.5   4.2       0.29   11.3   1.1    2.1  2  CREPT        Cell-cycle alteration and expression-elevated pr


Domain annotation for each model (and alignments):
>> HisKA_2  Histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.7   2.8e+03      20      55 ..      63     100 ..      61     103 .. 0.71
   2 !  106.5   0.7   3.3e-34   5.4e-31       1      76 []     490     565 ..     490     565 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.7
                           HisKA_2  20 qarkakdeevkealre..sqnRvlsialiheeLyksed 55 
                                       + +kak e++  +l+e  s nR + + ++ + L++++d
  gi|298674942|ref|YP_003726692.1|  63 NEDKAKGENIATMLSEyeSSNRSEVLNMLKRLLVQNKD 100
                                       56777777777777652267888888888888888877 PP

  == domain 2  score: 106.5 bits;  conditional E-value: 3.3e-34
                           HisKA_2   1 EihHRvkNnLqvisslLslqarkakdeevkealresqnRvlsialiheeLyksedletvdfseylekLvenlfksy 76 
                                       EihHRvkNnLqvisslLsl++ +++d++v ea+r+sqnRv+s+al heeLy+s+ + ++dfsey+++L++ l+++y
  gi|298674942|ref|YP_003726692.1| 490 EIHHRVKNNLQVISSLLSLESGNFDDPDVVEAFRDSQNRVRSMALAHEELYQSKHVADIDFSEYVDNLTNYLIQTY 565
                                       9***********************************************************************9987 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.5   4.6   7.6e-32   1.2e-28       5     246 ..      41     294 ..      37     296 .. 0.78
   2 ?   -0.3   0.6      0.46   7.6e+02     174     237 ..     624     682 ..     567     686 .. 0.69

  Alignments for each domain:
  == domain 1  score: 100.5 bits;  conditional E-value: 7.6e-32
                          dCache_1   5 eqaeeqllglaeqlanniedvldslenlaetlasnpslqdlleepnraneasreslqallksilksn.......... 71 
                                       + a++q+ + a+++an++++++++ ++  e      +++ +l+e++    ++r+++ ++lk +l  n          
  gi|298674942|ref|YP_003726692.1|  41 DLAYQQSIEKATSYANDFNTDMNEDKAKGE------NIATMLSEYE---SSNRSEVLNMLKRLLVQNkdligtyvay 108
                                       5688999999************77443333......4555678877...599**********888887788888888 PP

                          dCache_1  72 .........pdisgvylvdadGqviassdpssppnleg.......tddpadrdwykealaggggkpvisdpyvdqtg 132
                                                +d+ + ++ d+ G++i   ++++     g       + d+  +++y+ +++ +  k+v+++py +   
  gi|298674942|ref|YP_003726692.1| 109 epdafdnrdEDYVNTTYHDSTGRLI---PYWNRI---GgdvhcepLVDYETSNYYQLPKKLE--KTVVTEPYLY-Q- 175
                                       8888888888889999999999997...444333...23558999*****************..9*******75.5. PP

                          dCache_1 133 gkpvitiavpiyddsgkfiGvlaadldldnlqdllsniklgetgyvfivdsdGniiahpd.kdl.lgknlrdelkaq 207
                                       gk+++++++pi++ +g+f+G+ ++d++l+n+++++s++ + +tgy+f+ +++G++++hp+ k++  +k+l+d + + 
  gi|298674942|ref|YP_003726692.1| 176 GKLIVSYVSPIMK-NGTFVGIGGVDVSLENIDNIVSDVEIFDTGYAFMSSNTGILLSHPEkKQWiGNKTLYDFDDPK 251
                                       79**********9.6*********************************************55555455555555544 PP

                          dCache_1 208 ..ealekalakiesgvssvklngeeylva.yapip.tglgWyl 246
                                         + ++ +++++e+ + +++ +  +  v  y+pi+ +    +l
  gi|298674942|ref|YP_003726692.1| 252 isQMADEIQSGKEGHIETIDPSTGKNVVMfYQPIEtGEYSFIL 294
                                       955555555555555555553334555666*****53355554 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.46
                          dCache_1 174 etgyvfivdsdGniiahpdkdllgknlrdelkaq...ealekalakiesgvssvklngeeylvayap 237
                                       ++ + +iv+++G+ i++        +++  ++++   +  ++ + +i + +   k++g e++++++ 
  gi|298674942|ref|YP_003726692.1| 624 DNNHKLIVSDNGKGISD--------DIDFRESESlglQLVNTLVEQIDGTIELDKSQGTEFIITFKE 682
                                       33344444444444444........222222222444444555667788888888888888888875 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0         4   6.6e+03       9      21 ..     461     480 ..     459     504 .. 0.54
   2 !   40.3   0.5   2.3e-13   3.8e-10       6     110 ..     591     682 ..     587     684 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4
                                       HHHHHHHHHHHH.......H CS
                         HATPase_c   9 iisnlvdNavkf.......a 21 
                                       i+ n v+Na k+        
  gi|298674942|ref|YP_003726692.1| 461 ILTNGVENARKAmyeftteR 480
                                       78888999999877664321 PP

  == domain 2  score: 40.3 bits;  conditional E-value: 2.3e-13
                                       HHHHHHHHHHHHHHHHS...TTTEEEEEEEEEE.TEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHH CS
                         HATPase_c   6 LrqiisnlvdNavkfat...kageieveikase.ddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGl 78 
                                       L  ii++l++N++k+a     +gei +++ ++  ++ ++ v+DnG+Gi+  d++     f +          + lGl
  gi|298674942|ref|YP_003726692.1| 591 LGIIINELISNSLKHAFsddATGEININMYVEGdNNHKLIVSDNGKGISD-DID-----FRE---------SESLGL 652
                                       6679***********4443467788888887334799999********97.777.....788.........889*** PP

                                       HHHHHHHHHTTTEEEEEEETTTEEEEEEEEES CS
                         HATPase_c  79 sivkklvelmgGeiwvesepgrGttftftlpl 110
                                        +v+ lve+++G+i++++++  Gt+f++t+++
  gi|298674942|ref|YP_003726692.1| 653 QLVNTLVEQIDGTIELDKSQ--GTEFIITFKE 682
                                       ****************6666..*****99986 PP

>> HWE_HK  HWE histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.1   7.1e-09   1.2e-05       1      52 [.     490     543 ..     490     570 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 7.1e-09
                                       HHHHHHHHHHHHHHHHHHHHSSSXS-HH..HHHHHHHHHHHHHHHHHHHHHHCT CS
                            HWE_HK   1 ElnHRvKNlLavvqsiarqtlrsaesle..efaeklsgRLqALsaahdllsree 52 
                                       E++HRvKN L v++s+ +  + + ++++  e+ ++ ++R+++++ ah+ l +++
  gi|298674942|ref|YP_003726692.1| 490 EIHHRVKNNLQVISSLLSLESGNFDDPDvvEAFRDSQNRVRSMALAHEELYQSK 543
                                       89*****************9887776652234455578*********9988765 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.4e-05     0.023       8      52 ..     385     429 ..     382     430 .. 0.96
   2 ?    0.6   0.0      0.46   7.5e+02      17      46 ..     439     468 ..     436     474 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.4e-05
                                       HHHHHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHHH CS
                              HAMP   8 rPLrrLaraarriaaGdldtrlpvsgrDEiGeLarafNaMldrLr 52 
                                        P+++ +r+a+++++G+l+tr   + +  + eL+ ++++++++L+
  gi|298674942|ref|YP_003726692.1| 385 SPIQETMRVANSLSKGRLSTRFRLNVKGDFKELGDTLDHFSESLN 429
                                       69****************************************997 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.46
                                       HHHHTTTBTSSTCCTTSSSHHHHHHHHHHH CS
                              HAMP  17 arriaaGdldtrlpvsgrDEiGeLarafNa 46 
                                         +i++ d++  + v+g+  ++ L   +++
  gi|298674942|ref|YP_003726692.1| 439 LTAIQKEDFTRKVQVHGNGDFAILTNGVEN 468
                                       6789999**********9999988877665 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   3.5e-06    0.0056      21     113 ..     580     663 ..     571     680 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.5e-06
                       HATPase_c_2  21 raglseelldeirlaveEactNavehayleapegpvevrlesdeea.ltvevaDsGpg.fdpetlpdpteeepkesl 95 
                                       +  l+ +++  + + ++E+++N  +ha  ++ +g++++ + ++++   ++ v+D+G+g  d             + +
  gi|298674942|ref|YP_003726692.1| 580 KISLNMDTAIPLGIIINELISNSLKHAFSDDATGEININMYVEGDNnHKLIVSDNGKGiSDDI-----------DFR 645
                                       5678888899999**************************77776665999********65554...........556 PP

                       HATPase_c_2  96 kegGrGlalikglvDeve 113
                                       +++ +Gl l+++lv++++
  gi|298674942|ref|YP_003726692.1| 646 ESESLGLQLVNTLVEQID 663
                                       677889999999888873 PP

>> dCache_2  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.2       1.2     2e+03      54      76 ..      48      70 ..      30     105 .. 0.55
   2 !   16.2   0.0   2.9e-06    0.0047      83     257 ..     207     267 ..     198     288 .. 0.56
   3 ?    0.0   2.8      0.23   3.8e+02      33      67 ..     471     508 ..     460     588 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.2
                          dCache_2 54 veeaysiaeeiyekyknelseee 76
                                      +e+a s a++++ ++ +++++ e
  gi|298674942|ref|YP_003726692.1| 48 IEKATSYANDFNTDMNEDKAKGE 70
                                      33444444444444333222222 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 2.9e-06
                          dCache_2  83 ealrsirydggegyyfiidskgtlilhpdspsleGknlldlkdkdGryiiremiklakkkgeGfveytwpkpdekkp 159
                                       ++++                                                                         
  gi|298674942|ref|YP_003726692.1| 207 NIVS------------------------------------------------------------------------- 210
                                       4444......................................................................... PP

                          dCache_2 160 rkkisyvkyfepldwiIGtgaylddieeelkqellktlksirygnngyifiydtdgniilhplkkelngknll.evk 235
                                                                              ++ + ++gy+f+ +++g ++ hp kk+ +g+++l +++
  gi|298674942|ref|YP_003726692.1| 211 ---------------------------------------DVEIFDTGYAFMSSNTGILLSHPEKKQWIGNKTLyDFD 248
                                       .......................................44455555555555555555555555555555555555 PP

                          dCache_2 236 dkkgkllqelleaakkkgegfv 257
                                       d+k   ++++ + +++++eg +
  gi|298674942|ref|YP_003726692.1| 249 DPK---ISQMADEIQSGKEGHI 267
                                       555...4444444444444433 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.23
                          dCache_2  33 elie...yeknsleeslkesLksrveeaysiaeeiyek 67 
                                       + +     e++++ee  k++++ rv + +++++++   
  gi|298674942|ref|YP_003726692.1| 471 KAMYeftTERKQAEEIRKKEIHHRVKNNLQVISSLLSL 508
                                       33333335777777777777887777777777666554 PP

>> sCache_2  Single Cache domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0     1e-05     0.017      40     105 ..     204     266 ..     183     277 .. 0.84
   2 ?   -1.9   0.1       1.6   2.7e+03      10      43 ..     463     497 ..     450     503 .. 0.53

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1e-05
                          sCache_2  40 evkelvnglkfgdGkgYffvldedgtllvhPfnpqleGkn.asnlkDanGkyiirelvkeak.kkggg 105
                                       ++ ++v++    d  gY f+  ++g+ll hP ++q++G + ++++ D++    i ++ +e++ +k+g+
  gi|298674942|ref|YP_003726692.1| 204 NIDNIVSDVEIFD-TGYAFMSSNTGILLSHPEKKQWIGNKtLYDFDDPK----ISQMADEIQsGKEGH 266
                                       6677888888888.9***********************76268899998....888888888555555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.6
                          sCache_2  10 knqvetaisliea.vykqvesgkiteeeaqeevke 43 
                                       +n ve+a++++ +   ++ ++ +i ++e+  +vk+
  gi|298674942|ref|YP_003726692.1| 463 TNGVENARKAMYEfTTERKQAEEIRKKEIHHRVKN 497
                                       34444444444330334445555666666655555 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.4   2.6e-05     0.042       7      52 ..     595     646 ..     591     658 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.6e-05
                       HATPase_c_3   7 laelvdNsld...Adaen.....vkievnknrgktgeivieDdGkGmsee.elkn 52 
                                       + el+ Nsl    +         ++i++  +  ++ ++ + D+GkG+s + ++++
  gi|298674942|ref|YP_003726692.1| 595 INELISNSLKhafS---DdatgeININMYVEGDNNHKLIVSDNGKGISDDiDFRE 646
                                       5699****986442...2244566666655556789************9988876 PP

>> Phage_coat  Phage PP7 coat protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00032      0.52      32     107 ..     385     478 ..     359     487 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00032
                                       SSSSS--EEEEEEEEETTSSEEEEEEE.........EEE.....EEEEEXTTTSTTXSEEEEEE...EEEEE.EEEE CS
                        Phage_coat  32 gplvgrlrltaslrqngaktayrvnlk.........ldq.....advvdcstsvcgelpkvryt...qvwsh.dvti 90 
                                        p+   +r++ sl +    t +r+n+k         ld       +v+d s +v   + k  +t   qv    d +i
  gi|298674942|ref|YP_003726692.1| 385 SPIQETMRVANSLSKGRLSTRFRLNVKgdfkelgdtLDHfseslNNVIDDSNAVLTAIQKEDFTrkvQVHGNgDFAI 461
                                       555566666666666666666666666222221111222222224699999999999999766632256543599** PP

                                       ETTS-HHHHHHHHHHHH CS
                        Phage_coat  91 vansteasrkslydltk 107
                                       ++n  e +rk++y++t 
  gi|298674942|ref|YP_003726692.1| 462 LTNGVENARKAMYEFTT 478
                                       **************986 PP

>> CREPT  Cell-cycle alteration and expression-elevated protein in tumour
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.1   0.00018      0.29      37      95 ..      32      90 ..      25     101 .. 0.88
   2 ?   -1.5   0.1       1.6   2.6e+03     101     101 ..     475     475 ..     415     510 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00018
                             CREPT 37 lekikdkeeaekllkqveealellaeYnkrLeaeleeRkklakmledfleaqkellaka 95
                                      +++ ++++e  ++++++e+a +  +++n+ ++++  + +++a+ml+++ ++ ++++ + 
  gi|298674942|ref|YP_003726692.1| 32 INSTTSQQEDLAYQQSIEKATSYANDFNTDMNEDKAKGENIATMLSEYESSNRSEVLNM 90
                                      67778999999**************************************9999887655 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.6
                             CREPT 101 e 101
                                       e
  gi|298674942|ref|YP_003726692.1| 475 E 475
                                       1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (689 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       867  (0.0483574); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.61u 0.23s 00:00:00.84 Elapsed: 00:00:00.41
# Mc/sec: 5094.13
//
Query:       gi|298674943|ref|YP_003726693.1|  [L=135]
Description: response regulator receiver protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-22   79.0   0.2    3.3e-22   78.8   0.2    1.1  1  Response_reg  Response regulator receiver domain
  ------ inclusion threshold ------
      0.021   15.1   0.5       0.04   14.2   0.5    1.4  1  TrkA_N        TrkA-N domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8   0.2   3.7e-26   3.3e-22       1     111 [.       6     116 ..       6     117 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 3.7e-26
                                       EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSS.SEHHHHHHHHHHCTTTSEEEE CS
                      Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpg.mdGlellkeireedpelpvii 76 
                                       +l+v+D+ +v+  +++ l++ gy++   a++g+ea+++++  + dl+l+Di++ g +dG+e++++ire   ++pvi 
  gi|298674943|ref|YP_003726693.1|   6 ILVVEDENIVALDIKNRLKKLGYSVPSIASTGEEAIRKAEITSADLVLMDIMLKGdVDGIEAAERIRELY-DIPVIY 81 
                                       8**********************77779**************************999***********99.****** PP

                                       EESSTSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                      Response_reg  77 ltahseeedavealkagaddflsKpfdpeeLlkal 111
                                       lta+++e+ +++a     ++++sKpf++++L++ +
  gi|298674943|ref|YP_003726693.1|  82 LTAYADEKILERAKLTQPYGYISKPFKEKDLRTNI 116
                                       *******************************9987 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.5   4.4e-06      0.04      26     101 ..       8      88 ..       2      99 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.4e-06
                                       EEESSH....HHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-..SSSHHHHHHHHHHHHHHTSSSEEEEEE CS
                            TrkA_N  26 vidkde....erveelreeglevvvgdatdeevLeeagiekadaviaa..tgddeanilavllakelnpkkkiiara 96 
                                       v++++     +  ++l++ g+ v     t ee++++a+i +ad+v+    ++ d + i a++ ++el +  ++i  +
  gi|298674943|ref|YP_003726693.1|   8 VVEDENivalDIKNRLKKLGYSVPSIASTGEEAIRKAEITSADLVLMDimLKGDVDGIEAAERIRELYDI-PVIYLT 83 
                                       444444222233577888899999999****************99965227799***********99985.555444 PP

                                       SSGGG CS
                            TrkA_N  97 qdpeh 101
                                        ++++
  gi|298674943|ref|YP_003726693.1|  84 AYADE 88 
                                       44433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 815.32
//
Query:       gi|298674944|ref|YP_003726694.1|  [L=447]
Description: signal transduction histidine kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.1e-32  109.2   3.2    8.1e-32  109.2   3.2    2.2  2  HisKA_2      Histidine kinase
    1.1e-25   89.8   0.5      2e-19   69.6   0.4    2.4  2  PAS_3        PAS fold
    3.2e-17   62.7   1.7    3.8e-11   43.2   0.3    2.5  2  PAS_9        PAS domain
    5.6e-15   55.5   0.0    5.7e-09   36.2   0.0    2.2  2  PAS_4        PAS fold
    1.8e-14   53.7   0.1    3.3e-09   36.8   0.0    2.5  2  PAS          PAS fold
    5.6e-10   39.0   0.0      6e-09   35.7   0.0    2.5  2  PAS_8        PAS domain
    1.2e-08   35.4   0.1      4e-08   33.7   0.1    1.9  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    4.7e-07   30.4   0.5    1.1e-06   29.2   0.5    1.7  1  HWE_HK       HWE histidine kinase
     0.0012   18.8   0.0     0.0022   18.0   0.0    1.5  1  HATPase_c_2  Histidine kinase-like ATPase domain
     0.0013   18.9   0.2        1.9    8.6   0.0    2.8  2  PAS_11       PAS domain
     0.0039   17.0   0.0      0.011   15.6   0.0    1.7  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
  ------ inclusion threshold ------
      0.087   12.9   0.0       0.24   11.4   0.0    1.7  1  Stomoxyn     Insect antimicrobial peptide, stomoxyn
       0.13   12.5   1.8        1.6    8.9   0.1    2.9  3  PAS_7        PAS fold
       0.13   12.1   0.1       0.25   11.1   0.1    1.4  1  VanY         D-alanyl-D-alanine carboxypeptidase


Domain annotation for each model (and alignments):
>> HisKA_2  Histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.9   2.5e+03      24      42 ..     123     141 ..     118     143 .. 0.81
   2 !  109.2   3.2   6.3e-35   8.1e-32       1      76 []     257     332 ..     257     332 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.9
                           HisKA_2  24 akdeevkealresqnRvls 42 
                                       ++ +e+++al+es+++ ++
  gi|298674944|ref|YP_003726694.1| 123 TERKETEKALQESEKKFRT 141
                                       56789999****9998665 PP

  == domain 2  score: 109.2 bits;  conditional E-value: 6.3e-35
                           HisKA_2   1 EihHRvkNnLqvisslLslqarkakdeevkealresqnRvlsialiheeLyksedletvdfseylekLvenlfksy 76 
                                       EihHRvkNnLqvisslL+l+a+++++++v ea+++sqnRv+s+al he+Ly+s+dl+t++f+eyl++L+ +lf+sy
  gi|298674944|ref|YP_003726694.1| 257 EIHHRVKNNLQVISSLLNLEASNFESDDVVEAFKNSQNRVRSMALAHEKLYQSKDLKTINFGEYLKNLAMHLFQSY 332
                                       9*************************************************************************98 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.6   0.4   1.6e-22     2e-19       3      89 .]      33     119 ..      31     119 .. 0.95
   2 !   18.0   0.0     2e-06    0.0026       2      88 ..     160     241 ..     159     242 .. 0.89

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 1.6e-22
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvirde 78 
                                       +vs+++ +  Gy+p+++++ + s+ d++hpeD+e+vr+ + +++++g  ++ +eyRi +k G++rwv +r+++ +++
  gi|298674944|ref|YP_003726694.1|  33 FVSDSITQF-GYTPDDFTSGCYSYGDIIHPEDLEKVRSRISRHVEQGYkQFVHEYRIYTKTGDIRWVTERTFIRNNS 108
                                       677777666.*************************************99**************************** PP

                             PAS_3  79 ngkpvrvigva 89 
                                        gk+++++g++
  gi|298674944|ref|YP_003726694.1| 109 MGKVTHYQGII 119
                                       *********96 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 2e-06
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       i v+++ +++l ys++ell+   ++ d +hp D      +++e++kkg ++ +e   +++dG ++ +e ++++i d 
  gi|298674944|ref|YP_003726694.1| 160 IEVNQSACNYLNYSRDELLQM--KIND-IHPSDTTIDSGEMNELVKKGYSI-FETTHVNRDGAIIPIELSVQYI-DY 231
                                       899******************..6655.8*******************955.55556*****************.99 PP

                             PAS_3  79 ngkpvrvigv 88 
                                       +g p +++ +
  gi|298674944|ref|YP_003726694.1| 232 QGLPAFIVVT 241
                                       9999988765 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   1.5e-06    0.0019       9     104 .]      26     124 ..      17     124 .. 0.72
   2 !   43.2   0.3   2.9e-14   3.8e-11       2     103 ..     148     245 ..     147     246 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.5e-06
                             PAS_9   9 pdg.rilyaNeaalrllGyspeevlgks..itdlfvtdpeanerlraaleqgrk...kerevevvlirkngetfwvl 79 
                                        d+ ++++++++  ++ Gy+p+++      + d++ ++++ ++  +++ +   +   k++  e+ +++k+g   wv 
  gi|298674944|ref|YP_003726694.1|  26 VDNwPVEFVSDSITQF-GYTPDDFTSGCysYGDII-HPEDLEKVRSRISRHV-EqgyKQFVHEYRIYTKTGDIRWVT 99 
                                       4552566*******99.******998644488999.3333333333333333.3488******************65 PP

                             PAS_9  80 .ltaspvkdd.dgelvgiivilrDite 104
                                         t++  +++  g+++++ +i++Dite
  gi|298674944|ref|YP_003726694.1| 100 eRTFI--RNNsMGKVTHYQGIIIDITE 124
                                       34443..555599*************8 PP

  == domain 2  score: 43.2 bits;  conditional E-value: 2.9e-14
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwv 78 
                                       d+i+i+++dg+ + +N++a++ l ys++e+l+ +i d+   ++++  +  ++ e  +k    +e+++++++g  +++
  gi|298674944|ref|YP_003726694.1| 148 DAIFICDMDGNFIEVNQSACNYLNYSRDELLQMKINDIH--PSDTTIDSGEMNELVKKGYSIFETTHVNRDGAIIPI 222
                                       89*************************************..55555555555555555469**************** PP

                             PAS_9  79 lltaspvkdddgelvgiivilrDit 103
                                       +l++  +    ++l ++iv+ r++t
  gi|298674944|ref|YP_003726694.1| 223 ELSVQYIDY--QGLPAFIVVTRNLT 245
                                       *******54..45999999999999 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   3.3e-06    0.0042      19     110 .]      33     127 ..      15     127 .. 0.89
   2 !   36.2   0.0   4.4e-12   5.7e-09       1     109 [.     143     248 ..     143     249 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.3e-06
                             PAS_4  19 yaNaaaaelfgappeellGktla..ellpeedaarleralrrvlegeepiefleelll..pgeerhyelrllPlrde 91 
                                       +++ ++ + fg++p++++  ++   ++  +ed + +++ + r +e++  ++ +e++     g+ r++  r +   ++
  gi|298674944|ref|YP_003726694.1|  33 FVSDSITQ-FGYTPDDFTSGCYSygDIIHPEDLEKVRSRISRHVEQGYKQFVHEYRIYtkTGDIRWVTERTFIRNNS 108
                                       56666666.7888888877777769999999***********************9999*********99998888** PP

                             PAS_4  92 sGevigvlvisrDiTerrr 110
                                        G+v ++ +i++DiTer++
  gi|298674944|ref|YP_003726694.1| 109 MGKVTHYQGIIIDITERKE 127
                                       *****************85 PP

  == domain 2  score: 36.2 bits;  conditional E-value: 4.4e-12
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       +++++da++++d dg+++ +N++a+ ++ ++++ell ++  +++p  d +  +  ++++++ + +i+++++++++g+
  gi|298674944|ref|YP_003726694.1| 143 FNNTNDAIFICDMDGNFIEVNQSACNYLNYSRDELLQMKINDIHPS-DTTIDSGEMNELVKKGYSIFETTHVNRDGA 218
                                       7899*****************************************9.9***************************** PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerr 109
                                         ++el++  + d +G   +++v++r +T r+
  gi|298674944|ref|YP_003726694.1| 219 IIPIELSVQYI-DYQGL-PAFIVVTRNLTKRK 248
                                       *******9988.66666.88888889888886 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.8e-05     0.023       2     113 .]       8     122 ..       7     122 .. 0.91
   2 !   36.8   0.0   2.5e-12   3.3e-09       2      96 ..     138     229 ..     137     243 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.8e-05
                                       HHHHHHHHSSSEEEEEE.TTSBEEEECHHHHHHHSSTH.HHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCC CS
                               PAS   2 dlraileslpdpifvvD.edgrilyvNaaaeellGlsr.eevlgkslldliheedda.elaelleqlleqgeesrag 75 
                                       dl++i++++p  +f++   d + +++ +   +++G+++ +  +g   +++i++++d  +++++++++ eqg ++   
  gi|298674944|ref|YP_003726694.1|   8 DLESIIHNSPIIVFLWKaVDNWPVEFVSDSITQFGYTPdDFTSGCYSYGDIIHPEDLeKVRSRISRHVEQGYKQFVH 84 
                                       6899*************999999999999999******77788888888888887777******************* PP

                                       CEEEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  76 eisfklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       e ++ ++ g ++++  r+  + +  g+++++ g++ di
  gi|298674944|ref|YP_003726694.1|  85 EYRIYTKTGDIRWVTERTFIRNNSMGKVTHYQGIIIDI 122
                                       **99999999999999999999999**********998 PP

  == domain 2  score: 36.8 bits;  conditional E-value: 2.5e-12
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       ++r++++++ d+if+ D dg++++vN++a+  l++sr+e+l  +++ +ih+ d   + +  e ++++++  +++e++
  gi|298674944|ref|YP_003726694.1| 138 KFRTLFNNTNDAIFICDMDGNFIEVNQSACNYLNYSRDELLQMKIN-DIHPSDT--TIDSGEMNELVKKGYSIFETT 211
                                       6899******************************************.8888887..999999999999999999999 PP

                                       EECTTSSEEEEEEEEEEE CS
                               PAS  79 fklrdgrpihlevraspv 96 
                                          rdg +i++e+ +  +
  gi|298674944|ref|YP_003726694.1| 212 HVNRDGAIIPIELSVQYI 229
                                       9999********998765 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.84   1.1e+03       3      18 ..       9      27 ..       9      69 .. 0.68
   2 !   35.7   0.0   4.7e-12     6e-09       2      48 ..     138     184 ..     137     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.84
                             PAS_8  3 lralfesspdgiav...vd 18
                                      l++++++sp  +++   vd
  gi|298674944|ref|YP_003726694.1|  9 LESIIHNSPIIVFLwkaVD 27
                                      6789999999999844433 PP

  == domain 2  score: 35.7 bits;  conditional E-value: 4.7e-12
                             PAS_8   2 rlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellgql 48 
                                       ++r+lf++ +d+i+++d +g+ +++vNq+a+  l ys ++l+ +++ ++
  gi|298674944|ref|YP_003726694.1| 138 KFRTLFNNTNDAIFICDmDGN-FIEVNQSACNYLNYSrDELLQMKI-ND 184
                                       89***************5655.***************888888777.43 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.1   3.1e-11     4e-08       2     107 ..     354     446 ..     353     447 .] 0.82

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 3.1e-11
                                       HHHHHHHHHHHHHHHHHHHHS.TTTEEEEEEEEEE...TEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSS CS
                         HATPase_c   2 dekrLrqiisnlvdNavkfat.kageieveikase...ddlvisveDnGiGipkedlkklfekfsqddstkrggggt 74 
                                       +++ L  i+++l++N++k+a  +++++ v+ik s+    ++++ + DnG+Gip+++ +     f +          +
  gi|298674944|ref|YP_003726694.1| 354 KSIPLGIIVNELLSNSLKHAFsENESGVVNIKFSQgydTNYELLINDNGKGIPEDM-D-----FKE---------PE 415
                                       5678889************66555566666666456678**************954.4.....788.........88 PP

                                       SHHHHHHHHHHHHTTTEEEEEEETTTEEEEEEE CS
                         HATPase_c  75 GlGlsivkklvelmgGeiwvesepgrGttftft 107
                                        lGl +v+ lve+++G i+++++   Gt+f+++
  gi|298674944|ref|YP_003726694.1| 416 SLGLELVNTLVEQVDGMIELDKSC--GTEFRIK 446
                                       9*******************6666..9999986 PP

>> HWE_HK  HWE histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.5   8.9e-10   1.1e-06       1      52 [.     257     310 ..     257     342 .. 0.75

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 8.9e-10
                                       HHHHHHHHHHHHHHHHHHHHSSSXS-HHHHHHHH...HHHHHHHHHHHHHHHHCT CS
                            HWE_HK   1 ElnHRvKNlLavvqsiarqtlrsaesleefaekl...sgRLqALsaahdllsree 52 
                                       E++HRvKN L v++s+ +  +++ e +++++e++   ++R+++++ ah+ l +++
  gi|298674944|ref|YP_003726694.1| 257 EIHHRVKNNLQVISSLLNLEASNFE-SDDVVEAFknsQNRVRSMALAHEKLYQSK 310
                                       89***************99977544.4444555522278*********9988765 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.7e-06    0.0022      31     113 ..     357     430 ..     330     447 .] 0.81

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.7e-06
                       HATPase_c_2  31 eirlaveEactNavehayleapegpvevrlesdeea.ltvevaDsGpgfdpetlpdpteeepkeslkegGrGlalik 106
                                        + + v+E+++N  +ha  e+++g v+++++++ ++  ++ + D+G+g +             + ++++ +Gl l++
  gi|298674944|ref|YP_003726694.1| 357 PLGIIVNELLSNSLKHAFSENESGVVNIKFSQGYDTnYELLINDNGKGIPEDM----------DFKEPESLGLELVN 423
                                       57899************************99988777***********55542..........44456678888888 PP

                       HATPase_c_2 107 glvDeve 113
                                       +lv++v+
  gi|298674944|ref|YP_003726694.1| 424 TLVEQVD 430
                                       8888884 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0037       4.7      39      92 ..      54     107 ..      35     128 .. 0.75
   2 !    8.6   0.0    0.0015       1.9       4      45 ..     149     187 ..     146     203 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0037
                            PAS_11  39 siydLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvkvktksklfkn 92 
                                       s+ d++hp+dl++++s  +  +++  ++    yR+ ++++++ +v  ++ + +n
  gi|298674944|ref|YP_003726694.1|  54 SYGDIIHPEDLEKVRSRISRHVEQGYKQFVHEYRIYTKTGDIRWVTERTFIRNN 107
                                       3559*************999995666777888*******999888666655555 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0015
                            PAS_11   4 fttrldidgkIisvDtsaLrasfslglekeelvgrsiydLch 45 
                                        +++ d+dg++i+v++   +a   l+++++el+++ i d++ 
  gi|298674944|ref|YP_003726694.1| 149 AIFICDMDGNFIEVNQ---SACNYLNYSRDELLQMKINDIHP 187
                                       56889***********...9999***********99999753 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   8.4e-06     0.011       7      52 ..     362     413 ..     358     424 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 8.4e-06
                       HATPase_c_3   7 laelvdNsld.Adaen....vkievnknrgktgeivieDdGkGmsee.elkn 52 
                                       + el+ Nsl  A +en    v+i++++    + e+ i D+GkG++e+ ++k+
  gi|298674944|ref|YP_003726694.1| 362 VNELLSNSLKhAFSENesgvVNIKFSQGYDTNYELLINDNGKGIPEDmDFKE 413
                                       779******97777779999******999999*************9988876 PP

>> Stomoxyn  Insect antimicrobial peptide, stomoxyn
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00019      0.24       7      31 ..     197     220 ..     195     221 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                                       HHHHHHHHHHHHHHHHTHHHHTTTT CS
                          Stomoxyn   7 FNklvKKvKHTiSETAHVAKDaAVi 31 
                                        N lvKK    i ET HV +D A+i
  gi|298674944|ref|YP_003726694.1| 197 MNELVKK-GYSIFETTHVNRDGAII 220
                                       5999999.689************99 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1       0.2   2.6e+02      63     114 ..      71     129 ..      34     130 .. 0.59
   2 ?    8.9   0.1    0.0012       1.6       1      44 [.     143     185 ..     143     215 .. 0.85
   3 ?   -1.5   0.0       2.2   2.8e+03      44      68 ..     239     263 ..     227     300 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.2
                             PAS_7  63 verrlaaaragkphsfererpdgrvievrgnpl...pdgGfVttyt....DiTerrrae 114
                                       + r +++  ++  h +   +++g +  v++++       G Vt y+    DiTer+++e
  gi|298674944|ref|YP_003726694.1|  71 ISRHVEQGYKQFVHEYRIYTKTGDIRWVTERTFirnNSMGKVTHYQgiiiDITERKETE 129
                                       33333333344455566666677776666666655566788888876666999999988 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0012
                             PAS_7   1 lenmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleel 44 
                                       ++n +++i + D d++ + +N+  ++ l+++++ +  +++++++
  gi|298674944|ref|YP_003726694.1| 143 FNNTNDAIFICDMDGNFIEVNQSACNYLNYSRDEL-LQMKINDI 185
                                       58999**************************9887.67777776 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.2
                             PAS_7  44 llrynaergefgagdveaeverrla 68 
                                       ++  n ++ ++++ ++e+e+++r++
  gi|298674944|ref|YP_003726694.1| 239 VVTRNLTKRKHAEVTREKEIHHRVK 263
                                       4444444444444556666666654 PP

>> VanY  D-alanyl-D-alanine carboxypeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1    0.0002      0.25      24     107 ..      71     151 ..      65     162 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0002
                                       --EEEEE----HHHHHHHH..HHHHHHHHHHHHHHHS--TTT-GGGGTSEEEEEEGGGTT.--SCGGGHCHHHHHHH CS
                              VanY  24 ielalvsgfRsverQeelf.ekksvkeeklkeilrvsalpGaSeHhtGlaiDisdkeaeetkleesfeetkafkwlq 99 
                                       i+ ++ +g+ ++ +  +++ ++   ++ ++++  r +   G+  H  G+ iDi++++++e+ l+es   +k f+ l 
  gi|298674944|ref|YP_003726694.1|  71 ISRHVEQGYKQFVHEYRIYtKTGDIRWVTERTFIRNN-SMGKVTHYQGIIIDITERKETEKALQES---EKKFRTLF 143
                                       66788899***********555556666666666655.5699**************9999766554...55566666 PP

                                       HHGGGGTE CS
                              VanY 100 knaakygF 107
                                       +n ++  F
  gi|298674944|ref|YP_003726694.1| 144 NNTNDAIF 151
                                       66665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 2820.43
//
Query:       gi|298674945|ref|YP_003726695.1|  [L=129]
Description: response regulator receiver protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-23   82.2   0.2    3.3e-23   82.0   0.2    1.0  1  Response_reg  Response regulator receiver domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.0   0.2   1.8e-27   3.3e-23       1     111 [.       6     116 ..       6     117 .. 0.97

  Alignments for each domain:
  == domain 1  score: 82.0 bits;  conditional E-value: 1.8e-27
                                       EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSS.SEHHHHHHHHHHCTTTSEEEE CS
                      Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpg.mdGlellkeireedpelpvii 76 
                                       +++v+D+  v+  +++ l++ gy++ ++a++g++a++++k++++dl+l+Di + g +dG+e+++ i+++  ++pv+ 
  gi|298674945|ref|YP_003726695.1|   6 IMVVEDENSVALDIKNRLKKLGYTVAGTASTGENAIKKAKKDHPDLVLVDIVLKGeIDGIEVARYIHNNL-DIPVVY 81 
                                       89*********************7777****************************99*********9977.9***** PP

                                       EESSTSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                      Response_reg  77 ltahseeedavealkagaddflsKpfdpeeLlkal 111
                                       lta++++e +++a   + ++++ Kpf+ ++L++ +
  gi|298674945|ref|YP_003726695.1|  82 LTAYADDELIERAKHTEPYGYILKPFQDKDLRSNI 116
                                       *******************************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 931.02
//
Query:       gi|298674946|ref|YP_003726696.1|  [L=424]
Description: enolase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   1.3e-114  382.5   0.2   1.7e-114  382.1   0.2    1.1  1  Enolase_C  Enolase, C-terminal TIM barrel domain
    8.9e-57  190.9   0.1    1.5e-56  190.2   0.1    1.4  1  Enolase_N  Enolase, N-terminal domain
    1.4e-07   31.3   0.0    2.2e-07   30.7   0.0    1.2  1  MR_MLE_C   Enolase C-terminal domain-like
  ------ inclusion threshold ------
      0.025   13.7   0.0      0.065   12.4   0.0    1.6  2  MAAL_C     Methylaspartate ammonia-lyase C-terminus


Domain annotation for each model (and alignments):
>> Enolase_C  Enolase, C-terminal TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  382.1   0.2  3.8e-118  1.7e-114       3     287 ..     147     421 ..     145     423 .. 0.97

  Alignments for each domain:
  == domain 1  score: 382.1 bits;  conditional E-value: 3.8e-118
                                       EE-EE-EEEEE-GGGSSSS--SSEEEEE-TT-SSHHHHHHHHHHHHHHHHHHHHHCC.GGGG-B-TTS-B----SSH CS
                         Enolase_C   3 vlPvPalnvinGGshagnklalqefmilPvgassfkealrlGaevyhklksvlkkkygksatnvGdeGGfaPnlqsn 79 
                                        lPvP++nv+nGG+hagnkla+qefmi+P +a sf+e++++G+e+yh l ++l+ kyg  atnvGdeGG+aP ++ +
  gi|298674946|ref|YP_003726696.1| 147 NLPVPTMNVLNGGEHAGNKLAIQEFMIQPKEAGSFTESMQMGVETYHALGKILESKYGPAATNVGDEGGYAPPIDVT 223
                                       69*************************************************************************** PP

                                       HHHHHHHHHHHHHCT-TC.TBEEEEE--GGGCEETCTTEEECTTTTTT..GGCEEEHHHHHHHHHHHHHHS-EEEEE CS
                         Enolase_C  80 kealdliveaiekaGykg.kvkialdvassefykekdkkydldfkeeesdkskkltseqladlykelvkkyPivsie 155
                                       ++ald +v+a+e+aGy++ +++i+ld+a+sef+  + + y +d+k         + s++l+d+y el + yPi+sie
  gi|298674946|ref|YP_003726696.1| 224 SDALDCLVNAVEEAGYSEtDITIGLDAAASEFF--DGNSYSIDGKV--------MDSSELMDYYLELLDTYPILSIE 290
                                       ****************988**************..6689*999987........88999****************** PP

                                       S-S-TT-HHHHHHHHHHHTTTSEEEESTTTTT-HHHHHHHHHCT--SEEEE-HHHH-SHHHHHHHHHHHHHTT-EEE CS
                         Enolase_C 156 dpldeddweawkklteelgdkvqivGddltvtnpkrlkeaiekkaanalllkvnqiGsltesleavklakeagygvv 232
                                       dp+ e+ +e +++lt e   +  ivGddl+vtn++rl+++ie +aan lllkvnqiG+++es++a+ +a+++gy v+
  gi|298674946|ref|YP_003726696.1| 291 DPFHEEAFEDFAELTREAW-NTIIVGDDLFVTNVNRLSRGIEMDAANGLLLKVNQIGTISESFDAASMANRNGYNVI 366
                                       ****************999.5669***************************************************** PP

                                       EE--SC--S--HHHHHHHHCT-SEEE---S-SHHHHHHHHHHHHHHHHHGCC-EE CS
                         Enolase_C 233 vshrsGetedttiadlavglsaGqiktGaparserlakynqllrieeelgekaky 287
                                       vshrsGeted++i+d++v+l a  iktGaparser +kynqllriee+lg+ +++
  gi|298674946|ref|YP_003726696.1| 367 VSHRSGETEDSIISDISVALGADMIKTGAPARSERTSKYNQLLRIEENLGDVSRF 421
                                       ***************************************************9987 PP

>> Enolase_N  Enolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.2   0.1   3.3e-60   1.5e-56       1     131 []      12     140 ..      12     140 .. 0.98

  Alignments for each domain:
  == domain 1  score: 190.2 bits;  conditional E-value: 3.3e-60
                                       EEEEEEEEEE-TTS-EEEEEEEEETTC-EEEEE--B-BSSSSSS-B----SSTTSGGGT--HHHHHHHHHTHHHHHT CS
                         Enolase_N   1 IkkvkareildSrGnpTvevevttedgalgraavpsGaStgekealelrDgdkkrylgkgvekavenvnekiapali 77 
                                       I++++arei+dSrGnpTvev+v t +g +gr++vpsGaStg++ealelrD+ ++ry gkgv  av+nvn++i+++l+
  gi|298674946|ref|YP_003726696.1|  12 IENIHAREIIDSRGNPTVEVDVFTGNG-FGRSSVPSGASTGTNEALELRDK-DERYRGKGVISAVDNVNNTIKNELL 86 
                                       89**********************877.8*********************9.79*********************** PP

                                       TSBTT-HHHHHHHHHHHH-STT-TTT-HHHHHHHHHHHHHHHHHHHTS-HHHHH CS
                         Enolase_N  78 gldvtdqeeiDkllielDgtenksklGaNailavSlAvakaaAkakelplyryl 131
                                       g+dv+ q++iD lli+lDgt+nk +lGaNail+vS+A+akaaA+++++ply +l
  gi|298674946|ref|YP_003726696.1|  87 GMDVRYQRQIDGLLIDLDGTDNKMNLGANAILGVSMAIAKAAADSLNIPLYTHL 140
                                       ***************************************************997 PP

>> MR_MLE_C  Enolase C-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   4.9e-11   2.2e-07      34     156 ..     231     369 ..     210     405 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 4.9e-11
                                       HHHHHHHHTTTSTSEEEEE-TTT.S.............BHHHHHHHHHHHGG.GTESEEESSSSTTTHHHHHHHHHH CS
                          MR_MLE_C  34 vravreavgpgddvdlmvDanqa.w.............dlatAirvarelee.ldllwlEEPvppeddleglaelra 95 
                                       v+av ea   ++d+++ +Da ++ +             d ++ + +  el + + +l +E+P++ e   e+ ael++
  gi|298674946|ref|YP_003726696.1| 231 VNAVEEAGYSETDITIGLDAAASeFfdgnsysidgkvmDSSELMDYYLELLDtYPILSIEDPFHEE-AFEDFAELTR 306
                                       6677777666777777777777752455555666666677777777667756699*********95.6********8 PP

                                       HH.SSEEEESTTSSS.HHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEEBS CS
                          MR_MLE_C  96 ra.sipiaagEslys.radfrelleagavdivqpdvsrvgGitearkvaalaeafgvpvapHs 156
                                       +a ++ i+++    + + ++ + +e +a+  + ++v+++g i+e+ + a +a  +g++v++ +
  gi|298674946|ref|YP_003726696.1| 307 EAwNTIIVGDDLFVTnVNRLSRGIEMDAANGLLLKVNQIGTISESFDAASMANRNGYNVIVSH 369
                                       6677767776665444**************************************999988765 PP

>> MAAL_C  Methylaspartate ammonia-lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.59   2.7e+03     190     217 ..      98     125 ..      90     135 .. 0.73
   2 ?   12.4   0.0   1.4e-05     0.065     127     216 ..     302     388 ..     255     395 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.59
                            MAAL_C 190 gvgaylGGscnetdvsarvsvhvalatr 217
                                       g+ + l G+ n  + +a+++  v++a+ 
  gi|298674946|ref|YP_003726696.1|  98 GLLIDLDGTDNKMNLGANAILGVSMAIA 125
                                       5666678999999999999887777654 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 1.4e-05
                            MAAL_C 127 aelreklkekgikvelvaDe.WcntledirefvdaeaadlvqiktPDlGginntieavlyckekgvgaylGGscnet 202
                                       a    +l++++ +  +v D+ +  +++ + + ++ +aa+ + +k+  +G+i+++ +a  +++++g ++ +   + et
  gi|298674946|ref|YP_003726696.1| 302 A----ELTREAWNTIIVGDDlFVTNVNRLSRGIEMDAANGLLLKVNQIGTISESFDAASMANRNGYNVIVSHRSGET 374
                                       3....456677788888877356778889999********************************************* PP

                            MAAL_C 203 dvsarvsvhvalat 216
                                       + s    + val +
  gi|298674946|ref|YP_003726696.1| 375 EDSIISDISVALGA 388
                                       *9966656665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 2463.88
//
Query:       gi|298674947|ref|YP_003726697.1|  [L=168]
Description: PfpI family intracellular protease [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-56  190.8   0.0    1.6e-56  190.6   0.0    1.0  1  DJ-1_PfpI      DJ-1/PfpI family
      1e-05   25.3   0.0       0.01   15.5   0.0    2.2  2  ThiJ_like      ThiJ/PfpI family-like
    0.00068   19.5   0.0     0.0009   19.1   0.0    1.4  1  GATase         Glutamine amidotransferase class-I
  ------ inclusion threshold ------
      0.016   14.8   0.0      0.017   14.7   0.0    1.3  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
        0.1   12.3   0.0        0.3   10.8   0.0    1.8  2  Peptidase_C26  Peptidase C26
       0.12   11.4   0.0       0.13   11.3   0.0    1.3  1  GATase_5       CobB/CobQ-like glutamine amidotransferase doma


Domain annotation for each model (and alignments):
>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.6   0.0   5.4e-60   1.6e-56       1     164 [.       1     163 [.       1     164 [. 0.99

  Alignments for each domain:
  == domain 1  score: 190.6 bits;  conditional E-value: 5.4e-60
                                       EEEEEEEETTBEHHHHHHHHHHHHHTTEEEEEEESSTSEEEETTSEEEE-SEEGGGCTCCG-SEEEE--BHHHHHHH CS
                         DJ-1_PfpI   1 kkvlvlladgvedvElivpvdvlkragikvdvvsvdkeevkgsrGlkvtvdaslddvkaaeyDalvlpGGragperl 77 
                                       +kvl+l+a+g+ed El +p+ +lk++gi+v+++s +k++++g +G+++ vd+++d+++++ +D+l lpGG+a p+++
  gi|298674947|ref|YP_003726697.1|   1 MKVLILTAEGFEDRELLYPYTRLKEEGIEVKIASNNKGTINGIHGYSIDVDCAFDEINPEGFDVLFLPGGKA-PQKI 76 
                                       69**********************************************************************.**** PP

                                       HTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTTSEE--SGGGHHHHHHTTSEE-SSSEEEETTEEEESSGGG CS
                         DJ-1_PfpI  78 renekvvelvkefaekgklvaaICagpqlLaaagvlkgrrvTsypavkdklekagakyvdkrvvvdgnlvTsrgpga 154
                                       r+nekv+ ++k f +++k+vaaIC+gpq+L++a+vl+grr+Tsy +++++l  aga++vd++vv+dgnl+Tsrg ++
  gi|298674947|ref|YP_003726697.1|  77 RQNEKVLVITKYFIDNDKPVAAICHGPQILVSADVLNGRRATSYSSIRKELASAGAEVVDEEVVKDGNLLTSRGFQD 153
                                       ***************************************************************************** PP

                                       HHHHHHHHHH CS
                         DJ-1_PfpI 155 aiefalelle 164
                                       + +f++el++
  gi|298674947|ref|YP_003726697.1| 154 LHAFGRELMK 163
                                       *******997 PP

>> ThiJ_like  ThiJ/PfpI family-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0   0.00081       2.4       2      32 ..       7      37 ..       6      44 .. 0.88
   2 !   15.5   0.0   3.5e-06      0.01      84     143 ..      61     111 ..      46     123 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00081
                         ThiJ_like  2 adeGydvtevaipwkvlkdagfsveFvtekg 32
                                        eG++  e+  p+  lk++g++v+ ++++ 
  gi|298674947|ref|YP_003726697.1|  7 TAEGFEDRELLYPYTRLKEEGIEVKIASNNK 37
                                      679**********************998764 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 3.5e-06
                         ThiJ_like  84 eydlvllpGGsdkavrelleserlhsllveylklvkrekepskvlgaicqgvlalafakp 143
                                        +d+++lpGG+ +     + ++    ++++y+       +++k ++aic+g   l  a+ 
  gi|298674947|ref|YP_003726697.1|  61 GFDVLFLPGGKAPQK---IRQNEKVLVITKYF-----I-DNDKPVAAICHGPQILVSADV 111
                                       69********99854...55555566788888.....3.5799********999998875 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0     3e-07    0.0009      31      87 ..      52     109 ..      20     148 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3e-07
                                       SHHHHHHHTHHSTSEEEEEEESSCTT...TTTHHHHHHHHCTSTS-EEEETHHHHHHHHH CS
                            GATase  31 asaeeilellknpdgilvsgGpgspg...vegkieaikearenkiPiLGICLGmQllaie 87 
                                         ++ei  + +++d ++++gG    +    e+ + ++k++++n++P+  IC G Q+l+ +
  gi|298674947|ref|YP_003726697.1|  52 CAFDEI--NPEGFDVLFLPGGKAPQKirqNEKVLVITKYFIDNDKPVAAICHGPQILVSA 109
                                       333444..368999999999977777777888888999999****************976 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   5.7e-06     0.017      39      90 ..      60     108 ..      23     162 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.7e-06
                          GATase_3  39 edadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGe 90 
                                       e  d+++lpGgk      ++ +++++    k ++ +++pv +iC G q+L +
  gi|298674947|ref|YP_003726697.1|  60 EGFDVLFLPGGKAPQ---KIRQNEKVLVITKYFIDNDKPVAAICHGPQILVS 108
                                       669********9765...55666666777788999**************965 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       0.6   1.8e+03     155     179 ..      25      49 ..      20      64 .. 0.78
   2 ?   10.8   0.0    0.0001       0.3      95     120 ..      83     108 ..      55     126 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.6
                     Peptidase_C26 155 kgsllaellgseeievnslHhqaik 179
                                       ++++  +++++++  +n +H  +i+
  gi|298674947|ref|YP_003726697.1|  25 EEGIEVKIASNNKGTINGIHGYSID 49 
                                       5555567777888999999999987 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0001
                     Peptidase_C26  95 laLiraalergvPilgiCrGlqllnv 120
                                       l + +  +++++P+ +iC G q+l  
  gi|298674947|ref|YP_003726697.1|  83 LVITKYFIDNDKPVAAICHGPQILVS 108
                                       55667889***************965 PP

>> GATase_5  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   4.5e-05      0.13      68     115 ..      72     118 ..       2     133 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.5e-05
                          GATase_5  68 wakslllneklrealekflnredtlaLGiCnGfqlLvklglvpggeie 115
                                       + + ++ nek+    + f+++ d+ + +iC G q+Lv  ++++g +++
  gi|298674947|ref|YP_003726697.1|  72 APQKIRQNEKVLVITKYFIDN-DKPVAAICHGPQILVSADVLNGRRAT 118
                                       456788899999888888888.******************99985444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1086.14
//
Query:       gi|298674948|ref|YP_003726698.1|  [L=148]
Description: hypothetical protein Metev_1013 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-14   54.3   0.0    1.7e-14   54.1   0.0    1.1  1  DUF296    Plants and Prokaryotes Conserved (PCC) domain


Domain annotation for each model (and alignments):
>> DUF296  Plants and Prokaryotes Conserved (PCC) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   0.0   9.3e-19   1.7e-14       1     106 [.      10     125 ..      10     126 .. 0.89

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 9.3e-19
                                       TEEEEEE-TTSBHHHHHHHHHHHHT-SSEEEEEEEEEEEEEEEEECTTT...........EE-S-EEEEEEEEEEEE CS
                            DUF296   1 rphvlrlepGediveaieefarkrgiraacvlsaiGavsnvtrladgee...........kllgrfeilslsGtilp 66 
                                       r++ +r+++ e+++e++e++a  ++ir+a++   +Gav +++ l++g+            kl+++ ei+++ G+i+ 
  gi|298674948|ref|YP_003726698.1|  10 RVFTVRIDNKENLIEELENLATYEDIRSAVF-VLLGAVGEAN-LVTGPLekiippepvwsKLEKPSEIMGI-GNIFF 83 
                                       6899**************************9.**********.776666678888888887789*******.88888 PP

                                       TT....EEEEEEEEETTSEEEEEEEEEE.EEEEEEEEEEEEE-C CS
                            DUF296  67 dg....lHlhvslagedgqvvgGhlaegplvaattvevvvaefe 106
                                       ++    +Hlh s +++ + v  G+l+ g+++++ ++ev+++e++
  gi|298674948|ref|YP_003726698.1|  84 ENekpkIHLHTSTGNQ-EGVKVGCLR-GENETFMVIEVFIMELS 125
                                       334789*********6.78*******.99************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 922.98
//
Query:       gi|298674949|ref|YP_003726699.1|  [L=430]
Description: amino acid permease [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-43  149.2  58.9    2.6e-43  148.5  58.9    1.4  1  AA_permease_2   Amino acid permease
    4.1e-28   98.2  60.3    1.6e-27   96.3  60.4    1.8  1  AA_permease     Amino acid permease
    3.8e-09   35.8  25.2    3.8e-09   35.8  25.2    2.2  2  Spore_permease  Spore germination protein


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.5  58.9   4.3e-47   2.6e-43       1     396 [.      12     390 ..      12     427 .. 0.86

  Alignments for each domain:
  == domain 1  score: 148.5 bits;  conditional E-value: 4.3e-47
                     AA_permease_2   1 lsllsafalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkk 75 
                                       l+ll +++  +g ++g+gi+v    +a+ +g al++++++a +++s   +l y+Elss++p+ g +yvy+k+afg k
  gi|298674949|ref|YP_003726699.1|  12 LGLLELTVSGVGNILGAGIYVLIgkAAGLAGNALWMSFLFAGIAIS-FTGLSYMELSSMFPKAGAEYVYVKQAFGDK 87 
                                       6889999999***********98878888***************98.6889************************** PP

                     AA_permease_2  76 vaflsawfnwfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilki 152
                                       +afl++wf +++  +++++++  +++y+ +++g        +++ +ai+++++++li   g+k s +++ i++ + +
  gi|298674949|ref|YP_003726699.1|  88 MAFLVGWFVLVGETIAISTVALGFGGYFGTLFGT-------AVLPVAIILILVFTLILFTGVKLSVRFAIIMTATGV 157
                                       ******************************9973.......578899****************************** PP

                     AA_permease_2 153 llpliiliilglitv.dgggfsslstetdtffpngwpgvllgllivlwsfdGfesaanvseevkk..kdvpkaifig 226
                                        + l+++i++gl +  ++++ +           +  +g + + + v+++f Gfe ++  s+e k+  k++ ka++++
  gi|298674949|ref|YP_003726699.1| 158 -MGLLVVIVIGLPYMgSINYLD----------VTSLSGLFEASALVFFAFLGFEEIVRLSQETKNpeKTTTKALVLA 223
                                       .677888889998861223332..........334445566667799***************887779********* PP

                     AA_permease_2 227 llivlvlyllvniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvleala 303
                                       +++++ ly+l++++++ v ++ e+a++s    ++a ++  ++gk ++ ++++++ +s + a++  ++gssr+l+ +a
  gi|298674949|ref|YP_003726699.1| 224 IVVTVSLYILIALTAVSVYNWQELAKSSA---PLADVASVAFGKNAFELIIVIALFSTANAVLFMLLGSSRILYGMA 297
                                       *************************9887...68888888888988888888999********************** PP

                     AA_permease_2 304 rdgvlPrffakvn.kfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigalilrkkrphl 379
                                       ++g++P+ +a v+  + +p+ ai ++a+vs i  l f++    ++ +++++s+++++++++ + i+++ lr++   +
  gi|298674949|ref|YP_003726699.1| 298 EHGAIPNIIAWVHpSRRTPWIAISTIALVS-IS-LTFIG----DIATVANISNFMVFLIFITVNITLIRLRFCDSFK 368
                                       *************99***************.44.44543....79******************************** PP

                     AA_permease_2 380 krpgkilvaiig.....alfll 396
                                        rp +++++i       +l+++
  gi|298674949|ref|YP_003726699.1| 369 YRPFRVPLNIGNfpiipLLGTV 390
                                       **99988887664433322222 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.3  60.4   2.7e-31   1.6e-27       3     435 ..      18     405 ..      16     422 .. 0.83

  Alignments for each domain:
  == domain 1  score: 96.3 bits;  conditional E-value: 2.7e-31
                       AA_permease   3 lvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviG 79 
                                       +v  +g++ G+g++v +g++++ aG  +++ ++l+ag+ i +++ls  e+++++pk+g+ y+y+++  g++++f +G
  gi|298674949|ref|YP_003726699.1|  18 TVSGVGNILGAGIYVLIGKAAGLAGN-ALWMSFLFAGIAISFTGLSYMELSSMFPKAGAEYVYVKQAFGDKMAFLVG 93 
                                       67789********************9.99************************************************ PP

                       AA_permease  80 lnylfswitvlaleltaasiliqfwelvtdlpkawvt..gavflvvlliinlvgvkvygeaefilalikiiaiiafi 154
                                       +       + ++  ++++   ++f +++  l+ + v   ++++++v+++i + gvk++ ++ +i++   ++ ++ +i
  gi|298674949|ref|YP_003726699.1|  94 WF------VLVGETIAISTVALGFGGYFGTLFGTAVLpvAIILILVFTLILFTGVKLSVRFAIIMTATGVMGLLVVI 164
                                       **......7777777777777888888888887777788999**************************999999999 PP

                       AA_permease 155 ivgiillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeks 231
                                       ++g  ++ + +  +                    +        +++ + + + v+faf G+e ++ +++E+k+Pek+
  gi|298674949|ref|YP_003726699.1| 165 VIGLPYMGSINYLDV------------------TS--------LSGLFEASALVFFAFLGFEEIVRLSQETKNPEKT 215
                                       999433333333333..................24........67899999************************** PP

                       AA_permease 232 iPkailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssanssl 308
                                         ka   +++ ++ +Y+l++l+++++ +++ l   +     a++  ++ +  g +++  +i+++++ ++ ++++ +l
  gi|298674949|ref|YP_003726699.1| 216 TTKALVLAIVVTVSLYILIALTAVSVYNWQELAKSS-----APLADVASVAFGKNAFELIIVIALF-STANAVLFML 286
                                       ******************************955555.....3577777777788888877777766.5567888899 PP

                       AA_permease 309 ysasRvlyslakdglaP.kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwllii 384
                                         +sR+ly +a+ g++P  ++ ++  r+ P+ ai   +++s  + ++  +++          +is ++ +++++ ++
  gi|298674949|ref|YP_003726699.1| 287 LGSSRILYGMAEHGAIPnIIAWVHPSRRTPWIAISTIALVSISLTFIGDIATV--------ANISNFMVFLIFITVN 355
                                       99***************76777788999***9998888888877777777776........9*************** PP

                       AA_permease 385 lsylrfR..kalkyqgrsieelgfkaallplgvilvlaaliiillilalyayl 435
                                       ++++r+R   ++ky+     +++  +  +p ++ l+ ++ +i++l l+l+ ++
  gi|298674949|ref|YP_003726699.1| 356 ITLIRLRfcDSFKYRPF---RVPLNIGNFPIIPLLGTVSTMILFLHLNLTVII 405
                                       ****7773366777666...447777777777777777777777777776554 PP

>> Spore_permease  Spore germination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8  25.2   6.4e-13   3.8e-09      14     270 ..      24     275 ..      15     296 .. 0.82
   2 ?   -0.1  12.4     0.056   3.4e+02     110     202 ..     313     409 ..     300     420 .. 0.79

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 6.4e-13
                    Spore_permease  14 fqlGvgiltlprsvaeqatpdgWisvllagiiililvllmlkllkkfpektl.iellkkilgkwLGsllsilfilyF 89 
                                        +lG+gi +l + +a  a+   W+s l+agi+i +  l +++l++ fp+    + ++k+ +g ++++l + + ++  
  gi|298674949|ref|YP_003726699.1|  24 NILGAGIYVLIGKAAGLAGNALWMSFLFAGIAISFTGLSYMELSSMFPKAGAeYVYVKQAFGDKMAFLVGWFVLVGE 100
                                       689***************9899**************************97654899**************8888887 PP

                    Spore_permease  90 lllaafelRefseliqvflledtplwiiilllllvilYlvvkGieslar.eflfiivilliilllillfslklaeik 165
                                        + +++++  f+  + +     t +  + ++l+lv+ ++++ G++  +r  +++ ++ ++  l++i++    +  i+
  gi|298674949|ref|YP_003726699.1| 101 TIAISTVALGFGGYFGTLF--GTAVLPVAIILILVFTLILFTGVKLSVRfAIIMTATGVMGLLVVIVIGLPYMGSIN 175
                                       7777777888888877654..45555566677788899999****99996777777777777778888888888888 PP

                    Spore_permease 166 nlrPvlgngikpvlkslkttslsflgveillllvpflkdk.kkvkkaallgvlistllyllttlivilvlsveqlkk 241
                                       +l+    ++++ +++++  + ++flg+e ++ l +  k++ k++ ka++l+++++++ly+l+ l +++v+  ++l k
  gi|298674949|ref|YP_003726699.1| 176 YLD---VTSLSGLFEASALVFFAFLGFEEIVRLSQETKNPeKTTTKALVLAIVVTVSLYILIALTAVSVYNWQELAK 249
                                       887...578889999************977777777776616678******************************** PP

                    Spore_permease 242 atwptlsllkvievpefierlevllivvw 270
                                       +  p+ +++ v   +   + +e+++++++
  gi|298674949|ref|YP_003726699.1| 250 SSAPLADVASVAFGK---NAFELIIVIAL 275
                                       *99988877665555...66666665554 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.056
                    Spore_permease 110 edtplwiiilllllvilYlvvkGieslar..eflfiivilliilllillfslklaeiknlrPvlgngikpvlks..l 182
                                        +tp ++i  + l+ i ++ ++ i ++a   +f+++++++++ + li l + ++++ +  r  l+ g  p++    +
  gi|298674949|ref|YP_003726699.1| 313 RRTPWIAISTIALVSISLTFIGDIATVANisNFMVFLIFITVNITLIRLRFCDSFKYRPFRVPLNIGNFPIIPLlgT 389
                                       47999999999999999999999*****7666666666666666666667777777777776789999999887557 PP

                    Spore_permease 183 kttslsflgveillllvpfl 202
                                         t++ fl   + ++++ fl
  gi|298674949|ref|YP_003726699.1| 390 VSTMILFLHLNLTVIIYGFL 409
                                       77888899999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1019  (0.0568353); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.73u 0.36s 00:00:01.08 Elapsed: 00:00:00.50
# Mc/sec: 2563.71
//
Query:       gi|298674950|ref|YP_003726700.1|  [L=368]
Description: Tubulin/FtsZ GTPase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.2e-34  118.2   0.1    1.6e-33  116.6   0.0    1.8  2  Tubulin    Tubulin/FtsZ family, GTPase domain
    0.00076   18.8   0.0     0.0029   16.9   0.0    2.0  1  Tubulin_2  Tubulin like
  ------ inclusion threshold ------
       0.12   13.1   3.0          1   10.0   0.3    2.7  2  PglD_N     PglD N-terminal domain


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.6   0.0   2.6e-37   1.6e-33       2     195 ..       4     182 ..       3     184 .. 0.92
   2 ?   -2.2   0.0      0.67     4e+03      40      40 ..     266     266 ..     223     305 .. 0.48

  Alignments for each domain:
  == domain 1  score: 116.6 bits;  conditional E-value: 2.6e-37
                                       EEEEEEHHHHHHHHHHHHH...HHHCH....HHHT.....TTEEEEE....EEES...BHHHHHTS-GS......EE CS
                           Tubulin   2 iivigvGqcGnqignelwellakehgiqsdgdslesfFsesgkveyiprsvaidt...dpqvlneikagselfnpnk 75 
                                       +++ig GqcGn++++++ +    e +   +++++ +f+s+++ ++ +  ++ai+t   d ++l+ +ka+      ++
  gi|298674950|ref|YP_003726700.1|   4 VLIIGNGQCGNRVLDAINK----E-AF-GKKSKFAKFYSKQKYKSNV-ETIAINTainDLKELEFTKAK------DR 67 
                                       899****************....4.33.34689*******9999999.999****55566666666666......** PP

                                       EE--CCCCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEE CS
                           Tubulin  76 lllgkegagnngaggypevgkeaaeeileeirkevekcdslqgffitaslgGGTGSGlgpvilevlkeeypkalvvt 152
                                       +++     + +g+g++++vgk++ ee++e+i ++ve+   ++  f+++s +GGTGS+++p++++ lke+y + +v++
  gi|298674950|ref|YP_003726700.1|  68 IHI----PHLHGVGANRNVGKQVFEENKEHITRKVEDRGPFDVAFVITSSSGGTGSSFTPLLVKELKERY-DFPVYS 139
                                       ***....889***********************************************************9.99**** PP

                                       EEEE--GG.G-HHHHHHHHHHHHHHHHT.-SEEEEEEHHHHHCC CS
                           Tubulin 153 vvvlPsefsevvvepynailalkeliee.sdavividNdaLlki 195
                                        vvlP+++ e++++ +n++++lke++e+  d +i+ dN+ L+++
  gi|298674950|ref|YP_003726700.1| 140 LVVLPFRE-EGTLYLQNTAFSLKEIRESgTDGIILADNQFLKDL 182
                                       ******99.*******************9**********99875 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.67
                                       . CS
                           Tubulin  40 s 40 
                                       +
  gi|298674950|ref|YP_003726700.1| 266 E 266
                                       1 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   4.8e-07    0.0029      74     226 ..      36     165 ..      17     226 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.8e-07
                         Tubulin_2  74 ssaevdrilrnllreetasaypsieeWlppeleelrkapeseGAGqiRtvGRlalfanleeirealrdaikrlrgsa 150
                                       s++++++ +++ + ++     ++++e    +++ +  +p  +G G +R vG+ ++ +n e i ++++d+        
  gi|298674950|ref|YP_003726700.1|  36 SKQKYKSNVETIAINTA---INDLKELEFTKAKDRIHIPHLHGVGANRNVGKQVFEENKEHITRKVEDRGP------ 103
                                       44444444444433322...234555544577777778888*********************999999754...... PP

                         Tubulin_2 151 geeeglnv.fVvgSLaGGTGSGiflDvayllrkilkeekqkvkiiglvllPdvfplnkeggervkaNayaaLkELna 226
                                             +v fV++S +GGTGS+     + ll k+lke    + ++ lv+lP       e+g+ + +N++ +LkE+  
  gi|298674950|ref|YP_003726700.1| 104 -----FDVaFVITSSSGGTGSSF----TPLLVKELKERYD-FPVYSLVVLPFR-----EEGTLYLQNTAFSLKEIRE 165
                                       .....33339***********85....4466666666665.578999999985.....5688999999999999987 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.3   0.00017         1       1      54 [.       3      59 ..       3      89 .. 0.65
   2 ?    2.7   0.2     0.032   1.9e+02      46      75 ..     319     348 ..     284     350 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00017
                            PglD_N  1 kivIiGaGGhgkvvadiiean...geyeiigflDdn.kktevegypvlgkaiellksl 54
                                      +++IiG G  g  v+d i+++   ++ + + f+ ++ +k++ve + +    i +lk+l
  gi|298674950|ref|YP_003726700.1|  3 NVLIIGNGQCGNRVLDAINKEafgKKSKFAKFYSKQkYKSNVETIAINTA-INDLKEL 59
                                      799***************88755335666667777525777887554443.3333333 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.032
                            PglD_N  46 kaiellkslseeeyevvi.AIGnnkvRkkia 75 
                                       +++e+++++ e+ y+v i AIG+ + +k+ +
  gi|298674950|ref|YP_003726700.1| 319 STMESASEI-ENLYNVAIdAIGQEREKKNRI 348
                                       357778888.778999999***998887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2196.11
//
Query:       gi|298674951|ref|YP_003726701.1|  [L=414]
Description: hypothetical protein Metev_1016 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-09   36.9   0.0     0.0023   18.2   0.0    2.6  2  DUF11         Domain of unknown function DUF11
    1.1e-08   34.3   2.6    2.4e-07   29.9   2.2    2.2  2  BatD          Oxygen tolerance
    3.1e-08   33.2   4.1    7.1e-05   22.3   0.9    2.4  2  TRAP_beta     Translocon-associated protein beta (TRAPB)
    9.3e-07   29.1   6.6     0.0097   16.1   1.1    2.6  2  CARDB         CARDB
    5.4e-05   23.4   0.1     0.0055   16.9   0.0    2.9  3  NPCBM_assoc   NPCBM-associated, NEW3 domain of alpha-galactos
     0.0039   17.5   1.4      0.011   16.1   0.8    2.1  2  A2M_BRD       Alpha-2-macroglobulin bait region domain
  ------ inclusion threshold ------
      0.044   13.6   0.0       0.26   11.1   0.0    2.0  2  DUF974        Protein of unknown function (DUF974)
       0.45   10.8  15.3        7.4    6.9   1.4    3.6  3  Calycin_like  Calycin-like beta-barrel domain
       0.45   10.6   4.4       0.55   10.3   0.3    3.1  3  BsuPI         Intracellular proteinase inhibitor
        3.7    7.7   8.4        5.1    7.2   0.3    3.7  3  DUF3244       Domain of unknown function (DUF3244)


Domain annotation for each model (and alignments):
>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   5.2e-06    0.0093       1      40 [.     143     215 ..     143     266 .. 0.64
   2 !   18.2   0.0   1.3e-06    0.0023      10      84 ..     271     347 ..     255     357 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.2e-06
                             DUF11   1 ltKtvdksevrpGdtvtytltvtNtgpasangvvvtDtl.................................P 40 
                                       +tKtvd+ +v+ Gd+++  + ++Ntg ++a +v  +  +                                 P
  gi|298674951|ref|YP_003726701.1| 143 ITKTVDNDTVKVGDNIRIRVEAQNTGDDKAIDVEFSNSMqenfvleetiieksgpmsidegetetvyiyelsP 215
                                       79****************************9998877776666666666666666666666555555555552 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 1.3e-06
                             DUF11  10 vrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsv..gsLeagesatlsftvrvtrtaas 84 
                                       +  G+tvt t+  +Ntg asa+ v++    P g++y  +     +++ + +v  ++L + +++ +sf+v+++  ++ 
  gi|298674951|ref|YP_003726701.1| 271 LPRGETVTSTINIKNTGKASAEAVQIDIDIPDGMEYLGGDDEIEIIDGAPTVymENLGQEQEKEISFKVKANEIGTY 347
                                       5569*********************9988*********999944443333334689999999999999999887664 PP

>> BatD  Oxygen tolerance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   2.2   1.3e-10   2.4e-07      11     155 ..     142     286 ..     135     306 .. 0.82
   2 ?    2.5   0.0     0.029        52     373     450 ..     333     410 ..     327     413 .. 0.49

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 1.3e-10
                              BatD  11 eftasvdknevevgetfrLtftvngas..gepdfsap.slekdfevlsg..sqssstqiinGkssssssktwtytLa 82 
                                       ++t +vd+++v+vg+++r++++++++   ++ d++++ s++++f + ++  ++s  ++i  G++++     + y L 
  gi|298674951|ref|YP_003726701.1| 142 NITKTVDNDTVKVGDNIRIRVEAQNTGddKAIDVEFSnSMQENFVLEETiiEKSGPMSIDEGETET--V--YIYELS 214
                                       68889*******************998766677777646777888888899889999999888877..5..****** PP

                              BatD  83 pkkeGtltIpaatievdgk......tyksnpitikVlkseasqsssaisdedlflraevskksvYvqeqvlvtlkly 153
                                       p k+G++ +++ t++++++      + +sn  ti+V       +++++++ +l + +e+++ ++  +e v+ t+ + 
  gi|298674951|ref|YP_003726701.1| 215 PAKSGEFDLKPTTATFSNEadqdfpKASSNTPTITV-------EQAEKNKAELNINTEADSFTLPRGETVTSTINIK 284
                                       **************99665233344579********.......566777788*******************999987 PP

                              BatD 154 tr 155
                                         
  gi|298674951|ref|YP_003726701.1| 285 NT 286
                                       66 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.029
                              BatD 373 peitikVekga..aaasspasstsaspaqkeev..kllgkdirfikgeaslkkkgs..ff...lfwlllllplllfv 440
                                       +ei +kV++++  +  + +++ + ++ a++e++  ++++kdir         k+g+  f+    +++++l +l+++ 
  gi|298674951|ref|YP_003726701.1| 333 KEISFKVKANEigT-YNLATQLSYNNGADDEKItsESTTKDIRV--------KEGKfdFLlnqPIYVYVLPILVIIG 400
                                       56777786666531.22222222233333333300334444443........2233345567788888888888885 PP

                              BatD 441 vllllwrkrr 450
                                       v  +++ k r
  gi|298674951|ref|YP_003726701.1| 401 VGGWVYYKHR 410
                                       5444444443 PP

>> TRAP_beta  Translocon-associated protein beta (TRAPB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.9     4e-08   7.1e-05      17     126 ..     138     246 ..     126     266 .. 0.76
   2 !   12.4   0.3   4.2e-05     0.076      13     121 ..     253     366 ..     246     406 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 4e-08
                         TRAP_beta  17 sarvlvkKkilnrllvegedltveytiyNvGssaAldVslvDdsfpeeaFevvsgslsakw.erlapge.nvshsfv 91 
                                       ++++ + K++ n+ ++ g ++ ++++  N G+ +A+dV+++     +e+F + +   +++   +++ ge +  ++++
  gi|298674951|ref|YP_003726701.1| 138 TPIINITKTVDNDTVKVGDNIRIRVEAQNTGDDKAIDVEFSNS--MQENFVLEETIIEKSGpMSIDEGEtETVYIYE 212
                                       5678899*********************************965..47778776664444431467766515679*** PP

                         TRAP_beta  92 vepkksgsfngtaavvtYresekgaelqlalssep 126
                                       + p ksg f  ++++ t+ +  + + + +a s +p
  gi|298674951|ref|YP_003726701.1| 213 LSPAKSGEFDLKPTTATFSNEAD-QDFPKASSNTP 246
                                       ******************66666.55555555333 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 4.2e-05
                         TRAP_beta  13 qedasarvlvkKkilnrllvegedltveytiyNvGssaAldVslv.D..dsf....peeaFevvsgslsakwerlap 82 
                                       +e+++a++ ++ ++ +  l+ ge +t +++i N G+++A  V++  D  d++      ++ e++ g+ ++ +e l  
  gi|298674951|ref|YP_003726701.1| 253 AEKNKAELNINTEADSFTLPRGETVTSTINIKNTGKASAEAVQIDiDipDGMeylgGDDEIEIIDGAPTVYMENLGQ 329
                                       456677777777888888999***************999877763234455422456899***************** PP

                         TRAP_beta  83 genvshsfvvepkksgsfngtaavvtYresekgaelqla 121
                                       +++ + sf v++   g +n  a+ ++Y +  +  e+ ++
  gi|298674951|ref|YP_003726701.1| 330 EQEKEISFKVKANEIGTYNL-ATQLSYNNGAD-DEKITS 366
                                       *****************997.67899966555.332222 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.4   9.8e-06     0.018       6      81 ..     143     224 ..     138     233 .. 0.89
   2 !   16.1   1.1   5.4e-06    0.0097       4      88 ..     260     357 ..     257     371 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9.8e-06
                                       E.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE.EEEEE.....SEE-CTEEEEEEEEEE-S-S-C CS
                             CARDB   6 vtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv.gtvtv.....psLaagesttvsftwtteateg 76 
                                       +t+t+  +++ vg++++i+v+ +N+G++++ +++ +  + ++ v +++++      s++ ge++tv +    +a++g
  gi|298674951|ref|YP_003726701.1| 143 ITKTVDNDTVKVGDNIRIRVEAQNTGDDKAIDVEFSNSMQENFVlEETIIeksgpMSIDEGETETVYIYELSPAKSG 219
                                       68899999************************************6666669*99999*********99988888999 PP

                                       EEEEE CS
                             CARDB  77 evtlt 81 
                                       e +l+
  gi|298674951|ref|YP_003726701.1| 220 EFDLK 224
                                       88876 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 5.4e-06
                                       EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE.....EEEEE.........SEE-CTEEEEEE CS
                             CARDB   4 LtvtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv.....gtvtv.........psLaagesttvs 66 
                                       L +++++   ++  ge++t t+++kN+G+a+++a+++++ + +        +++++         ++L  ++++++s
  gi|298674951|ref|YP_003726701.1| 260 LNINTEADSFTLPRGETVTSTINIKNTGKASAEAVQIDIDIPDGMEylggdDEIEIidgaptvymENLGQEQEKEIS 336
                                       666666666667789************************99665555895544555888888899************ PP

                                       EEEE-S-S-CEEEEEEEESTT- CS
                             CARDB  67 ftwtteategevtltvvvDpdn 88 
                                       f+++++ + g++ l  +   +n
  gi|298674951|ref|YP_003726701.1| 337 FKVKAN-EIGTYNLATQLSYNN 357
                                       *****9.999999877766655 PP

>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.07   1.3e+02       3      29 ..     154     180 ..     152     184 .. 0.87
   2 !   16.9   0.0   3.1e-06    0.0055       3      33 ..     273     303 ..     271     306 .. 0.96
   3 ?   -2.7   0.0       4.2   7.5e+03      48      61 ..     328     341 ..     319     355 .. 0.50

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.07
                       NPCBM_assoc   3 pGetvtltltvtndgtaaatnvslsls 29 
                                        G+  ++++++ n+g++ a +v++s s
  gi|298674951|ref|YP_003726701.1| 154 VGDNIRIRVEAQNTGDDKAIDVEFSNS 180
                                       5888999***************99865 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 3.1e-06
                       NPCBM_assoc   3 pGetvtltltvtndgtaaatnvslslslPeG 33 
                                       +Getvt t+ ++n+g+a+a++v+++++ P+G
  gi|298674951|ref|YP_003726701.1| 273 RGETVTSTINIKNTGKASAEAVQIDIDIPDG 303
                                       7****************************98 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 4.2
                       NPCBM_assoc  48 apGetveatvkVtp 61 
                                          ++ e  +kV++
  gi|298674951|ref|YP_003726701.1| 328 GQEQEKEISFKVKA 341
                                       33444444444443 PP

>> A2M_BRD  Alpha-2-macroglobulin bait region domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       2.8     5e+03      86      93 ..      80      87 ..      53     114 .. 0.60
   2 !   16.1   0.8     6e-06     0.011       4     121 ..     146     282 ..     141     297 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.8
                                      EEEE---- CS
                                      xxxxxxxx RF
                           A2M_BRD 86 dsvqlpve 93
                                      ds  +++e
  gi|298674951|ref|YP_003726701.1| 80 DSFSFDFE 87
                                      44444444 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 6e-06
                                       EESSSS--TTSEEEEEEE-SS-............EE-TT-....BSS-----.-S...S........-EEEEEE--T CS
                                       xxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxx RF
                           A2M_BRD   4 spdkeeykvGetakltvkstfa............tverdstlylvlsrgnivssgekve....eidsstsfsfpvta 64 
                                       + d++++kvG++++++v+++              + ++++    vl+   i +sg   +    e  ++t++ +++++
  gi|298674951|ref|YP_003726701.1| 146 TVDNDTVKVGDNIRIRVEAQNTgddkaidvefsnSMQENF----VLEETIIEKSG---PmsidEGETETVYIYELSP 215
                                       56899*************9886666655544443333333....55555553344...2566666677789999999 PP

                                       T-----EE..EEEE..E-......-CEEEEEEE----.-GGGB-EEEEE.E.E...-SS.SEEEEEEE CS
                                       xxxxxxxx..xxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxx.x.xxxxxxx.xxxxxxxx RF
                           A2M_BRD  65 dmaPnarv..vvyyirrd......gevvadsvqlpvekdfenklsvsle.s.ynetrPg.eevtlkvk 121
                                       + + ++ +   +++   +      ++  +++ ++ ve+ ++nk ++ ++ + +++t+P+ e+vt +++
  gi|298674951|ref|YP_003726701.1| 216 AKSGEFDLkpTTATF-SNeadqdfPKASSNTPTITVEQAEKNKAELNINtEaDSFTLPRgETVTSTIN 282
                                       999999999544444.3347899**************************94599*****567766654 PP

>> DUF974  Protein of unknown function (DUF974)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.43   7.6e+02     132     166 ..     168     202 ..     141     225 .. 0.74
   2 ?   11.1   0.0   0.00014      0.26      13      92 ..     274     365 ..     269     391 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.43
                            DUF974 132 reevvLeaqleNvtedaivlekvklepeeglkaes 166
                                        ++ +++++  N ++++ vle++ +e + ++++++
  gi|298674951|ref|YP_003726701.1| 168 GDDKAIDVEFSNSMQENFVLEETIIEKSGPMSIDE 202
                                       56667788888888888888888888877777665 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00014
                            DUF974  13 GetFscylcvnnesaekevrdvrikaelqtpsqr......leLeeseeeekekelepgeslqkvvshelkelGnhvL 83 
                                       Get +++++++n+ + ++ + v+i +++    +       +e  + + +   ++l ++++ +   + + +e+G++ L
  gi|298674951|ref|YP_003726701.1| 274 GETVTSTINIKNTGK-ASAEAVQIDIDIPDGMEYlggddeIEIIDGAPTVYMENLGQEQEKEISFKVKANEIGTYNL 349
                                       9**************.999999988887666665666666666555555556666666655555555556******* PP

                            DUF974  84 avtVsYte.......a 92 
                                       a + sY++       +
  gi|298674951|ref|YP_003726701.1| 350 ATQLSYNNgaddekiT 365
                                       ******8766654332 PP

>> Calycin_like  Calycin-like beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   2.2    0.0054       9.7      24     123 ..      80     179 ..      59     180 .. 0.82
   2 ?    6.9   1.4    0.0041       7.4      20      64 ..     242     287 ..     227     300 .. 0.73
   3 ?    4.2   0.2     0.028        50      10      39 ..     321     350 ..     317     376 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0054
                                       -EEEEEE-SSS-EEEEEE-GG.G------EEEEEEEEE-SSSSSBEEEEEEEEE-TT--E...EEEEEEEEEETTEE CS
                      Calycin_like  24 akvtitknedgtvnlsLknfsfgelplGditvdnvkvtkeggsyttfsgsqkltlagggdaeeatvslsGtisgkkl 100
                                        + +   +++g+v+++L+   +g+l+  +i ++   ++k+  + + ++g  + +  +g+  +++t ++++++ +   
  gi|298674951|ref|YP_003726701.1|  80 DSFSFDFEDEGEVEVTLNSVFGGNLNRANISISLSDYDKDLHTKKVINGGHDEADFAGTPIINITKTVDNDTVKVGD 156
                                       5666677899********99999**********99999988666677777777777777777799999988888888 PP

                                       EEEEEEE..ETT-SS-EEEEEEE CS
                      Calycin_like 101 nltitikvkdgamtmpikvtFkG 123
                                       n+ i ++++++++   i+v F++
  gi|298674951|ref|YP_003726701.1| 157 NIRIRVEAQNTGDDKAIDVEFSN 179
                                       99999999999**********86 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0041
                                       -B-S-EEEEEE-SSS-EEEEEE-GG...G------EEEEEEEEE-SS CS
                      Calycin_like  20 sdadakvtitknedgtvnlsLknfs..fgelplGditvdnvkvtkeg 64 
                                       s+++ ++t++++e+++++l+++  +  f +lp G  + + +++++ g
  gi|298674951|ref|YP_003726701.1| 242 SSNTPTITVEQAEKNKAELNINTEAdsF-TLPRGETVTSTINIKNTG 287
                                       4444799999999999999999988866.666666666666666555 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.028
                                       EEEETTEE---B-S-EEEEEE-SSS-EEEE CS
                      Calycin_like  10 svsvggeespsdadakvtitknedgtvnls 39 
                                       +v++++  ++++++ + ++++ne gt+nl+
  gi|298674951|ref|YP_003726701.1| 321 TVYMENLGQEQEKEISFKVKANEIGTYNLA 350
                                       79999999999999**************97 PP

>> BsuPI  Intracellular proteinase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.3   0.00031      0.55       3      43 ..     147     188 ..     145     221 .. 0.85
   2 ?   -0.5   0.1      0.71   1.3e+03       9      28 ..     272     291 ..     263     297 .. 0.79
   3 ?   -1.5   0.0       1.4   2.6e+03      71      96 ..     330     354 ..     321     382 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00031
                                       EEEEEEE-SS-EEEEEEEEE-SS.S-EEEEESSS--EEEEEE CS
                             BsuPI   3 laleaeasgeavelaltvtNesd.eavtlqFssgqkydlvvk 43 
                                       ++ ++ + g++++++++ +N++d +a++++Fs++++ ++v++
  gi|298674951|ref|YP_003726701.1| 147 VDNDTVKVGDNIRIRVEAQNTGDdKAIDVEFSNSMQENFVLE 188
                                       6778889999***********862679*************96 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.71
                                       E-SS-EEEEEEEEE-SSS-E CS
                             BsuPI   9 asgeavelaltvtNesdeav 28 
                                        +ge+v  ++ ++N+++ + 
  gi|298674951|ref|YP_003726701.1| 272 PRGETVTSTINIKNTGKASA 291
                                       56789999999999998775 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.4
                                       T-EEEEEEEE.S---SEEEEEEEEE- CS
                             BsuPI  71 gesatyeetwdedlepGeYtleaelv 96 
                                       ++++  + ++ +  e G+Y+l  +l 
  gi|298674951|ref|YP_003726701.1| 330 EQEKEISFKV-KANEIGTYNLATQLS 354
                                       4444444444.455566666655543 PP

>> DUF3244  Domain of unknown function (DUF3244)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   1.1      0.11   1.9e+02      38      88 ..     166     214 ..     136     223 .. 0.67
   2 ?    0.4   0.1      0.38   6.8e+02      46      57 ..     247     258 ..     234     308 .. 0.55
   3 ?    7.2   0.3    0.0029       5.1      27      86 ..     289     350 ..     275     357 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.11
                                       ESS--SEEEEEEEETTT--EEEEEEE-GGGTTEEEEE-TTS-SEEEEEEEE CS
                           DUF3244  38 fesplsdvtitikdeetgevvyestivnasgstisidlsgeesgeYklelt 88 
                                       ++ +++ +++  +++ +++ v e+ti+++ +  +sid +ge +  Y+ el+
  gi|298674951|ref|YP_003726701.1| 166 NTGDDKAIDVEFSNSMQENFVLEETIIEK-SGPMSID-EGETETVYIYELS 214
                                       34455667777778888888888888866.4666666.6666666776666 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.38
                                       EEEEEETTT--E CS
                           DUF3244  46 titikdeetgev 57 
                                       tit+ ++e++++
  gi|298674951|ref|YP_003726701.1| 247 TITVEQAEKNKA 258
                                       666666654443 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0029
                                       EEEETTEEEEEESS--SEE....EEEEEETTT--EEEEEEE-GGGTTEEEEE-TTS-SEEEEEE CS
                           DUF3244  27 asiegnilsiefesplsdv....titikdeetgevvyestivnasgstisidlsgeesgeYkle 86 
                                       as+e+ ++ i++ + ++ +    +i i d     +vy ++  ++++++is++++  e g+Y+l 
  gi|298674951|ref|YP_003726701.1| 289 ASAEAVQIDIDIPDGMEYLggddEIEIIDG--APTVYMENLGQEQEKEISFKVKANEIGTYNLA 350
                                       677777888888888888888778999999..56777777788899***************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       908  (0.0506442); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.64u 0.35s 00:00:00.99 Elapsed: 00:00:00.51
# Mc/sec: 2461.11
//
Query:       gi|298674952|ref|YP_003726702.1|  [L=277]
Description: nicotinate-nucleotide pyrophosphorylase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-56  191.2   1.9    1.4e-56  190.9   1.9    1.1  1  QRPTase_C       Quinolinate phosphoribosyl transferase, C-ter
    8.5e-19   67.4   0.0    1.7e-18   66.4   0.0    1.5  1  QRPTase_N       Quinolinate phosphoribosyl transferase, N-ter
     0.0048   16.3   0.1      0.011   15.1   0.1    1.6  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
     0.0059   15.9   0.3     0.0097   15.3   0.3    1.4  1  TMP-TENI        Thiamine monophosphate synthase
  ------ inclusion threshold ------
      0.099   13.0   0.3       0.15   12.5   0.3    1.4  1  Radical_SAM     Radical SAM superfamily


Domain annotation for each model (and alignments):
>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.9   1.9   3.9e-60   1.4e-56       1     169 []     101     272 ..     101     272 .. 0.98

  Alignments for each domain:
  == domain 1  score: 190.9 bits;  conditional E-value: 3.9e-60
                                       HHHHHHHHHHHHHCT..SSEEEE-S---TTTHHHHHHHHHHTTSB--TSSTTTSEEE-HHHHHHHSSHHHHHHHHHH CS
                         QRPTase_C   1 iAtltarmveaaksa..kvrildTRkttPglrllekyAvliGGgdnhrlgLsdmvlikdnhiaaagsiveavksvre 75 
                                       iAt+t+++v+ ++    k+ i++TRkttPg+r++ek+Av +GGgd hr++Lsd+v+ikdnhi+++g  ++av+ + e
  gi|298674952|ref|YP_003726702.1| 101 IATQTRKCVDTVRCYsdKTDIACTRKTTPGIRKFEKMAVIAGGGDPHRYNLSDTVMIKDNHIKIMG-FENAVDIAVE 176
                                       9***********98888*************************************************.********** PP

                                       HHTTTSEEEEEESSHHHHHHHHHHT-SEEEEES--HHHHHHHHHHHHHHSTT..SEEEEESS--TTTHHHHHCTT-S CS
                         QRPTase_C  76 avdkevkievevesleeleevleaeadiimLDnfsveelkkaveelkeknkr..vlievSGgvtlenveeyaksgvd 150
                                        ++++ kieveves++++ ++++ ++diimLDn+++ e+ +++e+lk+kn +  v+ie SGg++ en+e+yak+g d
  gi|298674952|ref|YP_003726702.1| 177 LASFTQKIEVEVESVNDAIKAAQKGVDIIMLDNMKPAEIIRTIEILKNKNLKnnVIIEISGGINPENLEDYAKTGAD 253
                                       **********************************************99988888*********************** PP

                                       EEEECHHCHTB----EEEE CS
                         QRPTase_C 151 visvgalthsvkalDislk 169
                                       +is+++l+h ++++Dis++
  gi|298674952|ref|YP_003726702.1| 254 IISMSSLIHMSRWIDISME 272
                                       *****************95 PP

>> QRPTase_N  Quinolinate phosphoribosyl transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.4   0.0   4.8e-22   1.7e-18       1      89 []      14      99 ..      14      99 .. 0.96

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 4.8e-22
                                      CTT--HHHHHHGCTTSEEEEEEEESSSEEE-SHHHHHHHHHHHTTTEEEESS-TT-EEETTEEEEEEEEEHHHHHHHHH CS
                         QRPTase_N  1 igrgDlttealipeekkakaeiiakeegvvaGlevaeevfellpglevellvkDGervekgdvlleieGnarallsaER 79
                                      ig+ D+     + ++k  +a++++ +e+++aG++va+ +f+++ g+ + + + DG+++++ dv+++i G a +ll+aER
  gi|298674952|ref|YP_003726702.1| 14 IGYNDISC--KMVPDKPHEATVFTNQECTLAGIDVAKSFFDYF-GIDAATSFIDGDKAHPDDVIFTIFGGAVSLLRAER 89
                                      57889999..77889999*************************.*********************************** PP

                                      HHHHHHHHHH CS
                         QRPTase_N 80 vaLnllqrlS 89
                                      ++Ln+l ++S
  gi|298674952|ref|YP_003726702.1| 90 LVLNFLGHMS 99
                                      *********9 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   3.1e-06     0.011     157     197 ..     223     261 ..     206     262 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.1e-06
                                       HHHHHHHT---EEEEESS--TTTCHHHHHHT--EEEESHHH CS
                    Ribul_P_3_epim 157 rklidekeldlkievDGGvkldnieqiaeagadvlVagsav 197
                                       +++    + ++ ie+ GG++ +n e  a+ gad++ ++s +
  gi|298674952|ref|YP_003726702.1| 223 KNKNL--KNNVIIEISGGINPENLEDYAKTGADIISMSSLI 261
                                       33333..37899***********************999866 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.3   2.7e-06    0.0097      97     181 .]     182     261 ..     157     261 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.7e-06
                          TMP-TENI  97 liiGlSvhsleeaeeaealgadYigvGpifpTdtKkdaeplgleglkelaealeiPvvaiGGitlenvaevleagad 173
                                         i + v+s ++a +a+++g+d i++  +     K+ +  + +e lk+   + ++ +   GGi++en+++ +++gad
  gi|298674952|ref|YP_003726702.1| 182 QKIEVEVESVNDAIKAAQKGVDIIMLDNM-----KPAEIIRTIEILKNKNLKNNVIIEISGGINPENLEDYAKTGAD 253
                                       55666678888899999999999988776.....88888899999988888888888999***************** PP

                          TMP-TENI 174 gvavvsai 181
                                        +++ s i
  gi|298674952|ref|YP_003726702.1| 254 IISMSSLI 261
                                       ***99865 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3   4.1e-05      0.15      96     164 ..     173     248 ..      71     251 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.1e-05
                                       HHHHTT..-SEEEEEEBSSSHH.....HHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHH CS
                                       xxxxxx..xxxxxxxxxxxxxx.....xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  96 rllelg..vdrvslgleaadde.....kvlklmn.rghtfeevlealeklreagikrvvdrivglpGendeeleell 164
                                         +el   +  +++ +e+++d      k  ++++ ++  + e+++++e+l+++++k+  ++i +  G n e le+++
  gi|298674952|ref|YP_003726702.1| 173 IAVELAsfTQKIEVEVESVNDAikaaqKGVDIIMlDNMKPAEIIRTIEILKNKNLKN-NVIIEISGGINPENLEDYA 248
                                       3334444448899999999999998884444555588999****************5.5556566666888777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1730.91
//
Query:       gi|298674953|ref|YP_003726703.1|  [L=271]
Description: aspartate dehydrogenase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-36  123.8   0.9    5.9e-36  122.7   0.9    1.6  1  DUF108           Domain of unknown function DUF108
    2.9e-25   89.2   0.2    5.2e-25   88.4   0.2    1.4  1  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain
    2.8e-08   33.9   0.3    5.4e-08   33.0   0.3    1.4  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
      1e-06   29.5   0.0      2e-06   28.6   0.0    1.4  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
    9.1e-05   22.9   0.3    0.00032   21.1   0.3    1.8  2  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
     0.0005   20.6   0.1     0.0013   19.3   0.1    1.7  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
     0.0011   19.3   0.9     0.0034   17.6   0.9    1.8  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0016   18.5   0.2     0.0028   17.7   0.2    1.5  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
     0.0022   17.4   0.0     0.0037   16.6   0.0    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
      0.017   15.3   0.1      0.029   14.5   0.1    1.4  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
      0.087   13.1   0.6       0.19   12.0   0.1    1.9  2  TrkA_N           TrkA-N domain
       0.14   12.6   0.1       0.52   10.7   0.1    2.1  2  Gp_dh_N          Glyceraldehyde 3-phosphate dehydrogenase, NA


Domain annotation for each model (and alignments):
>> DUF108  Domain of unknown function DUF108
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.7   0.9   3.9e-39   5.9e-36       2      89 .]     170     257 ..     169     257 .. 0.98

  Alignments for each domain:
  == domain 1  score: 122.7 bits;  conditional E-value: 3.9e-39
                                       SS-EEEEEEEHHHHHHHSTTS-CHHHHHHHHHH.CCGEEEEEEEETT-SSEEEEEEEEETTEEEEEEEEE-EETTEE CS
                            DUF108   2 teptvlFeGsareaikkfPknvNvaaalaLaalgfdrvkvelvadpnldkniheieveGsfgefslevenkpspenP 78 
                                       +++tv+FeGsa+ea+k fP+nvNvaa+l+L ++gfd+++v+++adp ++knih+++v+G+fgef+++ven psp+nP
  gi|298674953|ref|YP_003726703.1| 170 KNETVVFEGSAAEAVKMFPANVNVAATLSLSGIGFDETSVKIIADPGAEKNIHNVTVKGNFGEFTTRVENLPSPTNP 246
                                       789************************************************************************** PP

                                       EEEHHHHHHHH CS
                            DUF108  79 ktsalaalsvi 89 
                                       kts+la ls+i
  gi|298674953|ref|YP_003726703.1| 247 KTSYLASLSAI 257
                                       *********86 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.4   0.2   3.5e-28   5.2e-25       1     117 []       8     121 ..       8     121 .. 0.98

  Alignments for each domain:
  == domain 1  score: 88.4 bits;  conditional E-value: 3.5e-28
                                       --SHHHHHHHHHHHH---SSEEEEEEEEESS.EEE-TTHHHHHT--CB---HHHHHHHHS-EEEEE-S--HHHHTTH CS
                     NAD_binding_3   1 GlGaiGsavleqlkrqqseielelvavadrd.sllskdrkallasealtldlddliahldpdvvVEcasseavaelv 76 
                                       G+GaiG++++++++++    e elvav+dr+   ls    +ll++e+++ +l+++++   +d+vVE as++a+ e+v
  gi|298674953|ref|YP_003726703.1|   8 GCGAIGTEICKAVDEGSI--ESELVAVYDRNkEHLSSLQSSLLNTEPVVYELQEMVK--HVDLVVESASQNAAYEIV 80 
                                       9**************996..8**********9999999*******************..****************** PP

                                       HHHHHTTEEEE-S--CGGG-HHHHHHHTSSSTTS--.EE-G CS
                     NAD_binding_3  77 lkaLkagkdvvtankgaladealyeeLreaaeangakiyve 117
                                       + aL++ +dv+++++ga++d++ +e+  + a+++g+kiy++
  gi|298674953|ref|YP_003726703.1|  81 TTALESSCDVMVMSVGAFVDKNFREKVTDIAKQKGCKIYLP 121
                                       ***************************************86 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.3   3.6e-11   5.4e-08       2     117 ..       3     115 ..       2     120 .. 0.82

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 3.6e-11
                                       EEEEETTTSHHHHHHHHHHHH.STTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH-SEEEE-S-H CS
                            DapB_N   2 kvavvGasGrmGkevvkavee.aedlelvaavdrkeselegkdagellglgklgvavtddleevlekadvliDFTtp 77 
                                       k+++vG+ G +G+e++kav+e + + elva++dr++++l+     +l ++  +  +v  +l+e+++++d +++  + 
  gi|298674953|ref|YP_003726703.1|   3 KLGIVGC-GAIGTEICKAVDEgSIESELVAVYDRNKEHLS-----SLQSSLLNTEPVVYELQEMVKHVDLVVESASQ 73 
                                       899****.************96789*********994333.....33333344568889****************** PP

                                       HHHHHHHHHHHHTT-EEEE--SS-..-HHHHHHHHHHTTTSE CS
                            DapB_N  78 eavlenlklalekgvklViGTTGl..seeelaeleelakkig 117
                                       +a++e + +ale+  ++ + + G   +++ +++++++ak+ g
  gi|298674953|ref|YP_003726703.1|  74 NAAYEIVTTALESSCDVMVMSVGAfvDKNFREKVTDIAKQKG 115
                                       *************99887777775567777888888887755 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   1.3e-09     2e-06       2      91 ..       3      92 ..       2      93 .. 0.91

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.3e-09
                                      EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHH.HHHTTHE.EESSHHHHHTCTTESEEEE-S-GGGHHHH CS
                      GFO_IDH_MocA  2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeav.aesfgve.aysdleelladpeidavivatpngtheel 78
                                      + +i+G+G ig++  +++ e + + e+va++d+++e    + +  ++ e ++ +l+e+++  ++d+v+     +  +e+
  gi|298674953|ref|YP_003726703.1|  3 KLGIVGCGAIGTEICKAVDEGSIESELVAVYDRNKEHLSSLqSSLLNTEpVVYELQEMVK--HVDLVVESASQNAAYEI 79
                                      78*******************9999***************94444455589999******..99***99999999**** PP

                                      HHHHHHTT-EEEE CS
                      GFO_IDH_MocA 79 akaaleagkhvll 91
                                      +  ale  ++v++
  gi|298674953|ref|YP_003726703.1| 80 VTTALESSCDVMV 92
                                      **********986 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.3   2.2e-07   0.00032       1      94 [.       3      91 ..       3     101 .. 0.88
   2 ?    2.3   0.0      0.15   2.2e+02      65      87 ..      86     108 ..      82     119 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.2e-07
                                      EEEEETTTSHHHHHHHHHHHC.TSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHHH CS
                    Semialdhyde_dh  1 kvaivGatGyvGqellrlLee.hpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpagv 78
                                      k +ivG  G++G+e+ + ++e + e elv+++ +++   + l+++ ++l +++ +++e   +e +k+vd+v+ ++++++
  gi|298674953|ref|YP_003726703.1|  3 KLGIVG-CGAIGTEICKAVDEgSIESELVAVYDRNK---EHLSSLQSSLLNTEPVVYEL--QEMVKHVDLVVESASQNA 75
                                      579***.9*************999999999999999...88888877777777777777..8889************** PP

                                      HHHHHHHHHHTTSEEE CS
                    Semialdhyde_dh 79 skelapklaeagvkvi 94
                                      + e++ +++e+ + v 
  gi|298674953|ref|YP_003726703.1| 76 AYEIVTTALESSCDVM 91
                                      ***********99765 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.15
                                       TT-SEEEE-SCHHHHHHHHHHHH CS
                    Semialdhyde_dh  65 kevdivflalpagvskelapkla 87 
                                       +++d+++++++a v k++ +k+ 
  gi|298674953|ref|YP_003726703.1|  86 SSCDVMVMSVGAFVDKNFREKVT 108
                                       68************999999883 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   8.4e-07    0.0013       1      94 [.       3      95 ..       3      98 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 8.4e-07
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.-EEECECHHHHHHH-SEEEE-S-HHHHHHHH CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.vkvtavdneeaaeeadvvvlavkpedveevl 78
                                      k+gi+G+G +g  + + ++ +g  ++e+v + +rn+e + +l+++l   +    + +e++++ d vv +   +++ e++
  gi|298674953|ref|YP_003726703.1|  3 KLGIVGCGAIGTEICK-AVDEGSIESELVAVYDRNKEHLSSLQSSLLnTEPVVYELQEMVKHVDLVVESASQNAAYEIV 80
                                      79*************9.778888777777788***********776547777789************988888887777 PP

                                      HHCGHHHHTTSEEEEE CS
                     F420_oxidored 79 selakdalkgklvisv 94
                                      + +  +++ + +v sv
  gi|298674953|ref|YP_003726703.1| 81 TTA-LESSCDVMVMSV 95
                                      666.355666666665 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.9   2.3e-06    0.0034       2     101 ..       5      95 ..       4     120 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.3e-06
                                       EEE--SHHHHHHHHHHHCTCCT-G.EEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-S CS
                   Sacchrp_dh_NADP   2 liiGaGsvGqavaellarhfdvda.eitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnls 77 
                                        i+G+G++G  + + + + + +++  ++v dr+ke+l  l +++         l+ e +   L++++k+ dlvv  +
  gi|298674953|ref|YP_003726703.1|   5 GIVGCGAIGTEICKAVDEGS-IESeLVAVYDRNKEHLSSLQSSL---------LNTEPVVYELQEMVKHVDLVVESA 71 
                                       69**********99888765.5555999********77775433.........333333333999************ PP

                                       SGGGHHHHHHHHHHHT-EEEESS- CS
                   Sacchrp_dh_NADP  78 ppissldvlkaCietgvhyvdtsi 101
                                        +  + +++ +++e  ++++  s+
  gi|298674953|ref|YP_003726703.1|  72 SQNAAYEIVTTALESSCDVMVMSV 95 
                                       ***************999988776 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.2   1.8e-06    0.0028      14      86 ..       3      74 ..       1     113 [. 0.81

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.8e-06
                                      EEEEES-SHHHHHHHHHHHCCT-CE..EEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSS CS
                      Shikimate_DH 14 kvlliGaGemaelvakhLlakgvkk..vvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisatase 86
                                      k  ++G G ++++++k+  + ++++  v+v  R+ e+ ++l ++l ++e     + el+e+++++d+v+ + + +
  gi|298674953|ref|YP_003726703.1|  3 KLGIVGCGAIGTEICKAVDEGSIESelVAVYDRNKEHLSSLQSSLLNTE---PVVYELQEMVKHVDLVVESASQN 74
                                      6679***************99765433999***************7774...44566777788999999887654 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   2.5e-06    0.0037      38     100 ..       3      72 ..       1      84 [. 0.73

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.5e-06
                                       EEEEES-SHHHHHHHHHHHHTT-E...EEEESSSHHHHH....CHHHHTCEECSHHHHHHH-SEEEE-S- CS
                      2-Hacid_dh_C  38 tvGiiGlGrIGqavakrlkafgmk...viaydrskkkee....eeeelgvelvsleellaesDivslhlp 100
                                       ++Gi+G+G+IG+++ k + +  ++   v +ydr+k++ +    +  +++  + +l+e++++ D v+  + 
  gi|298674953|ref|YP_003726703.1|   3 KLGIVGCGAIGTEICKAVDEGSIEselVAVYDRNKEHLSslqsSLLNTEPVVYELQEMVKHVDLVVESAS 72 
                                       79*****************66664233777888877555663333333334669*********9986655 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   1.9e-05     0.029       1      77 [.       3      85 ..       3     119 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.9e-05
                                      EEEEE--SHHHHHHHHHHHHTT-E...EEEE-SSHHHHHHHHHTT...EEE-SSHHHHHHHCSEEEE-SSSHHHHHHHH CS
                     NAD_binding_2  1 kigfiGlGvMGsnmalnllkagyk...vavynrtkekveelvaeg...akaaesieelvasldvvitmvkagkavdevi 73
                                      k+g++G G +G+++++ + +  ++   vavy+r+ke++ +l ++      ++++++e+v+++d+v+   ++++a + v+
  gi|298674953|ref|YP_003726703.1|  3 KLGIVGCGAIGTEICKAVDEGSIEselVAVYDRNKEHLSSLQSSLlntEPVVYELQEMVKHVDLVVESASQNAAYEIVT 81
                                      689***************765543334***********99999865545567888888888888877766666665555 PP

                                      HSHC CS
                     NAD_binding_2 74 egll 77
                                      + l 
  gi|298674953|ref|YP_003726703.1| 82 TALE 85
                                      5443 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00013      0.19       3      43 ..       6      49 ..       4      93 .. 0.86
   2 ?   -2.1   0.0       3.1   4.6e+03      54      69 ..     198     213 ..     160     226 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                                      EES-SHHHHHHHHHHHHTT...EEEEEEESSHHHHHHHHHTTSE CS
                            TrkA_N  3 iiGlGrvGrslaeeLsegg...kdvvvidkdeerveelreegle 43
                                      i+G+G +G+++++ + eg+   + v v d+++e++ +l+   l+
  gi|298674953|ref|YP_003726703.1|  6 IVGCGAIGTEICKAVDEGSiesELVAVYDRNKEHLSSLQSSLLN 49
                                      9****************98898779999******9999988755 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.1
                                       HHHHTTGGGESEEEE- CS
                            TrkA_N  54 vLeeagiekadaviaa 69 
                                        L  +g ++ ++ i+a
  gi|298674953|ref|YP_003726703.1| 198 SLSGIGFDETSVKIIA 213
                                       2333333333333333 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00035      0.52       2      57 ..       3      62 ..       2     101 .. 0.71
   2 ?   -2.5   0.0       4.5   6.8e+03      68      93 ..     189     214 ..     169     217 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00035
                                      EEEEESTSHHHHHHHHHHHHHT.TCEEEEEE-..TS-HHHH.HHHHHEETTTEC-SS-EE CS
                           Gp_dh_N  2 kvainGfGRIGrlvlralleek.elevvaind..ltdletl.ayllkyDsvhgrfkgeve 57
                                      k++i G G IG  +++a+ e + e e+va+ d    +l++l ++ll+ + v  ++++ v+
  gi|298674953|ref|YP_003726703.1|  3 KLGIVGCGAIGTEICKAVDEGSiESELVAVYDrnKEHLSSLqSSLLNTEPVVYELQEMVK 62
                                      89*****************8888*******994223444441345566666655555555 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.5
                                       EEEEEE--SSGGGS-CHHHTSSEEEE CS
                           Gp_dh_N  68 kkikvlaekdpeelpwkelgvdlVve 93 
                                        +++v a+ + + + ++e+ v+++ +
  gi|298674953|ref|YP_003726703.1| 189 ANVNVAATLSLSGIGFDETSVKIIAD 214
                                       45666777777778888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1633.56
//
Query:       gi|298674954|ref|YP_003726704.1|  [L=306]
Description: quinolinate synthetase complex subunit A [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   5.6e-124  413.2   4.9   6.3e-124  413.0   4.9    1.0  1  NadA          Quinolinate synthetase A protein
  ------ inclusion threshold ------
       0.06   13.6   0.2        1.2    9.3   0.0    2.3  2  NTP_transf_4  Sugar nucleotidyl transferase
       0.18   11.4   0.0        1.3    8.6   0.0    2.1  2  Sigma70_r4    Sigma-70, region 4


Domain annotation for each model (and alignments):
>> NadA  Quinolinate synthetase A protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  413.0   4.9  1.1e-127  6.3e-124       2     299 .]      10     301 ..       9     301 .. 0.98

  Alignments for each domain:
  == domain 1  score: 413.0 bits;  conditional E-value: 1.1e-127
                                       HHHHHHHHHTEEEEEETTS-HHHHHH-SEEE-HHHHHHHCCC-SSSEEEEES-HHHHHHHHHHSTTSEEE-SSTT-- CS
                              NadA   2 eikelkkeknavilaHnYqedeiqeiadfvGDSleLarkaaeteaevivfcGVhFMaetakiLspekkvllpdleag 78 
                                       +i++lk+eknavilaHnYq+deiq+iadfvGDSl L+r+a +++a++ivfcGV+FMae+a+iLspek+v++p+++ag
  gi|298674954|ref|YP_003726704.1|  10 NINKLKNEKNAVILAHNYQRDEIQDIADFVGDSLGLSREAVKQDADIIVFCGVDFMAESAAILSPEKTVIMPEIDAG 86 
                                       79*************************************************************************** PP

                                       -HHHCT--HHHHHHHHHHSTTS-EEEESSS-HHHHTT-SEEE-TTTHHHHHHHSS-SEEEEES-HHHHHHHHHHH.S CS
                              NadA  79 CsladmitaeeveelkeelpdaavvtYvNssaevKalsdivcTSsnavkvvealkekkilflPDqnLgryvakklge 155
                                       C++a m+t ++++e +ee+pdaavv+YvN+sa+vKa++di+cTS+nav+v+++l+e++i+f+PD+nL+++va+++ +
  gi|298674954|ref|YP_003726704.1|  87 CPMAAMVTPKSLREKREEYPDAAVVCYVNTSAAVKAECDICCTSANAVNVINSLDEDTIIFVPDKNLANFVASQT-D 162
                                       **************************************************************************9.6 PP

                                       EEEEESSSS-GCGGG--CHHHHHHHHCSTT-EEEE-TTS-HHHHHCSSEE--HHHHCCCCGTTSSSCEEEES-THHH CS
                              NadA 156 kkiilwkgaCsvHeefkaeeveelkeehpdakvlvHPEckeevveaadvvgSTsqiikavkeseakefiigTelglv 232
                                       k+ii w+g+C++H+++ a +v  +ke+hp+a++l+HPEc+++v+e ad + ST++++++v++s++kefiigTe+g++
  gi|298674954|ref|YP_003726704.1| 163 KTIIPWEGYCPTHHQILAGDVLLMKEQHPNAEFLAHPECRKDVLEIADKILSTTGMVNYVQQSDSKEFIIGTENGIL 239
                                       68*************************************************************************** PP

                                       HHHHHH-TTSEEE.....ECSSSSSTTGGG--HHHHHHHHHHT-S.B----HHHHHHHHHHHHHHHH CS
                              NadA 233 erlkkeapekefialsaeaaeeavCetMkkitleklleaLeeleeeeikvdeevaekAkkalermle 299
                                       +rl ke+p+k+f+++s    + a+C++Mk+itl+++ ++Le++e+ +i+v+e++++kAk+al++mle
  gi|298674954|ref|YP_003726704.1| 240 HRLDKENPDKTFYHAS----QYAICPNMKMITLDSVQKSLEKMEY-KIEVPEDIRKKAKRALDKMLE 301
                                       *************443....4689********************9.*******************96 PP

>> NTP_transf_4  Sugar nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.036   2.1e+02      77     109 ..     126     159 ..      87     166 .. 0.64
   2 ?    9.3   0.0    0.0002       1.2      35     149 ..     168     296 ..     163     303 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.036
                      NTP_transf_4  77 vlpdea.lveaikelkageallkgdellaarvte 109
                                       +++++a +v+ i++l++ + +++ d+ la +v +
  gi|298674954|ref|YP_003726704.1| 126 ICCTSAnAVNVINSLDEDTIIFVPDKNLANFVAS 159
                                       4444334999999999999999955555555544 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0002
                      NTP_transf_4  35 wekllgaatvsfltreyLaevyqekyPl.....nvleeeenllingrvlpdealveaikelkageallkgdellaar 106
                                       we ++ + + + l  + L  +++e++P      +++ ++++l i  ++l +  +v+ +++ + +e ++  ++ +  r
  gi|298674954|ref|YP_003726704.1| 168 WEGYCPT-HHQILAGDVL--LMKEQHPNaeflaHPECRKDVLEIADKILSTTGMVNYVQQSDSKEFIIGTENGILHR 241
                                       8999999.9999999999..99*****7799987777777************************************* PP

                      NTP_transf_4 107 vteaeaakleksllsd...................ekveleeeelkllrrpwDifskngeal 149
                                       +++++ +k     +s+                   ek+e++      ++ p Di +k ++al
  gi|298674954|ref|YP_003726704.1| 242 LDKENPDKTFYH-ASQyaicpnmkmitldsvqkslEKMEYK------IEVPEDIRKKAKRAL 296
                                       **9776665555.4446888888887776554444444444......666777766666666 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00021       1.3      26      39 ..      39      52 ..      33      53 .. 0.96
   2 ?   -0.4   0.0      0.14   8.3e+02      35      48 ..     286     299 ..     285     300 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00021
                                      HHHHHTS-HHHHHH CS
                        Sigma70_r4 26 IgerlgiSrerVrq 39
                                      +g+ lg+Sre+V+q
  gi|298674954|ref|YP_003726704.1| 39 VGDSLGLSREAVKQ 52
                                      79***********9 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHHH CS
                        Sigma70_r4  35 erVrqiekrAlrkL 48 
                                       e +r   krAl+k+
  gi|298674954|ref|YP_003726704.1| 286 EDIRKKAKRALDKM 299
                                       5699999*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       982  (0.0547716); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 1815.46
//
Query:       gi|298674955|ref|YP_003726705.1|  [L=281]
Description: prenyltransferase UbiA [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-38  133.1  20.2    2.5e-38  131.8  20.0    1.6  1  UbiA      UbiA prenyltransferase family


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.8  20.0   1.4e-42   2.5e-38      19     247 ..      34     269 ..      16     274 .. 0.83

  Alignments for each domain:
  == domain 1  score: 131.8 bits;  conditional E-value: 1.4e-42
                              UbiA  19 l.......llllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilgllllalll 88 
                                       +          l +++ ++++++a+na+NdyfD+eiDa   ++p RP++sG+i   +a+ f+i l+i+g++++ ++l
  gi|298674955|ref|YP_003726705.1|  34 AllgysfvYRTLSVFFVVFFVTGAGNAINDYFDYEIDAV--NKPSRPIPSGKIGLSKAFYFSITLFIIGVVIA-FTL 107
                                       3444444434556667789********************..********************************.*** PP

                              UbiA  89 npltallgllalllyvvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavflltwaialandl 165
                                       n+ t +++l++ l+++ Y +  lKr  + g++ +g   g  +l+g a+++ s   ++++l+++  l t++  +++d+
  gi|298674955|ref|YP_003726705.1| 108 NWITGIIALFNSLVLIYYAK-TLKRKAFSGNLSIGYLTGSTFLFGGAVYGISGLYALMILFILATLATTSREIVKDI 183
                                       *******************5.***************************9999999********************** PP

                              UbiA 166 rdregDrkagiktlpvvlGrkaarillalllavllla.llllllalllllylllalllaalallraarlvrrrdakk 241
                                       +d++gD+k   +tlp+ +G k++++++ ++ ++++++ +l + l ll+  yl++++l+ +++++    +v +++a+ 
  gi|298674955|ref|YP_003726705.1| 184 EDIKGDEKEKANTLPIHIGVKKSAYIASFIGFIAIVSsPLPYILSLLGINYLYIVALADIFFIVAITEIVFYKNASM 260
                                       *************************7555555555556666666666666666666666666666667777777777 PP

                              UbiA 242 aakff...l 247
                                        +k+f   +
  gi|298674955|ref|YP_003726705.1| 261 SSKLFkiaM 269
                                       777775542 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       999  (0.0557198); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 1699.06
//
Query:       gi|298674956|ref|YP_003726706.1|  [L=406]
Description: methionine adenosyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.9e-161  537.3   0.3   2.2e-161  537.1   0.3    1.0  1  AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synt
  ------ inclusion threshold ------
      0.059   13.7   0.2       0.24   11.7   0.2    2.1  2  SWIRM            SWIRM domain


Domain annotation for each model (and alignments):
>> AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synthetase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  537.1   0.3  2.4e-165  2.2e-161       2     396 .]       3     402 ..       2     402 .. 0.97

  Alignments for each domain:
  == domain 1  score: 537.1 bits;  conditional E-value: 2.4e-165
                                       -EEEEE-TTS-GTTSSEEEEEEE-TTSHHHHHHHHHHHHHHHHHHHHHHHHSS---EEEEEEEEE--EEEEETTEEE CS
                   AdoMet_Synthase   2 nivveelkkkpveeqevEivErKGiGHPDsiaDgiaeavsralskeylekfgailhhniDkvllvaGesepkfgGGe 78 
                                       niv+e+l+++p++eq++EivErKG+GHPD+i+D+++++vs++l+ eyl+k+g ilhhn+Dk++lv+G++e ++gGGe
  gi|298674956|ref|YP_003726706.1|   3 NIVIENLNTQPLQEQKLEIVERKGLGHPDYICDSLMDRVSVNLCSEYLKKLGYILHHNTDKGMLVSGKVEGELGGGE 79 
                                       9**************************************************************************** PP

                                       EEE-EEEEEEEEEEEEE.EEE--HHHHHHHHHHHHHHHH-SS--TTTSEEEEEEEEEEEEHHHHHHCH-SS...-BE CS
                   AdoMet_Synthase  79 viepieillsgratkevegekipveeialeaakeylkenlraldlekdvivdvklgkgsadLkdvferkkk.evpla 154
                                       +++p+ +++++rat e++g ++++e+i++++ake+++enlr++d++ +++++++l++gs++L+d+f+rkkk ev  a
  gi|298674956|ref|YP_003726706.1|  80 IVDPMLLVFGDRATFEADGIEFDIENIVTSTAKEWFSENLRFVDPS-QIQYQIELKSGSSELTDIFRRKKKnEVLGA 155
                                       *********************************************8.8********************99989**** PP

                                       SSSEEEEEEES--HHHHHHHHHHHHHTSHHHHHH-TTEEEEEEEEEEEETTEEEEEEEEEEEGGG--SHHHHHHHHH CS
                   AdoMet_Synthase 155 NDtSfgvgyaplseleklvleterllnskelkkklpevGeDiKvmglRekkkielTvavalvdrlvkdleeYlevke 231
                                       NDtS++vg+ap + +e +v ete++lns+++kk++pe+GeD+Kvmg+R++++i+lTva++l+d+++k+++eY+++k+
  gi|298674956|ref|YP_003726706.1| 156 NDTSAAVGFAPSTFTEWIVHETEKHLNSSTFKKEYPESGEDVKVMGVRNNNDIHLTVAMPLIDSYIKSEDEYFKRKN 232
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHSTTSE....EEEEE-TT-BGG..GTB--EESSSSGGGTT--EETTSS--TTSSB-TTS----S- CS
                   AdoMet_Synthase 232 eikeeveelakkltkere....vevevNtaDkke..eesvyltvtGtsaEegDdGsvGRGNRvnGlitpnrpmslEA 302
                                       ei +e++e+++k++++++    +++++Nt+D++    +++y tvtGtsaE++D+G+vGRGNRvnG+i++nrp s EA
  gi|298674956|ref|YP_003726706.1| 233 EIINEIDEFVSKYAETENnlpsTSISFNTLDEPGkgLNGIYTTVTGTSAEDADCGQVGRGNRVNGIIPLNRPSSAEA 309
                                       **********98877654222269*******98756899************************************** PP

                                       -TTS-TTT-HHHHHHHHHHHHHHHHHHH-TTEEEEEEEEEE-TTSBTTS-SEEEEEEEESSS---HHSHHHHHHHHH CS
                   AdoMet_Synthase 303 aaGKNPvsHvGKiYnvlaneiakeiveevegvkevyvrllsqiGkpidePlvasvqvilekgvsleevekeveeiid 379
                                       aaGKNPvsHvGKiYn+l+++ia +i++e+++v+e+yv+lls+iGkpid P++a+ q+ +e+g +l++v++ev+e+i+
  gi|298674956|ref|YP_003726706.1| 310 AAGKNPVSHVGKIYNALSHRIAYRIYNEIPDVSEAYVWLLSDIGKPIDAPRMATTQISMEAG-TLDSVKTEVHEVIN 385
                                       *********************************************************99988.8999********** PP

                                       HHHT-HHHHHHHHTTT- CS
                   AdoMet_Synthase 380 eelekieeiteeliegk 396
                                       +ele+i+++++el++gk
  gi|298674956|ref|YP_003726706.1| 386 SELENIQQFCMELAKGK 402
                                       *************9986 PP

>> SWIRM  SWIRM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       1.9   1.7e+04      78      87 ..      47      56 ..      39      56 .. 0.74
   2 ?   11.7   0.2   2.7e-05      0.24       6      53 ..     169     247 ..     166     262 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 1.9
                             SWIRM 78 hefLerwGlI 87
                                       e+L++ G+I
  gi|298674956|ref|YP_003726706.1| 47 SEYLKKLGYI 56
                                      4788888887 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 2.7e-05
                             SWIRM   6 FdpdslhpiEkellself..................ngk..............dktpeeYlkiRnkiialyrenpke 50 
                                       F    +h++Ek+l s+ f                  n +               k+++eY+k +n+ii++  e +++
  gi|298674956|ref|YP_003726706.1| 169 FTEWIVHETEKHLNSSTFkkeypesgedvkvmgvrnN-NdihltvamplidsyIKSEDEYFKRKNEIINEIDEFVSK 244
                                       666779************7777777777777777651.25667777777765459***************9998888 PP

                             SWIRM  51 ylt 53 
                                       y +
  gi|298674956|ref|YP_003726706.1| 245 YAE 247
                                       765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       737  (0.0411066); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 2450.26
//
Query:       gi|298674957|ref|YP_003726707.1|  [L=230]
Description: hypothetical protein Metev_1022 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-94  314.9   0.1    2.1e-94  314.7   0.1    1.0  1  PIN_5            PINc domain ribonuclease
     0.0045   17.1   0.0      0.016   15.3   0.0    1.9  2  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit
  ------ inclusion threshold ------
      0.082   12.7   0.1       0.13   12.1   0.1    1.2  1  Collectrin       Renal amino acid transporter


Domain annotation for each model (and alignments):
>> PIN_5  PINc domain ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  314.7   0.1   3.6e-98   2.1e-94       1     206 []       5     219 ..       5     219 .. 0.98

  Alignments for each domain:
  == domain 1  score: 314.7 bits;  conditional E-value: 3.6e-98
                             PIN_5   1 rfvlDTsaltdpevreklgeeeleeavkklldliaearlklgiscyip.psvykElkeflkreeveeeviakldtwl 76 
                                       rfvlDT+altd +vr++++ +el+++++++l+lia+arl+l+iscyip psvy+El+ef+k++++e+eviak+dtwl
  gi|298674957|ref|YP_003726707.1|   5 RFVLDTTALTDLQVRSQMEIDELCDGMQSILELIANARLQLDISCYIPfPSVYNELQEFAKNNNCEDEVIAKIDTWL 81 
                                       8**************************************************************************** PP

                             PIN_5  77 vkkspdryevkipaeilyeyveevrerinkGlrvaEeavreaaeeseklekee........eeeevgelikklRekY 145
                                       vkk+pdry+v+ip++i++eyv+++r+rinkG++vaE+a+ ++a+++++l++e+        e+e++g +i k+R+kY
  gi|298674957|ref|YP_003726707.1|  82 VKKTPDRYNVTIPSRIFHEYVTYMRDRINKGMNVAEDAILNTASQCMSLKEEDrdnfgeeiEREVIGGIIGKFRNKY 158
                                       ***********************************************99655467899999**************** PP

                             PIN_5 146 realRkGilDsaeDldvllLAkELdaavvssDeGikkwaeklGlrlveakkfpkvlkeylk 206
                                       r+alR+GilDsa+D+dvllLAkELdaavv+sD Gi+kwae+l +r+v+a++fp++l+eylk
  gi|298674957|ref|YP_003726707.1| 159 RSALRYGILDSAPDIDVLLLAKELDAAVVASDYGIQKWAEQLAVRYVPASTFPRMLQEYLK 219
                                       ***********************************************************96 PP

>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.7e-06     0.016      59     107 ..      58     104 ..      22     121 .. 0.80
   2 ?   -1.1   0.0      0.32   1.9e+03      18      49 ..     171     201 ..     163     221 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.7e-06
                   HicB_lk_antitox  59 ssieellanpeyaggiwalvdvdlskldgkaeriNitlpervlkriDaa 107
                                       ++++e+ +n+++++ +  ++++d+  ++++  r N+t+p+r+ ++  ++
  gi|298674957|ref|YP_003726707.1|  58 NELQEFAKNNNCEDEV--IAKIDTWLVKKTPDRYNVTIPSRIFHEYVTY 104
                                       5677778888888876..5789999*****************9986555 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.32
                   HicB_lk_antitox  18 PdlpGcfsagdtleeaianakeaielhlegli 49 
                                       Pd++ +   +++l+ a+  +   i+ + e+l+
  gi|298674957|ref|YP_003726707.1| 171 PDID-VLLLAKELDAAVVASDYGIQKWAEQLA 201
                                       6665.555678899999999999999988875 PP

>> Collectrin  Renal amino acid transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   2.1e-05      0.13      44     104 ..      58     118 ..      52     133 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.1e-05
                        Collectrin  44 nqtvefevenvlvlnetqrvSfwfvvtspknesklvpkeeveeairksrnrineaflLddk 104
                                       n+  ef  +n +  ++ +++ +w+v ++p+  + ++p +  +e +   r+rin+ +++ ++
  gi|298674957|ref|YP_003726707.1|  58 NELQEFAKNNNCEDEVIAKIDTWLVKKTPDRYNVTIPSRIFHEYVTYMRDRINKGMNVAED 118
                                       556677888888888999***********************************98877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1409.60
//
Query:       gi|298674958|ref|YP_003726708.1|  [L=221]
Description: cobalamin B12-binding domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.9e-24   85.0   0.7      6e-24   84.4   0.6    1.4  1  B12-binding    B12 binding domain
      1e-18   67.5   0.3    2.4e-18   66.3   0.0    1.8  2  B12-binding_2  B12 binding domain


Domain annotation for each model (and alignments):
>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.4   0.6   6.7e-28     6e-24       2     116 ..      94     203 ..      93     208 .. 0.88

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 6.7e-28
                       B12-binding   2 kvllatvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvellkri 78 
                                        ++++++ gd+h++G++++   l+ ag+ V++lg +v+ ed+++ +++ ++dv+glSa++t+++ ++k++v++++r+
  gi|298674958|ref|YP_003726708.1|  94 VAVVGVILGDIHDIGINLVSSLLKSAGITVYDLGKDVPYEDFIEIAKDVNADVIGLSAMMTTSMMGMKDVVKMARRE 170
                                       57999********************************************************************9999 PP

                       B12-binding  79 rprvkvvvGGahpsldpeetleaklgiddvvvgegeda 116
                                        p+vk+++GG +  +  +++ e  +g +d+   +++da
  gi|298674958|ref|YP_003726708.1| 171 IPDVKIMIGGGP--VSRDFCGE--IG-ADAYADDARDA 203
                                       9*********99..45555444..88.66455555555 PP

>> B12-binding_2  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   0.0   2.7e-22   2.4e-18       2      74 ..       8      80 ..       7      81 .. 0.97
   2 ?   -2.7   0.1      0.93   8.3e+03      18      37 ..     194     209 ..     191     212 .. 0.60

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 2.7e-22
                     B12-binding_2  2 aerlhwaivhgdkegieelidealaqgsaavdvlndvllpamkeVGdlfgagelflpqvllsaevmkkavahL 74
                                      ++ l++a+v+gdk+++ + ++++l+++ ++ +++ d++  +m++V +++++ge+f+p+ +ls+e+m++a+ +L
  gi|298674958|ref|YP_003726708.1|  8 LNGLANAVVNGDKDKAIKFAQKVLEENIDPYEAITDGCTRGMHVVSEKYDNGEMFIPHIMLSSEAMNEAITVL 80
                                      5789******************************************************************998 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.93
                     B12-binding_2  18 eelidealaqgsaavdvlnd 37 
                                       ++ +d a+    +a +++ +
  gi|298674958|ref|YP_003726708.1| 194 DAYADDAR----DAIEIVKE 209
                                       55566666....66666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1331.16
//
Query:       gi|298674959|ref|YP_003726709.1|  [L=414]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.5e-26   90.5   0.8    2.2e-25   89.2   0.0    2.0  2  OrfB_IS605      Probable transposase
    9.1e-12   44.7   0.3    2.4e-11   43.4   0.1    1.9  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.017   15.5   0.0      0.034   14.5   0.0    1.4  1  RuvX            Holliday junction resolvase


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.3      0.45   2.7e+03      47      84 ..      10      29 ..       2      40 .. 0.53
   2 !   89.2   0.0   3.7e-29   2.2e-25      15     119 ..     190     292 ..     176     293 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.45
                        OrfB_IS605 47 ksdykylakeiaelqsklkksknykkasrklarlhrkr 84
                                      k+d+++                   ++ +++++l++++
  gi|298674959|ref|YP_003726709.1| 10 KADKQK------------------YEVLKRITKLSKNL 29
                                      333333..................34444444444444 PP

  == domain 2  score: 89.2 bits;  conditional E-value: 3.7e-29
                        OrfB_IS605  15 gnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsrrrkhl 91 
                                        nk+++iDlG+nn+at+v+++gt+f+++gr lks +++++k +  lqs ++k++   k  +kl  l++kr+++++++
  gi|298674959|ref|YP_003726709.1| 190 YNKHLSIDLGVNNFATCVDTNGTAFIIEGRGLKSYNRWWNKVKSGLQSVYDKQG--IKSGQKLNWLFEKRKNKLNDF 264
                                       699**************************************************9..9******************** PP

                        OrfB_IS605  92 lhklathliktlkevgvetLnvgnmkdi 119
                                       +++ +++++k++ +++++++++g++kdi
  gi|298674959|ref|YP_003726709.1| 265 MNQSVNYIVKHCIDNNIGNIIIGELKDI 292
                                       *************************998 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       2.4   1.4e+04       9      22 ..     167     180 ..     167     181 .. 0.81
   2 !   43.4   0.1     4e-15   2.4e-11       1      69 []     311     385 ..     311     385 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 2.4
                    OrfB_Zn_ribbon   9 eykakeyGikveev 22 
                                       +y  +++ i++++ 
  gi|298674959|ref|YP_003726709.1| 167 KYNGQWFEIEYVYR 180
                                       68899999999885 PP

  == domain 2  score: 43.4 bits;  conditional E-value: 4e-15
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke......alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f+k+k++l+ k++ yGi+ +ev++ayTSkt +   +  ++      ++ +r +  ++ g  +++Dvn+a+Nil++
  gi|298674959|ref|YP_003726709.1| 311 FGKFKQKLRSKCEYYGINCIEVDEAYTSKTDALALEPIEKhqkymgKRVKRGLFQSSTGKLLNADVNGALNILRK 385
                                       89****************************887776666666688977788888888***************986 PP

>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   5.7e-06     0.034      36     107 ..     263     346 ..     241     362 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.7e-06
                                       H..HHHHHHHHHHHHHTT--EEEEE--......---..-SSS---SSTTHHHHHHHHHT....T-EEEEE--S---- CS
                              RuvX  36 k..ekdleelkelvkeeeveeiVvGlP......lnl..dgsegesakkvrkfaeeLakrl..kklpvelvDErlttv 100
                                       +  +++++ + + + ++++ +i++G        +n+  +++++ ++  + kf ++L++++  ++++ + vDE +t++
  gi|298674959|ref|YP_003726709.1| 263 DfmNQSVNYIVKHCIDNNIGNIIIGELkdikqnFNMgkKNNQTFQTIPFGKFKQKLRSKCeyYGINCIEVDEAYTSK 339
                                       14479999*****************8878888856611455555555669********9977899***********9 PP

                                       XXXXXXX CS
                              RuvX 101 eaerilr 107
                                       + + +l+
  gi|298674959|ref|YP_003726709.1| 340 TDALALE 346
                                       8776664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1052  (0.0586759); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2852.58
//
Query:       gi|298674960|ref|YP_003726710.1|  [L=733]
Description: AAA ATPase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.7e-97  320.8   0.1    3.7e-47  160.1   0.0    2.4  2  AAA              ATPase family associated with various cellul
    8.4e-34  115.1   0.3    5.5e-17   61.3   0.1    2.9  2  AAA_lid_3        AAA+ lid domain
    6.8e-24   83.9   1.0    1.1e-22   80.0   2.1    2.5  2  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    4.5e-16   59.4   0.0    4.8e-07   30.0   0.0    2.4  2  AAA_2            AAA domain (Cdc48 subfamily)
    5.3e-14   52.9   0.2    0.00017   22.1   0.0    4.1  3  AAA_16           AAA ATPase domain
    2.8e-13   49.9   0.0    2.3e-05   24.2   0.0    2.9  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    4.9e-13   48.7   0.0    1.9e-12   46.8   0.0    2.0  1  CDC48_2          Cell division protein 48 (CDC48), domain 2
    2.1e-10   40.8   0.0     0.0002   21.4   0.0    2.5  2  AAA_14           AAA domain
    3.2e-10   40.4   2.3     0.0072   16.6   0.1    4.3  4  AAA_22           AAA domain
    3.8e-10   39.5   0.0    0.00016   21.0   0.0    2.8  2  TIP49            TIP49 P-loop domain
    1.1e-09   38.4   2.8    0.00059   19.8   0.4    4.4  2  AAA_5            AAA domain (dynein-related subfamily)
    1.9e-09   37.8   0.0      0.001   19.2   0.0    2.6  2  AAA_33           AAA domain
    1.8e-08   34.2   0.7     0.0018   18.3   0.0    3.4  3  Vps4_C           Vps4 C terminal oligomerisation domain
    1.6e-07   31.2   0.3      0.082   12.6   0.1    3.8  2  Sigma54_activat  Sigma-54 interaction domain
    3.7e-07   30.1   0.0      0.032   14.0   0.0    2.7  2  AAA_24           AAA domain
    8.4e-07   29.6   0.0      0.051   14.1   0.0    2.7  2  AAA_18           AAA domain
    9.5e-07   28.7   0.0      0.039   13.7   0.0    2.4  2  IstB_IS21        IstB-like ATP binding protein
    2.1e-06   28.0   0.0      0.046   14.1   0.0    2.8  2  RNA_helicase     RNA helicase
      3e-06   27.8   0.0      0.095   13.2   0.0    2.6  2  ABC_tran         ABC transporter
    3.3e-06   26.8   2.6       0.54    9.8   0.0    4.3  4  AAA_25           AAA domain
    4.4e-06   26.2   0.1     0.0091   15.4   0.0    2.6  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    9.2e-06   25.7   1.0       0.31   10.9   0.1    4.1  4  ATPase_2         ATPase domain predominantly from Archaea
    1.1e-05   25.1   0.0      0.043   13.3   0.0    2.6  2  AAA_7            P-loop containing dynein motor region
    1.5e-05   25.0   0.0      0.014   15.2   0.0    2.6  2  Bac_DnaA         Bacterial dnaA  protein
    1.8e-05   25.0   0.0       0.19   12.0   0.0    2.5  2  AAA_28           AAA domain
    4.1e-05   22.9   0.0      0.043   13.0   0.0    2.5  2  DUF815           Protein of unknown function (DUF815)
    6.4e-05   22.5   0.5       0.13   11.7   0.1    2.7  2  PhoH             PhoH-like protein
    0.00014   21.9   0.4       0.34   10.8   0.0    3.7  4  NACHT            NACHT domain
    0.00028   20.2   0.0       0.11   11.7   0.0    2.2  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    0.00045   20.0   0.1       0.24   11.1   0.0    2.7  2  AAA_30           AAA domain
     0.0011   18.8   0.0      0.087   12.7   0.0    2.5  2  AAA_3            ATPase family associated with various cellul
     0.0012   18.3   0.1        6.6    6.1   0.0    4.0  4  TniB             Bacterial TniB protein
     0.0014   17.9   0.1        0.7    9.1   0.0    2.6  2  Zeta_toxin       Zeta toxin
     0.0016   18.2   1.5          6    6.5   0.0    4.3  4  Guanylate_kin    Guanylate kinase
     0.0016   17.6   0.1        1.4    8.0   0.0    2.3  2  Parvo_NS1        Parvovirus non-structural protein NS1
      0.002   18.1   0.0        1.4    8.9   0.0    2.6  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.002   18.6   0.0       0.68   10.3   0.0    3.1  2  AAA_17           AAA domain
     0.0031   16.4   0.0       0.43    9.4   0.0    2.3  2  AFG1_ATPase      AFG1-like ATPase
     0.0032   16.8   3.5       0.84    8.9   0.1    3.7  4  ATPase           KaiC
     0.0042   16.3   0.0        3.4    6.8   0.0    2.6  2  NB-ARC           NB-ARC domain
     0.0057   15.9   0.0        5.3    6.2   0.0    3.3  3  KAP_NTPase       KAP family P-loop domain
  ------ inclusion threshold ------
      0.011   15.5   0.2       0.91    9.2   0.0    2.7  2  Cytidylate_kin   Cytidylate kinase
      0.012   16.0   4.2       0.32   11.3   0.2    3.1  2  AAA_19           AAA domain
      0.047   13.8   0.0         12    6.1   0.0    2.7  2  Sigma54_activ_2  Sigma-54 interaction domain
      0.062   13.0   0.1         13    5.7   0.0    2.9  2  AAA_29           P-loop containing region of AAA domain
      0.073   12.8   0.0        8.9    6.0   0.0    2.7  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
      0.079   12.3   0.1        3.1    7.1   0.1    2.5  2  IPT              Isopentenyl transferase
       0.09   12.9   0.1          2    8.5   0.0    2.4  2  Cytidylate_kin2  Cytidylate kinase-like family
       0.11   12.3   0.0        4.1    7.1   0.0    2.3  2  AAA_11           AAA domain
       0.11   12.5   0.3        9.4    6.2   0.0    2.9  2  ResIII           Type III restriction enzyme, res subunit
       0.11   11.6   0.0        4.8    6.3   0.0    2.3  2  DAP3             Mitochondrial ribosomal death-associated pro
       0.15   11.7   0.2         43    3.7   0.0    3.3  3  Zot              Zonular occludens toxin (Zot)
       0.23   11.4   6.0         10    6.0   0.0    4.6  5  NTPase_1         NTPase
        3.6    7.3   4.7         46    3.7   0.1    3.5  4  AAA_21           AAA domain, putative AbiEii toxin, Type IV T


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.7   0.0     3e-49     1e-46       1     131 [.     215     344 ..     215     345 .. 0.98
   2 !  160.1   0.0   1.1e-49   3.7e-47       1     130 [.     487     616 ..     487     618 .. 0.97

  Alignments for each domain:
  == domain 1  score: 158.7 bits;  conditional E-value: 3e-49
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       v++yGp GtGKTl+akava e++++f+++sg+e++sky gese+k+re+f+ea++ a psi+fiDEid++a++r + 
  gi|298674960|ref|YP_003726710.1| 215 VMVYGPSGTGKTLIAKAVAYETDANFISLSGPEIMSKYYGESEEKLREIFEEAENDA-PSIIFIDEIDSIAPKRGEV 290
                                       689*****************************************************9.****************999 PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       + e+e+r+v+qLl+ +dg+k++ ++vivi+atnrp+++d+al+r gRfdr+ieie
  gi|298674960|ref|YP_003726710.1| 291 SGEVEQRIVAQLLSLMDGLKSR-GEVIVIAATNRPSSVDEALRRgGRFDREIEIE 344
                                       *********************7.66***************************997 PP

  == domain 2  score: 160.1 bits;  conditional E-value: 1.1e-49
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TT CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sg 76 
                                       v+lyGppGtGKT+lakav  e++++f++i+g+ellskyvgese+ ire+f++ak+ a p+++fiDEid++a++r ++
  gi|298674960|ref|YP_003726710.1| 487 VILYGPPGTGKTMLAKAVSGESEANFISIKGPELLSKYVGESERAIRETFRKAKQAA-PTVIFIDEIDSIAPRRgKS 562
                                       79******************************************************9.****************999 PP

                                       CCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEET CS
                               AAA  77 seseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkiei 130
                                       ++s+++ervv+q+lte+dg ++ ++ v+vi+atnr d +dpallr gRfdr +++
  gi|298674960|ref|YP_003726710.1| 563 NDSNVTERVVSQILTEMDGIEELKD-VVVIAATNRLDIVDPALLRpGRFDRMVYV 616
                                       9*********************755.*************************9997 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.0   2.7e-16   9.1e-14       1      41 [.     367     407 ..     367     425 .. 0.90
   2 !   61.3   0.1   1.7e-19   5.5e-17       1      37 [.     640     676 ..     640     699 .. 0.79

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 2.7e-16
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitme 41 
                                       d+ l+eLA  T+G++GADla+lc+eAa++Alr  +++i+ e
  gi|298674960|ref|YP_003726710.1| 367 DIVLDELADITHGFVGADLASLCKEAAMRALRKIMPHIKIE 407
                                       5669*****************************99976644 PP

  == domain 2  score: 61.3 bits;  conditional E-value: 1.7e-19
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgike 37 
                                       +vd+++LA  TeGySGAD++a+creAallAlr++ik 
  gi|298674960|ref|YP_003726710.1| 640 NVDIEKLANITEGYSGADIEAICREAALLALREVIKP 676
                                       7********************************7662 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.0   2.1   3.2e-25   1.1e-22       3      84 ..       8      89 ..       6      90 .. 0.97
   2 ?   -1.6   0.0       9.8   3.3e+03      20      42 ..     200     223 ..     200     246 .. 0.58

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 3.2e-25
                                      EEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEEE CS
                           CDC48_N  3 rVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtVr 81
                                       V++a+++dvg+gi+r+d+e m++lg  +gd++ei+ k++ +a++ p ++ d+ k++Ir+dg+tR+n gv+i+d V V+
  gi|298674960|ref|YP_003726710.1|  8 HVSRAYHKDVGKGIARVDRESMQKLGAVSGDIIEIRSKKQGYAVIQPFYENDTAKDVIRIDGNTRSNTGVGIDDIVVVS 86
                                      699**************************************************************************** PP

                                      EE- CS
                           CDC48_N 82 kae 84
                                      k++
  gi|298674960|ref|YP_003726710.1| 87 KIQ 89
                                      986 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 9.8
                                       -HHHHHHHTS-TTSEEEEEC.CCC CS
                           CDC48_N  20 dpedmeelglepgdvveieg.krk 42 
                                       +pe +++lg+ep + v + g + +
  gi|298674960|ref|YP_003726710.1| 200 HPELFQKLGIEPPKGVMVYGpSGT 223
                                       589999999999877777664443 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   1.5e-09   4.8e-07       6     105 ..     215     308 ..     211     340 .. 0.86
   2 !   26.8   0.0   1.4e-08   4.8e-06       7      99 ..     488     576 ..     483     583 .. 0.81

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 1.5e-09
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +++ gp+g+Gkt++aka+a   ++    ++i +   e++     + + ++++  ++   +ae++   i+++DEid i
  gi|298674960|ref|YP_003726710.1| 215 VMVYGPSGTGKTLIAKAVAYETDA----NFISLSGPEIMS----KYYGESEEKLREIFEEAENDApsIIFIDEIDSI 283
                                       6899****************9996....************....9999***************9999********** PP

                                       ------------H...HHHHHHHHHHH- CS
                             AAA_2  81 hpkessgadvSre...gVqrdLLqileg 105
                                       +p   ++ +vS+e    ++  LL +++g
  gi|298674960|ref|YP_003726710.1| 284 AP---KRGEVSGEveqRIVAQLLSLMDG 308
                                       **...66666665211455667777776 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 1.4e-08
                                       EEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG-- CS
                             AAA_2   7 lllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKih 81 
                                       +l gp g+Gkt+laka++   ++    ++i +   ell     + + +++   ++   +a++    ++++DEid i+
  gi|298674960|ref|YP_003726710.1| 488 ILYGPPGTGKTMLAKAVSGESEA----NFISIKGPELLS----KYVGESERAIRETFRKAKQAAptVIFIDEIDSIA 556
                                       678**************999985....************....55555566666666667776688*********** PP

                                       --..---------HHHHHHH CS
                             AAA_2  82 pk..essgadvSregVqrdL 99 
                                       p+  +s+ ++v +  V ++L
  gi|298674960|ref|YP_003726710.1| 557 PRrgKSNDSNVTERVVSQIL 576
                                       **977788888877777776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0     5e-07   0.00017      24     139 ..     212     317 ..     199     319 .. 0.75
   2 !   20.6   0.0   1.4e-06   0.00048      14      61 ..     474     518 ..     473     528 .. 0.82
   3 ?    4.6   0.0      0.11        38     122     147 ..     531     555 ..     526     565 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 5e-07
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrek 100
                                       p  v+++G+sG+GK+ ++++++ +  +    f++    +  ++  y    + l r e++++ +++   a    + ++
  gi|298674960|ref|YP_003726710.1| 212 PKGVMVYGPSGTGKTLIAKAVAYETDA---NFISLSGPEI-MSKYYGESEEKL-R-EIFEEAEND---APSIIFIDE 279
                                       589*******************54444...4766666666.334444477777.5.777777777...566777788 PP

                            AAA_16 101 leealaavpelagaeasrllellkrllallsrderplvl 139
                                       +++ +   +e++g+ ++r+ ++l +l++ l+++++ +++
  gi|298674960|ref|YP_003726710.1| 280 IDSIAPKRGEVSGEVEQRIVAQLLSLMDGLKSRGE-VIV 317
                                       888888999999*999***********99998777.443 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 1.4e-06
                            AAA_16  14 salervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcd 61 
                                       +++++v++  p+ v+l+G++G+GK+ l++++  + e++   f++ k  
  gi|298674960|ref|YP_003726710.1| 474 DLFKAVNTTPPRGVILYGPPGTGKTMLAKAVSGESEAN---FISIKGP 518
                                       57899999999******************999766666...6666655 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.11
                            AAA_16 122 llkrllallsrderplvlvlDdlqwa 147
                                       ++++ ++++++ + p+v+++D+++ +
  gi|298674960|ref|YP_003726710.1| 531 AIRETFRKAKQ-AAPTVIFIDEIDSI 555
                                       67888899999.899********965 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0     7e-08   2.3e-05      34     103 ..     213     290 ..     206     332 .. 0.85
   2 !   22.5   0.0   2.4e-07   7.8e-05      35      98 ..     486     557 ..     478     609 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 7e-08
                            RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsravee 102
                                         v++yGp G Gkt +ak +a e ++++ + sgP +      e +  l  ++ + e++   ++fidei  ++++  e
  gi|298674960|ref|YP_003726710.1| 213 KGVMVYGPSGTGKTLIAKAVAYETDANFISLSGPEImskyygESEEKLREIFEEAENDapSIIFIDEIDSIAPKRGE 289
                                       5699******************************994433333456788898887764337*******999887666 PP

                            RuvB_N 103 v 103
                                       v
  gi|298674960|ref|YP_003726710.1| 290 V 290
                                       5 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 2.4e-07
                            RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsr 98 
                                        v+lyGpPG Gkt lak ++ e ++++ +  gP l      e ++ +   + + ++    v+fidei  +++
  gi|298674960|ref|YP_003726710.1| 486 GVILYGPPGTGKTMLAKAVSGESEANFISIKGPELlskyvgESERAIRETFRKAKQAapTVIFIDEIDSIAP 557
                                       599******************************873222222233344444433332226999999988765 PP

>> CDC48_2  Cell division protein 48 (CDC48), domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.0   5.8e-15   1.9e-12       8      62 ..     110     165 ..     108     167 .. 0.94

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 5.8e-15
                                       H.HHHCCCTTEEE-TTEEEEECCTCCCEEEEEEEECCCCSCEEECTSCCEEESTTC CS
                           CDC48_2   8 a.ylkrqFlgrpvtkGdlvvfefkgqeiklvVvstePkgpvgitetTeielgtkpv 62 
                                       a yl r ++grpvt G+ v++e  + ++ +vVvs++P+gp+++t++T+i+l ++ v
  gi|298674960|ref|YP_003726710.1| 110 AqYLSRMLEGRPVTRGEWVRVETVNEPLYFVVVSIKPAGPAVVTNDTSIRLKDESV 165
                                       44*************************************************99877 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   5.9e-07    0.0002       5      85 ..     215     304 ..     212     339 .. 0.74
   2 !   16.7   0.0   1.8e-05    0.0058       5      76 ..     487     555 ..     484     594 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 5.9e-07
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev..... 76 
                                       +++ G+  +GKT ++k +++e      +++ ++  +   k + ++e+ l++i+e+++++  +++f+DEi  +     
  gi|298674960|ref|YP_003726710.1| 215 VMVYGPSGTGKTLIAKAVAYETD---ANFISLSGPEIMSKYYGESEEKLREIFEEAENDAPSIIFIDEIDSIapkrg 288
                                       7899***************9888...89999988888887777666555555555566699********99865555 PP

                            AAA_14  77 .......pewekalks 85 
                                              +++   l s
  gi|298674960|ref|YP_003726710.1| 289 evsgeveQRIVAQLLS 304
                                       5555555555555555 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1.8e-05
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                       +++ G+  +GKT+l+k +  e+     +++ i+  +   k   ++e+ +++ ++k+k+   t++f+DEi  +
  gi|298674960|ref|YP_003726710.1| 487 VILYGPPGTGKTMLAKAVSGESE---ANFISIKGPELLSKYVGESERAIRETFRKAKQAAPTVIFIDEIDSI 555
                                       799************99998877...88888887776666655655444444444455689********877 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   2.2e-05    0.0072       8      59 ..     215     266 ..     210     270 .. 0.79
   2 ?    4.5   0.0      0.12        39      72     118 ..     254     308 ..     242     322 .. 0.72
   3 !   14.2   0.1   0.00012      0.04       8      29 ..     487     508 ..     482     525 .. 0.81
   4 ?    3.7   0.0      0.21        70      77     105 ..     531     559 ..     519     593 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.2e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsstsskdllre 59 
                                       ++v+G+sGtGKT+ ++ ++++ d+ +++   +pe++ +++  s+++++++++e
  gi|298674960|ref|YP_003726710.1| 215 VMVYGPSGTGKTLIAKAVAYETDA-NFISLSGPEIMsKYYGESEEKLREIFEE 266
                                       689******************863.4444478887778888888888888876 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.12
                            AAA_22  72 rlsseellealeqalraravielliiDEaqhlr....s......eealeeLrsllnl 118
                                       + s+e l+e +e+a +++    ++ iDE++ +     +      ++++ +L sl++ 
  gi|298674960|ref|YP_003726710.1| 254 GESEEKLREIFEEAENDAPS--IIFIDEIDSIApkrgEvsgeveQRIVAQLLSLMDG 308
                                       56778888888888888877..*********98765415566667777777777774 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 0.00012
                            AAA_22   8 lvvtGesGtGKTtllrrlleql 29 
                                       ++++G++GtGKT+l++ +  + 
  gi|298674960|ref|YP_003726710.1| 487 VILYGPPGTGKTMLAKAVSGES 508
                                       689*************987665 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.21
                            AAA_22  77 ellealeqalraravielliiDEaqhlr..s 105
                                       +++e++++a +a+  + ++ iDE++ +   +
  gi|298674960|ref|YP_003726710.1| 531 AIRETFRKAKQAA--PTVIFIDEIDSIAprR 559
                                       3334444444444..46********996541 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.6e-05    0.0088      51      97 ..     213     257 ..     205     269 .. 0.84
   2 !   21.0   0.0   4.9e-07   0.00016      51     106 ..     485     539 ..     474     558 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.6e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte 97 
                                       ++v++ GpsgtGkt +a a++ e   d  f++lsg e+ s     +e
  gi|298674960|ref|YP_003726710.1| 213 KGVMVYGPSGTGKTLIAKAVAYET--DANFISLSGPEIMSKYYGESE 257
                                       89******************9985..689*********998765554 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 4.9e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte.vltqalrks 106
                                       r+v+l Gp+gtGkt la a+s e  ++  f++++g e+ s  v  +e ++ +++rk+
  gi|298674960|ref|YP_003726710.1| 485 RGVILYGPPGTGKTMLAKAVSGE--SEANFISIKGPELLSKYVGESErAIRETFRKA 539
                                       89*******************98..5689**************9998679999**98 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.1   0.00019     0.062       2     135 ..     215     332 ..     214     334 .. 0.67
   2 !   19.8   0.4   1.8e-06   0.00059       1     134 [.     486     604 ..     486     610 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00019
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEver 76 
                                       v++ Gp+GtgK+ +a+ +a  + +++    +++ +++           g+ + +  ++ ++a+   ++i+++DE++ 
  gi|298674960|ref|YP_003726710.1| 215 VMVYGPSGTGKTLIAKAVAYETDANFISLSGPEIMSKYY---------GESEEKLREIFEEAEndAPSIIFIDEIDS 282
                                       899******************999999888888665432.........23333345556666666788888888888 PP

                                       --H...HHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHH CS
                             AAA_5  77 aes...evlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalr 135
                                       + +   ev +++ + +  + l+l++g +  ++        + via++n+++    ++++alr
  gi|298674960|ref|YP_003726710.1| 283 IAPkrgEVSGEVEQRIVAQLLSLMDGLKSRGE--------VIVIAATNRPS----SVDEALR 332
                                       77522256666666666666666666555544........77777777777....5555665 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 1.8e-06
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                       +v+L GppGtgK++la+ ++   ++++  + +++ +++     +r i          +  r+a+   + ++++DE++
  gi|298674960|ref|YP_003726710.1| 486 GVILYGPPGTGKTMLAKAVSGESEANFISIKGPELLSKYVGESERAI---------RETFRKAKqaAPTVIFIDEID 553
                                       59*******************99999999999986666555555555.........555555555678999****** PP

                                       G--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHH CS
                             AAA_5  76 raesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspal 134
                                        + +   +s  s   er ++  +  ++++  ++  l+++ via++n+ld     ++pal
  gi|298674960|ref|YP_003726710.1| 554 SIAPRRGKSNDSNVTERVVS--QILTEMDGIEE--LKDVVVIAATNRLD----IVDPAL 604
                                       99999998888888888888..33333333222..44599999999998....445555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   3.1e-06     0.001       2      81 ..     215     324 ..     215     370 .. 0.79
   2 !   15.9   0.0   3.2e-05     0.011       2      50 ..     487     537 ..     487     622 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.1e-06
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt............................dy 48 
                                       v++ G++G+GK+  a+ ++ +++  ++ ls ++++++++g+ +++++                             +
  gi|298674960|ref|YP_003726710.1| 215 VMVYGPSGTGKTLIAKAVAYETDanFISLSGPEIMSKYYGESEEKLReifeeaendapsiifideidsiapkrgeVS 291
                                       7999***************999999999***********97777776778888888888999999999988887766 PP

                            AAA_33  49 trvldrlyqilnelarkalsagrnvildatnls 81 
                                        +v++r+ ++l  l +   s+g  +++ atn+ 
  gi|298674960|ref|YP_003726710.1| 292 GEVEQRIVAQLLSLMDGLKSRGEVIVIAATNRP 324
                                       678888999998888766666666777777754 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 3.2e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqsktdytr 50 
                                       v+l G+pG+GK+ la+ +  +    ++ +  ++l+++++g+ ++ +++  r
  gi|298674960|ref|YP_003726710.1| 487 VILYGPPGTGKTMLAKAVSGESEanFISIKGPELLSKYVGESERAIRETFR 537
                                       7899**************999887888899999999999866665553333 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00088      0.29      18      44 ..     409     435 ..     403     444 .. 0.90
   2 ?    0.6   0.0       1.7   5.7e+02      15      43 ..     448     484 ..     443     485 .. 0.74
   3 !   18.3   0.0   5.3e-06    0.0018      22      54 ..     684     717 ..     674     720 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00088
                            Vps4_C  18 dipsdkllePpvtlkDflkalkkarpt 44 
                                       +ip+d l   +vt +Df +alk+  p+
  gi|298674960|ref|YP_003726710.1| 409 EIPPDILDSLKVTKNDFYEALKNIEPS 435
                                       7999999999**************998 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.7
                            Vps4_C  15 twmdip........sdkllePpvtlkDflkalkkarp 43 
                                       +w di          ++ +e p+++ D+ ka++++ p
  gi|298674960|ref|YP_003726710.1| 448 NWDDIGgldnakqeLSEAVEWPLKYPDLFKAVNTTPP 484
                                       566655555554445677889***********99987 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 5.3e-06
                            Vps4_C  22 dklleP.pvtlkDflkalkkarptVskeDLekhe 54 
                                       +++ ++ +++ ++f+ka+++++pt sk+D++ ++
  gi|298674960|ref|YP_003726710.1| 684 KDIANRiKINWSHFEKAIARTKPTTSKKDMQFYD 717
                                       5566666999*******************98765 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   0.00025     0.082      23      52 ..     213     239 ..     202     334 .. 0.85
   2 !   12.5   0.0   0.00027     0.088      23     142 ..     485     595 ..     471     618 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00025
                                       S-EEEECSTTSSHHHHHHHHHHHSTTTTS- CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekp 52 
                                         v++ G sGtGK+l+a+a+  +++   ++
  gi|298674960|ref|YP_003726710.1| 213 KGVMVYGPSGTGKTLIAKAVAYETD---AN 239
                                       579***************9976544...44 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00027
                                       S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEHHHHHTTTSEEEE CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekkGlfekadgGtlfL 99 
                                         v++ G  GtGK++la+a+  +s+   ++f+++       ell s+  G ++ a   + +    + ++a   ++f+
  gi|298674960|ref|YP_003726710.1| 485 RGVILYGPPGTGKTMLAKAVSGESE---ANFISIKGP----ELL-SKYVGESERAIRETFR----KAKQAAPTVIFI 549
                                       6799**************9976665...789888653....344.4455666555544444....557888888888 PP

                                       ETGGGS-HHHHHHHHHHHHHSEEESBTSSS...EEE--EEEEEEES CS
                   Sigma54_activat 100 DeigelplelQekLlrvlqegevervGssk...eikvdvriiaatn 142
                                       Dei ++ ++  +     + e+ v+++ ++    e   dv +iaatn
  gi|298674960|ref|YP_003726710.1| 550 DEIDSIAPRRGKSNDSNVTERVVSQILTEMdgiEELKDVVVIAATN 595
                                       8888887765555444444444444433221112334666666666 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   0.00017     0.056       5      76 ..     215     282 ..     212     291 .. 0.61
   2 !   14.0   0.0   9.7e-05     0.032       5      42 ..     487     527 ..     484     561 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00017
                            AAA_24   5 iliyGpsgiGKTtlakel..gpkplfidtekGlksldadkfpdie...swedfldevvelaaeladyktlviDtide 76 
                                       +++yGpsg+GKT +ak    + ++ fi + +        ++ +     s e++++ ++e + + +  ++++iD id 
  gi|298674960|ref|YP_003726710.1| 215 VMVYGPSGTGKTLIAKAVayETDANFISLSG-------PEIMSKYygeSEEKLREIFEEAENDAP--SIIFIDEIDS 282
                                       89*************9985544444444433.......222211122255555555555544444..6677777765 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 9.7e-05
                            AAA_24   5 iliyGpsgiGKTtlakel..gpkplfidtek.Glksldadk 42 
                                       +++yGp+g+GKT+lak    + ++ fi + +  l s ++ +
  gi|298674960|ref|YP_003726710.1| 487 VILYGPPGTGKTMLAKAVsgESEANFISIKGpELLSKYVGE 527
                                       789*************9987555555555443445555555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   0.00042      0.14       1      81 [.     215     320 ..     215     353 .. 0.73
   2 !   14.1   0.0   0.00015     0.051       1      25 [.     487     518 ..     487     596 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00042
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.................gvnlrdvakenglllevdpe..........aldes 49 
                                       +++ G++G+GKt +ak+++ ++ ++                  ++lr+++ e +   +   +            + s
  gi|298674960|ref|YP_003726710.1| 215 VMVYGPSGTGKTLIAKAVAYETdANfislsgpeimskyygesEEKLREIFEEAENDAPSIIFideidsiapkRGEVS 291
                                       789***************88876556888888888888888855555555555555555555555777777777777 PP

                            AAA_18  50 krldedkldklldaleenssaleegknlvidg 81 
                                        ++++  +++ll+++++  s    g+++vi  
  gi|298674960|ref|YP_003726710.1| 292 GEVEQRIVAQLLSLMDGLKS---RGEVIVIAA 320
                                       78888888888888888765...677777765 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 0.00015
                            AAA_18   1 IlltGtpGvGKttlakeLskrl..gf.....g 25 
                                       ++l G+pG+GKt lak++s +   +f      
  gi|298674960|ref|YP_003726710.1| 487 VILYGPPGTGKTMLAKAVSGESeaNFisikgP 518
                                       79****************54431233544441 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   0.00027     0.091      45      71 ..     210     236 ..     199     244 .. 0.85
   2 !   13.7   0.0   0.00012     0.039      49      71 ..     486     508 ..     475     556 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00027
                         IstB_IS21  45 ekkenivllGpsGvGKshlaialgvea 71 
                                       e  +++++ GpsG+GK+ +a a+++e+
  gi|298674960|ref|YP_003726710.1| 210 EPPKGVMVYGPSGTGKTLIAKAVAYET 236
                                       5567899***************99875 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00012
                         IstB_IS21  49 nivllGpsGvGKshlaialgvea 71 
                                       +++l Gp+G+GK+ la a++ e 
  gi|298674960|ref|YP_003726710.1| 486 GVILYGPPGTGKTMLAKAVSGES 508
                                       799**************987654 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0    0.0012      0.41       1      23 [.     215     237 ..     215     284 .. 0.74
   2 !   14.1   0.0   0.00014     0.046       1     106 [.     487     595 ..     487     596 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0012
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakall 23 
                                       +++yGpsg+GK+++ak +a +  
  gi|298674960|ref|YP_003726710.1| 215 VMVYGPSGTGKTLIAKAVAYETD 237
                                       689*************9655443 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 0.00014
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl...klkkkdsvysrnpeddfwdgYt.....gqevvvidDfgqvkdee.nps 68 
                                       ++lyGp+g+GK++lak ++ + + ++   k ++  s y++++e  + + ++      ++v+ id++ ++  +  + +
  gi|298674960|ref|YP_003726710.1| 487 VILYGPPGTGKTMLAKAVSGESEANFisiKGPELLSKYVGESERAIRETFRkakqaAPTVIFIDEIDSIAPRRgKSN 563
                                       689**************777777655566333333334444433333333211124556777777777777776666 PP

                      RNA_helicase  69 dlaelirlvsstpyplnmasleekgtlftSkvvivtsN 106
                                       d +   r+vs   + ++m+ +ee     + +vvi+ +N
  gi|298674960|ref|YP_003726710.1| 564 DSNVTERVVSQ--ILTEMDGIEEL----KDVVVIAATN 595
                                       77777777764..45556666654....3455555555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00078      0.26       6      67 ..     207     266 ..     205     329 .. 0.78
   2 !   13.2   0.0   0.00029     0.095      14      74 ..     487     546 ..     478     597 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00078
                                       EEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe 67 
                                       l +++ + v + G++G+GK+ ++k++a +++  +  i l g ++ ++   +++++++ +++e
  gi|298674960|ref|YP_003726710.1| 207 LGIEPPKGVMVYGPSGTGKTLIAKAVAYETD--ANFISLSGPEIMSKYYGESEEKLREIFEE 266
                                       6778888999****************98876..57777777777776666677776666666 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00029
                                       EEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                          ABC_tran  14 vaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpel 74 
                                       v + G+ G+GK+ L+k+++g+++  +  i ++g +l ++   ++++ i+  + + +q  p++
  gi|298674960|ref|YP_003726710.1| 487 VILYGPPGTGKTMLAKAVSGESE--ANFISIKGPELLSKYVGESERAIRETFRKaKQAAPTV 546
                                       7899*****************96..5777778877777444444444444433333333433 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.041        14      36      55 ..     215     234 ..     208     238 .. 0.86
   2 ?    2.5   0.0      0.29        96     128     177 ..     258     307 ..     247     325 .. 0.79
   3 !    9.8   0.0    0.0016      0.54      36      50 ..     487     501 ..     484     507 .. 0.89
   4 ?    5.8   0.1     0.028       9.2     128     181 ..     530     588 ..     518     594 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.041
                            AAA_25  36 allaGapgtGKttlaldlal 55 
                                       ++++G++gtGKt +a  +a+
  gi|298674960|ref|YP_003726710.1| 215 VMVYGPSGTGKTLIAKAVAY 234
                                       589**********9977775 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.29
                            AAA_25 128 advdaleaaieevegvrlvviDplsralggdensnsdv.galvealeriar 177
                                       ++++++ +++e    +  + iD ++++ +   + + +v +++v++l ++ +
  gi|298674960|ref|YP_003726710.1| 258 EKLREIFEEAEN-DAPSIIFIDEIDSIAPKRGEVSGEVeQRIVAQLLSLMD 307
                                       456667777777.44***************777777776999999988765 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0016
                            AAA_25  36 allaGapgtGKttla 50 
                                       ++l+G+pgtGKt+la
  gi|298674960|ref|YP_003726710.1| 487 VILYGPPGTGKTMLA 501
                                       69************8 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.028
                            AAA_25 128 advdaleaaieevegvrlvviDplsralgg.densnsd.....vgalvealeriarrtga 181
                                       +++++  +++++ + + ++ iD ++++ +  ++ ++s      v+++++ ++ i++ +++
  gi|298674960|ref|YP_003726710.1| 530 RAIRETFRKAKQ-AAPTVIFIDEIDSIAPRrGKSNDSNvtervVSQILTEMDGIEELKDV 588
                                       678888899999.56***********9999644444443334335555555555555555 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0051       1.7      25      42 ..     215     232 ..     212     236 .. 0.89
   2 !   15.4   0.0   2.7e-05    0.0091      25      43 ..     487     505 ..     480     552 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0051
                      Mg_chelatase  25 lllvGppGsGKtmlakrl 42 
                                       ++++Gp+G+GKt++ak++
  gi|298674960|ref|YP_003726710.1| 215 VMVYGPSGTGKTLIAKAV 232
                                       7899***********987 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 2.7e-05
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       ++l+GppG+GKtmlak+++
  gi|298674960|ref|YP_003726710.1| 487 VILYGPPGTGKTMLAKAVS 505
                                       79**************976 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       4.3   1.4e+03     146     193 ..     137     184 ..     131     194 .. 0.82
   2 !   10.9   0.1   0.00092      0.31      17     122 ..     209     318 ..     201     322 .. 0.51
   3 ?    2.1   0.0      0.46   1.5e+02     103     164 ..     257     321 ..     239     348 .. 0.68
   4 !    9.3   0.1    0.0029      0.96      13      95 ..     477     556 ..     473     592 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 4.3
                          ATPase_2 146 lnliesltkekhlcvviclsSeglfiervyneselegrhkyilvddld 193
                                       l++++   k    +vv   +S  l  e v++e+e  +r +y ++  l+
  gi|298674960|ref|YP_003726710.1| 137 LYFVVVSIKPAGPAVVTNDTSIRLKDESVDSEGETTERITYEDIGGLK 184
                                       6677777888888899999999999**************998887774 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00092
                          ATPase_2  17 repneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie......eeeekkklekal..... 82 
                                        ep + +++YGp g GKt + k ++ +  d ++      +  e+ ++++ e+ e      ee               
  gi|298674960|ref|YP_003726710.1| 209 IEPPKGVMVYGPSGTGKTLIAKAVAYET-DANFI---SLSGPEIMSKYYGESEEklreifEEA--------Endaps 273
                                       56777899*********97777766665.54542...22333333333333311111222222........122222 PP

                          ATPase_2  83 ......giavpkaeleeilkeksklvfkaielllekikkkgkkiii 122
                                              + +   +  e++ e  + + +++ +l++ +k +g  i+i
  gi|298674960|ref|YP_003726710.1| 274 iifideIDSIAP-KRGEVSGEVEQRIVAQLLSLMDGLKSRGEVIVI 318
                                       223342222222.223555566666666677777777777665555 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.46
                          ATPase_2 103 fkaielllekikkkgkkiiiiiDelqkli....dlglngaellvkeLlnliesltkekhlcvvicl 164
                                       ++++ +++e+ ++++   ii+iDe+  +     ++  + ++  v++Ll+l++ l ++ +++v+ ++
  gi|298674960|ref|YP_003726710.1| 257 EEKLREIFEEAENDAP-SIIFIDEIDSIApkrgEVSGEVEQRIVAQLLSLMDGLKSRGEVIVIAAT 321
                                       5556666666666644.6899999988761111444447788999999999997777777666544 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.0029
                          ATPase_2  13 eilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekalgiavpka 89 
                                       + ++++p + + +YGp g GKt L k +  ++ + ++  i   +l +++  + ++ i+e+  k   ++a+ +++  +
  gi|298674960|ref|YP_003726710.1| 477 KAVNTTPPRGVILYGPPGTGKTMLAKAVSGES-EANFISIKGPELLSKYVGESERAIRETFRKA--KQAAPTVIFID 550
                                       5667778888999*********9999876666.5566666666666666666666655443333..44444455555 PP

                          ATPase_2  90 eleeil 95 
                                       e++ i 
  gi|298674960|ref|YP_003726710.1| 551 EIDSIA 556
                                       555444 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   0.00013     0.043      30      63 ..     209     241 ..     200     282 .. 0.85
   2 !    9.0   0.0    0.0028      0.93      35      60 ..     486     510 ..     477     556 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00013
                             AAA_7  30 lknkkpvllvGptGtGKtviikdllkkldkekyl 63 
                                       ++  k v+++Gp+GtGKt+i+k +  + d  +++
  gi|298674960|ref|YP_003726710.1| 209 IEPPKGVMVYGPSGTGKTLIAKAVAYETD-ANFI 241
                                       666789****************9988888.4444 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0028
                             AAA_7  35 pvllvGptGtGKtviikdllkkldke 60 
                                        v+l+Gp GtGKt+++k +  + +  
  gi|298674960|ref|YP_003726710.1| 486 GVILYGPPGTGKTMLAKAVSGESE-A 510
                                       699************999876665.4 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   4.2e-05     0.014      37     178 ..     215     358 ..     210     379 .. 0.77
   2 ?    6.8   0.0     0.016       5.3      37     110 ..     487     556 ..     478     629 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.2e-05
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHT.T-SEEEEE-GGGGTT- CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklr.kvDvLliDDiqflagk 112
                                       +++yg++G Gkt + ka+++e+ +n+     + l++ e +++     ++k  e f e    +  ++ iD+i  +a k
  gi|298674960|ref|YP_003726710.1| 215 VMVYGPSGTGKTLIAKAVAYETDANF-----ISLSGPEIMSKYYGESEEKLREIFEEAENdAPSIIFIDEIDSIAPK 286
                                       789**************999876665.....568999999999988888888889887773557999*******999 PP

                                       .........HHHHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHHH CS
                          Bac_DnaA 113 .........ektqeelfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkkk 178
                                                +++  +l+ +++ l   g+ +v+++   P++++e   r   rf++   ++ie pd++ rl+ilk +
  gi|298674960|ref|YP_003726710.1| 287 rgevsgeveQRIVAQLLSLMDGLKSRGEVIVIAATNRPSSVDEALRR-GGRFDR--EIEIEIPDRDARLEILKVH 358
                                       33333222223445677777888889999*********988765433.567777..5778889********9855 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.016
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHT.T-SEEEEE-GGGGT CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklr.kvDvLliDDiqfla 110
                                       +++yg+ G Gkt L ka++ e ++n+ +     +++ e l++ v   +    e+f++  + +  v+ iD+i  +a
  gi|298674960|ref|YP_003726710.1| 487 VILYGPPGTGKTMLAKAVSGESEANFIS-----IKGPELLSKYVGESERAIRETFRKAKQaAPTVIFIDEIDSIA 556
                                       789*************998877666654.....556666666666666666666766555244567777777776 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0    0.0016      0.54       2      49 ..     215     267 ..     214     282 .. 0.76
   2 !   12.0   0.0   0.00056      0.19       2      37 ..     487     527 ..     486     552 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0016
                            AAA_28   2 ivitGgestGKTtlleaLa....argypvv.pEaareileeklakgedalpwv 49 
                                       +++ G+++tGKT +++a a    a+ ++   pE++ +++ e  +k +++ +++
  gi|298674960|ref|YP_003726710.1| 215 VMVYGPSGTGKTLIAKAVAyetdANFISLSgPEIMSKYYGESEEKLREIFEEA 267
                                       6799***************7443335666688888888888777777666655 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00056
                            AAA_28   2 ivitGgestGKTtlleaLa...argypvv..pEaareilee 37 
                                       +++ G+++tGKT l++a +   + ++  +  pE   +++ e
  gi|298674960|ref|YP_003726710.1| 487 VILYGPPGTGKTMLAKAVSgesEANFISIkgPELLSKYVGE 527
                                       789***************96442243333467766666654 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0075       2.5      52     116 ..     211     280 ..     203     358 .. 0.63
   2 !   13.0   0.0   0.00013     0.043      16      81 ..     438     512 ..     426     554 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0075
                            DUF815  52 pannvLLwGarGtGKSslvkallneyaeegLrli..evekedl....kelpklvellrerperfilfvDDL 116
                                       p + v+++G  GtGK  + ka+  e+ ++ + l   e+  +      ++l +++e+  e++   i+f+D +
  gi|298674960|ref|YP_003726710.1| 211 PPKGVMVYGPSGTGKTLIAKAVAYETDANFISLSgpEIMSKYYgeseEKLREIFEEA-ENDAPSIIFIDEI 280
                                       56779*******************999998655322666554410003444444443.3455678888865 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00013
                            DUF815  16 lepveevdevklddLvgidkqkealvente.........qfleglpannvLLwGarGtGKSslvkallneyaeeg 81 
                                        e v ev ++++dd+ g+d+ k++l e +e         + ++ +p + v+L+G  GtGK  l ka+  e +++ 
  gi|298674960|ref|YP_003726710.1| 438 REVVVEVAHINWDDIGGLDNAKQELSEAVEwplkypdlfKAVNTTPPRGVILYGPPGTGKTMLAKAVSGESEANF 512
                                       567889999****************999874443332223466778888******************98887765 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.1   0.00039      0.13      22      42 ..     215     235 ..     206     240 .. 0.87
   2 !    8.0   0.1    0.0055       1.8      22      39 ..     487     504 ..     475     511 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00039
                                       EEEE--TTSSTTHHHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavalave 42 
                                       v++ Gp+GtGKt++a a+a e
  gi|298674960|ref|YP_003726710.1| 215 VMVYGPSGTGKTLIAKAVAYE 235
                                       7899***********999975 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0055
                                       EEEE--TTSSTTHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylaval 39 
                                       v+  Gp GtGKt+la a+
  gi|298674960|ref|YP_003726710.1| 487 VILYGPPGTGKTMLAKAV 504
                                       7889**********9876 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.046        15       3      23 ..     215     235 ..     213     241 .. 0.88
   2 ?    0.4   0.0       1.6   5.2e+02      62     135 ..     253     327 ..     237     346 .. 0.64
   3 !   10.8   0.0     0.001      0.34       3      20 ..     487     504 ..     485     511 .. 0.88
   4 ?   -1.3   0.0       5.5   1.8e+03      58     100 ..     521     563 ..     518     587 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.046
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       v++ G++G GKT  ++ +a +
  gi|298674960|ref|YP_003726710.1| 215 VMVYGPSGTGKTLIAKAVAYE 235
                                       7899***********999876 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.6
                                       CTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH............HHHHHCTTTTT--EEEEEEECCCHHHH CS
                             NACHT  62 lpepaapvsevwavllelperlLlilDglDelvtdlgq...kekqpvrtlLselirkkllpeasllltvrpralrdl 135
                                       + e++++ +e++++    + ++ + +D +D ++ + g+   + +q++   L +l+ + l ++  +++++ +++ + +
  gi|298674960|ref|YP_003726710.1| 253 YGESEEKLREIFEEAENDAPSI-IFIDEIDSIAPKRGEvsgEVEQRIVAQLLSLMDG-LKSRGEVIVIAATNRPSSV 327
                                       5666666666555544444444.5579999999999999996666666677788888.4444444444444444343 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.001
                                       EEEEC-TTTCHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqkl 20 
                                       vil G++G GKT+L++ +
  gi|298674960|ref|YP_003726710.1| 487 VILYGPPGTGKTMLAKAV 504
                                       89*************987 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 5.5
                                       HCCCCTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH.. CS
                             NACHT  58 lfsqlpepaapvsevwavllelperlLlilDglDelvtdlgq.k 100
                                       l +   e++++++e     ++++  +++ +D +D ++   g+ +
  gi|298674960|ref|YP_003726710.1| 521 LSKYVGESERAIRE-TFRKAKQAAPTVIFIDEIDSIAPRRGKsN 563
                                       55556666666666.22335677777888899998888777643 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00033      0.11       4      55 ..     215     260 ..     212     290 .. 0.70
   2 ?    6.4   0.0     0.013       4.5       4      45 ..     487     521 ..     484     572 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00033
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvl.vlrealakke 55 
                                       v+V G +GtGKt+++ ++++e         a+++s ++p+++ +++ + ++k 
  gi|298674960|ref|YP_003726710.1| 215 VMVYGPSGTGKTLIAKAVAYET-------DANFISLSGPEIMsKYYGESEEKL 260
                                       78*******************9.......566666666665424444444444 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.013
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvl 45 
                                       v+  G +GtGKt+++ ++  e        +a+++s  +p++l
  gi|298674960|ref|YP_003726710.1| 487 VILYGPPGTGKTMLAKAVSGES-------EANFISIKGPELL 521
                                       6779**********99888877.......4555554444444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.032        11      21      39 ..     215     233 ..     203     243 .. 0.85
   2 !   11.1   0.0   0.00072      0.24      10      39 ..     476     505 ..     473     518 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.032
                            AAA_30  21 avltGpAGtGKttalkalr 39 
                                       +++ Gp GtGKt + ka++
  gi|298674960|ref|YP_003726710.1| 215 VMVYGPSGTGKTLIAKAVA 233
                                       5789*********999986 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00072
                            AAA_30  10 vealltsgdrvavltGpAGtGKttalkalr 39 
                                       ++a+ t++ r ++l Gp+GtGKt++ ka+ 
  gi|298674960|ref|YP_003726710.1| 476 FKAVNTTPPRGVILYGPPGTGKTMLAKAVS 505
                                       677778888899************999986 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.16        52       2      28 ..     215     241 ..     214     294 .. 0.88
   2 !   12.7   0.0   0.00026     0.087       2     116 ..     487     600 ..     486     615 .. 0.63

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.16
                             AAA_3   2 vllegvPGlaktllvkalakaldlefk 28 
                                       v++ g  G++ktl++ka+a   d++f 
  gi|298674960|ref|YP_003726710.1| 215 VMVYGPSGTGKTLIAKAVAYETDANFI 241
                                       6788899************99999885 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00026
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappkt 78 
                                       v+l g PG++kt+l+ka++   +++f  i+  p+ll   + G +     +++f+  k      +++ dei+  +p+ 
  gi|298674960|ref|YP_003726710.1| 487 VILYGPPGTGKTMLAKAVSGESEANFISIK-GPELLSKYV-GESERA-IRETFRKAKQ-AAPTVIFIDEIDSIAPRR 559
                                       7899**********************9998.699997655.554322.2233433332.335688999999888876 PP

                             AAA_3  79 qsalleameer....qvtvegethklpepflvlatqnPieqe 116
                                         +    + er     +t  +   +l++  +v+a+ n ++  
  gi|298674960|ref|YP_003726710.1| 560 GKSNDSNVTERvvsqILTEMDGIEELKD-VVVIAATNRLDIV 600
                                       5444444444400004444555555554.5667777776655 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.022       7.3      26      55 ..     203     232 ..     195     245 .. 0.82
   2 ?   -1.5   0.1       4.2   1.4e+03      69     149 ..     351     432 ..     336     442 .. 0.68
   3 ?    6.1   0.0      0.02       6.6      25      54 ..     474     503 ..     460     512 .. 0.84
   4 ?   -0.2   0.0       1.7   5.7e+02     110     132 ..     534     556 ..     521     578 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.022
                              TniB  26 LleypkrkrmpnlllvGdsnnGKtmivekF 55 
                                       L+++   + ++ ++++G+s +GKt i++  
  gi|298674960|ref|YP_003726710.1| 203 LFQKLGIEPPKGVMVYGPSGTGKTLIAKAV 232
                                       6666666777899*************9865 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.2
                              TniB  69 kvpvlvvqappkpdekrlyaaiLealgaplkararvskleqqvlrllrelkvrvLiiDEih.nllagsarkqrefln 144
                                       ++++l v+++  p ++++    L+ +   +   + +s  +++++r lr++++++ i  Ei  ++l     +++ f +
  gi|298674960|ref|YP_003726710.1| 351 RLEILKVHTRGMPFDNDIVLDELADITHGFVGADLASLCKEAAMRALRKIMPHIKIEEEIPpDILDSLKVTKNDFYE 427
                                       55667777777777777776667777777766667777778888888888888888777743677777777777777 PP

                              TniB 145 alksL 149
                                       alk++
  gi|298674960|ref|YP_003726710.1| 428 ALKNI 432
                                       77776 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.02
                              TniB  25 eLleypkrkrmpnlllvGdsnnGKtmivek 54 
                                       +L+++ + + ++ ++l+G++ +GKtm+++ 
  gi|298674960|ref|YP_003726710.1| 474 DLFKAVNTTPPRGVILYGPPGTGKTMLAKA 503
                                       6777778888899**************986 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 1.7
                              TniB 110 qvlrllrelkvrvLiiDEihnll 132
                                       ++ r  ++  + v+ iDEi+++ 
  gi|298674960|ref|YP_003726710.1| 534 ETFRKAKQAAPTVIFIDEIDSIA 556
                                       445556778899*******9986 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.021       6.9      14      51 ..     210     245 ..     202     262 .. 0.88
   2 !    9.1   0.0    0.0021       0.7      15      51 ..     483     517 ..     474     526 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.021
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrldp 51 
                                       e Pk +++ G +G GK+ +a++++ e+  + n++ l++
  gi|298674960|ref|YP_003726710.1| 210 EPPKGVMVYGPSGTGKTLIAKAVAYET--DANFISLSG 245
                                       569999*******************98..788888865 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0021
                        Zeta_toxin  15 rPklillgGqpGAGKselaellkdelerqgnvvrldp 51 
                                        P  ++l G pG GK+ la+++  e   + n++ +++
  gi|298674960|ref|YP_003726710.1| 483 PPRGVILYGPPGTGKTMLAKAVSGES--EANFISIKG 517
                                       58889********************8..899998875 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.17        57       4      30 ..     214     240 ..     212     248 .. 0.83
   2 ?    2.1   0.0      0.41   1.4e+02      75      95 ..     249     269 ..     240     286 .. 0.82
   3 ?    6.5   0.0     0.018         6       3      30 ..     485     512 ..     483     517 .. 0.84
   4 ?    1.6   0.1       0.6     2e+02     110     162 ..     539     589 ..     523     598 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.17
                                       EEEEESTTTSSHHHHHHHHHHHSTTTE CS
                     Guanylate_kin   4 pvvlvgpsgaGksslkkaLlselpekf 30 
                                        v++ gpsg+Gk  + ka+  e   +f
  gi|298674960|ref|YP_003726710.1| 214 GVMVYGPSGTGKTLIAKAVAYETDANF 240
                                       58899************9988877777 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.41
                                       TTEEEEEEHHHHHHHHHTTSE CS
                     Guanylate_kin  75 sgnlygtsveaieevlekgki 95 
                                        +++yg+s e+ +e++e++ +
  gi|298674960|ref|YP_003726710.1| 249 MSKYYGESEEKLREIFEEAEN 269
                                       689*************99865 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.018
                                       SEEEEESTTTSSHHHHHHHHHHHSTTTE CS
                     Guanylate_kin   3 rpvvlvgpsgaGksslkkaLlselpekf 30 
                                       r v+l gp g+Gk +l ka+  e + +f
  gi|298674960|ref|YP_003726710.1| 485 RGVILYGPPGTGKTMLAKAVSGESEANF 512
                                       779***************9977776666 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.6
                                       HTTTTEEEEEEEESSHHHHHHHHTTSSSSHHHHHHHHH.HHHHHHHGGG.C.SSEE CS
                     Guanylate_kin 110 kaelspiivFikppslkelqrrlksrgkeqeeklakrl.aaaekelqey.e.fdvv 162
                                       +++ +p ++Fi     +e++    +rgk++  ++ +r+ +++  e+    e  dvv
  gi|298674960|ref|YP_003726710.1| 539 AKQAAPTVIFI-----DEIDSIAPRRGKSNDSNVTERVvSQILTEMDGIeElKDVV 589
                                       45889999999.....7777777789999999888886256777777664454554 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0075       2.5     117     137 ..     215     235 ..     209     239 .. 0.89
   2 !    8.0   0.0    0.0041       1.4     117     134 ..     487     504 ..     479     526 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0075
                         Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                                       v++yGp  tGkt +a+a a+ 
  gi|298674960|ref|YP_003726710.1| 215 VMVYGPSGTGKTLIAKAVAYE 235
                                       789**************9986 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0041
                         Parvo_NS1 117 vwfyGpantGktnlaeaI 134
                                       v +yGp+ tGkt+la+a 
  gi|298674960|ref|YP_003726710.1| 487 VILYGPPGTGKTMLAKAV 504
                                       789************986 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.027       9.1      19      46 ..     212     239 ..     194     261 .. 0.73
   2 !    8.9   0.0    0.0044       1.4      21      51 ..     482     518 ..     456     532 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.027
                                       TEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve 46 
                                        + ++ +G+ G+GKT +++++a + + +
  gi|298674960|ref|YP_003726710.1| 212 PKGVMVYGPSGTGKTLIAKAVAYETDAN 239
                                       445999***************9888766 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0044
                                       E....EEEEESTTSSHHHHHHHHHHHTT--..----T CS
                              TsaE  21 v....ilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                       +    ++L+G+ G+GKT+l++++  + + +  ++k P
  gi|298674960|ref|YP_003726710.1| 482 TpprgVILYGPPGTGKTMLAKAVSGESEANfiSIKGP 518
                                       144449***************9988777665556655 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.098        33       1      26 [.     218     243 ..     218     301 .. 0.71
   2 !   10.3   0.0    0.0021      0.68       1      69 [.     490     559 ..     490     622 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.098
                                       EE-TTSSHHHHHHHHHHHHTEEEEEH CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsa 26 
                                       +G+ G GK+ +++ ++ + +  ++s 
  gi|298674960|ref|YP_003726710.1| 218 YGPSGTGKTLIAKAVAYETDANFISL 243
                                       79**********99998775555553 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0021
                                       EE-TTSSHHHHHHHHHHHH..TEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHH CS
                            AAA_17   1 lGgPGsGKgtqceklveky..gfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeea 69 
                                       +G+PG GK+ +++ +  +   +f  +   +ll + + +++    r+ +rk+++     +    +++ia ++
  gi|298674960|ref|YP_003726710.1| 490 YGPPGTGKTMLAKAVSGESeaNFISIKGPELLSKYVGESER-AIRETFRKAKQAAPTVIFIDEIDSIAPRR 559
                                       7***********99986552266667767777777766665.68899998877665554444444555444 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.042        14      58      79 ..     208     229 ..     192     239 .. 0.81
   2 !    9.4   0.0    0.0013      0.43      55      79 ..     477     501 ..     439     505 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.042
                       AFG1_ATPase  58 svepvrglYlwGgvGrGKtylm 79 
                                         ep++g+ ++G+ G GKt + 
  gi|298674960|ref|YP_003726710.1| 208 GIEPPKGVMVYGPSGTGKTLIA 229
                                       468****************875 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0013
                       AFG1_ATPase  55 krksvepvrglYlwGgvGrGKtylm 79 
                                       k  +++p+rg+ l+G+ G GKt+l 
  gi|298674960|ref|YP_003726710.1| 477 KAVNTTPPRGVILYGPPGTGKTMLA 501
                                       345789*****************95 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.1    0.0025      0.84      13      42 ..     206     235 ..     201     243 .. 0.83
   2 ?   -1.0   0.0       2.8   9.2e+02     110     154 ..     259     309 ..     235     326 .. 0.64
   3 ?    5.3   0.1     0.033        11      22      37 ..     487     502 ..     482     516 .. 0.88
   4 ?   -0.3   0.0       1.7   5.5e+02     144     176 ..     532     567 ..     513     589 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0025
                            ATPase  13 kgGipegrvvlitGepGtGKtifalqFlik 42 
                                       k Gi   + v ++G +GtGKt++a+  +++
  gi|298674960|ref|YP_003726710.1| 206 KLGIEPPKGVMVYGPSGTGKTLIAKAVAYE 235
                                       5578888889*************9987776 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.8
                            ATPase 110 elaeaikeika...krvviDsitgl...ayeekeavaReilrqlvrvlkkl 154
                                       +l+e+ +e +    + + iD i+++     e + +v  +i+ ql++ + +l
  gi|298674960|ref|YP_003726710.1| 259 KLREIFEEAENdapSIIFIDEIDSIapkRGEVSGEVEQRIVAQLLSLMDGL 309
                                       444444444433335666666666632144555566677777887777655 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.033
                            ATPase  22 vlitGepGtGKtifal 37 
                                       v ++G pGtGKt++a+
  gi|298674960|ref|YP_003726710.1| 487 VILYGPPGTGKTMLAK 502
                                       6789*********997 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 1.7
                            ATPase 144 lrqlvrvlkklgvTailvsekss...seeaaggygv 176
                                       +r+ +r  k+   T i++ e++s     ++ +  +v
  gi|298674960|ref|YP_003726710.1| 532 IRETFRKAKQAAPTVIFIDEIDSiapRRGKSNDSNV 567
                                       555556666666666666666664443333333333 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.013       4.3      22      43 ..     214     235 ..     201     242 .. 0.79
   2 ?    6.8   0.0      0.01       3.4      23      43 ..     487     507 ..     478     513 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.013
                                       EEEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC  22 vvalvGmgGvGKttlakqilnk 43 
                                        v ++G  G GKt +ak +  +
  gi|298674960|ref|YP_003726710.1| 214 GVMVYGPSGTGKTLIAKAVAYE 235
                                       4889************998765 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.01
                                       EEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC  23 valvGmgGvGKttlakqilnk 43 
                                       v l+G +G GKt lak +  +
  gi|298674960|ref|YP_003726710.1| 487 VILYGPPGTGKTMLAKAVSGE 507
                                       679************998766 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.016       5.3     139     189 ..     226     287 ..     104     333 .. 0.72
   2 ?    2.0   0.0      0.29        97      14      41 ..     478     505 ..     470     513 .. 0.80
   3 ?    3.3   0.0      0.12        41     166     188 ..     534     558 ..     521     562 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.016
                        KAP_NTPase 139 s............raaklkeeaplkklqteveelladmektLdalqkrlVvviDdLDrcetee 189
                                       +            +   l+  + + k   e ee+l +++++ ++ + + +++iD++D++ +++
  gi|298674960|ref|YP_003726710.1| 226 TliakavayetdaNFISLSGPEIMSKYYGESEEKLREIFEEAEN-DAPSIIFIDEIDSIAPKR 287
                                       04444445555556666667777777777888888888888887.99***********98876 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.29
                        KAP_NTPase  14 eptlatpivvgLygkWGsGKssllnkle 41 
                                         + ++p  v Lyg+ G+GK+ l + + 
  gi|298674960|ref|YP_003726710.1| 478 AVNTTPPRGVILYGPPGTGKTMLAKAVS 505
                                       455689999************9988765 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.12
                        KAP_NTPase 166 ktLda..lqkrlVvviDdLDrcete 188
                                       +t+++  +  + V++iD++D++ + 
  gi|298674960|ref|YP_003726710.1| 534 ETFRKakQAAPTVIFIDEIDSIAPR 558
                                       444445678899*********9876 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0028      0.91       3      28 ..     217     242 ..     215     245 .. 0.89
   2 ?    3.5   0.0      0.16        52       3      27 ..     489     513 ..     487     516 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0028
                                       EE-STTSSHHHHHHHHHHHHT-EEEE CS
                    Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyld 28 
                                       + GP+g+GK  +a+a+a + ++++++
  gi|298674960|ref|YP_003726710.1| 217 VYGPSGTGKTLIAKAVAYETDANFIS 242
                                       67*****************9999986 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.16
                                       EE-STTSSHHHHHHHHHHHHT-EEE CS
                    Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyl 27 
                                       + GP g+GK  +a+a++ + +++++
  gi|298674960|ref|YP_003726710.1| 489 LYGPPGTGKTMLAKAVSGESEANFI 513
                                       56***************99998887 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.3      0.15        50      11      30 ..     213     232 ..     209     241 .. 0.82
   2 ?   11.3   0.2   0.00098      0.32       3      33 ..     477     507 ..     476     580 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.15
                            AAA_19  11 kvllvtaGpGtGKTrvlkhi 30 
                                       k ++v ++ GtGKT + k++
  gi|298674960|ref|YP_003726710.1| 213 KGVMVYGPSGTGKTLIAKAV 232
                                       55899*********987765 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00098
                            AAA_19   3 eavealkekvllvtaGpGtGKTrvlkhival 33 
                                       +av++++ + +++ ++pGtGKT + k++  +
  gi|298674960|ref|YP_003726710.1| 477 KAVNTTPPRGVILYGPPGTGKTMLAKAVSGE 507
                                       5888999999************987766544 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.094        31      24      80 ..     215     282 ..     210     288 .. 0.55
   2 ?    6.1   0.0     0.035        12      24      80 ..     487     554 ..     474     562 .. 0.59

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.094
                                       EEEEEETT--HHHHHHCC--TTS-E.E--SSTTHHH.......H-HHHHHHHT...TTSEEEEEE-TT CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpw.leifvverla.......klpldlleqa...kggtLylkdiad 80 
                                       v + G+ G+gk+l+A++ + +   + +++   e  +       +   +++e+a    + ++++ +i++
  gi|298674960|ref|YP_003726710.1| 215 VMVYGPSGTGKTLIAKAVAYETDANfISLSGPEIMSkyygeseEKLREIFEEAendAPSIIFIDEIDS 282
                                       8899************9875443321222211111100111113446666666443455666666665 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.035
                                       EEEEEETT--HHHHHHCC--TTS-E.E--SSTTHHHH-H...........HHHHHHTTTSEEEEEE-TT CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpw.leifvverlaklp...........ldlleqakggtLylkdiad 80 
                                       v l G++G+gk++ A++ + +s+ + ++i+  e l+k              +  +qa + ++++ +i++
  gi|298674960|ref|YP_003726710.1| 487 VILYGPPGTGKTMLAKAVSGESEANfISIKGPELLSK-YvgeserairetFRKAKQAAPTVIFIDEIDS 554
                                       899**************99877664133333322222.0233333332223333335666677777666 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.038        13      21      39 ..     212     229 ..     202     234 .. 0.74
   2 ?    3.7   0.0      0.15        50      20      39 ..     483     501 ..     474     505 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.038
                            AAA_29  21 lkgatlltGpsGsGKSTll 39 
                                       +kg +++ GpsG+GK+ + 
  gi|298674960|ref|YP_003726710.1| 212 PKG-VMVYGPSGTGKTLIA 229
                                       356.99*********8665 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.15
                            AAA_29  20 dlkgatlltGpsGsGKSTll 39 
                                        ++g ++l Gp G+GK+ l 
  gi|298674960|ref|YP_003726710.1| 483 PPRG-VILYGPPGTGKTMLA 501
                                       3467.99*********9875 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.14        46       2      22 ..     213     233 ..     212     237 .. 0.87
   2 ?    6.0   0.0     0.027       8.9       4      24 ..     487     507 ..     484     512 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.14
                         PduV-EutP   2 kkilliGkvgsGKttLtqalk 22 
                                       k +++ G++g+GKt +++a+ 
  gi|298674960|ref|YP_003726710.1| 213 KGVMVYGPSGTGKTLIAKAVA 233
                                       679***********9999875 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.027
                         PduV-EutP   4 illiGkvgsGKttLtqalkge 24 
                                       ++l G+ g+GKt L++a++ge
  gi|298674960|ref|YP_003726710.1| 487 VILYGPPGTGKTMLAKAVSGE 507
                                       89****************997 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1    0.0095       3.1       5      32 ..     216     243 ..     213     245 .. 0.93
   2 ?    2.4   0.0      0.26        87       5      31 ..     488     514 ..     485     540 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0095
                               IPT   5 lifGatttGKtaeaiklaketgapvivl 32 
                                       +++G+ +tGKt  a ++a et a  i+l
  gi|298674960|ref|YP_003726710.1| 216 MVYGPSGTGKTLIAKAVAYETDANFISL 243
                                       69********************999987 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.26
                               IPT   5 lifGatttGKtaeaiklaketgapviv 31 
                                       +++G+ +tGKt  a +++ e  a  i+
  gi|298674960|ref|YP_003726710.1| 488 ILYGPPGTGKTMLAKAVSGESEANFIS 514
                                       68**************99988887776 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0061         2       8      53 ..     221     268 ..     217     314 .. 0.86
   2 ?    1.6   0.0       0.8   2.6e+02       8      81 ..     493     567 ..     489     592 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0061
                   Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeev.eevde.r 53 
                                        G+g++ i++a+A +   +f++   +e ++k  g see++ e ++e +
  gi|298674960|ref|YP_003726710.1| 221 SGTGKTLIAKAVAYETDANFISLSGPEIMSKYYGESEEKLrEIFEEaE 268
                                       59**************************************66666642 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.8
                   Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeev.eevdersrlssflskllaarvagdtldeklddel 81 
                                        G+g++ +++a++ + + +f++ + +e ++k  g se  + e++ +++ ++ ++  +   +  +   +++ d+++
  gi|298674960|ref|YP_003726710.1| 493 PGTGKTMLAKAVSGESEANFISIKGPELLSKYVGESERAIrETFRKAKQAAPTVIFIDEIDSIAPRRGKSNDSNV 567
                                       599********************9999999999999999866666644333333333333322222244444443 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.29        97      20      34 ..     215     229 ..     201     263 .. 0.81
   2 ?    7.1   0.0     0.012       4.1      20      34 ..     487     501 ..     474     566 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.29
                            AAA_11  20 tliqGPPGtgKTkti 34 
                                       +++ GP GtgKT   
  gi|298674960|ref|YP_003726710.1| 215 VMVYGPSGTGKTLIA 229
                                       789*********543 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.012
                            AAA_11  20 tliqGPPGtgKTkti 34 
                                       +++ GPPGtgKT   
  gi|298674960|ref|YP_003726710.1| 487 VILYGPPGTGKTMLA 501
                                       5789********654 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.028       9.4      19      48 ..     207     236 ..     189     244 .. 0.80
   2 ?    2.8   0.0      0.32   1.1e+02      23      42 ..     483     502 ..     454     515 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.028
                                       ....TTSEEEEEESTTSTHHHHHHHHHHHH CS
                            ResIII  19 lkskrdkrglikmaTGtGKTlvaaklierl 48 
                                       l ++  k +++  + GtGKTl+a +++++ 
  gi|298674960|ref|YP_003726710.1| 207 LGIEPPKGVMVYGPSGTGKTLIAKAVAYET 236
                                       4446778889999**********8888776 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.32
                                       TTSEEEEEESTTSTHHHHHH CS
                            ResIII  23 rdkrglikmaTGtGKTlvaa 42 
                                         + +++  + GtGKT++a 
  gi|298674960|ref|YP_003726710.1| 483 PPRGVILYGPPGTGKTMLAK 502
                                       44566788999******984 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.17        57      22      55 ..     211     243 ..     201     253 .. 0.80
   2 ?    6.3   0.0     0.014       4.8      19      43 ..     480     503 ..     470     524 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.17
                                       ---EEEEE-SSSSSTTTTHHHHHHHGGGS--EEE CS
                              DAP3  22 kvkrlvltGekgsGKSvlLlqalayAlekgwvvl 55 
                                       + k ++++G  g+GK++ +++a+ay ++++++ l
  gi|298674960|ref|YP_003726710.1| 211 PPKGVMVYGPSGTGKTL-IAKAVAYETDANFISL 243
                                       5566899********85.7899999888888765 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.014
                                       SSS---EEEEE-SSSSSTTTTHHHH CS
                              DAP3  19 kkkkvkrlvltGekgsGKSvlLlqa 43 
                                       ++++   ++l+G +g+GK++l ++a
  gi|298674960|ref|YP_003726710.1| 480 NTTPPRGVILYGPPGTGKTML-AKA 503
                                       66777789**********984.555 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.13        43       4      62 ..     216     279 ..     215     286 .. 0.71
   2 ?    3.1   0.0       0.2        65      63     107 ..     254     298 ..     233     336 .. 0.67
   3 ?    2.8   0.0      0.25        82       4      61 ..     488     550 ..     487     580 .. 0.64

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.13
                               Zot   4 lvtGapGsgKtsga..vkkdllp..alkegRkiitnidGlrlerieqvlgekvs.tarliridn 62 
                                       +v+G+ G+gKt+ a  v  +      + +g +i+ +  G   e+++ +++e+ + ++ +i+id+
  gi|298674960|ref|YP_003726710.1| 216 MVYGPSGTGKTLIAkaVAYETDAnfISLSGPEIMSKYYGESEEKLREIFEEAENdAPSIIFIDE 279
                                       6899999999975411544333332444799999999999999999999988888888998883 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.2
                               Zot  63 pegaetlkefakwatidkgallviDEcqeifpvrakegrkdpevi 107
                                        e++e+l e++  a  d  ++++iDE   i p+r +   +++++i
  gi|298674960|ref|YP_003726710.1| 254 GESEEKLREIFEEAENDAPSIIFIDEIDSIAPKRGEVSGEVEQRI 298
                                       5788889999999998999***********999987655554443 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.25
                               Zot   4 lvtGapGsgKts..gavkkdllp.alk.egRkiitnidGlrlerieqvlgekvs.tarlirid 61 
                                       + +G+pG+gKt+  +av+ +    ++  +g ++  +  G   ++i+  ++++++ ++ +i+id
  gi|298674960|ref|YP_003726710.1| 488 ILYGPPGTGKTMlaKAVSGESEAnFISiKGPELLSKYVGESERAIRETFRKAKQaAPTVIFID 550
                                       568888888886113455433332222356666666666666666666666666666666666 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.53   1.7e+02       2      23 ..     215     236 ..     214     250 .. 0.79
   2 ?    0.4   0.2       1.6   5.2e+02      82     107 ..     257     283 ..     245     313 .. 0.71
   3 ?   -1.6   0.0       6.9   2.3e+03      87     122 ..     435     470 ..     421     476 .. 0.73
   4 ?    6.0   0.0     0.031        10       2      32 ..     487     517 ..     486     521 .. 0.83
   5 ?    1.1   0.0      0.95   3.2e+02      80     104 ..     527     552 ..     521     577 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.53
                                       EEEE--TTSSHHHHHHHHHHHH CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlell 23 
                                       v++ Gp+G+GKt + k v+ + 
  gi|298674960|ref|YP_003726710.1| 215 VMVYGPSGTGKTLIAKAVAYET 236
                                       6789*******99988887665 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHHH.HHH-EEEE---STT CS
                          NTPase_1  82 eelalealrkal.seadviviDEiGkm 107
                                       ee   e++++a    + +i iDEi ++
  gi|298674960|ref|YP_003726710.1| 257 EEKLREIFEEAEnDAPSIIFIDEIDSI 283
                                       55556666776634445*******766 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 6.9
                                       HHHHHHHHHH-EEEE---STTGGG-HHHHHHHHHHH CS
                          NTPase_1  87 ealrkalseadviviDEiGkmElkskkfkeaveevL 122
                                       +a+r+ + e   i  D iG +    ++++eave  L
  gi|298674960|ref|YP_003726710.1| 435 SAMREVVVEVAHINWDDIGGLDNAKQELSEAVEWPL 470
                                       55555555555566799**********999998655 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.031
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       v++ GppG+GKt l k v+ + + + ++++G
  gi|298674960|ref|YP_003726710.1| 487 VILYGPPGTGKTMLAKAVSGESEANFISIKG 517
                                       7899***********9999887666666655 PP

  == domain 5  score: 1.1 bits;  conditional E-value: 0.95
                                       HHHHHHHHHHHHHH.HHH-EEEE--- CS
                          NTPase_1  80 sfeelalealrkal.seadviviDEi 104
                                       + e+ + e +rka    + vi iDEi
  gi|298674960|ref|YP_003726710.1| 527 ESERAIRETFRKAKqAAPTVIFIDEI 552
                                       5677888888988844455******9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1      0.14        46       3      20 ..     216     233 ..     215     259 .. 0.77
   2 ?   -0.6   0.1       2.7   8.9e+02     256     268 ..     270     282 ..     263     283 .. 0.82
   3 ?    2.2   0.0      0.38   1.3e+02       3      20 ..     488     505 ..     487     531 .. 0.80
   4 ?   -0.6   0.0       2.7   9.1e+02     258     268 ..     544     554 ..     531     554 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.14
                            AAA_21   3 vliGpNgsGKSnLLdald 20 
                                       +++Gp g+GK+ + +a  
  gi|298674960|ref|YP_003726710.1| 216 MVYGPSGTGKTLIAKAVA 233
                                       68***********99983 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.7
                            AAA_21 256 kkgsllliDEpEn 268
                                       + +s+++iDE+++
  gi|298674960|ref|YP_003726710.1| 270 DAPSIIFIDEIDS 282
                                       4459*******97 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.38
                            AAA_21   3 vliGpNgsGKSnLLdald 20 
                                       +l+Gp g+GK+ L +a +
  gi|298674960|ref|YP_003726710.1| 488 ILYGPPGTGKTMLAKAVS 505
                                       79***********99985 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 2.7
                            AAA_21 258 gsllliDEpEn 268
                                       +++++iDE+++
  gi|298674960|ref|YP_003726710.1| 544 PTVIFIDEIDS 554
                                       29*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (733 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        54  (0.00301188); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              54  [number of targets reported over threshold]
# CPU time: 0.74u 0.31s 00:00:01.05 Elapsed: 00:00:00.47
# Mc/sec: 4694.25
//
Query:       gi|298674961|ref|YP_003726711.1|  [L=232]
Description: hypothetical protein Metev_1027 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.3e-92  308.3   0.0    3.7e-92  308.2   0.0    1.0  1  4HFCP_synth  4-HFC-P synthase
     0.0012   18.6   0.0      0.012   15.4   0.0    2.1  2  QRPTase_C    Quinolinate phosphoribosyl transferase, C-termin


Domain annotation for each model (and alignments):
>> 4HFCP_synth  4-HFC-P synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  308.2   0.0   4.1e-96   3.7e-92       1     227 [.       3     228 ..       3     229 .. 0.99

  Alignments for each domain:
  == domain 1  score: 308.2 bits;  conditional E-value: 4.1e-96
                                       EEE--SSHHHHHHHHHHT-SEEEE--GGG-TT----HHHHHHHHHHS-TTSEEEEEEEEE-S-HHHHHHHHHHHHHT CS
                       4HFCP_synth   1 LLvSvrnleEaelalaggadiiDvKnPaeGsLGalfpevireivevvpgsvpvSaaiGdlpekpgtvslaalgaaaa 77 
                                       LLvS++n+eEa +a++ggadiiDvKnP+eGsLGa+fp+vi+e+++ +++++p+Sa+iGd+++kpgt+slaa+gaa++
  gi|298674961|ref|YP_003726711.1|   3 LLVSPINTEEAVSACNGGADIIDVKNPKEGSLGANFPWVIKEVKDSIDSKKPISATIGDFNYKPGTASLAAYGAASS 79 
                                       8**************************************************************************** PP

                                       T-SEEEEEE-S--SHHHHHHHHHHHHHHHHHH-TTSEEEEEEETTGGGTT---GGGHHHHHHHHT-SEEEEE-SS-S CS
                       4HFCP_synth  78 gvdyvKvGlaglkkeeealealkavvkavkeedkekkvvavlyaDaervasvsplellelaaeagaagvmlDTadKd 154
                                       g++y+KvGl+++++ee+a+++l++++++vk++d++kkvva++y+D++r++s+sp++l+e+ a+ag+++vm+DT +Kd
  gi|298674961|ref|YP_003726711.1|  80 GAEYIKVGLYDIQTEEQAYDMLENITNSVKSYDSNKKVVACGYSDYQRINSISPMKLPEIGANAGVDLVMMDTGHKD 156
                                       ***************************************************************************** PP

                                       S--HHHHS-HHHHHHHHHHHHHTT-EEEE-SS--GGGHHHHHHTT-SEEEESGGGBTTSSTTSSB-HHHHHHH CS
                       4HFCP_synth 155 gkslldflseeelaefveeareaglltaLAGslkledlpaLkklkpdilGvRgavCeegdRngkidaelvekl 227
                                       gks++ f+se++l+efv+ a+++gl+taLAGs+k++dl+ Lk++kpdi+GvRg+vC +gdRn+ +++elv+k+
  gi|298674961|ref|YP_003726711.1| 157 GKSTFYFMSENTLSEFVDLAHSYGLETALAGSIKFDDLEPLKRIKPDIIGVRGIVC-GGDRNTIVQEELVTKV 228
                                       ********************************************************.*************997 PP

>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.031   2.8e+02      85     113 ..       5      33 ..       1      58 [. 0.77
   2 !   15.4   0.0   1.4e-06     0.012      26     154 ..      65     207 ..      43     213 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.031
                                       EEESSHHHHHHHHHHT-SEEEEES--HHH CS
                         QRPTase_C  85 vevesleeleevleaeadiimLDnfsvee 113
                                       v   + ee+  + + +adii + n++   
  gi|298674961|ref|YP_003726711.1|   5 VSPINTEEAVSACNGGADIIDVKNPKEGS 33 
                                       55568899999*********999997644 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.4e-06
                                       -TTTHHHHHHHHHHTTSB--TSSTTTSEEE-HHHHHHHSSHHHHHHHHHHHHTTTSEEEEEESSHHHHHHHHH.... CS
                         QRPTase_C  26 tPglrllekyAvliGGgdnhrlgLsdmvlikdnhiaaagsiveavksvreavdkevkievevesleeleevle.... 98 
                                        Pg++ l+ y +   G++  ++gL+d+ +       ++ +i++ vks +++ +    +    + ++ ++ +      
  gi|298674961|ref|YP_003726711.1|  65 KPGTASLAAYGAASSGAEYIKVGLYDIQTEE-QAYDMLENITNSVKSYDSNKKV---VACGYSDYQRINSISPmklp 137
                                       69************************98855.5567788899999998877532...45555555555555444556 PP

                                       .....HT-SEEEEES-...........-HHHHHHHHHHHHHHSTTSEEEEESS--TTTHHHHHCTT-SEEEE CS
                         QRPTase_C  99 .....aeadiimLDnf...........sveelkkaveelkeknkrvlievSGgvtlenveeyaksgvdvisv 154
                                            a++d++m+D+            s ++l ++v++   +   +++  +G+++ +++e +++++ d+i+v
  gi|298674961|ref|YP_003726711.1| 138 eiganAGVDLVMMDTGhkdgkstfyfmSENTLSEFVDLA--HSYGLETALAGSIKFDDLEPLKRIKPDIIGV 207
                                       6665688********999999998888889999999954..444489999************9999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1781.22
//
Query:       gi|298674962|ref|YP_003726712.1|  [L=235]
Description: histidine biosynthesis protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.5e-33  114.1   0.7    7.4e-33  113.9   0.7    1.0  1  His_biosynth  Histidine biosynthesis protein
  ------ inclusion threshold ------
      0.035   13.4   1.1       0.33   10.2   0.2    2.0  2  ThiG          Thiazole biosynthesis protein ThiG


Domain annotation for each model (and alignments):
>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.9   0.7   8.3e-37   7.4e-33       3     228 ..       5     229 ..       3     230 .. 0.87

  Alignments for each domain:
  == domain 1  score: 113.9 bits;  conditional E-value: 8.3e-37
                                       EEEEEEETTEEEEECTTCS........TCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHC..TTHHHHHHHHHHHH CS
                      His_biosynth   3 ipalDlkdGkvVrlvkGdr........fqelryagdpvelakryeeegadelhvvDldaak..egreanldlveeia 69 
                                       + +lD+ + +vV+ + Gdr         ++   + +p+   +  e    +e++ +Dl+  +   + ++n+++++ i 
  gi|298674962|ref|YP_003726712.1|   5 VLVLDIYNRNVVHAKGGDRkhyhpinqTSKICNSSNPI---EIIETVRPKEVYAADLNILQgtGSCNTNYEVISSIS 78 
                                       669****************6666653333333334444...55566678888888887766445678999******* PP

                                       HH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEECEEEEETTTTEEEE CS
                      His_biosynth  70 eevfipvqvGGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarrgykvaikgwreetg 146
                                       e+     +v+ GI s++d+ ++l++ adk+++gt+++ + ++i+++a  +++ +i v+iD +++ k++    +    
  gi|298674962|ref|YP_003726712.1|  79 EK--TSTMVDMGITSFNDISDALSI-ADKIVLGTETA-SIDVISKAAYYYPG-RINVSIDKKDN-KILKTDPDIP-- 147
                                       **..8999*****************.*********86.678***********.*******9999.7777666666.. PP

                                       EEHHHHHHHHHHTT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTCSEEEESHHH CS
                      His_biosynth 147 ldavelakkleelgageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelksegvdavivgsal 223
                                        +++e++k l++++++++++ d+d++Gt sG+d e+++++ +  k+ ++ +GGv++++d+++lk++gv++++v++al
  gi|298674962|ref|YP_003726712.1| 148 DNPFEIIKILNDVNIQDVIVLDMDSVGTSSGVDSEFLSNVVSCSKHDILLGGGVRDVDDIETLKNAGVKGALVATAL 224
                                       79*************************************************************************** PP

                                       HTTSS CS
                      His_biosynth 224 yegel 228
                                       +++++
  gi|298674962|ref|YP_003726712.1| 225 HNRSI 229
                                       *9876 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1    0.0098        88     156     205 ..      63     109 ..      56     124 .. 0.73
   2 ?   10.2   0.2   3.7e-05      0.33     141     217 ..     158     234 ..     114     235 .] 0.87

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.0098
                                       TS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESH CS
                              ThiG 156 GsglGllnkealkiiieeakvPvivDAGigspsdaaqamelGadavllnt 205
                                       G+g   +n e+++ i e+++   +vD Gi s +d+  a+ +  d ++l t
  gi|298674962|ref|YP_003726712.1|  63 GTGSCNTNYEVISSISEKTS--TMVDMGITSFNDISDALSIA-DKIVLGT 109
                                       66666777777888877665..68999999999999999885.4444444 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 3.7e-05
                                       HHTT-SEBEEB.SSSTTS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHH CS
                              ThiG 141 eevGcaavmPl.aapiGsglGllnkealkiiieeakvPvivDAGigspsdaaqamelGadavllntavaeakdpvam 216
                                       ++v ++ v+ l    +G++ G+   e+l+ +++  k  +++  G++   d+ +  + G+++ l++ta+ + + pv+m
  gi|298674962|ref|YP_003726712.1| 158 NDVNIQDVIVLdMDSVGTSSGVD-SEFLSNVVSCSKHDILLGGGVRDVDDIETLKNAGVKGALVATALHNRSIPVEM 233
                                       55555554444245799999986.57899999999***************************************999 PP

                                       H CS
                              ThiG 217 A 217
                                        
  gi|298674962|ref|YP_003726712.1| 234 V 234
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.92
# Mc/sec: 775.44
//
Query:       gi|298674963|ref|YP_003726713.1|  [L=79]
Description: hypothetical protein Metev_1029 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 536.55
//
Query:       gi|298674964|ref|YP_003726714.1|  [L=199]
Description: thymidylate kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.5e-45  153.1   0.0    7.5e-45  152.9   0.0    1.0  1  Thymidylate_kin  Thymidylate kinase
    1.3e-08   35.0   0.1    2.6e-08   34.0   0.1    1.5  1  dNK              Deoxynucleoside kinase
    2.6e-06   28.0   0.0    5.5e-06   27.0   0.0    1.5  1  AAA_18           AAA domain
    1.3e-05   25.4   0.0    3.4e-05   24.0   0.0    1.8  1  AAA_33           AAA domain
     0.0025   17.1   0.0     0.0055   16.0   0.0    1.8  1  Zeta_toxin       Zeta toxin
     0.0049   17.1   0.0     0.0065   16.7   0.0    1.3  1  AAA_28           AAA domain
  ------ inclusion threshold ------
      0.013   15.8   0.0       0.48   10.7   0.0    2.2  2  AAA_22           AAA domain
      0.042   13.9   0.3        1.2    9.2   0.0    2.3  2  AAA_14           AAA domain
       0.05   14.0   0.0        2.1    8.8   0.0    2.5  1  AAA_17           AAA domain


Domain annotation for each model (and alignments):
>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.9   0.0   3.8e-48   7.5e-45       1     185 []       8     191 ..       8     191 .. 0.92

  Alignments for each domain:
  == domain 1  score: 152.9 bits;  conditional E-value: 3.8e-48
                                       EEESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHHHHHHHTTHHHHHHHH CS
                   Thymidylate_kin   1 iEGlDGaGKttqaellkerlkeegikvvltrepggteiGekirelllkeeeleeqteallfaadriehleekikpal 77 
                                       +EG+DG+GK+t++e l+++ + +   vv+trep+++ iG+ + +++    + ++ +e +lf+ d++eh+++ i pa+
  gi|298674964|ref|YP_003726714.1|   8 LEGIDGSGKSTITERLMNHPSLSN--VVFTREPTKNWIGKAVEQAIR--SDTDQIAEFFLFTSDHAEHISKTIYPAI 80 
                                       6****************9977666..9******************99..8999999********************* PP

                                       HTT-EEEEES-HHHHHHHHHTTTTTT....CHHHHHHGGGTTSE-SEEEEEESSHHHHHTSCCTTSSTTTSHHHHHH CS
                   Thymidylate_kin  78 kqgktvivdRylfSslaYqgakegvd....ldlvlslnedvllkPdltflldvdpevalkRlakrdeldeeeeeqld 150
                                       ++gk vi+dRyl+S +aYqg++ +      +++v+++++  +  Pdlt++ld+dpe a++R++ r+e  ++++e+ +
  gi|298674964|ref|YP_003726714.1|  81 ENGKNVISDRYLDSRCAYQGVTLSEKfedpIKWVQKIHDGWTIIPDLTIFLDIDPEFAIERCGNRGE--QTKFEKME 155
                                       ********************95543311336788888888777************************..9******* PP

                                       HHHHHHHHHHHHHH.TTSTEEEEETTS-HHHHHHHH CS
                   Thymidylate_kin 151 flrkvrerylelak.ederiliidasksieevheeI 185
                                       fl++v  +y++l+k ++er++++d s++ieev++++
  gi|298674964|ref|YP_003726714.1| 156 FLQQVYDNYQRLMKdNPERFVVVDSSQPIEEVEKDV 191
                                       ********************************9975 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.1   1.3e-11   2.6e-08       1     199 [.       6     195 ..       6     199 .] 0.73

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 1.3e-11
                                       EEEEESTTSSHHHHHHHHHCCST...CEEEE-HHHHCCSSSSHHHHHHHHSHHHHH..HHHHHHHHHHHHHHHHCHH CS
                               dNK   1 ivveGnIgaGKstlvklLskklg...vkvfeEpvdkwtnvqknlLekfYkdpsrws..falqtyvllsrlkqqleal 72 
                                       i++eG  g+GKst++++L ++     v++ +Ep ++w  + k + + +  d  + +  f +      +  k +  a+
  gi|298674964|ref|YP_003726714.1|   6 ITLEGIDGSGKSTITERLMNHPSlsnVVFTREPTKNW--IGKAVEQAIRSDTDQIAefFLFTSDHAEHISKTIYPAI 80 
                                       789***************998655459999*******..55555555555555544225666666777777777777 PP

                                       SSS-EEEEES-HHHHHHTHHHHHHHTTSS-HHHHHHHHHHHHHHH..HHCCH-SEEEEEE--HHHHHHHHHHCTTCC CS
                               dNK  73 atkqvvvleRsiysdryiFakalaekgtlseeelkiykelldnll..eelakpdlliYLkasletclerikkRgree 147
                                       +++++v+ +R   s +       a +g+   e+++   ++ +++   +++  pdl i+L++++e   er  +Rg++ 
  gi|298674964|ref|YP_003726714.1|  81 ENGKNVISDRYLDSRC-------AYQGVTLSEKFEDPIKWVQKIHdgWTII-PDLTIFLDIDPEFAIERCGNRGEQT 149
                                       9999999999887777.......3455555566666666666666444466.9*********************998 PP

                                       CTTS-HHHHHHHHHHHHHHHTSGGCS-EEEEETSS.-TTTHCCHHHHHHHHH CS
                               dNK 148 ekkieldYlekLhekyeewlkklnevpvlvidveeldlvaeeekredvveev 199
                                        k  ++++l+++  +y+  +k  n    +v+d ++      ee ++dvv+ +
  gi|298674964|ref|YP_003726714.1| 150 -KFEKMEFLQQVYDNYQRLMKD-NPERFVVVDSSQ----PIEEVEKDVVDII 195
                                       .455788999999999988888.555677777777....5666666666655 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   2.7e-09   5.5e-06       1     122 [.       6     150 ..       6     161 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 2.7e-09
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskrldedkldklldaleenss........ 69 
                                       I l G+ G+GK+t++++L ++      l+ v++ +++   +  +a+++  r d+d+ ++ +     +++        
  gi|298674964|ref|YP_003726714.1|   6 ITLEGIDGSGKSTITERLMNH----PSLSNVVFTREPTKNWIGKAVEQAIRSDTDQIAEFFLFTSDHAEhisktiyp 78 
                                       899***************776....69*****************888888888888777776666666688899999 PP

                            AAA_18  70 aleegknlvidghlaeleseaakdikk.......................vvLtaspeelleRlekRgyeeakike 122
                                       a e+gkn++ d  l   + ++ + +                         ++L+ +pe  +eR  +Rg+++    +
  gi|298674964|ref|YP_003726714.1|  79 AIENGKNVISDRYLDSRCAYQGVTLSEkfedpikwvqkihdgwtiipdltIFLDIDPEFAIERCGNRGEQT----K 150
                                       8899999854544444444444444445566999999*******************************765....3 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   1.7e-08   3.4e-05       1     122 [.       5     149 ..       5     172 .. 0.64

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.7e-08
                            AAA_33   1 lvllvGlpGsGKstlaerllkklg...avllssdt..lrrrlfg....tdqqsktdytrvldrlyqilnelarkals 68 
                                       l+ l G  GsGKst  erl+++     +v+ +++t  ++ + ++    +d +++ +   ++++  +++++++  a +
  gi|298674964|ref|YP_003726714.1|   5 LITLEGIDGSGKSTITERLMNHPSlsnVVFTREPTknWIGKAVEqairSDTDQIAEFFLFTSDHAEHISKTIYPAIE 81 
                                       68899***************6666999888888888855555552333555556666668888999999******** PP

                            AAA_33  69 agrnvildatnlsrrer.........arflklarrlg.....vpvrivvvetdeetlkeRlakRaang 122
                                        g+nvi d  + sr++          ++ +k++++++      p++ ++++ d+e + eR   R +++
  gi|298674964|ref|YP_003726714.1|  82 NGKNVISDRYLDSRCAYqgvtlsekfEDPIKWVQKIHdgwtiIPDLTIFLDIDPEFAIERCGNRGEQT 149
                                       *******8774444333233333222333333332221111145888888888888888888888864 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.7e-06    0.0055      17     107 ..       4      95 ..       2     194 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.7e-06
                        Zeta_toxin  17 klillgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPeyee.ilkadpkkase..ltqkdaselvekllqe 90 
                                       kli l G  G+GKs++ e l +      + v++ +   ++ + ++ e +++ d ++ +e  l+ +d  e   k++  
  gi|298674964|ref|YP_003726714.1|   4 KLITLEGIDGSGKSTITERLMNHP--SLSNVVFTREPTKNWIGKAVEqAIRSDTDQIAEffLFTSDHAEHISKTIYP 78 
                                       68889999************9996..8899999999****998875515667888888733568999999999**** PP

                        Zeta_toxin  91 aiengyniivegtlrsp 107
                                       aieng n+i ++ l+s 
  gi|298674964|ref|YP_003726714.1|  79 AIENGKNVISDRYLDSR 95 
                                       ***********999874 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   3.3e-06    0.0065       2     145 ..       6     164 ..       5     186 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.3e-06
                            AAA_28   2 ivitGgestGKTtlleaLaar....gypvvpEaareileeklakgedalpwv.edllafaervleeqleeeaaa.aa 72 
                                       i + G  ++GK+t++e+L ++    +++  +E+    + +  ++  +   ++ +++  f +   e+  ++   a ++
  gi|298674964|ref|YP_003726714.1|   6 ITLEGIDGSGKSTITERLMNHpslsNVVFTREPTKNWIGKAVEQAIRSDTDQiAEFFLFTSDHAEHISKTIYPAiEN 82 
                                       6678889**************987656666*****99988885554422222355666665444444444444469* PP

                            AAA_28  73 nkvlfcDrglldtlaYaraygge.aeae..leaaarekry...dlvfllppapei..dddgeRre.dleereaider 140
                                       +k +++Dr l   +aY  +   e  e +  +++++        dl ++l+ +pe+  ++ g+R e +  e +++ ++
  gi|298674964|ref|YP_003726714.1|  83 GKNVISDRYLDSRCAYQGVTLSEkFEDPikWVQKIHDGWTiipDLTIFLDIDPEFaiERCGNRGEqTKFEKMEFLQQ 159
                                       ****************9555444244433366666644434558888888888665677788854243444444444 PP

                            AAA_28 141 lreal 145
                                       + + +
  gi|298674964|ref|YP_003726714.1| 160 VYDNY 164
                                       44444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00024      0.48       5      29 ..       3      27 ..       1      87 [. 0.84
   2 ?    3.3   0.0     0.046        92      68     103 ..     149     184 ..     128     196 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00024
                            AAA_22  5 agilvvtGesGtGKTtllrrlleql 29
                                       +++++ G  G+GK+t  +rl++  
  gi|298674964|ref|YP_003726714.1|  3 GKLITLEGIDGSGKSTITERLMNHP 27
                                      678999***************9976 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.046
                            AAA_22  68 lkaerlsseellealeqalrarav...ielliiDEaqhl 103
                                       +k    ++ e+l++++++ ++ ++    +++++D  q +
  gi|298674964|ref|YP_003726714.1| 149 TKF---EKMEFLQQVYDNYQRLMKdnpERFVVVDSSQPI 184
                                       344...7888999999999999999999******98877 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0006       1.2       2      27 ..       3      28 ..       2      87 .. 0.77
   2 ?    2.9   0.1     0.051     1e+02      42      86 ..     150     194 ..     139     198 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0006
                            AAA_14  2 rkilvitGaRrvGKTtllkqlikell 27
                                      +k+++++G+  +GK+t+ ++l+++  
  gi|298674964|ref|YP_003726714.1|  3 GKLITLEGIDGSGKSTITERLMNHPS 28
                                      68999***************997654 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.051
                            AAA_14  42 rdkkladpekllelileklkeekktylflDEiqevpewekalksl 86 
                                       +++k++  +++++ +++++k++ +++++ D  q ++e+ek + ++
  gi|298674964|ref|YP_003726714.1| 150 KFEKMEFLQQVYDNYQRLMKDNPERFVVVDSSQPIEEVEKDVVDI 194
                                       444555445677777777666788999999999999998877665 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0011       2.1       2      22 ..      10      30 ..       9     158 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0011
                                      E-TTSSHHHHHHHHHHHHTEE CS
                            AAA_17  2 GgPGsGKgtqceklvekygft 22
                                      G+ GsGK+t+ e+l+ +  ++
  gi|298674964|ref|YP_003726714.1| 10 GIDGSGKSTITERLMNHPSLS 30
                                      788999999999997765444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      652  (0.0363657); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1432.18
//
Query:       gi|298674965|ref|YP_003726715.1|  [L=45]
Description: hypothetical protein Metev_1031 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00014   21.9   0.3    0.00015   21.8   0.3    1.0  1  HypA            Hydrogenase/urease nickel incorporation, meta
    0.00017   21.6   2.2    0.00024   21.1   2.2    1.3  1  Zn-ribbon_8     Zinc ribbon domain
     0.0065   16.5   0.3     0.0073   16.3   0.3    1.1  1  zinc_ribbon_6   Zinc-ribbon
     0.0085   15.8   2.1       0.02   14.6   0.1    2.0  2  Ribosomal_S27e  Ribosomal protein S27
     0.0088   16.0   0.9      0.041   13.8   0.1    2.0  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
  ------ inclusion threshold ------
      0.023   14.5   4.8        1.8    8.5   0.5    2.1  2  TFIIS_C         Transcription factor S-II (TFIIS)
      0.037   13.8   1.1        0.4   10.5   0.4    2.0  2  zinc_ribbon_5   zinc-ribbon domain
      0.039   13.9   0.8      0.056   13.4   0.8    1.3  1  Prok-RING_1     Prokaryotic RING finger family 1
      0.048   13.0   0.2      0.048   13.0   0.2    1.0  1  FAM35_C         Protein family FAM35, C-terminal
      0.052   13.2   1.0      0.095   12.4   1.0    1.5  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
       0.14   12.1   4.0        1.1    9.2   0.8    2.1  2  zinc_ribbon_4   zinc-ribbon domain
        0.2   11.4   5.7        2.5    7.9   0.6    2.1  2  Rubredoxin_2    Rubredoxin metal binding domain
       0.22   11.7   4.7        1.6    9.0   0.2    2.1  2  zf-AN1          AN1-like Zinc finger
       0.75   10.8   4.5        9.9    7.3   0.6    2.2  2  zf-C2H2_4       C2H2-type zinc finger
        1.2    9.7   4.0          6    7.5   0.5    2.2  2  zf-C2H2         Zinc finger, C2H2 type
        2.6    7.9   5.4         11    5.9   0.2    2.1  2  zf-H2C2_5       C2H2-type zinc-finger domain


Domain annotation for each model (and alignments):
>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.3   1.3e-07   0.00015      64      98 ..       7      43 ..       4      45 .] 0.84

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.3e-07
                                      EEEE--EEEETTTS-EEECHHH..HHS-TTTSSS-EE CS
                              HypA 64 ieevpvkvrCreCgkefeleek..alrCpkCgsadve 98
                                      i++  v +rC+ C+ ef+++ +   ++Cp+Cgs+d++
  gi|298674965|ref|YP_003726715.1|  7 INQSMVFFRCNICSFEFQEDPNfmPIKCPQCGSEDTQ 43
                                      67778899**********88754567*******9976 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   2.2   2.2e-07   0.00024       6      38 ..      14      44 ..      13      45 .] 0.81

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.2e-07
                       Zn-ribbon_8  6 YrCeeCghefevlqsisdapltaCPeCgs.evrr 38
                                      +rC+ C  ef +   ++   +++CP+Cgs +++r
  gi|298674965|ref|YP_003726715.1| 14 FRCNICSFEFQEDPNFM---PIKCPQCGSeDTQR 44
                                      8******8887555555...677******99998 PP

>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.3   6.5e-06    0.0073      23      58 ..       7      42 ..       4      43 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.5e-06
                     zinc_ribbon_6 23 yknkkvkilCnDCekksevkfhvlglkCkeCgSYNT 58
                                      +++++v   Cn C+ + + +  ++ +kC +CgS +T
  gi|298674965|ref|YP_003726715.1|  7 INQSMVFFRCNICSFEFQEDPNFMPIKCPQCGSEDT 42
                                      577889999************************777 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.2      0.23   2.5e+02      27      33 ..      14      20 ..       6      26 .. 0.74
   2 !   14.6   0.1   1.8e-05      0.02       4      18 ..      28      42 ..      25      43 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.23
                                      EEESSST CS
                    Ribosomal_S27e 27 vkCisCg 33
                                        C +C+
  gi|298674965|ref|YP_003726715.1| 14 FRCNICS 20
                                      4799998 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.8e-05
                                      -EEEEE-TTTS-EEE CS
                    Ribosomal_S27e  4 kFldvkCpdCenetv 18
                                      +F+ +kCp+C+ e +
  gi|298674965|ref|YP_003726715.1| 28 NFMPIKCPQCGSEDT 42
                                      8*********99875 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.39   4.4e+02      22      29 ..      16      23 ..       9      24 .. 0.78
   2 !   13.8   0.1   3.6e-05     0.041       3      13 ..      31      42 ..      29      42 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.39
                    PhnA_Zn_Ribbon 22 CpeCahEw 29
                                      C  C+ E+
  gi|298674965|ref|YP_003726715.1| 16 CNICSFEF 23
                                      88888887 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 3.6e-05
                    PhnA_Zn_Ribbon  3 p.kCplCaSeyt 13
                                      p kCp+C+Se t
  gi|298674965|ref|YP_003726715.1| 31 PiKCPQCGSEDT 42
                                      669******965 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.5    0.0016       1.8      26      39 .]      11      24 ..       8      24 .. 0.87
   2 ?    8.4   0.4    0.0017       1.9       1      10 [.      32      41 ..      32      43 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0016
                           TFIIS_C 26 tvfykCtkCghrWr 39
                                       vf++C+ C ++++
  gi|298674965|ref|YP_003726715.1| 11 MVFFRCNICSFEFQ 24
                                      79*******99985 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0017
                           TFIIS_C  1 akCpkCgsre 10
                                      +kCp+Cgs++
  gi|298674965|ref|YP_003726715.1| 32 IKCPQCGSED 41
                                      69*****987 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.14   1.5e+02      19      32 ..       7      20 ..       3      24 .. 0.62
   2 ?   10.5   0.4   0.00036       0.4       1      10 [.      30      39 ..      30      40 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.14
                     zinc_ribbon_5 19 lKksgkkVrCakCa 32
                                      + +s +  rC  C 
  gi|298674965|ref|YP_003726715.1|  7 INQSMVFFRCNICS 20
                                      55566666776664 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00036
                     zinc_ribbon_5  1 LiirCpdCdt 10
                                      + i+Cp+C++
  gi|298674965|ref|YP_003726715.1| 30 MPIKCPQCGS 39
                                      669*****98 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.8     5e-05     0.056       6      28 ..      15      39 ..      11      43 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5e-05
                       Prok-RING_1  6 kCpvCgkelkeedDi..VvCpeCgt 28
                                      +C++C+ e++e+     + Cp+Cg+
  gi|298674965|ref|YP_003726715.1| 15 RCNICSFEFQEDPNFmpIKCPQCGS 39
                                      7***********7763468****97 PP

>> FAM35_C  Protein family FAM35, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   4.3e-05     0.048      44      74 ..       8      39 ..       2      45 .] 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.3e-05
                           FAM35_C 44 s.ditytGCakCgleletDenkiykqCysCLp 74
                                      + ++++  C+ C+ e + D n +  +C +C  
  gi|298674965|ref|YP_003726715.1|  8 NqSMVFFRCNICSFEFQEDPNFMPIKCPQCGS 39
                                      44899*************************65 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.0   8.5e-05     0.095       3      25 ..      16      39 ..      14      40 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.5e-05
                                      -SSS--B--.--SSS----SSS-- CS
                    DNA_RNApol_7kD  3 CgeCgaevs.lkkgdpiRCkeCGh 25
                                      C  C+ e++ + +  pi+C +CG+
  gi|298674965|ref|YP_003726715.1| 16 CNICSFEFQeDPNFMPIKCPQCGS 39
                                      888999998788889********6 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.032        36       3      13 ..      14      24 ..       7      28 .. 0.85
   2 ?    9.2   0.8   0.00099       1.1       1      10 [.      30      39 ..      30      40 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.032
                     zinc_ribbon_4  3 itCpsCkakye 13
                                      ++C  C+++++
  gi|298674965|ref|YP_003726715.1| 14 FRCNICSFEFQ 24
                                      68999999986 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00099
                     zinc_ribbon_4  1 MkitCpsCka 10
                                      M i Cp+C++
  gi|298674965|ref|YP_003726715.1| 30 MPIKCPQCGS 39
                                      899*****86 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.5    0.0059       6.6       1      10 [.      14      23 ..      14      25 .. 0.88
   2 ?    7.9   0.6    0.0022       2.5      16      22 ..      33      39 ..      33      44 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0059
                      Rubredoxin_2  1 YvCsqCGfes 10
                                      ++C+ C+fe+
  gi|298674965|ref|YP_003726715.1| 14 FRCNICSFEF 23
                                      8*******97 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0022
                      Rubredoxin_2 16 rCpsCgs 22
                                      +Cp+Cgs
  gi|298674965|ref|YP_003726715.1| 33 KCPQCGS 39
                                      7999997 PP

>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.8     0.024        27      11      23 ..      11      23 ..       5      25 .. 0.77
   2 ?    9.0   0.2    0.0014       1.6      11      21 ..      29      39 ..      24      40 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.024
                            zf-AN1 11 flpfkCryCgkvF 23
                                      ++ f+C+ C+ +F
  gi|298674965|ref|YP_003726715.1| 11 MVFFRCNICSFEF 23
                                      345******9877 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0014
                            zf-AN1 11 flpfkCryCgk 21
                                      f+p+kC++Cg 
  gi|298674965|ref|YP_003726715.1| 29 FMPIKCPQCGS 39
                                      899******96 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.6    0.0088       9.9       1      11 [.      14      22 ..      14      29 .. 0.77
   2 ?    5.6   0.2     0.032        36       2       7 ..      33      38 ..      32      42 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0088
                         zf-C2H2_4  1 fkCpiCgksFs 11
                                      f+C iC  sF 
  gi|298674965|ref|YP_003726715.1| 14 FRCNIC--SFE 22
                                      89****..664 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.032
                         zf-C2H2_4  2 kCpiCg 7 
                                      kCp+Cg
  gi|298674965|ref|YP_003726715.1| 33 KCPQCG 38
                                      8****6 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.5    0.0053         6       1      10 [.      14      23 ..      14      26 .. 0.91
   2 ?    3.7   0.2     0.087        97       2       7 ..      33      38 ..      32      43 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0053
                                      EEETTTTEEE CS
                           zf-C2H2  1 ykCpdCgksF 10
                                      ++C++C+  F
  gi|298674965|ref|YP_003726715.1| 14 FRCNICSFEF 23
                                      8******988 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.087
                                      EETTTT CS
                           zf-C2H2  2 kCpdCg 7 
                                      kCp Cg
  gi|298674965|ref|YP_003726715.1| 33 KCPQCG 38
                                      8****8 PP

>> zf-H2C2_5  C2H2-type zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.2    0.0096        11       1       8 [.      14      21 ..      14      22 .. 0.93
   2 ?    4.5   0.9     0.027        30       2       6 ..      33      37 ..      33      38 .. 0.96

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0096
                         zf-H2C2_5  1 YKCsqCDY 8 
                                      ++C+ C++
  gi|298674965|ref|YP_003726715.1| 14 FRCNICSF 21
                                      8******9 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.027
                         zf-H2C2_5  2 KCsqC 6 
                                      KC+qC
  gi|298674965|ref|YP_003726715.1| 33 KCPQC 37
                                      9**** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 339.21
//
Query:       gi|298674966|ref|YP_003726716.1|  [L=222]
Description: hypothetical protein Metev_1032 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.7e-65  218.5   0.0    8.7e-65  218.3   0.0    1.0  1  DUF166    Domain of unknown function
    8.5e-05   22.7   0.0    0.00017   21.7   0.0    1.5  1  DapB_N    Dihydrodipicolinate reductase, N-terminus


Domain annotation for each model (and alignments):
>> DUF166  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.3   0.0   9.7e-69   8.7e-65       2     219 ..       6     217 ..       5     218 .. 0.98

  Alignments for each domain:
  == domain 1  score: 218.3 bits;  conditional E-value: 9.7e-69
                            DUF166   2 vltsgeyGervvenilnepdferslivavvevpeeldefiedpeelLpe......lkeaDiviaytlhpDlllelae 72 
                                       v+t+g+yG+r+++++++++df+    ++++e+p +l+efi++p+ ++++      +++aDi+i+y+lhpDl+ e+a+
  gi|298674966|ref|YP_003726716.1|   6 VITRGKYGKRLIDTLRSKSDFN----IVTAELPTKLPEFIDEPDVYFNNldldnkVFKADILITYSLHPDLTSEIAR 78 
                                       9*********************....9********************99999999********************** PP

                            DUF166  73 kakekkvkalivpaeapkaglrkelkekleelgievavpkpfCsleeegkpkideFleefGkPelevevkdgkikkV 149
                                       +a +++v+alivp  + + + ++el++ ++e+gi+++v++++C+l+  + p+++eF++ fG+P l+++ ++ ki++V
  gi|298674966|ref|YP_003726716.1|  79 IAGRSGVRALIVPGGTSR-APINELERYSKEYGIHIEVDDICCALD--SCPETSEFTSIFGRPALKIKTDERKITDV 152
                                       *****************9.**************************6..6**************************** PP

                            DUF166 150 eVlrsapCGstwyvakklkGkeveeaeekageahqsYpClAsmerdfelketklhkAgyihkeavekAlk 219
                                       +V+r+apCGstwy+a++l+G+++++a +  g+ +q+YpC+A+++     +++++h+++++hk+a+ekA++
  gi|298674966|ref|YP_003726716.1| 153 DVIRGAPCGSTWYMAENLIGTDIKDAASYGGLLIQQYPCRAVRG-----GKGGIHESAELHKKAIEKAIE 217
                                       ********************************************.....*******************98 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   1.9e-08   0.00017       9     118 ..       9     111 ..       2     115 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.9e-08
                                       TSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEB.SSHHHHHHH-SEEEE-S.-HHHHHHH CS
                            DapB_N   9 sGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavt.ddleevlekadvliDFT.tpeavlen 83 
                                       +G+ Gk++++++++++d+++v a   ++       + e+++    +v ++  dl++ + kad+li ++ +p+ + e 
  gi|298674966|ref|YP_003726716.1|   9 RGKYGKRLIDTLRSKSDFNIVTAELPTK-------LPEFIDE--PDVYFNnLDLDNKVFKADILITYSlHPDLTSEI 76 
                                       6********************9976666.......5555554..5555553678888888********99******* PP

                                       HHHHHHTT-EEEE--SS--HHHHHHHHHHTTTSEE CS
                            DapB_N  84 lklalekgvklViGTTGlseeelaeleelakkigv 118
                                       +++a ++gv++ i   G s++ ++ele+++k+ g+
  gi|298674966|ref|YP_003726716.1|  77 ARIAGRSGVRALIVPGGTSRAPINELERYSKEYGI 111
                                       *******************************9776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.34s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1298.61
//
Query:       gi|298674967|ref|YP_003726717.1|  [L=573]
Description: PHP domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-18   67.0   1.4    1.5e-16   60.5   0.1    3.6  3  HHH_8            Helix-hairpin-helix domain
    2.4e-16   59.7   0.0    5.3e-16   58.5   0.0    1.6  1  DNA_pol_B_thumb  DNA polymerase beta thumb
    1.7e-13   50.9   0.2    1.6e-09   38.2   0.0    3.7  5  HHH_5            Helix-hairpin-helix domain
    9.9e-07   29.2   0.6    2.4e-06   27.9   0.2    2.0  2  PHP              PHP domain
    2.3e-05   24.0   0.0     0.0085   15.9   0.0    3.0  2  HHH              Helix-hairpin-helix motif
    0.00012   21.8   0.0    0.00089   19.0   0.0    2.6  3  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
     0.0003   21.0   0.0      0.032   14.5   0.0    2.8  2  Cdd1             Pathogenicity locus
    0.00094   18.7   0.8     0.0027   17.2   0.0    2.2  3  RNase_P_p30      RNase P subunit p30
  ------ inclusion threshold ------
      0.041   14.0   0.0         17    5.6   0.0    2.8  2  TfoX_C           TfoX C-terminal domain
      0.041   14.1   0.3       0.24   11.6   0.0    2.4  2  DNA_pol_B_palm   DNA polymerase beta palm


Domain annotation for each model (and alignments):
>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.5   0.1   8.2e-20   1.5e-16       1      67 [.       3      71 ..       3      72 .. 0.96
   2 ?    1.9   0.0      0.16   2.9e+02      46      60 ..      91     104 ..      80     107 .. 0.77
   3 ?    0.8   0.1      0.36   6.5e+02      31      57 ..     112     136 ..     110     149 .. 0.76

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 8.2e-20
                                      HHHHHHHHHHHHHHHHHCT--CCCHHHHHHHHCCCCC-SS-HHHH.TT.HCTTSTT--HHHHHHHHHHH CS
                             HHH_8  1 NkeiadaLeeladllelkgedpfrvraYrrAaraiealpeeitsl.ee.eltklpgiGkkiaakieeil 67
                                      N++ia++++++a++le++++++++++aY rA   i++l+e+i++l e+ +l ++pg+Gk+  +ki  il
  gi|298674967|ref|YP_003726717.1|  3 NHDIARIFSKTAKMLEFQNASSYKIKAYNRASYRIKNLKEDINNLhEDdRLDSIPGVGKSFKNKIVDIL 71
                                      99*******************************************64479****************998 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.16
                                       TTHCTTSTT--HHHH CS
                             HHH_8  46 eeeltklpgiGkkia 60 
                                       ee l ++pg+G++i 
  gi|298674967|ref|YP_003726717.1|  91 EE-LMAIPGMGPRIT 104
                                       55.99*******996 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.36
                                       HHCCCCC-SS-HHHHTTHCTTSTT--H CS
                             HHH_8  31 AaraiealpeeitsleeeltklpgiGk 57 
                                        +r+i++l+e+ ++ +  +++lp++G+
  gi|298674967|ref|YP_003726717.1| 112 GIRTIDDLKEAART-HR-IRRLPNMGA 136
                                       58999999999999.66.999**9994 PP

>> DNA_pol_B_thumb  DNA polymerase beta thumb
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.5   0.0     3e-19   5.3e-16       3      70 .]     255     315 ..     253     315 .. 0.98

  Alignments for each domain:
  == domain 1  score: 58.5 bits;  conditional E-value: 3e-19
                                       HHHHS-HHHHHHHHHHHHCTTEEEETTEEE.......ETCCCEEEC-SSHHHHHHHCTS----GGGTT CS
                   DNA_pol_B_thumb   3 lyfTGsktFnrdlRrlakkkglkLnssglrdekgkaeddddgelvevetErdvfelLglpyipPeeRe 70 
                                       ++ TGsk++n++l+++a +++l+L++ gl        + +dg++++++tE d+++ +gl+yipPe+Re
  gi|298674967|ref|YP_003726717.1| 255 IHLTGSKKHNIHLQQIASSMNLHLSKFGLI-------NLEDGNKLTSKTENDIYQKMGLDYIPPELRE 315
                                       799***************************.......9*****************************7 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.039        69      34      45 ..      50      61 ..      37      73 .. 0.71
   2 !   19.2   0.0     8e-07    0.0014       3      46 ..      52     102 ..      50     103 .. 0.88
   3 !   38.2   0.0   8.9e-13   1.6e-09       2      56 ..      91     147 ..      90     148 .. 0.93
   4 ?   -3.9   0.0        10   1.8e+04      45      54 ..     151     160 ..     151     161 .. 0.82
   5 ?   -2.3   0.0       3.9     7e+03       7      49 ..     509     518 ..     507     520 .. 0.50

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.039
                                      HHHHHTSTTS-H CS
                             HHH_5 34 veeLakipGiGk 45
                                       ++L +ipG+Gk
  gi|298674967|ref|YP_003726717.1| 50 DDRLDSIPGVGK 61
                                      468888888887 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 8e-07
                                       HHHTSTT--HH...HHHHHHTTT.--SHHHHHHS...-HHHHHTSTTS-HH CS
                             HHH_5   3 eLlsvsGiGpk...tAlallsaG.iesvedlaaa...dveeLakipGiGkk 46 
                                        L s++G+G++    ++ +l++G ++ +e++ ++   ++eeL +ipG+G++
  gi|298674967|ref|YP_003726717.1|  52 RLDSIPGVGKSfknKIVDILNTGtFSEYEKIRQEipvNIEELMAIPGMGPR 102
                                       799*******96667777****98999******977789**********96 PP

  == domain 3  score: 38.2 bits;  conditional E-value: 8.9e-13
                                       HHHHTSTT--HHHHHHHHTT.T--SHHHHHHS-H.HHHHTSTTS-HHHHHHHHHHHH CS
                             HHH_5   2 eeLlsvsGiGpktAlallsa.Giesvedlaaadv.eeLakipGiGkktAeriilelk 56 
                                       eeL+ ++G+Gp++   l++  Gi++++dl++a++ +++ ++p +G+ + eri+ ++k
  gi|298674967|ref|YP_003726717.1|  91 EELMAIPGMGPRITQFLYKRlGIRTIDDLKEAARtHRIRRLPNMGAIKEERILNAIK 147
                                       89******************99********998538****************99887 PP

  == domain 4  score: -3.9 bits;  conditional E-value: 10
                                       HHHHHHHHHH CS
                             HHH_5  45 kktAeriile 54 
                                       k+ A+ri+le
  gi|298674967|ref|YP_003726717.1| 151 KRGADRILLE 160
                                       5679***998 PP

  == domain 5  score: -2.3 bits;  conditional E-value: 3.9
                                       STT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHH CS
                             HHH_5   7 vsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAe 49 
                                       +                                  +i +ktA+
  gi|298674967|ref|YP_003726717.1| 509 L---------------------------------NDINAKTAK 518
                                       4.................................455556655 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.2   1.4e-09   2.4e-06       1     165 [.     340     501 ..     340     503 .. 0.65
   2 ?   -3.6   0.0       6.8   1.2e+04      21      37 ..     514     530 ..     511     539 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.4e-09
                                       EEEE--CCC.--.S-H..HHHHHHHHHCT-SEEEEEEEEBTT............HHHHHHHHHHHHTTTTSEEEEEE CS
                                       xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP   1 dlHvHteys.lldgalsieelvkkakelglkaiaiTDhgnlf............gyvefykaakkkykagikpiiGl 64 
                                       dlH+H++ s ++ +++  +++++ a++lg++ +ai Dh+                 ++++++++ +y ++++++ G+
  gi|298674967|ref|YP_003726717.1| 340 DLHIHSNWSdGK-STI--QQIADNARSLGYEYVAICDHSKSRanasglsegqllRRMDEIEKINSRY-DDFRILAGT 412
                                       89*******444.777..**********************999********9999999999998888.8******** PP

                                       E.......................E....EHHHHHHHHHHHHH...........HHHHHH....S............ CS
                                       xxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx....xxxxxxxxxxxxx RF
                               PHP  65 eayvaddse.....kerpshltllaknqeGyknllkllskaylegf.yrkpridkellek....hsegLivlsgclk 131
                                       e++++ +       +               + + ++ +++a   gf ++k+ i+k ++++    + + L   +g + 
  gi|298674967|ref|YP_003726717.1| 413 ECDIKANASldynsN---------------ILEKMDIVIAAIHTGFdEDKKTITKRIVRAleneYVNVLAHPTGRRL 474
                                       *88887776222220...............22224444444444444444444444444422223122222333333 PP

                                       ......TTGGHHHHHHHHHHHHHHHC.T-EEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP 132 GevfealdlieveekaeealeelakifgdyiEin 165
                                       Ge +      e++   ++ +e+ +++ ++++Ein
  gi|298674967|ref|YP_003726717.1| 475 GERA------EYDVDMDKLMETAKRN-NKILEIN 501
                                       3222......3444466677777776.7777776 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 6.8
                                       HHHHHHCT-SEEEEEEE CS
                                       xxxxxxxxxxxxxxxxx RF
                               PHP  21 vkkakelglkaiaiTDh 37 
                                       +k+ake+g++ +  TD 
  gi|298674967|ref|YP_003726717.1| 514 AKTAKEMGIPLVINTDA 530
                                       58899999999988885 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.016        28      13      29 ..      53      69 ..      51      70 .. 0.81
   2 !   15.9   0.0   4.8e-06    0.0085       4      21 ..      84     101 ..      81     102 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.016
                                      HHTSTT-SHHHHHHHHH CS
                               HHH 13 LlalPGVGpktAeaIls 29
                                      L ++PGVG++  ++I +
  gi|298674967|ref|YP_003726717.1| 53 LDSIPGVGKSFKNKIVD 69
                                      789*****987777765 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 4.8e-06
                                       HHHTSSHHHHHTSTT-SH CS
                               HHH   4 glipasreeLlalPGVGp 21 
                                        +ip ++eeL+a+PG Gp
  gi|298674967|ref|YP_003726717.1|  84 QEIPVNIEELMAIPGMGP 101
                                       689**************9 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0     5e-07   0.00089       2      30 ..      92     121 ..      91     135 .. 0.87
   2 ?   -2.5   0.0       2.6   4.6e+03       3      18 ..     213     230 ..     212     231 .. 0.67
   3 ?   -4.0   0.0         8   1.4e+04      39      45 ..     302     308 ..     301     308 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 5e-07
                   DNA_pol_lambd_f   2 lFtkvyGVGpktAkkwyak.Girtledlra 30 
                                       +++ + G Gp++ + +y++ Girt++dl++
  gi|298674967|ref|YP_003726717.1|  92 ELMAIPGMGPRITQFLYKRlGIRTIDDLKE 121
                                       799**************************9 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.6
                   DNA_pol_lambd_f   3 FtkvyGVG..pktAkkwy 18 
                                       Ft++ GV     +A kw+
  gi|298674967|ref|YP_003726717.1| 213 FTRIKGVQtiLNKADKWV 230
                                       677777754456888887 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 8
                   DNA_pol_lambd_f  39 qqiGlky 45 
                                       q++Gl y
  gi|298674967|ref|YP_003726717.1| 302 QKMGLDY 308
                                       99***98 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.047        84       7      25 ..      52      70 ..      47      90 .. 0.78
   2 !   14.5   0.0   1.8e-05     0.032       5      39 ..      90     125 ..      87     143 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.047
                              Cdd1  7 elqdiPniGkalaedlvel 25
                                      +l +iP++Gk++ +++v++
  gi|298674967|ref|YP_003726717.1| 52 RLDSIPGVGKSFKNKIVDI 70
                                      799*********9998865 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.8e-05
                              Cdd1   5 lkelqdiPniGkalaedlv.elGirsveelkgedpe 39 
                                       ++el  iP+ G+++ + l+ +lGir++++lk+   +
  gi|298674967|ref|YP_003726717.1|  90 IEELMAIPGMGPRITQFLYkRLGIRTIDDLKEAART 125
                                       7899**************978**********97655 PP

>> RNase_P_p30  RNase P subunit p30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       3.4   6.1e+03      57      76 ..      20      39 ..      11      48 .. 0.65
   2 ?   -2.0   0.0       1.1     2e+03      22      54 ..     173     203 ..     162     225 .. 0.58
   3 !   17.2   0.0   1.5e-06    0.0027       2      95 ..     340     437 ..     339     479 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3.4
                                      HHHHHHH..HHSSEEEEEEE CS
                       RNase_P_p30 57 lkkelsglkllsRvtlvvsd 76
                                      ++ +++++k ++R    +++
  gi|298674967|ref|YP_003726717.1| 20 QNASSYKIKAYNRASYRIKN 39
                                      45566778888887665555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.1
                                       HHHHH-SEEEEEEEEEESS---HHHHH...... CS
                       RNase_P_p30  22 laelgytgvainftveaekekkpnasepikeel 54 
                                       l++  yt v +  +v+ +ke  +n +     + 
  gi|298674967|ref|YP_003726717.1| 173 LETIPYTKVSVVGSVRRQKETVNNINL--IVTT 203
                                       556666777777777644444444333..3333 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 1.5e-06
                                       EEEE-SH..........HHHHHHHHH-SEEEEEEEEEESS---HHHHH...........HHHHHHHH..HHSSEEEE CS
                       RNase_P_p30   2 dlnipwpsddskkks.rtiktlaelgytgvainftveaekekkpnase....pikeelkelkkelsglkllsRvtlv 73 
                                       dl+i+ + +d k++  +++  +++lgy+ vai+ + + ++ +    se    ++  e+++ +++  ++++l + ++ 
  gi|298674967|ref|YP_003726717.1| 340 DLHIHSNWSDGKSTIqQIADNARSLGYEYVAICDHSK-SRANASGLSEgqllRRMDEIEKINSRYDDFRILAGTECD 415
                                       55665554433333237999***************99.55555555556788777788888888888********** PP

                                       EEES-H.HHHHHHHHH--EEEE CS
                       RNase_P_p30  74 vsdpsklqrlskvrqkfdllav 95 
                                       ++ +++l  +s++  k+d++ +
  gi|298674967|ref|YP_003726717.1| 416 IKANASLDYNSNILEKMDIVIA 437
                                       ******************9864 PP

>> TfoX_C  TfoX C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0    0.0094        17       4      33 ..      92     122 ..      89     126 .. 0.85
   2 ?    5.6   0.1    0.0097        17       2      22 ..     125     146 ..     124     148 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0094
                            TfoX_C   4 rLkdLpNlglklerlL.kkaGIktveeLrel 33 
                                       +L  +p +g+++ + L k+ GI+t+++L+e 
  gi|298674967|ref|YP_003726717.1|  92 ELMAIPGMGPRITQFLyKRLGIRTIDDLKEA 122
                                       6888999*******994469********986 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0097
                            TfoX_C   2 knrLkdLpNlg.lklerlLkka 22 
                                       ++r+++LpN+g +k er+L+++
  gi|298674967|ref|YP_003726717.1| 125 THRIRRLPNMGaIKEERILNAI 146
                                       689*******956899999987 PP

>> DNA_pol_B_palm  DNA polymerase beta palm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00014      0.24      11      50 ..     166     204 ..     156     230 .. 0.75
   2 ?   -1.4   0.1       1.4   2.6e+03      43      73 ..     432     461 ..     430     468 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
                                       HHHHHHHHHHH-TT-EEEE-HHHHTT-SEESSEEEEEEBT CS
                    DNA_pol_B_palm  11 ealvkkaakeldpevevivcGSYRRgaessGDvDvlitkk 50 
                                       ++ +k+ +++  p ++v v+GS RR++e+   + +++t +
  gi|298674967|ref|YP_003726717.1| 166 ADDIKSILET-IPYTKVSVVGSVRRQKETVNNINLIVTTD 204
                                       3344444433.36689*********************986 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.4
                                       EEEEEEBTTBSTTSS--HHHHHHHHHHHHHT CS
                    DNA_pol_B_palm  43 vDvlitkkdakseskklkklleklvkklkkk 73 
                                       +D++i   ++  + +++k++++++v++l+++
  gi|298674967|ref|YP_003726717.1| 432 MDIVIAAIHTGFD-EDKKTITKRIVRALENE 461
                                       6888887777774.47899999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (573 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.49
# Mc/sec: 3523.07
//
Query:       gi|298674968|ref|YP_003726718.1|  [L=476]
Description: methanogenesis marker protein 14 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   2.2e-235  781.3   3.8   2.5e-235  781.1   3.8    1.0  1  DUF2114     Uncharacterized protein conserved in archaea (DUF
  ------ inclusion threshold ------
       0.02   14.7   0.0          7    6.4   0.0    2.7  3  Pan_kinase  Type III pantothenate kinase
      0.021   14.7   0.0       0.04   13.8   0.0    1.4  1  R_equi_Vir  Rhodococcus equi virulence-associated protein
      0.079   12.4   0.0       0.15   11.6   0.0    1.3  1  ASFV_360    African swine fever virus multigene family 360 pr


Domain annotation for each model (and alignments):
>> DUF2114  Uncharacterized protein conserved in archaea (DUF2114)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  781.1   3.8  5.6e-239  2.5e-235       1     449 []      22     474 ..      22     474 .. 0.99

  Alignments for each domain:
  == domain 1  score: 781.1 bits;  conditional E-value: 5.6e-239
                           DUF2114   1 eyyivasvelGntttkciltatnletgktyllnktvkmtrdvrkpkegeevfgktlagveltresvaelvrdtlles 77 
                                       +y++vasve+Gntttkcil+atnle+gkt++++k+v+mtrdvrkpk+ge+vfgktl+gve+tresvaelvrdtll++
  gi|298674968|ref|YP_003726718.1|  22 PYFVVASVEVGNTTTKCILMATNLEDGKTRHITKNVRMTRDVRKPKSGETVFGKTLSGVEFTRESVAELVRDTLLDA 98 
                                       7**************************************************************************** PP

                           DUF2114  78 lkkakldieedldfvvrstGvvagfdspeevgelikaladGCleagvppkkmtpamskenlpeklrkyslldkvvfd 154
                                       +kkakld+++dl+fvvrstGvvagfd p++vge+ika+adGCl+a++pp+kmtp+ms +n+p+++rkys+l++v+fd
  gi|298674968|ref|YP_003726718.1|  99 VKKAKLDVKTDLNFVVRSTGVVAGFDVPDDVGEFIKAMADGCLMADIPPNKMTPPMSLDNIPKEYRKYSKLNQVIFD 175
                                       ***************************************************************************** PP

                           DUF2114 155 GavasvvpPkgktgvevvanemegeLvtaGikegakwtdvdfrnPcisidfGttLdGrivndeePyaktvgnfcGla 231
                                       Gavasv pP+g+tgvevvanemegeLvtaGikegakw+d+d+rnPcisidfGttL+Gri++++ePya+t+gn+cG+a
  gi|298674968|ref|YP_003726718.1| 176 GAVASVNPPTGATGVEVVANEMEGELVTAGIKEGAKWADIDYRNPCISIDFGTTLAGRIISPDEPYANTIGNLCGYA 252
                                       ***************************************************************************** PP

                           DUF2114 232 GaipdaivrGtglvdkklgaaldlfkekkkk....kkkkkkikeyaekihelidiekvPkdrerfGtvPvdakaaee 304
                                       Gaipdai+rGtg vd++lg+al++f++k ++    k+k+k+i++yaekihe+i+ie+vP dr+++G+vPv+++aa++
  gi|298674968|ref|YP_003726718.1| 253 GAIPDAIIRGTGRVDENLGTALEIFDQKVMNfiklKMKDKAIQNYAEKIHEHINIERVPVDRNKYGSVPVNPSAAKD 329
                                       **************************9988789999***************************************** PP

                           DUF2114 305 agvvliGcdvgengsdlekleeigaeilekeglkvllavldevsakivkrlievaveeglveektaiGitGragitG 381
                                       +gv+liGcdvgengsdl+kl+e+g+ei++kegl+v++av+d v+ak+v+rli+va+eeglv ++taiG++Gra++tG
  gi|298674968|ref|YP_003726718.1| 330 SGVTLIGCDVGENGSDLDKLMELGNEIYKKEGLQVVYAVIDVVMAKVVYRLIKVAKEEGLVFDDTAIGLSGRAALTG 406
                                       ***************************************************************************** PP

                           DUF2114 382 kkpelilekieelglyddkeenvvfvddgLarGaavmarCmnslGtpknPlGGvrggkCilkkriklq 449
                                       +kp+l+le+++el+++d+++e+vvfvddgLarGaavmarCmnslGtp+nPlGG+rggkCil++riklq
  gi|298674968|ref|YP_003726718.1| 407 NKPKLVLEYLDELQIHDKIDEHVVFVDDGLARGAAVMARCMNSLGTPSNPLGGHRGGKCILGERIKLQ 474
                                       ******************************************************************97 PP

>> Pan_kinase  Type III pantothenate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0016         7       4     105 ..      29     130 ..      27     137 .. 0.60
   2 ?    5.1   0.0    0.0041        18     120     144 ..     217     241 ..     208     245 .. 0.83
   3 ?   -2.6   0.0      0.92   4.1e+03      34      76 ..     344     386 ..     338     391 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0016
                                       EEE-SSEEEEEEEETTCCEE..TEEEEEEEEESCHHHHHHHHHHCHCCCCEGCEEEEEEESSCHHHHHHHHHHHHH. CS
                        Pan_kinase   4 iDiGNtrikwalfegeella..swriastaasrtadelaellesllkaagleieaviissVvpaavaalleallky. 77 
                                       +++GNt +k  l+  ++l +  +++i + +++ t d ++    +++  ++l+  +    sV++ + ++ll+a++k+ 
  gi|298674968|ref|YP_003726718.1|  29 VEVGNTTTKCILM-ATNLEDgkTRHI-TKNVRMTRDVRKPKSGETVFGKTLSGVEFTRESVAELVRDTLLDAVKKAk 103
                                       79***********.455666433333.66666665555555555544444444456677777777777777777762 PP

                                       ..HSS-EEEES.CSSECTCEE-SSSGGGS- CS
                        Pan_kinase  78 ..fkveplvvrssaaklgltngydnpkelG 105
                                         +k++  +v      +g+  g+d p+ +G
  gi|298674968|ref|YP_003726718.1| 104 ldVKTDLNFVV---RSTGVVAGFDVPDDVG 130
                                       11223333344...4556666666665555 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0041
                                       TTSEEEEEEESSEEEEEEEETTSEE CS
                        Pan_kinase 120 pgkpllvvdfGTAttfdavsadgey 144
                                        ++p++ +dfGT +   ++s d+ y
  gi|298674968|ref|YP_003726718.1| 217 YRNPCISIDFGTTLAGRIISPDEPY 241
                                       4679**********99999998877 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.92
                                       SCHHHHHHHHHHCHCCCCEGCEEEEEEESSCHHHHHHHHHHHH CS
                        Pan_kinase  34 rtadelaellesllkaagleieaviissVvpaavaalleallk 76 
                                       ++ d+l el +++ k++gl++  ++i  V+ ++v++l++++++
  gi|298674968|ref|YP_003726718.1| 344 SDLDKLMELGNEIYKKEGLQVVYAVIDVVMAKVVYRLIKVAKE 386
                                       5667888888889999999887777777777777777776655 PP

>> R_equi_Vir  Rhodococcus equi virulence-associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     9e-06      0.04      71     118 ..     362     407 ..     322     418 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9e-06
                                       XXEEEEEEEEEEE-SSEEEEEEEECT--EEEEEEECEE-SEEEEEEEE CS
                        R_equi_Vir  71 qekqYdVhGvvvSavvYqklkisvdggktFdGdaGGlsiPGaaalwGt 118
                                        +  Y+V  vv+  vvY+ +k+  ++g +Fd  a Gls  G aal G+
  gi|298674968|ref|YP_003726718.1| 362 LQVVYAVIDVVMAKVVYRLIKVAKEEGLVFDDTAIGLS--GRAALTGN 407
                                       4567******************************9998..77777775 PP

>> ASFV_360  African swine fever virus multigene family 360 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.3e-05      0.15      93     143 ..     266     316 ..     264     326 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.3e-05
                          ASFV_360  93 vkynlteaiqyfyqryrdfkewrlicalsfnnvfdlheiyrtekvnmdide 143
                                       v  nl +a++ f+q++++f + +++     n   ++he +++e+v +d ++
  gi|298674968|ref|YP_003726718.1| 266 VDENLGTALEIFDQKVMNFIKLKMKDKAIQNYAEKIHEHINIERVPVDRNK 316
                                       56799******************************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 2860.46
//
Query:       gi|298674969|ref|YP_003726719.1|  [L=133]
Description: thioredoxin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-28   98.9   0.1    1.7e-28   98.6   0.1    1.2  1  Thioredoxin    Thioredoxin
    1.5e-07   31.9   0.3    1.1e-06   29.0   0.1    2.2  2  Thioredoxin_2  Thioredoxin-like domain
    2.2e-07   30.5   0.0    2.4e-07   30.4   0.0    1.1  1  OST3_OST6      OST3 / OST6 family, transporter family
    4.6e-07   30.1   0.1    0.00095   19.4   0.0    2.5  3  Thioredoxin_8  Thioredoxin-like
    2.9e-05   24.0   0.2      0.001   19.0   0.1    2.1  2  AhpC-TSA       AhpC/TSA family
    6.7e-05   22.9   0.0    8.8e-05   22.5   0.0    1.4  1  Thioredoxin_6  Thioredoxin-like domain
    0.00025   21.0   0.4    0.00054   20.0   0.0    1.8  2  Thioredoxin_3  Thioredoxin domain
    0.00066   19.5   0.2    0.00097   18.9   0.2    1.4  1  Thioredoxin_9  Thioredoxin
     0.0034   17.5   0.0     0.0056   16.8   0.0    1.4  1  Thioredoxin_7  Thioredoxin-like
     0.0042   16.8   0.2      0.019   14.7   0.1    1.9  2  Redoxin        Redoxin
     0.0054   16.6   0.1      0.013   15.4   0.0    1.6  1  TraF           F plasmid transfer operon protein
  ------ inclusion threshold ------
      0.022   14.9   0.2      0.098   12.9   0.0    2.1  2  Glutaredoxin   Glutaredoxin
      0.047   13.7   0.0      0.063   13.2   0.0    1.4  1  HyaE           Hydrogenase-1 expression protein HyaE


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.6   0.1   1.3e-31   1.7e-28       4     101 ..      33     129 ..      30     131 .. 0.96

  Alignments for each domain:
  == domain 1  score: 98.6 bits;  conditional E-value: 1.3e-31
                                       ESSHHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEE CS
                       Thioredoxin   4 vltkenFeeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfk 80 
                                        +t++n +e+v+k   lv+++++A+wCg+Ck++aP +e+la+e+++k ++ak+dvd+n++ akk+++++iPtl++fk
  gi|298674969|ref|YP_003726719.1|  33 DVTDSNVDETVSK-YPLVVIDCWAEWCGPCKKIAPAIEELASEYQGKAVFAKLDVDNNQESAKKFGISSIPTLLIFK 108
                                       57999********.*************************************************************** PP

                                       TTEEEEEEESS-HHHHHHHHH CS
                       Thioredoxin  81 ngkevkkyegarekeklaafl 101
                                       n   ++ + ga +k+++++ l
  gi|298674969|ref|YP_003726719.1| 109 NKVLIDYIIGAVSKQDIIKRL 129
                                       ****************99876 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       4.7   6.4e+03      52      53 ..      17      18 ..       3      40 .. 0.52
   2 !   29.0   0.1   8.3e-10   1.1e-06       8     108 ..      49     128 ..      42     129 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.7
                     Thioredoxin_2 52 ai 53
                                      +i
  gi|298674969|ref|YP_003726719.1| 17 EI 18
                                      11 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 8.3e-10
                     Thioredoxin_2   8 vlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPti 84 
                                       v+++ ++++C+ Ckk+   ++el    +      ++ +++++  +++ ++e              a+k+g+++ Pt+
  gi|298674969|ref|YP_003726719.1|  49 VVIDCWAEWCGPCKKIAPAIEEL---ASE-----YQGKAVFAKLDVDNNQE-------------SAKKFGISSIPTL 104
                                       567778*************9999...444.....56665555555555555.............57**********6 PP

                     Thioredoxin_2  85 vfldgkeivarlpGyvpaeeleal 108
                                       +++  k  ++ + G+v+++++ + 
  gi|298674969|ref|YP_003726719.1| 105 LIFKNKVLIDYIIGAVSKQDIIKR 128
                                       6555555999*******9998775 PP

>> OST3_OST6  OST3 / OST6 family, transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   1.7e-10   2.4e-07      46     105 ..      58     110 ..      19     125 .. 0.90

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 1.7e-10
                         OST3_OST6  46 CelCrefepefelvakswrkdekskskklfFakvdfdegkdvFqklglnsaPhlllfppk 105
                                       C +C++++p +e +a+ ++ +        +Fak+d+d++++  +k+g++s+P ll+f+ k
  gi|298674969|ref|YP_003726719.1|  58 CGPCKKIAPAIEELASEYQGK-------AVFAKLDVDNNQESAKKFGISSIPTLLIFKNK 110
                                       *****************9999.......5****************************975 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       5.8   7.9e+03      70      78 ..      14      22 ..       5      37 .. 0.58
   2 !   19.4   0.0   6.9e-07   0.00095       3      47 ..      48      90 ..      46      92 .. 0.83
   3 !   10.6   0.0    0.0004      0.55      66      91 ..      84     109 ..      76     111 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 5.8
                                      -HHHHTT-S CS
                     Thioredoxin_8 70 krnklkkky 78
                                      k+++++k +
  gi|298674969|ref|YP_003726719.1| 14 KIKEIQKSM 22
                                      333333333 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 6.9e-07
                                      EEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS-H CS
                     Thioredoxin_8  3 vvlLyfgaswcppckaftpklkelyeklkkkkkveivyvsldkke 47
                                      +v++ ++a+wc pck++ p + el ++++   k ++  + +d+++
  gi|298674969|ref|YP_003726719.1| 48 LVVIDCWAEWCGPCKKIAPAIEELASEYQ--GKAVFAKLDVDNNQ 90
                                      5899************************9..66666666666655 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.0004
                                       E-TT-HHHHTT-S--TT-SEEEEE-T CS
                     Thioredoxin_8  66 fddkkrnklkkkynvkaiPtlvvldk 91 
                                        d +++++ +kk+++++iPtl++ ++
  gi|298674969|ref|YP_003726719.1|  84 LDVDNNQESAKKFGISSIPTLLIFKN 109
                                       5667899***************9875 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   7.4e-07     0.001      27      59 ..      48      79 ..      29      83 .. 0.85
   2 ?    3.0   0.0     0.066        91      88     123 ..      86     115 ..      80     116 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 7.4e-07
                                      EEEEEEESTST-CCHHHHHHHHHHCHHHCCCTT CS
                          AhpC-TSA 27 pvvlffypkdwcpvCttelpalaklyeefkerg 59
                                       vv+ ++++ wc +C++ +pa+++l+ e++ + 
  gi|298674969|ref|YP_003726719.1| 48 LVVIDCWAE-WCGPCKKIAPAIEELASEYQGKA 79
                                      699******.*******************9765 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.066
                                       E-TTSHHHHHTT-EETTTTECSCEEEEE-TTSBEEE CS
                          AhpC-TSA  88 sDeegkvakaygvlkeekglalratfvidkegkiry 123
                                        D++++ ak++g+        +++  +++++  i y
  gi|298674969|ref|YP_003726719.1|  86 VDNNQESAKKFGIS------SIPTLLIFKNKVLIDY 115
                                       699***********......7777777777666655 PP

>> Thioredoxin_6  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   6.4e-08   8.8e-05      83     161 ..      35     110 ..       8     127 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 6.4e-08
                                       SHHHHHHHHTSS--EEEEEEE-TTSTTHHHHHHHHHHHHHHTTTT-EEEEEETTGGHHHHHHTT--GGG-SEEEEEE CS
                     Thioredoxin_6  83 tpenaeelfeeglppllllflkkddeeteklkkaiekvakefkdkinfaladaksfkrpleylglsssdlPvivivd 159
                                       t+ n++e  ++  p++++    +     +k+  aie++a e+++k  fa +d++++++  + +g+s  ++P++ i++
  gi|298674969|ref|YP_003726719.1|  35 TDSNVDETVSKY-PLVVIDCWAEWCGPCKKIAPAIEELASEYQGKAVFAKLDVDNNQESAKKFGIS--SIPTLLIFK 108
                                       555555544444.555555554444445788889********************************..******998 PP

                                       SS CS
                     Thioredoxin_6 160 sa 161
                                       ++
  gi|298674969|ref|YP_003726719.1| 109 NK 110
                                       54 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       3.2   4.3e+03      37      47 ..       5      15 ..       1      24 [. 0.56
   2 !   20.0   0.0   3.9e-07   0.00054      10      55 ..      58     106 ..      49     129 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.2
                                      TTHHHHHHCT- CS
                     Thioredoxin_3 37 tdfeeiekygV 47
                                      +++eei k ++
  gi|298674969|ref|YP_003726719.1|  5 EELEEIRKKKI 15
                                      55555544443 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 3.9e-07
                                       STTCHHHHHHHHHHCHCCTCECEEECC..TTHHHH.HHCT-SSSSEEEC CS
                     Thioredoxin_3  10 CakCpklekavkeaaaekgikaevekv..tdfeei.ekygVmsvPalvi 55 
                                       C  C+k++ a++e+a e + ka + k    +++e  +k+g+ s+P+l+i
  gi|298674969|ref|YP_003726719.1|  58 CGPCKKIAPAIEELASEYQGKAVFAKLdvDNNQESaKKFGISSIPTLLI 106
                                       999***************999966554437777779***********65 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.2   7.1e-07   0.00097      49     107 ..      54     110 ..       2     119 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 7.1e-07
                                       --TT-HHHHHHHHHHHHHH.HH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE-TT CS
                     Thioredoxin_9  49 tedwCgDaavnvPvlakia.elnpnievkillrdenlelmdqyltngaraiPtliildee 107
                                        ++wCg +  + P+++++a e++ +  +  l  d+n+e  +++   g  +iPtl+i++++
  gi|298674969|ref|YP_003726719.1|  54 WAEWCGPCKKIAPAIEELAsEYQGKAVFAKLDVDNNQESAKKF---GISSIPTLLIFKNK 110
                                       479**************99567778888999999999999999...88*******99876 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0     4e-06    0.0056      20      82 ..      49     108 ..      37     109 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4e-06
                                       EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG.-TT-.--SSEEEEE- CS
                     Thioredoxin_7  20 vlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdanilelde.qgvPvvafld 82 
                                       v ++  a+wc++C++++ + ++     + +++k v+ ++dv++++++  +  + + +P++++++
  gi|298674969|ref|YP_003726719.1|  49 VVIDCWAEWCGPCKKIAPAIEEL--ASE-YQGKAVFAKLDVDNNQESA-KKFGiSSIPTLLIFK 108
                                       3458899**********998876..666.****************987.4333467***99985 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   1.3e-05     0.019      31      63 ..      49      80 ..      31      96 .. 0.87
   2 ?    0.5   0.0      0.32   4.4e+02      92     134 ..      87     119 ..      76     127 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                                      EEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTT CS
                           Redoxin 31 vvvnfvpgafcPtCsaehpyleklaellkekgv 63
                                      vv+  ++  +c++C++ +p++e+la ++  k+v
  gi|298674969|ref|YP_003726719.1| 49 VVIDCWAE-WCGPCKKIAPAIEELASEYQGKAV 80
                                      68899999.***************999988876 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.32
                                       -TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEESS CS
                           Redoxin  92 DgsaaftkalGlrleedaseglrtpryavidedgkvvylevep 134
                                       D +++ +k++G          + +  + +i ++++++ ++ ++
  gi|298674969|ref|YP_003726719.1|  87 DNNQESAKKFG----------ISSIPTLLIFKNKVLIDYIIGA 119
                                       45555556666..........4455556666777777666665 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   9.3e-06     0.013     141     222 ..      58     128 ..      50     130 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9.3e-06
                              TraF 141 cpyceaqapilqafadkyglevraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlvdpksqkvvpvaaGllsld 217
                                       c+ c++ ap ++++a +y+ + ++ ++d   ++e          a+++g++++P+l++++ k    +    G++s +
  gi|298674969|ref|YP_003726719.1|  58 CGPCKKIAPAIEELASEYQGKAVFAKLDVDNNQE---------SAKKFGISSIPTLLIFKNKV--LIDYIIGAVSKQ 123
                                       999***************9999888888776644.........466*************9983..222234778888 PP

                              TraF 218 eleer 222
                                       ++ +r
  gi|298674969|ref|YP_003726719.1| 124 DIIKR 128
                                       77777 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.87   1.2e+03      36      45 ..      17      26 ..       3      52 .. 0.53
   2 ?   12.9   0.0   7.1e-05     0.098       7      55 ..      56     106 ..      44     112 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.87
                                      HHHHHHHHHH CS
                      Glutaredoxin 36 eireelkels 45
                                      ei++ ++++s
  gi|298674969|ref|YP_003726719.1| 17 EIQKSMERRS 26
                                      4444444444 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 7.1e-05
                                       TSSHHHHHHHHHHHHTTGG......EEEEEGCCSHHHHHHHHHHHTSSSSSEEEE CS
                      Glutaredoxin   7 ptCpyCkkakrlLkelgvk......feeidvdkdeeireelkelsgvrtvPqvfi 55 
                                        +C+ Ckk+  + +el  +      f+  dvd+++e  ++     g++++P++ i
  gi|298674969|ref|YP_003726719.1|  56 EWCGPCKKIAPAIEELASEyqgkavFAKLDVDNNQESAKKF----GISSIPTLLI 106
                                       79********9998888554444458999999985555554....9999999987 PP

>> HyaE  Hydrogenase-1 expression protein HyaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.6e-05     0.063      49      99 ..      67     116 ..      18     124 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.6e-05
                                       HHHHHHCT-TTS-EEEEEETHHHHHHHHHCCT-TSSSEEEEEETTEEEEEE CS
                              HyaE  49 vlpEllkaFpnalraavvadreqeealaerfgvlktPsllflrdgeylgvl 99 
                                        + El  +++  +  a +   +++++ a++fg++  P+ll+++++ ++  +
  gi|298674969|ref|YP_003726719.1|  67 AIEELASEYQGKAVFAKLD-VDNNQESAKKFGISSIPTLLIFKNKVLIDYI 116
                                       5778888888877666665.77778889**************998776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       833  (0.046461); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 818.58
//
Query:       gi|298674970|ref|YP_003726720.1|  [L=340]
Description: restriction endonuclease [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      4e-31  107.4   0.2      7e-31  106.6   0.2    1.4  1  Mrr_cat    Restriction endonuclease
    1.4e-10   41.1   0.1      3e-10   40.1   0.1    1.5  1  Mrr_cat_2  Restriction endonuclease
     0.0013   18.6   1.1     0.0034   17.3   0.4    2.0  2  DUF2691    Protein of unknown function (DUF2691)
  ------ inclusion threshold ------
       0.11   12.7   2.2       0.88    9.8   0.1    2.5  2  PBP5_C     Penicillin-binding protein 5, C-terminal domain


Domain annotation for each model (and alignments):
>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.6   0.2   1.6e-34     7e-31       2     115 .]      10     122 ..       9     122 .. 0.97

  Alignments for each domain:
  == domain 1  score: 106.6 bits;  conditional E-value: 1.6e-34
                                       TTT-TTCHHHHHHHHHHHHSSSEEE---B-TTSSB--EEEETTEEEE.EEEEEEE--TS-B-HHHHHHHHHHCTTS. CS
                           Mrr_cat   2 dkmspkeFeklvaellealGykeveltgrsgDggiDliakkdplgse.rilvqaKryknkvgvkeVqeligalkkrg 77 
                                        +m+p++Feklva l+ ++Gyk  e+t++s+D g+D+++k +++g   ++lvqaKry+++vgvke++e  +   +  
  gi|298674970|ref|YP_003726720.1|  10 LQMDPYDFEKLVAYLFTNMGYK-AEVTNQSRDDGVDVVLKLEKFGLShKWLVQAKRYSKTVGVKEIREYSSLRYQDD 85 
                                       68*******************9.9*********************966***************************** PP

                                       .SEEEEEESS-B-HHHHHHHHTT--EEEE-HHHHHHHH CS
                           Mrr_cat  78 adkgifvttsdftkaAreeaeelnkieLldgdeLaell 115
                                       ++  i+vtt++ft++A+ ea++ ++++L++g  L+e+l
  gi|298674970|ref|YP_003726720.1|  86 VEGIIVVTTDEFTDDAKTEAKK-HNLKLIEGGLLVEML 122
                                       **********************.***********9996 PP

>> Mrr_cat_2  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.1   6.7e-14     3e-10       2     106 ..      12     114 ..      11     123 .. 0.83

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 6.7e-14
                         Mrr_cat_2   2 tdpayaee.fkeVwlwkewpeekrlgkkDtGIDlVake..rkegeywAIQcKfYaedekiqkedidsFlsasgkkkf 75 
                                       +dp   e+ ++ +++  +++ e + +++D G+D+V k    + ++ w +Q+K+Y+  +++  ++i+++ s+  ++  
  gi|298674970|ref|YP_003726720.1|  12 MDPYDFEKlVAYLFTNMGYKAEVTNQSRDDGVDVVLKLekFGLSHKWLVQAKRYS--KTVGVKEIREYSSLRYQDD- 85 
                                       67887777788888899999999999*********9984456679999*******..69***********999876. PP

                         Mrr_cat_2  76 tkrliisTtdkwsknaeealknqkipvkrid 106
                                       ++++i++Ttd+++ +a++   ++k++ k+i+
  gi|298674970|ref|YP_003726720.1|  86 VEGIIVVTTDEFTDDAKTE--AKKHNLKLIE 114
                                       6789999*********998..5555566665 PP

>> DUF2691  Protein of unknown function (DUF2691)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.4   7.5e-07    0.0034      45     141 ..     152     255 ..     135     262 .. 0.79
   2 ?   -1.2   0.0      0.36   1.6e+03      50      97 ..     286     330 ..     254     339 .. 0.45

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 7.5e-07
                           DUF2691  45 L..dealFpeeeevlegeelkktlkkkdyYliFadlkafpkkk...lakdiktyeeflkskcelvllivDssyvtiy 116
                                       L  de++  +e+ v++g++l+  +++k+ Yli + l +f +k+    + ++++       + e+ ll+  +  + i+
  gi|298674970|ref|YP_003726720.1| 152 LknDESVMANEPAVVKGQKLMVAVTNKNIYLIKKTLGIFSRKTdiyRQINVNNIVGIHTNNREIYLLTGQNGDIEIF 228
                                       24489999*******************************98862224678889999999999*****9999998888 PP

                           DUF2691 117 ckdqeiieklyknake..qgfedieyi 141
                                         + +  ekl+++  +   ++++ ey+
  gi|298674970|ref|YP_003726720.1| 229 NIHPKKPEKLFETFSNlkAEYTKGEYL 255
                                       888888888877655411567777775 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.36
                           DUF2691  50 FpeeeevlegeelkktlkkkdyYliFadlkafpkkklakdiktyeefl 97 
                                       F+ ++ v +g + +   kk++  + F+  k+ +++    d+++ +e+ 
  gi|298674970|ref|YP_003726720.1| 286 FNLKNIVGTGVTNTGLFKKQKLVVWFSSDKVNKYE---IDVDNVQEWQ 330
                                       33333333444444444445555555544444444...3444444444 PP

>> PBP5_C  Penicillin-binding protein 5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.3     0.057   2.6e+02       7      39 ..     152     185 ..     149     196 .. 0.81
   2 ?    9.8   0.1    0.0002      0.88      23      90 ..     212     283 ..     192     284 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.057
                                       EXTTCES..EEEEEESSSSSEEEEEESSXEEEEEE CS
                            PBP5_C   7 ykkgkvv..ktvsvlkgkekeVplvakediyvtvk 39 
                                       +k++++v  ++  v kg++  + +v++++iy++ k
  gi|298674970|ref|YP_003726720.1| 152 LKNDESVmaNEPAVVKGQKL-MVAVTNKNIYLIKK 185
                                       56677778888889999999.77889999999855 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0002
                                       SSEEEEEESSXEEEEEETTHCCTEEEEEEESSSEESGBGTTSEEEEEEEEETTEEEEE....EEEEESSXBX CS
                            PBP5_C  23 ekeVplvakediyvtvkkgekkklkakvelkksleapikkGqkvGklkvyldgkliak....vplvakedve 90 
                                        +e+ l++ ++ ++ +++   kk ++ +e  ++l+a  +kG+ + k +++++g li +     +l ++++ve
  gi|298674970|ref|YP_003726720.1| 212 NREIYLLTGQNGDIEIFNIHPKKPEKLFETFSNLKAEYTKGEYLLKFEIKKEGYLILTskrlMDLNSDNEVE 283
                                       56778888888888888888899999999999************************9999977999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 2061.86
//
Query:       gi|298674971|ref|YP_003726721.1|  [L=934]
Description: heavy metal translocating P-type ATPase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-56  189.7   4.2    1.3e-55  187.7   2.6    2.4  2  E1-E2_ATPase     E1-E2 ATPase
    1.6e-44  152.7   4.6    3.2e-44  151.7   4.6    1.5  1  Hydrolase        haloacid dehalogenase-like hydrolase
    6.1e-44  148.3  19.2    9.5e-15   54.8   0.4    4.5  4  HMA              Heavy-metal-associated domain
    6.3e-06   26.1   3.4      6e-05   22.9   1.3    2.4  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
     0.0018   18.4   0.2        1.9    8.6   0.0    3.4  4  Tox-PL-2         Papain fold toxin 2
  ------ inclusion threshold ------
      0.014   15.8   3.0         16    6.0   0.1    4.4  4  Fer2_BFD         BFD-like [2Fe-2S] binding domain
      0.019   15.0   4.0        9.7    6.3   0.1    3.8  3  Thioredoxin_3    Thioredoxin domain
      0.064   13.7   0.0       0.32   11.4   0.0    2.0  1  HAD              haloacid dehalogenase-like hydrolase
      0.092   12.9   0.7        4.2    7.6   0.0    3.3  3  FeS_assembly_P   Iron-sulfur cluster assembly protein
       0.11   12.2   0.2       0.27   10.8   0.2    1.7  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
       0.12   12.1   0.0        2.1    8.1   0.0    2.4  2  Rhabdo_matrix    Rhabdovirus matrix protein
       0.33   11.0   2.7        3.2    7.9   0.1    3.0  2  RRM_3            RNA binding motif


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.23   3.4e+02      61     160 ..     214     321 ..     201     323 .. 0.61
   2 !  187.7   2.6   8.7e-59   1.3e-55       2     180 ..     406     597 ..     405     598 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.23
                                       -EE-..G-TTEE-TT-EEEE-EEEEEEEE-TTTSTTTTTS.TTS--------HHHHHHHHH..HHHHHHHHHHHHHH CS
                      E1-E2_ATPase  61 pvek..ekgdmvfsGtvvvsgeakavVtatgedtelgkia.rlveeakskktplqkkldkl..gkvlvpvvlliall 132
                                        v    ek + v+ ++ v    +k  V  +g + + +k   ++ +e ++++t+++++ ++l  ++ lv+ + l  + 
  gi|298674971|ref|YP_003726721.1| 214 SVNLplEKAHLVYDSSLVSVTDMKSAVEDIGYSATSEKKElESDREREARETEMKQQRTNLiiAAALVLPISLGDMS 290
                                       44445578889999999999999999999998766554330333333344444444333330033344445555555 PP

                                       HHHS-STTTSSTT...HHHHHHHHHHHHHS- CS
                      E1-E2_ATPase 133 vflialllgksla...eallralallvaaiP 160
                                       +++ ++l++ +++   e+ll+ l+++v++ P
  gi|298674971|ref|YP_003726721.1| 291 TAFPNILWFVPPFlanEILLFLLTTIVMIFP 321
                                       6666666666666777888888888888877 PP

  == domain 2  score: 187.7 bits;  conditional E-value: 8.7e-59
                                       SS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE CS
                      E1-E2_ATPase   2 llpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvs 78 
                                       l+++ta+vi dg+e+ei+++++++G iv++++g+++p+Dg++ +gs+ vdes++TGEs pv+k+ gd+v++ t+++s
  gi|298674971|ref|YP_003726721.1| 406 LKAKTARVIVDGEEKEIPVEDVEIGNIVVVRPGEKIPVDGEVTDGSSAVDESMITGESIPVDKDPGDTVIGATINKS 482
                                       6789************************************************************************* PP

                                       -EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT.......... CS
                      E1-E2_ATPase  79 geakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgksla.......... 145
                                       g++k+++ ++g++t l++i++lve+a+s+k+plq+++d +++ ++++v +ial++f++++l+g +++          
  gi|298674971|ref|YP_003726721.1| 483 GTLKFRASKVGSETALAQIIQLVENAQSSKPPLQRIADVVAGNFILAVHIIALVTFMVWFLIGYEAFdvslfsnits 559
                                       *************************************************************99999999999***** PP

                                       ...HHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHHHHH CS
                      E1-E2_ATPase 146 ...eallralallvaaiPcaLplavplalalgarrlak 180
                                          ++ll a+++lv+++Pca +la+p a+++g+++ a+
  gi|298674971|ref|YP_003726721.1| 560 pflFSLLIAITVLVISCPCAVGLATPAAIMVGTGKGAE 597
                                       **********************************9987 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.7   4.6   2.2e-47   3.2e-44       2     209 ..     615     830 ..     614     831 .. 0.92

  Alignments for each domain:
  == domain 1  score: 151.7 bits;  conditional E-value: 2.2e-47
                                       SEEEEESBTTTBCHHHHHHHHHHHH......CHHHHHHHHHHHHCHHHHHHHHHHHHHHHHH...HHHHHETTTE.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxx.. RF
                         Hydrolase   2 ktvvfDkdGTLttgepsvedvivsa......alalaaaletgsehpigkalvaaakarsgal...tgfatfigrg.. 67 
                                       +t+vfDk+GTLt gep+++dv+          l +aa  e gsehp+g+a+v+ a+ar ++l   ++f  ++g+g  
  gi|298674971|ref|YP_003726721.1| 615 DTIVFDKTGTLTVGEPELTDVVGTDdysddeVLRIAATVEKGSEHPLGEAIVKGAQARDINLktaENFKNIPGHGve 691
                                       89**********************955655556666666666****************7777778************ PP

                                       ......HHHHTHHHHHHHH.HCHHHHHHHHHHHHHHCHHHHHH..TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTE CS
                                       ......xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  68 ......ayaigkpewltal.dippdlgaaigsaqsqgrtvall..qaralavftiadplkvkpeaaeavasLkaagi 135
                                             +++ g +++++++    + l++++++ + +g+t++l   ++ a +v+++ad+  +k+  ++av + +++gi
  gi|298674971|ref|YP_003726721.1| 692 aslegkRILLGTRKLMDDNdIDISGLDKKMEEFENDGKTAMLIasDNTAIGVVAVADT--LKENSKHAVDKVHKMGI 766
                                       *******************5445789****************99999***********..***************** PP

                                       EEEEEESSEHHHHHHHHHHTTGGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 136 evvlltgdnpetaeraanqlGddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaA 209
                                       e +++tgdn++tae++ +q+G           + + ++++pe+k   i+ Lq +++ vamVGDg+nDa+al + 
  gi|298674971|ref|YP_003726721.1| 767 EAIMITGDNKRTAEAIGRQVG----------MDRVLSEVLPEQKASEIKNLQNEGRVVAMVGDGINDAPALTQS 830
                                       *********************..........6666************************************876 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.8   0.4   6.4e-18   9.5e-15       1      62 []       6      67 ..       6      67 .. 0.97
   2 !   51.7   2.0   6.1e-17   9.1e-14       2      61 ..     118     177 ..     117     178 .. 0.97
   3 !   52.0   0.7   4.7e-17     7e-14       2      61 ..     186     245 ..     185     246 .. 0.97
   4 ?   -1.0   0.1       1.6   2.4e+03      33      51 ..     406     421 ..     405     428 .. 0.79

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 6.4e-18
                               HMA  1 tvrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagyk 62
                                      t++v gm C +C+++v++++sel+gVesv+vdl++  + V++d e ++l +i++a+ +agy+
  gi|298674971|ref|YP_003726721.1|  6 TIKVYGMSCKHCVKSVTDAISELEGVESVDVDLENEWAIVTFDSETVNLDDIRQAVTDAGYQ 67
                                      68899*******************************************************95 PP

  == domain 2  score: 51.7 bits;  conditional E-value: 6.1e-17
                               HMA   2 vrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagy 61 
                                       ++v gm+Ca+Ca+ vekvL++ +gV s++v+ a  ++ V++d++ ++ ++++ a+ ++gy
  gi|298674971|ref|YP_003726721.1| 118 FKVTGMTCASCAKNVEKVLKKQSGVVSATVNIALEKASVTYDPSVVSSKELKDAVVSIGY 177
                                       8999*****************************************99899*********9 PP

  == domain 3  score: 52.0 bits;  conditional E-value: 4.7e-17
                               HMA   2 vrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagy 61 
                                       +++ gm+Ca+Ca+ vekvL++l+gVesv+v+l   ++  ++d + +++ + + a+e++gy
  gi|298674971|ref|YP_003726721.1| 186 LNIGGMTCASCAKNVEKVLKKLEGVESVSVNLPLEKAHLVYDSSLVSVTDMKSAVEDIGY 245
                                       5789*******************************************************9 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 1.6
                               HMA  33 latktvtVegdaestklrk 51 
                                       l++kt+ V +d e+   ++
  gi|298674971|ref|YP_003726721.1| 406 LKAKTARVIVDGEE---KE 421
                                       6789999*999999...33 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.063        94      15      56 ..     749     790 ..     743     795 .. 0.89
   2 !   22.9   1.3     4e-08     6e-05     198     252 ..     806     861 ..     799     863 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.063
                                       ---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCS CS
                       Hydrolase_3  15 kisektkeaikklkekgikvviATGRslravlpvleelgldl 56 
                                       +++e++k+a+ k+++ gi+ +  TG + r+++ + +++g+d 
  gi|298674971|ref|YP_003726721.1| 749 TLKENSKHAVDKVHKMGIEAIMITGDNKRTAEAIGRQVGMDR 790
                                       67899**************************99999999874 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 4e-08
                                       HCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGG.THHH CS
                       Hydrolase_3 198 elnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnne.dGVa 252
                                       +l+ +   v+ +GDg ND + L+++++g+Amg +++ + + A+ v  +n+  d +a
  gi|298674971|ref|YP_003726721.1| 806 NLQNEGRVVAMVGDGINDAPALTQSDIGIAMGAGTDVAMESAKIVLIKNDLiDVIA 861
                                       555566678999*********************************99998777666 PP

>> Tox-PL-2  Papain fold toxin 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0         2   2.9e+03      14      40 ..      10      37 ..       3      77 .. 0.63
   2 !    8.6   0.0    0.0013       1.9      10      33 ..     117     140 ..     110     177 .. 0.76
   3 ?    5.5   0.0     0.012        19      12      31 ..     187     206 ..     179     237 .. 0.79
   4 ?   -3.5   0.0       7.5   1.1e+04      33      51 ..     693     711 ..     687     728 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2
                          Tox-PL-2 14 klleCveCAaalekyLke.qgisGkrlk 40
                                        ++C++C + +++++ e +g++   + 
  gi|298674971|ref|YP_003726721.1| 10 YGMSCKHCVKSVTDAISElEGVESVDVD 37
                                      5678999999998887653455555555 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0013
                          Tox-PL-2  10 vkrfklleCveCAaalekyLkeqg 33 
                                         +++ + C +CA+++ek Lk+q 
  gi|298674971|ref|YP_003726721.1| 117 NFKVTGMTCASCAKNVEKVLKKQS 140
                                       55678899************9983 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.012
                          Tox-PL-2  12 rfklleCveCAaalekyLke 31 
                                       ++  + C +CA+++ek Lk+
  gi|298674971|ref|YP_003726721.1| 187 NIGGMTCASCAKNVEKVLKK 206
                                       566789************97 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 7.5
                          Tox-PL-2  33 gisGkrlklktksaedaas 51 
                                        ++Gkr+ l t++  d ++
  gi|298674971|ref|YP_003726721.1| 693 SLEGKRILLGTRKLMDDND 711
                                       6789999999988877554 PP

>> Fer2_BFD  BFD-like [2Fe-2S] binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0       0.3   4.4e+02      35      50 ..      11      26 ..       4      27 .. 0.85
   2 ?   -0.9   0.0       1.5   2.2e+03       7      28 ..      51      72 ..      50      81 .. 0.74
   3 ?    6.0   0.1     0.011        16      34      50 ..     121     137 ..     116     138 .. 0.89
   4 ?    5.0   0.0     0.021        31      35      50 ..     190     205 ..     163     206 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.3
                          Fer2_BFD 35 gtgCggCrpaieeiLa 50
                                      g+ C+ C++ + + + 
  gi|298674971|ref|YP_003726721.1| 11 GMSCKHCVKSVTDAIS 26
                                      899******9988765 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.5
                          Fer2_BFD  7 gvtegeIrdairraglttveev 28
                                       v+ ++Ir+a++ ag +  eev
  gi|298674971|ref|YP_003726721.1| 51 TVNLDDIRQAVTDAGYQPGEEV 72
                                      577899*****88887766666 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.011
                          Fer2_BFD  34 agtgCggCrpaieeiLa 50 
                                       +g+ C++C + +e++L+
  gi|298674971|ref|YP_003726721.1| 121 TGMTCASCAKNVEKVLK 137
                                       6899**********997 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.021
                          Fer2_BFD  35 gtgCggCrpaieeiLa 50 
                                       g+ C++C + +e++L+
  gi|298674971|ref|YP_003726721.1| 190 GMTCASCAKNVEKVLK 205
                                       566**********997 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1    0.0065       9.7       2      35 ..       6      40 ..       5      52 .. 0.76
   2 ?    5.4   0.2     0.013        19       2      31 ..     117     145 ..     116     163 .. 0.70
   3 ?    2.1   0.0      0.14     2e+02       5      23 ..     188     207 ..     184     228 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0065
                                      EEEEESSSSTTCH.HHHHHHHHHCHCCTCECEEEC CS
                     Thioredoxin_3  2 eikvlgpgCakCp.klekavkeaaaekgikaevek 35
                                      +ikv g +C++C   ++ a+ e+   + +++++e+
  gi|298674971|ref|YP_003726721.1|  6 TIKVYGMSCKHCVkSVTDAISELEGVESVDVDLEN 40
                                      79**********97777777777666666666665 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.013
                                       EEEEESSSSTTCHHHHHHHHHHCHCC.T.CEC CS
                     Thioredoxin_3   2 eikvlgpgCakCpklekavkeaaaek.g.ika 31 
                                       ++kv g +Ca C    k+v+++++++ g ++a
  gi|298674971|ref|YP_003726721.1| 117 NFKVTGMTCASCA---KNVEKVLKKQsGvVSA 145
                                       6899999****99...5555555555444444 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.14
                                       EESSSSTTCH.HHHHHHHHH CS
                     Thioredoxin_3   5 vlgpgCakCp.klekavkea 23 
                                       + g +Ca C  ++ek++k++
  gi|298674971|ref|YP_003726721.1| 188 IGGMTCASCAkNVEKVLKKL 207
                                       55778888885666665554 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00021      0.32      88     187 ..     752     827 ..     722     828 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00021
                               HAD  88 pgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkvaalrewlaa 164
                                       +  + +++++++ G++ ++++g +++ +e++ +++g d+vl++                  v  e+k+++++  l+ 
  gi|298674971|ref|YP_003726721.1| 752 ENSKHAVDKVHKMGIEAIMITGDNKRTAEAIGRQVGMDRVLSE------------------VLPEQKASEIKN-LQN 809
                                       55566788889*************************8888888..................334455666666.222 PP

                               HAD 165 egegidleevvayGDspsDlpll 187
                                       e        v  +GD+++D p+l
  gi|298674971|ref|YP_003726721.1| 810 E-----GRVVAMVGDGINDAPAL 827
                                       2.....22344458888888876 PP

>> FeS_assembly_P  Iron-sulfur cluster assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0       0.3   4.5e+02      55      72 ..      19      36 ..      13      38 .. 0.81
   2 ?   -0.6   0.0         1   1.5e+03      39      72 ..     117     147 ..     112     149 .. 0.72
   3 ?    7.6   0.0    0.0028       4.2      37      72 ..     183     215 ..     158     217 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.3
                                      HHHHHHHC.STT--EEEE CS
                    FeS_assembly_P 55 adaeaalralpgvevveV 72
                                      +++ +a+  l+gve+v V
  gi|298674971|ref|YP_003726721.1| 19 KSVTDAISELEGVESVDV 36
                                      6899********666665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1
                                       EE--SSTT-TTHHHHHHHHHHHHC.STT--EEEE CS
                    FeS_assembly_P  39 ditltypacslaeairadaeaalralpgvevveV 72 
                                        + +t + c+     ++ +e+ l++  gv +++V
  gi|298674971|ref|YP_003726721.1| 117 NFKVTGMTCA---SCAKNVEKVLKKQSGVVSATV 147
                                       5566666666...78899**********555555 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0028
                                       EEEE--SSTT-TTHHHHHHHHHHHHC.STT--EEEE CS
                    FeS_assembly_P  37 svditltypacslaeairadaeaalralpgvevveV 72 
                                       ++d++++ + c+     ++ +e+ l++l+gve+v+V
  gi|298674971|ref|YP_003726721.1| 183 TIDLNIGGMTCA---SCAKNVEKVLKKLEGVESVSV 215
                                       566777766777...899************777776 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00018      0.27      21      85 ..     728     793 ..     726     816 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00018
                                       HHHHHHHHH.TTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC...EEEEEE CS
                   Methyltr_RsmB-F  21 gKTthiael.mknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgg.elfDriLl 85 
                                       gKT+ + +  +   g+v   d+ ke  k+ ++ ++++g++ +i++++D +++ + +g    +Dr+L 
  gi|298674971|ref|YP_003726721.1| 728 GKTAMLIASdNTAIGVVAVADTLKENSKHAVDKVHKMGIE-AIMITGDNKRTAEAIGRqVGMDRVLS 793
                                       89998877735555666667999*****************.99999******9999984569**995 PP

>> Rhabdo_matrix  Rhabdovirus matrix protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.21   3.2e+02     123     152 ..     475     504 ..     460     521 .. 0.77
   2 ?    8.1   0.0    0.0014       2.1      80     140 ..     652     712 ..     642     731 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.21
                     Rhabdo_matrix 123 egatitftgrflfssshvgcddnrtklagl 152
                                        gati  +g + f +s+vg +   +++  l
  gi|298674971|ref|YP_003726721.1| 475 IGATINKSGTLKFRASKVGSETALAQIIQL 504
                                       69*****************99877776655 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0014
                     Rhabdo_matrix  80 kvnfgsrkpapqttyqvtkarevylqtqplekkipmqtysvstegatitftgrflfssshv 140
                                        v+ gs +p  ++  + ++ar++ l+t    k+ip +    s eg  i +  r l+    +
  gi|298674971|ref|YP_003726721.1| 652 TVEKGSEHPLGEAIVKGAQARDINLKTAENFKNIPGHGVEASLEGKRILLGTRKLMDDNDI 712
                                       57789*******************************************9999998765544 PP

>> RRM_3  RNA binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1    0.0021       3.2       4      61 ..       7      69 ..       5     105 .. 0.74
   2 ?    1.8   0.1      0.16   2.4e+02       5      88 ..     187     268 ..     184     275 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0021
                                      EEEEE-SSS--HHHHHHHCHCCS-ECEEEE-TTSSEEEEEESSHHH.HHHHHHHHHHC....- CS
                             RRM_3  4 lklsGlnkelsredikellsklgevayvdyekgdkegevrFkedee.akkalekatea....k 61
                                      +k+ G++ + +++++ +++s+l+ v+ vd+  +++ + v F+++      + ++ t+a     
  gi|298674971|ref|YP_003726721.1|  7 IKVYGMSCKHCVKSVTDAISELEGVESVDVDLENEWAIVTFDSETVnLDDIRQAVTDAgyqpG 69
                                      6889999999*******************************9986534555555555544453 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.16
                                       EEEE-SSS--HHHHHHHCHCCS-ECEEEE-TTSSEEEEEESSHHHHHHHHHHHHHC-B-CCTSSEEEEE--HHHHHH CS
                             RRM_3   5 klsGlnkelsredikellsklgevayvdyekgdkegevrFkedeeakkalekateaklkikdaevtlelLeGeeEke 81 
                                        + G++ +++ +++ ++l+kl+ v+ v ++   +++++ ++++  +   +++a+e   +   a  + + Le ++E+e
  gi|298674971|ref|YP_003726721.1| 187 NIGGMTCASCAKNVEKVLKKLEGVESVSVNLPLEKAHLVYDSSLVSVTDMKSAVED--IGYSATSEKKELESDRERE 261
                                       67789999999*****************************9997777777777776..4444555556677777777 PP

                                       HHHHHHH CS
                             RRM_3  82 ywkkile 88 
                                       + ++ ++
  gi|298674971|ref|YP_003726721.1| 262 ARETEMK 268
                                       7655444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (934 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       997  (0.0556082); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.85u 0.32s 00:00:01.17 Elapsed: 00:00:00.52
# Mc/sec: 5414.36
//
Query:       gi|298674972|ref|YP_003726722.1|  [L=75]
Description: hypothetical protein Metev_1038 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.016   15.1   4.1       0.45   10.4   0.1    2.1  2  DUF2970        Protein of unknown function (DUF2970)
      0.023   14.4   2.0      0.026   14.2   2.0    1.1  1  Keratin_assoc  Keratinocyte-associated protein 2
       0.32   11.0   3.4        2.7    8.0   0.1    2.2  2  PilX_N         PilX N-terminal
       0.33   10.7   4.6       0.41   10.4   4.6    1.2  1  S_2TMBeta      SMODS-associating 2TM, beta-strand rich effect
       0.79    9.8   3.7       0.92    9.6   3.7    1.2  1  Vma12          Endoplasmic reticulum-based factor for assembl


Domain annotation for each model (and alignments):
>> DUF2970  Protein of unknown function (DUF2970)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.9    0.0032        11      29      47 ..      10      28 ..       4      31 .. 0.86
   2 ?   10.4   0.1   0.00012      0.45      36      53 ..      44      61 ..      35      63 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0032
                           DUF2970 29 splhviivGlilaalfvll 47
                                      s+++ ii+ ++ ++lf +l
  gi|298674972|ref|YP_003726722.1| 10 SLVASIITSVVITVLFMFL 28
                                      78999***********875 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00012
                           DUF2970 36 vGlilaalfvllLillVk 53
                                      v +i+ alfv+lL ++V+
  gi|298674972|ref|YP_003726722.1| 44 VDIIGGALFVFLLTMIVS 61
                                      669**************7 PP

>> Keratin_assoc  Keratinocyte-associated protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   2.0   7.2e-06     0.026       5      54 ..      12      60 ..       6      72 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.2e-06
                     Keratin_assoc  5 tslllssllavlvfalmqlyksklasselltilgGflgsllFvllLTavg 54
                                      ++++++s+++ ++f  + ++k++   s + t +  ++g  lFv+lLT++ 
  gi|298674972|ref|YP_003726722.1| 12 VASIITSVVITVLFMFLAIIKNNTDISPMYTQV-DIIGGALFVFLLTMIV 60
                                      445666677777899999999999999888865.699999*******985 PP

>> PilX_N  PilX N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.8     0.016        57       4      22 ..      17      36 ..      13      37 .. 0.83
   2 ?    8.0   0.1   0.00076       2.7       6      23 ..      47      64 ..      44      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.016
                            PilX_N  4 a.Lvvtllllavltllgvat 22
                                      + +v+t+l++++  +++++ 
  gi|298674972|ref|YP_003726722.1| 17 TsVVITVLFMFLAIIKNNTD 36
                                      558999******99999875 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00076
                            PilX_N  6 vvtllllavltllgvati 23
                                      + ++l++++lt++++a+i
  gi|298674972|ref|YP_003726722.1| 47 IGGALFVFLLTMIVSASI 64
                                      6799***********986 PP

>> S_2TMBeta  SMODS-associating 2TM, beta-strand rich effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   4.6   0.00012      0.41       2      54 ..      14      68 ..      11      75 .] 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00012
                         S_2TMBeta  2 allsvilsyllsavlslissllellle..alsvigtaviflllyllfdkklWklk 54
                                      ++++ +++++l  +l +i++++++ +     ++ig a++++ll+++ +  +W   
  gi|298674972|ref|YP_003726722.1| 14 SIITSVVITVLFMFLAIIKNNTDISPMytQVDIIGGALFVFLLTMIVSASIWPSI 68
                                      4778888899999999999999955552266778899999************765 PP

>> Vma12  Endoplasmic reticulum-based factor for assembly of V-ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   3.7   0.00026      0.92      72     103 ..       4      35 ..       1      69 [. 0.70

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00026
                             Vma12  72 evnrqlilvlNiliSvvavffavwialrsart 103
                                       +++ + +lv  i+ Svv+++ +++ a+ +  t
  gi|298674972|ref|YP_003726722.1|   4 NLKGKYSLVASIITSVVITVLFMFLAIIKNNT 35 
                                       5678899*****************99865544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1204  (0.0671538); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 491.02
//
Query:       gi|298674973|ref|YP_003726723.1|  [L=326]
Description: radical SAM domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      4e-13   50.1   0.1    5.7e-13   49.6   0.1    1.2  1  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.1   3.2e-17   5.7e-13       1     162 [.      94     248 ..      94     253 .. 0.88

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 3.2e-17
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTC.C CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlakla.v 75 
                                       +++++ C ++C+fC++p+       g++++ +e+l+ + e+ ++ g  k + +++g  +   ++v+ + +++k+  +
  gi|298674973|ref|YP_003726723.1|  94 ITISEKCVYDCKFCPVPK-----LNGKIKTFDEVLQYIHEA-HSTGgMKAISITSGVADTPEKEVDRTVEIVKEVkK 164
                                       578999***********6.....8*****************.68888*********999998888888888888655 PP

                                       CTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET.EEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                       Radical_SAM  76 pgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikr.vvdrivg 151
                                        ++ i v++ +t +     +rl+e+g   +  ++e+ d ++++k + +g++++ +l+ l  + +  +k+ v+++ ++
  gi|298674973|ref|YP_003726723.1| 165 YNVPIGVSIYPTND---SSKRLKEAGAYEIKYNVETMDRDVYQKAC-GGQELDVILKHLSEAVKIFGKNkVFSNFII 237
                                       56666666666664...88*********************999999.99****************777799999999 PP

                                       BTTTSHHHHHH CS
                                       xxxxxxxxxxx RF
                       Radical_SAM 152 lpGendeelee 162
                                       + Ge+de++e+
  gi|298674973|ref|YP_003726723.1| 238 GLGESDETVEK 248
                                       999****9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2472.09
//
Query:       gi|298674974|ref|YP_003726724.1|  [L=386]
Description: coenzyme F420 hydrogenase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-36  125.3   0.0    1.8e-36  125.3   0.0    1.9  2  FrhB_FdhB_C    Coenzyme F420 hydrogenase/dehydrogenase, beta 
    3.4e-24   84.8   0.1    9.3e-23   80.2   0.1    2.5  2  FrhB_FdhB_N    Coenzyme F420 hydrogenase/dehydrogenase, beta 
    8.2e-07   29.0   2.1    2.3e-06   27.6   2.1    1.7  1  YHS            YHS domain
    6.9e-05   22.5  14.7     0.0097   15.7   3.5    2.7  2  Fer4           4Fe-4S binding domain
    0.00073   19.6  13.3    0.00073   19.6  13.3    2.7  3  Fer4_10        4Fe-4S dicluster domain
     0.0044   17.1  13.4     0.0044   17.1  13.4    3.0  3  Fer4_9         4Fe-4S dicluster domain
     0.0047   17.3   1.5     0.0047   17.3   1.5    3.6  3  Fer4_4         4Fe-4S binding domain
  ------ inclusion threshold ------
      0.016   15.3  17.4       0.11   12.6   2.9    2.9  2  Fer4_6         4Fe-4S binding domain
      0.016   15.9   1.0      0.016   15.9   1.0    2.6  2  ATPase-cat_bd  Putative metal-binding domain of cation transp
      0.016   15.3  11.5      0.051   13.7  11.5    1.9  1  Fer4_21        4Fe-4S dicluster domain
      0.075   13.6  18.2       0.31   11.6   2.4    3.1  4  Fer4_17        4Fe-4S dicluster domain
       0.15   12.2  19.7       0.24   11.6   4.2    3.4  3  Fer4_2         4Fe-4S binding domain
       0.26   11.7  18.2      0.099   13.1   2.1    3.0  4  Fer4_8         4Fe-4S dicluster domain
       0.44   11.3   8.8        1.7    9.4   0.1    2.9  2  Fer4_15        4Fe-4S single cluster domain
       0.54   11.2  15.2       0.38   11.7   0.5    3.2  3  Fer4_16        4Fe-4S double cluster binding domain
       0.56   10.8  21.8       0.33   11.6  15.3    3.2  3  Fer4_7         4Fe-4S dicluster domain
        1.3    9.2   8.9       0.27   11.5   1.1    2.6  2  Fer4_18        4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   2.2       5.4   5.7e+03      73     100 ..      50      79 ..      16     110 .. 0.62
   2 !  125.3   0.0   1.7e-39   1.8e-36       2     154 ..     209     360 ..     208     361 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5.4
                       FrhB_FdhB_C  73 elkdekeislkelee..firpsCkvCkdkt 100
                                       +l+d+++is  +l++  +++  C  C    
  gi|298674974|ref|YP_003726724.1|  50 TLEDKEKISFGKLNKeiIKPGICTLCGACA 79 
                                       344455556665555553333444444333 PP

  == domain 2  score: 125.3 bits;  conditional E-value: 1.7e-39
                       FrhB_FdhB_C   2 kkvavvGtPCqiaalrklqk......kklkekilltiglfCggnfspealrklleelgvdpedvkklefrgkgkfrv 72 
                                       + +a+vGt+C+i a+ k+qk      + + ++  l +glfC+++f++++++++ e +g++ e + ++++r kg+f+ 
  gi|298674974|ref|YP_003726724.1| 209 RSIAFVGTSCNIDAVTKMQKspygflHMFMRANILKLGLFCMDTFYYDGIKEFVENHGMKLEAIDSMKIR-KGRFEF 284
                                       789***********************8889999************************************7.****** PP

                       FrhB_FdhB_C  73 elkd.ekeislkeleefirpsCkvCkdktaelADisvGdvwgpekkgdddegvstvlvrtekgeellekaveagele 148
                                       ++ d + +++l+++++++++sC++C+d  +e+ADis+G +      g +++g +tv++r+ +g e++++av++g+++
  gi|298674974|ref|YP_003726724.1| 285 YMGDeVRSYNLSDFDSYRSSSCRFCTDLASENADISFGGI------G-SPDGCTTVIARSGMGYEIFNEAVDRGYIK 354
                                       ***9988999******************************......9.***************************** PP

                       FrhB_FdhB_C 149 leelde 154
                                       +++l++
  gi|298674974|ref|YP_003726724.1| 355 ARQLTQ 360
                                       *99876 PP

>> FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.2   0.1   8.8e-26   9.3e-23      14      77 ..     136     200 ..     126     201 .. 0.93
   2 ?    1.6   0.0      0.29   3.1e+02      18      42 ..     337     361 ..     332     373 .. 0.81

  Alignments for each domain:
  == domain 1  score: 80.2 bits;  conditional E-value: 8.8e-26
                       FrhB_FdhB_N  14 kaqsGGivtallkylLeegiidgvivvaps.kdpwrpkpviattkeellaaaGskYtlspnlklL 77 
                                       ++q+G +vt++l+y+L+eg+id++iv++ s ++pw+p+p++at+ eel++a+GskY +s+++++L
  gi|298674974|ref|YP_003726724.1| 136 EGQDGAVVTSMLAYALDEGLIDCAIVTTTSnEEPWKPIPIVATSYEELVKARGSKYIHSMTMEAL 200
                                       69**************************9999*****************************9998 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.29
                       FrhB_FdhB_N  18 GGivtallkylLeegiidgvivvap 42 
                                        G+  +++ ++ ++g+i +   +++
  gi|298674974|ref|YP_003726724.1| 337 SGMGYEIFNEAVDRGYIKARQLTQK 361
                                       59999************88666665 PP

>> YHS  YHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   2.1   2.1e-09   2.3e-06       2      39 ..       3      39 ..       3      42 .. 0.94

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 2.1e-09
                               YHS  2 tdPvcgmkvdkekaeekseYkGkeYyFcSegCkdkFed 39
                                      +dP c++ v  e +e+ se +Gk  yFc+++Ck kF++
  gi|298674974|ref|YP_003726724.1|  3 IDPICKKEV-SESSEYVSESGGKNQYFCCPECKKKFDE 39
                                      59*******.777***********************96 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   3.5   0.00019       0.2       3      18 ..      67      82 ..      65      84 .. 0.88
   2 !   15.7   3.5   9.2e-06    0.0097       6      19 ..      96     109 ..      94     110 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00019
                                      EETTTSSS-THHHHHS CS
                              Fer4  3 ideekCigCGaCvevC 18
                                      i +  C+ CGaC+  C
  gi|298674974|ref|YP_003726724.1| 67 IKPGICTLCGACAATC 82
                                      77889*********99 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 9.2e-06
                                       TTSSS-THHHHHST CS
                              Fer4   6 ekCigCGaCvevCP 19 
                                        kC++CG C++ CP
  gi|298674974|ref|YP_003726724.1|  96 GKCTACGVCYNQCP 109
                                       69************ PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   7.9     0.015        16      23      55 ..      34      82 ..      27      83 .. 0.64
   2 !   19.6  13.3   6.9e-07   0.00073       3      56 .]      66     109 ..      64     109 .. 0.95
   3 ?   -1.3   0.0       2.4   2.5e+03      39      49 ..     300     310 ..     288     315 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.015
                           Fer4_10 23 l...............tsvgakgeaseeeavrk.kvekCtgcgaCveaC 55
                                                      t  +++++  ++  +++ k++ Ct cgaC++ C
  gi|298674974|ref|YP_003726724.1| 34 KkkfdelensvirlrrTLEDKEKISFGKLNKEIiKPGICTLCGACAATC 82
                                      4455555555555555555556666666666666899999999999999 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 6.9e-07
                           Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +i +  C+ Cg+C + C          + + +e+++ k  +kCt+cg C+ +CP
  gi|298674974|ref|YP_003726724.1|  66 IIKPGICTLCGACAATC----------ESIVIEGEQPKLRGKCTACGVCYNQCP 109
                                       688999***********..........89************************9 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.4
                           Fer4_10  39 rkkvekCtgcg 49 
                                       +  +++C +c+
  gi|298674974|ref|YP_003726724.1| 300 SYRSSSCRFCT 310
                                       55667777775 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   6.4    0.0078       8.2       8      48 ..      29      84 ..      25      87 .. 0.67
   2 !   17.1  13.4   4.2e-06    0.0044       2      49 ..      72     111 ..      71     113 .. 0.87
   3 ?   -0.9   0.0       1.8   1.9e+03      33      40 ..     301     310 ..     278     331 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0078
                            Fer4_9  8 CveaCpagvvvedaaerkarlraase...............eaCigCgaCveaCpk 48
                                      C + C+++  + +++    r + +++                 C+ CgaC++ C++
  gi|298674974|ref|YP_003726724.1| 29 CCPECKKKFDELENSVIRLRRTLEDKekisfgklnkeiikpGICTLCGACAATCES 84
                                      5556666666555555555544444466777777777888877999****999986 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 4.2e-06
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                       Ct CgaC + C++ v+++++ +   +        C+ Cg C++ Cp++
  gi|298674974|ref|YP_003726724.1|  72 CTLCGACAATCESIVIEGEQPKLRGK--------CTACGVCYNQCPRT 111
                                       ************99998887766544........************97 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.8
                            Fer4_9  33 e..eaCigCg 40 
                                       +  ++C +C 
  gi|298674974|ref|YP_003726724.1| 301 YrsSSCRFCT 310
                                       3556788776 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   1.7   0.00082      0.86       4      15 ..      72      83 ..      63      86 .. 0.92
   2 !   17.3   1.5   4.5e-06    0.0047       3      15 ..      97     109 ..      95     121 .. 0.92
   3 ?   -0.9   0.2       3.1   3.2e+03       7      12 ..     306     311 ..     304     311 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00082
                            Fer4_4  4 CigCgsCvaaCP 15
                                      C+ Cg+C a+C+
  gi|298674974|ref|YP_003726724.1| 72 CTLCGACAATCE 83
                                      ***********8 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 4.5e-06
                            Fer4_4   3 rCigCgsCvaaCP 15 
                                       +C+ Cg+C++ CP
  gi|298674974|ref|YP_003726724.1|  97 KCTACGVCYNQCP 109
                                       7************ PP

  == domain 3  score: -0.9 bits;  conditional E-value: 3.1
                            Fer4_4   7 CgsCva 12 
                                       C+ C++
  gi|298674974|ref|YP_003726724.1| 306 CRFCTD 311
                                       999986 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.9    0.0001      0.11       4      23 ..      67      86 ..      66      87 .. 0.86
   2 ?   12.4   1.6   0.00012      0.13       7      20 ..      96     109 ..      95     119 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0001
                            Fer4_6  4 idpdkCigCgdCvrvCPega 23
                                      i+p  C+ Cg+C++ C   +
  gi|298674974|ref|YP_003726724.1| 67 IKPGICTLCGACAATCESIV 86
                                      68899***********8655 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00012
                            Fer4_6   7 dkCigCgdCvrvCP 20 
                                        kC+ Cg C++ CP
  gi|298674974|ref|YP_003726724.1|  96 GKCTACGVCYNQCP 109
                                       59************ PP

>> ATPase-cat_bd  Putative metal-binding domain of cation transport ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   1.0   1.5e-05     0.016       5      36 ..       7      38 ..       6      46 .. 0.90
   2 ?   -0.0   0.5       1.4   1.5e+03      28      42 ..      75      89 ..      54      92 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.5e-05
                     ATPase-cat_bd  5 CglpveesaklkaeiegeerefCCkGCqavaq 36
                                      C+++v+es+++ +e  g++++fCC+ C+  ++
  gi|298674974|ref|YP_003726724.1|  7 CKKEVSESSEYVSESGGKNQYFCCPECKKKFD 38
                                      9**************************97665 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.4
                     ATPase-cat_bd 28 CkGCqavaqliveag 42
                                      C  C+a ++ iv +g
  gi|298674974|ref|YP_003726724.1| 75 CGACAATCESIVIEG 89
                                      999******999777 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7  11.5   4.8e-05     0.051       3      52 ..      67     109 ..      65     114 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.8e-05
                           Fer4_21   3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCP 52 
                                       i++  C  Cg C+ +Ce      i i++++  + +  +C++C +C++ CP
  gi|298674974|ref|YP_003726724.1|  67 IKPGICTLCGACAATCE-----SIVIEGEQ--PKLRGKCTACGVCYNQCP 109
                                       78889************.....47776554..67899************* PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   4.7     0.002       2.1       8      58 ..      29      84 ..      25      87 .. 0.56
   2 ?    9.6   3.3    0.0013       1.3      45      58 ..      97     110 ..      88     113 .. 0.66
   3 ?   11.6   2.4    0.0003      0.31       1      20 [.      97     116 ..      97     143 .. 0.76
   4 ?   -2.1   0.1       5.6   5.9e+03       4      10 ..     305     311 ..     304     338 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.002
                           Fer4_17  8 ClpeCpsyeaydnepkkllraaklglleeaeke......ekaslCieCgeCerkCPq 58
                                      C peC    + + e+  ++ + +l+++e+++         k + C+ Cg C++ C +
  gi|298674974|ref|YP_003726724.1| 29 CCPECKKKFD-ELENSVIRLRRTLEDKEKISFGklnkeiIKPGICTLCGACAATCES 84
                                      5555654333.223344444444544444322233332448899***********75 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0013
                           Fer4_17  45 lCieCgeCerkCPq 58 
                                       +C+ Cg C  +CP 
  gi|298674974|ref|YP_003726724.1|  97 KCTACGVCYNQCPR 110
                                       66666666666665 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.0003
                           Fer4_17   1 rCiqCgyClpeCpsyeaydn 20 
                                       +C+ Cg C ++Cp+ + +++
  gi|298674974|ref|YP_003726724.1|  97 KCTACGVCYNQCPRTITTEE 116
                                       69999999999999877655 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 5.6
                           Fer4_17   4 qCgyClp 10 
                                       +C++C++
  gi|298674974|ref|YP_003726724.1| 305 SCRFCTD 311
                                       6888887 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   2.7    0.0016       1.7       6      20 ..      68      82 ..      65      84 .. 0.87
   2 ?   11.6   4.2   0.00023      0.24       9      21 ..      97     109 ..      92     110 .. 0.91
   3 ?   -0.7   0.2       1.9     2e+03      12      18 ..     305     311 ..     304     312 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0016
                            Fer4_2  6 dtdrCigCgaCvsaC 20
                                       + +C+ CgaC   C
  gi|298674974|ref|YP_003726724.1| 68 KPGICTLCGACAATC 82
                                      6789*******9999 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00023
                            Fer4_2   9 rCigCgaCvsaCP 21 
                                       +C++Cg C++ CP
  gi|298674974|ref|YP_003726724.1|  97 KCTACGVCYNQCP 109
                                       8********99*9 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.9
                            Fer4_2  12 gCgaCvs 18 
                                       +C+ C++
  gi|298674974|ref|YP_003726724.1| 305 SCRFCTD 311
                                       6999985 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   6.6     0.052        55      50      62 ..      71      83 ..      19      86 .. 0.71
   2 ?    8.3   2.6    0.0029       3.1       5      18 ..      72      85 ..      68      96 .. 0.73
   3 ?   10.9   3.3   0.00046      0.49      50      63 ..      97     110 ..      87     112 .. 0.73
   4 ?   13.1   2.1   9.4e-05     0.099       4      19 ..      97     112 ..      95     163 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.052
                            Fer4_8 50 sCttcgaCtevCp 62
                                       Ct cgaC+  C 
  gi|298674974|ref|YP_003726724.1| 71 ICTLCGACAATCE 83
                                      5666666666664 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0029
                            Fer4_8  5 CieCgaCqsaCpvl 18
                                      C+ CgaC ++C ++
  gi|298674974|ref|YP_003726724.1| 72 CTLCGACAATCESI 85
                                      88888888888655 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00046
                            Fer4_8  50 sCttcgaCtevCpv 63 
                                       +Ct+cg C ++Cp 
  gi|298674974|ref|YP_003726724.1|  97 KCTACGVCYNQCPR 110
                                       67777777777776 PP

  == domain 4  score: 13.1 bits;  conditional E-value: 9.4e-05
                            Fer4_8   4 kCieCgaCqsaCpvlr 19 
                                       kC+ Cg C ++Cp   
  gi|298674974|ref|YP_003726724.1|  97 KCTACGVCYNQCPRTI 112
                                       6777777777777333 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   1.1     0.016        17       8      22 ..      72      86 ..      69      93 .. 0.82
   2 ?    9.4   0.1    0.0016       1.7       6      26 ..      96     116 ..      95     154 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.016
                           Fer4_15  8 CigcglCvaeapevf 22
                                      C+ cg+C+a ++ ++
  gi|298674974|ref|YP_003726724.1| 72 CTLCGACAATCESIV 86
                                      ***********7654 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0016
                           Fer4_15   6 daCigcglCvaeapevfelde 26 
                                        +C+ cg+C+  +p+ ++ +e
  gi|298674974|ref|YP_003726724.1|  96 GKCTACGVCYNQCPRTITTEE 116
                                       58*************998875 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   7.8      0.88   9.3e+02      44      64 ..      62      82 ..      21      84 .. 0.58
   2 ?    7.3   2.6    0.0087       9.1       2      20 ..      72      90 ..      71      96 .. 0.85
   3 ?   11.7   0.5   0.00036      0.38       1      20 [.      97     116 ..      97     138 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.88
                           Fer4_16 44 deekckkqeaitgCdiCqdvC 64
                                       +++  k + +t C++C+++C
  gi|298674974|ref|YP_003726724.1| 62 LNKEIIKPGICTLCGACAATC 82
                                      333333445678888888888 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0087
                           Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                      C+ Cg+Ca +C + +i+++
  gi|298674974|ref|YP_003726724.1| 72 CTLCGACAATCESIVIEGE 90
                                      9**********99999887 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00036
                           Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                       +C+ Cg C + CP    +e+
  gi|298674974|ref|YP_003726724.1|  97 KCTACGVCYNQCPRTITTEE 116
                                       5************9877665 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   5.9    0.0044       4.6      14      49 ..      42      83 ..      27      86 .. 0.57
   2 ?   11.6  15.3   0.00031      0.33       2      50 ..      72     110 ..      71     112 .. 0.87
   3 ?   -0.7   0.1       2.1   2.2e+03       4      11 ..     305     312 ..     297     333 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0044
                            Fer4_7 14 vkaieldeeenekgt......ekveidpekClgCgaCvavCP 49
                                      +++i+l+   ++k++       k  i+p  C+ CgaC+a+C 
  gi|298674974|ref|YP_003726724.1| 42 NSVIRLRRTLEDKEKisfgklNKEIIKPGICTLCGACAATCE 83
                                      455555544444433333334555678888999999999995 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00031
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPt 50 
                                       C+ CgaC+a+C + +ie ++        k      kC+ Cg+C + CP 
  gi|298674974|ref|YP_003726724.1|  72 CTLCGACAATCESIVIEGEQP-------K---LRGKCTACGVCYNQCPR 110
                                       *****************9775.......2...3469************7 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 2.1
                            Fer4_7   4 gCgaCvaa 11 
                                        C++C++ 
  gi|298674974|ref|YP_003726724.1| 305 SCRFCTDL 312
                                       48888765 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   1.7      0.46   4.9e+02      59      72 ..      70      83 ..      45      91 .. 0.68
   2 ?   11.5   1.1   0.00025      0.27      53      81 ..      90     118 ..      84     123 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.46
                           Fer4_18 59 gdcidcescvkvcP 72
                                      g c+ c++c + c 
  gi|298674974|ref|YP_003726724.1| 70 GICTLCGACAATCE 83
                                      55777777766664 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00025
                           Fer4_18  53 rkekgagdcidcescvkvcPtgidirkGl 81 
                                       ++ k  g+c++c++c + cP  i   +Gl
  gi|298674974|ref|YP_003726724.1|  90 EQPKLRGKCTACGVCYNQCPRTITTEEGL 118
                                       5678899****************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.61u 0.25s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2518.61
//
Query:       gi|298674975|ref|YP_003726725.1|  [L=93]
Description: glutamyl-tRNA(Gln) amidotransferase subunit C [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-20   73.3   0.9    2.1e-20   72.8   0.9    1.2  1  Glu-tRNAGln  Glu-tRNAGln amidotransferase C subunit
  ------ inclusion threshold ------
      0.082   12.9   0.2       0.12   12.4   0.2    1.4  1  DUF2420      Protein of unknown function (DUF2420)


Domain annotation for each model (and alignments):
>> Glu-tRNAGln  Glu-tRNAGln amidotransferase C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.8   0.9   2.3e-24   2.1e-20       1      61 [.      18      88 ..      18      88 .. 0.94

  Alignments for each domain:
  == domain 1  score: 72.8 bits;  conditional E-value: 2.3e-24
                                      --HHHHHHHHHHHHHHHHHHTTCGCS--TT----S.......-EB-S--.....HHHHHTT-SSEETTEEE CS
                       Glu-tRNAGln  1 lseeEleklakelnsildyveqLqevdttgveplthp.....vlReDev.....reelLknApetedgyfv 61
                                      ++e++++++a++ln++l+++eqL+evdt++v+p++h+     v+ReD++     ++++L+n +++++gyf+
  gi|298674975|ref|YP_003726725.1| 18 IDEKDADEYASQLNDVLNHFEQLDEVDTENVPPTYHVidlvnVFREDVAresltQDKALENTSSSKEGYFK 88
                                      58999******************************************7567998888*************8 PP

>> DUF2420  Protein of unknown function (DUF2420)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   1.4e-05      0.12      45      82 ..      15      50 ..       3      64 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.4e-05
                           DUF2420 45 dltltEdnvynkdislndilsifkiLkenskseedvpe 82
                                       +++ E++    + +lnd+l+ f++L e +  +e+vp 
  gi|298674975|ref|YP_003726725.1| 15 RIEIDEKDADEYASQLNDVLNHFEQLDEVD--TENVPP 50
                                      68999999999*******************..777773 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 687.81
//
Query:       gi|298674976|ref|YP_003726726.1|  [L=475]
Description: glutamyl-tRNA(Gln) amidotransferase subunit A [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   5.1e-159  530.0   0.1   5.8e-159  529.8   0.1    1.0  1  Amidase   Amidase


Domain annotation for each model (and alignments):
>> Amidase  Amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  529.8   0.1  3.2e-163  5.8e-159       1     451 []      21     454 ..      21     454 .. 0.98

  Alignments for each domain:
  == domain 1  score: 529.8 bits;  conditional E-value: 3.2e-163
                                       HHHHHHHHHHHHHHHHH--EEEEEHCCCCHHHHT---TTT......TTTT-EEEEETTB--TTSB--TTSGGGTT-B CS
                           Amidase   1 elveaflkrieavneklnalvtvfieealaqAakldkkrargkekgpLhGvPisvKDnidvkgvpttaGskalenyp 77 
                                       e+++++l++i++  +k+n  + ++++ea ++A+ +dk+      +g L+GvP++vKDni++ g+ptt++s++le+y+
  gi|298674976|ref|YP_003726726.1|  21 EVLNSYLEKINK--SKMN-GYSTVYDEAVEEARDIDKNGH----NGILAGVPVAVKDNISTDGIPTTCCSRILEGYT 90 
                                       7999******99..9999.99999************9986....********************************* PP

                                       -SS--HHHHHHHHTT-EEEEEE--SGGG-SSSSTT-TT---BBTTCTCCB--SSSHHHHHHHHTTSSSCEEEEESSS CS
                           Amidase  78 aekDatvverLkkaGavilgkTnmdefamgsstensvfgptrNPwdksrtpGGSSGGsAAavAaglvplaiGtDtGG 154
                                       +++Da+vverLk++Ga+++gkTnmdefamg+ste+s++gpt NPwd+ ++pGGSSGGsAA++Aa+ +p+++G+DtGG
  gi|298674976|ref|YP_003726726.1|  91 PPYDAHVVERLKSEGAIVIGKTNMDEFAMGTSTETSCYGPTLNPWDTGKVPGGSSGGSAAVIAADEAPVSLGSDTGG 167
                                       ***************************************************************************** PP

                                       TTHHHHHHCTSEEEE--TTSC--TTB--SSTTT-EEEEEESSHHHHHHHHHHHBS--TT-TTS----HHHHHHHHCT CS
                           Amidase 155 SiRiPAsfcglvGlKPtygrvSragvvalessldvvGplarsvedlalllrvilgedpkdstssvipeesedlaeel 231
                                       S+R+PAs+cg+vGlKPtyg vSr+g++++++sl+++Gpla +v+d+a++++vi g+d++dsts +   ++ +++++l
  gi|298674976|ref|YP_003726726.1| 168 SVRCPASYCGVVGLKPTYGTVSRYGLISYANSLEQIGPLANNVSDVAIMMDVIGGHDTRDSTSVS---QKTNYQNAL 241
                                       ****************************************************************8...679****** PP

                                       T---TT-EEEEEGGGCSS---CCHHHHHHHHHHHHHCTT-EEEEEE-CCGGGHHHHHHHHHHHHHHHHTTT-SSSSS CS
                           Amidase 232 kkslkglriGvvkedgvasldpevqravekalkaLeeaGhevvevelpsleealslyylilvaeassnlarylgvry 308
                                       k + +gl+iG+++e++ + + pev+++v +a+++ e++G++ ++v++p+  +als+yy+i+++eassnlar++g ry
  gi|298674976|ref|YP_003726726.1| 242 KDDVNGLKIGIPEEYFGEGIYPEVEESVWNAIHKFEDMGATWEKVSMPNTSYALSAYYIIAMSEASSNLARFDGTRY 318
                                       ***************************************************************************** PP

                                       ---SS-SCCCCCCCHHHHCCS-HHHHHHHHHHHHHCSCCCCCCCHHHHHHHHHHHHHHHHHHCCCBSEEEEESSSSS CS
                           Amidase 309 erlsetkvlsellpksraellgeevkrrielgnyalsaeasskyylkaqkvrrllrrefakafeelDvllsPtaptp 385
                                          ++ ++++ + +++ra+++g+ev+rri lg+yalsa++++kyylka kvr+l++++f +a+  +Dvl++Pt+pt+
  gi|298674976|ref|YP_003726726.1| 319 GYRADGDNWHVMASRTRAQGFGTEVQRRILLGTYALSAGYYDKYYLKALKVRTLVKQDFENALSNVDVLMTPTMPTT 395
                                       666666777******************************************************************** PP

                                       --BCCCCCHHHCSHHHHHGCCTTT...HHHHHTT--EEEEECCCCT.TECEEEEEEESTT-HHHHH CS
                           Amidase 386 aprlgekdktidsytvlynlldftavvvpvnlaglpalsvpagksedglPvGvqvigkafqeetlL 451
                                       a++lgek    +++++ly+ ++ t   vpvnlag p++svp+g+s+ glP+G+q+igk+f+e+t+L
  gi|298674976|ref|YP_003726726.1| 396 AFKLGEKI---KDPLSLYLADVNT---VPVNLAGVPSISVPCGFSD-GLPIGLQIIGKHFNESTIL 454
                                       *******7...79***********...*****************96.****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3407.04
//
Query:       gi|298674977|ref|YP_003726727.1|  [L=473]
Description: glutamyl-tRNA(Gln) amidotransferase subunit B [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   1.1e-103  346.3   0.0   1.8e-103  345.7   0.0    1.3  1  GatB_N     GatB/GatE catalytic domain
    1.1e-43  148.6   3.6    1.9e-43  147.9   3.6    1.4  1  GatB_Yqey  GatB domain


Domain annotation for each model (and alignments):
>> GatB_N  GatB/GatE catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  345.7   0.0    2e-107  1.8e-103       1     270 [.       9     287 ..       9     290 .. 0.97

  Alignments for each domain:
  == domain 1  score: 345.7 bits;  conditional E-value: 2e-107
                                       EEEEEEEEEEB--.SB-SSSSSBSSSSCESTTSS--TTTTTSTT..--EEHHHHHHHHHHHHHTTEEE-SEE-EEEE CS
                                       xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N   1 lviGlEiHaqlkt.ksKlFssasteeegeepnsevsevdlalPGtlPvlnkeavelaikaalalnceiaeeskfdRK 76 
                                       +viGlEiH+ql++ +sK+F+++st  +++epns++++v+l+lPG+lPv+n++ave+a+k++lalnc+i e+++f+RK
  gi|298674977|ref|YP_003726727.1|   9 VVIGLEIHVQLNKlNSKMFCACSTDYHNSEPNSNTCPVCLGLPGSLPVINEKAVESAMKVGLALNCDIVEQTQFHRK 85 
                                       69*********998*********8778899*********************************************** PP

                                       E-TCTTCTTSEEEEESSS.SEEEEEEEE.....TEEEEEEEEEEEE---EEEE....EETTEEEEETTSTT-EEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxx RF
                            GatB_N  77 nyfypdlpkgyQitqkeeplakeGslel.....ekkvrierihlEeDaaksvh....eekeeslvdlnRaGvpLiEi 144
                                       nyfypdlpkg+Qitq++ p+a++G++ +     e+ vri+r+h+EeD ++++h    e+++ +l+d+nR+G++L+Ei
  gi|298674977|ref|YP_003726727.1|  86 NYFYPDLPKGFQITQYDYPIANDGKIAIesdegEHVVRIKRAHMEEDPGRMMHigniEKSKGTLIDYNRSGMALLEI 162
                                       ***************************9999988889*****************99978889*************** PP

                                       EE-STB-SHHHHHHHHHHHHHHHHHHTSB--SGGGTTEEEEEEEEECTSETTSSS.--EEEEEE-SHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 145 vtepdlrspeearavveklrellralgvsdgnmeeGslRcDvNvSvreeekgeeegtrvEiKnlnslksiekaieye 221
                                       vtepd+r+p+ear++++klr+++++l+v d n+ eG++R+D+N+S++        g r+E+Kn++s k  e+a+ ye
  gi|298674977|ref|YP_003726727.1| 163 VTEPDIRNPKEARRFLDKLRNIIEYLEVFDSNL-EGAMRVDANISLQG-------GSRTEVKNISSHKGAERALLYE 231
                                       *********************************.7************4.......49******************** PP

                                       HHHHHHHH.......-EEEEEETTTTEEEEECC----...-EEE-TTS--EE--HH CS
                                       xxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 222 ierqiell.......qeTrkfdedkgetvslRskeeaedYryfpepdlppleisee 270
                                       i rq +++        eTr+fde+kg tv lRske+++dYryfpepdl+p+++ ++
  gi|298674977|ref|YP_003726727.1| 232 IMRQKNIMrrggeviMETRHFDEEKGCTVGLRSKEAEHDYRYFPEPDLTPIRVADR 287
                                       ****************************************************9876 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.9   3.6   2.1e-47   1.9e-43       1     148 []     328     471 ..     328     471 .. 0.98

  Alignments for each domain:
  == domain 1  score: 147.9 bits;  conditional E-value: 2.1e-47
                                       HHHHHHHHHSS.HHHHHHHHHTCHHHHHHHHTXXTTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHHTXXHH CS
                         GatB_Yqey   1 dffeevvkegadaklaanwllnellgelnkegleieelkltpeqlaellkliaegkIskkiakevleelleegkspe 77 
                                       +ffee++ke  d+k+ a+w+++ l geln+++l++++  ++ e++  +++++ ++kI++k+a ev++++l+ g++p+
  gi|298674977|ref|YP_003726727.1| 328 EFFEEIAKEV-DPKTSASWVADVLKGELNYRELTVDA--FKVEDMISIIQMVTQDKITEKSAVEVIRQILDYGGKPD 401
                                       59*******7.**************************..9******************************99***** PP

                                       HHHHHCTXXXXXXSSXHHHHHHHHHHTXHHHHHHHTTXXTTSTHHHHHHHHHTTSSXSXHHHHHHHHHHHS CS
                         GatB_Yqey  78 eiieekgLkqisdeeeleklveeviaenpkavedyksgkekalkflvGqvMkktkGkadpklvnellkekL 148
                                       ei++e+gL ++++ + + k+v e+i+en++av+dy +gkek+l++lvGqvMkkt+G+ad+k+v+ell ++L
  gi|298674977|ref|YP_003726727.1| 402 EIVRENGLLKVEE-DVVSKAVTETIQENEQAVNDYFAGKEKSLNYLVGQVMKKTRGRADAKEVRELLVDEL 471
                                       ***********97.*****************************************************8876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3482.59
//
Query:       gi|298674978|ref|YP_003726728.1|  [L=131]
Description: hypothetical protein Metev_1046 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-16   60.4   0.0    1.7e-16   60.3   0.0    1.0  1  DUF498         Protein of unknown function (DUF498/DUF598)
  ------ inclusion threshold ------
      0.035   14.5   0.1       0.11   12.9   0.0    1.8  2  DUF1104        Protein of unknown function (DUF1104)
       0.11   11.9   0.0       0.12   11.7   0.0    1.1  1  Indigoidine_A  Indigoidine synthase A like protein
       0.13   12.8   1.1        0.4   11.3   1.1    1.9  1  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> DUF498  Protein of unknown function (DUF498/DUF598)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.0   3.7e-20   1.7e-16       1     109 []      12     128 ..      12     128 .. 0.91

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 3.7e-20
                                       EEEEESSEEEETTEEESSEEEE-SSSE.EE-T.....HCS.TTCEECHHHHHHCT..T..SEEEEE-TTS.-----H CS
                            DUF498   1 idaygeggfelngvkysgsllvlpeea.fawd.....vak.aedlteeslellellepkpellilGtGkr.qlplsp 69 
                                       id++++g+++++g+ky ++++++p+++  +++     +++ +++l +e+++++    ++++++++G G++ +l+l +
  gi|298674978|ref|YP_003726728.1|  12 IDGTEFGSITIDGKKYGHDVVIYPQKIeKRMKeisknKYGsGHKLCKEEMQEYLKNLDNIDTVVVGNGQNgVLQLLD 88 
                                       899**********************99555546777656779**********9666789****************** PP

                                       HHHHHHHCCTSEEEEE-HHHHHHHHHHHHHHT--EEEEEE CS
                            DUF498  70 evrealnelgigvevmdtraAartyNllaaegrrVaaaLi 109
                                       e+ ++l+++g++v   +t++A+  +N  ++ +++V+++++
  gi|298674978|ref|YP_003726728.1|  89 ETEKMLEDKGVEVINRKTPEAINDFNQKIQTKNKVLGIFH 128
                                       ***********************************99886 PP

>> DUF1104  Protein of unknown function (DUF1104)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.5e-05      0.11      11      60 ..      20      69 ..       8      79 .. 0.84
   2 ?   -0.5   0.0      0.36   1.6e+03      16      48 ..     104     117 ..      82     124 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.5e-05
                                      HHTTTTS-GGGHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHTTS- CS
                           DUF1104 11 iklaGkvapeevldykmevaKrlkslkekekkkfkkklkeaaeknlekmt 60
                                      i + Gk+  ++v+ y   ++Kr+k++++++  + +k  ke++++ l+++ 
  gi|298674978|ref|YP_003726728.1| 20 ITIDGKKYGHDVVIYPQKIEKRMKEISKNKYGSGHKLCKEEMQEYLKNLD 69
                                      566799999*********************99999999999999998875 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.36
                                       TS-GGGHHHHHHHHHHHHHHS-HHHHHHHHHHH CS
                           DUF1104  16 kvapeevldykmevaKrlkslkekekkkfkkkl 48 
                                        ++pe + d++                   +k+
  gi|298674978|ref|YP_003726728.1| 104 RKTPEAINDFN-------------------QKI 117
                                       33333333333...................333 PP

>> Indigoidine_A  Indigoidine synthase A like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.8e-05      0.12     135     178 ..      65     109 ..      48     124 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.8e-05
                                       HHHHTTS-EEEEESBB-TTS-H.HHHHHHHHHTT--EEEES-SB- CS
                     Indigoidine_A 135 LteLartpvavvcaGvksiLdi.prtleyLetqgvpvvtyktdef 178
                                       L++L + +++vv  G + +L + ++t  +Le +gv v+  kt e 
  gi|298674978|ref|YP_003726728.1|  65 LKNLDNIDTVVVGNGQNGVLQLlDETEKMLEDKGVEVINRKTPEA 109
                                       899*****************96379999**********9987654 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.1   8.9e-05       0.4      34      72 ..      83     116 ..      59     123 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.9e-05
                                       SSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTS CS
                         Pyr_redox  34 llrllDeeaskilqeklekngievllntkveeiegsedg 72 
                                       +l+llDe+     ++ le++g+ev+  +++e+i+  +++
  gi|298674978|ref|YP_003726728.1|  83 VLQLLDET-----EKMLEDKGVEVINRKTPEAINDFNQK 116
                                       44555555.....99******************965554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1431  (0.0798148); expected 358.6 (0.02)
Passed bias filter:                      881  (0.0491383); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.20s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1071.15
//
Query:       gi|298674979|ref|YP_003726729.1|  [L=173]
Description: PfpI family intracellular protease [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.4e-40  138.1   0.3    2.6e-40  137.9   0.3    1.0  1  DJ-1_PfpI   DJ-1/PfpI family
    0.00022   21.0   0.0     0.0023   17.7   0.0    1.9  1  ThiJ_like   ThiJ/PfpI family-like
     0.0099   15.5   0.1      0.013   15.2   0.1    1.3  1  Catalase_C  C-terminal domain found in long catalases
  ------ inclusion threshold ------
      0.064   12.9   0.0        0.1   12.2   0.0    1.3  1  GATase_3    CobB/CobQ-like glutamine amidotransferase domain
      0.075   12.8   0.0       0.15   11.8   0.0    1.5  1  GATase      Glutamine amidotransferase class-I
      0.082   12.4   0.0        0.1   12.1   0.0    1.1  1  DUF705      Protein of unknown function (DUF705)
      0.091   12.7   0.1       0.73    9.7   0.1    2.0  2  DUF2124     Uncharacterized protein conserved in archaea (DUF


Domain annotation for each model (and alignments):
>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.9   0.3     1e-43   2.6e-40       1     164 [.       4     170 ..       4     171 .. 0.98

  Alignments for each domain:
  == domain 1  score: 137.9 bits;  conditional E-value: 1e-43
                                       EEEEEEEE.TTBEHHHHHHHHHHHHHTTEEEEEEESSTSEEEETTSEEEE-SEEGGGCTCCG-SEEEE--BHHHHHH CS
                         DJ-1_PfpI   1 kkvlvlla.dgvedvElivpvdvlkragikvdvvsvdkeevkgsrGlkvtvdaslddvkaaeyDalvlpGGragper 76 
                                       kkvl+++a ++++d E+++p +v++++g++v+v+s+d+++ +g+ G + ++d +++d++ ++yDa+v+ GG  + e+
  gi|298674979|ref|YP_003726729.1|   4 KKVLMVIAqENFRDEEFFEPKKVFENNGVDVTVASTDTKTATGMLGGTAKPDIKISDADMDDYDAIVISGGSGSKEY 80 
                                       79*****999******************************************************************* PP

                                       HHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTTSEE--SGGGH..HHHHHTTSEE-SSSEEEETTEEEESS CS
                         DJ-1_PfpI  77 lrenekvvelvkefaekgklvaaICagpqlLaaagvlkgrrvTsypavk..dklekagakyvdkrvvvdgnlvTsrg 151
                                       l++ne++ elv ++++++k+v aIC +p++La+ g+l+g++vT +   +  +++++ ga y+ + vv ++n++T +g
  gi|298674979|ref|YP_003726729.1|  81 LWDNEQLHELVNKAYKDDKIVSAICVSPVVLAKSGILEGKNVTVFDDPNsiNEVKECGACYENEGVVNCENIITGKG 157
                                       *********************************************8888779************************* PP

                                       GGGHHHHHHHHHH CS
                         DJ-1_PfpI 152 pgaaiefalelle 164
                                       p+ a++f++++l+
  gi|298674979|ref|YP_003726729.1| 158 PDYAEQFGEAVLD 170
                                       ********99986 PP

>> ThiJ_like  ThiJ/PfpI family-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   8.8e-07    0.0023      80     141 ..      31     114 ..      16     152 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 8.8e-07
                         ThiJ_like  80 F..............................sleeydlvllpGGsdkavrelleserlhsllveylklvkrekepsk 126
                                                                      ++++yd++ + GGs+     l ++e+lh+l+++         +++k
  gi|298674979|ref|YP_003726729.1|  31 GvdvtvastdtktatgmlggtakpdikisdaDMDDYDAIVISGGSGSKE-YLWDNEQLHELVNKAY-------KDDK 99 
                                       335555555556666666666666666666699************9975.67899****9988766.......568* PP

                         ThiJ_like 127 vlgaicqgvlalafa 141
                                       +++aic   ++la++
  gi|298674979|ref|YP_003726729.1| 100 IVSAICVSPVVLAKS 114
                                       ******998888876 PP

>> Catalase_C  C-terminal domain found in long catalases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1     5e-06     0.013      21     130 ..      21     128 ..       2     146 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5e-06
                        Catalase_C  21 kalaaalaaegvdvtvvaeklgsaeg.vnrT......YstadaveFDaivvadgaeslfsakataasslfpagrplq 90 
                                        + ++ ++++gvdvtv     ++a+g +  T       s ad  ++Daiv+ +g        + +++ l  +++  +
  gi|298674979|ref|YP_003726729.1|  21 FEPKKVFENNGVDVTVASTDTKTATGmLGGTakpdikISDADMDDYDAIVISGG--------SGSKEYLWDNEQLHE 89 
                                       5557889999999999987777666643333334444899999***********........3556789999***** PP

                        Catalase_C  91 llldayrhgKpigalGsgaealkaagisaeepGVyvadsa 130
                                       l+++ay+  K + a+  +  +l+++gi  e++ V v d+ 
  gi|298674979|ref|YP_003726729.1|  90 LVNKAYKDDKIVSAICVSPVVLAKSGIL-EGKNVTVFDDP 128
                                       ***************9999999999996.46667666654 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     4e-05       0.1      29      84 ..      55     107 ..      47     124 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4e-05
                          GATase_3  29 fvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGG 84 
                                        ++++d ++ +d+d++++ Gg+    +  l ++++l e +++a+++++ v +iC  
  gi|298674979|ref|YP_003726729.1|  55 DIKISDADM-DDYDAIVISGGSGS--KEYLWDNEQLHELVNKAYKDDKIVSAICVS 107
                                       567788888.56********9865..455667779*******************65 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.8e-05      0.15      18      79 ..      28     106 ..      23     115 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.8e-05
                                       HHTT-EEEEEETTSHHHHH............HH.THHSTSEEEEEEESSCTT....TTTHHHHHHHHCTSTS-EEEE CS
                            GATase  18 velgvkvevvpidasaeei............le.llknpdgilvsgGpgspg....vegkieaikearenkiPiLGI 77 
                                        ++gv+v+v   d++  +              +   +++d+i++sgG gs++     e+  e++++a + ++ +  I
  gi|298674979|ref|YP_003726729.1|  28 ENNGVDVTVASTDTKTATGmlggtakpdikiSDaDMDDYDAIVISGGSGSKEylwdNEQLHELVNKAYKDDKIVSAI 104
                                       56667777777666544446777777775542234789**************9998899999999999988888888 PP

                                       TH CS
                            GATase  78 CL 79 
                                       C 
  gi|298674979|ref|YP_003726729.1| 105 CV 106
                                       86 PP

>> DUF705  Protein of unknown function (DUF705)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     4e-05       0.1     188     261 ..      59     127 ..      54     151 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4e-05
                            DUF705 188 revglerslFkiilsgGrtveeekldalkkrflkekivlditnskrlPksvkvvlkyLsdknleffksitLvDD 261
                                        +++++ ++  i++sgG+ ++e+  d+++ + l++k + d +++  +  s+ v  k     ++  +k +t+ DD
  gi|298674979|ref|YP_003726729.1|  59 SDADMD-DYDAIVISGGSGSKEYLWDNEQLHELVNKAYKDDKIVSAICVSPVVLAK----SGILEGKNVTVFDD 127
                                       688999.999****************99999999*********9999999977554....44555555555555 PP

>> DUF2124  Uncharacterized protein conserved in archaea (DUF2124)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.014        36      63     101 ..      27      64 ..      15      66 .. 0.77
   2 ?    9.7   0.1   0.00029      0.73      68     119 ..      56     108 ..      33     120 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.014
                                       EETTEEEEEEE-.-S-EEEEEEEGGGGSTTTS--HHHHH CS
                           DUF2124  63 vtdvGmqleeeaeeekadvvvllGGlampkikveaedvk 101
                                       +++ G++++ +  +++  +  +lGG a p ik++ +d+ 
  gi|298674979|ref|YP_003726729.1|  27 FENNGVDVTVAS-TDTKTATGMLGGTAKPDIKISDADMD 64 
                                       677788888777.444555679***********999986 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00029
                                       EEEEEE-.-S-EEEEEEEGGGGSTTTS--HHHHHHHHHHH..EEEEEEEEEETT CS
                           DUF2124  68 mqleeeaeeekadvvvllGGlampkikveaedvkelieki..ekkkviGvcfms 119
                                       ++++++   ++ d++v+ GG   +++  + e+++el++k+  ++k v  +c   
  gi|298674979|ref|YP_003726729.1|  56 IKISDAD-MDDYDAIVISGGSGSKEYLWDNEQLHELVNKAykDDKIVSAICVSP 108
                                       4566665.8899**************************9985555566788765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1243.89
//
Query:       gi|298674980|ref|YP_003726730.1|  [L=195]
Description: hypothetical protein Metev_1048 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.2e-29  101.0   0.0    6.1e-29  100.5   0.0    1.2  1  UPF0029     Uncharacterized protein family UPF0029
    1.9e-05   24.4   0.2    3.8e-05   23.5   0.2    1.5  1  DUF1949     Domain of unknown function (DUF1949)
  ------ inclusion threshold ------
      0.064   13.5   0.4       0.15   12.3   0.1    1.7  2  OrfB_IS605  Probable transposase


Domain annotation for each model (and alignments):
>> UPF0029  Uncharacterized protein family UPF0029
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.5   0.0     1e-32   6.1e-29       1     105 []      13     119 ..      13     119 .. 0.95

  Alignments for each domain:
  == domain 1  score: 100.5 bits;  conditional E-value: 1e-32
                                       TTEEEEEEEEE-SSHHHHHHHHHHH--..TTSSEEEEEE....EE....TTEE-TTSST..SHHHHHHHHHHTTB-S CS
                           UPF0029   1 kkSrFiavlaaveseeevkaileelkkenkkathniyAyrlrqkvekvnedsdddgEpa..AGkkllelLekeklen 75 
                                       k+S F++++ +v+ e+e+++++e++k+++k+a hn++Ay +++ + ++  ++dddgEpa  +Gk++++++  ++++n
  gi|298674980|ref|YP_003726730.1|  13 KNSVFLGYAEPVNGETEARKFIEKIKNRHKDAAHNVSAYIIKNSN-ELTVKYDDDGEPAgsSGKPVYKVMDLKNIQN 88 
                                       78*************************************555555.69999************************** PP

                                       EEEEEEEE--SS--HHHHH.HHHHHHHHHHH CS
                           UPF0029  76 vlvvvtRwfGGikLGpgrl.raiseaareaL 105
                                       ++vvv+R+fGGikLG g+l ra++e+a ea+
  gi|298674980|ref|YP_003726730.1|  89 AVVVVSRYFGGIKLGFGGLtRAYRETAIEAI 119
                                       *************************998875 PP

>> DUF1949  Domain of unknown function (DUF1949)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.2   6.4e-09   3.8e-05       1      55 [.     135     188 ..     135     189 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 6.4e-09
                           DUF1949   1 ltvdYadlgkverlLeqfgativdteYtddVtltlavpeeeveafkaaLtdltsG 55 
                                       +++dY+ +   + l+eq+ ++i +++Y d V+++  + e+  + f ++L  +t +
  gi|298674980|ref|YP_003726730.1| 135 IRFDYSCIKDAKTLIEQY-GKIDEEHYFDVVEFITDINEDLTDDFVQKLKSITKD 188
                                       6799**************.*******************************99976 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   2.5e-05      0.15      75     108 ..      28      61 ..      24      63 .. 0.90
   2 ?   -2.9   0.0       1.2   7.4e+03      88     112 ..     167     191 ..     162     195 .] 0.53

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.5e-05
                        OrfB_IS605  75 rklarlhrkrsrrrkhllhklathliktlkevgv 108
                                       ++ ++  +k+++r k+++h+++ ++ik+  e+ v
  gi|298674980|ref|YP_003726730.1|  28 TEARKFIEKIKNRHKDAAHNVSAYIIKNSNELTV 61 
                                       6889999*********************999877 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.2
                        OrfB_IS605  88 rkhllhklathliktlkevgvetLn 112
                                       +++  + l+ + +++lk +  ++++
  gi|298674980|ref|YP_003726730.1| 167 ITDINEDLTDDFVQKLKSITKDKVI 191
                                       4555555555555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       944  (0.0526521); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 1560.41
//
Query:       gi|298674981|ref|YP_003726731.1|  [L=410]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-22   79.2   0.2    1.1e-21   77.3   0.0    2.0  2  OrfB_IS605      Probable transposase
    1.1e-10   41.3   0.4    3.9e-10   39.5   0.1    2.2  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    0.00055   19.7   0.3     0.0017   18.2   0.3    1.8  1  DUF919          Nucleopolyhedrovirus protein of unknown funct
     0.0078   16.6   0.0      0.019   15.3   0.0    1.6  1  RuvX            Holliday junction resolvase
  ------ inclusion threshold ------
       0.12   12.2   0.1       0.25   11.2   0.0    1.5  2  MOR2-PAG1_C     Cell morphogenesis C-terminal


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.3      0.91   3.3e+03      37      55 ..      31      49 ..      11      87 .. 0.58
   2 !   77.3   0.0     3e-25   1.1e-21      10     119 ..     185     292 ..     176     293 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.91
                        OrfB_IS605 37 twflykgrrlksdykylak 55
                                      + +ly+ r+++ +y ++ +
  gi|298674981|ref|YP_003726731.1| 31 NFTLYNIRQYFFNYGKYLN 49
                                      3344555444444433333 PP

  == domain 2  score: 77.3 bits;  conditional E-value: 3e-25
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsr 86 
                                        ++ + n++++iDlG+ n+at+vt++gt+f+ +gr +ks +++++ke+ +lqs ++k++       k+   +rkr  
  gi|298674981|ref|YP_003726731.1| 185 IAELDYNSHLSIDLGVDNFATCVTTNGTAFILDGRGIKSYNRWWNKEKSRLQSVYDKQG--LDDGLKINQFSRKRFW 259
                                       66677899**************************************************9..9*************** PP

                        OrfB_IS605  87 rrkhllhklathliktlkevgvetLnvgnmkdi 119
                                       ++++++++ +++++k++ e+ ++++++g++k+i
  gi|298674981|ref|YP_003726731.1| 260 KINDFMNQCVNYIVKHCLENRIGNIVIGELKEI 292
                                       ******************************987 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.3   4.6e+03       9      21 ..     167     179 ..     165     181 .. 0.88
   2 !   39.5   0.1   1.1e-13   3.9e-10       1      69 []     311     385 ..     311     385 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.3
                    OrfB_Zn_ribbon   9 eykakeyGikvee 21 
                                       +yk +++ i++++
  gi|298674981|ref|YP_003726731.1| 167 KYKGRWFEIEYVY 179
                                       79*******9987 PP

  == domain 2  score: 39.5 bits;  conditional E-value: 1.1e-13
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke......alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f+++k++l+ k++ +Gik++ev++ayTSk  +   +  ++      ++s+r    ++ g  +++D+n+a+Nil++
  gi|298674981|ref|YP_003726731.1| 311 FARFKQKLASKCEYHGIKYHEVDEAYTSKVDALALEPIRKhkkylgRRSKRGIFQSSTGRLINADINGALNILRK 385
                                       899**************************8766655544445588*9*************************986 PP

>> DUF919  Nucleopolyhedrovirus protein of unknown function (DUF919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.3   4.6e-07    0.0017      15      58 ..       4      45 ..       2      47 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.6e-07
                            DUF919 15 qaKrkltiksqHfErlkkitKnpkElqdlekklnklRqeFLnfg 58
                                       +K  l+ + q +E lk++tK +k l +   +l ++Rq+F+n+g
  gi|298674981|ref|YP_003726731.1|  4 TQKNHLRADKQTYETLKRLTKLSKNLYNF--TLYNIRQYFFNYG 45
                                      58999******************888765..8***********9 PP

>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   5.3e-06     0.019      37     106 ..     266     345 ..     250     366 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.3e-06
                                       HHHHHHHHHHHHHTT--EEEEE--........----SSS---SSTTHHHHHHHHHT....T-EEEEE--S----XXX CS
                              RuvX  37 ekdleelkelvkeeeveeiVvGlP........lnldgsegesakkvrkfaeeLakrl..kklpvelvDErlttveae 103
                                       ++ ++ + + + e+++ +iV+G          +  +++++ ++  +++f ++La+++  ++++ + vDE +t++  +
  gi|298674981|ref|YP_003726731.1| 266 NQCVNYIVKHCLENRIGNIVIGELkeikqeqnTGKQNNQNFQTIPFARFKQKLASKCeyHGIKYHEVDEAYTSKVDA 342
                                       6889999***************986776665555566667777778999*****99977899***********9765 PP

                                       XXX CS
                              RuvX 104 ril 106
                                        +l
  gi|298674981|ref|YP_003726731.1| 343 LAL 345
                                       555 PP

>> MOR2-PAG1_C  Cell morphogenesis C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.8   6.5e+03      74      89 ..      13      28 ..      10      29 .. 0.82
   2 ?   11.2   0.0   6.9e-05      0.25     146     180 ..     250     284 ..     233     302 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.8
                       MOR2-PAG1_C 74 eatlellskLtklsdd 89
                                      ++t e+l++Ltkls++
  gi|298674981|ref|YP_003726731.1| 13 KQTYETLKRLTKLSKN 28
                                      6899999999999875 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 6.9e-05
                       MOR2-PAG1_C 146 ltsyakgrfrtkddflkqvvkalreayfpehesea 180
                                       +++++++rf + +df++q+v+++ ++++++   ++
  gi|298674981|ref|YP_003726731.1| 250 INQFSRKRFWKINDFMNQCVNYIVKHCLENRIGNI 284
                                       478************************98766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       977  (0.0544927); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2812.94
//
Query:       gi|298674982|ref|YP_003726732.1|  [L=142]
Description: hypothetical protein Metev_1050 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.029   14.8   0.6      0.054   13.9   0.6    1.4  1  L71       L71 family


Domain annotation for each model (and alignments):
>> L71  L71 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.6     3e-06     0.054       7      52 ..       9      54 ..       6      63 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3e-06
                               L71  7 ekCercerrlgkrddnveilNreCrrktrrryrWrnitRCeLqkaa 52
                                      + C++  + +g+ +d+++il ++ +++++   +W nit  +L++ +
  gi|298674982|ref|YP_003726732.1|  9 AICDARLELMGEYKDELDILENNSQQNRNLIKNWLNITNTDLSQCK 54
                                      6799*******************999999999*******9998644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1079.09
//
Query:       gi|298674983|ref|YP_003726733.1|  [L=133]
Description: hypothetical protein Metev_1051 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-63  210.3   1.4    6.7e-63  210.2   1.4    1.0  1  DUF1699   Protein of unknown function (DUF1699)


Domain annotation for each model (and alignments):
>> DUF1699  Protein of unknown function (DUF1699)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.2   1.4   3.7e-67   6.7e-63       1     129 [.       1     129 [.       1     130 [. 0.99

  Alignments for each domain:
  == domain 1  score: 210.2 bits;  conditional E-value: 3.7e-67
                           DUF1699   1 mkirvvsskeeietlnenekivHlafrpsntdilslvkkcpklkaiqvpeSykktlsksakmfleiqgiellegdvw 77 
                                       mkirvvs+k+eie+l+e+e+ivHlafrpsntdi+++v+kcp+lk++++p+Sykktls+sakmfle+qg++llegdvw
  gi|298674983|ref|YP_003726733.1|   1 MKIRVVSAKDEIENLDESEEIVHLAFRPSNTDIFTIVSKCPNLKVLHLPSSYKKTLSESAKMFLEMQGVDLLEGDVW 77 
                                       9**************************************************************************** PP

                           DUF1699  78 ghrkdineyyevseevierikelkseglseeeiaeklsketklspdlikfll 129
                                       ghrkdiney+evs++v+++i+elk++g++ee+i+ek++ket+ls+d++kfl+
  gi|298674983|ref|YP_003726733.1|  78 GHRKDINEYSEVSRNVYKKIDELKEKGIDEEKIVEKMEKETNLSSDFVKFLV 129
                                       **************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       927  (0.0517039); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1057.64
//
Query:       gi|298674984|ref|YP_003726734.1|  [L=352]
Description: CaCA family Na+/Ca+ antiporter [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.8e-54  183.2  42.3    1.7e-28   99.5  16.2    2.0  2  Na_Ca_ex    Sodium/calcium exchanger protein
  ------ inclusion threshold ------
        3.2    7.8  12.3       0.23   11.5   2.1    2.9  3  Flg_bb_rod  Flagella basal body rod protein


Domain annotation for each model (and alignments):
>> Na_Ca_ex  Sodium/calcium exchanger protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.5  16.2   1.9e-32   1.7e-28       3     150 ..       8     147 ..       6     147 .. 0.90
   2 !   89.9  18.1   1.7e-29   1.5e-25       3     150 ..     201     341 ..     199     342 .. 0.88

  Alignments for each domain:
  == domain 1  score: 99.5 bits;  conditional E-value: 1.9e-32
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex   3 fvlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnl 79 
                                       ++++i +ll ++ ++d++v+ a+ iak lg+s+ v+Gltl+++g+s+pEl+ss++a+ ++  +++ign++Gsni+n+
  gi|298674984|ref|YP_003726734.1|   8 LIILITALLSLVKGSDYFVEYASTIAKLLGVSEFVIGLTLVSIGTSIPELASSMAAVFQQAEEIVIGNIIGSNIANI 84 
                                       6899************************************************************************* PP

                                       HTHHHHHHHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex  80 llviGlialigslkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvllllYalylvlsl 150
                                        lv+G+++l++ +k d++ lk d  +++l+a++l++ v+ l         ++++e++++l+lY+ y+++s+
  gi|298674984|ref|YP_003726734.1|  85 ALVVGFAVLFANIKTDRKILKKDG-YIMLFAVILFF-VFSLD------YYISRFEAIIFLFLYLSYIFYSW 147
                                       ***********9999999988777.55555555544.33334......67******************986 PP

  == domain 2  score: 89.9 bits;  conditional E-value: 1.7e-29
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex   3 fvlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnl 79 
                                       fv++ +s ++++++a ++++ a ++a++++is++++G+ l+Alg+slpEl+++ ++a++g++ l +gnv+Gsni n+
  gi|298674984|ref|YP_003726734.1| 201 FVILSISGFAVILGARYFIQQAVYFANIFNISDTIIGISLVALGTSLPELMVTATSAKKGYGYLILGNVIGSNITNT 277
                                       7899999999******************************************************************* PP

                                       HTHHHHHHHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex  80 llviGlialigslkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvllllYalylvlsl 150
                                       +l++Gl++l+ +    +  +  dl ++++  +++l+++lll++ +  +++l++ eg+ lll+Y+l++  +l
  gi|298674984|ref|YP_003726734.1| 278 FLILGLSGLVVP---LGI-VGTDL-FFIMPFMIFLSAILLLFVWT--QWELKRPEGVFLLLVYILFITTLL 341
                                       **********44...332.35566.66666777777777766554..6******************98765 PP

>> Flg_bb_rod  Flagella basal body rod protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   2.1   2.5e-05      0.23      16      30 ..      75      90 ..      75      90 .. 0.96
   2 ?   -1.5   0.1      0.29   2.6e+03      13      26 ..     219     232 ..     219     234 .. 0.79
   3 ?    2.6   0.4     0.015   1.4e+02      16      24 ..     268     276 ..     268     278 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.5e-05
                        Flg_bb_rod 16 dvianNiANan.TtGy 30
                                      ++i++NiAN+  ++G+
  gi|298674984|ref|YP_003726734.1| 75 NIIGSNIANIAlVVGF 90
                                      89************99 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.29
                        Flg_bb_rod  13 ialdvianNiANan 26 
                                       i+++v+ +Ni N++
  gi|298674984|ref|YP_003726734.1| 219 IQQAVYFANIFNIS 232
                                       68999999998876 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.015
                        Flg_bb_rod  16 dvianNiAN 24 
                                       +vi++Ni N
  gi|298674984|ref|YP_003726734.1| 268 NVIGSNITN 276
                                       8******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       964  (0.0537676); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2693.04
//
Query:       gi|298674985|ref|YP_003726735.1|  [L=372]
Description: hypothetical protein Metev_1053 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.6e-73  246.7   0.8      2e-73  246.4   0.8    1.1  1  DUF2117     Uncharacterized protein conserved in archaea (DUF
     0.0075   15.5   0.1      0.011   15.0   0.1    1.2  1  NAD_kinase  ATP-NAD kinase


Domain annotation for each model (and alignments):
>> DUF2117  Uncharacterized protein conserved in archaea (DUF2117)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.4   0.8   2.2e-77     2e-73       1     212 []      76     288 ..      76     288 .. 0.98

  Alignments for each domain:
  == domain 1  score: 246.4 bits;  conditional E-value: 2.2e-77
                           DUF2117   1 DivfLlnygksketGhvFgkiVver.skekkpliqierpgekdgeiilwnekaeklakklseelglkivkpeeveke 76 
                                       Div+Ll ++ks+ +Gh+Fg++V+e+ ++ k p++qie++g+  g ii+w+++++++ak+ls+ lglki++p+++++ 
  gi|298674985|ref|YP_003726735.1|  76 DIVCLLTQSKSVDNGHIFGNMVIEKlDNPKLPVLQIETQGS--GVIIPWTKNSTNHAKSLSDLLGLKISTPMNIVSG 150
                                       9************************8999********9998..********************************** PP

                           DUF2117  77 iveskgkrvvrkiagvspgenilvnGiviGkaeseevtivaedgkivdikggeiKehGvekLgk......vdlekai 147
                                       i+ + g++++r+i+gvspge +++nGi+iG+aes++vtiva++g+i +i+gg+iK+hGvekL+k      vd+e+a+
  gi|298674985|ref|YP_003726735.1| 151 IY-KCGSTIKREISGVSPGECVFLNGIIIGRAESNKVTIVADNGFIKSIEGGTIKQHGVEKLHKydkrvpVDIENAW 226
                                       99.99************************************************************************ PP

                           DUF2117 148 vktgllRrskvkekllkkkklkkkkekkvgkvvlidHaaedvlelakkadlvvtvGDDTTavagd 212
                                       +ktgllRr   + +++ ++k+++++++++++vvlidH+a+++++l  k+d++vt+GDDTT+va+d
  gi|298674985|ref|YP_003726735.1| 227 IKTGLLRR---SCNYSPQVKYNSTGSNNGFRVVLIDHDADNCFDLDFKVDMAVTIGDDTTIVAAD 288
                                       ********...6788899999******************************************98 PP

>> NAD_kinase  ATP-NAD kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   1.2e-06     0.011      69     110 ..     262     302 ..     216     305 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-06
                                       CCC-TTTTTSSSEEEEEE-HHHHHHHHHHHHHCT-EEEEEES CS
                        NAD_kinase  69 kaleafadagvdliivvGGDGTaldvarllqkaeiPvlgvna 110
                                       ++ +   d +vd+++++G+D T+ ++  ++ + ++Pv+g+  
  gi|298674985|ref|YP_003726735.1| 262 ADNCFDLDFKVDMAVTIGDDTTIVAA-DIFYRFAVPVIGIVD 302
                                       5555567899**********999865.566668******965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2827.79
//
Query:       gi|298674986|ref|YP_003726736.1|  [L=126]
Description: hypothetical protein Metev_1054 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00058   20.0   0.0     0.0011   19.1   0.0    1.5  1  HTH_34    Winged helix DNA-binding domain
     0.0019   18.1   0.0     0.0038   17.1   0.0    1.5  1  PadR      Transcriptional regulator PadR-like family
  ------ inclusion threshold ------
      0.047   13.6   0.0      0.069   13.0   0.0    1.3  1  TrmB      Sugar-specific transcriptional regulator TrmB


Domain annotation for each model (and alignments):
>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.8e-07    0.0011       5      63 ..      32      92 ..      30     103 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.8e-07
                            HTH_34  5 vlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYiev..dkefkgkkprtllriTp 63
                                      +l+yL+ v++a+ +e+  ++++ + + s+ ++++ ++++i++  +k+  +++p  ++++T 
  gi|298674986|ref|YP_003726736.1| 32 ALTYLSNVKRASSQEIEMCTGLRQPEVSIAMRTMRDNNWINIynKKTAGKGRPTKIYELTT 92
                                      799*************************************985456666778999999995 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   6.4e-07    0.0038      37      66 ..      61      91 ..      45      93 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.4e-07
                                      HHHHHHHTTSEEEEEE-S.TSSS-EEEEEES CS
                              PadR 37 aLkrLekeglvesewees.gegpprkyYrlT 66
                                      a+++++++++++ +++++ g+g+p+k+Y+lT
  gi|298674986|ref|YP_003726736.1| 61 AMRTMRDNNWINIYNKKTaGKGRPTKIYELT 91
                                      5789************999***********9 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.2e-05     0.069       1      65 [.      20      91 ..      20      94 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.2e-05
                                      HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.......TTEEEE- CS
                              TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.......pklYrav 65
                                      L+ lG+s + a + ++L + ++a+ +ei  ++g+ ++ v  ++r + d  ++++  ++       +k+Y+ +
  gi|298674986|ref|YP_003726736.1| 20 LKSLGMSRNVATALTYLSNVKRASSQEIEMCTGLRQPEVSIAMRTMRDNNWINIYNKKtagkgrpTKIYELT 91
                                      7899*************************************************9988878888866688765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       916  (0.0510904); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 880.04
//
Query:       gi|298674987|ref|YP_003726737.1|  [L=76]
Description: hypothetical protein Metev_1055 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0089   16.1   0.4       0.01   15.9   0.4    1.1  1  FKBP_N_2  BDBT FKBP like N-terminal
  ------ inclusion threshold ------
       0.07   13.8   0.2      0.088   13.5   0.2    1.3  1  ThiS      ThiS family


Domain annotation for each model (and alignments):
>> FKBP_N_2  BDBT FKBP like N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.4   1.1e-06      0.01      15      73 ..      11      64 ..       2      74 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.1e-06
                          FKBP_N_2 15 lgfqklekPtevsscivlveklqnveerkdqllekleleeekeiviGeal.teideyier 73
                                       +++    P + s  +v++ek        ++ll+kl+++ee +iv+ +++ t+id +ie+
  gi|298674987|ref|YP_003726737.1| 11 VDVK--IVPDDNSEQSVNIEKG----ATYEDLLKKLDINEESVIVLNDGNaTPIDGVIES 64
                                      5544..5699999999999998....778899**************9997489*****97 PP

>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   9.8e-06     0.088      13      77 .]      22      76 .]       9      76 .] 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.8e-06
                                      CEEEEESSTSBHHHHHHHHHHHTCHHGTTTTEEEEETTEEEGCCTTTSB--TTCEEEEEESTTC- CS
                              ThiS 13 eeelelaegstvaelleaLgerypelalerrvavavNgeivprlwldtelkdgDevailppVaGG 77
                                      e+ + ++ g+t ++ll++L+ +       + v+v+ +g+  p    d ++ +g ++ +l + +GG
  gi|298674987|ref|YP_003726737.1| 22 EQSVNIEKGATYEDLLKKLDINE------ESVIVLNDGNATPI---DGVIESG-KIQVLKITSGG 76
                                      78889999*************99......88888888887777...6666555.56777776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 561.92
//
Query:       gi|298674988|ref|YP_003726738.1|  [L=58]
Description: hypothetical protein Metev_1056 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       940  (0.052429); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 415.03
//
Query:       gi|298674989|ref|YP_003726739.1|  [L=240]
Description: ApbE family lipoprotein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1770.71
//
Query:       gi|298674990|ref|YP_003726740.1|  [L=132]
Description: 4Fe-4S ferredoxin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-13   49.8  14.2      5e-07   29.3   2.2    2.3  2  Fer4          4Fe-4S binding domain
    7.1e-12   45.3  22.3    1.6e-08   34.6  13.0    1.9  2  Fer4_9        4Fe-4S dicluster domain
    2.3e-11   43.2  15.3    1.8e-06   27.8   2.3    2.3  2  Fer4_6        4Fe-4S binding domain
    8.7e-11   42.2  11.5    1.5e-10   41.5  11.5    1.4  1  Fer4_7        4Fe-4S dicluster domain
    5.3e-09   35.9  12.6    0.00017   21.8   3.1    2.2  2  Fer4_4        4Fe-4S binding domain
    8.5e-09   35.4  13.2    1.4e-08   34.7  13.2    1.4  1  Fer4_10       4Fe-4S dicluster domain
      1e-08   36.0  11.4    0.00037   21.4   1.0    2.3  2  Fer4_16       4Fe-4S double cluster binding domain
    8.9e-08   31.8  15.9    0.00032   20.6   3.7    2.4  2  Fer4_2        4Fe-4S binding domain
    1.4e-07   31.9   4.1     0.0064   17.0   0.9    2.2  2  Fer4_17       4Fe-4S dicluster domain
    1.6e-07   31.7   4.4     0.0046   17.4   0.1    2.2  2  Fer4_8        4Fe-4S dicluster domain
    8.6e-07   29.0  14.3     0.0021   18.2   3.0    2.1  2  Fer4_21       4Fe-4S dicluster domain
    2.2e-06   28.1  16.3    0.00034   21.1   4.1    2.3  2  Fer4_13       4Fe-4S single cluster domain of Ferredoxin I
    2.8e-05   24.3  11.8    0.00031   20.9  12.3    2.0  2  Fer4_18       4Fe-4S dicluster domain
    3.4e-05   24.6   6.3       0.03   15.2   0.2    2.1  2  Fer4_22       4Fe-4S dicluster domain
    0.00011   22.8  18.4      0.037   14.9   5.1    2.2  2  Fer4_3        4Fe-4S binding domain
     0.0041   17.2   5.2     0.0066   16.5   5.2    1.3  1  Fer4_19       Divergent 4Fe-4S mono-cluster
  ------ inclusion threshold ------
      0.013   16.2  10.6       0.18   12.6   2.7    2.6  2  Fer4_15       4Fe-4S single cluster domain
        3.2    8.2  10.8         19    5.7   2.8    2.3  2  Keratin_matx  Keratin, high-sulphur matrix protein
        4.9    7.3   8.2         13    5.9   8.1    1.8  2  ETF_QO        Electron transfer flavoprotein-ubiquinone oxido


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   4.3     5e-09   4.8e-06       3      23 ..      74      94 ..      72      95 .. 0.89
   2 !   29.3   2.2   5.3e-10     5e-07       5      23 ..     106     124 ..     102     125 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 5e-09
                                      EETTTSSS-THHHHHSTTTEE CS
                              Fer4  3 ideekCigCGaCvevCPvgAI 23
                                       d + C+ CGaCv++CP ++ 
  gi|298674990|ref|YP_003726740.1| 74 RDDDECVDCGACVSICPKNVF 94
                                      599**************9975 PP

  == domain 2  score: 29.3 bits;  conditional E-value: 5.3e-10
                                       TTTSSS-THHHHHSTTTEE CS
                              Fer4   5 eekCigCGaCvevCPvgAI 23 
                                       +e Ci CG+C++ CP+gA+
  gi|298674990|ref|YP_003726740.1| 106 PENCIQCGTCIKTCPHGAL 124
                                       89****************8 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   1.8     1e-07   9.9e-05      31      49 ..      74      92 ..      43      94 .. 0.75
   2 !   34.6  13.0   1.6e-11   1.6e-08       1      50 [.      78     123 ..      78     124 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1e-07
                            Fer4_9 31 aseeaCigCgaCveaCpkg 49
                                      +++++C++CgaCv +Cpk+
  gi|298674990|ref|YP_003726740.1| 74 RDDDECVDCGACVSICPKN 92
                                      22257************98 PP

  == domain 2  score: 34.6 bits;  conditional E-value: 1.6e-11
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                       +C++CgaCv+ Cp++v++ d++ + +   +    +Ci+Cg+C++ Cp+ga
  gi|298674990|ref|YP_003726740.1|  78 ECVDCGACVSICPKNVFKIDENWNVNMEPE----NCIQCGTCIKTCPHGA 123
                                       5*****************999888877543....7*************97 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   5.4   2.7e-07   0.00026       4      23 ..      74      93 ..      71      94 .. 0.87
   2 !   27.8   2.3   1.9e-09   1.8e-06       4      24 .]     104     124 ..     102     124 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.7e-07
                            Fer4_6  4 idpdkCigCgdCvrvCPega 23
                                       d+d C++Cg+Cv++CP ++
  gi|298674990|ref|YP_003726740.1| 74 RDDDECVDCGACVSICPKNV 93
                                      68999************886 PP

  == domain 2  score: 27.8 bits;  conditional E-value: 1.9e-09
                            Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                                         p++Ci+Cg C++ CP+ga+
  gi|298674990|ref|YP_003726740.1| 104 MEPENCIQCGTCIKTCPHGAL 124
                                       569****************97 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5  11.5   1.6e-13   1.5e-10       2      52 .]      79     123 ..      72     123 .. 0.94

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 1.6e-13
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       C+ CgaCv+ Cp +++++de         v+++pe+C++Cg C+++CP+ga
  gi|298674990|ref|YP_003726740.1|  79 CVDCGACVSICPKNVFKIDEN------WNVNMEPENCIQCGTCIKTCPHGA 123
                                       ******************996......45899*****************98 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   3.1   1.8e-07   0.00017       2      16 ..      77      91 ..      76      95 .. 0.91
   2 !   19.4   2.0   1.1e-06     0.001       1      15 [.     106     120 ..     106     128 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.8e-07
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      + C++Cg+Cv++CP 
  gi|298674990|ref|YP_003726740.1| 77 DECVDCGACVSICPK 91
                                      78************6 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 1.1e-06
                            Fer4_4   1 qerCigCgsCvaaCP 15 
                                       +e+Ci+Cg C+ +CP
  gi|298674990|ref|YP_003726740.1| 106 PENCIQCGTCIKTCP 120
                                       69************9 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7  13.2   1.5e-11   1.4e-08       3      56 .]      73     120 ..      71     120 .. 0.95

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 1.5e-11
                           Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                        +ddd C+ Cg+Cv+ CP       +  +++e+  v+  +e+C++cg C++ CP
  gi|298674990|ref|YP_003726740.1|  73 NRDDDECVDCGACVSICPK------NVFKIDENWNVNMEPENCIQCGTCIKTCP 120
                                       689****************......999999**********************9 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   1.0     4e-07   0.00037       2      29 ..      79     104 ..      78     108 .. 0.83
   2 !   19.6   3.5   1.4e-06    0.0013       1      19 [.     108     126 ..     108     131 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 4e-07
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeieare 29 
                                       C++Cg+C+++CP n++k +  ++++ ++
  gi|298674990|ref|YP_003726740.1|  79 CVDCGACVSICPKNVFKID--ENWNVNM 104
                                       ****************999..6666655 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.4e-06
                           Fer4_16   1 rCgtCgkCaevCPtnaike 19 
                                       +C++Cg C+++CP++a++ 
  gi|298674990|ref|YP_003726740.1| 108 NCIQCGTCIKTCPHGALSI 126
                                       6***************985 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   4.3     6e-06    0.0056       6      21 ..      75      90 ..      72      91 .. 0.89
   2 !   20.6   3.7   3.4e-07   0.00032       6      22 .]     105     121 ..     103     121 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6e-06
                            Fer4_2  6 dtdrCigCgaCvsaCP 21
                                      d d C+ CgaCvs CP
  gi|298674990|ref|YP_003726740.1| 75 DDDECVDCGACVSICP 90
                                      5578***********9 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 3.4e-07
                            Fer4_2   6 dtdrCigCgaCvsaCPa 22 
                                       ++++Ci+Cg+C++ CP+
  gi|298674990|ref|YP_003726740.1| 105 EPENCIQCGTCIKTCPH 121
                                       689*************7 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   1.1e-05     0.011      44      60 ..      77      93 ..      41      94 .. 0.84
   2 !   17.0   0.9   6.8e-06    0.0064      44      59 ..     107     122 ..      95     129 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.1e-05
                           Fer4_17 44 slCieCgeCerkCPqgl 60
                                      ++C+ Cg C++ CP+++
  gi|298674990|ref|YP_003726740.1| 77 DECVDCGACVSICPKNV 93
                                      79************986 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 6.8e-06
                           Fer4_17  44 slCieCgeCerkCPqg 59 
                                       ++Ci+Cg C + CP+g
  gi|298674990|ref|YP_003726740.1| 107 ENCIQCGTCIKTCPHG 122
                                       5666666666666654 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   4.9e-06    0.0046      49      65 .]      77      93 ..      31     102 .. 0.78
   2 !   15.4   1.6     2e-05     0.019       3      17 ..     107     121 ..     105     131 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.9e-06
                            Fer4_8 49 wsCttcgaCtevCpvgi 65
                                      ++C+ cgaC++ Cp+++
  gi|298674990|ref|YP_003726740.1| 77 DECVDCGACVSICPKNV 93
                                      67888888888888765 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 2e-05
                            Fer4_8   3 ekCieCgaCqsaCpv 17 
                                       e+Ci+Cg C ++Cp 
  gi|298674990|ref|YP_003726740.1| 107 ENCIQCGTCIKTCPH 121
                                       689********9994 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   3.7   9.1e-06    0.0085      35      52 ..      73      90 ..      57      96 .. 0.75
   2 !   18.2   3.0   2.2e-06    0.0021       3      22 ..     104     123 ..     101     131 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.1e-06
                           Fer4_21 35 kvvedeCvGCnlCssvCP 52
                                      +  +deCv C  C+s+CP
  gi|298674990|ref|YP_003726740.1| 73 NRDDDECVDCGACVSICP 90
                                      456899999999999999 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 2.2e-06
                           Fer4_21   3 idedkCigCgkCliaCedts 22 
                                       +++++Ci+Cg C+++C+ ++
  gi|298674990|ref|YP_003726740.1| 104 MEPENCIQCGTCIKTCPHGA 123
                                       5789*************655 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   4.1   3.6e-07   0.00034       2      25 ..      75      99 ..      72     104 .. 0.88
   2 !   12.9   4.3   0.00013      0.12       3      18 ..     106     121 ..     102     122 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.6e-07
                           Fer4_13  2 DrdtCiacgaCvelaP.dvFeedde 25
                                      D d+C++cgaCv+++P +vF++d++
  gi|298674990|ref|YP_003726740.1| 75 DDDECVDCGACVSICPkNVFKIDEN 99
                                      669*************559*99986 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00013
                           Fer4_13   3 rdtCiacgaCvelaPd 18 
                                        ++Ci cg+C +++P+
  gi|298674990|ref|YP_003726740.1| 106 PENCIQCGTCIKTCPH 121
                                       689************5 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9  12.3   3.3e-07   0.00031      49      95 ..      67     119 ..      31     121 .. 0.78
   2 !   12.1   2.1   0.00018      0.17      56      74 ..     104     122 ..      92     130 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 3.3e-07
                           Fer4_18  49 ekeerkekgagdcidcescvkvcPtgi...dirkGlqle...ciscllcidac 95 
                                       + ++  ++++ +c+dc++cv++cP ++   d    + +e   ci+c+ ci +c
  gi|298674990|ref|YP_003726740.1|  67 QLDSPVNRDDDECVDCGACVSICPKNVfkiDENWNVNMEpenCIQCGTCIKTC 119
                                       45666678899*************875311555555553555**********9 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00018
                           Fer4_18  56 kgagdcidcescvkvcPtg 74 
                                        +  +ci+c++c+k cP g
  gi|298674990|ref|YP_003726740.1| 104 MEPENCIQCGTCIKTCPHG 122
                                       45679************87 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.2   3.2e-05      0.03      58      95 ..      50      92 ..      30      93 .. 0.68
   2 !   12.1   2.0   0.00028      0.27      72      94 ..      99     121 ..      91     123 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.2e-05
                           Fer4_22 58 kkerlrqrllhklsefkekf.....gesgCvGCgRCieacpvk 95
                                        e++r  l+ k +++ +       +   Cv Cg C++ cp++
  gi|298674990|ref|YP_003726740.1| 50 DFENFRDSLISKGAKVIQLDspvnrDDDECVDCGACVSICPKN 92
                                      55666666666665554433344448899***********987 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00028
                           Fer4_22  72 efkekfgesgCvGCgRCieacpv 94 
                                       +++ +++ + C+ Cg Ci++cp+
  gi|298674990|ref|YP_003726740.1|  99 NWNVNMEPENCIQCGTCIKTCPH 121
                                       67788899999999999999997 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   5.4   8.8e-05     0.083       1      14 [.      79      92 ..      79      93 .. 0.94
   2 !   14.9   5.1     4e-05     0.037       1      15 []     109     123 ..     109     123 .. 0.98

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.8e-05
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      C+ CgaCv  CP++
  gi|298674990|ref|YP_003726740.1| 79 CVDCGACVSICPKN 92
                                      999*********98 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 4e-05
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C++Cg+C + CP gA
  gi|298674990|ref|YP_003726740.1| 109 CIQCGTCIKTCPHGA 123
                                       *************99 PP

>> Fer4_19  Divergent 4Fe-4S mono-cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   5.2     7e-06    0.0066       9      61 ..      73     126 ..      69     129 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7e-06
                           Fer4_19   9 ednrelCihsgnCvk.glpevFdpkrkpwikpdeasteeiievverCPSGALsy 61 
                                         + + C   g Cv    ++vF+ +++  ++ + ++  +    +++CP GALs+
  gi|298674990|ref|YP_003726740.1|  73 NRDDDECVDCGACVSiCPKNVFKIDENWNVNMEPENCIQCGTCIKTCPHGALSI 126
                                       567788*********44568*******779**********************98 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.7   0.00019      0.18       4      26 ..      75      98 ..      72     100 .. 0.85
   2 ?    8.3   0.6    0.0041       3.9       2      19 ..     103     120 ..     102     125 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00019
                           Fer4_15  4 DrdaCigcglCvaea.pevfelde 26
                                      D d+C  cg+Cv  + ++vf++de
  gi|298674990|ref|YP_003726740.1| 75 DDDECVDCGACVSICpKNVFKIDE 98
                                      99*************557888886 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0041
                           Fer4_15   2 vvDrdaCigcglCvaeap 19 
                                         + ++Ci cg C++ +p
  gi|298674990|ref|YP_003726740.1| 103 NMEPENCIQCGTCIKTCP 120
                                       56789***********98 PP

>> Keratin_matx  Keratin, high-sulphur matrix protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1  10.1     0.062        58      20      63 ..      76     119 ..      69     119 .. 0.84
   2 ?    5.7   2.8      0.02        19      22      39 ..     108     124 ..     101     130 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.062
                      Keratin_matx  20 sdkscrcGvclpstcpheisllept.ccdtcpppccvpdsyvptc 63 
                                        d +  cG+c+ s cp+++  ++     +  p  c++  +++ tc
  gi|298674990|ref|YP_003726740.1|  76 DDECVDCGACV-SICPKNVFKIDENwNVNMEPENCIQCGTCIKTC 119
                                       478889****8.99*****99876615666799999999999998 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.02
                      Keratin_matx  22 kscrcGvclpstcpheis 39 
                                        + +cG c+  tcph   
  gi|298674990|ref|YP_003726740.1| 108 NCIQCGTCI-KTCPHGAL 124
                                       6789****9.69***765 PP

>> ETF_QO  Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   1.1      0.54   5.1e+02      72      86 ..      76      90 ..      38      99 .. 0.78
   2 ?    5.9   8.1     0.014        13      46      83 ..      85     117 ..      64     128 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.54
                                      CCC--S--HHHHH-T CS
                            ETF_QO 72 aqnCvhCktCdikdp 86
                                        +Cv C +C    p
  gi|298674990|ref|YP_003726740.1| 76 DDECVDCGACVSICP 90
                                      567888888854444 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.014
                                       HHHH-TTS-EEEEETTTTSSEEEEE-CCC--S--HHHH CS
                            ETF_QO  46 eqryCPagvyeivedeeakekklqinaqnCvhCktCdi 83 
                                       +  +CP +v++i e+      +++++ +nC+ C tC  
  gi|298674990|ref|YP_003726740.1|  85 CVSICPKNVFKIDEN-----WNVNMEPENCIQCGTCIK 117
                                       567899999998654.....578999**********44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       746  (0.0416086); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 939.02
//
Query:       gi|298674991|ref|YP_003726741.1|  [L=499]
Description: hypothetical protein Metev_1059 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   6.6e-142  472.5   0.6   6.6e-142  472.5   0.6    1.8  2  HcyBio          Homocysteine biosynthesis enzyme, sulfur-inco
      1e-26   93.1   6.0    7.8e-13   48.7   0.0    2.8  3  CBS             CBS domain
  ------ inclusion threshold ------
      0.039   14.4   0.6       0.34   11.4   0.3    2.5  2  Ribosomal_L9_C  Ribosomal protein L9, C-terminal domain


Domain annotation for each model (and alignments):
>> HcyBio  Homocysteine biosynthesis enzyme, sulfur-incorporation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  472.5   0.6  1.1e-145  6.6e-142       2     346 ..      19     354 ..      18     355 .. 0.99
   2 ?   -0.8   0.6     0.087   5.2e+02       3      35 ..     424     458 ..     422     468 .. 0.76

  Alignments for each domain:
  == domain 1  score: 472.5 bits;  conditional E-value: 1.1e-145
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            HcyBio   2 vVltaeelkklvrekgekkaaeevDVVttgTfgvmsssgallnlgvaepkikiekvwLngvpayaglaavdlylgat 78 
                                        V+taee++++v+e g++ aa+evDVVttgTfg+m+ssga+ln+g+aep+ik +k+wLn+v+ayaglaavd+y+g+t
  gi|298674991|ref|YP_003726741.1|  19 NVVTAEEMVDIVSELGTEGAAQEVDVVTTGTFGAMCSSGAFLNFGHAEPPIKFQKIWLNDVEAYAGLAAVDAYIGST 95 
                                       69*************************************************************************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            HcyBio  79 aeseddkeeeeyGGghviedLvagkeveleaeaketdcyprkeieteitlddlneailvnpRnayqnYnaavNssee 155
                                       + se+   + eyGG+hviedL++gk+++++a++++tdcyp k ++t+++++dln+ ++vnpRn +q+Yn+a+Ns+++
  gi|298674991|ref|YP_003726741.1|  96 QLSET--AGMEYGGAHVIEDLISGKSIDVHAKSYGTDCYPLKILDTTLNINDLNQTTMVNPRNGFQKYNVATNSTNR 170
                                       ****4..456******************************************************************* PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            HcyBio 156 tiytymgelkpnlgnatysgaGelsPllnDpelktigiGtrilLgGaeGyvigeGTqsspekkrengvplgpagtLa 232
                                       t++tym +l pn gn+tysg+G lsPl nDp+++tig+Gtri++gGa+Gyv+geG q++pe +         +gtL+
  gi|298674991|ref|YP_003726741.1| 171 TLHTYMSTLLPNHGNITYSGSGVLSPLSNDPNYETIGTGTRIFIGGAQGYVVGEGSQHNPEVN---------FGTLM 238
                                       ***********************************************************9998.........***** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                            HcyBio 233 vigdlkeMspeylrgafltsyGpelivgvgipiPvldeevleelavkdedielpvvDvserrrerktlgevsYael. 308
                                       v+g+lk+M+p+y+rga++ +yG++l++g+g+piPvl+e+++e++av+dedi+++++D+++++r+r++l ev+Yael 
  gi|298674991|ref|YP_003726741.1| 239 VQGNLKDMNPDYVRGASFYGYGTSLYMGIGVPIPVLNERIAENTAVRDEDIVTNILDYGVQSRDRPKLREVTYAELk 315
                                       ***************************************************************************** PP

                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            HcyBio 309 .GkieiegkevktarlsslkrareiaeeLkewiekgefl 346
                                        G ++++g+ev+t++lss+k ar iae  k++i++gef+
  gi|298674991|ref|YP_003726741.1| 316 sGYVDLNGREVPTSPLSSFKTARLIAEDCKDQIKNGEFF 354
                                       **************************************7 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.087
                                       xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx RF
                            HcyBio   3 Vltaeelkklvrekge..kkaaeevDVVttgTfgv 35 
                                       ++ta +++k v++++    k + + DVVt+ T ++
  gi|298674991|ref|YP_003726741.1| 424 IVTAWDISKAVAQEKYhiVKDFMTRDVVTATTEET 458
                                       7999999999998543114556677****999875 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       1.3   7.6e+03      17      47 ..       5      31 ..       3      32 .. 0.60
   2 !   48.7   0.0   1.3e-16   7.8e-13       1      55 [.     380     434 ..     380     436 .. 0.93
   3 !   46.6   0.8   5.8e-16   3.5e-12       1      56 [.     442     497 ..     442     498 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.3
                                      BHHHHHHHHHHHTSSEEEEEETTTBEEEEEE CS
                               CBS 17 tleealelmrekgvsrlPVVdedgklvGivt 47
                                      ++ee+ +++++   +++ VV   ++ v iv+
  gi|298674991|ref|YP_003726741.1|  5 SIEEINNKIKD---GSVNVV-TAEEMVDIVS 31
                                      78888888855...566455.2444666655 PP

  == domain 2  score: 48.7 bits;  conditional E-value: 1.3e-16
                                       HHHHSBSSCEEEETTSBHHHHHHH.HHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 Vgdimtrdvvtvppdttleealel.mrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       V++im r+vvt+  d++ +ea+++ m e+ +++lPVV ed klvGivt  D+ +a+
  gi|298674991|ref|YP_003726741.1| 380 VREIMARNVVTIQQDSSFHEAAKKiM-ESTFDHLPVVSEDSKLVGIVTAWDISKAV 434
                                       89**********************67.999*******99999**********8886 PP

  == domain 3  score: 46.6 bits;  conditional E-value: 5.8e-16
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       V+d+mtrdvvt++ ++t+  a+  + +k+vs+lPVVd++ ++vGi+t  D+ ++l+
  gi|298674991|ref|YP_003726741.1| 442 VKDFMTRDVVTATTEETIDIAAHHIDQKEVSALPVVDNERRVVGIITSNDISKLLA 497
                                       89***********************8888*******99999**********88875 PP

>> Ribosomal_L9_C  Ribosomal protein L9, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   5.6e-05      0.34       7      73 ..     401     464 ..     396     473 .. 0.76
   2 ?    0.1   0.0      0.19   1.1e+03      22      43 ..     477     498 ..     462     499 .] 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.6e-05
                                       HHHHSS..-EEEE--B-TT-BBSS---HHHHHHHHHHHT-----GGGEE-TTT-SBSSEEEEEEESS CS
                    Ribosomal_L9_C   7 aekLeakvkvtikakagedgklFGsVtakdIaealkkklgieidkkkieleepiktlGeyevtvkLh 73 
                                       a+k+  + ++     ++ed kl G Vta dI++a++++ +++i k  ++  + + ++ e ++++  h
  gi|298674991|ref|YP_003726741.1| 401 AKKIM-ESTFDHLPVVSEDSKLVGIVTAWDISKAVAQE-KYHIVKDFMTR-DVVTATTEETIDIAAH 464
                                       55565.333454555799*******************9.9***9998885.4477777777766665 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.19
                                       B-TT-BBSS---HHHHHHHHHH CS
                    Ribosomal_L9_C  22 agedgklFGsVtakdIaealkk 43 
                                       + ++ ++ G +t++dI++ l++
  gi|298674991|ref|YP_003726741.1| 477 VDNERRVVGIITSNDISKLLAS 498
                                       456788999*******999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (499 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 3452.91
//
Query:       gi|298674992|ref|YP_003726742.1|  [L=212]
Description: hypothetical protein Metev_1060 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.091   13.2   3.4        2.9    8.4   3.4    2.3  1  FtsX      FtsX-like permease family


Domain annotation for each model (and alignments):
>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   3.4   0.00016       2.9      22      91 ..      13     182 ..      12     187 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00016
                              FtsX  22 lteillitlvalviGlgl..............gllaaqllsdvllssvf............................ 56 
                                       ++e++ +t+++++iG++               g ++   +s  ++s++                             
  gi|298674992|ref|YP_003726742.1|  13 FSELIKYTIPGYLIGIVMaslldyygyqqnplGHWLVRTFSGEGESIFEgiysikqrlsgalgsiseaygwgklsgm 89 
                                       57888899999999988855555555555555333333333333333224445555555555555555555555555 PP

                              FtsX  57 ......................................................s....selkisidlitvliiivl 75 
                                                                                             +    ++ +++++ ++v+ii+ l
  gi|298674992|ref|YP_003726742.1|  90 sipwiidlfshlagvniygvegfyipyfyalsdqiganisglyylkrseyswlkGikryIHHPVMVSSLIVIIIVPL 166
                                       56666666666666666666666677777777777777777777777776666514567999999999999999999 PP

                              FtsX  76 llllallagllsiski 91 
                                       +llla ++g+ ++ +i
  gi|298674992|ref|YP_003726742.1| 167 GLLLARIIGFSPTNQI 182
                                       9999999999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1484.75
//
Query:       gi|298674993|ref|YP_003726743.1|  [L=150]
Description: cytidyltransferase-like domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-18   67.3   0.0    1.8e-18   67.1   0.0    1.0  1  CTP_transf_like  Cytidylyltransferase-like
     0.0027   17.6   0.0      0.048   13.6   0.0    2.1  2  FAD_syn          FAD synthetase
  ------ inclusion threshold ------
      0.012   14.8   0.1        2.9    7.0   0.0    2.1  2  HIGH_NTase1      HIGH Nucleotidyl Transferase


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.1   0.0   2.9e-22   1.8e-18       1     142 [.      16     143 ..      16     144 .. 0.91

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 2.9e-22
                                       EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHH CS
                   CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlelakevdevisvdpweltrevl 77 
                                       la GtFD++H GHl++l +a+kl++e l+v+v+     k+k kp++++++R+ m+  +  vd+++  ++  +  e +
  gi|298674993|ref|YP_003726743.1|  16 LATGTFDLLHPGHLHYLSEARKLGNE-LYVIVARESMIKHKPKPVIPENQRVTMVNSLDVVDKAVLGSETNIY-EPI 90 
                                       689***********************.************999*******************************.6** PP

                                       HHTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHHH CS
                   CTP_transf_like  78 kklkpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkire 142
                                       k++kpd  ++ ig d+  +   +  +e+ l+++++  ++++       + +  +++ +Ss ki+ 
  gi|298674993|ref|YP_003726743.1|  91 KNIKPD--VITIGYDQKFS---SDSIEKNLEELGINAKVVR-------INKLSDCSLCSSGKIID 143
                                       ******..*******8777...5788888888888888777.......88888888889888876 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0     8e-06     0.048       8      41 ..      14      47 ..       8      80 .. 0.74
   2 ?    2.3   0.0     0.024   1.4e+02     102     123 ..      90     110 ..      78     138 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8e-06
                           FAD_syn  8 avvtlGnFDGvHlGHqallkkaveaakekglpsv 41
                                       v++ G FD +H GH + l++a+++ +e  + ++
  gi|298674993|ref|YP_003726743.1| 14 RVLATGTFDLLHPGHLHYLSEARKLGNELYVIVA 47
                                      6899*********************988776554 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.024
                           FAD_syn 102 lveklkvkavvvGfdfrfGkkr 123
                                       ++ ++k  ++++G+d +f ++ 
  gi|298674993|ref|YP_003726743.1|  90 IK-NIKPDVITIGYDQKFSSDS 110
                                       44.7888889999999988763 PP

>> HIGH_NTase1  HIGH Nucleotidyl Transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0   0.00086       5.2      13      35 ..      24      46 ..      21      50 .. 0.89
   2 ?    7.0   0.0   0.00049       2.9      87     115 ..      66      94 ..      63     142 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.00086
                       HIGH_NTase1 13 fHnGHlyhlekakeltgadvvia 35
                                      +H GHl+ l++a++l ++ +vi+
  gi|298674993|ref|YP_003726743.1| 24 LHPGHLHYLSEARKLGNELYVIV 46
                                      7*************988888887 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00049
                       HIGH_NTase1  87 VslLnalgvvdslvFGsEsgdiealkkia 115
                                       V++ n+l+vvd+ v GsE++  e +k+i 
  gi|298674993|ref|YP_003726743.1|  66 VTMVNSLDVVDKAVLGSETNIYEPIKNIK 94 
                                       999******************99999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1081.13
//
Query:       gi|298674994|ref|YP_003726744.1|  [L=380]
Description: class I/II aminotransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-65  220.2   0.0    5.2e-65  220.0   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    0.00063   19.2   0.1     0.0012   18.3   0.1    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
     0.0019   17.6   0.0     0.0038   16.6   0.0    1.5  1  Beta_elim_lyase  Beta-eliminating lyase
      0.002   17.2   0.0     0.0053   15.8   0.0    1.7  2  Aminotran_5      Aminotransferase class-V
     0.0091   14.6   0.0      0.015   13.9   0.0    1.3  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
       0.01   14.8   0.1        1.4    7.7   0.0    2.4  2  Alliinase_C      Allinase
      0.053   12.2   0.0      0.077   11.7   0.0    1.3  1  OKR_DC_1         Orn/Lys/Arg decarboxylase, major domain


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  220.0   0.0     2e-68   5.2e-65       2     363 .]      30     375 ..      29     375 .. 0.94

  Alignments for each domain:
  == domain 1  score: 220.0 bits;  conditional E-value: 2e-68
                                       EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGag 78 
                                       dvi ++ +e+++d    t+ ++   ++   ++ ++ + y p+ g p+l++a+a+ l++++kl+ + + +++v++Ga+
  gi|298674994|ref|YP_003726744.1|  30 DVISFSLGEPDFD----TPRHICDSAAN--AMYNGETHYAPSAGIPQLKSAIAEKLQNENKLNADES-NILVTPGAK 99 
                                       799**********....99999999998..8999999********************9999999999.********* PP

                                       HHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEE CS
                     Aminotran_1_2  79 aliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilve 155
                                       ++i  +++   l+ +de +++dp + sy+++++++g+  v  p+++ +df+    ++ e +++      ktk+i+v+
  gi|298674994|ref|YP_003726744.1| 100 QAIFEIMMSV-LDQDDEAILFDPAWVSYEPCIKMAGAHPVWAPTNPDNDFK--PYDISEYVTD------KTKMIVVN 167
                                       **********.********************************88666665..4566676777......99****** PP

                                       SS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT.EEEEEESSSTTSSGGG-EE CS
                     Aminotran_1_2 156 sphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepn.llivgslsKafGlaGeRvG 231
                                       sp NPtG+v+ ++ le ++d+a  + l++++De+Y++  ++ + +++ +  ++   + +++v+++sK+++++G+R+G
  gi|298674994|ref|YP_003726744.1| 168 SPCNPTGSVYEKDVLENIADIAIDHDLFVLSDEIYEKIIYDRE-HIS-IGSMDGMQDrTITVNGFSKSYAMTGWRLG 242
                                       ****************************************954.445.66666666689****************** PP

                                       EEEEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSS CS
                     Aminotran_1_2 232 yilgnaavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgm 306
                                       y+++++++ + l k++++  s  ++ +q+   aal+ +++    + em+ ++ +rr++l+d+L++lg+k+  +q+++
  gi|298674994|ref|YP_003726744.1| 243 YACAHPDIFNNLLKIQSHSVSsaTTFVQHGGYAALNGPQE---PVYEMVNEFRARRDVLVDGLNSLGIKCNRPQGAF 316
                                       *********************9*****************7...8********************************* PP

                                       EEEEEETHH.CHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHHH CS
                     Aminotran_1_2 307 flltdlsae.takelskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelveal 363
                                       + + d+s+  t +e++++Ll+e +v+vtpg+ f+   ++++Ri++ +++++ ++e +e++
  gi|298674994|ref|YP_003726744.1| 317 YAFADVSEFgTGDEVAEELLKEAHVAVTPGSAFGPsgKNFIRISY-ATSQDRIQEGLERI 375
                                       *******98**************************99********.9********99998 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   4.6e-07    0.0012      57     144 ..     107     199 ..      85     200 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 4.6e-07
                                       HTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEE...EB-GGGB---...H CS
                   DegT_DnrJ_EryC1  57 algvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitertkaIl...pVhlyGqvad...m 127
                                          ++++de I     +v+   ++  +ga pv +  +pd    +p +i + +t +tk I+   p +  G v +   +
  gi|298674994|ref|YP_003726744.1| 107 MSVLDQDDEAILFDPAWVSYEPCIKMAGAHPVWAPTNPD-NDFKPYDISEYVTDKTKMIVvnsPCNPTGSVYEkdvL 182
                                       3345578***************************99976.589****************944457889999853447 PP

                                       HHHHHHHHHCT-EEEEE CS
                   DegT_DnrJ_EryC1 128 dalkaiaakhglkvieD 144
                                       +++ +ia +h+l v++D
  gi|298674994|ref|YP_003726744.1| 183 ENIADIAIDHDLFVLSD 199
                                       88889999******999 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.5e-06    0.0038      19     167 ..      53     199 ..      42     200 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.5e-06
                                       HCS----CCCT--HHHHHHHHHHHHHTT-SEEEE........ES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSST CS
                   Beta_elim_lyase  19 aaamlGdesYgedktvnrLedavaelfgkeaalf........vpqGtaAnsillkillqrgeevivtepahihfdet 87 
                                        a+  G+  Y+ + ++ +L+ a+ae +  e  l         +p   +A    ++ +l + +e i+ +pa +    +
  gi|298674994|ref|YP_003726744.1|  53 NAMYNGETHYAPSAGIPQLKSAIAEKLQNENKLNadesnilvTPGAKQAIFEIMMSVLDQDDEAILFDPAWVSYEPC 129
                                       45556777788888888888888885555555544444433233333333333344456666677777776665554 PP

                                       THHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EE CS
                   Beta_elim_lyase  88 gaiaelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygipl 164
                                            +ag++++ ++++ ++++++ ++ + +++      k+k+i++   +n   G v++ + l+++a+ia ++++ +
  gi|298674994|ref|YP_003726744.1| 130 ---IKMAGAHPVWAPTNPDNDFKPYDISEYVTD------KTKMIVVNSPCNP-TGSVYEKDVLENIADIAIDHDLFV 196
                                       ...5689************************99......699*********5.9********************999 PP

                                       EEE CS
                   Beta_elim_lyase 165 hlD 167
                                       + D
  gi|298674994|ref|YP_003726744.1| 197 LSD 199
                                       887 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.43   1.1e+03     289     345 ..       7      65 ..       2      75 .. 0.66
   2 !   15.8   0.0   2.1e-06    0.0053      56     175 ..      85     199 ..      44     201 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.43
                                       HHHCTSTTEEEES.-B-CTCB..SEEEEEETTCSHHHHHHHHHHTTEEEEEE-TTTHHH CS
                       Aminotran_5 289 erlkslpgvrlygpdkaerra..sivsfnfkgvhaedvatlLdeegIavrsGhhcaqpl 345
                                       er+k+++ +r+++ +++ r++   ++sf++ + + +  ++++d+++ a+  G+++  p+
  gi|298674994|ref|YP_003726744.1|   7 ERVKESETIRIANLANQLRKKniDVISFSLGEPDFDTPRHICDSAANAMYNGETHYAPS 65 
                                       66777777777665555444401567777777777888888888877777777777666 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 2.1e-06
                                       HT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGH CS
                       Aminotran_5  56 inaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldel 132
                                       +na++ ++i++t G+ +ai  +++s+   l+++de+++ +    +   p+ ++a   ga+ +++p +++   ++ ++
  gi|298674994|ref|YP_003726744.1|  85 LNADE-SNILVTPGAKQAIFEIMMSV---LDQDDEAILFDPAWVSYE-PCIKMA---GAHPVWAPTNPDNDFKPYDI 153
                                       78885.********************...9********998777766.777776...99****************** PP

                                       HHH--TTEEEEEEESBETTTTEB--...HHHHHHHHHHTT-EEEEE CS
                       Aminotran_5 133 ekllnektklvaithvsnvtGtiqp...veeigklakkkgalvlvD 175
                                        +++++ktk++ ++   n tG + +   +e+i+++a +++ +vl D
  gi|298674994|ref|YP_003726744.1| 154 SEYVTDKTKMIVVNSPCNPTGSVYEkdvLENIADIAIDHDLFVLSD 199
                                       *********************9744223677888887887777766 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   5.8e-06     0.015      70     173 ..      92     199 ..      71     205 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.8e-06
                                       EEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHH.TTCEEEEESTTSHHHHHHHCCTTEEEEEEES CS
                   Cys_Met_Meta_PP  70 alavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkk.lgievkfvdtsdleelekaikentklvylEt 145
                                        l+++    Ai+ +++++l + de ++ d ++ + +  +k    + +   ++  +  ++ ++ + ++++tk++ + +
  gi|298674994|ref|YP_003726744.1|  92 ILVTPGAKQAIFEIMMSVLDQDDEAILFDPAWVSYEPCIKMAGAHpVWAPTNPDNDFKPYDISEYVTDKTKMIVVNS 168
                                       344444567999999999999999999999998888888777666344555556667899***************** PP

                                       S-TTTT----...HHHHHHHHHHTT-EEEEE CS
                   Cys_Met_Meta_PP 146 ptnpllkvvD...iekiaklakkagvlvvvD 173
                                       p np+ +v     +e+ia++a ++++ v+ D
  gi|298674994|ref|YP_003726744.1| 169 PCNPTGSVYEkdvLENIADIAIDHDLFVLSD 199
                                       *****99974334688999998888888777 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.2    0.0056        14     129     207 ..     155     245 ..     147     266 .. 0.60
   2 ?    7.7   0.0   0.00055       1.4     303     362 ..     318     378 ..     308     379 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0056
                                       T-.--S..S-EEEEEESS-TTT------.--........-TT-....EEEEEE-TT-STTTS---S...-B--SEEE CS
                       Alliinase_C 129 ayvkkknpeefielvtsPnnPdgllrea.vv........kgse....akviyDlayYWPhytpits...kadedimL 189
                                       +yv++k  ++ + +v sP nP g + e+ v+        + ++    +  iy+ + Y  ++  i s    +d  i +
  gi|298674994|ref|YP_003726744.1| 155 EYVTDK--TK-MIVVNSPCNPTGSVYEKdVLeniadiaiD-HDlfvlSDEIYEKIIYDREHISIGSmdgMQDRTITV 227
                                       564444..33.44899*****9998654155322222211.111111223444555655555554322257788888 PP

                                       EEHHHHHS-GGG-EEEEE CS
                       Alliinase_C 190 ftlskltGhaGsrlGWal 207
                                         +sk    +G rlG+a 
  gi|298674994|ref|YP_003726744.1| 228 NGFSKSYAMTGWRLGYAC 245
                                       888888888888888875 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00055
                                       SEEEEEESSSS..-HHHHHHTTTEEEEEGGGGT.S-TTEEEEESSS-HHHHHHHHHHHHTS CS
                       Alliinase_C 303 ayaWlkcekeededcaevlrekkiltrsGevfe.aesryvrlsllkrdddfdvllerlkkl 362
                                       a+a +    ++de  +e+l+e+++    G+ f+ ++++++r+s   ++d  +  ler+k++
  gi|298674994|ref|YP_003726744.1| 318 AFADVSEFGTGDEVAEELLKEAHVAVTPGSAFGpSGKNFIRISYATSQDRIQEGLERIKSV 378
                                       455555555677778999**************9567899******************9986 PP

>> OKR_DC_1  Orn/Lys/Arg decarboxylase, major domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0     3e-05     0.077      79     140 ..      85     148 ..      70     204 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3e-05
                                       CT-SEEEE.ESSHHHHHHHHHHHHH--TTEEEEEESS--HHHHHHHHHS-EEEEEE--E.B-TT CS
                          OKR_DC_1  79 fgadksyf.vvnGTsssnkvvlnavltpgdlvlvdRNcHKSiehalvlsgatPvylepe.rnal 140
                                        +ad+s + v+ G   ++  ++++vl + d  ++   +  S e  + ++ga+Pv+  ++ +n +
  gi|298674994|ref|YP_003726744.1|  85 LNADESNIlVTPGAKQAIFEIMMSVLDQDDEAILFDPAWVSYEPCIKMAGAHPVWAPTNpDNDF 148
                                       689998762567999***999***9999887655557899***************998888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2723.79
//
Query:       gi|298674995|ref|YP_003726745.1|  [L=134]
Description: 6,7-dimethyl-8-ribityllumazine synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-28   99.7   0.0    1.4e-28   99.5   0.0    1.0  1  DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase


Domain annotation for each model (and alignments):
>> DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.5   0.0   7.6e-33   1.4e-28       3     138 ..       4     132 ..       2     134 .] 0.93

  Alignments for each domain:
  == domain 1  score: 99.5 bits;  conditional E-value: 7.6e-33
                                       EEEEEEESTTHHHHHHHHHHHHHHHHHCTTSSCCEEEEEESSCCCHHHHHHHHCTSTT-.SEEEEEEEEE--SSCHH CS
                     DMRL_synthase   3 riaiVvarfneeitdkllegaldelkeagvaeenidvvtVPGafElplaakklaesskyldavialGvvirGetphf 79 
                                       ++++V a+fn+++t ++    +++++ +g++    + + VPG++++pla+kk++e+ + +dav+++G+vi+G+t+h+
  gi|298674995|ref|YP_003726745.1|   4 NLGFVIAEFNRDLTYQMELLGKEHAEFLGAE--VKNKILVPGVYDMPLAIKKFCEQ-DDIDAVVTIGAVIEGSTEHD 77 
                                       6899*************************75..778899****************5.457***************** PP

                                       HHHHHHHHHHHHHHHHHCTS-EEEEEEEES.SHHCCHHCCTSTCCCHHHHHHHHHHHHHH CS
                     DMRL_synthase  80 eyvaeavskglmrvsldtgvPvifgvltvd.teeqaleraggkagnkGeeaaeaaleman 138
                                       e+v++++s++++++sl++++Pv+ g+  +  t+ +a+er      ++ ++a+e+a+++++
  gi|298674995|ref|YP_003726745.1|  78 EIVVQHASRKITDLSLEYNKPVTLGIAGPGmTRMEAHERL-----DYSKRAVESAVKLVQ 132
                                       ******************************9*********.....899999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1044.68
//
Query:       gi|298674996|ref|YP_003726746.1|  [L=154]
Description: riboflavin synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      6e-18   65.0   0.4    6.8e-18   64.8   0.4    1.1  1  DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
  ------ inclusion threshold ------
       0.09   13.1   0.5       0.66   10.4   0.0    2.1  2  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
       0.11   12.6   0.0       0.18   11.8   0.0    1.3  1  PAS            PAS fold


Domain annotation for each model (and alignments):
>> DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.8   0.4   1.1e-21   6.8e-18       3     137 ..       3     128 ..       1     132 [. 0.85

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 1.1e-21
                                       EEEEEEESTTHHHHHHHHHHHHHHHHHCTTSSCCEEEEEESSCCCHHHHHHHHCTSTT-.SEEEEEEEEE--SSCHH CS
                     DMRL_synthase   3 riaiVvarfneeitdkllegaldelkeagvaeenidvvtVPGafElplaakklaesskyldavialGvvirGetphf 79 
                                        i+iV ++f      ++ + alde++++    ++++++tVPG  +lp+a kkl+e++++ d vialG  + G+ +++
  gi|298674996|ref|YP_003726746.1|   3 TIGIVDTTF---ARFDMGSVALDEINKNAS--ARTVRITVPGIKDLPVASKKLLEEQGC-DIVIALG--MPGSAEKD 71 
                                       689999999...77899999******9995..59*********************6445.*******..9******* PP

                                       HHHHHHHHHHHHHHHHHCTS-EEEEEEEESSHHCCHHCCTSTC..CCHHHHHHHHHHHHH CS
                     DMRL_synthase  80 eyvaeavskglmrvsldtgvPvifgvltvdteeqaleraggka..gnkGeeaaeaalema 137
                                       +++a+++s+gl++++l t++ +i   +  d+ +  +e a   +  +n+++e+a ++++++
  gi|298674996|ref|YP_003726746.1|  72 KMCANQASQGLIQAQLMTNKHIIEVFVHEDEAANEKELA---QlmENRAREHAVNVVKLL 128
                                       *******************88887665555555555555...236************986 PP

>> Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00011      0.66      46      67 ..      47      68 ..      20      76 .. 0.85
   2 ?    0.9   0.1     0.095   5.6e+02      26      58 ..      92     125 ..      84     128 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00011
                                      HHHHHHHTT-SEEEESSSCHHH CS
                     Nitro_FeMo-Co 46 laqllaeegvdvvivgkiGpra 67
                                       ++ll+e+g+d+vi+ ++ ++a
  gi|298674996|ref|YP_003726746.1| 47 SKKLLEEQGCDIVIALGMPGSA 68
                                      5678899***********8776 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.095
                                       EEEEEE.E.GCCCTSSCSSTHHHHHHHHTT-SEE CS
                     Nitro_FeMo-Co  26 kivenr.veeaadaegggggklaqllaeegvdvv 58 
                                       +i+e+  +e +a++e++  + +++++ e+ v+vv
  gi|298674996|ref|YP_003726746.1|  92 HIIEVFvHEDEAANEKELAQLMENRAREHAVNVV 125
                                       4566666677888888888888888888888887 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     3e-05      0.18      41      80 ..      88     127 ..      82     140 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3e-05
                                       CTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEE CS
                               PAS  41 vlgkslldliheeddaelaelleqlleqgeesrageisfk 80 
                                       + +k++++++++ed+a   ++l ql+e++ +++a+++   
  gi|298674996|ref|YP_003726746.1|  88 MTNKHIIEVFVHEDEAANEKELAQLMENRAREHAVNVVKL 127
                                       789******************************9998655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1231.09
//
Query:       gi|298674997|ref|YP_003726747.1|  [L=383]
Description: class V aminotransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-42  145.0   0.0    3.5e-42  144.7   0.0    1.1  1  Aminotran_5      Aminotransferase class-V
  ------ inclusion threshold ------
        0.1   11.8   0.0        0.2   10.9   0.0    1.5  1  Beta_elim_lyase  Beta-eliminating lyase
       0.15   11.1   0.0       0.26   10.3   0.0    1.2  1  FAD_binding_2    FAD binding domain
       0.18   11.5   0.0       0.38   10.5   0.0    1.5  1  NUDIX_5          NUDIX, or N-terminal NPxY motif-rich,  regio


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.7   0.0   7.8e-46   3.5e-42      22     358 ..      27     339 ..       7     351 .. 0.88

  Alignments for each domain:
  == domain 1  score: 144.7 bits;  conditional E-value: 7.8e-46
                                       HHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHH.HHHHHHHHCCCC-TTTSEEEEETTS CS
                       Aminotran_5  22 yytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtte.ainlvalslarslkpgdeivvteae 97 
                                                  ++ h+g e++++++++ + +++++n+++  +i ++sG+++ ++++++ +     ++ d++++ e++
  gi|298674997|ref|YP_003726747.1|  27 P----------MINHRGDEFAEIYDDCCNILKDVFNTQN--DISVISGSGSaGMEAAIGCT---TNNNDNVITIENG 88 
                                       3..........789************************7..99999999996778777777...89*********** PP

                                       HGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEE CS
                       Aminotran_5  98 hhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlv 174
                                       + +++   + +a+r g  +  ++ +++  +dld++e+ll+e ++ va+ h++++ G+++p +e+gklakk++al+++
  gi|298674997|ref|YP_003726747.1|  89 KFGER--FKLIADRYGNAL-PVESEWGEPIDLDKVENLLAEGANSVAMVHNETSAGVLNPAKEVGKLAKKYDALFIM 162
                                       *****..*******99999.999****************************************************** PP

                                       E-TTTTTTS---HHHHTESEEEEETTT.TTSSTT-EEEEEEHHHHHTS..SS.STTSEEEEETTEEEEHCTTGGGS. CS
                       Aminotran_5 175 DaaqavghipidvkklgvDflafsghK.llgPtGiGvlyvrkellekleplllggemveevsleettfaeapskfea 250
                                       D+ +++g  +++v+++gvD++ ++++K + +P+G +++++++++ e++e +    ++++   ++e+  +++ +    
  gi|298674997|ref|YP_003726747.1| 163 DGITSIGGDEVKVDDWGVDIAIAGSQKcIGAPPGMSMVSISDRAYEAMENVDNKPYYLDLEAYKESLDKDKTQTPY- 238
                                       ***************************8888******************************997777455544444. PP

                                       SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEE..TTCSHHHHH CS
                       Aminotran_5 251 GTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnf..kgvhaedva 325
                                        Tp v+ ++gl++ l +++e g+++  +++++ ++++++++++++       d++ + +++vs     +gv+ ed++
  gi|298674997|ref|YP_003726747.1| 239 -TPAVPLFYGLQESLHIVNEEGIDNRINRHRTYSKAVRNAMDAIGLEMYPTLDENTQYSNTVSAMSapEGVSGEDIK 314
                                       .9*****************************************98776655566677777776655579******** PP

                                       HHHHHTTEEEEEE-TTTHHHHHHTT.S-EEEEE CS
                       Aminotran_5 326 tlLdeegIavrsGhhcaqplmkrlalegtvRaS 358
                                       + + ++gI + +G++ +         ++++R++
  gi|298674997|ref|YP_003726747.1| 315 KDMLKRGIVIVGGQERL--------KDKIFRIG 339
                                       *************9987........55555555 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   4.6e-05       0.2      29     169 ..      35     165 ..      16     289 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.6e-05
                                       T--HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH-..-TTEEEEEETT-HHHHSST.THHHHCC--EEEEE- CS
                   Beta_elim_lyase  29 gedktvnrLedavaelfgkeaalfvpqGtaAnsillkill..qrgeevivtepahihfdet.gaiaelagvklrdlk 102
                                       + ++ + + ++ ++++f ++  + v +G ++  +  +i +  + +++vi  e  ++ f e  + ia   g  + +++
  gi|298674997|ref|YP_003726747.1|  35 EFAEIYDDCCNILKDVFNTQNDISVISGSGSAGMEAAIGCttNNNDNVITIE--NGKFGERfKLIADRYGN-ALPVE 108
                                       5556667777788888888888888876666555555555204444444333..55555553444444333.56666 PP

                                       EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEET CS
                   Beta_elim_lyase 103 nkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgA 169
                                       ++    +dl+k+e++++e ga  + ++++  ++   +       l+  +ev ++akky+  +++Dg 
  gi|298674997|ref|YP_003726747.1| 109 SEWGEPIDLDKVENLLAE-GA--NSVAMVHNETSAGV-------LNPAKEVGKLAKKYDALFIMDGI 165
                                       666678************.66..67777776655554.......55668999*************94 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   5.8e-05      0.26       3      32 ..      59      89 ..      58      92 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 5.8e-05
                                      EEE--SHHHHHHHHHHHHTTT.-EEEEESSS CS
                     FAD_binding_2  3 iViGsGlAGLaAAleaaeaGl.kvavvekeq 32
                                      ++ GsG AG+ AA+ ++ ++  +v+ +e+++
  gi|298674997|ref|YP_003726747.1| 59 VISGSGSAGMEAAIGCTTNNNdNVITIENGK 89
                                      788***************98889*9999875 PP

>> NUDIX_5  NUDIX, or N-terminal NPxY motif-rich,  region of KRIT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   8.5e-05      0.38      97     125 ..     231     259 ..     227     282 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8.5e-05
                           NUDIX_5  97 kdnskpskspgsPsFycLqdilrvcsess 125
                                       kd++++ ++p  P Fy Lq+ l++++e++
  gi|298674997|ref|YP_003726747.1| 231 KDKTQTPYTPAVPLFYGLQESLHIVNEEG 259
                                       99************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2882.06
//
Query:       gi|298674998|ref|YP_003726748.1|  [L=185]
Description: transcriptional regulator, XRE family [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-22   78.6   0.4    8.6e-11   42.1   0.1    2.3  2  CBS             CBS domain
    1.7e-12   47.2   0.0      5e-12   45.7   0.0    1.7  2  HTH_3           Helix-turn-helix
    2.5e-07   30.6   0.0    4.7e-07   29.7   0.0    1.4  1  HTH_19          Helix-turn-helix domain
      1e-06   29.0   0.0    1.6e-06   28.3   0.0    1.2  1  HTH_31          Helix-turn-helix domain
    0.00018   21.3   0.0    0.00029   20.6   0.0    1.3  1  HTH_25          Helix-turn-helix domain
     0.0013   18.7   0.0     0.0045   16.9   0.0    1.9  2  Pou             Pou domain - N-terminal to homeobox domain
     0.0042   17.5   0.0      0.014   15.8   0.0    1.9  2  HTH_26          Cro/C1-type HTH DNA-binding domain
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.028   14.4   0.0    1.5  1  HTH_37          Helix-turn-helix domain
        0.1   12.7   0.0       0.17   12.0   0.0    1.4  1  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito
       0.12   12.0   0.0       0.73    9.4   0.0    2.3  3  HTH_24          Winged helix-turn-helix DNA-binding


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.1   4.8e-14   8.6e-11       2      55 ..      67     119 ..      66     121 .. 0.94
   2 !   34.6   0.0     1e-11   1.9e-08       1      56 [.     132     184 ..     132     185 .] 0.94

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 4.8e-14
                                       HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       + im++dvv+++pd t+ +a+++m+++g+s++PV+ ed  +vG v++  +l+++
  gi|298674998|ref|YP_003726748.1|  67 KNIMHTDVVYISPDKTINDAVNIMEKHGYSQVPVL-EDWSCVGSVSEDMILKVM 119
                                       689*********************9999*******.899********9999875 PP

  == domain 2  score: 34.6 bits;  conditional E-value: 1e-11
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       ++d+m +++++++p+t +  +++++++  +s+++++ ++gk+ G++t++Dl+++l+
  gi|298674998|ref|YP_003726748.1| 132 IRDVMMSPLPVISPETFINAVFNMFEQ--FSAVLIM-DNGKYTGMITKHDLMKLLH 184
                                       589**********************66..****999.6**************9986 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.0   2.8e-15     5e-12       1      49 [.       9      57 ..       9      60 .. 0.95
   2 ?   -2.8   0.0       3.9   6.9e+03       5      12 ..      90      97 ..      89      99 .. 0.84

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 2.8e-15
                                      HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHT CS
                             HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLg 49
                                      lk++R++lg +q eLA+++Gvs+  i+riE ++  P+l+t+kk+ +a++
  gi|298674998|ref|YP_003726748.1|  9 LKRKRNELGFTQNELAKMTGVSQPLIARIEANDVDPRLSTVKKIYDAFQ 57
                                      89******************************************87775 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.9
                                      HHHTTHHH CS
                             HTH_3  5 Rkqlglsq 12
                                      ++++g+sq
  gi|298674998|ref|YP_003726748.1| 90 MEKHGYSQ 97
                                      6899***9 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   2.6e-10   4.7e-07       2      51 ..       7      55 ..       6      57 .. 0.94

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 2.6e-10
                            HTH_19  2 erLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaea 51
                                      e+Lk+ R elg+tq ela+++g+s+  i+ iE +   +p  ++++ki+ a
  gi|298674998|ref|YP_003726748.1|  7 ENLKRKRNELGFTQNELAKMTGVSQPLIARIEANDV-DPRLSTVKKIYDA 55
                                      99********************************98.9999***999865 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   9.1e-10   1.6e-06       6      54 ..       9      56 ..       6      64 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 9.1e-10
                            HTH_31  6 LralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaral 54
                                      L++ R++ G +q e+A+ +gvs+  + r+E    + p+++++ ++ +a+
  gi|298674998|ref|YP_003726748.1|  9 LKRKRNELGFTQNELAKMTGVSQPLIARIEANDVD-PRLSTVKKIYDAF 56
                                      8999******************************7.*******999886 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.6e-07   0.00029       2      36 ..       9      43 ..       8      45 .. 0.96

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.6e-07
                                      HHHHHHTTT--HHHHHHHSS--HHHHHHHHCT--T CS
                            HTH_25  2 LraaRearglsleevaketkIrkdylealEeddfd 36
                                      L+++R ++g +  e+ak t +++ ++ ++E++d+d
  gi|298674998|ref|YP_003726748.1|  9 LKRKRNELGFTQNELAKMTGVSQPLIARIEANDVD 43
                                      99******************************986 PP

>> Pou  Pou domain - N-terminal to homeobox domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.5e-06    0.0045      10      53 ..       6      43 ..       3      53 .. 0.84
   2 ?   -3.1   0.0       4.3   7.8e+03      61      67 ..      98     104 ..      88     104 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.5e-06
                               Pou 10 akefkqkRiklgltQadvglaLgklygkefSqttIcrFEkLdls 53
                                      a+++k+kR +lg+tQ+++++    +  + +Sq  I r+E+ d+ 
  gi|298674998|ref|YP_003726748.1|  6 AENLKRKRNELGFTQNELAK----M--TGVSQPLIARIEANDVD 43
                                      899************98665....4..4589********98775 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.3
                               Pou  61 kplLekW 67 
                                        p+Le W
  gi|298674998|ref|YP_003726748.1|  98 VPVLEDW 104
                                       3666666 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   7.9e-06     0.014       1      50 [.       8      56 ..       8      58 .. 0.90
   2 ?   -3.9   0.0        10   1.8e+04       4      12 ..     117     125 ..     115     127 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.9e-06
                            HTH_26  1 kLrelmadrgitkseLargtgisaatlsrlvkgkpervsldtLdkiCdaL 50
                                      +L++   + g t++eLa++tg+s++ ++r+  + +  ++l+t  ki da+
  gi|298674998|ref|YP_003726748.1|  8 NLKRKRNELGFTQNELAKMTGVSQPLIARIEANDV-DPRLSTVKKIYDAF 56
                                      57777778899***********************6.9*********9987 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 10
                            HTH_26   4 elmadrgit 12 
                                       ++m d++i+
  gi|298674998|ref|YP_003726748.1| 117 KVMTDNKIN 125
                                       789999986 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.6e-05     0.028      22      54 ..       8      40 ..       5      47 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.6e-05
                                      HHHHHHHHCT--HHHHHHHHT--HHHHHHHHTT CS
                            HTH_37 22 aiaeliekrelsqseaaqllgiaqPkvsrllrg 54
                                       +++++ +++ +q e+a+++g++qP + r++  
  gi|298674998|ref|YP_003726748.1|  8 NLKRKRNELGFTQNELAKMTGVSQPLIARIEAN 40
                                      589999********************9999865 PP

>> MqsA_antitoxin  Antitoxin component of bacterial toxin-antitoxin system, MqsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   9.7e-05      0.17      71     116 ..       6      51 ..       2      64 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.7e-05
                    MqsA_antitoxin  71 pafiarvrkkleldqreaaeifGgGvnafsryekGkvrpplalvkl 116
                                       ++ ++r r++l+++q+e+a++ G+     +r e+  v p l++vk 
  gi|298674998|ref|YP_003726748.1|   6 AENLKRKRNELGFTQNELAKMTGVSQPLIARIEANDVDPRLSTVKK 51 
                                       5678899***********************************9984 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00041      0.73      19      36 ..      19      36 ..      17      37 .. 0.90
   2 ?   -3.5   0.0       4.4   7.9e+03       4      14 ..      48      58 ..      46      60 .. 0.66
   3 ?   -1.2   0.0      0.83   1.5e+03      33      46 ..      82      95 ..      79      95 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00041
                            HTH_24 19 sqreLAerlglSpstvnr 36
                                      +q+eLA+++g+S++ + r
  gi|298674998|ref|YP_003726748.1| 19 TQNELAKMTGVSQPLIAR 36
                                      8***********998876 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.4
                            HTH_24  4 tdrkILelLqk 14
                                      t +kI+ + qk
  gi|298674998|ref|YP_003726748.1| 48 TVKKIYDAFQK 58
                                      45677777776 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.83
                            HTH_24 33 tvnrrlkrLeeeGl 46
                                      t+n  ++ +e+ G+
  gi|298674998|ref|YP_003726748.1| 82 TINDAVNIMEKHGY 95
                                      89999999*99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1296.91
//
Query:       gi|298674999|ref|YP_003726749.1|  [L=758]
Description: AAA ATPase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-94  311.6   0.0    4.2e-46  156.6   0.0    2.5  2  AAA              ATPase family associated with various cellul
    2.1e-30  104.2   0.9    2.8e-16   59.1   0.2    2.7  2  AAA_lid_3        AAA+ lid domain
    1.8e-25   88.9   0.7      5e-24   84.3   2.4    2.6  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    2.9e-16   60.3   0.0    6.2e-07   29.9   0.0    3.5  3  AAA_16           AAA ATPase domain
    2.9e-14   53.6   0.0    2.7e-06   27.6   0.0    2.6  2  AAA_2            AAA domain (Cdc48 subfamily)
    6.7e-13   48.7   0.0    4.9e-05   23.1   0.0    2.8  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    3.9e-12   45.8   0.4      1e-11   44.4   0.1    1.9  1  CDC48_2          Cell division protein 48 (CDC48), domain 2
    1.8e-10   41.2   0.0    0.00051   20.2   0.0    2.9  2  AAA_33           AAA domain
    3.1e-10   40.4   0.1     0.0019   18.5   0.0    3.9  3  AAA_22           AAA domain
    5.9e-10   39.3   3.6     0.0026   17.7   0.4    4.6  3  AAA_5            AAA domain (dynein-related subfamily)
    1.1e-09   38.0   0.1    0.00086   18.6   0.0    3.2  3  TIP49            TIP49 P-loop domain
    8.5e-09   35.5   0.0     0.0025   17.8   0.0    2.5  2  AAA_14           AAA domain
    3.5e-08   33.4   0.0      0.013   15.3   0.0    3.0  3  IstB_IS21        IstB-like ATP binding protein
    6.9e-08   33.1   0.0      0.025   15.1   0.0    3.1  2  AAA_18           AAA domain
    1.6e-07   31.2   0.0      0.014   15.1   0.0    3.1  2  Sigma54_activat  Sigma-54 interaction domain
    2.3e-07   30.4   0.2     0.0089   15.4   0.0    2.8  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    3.9e-07   30.1   0.2       0.29   11.0   0.0    4.1  4  NACHT            NACHT domain
    7.8e-07   28.8   0.0      0.022   14.3   0.0    2.6  2  AAA_7            P-loop containing dynein motor region
      2e-06   28.4   0.0      0.025   15.1   0.0    2.6  2  ABC_tran         ABC transporter
    5.7e-06   26.2   0.0      0.022   14.5   0.0    2.7  2  AAA_24           AAA domain
    8.2e-06   25.2   0.1       0.13   11.5   0.0    2.6  2  Zeta_toxin       Zeta toxin
    8.7e-06   26.1   0.0       0.14   12.4   0.0    2.5  2  AAA_28           AAA domain
    1.4e-05   25.5   0.0       0.13   12.7   0.0    3.1  2  RNA_helicase     RNA helicase
    2.2e-05   24.4   0.0        0.3   11.1   0.0    2.6  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    4.2e-05   23.5   0.0       0.12   12.1   0.0    2.4  2  AAA_11           AAA domain
    6.4e-05   22.5   0.1       0.47    9.9   0.0    2.7  2  PhoH             PhoH-like protein
     0.0001   22.1   0.1       0.57    9.9   0.0    2.4  2  AAA_30           AAA domain
    0.00011   22.1   0.0        0.5   10.2   0.0    2.6  2  AAA_3            ATPase family associated with various cellul
    0.00014   21.1   0.0        0.3   10.2   0.0    2.9  3  NB-ARC           NB-ARC domain
    0.00016   20.9   0.0       0.13   11.5   0.0    2.7  2  DUF815           Protein of unknown function (DUF815)
    0.00026   20.2   0.0       0.23   10.5   0.0    2.2  2  Parvo_NS1        Parvovirus non-structural protein NS1
    0.00032   20.6   0.1       0.58   10.2   0.0    2.9  2  Vps4_C           Vps4 C terminal oligomerisation domain
    0.00036   19.9   0.0       0.17   11.1   0.0    2.2  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    0.00048   19.6   2.3       0.36   10.1   0.1    3.6  3  ATPase           KaiC
    0.00053   20.0   0.0       0.82    9.5   0.0    3.2  2  ATPase_2         ATPase domain predominantly from Archaea
    0.00087   18.9   5.5       0.43   10.1   0.4    3.8  3  AAA_25           AAA domain
     0.0016   18.8   0.2        2.2    8.6   0.0    2.7  2  AAA_19           AAA domain
     0.0019   18.6   0.0        1.3    9.5   0.0    3.3  3  AAA_17           AAA domain
     0.0052   16.9   0.0        3.3    7.8   0.0    2.6  2  Sigma54_activ_2  Sigma-54 interaction domain
  ------ inclusion threshold ------
       0.01   15.7   0.0        2.5    7.9   0.0    3.0  2  Bac_DnaA         Bacterial dnaA  protein
       0.01   15.8   0.0         10    6.0   0.0    3.3  2  NTPase_1         NTPase
       0.01   15.1   0.1       0.65    9.2   0.0    2.7  2  KAP_NTPase       KAP family P-loop domain
      0.012   14.5   0.0       0.89    8.4   0.0    2.4  2  AFG1_ATPase      AFG1-like ATPase
      0.013   15.6   0.0        7.3    6.6   0.0    2.4  2  ResIII           Type III restriction enzyme, res subunit
      0.018   14.8   0.1        6.2    6.5   0.0    2.4  2  Cytidylate_kin   Cytidylate kinase
      0.022   14.5   0.1         16    5.1   0.0    4.1  4  Guanylate_kin    Guanylate kinase
      0.023   14.1   0.0        3.8    6.9   0.0    3.2  4  TniB             Bacterial TniB protein
      0.033   13.7   0.0        0.1   12.1   0.0    1.9  1  UFD1             Ubiquitin fusion degradation protein UFD1
      0.039   13.7   0.0        4.7    6.9   0.0    2.5  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
       0.05   12.7   0.0        9.9    5.1   0.0    2.8  2  T2SSE            Type II/IV secretion system protein
      0.067   13.0   0.0         10    5.9   0.0    2.4  2  CPT              Chloramphenicol phosphotransferase-like prot
      0.076   12.6   0.0         15    5.1   0.0    2.4  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
       0.13   12.4   0.1         29    4.8   0.0    2.8  2  SKI              Shikimate kinase
       0.13   12.0   0.0         16    5.2   0.0    2.3  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.6   0.0   1.3e-48   4.2e-46       1     130 [.     248     376 ..     248     378 .. 0.97
   2 !  152.6   0.0   2.2e-47   7.3e-45       1     131 [.     521     652 ..     521     653 .. 0.96

  Alignments for each domain:
  == domain 1  score: 156.6 bits;  conditional E-value: 1.3e-48
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       vll GppGtGKTlla+ava+e++++f++i+g+e++sk+ gese++ire+f+ea+++  p i+f+DE+d++a++r + 
  gi|298674999|ref|YP_003726749.1| 248 VLLQGPPGTGKTLLARAVANESDAYFISINGPEIMSKFYGESEQRIREVFDEAEKNT-PAIIFLDELDSIAPKRAEV 323
                                       79***************************************************9997.****************99* PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEET CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkiei 130
                                       + e+e+rvv+qLl+ +dg+k++++ vi+igatnrp+ ld al+r gRfdr+ie+
  gi|298674999|ref|YP_003726749.1| 324 TGEVERRVVAQLLSLMDGLKERKN-VILIGATNRPEALDIALRRpGRFDREIEL 376
                                       *********************855.**************************986 PP

  == domain 2  score: 152.6 bits;  conditional E-value: 2.2e-47
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH..T CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr..s 75 
                                       v+lyGppGtGKT+lakava+e++++f+  +gs+llsk+ gesek+i+e+f++a++ a p+++f+DE+da+a+ r  +
  gi|298674999|ref|YP_003726749.1| 521 VMLYGPPGTGKTMLAKAVANESDANFIAAKGSDLLSKWYGESEKRIAEVFSRARQVA-PTVIFLDELDAIAPVRgsT 596
                                       69******************************************************9.****************966 PP

                                       TCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  76 gseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                        +e +++ervvnqLl+eldg+++ ++ v+vigatnrpd +dpallr gRfd+ i ++
  gi|298674999|ref|YP_003726749.1| 597 VGEPQVTERVVNQLLSELDGLEELRG-VVVIGATNRPDIVDPALLRpGRFDELIMVP 652
                                       669********************866.*************************99876 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.0     9e-14     3e-11       1      40 [.     400     439 ..     400     442 .. 0.95
   2 !   59.1   0.2   8.3e-19   2.8e-16       1      44 [.     675     720 ..     675     721 .. 0.94

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 9e-14
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitm 40 
                                       dvdl++LAe T G++GAD+a+l reAa+  lrr ++ei+ 
  gi|298674999|ref|YP_003726749.1| 400 DVDLNKLAEITYGFVGADIASLAREAAMGVLRRILPEIDL 439
                                       9********************************9999875 PP

  == domain 2  score: 59.1 bits;  conditional E-value: 8.3e-19
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgik.e.itmedfe 44 
                                       dv+++eL++rTeGy+GAD+aa+c++A++ Alr++i  e +++++f 
  gi|298674999|ref|YP_003726749.1| 675 DVSIDELVARTEGYTGADIAAICKKAGRFALRENIMaEnVKQSHFL 720
                                       9*********************************98658*****96 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.3   2.4   1.5e-26     5e-24       1      84 [.      11      94 ..      11      95 .. 0.98

  Alignments for each domain:
  == domain 1  score: 84.3 bits;  conditional E-value: 1.5e-26
                                      CEEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEE CS
                           CDC48_N  1 rLrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVt 79
                                      +L+Vaea+q+dvg+g+vrid++  +++g+++ dvve++g+r+T aiv +  p d++k+iIrmdg++R+n + si d +t
  gi|298674999|ref|YP_003726749.1| 11 KLKVAEANQNDVGKGVVRIDKASRDKIGVREYDVVELRGRRTTSAIVRREFPADSSKDIIRMDGLIRTNSKTSISDNIT 89
                                      69***************************************************************************** PP

                                      EEEE- CS
                           CDC48_N 80 Vrkae 84
                                      V+kae
  gi|298674999|ref|YP_003726749.1| 90 VKKAE 94
                                      ***97 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   1.9e-09   6.2e-07      17     140 ..     238     351 ..     235     351 .. 0.75
   2 !   20.3   0.0   1.8e-06   0.00059      15      63 ..     509     554 ..     507     570 .. 0.83
   3 ?    5.8   0.0     0.049        16     124     170 .]     567     626 ..     560     626 .. 0.62

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 1.9e-09
                            AAA_16  17 ervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesae 93 
                                       +++    p  vll G++G+GK+ l+r++++   +++++f++ +  +      +s +    + e+ +r++ deae++ 
  gi|298674999|ref|YP_003726749.1| 238 DSLGIEAPKGVLLQGPPGTGKTLLARAVAN---ESDAYFISINGPEI-----MSKFYG--ESEQRIREVFDEAEKNT 304
                                       5556667899*******************6...6669**********.....333333..34588888888866655 PP

                            AAA_16  94 leawrekleeala.avpelagaeasrllellkrllallsrderplvlv 140
                                       ++      ++++a   +e++g+ ++r+ ++l +l++ l++++  ++l+
  gi|298674999|ref|YP_003726749.1| 305 PAIIFLDELDSIApKRAEVTGEVERRVVAQLLSLMDGLKERKN-VILI 351
                                       555554444444448899999999***********99999554.7664 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 1.8e-06
                            AAA_16  15 alervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63 
                                       a++r+    p  v+l+G++G+GK+ l+++++++  ++   f+++k  +l
  gi|298674999|ref|YP_003726749.1| 509 AFRRLGVEAPKGVMLYGPPGTGKTMLAKAVANESDAN---FIAAKGSDL 554
                                       677777778899*******************977776...888777766 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.049
                            AAA_16 124 krllallsrderplvlvlDdlq..............wade.aslqllaaLlrlleskpllvv 170
                                       ++ ++++++   p+v++lD+l+                 e    qll++L  l e + ++v+
  gi|298674999|ref|YP_003726749.1| 567 AEVFSRARQ-VAPTVIFLDELDaiapvrgstvgepqVT-ErVVNQLLSELDGLEELRGVVVI 626
                                       455566677.667*********5555555555555222.23555567777777766666665 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   8.2e-09   2.7e-06       6     105 ..     248     341 ..     245     347 .. 0.90
   2 !   23.0   0.0   2.1e-07   7.1e-05       6     104 ..     521     615 ..     518     618 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 8.2e-09
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll gp g+Gkt+la+a+a+  ++     +i ++  e++     + + ++++  ++   +ae++   i++lDE+d i
  gi|298674999|ref|YP_003726749.1| 248 VLLQGPPGTGKTLLARAVANESDA----YFISINGPEIMS----KFYGESEQRIREVFDEAEKNTpaIIFLDELDSI 316
                                       6899******************96....************....99999999999999999999999********** PP

                                       ---.---------HHHHHHHHHHHH- CS
                             AAA_2  81 hpk.essgadvSregVqrdLLqileg 105
                                       +pk  + + +v r  V+  LL +++g
  gi|298674999|ref|YP_003726749.1| 317 APKrAEVTGEVERR-VVAQLLSLMDG 341
                                       **987888888776.66778899987 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 2.1e-07
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       ++l gp g+Gkt+laka+a+  ++    ++i a  s+ll     + + ++++  ++   +a +    +++lDE+d i
  gi|298674999|ref|YP_003726749.1| 521 VMLYGPPGTGKTMLAKAVANESDA----NFIAAKGSDLLS----KWYGESEKRIAEVFSRARQVAptVIFLDELDAI 589
                                       5789******************96....************....99999999999999999998888********** PP

                                       ---..---------HHHHHHHHHHHH CS
                             AAA_2  81 hpk..essgadvSregVqrdLLqile 104
                                       +p   ++ g+    e V++ LL  l+
  gi|298674999|ref|YP_003726749.1| 590 APVrgSTVGEPQVTERVVNQLLSELD 615
                                       **887566666667888888887666 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   2.7e-07     9e-05      33     103 ..     245     323 ..     240     373 .. 0.76
   2 !   23.1   0.0   1.5e-07   4.9e-05      31      94 ..     516     587 ..     481     599 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.7e-07
                            RuvB_N  33 ldhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsrave 101
                                          vll+GpPG Gkt la+ +a+e ++ + +  gP +      e ++ +  ++ + e++   ++f+de+  ++++  
  gi|298674999|ref|YP_003726749.1| 245 PKGVLLQGPPGTGKTLLARAVANESDAYFISINGPEImskfygESEQRIREVFDEAEKNtpAIIFLDELDSIAPKRA 321
                                       5679*******************************983333333345677777666655225888888888877766 PP

                            RuvB_N 102 ev 103
                                       ev
  gi|298674999|ref|YP_003726749.1| 322 EV 323
                                       65 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 1.5e-07
                            RuvB_N  31 ealdhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideih 94 
                                       ea   v+lyGpPG Gkt lak +a+e ++++ ++ g  l      e ++ +a ++++ ++    v+f+de+ 
  gi|298674999|ref|YP_003726749.1| 516 EAPKGVMLYGPPGTGKTMLAKAVANESDANFIAAKGSDLlskwygESEKRIAEVFSRARQVapTVIFLDELD 587
                                       67778*************************988877654232222334556666666554322577777765 PP

>> CDC48_2  Cell division protein 48 (CDC48), domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.1     3e-14     1e-11       8      64 .]     116     199 ..     111     199 .. 0.84

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 3e-14
                                       H.HHHCCCTTEEE-TTEEE........................EECCT.....CCCEEEEEEEECCCCSCEEECTSC CS
                           CDC48_2   8 a.ylkrqFlgrpvtkGdlv........................vfefk.....gqeiklvVvstePkgpvgitetTe 54 
                                       a  l++ F +r v+kGd +                        +   +     ++e+k  +vst+P+g+v+it++Te
  gi|298674999|ref|YP_003726749.1| 116 AeILRSIFKNRTVSKGDFIsttnvrkpkdtygkgmmyedffqdM---FsssfgLGEVKIQIVSTSPSGIVKITDSTE 189
                                       44899**************9999999999999988777766663...044456************************ PP

                                       CEEESTTCCE CS
                           CDC48_2  55 ielgtkpvev 64 
                                       +el ++ vev
  gi|298674999|ref|YP_003726749.1| 190 VELLPESVEV 199
                                       *****99985 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   1.5e-06   0.00051       2      47 ..     248     309 ..     248     379 .. 0.73
   2 !   17.6   0.0   9.6e-06    0.0032       2     113 ..     521     674 ..     521     677 .. 0.64

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.5e-06
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt..............d 47 
                                       vll G+pG+GK+ la+ ++++ +  ++ ++ ++++++ +g+ +q+++               
  gi|298674999|ref|YP_003726749.1| 248 VLLQGPPGTGKTLLARAVANESDayFISINGPEIMSKFYGESEQRIRevfdeaekntpaiiF 309
                                       6899***************99999778899*********98888887444444444444440 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 9.6e-06
                            AAA_33   2 vllvGlpGsGKstlaerllkklgavllssdt..lrrrlfgtdqqskt.............................. 46 
                                       v+l G+pG+GK+ la+ ++++ +a +++     l+++ +g+ ++++                               
  gi|298674999|ref|YP_003726749.1| 521 VMLYGPPGTGKTMLAKAVANESDANFIAAKGsdLLSKWYGESEKRIAevfsrarqvaptvifldeldaiapvrgstv 597
                                       799******************99666655433455555555555444455555555555666666666666665555 PP

                            AAA_33  47 dytrvldrlyqilnelarkalsagrnvildat.........nlsrrerarflkl.arrlgvpvrivvvetdeetlke 113
                                         ++v++r+ ++l   ++   + ++ v++ at         +l++ ++++++ + +++ +++ +i+ v+t+e +l++
  gi|298674999|ref|YP_003726749.1| 598 GEPQVTERVVNQLLSELDGLEELRGVVVIGATnrpdivdpaLLRPGRFDELIMVpVPDKEARLKILEVHTSEMELAD 674
                                       44566666666666666555555555666555444444444777777777666667888888888888888877765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   0.00014     0.047       9      32 ..     249     272 ..     243     288 .. 0.82
   2 ?    2.2   0.0       0.6     2e+02      86     132 ..     297     355 ..     285     360 .. 0.67
   3 !   18.5   0.0   5.7e-06    0.0019       8      38 ..     521     562 ..     516     627 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00014
                            AAA_22   9 vvtGesGtGKTtllrrlleqldee 32 
                                       ++ G++GtGKT+l+r ++++ d++
  gi|298674999|ref|YP_003726749.1| 249 LLQGPPGTGKTLLARAVANESDAY 272
                                       788****************98654 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.6
                            AAA_22  86 lrarav..ielliiDEaqhlr..s........eealeeLrsllnlsrkgvqliLvGtpe 132
                                       ++++ +  ++++ +DE + +   +         +++ +L sl++  +    +iL+G ++
  gi|298674999|ref|YP_003726749.1| 297 FDEAEKntPAIIFLDELDSIApkRaevtgeveRRVVAQLLSLMDGLKERKNVILIGATN 355
                                       33333455689*********886245666777888999999998855555667777765 PP

  == domain 3  score: 18.5 bits;  conditional E-value: 5.7e-06
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee...........e 38 
                                       ++++G++GtGKT+l++ ++++ d+   a++            
  gi|298674999|ref|YP_003726749.1| 521 VMLYGPPGTGKTMLAKAVANESDANFIAAKgsdllskwygeS 562
                                       689******************987776666666666666652 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       4.6   1.5e+03      65      81 ..      66      82 ..      40     135 .. 0.58
   2 !   17.7   0.4   7.9e-06    0.0026       1      85 [.     247     324 ..     247     366 .. 0.60
   3 !   17.3   0.1   1.1e-05    0.0037       1      78 [.     520     590 ..     520     642 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 4.6
                                      G-SEEEEESGGG--HHH CS
                             AAA_5 65 egeilvlDEveraesev 81
                                      +++i+++D++ r +s++
  gi|298674999|ref|YP_003726749.1| 66 SKDIIRMDGLIRTNSKT 82
                                      44444444444444433 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 7.9e-06
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                       +vlL+GppGtgK+ la+ +a    + +  +++++ +++  + g+ e      ++   ++ ++a+  +++i++lDE++
  gi|298674999|ref|YP_003726749.1| 247 GVLLQGPPGTGKTLLARAVANESDAYFISINGPEIMSK--FYGESE------QRI-REVFDEAEknTPAIIFLDELD 314
                                       59*****************9998888888888887765..344444......122.333344444688888888888 PP

                                       G--HHHHHHH CS
                             AAA_5  76 raesevlnsL 85 
                                        + ++ +++ 
  gi|298674999|ref|YP_003726749.1| 315 SIAPKRAEVT 324
                                       8876655555 PP

  == domain 3  score: 17.3 bits;  conditional E-value: 1.1e-05
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEver 76 
                                       +v+L GppGtgK++la+ +a    +++    ++      dl+ ++   ++ +++   ++ ra +  + +++lDE++ 
  gi|298674999|ref|YP_003726749.1| 520 GVMLYGPPGTGKTMLAKAVANESDANFIAAKGS------DLLSKWY--GESEKRIAEVFSRARQvAPTVIFLDELDA 588
                                       59***************9998877777665554......4666666..45555555555555556777777777775 PP

                                       -- CS
                             AAA_5  77 ae 78 
                                       + 
  gi|298674999|ref|YP_003726749.1| 589 IA 590
                                       54 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0         3     1e+03     133     198 ..      89     155 ..      78     164 .. 0.76
   2 !   18.6   0.0   2.6e-06   0.00086      50      93 ..     245     286 ..     241     300 .. 0.86
   3 !   15.3   0.0   2.7e-05     0.009      50      97 ..     518     563 ..     512     578 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3
                                       SS-..TTS--EEEEEE-SS-EEEEEE-HHHHHHHHHHT.--TT-EEEEETTT--EEE-SSS-SS--- CS
                             TIP49 133 plskekkikevkitlktakeekklklgskiaeellkek.vkegDviviekesGkvkklGrsearake 198
                                       +++k++ +++ ++tl  + +  +++   +i  ++ k++ v++gD i   + +      G+++ +++ 
  gi|298674999|ref|YP_003726749.1|  89 TVKKAEWKEAKHVTLAPVTKGVRIHAPAEILRSIFKNRtVSKGDFISTTNVRKPKDTYGKGMMYEDF 155
                                       445667778889999999999999999999999888654999**99987777666777777776665 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 2.6e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  50 GravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslev 93 
                                        ++vLl+Gp+gtGkt la a+++e  +d  f++++g e+ s   
  gi|298674999|ref|YP_003726749.1| 245 PKGVLLQGPPGTGKTLLARAVANE--SDAYFISINGPEIMSKFY 286
                                       589*******************99..5799*********99755 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 2.7e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  50 GravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte 97 
                                        ++v+l Gp+gtGkt la a+++e  +d  f+a +gs++ s     +e
  gi|298674999|ref|YP_003726749.1| 518 PKGVMLYGPPGTGKTMLAKAVANE--SDANFIAAKGSDLLSKWYGESE 563
                                       589*******************99..5789********9997665555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   7.6e-06    0.0025       4     116 ..     247     369 ..     244     380 .. 0.73
   2 !   15.3   0.0   4.7e-05     0.016       5      76 ..     521     589 ..     517     657 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 7.6e-06
                            AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe.kllelileklkeekktylflDEiqev... 76 
                                        ++++G+  +GKT l++ +++e+      ++ in  +   k + ++e ++ e++ e  +++   ++flDE   +   
  gi|298674999|ref|YP_003726749.1| 247 GVLLQGPPGTGKTLLARAVANESD---AYFISINGPEIMSKFYGESEqRIREVFDEA-EKNTPAIIFLDELDSIapk 319
                                       5899****************8888...888888888877766555552455555554.4458999*******99888 PP

                            AAA_14  77 .........pewekalkslvd..egknldvivtGSnskllskeiatslagr 116
                                                +++   l sl+d  + ++ +vi+ G  +     +ia +  gr
  gi|298674999|ref|YP_003726749.1| 320 raevtgeveRRVVAQLLSLMDglK-ERKNVILIGATNRPEALDIALRRPGR 369
                                       888888888777777777777532.45578888877766666666555555 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 4.7e-05
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe.kllelileklkeekktylflDEiqev 76 
                                       +++ G+  +GKT+l+k +++e+     +++  +  d   k + ++e ++ e++ +  ++   t++flDE   +
  gi|298674999|ref|YP_003726749.1| 521 VMLYGPPGTGKTMLAKAVANESD---ANFIAAKGSDLLSKWYGESEkRIAEVFSRA-RQVAPTVIFLDELDAI 589
                                       7899***************9988...999999999998888776663566666665.444789******9887 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   0.00011     0.036      44      70 ..     242     268 ..     233     277 .. 0.88
   2 ?   -0.6   0.0       2.8   9.4e+02      29      56 ..     326     354 ..     315     356 .. 0.79
   3 !   15.3   0.0   3.8e-05     0.013      45      71 ..     516     542 ..     509     589 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00011
                         IstB_IS21  44 iekkenivllGpsGvGKshlaialgve 70 
                                       ie+ ++++l Gp+G+GK+ la a++ e
  gi|298674999|ref|YP_003726749.1| 242 IEAPKGVLLQGPPGTGKTLLARAVANE 268
                                       6777899****************9976 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.8
                         IstB_IS21  29 sldkrkvkeLat.lsfiekkenivllGps 56 
                                       ++++r v++L + ++ +++++n++l+G +
  gi|298674999|ref|YP_003726749.1| 326 EVERRVVAQLLSlMDGLKERKNVILIGAT 354
                                       6788888887551689999*******976 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 3.8e-05
                         IstB_IS21  45 ekkenivllGpsGvGKshlaialgvea 71 
                                       e+ ++++l Gp+G+GK+ la a++ e 
  gi|298674999|ref|YP_003726749.1| 516 EAPKGVMLYGPPGTGKTMLAKAVANES 542
                                       667889****************99764 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   0.00011     0.036       1      66 [.     248     341 ..     248     385 .. 0.62
   2 !   15.1   0.0   7.5e-05     0.025       1      35 [.     521     551 ..     521     624 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 0.00011
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf....................gvnlrdvakenglllevdpe.......aldes 49 
                                       +ll G+pG+GKt la++++++  ++                     +++ d a +n + + + +e         + +
  gi|298674999|ref|YP_003726749.1| 248 VLLQGPPGTGKTLLARAVANESdAYfisingpeimskfygeseqrIREVFDEAEKNTPAIIFLDEldsiapkRAEVT 324
                                       7899**************99976668888888666666666644444444444444444444444555555444445 PP

                            AAA_18  50 krldedkldklldalee 66 
                                        ++++ ++++ll+++++
  gi|298674999|ref|YP_003726749.1| 325 GEVERRVVAQLLSLMDG 341
                                       55555555555555555 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 7.5e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvaken 35 
                                       ++l G+pG+GKt lak+++++       +++a+++
  gi|298674999|ref|YP_003726749.1| 521 VMLYGPPGTGKTMLAKAVANES----DANFIAAKG 551
                                       789***************9884....333333332 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   4.1e-05     0.014      22      62 ..     245     282 ..     238     363 .. 0.78
   2 !   11.9   0.0   0.00039      0.13      20      48 ..     516     544 ..     500     557 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.1e-05
                                       SS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS- CS
                   Sigma54_activat  22 dlsvlitGesGtGKellaraiheaskrkekpfvavncaaip 62 
                                       +  vl++G  GtGK+llara+ ++s+   + f+++n  +i 
  gi|298674999|ref|YP_003726749.1| 245 PKGVLLQGPPGTGKTLLARAVANESD---AYFISINGPEIM 282
                                       5679****************998776...789999976653 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00039
                                       TSSS-EEEECSTTSSHHHHHHHHHHHSTT CS
                   Sigma54_activat  20 ktdlsvlitGesGtGKellaraiheaskr 48 
                                       + +  v++ G  GtGK++la+a+ ++s+ 
  gi|298674999|ref|YP_003726749.1| 516 EAPKGVMLYGPPGTGKTMLAKAVANESDA 544
                                       556789****************9988763 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00032      0.11      25      42 ..     248     265 ..     242     268 .. 0.90
   2 !   15.4   0.0   2.7e-05    0.0089      25      42 ..     521     538 ..     506     541 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00032
                      Mg_chelatase  25 lllvGppGsGKtmlakrl 42 
                                       +ll GppG+GKt+la+++
  gi|298674999|ref|YP_003726749.1| 248 VLLQGPPGTGKTLLARAV 265
                                       89*************987 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 2.7e-05
                      Mg_chelatase  25 lllvGppGsGKtmlakrl 42 
                                       ++l+GppG+GKtmlak++
  gi|298674999|ref|YP_003726749.1| 521 VMLYGPPGTGKTMLAKAV 538
                                       89*************987 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0    0.0012      0.41       3      22 ..     248     267 ..     246     271 .. 0.90
   2 ?    0.4   0.0       1.7   5.6e+02      62     125 ..     286     351 ..     280     379 .. 0.63
   3 !   11.0   0.0   0.00087      0.29       3      23 ..     521     541 ..     519     550 .. 0.89
   4 ?    2.4   0.0      0.41   1.3e+02      55     111 ..     552     613 ..     542     640 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0012
                                       EEEEC-TTTCHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklal 22 
                                       v+lqG++G GKT L++ +a 
  gi|298674999|ref|YP_003726749.1| 248 VLLQGPPGTGKTLLARAVAN 267
                                       79**************9986 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.7
                                       CTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH............HHHHHCTTTTT--EEEE CS
                             NACHT  62 lpepaapvsevwavllelperlLlilDglDelvtdlgq...kekqpvrtlLselirkkllpeaslll 125
                                       + e++++++ev+ +  ++   + + lD lD ++ +  +   + +++v   L +l+ +   +++ +l+
  gi|298674999|ref|YP_003726749.1| 286 YGESEQRIREVFDEAEKNT-PAIIFLDELDSIAPKRAEvtgEVERRVVAQLLSLMDGLKERKNVILI 351
                                       5677777888777755554.45555899999998777788844445555555787774444444444 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00087
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       v+l G++G GKT+L++ +a +
  gi|298674999|ref|YP_003726749.1| 521 VMLYGPPGTGKTMLAKAVANE 541
                                       7899************99875 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.41
                                       CHHHCCCCTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH...............HHH CS
                             NACHT  55 adllfsqlpepaapvsevwavllelperlLlilDglDelvtdlgq......kekqpvrtlLse 111
                                        dll + + e+++++ ev++ ++++   +++ lD lD ++   g        +++ v++lLse
  gi|298674999|ref|YP_003726749.1| 552 SDLLSKWYGESEKRIAEVFS-RARQVAPTVIFLDELDAIAPVRGStvgepqVTERVVNQLLSE 613
                                       58999999999999999554.666667777889******999998885444444444445544 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00044      0.15      30      58 ..     242     270 ..     235     318 .. 0.85
   2 !   14.3   0.0   6.6e-05     0.022      28      61 ..     513     545 ..     506     553 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00044
                             AAA_7  30 lknkkpvllvGptGtGKtviikdllkkld 58 
                                       +++ k vll Gp GtGKt++++ + ++ d
  gi|298674999|ref|YP_003726749.1| 242 IEAPKGVLLQGPPGTGKTLLARAVANESD 270
                                       667789****************9999887 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 6.6e-05
                             AAA_7  28 lllknkkpvllvGptGtGKtviikdllkkldkek 61 
                                       l +++ k v+l+Gp GtGKt+++k + ++ d  +
  gi|298674999|ref|YP_003726749.1| 513 LGVEAPKGVMLYGPPGTGKTMLAKAVANESD-AN 545
                                       56788899*****************999988.44 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0    0.0021      0.69       5      67 ..     239     299 ..     238     352 .. 0.76
   2 !   15.1   0.0   7.4e-05     0.025       7      76 ..     514     582 ..     511     634 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0021
                                       EEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   5 slklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe 67 
                                       sl +++ + v + G+ G+GK+ L++++a++++     i ++g ++ ++   +++++i+ ++ e
  gi|298674999|ref|YP_003726749.1| 239 SLGIEAPKGVLLQGPPGTGKTLLARAVANESDA--YFISINGPEIMSKFYGESEQRIREVFDE 299
                                       67788889999******************9975..4555577777776666777777666666 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 7.4e-05
                                       EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                          ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltv 76 
                                        +++ + v + G+ G+GK+ L+k++a++++  +  i  +g dl ++   +++k+i+ ++    q+ p++  
  gi|298674999|ref|YP_003726749.1| 514 GVEAPKGVMLYGPPGTGKTMLAKAVANESD--ANFIAAKGSDLLSKWYGESEKRIAEVFSRaRQVAPTVIF 582
                                       677778899*******************97..688999999999999999999999988886677776644 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0033       1.1       5      33 ..     248     278 ..     244     326 .. 0.65
   2 !   14.5   0.0   6.7e-05     0.022       4      25 ..     520     543 ..     517     593 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0033
                            AAA_24   5 iliyGpsgiGKTtlakel..gpkplfidtek 33 
                                       +l+ Gp+g+GKT la+    + ++ fi +++
  gi|298674999|ref|YP_003726749.1| 248 VLLQGPPGTGKTLLARAVanESDAYFISING 278
                                       7999************998878888887765 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 6.7e-05
                            AAA_24   4 kiliyGpsgiGKTtlakel..gpk 25 
                                        +++yGp+g+GKT+lak    + +
  gi|298674999|ref|YP_003726749.1| 520 GVMLYGPPGTGKTMLAKAVanESD 543
                                       589*************99865444 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0    0.0004      0.13      14      50 ..     243     277 ..     235     294 .. 0.86
   2 !   10.9   0.0   0.00062      0.21      14      47 ..     516     547 ..     506     556 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0004
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrld 50 
                                       e Pk +ll G pG GK+ la+++++e   +  ++ ++
  gi|298674999|ref|YP_003726749.1| 243 EAPKGVLLQGPPGTGKTLLARAVANES--DAYFISIN 277
                                       78***********************98..55555555 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00062
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvv 47 
                                       e Pk ++l G pG GK+ la+++++e   + n++
  gi|298674999|ref|YP_003726749.1| 516 EAPKGVMLYGPPGTGKTMLAKAVANES--DANFI 547
                                       89***********************98..55555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0    0.0011      0.36       2      37 ..     248     288 ..     247     321 .. 0.72
   2 !   12.4   0.0   0.00041      0.14       2      44 ..     521     564 ..     520     582 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0011
                            AAA_28   2 ivitGgestGKTtlleaLaar....gypvv.pEaareilee 37 
                                       + + G+++tGKT l++a a++     +++  pE++ +++ e
  gi|298674999|ref|YP_003726749.1| 248 VLLQGPPGTGKTLLARAVANEsdayFISINgPEIMSKFYGE 288
                                       6788***************7654323333366666665544 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00041
                            AAA_28   2 ivitGgestGKTtlleaLaar.gypvvpEaareileeklakged 44 
                                       +++ G+++tGKT l++a a++ + + ++  + ++l++ + + e+
  gi|298674999|ref|YP_003726749.1| 521 VMLYGPPGTGKTMLAKAVANEsDANFIAAKGSDLLSKWYGESEK 564
                                       6899***************8756777766666666666555555 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0049       1.6       1      22 [.     248     269 ..     248     310 .. 0.81
   2 !   12.7   0.0   0.00039      0.13       1      23 [.     521     543 ..     521     578 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0049
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakal 22 
                                       ++l+Gp+g+GK++la+ +a++ 
  gi|298674999|ref|YP_003726749.1| 248 VLLQGPPGTGKTLLARAVANES 269
                                       5799************987765 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00039
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakall 23 
                                       ++lyGp+g+GK++lak +a++  
  gi|298674999|ref|YP_003726749.1| 521 VMLYGPPGTGKTMLAKAVANESD 543
                                       689**************887654 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0    0.0014      0.48      19      44 ..     245     270 ..     226     290 .. 0.79
   2 !   11.1   0.0   0.00091       0.3       8      43 ..     511     542 ..     491     552 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0014
                                       TEEEEEEESTTSSHHHHHHHHHHHTT CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglakalg 44 
                                        + +lL+G+ G+GKT l+r++a++ +
  gi|298674999|ref|YP_003726749.1| 245 PKGVLLQGPPGTGKTLLARAVANESD 270
                                       4469*****************99865 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00091
                                       HHHHHHHHHCHTEEEEEEESTTSSHHHHHHHHHHHT CS
                              TsaE   8 ealgkklakalgdvilLeGdLGaGKTtlvrglakal 43 
                                       ++lg +      + ++L+G+ G+GKT+l++++a++ 
  gi|298674999|ref|YP_003726749.1| 511 RRLGVEA----PKGVMLYGPPGTGKTMLAKAVANES 542
                                       3333333....346******************9876 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00037      0.12      17      41 ..     245     269 ..     233     307 .. 0.80
   2 !    8.8   0.0    0.0038       1.3      15      40 ..     516     541 ..     505     573 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00037
                            AAA_11  17 seitliqGPPGtgKTktivellsql 41 
                                       ++ +l+qGPPGtgKT    ++ ++ 
  gi|298674999|ref|YP_003726749.1| 245 PKGVLLQGPPGTGKTLLARAVANES 269
                                       55589**********8887777765 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0038
                            AAA_11  15 seseitliqGPPGtgKTktivellsq 40 
                                       + ++ +++ GPPGtgKT    ++ ++
  gi|298674999|ref|YP_003726749.1| 516 EAPKGVMLYGPPGTGKTMLAKAVANE 541
                                       55666899*********777666665 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0018      0.59      22      40 ..     248     266 ..     237     271 .. 0.85
   2 !    9.9   0.0    0.0014      0.47      22      41 ..     521     540 ..     508     546 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0018
                                       EEEE--TTSSTTHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavala 40 
                                       v   Gp GtGKt+la a+a
  gi|298674999|ref|YP_003726749.1| 248 VLLQGPPGTGKTLLARAVA 266
                                       7789***********9998 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0014
                                       EEEE--TTSSTTHHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavalav 41 
                                       v+  Gp GtGKt+la a+a 
  gi|298674999|ref|YP_003726749.1| 521 VMLYGPPGTGKTMLAKAVAN 540
                                       7899***********99985 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0     0.002      0.67      21      40 ..     248     267 ..     240     276 .. 0.87
   2 !    9.9   0.0    0.0017      0.57      11      40 ..     511     540 ..     506     585 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.002
                            AAA_30  21 avltGpAGtGKttalkalre 40 
                                       ++l+Gp+GtGKt + +a+++
  gi|298674999|ref|YP_003726749.1| 248 VLLQGPPGTGKTLLARAVAN 267
                                       689***********999975 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0017
                            AAA_30  11 ealltsgdrvavltGpAGtGKttalkalre 40 
                                       ++l  +  + ++l Gp+GtGKt++ ka+++
  gi|298674999|ref|YP_003726749.1| 511 RRLGVEAPKGVMLYGPPGTGKTMLAKAVAN 540
                                       55555555567899**********999976 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0    0.0015       0.5       2      30 ..     248     276 ..     247     289 .. 0.89
   2 !    9.2   0.0    0.0031         1       2      28 ..     521     547 ..     520     597 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0015
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       vll+g PG++ktll++a+a+  d+ f  i
  gi|298674999|ref|YP_003726749.1| 248 VLLQGPPGTGKTLLARAVANESDAYFISI 276
                                       89*****************9998887655 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0031
                             AAA_3   2 vllegvPGlaktllvkalakaldlefk 28 
                                       v+l g PG++kt+l+ka+a+  d++f 
  gi|298674999|ref|YP_003726749.1| 521 VMLYGPPGTGKTMLAKAVANESDANFI 547
                                       78999***************9999885 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0078       2.6      23      45 ..     248     270 ..     236     274 .. 0.88
   2 !   10.2   0.0    0.0009       0.3      23      45 ..     521     543 ..     510     547 .. 0.88
   3 ?   -1.9   0.0       4.6   1.5e+03     120     149 ..     648     678 ..     643     698 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0078
                                       EEEEESTTSSHHHHHHHHCCSHC CS
                            NB-ARC  23 valvGmgGvGKttlakqilnksd 45 
                                       v l G +G GKt la+ + n+sd
  gi|298674999|ref|YP_003726749.1| 248 VLLQGPPGTGKTLLARAVANESD 270
                                       6799***************9976 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0009
                                       EEEEESTTSSHHHHHHHHCCSHC CS
                            NB-ARC  23 valvGmgGvGKttlakqilnksd 45 
                                       v l+G +G GKt lak + n+sd
  gi|298674999|ref|YP_003726749.1| 521 VMLYGPPGTGKTMLAKAVANESD 543
                                       789****************9965 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 4.6
                                       ....HHHHCHTTSEEE.EEESBCCCCCCS-S CS
                            NB-ARC 120 kigvvlparenrlrvl.lTTRdeevanavsa 149
                                        i+v++p++e rl++l + T ++e+a+ vs 
  gi|298674999|ref|YP_003726749.1| 648 LIMVPVPDKEARLKILeVHTSEMELADDVSI 678
                                       4889999999999998677778888777765 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.012       3.9      54     116 ..     246     313 ..     238     375 .. 0.65
   2 !   11.5   0.0   0.00038      0.13      24      80 ..     480     545 ..     465     586 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.012
                            DUF815  54 nnvLLwGarGtGKSslvkallneyaeegLrli..evekedlkelpklvellr...erperfilfvDDL 116
                                       + vLL G  GtGK  l +a+ ne  +  + +   e+  +   e ++ ++++    e+++  i+f+D L
  gi|298674999|ref|YP_003726749.1| 246 KGVLLQGPPGTGKTLLARAVANESDAYFISINgpEIMSKFYGESEQRIREVFdeaEKNTPAIIFLDEL 313
                                       579*******************9887765442225544444333333333321113344567777766 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00038
                            DUF815  24 evklddLvgidkqkeal.......venteqfle.glpa.nnvLLwGarGtGKSslvkallneyaee 80 
                                       +v++dd+ g+++ ke l       ++n+e+f + g +a + v+L+G  GtGK  l ka+ ne  ++
  gi|298674999|ref|YP_003726749.1| 480 NVTWDDVGGLEEVKELLseavewpLKNAEAFRRlGVEApKGVMLYGPPGTGKTMLAKAVANESDAN 545
                                       56677777777777766222222235777775434444378*******************997665 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0069       2.3     117     141 ..     248     272 ..     244     277 .. 0.90
   2 !   10.5   0.0   0.00068      0.23     117     138 ..     521     542 ..     516     545 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0069
                         Parvo_NS1 117 vwfyGpantGktnlaeaIakavply 141
                                       v++ Gp+ tGkt la+a a+ ++ y
  gi|298674999|ref|YP_003726749.1| 248 VLLQGPPGTGKTLLARAVANESDAY 272
                                       7889***************988876 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00068
                         Parvo_NS1 117 vwfyGpantGktnlaeaIakav 138
                                       v++yGp+ tGkt+la+a a+ +
  gi|298674999|ref|YP_003726749.1| 521 VMLYGPPGTGKTMLAKAVANES 542
                                       789**************99865 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.2     0.017       5.7      19      44 ..     444     469 ..     436     473 .. 0.86
   2 !   10.2   0.0    0.0017      0.58      22      54 ..     707     739 ..     694     741 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.017
                            Vps4_C  19 ipsdkllePpvtlkDflkalkkarpt 44 
                                       ip+d l + +vt  Df++alk + p+
  gi|298674999|ref|YP_003726749.1| 444 IPKDVLDQLQVTKMDFDNALKDVSPS 469
                                       778888888**************998 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0017
                            Vps4_C  22 dkllePpvtlkDflkalkkarptVskeDLekhe 54 
                                       + +++ +v+ ++flka+++  p+V++e ++ +e
  gi|298674999|ref|YP_003726749.1| 707 ENIMAENVKQSHFLKAIEEIGPSVTSEVVKYYE 739
                                       5678889*******************9999887 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0    0.0005      0.17       4      44 ..     248     281 ..     245     322 .. 0.76
   2 ?    6.6   0.0     0.012       3.9       5      25 ..     522     542 ..     518     573 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0005
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplv 44 
                                       vl +G +GtGKt+++ ++++e         a ++s N+p++
  gi|298674999|ref|YP_003726749.1| 248 VLLQGPPGTGKTLLARAVANES-------DAYFISINGPEI 281
                                       789*************999998.......555666666654 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.012
                           DUF2075   5 lVtGvaGtGKtvvllnllael 25 
                                       +  G +GtGKt+++ ++++e 
  gi|298674999|ref|YP_003726749.1| 522 MLYGPPGTGKTMLAKAVANES 542
                                       6689***********999997 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.2       2.7     9e+02     182     212 ..      24      54 ..      10      60 .. 0.87
   2 !   10.1   0.1    0.0011      0.36      14      37 ..     240     263 ..     234     349 .. 0.86
   3 ?    6.5   0.0     0.014       4.6      19      37 ..     518     536 ..     504     545 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.7
                            ATPase 182 dgvivLdlkeieeelvRtleivkmRgtkhsk 212
                                       +gv+++d+ + ++  vR  ++v +Rg ++ +
  gi|298674999|ref|YP_003726749.1|  24 KGVVRIDKASRDKIGVREYDVVELRGRRTTS 54 
                                       69***********************998876 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0011
                            ATPase  14 gGipegrvvlitGepGtGKtifal 37 
                                        Gi   + vl+ G pGtGKt++a 
  gi|298674999|ref|YP_003726749.1| 240 LGIEAPKGVLLQGPPGTGKTLLAR 263
                                       48889999**************96 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.014
                            ATPase  19 grvvlitGepGtGKtifal 37 
                                        + v ++G pGtGKt++a+
  gi|298674999|ref|YP_003726749.1| 518 PKGVMLYGPPGTGKTMLAK 536
                                       566899***********97 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.026       8.8      24     122 ..     249     350 ..     239     352 .. 0.52
   2 !    9.5   0.0    0.0025      0.82      23      45 ..     521     543 ..     511     615 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.026
                          ATPase_2  24 fiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal...............gia 85 
                                       ++ Gp g GKt L + ++++++       y+i++++ +i ++       e+++++++++               ++ 
  gi|298674999|ref|YP_003726749.1| 249 LLQGPPGTGKTLLARAVANESDA------YFISINGPEIMSKFYG----ESEQRIREVFdeaekntpaiifldeLDS 315
                                       56699999999999988888844......4444444444333333....2222222222222233333444454333 PP

                          ATPase_2  86 vpkaeleeilkeksklvfkaielllekikkkgkkiii 122
                                       +  +++ e+  e  + v +++ +l++ +k+++  +i+
  gi|298674999|ref|YP_003726749.1| 316 IAPKRA-EVTGEVERRVVAQLLSLMDGLKERK-NVIL 350
                                       333333.3445666666666767777776663.3444 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0025
                          ATPase_2  23 yfiYGpegsGKtaLlkeiienle 45 
                                       +++YGp g GKt L k ++++++
  gi|298674999|ref|YP_003726749.1| 521 VMLYGPPGTGKTMLAKAVANESD 543
                                       689*************9999883 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.034        11      36      52 ..     248     264 ..     241     268 .. 0.85
   2 ?    3.1   0.1      0.18        61     127     176 ..     290     339 ..     265     353 .. 0.77
   3 !   10.1   0.4    0.0013      0.43      36      54 ..     521     539 ..     514     626 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.034
                            AAA_25  36 allaGapgtGKttlald 52 
                                       +ll G+pgtGKt la  
  gi|298674999|ref|YP_003726749.1| 248 VLLQGPPGTGKTLLARA 264
                                       6899*********9965 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.18
                            AAA_25 127 tadvdaleaaieevegvrlvviDplsralggdensnsdv.galvealeria 176
                                       ++ ++++ +++e+ + ++ + +D l+++ +   +   +v +++v++l ++ 
  gi|298674999|ref|YP_003726749.1| 290 EQRIREVFDEAEK-NTPAIIFLDELDSIAPKRAEVTGEVeRRVVAQLLSLM 339
                                       4567778888889.78***************77777887788888877664 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.0013
                            AAA_25  36 allaGapgtGKttlaldla 54 
                                       ++l+G+pgtGKt+la  +a
  gi|298674999|ref|YP_003726749.1| 521 VMLYGPPGTGKTMLAKAVA 539
                                       68***********996555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1     0.015       4.9      12      32 ..     247     267 ..     242     352 .. 0.84
   2 !    8.6   0.0    0.0066       2.2      11      33 ..     519     541 ..     511     634 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.015
                            AAA_19  12 vllvtaGpGtGKTrvlkhiva 32 
                                        +l+ ++pGtGKT + +++ +
  gi|298674999|ref|YP_003726749.1| 247 GVLLQGPPGTGKTLLARAVAN 267
                                       5899*********88776654 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0066
                            AAA_19  11 kvllvtaGpGtGKTrvlkhival 33 
                                       k +++ ++pGtGKT + k++ ++
  gi|298674999|ref|YP_003726749.1| 519 KGVMLYGPPGTGKTMLAKAVANE 541
                                       457899********988777655 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       9.6   3.2e+03      51      98 ..      47      94 ..      27     139 .. 0.67
   2 ?    5.1   0.0     0.088        29       2      25 ..     252     275 ..     251     322 .. 0.77
   3 !    9.5   0.0    0.0038       1.3       1      32 [.     524     557 ..     524     583 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 9.6
                                      HHHHHHHHHHHHHHHHHHHHSSEEEEEE-SEEEETTEEEESSHHHHHH CS
                            AAA_17 51 leekkelqkeaaekiaeeakkkgvlvdghprikeqagfldglpkevle 98
                                      l+ ++ + +++ ++   +++k+ + +dg  r++ +  + d+++++  e
  gi|298674999|ref|YP_003726749.1| 47 LRGRRTTSAIVRREFPADSSKDIIRMDGLIRTNSKTSISDNITVKKAE 94
                                      555555556666666666777788888888888887777777765444 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.088
                                       E-TTSSHHHHHHHHHHHHTEEEEE CS
                            AAA_17   2 GgPGsGKgtqceklvekygfthls 25 
                                       G+PG GK+ +++ ++ + +  ++s
  gi|298674999|ref|YP_003726749.1| 252 GPPGTGKTLLARAVANESDAYFIS 275
                                       9**********9999887666555 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0038
                                       EE-TTSSHHHHHHHHHHHHTEEEEEH..HHHHHH CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsa..Gdllre 32 
                                       +G+PG GK+ +++ ++ + +  ++ a  +dll +
  gi|298674999|ref|YP_003726749.1| 524 YGPPGTGKTMLAKAVANESDANFIAAkgSDLLSK 557
                                       7**************9887555554332888765 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0      0.01       3.3      23      46 ..     247     270 ..     242     322 .. 0.73
   2 ?    6.2   0.0     0.031        10      23      47 ..     520     544 ..     512     588 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.01
                                       -EEEEEETT--HHHHHHCC--TTS CS
                   Sigma54_activ_2  23 pvfltGekGsgkelvArlLhknsg 46 
                                        v+l G++G+gk+l Ar+ +++s 
  gi|298674999|ref|YP_003726749.1| 247 GVLLQGPPGTGKTLLARAVANESD 270
                                       59****************998775 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.031
                                       -EEEEEETT--HHHHHHCC--TTS- CS
                   Sigma54_activ_2  23 pvfltGekGsgkelvArlLhknsgp 47 
                                        v l G++G+gk++ A++ +++s  
  gi|298674999|ref|YP_003726749.1| 520 GVMLYGPPGTGKTMLAKAVANESDA 544
                                       5899**************9998765 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.098        33      37     177 ..     248     390 ..     243     438 .. 0.68
   2 ?    7.9   0.0    0.0074       2.5      37      66 ..     521     550 ..     511     562 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.098
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHTT-.SEEEEE-GGGGTT- CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklrkv.DvLliDDiqflagk 112
                                       +++ g+ G Gkt L +a++ne     +++  + +++ e ++++    +++  e f e  +++  ++ +D++  +a k
  gi|298674999|ref|YP_003726749.1| 248 VLLQGPPGTGKTLLARAVANE-----SDAYFISINGPEIMSKFYGESEQRIREVFDEAEKNTpAIIFLDELDSIAPK 319
                                       678888899999998888775.....455556677777777777777777777777766655134557777777776 PP

                                       H.........HHHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHH CS
                          Bac_DnaA 113 e.........ktqeelfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkk 177
                                                 ++  +l+ +++ l e ++ +++ +   P++l+ +  r   rf++   ++++ pd+e r++il+ 
  gi|298674999|ref|YP_003726749.1| 320 RaevtgeverRVVAQLLSLMDGLKERKNVILIGATNRPEALD-IALRRPGRFDR--EIELHVPDTEGRMEILQI 390
                                       422211111123345667777777777788888888888875.55666778877..467777888888888864 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0074
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS- CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelr 66 
                                       +++yg+ G Gkt L ka++ne  +n+ +++
  gi|298674999|ref|YP_003726749.1| 521 VMLYGPPGTGKTMLAKAVANESDANFIAAK 550
                                       79******************9988876665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.033        11       2      32 ..     248     278 ..     247     346 .. 0.85
   2 ?    6.0   0.0      0.03        10       2      23 ..     521     542 ..     520     554 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.033
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       v++ GppG+GKt l + v+++ +   ++++G
  gi|298674999|ref|YP_003726749.1| 248 VLLQGPPGTGKTLLARAVANESDAYFISING 278
                                       6899************999987766666666 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.03
                                       EEEE--TTSSHHHHHHHHHHHH CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlell 23 
                                       v++ GppG+GKt l k v+++ 
  gi|298674999|ref|YP_003726749.1| 521 VMLYGPPGTGKTMLAKAVANES 542
                                       6789************999876 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0019      0.65     162     200 ..     291     331 ..     243     351 .. 0.88
   2 ?    2.7   0.0      0.18        60      23      47 ..     521     545 ..     515     615 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0019
                        KAP_NTPase 162 admektLda..lqkrlVvviDdLDrceteevlqlleavkll 200
                                       +++ + +d+  ++++ ++++D+LD++ ++++  + e+ + +
  gi|298674999|ref|YP_003726749.1| 291 QRIREVFDEaeKNTPAIIFLDELDSIAPKRAEVTGEVERRV 331
                                       456666666778******************99998876655 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.18
                        KAP_NTPase  23 vgLygkWGsGKssllnkledelkef 47 
                                       v+Lyg+ G+GK+ l + + +e + +
  gi|298674999|ref|YP_003726749.1| 521 VMLYGPPGTGKTMLAKAVANESDAN 545
                                       899*********9999888876665 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.098        33      60      78 ..     243     261 ..     236     272 .. 0.89
   2 ?    8.4   0.0    0.0027      0.89      56      79 ..     512     535 ..     490     547 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.098
                       AFG1_ATPase  60 epvrglYlwGgvGrGKtyl 78 
                                       e+++g+ l+G+ G GKt l
  gi|298674999|ref|YP_003726749.1| 243 EAPKGVLLQGPPGTGKTLL 261
                                       799**************98 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0027
                       AFG1_ATPase  56 rksvepvrglYlwGgvGrGKtylm 79 
                                       r  ve+++g+ l+G+ G GKt+l 
  gi|298674999|ref|YP_003726749.1| 512 RLGVEAPKGVMLYGPPGTGKTMLA 535
                                       34689*****************96 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.022       7.3      22      46 ..     243     267 ..     217     313 .. 0.80
   2 ?    6.5   0.0     0.023       7.6      21      73 ..     506     561 ..     486     588 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.022
                                       .TTSEEEEEESTTSTHHHHHHHHHH CS
                            ResIII  22 krdkrglikmaTGtGKTlvaaklie 46 
                                       +  k +l++ + GtGKTl+a +++ 
  gi|298674999|ref|YP_003726749.1| 243 EAPKGVLLQGPPGTGKTLLARAVAN 267
                                       7889999***********9976655 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.023
                                       ...........TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHH CS
                            ResIII  21 s.........krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtlee 73 
                                       +         +  k +++  + GtGKT++a +++ +   +      ++ + + +ll++++ e
  gi|298674999|ref|YP_003726749.1| 506 NaeafrrlgvEAPKGVMLYGPPGTGKTMLAKAVANESDAN------FIAAKGSDLLSKWYGE 561
                                       14445555557788899999********998887776664......3345566666666655 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0      0.03       9.9       3      27 ..     250     274 ..     248     278 .. 0.88
   2 ?    6.5   0.0     0.019       6.2       3      27 ..     523     547 ..     521     551 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.03
                                       EE-STTSSHHHHHHHHHHHHT-EEE CS
                    Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyl 27 
                                       + GP g+GK  +ara+a++ ++ ++
  gi|298674999|ref|YP_003726749.1| 250 LQGPPGTGKTLLARAVANESDAYFI 274
                                       78****************9988776 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.019
                                       EE-STTSSHHHHHHHHHHHHT-EEE CS
                    Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyl 27 
                                       + GP g+GK  +a+a+a++ +++++
  gi|298674999|ref|YP_003726749.1| 523 LYGPPGTGKTMLAKAVANESDANFI 547
                                       67*****************999987 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.88   2.9e+02       3      30 ..     246     273 ..     244     280 .. 0.84
   2 ?    1.7   0.0      0.53   1.8e+02      75      98 ..     282     310 ..     276     324 .. 0.78
   3 ?    5.1   0.0     0.049        16       3      30 ..     519     546 ..     517     550 .. 0.87
   4 ?    0.1   0.0       1.6   5.4e+02      76      96 ..     556     576 ..     544     593 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.88
                                       SEEEEESTTTSSHHHHHHHHHHHSTTTE CS
                     Guanylate_kin   3 rpvvlvgpsgaGksslkkaLlselpekf 30 
                                       + v l gp g+Gk  l  a+ +e   +f
  gi|298674999|ref|YP_003726749.1| 246 KGVLLQGPPGTGKTLLARAVANESDAYF 273
                                       568999***********99998888777 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.53
                                       TTEEEEEEHHHHHHHHHTTSE.....EEE CS
                     Guanylate_kin  75 sgnlygtsveaieevlekgki.....viL 98 
                                        ++ yg+s + i+ev++++ +     ++L
  gi|298674999|ref|YP_003726749.1| 282 MSKFYGESEQRIREVFDEAEKntpaiIFL 310
                                       5789***********98876545544455 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.049
                                       SEEEEESTTTSSHHHHHHHHHHHSTTTE CS
                     Guanylate_kin   3 rpvvlvgpsgaGksslkkaLlselpekf 30 
                                       + v+l gp g+Gk +l ka+ +e   +f
  gi|298674999|ref|YP_003726749.1| 519 KGVMLYGPPGTGKTMLAKAVANESDANF 546
                                       6689***************999887776 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 1.6
                                       TEEEEEEHHHHHHHHHTTSEE CS
                     Guanylate_kin  76 gnlygtsveaieevlekgkiv 96 
                                       ++ yg+s + i ev+  +++v
  gi|298674999|ref|YP_003726749.1| 556 SKWYGESEKRIAEVFSRARQV 576
                                       689**************9995 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.19        62      26      58 ..     236     268 ..     221     280 .. 0.83
   2 ?   -2.6   0.0       9.5   3.2e+03     139     151 ..     328     340 ..     287     365 .. 0.53
   3 ?    6.9   0.0     0.011       3.8      34      59 ..     517     542 ..     505     553 .. 0.82
   4 ?   -2.1   0.0       6.7   2.2e+03     109     132 ..     567     590 ..     560     607 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.19
                              TniB  26 LleypkrkrmpnlllvGdsnnGKtmivekFarl 58 
                                       L++    + ++ +ll G++ +GKt +++  a++
  gi|298674999|ref|YP_003726749.1| 236 LFDSLGIEAPKGVLLQGPPGTGKTLLARAVANE 268
                                       666666677899*************99887765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 9.5
                              TniB 139 qreflnalksLgn 151
                                        r+++++l sL++
  gi|298674999|ref|YP_003726749.1| 328 ERRVVAQLLSLMD 340
                                       3333333333333 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.011
                              TniB  34 rmpnlllvGdsnnGKtmivekFarlh 59 
                                        ++ ++l+G++ +GKtm+++  a++ 
  gi|298674999|ref|YP_003726749.1| 517 APKGVMLYGPPGTGKTMLAKAVANES 542
                                       56789**************9887765 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 6.7
                              TniB 109 qqvlrllrelkvrvLiiDEihnll 132
                                       ++v +  r++ + v+ +DE++ + 
  gi|298674999|ref|YP_003726749.1| 567 AEVFSRARQVAPTVIFLDELDAIA 590
                                       456677799999*******99875 PP

>> UFD1  Ubiquitin fusion degradation protein UFD1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00031       0.1      63     143 ..      60     140 ..      44     194 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00031
                              UFD1  63 eFtae..egtvylPewmmenlgleegdlveiesvslpkgkfvklqpqsedfldisdpkavLekaLrnfatLtkgdvi 137
                                       eF a+  ++ + +   + +n + + +d +++++++ +++k v+l p + + ++i+ p ++L + ++n  t++kgd i
  gi|298674999|ref|YP_003726749.1|  60 EFPADssKDIIRMDGLIRTNSKTSISDNITVKKAEWKEAKHVTLAPVT-KGVRIHAPAEILRSIFKN-RTVSKGDFI 134
                                       666541156788888999999*************************95.5689********998887.789*****9 PP

                              UFD1 138 eikynd 143
                                       + +  +
  gi|298674999|ref|YP_003726749.1| 135 STTNVR 140
                                       877644 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0       0.1        35       2      27 ..     246     271 ..     245     275 .. 0.87
   2 ?    6.9   0.0     0.014       4.7       2      24 ..     519     541 ..     518     545 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.1
                         PduV-EutP   2 kkilliGkvgsGKttLtqalkgeelk 27 
                                       k +ll G+ g+GKt L++a+ +e+  
  gi|298674999|ref|YP_003726749.1| 246 KGVLLQGPPGTGKTLLARAVANESDA 271
                                       5699****************998755 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.014
                         PduV-EutP   2 kkilliGkvgsGKttLtqalkge 24 
                                       k ++l G+ g+GKt L++a+ +e
  gi|298674999|ref|YP_003726749.1| 519 KGVMLYGPPGTGKTMLAKAVANE 541
                                       679****************9987 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.058        19     130     153 ..     246     269 ..     232     279 .. 0.83
   2 ?    5.1   0.0      0.03       9.9     116     152 ..     505     541 ..     418     549 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.058
                             T2SSE 130 glilvsGgTgsGKttllyallkei 153
                                       + +l+ G+ g+GKt l+ a+ +e 
  gi|298674999|ref|YP_003726749.1| 246 KGVLLQGPPGTGKTLLARAVANES 269
                                       6789************99988775 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.03
                             T2SSE 116 ekiaevlrkavrerglilvsGgTgsGKttllyallke 152
                                       ++ +++ r  v++ + +++ G+ g+GKt l+ a+ +e
  gi|298674999|ref|YP_003726749.1| 505 KNAEAFRRLGVEAPKGVMLYGPPGTGKTMLAKAVANE 541
                                       666777777788889999*************998876 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0      0.03        10       4      33 ..     248     277 ..     246     308 .. 0.86
   2 ?    4.4   0.0     0.091        30       4      32 ..     521     549 ..     519     569 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.03
                                       EEEEE-TTSSHHHHHHHHHHHSSS-EEEEE CS
                               CPT   4 ilLnGgsssGKsslaralqevldepwlhlg 33 
                                       +lL+G + +GK+ lara+ + +d+ ++ ++
  gi|298674999|ref|YP_003726749.1| 248 VLLQGPPGTGKTLLARAVANESDAYFISIN 277
                                       89*********************9999886 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.091
                                       EEEEE-TTSSHHHHHHHHHHHSSS-EEEE CS
                               CPT   4 ilLnGgsssGKsslaralqevldepwlhl 32 
                                       ++L G + +GK+ la+a+ + +d+ +++ 
  gi|298674999|ref|YP_003726749.1| 521 VMLYGPPGTGKTMLAKAVANESDANFIAA 549
                                       89*********************999875 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.059        20       4      26 ..     249     271 ..     247     286 .. 0.82
   2 ?    5.1   0.0     0.045        15       4      27 ..     522     545 ..     520     552 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.059
                                       EEEESTTCCHHHHHHHHHCT--S CS
                              cobW   4 vltGflGsGKTtLlnhllenrag 26 
                                       +l G++G+GKT L +++ ++++ 
  gi|298674999|ref|YP_003726749.1| 249 LLQGPPGTGKTLLARAVANESDA 271
                                       689********998888776655 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.045
                                       EEEESTTCCHHHHHHHHHCT--SS CS
                              cobW   4 vltGflGsGKTtLlnhllenragl 27 
                                       +l G++G+GKT+L +++ ++++ +
  gi|298674999|ref|YP_003726749.1| 522 MLYGPPGTGKTMLAKAVANESDAN 545
                                       689**********99988776655 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.086        29       1      24 [.     254     277 ..     254     304 .. 0.69
   2 ?    4.7   0.0     0.092        30       1      21 [.     527     547 ..     527     574 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.086
                                       TTSSHHHHHHHHHHHHTSEEEEHH CS
                               SKI   1 mGaGKstvGkllAkklglefiDlD 24 
                                       +G+GK+ +++++A++ +  fi + 
  gi|298674999|ref|YP_003726749.1| 254 PGTGKTLLARAVANESDAYFISIN 277
                                       69****************999775 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.092
                                       TTSSHHHHHHHHHHHHTSEEE CS
                               SKI   1 mGaGKstvGkllAkklglefi 21 
                                       +G+GK+ ++k++A++ + +fi
  gi|298674999|ref|YP_003726749.1| 527 PGTGKTMLAKAVANESDANFI 547
                                       69**************99998 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.047        16       3      70 ..     250     312 ..     248     317 .. 0.76
   2 ?    4.4   0.0     0.083        28       5      70 ..     525     585 ..     521     590 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.047
                   Viral_helicase1   3 vhGvpGcGKStlirkllrts..liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDE 70 
                                        +G pG GK+ l r ++++s  + +++n p  e+ ++   +++++  + +d+++++        i++lDE
  gi|298674999|ref|YP_003726749.1| 250 LQGPPGTGKTLLARAVANESdaYFISINGP--EIMSKFYGESEQRIREVFDEAEKNTP-----AIIFLDE 312
                                       6799***************99544444444..77777667888888888888888764.....4888888 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.083
                   Viral_helicase1   5 GvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDE 70 
                                       G pG GK+ l + ++++s  ++ + +    ll+++  +++++  + +  + +   +     +++lDE
  gi|298674999|ref|YP_003726749.1| 525 GPPGTGKTMLAKAVANESdANFIAAKG-SDLLSKWYGESEKRIAEVFSRARQV--A---PTVIFLDE 585
                                       78***************8766666666.6777777655555555544433332..2...24677776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (758 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        54  (0.00301188); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              54  [number of targets reported over threshold]
# CPU time: 0.81u 0.34s 00:00:01.15 Elapsed: 00:00:00.49
# Mc/sec: 4634.40
//
Query:       gi|298675000|ref|YP_003726750.1|  [L=458]
Description: monomethylamine methyltransferase MtmB [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   6.7e-225  747.0   0.7   7.5e-225  746.8   0.7    1.0  1  MtmB      Monomethylamine methyltransferase MtmB


Domain annotation for each model (and alignments):
>> MtmB  Monomethylamine methyltransferase MtmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  746.8   0.7  4.2e-229  7.5e-225       2     450 .]       8     456 ..       7     456 .. 1.00

  Alignments for each domain:
  == domain 1  score: 746.8 bits;  conditional E-value: 4.2e-229
                              MtmB   2 dvydaykrakkGekveedewdyveipqkaeelkekydikfenefiPededladrlfqaGlelLvetGvycidtervi 78 
                                       +vyd+y+rak+Gek+++d+wd ++ip+ka elk+ky ++f++ef+P+d+d++++lf+aG+e+L+e+G+yc+dt+r++
  gi|298675000|ref|YP_003726750.1|   8 TVYDFYDRAKTGEKTTQDDWDLMTIPMKAGELKQKYGLDFGDEFVPTDKDMMENLFNAGFEMLLECGIYCTDTKRIV 84 
                                       8**************************************************************************** PP

                              MtmB  79 kvteeeilegikkapkklelGegkdaveleerksndskkPiiqgGPtGapvsedvfleviqsyaqeplvdtivsGvl 155
                                       k+te+ei+++i++++k+++lG+g+dav++++r++ d++kP+iqgGPtGapvsedvf++v++sya e   d iv+Gv+
  gi|298675000|ref|YP_003726750.1|  85 KYTEDEIWDAINNVDKEFTLGTGRDAVTVRKREVGDKRKPLIQGGPTGAPVSEDVFVPVHMSYAMERECDLIVNGVM 161
                                       ***************************************************************************** PP

                              MtmB 156 etvegkeaktksPfeikatlaearlvkeatslagrpglalkGpetplsaagrlaadlaeglresdshevsqLnelki 232
                                       ++++gk+++++sP+e+ a+++e rl+kea++++grpg++l+Gpet+lsa g+++ad+ +gl++ dshevsqLnelki
  gi|298675000|ref|YP_003726750.1| 162 TSIRGKSPVPGSPYEVLAAKSESRLIKEACAMCGRPGMGLOGPETSLSAPGNISADAVGGLNPADSHEVSQLNELKI 238
                                       ***************************************************************************** PP

                              MtmB 233 dvealnliagykangdvilveqmPifGGyaggieetaivdvattlasfvltdasfhldGpihirwgstttretlqia 309
                                       d++a++++a+y+an+dvi+ eqmPifGGyaggieetaivdvatt+++f++ +a++hldGp+hirwgst+tre+l+ia
  gi|298675000|ref|YP_003726750.1| 239 DLDAIAVVAHYQANSDVIMDEQMPIFGGYAGGIEETAIVDVATTINAFLMNNATWHLDGPVHIRWGSTNTREALKIA 315
                                       ***************************************************************************** PP

                              MtmB 310 ahaaaaidantdlllanqyytlaGpctemclletaaqaiadtasGrellsGvaaakGvvkdkttGlearlmgevaia 386
                                       ++++a+i+++td++l+nqyy++aGpctemclle+aaq+++dtasGre+lsGva+akGv +dkttG+ear+mge a+a
  gi|298675000|ref|YP_003726750.1| 316 GWTSATIKEHTDMILGNQYYPCAGPCTEMCLLEAAAQSMTDTASGREILSGVASAKGVGQDKTTGMEARMMGETARA 392
                                       ***************************************************************************** PP

                              MtmB 387 aaglevsevneildklvskyeknyakaPaGkrfqeCydvktvePtdeyldvydkalkkleelGl 450
                                       +ag++++evn+ildklv +ye+++ + P+ k+fqeCyd++t++P dey++vyd a kkle+lGl
  gi|298675000|ref|YP_003726750.1| 393 TAGMDINEVNKILDKLVGMYENDFGNLPEDKTFQECYDISTITPIDEYVNVYDGAKKKLEDLGL 456
                                       **************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.35s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 2614.34
//
Query:       gi|298675001|ref|YP_003726751.1|  [L=217]
Description: methyltransferase cognate corrinoid protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-23   82.7   0.1    3.9e-23   81.7   0.1    1.5  1  B12-binding_2  B12 binding domain
    1.4e-17   63.8   0.4    2.6e-17   63.0   0.4    1.4  1  B12-binding    B12 binding domain


Domain annotation for each model (and alignments):
>> B12-binding_2  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.7   0.1   4.4e-27   3.9e-23       3      75 .]       8      80 ..       6      80 .. 0.97

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 4.4e-27
                     B12-binding_2  3 erlhwaivhgdkegieelidealaqgsaavdvlndvllpamkeVGdlfgagelflpqvllsaevmkkavahLe 75
                                      e+l++ai++ d eg++ l++eal++g +av+++n++l p+mk+VGd+f++ge flpq +++a++m+ a++++e
  gi|298675001|ref|YP_003726751.1|  8 EKLKNAIINQDIEGCKNLTKEALDAGLSAVEIVNKGLTPGMKVVGDKFESGEAFLPQIMMAAKAMQGAMEYIE 80
                                      89********************************************************************986 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.0   0.4   2.9e-21   2.6e-17       4     119 ..      96     207 ..      93     209 .. 0.89

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 2.9e-21
                       B12-binding   4 llatvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvgl..Salltsqleavkelvel..lk 76 
                                       +  + +gd+h++G +++  +l+++gf++++lg++v++++++++i++ k d ++l  Sal+t+++ + kel++l  ++
  gi|298675001|ref|YP_003726751.1|  96 VTFVQEGDIHDIGHRLVTTMLQANGFDIVDLGVDVPDDNVLEEIEKQKDDQILLvgSALMTTSMLGQKELMNLigEA 172
                                       5667789*****************************************99988889********************* PP

                       B12-binding  77 rirprvkvvvGGahpsldpeetleaklgiddvvvgegedalea 119
                                       + r++vkv++GGa+++  + +   + +g +d    ++e+a+ea
  gi|298675001|ref|YP_003726751.1| 173 GLRDKVKVMLGGAPVTQKWID---E-IG-AD---ATAENAAEA 207
                                       *************96666666...6.99.55...588877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1338.30
//
Query:       gi|298675002|ref|YP_003726752.1|  [L=376]
Description: major facilitator superfamily protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      7e-35  120.6  74.4    1.3e-27   96.6  40.3    2.0  2  MFS_1       Major Facilitator Superfamily
  ------ inclusion threshold ------
       0.98    8.2  21.7      0.036   12.9  11.9    2.2  2  MFS_1_like  MFS_1 like family


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.6  40.3   1.5e-31   1.3e-27       3     326 ..      10     320 ..       8     322 .. 0.71
   2 !   37.6  26.1   1.3e-13   1.2e-09       1     165 [.     219     372 ..     219     376 .] 0.89

  Alignments for each domain:
  == domain 1  score: 96.6 bits;  conditional E-value: 1.5e-31
                             MFS_1   3 laaflsalarsilgpalpl.alaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglll 78 
                                        ++f+++  ++++ p+lp+ a a++ + +p   +ll+++y+++a+++++p+G l+d +G  r+++lg+l+++++++l
  gi|298675002|ref|YP_003726752.1|  10 TTIFVMMGLSDAVVPILPElAAANHSN-NPMISSLLFSTYFIAALITMIPFGILTDIYGNVRFIMLGILMTFVSGYL 85 
                                       678999999999******844444444.7777888***************************999999999999777 PP

                             MFS_1  79 llfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfy 155
                                       +l++++lw+ll++r++ G ++ga+fpa+ ++++++++   r++++g +s   ++G ++g +++g+l+ s g     +
  gi|298675002|ref|YP_003726752.1|  86 ILITNNLWILLFARIIEGSACGAFFPAAFSMLSRYTK---RNQYFGEFSFLLNAGLAVGVAISGVLT-STGLKNGIL 158
                                       7766999*****************************5...6**************************.667676667 PP

                             MFS_1 156 ilaivsllafv..lfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvl.w...illialllfffgfsg. 225
                                       +++++s ++f+  + ++    ++ +++          + +  +++ +   lkd +  +    ++ +++l+ff+f + 
  gi|298675002|ref|YP_003726752.1| 159 LFTAISGILFIvaIPVWNKSKTEINNPGLGIN----DKIENTWIK-IYTQLKDTFYtLfngNYINIWILTFFVFGAp 230
                                       77777777666233333334444444444333....448888888.3333333333224554666666666666662 PP

                             MFS_1 226 ..lltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssa 300
                                         +++l p y  e++  +   ++g+++a l++ ++i ++l+gr   +     +++++ ++l+++++g +++ ++   
  gi|298675002|ref|YP_003726752.1| 231 tvFVALYPDY-SEDFLSK--TMLGITIASLYVSAMITSFLIGRSGFK-----YNTMIKAGLIIISAGAIIAINY--- 296
                                       2255555555.5555555..888866666666665555555555544.....6667777777777776666666... PP

                             MFS_1 301 vllllvlvliGfglgfvfpsllalas 326
                                          + +++++G+g+g  ++ l  ++s
  gi|298675002|ref|YP_003726752.1| 297 --PISGFIIMGIGGGSGMVGLPIAVS 320
                                       ..466888888866666666655555 PP

  == domain 2  score: 37.6 bits;  conditional E-value: 1.3e-13
                             MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgll 77 
                                       +++++f+++ a +++ +++p  ++ed+  s++ +g+ ++  ++ a+++s+++Gr + ++    ++ +gl++ ++g +
  gi|298675002|ref|YP_003726752.1| 219 IWILTFFVFGAPTVFVALYP-DYSEDFL-SKTMLGITIASLYVSAMITSFLIGRSGFKY--NTMIKAGLIIISAG-A 290
                                       68999999999999999999.9*****9.**************************9998..66889999999999.8 PP

                             MFS_1  78 lllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravf 154
                                       +++  ++++  + + +++G+g+ ++  +g+ +++   +  +rg+ +gll++++ +G  l pl++g+l+ +l+++++f
  gi|298675002|ref|YP_003726752.1| 291 IIA--INYP--ISGFIIMGIGG-GSGMVGLPIAVSHLNV-NRGLSMGLLNTCTYAGLGLMPLFAGVLTPYLSFEWIF 361
                                       888..7877..99999*****5.5555666666667777.9************************************ PP

                             MFS_1 155 yilaivsllaf 165
                                       ++ +i+  +++
  gi|298675002|ref|YP_003726752.1| 362 LLDGIIIGISV 372
                                       *******9983 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9  11.9     4e-06     0.036     259     374 ..      37     149 ..       2     162 .. 0.75
   2 ?   -0.9   5.5     0.063   5.6e+02     180     280 ..     154     269 ..     123     305 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4e-06
                        MFS_1_like 259 ntllGslva.lgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaa 334
                                       n +++sl++    +a +++ +    l++++G v+ +++++l++++   l+ i++n+w++l++ +++g ++g+++ aa
  gi|298675002|ref|YP_003726752.1|  37 NPMISSLLFsTYFIAALITMIPFGILTDIYGNVRFIMLGILMTFVSGYLILITNNLWILLFARIIEGSACGAFFPAA 113
                                       3444444440445778888888899**************************************************** PP

                        MFS_1_like 335 veyvskiapksleatgqgllsglyfglGralGsliGGllw 374
                                        +  s+ + ++   ++ g +s l   +G a+G  i+G+l 
  gi|298675002|ref|YP_003726752.1| 114 FSMLSRYTKRN---QYFGEFSFL-LNAGLAVGVAISGVLT 149
                                       ***99877654...455656544.6677788888888775 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.063
                        MFS_1_like 180 sallyvlaallvisllvvlilnetekesklkvtksl...................qvllnilknpevi.ifllvali 236
                                       +  +++++a+  i ++v       + +sk+++ + +                   ++ + +l n ++i i +l+ ++
  gi|298675002|ref|YP_003726752.1| 154 KNGILLFTAISGILFIV---AIPVWNKSKTEINN-PglgindkientwikiytqlKDTFYTLFNGNYInIWILTFFV 226
                                       44444444444444444...33334445555553.456777788888888888884444455555544144444445 PP

                        MFS_1_like 237 lg...mswgiienFlflYLkelgasntllGslvalgvvaei.plfffa 280
                                        g   ++++++  + + +L     s+t+lG+++a   v+ + + f+++
  gi|298675002|ref|YP_003726752.1| 227 FGaptVFVALYPDYSEDFL-----SKTMLGITIASLYVSAMiTSFLIG 269
                                       4422245666666666666.....999999999866665540445544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 2303.35
//
Query:       gi|298675003|ref|YP_003726753.1|  [L=167]
Description: hypothetical protein Metev_1071 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.039   13.8   0.2      0.075   12.9   0.2    1.4  1  DUF5089      Domain of unknown function (DUF5089)
       0.12   12.4   2.3        5.9    7.0   0.1    2.7  3  Phage_Orf51  Phage Conserved Open Reading Frame 51


Domain annotation for each model (and alignments):
>> DUF5089  Domain of unknown function (DUF5089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   8.4e-06     0.075     149     178 ..      80     109 ..      78     111 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.4e-06
                           DUF5089 149 lkslkkeaevQnkeikkqkskikdItkvne 178
                                       lk l++++ +Q++ +k+qk++++dI  +ne
  gi|298675003|ref|YP_003726753.1|  80 LKMLNSKSLKQSEDVKSQKNNTNDIDGYNE 109
                                       899**********************99987 PP

>> Phage_Orf51  Phage Conserved Open Reading Frame 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1   0.00065       5.9      30      56 ..       5      31 ..       2      45 .. 0.84
   2 ?   -2.7   0.0       0.7   6.3e+03       4      13 ..      59      68 ..      57      74 .. 0.76
   3 ?    4.5   0.2    0.0039        35       7      30 ..     140     163 ..     134     166 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00065
                       Phage_Orf51 30 ihvvngtyyfhghivpgwqgvkktfdt 56
                                       h+  gt y+ g+i p ++  k+ + t
  gi|298675003|ref|YP_003726753.1|  5 YHIETGTLYINGYITPAYKFEKNEIGT 31
                                      69999************9987776665 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.7
                       Phage_Orf51  4 sarkeylnqf 13
                                      s++k yln f
  gi|298675003|ref|YP_003726753.1| 59 SCKKLYLNIF 68
                                      6678899977 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.0039
                       Phage_Orf51   7 keylnqffgskrylyqdnervahi 30 
                                        ey  q++   r  yqd e v  i
  gi|298675003|ref|YP_003726753.1| 140 EEYTRQYLYRARKKYQDFEDVFGI 163
                                       69*****************99766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1125  (0.0627475); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1074.03
//
Query:       gi|298675004|ref|YP_003726754.1|  [L=109]
Description: hypothetical protein Metev_1072 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-34  117.0   1.5    4.1e-34  116.7   1.5    1.1  1  DUF2551          Protein of unknown function (DUF2551)
     0.0084   16.5   0.1      0.015   15.7   0.1    1.5  1  Penicillinase_R  Penicillinase repressor
  ------ inclusion threshold ------
      0.062   13.0   0.0       0.12   12.1   0.0    1.6  1  Ribosomal_L12_N  Ribosomal protein L7/L12 dimerisation domain
      0.076   12.9   0.7       0.19   11.7   0.5    1.9  1  Imm6             Immunity protein Imm6


Domain annotation for each model (and alignments):
>> DUF2551  Protein of unknown function (DUF2551)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.7   1.5   9.2e-38   4.1e-34       1      83 []      12      94 ..      12      94 .. 0.99

  Alignments for each domain:
  == domain 1  score: 116.7 bits;  conditional E-value: 9.2e-38
                           DUF2551  1 LkkylerDksGiRrevLklfleakkltveeiyeklkekfdvsykgvasmvGliasrlGIlkvkkeskgeknvYsLkeey 79
                                      L+k++e D+sG+R++vL++fl++k++tv+++ye++k+kf++s+++vasmvG+i+s+lGIl+++kes+++++vY+Lk+ey
  gi|298675004|ref|YP_003726754.1| 12 LQKFVELDTSGLRSSVLSFFLKEKNVTVDDLYEAIKTKFNISRSSVASMVGYIHSKLGILRAYKESYKTHMVYTLKDEY 90
                                      89***************************************************************************** PP

                           DUF2551 80 adlv 83
                                      +dl+
  gi|298675004|ref|YP_003726754.1| 91 VDLI 94
                                      *997 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   3.2e-06     0.015       6      59 ..      25      79 ..      20     104 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.2e-06
                                      SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHT.TS-EEEEETTE CS
                   Penicillinase_R  6 aevmeilwekgeatvkevveeleeekelaysTVktllrrLvkK.gllsrekegra 59
                                      + v+  + +++++tv+++ e+++ + + ++s+V+++++  + K g+l+++ke  +
  gi|298675004|ref|YP_003726754.1| 25 SSVLSFFLKEKNVTVDDLYEAIKTKFNISRSSVASMVGYIHSKlGILRAYKESYK 79
                                      67999999*********************************99778888877333 PP

>> Ribosomal_L12_N  Ribosomal protein L7/L12 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.7e-05      0.12      17      38 ..      39      61 ..      32      70 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.7e-05
                                      HHHHHHHHHHHTTHHHH.HHHHH CS
                   Ribosomal_L12_N 17 lseLvkalEekFGVsAA.APvav 38
                                      + +L +a+++kF++s +  + +v
  gi|298675004|ref|YP_003726754.1| 39 VDDLYEAIKTKFNISRSsVASMV 61
                                      5699***********65234333 PP

>> Imm6  Immunity protein Imm6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.5   4.1e-05      0.19      36      54 ..      30      48 ..       3      98 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.1e-05
                              Imm6 36 kwlegenvtadeLydlldn 54
                                       +l+++nvt+d+Ly+ +  
  gi|298675004|ref|YP_003726754.1| 30 FFLKEKNVTVDDLYEAIKT 48
                                      59*************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 673.98
//
Query:       gi|298675005|ref|YP_003726755.1|  [L=135]
Description: hypothetical protein Metev_1073 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0099   15.7   0.0      0.018   14.9   0.0    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
       0.16   12.1   0.0       0.27   11.4   0.0    1.4  1  B-block_TFIIIC  B-block binding subunit of TFIIIC


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0     2e-06     0.018      23      60 ..      68     105 ..      65     111 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2e-06
                                       CHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT CS
                              TrmB  23 atadeiaeelgvprskvYevLrsLedkGlVerekgrpk 60 
                                       ++ ++i +el++ r++ Y++ ++L+ +Gl++++ ++++
  gi|298675005|ref|YP_003726755.1|  68 SEWKDIIKELDIGRASFYSMRNKLLGAGLITTRNQEYR 105
                                       67789**************************9988875 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0     3e-05      0.27      22      53 ..      71     102 ..      70     117 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3e-05
                    B-block_TFIIIC  22 sdLakeskqdprslfyrlksLekkgLIvkqsi 53 
                                       +d++ke+++   s+++ +++L   gLI+ ++ 
  gi|298675005|ref|YP_003726755.1|  71 KDIIKELDIGRASFYSMRNKLLGAGLITTRNQ 102
                                       5899************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.33s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 814.04
//
Query:       gi|298675006|ref|YP_003726756.1|  [L=238]
Description: putative circadian clock protein KaiC [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-45  155.4   0.2    1.7e-45  155.2   0.2    1.0  1  ATPase         KaiC
    2.9e-06   26.2   0.1    4.5e-06   25.6   0.1    1.2  1  GvpD           GvpD gas vesicle protein
    3.9e-05   23.1   0.0    5.1e-05   22.7   0.0    1.4  1  DnaB_C         DnaB-like helicase C terminal domain
    0.00017   21.2   0.0    0.00024   20.7   0.0    1.3  1  RecA           recA bacterial DNA recombination protein
     0.0018   18.1   0.1     0.0054   16.5   0.0    1.8  2  IstB_IS21      IstB-like ATP binding protein
     0.0066   16.2   0.4      0.013   15.2   0.4    1.5  1  AAA_24         AAA domain
      0.009   15.9   0.7      0.033   14.1   0.7    1.9  1  NTPase_1       NTPase
     0.0098   15.2   0.0      0.011   15.1   0.0    1.2  1  DUF2075        Uncharacterized conserved protein (DUF2075)
  ------ inclusion threshold ------
      0.011   14.8   0.0      0.016   14.2   0.0    1.2  1  T2SSE          Type II/IV secretion system protein
      0.014   15.7   0.2       0.04   14.2   0.1    1.8  2  AAA_22         AAA domain
      0.017   14.7   0.1      0.028   14.0   0.1    1.5  1  AAA_25         AAA domain
      0.023   14.3   0.4       0.08   12.5   0.0    2.1  3  Ras            Ras family
      0.031   13.5   1.2       0.04   13.2   1.2    1.5  1  Rad51          Rad51
      0.035   14.1   0.0      0.059   13.4   0.0    1.4  1  ResIII         Type III restriction enzyme, res subunit
      0.077   13.0   0.1       0.33   11.0   0.0    2.0  2  AAA_14         AAA domain
       0.16   12.4   0.0        0.2   12.0   0.0    1.3  1  AAA_16         AAA ATPase domain
       0.23   10.4   0.3       0.36    9.7   0.3    1.2  1  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.2   0.2   1.6e-48   1.7e-45       2     229 ..       5     234 ..       4     236 .. 0.90

  Alignments for each domain:
  == domain 1  score: 155.2 bits;  conditional E-value: 1.6e-48
                            ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekle 78 
                                       +tgI +lD  ++gG+p+g+ + itG++GtGKtif+lqFl k + + g+++ +v++ee++ed+  +a  l   l+++ 
  gi|298675006|ref|YP_003726756.1|   5 STGIDELDGKISGGFPKGKGIVITGSSGTGKTIFGLQFLNKACHD-GKKCTIVATEETPEDILTHADVLNLSLRDFY 80 
                                       7********************************************.******************************* PP

                            ATPase  79 eegklaiidasesaeesaee....kdkedleel.ieelaeaikeikakrvviDsitglayeekeavaReilrqlvrv 150
                                       ++g l i+d++++++ ++ee         +e + +eel + ++    + vviD+i++++   ++ ++R+ +++l+++
  gi|298675006|ref|YP_003726756.1|  81 NNGYLEIVDTYRKRAFETEEsdirGAGLTIERIdLEELPNLVS-NDSEVVVIDNIGVYSIGLSTYEFRNNFDTLTYE 156
                                       **************99998855432222333331344455444.3569**********9999*************** PP

                            ATPase 151 lkklgvTailvsekssseeaaggygveefivdgvivLdlkeiee..elvRtleivkmRgtkhskkehpfeIteegik 225
                                       l+++g  a+ v++   +  ++ +y+++e++  g i+L  ke+ +  +++R++ i kmR t++s + + ++It++gi+
  gi|298675006|ref|YP_003726756.1| 157 LSENGYSALYVMD---ETAHNLTYNLAEYSTFGSIKLMIKENPYteKMERYMYIPKMRDTEISLELMLYDITSGGIT 230
                                       *************...78899*********************9999******************************9 PP

                            ATPase 226 vlee 229
                                        le+
  gi|298675006|ref|YP_003726756.1| 231 LLES 234
                                       9875 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.1   4.3e-09   4.5e-06       9     205 ..      21     224 ..      17     233 .. 0.65

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 4.3e-09
                              GvpD   9 aGktllikGaPGtGktlftlrgldvlrre.sdvlyvstrvddetvseayfsgeaeldktalldllkdpl..eldldv 82 
                                        Gk ++i G  GtGkt+f l++l+   ++ ++   v+t  + e +       +a++ +  l d++++++  ++d+ +
  gi|298675006|ref|YP_003726756.1|  21 KGKGIVITGSSGTGKTIFGLQFLNKACHDgKKCTIVATEETPEDIL-----THADVLNLSLRDFYNNGYleIVDTYR 92 
                                       599********************97655515666777776666654.....34445555555555555432344444 PP

                              GvpD  83 dvPiek..ldlesllefvdeiaaiatkliialdswelvyeyla......erydsPediktvkndlvvlaresgvrlv 151
                                       +  +e+   d+      ++ i       +++ ds  +v++ +         y+  +++ t++ +l    ++    l 
  gi|298675006|ref|YP_003726756.1|  93 KRAFETeeSDIRGAGLTIERIDLEELPNLVSNDSEVVVIDNIGvysiglSTYEFRNNFDTLTYELS---ENGYSALY 166
                                       444433113344444444444444444455555544555554411111168999999999999999...77777888 PP

                              GvpD 152 lvletaan...srleyivdGvvtlnvkeddr.grlrrdlrleklrGvrignrlqPftl 205
                                       ++ eta+n   +  ey   G + l +ke+    ++ r + + k+r   i   l  + +
  gi|298675006|ref|YP_003726756.1| 167 VMDETAHNltyNLAEYSTFGSIKLMIKENPYtEKMERYMYIPKMRDTEISLELMLYDI 224
                                       899999883324469*************97515789*********9988776665555 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   4.9e-08   5.1e-05       2      64 ..       4      66 ..       3     137 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 4.9e-08
                                      BXSSTHHHH.HHCTSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHH CS
                                      xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  2 lstgfkdLD.kltsGlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlv 64
                                      lstg ++LD k+ +G+ kg+ i+i + +++Gkt + l++ ++a+++ k +++++  e + e+++
  gi|298675006|ref|YP_003726756.1|  4 LSTGIDELDgKISGGFPKGKGIVITGSSGTGKTIFGLQFLNKACHDGK-KCTIVATEETPEDIL 66
                                      689******777889*************************99997555.667777766666654 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   2.3e-07   0.00024      32      92 ..       2      61 ..       1      90 [. 0.89

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.3e-07
                                      -EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS-- CS
                              RecA 32 etissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafidaeha 92
                                      e +s+G   ld  +  GG+pkG+ i i G+  +Gkt + l+ + +a + g+ ++ + +e +
  gi|298675006|ref|YP_003726756.1|  2 ERLSTGIDELDGKIS-GGFPKGKGIVITGSSGTGKTIFGLQFLNKACHDGKKCTIVATEET 61
                                      568899999998887.**************************************9999875 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   5.1e-06    0.0054      47      88 ..      22      63 ..      18     101 .. 0.85
   2 ?   -2.4   0.0       3.3   3.5e+03     109     120 ..     126     137 ..     120     142 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.1e-06
                         IstB_IS21 47 kenivllGpsGvGKshlaialgveavraglsvlfvrvedLve 88
                                       ++iv++G sG+GK+ +   +  +a+++g++ + v +e+  e
  gi|298675006|ref|YP_003726756.1| 22 GKGIVITGSSGTGKTIFGLQFLNKACHDGKKCTIVATEETPE 63
                                      5789**************************999888876555 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.3
                         IstB_IS21 109 vdllilDdlgll 120
                                       ++++++D++g+ 
  gi|298675006|ref|YP_003726756.1| 126 SEVVVIDNIGVY 137
                                       6899*****986 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.4   1.2e-05     0.013       3      74 ..      23     134 ..      21     148 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-05
                            AAA_24   3 lkiliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdieswedfldevvel............. 59 
                                       + i+i+G+sg+GKT + +++       g+k  ++ te+   ++  +  +   s+ df++                  
  gi|298675006|ref|YP_003726756.1|  23 KGIVITGSSGTGKTIFGLQFlnkachdGKKCTIVATEETPEDILTHADVLNLSLRDFYNNGYLEivdtyrkrafete 99 
                                       679*****************888888888888888888665555555443334444444333223444455566666 PP

                            AAA_24  60 ....................aaeladyktlviDti 74 
                                                           +   +d +++viD+i
  gi|298675006|ref|YP_003726756.1| 100 esdirgagltieridleelpNLVSNDSEVVVIDNI 134
                                       66666666666666666666666666666666666 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.7   3.1e-05     0.033       2     106 ..      25     136 ..      24     195 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.1e-05
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-------EEEEEET.T...--EEEEEETT---SSEETTEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevreggrrigFkivdlas...geegiLarveakreprvgkyv 75 
                                       ++iTG++G+GKt +  + l++  ++g k + + tee  e+   +  ++ +l+     ++g+L  v++ r+  ++   
  gi|298675006|ref|YP_003726756.1|  25 IVITGSSGTGKTIFGLQFLNKACHDGKKCTIVATEETPEDIL-THADVLNLSLrdfYNNGYLEIVDTYRKRAFETEE 100
                                       79******************999******9999999986543.3334444422111568899999955555554444 PP

                                       E-HHH....HHHHHHHHHHHHH.HHH-EEEE---ST CS
                          NTPase_1  76 vdves....feelalealrkal.seadviviDEiGk 106
                                        d+      +e++ le l + + ++++v+viD iG 
  gi|298675006|ref|YP_003726756.1| 101 SDIRGagltIERIDLEELPNLVsNDSEVVVIDNIGV 136
                                       444444477899999999998878888********5 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0     1e-05     0.011       4      26 ..      25      51 ..      22     132 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1e-05
                           DUF2075  4 vlVtGvaGtGKtvvllnllael....e 26
                                      +++tG +GtGKt+ +l++l+++    +
  gi|298675006|ref|YP_003726756.1| 25 IVITGSSGTGKTIFGLQFLNKAchdgK 51
                                      89******************9833330 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.6e-05     0.016     131     182 ..      24      77 ..      13      93 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.6e-05
                             T2SSE 131 lilvsGgTgsGKttllyallkeinks..derivtvEDpvEiqleganqvqlnak 182
                                        i+++G  g+GKt++    l++  ++  +  iv  E + E  l +a++++l  +
  gi|298675006|ref|YP_003726756.1|  24 GIVITGSSGTGKTIFGLQFLNKACHDgkKCTIVATEETPEDILTHADVLNLSLR 77 
                                       69************988888877766556679999*****99999999988765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   3.8e-05      0.04       8      44 ..      25      66 ..      21     135 .. 0.62
   2 ?   -2.2   0.0       4.3   4.6e+03      86     103 ..     158     175 ..     147     191 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.8e-05
                            AAA_22  8 lvvtGesGtGKTtllrrlleqldeeakaee.....erpevvf 44
                                      +v+tG sGtGKT    ++l++++ + k  +     e pe ++
  gi|298675006|ref|YP_003726756.1| 25 IVITGSSGTGKTIFGLQFLNKACHDGKKCTivateETPEDIL 66
                                      89*******************974433222444443333333 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.3
                            AAA_22  86 lraravielliiDEaqh.l 103
                                       +++ +  +l + DE  h l
  gi|298675006|ref|YP_003726756.1| 158 SENGYS-ALYVMDETAHnL 175
                                       444455.788888866657 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   2.6e-05     0.028      22      81 ..      11      60 ..       1     136 [. 0.71

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.6e-05
                            AAA_25 22 rrwlvkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEd 81
                                      ++  + g  p+g+ ++++G +gtGKt + l+   + +  Gk           k+ +v++E+
  gi|298675006|ref|YP_003726756.1| 11 LDGKISGGFPKGKGIVITGSSGTGKTIFGLQFLNKAChDGK-----------KCTIVATEE 60
                                      555567667**********************9988886666...........444444444 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   7.6e-05      0.08       2      54 ..      25      78 ..      24      97 .. 0.82
   2 ?   -1.6   0.0       1.7   1.8e+03      67      96 ..     165     194 ..     160     215 .. 0.79
   3 ?   -2.4   0.0       2.9     3e+03      59      83 ..     202     226 ..     197     227 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.6e-05
                                      EEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSE.EEEEEEEEETTEEEEEEEEE CS
                               Ras  2 lvlvGdsavGKtslllrfvkdkFkeeyesTigv.dfytkeievdgkevkleiwD 54
                                      +v+ G+s++GKt + l+f ++  ++ ++ Ti + +++ ++i ++   ++l++ D
  gi|298675006|ref|YP_003726756.1| 25 IVITGSSGTGKTIFGLQFLNKACHDGKKCTIVAtEETPEDILTHADVLNLSLRD 78
                                      799***************************943145556666666666666655 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.7
                                       HHHTTESEEEEEEETTBHHHHHTHHHHHHH CS
                               Ras  67 lyyrdaegillvyditsresfenvkkwvee 96 
                                       ly+ d ++  l+y++ + ++f ++k +++e
  gi|298675006|ref|YP_003726756.1| 165 LYVMDETAHNLTYNLAEYSTFGSIKLMIKE 194
                                       567777778889999999999999877776 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.9
                                       GGGHHHHHHHHTTESEEEEEEETTB CS
                               Ras  59 eefkslrelyyrdaegillvydits 83 
                                       e++  + ++  ++ +  l++ydits
  gi|298675006|ref|YP_003726756.1| 202 ERYMYIPKMRDTEISLELMLYDITS 226
                                       6777777777777778889999986 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.2   3.8e-05      0.04      18      57 ..       3      42 ..       1     161 [. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.8e-05
                                      EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHH CS
                             Rad51 18 qlttGskklDelLgGGietgsiteifGefrsGktqlchtl 57
                                      +l+tG  +lD  ++GG++ g+   i G +++Gkt +  ++
  gi|298675006|ref|YP_003726756.1|  3 RLSTGIDELDGKISGGFPKGKGIVITGSSGTGKTIFGLQF 42
                                      699*******************************998764 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.6e-05     0.059      23     157 ..      21     192 ..       2     205 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.6e-05
                                       TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSH...HHHHHHH...HHGGGGTGG............. CS
                            ResIII  23 rdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprk...slleqtl...eefkkflseayke......... 84 
                                       + k ++i    GtGKT+  +++  +  + gk  k+ +++ ++   ++l  +      +++f+++ y e         
  gi|298675006|ref|YP_003726756.1|  21 KGKGIVITGSSGTGKTIFGLQFLNKACHDGK--KCTIVATEEtpeDILTHADvlnLSLRDFYNNGYLEivdtyrkra 95 
                                       5677889999***************999877..67766665534444444445554445555555555322222123 PP

                                       ...GEEEESSS-B--...............-SEEEEEHHHHHHTH..................HHHTTT-S.EEEEE CS
                            ResIII  85 ...igkkvsgdkkka........kekdstnkkilvttiqsldadseee..........eeeseellrdrfd.viiiD 139
                                          ++ +++g + ++         +  s++++++v+    ++++              + + e  ++++   ++++D
  gi|298675006|ref|YP_003726756.1|  96 fetEESDIRGAGLTIeridleelPNLVSNDSEVVVIDNIGVYSIG--LstyefrnnfdTLTYELSENGY-SaLYVMD 169
                                       322333333333333445555554455555555555555555555..0346666655333333333333.26999** PP

                                       T.GGGTTS.....TTTHHHHHT- CS
                            ResIII 140 E.aHrlgak....kswreilekf 157
                                       E aH+l+++    +++ +i+ ++
  gi|298675006|ref|YP_003726756.1| 170 EtAHNLTYNlaeySTFGSIKLMI 192
                                       98899999754443555555544 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00032      0.33       3      67 ..      23      85 ..      21      94 .. 0.75
   2 ?   -0.5   0.0       1.1   1.2e+03      64      75 ..     125     136 ..      89     199 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00032
                            AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekkty 67
                                      k +vitG   +GKT +  q++++   + +++  ++ ++ +++ l++  ++l+l l+ +++ + ++
  gi|298675006|ref|YP_003726756.1| 23 KGIVITGSSGTGKTIFGLQFLNKACHDGKKCTIVATEETPEDILTHA-DVLNLSLRDFYN-NGYL 85
                                      679******************99998889999999888777655544.566666665544.4444 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.1
                            AAA_14  64 kktylflDEiqe 75 
                                       + +++++D i  
  gi|298675006|ref|YP_003726756.1| 125 DSEVVVIDNIGV 136
                                       445555555543 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00019       0.2      24      52 ..      20      53 ..       8     135 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00019
                            AAA_16 24 p..elvllsGesGvGKsslvrellralekd...g 52
                                      p    ++++G sG+GK+    ++l+ ++ d    
  gi|298675006|ref|YP_003726756.1| 20 PkgKGIVITGSSGTGKTIFGLQFLNKACHDgkkC 53
                                      355899************9999999999885431 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.3   0.00034      0.36      17      49 ..      24      56 ..      21      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00034
                     TrwB_AAD_bind 17 hilivGttGsGKtqalekllrairargdraivl 49
                                       i+i+G+ G+GKt    ++l+++ + g+++ ++
  gi|298675006|ref|YP_003726756.1| 24 GIVITGSSGTGKTIFGLQFLNKACHDGKKCTIV 56
                                      689********************9999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 1394.01
//
Query:       gi|298675007|ref|YP_003726757.1|  [L=309]
Description: TM helix repeat-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-26   89.9  17.3    5.5e-12   45.5   1.0    5.4  7  TM_helix  Conserved TM helix


Domain annotation for each model (and alignments):
>> TM_helix  Conserved TM helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   1.8   6.9e-15   1.2e-10       3      49 ..      10      56 ..       8      57 .. 0.96
   2 ?   -0.9   0.0     0.092   1.7e+03      37      47 ..      62      72 ..      60      75 .. 0.79
   3 ?   -0.0   0.4     0.051   9.1e+02       5      23 ..      76      94 ..      73      95 .. 0.86
   4 !   45.5   1.0   3.1e-16   5.5e-12       2      49 ..     102     149 ..     101     150 .. 0.96
   5 ?   -3.5   0.1      0.59   1.1e+04      22      27 ..     174     179 ..     165     182 .. 0.48
   6 !   27.6   1.0   1.2e-10   2.1e-06       4      48 ..     197     241 ..     194     243 .. 0.94
   7 ?   -3.3   0.8      0.53   9.6e+03      17      27 ..     250     260 ..     247     270 .. 0.63

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 6.9e-15
                                      XXSXXHHHHTTHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS-H CS
                          TM_helix  3 lnnllnellsflPnLvgAilILlvGwiiAkfvsrlvtkllaktgidd 49
                                      l n++++ + f+P Lv+ i++L+vG +++k + +l +++l+k+g+d 
  gi|298675007|ref|YP_003726757.1| 10 LYNMVSQMIEFIPLLVAIIVLLIVGRFVGKGLGKLGSRILEKIGLDI 56
                                      78*******************************************95 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.092
                                      HHHHHHHHHTS CS
                          TM_helix 37 lvtkllaktgi 47
                                      +++k++ k++i
  gi|298675007|ref|YP_003726757.1| 62 AIGKMISKSNI 72
                                      68999999998 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.051
                                      SXXHHHHTTHSHHHHHHHH CS
                          TM_helix  5 nllnellsflPnLvgAilI 23
                                      ++ ++++   + Lv A++I
  gi|298675007|ref|YP_003726757.1| 76 GFFDTIIRWFVYLVFAVII 94
                                      678999999999*****99 PP

  == domain 4  score: 45.5 bits;  conditional E-value: 3.1e-16
                                       XXXSXXHHHHTTHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS-H CS
                          TM_helix   2 plnnllnellsflPnLvgAilILlvGwiiAkfvsrlvtkllaktgidd 49 
                                        ++++l+++++f+P +  A++IL+vG+++  f+++lv+k+l++t ++d
  gi|298675007|ref|YP_003726757.1| 102 IVSDFLTDVIAFIPLIASAAIILVVGFLVVDFLADLVKKVLETTELND 149
                                       699*****************************************9987 PP

  == domain 5  score: -3.5 bits;  conditional E-value: 0.59
                                       HHHHHH CS
                          TM_helix  22 lILlvG 27 
                                       lI l G
  gi|298675007|ref|YP_003726757.1| 174 LIKLFG 179
                                       333333 PP

  == domain 6  score: 27.6 bits;  conditional E-value: 1.2e-10
                                       XSXXHHHHTTHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS- CS
                          TM_helix   4 nnllnellsflPnLvgAilILlvGwiiAkfvsrlvtkllaktgid 48 
                                        +l++ ++ +lPnL + ilIL+ G++ + +  + +++ ++ + i+
  gi|298675007|ref|YP_003726757.1| 197 ADLVGRIVEYLPNLAAGILILIGGLLAIGVFEKYLDNFMKGMSIE 241
                                       6899************************************99997 PP

  == domain 7  score: -3.3 bits;  conditional E-value: 0.53
                                       HHHHHHHHHHH CS
                          TM_helix  17 LvgAilILlvG 27 
                                       L g +l+L++ 
  gi|298675007|ref|YP_003726757.1| 250 LRGVLLLLVIF 260
                                       55666666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1023  (0.0570584); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 1847.35
//
Query:       gi|298675008|ref|YP_003726758.1|  [L=70]
Description: hypothetical protein Metev_1076 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.19   11.8   6.0       0.44   10.6   0.1    2.1  2  ETRAMP           Malarial early transcribed membrane protein 
       0.86    9.6   3.6        4.7    7.2   0.3    2.2  2  Gram_pos_anchor  LPXTG cell wall anchor motif
        5.5    6.9  10.1       0.26   11.1   1.4    2.0  2  LapA_dom         Lipopolysaccharide assembly protein A domain


Domain annotation for each model (and alignments):
>> ETRAMP  Malarial early transcribed membrane protein (ETRAMP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   7.4e-05      0.44      51      76 ..       7      32 ..       2      39 .. 0.86
   2 ?    3.8   2.0    0.0098        59      55      78 ..      41      64 ..      35      69 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 7.4e-05
                            ETRAMP 51 kkkKliiistiatalallvasalGlg 76
                                      k +K+ ii ++a+++al +++ +G++
  gi|298675008|ref|YP_003726758.1|  7 KPNKNPIILLVAIGIALSAGLFYGMM 32
                                      589999******************87 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.0098
                            ETRAMP 55 liiistiatalallvasalGlgiy 78
                                      +++i t++++ +l+va++  + +y
  gi|298675008|ref|YP_003726758.1| 41 IMVILTASAVGLLAVAITKLISYY 64
                                      455555555555555444334444 PP

>> Gram_pos_anchor  LPXTG cell wall anchor motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.3   0.00079       4.7      15      35 ..       9      29 ..       8      31 .. 0.90
   2 ?    3.5   0.3     0.012        71      20      30 ..      45      55 ..      35      62 .. 0.51

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00079
                                      XXXXXXXXXXXXXXXXXXXXX CS
                   Gram_pos_anchor 15 ngnifltaaGllallggllLl 35
                                      n+n++ +++++ ++l+++l++
  gi|298675008|ref|YP_003726758.1|  9 NKNPIILLVAIGIALSAGLFY 29
                                      78999*****99**9999997 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.012
                                      XXXXXXXXXXX CS
                   Gram_pos_anchor 20 ltaaGllallg 30
                                      lta ++ +l++
  gi|298675008|ref|YP_003726758.1| 45 LTASAVGLLAV 55
                                      33333333332 PP

>> LapA_dom  Lipopolysaccharide assembly protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   4.1       0.1   6.2e+02      23      42 ..      13      33 ..      11      36 .. 0.52
   2 ?   11.1   1.4   4.4e-05      0.26      11      43 ..      33      64 ..      28      70 .] 0.82

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.1
                          LapA_dom 23 llvafgiGa.llgwllslwsy 42
                                      +++ ++iG+ l ++l+  +++
  gi|298675008|ref|YP_003726758.1| 13 IILLVAIGIaLSAGLFYGMMW 33
                                      455555555344445544455 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 4.4e-05
                          LapA_dom 11 lfaqvelpLsllllvafgiGallgwllslwsyl 43
                                      +fa+ e +L++++l a ++G+l++ ++ l+sy 
  gi|298675008|ref|YP_003726758.1| 33 WFAE-EQNLIMVILTASAVGLLAVAITKLISYY 64
                                      4666.999*****************99998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       871  (0.0485805); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 427.92
//
Query:       gi|298675009|ref|YP_003726759.1|  [L=334]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.6e-23   80.2   0.3    3.3e-22   78.2   0.0    2.3  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    8.2e-05   22.8   0.7    0.00019   21.7   0.7    1.5  1  OrfB_IS605      Probable transposase
  ------ inclusion threshold ------
      0.017   15.1   4.6       0.16   12.0   0.4    3.0  3  HypA            Hydrogenase/urease nickel incorporation, meta
      0.069   13.1   0.2      0.069   13.1   0.2    2.3  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
      0.071   13.2   5.4       0.29   11.3   1.3    2.5  2  UPF0547         Uncharacterised protein family UPF0547
      0.074   12.4   0.2      0.074   12.4   0.2    2.7  2  FAM76           FAM76 protein
      0.078   12.6   1.0       0.16   11.6   1.0    1.5  1  Zn_ribbon_17    Zinc-ribbon, C4HC2 type
       0.13   11.8   2.8          1    8.9   2.9    2.3  1  Mu-like_Com     Mu-like prophage protein Com
       0.64   10.1   3.0        1.5    8.9   3.0    1.8  1  DZR             Double zinc ribbon
        3.2    7.6   7.0        3.4    7.5   0.8    3.0  3  zinc_ribbon_2   zinc-ribbon domain


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1         3   5.4e+03      33      49 ..     214     231 ..     209     235 .. 0.56
   2 !   78.2   0.0   1.9e-25   3.3e-22       1      68 [.     244     309 ..     244     310 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3
                    OrfB_Zn_ribbon  33 eCgsknke.alsgrtfkC 49 
                                       +Cg ++++ +  ++  kC
  gi|298675009|ref|YP_003726759.1| 214 NCGIRMENlKGIRDSAKC 231
                                       566666664444444444 PP

  == domain 2  score: 78.2 bits;  conditional E-value: 1.9e-25
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       f++l+ +leyka+  G+k+e v+p+yTS++Cs+Cg+ + +   g+ fkCp+Cg++ + D nAa+Ni+ 
  gi|298675009|ref|YP_003726759.1| 244 FYQLQFMLEYKARLLGVKIEFVEPEYTSQDCSRCGYLGIR--YGEAFKCPHCGHVDHVDANAAFNIAM 309
                                       899*************************************..************************96 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.7     1e-07   0.00019       3     107 ..     118     214 ..     113     225 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1e-07
                        OrfB_IS605   3 pvevevelpkpkgnkaagiDlGin.nLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrkla 78 
                                        v+v++  ++ ++++ +g+Dl+   ++a++++ ++  + + g++++    ++++ +++lq k k         +k++
  gi|298675009|ref|YP_003726759.1| 118 SVTVPE-REQIEPENYLGVDLNTTgHIAVMSNPKTGKIWKLGKKAQHIHLKYKNDRRKLQVKGKY--------KKVK 185
                                       344443.88999**********87367777777766677889******************98443........5799 PP

                        OrfB_IS605  79 rlhrkrsrrrkhllhklathliktlkevg 107
                                        + ++ sr++++l hk+++++++t  +++
  gi|298675009|ref|YP_003726759.1| 186 QVKDRESRIVRDLNHKISSKIVETAAANN 214
                                       9**********************988775 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.034        62       9      34 ..      46      72 ..      40      77 .. 0.75
   2 ?   -3.1   0.0       4.4   7.9e+03      25      42 ..     113     130 ..     103     132 .. 0.74
   3 ?   12.0   0.4   9.1e-05      0.16      58      96 ..     258     297 ..     205     309 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.034
                                      HHHHHHHHHH.CCTT..EEEEEEEEEE CS
                              HypA  9 sivevveeea.keaaarkvtkvkvevG 34
                                      +i +++ ++  k+++a+kvt+vk+++ 
  gi|298675009|ref|YP_003726759.1| 46 AISNQILKKYaKDKSAKKVTSVKLTIP 72
                                      5666666666377999********986 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.4
                                       EEEEEEEEEETTCT--HH CS
                              HypA  25 kvtkvkvevGelsgvepe 42 
                                       k   v v+v e +++epe
  gi|298675009|ref|YP_003726759.1| 113 KYVYVSVTVPEREQIEPE 130
                                       555688999999999987 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 9.1e-05
                                       TT-EEE.EEEE--EEEETTTS-EEECHHHHHS-TTTSSS- CS
                              HypA  58 egaeLe.ieevpvkvrCreCgkefeleekalrCpkCgsad 96 
                                        g ++e +e +  +  C++Cg+ +    +a++Cp+Cg+ d
  gi|298675009|ref|YP_003726759.1| 258 LGVKIEfVEPEYTSQDCSRCGYLGIRYGEAFKCPHCGHVD 297
                                       4455553455556778*****8887655689******975 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   4.5    0.0026       4.6      13      26 ..     282     295 ..     270     295 .. 0.88
   2 ?   13.1   0.2   3.9e-05     0.069      13      27 ..     282     296 ..     279     306 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0026
                     Zn_Tnp_IS1595  13 lrWpngfvCPhCgs 26 
                                       +r+++ f CPhCg+
  gi|298675009|ref|YP_003726759.1| 282 IRYGEAFKCPHCGH 295
                                       79999999****95 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 3.9e-05
                     Zn_Tnp_IS1595  13 lrWpngfvCPhCgsr 27 
                                       +r+++ f CPhCg+ 
  gi|298675009|ref|YP_003726759.1| 282 IRYGEAFKCPHCGHV 296
                                       799**********86 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2     0.051        91      15      22 ..     272     279 ..     271     280 .. 0.88
   2 ?   11.3   1.3   0.00016      0.29      16      24 ..     289     297 ..     286     298 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.051
                           UPF0547  15 qfCphCGy 22 
                                       q C+ CGy
  gi|298675009|ref|YP_003726759.1| 272 QDCSRCGY 279
                                       78*****9 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00016
                           UPF0547  16 fCphCGyvF 24 
                                       +CphCG+v+
  gi|298675009|ref|YP_003726759.1| 289 KCPHCGHVD 297
                                       8******96 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -7.4  11.1        10   1.8e+04     233     233 ..     159     159 ..       4     236 .. 0.48
   2 ?   12.4   0.2   4.1e-05     0.074      78     103 ..     269     294 ..     262     307 .. 0.88

  Alignments for each domain:
  == domain 1  score: -7.4 bits;  conditional E-value: 10
                             FAM76 233 k 233
                                       k
  gi|298675009|ref|YP_003726759.1| 159 K 159
                                       2 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 4.1e-05
                             FAM76  78 FigskCqRCtnsekkyGkpvtCeqCk 103
                                       ++++ C+RC +   +yG++ +C +C 
  gi|298675009|ref|YP_003726759.1| 269 YTSQDCSRCGYLGIRYGEAFKCPHCG 294
                                       7899*********************6 PP

>> Zn_ribbon_17  Zinc-ribbon, C4HC2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.0   8.9e-05      0.16       6      34 ..     273     303 ..     269     317 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.9e-05
                      Zn_ribbon_17   6 sCayCe.lavk.grvvlcgvCeHvlHasCar 34 
                                        C+ C  l ++ g  + c+ C+Hv H +  +
  gi|298675009|ref|YP_003726759.1| 273 DCSRCGyLGIRyGEAFKCPHCGHVDHVDANA 303
                                       5666642445438899**********98655 PP

>> Mu-like_Com  Mu-like prophage protein Com
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   2.9   0.00056         1      25      40 ..     288     303 ..     272     314 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00056
                       Mu-like_Com  25 iKCPRCGtLnHlkaes 40 
                                        KCP CG + H+ a++
  gi|298675009|ref|YP_003726759.1| 288 FKCPHCGHVDHVDANA 303
                                       48**********9875 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   3.0   0.00086       1.5      12      37 ..     271     296 ..     213     316 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00086
                               DZR  12 arfCseCgtklkavaaedrCpsCgek 37 
                                       ++ Cs+Cg    ++ ++ +Cp+Cg+ 
  gi|298675009|ref|YP_003726759.1| 271 SQDCSRCGYLGIRYGEAFKCPHCGHV 296
                                       34466666665566666666666666 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.069   1.2e+02      16      21 ..     274     279 ..     270     280 .. 0.71
   2 ?    7.5   0.8    0.0019       3.4       1      21 [.     289     295 ..     285     296 .. 0.61
   3 ?   -3.0   0.0       3.9   7.1e+03      19      21 ..     315     317 ..     314     318 .. 0.52

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.069
                     zinc_ribbon_2  16 CpyCGt 21 
                                       C++CG+
  gi|298675009|ref|YP_003726759.1| 274 CSRCGY 279
                                       777775 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0019
                     zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCGt 21 
                                       +Cp+CG              +
  gi|298675009|ref|YP_003726759.1| 289 KCPHCG--------------H 295
                                       455555..............4 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 3.9
                     zinc_ribbon_2  19 CGt 21 
                                       CG+
  gi|298675009|ref|YP_003726759.1| 315 CGA 317
                                       554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1413  (0.0788109); expected 358.6 (0.02)
Passed bias filter:                      674  (0.0375927); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 1996.45
//
Query:       gi|298675010|ref|YP_003726760.1|  [L=341]
Description: hypothetical protein Metev_1078 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.3e-37  126.8   3.2      1e-36  126.3   3.2    1.1  1  DUF21            Cyclin M transmembrane N-terminal domain
  ------ inclusion threshold ------
      0.065   13.5   0.6        2.3    8.5   0.2    2.4  2  Par3_HAL_N_term  N-terminal of Par3 and HAL proteins


Domain annotation for each model (and alignments):
>> DUF21  Cyclin M transmembrane N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.3   3.2   1.1e-40     1e-36       1     169 [.       8     167 ..       8     176 .. 0.96

  Alignments for each domain:
  == domain 1  score: 126.3 bits;  conditional E-value: 1.1e-40
                             DUF21   1 liivlllllsaffsgaEtAlvslsrlrleelaekgkkkakrllkllknperlLstlligntlvnillsalatalfve 77 
                                       ++i+++l  sa+fsg++++l+ lsrl le  ae+++k+a ++l+l+++ ++lL+tll gn+ vn+ll++l++++++ 
  gi|298675010|ref|YP_003726760.1|   8 ILIIFCLSQSAIFSGLTIGLFGLSRLGLEIEAETRHKNAIKILQLRRDANFLLTTLLWGNMSVNVLLTLLTNSIMAG 84 
                                       6899***********************************************************************99 PP

                             DUF21  78 llaegalavviatviv.tllilvfgEilPkslalkyaekialalapplrvlmvllyPlvwllskllnlilesesepa 153
                                         a          +++ t+ i +fgEi+P++++++ya+k+   l+p++++++v++yP++++   ll++ l++e+ ++
  gi|298675010|ref|YP_003726760.1|  85 ATA----------FLFsTFSITLFGEIAPQAYFTRYALKVGGHLVPIVKIYQVIFYPVAKPSAILLDKWLGKERMQF 151
                                       997..........7888************************************************************ PP

                             DUF21 154 vseeelkklveeseee 169
                                       ++ee l+ ++e + e+
  gi|298675010|ref|YP_003726760.1| 152 FKEEYLRIMLEKHIES 167
                                       ***********99987 PP

>> Par3_HAL_N_term  N-terminal of Par3 and HAL proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.011     1e+02      35      65 ..     173     204 ..     158     209 .. 0.76
   2 ?    8.5   0.2   0.00026       2.3      20      69 ..     212     261 ..     202     264 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.011
                   Par3_HAL_N_term  35 kkatekdsdslvkvhsles.kdggiLDpDDll 65 
                                        k+ +  + +++++  ++  ++g+i+DpD ++
  gi|298675010|ref|YP_003726760.1| 173 SKMEGLGALNFLQIDDISIsQEGSIIDPDSVI 204
                                       5666666677899999998799*******876 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00026
                   Par3_HAL_N_term  20 ellvrdLikqavqRykkatekdsdslvkvhsleskdggiLDpDDlladvv 69 
                                       +    d++++  + + +  +k+ +++v ++  +++   +LD D  l+dv+
  gi|298675010|ref|YP_003726760.1| 212 RPVFPDITRDPSDPFLQKLQKSDKKWVIITDSDDEPVMVLDSDAFLRDVI 261
                                       55556777777788899999****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 2017.49
//
Query:       gi|298675011|ref|YP_003726761.1|  [L=804]
Description: phosphoenolpyruvate synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   4.9e-116  387.6   0.0   6.9e-116  387.1   0.0    1.2  1  PPDK_N           Pyruvate phosphate dikinase, PEP/pyruvate bi
    6.4e-55  186.3   0.0      1e-54  185.7   0.0    1.2  1  PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
    2.5e-21   75.1   0.4    6.4e-21   73.8   0.4    1.8  1  PEP-utilizers    PEP-utilising enzyme, mobile domain


Domain annotation for each model (and alignments):
>> PPDK_N  Pyruvate phosphate dikinase, PEP/pyruvate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  387.1   0.0  1.1e-119  6.9e-116       2     316 ..      16     345 ..      15     356 .. 0.97

  Alignments for each domain:
  == domain 1  score: 387.1 bits;  conditional E-value: 1.1e-119
                            PPDK_N   2 elvGGKganLael...lneagipvPpgfaitadafrefleengleekideelkeldvddvdelrkaskeirelilsa 75 
                                       ++vGGK+a+L+e+   l ++gi++P+gfa+tada++++le++g+ +++++ ++ ld++dv++l+k++k++r+lil+a
  gi|298675011|ref|YP_003726761.1|  16 PVVGGKNASLGEMyrkLVSEGINIPNGFAVTADAYWHVLESGGVLDELKKTMDGLDITDVSDLSKRGKKARNLILDA 92 
                                       68***********99877899******************************************************** PP

                            PPDK_N  76 elPeeleeaikeayeelgkkfgdeelpvaVRSSataEDlpkasfaGqqdtyLnvggeeevleaikavfaSlfnerAi 152
                                        +P++l ++ik+ay+ l++++g + ++vaVRSSataEDlp+asfaGqq+tyLn++g +++ +a+ ++faSlf++rAi
  gi|298675011|ref|YP_003726761.1|  93 GIPQDLWDEIKQAYDYLCEQYGPN-TDVAVRSSATAEDLPNASFAGQQETYLNIHGYHSLKDACIRCFASLFTDRAI 168
                                       *********************997.9*************************************************** PP

                            PPDK_N 153 lYrkekgldheevalavvvqkmvnsdlgasGVafsldpetGfkdevlinasyGlGeaVVaGrvtpdefvvekstrk. 228
                                       +Yr+++++dh++v+l+++++kmv+sdl++sGV f+ld+etGf+d+vli+ syGlGe+VV+G+v+pdef+v+k+t k 
  gi|298675011|ref|YP_003726761.1| 169 TYRENNNFDHFKVGLSIGIMKMVRSDLASSGVIFTLDTETGFRDVVLITGSYGLGENVVQGQVNPDEFYVFKPTFKk 245
                                       **************************************************************************999 PP

                            PPDK_N 229 ....ilekkigekeikivydekeeg..tkevevpeeereklaLsdeeveeLaeiakkiekhyg......tpmdiEfa 293
                                           i++k +g+keik+vy + e++  t++v+vp+++r++++++++e+ +La +a kie++y+      +pmdiE+a
  gi|298675011|ref|YP_003726761.1| 246 gyssIISKYLGNKEIKMVYGRGESKtlTRNVNVPDADRKRFCINNDEILTLAGYAIKIEDYYSryykksQPMDIEWA 322
                                       **********************999999************************************************* PP

                            PPDK_N 294 ideeegklyllQaRpetrtsekk 316
                                       +d+e+g+++++QaRpet++s+k 
  gi|298675011|ref|YP_003726761.1| 323 KDGETGQIFIVQARPETVQSQKD 345
                                       *******************9975 PP

>> PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.7   0.0   1.7e-58     1e-54      19     289 ..     490     795 ..     475     800 .. 0.88

  Alignments for each domain:
  == domain 1  score: 185.7 bits;  conditional E-value: 1.7e-58
                                       BCEEEEEESSCHHHHHHHHCTXSSEEEEEHHHHCTTSCC..HHHHHH.............................. CS
                   PEP-utilizers_C  19 kikvlaNidtpedaekalengaeGiGLlRtEflfmaree..lpteee.............................. 63 
                                       ++k+++Ni++pe a ++++ + +G+GL R Ef++ +  +  + +++                               
  gi|298675011|ref|YP_003726761.1| 490 ETKMMMNIGNPEIAFSYARIPNDGVGLARLEFIISSYIKvhPMALIHpekiedenvmkkidgltagyssreeyfvdk 566
                                       6899*****************************9988442244444478899************************9 PP

                                       HHHHHHHHHHHTTTSEEEEEXXXSSCC..GGSGGCHH.HH.XSXGGGSSXTHHHHCCS..HHHHHHHHHHHHHHCCC CS
                   PEP-utilizers_C  64 qaeaykkvleamngrpvvvRtlDiggd..kelpelke.epeevNPmlGfRgirlglse..pelfetqlrAllrasaa 135
                                       + +    +++a+++ pvvvR+ D++++   +l  +++ e +e NPmlGfRg +++++   +e f  + +A++r++ +
  gi|298675011|ref|YP_003726761.1| 567 LSQGVGMLAAAFYPNPVVVRMSDFKSNeyANLIGGEYfEIKENNPMLGFRGASRYTHDnyREGFSLECKAMKRVRDE 643
                                       999999999*****************944456555541568***********999987679**************96 PP

                                       C...EEEEEESSXXSHHHHHHHHHHHHHHHHHHHHCTCTX.XTTXEEEEEEXSHHHHHTHHHHCTTSSEEEEXHHHH CS
                   PEP-utilizers_C 136 g...kleimlPmvasveeleeakkiieevkeelekegvkk.kkkvkvGiMiEvpsaalladklakevdFfSiGtNDL 208
                                       +   +l im+P+ ++++e e+  k +e+        g+k+ +++++v +M E+p  +ll+d++ +  d+fSiG+NDL
  gi|298675011|ref|YP_003726761.1| 644 MgltNLVIMIPFCRTIKEGENVIKELENN-------GLKRgENGLEVYVMCEIPNNILLIDEFSEFFDGFSIGSNDL 713
                                       6667**********999977655555544.......44431679********************************* PP

                                       HHHHHTXXCCCHCHHHHSXTTTCHHCCCHHHHHHHHHHCCXEEEEESCCCC.SCCCHHHHHHCTXSEEEEXGGGHHH CS
                   PEP-utilizers_C 209 tQytlavdRdneevaklydplepavlrlikevikaaeekglkvgiCGelag.dpsavellvglGldelSmsaasvpa 284
                                       tQ+tl++dRd++ ++k +d+ +  v++ +   i+ a++++ + g+CG++++ +p+ +e+lv+ G+d++S++++++++
  gi|298675011|ref|YP_003726761.1| 714 TQLTLGIDRDSDILSKEFDERDSGVKKSLCAAIQGAKRNNRHSGLCGQAPSdYPEFAEFLVKEGIDSISLNPDALMK 790
                                       ***************************************************77*********************998 PP

                                       HHHHH CS
                   PEP-utilizers_C 285 araal 289
                                       +  ++
  gi|298675011|ref|YP_003726761.1| 791 TTLKV 795
                                       87666 PP

>> PEP-utilizers  PEP-utilising enzyme, mobile domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.8   0.4   1.1e-24   6.4e-21       2      73 .]     388     464 ..     387     464 .. 0.93

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 1.1e-24
                                       --S-EEEEES---HHHHTTS-GEEEEEES--TTHHHHHHHHHHTT--EEE--SSHH......HH--TEEEEEETTTT CS
                     PEP-utilizers   2 leegvILvaeetspsdiagldkaaGivterGGmtSHaAivArelgiPaVvgvgeati.....elkegdlitvDgstG 73 
                                       +++g+IL+a+ t+p++ + ++ a +ivt++GG+tSHaAiv+relg+PaVvg+ +        ++++g  itv +++G
  gi|298675011|ref|YP_003726761.1| 388 FKPGEILIADTTTPDWEPVMKTAGAIVTNKGGRTSHAAIVSRELGVPAVVGAVDENGlesteKIQTGNKITVSCAEG 464
                                       6899************************************************9987688887888889999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (804 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.27s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 5005.78
//
Query:       gi|298675012|ref|YP_003726762.1|  [L=253]
Description: beta-lactamase-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-23   82.3   0.0    3.7e-23   82.1   0.0    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
    4.3e-11   43.2   0.2    1.5e-10   41.4   0.2    1.7  1  Lactamase_B    Metallo-beta-lactamase superfamily
    4.9e-05   23.3   0.0    0.00014   21.8   0.0    1.7  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.1   0.0   6.2e-27   3.7e-23       3     168 ..      31     185 ..      29     217 .. 0.84

  Alignments for each domain:
  == domain 1  score: 82.1 bits;  conditional E-value: 6.2e-27
                                       EEES--TTHHHH.HTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC....C--EEEEEEEEHHHHHHCCTTC CS
                     Lactamase_B_2   3 iLiDagpdlrqq.alralqPvelrdelppidaVllthaHyDHlaglltlre....lrpkklplyapkgvlavleanf 74 
                                       iL+D+g +++   ++++       ++  +id V+l+h H DH+a++l+l +    + ++++++y+p+g+ + ++  +
  gi|298675012|ref|YP_003726762.1|  31 ILFDCGSGILNRiFESRY-----NHT--DIDTVVLSHLHLDHVADVLCLIKanwlCDKTNITIYGPEGTNEWMTGLL 100
                                       9*******9988644333.....355..**************************655556**************998 PP

                                       GHHHCHTT.TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHH CS
                     Lactamase_B_2  75 vylaleee.pavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipeei 150
                                       +     +    +n+ e+ +g++f++++++++it+    h+ +          lG+rie+gg +++y+gDt+ ++ +i
  gi|298675012|ref|YP_003726762.1| 101 KIYGYLQGkSDTNIIEVSAGDTFTPDGVNCKITCSKGVHSVPS---------LGYRIESGGSTIVYSGDTEPCK-SI 167
                                       766655555899*************99***************9.........*******************999.88 PP

                                       HHHHCT-SEEEEE-S-SS CS
                     Lactamase_B_2 151 gerlggadllllditaye 168
                                        ++ ++adll++++ +  
  gi|298675012|ref|YP_003726762.1| 168 MDLSQDADLLIHECSFPC 185
                                       88*********9988654 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.2   2.5e-14   1.5e-10      10     152 ..      23     162 ..      15     180 .. 0.79

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 2.5e-14
                                       EEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHH CS
                       Lactamase_B  10 liegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmee 86 
                                       + e +g+ iL+D+G++  +  +       +++  d+d+v+l+HlHlDH++++  l++a + +   +  ++    ++e
  gi|298675012|ref|YP_003726762.1|  23 IAEIEGKPILFDCGSGILNRIFE-----SRYNHTDIDTVVLSHLHLDHVADVLCLIKANWLCDKTNITIYGPEGTNE 94 
                                       34599*****************9.....6***********************9999999999999988888888888 PP

                                       HHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHE...CTTSTSCCEEEEEETTCCEEEECTTT CS
                       Lactamase_B  87 addaasrkglllagvsadkpdvdeeeldgnaggrralyvt...ggpghghghgvveygggkvlftGDal 152
                                        +++  +  + + ++  d +++    +d+++++++  ++t   g +   ++++++e+gg +++++GD+ 
  gi|298675012|ref|YP_003726762.1|  95 WMTGLLKIYG-YLQGKSDTNIIEVSAGDTFTPDGVNCKITcskGVHSVPSLGYRIESGGSTIVYSGDTE 162
                                       8777666655.4455555555555555555555555554333388999999999*************96 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   2.3e-08   0.00014      12     132 ..      24     177 ..      19     181 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.3e-08
                     Lactamase_B_3  12 letagarilvDPfka....nlgyeppaeeaDlvlisqaledHahletlkql.......................... 58 
                                        e++g+ il D +++      + +++  ++D v++s+ + dH +      +                          
  gi|298675012|ref|YP_003726762.1|  24 AEIEGKPILFDCGSGilnrIFESRYNHTDIDTVVLSHLHLDHVADVLC-LIkanwlcdktnitiygpegtnewmtgl 99 
                                       578899999999854442356677888***************976533.2245799998888888888888888888 PP

                     Lactamase_B_3  59 aenvkvleegeslev......ggleiravatshdavggsergenngflleqdgltiyhlGhlahelsseelkelgrv 129
                                        +++ +l++++++++      + +   +v+ +++ ++g +  +  g+++e++g ti++ G++     ++  +  +++
  gi|298675012|ref|YP_003726762.1| 100 LKIYGYLQGKSDTNIievsagDTFTPDGVNCKITCSKGVHSVPSLGYRIESGGSTIVYSGDTEP--CKSIMDLSQDA 174
                                       6666666666554441112112344445555557778889999******************986..44444455556 PP

                     Lactamase_B_3 130 Dvv 132
                                       D++
  gi|298675012|ref|YP_003726762.1| 175 DLL 177
                                       655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1787.63
//
Query:       gi|298675013|ref|YP_003726763.1|  [L=367]
Description: uroporphyrinogen decarboxylase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-78  264.3   0.0    1.8e-78  264.1   0.0    1.0  1  URO-D     Uroporphyrinogen decarboxylase (URO-D)
  ------ inclusion threshold ------
      0.013   14.2   0.1      0.018   13.8   0.1    1.1  1  CAGE1     Cancer-associated gene protein 1 family


Domain annotation for each model (and alignments):
>> URO-D  Uroporphyrinogen decarboxylase (URO-D)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  264.1   0.0     2e-82   1.8e-78       1     345 [.       6     365 ..       6     366 .. 0.93

  Alignments for each domain:
  == domain 1  score: 264.1 bits;  conditional E-value: 2e-82
                                       ----HHHHHHTT---SS--B--TT-SSTTSHHHHHHHTSSSHHHHHH-HHHHHHHHHHHHHHH--S-EE-S--T.TG CS
                             URO-D   1 tknerllralrgekvdrvPvwlmRqaGrylpeyraeragvsflelcknpelaaevtlqpvrrfglDaailfsdi.lv 76 
                                       t++er+++al+ ++vdrvP+ +  +  + ++  + +r+++s+++++++ e +a++++ +++++++D+++ ++++ lv
  gi|298675013|ref|YP_003726763.1|   6 TSKERFINALEMKDVDRVPYGY-LW--FGAGDAVLKRMNTSMKDVYYSSEGIAKAQMLAREMYHHDNVMSPWGClLV 79 
                                       689*******************.55..789999***************************************9989* PP

                                       GGGGGT-EEEEETTTEEEEE--S-.....GGGS----GGG.G..HHHHHHHHHHHHH.--SS-EEEEEE-HHHHHHH CS
                             URO-D  77 eaealGlevefeegegPvvekpvr.taedveklevpddveegrlpyvleaikllkkelggevpligfvgaPftlasy 152
                                       eaealG+ v+++e+++P v+++++ + ++++ +e+++ ++ +r+++v +++++lkkel++ev ++g +++P++la++
  gi|298675013|ref|YP_003726763.1|  80 EAEALGTIVNIKEDRYPTVAEYALkSSKEYDTIEPQNIKKSERIETVSKSVSILKKELNDEVFITGSIMSPLMLATQ 156
                                       ***********************************9997659*********************************** PP

                                       HHCTT-SS-HHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEE..TTGGGS-HHHHHHHTHHHHHHH CS
                             URO-D 153 lveGgskgfekllkllykdpeevhklldkltdvvieylkaqieagAdaiqifD..swagllspedfeefvlpylkri 227
                                       ++     ++ kl++ +++++e+vh ll++ltd +i y+++++e g+d   + +   +a+l+sp++ +ef+l+y+k++
  gi|298675013|ref|YP_003726763.1| 157 VL-----EMVKLCEEMIMEKENVHYLLERLTDGSILYADRMLEEGVDGFLVENgeNTADLFSPQMADEFALKYTKKL 228
                                       **.....********************************************************************** PP

                                       HHHHHH.H--S-EEEEESSHH.HHHHHHTTS--SEEE-...................-TTS-HHHHHH....SS... CS
                             URO-D 228 vdevkaegpkvpvilfikgagaeiledlaelgadvlsl...................dwtvdlkeaar....evg.d 280
                                       +++++++g+  +vi ++++++ +++e+  +++ d++++                   +++ ++    r    ++   
  gi|298675013|ref|YP_003726763.1| 229 YNHIHKNGG--YVISHNCAEH-AFHEKDVSMKPDAMNFafgdvsslgnrygveciknHNHKNIGCGPRycfkDFEkY 302
                                       *******99..*********9.79999999*****999999999999999999988855555533333555555556 PP

                                       ..EEE--B-G.GGGG.S-HHHHHHHHHHHHT.T---SSSEEB-BSS---TTS-HHHHHHHHHHHHT CS
                             URO-D 281 kvalqGnldPialLl.gspeeiekevkeilekgaggkkgyilnlGhgippetppenvkalveavke 345
                                       +++l+Gn++P  +   gs ++ie+ev+++++  a+++kg+il++G++ip++t+ e++ +l++++k+
  gi|298675013|ref|YP_003726763.1| 303 RTCLMGNINP-NVFGnGSLDDIENEVESCIK--AAPNKGFILSTGCEIPLGTKQEKMDTLWNTMKS 365
                                       99********.68888***************..5899*************************9987 PP

>> CAGE1  Cancer-associated gene protein 1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1     2e-06     0.018     118     243 ..      96     222 ..      79     246 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2e-06
                             CAGE1 118 sytekPelq.shvynyakdsnikqdsfkEenpvetsistnkdqlaeecvrq.ssrSpplihcs.getlkftEkslak 191
                                       +++ + +l+ s+ y   + +nik+ +  E   v  s+s+ k +l +e+++  s  Sp ++ ++  e +k+ E+ +++
  gi|298675013|ref|YP_003726763.1|  96 PTVAEYALKsSKEYDTIEPQNIKKSERIET--VSKSVSILKKELNDEVFITgSIMSPLMLATQvLEMVKLCEEMIME 170
                                       555555554156788888999998877775..666888888899999877736678887777668************ PP

                             CAGE1 192 stakesalnlsqpqsflykenvlsdvekpfykensfnllDlranykteeiav 243
                                       +      l+     s+ly + +l++  + f  en  n+ Dl   + ++e a+
  gi|298675013|ref|YP_003726763.1| 171 KENVHYLLERLTDGSILYADRMLEEGVDGFLVENGENTADLFSPQMADEFAL 222
                                       ****************************************998888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2800.55
//
Query:       gi|298675014|ref|YP_003726764.1|  [L=63]
Description: hypothetical protein Metev_1082 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0077   16.1   0.0      0.039   13.9   0.0    1.9  1  EF-hand_6  EF-hand domain
  ------ inclusion threshold ------
      0.019   15.4   0.1      0.025   15.0   0.1    1.2  1  EF-hand_7  EF-hand domain pair


Domain annotation for each model (and alignments):
>> EF-hand_6  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   4.4e-06     0.039       5      28 ..      14      37 ..      12      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.4e-06
                         EF-hand_6  5 aFklfDkdgdGkidaeElrkalrk 28
                                      +++ +D + d  id++El ka+++
  gi|298675014|ref|YP_003726764.1| 14 KYHSYDSNQDYVIDRSELSKAIND 37
                                      6788****************9985 PP

>> EF-hand_7  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   2.8e-06     0.025       7      37 ..      14      43 ..      10      60 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.8e-06
                         EF-hand_7  7 aFkelDtdgdgyldkeellrllrkifqgage 37
                                      ++ ++D+++d  +d++el +++   ++g+  
  gi|298675014|ref|YP_003726764.1| 14 KYHSYDSNQDYVIDRSELSKAINDYYAGK-L 43
                                      6899****************999887764.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 502.32
//
Query:       gi|298675015|ref|YP_003726765.1|  [L=396]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-22   79.3   0.0    5.1e-22   78.3   0.0    1.5  1  OrfB_IS605      Probable transposase
    2.3e-12   46.6   0.0    4.9e-12   45.6   0.0    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0002   20.7   0.1     0.0002   20.7   0.1    1.6  2  Glyco_hydro_97  Glycoside hydrolase 97
  ------ inclusion threshold ------
        0.1   11.8   0.0       0.17   11.1   0.0    1.3  1  EAP30           EAP30/Vps36 family


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.3   0.0   1.1e-25   5.1e-22       2     117 ..     164     278 ..     163     281 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 1.1e-25
                        OrfB_IS605   2 ipvevevelpkpkgnkaagiDlGinnLatvvtedgtw.flykgrrlksdykylakeiaelqsklkksknykkasrkl 77 
                                       i++e + e+p p++++ a+iDlGinn++t+v++ g+  +++kg  +ks ++ ++k+  +l s+++k +   k s+kl
  gi|298675015|ref|YP_003726765.1| 164 IVYEKDLETPDPNEENIASIDLGINNIVTMVNNIGEKpIVIKGGVAKSINQFYNKKSGKLKSIYDKLG--IKNSKKL 238
                                       88999999****************************99*****************************9..9****** PP

                        OrfB_IS605  78 arlhrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       ++l++k + ++++++hk+++++++ + + +++tL++g+  
  gi|298675015|ref|YP_003726765.1| 239 KKLYHKYKMKINDFFHKASKRVVDFCVKHNIGTLVIGYNE 278
                                       *************************************986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.0   1.1e-15   4.9e-12       1      69 []     299     373 ..     299     373 .. 0.96

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 1.1e-15
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke......alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f++l eql+yka++ G kv+e +++yTSk +   g+ +++      ++ +r + +++ g+ +++Dvn+a+Ni+k+
  gi|298675015|ref|YP_003726765.1| 299 FHRLLEQLKYKAEDVGLKVIEQEESYTSKCSFLDGEPVERrtsylgKRIKRGLFRSSNGTIINADVNGAYNIMKK 373
                                       899**************************999******999*****99999999999****************96 PP

>> Glyco_hydro_97  Glycoside hydrolase 97
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.2      0.69   3.1e+03       1      22 [.      76      97 ..      76     115 .. 0.69
   2 !   20.7   0.1   4.5e-08    0.0002      34     106 ..     254     325 ..     215     343 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.69
                    Glyco_hydro_97  1 DtsWikpgkyvwdWwemiagke 22
                                      D +Wi   +++ dW ++ +++ 
  gi|298675015|ref|YP_003726765.1| 76 DKNWISFFQSIKDWEKNPENYY 97
                                      6678888888888877766654 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 4.5e-08
                    Glyco_hydro_97  34 tetvkryiDfAaengleyvlvegwdegWee..kkkkekefdftkpypdfdleelvaYakekgvgvelwlhsetsg 106
                                        +  kr +Df+ ++++ ++++ g++egW++  ++ k ++++ ++++p  +l e ++Y k+ +vg++++ ++e ++
  gi|298675015|ref|YP_003726765.1| 254 HKASKRVVDFCVKHNIGTLVI-GYNEGWKQevDMGK-RNNQKFTQIPFHRLLEQLKY-KAEDVGLKVIEQEESYT 325
                                       56789****************.*******9865554.45555667788888888888.44466788887777654 PP

>> EAP30  EAP30/Vps36 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   3.8e-05      0.17      63     124 ..     223     281 ..     207     346 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.8e-05
                             EAP30  63 ftkmcaslGvdplsskkseslgfl...ellglgdfyyeLavqivevclatraengglisleelya 124
                                        +++ ++lG+     k+s++l++l     ++++df+ + ++++v++c + +     +i   e ++
  gi|298675015|ref|YP_003726765.1| 223 LKSIYDKLGI-----KNSKKLKKLyhkYKMKINDFFHKASKRVVDFCVKHN-IGTLVIGYNEGWK 281
                                       4458899999.....3344555666666777****************9543.2225555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1004  (0.0559987); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.19s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 3040.25
//
Query:       gi|298675016|ref|YP_003726766.1|  [L=71]
Description: hypothetical protein Metev_1084 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      5e-07   29.9   0.1    6.1e-07   29.6   0.1    1.2  1  DUF1059        Protein of unknown function (DUF1059)
  ------ inclusion threshold ------
      0.019   15.3   0.2      0.025   15.0   0.2    1.2  1  PLAC9          Placenta-specific protein 9
      0.034   14.3   0.0      0.039   14.1   0.0    1.1  1  zf-C2H2_aberr  Aberrant zinc-finger
      0.051   13.6   1.9      0.086   12.9   1.5    1.5  2  Spore_Cse60    Sporulation protein Cse60


Domain annotation for each model (and alignments):
>> DUF1059  Protein of unknown function (DUF1059)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.1   1.3e-10   6.1e-07       1      54 [.       1      58 [.       1      60 [. 0.86

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 1.3e-10
                           DUF1059  1 mkefkCgD..vgpdCgfeitaeteeEvlrkvaeHakaaHg..lteippelvekiksaI 54
                                      mk +k     +g++C++++ +++ eEv +k+ +H  ++H+  l ++ ++ ++  k++I
  gi|298675016|ref|YP_003726766.1|  1 MKIIKGNNlgLGIKCDYMAVGNSVEEVEEKIFDHLEKEHKetLDNLDEDDIKDLKYRI 58
                                      5666666655799***************************777788999999999999 PP

>> PLAC9  Placenta-specific protein 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.2   5.5e-06     0.025      16      54 ..      14      48 ..       5      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.5e-06
                             PLAC9 16 aCdrhlavqsrldvieetvektvehleaevkGllgqlee 54
                                      +Cd ++av +    +ee+ ek  +hle e k  l  l+e
  gi|298675016|ref|YP_003726766.1| 14 KCD-YMAVGN---SVEEVEEKIFDHLEKEHKETLDNLDE 48
                                      566.788875...5799999*************999987 PP

>> zf-C2H2_aberr  Aberrant zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   8.7e-06     0.039      35      79 ..      11      52 ..       5      62 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.7e-06
                     zf-C2H2_aberr 35 fslkCpvrkCsesivelentelleehlekehaakllellkeleie 79
                                        +kC ++   +s+ e+   e +++hlekeh  + l+ l e +i+
  gi|298675016|ref|YP_003726766.1| 11 LGIKCDYMAVGNSVEEV--EEKIFDHLEKEHK-ETLDNLDEDDIK 52
                                      569******98888765..578*********9.778888877775 PP

>> Spore_Cse60  Sporulation protein Cse60
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.39   1.7e+03      37      49 ..      19      31 ..       4      32 .. 0.72
   2 ?   12.9   1.5   1.9e-05     0.086      14      41 ..      34      61 ..      23      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.39
                       Spore_Cse60 37 nvaaiieeeeeqi 49
                                       v+ ++ee ee+i
  gi|298675016|ref|YP_003726766.1| 19 AVGNSVEEVEEKI 31
                                      4677778888877 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 1.9e-05
                       Spore_Cse60 14 DLekevneFLkkldddqliDikYnvaai 41
                                       Leke  e L++ld+d + D+kY ++  
  gi|298675016|ref|YP_003726766.1| 34 HLEKEHKETLDNLDEDDIKDLKYRISTL 61
                                      499999******************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1101  (0.0614089); expected 358.6 (0.02)
Passed bias filter:                      780  (0.0435049); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 493.81
//
Query:       gi|298675017|ref|YP_003726767.1|  [L=169]
Description: putative small multi-drug export [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-33  115.2   1.6    3.4e-33  114.8   1.6    1.2  1  Sm_multidrug_ex  Putative small multi-drug export protein


Domain annotation for each model (and alignments):
>> Sm_multidrug_ex  Putative small multi-drug export protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.8   1.6   1.9e-37   3.4e-33       1     121 []      30     152 ..      30     152 .. 0.98

  Alignments for each domain:
  == domain 1  score: 114.8 bits;  conditional E-value: 1.9e-37
                   Sm_multidrug_ex   1 Elrgaiplgi.llgldpllallvsvlgnllpvplillflrkllellkkkkllkklfekleekaek.ksekiekygfl 75 
                                       Elrgaip++i +++++pl++++++v+gn++p++ +l  l+ l++ l+++k+l++l+ekl +k+++ +s k+ekyg++
  gi|298675017|ref|YP_003726767.1|  30 ELRGAIPIAItVYKMNPLVSYCLAVIGNIIPIYPVLASLDVLTRKLRRFKTLDSLIEKLFSKTHRcHSAKFEKYGTI 106
                                       9*********777***************************999999*******************9*********** PP

                   Sm_multidrug_ex  76 GLllFvaiPLpgTGawtGsliasllglkkkkallaillGvliaglI 121
                                       +L+  va+PLp+TG w+G+++a+++g++kk++++ai++G+l++g+I
  gi|298675017|ref|YP_003726767.1| 107 ALVPIVALPLPMTGGWSGCVAAFIFGIQKKHSFPAIVAGILLSGVI 152
                                       ********************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1258.96
//
Query:       gi|298675018|ref|YP_003726768.1|  [L=176]
Description: hypothetical protein Metev_1087 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-07   31.8   0.0    2.1e-07   31.2   0.0    1.3  1  Cytochrome_CBB3  Cytochrome C oxidase, cbb3-type, subunit III
    1.6e-07   32.3   0.0    2.7e-07   31.6   0.0    1.3  1  Cytochrom_C      Cytochrome c
  ------ inclusion threshold ------
      0.044   14.0   0.0      0.072   13.3   0.0    1.4  1  Chordopox_A13L   Chordopoxvirus A13L protein


Domain annotation for each model (and alignments):
>> Cytochrome_CBB3  Cytochrome C oxidase, cbb3-type, subunit III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   3.5e-11   2.1e-07      13      67 .]      89     171 ..      83     171 .. 0.76

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 3.5e-11
                   Cytochrome_CBB3  13 nCasCHgkggag...........pslagrdwep...........dalvdiiknGk...g.....aMpafggqlsdee 59 
                                       +C+ CHg++g+g           p+++ ++++            ++++++i++G+   g      Mp ++  +sd++
  gi|298675018|ref|YP_003726768.1|  89 SCVDCHGADGKGnrpirmnykipPDITYSALTSdehdehpvytdETIKRAIRKGIdpsGnlldsTMPRWH--MSDKD 163
                                       8******8888889999999999666644333223444678888**********85552455558****7..8**** PP

                   Cytochrome_CBB3  60 lwalvaYl 67 
                                       ++++v+Yl
  gi|298675018|ref|YP_003726768.1| 164 VDDVVEYL 171
                                       *******8 PP

>> Cytochrom_C  Cytochrome c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   4.5e-11   2.7e-07      11      91 ..      89     174 ..      76     175 .. 0.75

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 4.5e-11
                                       TGGGTB-SSSBSSS.........--HHHHHHHTTT-HHHHHHHHTTSS--S..SSHHHHHHHGGGGGGG.TT--HHH CS
                       Cytochrom_C  11 nCaaCHgvegggakqgg.....gptlsgaaerasaasigasvanpaavsap..rddfekkkltaemparkerlteqe 80 
                                        C+ CHg++g+g+ +        p+++  a + ++  +  ++++   + a   + d+ ++ l + mp    ++++++
  gi|298675018|ref|YP_003726768.1|  89 SCVDCHGADGKGNRPIRmnykiPPDITYSALTSDEHDEHPVYTDETIKRAIrkGIDPSGNLLDSTMPR--WHMSDKD 163
                                       7************98879****7777777766666666666665555555511455555555556665..5****** PP

                                       HHHHHHHHHTT CS
                       Cytochrom_C  81 iadlaaYLksl 91 
                                       ++d+++YLk+l
  gi|298675018|ref|YP_003726768.1| 164 VDDVVEYLKKL 174
                                       ********987 PP

>> Chordopox_A13L  Chordopoxvirus A13L protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.2e-05     0.072       4      51 ..       5      56 ..       1      67 [. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.2e-05
                    Chordopox_A13L  4 dlllliiCvaivg....livYgiYnrkketqttnpstveeyeeedniKtgfv 51
                                       ++l+ii +++v+    l++Y +Y  + +++   p  + +  +++n+Kt+f 
  gi|298675018|ref|YP_003726768.1|  5 TIILIIILAIVVAgsipLLIYQLYPPNIDENSYGPTGPGRSYQDQNLKTSFE 56
                                      466666666665455559******9988888888888777777888****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1278.19
//
Query:       gi|298675019|ref|YP_003726769.1|  [L=335]
Description: hypothetical protein Metev_1089 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.13   12.7   2.7        5.8    7.4   0.4    3.0  3  Inhibitor_I29  Cathepsin propeptide inhibitor domain (I29)


Domain annotation for each model (and alignments):
>> Inhibitor_I29  Cathepsin propeptide inhibitor domain (I29)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0    0.0043        77      25      36 ..      18      29 ..       2      43 .. 0.85
   2 ?   -2.3   0.0      0.36   6.5e+03      25      38 ..     115     129 ..      99     138 .. 0.65
   3 ?    7.4   0.4   0.00032       5.8      17      35 ..     286     305 ..     278     312 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0043
                     Inhibitor_I29 25 FkeNlrqiqehN 36
                                      F +N++qi+e N
  gi|298675019|ref|YP_003726769.1| 18 FYKNMEQIKEMN 29
                                      99********** PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.36
                     Inhibitor_I29  25 FkeNlrqiqehN.an 38 
                                       F++ ++  ++ N +n
  gi|298675019|ref|YP_003726769.1| 115 FEKECIDTRNINdIN 129
                                       778888888888323 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.00032
                     Inhibitor_I29  17 einerf.enFkeNlrqiqeh 35 
                                       +i++ f e+++eN +qi++ 
  gi|298675019|ref|YP_003726769.1| 286 DIEKHFlEIWQENYNQINNI 305
                                       6788899**********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1297  (0.0723409); expected 358.6 (0.02)
Passed bias filter:                      622  (0.0346924); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2175.45
//
Query:       gi|298675020|ref|YP_003726770.1|  [L=464]
Description: hypothetical protein Metev_1090 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.3e-56  189.0  14.2    8.3e-56  189.0  14.2    2.7  2  DUF92     Integral membrane protein DUF92
  ------ inclusion threshold ------
       0.16   10.8   0.3       0.33    9.8   0.3    1.5  1  DUF5423   Family of unknown function (DUF5423)


Domain annotation for each model (and alignments):
>> DUF92  Integral membrane protein DUF92
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   1.6     0.052   4.7e+02       9      42 ..     132     165 ..     127     183 .. 0.74
   2 !  189.0  14.2   9.3e-60   8.3e-56       2     235 ..     231     449 ..     230     450 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.052
                             DUF92   9 ralrkksLtpsGalaavlvgvlialaplgllffl 42 
                                       +a++k +Lt++ +++ + vg+++ + ++++ +f+
  gi|298675020|ref|YP_003726770.1| 132 IAYKKYTLTLTSIIVLLGVGIITSFLSSSWIIFW 165
                                       5899999999999999999999888877765443 PP

  == domain 2  score: 189.0 bits;  conditional E-value: 9.3e-60
                             DUF92   2 ltlllalralrkksLtpsGalaavlvgvlialaplgllffllllvFfllgslltkvkkkvKa..kleeekegaRdav 76 
                                       ++lll+++a++ +  + s++l+a+l+gvli+   + + +f+lll+Ff+lg ++tk+k+k K+  +++++++g R+++
  gi|298675020|ref|YP_003726770.1| 231 FSLLLGILAYKAGIADISALLSAALLGVLIIGF-GDFFWFILLLMFFILGGIFTKYKYKYKEsiGIAQSEGGIRSYE 306
                                       6799************************99999.9999************************99999999999**** PP

                             DUF92  77 qVlanslvalllally.....lasdlllvgivasyAavaaDTlaSElGkilskskprlittlkkvppGtnGgVsllG 148
                                       +V++ns++al+la++y     + s+l+++++++++A++++DTlaSE+G + +k+kpr+ittlk+++pGt+G++s+lG
  gi|298675020|ref|YP_003726770.1| 307 NVFSNSTAALCLAIAYgiypeY-SSLIIFAYLGAVATATGDTLASEIG-TTAKAKPRIITTLKPTNPGTDGAISVLG 381
                                       ****************876643.99***********************.55566*********************** PP

                             DUF92 149 llasllGalliallavlllllel...lillltlaGllGsllDSlLGatlqasvvdkrtgkvvegeggekvvsGldlL 222
                                        +a++lG+++i+lla+l+ ++++    ++++t+ G++G+++DSl+Gat+q++                      ++L
  gi|298675020|ref|YP_003726770.1| 382 EIAAVLGSICIGLLAYLFGMVDNlllSLVIGTAGGFIGTNIDSLIGATIQEK----------------------HFL 436
                                       **************99999999999878889999******************......................789 PP

                             DUF92 223 dNnaVNllsallt 235
                                       +N++VN+++++++
  gi|298675020|ref|YP_003726770.1| 437 SNSGVNFVATFAG 449
                                       9999999999876 PP

>> DUF5423  Family of unknown function (DUF5423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.3   3.6e-05      0.33      13      62 ..      75     123 ..      68     160 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 3.6e-05
                           DUF5423  13 rhpklryvydialiaisilcivsiilwtqgsglalfaiapalaigalgvt 62 
                                       ++pk+r  y++ +++i+il ++  il        l+ i+ a+ai ++gv+
  gi|298675020|ref|YP_003726770.1|  75 KKPKIRSSYNL-VVSITILLLIGAILDFTSFSYPLYVISGAFAISTFGVS 123
                                       78*******98.578999999999998888999***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       910  (0.0507558); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 3269.56
//
Query:       gi|298675021|ref|YP_003726771.1|  [L=370]
Description: PAS/PAC sensor signal transduction histidine kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-31  108.9   0.7    2.9e-31  108.3   0.2    1.6  2  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    1.3e-21   76.4   0.6    2.9e-21   75.2   0.1    1.9  2  HisKA        His Kinase A (phospho-acceptor) domain
    3.6e-12   46.3   0.0    7.3e-12   45.3   0.0    1.5  1  PAS          PAS fold
    5.5e-11   42.6   0.0    1.1e-10   41.6   0.0    1.6  1  PAS_9        PAS domain
    2.7e-06   27.3   0.0    5.7e-06   26.2   0.0    1.6  1  PAS_8        PAS domain
     0.0023   17.8   0.1     0.0062   16.4   0.1    1.8  1  HATPase_c_5  GHKL domain
     0.0029   17.5   0.1     0.0094   15.8   0.0    2.0  2  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
  ------ inclusion threshold ------
      0.011   16.0   0.0      0.026   14.8   0.0    1.6  1  PAS_3        PAS fold
       0.12   12.6   0.0       0.22   11.8   0.0    1.4  1  PAS_4        PAS fold


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       5.2     1e+04       4      27 ..       6      28 ..       4      76 .. 0.68
   2 !  108.3   0.2   1.5e-34   2.9e-31       2     111 ..     253     362 ..     252     363 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5.2
                                      HHHHHHHHHHHHHHHHHHSTTTEE CS
                         HATPase_c  4 krLrqiisnlvdNavkfatkagei 27
                                      +r+r +i  + d+ + +   +g+i
  gi|298675021|ref|YP_003726771.1|  6 ERFRTVIELAADAIIAH-DFDGDI 28
                                      67777777777777776.444444 PP

  == domain 2  score: 108.3 bits;  conditional E-value: 1.5e-34
                                       HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTSSSHH CS
                         HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsq.ddstkrggggtGlG 77 
                                       d ++Lrqi+ nl+ Na+kf t++g+i+ e++  ++++++sv D+GiGip+++++++fe+f q d+stkr++ gtGlG
  gi|298675021|ref|YP_003726771.1| 253 DNIKLRQILYNLIYNAIKF-TNNGSITTEVDFVDNNYQFSVIDTGIGIPEDKQDEIFESFKQlDSSTKRRHAGTGLG 328
                                       7889***************.99*******998778****************************************** PP

                                       HHHHHHHHHHTTTEEEEEEETTTEEEEEEEEESS CS
                         HATPase_c  78 lsivkklvelmgGeiwvesepgrGttftftlple 111
                                       l++vk+lve +gG i+ves+ g+G++ftft+p++
  gi|298675021|ref|YP_003726771.1| 329 LTLVKRLVEIHGGYIEVESKYGEGSRFTFTIPMQ 362
                                       *******************************986 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.2   0.1   1.5e-24   2.9e-21       1      67 []     138     206 ..     138     206 .. 0.95
   2 ?   -2.5   0.0       2.7   5.4e+03      51      61 ..     217     225 ..     213     229 .. 0.78

  Alignments for each domain:
  == domain 1  score: 75.2 bits;  conditional E-value: 1.5e-24
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                             HisKA   1 slgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsrieag 67 
                                       +++++la+v+HELrtPL++i+g+++++ +   gkl+ ++  yl++i+++++ l++l++dlLdls+ie+g
  gi|298675021|ref|YP_003726771.1| 138 AKSELLANVSHELRTPLTSIIGFSDIMLKGkaGKLNNNQINYLNKIHKSGQNLLDLINDLLDLSKIESG 206
                                       589***********************9666699**********************************97 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.7
                                       HHHHHHHHHHH CS
                             HisKA  51 ldhlvedlLdl 61 
                                       l++++edl  +
  gi|298675021|ref|YP_003726771.1| 217 LTEIIEDL--M 225
                                       78999999..4 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.0   3.7e-15   7.3e-12       1     113 []       6     115 ..       6     115 .. 0.95

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 3.7e-15
                                       HHHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCE CS
                               PAS   1 edlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesragei 77 
                                       e++r+++e ++d+i++ D dg+i+yvN+ a e lG++ +e+l+ +++d  + ++++  ++++++ l+  ++ r++  
  gi|298675021|ref|YP_003726771.1|   6 ERFRTVIELAADAIIAHDFDGDIVYVNELAYENLGYTKSELLSMNIMDIEPYNENYNSRKRYRNKLSIHNSYRIETS 82 
                                       689***********************************************************************999 PP

                                       EEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  78 sfklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                        +++  g+++++ev  + +   ++    +lg++rdi
  gi|298675021|ref|YP_003726771.1|  83 HERK-YGSIYPVEVKITRIDLDSEP--VILGFCRDI 115
                                       9999.**********9988888776..9******98 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.0   5.7e-14   1.1e-10       4     104 .]      19     117 ..      16     117 .. 0.85

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 5.7e-14
                             PAS_9   4 ilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwv 78 
                                       i+  + dg i+y+Ne a + lGy++ e+l  +i d+    ++ ++++r r+ l  +    ++ e+ + rk g+ ++v
  gi|298675021|ref|YP_003726771.1|  19 IIAHDFDGDIVYVNELAYENLGYTKSELLSMNIMDIEpyNENYNSRKRYRNKLSIHN--SYRIETSHERKYGSIYPV 93 
                                       55555799*****************************54444445555555555555..****************** PP

                             PAS_9  79 lltaspvkdddgelvgiivilrDite 104
                                       +++++++  d++ +++  +++rDit+
  gi|298675021|ref|YP_003726771.1|  94 EVKITRIDLDSEPVIL--GFCRDITT 117
                                       *******999999999..******95 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   2.9e-09   5.7e-06       1      45 [.       6      51 ..       6      70 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 2.9e-09
                             PAS_8  1 erlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgell 45
                                      er+r+++e ++d+i+  d +gd iv+vN+ a+e lGy+  +l+ + +
  gi|298675021|ref|YP_003726771.1|  6 ERFRTVIELAADAIIAHDfDGD-IVYVNELAYENLGYTkSELLSMNI 51
                                      7**************999****.*************99777666544 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   3.1e-06    0.0062       1      92 [.     252     350 ..     252     362 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.1e-06
                       HATPase_c_5   1 ikdldlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg.......ek....kkle.sskskke 65 
                                       ++++ l  il nl+ NAi   ++ +     I+ +v   ++++ +s+  +  g       e+    k+l  s+k+++ 
  gi|298675021|ref|YP_003726771.1| 252 MDNIKLRQILYNLIYNAIKFTNNGS-----ITTEVDFVDNNYQFSVIDTGIGipedkqdEIfesfKQLDsSTKRRHA 323
                                       567789999********98877655.....77777777777777777774444444444335445555557799999 PP

                       HATPase_c_5  66 ehGiGlksireivkkykgnlsieaedg 92 
                                         G+Gl+ ++++v+ ++g +++e + g
  gi|298675021|ref|YP_003726771.1| 324 GTGLGLTLVKRLVEIHGGYIEVESKYG 350
                                       9*****************999887644 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.7   3.4e+03      90     120 ..     115     147 ..     109     156 .. 0.62
   2 !   15.8   0.0   4.7e-06    0.0094       5      76 ..     259     328 ..     255     370 .] 0.63

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.7
                       HATPase_c_3  90 vitkkegess..tltldvdkidkenekvleelt 120
                                       ++t+k+ e++   ++l+ +++++ +++ l++++
  gi|298675021|ref|YP_003726771.1| 115 ITTRKQAEENliIAKLEAEATSQAKSELLANVS 147
                                       455555444434777777777777666666554 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 4.7e-06
                       HATPase_c_3   5 kAlaelvdNsld.AdaenvkievnknrgktgeivieDdGkGmseeelknalr.latsskeakrkstslGkkGiG 76 
                                       + l  l+ N++   +  +++ ev++ + ++ ++++ D G G++e++ ++ ++ + + + ++kr +      G+G
  gi|298675021|ref|YP_003726771.1| 259 QILYNLIYNAIKfTNNGSITTEVDFVD-NNYQFSVIDTGIGIPEDKQDEIFEsFKQLDSSTKRRHAG---TGLG 328
                                       66889999***9888899999999986.689*************98887774244444443332222...2222 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.3e-05     0.026       1      83 [.      28     107 ..      28     112 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.3e-05
                             PAS_3   1 iiyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvird 77 
                                       i+yv+e  +e lGy+++ell+   +++d+    +  + r+ + + l+   +y +e    rk G+++ ve +++ i d
  gi|298675021|ref|YP_003726771.1|  28 IVYVNELAYENLGYTKSELLSM--NIMDIEPYNENYNSRKRYRNKLSIHNSYRIETSHERKYGSIYPVEVKITRI-D 101
                                       589*******************..************************************************999.8 PP

                             PAS_3  78 engkpv 83 
                                        +++pv
  gi|298675021|ref|YP_003726771.1| 102 LDSEPV 107
                                       888777 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00011      0.22       5     110 .]      16     120 ..      12     120 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                             PAS_4   5 pdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pgeerh 80 
                                        da+++ d dg ++y+N+ a e +g++  ell +   ++ p     + +  +r  l+ + +++ ++ + +  g+  +
  gi|298675021|ref|YP_003726771.1|  16 ADAIIAHDFDGDIVYVNELAYENLGYTKSELLSMNIMDIEPYNENYNSRKRYRNKLSIHNSYRIETSHERkYGSIYP 92 
                                       5889999***********9999***************99998888888999999999999999999999999***** PP

                             PAS_4  81 yelrllPlrdesGevigvlvisrDiTerrr 110
                                       +e+ ++++ d + e   +l+++rDiT r++
  gi|298675021|ref|YP_003726771.1|  93 VEVKITRI-DLDSE-PVILGFCRDITTRKQ 120
                                       ********.78888.889*********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.49u 0.21s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2823.84
//
Query:       gi|298675022|ref|YP_003726772.1|  [L=141]
Description: hypothetical protein Metev_1092 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-07   32.0  16.1    1.5e-07   31.8  16.1    1.1  1  DUF420         Protein of unknown function (DUF420)


Domain annotation for each model (and alignments):
>> DUF420  Protein of unknown function (DUF420)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8  16.1   8.4e-12   1.5e-07       4     132 .]      11     134 ..       8     134 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 8.4e-12
                            DUF420   4 lnavlnalaavllllglvaikkgkieaHrklmllafvlsalFlvlYllkhalagetkfggpeeegvirpvYlaiLit 80 
                                       l+ ++  l ++++++g+++ kkgki++H k+m +a+v+ +l +v+ ++  +      ++   e  + + ++ + L++
  gi|298675022|ref|YP_003726772.1|  11 LHLIVQFLIILTVIMGVYLFKKGKIRNHCKIMPAALVVQILTVVFIMTPSMSR----YV---EGIIPNLLFNIELWV 80 
                                       6788999999****************************999888777777666....66...334557889999*** PP

                            DUF420  81 HivLavvvvplvlvtlvlalkg...kfekHrkiaritvpiwlyvavtGvvvYllL 132
                                       H ++ +vv+ l  + ++l++++    + +  k+ + t+++w+++++ G+  Yl+L
  gi|298675022|ref|YP_003726772.1|  81 HHIVGLVVILLGGY-IYLGFRKkikFVVNRTKLMKSTFWMWILTFLIGLHLYLML 134
                                       *****999888877.7789988453355889***********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1058  (0.0590105); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1056.19
//
Query:       gi|298675023|ref|YP_003726773.1|  [L=244]
Description: hypothetical protein Metev_1094 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.3e-20   70.3   0.7    4.4e-09   35.8   0.0    2.9  3  HTH_24     Winged helix-turn-helix DNA-binding
    5.2e-07   29.5   0.0      0.046   13.6   0.0    2.3  2  MarR       MarR family
    4.4e-06   26.5   0.0      0.012   15.5   0.0    2.4  2  TrmB       Sugar-specific transcriptional regulator TrmB
    0.00025   20.9   0.0       0.57   10.1   0.0    2.2  2  MarR_2     MarR family
     0.0012   18.9   0.0     0.0023   18.0   0.0    1.5  1  HTH_20     Helix-turn-helix domain
     0.0014   18.5   0.0      0.022   14.6   0.0    2.4  2  HTH_5      Bacterial regulatory protein, arsR family
     0.0031   17.4   0.0       0.46   10.5   0.0    2.2  2  HTH_Crp_2  Crp-like helix-turn-helix domain
     0.0064   16.3   0.0       0.73    9.7   0.0    2.3  2  HTH_IclR   IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.075   13.4   0.0       0.21   12.0   0.0    1.7  1  FaeA       FaeA-like protein


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.0   2.2e-12   4.4e-09       2      48 .]      94     140 ..      93     140 .. 0.95
   2 ?   -0.5   0.1      0.47   9.4e+02       2       9 ..     158     165 ..     157     168 .. 0.89
   3 !   31.6   0.0   4.5e-11     9e-08       3      47 ..     171     215 ..     169     216 .. 0.94

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 2.2e-12
                            HTH_24   2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                       +e++ k+++++ k+p++++++L++ +g+ ++ +++++k Le++  I+
  gi|298675023|ref|YP_003726773.1|  94 NENRNKVYNYIVKHPGCTIKDLSDGVGINRGSTKYHIKTLERNDKIE 140
                                       78899*************************************99885 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.47
                            HTH_24   2 detdrkIL 9  
                                       +e+drkI+
  gi|298675023|ref|YP_003726773.1| 158 NEIDRKII 165
                                       89*****7 PP

  == domain 3  score: 31.6 bits;  conditional E-value: 4.5e-11
                            HTH_24   3 etdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                        t +++L  +   p+i+++eL+e+  lS+stvn+++ +++++ +I
  gi|298675023|ref|YP_003726773.1| 171 TTSKDLLISILNYPGITNTELSEMHYLSKSTVNWYITKFQNDDII 215
                                       578899999**********************************99 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   2.3e-05     0.046      14      48 ..     106     140 ..     103     144 .. 0.91
   2 !   13.5   0.0   2.6e-05     0.052       7      42 ..     175     210 ..     170     218 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.3e-05
                                       HSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR  14 eqgplsvseLakklgvskstvtrvldrLekkGlie 48 
                                        ++++++++L + +g++++++   +++Le+++ ie
  gi|298675023|ref|YP_003726773.1| 106 KHPGCTIKDLSDGVGINRGSTKYHIKTLERNDKIE 140
                                       69***************************998665 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 2.6e-05
                                       HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHH CS
                              MarR   7 viLrilyeqgplsvseLakklgvskstvtrvldrLe 42 
                                       ++L ++ + ++++++eL ++ ++skstv   +++  
  gi|298675023|ref|YP_003726773.1| 175 DLLISILNYPGITNTELSEMHYLSKSTVNWYITKFQ 210
                                       6899************************88777766 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0     6e-06     0.012      11      60 ..      98     147 ..      91     163 .. 0.91
   2 !    8.9   0.0   0.00071       1.4      13      63 ..     176     227 ..     170     231 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6e-06
                                       CCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT CS
                              TrmB  11 akvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpk 60 
                                        kvY +++k+   t+++++  +g+ r +    ++ Le+ + +e++k+ ++
  gi|298675023|ref|YP_003726773.1|  98 NKVYNYIVKHPGCTIKDLSDGVGINRGSTKYHIKTLERNDKIETIKSGKY 147
                                       59*******************************************97654 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00071
                                       HCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.STTTEEE CS
                              TrmB  13 vYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek.grpklYr 63 
                                         + +l++   t +e++e+  +++s+v+ ++ +  + +++  ++ g++k+Y 
  gi|298675023|ref|YP_003726773.1| 176 LLISILNYPGITNTELSEMHYLSKSTVNWYITKFQNDDIIIAKQtGKYKKYY 227
                                       5678999*******************************99887757788996 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00029      0.57      13      54 ..     103     142 ..     100     146 .. 0.88
   2 !    8.6   0.0   0.00084       1.7       9      48 ..     175     212 ..     170     222 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00029
                                       HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  13 aLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54 
                                       ++  +pg  +t+++l +  g+ ++++ +++k L++   +e+ 
  gi|298675023|ref|YP_003726773.1| 103 YIVKHPG--CTIKDLSDGVGINRGSTKYHIKTLERNDKIETI 142
                                       68889**..************************998777765 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00084
                                       HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHT CS
                            MarR_2   9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaa 48 
                                       ++L  + + pg  +t +el +   lsks+v+  + +++  
  gi|298675023|ref|YP_003726773.1| 175 DLLISILNYPG--ITNTELSEMHYLSKSTVNWYITKFQND 212
                                       899********..*****************9888888766 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.2e-06    0.0023       7      60 ..      91     145 ..      85     146 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.2e-06
                                       HS-.HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20   7 Lah.PvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60 
                                       +++ + R +++ ++    g t ++l + +++ + +  yH+++Le+ + +e+ ++g
  gi|298675023|ref|YP_003726773.1|  91 FDNnENRNKVYNYIVKHPGCTIKDLSDGVGINRGSTKYHIKTLERNDKIETIKSG 145
                                       566678888888888999*********************************9998 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.1e-05     0.022       2      41 ..      95     135 ..      94     140 .. 0.89
   2 ?    0.9   0.0      0.21   4.3e+02      18      32 ..     188     202 ..     184     215 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.1e-05
                                       HHHHHHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHHHH CS
                             HTH_5   2 ptRlkILklLaege.lcvcelaeelglsqstvShHLkkLre 41 
                                       ++R k+ ++  + + +++ +l++ +g++++ + +H k L+ 
  gi|298675023|ref|YP_003726773.1|  95 ENRNKVYNYIVKHPgCTIKDLSDGVGINRGSTKYHIKTLER 135
                                       678888888889888************************96 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.21
                                       HHHHHHHHTS-HHHH CS
                             HTH_5  18 vcelaeelglsqstv 32 
                                        +el+e+  ls+stv
  gi|298675023|ref|YP_003726773.1| 188 NTELSEMHYLSKSTV 202
                                       6899***9******9 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.014        27      22      55 ..     110     146 ..      82     159 .. 0.79
   2 !   10.5   0.0   0.00023      0.46      22      52 ..     186     216 ..     168     225 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.014
                                       HHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE..E.TE CS
                         HTH_Crp_2  22 ltqeelAsmlGltretvsrilseLkreglis..r.gr 55 
                                        t ++l++ +G++r ++   ++ L+r   i+  + g+
  gi|298675023|ref|YP_003726773.1| 110 CTIKDLSDGVGINRGSTKYHIKTLERNDKIEtiKsGK 146
                                       6789***********************9999643333 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00023
                                       HHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE CS
                         HTH_Crp_2  22 ltqeelAsmlGltretvsrilseLkreglis 52 
                                       +t++el++m  l+ +tv+  +++++++ +i 
  gi|298675023|ref|YP_003726773.1| 186 ITNTELSEMHYLSKSTVNWYITKFQNDDIII 216
                                       8****************************96 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   0.00037      0.73      15      44 ..     107     135 ..     102     141 .. 0.87
   2 ?    4.2   0.0     0.019        38      18      36 ..     185     203 ..     175     212 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00037
                                       TBSS-BHHHHHHHHTS-HHHHHHHHHHHHH CS
                          HTH_IclR  15 apqeltlselArrtglpkStvhRlLqtLve 44 
                                       +p+  t+++l++  g+++ ++  +++tL++
  gi|298675023|ref|YP_003726773.1| 107 HPG-CTIKDLSDGVGINRGSTKYHIKTLER 135
                                       444.69**********************98 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.019
                                       S-BHHHHHHHHTS-HHHHH CS
                          HTH_IclR  18 eltlselArrtglpkStvh 36 
                                       + t++el++   l+kStv 
  gi|298675023|ref|YP_003726773.1| 185 GITNTELSEMHYLSKSTVN 203
                                       4799*************95 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0001      0.21       3      49 ..      98     143 ..      96     149 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0001
                                       HHHHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE- CS
                              FaeA   3 eeIleylnsikapckTreiAdalglsaYQaRyYLeqLekegkikrsp 49 
                                       +++ +y+ + + +c+ +++ d +g+     +y +++Le+  ki+   
  gi|298675023|ref|YP_003726773.1|  98 NKVYNYIVK-HPGCTIKDLSDGVGINRGSTKYHIKTLERNDKIETIK 143
                                       78899****.*********************************9655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       843  (0.0470188); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1743.96
//
Query:       gi|298675024|ref|YP_003726774.1|  [L=153]
Description: hypothetical protein Metev_1095 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1177.44
//
Query:       gi|298675025|ref|YP_003726775.1|  [L=261]
Description: hypothetical protein Metev_1096 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0067   16.0   1.6      0.011   15.3   1.6    1.3  1  DUF2140         Uncharacterized protein conserved in bacteria
  ------ inclusion threshold ------
      0.022   14.4   0.6      0.028   14.0   0.6    1.2  1  tRNA_anti-like  tRNA_anti-like
      0.077   12.8   1.6       0.13   12.0   1.6    1.3  1  SPC25           Microsomal signal peptidase 25 kDa subunit (S
       0.25   11.0   6.6        1.7    8.4   1.4    2.8  2  DUF2963         Protein of unknown function (DUF2963)


Domain annotation for each model (and alignments):
>> DUF2140  Uncharacterized protein conserved in bacteria (DUF2140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   1.6   2.5e-06     0.011      12      81 ..      11      80 ..       9      90 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.5e-06
                           DUF2140 12 alllllvavvlvrvfapseestekssekekkseaeftitttkkqlnalinkylkkkqkdeklkykveldd 81
                                      +ll+++++v++v+v+++s e++  +s++ +k +++ ++++t ++ +++ +  lk  +++++ +y+v l++
  gi|298675025|ref|YP_003726775.1| 11 GLLVATMLVCMVFVTTVSAENSMAASSEMNKTYTKGNVEITLDKNENMNSAKLKVTSNESTYNYRVNLSK 80
                                      689999999***********99999999999999********999999999****************954 PP

>> tRNA_anti-like  tRNA_anti-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.6   6.3e-06     0.028       6      90 ..       7      91 ..       1     116 [. 0.87

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.3e-06
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX---HHHHHTS-..............EEEHHHHHHHHHH-HHHHHHHH CS
                    tRNA_anti-like  6 kkilviilivilllfvialvaqaaesardkekaekedadatlaeakakpeavaekasqisArdLlaeYdkNevkadkkY 84
                                      ++i +++++ +l+ +v++    a++s+ +++  +k+ +++++++   k e+      +++ ++ + +Y+ N +k+++kY
  gi|298675025|ref|YP_003726775.1|  7 RQIEGLLVATMLVCMVFVTTVSAENSMAASSEMNKTYTKGNVEITLDKNENMNSAKLKVTSNESTYNYRVNLSKSESKY 85
                                      5677888999999999999889999999**************99999999999999*********************** PP

                                      TT-EEE CS
                    tRNA_anti-like 85 kGkiie 90
                                        ki  
  gi|298675025|ref|YP_003726775.1| 86 IAKIYN 91
                                      998865 PP

>> SPC25  Microsomal signal peptidase 25 kDa subunit (SPC25)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.6   2.9e-05      0.13      69     153 ..      16     101 ..      11     104 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.9e-05
                             SPC25  69 lsgiltlystfvekntifvgkrktgskrie.kitissslkklsptytltvsykdksnkgkslkakeleksvgewFde 144
                                        + + ++++t+v +++ + ++++ +++ ++ +++i+ + +++ +  +l+v+ ++++ +++++ +k+ +k ++++ ++
  gi|298675025|ref|YP_003726775.1|  16 TMLVCMVFVTTVSAENSMAASSEMNKTYTKgNVEITLDKNENMNSAKLKVTSNESTYNYRVNLSKSESKYIAKIYNS 92 
                                       5667777888888888888888888776668777777779999*************999999999999999****** PP

                             SPC25 145 dGylveeef 153
                                       dG+l  +++
  gi|298675025|ref|YP_003726775.1|  93 DGKLINKKY 101
                                       ****99887 PP

>> DUF2963  Protein of unknown function (DUF2963)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.4   0.00037       1.7       9      30 ..      84     105 ..      82     106 .. 0.85
   2 ?    4.3   0.3    0.0075        34      31      43 ..     165     177 ..     157     181 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00037
                           DUF2963   9 kki.deYnpqtgkkiKrtnYqed 30 
                                       k+i + Yn++ gk+i +++Y  +
  gi|298675025|ref|YP_003726775.1|  84 KYIaKIYNSD-GKLINKKYYSSN 105
                                       688669****.*********765 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0075
                           DUF2963  31 GktinsIeeyDde 43 
                                        k i++I+ yD  
  gi|298675025|ref|YP_003726775.1| 165 PKGIDYINVYDGK 177
                                       466********43 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1360  (0.0758548); expected 358.6 (0.02)
Passed bias filter:                      636  (0.0354733); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1918.41
//
Query:       gi|298675026|ref|YP_003726776.1|  [L=411]
Description: hypothetical protein Metev_1098 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-14   53.1   1.0    4.9e-14   53.1   1.0    2.2  4  Peptidase_C39_2  Peptidase_C39 like family
  ------ inclusion threshold ------
      0.026   14.9   0.2      0.076   13.4   0.2    1.8  1  Inhibitor_I69    Spi protease inhibitor


Domain annotation for each model (and alignments):
>> Peptidase_C39_2  Peptidase_C39 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1      0.74   6.6e+03      64      84 ..      52      71 ..      15      96 .. 0.51
   2 ?   -1.9   0.1      0.51   4.6e+03      79      91 ..     134     146 ..      71     187 .. 0.60
   3 ?   -2.1   0.0      0.56     5e+03     105     105 ..     160     160 ..     114     216 .. 0.56
   4 !   53.1   1.0   5.5e-18   4.9e-14       3     144 .]     251     389 ..     249     389 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.74
                   Peptidase_C39_2 64 gvynepivklaekyglkvsdt 84
                                      ++y + + ++ ek+ + ++d+
  gi|298675026|ref|YP_003726776.1| 52 SYYVQYVPNVTEKVEK-FQDW 71
                                      2233333333333332.4444 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.51
                   Peptidase_C39_2  79 lkvsdtrgssiee 91 
                                       +k  +++++ +++
  gi|298675026|ref|YP_003726776.1| 134 NKTESLVKEHVNK 146
                                       2222222222222 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.56
                   Peptidase_C39_2 105 s 105
                                        
  gi|298675026|ref|YP_003726776.1| 160 G 160
                                       1 PP

  == domain 4  score: 53.1 bits;  conditional E-value: 5.5e-18
                   Peptidase_C39_2   3 vplynQldelpngCeptslamvlsyl...gkk......vtqnelakelktnssgdpntgfvgnitdksglgvynepi 70 
                                       vp y +     +gC+pt+ amvl y+   g+          +ela+ ++t ++ + +t+   +i++  +  + n+ +
  gi|298675026|ref|YP_003726776.1| 251 VPAYEW----YKGCSPTASAMVLGYWknnGYPgfpeeiTLIEELANAMGTSNWPEGTTWP-IEIDNGIEEVCDNHGY 322
                                       888888....99**************9886634534433356677777777765666654.4666667777777777 PP

                   Peptidase_C39_2  71 vklaekyglkvsdtrgssieevkkeidagkPvvvsvttfkplndgeikftssgHlvvitGYdekg.krvyvnDPa 144
                                       +++ ++  +        s++ev+++++++ P+v+++   + ++++  +  +++H+v+++GY++++ ++++++D++
  gi|298675026|ref|YP_003726776.1| 323 NNFDANNDY------YVSWNEVINNVNSDEPFVINML--SGGTGSGHSQPYGEHSVTCVGYSDNTeDYIFIHDTW 389
                                       777666666......78*******************4..55577889****************88799*****87 PP

>> Inhibitor_I69  Spi protease inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   8.5e-06     0.076       3      77 ..      41     122 ..      39     142 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.5e-06
                     Inhibitor_I69   3 pvseeeAlkiAekffaqngaktaasaasqssl....sseattsasasepayYVfn...ygdgkGFvIVsaddrappi 72 
                                       ++s e+A+ +A+ +++   + t++  + q       ++++   + + e++ Y fn   +g+ +G++++sa+++ +p+
  gi|298675026|ref|YP_003726776.1|  41 NISLEKARLVASYYVQYVPNVTEKVEKFQDWNdatvKKSEIFYNLKGEKSAYAFNvtvNGEYSGYILISATKDNYPV 117
                                       799999*****9999988888776555544337788555555555555555555511166778************** PP

                     Inhibitor_I69  73 LaYsd 77 
                                       L +s+
  gi|298675026|ref|YP_003726776.1| 118 LEFSK 122
                                       97775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1366  (0.0761894); expected 358.6 (0.02)
Passed bias filter:                      672  (0.0374812); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.52
# Mc/sec: 2400.51
//
Query:       gi|298675027|ref|YP_003726777.1|  [L=400]
Description: carbohydrate-binding and sugar hydrolysis protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-45  155.0 122.7    1.4e-19   70.3  35.2    3.1  3  NosD             Periplasmic copper-binding protein (NosD)
    1.1e-36  126.1 135.7    9.1e-18   64.6  39.2    3.5  4  Beta_helix       Right handed beta helix region


Domain annotation for each model (and alignments):
>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.3  35.2   1.6e-23   1.4e-19       4     173 ..      46     228 ..      43     229 .. 0.81
   2 !   64.6  29.1   8.7e-22   7.8e-18      59     172 ..     205     315 ..     202     316 .. 0.96
   3 !   47.7  42.4   1.3e-16   1.2e-12      39     180 ..     229     368 ..     228     379 .. 0.86

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 1.6e-23
                              NosD   4 aisgdevlvsa..rgngiqlens............egseisnneisnsrdgilldnssnntitgntienl....ryG 62 
                                       a sgd+++v+   +     +en+            ++ e +  + +++++++   ns++++i+g +i       ++G
  gi|298675027|ref|YP_003726777.1|  46 ANSGDNIVVYPgkY-----IENIvidkevsiesksKNPENTVIQSKTPEKNVIQVNSNKVNISGFKIMGVkntnQSG 117
                                       56677777774442.....33332222244544332222244555566677788899999999996655555679** PP

                              NosD  63 ihlensesntiedntlssnesGialmsssnntlenNtisnnenyGillsdssnntisnNtis.nnnkGiflensssn 138
                                       ++l+  e+++i+++++s+n +G+++ +s+ ntl nNt+++n+n+Gi+l++s+nn + nN +  n+ +Gifl++s +n
  gi|298675027|ref|YP_003726777.1| 118 VYLDRVEKCNISNSIFSKNFNGVSFFKSEWNTLVNNTVKSNKNHGIYLKKSKNNRVINNIVGsNSRYGIFLQRSINN 194
                                       *************************************************************76************** PP

                              NosD 139 titgNriesnqkiGilllsssegntiynNyFinns 173
                                        i  N+i+++ + Gi+ +++s++n + +N F++n+
  gi|298675027|ref|YP_003726777.1| 195 NIITNHIQNHSNNGIM-VDHSNNNFLGDNKFFDNE 228
                                       ****************.***************996 PP

  == domain 2  score: 64.6 bits;  conditional E-value: 8.7e-22
                              NosD  59 lryGihlensesntiedntlssnesGialmsssnntlenNtisnnenyGillsdssnntisnNtisnnnkGiflens 135
                                       +++Gi+++ s++n + dn++++ne+Gi+++ss+ n l+ N+isnn++ Gi    s++n++ nN i++n+ Gifl++ 
  gi|298675027|ref|YP_003726777.1| 205 SNNGIMVDHSNNNFLGDNKFFDNEYGIYIHSSQSNKLKVNNISNNKI-GIQGGLSNKNELINNSILKNKVGIFLYKC 280
                                       579********************************************.***************************** PP

                              NosD 136 ssntitgNriesnqkiGilllsssegntiynNyFinn 172
                                       ++n i  N i++n   Gil l++s +n+i nN++ n+
  gi|298675027|ref|YP_003726777.1| 281 NGNDIIANIINENIHKGIL-LQYSVDNKISNNTL-NS 315
                                       *******************.**************.53 PP

  == domain 3  score: 47.7 bits;  conditional E-value: 1.3e-16
                              NosD  39 dgilldnssnntitgntienlryGihlensesntiedntlssnesGialmsssnntlenNtisnnenyGillsdssn 115
                                       +gi++ +s++n+++ n i+n++ Gi    s++n + +n + +n+ Gi+l++ ++n +  N+i++n  +Gill++s +
  gi|298675027|ref|YP_003726777.1| 229 YGIYIHSSQSNKLKVNNISNNKIGIQGGLSNKNELINNSILKNKVGIFLYKCNGNDIIANIINENIHKGILLQYSVD 305
                                       68999999999999999999999999999999999999999999999999999996669999999999999999999 PP

                              NosD 116 ntisnNtisnnnkGiflens.ssntitgNriesnqkiGilllsssegntiynNyFinnsenvkydg 180
                                       n+isnNt  +n+ Gi +e+  s+nt+  N++++n    i   ++++ n+i nNy+ nns +  +++
  gi|298675027|ref|YP_003726777.1| 306 NKISNNTLNSNGLGIIMEDFsSNNTVHYNSLSKN-RANIR--ANYSINQIKNNYMNNNSSQNLNSD 368
                                       9999999999999999999669999999999999.89998..777799999999966665554444 PP

>> Beta_helix  Right handed beta helix region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   1.7      0.19   1.7e+03     100     129 ..      34      65 ..      17      86 .. 0.62
   2 !   64.6  39.2     1e-21   9.1e-18       3     157 ..      93     245 ..      91     246 .. 0.94
   3 !   51.0  38.1   1.5e-17   1.4e-13      12     144 ..     195     321 ..     193     324 .. 0.95
   4 !   38.1  42.4   1.5e-13   1.3e-09       1     158 []     229     379 ..     229     379 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.19
                                       -S--EEES-EEESTT--SEE---TT..---EE CS
                        Beta_helix 100 ssnntienNiidnnagsGividdss..snvtv 129
                                       ++ ++i++ + d+n+g+ iv+++++   n+++
  gi|298675027|ref|YP_003726777.1|  34 NNYTSIKKAVNDANSGDNIVVYPGKyiENIVI 65 
                                       44466777777777788888888884333333 PP

  == domain 2  score: 64.6 bits;  conditional E-value: 1e-21
                                       EEE-SS-E.EEESEEEES-...SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT- CS
                        Beta_helix   3 isingssnvtiknntisns...ggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfg 76 
                                       i +n++++ +i++++i+++   +++G+yl+  +++ i+n+ +++ +++G++  +s+ nt+ nnt+  n++ gi+l++
  gi|298675027|ref|YP_003726777.1|  93 IQVNSNKV-NISGFKIMGVkntNQSGVYLDRVEKCNISNSIFSK-NFNGVSFFKSEWNTLVNNTVKSNKNHGIYLKK 167
                                       45555555.*****************************999999.******************************** PP

                                       -S--EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EE CS
                        Beta_helix  77 asnnlienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtv 153
                                       ++nn + nn +  n+++Gi+l+ s nn i  N+i n +++Gi +d s+ n+   +N++++n  +Gi++ +s+s +++
  gi|298675027|ref|YP_003726777.1| 168 SKNNRVINNIVGSNSRYGIFLQRSINNNIITNHIQNHSNNGIMVDHSN-NNFLGDNKFFDNE-YGIYIHSSQS-NKL 241
                                       ************************************************.8889********8.*******999.777 PP

                                       ES-E CS
                        Beta_helix 154 rnNt 157
                                       + N+
  gi|298675027|ref|YP_003726777.1| 242 KVNN 245
                                       7666 PP

  == domain 3  score: 51.0 bits;  conditional E-value: 1.5e-17
                                       EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEE CS
                        Beta_helix  12 tiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnlienneit 88 
                                       +i  n+i+n +++Gi++++s+n+ + +n++ + +++Giyi++s+ n+++ n+is+n+  gi    +++n + nn i 
  gi|298675027|ref|YP_003726777.1| 195 NIITNHIQNHSNNGIMVDHSNNNFLGDNKFFD-NEYGIYIHSSQSNKLKVNNISNNK-IGIQGGLSNKNELINNSIL 269
                                       6889999999**********************.************************.******************* PP

                                       S-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE- CS
                        Beta_helix  89 dnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiav 144
                                       +n+  Gi+l+ ++ n+i  Nii++n + Gi +++s  +++++nNt+++n+  Gi +
  gi|298675027|ref|YP_003726777.1| 270 KNKV-GIFLYKCNGNDIIANIINENIHKGILLQYSV-DNKISNNTLNSNG-LGI-I 321
                                       **87.*******************************.************7.777.4 PP

  == domain 4  score: 38.1 bits;  conditional E-value: 1.5e-13
                                       -SEEE-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT-- CS
                        Beta_helix   1 sgisingssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfga 77 
                                       +gi+i +s++ ++k n+isn ++ Gi+ + s+++ + nn i + +  Gi ++++++n i  n i++n + gi l+++
  gi|298675027|ref|YP_003726777.1| 229 YGIYIHSSQSNKLKVNNISN-NKIGIQGGLSNKNELINNSILK-NKVGIFLYKCNGNDIIANIINENIHKGILLQYS 303
                                       68999999999999999999.5999999999999999999999.999999999999999999999999999999999 PP

                                       S--EEES-EEES-SS-SEE-TT.-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EE CS
                        Beta_helix  78 snnlienneitdnggsGiylny.ssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtv 153
                                         n i+nn+ + ng  Gi +++ ssnnt+++N ++ n+ + i  ++s   + ++nN ++nn+  + +++++s+++ +
  gi|298675027|ref|YP_003726777.1| 304 VDNKISNNTLNSNGL-GIIMEDfSSNNTVHYNSLSKNR-ANIRANYSI--NQIKNNYMNNNS--SQNLNSDSHEIPF 374
                                       999999999999988.9999977999999999999999.888888888..666999999988..5556777777888 PP

                                       ES-E. CS
                        Beta_helix 154 rnNti 158
                                        n t+
  gi|298675027|ref|YP_003726777.1| 375 INSTF 379
                                       87775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1271  (0.0708907); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.34s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 2365.34
//
Query:       gi|298675028|ref|YP_003726778.1|  [L=472]
Description: ammonium transporter [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   8.3e-125  416.6  38.1     1e-124  416.3  38.1    1.1  1  Ammonium_transp  Ammonium Transporter Family
  ------ inclusion threshold ------
        1.3    8.4  28.4       0.12   11.8   3.3    3.1  3  DUF373           Domain of unknown function (DUF373)


Domain annotation for each model (and alignments):
>> Ammonium_transp  Ammonium Transporter Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  416.3  38.1  1.1e-128    1e-124       1     399 []      51     463 ..      51     463 .. 0.96

  Alignments for each domain:
  == domain 1  score: 416.3 bits;  conditional E-value: 1.1e-128
                                       HHHHHHHHHHHHHHHHHHHHHHHHSSGGGHHHHHHHHHHHHHHHHHHHHHTHHHHHHSSCBSSSSSCE-TTTTSCCG CS
                   Ammonium_transp   1 aflllsaalvifmqagfalleaglvrsknvlnilvknlldlavvvllyvlfGyslafgkskgvsgfignlglsaagv 77 
                                       ++l+ls a+v++m+agf l+eagl+rskn+ nil+kn++ + ++vl+y+++G+++++g++    g++g+ +++++g+
  gi|298675028|ref|YP_003726778.1|  51 VWLILSGAIVFLMHAGFSLVEAGLTRSKNTANILMKNFMTISLGVLVYWAVGWAIMYGTD--AAGLVGTSQFFLSGA 125
                                       7**********************************************************9..**********99999 PP

                                       CCTTCCHHHHHHHHHHHHHHHHHHHHHHCTTTB-HHHHHHHHHHHHHHTHHHHHHHHHS.SSHHHHTT--....... CS
                   Ammonium_transp  78 qdetlldglfflfqlafaataitivsgavaerikfsayllfsallgtlvyppvahwvwgeggwlaklgvl....... 147
                                       ++ +l++   + fq++faata+tivsgavaer++f+ayl++++l++ l+yp+++hwvw+   ++   g+        
  gi|298675028|ref|YP_003726778.1| 126 DN-SLWNS--WWFQMVFAATAATIVSGAVAERMEFKAYLIYAILMVALIYPVYGHWVWSGSELALLTGADsfivnai 199
                                       88.67676..99***********************************************744444444446677777 PP

                                       .....-SSSTTTTHHHHHHHHHHHHHHHS-STTTTG.TTTSS--GSBHHHHHHHHHHHHHHHHHHHHGGGSSSSHHH CS
                   Ammonium_transp 148 ....iDfAgstvVHlvggvagLaaalvlgkregrfe.gkeeaikghnlpfavlGtllLwfgWfgFNaGsaltankra 219
                                           +DfAgs+vVH+vgg+a+Laa+++lg+r+g+f  g++ ai+ghnl +a+lGtl+L+fgW gFN+Gs+l a++++
  gi|298675028|ref|YP_003726778.1| 200 gtslHDFAGSSVVHAVGGYAALAAVIILGPRIGKFRdGEPVAIPGHNLAYAFLGTLILAFGWIGFNGGSTLDATDAY 276
                                       7789************************************************************************* PP

                                       HH.HHHHHHHHHHHHHHHHHHHHHHHCSS-BHHHHHHHHHHHHHHHTTTTTTS-HHHHHHHHHHHHHHHHHHHHHHH CS
                   Ammonium_transp 220 raraavtTllAaaagaltallisrlkegkinvlglanGilAGlVAiTaacavvepwgAliiGlvAgvlsvlgvkklk 296
                                        ++++v+T +Aaaaga+ a+l++++k+gk++   +anG+lAGlVAiTa c+ ve w+AliiG+++g+++++gv + +
  gi|298675028|ref|YP_003726778.1| 277 MNLVIVNTFIAAAAGAVSAMLVTWVKTGKPDPSLTANGLLAGLVAITAPCGSVENWAALIIGTIGGIIVYAGVMFNE 353
                                       *************************************************************************9899 PP

                                       HHHTC-CTTHHHHHHHHHHHHHHHHHHHHTSHHHC.......SSHSSTTGGGT-CHHHHHHHHHHHHHHHHHHHHHH CS
                   Ammonium_transp 297 eklkidDsldvvavHgvgGiwGllavgifaaekvv.......askisggllsgegkqlvvqligilvilayafvvtl 366
                                       + lk+dD++++++vHg +G wGll vgif+    +       ++   +gl++g+ +q+ +ql+g++v +++af+ ++
  gi|298675028|ref|YP_003726778.1| 354 NVLKVDDPVGAISVHGYSGSWGLLSVGIFSVGLGNgiledavYAASVPGLIYGGVSQFLIQLVGVIVNIIWAFGASF 430
                                       99****************************99888999999999999****************************** PP

                                       HHHHHHHHHTTSB--HHHHHHSHHHHHHSSSSB CS
                   Ammonium_transp 367 illlllklllgLrvseeeeevglDvaehgetay 399
                                       +++++++ ++g rvsee+e +glD+ ehg +ay
  gi|298675028|ref|YP_003726778.1| 431 FIFKIIDVIIGTRVSEEDEITGLDTVEHGIEAY 463
                                       *****************************9988 PP

>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1  10.8    0.0015        13     214     320 ..       6     115 ..       2     148 .. 0.63
   2 ?   -0.2   1.6     0.059   5.3e+02     207     266 ..     143     215 ..     135     292 .. 0.51
   3 ?   11.8   3.3   1.3e-05      0.12     160     289 ..     312     443 ..     308     454 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0015
                            DUF373 214 leegritfvtyvvallllligiisgyislesvssasvssglltlilafiygavewlalailtaslgkiideylkree 290
                                       ++++rit+v+++  l+l+l+ + ++ ++ +s++++++s + l+ +l+f+  ++   a+++l+ +  +++++ l +++
  gi|298675028|ref|YP_003726778.1|   6 IKSKRITLVIAT--LILVLLTLTNSAYA-TSIEENAASITSLETTLTFVWLILS-GAIVFLMHAGFSLVEAGL-TRS 77 
                                       555666655443..34444444444443.5677766677777777776654433.345555566667777777.557 PP

                            DUF373 291 kdiarllllpflvlaiglvlygasaylls........l 320
                                       k++a++l+  f+++++g+++y a+++ +         +
  gi|298675028|ref|YP_003726778.1|  78 KNTANILMKNFMTISLGVLVYWAVGWAIMygtdaaglV 115
                                       99999***************888887744455555550 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.059
                            DUF373 207 leklkesleegritfvtyvvallllligiisgyislesvssasvssglltlilafiyg................av 266
                                       ++++ +   ++r+ f +y++ ++l++  +i+ ++  + +s   ++  llt + +fi +                av
  gi|298675028|ref|YP_003726778.1| 143 AATIVSGAVAERMEFKAYLIYAILMVA-LIYPVYGHWVWSG--SELALLTGADSFIVNaigtslhdfagssvvhAV 215
                                       444455555566666666665555433.3333333343433..223444444444444333333334444433344 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 1.3e-05
                            DUF373 160 plGlllliyalllllglpelalaiillllGlylllrGfgldelleelleklkesleegritfvtyvvallllligii 236
                                         Gll  ++a+++  g++e  +a+i++ +G+++++ G+ ++e++ ++ + +   ++    +    ++++ ++ +g+ 
  gi|298675028|ref|YP_003726778.1| 312 ANGLLAGLVAITAPCGSVENWAALIIGTIGGIIVYAGVMFNENVLKVDDPVGA-ISVHGYSGSWGLLSVGIFSVGLG 387
                                       55777778888888999999999*******************88755555544.44444566677899999999999 PP

                            DUF373 237 sgyislesvss....asvssglltlilafiygavewlalailtaslgkiideylkre 289
                                       +g+ + ++v++    + ++ g+ + +++++  +v+++++ +   ++ kiid ++ ++
  gi|298675028|ref|YP_003726778.1| 388 NGILE-DAVYAasvpGLIYGGVSQFLIQLVGVIVNIIWAFGASFFIFKIIDVIIGTR 443
                                       99988.55555456666666777777777777999999999999*******999666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       898  (0.0500865); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 3146.86
//
Query:       gi|298675029|ref|YP_003726779.1|  [L=114]
Description: nitrogen regulatory protein P-II [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-39  132.9   2.1      6e-39  132.8   2.1    1.0  1  P-II      Nitrogen regulatory protein P-II


Domain annotation for each model (and alignments):
>> P-II  Nitrogen regulatory protein P-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.8   2.1   3.3e-43     6e-39       1     102 []       6     107 ..       6     107 .. 0.99

  Alignments for each domain:
  == domain 1  score: 132.8 bits;  conditional E-value: 3.3e-43
                                       EEEEEEGGGHHHHHHHHHHTTGGCEEEEEEEEEESTCCEEEECTTEEEEEEEEEEEEEEEEEEGGGHHHHHHHHHHH CS
                              P-II   1 ieaiirpekleevkeaLekagvkgltvtevkGrGkqkghtelyrgaeyevellpkvkleivvsdedvekvveaiika 77 
                                       ieai+rp+k+++vk++Le+ag+++lt  +vkGrGkqkg ++  rg++y v++lpk k+e+vvsd+dv++v+++i+k+
  gi|298675029|ref|YP_003726779.1|   6 IEAIVRPTKVDHVKTELEDAGFESLTQYDVKGRGKQKGVVQQWRGRKYCVDMLPKSKIEMVVSDDDVNTVIDIIQKT 82 
                                       89*************************************************************************** PP

                                       H-SSSTTSEEEEEEEESEEEETTTT CS
                              P-II  78 aktgeiGDGkiFvlpveevirirtg 102
                                       a tgeiGDGkiFv+pve+v+rirt+
  gi|298675029|ref|YP_003726779.1|  83 ASTGEIGDGKIFVSPVESVVRIRTN 107
                                       ***********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 897.94
//
Query:       gi|298675030|ref|YP_003726780.1|  [L=135]
Description: blue (type 1) copper domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.8e-13   49.4   0.1    4.7e-13   49.1   0.1    1.1  1  Cupredoxin_1  Cupredoxin-like domain
    6.8e-11   42.5   2.3    3.3e-09   37.1   2.3    2.1  1  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
     0.0077   16.7   1.4       0.01   16.3   0.6    1.5  2  DUF2190       Uncharacterized conserved protein (DUF2190)
  ------ inclusion threshold ------
       0.17   10.6   0.4       0.22   10.3   0.4    1.1  1  ATHILA        ATHILA ORF-1 family


Domain annotation for each model (and alignments):
>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.1   1.1e-16   4.7e-13      16     104 .]      24     117 ..       8     117 .. 0.84

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 1.1e-16
                      Cupredoxin_1  16 a..........aaaektveitvkdggfePskievkagekvklkiknkdktpeefesedlgeekvlapgktttitiap 82 
                                       +          + a +t ++ ++d +f+P++i++  g   +++++n+d+t ++++s++++   +l++g+t+t t+  
  gi|298675030|ref|YP_003726780.1|  24 QqnggtedngeDGAVETTNVIMEDIQFKPATIQISVGD--TVTWTNEDSTEHTVTSDNFDS-GNLEQGETFTHTF-- 95 
                                       3356655555456677899*******************..89******************9.9************.. PP

                      Cupredoxin_1  83 lkpGeYeftcdmhmdakGkliV 104
                                        ++G Y++ c +h+ + G++iV
  gi|298675030|ref|YP_003726780.1|  96 NEAGVYDYQCTIHPSMTGTVIV 117
                                       9********************9 PP

>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   2.3   7.4e-13   3.3e-09       7      98 ..      43     117 ..      37     118 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 7.4e-13
                                       ETTETSEEESSEEEEETTEEEEEEEESSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSEEEEEE CS
                       Copper-bind   7 vesgdlqFetkeitvkkgekvtfvnlavmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfdeagtYkff 83 
                                       v  +d+qF++++i+++ g++vt++n ++  H v  d       +d+ ++++         Ge+++ tf+eag Y++ 
  gi|298675030|ref|YP_003726780.1|  43 VIMEDIQFKPATIQISVGDTVTWTNEDSTEHTVTSD--N----FDSGNLEQ---------GETFTHTFNEAGVYDYQ 104
                                       556789*******************99999988654..3....45556665.........9**************** PP

                                       ETTTTTTTSEEEEEE CS
                       Copper-bind  84 CsPHaaagMkgkvtv 98 
                                       C+ H +  M g+v+v
  gi|298675030|ref|YP_003726780.1| 105 CTIHPS--MTGTVIV 117
                                       *****4..6****98 PP

>> DUF2190  Uncharacterized conserved protein (DUF2190)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.6   2.2e-06      0.01      37      79 ..      29      76 ..       9      92 .. 0.75
   2 ?   -1.2   0.0      0.67     3e+03      52      52 ..     101     101 ..      70     133 .. 0.58

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.2e-06
                           DUF2190 37 daaaGetvtvaveGvf......veaaaaiavGdkVywdasgkvltt.tta 79
                                      + ++Ge ++v+++ v+      + a+  i+vGd+V+w++++    + t  
  gi|298675030|ref|YP_003726780.1| 29 TEDNGEDGAVETTNVImediqfKPATIQISVGDTVTWTNEDST--EhTVT 76
                                      44799*******999999999988989***********99875..22233 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.67
                           DUF2190  52 f 52 
                                       +
  gi|298675030|ref|YP_003726780.1| 101 Y 101
                                       2 PP

>> ATHILA  ATHILA ORF-1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.4     5e-05      0.22     345     406 ..      40      98 ..      37     107 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 5e-05
                            ATHILA 345 vTtieekenIdfkPskeilsappedeaelteeaeeedvdeededeeaelekfdtsqyhFeeh 406
                                       +T+++  e+I+fkP++ +   +  d + +t+e+ +e   ++d+ +  +le+ +t   +F+e 
  gi|298675030|ref|YP_003726780.1|  40 TTNVI-MEDIQFKPATIQI--SVGDTVTWTNEDSTEHTVTSDNFDSGNLEQGETFTHTFNEA 98 
                                       56664.689******6666..889***********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 950.71
//
Query:       gi|298675031|ref|YP_003726781.1|  [L=451]
Description: coenzyme F390 synthetase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-15   55.8   0.0    3.7e-15   55.4   0.0    1.1  1  AMP-binding  AMP-binding enzyme
  ------ inclusion threshold ------
      0.029   14.4   0.0       0.35   10.9   0.0    2.1  2  SIS_2        SIS domain
       0.14   12.1   0.0       0.22   11.4   0.0    1.2  1  DUF1478      Protein of unknown function (DUF1478)


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.4   0.0   6.2e-19   3.7e-15     139     327 ..      74     260 ..      14     293 .. 0.72

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 6.2e-19
                                       HCCCCSCTTS-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHH.HHHCSCCTTT-EEEESS-TTSC CS
                       AMP-binding 139 eeeeseekaekpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslk.letrfklkeddvvlsilplahi 214
                                       +++++e    +  e +++  +d+ ++  TSGT G PK   l+ + +  ++ ++k     ++++++d+v++++++   
  gi|298675031|ref|YP_003726781.1|  74 HNQPPET---NSFEFKSVGWEDVFTVHETSGTSGVPKSFFLTWKDWERFAEKYKrTFISQGFGPGDRVVVCASYGMN 147
                                       2332222...2346667899********************************986333467889************* PP

                                       HHHHHHHHHHHHTT-EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHH..HHCCCHH.CHHHHCCGTT-SEE CS
                       AMP-binding 215 fglilelllallsGatvvllpkdaaldpklllelieklkvtviagvPrvleal..lesgalk.aakkakdlsslrlv 288
                                       +g  + +l+a   G+++ +++++ +++    +++i+ +++t i  v  v++ l  ++ + +k   +   + ss++ +
  gi|298675031|ref|YP_003726781.1| 148 VGANTMTLAARDIGMSI-IPEGKCTFP----VRVITSYEPTGI--VGNVFKLLrlAN-RMKKeGLEP--SESSIERL 214
                                       **977777777777744.556666655....89********66..556666664233.223312333..67899999 PP

                                       EEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSEC.EE......C CS
                       AMP-binding 289 llggeplspellrffralfgeevlegYGlTEttgvv.tv......l 327
                                       ++gge+  +e+ + ++++ g++v+++YG TE t++  +       +
  gi|298675031|ref|YP_003726781.1| 215 VVGGESFAEEARDYLSEIWGCNVFNTYGSTEGTMCGeCSeinglhV 260
                                       9********************************9985323334330 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.058   3.5e+02      98     119 ..      85     106 ..      38     117 .. 0.69
   2 ?   10.9   0.0   5.8e-05      0.35      89     134 ..     121     165 ..     111     166 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.058
                                       HTT--TT-EEEEE-SS--SHHH CS
                             SIS_2  98 lvrlkpgDvLlviSnsGnnavv 119
                                          +  +Dv+ v+ +sG + v+
  gi|298675031|ref|YP_003726781.1|  85 FKSVGWEDVFTVHETSGTSGVP 106
                                       4556679**********99987 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 5.8e-05
                                       TTHHHHHHHHTT--TT-EEEEE-SS--SHHHHHHHHHHHHHT-EEE CS
                             SIS_2  89 egyakqilrlvrlkpgDvLlviSnsGnnavvveaaeaakergmkvi 134
                                       e y +++ ++  + pgD  +v  + G n  +  + +aa+++gm +i
  gi|298675031|ref|YP_003726781.1| 121 EKYKRTFISQ-GFGPGDRVVVCASYGMNVGANTMTLAARDIGMSII 165
                                       5566666666.89*******************************98 PP

>> DUF1478  Protein of unknown function (DUF1478)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.7e-05      0.22      73     123 ..     101     153 ..      93     171 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.7e-05
                           DUF1478  73 gttgcprelfl...dlyrfiptltrtlltslgcgpggavvlrsgyrslvlacsl 123
                                       gt+g+p+ +fl   d  rf     rt++ s g gpg  vv+ + y   v a ++
  gi|298675031|ref|YP_003726781.1| 101 GTSGVPKSFFLtwkDWERFAEKYKRTFI-SQGFGPGDRVVVCASYGMNVGANTM 153
                                       9*********9666789********986.78**********9999877766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3327.19
//
Query:       gi|298675032|ref|YP_003726782.1|  [L=728]
Description: hypothetical protein Metev_1104 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-76  255.1   0.0    3.5e-75  251.4   0.0    2.4  2  Thioredox_DsbH  Protein of unknown function, DUF255
    4.1e-12   46.1   0.0    8.7e-12   45.1   0.0    1.6  1  Thioredoxin_7   Thioredoxin-like
    4.3e-06   26.4   0.3    6.5e-05   22.5   0.0    2.1  2  Glyco_hydro_9   Glycosyl hydrolase family 9
    5.5e-05   22.8   4.2     0.0031   17.1   0.1    2.8  2  Glyco_hydro_76  Glycosyl hydrolase family 76
    8.9e-05   21.7   2.5      0.046   12.8   0.1    2.5  2  Glyco_hydro_88  Glycosyl Hydrolase Family 88
    0.00042   19.7   0.1        1.4    8.0   0.1    3.2  3  GlcNAc_2-epim   N-acylglucosamine 2-epimerase (GlcNAc 2-epime
     0.0035   16.0   2.2         12    4.4   0.0    4.5  5  LANC_like       Lanthionine synthetase C-like protein
  ------ inclusion threshold ------
      0.036   14.5   0.0      0.099   13.1   0.0    1.8  1  Thioredoxin_2   Thioredoxin-like domain


Domain annotation for each model (and alignments):
>> Thioredox_DsbH  Protein of unknown function, DUF255
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  251.4   0.0   1.6e-78   3.5e-75       2     162 ..      13     173 ..      12     174 .. 0.98
   2 ?    0.6   0.0      0.22   4.8e+02      75     108 ..     389     422 ..     361     430 .. 0.76

  Alignments for each domain:
  == domain 1  score: 251.4 bits;  conditional E-value: 1.6e-78
                    Thioredox_DsbH   2 nrlaeekspYllqhaknpvdWypwgeealekakeedkpillsiGysachWChvmekesfedeevaallnesfvsvkv 78 
                                       n+l++ekspYllqha npv+Wypwg+ea+ekak+edkpi+lsiGys+chWChvme+esfed+e+a++ln++fv++kv
  gi|298675032|ref|YP_003726782.1|  13 NHLINEKSPYLLQHAYNPVNWYPWGDEAFEKAKNEDKPIFLSIGYSTCHWCHVMENESFEDPEIAQILNDNFVCIKV 89 
                                       99*************************************************************************** PP

                    Thioredox_DsbH  79 DreerPdldkiymeavqaltgsggWPlnvfltpdlkpffggtYfpkeeregrpgflevlekiaelweeereeleeea 155
                                       DreerPd+d++ym+++qaltg+ggWPl++++tp++kpf ++tY+pke+r g +g++++l +i+++w++++ el ++a
  gi|298675032|ref|YP_003726782.1|  90 DREERPDIDSTYMDVCQALTGRGGWPLTIIMTPEKKPFSAATYLPKESRFGLTGLIDLLPRISDMWSKQKRELVSRA 166
                                       ***************************************************************************** PP

                    Thioredox_DsbH 156 eelleal 162
                                       e++++++
  gi|298675032|ref|YP_003726782.1| 167 EQITSSV 173
                                       **99875 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.22
                    Thioredox_DsbH  75 svkvDreerPdldkiymeavqaltgsggWPlnvf 108
                                       ++ +D e   +ld+++ ++ +a +++g+W  n++
  gi|298675032|ref|YP_003726782.1| 389 PLYIDVEPDEELDEFHEKLNEAREKRGAWKRNLL 422
                                       56788898999******************88876 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.0   3.9e-15   8.7e-12       2      65 ..      33      96 ..      32     122 .. 0.83

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 3.9e-15
                                      --SSHHHHHHHHHHHT--EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-G CS
                     Thioredoxin_7  2 wlsdldealakaaergkpvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterda 65
                                      w+ + dea++ka+ + kp+++ +g s+c+ C+++e +  +d+e++++l+++fv+ +vd +er +
  gi|298675032|ref|YP_003726782.1| 33 WYPWGDEAFEKAKNEDKPIFLSIGYSTCHWCHVMENESFEDPEIAQILNDNFVCIKVDREERPD 96
                                      999**********************************99999****9************99976 PP

>> Glyco_hydro_9  Glycosyl hydrolase family 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.057   1.3e+02     211     242 ..     284     321 ..     254     383 .. 0.65
   2 !   22.5   0.0   2.9e-08   6.5e-05     135     252 ..     446     559 ..     407     629 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.057
                                       HHHHHHHHHHHH--HHHHHHHHHCC.TTSST........ CS
                     Glyco_hydro_9 211 llwAaawlykatkeasylddaksyyskeaas.......s 242
                                       l +A +++y+at++ +y++ a++  +    +       +
  gi|298675032|ref|YP_003726782.1| 284 LSMAYIEVYQATGKIEYKNTARDVFTYAL-RdltskegG 321
                                       55677778888877777777765443222.134444330 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 2.9e-08
                                       EEEEETTC--HHHHHHHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHHHHHHH-.-..TT.--TGTTTTTTS--SSH CS
                     Glyco_hydro_9 135 vykvdesnpgtdaaaetAAalAaasrvfkksdpayAaklleaAkklyafadkyr.ky.ad.siaeaagggfYnssdk 208
                                       v+ +++++  td  + + Aal+  + vf+  d++yA++  +aA  + + ++ ++ ++ ++  ++++  +gf +  d 
  gi|298675032|ref|YP_003726782.1| 446 VHPAKDDKILTDWNGLMIAALSKGAQVFN--DKEYANSARKAADFIIKNMSDSSgQLmHRyRDGDSDIHGFID--DY 518
                                       4445566668899999************4..******999999988888853333321221112122222333..35 PP

                                       HHHHHHHHHHHHHH--HHHHHHHHHCC.TTSST...BTTB-HHH CS
                     Glyco_hydro_9 209 DellwAaawlykatkeasylddaksyyskeaasssfsWdnkvag 252
                                         l w+ ++ly++t e +yl++a + ++      ++ Wd+++ g
  gi|298675032|ref|YP_003726782.1| 519 AFLTWGLIELYETTFEVKYLEKALEFNNYL---INHFWDDNNGG 559
                                       5899**********8889*****9866533...23489996666 PP

>> Glyco_hydro_76  Glycosyl hydrolase family 76
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.4    0.0029       6.6      40     136 ..     219     321 ..     188     334 .. 0.60
   2 !   17.1   0.1   1.4e-06    0.0031      51     181 ..     479     611 ..     443     623 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0029
                                       HHHHHHHHHHHHCTTCCCHHHHHH........HHHCCCT......CEE-.SSSTTCTCSSEHHHHHHHHHHHHHHHH CS
                    Glyco_hydro_76  40 alfgalidywrltgdstyndlitq........allaqag......enyd.ympanqsrtegnDDqafwglaamtaae 101
                                       + ++ l+ yw++t++++  +++++        +++ + g      +  + +m ++ ++ + + Dqa   +a ++ ++
  gi|298675032|ref|YP_003726782.1| 219 HNLMFLMRYWERTSNNKALEMVEKtlknmrigGIYDHIGfgfhrySTDRyWMIPHFEK-MLY-DQALLSMAYIEVYQ 293
                                       5578899999999999888888883333333333334442222211111122222222.222.56666666666666 PP

                                       H.....H--HHHHHHHHHHHHHHHHCB-SCSCCS- CS
                    Glyco_hydro_76 102 rnfpeptdepswLalAqavfntqasrwdeetcgGG 136
                                       +     t++ ++ + A+ vf +  +   +++  GG
  gi|298675032|ref|YP_003726782.1| 294 A-----TGKIEYKNTARDVFTYALRDLTSKE--GG 321
                                       5.....9999999999999977766665553..55 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.4e-06
                                       HCTTCCCHHHHHHHHHCCCTCE.E-SSSTTCTCSSEHHHHHHHHHHHHHHHHH.....H--HHHHHHHHHHHHHHHH CS
                    Glyco_hydro_76  51 ltgdstyndlitqallaqagen.ydympanqsrtegnDDqafwglaamtaaernfpeptdepswLalAqavfntqas 126
                                       + +  +  d i + +   +g+  ++y     +   + DD af +   ++ +e++f+ +     +L+ A ++ n++++
  gi|298675032|ref|YP_003726782.1| 479 ANSARKAADFIIKNMSDSSGQLmHRYRDGDSDIHGFIDDYAFLTWGLIELYETTFEVK-----YLEKALEFNNYLIN 550
                                       2333355566666777788877555888888888999*****99999*****966665.....************** PP

                                       C.B-SCSCCS-BBSE.......C..ESS--SEEEHHHHHHHHHHHHHHHHHH--CHHHHHHHH CS
                    Glyco_hydro_76 127 r.wdeetcgGGlrWq.......iftwnsgydyknsisngplfqlaarLarytgnetYlewAek 181
                                       + wd++  +GG +         i++ ++ yd      n+ ++   +rL r+tgn ++ ++A+ 
  gi|298675032|ref|YP_003726782.1| 551 HfWDDN--NGGFYFTpdnaetpIVRKKEIYDGASPSGNSVALMNLMRLGRMTGNPELEKKASD 611
                                       ****98..6**9986322222234444555666666677777777888888888888887765 PP

>> Glyco_hydro_88  Glycosyl Hydrolase Family 88
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.6   0.00052       1.2      38     118 ..     224     324 ..     219     343 .. 0.79
   2 !   12.8   0.1     2e-05     0.046      88     174 ..     473     561 ..     436     622 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00052
                                       HHHHHHHH--HHHHHHHHHHHHHCCCTTS-.....................CTTSGGGTGHHHHHHHHHHHH-THHH CS
                    Glyco_hydro_88  38 lleayeatgdkeyldyakawadslideggk.....................telelDdidigllllllyeltkdery 93 
                                       l++++e t +++ l++++++ +++   g                       +++  D++ + + ++  y+ t++ +y
  gi|298675032|ref|YP_003726782.1| 224 LMRYWERTSNNKALEMVEKTLKNMRIGGIYdhigfgfhrystdrywmiphfEKMLYDQALLSMAYIEVYQATGKIEY 300
                                       56788888888888888886666666665566666666666677777777888888999999999999999999999 PP

                                       HHHHHHHHHHHHHCS-B.TTS.B.S CS
                    Glyco_hydro_88  94 keaaeeladyvlakpprtseGgfwh 118
                                       k++a++++ y l++  + +eGgf  
  gi|298675032|ref|YP_003726782.1| 301 KNTARDVFTYALRDLTS-KEGGFYS 324
                                       99999999999998888.8899875 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2e-05
                                       H-THHHHHHHHHHHHHHHHCS-B.TTS.B.S....BTTSTTEEETHHHHHHHHHHHHHHHHHCGTHHHHHHHHHHHH CS
                    Glyco_hydro_88  88 tkderykeaaeeladyvlakpprtseGgfwh....kkkepeqlWlDgLfMaipllaklskvtgepkyldeaikqfll 160
                                        +d++y + a+++ad++++++++ s G ++h     +   +   +D+       l++l+++t e kyl++a++   +
  gi|298675032|ref|YP_003726782.1| 473 FNDKEYANSARKAADFIIKNMSD-SSGQLMHryrdGDSDIHGF-IDDYAFLTWGLIELYETTFEVKYLEKALEFNNY 547
                                       45778888888888888888888.6677777555333333333.444444566677888888888888888888888 PP

                                       HHHHHBETTTSEB- CS
                    Glyco_hydro_88 161 tarhlfdpetGlyy 174
                                         +h  d ++G +y
  gi|298675032|ref|YP_003726782.1| 548 LINHFWDDNNGGFY 561
                                       88887777777666 PP

>> GlcNAc_2-epim  N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.1   0.00064       1.4     219     333 ..     223     337 ..     220     346 .. 0.83
   2 ?    1.5   0.0     0.062   1.4e+02     281     316 ..     463     498 ..     433     516 .. 0.76
   3 !    6.0   0.0    0.0028       6.2     232     269 ..     535     572 ..     519     630 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00064
                                       HHHHHHHHTT----THHHHHHHHHHHHHHHHBS-SSS.SB-.S-B-TTS-BSS--EEHHHHHHHHHHHHHHHHHH-- CS
                     GlcNAc_2-epim 219 LlldlallkreraakllekArkLfetalakgwdkdrg.glv.ytldaagkpvddakllWpqtEalkaaaalaeltge 293
                                       +l++++  +r++++k+le  +k  +++   g+    g g++ y +d++ ++++ +k+l  q+    a +  ++ tg+
  gi|298675032|ref|YP_003726782.1| 223 FLMRYW--ERTSNNKALEMVEKTLKNMRIGGIYDHIGfGFHrYSTDRYWMIPHFEKMLYDQALLSMAYIEVYQATGK 297
                                       788888..799999999999999999999999999999987467999999999999999999988888999999999 PP

                                       CHHHHHHHHHHHHHHHHTB-TTTSSB-SEE-TTS-.B---- CS
                     GlcNAc_2-epim 294 arylewyarvaeylerhlidpekGlWfdkldadge.vaekv 333
                                        +y + ++ v  y  r l ++ +G  +  +dad e v+ k 
  gi|298675032|ref|YP_003726782.1| 298 IEYKNTARDVFTYALRDLTSK-EGGFYSAVDADSEgVEGKF 337
                                       999999999999999996555.5667889999988777665 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.062
                                       HHHHHHHHHHH--CHHHHHHHHHHHHHHHHTB-TTT CS
                     GlcNAc_2-epim 281 lkaaaalaeltgearylewyarvaeylerhlidpek 316
                                       ++a+ ++a++  +++y+++++++a+++ +++ d   
  gi|298675032|ref|YP_003726782.1| 463 IAALSKGAQVFNDKEYANSARKAADFIIKNMSDSSG 498
                                       788888999999999999999999999999887654 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0028
                                       -THHHHHHHHHHHHHHHHBS-SSSSB-S-B-TTS-BSS CS
                     GlcNAc_2-epim 232 akllekArkLfetalakgwdkdrgglvytldaagkpvd 269
                                        k+lekA +  +  +++ wd ++gg+++t d+a++p +
  gi|298675032|ref|YP_003726782.1| 535 VKYLEKALEFNNYLINHFWDDNNGGFYFTPDNAETPIV 572
                                       33344444444444444444444444444444444433 PP

>> LANC_like  Lanthionine synthetase C-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.44   9.8e+02     173     198 ..     222     247 ..     221     254 .. 0.76
   2 ?    3.2   0.1     0.012        27      16      57 ..     286     324 ..     282     374 .. 0.72
   3 ?    2.8   0.0     0.015        35     232     261 ..     464     493 ..     459     499 .. 0.73
   4 ?   -1.1   0.0      0.24   5.5e+02     112     140 ..     522     549 ..     515     576 .. 0.75
   5 !    4.4   0.0    0.0053        12      15      62 ..     590     643 ..     576     686 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.44
                                       HHHHCCCHT.-HHHHHHHHHHHHHHH CS
                         LANC_like 173 lallalykgtksekllelikkllkyl 198
                                        +l+++++ t ++k le+++k+lk +
  gi|298675032|ref|YP_003726782.1| 222 MFLMRYWERTSNNKALEMVEKTLKNM 247
                                       56788888888888888888887766 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHTHHHHHHHHHHHHHHHHHHHCCH.-S--STTT CS
                         LANC_like  16 llllelykvtknekylklahkylekikkelselglesisffs 57 
                                       ++++e+y++t++ +y+++a++ + ++ + l +   +  +f+s
  gi|298675032|ref|YP_003726782.1| 286 MAYIEVYQATGKIEYKNTARDVFTYALRDLTS---KEGGFYS 324
                                       67788888888888888888888888887777...5555554 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.015
                                       HHHHHHHHHHT-HHHHHHHHHHHHHHHHH- CS
                         LANC_like 232 lallkagkalneeelleeaeealevvlkkg 261
                                        al k ++++n++e+ ++a++a++ ++k+ 
  gi|298675032|ref|YP_003726782.1| 464 AALSKGAQVFNDKEYANSARKAADFIIKNM 493
                                       467777788888888888888888887764 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 0.24
                                       HHHHHHHHHHH-SGHHHHHHHHHHHHHHH CS
                         LANC_like 112 lsyllllneetkieedllkqilkylvelg 140
                                        + l++l+e+t +e ++l+++l++ ++l+
  gi|298675032|ref|YP_003726782.1| 522 TWGLIELYETT-FEVKYLEKALEFNNYLI 549
                                       57788888888.88888888888877777 PP

  == domain 5  score: 4.4 bits;  conditional E-value: 0.0053
                                       HHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHCC......H.-S--STTTSHHHH CS
                         LANC_like  15 allllelykvtknekylklahkylekikkelse......lglesisffsGaagi 62 
                                       ++ l +l+++t+n++++k a++ +++  k+ls+      ++++ + f  G ++ 
  gi|298675032|ref|YP_003726782.1| 590 LMNLMRLGRMTGNPELEKKASDSIKSFSKSLSRnpiastHSMQALDFVQGPSSE 643
                                       4558899**************************888777777777777777765 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.4e-05     0.099       1      58 [.      44      94 ..      44     136 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.4e-05
                     Thioredoxin_2  1 akgngkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcake 58
                                      ak + kp+++ +  ++C  C+ +++e +e++++ ++     l+++  ++ +++++++ 
  gi|298675032|ref|YP_003726782.1| 44 AKNEDKPIFLSIGYSTCHWCHVMENESFEDPEIAQI-----LNDN--FVCIKVDREER 94
                                      57789*******************************.....9998..55555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (728 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 5360.88
//
Query:       gi|298675033|ref|YP_003726783.1|  [L=235]
Description: exsB protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-60  202.5   0.0    6.3e-60  202.3   0.0    1.0  1  QueC           Queuosine biosynthesis protein QueC
    1.9e-05   24.5   0.0    0.00051   19.8   0.0    2.1  2  ATP_bind_3     PP-loop family
     0.0013   18.4   0.0       0.32   10.5   0.0    2.3  2  ThiI           Thiamine biosynthesis protein (ThiI)
  ------ inclusion threshold ------
      0.019   14.6   0.0      0.027   14.2   0.0    1.1  1  Asn_synthase   Asparagine synthase
      0.026   13.6   0.0      0.035   13.2   0.0    1.2  1  NAD_synthase   NAD synthase
      0.031   14.2   0.1      0.083   12.9   0.1    1.7  2  Fer2           2Fe-2S iron-sulfur cluster binding domain
      0.039   12.8   0.0       0.06   12.1   0.0    1.3  1  tRNA_Me_trans  tRNA methyl transferase


Domain annotation for each model (and alignments):
>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.3   0.0   2.5e-63   6.3e-60       2     209 ..       3     219 ..       2     220 .. 0.94

  Alignments for each domain:
  == domain 1  score: 202.3 bits;  conditional E-value: 2.5e-63
                                       EEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-T.TSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCGGG----- CS
                              QueC   2 avvllSGGlDSttvlalakkegkevealtfdYgqr.hkkeleaakkiakelgveehkildldllkelggsaLtdeei 77 
                                       a+ llS GlDS ++l++a++  +   a+ fdYgqr +kke+e+ kki++++g+ + ++++ld+l+++++++L+++++
  gi|298675033|ref|YP_003726783.1|   3 AISLLSSGLDSVAALTIAREITDVKLAIIFDYGQRsAKKEIEYSKKICTHFGI-DYEVIKLDWLEKITNTSLVNKKE 78 
                                       899****************9999999*********99****************.*********************** PP

                                       ----...--..............--------TTHHHHHHHHHHHHHHHHT-SEEEE---S-STT--GGGSHHHHHHH CS
                              QueC  78 evpk...eelee...........eelpntfVpaRNliflslaasyaealgaeaiiiGvneedfsgYPDcrdefvkal 140
                                       +vp+       +           e+++n++Vp+RN ifl + a++ae+l++e +i+G+n+e+ +++PD+++efv+++
  gi|298675033|ref|YP_003726783.1|  79 DVPEltlD---DvsgknatekteESAKNVWVPNRNGIFLNISAGFAESLECEYVIVGFNSEEGQTFPDNSPEFVDSM 152
                                       ****5551...44445555566699**************************************************** PP

                                       HHHHHHHHTS--EEE-TTTT--HHHHHHHHHHTTHHHHH-B-STTS.-BTTTTSSSHHHHHHHHHHHHH CS
                              QueC 141 nkalnlgedkkieieaPlidlsKaeivklgkelgvpleetlsCYegeeegkaCgeCdaCalRkkgfeea 209
                                       n+ l++++ + ++i aPl+d +K++i++ + + g ple ++sCY+g  ++ +Cg C++C++Rk++f+e+
  gi|298675033|ref|YP_003726783.1| 153 NTCLSYSTRNGVKILAPLVDYNKKDIINQALKSGTPLEWSWSCYHG--RDLPCGVCESCIRRKHAFNEL 219
                                       **********************************************..668***************986 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0     2e-07   0.00051       6      73 ..       7      70 ..       3      79 .. 0.83
   2 ?    2.5   0.0     0.043   1.1e+02     131     156 ..     157     182 ..     143     191 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2e-07
                                      --SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H.HHCTT CS
                        ATP_bind_3  6 vSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv.akkkg 73
                                      +S GlDS+a l ++ +  +       ai +d+g r+ +k+e e+ k++c++++i++e+ k+d+ +k ++
  gi|298675033|ref|YP_003726783.1|  7 LSSGLDSVAALTIAREITD----VKLAIIFDYGQRS-AKKEIEYSKKICTHFGIDYEVIKLDWlEKITN 70
                                      69***********999977....457899****985.788999*******************9533333 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.043
                                       SEEEETTCCEE-CCCT--HHHHHHHH CS
                        ATP_bind_3 131 easeiasirlvRPlLkvskeeleeyl 156
                                       ++s++++++++ Pl++++k+++ + +
  gi|298675033|ref|YP_003726783.1| 157 SYSTRNGVKILAPLVDYNKKDIINQA 182
                                       45667889999999999999998765 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0    0.0033       8.6       6      59 ..       3      53 ..       2      81 .. 0.69
   2 !   10.5   0.0   0.00013      0.32     137     161 ..     163     187 ..     109     199 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0033
                              ThiI  6 vlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaey 59
                                      +++LlS G+DS Vaa  + +    v+l  +++  + +  a++ +e   ++ +++
  gi|298675033|ref|YP_003726783.1|  3 AISLLSSGLDS-VAALTIAREITDVKLAIIFD--YGQRSAKKEIEYSKKICTHF 53
                                      689*******9.89988888888888766654..44444444555555555444 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00013
                              ThiI 137 nllilrPLigldKeeiiklAkeigt 161
                                        + il PL+ ++K++ii+ A + gt
  gi|298675033|ref|YP_003726783.1| 163 GVKILAPLVDYNKKDIINQALKSGT 187
                                       468*****************99888 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     1e-05     0.027      22      75 ..       5      58 ..       3      71 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1e-05
                      Asn_synthase 22 alLSGGlDSSliaalaarqsk.splktFsigfeekgsdeakyakevaehlgteht 75
                                      +lLS GlDS +   +a++ ++ + +  F  g    + +e++y k+++ h+g++  
  gi|298675033|ref|YP_003726783.1|  5 SLLSSGLDSVAALTIAREITDvKLAIIFDYGQ-RSAKKEIEYSKKICTHFGIDYE 58
                                      69*****************9722223344444.79*****************943 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.4e-05     0.035      25      99 ..       7      80 ..       1      94 [. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                                      E-SSHHHHHHHHHHHHHHTCGEEEEEE--.SSSTTHHHHHHHHHHHHHHTSEEEE---HHHHHHHHHHHHHHH-HH CS
                      NAD_synthase 25 lSGGvDSslvaalavkalgkenvlalllP.ssvsseedvedalalaenlgievktidikpivrafeqelkeakedl 99
                                      lS G+DS  + ++a+++   +  la+++  ++ s ++++e +++++ ++gi++++i+++   ++ + +l ++ked+
  gi|298675033|ref|YP_003726783.1|  7 LSSGLDSVAALTIAREIT--DVKLAIIFDyGQRSAKKEIEYSKKICTHFGIDYEVIKLDWLEKITNTSLVNKKEDV 80
                                      9******99999999988..788999999999**************************999888888777766554 PP

>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.9   7.5e+03      55      74 ..     138     156 ..     126     159 .. 0.55
   2 ?   12.9   0.1   3.2e-05     0.083      16      44 ..     176     207 ..     170     221 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.9
                                       TSSSSTHHHHHTTEEEEGGG CS
                              Fer2  55 detelegeeldegklrlaCq 74 
                                       ++t+ ++++ +  + + +C 
  gi|298675033|ref|YP_003726783.1| 138 GQTFPDNSP-EFVDSMNTCL 156
                                       356666665.4555567776 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 3.2e-05
                                       THBHHHHHHHTTTTTSTTSSSSSS...SSTTE CS
                              Fer2  16 ettlldaaeenggidipysCgggg...CgtCl 44 
                                       + ++ +a+++   ++  +sC++g    Cg+C 
  gi|298675033|ref|YP_003726783.1| 176 KDIINQALKSGTPLEWSWSCYHGRdlpCGVCE 207
                                       45699*****99**********7777888886 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.3e-05      0.06       5      70 ..       5      62 ..       1      77 [. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.3e-05
                     tRNA_Me_trans  5 valSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdf 70
                                       +lS+G DS vaa+ ++++    + v l+++ + ++     +a++++++ ++++ ++gi +ev+++
  gi|298675033|ref|YP_003726783.1|  5 SLLSSGLDS-VAALTIAREI---TDVKLAIIFDYGQR----SAKKEIEYSKKICTHFGIDYEVIKL 62
                                      679*****7.7888887765...55667777774444....5999****************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1777.90
//
Query:       gi|298675034|ref|YP_003726784.1|  [L=184]
Description: hypothetical protein Metev_1106 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-71  238.0   6.1    5.6e-71  237.8   6.1    1.0  1  DUF366    Domain of unknown function (DUF366)


Domain annotation for each model (and alignments):
>> DUF366  Domain of unknown function (DUF366)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.8   6.1   3.1e-75   5.6e-71       1     183 []       1     179 [.       1     179 [. 0.97

  Alignments for each domain:
  == domain 1  score: 237.8 bits;  conditional E-value: 3.1e-75
                            DUF366   1 mkvlvleekikYdGsqlsslwaykefgiqgdsivafrGecevkleelvDleDvkeeeeIksedmlhfivehFdstdl 77 
                                       m++++l+++ +YdGsq+sslway+ +g+q+dsi+ frG+c+v++++++DleD++e+e I+s+dm+hfi+ehFdst+l
  gi|298675034|ref|YP_003726784.1|   1 MECIYLNNR-NYDGSQISSLWAYNIAGVQDDSIIYFRGTCNVEIDHMIDLEDKRENEAIYSSDMIHFIIEHFDSTNL 76 
                                       667777665.9****************************************************************** PP

                            DUF366  78 klavlrQrllvaivkevleekgvklkreGdDlyvndkKLsvsiataslvsvkiHlglNvesegtpvetigLkdlgi. 153
                                       kl++ rQrl+++iv+e+l++kg+++kreGdDl++n++KLsvsia++s+vs+kiH+g+Nv ++     ++ Lk +g+ 
  gi|298675034|ref|YP_003726784.1|  77 KLVYSRQRLFASIVSEILMDKGFNIKREGDDLFINNRKLSVSIASTSAVSQKIHFGINVIHD----YYADLKSIGFe 149
                                       **************************************************************....9999****998 PP

                            DUF366 154 eedieelaeevakkyaeeiediekdirKvr 183
                                       e++ie+l+ e+a++y++e++diekd+rK+r
  gi|298675034|ref|YP_003726784.1| 150 ESKIEQLMCEIAESYVNELDDIEKDLRKSR 179
                                       899*************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1403.81
//
Query:       gi|298675035|ref|YP_003726785.1|  [L=239]
Description: radical SAM domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.2e-10   40.3   1.3    8.3e-10   39.3   1.1    1.7  2  Radical_SAM  Radical SAM superfamily
    1.4e-08   34.8   1.2    3.5e-08   33.6   0.8    2.0  1  Fer4_14      4Fe-4S single cluster domain
    3.3e-07   30.7   0.1    1.2e-06   28.8   0.1    2.0  1  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   1.1   1.4e-13   8.3e-10       3     166 ..      27     187 ..      25     215 .. 0.86
   2 ?   -2.2   0.0      0.76   4.6e+03     124     146 ..     206     227 ..     190     230 .. 0.76

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 1.4e-13
                                       EESEESS--TTTSCCTT.............HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHH CS
                                       xxxxxxxxxxxxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpet.............vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvel 66 
                                        + gCnl+C +C++ +               + e  +  l+v  ++e +++++ +  v+ v l+ggepl ++df++ 
  gi|298675035|ref|YP_003726785.1|  27 RFIGCNLQCQYCDTQREyvdfcrfeenpgsDEFELIPNPLDVNTVAESIESFS-S--VHSVSLTGGEPLIHADFIKN 100
                                       567************************99999999999999999999999995.4..*****************888 PP

                                       HHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  67 lerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagik 143
                                       l   a l        +e+n tl  +e++++ ++  v  vs ++++++++++ +       +e++++++++l+    +
  gi|298675035|ref|YP_003726785.1| 101 LQISAPL-------YLESNMTL--PEMAKKVKD-KVSFVSGDVKIINEFECDDFE---THIEKTIDSFKILKTTESR 164
                                       8888776.......9*******..6********.88*************544444...7788888888888888888 PP

                                       TEEEEEEEBTTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 144 rvvdrivglpGendeeleellel 166
                                       +++  iv+l++   e + ++++ 
  gi|298675035|ref|YP_003726785.1| 165 DCFCKIVVLENTKIEYVLDIMDK 187
                                       88888888888888877777664 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.76
                                       TSHHHHHHHHHHHHHHTTSETEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 124 ghtfeevlealeklreagikrvv 146
                                       +++++++l+  + l ++gi+ ++
  gi|298675035|ref|YP_003726785.1| 206 RPSVQHLLQIQKQLLDKGIN-TK 227
                                       47888888888999999888.44 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.8   5.8e-12   3.5e-08       1     109 [.      24     130 ..      24     142 .. 0.68

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 5.8e-12
                           Fer4_14   1 lfvrlsgCnlsCkgCdnketwks...........elgkpqteelleqilkdlkkseikiqglvltGGePLhyenkke 66 
                                       +fvr+ gCnl+C+ Cd++ ++ +           e + + +  ++ + +++  +s ++ + ++ltGGePL++     
  gi|298675035|ref|YP_003726785.1|  24 VFVRFIGCNLQCQYCDTQREYVDfcrfeenpgsdEFELIPNPLDV-NTVAESIESFSSVHSVSLTGGEPLIH----- 94 
                                       69**************88877766776665555422222222233.333345556666788*********99..... PP

                           Fer4_14  67 llklvkrlkeeypekkiwletngtleielektpdlkekleals 109
                                         +++k+l+ +    +  le+n tl  e+   ++ k+k+  +s
  gi|298675035|ref|YP_003726785.1|  95 -ADFIKNLQISA---PLYLESNMTLP-EMA--KKVKDKVSFVS 130
                                       .77888887777...78888888888.433..56777777777 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.1     2e-10   1.2e-06       1      67 [.      12      95 ..      12     173 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 2e-10
                           Fer4_12  1 lnGeG....vr.lslfvsgCnlsCkgCf.nketwsfk.............sgkeftkelleeiiedlkkesiegltllG 60
                                      ++GeG    vr +++++ gCnl+C++C  ++e  +f                ++ + ++ +e ie++  +s+  ++l+G
  gi|298675035|ref|YP_003726785.1| 12 VQGEGpyvgVRqVFVRFIGCNLQCQYCDtQREYVDFCrfeenpgsdefelIPNPLDVNTVAESIESF--SSVHSVSLTG 88
                                      5778776656657999**********96144455444566666554444444555677777777777..999******* PP

                           Fer4_12 61 GEPllpe 67
                                      GEPl ++
  gi|298675035|ref|YP_003726785.1| 89 GEPLIHA 95
                                      ****943 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1788.19
//
Query:       gi|298675036|ref|YP_003726786.1|  [L=116]
Description: 6-pyruvoyl-tetrahydropterin synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-28   99.5   0.0    1.4e-28   99.3   0.0    1.0  1  PTPS      6-pyruvoyl tetrahydropterin synthase
  ------ inclusion threshold ------
      0.077   13.3   0.1      0.094   13.0   0.1    1.1  1  DUF5071   Domain of unknown function (DUF5071)


Domain annotation for each model (and alignments):
>> PTPS  6-pyruvoyl tetrahydropterin synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.3   0.0   1.6e-32   1.4e-28       7     121 ..      11     112 ..       6     114 .. 0.94

  Alignments for each domain:
  == domain 1  score: 99.3 bits;  conditional E-value: 1.6e-32
                                       EEEEEE--TTTTGGGGSTEEEEEEEEEEEEEC-STCTTBSS-HHHHHHHHHHHHHCTTTEECCCC-CCHHCCS.--H CS
                              PTPS   7 eFdaaHrlrkhegkcrnlHGHnykvevtvegeeldetgmvvdfgelkealkeileelDhkflnaddpeleellspTa 83 
                                       ++d aH+l++he  c+ +HGH+y+vev +ege  ++ gmv+df++lk+++k+il+ +Dh++ln ++ ++     p++
  gi|298675036|ref|YP_003726786.1|  11 SIDTAHYLPGHE-TCGIVHGHTYRVEVVIEGE--KNGGMVMDFADLKKIVKDILKDYDHTLLN-NILSY-----PSS 78 
                                       7899*****999.9******************..999*************************9.55555.....9** PP

                                       HHHHHHHHHHHHHHHGCCCGCEEEEEEEEETTEEEEEE CS
                              PTPS  84 EnlaklifeelkerlqekevklskvrvwEtpnswaeyr 121
                                       Enl++ i+ +l+e+l      l kvr+wE +++w+e++
  gi|298675036|ref|YP_003726786.1|  79 ENLCENIYSKLSEKL----KMLVKVRIWEGEGKWCEID 112
                                       ***************....8999************986 PP

>> DUF5071  Domain of unknown function (DUF5071)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1     1e-05     0.094      54     113 ..      51     113 ..      46     116 .] 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1e-05
                                       GGTHHHHHHHHHSS-HHHHHHHHHHHG.GGS-HHHHHHHHHHHHHHHTS--S.SHHHH.HHHH CS
                           DUF5071  54 eelvkeiaeiLeknDeewkyfvleflv.eklpveskkklkeelerlveepte.dEkee.elde 113
                                        +l+k +++iL+  D++  +++l + + e+l ++   kl e+l+ lv+      E ++ e+d+
  gi|298675036|ref|YP_003726786.1|  51 ADLKKIVKDILKDYDHTLLNNILSYPSsENLCENIYSKLSEKLKMLVKVRIWeGEGKWcEIDS 113
                                       578999******************97526788888899********98765434544446665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 856.29
//
Query:       gi|298675037|ref|YP_003726787.1|  [L=315]
Description: radical SAM domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.1e-26   92.0   0.2    7.5e-26   91.5   0.2    1.3  1  Radical_SAM  Radical SAM superfamily
    6.6e-07   29.5   0.1    1.6e-06   28.2   0.1    1.6  1  Fer4_14      4Fe-4S single cluster domain
    6.3e-05   23.3   0.1    0.00012   22.4   0.1    1.6  1  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.5   0.2   1.3e-29   7.5e-26       3     165 ..      43     222 ..      41     242 .. 0.92

  Alignments for each domain:
  == domain 1  score: 91.5 bits;  conditional E-value: 1.3e-29
                                       EESEESS--TTTSCCTT....HHHHHHHHHHHHHHHHHHHHHHH.HHTT.SEEEEEESSTGGGSTTHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpet....vrregrgrslsveeileevkelk.aekg.vkevilgggepllypdfvellerlakl 73 
                                       v + Cn +C++C+r  +     r+++++++l+++e le+ +++  +++  +   i g g+pl+++ +++++++l+k+
  gi|298675037|ref|YP_003726787.1|  43 VAPKCNIQCKYCIRDNDcvneCRPGVTSKVLTPQEALEKTRQVLeEHPFiKVIAIAGPGDPLAND-ETFETFKLIKE 118
                                       6789****************************************66666666667789*****88.55888888888 PP

                                       CCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHH...............HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...............xxxxxxxx RF
                       Radical_SAM  74 avpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtf...............eevleale 135
                                       + p++ i+++tng+ + ++ ++ +l++gv +++++++a+d+e +++ ++++  +                 +le+++
  gi|298675037|ref|YP_003726787.1| 119 EFPNVIICMSTNGLAL-PDRIDDMLDAGVQTLTVTVNAVDPE-IQRQICDRVVYngklykgkeaaelliNNQLEGIK 193
                                       89**************.*************************.99999855555699******************** PP

                                       HHHHTTSETEEEEEEEBTTTSHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 136 klreagikrvvdrivglpGendeeleelle 165
                                       ++ eagi  +++++v++p +nd++++++++
  gi|298675037|ref|YP_003726787.1| 194 RAIEAGIV-IKINTVLVPDVNDDHVVDIAK 222
                                       ********.*****************9987 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.1   2.8e-10   1.6e-06       7      92 ..      46     134 ..      42     158 .. 0.73

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 2.8e-10
                           Fer4_14   7 gCnlsCkgCdnketwks......elgkpqteelleqilkdlkkseikiqglvltG.GePLhyenkkellklvkrlke 76 
                                       +Cn++Ck C + ++  +      +++    +e le+  + l+++ + i+ + + G G+PL  +n++++ +  k +ke
  gi|298675037|ref|YP_003726787.1|  46 KCNIQCKYCIRDNDCVNecrpgvTSKVLTPQEALEKTRQVLEEHPF-IKVIAIAGpGDPL--ANDETF-ETFKLIKE 118
                                       8******999555444425555566666667777666656677777.888**********..666665.55699*** PP

                           Fer4_14  77 eypekkiwletngtle 92 
                                       e+p++ i + tng++ 
  gi|298675037|ref|YP_003726787.1| 119 EFPNVIICMSTNGLAL 134
                                       *************875 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1     2e-08   0.00012      12      98 ..      44     136 ..      10     163 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2e-08
                           Fer4_12  12 vsgCnlsCkgCfnketwsfk.......sgkeftkelleeiiedlkk.esiegltllG.GEPllpenaeallelvkev 79 
                                       +  Cn++Ck+C+  +   ++       s+  +++e+le+  + l++ + i+ + + G G+Pl+  n+e++ e +k +
  gi|298675037|ref|YP_003726787.1|  44 APKCNIQCKYCIRDNDC-VNecrpgvtSKVLTPQEALEKTRQVLEEhPFIKVIAIAGpGDPLA--NDETF-ETFKLI 116
                                       458********955444.22244555344555699999999999854999*************..66665.56799* PP

                           Fer4_12  80 keekp.ekdiwlytgytlee 98 
                                       kee+p    +++++g  l +
  gi|298675037|ref|YP_003726787.1| 117 KEEFPnVIICMSTNGLALPD 136
                                       *****445566667766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       931  (0.051927); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1807.62
//
Query:       gi|298675038|ref|YP_003726788.1|  [L=328]
Description: methanogenesis marker protein 2 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-18   67.2   0.4    3.1e-18   66.2   0.4    1.5  1  AIRS      AIR synthase related protein, N-terminal domain
    2.9e-16   60.0   0.0    4.7e-16   59.3   0.0    1.3  1  AIRS_C    AIR synthase related protein, C-terminal domain


Domain annotation for each model (and alignments):
>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.2   0.4   3.5e-22   3.1e-18       1      93 [.      45     150 ..      45     151 .. 0.86

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 3.5e-22
                                       SSSEE.........EEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC...HHHHHHHHHHHH CS
                              AIRS   1 dDaav.........vvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp...wleevvrglaea 65 
                                       dDaav         ++++ds  ++++ +    +G++av +n++D+aamGArPla++++++ +    ++ +++g+ ++
  gi|298675038|ref|YP_003726788.1|  45 DDAAVididgndviLFAADSIWEKLMKASPWWAGYTAVLANVNDIAAMGARPLAMVDVISSSdkdSCNTLLKGITDG 121
                                       899944445555458888988888777665558******************************************** PP

                                       HHHTT-EEEEEEEEEESS.EEEEEEEEEE CS
                              AIRS  66 aeelgvplvgGdtsfsne.ptisvtavGl 93 
                                       ++++gvp+vgG+++ ++   +i+v+++G+
  gi|298675038|ref|YP_003726788.1| 122 IKKFGVPMVGGHLHPDTPySSIAVAIIGI 150
                                       **************996558899999998 PP

>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.3   0.0   5.2e-20   4.7e-16      38     150 ..     191     300 ..     163     305 .. 0.89

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 5.2e-20
                                       HHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHHHHHHTTTEEEEEECGTHHHHHHHHHHHHHHHCSTTTE CS
                            AIRS_C  38 lgdvlleptliyvkralaalkglvkaahDvTgGGLlgalaemapasgvgaeidldkvpifdelesplemllsensGr 114
                                         d++ ++++  v++ + ++ +l+++ +D+++ G +g+l ++++ s+vga +d+dk+p+ d + + ++ l++ +  +
  gi|298675038|ref|YP_003726788.1| 191 FKDPETVRNRYLVMQTIGEK-KLATSGKDISNPGTIGTLGMLCETSNVGASVDIDKIPFPDGV-ELEQWLKVYTATG 265
                                       67999999999999999997.****************************************99.77888889***** PP

                                       EEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESSS CS
                            AIRS_C 115 llvavppeeadavlaileeeglpeaavIGevtakee 150
                                       ++++v +e+ d+++++++++g+ +a+vIGe+ +  +
  gi|298675038|ref|YP_003726788.1| 266 YILTVNSENVDECIQVFNDAGI-TASVIGEINDTLK 300
                                       **********************.7*******98755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1950.39
//
Query:       gi|298675039|ref|YP_003726789.1|  [L=98]
Description: hypothetical protein Metev_1111 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.35s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 590.39
//
Query:       gi|298675040|ref|YP_003726790.1|  [L=448]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-27   96.2   0.2      3e-27   95.2   0.2    1.5  1  OrfB_IS605      Probable transposase
    7.6e-22   77.0   0.6    1.9e-21   75.8   0.6    1.7  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    5.8e-09   35.3   0.1    1.4e-08   34.1   0.1    1.6  1  HTH_OrfB_IS605  Helix-turn-helix domain
     0.0025   17.5   1.5          1    9.2   0.2    2.8  2  zinc_ribbon_2   zinc-ribbon domain
     0.0044   16.2   1.4     0.0074   15.5   1.4    1.3  1  RuvC_1          RuvC nuclease domain
  ------ inclusion threshold ------
      0.017   15.1   1.1      0.042   13.8   1.1    1.6  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
      0.037   13.6   0.2         10    5.7   0.0    2.6  2  TF_Zn_Ribbon    TFIIB zinc-binding
      0.087   12.8   0.6        8.5    6.4   0.1    2.5  2  Nudix_N_2       Nudix N-terminal
       0.11   12.0   1.2        5.3    6.6   0.2    2.7  2  zf-ribbon_3     zinc-ribbon domain
       0.13   12.3   0.7       0.37   10.8   0.7    1.8  1  DZR             Double zinc ribbon
        4.1    7.2   5.8         49    3.7   5.8    2.3  1  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.2   0.2   1.9e-30     3e-27       3     117 ..     207     318 ..     205     321 .. 0.97

  Alignments for each domain:
  == domain 1  score: 95.2 bits;  conditional E-value: 1.9e-30
                        OrfB_IS605   3 pvevevelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklar 79 
                                        ve+++++ + ++++a+giDlG++ ++t+++ d   f+  +r+l++++k+lake+++l++   ks+nykk+++k+ r
  gi|298675040|ref|YP_003726790.1| 207 TVELPENPVPSTPENAVGIDLGLKSFITTSNDD---FVEPPRFLRKAEKRLAKEQRKLSRMEFKSNNYKKQKQKVNR 280
                                       68999999999**********************...***************************************** PP

                        OrfB_IS605  80 lhrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       +hrk++  r+h+ h l++ l+++++ ++ e+L+++n++
  gi|298675040|ref|YP_003726790.1| 281 IHRKVASARNHFSHCLSKLLVEKYDLIVFEDLKIKNLV 318
                                       ***********************************997 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.8   0.6   1.1e-24   1.9e-21       1      69 []     332     402 ..     332     402 .. 0.98

  Alignments for each domain:
  == domain 1  score: 75.8 bits;  conditional E-value: 1.1e-24
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke..alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       ++kl + + yka e+G+ v ++np +T + Cs+Cg k+ke  +l +r f+C++Cg+e+drD+nAa+Nil +
  gi|298675040|ref|YP_003726790.1| 332 WNKLVQHVTYKAAERGKIVDKINPDNTTQVCSHCGTKKKEklRLGDRIFYCSKCGLEIDRDLNAAVNILTK 402
                                       99******************************************************************975 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.1   8.6e-12   1.4e-08       5      44 ..      14      53 ..      12      55 .. 0.93

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 8.6e-12
                    HTH_OrfB_IS605  5 aykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayee 44
                                        ++ + PT eQe kl++t++ +R  +N+ L+ r + y +
  gi|298675040|ref|YP_003726790.1| 14 NLRFKIHPTLEQEKKLNETLEYCRSTWNHLLSIRVDLYDR 53
                                      6799******************************999975 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.2   0.00061         1       9      22 ..     354     368 ..     352     369 .. 0.74
   2 !    6.4   0.1    0.0048       7.8       1      10 [.     381     390 ..     381     395 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00061
                     zinc_ribbon_2   9 lqdnakF.CpyCGtp 22 
                                       ++dn +  C++CGt+
  gi|298675040|ref|YP_003726790.1| 354 NPDNTTQvCSHCGTK 368
                                       667666679999997 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0048
                     zinc_ribbon_2   1 fCpnCGaelq 10 
                                       +C++CG e++
  gi|298675040|ref|YP_003726790.1| 381 YCSKCGLEID 390
                                       7999998885 PP

>> RuvC_1  RuvC nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   1.4   4.5e-06    0.0074      60     210 ..     258     404 ..     223     410 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.5e-06
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            RuvC_1  60 relLderekerekarknWqkiekikelKegYlsqvvhkiaklaikynaivvlEdLnlgFkrgrqkvekqvyqkfEka 136
                                       + +L+++e + ++ +k+ qk+++i+    +  ++  h ++kl++++  ++v+EdL ++   + +k+ k++     ++
  gi|298675040|ref|YP_003726790.1| 258 QRKLSRMEFKSNNYKKQKQKVNRIHRKVASARNHFSHCLSKLLVEKYDLIVFEDLKIKNLVKNNKLAKSISDVSWNK 334
                                       578999999999999*********998888899999***************************************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            RuvC_1 137 LidklnylvdkkkkeeeaggllkayqltakvesfeklgkqaG.ilfyvpaayTkklslpedadaNgayniarkgl 210
                                       L++++ y + +  k  ++ +  ++ q+ ++  + +k +   G  +fy      +k+ l++d d N+a ni  k  
  gi|298675040|ref|YP_003726790.1| 335 LVQHVTYKAAERGKIVDKINPDNTTQVCSHCGTKKKEKLRLGdRIFYC-----SKCGLEIDRDLNAAVNILTKSS 404
                                       ***********9999999***********9988887776666246665.....6789999999999999988865 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.1   2.5e-05     0.042      18      44 ..     359     386 ..     355     388 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.5e-05
                     Zn_Tnp_IS1595  18 gfvCPhCgsr..kayriktrglfqCkeCr 44 
                                       ++vC hCg +  +  r+ + + f C++C+
  gi|298675040|ref|YP_003726790.1| 359 TQVCSHCGTKkkEKLRLGD-RIFYCSKCG 386
                                       589*******777777777.********7 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.011        17      14      27 ..     354     367 ..     349     372 .. 0.86
   2 ?    5.7   0.0    0.0063        10      20      32 ..     380     392 ..     378     395 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.011
                                       ETSTTCEEESSSSB CS
                      TF_Zn_Ribbon  14 DpergelvCtdCGl 27 
                                       +p++++ vC+ CG+
  gi|298675040|ref|YP_003726790.1| 354 NPDNTTQVCSHCGT 367
                                       6899999******7 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0063
                                       EEESSSSBEEEEC CS
                      TF_Zn_Ribbon  20 lvCtdCGlVledn 32 
                                       ++C++CGl ++ +
  gi|298675040|ref|YP_003726790.1| 380 FYCSKCGLEIDRD 392
                                       79******99865 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1    0.0052       8.5       3      18 ..     362     377 ..     360     379 .. 0.85
   2 ?    4.0   0.0     0.029        47       2      11 ..     381     390 ..     380     395 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0052
                                       -TTT--B-EEE--TT- CS
                         Nudix_N_2   3 CsqCGtpvelripdgD 18 
                                       Cs+CGt+ + ++  gD
  gi|298675040|ref|YP_003726790.1| 362 CSHCGTKKKEKLRLGD 377
                                       9999999998888887 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.029
                                       B-TTT--B-E CS
                         Nudix_N_2   2 FCsqCGtpve 11 
                                       +Cs+CG ++ 
  gi|298675040|ref|YP_003726790.1| 381 YCSKCGLEID 390
                                       9*****7765 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.2    0.0032       5.3      17      25 ..     360     368 ..     352     370 .. 0.76
   2 ?    3.1   0.0     0.042        68       4       9 ..     381     386 ..     380     393 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0032
                       zf-ribbon_3  17 nvCpyCGtk 25 
                                       +vC +CGtk
  gi|298675040|ref|YP_003726790.1| 360 QVCSHCGTK 368
                                       678888875 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.042
                       zf-ribbon_3   4 rCPnCG 9  
                                       +C++CG
  gi|298675040|ref|YP_003726790.1| 381 YCSKCG 386
                                       688887 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.7   0.00023      0.37      11      40 ..     358     391 ..     351     398 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00023
                               DZR  11 darfCseCgtklkavaa....edrCpsCgekvdp 40 
                                         ++Cs+Cgtk k+  +       C++Cg ++d 
  gi|298675040|ref|YP_003726790.1| 358 TTQVCSHCGTKKKEKLRlgdrIFYCSKCGLEIDR 391
                                       4567777777766555566656667777766655 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   5.8      0.03        49       2      30 ..     358     388 ..     357     389 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.03
                     zf-NADH-PPase   2 thrFCgrCGapte..paeggwarvCpaCgle 30 
                                       t++ C++CG++ +  +  g++   C+ Cgle
  gi|298675040|ref|YP_003726790.1| 358 TTQVCSHCGTKKKekLRLGDRIFYCSKCGLE 388
                                       8999*****9865114455777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1380  (0.0769703); expected 358.6 (0.02)
Passed bias filter:                      640  (0.0356964); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.66u 0.35s 00:00:01.01 Elapsed: 00:00:01.23
# Mc/sec: 1102.24
//
Query:       gi|298675041|ref|YP_003726791.1|  [L=134]
Description: hypothetical protein Metev_1113 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-28   99.6   0.1    1.6e-28   99.3   0.1    1.1  1  TrmO      tRNA-methyltransferase O


Domain annotation for each model (and alignments):
>> TrmO  tRNA-methyltransferase O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.3   0.1   9.2e-33   1.6e-28      12     117 ..      29     128 ..      23     130 .. 0.93

  Alignments for each domain:
  == domain 1  score: 99.3 bits;  conditional E-value: 9.2e-33
                                       -EEEEEE-HHH..HGGGTTGGG-SEEEEEEE-TTS...-.SS--E-TT-.SS-E.EGGGS--S-SSS-EEEEEEEEE CS
                              TrmO  12 aeaeielepeynseealegleefshlwllfvfhenaekklkakvrpprlggnervGvfatRsphRpnpiglsvvkle 88 
                                       + ++i + +e+  +++l  +++f++l ++f+f++    +  ++++++r++g  r Gvfa+R+p+Rpn ig+++vkle
  gi|298675041|ref|YP_003726791.1|  29 SVSKIIIYDEF--KDGLYRVTDFDRLEVIFYFDKF---NNYELIQKRRIDG-IRAGVFASRTPKRPNGIGITTVKLE 99 
                                       56789999999..9*******************88...34789*******9.788********************** PP

                                       EEETTEEEEES----TT-EEEEEEE--HH CS
                              TrmO  89 kvegnvlevsgvDlldgtpvlDiKPYvpy 117
                                       kv +n+l+v+g+D+ld+tpvlDiKPYv++
  gi|298675041|ref|YP_003726791.1| 100 KVVDNILHVKGLDALDKTPVLDIKPYVES 128
                                       ***************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 773.98
//
Query:       gi|298675042|ref|YP_003726792.1|  [L=267]
Description: hypothetical protein Metev_1114 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.2e-20   70.5   0.2    1.9e-19   69.6   0.2    1.6  1  DUF1724   Domain of unknown function (DUF1724)
    0.00085   19.3   2.0     0.0017   18.3   0.2    2.4  3  HTH_45    Winged helix-turn-helix
     0.0069   16.3   0.2      0.021   14.8   0.1    1.8  2  MarR      MarR family
  ------ inclusion threshold ------
      0.016   15.0   0.1       0.03   14.2   0.1    1.5  1  HTH_5     Bacterial regulatory protein, arsR family
      0.035   14.0   0.1      0.081   12.9   0.1    1.7  1  HTH_11    HTH domain
      0.036   12.9   0.0      0.064   12.0   0.0    1.3  1  WAPL      Wings apart-like protein regulation of heterochroma
      0.081   13.1   0.0       0.27   11.4   0.0    2.0  1  HTH_34    Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> DUF1724  Domain of unknown function (DUF1724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.6   0.2   7.3e-23   1.9e-19       4      61 ..     199     256 ..     196     257 .. 0.96

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 7.3e-23
                           DUF1724   4 yvydeeikplsltvtDkflslslfdkdgkydhkdlisfdesAlkWGeeLFeyYlkrSe 61 
                                        +y++e++ +s+ v+Dk ++l+l+dk+gk+ hk++is+d+sA+kWG+eL +yY + S+
  gi|298675042|ref|YP_003726792.1| 199 LLYNDEMGVASILVSDKLTYLNLLDKNGKFNHKKIISYDDSAVKWGQELVQYYTNIST 256
                                       68*****************************************************998 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.2   6.6e-07    0.0017      15      72 ..      22      79 ..      17      84 .. 0.88
   2 ?   -3.1   0.0       3.2   8.3e+03       6      25 ..     127     145 ..     126     147 .. 0.65
   3 ?   -1.8   0.0       1.2   3.2e+03      39      51 ..     218     230 ..     212     256 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 6.6e-07
                            HTH_45 15 isegeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlelleklkel 72
                                      +s+g ++   i  k n + + +   +++L e+ li k++e Y lTe G+ +++kl  +
  gi|298675042|ref|YP_003726792.1| 22 LSKGPQNRDDIRNKLNVTSSSIMPQIKILEENYLIVKENEYYHLTEIGKAIVDKLIPF 79
                                      467888889999999999999*******************************998655 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.2
                            HTH_45   6 eIiadILeaisegeakkTki 25 
                                       eI  ++L+ + +++++ T+i
  gi|298675042|ref|YP_003726792.1| 127 EIPQELLDGL-KESNSVTAI 145
                                       6777777777.556666665 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.2
                            HTH_45  39 YLdmLvekglikk 51 
                                       YL+ L ++g  ++
  gi|298675042|ref|YP_003726792.1| 218 YLNLLDKNGKFNH 230
                                       8888877775533 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1     8e-06     0.021       9      48 ..      18      57 ..      16      60 .. 0.92
   2 ?   -3.3   0.0       3.4   8.8e+03       8      20 ..     105     117 ..     104     119 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 8e-06
                                      HHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR  9 LrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                      L++l ++gp++  ++ +kl+v++s++  +++ Le++ li 
  gi|298675042|ref|YP_003726792.1| 18 LMLLLSKGPQNRDDIRNKLNVTSSSIMPQIKILEENYLIV 57
                                      889999****************************997775 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.4
                                       HHHHHHHSTTEEH CS
                              MarR   8 iLrilyeqgplsv 20 
                                       +L+ ++e g+ ++
  gi|298675042|ref|YP_003726792.1| 105 LLTRIRELGDYKI 117
                                       6788888887665 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.2e-05      0.03       2      42 ..      13      53 ..      12      58 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.2e-05
                                      HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHT CS
                             HTH_5  2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLrea 42
                                       +R  ++ lL++g++   ++ ++l+++ s +  + k+L+e 
  gi|298675042|ref|YP_003726792.1| 13 DKRKNLMLLLSKGPQNRDDIRNKLNVTSSSIMPQIKILEEN 53
                                      6899**********************************996 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   3.2e-05     0.081       8      48 ..      19      58 ..      14      64 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.2e-05
                            HTH_11  8 lLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIes 48
                                      +Ll ++gp + +++  +Lnv+ + +   Ik+Lee  + I++
  gi|298675042|ref|YP_003726792.1| 19 MLLLSKGPQNRDDIRNKLNVTSSSIMPQIKILEEN-YLIVK 58
                                      45578888999**********************98.35554 PP

>> WAPL  Wings apart-like protein regulation of heterochromatin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.5e-05     0.064     216     272 ..      28      83 ..      10     146 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.5e-05
                              WAPL 216 a..kkdtrsdetlsllerclsvLEnvtflseenqayllrlkkkqlvikliklLqdissq 272
                                       +  + +++ + t+s +   +++LE   +  +en+ y+l+  +k +v+kli +L+     
  gi|298675042|ref|YP_003726792.1|  28 NrdDIRNKLNVTSSSIMPQIKILEENYLIVKENEYYHLTEIGKAIVDKLIPFLET---L 83 
                                       3356777777889999999**********************************73...3 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00011      0.27       9      46 ..      21      57 ..      16      83 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                            HTH_34  9 LasvdeadfvelkealeatdgnLsvhlkkLekagYiev 46
                                      L+s+   +  +++++l++t++ +  ++k+Le++ Y+ v
  gi|298675042|ref|YP_003726792.1| 21 LLSKGPQNRDDIRNKLNVTSSSIMPQIKILEEN-YLIV 57
                                      55555566689********************86.5544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1621.35
//
Query:       gi|298675043|ref|YP_003726793.1|  [L=241]
Description: hypothetical protein Metev_1115 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-25   88.4   0.1    5.7e-25   87.8   0.1    1.3  1  Thg1      tRNAHis guanylyltransferase
      7e-10   39.1   1.0      1e-09   38.6   1.0    1.2  1  Thg1C     Thg1 C terminal domain


Domain annotation for each model (and alignments):
>> Thg1  tRNAHis guanylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.8   0.1   6.3e-29   5.7e-25       4     124 ..       1     118 [.       1     119 [. 0.94

  Alignments for each domain:
  == domain 1  score: 87.8 bits;  conditional E-value: 6.3e-29
                              Thg1   4 vkefeqddkllpntlivvRiDGrgFhkfskkhkfekPnDeralklmneaakelvkefe.divlaYgqSDEislvlsk 79 
                                       +k+ e   +l    +++vRiDGr+F+k  +++++ekP+D++++++m++a + ++k+   ++v+aY++SDEi+l +++
  gi|298675043|ref|YP_003726793.1|   1 MKKREIYADLRCAPPLIVRIDGRNFKKTLSRQNLEKPYDKKFASAMTDAIELFLKKSGiSPVFAYSFSDEINLFFDD 77 
                                       677887888888999****************************************99669***************** PP

                              Thg1  80 etklynrraqklvslvaslftaafvkllskafeelpsFDarvvly 124
                                        t  +++r++kl s++ s++++a ++++ +      sFD+r+v++
  gi|298675043|ref|YP_003726793.1|  78 IT--FDGRVEKLDSVIPSFLSSALTMQMDSDEP--LSFDSRIVPL 118
                                       99..*************************9987..8******986 PP

>> Thg1C  Thg1 C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   1.0   1.1e-13     1e-09       2      82 ..     122     200 ..     121     224 .. 0.84

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 1.1e-13
                             Thg1C   2 nlrDYlsWRqvDchinnlYNttFWalvqkgglteqeaeeeLkgtlskdkneiLfsefginYnnepeifrkGsvlvre 78 
                                       ++ +Y+ WRq ++  n +    +++l+  +g +e+ea +++kg  s+d +e+Lf++ gin ++ p+ +r+G +++++
  gi|298675043|ref|YP_003726793.1| 122 QISEYMVWRQSEAWRNCINSYGYYTLL-SEGWSENEAARHMKGLKSSDIHEMLFKR-GINLAKVPQWHRRGIMVYKT 196
                                       6889*********99888888899999.89************************87.9*************999997 PP

                             Thg1C  79 keke 82 
                                       k + 
  gi|298675043|ref|YP_003726793.1| 197 KYEI 200
                                       6554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1484.58
//
Query:       gi|298675044|ref|YP_003726794.1|  [L=89]
Description: PRC-barrel domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-14   54.2   1.8    1.5e-14   53.8   1.8    1.1  1  PRC       PRC-barrel domain


Domain annotation for each model (and alignments):
>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.8   1.8   8.6e-19   1.5e-14       5      73 ..       4      73 ..       2      77 .. 0.92

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 8.6e-19
                                      CS---TT-EEEETTSSEEEEEEEEEEETTTTEEEEEEEEETTT.......-EEEEEGG.CEECCCTEEEET CS
                               PRC  5 rasdliGkeVytedGeklGkVkDvvidekegrvralvvsvggflgi..gekevliPfdlavkigkdriivd 73
                                      ++s+l G+ Vyt+ G+++Gk++D+v+d ++ +v++l +s+ ++  +    k v+iP++ +v + +d++i++
  gi|298675044|ref|YP_003726794.1|  4 EISSLFGLNVYTNAGTYVGKISDMVLDVNNRKVTGLAISDINREIFdvPTKGVIIPYR-WVVTSGDIVIIR 73
                                      589****************************************555************.888888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 556.25
//
Query:       gi|298675045|ref|YP_003726795.1|  [L=307]
Description: malate dehydrogenase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-39  135.4   0.4    2.2e-39  134.8   0.4    1.3  1  Ldh_1_N         lactate/malate dehydrogenase, NAD binding dom
    2.4e-30  105.6   0.0    4.1e-30  104.9   0.0    1.3  1  Ldh_1_C         lactate/malate dehydrogenase, alpha/beta C-te
    0.00045   19.9   1.8      0.002   17.7   1.7    2.0  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
     0.0022   17.6   0.7      0.013   15.1   0.1    2.5  3  Glyco_hydro_4   Family 4 glycosyl hydrolase
     0.0048   15.9   0.1     0.0087   15.1   0.1    1.4  1  3Beta_HSD       3-beta hydroxysteroid dehydrogenase/isomerase
  ------ inclusion threshold ------
      0.064   13.8   0.2       0.46   11.1   0.0    2.2  2  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
       0.12   11.7   0.2       0.23   10.8   0.2    1.4  1  ThiF            ThiF family


Domain annotation for each model (and alignments):
>> Ldh_1_N  lactate/malate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.8   0.4   8.6e-43   2.2e-39       1     141 []       2     141 ..       2     141 .. 0.98

  Alignments for each domain:
  == domain 1  score: 134.8 bits;  conditional E-value: 8.6e-43
                                       EEEEEETTTSHHHHHHHHHHHHTTSSSEEEEE-SSHHHHHHHHHHHHHCHCCSTS-EEEEE.SSGGGGTTESEEEE- CS
                           Ldh_1_N   1 vkvavvGaaGgiGqslalllankkladelaLlDiakekleGvaldlshistflsvkvkvse.keeealkdadvvvit 76 
                                       +k++v+Ga G++G++    la+ +l+d +++ Di +   +G+ ldl + +  +  ++ +++ +++++++++dvvv+t
  gi|298675045|ref|YP_003726795.1|   2 TKISVIGA-GNVGATAVQRLAELELGD-IVMTDIIEGLPQGKSLDLMQSAPVMGYDTDITGtNDYKDIEGSDVVVVT 76 
                                       69******.******************.********************99999999999988*************** PP

                                       -S-SS-TTTTHHHHHHHHHHHHHHHHHHHHHHTTTSEEEE-SSSHHHHHHHHHHHHTS-GGGEEE CS
                           Ldh_1_N  77 agvprkpGetRddLlkvNakIvkeiveaiakvapnaivlvvsNPvdiltevlkkasglpkkrvig 141
                                       ag+prkpG++RddLl++Na+I+k+++e+i+ +ap+ +++ v+NP di+t+++ +++g++++rv+g
  gi|298675045|ref|YP_003726795.1|  77 AGMPRKPGMSRDDLLDKNANITKDVCENIKTHAPDSTIITVTNPLDIMTYAALEVTGFEHNRVFG 141
                                       ***************************************************************98 PP

>> Ldh_1_C  lactate/malate dehydrogenase, alpha/beta C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.9   0.0   1.6e-33   4.1e-30       2     162 ..     145     304 ..     144     306 .. 0.95

  Alignments for each domain:
  == domain 1  score: 104.9 bits;  conditional E-value: 1.6e-33
                                       HHHHHHHHHHHHHHHTS-GGGEE--EEBSSST..........ETTEEHHHHHTTSTTSTHHHHHHHHHHHHHHHHHH CS
                           Ldh_1_C   2 tLDivRaktflaekagvtprsvkvtViGgHsg..........vtiipllsqvkellklsekqleeliervqnggdev 68 
                                        LD+ R++tf+a + g + ++v+++V+GgH++          v +ip+      +  +se+ ++ l+er+ +gg+e+
  gi|298675045|ref|YP_003726795.1| 145 VLDSSRFETFIAMELGCSIQDVNAMVLGGHGDlmvplpqystVSGIPI------TEIMSEDTINRLVERTIHGGAEI 215
                                       59*******************************999888877777777......557999***************** PP

                                       HHHHTTSSSS-HHHHHHHHHHHHHHHTTHTEEEEEEEEEESCCCECCSSEEEEEEEEEEETTEEEEE-------HHH CS
                           Ldh_1_C  69 vkakkGagsatlsmAvAgakfveallrdtkeilsagvyldgevglkdqeieyfsvPvvlgknGvekvleilklndfe 145
                                       v+  k +gsa+++  ++++k+v+++++d k+il+a++yl+ge+gl+d   +y++vPv lgk Gve ++e l l+d +
  gi|298675045|ref|YP_003726795.1| 216 VEHLK-EGSAFYAPSASIVKMVDSVVNDKKRILPAAAYLNGEYGLND---IYLGVPVKLGKGGVEDIIE-LDLTDDQ 287
                                       **876.8****************************************...9******************.******* PP

                                       HHHHHHHHHHHHHHHHH CS
                           Ldh_1_C 146 eekleksvkeLkkeiek 162
                                       ++kl +s +  k+ei k
  gi|298675045|ref|YP_003726795.1| 288 KQKLSQSGASVKEEIAK 304
                                       **************987 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   1.7   7.7e-07     0.002       2     119 ..       3     117 ..       2     129 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 7.7e-07
                                       EEEEE--STTHHHHHHHHHHCT.SEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHHHCHTTTEEEES-HHHHHHC- CS
                    UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeig.hevigvDideekvdklnsgkipiyepgLeelvkkavesgrlsfttdvekaveea 77 
                                       kisviG+G vG++    lae+   ++++ Di    ++ l +gk+     +L++       ++ +++t+d++  +e +
  gi|298675045|ref|YP_003726795.1|   3 KISVIGAGNVGATAVQRLAELElGDIVMTDI----IEGLPQGKSL----DLMQSAPVMGYDTDITGTNDYKD-IEGS 70 
                                       8*******************99789*****9....9999999974....555555555556789******99.**** PP

                                       SEEEE-----B-T...TTTCB-T.....HHHHHHHHHHHHHHHCEEEEEE CS
                    UDPG_MGDP_dh_N  78 dvifiaVgTPskk...kgkaaDl.....kyvesaarsiaealkkgkvvvv 119
                                       dv++++ g P k    +    Dl     +  ++++++i+ ++ + +++ v
  gi|298675045|ref|YP_003726795.1|  71 DVVVVTAGMPRKPgmsR---DDLldknaNITKDVCENIKTHAPDSTIITV 117
                                       ************95442...333222225678888888888888777755 PP

>> Glyco_hydro_4  Family 4 glycosyl hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.32   8.2e+02      71      92 ..      23      44 ..       3      86 .. 0.58
   2 !   15.1   0.1     5e-06     0.013     125     159 ..      99     133 ..      93     143 .. 0.87
   3 ?   -2.8   0.0       1.5   3.8e+03     119     142 ..     207     234 ..     185     246 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.32
                                      HTT-SEEEE---TTHHHHHHHH CS
                     Glyco_hydro_4 71 lkdadfVitairvGlekareid 92
                                      l+  d+V+t i  Gl + + +d
  gi|298675045|ref|YP_003726795.1| 23 LELGDIVMTDIIEGLPQGKSLD 44
                                      3444555555555544444444 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 5e-06
                                       HHHHHHHHHH-TTSEEEE-SSSHHHHHHHHHHHST CS
                     Glyco_hydro_4 125 leIakdieelcPdawvlnytNPaavvteallrlvp 159
                                        +++++i+  +Pd++++  tNP+ ++t a l +++
  gi|298675045|ref|YP_003726795.1|  99 KDVCENIKTHAPDSTIITVTNPLDIMTYAALEVTG 133
                                       699************************99987765 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHHHHHH....H-TTSEEEE CS
                     Glyco_hydro_4 119 rtipvlleIakdiee....lcPdawvln 142
                                       rti   +eI+++++e    ++P a +++
  gi|298675045|ref|YP_003726795.1| 207 RTIHGGAEIVEHLKEgsafYAPSASIVK 234
                                       6777777777777764444556665555 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   3.4e-06    0.0087       5     104 ..       8     106 ..       5     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.4e-06
                         3Beta_HSD   5 gaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk..viegDvtdkdkleealegvdvvihlaslvdv 79 
                                       gaG +G++ v++L +le l ++ + D+ e+ +  ++l  ++ +      +D+t +++ ++ +eg+dvv+++a++   
  gi|298675045|ref|YP_003726795.1|   8 GAGNVGATAVQRLAELE-LGDIVMTDIIEGLPQGKSLDLMQSAPvmGYDTDITGTNDYKD-IEGSDVVVVTAGMPRK 82 
                                       6799************9.8*******988766655555555554336789*****99865.8*************** PP

                         3Beta_HSD  80 agkltedeimkvnvkGTrnvleacv 104
                                        g+ ++d + + n + T+ v e  +
  gi|298675045|ref|YP_003726795.1|  83 PGMSRDD-LLDKNANITKDVCENIK 106
                                       **77666.88889999999988765 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00018      0.46       1      68 [.       3      76 ..       3      84 .. 0.73
   2 ?   -0.2   0.0      0.59   1.5e+03      74      97 .]      98     120 ..      94     120 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00018
                                      EEEEETTSHHHHHHHHHHHHTTS...-GGCEEEEEESSCCCHHHHHHHHC.....-EEECECHHHHHHH-SEEEE- CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaaga...qpheivvansrnpekaeelaeelg.....vkvtavdneeaaeeadvvvla 68
                                      ki +iGaGn+g++ +++l++        ++i+ +  ++ ++++ ++++        ++t+++  + +e +dvvv++
  gi|298675045|ref|YP_003726795.1|  3 KISVIGAGNVGATAVQRLAELELgdiVMTDIIEG-LPQGKSLDLMQSA-PvmgydTDITGTNDYKDIEGSDVVVVT 76
                                      799***************9987666777777766.5555655555433.334566777877777778888888876 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.59
                                       HHHHHHHCGHHHHTTSEEEEESSS CS
                     F420_oxidored  74 veevlselakdalkgklvisvlag 97 
                                       +++v++++ k    ++++i+v+++
  gi|298675045|ref|YP_003726795.1|  98 TKDVCENI-KTHAPDSTIITVTNP 120
                                       68999999.8889999****9996 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   8.8e-05      0.23      19      49 ..       2      32 ..       1      33 [. 0.95

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 8.8e-05
                                      SEEEEE--SHHHHHHHHHHHHHTTTEEEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 19 skvllvGaGglGsellknLalsGvgkltlvD 49
                                      +k+ ++GaG +G  +++ La + +g + ++D
  gi|298675045|ref|YP_003726795.1|  2 TKISVIGAGNVGATAVQRLAELELGDIVMTD 32
                                      5899*************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 1799.38
//
Query:       gi|298675046|ref|YP_003726796.1|  [L=124]
Description: hypothetical protein Metev_1118 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-42  144.5   0.0    1.7e-42  144.3   0.0    1.0  1  DHNA      Dihydroneopterin aldolase


Domain annotation for each model (and alignments):
>> DHNA  Dihydroneopterin aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.3   0.0   9.3e-47   1.7e-42       1     107 [.       9     116 ..       9     117 .. 0.98

  Alignments for each domain:
  == domain 1  score: 144.3 bits;  conditional E-value: 9.3e-47
                                       -HHHHHHHHHHHHHHHHHHHHTT-EESTTTHHHHHHHHHHHHHTSTTEEEEEEEE-S-..GGCC-S.TS-EE--TTT CS
                              DHNA   1 tdrerAvFEagiklgalyHqfvGtPvseesaeslekaieesielQPfvedvkvkidrekleeklee.fgYteLtgem 76 
                                       +d+e+AvFEagiklgalyHqf+G+P++ e+++slekai++si++QP+v+++kv+i+r++++++l+  fgY+eL+g m
  gi|298675046|ref|YP_003726796.1|   9 SDSEQAVFEAGIKLGALYHQFTGSPLTLETVDSLEKAISQSISVQPYVKNIKVTINRDMVRSRLNGeFGYCELEGCM 85 
                                       689************************************************************9988********** PP

                                       EEEEEEEEETTEEEEEEEEEETTTTEEEEEE CS
                              DHNA  77 ldveitvkyeeaevkarleyieeldYplmkv 107
                                       ldv ++++y+e+e+k++l+y+e+l+Yplmk+
  gi|298675046|ref|YP_003726796.1|  86 LDVVLDISYKEKEAKVSLKYDEKLNYPLMKI 116
                                       *****************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 758.55
//
Query:       gi|298675047|ref|YP_003726797.1|  [L=227]
Description: CDP-diacylglycerol/serine O-phosphatidyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-11   45.0   0.4    1.4e-11   45.0   0.4    3.5  3  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
  ------ inclusion threshold ------
      0.037   14.1   1.9       0.31   11.1   0.1    2.4  2  DUF4267          Domain of unknown function (DUF4267)
        5.7    6.4  29.9       0.85    9.1  25.2    2.0  2  ABC2_membrane_5  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.4   2.4e-15   1.4e-11       2      66 .]       9      71 ..       8      71 .. 0.92
   2 ?   -0.9   0.1       0.5     3e+03      26      42 ..      88     107 ..      73     123 .. 0.52
   3 ?   -3.3   8.6       2.7   1.6e+04       8      27 ..     153     177 ..     126     215 .. 0.51

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 2.4e-15
                                      -HHHHHHHHHHHHHHHHHGGGS-H..HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                   CDP-OH_P_transf  2 lPnaiTllrlllsvlailllltyyplvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                      +P++i++++ l++++a+l +l  ++  la++l+l a+++D+lDG++AR  ++  +lG+ lDslaD
  gi|298675047|ref|YP_003726797.1|  9 IPDLISISNALFGISAMLAVLDNNH-HLAAVLILTAAIADGLDGFIARYIES-GELGEHLDSLAD 71
                                      7****************98877777.9999999999999***********66.77*********9 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.5
                                       ......HHHHHHHHHHHHHTT CS
                   CDP-OH_P_transf  26 p....lvlailllliasltDa 42 
                                       +    + +++  +++++++++
  gi|298675047|ref|YP_003726797.1|  88 GsqfpY-VMMGAVFVYFICGI 107
                                       233432.22223334455554 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 2.7
                                       HHHHHHHHHHHHGGGS-H.......... CS
                   CDP-OH_P_transf   8 llrlllsvlailllltyyp........l 27 
                                       +l l+l   +il++ ty +        l
  gi|298675047|ref|YP_003726797.1| 153 ILTLIL---SILMISTYTYpkirgmktL 177
                                       222222...2222222222455555441 PP

>> DUF4267  Domain of unknown function (DUF4267)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   5.1e-05      0.31      47     101 ..      17      77 ..      10      88 .. 0.70
   2 ?    2.0   0.1     0.036   2.1e+02      41      59 ..     170     188 ..     164     213 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.1e-05
                           DUF4267  47 dlalGlallvlslqgnrralgvvlllgavvglgDalivwrqggaekt......aalghlvt 101
                                       +  +G+  ++++l+ n++ ++v++l +a+++  D++i +     e +      a ++ +++
  gi|298675047|ref|YP_003726797.1|  17 NALFGISAMLAVLDNNHHLAAVLILTAAIADGLDGFIARYIESGELGehldslADIISFGA 77 
                                       6678999999999************************944333233223444533444444 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.036
                           DUF4267  41 alkGvRdlalGlallvlsl 59 
                                       ++ G+ +la+G++++++ +
  gi|298675047|ref|YP_003726797.1| 170 KIRGMKTLAFGFVFFIIIV 188
                                       677999*********9987 PP

>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1      0.71   4.2e+03      29      29 ..      27      27 ..       9      46 .. 0.42
   2 ?    9.1  25.2   0.00014      0.85      23     134 ..      79     192 ..      68     218 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.71
                   ABC2_membrane_5 29 l 29
                                      +
  gi|298675047|ref|YP_003726797.1| 27 A 27
                                      1 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00014
                   ABC2_membrane_5  23 llaiiiliflndsvlli.fsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitl 98 
                                        ++ii++i++++ ++++ +++++ +i+   il + + + k +  k +  LP+t + +V + Yl+v+   ++++ i++
  gi|298675047|ref|YP_003726797.1|  79 PVVIIYAIYGSQFPYVMmGAVFVYFICG--ILRLARFNTKTNNIKDFEGLPITASGVVLASYLLVYQKYIFSSAIII 153
                                       4566777777777775514444444444..4899999***************************9987777777777 PP

                   ABC2_membrane_5  99 llliiavlikgnvtisev..llsiliglvialif.laiv 134
                                       l+li++ l+ +++t   +  ++++++g+v+++i+ ++ +
  gi|298675047|ref|YP_003726797.1| 154 LTLILSILMISTYTYPKIrgMKTLAFGFVFFIIIvGSYF 192
                                       777666666666554443214455555544444412222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       975  (0.0543812); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1379.59
//
Query:       gi|298675048|ref|YP_003726798.1|  [L=221]
Description: phosphatidylserine decarboxylase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.5e-27   93.9   0.3    3.4e-21   75.7   0.0    2.1  2  PS_Dcarbxylase  Phosphatidylserine decarboxylase
  ------ inclusion threshold ------
      0.075   13.2   0.1        1.5    9.1   0.1    2.6  2  Peptidase_M23   Peptidase family M23


Domain annotation for each model (and alignments):
>> PS_Dcarbxylase  Phosphatidylserine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   4.1e-07    0.0037       4      35 ..      45      76 ..      42      79 .. 0.90
   2 !   75.7   0.0   3.8e-25   3.4e-21      73     199 ..      80     198 ..      75     199 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.1e-07
                    PS_Dcarbxylase  4 ffvrklkdgaRpidddpgaivsPaDgrilqig 35
                                      f +++++d++R +++ ++++vsPaDg++  i+
  gi|298675048|ref|YP_003726798.1| 45 FSIWFFRDPVRHPKKCNKCMVSPADGKVIDIR 76
                                      789**********999999*********9886 PP

  == domain 2  score: 75.7 bits;  conditional E-value: 3.8e-25
                    PS_Dcarbxylase  73 vviyLspgdyHryhaPvsgkveerrhipGellsvnpsalkelrglftlneRvvlvie.wkGkvavvpvGatnvgsiv 148
                                       + i+++ +d+H+++ P +g++ +  + +G +l++  ++ ++       neR+ + i+ ++G+  v++++++++++i 
  gi|298675048|ref|YP_003726798.1|  80 ICIFMNFNDVHVNRTPLEGEIIKTSYTNGSFLPAFYKDSEK-------NERNEITIKtEYGNTKVTQIAGLIARRII 149
                                       789***************************99776655554.......6********559***************** PP

                    PS_Dcarbxylase 149 lnvlkgdelkkGeelGyFqfGStvvlvfeagkfieslvekgqkvkmGeklg 199
                                       ++v +gd +++G+++G++ fGS+v++ ++ +  ++     ++kv +Ge+++
  gi|298675048|ref|YP_003726798.1| 150 TYVDEGDLISQGQRIGMICFGSRVDVTVPDN--FDIVCDIKDKVTAGESII 198
                                       *****************************99..667888899999999986 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1   0.00017       1.5      34      72 ..     125     167 ..      57     178 .. 0.78
   2 ?   -1.5   0.0      0.34   3.1e+03      60      70 ..     188     198 ..     181     210 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00017
                                       EEEEEEEECTCEEEEEEEESEES....S-TTEEE-TTCEEEEE CS
                     Peptidase_M23  34 Gnvviidhgdgystlyahlskis....vkegqkVkaGqvIGtv 72 
                                         ++  + g+  +t +a l + +    v+eg+ +++Gq IG +
  gi|298675048|ref|YP_003726798.1| 125 EITIKTEYGNTKVTQIAGLIARRiityVDEGDLISQGQRIGMI 167
                                       33444444666667777766644456799************76 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.34
                                       TEEE-TTCEEE CS
                     Peptidase_M23  60 gqkVkaGqvIG 70 
                                       ++kV aG+ I 
  gi|298675048|ref|YP_003726798.1| 188 KDKVTAGESII 198
                                       68888888653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1608.84
//
Query:       gi|298675049|ref|YP_003726799.1|  [L=277]
Description: exosortase EpsH-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-11   44.0  18.1    2.6e-11   43.6  18.1    1.2  1  Exosortase_EpsH  Transmembrane exosortase (Exosortase_EpsH)
  ------ inclusion threshold ------
       0.26   11.0   0.5       0.88    9.3   0.1    2.0  2  DSX_dimer        Doublesex dimerisation domain


Domain annotation for each model (and alignments):
>> Exosortase_EpsH  Transmembrane exosortase (Exosortase_EpsH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6  18.1   2.9e-15   2.6e-11      67     254 ..      41     249 ..       4     251 .. 0.63

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 2.9e-15
                   Exosortase_EpsH  67 allgelsrvlllsalslv.lillglvllllG....................lralrlllfpllll.llalPlpavlv 121
                                       ++l+ l  +++ + + ++  i +g++++ll                     + ++  +  +++l  ++++P   + +
  gi|298675049|ref|YP_003726799.1|  41 WFLQPLHYIKINDYFNVTlTIGIGAFCILLSytmikeyrmspgestftsgsTDVTTMATIATALGsVFYFP--FSQI 115
                                       33333333333333333333333444444443344445777777777666644444445566666688888..5566 PP

                   Exosortase_EpsH 122 aqlslpLqllvaavagfllsllgipvereG.nviqlptgqveVaeaCsGlrsllallalglllallfrrrlw.krkl 196
                                       ++l+ +L+++v+++++++l+ lg+p+e+   n+i+l+ ++v +  aC+ ++s+      +l+ +l+++++++ k+ +
  gi|298675049|ref|YP_003726799.1| 116 PALNEWLITVVTQQVVWILHGLGYPAEMISwNLITLNGYTVKIILACTAIESI------ALFTGLIVAVTAPiKKLF 186
                                       88999*********************77666******************6665......555555555555546768 PP

                   Exosortase_EpsH 197 llllaavpiaflaNlvRilllvl..layhygpeaaegllH.....eiaGwllfgvalllllgllp 254
                                         ++++vp+++ +Nl+R ++ v+  + +++gp+++ + +H      +aG++l++ +++++l++lp
  gi|298675049|ref|YP_003726799.1| 187 TAFMVSVPVIYGLNLFRDVFVVVayAYQWFGPNSF-DIAHhfiakSGAGVVLLV-IAFIVLRILP 249
                                       8999*************8888551155678*****.888844443344444444.4477777776 PP

>> DSX_dimer  Doublesex dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1      0.29   2.6e+03       9      27 ..      33      49 ..      29      52 .. 0.69
   2 ?    9.3   0.1   9.8e-05      0.88       8      23 ..     130     145 ..     125     154 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.29
                         DSX_dimer  9 qWlleklGyPWemmPlmyv 27
                                       Wll      W + Pl y+
  gi|298675049|ref|YP_003726799.1| 33 GWLLF--SVHWFLQPLHYI 49
                                      57764..346888888886 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 9.8e-05
                         DSX_dimer   8 aqWlleklGyPWemmP 23 
                                         W+l  lGyP em+ 
  gi|298675049|ref|YP_003726799.1| 130 VVWILHGLGYPAEMIS 145
                                       56************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 2245.85
//
Query:       gi|298675050|ref|YP_003726800.1|  [L=138]
Description: NUDIX hydrolase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.1e-20   71.0   0.0      1e-19   70.8   0.0    1.0  1  NUDIX     NUDIX domain
  ------ inclusion threshold ------
      0.034   13.6   0.0       0.13   11.8   0.0    1.8  2  DUF4916   Domain of unknown function (DUF4916)


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.8   0.0   1.2e-23     1e-19       4     125 ..       8     121 ..       5     128 .. 0.82

  Alignments for each domain:
  == domain 1  score: 70.8 bits;  conditional E-value: 1.2e-23
                                       EEEEEE.EEETTSEEEEEEESSSSTTT.EESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEE CS
                             NUDIX   4 ravgvv.llnekgevLlvrrskkpfpg.WelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpy 78 
                                        +v +v +ln+k  ++lv+r++ p +g ++lPgG+ve gEt e+A+ REl+EEtGl+ e ++llg    ++++++++
  gi|298675050|ref|YP_003726800.1|   8 LTVDAVtILNGK--IVLVKRKNPPYQGkFALPGGFVEIGETTENAVKRELKEETGLSGEIVKLLG----VYSDPDRD 78 
                                       578888899*99..*******999999889***********************************....77888888 PP

                                       EEEEEEEEEEEEEECSGCSSTSTTTEEEEEEEEHHHHHHHHTHCTHH CS
                             NUDIX  79 gdeheilyvfleevegelepndenevsevrwvpleellkeklaaesr 125
                                       ++ h +++++l  + g+  p ++ + ++++ ++++++  ++la ++ 
  gi|298675050|ref|YP_003726800.1|  79 PRGHTVSVCYL--LIGKGVPVADTDAKDIEVFDITKI--PELAFDHN 121
                                       889*******9..445555555677778888888888..44444444 PP

>> DUF4916  Domain of unknown function (DUF4916)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0     0.083   7.5e+02      55      79 ..      36      60 ..      10      66 .. 0.80
   2 ?   11.8   0.0   1.4e-05      0.13     108     144 ..      77     113 ..      70     131 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.083
                                      -EEEE--TT--HHHHHHHHHHHHH- CS
                           DUF4916 55 lvsGrvlyhetvreallrhiekdlG 79
                                      l  G v   et  +a+ r+++++ G
  gi|298675050|ref|YP_003726800.1| 36 LPGGFVEIGETTENAVKRELKEETG 60
                                      5567788889999999999887766 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 1.4e-05
                                       E-TT-EEEEEEEEEEB-S-----TTEEEEEEE-HHHH CS
                           DUF4916 108 tdprqhavslayvvpvaGdceprqdaleleWltpeea 144
                                        dpr h+vs++y++  +G   +  da ++e ++ ++ 
  gi|298675050|ref|YP_003726800.1|  77 RDPRGHTVSVCYLLIGKGVPVADTDAKDIEVFDITKI 113
                                       79*************9**999999**99999887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 951.92
//
Query:       gi|298675051|ref|YP_003726801.1|  [L=103]
Description: transcription termination factor Tfs [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-17   63.7  17.2    1.1e-17   63.6   5.1    3.1  3  TFIIS_C          Transcription factor S-II (TFIIS)
    2.7e-07   30.4  11.7    1.7e-06   27.8   2.4    3.2  3  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
    3.7e-05   23.3  11.5          2    8.2   0.2    4.1  4  zinc_ribbon_2    zinc-ribbon domain
      6e-05   22.8   7.7    0.00012   21.8   3.4    2.3  2  TackOD1          Thaumarchaeal output domain 1
    0.00058   19.7  15.6       0.35   10.8   0.7    4.1  4  zinc_ribbon_4    zinc-ribbon domain
     0.0019   18.3   9.1       0.42   10.8   2.6    3.9  3  Zn-ribbon_8      Zinc ribbon domain
     0.0022   17.9  12.2      0.014   15.3   2.1    2.7  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0022   17.6   9.9       0.52   10.0   0.0    3.4  3  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
      0.003   17.9   0.7      0.003   17.9   0.7    2.9  3  GFA              Glutathione-dependent formaldehyde-activatin
     0.0042   17.0   9.0      0.077   12.9   0.3    3.7  3  Nudix_N_2        Nudix N-terminal
     0.0079   16.2  15.8        1.8    8.7   0.4    4.2  4  zf-ACC           Acetyl-coA carboxylase zinc finger domain
  ------ inclusion threshold ------
      0.012   15.7  10.8       0.22   11.6   1.0    2.9  2  DZR              Double zinc ribbon
      0.023   14.9   9.3        3.2    8.0   2.6    3.2  3  zf-AN1           AN1-like Zinc finger
       0.04   14.1   8.9        0.6   10.3   8.9    2.3  1  FYVE             FYVE zinc finger
      0.042   13.3  14.1       0.19   11.2   3.7    3.6  3  zf-ribbon_3      zinc-ribbon domain
      0.055   13.5   9.0         33    4.5   9.0    2.5  1  zinc-ribbons_6   zinc-ribbons
      0.064   13.6   0.4      0.064   13.6   0.4    2.1  2  DUF3268          zinc-finger-containing domain
      0.076   13.7   6.2        2.9    8.7   0.2    2.8  3  zinc-ribbon_6    zinc-ribbon domain
      0.099   12.3   9.4        5.5    6.7   0.0    4.0  4  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.11   12.0  12.1       0.67    9.5   1.1    3.5  3  TF_Zn_Ribbon     TFIIB zinc-binding
       0.12   12.0   1.3      0.088   12.4   0.4    1.3  1  UCH_1            Ubiquitin carboxyl-terminal hydrolase
       0.14   12.4  13.1        0.2   11.9   2.2    3.0  2  IBR              IBR domain, a half RING-finger domain
       0.32   10.9   4.1         20    5.2   0.0    3.2  3  DUF951           Bacterial protein of unknown function (DUF95
       0.34   10.8  11.7        3.1    7.8   0.1    3.6  3  HalOD2           Halobacterial output domain 2
       0.49   10.1   9.4          6    6.7   0.1    3.5  3  Ribosomal_S27e   Ribosomal protein S27
       0.51   10.7   8.5        7.5    6.9   3.8    2.9  2  Rpr2             RNAse P Rpr2/Rpp21/SNM1 subunit domain
       0.61   10.1  10.7        9.3    6.3   5.5    2.7  2  HypA             Hydrogenase/urease nickel incorporation, met
       0.62   10.2  11.6        8.4    6.6   0.1    3.9  4  UPF0547          Uncharacterised protein family UPF0547
       0.86    9.5  11.1         22    5.0   0.2    4.1  4  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
       0.91    9.6  13.8          9    6.4   0.1    3.8  3  ADK_lid          Adenylate kinase, active site lid
        1.2    9.0  12.5          9    6.2   0.2    4.0  4  HscB_4_cys       Co-chaperone HscB tetracysteine metal bindin
        1.2    9.9  11.6       0.34   11.7   1.3    3.0  3  zinc_ribbon_15   zinc-ribbon family
        1.4    9.3  11.0          5    7.5   0.1    4.0  4  zf-LITAF-like    LITAF-like zinc ribbon domain
        1.6    8.9   9.4        3.5    7.8   0.3    3.1  2  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
        1.7    8.3   9.2        9.8    5.9   0.1    3.5  3  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
        1.9    8.3  13.4        2.1    8.2   0.1    3.5  3  zf-C2H2_11       zinc-finger C2H2-type
        3.3    8.5  15.6          7    7.5   0.1    3.7  4  zf-3CxxC_2       Zinc-binding domain
        4.6    7.1  20.4        1.6    8.5   1.8    4.2  4  Rubredoxin_2     Rubredoxin metal binding domain
          6    7.1   0.0          6    7.1   0.0    3.3  3  DiS_P_DiS        Bacterial Peptidase A24 N-terminal domain
        6.8    6.8  17.2        1.4    8.9   4.0    3.0  3  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
          7    6.7  10.1       0.66   10.0   0.7    2.8  2  Ogr_Delta        Ogr/Delta-like zinc finger
        7.8    6.3  14.2         29    4.5   0.0    4.1  4  A2L_zn_ribbon    A2L zinc ribbon domain


Domain annotation for each model (and alignments):
>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.2      0.19        83       3       8 ..       4       9 ..       2      11 .. 0.85
   2 ?    4.8   0.5     0.061        26      30      36 ..      19      25 ..      16      27 .. 0.65
   3 !   63.6   5.1   2.5e-20   1.1e-17       1      39 []      62     100 ..      62     100 .. 0.98

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.19
                           TFIIS_C 3 CpkCgs 8
                                     CpkC+s
  gi|298675051|ref|YP_003726801.1| 4 CPKCKS 9
                                     ****96 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.061
                           TFIIS_C 30 kCtkCgh 36
                                      kC kCgh
  gi|298675051|ref|YP_003726801.1| 19 KCRKCGH 25
                                      5666665 PP

  == domain 3  score: 63.6 bits;  conditional E-value: 2.5e-20
                           TFIIS_C   1 akCpkCgsreayffqlQtRsaDEpmtvfykCtkCghrWr 39 
                                       akC++Cg++ ay++ +Q+RsaDE++t+f+kCtkCg +Wr
  gi|298675051|ref|YP_003726801.1|  62 AKCQECGHTVAYWWLRQLRSADESETRFFKCTKCGATWR 100
                                       59************************************8 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   2.4   3.9e-09   1.7e-06       1      30 [.       1      26 [.       1      32 [. 0.89
   2 ?    1.1   0.2      0.89   3.8e+02       4       8 ..      64      68 ..      61      70 .. 0.86
   3 ?    6.5   0.1     0.018       7.7      16      29 ..      83      97 ..      79      98 .. 0.74

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 3.9e-09
                                      EEBESTTTSBEEEEECSCCCEEEESSSS-E CS
                    RNA_POL_M_15KD  1 lkFCpkCgNlLlpkedkegknfeCrqCgYe 30
                                      ++FCpkC++l+ p +   +    Cr+Cg +
  gi|298675051|ref|YP_003726801.1|  1 MEFCPKCKSLMFPVDNSMK----CRKCGHI 26
                                      99***********999999....****966 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.89
                                      ESTTT CS
                    RNA_POL_M_15KD  4 CpkCg 8 
                                      C++Cg
  gi|298675051|ref|YP_003726801.1| 64 CQECG 68
                                      88887 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.018
                                      CSCCCE.EEESSSS- CS
                    RNA_POL_M_15KD 16 dkegkn.feCrqCgY 29
                                      d++ ++ f C +Cg+
  gi|298675051|ref|YP_003726801.1| 83 DESETRfFKCTKCGA 97
                                      5556667******96 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.4     0.023        10      15      19 ..       3       7 ..       2      11 .. 0.77
   2 !    8.1   0.1    0.0053       2.3      11      21 ..      15      25 ..      12      26 .. 0.83
   3 ?    6.5   0.1     0.016       6.9       1       8 [.      63      70 ..      57      72 .. 0.68
   4 !    8.2   0.2    0.0047         2       1       7 [.      91      97 ..      88     101 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.023
                     zinc_ribbon_2 15 FCpyC 19
                                      FCp+C
  gi|298675051|ref|YP_003726801.1|  3 FCPKC 7 
                                      77777 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0053
                     zinc_ribbon_2 11 dnakFCpyCGt 21
                                      dn+  C +CG+
  gi|298675051|ref|YP_003726801.1| 15 DNSMKCRKCGH 25
                                      78888999997 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.016
                     zinc_ribbon_2  1 fCpnCGae 8 
                                      +C +CG++
  gi|298675051|ref|YP_003726801.1| 63 KCQECGHT 70
                                      56666665 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.0047
                     zinc_ribbon_2  1 fCpnCGa 7 
                                      +C++CGa
  gi|298675051|ref|YP_003726801.1| 91 KCTKCGA 97
                                      7888887 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   3.4   2.9e-07   0.00012      88     157 ..       2      72 ..       1      79 [. 0.81
   2 ?    2.9   0.1      0.18        76      95     112 ..      81      98 ..      77     102 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.9e-07
                           TackOD1  88 evCpkCkSidieeqelihhftCgnv...gpeeeflkegkleCpkCktkLrhiGvDYdrplevykCnsCkslfs 157
                                       e CpkCkS  +  ++++++ +Cg++   g+ ++f+ +++ e  + + ++ +  vD   p +  kC++C+++++
  gi|298675051|ref|YP_003726801.1|   2 EFCPKCKSLMFPVDNSMKCRKCGHIkgsGSSDTFVSRTEKE--NREVTVLEGEVDQGLPTTEAKCQECGHTVA 72 
                                       78**********************93333556676666544..556777788899999***********9876 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.18
                           TackOD1  95 SidieeqelihhftCgnv 112
                                       S+d +e+ ++++ +Cg++
  gi|298675051|ref|YP_003726801.1|  81 SADESETRFFKCTKCGAT 98 
                                       777788888888888865 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.2      0.29   1.2e+02       5       9 ..       4       8 ..       3      12 .. 0.68
   2 !    8.5   0.2    0.0043       1.8      25      34 ..      17      26 ..      13      26 .. 0.89
   3 ?    6.9   0.3     0.014         6      24      34 ..      60      70 ..      58      71 .. 0.87
   4 !   10.8   0.7   0.00083      0.35      26      36 .]      90     100 ..      84     100 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.29
                     zinc_ribbon_4 5 CpsCk 9
                                     Cp+Ck
  gi|298675051|ref|YP_003726801.1| 4 CPKCK 8
                                     66665 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0043
                     zinc_ribbon_4 25 kvrCskCghv 34
                                      +++C kCgh+
  gi|298675051|ref|YP_003726801.1| 17 SMKCRKCGHI 26
                                      68*******6 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.014
                     zinc_ribbon_4 24 vkvrCskCghv 34
                                      ++++C  Cgh+
  gi|298675051|ref|YP_003726801.1| 60 TEAKCQECGHT 70
                                      579*******7 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 0.00083
                     zinc_ribbon_4  26 vrCskCghvFr 36 
                                        +C+kCg+++r
  gi|298675051|ref|YP_003726801.1|  90 FKCTKCGATWR 100
                                       69********7 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.18        76      29      34 ..       4       9 ..       1      12 [. 0.80
   2 ?    5.0   0.1     0.063        27       7      14 ..      19      26 ..      17      40 .. 0.89
   3 !   10.8   2.6   0.00097      0.42       7      35 ..      63      98 ..      58     100 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.18
                       Zn-ribbon_8 29 CPeCgs 34
                                      CP+C+s
  gi|298675051|ref|YP_003726801.1|  4 CPKCKS 9 
                                      ****87 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.063
                       Zn-ribbon_8  7 rCeeCghe 14
                                      +C++Cgh 
  gi|298675051|ref|YP_003726801.1| 19 KCRKCGHI 26
                                      89999985 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00097
                       Zn-ribbon_8  7 rCeeCghefe.....vlqsisdap..ltaCPeCgse 35
                                      +C+eCgh+       +l+s+++++    +C +Cg++
  gi|298675051|ref|YP_003726801.1| 63 KCQECGHTVAywwlrQLRSADESEtrFFKCTKCGAT 98
                                      8************7777766633332445****985 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.4    0.0026       1.1      25      48 ..      14      36 ..       8      47 .. 0.79
   2 !   15.3   2.1   3.4e-05     0.014      29      56 ..      62      99 ..      52     103 .] 0.91

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0026
                    OrfB_Zn_ribbon 25 ayTSktCseCgsknkealsgrtfk 48
                                         S +C +Cg+++    s++tf+
  gi|298675051|ref|YP_003726801.1| 14 VDNSMKCRKCGHIKGS-GSSDTFV 36
                                      56899********998.6666665 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 3.4e-05
                    OrfB_Zn_ribbon 29 ktCseCgsknke..........alsgrtfkCpnCgfea 56
                                       +C eCg+++ +          + ++r fkC++Cg+++
  gi|298675051|ref|YP_003726801.1| 62 AKCQECGHTVAYwwlrqlrsadESETRFFKCTKCGATW 99
                                      68******************99999**********997 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   3.1     0.015       6.4      14      25 ..      14      25 ..       3      26 .. 0.68
   2 !   10.0   0.0    0.0012      0.52      19      29 ..      63      73 ..      57      73 .. 0.85
   3 ?    3.7   0.2      0.12        50      19      25 ..      91      97 ..      86     100 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.015
                                      SSS----SSS-- CS
                    DNA_RNApol_7kD 14 kgdpiRCkeCGh 25
                                         + +C++CGh
  gi|298675051|ref|YP_003726801.1| 14 VDNSMKCRKCGH 25
                                      44569******9 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0012
                                      --SSS-----B CS
                    DNA_RNApol_7kD 19 RCkeCGhRilY 29
                                      +C+eCGh + Y
  gi|298675051|ref|YP_003726801.1| 63 KCQECGHTVAY 73
                                      8******8876 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.12
                                      --SSS-- CS
                    DNA_RNApol_7kD 19 RCkeCGh 25
                                      +C++CG 
  gi|298675051|ref|YP_003726801.1| 91 KCTKCGA 97
                                      6888884 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.2     0.085        36      50      61 ..       2      13 ..       1      19 [. 0.79
   2 !   17.9   0.7     7e-06     0.003       4      61 ..      19      73 ..      16      81 .. 0.86
   3 ?    1.3   0.3         1   4.3e+02      44      58 ..      84      98 ..      75     101 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.085
                               GFA 50 sfCpeCgsplys 61
                                      +fCp+C s ++ 
  gi|298675051|ref|YP_003726801.1|  2 EFCPKCKSLMFP 13
                                      6*******9985 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 7e-06
                               GFA  4 hCsdCrkasgsaftanavvkaealellegelkeykktadsgnkvtrsfCpeCgsplys 61
                                      +C++C +++gs+ +  +v ++e+    + e+++ + + d+g + t+  C+eCg ++ +
  gi|298675051|ref|YP_003726801.1| 19 KCRKCGHIKGSGSSDTFVSRTEKE---NREVTVLEGEVDQGLPTTEAKCQECGHTVAY 73
                                      6*********99988888776654...468999999999**************99875 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 1
                               GFA 44 gnkvtrsfCpeCgsp 58
                                      +++ +   C +Cg++
  gi|298675051|ref|YP_003726801.1| 84 ESETRFFKCTKCGAT 98
                                      44555577****975 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2      0.19        81       2       7 ..       3       8 ..       2      11 .. 0.80
   2 ?    4.3   0.3     0.088        38      25      31 ..      20      26 ..      18      27 .. 0.75
   3 !   12.9   0.3   0.00018     0.077       3      30 ..      64      97 ..      64      99 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.19
                                     B-TTT- CS
                         Nudix_N_2 2 FCsqCG 7
                                     FC++C 
  gi|298675051|ref|YP_003726801.1| 3 FCPKCK 8
                                     999995 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.088
                                      ETTTTEE CS
                         Nudix_N_2 25 CpaCgti 31
                                      C +Cg+i
  gi|298675051|ref|YP_003726801.1| 20 CRKCGHI 26
                                      7888887 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 0.00018
                                      -TTT--B-E.....EE--TT-SS-EEE.ETTTTE CS
                         Nudix_N_2  3 CsqCGtpve.....lripdgDnreRlv.CpaCgt 30
                                      C++CG++v+     +   ++++++R+  C++Cg+
  gi|298675051|ref|YP_003726801.1| 64 CQECGHTVAywwlrQLRSADESETRFFkCTKCGA 97
                                      ********98887444558999999755****97 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.2     0.043        18       4      12 ..       4      12 ..       4      13 .. 0.84
   2 ?    4.3   0.5     0.098        42       3      10 ..      19      26 ..      18      26 .. 0.85
   3 ?    7.0   0.2     0.015       6.2       3      11 ..      63      71 ..      62      73 .. 0.89
   4 !    8.7   0.4    0.0041       1.8       1      10 [.      89      98 ..      89      98 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.043
                            zf-ACC  4 CpsCgemly 12
                                      Cp+C+++++
  gi|298675051|ref|YP_003726801.1|  4 CPKCKSLMF 12
                                      999999875 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.098
                            zf-ACC  3 KCpsCgem 10
                                      KC +Cg++
  gi|298675051|ref|YP_003726801.1| 19 KCRKCGHI 26
                                      9****986 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.015
                            zf-ACC  3 KCpsCgeml 11
                                      KC +Cg+++
  gi|298675051|ref|YP_003726801.1| 63 KCQECGHTV 71
                                      9*****998 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.0041
                            zf-ACC  1 WtKCpsCgem 10
                                      ++KC++Cg++
  gi|298675051|ref|YP_003726801.1| 89 FFKCTKCGAT 98
                                      79******85 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.0   0.00051      0.22      13      36 ..       2      25 ..       1      32 [. 0.74
   2 ?    7.1   3.1     0.013       5.7      10      37 ..      59      98 ..      54     103 .] 0.62

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00051
                               DZR 13 rfCseCgtklkavaaedrCpsCge 36
                                      +fC++C++ + +v ++ +C +Cg+
  gi|298675051|ref|YP_003726801.1|  2 EFCPKCKSLMFPVDNSMKCRKCGH 25
                                      477777777777777777777776 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.013
                               DZR 10 pdarfCseCgtklkavaa.............edrCpsCgek 37
                                           C+eCg+++  +                 +C +Cg+ 
  gi|298675051|ref|YP_003726801.1| 59 TTEAKCQECGHTVA-YWWlrqlrsadesetrFFKCTKCGAT 98
                                      55667888888853.22245555566777766677777764 PP

>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   2.6    0.0075       3.2       1      21 [.       4      25 ..       3      26 .. 0.81
   2 ?    3.9   0.1      0.15        62      14      22 ..      62      70 ..      52      71 .. 0.76
   3 ?    6.1   0.1     0.029        12      10      21 ..      86      97 ..      79      99 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0075
                            zf-AN1  1 CsfksCkkkdflp...fkCryCgk 21
                                      C  ++Ck++ f +   +kCr+Cg+
  gi|298675051|ref|YP_003726801.1|  4 C--PKCKSLMFPVdnsMKCRKCGH 25
                                      4..48*****844778******96 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.15
                            zf-AN1 14 fkCryCgkv 22
                                       kC++Cg++
  gi|298675051|ref|YP_003726801.1| 62 AKCQECGHT 70
                                      79****986 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.029
                            zf-AN1 10 dflpfkCryCgk 21
                                      ++  fkC +Cg 
  gi|298675051|ref|YP_003726801.1| 86 ETRFFKCTKCGA 97
                                      5566******97 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   8.9    0.0014       0.6      11      66 ..       3      71 ..       1     101 [. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0014
                                      B-TTT--B--SSS--EE-TTT--EE-STTS-EEE.EEGGGTEEEEE.............EE-HHHHHHH CS
                              FYVE 11 kCeiCakkFsllrrrhhCrlCGkvvCekCssklvallekeaeeksv.............rvCkeClael 66
                                       C++C++    +     Cr CG++  +  s+++v+ +eke+ e  v               C+eC +++
  gi|298675051|ref|YP_003726801.1|  3 FCPKCKSLMFPVDNSMKCRKCGHIKGSGSSDTFVSRTEKENREVTVlegevdqglptteAKCQECGHTV 71
                                      6*****98888899*****************99999966555555577777777777776677776654 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   3.7   0.00044      0.19       2      24 ..       1      25 [.       1      26 [. 0.89
   2 ?    4.2   0.1     0.073        31       3      10 ..      62      69 ..      57      72 .. 0.65
   3 ?    3.4   0.4      0.13        55      18      24 ..      91      97 ..      90      98 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00044
                       zf-ribbon_3  2 tvrCPnCGa.p.lssddnvCpyCGt 24
                                      + +CP+C++   + +  ++C +CG+
  gi|298675051|ref|YP_003726801.1|  1 MEFCPKCKSlMfPVDNSMKCRKCGH 25
                                      679******867999999******6 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.073
                       zf-ribbon_3  3 vrCPnCGa 10
                                       +C +CG+
  gi|298675051|ref|YP_003726801.1| 62 AKCQECGH 69
                                      45666666 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.13
                       zf-ribbon_3 18 vCpyCGt 24
                                      +C++CG+
  gi|298675051|ref|YP_003726801.1| 91 KCTKCGA 97
                                      5888885 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   9.0     0.078        33       3      24 ..       4      25 ..       2     102 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.078
                                      -SSS-S--EE-SSEEE-TTT-- CS
                    zinc-ribbons_6  3 CpeCqqelekrgeqyhCeaCqe 24
                                      Cp+C++ +   +++++C++C +
  gi|298675051|ref|YP_003726801.1|  4 CPKCKSLMFPVDNSMKCRKCGH 25
                                      9999999998888899998876 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       2.1   8.8e+02       2      17 ..      17      32 ..      16      48 .. 0.65
   2 ?   13.6   0.4   0.00015     0.064       3      39 ..      62      98 ..      60     101 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 2.1
                           DUF3268  2 ttrCpyCGekvilvsa 17
                                      +++C+ CG+     s+
  gi|298675051|ref|YP_003726801.1| 17 SMKCRKCGHIKGSGSS 32
                                      5789999886555444 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.00015
                           DUF3268  3 trCpyCGekvilvsaseiYkerskgkllylCpkCday 39
                                       +C+ CG++v++   +++ ++ + ++ ++ C+kC+a 
  gi|298675051|ref|YP_003726801.1| 62 AKCQECGHTVAYWWLRQLRSADESETRFFKCTKCGAT 98
                                      68*********************************96 PP

>> zinc-ribbon_6  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.2    0.0067       2.9       4      41 ..       4      43 ..       2      55 .. 0.74
   2 ?    6.9   0.1     0.023       9.9      15      28 ..      61      74 ..      51      91 .. 0.77
   3 ?    0.5   0.2       2.4     1e+03       2       9 ..      90      97 ..      89     100 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0067
                     zinc-ribbon_6  4 CeqCgqllff..enssClkCgaalgfapeelellaleeae 41
                                      C +C++l+f   ++++C kCg+  g  ++++ ++  e+++
  gi|298675051|ref|YP_003726801.1|  4 CPKCKSLMFPvdNSMKCRKCGHIKGSGSSDTFVSRTEKEN 43
                                      99**999884335679*****9988777776666655554 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.023
                     zinc-ribbon_6 15 nssClkCgaalgfa 28
                                      + +C++Cg+++++ 
  gi|298675051|ref|YP_003726801.1| 61 EAKCQECGHTVAYW 74
                                      67899999999996 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 2.4
                     zinc-ribbon_6  2 feCeqCgq 9 
                                      f+C++Cg 
  gi|298675051|ref|YP_003726801.1| 90 FKCTKCGA 97
                                      77888875 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.059        25       4      11 ..       3      10 ..       1      15 [. 0.82
   2 ?    1.2   0.2      0.66   2.8e+02       3      10 ..      18      25 ..      16      26 .. 0.80
   3 ?    6.7   0.0     0.013       5.5       4      15 ..      63      74 ..      60      78 .. 0.82
   4 ?    3.7   0.2      0.11        46       3      10 ..      90      97 ..      88      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.059
                            zf_UBZ  4 lCerCgke 11
                                      +C++C++ 
  gi|298675051|ref|YP_003726801.1|  3 FCPKCKSL 10
                                      8****975 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.66
                            zf_UBZ  3 ylCerCgk 10
                                        C +Cg+
  gi|298675051|ref|YP_003726801.1| 18 MKCRKCGH 25
                                      57****96 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.013
                            zf_UBZ  4 lCerCgkeipes 15
                                       C++Cg+++  +
  gi|298675051|ref|YP_003726801.1| 63 KCQECGHTVAYW 74
                                      6******99755 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.11
                            zf_UBZ  3 ylCerCgk 10
                                      + C +Cg+
  gi|298675051|ref|YP_003726801.1| 90 FKCTKCGA 97
                                      89****97 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   3.9      0.03        13       3      27 ..       4      25 ..       2      41 .. 0.83
   2 ?    3.8   0.1     0.096        41       2       8 ..      63      69 ..      58      74 .. 0.63
   3 ?    9.5   1.1    0.0016      0.67       2      29 ..      63      99 ..      62     103 .] 0.76

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.03
                                      ETTTTCEECHEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon  3 CPnCgstnlveDpergelvCtdCGl 27
                                      CP+C+s ++ +D   + + C +CG 
  gi|298675051|ref|YP_003726801.1|  4 CPKCKSLMFPVD---NSMKCRKCGH 25
                                      ******766555...5589999997 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.096
                                      EETTTTC CS
                      TF_Zn_Ribbon  2 kCPnCgs 8 
                                      kC +Cg+
  gi|298675051|ref|YP_003726801.1| 63 KCQECGH 69
                                      4555555 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0016
                                      EETTTTCEE.C........HEETSTTCEEESSSSBEE CS
                      TF_Zn_Ribbon  2 kCPnCgstn.l........veDpergelvCtdCGlVl 29
                                      kC +Cg+t  +          + e+  + Ct+CG+ +
  gi|298675051|ref|YP_003726801.1| 63 KCQECGHTVaYwwlrqlrsADESETRFFKCTKCGATW 99
                                      89999998645999998844446666679*****866 PP

>> UCH_1  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.4   0.00021     0.088     136     201 ..      11      69 ..       5      84 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00021
                                       xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx.x RF
                             UCH_1 136 gtkaettirclkCgsek.srksstlvldlkyPkpsnekkeakvtfasilkssler.ekttrawCekC.k 201
                                        + + ++++c+kCg+ k s +s+t+v  +    + +e+     +  ++l+  +++   tt+a C++C +
  gi|298675051|ref|YP_003726801.1|  11 MFPVDNSMKCRKCGHIKgSGSSDTFVSRT----E-KEN-----REVTVLEGEVDQgLPTTEAKCQECgH 69 
                                       378999***********9********544....2.222.....33578888888866678999999944 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.2   0.00046       0.2      20      46 ..       3      25 ..       1      27 [. 0.88
   2 ?    3.6   3.5      0.19        80      20      45 ..      63      96 ..      33     101 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00046
                               IBR 20 wCprpdCeaiieksegcksvtCskCgf 46
                                       Cp  +C++++ + ++  s++C+kCg+
  gi|298675051|ref|YP_003726801.1|  3 FCP--KCKSLMFPVDN--SMKCRKCGH 25
                                      7*9..******99999..789****98 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.19
                               IBR 20 wCprpdCeaii........eksegcks..vtCskCg 45
                                      +C   +C++ +        ++ +++++   +C+kCg
  gi|298675051|ref|YP_003726801.1| 63 KCQ--ECGHTVaywwlrqlRSADESETrfFKCTKCG 96
                                      454..5555555555554422222111346677776 PP

>> DUF951  Bacterial protein of unknown function (DUF951)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.3     0.076        32      28      39 ..      15      26 ..       5      27 .. 0.89
   2 ?    5.2   0.0     0.048        20      32      40 ..      63      71 ..      59      77 .. 0.88
   3 ?    1.0   0.1      0.96   4.1e+02      31      38 ..      90      97 ..      88      99 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.076
                            DUF951 28 diklkClgcgre 39
                                      d  +kC +cg++
  gi|298675051|ref|YP_003726801.1| 15 DNSMKCRKCGHI 26
                                      6679******96 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.048
                            DUF951 32 kClgcgrev 40
                                      kC++cg+ v
  gi|298675051|ref|YP_003726801.1| 63 KCQECGHTV 71
                                      9******98 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.96
                            DUF951 31 lkClgcgr 38
                                      +kC++cg 
  gi|298675051|ref|YP_003726801.1| 90 FKCTKCGA 97
                                      59****95 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.029        12      33      45 ..      19      31 ..      16      37 .. 0.80
   2 ?    4.6   0.3     0.071        30      33      41 ..      63      71 ..      51      75 .. 0.85
   3 ?    7.8   0.1    0.0073       3.1      32      40 ..      90      98 ..      78     103 .] 0.80

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.029
                            HalOD2 33 kCtrCGevqaaAd 45
                                      kC +CG+++ + +
  gi|298675051|ref|YP_003726801.1| 19 KCRKCGHIKGSGS 31
                                      9******987755 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.071
                            HalOD2 33 kCtrCGevq 41
                                      kC +CG++ 
  gi|298675051|ref|YP_003726801.1| 63 KCQECGHTV 71
                                      899999986 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0073
                            HalOD2 32 WkCtrCGev 40
                                      +kCt+CG++
  gi|298675051|ref|YP_003726801.1| 90 FKCTKCGAT 98
                                      578888876 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   2.4      0.24     1e+02      27      35 ..      18      26 ..       3      30 .. 0.58
   2 ?    6.7   0.1     0.014         6      23      36 ..      58      71 ..      55      73 .. 0.74
   3 ?    3.2   0.1      0.16        70      26      35 ..      89      98 ..      84     100 .. 0.68

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.24
                                      EEESSSTCE CS
                    Ribosomal_S27e 27 vkCisCgkv 35
                                      +kC +Cg++
  gi|298675051|ref|YP_003726801.1| 18 MKCRKCGHI 26
                                      466666654 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.014
                                      -SS-EEESSSTCEE CS
                    Ribosomal_S27e 23 aatvvkCisCgkvL 36
                                      + t  kC+ Cg+++
  gi|298675051|ref|YP_003726801.1| 58 PTTEAKCQECGHTV 71
                                      56777888888877 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.16
                                      -EEESSSTCE CS
                    Ribosomal_S27e 26 vvkCisCgkv 35
                                        kC +Cg +
  gi|298675051|ref|YP_003726801.1| 89 FFKCTKCGAT 98
                                      5577777764 PP

>> Rpr2  RNAse P Rpr2/Rpp21/SNM1 subunit domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.2     0.066        28      46      60 ..       2      16 ..       1      19 [. 0.85
   2 ?    6.9   3.8     0.018       7.5      47      80 ..      19      68 ..      14      96 .. 0.59

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.066
                                      TB-TTT--B--CTTT CS
                              Rpr2 46 tvCkkCgsvlipgvt 60
                                      ++C kC+s++ p  +
  gi|298675051|ref|YP_003726801.1|  2 EFCPKCKSLMFPVDN 16
                                      69********99766 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.018
                                      B-TTT--B--CTTTEEEEEE-SSS-E............................ CS
                              Rpr2 47 vCkkCgsvlipgvtcsvrvenkskkkkkkkkka....................d 80
                                       C+kCg++  +g++ +   +  +k+++   + +                     
  gi|298675051|ref|YP_003726801.1| 19 KCRKCGHIKGSGSSDTFVSRT-EKENR---EVTvlegevdqglptteakcqecG 68
                                      5*******9999988887654.33222...222455788888866544444440 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   1.8     0.038        16      73      95 ..       4      26 ..       1      40 [. 0.76
   2 ?    6.3   5.5     0.022       9.3      67      94 ..      58      97 ..      11     102 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.038
                                      ETTTS-EEECHHHHHS-TTTSSS CS
                              HypA 73 CreCgkefeleekalrCpkCgsa 95
                                      C +C++ +   +++++C kCg+ 
  gi|298675051|ref|YP_003726801.1|  4 CPKCKSLMFPVDNSMKCRKCGHI 26
                                      99999777654456899999975 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.022
                                      E--EEEETTTS-EEECHH.HHH...........S-TTTSS CS
                              HypA 67 vpvkvrCreCgkefelee.kal...........rCpkCgs 94
                                         +++C+eCg+++     ++l           +C kCg+
  gi|298675051|ref|YP_003726801.1| 58 PTTEAKCQECGHTVAYWWlRQLrsadesetrffKCTKCGA 97
                                      4567788888888773322222556777888888888886 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.6      0.29   1.2e+02      14      20 ..       1       7 [.       1       9 [. 0.73
   2 ?    6.3   0.1     0.025        11      15      23 ..      18      26 ..      15      26 .. 0.83
   3 ?    6.6   0.1      0.02       8.4      15      22 ..      62      69 ..      54      72 .. 0.74
   4 ?   -0.3   0.1       2.8   1.2e+03      16      21 ..      91      96 ..      91     100 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.29
                           UPF0547 14 aqfCphC 20
                                      ++fCp C
  gi|298675051|ref|YP_003726801.1|  1 MEFCPKC 7 
                                      5678877 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.025
                           UPF0547 15 qfCphCGyv 23
                                       +C+ CG++
  gi|298675051|ref|YP_003726801.1| 18 MKCRKCGHI 26
                                      58*****95 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.02
                           UPF0547 15 qfCphCGy 22
                                       +C +CG+
  gi|298675051|ref|YP_003726801.1| 62 AKCQECGH 69
                                      57999998 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 2.8
                           UPF0547 16 fCphCG 21
                                      +C  CG
  gi|298675051|ref|YP_003726801.1| 91 KCTKCG 96
                                      588898 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1      0.11        47      14      23 ..       4      13 ..       2      16 .. 0.68
   2 ?    5.0   0.2     0.052        22      13      19 ..      19      25 ..      18      26 .. 0.86
   3 ?    2.0   0.3      0.47     2e+02      13      21 ..      63      71 ..      62      73 .. 0.82
   4 ?    3.9   0.1      0.12        50      13      19 ..      91      97 ..      82      99 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.11
                           DUF35_N 14 CpdCGtvqfP 23
                                      Cp+C ++ fP
  gi|298675051|ref|YP_003726801.1|  4 CPKCKSLMFP 13
                                      6666666666 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.052
                           DUF35_N 13 rCpdCGt 19
                                      +C++CG+
  gi|298675051|ref|YP_003726801.1| 19 KCRKCGH 25
                                      8*****8 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.47
                           DUF35_N 13 rCpdCGtvq 21
                                      +C  CG+ +
  gi|298675051|ref|YP_003726801.1| 63 KCQECGHTV 71
                                      8*****975 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.12
                           DUF35_N 13 rCpdCGt 19
                                      +C++CG+
  gi|298675051|ref|YP_003726801.1| 91 KCTKCGA 97
                                      7999997 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   4.8      0.28   1.2e+02       4      28 ..       4      24 ..       3      26 .. 0.68
   2 ?    6.4   0.1     0.021         9      17      29 ..      57      69 ..      52      72 .. 0.86
   3 ?    4.0   0.1      0.12        51       4      11 ..      92      99 ..      90     102 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.28
                                      -TTT--EEETTTB--SSTTB-TTT- CS
                           ADK_lid  4 CpkCGrsYhvvfnpPkveglCDkCG 28
                                      CpkC+      + p  + ++C kCG
  gi|298675051|ref|YP_003726801.1|  4 CPKCKSL----MFPVDNSMKCRKCG 24
                                      6666642....2356799******9 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.021
                                      --SSTTB-TTT-- CS
                           ADK_lid 17 pPkveglCDkCGe 29
                                       P +e +C +CG 
  gi|298675051|ref|YP_003726801.1| 57 LPTTEAKCQECGH 69
                                      5899********7 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.12
                                      -TTT--EE CS
                           ADK_lid  4 CpkCGrsY 11
                                      C kCG+++
  gi|298675051|ref|YP_003726801.1| 92 CTKCGATW 99
                                      89999885 PP

>> HscB_4_cys  Co-chaperone HscB tetracysteine metal binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.2     0.021         9      19      26 ..       3      10 ..       2      10 .. 0.87
   2 ?    5.9   0.1     0.026        11       2      18 ..      19      35 ..      19      36 .. 0.87
   3 ?    0.8   0.4         1   4.3e+02       3      10 ..      64      71 ..      63      74 .. 0.78
   4 ?    2.0   0.2      0.44   1.9e+02       3       8 ..      92      97 ..      82     101 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.021
                                      B-TTT--B CS
                        HscB_4_cys 19 FCpqCRAL 26
                                      FCp+C  L
  gi|298675051|ref|YP_003726801.1|  3 FCPKCKSL 10
                                      *****876 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.026
                                      B-SSS--B--SS-S--- CS
                        HscB_4_cys  2 rCWnCGgpgapgrgdef 18
                                      +C +CG+  + g  d f
  gi|298675051|ref|YP_003726801.1| 19 KCRKCGHIKGSGSSDTF 35
                                      599****9999999987 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 1
                                      -SSS--B- CS
                        HscB_4_cys  3 CWnCGgpg 10
                                      C  CG+  
  gi|298675051|ref|YP_003726801.1| 64 CQECGHTV 71
                                      889**976 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.44
                                      -SSS-- CS
                        HscB_4_cys  3 CWnCGg 8 
                                      C +CG 
  gi|298675051|ref|YP_003726801.1| 92 CTKCGA 97
                                      555554 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   1.1       1.5   6.6e+02      80      85 ..       2       7 ..       1       8 [. 0.80
   2 ?   11.7   1.3   0.00079      0.34      36      75 ..      16      71 ..      11      74 .. 0.75
   3 ?    2.5   0.0      0.59   2.5e+02      37      45 ..      89      97 ..      77     103 .] 0.59

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 1.5
                    zinc_ribbon_15 80 kyCpkC 85
                                      ++CpkC
  gi|298675051|ref|YP_003726801.1|  2 EFCPKC 7 
                                      799999 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00079
                    zinc_ribbon_15 36 pylacskCkslleaskelgkeiekkesse.................kkeCknCgkev 75
                                        ++c+kC+++ ++ ++  + ++++e+++                 + +C++Cg++v
  gi|298675051|ref|YP_003726801.1| 16 NSMKCRKCGHIKGSGSS-DTFVSRTEKENrevtvlegevdqglpttEAKCQECGHTV 71
                                      4699*****98877653.3333333333346799********************998 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.59
                    zinc_ribbon_15 37 ylacskCks 45
                                      +++c+kC++
  gi|298675051|ref|YP_003726801.1| 89 FFKCTKCGA 97
                                      444444444 PP

>> zf-LITAF-like  LITAF-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.4      0.38   1.6e+02      58      65 ..       3      10 ..       1      15 [. 0.77
   2 ?    2.8   0.5      0.33   1.4e+02       5      25 ..      17      45 ..      14      50 .. 0.62
   3 ?    7.5   0.1     0.012         5      54      69 ..      59      74 ..      54      75 .. 0.85
   4 ?    1.4   0.0      0.93     4e+02      58      65 ..      91      98 ..      83     103 .] 0.73

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.38
                     zf-LITAF-like 58 yCpnCgal 65
                                      +Cp+C++l
  gi|298675051|ref|YP_003726801.1|  3 FCPKCKSL 10
                                      58888876 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.33
                     zf-LITAF-like  5 qvdCpaCqqrv........vTsveyksgk 25
                                      +++C +C++          v+++e+++  
  gi|298675051|ref|YP_003726801.1| 17 SMKCRKCGHIKgsgssdtfVSRTEKENRE 45
                                      56777777766666665556666665555 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.012
                     zf-LITAF-like 54 dvehyCpnCgallgty 69
                                       +e +C++Cg++++++
  gi|298675051|ref|YP_003726801.1| 59 TTEAKCQECGHTVAYW 74
                                      67899********997 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.93
                     zf-LITAF-like 58 yCpnCgal 65
                                      +C++Cga+
  gi|298675051|ref|YP_003726801.1| 91 KCTKCGAT 98
                                      67777765 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.3    0.0081       3.5       2      23 ..       4      24 ..       3      49 .. 0.90
   2 ?    2.2   3.6      0.45   1.9e+02      10      24 ..      72      97 ..      56     100 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0081
                          zf-Mss51  2 CPvpkhkqtapkhvdfeCpdCG 23
                                      CP +k+ +  p + +++C +CG
  gi|298675051|ref|YP_003726801.1|  4 CPKCKSLM-FPVDNSMKCRKCG 24
                                      ****7666.89**********9 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.45
                          zf-Mss51 10 t...........apkhvdfeCpdCGi 24
                                      +           +++   f+C +CG 
  gi|298675051|ref|YP_003726801.1| 72 AywwlrqlrsadESETRFFKCTKCGA 97
                                      35555555555456666788888885 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.4      0.16        67       8      15 ..      19      26 ..      15      27 .. 0.89
   2 ?    3.7   0.1      0.11        49       8      16 ..      63      71 ..      61      73 .. 0.90
   3 ?    5.9   0.1     0.023       9.8       4      13 ..      87      96 ..      84      98 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.16
                                      E-TTT--E CS
                   Desulfoferrod_N  8 kCevCGni 15
                                      kC  CG i
  gi|298675051|ref|YP_003726801.1| 19 KCRKCGHI 26
                                      9*****87 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.11
                                      E-TTT--EE CS
                   Desulfoferrod_N  8 kCevCGniV 16
                                      kC+ CG  V
  gi|298675051|ref|YP_003726801.1| 63 KCQECGHTV 71
                                      9*****988 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.023
                                      T-EEE-TTT- CS
                   Desulfoferrod_N  4 levYkCevCG 13
                                      +  +kC+ CG
  gi|298675051|ref|YP_003726801.1| 87 TRFFKCTKCG 96
                                      5679****** PP

>> zf-C2H2_11  zinc-finger C2H2-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1    0.0049       2.1       3      11 ..      16      24 ..      15      26 .. 0.90
   2 ?    4.0   0.4     0.099        42       5      11 ..      62      68 ..      59      70 .. 0.85
   3 ?    4.7   0.1     0.061        26       5      12 ..      90      97 ..      87      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0049
                        zf-C2H2_11  3 stcqCleCG 11
                                      ++++C++CG
  gi|298675051|ref|YP_003726801.1| 16 NSMKCRKCG 24
                                      89******9 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.099
                        zf-C2H2_11  5 cqCleCG 11
                                       +C+eCG
  gi|298675051|ref|YP_003726801.1| 62 AKCQECG 68
                                      59****9 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.061
                        zf-C2H2_11  5 cqCleCGl 12
                                      ++C++CG 
  gi|298675051|ref|YP_003726801.1| 90 FKCTKCGA 97
                                      69*****6 PP

>> zf-3CxxC_2  Zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   2.7         5   2.1e+03       9      14 ..      19      24 ..       2      29 .. 0.59
   2 ?    2.8   0.4      0.46     2e+02       9      21 ..      19      31 ..      16      41 .. 0.79
   3 ?    7.5   0.1     0.016         7      28      51 ..      62      85 ..      58      89 .. 0.80
   4 ?    6.8   1.7     0.026        11       8      17 ..      90      99 ..      87     101 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 5
                        zf-3CxxC_2  9 kCekCg 14
                                      kC+kCg
  gi|298675051|ref|YP_003726801.1| 19 KCRKCG 24
                                      444444 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.46
                        zf-3CxxC_2  9 kCekCgkeWsSan 21
                                      kC+kCg+   S+ 
  gi|298675051|ref|YP_003726801.1| 19 KCRKCGHIKGSGS 31
                                      8999999877775 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.016
                        zf-3CxxC_2 28 QeCkkCkekvepyklrekdkkkga 51
                                       +C++C+++v  + lr+++  +++
  gi|298675051|ref|YP_003726801.1| 62 AKCQECGHTVAYWWLRQLRSADES 85
                                      59***********99997766654 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.026
                        zf-3CxxC_2  8 fkCekCgkeW 17
                                      fkC+kCg +W
  gi|298675051|ref|YP_003726801.1| 90 FKCTKCGATW 99
                                      9********* PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.6      0.54   2.3e+02      17      22 ..       4       9 ..       3       9 .. 0.90
   2 ?    3.9   0.4       0.1        43       3       8 ..      20      25 ..      19      29 .. 0.78
   3 ?    8.5   1.8    0.0038       1.6       3      14 ..      64      75 ..      63      75 .. 0.89
   4 ?    5.2   0.3      0.04        17       1       9 [.      90      98 ..      90     102 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.54
                      Rubredoxin_2 17 CpsCgs 22
                                      Cp C+s
  gi|298675051|ref|YP_003726801.1|  4 CPKCKS 9 
                                      ****96 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.1
                      Rubredoxin_2  3 CsqCGf 8 
                                      C++CG+
  gi|298675051|ref|YP_003726801.1| 20 CRKCGH 25
                                      999997 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0038
                      Rubredoxin_2  3 CsqCGfesakwf 14
                                      C++CG++ a w+
  gi|298675051|ref|YP_003726801.1| 64 CQECGHTVAYWW 75
                                      *******99986 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.04
                      Rubredoxin_2  1 YvCsqCGfe 9 
                                      + C +CG++
  gi|298675051|ref|YP_003726801.1| 90 FKCTKCGAT 98
                                      78*****97 PP

>> DiS_P_DiS  Bacterial Peptidase A24 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   3.1       4.9   2.1e+03      27      35 ..      17      25 ..       4      28 .. 0.59
   2 ?    7.1   0.0     0.014         6      23      40 ..      57      74 ..      33      79 .. 0.81
   3 ?    0.2   0.1         2   8.4e+02      29      36 ..      91      98 ..      84     103 .] 0.71

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 4.9
                         DiS_P_DiS 27 rSrCpkCgh 35
                                      + +C kCgh
  gi|298675051|ref|YP_003726801.1| 17 SMKCRKCGH 25
                                      345666665 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.014
                         DiS_P_DiS 23 lvkprSrCpkCghklkwl 40
                                      l + +++C++Cgh+++ +
  gi|298675051|ref|YP_003726801.1| 57 LPTTEAKCQECGHTVAYW 74
                                      5677899******99876 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 2
                         DiS_P_DiS 29 rCpkCghk 36
                                      +C+kCg++
  gi|298675051|ref|YP_003726801.1| 91 KCTKCGAT 98
                                      57777765 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   5.4      0.51   2.2e+02      21      45 ..       4      25 ..       2      26 .. 0.71
   2 ?    2.7   0.5      0.29   1.3e+02      19      26 ..      18      25 ..      12      34 .. 0.75
   3 ?    8.9   4.0    0.0033       1.4      19      45 ..      62      97 ..      56      98 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.51
                     Zn_Tnp_IS1595 21 CPhCgsrkayriktrglfqCkeCrk 45
                                      CP+C+  ++ +  +    +C++C++
  gi|298675051|ref|YP_003726801.1|  4 CPKCK--SLMFPVD-NSMKCRKCGH 25
                                      9***9..4454444.5778999886 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.29
                     Zn_Tnp_IS1595 19 fvCPhCgs 26
                                        C +Cg+
  gi|298675051|ref|YP_003726801.1| 18 MKCRKCGH 25
                                      45777775 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0033
                     Zn_Tnp_IS1595 19 fvCPhCgsr.kayrikt........rglfqCkeCrk 45
                                        C  Cg++  ++ +++         + f+C +C++
  gi|298675051|ref|YP_003726801.1| 62 AKCQECGHTvAYWWLRQlrsadeseTRFFKCTKCGA 97
                                      57*******77777777999**************97 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1      0.29   1.2e+02       2       9 ..       4      11 ..       3      12 .. 0.86
   2 ?   10.0   0.7    0.0016      0.66       1      37 [.      63      99 ..      63     102 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.29
                         Ogr_Delta  2 CPhCgapa 9 
                                      CP+C++ +
  gi|298675051|ref|YP_003726801.1|  4 CPKCKSLM 11
                                      ****9866 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0016
                         Ogr_Delta  1 rCPhCgapaaartsrnl.skdvre.ryyqCsnfeCgatf 37
                                      +C +Cg+  a +  r+l s+d  e r++ C+   Cgat 
  gi|298675051|ref|YP_003726801.1| 63 KCQECGHTVAYWWLRQLrSADESEtRFFKCTK--CGATW 99
                                      699****999999998746666669******9..**995 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.2      0.13        56      22      27 ..       2       7 ..       1      11 [. 0.85
   2 ?    3.0   0.8       0.2        85       3      11 ..      17      25 ..      15      27 .. 0.68
   3 ?    4.5   0.0     0.067        29      24      30 ..      64      70 ..      61      77 .. 0.73
   4 ?    2.7   0.4      0.26   1.1e+02       6      10 ..      92      96 ..      90      98 .. 0.59

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.13
                     A2L_zn_ribbon 22 lvCieC 27
                                      ++C++C
  gi|298675051|ref|YP_003726801.1|  2 EFCPKC 7 
                                      89**** PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.2
                     A2L_zn_ribbon  3 lkvCsvCgg 11
                                        +C +Cg+
  gi|298675051|ref|YP_003726801.1| 17 SMKCRKCGH 25
                                      457888887 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.067
                     A2L_zn_ribbon 24 CieCgas 30
                                      C+eCg +
  gi|298675051|ref|YP_003726801.1| 64 CQECGHT 70
                                      7777754 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.26
                     A2L_zn_ribbon  6 CsvCg 10
                                      C++Cg
  gi|298675051|ref|YP_003726801.1| 92 CTKCG 96
                                      66665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       890  (0.0496402); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        60  (0.00334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              42  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 692.01
//
Query:       gi|298675052|ref|YP_003726802.1|  [L=245]
Description: proliferating cell nuclear antigen PcnA [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.8e-13   48.9   2.1    2.3e-12   46.7   0.4    2.3  2  PCNA_N         Proliferating cell nuclear antigen, N-terminal
    4.2e-10   39.9   0.0    4.4e-08   33.3   0.0    2.8  2  PCNA_C         Proliferating cell nuclear antigen, C-terminal
     0.0052   16.3   0.0      0.023   14.2   0.0    1.9  2  Rad9           Rad9
  ------ inclusion threshold ------
      0.035   14.2   0.6       0.16   12.1   0.2    2.1  2  DNA_pol3_beta  DNA polymerase III beta subunit, N-terminal do
      0.073   12.1   0.0        1.7    7.6   0.0    2.1  2  Rad1           Repair protein Rad1/Rec1/Rad17


Domain annotation for each model (and alignments):
>> PCNA_N  Proliferating cell nuclear antigen, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.4   6.5e-16   2.3e-12       8     101 ..       7      99 ..       1     107 [. 0.92
   2 ?    0.2   0.0      0.16   5.9e+02      80     104 ..     153     177 ..     141     201 .. 0.79

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 6.5e-16
                                       SHHHHHHHHHHHTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS-EEEEEEHHHHHHHHTTSTT CS
                            PCNA_N   8 qasllkklleaikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrCDrnlalgvnlnslskilkcann 84 
                                       +a ll+  +e +  lv+e+ + ++++Gis++a+D + va+v+++l s++f+++  D    +g++l+ +s il +a++
  gi|298675052|ref|YP_003726802.1|   7 DAYLLRDSVEILSVLVDEIRLRTSSDGISVKAVDPANVAMVTFNLDSSAFDDFEADE-GEIGLDLTKISDILGVADK 82 
                                       578999999***********************************************6.579**************** PP

                                       TSEEEEEEETTSSEEEE CS
                            PCNA_N  85 edsvtlkaedeadtlal 101
                                       +d+v ++ +++++++++
  gi|298675052|ref|YP_003726802.1|  83 NDKVYMELNENSQNMSI 99 
                                       ***********999976 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.16
                                       TTSTTTSEEEEEEETTSSEEEEEEE CS
                            PCNA_N  80 kcannedsvtlkaedeadtlalvfe 104
                                        ++ n+d+  ++ae ++d++ l + 
  gi|298675052|ref|YP_003726802.1| 153 LLGVNDDVFYMEAEGDTDKVRLDLP 177
                                       5677999999999999999988665 PP

>> PCNA_C  Proliferating cell nuclear antigen, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.028     1e+02      46      76 ..      63      93 ..      57     102 .. 0.89
   2 !   33.3   0.0   1.2e-11   4.4e-08       1     127 [.     121     240 ..     121     241 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.028
                                      EETTEEEEEEE--BEESSSGGGCBEEEESS- CS
                            PCNA_C 46 sGdiGsasivlkqvkdvdkeeeavklelkep 76
                                      +G+iG   +++++   v+++++ v +el+e 
  gi|298675052|ref|YP_003726802.1| 63 EGEIGLDLTKISDILGVADKNDKVYMELNEN 93
                                      69*************************9986 PP

  == domain 2  score: 33.3 bits;  conditional E-value: 1.2e-11
                                       ----SS-SEEEEEEHHHHHHHHHHHTTT-SEEEEEEETTEEEEEEEETTEEEEEEE--BEESSSGGGCBEEEESS-E CS
                            PCNA_C   1 gipdseydavvklpssefaricrdlsqlsdsvvisvtkegvkfsasGdiGsasivlkqvkdvdkeeeavklelkepv 77 
                                       +ip++e  a + l  ++  r ++   ++sd + + v  +     a+Gd  +  + l         ++ + l+  + v
  gi|298675052|ref|YP_003726802.1| 121 KIPQLELPAEIILNGTDLRRAVKAAEKISDHMLLGVNDDVFYMEAEGDTDKVRLDL-------PRDQLIDLKP-DDV 189
                                       699999999999***********************************976653333.......3456666765.468 PP

                                       EEEEEHHHHHHHGGGGGC-SEEEEEEETTSEEEEEEEETTC.EEEEEEE-B CS
                            PCNA_C  78 tltfalkYlaeftkatsLservtlslssevPlvveykikdv.gllayllak 127
                                          f+l+Yl +++k +s s++v l+l ++ P++++++i+++ g + ylla+
  gi|298675052|ref|YP_003726802.1| 190 RSLFSLDYLSDIVKPASKSNEVVLELGQDFPIKINFEIANGiGKVGYLLAP 240
                                       999***********************************9852777888887 PP

>> Rad9  Rad9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   6.3e-06     0.023       4      53 ..      14      63 ..      11     103 .. 0.81
   2 ?   -0.5   0.0      0.19   6.9e+02       1      27 [.     138     164 ..     138     166 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.3e-06
                              Rad9  4 alqclsrigdelyleisedglelrtvnssrSayalvtlkksfFdkyekev 53
                                      +++ ls + de+ l  s dg+++++v+ ++ a ++++l +s Fd +e + 
  gi|298675052|ref|YP_003726802.1| 14 SVEILSVLVDEIRLRTSSDGISVKAVDPANVAMVTFNLDSSAFDDFEADE 63
                                      578899999*************************************5443 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.19
                              Rad9   1 laralqclsrigdelyleisedglelr 27 
                                       l ra++++ +i+d + l  ++d + ++
  gi|298675052|ref|YP_003726802.1| 138 LRRAVKAAEKISDHMLLGVNDDVFYME 164
                                       5699*************9999988776 PP

>> DNA_pol3_beta  DNA polymerase III beta subunit, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   4.5e-05      0.16      32     114 ..      24     113 ..       8     120 .. 0.86
   2 ?   -0.5   0.0      0.36   1.3e+03      68      92 ..     201     225 ..     191     229 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.5e-05
                                       EEEEEEETTEEEEEEE-SSEEEEEEEESEEE......EE-EEEEEEHHHHHHHHHHSSTTSEEEEEEET..TEEEEE CS
                     DNA_pol3_beta  32 gvllevkdsqlsltgtDleisiestisaese......eeegkvlvparllldivkaLpndkkvkisvne..qkllii 100
                                        + l  +++++s+++ D    + +t+++ s+      + eg++ +   +++di+   +++ kv +++ne  q+++i 
  gi|298675052|ref|YP_003726802.1|  24 EIRLRTSSDGISVKAVDPANVAMVTFNLDSSafddfeADEGEIGLDLTKISDILGVADKNDKVYMELNEnsQNMSIN 100
                                       57899999*********98888888888888899999999*****************************76777777 PP

                                       EETTEEEEEE-BEG CS
                     DNA_pol3_beta 101 ksgssrfslstlsa 114
                                         gs  ++ls l+ 
  gi|298675052|ref|YP_003726802.1| 101 -IGSFSYTLSLLDP 113
                                       .9999999998875 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.36
                                       EEEEHHHHHHHHHHSSTTSEEEEEE CS
                     DNA_pol3_beta  68 vlvparllldivkaLpndkkvkisv 92 
                                       ++ pa++ +++v +L +d ++ki++
  gi|298675052|ref|YP_003726802.1| 201 IVKPASKSNEVVLELGQDFPIKINF 225
                                       4556666666666666666666665 PP

>> Rad1  Repair protein Rad1/Rec1/Rad17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.014        50      23      67 ..      23      85 ..      15     119 .. 0.65
   2 ?    7.6   0.0   0.00048       1.7     159     224 ..     121     182 ..     104     225 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.014
                              Rad1 23 dkalvqissdGlkf.ivednrvlqaqafldkalFtsYtfenaqdd...................e 67
                                      d++ +  ssdG+++  v+ + v   +  ld++ F++++ ++   +                   +
  gi|298675052|ref|YP_003726802.1| 23 DEIRLRTSSDGISVkAVDPANVAMVTFNLDSSAFDDFEADEG--EigldltkisdilgvadkndK 85
                                      566677899999994478889999999999999999998332..244666666666666554331 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00048
                              Rad1 159 eldrqevvlkvilkselLhsalteLdatskklkilassekkapvfalsakgelgssevefpneksv 224
                                       +  + e+ +++il++  L+ a++  +++s+++ + +++     vf ++a+g++ ++++++p ++ +
  gi|298675052|ref|YP_003726802.1| 121 KIPQLELPAEIILNGTDLRRAVKAAEKISDHMLLGVND----DVFYMEAEGDTDKVRLDLPRDQLI 182
                                       5556678899*********************9999999....4******************99864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1666.58
//
Query:       gi|298675053|ref|YP_003726803.1|  [L=349]
Description: DNA primase large subunit [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      9e-37  126.9   0.6    5.1e-36  124.4   0.6    1.8  1  DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large s
     0.0057   16.9   0.1     0.0057   16.9   0.1    2.8  3  DUF4883          DOmain of unknown function (DUF4883)
  ------ inclusion threshold ------
      0.046   14.2   0.2        0.2   12.2   0.1    2.1  2  TFIID_20kDa      Transcription initiation factor TFIID subuni
      0.046   13.8   0.0       0.19   11.9   0.0    2.1  1  Skp1             Skp1 family, dimerisation domain
      0.058   13.5   0.1       0.26   11.4   0.1    2.0  2  Mut7-C           Mut7-C RNAse domain


Domain annotation for each model (and alignments):
>> DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.4   0.6   1.4e-39   5.1e-36       2     206 ..     131     313 ..     130     332 .. 0.86

  Alignments for each domain:
  == domain 1  score: 124.4 bits;  conditional E-value: 1.4e-39
                                       EEEEEHHHHHHHTT.-G.......GS-EETTEEEE-HHHHHHHHHHHHHHHHHH..........HHGGGSSS---HH CS
                   DNA_primase_lrg   2 fykvpfedvldlvk.rr.......rvllkkGyaylpkeeleslllekfrkrlekalestkeslpeleeeikederek 70 
                                        + ++f+d+++l++  +       ++ lk+Gy+ +++ee+ +ll e++r+r+++al   + s++       +  ++ 
  gi|298675053|ref|YP_003726803.1| 131 HFAMHFTDYIKLANtMKdlkwklvNRRLKQGYVHITHEEVARLLQEAIRDRIQNALPL-DVSSEA-----CNNCNSY 201
                                       5899**********633699*************************************9.444333.....4444555 PP

                                       HHHHHCT--.............TTSSTTGGSHHHHTT--HHHHCCHHHHCCCSS--CHHHHHHHHHHHHCT--CHHH CS
                   DNA_primase_lrg  71 leellealsesyvaedvqeeedskisaknidklakesfPpCmrelleglkknghlkhegrlqltlFlkdiglsldei 147
                                       ++e++e l+          +++s+++ ++++++  esfPpC+ ++++g+  + +l h+ r++lt+Fl ++g+s+dei
  gi|298675053|ref|YP_003726803.1| 202 IDEIKEVLQ----------NRKSDVNIDEMGEVDTESFPPCISNAISGVSTGANLGHSMRFALTSFLLNVGMSVDEI 268
                                       666666666..........6669999999************************************************ PP

                                       HCCCHCHST..HHHHHH.HTHCHCHHHCC-STT--------HHHHHHS....TT---S.-H CS
                   DNA_primase_lrg 148 lelwkeaftrteekFdk.eyrynirhnyGkegkrtnyspysCekiltkpppgkgdahg.Cp 206
                                       ++++  +     ++Fd+ ++ry+i+h++G   ++  y+p+sC+++         +++g C+
  gi|298675053|ref|YP_003726803.1| 269 VDMFNVS-----PDFDEeKTRYQIEHIAG--SSGSPYTPPSCQTM---------KTYGnCY 313
                                       ******8.....*****************..88889*********.........6666663 PP

>> DUF4883  DOmain of unknown function (DUF4883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   1.6e-06    0.0057      54     111 ..      87     144 ..      69     151 .. 0.73
   2 ?   -0.8   0.0      0.49   1.7e+03       3      22 ..     197     215 ..     195     227 .. 0.72
   3 ?    0.1   0.5      0.26   9.2e+02       4      22 ..     326     344 ..     322     347 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.6e-06
                           DUF4883  54 enfiekekkleekpeyklfitfesekyvidvyneklisvypwDgkykkdyidiknipa 111
                                       ++++ +  +l e ++    +  e++++++++ n+  +s++p+D+++ + + d  ++ +
  gi|298675053|ref|YP_003726803.1|  87 DSYLIRRYALAEAESASKLLKTENKDFLVEIANDFNVSITPFDSHFAMHFTDYIKLAN 144
                                       55555555555555555556778888********************997777655544 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.49
                           DUF4883   3 snfyYtnllakklksnkklk 22 
                                       +++ Y++++++ l++  k  
  gi|298675053|ref|YP_003726803.1| 197 NCNSYIDEIKEVLQNR-KSD 215
                                       6788999999966654.444 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.26
                           DUF4883   4 nfyYtnllakklksnkklk 22 
                                       ++yY ++l+kk k++k+++
  gi|298675053|ref|YP_003726803.1| 326 LNYYRKKLYKKAKKEKEKS 344
                                       5899*****9999988765 PP

>> TFIID_20kDa  Transcription initiation factor TFIID subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   5.6e-05       0.2      15      47 ..     103     135 ..      95     152 .. 0.89
   2 ?   -1.7   0.0       1.2   4.2e+03      36      51 ..     200     215 ..     197     220 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.6e-05
                                       S----HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       TFIID_20kDa  15 etkldedvedlLleiaddFvesvtkfacklakh 47 
                                       ++ l  + +d L+eia+dF  s+t f +++a h
  gi|298675053|ref|YP_003726803.1| 103 SKLLKTENKDFLVEIANDFNVSITPFDSHFAMH 135
                                       56688999*******************999987 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHTT-S CS
                       TFIID_20kDa  36 svtkfacklakhRksd 51 
                                       s ++ + ++ ++Rksd
  gi|298675053|ref|YP_003726803.1| 200 SYIDEIKEVLQNRKSD 215
                                       5566677788899998 PP

>> Skp1  Skp1 family, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   5.3e-05      0.19      17      38 ..     262     283 ..     249     289 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.3e-05
                              Skp1  17 gktpeeiReiFnIenDftpEEe 38 
                                       g++++ei  +Fn+  Df +E+ 
  gi|298675053|ref|YP_003726803.1| 262 GMSVDEIVDMFNVSPDFDEEKT 283
                                       89****************9975 PP

>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.66   2.4e+03      43      84 ..      79     125 ..      69     131 .. 0.70
   2 ?   11.4   0.1   7.3e-05      0.26      51     105 ..     152     207 ..     145     233 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.66
                            Mut7-C  43 rillTr..dreLlkraklkkg...vlltsrdveeqlreviarlglkl 84 
                                       ril+++  d+ L++r  l+++     l +++ ++ l+e+ +++++++
  gi|298675053|ref|YP_003726803.1|  79 RILVSCinDSYLIRRYALAEAesaSKLLKTENKDFLVEIANDFNVSI 125
                                       67776544777888777766665544567777888888888877665 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 7.3e-05
                            Mut7-C  51 eLlkraklkkgvlltsrdveeqlrevia.rlglklslkpelsrCvaCngeleevek 105
                                       +L++r+ ++  v +t+++v++ l+e i+ r++ +l l+   + C +Cn+ ++e+++
  gi|298675053|ref|YP_003726803.1| 152 KLVNRRLKQGYVHITHEEVARLLQEAIRdRIQNALPLDVSSEACNNCNSYIDEIKE 207
                                       67888887777999***********98537999999*************9888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       919  (0.0512577); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2584.80
//
Query:       gi|298675054|ref|YP_003726804.1|  [L=440]
Description: cobyrinic acid a,c-diamide synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-33  116.4   0.1    1.7e-33  115.9   0.1    1.2  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    7.8e-21   74.8   2.4      1e-18   67.9   3.3    2.5  2  AAA_26         AAA domain
    1.2e-19   70.7   0.1      2e-19   69.9   0.1    1.4  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
  ------ inclusion threshold ------
      0.024   14.5   0.0      0.074   13.0   0.0    1.7  2  AAA_31         AAA domain
      0.056   12.7   0.1       0.17   11.1   0.0    1.8  2  DUF1611        Domain of unknown function (DUF1611_C) P-loop 
      0.058   13.0   0.0      0.099   12.3   0.0    1.3  1  Peptidase_S51  Peptidase family S51
      0.095   12.6   0.6          1    9.2   0.1    2.4  3  NTPase_1       NTPase
       0.11   12.2   0.0       0.24   11.1   0.0    1.5  1  GATase         Glutamine amidotransferase class-I
       0.15   11.9   0.0       0.33   10.8   0.0    1.5  1  SNO            SNO glutamine amidotransferase family


Domain annotation for each model (and alignments):
>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.9   0.1   8.7e-37   1.7e-33       1     190 [.     241     421 ..     241     426 .. 0.88

  Alignments for each domain:
  == domain 1  score: 115.9 bits;  conditional E-value: 8.7e-37
                          GATase_3   1 kiavirlpaisnyt..dldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeag 75 
                                       +i+v ++ a+ +y+   ld  ++ ++   +f+p  + +l +d+d ++l+Gg++++    l+++ ++  ++k++a++g
  gi|298675054|ref|YP_003726804.1| 241 TIGVGMDGAFCFYYqdMLDSFRQCGADIEFFSP-VQGEL-PDVDGIYLGGGYPELYIEDLEKS-KTTSELKNLAADG 314
                                       58899999*******669**********9****.66779.56**************9999988.88999******** PP

                          GATase_3  76 gpvlgiCGGlqmLGeeiedpegvegeageveglglLdietefek.ekltgqvegevelaaegeevkGyEiHsGrtil 151
                                       +p++g+CGG+q+L++++e ++ v     e+++ ++++++t++++  k++g++++e++ +  + ++ G+E+H+++t  
  gi|298675054|ref|YP_003726804.1| 315 MPIYGECGGMQYLCSSYEIDD-V-----EYKMADVFPANTRMTNkLKALGHTKAEASGEFINGTLLGHEFHYSTTEC 385
                                       *****************7654.5.....9***************4477877777755555568899*********** PP

                          GATase_3 152 kekakpllkvkvggnng.ekdGavkksedgnvlGtYlHgl 190
                                       +++ak  +++++g++++ +kdG+ ++    n +++Y+H +
  gi|298675054|ref|YP_003726804.1| 386 SRDAKLEYEMIRGKGIEdGKDGLSEH----NSIASYMHAH 421
                                       **********99777777******87....********98 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.9   3.3   5.1e-22     1e-18       2     195 ..       4     182 ..       3     185 .. 0.81
   2 ?   -3.1   0.0         3   5.9e+03      24      43 ..     260     279 ..     258     304 .. 0.83

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 5.1e-22
                            AAA_26   2 tifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiqtgieededselikellgldqtyelpeplalsaplspela 78 
                                       +++++gt  gvGKT+vs+g+++al++++ kv+ +K    +i    d+ + + +++ ++ +  ++++++++++     
  gi|298675054|ref|YP_003726804.1|   4 SVLIAGTHSGVGKTTVSMGIMAALSKRNLKVQPYKVGPDYI----DPTHHTAICKKPSRN--LDTYMMDEEY----- 69 
                                       799***************************99888544444....788888888655544..5779998653..... PP

                            AAA_26  79 arqegedidlekivkelekdadivvVEGagglgvpitee..llnadiaknlgapvilVarggl..gtinqllltiea 151
                                            ++i      +  ++dadi v+EG+ gl +++ ++   + a +ak +gapvilV++++   +++ ++l  ++ 
  gi|298675054|ref|YP_003726804.1|  70 ---IRRSI------EYSSNDADISVIEGVMGLYDGVDSTeiSSSAHVAKVIGAPVILVVNVHGmsRSVGAILKGYSE 137
                                       ...22334......45789*************977554434999****************96532678888877777 PP

                            AAA_26 152 lrqknvrvlGvilNkvrnpenvetlekksg..ipvlGvvPylpdle 195
                                       + + +v+v+Gv+lNkv +++  ++++ + +  ipv+G++P +++++
  gi|298675054|ref|YP_003726804.1| 138 YDK-DVNVAGVVLNKVGSQRHAQMIKDALPsdIPVVGALPKNQNVS 182
                                       766.8***********************87669********99876 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3
                            AAA_26  24 alkrkgvkvgyfKPiqtgie 43 
                                       +++++g+ + +f P+q ++ 
  gi|298675054|ref|YP_003726804.1| 260 SFRQCGADIEFFSPVQGELP 279
                                       56789999999*99997765 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9   0.1     1e-22     2e-19       1     125 [.       5     187 ..       5     190 .. 0.89

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 1e-22
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH....HTTEB-HHHH................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxx................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai....leglendiep................... 54 
                                       ++ia+t +GvGKTt++ ++++al++r+l+V++++++p+    ++     ++ +    +                   
  gi|298675054|ref|YP_003726804.1|   5 VLIAGTHSGVGKTTVSMGIMAALSKRNLKVQPYKVGPDYIDPTHhtaiCKKPSR---Nldtymmdeeyirrsieyss 78 
                                       68************************************7776666655222222...13557888888888****** PP

                                       .........................................CCHCCCHHHHHHCHCHHHH.....EEEEEEEEESS. CS
                                       .........................................xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx RF
                              CbiA  55 .........................................dlkrllellealgkkkall...lkiagvvlnrvdge 87 
                                                                                ++  +++++ a+ k+++     +++agvvln+v+++
  gi|298675054|ref|YP_003726804.1|  79 ndadisviegvmglydgvdsteisssahvakvigapvilvvNVHGMSRSVGAILKGYSEYdkdVNVAGVVLNKVGSQ 155
                                       *****************************************9999999**9999999988999************** PP

                                       ..-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  88 neetllkealeelkqrygvpvlgviprdeavaeaparg 125
                                       ++ +++k+al        +pv+g +p++++v   p+r+
  gi|298675054|ref|YP_003726804.1| 156 RHAQMIKDALPS-----DIPVVGALPKNQNV-SVPSRH 187
                                       *********999.....89***********9.566665 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.7e-05     0.074       9      34 ..      10      35 ..       3      97 .. 0.77
   2 ?   -2.5   0.0         2     4e+03      86     112 ..     329     355 ..     317     369 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.7e-05
                            AAA_31  9 qKGGvGKTTtsvnlaaalaklgkkvL 34
                                         GvGKTT s+ + aal+k++ kv 
  gi|298675054|ref|YP_003726804.1| 10 THSGVGKTTVSMGIMAALSKRNLKVQ 35
                                      567*********************95 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2
                            AAA_31  86 ssidLaeaeielvelekkeeilkelle 112
                                       ss ++ ++e +++++   +++++++l+
  gi|298675054|ref|YP_003726804.1| 329 SSYEIDDVEYKMADVFPANTRMTNKLK 355
                                       444444444444444444444444444 PP

>> DUF1611  Domain of unknown function (DUF1611_C) P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   8.8e-05      0.17      14      48 ..       4      38 ..       1      51 [. 0.89
   2 ?   -2.9   0.0       1.7   3.4e+03      82      97 ..      77      90 ..      60     104 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.8e-05
                           DUF1611 14 rvlvvGTdcavGKrttaleleealeerGlkaafva 48
                                       vl+ GT + vGK t ++ + +al +r lk++   
  gi|298675054|ref|YP_003726804.1|  4 SVLIAGTHSGVGKTTVSMGIMAALSKRNLKVQPYK 38
                                      69**************************9987655 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.7
                           DUF1611 82 aaeeeepdlilveGQg 97
                                         ++++d+ ++eG  
  gi|298675054|ref|YP_003726804.1| 77 S--SNDADISVIEGVM 90
                                      2..2444666676655 PP

>> Peptidase_S51  Peptidase family S51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     5e-05     0.099      48     138 ..     253     336 ..     246     383 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5e-05
                                       HHHHHHHHHHHTT-EEEE--TTTS-HHHHHHHHHHSSEEEE--S-HHHHHHHHHHTTHHHHHHHHHHTT-EEEEETH CS
                     Peptidase_S51  48 yvekvrkaleklglevdeLelskdpeeeieeklleadviyvgGGntfrLlkllketgldkllreavqqglvyiGvSA 124
                                       y +++ + +++ g++++   ++ + + e+ +     d+iy+gGG     ++ l++ ++ + l++  ++g+++ G   
  gi|298675054|ref|YP_003726804.1| 253 YYQDMLDSFRQCGADIE---FFSPVQGELPD----VDGIYLGGGYPELYIEDLEKSKTTSELKNLAADGMPIYGECG 322
                                       66777777777776544...45555666666....*****************************************9 PP

                                       HHHTTSSB-GGGTT CS
                     Peptidase_S51 125 Gaivagesiettsy 138
                                       G    ++s e +++
  gi|298675054|ref|YP_003726804.1| 323 GMQYLCSSYEIDDV 336
                                       99888777766654 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1   0.00052         1       3      31 ..       6      35 ..       4      38 .. 0.86
   2 ?   -3.9   0.0       5.6   1.1e+04      82     101 ..      67      86 ..      55      90 .. 0.74
   3 ?    0.7   0.0      0.21   4.2e+02     111     137 ..     154     180 ..     150     205 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00052
                                      EEE-.-TTSSHHHHHHHHHHHH...GGGEE CS
                          NTPase_1  3 fiTG.ppGvGKtTlvkkvlellkssgvkvg 31
                                      +i G ++GvGKtT+   ++ +l+++++kv+
  gi|298675054|ref|YP_003726804.1|  6 LIAGtHSGVGKTTVSMGIMAALSKRNLKVQ 35
                                      5666257********************997 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 5.6
                                       HHHHHHHHHHHHHHH-EEEE CS
                          NTPase_1  82 eelalealrkalseadvivi 101
                                       ee++ ++++ + ++ad+ vi
  gi|298675054|ref|YP_003726804.1|  67 EEYIRRSIEYSSNDADISVI 86 
                                       56777788888889999988 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.21
                                       -HHHHHHHHHHHTTTSEEEEE--SS-- CS
                          NTPase_1 111 skkfkeaveevLksekpvlavihrrkd 137
                                       s++ +++++++L s+ pv++ ++++++
  gi|298675054|ref|YP_003726804.1| 154 SQRHAQMIKDALPSDIPVVGALPKNQN 180
                                       678899*****************9973 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00012      0.24      39      91 ..     277     342 ..     253     396 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                                       THHSTSEEEEEEESSCTT.....TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTT........E CS
                            GATase  39 llknpdgilvsgGpgspg.....vegkieaikearenkiPiLGICLGmQllaiefgr........k 91 
                                       +l ++dgi + gG  + +       ++ + +k+++  ++Pi G C GmQ l+ ++          +
  gi|298675054|ref|YP_003726804.1| 277 ELPDVDGIYLGGGYPELYiedleKSKTTSELKNLAADGMPIYGECGGMQYLCSSYEIddveykmaD 342
                                       35689********999998874433333445666668**************999987444333332 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00017      0.33      29      91 ..     276     337 ..     246     347 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00017
                                       GGGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEETTBSS- CS
                               SNO  29 edlaevdaliiPGGestamskliertglyedllefvknsekvvlGtCaGlillskelenelvk 91 
                                        +l +vd++ + GG        +e+ +   +l++ ++++  +++G C G+ +l+   e+++v+
  gi|298675054|ref|YP_003726804.1| 276 GELPDVDGIYLGGGYPELYIEDLEKSKTTSELKNLAADG-MPIYGECGGMQYLCSSYEIDDVE 337
                                       579999*****9999888777778888899******999.9*************999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.57u 0.21s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3191.04
//
Query:       gi|298675055|ref|YP_003726805.1|  [L=308]
Description: molybdenum cofactor biosynthesis protein A [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.2e-31  108.6   0.1    8.6e-31  107.6   0.0    1.5  2  Radical_SAM  Radical SAM superfamily
    8.8e-20   70.9   0.2    1.5e-19   70.2   0.2    1.4  1  Mob_synth_C  Molybdenum Cofactor Synthesis C
    4.4e-08   33.3   0.1    1.1e-07   32.0   0.1    1.6  1  Fer4_14      4Fe-4S single cluster domain
    6.2e-07   29.8   0.0    1.4e-06   28.6   0.0    1.7  1  Fer4_12      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.062   13.7   0.0       0.13   12.6   0.0    1.5  1  HIPIP        High potential iron-sulfur protein


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.6   0.0   2.4e-34   8.6e-31       1     167 []      26     184 ..      26     184 .. 0.97
   2 ?   -3.1   0.0       2.6   9.2e+03     105     122 ..     209     234 ..     198     245 .. 0.62

  Alignments for each domain:
  == domain 1  score: 107.6 bits;  conditional E-value: 2.4e-34
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpg 77 
                                       +++t+ Cnl+C++C+      +    +++sv++i ++v  ++   gv+ + ++ggepl+++df+++l  l  l    
  gi|298675055|ref|YP_003726805.1|  26 ISITNRCNLNCIYCHHEG---NSSSKKEMSVDDISKIVHTAS-CYGVNKIKFSGGEPLVRDDFEQILQSLPPL---- 94 
                                       689**************8...8*******************7.556************************997.... PP

                                       EEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  78 iritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglp 153
                                        +i+ +tng+l+ ++ + +l+ +g+dr++++l+++d+e+++ +++ +++t+e+v+e++++  +ag+ +v+ ++++l+
  gi|298675055|ref|YP_003726805.1|  95 KEISATTNGVLL-KDRAHELKAAGLDRINISLDTLDPECYQFITGgKQGTLEQVIEGIKASVDAGLTPVKLNVILLK 170
                                       8***********.**************************************************************** PP

                                       TTSHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxx RF
                       Radical_SAM 154 Gendeeleellell 167
                                       G nd +++e++e++
  gi|298675055|ref|YP_003726805.1| 171 GINDTKIDEMIEFI 184
                                       ***********997 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.6
                                       EEEEEBSSSHH........HHHHHHT CS
                                       xxxxxxxxxxx........xxxxxxx RF
                       Radical_SAM 105 vslgleaadde........kvlklmn 122
                                       + ++++a+ +e        +v+ +++
  gi|298675055|ref|YP_003726805.1| 209 YRVDIQAIENElesradeiRVRSMHR 234
                                       55566666666555555555555554 PP

>> Mob_synth_C  Molybdenum Cofactor Synthesis C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.2   0.2   4.3e-23   1.5e-19       2     121 ..     192     302 ..     191     308 .] 0.79

  Alignments for each domain:
  == domain 1  score: 70.2 bits;  conditional E-value: 4.3e-23
                                       EEEEEE---B-TTSSB--SSB--HHHHHHHHHHHS-EEEE-..-SST-SSEEEEETTT--EEEEE-TTTS-.-GGG- CS
                       Mob_synth_C   2 elrfIElmpvgegeewrekkvvsadeilerieerlalleak..ketkgpakrykikdgkgeiglIapvsep.FCasC 75 
                                        l++IElm+++       + + +++  ++ ie++l++++++   ++++ +k+y i++++  i+l++p++++ FCa+C
  gi|298675055|ref|YP_003726805.1| 192 ILQLIELMDFE------FEVYHQYRVDIQAIENELESRADEirVRSMHRRKKYIIDSAE--IELVRPIDNTqFCANC 260
                                       589******99......356777777777777777777666324559********8887..*********99***** PP

                                       -EEEE-TTSEEESSSS-SS-.EEHHHHHHTT--HHHHHHHHHHHHHT CS
                       Mob_synth_C  76 nRlRltadGklktCLfaeee.idlrdllregaseeeLkelikealar 121
                                       nRlR+tadGklk+CL  +++ +d+ ++  e++      el+k a++r
  gi|298675055|ref|YP_003726805.1| 261 NRLRVTADGKLKPCLLVDNNlVDVSEASSEKM-----DELLKLAVSR 302
                                       *****************999999998877765.....3445555544 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.1     3e-11   1.1e-07       5     114 ..      29     124 ..      26     127 .. 0.76

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 3e-11
                           Fer4_14   5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypek 81 
                                       +++Cnl+C  C ++   +s+++k+ + +++++i+   ++s +  +++ ++GGePL     +++ ++++ l      k
  gi|298675055|ref|YP_003726805.1|  29 TNRCNLNCIYCHHEG--NSSSKKEMSVDDISKIV--HTASCYGVNKIKFSGGEPLVR---DDFEQILQSLPP---LK 95 
                                       79**********999..9999999**********..6666666799*********54...667777666654...46 PP

                           Fer4_14  82 kiwletngtleielektpdlkeklealskidll 114
                                       +i   tng+l ++     +++ k   l+ i+++
  gi|298675055|ref|YP_003726805.1|  96 EISATTNGVLLKDR----AHELKAAGLDRINIS 124
                                       99999999998553....344455555555555 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0     4e-10   1.4e-06      12      80 ..      29      92 ..      14     127 .. 0.70

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 4e-10
                           Fer4_12 12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevk 80
                                      +++Cnl+C +C+ +   s  s+ke++ + + +i++ ++ + ++++ ++GGEPl+   ++++ ++++++ 
  gi|298675055|ref|YP_003726805.1| 29 TNRCNLNCIYCHHEGNSS--SKKEMSVDDISKIVHTASCYGVNKIKFSGGEPLV---RDDFEQILQSLP 92
                                      789*********766555..55666677899******9****************...555555555544 PP

>> HIPIP  High potential iron-sulfur protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.7e-05      0.13      10      57 ..     238     283 ..     233     286 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.7e-05
                                       -BSSGGGSSHHHH--SSGG-SGGGBTTEESTSTTSEEEETTSTTEBEE CS
                             HIPIP  10 YvedaakadkakharyeegqhCanCalyqkkeeaewgpCtlfagklVa 57 
                                       Y  d a+++    + +++ q+CanC     +++++ +pC l++++lV 
  gi|298675055|ref|YP_003726805.1| 238 YIIDSAEIE--LVRPIDNTQFCANCNRLRVTADGKLKPCLLVDNNLVD 283
                                       666777776..45667799********9999999********999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2211.91
//
Query:       gi|298675056|ref|YP_003726806.1|  [L=50]
Description: hypothetical protein Metev_1128 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 374.53
//
Query:       gi|298675057|ref|YP_003726807.1|  [L=262]
Description: stationary-phase survival protein SurE [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-53  179.6   0.0      7e-53  179.3   0.0    1.1  1  SurE      Survival protein SurE
  ------ inclusion threshold ------
      0.081   12.1   0.1       0.11   11.7   0.1    1.2  1  SIL1      Nucleotide exchange factor SIL1


Domain annotation for each model (and alignments):
>> SurE  Survival protein SurE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.3   0.0   7.8e-57     7e-53       1     192 [.       5     198 ..       5     201 .. 0.94

  Alignments for each domain:
  == domain 1  score: 179.3 bits;  conditional E-value: 7.8e-57
                                       EEEE-SS-TT-HHHHHHHHHHTTTTSEEEEEEESSS-TTCTTS--SSSEEEEEEEECSTTTCEEEESS-HHHHHHHH CS
                              SurE   1 iLltNDDGieapgiralvealaaaghevvvvaPdserSgigkaltleeplrveseeeeeeeeeyavsGtPadcvkla 77 
                                       iLltNDDG+ ++gi a ++++++ g +v+++aP+ ++Sg+g++++l eplr+++++  ++ ++y++ GtP+d v l+
  gi|298675057|ref|YP_003726807.1|   5 ILLTNDDGVYSAGISAAYNSIKDLG-DVTIAAPAVQQSGVGRSISLFEPLRITKANI-DGVKAYSIGGTPTDSVILG 79 
                                       8*********************888.*************************997766.9****************** PP

                                       HHTTTTTS.SSEEEEEEEES---GGGG.GG-HHHHHHHHHHHTTSEEEEEEEESSS.....SS-SSS---HHHHHHH CS
                              SurE  78 leellkekkpdlVvSGiNhGaNlgtdv.lySGTvgAaleaalegipaiAvSlaskk.....eeekkeedtfeaaakv 148
                                       + +l++e kpdl++SG N G+N++td+ ++SGT+gAale+a  gipaiA S+++++     ++ ++ +++fe  +++
  gi|298675057|ref|YP_003726807.1|  80 IFKLMDE-KPDLLLSGFNIGENISTDTvTTSGTIGAALEGASYGIPAIAASIQVTDeglkfDDLRDYQHDFEVGKNI 155
                                       *****65.7******************9*************************9999**99666677888******* PP

                                       HHHHHTTETTS-...SS-EEEEEEESS.GCG-SEEEE-B--CCS CS
                              SurE 149 aaklveklieklllekvellnvNvPeleeeeikgvkvtrlgrrr 192
                                       ++++++k+i++ l ++v+llnvN+P++ e++ + +++t+l+r+ 
  gi|298675057|ref|YP_003726807.1| 156 INRIAKKVIHHGLPDNVDLLNVNIPHMAEDDTE-IEITQLARKF 198
                                       *************************88888766.88*9999875 PP

>> SIL1  Nucleotide exchange factor SIL1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   1.2e-05      0.11      27      52 ..     136     161 ..     123     204 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.2e-05
                              SIL1  27 ekaLddlielshDykfGvkiishefe 52 
                                         ++ddl ++ hD+++G +ii+   +
  gi|298675057|ref|YP_003726807.1| 136 GLKFDDLRDYQHDFEVGKNIINRIAK 161
                                       568******************87654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 2119.84
//
Query:       gi|298675058|ref|YP_003726808.1|  [L=226]
Description: FkbM family methyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-08   35.1   0.1    1.8e-07   31.3   0.1    2.1  1  Methyltransf_21  Methyltransferase FkbM domain
    0.00018   21.2   0.0    0.00026   20.7   0.0    1.2  1  Methyltransf_22  Methyltransferase domain
    0.00087   19.1   0.1     0.0035   17.1   0.0    2.0  2  Met_10           Met-10+ like-protein
      0.001   18.2   0.0     0.0017   17.5   0.0    1.4  1  DREV             DREV methyltransferase
  ------ inclusion threshold ------
      0.029   14.2   0.0      0.035   14.0   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
      0.043   12.9   0.0      0.055   12.5   0.0    1.3  1  RrnaAD           Ribosomal RNA adenine dimethylase


Domain annotation for each model (and alignments):
>> Methyltransf_21  Methyltransferase FkbM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.1   6.1e-11   1.8e-07       1     163 [.      77     202 ..      77     212 .. 0.75

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 6.1e-11
                   Methyltransf_21   1 dvGanigvwdsfanltarlcggggevlaiEPvpnslpkfeklranlltlavgndvglyelivegksggkyfpfavgd 77 
                                       d+Ga ig  ++ +    + +++ ++++a+EP+     ++++l  n   + ++          + +     +p+a ++
  gi|298675058|ref|YP_003726808.1|  77 DIGAGIG--AFSL----KVHQKVDHIYAVEPL-----WKNELSKN---CELS-------GADNVT----ILPYALSS 128
                                       8999999..4444....346789999999996.....88999888...4444.......244566....88899999 PP

                   Methyltransf_21  78 tngfstssvlggedaryievpvvtld...sfleeikksridllkiDvEGaElevLeG.aqkglkrcqpnlivvEvhk 150
                                       ++ +++ +       r  +v+ +tl+   +++  +    +d+lk+D+EG+E+++  + + kg++r     i  Evh+
  gi|298675058|ref|YP_003726808.1| 129 DDLSIEYE------DRKANVEGKTLSelkELCGGH----VDFLKMDCEGGEWSIK-PrELKGIRR-----IEAEVHS 189
                                       98888886......568999999998665666666....**************96.77*******.....999**** PP

                   Methyltransf_21 151 fkefetelfdeir 163
                                       f+ +  ++f +++
  gi|298675058|ref|YP_003726808.1| 190 FNGENMNDFVKML 202
                                       9954444444443 PP

>> Methyltransf_22  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   8.6e-08   0.00026     160     242 ..     145     217 ..     115     223 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 8.6e-08
                   Methyltransf_22 160 ltlqdtlkklgh.klrtidvlkidcekcewenykdwvevdirqilvevhglpskkaaplaasdffdafrkasyvrfs 235
                                       +tl++    l+      +d lk+dce  ew+        +ir+i  evh+  +++       df + ++ +++++  
  gi|298675058|ref|YP_003726808.1| 145 KTLSE----LKElCGGHVDFLKMDCEGGEWSIKPRE-LKGIRRIEAEVHSFNGENMN-----DFVKMLESNDFIVR- 210
                                       44444....444345679************975554.469***********999877.....***********655. PP

                   Methyltransf_22 236 kevnvfn 242
                                       k+ n  n
  gi|298675058|ref|YP_003726808.1| 211 KKKNACN 217
                                       5555544 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.2e-06    0.0035      90     131 ..      61     100 ..      48     130 .. 0.85
   2 ?   -1.8   0.0      0.75   2.3e+03      35      72 ..     180     216 ..     161     220 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.2e-06
                                       HHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEE CS
                            Met_10  90 ErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaid 131
                                       E   +    +++++V+d+ AGiG f++ + +  k   ++a++
  gi|298675058|ref|YP_003726808.1|  61 ESDYIFDDLNPDDIVLDIGAGIGAFSLKVHQ--KVDHIYAVE 100
                                       6667788899****************99988..9999***97 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.75
                                       -SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTE CS
                            Met_10  35 vktvlrkvsevegefRtfelevlaGsdstetihkEngc 72 
                                       ++ +  +v++ +ge  +  +++l  +d  ++ +k n+c
  gi|298675058|ref|YP_003726808.1| 180 IRRIEAEVHSFNGENMNDFVKMLESND-FIVRKKKNAC 216
                                       455555555556666666666666666.6777777766 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   5.6e-07    0.0017      94     127 ..      71     104 ..      15     114 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.6e-07
                              DREV  94 edkklldlGaGdGeitkrvaptfeevyatelset 127
                                        d  +ld+GaG G  + +v + ++++ya e  ++
  gi|298675058|ref|YP_003726808.1|  71 PDDIVLDIGAGIGAFSLKVHQKVDHIYAVEPLWK 104
                                       35679************************97775 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.2e-05     0.035      15      59 ..      64     107 ..      54     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.2e-05
                   Methyltransf_23  15 rllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeavei 59 
                                        +++ l+++  vLdiG+G G ++    +++ ++++v++  +++e+
  gi|298675058|ref|YP_003726808.1|  64 YIFDDLNPDDIVLDIGAGIGAFSLKVHQKVDHIYAVEPL-WKNEL 107
                                       5677789999*******************99******94.55554 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.8e-05     0.055      27      59 ..      68     100 ..      12     123 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.8e-05
                                       -GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE- CS
                            RrnaAD  27 nleekltvleigpGkGilTeeLakrakqvvvlE 59 
                                       +l++++ vl+ig+G G+++ ++ + +++  ++E
  gi|298675058|ref|YP_003726808.1|  68 DLNPDDIVLDIGAGIGAFSLKVHQKVDHIYAVE 100
                                       45689*****************99999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 1833.66
//
Query:       gi|298675059|ref|YP_003726809.1|  [L=264]
Description: peroxiredoxin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      6e-30  103.7   0.0    8.5e-30  103.2   0.0    1.2  1  AhpC-TSA    AhpC/TSA family
    7.8e-11   41.9   0.0    4.5e-10   39.4   0.0    2.0  1  Redoxin     Redoxin
    5.9e-10   38.8   0.0    1.3e-09   37.8   0.0    1.6  1  1-cysPrx_C  C-terminal domain of 1-Cys peroxiredoxin


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.2   0.0   1.4e-33   8.5e-30       1     123 [.      19     177 ..      19     178 .. 0.97

  Alignments for each domain:
  == domain 1  score: 103.2 bits;  conditional E-value: 1.4e-33
                                       TTSB----EEESTTCEEEEC.HHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHH CS
                          AhpC-TSA   1 vgdkapdfelknadgetvsl.sdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkf 76 
                                       +gd ap f++  +  +++++ +dykgk+v++f +p+d++pvCtte  ++a + eefke++ e++g+s+ds +sh  +
  gi|298675059|ref|YP_003726809.1|  19 IGDNAPAFKADSTV-GEINFpNDYKGKWVIFFSHPGDFTPVCTTEFLKFAHMQEEFKELNTELLGLSIDSIYSHITW 94 
                                       89********9887.677777******************************************************** PP

                                       HHH-H.............SSEEEE-TTSHHHHHTT-EETT........................TTECSCEEEEE-T CS
                          AhpC-TSA  77 iekes............lnfpllsDeegkvakaygvlkee........................kglalratfvidk 117
                                        + ++            ++fp++ D + kva++yg+++++                        ++ ++ra+f+id+
  gi|298675059|ref|YP_003726809.1|  95 LKSIRdnikykgygnidITFPIIDDLNMKVAQKYGMIHPKakwsqeevmeqlrttgkskskdsfSTHTVRAVFIIDP 171
                                       ***************************************************************************** PP

                                       TSBEEE CS
                          AhpC-TSA 118 egkiry 123
                                       + +ir+
  gi|298675059|ref|YP_003726809.1| 172 HAIIRA 177
                                       ****96 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.0   7.5e-14   4.5e-10       3     107 ..      20     132 ..      18     196 .. 0.82

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 7.5e-14
                                       TSBB---ECCEETTCEEEEEHHH.HTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHHH CS
                           Redoxin   3 gdkaPdftlplaatdgnsvslse.fkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvke 78 
                                       gd aP+f+  +  +   +++    +kgk v+ ++ pg f+P+C++e +++++ +e++ke + + +++++d+      
  gi|298675059|ref|YP_003726809.1|  20 GDNAPAFKA-D--STVGEINFPNdYKGKWVIFFSHPGDFTPVCTTEFLKFAHMQEEFKELNTELLGLSIDSIYSHIT 93 
                                       8999***94.4..66666666666*********************************************99999555 PP

                                       HHHH............TT-TSEEEE-TTSHHHHHTT-TTEE CS
                           Redoxin  79 fwgk............eglkfpvlsDgsaaftkalGlrlee 107
                                       ++++             +++fp++ D + ++++++G+    
  gi|298675059|ref|YP_003726809.1|  94 WLKSirdnikykgygnIDITFPIIDDLNMKVAQKYGMI--H 132
                                       55556667999999876778999999**********54..3 PP

>> 1-cysPrx_C  C-terminal domain of 1-Cys peroxiredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.0   2.1e-13   1.3e-09       1      39 [.     198     236 ..     198     237 .. 0.96

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 2.1e-13
                                       HHHHHHHHT-BB-TTT.TBT-EEE---SSHHHHHHHHHH CS
                        1-cysPrx_C   1 ALQladkhgvatPAnWkpGdkvivpPpateedavkryle 39 
                                       A+Q +d+++v tP +W pGd+ i+ Pp+t+e a++r +e
  gi|298675059|ref|YP_003726809.1| 198 AMQKSDEENVQTPEGWYPGDDLIINPPKTYESAIERIKE 236
                                       89**********************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2140.69
//
Query:       gi|298675060|ref|YP_003726810.1|  [L=112]
Description: PPE repeat-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-06   27.6   3.8     0.0081   15.9   0.1    3.0  4  GLTT            GLTT repeat (6 copies)
     0.0034   17.2   7.6      0.022   14.7   4.8    2.2  2  Pentapeptide_2  Pentapeptide repeats (8 copies)


Domain annotation for each model (and alignments):
>> GLTT  GLTT repeat (6 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1      0.43   3.9e+03      13      17 ..      26      30 ..      25      30 .. 0.44
   2 ?   -2.7   0.0      0.63   5.6e+03       7      11 ..      43      47 ..      43      52 .. 0.50
   3 !   15.9   0.1     9e-07    0.0081       5      27 ..      61      83 ..      60      84 .. 0.92
   4 !   11.8   0.0   1.7e-05      0.16       6      22 ..      87     103 ..      85     104 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.43
                              GLTT 13 vtmGL 17
                                      v++GL
  gi|298675060|ref|YP_003726810.1| 26 VVLGL 30
                                      44554 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.63
                              GLTT  7 LvslG 11
                                      Lvs+G
  gi|298675060|ref|YP_003726810.1| 43 LVSAG 47
                                      33333 PP

  == domain 3  score: 15.9 bits;  conditional E-value: 9e-07
                              GLTT  5 lGLvslGLvtmGLvtlGLvtmGL 27
                                       G++s+G+ + GL++ G+ ++G+
  gi|298675060|ref|YP_003726810.1| 61 TGIFSAGIFSAGLFAVGVFSIGV 83
                                      69******************998 PP

  == domain 4  score: 11.8 bits;  conditional E-value: 1.7e-05
                              GLTT   6 GLvslGLvtmGLvtlGL 22 
                                       G++s+G+ +mG+ ++GL
  gi|298675060|ref|YP_003726810.1|  87 GIFSIGIFSMGIYAIGL 103
                                       8999*******999998 PP

>> Pentapeptide_2  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   4.8   2.4e-06     0.022       3      39 ..      51      87 ..      45      88 .. 0.96
   2 !   13.3   7.1   6.3e-06     0.057       3      39 ..      61      97 ..      57      98 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.4e-06
                    Pentapeptide_2  3 tGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39
                                      +G+l +G++ tG f  G  + G f +G + +G + +G
  gi|298675060|ref|YP_003726810.1| 51 IGYLSAGNFSTGIFSAGIFSAGLFAVGVFSIGVFSFG 87
                                      799*******************************998 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 6.3e-06
                    Pentapeptide_2  3 tGslNsGsgNtGffNlGsgNtGsfNlGsgNtGsgntG 39
                                      tG++ +G +  G+f +G  ++G f +G + +G++  G
  gi|298675060|ref|YP_003726810.1| 61 TGIFSAGIFSAGLFAVGVFSIGVFSFGIFSIGIFSMG 97
                                      89*******************************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       868  (0.0484132); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 825.60
//
Query:       gi|298675061|ref|YP_003726811.1|  [L=405]
Description: peptidase U32 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-83  279.4   0.0    2.1e-83  279.1   0.0    1.1  1  Peptidase_U32  Peptidase family U32
  ------ inclusion threshold ------
      0.032   14.6   0.4      0.076   13.4   0.4    1.6  1  GTP_EFTU_D2    Elongation factor Tu domain 2
       0.12   12.7   0.0       0.24   11.7   0.0    1.5  1  RGS            Regulator of G protein signaling domain


Domain annotation for each model (and alignments):
>> Peptidase_U32  Peptidase family U32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  279.1   0.0   3.5e-87   2.1e-83       1     231 [.      79     302 ..      79     304 .. 0.95

  Alignments for each domain:
  == domain 1  score: 279.1 bits;  conditional E-value: 3.5e-87
                     Peptidase_U32   1 leklrkyleklaelgvdavivqDpgvlelareeapelelhlStqanitnseavrflkelGasrvvlaRElsleeika 77 
                                       l++l k l+++ ++++davi +Dp+v++ a ++   l +h+Stqan++n+++++f+k lGasrv+l+REl+le+ik+
  gi|298675061|ref|YP_003726811.1|  79 LQELDKVLDDVSKVNIDAVIAWDPAVIKKAVDK--GLDIHISTQANVSNWATAEFYKTLGASRVILSRELTLEQIKD 153
                                       578999**************************9..****************************************** PP

                     Peptidase_U32  78 ikekvpdvelEvfvhGalcvaysGrcllssylsgrsanrgecaqpcrldyrlieekekgeeepieedekgtyllspk 154
                                       i++++ d+elEvfvhGa+c a+sGrc+ls+y+ g+san+gec+qpcr++++l  e+ ++ e       +g+ylls+k
  gi|298675061|ref|YP_003726811.1| 154 IRKNT-DIELEVFVHGAMCQAVSGRCYLSAYIVGKSANCGECSQPCRWQWTLHGENGEQIEL------EGKYLLSTK 223
                                       *****.*********************************************88887543333......377****** PP

                     Peptidase_U32 155 dlclieelpelleaGvdslKIeGRmkspeyvatvvrvYreaidallagr..eevkeelkeeleklanrgltsgfllg 229
                                       dlc+ie++pel++ Gvd++K+eGR+++++y+ tv ++Yrea+d++l+g+  +++++ +k +l + +nrg+++gf++g
  gi|298675061|ref|YP_003726811.1| 224 DLCMIEHIPELVNSGVDAFKVEGRLRNTSYINTVSKCYREALDNYLNGTytNQKAQFWKTKLIQEYNRGFSTGFYFG 300
                                       *************************************************97777889*******************9 PP

                     Peptidase_U32 230 rk 231
                                       ++
  gi|298675061|ref|YP_003726811.1| 301 TP 302
                                       97 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.4   1.3e-05     0.076      13      61 ..     345     390 ..     344     397 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.3e-05
                                       EETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEES CS
                       GTP_EFTU_D2  13 lkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaik 61 
                                       l++Gd ++i g +t    i  ++ sl t+++ + +a++g+ +G  v+ k
  gi|298675061|ref|YP_003726811.1| 345 LQVGDDIVIEGATT---YIEQKVESLVTNRKHLSTAEKGQLVGMSVRDK 390
                                       789******88777...899************************99866 PP

>> RGS  Regulator of G protein signaling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.9e-05      0.24       9      71 ..     259     343 ..     252     363 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.9e-05
                                       HHHHHHHHHHHHHTTCTHHHHHHHH..HHHHHTS....................SHHHHHHHHHHHHHHHHTSTTST CS
                               RGS   9 qpgrslFreFlesefseenlsFwla..veefkka....................keqeelkkkakeIyneylapssp 63 
                                       + +r+++ ++l+ ++ +++ +Fw+   ++e+++                      + +++k++a  I+ +y  ++s+
  gi|298675061|ref|YP_003726811.1| 259 KCYREALDNYLNGTYTNQKAQFWKTklIQEYNRGfstgfyfgtpgpeglnpdsdMNISSVKREAVGIITNYYPKQSA 335
                                       4589999****************86669*****9*******************9999***************99999 PP

                                       TSSTS-HH CS
                               RGS  64 kelnidkk 71 
                                        ++++ ++
  gi|298675061|ref|YP_003726811.1| 336 ASVDLREQ 343
                                       99998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.84
# Mc/sec: 1456.78
//
Query:       gi|298675062|ref|YP_003726812.1|  [L=370]
Description: cytochrome c biogenesis protein transmembrane region [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-14   54.6  13.7    2.2e-14   53.9  13.7    1.3  1  DsbD           Cytochrome C biogenesis protein transmembrane 
    4.9e-10   39.3   0.5    9.5e-10   38.4   0.5    1.4  1  Thioredoxin_3  Thioredoxin domain
    4.4e-07   29.8   0.1    7.8e-07   29.0   0.1    1.4  1  Thioredoxin    Thioredoxin
    5.6e-07   29.7  12.8    1.3e-06   28.5  12.8    1.7  1  DsbD_2         Cytochrome C biogenesis protein transmembrane 
  ------ inclusion threshold ------
      0.014   15.8   1.4       0.35   11.3   0.1    2.9  2  DUF2231        Predicted membrane protein (DUF2231)
       0.02   15.2   2.8        1.6    9.0   0.2    2.9  3  DUF1772        Domain of unknown function (DUF1772)
       0.02   15.1   0.1      0.041   14.1   0.1    1.5  1  Glutaredoxin   Glutaredoxin
       0.11   12.4   0.1       0.34   10.7   0.1    1.7  1  TraF           F plasmid transfer operon protein
       0.12   12.8   0.3        0.4   11.1   0.3    1.8  1  Thioredoxin_2  Thioredoxin-like domain


Domain annotation for each model (and alignments):
>> DsbD  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9  13.7   1.1e-17   2.2e-14       2     211 ..     152     365 ..     151     367 .. 0.81

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 1.1e-17
                              DsbD   2 flaGllsflsPCilpliPaylsyisgvsvedvktekkkvkvllkallFvlGlslvfvslglsaaflgqllkdvkevi 78 
                                       + aG+l+ + PC+l+++ a+++ ++ +s +++++       l+    F  G+ ++++ +g+++ + ++ + +++e+i
  gi|298675062|ref|YP_003726812.1| 152 LIAGILAGFNPCLLAVM-AFMASVTLTSEGNRRDM------LTIVAGFCAGIFITYTVVGMGILKTINSMPEIHETI 221
                                       78************987.67777787888887774......677789*****************************9 PP

                              DsbD  79 rrvaglivillGlhflgvfkievleklkll............lkikkkaelsvlgalllGltFalgwsPCigPvlas 143
                                       +  + +  ++ Gl    +++   +++  +              +ik k+ l  + +l +G +F+l+ +PC+g v  s
  gi|298675062|ref|YP_003726812.1| 222 TLFMVT--LIGGLGAWHIYDAYYMKTRDKStfktpkslisfmGNIKGKNIL--MLSLFAGGLFSLVKAPCVGAVYLS 294
                                       988655..5567888888996666655555677888888875555555555..778999999*************** PP

                              DsbD 144 vlalaaskeslakgallllvyvlGlaipfllv.gll.lellkkklkslk.kyskaveiaggvllvllGvll 211
                                       +l +  ++ ++ +g+l+l vy  G + p++++ gll ++l   ++  ++ k  + ++ ++gv+l++l +ll
  gi|298675062|ref|YP_003726812.1| 295 ILDMMMTRVEVVEGTLYLAVYNFGVVFPVFILgGLLaFGLNPDTVTEFReKRRSEIRLITGVVLIILAILL 365
                                       ***************************9655516662456667788886256678************9997 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.5   4.8e-13   9.5e-10       7      61 ..      45     101 ..      38     104 .. 0.91

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 4.8e-13
                                       SSSSTTCHHHHHHHHHHCHCC.TCECEEECC.TTHHHHHHCT-SSSSEEECTTCEEE CS
                     Thioredoxin_3   7 gpgCakCpklekavkeaaaek.gikaevekv.tdfeeiekygVmsvPalvidgkvvv 61 
                                         gC kC+k++ +++ +++++ +i+++ +++ t ++++++ygV++vP lvi++  ++
  gi|298675062|ref|YP_003726812.1|  45 ENGCSKCQKIAPVIENVVDNSeNINYSSYEIsTSYNQMKEYGVYTVPVLVINESTKI 101
                                       579******************77***888888********************99876 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.1   3.9e-10   7.8e-07      15      93 ..      33     111 ..      30     123 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 3.9e-10
                                       TTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTE.EEEEEES CS
                       Thioredoxin  15 akekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngk.evkkyeg 90 
                                       ++++++ +  Fy + C +C+++aP++e++ ++ + ++     ++ ++ +  k+y+v  +P l++ ++ k + ++y+g
  gi|298675062|ref|YP_003726812.1|  33 SAQDDTRVEYFYENGCSKCQKIAPVIENVVDNSE-NINYSSYEISTSYNQMKEYGVYTVPVLVINESTKiTYQDYKG 108
                                       55566667789********************999.***************************999999999999999 PP

                                       S-H CS
                       Thioredoxin  91 are 93 
                                       + +
  gi|298675062|ref|YP_003726812.1| 109 NIT 111
                                       865 PP

>> DsbD_2  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5  12.8   6.7e-10   1.3e-06       2     198 ..     151     363 ..     147     364 .. 0.73

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 6.7e-10
                            DsbD_2   2 afllgLlgsl.hClgmCggivlalslskp..kra.la.lllynlGRilsYallGalvgllgsvlqlageleglrall 73 
                                       ++++g+l+++ +Cl+   +++++++l+++  +r  l   + + +G  ++Y+++G+ +    +++  +   e ++ ++
  gi|298675062|ref|YP_003726812.1| 151 VLIAGILAGFnPCLLAVMAFMASVTLTSEgnRRDmLTiVAGFCAGIFITYTVVGMGILKTINSMPEIH--ETITLFM 225
                                       68899999999*************99996324443335889*************86655555553333..2344444 PP

                            DsbD_2  74 gvllgllllllglkll.lkkkllklerlgkllsrllkklakklkslasalllGllnGll..pC.glvysalllal.a 145
                                         l+g l+++ + ++  +k + +++ +++k l +++++++ k + l  +l++G l++l+  pC g vy+ +l ++ +
  gi|298675062|ref|YP_003726812.1| 226 VTLIGGLGAWHIYDAYyMKTRDKSTFKTPKSLISFMGNIKGK-NILMLSLFAGGLFSLVkaPCvGAVYLSILDMMmT 301
                                       445555554444443323444444556677777777777775.667778999999999777**98999777755505 PP

                            DsbD_2 146 sgsaleGalvmlaFgLGTlpalllfglllgll.........skklrkkllrlagvllillgl 198
                                         +++eG l+++++  G + +++++g ll++          ++k r +++ ++gv+li+l++
  gi|298675062|ref|YP_003726812.1| 302 RVEVVEGTLYLAVYNFGVVFPVFILGGLLAFGlnpdtvtefREKRRSEIRLITGVVLIILAI 363
                                       679***********************999996588887777778888888899999999987 PP

>> DUF2231  Predicted membrane protein (DUF2231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00018      0.35      12      80 ..     187     259 ..     183     281 .. 0.82
   2 ?    2.2   0.1      0.12   2.4e+02      20      57 ..     325     365 ..     306     368 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00018
                           DUF2231  12 alvigflaalaGlvelllaepsirakktallHavggvlllalivaltvW....rfvlrlreeeqvsplylals 80 
                                        +v+gf a ++ ++ ++ +   ++ +++  +H ++ ++++ li +l +W     +++++r++++ +    ++s
  gi|298675062|ref|YP_003726812.1| 187 TIVAGFCAGIFITYTVVGMGILKTINSMPEIHETITLFMVTLIGGLGAWhiydAYYMKTRDKSTFKTPKSLIS 259
                                       56777888888888888877777899999********************999999999999987766655555 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.12
                           DUF2231  20 alaGlvelllaepsi....rakktallHavggvlllalival 57 
                                       +l Gl+ ++l+ p +    r+k+   +  ++gv+l++l+++l
  gi|298675062|ref|YP_003726812.1| 325 ILGGLLAFGLN-PDTvtefREKRRSEIRLITGVVLIILAILL 365
                                       45567777777.44458889999999999******9999885 PP

>> DUF1772  Domain of unknown function (DUF1772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.1   2.2e+03       3      18 ..      21      36 ..      12      56 .. 0.64
   2 ?    9.0   0.2   0.00082       1.6      38      86 ..     160     206 ..     120     244 .. 0.63
   3 ?    5.2   0.1     0.013        25      27      77 ..     310     363 ..     278     369 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.1
                           DUF1772  3 ilafslfvvPallslp 18
                                      il + lf vP++++++
  gi|298675062|ref|YP_003726812.1| 21 ILIILLFLVPTVSAQD 36
                                      4444455555555555 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00082
                           DUF1772  38 vfpplallsalafa.ylaaraasrgarllylaaaallllsivp.yTllvmv 86 
                                       + p  +ll++ af+  ++   +   +r ++ ++ a ++++i++ yT++ m 
  gi|298675062|ref|YP_003726812.1| 160 FNP--CLLAVMAFMaSVTL-TSEGNRRDML-TIVAGFCAGIFItYTVVGMG 206
                                       333..34444444412222.2333333333.4455555677777***9993 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.013
                           DUF1772  27 qwrrlfkrgkavfpplallsalafayla......araasrgarllylaaaallllsi 77 
                                       +  ++++ g +vfp++ l+ +laf+ l       +r ++r+  +l++++ ++ +l+i
  gi|298675062|ref|YP_003726812.1| 310 LYLAVYNFG-VVFPVFILGGLLAFG-LNpdtvteFREKRRSEIRLITGVVLI-ILAI 363
                                       556678778.99************9.6679**99889999999998554333.3334 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1     2e-05     0.041       1      57 [.      40      97 ..      40      99 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2e-05
                                      EEEEESTSSHHHHHHHHHH.....HHTTGGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEETT CS
                      Glutaredoxin  1 vvlftkptCpyCkkakrlL.....kelgvkfeeidvdkdeeireelkelsgvrtvPqvfidg 57
                                      v++f  ++C  C+k+  +      ++ ++++  ++++       ++ke+ gv tvP+++i++
  gi|298675062|ref|YP_003726812.1| 40 VEYFYENGCSKCQKIAPVIenvvdNSENINYSSYEISTS---YNQMKEY-GVYTVPVLVINE 97
                                      7899999*******99999888888888**********7...999****.**********96 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00017      0.34     135     197 ..      42      94 ..      34     103 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00017
                              TraF 135 fFyrgkcpyceaqapilqafadkyglevraVsvdgrplpelpnarvdkgqaarlgvkrtPalv 197
                                       +Fy+++c+ c++ ap+++++ d+ +     ++     +        + +q++++gv ++P+lv
  gi|298675062|ref|YP_003726812.1|  42 YFYENGCSKCQKIAPVIENVVDNSE----NINYSSYEIS------TSYNQMKEYGVYTVPVLV 94 
                                       8*****************9988753....2222222221......222355566666666665 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.3    0.0002       0.4      11      99 ..      42     109 ..      37     117 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0002
                     Thioredoxin_2  11 vftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPtivfl 87 
                                       +f+ ++C  C+k+  +++++           +++s     ++i ++  +      i +++  +++ygv  +P +v+ 
  gi|298675062|ref|YP_003726812.1|  42 YFYENGCSKCQKIAPVIENV-----------VDNS-----ENINYSSYE------ISTSYNQMKEYGVYTVPVLVIN 96 
                                       68999999999999999999...........5555.....888888888......788999999*********9998 PP

                     Thioredoxin_2  88 dgk.eivarlpGy 99 
                                       + +   +  ++G 
  gi|298675062|ref|YP_003726812.1|  97 ESTkITYQDYKGN 109
                                       8886555566665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       968  (0.0539907); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2387.63
//
Query:       gi|298675063|ref|YP_003726813.1|  [L=151]
Description: hypothetical protein Metev_1135 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.097   12.1   0.0       0.12   11.9   0.0    1.2  1  DUF769    Xylella fastidiosa protein of unknown function (DUF


Domain annotation for each model (and alignments):
>> DUF769  Xylella fastidiosa protein of unknown function (DUF769)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   6.4e-06      0.12     111     174 ..      80     143 ..      50     148 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.4e-06
                            DUF769 111 vlreldgtpqkkvdkwwkidrlqtaelvGGdevqfgidsavsesvegvikagvalveagikerk 174
                                        + +ldgtp ++ ++ wk++++ ++    G +  + +++ vs   +  ++ +++ v++ + ++k
  gi|298675063|ref|YP_003726813.1|  80 TVYNLDGTPVQNETNVWKVEAMERTCACSGIDDLYVVEGYVSADTGELLEISTKTVSEQNYDKK 143
                                       3469******************999888888878899999999999988888888887766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       916  (0.0510904); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 995.95
//
Query:       gi|298675064|ref|YP_003726814.1|  [L=459]
Description: deoxyribodipyrimidine photo-lyase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-73  245.4   2.4    5.8e-73  244.7   2.4    1.3  1  FAD_binding_7   FAD binding domain of DNA photolyase
      2e-44  151.5   0.0    3.6e-44  150.6   0.0    1.4  1  DNA_photolyase  DNA photolyase


Domain annotation for each model (and alignments):
>> FAD_binding_7  FAD binding domain of DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  244.7   2.4   6.5e-77   5.8e-73       2     199 ..     265     452 ..     264     454 .. 0.95

  Alignments for each domain:
  == domain 1  score: 244.7 bits;  conditional E-value: 6.5e-77
                                       HHHHHHHHHHHHHHHCSTTTTTSSTTGCCTT------HH.HHHHHHTT-SS-HHHHHHHHHHHHHS---HHHHHHHH CS
                     FAD_binding_7   2 lreLlwrefyyallaaepelaeralkekfdripweeseeekleaWkeGrTGfPlvDAamrqLretGwmhnrlRmiva 78 
                                       +++L+wr+fy++l++++p + ++++k+kfd+i+w+++++ k+++W++G+TGfP+vDA++r+++ tG+mhnr+Rmi+a
  gi|298675064|ref|YP_003726814.1| 265 ITQLYWRDFYTYLAHHYPYIFKQSFKKKFDSIEWDNDSD-KFKKWCAGETGFPIVDAGIREMNYTGYMHNRVRMITA 340
                                       579*******************************88766.7************************************ PP

                                       HHHCTTT-B-HHHHHHHHHHH-TT--CCHHHHHHHHHCT-STTS-STT----CCCCHHHCSTT-HHHHHH-GGGTTS CS
                     FAD_binding_7  79 sFltkdLlidWregeevFeellvDadlasnagnwqwlagtgadaapafrifnpvkqgkkfDpegeyirrwvpeLkkl 155
                                       sFl+kdL+idW++ge++F+++lvD+d ++n gnwqw+a+tg da+p+frifnp++q+kkfD+e+ yi++w+ eL+++
  gi|298675064|ref|YP_003726814.1| 341 SFLVKDLHIDWKWGEQYFARKLVDYDKSVNIGNWQWSASTGPDAQPFFRIFNPWSQQKKFDSECIYIKKWIEELRNV 417
                                       ***************************************************************************** PP

                                       -HHHHT-GGGSGCHHHHHHT--TTTSS---SS-HHHHHHHHHHH CS
                     FAD_binding_7 156 pakyihepwkapaeeqkkagvvlgkdYpkpivdhkearkralea 199
                                       + k ih+            + +    Yp+pi++hk++r++ l+ 
  gi|298675064|ref|YP_003726814.1| 418 SCKSIHNLE---------NKNTFIPGYPEPIINHKTEREKSLAV 452
                                       ******744.........23467889*************99876 PP

>> DNA_photolyase  DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.6   0.0   4.1e-48   3.6e-44       2     160 ..       8     166 ..       7     172 .. 0.94

  Alignments for each domain:
  == domain 1  score: 150.6 bits;  conditional E-value: 4.1e-48
                                       EEEESS---STT-HHHHHHHCTTSEEEEEEEE-HH..HHTCGS-CHHHHHHHHHHHHHHHHHHHHTT--EEEEESSH CS
                    DNA_photolyase   2 lvWfrrDlRlhDNpALaaAaasgepvipvfvldpe..kahklrvgaarvdfllesLadLdeeLrelgirLvvrrgdp 76 
                                       ++ frrDlR+ DN+ L +A++++e vip+f++dp+  + +++ +++++ +fl+esL+dL+++L+++g +L++++g +
  gi|298675064|ref|YP_003726814.1|   8 IFIFRRDLRVDDNTGLDYALENSEYVIPCFIFDPRliE-KNDNFNPNSFQFLIESLEDLKHQLNDKGAKLYLFHGIA 83 
                                       677********************************853.44468********************************* PP

                                       HHHHHHHHHHCTECEEEEE---SHHHHHHHHHHHHHHHHCTSEEEEE--SSSS-HHHHHTTTSSSHSSHHHHHHCHH CS
                    DNA_photolyase  77 advlpelakelgasavvanreyepdererdeavkealrkagievesfddhtlvepgevktkkgkpykvFtpfrkrwl 153
                                       ++v+ +l++++ ++av++nr+y+p+ ++rdea k+a++  +++++s++d +l +p+++kt+kg+py vFtpf+k++ 
  gi|298675064|ref|YP_003726814.1|  84 ENVVTNLINKNLIDAVFVNRDYTPFSKKRDEAFKKACEMYNVDFISCNDLLLNNPDKIKTQKGTPYTVFTPFFKKAS 160
                                       **************************************************************************998 PP

                                       HHHCS-T CS
                    DNA_photolyase 154 kelkepl 160
                                       k ++ +l
  gi|298675064|ref|YP_003726814.1| 161 K-FDVNL 166
                                       7.55544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3432.29
//
Query:       gi|298675065|ref|YP_003726815.1|  [L=906]
Description: DEAD/DEAH box helicase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-27   95.2   0.0    1.2e-26   93.6   0.0    1.8  2  DEAD             DEAD/DEAH box helicase
    9.9e-17   61.5   0.0    2.3e-16   60.3   0.0    1.7  1  DUF1998          Domain of unknown function (DUF1998)
    2.5e-15   56.8   0.1    1.6e-14   54.2   0.0    2.4  2  Helicase_C       Helicase conserved C-terminal domain
    8.1e-13   47.6   8.7     0.0007   19.3   0.5    3.8  3  TPR_1            Tetratricopeptide repeat
    1.2e-12   47.0   6.2     0.0002   21.3   0.3    3.7  3  TPR_2            Tetratricopeptide repeat
    1.5e-11   44.6   0.0    3.8e-11   43.3   0.0    1.7  1  ResIII           Type III restriction enzyme, res subunit
    3.3e-11   42.7   1.3    9.4e-05   22.0   0.2    2.6  2  TPR_11           TPR repeat
    1.6e-10   40.3   4.0      0.026   14.7   0.1    4.0  3  TPR_8            Tetratricopeptide repeat
    5.4e-10   39.6   0.4    3.9e-06   27.3   0.0    2.4  2  TPR_19           Tetratricopeptide repeat
    1.5e-07   31.5   0.0    0.00064   19.8   0.0    2.4  2  TPR_9            Tetratricopeptide repeat
    1.4e-05   25.1   6.6     0.0098   15.9   0.2    3.5  3  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
      3e-05   24.5   0.0      0.095   13.6   0.0    3.0  3  TPR_14           Tetratricopeptide repeat
    0.00014   22.4   0.0       0.31   11.7   0.0    2.4  2  TPR_16           Tetratricopeptide repeat
    0.00036   20.8   0.5      0.019   15.2   0.4    2.6  2  TPR_12           Tetratricopeptide repeat
    0.00087   19.5   4.7     0.0016   18.6   4.7    1.5  1  ANAPC3           Anaphase-promoting complex, cyclosome, subun
     0.0095   16.0   1.5        0.5   10.5   0.1    3.2  3  MIT              MIT (microtubule interacting and transport) 
  ------ inclusion threshold ------
      0.023   14.2   0.0      0.058   12.9   0.0    1.7  1  Glycos_transf_1  Glycosyl transferases group 1
       0.25   11.8   0.8         21    5.6   0.1    2.7  2  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
        5.2    7.7  11.9       0.17   12.4   0.2    3.5  2  TPR_17           Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.6   0.0   1.2e-29   1.2e-26       2     170 ..      56     225 ..      55     230 .. 0.86
   2 ?   -2.2   0.0       3.3   3.1e+03      44      94 ..     286     337 ..     276     354 .. 0.64

  Alignments for each domain:
  == domain 1  score: 93.6 bits;  conditional E-value: 1.2e-29
                                       HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTT..STS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxx RF
                              DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkky..idl 76 
                                       + Q eai++i +g++++++  T+sGKTl +lipv+++++   +++   +++v+P+ +L++++++++++f ++  +d+
  gi|298675065|ref|YP_003726815.1|  56 KHQVEAIENIRNGKNIVLSTGTASGKTLSYLIPVFEHLT---DNNDATVIYVSPLNALVNDQVKKFQNFRDEtgLDI 129
                                       689***********************************6...588889***********************834558 PP

                                       EEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHH...HCTSSH....CTTEEEEEEETHHHHHHTTTHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  77 rvlliiggvaardqlskldngvdivvgtpgrlddll...stgkln....lsqvrflVlDEadrlldqgfsdfinril 146
                                        ++ +ig+ + ++++s+  n+ +i++++p++l+  l   +  + +    ls++++++lDE + +     +  + ++l
  gi|298675065|ref|YP_003726815.1| 130 DINRFIGSIPDEEKKSAK-NNSRIIFTNPEMLHMSLlqwK--H-QwfrvLSNLKYIILDESHYYRGV-LGSNMANLL 201
                                       888899988887777777.9*************9553542..2.22346*****************9.99999999* PP

                                       HHSHHHCTTSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 147 nqlpqitcdgklqrqvivlSATlp 170
                                       ++l++ ++   ++ q i+++AT+ 
  gi|298675065|ref|YP_003726815.1| 202 RRLERVCNYYGSNPQYICCTATIG 225
                                       ***776666559999*******96 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.3
                                       TSTS-EEEEEESSHHHHHHHHHHHHHHTTTST..SEEEEEETTSSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx RF
                              DEAD  44 gktgpkalivePtreLaeqtlnnlkkfkkyid..lrvlliiggvaardqlskl 94 
                                        ++g + +i + +r+ ae ++  +kk +++ d   +v++ + g   +d+++++
  gi|298675065|ref|YP_003726815.1| 286 VQDGYQSIIFTRSRQKAERMALSAKKELETRDssEKVCS-YRGGYHKDDRENI 337
                                       567888999999999999999999999998663334443.3333333444444 PP

>> DUF1998  Domain of unknown function (DUF1998)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.0   2.5e-19   2.3e-16       2      83 .]     656     735 ..     655     735 .. 0.95

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 2.5e-19
                           DUF1998   2 ehalinalplflqcdesdlgteckapedeprkrpariliydavpgGaGiaekaaelleellraalelieecdCeeaG 78 
                                       eh +i + p++l  d++d+g+ +k+++++   ++ +i+iyd++ gG+G+ae++++ l e+l+ +l+ ie+c+C+ +G
  gi|298675065|ref|YP_003726815.1| 656 EHGMIAMYPIHLLADRNDVGGLSKSNHSD-IGDKSGIFIYDGHNGGVGYAENGYHKLIEMLDVTLNAIENCPCN-DG 730
                                       899********************977665.6899***************************************8.** PP

                           DUF1998  79 CpaCl 83 
                                       Cp+C+
  gi|298675065|ref|YP_003726815.1| 731 CPSCI 735
                                       ****7 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       5.1   4.8e+03      11      57 ..      92     145 ..      81     151 .. 0.60
   2 !   54.2   0.0   1.7e-17   1.6e-14      11     110 ..     284     389 ..     273     390 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 5.1
                                       HHTTTTSEEEEEESSHHHHHH..HHHHHHHT......TSTEEEESTTSTHHHHHH CS
                        Helicase_C  11 kleeeggkilifvntidrlek..vklllekk......gikvavlhgelpqneree 57 
                                       +l+ +++ ++i+v   + l +  vk + +++      +i + ++ g++p +e++ 
  gi|298675065|ref|YP_003726815.1|  92 HLTDNNDATVIYVSPLNALVNdqVKKF-QNFrdetglDIDINRFIGSIPDEEKKS 145
                                       455666666666666663322244555.122345567788888888888888765 PP

  == domain 2  score: 54.2 bits;  conditional E-value: 1.7e-17
                                       HHTTTTSEEEEEESSHHHHHH.....HHHHHHHT......TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGG CS
                        Helicase_C  11 kleeeggkilifvntidrlek.....vklllekk......gikvavlhgelpqnereeileqfnkgesdvLiatdva 76 
                                       ++ ++g++++if+++++++e+      k     +      + kv+ + g   +++re i +q  +g+ + +i+t+++
  gi|298675065|ref|YP_003726815.1| 284 TFVQDGYQSIIFTRSRQKAERmalsaKK-----EletrdsSEKVCSYRGGYHKDDRENIEKQLSEGTLRGVISTNAL 355
                                       56799************99874444333.....23344679************************************ PP

                                       TSSSTSTTESEEEESSSSSSHHHHHHHHTTSSST CS
                        Helicase_C  77 erGidipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                       e Gidi ++++++  ++p +v + +q++GR+gR+
  gi|298675065|ref|YP_003726815.1| 356 ELGIDIGGLDVCVLDGYPGTVMNTKQQAGRAGRG 389
                                       *********************************7 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   2.2e-06    0.0021       1      34 []     789     822 ..     789     822 .. 0.96
   2 !   14.0   0.3   3.6e-05     0.034       1      29 [.     823     851 ..     823     852 .. 0.96
   3 !   19.3   0.5   7.4e-07    0.0007       7      34 .]     863     890 ..     857     890 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.2e-06
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+ +  +G ++ k +k++ A e+++ AL+l+P+n
  gi|298675065|ref|YP_003726815.1| 789 ADEWIKKGRVFGKEKKHKNACECFDNALQLEPDN 822
                                       78899***************************98 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3.6e-05
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALe 29 
                                       a+aly ++ a+f+l +y++  e+ +k+Le
  gi|298675065|ref|YP_003726815.1| 823 ANALYDKAKACFHLRMYEQSSECINKVLE 851
                                       78**************************9 PP

  == domain 3  score: 19.3 bits;  conditional E-value: 7.4e-07
                                       HHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   7 lGnayfklgkydeAleyyekALelnPnn 34 
                                       +G  + +lgky+ Al+ ++kAL+l+P+n
  gi|298675065|ref|YP_003726815.1| 863 KGINLVNLGKYQAALDEFNKALKLEPDN 890
                                       6666779*******************98 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   8.2e-06    0.0078       1      34 []     789     822 ..     789     822 .. 0.95
   2 !   10.9   0.2   0.00044      0.42       1      29 [.     823     851 ..     823     855 .. 0.94
   3 !   21.3   0.3   2.1e-07    0.0002       7      34 .]     863     890 ..     857     890 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.2e-06
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a+ +   G++  k ++++ A e+f+ Al+l+P+n
  gi|298675065|ref|YP_003726815.1| 789 ADEWIKKGRVFGKEKKHKNACECFDNALQLEPDN 822
                                       678999**************************98 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00044
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAle 29 
                                       a aly  ++a+++l  ye+  e+ +k+le
  gi|298675065|ref|YP_003726815.1| 823 ANALYDKAKACFHLRMYEQSSECINKVLE 851
                                       689************************98 PP

  == domain 3  score: 21.3 bits;  conditional E-value: 2.1e-07
                             TPR_2   7 lGlayyklgdyeeAleafekAleldPnn 34 
                                        G  + +lg+y+ Al+ f+kAl+l+P+n
  gi|298675065|ref|YP_003726815.1| 863 KGINLVNLGKYQAALDEFNKALKLEPDN 890
                                       688999********************98 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   0.0     4e-14   3.8e-11       3     154 ..      53     208 ..      51     226 .. 0.76

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 4e-14
                                       EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGT CS
                            ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkfl 78 
                                       +l+++Q eaien++      + k++++   T +GKTl + + + e+l+ + +   ++ + p ++l++   ++f++f 
  gi|298675065|ref|YP_003726815.1|  53 NLYKHQVEAIENIR------NGKNIVLSTGTASGKTLSYlIPVFEHLTDN-NDATVIYVSPLNALVNDQVKKFQNFR 122
                                       6899*********6......678999999999*******67777777776.556*********************** PP

                                       GG......GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-S..EEEEETGGGTTS...T. CS
                            ResIII  79 seayke..igkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfd..viiiDEaHrlgak..k. 148
                                       +e+  +  i+ ++ +  +++k+++++n++i++t+ ++l+ ++    +++++  r  ++  +ii DE+H +++   + 
  gi|298675065|ref|YP_003726815.1| 123 DETGLDidINRFIGSIPDEEKKSAKNNSRIIFTNPEMLHMSL---LQWKHQWFRVLSNlkYIILDESHYYRGVlgSn 196
                                       ***999995555555555555557******************...888888877666667********999865522 PP

                                       ......TTHHHH CS
                            ResIII 149 ......swreil 154
                                               +++ 
  gi|298675065|ref|YP_003726815.1| 197 manllrRLERVC 208
                                       223333444444 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   8.7e-07   0.00082       1      37 [.     796     832 ..     796     836 .. 0.87
   2 !   22.0   0.2     1e-07   9.4e-05       6      30 ..     869     893 ..     866     894 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 8.7e-07
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGla 37 
                                       G+++ +  k ++A e++ +Al+l Pdna+a+y  ++a
  gi|298675065|ref|YP_003726815.1| 796 GRVFGKEKKHKNACECFDNALQLEPDNANALYDKAKA 832
                                       56666778999*********************99887 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 1e-07
                            TPR_11   6 eqGkyeeAieaYkkAlkldPdnaea 30 
                                        +Gky +A+ +++kAlkl Pdn+ +
  gi|298675065|ref|YP_003726815.1| 869 NLGKYQAALDEFNKALKLEPDNPKI 893
                                       58*********************87 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   4.8e-05     0.045       4      34 .]     792     822 ..     791     822 .. 0.96
   2 !   10.3   0.3    0.0007      0.66       1      30 [.     823     852 ..     823     852 .. 0.95
   3 !   14.7   0.1   2.8e-05     0.026      11      34 .]     867     890 ..     862     890 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.8e-05
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       + ++g++  k +++++A e++  al+l+pdn
  gi|298675065|ref|YP_003726815.1| 792 WIKKGRVFGKEKKHKNACECFDNALQLEPDN 822
                                       889**************************97 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0007
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekalel 30 
                                       a a+y ++++++ l  ye++ e+++k+le+
  gi|298675065|ref|YP_003726815.1| 823 ANALYDKAKACFHLRMYEQSSECINKVLEM 852
                                       679*************************96 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 2.8e-05
                                       HHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8  11 ylklgdyeeAkeyyekaleldpdn 34 
                                       + +lg+y++A   ++kal+l+pdn
  gi|298675065|ref|YP_003726815.1| 867 LVNLGKYQAALDEFNKALKLEPDN 890
                                       679*******************97 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   4.1e-09   3.9e-06       4      65 ..     802     863 ..     801     865 .. 0.95
   2 !   10.2   0.1   0.00091      0.85       5      29 ..     871     895 ..     867     904 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 4.1e-09
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasLl 65 
                                       e+++ +A + + +alq +p+na+a+++ A+a++ l  +++  +++++++e+  ++a++++L+
  gi|298675065|ref|YP_003726815.1| 802 EKKHKNACECFDNALQLEPDNANALYDKAKACFHLRMYEQSSECINKVLEMGYNTANLRKLK 863
                                       7789999999*********************************************9999997 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00091
                            TPR_19   5 gdyaeAlalleqalqedpknaearl 29 
                                       g+y++Al+ + +al+ +p+n+ ++ 
  gi|298675065|ref|YP_003726815.1| 871 GKYQAALDEFNKALKLEPDNPKIQK 895
                                       89999*************9999875 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00027      0.25       8      55 ..     802     849 ..     798     852 .. 0.89
   2 !   19.8   0.0   6.8e-07   0.00064      16      69 ..     844     897 ..     838     899 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00027
                             TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeay 55 
                                       e+++  a ++ +  l+l Pd +  ++d + + ++l  +++  ++ +  
  gi|298675065|ref|YP_003726815.1| 802 EKKHKNACECFDNALQLEPDNANALYDKAKACFHLRMYEQSSECINKV 849
                                       678999******************************999998887665 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 6.8e-07
                             TPR_9  16 avverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaeair 69 
                                       ++++ +l +  +++ +r   G+ l+ lG ++aAl++++ +l l+pd+p +  ++
  gi|298675065|ref|YP_003726815.1| 844 ECINKVLEMGYNTANLRKLKGINLVNLGKYQAALDEFNKALKLEPDNPKIQKLK 897
                                       799999*****************************************9987776 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.3    0.0031       2.9      15      38 ..     803     826 ..     800     827 .. 0.90
   2 ?    3.9   0.1     0.062        58       4      31 ..     826     853 ..     824     865 .. 0.82
   3 !   15.9   0.2     1e-05    0.0098      13      48 ..     869     904 ..     864     905 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0031
                                       T-HHHHHHHHHHHHHHTTS-HHHH CS
                        Fis1_TPR_C  15 geYseArryvdalLeiEPenrQaq 38 
                                       +++++A ++ d  L++EP+n +a+
  gi|298675065|ref|YP_003726815.1| 803 KKHKNACECFDNALQLEPDNANAL 826
                                       7899****************9985 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.062
                                       HHHHHHHHHHHT-HHHHHHHHHHHHHHT CS
                        Fis1_TPR_C   4 lYylAlGhyklgeYseArryvdalLeiE 31 
                                       lY  A +++ l+ Y+++ ++++ +Le+ 
  gi|298675065|ref|YP_003726815.1| 826 LYDKAKACFHLRMYEQSSECINKVLEMG 853
                                       778899*******************985 PP

  == domain 3  score: 15.9 bits;  conditional E-value: 1e-05
                                       HHT-HHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHH CS
                        Fis1_TPR_C  13 klgeYseArryvdalLeiEPenrQaqsLkeliedki 48 
                                        lg+Y+ A+   +  L++EP+n   q+Lk+  e+++
  gi|298675065|ref|YP_003726815.1| 869 NLGKYQAALDEFNKALKLEPDNPKIQKLKSDTEKQL 904
                                       79***************************9999886 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0078       7.4       5      43 ..     793     831 ..     789     832 .. 0.82
   2 ?    1.3   0.0      0.87   8.2e+02       2      29 ..     824     851 ..     823     852 .. 0.89
   3 !   13.6   0.0    0.0001     0.095       6      40 ..     862     896 ..     857     900 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0078
                            TPR_14   5 lalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                        + ++++    +++ A ++++ al+l Pd+a a++  a+
  gi|298675065|ref|YP_003726815.1| 793 IKKGRVFGKEKKHKNACECFDNALQLEPDNANALYDKAK 831
                                       555666667788999****************99987776 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.87
                            TPR_14   2 eallalaeallalGdpdeAiallrrala 29 
                                       +al++ a+a+++l+ ++++ ++ +++l+
  gi|298675065|ref|YP_003726815.1| 824 NALYDKAKACFHLRMYEQSSECINKVLE 851
                                       799**************99999888875 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 0.0001
                            TPR_14   6 alaeallalGdpdeAiallrralalaPddaeawll 40 
                                       + +  l +lG++++A++ +++al+l Pd++ ++ l
  gi|298675065|ref|YP_003726815.1| 862 LKGINLVNLGKYQAALDEFNKALKLEPDNPKIQKL 896
                                       55666899**********************99876 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0042       3.9       4      48 ..     796     837 ..     793     841 .. 0.83
   2 !   11.7   0.0   0.00033      0.31       4      34 ..     864     891 ..     862     901 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0042
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqg 48 
                                       +r + + ++   A + ++ al +    Pd+a Al+ ++ a++++ 
  gi|298675065|ref|YP_003726815.1| 796 GRVFGKEKKHKNACECFDNALQLE---PDNANALYDKAKACFHLR 837
                                       6666666677777899********...***************985 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00033
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPdaa 34 
                                       +  ++++g+y++A+  ++ alk+    Pd++
  gi|298675065|ref|YP_003726815.1| 864 GINLVNLGKYQAALDEFNKALKLE---PDNP 891
                                       66799*******************...6655 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.1    0.0016       1.5       9      74 ..     795     852 ..     791     852 .. 0.90
   2 !   15.2   0.4     2e-05     0.019       3      74 ..     823     886 ..     821     887 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0016
                            TPR_12   9 laavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                        + v  + +++  A+e+++ al++      pd+   a++l++ + +++ l  ye+  e  +++l++
  gi|298675065|ref|YP_003726815.1| 795 KGRVFGKEKKHKNACECFDNALQLE-----PDN---ANALYDKAKACFHLRMYEQSSECINKVLEM 852
                                       5677778999***********9999.....998...99********************99999997 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 2e-05
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       a+al+  a ++++l  y+++ e+ +k+le+       +  +ta+ +   g+ +  lg+y++Al+ +++al++
  gi|298675065|ref|YP_003726815.1| 823 ANALYDKAKACFHLRMYEQSSECINKVLEMG------Y--NTANLRKLKGINLVNLGKYQAALDEFNKALKL 886
                                       6677777778888888888888888887777......2..49999999999999999999999999999975 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   4.7   1.7e-06    0.0016       3      81 ..     803     882 ..     801     883 .. 0.96

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.7e-06
                                       T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                       +++knA  +++ +l+ e+++++++y +A++ +++  y++  e ++k  +   ++ + r l++  l+ L+ky+ A++ 
  gi|298675065|ref|YP_003726815.1| 803 KKHKNACECFDNALQLEPDNANALYDKAKACFHLRMYEQSSECINKVlEMGYNTANLRKLKGINLVNLGKYQAALDE 879
                                       789************************************************************************98 PP

                                       H-S CS
                            ANAPC3  79 Lek 81 
                                       + k
  gi|298675065|ref|YP_003726815.1| 880 FNK 882
                                       876 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.19   1.8e+02      26      42 ..     804     822 ..     801     835 .. 0.68
   2 ?   -0.6   0.1       1.5   1.4e+03      24      46 ..     836     860 ..     827     864 .. 0.80
   3 !   10.5   0.1   0.00053       0.5      26      54 ..     872     901 ..     870     905 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.19
                               MIT  26 lYkealelLlqalk.e.kn 42 
                                       + k+a+e +  al+ e +n
  gi|298675065|ref|YP_003726815.1| 804 KHKNACECFDNALQlEpDN 822
                                       5689999999999966433 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.5
                               MIT  24 lelYkealelLlqalk.e.kneerr 46 
                                       l++Y+++ e ++++l    ++++ r
  gi|298675065|ref|YP_003726815.1| 836 LRMYEQSSECINKVLEmGyNTANLR 860
                                       689***********98556555555 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00053
                               MIT  26 lYkealelLlqalk.ekneerrellrekie 54 
                                       +Y+ al+ +++alk e +  + ++l++ +e
  gi|298675065|ref|YP_003726815.1| 872 KYQAALDEFNKALKlEPDNPKIQKLKSDTE 901
                                       8*************9966688888887766 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.1e-05     0.058       8      99 ..      62     156 ..      56     164 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.1e-05
                                       HTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.....STTHHHHHHHHHHHCTTCGG.GEEE CS
                   Glycos_transf_1   8 klgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG....ngeeekelkklaeelelsdnv.iflg 79 
                                        ++++++k+i+ls g  +  K +++li +f++l ++ n+ +++ +        ++ k++++  +e +l  ++ +f+g
  gi|298675065|ref|YP_003726815.1|  62 IENIRNGKNIVLSTGTASG-KTLSYLIPVFEHLTDN-NDATVIYVSPlnalVNDQVKKFQNFRDETGLDIDInRFIG 136
                                       678899***********99.*************987.6666666666999867899************988846*** PP

                                       CCHSSSHHHHHHCESEEEEE CS
                   Glycos_transf_1  80 evsredleellknadifvlp 99 
                                        +++e++++ ++n+ i++ +
  gi|298675065|ref|YP_003726815.1| 137 SIPDEEKKSAKNNSRIIFTN 156
                                       ****************9976 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.053        50      69     122 ..     789     842 ..     766     858 .. 0.78
   2 ?    5.6   0.1     0.022        21      78     117 ..     866     905 ..     834     906 .] 0.78

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.053
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SS CS
                   Alkyl_sulf_dimr  69 aekvlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaes 122
                                       a++ ++k +   ke++ + a+e  +++++ +p+na+a   ka+a  +l   ++s
  gi|298675065|ref|YP_003726815.1| 789 ADEWIKKGRVFGKEKKHKNACECFDNALQLEPDNANALYDKAKACFHLRMYEQS 842
                                       6677788888889999******************99988888776666554444 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.022
                                       HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHH CS
                   Alkyl_sulf_dimr  78 ealkegdyrwaaellnhlvfadpenaeakelkadaleqlg 117
                                       + ++ g+y++a+   n+++  +p+n + ++lk d+ +ql+
  gi|298675065|ref|YP_003726815.1| 866 NLVNLGKYQAALDEFNKALKLEPDNPKIQKLKSDTEKQLS 905
                                       456889****************************999886 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   0.00018      0.17       1      24 [.     811     834 ..     811     846 .. 0.86
   2 ?    2.4   0.1      0.26   2.5e+02       2      14 ..     880     892 ..     879     894 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00018
                            TPR_17   1 lylkaleldPnnadaynnLAelll 24 
                                       ++ +al+l+P+na+a++ +A++  
  gi|298675065|ref|YP_003726815.1| 811 CFDNALQLEPDNANALYDKAKACF 834
                                       799*****************9865 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.26
                            TPR_17   2 ylkaleldPnnad 14 
                                       + kal+l+P+n++
  gi|298675065|ref|YP_003726815.1| 880 FNKALKLEPDNPK 892
                                       89*********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (906 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.63u 0.22s 00:00:00.85 Elapsed: 00:00:00.41
# Mc/sec: 6694.43
//
Query:       gi|298675066|ref|YP_003726816.1|  [L=396]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-22   80.1   0.0    2.9e-22   79.1   0.0    1.5  1  OrfB_IS605      Probable transposase
      7e-12   45.1   0.0    1.5e-11   44.0   0.0    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    2.9e-05   23.5   0.1    5.2e-05   22.7   0.1    1.4  1  Glyco_hydro_97  Glycoside hydrolase 97
  ------ inclusion threshold ------
      0.093   13.1   0.9       0.21   12.0   0.9    1.6  1  HEPN_Swt1       Swt1-like HEPN
       0.15   11.3   0.0       0.25   10.6   0.0    1.4  1  EAP30           EAP30/Vps36 family


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.1   0.0   8.2e-26   2.9e-22       2     117 ..     164     278 ..     163     281 .. 0.97

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 8.2e-26
                        OrfB_IS605   2 ipvevevelpkpkgnkaagiDlGinnLatvvtedgtw.flykgrrlksdykylakeiaelqsklkksknykkasrkl 77 
                                       i++e + e+p p++++ a+iDlGinn++t+v++ g+  +++kg  +ks ++ ++k+  +l s+++k +   k s+kl
  gi|298675066|ref|YP_003726816.1| 164 IVYEKDLETPDPNEENIASIDLGINNIVTMVNNIGEKpIVIKGGVAKSINQFYNKKSGKLKSIYDKLG--IKNSKKL 238
                                       88999999****************************99*****************************9..9****** PP

                        OrfB_IS605  78 arlhrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       ++l++k + ++++++hk+++++++ + + +++tL++g+  
  gi|298675066|ref|YP_003726816.1| 239 KKLYHKYKMKINDFFHKASKRIVDFCVKHNIGTLVIGYNE 278
                                       *************************************986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.0   4.2e-15   1.5e-11       1      69 []     299     373 ..     299     373 .. 0.96

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 4.2e-15
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke......alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f++l eql+yka++ G kv+e +++yTSk +   g+ +++      ++ +r + +++ g+ +++Dvn+a+Ni+k+
  gi|298675066|ref|YP_003726816.1| 299 FHRLPEQLKYKAEDVGLKVIEQEESYTSKCSFLDGEPVERrtsyigKRIKRGLFRSSNGTIINADVNGAYNIMKK 373
                                       78999************************999******999*****99999999999****************96 PP

>> Glyco_hydro_97  Glycoside hydrolase 97
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1   1.4e-08   5.2e-05      34     107 ..     254     326 ..     215     345 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.4e-08
                    Glyco_hydro_97  34 tetvkryiDfAaengleyvlvegwdegWee..kkkkekefdftkpypdfdleelvaYakekgvgvelwlhsetsgn 107
                                        +  kr +Df+ ++++ ++++ g++egW++      +++++ ++++p  +l+e ++Y k+ +vg++++ ++e +++
  gi|298675066|ref|YP_003726816.1| 254 HKASKRIVDFCVKHNIGTLVI-GYNEGWKQevY-MGKRNNQKFTQIPFHRLPEQLKY-KAEDVGLKVIEQEESYTS 326
                                       56789****************.*******9954.445666777899***********.555678999888887555 PP

>> HEPN_Swt1  Swt1-like HEPN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.9   5.7e-05      0.21       9      70 ..      25      85 ..      18      97 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.7e-05
                         HEPN_Swt1  9 gLrpfverelskayged..wweeveaslekdeeekkesekeiskldvqdllrvitenWkevFkk 70
                                       L++  + ++++++++d  w++  e    +++ ++ e+ + +  +++q+ l+++++nWk++F++
  gi|298675066|ref|YP_003726816.1| 25 NLYNQANFIVKQSLNDDgdWVRYEEL---NKQLKGTENYSVLPTQTAQQTLKLMDKNWKSFFQS 85
                                      56655566666766666645544444...444444455666677889999**********7765 PP

>> EAP30  EAP30/Vps36 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   6.9e-05      0.25      63     109 ..     223     267 ..     207     324 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 6.9e-05
                             EAP30  63 ftkmcaslGvdplsskkseslgfl...ellglgdfyyeLavqivevclat 109
                                        +++ ++lG+     k+s++l++l     ++++df+ + +++iv++c + 
  gi|298675066|ref|YP_003726816.1| 223 LKSIYDKLGI-----KNSKKLKKLyhkYKMKINDFFHKASKRIVDFCVKH 267
                                       4458899999.....3344555666666777****************954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1070  (0.0596798); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2840.41
//
Query:       gi|298675067|ref|YP_003726817.1|  [L=1104]
Description: PAS/PAC sensor signal transduction histidine kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.6e-50  167.7   9.8    1.7e-11   44.2   0.0    5.9  6  PAS_9          PAS domain
    2.3e-40  136.8   0.7      3e-18   65.9   0.2    6.3  5  PAS_3          PAS fold
    2.1e-39  134.0   0.2    9.9e-11   41.6   0.0    6.3  5  PAS            PAS fold
    3.1e-39  133.6   0.0    3.1e-08   33.9   0.0    5.3  5  PAS_4          PAS fold
    1.2e-26   93.4   0.5    3.4e-26   91.9   0.1    2.0  1  HATPase_c      Histidine kinase-, DNA gyrase B-, and HSP90-li
    2.3e-19   69.0   0.0    8.9e-05   22.4   0.0    5.3  5  PAS_8          PAS domain
    5.6e-17   61.5   3.9    3.2e-14   52.7   0.0    4.7  5  HisKA          His Kinase A (phospho-acceptor) domain
    1.8e-12   47.4   0.2    4.9e-08   33.1   0.0    4.4  5  PAS_11         PAS domain
      2e-08   34.8   3.0      0.073   13.7   0.0    5.1  4  PAS_10         PAS domain
    5.6e-06   26.5   0.7       0.14   12.4   0.0    4.6  5  PAS_7          PAS fold
     0.0011   19.2   0.0     0.0025   18.1   0.0    1.5  1  GAF_2          GAF domain
     0.0035   17.0   3.1        1.7    8.3   0.1    3.4  4  PAS_12         UPF0242 C-terminal PAS-like domain
  ------ inclusion threshold ------
      0.015   15.1   0.0      0.049   13.5   0.0    1.9  1  HATPase_c_3    Histidine kinase-, DNA gyrase B-, and HSP90-li
      0.088   12.6   1.5       0.25   11.2   0.1    2.3  2  PAN_3          PAN-like domain
       0.13   12.5   0.1       0.44   10.8   0.1    2.0  1  Fascin         Fascin domain
        1.6    8.6   5.7         12    5.7   1.8    3.7  3  Mt_ATP-synt_D  ATP synthase D chain, mitochondrial (ATP5H)


Domain annotation for each model (and alignments):
>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.0   1.6e-14   1.7e-11       1     104 []      48     147 ..      48     147 .. 0.91
   2 !   33.6   0.6   3.2e-11   3.6e-08       5     104 .]     190     293 ..     186     293 .. 0.81
   3 ?   -2.7   0.0       6.3   7.1e+03      30      57 ..     326     353 ..     312     365 .. 0.75
   4 !   27.5   0.0   2.6e-09   2.9e-06       3     104 .]     494     592 ..     492     592 .. 0.87
   5 !   36.7   0.0   3.4e-12   3.9e-09       6     104 .]     620     718 ..     615     718 .. 0.92
   6 !   27.1   0.0   3.4e-09   3.8e-06       4     104 .]     744     843 ..     741     843 .. 0.86

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 1.6e-14
                             PAS_9   1 pdgilidnpdgrilyaNeaalrllGyspeevlgksitdlf.vtdpeanerlraaleqgrkkerevevvlirkngetf 76 
                                       pd i i n+d++i+ +N+a  ++l  speev gk++++++  ++p + +  ++++++++  + +v+  +       +
  gi|298675067|ref|YP_003726817.1|  48 PDVIGIQNTDHEIICYNKAGYKFLNVSPEEVKGKKCFEIIgRQSPCDICATKNVYKTKQ--PSQVQKYIESM---GV 119
                                       56788999********************************9999999999999999999..77777666666...57 PP

                             PAS_9  77 wvlltaspvkdddgelvgiivilrDite 104
                                       w +++a+pv+d++gel+ ii  lrDit+
  gi|298675067|ref|YP_003726817.1| 120 WLDVRAYPVQDENGELTQIIEHLRDITT 147
                                       **************************95 PP

  == domain 2  score: 33.6 bits;  conditional E-value: 3.2e-11
                             PAS_9   5 li..dnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrk...kerevevvlirknge 74 
                                       +i   + + +i+ +N++ +++lGy+++ ++g +i+d++    + + ++   ++l+   +   +++++e+ + + +ge
  gi|298675067|ref|YP_003726817.1| 190 IIlaLDCNQNITLVNNKGCEILGYNKDKIVGSNIFDIIpeRYKNDIKSVSGKLLN---EgiqTAQRFENPILTGTGE 263
                                       4423445669****************************33333333333333333...2666*************** PP

                             PAS_9  75 tfwvlltaspvkdddgelvgiivilrDite 104
                                       +  +  + + +kd++g+++g ++  +Dite
  gi|298675067|ref|YP_003726817.1| 264 ERIISWHNTVLKDQNGNITGTLSSGIDITE 293
                                       *****************************8 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 6.3
                             PAS_9  30 evlgksitdlfvtdpeanerlraaleqg 57 
                                       ++++ks++ l++t  ++n  ++ + e+g
  gi|298675067|ref|YP_003726817.1| 326 QLIQKSCELLVETRGYHNAWIALMDENG 353
                                       6899999999988888887777766666 PP

  == domain 4  score: 27.5 bits;  conditional E-value: 2.6e-09
                             PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfwv 78 
                                       + ++ + +g+ l++N+ a + lGys+ee+l    + +   d+ ++ ++++ ++++ +   +++e  +++k+g++++v
  gi|298675067|ref|YP_003726817.1| 494 AAFVHDLEGNFLDVNDVAVQRLGYSREELLAMGPKGID--DETSKIKIKNRINSILDdGYFAFEASHVTKTGKKIPV 568
                                       55666699********************9998877776..77777777777777777777***************** PP

                             PAS_9  79 lltaspvkdddgelvgiivilrDite 104
                                        ++ s v  +++  ++  +i rDite
  gi|298675067|ref|YP_003726817.1| 569 AINSSLVEYEGKPAIL--SIARDITE 592
                                       *******999999999..*******8 PP

  == domain 5  score: 36.7 bits;  conditional E-value: 3.4e-12
                             PAS_9   6 idnpdgril.yaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfwvll 80 
                                        ++++g +  y++++ + +lGy+p  ++gk+++d++ +++++n+ ++ +++ + + k  +ve  +++ +g ++w + 
  gi|298675067|ref|YP_003726817.1| 620 QTDEKG-VFeYVSPSHEYILGYKPHYLVGKNVFDFV-HPEDRNKLKHLFYKCINNqKSATVEHRYQHADGYYLWLET 694
                                       478999.666**************************.99999999999999999999******************** PP

                             PAS_9  81 taspvkdddgelvgiivilrDite 104
                                           v+d+d++ v +i+  r++te
  gi|298675067|ref|YP_003726817.1| 695 VGNVVYDEDENDVKAIFGTRNVTE 718
                                       ********9999999***9*9998 PP

  == domain 6  score: 27.1 bits;  conditional E-value: 3.4e-09
                             PAS_9   4 ilidnpdgrilyaNeaalrllGyspeevlgks.itdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfw 77 
                                       ++i +++ + l +N+ +++l Gys+ee+  ++ +td++  ++ p+ +e+  ++l + ++ +r +e  +i++n+++ +
  gi|298675067|ref|YP_003726817.1| 744 TAIADENSTFLLVNREFEKLSGYSKEEIEKRKnWTDFIveEDLPYLRENYYKLLANSTSVPRKYEFRFIDRNNNQKY 820
                                       6788899********************998885788888888899999999999999989***************** PP

                             PAS_9  78 vlltaspvkdddgelvgiivilrDite 104
                                       + + +  +   ++++   i++l Dite
  gi|298675067|ref|YP_003726817.1| 821 ISMAVNSIP--ERKIA--IATLLDITE 843
                                       888888886..54455..5******98 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.012        14      66      86 ..     119     139 ..      60     140 .. 0.70
   2 !   18.0   0.0   2.3e-06    0.0025       3      84 ..     202     283 ..     200     287 .. 0.91
   3 ?    2.5   0.0      0.16   1.8e+02       3      22 ..     506     525 ..     504     585 .. 0.69
   4 !   65.9   0.2   2.7e-21     3e-18       3      84 ..     629     708 ..     627     711 .. 0.96
   5 !   35.8   0.0   6.5e-12   7.3e-09       3      68 ..     755     821 ..     753     832 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.012
                             PAS_3  66 rwveararvirdengkpvrvi 86 
                                       +w++ ra++++deng+ +++i
  gi|298675067|ref|YP_003726817.1| 119 VWLDVRAYPVQDENGELTQII 139
                                       699*************99886 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 2.3e-06
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.py.egeyRirrkdGeyrwveararvird 77 
                                        v+++ +eilGy ++ + g+  ++ d++     + +++   ++l++g      +e  i++  Ge r ++++ +v++d
  gi|298675067|ref|YP_003726817.1| 202 LVNNKGCEILGYNKDKIVGS--NIFDIIPERYKNDIKSVSGKLLNEGIqTAqRFENPILTGTGEERIISWHNTVLKD 276
                                       589999**************..************************99533488899******************** PP

                             PAS_3  78 engkpvr 84 
                                       +ng+++ 
  gi|298675067|ref|YP_003726817.1| 277 QNGNITG 283
                                       ***9875 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.16
                             PAS_3   3 yvserveeilGyspeellgk 22 
                                        v++   + lGys+eell+ 
  gi|298675067|ref|YP_003726817.1| 506 DVNDVAVQRLGYSREELLAM 525
                                       6888889999*******988 PP

  == domain 4  score: 65.9 bits;  conditional E-value: 2.7e-21
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirden 79 
                                       yvs++ e ilGy p+ l gk  ++ d+vhpeDr+++++ + ++++++++ ++e+R++++dG y w+e+ ++v++de+
  gi|298675067|ref|YP_003726817.1| 629 YVSPSHEYILGYKPHYLVGK--NVFDFVHPEDRNKLKHLFYKCINNQKSATVEHRYQHADGYYLWLETVGNVVYDED 703
                                       9*******************..******************************************************9 PP

                             PAS_3  80 gkpvr 84 
                                        + v+
  gi|298675067|ref|YP_003726817.1| 704 ENDVK 708
                                       88665 PP

  == domain 5  score: 35.8 bits;  conditional E-value: 6.5e-12
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge..pyegeyRirrkdGeyrwv 68 
                                        v++++e++ Gys+ee++++ ++w d++  eD++++re++ ++l++ +  p + e+R++ ++    ++
  gi|298675067|ref|YP_003726817.1| 755 LVNREFEKLSGYSKEEIEKR-KNWTDFIVEEDLPYLRENYYKLLANSTsvPRKYEFRFIDRNNNQKYI 821
                                       689*****************.9**********************88886666999***9998766655 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   3.1e-05     0.034       4     113 .]      41     145 ..      40     145 .. 0.79
   2 !   23.0   0.0   5.5e-08   6.1e-05       8     108 ..     185     286 ..     178     291 .. 0.65
   3 !   18.1   0.0   1.9e-06    0.0021       2      43 ..     483     524 ..     482     590 .. 0.78
   4 !   41.6   0.0   8.9e-14   9.9e-11       2     102 ..     606     705 ..     605     714 .. 0.87
   5 !   29.0   0.0   7.5e-10   8.4e-07       2      95 ..     732     827 ..     731     841 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.1e-05
                                       HHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEE CS
                               PAS   4 raileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfk 80 
                                       ++i++++pd i + + d++i+  N+a  ++l+ s+eev gk+ ++ i  +++     + +++   +++++++++ ++
  gi|298675067|ref|YP_003726817.1|  41 DTIFDAIPDVIGIQNTDHEIICYNKAGYKFLNVSPEEVKGKKCFEIIGRQSP--CDICATKNVYKTKQPSQVQKYIE 115
                                       6899***************************************976655544..44455555545555555555444 PP

                                       CTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  81 lrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                             ++l+vra pv d+ ge+++++  lrdi
  gi|298675067|ref|YP_003726817.1| 116 S---MGVWLDVRAYPVQDENGELTQIIEHLRDI 145
                                       4...79999999999999999999999888876 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 5.5e-08
                                       HHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH...HHHHHHHHHHHHTT-ECCCCEEEEC CS
                               PAS   8 eslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda...elaelleqlleqgeesrageisfkl 81 
                                       + + + i+++D + +i++vN + +e+lG++ + ++g++++d i+e +      +  +l++   q+ ++    i ++ 
  gi|298675067|ref|YP_003726817.1| 185 DVSGTIILALDCNQNITLVNNKGCEILGYNKDKIVGSNIFDIIPERYKNdikSVSGKLLNEGIQTAQRFENPI-LT- 259
                                       5577899**********************************99987655443222222222222222222222.22. PP

                                       TTSSEEEEEEEEEEEEETTEEEEEEEE CS
                               PAS  82 rdgrpihlevraspvrdaggeilgflg 108
                                         g+++ +  +++ + d  g+i+g l 
  gi|298675067|ref|YP_003726817.1| 260 GTGEERIISWHNTVLKDQNGNITGTLS 286
                                       256666666666666666666666555 PP

  == domain 3  score: 18.1 bits;  conditional E-value: 1.9e-06
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTT CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlg 43 
                                       +++ i++ + d+ fv D  g++l vN+ a + lG+sree+l 
  gi|298675067|ref|YP_003726817.1| 483 QYQDIFNGMNDAAFVHDLEGNFLDVNDVAVQRLGYSREELLA 524
                                       7999***********************************975 PP

  == domain 4  score: 41.6 bits;  conditional E-value: 8.9e-14
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                        +r+i +++ d +  +De+g++ yv+++ e +lG+++  ++gk+++d++h+ed+ +l+ l+ +++ ++++s ++e++
  gi|298675067|ref|YP_003726817.1| 606 LYRRITNNMLDLVSQTDEKGVFEYVSPSHEYILGYKPHYLVGKNVFDFVHPEDRNKLKHLFYKCI-NNQKSATVEHR 681
                                       69**************************************************9986665555555.55666667777 PP

                                       EECTTSSEEEEEEEEEEEEETTEE CS
                               PAS  79 fklrdgrpihlevraspvrdagge 102
                                           dg + +le+  + v+d++++
  gi|298675067|ref|YP_003726817.1| 682 YQHADGYYLWLETVGNVVYDEDEN 705
                                       7777*****************987 PP

  == domain 5  score: 29.0 bits;  conditional E-value: 7.5e-10
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHC.TTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCC CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreev.lgkslldliheedda.elaelleqlleqgeesrage 76 
                                       ++r+i+e++ +++ + De+  +l+vN+++e+l G+s ee+  +k+  d+i+eed    +   ++ l+++++ +r +e
  gi|298675067|ref|YP_003726817.1| 732 RYRTIFETTGSATAIADENSTFLLVNREFEKLSGYSKEEIeKRKNWTDFIVEEDLPyLRENYYKLLANSTSVPRKYE 808
                                       89***********************************8873688999999999876444445556667778889999 PP

                                       EEEECTTSSEEEEEEEEEE CS
                               PAS  77 isfklrdgrpihlevrasp 95 
                                        +f  r++  +++ + +++
  gi|298675067|ref|YP_003726817.1| 809 FRFIDRNNNQKYISMAVNS 827
                                       9988866666666655554 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   2.7e-11   3.1e-08       1     109 [.      44     149 ..      44     150 .. 0.93
   2 !   32.9   0.0   5.3e-11     6e-08       1     109 [.     184     295 ..     184     296 .. 0.86
   3 !   17.4   0.0   3.6e-06     0.004       1     109 [.     488     594 ..     488     595 .. 0.95
   4 !   25.9   0.0   7.9e-09   8.8e-06       6     109 ..     616     720 ..     611     721 .. 0.93
   5 !   17.0   0.0   4.7e-06    0.0053       2     110 .]     738     846 ..     737     846 .. 0.90

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 2.7e-11
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       +d++pd++ + ++d  ++ +N+a+ + + ++pee+ Gk+++e+   ++  ++ +a + v ++++p + + +      
  gi|298675067|ref|YP_003726817.1|  44 FDAIPDVIGIQNTDHEIICYNKAGYKFLNVSPEEVKGKKCFEIIGRQSPCDI-CATKNVYKTKQPSQVQKYIES--M 117
                                       79****************************************9998555555.67899***********98888..9 PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerr 109
                                       ++++++r++P+ de+Ge   +++++rDiT ++
  gi|298675067|ref|YP_003726817.1| 118 GVWLDVRAYPVQDENGELTQIIEHLRDITTEK 149
                                       9****************************886 PP

  == domain 2  score: 32.9 bits;  conditional E-value: 5.3e-11
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll... 74 
                                       ld +  ++++ld +++++ +N+ ++e++g+  + ++G+  +++ pe+ + ++ +   ++l ++  ++ + + ++   
  gi|298675067|ref|YP_003726817.1| 184 LDVSGTIILALDCNQNITLVNNKGCEILGYNKDKIVGSNIFDIIPERYKNDIKSVSGKLLNEG-IQTAQRFENPilt 259
                                       57778889999************************************8888888888888776.3333333333345 PP

                             PAS_4  75 .pgeerhyelrllPlrdesGevigvlvisrDiTerr 109
                                         geer+++++ + l+d +G + g+l  ++DiTer+
  gi|298675067|ref|YP_003726817.1| 260 gTGEERIISWHNTVLKDQNGNITGTLSSGIDITERK 295
                                       88********************************97 PP

  == domain 3  score: 17.4 bits;  conditional E-value: 3.6e-06
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       ++ ++da +v d +g++l++N  a + +g+++eell + +  +  e ++  + + ++  l+ + +++++ +++  g+
  gi|298675067|ref|YP_003726817.1| 488 FNGMNDAAFVHDLEGNFLDVNDVAVQRLGYSREELLAMGPKGIDDETSKIKIKNRINSILDDGYFAFEASHVTKTGK 564
                                       567899***********************************776788****************************** PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerr 109
                                         ++ ++ + + + +G+  ++l i+rDiTer+
  gi|298675067|ref|YP_003726817.1| 565 KIPVAINSSLV-EYEGK-PAILSIARDITERK 594
                                       **********9.68***.9************8 PP

  == domain 4  score: 25.9 bits;  conditional E-value: 7.9e-09
                             PAS_4   6 dalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pgeerhy 81 
                                       d++   d+ g+++y++++ ++++g+ p+ l+Gk +++++ +ed+  l +   +++  +++++ ++ + + +g   ++
  gi|298675067|ref|YP_003726817.1| 616 DLVSQTDEKGVFEYVSPSHEYILGYKPHYLVGKNVFDFVHPEDRNKLKHLFYKCINNQKSATVEHRYQHaDGYYLWL 692
                                       667778************999****************99999***************************88888888 PP

                             PAS_4  82 elrllPlrdesGevigvlvisrDiTerr 109
                                       e+  + + de+   + +++ +r +Ter+
  gi|298675067|ref|YP_003726817.1| 693 ETVGNVVYDEDENDVKAIFGTRNVTERK 720
                                       8888**********************98 PP

  == domain 5  score: 17.0 bits;  conditional E-value: 4.7e-06
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktla.ellpeedaarleralrrvlegeepiefleelll... 74 
                                       + +  a+a+ d+++++l +N+++++l g++ ee+  ++ + ++  eed + l++++ ++l+  +++ +  e ++   
  gi|298675067|ref|YP_003726817.1| 738 ETTGSATAIADENSTFLLVNREFEKLSGYSKEEIEKRKNWtDFIVEEDLPYLRENYYKLLANSTSVPRKYEFRFidr 814
                                       6677899*********************************9************************999999999999 PP

                             PAS_4  75 pgeerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                       +  ++++++ ++ +   + +   +++++ DiTer++
  gi|298675067|ref|YP_003726817.1| 815 NNNQKYISMAVNSIP--ERK--IAIATLLDITERKQ 846
                                       999999999997773..344..7899999****985 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.9   0.1     3e-29   3.4e-26       1     109 [.     985    1099 ..     985    1101 .. 0.91

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 3e-29
                                        EHHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEE..EE...TEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCH CS
                         HATPase_c    1 gdekrLrqiisnlvdNavkfatkageieveika..se...ddlvisveDnGiGipkedlkklfekfsq.ddstkr 69  
                                        gd++ Lrq++ +l+dNa kf++++g+i+++     ++   + ++i v+DnGiGi ke ++ +f+ f+q d+s +r
  gi|298675067|ref|YP_003726817.1|  985 GDKDYLRQVLVHLMDNARKFTSSGGKIQIHAFNdaDKsmdNFVHIIVKDNGIGIKKESIPDIFKLFYQiDGSMTR 1059
                                        78999***************7788877776664542266689999****************************** PP

                                        TSTSSSHHHHHHHHHHHHTTTEEEEEEETTTEEEEEEEEE CS
                         HATPase_c   70 ggggtGlGlsivkklvelmgGeiwvesepgrGttftftlp 109 
                                        +++gtGlG+++++k++e+++G iwv+se++ Gt+++++lp
  gi|298675067|ref|YP_003726817.1| 1060 KYEGTGLGMYLCNKIIETHNGYIWVDSEENAGTDVHVKLP 1099
                                        *************************************998 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.026        29       4      46 ..      41      84 ..      40     101 .. 0.84
   2 !   14.8   0.0   1.9e-05     0.021      14      50 ..     191     228 ..     184     239 .. 0.75
   3 !   22.4   0.0   7.9e-08   8.9e-05       2      42 ..     483     524 ..     482     538 .. 0.86
   4 ?   -1.2   0.0       1.9   2.2e+03       2      37 ..     606     641 ..     605     668 .. 0.72
   5 !   19.3   0.0   7.3e-07   0.00082       2      46 ..     732     777 ..     731     800 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.026
                             PAS_8  4 ralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellg 46
                                       ++f+++pd i + +++  i+ +N+a +++l +s +++kg+++ 
  gi|298675067|ref|YP_003726817.1| 41 DTIFDAIPDVIGIQNTDHEIICYNKAGYKFLNVSpEEVKGKKCF 84
                                      589*********9996678*********************9995 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.9e-05
                             PAS_8  14 iavvd.lgdrivdvNqaalellGys.adlkgellgqllp 50 
                                       i+ +d +++ i+ vN++ +e+lGy+ + + g+ + +++p
  gi|298675067|ref|YP_003726817.1| 191 ILALDcNQN-ITLVNNKGCEILGYNkDKIVGSNIFDIIP 228
                                       344778888.**************977776665544444 PP

  == domain 3  score: 22.4 bits;  conditional E-value: 7.9e-08
                             PAS_8   2 rlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkg 42 
                                       +++ +f+ ++d+ +v d +g+ ++dvN+ a + lGys ++l++
  gi|298675067|ref|YP_003726817.1| 483 QYQDIFNGMNDAAFVHDlEGN-FLDVNDVAVQRLGYSrEELLA 524
                                       79*************996666.***************777766 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 1.9
                             PAS_8   2 rlralfesspdgiavvd.lgdrivdvNqaalellGys 37 
                                        +r + +++ d +  +d  g  + +v ++ + +lGy+
  gi|298675067|ref|YP_003726817.1| 606 LYRRITNNMLDLVSQTDeKG-VFEYVSPSHEYILGYK 641
                                       69999999999999999454.5999999999999987 PP

  == domain 5  score: 19.3 bits;  conditional E-value: 7.3e-07
                             PAS_8   2 rlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellg 46 
                                       r+r++fe+   + a++d +  +++ vN+ +++l Gys +++   + +
  gi|298675067|ref|YP_003726817.1| 732 RYRTIFETTGSATAIADeNS-TFLLVNREFEKLSGYSkEEIEKRKNW 777
                                       9****************444.5***************7766655544 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.9   2.1e+03      45      64 ..     129     148 ..     126     150 .. 0.81
   2 ?    4.5   0.1     0.033        37      28      55 ..     293     318 ..     273     320 .. 0.86
   3 ?   -2.2   0.0       3.9   4.4e+03      12      40 ..     452     484 ..     449     493 .. 0.64
   4 ?    0.9   0.2      0.42   4.7e+02      41      63 ..     596     619 ..     582     623 .. 0.70
   5 !   52.7   0.0   2.9e-17   3.2e-14       1      66 [.     871     938 ..     871     939 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHHHHHHHCCH CS
                             HisKA  45 esearrldhlvedlLdlsri 64 
                                       ++e   l++++e l+d++++
  gi|298675067|ref|YP_003726817.1| 129 QDENGELTQIIEHLRDITTE 148
                                       56667899********9875 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.033
                                       HC..T-HSSCHHHHHHHHHHHHHHHHHH CS
                             HisKA  28 kregklteelkeyletiesearrldhlv 55 
                                       +r  kl ee ++yl+++ + +r +++l+
  gi|298675067|ref|YP_003726817.1| 293 ER--KLAEEKQDYLNQVLRAIRNVNQLI 318
                                       56..899*******************98 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3.9
                                       HHHHHHHHHHHHHHHHHC......T-HSSCHHH CS
                             HisKA  12 ELrtPLsailgnaeaLkre....gklteelkey 40 
                                       EL + Ls  l n+e+  ++    +k  ++lk+y
  gi|298675067|ref|YP_003726817.1| 452 ELTNDLSYALYNLEIEDEKikayNKVQQSLKQY 484
                                       888999999999999544454443333444444 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.42
                                       HHHHHHHHHHH.HHHHHHHHHHCC CS
                             HisKA  41 letiesearrl.dhlvedlLdlsr 63 
                                       +e++ +e + l +++ +++Ldl +
  gi|298675067|ref|YP_003726817.1| 596 IEKALKENEKLyRRITNNMLDLVS 619
                                       4444555554449********987 PP

  == domain 5  score: 52.7 bits;  conditional E-value: 2.9e-17
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                             HisKA   1 slgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsriea 66 
                                       ++ +f+++++HELrtP+++i+g++e++ +e  g l+e++ke  ++i+++ +rl+ l+e lL   ++++
  gi|298675067|ref|YP_003726817.1| 871 MKDEFISNLSHELRTPITSIKGFSELIYNEklGTLNEKQKEGMDSIVKSCDRLRWLIESLLYVNKLQT 938
                                       689************************444589****************************9999876 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0         9     1e+04      49      64 ..     135     150 ..     131     155 .. 0.71
   2 ?    0.8   0.0      0.47   5.3e+02       8      47 ..     194     230 ..     189     252 .. 0.80
   3 ?   -1.4   0.0       2.2   2.5e+03       6      36 ..     496     523 ..     492     528 .. 0.85
   4 !   33.1   0.0   4.4e-11   4.9e-08      23     110 ..     633     719 ..     617     722 .. 0.90
   5 !    7.0   0.0    0.0056       6.3      28      91 ..     764     831 ..     744     834 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 9
                            PAS_11  49 lstlkshlrevissng 64 
                                       l+++ +hlr+++ +++
  gi|298675067|ref|YP_003726817.1| 135 LTQIIEHLRDITTEKE 150
                                       778899*****94444 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.47
                            PAS_11   8 ldidgkIisvDtsaLrasfslglekeelvgrsiydLchpq 47 
                                       ld + +I+ v++   ++   lg++k+++vg  i+d++ ++
  gi|298675067|ref|YP_003726817.1| 194 LDCNQNITLVNN---KGCEILGYNKDKIVGSNIFDIIPER 230
                                       677778888888...888899**************98665 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.2
                            PAS_11   6 trldidgkIisvDtsaLrasfslglekeelv 36 
                                       + +d++g++++v+     a  +lg+++eel+
  gi|298675067|ref|YP_003726817.1| 496 FVHDLEGNFLDVND---VAVQRLGYSREELL 523
                                       789**********9...88889999998875 PP

  == domain 4  score: 33.1 bits;  conditional E-value: 4.4e-11
                            PAS_11  23 rasfslglekeelvgrsiydLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvkvktksklfknqksneqd 99 
                                       ++++ lg++ + lvg+ ++d++hp+d+ +lk  + + i +n+++++   R + +++ ++++ t++ + ++++ n+++
  gi|298675067|ref|YP_003726817.1| 633 SHEYILGYKPHYLVGKNVFDFVHPEDRNKLKHLFYKCI-NNQKSATVEHRYQHADGYYLWLETVGNVVYDEDENDVK 708
                                       7899**********************************.8888888899**************************** PP

                            PAS_11 100 fimathtllse 110
                                        i +t  + ++
  gi|298675067|ref|YP_003726817.1| 709 AIFGTRNVTER 719
                                       **999988765 PP

  == domain 5  score: 7.0 bits;  conditional E-value: 0.0056
                            PAS_11  28 lglekeelv.grsiydLchpqdlstlkshlrevi.ssngeatsslyRLrl..sqdkfvkvktksklfk 91 
                                        g++kee+  ++ + d++ ++dl  l++ + + + +s+   ++  +R++   +++k++++  +s  ++
  gi|298675067|ref|YP_003726817.1| 764 SGYSKEEIEkRKNWTDFIVEEDLPYLRENYYKLLaNSTSVPRKYEFRFIDrnNNQKYISMAVNSIPER 831
                                       5677777651679****************999996777777777799987667889999999987765 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   8.2e-05     0.092      17     106 .]      56     146 ..      42     146 .. 0.94
   2 !   13.7   0.0   6.5e-05     0.073       7     106 .]     186     292 ..     180     292 .. 0.79
   3 ?    2.9   0.0      0.15   1.7e+02      21      73 ..     627     680 ..     618     694 .. 0.71
   4 ?   -0.3   0.1       1.4   1.6e+03      42      81 ..     694     733 ..     692     737 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.2e-05
                            PAS_10  17 dnlqirrFtpaakklfklipadv.Grpladihpkkavknveeviealrtgekdevevvvpkngkwvlvrylpyrded 92 
                                       ++ +i+++++a  k++++ p++v G +  +i  +++  ++    +  +t++  +v++++++ g w  vr  p++de+
  gi|298675067|ref|YP_003726817.1|  56 TDHEIICYNKAGYKFLNVSPEEVkGKKCFEIIGRQSPCDICATKNVYKTKQPSQVQKYIESMGVWLDVRAYPVQDEN 132
                                       678999*****999****9999889******999999999999999******************************* PP

                            PAS_10  93 geiaGvvetfvDit 106
                                       ge   ++e + Dit
  gi|298675067|ref|YP_003726817.1| 133 GELTQIIEHLRDIT 146
                                       **********9997 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 6.5e-05
                            PAS_10   7 stpieltflDdnlqirrFtpaakklfkli.padvGrpladihpkkavknveeviealrtgek.devevvvp.....k 76 
                                            ++ lD n +i+  +++  +++ ++ ++ vG ++ di p+++++++++v  +l ++     ++++ p      
  gi|298675067|ref|YP_003726817.1| 186 VSGTIILALDCNQNITLVNNKGCEILGYNkDKIVGSNIFDIIPERYKNDIKSVSGKLLNEGIqTAQRFENPiltgtG 262
                                       5555678899999999999987777666515679********************99988665144445545667778 PP

                            PAS_10  77 ngkwvlvrylpyrdedgeiaGvvetfvDit 106
                                       +++++      ++d++g+i G++   +Dit
  gi|298675067|ref|YP_003726817.1| 263 EERIISWHNTVLKDQNGNITGTLSSGIDIT 292
                                       8**********************9999996 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.15
                            PAS_10  21 irrFtpaakklfklipa.dvGrpladihpkkavknveeviealrtgekdevevv 73 
                                       + + +p+++ ++ ++p   vG ++ d+++++  +++++++ ++++++k     +
  gi|298675067|ref|YP_003726817.1| 627 FEYVSPSHEYILGYKPHyLVGKNVFDFVHPEDRNKLKHLFYKCINNQKSATVEH 680
                                       55555566655555554148***********************99998544333 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 1.4
                            PAS_10  42 pladihpkkavknveeviealrtgekdevevvvpkngkwv 81 
                                       ++ +++ ++ +++v+ ++ +   +e+++ e+  ++++k +
  gi|298675067|ref|YP_003726817.1| 694 TVGNVVYDEDENDVKAIFGTRNVTERKKTEIALKESEKRY 733
                                       67899999******************99999987555544 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.43   4.8e+02       8      55 ..      51      97 ..      44     153 .. 0.64
   2 ?   -0.8   0.1       1.5   1.7e+03      42      78 ..     143     181 ..     126     193 .. 0.56
   3 !    7.4   0.0    0.0043       4.8       8     115 .]     191     299 ..     184     299 .. 0.77
   4 ?   -2.4   0.0       4.8   5.3e+03     102     114 ..     585     597 ..     577     598 .. 0.82
   5 !   12.4   0.0   0.00012      0.14       9     115 .]     745     849 ..     737     849 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.43
                             PAS_7  8 isvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefg 55
                                      i + + d++++++N+   + l++++e v  g++  e++  ++    ++
  gi|298675067|ref|YP_003726817.1| 51 IGIQNTDHEIICYNKAGYKFLNVSPEEV-KGKKCFEIIGRQSPCDICA 97
                                      5666788999999999999999999999.6777666665554444444 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.5
                             PAS_7  42 eellrynaergefg..agdveaeverrlaaaragkphsf 78 
                                       ++++     ++e++  + + e+ +e+r+++++++k    
  gi|298675067|ref|YP_003726817.1| 143 RDITTEKEMEKELEksHIELEKRIEERTEQLKQEKDLMK 181
                                       333333333333332234466678888887777765555 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0043
                             PAS_7   8 isvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaeverrlaaaragkphsfererpd 84 
                                       i+ +D +++++++N++ +e+l++ ++ + vg ++ +++  + ++ +++ + + + +++ ++ a++++++ +   + +
  gi|298675067|ref|YP_003726817.1| 191 ILALDCNQNITLVNNKGCEILGYNKDKI-VGSNIFDIIPERYKN-DIK-SVSGKLLNEGIQTAQRFENPILT-GTGE 263
                                       667999**********************.********9877444.444.35566777788777777766555.5688 PP

                             PAS_7  85 grvievrgnplpd.....gGfVttytDiTerrraee 115
                                       +r+i+ +++ l d      G++++  DiTer+ aee
  gi|298675067|ref|YP_003726817.1| 264 ERIISWHNTVLKDqngniTGTLSSGIDITERKLAEE 299
                                       999999999996533223577778889999998875 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 4.8
                             PAS_7 102 ttytDiTerrrae 114
                                       ++  DiTer++ e
  gi|298675067|ref|YP_003726817.1| 585 SIARDITERKKIE 597
                                       5678*****9987 PP

  == domain 5  score: 12.4 bits;  conditional E-value: 0.00012
                             PAS_7   9 svfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaeverrlaaaragkphsfererpdg 85 
                                       ++ D++   +++Nr++ +l ++++e ++  ++ ++++    e   + +++  + +++ + ++ ++ + +f  + ++ 
  gi|298675067|ref|YP_003726817.1| 745 AIADENSTFLLVNREFEKLSGYSKEEIEKRKNWTDFIVE--EDLPYLRENYYKLLANST-SVPRKYEFRFIDRNNNQ 818
                                       688999*********************999998887743..344444677778888888.555666666677789** PP

                             PAS_7  86 rvievrgnplpd.gGfVttytDiTerrraee 115
                                       + i++  n +p+ +  ++t  DiTer+++ee
  gi|298675067|ref|YP_003726817.1| 819 KYISMAVNSIPErKIAIATLLDITERKQSEE 849
                                       **********9945679***********996 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   2.3e-06    0.0025       7     137 ..     327     461 ..     322     461 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.3e-06
                                       HHHHHHHHHHHS.S..EEEEEEE-TTS-EEEE.....EEEES-TTSTT-S-B---TT.HHH...HHHHHTS-EEES- CS
                             GAF_2   7 lldlvldelvel.gaalgyillvdddgglrla.....awgeaeeefgaaldrplgeg.lvg...ealrtgrpvilnd 73 
                                       l +  ++ lve+ g + ++i+l d++gg          +g+  e+   +   +l +g l+    +al +   +++ +
  gi|298675067|ref|YP_003726817.1| 327 LIQKSCELLVETrGYHNAWIALMDENGG--GGfnnivQAGMGAEFAYIKD--KLKDGgLIDcvqKALNQSDTIVVKN 399
                                       78899*******88**********9888..33222223333333333333..45555565555699999******** PP

                                       GGG-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  74 leedpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                       + +    ++l   +++ ++ l   l +++r++G+l++    +++ d ++l+l++el ++++ a+
  gi|298675067|ref|YP_003726817.1| 400 PVSACVNCPL--PDVHKGNNLTRKLEYNNRTYGILSVTVPSEYGKDNDELDLFDELTNDLSYAL 461
                                       8885665555..58888899*****8889********888888889**************9997 PP

>> PAS_12  UPF0242 C-terminal PAS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.1    0.0015       1.7      56     100 ..     187     232 ..     129     246 .. 0.77
   2 ?   -3.7   0.0       7.6   8.5e+03      70      90 ..     505     525 ..     500     545 .. 0.76
   3 ?   -2.7   0.0       3.7   4.2e+03       4      27 ..     661     684 ..     659     689 .. 0.81
   4 !    7.3   0.1     0.003       3.3      54     139 ..     738     829 ..     730     838 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0015
                            PAS_12  56 lgailvysqkenkllfaNaqirallGwssdkfl.qdfseivqegle 100
                                       +g+i++    ++ +  +N++  ++lG+++dk++ ++ ++i+ e ++
  gi|298675067|ref|YP_003726817.1| 187 SGTIILALDCNQNITLVNNKGCEILGYNKDKIVgSNIFDIIPERYK 232
                                       56777777889999******************94567899887654 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 7.6
                            PAS_12  70 lfaNaqirallGwssdkflqd 90 
                                       l +N+   + lG+s +++l  
  gi|298675067|ref|YP_003726817.1| 505 LDVNDVAVQRLGYSREELLAM 525
                                       567888888999999998765 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 3.7
                            PAS_12   4 easillkkcieiaqkitgansftn 27 
                                       ++++l+ kci+  +  t+ ++++ 
  gi|298675067|ref|YP_003726817.1| 661 KLKHLFYKCINNQKSATVEHRYQH 684
                                       5789999****9999999888865 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.003
                            PAS_12  54 EnlgailvysqkenkllfaNaqirallGwssdkflqdfs..e.ivqegleeWkra...laklsskteskirlvlKtK 124
                                       E++g+    +  +   l +N+++++l G+s++++ ++ +  + iv+e l   +++   l + s+++ +k ++ +  +
  gi|298675067|ref|YP_003726817.1| 738 ETTGSATAIADENSTFLLVNREFEKLSGYSKEEIEKRKNwtDfIVEEDLPYLRENyykLLANSTSVPRKYEFRFIDR 814
                                       5666666778888899*****************98775422337888876555541113344667778888888888 PP

                            PAS_12 125 agqevllncllgiip 139
                                       ++++ ++++ +  ip
  gi|298675067|ref|YP_003726817.1| 815 NNNQKYISMAVNSIP 829
                                       888888888888877 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   4.4e-05     0.049       5      58 ..     992    1051 ..     989    1071 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.4e-05
                       HATPase_c_3    5 kAlaelvdNsld..Adaenvkievnknrgkt....geivieDdGkGmseeelknalrlat 58  
                                        ++l+ l dN+    ++  +++i++ ++  k+      i ++D+G G+++e + + ++l  
  gi|298675067|ref|YP_003726817.1|  992 QVLVHLMDNARKftSSGGKIQIHAFNDADKSmdnfVHIIVKDNGIGIKKESIPDIFKLFY 1051
                                        6899999**9874477778888877665444566689*************9999888654 PP

>> PAN_3  PAN-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2       1.3   1.5e+03      34      58 ..      82     106 ..      79     116 .. 0.80
   2 ?   11.2   0.1   0.00023      0.25      24      62 ..     383     421 ..     371     426 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.3
                             PAN_3  34 tCilayknsenCtlfeignvstvkk 58 
                                       +C+ +  ++++C +++ +nv + k+
  gi|298675067|ref|YP_003726817.1|  82 KCFEIIGRQSPCDICATKNVYKTKQ 106
                                       68888888999****9999988776 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00023
                             PAN_3  24 dCvqkCledstCilayknsenCtlfeignvstvkkiess 62 
                                       dCvqk l++s+ i++ +  + C+++   +v++ ++++++
  gi|298675067|ref|YP_003726817.1| 383 DCVQKALNQSDTIVVKNPVSACVNCPLPDVHKGNNLTRK 421
                                       8***************99*************99998765 PP

>> Fascin  Fascin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00039      0.44      40      96 ..     682     743 ..     654     753 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00039
                                       EEETTSEEEEE-TTSBEEEEESS--GGGEEEEEEE....TCEEEEEETTSCEEE.ECTTTEE CS
                            Fascin  40 LrshngkYlsldkdGrvvaeaetkeedtlFelefr....grwallresngryLg.igkeglL 96 
                                        + ++g+Yl l++ G+vv+++++++ ++ F  +         ++l+es++ry +  +++g  
  gi|298675067|ref|YP_003726817.1| 682 YQHADGYYLWLETVGNVVYDEDENDVKAIFGTRNVterkKTEIALKESEKRYRTiFETTGSA 743
                                       46899*************************87665554566799999999997766666655 PP

>> Mt_ATP-synt_D  ATP synthase D chain, mitochondrial (ATP5H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   1.8     0.011        12      90     126 ..     150     186 ..     138     191 .. 0.74
   2 ?    1.6   0.0      0.21   2.3e+02      51      89 ..     368     406 ..     365     423 .. 0.88
   3 ?   -2.3   0.3       3.3   3.7e+03      93     121 ..     845     872 ..     818     879 .. 0.56

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.011
                                       HHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHT-XXXX CS
                     Mt_ATP-synt_D  90 aeekevkkeikefkeeskkrieelekeleklksllpf 126
                                       ++eke +k++ e  +  ++r e+l++e + +k+ l++
  gi|298675067|ref|YP_003726817.1| 150 EMEKELEKSHIELEKRIEERTEQLKQEKDLMKKYLDV 186
                                       5677777777777777777777777777777777665 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.21
                                       -HHHHHHHSSSTTHHHHHHHHHHH--------TTTTHHH CS
                     Mt_ATP-synt_D  51 dWayYkknvakeglVdeFekkYealkipypedkyteevd 89 
                                       ++ay k++++  gl+d  +k+ ++ ++++ ++++++ v+
  gi|298675067|ref|YP_003726817.1| 368 EFAYIKDKLKDGGLIDCVQKALNQSDTIVVKNPVSACVN 406
                                       699**********************99999988887776 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 3.3
                                       HHHHHHCHHHHHHHHHHHHHHHHHHHHHT CS
                     Mt_ATP-synt_D  93 kevkkeikefkeeskkrieelekeleklk 121
                                       k+++++   + e+  k+ eel+ el+k+k
  gi|298675067|ref|YP_003726817.1| 845 KQSEETLRIYSEKLSKTNEELR-ELDKMK 872
                                       3334444444444444444443.444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1445  (0.0805957); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.84u 0.32s 00:00:01.15 Elapsed: 00:00:00.49
# Mc/sec: 6730.25
//
Query:       gi|298675068|ref|YP_003726818.1|  [L=797]
Description: PAS/PAC sensor signal transduction histidine kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.4e-25   87.9   3.1    9.7e-10   38.6   0.1    3.7  3  PAS_9          PAS domain
    3.1e-21   76.0   0.2    2.4e-20   73.1   0.0    2.5  2  HATPase_c      Histidine kinase-, DNA gyrase B-, and HSP90-li
    3.5e-20   72.1   0.0    3.6e-07   30.2   0.0    3.9  3  PAS            PAS fold
    3.3e-16   58.9   0.1    1.5e-07   31.3   0.1    3.8  3  PAS_8          PAS domain
    2.4e-15   56.8   0.0     0.0012   19.0   0.0    3.3  3  PAS_4          PAS fold
    1.5e-08   34.8   0.0      0.015   15.5   0.0    3.6  3  PAS_3          PAS fold
    0.00016   22.3   0.0    0.00033   21.3   0.0    1.5  1  GAF            GAF domain
    0.00034   20.9   0.0    0.00076   19.8   0.0    1.5  1  GAF_2          GAF domain
     0.0044   17.3   0.0     0.0089   16.4   0.0    1.5  1  GAF_3          GAF domain
     0.0052   16.8   1.3      0.017   15.1   0.0    2.6  3  HisKA          His Kinase A (phospho-acceptor) domain
  ------ inclusion threshold ------
       0.13   12.2   0.0       0.39   10.7   0.0    1.7  2  HATPase_c_2    Histidine kinase-like ATPase domain
       0.23   11.7   0.4       0.58   10.4   0.4    1.6  1  Ribosomal_L22  Ribosomal protein L22p/L17e


Domain annotation for each model (and alignments):
>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.1   6.5e-13   9.7e-10       2     103 ..     214     312 ..     213     313 .. 0.88
   2 !   16.7   0.0   4.4e-06    0.0066      16     104 .]     348     436 ..     336     436 .. 0.85
   3 !   31.2   0.0   1.3e-10     2e-07       2     103 ..     460     558 ..     459     559 .. 0.91

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 6.5e-13
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfw 77 
                                        g++ ++++g+i+ +N+ +++++ +s+e ++g +i++l   ++e ++ +r+al+  ++  e e+ +vl+ kn   + 
  gi|298675068|ref|YP_003726818.1| 214 LGVFSTDSNGEIIQCNKYLIDITKSSKEKIIGLNIFNLP-VNSEIKNCIRNALDGYTQfYEGEYKTVLTGKN---LK 286
                                       6899999********************************.*****************665555666666665...46 PP

                             PAS_9  78 vlltaspvkdddgelvgiivilrDit 103
                                       +++ ++p  ++dg++vg+i++++D+t
  gi|298675068|ref|YP_003726818.1| 287 IRAYFTPDTSEDGKIVGCIGTITDLT 312
                                       67888999****************99 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 4.4e-06
                             PAS_9  16 aNeaalrllGyspeevlgksitdlf.vtdpeanerlraaleqgrkkerevevvlirkngetfwvlltaspvkdddge 91 
                                       +N+  ++++G+ +e++   +i d+  ++ ++  + l++++ + + +  + +  li+knge     +t++p +d +g 
  gi|298675068|ref|YP_003726818.1| 348 VNKPHANFFGFRKEDLEYNDIYDVHlKQTAYLIKGLSDYVFENK-SRLQTTEKLINKNGELRNLSITLTPEFDYNGD 423
                                       8999999********99999999998555555555555544444.599***************99*******99*** PP

                             PAS_9  92 lvgiivilrDite 104
                                       +  +i+  +Dite
  gi|298675068|ref|YP_003726818.1| 424 VDYVICSGEDITE 436
                                       ************8 PP

  == domain 3  score: 31.2 bits;  conditional E-value: 1.3e-10
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetf 76 
                                       d++l+ + dg+ l++N +a+++lGys++++l   ++d+   ++  + n +++++++ gr     +e+ +i+++g+t+
  gi|298675068|ref|YP_003726818.1| 460 DAVLVQDLDGNFLDVNLTACEFLGYSKADILKMGYKDIDalEQVGNLNAFENDLYRHGR---AVFETKYIKNDGSTI 533
                                       7899999*************************999998876677777777888888887...9************** PP

                             PAS_9  77 wvlltaspvkdddgelvgiivilrDit 103
                                        v+++ + ++ +++  ++  ++ rDit
  gi|298675068|ref|YP_003726818.1| 534 SVEVNSRFIQYQGKPAIL--LVARDIT 558
                                       **********99999999..******9 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.8   2.7e+03      54      84 ..      38      69 ..      27      82 .. 0.80
   2 !   73.1   0.0   1.6e-23   2.4e-20       7     110 ..     694     796 ..     690     797 .] 0.93

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.8
                                      HTGTCSTTCH.HCSTCHTSTSSSHHHHHHHHH CS
                         HATPase_c 54 lkklfekfsq.ddstkrggggtGlGlsivkkl 84
                                      + ++f++fs+ d++ k++ g  G+ +s  +++
  gi|298675068|ref|YP_003726818.1| 38 ITNIFGRFSDvDAKIKDSLGKLGVLFSSTRSY 69
                                      4589******9888888889999888877765 PP

  == domain 2  score: 73.1 bits;  conditional E-value: 1.6e-23
                                       HHHHHHHHHHHHHHHSTTTEEEEEEEEEE..TEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHH CS
                         HATPase_c   7 rqiisnlvdNavkfatkageieveikase..ddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsiv 81 
                                       +q++ nl++Navk++++++++ + i+  +  +  ++s +D G Gip ed + +f++f++   +k++ +g+GlGl+iv
  gi|298675068|ref|YP_003726818.1| 694 EQVFANLLSNAVKYSPENSRVIIDID--DigKFWKVSFTDFGEGIPDEDKETIFTRFQR--LEKDSVKGSGLGLAIV 766
                                       79************999999999999..444799*************************..7788999********* PP

                                       HHHHHHTTTEEEEEEET.TTEEEEEEEEES CS
                         HATPase_c  82 kklvelmgGeiwvesep.grGttftftlpl 110
                                       k+++el++Ge+ v+++p grG+ f++tl++
  gi|298675068|ref|YP_003726818.1| 767 KQIIELHDGEVGVDDNPeGRGSVFWVTLKK 796
                                       *************88888*********986 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   2.4e-10   3.6e-07       4     112 ..     206     310 ..     203     311 .. 0.95
   2 !   10.3   0.0   0.00034      0.52       2     113 .]     324     434 ..     323     434 .. 0.93
   3 !   27.0   0.0   2.3e-09   3.4e-06       2     113 .]     450     557 ..     449     557 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 2.4e-10
                                       HHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEE CS
                               PAS   4 raileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfk 80 
                                       r+++e+lp ++f +D +g+i+ +N+   +++  s e ++g +++ l ++    e + +++++l   +++  ge +  
  gi|298675068|ref|YP_003726818.1| 206 RSLIENLPLGVFSTDSNGEIIQCNKYLIDITKSSKEKIIGLNIFNLPVNS---EIKNCIRNALDGYTQFYEGEYKTV 279
                                       789*****************************************887765...5*********************** PP

                                       CTTSSEEEEEEEEEEEEETTEEEEEEEEEEEE CS
                               PAS  81 lrdgrpihlevraspvrdaggeilgflgvlrd 112
                                       l  g+   ++   +p ++++g+i g +g++ d
  gi|298675068|ref|YP_003726818.1| 280 L-TGKNLKIRAYFTPDTSEDGKIVGCIGTITD 310
                                       *.***************************998 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00034
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       +++ +++++++ i+    +    +vN+  + ++G++ e++    ++d+   ++ +  + l   + e++++ ++ e+ 
  gi|298675068|ref|YP_003726818.1| 324 KMEKVIDNIDTHIWYFADRRTYGLVNKPHANFFGFRKEDLEYNDIYDVHLKQTAYLIKGLSDYVFENKSRLQTTEKL 400
                                       68999*****************************************9998887778888888999999999999999 PP

                                       EECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  79 fklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       +++ +g+ + l ++ +p +d  g + ++++ + di
  gi|298675068|ref|YP_003726818.1| 401 INK-NGELRNLSITLTPEFDYNGDVDYVICSGEDI 434
                                       999.***************************9998 PP

  == domain 3  score: 27.0 bits;  conditional E-value: 2.3e-09
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       ++r+++e+l+d+++v D dg++l vN +a+e+lG+s  ++l    + +i       l +    ++ ++   r+g+  
  gi|298675068|ref|YP_003726818.1| 450 RYRTLFEDLIDAVLVQDLDGNFLDVNLTACEFLGYSKADILKMG-YKDIDA-----LEQVGNLNAFENDLYRHGRAV 520
                                       79***********************************9988554.457765.....444444445555555555555 PP

                                       EEC....TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  79 fkl....rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       f++     dg++i +ev+ + +   g+    +l+v+rdi
  gi|298675068|ref|YP_003726818.1| 521 FETkyikNDGSTISVEVNSRFIQYQGKP--AILLVARDI 557
                                       5555555699999999998888887766..899999987 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.4e-07   0.00021       2      48 ..     204     248 ..     203     268 .. 0.80
   2 ?    1.4   0.0      0.23   3.5e+02       4      40 ..     326     363 ..     323     380 .. 0.72
   3 !   31.3   0.1   9.9e-11   1.5e-07       2      42 ..     450     491 ..     449     509 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.4e-07
                             PAS_8   2 rlralfesspdgiavvd.lgdrivdvNqaalellGysadlkgellg.ql 48 
                                       r+r+l+e++p g++ +d +g+ i+++N+  ++++  s  +k++ +g ++
  gi|298675068|ref|YP_003726818.1| 204 RHRSLIENLPLGVFSTDsNGE-IIQCNKYLIDITK-S--SKEKIIGlNI 248
                                       9****************8888.************8.6..6777666433 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.23
                             PAS_8   4 ralfesspdgiav.vdlgdrivdvNqaalellGys.adl 40 
                                       + ++++++  i+  +d+ +    vN+  + ++G++ +dl
  gi|298675068|ref|YP_003726818.1| 326 EKVIDNIDTHIWYfADRRT-YGLVNKPHANFFGFRkEDL 363
                                       6788999999996335444.889**********664443 PP

  == domain 3  score: 31.3 bits;  conditional E-value: 9.9e-11
                             PAS_8   2 rlralfesspdgiavvdlgdrivdvNqaalellGys.adlkg 42 
                                       r+r+lfe + d+++v dl+++++dvN +a+e+lGys ad++ 
  gi|298675068|ref|YP_003726818.1| 450 RYRTLFEDLIDAVLVQDLDGNFLDVNLTACEFLGYSkADILK 491
                                       9****************6666***************998876 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   5.5e-06    0.0083       2     106 ..     210     312 ..     209     316 .. 0.91
   2 !   19.0   0.0   8.4e-07    0.0012      17     108 ..     345     437 ..     330     439 .. 0.83
   3 !   17.8   0.0     2e-06     0.003       1     109 [.     455     561 ..     455     562 .. 0.96

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.5e-06
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pge 77 
                                       ++lp +++  d++g ++ +N+   ++ + + e ++G   +  lp  +  ++ + +r +l+g +  ++ e+ +   g+
  gi|298675068|ref|YP_003726818.1| 210 ENLPLGVFSTDSNGEIIQCNKYLIDITKSSKEKIIGLNIFN-LP--VNSEIKNCIRNALDGYTQFYEGEYKTVlTGK 283
                                       899************************************95.55..89*************8777666665558999 PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiT 106
                                          +   ++P   e+G+++g++++++D+T
  gi|298675068|ref|YP_003726818.1| 284 NLKIRAYFTPDTSEDGKIVGCIGTITDLT 312
                                       99999999********************9 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 8.4e-07
                             PAS_4  17 vlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pgeerhyelrllPlrdes 92 
                                       +  +N+  a  fg++ e+l     ++++ ++ a  +    + v e + +++++e l   +ge r ++++l+P +d +
  gi|298675068|ref|YP_003726818.1| 345 YGLVNKPHANFFGFRKEDLEYNDIYDVHLKQTAYLIKGLSDYVFENKSRLQTTEKLINkNGELRNLSITLTPEFDYN 421
                                       55666666667777777777777777777777777777888899999999999999999****************** PP

                             PAS_4  93 GevigvlvisrDiTer 108
                                       G+v+ v++ + DiTe 
  gi|298675068|ref|YP_003726818.1| 422 GDVDYVICSGEDITEH 437
                                       **************96 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 2e-06
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       ++ l da++v d dg++l++N +a+e +g++ +++l + + ++   e+ ++l +  + + + +++++++ + + +g+
  gi|298675068|ref|YP_003726818.1| 455 FEDLIDAVLVQDLDGNFLDVNLTACEFLGYSKADILKMGYKDIDALEQVGNLNAFENDLYRHGRAVFETKYIKNDGS 531
                                       678899***********************************999999****************************** PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerr 109
                                       +  +e++ + +   +G+  ++l+++rDiT r+
  gi|298675068|ref|YP_003726818.1| 532 TISVEVNSRFI-QYQGK-PAILLVARDITGRK 561
                                       ********999.68***.9**********997 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.042        63      37      89 .]     256     308 ..     251     308 .. 0.84
   2 !   15.5   0.0     1e-05     0.015       5      87 ..     349     429 ..     347     430 .. 0.87
   3 !   10.9   0.0   0.00029      0.43       3      83 ..     473     549 ..     471     554 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.042
                             PAS_3  37 rvrealqealkkge.pyegeyRirrkdGeyrwveararvirdengkpvrvigva 89 
                                       ++++++ +al++ +  yegey+ +   G+   ++a+ ++  +e+gk+v  ig++
  gi|298675068|ref|YP_003726818.1| 256 EIKNCIRNALDGYTqFYEGEYKTVLT-GKNLKIRAYFTPDTSEDGKIVGCIGTI 308
                                       56788889998888688****99986.555589*******************96 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1e-05
                             PAS_3   5 serveeilGyspeellgkveswldlvhpeDrervrealqeal.kkgepyegeyRirrkdGeyrwveararvirdeng 80 
                                       ++   + +G+++e+l+ +  +++d vh    +++ + l +++ ++++++++  ++++k+Ge r ++ + ++ +d ng
  gi|298675068|ref|YP_003726818.1| 349 NKPHANFFGFRKEDLEYN--DIYD-VHLKQTAYLIKGLSDYVfENKSRLQTTEKLINKNGELRNLSITLTPEFDYNG 422
                                       5667789***********..****.57777788888888888466669***************************** PP

                             PAS_3  81 kpvrvig 87 
                                        +++vi+
  gi|298675068|ref|YP_003726818.1| 423 DVDYVIC 429
                                       ***9987 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00029
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirden 79 
                                        v+ + +e lGys++++l+    ++d+   e   ++++  +++ + g+   +e ++++ dG+++ ve   r i + +
  gi|298675068|ref|YP_003726818.1| 473 DVNLTACEFLGYSKADILKM--GYKDIDALEQVGNLNAFENDLYRHGR-AVFETKYIKNDGSTISVEVNSRFI-QYQ 545
                                       5677889*************..66666666666666555555556666.4567777*****************.888 PP

                             PAS_3  80 gkpv 83 
                                       gkp 
  gi|298675068|ref|YP_003726818.1| 546 GKPA 549
                                       8886 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   2.2e-07   0.00033      55     133 .]     112     189 ..      63     189 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.2e-07
                                       HHHHSSSEEEST.GG.TSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEE.SSSCSHHHHHHHHHHHHHH CS
                               GAF  55 vlatgqplvipd.st.pdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhn.psppftreelellqvladq 128
                                        l+++++++++d +t pd+   +   ++ll+   +rs++ +Pl+ ++el G + l+n +++ ++ + l++lq+++d 
  gi|298675068|ref|YP_003726818.1| 112 ELKKDEVIHVNDvATlPDEALKE---KNLLGKGDVRSFIIIPLHINDELSGFIGLDNiTTD-YRIDNLNILQMVSDV 184
                                       57789999***964467777777...78*****************************8888.**************9 PP

                                       HHHHH CS
                               GAF 129 vaval 133
                                       ++ +l
  gi|298675068|ref|YP_003726818.1| 185 IGTEL 189
                                       99876 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   5.1e-07   0.00076      67     134 ..     117     186 ..     106     189 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.1e-07
                                       S-EEES-GGG..-S-HHHHH.HHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHH CS
                             GAF_2  67 rpvilndlee..dpdkkglp.aghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqia 134
                                       + + +nd+++  d++ k  + +g+ ++rsf+++Pl  ++++ G+++l  n   ++  ++l +L+++++ i+
  gi|298675068|ref|YP_003726818.1| 117 EVIHVNDVATlpDEALKEKNlLGKGDVRSFIIIPLHINDELSGFIGL-DNITTDYRIDNLNILQMVSDVIG 186
                                       567799999955444444448**************88889******9.566666*************9997 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0     6e-06    0.0089       2     127 ..      48     189 ..      47     190 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6e-06
                             GAF_3   2 ldellekllkllvkllgaevgalllldedgnklqvaagw..dgkpalsesld.edsalarralssg...evvsepsf 72 
                                       +d  + ++l +l  l++++++ ++l+ + ++++  ++ w  +g + ++e l    + ++ +++++    ev++++++
  gi|298675068|ref|YP_003726818.1|  48 VDAKIKDSLGKLGVLFSSTRSYVFLFKNNKKTMDNTHEWcyTGIEPWKEKLQnLSTDVFPWLMNELkkdEVIHVNDV 124
                                       67778888999999***********************************9988999999999998755589***998 PP

                             GAF_3  73 aeedglpd...........raalavPLvagrqviGvlalastkprafdaedlelleslArqiatai 127
                                       a  +   +           r+ +++PL + +++ G+++l    +  ++ ++l  l+ ++++i+t++
  gi|298675068|ref|YP_003726818.1| 125 ATLPDEALkeknllgkgdvRSFIIIPLHINDELSGFIGLDNITTD-YRIDNLNILQMVSDVIGTEL 189
                                       7754422244444445666888*****************888866.99999*****9999999986 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0         4     6e+03      43      58 ..     197     212 ..     178     214 .. 0.78
   2 ?   -2.3   0.1       3.2   4.7e+03      42      60 ..     442     460 ..     433     462 .. 0.83
   3 !   15.1   0.0   1.2e-05     0.017       4      66 ..     583     644 ..     580     645 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4
                                       HHHHHHHHHHHHHHHH CS
                             HisKA  43 tiesearrldhlvedl 58 
                                        +e++++r ++l+e+l
  gi|298675068|ref|YP_003726818.1| 197 ALEQSEKRHRSLIENL 212
                                       4566777999999987 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.2
                                       HHHHHHHHHHHHHHHHHHH CS
                             HisKA  42 etiesearrldhlvedlLd 60 
                                       ++ie+++ r + l edl d
  gi|298675068|ref|YP_003726818.1| 442 KRIEESEIRYRTLFEDLID 460
                                       78999999********987 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 1.2e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHH.HC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                             HisKA   4 rflagvaHELrtPLsailgnaeaL.kregklteelkeyletiesearrldhlvedlLdlsriea 66 
                                        f+  + H+L +P  +++g++++L +   ++++   + l++i+ + + l +l+++   +++++a
  gi|298675068|ref|YP_003726818.1| 583 MFTDILRHDLLNPAGVVKGFTQLLiSM--ENDDYKLDVLNKIKASNEKLIELIQNASYFAKLDA 644
                                       5778899****************9644..34555556*******************99999986 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       7.4   1.1e+04       4      25 ..     573     594 ..     571     596 .. 0.82
   2 ?   10.7   0.0   0.00026      0.39      40     110 ..     701     771 ..     692     792 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 7.4
                       HATPase_c_2   4 dpehvrtvrevaeavlrragls 25 
                                       ++eh+ ++ ++++++lr+  l+
  gi|298675068|ref|YP_003726818.1| 573 KLEHSNKLKDMFTDILRHDLLN 594
                                       6899999********9886665 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00026
                       HATPase_c_2  40 ctNavehayleapegpvevrlesdeealtvevaDsGpg.fdpe..tlpdpteeepkeslkegGrGlalikglvD 110
                                       ++Nav++  +   + +v + +++ ++  +v+++D G+g  d    t+  + +   k+s k +G+Gla++k++ +
  gi|298675068|ref|YP_003726818.1| 701 LSNAVKYSPE---NSRVIIDIDDIGKFWKVSFTDFGEGiPDEDkeTIFTRFQRLEKDSVKGSGLGLAIVKQIIE 771
                                       6777777775...367999999999999******8888655441166666666669**************9865 PP

>> Ribosomal_L22  Ribosomal protein L22p/L17e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.4   0.00039      0.58       5      64 ..     621     680 ..     618     684 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00039
                                       EESS-HHHHHHHHHHHTTSBHHHHHHHHHT-SSTTHHHHHHHHHHHHHHHH..HT-GGGE CS
                     Ribosomal_L22   5 nlrvsfkklrevarlIrgmkveeAlkyLkfskkkaakfvlklLknaeanaelkgldvdsl 64 
                                       +++ s  kl e+++        +A++ L+f+k+  + ++++++   e++a+ k+ d + l
  gi|298675068|ref|YP_003726818.1| 621 KIKASNEKLIELIQNASYFAKLDAMEDLEFEKQDISAILKSVVSDFEQQAKDKNIDIEFL 680
                                       6788888999999999999999********************************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (797 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       929  (0.0518155); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.60u 0.24s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 5735.98
//
Query:       gi|298675069|ref|YP_003726819.1|  [L=652]
Description: phosphoadenosine phosphosulfate reductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.9e-41  139.8   0.0    1.6e-40  138.9   0.0    1.5  1  PAPS_reduct   Phosphoadenosine phosphosulfate reductase famil
    3.9e-05   24.2  11.6    3.9e-05   24.2  11.6    3.0  4  Fer4_7        4Fe-4S dicluster domain
    4.8e-05   23.4  12.4    4.8e-05   23.4  12.4    2.7  2  Fer4_10       4Fe-4S dicluster domain
    8.3e-05   22.7  13.0    8.3e-05   22.7  13.0    3.1  4  Fer4_9        4Fe-4S dicluster domain
     0.0012   18.7   0.1     0.0027   17.6   0.1    1.6  1  TBP           Transcription factor TFIID (or TATA-binding pro
     0.0024   17.6   6.4     0.0024   17.6   6.4    3.6  4  Fer4          4Fe-4S binding domain
     0.0068   17.3  12.7       0.02   15.8   2.3    4.5  4  Fer4_16       4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
      0.053   12.6   0.0       0.11   11.6   0.0    1.5  1  NAD_synthase  NAD synthase
       0.11   12.7   0.2       0.11   12.7   0.2    2.6  3  DUF1827       Domain of unknown function (DUF1827)
       0.16   11.7   0.0       0.36   10.6   0.0    1.6  1  ATP_bind_3    PP-loop family
        1.2    9.3  10.8        5.8    7.2  10.8    2.2  1  Fer4_18       4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.9   0.0     1e-43   1.6e-40       3     173 ..     261     435 ..     259     436 .. 0.95

  Alignments for each domain:
  == domain 1  score: 138.9 bits;  conditional E-value: 1e-43
                                       EEE--SSCTCHHHHHHHHHHCTTH..EEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-TH CS
                       PAPS_reduct   3 vvsvsgGkdslVllhLalkafkpv..pvvfvdtghefpetiefvdeleeryglrlkvyepeeevaekinaekhgssl 77 
                                        vs+sgGkdslV+l+L++ka+k++  + +f++tg e+pet+ef  +++++ ++++      ++++ek+  ++ + ++
  gi|298675069|ref|YP_003726819.1| 261 HVSFSGGKDSLVVLDLTRKALKNRelKAFFINTGIEYPETVEFARRFTSENNIDFVESGAGNKFWEKVGDFGPPAKD 337
                                       69*********************7668************************************************** PP

                                       HHCHHHHHHTHHHHHHHHHCT...TECEEE----CCCTTTTTTSSSEEECTTT-SCEEE-CCCT--HHHHHHHHHHC CS
                       PAPS_reduct  78 yeeaaeriaKveplkkaLekl...dedalltGaRrdesksraklpiveidedfekslrvfPllnWteedvwqyilre 151
                                       +++ +++++K+ p++  ++k    +  +++ G R +es+sr++++ +e +   +++l++fP+ +W+  + w yi+ +
  gi|298675069|ref|YP_003726819.1| 338 FRW-CCKVCKLAPANTIIDKCsekGMCLTVDGKRTYESFSRSAISTIEQNPFVPNQLNIFPIKDWKAIELWLYIYWQ 413
                                       ***.***************994334457899********************************************** PP

                                       T--B-CCCCTT-SS--BCTTB- CS
                       PAPS_reduct 152 nipynpLydqgfrsiGcvpctg 173
                                       +++ynpLyd gf+++Gc+ c++
  gi|298675069|ref|YP_003726819.1| 414 KLEYNPLYDMGFERVGCYLCPA 435
                                       ********************87 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       6.4   1.1e+04      29      44 ..      20      35 ..       8      38 .. 0.58
   2 ?   -3.3   0.3       9.3   1.5e+04       4      10 ..      43      49 ..      41      50 .. 0.78
   3 ?   -3.2   1.8       8.2   1.3e+04      34      46 ..     353     365 ..     335     366 .. 0.69
   4 !   24.2  11.6   2.4e-08   3.9e-05       1      48 [.     599     643 ..     599     645 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 6.4
                            Fer4_7 29 ekveidpekClgCgaC 44
                                      ++++++ ++   C++C
  gi|298675069|ref|YP_003726819.1| 20 KQITYNKNYIFWCNRC 35
                                      5555555555555555 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 9.3
                            Fer4_7  4 gCgaCva 10
                                      +Cg C +
  gi|298675069|ref|YP_003726819.1| 43 ECGICNN 49
                                      6999976 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 8.2
                            Fer4_7  34 dpekClgCgaCva 46 
                                         +kC+  g+C +
  gi|298675069|ref|YP_003726819.1| 353 IIDKCSEKGMCLT 365
                                       4567777777766 PP

  == domain 4  score: 24.2 bits;  conditional E-value: 2.4e-08
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveid.pekClgCgaCvavC 48 
                                       +C +Cg C + Cpv+a++l + +++     ++i   e+C+ Cg+C + C
  gi|298675069|ref|YP_003726819.1| 599 KCKKCGICKDICPVGAVKLSDGTENH----TNITiDESCTKCGKCTQSC 643
                                       7******************9985443....34432689*********** PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1       8.7   1.4e+04      19      26 ..     433     437 ..     430     450 .. 0.55
   2 !   23.4  12.4     3e-08   4.8e-05       7      55 ..     598     643 ..     594     644 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 8.7
                           Fer4_10  19 CPadltsv 26 
                                       CPa     
  gi|298675069|ref|YP_003726819.1| 433 CPAA---L 437
                                       8883...3 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 3e-08
                           Fer4_10   7 dtCirCgkCvkaCPadltsvgakgeaseeeavrk.kvekCtgcgaCveaC 55 
                                        +C +Cg C++ CP+      +k  +  e++ ++   e+Ct+cg+C+++C
  gi|298675069|ref|YP_003726819.1| 598 VKCKKCGICKDICPV----GAVKLSDGTENHTNItIDESCTKCGKCTQSC 643
                                       58*************....555555555555555499************* PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.4       3.6   5.8e+03      36      40 ..      32      36 ..      10      49 .. 0.60
   2 ?   -1.5   1.8       1.9   3.1e+03       8      26 ..     341     362 ..     339     370 .. 0.78
   3 ?   -3.5   0.0       7.6   1.2e+04      10      22 ..     432     443 ..     429     454 .. 0.60
   4 !   22.7  13.0   5.1e-08   8.3e-05       1      46 [.     599     643 ..     599     644 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.6
                            Fer4_9 36 CigCg 40
                                      C  C+
  gi|298675069|ref|YP_003726819.1| 32 CNRCN 36
                                      44443 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.9
                            Fer4_9   8 CveaC...pagvvvedaaerka 26 
                                       C ++C   pa++++++++e+ +
  gi|298675069|ref|YP_003726819.1| 341 CCKVCklaPANTIIDKCSEKGM 362
                                       7777888899999988887765 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 7.6
                            Fer4_9  10 eaCpagvvvedaa 22 
                                         Cpa +  e + 
  gi|298675069|ref|YP_003726819.1| 432 L-CPAALSAEYQR 443
                                       3.77776655555 PP

  == domain 4  score: 22.7 bits;  conditional E-value: 5.1e-08
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaC 46 
                                       kC +Cg C + Cp g+v+ +++++   +   +e +C++Cg+C++ C
  gi|298675069|ref|YP_003726819.1| 599 KCKKCGICKDICPVGAVKLSDGTENHTNITIDE-SCTKCGKCTQSC 643
                                       7********************999998877766.9*********** PP

>> TBP  Transcription factor TFIID (or TATA-binding protein, TBP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   1.7e-06    0.0027      47      84 ..     560     596 ..     541     597 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.7e-06
                                       TTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHHHHH CS
                               TBP  47 epkvtaliFssGkvvitGakseeelreaakkiapilkk 84 
                                         ++++++FssG++++t ak+++e++ ++k+  + lk+
  gi|298675069|ref|YP_003726819.1| 560 TDTASIKVFSSGNIQVT-AKTKDESHSVFKETTRQLKR 596
                                       46899************.*************9999985 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.5       2.3   3.7e+03      11      14 ..      44      47 ..      42      49 .. 0.86
   2 ?   -3.1   0.8         5   8.1e+03       9      14 ..     428     433 ..     428     433 .. 0.90
   3 !   17.6   6.4   1.5e-06    0.0024       7      23 ..     599     615 ..     597     616 .. 0.94
   4 !    9.1   3.6   0.00072       1.2       5      18 ..     630     643 ..     627     643 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.3
                                      -THH CS
                              Fer4 11 CGaC 14
                                      CG+C
  gi|298675069|ref|YP_003726819.1| 44 CGIC 47
                                      **** PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5
                                       SS-THH CS
                              Fer4   9 igCGaC 14 
                                       +gC +C
  gi|298675069|ref|YP_003726819.1| 428 VGCYLC 433
                                       79***9 PP

  == domain 3  score: 17.6 bits;  conditional E-value: 1.5e-06
                                       TSSS-THHHHHSTTTEE CS
                              Fer4   7 kCigCGaCvevCPvgAI 23 
                                       kC +CG+C ++CPvgA 
  gi|298675069|ref|YP_003726819.1| 599 KCKKCGICKDICPVGAV 615
                                       8***************7 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.00072
                                       TTTSSS-THHHHHS CS
                              Fer4   5 eekCigCGaCvevC 18 
                                        e C++CG+C + C
  gi|298675069|ref|YP_003726819.1| 630 DESCTKCGKCTQSC 643
                                       578********999 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   3.8       1.5   2.5e+03      33      61 ..       8      36 ..       2      50 .. 0.70
   2 !   15.5   3.0   1.6e-05     0.026      29      66 ..     575     612 ..     562     613 .. 0.77
   3 !   15.8   2.3   1.2e-05      0.02       1      20 [.     599     618 ..     599     631 .. 0.80
   4 ?    3.2   5.9      0.11   1.7e+02       2      12 ..     633     643 ..     632     645 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.5
                           Fer4_16 33 yntaekkdlaedeekckkqeaitgCdiCq 61
                                      +++   ++++++++ +++++ i+ C++C+
  gi|298675069|ref|YP_003726819.1|  8 KRKSRPRNYKKQKQITYNKNYIFWCNRCN 36
                                      45555667777777777777788888885 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.6e-05
                           Fer4_16  29 ecisyntaekkdlaedeekckkqeaitgCdiCqdvCPa 66 
                                        + +++++ +  ++e++++ k++ +++ C+iC+d+CP+
  gi|298675069|ref|YP_003726819.1| 575 VTAKTKDESHSVFKETTRQLKRAVKCKKCGICKDICPV 612
                                       444556677888999999999999*************8 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 1.2e-05
                           Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                       +C++Cg C ++CP++a+k  
  gi|298675069|ref|YP_003726819.1| 599 KCKKCGICKDICPVGAVKLS 618
                                       5***************9977 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.11
                           Fer4_16   2 CgtCgkCaevC 12 
                                       C++CgkC+++C
  gi|298675069|ref|YP_003726819.1| 633 CTKCGKCTQSC 643
                                       99******999 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.7e-05      0.11       5      71 ..     242     310 ..     237     319 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.7e-05
                                       HHHHHHHHHHHCTTSE..EEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHH CS
                      NAD_synthase   5 lvdflkeyvkkagakg..vvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaen 71 
                                        ++ +k  v++++ k+  v +  SGG DS +v  l++kal + + +a  + +  + +e ve a+ +  +
  gi|298675069|ref|YP_003726819.1| 242 AMNTIKGIVNQKEYKNlpVHVSFSGGKDSLVVLDLTRKALKNRELKAFFINTGIEYPETVEFARRFTSE 310
                                       567788888888887622567899****************99999999999999999999888888766 PP

>> DUF1827  Domain of unknown function (DUF1827)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       8.3   1.3e+04      44      55 ..     142     153 ..     133     177 .. 0.58
   2 ?    0.2   0.1      0.54   8.9e+02      36      63 ..     204     231 ..     193     288 .. 0.57
   3 ?   12.7   0.2   6.8e-05      0.11      10      58 ..     549     596 ..     541     599 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 8.3
                                       EEEEEEEESSS- CS
                           DUF1827  44 hveivlsnkkRa 55 
                                       ++ + +++ kR+
  gi|298675069|ref|YP_003726819.1| 142 KKTVTVKDTKRH 153
                                       333444444444 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.54
                                       EEEEEETTEEEEEEEESSS---HHHHHH CS
                           DUF1827  36 vvyteapkhveivlsnkkRaikeeEief 63 
                                       v+ +++ ++ e+ ls+k+  +++  i  
  gi|298675069|ref|YP_003726819.1| 204 VLKVKKIDNSEVTLSEKNPDLNDVIIAN 231
                                       4444444444444444444333322222 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 6.8e-05
                                       -HHHHHHHHHHSS-SEEEEEEETTEEEEEEEETTEEEEEEEESSS---H CS
                           DUF1827  10 yselvkkqLenTdaklvkvYslGnttvvyteapkhveivlsnkkRaike 58 
                                       +s+ +   L +Td+  +kv+s Gn++v   +++++   v+++ +R++k+
  gi|298675069|ref|YP_003726819.1| 549 FSQDLGTLLVKTDTASIKVFSSGNIQVTA-KTKDESHSVFKETTRQLKR 596
                                       678888899*****************985.5566666778888888875 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00022      0.36       3      40 ..     261     296 ..     259     321 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00022
                                       EEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSS CS
                        ATP_bind_3   3 lvAvSgGlDSmaLllllaklkkklgiklvaihvdhglr 40 
                                        v +SgG DS++ l l+ k  k+   +l a+ ++ g+ 
  gi|298675069|ref|YP_003726819.1| 261 HVSFSGGKDSLVVLDLTRKALKN--RELKAFFINTGIE 296
                                       699***************99775..5667777766654 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2  10.8    0.0035       5.8      38      95 ..     577     643 ..     553     648 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0035
                           Fer4_18  38 agrkkekkalkekeerkekgagdcidcescvkvcPtg.idirkGlql........eciscllcidac 95 
                                       a++k e++++ ++ +r+ k a +c +c+ c ++cP+g + + +G           +c +c++c  +c
  gi|298675069|ref|YP_003726819.1| 577 AKTKDESHSVFKETTRQLKRAVKCKKCGICKDICPVGaVKLSDGTENhtnitideSCTKCGKCTQSC 643
                                       3444444555566677889999*************98578999964311112222699999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (652 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1179  (0.0657594); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 4656.09
//
Query:       gi|298675070|ref|YP_003726820.1|  [L=384]
Description: geranylgeranyl reductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-19   70.4   0.0    1.7e-15   57.2   0.0    2.7  2  FAD_binding_3   FAD binding domain
      1e-11   44.7   0.2    3.3e-05   23.3   0.0    2.2  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    5.6e-10   38.9   0.1    1.5e-06   27.7   0.0    2.2  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    6.7e-10   38.4   0.0    4.1e-05   22.6   0.0    2.3  2  Trp_halogenase  Tryptophan halogenase
    3.5e-09   36.7   0.0     0.0013   18.4   0.0    2.1  2  DAO             FAD dependent oxidoreductase
      7e-08   31.6   0.1    1.1e-05   24.3   0.0    2.1  2  HI0933_like     HI0933-like protein
    4.6e-07   29.5   0.0    7.6e-07   28.8   0.0    1.3  1  FAD_oxidored    FAD dependent oxidoreductase
    5.7e-07   28.9   0.0    1.8e-06   27.2   0.0    1.7  2  Lycopene_cycl   Lycopene cyclase protein
    6.1e-06   25.6   0.0    1.5e-05   24.3   0.0    1.6  2  FAD_binding_2   FAD binding domain
    2.4e-05   23.6   0.1    5.3e-05   22.5   0.1    1.5  1  GIDA            Glucose inhibited division protein A
    7.6e-05   22.1   0.0    0.00068   18.9   0.0    2.0  2  Thi4            Thi4 family
    0.00018   21.7   0.0      0.001   19.2   0.0    2.2  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
     0.0027   18.2   0.0        4.6    7.9   0.0    2.6  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.023   14.8   0.0      0.041   13.9   0.0    1.4  1  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
       0.17   11.8   0.0        1.9    8.5   0.0    2.2  2  NAD_binding_9   FAD-NAD(P)-binding


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   0.0   1.4e-18   1.7e-15       2     177 ..       2     159 ..       1     187 [. 0.83
   2 !    9.7   0.0   0.00039      0.46     278     319 ..     251     292 ..     247     321 .. 0.74

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 1.4e-18
                                       EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEE CS
                     FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmellrqlGledrilaegapnelmgealyn 78 
                                       +dVlI+GaGpaG ++a+  +e+G +++l+ek++   ++p a+ ++qr +++l+             p++l++   y+
  gi|298675070|ref|YP_003726820.1|   2 YDVLIIGAGPAGTTAAKHTAEKGLDTLLIEKQKLPRKKPCAGLVSQRALNSLEF----------EIPKHLIKRYCYG 68 
                                       69*************************************************986..........3467777777777 PP

                                       ECCCCCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEE CS
                     FAD_binding_3  79 elsdtpkaradlelesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvra 155
                                       +  +++  +  le +   +   +++ +e++ +L+++a+++g+++  +t v+s++++++ v+ + ++        ++a
  gi|298675070|ref|YP_003726820.1|  69 T--RIKYKNHVLESKLDRPVGILVSRDEFDYYLSQQATKKGAEILDNTSVNSVNAENDYVAVNTTKGL------FKA 137
                                       7..3333344444334445556788999********************************99999885......99* PP

                                       EEEEE--GTT-HHHHHHTGGEE CS
                     FAD_binding_3 156 kYlvGaDGgrStvrktlgiefe 177
                                       + ++GaDG++S++++ +    e
  gi|298675070|ref|YP_003726820.1| 138 RIVIGADGVNSICARYVRSGSE 159
                                       *************998874444 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00039
                                       ESSSEETTEEE-GGGTEEE-STTSHHHHHHHHHHHHHHHHHH CS
                     FAD_binding_3 278 aekyrkgrvflaGDAaHihpPtgGqGlNtaiqDavnLawkLa 319
                                        ++ +++rv l+GDAa  +    G G+  ai+     a   +
  gi|298675070|ref|YP_003726820.1| 251 KRDVHSDRVILVGDAAGFVDAFLGEGISYAIMSGKIAANTVI 292
                                       57889**********************999987665555544 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   4.5e-07   0.00054       1      32 [.       5      35 ..       5      37 .. 0.93
   2 !   23.3   0.0   2.8e-08   3.3e-05      78     141 ..      90     153 ..      78     178 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.5e-07
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgni 32
                                      +IiGaGPaG +aa +  ++gl d l +Ek+++
  gi|298675070|ref|YP_003726820.1|  5 LIIGAGPAGTTAAKHTAEKGL-DTLLIEKQKL 35
                                      6********************.789****975 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 2.8e-08
                       Pyr_redox_3  78 lsrkealeYlrevaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGefdkPnkl 141
                                       +sr+e+ +Yl++ a+++  +i  +++V+sv+ e++   v+t+k+ ++A+ vi A G  ++  + 
  gi|298675070|ref|YP_003726820.1|  90 VSRDEFDYYLSQQATKKGAEILDNTSVNSVNAENDYVAVNTTKGLFKARIVIGADGVNSICARY 153
                                       5799999***********************************************9987666555 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   1.3e-09   1.5e-06       1      41 [.       2      41 ..       2      84 .. 0.74
   2 !    9.6   0.0    0.0004      0.48     181     256 ..      91     164 ..      66     171 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.3e-09
                                      CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcl 41
                                      +dv++iG+GpAG++aa++ a++g++++l+e ++ ++  ++ 
  gi|298675070|ref|YP_003726820.1|  2 YDVLIIGAGPAGTTAAKHTAEKGLDTLLIE-KQKLPRKKPC 41
                                      69***************************6.4444444443 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0004
                                       S-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 181 ldkelsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpstelleeklglelderg 256
                                         +e+  +l ++ +k+G e+  +tsv+ ++++++ +  v++++  ++a+ v+ a Gv    + +  ++g e++++ 
  gi|298675070|ref|YP_003726820.1|  91 SRDEFDYYLSQQATKKGAEILDNTSVNSVNAEND-YVAVNTTKGLFKARIVIGADGVNSICARY-VRSGSETNRNA 164
                                       45789999*************************8.6667777777***********98877666.77777776665 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   1.8e-05     0.021       1      41 [.       3      40 ..       3      69 .. 0.87
   2 !   22.6   0.0   3.4e-08   4.1e-05     152     368 ..      91     313 ..      56     330 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.8e-05
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS---SS CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlveseeigtvgv 41
                                      +++i+G+G+aG +aA + a+ +   l+ +l+e++++++ + 
  gi|298675070|ref|YP_003726820.1|  3 DVLIIGAGPAGTTAAKHTAEKG---LDTLLIEKQKLPRKKP 40
                                      699*************999988...9***********9765 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 3.4e-08
                                       -HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG-IIIIIIT---EEE-TTT CS
                    Trp_halogenase 152 daalyakfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfrgllieqaLktgfedwsdv 228
                                        + +++ +L + a+++G ++++ ++v+ +  e+++v+ +++++g  ++a+++i + G +++    + ++g e+  + 
  gi|298675070|ref|YP_003726820.1|  91 SRDEFDYYLSQQATKKGAEILDNTSVNSVNAENDYVA-VNTTKGL-FKARIVIGADGVNSICARYV-RSGSETNRNA 164
                                       57889**********************99999***96.7777887.9*************998887.8888888877 PP

                                       ----EEEEEEEE--H.---SSEE..EEE-SSEEEEEEEETTEEEEEEEE-TTTS-HHHHHHHHHHHCT--T.TTS-. CS
                    Trp_halogenase 229 LltdrAlavqvesee.lvepytr..ataekaGWtWkiPLqhrlgnGyvyssahadddeAlaellaeldgkl.eaep. 300
                                       +   + + +++e  + +    t+      k+G +W  P  + ++ G+    +   + + l++    ++ +  ++ + 
  gi|298675070|ref|YP_003726820.1| 165 FSLISEVPASIEYINnKYLDITEvdFGRVKNGYFWTFPKDNHISVGLGLFDNSS-ESKPLKTYYDYIKDQYfDYLKp 240
                                       766566655555544455556663345679***********9999987765544.5555555555554432133331 PP

                                       ..EEEE---EEES-SEETTEEE-CCCTEE--CCCS-HHHHHHH....HHHHHHHT--BTT--HHHHHHHHHHHH CS
                    Trp_halogenase 301 ..rkirfttGrrkqawvknvvalGlasgfvePlestsihliqa....alrrLlallpdksdepaaiaefnreva 368
                                         + i++  G+++ + +  v+++G+a+gfv++  + +i  +      a++++++ + ++ +++ + + +  + +
  gi|298675070|ref|YP_003726820.1| 241 rgHFIPI-GGYKRDVHSDRVILVGDAAGFVDAFLGEGISYAIMsgkiAANTVIEAFEENDFSEDKFSTYLTRCE 313
                                       2234443.689999***********************99888778889********999999888888766655 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.1e-06    0.0013       1      31 [.       3      35 ..       3      76 .. 0.93
   2 !   16.6   0.0   3.9e-06    0.0047     151     351 ..      98     289 ..      85     290 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.1e-06
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdi 31
                                      dv+iiG+G +G ++A + a++g  ++l+ek++ 
  gi|298675070|ref|YP_003726820.1|  3 DVLIIGAGPAGTTAAKHTAEKGldTLLIEKQKL 35
                                      8*****************************965 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 3.9e-06
                                       HHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GGGHHHH..HTT..CTTTSEEEEEEEE CS
                               DAO 151 alaraaealGveilegtevtgleeedgkvwgverttpgendaadavVnaaGawsdll..gll..keldlpispvrgq 223
                                       +l ++a ++G+eil +t v ++++e ++ + v +tt+g   +a+ v+ a G+ s  +  + +  +      + + + 
  gi|298675070|ref|YP_003726820.1|  98 YLSQQATKKGAEILDNTSVNSVNAE-NDYVAV-NTTKGLF-KARIVIGADGVNS--IcaRYVrsGSE--TNRNAFSL 167
                                       57788*****************665.344555.7887874.5688******998..43333332212..22444444 PP

                                       EEEEEECCTHSTGSGCSEEEEEEEETTTTEEEEEETTSEEEEEESSEEETTCSSTSCSHHHHHHHHHHHHHHSGGGC CS
                               DAO 224 vlvlkplseklvspaailpvpetdddgrgvyvtprkdgrvlvGgtadeesgdddpevdeedidellealrklfPqlg 300
                                       +  +    e  + +++  ++ +  + + g++ t +kd+++ vG     + + +  ++    +d++ ++  +++   g
  gi|298675070|ref|YP_003726820.1| 168 ISEVPASIEYINNKYLDITEVDFGRVKNGYFWTFPKDNHISVGLGL-FDNSSE-SKPLKTYYDYIKDQYFDYLKPRG 242
                                       4444222223334454444444888888999999999*****9987.444444.5999999***********96668 PP

                                       GEEEEEEE.EEEE.TTSSEEEEEEETEEEEEEEEECTTTHHHHHHHHHHHHHH CS
                               DAO 301 dvlrkwaG.lrpl.pdglpligetpgvkglylatGhsghGltlapatGkllae 351
                                       ++     G  r+   d+  l+g +    g++ a  + g G++ a+++Gk++a+
  gi|298675070|ref|YP_003726820.1| 243 HFIP-IGGyKRDVhSDRVILVGDA---AGFVDA--FLGEGISYAIMSGKIAAN 289
                                       8773.4441366447999999984...577777..567999999999999885 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   9.5e-09   1.1e-05       1      38 [.       2      39 ..       2      44 .. 0.91
   2 !    5.2   0.0    0.0059       7.1     115     167 ..      99     149 ..      96     162 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 9.5e-09
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HH CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklgrK 38
                                      +dv++iG+G+AG  aA + a++g ++ll+ek+k + +K
  gi|298675070|ref|YP_003726820.1|  2 YDVLIIGAGPAGTTAAKHTAEKGLDTLLIEKQKLPRKK 39
                                      59*****************************9777666 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0059
                                       HHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS- CS
                       HI0933_like 115 llkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlSi 167
                                       l ++++++g ++  +t+v+sv++e+d  + v+t +++ ++a+ ++ A G +Si
  gi|298675070|ref|YP_003726820.1|  99 LSQQATKKGAEILDNTSVNSVNAENDY-VAVNT-TKGLFKARIVIGADGVNSI 149
                                       78999****************988887.99999.9999***999999999887 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   6.4e-10   7.6e-07       1     142 [.       3     143 ..       3     152 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 6.4e-10
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaeeqvvtgiareflerlrq..rgga.r 74 
                                       Dv+++G+gpaG++AA   a++G  +lL+e+++       +glv+    n  e ++ + ++++++   r   +++  +
  gi|298675070|ref|YP_003726820.1|   3 DVLIIGAGPAGTTAAKHTAEKGLDTLLIEKQKLPRKKPCAGLVSQRALNSLEFEIPKHLIKRYCYGTRIkyKNHVlE 79 
                                       9****************************999988888888888888888777777777777776554311222211 PP

                      FAD_oxidored  75 lkkrskwn....tfepevakavleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvfiDA 142
                                         ++ + +     +  + +   l +  +++g ++l nt + +v+ e+ +  +v++     +  ++A+++i A
  gi|298675070|ref|YP_003726820.1|  80 --SKLD-RpvgiLVSRDEFDYYLSQQATKKGAEILDNTSVNSVNAEN-DYVAVNTT----KGLFKARIVIGA 143
                                       ..2222.2334467777777777777799999999999999999996.67777774....678888888866 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   1.5e-09   1.8e-06       1     145 [.       3     150 ..       3     163 .. 0.79
   2 ?   -1.5   0.0      0.83   9.9e+02     243     297 ..     245     298 ..     242     311 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 1.5e-09
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnnyvWsdefedlga.....leecvehsWsgtivylddg 72 
                                       Dv++iGaGpAg   A++   a++gl  +lie  ++l++         +++l++      +++++    gt+++ +++
  gi|298675070|ref|YP_003726820.1|   3 DVLIIGAGPAGTTAAKHT--AEKGLDTLLIEK-QKLPRKKPCAGLVSQRALNSlefeiPKHLIKRYCYGTRIKYKNH 76 
                                       9*****************..**********76.55657777789999999999444433567777788888988888 PP

                     Lycopene_cycl  73 k.killgraYg.rvsskrlkeellerlvengvkll.eakvesveeeeageslvvleggr.kirarlvvdarglaslk 145
                                         + +l+r+ g  vs++++   l ++  ++g++ l +  v+sv++e++   +v+++  +   +ar+v+ a g+ s +
  gi|298675070|ref|YP_003726820.1|  77 VlESKLDRPVGiLVSRDEFDYYLSQQATKKGAEILdNTSVNSVNAEND---YVAVNTTKgLFKARIVIGADGVNSIC 150
                                       724567798873599*************77776551667999999988...66666666478**********88766 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.83
                     Lycopene_cycl 243 iPvtlggslprleqk.vlaiGaaaglvhPaTGYsvarslaeapllasaiaaalres 297
                                       iP+  gg  + +++  v+ +G aag v    G  +  ++   ++ a+ + +a +e+
  gi|298675070|ref|YP_003726820.1| 245 IPI--GGYKRDVHSDrVILVGDAAGFVDAFLGEGISYAIMSGKIAANTVIEAFEEN 298
                                       899..88888887766999******9988888777777777777777777776655 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   1.2e-08   1.5e-05       1      32 [.       3      34 ..       3      38 .. 0.96
   2 ?   -2.5   0.0       1.6     2e+03     146     173 ..      98     125 ..      80     149 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.2e-08
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSS CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeq 32
                                      Dv++iG+G AG +AA   ae+Gl+++++ek +
  gi|298675070|ref|YP_003726820.1|  3 DVLIIGAGPAGTTAAKHTAEKGLDTLLIEKQK 34
                                      9****************************975 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.6
                                       HHHHHHHTCTEEEEESEEEEEEEECTTE CS
                     FAD_binding_2 146 rlvesarkagvdfqerteadeLivedgr 173
                                        l ++a k g +++++t++++++ e++ 
  gi|298675070|ref|YP_003726820.1|  98 YLSQQATKKGAEILDNTSVNSVNAENDY 125
                                       5678888999999999999999988873 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.1   4.5e-08   5.3e-05       1      54 [.       3      55 ..       3     171 .. 0.67

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 4.5e-08
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SSSSEEE-TTHHHHHH CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldtiaelsCnpsiggiakgllvr 54
                                      dv +iG+G AG+ AA ++a++G+++lLi +k +   + +C   +   a   l  
  gi|298675070|ref|YP_003726820.1|  3 DVLIIGAGPAGTTAAKHTAEKGLDTLLI-EKQKLPRKKPCAGLVSQRALNSLEF 55
                                      799*************************.4444445555555555555555555 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   5.7e-07   0.00068      19      50 ..       3      33 ..       1      36 [. 0.94
   2 ?    0.7   0.0      0.21   2.6e+02      43      96 ..      74     131 ..      61     148 .. 0.64

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5.7e-07
                                      EEEEE--SHHHHHHHHHHHHCTTS-EEEEESS CS
                              Thi4 19 DvvivGaGssGLtaayylakkpdlkvailers 50
                                      Dv+i+GaG++G taa+  a+k +l ++++e++
  gi|298675070|ref|YP_003726820.1|  3 DVLIIGAGPAGTTAAKHTAEK-GLDTLLIEKQ 33
                                      9********************.********86 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.21
                                       -EEEEESSSS--TTTTTTSTTBSEEEEE...TTTHHHHHHTT---EE.ESSEEEESEH CS
                              Thi4  43 kvailersvspGGGawlGGqlfsaivvr...kpakelLdelgikyed.egdyvvvkda 96 
                                       k  +le+++    G+      f++ + +   k++ e+Ld+  +++ + e+dyv v+ +
  gi|298675070|ref|YP_003726820.1|  74 KNHVLESKLDRPVGILVSRDEFDYYLSQqatKKGAEILDNTSVNSVNaENDYVAVNTT 131
                                       5566666666666666666667666654111566789999999876515566666543 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   8.8e-07     0.001       1      28 [.       6      33 ..       6      37 .. 0.96
   2 ?   -1.4   0.0       2.4   2.8e+03      42      67 ..     204     229 ..     192     230 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 8.8e-07
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekr 28
                                      I+GaG +G +aA + a++g+d ll+ek+
  gi|298675070|ref|YP_003726820.1|  6 IIGAGPAGTTAAKHTAEKGLDTLLIEKQ 33
                                      9*************************98 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.4
                                       TCEECTS---EEETTHHHHCHHHHCC CS
                     NAD_binding_8  42 gvrvdygahifhgsgyypnvrrllre 67 
                                       ++ + +g   f  s++++ +++++++
  gi|298675070|ref|YP_003726820.1| 204 DNHISVGLGLFDNSSESKPLKTYYDY 229
                                       36677888888777889999999887 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0038       4.6       2      35 ..       4      37 ..       3      56 .. 0.89
   2 !    7.8   0.0    0.0042         5      44      77 ..      97     129 ..      77     133 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0038
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      v+++G+G  g  +A+  ae g ++ ++e ++ ++
  gi|298675070|ref|YP_003726820.1|  4 VLIIGAGPAGTTAAKHTAEKGLDTLLIEKQKLPR 37
                                      89**************************998777 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0042
                                       HHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEE CS
                         Pyr_redox  44 kilqeklekngievllntkveeiegsedgvesvk 77 
                                        +l ++ +k+g e+l nt+v++++ ++d   +v 
  gi|298675070|ref|YP_003726820.1|  97 YYLSQQATKKGAEILDNTSVNSVNAENDY-VAVN 129
                                       57888999****************99985.3455 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.5e-05     0.041      14      65 ..       3      54 ..       1      65 [. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.5e-05
                                      EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEE CS
                      Shikimate_DH 14 kvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealk 65
                                       vl+iGaG  ++ +akh ++kg++ +++    l r k  a  +++  ++ l+
  gi|298675070|ref|YP_003726820.1|  3 DVLIIGAGPAGTTAAKHTAEKGLDTLLIEKQKLPRKKPCAGLVSQRALNSLE 54
                                      69************************99888888887777776666555555 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0016       1.9       2      19 ..       6      23 ..       5      44 .. 0.83
   2 ?    0.8   0.0      0.37   4.5e+02      90     123 ..      89     122 ..      67     148 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0016
                     NAD_binding_9  2 ivGaGprGlavlerLlar 19
                                      i+GaGp+G++++++ +++
  gi|298675070|ref|YP_003726820.1|  6 IIGAGPAGTTAAKHTAEK 23
                                      9*************9887 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.37
                     NAD_binding_9  90 fvpRalyGrYlrdlfeellarlpegvtvevhrae 123
                                        v+R  +  Yl++++++  a+  ++++v+ ++ae
  gi|298675070|ref|YP_003726820.1|  89 LVSRDEFDYYLSQQATKKGAEILDNTSVNSVNAE 122
                                       6899999999999999999888888788777664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2739.00
//
Query:       gi|298675071|ref|YP_003726821.1|  [L=481]
Description: multi antimicrobial extrusion protein MatE [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-19   68.8  20.0    4.9e-19   68.8  20.0    3.6  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
    2.6e-17   63.1  21.0    2.6e-17   63.1  21.0    2.3  2  Polysacc_synt    Polysaccharide biosynthesis protein
    1.1e-16   60.9  14.5    1.1e-16   60.9  14.5    2.1  2  Polysacc_synt_3  Polysaccharide biosynthesis protein
    1.6e-12   47.4   4.3    1.6e-12   47.4   4.3    4.0  4  MatE             MatE
    2.8e-08   32.8  33.8    2.8e-08   32.8  32.7    1.6  1  MurJ             Lipid II flippase MurJ


Domain annotation for each model (and alignments):
>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.4   5.4         5   1.8e+04     119     133 ..      77     101 ..       6     116 .. 0.46
   2 !   14.8   6.4   6.4e-06     0.023       2     100 ..     120     218 ..     119     251 .. 0.80
   3 ?   -2.5   0.0       1.4   4.9e+03      91     108 ..     294     308 ..     268     325 .. 0.55
   4 !   68.8  20.0   1.4e-22   4.9e-19       4     142 ..     335     465 ..     332     466 .. 0.93

  Alignments for each domain:
  == domain 1  score: -4.4 bits;  conditional E-value: 5
                   Polysacc_synt_C 119 a..........alalllavlvgalv 133
                                       +          ++++l +  +   v
  gi|298675071|ref|YP_003726821.1|  77 EdfqdifysflSIVILTGFSASLMV 101
                                       2333332221111222222222222 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 6.4e-06
                   Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllli.plfgivGaaiatvlallvvavlnlyal 77 
                                       ++il+ +i++ sl+ +l +++ ++ + k+  + lv   ++ ++l  +++    g++Ga+++ +   +v ++   +++
  gi|298675071|ref|YP_003726821.1| 120 VQILSAIIFLESLNGILFNYFRATQQIKKHSVLLVTKTVLFIVLVSFFVlMGEGLTGALAGLLTKDIVLLLATTVII 196
                                       79***********************************************334489********************** PP

                   Polysacc_synt_C  78 rrllgiklellrrllkpllaalv 100
                                         ++gik   ++++ k +l+  +
  gi|298675071|ref|YP_003726821.1| 197 GAEIGIKRPRFTNI-KEYLSFGL 218
                                       *******9546666.55555544 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.4
                   Polysacc_synt_C  91 llkpllaalvmgivvyll 108
                                        lk++la+ + ++     
  gi|298675071|ref|YP_003726821.1| 294 SLKYFLAVGIPAVF---G 308
                                       33555555555544...2 PP

  == domain 4  score: 68.8 bits;  conditional E-value: 1.4e-22
                   Polysacc_synt_C   4 ilalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyalrrl 80 
                                       ++als++++++++++  ++   +++k++ k+ +++a+++++ln+l ip++gi+Gaa  t+l+++v+++l+ y+ +++
  gi|298675071|ref|YP_003726821.1| 335 FVALSALVFGVFIIFEKVIYLEKKTKTIGKIWMFAAVLNFGLNILIIPYIGIIGAAGTTLLSFIVGLCLIAYYSSKY 411
                                       679************************************************************************** PP

                   Polysacc_synt_C  81 lgiklellrrllkpllaalvmgivvylllllllgllllaalalllavlvgalvYlllllllr 142
                                       l++++  +r + k l+a+++m+++   + ++ +  l+      l+ ++++a++Y+++l+ll+
  gi|298675071|ref|YP_003726821.1| 412 LKFDV-NFRFISKSLFASILMSLI---VISWDPVNLF----DALVMIGICAVFYFAVLILLK 465
                                       *****.6*****************...8888887666....44677778**********998 PP

>> Polysacc_synt  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.1  21.0   7.3e-21   2.6e-17      10     269 ..      16     273 ..       7     275 .. 0.83
   2 !    4.3  13.1    0.0063        23      56     208 ..     271     430 ..     267     451 .. 0.75

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 7.3e-21
                     Polysacc_synt  10 lsqlitkllafvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrekkelvslillnvllvll 86 
                                       + +l+  l +++ l++l+  ++ e +G+  +++ +v++  +++ lGl+aa vr+    ++  e+++ i+ + l++++
  gi|298675071|ref|YP_003726821.1|  16 ITNLVGSLSGLILLPILTKNMPVESYGIWVQIIVTVGIVPNIVMLGLPAAMVRYLPSVKKA-EDFQDIFYSFLSIVI 91 
                                       5678888889********************************************9888764.666666666666666 PP

                     Polysacc_synt  87 vlvllfllllliaa......flglpelavlylilalmllllvgvasfrrglfqglermkyaavsqvveqlsrvilvl 157
                                       ++   + l+ ++ a      ++++  lav +l ++++   l + +    ++f++ +  k  +v  v + + +++lv 
  gi|298675071|ref|YP_003726821.1|  92 LTGFSASLMVYLLAgsiasvLFDGNTLAVQILSAIIF---LESLNGILFNYFRATQQIKKHSVLLVTKTVLFIVLVS 165
                                       5543333333332335555777777777665544444...5688888999*************************** PP

                     Polysacc_synt 158 iavflfldivaavlgavlaalvggivslavlrkkf.rprfvilslklvrellsfsapltisslaillytyidsillg 233
                                       ++v+++  +++a++g++   +v +++  +++  +   +r  +    +++e lsf++p + +s++  + + +d+++++
  gi|298675071|ref|YP_003726821.1| 166 FFVLMGEGLTGALAGLLTKDIVLLLATTVIIGAEIgIKRPRFT---NIKEYLSFGLPNVPGSMSQWVVNSSDRYVIS 239
                                       *******************************988853444444...66***************************** PP

                     Polysacc_synt 234 lllgaeavGiYnaayqllvaisgllapivtaalfPv 269
                                        +lg++avG Y+ +y+l +++ ++lap +   + P+
  gi|298675071|ref|YP_003726821.1| 240 GFLGTSAVGLYSPGYTLGNIVRMFLAPLNF--MLPM 273
                                       **************************9876..5555 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0063
                     Polysacc_synt  56 lnaalvreiakyrekkelvslillnvl.lvllvlvllfllllliaa....flglpelav....lylilalmllllvg 123
                                       l+ +l+++ ++++ +  +v++il+ +l   l v +  ++ l ++++    +l+ pe a+    + ++ al+ l++  
  gi|298675071|ref|YP_003726821.1| 271 LPMILSKYYDENNLD--EVKKILSYSLkYFLAVGIPAVFGLSFLSEqillILSTPEIASkgyqITPFVALSALVFGV 345
                                       788999999999994..555555444413333444444444455455666999999887433345556666678999 PP

                     Polysacc_synt 124 vasfrrglfqglermkyaavsqvveqlsrvilvliavflfldivaavlgavlaalvggivslavlrkkfr..prfvi 198
                                       +++f   ++ +++  +   +++++ +l +  l ++ + +++ i +a+++++l+ +vg+ + ++++ k+++  ++f +
  gi|298675071|ref|YP_003726821.1| 346 FIIFEKVIYLEKKTKTIGKIWMFAAVLNFG-LNILIIPYIG-IIGAAGTTLLSFIVGLCLIAYYSSKYLKfdVNFRF 420
                                       99999*************************.6677777888.9**********************999965688888 PP

                     Polysacc_synt 199 lslklvrell 208
                                       +s++l+  +l
  gi|298675071|ref|YP_003726821.1| 421 ISKSLFASIL 430
                                       8666665544 PP

>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9  14.5   3.1e-20   1.1e-16       8     283 ..      38     320 ..      31     324 .. 0.89
   2 ?   -1.8   4.2       0.4   1.4e+03      84     177 ..     332     424 ..     326     448 .. 0.79

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 3.1e-20
                   Polysacc_synt_3   8 pedFGvvaialvvislanlfvdmGlssaliqke..dlteedlstvftf....nlvlgllialvlfllapliasfynq 78 
                                        e +G+   ++v ++++  +v +Gl  a+++      ++ed++ +f++     +++g+ ++l+++lla +ias++ +
  gi|298675071|ref|YP_003726821.1|  38 VESYGIWVQIIVTVGIVPNIVMLGLPAAMVRYLpsVKKAEDFQDIFYSflsiVILTGFSASLMVYLLAGSIASVLFD 114
                                       689****************************9852344559*****9622225688*****************7654 PP

                   Polysacc_synt_3  79 pelvtvlrvlalvlilsglssvqeallrrelkFkklfkitlvssvvgvivaivlAllglgvwALvigtllssllslv 155
                                        +    +++l+  ++l++l+ +  +++r   + kk ++  ++ +v+ +++    +l+g g+   + g l+++++ l+
  gi|298675071|ref|YP_003726821.1| 115 GN-TLAVQILSAIIFLESLNGILFNYFRATQQIKKHSVLLVTKTVLFIVLVSFFVLMGEGLTGALAGLLTKDIVLLL 190
                                       44.4468********************************999999998888899*********************** PP

                   Polysacc_synt_3 156 llwlaskwrprlkf.slkslkelfsfglklllsnllnylarnldnlliGkvlssaaLGlYsvakrlaslpvaeitsv 231
                                       + ++++   + +k  +++++ke++sfgl  +  ++ +++++++d  +i  +l+++a+GlYs +++l +++  ++ ++
  gi|298675071|ref|YP_003726821.1| 191 ATTVIIGAEIGIKRpRFTNIKEYLSFGLPNVPGSMSQWVVNSSDRYVISGFLGTSAVGLYSPGYTLGNIVR-MFLAP 266
                                       *****9999888642789************************************************99865.56689 PP

                   Polysacc_synt_3 232 iakVlfPalSrlqddk..kklrelylkvlrlialivlPiavglavvaellvkvl 283
                                       ++ +l  +lS+  d++  +++++ +  +l+    + +P+++gl +++e ++ +l
  gi|298675071|ref|YP_003726821.1| 267 LNFMLPMILSKYYDENnlDEVKKILSYSLKYFLAVGIPAVFGLSFLSEQILLIL 320
                                       999999999*9976542279****************************998876 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.4
                   Polysacc_synt_3  84 vlrvlalvlilsglssvqeallrrelkFkklfkitlvssvvgvivaivlAllglgvwALvigtllssllslvllwla 160
                                       ++ ++al+ ++ g++ + e  +  e k k++ ki +++ v+ + + i++ + + g+   +  tlls ++ l+l+ ++
  gi|298675071|ref|YP_003726821.1| 332 ITPFVALSALVFGVFIIFEKVIYLEKKTKTIGKIWMFAAVLNFGLNILI-IPYIGIIGAAGTTLLSFIVGLCLIAYY 407
                                       6667788888888888888888888889999999999999998888865.556788888999999999999999999 PP

                   Polysacc_synt_3 161 skwrprlkfslkslkel 177
                                       s+  +++ ++++ +++ 
  gi|298675071|ref|YP_003726821.1| 408 SSKYLKFDVNFRFISKS 424
                                       99888888888776654 PP

>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3  11.5     0.065   2.3e+02      30     154 ..      40     162 ..      16     170 .. 0.82
   2 ?    2.0   0.0      0.04   1.4e+02      48      66 ..     188     206 ..     185     218 .. 0.78
   3 !   47.4   4.3   4.3e-16   1.6e-12       6     160 ..     224     378 ..     219     379 .. 0.96
   4 ?   -2.1   0.3      0.75   2.7e+03      81     101 ..     447     467 ..     441     475 .. 0.60

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.065
                              MatE  30 avsialsilsllfvfllglstalttlvgqalGa.knfkrakealrqglilllllsliiallvllfseqilslftqde 105
                                       +++i  +i+  +++++  ++ +l + + ++l + k+ ++++ +++  l +++l ++ ++l+v+l++  i+s++ + +
  gi|298675071|ref|YP_003726821.1|  40 SYGIWVQIIVTVGIVPNIVMLGLPAAMVRYLPSvKKAEDFQDIFYSFLSIVILTGFSASLMVYLLAGSIASVLFDGN 116
                                       6677777777777777777777777777777553778999999999**************************99998 PP

                              MatE 106 evlelakrylrililgipalalqlvlsgilrgagktkvplyislislll 154
                                       +   la ++l+++i+ + ++++++ + ++ + ++k  v l+   + +++
  gi|298675071|ref|YP_003726821.1| 117 T---LAVQILSAIIFLESLNGILFNYFRATQQIKKHSVLLVTKTVLFIV 162
                                       5...9************99999999999999999988877777666633 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.04
                              MatE  48 lstalttlvgqalGaknfk 66 
                                       l  a+t+++g ++G k+++
  gi|298675071|ref|YP_003726821.1| 188 LLLATTVIIGAEIGIKRPR 206
                                       678************9864 PP

  == domain 3  score: 47.4 bits;  conditional E-value: 4.3e-16
                              MatE   6 nllesllslidtllvgrl.gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglillll 81 
                                       ++ +++++  d ++++++ g++a++ +s + ++ +++ +fl  l+  l  + ++++ ++n +++k++l ++l+  l+
  gi|298675071|ref|YP_003726821.1| 224 SMSQWVVNSSDRYVISGFlGTSAVGLYSPGYTLGNIVRMFLAPLNFMLPMILSKYYDENNLDEVKKILSYSLKYFLA 300
                                       6789999********************************************************************** PP

                              MatE  82 lsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislllnipl 158
                                       +++++++ + ++seqil ++ +++e+++++ ++ ++++l+++++++++++ ++    +ktk++  i +++++ln+ l
  gi|298675071|ref|YP_003726821.1| 301 VGIPAVFGLSFLSEQILLIL-STPEIASKGYQITPFVALSALVFGVFIIFEKVIYLEKKTKTIGKIWMFAAVLNFGL 376
                                       *****************999.5666**************************************************99 PP

                              MatE 159 ny 160
                                       n 
  gi|298675071|ref|YP_003726821.1| 377 NI 378
                                       96 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 0.75
                              MatE  81 llsliiallvllfseqilslf 101
                                       l+++ i+++ ++   ++l+ f
  gi|298675071|ref|YP_003726821.1| 447 LVMIGICAVFYFAVLILLKGF 467
                                       555556666555555555555 PP

>> MurJ  Lipid II flippase MurJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8  32.7   7.9e-12   2.8e-08      64     426 ..      83     436 ..      74     460 .. 0.78

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 7.9e-12
                              MurJ  64 ilvlllvtligilaapllirllatgfdeetlelavsllrillpylllvslsavfgavLnarkk...FfapafsPvll 137
                                       +++ l++++++ + a l+++lla  ++   +   +  ++il   ++l sl ++++    a ++     +  ++ ++l
  gi|298675071|ref|YP_003726821.1|  83 FYSFLSIVILTGFSASLMVYLLAGSIASVLFDGNTLAVQILSAIIFLESLNGILFNYFRATQQikkHSVLLVTKTVL 159
                                       6788999*******************666666666667888888888888888887777665500055555555555 PP

                              MurJ 138 NvsvIltllllanklgeeailaLaiGvliGgvlqllvqlpalkkaglllkprfafrdeglkkflklllptllg.vsv 213
                                        ++ + + +l+ + l+     aLa  ++   vl l+ +++  +++g++ +prf     ++k+ l   lp + g +s 
  gi|298675071|ref|YP_003726821.1| 160 FIVLVSFFVLMGEGLT----GALAGLLTKDIVLLLATTVIIGAEIGIK-RPRFT----NIKEYLSFGLPNVPGsMSQ 227
                                       5555555444444444....5677667777777777777777777776.99888....5666777777777551566 PP

                              MurJ 214 sqlnllvdtalAsflaegsvsilayadrilqlPlglfgvsistvlLPr.lSrsakekdedevrdllsqairltllll 289
                                         +n+    +++ fl +++v +++ +  + +  + +f ++ ++ +LP  lS+ ++e++ dev++ ls +++  l++ 
  gi|298675071|ref|YP_003726821.1| 228 WVVNSSDRYVISGFLGTSAVGLYSPGYTLGN-IVRMF-LAPLNFMLPMiLSKYYDENNLDEVKKILSYSLKYFLAVG 302
                                       6678888888888887777777666655554.45666.688899999736*************************** PP

                              MurJ 290 ipvsfgllvlskpivsllferGnFseedveataevLaayalgLipyalvklllrvfYAredtktPvkislislvlni 366
                                       ip++fgl +ls++i+ +l      ++e + +  ++    al+ + + ++ ++ +v Y ++ tkt  ki ++++vln 
  gi|298675071|ref|YP_003726821.1| 303 IPAVFGLSFLSEQILLILS-----TPEIASKGYQITPFVALSALVFGVFIIFEKVIYLEKKTKTIGKIWMFAAVLNF 374
                                       ***************9997.....9999999999999**************************************** PP

                              MurJ 367 llsllllpplgvvglalatslsaliglvllyvllrkrlk..lteargiktflaklvvllala 426
                                       +l++l++p++g +g a  t ls+++gl l+ ++  k lk  + +  + k  +a++++ l+++
  gi|298675071|ref|YP_003726821.1| 375 GLNILIIPYIGIIGAAGTTLLSFIVGLCLIAYYSSKYLKfdVNFRFISKSLFASILMSLIVI 436
                                       ************************************99843233333333334444434333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       920  (0.0513135); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.24s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3370.46
//
Query:       gi|298675072|ref|YP_003726822.1|  [L=161]
Description: membrane-flanked domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-17   62.5   0.1    4.4e-17   62.0   0.1    1.2  1  bPH_2     Bacterial PH domain
  ------ inclusion threshold ------
      0.097   12.8   0.0       0.18   11.9   0.0    1.5  1  bPH_4     Bacterial PH domain


Domain annotation for each model (and alignments):
>> bPH_2  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.0   0.1   4.9e-21   4.4e-17       2      79 ..      75     149 ..      74     150 .. 0.95

  Alignments for each domain:
  == domain 1  score: 62.0 bits;  conditional E-value: 4.9e-21
                             bPH_2   2 rattytitdrrvvvrsGillrktldiplerIqavsleqsllqrrlglgtivietaggsraevelplrsvpdaeelae 78 
                                       r+++y+i+++++ +++Gi+  +++ ip+ r+q+v++e ++++r++gl+t++i+ta  +   + +p++s+++ +el+ 
  gi|298675072|ref|YP_003726822.1|  75 RFWRYEIRENEIDIQHGIFIVRRTLIPMVRVQHVDTEHGPVMRFFGLATLRISTAATN---HYIPALSKEKSAELMG 148
                                       8899******************************************************...5********9999976 PP

                             bPH_2  79 l 79 
                                       +
  gi|298675072|ref|YP_003726822.1| 149 Q 149
                                       6 PP

>> bPH_4  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     2e-05      0.18       2      54 ..      78     132 ..      77     150 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2e-05
                             bPH_4   2 kYeitegvLliksG..firkk.IpiedIkkirktksplsspalsldrleIkygkyd 54 
                                       +Yei e+++ i++G  ++r++ Ip+ +++++   + p+++ +  l  l I +++ +
  gi|298675072|ref|YP_003726822.1|  78 RYEIRENEIDIQHGifIVRRTlIPMVRVQHVDTEHGPVMR-FFGLATLRISTAATN 132
                                       7*************94456669*************99986.455666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1252.31
//
Query:       gi|298675073|ref|YP_003726823.1|  [L=473]
Description: membrane-flanked domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-36  123.0   0.2      5e-13   49.0   0.1    3.2  3  bPH_2     Bacterial PH domain
  ------ inclusion threshold ------
      0.012   16.0   1.1        6.8    7.2   0.1    2.8  3  Rtt106    Histone chaperone Rttp106-like
      0.044   13.5   3.5      0.073   12.8   0.3    2.3  2  DUF1345   Protein of unknown function (DUF1345)
       0.31   11.1   3.4        2.6    8.2   0.1    3.5  4  bPH_4     Bacterial PH domain
        5.1    5.8  11.7      0.064   12.0   0.5    2.6  3  DUF2207   Predicted membrane protein (DUF2207)
        9.2    6.4   8.2         16    5.6   3.2    2.5  2  DHHC      DHHC palmitoyltransferase


Domain annotation for each model (and alignments):
>> bPH_2  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.1   1.7e-16     5e-13       1      80 []      55     135 ..      55     135 .. 0.95
   2 !   48.0   0.0   3.6e-16   1.1e-12       1      73 [.     244     324 ..     244     326 .. 0.95
   3 !   22.6   0.0     3e-08   8.9e-05       7      79 ..     396     469 ..     390     470 .. 0.85

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 1.7e-16
                             bPH_2   1 yrattytitdrrvvvrsGillrktldiplerIqavsleqsllqrrlglgtivietaggsrae.velplrsvpdaeel 76 
                                       ++ +ty+ ++  +++++G+l++k++ i++er+q+v++++++l ++l+++++++ tag++ ++  +l ++s+++ +++
  gi|298675073|ref|YP_003726823.1|  55 WYLYTYQYEEGYLHIKKGLLFKKERSIKRERVQTVNVRTNILLKLLRVASVQVKTAGSGMESeLTLTAVSIDETQKI 131
                                       5668999****************************************************9778************** PP

                             bPH_2  77 aell 80 
                                       +++l
  gi|298675073|ref|YP_003726823.1| 132 KAHL 135
                                       9986 PP

  == domain 2  score: 48.0 bits;  conditional E-value: 3.6e-16
                             bPH_2   1 yrattytitdrrvvvrsGillrktldiplerIqavsleqsllqrrlglgtivietaggsrae........velplrs 69 
                                       y+++t t +d+ + +  Gi+++k++++ l+r+qavs++++ll++++gl++++ e+aggs+++        + l +r 
  gi|298675073|ref|YP_003726823.1| 244 YANFTLTRQDDSLKISWGIIEQKEYNLDLNRVQAVSVQDGLLRQPFGLCSVSAEVAGGSSEKqdyitrlyPLLHFRE 320
                                       899********************************************************988999999999999998 PP

                             bPH_2  70 vpda 73 
                                       +p++
  gi|298675073|ref|YP_003726823.1| 321 LPKF 324
                                       8876 PP

  == domain 3  score: 22.6 bits;  conditional E-value: 3e-08
                             bPH_2   7 titdrrvvvrsGillrktldiplerIqavsleqsllqrrlglgtivietaggsrae.velplrsvpdaeelael 79 
                                       ++ ++++++r   + r  + i  ++Iq+++++++++qrr  l t+++++ ++ + + +++++++ ++ +++ ++
  gi|298675073|ref|YP_003726823.1| 396 ALGNKQLTLRFRNIHRYHVFILKNHIQSMQISTNPFQRRSDLSTVRVSVLSSPAGKdFKIADVDNEENKKIWQW 469
                                       56789999999999999999****************************98888755688888888877777666 PP

>> Rtt106  Histone chaperone Rttp106-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0031       9.1      18      84 ..      63     139 ..      49     143 .. 0.62
   2 ?   -3.3   0.0       4.2   1.2e+04      50      73 ..     243     268 ..     236     274 .. 0.60
   3 ?    7.2   0.1    0.0023       6.8      29      82 ..     413     472 ..     400     473 .] 0.79

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0031
                            Rtt106  18 ekgllfgfkkPllfiplediesvsfeRv.......svtsrtfdlvvel....kkeeveFsmidqeelegidefvksk 83 
                                       e+g l+ +kk llf + ++i++ + + v           r  ++ v++     + e++++ ++ +e ++i++ ++++
  gi|298675073|ref|YP_003726823.1|  63 EEGYLH-IKKGLLFKKERSIKRERVQTVnvrtnilLKLLRVASVQVKTagsgMESELTLTAVSIDETQKIKAHLEKH 138
                                       444455.555555544444444333311112224444455666666666655449*******************999 PP

                            Rtt106  84 g 84 
                                       +
  gi|298675073|ref|YP_003726823.1| 139 K 139
                                       7 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.2
                            Rtt106  50 rtfdlvvelkk..eeveFsmidqeel 73 
                                       r  ++++++++   +++ + i+q+e+
  gi|298675073|ref|YP_003726823.1| 243 RYANFTLTRQDdsLKISWGIIEQKEY 268
                                       45566666655333444456777776 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0023
                            Rtt106  29 llfiplediesvsfeRvsvtsrtfdlvvel.......kkeeveFsmidqeelegidefvks 82 
                                        +fi  ++i+s++++ ++  +r  dl+ ++        ++++++  +d ee ++i +++++
  gi|298675073|ref|YP_003726823.1| 413 HVFILKNHIQSMQIS-TNPFQRRSDLSTVRvsvlsspAGKDFKIADVDNEENKKIWQWFSR 472
                                       577788889999999.777777778776665667655449******************976 PP

>> DUF1345  Protein of unknown function (DUF1345)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.3       0.1   3.1e+02      77     122 ..      36      79 ..       6      83 .. 0.72
   2 ?   12.8   0.3   2.4e-05     0.073      65     110 ..     207     252 ..     171     268 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.1
                           DUF1345  77 llhlalavatvvlsWllvh.tvfalhYahlyyekkeeeggldFpgte 122
                                       l+++a+ ++ ++ls  + +  +++ +Y++ y    + ++gl F++++
  gi|298675073|ref|YP_003726823.1|  36 LVWIAIVFLVLLLSYSAAKwYLYTYQYEEGYL---HIKKGLLFKKER 79 
                                       56677777777777777662479999999999...888888888765 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2.4e-05
                           DUF1345  65 lasakaekpaekllhlalavatvvlsWllvhtvfalhYahlyyekk 110
                                       l+++  e++ + ++ +++ ++ +++sW+l  +vf ++Ya+   +++
  gi|298675073|ref|YP_003726823.1| 207 LEQVVPESGVNMIFLVIILLILLLISWILSTIVFMVRYANFTLTRQ 252
                                       3566666677778899999999*****************9776444 PP

>> bPH_4  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1   0.00089       2.6       2      36 ..      59      96 ..      58     107 .. 0.81
   2 ?   -0.8   0.1      0.54   1.6e+03      29      60 ..     135     167 ..     125     169 .. 0.71
   3 ?   -0.7   0.0      0.54   1.6e+03       6      21 ..     252     268 ..     246     289 .. 0.70
   4 ?    0.2   0.0      0.27   7.9e+02      21      49 ..     416     445 ..     397     462 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00089
                             bPH_4  2 kYeitegvLliksG.firkk..IpiedIkkirktkspl 36
                                      +Y+ +eg L+ik G +++k+  I+ e+++++   +++l
  gi|298675073|ref|YP_003726823.1| 59 TYQYEEGYLHIKKGlLFKKErsIKRERVQTVNVRTNIL 96
                                      7999***********99999566667788887777776 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.54
                             bPH_4  29 irktksplsspalsldrleIkygkydt.ilisP 60 
                                        +k+k   s++ +s + ++ +y+k+ +   isP
  gi|298675073|ref|YP_003726823.1| 135 LEKHKPYKSQKTSSDETITETYEKEVNtYRISP 167
                                       556666666888888888888986655599999 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.54
                             bPH_4   6 tegvLliksGfirkk.I 21 
                                       ++++L+i+ G+i++k +
  gi|298675073|ref|YP_003726823.1| 252 QDDSLKISWGIIEQKeY 268
                                       7999******9988753 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.27
                             bPH_4  21 IpiedIkkirktkspls.spalsldrleIk 49 
                                       I  ++I++++ +++p+  ++ ls+ r+ + 
  gi|298675073|ref|YP_003726823.1| 416 ILKNHIQSMQISTNPFQrRSDLSTVRVSVL 445
                                       566899999999999998888998888775 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   2.2     0.095   2.8e+02     400     448 ..      24      69 ..       4      77 .. 0.38
   2 ?   12.0   0.5   2.1e-05     0.064     316     430 ..      90     239 ..      62     253 .. 0.53
   3 ?   -1.5   0.1      0.27   8.1e+02     205     230 ..     351     376 ..     338     403 .. 0.47

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.095
                           DUF2207 400 lallllvlllvfllilllillliaiivlllfsrllgrrteeGaellakw 448
                                       l   l ++ ++fl+++++++l++++ + +      + +t ++ e + ++
  gi|298675073|ref|YP_003726823.1|  24 LRDDLSGMDFSFLVWIAIVFLVLLLSYSAA---KWYLYTYQYEEGYLHI 69 
                                       222222222444444444444443333333...3333344444444333 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 2.1e-05
                           DUF2207 316 dpyEkalldlLfdkseeg.ks...........lkeikkyakkskk...kakkfkkalkkwksavkk.........ke 368
                                       +   + ll+lL  +s +  +                            + +k+k++l+       k         ++
  gi|298675073|ref|YP_003726823.1|  90 NVRTNILLKLLRVASVQVkTAgsgmeseltltA-----------VsidETQKIKAHLE-------KhkpyksqktSS 148
                                       555555666665333333222323322222220...........12223333333333.......333333345545 PP

                           DUF2207 369 rgyfdkkgkkklkklsalglgliilglilillallllvll.............................lvfllill 416
                                        + ++++ +k+ +++++  + l+++g   + + ll+ +++                             ++fl+i+l
  gi|298675073|ref|YP_003726823.1| 149 DETITETYEKEVNTYRISPWNLFLAGATSGRFMLLFSIIAaafsqiypyipetylrlvleqvvpesgvnMIFLVIIL 225
                                       555555555555555555555555555555444444444355556788**************999987777777777 PP

                           DUF2207 417 lillliaiivlllf 430
                                       lillli++i+  + 
  gi|298675073|ref|YP_003726823.1| 226 LILLLISWILSTIV 239
                                       77777777665554 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.27
                           DUF2207 205 slallillilllillllllllllikl 230
                                       ++++  +++ll+illl  + +  i+l
  gi|298675073|ref|YP_003726823.1| 351 YIIRSSIPVLLVILLLQMVPYGWISL 376
                                       33333333333333333333322222 PP

>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.2     0.041   1.2e+02      53      88 ..      34      69 ..      28     105 .. 0.75
   2 ?    5.6   3.2    0.0053        16      59     126 ..     180     248 ..     169     256 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.041
                              DHHC 53 lfllylllllilalvlllialvklveeekkseflav 88
                                       fl+++++++++ l+ ++ a ++l+++++++ +l +
  gi|298675073|ref|YP_003726823.1| 34 SFLVWIAIVFLVLLLSYSAAKWYLYTYQYEEGYLHI 69
                                      567777777777777777777777777766665544 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0053
                              DHHC  59 llllilalvlllialvklveeekkseflavtllkkllsilllvlsllfllllgllllfhlylil.rnlT 126
                                       ++ll+ ++ +++  ++ +++e +   +l    +++ +++++lv+ ll+lll++ +l + +++++  n+T
  gi|298675073|ref|YP_003726823.1| 180 FMLLFSIIAAAFSQIYPYIPETYLRLVLEQVVPESGVNMIFLVIILLILLLISWILSTIVFMVRyANFT 248
                                       577788888888999999999999999988888888888888888888888888888777777656666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1199  (0.0668749); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 3454.57
//
Query:       gi|298675074|ref|YP_003726824.1|  [L=324]
Description: phosphoesterase RecJ domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-06   27.0   0.2      7e-06   26.2   0.2    1.4  1  DHH       DHH family


Domain annotation for each model (and alignments):
>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.2   3.9e-10     7e-06       8      61 ..       3      89 ..       1     119 [. 0.83

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 3.9e-10
                                      CSSSHHHHHH.HHHHHH.................................CECS--TCGGCGCCHHCCCSEEEEEEE-S CS
                                      xxxxxxxxxx.xxxxxx.................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH  8 knpDtDsigS.aialan.................................llvDhneksqavegeakeeaedviiiDHH 52
                                      ++ DtD+i+S ai++++                                 ++ D+ ++++  ++  +++++++ i DHH
  gi|298675074|ref|YP_003726824.1|  3 HHWDTDGICSaAILFEYlgkefdtyvphignyfftvdeidkiskknydfiIIADMAIPEDNIVDLKNKSGVQIYIFDHH 81
                                      689*******99999998888888888888888777777777777777777*************9************** PP

                                      ---SS---S CS
                                      xxxxxxxxx RF
                               DHH 53 rlgeefetl 61
                                       +  +++++
  gi|298675074|ref|YP_003726824.1| 82 LQD-NIQRN 89
                                      *98.55555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2251.17
//
Query:       gi|298675075|ref|YP_003726825.1|  [L=181]
Description: adenylylsulfate kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-60  203.5   0.0      2e-60  203.3   0.0    1.0  1  APS_kinase       Adenylylsulphate kinase
    3.9e-08   33.1   0.0    4.6e-08   32.8   0.0    1.1  1  KTI12            Chromatin associated protein KTI12
    1.3e-06   28.7   0.0    2.2e-06   27.9   0.0    1.5  1  AAA_33           AAA domain
    1.6e-05   25.4   0.0    2.9e-05   24.6   0.0    1.5  1  AAA_18           AAA domain
    5.6e-05   22.6   0.0    7.3e-05   22.2   0.0    1.2  1  6PF2K            6-phosphofructo-2-kinase
     0.0017   18.3   0.0      0.004   17.1   0.0    1.6  2  Ploopntkinase3   P-loop Nucleotide Kinase3
     0.0021   17.8   0.0     0.0027   17.5   0.0    1.2  1  AAA_30           AAA domain
     0.0021   17.1   0.0      0.004   16.2   0.0    1.4  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0036   17.2   0.2      0.006   16.5   0.2    1.5  1  NTPase_1         NTPase
     0.0038   17.6   0.0     0.0049   17.3   0.0    1.3  1  AAA_16           AAA ATPase domain
     0.0085   16.3   0.1      0.018   15.3   0.0    1.5  2  AAA_28           AAA domain
  ------ inclusion threshold ------
      0.012   16.0   0.0      0.053   13.9   0.0    2.0  2  RNA_helicase     RNA helicase
      0.014   15.5   0.0      0.018   15.1   0.0    1.2  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
      0.018   14.6   0.0      0.034   13.8   0.0    1.6  2  SRP54            SRP54-type protein, GTPase domain
      0.038   13.7   0.0      0.058   13.1   0.0    1.3  1  PRK              Phosphoribulokinase / Uridine kinase family
      0.042   13.8   0.0      0.067   13.2   0.0    1.4  1  AAA_5            AAA domain (dynein-related subfamily)
      0.045   14.2   0.2      0.096   13.1   0.1    1.7  1  AAA_17           AAA domain
      0.063   12.5   0.0      0.075   12.2   0.0    1.2  1  NB-ARC           NB-ARC domain
      0.069   12.8   0.1       0.15   11.8   0.1    1.6  2  Thymidylate_kin  Thymidylate kinase
      0.082   13.2   0.0       0.14   12.5   0.0    1.5  1  AAA_22           AAA domain
      0.094   12.6   0.0       0.51   10.2   0.0    2.1  3  Sigma54_CBD      Sigma-54 factor, core binding domain
       0.12   12.9   0.1       0.16   12.5   0.0    1.3  1  ABC_tran         ABC transporter
       0.15   11.7   0.2       0.31   10.7   0.1    1.6  2  AAA_24           AAA domain
        0.2   11.1   0.0        0.3   10.5   0.0    1.3  1  ParA             NUBPL iron-transfer P-loop NTPase
       0.23   11.3   0.5          3    7.6   0.0    2.1  2  dNK              Deoxynucleoside kinase


Domain annotation for each model (and alignments):
>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.3   0.0   2.8e-63     2e-60       2     154 ..       9     158 ..       8     162 .. 0.98

  Alignments for each domain:
  == domain 1  score: 203.3 bits;  conditional E-value: 2.8e-63
                                       -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--SSHHHHHHHHHHHHHHHHHHHHTT-EEE CS
                        APS_kinase   2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgfseedRkenirrvaevaklladaglivl 78 
                                       g+vvwltGl g+GKsti+ +l k  +ekg  ++++dGd++R+gL+ dLgf++edR+e+ rrva+v+klla++g+ v 
  gi|298675075|ref|YP_003726825.1|   9 GFVVWLTGLPGTGKSTISAELTKIFQEKGFCTETMDGDEIRKGLSADLGFTKEDRQEHARRVAFVSKLLARNGVAVN 85 
                                       89*************************************************************************** PP

                                       EE----SHHHHHHHHHHHHCHTEEEEEEEE--HHHHHHHTTTSHHHHHHTTSSSSHTTTSS-----SS-SEEEETT CS
                        APS_kinase  79 vafisPyreeReaarelleealkfievfvdtplevceerDpkglYkkareGeikeftGidspYeaPenpelvvdtd 154
                                       va+isPyr+ Re+ar+ +e   +f+ev+v+tplevc+erDpkglY+ka++Gei+++tG +++Ye+P npe+v+dt 
  gi|298675075|ref|YP_003726825.1|  86 VALISPYRSFREHARNEIE---NFVEVYVKTPLEVCMERDPKGLYAKAQQGEITDLTGYQDTYEEPLNPEVVIDTC 158
                                       *******************...5**************************************************986 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0   6.4e-11   4.6e-08       4     122 ..      12     128 ..      10     164 .. 0.80

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 6.4e-11
                                       EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH..TTSSS--GGGHHHHHHHHHHHHHHHHTT.SEEE.E-S CS
                             KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvviddeslg.iekdsykdsakekalRsslrsavkrdLskekvVI.vDs 78 
                                       v ltGlP +GKst+++eL k ++e++     +d + ++ + + +   +++ ++  ++  + v++ L ++ v + v  
  gi|298675075|ref|YP_003726825.1|  12 VWLTGLPGTGKSTISAELTKIFQEKGFCTETMDGDEIRkGLSADLGFTKEDRQEHARRVAFVSKLLARNGVAVnVAL 88 
                                       679*****************************9666665888888999999999999999********998661555 PP

                                       ---SHHHHHHHHHHHHHTT-EEEEEEEE--HHHHHHHHHHTT-S CS
                             KTI12  79 lnyikgfRYeLyciakaakttlcvvyvvapldvlvkwneereek 122
                                       +  +++fR      a++   +++ vyv++pl+v+++++ +   +
  gi|298675075|ref|YP_003726825.1|  89 ISPYRSFR----EHARNEIENFVEVYVKTPLEVCMERDPKGLYA 128
                                       56677777....57**********************99444333 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   3.1e-09   2.2e-06       1     115 [.      11     122 ..      11     148 .. 0.70

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 3.1e-09
                            AAA_33   1 lvllvGlpGsGKstlaerl...lkklg..avllssdtlrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrn 72 
                                       +v+l GlpG+GKst + +l    ++ g  +++ + d++r+ l ++   +k+d+++ + r+      ++  +l a+++
  gi|298675075|ref|YP_003726825.1|  11 VVWLTGLPGTGKSTISAELtkiFQEKGfcTETMDGDEIRKGLSADLGFTKEDRQEHARRVA-----FVS-KLLARNG 81 
                                       799***************96667777799999************88888877555444443.....442.3334444 PP

                            AAA_33  73 vildatnls......rrerarflklarrlgvpvrivvvetdeetlkeRl 115
                                       v +   ++s      +++r ++ ++++        v+v+t+ e++ eR 
  gi|298675075|ref|YP_003726825.1|  82 VAVNVALISpyrsfrEHARNEIENFVE--------VYVKTPLEVCMERD 122
                                       444444444110022455555555555........99********9996 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0     4e-08   2.9e-05       1     109 [.      12     121 ..      12     136 .. 0.65

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 4e-08
                            AAA_18   1 IlltGtpGvGKttlakeL....skrlgf..gvnlrdvakenglllevdpealdeskrldedkldklldaleenssal 71 
                                       ++ltG pG+GK+t++ eL    +++ gf   +  +d ++++ + +  + +   e +++   +++ ++++l +n    
  gi|298675075|ref|YP_003726825.1|  12 VWLTGLPGTGKSTISAELtkifQEK-GFctETMDGDEIRKGLSADLGFTK---EDRQEHARRVAFVSKLLARNG--- 81 
                                       78****************4444444.235555555555555544444444...555566666666666666653... PP

                            AAA_18  72 eegknl.vidghlaeleseaakdikk..vvLtaspeelleR 109
                                         + n+ +i+  ++  e +++ + ++  v+++++ e+++eR
  gi|298675075|ref|YP_003726825.1|  82 -VAVNVaLISPYRSFREHARNEIENFveVYVKTPLEVCMER 121
                                       .3444426665555555555555555889999999999998 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0     1e-07   7.3e-05       9      59 ..       5      55 ..       1      82 [. 0.83

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1e-07
                                      T..S-EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHHHHHHSS CS
                             6PF2K  9 lknsklvivlvGLpargKtyiskkltrylkwlgvrtkvFnvgkyrreaska 59
                                      ++n+ +v+ l GLp +gK++is +lt+  +  g+ t + +  ++r+  s  
  gi|298675075|ref|YP_003726825.1|  5 NSNNGFVVWLTGLPGTGKSTISAELTKIFQEKGFCTETMDGDEIRKGLSAD 55
                                      467889999***************************999999999877654 PP

>> Ploopntkinase3  P-loop Nucleotide Kinase3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   5.5e-06     0.004       5      32 ..      11      38 ..       7      57 .. 0.85
   2 ?   -1.3   0.0       2.4   1.7e+03     156     156 ..      98      98 ..      44     150 .. 0.59

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.5e-06
                    Ploopntkinase3  5 liylvGqPGaGkstlmaeltkgfdrskv 32
                                      +++l G PG+Gkst+ aeltk f+ + +
  gi|298675075|ref|YP_003726825.1| 11 VVWLTGLPGTGKSTISAELTKIFQEKGF 38
                                      689*******************998755 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.4
                    Ploopntkinase3 156 a 156
                                       +
  gi|298675075|ref|YP_003726825.1|  98 H 98 
                                       2 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   3.7e-06    0.0027      17      47 ..       8      38 ..       3      91 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.7e-06
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaweaagg 47
                                      +  v+ ltG +GtGK+t+ ++l+++++++g+
  gi|298675075|ref|YP_003726825.1|  8 NGFVVWLTGLPGTGKSTISAELTKIFQEKGF 38
                                      456889*********************9984 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   5.5e-06     0.004      28      57 ..       8      37 ..       2      44 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.5e-06
                                      -SEEEEEEE-TTSSHHHHHHHHHHHHHCTT CS
                              MeaB 28 raqvvGltGvPGaGkstlvealglelrrrG 57
                                      +  vv ltG+PG+Gkst+  +l+  ++++G
  gi|298675075|ref|YP_003726825.1|  8 NGFVVWLTGLPGTGKSTISAELTKIFQEKG 37
                                      567899********************9998 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2   8.4e-06     0.006       2      48 ..      12      59 ..      11     108 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8.4e-06
                                      EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE---.----EEE CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevreg.grrigFk 48
                                      v +TG pG+GK+T+   +++  +++g+  + +   e+r+g     gF+
  gi|298675075|ref|YP_003726825.1| 12 VWLTGLPGTGKSTISAELTKIFQEKGFCTETMDGDEIRKGlSADLGFT 59
                                      789*******************99988777777777775523445555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   6.8e-06    0.0049      26      59 ..      11      44 ..       2     121 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 6.8e-06
                            AAA_16 26 lvllsGesGvGKsslvrellralekdggiflrgk 59
                                      +v l+G +G+GKs++  el + ++++g+ + + +
  gi|298675075|ref|YP_003726825.1| 11 VVWLTGLPGTGKSTISAELTKIFQEKGFCTETMD 44
                                      689*****************99988843333333 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.6e-05     0.018       2      61 ..      12      78 ..      11      84 .. 0.77
   2 ?   -2.9   0.0       9.7     7e+03      83     100 ..     136     153 ..     133     160 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.6e-05
                            AAA_28  2 ivitGgestGKTtlleaLa....ar..gypvv..pEaareileeklakgedalpwvedllafaervle 61
                                      + +tG ++tGK+t++++L+    ++   ++++   E+   +  ++++++ed  ++ ++++af +++l+
  gi|298675075|ref|YP_003726825.1| 12 VWLTGLPGTGKSTISAELTkifqEKgfCTETMdgDEIRKGLSADLGFTKEDRQEH-ARRVAFVSKLLA 78
                                      679****************665434443556677888888888888888887776.588888887775 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 9.7
                            AAA_28  83 ldtlaYarayggeaeael 100
                                        d + Y ++y+++ ++e+
  gi|298675075|ref|YP_003726825.1| 136 TDLTGYQDTYEEPLNPEV 153
                                       677889999999866664 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   7.3e-05     0.053       1      25 [.      12      36 ..      12      70 .. 0.84
   2 ?   -0.8   0.0       2.9   2.1e+03      66      88 ..      99     121 ..      91     131 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.3e-05
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkk 25
                                      +wl+G +g+GKSt++ eL+k +++k
  gi|298675075|ref|YP_003726825.1| 12 VWLTGLPGTGKSTISAELTKIFQEK 36
                                      7****************99988765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.9
                      RNA_helicase  66 npsdlaelirlvsstpyplnmas 88 
                                         +++++++++   tp++++m +
  gi|298675075|ref|YP_003726825.1|  99 ARNEIENFVEVYVKTPLEVCMER 121
                                       45689999999999999999987 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   2.5e-05     0.018       9      95 ..      19     105 ..      13     137 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.5e-05
                                       TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.HTTEB-HHHHCCHCCCHHHHHHCHCHHHH..EEEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlai.leglendiepdlkrllellealgkkkalllkiagvvlnrv 84 
                                       G+GK+t++a L ++++++g+ +   D D  ++ l+  l  +++d+++ + r + ++++l  ++ +++++a + + r 
  gi|298675075|ref|YP_003726825.1|  19 GTGKSTISAELTKIFQEKGFCTETMDGDEIRKGLSAdLGFTKEDRQEHARR-VAFVSKLLARNGVAVNVALISPYRS 94 
                                       9*******************9999999988888887444455555555555.6666666666555566666666665 PP

                                       SS...-TTCHH CS
                                       xxxxxxxxxxx RF
                              CbiA  85 dgeneetllke 95 
                                         e++ +++++
  gi|298675075|ref|YP_003726825.1|  95 FREHARNEIEN 105
                                       55544444444 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.8e-05     0.034       3      43 ..      11      51 ..       9      88 .. 0.89
   2 ?   -3.1   0.0       7.1   5.1e+03      32      46 ..     153     167 ..     143     175 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.8e-05
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTT CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaa 43
                                      v+ l Gl G+GK t  a L ++++++g  +  +  D  R +
  gi|298675075|ref|YP_003726825.1| 11 VVWLTGLPGTGKSTISAELTKIFQEKGFCTETMDGDEIRKG 51
                                      7889**********************999998888888877 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.1
                                       EEEEEESTSSTTHHH CS
                             SRP54  32 vllvaaDtfRaaAve 46 
                                       v++ ++Dt   +A+e
  gi|298675075|ref|YP_003726825.1| 153 VVIDTCDTTPEGAAE 167
                                       556666666555555 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   8.2e-05     0.058       3      60 ..      13      69 ..      11      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.2e-05
                               PRK  3 gvagsSGaGkttvarklekifgrekvkaaeiegdsflrldraekdleleerkrakeke 60
                                       ++g  G Gk+t++++l+kif++++  + +++gd++ +  +a+   + e+r++   ++
  gi|298675075|ref|YP_003726825.1| 13 WLTGLPGTGKSTISAELTKIFQEKGFCTETMDGDEIRKGLSADLGFTKEDRQEHA-RR 69
                                      579999*****************99999999999999888888888888777654.44 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   9.3e-05     0.067       2      28 ..      12      38 ..      11      72 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.3e-05
                                      EEEE--SSSSHHHHHHHGGGGBS--EE CS
                             AAA_5  2 vlLvGppGtgKselaerlaaalnreve 28
                                      v L G pGtgKs+++ +l + ++ + +
  gi|298675075|ref|YP_003726825.1| 12 VWLTGLPGTGKSTISAELTKIFQEKGF 38
                                      5699****************9976654 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   0.00013     0.096       1      37 [.      15      55 ..      15     125 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00013
                                      EE-TTSSHHHHHHHHHHHH...TEEEEEH.HHHHHHHHHTT CS
                            AAA_17  1 lGgPGsGKgtqceklveky...gfthlsa.Gdllreeakrg 37
                                      +G+PG GK+t++++l + +   gf   ++ Gd +r+  + +
  gi|298675075|ref|YP_003726825.1| 15 TGLPGTGKSTISAELTKIFqekGFCTETMdGDEIRKGLSAD 55
                                      7************9986552225555444688888765544 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0    0.0001     0.075      19      47 ..       8      36 ..       1      70 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0001
                                      CSEEEEEEESTTSSHHHHHHHHCCSHCCC CS
                            NB-ARC 19 qslvvalvGmgGvGKttlakqilnksdev 47
                                      + +vv l G +G GK+t++++  + ++e 
  gi|298675075|ref|YP_003726825.1|  8 NGFVVWLTGLPGTGKSTISAELTKIFQEK 36
                                      4499****************998887765 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1    0.0002      0.15       3      47 ..      16      57 ..      14      85 .. 0.75
   2 ?   -1.9   0.0       3.1   2.2e+03     123     134 ..     110     121 ..      89     156 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0002
                                      ESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHH CS
                   Thymidylate_kin  3 GlDGaGKttqaellkerlkeegikvvltrepggteiGekirelll 47
                                      Gl G+GK+t+++ l + ++e+g   + t   +g ei++ + + l 
  gi|298675075|ref|YP_003726825.1| 16 GLPGTGKSTISAELTKIFQEKG---FCTETMDGDEIRKGLSADLG 57
                                      999*******************...45666666677776666666 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.1
                                       EEESSHHHHHTS CS
                   Thymidylate_kin 123 lldvdpevalkR 134
                                       +++++ ev+++R
  gi|298675075|ref|YP_003726825.1| 110 YVKTPLEVCMER 121
                                       333333444443 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00019      0.14       9      36 ..      13      40 ..       6      90 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00019
                            AAA_22  9 vvtGesGtGKTtllrrlleqldeeakae 36
                                       +tG +GtGK+t  ++l++ ++e  + +
  gi|298675075|ref|YP_003726825.1| 13 WLTGLPGTGKSTISAELTKIFQEKGFCT 40
                                      589***************9998765544 PP

>> Sigma54_CBD  Sigma-54 factor, core binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.7   1.2e+03      32      58 ..      25      60 ..      19      84 .. 0.60
   2 ?   -2.3   0.0       4.6   3.3e+03      61      80 ..     110     129 ..      94     132 .. 0.71
   3 ?   10.2   0.0   0.00072      0.51       5      47 ..     138     180 ..     134     181 .] 0.90

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.7
                       Sigma54_CBD 32 iaeylienLdedGYleesle..eiaeel.......e 58
                                      i   l +   e+G+ +e+++  ei + l       +
  gi|298675075|ref|YP_003726825.1| 25 ISAELTKIFQEKGFCTETMDgdEIRKGLsadlgftK 60
                                      566677777888888866541144444444445542 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.6
                       Sigma54_CBD  61 eveavlkliqsldPaGvgAr 80 
                                        v++ l++ ++ dP G  A+
  gi|298675075|ref|YP_003726825.1| 110 YVKTPLEVCMERDPKGLYAK 129
                                       56677888889999998886 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00072
                       Sigma54_CBD   5 laaaeeslqehLleQlallelseeereiaeylienLdedGYle 47 
                                       l+  +++ +e L+ ++ + +++++ + +ae+++ +Lde GY++
  gi|298675075|ref|YP_003726825.1| 138 LTGYQDTYEEPLNPEVVIDTCDTTPEGAAETIVSKLDELGYFS 180
                                       56678899999******************************96 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00022      0.16       9      52 ..       7      61 ..       3     132 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00022
                                      ETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE..EETTCEGGG..........B CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxx..........x RF
                          ABC_tran  9 kegekvaivGenGaGKStLlkllagllkpteGei..lldgkdlke..........q 52
                                      ++g +v ++G  G+GKSt+ + l++  +  +G    ++dg+++++          +
  gi|298675075|ref|YP_003726825.1|  7 NNGFVVWLTGLPGTGKSTISAELTKIFQE-KGFCteTMDGDEIRKglsadlgftkE 61
                                      5788999****************999984.55442244555555555544554443 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00043      0.31       4      25 ..      11      31 ..       8      60 .. 0.83
   2 ?   -2.0   0.0       3.6   2.5e+03      69      75 ..     153     159 ..      99     174 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00043
                            AAA_24  4 kiliyGpsgiGKTtlakelgpk 25
                                       ++++G +g+GK+t+ +el  k
  gi|298675075|ref|YP_003726825.1| 11 VVWLTGLPGTGKSTISAEL-TK 31
                                      79***************99.33 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.6
                            AAA_24  69 lviDtid 75 
                                       +viDt d
  gi|298675075|ref|YP_003726825.1| 153 VVIDTCD 159
                                       5566655 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00042       0.3      10      57 ..      15      62 ..       8      88 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00042
                              ParA 10 SgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeek 57
                                       g  G GKSt++++l+  +++kg+ +  +D D +   +   lg ++e+
  gi|298675075|ref|YP_003726825.1| 15 TGLPGTGKSTISAELTKIFQEKGFCTETMDGDEIRKGLSADLGFTKED 62
                                      56679*************************997666666556655544 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.22   1.6e+02       4      29 ..      15      41 ..      12      56 .. 0.78
   2 ?    7.6   0.0    0.0042         3      85     139 ..      66     121 ..      60     153 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.22
                                      EESTTSSHHHHHHHHHCCST.CEEEE- CS
                               dNK  4 eGnIgaGKstlvklLskklg.vkvfeE 29
                                       G  g GKst+   L+k ++   +++E
  gi|298675075|ref|YP_003726825.1| 15 TGLPGTGKSTISAELTKIFQeKGFCTE 41
                                      57789******9999998874444455 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0042
                                       HHHHHTHHH.HHHHTTSS-HHH.HHHHHHHHHHHHHHCCH-SEEEEEE--HHHHHHH CS
                               dNK  85 ysdryiFak.alaekgtlseee.lkiykelldnlleelakpdlliYLkasletcler 139
                                       +  r  F++ +la++g++ +++ +  y ++++ + +e++   + +Y+k++le+c+er
  gi|298675075|ref|YP_003726825.1|  66 HARRVAFVSkLLARNGVAVNVAlISPYRSFREHARNEIE-NFVEVYVKTPLEVCMER 121
                                       555555664145566666555525779999999999999.7788***********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1321.14
//
Query:       gi|298675076|ref|YP_003726826.1|  [L=464]
Description: anion transporter [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-75  255.4  36.6    1.5e-75  255.1  36.6    1.0  1  Na_sulph_symp  Sodium:sulfate symporter transmembrane region
    5.9e-38  130.8  47.9    1.5e-22   80.2  19.2    2.2  2  CitMHS         Citrate transporter
  ------ inclusion threshold ------
      0.028   13.2  41.0       0.26   10.1  21.7    2.9  2  DctM           Tripartite ATP-independent periplasmic transpo


Domain annotation for each model (and alignments):
>> Na_sulph_symp  Sodium:sulfate symporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  255.1  36.6   2.5e-79   1.5e-75       7     470 ..      12     460 ..       5     462 .. 0.94

  Alignments for each domain:
  == domain 1  score: 255.1 bits;  conditional E-value: 2.5e-79
                     Na_sulph_symp   7 lllllvvlliilllPapdgleskawrllaifiaaivglileplplavialialsllavligvlaakalsevlsgfss 83 
                                        +  l++l+ i+l P p+gl+++++  l+ifi+ai+ + +++lpl v+ l+ + ll++l  + +    +++ s f +
  gi|298675076|ref|YP_003726826.1|  12 IIFSLIILAGIFLAPSPEGLTVEGKNALGIFIVAIILWTTNALPLSVTGLFVIVLLPLLDVMSS----KDAFSLFGN 84 
                                       455689999************************************************9999999....9******** PP

                     Na_sulph_symp  84 dttlLvfaalliaaavektgLgkRiAlvlvkivGkrtliLgyalvladlllapatpsntAraggivfpvikslssaf 160
                                        +++ +++a+++aa+++ktgL kR+Al +++ +G +++ L  +++++  l++ ++p  +   ++i+fpv++ ++  +
  gi|298675076|ref|YP_003726826.1|  85 RAVFFILGAFILAAGMMKTGLSKRLALKMLSRFGGTPRNLLAGIMISSALMSFIMPEHA--VAAIMFPVVSTIADNL 159
                                       ********************************************************875..578************* PP

                     Na_sulph_symp 161 gsepekqserkigaylmltvvqsasitsiaflTamApNllllglinsilgveitwasWflaaiptgvillllvplll 237
                                       + ep ++   + g  l l+ + +a i+++ +l + A N+l+++++++  g+ei++ +W +aaip+  ++l++   +l
  gi|298675076|ref|YP_003726826.1| 160 DLEPLDS---EYGTLLFLSLAWGAIIGGVGTLLGGARNPLAIAMLKENTGIEISFFEWCVAAIPIVFVMLVIGFVVL 233
                                       ****995...47***************************************************************** PP

                     Na_sulph_symp 238 yvlyppeikkkeeakavaktelkelGpltarekallilfvlllllWifgeslnidattvaivvlvillllrvldWkD 314
                                         +++  ++ ++ ak+v ++el+ +G + + ek+  +++vl +l Wif ++  +  +++ai++ v +++l+v++W+D
  gi|298675076|ref|YP_003726826.1| 234 NYFFKVDVDDVKPAKRVLEKELNRIGSMDIYEKKSGAILVLTILSWIFLGHD-FGLAAIAILGAVAIFILNVVNWED 309
                                       ************************************************9987.999********************9 PP

                     Na_sulph_symp 315 ivkqktaWntllllgglialakllersgliewlgnklttslsglspavaiiiilslfvlvhylfaSatAttaallpi 391
                                       i  +   W+++l++gg i++ + l+++g  +wl+n+   s   l p +++   +sl+    ++  S++A +a+l+pi
  gi|298675076|ref|YP_003726826.1| 310 IE-SDVNWGVILMYGGAISIGSALSQTGAAQWLANQALDSFV-LTPILLM-LGISLVAKFLTEGISNSAAVAILIPI 383
                                       85.6789****************************8776666.4444433.34566666778899************ PP

                     Na_sulph_symp 392 llavaqaipgappllvalllalatslagfllpyatgpnpivfgagylkvkdywrlGfilsiigllillllgalwwkl 468
                                         +v+ ++ g++p+ ++ l+a+ ++la f+ p++t+pn+i++++gy ++kd    G+il++ + + +++++ ++w +
  gi|298675076|ref|YP_003726826.1| 384 GFSVGDVV-GINPVAMVYLIAIPSGLA-FMFPMGTPPNAIAYSSGYYEIKDVLVPGLILNLTSWIAFIIMALVYWPI 458
                                       ********.******************.***********************************************99 PP

                     Na_sulph_symp 469 Lv 470
                                       ++
  gi|298675076|ref|YP_003726826.1| 459 IG 460
                                       86 PP

>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.2  19.2   2.5e-26   1.5e-22       1     166 [.      46     233 ..      44     272 .. 0.80
   2 !   56.2  20.9   5.1e-19   3.1e-15       2     162 ..     273     454 ..     271     462 .. 0.83

  Alignments for each domain:
  == domain 1  score: 80.2 bits;  conditional E-value: 2.5e-26
                                       xxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS   1 lvllileklrldvvallvlvll....vltieealsgiaspiillllgamiigaaleetGlfdrlaakllrlaggkrd 73 
                                       ++l+ + +l+l+v+ l+v+vll    v++ ++a+s +++ +++++lga+i++a++ +tGl +rla k+l+++gg ++
  gi|298675076|ref|YP_003726826.1|  46 IILWTTNALPLSVTGLFVIVLLplldVMSSKDAFSLFGNRAVFFILGAFILAAGMMKTGLSKRLALKMLSRFGGTPR 122
                                       57888888***************999999999********************************************* PP

                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                            CitMHS  74 .llvllvlltallsafvsndgvvlimipivlslakrlkklppl.......lliplalaaniggaltpiGtpttraa. 141
                                        ll+ +++ +al+s ++   +v++im p+v ++a    +l pl       l++ la +a igg+ t+ G+   r + 
  gi|298675076|ref|YP_003726826.1| 123 nLLAGIMISSALMSFIMPEHAVAAIMFPVVSTIADN-LDLEPLdseygtlLFLSLAWGAIIGGVGTLLGGA--RNPl 196
                                       **********************************96.8888888******999******************..3332 PP

                                       .........xxxxxxxxxxxx...........xxxxxxxx..xxxxx RF
                            CitMHS 142 .........arpglslpnlll...........lalllvgl..lplvl 166
                                                           +           +++++v+l   ++vl
  gi|298675076|ref|YP_003726826.1| 197 aiamlkentG----------IeisffewcvaaIPIVFVMLviGFVVL 233
                                       2444444430..........144444443333333333221122222 PP

  == domain 2  score: 56.2 bits;  conditional E-value: 5.1e-19
                                       xxxxxxx......xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS   2 vllilek......lrldvvallvlvll....vltieealsgiaspiillllgamiigaaleetGlfdrlaakllrla 68 
                                       vl il++       +l+++a+l++v+     v+  e++ s + +++il+++ga+ ig+al++tG++++la+  l  +
  gi|298675076|ref|YP_003726826.1| 273 VLTILSWiflghdFGLAAIAILGAVAIfilnVVNWEDIESDVNWGVILMYGGAISIGSALSQTGAAQWLANQALDSF 349
                                       556666666667789999********9***********************************************999 PP

                                       xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS  69 ggkrd.llvllvlltallsafvsndgvvlimipivlslakrlkklppllliplalaaniggaltpiGtpttraaarp 144
                                          +  l++ ++l++ +l+  +sn ++v+i+ipi +s++  ++ +p++++ ++a+++++   + p+Gtp        
  gi|298675076|ref|YP_003726826.1| 350 VLTPIlLMLGISLVAKFLTEGISNSAAVAILIPIGFSVGDVVGINPVAMVYLIAIPSGLAF-MFPMGTP-------- 417
                                       9999999999*******************************99999999999*******99.99*****........ PP

                                       xxxxxxxxx.......................xxxxxxxxx RF
                            CitMHS 145 glslpnlll.......................lalllvgll 162
                                           pn ++                       +a ++ +l+
  gi|298675076|ref|YP_003726826.1| 418 ----PNAIAyssgyyeikdvlvpglilnltswIAFIIMALV 454
                                       ....6666666666666666663333343333333333333 PP

>> DctM  Tripartite ATP-independent periplasmic transporter, DctM component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7  19.2    0.0038        23     276     406 ..      85     228 ..       7     239 .. 0.72
   2 ?   10.1  21.7   4.4e-05      0.26     163     408 ..     207     454 ..     195     459 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0038
                              DctM 276 aavlfilaaagifaglltltgvplkls.elllslsggkllfLilvnllvlvlGmfldttaaiiilvpilaPaaaklg 351
                                        av+fil a  i+a  ++ tg++ +l+ ++l+  +g++  +L+ +++ + ++ ++++  a++ i+ p++  +a++l+
  gi|298675076|ref|YP_003726826.1|  85 RAVFFILGAF-ILAAGMMKTGLSKRLAlKMLSRFGGTPRNLLAGIMISSALMSFIMPEHAVAAIMFPVVSTIADNLD 160
                                       5688888665.666666889999999934555566666889999********************************* PP

                              DctM 352 idp..ihfgvvivlnlsiglitPPvGlalfvass...ia........kvsveeivkalvPflvvlvva 406
                                       ++p    +g +++l l+ g i   vG+ l  a++   ia        ++s+ e  +a++P ++v++v+
  gi|298675076|ref|YP_003726826.1| 161 LEPldSEYGTLLFLSLAWGAIIGGVGTLLGGARNplaIAmlkentgiEISFFEWCVAAIPIVFVMLVI 228
                                       ***44357788888888888887777777776642224477777777889999999999987776553 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 4.4e-05
                              DctM 163 lgvsigdlfaaaiipglllavglllavaiaak..kenlrsktkaelkrlgqalkeai....palllpliiligillg 233
                                        ++s ++  +aai   ++++v+ +++  ++ k   +++++ ++ ++k+l ++   +i       +l+l il  i+lg
  gi|298675076|ref|YP_003726826.1| 207 IEISFFEWCVAAIPIVFVMLVIGFVVLNYFFKvdVDDVKPAKRVLEKELNRIGSMDIyekkSGAILVLTILSWIFLG 283
                                       56788899999997777766655555444444358889999998888888888887755556788888888888888 PP

                              DctM 234 iftpteagavavvyalviallvyrrltleevaaallstakttaavlfilaaagifaglltltgvplklse.lllsls 309
                                              +a+a+++a +i +l    +++e++ +       +   v+++  +a  +  +l+ tg++++l++ +l s  
  gi|298675076|ref|YP_003726826.1| 284 HDFGL--AAIAILGAVAIFIL--NVVNWEDIES------DVNWGVILMYGGAISIGSALSQTGAAQWLANqALDSFV 350
                                       84444..44555555444444..4458888765......45566788889999999999*********973677899 PP

                              DctM 310 ggkllfLilvnllvlvlGmfldttaaiiilvpilaPaaaklgidpihfgvvivlnlsigli....tPPvGlalfva. 381
                                        +++l+++ + l+  +l  +++ +aa+ il pi + + + +gi+p+++  +i +   ++++    tPP ++a   + 
  gi|298675076|ref|YP_003726826.1| 351 LTPILLMLGISLVAKFLTEGISNSAAVAILIPIGFSVGDVVGINPVAMVYLIAIPSGLAFMfpmgTPPNAIAYSSGy 427
                                       999988888888888*********************************99999888777774444777777654331 PP

                              DctM 382 ssiakvsveeivkalvPflvvlvvalv 408
                                        +i  v v +++  l  ++  +++alv
  gi|298675076|ref|YP_003726826.1| 428 YEIKDVLVPGLILNLTSWIAFIIMALV 454
                                       355567777777777777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 3020.05
//
Query:       gi|298675077|ref|YP_003726827.1|  [L=145]
Description: hypothetical protein Metev_1149 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.8e-06   26.7   2.9    1.4e-05   25.6   2.9    1.6  1  Usp             Universal stress protein family
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.027   14.5   0.0    1.5  1  DNA_photolyase  DNA photolyase
      0.018   15.2   0.2          3    8.0   0.0    2.2  2  LPD7            Large polyvalent protein-associated domain 7
      0.023   14.1   0.1      0.048   13.1   0.0    1.4  2  AP_endonuc_2    Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   2.9   3.2e-09   1.4e-05       4     113 ..       6     128 ..       3     145 .] 0.92

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 3.2e-09
                                       EEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH.......... CS
                               Usp   4 rIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada.......... 70 
                                       +I+Va+  ++  k+ +++Al++a++++a+li+l v d    ++v+   + ++   +e  ++  +  +          
  gi|298675077|ref|YP_003726827.1|   6 TIMVAFSATSIHKEPAKRALDMAQEKNAKLIVLSVRDKNITEKVAKVTQNHGFLGKEIVKDLMKDIKkdrdeliser 82 
                                       8*********************************************999999888888888777777889******* PP

                                       ...HHHHHHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCC CS
                               Usp  71 ...akaaaeaggvkvevvveegdpaeeilevaeeedadliVvGsrg 113
                                            ++ae++g++ ++ ++ gd  e  +eva ++++d ++v   g
  gi|298675077|ref|YP_003726827.1|  83 lgrIGEEAEKRGIDYKTLQLKGDFVENVVEVAGKHGVDTVLVEDMG 128
                                       ****************************************997666 PP

>> DNA_photolyase  DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   6.1e-06     0.027      15      95 ..      23     125 ..      21     139 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.1e-06
                                       HHHHHHHCTTSEEEEEEEE-HH...HHTCG....................S-CHHHHHHHHHHHHHHHHHHHHTT-- CS
                    DNA_photolyase  15 pALaaAaasgepvipvfvldpe...kahkl....................rvgaarvdfllesLadLdeeLrelgir 68 
                                       +AL  A+++++++i++ v d++   k                         +++ r +++ e+L ++ ee +++gi+
  gi|298675077|ref|YP_003726827.1|  23 RALDMAQEKNAKLIVLSVRDKNiteK---VakvtqnhgflgkeivkdlmkDIKKDRDELISERLGRIGEEAEKRGID 96 
                                       69999999999999999999997652...23346677889999999988888888888*****************76 PP

                                       ..EEEEESSHHHHHHHHHHHCTECEEEEE CS
                    DNA_photolyase  69 ..Lvvrrgdpadvlpelakelgasavvan 95 
                                          + ++gd ++ ++e+a ++g+++v+++
  gi|298675077|ref|YP_003726827.1|  97 ykTLQLKGDFVENVVEVAGKHGVDTVLVE 125
                                       115666788*****************987 PP

>> LPD7  Large polyvalent protein-associated domain 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1    0.0045        20      31      75 ..       9      58 ..       2      78 .. 0.73
   2 ?    8.0   0.0   0.00067         3      49      78 ..      92     122 ..      87     136 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0045
                              LPD7 31 v...tsddddeavaaalelAqak.wgsltvs.GseeFkreaweaaaergl 75
                                      v   +++  +e ++ al++Aq+k  + + +s  ++   ++++++ + +g+
  gi|298675077|ref|YP_003726827.1|  9 VafsATSIHKEPAKRALDMAQEKnAKLIVLSvRDKNITEKVAKVTQNHGF 58
                                      555544445677899********668888886777888888888888887 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00067
                              LPD7  49 ak...wgsltvsGseeFkreaweaaaerglevt 78 
                                       ++   +++l+++G+  F++ ++e+a ++g+++ 
  gi|298675077|ref|YP_003726827.1|  92 KRgidYKTLQLKGD--FVENVVEVAGKHGVDTV 122
                                       55544689999999..*************9987 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.1e-05     0.048      72     126 ..      21      96 ..      10      98 .. 0.90
   2 ?   -2.7   0.0      0.72   3.2e+03     116     127 ..     110     122 ..     104     133 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.1e-05
                                       HHHHHHHHHHHTBSEEEEEBCC.....................GBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSE CS
                      AP_endonuc_2  72 lkraielaaaLGapllvlhpGt.....................agagpkgseeeawerlaeslneladyaekegvk 126
                                       +kra+++a++ +a+l+vl + +                       ++ k+ ++++ e++ e+l +++++aek+g+ 
  gi|298675077|ref|YP_003726827.1|  21 AKRALDMAQEKNAKLIVLSVRDknitekvakvtqnhgflgkeiVKDLMKDIKKDRDELISERLGRIGEEAEKRGID 96 
                                       79*****************888*************888888886678888888*********************85 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.72
                                       HHHHHHHHTSE.E CS
                      AP_endonuc_2 116 ladyaekegvk.l 127
                                       ++++a k+gv  +
  gi|298675077|ref|YP_003726827.1| 110 VVEVAGKHGVDtV 122
                                       4555555555423 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       944  (0.0526521); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1071.92
//
Query:       gi|298675078|ref|YP_003726828.1|  [L=245]
Description: nucleotidyl transferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.8e-44  150.1   0.0    8.7e-44  150.0   0.0    1.0  1  NTP_transferase  Nucleotidyl transferase
    1.8e-13   51.1   0.0    2.2e-13   50.9   0.0    1.1  1  NTP_transf_3     MobA-like NTP transferase domain
    3.5e-09   36.7   0.0    1.7e-08   34.5   0.0    1.9  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
     0.0077   16.0   0.1      0.013   15.3   0.1    1.4  1  Glycos_transf_2  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.0   0.0   1.9e-47   8.7e-44       1     246 [.       2     238 ..       2     240 .. 0.93

  Alignments for each domain:
  == domain 1  score: 150.0 bits;  conditional E-value: 1.9e-47
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEE CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevli 77 
                                       k++I a GsGtRL P t++++k l+pv++k  +i++ ++  +n+gi++ i ++ + +++ + ++l++g++fgv++++
  gi|298675078|ref|YP_003726828.1|   2 KGLIPAAGSGTRLGPFTHAMPKELLPVGDK-AVIEHAVESFVNAGIDD-ITIVVSPKKHGLSDYLGSGKRFGVNITY 76 
                                       57899*************************.*****************.7777778999****************** PP

                                       EEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEEC CS
                   NTP_transferase  78 alepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGviead 154
                                       ++++ + g+A+Av  ++ +++ +     ++vLg++ +  d++ + +k++ e+++  ++t+g+++v++ t+ G+i+++
  gi|298675078|ref|YP_003726828.1|  77 VVQDDRLGLANAVEAGEHVINGSPF---AVVLGDNFFSPDTILQDLKQFHENNK-ADATVGVMEVSDVTRHGIIKTN 149
                                       *********************9997...9***********77777777777666.59*******************9 PP

                                       TTSBEEEEECS-SSHSH.CSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EE CS
                   NTP_transferase 155 eegrverfvEKPkeaka.selassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWs 230
                                       ++ ++ +++EKP+++ka s+l  +G Yvf++++++ + +d ++  + e ++td ++ ++e+gk+ ++   ++     
  gi|298675078|ref|YP_003726828.1| 150 GN-NIVDLIEKPEADKApSKLGIAGMYVFEPQIFDAI-RDTKPGYKDEYQLTDSIKILVEQGKNVVYREIDGI--HI 222
                                       85.999***********7788889*************.88***************************999996..5* PP

                                       EXSSHHHHHHHHHHHH CS
                   NTP_transferase 231 DvGtldslleanekla 246
                                       DvGt+++l++an+ ++
  gi|298675078|ref|YP_003726828.1| 223 DVGTPEDLMKANDYYL 238
                                       ***********99876 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   0.0   4.8e-17   2.2e-13       2     122 ..       4     134 ..       3     175 .. 0.82

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 4.8e-17
                                       EEEEESS-TTTT..T...THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHH...TTCT..S-EEE-T CS
                      NTP_transf_3   2 viLAGGrSsRmg..g...dKallplggkpllervldalraagvdevvvvggd..eevlaal...arlg..vrvvede 66 
                                       +i A+G ++R+g  +   +K llp+g+k ++e++++++  ag+d++++v+ +  + + ++l   +r+g  +++v+++
  gi|298675078|ref|YP_003726828.1|   4 LIPAAGSGTRLGpfThamPKELLPVGDKAVIEHAVESFVNAGIDDITIVVSPkkHGLSDYLgsgKRFGvnITYVVQD 80 
                                       677*********651578*******************************9884333444443334555335556665 PP

                                       TSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEE CS
                      NTP_transf_3  67 dpgkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvpt 122
                                           g + ++ a+ + + + ++++v+++D  + +  +++ l + +++++ad++v +
  gi|298675078|ref|YP_003726828.1|  81 -DRLGLANAVEAGEHVI-NGSPFAVVLGDNFFSPDTILQDLKQFHENNKADATVGV 134
                                       .379**********999.8***********99888888888888888888888765 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.0   3.9e-12   1.7e-08       4     218 ..       4     236 ..       1     240 [. 0.68

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 3.9e-12
                                       EEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGG....CCEEEEE- CS
                              IspD   4 vipAAGsGkRmk...aglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllld....ksiqlvaG 73 
                                       +ipAAGsG+R++     +pK +l + +++++eh+v+++ +   +d i +vvs+++ +    l +      +i+ v+ 
  gi|298675078|ref|YP_003726828.1|   4 LIPAAGSGTRLGpftHAMPKELLPVGDKAVIEHAVESFVN-AGIDDITIVVSPKKHGLSDYLGSGkrfgVNITYVVQ 79 
                                       8*********96443789*********************9.88************8888888777777766777776 PP

                                       -SSH..HHHHHHHHHTTSSTTSEEEE--T.T-TT--HHHHHHHHHHHHTTCSEEEEEEE-SSEEEEE..ETTT.BEE CS
                              IspD  74 GdeR..aesVlnglkalegeakfVLvHDa.ARpllkaadiaellaaaeqstqgailalpvkDtikrv..eadg.lva 144
                                        d    a++V +g ++++g+   V++ D    p +  +d+++  + +  +  +++ ++ v+D  + +  +++g  ++
  gi|298675078|ref|YP_003726828.1|  80 DDRLglANAVEAGEHVINGSPFAVVLGDNfFSPDTILQDLKQFHENN--KADATVGVMEVSDVTRHGiiKTNGnNIV 154
                                       554244899***********966666664134444444444443333..3578899999999755321122222444 PP

                                       EEETG.......T..TE..EEEEEEEEEEHHHHHHHHHHHHHCT---SSHHHHHHHTT--EEEEE--TTG----SHH CS
                              IspD 145 etedR.......e..gL..waaqtPqgFrvdlllaahakgeqegaeitDdaslvekiGlsvkvVeGeednlKittpe 210
                                       + +++       +  g+    +  Pq F+   ++++     ++ ++ tD ++++ + G +v   e +   + + tpe
  gi|298675078|ref|YP_003726828.1| 155 DLIEKpeadkapSklGIagMYVFEPQIFD--AIRDTKPG-YKDEYQLTDSIKILVEQGKNVVYREIDGIHIDVGTPE 228
                                       44433111111111122222355677764..45555443.4555999999999999999999999999999999999 PP

                                       HHHHHHHH CS
                              IspD 211 DlalAeai 218
                                       Dl+ A+ +
  gi|298675078|ref|YP_003726828.1| 229 DLMKANDY 236
                                       99999754 PP

>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   2.9e-06     0.013      15     133 ..      36     175 ..      30     216 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.9e-06
                                       HHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SSEEEEEESSEE CS
                   Glycos_transf_2  15 etlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgdyilflDaDde 91 
                                        ++es ++      ++i +v    + ++ + l +  + + +++++ ++ + G+a+a+ ag    +g  ++++  D  
  gi|298675078|ref|YP_003726828.1|  36 HAVESFVNA---GIDDITIVVSPKKHGLSDYLGSGKRFGVNITYVVQDDRLGLANAVEAGEHVINGSPFAVVLGDNF 109
                                       555555555...33333333344444666666666668889**************************9999999999 PP

                                       E-TT.HHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS.......................E CS
                   Glycos_transf_2  92 pdpd.wleklvealekdgadvvlgqrprifgetdeiernkrv.......................g 133
                                       ++pd  l++l ++ e++ ad+ +g   ++++ ++ i ++ ++                       +
  gi|298675078|ref|YP_003726828.1| 110 FSPDtILQDLKQFHENNKADATVGVMEVSDVTRHGIIKTNGNnivdliekpeadkapsklgiagmY 175
                                       999966777777777777888888888877777777777665555555555555555544444440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1537.12
//
Query:       gi|298675079|ref|YP_003726829.1|  [L=375]
Description: family 2 glycosyl transferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-22   79.0   0.4    5.1e-22   78.5   0.4    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    2.5e-15   57.0   0.0    3.6e-15   56.5   0.0    1.1  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    1.3e-10   41.5   0.7      4e-10   40.0   0.7    1.8  1  Glyco_trans_2_3  Glycosyl transferase family group 2
    8.4e-07   28.7   0.8    1.3e-06   28.1   0.8    1.2  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
    8.6e-06   25.3   0.0    1.4e-05   24.6   0.0    1.3  1  Glyco_transf_21  Glycosyl transferase family 21
    0.00022   20.0   7.5     0.0019   16.9   0.0    2.4  3  Chitin_synth_2   Chitin synthase
    0.00089   18.7   0.0     0.0014   18.1   0.0    1.3  1  Anp1             Anp1
  ------ inclusion threshold ------
      0.057   13.9   0.2       0.14   12.7   0.2    1.7  1  Glyco_tranf_2_4  Glycosyl transferase family 2
        0.1   12.7   0.0        0.2   11.8   0.0    1.4  1  DUF2694          Protein of unknown function (DUF2694)
        1.1    9.3   5.9         15    5.6   0.1    3.1  4  DUF4898          Domain of unknown function (DUF4898)
        4.8    5.7   7.3        6.7    5.3   7.3    1.2  1  Ndc1_Nup         Nucleoporin protein Ndc1-Nup


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.5   0.4   3.1e-25   5.1e-22       1     128 [.      44     174 ..      44     212 .. 0.80

  Alignments for each domain:
  == domain 1  score: 78.5 bits;  conditional E-value: 3.1e-25
                                       EEEEEESS-TTTHHHHHHHHHHH.GGCCEEEEEEEEES-SSCHHHHHGGGCH.C-TTEEEEEESSS-HHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaq.dpypdfeiivvDDgStDetveileelak.edprvrvirreenvGkagalnagl 75 
                                       +vviptyNeek ++  ++ l+++ +p ++++ ivvDD S+D+tve+++++ + ++    +i ++ ++G   ++n g+
  gi|298675079|ref|YP_003726829.1|  44 TVVIPTYNEEKVIEHRIKNLRDInYPTDKIHAIVVDDRSSDNTVELAKDAFDkYNVSGEIIVKDSRTGTNESVNLGV 120
                                       69**************************************************98999999***************** PP

                                       HH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCE.EEEEEEEEECCCCCCCH CS
                   Glycos_transf_2  76 raatgdyilflDaDdepdpdwleklvealekdgadv.vlgqrprifgetdeier 128
                                       + a++d++++ DaD++++++ l   ++ l  d++ + v+g    i +e+ + + 
  gi|298675079|ref|YP_003726829.1| 121 KSARTDIVVTTDADVVFEDNALDYAIGTLLSDDNIGaVCGELEPIVKEKSFTTG 174
                                       ***********************9999988775555044444444444444444 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   0.0   2.2e-18   3.6e-15       1     226 [.      40     261 ..      40     263 .. 0.88

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 2.2e-18
                   Glyco_tranf_2_3   1 prdlavlVptfneedvlgevlesllaqeypr..vevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgk 75 
                                       p+d++v++pt+nee+v++  + +l  + yp+  ++ +vv+d+s++ t+e a+ + +++   +  ++v++    +tg+
  gi|298675079|ref|YP_003726829.1|  40 PPDITVVIPTYNEEKVIEHRIKNLRDINYPTdkIHAIVVDDRSSDNTVELAKDAFDKYNVSG-EIIVKDS---RTGT 112
                                       778**************************77679999***************9989997544.7777755...5789 PP

                   Glyco_tranf_2_3  76 sralnealravksdlvllvDdDtvvePdtlkrllqff.ltpkvgavgtpvfll.nrstlvsalgalefaerhlrfla 150
                                        +++n +++ +++d+v+  D+D+v e+++l+++  ++  ++++gav +  +    ++++++ + +  +   + +++ 
  gi|298675079|ref|YP_003726829.1| 113 NESVNLGVKSARTDIVVTTDADVVFEDNALDYAIGTLlSDDNIGAVCGELEPIvKEKSFTTGSEK-AYRSVYGKMCT 188
                                       9999********************************988889***99988664389999999988.56677777777 PP

                   Glyco_tranf_2_3 151 arral.gvltlnGsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaavrevfpsslkayikqrnR 226
                                           + ++ ++nG + + r + +  +    p+ + + D+ ++l++ r+g+r  y + a  +e+ +++l++ ++q+ R
  gi|298675079|ref|YP_003726829.1| 189 WESHIhSTYCFNGPLIALRKKAFSPI----PATHGASDAGMALEIIRNGYRCIYEANAKFYEYITENLTQQRRQKIR 261
                                       77555168******************....556779******************99999***********9999977 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.7   2.4e-13     4e-10       1     193 [.     127     315 ..     127     367 .. 0.78

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 2.4e-13
                   Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaela.spevaivqgpvlv.mnvanwleelaalffaedhgkdilvrealgrvvpsvGs 75 
                                       i++  DaD v   + l +++  l  ++++++v+g   + +  +++++   ++ +   +gk++ + + ++++  + G 
  gi|298675079|ref|YP_003726829.1| 127 IVVTTDADVVFEDNALDYAIGTLLsDDNIGAVCGELEPiVKEKSFTTGSEKAYR-SVYGKMCTWESHIHSTYCFNGP 202
                                       68999***************9777479********7762566666666666655.69******************** PP

                   Glyco_trans_2_3  76 gaflrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGcel..ekli 150
                                        ++lr +a++ +   +   ++ + D  m+l + r+Gyr+++ + + ++e+   +l   +rQ+ R     +    ++i
  gi|298675079|ref|YP_003726829.1| 203 LIALRKKAFSPI---P--ATHGASDAGMALEIIRNGYRCIYEANAKFYEYITENLTQQRRQKIRRSSRLQEatLHNI 274
                                       *******99877...6..68999**************************************9997666422343334 PP

                   Glyco_trans_2_3 151 llvrllgylgsllwsalplhlallllfsllalalvllllllla 193
                                        l++    +g++ +  lp +++++++ ++  ++ v+l+ ++l 
  gi|298675079|ref|YP_003726829.1| 275 NLIS--SKYGKFGTLILPMRFLMFFVVPVMFFVSVILWSVFLS 315
                                       3331..2244444444444444444444444444444443332 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.8   7.9e-10   1.3e-06       1      95 [.      44     138 ..      44     154 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 7.9e-10
                   Glyco_tranf_2_2   1 svviplraseerhyieervlqkak.yy.deeielivvddgSsekfleevssiidlnllv.ylkdeddkayslaaarN 74 
                                       +vvip +++e+   ie r+++ +   y  ++i+ ivvdd Ss++++e  +   d+      +   +d   +   + N
  gi|298675079|ref|YP_003726829.1|  44 TVVIPTYNEEKV--IEHRIKNLRDiNYpTDKIHAIVVDDRSSDNTVELAKDAFDKYNVSgEII-VKDSRTGTNESVN 117
                                       79********99..*****665541346999***************99998776544331322.334567999**** PP

                   Glyco_tranf_2_2  75 rGaskaesdlvlFlDaDcfis 95 
                                       +G++ a +d+v+  DaD  + 
  gi|298675079|ref|YP_003726829.1| 118 LGVKSARTDIVVTTDADVVFE 138
                                       *****************8765 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   8.6e-09   1.4e-05       4     116 ..     100     214 ..      98     265 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 8.6e-09
                   Glyco_transf_21   4 r.rllvsgdpvgvnpKvnnllqaleaakydllvisDsdvrvkpdyLeellaa.ledpkvglVts.lpvgsdakglaa 77 
                                       + +++v+++++g+n  v   + ++++a++d++v+ D+dv+++ ++L+   ++ l+d+++g V++ l   +++k++++
  gi|298675079|ref|YP_003726829.1| 100 SgEIIVKDSRTGTNESV---NLGVKSARTDIVVTTDADVVFEDNALDYAIGTlLSDDNIGAVCGeLEPIVKEKSFTT 173
                                       55688999999999998...568899********************97665516779******97778********* PP

                   Glyco_transf_21  78 aleaaflntl..agvlqaklsglgfavGksmalrreaLeai 116
                                         e+a+ + +  + ++ ++   + + +G  +alr++a+  i
  gi|298675079|ref|YP_003726829.1| 174 GSEKAYRSVYgkMCTWESHIHSTYCFNGPLIALRKKAFSPI 214
                                       ******955512666666899***************99876 PP

>> Chitin_synth_2  Chitin synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.4   2.3e+03      27      63 ..      43      78 ..      17      80 .. 0.66
   2 !   16.9   0.0   1.2e-06    0.0019     195     287 ..     118     209 ..     113     215 .. 0.82
   3 !    4.9   3.1    0.0052       8.5     369     467 ..     265     354 ..     237     363 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.4
                    Chitin_synth_2 27 ticlvtaysegeeglrttldslastdyddkrklllvv 63
                                      + +++++y e+ + + + +  l  ++y+  +   +vv
  gi|298675079|ref|YP_003726829.1| 43 ITVVIPTYNEE-KVIEHRIKNLRDINYPTDKIHAIVV 78
                                      34567888774.5688888888888888765444444 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1.2e-06
                    Chitin_synth_2 195 iGvspdfyeivlmvdadtkvapdsltrlvaalvkdpeilglcGetkiankkeswvtaiqvfeyyishhlskafesvf 271
                                       +Gv++++ +iv++ dad   + ++l   + +l++d +i ++cGe +   k++s+ t      y   + +  ++es  
  gi|298675079|ref|YP_003726829.1| 118 LGVKSARTDIVVTTDADVVFEDNALDYAIGTLLSDDNIGAVCGELEPIVKEKSFTTGSEK-AYRSVYGKMCTWESHI 193
                                       699999****************************************99******997543.3444455666777777 PP

                    Chitin_synth_2 272 GsvtclPGcfslyrik 287
                                        s  c+ G + + r k
  gi|298675079|ref|YP_003726829.1| 194 HSTYCFNGPLIALRKK 209
                                       7777777766666655 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.0052
                    Chitin_synth_2 369 rwinstvhnllelvlvrdlcGtfcfsmrfvvfieligtvvlPvaiaftlylivasilksklvpviplvllaivlGlp 445
                                       r  ++t+hn+  +       Gt+++ mrf++f+      v+P  ++f + +i+ s++ s++  v  lv++a   G  
  gi|298675079|ref|YP_003726829.1| 265 RLQEATLHNINLISSKYGKFGTLILPMRFLMFF------VVP--VMFFVSVILWSVFLSQFNIVFGLVIIAGFAG-- 331
                                       455689999765555667889999999999985......556..5799999999999999999999998886655.. PP

                    Chitin_synth_2 446 aili.vltarkleyvawllvyll 467
                                       a++  +  ++ l+   w  vyll
  gi|298675079|ref|YP_003726829.1| 332 ALISgLWSSNILSSFIWHQVYLL 354
                                       33331345556778888888887 PP

>> Anp1  Anp1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   8.3e-07    0.0014      11      80 ..      31      98 ..      26     183 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 8.3e-07
                              Anp1 11 estadaaenkekvLiltplrdaekflpeyfenllkltyphelidLaflvsdtsegdktlealeeelkklq 80
                                      e++ ++++n  ++ +++p  ++ek++++ ++nl  ++yp+++i+ a++v d s  d+t+e  +++++k++
  gi|298675079|ref|YP_003726829.1| 31 ENSGNKIKNPPDITVVIPTYNEEKVIEHRIKNLRDINYPTDKIH-AIVVDDRS-SDNTVELAKDAFDKYN 98
                                      6778999************************************8.77787777.7889888888888877 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   8.3e-05      0.14       1      81 [.      50     134 ..      50     142 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.3e-05
                   Glyco_tranf_2_4   1 rneadiLpeflahhlalgf..d..rilvydndstDgtrailkelpevkllhvdksy..ederrq.vellkallarya 70 
                                       +ne++++++ ++ ++++ +  d  + +v+d+ s+D+t ++ k     + ++v +++  +d+r++ +e  +    + a
  gi|298675079|ref|YP_003726829.1|  50 YNEEKVIEHRIKNLRDINYptDkiHAIVVDDRSSDNTVELAKDA--FDKYNVSGEIivKDSRTGtNESVNLGV-KSA 123
                                       59999999999999999876533479**************9984..333333333323555555223333333.334 PP

                   Glyco_tranf_2_4  71 eadwvlvvDaD 81 
                                       ++d v++ DaD
  gi|298675079|ref|YP_003726829.1| 124 RTDIVVTTDAD 134
                                       66777777766 PP

>> DUF2694  Protein of unknown function (DUF2694)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00012       0.2       4      50 ..      90     136 ..      87     152 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                           DUF2694   4 anpafdtvhpsgdvlvrscrggylhsvalseaameadaerlaeaill 50 
                                       a+ afd    sg+++v+  r g   sv l   +  +d    ++a ++
  gi|298675079|ref|YP_003726829.1|  90 AKDAFDKYNVSGEIIVKDSRTGTNESVNLGVKSARTDIVVTTDADVV 136
                                       5679************************9877766665555554444 PP

>> DUF4898  Domain of unknown function (DUF4898)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1    0.0093        15      39      64 ..      41      65 ..      38      67 .. 0.84
   2 ?   -2.5   0.1       3.2   5.2e+03      43      68 ..      75      99 ..      69     110 .. 0.62
   3 ?   -2.1   0.0       2.3   3.7e+03      43      69 ..     103     130 ..      97     131 .. 0.76
   4 ?    5.2   0.1     0.012        19       7      46 ..     260     300 ..     258     303 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0093
                           DUF4898 39 kkivvvvpsdledekvikesvkkars 64
                                       +i+vv+p   e ekvi++ +k+ r+
  gi|298675079|ref|YP_003726829.1| 41 PDITVVIPTYNE-EKVIEHRIKNLRD 65
                                      6899****9777.*********9885 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.2
                           DUF4898 43 vvvpsdledekvikesvkkarsslsv 68
                                       +v +d+  ++   e+ k a+++ +v
  gi|298675079|ref|YP_003726829.1| 75 AIVVDDRS-SDNTVELAKDAFDKYNV 99
                                      34445555.45556777777777666 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.3
                           DUF4898  43 vvvpsdled.ekvikesvkkarsslsvt 69 
                                       ++v +++ + +++++  vk+ar+++ vt
  gi|298675079|ref|YP_003726829.1| 103 IIVKDSRTGtNESVNLGVKSARTDIVVT 130
                                       6666777776777888899999998886 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.012
                           DUF4898   7 ikkskkikfvkkislkiIsd.yekffnfilPkdkkivvvvp 46 
                                       i +s + +     ++++Is+ y kf  +ilP    ++ vvp
  gi|298675079|ref|YP_003726829.1| 260 IRRSSRLQEATLHNINLISSkYGKFGTLILPMRFLMFFVVP 300
                                       6777788888888899997449**********977776666 PP

>> Ndc1_Nup  Nucleoporin protein Ndc1-Nup
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   7.3    0.0041       6.7     191     263 ..     295     357 ..     242     366 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0041
                          Ndc1_Nup 191 lllvspiiyylllrsfiwslalillrlflnlprsaapppldslpfnlsLllrtlllgflllllwelanllFdv 263
                                       +++v p  +++++  ++ws++l+ + ++++l          + +f   L+  ++ +++l  ++w+ ++llF+ 
  gi|298675079|ref|YP_003726829.1| 295 MFFVVP--VMFFVSVILWSVFLSQFNIVFGLVI--------IAGFAGALISGLWSSNILSSFIWHQVYLLFSL 357
                                       111222..2355566666654444444444444........7778**************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1027  (0.0572815); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2742.47
//
Query:       gi|298675080|ref|YP_003726830.1|  [L=430]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-22   79.3   0.6      8e-22   77.7   0.6    1.9  1  OrfB_IS605      Probable transposase
    2.1e-08   34.0   0.0    5.2e-08   32.7   0.0    1.7  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.015   15.4   0.1      0.015   15.4   0.1    2.2  2  DUF986          Protein of unknown function (DUF986)
       0.02   15.2   0.1      0.043   14.2   0.1    1.5  1  CRF1            Transcription factor CRF1
       0.02   14.8   2.0      0.043   13.7   2.0    1.5  1  PhaP_Bmeg       Polyhydroxyalkanoic acid inclusion protein (P


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.7   0.6   2.2e-25     8e-22       4     119 ..     181     297 ..     178     298 .. 0.92

  Alignments for each domain:
  == domain 1  score: 77.7 bits;  conditional E-value: 2.2e-25
                        OrfB_IS605   4 vevevelpkpkgnkaagiDlGinnLatvv.tedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklar 79 
                                       ++ + +    ++n+ ++iDlG+ n+at v t++gt+++++g+++ks ++ ++ke+a+lq  ++k++  +k +++l+r
  gi|298675080|ref|YP_003726830.1| 181 YDKKLQDMNLDKNQYLSIDLGLDNFATFVeTSTGTAEIIDGKHIKSINQFYNKEKARLQGVKDKQGMEHKFTKRLSR 257
                                       5555556667899**************773678999***************************************** PP

                        OrfB_IS605  80 lhrkrsrrrkhllhklathliktlkevgvetLnvgnmkdi 119
                                       l +kr ++++++l+  + +++kt+ ++ ++++++g++k+i
  gi|298675080|ref|YP_003726830.1| 258 LTNKRDNKVDEFLNRSVDYIVKTCIDKDIGNIVIGELKEI 297
                                       *************************************987 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0   1.5e-11   5.2e-08       4      69 .]     319     390 ..     316     390 .. 0.85

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 1.5e-11
                    OrfB_Zn_ribbon   4 lkeqleykakeyGikveevnpayTSktCseCgsknke......alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       +k +l+ k+  yGi+++e +++yTSkt +   +  ++      ++ +r +  ++ g  +++Dvn+a+Nil++
  gi|298675080|ref|YP_003726830.1| 319 FKSKLQSKCDLYGINYIEEDESYTSKTDALSLEPIRKheeymgRRIKRGLFKSSTGQLLNADVNGALNILRK 390
                                       899***********************9776665555555699978888888888***************986 PP

>> DUF986  Protein of unknown function (DUF986)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   1.0      0.21   7.5e+02      96     118 ..      41      63 ..      36      82 .. 0.69
   2 ?   15.4   0.1   4.2e-06     0.015      88     140 ..     165     217 ..     161     221 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.21
                            DUF986  96 ffyanifieYkkikainlsedgi 118
                                       +fy+n f++Y++  +    +d++
  gi|298675080|ref|YP_003726830.1|  41 YFYNNKFLPYTNNYHYCKDNDNY 63 
                                       8*********9876665555554 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 4.2e-06
                            DUF986  88 klllKeeGffyanifieYkkikainlsedgilvidlekrrllikvkklddlek 140
                                       +++ K++G fy+  ++  kk++++nl  +++l idl   ++   v++   + +
  gi|298675080|ref|YP_003726830.1| 165 RIVPKHDGKFYQMQYVYDKKLQDMNLDKNQYLSIDLGLDNFATFVETSTGTAE 217
                                       6788*******************************988777777776665555 PP

>> CRF1  Transcription factor CRF1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.2e-05     0.043      43     108 ..     207     273 ..     198     275 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.2e-05
                              CRF1  43 tWakednkpfgiiDGlstkSLqekdkedactkgentanngagaqtlnetse.sdkdelsLddlLntS 108
                                       t++++ +    iiDG++ kS+++  +++++  +  + ++g +++ +++ s  ++k +  +d++Ln S
  gi|298675080|ref|YP_003726830.1| 207 TFVETSTGTAEIIDGKHIKSINQFYNKEKARLQGVKDKQGMEHKFTKRLSRlTNKRDNKVDEFLNRS 273
                                       78888888999**********87666666666667777788777777766668999999*****987 PP

>> PhaP_Bmeg  Polyhydroxyalkanoic acid inclusion protein (PhaP_Bmeg)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   2.0   1.2e-05     0.043      22      94 ..     225     298 ..     221     314 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.2e-05
                         PhaP_Bmeg  22 erfaslskqvEqltLkalkqqqdlvkeltkalselekeskqltaeledqlqktven..lrskaGnkvednieEwt 94 
                                       + ++++ +  E++ L+ +k++q + +++tk ls+l ++  +   e++++ ++++ +  + ++ Gn v  +++E +
  gi|298675080|ref|YP_003726830.1| 225 KSINQFYN-KEKARLQGVKDKQGMEHKFTKRLSRLTNKRDNKVDEFLNRSVDYIVKtcIDKDIGNIVIGELKEIK 298
                                       55666654.599**************************99999*********99773357888888777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 3134.76
//
Query:       gi|298675081|ref|YP_003726831.1|  [L=747]
Description: multi-sensor signal transduction histidine kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-33  115.3   0.2    6.8e-33  113.5   0.1    2.1  2  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    1.1e-21   76.6   0.1    5.6e-21   74.4   0.0    2.3  2  HisKA        His Kinase A (phospho-acceptor) domain
      6e-18   64.9   0.0    1.1e-08   35.0   0.0    2.7  2  PAS          PAS fold
    1.9e-17   63.5   0.0    4.7e-10   39.7   0.0    2.7  2  PAS_4        PAS fold
    1.9e-17   63.4   0.4    3.6e-08   33.6   0.0    2.8  2  PAS_9        PAS domain
    4.9e-14   52.0   0.3    5.3e-08   32.7   0.1    2.7  2  PAS_8        PAS domain
    6.7e-08   32.7   0.0     0.0031   17.8   0.0    2.7  2  PAS_3        PAS fold
    7.5e-05   22.6   0.0    0.00017   21.5   0.0    1.6  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
  ------ inclusion threshold ------
      0.031   12.5   0.2       0.06   11.5   0.2    1.4  1  HOOK         HOOK protein
       0.16   11.9   0.0       0.16   11.9   0.0    2.3  2  HATPase_c_5  GHKL domain


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       5.4   9.7e+03       3      27 ..     375     398 ..     373     422 .. 0.79
   2 !  113.5   0.1   3.8e-36   6.8e-33       2     111 ..     623     733 ..     622     734 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 5.4
                                       HHHHHHHHHHHHHHHHHHHSTTTEE CS
                         HATPase_c   3 ekrLrqiisnlvdNavkfatkagei 27 
                                       e+r+r +i ++ d+ + +   +g+i
  gi|298675081|ref|YP_003726831.1| 375 EQRFRTLIEHAADAIIVH-DFDGNI 398
                                       789999999999999988.555544 PP

  == domain 2  score: 113.5 bits;  conditional E-value: 3.8e-36
                                       HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEE.TEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTSSSH CS
                         HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikase.ddlvisveDnGiGipkedlkklfekfsq.ddstkrggggtGl 76 
                                       de +L++i+ nl+ N+vkf t++g+i+++++ +e +++++sv D+GiGip e+l+++fe+f q d +t+r+++gtGl
  gi|298675081|ref|YP_003726831.1| 623 DELKLKHILYNLLYNSVKF-TDDGSITIKLDLDEnNNYKFSVVDSGIGIPNEKLNQIFEPFKQlDTGTSRKYSGTGL 698
                                       8999***************.99*********97779***************************************** PP

                                       HHHHHHHHHHHTTTEEEEEEETTTEEEEEEEEESS CS
                         HATPase_c  77 GlsivkklvelmgGeiwvesepgrGttftftlple 111
                                       Gl++vk+lvel+gG+iwvese g G++ftft+p +
  gi|298675081|ref|YP_003726831.1| 699 GLTLVKRLVELHGGNIWVESEVGTGSKFTFTIPSD 733
                                       *******************************9975 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       5.9   1.1e+04      50      66 ..     486     502 ..     463     502 .. 0.82
   2 !   74.4   0.0   3.1e-24   5.6e-21       1      67 []     508     576 ..     508     576 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 5.9
                                       HHHHHHHHHHHHCCHHH CS
                             HisKA  50 rldhlvedlLdlsriea 66 
                                        ++++ ed L ++++ea
  gi|298675081|ref|YP_003726831.1| 486 TMQKQTEDNLVYAKMEA 502
                                       57888999999999885 PP

  == domain 2  score: 74.4 bits;  conditional E-value: 3.1e-24
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                             HisKA   1 slgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsrieag 67 
                                       ++++++a+v+HELrtPL++i+g++++L +   g+l++++++yl +i++ +++l ++++++Ldls+i++g
  gi|298675081|ref|YP_003726831.1| 508 AKSDMIANVSHELRTPLTTIIGFSDVLLKGkaGDLNDSQEKYLSKIHDRGQQLHNIINEMLDLSKIDSG 576
                                       589***********************9777799**********************************97 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   1.8e-09   3.3e-06       3      97 ..     258     350 ..     256     361 .. 0.72
   2 !   35.0   0.0   6.1e-12   1.1e-08       2     113 .]     377     485 ..     376     485 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1.8e-09
                                       HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEE CS
                               PAS   3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisf 79 
                                       +r+ ++ +p  ifv+D+ g+ + vN++a +++ ++ +e+l+ +++dl +  d +e++ l+ + l ++ + ++ e  f
  gi|298675081|ref|YP_003726831.1| 258 FRSYVDYAPFWIFVIDRHGNYVDVNPTASSMTEYTMNELLSMNIVDLHPS-DAYEQVNLVFNELVDTGSIST-ELPF 332
                                       66677889999**********************************76655.555666666666666655555.3334 PP

                                       ECTTSSEEEEEEEEEEEE CS
                               PAS  80 klrdgrpihlevraspvr 97 
                                        +++g  + + v+a+++ 
  gi|298675081|ref|YP_003726831.1| 333 ITKNGDRRIWIVEAVKLN 350
                                       445777777777777655 PP

  == domain 2  score: 35.0 bits;  conditional E-value: 6.1e-12
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       ++r+++e+++d+i+v D dg+ilyvN+ a+e lG+  + +l+ ++ d+ +  d + +++++++  +  ++   +   
  gi|298675081|ref|YP_003726831.1| 377 RFRTLIEHAADAIIVHDFDGNILYVNELACESLGYIKDKLLSMNVTDFDPYVDVDVFRDKYWNKTSPDTSYLVETYH 453
                                       89********************************************9999885555666666666666666666666 PP

                                       EECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  79 fklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                        +  dg+++++evr + +  +g+    +lg++rdi
  gi|298675081|ref|YP_003726831.1| 454 KRS-DGTIYPVEVRLTRIDLGGKP--AILGFVRDI 485
                                       666.***********999998776..********8 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.0   2.6e-13   4.7e-10       3     109 ..     264     365 ..     262     366 .. 0.96
   2 !   21.1   0.0   1.5e-07   0.00027       2     109 ..     383     489 ..     382     490 .. 0.91

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 2.6e-13
                             PAS_4   3 slpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgeer 79 
                                         p++++v+d++g+++++N++a ++  ++  ell +   +l+p ++ +++    +++++++   ++l + + +g++r
  gi|298675081|ref|YP_003726831.1| 264 YAPFWIFVIDRHGNYVDVNPTASSMTEYTMNELLSMNIVDLHPSDAYEQVNLVFNELVDTGSISTELPFITKNGDRR 340
                                       5799*********************************************************99999999999***** PP

                             PAS_4  80 hyelrllPlrdesGevigvlvisrDiTerr 109
                                       ++ ++++ l +     + +l++++DiTer+
  gi|298675081|ref|YP_003726831.1| 341 IWIVEAVKLNE-----DRFLGFTTDITERK 365
                                       *********76.....89**********97 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 1.5e-07
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pge 77 
                                       ++  da++v d dg++ly+N+ a+e +g+  + ll + + ++ p  d + +++ +    + ++++  ++++++ +g 
  gi|298675081|ref|YP_003726831.1| 383 EHAADAIIVHDFDGNILYVNELACESLGYIKDKLLSMNVTDFDPYVDVDVFRDKYWNKTSPDTSYLVETYHKRsDGT 459
                                       78899************************************999999999999888888888888888888889*** PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerr 109
                                         ++e+rl+++ d  G+  ++l+++rDiT ++
  gi|298675081|ref|YP_003726831.1| 460 IYPVEVRLTRI-DLGGK-PAILGFVRDITMQK 489
                                       ***********.66666.***********987 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.1   2.1e-09   3.8e-06       4     104 .]     269     363 ..     266     363 .. 0.82
   2 !   33.6   0.0     2e-11   3.6e-08       2     103 ..     387     486 ..     386     487 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 2.1e-09
                             PAS_9   4 ilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkng.etfw 77 
                                       i++++ +g+ +++N++a  ++ y+ +e+l  +i dl   +  ++ n  +++++++g+    + e+ +i+kng +++w
  gi|298675081|ref|YP_003726831.1| 269 IFVIDRHGNYVDVNPTASSMTEYTMNELLSMNIVDLHpsDAYEQVNLVFNELVDTGS---ISTELPFITKNGdRRIW 342
                                       66778********************************77777777777777777777...************66666 PP

                             PAS_9  78 vlltaspvkdddgelvgiivilrDite 104
                                           + +vk +++++    ++ +Dite
  gi|298675081|ref|YP_003726831.1| 343 ---IVEAVKLNEDRFL---GFTTDITE 363
                                       ...5666666666655...69999997 PP

  == domain 2  score: 33.6 bits;  conditional E-value: 2e-11
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetf 76 
                                       d+i++ + dg+ily+Ne a++ lGy ++ +l  ++td+   v+ +  +++ ++       + + ve+ + r++g+ +
  gi|298675081|ref|YP_003726831.1| 387 DAIIVHDFDGNILYVNELACESLGYIKDKLLSMNVTDFDpyVDVDVFRDKYWNKTSPD--TSYLVETYHKRSDGTIY 461
                                       67888779******************************94444444444444444444..6**************** PP

                             PAS_9  77 wvlltaspvkdddgelvgiivilrDit 103
                                       +v+++++++  +++  ++  +++rDit
  gi|298675081|ref|YP_003726831.1| 462 PVEVRLTRIDLGGKPAIL--GFVRDIT 486
                                       *********777777777..******9 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   3.2e-06    0.0058       2      47 ..     257     302 ..     256     320 .. 0.79
   2 !   32.7   0.1     3e-11   5.3e-08       1      55 [.     376     427 ..     376     439 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.2e-06
                             PAS_8   2 rlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellgq 47 
                                       ++r+ ++ +p  i+v+d  g+  vdvN++a  ++ y+ ++l+ + + +
  gi|298675081|ref|YP_003726831.1| 257 KFRSYVDYAPFWIFVIDrHGN-YVDVNPTASSMTEYTmNELLSMNI-V 302
                                       79999************5555.***************666666544.3 PP

  == domain 2  score: 32.7 bits;  conditional E-value: 3e-11
                             PAS_8   1 erlralfesspdgiavvd.lgdrivdvNqaalellGysadlkgellgqllpvlrpl 55 
                                       +r+r+l+e+++d+i+v d +g+ i++vN+ a+e lG    +k++ll   +++++p+
  gi|298675081|ref|YP_003726831.1| 376 QRFRTLIEHAADAIIVHDfDGN-ILYVNELACESLG-Y--IKDKLLSMNVTDFDPY 427
                                       7***************999999.*************.4..7777777666666665 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.7e-06    0.0031       2      69 ..     279     343 ..     278     355 .. 0.87
   2 !   12.2   0.0   9.2e-05      0.17       2      83 ..     399     477 ..     398     482 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.7e-06
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeD.rervrealqealkkgepyegeyRirrkdGeyrwve 69 
                                       + v+++ + ++ y+ +ell+   ++ dl hp D  e+v+  ++e++++g+ +++e  +++k+G+ r + 
  gi|298675081|ref|YP_003726831.1| 279 VDVNPTASSMTEYTMNELLSM--NIVDL-HPSDaYEQVNLVFNELVDTGS-ISTELPFITKNGDRRIWI 343
                                       689******************..99997.66665************9999.9***********987665 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 9.2e-05
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       +yv+e  +e lGy ++ ll+   ++ d+    D + +r+++++  + +++y +e   +r dG+++ ve r + i d 
  gi|298675081|ref|YP_003726831.1| 399 LYVNELACESLGYIKDKLLSM--NVTDFDPYVDVDVFRDKYWNKTSPDTSYLVETYHKRSDGTIYPVEVRLTRI-DL 472
                                       89*******************..****************************999999*************9999.87 PP

                             PAS_3  79 ngkpv 83 
                                        gkp 
  gi|298675081|ref|YP_003726831.1| 473 GGKPA 477
                                       77776 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   9.3e-08   0.00017       6      77 ..     630     700 ..     625     738 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 9.3e-08
                       HATPase_c_3   6 AlaelvdNsld.AdaenvkievnknrgktgeivieDdGkGmseeelknalrlatsskeakrkstslGkkGiGl 77 
                                        l  l+ Ns+   d  +++i+++ +++++ ++++ D G G+++e+l + +++ ++  +   +s++++  G+Gl
  gi|298675081|ref|YP_003726831.1| 630 ILYNLLYNSVKfTDDGSITIKLDLDENNNYKFSVVDSGIGIPNEKLNQIFEPFKQLDTG--TSRKYSGTGLGL 700
                                       5788999**9999999**********************************988887774..799999999996 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   3.4e-05      0.06     555     611 ..     219     274 ..     213     295 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.4e-05
                              HOOK 555 kkkeqleelepklssnkqkieeleeaLkkkdedlkameerYkkyveKAksViktLdp 611
                                       + k +++e+++++s +   i e+++ Lkk++edlk  e+++++yv+ A   i  +d 
  gi|298675081|ref|YP_003726831.1| 219 REKDLFQEVANDISYSLYNI-EMKKELKKREEDLKESENKFRSYVDYAPFWIFVIDR 274
                                       56677888888888877766.799**********************99766666665 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.6       2.9   5.3e+03      52      52 ..     113     113 ..      62     170 .. 0.44
   2 ?   11.9   0.0     9e-05      0.16       4      91 ..     625     720 ..     622     730 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.9
                       HATPase_c_5  52 g 52 
                                       +
  gi|298675081|ref|YP_003726831.1| 113 Q 113
                                       2 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 9e-05
                       HATPase_c_5   4 ldlcvilgnlLdNAieacskieeekrfIrltvrekkks......liisieNsyegek....kkle.sskskkeehGi 69 
                                       l l  il nlL N++   ++ +     I+l + e+++         i i N+  +++    k+l   +++k +  G+
  gi|298675081|ref|YP_003726831.1| 625 LKLKHILYNLLYNSVKFTDDGS---ITIKLDLDENNNYkfsvvdSGIGIPNEKLNQIfepfKQLDtGTSRKYSGTGL 698
                                       6678899999999886665544...56666666655442121112244555555555666666663457788999** PP

                       HATPase_c_5  70 Glksireivkkykgnlsieaed 91 
                                       Gl+ ++++v+ ++gn+++e e 
  gi|298675081|ref|YP_003726831.1| 699 GLTLVKRLVELHGGNIWVESEV 720
                                       *****************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (747 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1012  (0.0564449); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.42
# Mc/sec: 5384.44
//
Query:       gi|298675082|ref|YP_003726832.1|  [L=677]
Description: PAS/PAC sensor signal transduction histidine kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.2e-32  110.7   0.0    3.1e-11   43.5   0.0    3.8  4  PAS_4           PAS fold
    1.3e-26   92.9   7.4    7.3e-11   42.2   0.1    3.8  3  PAS_9           PAS domain
    4.1e-25   88.5   0.8      1e-24   87.2   0.0    2.1  2  HATPase_c       Histidine kinase-, DNA gyrase B-, and HSP90-l
    1.9e-18   66.5   0.0    4.8e-06   26.6   0.0    4.3  3  PAS             PAS fold
    4.1e-14   52.4   0.0    1.6e-13   50.5   0.0    2.1  1  HisKA           His Kinase A (phospho-acceptor) domain
    4.5e-11   42.5   0.0     0.0014   18.6   0.0    3.8  3  PAS_8           PAS domain
    3.6e-09   37.2   5.2     0.0034   17.9   0.1    4.1  4  PAS_10          PAS domain
    1.8e-08   34.5   0.1    2.5e-05   24.5   0.0    4.1  4  PAS_3           PAS fold
    0.00041   20.2   2.6     0.0064   16.4   0.3    2.7  2  PAS_6           YheO-like PAS domain
    0.00072   19.4   0.1     0.0019   18.0   0.1    1.7  1  HATPase_c_3     Histidine kinase-, DNA gyrase B-, and HSP90-l
      0.002   17.8   5.2      0.019   14.7   1.7    3.0  2  LUC7            LUC7 N_terminus
     0.0049   16.7   0.1     0.0049   16.7   0.1    2.9  3  HATPase_c_5     GHKL domain
  ------ inclusion threshold ------
      0.033   14.1   0.2      0.033   14.1   0.2    2.6  3  DUF1151         Protein of unknown function (DUF1151)
      0.048   13.8   0.9         26    5.0   0.0    4.4  3  PAS_7           PAS fold
       0.19   11.9   9.3       0.26   11.4   3.0    2.9  2  NYD-SP28_assoc  Sperm tail C-terminal domain
        2.4    8.5   6.1       0.88    9.9   0.1    3.1  3  Flu_NS2         Influenza non-structural protein (NS2)


Domain annotation for each model (and alignments):
>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   4.3e-10   4.9e-07       4     109 ..      52     154 ..      49     155 .. 0.92
   2 !   43.5   0.0   2.8e-14   3.1e-11       3     108 ..     191     299 ..     189     301 .. 0.93
   3 !   32.7   0.0   6.4e-11   7.1e-08       1     110 []     317     427 ..     317     427 .. 0.97
   4 ?   -2.7   0.0       6.4   7.2e+03      11      28 ..     557     574 ..     553     577 .. 0.80

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 4.3e-10
                             PAS_4   4 lpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgeerh 80 
                                       +pd+l + d++ +++ +N+a+ + f + pee+ Gk+++e+     ++   +a  +v ++++p + + +      + +
  gi|298675082|ref|YP_003726832.1|  52 IPDILGIQDTNHNIIKYNKAGYSFFNLKPEEVAGKKCYEIIGR-NKPCKICATSKVYKSKKPEHVVKYIEE--MDIW 125
                                       79*************************************9887.8888889999*****988777775555..**** PP

                             PAS_4  81 yelrllPlrdesGevigvlvisrDiTerr 109
                                       +++r++P++d +G    v++++rDiT+++
  gi|298675082|ref|YP_003726832.1| 126 FDVRAYPIFDNNGNLTNVMEHLRDITQEK 154
                                       **************************987 PP

  == domain 2  score: 43.5 bits;  conditional E-value: 2.8e-14
                             PAS_4   3 slpdalavldpdgrvlyaNaaaaelfgappeellGktlae.llpeedaarleralrrvlegeepiefleelll..pg 76 
                                        + ++++vld ++r++ +N+ ++e++g++  el+Gk ++e ++p e  + + ++ + +++g+e     + +    +g
  gi|298675082|ref|YP_003726832.1| 191 ISGAIIIVLDNNQRIELINNKGCEVLGYDKTELIGKNMYEnFVPREYMDKVNNISNNLIQGHEDNNNFINPIIgkNG 267
                                       578899*********************************8466666****************999999988879*** PP

                             PAS_4  77 eerhyelrllPlrdesGevigvlvisrDiTer 108
                                       eer++++  + l+d++G +ig+l  ++D+Te+
  gi|298675082|ref|YP_003726832.1| 268 EERIISWYNSVLKDDNGSIIGTLSSGIDVTEL 299
                                       ******************************96 PP

  == domain 3  score: 32.7 bits;  conditional E-value: 6.4e-11
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaae.lfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.p 75 
                                       ++ +p++l+ + ++g+++++N+++ e l   + ee l   l e  p+    ++++ lr++ + ++ ++ +  +    
  gi|298675082|ref|YP_003726832.1| 317 FEESPVGLLKCKSNGKIVDVNKRILEiLNSPSKEETLKFNLLE-SPHIKNSGFDEELRKAFSNNRIVKNERKYISfW 392
                                       789***********************9999************9.6999***************************** PP

                             PAS_4  76 geerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                       g+ r++   ++Pl de+G v   ++ + DiT+r++
  gi|298675082|ref|YP_003726832.1| 393 GRKRWIYYKIVPLGDEEGNVNESIIALDDITQRKE 427
                                       *********************************85 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 6.4
                             PAS_4  11 ldpdgrvlyaNaaaaelf 28 
                                       +d+++  ++aN+++ e +
  gi|298675082|ref|YP_003726832.1| 557 IDSNLPLVDANPEYLEQV 574
                                       68999999*****99855 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.1   6.5e-14   7.3e-11       4     104 .]      56     152 ..      53     152 .. 0.80
   2 !   31.0   1.6     2e-10   2.3e-07       4     104 .]     196     298 ..     193     298 .. 0.82
   3 !   20.9   0.0   2.8e-07   0.00032       1     104 []     321     424 ..     321     424 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 6.5e-14
                             PAS_9   4 ilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwvll 80 
                                         i +++++i+++N+a   ++  +peev gk++ +++    +  ++++a  +  +   +  e v  + ++  +w+++
  gi|298675082|ref|YP_003726832.1|  56 LGIQDTNHNIIKYNKAGYSFFNLKPEEVAGKKCYEII--GRNKPCKICATSKVYK--SKKPEHVVKYIEEMDIWFDV 128
                                       457889*******************************..5555555555555555..4445555555556679**** PP

                             PAS_9  81 taspvkdddgelvgiivilrDite 104
                                       +a+p++d++g+l+ +   lrDit+
  gi|298675082|ref|YP_003726832.1| 129 RAYPIFDNNGNLTNVMEHLRDITQ 152
                                       ***********************7 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 2e-10
                             PAS_9   4 ilidnpdgrilyaNeaalrllGyspeevlgksitdlf...vtdpeanerlraaleqgrkkerevevvlirkngetfw 77 
                                       i++ +++ ri+ +N++ +++lGy++ e++gk++ + f   +  ++ n+  +++++ ++    ++ + +i knge+  
  gi|298675082|ref|YP_003726832.1| 196 IIVLDNNQRIELINNKGCEVLGYDKTELIGKNMYENFvprEYMDKVNNISNNLIQGHE-DNNNFINPIIGKNGEERI 271
                                       444779999***********************88888455444444444444444444.8889999999******** PP

                             PAS_9  78 vlltaspvkdddgelvgiivilrDite 104
                                       +    s +kdd+g ++g ++  +D+te
  gi|298675082|ref|YP_003726832.1| 272 ISWYNSVLKDDNGSIIGTLSSGIDVTE 298
                                       **999********************98 PP

  == domain 3  score: 20.9 bits;  conditional E-value: 2.8e-07
                             PAS_9   1 pdgilidnpdgrilyaNeaalrllGys.peevlgksitdlf....vtdpeanerlraaleqgrkkerevevvlirkn 72 
                                       p+g l + ++g+i+++N+  l++l +  +ee l    ++l+     +++  +e+lr+a+ + r      e  +i   
  gi|298675082|ref|YP_003726832.1| 321 PVGLLKCKSNGKIVDVNKRILEILNSPsKEETLK---FNLLesphIKNSGFDEELRKAFSNNR--IVKNERKYISFW 392
                                       56778899****************9763555454...5555566899****************..999999999999 PP

                             PAS_9  73 getfwvlltaspvkdddgelvgiivilrDite 104
                                       g++ w+  +++p+ d++g++   i+ l Dit+
  gi|298675082|ref|YP_003726832.1| 393 GRKRWIYYKIVPLGDEEGNVNESIIALDDITQ 424
                                       ******************************97 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       6.8   7.6e+03      37      81 ..     275     327 ..     239     342 .. 0.53
   2 !   87.2   0.0     9e-28     1e-24       4     109 ..     569     674 ..     566     676 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 6.8
                                       EEEEEEEESS.......SSSTTHHHTGTCSTTCH.HCSTCHTSTSSSHHHHHH CS
                         HATPase_c  37 dlvisveDnG.......iGipkedlkklfekfsq.ddstkrggggtGlGlsiv 81 
                                       ++++   DnG        Gi++ +l +l  ++++ ++++k+  + + +Gl  +
  gi|298675082|ref|YP_003726832.1| 275 YNSVLKDDNGsiigtlsSGIDVTELINLKNSLQEsKNQYKQLFEESPVGLLKC 327
                                       44554555555555555677777766555555555555555555555666555 PP

  == domain 2  score: 87.2 bits;  conditional E-value: 9e-28
                                       HHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTSSSHHHH CS
                         HATPase_c   4 krLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsq.ddstkrggggtGlGls 79 
                                       + L+q++ +++dNa kf++++g+++v+   ++++l+i v+DnGiGi++e  +++f+ f+q dds+kr+++gtG G++
  gi|298675082|ref|YP_003726832.1| 569 EYLEQVFVHILDNACKFTPSGGKVDVHAF-DDGNLHIIVSDNGIGIDEESANNIFDLFYQkDDSSKRRYSGTGAGMY 644
                                       6799*************778888888777.668******************************************** PP

                                       HHHHHHHHTTTEEEEEEETTTEEEEEEEEE CS
                         HATPase_c  80 ivkklvelmgGeiwvesepgrGttftftlp 109
                                        +kk++e+++G+iwves+ ++Gt++++ lp
  gi|298675082|ref|YP_003726832.1| 645 FCKKIIEKHHGNIWVESKIKEGTDVHIILP 674
                                       **************************9988 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0    0.0003      0.34       8      50 ..      50      92 ..      45     150 .. 0.68
   2 !   26.6   0.0   4.3e-09   4.8e-06      11     102 ..     193     285 ..     186     296 .. 0.78
   3 !   23.5   0.0   3.8e-08   4.2e-05       2     113 .]     312     422 ..     311     422 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0003
                                      HHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGB CS
                               PAS  8 eslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldli 50
                                      + +pd   + D +++i+  N+a  ++++l++eev gk+ ++ i
  gi|298675082|ref|YP_003726832.1| 50 DFIPDILGIQDTNHNIIKYNKAGYSFFNLKPEEVAGKKCYEII 92
                                      55666666779**************************998644 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 4.3e-09
                                       SSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEEC.TTSSE CS
                               PAS  11 pdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfkl.rdgrp 86 
                                        + i+v+D + ri ++N + +e lG++  e++gk++++ +++ +  + +  ++++l qg+e ++  i+    ++g++
  gi|298675082|ref|YP_003726832.1| 193 GAIIIVLDNNQRIELINNKGCEVLGYDKTELIGKNMYENFVPREYMDKVNNISNNLIQGHEDNNNFINPIIgKNGEE 269
                                       6789*************************************998888888888888888887776665555667766 PP

                                       EEEEEEEEEEEETTEE CS
                               PAS  87 ihlevraspvrdagge 102
                                       + +   +s + d  g 
  gi|298675082|ref|YP_003726832.1| 270 RIISWYNSVLKDDNGS 285
                                       6666666666666555 PP

  == domain 3  score: 23.5 bits;  conditional E-value: 3.8e-08
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTH.HHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsr.eevlgkslldliheeddaelaelleqlleqgeesragei 77 
                                       ++++++e +p++ +    +g+i+ vN+ + e+l+ +  ee l  +ll + ++ +++ + e+l+++ ++++  +++++
  gi|298675082|ref|YP_003726832.1| 312 QYKQLFEESPVGLLKCKSNGKIVDVNKRILEILNSPSkEETLKFNLL-ESPHIKNSGFDEELRKAFSNNRIVKNERK 387
                                       7999*********************************6777777777.66677899******************999 PP

                                       EEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  78 sfklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                        + +  gr++++    +p++d++g++ + +  l di
  gi|298675082|ref|YP_003726832.1| 388 YISF-WGRKRWIYYKIVPLGDEEGNVNESIIALDDI 422
                                       9999.*********************9999888886 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   0.0   1.4e-16   1.6e-13       1      61 [.     452     514 ..     452     520 .. 0.92

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 1.4e-16
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHH CS
                             HisKA   1 slgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdl 61 
                                       +++rf+++v+HELrtP++ i+g++ +L ++  g+l++++ +++ +i ++ +rl+ l+++l  +
  gi|298675082|ref|YP_003726832.1| 452 MKNRFISNVSHELRTPITNIKGYSNLLNNKklGELNDKQSKAVSVISQSCERLRWLIDTLIHI 514
                                       699************************88889**************************99765 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.08        90      14      49 ..      56      92 ..      46     103 .. 0.75
   2 !   15.8   0.0   9.7e-06     0.011       9      45 ..     191     228 ..     184     243 .. 0.74
   3 !   18.6   0.0   1.3e-06    0.0014       2      51 ..     312     360 ..     311     376 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.08
                             PAS_8 14 iavvdlgdrivdvNqaalellGys.adlkgellgqll 49
                                      + + d++ +i+ +N+a + ++ ++ +++ g+++ +++
  gi|298675082|ref|YP_003726832.1| 56 LGIQDTNHNIIKYNKAGYSFFNLKpEEVAGKKCYEII 92
                                      445673336*************999999999986554 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 9.7e-06
                             PAS_8   9 sspdgiavvdlgdrivdvNqaalellGys.adlkgell 45 
                                        s   i+v+d+++ri  +N++ +e lGy+  +l+g+ +
  gi|298675082|ref|YP_003726832.1| 191 ISGAIIIVLDNNQRIELINNKGCEVLGYDkTELIGKNM 228
                                       55556777897789*************99555555444 PP

  == domain 3  score: 18.6 bits;  conditional E-value: 1.3e-06
                             PAS_8   2 rlralfesspdgiavvd.lgdrivdvNqaalellGysadlkgellg.qllpv 51 
                                       ++++lfe sp+g++ ++ +g+ ivdvN++ le+l  +  +k+e+l  +ll+ 
  gi|298675082|ref|YP_003726832.1| 312 QYKQLFEESPVGLLKCKsNGK-IVDVNKRILEILNSP--SKEETLKfNLLES 360
                                       79************7676666.*************66..9999998666554 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       8.8   9.9e+03      61      72 ..      18      29 ..       6      49 .. 0.48
   2 !   17.9   0.1   3.1e-06    0.0034      16     106 .]      60     151 ..      56     151 .. 0.96
   3 !   15.2   0.2   2.1e-05     0.024      12     106 .]     196     297 ..     186     297 .. 0.88
   4 ?    3.8   0.0     0.076        86      63     106 .]     382     423 ..     361     423 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 8.8
                            PAS_10 61 alrtgekdevev 72
                                      +lr++++d ++ 
  gi|298675082|ref|YP_003726832.1| 18 ELRNQNSDLQKR 29
                                      444444443332 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 3.1e-06
                            PAS_10  16 DdnlqirrFtpaakklfklipadv.Grpladihpkkavknveeviealrtgekdevevvvpkngkwvlvrylpyrde 91 
                                       D+n +i+++++a  ++f+l+p++v G +  +i  +++  ++    +  ++++ ++v +++++ + w+ vr  p+ d+
  gi|298675082|ref|YP_003726832.1|  60 DTNHNIIKYNKAGYSFFNLKPEEVaGKKCYEIIGRNKPCKICATSKVYKSKKPEHVVKYIEEMDIWFDVRAYPIFDN 136
                                       99*******************9877**********9999999999******************************** PP

                            PAS_10  92 dgeiaGvvetfvDit 106
                                       +g+   v+e + Dit
  gi|298675082|ref|YP_003726832.1| 137 NGNLTNVMEHLRDIT 151
                                       *************97 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 2.1e-05
                            PAS_10  12 ltflDdnlqirrFtpaakklfklipad.vGrpl.adihpkkavknveeviealrtgekdevevvvp.....kngkwv 81 
                                       ++ lD+n +i   +++  +++ + +++ +G ++ ++++p++++++v+++ ++l++g +d+ ++  p      +++++
  gi|298675082|ref|YP_003726832.1| 196 IIVLDNNQRIELINNKGCEVLGYDKTElIGKNMyENFVPREYMDKVNNISNNLIQGHEDNNNFINPiigknGEERII 272
                                       7899***********99999999887647*9995689**************************99999865568999 PP

                            PAS_10  82 lvrylpyrdedgeiaGvvetfvDit 106
                                         + + ++d++g+i G++   +D+t
  gi|298675082|ref|YP_003726832.1| 273 SWYNSVLKDDNGSIIGTLSSGIDVT 297
                                       999999**********998888875 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.076
                            PAS_10  63 rtgekdevevvvpkngkwvlvrylpyrdedgeiaGvvetfvDit 106
                                        ++e+++ +++   +++w++ ++ p+ de+g+++  ++ + Dit
  gi|298675082|ref|YP_003726832.1| 382 VKNERKYISFW--GRKRWIYYKIVPLGDEEGNVNESIIALDDIT 423
                                       33344444444..88*****************998888887775 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.3   1.5e+03       2      30 ..      66      92 ..      65      94 .. 0.88
   2 ?    3.8   0.0     0.065        73      66      85 ..     124     143 ..     123     145 .. 0.90
   3 !   24.5   0.0   2.2e-08   2.5e-05       4      84 ..     208     288 ..     205     292 .. 0.91
   4 ?   -0.3   0.0       1.2   1.3e+03      38      82 ..     368     412 ..     333     416 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.3
                             PAS_3  2 iyvserveeilGyspeellgkveswldlv 30
                                      i  +++ +  + + pee+ gk  ++++++
  gi|298675082|ref|YP_003726832.1| 66 IKYNKAGYSFFNLKPEEVAGK--KCYEII 92
                                      7789999999***********..998876 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.065
                             PAS_3  66 rwveararvirdengkpvrv 85 
                                       +w++ ra++i+d+ng+ + v
  gi|298675082|ref|YP_003726832.1| 124 IWFDVRAYPIFDNNGNLTNV 143
                                       6**************98765 PP

  == domain 3  score: 24.5 bits;  conditional E-value: 2.2e-08
                             PAS_3   4 vserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvirden 79 
                                       ++++ +e+lGy++ el+gk + + ++v  e  ++v++  ++++++ e   ++   i+ k+Ge r ++++ +v++d+n
  gi|298675082|ref|YP_003726832.1| 208 INNKGCEVLGYDKTELIGK-NMYENFVPREYMDKVNNISNNLIQGHEdNNNFINPIIGKNGEERIISWYNSVLKDDN 283
                                       688999*************.88888888888************9999666999************************ PP

                             PAS_3  80 gkpvr 84 
                                       g ++ 
  gi|298675082|ref|YP_003726832.1| 284 GSIIG 288
                                       *9875 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 1.2
                             PAS_3  38 vrealqealkkgepyegeyRirrkdGeyrwveararvirdengkp 82 
                                       + e+l +a+++++ ++ e +++   G  rw+  +++++ de+g++
  gi|298675082|ref|YP_003726832.1| 368 FDEELRKAFSNNRIVKNERKYISFWGRKRWIYYKIVPLGDEEGNV 412
                                       556666777777777777777777889999999999999999987 PP

>> PAS_6  YheO-like PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.3   5.7e-06    0.0064      43     113 ..     234     303 ..     206     305 .. 0.89
   2 ?    2.9   0.1     0.085        95      53      86 ..     417     450 ..     409     459 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.7e-06
                             PAS_6  43 gRkvGdpltdlvlellkeeeeeeedvlvnyktktkdgkilksstifirdekgkliglLCiNldlskleaae 113
                                        R+  d+++++  +l++ +e++ ++ + +  +k+ +++i+     +++d++g++ig L+  +d+++l +++
  gi|298675082|ref|YP_003726832.1| 234 PREYMDKVNNISNNLIQGHEDN-NNFINPIIGKNGEERIISWYNSVLKDDNGSIIGTLSSGIDVTELINLK 303
                                       5778888899999999988888.99*****************************************99876 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.085
                             PAS_6  53 lvlellkeeeeeeedvlvnyktktkdgkilksst 86 
                                       ++l+ +++++e+e++ l+ y+  +k +++lks +
  gi|298675082|ref|YP_003726832.1| 417 IALDDITQRKETETQLLKYYDDLQKANRELKSLS 450
                                       68899999999999999999999********987 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   1.7e-06    0.0019       5      79 ..     573     645 ..     569     667 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.7e-06
                       HATPase_c_3   5 kAlaelvdNsld..AdaenvkievnknrgktgeivieDdGkGmseeelknalrlatsskeakrkstslGkkGiGlkl 79 
                                       ++ + ++dN+     +  +v++++ ++   +  i + D+G G++ee   n + l  ++ +  ++++ ++  G G+ +
  gi|298675082|ref|YP_003726832.1| 573 QVFVHILDNACKftPSGGKVDVHAFDD--GNLHIIVSDNGIGIDEESANNIFDLFYQKDD--SSKRRYSGTGAGMYF 645
                                       566778888877334455566666665..579*********************9999888..478888888999765 PP

>> LUC7  LUC7 N_terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   1.7   1.7e-05     0.019     159     213 ..     148     207 ..       3     240 .. 0.77
   2 ?    3.0   0.1     0.063        70     147     180 ..     408     452 ..     401     500 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.7e-05
                                       XXXXXXXXXXXXXXXXXXXX.......XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              LUC7 159 keveelkeekeeleqqyeaaa.....aneeseasqekkmkvCeiCGaflivgDaqqRied 213
                                       + + + k+  +++++q ++ +     ++++ e   +k  k  +i+Ga++iv D++qRie 
  gi|298675082|ref|YP_003726832.1| 148 RDITQEKKLENKIKDQRNNLEkivyeRTKQLEIERDKAQKYLDISGAIIIVLDNNQRIEL 207
                                       33333333333333333332266666789999999***********************84 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.063
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX............. CS
                              LUC7 147 eeGkVdeaqklmkeveelkeekeeleqqyeaaa...........a 180
                                       eeG+V+e+   ++ + + ke+ ++l + y++ +            
  gi|298675082|ref|YP_003726832.1| 408 EEGNVNESIIALDDITQRKETETQLLKYYDDLQkanrelkslseM 452
                                       69************************9999887444444444430 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.3       3.7   4.1e+03      14      42 ..     140     167 ..     137     191 .. 0.69
   2 ?   -2.0   0.3       3.1   3.5e+03      27      52 ..     255     280 ..     241     319 .. 0.61
   3 !   16.7   0.1   4.4e-06    0.0049       6      90 ..     571     662 ..     566     673 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.7
                       HATPase_c_5  14 LdNAieacskieeekrfIrltvrekkksl 42 
                                       L N +e  ++i++ +++++ +++ + ++l
  gi|298675082|ref|YP_003726832.1| 140 LTNVMEHLRDITQ-EKKLENKIKDQRNNL 167
                                       5677788888775.777777777666554 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.1
                       HATPase_c_5  27 ekrfIrltvrekkksliisieNsyeg 52 
                                       ++ fI+  + ++ +  iis  Ns+ +
  gi|298675082|ref|YP_003726832.1| 255 NNNFINPIIGKNGEERIISWYNSVLK 280
                                       55677777777777777777776544 PP

  == domain 3  score: 16.7 bits;  conditional E-value: 4.4e-06
                       HATPase_c_5   6 lcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyegek...........kklesskskkeehGiGl 71 
                                       l  ++  +LdNA   c+ ++ +  ++++++  + +  ii  +N +  ++           +k  ssk++ +  G G+
  gi|298675082|ref|YP_003726832.1| 571 LEQVFVHILDNA---CKFTP-SGGKVDVHAFDDGNLHIIVSDNGIGIDEesannifdlfyQKDDSSKRRYSGTGAGM 643
                                       567899999997...66666.4789******************976633234455666667777999999999**** PP

                       HATPase_c_5  72 ksireivkkykgnlsieae 90 
                                          ++i++k++gn+++e +
  gi|298675082|ref|YP_003726832.1| 644 YFCKKIIEKHHGNIWVESK 662
                                       **************99875 PP

>> DUF1151  Protein of unknown function (DUF1151)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   1.6       3.2   3.6e+03      55      80 ..       7      32 ..       1      41 [. 0.54
   2 ?   14.1   0.2   2.9e-05     0.033      41      94 ..     136     186 ..     123     192 .. 0.83
   3 ?   -3.2   0.4       7.2   8.1e+03      75      97 ..     429     451 ..     422     466 .. 0.48

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.2
                           DUF1151 55 eqvlkqkkeeeeakkkkseLeqelek 80
                                      +   +  +e +e ++++s+L++ l +
  gi|298675082|ref|YP_003726832.1|  7 KSKNQLLQEIKELRNQNSDLQKRLTE 32
                                      33333344445555566666666654 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 2.9e-05
                           DUF1151  41 eKpELqrvlekrkeeqvlkqkkeeeeakkkkseLeqelekraqrleelekeeek 94 
                                       +   L  v+e+ +   + ++kk e++ k+++++Le+ + +r ++le  e+++ +
  gi|298675082|ref|YP_003726832.1| 136 NNGNLTNVMEHLRD--ITQEKKLENKIKDQRNNLEKIVYERTKQLE-IERDKAQ 186
                                       5567999******6..9999999**********************9.4444433 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 7.2
                           DUF1151  75 eqelekraqrleelekeeekqke 97 
                                       e++l+k    l+++++e ++ +e
  gi|298675082|ref|YP_003726832.1| 429 ETQLLKYYDDLQKANRELKSLSE 451
                                       55555555555544444444333 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.39   4.4e+02      11      55 ..      59     102 ..      50     158 .. 0.79
   2 ?    5.0   0.0     0.023        26       8      33 ..     196     221 ..     189     233 .. 0.86
   3 ?    2.3   0.1      0.16   1.8e+02       7      33 ..     323     349 ..     317     430 .. 0.63

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.39
                             PAS_7  11 fDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefg 55 
                                        D +++++ +N+   + ++l +e v +g++  e++  n+  + ++
  gi|298675082|ref|YP_003726832.1|  59 QDTNHNIIKYNKAGYSFFNLKPEEV-AGKKCYEIIGRNKPCKICA 102
                                       6889999999999999999999999.8999999998776554444 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.023
                             PAS_7   8 isvfDadlrLvawNrrylelldlpee 33 
                                       i+v+D+++r+ ++N++ +e+l++ ++
  gi|298675082|ref|YP_003726832.1| 196 IIVLDNNQRIELINNKGCEVLGYDKT 221
                                       79*******************99876 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.16
                             PAS_7   7 GisvfDadlrLvawNrrylelldlpee 33 
                                       G++   +++++v +N+r+le+l+ p++
  gi|298675082|ref|YP_003726832.1| 323 GLLKCKSNGKIVDVNKRILEILNSPSK 349
                                       555566777888888888888888865 PP

>> NYD-SP28_assoc  Sperm tail C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   3.0   0.00023      0.26      34      58 ..       8      32 ..       7      33 .. 0.91
   2 ?    2.8   0.5      0.11   1.2e+02      39      55 ..     429     449 ..     422     451 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00023
                    NYD-SP28_assoc 34 eRaklieetesLekqNeeLrnlLkq 58
                                       + +l++e+++L++qN+ L+++L++
  gi|298675082|ref|YP_003726832.1|  8 SKNQLLQEIKELRNQNSDLQKRLTE 32
                                      5789******************987 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.11
                    NYD-SP28_assoc  39 ieet....esLekqNeeLrnl 55 
                                        ++     + L+k N eL++l
  gi|298675082|ref|YP_003726832.1| 429 ETQLlkyyDDLQKANRELKSL 449
                                       444444449*********987 PP

>> Flu_NS2  Influenza non-structural protein (NS2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1       1.2   1.4e+03      35      61 ..       5      31 ..       1      52 [. 0.66
   2 ?   -2.0   0.2       4.1   4.6e+03      44      73 ..     142     173 ..     135     185 .. 0.65
   3 ?    9.9   0.1   0.00079      0.88      19      89 ..     475     545 ..     467     549 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.2
                                      X-CHHHHHHHHHHHHHHHHHHHHHC-- CS
                           Flu_NS2 35 nekwreqlgqkreeirllieelrhklk 61
                                      +ek ++ql q   e+r    +l+ +l 
  gi|298675082|ref|YP_003726832.1|  5 DEKSKNQLLQEIKELRNQNSDLQKRLT 31
                                      677778888888777777766665443 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.1
                                       HHHHHHHHHHHHHH..HC----TTSHHHHHHH CS
                           Flu_NS2  44 qkreeirllieelr..hklkiaessieqivsl 73 
                                         +e++r +++e +   k+k   + +e+iv+ 
  gi|298675082|ref|YP_003726832.1| 142 NVMEHLRDITQEKKleNKIKDQRNNLEKIVYE 173
                                       55677777777655336666666777888764 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00079
                                       XXXXXXXXXXXXXXXXX-CHHHHHHHHHHHHHHHHHHHHHC---.-TTSHHHHHHHHHHHHHHHHHHHHHH- CS
                           Flu_NS2  19 gelvmkstdlhslqnrnekwreqlgqkreeirllieelrhklki.aessieqivslsllelllevkdvvevy 89 
                                       ++l+     l  l++++ k    + q  e +r+li+ l h   + +++ i+    +sl  ll +v  +  vy
  gi|298675082|ref|YP_003726832.1| 475 SNLL-NNKKLGELNDKQSKAVSVISQSCERLRWLIDTLIHINILeSDNGIQHTQKISLSSLLNNVVSENSVY 545
                                       5555.556667788999999999****************865542567787777777777777776666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (677 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1953  (0.10893); expected 358.6 (0.02)
Passed bias filter:                      777  (0.0433376); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.68u 0.27s 00:00:00.95 Elapsed: 00:00:00.44
# Mc/sec: 4615.79
//
Query:       gi|298675083|ref|YP_003726833.1|  [L=862]
Description: PAS/PAC sensor signal transduction histidine kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.1e-47  158.8   2.0    1.5e-17   63.6   0.1    4.9  5  PAS_3        PAS fold
    4.4e-47  158.6   7.0    1.1e-10   41.7   0.0    5.8  6  PAS_9        PAS domain
    9.6e-39  131.9   0.0      6e-12   45.6   0.0    5.4  5  PAS          PAS fold
    2.2e-38  130.9   0.0    5.7e-08   33.0   0.0    5.2  5  PAS_4        PAS fold
    4.2e-20   72.3   0.1    1.2e-19   70.8   0.1    1.9  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    5.7e-17   61.3   0.0    2.3e-06   27.5   0.0    5.5  5  PAS_8        PAS domain
    7.5e-07   29.3   0.1      0.099   12.8   0.0    4.2  4  PAS_7        PAS fold
    2.9e-06   27.4   0.0    5.9e-05   23.2   0.0    2.7  2  PAS_11       PAS domain
    5.5e-05   23.1   0.5    0.00026   21.0   0.1    2.4  2  HisKA        His Kinase A (phospho-acceptor) domain
     0.0046   16.9   0.0      0.031   14.2   0.0    2.2  2  HATPase_c_2  Histidine kinase-like ATPase domain
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.057   13.4   0.0    2.3  1  NOGCT        NOGCT (NUC087) domain
      0.021   14.6   0.1      0.067   13.0   0.1    1.8  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
       0.11   12.2   0.6       0.44   10.3   0.2    2.3  2  SPOB_a       Sensor_kinase_SpoOB-type, alpha-helical domain


Domain annotation for each model (and alignments):
>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0    0.0064       8.9       4      85 ..      29     108 ..      28     112 .. 0.83
   2 !   63.6   0.1   1.1e-20   1.5e-17       2      86 ..     153     235 ..     152     237 .. 0.97
   3 !   59.1   0.1   2.9e-19   4.1e-16       3      89 .]     278     367 ..     276     367 .. 0.93
   4 ?   -2.1   0.0       3.6   4.9e+03      66      86 ..     468     489 ..     466     492 .. 0.84
   5 !   25.1   0.0   1.2e-08   1.6e-05       3      86 ..     534     615 ..     532     618 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0064
                             PAS_3   4 vserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvirden 79 
                                       ++++  + lG+ + +l++   +++d++  e+ e + +  ++++k++e  y++e+ +++  Ge   ++ + ++i d+ 
  gi|298675083|ref|YP_003726833.1|  29 ANKAHADFLGINKKDLENA--NLYDFLSKEEAESCVKGNKQVFKTKEnTYTEEW-VQNGKGEKKLLSITKSPIIDSC 102
                                       57888999***********..**************************7888777.6666777777777777777777 PP

                             PAS_3  80 gkpvrv 85 
                                       g++ +v
  gi|298675083|ref|YP_003726833.1| 103 GNVEFV 108
                                       776665 PP

  == domain 2  score: 63.6 bits;  conditional E-value: 1.1e-20
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       +y+ ++ e ++Gy pe l+gk  ++ld+vhp+D e + e++q+ l++  p ++eyR+++ dG y+w+e+ ++vi+d+
  gi|298675083|ref|YP_003726833.1| 153 VYAGPSHELVIGYKPENLTGK--NVLDFVHPDDYEWMVEEYQQFLQTLNPKKVEYRYLHSDGYYIWLETIGNVIHDD 227
                                       79999****************..***********************99999************************** PP

                             PAS_3  79 ngkpvrvi 86 
                                        g++ rv+
  gi|298675083|ref|YP_003726833.1| 228 YGNVKRVV 235
                                       ****9986 PP

  == domain 3  score: 59.1 bits;  conditional E-value: 2.9e-19
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge..pyege...yRirrkdGeyrwveararv 74 
                                       yvse+v +++Gys+ ++++++ s++d++ p+D+ rv +++  + ++    ++  +   yRi++k+  +rwv++r+++
  gi|298675083|ref|YP_003726833.1| 278 YVSENVIDTFGYSAGDFTANKLSYADVINPDDLGRVVSEVYYYSNDPDcvKF--QhkpYRIITKNENIRWVDDRTYI 352
                                       9*******************************************99884555..4447******************* PP

                             PAS_3  75 irdengkpvrvigva 89 
                                       +rd++g+++ ++g++
  gi|298675083|ref|YP_003726833.1| 353 LRDDDGNVTNYQGII 367
                                       *************85 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 3.6
                             PAS_3  66 rwveararvi.rdengkpvrvi 86 
                                        w+e + +++ + +ng++  v+
  gi|298675083|ref|YP_003726833.1| 468 KWFEIYSYPViNGDNGEISSVV 489
                                       6999999999999999998876 PP

  == domain 5  score: 25.1 bits;  conditional E-value: 1.2e-08
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeD.rervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       +v+++++ i+Gy ++el gk   +  +v pe+  +++ + +++ +k+  +++ge+ ++ kd     + a+a+ ++d 
  gi|298675083|ref|YP_003726833.1| 534 SVNPAYCSIYGYNSDELVGK---HFTVVVPEEyKKELSSLHDRFIKGIDELSGEWPVIDKDSNPKTILATATKVQDF 607
                                       69******************...77777777735556666666776666*************************999 PP

                             PAS_3  79 ngkpvrvi 86 
                                       + +p +v 
  gi|298675083|ref|YP_003726833.1| 608 DDEPKKVT 615
                                       99998875 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.1   8.5e-09   1.2e-05      16     104 .]      29     117 ..      22     117 .. 0.92
   2 !   41.7   0.0   7.6e-14   1.1e-10       2     104 .]     141     243 ..     140     243 .. 0.89
   3 !   24.7   0.0   1.5e-08   2.1e-05       4     104 .]     266     372 ..     262     372 .. 0.82
   4 !   26.7   0.0   3.7e-09   5.1e-06       2     104 .]     396     497 ..     395     497 .. 0.90
   5 !   39.3   0.0   4.3e-13     6e-10       1     103 [.     520     621 ..     520     622 .. 0.93
   6 ?   -3.0   0.1       6.3   8.6e+03      43      82 ..     715     752 ..     684     762 .. 0.64

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 8.5e-09
                             PAS_9  16 aNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwvlltaspvkdddg 90 
                                       aN+a +++lG +++++ + ++ d++  +++++  +  ++++++++      e   ++ +ge+ +  +t sp++d+ g
  gi|298675083|ref|YP_003726833.1|  29 ANKAHADFLGINKKDLENANLYDFLskEEAESCVKGNKQVFKTKE--NTYTEEWVQNGKGEKKLLSITKSPIIDSCG 103
                                       8************************88888888888888888888..888888888888999999**********99 PP

                             PAS_9  91 elvgiivilrDite 104
                                       ++ ++ +  +Dite
  gi|298675083|ref|YP_003726833.1| 104 NVEFVTCSAEDITE 117
                                       *************8 PP

  == domain 2  score: 41.7 bits;  conditional E-value: 7.6e-14
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetf 76 
                                       d+++++++ g  +ya ++ + ++Gy+pe + gk++ d++  ++ +   e+ +++l+++   ++ ve+ + +++g ++
  gi|298675083|ref|YP_003726833.1| 141 DMVALTDKYGYFVYAGPSHELVIGYKPENLTGKNVLDFVhpDDYEWMVEEYQQFLQTLN--PKKVEYRYLHSDGYYI 215
                                       567788999******************************55555555666666666666..**************** PP

                             PAS_9  77 wvlltaspvkdddgelvgiivilrDite 104
                                       w +     ++dd g+++++++ +rDite
  gi|298675083|ref|YP_003726833.1| 216 WLETIGNVIHDDYGNVKRVVFSSRDITE 243
                                       ***************************8 PP

  == domain 3  score: 24.7 bits;  conditional E-value: 1.5e-08
                             PAS_9   4 ilidnpdgril.yaNeaalrllGyspeevlgks..itdlfvtdpeanerlraaleqgrk....kerevevvlirkng 73 
                                       +l  n+dg  + y++e +++ +Gys+ ++   +  + d++ ++++  + +++++    +    k++++++ +i+kn+
  gi|298675083|ref|YP_003726833.1| 266 FLWANEDGWPVkYVSENVIDTFGYSAGDFTANKlsYADVI-NPDDLGRVVSEVYYYSNDpdcvKFQHKPYRIITKNE 341
                                       44489***9999****************766655599999.444444444444444444559*************** PP

                             PAS_9  74 etfwvlltaspvkdddgelvgiivilrDite 104
                                       +  wv+ + + ++dddg+++ + +i+ Dite
  gi|298675083|ref|YP_003726833.1| 342 NIRWVDDRTYILRDDDGNVTNYQGIILDITE 372
                                       ******999999******************8 PP

  == domain 4  score: 26.7 bits;  conditional E-value: 3.7e-09
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspee.vlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirknget 75 
                                       dgi ++++d++i+++N +++++  y ++  + gk++   +  +++p +++  + a+++g+    + ++v   +  ++
  gi|298675083|ref|YP_003726833.1| 396 DGISVIDSDFNIVRVNSKMNEW--YEENVpLEGKKCYHAYqyYESPCEKCPTDSAFRTGK---TQMDIVTGLPGSKP 467
                                       7999999***************..66666799****************************...6667777777789* PP

                             PAS_9  76 fwvlltaspvkdd.dgelvgiivilrDite 104
                                        w+++  +pv+++ +ge+ +++ ++rDi++
  gi|298675083|ref|YP_003726833.1| 468 KWFEIYSYPVINGdNGEISSVVEFVRDISD 497
                                       *************9999999********96 PP

  == domain 5  score: 39.3 bits;  conditional E-value: 4.3e-13
                             PAS_9   1 pdgilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirknget 75 
                                       p+gi+i++++g   ++N+a + ++Gy+++e++gk++t ++  + ++e  +  +++++ ++  e ++e   i+k+ ++
  gi|298675083|ref|YP_003726833.1| 520 PVGICITDKNGYFDSVNPAYCSIYGYNSDELVGKHFTVVVpeEYKKELSSLHDRFIKGID--ELSGEWPVIDKDSNP 594
                                       78*********999**************************88888888888888999999..*************** PP

                             PAS_9  76 fwvlltaspvkdddgelvgiivilrDit 103
                                         +l+ta+ v+d d+e +  + +++Dit
  gi|298675083|ref|YP_003726833.1| 595 KTILATATKVQDFDDEPKK-VTFVIDIT 621
                                       **********999999998.78999998 PP

  == domain 6  score: -3.0 bits;  conditional E-value: 6.3
                             PAS_9  43 dpeanerlraaleqgrkkerevevvlirkngetfwvllta 82 
                                         +  e ++++++++r + +e+++++   n+++++  +++
  gi|298675083|ref|YP_003726833.1| 715 RFDIGEIIEEVIDNMRFSMYEKNIDIKFVNNGPYY--ANL 752
                                       44556677777777776666666666666667776..444 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   4.9e-05     0.068      26     113 .]      29     115 ..      28     115 .. 0.93
   2 !   41.6   0.0   7.2e-14   9.9e-11       2     113 .]     131     241 ..     130     241 .. 0.96
   3 !   15.9   0.0   7.1e-06    0.0098       5     113 .]     256     370 ..     253     370 .. 0.91
   4 !    8.5   0.1    0.0014       1.9       2      32 ..     386     416 ..     385     417 .. 0.91
   5 !   45.6   0.0   4.3e-15     6e-12       2     110 ..     511     618 ..     510     620 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.9e-05
                                       ECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEEEEEEEEETTEE CS
                               PAS  26 vNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfklrdgrpihlevraspvrdagge 102
                                       +N+a +++lG++ +++ + +l+d+++ e+ +  ++  +q+ +++e+  ++e   +  +g+++ l ++ sp++d  g+
  gi|298675083|ref|YP_003726833.1|  29 ANKAHADFLGINKKDLENANLYDFLSKEEAESCVKGNKQVFKTKENTYTEEWVQNG-KGEKKLLSITKSPIIDSCGN 104
                                       79*************************98888888889999999999999999999.******************** PP

                                       EEEEEEEEEES CS
                               PAS 103 ilgflgvlrdi 113
                                       +  + + + di
  gi|298675083|ref|YP_003726833.1| 105 VEFVTCSAEDI 115
                                       *9999999887 PP

  == domain 2  score: 41.6 bits;  conditional E-value: 7.2e-14
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                        +r+i e++ d++ ++D+ g ++y+ ++ e   G+++e + gk++ld++h++d + ++e+++q l++ ++++ + + 
  gi|298675083|ref|YP_003726833.1| 131 LFREITENMQDMVALTDKYGYFVYAGPSHELVIGYKPENLTGKNVLDFVHPDDYEWMVEEYQQFLQTLNPKKVEYRY 207
                                       6899*************************************************99***************9999999 PP

                                       EECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  79 fklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       +   dg +i+le+  + + d  g+++ +++  rdi
  gi|298675083|ref|YP_003726833.1| 208 LHS-DGYYIWLETIGNVIHDDYGNVKRVVFSSRDI 241
                                       999.**********************999998887 PP

  == domain 3  score: 15.9 bits;  conditional E-value: 7.1e-06
                                       HHHHHSSSEEEEEE.TTSB.EEEECHHHHHHHSSTH.HHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   5 aileslpdpifvvD.edgr.ilyvNaaaeellGlsr.eevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       +i++s+p+  f++  edg+ + yv+++  + +G+s+ +   +k  + +++++dd  ++     ++++  ++  ++++
  gi|298675083|ref|YP_003726833.1| 256 SIINSSPAVAFLWAnEDGWpVKYVSENVIDTFGYSAgDFTANKLSYADVINPDDLGRVVSEVYYYSNDPDCVKFQHK 332
                                       69***********99****667**************99999999999999999988888888888888888888887 PP

                                       EEC...TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  79 fkl...rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                         +   ++  +++++ r+  +rd +g+++ + g++ di
  gi|298675083|ref|YP_003726833.1| 333 PYRiitKNENIRWVDDRTYILRDDDGNVTNYQGIILDI 370
                                       777999****************************9997 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.0014
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHH CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaee 32 
                                       +l+ ++es+ d+i v+D d +i+ vN++++e
  gi|298675083|ref|YP_003726833.1| 386 MLDDVFESIQDGISVIDSDFNIVRVNSKMNE 416
                                       567789**********************976 PP

  == domain 5  score: 45.6 bits;  conditional E-value: 4.3e-15
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       +l+ i++++p++i+++D++g +  vN+a++++ G++ +e++gk++  +++ee+  el +l  + ++   e ++++  
  gi|298675083|ref|YP_003726833.1| 511 MLQDIIQNIPVGICITDKNGYFDSVNPAYCSIYGYNSDELVGKHFTVVVPEEYKKELSSLHDRFIKGIDELSGEWPV 587
                                       7899***********************************************99999999999999999999999999 PP

                                       EECTTSSEEEEEEEEEEEEETTEEEEEEEEEE CS
                               PAS  79 fklrdgrpihlevraspvrdaggeilgflgvl 110
                                       +++ d  p+ ++ +a++v d ++e++ + +v+
  gi|298675083|ref|YP_003726833.1| 588 IDK-DSNPKTILATATKVQDFDDEPKKVTFVI 618
                                       999.*******************998777765 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0     3e-08   4.2e-05      14     110 .]      23     120 ..      12     120 .. 0.95
   2 !   32.0   0.0   8.6e-11   1.2e-07       2     109 ..     137     245 ..     136     246 .. 0.92
   3 !    9.1   0.0    0.0011       1.5       3     109 ..     260     374 ..     258     375 .. 0.81
   4 !   26.7   0.0   3.7e-09   5.1e-06       1     109 [.     391     499 ..     391     500 .. 0.92
   5 !   33.0   0.0   4.1e-11   5.7e-08       3     109 ..     518     624 ..     516     625 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 3e-08
                             PAS_4  14 dgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pgeerhyelrllPlr 89 
                                       ++++  aN+a a+ +g+  ++l +  l+++l++e a+      ++v +++e  +++e +    ge + ++++++P+ 
  gi|298675083|ref|YP_003726833.1|  23 EYNYGGANKAHADFLGINKKDLENANLYDFLSKEEAESCVKGNKQVFKTKENTYTEEWVQNgKGEKKLLSITKSPII 99 
                                       678888***************************************************99999*************** PP

                             PAS_4  90 desGevigvlvisrDiTerrr 110
                                       d+ G v +v + + DiTe r+
  gi|298675083|ref|YP_003726833.1| 100 DSCGNVEFVTCSAEDITEKRE 120
                                       ******************985 PP

  == domain 2  score: 32.0 bits;  conditional E-value: 8.6e-11
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgee 78 
                                       ++++d++a  d+ g ++ya ++ + ++g+ pe l+Gk + +++ ++d +   + +++ l++  p + +  +l++++ 
  gi|298675083|ref|YP_003726833.1| 137 ENMQDMVALTDKYGYFVYAGPSHELVIGYKPENLTGKNVLDFVHPDDYEWMVEEYQQFLQTLNPKKVEYRYLHSDGY 213
                                       799******************9888****************99999***************************5555 PP

                             PAS_4  79 rhyelrl.lPlrdesGevigvlvisrDiTerr 109
                                        +++ ++ + ++d+ G v  v++ srDiTe +
  gi|298675083|ref|YP_003726833.1| 214 YIWLETIgNVIHDDYGNVKRVVFSSRDITEHK 245
                                       55555555*********************976 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0011
                             PAS_4   3 slpdalavl.dpdg.rvlyaNaaaaelfgappeellGktla..ellpeedaarleralrrvlegeepiefleelll. 74 
                                       s+p++ + + ++dg  v y++++  + fg+++ +++  +l   ++ +++d +r+ + +       + ++f++ + + 
  gi|298675083|ref|YP_003726833.1| 260 SSPAVAFLWaNEDGwPVKYVSENVIDTFGYSAGDFTANKLSyaDVINPDDLGRVVSEVYYYSNDPDCVKFQHKPYRi 336
                                       56666666666666235677777777788888888877777778888888888888888888889999999988889 PP

                             PAS_4  75 ...pgeerhyelrllPlrdesGevigvlvisrDiTerr 109
                                          +   r+++ r + lrd++G v  + +i+ DiTe +
  gi|298675083|ref|YP_003726833.1| 337 itkNENIRWVDDRTYILRDDDGNVTNYQGIILDITENK 374
                                       9999*******************************975 PP

  == domain 4  score: 26.7 bits;  conditional E-value: 3.7e-09
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       ++s++d++ v+d+d++++++N  + e++  +   l Gk+++  +     +   ++ + + ++++++ +  + l++ +
  gi|298675083|ref|YP_003726833.1| 391 FESIQDGISVIDSDFNIVRVNSKMNEWY-EENVPLEGKKCYHAYQYYESPCEKCPTDSAFRTGKTQMDIVTGLPGSK 466
                                       79************************65.5788********98888899999************************* PP

                             PAS_4  78 erhyelrllPlrd.esGevigvlvisrDiTerr 109
                                       ++++e+  +P+ + ++Ge+  v++++rDi++r+
  gi|298675083|ref|YP_003726833.1| 467 PKWFEIYSYPVINgDNGEISSVVEFVRDISDRV 499
                                       **********86626677************997 PP

  == domain 5  score: 33.0 bits;  conditional E-value: 4.1e-11
                             PAS_4   3 slpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pgee 78 
                                       ++p+++++ d++g +  +N+a+++++g+  +el+Gk++  ++pee + +l++  +r ++g + ++ +  + + +  +
  gi|298675083|ref|YP_003726833.1| 518 NIPVGICITDKNGYFDSVNPAYCSIYGYNSDELVGKHFTVVVPEEYKKELSSLHDRFIKGIDELSGEWPVIDkDSNP 594
                                       89**********************************************************99999999999999999 PP

                             PAS_4  79 rhyelrllPlrdesGevigvlvisrDiTerr 109
                                       ++++ +++ + d + e    + +++DiT r+
  gi|298675083|ref|YP_003726833.1| 595 KTILATATKVQDFDDE-PKKVTFVIDITGRK 624
                                       9999999999998888.55556778888887 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.8   0.1     9e-23   1.2e-19       6     110 ..     756     859 ..     751     861 .. 0.92

  Alignments for each domain:
  == domain 1  score: 70.8 bits;  conditional E-value: 9e-23
                                       HHHHHHHHHHHHHHHHSTTTEEEEEEEEEE.TEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHH CS
                         HATPase_c   6 LrqiisnlvdNavkfatkageieveikase.ddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsiv 81 
                                       ++q++ nl+ N++k++++++ i+vei   + d+ +++++D G+Gi+++d k +f++f +  ++  + +g G+Gl+iv
  gi|298675083|ref|YP_003726833.1| 756 IEQAFTNLINNSIKYNPENSGIKVEIFD-DiDYWKVQIKDEGPGISEQDKKYIFDRFKR--GEGKKVSGKGIGLAIV 829
                                       689************99**********4.359***************************..5666778********* PP

                                       HHHHHHTTTEEEEEEET.TTEEEEEEEEES CS
                         HATPase_c  82 kklvelmgGeiwvesep.grGttftftlpl 110
                                       +k+v+ ++G++ ve++p g+G+ f+++l++
  gi|298675083|ref|YP_003726833.1| 830 QKIVDIHEGSVGVEDNPdGKGSMFWVKLKK 859
                                       *************99999*********986 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.51     7e+02      26      42 ..      29      46 ..       8      70 .. 0.70
   2 !    7.2   0.0    0.0039       5.3       1      63 [.     130     195 ..     130     199 .. 0.76
   3 ?    3.2   0.0     0.068        94       5      55 ..     256     308 ..     254     314 .. 0.77
   4 !   14.8   0.0   1.6e-05     0.022       5      35 ..     389     419 ..     385     450 .. 0.77
   5 !   27.5   0.0   1.7e-09   2.3e-06       3      47 ..     512     557 ..     510     574 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.51
                             PAS_8 26 vNqaalellGys.adlkg 42
                                      +N+a +++lG + +dl  
  gi|298675083|ref|YP_003726833.1| 29 ANKAHADFLGINkKDLEN 46
                                      9*********66555444 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0039
                             PAS_8   1 erlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellgqllpvlrplle..daeqll 63 
                                       e +r + e+++d +a++d  g  +v++ ++ +   Gy+ + l g+ + ++++  ++++   +++q+l
  gi|298675083|ref|YP_003726833.1| 130 ELFREITENMQDMVALTDkYGY-FVYAGPSHELVIGYKpENLTGKNVLDFVHPDDYEWMveEYQQFL 195
                                       6799**************7777.***99999999999977777777764444444444447777766 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.068
                             PAS_8   5 alfesspdgiav.vd.lgdrivdvNqaalellGys.adlkgellgqllpvlrpl 55 
                                       ++++ssp   ++ ++ +g+ + +v +  ++ +Gys  d+ + +l  + +v++p 
  gi|298675083|ref|YP_003726833.1| 256 SIINSSPAVAFLwANeDGWPVKYVSENVIDTFGYSaGDFTANKL-SYADVINPD 308
                                       68888888555524433336999************999999999.888887775 PP

  == domain 4  score: 14.8 bits;  conditional E-value: 1.6e-05
                             PAS_8   5 alfesspdgiavvd.lgdrivdvNqaalellG 35 
                                        +fes++dgi v+d +  +iv vN ++ e + 
  gi|298675083|ref|YP_003726833.1| 389 DVFESIQDGISVIDsDF-NIVRVNSKMNEWYE 419
                                       69************444.6******9988776 PP

  == domain 5  score: 27.5 bits;  conditional E-value: 1.7e-09
                             PAS_8   3 lralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellgq 47 
                                       l+ ++ ++p+gi+++d +g  +  vN+a++ ++Gy+ ++l g+ + +
  gi|298675083|ref|YP_003726833.1| 512 LQDIIQNIPVGICITDkNGY-FDSVNPAYCSIYGYNsDELVGKHFTV 557
                                       7899************9999.***************66666654433 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.76   1.1e+03      79     114 ..      82     122 ..      48     123 .. 0.64
   2 ?   -2.3   0.0       3.6     5e+03     101     114 ..     235     248 ..     191     249 .. 0.86
   3 !   10.3   0.0   0.00042      0.58       1      28 [.     391     418 ..     391     423 .. 0.90
   4 !   12.8   0.0   7.2e-05     0.099       1      45 [.     516     559 ..     516     578 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.76
                             PAS_7  79 ererpdgrvievrgnplpdgG....fVt.tytDiTerrrae 114
                                       +  + + + ++++++p+ d +    fVt + +DiTe+r+ e
  gi|298675083|ref|YP_003726833.1|  82 QNGKGEKKLLSITKSPIIDSCgnveFVTcSAEDITEKREYE 122
                                       44444556777777777553323334442568****99987 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.6
                             PAS_7 101 VttytDiTerrrae 114
                                       V +  DiTe+++ e
  gi|298675083|ref|YP_003726833.1| 235 VFSSRDITEHKELE 248
                                       67788999999866 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00042
                             PAS_7   1 lenmsqGisvfDadlrLvawNrrylell 28 
                                       +e++++Gisv+D+d ++v +N+++ e +
  gi|298675083|ref|YP_003726833.1| 391 FESIQDGISVIDSDFNIVRVNSKMNEWY 418
                                       589******************9988765 PP

  == domain 4  score: 12.8 bits;  conditional E-value: 7.2e-05
                             PAS_7   1 lenmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleell 45 
                                       ++n++ Gi++ D+++    +N  y++++++ ++ + vg++++ ++
  gi|298675083|ref|YP_003726833.1| 516 IQNIPVGICITDKNGYFDSVNPAYCSIYGYNSDEL-VGKHFTVVV 559
                                       689***************************99988.898887665 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.43     6e+02      28      64 ..      37      73 ..      33      80 .. 0.83
   2 !   23.2   0.0   4.3e-08   5.9e-05      13     103 ..     151     237 ..     140     246 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.43
                            PAS_11 28 lglekeelvgrsiydLchpqdlstlkshlrevissng 64
                                      lg++k++l +  +yd++++++ ++  +  ++v+ +++
  gi|298675083|ref|YP_003726833.1| 37 LGINKKDLENANLYDFLSKEEAESCVKGNKQVFKTKE 73
                                      589999***************9999999999993333 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 4.3e-08
                            PAS_11  13 kIisvDtsaLrasfslglekeelvgrsiydLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvkvktkskl 89 
                                        ++   +   +++++ g++ e+l+g+ + d++hp+d +++ + +++ + ++ + ++  yR   s++ ++++ t + +
  gi|298675083|ref|YP_003726833.1| 151 YFVYAGP---SHELVIGYKPENLTGKNVLDFVHPDDYEWMVEEYQQFL-QTLNPKKVEYRYLHSDGYYIWLETIGNV 223
                                       5666666...889999********************************.999999999***************9999 PP

                            PAS_11  90 fknqksneqdfima 103
                                         + + n   ++ +
  gi|298675083|ref|YP_003726833.1| 224 IHDDYGNVKRVVFS 237
                                       98888777776665 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       2.4   3.4e+03      35      52 ..     123     143 ..     106     148 .. 0.52
   2 !   21.0   0.1   1.9e-07   0.00026       5      65 ..     647     706 ..     643     707 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.4
                                       SSCHH...HHHHHHHHHHHHH CS
                             HisKA  35 eelke...yletiesearrld 52 
                                        +lke   +++ i ++ + + 
  gi|298675083|ref|YP_003726833.1| 123 TRLKEneeLFREITENMQDMV 143
                                       333332224555555544444 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 1.9e-07
                                       HHHHHHHHHHHHHHHHHHHHHHH.HC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHH CS
                             HisKA   5 flagvaHELrtPLsailgnaeaL.kregklteelkeyletiesearrldhlvedlLdlsrie 65 
                                       f+  + H+L +P+  ++g+a +L k+  +++e+  + l++++ + +r  +l+e+   l+ri+
  gi|298675083|ref|YP_003726833.1| 647 FTDILRHDLLNPVGIVKGYANLLyKK--ETDENKLKILDKMIINNERAIELIENAGNLARID 706
                                       667799*****************755..47788888******************99999987 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.91   1.3e+03       3      24 ..     635     656 ..     633     660 .. 0.84
   2 !   14.2   0.0   2.3e-05     0.031      38     112 ..     758     836 ..     747     855 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.91
                       HATPase_c_2   3 adpehvrtvrevaeavlrragl 24 
                                       +++e++ ++re+++++lr+  l
  gi|298675083|ref|YP_003726833.1| 635 NELERLNEIREIFTDILRHDLL 656
                                       68999***********998666 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 2.3e-05
                       HATPase_c_2  38 EactNavehayleap.egpvevrlesdeealtvevaDsGpg.fdpe..tlpdpteeepkeslkegGrGlalikglvD 110
                                        a+tN ++   + +p +  ++v++ +d +  +v+++D+Gpg  +     + d+ + +   +    G+Gla+++++vD
  gi|298675083|ref|YP_003726833.1| 758 QAFTNLINNSIKYNPeNSGIKVEIFDDIDYWKVQIKDEGPGiSEQDkkYIFDRFKRGEGKKVSGKGIGLAIVQKIVD 834
                                       5788888888888886788999999***************953333113456777777899999************* PP

                       HATPase_c_2 111 ev 112
                                         
  gi|298675083|ref|YP_003726833.1| 835 IH 836
                                       76 PP

>> NOGCT  NOGCT (NUC087) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.1e-05     0.057      38      53 ..     167     182 ..     165     182 .. 0.96

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.1e-05
                             NOGCT  38 PEildGkNvaDFidpd 53 
                                       PE l GkNv DF++pd
  gi|298675083|ref|YP_003726833.1| 167 PENLTGKNVLDFVHPD 182
                                       9999***********9 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   4.8e-05     0.067       4      79 ..     757     826 ..     755     833 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.8e-05
                       HATPase_c_3   4 ekAlaelvdNsldAdaen..vkievnknrgktgeivieDdGkGmseeelknal.rlatsskeakrkstslGkkGiGl 77 
                                       e+A + l++Ns+  + en  +k+e+ ++  +  +++i+D+G G+se++ k  + r+ + + +      +++ kGiG 
  gi|298675083|ref|YP_003726833.1| 757 EQAFTNLINNSIKYNPENsgIKVEIFDD-IDYWKVQIKDEGPGISEQDKKYIFdRFKRGEGK------KVSGKGIG- 825
                                       67999********999996777777776.4789**************988877344444444......56777887. PP

                       HATPase_c_3  78 kl 79 
                                        l
  gi|298675083|ref|YP_003726833.1| 826 -L 826
                                       .3 PP

>> SPOB_a  Sensor_kinase_SpoOB-type, alpha-helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2   0.00032      0.44       6      36 ..     637     668 ..     633     695 .. 0.79
   2 ?   -3.2   0.0       5.2   7.1e+03      43      53 ..     719     729 ..     712     730 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00032
                            SPOB_a   6 ikelkeliklL.rsqRHDflNhLQvIsGylqL 36 
                                       +++l+e+ +++   +RHD lN   +++Gy  L
  gi|298675083|ref|YP_003726833.1| 637 LERLNEIREIFtDILRHDLLNPVGIVKGYANL 668
                                       556666667776679**************987 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.2
                            SPOB_a  43 eeyieevvkel 53 
                                        e+ieev++++
  gi|298675083|ref|YP_003726833.1| 719 GEIIEEVIDNM 729
                                       58999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (862 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.76u 0.32s 00:00:01.08 Elapsed: 00:00:00.50
# Mc/sec: 5181.31
//
Query:       gi|298675084|ref|YP_003726834.1|  [L=121]
Description: hypothetical protein Metev_1157 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-05   24.0  11.6      4e-05   23.7  11.6    1.1  1  DUF4870         Domain of unknown function (DUF4870)
  ------ inclusion threshold ------
      0.095   12.5   4.2       0.12   12.2   4.2    1.1  1  TIC20           Chloroplast import apparatus Tic20-like
       0.23   11.9   6.6       0.16   12.4   4.5    1.7  2  DUF4231         Protein of unknown function (DUF4231)
        1.7    8.6   5.2        1.9    8.4   2.5    1.9  2  DUF3754         Protein of unknown function (DUF3754)
        3.2    7.7  15.7        1.9    8.5   0.2    2.9  3  DUF4389         Domain of unknown function (DUF4389)
        8.4    6.7  23.7        8.7    6.7   6.3    2.3  2  DUF4064         Protein of unknown function (DUF4064)


Domain annotation for each model (and alignments):
>> DUF4870  Domain of unknown function (DUF4870)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7  11.6   1.3e-08     4e-05      14     106 ..      15     113 ..       7     116 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.3e-08
                           DUF4870  14 sklliplgniilPlviwllkkdksefvdeqgkealNFqislliysiilivlsllvligf..ll.....lllllllll 83 
                                       + +l+ ++++i  ++ ++++k++ e v+ ++++++     l+i+ i++ +++ ++ +gf  ++     ++++l++l+
  gi|298675084|ref|YP_003726834.1|  15 AGVLAYVLGFISGIIFLFIEKEN-ESVRFHAAQSIVVFGALFILNIVISAIAGILAFGFlsFIsmilsFIATLIGLI 90 
                                       55677889999999999999999.9********99999999999888888888888888752255567888999*** PP

                           DUF4870  84 nlvlviiaaikanegeeyryplt 106
                                        ++l i+ +  a++g++ r p  
  gi|298675084|ref|YP_003726834.1|  91 TIILWIYLMFMAYKGNQTRLPAV 113
                                       *******************9975 PP

>> TIC20  Chloroplast import apparatus Tic20-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   4.2   3.9e-05      0.12     106     181 .]      36     117 ..      11     117 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.9e-05
                             TIC20 106 lprylRFhvmlailLdvalqvvllesnfnPli......gfklklgmylwagvalalivtllecvrsaLlGkyprlPl 176
                                        +  +RFh+ ++i+   al ++ +  +   +i       f  +++ ++ + ++l++i++ ++ +  a  G+ +rlP 
  gi|298675084|ref|YP_003726834.1|  36 ENESVRFHAAQSIVVFGALFILNIVISAIAGIlafgflSFISMILSFIATLIGLITIILWIYLMFMAYKGNQTRLPA 112
                                       34569********998888885444444444332322234445556777889************************* PP

                             TIC20 177 vseaA 181
                                       v+e A
  gi|298675084|ref|YP_003726834.1| 113 VAEIA 117
                                       **976 PP

>> DUF4231  Protein of unknown function (DUF4231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.51   1.5e+03      48      62 ..      17      31 ..       4      49 .. 0.49
   2 ?   12.4   4.5   5.4e-05      0.16      10      81 ..      44     115 ..      32     119 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.51
                           DUF4231 48 iltallsalvailaa 62
                                      +l+ +l+ ++ i+  
  gi|298675084|ref|YP_003726834.1| 17 VLAYVLGFISGIIFL 31
                                      333333333333322 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 5.4e-05
                           DUF4231  10 asrakrrfrllrlitivlgallpilvssklgagvsvlkiltallsalvailaaleeffrykerWrryRstaE 81 
                                       a ++   f  l ++ iv++a++ il+ + l   +++l ++++l++++++il ++  f+ yk + +r  ++aE
  gi|298675084|ref|YP_003726834.1|  44 AAQSIVVFGALFILNIVISAIAGILAFGFLSFISMILSFIATLIGLITIILWIYLMFMAYKGNQTRLPAVAE 115
                                       556666677788999************99999****************************998877777776 PP

>> DUF3754  Protein of unknown function (DUF3754)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1     0.023        68      63     103 ..      20      59 ..       5      62 .. 0.73
   2 ?    8.4   2.5   0.00065       1.9      63     118 ..      55     109 ..      52     119 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.023
                           DUF3754  63 lgvpaivglvavllkllkaeklknklssliaaliavlalgg 103
                                         +  i g+++++++  + e+++  + + i ++ a++ l +
  gi|298675084|ref|YP_003726834.1|  20 YVLGFISGIIFLFIEK-ENESVRFHAAQSIVVFGALFILNI 59 
                                       4455566777777777.999999999999999999988765 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00065
                           DUF3754  63 lgvpaivglvavllkllkaeklknklssliaaliavlalggfafrqyvkyknkkir 118
                                       + ++++++++a +l++  + ++ +++ s+ia+li ++++++++   +++yk  ++r
  gi|298675084|ref|YP_003726834.1|  55 FILNIVISAIAGILAF-GFLSFISMILSFIATLIGLITIILWIYLMFMAYKGNQTR 109
                                       7788999999999999.99999999**************************99988 PP

>> DUF4389  Domain of unknown function (DUF4389)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.2   0.00063       1.9      19      47 ..      13      41 ..      10      51 .. 0.89
   2 ?   -1.2   3.4      0.66     2e+03      10      26 ..      54      70 ..      42      80 .. 0.50
   3 ?    5.3   5.2    0.0064        19      14      39 ..      76     101 ..      69     114 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00063
                           DUF4389 19 slaslvlwvvvvvqflivLvtgrpnepLr 47
                                      ++a+++++v+ ++  +i L+  ++ne++r
  gi|298675084|ref|YP_003726834.1| 13 NIAGVLAYVLGFISGIIFLFIEKENESVR 41
                                      6899**********************987 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.66
                           DUF4389 10 lmllfaivlslaslvlw 26
                                      l +l +++ ++a+++++
  gi|298675084|ref|YP_003726834.1| 54 LFILNIVISAIAGILAF 70
                                      33444444444444433 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.0064
                           DUF4389  14 faivlslaslvlwvvvvvqflivLvt 39 
                                       + ++ls+  +++++++++ ++++ ++
  gi|298675084|ref|YP_003726834.1|  76 ISMILSFIATLIGLITIILWIYLMFM 101
                                       678999****************9997 PP

>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2  11.3     0.017        50      11      76 ..      14      70 ..      10      76 .. 0.67
   2 ?    6.7   6.3    0.0029       8.7       5      34 ..      77     106 ..      71     118 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.017
                           DUF4064 11 IGgilgillglllllflfllssgefsqelteeqalsgedasavleflstllivlgvialiaivlgi 76
                                      I+g+l  +lg++ +++++++ ++++s  +         +a+++  +++ l+i+ +vi+ ia++l +
  gi|298675084|ref|YP_003726834.1| 14 IAGVLAYVLGFISGIIFLFIEKENESVRF---------HAAQSIVVFGALFILNIVISAIAGILAF 70
                                      56666666666666665666665555554.........6677777888888888888888888765 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0029
                           DUF4064   5 eiiLglIGgilgillglllllflfllssge 34 
                                        +iL++I+  +g++ ++l ++ +f+  +g+
  gi|298675084|ref|YP_003726834.1|  77 SMILSFIATLIGLITIILWIYLMFMAYKGN 106
                                       356666666666666666666666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1406  (0.0784204); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 888.92
//
Query:       gi|298675085|ref|YP_003726835.1|  [L=263]
Description: hypothetical protein Metev_1158 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2113.79
//
Query:       gi|298675086|ref|YP_003726836.1|  [L=296]
Description: response regulator receiver protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.4e-48  163.2   3.0    6.2e-48  162.7   3.0    1.2  1  MetOD1        Metanogen output domain 1
    2.2e-29  101.9   0.6      5e-29  100.7   0.6    1.6  1  Response_reg  Response regulator receiver domain
  ------ inclusion threshold ------
       0.03   13.7   0.8       0.35   10.2   0.2    2.3  2  IPT           Isopentenyl transferase
        0.1   11.3   0.4       0.15   10.8   0.4    1.2  1  DUF1864       Domain of unknown function (DUF1864)


Domain annotation for each model (and alignments):
>> MetOD1  Metanogen output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.7   3.0   1.4e-51   6.2e-48       2     154 ..     136     294 ..     135     295 .. 0.98

  Alignments for each domain:
  == domain 1  score: 162.7 bits;  conditional E-value: 1.4e-51
                            MetOD1   2 lkkkkvkaelrsfllsaiPtlaskippeekkilikqfadrveknlkpkfkeelk.....eaekeeedaekvlkayie 73 
                                       l+++++++++r++l+ +iPtl++++p+e+kkili+q+++++e+ +++ + +++k     e ++e+ ++++v k+++e
  gi|298675086|ref|YP_003726836.1| 136 LNELYTQHQIRNILTGIIPTLLQQLPKEKKKILIHQMVKEIESLFNEIYVSNNKykdtlELDSENINPDNVKKTCTE 212
                                       78999************************************************************************ PP

                            MetOD1  74 wlnqlfanfgiktekkedeknvlleftnCpWge.earknPifCllcraivsrsftwtglkgsveqkktlgngdekCv 149
                                       ++n+l+a+f++k+ +++d+  ++le+t CpWg+ +a++nPi+C+l+++i++++++++++++s+++ kt+gng+++C+
  gi|298675086|ref|YP_003726836.1| 213 VMNYLGADFIAKEPDSKDNVLFALENTICPWGAsQAKMNPILCNLTKKIFYNVASKAYSNVSINTVKTIGNGNCSCY 289
                                       ***************************************************************************** PP

                            MetOD1 150 Feikv 154
                                       Fei +
  gi|298675086|ref|YP_003726836.1| 290 FEILK 294
                                       **986 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.7   0.6   1.1e-32     5e-29       1     111 [.      10     119 ..      10     120 .. 0.96

  Alignments for each domain:
  == domain 1  score: 100.7 bits;  conditional E-value: 1.1e-32
                                       EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCT..TTSEEE CS
                      Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireed..pelpvi 75 
                                       +livdD+p ++ell+++l+  gy ++ +a +g+ea+++++++++d+illD++mp+++G+e++++i+++d  + +pv+
  gi|298675086|ref|YP_003726836.1|  10 ILIVDDEPELVELLADYLD--GY-NTIAAYNGQEAINIIESDNIDVILLDVMMPDINGFEVCTHIKNDDslNYIPVL 83 
                                       8*****************9..99.7778***************************************998888**** PP

                                       EEESSTSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                      Response_reg  76 iltahseeedavealkagaddflsKpfdpeeLlkal 111
                                       ++ta s++++++++l+ gaddfl+Kp+d eeL +++
  gi|298675086|ref|YP_003726836.1|  84 MITALSDHDNKIHGLDSGADDFLTKPVDGEELNARV 119
                                       ********************************9988 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.046   2.1e+02     169     197 ..      23      52 ..      12      75 .. 0.77
   2 ?   10.2   0.2   7.8e-05      0.35     136     172 ..     116     152 ..     112     172 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.046
                               IPT 169 led.idGyryildyarkkkvtidklanlda 197
                                       l+d +dGy++i  y  ++ ++i +  n+d 
  gi|298675086|ref|YP_003726836.1|  23 LADyLDGYNTIAAYNGQEAINIIESDNIDV 52 
                                       554379***********9999988777776 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 7.8e-05
                               IPT 136 kkRvrqmlrpeeegaslldElaelwkepkarailedi 172
                                        +Rvr  lr+++ +  l++ l el+++++ r+il +i
  gi|298675086|ref|YP_003726836.1| 116 NARVRSALRIKKLHDELMKNLNELYTQHQIRNILTGI 152
                                       58********************************998 PP

>> DUF1864  Domain of unknown function (DUF1864)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.4   3.3e-05      0.15      11      60 ..     125     175 ..     116     182 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.3e-05
                           DUF1864  11 irarfvelnseLeelyfqqedkadvegvgeelkeaLeeegra.likallae 60 
                                       i++   el+++L+ely q + ++  +g++ +l ++L++e ++ li+++++e
  gi|298675086|ref|YP_003726836.1| 125 IKKLHDELMKNLNELYTQHQIRNILTGIIPTLLQQLPKEKKKiLIHQMVKE 175
                                       7777889*****************************999876256677666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1016  (0.056668); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 2214.61
//
Query:       gi|298675087|ref|YP_003726837.1|  [L=252]
Description: hypothetical protein Metev_1160 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.089   13.2   0.1       0.18   12.2   0.1    1.6  1  Lar_restr_allev  Restriction alleviation protein Lar
        0.1   12.8   1.2        0.3   11.3   1.2    1.8  1  zf-piccolo       Piccolo Zn-finger
        2.1    8.4   4.8         19    5.4   0.1    2.7  3  zf-Sec23_Sec24   Sec23/Sec24 zinc finger


Domain annotation for each model (and alignments):
>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   3.1e-05      0.18       4      51 ..      19      64 ..      16      77 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.1e-05
                   Lar_restr_allev  4 kpCPfCggravlersqrvvaeigqcvyCadCgastpwfkiaedeaeae 51
                                        CP C+ +++++ s+  + e   + +C+ Cg++t+     ++e++  
  gi|298675087|ref|YP_003726837.1| 19 ITCPLCNTDGKIHISNIETGE--STDICMFCGYNTHNEIAVDKEKDYL 64
                                      57*************999876..4899******655555555554444 PP

>> zf-piccolo  Piccolo Zn-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.2   4.9e-05       0.3       2      46 ..      20      59 ..      19      66 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.9e-05
                        zf-piccolo  2 lCplCktelnvgskeppnyntCteCkkqvCnlCGFnptphltekk 46
                                      +CplC+t+ +++     n +t     + +C  CG+n + +++  k
  gi|298675087|ref|YP_003726837.1| 20 TCPLCNTDGKIHI---SNIETGE--STDICMFCGYNTHNEIAVDK 59
                                      7******999994...4444443..578********988766544 PP

>> zf-Sec23_Sec24  Sec23/Sec24 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1    0.0032        19      21      33 ..      16      28 ..       1      33 [. 0.72
   2 ?    4.8   0.2    0.0049        29      15      33 ..      33      51 ..      31      56 .. 0.80
   3 ?   -2.6   0.1      0.99   5.9e+03      10      23 ..     107     120 ..     106     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0032
                    zf-Sec23_Sec24 21 gkrwiCnfCnhkn 33
                                      +   +C++Cn+  
  gi|298675087|ref|YP_003726837.1| 16 KEAITCPLCNTDG 28
                                      56689*****975 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0049
                    zf-Sec23_Sec24 15 ckidfggkrwiCnfCnhkn 33
                                      ++i  g ++ iC fC+  +
  gi|298675087|ref|YP_003726837.1| 33 SNIETGESTDICMFCGYNT 51
                                      5677888899*****9875 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.99
                    zf-Sec23_Sec24  10 ylNpfckidfggkr 23 
                                       ++N   ki+ ++k+
  gi|298675087|ref|YP_003726837.1| 107 VINFIDKIQTNKKS 120
                                       78999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1051  (0.0586201); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1678.59
//
Query:       gi|298675088|ref|YP_003726838.1|  [L=306]
Description: hypothetical protein Metev_1161 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-39  134.6   1.0    6.1e-39  133.5   1.1    1.4  2  MetOD1    Metanogen output domain 1
    4.6e-06   26.9   0.0    2.3e-05   24.6   0.0    2.0  1  PAS_4     PAS fold


Domain annotation for each model (and alignments):
>> MetOD1  Metanogen output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       0.8   7.2e+03       9      24 ..      11      26 ..       7      48 .. 0.65
   2 !  133.5   1.1   6.8e-43   6.1e-39       6     152 ..     149     304 ..     143     306 .] 0.96

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.8
                            MetOD1  9 aelrsfllsaiPtlas 24
                                      +el++ +++++P  ++
  gi|298675088|ref|YP_003726838.1| 11 NELKDYIIKSLPDNLT 26
                                      6666677777665544 PP

  == domain 2  score: 133.5 bits;  conditional E-value: 6.8e-43
                            MetOD1   6 kvkaelrsfllsaiPtlaskippeekkilikqfadrveknlkpkfkeelk.........eaekeeedaekvlkayie 73 
                                       + ++++r++l+  iPtl+++ p++ +ki++kq+ d+ve+ + ++ +++lk         +++ e+ ++++v+ + +e
  gi|298675088|ref|YP_003726838.1| 149 YKQNQIRKILTGTIPTLLKESPKDRRKIVVKQMLDMVENCMFHQNTSTLKsqqidckssKFKYEDVNSNNVGYMSCE 225
                                       579******************************************************99999*************** PP

                            MetOD1  74 wlnqlfanfgiktekkedeknvlleftnCpWge.earknPifCllcraivsrsftwtglkgsveqkktlgngdekCv 149
                                       ++nql+++f  +   ++++ ++++++t CpWg+ +a++nPi+C+l+++i+sr++t+++ + +ve+ kt+gngd++C+
  gi|298675088|ref|YP_003726838.1| 226 VMNQLGGDFSLESF-DKEGLRFAVKGTGCPWGAeQAKSNPILCNLTKGIISRVITKVYNDAKVETLKTMGNGDKCCY 301
                                       ************98.69999************99******************************************* PP

                            MetOD1 150 Fei 152
                                       F i
  gi|298675088|ref|YP_003726838.1| 302 FII 304
                                       *87 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   2.6e-09   2.3e-05       2     109 ..      19     135 ..      18     136 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.6e-09
                             PAS_4   2 dslpdalavldpdgrvlyaNaa...aaelfgappeellGktla.ellpee......daarleralrrvlegeepief 68 
                                        slpd+l+vld+dg++ly+N     +a+  g++p+ +   t + ++  +        a   ++ +r v++g++ i++
  gi|298675088|ref|YP_003726838.1|  19 KSLPDNLTVLDTDGTILYVNDLwriFASNNGLDPDMCSEGTNYlDVCDHAygknseEAYVAANGIRDVITGKKDIFE 95 
                                       589*****************999998887888888776555555777777666655555556779************ PP

                             PAS_4  69 leelll.pgeerhyelrllPlrdesGevigvlvisrDiTerr 109
                                       le++ + p++ r+y++ ++Pl +    +  vl++   iTer+
  gi|298675088|ref|YP_003726838.1|  96 LEYPCHaPDKNRWYLMKVIPLNK--RYPTPVLIYHLNITERK 135
                                       ***999***************54..55778888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2301.85
//
Query:       gi|298675089|ref|YP_003726839.1|  [L=341]
Description: transcription factor tFIIB cyclin-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-44  148.8   2.0    3.3e-21   75.1   0.1    2.3  2  TFIIB           Transcription factor TFIIB repeat
    2.6e-17   62.0   1.6    2.6e-17   62.0   1.6    2.1  3  TF_Zn_Ribbon    TFIIB zinc-binding
    8.5e-05   22.0   0.7      0.023   14.2   0.1    3.0  2  Sigma70_r4      Sigma-70, region 4
    0.00015   21.6   0.4    0.00036   20.4   0.4    1.7  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0017   18.4   4.9      0.039   14.0   3.2    2.7  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain
  ------ inclusion threshold ------
      0.014   15.2   0.2      0.051   13.4   0.2    2.0  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
      0.039   14.5   0.1        3.3    8.4   0.0    2.6  2  RPA_interact_C  Replication protein A interacting C-terminal
      0.078   13.1   5.7       0.13   12.4   0.4    3.1  3  Zn-ribbon_8     Zinc ribbon domain
      0.085   12.3   0.3       0.25   10.8   0.1    1.9  2  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
       0.12   12.1   0.0         11    5.7   0.0    2.3  2  Cyclin_N        Cyclin, N-terminal domain
       0.12   12.4   2.2       0.14   12.2   0.5    1.9  2  Elf1            Transcription elongation factor Elf1 like
       0.16   12.3   5.0        7.8    6.9   0.1    3.4  3  HTH_31          Helix-turn-helix domain
        0.2   11.1   3.4        1.9    8.0   3.4    2.3  1  zf-ribbon_3     zinc-ribbon domain
       0.23   11.1   1.1       0.54    9.9   0.1    2.1  2  zf-tcix         Putative treble-clef, zinc-finger, Zn-binding
       0.33   11.2   2.3        2.9    8.1   0.9    2.3  2  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
       0.37   10.6   2.5        5.6    6.8   2.5    2.4  1  A2L_zn_ribbon   A2L zinc ribbon domain
        1.8    8.6   4.1        2.1    8.4   0.5    2.9  2  Nudix_N_2       Nudix N-terminal


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.4   0.3   1.1e-23   1.1e-20       2      71 .]     161     230 ..     160     230 .. 0.97
   2 !   75.1   0.1   3.2e-24   3.3e-21       1      71 []     254     324 ..     254     324 .. 0.99

  Alignments for each domain:
  == domain 1  score: 73.4 bits;  conditional E-value: 1.1e-23
                                       HHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   2 krfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                        r+a+al+Lp +V++ A  ++++a++++++ Grs +g+aAA+ly Acr++ v rt+ ei +v++Vs  +i
  gi|298675089|ref|YP_003726839.1| 161 DRMASALGLPRTVRETAAVVYRKAVDKNLIRGRSIEGVAAAALYAACRQCSVPRTLDEIGEVSRVSRIEI 230
                                       69***************************************************************98776 PP

  == domain 2  score: 75.1 bits;  conditional E-value: 3.2e-24
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       ++rf++ l+L+ +V+++ +e++++a+e+++++Gr p+g+aAA++yiA+ +++++rtq+e+++v+ V+e+ti
  gi|298675089|ref|YP_003726839.1| 254 VPRFCSGLKLKSEVQSKGVEILRQASEKEITSGRGPTGVAAAAIYIASMLCGERRTQREVADVAGVTEVTI 324
                                       689******************************************************************98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.0   1.6   2.5e-20   2.6e-17       2      43 .]      44      85 ..      43      85 .. 0.98
   2 ?   -3.6   0.1       7.7   8.1e+03       3      10 ..     207     214 ..     206     218 .. 0.70
   3 ?   -3.0   0.0       5.2   5.5e+03      24      39 ..     257     273 ..     256     274 .. 0.81

  Alignments for each domain:
  == domain 1  score: 62.0 bits;  conditional E-value: 2.5e-20
                                      EETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                                      kCP+Cgs nl+ D+er+elvC+dCGlV++ + +degpewr+f
  gi|298675089|ref|YP_003726839.1| 44 KCPECGSINLEQDYERAELVCSDCGLVVDAELVDEGPEWRAF 85
                                      8***************************************98 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 7.7
                                       ETTTTCEE CS
                      TF_Zn_Ribbon   3 CPnCgstn 10 
                                       C  C+ ++
  gi|298675089|ref|YP_003726839.1| 207 CRQCSVPR 214
                                       89998875 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 5.2
                                       SS.SBEEEECCCCCCCH CS
                      TF_Zn_Ribbon  24 dC.GlVlednsidegpe 39 
                                       +C Gl l  +  ++g+e
  gi|298675089|ref|YP_003726839.1| 257 FCsGLKLKSEVQSKGVE 273
                                       69999999888888776 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.017        18      20      34 ..     213     227 ..     208     241 .. 0.90
   2 !   14.2   0.1   2.1e-05     0.023      18      43 ..     305     330 ..     296     335 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.017
                                       T--HHHHHHHHTS-H CS
                        Sigma70_r4  20 glTleEIgerlgiSr 34 
                                       ++Tl EIge+  +Sr
  gi|298675089|ref|YP_003726839.1| 213 PRTLDEIGEVSRVSR 227
                                       69********99998 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 2.1e-05
                                       TTT--HHHHHHHHTS-HHHHHHHHHH CS
                        Sigma70_r4  18 geglTleEIgerlgiSrerVrqiekr 43 
                                       ge +T+ E++++ g+++ ++r + k+
  gi|298675089|ref|YP_003726839.1| 305 GERRTQREVADVAGVTEVTIRNRYKE 330
                                       799*******************9986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.4   3.4e-07   0.00036      29      60 ..      43      75 ..      16      76 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.4e-07
                    OrfB_Zn_ribbon 29 ktCseCgsknke.alsgrtfkCpnCgfeadrDv 60
                                       +C+eCgs+n e + ++ +++C++Cg++ d+ +
  gi|298675089|ref|YP_003726839.1| 43 NKCPECGSINLEqDYERAELVCSDCGLVVDAEL 75
                                      58********99999***************976 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   3.2   3.7e-05     0.039       3      26 .]      44      67 ..      43      67 .. 0.95
   2 ?    3.2   0.0     0.089        94       9      20 ..     178     189 ..     177     189 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.7e-05
                            zf-ACC  3 KCpsCgemlykkeLernlyVCPkC 26
                                      KCp+Cg++ + ++ er   VC  C
  gi|298675089|ref|YP_003726839.1| 44 KCPECGSINLEQDYERAELVCSDC 67
                                      9***************99999988 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.089
                            zf-ACC   9 emlykkeLernl 20 
                                       +++y+k +++nl
  gi|298675089|ref|YP_003726839.1| 178 AVVYRKAVDKNL 189
                                       79*********7 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   4.8e-05     0.051      17      41 ..     307     331 ..     305     332 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.8e-05
                     HTH_AsnC-type  17 RisyaeLAervGlSestvlrRvrrL 41 
                                       R++ +e+A+  G++e t+++R++ L
  gi|298675089|ref|YP_003726839.1| 307 RRTQREVADVAGVTEVTIRNRYKEL 331
                                       99********************988 PP

>> RPA_interact_C  Replication protein A interacting C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0031       3.3       2      27 ..      45      73 ..      44     120 .. 0.82
   2 ?    3.5   0.0     0.098     1e+02      65      78 ..     199     212 ..     184     215 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0031
                    RPA_interact_C  2 CPvCkkrklkets..evifCe.Cglrlet 27
                                      CP C + +l+++     ++C+ Cgl ++ 
  gi|298675089|ref|YP_003726839.1| 45 CPECGSINLEQDYerAELVCSdCGLVVDA 73
                                      **********9653477***99**98877 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.098
                    RPA_interact_C  65 gveaLlaeCeeCdf 78 
                                         +aL+a C++C++
  gi|298675089|ref|YP_003726839.1| 199 AAAALYAACRQCSV 212
                                       5689********97 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.4   0.00012      0.13      15      38 ..      30      55 ..      25      57 .. 0.76
   2 ?    2.2   0.1      0.19     2e+02       5      16 ..      61      72 ..      56      83 .. 0.71
   3 ?   -1.8   0.1       3.4   3.6e+03      28      32 ..     205     210 ..     196     215 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                       Zn-ribbon_8 15 fevlqsis.dapltaCPeCgs.evrr 38
                                       e+  s+  ++p  +CPeCgs ++++
  gi|298675089|ref|YP_003726839.1| 30 KEKEKSSEiESPVNKCPECGSiNLEQ 55
                                      556666666778788******99986 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.19
                       Zn-ribbon_8  5 eYrCeeCghefe 16
                                      e  C +Cg + +
  gi|298675089|ref|YP_003726839.1| 61 ELVCSDCGLVVD 72
                                      345888886655 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 3.4
                       Zn-ribbon_8  28 a.CPeC 32 
                                       a C +C
  gi|298675089|ref|YP_003726839.1| 205 AaCRQC 210
                                       447777 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       4.5   4.7e+03      23      35 ..     188     200 ..     182     201 .. 0.75
   2 ?   10.8   0.1   0.00024      0.25      22      50 ..     302     330 ..     294     332 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.5
                      HTH_Tnp_ISL3  23 lllesrsvkavAr 35 
                                        l+++rs+  vA+
  gi|298675089|ref|YP_003726839.1| 188 NLIRGRSIEGVAA 200
                                       5778889999996 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00024
                      HTH_Tnp_ISL3  22 elllesrsvkavArqlgvSwtTVwrildr 50 
                                       +l+ e+r+ ++vA+  gv++ T+++++++
  gi|298675089|ref|YP_003726839.1| 302 MLCGERRTQREVADVAGVTEVTIRNRYKE 330
                                       577788*******************9987 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1      0.03        32      42      90 ..     164     212 ..     146     246 .. 0.81
   2 ?    5.7   0.0     0.011        11      32     102 ..     248     320 ..     223     336 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.03
                                       HHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSS CS
                          Cyclin_N  42 aekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveei 90 
                                       a+ + l + +  +a++++ + + k+ ++ + ++ v+a++L+ A++   +
  gi|298675089|ref|YP_003726839.1| 164 ASALGLPRTVRETAAVVYRKAVDKNLIRGRSIEGVAAAALYAACRQCSV 212
                                       556667777777899999999999999999**************97433 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHH..HSSS---HHHHHHHT CS
                          Cyclin_N  32 ailidwlvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKv..eeisppkledlvyit 102
                                       ++ id++ + ++ +kl++e+    v++l +  +k++++ +    v+a+++++A+ +  e+    ++ d++ +t
  gi|298675089|ref|YP_003726839.1| 248 TSPIDYVPRFCSGLKLKSEVQSKGVEILRQASEKEITSGRGPTGVAAAAIYIASMLcgERRTQREVADVAGVT 320
                                       5568999999*******************************************98766555555666665555 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.5   0.00014      0.14       3      56 ..      25      72 ..      19      79 .. 0.74
   2 ?   -2.4   0.1         5   5.2e+03      46      53 ..     205     212 ..     200     219 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                              Elf1  3 RkkkakkrkkkkkkklptkFdCpfCnheksvevkldkkekiaevsCkvCgesfe 56
                                      Rk+k+k +k+k+++  + + +Cp C++      +l++  ++ae+ C+ Cg+ ++
  gi|298675089|ref|YP_003726839.1| 25 RKEKEK-EKEKSSEIESPVNKCPECGSI-----NLEQDYERAELVCSDCGLVVD 72
                                      555554.344444444556789999976.....99**************98665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5
                              Elf1  46 vsCkvCge 53 
                                       + C++C+ 
  gi|298675089|ref|YP_003726839.1| 205 AACRQCSV 212
                                       67888875 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.047        50      44      62 ..     157     175 ..     139     178 .. 0.84
   2 ?    1.3   0.2      0.43   4.5e+02      28      40 ..     222     234 ..     191     246 .. 0.81
   3 ?    6.9   0.1    0.0074       7.8      14      32 ..     307     325 ..     273     326 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.047
                            HTH_31  44 pavlealaralgldpaera 62 
                                       ++ l+++a algl++  r+
  gi|298675089|ref|YP_003726839.1| 157 LSELDRMASALGLPRTVRE 175
                                       6789**********98776 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.43
                            HTH_31  28 estlsrlEqGrrg 40 
                                       +s++sr+E Gr  
  gi|298675089|ref|YP_003726839.1| 222 VSRVSRIEIGRTY 234
                                       6889999999986 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0074
                            HTH_31  14 GLsqeevAerlgvsestls 32 
                                       + +q+evA+ +gv+e t++
  gi|298675089|ref|YP_003726839.1| 307 RRTQREVADVAGVTEVTIR 325
                                       78************99986 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   3.4    0.0018       1.9       3      24 ..      43      69 ..      41      71 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0018
                       zf-ribbon_3  3 vrCPnCGa.plssd....dnvCpyCGt 24
                                      ++CP+CG+ +l+ d      vC  CG 
  gi|298675089|ref|YP_003726839.1| 43 NKCPECGSiNLEQDyeraELVCSDCGL 69
                                      58******8898774444567777775 PP

>> zf-tcix  Putative treble-clef, zinc-finger, Zn-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00052      0.54      10      20 ..      42      52 ..      37      54 .. 0.91
   2 ?   -1.9   0.1       2.5   2.6e+03      13      17 ..      64      68 ..      63      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00052
                           zf-tcix 10 vrkCpkCGtyN 20
                                      v kCp+CG +N
  gi|298675089|ref|YP_003726839.1| 42 VNKCPECGSIN 52
                                      67*******99 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.5
                           zf-tcix 13 CpkCG 17
                                      C+ CG
  gi|298675089|ref|YP_003726839.1| 64 CSDCG 68
                                      ****9 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.9    0.0027       2.9      17      40 .]      44      68 ..      42      68 .. 0.89
   2 ?    1.9   0.0      0.25   2.6e+02      16      25 ..     205     214 ..     201     222 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0027
                     Auto_anti-p27 17 tCpvCgvPLmrdr.kggkvyCvaCd 40
                                       Cp+Cg++ +++  ++ +++C  C+
  gi|298675089|ref|YP_003726839.1| 44 KCPECGSINLEQDyERAELVCSDCG 68
                                      5********99988899*****996 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.25
                     Auto_anti-p27  16 etCpvCgvPL 25 
                                       + C +C+vP 
  gi|298675089|ref|YP_003726839.1| 205 AACRQCSVPR 214
                                       46*******7 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   2.5    0.0053       5.6       5      30 ..      44      70 ..      43      71 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0053
                     A2L_zn_ribbon  5 vCsvCggngiln.seqgylvCieCgas 30
                                      +C  Cg+ ++ +  e+++lvC +Cg++
  gi|298675089|ref|YP_003726839.1| 44 KCPECGSINLEQdYERAELVCSDCGLV 70
                                      677788877777779999*******86 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.5    0.0019       2.1       3      31 ..      45      70 ..      45      72 .. 0.84
   2 ?   -1.6   0.2       2.6   2.8e+03       3       7 ..     207     211 ..     206     216 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0019
                                      -TTT--B-EEE--TT-SS-EEEETTTTEE CS
                         Nudix_N_2  3 CsqCGtpvelripdgDnreRlvCpaCgti 31
                                      C++CG+     ++++ +r  lvC++Cg +
  gi|298675089|ref|YP_003726839.1| 45 CPECGSI---NLEQDYERAELVCSDCGLV 70
                                      9999986...6666679999*******87 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.6
                                       -TTT- CS
                         Nudix_N_2   3 CsqCG 7  
                                       C+qC 
  gi|298675089|ref|YP_003726839.1| 207 CRQCS 211
                                       77875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1182  (0.0659267); expected 358.6 (0.02)
Passed bias filter:                      680  (0.0379274); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2571.94
//
Query:       gi|298675090|ref|YP_003726840.1|  [L=401]
Description: HNH endonuclease [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-64  215.2   4.4    9.7e-64  214.4   4.4    1.4  1  RRXRR     RRXRR protein
      8e-11   41.9   7.6    1.8e-10   40.8   7.6    1.7  1  HNH       HNH endonuclease
    3.1e-06   26.9   4.6    7.7e-06   25.7   4.6    1.7  1  HNH_5     HNH endonuclease
    0.00019   21.5   0.4    0.00074   19.6   0.4    2.0  1  HNH_2     HNH endonuclease
  ------ inclusion threshold ------
        4.1    7.1   6.5        1.3    8.7   2.8    2.0  2  zf_UBZ    Ubiquitin-Binding Zinc Finger


Domain annotation for each model (and alignments):
>> RRXRR  RRXRR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.4   4.4   2.7e-67   9.7e-64       1     174 []       3     176 ..       3     176 .. 0.99

  Alignments for each domain:
  == domain 1  score: 214.4 bits;  conditional E-value: 2.7e-67
                             RRXRR   1 VfVldkegkplmPtkpkrarklLkqgkAkvvrrkpftiqLkeesseesvqpvelklDpGskvtGiavvsekkvllka 77 
                                       VfV++k++kplmPt+p++ar+lLk+gkAkvvrr+pfti+L++e++e++ qpv+ ++D+Gsk++G+a+v +++vl+++
  gi|298675090|ref|YP_003726840.1|   3 VFVISKNKKPLMPTRPAKARRLLKSGKAKVVRRTPFTIKLLYETTEYT-QPVVAGMDSGSKHIGCAAVVNDEVLYQS 78 
                                       9***********************************************.**************************** PP

                             RRXRR  78 elelrgkdikkkleeRrelRraRRsrktryrqaRfdnR..kkkegwLapslqhrvqthlrvvkrlakllpitkivve 152
                                       e+elr  d+++k+++R+ +Rr+RRsrktryr++RfdnR  +kke+++aps++++vq+h r  + ++++lp++k+ ve
  gi|298675090|ref|YP_003726840.1|  79 EVELRD-DVSRKMKDRADYRRNRRSRKTRYRKPRFDNRgnSKKENRIAPSIKNKVQSHDRERRFVESILPVKKWIVE 154
                                       *****9.********************************99************************************ PP

                             RRXRR 153 lvkfDiqklenpeisgaeyqqG 174
                                       +++fDi+k++np++sg+ yq+G
  gi|298675090|ref|YP_003726840.1| 155 TASFDIHKITNPNVSGTGYQNG 176
                                       ********************98 PP

>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   7.6     5e-14   1.8e-10       1      46 [.     196     240 ..     196     241 .. 0.95

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 5e-14
                               HNH   1 CeyCgrkfhksealevdHiipisqggaddieNlqllCksCHnkkhd 46 
                                       C+ C++  ++ + le++Hi+ +s+gg+d  +Nl++lC++CH k+hd
  gi|298675090|ref|YP_003726840.1| 196 CQKCKNRSKD-PKLECHHIVFRSNGGTDRPDNLITLCETCHGKLHD 240
                                       *******777.7*********************************8 PP

>> HNH_5  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   4.6   2.2e-09   7.7e-06       1      44 [.     196     239 ..     196     247 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 2.2e-09
                             HNH_5   1 CiyCgkeiaekelseeHIiPeslGGkltisnlvtlCkkCNqkkg 44 
                                       C+ C+++ ++ +l+  HI+ +s GG+  ++nl tlC++C+ k+ 
  gi|298675090|ref|YP_003726840.1| 196 CQKCKNRSKDPKLECHHIVFRSNGGTDRPDNLITLCETCHGKLH 239
                                       9***************************************9984 PP

>> HNH_2  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.4   2.1e-07   0.00074       8      72 .]     205     246 ..     196     246 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.1e-07
                             HNH_2   8 dpslleaAHIiPwslssffndlilnrfeigrillekgstidspsNgllLspdiHklFdqflfafe 72 
                                       dp  le++HI+           ++n +            +d+p+N+++L+ ++H   +++ f+++
  gi|298675090|ref|YP_003726840.1| 205 DP-KLECHHIVF----------RSNGG------------TDRPDNLITLCETCHGKLHDGEFTIN 246
                                       44.667777766..........55555............***********************996 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   2.8   0.00037       1.3       1      20 [.     192     211 ..     192     212 .. 0.94
   2 ?   -1.3   0.1      0.47   1.7e+03       4      11 ..     230     237 ..     229     243 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00037
                            zf_UBZ   1 dtylCerCgkeipeselqEH 20 
                                       d+y+C++C+ +  +++l++H
  gi|298675090|ref|YP_003726840.1| 192 DNYTCQKCKNRSKDPKLECH 211
                                       79****************99 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.47
                            zf_UBZ   4 lCerCgke 11 
                                       lCe C+ +
  gi|298675090|ref|YP_003726840.1| 230 LCETCHGK 237
                                       7****865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       940  (0.052429); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2905.50
//
Query:       gi|298675091|ref|YP_003726841.1|  [L=996]
Description: PAS/PAC sensor signal transduction histidine kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.4e-57  190.0   5.7    3.4e-12   46.5   0.0    6.6  6  PAS_9        PAS domain
    8.5e-50  167.5   0.0    2.2e-10   40.5   0.0    7.0  6  PAS          PAS fold
    1.6e-45  153.8   0.0    8.9e-12   45.2   0.0    7.7  6  PAS_4        PAS fold
    4.3e-39  131.9   0.1    9.2e-09   35.1   0.0    6.4  6  PAS_8        PAS domain
    1.3e-31  109.4   0.0    3.1e-31  108.2   0.0    1.7  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    5.4e-23   81.1   0.1     0.0002   21.5   0.0    6.5  5  PAS_3        PAS fold
    3.9e-21   74.9   0.1    3.9e-21   74.9   0.1    2.2  3  HisKA        His Kinase A (phospho-acceptor) domain
    3.6e-08   33.6   4.3        1.4    9.1   0.0    7.5  8  PAS_7        PAS fold
    4.7e-05   23.3   0.2       0.11   12.4   0.1    4.0  4  MEKHLA       MEKHLA domain
      0.001   18.7   1.7        7.2    6.2   0.0    4.7  6  PAS_12       UPF0242 C-terminal PAS-like domain
  ------ inclusion threshold ------
      0.018   15.0   0.0      0.089   12.7   0.0    2.2  2  HATPase_c_5  GHKL domain
      0.096   12.6   0.0       0.24   11.4   0.0    1.6  1  HATPase_c_2  Histidine kinase-like ATPase domain


Domain annotation for each model (and alignments):
>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   5.3e-06    0.0079       6      84 ..      25     118 ..      17     131 .. 0.60
   2 !   13.9   0.1   3.2e-05     0.048       2     104 .]     136     255 ..     133     255 .. 0.53
   3 !   46.5   0.0   2.3e-15   3.4e-12       1     104 []     278     388 ..     277     388 .. 0.88
   4 !   39.5   0.0   3.6e-13   5.4e-10       2     104 .]     408     507 ..     407     507 .. 0.97
   5 !   30.8   0.0   1.8e-10   2.7e-07       2     104 .]     531     627 ..     530     627 .. 0.79
   6 !   39.6   0.0   3.3e-13     5e-10       4     103 ..     653     750 ..     650     750 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.3e-06
                             PAS_9   6 idnpdg.....rilyaNeaalrllGyspeevlgksitdlf.............vtdpeanerlraaleqgrkkerev 64 
                                       i+n+dg     +i+++N+a + + G +++ev+g+  ++++             v +  ++  ++ ++       ++ 
  gi|298675091|ref|YP_003726841.1|  25 IYNSDGypvdyKIIDINPAYESIVGLKRDEVVGQLASNIYdtgeapflhtyakVAETGEQTCFETYFSLF---GKHI 98 
                                       466777777779****************************644444444333222222222222222222...3444 PP

                             PAS_9  65 evvlirkngetfwvlltasp 84 
                                        ++ i +n ++f + +t ++
  gi|298675091|ref|YP_003726841.1|  99 RITVISPNKSKFITIFTDIT 118
                                       44444444444444444333 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 3.2e-05
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlf..............vtdpeanerlraaleqgrk..... 59 
                                       + i++++++ ri ++N++a+ + G++++e++g +  + +                         ++ ++ +      
  gi|298675091|ref|YP_003726841.1| 136 MVIMMVDSERRIFKVNKSAELFSGTTSDEMVGLRGGEALrclnslsnpdgcgfG----------QYCQECKVkntvi 202
                                       55677989999**********************955555555565544444442..........2222222222233 PP

                             PAS_9  60 .........kerevevvlirkngetfwvlltaspvkdddgelvgiivilrDite 104
                                                   e  + ++ + + ++++ l  + ++++d++ + +iv l Dite
  gi|298675091|ref|YP_003726841.1| 203 dtfetgnnhYNVETSLPFMIDGDVKYLTFLISTSLINNDEKPK-VIVSLLDITE 255
                                       3222244232222222233333333334433334444444444.4577777776 PP

  == domain 3  score: 46.5 bits;  conditional E-value: 2.3e-15
                             PAS_9   1 pdgilidnpdgrilyaNeaalrllGyspeevlgksitdlf....vtdpeanerlraaleqgrk...kerevevvlir 70 
                                       p++i  +n++g+i+yaN aa+++lG s+ e+ g+ ++++     +++ +   + +  +e  +k   ++++v   +  
  gi|298675091|ref|YP_003726841.1| 278 PVCITKVNKNGNIVYANSAAENVLGLSKSEIEGRTYDNVKwkitDFKGNLFPETELPFELVQKyqkPVYDVRHAIEW 354
                                       45666699***************************99999887766666666666666666668889********** PP

                             PAS_9  71 kngetfwvlltaspvkdddgelvgiivilrDite 104
                                       +ng++ +  ++a+p++dd+g++ +ii++++Dit+
  gi|298675091|ref|YP_003726841.1| 355 PNGQRKLLSINAAPIFDDNGNFGSIIATIEDITA 388
                                       ********************************95 PP

  == domain 4  score: 39.5 bits;  conditional E-value: 3.6e-13
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwv 78 
                                       ++i+i + dg ++yaN a l++  y++ee+lgk+it++  + +e++ ++ ++l +     +  e    +k g+ f v
  gi|298675091|ref|YP_003726841.1| 408 NAIAISDLDGYLTYANSASLDMWEYNKEEILGKHITEFW-QYKENAINVYHYLHENG--SWKSEGKAKTKHGNVFDV 481
                                       6899999***999**************************.*****************..****************** PP

                             PAS_9  79 lltaspvkdddgelvgiivilrDite 104
                                          +  v d++g+ v+i++ ++Dit+
  gi|298675091|ref|YP_003726841.1| 482 YSLINLVNDESGKPVAIAGSFVDITK 507
                                       *999***999**************95 PP

  == domain 5  score: 30.8 bits;  conditional E-value: 1.8e-10
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetf 76 
                                        gi++++++g+ +++N+aa+ ++Gy+++e+l  +i dl     ++ a + ++++le+g+    + e+ +i+kn++  
  gi|298675091|ref|YP_003726841.1| 531 IGIFVIDKNGNYVDVNPAACHIIGYTKDELLSMNIIDLHpdNAHELAGQIFEELLENGK---VSAELPFITKNDSLR 604
                                       6899999********************************55555555566666666666...999999999999766 PP

                             PAS_9  77 wvlltaspvkdddgelvgiivilrDite 104
                                       +  l a+ + +d+     +i++ +Dit+
  gi|298675091|ref|YP_003726841.1| 605 YWILDAVKLLEDK-----YIGFTTDITD 627
                                       6667776666554.....6678888885 PP

  == domain 6  score: 39.6 bits;  conditional E-value: 3.3e-13
                             PAS_9   4 ilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwv 78 
                                       i+  + dg+i+y+N+ a++ lGys+ee+l  +i d+    ++ + +   ++ l   +   + ve+ l+rk+g+++++
  gi|298675091|ref|YP_003726841.1| 653 IIAHDFDGNIVYVNNLACENLGYSKEELLSMNIADISayINSYDPKTVYWEKLSPSD--SYLVETKLRRKDGSYYPA 727
                                       55555799*****************************76666666666666666666..9***************** PP

                             PAS_9  79 lltaspvkdddgelvgiivilrDit 103
                                       +++++++  +++ +++  +++r it
  gi|298675091|ref|YP_003726841.1| 728 EVKLTRIDLKGRSVIL--GFVREIT 750
                                       *******888888888..9999998 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0    0.0002       0.3      22      47 ..      36      61 ..      33     110 .. 0.82
   2 !   14.2   0.0   2.2e-05     0.033       2      43 ..     126     167 ..     125     169 .. 0.95
   3 !   26.7   0.0   2.8e-09   4.2e-06       3     113 .]     270     386 ..     268     386 .. 0.81
   4 !   24.9   0.0   1.1e-08   1.6e-05       3     112 ..     399     504 ..     397     505 .. 0.84
   5 !   40.5   0.0   1.5e-13   2.2e-10       2      99 ..     521     616 ..     520     625 .. 0.81
   6 !   40.4   0.0   1.6e-13   2.4e-10       1     113 []     640     749 ..     640     749 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0002
                                      BEEEECHHHHHHHSSTHHHCTTSBGG CS
                               PAS 22 rilyvNaaaeellGlsreevlgksll 47
                                      +i+ +N+a+e++ Gl+r+ev+g+  +
  gi|298675091|ref|YP_003726841.1| 36 KIIDINPAYESIVGLKRDEVVGQLAS 61
                                      7999******************9765 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 2.2e-05
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTT CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlg 43 
                                       +l++i e+ p  i++vD   ri+ vN++ae + G + +e++g
  gi|298675091|ref|YP_003726841.1| 126 ELKTIYENVPMVIMMVDSERRIFKVNKSAELFSGTTSDEMVG 167
                                       6899**********************************9998 PP

  == domain 3  score: 26.7 bits;  conditional E-value: 2.8e-09
                                       HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH......HHHHHHHHHHHHTT-EC CS
                               PAS   3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda......elaelleqlleqgeesr 73 
                                       ++ + e++p+ i  v+++g+i+y+N+aae  lGls +e+ g+++  + +  +d       e+   +e + + +++  
  gi|298675091|ref|YP_003726841.1| 270 FEKVAETSPVCITKVNKNGNIVYANSAAENVLGLSKSEIEGRTYDNVKWKITDFkgnlfpETELPFELVQKYQKPVY 346
                                       788899999**********************************9887777665456666666666666666666666 PP

                                       CCCEEEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  74 ageisfklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       ++++ ++ ++g  + l ++a+p++d  g+   ++ ++ di
  gi|298675091|ref|YP_003726841.1| 347 DVRHAIEWPNGQRKLLSINAAPIFDDNGNFGSIIATIEDI 386
                                       6666666699999999999999999999999999999987 PP

  == domain 4  score: 24.9 bits;  conditional E-value: 1.1e-08
                                       HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEE CS
                               PAS   3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisf 79 
                                       +++ les++++i + D dg  +y+N+a  ++  ++ ee+lgk++ +++  ++    a  +  +l+++ +++++ +  
  gi|298675091|ref|YP_003726841.1| 399 MKNTLESSINAIAISDLDGYLTYANSASLDMWEYNKEEILGKHITEFWQYKE---NAINVYHYLHENGSWKSEGKAK 472
                                       67889*******************************************9884...6677777777777777777766 PP

                                       ECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEE CS
                               PAS  80 klrdgrpihlevraspvrdaggeilgflgvlrd 112
                                       ++ +g ++ +    + v d++g++  + g + d
  gi|298675091|ref|YP_003726841.1| 473 TK-HGNVFDVYSLINLVNDESGKPVAIAGSFVD 504
                                       66.999999999999999999988777776655 PP

  == domain 5  score: 40.5 bits;  conditional E-value: 1.5e-13
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       +lr+ ++++p +ifv+D++g+ + vN+aa+ + G++ +e+l+ +++dl + +  +ela ++ + l+++ + +a+   
  gi|298675091|ref|YP_003726841.1| 521 QLRNYIDNSPIGIFVIDKNGNYVDVNPAACHIIGYTKDELLSMNIIDLHP-DNAHELAGQIFEELLENGKVSAELP- 595
                                       68999*****************************************6664.4444999999999999988888544. PP

                                       EECTTSSEEEEEEEEEEEEET CS
                               PAS  79 fklrdgrpihlevraspvrda 99 
                                       f +++ + +++ + a+++++ 
  gi|298675091|ref|YP_003726841.1| 596 FITKNDSLRYWILDAVKLLED 616
                                       444477777777777776665 PP

  == domain 6  score: 40.4 bits;  conditional E-value: 1.6e-13
                                       HHHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCE CS
                               PAS   1 edlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesragei 77 
                                       e++r++ e+++d+i++ D dg+i+yvN  a+e lG+s ee+l+ ++  +i+   ++  ++  + + e  ++s ++ +
  gi|298675091|ref|YP_003726841.1| 640 ERFRTLTEQAADAIIAHDFDGNIVYVNNLACENLGYSKEELLSMNIA-DISAYINS--YDPKTVYWEKLSPSDSYLV 713
                                       6899*******************************************.56666664..4444444444444444444 PP

                                       EEEC..TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  78 sfkl..rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                         kl  +dg+++++ev  + +  +g     +lg++r i
  gi|298675091|ref|YP_003726841.1| 714 ETKLrrKDGSYYPAEVKLTRIDLKGRS--VILGFVREI 749
                                       4444448***********999999877..899998876 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   3.7e-06    0.0055      14     109 ..      34     121 ..      33     122 .. 0.81
   2 !   11.5   0.0   0.00019      0.28       2      70 ..     132     206 ..     131     258 .. 0.63
   3 !   29.5   0.0   4.5e-10   6.7e-07       2     107 ..     275     388 ..     274     391 .. 0.92
   4 !   23.3   0.0   3.8e-08   5.7e-05       1     109 [.     403     509 ..     403     510 .. 0.86
   5 !   45.2   0.0     6e-15   8.9e-12       2     110 .]     527     630 ..     526     630 .. 0.98
   6 !   16.1   0.0   6.8e-06      0.01       2     110 .]     647     754 ..     646     754 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.7e-06
                             PAS_4  14 dgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgeerhyelrl.lPlr 89 
                                       d++++++N+a+++++g+ ++e++G+    ++ +   a++ + +++v+e++e   f+++  l   ++h+ +++ +P +
  gi|298675091|ref|YP_003726841.1|  34 DYKIIDINPAYESIVGLKRDEVVGQLASNIYDT-GEAPFLHTYAKVAETGEQTCFETYFSL--FGKHIRITViSPNK 107
                                       899***********************9998888.888999999999998877666666655..46777777746665 PP

                             PAS_4  90 desGevigvlvisrDiTerr 109
                                               ++ i++DiT +r
  gi|298675091|ref|YP_003726841.1| 108 S------KFITIFTDITSQR 121
                                       5......8999999999877 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00019
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee......daarleralrrvlegeepiefle 70 
                                       +++p ++ ++d++ r+  +N++a+   g + +e++G +  e l         d+ ++ ++ +++   +++i++ e
  gi|298675091|ref|YP_003726841.1| 132 ENVPMVIMMVDSERRIFKVNKSAELFSGTTSDEMVGLRGGEALRCLnslsnpDGCGFGQYCQECKVKNTVIDTFE 206
                                       899*******************999***********998875433233344455555555555555555555555 PP

  == domain 3  score: 29.5 bits;  conditional E-value: 4.5e-10
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee.......daarleralrrvlegeepieflee 71 
                                       + +p++++ ++++g+++yaN aa+ ++g++  e+ G+t+  +  +        + ++ e + + v + ++p++++ +
  gi|298675091|ref|YP_003726841.1| 275 ETSPVCITKVNKNGNIVYANSAAENVLGLSKSEIEGRTYDNV-KWKitdfkgnLFPETELPFELVQKYQKPVYDVRH 350
                                       679************************************943.3333667778***********************9 PP

                             PAS_4  72 lll..pgeerhyelrllPlrdesGevigvlvisrDiTe 107
                                            +g+++ +++++ P++d++G    +++++ DiT+
  gi|298675091|ref|YP_003726841.1| 351 AIEwpNGQRKLLSINAAPIFDDNGNFGSIIATIEDITA 388
                                       999**********************************7 PP

  == domain 4  score: 23.3 bits;  conditional E-value: 3.8e-08
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       l+s+  a+a+ d dg  +yaN a+ ++  +  ee+lGk+  e++      + + ++ + l ++ +++++   ++ + 
  gi|298675091|ref|YP_003726841.1| 403 LESSINAIAISDLDGYLTYANSASLDMWEYNKEEILGKHITEFWQ---YKENAINVYHYLHENGSWKSEGKAKT-KH 475
                                       6899999************************************97...56777777788888889999999999.55 PP

                             PAS_4  78 erhyelrl..lPlrdesGevigvlvisrDiTerr 109
                                       + ++++    + + desG+++++ + ++DiT r+
  gi|298675091|ref|YP_003726841.1| 476 GNVFDVYSliNLVNDESGKPVAIAGSFVDITKRK 509
                                       55555544459999*****************997 PP

  == domain 5  score: 45.2 bits;  conditional E-value: 6e-15
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgee 78 
                                       d++p +++v+d++g+++++N+aa++++g++ +ell +   +l+p+ + +   ++ +++le +++  +l + + +++ 
  gi|298675091|ref|YP_003726841.1| 527 DNSPIGIFVIDKNGNYVDVNPAACHIIGYTKDELLSMNIIDLHPDNAHELAGQIFEELLENGKVSAELPFITKNDSL 603
                                       89*************************************************************************** PP

                             PAS_4  79 rhyelrllPlrdesGevigvlvisrDiTerrr 110
                                       r++ l ++ l++     + ++++++DiT+r+r
  gi|298675091|ref|YP_003726841.1| 604 RYWILDAVKLLE-----DKYIGFTTDITDRKR 630
                                       **********99.....99***********97 PP

  == domain 6  score: 16.1 bits;  conditional E-value: 6.8e-06
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee.daarleralrrvlegeepiefleelllpge 77 
                                       ++  da+++ d dg+++y+N+ a+e +g++ eell +  a++     + ++   +++++  ++  + ++  ++ +g+
  gi|298675091|ref|YP_003726841.1| 647 EQAADAIIAHDFDGNIVYVNNLACENLGYSKEELLSMNIADISAYInSYDPKTVYWEKLSPSDSYLVETKLRRKDGS 723
                                       6788999*********************************98776689***********999766666665555*** PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerrr 110
                                         + e+ l+++ d +G+   +l+++r+iT r++
  gi|298675091|ref|YP_003726841.1| 724 YYPAEVKLTRI-DLKGR-SVILGFVREITIRKQ 754
                                       ***********.99***.999********9985 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   5.1e-06    0.0076       6      53 ..      11      68 ..       6      83 .. 0.75
   2 !   16.1   0.0   5.6e-06    0.0084       3      55 ..     127     180 ..     126     189 .. 0.86
   3 !   17.2   0.0   2.5e-06    0.0038       2      46 ..     269     314 ..     268     337 .. 0.78
   4 !   13.4   0.0   3.9e-05     0.059       7      44 ..     403     441 ..     398     456 .. 0.81
   5 !   35.1   0.0   6.2e-12   9.2e-09       1      58 [.     520     576 ..     520     587 .. 0.76
   6 !   24.6   0.0   1.2e-08   1.8e-05       1      44 [.     640     684 ..     640     700 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.1e-06
                             PAS_8  6 lfesspdgiav...vd.lgd.....rivdvNqaalellGys.adlkgellgqllpvlr 53
                                      ++ ++++g++    ++  ++     +i+d+N+a++ + G++ +++ g+l  ++ +  +
  gi|298675091|ref|YP_003726841.1| 11 VYKTMNEGVCFheiIYnSDGypvdyKIIDINPAYESIVGLKrDEVVGQLASNIYDTGE 68
                                      66789999996555333444677779***************9***9999986655544 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 5.6e-06
                             PAS_8   3 lralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpvlrpl 55 
                                       l++++e++p  i++vd  +ri  vN++a+ + G + +++ g   g+ l+ l++l
  gi|298675091|ref|YP_003726841.1| 127 LKTIYENVPMVIMMVDSERRIFKVNKSAELFSGTTsDEMVGLRGGEALRCLNSL 180
                                       789*************7779*************888999888888887777765 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 2.5e-06
                             PAS_8   2 rlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellg 46 
                                       +++ + e+sp+ i  v+ +g+ iv++N aa+  lG+s  ++ g + +
  gi|298675091|ref|YP_003726841.1| 269 FFEKVAETSPVCITKVNkNGN-IVYANSAAENVLGLSkSEIEGRTYD 314
                                       578888888888886776888.*************999999888765 PP

  == domain 4  score: 13.4 bits;  conditional E-value: 3.9e-05
                             PAS_8   7 fesspdgiavvd.lgdrivdvNqaalellGys.adlkgel 44 
                                       +ess ++ia+ d +g  ++++N a l+++ y+ ++++g+ 
  gi|298675091|ref|YP_003726841.1| 403 LESSINAIAISDlDGY-LTYANSASLDMWEYNkEEILGKH 441
                                       789999****995555.**************977777654 PP

  == domain 5  score: 35.1 bits;  conditional E-value: 6.2e-12
                             PAS_8   1 erlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellgqllpvlrplle.d 58 
                                       ++lr+ +++sp gi+v+d +g+  vdvN+aa+++ Gy+ ++l+ +   ++++ ++++ +  
  gi|298675091|ref|YP_003726841.1| 520 QQLRNYIDNSPIGIFVIDkNGN-YVDVNPAACHIIGYTkDELLSM---NIIDLHPDNAHeL 576
                                       578999************8888.***************6666664...5555555555543 PP

  == domain 6  score: 24.6 bits;  conditional E-value: 1.2e-08
                             PAS_8   1 erlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgel 44 
                                       er+r+l e+++d+i+  d +g+ iv+vN+ a+e lGys ++l+ + 
  gi|298675091|ref|YP_003726841.1| 640 ERFRTLTEQAADAIIAHDfDGN-IVYVNNLACENLGYSkEELLSMN 684
                                       7**************9999999.**************977766554 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.2   0.0   2.1e-34   3.1e-31       2     110 ..     887     995 ..     886     996 .] 0.97

  Alignments for each domain:
  == domain 1  score: 108.2 bits;  conditional E-value: 2.1e-34
                                       HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTSSSHH CS
                         HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsq.ddstkrggggtGlG 77 
                                       d+++Lrqi+ nlv Navkf t++g+++v+++ +++d  +sv D+GiGip ++++++f++f q d++++r+++gtGlG
  gi|298675091|ref|YP_003726841.1| 887 DKIKLRQILYNLVYNAVKF-TEQGSVTVKLDWNDNDMLFSVIDTGIGIPADKQDEIFDSFKQlDSGASRRYSGTGLG 962
                                       7899***************.***********9889****************************************** PP

                                       HHHHHHHHHHTTTEEEEEEETTTEEEEEEEEES CS
                         HATPase_c  78 lsivkklvelmgGeiwvesepgrGttftftlpl 110
                                       l++v++lve++gG+iwvese+ +G++f f +p+
  gi|298675091|ref|YP_003726841.1| 963 LALVERLVEMHGGKIWVESEEREGSRFSFIIPE 995
                                       *****************************9986 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.08   1.2e+02       2      31 ..      38      64 ..      37     102 .. 0.72
   2 !   10.2   0.0   0.00049      0.73       1      88 [.     290     382 ..     290     383 .. 0.78
   3 !   17.0   0.1   3.7e-06    0.0055       2      87 ..     420     500 ..     419     502 .. 0.85
   4 !   19.9   0.0   4.5e-07   0.00067       2      68 ..     543     606 ..     542     618 .. 0.87
   5 !   21.5   0.0   1.4e-07    0.0002       1      83 [.     662     741 ..     662     746 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.08
                             PAS_3  2 iyvserveeilGyspeellgkveswldlvh 31
                                      i +++++e i+G+ ++e+ g+   +++ ++
  gi|298675091|ref|YP_003726841.1| 38 IDINPAYESIVGLKRDEVVGQ---LASNIY 64
                                      889***************999...444444 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00049
                             PAS_3   1 iiyvserveeilGyspeellgk.veswldlvhpeD...rervrealqealkkge.pyegeyRirrkdGeyrwveara 72 
                                       i+y++ + e++lG+s++e++g+ +++++  +        ++++  ++ + k ++ +y++ + i +++G+   ++  a
  gi|298675091|ref|YP_003726841.1| 290 IVYANSAAENVLGLSKSEIEGRtYDNVKWKITDFKgnlFPETELPFELVQKYQKpVYDVRHAIEWPNGQRKLLSINA 366
                                       589999999999999999999975544433333221145555566666778888889******************** PP

                             PAS_3  73 rvirdengkpvrvigv 88 
                                        +i+d+ng+   +i++
  gi|298675091|ref|YP_003726841.1| 367 APIFDDNGNFGSIIAT 382
                                       *********9999887 PP

  == domain 3  score: 17.0 bits;  conditional E-value: 3.7e-06
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       +y++ +  +++ y +ee+lgk  ++ ++    +  ++ + + ++l ++++++ e + ++k+G ++ v + ++ ++de
  gi|298675091|ref|YP_003726841.1| 420 TYANSASLDMWEYNKEEILGK--HITEFWQYKE--NAINVY-HYLHENGSWKSEGKAKTKHGNVFDVYSLINLVNDE 491
                                       69999****************..7777765444..444444.46667777*************************** PP

                             PAS_3  79 ngkpvrvig 87 
                                       +gkpv + g
  gi|298675091|ref|YP_003726841.1| 492 SGKPVAIAG 500
                                       *****9988 PP

  == domain 4  score: 19.9 bits;  conditional E-value: 4.5e-07
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeD.rervrealqealkkgepyegeyRirrkdGeyrwv 68 
                                       + v+++ ++i+Gy+++ell+   +++dl hp+   e + + ++e+l++g+ ++ e  +++k+ + r++
  gi|298675091|ref|YP_003726841.1| 543 VDVNPAACHIIGYTKDELLSM--NIIDL-HPDNaHELAGQIFEELLENGK-VSAELPFITKNDSLRYW 606
                                       689******************..99996.8888799999*******9999.8**********999864 PP

  == domain 5  score: 21.5 bits;  conditional E-value: 1.4e-07
                             PAS_3   1 iiyvserveeilGyspeellgk.veswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvir 76 
                                       i+yv++  +e lGys+eell+  + ++  ++   D +     ++e l+   +y +e ++rrkdG+y+  e + + i 
  gi|298675091|ref|YP_003726841.1| 662 IVYVNNLACENLGYSKEELLSMnIADISAYINSYDPKT---VYWEKLSPSDSYLVETKLRRKDGSYYPAEVKLTRI- 734
                                       5899******************9999999999999665...57999*999*****************999998888. PP

                             PAS_3  77 dengkpv 83 
                                       d +g+ v
  gi|298675091|ref|YP_003726841.1| 735 DLKGRSV 741
                                       7777665 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       6.9     1e+04      38      56 ..     509     527 ..     503     528 .. 0.76
   2 ?   -3.5   0.1       7.4   1.1e+04      36      56 ..     627     647 ..     610     650 .. 0.57
   3 !   74.9   0.1   2.6e-24   3.9e-21       1      67 []     772     840 ..     772     840 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 6.9
                                       HHHHHHHHHHHHHHHHHHH CS
                             HisKA  38 keyletiesearrldhlve 56 
                                       k y e++++++++l++ ++
  gi|298675091|ref|YP_003726841.1| 509 KSYEEKLKKSEQQLRNYID 527
                                       5677888889999988886 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 7.4
                                       SCHHHHHHHHHHHHHHHHHHH CS
                             HisKA  36 elkeyletiesearrldhlve 56 
                                       + k+  e ++++++r + l e
  gi|298675091|ref|YP_003726841.1| 627 DRKRIEEELRESEERFRTLTE 647
                                       445555666666667666665 PP

  == domain 3  score: 74.9 bits;  conditional E-value: 2.6e-24
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                             HisKA   1 slgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsrieag 67 
                                       +++++la+v+HELrtPL++i+g++++L +   g+l+e++k yl ++++++++l++l+ d+Ldls+ie+g
  gi|298675091|ref|YP_003726841.1| 772 AKSELLANVSHELRTPLTSIIGFSDILLKGklGDLNESQKTYLSKVHRSGKHLLDLITDILDLSKIESG 840
                                       589***********************9777799**********************************97 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.017        26      96     114 ..     106     124 ..      61     125 .. 0.81
   2 ?    0.8   0.0      0.35   5.3e+02       2      27 ..     132     156 ..     131     182 .. 0.78
   3 ?   -2.4   0.0       3.5   5.2e+03     101     114 ..     247     260 ..     246     261 .. 0.80
   4 !    9.1   0.0   0.00097       1.4      11     114 ..     284     393 ..     278     394 .. 0.68
   5 ?    4.1   0.0     0.033        49       5      50 ..     407     451 ..     403     481 .. 0.88
   6 ?   -2.8   0.0       4.6   6.9e+03     103     115 .]     501     513 ..     488     513 .. 0.86
   7 ?    5.3   0.1     0.014        21       1      44 [.     526     568 ..     526     633 .. 0.72
   8 ?    1.6   0.0       0.2     3e+02       3      48 ..     648     692 ..     646     700 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.017
                             PAS_7  96 pdgGfVttytDiTerrrae 114
                                        +  f+t++tDiT +r+++
  gi|298675091|ref|YP_003726841.1| 106 NKSKFITIFTDITSQRKTD 124
                                       55569**********9975 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.35
                             PAS_7   2 enmsqGisvfDadlrLvawNrrylel 27 
                                       en++  i+++D++ r+  +N+   el
  gi|298675091|ref|YP_003726841.1| 132 ENVPMVIMMVDSERRIFKVNKSA-EL 156
                                       688888**************975.44 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 3.5
                             PAS_7 101 VttytDiTerrrae 114
                                       +++  DiTer++++
  gi|298675091|ref|YP_003726841.1| 247 IVSLLDITERKKTQ 260
                                       56678******987 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.00097
                             PAS_7  11 fDadlrLvawNrrylelldlpeelvqvgvpleellryn.aergefg.agdveaeverrlaaara...gkphsferer 82 
                                       +++++++v  N+   ++l+l+++ +  g++++++   +   +g++  + +      + ++++++   + +h++e   
  gi|298675091|ref|YP_003726841.1| 284 VNKNGNIVYANSAAENVLGLSKSEI-EGRTYDNVKWKItDFKGNLFpETELPF---ELVQKYQKpvyDVRHAIEWPN 356
                                       6677777888888888888888877.666666664333144555552222222...233333333337899999999 PP

                             PAS_7  83 pdgrvievrgnpl.....pdgGfVttytDiTerrrae 114
                                        + + +++++ p+       g +++t +DiT+++++e
  gi|298675091|ref|YP_003726841.1| 357 GQRKLLSINAAPIfddngNFGSIIATIEDITAYKEKE 393
                                       99***********7665555899***********987 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.033
                             PAS_7   5 sqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynae 50 
                                        ++i++ D d+ L+  N+  l++ ++ +e +  g++++e+ +y  +
  gi|298675091|ref|YP_003726841.1| 407 INAIAISDLDGYLTYANSASLDMWEYNKEEI-LGKHITEFWQYKEN 451
                                       57899***********************999.99999999998765 PP

  == domain 6  score: -2.8 bits;  conditional E-value: 4.6
                             PAS_7 103 tytDiTerrraee 115
                                       ++ DiT+r+  ee
  gi|298675091|ref|YP_003726841.1| 501 SFVDITKRKSYEE 513
                                       689*****99875 PP

  == domain 7  score: 5.3 bits;  conditional E-value: 0.014
                             PAS_7   1 lenmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleel 44 
                                       ++n + Gi v+D++++ v +N   +++ +++++ +   +++ +l
  gi|298675091|ref|YP_003726841.1| 526 IDNSPIGIFVIDKNGNYVDVNPAACHIIGYTKDEL-LSMNIIDL 568
                                       578889**********************9998877.55555555 PP

  == domain 8  score: 1.6 bits;  conditional E-value: 0.2
                             PAS_7   3 nmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellryn 48 
                                       +  ++i+  D d+++v +N+  +e l++++e +   ++++++ +y+
  gi|298675091|ref|YP_003726841.1| 648 QAADAIIAHDFDGNIVYVNNLACENLGYSKEEL-LSMNIADISAYI 692
                                       556789999********************9999.899999998886 PP

>> MEKHLA  MEKHLA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.58   8.7e+02      43      70 ..     282     309 ..     251     319 .. 0.68
   2 !   12.4   0.1   7.4e-05      0.11      48     116 ..     416     481 ..     392     507 .. 0.70
   3 ?   -1.3   0.0       1.2   1.9e+03      47      97 ..     538     588 ..     495     601 .. 0.54
   4 ?    5.1   0.0     0.013        20      23      76 ..     635     687 ..     623     696 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.58
                            MEKHLA  43 hslkadpvfnyaNqaaldllettweelt 70 
                                        +++++   +yaN aa ++l ++ +e+ 
  gi|298675091|ref|YP_003726841.1| 282 TKVNKNGNIVYANSAAENVLGLSKSEIE 309
                                       4556667889******999999888776 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 7.4e-05
                            MEKHLA  48 dpvfnyaNqaaldllettweeltdlpsrksaepeekeeRealLekvaeqgfvenysGvrisstGrrfsi 116
                                       d  ++yaN a+ld++e++ ee+   + ++  + +e++   +  + + e+g  +  +G   +++G  f +
  gi|298675091|ref|YP_003726841.1| 416 DGYLTYANSASLDMWEYNKEEILGKHITEFWQYKENAI--NVYHYLHENGSWK-SEGKAKTKHGNVFDV 481
                                       56789****************99888888777555444..4445555555533.555556666665555 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.2
                            MEKHLA  47 adpvfnyaNqaaldllettweeltdlpsrksaepeekeeRealLekvaeqg 97 
                                       ++  ++  N aa ++  +t +el ++       ++++e   + +e++ e+g
  gi|298675091|ref|YP_003726841.1| 538 KNGNYVDVNPAACHIIGYTKDELLSMNIIDLHPDNAHELAGQIFEELLENG 588
                                       333444446666666666666666666666555555555556666666665 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.013
                            MEKHLA  23 sesaeelakaLfe.apfavlshslkadpvfnyaNqaaldllettweeltdlpsrk 76 
                                        +++ee  ++L e a +a+++h+++     +y N+ a + l ++ eel ++    
  gi|298675091|ref|YP_003726841.1| 635 LRESEERFRTLTEqAADAIIAHDFD--GNIVYVNNLACENLGYSKEELLSMNIAD 687
                                       4456777888887799*******86..668899***************9998765 PP

>> PAS_12  UPF0242 C-terminal PAS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.54     8e+02      66      98 ..      34      67 ..      25      86 .. 0.78
   2 ?    2.5   0.0     0.066        99      44      88 ..     120     166 ..     109     168 .. 0.89
   3 ?    3.9   0.0     0.025        37      60      96 ..     281     317 ..     268     340 .. 0.80
   4 ?   -2.4   0.1       2.2   3.3e+03      66     136 ..     416     486 ..     400     490 .. 0.57
   5 ?   -3.6   0.0       5.2   7.8e+03      71      89 ..     544     562 ..     528     565 .. 0.79
   6 !    6.2   0.0    0.0048       7.2      54      90 ..     647     683 ..     636     698 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.54
                            PAS_12 66 enkllfaNaqirallGwssdkflqdf.seivqeg 98
                                      + k++ +N   ++++G+  d+++ +  s+i + g
  gi|298675091|ref|YP_003726841.1| 34 DYKIIDINPAYESIVGLKRDEVVGQLaSNIYDTG 67
                                      679999**************99976514455555 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.066
                            PAS_12  44 lRrLfDsLrs..EnlgailvysqkenkllfaNaqirallGwssdkfl 88 
                                       +R+  D+L+   En  ++++    e++++ +N+  + + G  sd+++
  gi|298675091|ref|YP_003726841.1| 120 QRKTDDELKTiyENVPMVIMMVDSERRIFKVNKSAELFSGTTSDEMV 166
                                       6788888986559***********************99999999876 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.025
                            PAS_12  60 lvysqkenkllfaNaqirallGwssdkflqdfseivq 96 
                                       +   +k+  +++aN+  +++lG+s+ ++  +  + v+
  gi|298675091|ref|YP_003726841.1| 281 ITKVNKNGNIVYANSAAENVLGLSKSEIEGRTYDNVK 317
                                       555678899***************9998777666665 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 2.2
                            PAS_12  66 enkllfaNaqirallGwssdkflqdfseivqegleeWkralaklssktes...kirlvlKtKagqevllncllg 136
                                       +  l +aN+ + ++  ++++++l +    ++e  +  ++a++  +  +e+   k + ++KtK+g+   ++ l+ 
  gi|298675091|ref|YP_003726841.1| 416 DGYLTYANSASLDMWEYNKEEILGKH---ITEFWQYKENAINVYHYLHENgswKSEGKAKTKHGNVFDVYSLIN 486
                                       55667888888888888888776543...333333333344433333332212555566777776666666555 PP

  == domain 5  score: -3.6 bits;  conditional E-value: 5.2
                            PAS_12  71 faNaqirallGwssdkflq 89 
                                        +N    +++G+ +d++l+
  gi|298675091|ref|YP_003726841.1| 544 DVNPAACHIIGYTKDELLS 562
                                       578889999****999876 PP

  == domain 6  score: 6.2 bits;  conditional E-value: 0.0048
                            PAS_12  54 EnlgailvysqkenkllfaNaqirallGwssdkflqd 90 
                                       E+++  ++   ++  ++++N+   + lG+s++++l+ 
  gi|298675091|ref|YP_003726841.1| 647 EQAADAIIAHDFDGNIVYVNNLACENLGYSKEELLSM 683
                                       66667777788999******************99864 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       3.8   5.7e+03       3      21 ..     392     410 ..     386     416 .. 0.67
   2 ?   12.7   0.0   5.9e-05     0.089       4      92 ..     889     984 ..     886     992 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.8
                       HATPase_c_5   3 dldlcvilgnlLdNAieac 21 
                                       + d   ++ n L+ +i+a 
  gi|298675091|ref|YP_003726841.1| 392 KEDTLHLMKNTLESSINAI 410
                                       4566667777777666664 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 5.9e-05
                       HATPase_c_5   4 ldlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg.......ek....kkless.kskkeehG 68 
                                       + l  il nl  NA+   ++      ++++++ ++++++++s+  +  g       e+    k+l s  +++ +  G
  gi|298675091|ref|YP_003726841.1| 889 IKLRQILYNLVYNAVKFTEQ-----GSVTVKLDWNDNDMLFSVIDTGIGipadkqdEIfdsfKQLDSGaSRRYSGTG 960
                                       56778999999999876665.....459***************9996666666555225444556554366778899 PP

                       HATPase_c_5  69 iGlksireivkkykgnlsieaedg 92 
                                       +Gl  ++++v+ ++g++++e e++
  gi|298675091|ref|YP_003726841.1| 961 LGLALVERLVEMHGGKIWVESEER 984
                                       99*****************99875 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00016      0.24      40     110 ..     895     971 ..     888     985 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                       HATPase_c_2  40 ctNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeep........keslkegGrGlalikgl 108
                                       ++N v  a +  ++g+v+v+l+ +++ + ++v D G g ++ ++++     +        +      G+Glal+++l
  gi|298675091|ref|YP_003726841.1| 895 LYNLVYNAVKFTEQGSVTVKLDWNDNDMLFSVIDTGIGIPADKQDEIFD--SfkqldsgaSRRYSGTGLGLALVERL 969
                                       68888888888999**********************9966654433222..124557877777788899******99 PP

                       HATPase_c_2 109 vD 110
                                       v+
  gi|298675091|ref|YP_003726841.1| 970 VE 971
                                       86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (996 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       913  (0.0509231); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.61u 0.23s 00:00:00.84 Elapsed: 00:00:00.41
# Mc/sec: 7315.00
//
Query:       gi|298675092|ref|YP_003726842.1|  [L=734]
Description: signal transduction histidine kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.9e-42  141.9   1.1      1e-18   67.4   0.5    4.2  4  PAS_3            PAS fold
    3.8e-35  120.3   8.1    4.9e-12   46.0   0.0    4.6  4  PAS_9            PAS domain
      1e-31  109.4   0.0    1.9e-10   40.9   0.0    4.4  4  PAS_4            PAS fold
    4.7e-29  100.3   5.1    4.7e-29  100.3   5.1    2.4  1  HisKA_2          Histidine kinase
    6.6e-21   74.4   0.1    1.8e-13   50.5   0.0    4.6  4  PAS              PAS fold
    2.4e-07   30.9   0.0    3.4e-05   23.9   0.0    2.9  2  PAS_11           PAS domain
    1.6e-06   28.6   0.0    1.2e-05   25.7   0.0    2.4  1  HATPase_c        Histidine kinase-, DNA gyrase B-, and HSP90-
    4.6e-06   27.2   1.8    6.2e-06   26.8   0.3    2.0  1  HWE_HK           HWE histidine kinase
    8.4e-05   22.5   0.0       0.32   11.1   0.0    4.4  4  PAS_8            PAS domain
    8.8e-05   22.5   0.0    0.00018   21.5   0.0    1.5  1  HATPase_c_2      Histidine kinase-like ATPase domain
    0.00033   20.9   0.1     0.0023   18.2   0.1    2.2  2  Gluconate_2-dh3  Gluconate 2-dehydrogenase subunit 3
     0.0016   19.0   1.8       0.19   12.3   0.0    3.9  4  PAS_10           PAS domain
     0.0067   17.0   7.7      0.019   15.6   0.8    2.8  2  U1snRNP70_N      U1 small nuclear ribonucleoprotein of 70kDa 
  ------ inclusion threshold ------
      0.022   14.9   3.1       0.61   10.3   0.0    4.4  6  PAS_7            PAS fold
      0.061   13.1   0.3        2.1    8.2   0.0    2.5  2  HATPase_c_3      Histidine kinase-, DNA gyrase B-, and HSP90-
      0.093   12.0   4.8       0.28   10.4   4.8    1.9  1  CorA             CorA-like Mg2+ transporter protein
       0.19   11.4   3.5       0.24   11.2   0.4    2.8  2  SPOB_a           Sensor_kinase_SpoOB-type, alpha-helical doma


Domain annotation for each model (and alignments):
>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.033        34       4      86 ..      31     111 ..      29     114 .. 0.82
   2 !   64.9   0.0   5.8e-21   6.1e-18       2      86 ..     155     237 ..     154     239 .. 0.96
   3 !   67.4   0.5   9.6e-22     1e-18       3      89 .]     282     371 ..     280     371 .. 0.95
   4 ?   -1.4   0.0       2.8     3e+03      19      75 ..     428     481 ..     397     493 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.033
                             PAS_3   4 vserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirdeng 80 
                                       ++++  + lG++++e+ +   s++d+   +  ++++++ ++++k +e++++   +++  G  r ++ + ++  d+ +
  gi|298675092|ref|YP_003726842.1|  31 ANKAHADFLGLDKSEFGNV--SIYDIFTKDVADYFFKDNKKIFKIKEKIHTREWFKNSKGVSRLLSITKTPKLDSCN 105
                                       57889999***********..**********************9999997766678888877777777776666666 PP

                             PAS_3  81 kpvrvi 86 
                                       ++ ++i
  gi|298675092|ref|YP_003726842.1| 106 NVEYII 111
                                       666665 PP

  == domain 2  score: 64.9 bits;  conditional E-value: 5.8e-21
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       +y+ ++++  lGy pe l+gk  s+ ++vhp+D++r++++++ +l++  p + eyR++++dG+y w+e++++ i+d+
  gi|298675092|ref|YP_003726842.1| 155 VYAGPTYKSNLGYNPEHLIGK--SVFNFVHPDDLDRIKSEFNSLLETLIPRKSEYRCLHADGHYLWLETYGNFIYDD 229
                                       7899999**************..****************************************************** PP

                             PAS_3  79 ngkpvrvi 86 
                                        g++ +++
  gi|298675092|ref|YP_003726842.1| 230 IGNIKKIV 237
                                       **999887 PP

  == domain 3  score: 67.4 bits;  conditional E-value: 9.6e-22
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyege...yRirrkdGeyrwveararvir 76 
                                       yvs++v +i+Gy  +++ +++ s++d++hp+D+erv+++++++ ++  +++++   yRi++k+  +rwv++r+++ir
  gi|298675092|ref|YP_003726842.1| 282 YVSNNVVDIFGYYVDDFNDDKLSYADIIHPDDIERVKSEVETYSENPDRFKFQhkpYRIITKNRNIRWVDDRTTIIR 358
                                       9*******************************************999977666678********************* PP

                             PAS_3  77 dengkpvrvigva 89 
                                       ++ g++++++gv+
  gi|298675092|ref|YP_003726842.1| 359 NDCGEITHYQGVI 371
                                       ***********96 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 2.8
                             PAS_3  19 llgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvi 75 
                                       l+gk  +++++ h  D +  +    +alk+g+  e+ +    ++ ++ w+e + +++
  gi|298675092|ref|YP_003726842.1| 428 LEGK--KCYQVYHNNDKPCDYCPTSRALKTGK-TETNIVPGLPNSKIEWLEIYSYPM 481
                                       4455..77777777777766666666676666.344444444555555555555555 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.3     6e-08   6.3e-05       5     104 .]      21     119 ..      17     119 .. 0.91
   2 !   46.0   0.0   4.6e-15   4.9e-12       2     104 .]     143     245 ..     142     245 .. 0.87
   3 !   20.5   0.3   3.9e-07   0.00042       7     104 .]     273     376 ..     265     376 .. 0.81
   4 !   32.4   0.0     8e-11   8.5e-08       2     104 .]     400     501 ..     399     501 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 6e-08
                             PAS_9   5 lidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwvl 79 
                                       +++ ++ +   aN+a +++lG ++ e+ + si d+f  + +++  ++ +++++ ++    +    + +++g   +  
  gi|298675092|ref|YP_003726842.1|  21 IFI-DEQTYYIANKAHADFLGLDKSEFGNVSIYDIFtkDVADYFFKDNKKIFKIKE--KIHTREWFKNSKGVSRLLS 94 
                                       335.4555889*************************99999999999999999999..99***************** PP

                             PAS_9  80 ltaspvkdddgelvgiivilrDite 104
                                       +t +p  d+ +++  ii+  +Dite
  gi|298675092|ref|YP_003726842.1|  95 ITKTPKLDSCNNVEYIICSAEDITE 119
                                       *********999999*********8 PP

  == domain 2  score: 46.0 bits;  conditional E-value: 4.6e-15
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk..kerevevvlirkngetf 76 
                                       ++i++++++g+ +ya ++ +  lGy+pe ++gks+++++  +p++ +r++  ++++ +  ++r  e+ + + +g ++
  gi|298675092|ref|YP_003726842.1| 143 EMICLTDKNGNFVYAGPTYKSNLGYNPEHLIGKSVFNFV--HPDDLDRIKSEFNSLLEtlIPRKSEYRCLHADGHYL 217
                                       6789999********************************..44444444444444444488**************** PP

                             PAS_9  77 wvlltaspvkdddgelvgiivilrDite 104
                                       w +     ++dd g+++ i+++ rDit+
  gi|298675092|ref|YP_003726842.1| 218 WLETYGNFIYDDIGNIKKIVFTGRDITK 245
                                       **************************95 PP

  == domain 3  score: 20.5 bits;  conditional E-value: 3.9e-07
                             PAS_9   7 dnpdg.rilyaNeaalrllGyspeevlgks..itdlfvtdpeanerlraaleqgrk.....kerevevvlirknget 75 
                                       d ++g +++y+++ + +++Gy  +++   +  + d++  +p++ er++  +e+ ++     k++++++ +i+kn++ 
  gi|298675092|ref|YP_003726842.1| 273 DEESGwPVEYVSNNVVDIFGYYVDDFNDDKlsYADII--HPDDIERVKSEVETYSEnpdrfKFQHKPYRIITKNRNI 347
                                       456665555***********99999998776699999..555555555555555556888***************** PP

                             PAS_9  76 fwvlltaspvkdddgelvgiivilrDite 104
                                        wv+ + + +++d ge++++ +++ Dit+
  gi|298675092|ref|YP_003726842.1| 348 RWVDDRTTIIRNDCGEITHYQGVILDITD 376
                                       ****99*********************96 PP

  == domain 4  score: 32.4 bits;  conditional E-value: 8e-11
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGys.peevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirknget 75 
                                       dgi ++++d+++++aN ++ ++  y+    + gk++ +++   ++p + +  ++al++g+    e ++v   +n + 
  gi|298675092|ref|YP_003726842.1| 400 DGISVIDTDFNVIRANSKMGEW--YKvNTPLEGKKCYQVYhnNDKPCDYCPTSRALKTGK---TETNIVPGLPNSKI 471
                                       7999999***************..55234499********55555555555555555555...9************* PP

                             PAS_9  76 fwvlltaspvkdd.dgelvgiivilrDite 104
                                        w ++  +p+ d   ge+ g++ ++rDite
  gi|298675092|ref|YP_003726842.1| 472 EWLEIYSYPMNDRyTGEILGVVEFVRDITE 501
                                       *****************************8 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   7.7e-05     0.081       3     108 ..      14     120 ..      12     122 .. 0.89
   2 !   36.2   0.0   5.4e-12   5.7e-09       3     110 .]     140     248 ..     138     248 .. 0.91
   3 !   13.9   0.0   4.5e-05     0.048      17     109 ..     280     378 ..     268     379 .. 0.96
   4 !   40.9   0.0   1.8e-13   1.9e-10       1     108 [.     395     502 ..     395     504 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.7e-05
                             PAS_4   3 slpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pgee 78 
                                       +++  ++++ +++++  aN+a a+ +g++  e+ + + ++++++++a+ +  + ++  + +e i++ e  +   g  
  gi|298675092|ref|YP_003726842.1|  14 QTNTQIFIFIDEQTYYIANKAHADFLGLDKSEFGNVSIYDIFTKDVADYFFKDNKKIFKIKEKIHTREWFKNsKGVS 90 
                                       555566667667788889******************************9999999999988888888877777**** PP

                             PAS_4  79 rhyelrllPlrdesGevigvlvisrDiTer 108
                                       r ++++++P +d+   v  +++ + DiTe 
  gi|298675092|ref|YP_003726842.1|  91 RLLSITKTPKLDSCNNVEYIICSAEDITEK 120
                                       ****************************97 PP

  == domain 2  score: 36.2 bits;  conditional E-value: 5.4e-12
                             PAS_4   3 slpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pgee 78 
                                       ++ ++++  d++g+++ya +++ + +g+ pe+l+Gk+++ ++ ++d +r+ +  + +le+  p +++   l+ +g  
  gi|298675092|ref|YP_003726842.1| 140 NMVEMICLTDKNGNFVYAGPTYKSNLGYNPEHLIGKSVFNFVHPDDLDRIKSEFNSLLETLIPRKSEYRCLHaDGHY 216
                                       667899**********************************99999***********************999955555 PP

                             PAS_4  79 rhyelrllPlrdesGevigvlvisrDiTerrr 110
                                        ++e+  + + d+ G +  +++++rDiT r++
  gi|298675092|ref|YP_003726842.1| 217 LWLETYGNFIYDDIGNIKKIVFTGRDITKRKQ 248
                                       5555555999*******************985 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 4.5e-05
                             PAS_4  17 vlyaNaaaaelfgappeellGktla..ellpeedaarleralrrvlegeepiefleelll....pgeerhyelrllP 87 
                                       v+y++++  ++fg+  +++ + +l   ++  ++d +r+ + ++   e  ++ +f++ + +    ++  r+++ r + 
  gi|298675092|ref|YP_003726842.1| 280 VEYVSNNVVDIFGYYVDDFNDDKLSyaDIIHPDDIERVKSEVETYSENPDRFKFQHKPYRiitkNRNIRWVDDRTTI 356
                                       7899999999**********9999999999999***********************9999***************** PP

                             PAS_4  88 lrdesGevigvlvisrDiTerr 109
                                       +r++ Ge+ ++ +++ DiT+r+
  gi|298675092|ref|YP_003726842.1| 357 IRNDCGEITHYQGVILDITDRK 378
                                       ********************97 PP

  == domain 4  score: 40.9 bits;  conditional E-value: 1.8e-13
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       ++s++d++ v+d+d++v++aN  + e++++    l Gk++++++   d++   ++  r+l+++++ +     l++ +
  gi|298675092|ref|YP_003726842.1| 395 FESIQDGISVIDTDFNVIRANSKMGEWYKVN-TPLEGKKCYQVYHNNDKPCDYCPTSRALKTGKTETNIVPGLPNSK 470
                                       79************************99985.79********99999999999************************ PP

                             PAS_4  78 erhyelrllPlrdesGe.vigvlvisrDiTer 108
                                        +++e+  +P+ d+  + ++gv++++rDiTe 
  gi|298675092|ref|YP_003726842.1| 471 IEWLEIYSYPMNDRYTGeILGVVEFVRDITEK 502
                                       ***********9996555************96 PP

>> HisKA_2  Histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.3   5.1   4.4e-32   4.7e-29       1      76 []     544     619 ..     544     619 .. 0.99

  Alignments for each domain:
  == domain 1  score: 100.3 bits;  conditional E-value: 4.4e-32
                           HisKA_2   1 EihHRvkNnLqvisslLslqarkakdeevkealresqnRvlsialiheeLyksedletvdfseylekLvenlfksy 76 
                                       E+hHR+kNnLqvisslL+lq++k++d++v+ea+r++qnRv+s++l+h+++y++++le++++++y+e+Lve+l+++y
  gi|298675092|ref|YP_003726842.1| 544 ELHHRIKNNLQVISSLLNLQSEKFNDDTVNEAFRDTQNRVISMSLVHQKIYHTKGLESINIRDYIEDLVEHLISLY 619
                                       99**********************************************************************9976 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.15   1.6e+02      26     113 .]      31     117 ..      11     117 .. 0.73
   2 !   50.5   0.0   1.7e-16   1.8e-13       2     113 .]     133     243 ..     132     243 .. 0.95
   3 !   11.1   0.0   0.00028      0.29      25     113 .]     282     374 ..     258     374 .. 0.86
   4 ?    4.4   0.0     0.034        36       4      32 ..     392     420 ..     389     426 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.15
                                       ECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEEEEEEEEETTE CS
                               PAS  26 vNaaaeellGlsreevlgkslldliheedda.elaelleqlleqgeesrageisfklrdgrpihlevraspvrdagg 101
                                       +N+a +++lGl+ +e  + s++d +  +  a ++ +  ++  + +e+ ++ e  fk  +g  + l ++ +p +d   
  gi|298675092|ref|YP_003726842.1|  31 ANKAHADFLGLDKSEFGNVSIYDIFTKD-VAdYFFKDNKKIFKIKEKIHTREW-FKNSKGVSRLLSITKTPKLDSCN 105
                                       6788888888888888888888555444.334555555555555555555443.33358889*************** PP

                                       EEEEEEEEEEES CS
                               PAS 102 eilgflgvlrdi 113
                                       ++ ++++ + di
  gi|298675092|ref|YP_003726842.1| 106 NVEYIICSAEDI 117
                                       *******99997 PP

  == domain 2  score: 50.5 bits;  conditional E-value: 1.7e-16
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                        +r+i  ++ ++i+++D++g+++y+ +++ + lG+++e ++gks++ ++h++d +  ++++  lle+  +++++ ++
  gi|298675092|ref|YP_003726842.1| 133 LFREITKNMVEMICLTDKNGNFVYAGPTYKSNLGYNPEHLIGKSVFNFVHPDDLDRIKSEFNSLLETLIPRKSEYRC 209
                                       68899999*********************************************999999999999999999999999 PP

                                       EECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  79 fklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       +   dg + +le+  + ++d  g+i+ +++++rdi
  gi|298675092|ref|YP_003726842.1| 210 LHA-DGHYLWLETYGNFIYDDIGNIKKIVFTGRDI 243
                                       999.******************************8 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00028
                                       EECHHHHHHHSSTHHHCT.TSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEEC...TTSSEEEEEEEEEEEE CS
                               PAS  25 yvNaaaeellGlsreevl.gkslldliheeddaelaelleqlleqgeesrageisfkl...rdgrpihlevraspvr 97 
                                       yv+ +  +++G+  ++    k  + +i+++dd e+++   + ++++ ++  ++++  +   ++  +++++ r++ +r
  gi|298675092|ref|YP_003726842.1| 282 YVSNNVVDIFGYYVDDFNdDKLSYADIIHPDDIERVKSEVETYSENPDRFKFQHKPYRiitKNRNIRWVDDRTTIIR 358
                                       67777777888888555514566889999**********************99988779999*************** PP

                                       ETTEEEEEEEEEEEES CS
                               PAS  98 daggeilgflgvlrdi 113
                                       +  gei+++ gv+ di
  gi|298675092|ref|YP_003726842.1| 359 NDCGEITHYQGVILDI 374
                                       *************998 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.034
                                       HHHHHHSSSEEEEEETTSBEEEECHHHHH CS
                               PAS   4 raileslpdpifvvDedgrilyvNaaaee 32 
                                       +  +es+ d+i v+D d +++ +N+++ e
  gi|298675092|ref|YP_003726842.1| 392 DDTFESIQDGISVIDTDFNVIRANSKMGE 420
                                       56689********************9975 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   3.2e-08   3.4e-05       9      91 ..     149     227 ..     142     237 .. 0.89
   2 ?    3.6   0.0     0.068        72      38      80 ..     303     347 ..     293     372 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 3.2e-08
                            PAS_11   9 didgkIisvDtsaLrasfslglekeelvgrsiydLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvkvkt 85 
                                       d +g+++   +     +  lg++ e l+g+s+++++hp+dl ++ks +   + ++   ++s yR   ++++++++ t
  gi|298675092|ref|YP_003726842.1| 149 DKNGNFVYAGP---TYKSNLGYNPEHLIGKSVFNFVHPDDLDRIKSEFNSLL-ETLIPRKSEYRCLHADGHYLWLET 221
                                       66777777777...778889********************************.999999****************** PP

                            PAS_11  86 ksklfk 91 
                                        + + +
  gi|298675092|ref|YP_003726842.1| 222 YGNFIY 227
                                       887765 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.068
                            PAS_11  38 rsiydLchpqdlstlkshlrevissngeatssl..yRLrlsqdkf 80 
                                       +s+ d++hp+d +++ks  +   +++++++ +   yR+++++ ++
  gi|298675092|ref|YP_003726842.1| 303 LSYADIIHPDDIERVKSEVETYSENPDRFKFQHkpYRIITKNRNI 347
                                       6899*************9977765555544333459999854443 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   1.2e-08   1.2e-05       5     107 ..     642     731 ..     638     733 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.2e-08
                                       HHHHHHHHHHHHHHHHHS...TTTEEEEEEEEEE.TEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSS.H CS
                         HATPase_c   5 rLrqiisnlvdNavkfat...kageieveikase.ddlvisveDnGiGipkedlkklfekfsqddstkrggggtG.l 76 
                                        L  +i++lv+N++k+a    + ge+ v    +e + +++ v+DnG+Gip+ d++     +++           G l
  gi|298675092|ref|YP_003726842.1| 642 PLGMLINELVSNSLKYAYsedEYGELNVIFYETEpGIYTLIVSDNGKGIPE-DID-----LDN----------PGsL 702
                                       67789***********554123334444444333689999**********8.455.....334..........3338 PP

                                       HHHHHHHHHHHTTTEEEEEEETTTEEEEEEE CS
                         HATPase_c  77 GlsivkklvelmgGeiwvesepgrGttftft 107
                                       Gl + k+lv++++G+++++ +   Gt+f+++
  gi|298675092|ref|YP_003726842.1| 703 GLQLIKSLVDQINGDFKLHGNN--GTEFVIN 731
                                       9******9999******97777..9999876 PP

>> HWE_HK  HWE histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.3   5.9e-09   6.2e-06       1      67 [.     544     613 ..     544     627 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 5.9e-09
                                       HHHHHHHHHHHHHHHHHHHHSS..SXS-HHHHHHHHHHHHHHHHHHHHHHHHCT.TS-EEHHHHHHHHHH CS
                            HWE_HK   1 ElnHRvKNlLavvqsiarqtlr..saesleefaeklsgRLqALsaahdllsree.wagaeLaelleeela 67 
                                       El+HR+KN L v++s+ +  ++  + ++++e+ ++ ++R+ ++s +h+ + +++  +++++++ +e+ ++
  gi|298675092|ref|YP_003726842.1| 544 ELHHRIKNNLQVISSLLNLQSEkfNDDTVNEAFRDTQNRVISMSLVHQKIYHTKgLESINIRDYIEDLVE 613
                                       9****************9877623467889999999***********98665541456666655555444 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.24   2.5e+02      25      46 ..      28      47 ..       9      70 .. 0.63
   2 ?    0.7   0.0      0.55   5.8e+02       1      43 [.     132     175 ..     132     200 .. 0.71
   3 ?    2.1   0.0      0.19     2e+02      17      53 ..     270     310 ..     251     324 .. 0.64
   4 !   11.1   0.0   0.00031      0.32       7      37 ..     395     425 ..     389     452 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.24
                             PAS_8 25 d..vNqaalellGysadlkgellg 46
                                      +  +N+a +++lG+    + +++g
  gi|298675092|ref|YP_003726842.1| 28 YyiANKAHADFLGL----DKSEFG 47
                                      1459*********5....555454 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.55
                             PAS_8   1 erlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkge 43 
                                       e +r +  ++ + i+++d +g+ +v++ +++   lGy+ + l+g+
  gi|298675092|ref|YP_003726842.1| 132 ELFREITKNMVEMICLTDkNGN-FVYAGPTYKSNLGYNpEHLIGK 175
                                       57888999999*****998888.9998777777777765554444 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.19
                             PAS_8  17 vdlgdr....ivdvNqaalellGys.adlkgellgqllpvlr 53 
                                       +++++     + +v +   +++Gy  +d+ +++l  + + ++
  gi|298675092|ref|YP_003726842.1| 270 WKNDEEsgwpVEYVSNNVVDIFGYYvDDFNDDKLS-YADIIH 310
                                       4444434566889999999******9999998884.444333 PP

  == domain 4  score: 11.1 bits;  conditional E-value: 0.00031
                             PAS_8   7 fesspdgiavvdlgdrivdvNqaalellGys 37 
                                       fes++dgi v+d++ +++ +N ++ e + ++
  gi|298675092|ref|YP_003726842.1| 395 FESIQDGISVIDTDFNVIRANSKMGEWYKVN 425
                                       9***********5556******998777665 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   1.7e-07   0.00018      32     119 ..     643     726 ..     632     732 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.7e-07
                       HATPase_c_2  32 irlaveEactNavehayleapegpvevr.lesdeealtvevaDsGpgfdpetlpdpteeepkeslkegGrGlalikg 107
                                       + + ++E+++N  ++ay e++ g+++v  +e +++  t+ v+D+G+g +             + + +g +Gl lik+
  gi|298675092|ref|YP_003726842.1| 643 LGMLINELVSNSLKYAYSEDEYGELNVIfYETEPGIYTLIVSDNGKGIPEDI----------DLDNPGSLGLQLIKS 709
                                       56789****************7666666377777779**********76653..........7788999******** PP

                       HATPase_c_2 108 lvDev..ey...dgegn 119
                                       lvD++  ++   +++g+
  gi|298675092|ref|YP_003726842.1| 710 LVDQIngDFklhGNNGT 726
                                       ***99554455555555 PP

>> Gluconate_2-dh3  Gluconate 2-dehydrogenase subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.3   1.4e+03      90     116 ..     119     145 ..     100     153 .. 0.76
   2 !   18.2   0.1   2.2e-06    0.0023      25      86 ..     488     549 ..     479     599 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.3
                   Gluconate_2-dh3  90 kgtgealeasaeahfFsllreltlegy 116
                                       ++++ + +++++++ F+++ ++++e+ 
  gi|298675092|ref|YP_003726842.1| 119 EKNQSEKQKKKSEELFREITKNMVEMI 145
                                       45556677778899****999999865 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 2.2e-06
                   Gluconate_2-dh3  25 keagvaafidrqladaplppeqeayrkglaaldayaraeygksFveldgaqqdalLealeke 86 
                                       + +gv++f+  + +++ ++ + e y+ +l++++++++++ +k+  e+++a++ ++Le   + 
  gi|298675092|ref|YP_003726842.1| 488 EILGVVEFVRDITEKTKTERQLEKYSTELKQINEELENRVQKQTEEIKNAERLRVLELHHRI 549
                                       5589****************************************************987765 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.14   1.5e+02      12     106 .]     145     244 ..     135     244 .. 0.69
   2 ?   -0.5   0.1       1.8   1.9e+03      67      96 ..     318     348 ..     299     375 .. 0.67
   3 !   12.3   0.0   0.00018      0.19       5     106 .]     395     500 ..     391     500 .. 0.86
   4 ?   -2.9   0.1       9.7     1e+04      55      66 ..     527     538 ..     508     578 .. 0.57

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.14
                            PAS_10  12 ltflDdnlqirrFtpaakklfklipad.vGrpladihpk....kavknveeviealrtgekdevevvvpkngkwvlv 83 
                                       +   D+n ++ +  p++k+ + ++p+  +G ++ +++++    ++++++++++e+l+ +++++   + +    w   
  gi|298675092|ref|YP_003726842.1| 145 ICLTDKNGNFVYAGPTYKSNLGYNPEHlIGKSVFNFVHPddldRIKSEFNSLLETLIPRKSEYRCLHADGHYLWLET 221
                                       44557777777777777666666655438******966625655666678888888888888887777766667777 PP

                            PAS_10  84 rylpyrdedgeiaGvvetfvDit 106
                                       +   ++d+ g+i+ +v t  Dit
  gi|298675092|ref|YP_003726842.1| 222 YGNFIYDDIGNIKKIVFTGRDIT 244
                                       77777888888888888888875 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.8
                            PAS_10  67 kdevevvvpkngkw.vlvrylpyrdedgeia 96 
                                       k eve++ ++++++ ++++  ++ +++++i+
  gi|298675092|ref|YP_003726842.1| 318 KSEVETYSENPDRFkFQHKPYRIITKNRNIR 348
                                       3445555556666556666666666666654 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00018
                            PAS_10   5 LnstpieltflDdnlqirrFtpaakklfklipadvGrpladi.hpkkavknveeviealrtgekdevevvv.p.kng 78 
                                       ++s++ ++  +D++ +++r + +  + +k++    G +  ++ h++++  +      al+tg++++  v+  p ++ 
  gi|298675092|ref|YP_003726842.1| 395 FESIQDGISVIDTDFNVIRANSKMGEWYKVNTPLEGKKCYQVyHNNDKPCDYCPTSRALKTGKTETNIVPGlPnSKI 471
                                       67778888999999999999999999999999999999999977779999999999999999999887666435778 PP

                            PAS_10  79 kwvlvrylpyrde.dgeiaGvvetfvDit 106
                                       +w  ++  p++d  +gei Gvve++ Dit
  gi|298675092|ref|YP_003726842.1| 472 EWLEIYSYPMNDRyTGEILGVVEFVRDIT 500
                                       99********99658*************7 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 9.7
                            PAS_10  55 veeviealrtge 66 
                                       v++ +e++++ e
  gi|298675092|ref|YP_003726842.1| 527 VQKQTEEIKNAE 538
                                       333333333333 PP

>> U1snRNP70_N  U1 small nuclear ribonucleoprotein of 70kDa MW N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   1.1     0.069        73      28      85 ..      78     137 ..      67     141 .. 0.63
   2 !   15.6   0.8   1.8e-05     0.019      13      84 ..     467     537 ..     466     539 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.069
                       U1snRNP70_N  28 ekrktkkkitGvaaflselke...deeeqeppektetkeekkererkekkekkeekleeal 85 
                                       ++r+  k+ +Gv+ +ls  k+   d   ++ +    + e  +e+++ ek++kk e+l +++
  gi|298675092|ref|YP_003726842.1|  78 HTREWFKNSKGVSRLLSITKTpklD-SCNNVEYIICSAEDITEKNQSEKQKKKSEELFREI 137
                                       4443357899******999875532.22223334556666777777777777777766654 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.8e-05
                       U1snRNP70_N  13 prpplpylppldydpekrktkkkitGvaaflselkedeeeqeppektetkeekkererkekkekkeekleea 84 
                                       p+ ++++l+  +y++++r t  +i Gv +f++ + e+++++ + ek  t+ ++  +e +++ +k+ e++++a
  gi|298675092|ref|YP_003726842.1| 467 PNSKIEWLEIYSYPMNDRYT-GEILGVVEFVRDITEKTKTERQLEKYSTELKQINEELENRVQKQTEEIKNA 537
                                       67789999999*********.78***********99888888888888899999999999999999998875 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       4.7   4.9e+03     101     114 ..     111     124 ..      76     125 .. 0.83
   2 ?   -1.4   0.0       2.4   2.5e+03       2      35 ..     139     172 ..     138     184 .. 0.80
   3 ?   -1.2   0.0       2.1   2.2e+03     100     115 .]     236     251 ..     233     251 .. 0.86
   4 ?   -1.6   0.0       2.9     3e+03      87     114 ..     371     381 ..     318     382 .. 0.65
   5 ?   10.3   0.0   0.00058      0.61       1      30 [.     395     424 ..     395     456 .. 0.89
   6 ?   -0.3   0.1       1.1   1.2e+03      98     114 ..     490     506 ..     467     509 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.7
                             PAS_7 101 VttytDiTerrrae 114
                                       + + +DiTe+ ++e
  gi|298675092|ref|YP_003726842.1| 111 ICSAEDITEKNQSE 124
                                       56779999999887 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.4
                             PAS_7   2 enmsqGisvfDadlrLvawNrrylelldlpeelv 35 
                                       +nm + i++ D++++ v     y + l++ +e +
  gi|298675092|ref|YP_003726842.1| 139 KNMVEMICLTDKNGNFVYAGPTYKSNLGYNPEHL 172
                                       589999*********9999888888888866655 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 2.1
                             PAS_7 100 fVttytDiTerrraee 115
                                       +V t  DiT+r++ e+
  gi|298675092|ref|YP_003726842.1| 236 IVFTGRDITKRKQLEQ 251
                                       588999*****99875 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 2.9
                             PAS_7  87 vievrgnplpdgGfVttytDiTerrrae 114
                                       +                  DiT+r+ ae
  gi|298675092|ref|YP_003726842.1| 371 I-----------------LDITDRKMAE 381
                                       2.................2777777666 PP

  == domain 5  score: 10.3 bits;  conditional E-value: 0.00058
                             PAS_7   1 lenmsqGisvfDadlrLvawNrrylelldl 30 
                                       +e++++Gisv+D d +++  N+++ e +++
  gi|298675092|ref|YP_003726842.1| 395 FESIQDGISVIDTDFNVIRANSKMGEWYKV 424
                                       589********************9998876 PP

  == domain 6  score: -0.3 bits;  conditional E-value: 1.1
                             PAS_7  98 gGfVttytDiTerrrae 114
                                        G+V    DiTe+ ++e
  gi|298675092|ref|YP_003726842.1| 490 LGVVEFVRDITEKTKTE 506
                                       4999999*****99887 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1      0.15   1.6e+02      80     125 ..     491     535 ..     484     544 .. 0.80
   2 ?    8.2   0.0     0.002       2.1       8      52 ..     648     698 ..     645     713 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.15
                       HATPase_c_3  80 Aslslgkkltvitkkegesstltldvdkidkenekvleeltveeie 125
                                        ++ + +++t  tk+e + ++++ ++++i++e e+ +++ t+e i+
  gi|298675092|ref|YP_003726842.1| 491 GVVEFVRDITEKTKTERQLEKYSTELKQINEELENRVQKQTEE-IK 535
                                       567788899999*****************99999988876655.44 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.002
                       HATPase_c_3   8 aelvdNsld.Adaen....vkievnknrgktgeivieDdGkGmsee.elkn 52 
                                        elv Nsl  A +e      ++ + + +    ++ + D+GkG++e+ +l+n
  gi|298675092|ref|YP_003726842.1| 648 NELVSNSLKyAYSEDeygeLNVIFYETEPGIYTLIVSDNGKGIPEDiDLDN 698
                                       69999999975555566666666665554568999*********9988887 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   4.8   0.00027      0.28     123     203 ..     505     585 ..     485     623 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00027
                              CorA 123 lfellekleeeldeledeledstkkeilrelaqlr.rrlvklrralapnrevlkrllakaddkllddedkeylrdll 198
                                        +++lek ++el+++ +el +++ +++ +e+ + +  r+ +l++ +++n +v+++ll+   +k  dd+ +e +rd +
  gi|298675092|ref|YP_003726842.1| 505 TERQLEKYSTELKQINEEL-ENRVQKQTEEIKNAErLRVLELHHRIKNNLQVISSLLNLQSEKFNDDTVNEAFRDTQ 580
                                       56889**************.666666777777776367********************8888888888888899999 PP

                              CorA 199 deler 203
                                       +++ +
  gi|298675092|ref|YP_003726842.1| 581 NRVIS 585
                                       99877 PP

>> SPOB_a  Sensor_kinase_SpoOB-type, alpha-helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.2       3.5   3.7e+03      39      56 ..     502     519 ..     492     524 .. 0.62
   2 ?   11.2   0.4   0.00022      0.24      18      53 ..     544     579 ..     527     587 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.5
                            SPOB_a  39 ydkaeeyieevvkelkee 56 
                                        +k e ++e++++elk++
  gi|298675092|ref|YP_003726842.1| 502 KTKTERQLEKYSTELKQI 519
                                       456666666666666665 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00022
                            SPOB_a  18 sqRHDflNhLQvIsGylqLgkydkaeeyieevvkel 53 
                                        ++H   N+LQvIs++l L+     ++ ++e+ +++
  gi|298675092|ref|YP_003726842.1| 544 ELHHRIKNNLQVISSLLNLQSEKFNDDTVNEAFRDT 579
                                       468999*************98766666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (734 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1967  (0.109711); expected 358.6 (0.02)
Passed bias filter:                      693  (0.0386525); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.62u 0.25s 00:00:00.87 Elapsed: 00:00:00.40
# Mc/sec: 5528.15
//
Query:       gi|298675093|ref|YP_003726843.1|  [L=383]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-28   98.3   2.0      8e-28   97.1   2.0    1.5  1  OrfB_IS605      Probable transposase
    1.4e-23   82.6   0.3    2.8e-23   81.6   0.3    1.5  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    4.4e-20   70.9   1.4    9.3e-20   69.8   1.4    1.6  1  HTH_OrfB_IS605  Helix-turn-helix domain
     0.0065   16.6   0.3      0.016   15.3   0.3    1.6  1  zf-piccolo      Piccolo Zn-finger
  ------ inclusion threshold ------
      0.046   13.5   4.4       0.29   10.9   1.7    2.4  2  Phage_GP20      Phage minor structural protein GP20
      0.047   13.5   1.9       0.43   10.4   0.3    2.4  2  LemA            LemA family
          1   10.2   4.1        1.5    9.7   0.5    2.5  2  Ima1_N          Ima1 N-terminal domain
          1    9.6   7.8       0.26   11.5   1.8    2.3  2  MapZ_EC1        MapZ extracellular domain 1


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.1   2.0   3.6e-31     8e-28       9     117 ..     179     284 ..     168     286 .. 0.94

  Alignments for each domain:
  == domain 1  score: 97.1 bits;  conditional E-value: 3.6e-31
                        OrfB_IS605   9 elpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrs 85 
                                       +++k ++n+++g+D+Gi+++a++++++   ++ ++r lk+  ++l+  +++l++k+k+s+ny+k + ++a++h+k++
  gi|298675093|ref|YP_003726843.1| 179 QKYKFDQNNTVGVDVGIKDFAVTSDGE---KIDNPRYLKNSIERLKVLQKRLSRKKKGSNNYRKLKHQIAKYHEKIA 252
                                       378999*********************...*********************************************** PP

                        OrfB_IS605  86 rrrkhllhklathliktlkevgvetLnvgnmk 117
                                       ++r +++hkl+++li ++++v++e Lnv+++ 
  gi|298675093|ref|YP_003726843.1| 253 NQREDFQHKLSSRLISENQAVALECLNVKGLL 284
                                       *****************************986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.6   0.3   1.2e-26   2.8e-23       1      68 [.     298     367 ..     298     368 .. 0.98

  Alignments for each domain:
  == domain 1  score: 81.6 bits;  conditional E-value: 1.2e-26
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpay.TSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       ++++ ++leyka++yG++++++ ++  +Sk C++Cg+ +++ +l++r+++Cp+C++ +drD+nA++Ni k
  gi|298675093|ref|YP_003726843.1| 298 WSSFVQKLEYKAEWYGKNIIKIGRFDpSSKICHVCGYHHQDlELKDREWECPDCKTIHDRDINASVNIKK 367
                                       99******************************************************************87 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.8   1.4   4.2e-23   9.3e-20       1      47 []       9      54 ..       9      54 .. 0.98

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 4.2e-23
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeegk 47
                                      M lkaykyr yP++ Q+e++a+++G++Rf+YN+aL+ +++ ye+ gk
  gi|298675093|ref|YP_003726843.1|  9 M-LKAYKYRMYPNQIQQELIAKHIGACRFIYNWALENKIKSYEQDGK 54
                                      8.******************************************997 PP

>> zf-piccolo  Piccolo Zn-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.3   7.1e-06     0.016      28      55 ..     326     353 ..     322     356 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7.1e-06
                        zf-piccolo  28 kqvCnlCGFnptphltekkeWlclnCQt 55 
                                       +++C +CG+  ++   + +eW c  C t
  gi|298675093|ref|YP_003726843.1| 326 SKICHVCGYHHQDLELKDREWECPDCKT 353
                                       79************************86 PP

>> Phage_GP20  Phage minor structural protein GP20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.048   1.1e+02     113     136 ..      51      77 ..      24      88 .. 0.71
   2 ?   10.9   1.7   0.00013      0.29      32      90 ..     218     276 ..     205     286 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.048
                        Phage_GP20 113 edgelkg...LdeqikkLkesdkyLFe 136
                                       +dg+ +    L++qi  Lk+++++L e
  gi|298675093|ref|YP_003726843.1|  51 QDGKAISrfeLNKQIRVLKQDHEWLNE 77 
                                       455555334488888888888888876 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00013
                        Phage_GP20  32 eqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeyeakiadlkldnaielaLk 90 
                                       e+lk  +k L+  kk +++  +L+ qi+++ +k++++ ++ + k++ + +++    aL+
  gi|298675093|ref|YP_003726843.1| 218 ERLKVLQKRLSRKKKGSNNYRKLKHQIAKYHEKIANQREDFQHKLSSRLISENQAVALE 276
                                       6788889999999********************************99888776666666 PP

>> LemA  LemA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1     0.075   1.7e+02      30      82 ..      60     112 ..      42     116 .. 0.82
   2 ?   10.4   0.3   0.00019      0.43      58     107 ..     211     261 ..     199     268 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.075
                              LemA  30 EketleevteaRakaaeaesveekaeaenqlssalsrllavaEnYPdLkanen 82 
                                       E +   +v +  ++  ++ + ++ + a  +l++a+ +++     +P++k+++n
  gi|298675093|ref|YP_003726843.1|  60 ELNKQIRVLKQDHEWLNEINSQSLQGATLNLENAFTKFFREKSGFPKFKSKKN 112
                                       55555566666666788889999999************************987 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00019
                              LemA  58 nqlssalsrllavaEnY.PdLkanenfleLqeelegtEnriavaRrrYnea 107
                                       + l+++++rl +++ +   + k ++n+++L++++++  ++ia++R++++++
  gi|298675093|ref|YP_003726843.1| 211 RYLKNSIERLKVLQKRLsRKKKGSNNYRKLKHQIAKYHEKIANQREDFQHK 261
                                       5667777777777666414557899**********************9876 PP

>> Ima1_N  Ima1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.2       0.3   6.7e+02     105     121 ..     236     252 ..     201     316 .. 0.59
   2 ?    9.7   0.5   0.00066       1.5       3      32 ..     329     358 ..     328     375 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.3
                            Ima1_N 105 eyeekeealeeykkele 121
                                       +y++ ++++ +y++++ 
  gi|298675093|ref|YP_003726843.1| 236 NYRKLKHQIAKYHEKIA 252
                                       33333333333333332 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00066
                            Ima1_N   3 CffCnkkskvkyeeknsfeCpsCeayNgfd 32 
                                       C+ C+ + +    +++++eCp+C+ +   d
  gi|298675093|ref|YP_003726843.1| 329 CHVCGYHHQDLELKDREWECPDCKTIHDRD 358
                                       ********999999999******9876555 PP

>> MapZ_EC1  MapZ extracellular domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.4      0.21   4.6e+02      48      84 ..      42      81 ..      39      93 .. 0.74
   2 ?   11.5   1.8   0.00012      0.26      26      78 ..     196     254 ..     175     277 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.21
                          MapZ_EC1 48 LekkLeklk.gskeYk..klkkkldslkkqisaieavNsq 84
                                      Le+k++ ++ + k  +  +l+k++  lk+  + ++++Nsq
  gi|298675093|ref|YP_003726843.1| 42 LENKIKSYEqDGKAISrfELNKQIRVLKQDHEWLNEINSQ 81
                                      5666666664333332227999999999999999999997 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00012
                          MapZ_EC1  26 aafftddketflkn.....sefaklseLekkLeklk.gskeYkklkkkldslkkqisai 78 
                                       ++f ++++ +++ n     + ++ l+ L+k L   k gs++Y+klk+++++  ++i+ +
  gi|298675093|ref|YP_003726843.1| 196 KDFAVTSDGEKIDNprylkNSIERLKVLQKRLSRKKkGSNNYRKLKHQIAKYHEKIANQ 254
                                       555555555555552222123688999*****98777*****************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1506  (0.083998); expected 358.6 (0.02)
Passed bias filter:                      660  (0.0368119); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2733.25
//
Query:       gi|298675094|ref|YP_003726844.1|  [L=121]
Description: hypothetical protein Metev_1167 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0011   19.7   0.0     0.0016   19.2   0.0    1.3  1  Cadherin_C_2  Cadherin cytoplasmic C-terminal


Domain annotation for each model (and alignments):
>> Cadherin_C_2  Cadherin cytoplasmic C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   8.8e-08    0.0016       1      40 [.       7      45 ..       7      86 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 8.8e-08
                      Cadherin_C_2  1 kltlYLviaLasvSflFLltvivlvavrlrkerksaalqk 40
                                      +l ++L++aLa++S l L+ vi + av l +  ++ + + 
  gi|298675094|ref|YP_003726844.1|  7 NLSIILIVALALISTLALAYVIDF-AVTLNEPAENYTETV 45
                                      6899******************99.777765555444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       746  (0.0416086); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 949.99
//
Query:       gi|298675095|ref|YP_003726845.1|  [L=394]
Description: hypothetical protein Metev_1168 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2918.12
//
Query:       gi|298675096|ref|YP_003726846.1|  [L=422]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.6e-24   84.7   1.7    1.1e-23   83.7   0.0    2.3  3  OrfB_IS605      Probable transposase
    1.5e-10   40.8   0.2    4.6e-10   39.3   0.1    1.9  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    0.00014   21.7   2.2    0.00021   21.1   0.7    2.1  2  Pentapeptide_2  Pentapeptide repeats (8 copies)
     0.0047   16.7   0.5      0.012   15.4   0.5    1.7  1  DUF919          Nucleopolyhedrovirus protein of unknown funct


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.81   3.6e+03      37      59 ..      39      61 ..      28      74 .. 0.74
   2 !   83.7   0.0   2.5e-27   1.1e-23      10     119 ..     185     292 ..     176     293 .. 0.94
   3 ?   -3.0   0.2       1.8     8e+03      42      70 ..     340     369 ..     338     376 .. 0.45

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.81
                        OrfB_IS605 37 twflykgrrlksdykylakeiae 59
                                      + f+++g+ l++d  y + +  e
  gi|298675096|ref|YP_003726846.1| 39 QYFFNHGKYLDKDTAYHTVKENE 61
                                      56888999999999988877666 PP

  == domain 2  score: 83.7 bits;  conditional E-value: 2.5e-27
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsr 86 
                                        ++ + n++++iDlG+ n+at+vt++gt+f+ +gr +ks +++++ke+ +lqs ++k++       k+ r ++kr  
  gi|298675096|ref|YP_003726846.1| 185 IAELDYNNHLSIDLGVDNFATCVTTSGTAFILDGRGIKSYNRWWNKEKSRLQSVYDKQN--VDDGIKMDRFSNKRFW 259
                                       6667789***************************************************9..9*************** PP

                        OrfB_IS605  87 rrkhllhklathliktlkevgvetLnvgnmkdi 119
                                       ++++++++ ++h++k++ e+ ++++++g+mk+i
  gi|298675096|ref|YP_003726846.1| 260 KINDFMNQCVNHIVKHCLENRIGNVIIGEMKEI 292
                                       *******************************87 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.8
                        OrfB_IS605  42 kgrrlksdykylakeiaelqsk.lkkskny 70 
                                       +g ++ + +++++ + + l+s  + k+k+y
  gi|298675096|ref|YP_003726846.1| 340 HGIKYHEVNEAYTSKVDALASEpIRKHKKY 369
                                       555555555555555555444314444433 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.4   6.4e+03       9      21 ..     167     179 ..     165     181 .. 0.88
   2 !   39.3   0.1     1e-13   4.6e-10       1      69 []     326     400 ..     326     400 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.4
                    OrfB_Zn_ribbon   9 eykakeyGikvee 21 
                                       +yk +++ i++++
  gi|298675096|ref|YP_003726846.1| 167 KYKGRWFEIEFVY 179
                                       79*******9987 PP

  == domain 2  score: 39.3 bits;  conditional E-value: 1e-13
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSkt...CseCgsknke...alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f+++k +++ k++ +Gik++evn+ayTSk     se  +k+k+   ++s+r    ++ g  +++D+n+a+Nil++
  gi|298675096|ref|YP_003726846.1| 326 FARFKYKIASKCEYHGIKYHEVNEAYTSKVdalASEPIRKHKKylgKRSKRGIFQSSTGRLINADINGALNILRK 400
                                       899**************************7333566666666699*9*************************986 PP

>> Pentapeptide_2  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.7   4.7e-08   0.00021      12      33 ..     297     318 ..     295     323 .. 0.52
   2 ?   -2.6   0.0       1.2   5.4e+03      11      17 ..     410     416 ..     407     417 .. 0.36

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 4.7e-08
                    Pentapeptide_2  12 NtGffNlGsgNtGsfNlGsgNt 33 
                                       N+G  N+G  N+G +N+G  Nt
  gi|298675096|ref|YP_003726846.1| 297 NIGKQNIGKQNIGKQNIGKQNT 318
                                       4555555555555555555554 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.2
                    Pentapeptide_2  11 gNtGffN 17 
                                       + +G++N
  gi|298675096|ref|YP_003726846.1| 410 TDSGDVN 416
                                       3333333 PP

>> DUF919  Nucleopolyhedrovirus protein of unknown function (DUF919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.5   2.7e-06     0.012      15      58 ..       4      45 ..       2      47 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.7e-06
                            DUF919 15 qaKrkltiksqHfErlkkitKnpkElqdlekklnklRqeFLnfg 58
                                       +K  l+ + q +E lk++tK +k l +   +l ++Rq+F+n g
  gi|298675096|ref|YP_003726846.1|  4 TQKNHLRADKQTYETLKRLTKLSKNLYNF--TLYTIRQYFFNHG 45
                                      58999******************888765..8**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1004  (0.0559987); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2783.95
//
Query:       gi|298675097|ref|YP_003726847.1|  [L=107]
Description: hypothetical protein Metev_1170 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-15   58.0   6.9    1.8e-15   57.8   6.9    1.1  1  DUF5320   Family of unknown function (DUF5320)
  ------ inclusion threshold ------
      0.052   13.5   0.1      0.059   13.3   0.1    1.1  1  DUF2612   Protein of unknown function (DUF2612)


Domain annotation for each model (and alignments):
>> DUF5320  Family of unknown function (DUF5320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.8   6.9     2e-19   1.8e-15       1      69 [.       1      63 [.       1      81 [. 0.81

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 2e-19
                           DUF5320  1 MPrgdgtGpmGlGpmtGrglGyCagadapgyansagfGrgrggrglgrgfgrrrraggarlaaaetaea 69
                                      MP+gd+tGp G GpmtGr lG C g++++g +++   Gr   g  +grgf ++++++g +  + +   +
  gi|298675097|ref|YP_003726847.1|  1 MPGGDRTGPEGKGPMTGRRLGPCLGSQTAGSMSNNSAGR---GLARGRGFAFNKNGSGFGKSNFR---K 63
                                      **********************************99999...89999999998888887777222...2 PP

>> DUF2612  Protein of unknown function (DUF2612)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   6.6e-06     0.059      71     102 ..      46      74 ..      39     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.6e-06
                           DUF2612  71 yfgFdeaglgFdqgsfkrrsdsttgltsLdde 102
                                        f+F+++g gF++ +f+++sd t+++   dd 
  gi|298675097|ref|YP_003726847.1|  46 GFAFNKNGSGFGKSNFRKNSDTTKSF---DDS 74 
                                       59*******************99966...443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 835.56
//
Query:       gi|298675098|ref|YP_003726848.1|  [L=333]
Description: radical SAM domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.2e-10   39.7   0.1    1.8e-09   38.2   0.1    1.7  2  Radical_SAM    Radical SAM superfamily
    0.00063   19.9   0.6     0.0021   18.2   0.6    1.8  1  Fer4_14        4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.037   13.9   0.1      0.082   12.7   0.0    1.6  2  BP28CT         BP28CT (NUC211) domain
      0.054   13.4   1.1       0.17   11.7   0.1    2.2  3  Mt_ATP-synt_D  ATP synthase D chain, mitochondrial (ATP5H)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.1     4e-13   1.8e-09       6     141 ..      31     171 ..      30     190 .. 0.79
   2 ?   -2.4   0.0       1.2   5.6e+03     112     140 ..     273     301 ..     268     307 .. 0.74

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 4e-13
                                       EESS--TTTSCCTT.....HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESS.TGGGSTTHHHHHHHHHHTCC CS
                                       xxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   6 gCnlrCsfCarpet.....vrregrgrslsveeileevkelkaekg.vkevilggg.epllypdfvellerlaklav 75 
                                        Cn++C++C+ ++t        ++ g + ++e i ++vk    +   v++++++g  ep+l+ ++   +++++ +  
  gi|298675098|ref|YP_003726848.1|  31 NCNFDCVYCQLGHTdfkvsYPENVEGLVTTQEAINALVKHK-NRIIdVDYITFSGTcEPTLNLEIGNMIKQIKNI-- 104
                                       6*****************65556666666666666666665.45555*****99755******************.. PP

                                       CTEEEEEEECSSCHG.HHHHHHHHHTT..-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxx.xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  76 pgiritvetngtlpd.eeklerllelg..vdrvslgleaaddekvlklmnrghtfeevlealeklreag 141
                                         + ++v+tn  l + +++ + ll+    + ++  g e + +  + ++  +g  +e ++++lek+ +  
  gi|298675098|ref|YP_003726848.1| 105 THVPVCVITNSSLMErKDVRQNLLNSDlvIATLVTGFEETFKA-INRPY-PGIKLENIINGLEKFSKQK 171
                                       7************996555556666556677777777777777.88888.***************9985 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.2
                                       SSHHHHHHHHT.CTSHHHHHHHHHHHHHHT CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 112 addekvlklmn.rghtfeevlealeklrea 140
                                       ++d+ +  l+  r+ tfe++ ++l + +++
  gi|298675098|ref|YP_003726848.1| 273 LNDD-IYSLISrRPCTFEQICDSLGAENDK 301
                                       5677.6666666999999999988766665 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.6   4.8e-07    0.0021       7      95 ..      31     121 ..      28     137 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.8e-07
                           Fer4_14   7 gCnlsCkgCd.....nketwkselgkpqteelleqilkdlkkseikiqglvltG.GePLhyenkkellklvkrlkee 77 
                                        Cn+ C+ C       k ++ ++++   t ++  + l + k++ i+ + ++++G  eP +     e+ +++k++k+ 
  gi|298675098|ref|YP_003726848.1|  31 NCNFDCVYCQlghtdFKVSYPENVEGLVTTQEAINALVKHKNRIIDVDYITFSGtCEPTLN---LEIGNMIKQIKNI 104
                                       7********997776677777777666555555566669999999*********99**955...5677788888776 PP

                           Fer4_14  78 ypekkiwletngtleiel 95 
                                       + ++++ + tn +l+   
  gi|298675098|ref|YP_003726848.1| 105 T-HVPVCVITNSSLMERK 121
                                       6.7899999999999333 PP

>> BP28CT  BP28CT (NUC211) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.8e-05     0.082      81     128 ..     130     177 ..     112     218 .. 0.78
   2 ?   -2.5   0.0      0.88   3.9e+03      94     123 ..     236     264 ..     235     296 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.8e-05
                                       HHHHHHHHHHHHH--------TTHHHHHHHHHHHHH---------HH. CS
                            BP28CT  81 RlitfykllnklaekLkslftsYasyllenavelLkalnekseeskek 128
                                         +++  l++ + e++k +  +Y +  len+++ L++++++++++k++
  gi|298675098|ref|YP_003726848.1| 130 SDLVIATLVTGFEETFKAINRPYPGIKLENIINGLEKFSKQKNQNKKT 177
                                       5678889*******************************8654444442 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.88
                                       --------TTHHHHHHHHHHHHH------- CS
                            BP28CT  94 ekLkslftsYasyllenavelLkalnekse 123
                                       ekLk++  ++ s +  + vel  a+ +k++
  gi|298675098|ref|YP_003726848.1| 236 EKLKQISDKFTSVFGSEKVELTFAN-SKKK 264
                                       5677777777777766666654222.2222 PP

>> Mt_ATP-synt_D  ATP synthase D chain, mitochondrial (ATP5H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   3.8e-05      0.17      59     116 ..     132     189 ..     122     216 .. 0.83
   2 ?   -0.8   0.1      0.27   1.2e+03      96     135 ..     251     292 ..     229     306 .. 0.58
   3 ?   -2.6   0.0      0.98   4.4e+03      24      44 ..     290     310 ..     276     328 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.8e-05
                                       SSSTTHHHHHHHHHHH--------TTTTHHHHHHHHHHHHCHHHHHHHHHHHHHHHHH CS
                     Mt_ATP-synt_D  59 vakeglVdeFekkYealkipypedkyteevdaeekevkkeikefkeeskkrieeleke 116
                                       +  + lV+ Fe+ ++a++ pyp  k ++ ++  ek +k++ ++ k+e + +i  +e++
  gi|298675098|ref|YP_003726848.1| 132 LVIATLVTGFEETFKAINRPYPGIKLENIINGLEKFSKQKNQNKKTELAIEIMLIESK 189
                                       55678**********************9999999999998888888877777666554 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.27
                                       HHHCHHHHHHHHHHHHHHHHH..HHHHT-XXXXXXXXXXXXX CS
                     Mt_ATP-synt_D  96 kkeikefkeeskkrieeleke..leklksllpfeemtmedfa 135
                                        ++++   ++skk++++++++   + + sl+     t+e+++
  gi|298675098|ref|YP_003726848.1| 251 SEKVELTFANSKKKVSKYTHKnlNDDIYSLISRRPCTFEQIC 292
                                       455566666666666666543112455555555555555555 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.98
                                       HHHHHHHHHHHHHHHHHHHS- CS
                     Mt_ATP-synt_D  24 aqfkalkaksdeylrrvaklP 44 
                                       +   +l a++d+++++++kl 
  gi|298675098|ref|YP_003726848.1| 290 QICDSLGAENDKVKSSLEKLI 310
                                       555566666666666666653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1170  (0.0652574); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2422.84
//
Query:       gi|298675099|ref|YP_003726849.1|  [L=153]
Description: hypothetical protein Metev_1173 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    9.6e-21   74.2   0.0    1.2e-20   73.8   0.0    1.1  1  DUF134      Protein of unknown function  DUF134
  ------ inclusion threshold ------
      0.025   14.8   4.4       0.04   14.1   4.4    1.4  1  IBR         IBR domain, a half RING-finger domain
      0.074   12.9   0.0       0.13   12.2   0.0    1.4  1  Phage_NinH  Phage NinH protein
       0.14   12.0   0.0       0.21   11.4   0.0    1.3  1  HTH_30      PucR C-terminal helix-turn-helix domain
        1.1    9.5  10.4        1.7    8.8   1.6    2.3  2  UPF0547     Uncharacterised protein family UPF0547
        2.3    8.3   8.1          7    6.7   8.1    1.9  1  HypA        Hydrogenase/urease nickel incorporation, metalloc


Domain annotation for each model (and alignments):
>> DUF134  Protein of unknown function  DUF134
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.8   0.0   4.1e-24   1.2e-20       5      96 ..       2      95 ..       1      97 [. 0.95

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 4.1e-24
                            DUF134  5 grprklrdileePkvrifkPeaveetg..kvaisldeleairlvdyedlkqeeaaklmGiskatlwrlltearkkiaka 81
                                       rp+k r + +eP+v  fkP +v++     v+i++dele++rl+  e+l+q e+a++m i ++t+ r+ ++a +ki++a
  gi|298675099|ref|YP_003726849.1|  2 VRPKKQRIVDIEPEVSDFKPSGVPLSSldEVNITIDELESLRLIYLENLNQTESARKMMIHQSTFQRISQQAIEKITNA 80
                                      59********************99887546************************************************* PP

                            DUF134 82 lveGraiilkGGeyk 96
                                      l++G+ai + GG+y+
  gi|298675099|ref|YP_003726849.1| 81 LINGKAIKIGGGNYT 95
                                      *************97 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   4.4   1.3e-05      0.04      21      46 ..     120     147 ..     100     149 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.3e-05
                               IBR  21 CprpdCeaiiekseg..cksvtCskCgf 46 
                                       C  pdC++  ++++g  c++v+C++C++
  gi|298675099|ref|YP_003726849.1| 120 CICPDCGYEQSHQKGipCNQVKCPECSK 147
                                       6666******99999***********87 PP

>> Phage_NinH  Phage NinH protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.3e-05      0.13      18      39 ..      51      72 ..      41      91 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.3e-05
                        Phage_NinH 18 nqtEvARrlkcsRatvRkYvrD 39
                                      nqtE AR++  + +t  +  + 
  gi|298675099|ref|YP_003726849.1| 51 NQTESARKMMIHQSTFQRISQQ 72
                                      ***************9887654 PP

>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   7.1e-05      0.21       2      30 ..      39      67 ..      39      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.1e-05
                                      ..HHHHHHHTTT-HHHHHHHHTS-HHHHH CS
                            HTH_30  2 leTLraylenggnisatAkaLhvHrnTlr 30
                                      le Lr    ++ n ++ A+++ +H  T++
  gi|298675099|ref|YP_003726849.1| 39 LESLRLIYLENLNQTESARKMMIHQSTFQ 67
                                      57788777788****************85 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.6   0.00056       1.7      14      23 ..     119     128 ..     116     129 .. 0.80
   2 ?    5.3   1.8    0.0069        21       2       7 ..     141     146 ..     133     147 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00056
                           UPF0547  14 aqfCphCGyv 23 
                                       + +Cp+CGy+
  gi|298675099|ref|YP_003726849.1| 119 TCICPDCGYE 128
                                       669******7 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0069
                           UPF0547   2 vCPeCe 7  
                                       +CPeC+
  gi|298675099|ref|YP_003726849.1| 141 KCPECS 146
                                       466665 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   8.1    0.0023         7      69      95 ..     118     148 ..      26     152 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0023
                                       -EEEETTTS-EEECHH..H..HHS-TTTSSS CS
                              HypA  69 vkvrCreCgkefelee..k..alrCpkCgsa 95 
                                        ++ C +Cg+e ++++     +++Cp+C++ 
  gi|298675099|ref|YP_003726849.1| 118 GTCICPDCGYEQSHQKgiPcnQVKCPECSKL 148
                                       5789*********8876624588*****985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1195  (0.0666518); expected 358.6 (0.02)
Passed bias filter:                      763  (0.0425568); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1134.61
//
Query:       gi|298675100|ref|YP_003726850.1|  [L=368]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.8e-25   86.8   3.5    1.5e-24   85.7   1.0    2.6  3  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    3.5e-10   40.2   1.5    3.5e-10   40.2   1.5    1.6  2  OrfB_IS605      Probable transposase
  ------ inclusion threshold ------
      0.067   13.2   0.1       0.13   12.3   0.1    1.5  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.15   12.2   1.6       0.89    9.7   0.1    2.2  2  UPF0547         Uncharacterised protein family UPF0547
        0.8    9.4   6.5          3    7.6   6.5    2.0  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
          1    9.4   4.8        2.7    8.0   4.8    1.7  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
        1.4    9.1   5.9         13    6.0   1.9    3.0  2  DUF2387         Probable metal-binding protein (DUF2387)
        2.2    8.1   4.5         22    4.9   0.4    2.4  2  Rubredoxin_2    Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.38   8.4e+02      15      28 ..     194     207 ..     167     213 .. 0.75
   2 ?   -0.1   0.0      0.41   9.1e+02      15      30 ..     194     209 ..     188     237 .. 0.83
   3 !   85.7   1.0   6.5e-28   1.5e-24       1      69 []     284     353 ..     284     353 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.38
                    OrfB_Zn_ribbon  15 yGikveevnpayTS 28 
                                       +G k  e+ ++yTS
  gi|298675100|ref|YP_003726850.1| 194 KGSKADEIRERYTS 207
                                       46677777777777 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.41
                    OrfB_Zn_ribbon  15 yGikveevnpayTSkt 30 
                                       +G k  e+ ++yTS +
  gi|298675100|ref|YP_003726850.1| 194 KGSKADEIRERYTSLK 209
                                       5788889999999965 PP

  == domain 3  score: 85.7 bits;  conditional E-value: 6.5e-28
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f++l+ ++ ykak +G++v+ +np yTS++CseCg+++k+ ++++ +fkC++Cg++ ++D+nA+ Ni++r
  gi|298675100|ref|YP_003726850.1| 284 FSELTDFILYKAKLEGVPVVIINPMYTSQQCSECGYIDKNnRQKQANFKCKRCGHRENADYNASKNIAHR 353
                                       899*************************************9**************************997 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   1.5   1.6e-13   3.5e-10      11     106 ..     167     253 ..     158     263 .. 0.86
   2 ?   -3.2   0.1       4.2   9.5e+03      40      68 ..     320     348 ..     311     354 .. 0.64

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 1.6e-13
                        OrfB_IS605  11 pkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsrr 87 
                                       +++  + + g+DlG+ n+at+++++    +ykg ++++  ++++  + +lqsk   s     a++ l++l++k +r+
  gi|298675100|ref|YP_003726850.1| 167 EVKCYEDVMGVDLGVVNIATTSDNE----VYKGSKADEIRERYTSLKSRLQSKGTWS-----AKKHLKKLSKKERRF 234
                                       555567789****************....************************6666.....79999********** PP

                        OrfB_IS605  88 rkhllhklathliktlkev 106
                                        ++l h +a++l+k+ k++
  gi|298675100|ref|YP_003726850.1| 235 KRDLNHRVAKQLVKRAKDT 253
                                       *************998765 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.2
                        OrfB_IS605  40 lykgrrlksdykylakeiaelqsklkksk 68 
                                       + k +r k+++++ +++  +    ++ sk
  gi|298675100|ref|YP_003726850.1| 320 IDKNNRQKQANFKCKRCGHRENADYNASK 348
                                       55556666666666666666555555555 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   5.7e-05      0.13      60      96 ..     295     340 ..     243     350 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.7e-05
                                       -EEE......EEEE--EEEETTTS-EEECHH..H.HHS-TTTSSS- CS
                              HypA  60 aeLe......ieevpvkvrCreCgkefelee..k.alrCpkCgsad 96 
                                       a+Le      i+ +  + +C+eCg+  + ++  + +++C++Cg+++
  gi|298675100|ref|YP_003726850.1| 295 AKLEgvpvviINPMYTSQQCSECGYIDKNNRqkQaNFKCKRCGHRE 340
                                       5555555545777788999*****9888555333788*****9874 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1    0.0004      0.89      15      25 ..     312     322 ..     310     323 .. 0.87
   2 ?    1.5   0.2      0.15   3.3e+02      16      22 ..     332     338 ..     329     339 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0004
                           UPF0547  15 qfCphCGyvFq 25 
                                       q C++CGy+++
  gi|298675100|ref|YP_003726850.1| 312 QQCSECGYIDK 322
                                       89******986 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.15
                           UPF0547  16 fCphCGy 22 
                                       +C  CG+
  gi|298675100|ref|YP_003726850.1| 332 KCKRCGH 338
                                       5777887 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   6.5    0.0014         3       3      26 ..     314     339 ..     313     340 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0014
                                       -SSS-..-B----SSS----SSS--- CS
                    DNA_RNApol_7kD   3 CgeCg..aevslkkgdpiRCkeCGhR 26 
                                       C eCg  +++  +k++  +Ck CGhR
  gi|298675100|ref|YP_003726850.1| 314 CSECGyiDKNNRQKQANFKCKRCGHR 339
                                       9999966788899999*********9 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   4.8    0.0012       2.7      19      45 ..     312     338 ..     308     339 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0012
                     Zn_Tnp_IS1595  19 fvCPhCgsr.kayriktrglfqCkeCrk 45 
                                       + C  Cg+  k  r k+   f+Ck+C++
  gi|298675100|ref|YP_003726850.1| 312 QQCSECGYIdKNNRQKQ-ANFKCKRCGH 338
                                       57*******77777777.********98 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.034        75      38      73 ..     223     258 ..     220     260 .. 0.87
   2 ?    6.0   1.9     0.006        13      31      49 ..     312     330 ..     306     357 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.034
                           DUF2387  38 ftdelsekgqsvakelktrvnkdeekeasakvqtvq 73 
                                       ++ +ls+k++ ++++l+ rv+k+  k+a+++ +++ 
  gi|298675100|ref|YP_003726850.1| 223 HLKKLSKKERRFKRDLNHRVAKQLVKRAKDTSRAIA 258
                                       7889999****************9999988887775 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.006
                           DUF2387  31 rECvsCgftdelsekgqsv 49 
                                         C +Cg++d+ + ++q+ 
  gi|298675100|ref|YP_003726850.1| 312 QQCSECGYIDKNNRQKQAN 330
                                       57999*****999995543 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.3     0.014        31       2       8 ..     313     319 ..     313     322 .. 0.89
   2 ?    4.9   0.4    0.0097        22       1      10 [.     331     340 ..     331     342 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.014
                      Rubredoxin_2   2 vCsqCGf 8  
                                       +Cs+CG+
  gi|298675100|ref|YP_003726850.1| 313 QCSECGY 319
                                       7*****9 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0097
                      Rubredoxin_2   1 YvCsqCGfes 10 
                                       + C++CG++ 
  gi|298675100|ref|YP_003726850.1| 331 FKCKRCGHRE 340
                                       78*****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1069  (0.0596241); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2617.04
//
Query:       gi|298675101|ref|YP_003726851.1|  [L=533]
Description: hypothetical protein Metev_1177 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   1.1e-129  432.6   1.0   1.4e-129  432.2   1.0    1.1  1  DUF790     Protein of unknown function (DUF790)
  ------ inclusion threshold ------
       0.77    9.5   3.7          1    9.1   0.1    2.9  4  PI3K_p85B  PI3-kinase family, p85-binding domain
       0.94    8.4   2.0         12    4.7   0.2    2.2  2  GGGtGRT    GGGtGRT protein


Domain annotation for each model (and alignments):
>> DUF790  Protein of unknown function (DUF790)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  432.2   1.0  2.4e-133  1.4e-129       1     387 []       1     407 [.       1     407 [. 0.97

  Alignments for each domain:
  == domain 1  score: 432.2 bits;  conditional E-value: 2.4e-133
                            DUF790   1 MLpsdllrvrrrggkivpkflkeenlelaaelielfeehvGekrgeleeelkeleeeatdyklvrGLakllereaef 77 
                                       MLps+ll++++++gk++p +++++++++a+ lie+f++++G+++g+l+ee++ +ee  ++y+l+rGL+++l r++++
  gi|298675101|ref|YP_003726851.1|   1 MLPSELLVTKTYKGKVKPVYASSKHIKTADMLIEAFNRNIGNTYGNLMEEIQGFEE--MNYRLIRGLTQILLRKCRI 75 
                                       ********************************************************..7****************** PP

                            DUF790  78 etespldpeelReevFeaaaeavvseeereevleevaeelgvspeeveealyadleenkiLtefeeitpeeLlkrYN 154
                                       e++ ++dp elR++vF ++++ ++s+eer+++l +va+++++s++e+e++l+ad++enki+++f++i+++eLlk+YN
  gi|298675101|ref|YP_003726851.1|  76 ESNVDIDPVELRQAVFGECSKIITSREERDNILYNVAKKYSISKNELEQNLWADIDENKIIKHFQPISSDELLKQYN 152
                                       ***************************************************************************** PP

                            DUF790 155 lslvqtlLfkatelrirvsdaeykelfravkllgLmyeieedaee............gleitvdGPaslfkaterYG 219
                                       +sl+qtl+fka++l+i+++  ++k++++av + +Lmy+++e + +            ++++++dGPas+fk+terYG
  gi|298675101|ref|YP_003726851.1| 153 ISLIQTLFFKAVDLDIKIKG-NFKNVLQAVLRSRLMYSFNEVPVSnnnneeidrgieTVNLHIDGPASIFKMTERYG 228
                                       ********************.9*******************9998999***************************** PP

                            DUF790 220 lalAkllpallkvekWeleAeikdrd.kkkrelrfeldsedsglvshyeeeke...............fdssveeef 280
                                        ++Akl+p++l++++W+++A+i++++ + kr+l+f+++s+d+++  ++++++                fdss+e ef
  gi|298675101|ref|YP_003726851.1| 229 KSFAKLVPHILECHSWSIRADISHKTtSGKRVLEFTASSSDDIFGLKTSQNRIkespntlydnnkkteFDSSIEYEF 305
                                       **************************999**********9987765555544467999******************* PP

                            DUF790 281 aerfeklktdwelerepellkiggsvmiPDFaleekdgrrvyleIvGfwtpeylkkKleklrkaerkelivavserl 357
                                       a+   +   +w+l+rep++lk+g++++iPDF+l +k++ +vy+eI+Gfwt++ylkkK++k+++++ +++i++++++l
  gi|298675101|ref|YP_003726851.1| 306 AQFSFR---EWSLDREPAILKAGKYAFIPDFSL-KKGNITVYVEIIGFWTHDYLKKKIAKVNEVD-VPIILLINNKL 377
                                       *98744...8***********************.******************************9.*********** PP

                            DUF790 358 klekagvkakdlrvilfkdklrvkdVlevl 387
                                       k++++++k+k+++v+++++k+++k+++++l
  gi|298675101|ref|YP_003726851.1| 378 KCSESDFKSKNADVMFYNRKIPYKQIMQIL 407
                                       ***************************986 PP

>> PI3K_p85B  PI3-kinase family, p85-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.75   4.5e+03      12      33 ..     120     141 ..     111     144 .. 0.74
   2 ?   -3.0   0.0       1.1   6.3e+03      27      52 ..     178     203 ..     175     214 .. 0.72
   3 ?   -0.3   0.1      0.15   9.1e+02      39      61 ..     403     425 ..     398     436 .. 0.86
   4 ?    9.1   0.1   0.00018         1      15      40 ..     442     467 ..     425     479 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.75
                         PI3K_p85B  12 seiKeeLweeakkyplfgllkd 33 
                                       +e+ ++Lw  + + +  ++ + 
  gi|298675101|ref|YP_003726851.1| 120 NELEQNLWADIDENKIIKHFQP 141
                                       5777899999888887777665 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.1
                         PI3K_p85B  27 lfgllkdpsdYvFvginqtaekeely 52 
                                       l  +l +  +Y F  +  + + +e +
  gi|298675101|ref|YP_003726851.1| 178 LQAVLRSRLMYSFNEVPVSNNNNEEI 203
                                       56677778889999998855555544 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.15
                         PI3K_p85B  39 FvginqtaekeelyDEtrrLcdv 61 
                                       +++i +++e++el+ E+ r+ ++
  gi|298675101|ref|YP_003726851.1| 403 IMQILKRYEEKELEKEHDRIKNI 425
                                       6788899***********99776 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.00018
                         PI3K_p85B  15 KeeLweeakkyplfgllkdpsdYvFv 40 
                                       Ke++w++a k++l + l+d s+Y++ 
  gi|298675101|ref|YP_003726851.1| 442 KENVWKKALKQKLEDQLNDDSEYLIF 467
                                       9**********************875 PP

>> GGGtGRT  GGGtGRT protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1    0.0074        44       5      59 ..     102     154 ..      98     177 .. 0.82
   2 ?    4.7   0.2     0.002        12       8      57 ..     400     449 ..     393     458 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.0074
                           GGGtGRT   5 erriekiekvlkeygiksleeakelckekgidveeivkevqpiafenavwayvlG 59 
                                       e+r + + +v k+y+i++ e  ++l   ++id ++i+k+ qpi+ ++    y + 
  gi|298675101|ref|YP_003726851.1| 102 EERDNILYNVAKKYSISKNELEQNLW--ADIDENKIIKHFQPISSDELLKQYNIS 154
                                       67777788899999999877666654..689**************9999888765 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.002
                           GGGtGRT   8 iekiekvlkeygiksleeakelckekgidveeivkevqpiafenavwayv 57 
                                        ++i ++lk+y+ k+le+ ++ +k+ ++ +++ + +++++a ++ vw   
  gi|298675101|ref|YP_003726851.1| 400 YKQIMQILKRYEEKELEKEHDRIKNIDVPPDKNIININDLAEKENVWKKA 449
                                       379**************************************999999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (533 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1186  (0.0661498); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.23s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3880.96
//
Query:       gi|298675102|ref|YP_003726852.1|  [L=453]
Description: type III restriction protein res subunit [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-26   94.0   0.1    1.2e-25   90.5   0.0    2.5  3  ResIII         Type III restriction enzyme, res subunit
    3.3e-19   69.1   0.3    6.5e-19   68.1   0.3    1.4  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
    1.6e-16   59.9   0.0    4.2e-16   58.5   0.0    1.8  1  XPB_DRD        Xeroderma pigmentosum group B helicase damage 
    1.9e-15   57.2   1.0    2.2e-14   53.8   0.1    2.6  3  Helicase_C     Helicase conserved C-terminal domain
    4.3e-08   33.1   0.0    1.4e-07   31.4   0.0    1.9  1  DEAD           DEAD/DEAH box helicase
  ------ inclusion threshold ------
      0.087   12.3   0.0       0.17   11.3   0.0    1.5  1  PhoH           PhoH-like protein


Domain annotation for each model (and alignments):
>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.5   0.0   3.9e-29   1.2e-25       2     171 .]      77     216 ..      76     216 .. 0.95
   2 ?   -1.3   0.1      0.66     2e+03      85     120 ..     250     284 ..     231     315 .. 0.63
   3 ?    0.0   0.0      0.25   7.5e+02      50      84 ..     331     383 ..     319     444 .. 0.69

  Alignments for each domain:
  == domain 1  score: 90.5 bits;  conditional E-value: 3.9e-29
                                       -EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGT CS
                            ResIII   2 lelreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkfl 78 
                                       ++lr+yQ++ai +++     +++ +g+i+++TG+GKT++ + +i+++ +      ++++vp+++l+eq+++ ++k +
  gi|298675102|ref|YP_003726852.1|  77 IQLRDYQQDAISSWI-----QNNYQGVIVLPTGSGKTFIGVDAIAYCNT-----PVIVIVPTIDLMEQWRSILSKAF 143
                                       79************9.....7899************************9.....8***************9999999 PP

                                       GG....GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHHHH CS
                            ResIII  79 seaykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswreile 155
                                       s +   ig    g+k+++         i+v+t++s++ +         e+  +rf++i++DE+H+l a + +r i+e
  gi|298675102|ref|YP_003726852.1| 144 SIE---IGALGGGKKDIQ--------PITVSTYDSAYIHA--------EKIGNRFNFIVFDEVHHLPA-EGYRTIAE 200
                                       987...788888888888........**************........9*******************.******** PP

                                       T---SEEEEEESS-S- CS
                            ResIII 156 kfkeavllglTATper 171
                                       +f + +++glTAT er
  gi|298675102|ref|YP_003726852.1| 201 MFIAPYRMGLTATYER 216
                                       *************875 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.66
                                       GEEEESSS-B--.......-SEEEEEHHHHHHTH.. CS
                            ResIII  85 igkkvsgdkkkakekdstnkkilvttiqsldadsee 120
                                       i+k++   k++ ++k+ + ++ ++t + + +++s++
  gi|298675102|ref|YP_003726852.1| 250 IEKITVALKDE-EKKEYKRNHSIFTDYLKKKNISMK 284
                                       33333333333.366777888888877776666644 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.25
                                       S.....-EEEE.ESSHHHHHHHHHHG..................GGGTGG.... CS
                            ResIII  50 kkgkeekflfl.vprkslleqtleef..................kkflseayke 84 
                                       kk ++  f+f+    ++l+ +  +ef                  +kf+s +y++
  gi|298675102|ref|YP_003726852.1| 331 KK-HIHDFVFIfTEHNQLVYRISDEFlippityktttrernlilEKFKSGTYNA 383
                                       44.344555541566789999999997777776666666555555555555544 PP

>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.1   0.3   2.2e-22   6.5e-19      59     182 ..     334     450 ..     303     451 .. 0.87

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 2.2e-22
                     ERCC3_RAD25_C  59 rgDkiivfsDnvfaLkeyakklkkpyiyGetseaerlkilqkfkknpkvntiflskvgDtsiDlPeanvliqisshf 135
                                         D + +f+++   + +++ ++  p i+ +t+++er  il+kfk+  ++n+i+ skv D+ iD+Pea+v i + s +
  gi|298675102|ref|YP_003726852.1| 334 IHDFVFIFTEHNQLVYRISDEFLIPPITYKTTTRERNLILEKFKSG-TYNAIVTSKVLDEGIDVPEASVGIIL-SGT 408
                                       36889999999999999999999999*****************976.89********************9965.568 PP

                     ERCC3_RAD25_C 136 gsrrqeaqrlGriLrakkksneeefnaffYsLvskDtkemaystkrq 182
                                       gs+r   qrlGriLr +k+     ++a  Y +vs +t+e++ s++r+
  gi|298675102|ref|YP_003726852.1| 409 GSKREYIQRLGRILRKQKG-----KEAVLYEIVSAETSEINTSKRRK 450
                                       ***************7665.....79***************999996 PP

>> XPB_DRD  Xeroderma pigmentosum group B helicase damage recognition domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.5   0.0   1.4e-19   4.2e-16       1      57 []       8      60 ..       8      60 .. 0.98

  Alignments for each domain:
  == domain 1  score: 58.5 bits;  conditional E-value: 1.4e-19
                                      EEEETTEEEECSSSTT...-CT.EEETTTTEEEEEGGGHHHHHHHHHCTT--EEEES CS
                           XPB_DRD  1 LrYdrGTllidgdprgkaslpfvewDeRvekyRapAlrYrdlveaLraagiefeDrv 57
                                      L+Y++GT+ i g+ +    +p++ wDeR++++Ra +l+Y++++++L+++ ie++D v
  gi|298675102|ref|YP_003726852.1|  8 LTYHQGTVKINGNIS----VPYAYWDERSKTFRAHGLYYKNIISYLKESSIEYKDSV 60
                                      89************9....************************************98 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.16   4.9e+02      18      49 ..     121     153 ..     115     176 .. 0.81
   2 ?   -2.6   0.0       2.4   7.1e+03      21      63 ..     271     311 ..     250     316 .. 0.54
   3 !   53.8   0.1   7.2e-18   2.2e-14       2     110 ..     322     424 ..     321     425 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.16
                                       EEEEEESSHHHHHH.HHHHHHHTTSTEEEESTT CS
                        Helicase_C  18 kilifvntidrlek.vklllekkgikvavlhge 49 
                                        ++++v+tid +e+  ++l + ++i++ +l g 
  gi|298675102|ref|YP_003726852.1| 121 PVIVIVPTIDLMEQwRSILSKAFSIEIGALGGG 153
                                       589*******99986777777779998888775 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.4
                                       EEESSHHHHHHHHHHHHHT.......TSTEEEESTTSTHHHHHHHHHHHH CS
                        Helicase_C  21 ifvntidrlekvklllekk.......gikvavlhgelpqnereeileqfn 63 
                                       if+ + +         +k+       +++ +v+ +    + r++ l++ +
  gi|298675102|ref|YP_003726852.1| 271 IFTDYLK---------KKNismkspgDFQKLVIRSGSDPEARKALLARNR 311
                                       3333333.........3333333344667777777777777777666655 PP

  == domain 3  score: 53.8 bits;  conditional E-value: 7.2e-18
                                       HHHHHHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTS CS
                        Helicase_C   2 kleallellkleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaer 78 
                                       k+e+l ++l ++++++ + if++  + ++  ++     ++ + +++ +++++er+ ile+f++g+++ +++++v+ +
  gi|298675102|ref|YP_003726852.1| 322 KVEKLRDIL-KKHIHDFVFIFTEHNQLVY--RIS---DEFLIPPITYKTTTRERNLILEKFKSGTYNAIVTSKVLDE 392
                                       788999999.7899999999999999996..555...5689999********************************* PP

                                       SSTSTTESEEEESSSSSSHHHHHHHHTTSSST CS
                        Helicase_C  79 GidipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                       Gid+p++++ i+++   + ++yiqr GR+ R 
  gi|298675102|ref|YP_003726852.1| 393 GIDVPEASVGIILSGTGSKREYIQRLGRILRK 424
                                       *****************************995 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.0   4.7e-11   1.4e-07       2     147 ..      81     204 ..      80     218 .. 0.76

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 4.7e-11
                                       HHHHHHHHHHHTTC.EEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSE CS
                                       xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   2 diQaeaiplilggg.dvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlr 77 
                                       d+Q+ ai   ++++ + ++  +TGsGKT + + ++           ++ +++++Pt  L+eq  + l+k ++ i  +
  gi|298675102|ref|YP_003726852.1|  81 DYQQDAISSWIQNNyQGVIVLPTGSGKTFIGVDAIA--------YCNTPVIVIVPTIDLMEQWRSILSKAFS-I--E 146
                                       7899999999966559999**********9777777........334579**********************.3..3 PP

                                       EEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  78 vlliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinriln 147
                                       +   +gg ++     ++     i+v+t +    + ++     ++++f+V+DE++ l  +g++   +  ++
  gi|298675102|ref|YP_003726852.1| 147 IG-ALGGGKK-----DI---QPITVSTYDSAYIHAEKI---GNRFNFIVFDEVHHLPAEGYRTIAEMFIA 204
                                       33.4565555.....34...467888888887777533...3799**************99988776655 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   5.7e-05      0.17       2      38 ..      77     113 ..      76     126 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.7e-05
                                       ----SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHH CS
                              PhoH   2 ikpktkeQkeylealkkndivfaiGpaGtGKtylava 38 
                                       i+ ++ +Q+++ + +++n   +++ p+G+GKt++ v 
  gi|298675102|ref|YP_003726852.1|  77 IQLRDYQQDAISSWIQNNYQGVIVLPTGSGKTFIGVD 113
                                       888999**********99999999*********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3275.36
//
Query:       gi|298675103|ref|YP_003726853.1|  [L=146]
Description: UspA domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-37  128.5   0.1    2.9e-37  128.3   0.1    1.0  1  Usp              Universal stress protein family
  ------ inclusion threshold ------
      0.031   14.5   0.1      0.077   13.2   0.0    1.7  2  VWA              von Willebrand factor type A domain
      0.034   14.9   0.1      0.061   14.0   0.1    1.4  1  DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomer
        0.2   11.6   0.0       0.41   10.6   0.0    1.5  1  DNA_photolyase   DNA photolyase


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.3   0.1   6.5e-41   2.9e-37       2     141 .]       5     145 ..       4     145 .. 0.98

  Alignments for each domain:
  == domain 1  score: 128.3 bits;  conditional E-value: 6.5e-41
                                       -SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH.HHHHHHC CS
                               Usp   2 ykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada.akaaaea 77 
                                       y +Il+a+Dgse+sk+A++ +++lak++ga+++ +++i+p + +++  +++ a+ + ++ +++ ++a++  ++  ++
  gi|298675103|ref|YP_003726853.1|   5 YNKILIATDGSENSKNAVQSGINLAKNTGAKVYTVYIIEPVSAAMSRKGPDWAKSAMEMMRKEGEKATEyVEKIGQE 81 
                                       89**************************************************************9999999999*** PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       ++++ve +++egdpaee +++a+++d++liV+G+rg+sg++r+++GSv+++v+rh+++ VlvV+
  gi|298675103|ref|YP_003726853.1|  82 ADIDVESIILEGDPAEEVIKFADKNDINLIVMGTRGLSGIKRFMVGSVADKVVRHSEKEVLVVP 145
                                       ***************************************************************7 PP

>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.7e-05     0.077     106     140 ..       7      53 ..       2      92 .. 0.77
   2 ?   -0.8   0.0      0.36   1.6e+03     122     139 ..      98     115 ..      68     136 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.7e-05
                                       EEEEEESS--CS.SHTHHHHHHHHGCTEEEEEEEE...........S CS
                               VWA 106 viilltdGksnd.gdpkeaaneakeqgikvfavGv...........g 140
                                        i++ tdG +n+ + ++  +n ak+ g kv++v +           g
  gi|298675103|ref|YP_003726853.1|   7 KILIATDGSENSkNAVQSGINLAKNTGAKVYTVYIiepvsaamsrkG 53 
                                       58899*******55*******************99666666665543 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.36
                                       HHHHHHHGCTEEEEEEEE CS
                               VWA 122 eaaneakeqgikvfavGv 139
                                       e+++ a +++i++++ G 
  gi|298675103|ref|YP_003726853.1|  98 EVIKFADKNDINLIVMGT 115
                                       344444455666666665 PP

>> DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.4e-05     0.061      60     127 ..      73     144 ..      55     146 .] 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.4e-05
                                       HHHHHHHHHTTS..SSEEEESH..HHHHHHHCHTT-SEEEE--SSGGGHHHHHHHHHTTSEEEE--SHHHHH CS
                   DXP_reductoisom  60 eelkealkekel..ktevlvGe..ealkelaeeeeadvvvaaivGaaGLkptlaaikagkriaLANKEsLVv 127
                                       e +++  +e+++  +  +l G+  e +++ a +++++++v +  G+ G+k  +    a+k +  + KE LVv
  gi|298675103|ref|YP_003726853.1|  73 EYVEKIGQEADIdvESIILEGDpaEEVIKFADKNDINLIVMGTRGLSGIKRFMVGSVADKVVRHSEKEVLVV 144
                                       44444444444322555666753367889999**************************************97 PP

>> DNA_photolyase  DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   9.2e-05      0.41      18      95 ..      27     114 ..      21     123 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 9.2e-05
                                       HHHHCTTSEEEEEEEE-HH..HHTCG............S-CHHHHHHHHHHHHHHHHHHHHTT--EEEEESSHHHHH CS
                    DNA_photolyase  18 aaAaasgepvipvfvldpe..kahkl............rvgaarvdfllesLadLdeeLrelgirLvvrrgdpadvl 80 
                                       + A ++g++v+ v++++p   +   +            ++  +  +   e ++++ +e ++ +++ ++++gdpa+++
  gi|298675103|ref|YP_003726853.1|  27 NLAKNTGAKVYTVYIIEPVsaA---MsrkgpdwaksamEMMRKEGEKATEYVEKIGQE-ADIDVESIILEGDPAEEV 99 
                                       56888999**********9541...233445455554444444444666777777777.5788999*********** PP

                                       HHHHHHCTECEEEEE CS
                    DNA_photolyase  81 pelakelgasavvan 95 
                                        ++a +++++ +v+ 
  gi|298675103|ref|YP_003726853.1| 100 IKFADKNDINLIVMG 114
                                       *********999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1095.51
//
Query:       gi|298675104|ref|YP_003726854.1|  [L=130]
Description: FG-GAP repeat-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-11   43.4   2.9    7.4e-11   42.5   2.9    1.5  1  VCBS             Repeat domain in Vibrio, Colwellia, Bradyrhi
    4.2e-09   36.4   1.9    9.8e-05   22.4   0.1    2.5  2  FG-GAP           FG-GAP repeat
     0.0016   18.5   0.7        1.8    8.8   0.0    2.5  3  Dockerin_1       Dockerin type I domain
     0.0022   17.4   0.5       0.14   11.6   0.1    2.3  2  TcdB_toxin_midN  Insecticide toxin TcdB middle/N-terminal reg
  ------ inclusion threshold ------
      0.017   14.8   0.2       0.13   12.0   0.1    2.0  1  PliI             Periplasmic lysozyme inhibitor of I-type lys


Domain annotation for each model (and alignments):
>> VCBS  Repeat domain in Vibrio, Colwellia, Bradyrhizobium and Shewanella
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   2.9   2.1e-14   7.4e-11       1      56 [.      74     127 ..      74     128 .. 0.89

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 2.1e-14
                              VCBS   1 DldgDGrlDlvvandgglrvyrnngdGtftdvtktslgg.sgggtgvavgDlDgDGd 56 
                                       Dl+gDG++D++v+  g +++y ++g+G ft    +++++ s + ++v ++D++gDG 
  gi|298675104|ref|YP_003726854.1|  74 DLNGDGKQDIIVTKHGVNYLYKGDGKGGFTA---YKMHDkSKNTNSVSIADVNGDGI 127
                                       9**************************9985...55555477788***********6 PP

>> FG-GAP  FG-GAP repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1   2.7e-08   9.8e-05       3      21 ..      68      86 ..      66     100 .. 0.76
   2 !   13.2   0.3     2e-05     0.072       3      15 ..     115     127 ..     113     128 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2.7e-08
                                      SSEEEESTSSSSS-EEEEE CS
                            FG-GAP  3 yslavgDvNGDGyaDLavG 21
                                       sl+ +D+NGDG++D++v+
  gi|298675104|ref|YP_003726854.1| 68 RSLTHADLNGDGKQDIIVT 86
                                      68999*************8 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2e-05
                                       SSEEEESTSSSSS CS
                            FG-GAP   3 yslavgDvNGDGy 15 
                                       +s++ +DvNGDG 
  gi|298675104|ref|YP_003726854.1| 115 NSVSIADVNGDGI 127
                                       79**********5 PP

>> Dockerin_1  Dockerin type I domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.2     8e+03      29      39 ..      29      39 ..      23      42 .. 0.75
   2 !    8.8   0.0    0.0005       1.8      26      45 ..      62      81 ..      49      84 .. 0.83
   3 !    7.9   0.1   0.00098       3.5      27      44 ..     110     127 ..      90     130 .] 0.76

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.2
                                      TSCCCHGGGST CS
                        Dockerin_1 29 ssssngkaaDv 39
                                      +s+++++ +Dv
  gi|298675104|ref|YP_003726854.1| 29 QSNKMQTGYDV 39
                                      56777888888 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0005
                                      EBTTSCCCHGGGSTT-SSCE CS
                        Dockerin_1 26 egqssssngkaaDvNgDGrv 45
                                      ++++ +   ++aD+NgDG+ 
  gi|298675104|ref|YP_003726854.1| 62 GNPEYTRSLTHADLNGDGKQ 81
                                      66777788999*******96 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.00098
                                       BTTSCCCHGGGSTT-SSC CS
                        Dockerin_1  27 gqssssngkaaDvNgDGr 44 
                                       ++++++    aDvNgDG 
  gi|298675104|ref|YP_003726854.1| 110 KSKNTNSVSIADVNGDGI 127
                                       55566777889*****95 PP

>> TcdB_toxin_midN  Insecticide toxin TcdB middle/N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.1   3.8e-05      0.14      17      52 ..      58      91 ..      28     106 .. 0.76
   2 !    4.2   0.1    0.0067        24      29      41 ..     115     127 ..     103     129 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.8e-05
                   TcdB_toxin_midN 17 tirvgtstsvedtnlslaDldGdGladlvltipsag 52
                                       +  g + +     l+ aDl+GdG+ d+++t  + +
  gi|298675104|ref|YP_003726854.1| 58 NMIRGNPEYTR--SLTHADLNGDGKQDIIVTKHGVN 91
                                      44444444433..3689***********99987776 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0067
                   TcdB_toxin_midN  29 tnlslaDldGdGl 41 
                                         +s+aD++GdG 
  gi|298675104|ref|YP_003726854.1| 115 NSVSIADVNGDGI 127
                                       358********97 PP

>> PliI  Periplasmic lysozyme inhibitor of I-type lysozyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   3.5e-05      0.13      60      81 ..      68      89 ..      35     124 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.5e-05
                                      EEEEEE-SSSSSS-EEEEEEE- CS
                              PliI 60 eevkladvngdkkkelvvlkrs 81
                                       +++ ad+ngd+k++++v+k+ 
  gi|298675104|ref|YP_003726854.1| 68 RSLTHADLNGDGKQDIIVTKHG 89
                                      56899*************9864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 951.17
//
Query:       gi|298675105|ref|YP_003726855.1|  [L=41]
Description: plasma-membrane proton-efflux P-type ATPase, partial [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.017   15.1   0.1      0.019   15.0   0.1    1.1  1  DUF2148   Uncharacterized protein containing a ferredoxin dom


Domain annotation for each model (and alignments):
>> DUF2148  Uncharacterized protein containing a ferredoxin domain (DUF2148)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1     1e-06     0.019       8      25 ..      13      30 ..       9      38 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1e-06
                           DUF2148  8 kaiDlGiAlgsavkvaad 25
                                      k  D+GiA+ sa ++a+ 
  gi|298675105|ref|YP_003726855.1| 13 KKADVGIAVSSATAAAKY 30
                                      779************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      156  (0.00870099); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.63
# Mc/sec: 195.37
//
Query:       gi|298675106|ref|YP_003726856.1|  [L=258]
Description: transcriptional regulator TrmB [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-23   82.1   0.0    3.4e-23   81.3   0.0    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0024   17.6   0.0      0.004   16.9   0.0    1.3  1  HTH_IclR        IclR helix-turn-helix domain
     0.0028   16.9   0.1     0.0043   16.3   0.1    1.3  1  Regulator_TrmB  Archaeal transcriptional regulator TrmB
     0.0032   17.0   1.3       0.02   14.4   0.0    3.0  4  HTH_24          Winged helix-turn-helix DNA-binding
     0.0095   15.9   0.0      0.026   14.4   0.0    1.8  1  MarR            MarR family
  ------ inclusion threshold ------
      0.032   14.6   0.0      0.082   13.3   0.0    1.7  1  Rrf2            Transcriptional regulator
      0.059   13.3   0.0       0.11   12.3   0.0    1.5  1  MarR_2          MarR family
      0.075   13.1   0.0       0.15   12.2   0.0    1.4  1  HTH_20          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.3   0.0   1.5e-26   3.4e-23       1      67 [.       5      71 ..       5      72 .. 0.98

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 1.5e-26
                                      HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--H CS
                              TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdp 67
                                      L+klGL+ yEa+vY++L+ lg ata+ei+  + vpr+kvY++++sLe+kG+Ve++ g p+++r+++p
  gi|298675106|ref|YP_003726856.1|  5 LKKLGLNGYEADVYITLVGLGDATAREISDSSSVPRPKVYDTIKSLEEKGFVEVQYGHPNRFRPMEP 71
                                      89**************************************************************998 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.8e-06     0.004      19      49 ..      27      57 ..      23      59 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.8e-06
                                      -BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR 19 ltlselArrtglpkStvhRlLqtLvelGyve 49
                                       t +e+++ + +p+++v+  +++L+e G+ve
  gi|298675106|ref|YP_003726856.1| 27 ATAREISDSSSVPRPKVYDTIKSLEEKGFVE 57
                                      5789**************************8 PP

>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   1.9e-06    0.0043       2      61 ..     107     166 ..     106     189 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.9e-06
                                       EEEESSHHHHHHHHHHHHHH-SSEEEEEE.-GGGHHHHHHHHHHHHHTT-EEEEEESS.--- CS
                    Regulator_TrmB   2 vwvvksretvierieelIesAenelivsl.pselLeelreeliaaaergvtVllliyp.ded 61 
                                       +w+vk++ +v +r++ lI++ ++e+++++ +  +L+e++ +l + +++++t +++i + +++
  gi|298675106|ref|YP_003726856.1| 107 IWMVKGNWAVTTRVQNLISTSQKEILIEVfDLDFLNEISNYL-DEIDKKIT-CIYIGKhEDQ 166
                                       8**************************97689**********.66677775.3333332333 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   9.1e-06      0.02      17      48 .]      26      57 ..      25      57 .. 0.94
   2 ?   -2.1   0.0       1.3   2.9e+03      33      42 ..     115     124 ..     115     126 .. 0.85
   3 ?   -1.9   0.3       1.2   2.6e+03       1       8 [.     148     155 ..     148     155 .. 0.93
   4 ?   -2.7   0.0         2   4.5e+03       4      16 ..     243     255 ..     242     256 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.1e-06
                            HTH_24 17 risqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      + + re+++ + ++++ v   +k Lee+G+++
  gi|298675106|ref|YP_003726856.1| 26 DATAREISDSSSVPRPKVYDTIKSLEEKGFVE 57
                                      6799**************************96 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.3
                            HTH_24  33 tvnrrlkrLe 42 
                                       +v++r+++L+
  gi|298675106|ref|YP_003726856.1| 115 AVTTRVQNLI 124
                                       5999****98 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.2
                            HTH_24   1 ldetdrkI 8  
                                       lde+d+kI
  gi|298675106|ref|YP_003726856.1| 148 LDEIDKKI 155
                                       79*****9 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 2
                            HTH_24   4 tdrkILelLqknp 16 
                                       ++++I e+L +++
  gi|298675106|ref|YP_003726856.1| 243 IHKNIVETLLQDS 255
                                       7899999999986 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   1.2e-05     0.026      16      50 ..      25      59 ..      19      65 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-05
                                      TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR 16 gplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      g+++  e+ + ++v ++ v  +++ Le+kG++e +
  gi|298675106|ref|YP_003726856.1| 25 GDATAREISDSSSVPRPKVYDTIKSLEEKGFVEVQ 59
                                      88999***************************975 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.7e-05     0.082      26      61 ..      27      62 ..      13      78 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.7e-05
                                      B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
                              Rrf2 26 vsseeiaerqnispsylekilakLrkaglvksvrGk 61
                                      ++++ei+++ +++++ +   ++ L+++g+v+++ G+
  gi|298675106|ref|YP_003726856.1| 27 ATAREISDSSSVPRPKVYDTIKSLEEKGFVEVQYGH 62
                                      799******************************997 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.1e-05      0.11      13      54 ..      20      59 ..       8      65 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.1e-05
                                      HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 13 aLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                       L   ++   t++e+ +   ++++ v  ++k L+++G+ve +
  gi|298675106|ref|YP_003726856.1| 20 TLVGLGD--ATAREISDSSSVPRPKVYDTIKSLEEKGFVEVQ 59
                                      4444444..8*****************************976 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   6.6e-05      0.15      25      56 ..      27      58 ..      16      60 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.6e-05
                                      B-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20 25 ltaselaerldlskntlsyHLrvLeeagLvev 56
                                      +ta e+ +  ++++  +++ ++ Lee g+vev
  gi|298675106|ref|YP_003726856.1| 27 ATAREISDSSSVPRPKVYDTIKSLEEKGFVEV 58
                                      68889999999********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1741.70
//
Query:       gi|298675107|ref|YP_003726857.1|  [L=245]
Description: ABC transporter-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-35  122.6   0.0    2.7e-35  121.8   0.0    1.3  1  ABC_tran     ABC transporter
    4.6e-10   39.8   3.2    1.6e-06   28.2   0.1    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    1.9e-06   28.5   1.0      3e-06   27.9   1.0    1.3  1  AAA_23       AAA domain
    7.3e-05   22.6   0.6      0.054   13.2   0.5    2.3  2  AAA_15       AAA ATPase domain
    0.00059   20.3   0.1     0.0038   17.7   0.1    2.2  1  AAA          ATPase family associated with various cellular a
    0.00062   19.5   0.1     0.0013   18.4   0.1    1.4  1  AAA_29       P-loop containing region of AAA domain
    0.00071   19.6   0.1     0.0013   18.7   0.0    1.5  2  Rad17        Rad17 P-loop domain
     0.0013   19.0   0.2     0.0046   17.2   0.2    1.9  1  AAA_22       AAA domain
     0.0025   17.3   0.1     0.0058   16.1   0.1    1.6  1  SMC_N        RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
       0.01   15.4   0.0      0.015   14.9   0.0    1.3  1  AAA_27       AAA domain
      0.019   14.6   0.3       0.14   11.7   0.0    2.0  2  SRP54        SRP54-type protein, GTPase domain
      0.026   13.2   0.0        1.7    7.2   0.0    2.1  2  AAA_13       AAA domain
      0.035   13.8   0.0        0.1   12.3   0.0    1.7  2  AAA_30       AAA domain
       0.09   12.7   0.8       0.39   10.6   0.0    2.2  3  RsgA_GTPase  RsgA GTPase
        0.1   13.2   0.0       0.23   12.1   0.0    1.6  1  TNT          Tuberculosis necrotizing toxin
       0.13   12.6   0.9        1.5    9.1   0.2    2.5  3  AAA_28       AAA domain
       0.22   11.7   0.3        6.3    7.0   0.1    2.3  2  AAA_33       AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.8   0.0   2.6e-38   2.7e-35       2     136 ..      20     162 ..      19     163 .. 0.97

  Alignments for each domain:
  == domain 1  score: 121.8 bits;  conditional E-value: 2.6e-38
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       + +s++++ege+ a++G+nGaGK+t lk+l+  l+pt+G+i+++g d+ + +++ +rk+igv++q+++l+++lt++e
  gi|298675107|ref|YP_003726857.1|  20 DGISFSVEEGEIFAFLGPNGAGKTTSLKILTTILHPTSGNIRVNGYDVLH-KKNDVRKSIGVIFQDNSLDDKLTAYE 95 
                                       789***********************************************.999*********************** PP

                                       H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n             e +e+++k+l +++l + k++ +    +++SgG+k+r+++ar l+  pk+l+lDEpt
  gi|298675107|ref|YP_003726857.1|  96 NmeyhavlykvpkeEIRERVDKLLGNVELLDRKNDLI----KTFSGGMKRRIEIARGLIHTPKVLFLDEPT 162
                                       ***********99989999************999999....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.5   9.4e-05     0.099       2      22 ..      32      52 ..      31      88 .. 0.79
   2 !   28.2   0.1   1.5e-09   1.6e-06     236     299 ..     134     195 ..      65     197 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.4e-05
                            AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                       ++ GpNg+GK++ L++l  +
  gi|298675107|ref|YP_003726857.1| 32 FAFLGPNGAGKTTSLKILTTI 52
                                      6899*************9655 PP

  == domain 2  score: 28.2 bits;  conditional E-value: 1.5e-09
                            AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsr.ngaQviltTHSp 299
                                        +S G+kr + ++  l+ ++   ++l++DEp +gL+ +  + l+e + + l++  +  v+ltTH+ 
  gi|298675107|ref|YP_003726857.1| 134 TFSGGMKRRIEIARGLIHTP---KVLFLDEPTLGLDAHTRAFLWEYIrD-LKEnSNLTVFLTTHNL 195
                                       46777877777777777777...9***********************63.444478********95 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   1.0   2.8e-09     3e-06      11     175 ..      17     193 ..       4     237 .. 0.64

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 2.8e-09
                            AAA_23  11 rdqe.idF...skgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayveltfenkd 83 
                                         ++ i F   +  ++++ GpNGaGKTT l  ++ +L   +++       + +  dv  +++++v++++ + f++++
  gi|298675107|ref|YP_003726857.1|  17 TAVDgISFsveEGEIFAFLGPNGAGKTTSLKILTTILHPTSGNI------RVNGYDVL-HKKNDVRKSIGVIFQDNS 86 
                                       33346888887779***********************9854333......34445665.555699999999998877 PP

                            AAA_23  84 gry....trsiererelskkkgkttkkaklellei....deleqfisellgskki.........ilnlilflgqerf 143
                                        ++    ++++e+   l+k  ++++++   +ll+     d ++++i++  g  k+           + +lfl++   
  gi|298675107|ref|YP_003726857.1|  87 LDDkltaYENMEYHAVLYKVPKEEIRERVDKLLGNvellDRKNDLIKTFSGGMKRrieiargliHTPKVLFLDEPTL 163
                                       76688888888888888887777777776666666455666666666655555552333333323333333333332 PP

                            AAA_23 144 eefelkdkkerleelekeleeledekkllekl 175
                                          +++++   l e++++l+e+++   +l ++
  gi|298675107|ref|YP_003726857.1| 164 --GLDAHTRAFLWEYIRDLKENSNLTVFLTTH 193
                                       ..223555557888888888887777766665 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.5   5.2e-05     0.054      24      83 ..      27      95 ..       1     136 [. 0.63
   2 !    7.5   0.0    0.0028       2.9     322     365 ..     151     194 ..     139     196 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.2e-05
                            AAA_15 24 e...ltvliGkNnsGKSsilealdlFlnnkekkn.........kkvikiekedleifeniseskdikIdvef 83
                                      e   +  + G+N++GK++ l++l  +l  + + n         +k+ ++ k+   if  +++s d k++ ++
  gi|298675107|ref|YP_003726857.1| 27 EegeIFAFLGPNGAGKTTSLKILTTILHPT-SGNirvngydvlHKKNDVRKSIGVIF--QDNSLDDKLTAYE 95
                                      3455899*****************999987.33356767776632222222222222..4444444444444 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0028
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                        ++++l+++EP + L       l++++++l ++++  v++tTH+
  gi|298675107|ref|YP_003726857.1| 151 HTPKVLFLDEPTLGLDAHTRAFLWEYIRDLKENSNLTVFLTTHN 194
                                       567899*************************************8 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   3.6e-06    0.0038       3     117 ..      34     200 ..      32     212 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.6e-06
                                       EESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSS........................................ CS
                               AAA   3 lyGppGtGKTllakavakelg..vefleisgsellsk........................................ 37 
                                       + Gp G GKT+  k + + l+  +  ++++g ++l k                                        
  gi|298675107|ref|YP_003726857.1|  34 FLGPNGAGKTTSLKILTTILHptSGNIRVNGYDVLHKkndvrksigvifqdnslddkltayenmeyhavlykvpkee 110
                                       78******************75466799******966799999999999999*****************999***** PP

                                       ....................STTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHH CS
                               AAA  38 ....................yvgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLltel 93 
                                                           +++  +  ++  ++ a+    +p++lf+DE      +           + + L + +
  gi|298675107|ref|YP_003726857.1| 111 irervdkllgnvelldrkndLIKTFSGGMKRRIEIARGLIhTPKVLFLDEPTLGLDAH----------TRAFLWEYI 177
                                       **********998888888766666666666666665555889*******77666666..........678888889 PP

                                       HHTTTSSSTEEEEEEESSGGGSTH CS
                               AAA  94 dgvkkkeskvivigatnrpdkldp 117
                                        ++k++ s+++v ++t++ d+ ++
  gi|298675107|ref|YP_003726857.1| 178 RDLKEN-SNLTVFLTTHNLDEAEK 200
                                       998885.66999999998887654 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   1.2e-06    0.0013      14      55 ..      21      63 ..      13      64 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.2e-06
                            AAA_29 14 ghtieidlkgatlltGpsGsGKSTllDAiqalLvpak.kvrfN 55
                                      g ++++++ +++ + Gp+G+GK+T l  ++++L p++ ++r N
  gi|298675107|ref|YP_003726857.1| 21 GISFSVEEGEIFAFLGPNGAGKTTSLKILTTILHPTSgNIRVN 63
                                      44555664449************************99777777 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.2e-06    0.0013      43     121 ..      27     106 ..       6     157 .. 0.79
   2 ?   -2.9   0.0       5.2   5.5e+03      73      91 ..     180     199 ..     175     234 .. 0.52

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.2e-06
                             Rad17  43 rkkriLLisGPsGCgkstvvkvLskelgikl.rewlnpvslkepdnqksdfkgltekesrflsqiesfkeleLkdak 118
                                       ++ +i    GP G gk+t +k+L+ +l +   +  +n+  + + +n +    g++ +++++  ++ +++++e ++  
  gi|298675107|ref|YP_003726857.1|  27 EEGEIFAFLGPNGAGKTTSLKILTTILHPTSgNIRVNGYDVLHKKNDVRKSIGVIFQDNSLDDKLTAYENMEYHAVL 103
                                       445688889****************99876615579**9999999999999999999999999*****999999888 PP

                             Rad17 119 ylk 121
                                       y++
  gi|298675107|ref|YP_003726857.1| 104 YKV 106
                                       843 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.2
                             Rad17  73 lrewlnpvslkepdn.qksd 91 
                                       l+e++n + +  ++n  + +
  gi|298675107|ref|YP_003726857.1| 180 LKENSNLTVFLTTHNlDEAE 199
                                       66777777766666642222 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.2   4.4e-06    0.0046       6     128 ..      30     191 ..      26     202 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.4e-06
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee.....................................erpevvfv 45 
                                        i +  G+ G+GKTt+l+ l+  l+  +   +                                     ++ + v++
  gi|298675107|ref|YP_003726857.1|  30 EIFAFLGPNGAGKTTSLKILTTILHPTSG--NirvngydvlhkkndvrksigvifqdnslddkltayenMEYHAVLY 104
                                       567788******************75444..2559999999999999999999999999998888887777777788 PP

                            AAA_22  46 tlpsstsskdllrellralglelkaerlsseellealeqalrarav........ielliiDEaqh.lr...seeale 110
                                       ++p+++  ++   +ll +++l   +      +l++++   +++r          +++l +DE    l+   ++ ++e
  gi|298675107|ref|YP_003726857.1| 105 KVPKEE-IRERVDKLLGNVELLDRK-----NDLIKTFSGGMKRRIEiarglihtPKVLFLDEPTLgLDahtRAFLWE 175
                                       888888.888888888888865555.....44444444444444334444899999*******9999987559**** PP

                            AAA_22 111 eLrsllnlsrkgvqliLv 128
                                       ++r+l +   ++++++L 
  gi|298675107|ref|YP_003726857.1| 176 YIRDLKE--NSNLTVFLT 191
                                       ****999..888877665 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   5.5e-06    0.0058      26     206 ..      31     202 ..       4     215 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.5e-06
                                       EEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEE.SSSSSSCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                             SMC_N  26 ftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkk.lkiekeevsisr 101
                                       + a +GpNG+GK+  l  +  +L  +s  ++r + + d++hk    ++  + ++ ++f++++ +   +  e+++   
  gi|298675107|ref|YP_003726857.1|  31 IFAFLGPNGAGKTTSLKILTTILHPTSG-NIRVNGY-DVLHK----KNDVRKSIGVIFQDNSLDdKLTAYENMEYHA 101
                                       55779************99999997777.***9876.67787....2333345667774443331333344444444 PP

                                       EEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 102 rvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkk 178
                                        +++  +   +i ++  +     ell +++  ++++SgG k  + +a  + i    p+   +lDe    LD++ ++ 
  gi|298675107|ref|YP_003726857.1| 102 VLYKVPK--EEIRERVDKLLGNVELLDRKNDLIKTFSGGMKRRIEIARGL-I--HTPKV-LFLDEPTLGLDAHTRAF 172
                                       4443333..2355666666666788888888999*******998887543.2..34554.569************** PP

                                       HHHHHHHHCTT..SEEEEE-SSHHHCCC-S CS
                                       xxxxxxxxxxx..xxxxxxxxxxxxxxxxx RF
                             SMC_N 179 vaellkekskn..aQfivislreemlekad 206
                                       + e+++  ++n    ++ ++++ +  ek  
  gi|298675107|ref|YP_003726857.1| 173 LWEYIRDLKENsnLTVFLTTHNLDEAEKIA 202
                                       ******888772245666777666666554 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.4e-05     0.015      10      69 ..      12      75 ..       6     123 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.4e-05
                            AAA_27 10 ryGkftdr.sldfsaeeadlhliyGpNEAGKstalrAisdllfGiper...tkdnflhdakkLr 69
                                      +y kft    ++fs ee ++   +GpN AGK+t+l+ ++ +l+  + +     ++ lh++++ r
  gi|298675107|ref|YP_003726857.1| 12 KYHKFTAVdGISFSVEEGEIFAFLGPNGAGKTTSLKILTTILHPTSGNirvNGYDVLHKKNDVR 75
                                      67777764269999999999999*****************999665441115678888888877 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00014      0.14       3      30 ..      31      58 ..      29      70 .. 0.79
   2 ?    1.0   0.0      0.27   2.8e+02      92     180 ..     136     223 ..      85     235 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegk 30
                                      +++++G++GaGKTt+l  L  +l+    
  gi|298675107|ref|YP_003726857.1| 31 IFAFLGPNGAGKTTSLKILTTILHPTSG 58
                                      6789************999888876655 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.27
                                       --SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEES.TTSSSSTTHHHHHHHHHT CS
                             SRP54  92 aGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltk.lDgdakgGaalsiaaelk 167
                                       +G ++   e+ + l ++ kv+  de  l lda t     + +++ ke+ ++t +  t  lD+  k    ++i ++  
  gi|298675107|ref|YP_003726857.1| 136 SGGMKRRIEIARGLIHTPKVLFLDEPTLGLDAHTRAFLWEYIRDLKENSNLTVFLTTHnLDEAEKIADRIAIIDK-- 210
                                       666667777777777777888888888888888888888888999999988887777437777776666655554.. PP

                                       S-EEEEE-SSSTT CS
                             SRP54 168 lPikfigvGekie 180
                                         i+ ig+ e+i+
  gi|298675107|ref|YP_003726857.1| 211 GQIQTIGTFEQIK 223
                                       3456666666665 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.012        13      22      39 ..      35      52 ..      29     131 .. 0.77
   2 ?    7.2   0.0    0.0016       1.7     524     582 ..     150     206 ..     141     239 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.012
                            AAA_13 22 YGwNGaGKTtLSrllrsl 39
                                       G NGaGKTt  ++l  +
  gi|298675107|ref|YP_003726857.1| 35 LGPNGAGKTTSLKILTTI 52
                                      59********87777665 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0016
                            AAA_13 524 igkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevkkntk 582
                                       i + k+ ++D P   LD+    +   +i++    +++   +f+ THnl+   ++ +++ 
  gi|298675107|ref|YP_003726857.1| 150 IHTPKVLFLDEPTLGLDAHTRAFLWEYIRDLK--ENSNLTVFLTTHNLDEAEKIADRIA 206
                                       56899**************************7..666678********98777777665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   9.5e-05       0.1      19      47 ..      30      58 ..      23     100 .. 0.83
   2 ?   -1.7   0.0       1.9     2e+03      52     131 ..     191     216 ..     172     236 .. 0.48

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.5e-05
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaagg 47
                                       + +  Gp G+GKtt+lk l+ +++   g
  gi|298675107|ref|YP_003726857.1| 30 EIFAFLGPNGAGKTTSLKILTTILHPTSG 58
                                      467789**************998877643 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.9
                            AAA_30  52 lAptgkaAkvLaeelgieastiakllkrlkgrarlepgtllivDEagmvdtkqlaallkaaekagakvilvGDerQl 128
                                        +++   A+++a+ + i                                                       D+ Q 
  gi|298675107|ref|YP_003726857.1| 191 TTHNLDEAEKIADRIAI------------------------------------------------------IDKGQI 213
                                       44444444444443333......................................................133333 PP

                            AAA_30 129 asV 131
                                       + +
  gi|298675107|ref|YP_003726857.1| 214 QTI 216
                                       333 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00037      0.39      78     126 ..       7      56 ..       1      66 [. 0.75
   2 ?    0.0   0.0      0.67   7.1e+02      62      97 ..      84     119 ..      60     125 .. 0.75
   3 ?   -2.9   0.0       5.1   5.4e+03      49      72 ..     186     208 ..     177     235 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00037
                                       EEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT---- CS
                       RsgA_GTPase  78 evllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelk 126
                                       e l+ + ++ ++++ ++  +++ ++ +++G+ G+GK+t ++ l+  l+  
  gi|298675107|ref|YP_003726857.1|   7 ENLKKKYHKFTAVDGISFSVEEgEIFAFLGPNGAGKTTSLKILTTILHPT 56 
                                       55555566667788888888888***************999887765555 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.67
                                       HHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHC CS
                       RsgA_GTPase  62 eeeleelkeelealgyevllvsaktkegleelkell 97 
                                       +++l++  +++e+++y+ +l ++ ++e  e++ +ll
  gi|298675107|ref|YP_003726857.1|  84 DNSLDDKLTAYENMEYHAVLYKVPKEEIRERVDKLL 119
                                       335778888999999999999888777766666655 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 5.1
                                       EEEEEE-GGG--HHHHHHHHHHHH CS
                       RsgA_GTPase  49 pvivlnKiDlleeeeeleelkeel 72 
                                       +++ l+  +l e e+ + +  + +
  gi|298675107|ref|YP_003726857.1| 186 LTVFLTTHNLDEAEK-IADRIAII 208
                                       445555555544444.33333333 PP

>> TNT  Tuberculosis necrotizing toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00022      0.23      30      71 ..       3      46 ..       1      68 [. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00022
                                      T--GGGGGS-EEEEEE.----..EEEEEB--BTTB----EEEEE CS
                               TNT 30 aLppsnlnknyhvYevlkple..veaGeiapwfgqpGgGvqyel 71
                                      a+  +nl+k+yh+++ ++ +   ve+Gei +  g +G G    l
  gi|298675107|ref|YP_003726857.1|  3 AIEVENLKKKYHKFTAVDGISfsVEEGEIFAFLGPNGAGKTTSL 46
                                      78999************988777**************9976555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.2    0.0014       1.5       2      21 ..      32      51 ..      31      69 .. 0.84
   2 ?    0.0   0.0      0.86     9e+02     103     121 ..      93     111 ..      74     133 .. 0.74
   3 ?    1.0   0.0      0.43   4.6e+02      50      99 ..     129     179 ..      90     204 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0014
                            AAA_28  2 ivitGgestGKTtlleaLaa 21
                                      ++++G+ ++GKTt l+ L+ 
  gi|298675107|ref|YP_003726857.1| 32 FAFLGPNGAGKTTSLKILTT 51
                                      589*************9984 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.86
                            AAA_28 103 aarekrydlvfllppapei 121
                                       a + ++y++v++  p +ei
  gi|298675107|ref|YP_003726857.1|  93 AYENMEYHAVLYKVPKEEI 111
                                       4567788999888888888 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.43
                            AAA_28  50 edllafaervleeqleeeaaa.aankvlfcDrglldtlaYarayggeaeae 99 
                                       +dl++  ++ ++ ++e ++   +++kvlf+D  +l   a  ra+ +e+ ++
  gi|298675107|ref|YP_003726857.1| 129 NDLIKTFSGGMKRRIEIARGLiHTPKVLFLDEPTLGLDAHTRAFLWEYIRD 179
                                       444444444444444444444666777777766666666666666655444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1     0.006       6.3       3      19 ..      33      49 ..      31      74 .. 0.80
   2 ?    2.2   0.0      0.17   1.8e+02      93     117 ..      95     117 ..      81     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.006
                            AAA_33  3 llvGlpGsGKstlaerl 19
                                       + G++G+GK+t ++ l
  gi|298675107|ref|YP_003726857.1| 33 AFLGPNGAGKTTSLKIL 49
                                      689*********88765 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.17
                            AAA_33  93 rrlgvpvrivvvetdeetlkeRlak 117
                                       +  +++ ++v  +++ e+++eR+ k
  gi|298675107|ref|YP_003726857.1|  95 E--NMEYHAVLYKVPKEEIRERVDK 117
                                       4..777899*************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       747  (0.0416643); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.54
# Mc/sec: 1360.21
//
Query:       gi|298675108|ref|YP_003726858.1|  [L=249]
Description: ABC-2 type transporter [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-39  133.8  15.4    5.5e-39  133.8  15.4    1.6  2  ABC2_membrane    ABC-2 type transporter
    1.1e-16   60.9  25.1    1.5e-16   60.4  25.1    1.2  1  ABC2_membrane_3  ABC-2 family transporter protein
    4.1e-09   36.1  13.4    4.1e-09   36.1  13.4    2.1  2  ABC2_membrane_2  ABC-2 family transporter protein
  ------ inclusion threshold ------
        4.9    7.3   5.9         35    4.6   0.2    3.2  3  CbtB             Probable cobalt transporter subunit (CbtB)


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.8  15.4   1.2e-42   5.5e-39       2     209 ..       4     214 ..       3     215 .. 0.96
   2 ?   -1.6   0.3      0.33   1.5e+03     107     121 ..     228     242 ..     221     246 .. 0.48

  Alignments for each domain:
  == domain 1  score: 133.8 bits;  conditional E-value: 1.2e-42
                     ABC2_membrane   2 qikallkreflqrwrdpslgllwrliqplllalvfgtvfgnlgnsedglnr.....pgllffsvlflafsaltsvap 73 
                                        i++++ r+++ +wr++  + +++++qp ++++ +g+  g + ++++gl++     pg+l++++lf +   + +v++
  gi|298675108|ref|YP_003726858.1|   4 SIRIMWIRQIKEYWRSKPRL-IASIVQPTIFLMALGFGLGPVFKQAGGLDYvqfltPGILGMAILFGS--VFNGVSL 77 
                                       5899*************999.9***************999655788888778889*************..999999* PP

                     ABC2_membrane  74 vferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldls...rfflflllllltalaassl 147
                                       +++++ g+l++ lv+p+ ++ + ++++ ++ ++ +++q++++l+++yf+ g++++   ++ l++l+++l+a+++s l
  gi|298675108|ref|YP_003726858.1|  78 LWDKQFGFLKETLVAPV-PRITLLIGRSIGGATTAVFQGIVLLAVSYFI-GFRMDsllHIPLVILFMFLIAFLFSLL 152
                                       *****************.******************************9.*****9888899*************** PP

                     ABC2_membrane 148 gllisalapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsnl 209
                                       g+ ++a + + e + ++++lv++p+++lsG+++pi+++p+ +  ia+lnPl+y+v++lr+++
  gi|298675108|ref|YP_003726858.1| 153 GISMGAKLDDPEAFPLIINLVIIPIFFLSGALFPINNLPSTVTTIAKLNPLSYGVDGLRGTM 214
                                       ***********************************************************998 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.33
                     ABC2_membrane 107 vsllqalifllivyf 121
                                       + l++++++l+i+ +
  gi|298675108|ref|YP_003726858.1| 228 ILLVVTFVLLIISSY 242
                                       444444444444433 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4  25.1   3.4e-20   1.5e-16     157     344 ..      51     241 ..      19     242 .. 0.88

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 3.4e-20
                   ABC2_membrane_3 157 snvasflvg.liliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll..afg 230
                                        ++++fl + ++ + ++f +++   vs++ +k+ + ++  lv++v ++++++++ +g ++ +++q +++l++  ++g
  gi|298675108|ref|YP_003726858.1|  51 LDYVQFLTPgILGMAILFGSVF-NGVSLLWDKQFGFLKETLVAPVPRITLLIGRSIGGATTAVFQGIVLLAVsyFIG 126
                                       5788899995666655555555.6669*********9999*******************************743555 PP

                   ABC2_membrane_3 231 lgipfg...nlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsii 304
                                         + ++   ++ l++l+++l +++++ lg  +++  +++e+  ++i +vi+++++++g+lfp+++lps++ +i+ ++
  gi|298675108|ref|YP_003726858.1| 127 --FRMDsllHIPLVILFMFLIAFLFSLLGISMGAKLDDPEAFPLIINLVIIPIFFLSGALFPINNLPSTVTTIAKLN 201
                                       ..66665558899**************************************************************** PP

                   ABC2_membrane_3 305 Pffapglgllrlitgdplweillsliilalfavvylllal 344
                                       P+++  +gl   + g + + i+++++il++ ++v+l+++ 
  gi|298675108|ref|YP_003726858.1| 202 PLSYGVDGLRGTMIGSSDFGIATDVGILLVVTFVLLIISS 241
                                       *************9998899*****************986 PP

>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   1.4     0.016        74     130     186 ..      25      77 ..      21      82 .. 0.74
   2 !   36.1  13.4   9.3e-13   4.1e-09     106     286 ..      86     247 ..      80     249 .] 0.84

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.016
                   ABC2_membrane_2 130 iglaiavallatvllalaiilalgivlaledllllvvasvlllllvvflalglllSs 186
                                       ++++   ++l ++ ++l+++ +    l++ ++l+  ++ +++l+     +++ ++S 
  gi|298675108|ref|YP_003726858.1|  25 ASIVQPTIFLMALGFGLGPVFKQAGGLDYVQFLTPGILGMAILF----GSVFNGVSL 77 
                                       445544566777789999**********************8887....444444443 PP

  == domain 2  score: 36.1 bits;  conditional E-value: 9.3e-13
                   ABC2_membrane_2 106 lkllLskPvsRdeillgKfigglaigla.iavallatvllalaiilalgivlaledllllvvasvlllllvvflalg 181
                                       lk  L  Pv+R ++l+g  igg++ +++ ++v+l +++ +  ++ +++  +++l  l+ +++a++++ll       g
  gi|298675108|ref|YP_003726858.1|  86 LKETLVAPVPRITLLIGRSIGGATTAVFqGIVLLAVSYFI--GFRMDSLLHIPLVILFMFLIAFLFSLL-------G 153
                                       677899**********************999999999655..778888888888777777777775555.......4 PP

                   ABC2_membrane_2 182 lllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeindflsllsptsa.yntllneilagsdlna 257
                                       + + + +    ea  l + l+++  ++ +++l+++++l+++ +        +  l+p s+  + l+++++ +sd   
  gi|298675108|ref|YP_003726858.1| 154 ISMGAKLD-DPEAFPLIINLVIIPIFFLSGALFPINNLPSTVTT-------IAKLNPLSYgVDGLRGTMIGSSD--- 219
                                       44555555.89*****************************8888.......88888888834566666666665... PP

                   ABC2_membrane_2 258 lgstatnllilllllavllvlgyvlFkrk 286
                                        +  at ++ill+++ vll+++ +lF+r 
  gi|298675108|ref|YP_003726858.1| 220 -FGIATDVGILLVVTFVLLIISSYLFERL 247
                                       .99************************96 PP

>> CbtB  Probable cobalt transporter subunit (CbtB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       1.4   6.5e+03      14      21 ..      34      41 ..      25      45 .. 0.53
   2 ?    4.4   0.1    0.0088        39      12      35 ..      55      78 ..      47      81 .. 0.81
   3 ?    4.6   0.2    0.0078        35      18      36 ..     117     134 ..     103     135 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.4
                              CbtB 14 vaAllLGl 21
                                      ++Al +Gl
  gi|298675108|ref|YP_003726858.1| 34 LMALGFGL 41
                                      33444444 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0088
                              CbtB 12 qlvaAllLGlllvylvgfsqaaal 35
                                      q ++  +LG++++++++f   ++l
  gi|298675108|ref|YP_003726858.1| 55 QFLTPGILGMAILFGSVFNGVSLL 78
                                      6666779***********877665 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.0078
                              CbtB  18 lLGlllvylvgfsqaaalH 36 
                                       +L l++ y++gf   ++lH
  gi|298675108|ref|YP_003726858.1| 117 VL-LAVSYFIGFRMDSLLH 134
                                       22.5667*********999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       806  (0.0449551); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.35s 00:00:00.95 Elapsed: 00:00:00.54
# Mc/sec: 1393.10
//
Query:       gi|298675109|ref|YP_003726859.1|  [L=644]
Description: nitrite and sulfite reductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-37  128.1   0.0    5.9e-37  126.9   0.0    1.7  1  FrhB_FdhB_C   Coenzyme F420 hydrogenase/dehydrogenase, beta s
    1.7e-28   99.1   0.1    3.2e-28   98.2   0.1    1.4  1  NIR_SIR       Nitrite and sulphite reductase 4Fe-4S domain
    1.9e-22   79.2   0.0    3.9e-22   78.2   0.0    1.5  1  FrhB_FdhB_N   Coenzyme F420 hydrogenase/dehydrogenase, beta s
    8.1e-17   60.3  39.4    2.9e-07   30.0   1.3    5.4  5  Fer4          4Fe-4S binding domain
    1.2e-12   47.4   0.0    3.2e-12   46.1   0.0    1.7  1  NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half 
    4.2e-10   40.1  31.1      0.001   19.6   4.6    5.0  3  Fer4_7        4Fe-4S dicluster domain
    8.3e-10   38.3  21.8    3.1e-05   23.8   3.2    4.7  4  Fer4_6        4Fe-4S binding domain
    1.7e-08   34.4  31.2    0.00059   19.9   0.1    4.3  3  Fer4_10       4Fe-4S dicluster domain
    3.5e-08   33.5  26.9     0.0026   17.9   3.8    3.8  3  Fer4_21       4Fe-4S dicluster domain
    5.2e-08   32.9  31.0    5.3e-06   26.5   9.9    4.2  5  Fer4_9        4Fe-4S dicluster domain
    1.3e-06   28.1  39.9    0.00076   19.4   1.6    5.4  5  Fer4_2        4Fe-4S binding domain
    4.3e-05   24.0  20.7      0.029   14.9   0.1    4.6  4  Fer4_13       4Fe-4S single cluster domain of Ferredoxin I
    0.00055   20.3  25.9      0.036   14.5   0.8    5.0  5  Fer4_8        4Fe-4S dicluster domain
     0.0006   20.3  26.1      0.054   14.0   0.6    5.0  5  Fer4_17       4Fe-4S dicluster domain
    0.00073   20.4  30.2       0.49   11.4   7.7    5.3  5  Fer4_16       4Fe-4S double cluster binding domain
    0.00081   20.1  31.1      0.033   14.9   1.3    4.6  4  Fer4_15       4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.021   15.0   1.4      0.021   15.0   1.4    2.8  2  Fer4_18       4Fe-4S dicluster domain
      0.028   14.9  38.3       0.11   13.1   2.4    5.7  5  Fer4_4        4Fe-4S binding domain
       0.03   15.1   2.5       0.03   15.1   2.5    4.4  4  Fer4_22       4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.9   0.0   6.3e-40   5.9e-37       2     151 ..     171     329 ..     170     333 .. 0.93

  Alignments for each domain:
  == domain 1  score: 126.9 bits;  conditional E-value: 6.3e-40
                       FrhB_FdhB_C   2 kkvavvGtPCqiaalrklqk................kklkekilltiglfCggnfspealrklleelgvdpedvkkl 62 
                                       ++va+vG+PCq+++ r+ q                 k +  +i ++iglfC++nf++++l  +le++g+d +++kk+
  gi|298675109|ref|YP_003726859.1| 171 ENVAMVGLPCQVYGTRRTQFfkglnvhpleigtdgeKANIPNIPYVIGLFCMENFNYDKLSGYLESIGIDLSKIKKY 247
                                       78*****************777888999999999998999************************************* PP

                       FrhB_FdhB_C  63 efrgkgkfrvelkd.ekeislkeleefirpsCkvCkdktaelADisvGdvwgpekkgdddegvstvlvrtekgeell 138
                                        +r   ++++ + + ++eislk++e+++ ++C++C+d ++++ADis G v      g ++ g++t+++r++kg ell
  gi|298675109|ref|YP_003726859.1| 248 AIR-LDEMIIMTDEgNVEISLKDIEDYVWDGCHICRDAVSKVADISAGHV------G-SSTGWTTLIARNAKGLELL 316
                                       **7.6666665555899*********************************......8.******************* PP

                       FrhB_FdhB_C 139 ekaveagelelee 151
                                       e+a+++g+le+++
  gi|298675109|ref|YP_003726859.1| 317 EAAEKDGYLETSD 329
                                       **********987 PP

>> NIR_SIR  Nitrite and sulphite reductase 4Fe-4S domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.2   0.1   3.4e-31   3.2e-28       9     154 ..     450     639 ..     445     643 .. 0.97

  Alignments for each domain:
  == domain 1  score: 98.2 bits;  conditional E-value: 3.4e-31
                                       CCSTCCCTBSS-SS-THHHHHHHHHHHCTCCCCTSSSS-BEEEEESSTCSTSSGGGSSEEEEEEEETTCEE...... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...... RF
                           NIR_SIR   9 tlcpgaglceeallDttelakaiedelepeygetylPrKfKiavsgcpnncvaveanDiglvgvkkdekei...... 79 
                                       t+cpg++ c+e +++t+ela++i+    ++++++  P+K+K+ ++gcpn cv++e+nDig+vg  ++++ +      
  gi|298675109|ref|YP_003726859.1| 450 TACPGTAYCPEGIVETKELANKIT----NQFAQRLTPHKMKVGIAGCPNSCVRAESNDIGIVGQMRPKIDEekctgc 522
                                       89**********************....***************************************9999****** PP

                                       ..............................................EEEEEE--B-SSSTC-TCEEEEEEEEEGGGH CS
                                       ..............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           NIR_SIR  80 ..............................................gfnilvGGglgrthgakktsarlgfvpeeev 110
                                                                                     g++i++GG+  r++ ++  ++   f++e+e+
  gi|298675109|ref|YP_003726859.1| 523 grcselcklnaisivagkavidrdlcincgwcvrgcphegavedktGYSIWIGGNDARRPTNGILLK--EFCTEDEM 597
                                       *******************************************************************..7******* PP

                                       HHHHHHHHHHHHHHS-CSSGGG-SHHHHHHHHHHHHHHHHHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           NIR_SIR 111 levveaivevyrdhgdrknrkkeRlkylverlGvekFrekveee 154
                                       +++++++ +v+    +r++  keRl+++++ +G  +F+++v +e
  gi|298675109|ref|YP_003726859.1| 598 VSIIDKLGKVFV--KYRTKPGKERLGNIIDLVGEGQFIKEVLSE 639
                                       ************..99************************9544 PP

>> FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.2   0.0   4.1e-25   3.9e-22       2      77 ..      91     163 ..      90     164 .. 0.95

  Alignments for each domain:
  == domain 1  score: 78.2 bits;  conditional E-value: 4.1e-25
                       FrhB_FdhB_N   2 vaArstdkeirkkaqsGGivtallkylLeegiidgvivvapskdpwrpkpviattkeellaaaGskYtlspnlklL 77 
                                        +Ar+t++ ir k+q+GG+vtall y++++g+idg++ +a      +p  +i+t+keel +++GskY+  p++++L
  gi|298675109|ref|YP_003726859.1|  91 TSARATNSTIRNKGQDGGAVTALLDYCFDNGLIDGAVNTADF---TKPSSRIVTNKEELQESQGSKYSALPVMSAL 163
                                       69***********************************99944...58***************************98 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   4.7   2.3e-09   2.2e-06       2      24 .]      13      35 ..      12      35 .. 0.94
   2 ?    0.8   0.3      0.51   4.8e+02      12      18 ..      53      59 ..      53      61 .. 0.90
   3 ?   -1.5   0.2       2.8   2.6e+03      10      17 ..     277     284 ..     276     284 .. 0.82
   4 !   30.0   1.3   3.1e-10   2.9e-07       1      24 []     512     535 ..     512     535 .. 0.94
   5 !   24.2   3.4   2.1e-08     2e-05       2      21 ..     542     561 ..     541     562 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 2.3e-09
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                      v+d+ +C+ CGaC+ vCP++ I+
  gi|298675109|ref|YP_003726859.1| 13 VVDKGLCTLCGACAAVCPYEIIE 35
                                      89******************996 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.51
                                      THHHHHS CS
                              Fer4 12 GaCvevC 18
                                      GaC +vC
  gi|298675109|ref|YP_003726859.1| 53 GACKDVC 59
                                      9****** PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.8
                                       S-THHHHH CS
                              Fer4  10 gCGaCvev 17 
                                       gC +C ++
  gi|298675109|ref|YP_003726859.1| 277 GCHICRDA 284
                                       9****875 PP

  == domain 4  score: 30.0 bits;  conditional E-value: 3.1e-10
                                       EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   1 vvideekCigCGaCvevCPvgAIt 24 
                                       ++ideekC+gCG+C e C  +AI+
  gi|298675109|ref|YP_003726859.1| 512 PKIDEEKCTGCGRCSELCKLNAIS 535
                                       68********************95 PP

  == domain 5  score: 24.2 bits;  conditional E-value: 2.1e-08
                                       EEETTTSSS-THHHHHSTTT CS
                              Fer4   2 videekCigCGaCvevCPvg 21 
                                       vid ++Ci+CG Cv  CP++
  gi|298675109|ref|YP_003726859.1| 542 VIDRDLCINCGWCVRGCPHE 561
                                       8*****************85 PP

>> NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.0   3.4e-15   3.2e-12       6      66 ..     378     436 ..     373     439 .. 0.92

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 3.4e-15
                      NIR_SIR_ferr   6 gkgyymvrlrvpnGritaeqlraladiaekygsgeirlTtrQnlqlhgvpeedleeileeL 66 
                                       g+  ++v +++ +G+ + e  +++a++a kyg+g++ +Ttr ++++ gv+ e+++++++e+
  gi|298675109|ref|YP_003726859.1| 378 GT--NFVKIKTNSGIADHEYISKVAELAGKYGDGTLEMTTRKSIEIQGVKGEHIDDLMSEV 436
                                       44..79****************************************************987 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   4.6   1.1e-06     0.001       2      48 ..      19      59 ..      18     119 .. 0.84
   2 !   18.3   6.4   2.7e-06    0.0026      10      52 .]     490     533 ..     450     533 .. 0.74
   3 !   14.2   0.6   5.1e-05     0.048      31      50 ..     541     560 ..     535     568 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.1e-06
                            Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekveidpekCl..gCgaCvavC 48
                                      C+ CgaC+a+Cp++ ie+de   ++         e+C+  g gaC +vC
  gi|298675109|ref|YP_003726859.1| 19 CTLCGACAAVCPYEIIEFDEN-GPRL-------KEECYrnGEGACKDVC 59
                                      ******************986.2322.......3445411233355555 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 2.7e-06
                            Fer4_7  10 aaCpvkaieldeeenek....gtekveidpekClgCgaCvavCPtga 52 
                                       a Cp+++++ +     +    g+++++id+ekC+gCg+C + C  +a
  gi|298675109|ref|YP_003726859.1| 490 AGCPNSCVRAESN---DigivGQMRPKIDEEKCTGCGRCSELCKLNA 533
                                       4577777776543...1334488999*****************8765 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 5.1e-05
                            Fer4_7  31 veidpekClgCgaCvavCPt 50 
                                       ++id + C++Cg Cv+ CP+
  gi|298675109|ref|YP_003726859.1| 541 AVIDRDLCINCGWCVRGCPH 560
                                       56677777777777777775 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   3.2   3.3e-08   3.1e-05       2      24 .]      12      34 ..      12      34 .. 0.94
   2 ?   -1.8   0.4       4.2   3.9e+03      17      23 ..     456     462 ..     450     463 .. 0.67
   3 !   18.4   1.4   1.7e-06    0.0016       2      19 ..     512     529 ..     511     534 .. 0.87
   4 !   23.8   2.3   3.3e-08   3.1e-05       1      23 [.     540     563 ..     540     564 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 3.3e-08
                            Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                      +++d+ +C+ Cg+C++vCP+ +i
  gi|298675109|ref|YP_003726859.1| 12 AVVDKGLCTLCGACAAVCPYEII 34
                                      689****************9987 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.2
                            Fer4_6  17 rvCPega 23 
                                       + CPeg+
  gi|298675109|ref|YP_003726859.1| 456 AYCPEGI 462
                                       5688885 PP

  == domain 3  score: 18.4 bits;  conditional E-value: 1.7e-06
                            Fer4_6   2 veidpdkCigCgdCvrvC 19 
                                       + id++kC+gCg+C   C
  gi|298675109|ref|YP_003726859.1| 512 PKIDEEKCTGCGRCSELC 529
                                       78************9888 PP

  == domain 4  score: 23.8 bits;  conditional E-value: 3.3e-08
                            Fer4_6   1 vveidpdkCigCgdCvrvCPe.ga 23 
                                       +++id+d+Ci Cg Cvr CP+ ga
  gi|298675109|ref|YP_003726859.1| 540 KAVIDRDLCINCGWCVRGCPHeGA 563
                                       689*****************6355 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   6.7   5.8e-06    0.0055       3      55 ..      13      59 ..      11      60 .. 0.81
   2 !   12.6   3.6   0.00011      0.11       3      19 ..     513     529 ..     511     538 .. 0.88
   3 !   19.9   0.1   6.3e-07   0.00059       1      22 [.     540     561 ..     540     588 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.8e-06
                           Fer4_10  3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcg..aCveaC 55
                                      v+d+  C+ Cg+C ++CP+        ++++ +e      e+C + g  aC ++C
  gi|298675109|ref|YP_003726859.1| 13 VVDKGLCTLCGACAAVCPY--------EIIEFDENGPRLKEECYRNGegACKDVC 59
                                      789999*************........7777777777777888886444999888 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00011
                           Fer4_10   3 vidddtCirCgkCvkaC 19 
                                       +id+++C++Cg+C + C
  gi|298675109|ref|YP_003726859.1| 513 KIDEEKCTGCGRCSELC 529
                                       79*************99 PP

  == domain 3  score: 19.9 bits;  conditional E-value: 6.3e-07
                           Fer4_10   1 kvvidddtCirCgkCvkaCPad 22 
                                       k+vid+d Ci+Cg Cv+ CP  
  gi|298675109|ref|YP_003726859.1| 540 KAVIDRDLCINCGWCVRGCPHE 561
                                       579*****************93 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   5.2   0.00074       0.7       1      51 [.      12      59 ..      12      65 .. 0.78
   2 !   17.9   3.8   2.7e-06    0.0026      13      57 ..     491     534 ..     484     537 .. 0.85
   3 !   17.9   0.5   2.8e-06    0.0026       1      21 [.     541     561 ..     541     570 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00074
                           Fer4_21  1 AridedkCigCgkCliaCedtshqaieidaktvlkvvedeCv..GCnlCssvC 51
                                      A++d+  C  Cg C+ +C+   ++ ie+d++   + +++eC   G   C +vC
  gi|298675109|ref|YP_003726859.1| 12 AVVDKGLCTLCGACAAVCP---YEIIEFDENG--PRLKEECYrnGEGACKDVC 59
                                      7899999999999999999...8999998654..5677778533777788887 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 2.7e-06
                           Fer4_21  13 kCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57 
                                        C  +C  +  + i i ++ + k+ e++C+GC  Cs+ C + ++i
  gi|298675109|ref|YP_003726859.1| 491 GCPNSCVRAESNDIGIVGQMRPKIDEEKCTGCGRCSELCKL-NAI 534
                                       5888888888888999999999999**************86.776 PP

  == domain 3  score: 17.9 bits;  conditional E-value: 2.8e-06
                           Fer4_21   1 AridedkCigCgkCliaCedt 21 
                                       A+id+d Ci+Cg C+  C+ +
  gi|298675109|ref|YP_003726859.1| 541 AVIDRDLCINCGWCVRGCPHE 561
                                       89****************964 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   6.0   3.6e-05     0.034       2      48 ..      19      61 ..      12      64 .. 0.81
   2 ?   -2.7   0.0       7.6   7.1e+03      38      43 ..     277     282 ..     255     284 .. 0.65
   3 !   13.4   7.2   6.7e-05     0.064      11      51 .]     491     534 ..     450     534 .. 0.63
   4 !   26.5   9.9   5.6e-09   5.3e-06       1      49 [.     518     561 ..     518     564 .. 0.91
   5 !   13.4   1.9     7e-05     0.066       2      23 ..     548     569 ..     547     576 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.6e-05
                            Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpk 48
                                      Ct CgaC ++Cp+++++ d+++   + +++++    g gaC ++C++
  gi|298675109|ref|YP_003726859.1| 19 CTLCGACAAVCPYEIIEFDENGPRLKEECYRN----GEGACKDVCQR 61
                                      9***************9999999998766555....33457777765 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.6
                            Fer4_9  38 gCgaCv 43 
                                       gC+ C 
  gi|298675109|ref|YP_003726859.1| 277 GCHICR 282
                                       344443 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 6.7e-05
                            Fer4_9  11 aCpagvvvedaaerkarlraase...eaCigCgaCveaCpkgai 51 
                                        Cp+  v+ +++   +  +++ +   e+C+gCg+C e C+ +ai
  gi|298675109|ref|YP_003726859.1| 491 GCPNSCVRAESNDIGIVGQMRPKideEKCTGCGRCSELCKLNAI 534
                                       345444444444444444444448999************99876 PP

  == domain 4  score: 26.5 bits;  conditional E-value: 5.6e-09
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                       kCtgCg+C e C+ ++++  a++  +  +      Ci Cg Cv  Cp++
  gi|298675109|ref|YP_003726859.1| 518 KCTGCGRCSELCKLNAISIVAGKAVIDRD-----LCINCGWCVRGCPHE 561
                                       7******************9999998874.....5************83 PP

  == domain 5  score: 13.4 bits;  conditional E-value: 7e-05
                            Fer4_9   2 CtgCgaCveaCpagvvvedaae 23 
                                       C++Cg Cv+ Cp++ +ved+ +
  gi|298675109|ref|YP_003726859.1| 548 CINCGWCVRGCPHEGAVEDKTG 569
                                       9999999999999998888766 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   2.8   8.2e-06    0.0078       3      22 .]      12      31 ..      10      31 .. 0.90
   2 ?   -2.2   0.7       6.2   5.9e+03      14      20 ..      53      59 ..      46      60 .. 0.76
   3 ?    0.6   0.2      0.79   7.4e+02      12      19 ..     277     284 ..     276     284 .. 0.87
   4 !   19.4   1.6   8.1e-07   0.00076       2      20 ..     511     529 ..     510     530 .. 0.92
   5 !   17.2   2.0   4.2e-06     0.004       2      22 .]     540     560 ..     539     560 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.2e-06
                            Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                                      +vvd   C+ CgaC  +CP+
  gi|298675109|ref|YP_003726859.1| 12 AVVDKGLCTLCGACAAVCPY 31
                                      579999*************5 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.2
                            Fer4_2 14 gaCvsaC 20
                                      gaC ++C
  gi|298675109|ref|YP_003726859.1| 53 GACKDVC 59
                                      6999999 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.79
                            Fer4_2  12 gCgaCvsa 19 
                                       gC +C++a
  gi|298675109|ref|YP_003726859.1| 277 GCHICRDA 284
                                       8****987 PP

  == domain 4  score: 19.4 bits;  conditional E-value: 8.1e-07
                            Fer4_2   2 pvvvdtdrCigCgaCvsaC 20 
                                       ++++d+++C+gCg C   C
  gi|298675109|ref|YP_003726859.1| 511 RPKIDEEKCTGCGRCSELC 529
                                       589************9999 PP

  == domain 5  score: 17.2 bits;  conditional E-value: 4.2e-06
                            Fer4_2   2 pvvvdtdrCigCgaCvsaCPa 22 
                                       ++v+d+d Ci+Cg Cv  CP+
  gi|298675109|ref|YP_003726859.1| 540 KAVIDRDLCINCGWCVRGCPH 560
                                       579*****************7 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   3.8    0.0055       5.2       1      17 [.      14      30 ..      14      62 .. 0.89
   2 ?   -0.7   0.1       2.3   2.2e+03      42      56 ..     483     497 ..     456     499 .. 0.72
   3 !   10.2   1.7   0.00088      0.83       1      16 [.     514     529 ..     514     531 .. 0.95
   4 !   14.9   0.1   3.1e-05     0.029       1      30 [.     543     572 ..     543     587 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0055
                           Fer4_13  1 VDrdtCiacgaCvelaP 17
                                      VD+  C+ cgaC++++P
  gi|298675109|ref|YP_003726859.1| 14 VDKGLCTLCGACAAVCP 30
                                      8999************* PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.3
                           Fer4_13  42 adaeeAadaCPvesI 56 
                                       ++++  +++CP +++
  gi|298675109|ref|YP_003726859.1| 483 HKMKVGIAGCPNSCV 497
                                       567778999*99987 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00088
                           Fer4_13   1 VDrdtCiacgaCvela 16 
                                       +D+++C++cg C el+
  gi|298675109|ref|YP_003726859.1| 514 IDEEKCTGCGRCSELC 529
                                       89************99 PP

  == domain 4  score: 14.9 bits;  conditional E-value: 3.1e-05
                           Fer4_13   1 VDrdtCiacgaCvelaPdvFeeddeggasv 30 
                                       +Drd Ci+cg Cv  +P+  + +d+ g+s+
  gi|298675109|ref|YP_003726859.1| 543 IDRDLCINCGWCVRGCPHEGAVEDKTGYSI 572
                                       8****************9777777777765 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.8   3.8e-05     0.036      49      65 .]      17      33 ..       9      33 .. 0.88
   2 ?    2.9   0.1      0.16   1.6e+02       4      17 ..      46      62 ..      44     120 .. 0.64
   3 ?   -2.7   0.0       9.2   8.7e+03      45      55 ..     272     282 ..     249     283 .. 0.65
   4 ?    4.3   7.4     0.059        56      49      62 ..     517     530 ..     449     533 .. 0.76
   5 !    9.2   0.2    0.0017       1.6      51      63 ..     548     560 ..     543     584 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.8e-05
                            Fer4_8 49 wsCttcgaCtevCpvgi 65
                                      + Ct cgaC+ vCp +i
  gi|298675109|ref|YP_003726859.1| 17 GLCTLCGACAAVCPYEI 33
                                      57************876 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.16
                            Fer4_8  4 kCieCg..aCqsaCp.v 17
                                      +C ++g  aC++ C  v
  gi|298675109|ref|YP_003726859.1| 46 ECYRNGegACKDVCQrV 62
                                      68888555999999631 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 9.2
                            Fer4_8  45 eealwsCttcg 55 
                                       ++ ++ C++c+
  gi|298675109|ref|YP_003726859.1| 272 DYVWDGCHICR 282
                                       45577888886 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.059
                            Fer4_8  49 wsCttcgaCtevCp 62 
                                       ++Ct+cg+C+e C+
  gi|298675109|ref|YP_003726859.1| 517 EKCTGCGRCSELCK 530
                                       67888888888886 PP

  == domain 5  score: 9.2 bits;  conditional E-value: 0.0017
                            Fer4_8  51 CttcgaCtevCpv 63 
                                       C +cg C++ Cp 
  gi|298675109|ref|YP_003726859.1| 548 CINCGWCVRGCPH 560
                                       5555555555553 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.6   5.8e-05     0.054      44      60 ..      17      33 ..       9      34 .. 0.88
   2 ?   -0.1   0.1       1.5   1.4e+03       6      17 ..      53      64 ..      46     105 .. 0.68
   3 ?   -2.3   0.0         7   6.6e+03      41      50 ..     273     282 ..     252     284 .. 0.71
   4 ?    5.8   6.2     0.022        21      32      57 ..     505     530 ..     451     534 .. 0.68
   5 !   11.5   0.6   0.00035      0.33      44      59 ..     546     561 ..     537     563 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.8e-05
                           Fer4_17 44 slCieCgeCerkCPqgl 60
                                      +lC+ Cg C+++CP+++
  gi|298675109|ref|YP_003726859.1| 17 GLCTLCGACAAVCPYEI 33
                                      58************986 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.5
                           Fer4_17  6 gyClpeCpsyea 17
                                      g+C ++C + + 
  gi|298675109|ref|YP_003726859.1| 53 GACKDVCQRVMT 64
                                      579999998766 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 7
                           Fer4_17  41 ekaslCieCg 50 
                                        +++ C+ C+
  gi|298675109|ref|YP_003726859.1| 273 YVWDGCHICR 282
                                       5677777765 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.022
                           Fer4_17  32 glleeaekeekaslCieCgeCerkCP 57 
                                       g+++++  +   ++C++Cg+C++ C 
  gi|298675109|ref|YP_003726859.1| 505 GIVGQMRPKIDEEKCTGCGRCSELCK 530
                                       44444433446689999999999995 PP

  == domain 5  score: 11.5 bits;  conditional E-value: 0.00035
                           Fer4_17  44 slCieCgeCerkCPqg 59 
                                       +lCi+Cg C+r CP++
  gi|298675109|ref|YP_003726859.1| 546 DLCINCGWCVRGCPHE 561
                                       6899999999999985 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   7.7   0.00051      0.49       2      32 ..      19      49 ..      18      69 .. 0.75
   2 ?   -0.7   0.0         3   2.8e+03      53      62 ..     274     283 ..     240     284 .. 0.66
   3 ?    3.9   7.5      0.11     1e+02      48      67 .]     513     532 ..     449     532 .. 0.65
   4 !   10.5   1.9     0.001      0.94       1      19 [.     518     536 ..     518     546 .. 0.83
   5 !   10.5   0.2   0.00096       0.9       2      18 ..     548     564 ..     547     585 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00051
                           Fer4_16  2 CgtCgkCaevCPtnaikekkekeiearecis 32
                                      C+ Cg+Ca vCP + i+ +++    ++ec  
  gi|298675109|ref|YP_003726859.1| 19 CTLCGACAAVCPYEIIEFDENGPRLKEECYR 49
                                      *****************99655555555544 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3
                           Fer4_16  53 aitgCdiCqd 62 
                                          gC iC d
  gi|298675109|ref|YP_003726859.1| 274 VWDGCHICRD 283
                                       3379999976 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.11
                           Fer4_16  48 ckkqeaitgCdiCqdvCPan 67 
                                       +  +e++tgC++C + C  n
  gi|298675109|ref|YP_003726859.1| 513 KIDEEKCTGCGRCSELCKLN 532
                                       33467899999999999765 PP

  == domain 4  score: 10.5 bits;  conditional E-value: 0.001
                           Fer4_16   1 rCgtCgkCaevCPtnaike 19 
                                       +C++Cg+C e C  nai+ 
  gi|298675109|ref|YP_003726859.1| 518 KCTGCGRCSELCKLNAISI 536
                                       5***************985 PP

  == domain 5  score: 10.5 bits;  conditional E-value: 0.00096
                           Fer4_16   2 CgtCgkCaevCPtnaik 18 
                                       C++Cg C+  CP++   
  gi|298675109|ref|YP_003726859.1| 548 CINCGWCVRGCPHEGAV 564
                                       ************95433 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   1.3   3.5e-05     0.033       2      28 ..      13      40 ..      12      53 .. 0.90
   2 ?   -2.4   0.0       9.2   8.6e+03      10      26 ..     277     293 ..     276     339 .. 0.57
   3 !   11.9   2.1    0.0003      0.28       2      19 ..     513     530 ..     513     543 .. 0.82
   4 !   13.9   1.5   7.4e-05      0.07       2      30 ..     542     571 ..     541     596 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.5e-05
                           Fer4_15  2 vvDrdaCigcglCvaeap.evfeldedg 28
                                      vvD+ +C+ cg+C+a++p e++e+de+g
  gi|298675109|ref|YP_003726859.1| 13 VVDKGLCTLCGACAAVCPyEIIEFDENG 40
                                      69***************65899999987 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 9.2
                           Fer4_15  10 gcglCvaeapevfelde 26 
                                       gc  C +++++v  +  
  gi|298675109|ref|YP_003726859.1| 277 GCHICRDAVSKVADISA 293
                                       66666666666554443 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.0003
                           Fer4_15   2 vvDrdaCigcglCvaeap 19 
                                       ++D+++C+gcg+C ++++
  gi|298675109|ref|YP_003726859.1| 513 KIDEEKCTGCGRCSELCK 530
                                       59**************96 PP

  == domain 4  score: 13.9 bits;  conditional E-value: 7.4e-05
                           Fer4_15   2 vvDrdaCigcglCvaeap.evfeldedgla 30 
                                       v+Drd+Ci cg Cv+ +p e  ++d+ g++
  gi|298675109|ref|YP_003726859.1| 542 VIDRDLCINCGWCVRGCPhEGAVEDKTGYS 571
                                       79***************6256667777766 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   1.4   2.3e-05     0.021      57     102 ..      15      66 ..       5      77 .. 0.75
   2 ?    7.9   7.0    0.0036       3.4      55      96 ..     513     559 ..     494     571 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.3e-05
                           Fer4_18  57 gagdcidcescvkvcPtgi.di.rkG..lqleciscll..cidacdkvmekl 102
                                       ++g c+ c++c +vcP +i +   +G  l+ ec   ++  c d c++vm   
  gi|298675109|ref|YP_003726859.1|  15 DKGLCTLCGACAAVCPYEIiEFdENGprLKEECYRNGEgaCKDVCQRVMTDA 66 
                                       5788************9973332345346779998754349*******9865 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0036
                           Fer4_18  55 ekgagdcidcescvkvcPt.gidirkGlqle....ciscllcidacd 96 
                                       + ++ +c+ c+ c ++c    i i  G  +     ci+c+ c+  c 
  gi|298675109|ref|YP_003726859.1| 513 KIDEEKCTGCGRCSELCKLnAISIVAGKAVIdrdlCINCGWCVRGCP 559
                                       456789***********973699*99986522445********9995 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   2.4   0.00011      0.11       3      16 ..      18      31 ..      15      32 .. 0.89
   2 ?    4.5   0.7     0.064        60       2      14 ..      45      59 ..      44      65 .. 0.88
   3 ?   -1.3   0.2       4.6   4.3e+03       6      12 ..     491     498 ..     490     499 .. 0.73
   4 ?    7.1   3.7    0.0093       8.8       2      15 ..     517     530 ..     516     532 .. 0.83
   5 ?   12.0   1.2   0.00026      0.24       2      15 ..     546     559 ..     544     570 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                            Fer4_4  3 rCigCgsCvaaCPq 16
                                       C+ Cg+C a+CP+
  gi|298675109|ref|YP_003726859.1| 18 LCTLCGACAAVCPY 31
                                      5************8 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.064
                            Fer4_4  2 erC..igCgsCvaaC 14
                                      e C  +g g+C ++C
  gi|298675109|ref|YP_003726859.1| 45 EECyrNGEGACKDVC 59
                                      778889********* PP

  == domain 3  score: -1.3 bits;  conditional E-value: 4.6
                            Fer4_4   6 gCg.sCva 12 
                                       gC+ sCv+
  gi|298675109|ref|YP_003726859.1| 491 GCPnSCVR 498
                                       78877987 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.0093
                            Fer4_4   2 erCigCgsCvaaCP 15 
                                       e+C+gCg+C   C+
  gi|298675109|ref|YP_003726859.1| 517 EKCTGCGRCSELCK 530
                                       89*******77775 PP

  == domain 5  score: 12.0 bits;  conditional E-value: 0.00026
                            Fer4_4   2 erCigCgsCvaaCP 15 
                                       + Ci+Cg Cv+ CP
  gi|298675109|ref|YP_003726859.1| 546 DLCINCGWCVRGCP 559
                                       67***********9 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.3     0.013        12      81      94 ..      18      31 ..       5      36 .. 0.69
   2 ?   -1.4   0.1       4.5   4.3e+03      57      92 ..     467     496 ..     450     504 .. 0.61
   3 ?   15.1   2.5   3.2e-05      0.03      72      94 ..     509     531 ..     497     533 .. 0.87
   4 ?    5.5   1.4     0.032        30      77      94 ..     543     560 ..     535     562 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.013
                           Fer4_22 81 gCvGCgRCieacpv 94
                                       C+ Cg C ++cp 
  gi|298675109|ref|YP_003726859.1| 18 LCTLCGACAAVCPY 31
                                      56666666666665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.5
                           Fer4_22  57 ekkerlrqrllhklsefkekfgesgCvGCgRCieac 92 
                                       e ++++ +++ ++l+ +k k+g  gC       ++c
  gi|298675109|ref|YP_003726859.1| 467 ELANKITNQFAQRLTPHKMKVGIAGC------PNSC 496
                                       44455555555555555555555555......3333 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 3.2e-05
                           Fer4_22  72 efkekfgesgCvGCgRCieacpv 94 
                                       +++ k++e++C+GCgRC+e c+ 
  gi|298675109|ref|YP_003726859.1| 509 QMRPKIDEEKCTGCGRCSELCKL 531
                                       5677899**************85 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.032
                           Fer4_22  77 fgesgCvGCgRCieacpv 94 
                                       +++  C+ Cg C++ cp+
  gi|298675109|ref|YP_003726859.1| 543 IDRDLCINCGWCVRGCPH 560
                                       578899999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (644 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.74u 0.32s 00:00:01.06 Elapsed: 00:00:00.51
# Mc/sec: 3784.78
//
Query:       gi|298675110|ref|YP_003726860.1|  [L=126]
Description: hypothetical protein Metev_1188 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.1e-07   30.3   0.0    4.7e-07   30.1   0.0    1.1  1  PTH2          Peptidyl-tRNA hydrolase PTH2
    0.00095   18.4   0.0     0.0011   18.3   0.0    1.1  1  Ribosomal_S2  Ribosomal protein S2
  ------ inclusion threshold ------
       0.14   12.2   0.3       0.33   11.0   0.1    1.7  2  PA28_alpha    Proteasome activator pa28 alpha subunit


Domain annotation for each model (and alignments):
>> PTH2  Peptidyl-tRNA hydrolase PTH2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   7.8e-11   4.7e-07      37     116 ..      49     125 ..      21     126 .] 0.84

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 7.8e-11
                                       ....CHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHHHTT-SEEEEEETSSSSSSTTCEEEEEEEEEEHHHHHHH CS
                              PTH2  37 s...nekellkeWeeegqkkivlkveseeeLlelaakakalglpaalirDagrtqiepgtkTvlaigPapksivdkv 110
                                       s   ++++ l++W +++q + +l++++ ++++++ ++a+  glp+  i D      + +    +aigP ++  + ++
  gi|298675110|ref|YP_003726860.1|  49 SsdkASEKNLDHWYDNNQSQQILRCSDFSDMEDIFEEAEYGGLPTISIYD------NNNDIMLIAIGPDKSGRISRL 119
                                       122222589*****************************************......89999**************** PP

                                       HTTSEB CS
                              PTH2 111 tgkLkl 116
                                       t++L  
  gi|298675110|ref|YP_003726860.1| 120 TSNLDK 125
                                       **9975 PP

>> Ribosomal_S2  Ribosomal protein S2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.8e-07    0.0011     122     187 ..      41     106 ..      20     119 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.8e-07
                      Ribosomal_S2 122 kkealklkkekekleknlggikkmkklPdlvvvldpkkekiavkEakklgipviaivDtnvdpdlv 187
                                       k ++++ +++ +  eknl++  + ++  +++ + d  + + + +Ea+  g p+i+i D n d  l+
  gi|298675110|ref|YP_003726860.1|  41 KISEVSKRSSDKASEKNLDHWYDNNQSQQILRCSDFSDMEDIFEEAEYGGLPTISIYDNNNDIMLI 106
                                       3333444455556699*********************************************98877 PP

>> PA28_alpha  Proteasome activator pa28 alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   5.4e-05      0.33      13      48 ..       4      39 ..       2      45 .. 0.89
   2 ?   -2.3   0.0      0.82   4.9e+03      43      50 ..      72      79 ..      68      87 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.4e-05
                        PA28_alpha 13 sltkeAEeLvskffPkkiveLdeLLkspsfnvsdls 48
                                      +l + +E+++ k+fP  +++L  + +++ ++ +dls
  gi|298675110|ref|YP_003726860.1|  4 KLSEFTEKFIPKTFPSECIQLIVYCTKSNLSADDLS 39
                                      677789****************99999999999998 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.82
                        PA28_alpha 43 nvsdlsev 50
                                      ++sd+s++
  gi|298675110|ref|YP_003726860.1| 72 RCSDFSDM 79
                                      55555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       875  (0.0488036); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 780.73
//
Query:       gi|298675111|ref|YP_003726861.1|  [L=249]
Description: type 11 methyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-16   61.1   0.0    2.5e-16   60.1   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    8.5e-15   55.2   0.0    1.4e-14   54.4   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    5.2e-13   49.1   0.0    2.1e-12   47.1   0.0    1.8  2  Methyltransf_31  Methyltransferase domain
    3.3e-09   36.4   0.0    1.6e-08   34.2   0.0    1.9  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    9.2e-07   29.5   0.0    1.5e-06   28.9   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    8.4e-06   25.4   0.0    1.5e-05   24.6   0.0    1.4  1  MTS              Methyltransferase small domain
    4.1e-05   23.1   0.0    8.3e-05   22.1   0.0    1.5  1  Methyltransf_4   Putative methyltransferase
    6.5e-05   22.8   0.0    8.9e-05   22.4   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
     0.0002   21.3   0.0    0.00094   19.1   0.0    1.9  2  Methyltransf_18  Methyltransferase domain
    0.00058   19.4   0.0    0.00074   19.1   0.0    1.2  1  Methyltransf_PK  AdoMet dependent proline di-methyltransferas
     0.0011   20.0   0.0     0.0019   19.2   0.0    1.3  1  Methyltransf_24  Methyltransferase domain
      0.004   16.8   0.0     0.0066   16.1   0.0    1.3  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
  ------ inclusion threshold ------
      0.013   15.0   0.0      0.015   14.9   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
      0.027   14.2   0.0       0.13   12.0   0.0    1.9  2  Methyltransf_16  Lysine methyltransferase
      0.044   13.2   0.0      0.063   12.7   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.087   12.6   0.0       0.13   12.0   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.091   12.5   0.0       0.12   12.2   0.0    1.2  1  DUF938           Protein of unknown function (DUF938)
       0.13   12.0   0.0       0.19   11.4   0.0    1.2  1  Met_10           Met-10+ like-protein
       0.13   11.9   0.0       0.23   11.1   0.0    1.4  1  UPF0020          Putative RNA methylase family UPF0020
       0.14   11.2   0.0       0.24   10.4   0.0    1.3  1  RrnaAD           Ribosomal RNA adenine dimethylase


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   0.0   2.8e-19   2.5e-16       1      97 []      40     135 ..      40     135 .. 0.95

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 2.8e-19
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgalh 75 
                                       +Ld+GcG G  t++la  ++++++t++Di + +l++  e+a+e+g+  ++  v+++++dlpfed++fDl+++ g++ 
  gi|298675111|ref|YP_003726861.1|  40 ILDIGCGIGMQTIHLAGICKDCHITATDIYQPYLDKLMENAAEKGVanRIFTVRASMDDLPFEDDEFDLIWCEGSIF 116
                                       8****************9999*************************999999********************87777 PP

                                       GSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  76 hlsdedlekalkeiarvLkpgG 97 
                                       +++   lek l+ ++r Lk gG
  gi|298675111|ref|YP_003726861.1| 117 IIE---LEKGLNYWKRFLKGGG 135
                                       776...999**********999 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   0.0   1.6e-17   1.4e-14       1      95 [.      41     138 ..      41     139 .. 0.94

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 1.6e-17
                                       EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CCC CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlhh 73 
                                       Ld+GcG G  + +la  +  ++++++D+ +  l+   e+a e+g+  ++  v+a++ +lpfed+ fDl+++  +++ 
  gi|298675111|ref|YP_003726861.1|  41 LDIGCGIGMQTIHLAGICkdCHITATDIYQPYLDKLMENAAEKGVanRIFTVRASMDDLPFEDDEFDLIWCEGSIFI 117
                                       8**************777889************999999999998887888************************** PP

                                       -CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  74 vedpekalkeiaRvLkpgGllv 95 
                                       + ++ek l+ ++R Lk gG+++
  gi|298675111|ref|YP_003726861.1| 118 I-ELEKGLNYWKRFLKGGGFIA 138
                                       *.6****************986 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.0   2.3e-15   2.1e-12       6     137 ..      39     184 ..      36     228 .. 0.85
   2 ?   -0.8   0.0       1.3   1.1e+03      33      60 ..     220     247 ..     205     249 .] 0.79

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 2.3e-15
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeq.gdieeleklledekfDlilsn 81 
                                       r+lD+GCG G  t+ la  ++++++++  Di +  + +  ena+++g+ n  F + +++ +l+  +ed+ fDli + 
  gi|298675111|ref|YP_003726861.1|  39 RILDIGCGIGMQTIHLA-GICKDCHITATDIYQPYLDKLMENAAEKGVANRIFTVrASMDDLP--FEDDEFDLIWCE 112
                                       89***************.99*****************************999999567777**..***********9 PP

                   Methyltransf_31  82 evlnaladpdkileeiervlkpggilliedprllaelp..akveeeskay....evvegak...........i 137
                                       + +  + +++k l+  +r lk gg ++++++ + +e+p  ++++ +++ay    +++e++k           +
  gi|298675111|ref|YP_003726861.1| 113 GSI-FIIELEKGLNYWKRFLKGGGFIALTEAVWFTENPseESLQLWQEAYpdikTIPETKKaiostgykvisS 184
                                       998.89999***********************99999999999999998877764444444444555555551 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.3
                   Methyltransf_31  33 GiDiseeaielArenaqklgldnveFeq 60 
                                       +i++s + ie+ r+++++ g+  + +++
  gi|298675111|ref|YP_003726861.1| 220 LIEFSRKEIEVFRKHSDEYGYAFFVMRK 247
                                       7999999999999999999998877765 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   1.8e-11   1.6e-08      50     171 ..      39     159 ..      22     183 .. 0.87
   2 ?   -0.5   0.0       0.7   6.3e+02     151     173 ..     220     242 ..     215     247 .. 0.83

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 1.8e-11
                                       EEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT-TTS-T-EEEEEEES- CS
                   Ubie_methyltran  50 kvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqanaeeLpfeddsfDvvtvsfG 125
                                       ++lD+ +G g  +++l+  + +  +++  Di +  L+   + + e+g+  +i  + a+  +Lpfedd fD++    G
  gi|298675111|ref|YP_003726861.1|  39 RILDIGCGIGMQTIHLAG-ICKDCHITATDIYQPYLDKLMENAAEKGVAnRIFTVRASMDDLPFEDDEFDLIWCE-G 113
                                       79**************87.567789************999999999998789999****************9887.5 PP

                                       GGG-S-HHHHHHHHHHHEEEEEEEEEEEE----SHHHHHHHHHHHH CS
                   Ubie_methyltran 126 lrnvtDklkaLkeayrvlkpGGrlvvlefskvelpllsqayelysk 171
                                          + + +k+L+   r lk GG +   e    + +  +++ +l+  
  gi|298675111|ref|YP_003726861.1| 114 SIFIIELEKGLNYWKRFLKGGGFIALTEAVWFTENPSEESLQLWQE 159
                                       557889*******************999998888888888888865 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.7
                                       EEEE----SHHHHHHHHHHHH.H CS
                   Ubie_methyltran 151 vlefskvelpllsqayelyskev 173
                                        +efs+ e++++++  + y + +
  gi|298675111|ref|YP_003726861.1| 220 LIEFSRKEIEVFRKHSDEYGYAF 242
                                       68**********99999887754 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   1.6e-09   1.5e-06       1      98 [.      41     136 ..      41     137 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.6e-09
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       L+iGcG G  + +l+   +d+++t++Di +  + d+  + a++++  n  ++++a  ++  ++ + fDl+++ + + 
  gi|298675111|ref|YP_003726861.1|  41 LDIGCGIGMQTIHLAGICKDCHITATDIYQPYL-DKLMENAAEKGVANRIFTVRASMDDLPFEDDEFDLIWCEGSIF 116
                                       8********************************.8888888888877777777777766666669*********999 PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgGr 98 
                                        + ++++ l+  ++ Lk gG 
  gi|298675111|ref|YP_003726861.1| 117 II-ELEKGLNYWKRFLKGGGF 136
                                       98.999999999999999997 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   1.7e-08   1.5e-05      32     103 ..      37     111 ..      26     132 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.7e-08
                                       CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC...EEEEE-STTTTSTTS-EEEEEE CS
                               MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle...vevvasdvleeveekkfdlivs 103
                                       + ++lD+GcG+G+ +++la  +++ ++t++d+    l+   en+++++++    +v+as     +e+++fdli +
  gi|298675111|ref|YP_003726861.1|  37 EPRILDIGCGIGMQTIHLAGICKDCHITATDIYQPYLDKLMENAAEKGVAnriFTVRASMDDLPFEDDEFDLIWC 111
                                       557**********************************************96533333333344567899999865 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   9.2e-08   8.3e-05       2      54 ..      37      89 ..      36     109 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 9.2e-08
                                      -EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEE CS
                    Methyltransf_4  2 apvvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlr 54
                                      +p +l+iGcG G  +++lA    d+ + + +i+++ ++k++++++++++ N  
  gi|298675111|ref|YP_003726861.1| 37 EPRILDIGCGIGMQTIHLAGICKDCHITATDIYQPYLDKLMENAAEKGVANRI 89
                                      5789*********************************************9944 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0     1e-07   8.9e-05       8     134 ..      22     158 ..      15     184 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1e-07
                   Methyltransf_23   8 elsdklerllpklraggrvLdiGcGtGillevlren..gfsvtgvDlspeaveiae.........kakkaqkdqfde 73 
                                       ++ +k  r+ p l++  r+LdiGcG G  + +l+     +++t+ D++    +++          ++++ +  ++  
  gi|298675111|ref|YP_003726861.1|  22 RCTEKAFRMIPSLPPEPRILDIGCGIGMQTIHLAGIckDCHITATDIYQPYLDKLMenaaekgvaNRIFTVRASM-- 96 
                                       5556666777889999***********8888887752356*******9665555447888886665555555555.. PP

                   Methyltransf_23  74 qeaaepqgkfdlIvlrevlehvpdppellrqiatllkpgGylllse..plaslkedrllldwl 134
                                       ++ +++++ fdlI +  ++  ++ +++ l+  ++ lk gG + l+e  +  + +++++l+ w+
  gi|298675111|ref|YP_003726861.1|  97 DDLPFEDDEFDLIWCEGSIFIIE-LEKGLNYWKRFLKGGGFIALTEavWFTENPSEESLQLWQ 158
                                       57778999********9997666.588999999999999999999966444447888888775 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0     1e-06   0.00094      13      71 ..      35      93 ..      24     113 .. 0.85
   2 ?   -0.6   0.0       1.2   1.1e+03     100     134 ..     207     241 ..     201     243 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1e-06
                   Methyltransf_18 13 ekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrl 71
                                      +++ r++DiG+  g+ +i+l+   k  +++a+Di +  l+k  en++++g+ ++i ++ 
  gi|298675111|ref|YP_003726861.1| 35 PPEPRILDIGCGIGMQTIHLAGICKDCHITATDIYQPYLDKLMENAAEKGVANRIFTVR 93
                                      45779******************9*9**************************9997654 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.2
                   Methyltransf_18 100 LeeakeklkkikklilqpnseaeelRkylvengfk 134
                                       Le+++++++++k+li  + +e+e +Rk   e g+ 
  gi|298675111|ref|YP_003726861.1| 207 LEAESKYNTDVKSLIEFSRKEIEVFRKHSDEYGYA 241
                                       7888899999999999999****999998888875 PP

>> Methyltransf_PK  AdoMet dependent proline di-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   8.3e-07   0.00074      57     166 ..      38     146 ..      19     186 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 8.3e-07
                   Methyltransf_PK  57 kvaldcGaGiGrvtknlLlkll.skvDlvepvekflekakeelaeekkkvgkvyvv..glqeftPeegrYdliWiqW 130
                                        ++ld+G+GiG  t +l       ++   +  + +l+k+ e+ ae k  + ++++v  ++++   e++++dliW+  
  gi|298675111|ref|YP_003726861.1|  38 PRILDIGCGIGMQTIHLAGICKdCHITATDIYQPYLDKLMENAAE-KGVANRIFTVraSMDDLPFEDDEFDLIWCEG 113
                                       689*********99998644333688999999********99998.666666666533799**99********9888 PP

                   Methyltransf_PK 131 cvghLtDedlvaflkrckkalkpnGlivvkenvake 166
                                        +  +  e+ +++ kr    lk +G+i + e v  +
  gi|298675111|ref|YP_003726861.1| 114 SIFIIELEKGLNYWKR---FLKGGGFIALTEAVWFT 146
                                       8877777777777766...68889999988876444 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   2.1e-06    0.0019       2     102 ..      42     138 ..      41     141 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.1e-06
                   Methyltransf_24   2 EiGvysGvstlwllralrrngagrlvavdhdpg.aeeaaalareaglddrvrlikadseealaslaagsiDllfiDg 77 
                                        iG+  G+ t++l+  +++ +   ++a d  +    + +++a+e+g+++r+  ++a ++++   ++++++Dl+++ g
  gi|298675111|ref|YP_003726861.1|  42 DIGCGIGMQTIHLAGICKDCH---ITATDIYQPyLDKLMENAAEKGVANRIFTVRASMDDL--PFEDDEFDLIWCEG 113
                                       69999*********9999987...68888866545678999999*********99988888..466679******** PP

                   Methyltransf_24  78 ghaaeavledleallprlapggvvl 102
                                       +    +  + l+ + + l+ gg++ 
  gi|298675111|ref|YP_003726861.1| 114 SIFIIELEKGLNYWKRFLKGGGFIA 138
                                       *999999999999999999999986 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   7.4e-06    0.0066       9      68 ..      37      94 ..      30     112 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7.4e-06
                                      T-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-C CS
                   Methyltr_RsmB-F  9 eetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDa 68
                                      e +ilD+ ++ G +T h+a +  +  +++A+d+ +  l++++en    gv n  ++++ a
  gi|298675111|ref|YP_003726861.1| 37 EPRILDIGCGIGMQTIHLAGI-CKDCHITATDIYQPYLDKLMENAAEKGVANR-IFTVRA 94
                                      678******************.56789*******************9999954.444444 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.7e-05     0.015       4      60 ..      40      98 ..      38     218 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.7e-05
                   Methyltransf_15  4 ilDlfsGaGGnviqfalv..fekviaieinleklacaqhNaevYgvsdkitlvlgdvfe 60
                                      ilD+ +G G ++i++a     +++ a +i +  l    +Na   gv+++i++v +++ +
  gi|298675111|ref|YP_003726861.1| 40 ILDIGCGIGMQTIHLAGIckDCHITATDIYQPYLDKLMENAAEKGVANRIFTVRASMDD 98
                                      8***************984456899***************************9987765 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00015      0.13      49     100 ..      39      89 ..      33     117 .. 0.76
   2 ?   -0.5   0.0         1     9e+02      75      94 ..     214     233 ..     202     238 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
                   Methyltransf_16  49 svlELGsGtGlvGlavaellpeakviltDlee.llellkknielnknalkskv 100
                                       ++l++G G G+  + +a   ++++++ tD+ +  l+ l++n +     +++++
  gi|298675111|ref|YP_003726861.1|  39 RILDIGCGIGMQTIHLAGICKDCHITATDIYQpYLDKLMENAAEK--GVANRI 89 
                                       79***************************9876777777776652..344444 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1
                   Methyltransf_16  75 ltDleellellkknielnkn 94 
                                        tD++ l+e+ +k ie+ ++
  gi|298675111|ref|YP_003726861.1| 214 NTDVKSLIEFSRKEIEVFRK 233
                                       59*************99664 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     7e-05     0.063     162     232 ..      37     111 ..      24     140 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7e-05
                              PrmA 162 geevlDvGtGSGiLaiaaakLgak.kvvavDiDevAvkvakeNaelNkvea.klevals.eell.keekadviva 232
                                       + ++lD+G+G G+ +i  a +  + +++a+Di +  ++   eNa+  +v++  ++v +s ++l+ ++ ++d+i +
  gi|298675111|ref|YP_003726861.1|  37 EPRILDIGCGIGMQTIHLAGICKDcHITATDIYQPYLDKLMENAAEKGVANrIFTVRASmDDLPfEDDEFDLIWC 111
                                       4589************9887765439************************9566665541555555789999977 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00014      0.13      71      97 ..      34      60 ..      17      96 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                                      --TT-EEEEES-TTSHHHHHHHHHHCT CS
                              PCMT 71 lkkgarvLevGsGsGyltavlarlvge 97
                                      l +  r+L++G+G G +t  la + ++
  gi|298675111|ref|YP_003726861.1| 34 LPPEPRILDIGCGIGMQTIHLAGICKD 60
                                      78899**************99998765 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00013      0.12      25      81 ..      37      92 ..      18     146 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                            DUF938 25 ttervLEiasGtGqHAvffApalpnlkwqpsdqdeelresiaawadelalsnlkpPl 81
                                      +  r+L+i+ G G   +++A   +  +  ++d  +   + ++  a+e +++n  + +
  gi|298675111|ref|YP_003726861.1| 37 EP-RILDIGCGIGMQTIHLAGICKDCHITATDIYQPYLDKLMENAAEKGVANRIFTV 92
                                      44.7****************************9999999*********999976544 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00021      0.19      88     158 ..      24      94 ..      19     131 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00021
                                       HHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES.-HHHHHHHHHHHHHTT-TTCEEEEES CS
                            Met_10  88 eaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidl.nPesvkylkeniklNkvekvvkpile 158
                                       ++   r++    +  +++d+  GiG  +i +a  +k+  + a d+ +P+  k++ en +   v++++ ++ +
  gi|298675111|ref|YP_003726861.1|  24 TEKAFRMIPSLPPEPRILDIGCGIGMQTIHLAGICKDCHITATDIyQPYLDKLM-ENAAEKGVANRIFTVRA 94 
                                       444569999999999*****************************9457666666.55566667776655554 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00026      0.23      75     127 ..      59     111 ..      42     113 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00026
                                       HH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE CS
                           UPF0020  75 aelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivt 127
                                       ++ ++ + D+ + ++++  eNa + gv+++i  + a + +L+ +++e+d+i +
  gi|298675111|ref|YP_003726861.1|  59 KDCHITATDIYQPYLDKLMENAAEKGVANRIFTVRASMDDLPFEDDEFDLIWC 111
                                       566799************************************8888****977 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00027      0.24      30      54 ..      36      60 ..      23      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00027
                                      TTSEEEEES-TTTCCHHHHHCC-SE CS
                            RrnaAD 30 ekltvleigpGkGilTeeLakrakq 54
                                      ++  +l+ig G G++T +La ++k 
  gi|298675111|ref|YP_003726861.1| 36 PEPRILDIGCGIGMQTIHLAGICKD 60
                                      6778*****************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 1461.42
//
Query:       gi|298675112|ref|YP_003726862.1|  [L=461]
Description: ATPase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.5e-19   68.6   4.1    1.4e-17   64.4   1.5    2.9  2  ATPase_2   ATPase domain predominantly from Archaea
    2.5e-18   66.3   0.5      1e-17   64.4   0.3    2.1  2  DUF234     Archaea bacterial proteins of unknown function
      3e-12   46.7   2.3    5.7e-12   45.8   0.9    2.2  2  AAA_14     AAA domain
    6.8e-08   33.1   0.0      1e-05   26.0   0.0    2.7  1  AAA_16     AAA ATPase domain
    5.6e-07   29.9   0.0      2e-06   28.1   0.0    1.9  3  AAA_22     AAA domain
      0.002   17.6   0.9       0.05   13.0   0.0    2.8  3  TniB       Bacterial TniB protein
     0.0075   16.4   0.3      0.028   14.6   0.0    2.2  2  DUF4143    Domain of unknown function (DUF4143)
  ------ inclusion threshold ------
      0.013   15.3   1.0      0.028   14.3   0.2    2.0  2  HTH_5      Bacterial regulatory protein, arsR family
      0.015   15.5   0.4      0.055   13.7   0.0    2.1  2  Roc        Ras of Complex, Roc, domain of DAPkinase
      0.027   14.7   0.0      0.056   13.7   0.0    1.5  1  UPF0102    Uncharacterised protein family UPF0102
      0.031   13.2   0.0      0.047   12.6   0.0    1.2  1  DUF4702    Domain of unknown function (DUF4702)
      0.051   13.6   0.1        1.9    8.5   0.0    2.5  2  HSDR_N_2   Type I restriction enzyme R protein N terminus (HS
      0.097   13.3   0.0        0.2   12.3   0.0    1.5  1  NFACT-R_1  NFACT protein RNA binding domain


Domain annotation for each model (and alignments):
>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.4   1.5     1e-20   1.4e-17       1     227 [.       3     199 ..       3     204 .. 0.79
   2 ?   -1.1   0.1       1.1   1.5e+03      71      71 ..     389     389 ..     326     440 .. 0.53

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 1e-20
                          ATPase_2   1 FfdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkk 77 
                                       F++Re+el+ + ++++++p ++++++G +++GKt L++++++ +++    + ++ + +++ +  ++ef       + 
  gi|298675112|ref|YP_003726862.1|   3 FYNREQELELMDTLYNNKP-SMIVLTGKRRVGKTELIRQFMKDRDS----IYFFVDSNKSIEILMQEF------TSI 68 
                                       9*******99999999865.56789*****************9944....445555555555567777......555 PP

                          ATPase_2  78 lekalgiavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnliesltk 154
                                       l++ l  ++p           +kl  +  e++l+ + +  k +++ iDe+q+    ++    +++++L+++++ + +
  gi|298675112|ref|YP_003726862.1|  69 LKESL--DLPD--Y-------IKL--ETPEQFLDFLVNHDKNLVVAIDEFQRFS--KIY--PSFIDQLQKYWDLKGE 128
                                       55555..3333..3.......122..4557788889999999************..666..88************** PP

                          ATPase_2 155 ekhlcvviclsSeglfie.rvyneselegrhky.ilvddldketalnflkegfkeleelskedfeeiyryvGGkP 227
                                       + +l+++i +sS g++++  ++++++l +r++  +++++++ +++ ++l+++   ++    +++ ++y ++GG +
  gi|298675112|ref|YP_003726862.1| 129 NSNLFLIISGSSIGMIRKiFIEDNAPLFKRADNlLTLKPFTVKEVFEMLDDM--GIR--DFDEKLNLYFLFGGTV 199
                                       ******************899************99*************9985..223..3345566666666665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.1
                          ATPase_2  71 e 71 
                                       e
  gi|298675112|ref|YP_003726862.1| 389 E 389
                                       1 PP

>> DUF234  Archaea bacterial proteins of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       3.8   5.2e+03      52      65 ..     111     124 ..      51     132 .. 0.71
   2 !   64.4   0.3   7.4e-21     1e-17       3      99 .]     319     412 ..     317     412 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3.8
                            DUF234  52 klpfrftkvGrwWk 65 
                                        +p  + ++ ++W+
  gi|298675112|ref|YP_003726862.1| 111 IYPSFIDQLQKYWD 124
                                       34555666666665 PP

  == domain 2  score: 64.4 bits;  conditional E-value: 7.4e-21
                            DUF234   3 rfvypnrseielgeseevlekikeelneyvgkvFEelvrelllelnkagklpfrftkvGrwWk.keeeiDivaldee 78 
                                        f+yp+ s+++ g ++ +l+k+++e+++++g  FE+++r+l++e +        ++kvG wW+ +++eiDiva+de+
  gi|298675112|ref|YP_003726862.1| 319 YFLYPQLSLYKAGYYKPLLNKVQKEWKRFTGDIFESVMRDLITEDIID-----SYSKVGPWWNrRGDEIDIVAFDEQ 390
                                       699****************************************66554.....599******84778********** PP

                            DUF234  79 ekkalfgEvKwkn.sekeakki 99 
                                       +kk+l++EvK ++ +e+e+++i
  gi|298675112|ref|YP_003726862.1| 391 NKKMLAVEVKNTElDENETRNI 412
                                       ************9877777765 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.9   4.1e-15   5.7e-12       3     129 ..      22     172 ..      20     174 .. 0.71
   2 ?   -2.2   0.0       2.9   3.9e+03      31      47 ..     392     408 ..     363     434 .. 0.58

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 4.1e-15
                            AAA_14   3 kilvitGaRrvGKTtllkqlikell................vkkesilyinldderdkkladpekllelileklkee 63 
                                        ++v+tG RrvGKT l++q++k++                  +  sil  +ld +++ kl++pe++l+++ ++   +
  gi|298675112|ref|YP_003726862.1|  22 SMIVLTGKRRVGKTELIRQFMKDRDsiyffvdsnksieilmQEFTSILKESLDLPDYIKLETPEQFLDFLVNH---D 95 
                                       579******************9999888995555554444444444444455555555566665666666665...5 PP

                            AAA_14  64 kktylflDEiqev....pewekalkslvd...egknldvivtGSnskllsk....eiatslagrvaeielyplsfaE 129
                                       k+ ++ +DE q+     p++ + l+++ d   e++nl +i++GS+ +++ k    + a  + +  + ++l p++++E
  gi|298675112|ref|YP_003726862.1|  96 KNLVVAIDEFQRFskiyPSFIDQLQKYWDlkgENSNLFLIISGSSIGMIRKifieDNAPLFKRADNLLTLKPFTVKE 172
                                       7899********988889999********7654489***********998743323334444444467788887777 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.9
                            AAA_14  31 esilyinldderdkkla 47 
                                       +++l +++++ ++++++
  gi|298675112|ref|YP_003726862.1| 392 KKMLAVEVKNTELDENE 408
                                       33344444443333322 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   7.3e-09     1e-05       1     147 [.       2     108 ..       2     135 .. 0.63

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 7.3e-09
                            AAA_16   1 rlvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqala 77 
                                       +++ Re+ele + ++++    + p++++l+G + vGK+ l+r++++   +d ++f+   +++           ++l 
  gi|298675112|ref|YP_003726862.1|   2 KFYNREQELELMDTLYN----NKPSMIVLTGKRRVGKTELIRQFMK--DRDSIYFFVDSNKSI----------EIL- 61 
                                       6999*****88888888....6679********************7..444455544444444..........233. PP

                            AAA_16  78 reellrqlldeaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqwa 147
                                         + ++ +l e   ++  ++        +             le+  ++l++l ++++ lv+ +D++q++
  gi|298675112|ref|YP_003726862.1|  62 M-QEFTSILKE---SLDLPDYI------K-------------LETPEQFLDFLVNHDKNLVVAIDEFQRF 108
                                       1.222333323...11111111......1.............1122233333344445566666666655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   1.5e-09     2e-06       4     130 ..      20     139 ..      17     148 .. 0.81
   2 ?   -2.9   0.0       5.5   7.6e+03      49      68 ..     271     290 ..     236     312 .. 0.64
   3 ?   -2.8   0.0       5.3   7.3e+03      52      99 ..     343     389 ..     329     423 .. 0.64

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1.5e-09
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseelle 80 
                                       + +++v+tG   +GKT l+r++++            ++ +++ + s +s + l++e+ ++l+++l+ +   + e  e
  gi|298675112|ref|YP_003726862.1|  20 KPSMIVLTGKRRVGKTELIRQFMKD-----------RDSIYFFVDSNKSIEILMQEFTSILKESLDLPDYIKLETPE 85 
                                       5689********************6...........34455555566668999*********99999777788888* PP

                            AAA_22  81 aleqalraravielliiDEaqhlrs...eealeeLrsllnl..srkgvqliLvGt 130
                                       ++ + l ++++  ++ iDE+q++ s   +  + +L + ++l  + +++ li+ G 
  gi|298675112|ref|YP_003726862.1|  86 QFLDFLVNHDKNLVVAIDEFQRF-SkiyPSFIDQLQKYWDLkgENSNLFLIISGS 139
                                       ***********9***********.6678888888877788766666666666665 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.5
                            AAA_22  49 sstsskdllrellralglel 68 
                                       s++s++  +++l + lg+  
  gi|298675112|ref|YP_003726862.1| 271 SLNSLSHYFHDLTELLGVVE 290
                                       33455666666666666554 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 5.3
                            AAA_22  52 sskdllrellralglelkaerlsseellealeqalrarav.ielliiDE 99 
                                       ++k +  ++++ + ++l +   +  + ++++   +++r++ i ++  DE
  gi|298675112|ref|YP_003726862.1| 343 EWKRFTGDIFESVMRDLIT--EDIIDSYSKVGPWWNRRGDeIDIVAFDE 389
                                       5667777777777666666..5555555555555555555555555554 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   3.6e-05      0.05      25      74 ..      11      62 ..       6      72 .. 0.78
   2 ?   -1.4   0.0      0.92   1.3e+03      20      57 ..     279     315 ..     261     318 .. 0.72
   3 ?    1.4   0.1      0.13   1.8e+02      66     127 ..     388     449 ..     378     452 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.6e-05
                              TniB 25 eLleypkrkrmpnlllvGdsnnGKtmivekFarlhppek..dedaekvpvlv 74
                                      eL+++  +++++ ++l G+  +GKt ++++F++++ +      +++++++l+
  gi|298675112|ref|YP_003726862.1| 11 ELMDTLYNNKPSMIVLTGKRRVGKTELIRQFMKDRDSIYffVDSNKSIEILM 62
                                      6888889999999*******************99876531134455666666 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.92
                              TniB  20 lerLeeLleypkrkrmpnlllvGdsnnGKtmivekFar 57 
                                       ++ L eLl +  ++++p     G+s+ GK  + e+F r
  gi|298675112|ref|YP_003726862.1| 279 FHDLTELLGVV-EHKIPVTDTKGKSKHGKYFLTENFFR 315
                                       55556666554.466788888999*****999999986 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.13
                              TniB  66 daekvpvlvvqappkpdekrlyaaiLealgaplkararvskleqqvlrllrelkvrvLiiDE 127
                                       d+++ ++l+v++ ++  +++  ++iL++l++++k  +  s+++ q     ++++ r Li DE
  gi|298675112|ref|YP_003726862.1| 388 DEQNKKMLAVEVKNTELDENETRNILNSLSEKVKLVKGSSNMQIQLGVAAKQIENRELISDE 449
                                       556677888999888888888999*********99999999999999999999999999998 PP

>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0         2   2.7e+03     103     117 ..      88     102 ..      36     103 .. 0.55
   2 !   14.6   0.0     2e-05     0.028      66     120 ..     345     400 ..     294     402 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2
                                       xxxxxxxxxxxxxxx RF
                           DUF4143 103 vDfvielkggkivpi 117
                                       +Df+++++++ +v+i
  gi|298675112|ref|YP_003726862.1|  88 LDFLVNHDKNLVVAI 102
                                       577776666666655 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 2e-05
                                       xxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                           DUF4143  66 senkGallEnlVaqeLlky..sekegaklyyyrdkngaEvDfvi.elkggkivpiEvK 120
                                       + + G ++E+ V+++L+++   ++ + k+  + +++g E+D+v  +++++k+ ++EvK
  gi|298675112|ref|YP_003726862.1| 345 KRFTGDIFES-VMRDLITEdiIDS-YSKVGPWWNRRGDEIDIVAfDEQNKKMLAVEVK 400
                                       3789999998.6788888877444.77888888889********65569999*****9 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2     2e-05     0.028       6      41 ..     249     284 ..     244     290 .. 0.91
   2 ?   -1.8   0.0       2.1   2.9e+03       6      14 ..     411     419 ..     410     424 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2e-05
                                       HHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHH CS
                             HTH_5   6 kILklLaegelcvcelaeelglsqstvShHLkkLre 41 
                                       +I+++ ++g+++ +e+++++++s   +Sh++  L e
  gi|298675112|ref|YP_003726862.1| 249 EIVSAISQGKCSLTEISDMTHVSLNSLSHYFHDLTE 284
                                       8*****************************998876 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.1
                                       HHHHHHTTS CS
                             HTH_5   6 kILklLaeg 14 
                                        IL++L+e+
  gi|298675112|ref|YP_003726862.1| 411 NILNSLSEK 419
                                       79****996 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     4e-05     0.055       2      23 ..      24      45 ..      23      74 .. 0.86
   2 ?   -2.6   0.0       4.6   6.3e+03      24      44 ..     387     407 ..     384     420 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4e-05
                                      EEEESSTTSSHHHHHHCHCT-C CS
                               Roc  2 vvlvGdsgvGKtsllkrfvedk 23
                                      +vl G+ +vGKt l+++f++d+
  gi|298675112|ref|YP_003726862.1| 24 IVLTGKRRVGKTELIRQFMKDR 45
                                      799****************986 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.6
                                       CC-EEETTTTEEEEEEECGGS CS
                               Roc  24 fsekekstigvdfltkevtki 44 
                                       f+e++k++++v+++++e+ + 
  gi|298675112|ref|YP_003726862.1| 387 FDEQNKKMLAVEVKNTELDEN 407
                                       788888888888888776443 PP

>> UPF0102  Uncharacterised protein family UPF0102
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.1e-05     0.056      21      45 ..     375     403 ..     367     425 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.1e-05
                                       EEETTEEEEEEE....TTEEEEEEEEE-. CS
                           UPF0102  21 wrcragEiDiia....tevlvfvEVKtRs 45 
                                       w+ r  EiDi+a    ++ ++ vEVK  +
  gi|298675112|ref|YP_003726862.1| 375 WNRRGDEIDIVAfdeqNKKMLAVEVKNTE 403
                                       554557**********889*******863 PP

>> DUF4702  Domain of unknown function (DUF4702)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.4e-05     0.047     258     293 ..      55      95 ..      33     104 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.4e-05
                           DUF4702 258 nkeiksllsq.....pasfdlPgyCslrePhrtldflaehr 293
                                       nk i  l++       +s+dlP y +l  P + ldfl +h 
  gi|298675112|ref|YP_003726862.1|  55 NKSIEILMQEftsilKESLDLPDYIKLETPEQFLDFLVNHD 95 
                                       5555555444111113689********************95 PP

>> HSDR_N_2  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.12   1.6e+02      21      94 ..      70     144 ..      55     153 .. 0.74
   2 ?    8.5   0.0    0.0014       1.9      36      68 ..     379     410 ..     366     423 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.12
                          HSDR_N_2  21 keliavekelqlgskkkraDivvykkdkkpllivecKapsvkiseevleqlksYlea..lkaeylvvtNglehivy 94 
                                       ke++++   ++l++ ++  D++v  ++ + +++++  +   ki    ++ql++Y      + +++++  g+++ ++
  gi|298675112|ref|YP_003726862.1|  70 KESLDLPDYIKLETPEQFLDFLVNHDK-NLVVAIDEFQRFSKIYPSFIDQLQKYWDLkgENSNLFLIISGSSIGMI 144
                                       566666667788888889999987755.888899888888999999********9874336777777777666655 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0014
                          HSDR_N_2  36 kkraDivvykkdkkpllivecKapsvkiseevl 68 
                                        + +Div +++++k +l+ve+K+ ++  +e + 
  gi|298675112|ref|YP_003726862.1| 379 GDEIDIVAFDEQNKKMLAVEVKNTELDENE-TR 410
                                       5679*******************9997754.44 PP

>> NFACT-R_1  NFACT protein RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00015       0.2       4      50 ..      16      63 ..      13      99 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                         NFACT-R_1  4 wFkssdgylvimGkDkqeneelikkyleesd.vwfhvdkessahvylr 50
                                       ++++ +++v+ Gk    + eli++ ++++d ++f vd++ s  ++++
  gi|298675112|ref|YP_003726862.1| 16 LYNNKPSMIVLTGKRRVGKTELIRQFMKDRDsIYFFVDSNKSIEILMQ 63
                                      5778899************************9***********99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.71u 0.34s 00:00:01.05 Elapsed: 00:00:00.52
# Mc/sec: 2660.96
//
Query:       gi|298675113|ref|YP_003726863.1|  [L=88]
Description: hypothetical protein Metev_1191 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 546.00
//
Query:       gi|298675114|ref|YP_003726864.1|  [L=548]
Description: hypothetical protein Metev_1193 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.5e-14   51.4  29.6    7.7e-08   31.9   7.2    3.0  3  NosD            Periplasmic copper-binding protein (NosD)
    4.3e-11   42.9  46.2    2.5e-07   30.7  39.6    3.2  3  Beta_helix      Right handed beta helix region
    0.00086   18.1   0.0     0.0016   17.2   0.0    1.4  1  Pectinesterase  Pectinesterase


Domain annotation for each model (and alignments):
>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.3     0.029   1.7e+02       2      79 ..      58     135 ..      57     152 .. 0.66
   2 !   31.9   7.2   1.3e-11   7.7e-08      30     132 ..     142     285 ..     120     289 .. 0.73
   3 !   25.0  13.1   1.6e-09   9.8e-06      82     166 ..     287     374 ..     282     375 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.029
                              NosD   2 nnaisgdevlvsargngiqlensegseisnneisnsrdgilldnssnntitgntienlryGihlensesntiedntl 78 
                                       nn+++gd + v   ++   ++  e +++   +++ s+++i   ++++++  ++  +  + + ++++++++ti++ t+
  gi|298675114|ref|YP_003726864.1|  58 NNSSDGDIIEVAPGTYSELVYMQERNDLIIRSTNGSEATIIDAKQTGKSPLNSPGTPTHPAFYVMDCNNITIKGFTI 134
                                       67777777666654444445555777777788888888885555556666666777779999999999966665444 PP

                              NosD  79 s 79 
                                       +
  gi|298675114|ref|YP_003726864.1| 135 N 135
                                       4 PP

  == domain 2  score: 31.9 bits;  conditional E-value: 1.3e-11
                              NosD  30 snneisnsrdgi.....lldnssnntitgntienlryGihlenses......ntiedntlssne...sGialmsssn 92 
                                       + nei +s d       ll++ssn+++++n ++n +yG++l++  +      n i++n++++n+    Gi l++   
  gi|298675114|ref|YP_003726864.1| 142 NTNEIYQSTDPYlmtpvLLYSSSNCKVQDNILHNFYYGVFLSGEAGfgpcndNLITNNKIDGNKlafFGINLYDDGT 218
                                       3344444444334455599***********************9999999999************9999*******97 PP

                              NosD  93 n.tlenNtisnnen....yGillsd.ssnntisnNti.....................snnnkGifl 132
                                          +enN+is+n+     y i+  + + n+tis+N++                     ++n++Gi++
  gi|298675114|ref|YP_003726864.1| 219 VdGMENNIISDNTVqncyYNIYAGFdAVNTTISGNVVsgspdlvdyfpsasytdppqeLDNGYGIKV 285
                                       7788888888888866667887765144578****99666666666666666666664466666665 PP

  == domain 3  score: 25.0 bits;  conditional E-value: 1.6e-09
                              NosD  82 esGialmsssnn.tlenNtisnnenyGillsdssnntisnNtisnnnkGiflens....ssntitgNriesnqkiGi 153
                                       ++G+a + + +   +++N+++++++ Gil ++ +  t+s+N + nnn+Gi +++     ++n+i  N i +n+++Gi
  gi|298675114|ref|YP_003726864.1| 287 GDGLASDGTVGGqLIKGNIVTDCKT-GILSNTFN-VTVSENIVCNNNNGIGIDDYlhqvTGNEIHYNDIRNNENYGI 361
                                       4788888888777**********99.*8777666.78*************999988889****************** PP

                              NosD 154 lllsssegntiyn 166
                                         +++++ n  yn
  gi|298675114|ref|YP_003726864.1| 362 INIAATDVNATYN 374
                                       *999999898886 PP

>> Beta_helix  Right handed beta helix region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   8.5   2.4e-08   0.00014      48     149 ..     118     218 ..      57     225 .. 0.68
   2 !   30.7  39.6   4.2e-11   2.5e-07       3     144 ..     158     363 ..     117     376 .. 0.72
   3 ?   -1.8   0.2       0.4   2.4e+03      52      75 ..     444     467 ..     406     495 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.4e-08
                                       SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-....SEE-TT-S--EEES-EEESTT--SEE- CS
                        Beta_helix  48 Giyilgssnntisnntisdnngggialfgasnnlienneitdnggs....GiylnyssnntienNiidnnagsGivi 120
                                        +y+  ++n+ti++ ti+d                + nei+   +      + l++ssn+++++Ni++n + +G+++
  gi|298675114|ref|YP_003726864.1| 118 AFYVMDCNNITIKGFTINDVI-----------LDANTNEIYQSTDPylmtPVLLYSSSNCKVQDNILHNFY-YGVFL 182
                                       344555555555555555555...........222233333333324444666666999999999999999.99999 PP

                                       --TT.....---EEES-EEES-S..SEEEE-TT-SS CS
                        Beta_helix 121 ddss.....snvtvtnNtitnnk..gaGiavvgsss 149
                                       + ++     +++ +tnN+i++nk    Gi+++++++
  gi|298675114|ref|YP_003726864.1| 183 SGEAgfgpcNDNLITNNKIDGNKlaFFGINLYDDGT 218
                                       999999999999999999999997777887777776 PP

  == domain 2  score: 30.7 bits;  conditional E-value: 4.2e-11
                                       EEE-SS-E.EEESEEEES-SS-SEEE-SSS-.......EEES-EEES..-SS-SEEE-TT......-S-EEES-EEE CS
                        Beta_helix   3 isingssnvtiknntisnsggyGiylrgssn......vvienneian..nsgsGiyilgs......snntisnntis 65 
                                       +++++ssn+++++n+++n  +yG++l g  +      ++i+nn+i +    ++Gi ++ +      +nn+is+nt+ 
  gi|298675114|ref|YP_003726864.1| 158 VLLYSSSNCKVQDNILHNF-YYGVFLSGEAGfgpcndNLITNNKIDGnkLAFFGINLYDDgtvdgmENNIISDNTVQ 233
                                       6778899999999999995.999999999999999999999999999777788888888888999999999999999 PP

                                       ---SEEE-TT--S--EEES-EEES-....................SS-SEE-TT....................... CS
                        Beta_helix  66 dnngggialfgasnnlienneitdn....................ggsGiylny....................... 99 
                                       ++++   a f+a n++i++n ++                      +g+Gi +++                       
  gi|298675114|ref|YP_003726864.1| 234 NCYYNIYAGFDAVNTTISGNVVSGSpdlvdyfpsasytdppqeldNGYGIKVTGdglasdgtvggqlikgnivtdck 310
                                       99955555558888888888888887777666666666666666544455555335533333222222222222222 PP

                                       ......-S--EEES-EEESTT--SEE---TT...---EEES-EEES-SSEEEE- CS
                        Beta_helix 100 ......ssnntienNiidnnagsGividdss...snvtvtnNtitnnkgaGiav 144
                                             + n+t+++Ni+ nn+ +Gi idd     ++++++ N i nn ++Gi +
  gi|298675114|ref|YP_003726864.1| 311 tgilsnTFNVTVSENIVCNNN-NGIGIDDYLhqvTGNEIHYNDIRNNENYGIIN 363
                                       222222666777777777777.77777777666777777777777777777744 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.4
                                       -TT-S-EEES-EEE---SEEE-TT CS
                        Beta_helix  52 lgssnntisnntisdnngggialf 75 
                                       +++ +++++n t +d++ g+i+++
  gi|298675114|ref|YP_003726864.1| 444 TNTGDIVLYNITLTDSKLGEINCS 467
                                       233555556666666655555544 PP

>> Pectinesterase  Pectinesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.6e-07    0.0016       2      69 ..      40     103 ..      39     141 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.6e-07
                                       EEE-TTS-SSBSSHHHHHHHS-SS-SS-EEEEE-SEEEE--EEE-TTS-SEEEEES-TTTEEEEE--- CS
                    Pectinesterase   2 vvvakdgsgkfktiseavaavpeksekrfviyvkaGvYeenvevekkktnvvlvGdGkektvitgskn 69 
                                       ++v +dg +++++i+ av++     ++  +i v  G+Y+e v +++++  ++   +G+e t+i +++ 
  gi|298675114|ref|YP_003726864.1|  40 ITVDDDGPADYSSIQYAVNNS----SDGDIIEVAPGTYSELVYMQERNDLIIRSTNGSEATIIDAKQT 103
                                       78999***********99865....45679******************9999***********98643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (548 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.56
# Mc/sec: 2943.19
//
Query:       gi|298675115|ref|YP_003726865.1|  [L=142]
Description: DNA polymerase beta domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-20   72.1   2.5    4.2e-20   71.6   2.5    1.2  1  Polbeta        Polymerase beta, Nucleotidyltransferase
    4.6e-10   39.7   1.3    6.5e-10   39.2   1.3    1.4  1  NTP_transf_2   Nucleotidyltransferase domain
  ------ inclusion threshold ------
       0.02   14.8   0.0      0.029   14.3   0.0    1.5  1  Adenyl_cycl_N  Adenylate cyclase NT domain


Domain annotation for each model (and alignments):
>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.6   2.5   7.1e-24   4.2e-20       1      91 [.       9     103 ..       9     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 71.6 bits;  conditional E-value: 7.1e-24
                                       -STTTTHHHHHHHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH.....SSSEEEEEETTTS- CS
                           Polbeta   1 ekikeilekekeielaylFGSrakgkareeSDiDlavllkekldleeelelaaeledi....klgkkvDlvdlneap 73 
                                       +k+++++  ++e++laylFGS+akg+ ++ SD+D+avll+e+l+++e ++l+ ++ d      + +++Dl ++n ap
  gi|298675115|ref|YP_003726865.1|   9 KKLEDYFTAKDEVILAYLFGSVAKGESNRLSDVDVAVLLDESLTKQEMFDLELKFIDDivgiLKVDDIDLTIMNLAP 85 
                                       799***************************************66666555555544444555999************ PP

                                       HHHHHHHHHS-EEEES-S CS
                           Polbeta  74 plllyeilkegkllyskd 91 
                                       ++l ++i+k+g +l s +
  gi|298675115|ref|YP_003726865.1|  86 LTLNFNIIKQGYILKSDE 103
                                       ***********9997765 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   1.3   1.1e-13   6.5e-10       1      87 [.       8     101 ..       6     135 .. 0.72

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 1.1e-13
                                       HHHHHHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEE... CS
                      NTP_transf_2   1 lkklleelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlv... 74 
                                       +kkl + +  ++ v+ ++lfGS+a+G+ ++ SD+D++v+l+e+  +++++   ++l++i + +  l++  +dl    
  gi|298675115|ref|YP_003726865.1|   8 IKKLEDYFTAKDEVILAYLFGSVAKGESNRLSDVDVAVLLDESLTKQEMF--DLELKFIDDIVGILKVDDIDLTimn 82 
                                       6788888888888******************************7754444..3333333333333334444444445 PP

                                       ......CEEECCCCTEEEE CS
                      NTP_transf_2  75 ......trekledpllvks 87 
                                              ++++++ ++ ks
  gi|298675115|ref|YP_003726865.1|  83 lapltlNFNIIKQGYILKS 101
                                       5555543333333555554 PP

>> Adenyl_cycl_N  Adenylate cyclase NT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   4.8e-06     0.029      91     134 ..      20      63 ..       3     124 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.8e-06
                     Adenyl_cycl_N  91 aieglylmGStgsiaqsekSDlDiWvchrselsaeelelLekKl 134
                                       ++   yl GS++    +  SD+D+ v  +++l+++e+  Le K 
  gi|298675115|ref|YP_003726865.1|  20 EVILAYLFGSVAKGESNRLSDVDVAVLLDESLTKQEMFDLELKF 63 
                                       444569**********************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 891.28
//
Query:       gi|298675116|ref|YP_003726866.1|  [L=473]
Description: DEXX-box ATPase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-28   98.6   4.0    2.5e-28   98.4   0.9    2.4  2  DUF234    Archaea bacterial proteins of unknown function
    1.5e-17   64.3   2.4    1.2e-15   58.1   2.4    2.5  1  ATPase_2  ATPase domain predominantly from Archaea
    9.8e-09   35.3   0.1    3.6e-08   33.5   0.1    2.0  1  AAA_14    AAA domain
    1.3e-05   25.1   0.0    2.7e-05   24.1   0.0    1.5  1  Mrr_cat   Restriction endonuclease
    0.00027   21.2   0.0    0.00082   19.7   0.0    1.8  1  AAA_22    AAA domain
     0.0095   15.9   1.2      0.034   14.1   0.1    2.4  2  HTH_45    Winged helix-turn-helix
  ------ inclusion threshold ------
       0.06   13.6   0.2       0.28   11.4   0.2    2.1  1  Roc       Ras of Complex, Roc, domain of DAPkinase
      0.075   13.4   0.3        2.5    8.4   0.1    2.7  2  AAA_16    AAA ATPase domain
       0.13   11.9   3.0       0.42   10.2   0.3    2.5  2  SatD      SatD family (SatD)


Domain annotation for each model (and alignments):
>> DUF234  Archaea bacterial proteins of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1       0.7   1.4e+03      19      70 ..      69     121 ..      56     133 .. 0.67
   2 !   98.4   0.9   1.2e-31   2.5e-28       1      93 [.     313     413 ..     313     418 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.7
                            DUF234  19 evlekikeel.neyvgk.vFEelvrelllelnkagklpfrftkvGrwWkkeeei 70 
                                       e+ +k+++++  +++g+ ++++++++l+ +  +++++ + f ++ r+ + +++i
  gi|298675116|ref|YP_003726866.1|  69 EIAKKFHQQFgLTFLGTpEWDDIFEQLFQYT-QNNQIIVVFDEFQRFLNINKNI 121
                                       4556666666567777636888888877744.4556777788888887765555 PP

  == domain 2  score: 98.4 bits;  conditional E-value: 1.2e-31
                            DUF234   1 wfrfvypnrseielgeseevlekikeelneyvgkvFEelvrelllelnkagklpfrftkvGrwW........kkeee 69 
                                       wfrfvyp+ seie+g+++ v+++i++eln++vg++FEe+++++l+e+nk+g l f+f k+G+ W        k+  e
  gi|298675116|ref|YP_003726866.1| 313 WFRFVYPYLSEIEIGNTSTVVDRIQSELNTFVGNTFEEITKQFLIEKNKKGDLGFTFGKIGKQWgryqkskgKNTYE 389
                                       ****************************************************************999998877888* PP

                            DUF234  70 iDivaldeeekkalfgEvKwknse 93 
                                       iD+ al+e+++++lf+E+Kw+n++
  gi|298675116|ref|YP_003726866.1| 390 IDLAALNENTNEILFCECKWQNQK 413
                                       **********************44 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   2.4   5.8e-19   1.2e-15       1     233 []       7     207 ..       7     207 .. 0.79

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 5.8e-19
                          ATPase_2   1 FfdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkk 77 
                                       F++R+ke+ + e+ ++++  +++ i G+++ GKt+++ e+++ + + ++    +         +l++     + + +
  gi|298675116|ref|YP_003726866.1|   7 FINRQKEVGYFENEYKKSDFRFISIIGRRRLGKTRFISEFLKDKTNFSY----IL------VPELNDL----NARVE 69 
                                       99***************************************99965443....22......2222332....22222 PP

                          ATPase_2  78 lekalgiavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnliesltk 154
                                       ++k++ ++++ + l       + + +  +e+l++  +++  +ii+++De+q+     +n  ++  + +++ i++  +
  gi|298675116|ref|YP_003726866.1|  70 IAKKFHQQFGLTFL------GTPEWDDIFEQLFQYTQNN--QIIVVFDEFQRFL--NIN--KNIFSIIQKNIDQYGQ 134
                                       33344333343333......2344455566666665554..8************..777..9999************ PP

                          ATPase_2 155 ekhlcvviclsSeglfiervyneselegrhky.ilvddldketalnflkegfkeleelskedfeeiyryvGGkPkal 230
                                         ++++v+ +sS g+++   ++ s+l+gr+++ ++ + +d+    + + +       ls e++ +iy++ GG Pk+l
  gi|298675116|ref|YP_003726866.1| 135 TSKMFLVVSGSSIGMMHGIFDHASPLYGRRTGqLEFESFDFFALNEWFPD-------LSIESKINIYSIYGGTPKYL 204
                                       ********************************999999966655555555.......58899*************** PP

                          ATPase_2 231 vel 233
                                       +e+
  gi|298675116|ref|YP_003726866.1| 205 EEV 207
                                       987 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.1   1.8e-11   3.6e-08       3     118 ..      27     165 ..      25     178 .. 0.66

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 1.8e-11
                            AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderd........kkladpe.............kllelile 58 
                                       + + i G Rr GKT ++ +++k++     ++ yi + + +d        k     +             + ++++ +
  gi|298675116|ref|YP_003726866.1|  27 RFISIIGRRRLGKTRFISEFLKDKT----NFSYILVPELNDlnarveiaK-----KfhqqfgltflgtpEWDDIFEQ 94 
                                       6789*****************9998....555555544444222444331.....1223345555666544455555 PP

                            AAA_14  59 k..lkeekktylflDEiqev....pewekalkslvdeg...knldvivtGSnskllsk..eiatslagrva 118
                                       +  ++++++ ++++DE q+     +++++++++ +d++   +++ ++v+GS+ +++    + a+ l gr +
  gi|298675116|ref|YP_003726866.1|  95 LfqYTQNNQIIVVFDEFQRFlninKNIFSIIQKNIDQYgqtSKMFLVVSGSSIGMMHGifDHASPLYGRRT 165
                                       43334479999*********6666667777777777444447899********999765566666666654 PP

>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   1.4e-08   2.7e-05      23     113 ..     375     471 ..     341     473 .] 0.80

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.4e-08
                                       S..EEE---B-TTSSB--EEEETTEEEEEEEEEEE--TS-B-HHHHHHHHHHCTT......S..SEEEEEESS-B-H CS
                           Mrr_cat  23 k..eveltgrsgDggiDliakkdplgserilvqaKryknkvgvkeVqeligalkk......rgadkgifvttsdftk 91 
                                       +  +++ +++++ + iDl a  ++   e ++ ++K++++k++v  +++li   k       ++ +   +v+ s+ft+
  gi|298675116|ref|YP_003726866.1| 375 QwgRYQKSKGKNTYEIDLAALNEN-TNEILFCECKWQNQKIDVGILKSLIDKSKFvdwhknKRIEYFAVVSKSGFTE 450
                                       1556788999999*****987654.5599******************998887765665546799999********* PP

                                       HHHHHHHTT--EEEE-HHHHHH CS
                           Mrr_cat  92 aAreeaeelnkieLldgdeLae 113
                                       +A e+a+e n+  L++ d++ +
  gi|298675116|ref|YP_003726866.1| 451 NALEFARE-NNFMLFTLDDFEN 471
                                       ********.*******999987 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   4.1e-07   0.00082       6     126 ..      27     141 ..      22     148 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 4.1e-07
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsstsskdllrellralglelkaerlsseellea 81 
                                       +++ ++G    GKT+ + ++l+ ++        + +++   +l+ ++ + ++++++ +++gl   + + + ++++e+
  gi|298675116|ref|YP_003726866.1|  27 RFISIIGRRRLGKTRFISEFLKDKT--------NFSYIlVPELNDLNARVEIAKKFHQQFGLTFLG-TPEWDDIFEQ 94 
                                       6899******************975........77777333555556999***********99999.********** PP

                            AAA_22  82 leqalraravielliiDEaqh.lr.seealeeL.rsllnl.srkgvqli 126
                                       l q+ ++ +   +++ DE+q+ l+ ++++++ + +++    +++++ l+
  gi|298675116|ref|YP_003726866.1|  95 LFQYTQNNQI--IVVFDEFQRfLNiNKNIFSIIqKNIDQYgQTSKMFLV 141
                                       ********99..*********6656677777773333333555555555 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       1.2   2.4e+03      10      28 ..     211     228 ..     207     229 .. 0.83
   2 !   14.1   0.1   1.7e-05     0.034       8      50 ..     244     287 ..     239     305 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.2
                            HTH_45  10 dILeaisegeakkTkimyk 28 
                                       +IL+ i      kT+++y+
  gi|298675116|ref|YP_003726866.1| 211 NILQEI-TRILDKTSMLYN 228
                                       689988.888899999996 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1.7e-05
                            HTH_45   8 iadILeaisegeakkTkimykanLsykllnkYLdmLve.kglik 50 
                                       +++IL++is+g +k+T i  ++ ++   l+ YL++Lv+  +l+k
  gi|298675116|ref|YP_003726866.1| 244 YFNILKNISQGVTKPTGIANNSGIKPTSLDYYLNTLVNdLDLVK 287
                                       689*********************************96146663 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00014      0.28       2     115 ..      29     142 ..      29     146 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
                                       EEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTT.T-HHH. CS
                               Roc   2 vvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrs.lhply. 76 
                                       + ++G  + GKt ++++f++dk + ++     ++ l+ +v+  k+++     +++ l +    G  + +   ++l+ 
  gi|298675116|ref|YP_003726866.1|  29 ISIIGRRRLGKTRFISEFLKDKTNFSYILVPELNDLNARVEIAKKFH-----QQFGLTF---LGTPEWDDiFEQLFq 97 
                                       569***********************999999999888874333332.....3344443...333333331344442 PP

                                       HCTSCEEEEEEE..GHHH....HCH.HHHHHHHHHHCSSS-EEEEE CS
                               Roc  77 lreaalailvyd..srss....enl.keWlkelkkvagkspvilvg 115
                                       +++++ +i+v+d  + ++    +n+ +   k++++++++s+++lv+
  gi|298675116|ref|YP_003726866.1|  98 YTQNNQIIVVFDefQ-RFlninKNIfSIIQKNIDQYGQTSKMFLVV 142
                                       567777778888542.331111233134567788888888888775 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0013       2.5      20      63 ..      22      77 ..       6     141 .. 0.63
   2 ?   -2.4   0.0       2.8   5.6e+03     126     145 ..     452     470 ..     448     472 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0013
                            AAA_16 20 rsgrpelvllsGesGvGKsslvrellralekd.............ggif.lrgkcdql 63
                                      ++++ + + ++G +  GK++ + e+l+   k+             ++ + ++ k++q 
  gi|298675116|ref|YP_003726866.1| 22 KKSDFRFISIIGRRRLGKTRFISEFLKD--KTnfsyilvpelndlNARVeIAKKFHQQ 77
                                      3567799999************999972..2223444444444444444444444444 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.8
                            AAA_16 126 llallsrderplvlvlDdlq 145
                                       +l+++++     +++lDd++
  gi|298675116|ref|YP_003726866.1| 452 ALEFARE-NNFMLFTLDDFE 470
                                       5677777.77799*****98 PP

>> SatD  SatD family (SatD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.3   0.00021      0.42      37      68 ..      97     128 ..      64     151 .. 0.77
   2 ?    1.3   0.2      0.11   2.2e+02     146     189 ..     404     449 ..     381     454 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00021
                              SatD  37 eeliskftitlGdefqallkvekkifqiidei 68 
                                       ++   +  i + defq +l+++k+if ii + 
  gi|298675116|ref|YP_003726866.1|  97 QYTQNNQIIVVFDEFQRFLNINKNIFSIIQKN 128
                                       455566678899****************9864 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.11
                              SatD 146 fikskwrasqle..vletllekkiyeekfdqkklaeklklsasals 189
                                       f  +kw+ ++++  +l++l++k+ + +  ++k++     +s+s ++
  gi|298675116|ref|YP_003726866.1| 404 FCECKWQNQKIDvgILKSLIDKSKFVDWHKNKRIEYFAVVSKSGFT 449
                                       6678999998773369*****************9999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 2840.64
//
Query:       gi|298675117|ref|YP_003726867.1|  [L=145]
Description: hypothetical protein Metev_1196 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-18   65.8   0.7    3.7e-18   65.5   0.7    1.1  1  DUF86         Protein of unknown function DUF86
  ------ inclusion threshold ------
      0.052   13.8   0.0      0.071   13.3   0.0    1.3  1  Phage_TAC_14  Phage tail assembly chaperone protein, TAC


Domain annotation for each model (and alignments):
>> DUF86  Protein of unknown function DUF86
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.5   0.7   4.1e-22   3.7e-18      15     116 ..      26     129 ..       7     132 .. 0.89

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 4.1e-22
                                       .TSTSCCGSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----SSC..HHHHHHHTTSS-HHHHHHHHHHHCCHHHH CS
                             DUF86  15 ldeeeflsdeleydavernlqvigEaaidiakhlakklgikkpgdy..ifeilaekgviaeepeepwrkmiglRNrL 89 
                                        ++ +++ +   + avern+q+++E++idi+  +++k+g+kkp+dy  ++ il ++ +i+e+++++++ ++  R++L
  gi|298675117|ref|YP_003726867.1|  26 TEKMDLQDNYEMRSAVERNIQIAIECVIDIGLVIISKEGLKKPEDYenVILILGKNAIIPEDFAKDFSTVASWRDAL 102
                                       3455666788899**************************************************************** PP

                                       HT-CCCTTHHHHHHHHHHTCHHHHHHH CS
                             DUF86  90 vHgYlgidpeivwsiikenlpdleefl 116
                                       vH   +i+ + + + ++e+l d+e++ 
  gi|298675117|ref|YP_003726867.1| 103 VHVDDEINTSLLENFLREQLGDFERYG 129
                                       ********************9999875 PP

>> Phage_TAC_14  Phage tail assembly chaperone protein, TAC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   7.9e-06     0.071      28      77 ..      18      65 ..       4      84 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.9e-06
                      Phage_TAC_14 28 ltalelleleekaeklsdaGngreasrlnvqlvldclvddkGkpipkedl 77
                                      +  l+ ++ e     l d  ++r a   n+q+ ++c++d     i ke l
  gi|298675117|ref|YP_003726867.1| 18 VNYLKTIDTE--KMDLQDNYEMRSAVERNIQIAIECVIDIGLVIISKEGL 65
                                      4445555544..35789999******************977666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 888.04
//
Query:       gi|298675118|ref|YP_003726868.1|  [L=94]
Description: DNA polymerase beta domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-17   62.2   0.8    4.8e-17   62.0   0.8    1.0  1  NTP_transf_2    Nucleotidyltransferase domain
    3.3e-15   56.0   1.0    3.6e-15   55.8   1.0    1.1  1  Polbeta         Polymerase beta, Nucleotidyltransferase
  ------ inclusion threshold ------
      0.027   14.7   0.0       0.03   14.5   0.0    1.2  1  DNA_pol_B_palm  DNA polymerase beta palm


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.0   0.8     8e-21   4.8e-17       6      94 ..      12      93 ..       7      94 .] 0.93

  Alignments for each domain:
  == domain 1  score: 62.0 bits;  conditional E-value: 8e-21
                                      HHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECCCCTE CS
                      NTP_transf_2  6 eelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekledpll 84
                                      + +k +++ +kv +fGS++rG+ l +SDiD+lv +++        ++ ++++e  + le l+ ++vdlv++++++ p l
  gi|298675118|ref|YP_003726868.1| 12 NTMKNKFGAKKVGVFGSFVRGEELDNSDIDILVEFEKGQ------KTFDNYMELKFYLEDLFDRKVDLVVISSIK-PQL 83
                                      67899999******************************4......678***************************.*** PP

                                      EEEEECEEEH CS
                      NTP_transf_2 85 vksileerpl 94
                                      +++il+e+++
  gi|298675118|ref|YP_003726868.1| 84 KDNILDEAVY 93
                                      *******998 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   1.0   6.1e-19   3.6e-15       6      84 ..      13      91 ..       8      94 .] 0.92

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 6.1e-19
                                      THHHHHHHHSTTEEEEEE-S------EEEEEEEESS-.--HHHHHHHHHHHHHH.SSSEEEEEETTTS-HHHHHHHHHS CS
                           Polbeta  6 ilekekeielaylFGSrakgkareeSDiDlavllkek.ldleeelelaaelediklgkkvDlvdlneapplllyeilke 83
                                      +++++ + + + +FGS+++g+  ++SDiD+ v +++  +++++++el+  led+   +kvDlv++++ +p l+ +il e
  gi|298675118|ref|YP_003726868.1| 13 TMKNKFGAKKVGVFGSFVRGEELDNSDIDILVEFEKGqKTFDNYMELKFYLEDL-FDRKVDLVVISSIKPQLKDNILDE 90
                                      67777789999*************************99****************.88*******************986 PP

                                      - CS
                           Polbeta 84 g 84
                                       
  gi|298675118|ref|YP_003726868.1| 91 A 91
                                      5 PP

>> DNA_pol_B_palm  DNA polymerase beta palm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   5.1e-06      0.03      24      60 ..      20      56 ..       2      88 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.1e-06
                                      T-EEEE-HHHHTT-S.EESSEEEEEEBTTBSTTSS--H CS
                    DNA_pol_B_palm 24 evevivcGSYRRgae.ssGDvDvlitkkdakseskklk 60
                                        +v v GS+ Rg+e +  D+D+l+  ++++++ ++  
  gi|298675118|ref|YP_003726868.1| 20 AKKVGVFGSFVRGEElDNSDIDILVEFEKGQKTFDN-Y 56
                                      3578899*****9875799*******9999987432.2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 599.51
//
Query:       gi|298675119|ref|YP_003726869.1|  [L=90]
Description: hypothetical protein Metev_1198 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.098   12.2   0.0       0.11   12.1   0.0    1.1  1  SatD      SatD family (SatD)


Domain annotation for each model (and alignments):
>> SatD  SatD family (SatD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   6.1e-06      0.11       1      57 [.       6      66 ..       6      85 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.1e-06
                              SatD  1 yialiGdiinskqiter..skvqkklkklleelnkky..aeeliskftitlGdefqallkv 57
                                      y  + Gd+i+s +  +   +kv   l + +  ++++   +e +  +f i  Gd fq++lk 
  gi|298675119|ref|YP_003726869.1|  6 YSVITGDLIDSSKFVDNewQKVASLLYESFRIVENEIvpNEAFRYEFEIYRGDSFQCVLKN 66
                                      56789****987665441256667777777777665523678999************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 567.74
//
Query:       gi|298675120|ref|YP_003726870.1|  [L=410]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.5e-23   81.7   0.2    2.8e-22   79.2   0.0    2.4  3  OrfB_IS605      Probable transposase
    4.8e-10   39.2   0.1    1.6e-09   37.6   0.1    1.9  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    0.00062   19.6   0.3     0.0017   18.2   0.3    1.7  1  DUF919          Nucleopolyhedrovirus protein of unknown funct
  ------ inclusion threshold ------
      0.038   14.4   0.0      0.085   13.2   0.0    1.5  1  RuvX            Holliday junction resolvase


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       1.1   5.1e+03      34      59 ..      28      53 ..      18      73 .. 0.54
   2 ?   -2.2   0.0         1   4.5e+03      10      45 ..      67     102 ..      51     108 .. 0.72
   3 !   79.2   0.0   6.4e-26   2.8e-22      10     119 ..     185     292 ..     176     293 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.1
                        OrfB_IS605 34 edgtwflykgrrlksdykylakeiae 59
                                      +  + +ly+ r+++ +y ++ +++  
  gi|298675120|ref|YP_003726870.1| 28 NLYNFTLYNIRQYFFNYGKYLNKNTA 53
                                      44445566666655555444443333 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtwflykgrr 45 
                                       + ++ +n++  +D G++ +  + +++ + ++ k+ +
  gi|298675120|ref|YP_003726870.1|  67 PSQVAQNTVETVDGGMKSFFKLLDKKRKGEYEKPVS 102
                                       556667777778888888888888887777777755 PP

  == domain 3  score: 79.2 bits;  conditional E-value: 6.4e-26
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsr 86 
                                        ++ + n++++iDlG+ n+at+vt++gt+f+ +gr +ks +++++ke+ +lqs ++k+        k+ r ++kr  
  gi|298675120|ref|YP_003726870.1| 185 IAELDYNSHLSIDLGVDNFATCVTTSGTAFILDGRGIKSYNRWWNKEKSRLQSVYDKQD--VDNGIKMDRFSNKRFW 259
                                       56667899**************************************************9..9*************** PP

                        OrfB_IS605  87 rrkhllhklathliktlkevgvetLnvgnmkdi 119
                                       ++++++++ ++h++k++ e+ ++++++g++k+i
  gi|298675120|ref|YP_003726870.1| 260 KINDFMNQCVNHIVKHCLENRIGNVVIGELKEI 292
                                       ******************************987 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.1   3.5e-13   1.6e-09       1      69 []     311     385 ..     311     385 .. 0.90

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 3.5e-13
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke......alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f+++k +l+ k+k +Gik++ev++ayTSk  +   +  k+      ++ +r    ++ g  +++D+n+a+Nil++
  gi|298675120|ref|YP_003726870.1| 311 FARFKYKLASKCKYHGIKYQEVDEAYTSKVDALALELIKKhkkylgKRPKRGIFQSSTGRLINADINGALNILRK 385
                                       899**************************9887766666666799999999999999***************986 PP

>> DUF919  Nucleopolyhedrovirus protein of unknown function (DUF919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.3   3.7e-07    0.0017      15      58 ..       4      45 ..       2      47 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.7e-07
                            DUF919 15 qaKrkltiksqHfErlkkitKnpkElqdlekklnklRqeFLnfg 58
                                       +K  l+ + q +E lk++tK +k l +   +l ++Rq+F+n+g
  gi|298675120|ref|YP_003726870.1|  4 TQKNHLRADKQTYETLKRLTKLSKNLYNF--TLYNIRQYFFNYG 45
                                      58999******************888765..8***********9 PP

>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.9e-05     0.085      37     106 ..     266     345 ..     253     361 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.9e-05
                                       HHHHHHHHHHHHHTT--EEEEE--........----SSS---SSTTHHHHHHHHHT....T-EEEEE--S----XXX CS
                              RuvX  37 ekdleelkelvkeeeveeiVvGlP........lnldgsegesakkvrkfaeeLakrl..kklpvelvDErlttveae 103
                                       ++ ++++ + + e+++ ++V+G          +  +++++ ++  +++f  +La+++  ++++   vDE +t++  +
  gi|298675120|ref|YP_003726870.1| 266 NQCVNHIVKHCLENRIGNVVIGELkeikqeqnIGKENTQNFQTIPFARFKYKLASKCkyHGIKYQEVDEAYTSKVDA 342
                                       68899*****************9867777655666677777788889999999999877889***********8755 PP

                                       XXX CS
                              RuvX 104 ril 106
                                        +l
  gi|298675120|ref|YP_003726870.1| 343 LAL 345
                                       444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       954  (0.0532099); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 2454.30
//
Query:       gi|298675121|ref|YP_003726871.1|  [L=190]
Description: hypothetical protein Metev_1200 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       840  (0.0468515); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1163.18
//
Query:       gi|298675122|ref|YP_003726872.1|  [L=410]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      5e-23   81.6   0.3    1.7e-22   79.9   0.0    2.0  2  OrfB_IS605      Probable transposase
    1.2e-10   41.2   0.3    4.9e-10   39.2   0.1    2.2  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0013   18.5   0.6     0.0037   17.1   0.6    1.8  1  DUF919          Nucleopolyhedrovirus protein of unknown funct
  ------ inclusion threshold ------
      0.034   14.5   0.0      0.079   13.3   0.0    1.6  1  RuvX            Holliday junction resolvase


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.2      0.78   3.5e+03      31      47 ..      25      41 ..       7      66 .. 0.52
   2 !   79.9   0.0   3.8e-26   1.7e-22       7     119 ..     182     292 ..     176     293 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.78
                        OrfB_IS605 31 vvtedgtwflykgrrlk 47
                                      ++ +  + +ly+ r+++
  gi|298675122|ref|YP_003726872.1| 25 LSKNLYNFTLYNIRQYF 41
                                      33333333444444444 PP

  == domain 2  score: 79.9 bits;  conditional E-value: 3.8e-26
                        OrfB_IS605   7 evelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrk 83 
                                       ++e    + n++++iDlG+ n+at+vt++gt+f+ +gr +ks +++++ke+ +lqs ++k++       k+ r ++k
  gi|298675122|ref|YP_003726872.1| 182 DEEIGNLDYNSHLSIDLGVDNFATCVTTSGTAFILDGRGIKSYNRWWNKEKSRLQSVYDKQN--VDDGIKMDRFSNK 256
                                       55566677899**************************************************9..9************ PP

                        OrfB_IS605  84 rsrrrkhllhklathliktlkevgvetLnvgnmkdi 119
                                       r  ++++++++ ++h++k++ e+ +++++ g+mk+i
  gi|298675122|ref|YP_003726872.1| 257 RFWKINDFMNQCVNHIVKHCLENRIGNIVNGEMKEI 292
                                       **********************************87 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.91   4.1e+03       9      21 ..     167     179 ..     162     183 .. 0.86
   2 !   39.2   0.1   1.1e-13   4.9e-10       1      69 []     311     385 ..     311     385 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.91
                    OrfB_Zn_ribbon   9 eykakeyGikvee 21 
                                       +yk +++ i++++
  gi|298675122|ref|YP_003726872.1| 167 KYKGRWFEIEFVY 179
                                       79*******9987 PP

  == domain 2  score: 39.2 bits;  conditional E-value: 1.1e-13
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke......alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f+++k++l+ k++ +Gik++ev++ayTSk  +   +  ++      ++s+r    ++ g  +++D+n+a+Nil++
  gi|298675122|ref|YP_003726872.1| 311 FARFKQKLASKCEYHGIKYHEVDEAYTSKVDALALEPIRKhkkylgKRSKRGIFQSSTGRLINADINGALNILRK 385
                                       899**************************8766655544445588*99************************986 PP

>> DUF919  Nucleopolyhedrovirus protein of unknown function (DUF919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.6   8.3e-07    0.0037      15      58 ..       4      45 ..       2      47 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 8.3e-07
                            DUF919 15 qaKrkltiksqHfErlkkitKnpkElqdlekklnklRqeFLnfg 58
                                       +K  l+ + q +E lk++tK +k l +   +l ++Rq+F+n++
  gi|298675122|ref|YP_003726872.1|  4 TQKNHLRADKQTYETLKRLTKLSKNLYNF--TLYNIRQYFFNYS 45
                                      58999******************888765..8***********8 PP

>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.8e-05     0.079      37     106 ..     266     345 ..     253     367 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.8e-05
                                       HHHHHHHHHHHHHTT--EEEEE--........----SSS---SSTTHHHHHHHHHT....T-EEEEE--S----XXX CS
                              RuvX  37 ekdleelkelvkeeeveeiVvGlP........lnldgsegesakkvrkfaeeLakrl..kklpvelvDErlttveae 103
                                       ++ ++++ + + e+++ +iV G          +  +++++ ++  +++f ++La+++  ++++ + vDE +t++  +
  gi|298675122|ref|YP_003726872.1| 266 NQCVNHIVKHCLENRIGNIVNGEMkeikqeqnIGKKNNQNFQTITFARFKQKLASKCeyHGIKYHEVDEAYTSKVDA 342
                                       6788999999999999999999887777776666677888888999*********9977899***********9766 PP

                                       XXX CS
                              RuvX 104 ril 106
                                        +l
  gi|298675122|ref|YP_003726872.1| 343 LAL 345
                                       555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1094  (0.0610185); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 2446.23
//
Query:       gi|298675123|ref|YP_003726873.1|  [L=105]
Description: DNA polymerase beta domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.3e-12   45.1   0.2    1.2e-11   44.8   0.2    1.1  1  NTP_transf_2    Nucleotidyltransferase domain
    1.6e-10   41.0   0.1    1.8e-10   40.8   0.1    1.1  1  Polbeta         Polymerase beta, Nucleotidyltransferase
  ------ inclusion threshold ------
      0.044   14.0   0.0      0.058   13.6   0.0    1.2  1  DNA_pol_B_palm  DNA polymerase beta palm


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.2     2e-15   1.2e-11       5      91 ..      20      98 ..      16     103 .. 0.90

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 2e-15
                                      HHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECCCCT CS
                      NTP_transf_2  5 leelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekledpl 83
                                      l el++++ v  + +fGSy r + +kgSD+D+lv +++         gl k+   +  l+ llg++vd+v++ +l+ p 
  gi|298675123|ref|YP_003726873.1| 20 LPELERKYNVSYLGIFGSYIREEETKGSDLDILVEFSKK-------LGLMKITGLENYLSDLLGVKVDIVPKRSLK-PC 90
                                      668899999999***************************.......899***********************9999.76 PP

                                      EEEEEECE CS
                      NTP_transf_2 84 lvksilee 91
                                      + ++ilee
  gi|298675123|ref|YP_003726873.1| 91 IGENILEE 98
                                      66666665 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.1     3e-14   1.8e-10       8      83 ..      25      98 ..      10     103 .. 0.88

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 3e-14
                                      HHHHHHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEEEETTTS-HHHHHHHHHS CS
                           Polbeta  8 ekekeielaylFGSrakgkareeSDiDlavllkekldleeelelaaelediklgkkvDlvdlneapplllyeilke 83
                                      +k+ +++ + +FGS+ +++ ++ SD+D+ v +++kl l +   l++ l+d+ lg kvD+v  ++ +p + ++il+e
  gi|298675123|ref|YP_003726873.1| 25 RKY-NVSYLGIFGSYIREEETKGSDLDILVEFSKKLGLMKITGLENYLSDL-LGVKVDIVPKRSLKPCIGENILEE 98
                                      344.9**********************************************.9*******9999999999999886 PP

>> DNA_pol_B_palm  DNA polymerase beta palm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   9.7e-06     0.058       8      51 ..      10      57 ..       9      81 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.7e-06
                                      HHHHHHHHHHHHHH-TT-EEE...E-HHHHTT-SEES.SEEEEEEBTT CS
                    DNA_pol_B_palm  8 ealealvkkaakeldpevevi...vcGSYRRgaessG.DvDvlitkkd 51
                                      e+l++++++++ el+++++v    + GSY R++e+ G D+D+l+  ++
  gi|298675123|ref|YP_003726873.1| 10 EQLQKILHDHLPELERKYNVSylgIFGSYIREEETKGsDLDILVEFSK 57
                                      578888899999999998775333789****9999888*****97654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 674.03
//
Query:       gi|298675124|ref|YP_003726874.1|  [L=93]
Description: plasmid stabilization system [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-10   41.5   0.1    1.9e-10   41.2   0.1    1.1  1  ParE_toxin       ParE toxin of type II toxin-antitoxin system
    0.00042   20.4   0.0    0.00051   20.1   0.0    1.1  1  Gp49             Phage derived protein Gp49-like (DUF891)
  ------ inclusion threshold ------
      0.015   15.3   0.1      0.025   14.5   0.1    1.5  1  ParE-like_toxin  ParE-like toxin of type II bacterial toxin-a
       0.15   12.4   0.0       0.22   12.0   0.0    1.3  1  SPOR             Sporulation related domain


Domain annotation for each model (and alignments):
>> ParE_toxin  ParE toxin of type II toxin-antitoxin system, parDE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.1   4.1e-14   1.9e-10       1      88 [.       5      87 ..       5      89 .. 0.87

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 4.1e-14
                                      EEEEHHHHHHHHHHHHHHHCC-HHHHHHHHHHHHHHHHHHHHTTTSEECTSTC.......CTTEEEEEECTEEEEEEEE CS
                        ParE_toxin  1 vrltprAlkdlkkiadyiardgpaakrfldaleealellaenpalgrprrelg.......lkglrririgdyriiYrid 72
                                      ++l+p + k lk +++++          +++++e +++l + p +  pr +++        k ++r+rig+yr+iY+i+
  gi|298675124|ref|YP_003726874.1|  5 IKLHPGVAKYLKSLDSNT----------KARIKEGIDTLSDKPYPENPRTDIKklkgtkgRKSFYRLRIGNYRVIYTIE 73
                                      689999999999998765..........78888888999999999999888889999***99****************6 PP

                                      TSTTEEEEEEEEEHHH CS
                        ParE_toxin 73 deelvvvilrvlhrse 88
                                       ee+++ + ++  r++
  gi|298675124|ref|YP_003726874.1| 74 -EETIL-VTDIIPREK 87
                                      .77888.*99998875 PP

>> Gp49  Phage derived protein Gp49-like (DUF891)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   1.1e-07   0.00051       1      63 [.      13      77 ..      13      89 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.1e-07
                              Gp49  1 eeldalpkkarakilaaldlleegg.pdlgkplvkkle.....dglwElrpksaggiiRvlyafdpgrk 63
                                      ++l++l+ +++a+i + +d l ++  p++++  +kkl+     +  + lr+    g +Rv+y+  ++  
  gi|298675124|ref|YP_003726874.1| 13 KYLKSLDSNTKARIKEGIDTLSDKPyPENPRTDIKKLKgtkgrKSFYRLRI----GNYRVIYTIEEETI 77
                                      589**********************999**************99*******....99******998874 PP

>> ParE-like_toxin  ParE-like toxin of type II bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   5.5e-06     0.025       4      83 ..       8      89 ..       5      93 .] 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.5e-06
                   ParE-like_toxin  4 trrfkkalkklkeklkadldkavkeiiedPelGeeKkGDLsgvfvyk.....fklnkqltllaYeldekkrvlvlllvG 77
                                       + ++k+lk l ++ ka++++ ++++ ++P+  ++++ D++ +   k     ++l+  ++++ Y+++e++++  +  + 
  gi|298675124|ref|YP_003726874.1|  8 HPGVAKYLKSLDSNTKARIKEGIDTLSDKPYPENPRT-DIKKLKGTKgrksfYRLRIGNYRVIYTIEEETIL--VTDII 83
                                      56789*************************9866654.7777765553335467888999999999999865..56666 PP

                   ParE-like_toxin 78 theNfY 83
                                      ++e  Y
  gi|298675124|ref|YP_003726874.1| 84 PREKGY 89
                                      666555 PP

>> SPOR  Sporulation related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.8e-05      0.22      16      51 ..      24      66 ..      18      68 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.8e-05
                                      HHHHHHHHHCCHH.T--.........EEECCSSSCEEEEESSB CS
                              SPOR 16 anAerlaakLrak.gfaaav......avvsgggglyrVrvGpf 51
                                      a+ ++ ++ L++k +++++       + ++g++++yr+r+G++
  gi|298675124|ref|YP_003726874.1| 24 ARIKEGIDTLSDKpYPENPRtdikklKGTKGRKSFYRLRIGNY 66
                                      5555555666666444444467788899*************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 597.37
//
Query:       gi|298675125|ref|YP_003726875.1|  [L=63]
Description: hypothetical protein Metev_1204 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.065   13.1   0.1      0.072   12.9   0.1    1.0  1  DUF4158   Domain of unknown function (DUF4158)


Domain annotation for each model (and alignments):
>> DUF4158  Domain of unknown function (DUF4158)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1     4e-06     0.072      85     123 ..      15      53 ..       5      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4e-06
                           DUF4158  85 salakyasreqtrrehlaeIrellgyrpfteadlrelee 123
                                       + l++y+s+ +t ++ l+++++ ++y++f e+++++le+
  gi|298675125|ref|YP_003726875.1|  15 DRLKSYGSKGETYSQILTRLMDEIDYESFMERQYKRLED 53 
                                       77999*****************************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 397.66
//
Query:       gi|298675126|ref|YP_003726876.1|  [L=1446]
Description: hypothetical protein Metev_1205 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.036   14.3   2.0      0.078   13.2   0.5    2.4  2  DUF4625       Domain of unknown function (DUF4625)
       0.04   14.0   2.4      0.058   13.5   0.3    2.5  2  SWC7          SWR1 chromatin-remodelling complex, sub-unit Sw
       0.16   12.1   0.4        8.5    6.7   0.0    2.7  2  TPR_7         Tetratricopeptide repeat
       0.26   11.5   2.0        5.7    7.3   0.3    3.1  3  TPR_2         Tetratricopeptide repeat
       0.31   11.4   2.2        1.5    9.2   0.2    3.2  2  TPR_8         Tetratricopeptide repeat
        0.4   10.6   4.8        4.5    7.3   0.2    3.2  3  TPR_1         Tetratricopeptide repeat
       0.72   10.4   6.4       0.84   10.2   0.1    3.5  3  Syntaxin-6_N  Syntaxin 6, N-terminal
        1.5    8.5   4.6         13    5.5   0.1    3.6  4  TPR_11        TPR repeat
        1.8    8.4  12.0        5.3    6.8   0.4    3.7  3  DUF724        Protein of unknown function (DUF724)
        5.6    8.0   6.0        2.3    9.2   1.5    2.7  2  CSN5_C        Cop9 signalosome subunit 5 C-terminal domain


Domain annotation for each model (and alignments):
>> DUF4625  Domain of unknown function (DUF4625)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.5   4.3e-05     0.078      11      69 ..     845     906 ..     831     931 .. 0.80
   2 ?   -4.1   0.0       9.7   1.7e+04      95     109 ..    1399    1413 ..    1389    1415 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.3e-05
                           DUF4625  11 dtekPvidllevsa.epeeeevlkiGetlhfeaklsdnealasykvdi..hnnfDhhshsse 69 
                                       + +kP +++l++ + + ++++ +++G+  ++e++l d e++++ k++i  ++n D+  h++ 
  gi|298675126|ref|YP_003726876.1| 845 QPKKPKLTDLNILElATSNGNNIHFGSPPSIEINLDDHEEIENWKISIvnEENTDQQYHHRL 906
                                       66899988776655259*******************************44456688777654 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 9.7
                           DUF4625   95 heeieiPadaeaGdY 109 
                                        +++i i +d+e G+Y
  gi|298675126|ref|YP_003726876.1| 1399 EKSIIIKDDFESGNY 1413
                                        6789999*******9 PP

>> SWC7  SWR1 chromatin-remodelling complex, sub-unit Swc7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3   3.3e-05     0.058       7      84 ..     126     203 ..     121     207 .. 0.93
   2 ?   -3.6   0.1       6.6   1.2e+04      44      80 ..     305     345 ..     297     357 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.3e-05
                              SWC7   7 eeLlkePivDeevlekfqshklvklyapelselqlrslkslveelfeegipeeeedepvtvvtLAnyyYskRieele 83 
                                       +++l + i+ ++ l+ f s+ l+ l+  e+ + + +++ks+ +++ + + + ee +++++ +++ + yY + +ee+e
  gi|298675126|ref|YP_003726876.1| 126 TNILFQGIIPNSCLNSFFSNMLIPLHKKEFFNYDFEEVKSFFRDWKKYESEIEEIENKIEDLKINKDYYLNELEEIE 202
                                       6788899**************************************9999888889999999*************998 PP

                              SWC7  84 e 84 
                                       +
  gi|298675126|ref|YP_003726876.1| 203 T 203
                                       6 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 6.6
                              SWC7  44 lkslveelfeegipeee....edepvtvvtLAnyyYskRie 80 
                                       l +l +elf ++ ++++    ++ p + ++    yY+k ++
  gi|298675126|ref|YP_003726876.1| 305 LDKLSTELFYRTWNNQDieylKNLPFNQLKSDIEYYNKLVN 345
                                       66667777777777666555555555555555566666665 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0047       8.5      12      32 ..    1270    1288 ..    1267    1292 .. 0.83
   2 ?    2.5   0.1       0.1   1.9e+02      11      22 ..    1304    1315 ..    1298    1323 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0047
                             TPR_7   12 lGdyeeAielyeqsLaltkdp 32  
                                         Gdy+e i +y++  a ++d 
  gi|298675126|ref|YP_003726876.1| 1270 NGDYKESILYYKR--ASESDK 1288
                                        69***********..877775 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.1
                             TPR_7   11 rlGdyeeAiely 22  
                                         +G+y++Ai++y
  gi|298675126|ref|YP_003726876.1| 1304 YMGEYKKAIDVY 1315
                                        58********99 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.3    0.0032       5.7      12      33 ..    1268    1289 ..    1262    1290 .. 0.87
   2 ?    2.0   0.0      0.17     3e+02      10      24 ..    1301    1315 ..    1300    1315 .. 0.86
   3 ?   -3.5   0.0       8.9   1.6e+04      13      20 ..    1409    1416 ..    1408    1418 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0032
                             TPR_2   12 yklgdyeeAleafekAleldPn 33  
                                        +++gdy+e + ++++A e d n
  gi|298675126|ref|YP_003726876.1| 1268 FNNGDYKESILYYKRASESDKN 1289
                                        789*************887765 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.17
                             TPR_2   10 ayyklgdyeeAleaf 24  
                                        + +++g+y++A++ +
  gi|298675126|ref|YP_003726876.1| 1301 SFIYMGEYKKAIDVY 1315
                                        6789********987 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 8.9
                             TPR_2   13 klgdyeeA 20  
                                        ++g+y eA
  gi|298675126|ref|YP_003726876.1| 1409 ESGNYTEA 1416
                                        78*****9 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.2   0.00086       1.5      12      33 ..    1268    1289 ..    1267    1290 .. 0.91
   2 ?   -1.3   0.1         2   3.5e+03      13      24 ..    1304    1315 ..    1301    1316 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00086
                                        HHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   12 lklgdyeeAkeyyekaleldpd 33  
                                        ++ gdy+e++ yy++a e d++
  gi|298675126|ref|YP_003726876.1| 1268 FNNGDYKESILYYKRASESDKN 1289
                                        589***************9986 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2
                                        HTT-HHHHHHHH CS
                             TPR_8   13 klgdyeeAkeyy 24  
                                         +g+y++A+ +y
  gi|298675126|ref|YP_003726876.1| 1304 YMGEYKKAIDVY 1315
                                        6899****9887 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       7.1   1.3e+04       8      26 ..     431     449 ..     429     449 .. 0.77
   2 ?    7.3   0.2    0.0025       4.5      12      29 ..    1268    1285 ..    1267    1290 .. 0.86
   3 ?    4.0   0.2     0.026        47      10      24 ..    1301    1315 ..    1300    1320 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 7.1
                                       HHHHHHTT-HHHHHHHHHH CS
                             TPR_1   8 GnayfklgkydeAleyyek 26 
                                       G + + + +y++ l++ ++
  gi|298675126|ref|YP_003726876.1| 431 GDIELINSQYEDSLADLKQ 449
                                       666667889***9999875 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0025
                                        HHTT-HHHHHHHHHHHHH CS
                             TPR_1   12 fklgkydeAleyyekALe 29  
                                        f++g+y+e + yy++A e
  gi|298675126|ref|YP_003726876.1| 1268 FNNGDYKESILYYKRASE 1285
                                        689************966 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.026
                                        HHHHTT-HHHHHHHH CS
                             TPR_1   10 ayfklgkydeAleyy 24  
                                         + ++g+y++A++ y
  gi|298675126|ref|YP_003726876.1| 1301 SFIYMGEYKKAIDVY 1315
                                        6789********987 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.4      0.26   4.7e+02      16      69 ..     162     210 ..     157     279 .. 0.72
   2 ?   -2.1   0.1       3.2   5.8e+03      37      37 ..     460     460 ..     392     493 .. 0.57
   3 ?   10.2   0.1   0.00047      0.84       6      66 ..     520     578 ..     515     601 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.26
                      Syntaxin-6_N  16 kaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLeetvrivek 69 
                                       +++s +r w++  ++      ee+++  ++L+ + +   ++le++e  ++i   
  gi|298675126|ref|YP_003726876.1| 162 EVKSFFRDWKKYESE-----IEEIENKIEDLKINKDYYLNELEEIETIISIWDT 210
                                       677888888874433.....6777777777777777777777777777754433 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.2
                      Syntaxin-6_N  37 e 37 
                                       +
  gi|298675126|ref|YP_003726876.1| 460 D 460
                                       2 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00047
                      Syntaxin-6_N   6 vkeeVqkslnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLeetvri 66 
                                       vk++  ++ + + +l+++ e++ +++   +++ + + ++eL +++++i+ ++++L++  + 
  gi|298675126|ref|YP_003726876.1| 520 VKKDLLNNYHGIDKLITKIEETDKSG--YSKNYYLSKKDELDNTIKDIKSQVSELNRDLEL 578
                                       56666666666666777776633333..358889999999999999999999999987754 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.61   1.1e+03       1      19 [.     431     449 ..     431     449 .. 0.92
   2 ?    5.5   0.1    0.0073        13       5      28 ..    1268    1291 ..    1264    1296 .. 0.83
   3 ?    2.2   0.2     0.081   1.5e+02       2      17 ..    1300    1315 ..    1300    1316 .. 0.87
   4 ?   -2.5   0.0       2.4   4.3e+03       5      13 ..    1408    1416 ..    1406    1419 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.61
                            TPR_11   1 GdayyeqGkyeeAieaYkk 19 
                                       Gd+     +ye++++++k+
  gi|298675126|ref|YP_003726876.1| 431 GDIELINSQYEDSLADLKQ 449
                                       89999999*******9997 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0073
                            TPR_11    5 yeqGkyeeAieaYkkAlkldPdna 28  
                                        +  G+y+e+i  Yk+A + d +  
  gi|298675126|ref|YP_003726876.1| 1268 FNNGDYKESILYYKRASESDKNLE 1291
                                        678**************9998865 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.081
                            TPR_11    2 dayyeqGkyeeAieaY 17  
                                        + +   G+y++Ai +Y
  gi|298675126|ref|YP_003726876.1| 1300 NSFIYMGEYKKAIDVY 1315
                                        567889*******999 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 2.4
                            TPR_11    5 yeqGkyeeA 13  
                                        +e G+y+eA
  gi|298675126|ref|YP_003726876.1| 1408 FESGNYTEA 1416
                                        899*****9 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2      0.18   3.2e+02     103     139 ..     169     205 ..     158     225 .. 0.69
   2 ?    5.6   1.1     0.007        13      90     167 ..     412     494 ..     405     513 .. 0.84
   3 ?    6.8   0.4    0.0029       5.3     125     182 ..     524     584 ..     512     588 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.18
                            DUF724 103 eqtklleerkklekkieeeesekrkleeeidelekki 139
                                       +++k+++e++++e+kie+ + +k  + +e++e+e  i
  gi|298675126|ref|YP_003726876.1| 169 DWKKYESEIEEIENKIEDLKINKDYYLNELEEIETII 205
                                       5666677777777777777777666666666666555 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.007
                            DUF724  90 lqsrlnkLlslkdeqtklleerkklekkieeeesekrkleeeid.....elekkilelerqlallkekkeaadkeia 161
                                       l + ln+ l+ +++++k++  ++ ++++ e+  ++ ++++++ +      + ++i++l+++l  l+e k++ ++e  
  gi|298675126|ref|YP_003726876.1| 412 LVDNLNQFLAYHEDYNKHKGDIELINSQYEDSLADLKQISQNSHlglndYTRENISDLKQKLGKLQEYKDKTSSEKE 488
                                       66789****************************99999999877777778899*************99999988887 PP

                            DUF724 162 rlksea 167
                                       +l    
  gi|298675126|ref|YP_003726876.1| 489 KLDYVL 494
                                       776555 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0029
                            DUF724 125 krkleeeidelekkilelerqlallk...ekkeaadkeiarlkseaekleeeledveqeFe 182
                                         +  + id+l  ki e  +   ++    +kk++ d+ i+++ks++++l+++le  e++F 
  gi|298675126|ref|YP_003726876.1| 524 LLNNYHGIDKLITKIEETDKSGYSKNyylSKKDELDNTIKDIKSQVSELNRDLELKEKHFV 584
                                       444445566666666666666555559999999*******************999999996 PP

>> CSN5_C  Cop9 signalosome subunit 5 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.2       2.3   4.2e+03       5      26 ..     333     354 ..     330     365 .. 0.81
   2 ?    9.2   1.5    0.0013       2.3       1      36 [.     451     486 ..     451     576 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.3
                            CSN5_C   5 LltNrdYatkqisDLaeKleka 26 
                                       L +  +Y +k ++D ++Kl+  
  gi|298675126|ref|YP_003726876.1| 333 LKSDIEYYNKLVNDENDKLKSK 354
                                       5667789999999999999875 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0013
                            CSN5_C   1 SqspLltNrdYatkqisDLaeKlekaessvsrsrsa 36 
                                       Sq++ l   dY+ + isDL++Kl k ++   +++s+
  gi|298675126|ref|YP_003726876.1| 451 SQNSHLGLNDYTRENISDLKQKLGKLQEYKDKTSSE 486
                                       788888889****************99887777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1169  (0.0652016); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.97u 0.34s 00:00:01.31 Elapsed: 00:00:00.53
# Mc/sec: 8278.87
//
Query:       gi|298675127|ref|YP_003726877.1|  [L=1607]
Description: DEAD/DEAH box helicase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      9e-20   71.2   0.0      2e-19   70.0   0.0    1.6  1  DEAD           DEAD/DEAH box helicase
    5.7e-12   46.0   0.0    2.3e-11   44.0   0.0    2.0  1  ResIII         Type III restriction enzyme, res subunit
    7.1e-11   42.7   0.1    7.1e-11   42.7   0.1    2.5  2  DUF1998        Domain of unknown function (DUF1998)
      9e-08   32.4   0.0    3.5e-07   30.5   0.0    2.1  1  Helicase_C     Helicase conserved C-terminal domain
     0.0027   16.8   0.0     0.0048   16.0   0.0    1.2  1  T2SSE          Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.053   13.4   0.2      0.053   13.4   0.2    2.8  4  eIF-5_eIF-2B   Domain found in IF2B/IF5
      0.059   13.5   0.0       0.14   12.3   0.0    1.6  1  DUF4107        Protein of unknown function (DUF4107)
       0.18   11.3   0.0       0.18   11.3   0.0    2.8  4  UvrD-helicase  UvrD/REP helicase N-terminal domain
       0.18   12.1   0.0       0.46   10.8   0.0    1.7  1  AAA_19         AAA domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.0   0.0     1e-22     2e-19       2     171 ..      91     296 ..      90     300 .. 0.78

  Alignments for each domain:
  == domain 1  score: 70.0 bits;  conditional E-value: 1e-22
                                       HHHHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHS....TTSTS-EEEEEESSHHHHHHHHHHHHHHTTT CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   2 diQaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyet....kgktgpkalivePtreLaeqtlnnlkkfkky 73 
                                       + Q++ai +i+ ++++ +va  TGsGKT++f+i +l+ ++++    +  +g +al++ P+ +La+++l+++++++k+
  gi|298675127|ref|YP_003726877.1|  91 KHQEKAIRNIInKNKNAVVATGTGSGKTEIFMITILNYLFKQqensELGPGVRALLLYPMNALANDQLKRMRTLLKN 167
                                       68*******996778*************************99999889999*************************7 PP

                                       ST.SEEEEEETT.....SSHHHHHHHH................HTT..CSEEEEEHHHHHHHH........HCTSSH CS
                                       xx.xxxxxxxxx.....xxxxxxxxxx................xxx..xxxxxxxxxxxxxxx........xxxxxx RF
                              DEAD  74 id.lrvlliigg.....vaardqlskl................dng..vdivvgtpgrlddll........stgkln 118
                                       +  ++    +g+      +ard+++++                + +  ++i++++  +l  l+             +
  gi|298675127|ref|YP_003726877.1| 168 CPeITFGRYTGEteenyRSARDKYKQMyheepldnefisrdkmK-EtpPHILLTNYAMLEYLMlrpsdhifF----D 239
                                       44233322233122233666677777788888888888876432.258*************88787544441....2 PP

                                       ...CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHC.TTSTTTSEEEEEESSBS.H CS
                                       ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx.x RF
                              DEAD 119 ...lsqvrflVlDEadrlldqgfsdfinrilnqlpqit.cdgklqrqvivlSATlp.k 171
                                           ++ +f+VlDEa+++     + +i+ ++++l++    + + + ++i+ SATl  +
  gi|298675127|ref|YP_003726877.1| 240 gsyADDWKFIVLDEAHTYDGA-KGIEISMLIRRLKDRVvGNIPGEIKCIATSATLGnS 296
                                       4459999*************9.7888888888887654155568899*******9744 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.0   1.1e-14   2.3e-11       4     148 ..      89     261 ..      87     292 .. 0.71

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 1.1e-14
                                       E-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S............-EEEEESSHHHHHHHHHH CS
                            ResIII   4 lreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkee.......kflflvprkslleqtlee 73 
                                       l+++Qe+ai+n++     +++k+++++  TG+GKT + + +i ++l k++e+       ++l+l p ++l +  l++
  gi|298675127|ref|YP_003726877.1|  89 LYKHQEKAIRNII-----NKNKNAVVATGTGSGKTEIFMITILNYLFKQQENselgpgvRALLLYPMNALANDQLKR 160
                                       789*********9.....8899***************9666666666666666**********************99 PP

                                       GGGGTGG....GEEEESSS-B--...............................-SEEEEEHHHHHHTH........ CS
                            ResIII  74 fkkflseaykeigkkvsgdkkka........................kekdstnkkilvttiqsldadseeeeeese 126
                                       ++ +l+++ + + + ++g+++++                         + ++t  +il+t++ +l   +  +     
  gi|298675127|ref|YP_003726877.1| 161 MRTLLKNCPEITFGRYTGETEENyrsardkykqmyheepldnefisrDKMKETPPHILLTNYAMLEYLM-LR----- 231
                                       966666665553333333333333333333344555555555555555555699999999999999988.32..... PP

                                       HHHTTT-S........EEEEETGGGTTS.T CS
                            ResIII 127 ellrdrfd........viiiDEaHrlgakk 148
                                         ++ +fd        +i+ DEaH + ++k
  gi|298675127|ref|YP_003726877.1| 232 PSDHIFFDgsyaddwkFIVLDEAHTYDGAK 261
                                       2222223334445777********988754 PP

>> DUF1998  Domain of unknown function (DUF1998)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.5       4.7   9.4e+03      70      82 ..     582     611 ..     578     612 .. 0.79
   2 !   42.7   0.1   3.6e-14   7.1e-11       3      83 .]    1495    1580 ..    1493    1580 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.7
                           DUF1998  70 ee.cdCee................aGCpaC 82 
                                       ++ cdC +                + CpaC
  gi|298675127|ref|YP_003726877.1| 582 NDiCDCGKnnyievvkvnskngnvHKCPAC 611
                                       444999449999999999999999999999 PP

  == domain 2  score: 42.7 bits;  conditional E-value: 3.6e-14
                           DUF1998    3 halinalplflqcdesdlgteckapedeprkrpariliydavpgGaGiaekaaellee......llraaleliee 71  
                                        +a++++++ +l++d+s++++ +++ + +     ++il++d vpgGaG  +++++   +      +l+ ++  +++
  gi|298675127|ref|YP_003726877.1| 1495 YAILEGASSTLGIDRSEIDGCLYSYKGD--PTSPAILLFDDVPGGAGHVKRITQ---DketisnILESTYTKMSN 1564
                                        899********************76665..69****************777655...2234666*********** PP

                           DUF1998   72 cdCee....aGCpaCl 83  
                                        c+C +    ++C+aCl
  gi|298675127|ref|YP_003726877.1| 1565 CNCGGedgnSSCYACL 1580
                                        ***5599********7 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   1.8e-10   3.5e-07      47     109 ..    1009    1071 ..     980    1073 .. 0.90

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 1.8e-10
                                        STTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSS CS
                        Helicase_C   47 hgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinfdlprnvtsyiqriGRtgR 109 
                                        +++l+++   +  ++f +ge++vL +++  e G+d+ +++ V++ ++p + ++y+qr+GR gR
  gi|298675127|ref|YP_003726877.1| 1009 TAQLTNEVAADLQTKFINGEVNVLSCSTTFELGVDVGELESVFMRNVPPSAANYVQRAGRSGR 1071
                                        567777888888899***********************************************9 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.4e-06    0.0048     101     158 ..      76     134 ..      57     136 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.4e-06
                             T2SSE 101 keltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKt.tllyallkeinksde 158
                                       + l+ +dl  ++ l +++++++r+ ++++++ +v+ gTgsGKt +++ ++l+++ k++e
  gi|298675127|ref|YP_003726877.1|  76 ELLESEDLPLDRPLYKHQEKAIRNIINKNKNAVVATGTGSGKTeIFMITILNYLFKQQE 134
                                       556778888888889****************************4455778888777655 PP

>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       1.4   2.8e+03     102     116 ..     559     574 ..     548     575 .. 0.62
   2 ?   -2.5   0.7       2.3   4.6e+03      86      98 ..     565     577 ..     560     594 .. 0.72
   3 ?   -3.0   0.4       3.2   6.3e+03      94     116 ..     589     613 ..     578     614 .. 0.64
   4 ?   13.4   0.2   2.7e-05     0.053      86     116 ..    1319    1348 ..    1298    1349 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.4
                                       C.SSSCEEEEESSSTC CS
                      eIF-5_eIF-2B 102 k.eerllvlkCkaCga 116
                                         +++   l C aCg+
  gi|298675127|ref|YP_003726877.1| 559 NdQKNNKHLICAACGS 574
                                       3434455588999996 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.3
                                       HHTSTSSSTSTCE CS
                      eIF-5_eIF-2B  86 eyVlCkeCkspet 98 
                                       + ++C  C+s + 
  gi|298675127|ref|YP_003726877.1| 565 KHLICAACGSIDK 577
                                       5566777777665 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 3.2
                                       TSTCEEECC..SSSCEEEEESSSTC CS
                      eIF-5_eIF-2B  94 kspetelek..eerllvlkCkaCga 116
                                       k+  +e++k  +++  v kC aC +
  gi|298675127|ref|YP_003726877.1| 589 KNNYIEVVKvnSKNGNVHKCPACTK 613
                                       444445555545666678*****86 PP

  == domain 4  score: 13.4 bits;  conditional E-value: 2.7e-05
                                        HHTSTSSSTSTCEEECCSSSCEEEEESSSTC CS
                      eIF-5_eIF-2B   86 eyVlCkeCkspetelekeerllvlkCkaCga 116 
                                        +yV+C++C++ +  l  +++ l  +Ck+C a
  gi|298675127|ref|YP_003726877.1| 1319 KYVICSNCHRYQRVLANSNESL-DHCKSCDA 1348
                                        8****************88888.8*****86 PP

>> DUF4107  Protein of unknown function (DUF4107)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     7e-05      0.14      23      90 ..     256     324 ..     252     345 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7e-05
                           DUF4107  23 tldknkGkivGavvkklkleklkkl.snlvadesenllGdddeiaknlkdfsdqlkGeklnlnrvvkek 90 
                                       t d  kG    + +++lk   +  + +++    ++  lG++d   k++ dfs++l Ge+++ n v +  
  gi|298675127|ref|YP_003726877.1| 256 TYDGAKGIEISMLIRRLKDRVVGNIpGEIKCIATSATLGNSDSDFKDVADFSNKLFGEHFDENDVIGPE 324
                                       667777777788888888877654427788888999***************************998744 PP

>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   8.9e-05      0.18       5      42 ..      93     133 ..      89     171 .. 0.82
   2 ?   -3.7   0.0       3.4   6.8e+03     195     242 ..     839     905 ..     816     913 .. 0.62
   3 ?   -2.1   0.1         1   2.1e+03     102     148 ..    1114    1166 ..    1112    1248 .. 0.62
   4 ?   -2.4   0.1       1.3   2.6e+03      36      57 ..    1542    1563 ..    1540    1564 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.9e-05
                                       HHHHHHS...-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSS CS
                     UvrD-helicase   5 qreaias...lggpilveAsAGsGKTfvlaerilrlikeee 42 
                                       q++ai++    +++ +v+ + GsGKT + +  il+ + +++
  gi|298675127|ref|YP_003726877.1|  93 QEKAIRNiinKNKNAVVATGTGSGKTEIFMITILNYLFKQQ 133
                                       66666655445999**************9999998887664 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.4
                                       CTTHHCHSS...................TSCSHHHHHHHHHHHHHHHHHHHHTCEEHHHHHHHHHHH CS
                     UvrD-helicase 195 spkelkkaf...................ekasdlqkkiaeflkeyqeqkkeenalDfsdllhallel 242
                                       spk+++++f                    + + + ++++ + k++  +k++++++D+ + ++++l+l
  gi|298675127|ref|YP_003726877.1| 839 SPKNNESYFrefgssktknikswvpnsdSHLNTRLDFLMRLSKKLGVNKDKKELIDLLKNIWKTLAL 905
                                       4444444444444444444444554444555666677777777777777777777776666666655 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1
                                        HHHHHHHHGGTTSHTTTEEECHHHHH......HCCHHHHHHHHHSCHSHTTTT CS
                     UvrD-helicase  102 qkilkkeanrigldpnfrildeedee......dlkqqellkelleksaddsln 148 
                                         ki+k+++++i l + ++i +++ ++      d+k  e lk+ l+++++d ++
  gi|298675127|ref|YP_003726877.1| 1114 EKIIKRHMYSIALAKFWKIHNDKFKNvdtfffDNKGPEYLKDYLDSKPKDIQD 1166
                                        58999999999999999999999876777777777777777777654444222 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 1.3
                                        HHHHTSSSTGGGEEEEESSHHH CS
                     UvrD-helicase   36 rlikeeeiepdrilvvTFTnkA 57  
                                        + i++ + ++++il +T+T+++
  gi|298675127|ref|YP_003726877.1| 1542 KRITQDKETISNILESTYTKMS 1563
                                        67999999***********986 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00023      0.46       1      43 [.      93     143 ..      93     262 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00023
                            AAA_19   1 qreav.e.alkekvllvtaGpGtGKTrvlkhivallvelggvkp......e 43 
                                       q++a+ +   k+k+ +v  G G+GKT++ +  +  ++  ++++       +
  gi|298675127|ref|YP_003726877.1|  93 QEKAIrNiINKNKNAVVATGTGSGKTEIFMITILNYLFKQQENSelgpgvR 143
                                       78888446778999*************987665444433333333455544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1607 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       815  (0.0454571); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 1.07u 0.30s 00:00:01.37 Elapsed: 00:00:00.54
# Mc/sec: 9009.40
//
Query:       gi|298675128|ref|YP_003726878.1|  [L=669]
Description: hypothetical protein Metev_1207 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-36  126.3   8.5    1.9e-36  126.3   8.5    3.3  2  DUF262    Protein of unknown function DUF262
    2.9e-29  101.7   4.0    2.9e-29  101.7   4.0    2.5  2  DUF1524   Protein of unknown function (DUF1524)
     0.0014   17.6   1.0     0.0023   16.9   1.0    1.2  1  Glypican  Glypican
     0.0055   17.3   3.2     0.0055   17.3   3.2    2.8  2  DUF643    Protein of unknown function (DUF643)


Domain annotation for each model (and alignments):
>> DUF262  Protein of unknown function DUF262
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.3   8.5   4.2e-40   1.9e-36       2     221 .]       9     225 ..       8     225 .. 0.81
   2 ?  -11.7  15.4         4   1.8e+04     151     164 ..     333     346 ..     229     661 .. 0.70

  Alignments for each domain:
  == domain 1  score: 126.3 bits;  conditional E-value: 4.2e-40
                            DUF262   2 edllskskrglriPdfQRpyvWeeeqveeLiedlla.....lkgyplGsivlw..skaads.ageleviDGQQRltT 70 
                                       + +ls+ ++ +++P++QR y+W+ +++++L++d+++     + +++lGs+v    +  + s  ++l +iDGQQRltT
  gi|298675128|ref|YP_003726878.1|   9 HTFLSGPQQ-FIVPIYQRTYSWDLKHCKKLWDDVERllsgqYVNHFLGSFVYInsDIYQVSsVPQLHIIDGQQRLTT 84 
                                       678999999.************************99****************9874444447*************** PP

                            DUF262  71 ltlllaatkeesekriknleaeiekekeeededrlkrreresdkellqkllrseklslee..keelaelnsltkkdl 145
                                       ++lll a           l+  ++       ++ +k++   s+k +  +l+++ ++++e   k  l++  s t+++l
  gi|298675128|ref|YP_003726878.1|  85 ISLLLQA-----------LIDVLQ-------NQDVKVKGVSSNKIRNYYLINTLEEEEELryKLVLNRNDSETYTNL 143
                                       *******...........222222.......3445666666666666666666555444434667777778888888 PP

                            DUF262 146 ..akeekrneeknlikayevieeilksa.......llsalktklslieieleseddedqayeiFerlNsrGvpLtas 213
                                         ++e ++n+ +n++k+y++++++++ +        l++l +kl ++ i+l    +ed  + iFe+lNs+G+ L++s
  gi|298675128|ref|YP_003726878.1| 144 leNRELNDNYSPNVYKNYKFFKDKIEGYepeylseILKTL-QKLMIVDISLN--PNEDNPQLIFESLNSTGLDLSQS 217
                                       9888999****************99999***755444444.77777777777..89999****************** PP

                            DUF262 214 ellkalll 221
                                       +l++++ll
  gi|298675128|ref|YP_003726878.1| 218 DLIRNYLL 225
                                       *****985 PP

  == domain 2  score: -11.7 bits;  conditional E-value: 4
                            DUF262 151 rneeknlikayevi 164
                                       +  ++ l+++y+  
  gi|298675128|ref|YP_003726878.1| 333 DVAYPFLLQVYDDY 346
                                       22222222222222 PP

>> DUF1524  Protein of unknown function (DUF1524)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1      0.87   3.9e+03     119     129 ..     325     351 ..     280     355 .. 0.51
   2 !  101.7   4.0   6.4e-33   2.9e-29       1     138 [.     413     548 ..     413     549 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.87
                           DUF1524 119 a................ekdewdeeai 129
                                       +                ++d+++e +i
  gi|298675128|ref|YP_003726878.1| 325 NeittlkvdvaypfllqVYDDYQENVI 351
                                       122223333444444445555555555 PP

  == domain 2  score: 101.7 bits;  conditional E-value: 6.4e-33
                           DUF1524   1 fprdeefrrallnaklysssrkklryilakelesalreedeeegeakkltiEHilPqslae.kw..egagqedeekr 74 
                                       fp+d+ef  +l++ ++y+ ++  ++y+l+ +le++ + + +e+ + + ++iEHi+Pq+++  ++  ++ g + ++ +
  gi|298675128|ref|YP_003726878.1| 413 FPSDDEFYYKLISIDVYNLRN--CKYLLS-KLENSHKWKIKEPINVDRYSIEHIMPQNPNLpDSwkKRLGRDYKQVQ 486
                                       699***************996..47****.***99999966666658888*********98633588999******* PP

                           DUF1524  75 eelvndlgNLtlltkslNsslsnkpfleKrdlykksslrlnrklaekdewdeeaiearqeaLak 138
                                       ++++++lgNLtl+    Ns+l +++f eK+++y+ks l+ln+ l+ +d+w+ee+i +r+e+Lak
  gi|298675128|ref|YP_003726878.1| 487 NQYLHTLGNLTLTV--HNSELGDMDFIEKKEAYDKSPLYLNDSLKGYDTWNEETIVERTEELAK 548
                                       **************..**********************************************98 PP

>> Glypican  Glypican
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   1.0   5.1e-07    0.0023     113     161 ..     258     308 ..     249     338 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.1e-07
                          Glypican 113 elFsktYgrlytqnaelfkelftelrryysgsnvnleealnefwa..rLle 161
                                       + F++ Y ++  +   +f+e++ e ++yy++s +  e+++n++++  +L  
  gi|298675128|ref|YP_003726878.1| 258 DNFMRDYLTIKLSRIPVFDEIYEEFKQYYKKSGITTEDVINDIYKysKLYV 308
                                       57999*************************************975215543 PP

>> DUF643  Protein of unknown function (DUF643)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   3.2   1.2e-06    0.0055      39      94 ..     278     336 ..     251     341 .. 0.88
   2 ?   -0.2   0.2      0.32   1.4e+03      21      87 ..     422     487 ..     406     493 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.2e-06
                            DUF643  39 avkkiqeykiktGksveeiindiiepekefik...dvlkdknlikkyknsknlkvdfsy 94 
                                        +++ ++y +k+G ++e++indi + +k ++k   ++ kd  l +k+++  +lkvd++y
  gi|298675128|ref|YP_003726878.1| 278 IYEEFKQYYKKSGITTEDVINDIYKYSKLYVKiafNMEKDEDLNNKFNEITTLKVDVAY 336
                                       5788899*********************9999444566999***************987 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.32
                            DUF643  21 klyeteqltleqkkqlysavkkiqeykiktGksveeiindiiepekefikdvlkdknlikkyknskn 87 
                                       kl  ++   l++ k l s +++  ++kik    v+    + i p+   + d  k k l + yk+++n
  gi|298675128|ref|YP_003726878.1| 422 KLISIDVYNLRNCKYLLSKLENSHKWKIKEPINVDRYSIEHIMPQNPNLPDSWK-KRLGRDYKQVQN 487
                                       555666666777777888888888888888888888877777777777888876.568888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (669 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1188  (0.0662614); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.72u 0.36s 00:00:01.08 Elapsed: 00:00:00.53
# Mc/sec: 3823.63
//
Query:       gi|298675129|ref|YP_003726879.1|  [L=82]
Description: AbrB family transcriptional regulator [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-09   36.1   0.1      6e-09   35.6   0.1    1.3  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
     0.0041   17.5   0.1     0.0066   16.9   0.0    1.5  1  PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin
  ------ inclusion threshold ------
      0.091   12.8   0.0       0.12   12.4   0.0    1.3  1  MraZ            MraZ protein, putative antitoxin-like


Domain annotation for each model (and alignments):
>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.1     1e-12     6e-09       2      40 ..      10      48 ..       9      54 .. 0.91

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 1e-12
                                      EETTEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCCCC CS
                    MazE_antitoxin  2 kvGnsgavriPkevrfelgireGdevelevdgdkiilrp 40
                                      k++++g+++iPke+r+  +++eG+++++   +d+i lr 
  gi|298675129|ref|YP_003726879.1| 10 KITKKGQISIPKEIRELENFKEGSKIVILAYDDRIELRS 48
                                      899******************************998875 PP

>> PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.1e-06    0.0066       2      35 ..       9      41 ..       8      68 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.1e-06
                    PrlF_antitoxin  2 stltergqttiPasvRkaLklkkgrdkiaytild 35
                                      +++t++gq  iP+ +R+  + k+g+ ki+    d
  gi|298675129|ref|YP_003726879.1|  9 AKITKKGQISIPKEIRELENFKEGS-KIVILAYD 41
                                      69********************987.66654443 PP

>> MraZ  MraZ protein, putative antitoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.9e-05      0.12      12      54 ..      13      57 ..       7      75 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.9e-05
                                      TTSEEE--CHHHH..HTTSCSEEEEEECCSEEEEEEHHHHHHHHH CS
                              MraZ 12 akGRlllPaklre..eaklekevvviGvsncLeiwpraeWekyee 54
                                      +kG +++P++ re   +k+   +v+ ++++++e++++++ ++ ++
  gi|298675129|ref|YP_003726879.1| 13 KKGQISIPKEIREleNFKEGSKIVILAYDDRIELRSMDQLDEKIS 57
                                      89********99643899999***************998754444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       856  (0.0477439); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 490.64
//
Query:       gi|298675130|ref|YP_003726880.1|  [L=110]
Description: hypothetical protein Metev_1209 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.1e-11   43.3   0.0    4.5e-11   43.1   0.0    1.0  1  PemK_toxin  PemK-like, MazF-like toxin of type II toxin-antit
  ------ inclusion threshold ------
      0.069   13.1   0.0      0.077   12.9   0.0    1.1  1  FliW        FliW protein


Domain annotation for each model (and alignments):
>> PemK_toxin  PemK-like, MazF-like toxin of type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.0   5.1e-15   4.5e-11       2     109 ..       6     106 ..       5     108 .. 0.85

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 5.1e-15
                                       TTEEEEEEE-S--TTS--SEEEEEE-S-HHHHCHSEEEEEEEESSSTSSGCSTTEEEE-HHHCSSSSSSSSEEEECC CS
                        PemK_toxin   2 rGeIvlvdldpsrgseqgkrRpvvVvsndafnekntvivvpltskdkdkkklpfhveleseildlngldkdswvkld 78 
                                       +G++v  ++ p +     k+Rp+ V+ +  ++    +i +++ts  k++    + ++l+ +  +   l+k+s ++  
  gi|298675130|ref|YP_003726880.1|   6 KGDVVVLPF-PFSDMSNSKKRPAFVLAKLPGE---DIILCMITSAVKTD---NYSITLNDNDFESGTLRKNSNIRPN 75 
                                       69*******.95555558********999887...7**********655...89999998722234466******** PP

                                       CEEEEEGGGEEEEEEE--HHHHHHHHHHHHH CS
                        PemK_toxin  79 qirtvdkarlrkkigklsredlaevqralak 109
                                        i+t dk+ +  k+g+l++++++ev+++l  
  gi|298675130|ref|YP_003726880.1|  76 RIFTADKSLILYKVGHLKNDKIDEVENKLVN 106
                                       ********9999***************9966 PP

>> FliW  FliW protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   8.5e-06     0.077      21      80 ..      21      80 ..      14     105 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.5e-06
                                      .STTS-EEEEEESS-TT-EEEEE-GGGT-TT------HHHHHHTT--SGGGEEEEEEEE- CS
                              FliW 21 eeeespflwLqsleeeelafvvidPflffpdYelelsdeelelleleseedvlvlvivtv 80
                                      ++++ p ++L  l  e++ + +i  ++  ++Y+++l+d++ e+  l++++++    i t+
  gi|298675130|ref|YP_003726880.1| 21 NSKKRPAFVLAKLPGEDIILCMITSAVKTDNYSITLNDNDFESGTLRKNSNIRPNRIFTA 80
                                      4556999**************************************999999876666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 780.46
//
Query:       gi|298675131|ref|YP_003726881.1|  [L=334]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.5e-25   86.7   0.4    3.5e-24   84.5   0.0    2.3  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    4.7e-05   23.6   0.7    0.00011   22.4   0.7    1.5  1  OrfB_IS605      Probable transposase
     0.0071   16.4   4.2      0.095   12.7   0.4    3.0  3  HypA            Hydrogenase/urease nickel incorporation, meta
  ------ inclusion threshold ------
       0.02   14.5   0.8      0.042   13.5   0.8    1.5  1  Zn_ribbon_17    Zinc-ribbon, C4HC2 type
      0.033   14.3   4.7       0.16   12.1   0.9    2.5  2  UPF0547         Uncharacterised protein family UPF0547
       0.38   10.8   2.9       0.52   10.4   1.6    1.9  1  DZR             Double zinc ribbon
        1.3    8.8   8.2        1.5    8.6   5.4    2.6  3  zinc_ribbon_2   zinc-ribbon domain
        1.4    8.7   6.8       0.62    9.8   2.6    2.6  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
        1.5    8.8   4.9       0.65   10.0   0.5    2.3  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
        1.6    8.7   4.7        2.4    8.1   0.2    3.2  3  zinc_ribbon_4   zinc-ribbon domain
        2.1    7.9   8.4       0.48    9.9   3.4    2.5  3  zf-ribbon_3     zinc-ribbon domain
        2.9    7.7   6.2         32    4.4   0.3    3.3  3  Rubredoxin_2    Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       1.8   2.8e+03      32      51 ..     213     233 ..     203     238 .. 0.66
   2 !   84.5   0.0   2.4e-27   3.5e-24       1      68 [.     244     309 ..     244     310 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.8
                    OrfB_Zn_ribbon  32 seCgsknke.alsgrtfkCpn 51 
                                       ++Cg ++++ +  ++  kC+n
  gi|298675131|ref|YP_003726881.1| 213 NNCGIRMENlKGIRDSAKCKN 233
                                       467766666555555555554 PP

  == domain 2  score: 84.5 bits;  conditional E-value: 2.4e-27
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       f++l+ +leyka+  G+k+e v+p+yTS++Cs+Cg+ + +  +g+ fkCp+Cg++ ++D nAa+Ni+ 
  gi|298675131|ref|YP_003726881.1| 244 FYQLQFMLEYKARLLGVKIEFVEPEYTSQDCSRCGYLGIR--NGDSFKCPHCGHVDHADANAAFNIAM 309
                                       899*************************************..************************96 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.7   7.4e-08   0.00011       3     107 ..     118     214 ..     113     225 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 7.4e-08
                        OrfB_IS605   3 pvevevelpkpkgnkaagiDlGin.nLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrkla 78 
                                        v+v++  ++ ++++ +g+Dl+   ++a++++ ++  + + g++++    ++++ +++lq k k         +k++
  gi|298675131|ref|YP_003726881.1| 118 SVTVPE-REQIEPENYLGVDLNTTgHIAVMSNPKTGKIWKLGKKAQHIHLKYKNDRRKLQVKGKY--------KKVK 185
                                       344443.88999**********87367777777766677889******************98443........5799 PP

                        OrfB_IS605  79 rlhrkrsrrrkhllhklathliktlkevg 107
                                        + ++ sr++++l hkl++++++t  +++
  gi|298675131|ref|YP_003726881.1| 186 QVKDRESRIVRDLNHKLSSKIVETAAANN 214
                                       9**********************988775 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.034        51       9      35 ..      46      73 ..      40      79 .. 0.75
   2 ?   -3.4   0.0       6.5   9.7e+03      27      42 ..     115     130 ..     105     132 .. 0.78
   3 !   12.7   0.4   6.4e-05     0.095      58      96 ..     258     297 ..     191     308 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.034
                                      HHHHHHHHHH.CCTT..EEEEEEEEEET CS
                              HypA  9 sivevveeea.keaaarkvtkvkvevGe 35
                                      +i +++ ++  k+++a+kvt+vk+++ +
  gi|298675131|ref|YP_003726881.1| 46 AISNQILKKYaKDKSAKKVTSVKLTIPN 73
                                      5666666666377999********9865 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 6.5
                                       EEEEEEEETTCT--HH CS
                              HypA  27 tkvkvevGelsgvepe 42 
                                         v v+v e +++epe
  gi|298675131|ref|YP_003726881.1| 115 VYVSVTVPEREQIEPE 130
                                       5688999999999987 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 6.4e-05
                                       TT-EEE.EEEE--EEEETTTS-EEECHHHHHS-TTTSSS- CS
                              HypA  58 egaeLe.ieevpvkvrCreCgkefeleekalrCpkCgsad 96 
                                        g ++e +e +  +  C++Cg+ +  + ++++Cp+Cg+ d
  gi|298675131|ref|YP_003726881.1| 258 LGVKIEfVEPEYTSQDCSRCGYLGIRNGDSFKCPHCGHVD 297
                                       4455553455556778*****9998777799******876 PP

>> Zn_ribbon_17  Zinc-ribbon, C4HC2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.8   2.8e-05     0.042       6      34 ..     273     303 ..     269     317 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.8e-05
                      Zn_ribbon_17   6 sCayCe.lav.kgrvvlcgvCeHvlHasCar 34 
                                        C+ C  l + +g  + c+ C+Hv Ha+  +
  gi|298675131|ref|YP_003726881.1| 273 DCSRCGyLGIrNGDSFKCPHCGHVDHADANA 303
                                       566664244415889************9765 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2     0.061        91      15      22 ..     272     279 ..     271     280 .. 0.88
   2 ?   12.1   0.9   0.00011      0.16      16      25 ..     289     298 ..     286     299 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.061
                           UPF0547  15 qfCphCGy 22 
                                       q C+ CGy
  gi|298675131|ref|YP_003726881.1| 272 QDCSRCGY 279
                                       78*****9 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00011
                           UPF0547  16 fCphCGyvFq 25 
                                       +CphCG+v+ 
  gi|298675131|ref|YP_003726881.1| 289 KCPHCGHVDH 298
                                       7******985 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.6   0.00035      0.52      27      49 .]     270     294 ..     213     294 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00035
                               DZR  27 aedrCpsCgek.vdpearf.CpeCG 49 
                                       +++ C++Cg+  + ++++f Cp+CG
  gi|298675131|ref|YP_003726881.1| 270 TSQDCSRCGYLgIRNGDSFkCPHCG 294
                                       3899*******999**********9 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.2     0.082   1.2e+02      16      21 ..     274     279 ..     270     281 .. 0.73
   2 ?    8.6   5.4     0.001       1.5       2      21 ..     274     295 ..     274     296 .. 0.93
   3 ?   -3.0   0.0       4.7   7.1e+03      19      21 ..     315     317 ..     314     318 .. 0.52

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.082
                     zinc_ribbon_2  16 CpyCGt 21 
                                       C++CG+
  gi|298675131|ref|YP_003726881.1| 274 CSRCGY 279
                                       777775 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.001
                     zinc_ribbon_2   2 CpnCGael.qdnakF.CpyCGt 21 
                                       C++CG+    +++ F Cp+CG+
  gi|298675131|ref|YP_003726881.1| 274 CSRCGYLGiRNGDSFkCPHCGH 295
                                       9999999879***********8 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 4.7
                     zinc_ribbon_2  19 CGt 21 
                                       CG+
  gi|298675131|ref|YP_003726881.1| 315 CGA 317
                                       554 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1         1   1.5e+03      22      26 ..     214     218 ..     213     233 .. 0.59
   2 ?    9.8   2.6   0.00041      0.62       2      25 ..     273     295 ..     273     296 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1
                                       SS--- CS
                    DNA_RNApol_7kD  22 eCGhR 26 
                                       +CG R
  gi|298675131|ref|YP_003726881.1| 214 NCGIR 218
                                       55555 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00041
                                       B-SSS--B----SSS----SSS-- CS
                    DNA_RNApol_7kD   2 iCgeCgaevslkkgdpiRCkeCGh 25 
                                       +C +Cg    +++gd+ +C +CGh
  gi|298675131|ref|YP_003726881.1| 273 DCSRCGY-LGIRNGDSFKCPHCGH 295
                                       5889985.78*************9 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   5.2     0.019        28      14      26 ..     283     295 ..     270     296 .. 0.56
   2 ?   10.0   0.5   0.00043      0.65      15      27 ..     284     296 ..     280     305 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.019
                     Zn_Tnp_IS1595  14 rWpngfvCPhCgs 26 
                                       r ++ f CPhCg+
  gi|298675131|ref|YP_003726881.1| 283 RNGDSFKCPHCGH 295
                                       3344466666663 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00043
                     Zn_Tnp_IS1595  15 WpngfvCPhCgsr 27 
                                        ++ f CPhCg+ 
  gi|298675131|ref|YP_003726881.1| 284 NGDSFKCPHCGHV 296
                                       46679******87 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       1.5   2.3e+03      30      36 .]     230     236 ..     228     236 .. 0.79
   2 ?    0.5   0.0       0.4   5.9e+02      28      33 ..     274     279 ..     265     280 .. 0.83
   3 ?    8.1   0.2    0.0016       2.4      22      34 ..     284     296 ..     283     296 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.5
                     zinc_ribbon_4  30 kCghvFr 36 
                                       kC+++F+
  gi|298675131|ref|YP_003726881.1| 230 KCKNTFK 236
                                       8999985 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.4
                     zinc_ribbon_4  28 CskCgh 33 
                                       Cs+Cg 
  gi|298675131|ref|YP_003726881.1| 274 CSRCGY 279
                                       999985 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0016
                     zinc_ribbon_4  22 kgvkvrCskCghv 34 
                                       +g + +C++Cghv
  gi|298675131|ref|YP_003726881.1| 284 NGDSFKCPHCGHV 296
                                       56789*******8 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       2.1   3.2e+03      21      25 ..     214     218 ..     213     219 .. 0.66
   2 ?    9.9   3.4   0.00032      0.48       5      25 ..     274     296 ..     272     296 .. 0.87
   3 ?   -2.3   0.0       2.3   3.4e+03       7      10 ..     314     317 ..     313     321 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.1
                       zf-ribbon_3  21 yCGtk 25 
                                       +CG +
  gi|298675131|ref|YP_003726881.1| 214 NCGIR 218
                                       67765 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00032
                       zf-ribbon_3   5 CPnCGap.lssddnv.CpyCGtk 25 
                                       C++CG + ++ +d++ Cp+CG++
  gi|298675131|ref|YP_003726881.1| 274 CSRCGYLgIRNGDSFkCPHCGHV 296
                                       99****7799999966*****86 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.3
                       zf-ribbon_3   7 nCGa 10 
                                       +CGa
  gi|298675131|ref|YP_003726881.1| 314 QCGA 317
                                       7887 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.2     0.037        55       3      10 ..     274     281 ..     273     284 .. 0.82
   2 ?    4.4   0.3     0.021        32       2      22 ..     289     295 ..     288     299 .. 0.57
   3 ?    0.9   0.0      0.26   3.8e+02       5      15 ..     314     324 ..     313     325 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.037
                      Rubredoxin_2   3 CsqCGfes 10 
                                       Cs+CG+  
  gi|298675131|ref|YP_003726881.1| 274 CSRCGYLG 281
                                       *****976 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.021
                      Rubredoxin_2   2 vCsqCGfesakwfGrCpsCgs 22 
                                                      Cp+Cg+
  gi|298675131|ref|YP_003726881.1| 289 K--------------CPHCGH 295
                                       4..............555554 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.26
                      Rubredoxin_2   5 qCGfesakwfG 15 
                                       qCG++s + +G
  gi|298675131|ref|YP_003726881.1| 314 QCGADSDASYG 324
                                       9****988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1432  (0.0798706); expected 358.6 (0.02)
Passed bias filter:                      659  (0.0367561); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2299.56
//
Query:       gi|298675132|ref|YP_003726882.1|  [L=104]
Description: hypothetical protein Metev_1211 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    0.00023   21.5   0.1    0.00043   20.7   0.1    1.4  1  EF-hand_7   EF-hand domain pair
    0.00028   20.2   1.0     0.0011   18.4   0.2    2.2  2  EF-hand_1   EF hand
    0.00039   20.1   0.3     0.0047   16.7   0.0    2.5  2  EF-hand_6   EF-hand domain
  ------ inclusion threshold ------
       0.03   14.5   4.1        3.7    7.8   0.1    2.8  3  Dockerin_1  Dockerin type I domain
      0.072   13.6   0.0      0.082   13.5   0.0    1.2  1  SpoIID      Stage II sporulation protein


Domain annotation for each model (and alignments):
>> EF-hand_7  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.1   1.2e-07   0.00043       3      53 ..      54     102 ..      52     102 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.2e-07
                         EF-hand_7   3 klkeaFke.lDtdgdgyldkeellrllrkifqgagegsklsdeelellfkef 53 
                                       ++++ F++ +D +++g ++k+e+++++   f     gs+++++ +  ++++f
  gi|298675132|ref|YP_003726882.1|  54 QVYQEFWMkYDINNNGDIEKSEVMNAINDYF---AQGSDMTKDNVMNVINKF 102
                                       567888888*************887777666...9*******9999888876 PP

>> EF-hand_1  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.26   9.3e+02       7      17 ..      43      53 ..      43      55 .. 0.82
   2 !   18.4   0.2   2.9e-07    0.0011       3      27 ..      57      81 ..      55      83 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.26
                                      HHHTTTSSSEE CS
                         EF-hand_1  7 refDkDgdGkI 17
                                      + fD+ gd  I
  gi|298675132|ref|YP_003726882.1| 43 KTFDVTGDTEI 53
                                      579****9877 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 2.9e-07
                                      HHHHHHHTTTSSSEEEHHHHHHHHH CS
                         EF-hand_1  3 keiFrefDkDgdGkIdfeEfkellk 27
                                      +e+++++D +++G I+++E +++++
  gi|298675132|ref|YP_003726882.1| 57 QEFWMKYDINNNGDIEKSEVMNAIN 81
                                      799*****************99876 PP

>> EF-hand_6  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.13   4.8e+02       7      19 ..      43      55 ..      43      57 .. 0.81
   2 !   16.7   0.0   1.3e-06    0.0047       3      27 ..      57      81 ..      55      93 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.13
                         EF-hand_6  7 klfDkdgdGkida 19
                                      k fD++gd +i  
  gi|298675132|ref|YP_003726882.1| 43 KTFDVTGDTEIQV 55
                                      579*****98875 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1.3e-06
                         EF-hand_6  3 reaFklfDkdgdGkidaeElrkalr 27
                                      +e+++++D +++G i ++E+++a++
  gi|298675132|ref|YP_003726882.1| 57 QEFWMKYDINNNGDIEKSEVMNAIN 81
                                      799*******************998 PP

>> Dockerin_1  Dockerin type I domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1    0.0011       3.8      26      45 ..      34      53 ..      25      56 .. 0.85
   2 ?    7.8   0.1     0.001       3.7      32      54 ..      58      80 ..      51      83 .. 0.78
   3 ?    4.2   2.0     0.014        49      37      53 ..      63      79 ..      62     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0011
                                      EBTTSCCCHGGGSTT-SSCE CS
                        Dockerin_1 26 egqssssngkaaDvNgDGrv 45
                                      +g  +++n+k++Dv+gD ++
  gi|298675132|ref|YP_003726882.1| 34 TGAITNENKKTFDVTGDTEI 53
                                      567899***********877 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.001
                                      CCHGGGSTT-SSCESHHHHHHHH CS
                        Dockerin_1 32 sngkaaDvNgDGrvnalDallvi 54
                                      +   ++D+N++G + +  ++  i
  gi|298675132|ref|YP_003726882.1| 58 EFWMKYDINNNGDIEKSEVMNAI 80
                                      66779********9988776655 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.014
                                      GSTT-SSCESHHHHHHH CS
                        Dockerin_1 37 aDvNgDGrvnalDallv 53
                                      +D+N++G + +  ++  
  gi|298675132|ref|YP_003726882.1| 63 YDINNNGDIEKSEVMNA 79
                                      89999999988776655 PP

>> SpoIID  Stage II sporulation protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.3e-05     0.082      51      85 ..      39      81 ..      11      96 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.3e-05
                                      ...--STT-S-TTTS-----.......H-HHH.THHHHHHHHH CS
                            SpoIID 51 redhkkfdvcddthcqvYqg.......etras.yeekveeAve 85
                                      +e++k+fdv+ dt+ qvYq+       +++ + ++++v +A++
  gi|298675132|ref|YP_003726882.1| 39 NENKKTFDVTGDTEIQVYQEfwmkydiNNNGDiEKSEVMNAIN 81
                                      3455669*************99999874444455666777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1087  (0.060628); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 733.46
//
Query:       gi|298675133|ref|YP_003726883.1|  [L=248]
Description: restriction endonuclease [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.5e-20   71.3   0.4      1e-19   70.6   0.4    1.3  1  Mrr_cat    Restriction endonuclease
    0.00024   21.0   0.2    0.00045   20.1   0.2    1.5  1  Mrr_cat_2  Restriction endonuclease
  ------ inclusion threshold ------
      0.067   13.4   0.1        1.7    8.9   0.0    2.6  3  BTB        BTB/POZ domain
       0.13   12.2   2.8        0.6   10.1   2.8    2.2  1  PBECR3     phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease


Domain annotation for each model (and alignments):
>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.6   0.4   2.3e-23     1e-19       1     114 [.     135     245 ..     135     246 .. 0.92

  Alignments for each domain:
  == domain 1  score: 70.6 bits;  conditional E-value: 2.3e-23
                                       HTTT-TTCHHHHHHHHHHHHSSSEEE---B-TTSSB--EEEETTEEEEEEEEEEE--T..S-B-HHHHHHHHHHCTT CS
                           Mrr_cat   1 ldkmspkeFeklvaellealGykeveltgrsgDggiDliakkdplgserilvqaKryk..nkvgvkeVqeligalkk 75 
                                       ldkms+ke+e+l+ ++++ +Gy  ve +g ++D g+D+++++ +   er++v +K+ +  +kv +++Vqe+++a ++
  gi|298675133|ref|YP_003726883.1| 135 LDKMSWKELEELLVSMYRDKGYL-VESVG-TKDMGADFVITEYG--VERTAVLIKHLNqgQKVTRNAVQEVAAAKDY 207
                                       689*******************9.***98.9**********976..567777777773348**************** PP

                                       S..SEEEEEESS-B-HHHHHHHHTT--EEEE-HHHHHHH CS
                           Mrr_cat  76 rgadkgifvttsdftkaAreeaeelnkieLldgdeLael 114
                                       ++++ ++++++++ft++A   ae+ n + L+ +++L ++
  gi|298675133|ref|YP_003726883.1| 208 YQCNGAMVISNQEFTQKALILAES-NDVSLIGREQLEDM 245
                                       ************************.***********998 PP

>> Mrr_cat_2  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.2     1e-07   0.00045      22     112 ..     157     244 ..     134     247 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1e-07
                         Mrr_cat_2  22 e.krlgkkDtGIDlVakerkegeywAIQcKfYaedekiqkedidsFlsasgkkkftkrliisTtdkwsknaeealkn 97 
                                         +++g+kD+G D V++e    e +A+  K  ++ +k++++ +++  +a++  +   +++is  + ++++a     +
  gi|298675133|ref|YP_003726883.1| 157 LvESVGTKDMGADFVITE-YGVERTAVLIKHLNQGQKVTRNAVQEVAAAKDYYQCNGAMVISNQE-FTQKALIL--A 229
                                       3467889***********.888999************************9999999999997655.88887655..6 PP

                         Mrr_cat_2  98 qkipvkridledLee 112
                                       ++ +v++i+ e+Le+
  gi|298675133|ref|YP_003726883.1| 230 ESNDVSLIGREQLED 244
                                       777899999999987 PP

>> BTB  BTB/POZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.2   5.5e+03      53      77 ..      35      59 ..      17      66 .. 0.54
   2 ?    8.9   0.0   0.00037       1.7      47      77 ..     126     156 ..     113     170 .. 0.78
   3 ?    1.3   0.0     0.085   3.8e+02      81     108 ..     195     222 ..     176     225 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.2
                                      EEEETTSGHHHHHHHHHHHHHSEEE CS
                               BTB 53 eielddvepeafealLefiYtgele 77
                                      e  l   e+ a + ++e +Y +  +
  gi|298675133|ref|YP_003726883.1| 35 EGCLVGLEHLAADTIIEHLYHDGYN 59
                                      3334455666677777777777655 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00037
                                       TTCCCEEEEETTSGHHHHHHHHHHHHHSEEE CS
                               BTB  47 eessvseielddvepeafealLefiYtgele 77 
                                       + +s+++ +ld+++ +++e+lL  +Y+++  
  gi|298675133|ref|YP_003726883.1| 126 SGNSTQNNNLDKMSWKELEELLVSMYRDKGY 156
                                       3444456789*****************9865 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.085
                                       GGGHHHHHHHHHHHT-HHHHHHHHHHHH CS
                               BTB  81 eenleelLaaadllqiprlkkaceeflk 108
                                       ++ ++e+ aa d++q++  + +  + ++
  gi|298675133|ref|YP_003726883.1| 195 RNAVQEVAAAKDYYQCNGAMVISNQEFT 222
                                       67788898999*****998877666655 PP

>> PBECR3  phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.8   0.00013       0.6      37      73 ..      84     119 ..      25     135 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00013
                            PBECR3  37 rHgnqstekdrgqidianipdiiknPDkviyggknkk 73 
                                        H ++ + ++++ i +++i+d i+nPD+   +++n+k
  gi|298675133|ref|YP_003726883.1|  84 YHNKSGDIQQMQLI-LDRIEDCIENPDSSDSKNQNQK 119
                                       47667777888888.************6555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1333  (0.0743488); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1442.90
//
Query:       gi|298675134|ref|YP_003726884.1|  [L=366]
Description: restriction endonuclease [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.6e-24   84.1   0.1    1.5e-23   83.0   0.1    1.7  1  Mrr_cat    Restriction endonuclease
      2e-05   24.5   0.0    4.6e-05   23.3   0.0    1.6  1  Mrr_cat_2  Restriction endonuclease
  ------ inclusion threshold ------
      0.022   15.2   0.3         13    6.3   0.0    3.5  3  HEAT_2     HEAT repeats


Domain annotation for each model (and alignments):
>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.0   0.1   2.6e-27   1.5e-23       2     115 .]     244     355 ..     243     355 .. 0.92

  Alignments for each domain:
  == domain 1  score: 83.0 bits;  conditional E-value: 2.6e-27
                                       TTT-TTCHHHHHHHHHHHHSSSEEE---B..-TTSSB--EEEETTEEEEEEEEEEE--TS-B-HHHHHHHHHHCTTS CS
                           Mrr_cat   2 dkmspkeFeklvaellealGykeveltgr..sgDggiDliakkdplgserilvqaKryknkvgvkeVqeligalkkr 76 
                                       dk++pk++e  v ++++++Gy    +t+    +D+g+D+i++k  lgser++vq+K++ +kvg  +Vqe+++++ ++
  gi|298675134|ref|YP_003726884.1| 244 DKLTPKQLELAVCKIYREKGYY-AIRTKNtnDKDQGADVILTK--LGSERVAVQVKQSGSKVGNSAVQEVVASVRYY 317
                                       689******************9.444444115689******98..99****************************** PP

                                       ..SEEEEEESS-B-HHHHHHHHTT--EEEE-HHHHHHHH CS
                           Mrr_cat  77 gadkgifvttsdftkaAreeaeelnkieLldgdeLaell 115
                                        ++ +++vt++++t++A + a++ n ++L+++deL +l+
  gi|298675134|ref|YP_003726884.1| 318 LCNSAMVVTNNYYTPEAVDLANA-NDVKLVNRDELRNLI 355
                                       ***********************.***********9985 PP

>> Mrr_cat_2  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   7.7e-09   4.6e-05      23     123 ..     270     364 ..     251     366 .] 0.85

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 7.7e-09
                         Mrr_cat_2  23 krlgkkDtGIDlVakerkegeywAIQcKfYaedekiqkedidsFlsasgkkkftkrliisTtdkwsknaeealknqk 99 
                                       k+++ kD+G D++ ++   +e +A+Q+K  ++ +k+ ++ +++ + as +    ++ +++T +  + +a +  +   
  gi|298675134|ref|YP_003726884.1| 270 KNTNDKDQGADVILTK-LGSERVAVQVK--QSGSKVGNSAVQEVV-ASVRYYLCNSAMVVTNNYYTPEAVDLAN--A 340
                                       67899*********99.99999******..999**********76.56777888888888***********944..4 PP

                         Mrr_cat_2 100 ipvkridledLeeseidwsklslg 123
                                        +vk+++ ++L+++ i   kl+++
  gi|298675134|ref|YP_003726884.1| 341 NDVKLVNRDELRNLIISHYKLFKK 364
                                       469*********999988887765 PP

>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.017     1e+02      53      77 ..      37      61 ..       9      68 .. 0.67
   2 ?    0.9   0.0       0.1     6e+02      29      46 ..     175     192 ..     158     195 .. 0.76
   3 ?    6.3   0.0    0.0021        13       3      43 ..     194     235 ..     192     239 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.017
                            HEAT_2 53 eaLgaigdpealpaLkelldddddd 77
                                      ++L+ ig+p+++++ +e+ +dd+ +
  gi|298675134|ref|YP_003726884.1| 37 QTLAGIGEPAVARVIEEMRKDDNPE 61
                                      5788888888888888888887754 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.1
                            HEAT_2  29 npealpaLvellededpa 46 
                                       +pe+ ++L ++l+ded +
  gi|298675134|ref|YP_003726884.1| 175 SPEIKELLEDMLKDEDFE 192
                                       678888888888888864 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0021
                            HEAT_2   3 aLlqalendpdpevrraairaLgrignpealpaLvell.ed.e 43 
                                        L ++l+n +d e + ++++ + +ign+  l+ L++l+ +d e
  gi|298675134|ref|YP_003726884.1| 194 RLQEYLKNTEDLEFKCQIAEIIHEIGNT-PLKDLLQLMnSDvE 235
                                       577899999******************6.99999999954444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       873  (0.0486921); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 2175.57
//
Query:       gi|298675135|ref|YP_003726885.1|  [L=544]
Description: copper-binding protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.6e-64  214.9 102.9    3.7e-51  173.7  54.3    2.1  2  NosD             Periplasmic copper-binding protein (NosD)
    7.1e-27   94.2  98.4    2.7e-19   69.6  55.1    3.3  4  Beta_helix       Right handed beta helix region
    0.00033   20.6  25.4    0.00033   20.6  25.4    3.5  4  Pectate_lyase_3  Pectate lyase superfamily protein


Domain annotation for each model (and alignments):
>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.4  40.6   8.3e-19     5e-15       2     154 ..      44     210 ..      43     210 .. 0.85
   2 !  173.7  54.3   6.2e-55   3.7e-51      33     238 ..     179     394 ..     177     397 .. 0.96

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 8.3e-19
                              NosD   2 nnaisgdevlvsargngiqlens............egseisnneisnsrdgilldnssnntitgntienl....ryG 62 
                                       n a+++d+++v+   ng++ en+             + + ++ +  +++d+++  + +n+ti+g  i+      ++G
  gi|298675135|ref|YP_003726885.1|  44 NAASDSDTIIVY---NGTYTENVdvnksvtilsesGNPDDTKVQAASTSDHVFNVTRDNVTISGFNITGAtvfeKAG 117
                                       778899999999...55555555443223333222444447778888999999999999999999888888999*** PP

                              NosD  63 ihlensesntiedntlssnesGialmsssnntlenNtisnnenyGillsdssnntisnNtis..nnnkGiflensss 137
                                       i+l++ ++n+i++n++s+n++G+ l +s  ntl+nNt+snn+n Gi l +ss+n+++nN++   +n +Gi+l++s++
  gi|298675135|ref|YP_003726885.1| 118 IFLDEVKNNNISNNKISNNYQGLRLLNSDINTLNNNTASNNNNDGINLYNSSSNKLNNNNANfnSNVDGISLYESNN 194
                                       *************************************************************6647779********* PP

                              NosD 138 ntitgNriesnqkiGil 154
                                       n + +N++++n   Gi+
  gi|298675135|ref|YP_003726885.1| 195 NNLNKNNVSYN-REGIY 210
                                       ***********.99998 PP

  == domain 2  score: 173.7 bits;  conditional E-value: 6.2e-55
                              NosD  33 eisnsrdgilldnssnntitgntienlryGihlensesntiedntlssne.sGialmsss.nntlenNtisnnenyG 107
                                       + +++ dgi l++s+nn++ +n ++ +r+Gi++++s++nt+++nt+s n+ +Gi+l++ s nntl+nNt+ nn++ G
  gi|298675135|ref|YP_003726885.1| 179 NFNSNVDGISLYESNNNNLNKNNVSYNREGIYFSESNNNTLNNNTVSYNReEGIILSDYSsNNTLNNNTVLNNKDDG 255
                                       5677889**********************************************9997655277************** PP

                              NosD 108 illsdssnntisnNtis.nnnkGiflensssntitgNriesnqkiGilllsssegntiynNyFinnsenvkydgsn. 182
                                       i +s+s+nn+++nNt+s n+n Gi++  s++n +++N i +n++ G+  + sse+ntiynN+F nn++n+++++s+ 
  gi|298675135|ref|YP_003726885.1| 256 IGISGSDNNKLNNNTVSnNKNVGISIFVSKNNILKSNIICNNTDLGFE-FPSSEDNTIYNNIF-NNENNTRITASSv 330
                                       *****************9******************************.**************.***********9* PP

                              NosD 183 .nneWnttktsgtniiggpylgGNyWsdydg.......eDadgDGigDtpYeindgviDylplv 238
                                         n+Wn tkt g ni+ggpy+gGNyW+ +dg       +Da++DG++D++++i +++ D lpl+
  gi|298675135|ref|YP_003726885.1| 331 tVNKWNITKTPGPNIVGGPYIGGNYWAHPDGtgfsqtcTDANNDGFCDSEFNIAENNNDSLPLT 394
                                       ******************************************************9999****97 PP

>> Beta_helix  Right handed beta helix region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.3         1   6.2e+03      32      39 ..      49      56 ..      33      74 .. 0.48
   2 !   69.6  55.1   4.6e-23   2.7e-19       5     158 .]      95     248 ..      91     248 .. 0.95
   3 !   38.9  35.3   1.3e-13   7.6e-10      31     124 ..     238     336 ..     237     388 .. 0.83
   4 ?   -3.3   3.0       1.2   7.2e+03      83      83 ..     402     402 ..     327     456 .. 0.50

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1
                                      S-.EEES- CS
                        Beta_helix 32 snvvienn 39
                                      s+++i  n
  gi|298675135|ref|YP_003726885.1| 49 SDTIIVYN 56
                                      22222211 PP

  == domain 2  score: 69.6 bits;  conditional E-value: 4.6e-23
                                       E-SS-E.EEESEEEES-...SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S CS
                        Beta_helix   5 ingssnvtiknntisns...ggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgas 78 
                                       ++++++ ti++++i+++    ++Gi+l++ +n+ i+nn+i+n ++ G+++l+s+ nt+ nnt s+nn++gi+l+++s
  gi|298675135|ref|YP_003726885.1|  95 VTRDNV-TISGFNITGAtvfEKAGIFLDEVKNNNISNNKISN-NYQGLRLLNSDINTLNNNTASNNNNDGINLYNSS 169
                                       555555.***********************************.********************************** PP

                                       --EEES-EEES-SS-.SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EEE CS
                        Beta_helix  79 nnlienneitdnggs.GiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtvr 154
                                        n ++nn+ + n+++ Gi+l+ s+nn +++N+++ n+  Gi++++s+ n+t +nNt++ n+ +Gi + ++ssn+t++
  gi|298675135|ref|YP_003726885.1| 170 SNKLNNNNANFNSNVdGISLYESNNNNLNKNNVSYNR-EGIYFSESN-NNTLNNNTVSYNREEGIILSDYSSNNTLN 244
                                       **********997766*********************.*********.***************************** PP

                                       S-E. CS
                        Beta_helix 155 nNti 158
                                       nNt+
  gi|298675135|ref|YP_003726885.1| 245 NNTV 248
                                       **96 PP

  == domain 3  score: 38.9 bits;  conditional E-value: 1.3e-13
                                       SS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-SEE-TT-S--EEES CS
                        Beta_helix  31 ssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnlienneitdnggsGiylnyssnntien 107
                                       ssn+++ nn++ nn ++Gi+i+gs+nn++ nnt+s+n+++gi +f ++nn+++ n i +n + G+++ +s++nti n
  gi|298675135|ref|YP_003726885.1| 238 SSNNTLNNNTVLNNKDDGIGISGSDNNKLNNNTVSNNKNVGISIFVSKNNILKSNIICNNTDLGFEFPSSEDNTIYN 314
                                       4666************************************************************************* PP

                                       -EEESTT.....--SEE---TT CS
                        Beta_helix 108 Niidnna.....gsGividdss 124
                                       Ni++n +     +s + ++ ++
  gi|298675135|ref|YP_003726885.1| 315 NIFNNENntritASSVTVNKWN 336
                                       ***8877444444444444444 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 1.2
                                       E CS
                        Beta_helix  83 e 83 
                                       e
  gi|298675135|ref|YP_003726885.1| 402 E 402
                                       2 PP

>> Pectate_lyase_3  Pectate lyase superfamily protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6  25.4   5.5e-08   0.00033      19     214 ..      37     232 ..      28     233 .. 0.76
   2 !   13.8  12.8   6.6e-06      0.04     132     214 ..     216     302 ..     216     303 .. 0.75
   3 !    4.9  16.7    0.0034        20     147     210 ..     255     320 ..     240     345 .. 0.51
   4 ?   -1.9   0.1      0.41   2.4e+03     144     169 ..     412     437 ..     365     475 .. 0.63

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 5.5e-08
                                       HHHHHHH......HTSS-EEE-SEEEEESS-EEE-SSEEE..EES-TTTEEEEE-TT-SS--SEEES-TT.T-.... CS
                   Pectate_lyase_3  19 aaiqkaiscasatttgavVYfPaGtYlvsspiilksgvqL..vGdgngrpvlkaaaafvgaglidgdpyv.sg.... 88 
                                         iq+ai +a+  ++ +++ +  GtY  +  + +ks + L   G++ + + ++aa+ ++  + +++d+++ sg    
  gi|298675135|ref|YP_003726885.1|  37 QKIQNAI-NAA--SDSDTIIVYNGTYTENVDV-NKSVTILseSGNP-DDTKVQAASTSDHVFNVTRDNVTiSGfnit 108
                                       57*****.444..4444444559***999998.6666666334777.666666666665555556666666666455 PP

                                       ..-EEEEEEEEEEEGGGG-SS---SSEEEES-EEEEEEEEEEES-SSEEE-SSS---TT---SS--EEEE..ES-EE CS
                   Pectate_lyase_3  89 gsealiatnnfyrqirnlkiditavapgatgihwqtaqatslenvefemseasgtkhqgifiengsggfl..ndlvf 163
                                       g+  +++   f+++++n  i+ ++++++++g++   ++  +l n+     +as+++++gi++ n+s++ l  n++ f
  gi|298675135|ref|YP_003726885.1| 109 GATVFEKAGIFLDEVKNNNISNNKISNNYQGLRLLNSDINTLNNN-----TASNNNNDGINLYNSSSNKLnnNNANF 180
                                       5599999999999******************88666666666665.....55556677*********9998899999 PP

                                       ES-SS-SEEE.S-EEEEEES-EEE-S--SEEE-TT-EEEEEEEEE.ESSSEEE CS
                   Pectate_lyase_3 164 sglgdigiav.gnqqftvrnitfnnattgievlwgwgwtlknvki.nncegGi 214
                                       +    +gi +  +++ +++++ ++ + +gi+++++++ tl+n+++ +n e+Gi
  gi|298675135|ref|YP_003726885.1| 181 NS-NVDGISLyESNNNNLNKNNVSYNREGIYFSESNNNTLNNNTVsYNREEGI 232
                                       99.999999988888888888888889*******999***9998856666687 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 6.6e-06
                                       S-SSEEE-SSS---TT--.-SS--EEEEES-EEES-SS-SEEE.S-EEEEEES-EEE-.S--SEEE-TT-EEEEE.E CS
                   Pectate_lyase_3 132 nvefemseasgtkhqgif.iengsggflndlvfsglgdigiav.gnqqftvrnitfnn.attgievlwgwgwtlk.n 204
                                       n+++++++ s + ++gi+  +++s+++ln+ ++ ++ d+gi + g+++  ++n+t++n  + gi++  +++ +lk n
  gi|298675135|ref|YP_003726885.1| 216 NNTLNNNTVSYNREEGIIlSDYSSNNTLNNNTVLNNKDDGIGIsGSDNNKLNNNTVSNnKNVGISIFVSKNNILKsN 292
                                       567777888866777777477888899966666666*******88999999999998867899**999777555516 PP

                                       EEEESSSEEE CS
                   Pectate_lyase_3 205 vkinncegGi 214
                                       +  nn+  G+
  gi|298675135|ref|YP_003726885.1| 293 IICNNTDLGF 302
                                       6667776676 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.0034
                                       T---SS--EEEEES-EEES-SS-SEEE..S-EEEEEES-EEE-S--SEEE-TT-EEEEEEEEEESS CS
                   Pectate_lyase_3 147 gifiengsggflndlvfsglgdigiav..gnqqftvrnitfnnattgievlwgwgwtlknvkinnc 210
                                       gi i+ + ++ ln+ ++s++ + gi +  +++++  +ni +nn+  g+e+ ++++ t+ n+ +nn 
  gi|298675135|ref|YP_003726885.1| 255 GIGISGSDNNKLNNNTVSNNKNVGISIfvSKNNILKSNIICNNTDLGFEFPSSEDNTIYNNIFNNE 320
                                       555555555555555555555555544323555555555555555555555544444444444332 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 0.41
                                       --TT---SS--EEEE.ES-EEES-SS- CS
                   Pectate_lyase_3 144 khqgifiengsggfl.ndlvfsglgdi 169
                                       + +g +i+ gs+ ++  +++ +g + i
  gi|298675135|ref|YP_003726885.1| 412 EPEGPTIQMGSQVTWtYNITNTG-SVI 437
                                       34444444455544434444444.333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (544 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       916  (0.0510904); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.70u 0.33s 00:00:01.03 Elapsed: 00:00:00.53
# Mc/sec: 3117.53
//
Query:       gi|298675136|ref|YP_003726886.1|  [L=320]
Description: hypothetical protein Metev_1217 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.1e-15   55.1   0.0    9.5e-05   22.5   0.0    4.1  4  Nitroreductase  Nitroreductase family
    1.1e-09   38.2   0.0    1.1e-05   25.1   0.0    3.4  3  TM1586_NiRdase  Putative TM nitroreductase
  ------ inclusion threshold ------
      0.032   13.9   0.0      0.059   13.0   0.0    1.4  1  DUF2271         Predicted periplasmic protein (DUF2271)


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   1.6e-08   9.5e-05      18      44 ..       2      28 ..       1      42 [. 0.89
   2 !    7.6   0.0    0.0006       3.6     110     144 ..      47      81 ..      32     104 .. 0.81
   3 !    7.3   0.0   0.00074       4.4       3      23 ..     109     130 ..     107     136 .. 0.91
   4 !   13.2   0.0   1.2e-05     0.071      79     170 .]     220     303 ..     142     303 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.6e-08
                                      HHHHHHHHHHHTS--GGG---EEEEEE CS
                    Nitroreductase 18 eelekileaarraPsagnlqpwrfvvv 44
                                      e + +i++ a+ aPs++n+qpw+f++ 
  gi|298675136|ref|YP_003726886.1|  2 ENINEIIRYATLAPSGHNTQPWKFYLE 28
                                      7899*********************85 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0006
                                       HHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGG CS
                    Nitroreductase 110 rayryalldagaaaqnllLaAtalGlgscpiggfd 144
                                        ++r+ ++++g+a++nll+ A+  G+ + +   fd
  gi|298675136|ref|YP_003726886.1|  47 PDDRELFISLGCALENLLIVAEHNGYSTNVEYSFD 81 
                                       5678999*******************999877776 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.00074
                                       H--B--.-B-S----HHHHHHH CS
                    Nitroreductase   3 kRrSiR.kFddepvpkeeleki 23 
                                       +R ++R k+d +++p+++l+k+
  gi|298675136|ref|YP_003726886.1| 109 QRQTTRsKYDGNSIPDDDLDKL 130
                                       8******************997 PP

  == domain 4  score: 13.2 bits;  conditional E-value: 1.2e-05
                                       HHHHHHHHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHH...HHHH CS
                    Nitroreductase  79 lklkaqkalagapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaae...evrk 152
                                       +++k   +++ +  l+vi           ++++   a++d+g   ++l+L Atal++    ++++ e  +   ++++
  gi|298675136|ref|YP_003726886.1| 220 QSKKDEINIRSSSSLLVI----------MSDDNSKIAWVDIGRSFERLVLNATALNIKNAHLNQPCEIPQlkeKLQE 286
                                       555666666777777777..........889999*************************999999955555557*** PP

                                       HHT-S..SEEEEEEEEE- CS
                    Nitroreductase 153 llglpdeeeivvliavGy 170
                                       +l + + +++++l+++Gy
  gi|298675136|ref|YP_003726886.1| 287 ILSIGN-KHPQLLLRIGY 303
                                       *****6.**********9 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   1.8e-09   1.1e-05     158     195 ..       2      38 ..       1      69 [. 0.87
   2 !    4.8   0.0    0.0031        19       2      33 ..     103     135 ..     102     190 .. 0.81
   3 !    4.8   0.0    0.0031        19      52     134 ..     218     294 ..     208     319 .. 0.69

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.8e-09
                                       HHHHHHHHHHHTS--GGG----EEE.E-SSEE.....E CS
                    TM1586_NiRdase 158 ewfkeileaarlAPsAlNqqpwrfelkdddeikikasv 195
                                       e+++ei++ a lAPs  N+qpw+f l++ ++iki+ + 
  gi|298675136|ref|YP_003726886.1|   2 ENINEIIRYATLAPSGHNTQPWKFYLEK-NQIKIFPDY 38 
                                       6899*********************877.7**997654 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0031
                                       HHHHHHH--B--.-B--S---HHHHHHHHH--- CS
                    TM1586_NiRdase   2 lyeaiekRhsvR.kYkdealeeelleelkeaie 33 
                                       ly+ai +R++ R kY+ ++++++ l++lk+ i 
  gi|298675136|ref|YP_003726886.1| 103 LYDAIPQRQTTRsKYDGNSIPDDDLDKLKSVIM 135
                                       699*********66**************99875 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.0031
                                       ...........-SSSSEEEE----SS.HHHHHHHHHHHHHHHHHHHHTT-EEEEES--SST...........T-S-E CS
                    TM1586_NiRdase  52 afkskvaklgkfkgvpnyialvgekk.edleekaGYygeqlvLkltalGlgtcWvggtykkkkakvelkkgeklviv 127
                                       + +sk  ++    + ++ ++++++++ + + + +G   e+lvL++tal+++   +    +  +       +ekl  +
  gi|298675136|ref|YP_003726886.1| 218 KAQSKKDEI-NIRSSSSLLVIMSDDNsKIAWVDIGRSFERLVLNATALNIKNAHLNQPCEIPQL------KEKLQEI 287
                                       445555666.55666777777787775667899****************998877754333333......5566666 PP

                                       EEEE-BS CS
                    TM1586_NiRdase 128 IalGyak 134
                                       +++G+ +
  gi|298675136|ref|YP_003726886.1| 288 LSIGNKH 294
                                       6666655 PP

>> DUF2271  Predicted periplasmic protein (DUF2271)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     1e-05     0.059      40      73 ..     165     198 ..     143     201 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1e-05
                           DUF2271  40 gegekwlkdlrqWwrksgrklkeeidgvsgaTra 73 
                                        ++e++ k+l++W r++ +++k+++dg+s+ T +
  gi|298675136|ref|YP_003726886.1| 165 MNDENFKKELTSWIRFNDSDTKKHLDGLSSKTMG 198
                                       5788999***********9999********9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 1909.16
//
Query:       gi|298675137|ref|YP_003726887.1|  [L=288]
Description: abortive infection protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-14   53.8   5.8    1.9e-14   53.8   5.8    2.5  3  CPBP      CPBP intramembrane metalloprotease


Domain annotation for each model (and alignments):
>> CPBP  CPBP intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   1.4       0.2   3.6e+03      31      31 ..      76      76 ..      10     115 .. 0.60
   2 !   53.8   5.8   1.1e-18   1.9e-14       6      91 ..     124     230 ..     119     231 .. 0.84
   3 ?   -2.5   0.0      0.38   6.8e+03      14      23 ..     235     244 ..     232     268 .. 0.63

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.2
                                      H CS
                              CPBP 31 l 31
                                      +
  gi|298675137|ref|YP_003726887.1| 76 I 76
                                      1 PP

  == domain 2  score: 53.8 bits;  conditional E-value: 1.1e-18
                                       HHHHHHHHHHHHHHHHHHTTCHHHHHHHH.S-HHHHHHHHHHHHHCSGGG.HHHH...................... CS
                              CPBP   6 lvfllalllapllEEllfRglllqllqergsstlailissilFglaHlpn.gpsv...................... 59 
                                         ++ ++lla+l+EE ++Rg+ l++lqe ++++ a+++ +il++++H+p  +  v                      
  gi|298675137|ref|YP_003726887.1| 124 PTLIGLSLLAGLGEEPGWRGFALPRLQEQYGPLNATFLLGILWAFWHIPVfF--Vdprsshgitdpiilgglvllta 198
                                       5677899**********************888*****************950..34455555566666677766666 PP

                                       HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              CPBP  60 llaalaGlvlgylylktgsllaaillHallnl 91 
                                       + ++l+ +++++++ +tgs+l  +llH+++n+
  gi|298675137|ref|YP_003726887.1| 199 VGIVLYTFFYTWIFNHTGSVLLMMLLHGGFNT 230
                                       9999999999********************97 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.38
                                       HHHHHHHHHH CS
                              CPBP  14 lapllEEllf 23 
                                       l+p++ E++f
  gi|298675137|ref|YP_003726887.1| 235 LVPFADEIVF 244
                                       5666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1734.50
//
Query:       gi|298675138|ref|YP_003726888.1|  [L=151]
Description: hypothetical protein Metev_1219 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.21   12.7   0.2        0.4   11.8   0.1    1.6  2  DUF5320   Family of unknown function (DUF5320)


Domain annotation for each model (and alignments):
>> DUF5320  Family of unknown function (DUF5320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.57     1e+04      49      52 ..      51      54 ..      26      78 .. 0.53
   2 ?   11.8   0.1   2.2e-05       0.4      66      99 .]     114     147 ..      93     147 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.57
                           DUF5320 49 gfgr 52
                                       +  
  gi|298675138|ref|YP_003726888.1| 51 FYSD 54
                                      2222 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 2.2e-05
                           DUF5320  66 taeaskeeekelLeeqaeaLeeeleaikkrlkel 99 
                                       +  ++ + +ke+L e++ +Le +l++i+ +l++l
  gi|298675138|ref|YP_003726888.1| 114 KFLPEFKPDKEILHEEKTYLECRLDEINHKLENL 147
                                       555677889**********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 912.80
//
Query:       gi|298675139|ref|YP_003726889.1|  [L=76]
Description: hypothetical protein Metev_1220 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0011   19.7   2.0     0.0035   18.1   2.0    1.8  1  VAPB_antitox  Putative antitoxin
  ------ inclusion threshold ------
      0.017   14.3   0.1      0.018   14.2   0.1    1.0  1  Taxilin       Myosin-like coiled-coil protein


Domain annotation for each model (and alignments):
>> VAPB_antitox  Putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   2.0   3.9e-07    0.0035       2      65 ..       4      59 ..       3      63 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.9e-07
                      VAPB_antitox  2 tIsIsdevYekLkklKr.egeSFsdvIerLlekkkkgkkkellelfgilseeeadeiekaskelr 65
                                      tIsI   ++ekL++l+r +++S++ +IerL+  +  + ++        ls+e ++ ie+a++ ++
  gi|298675139|ref|YP_003726889.1|  4 TISIVPRTKEKLDSLRRfPQKSYNSIIERLIIMSV-D-ED-------ELSDEAIQGIEEALEDIK 59
                                      9*****************************95333.2.22.......344455555555555554 PP

>> Taxilin  Myosin-like coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1     2e-06     0.018      67     117 ..      10      60 ..       2      70 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2e-06
                           Taxilin  67 laksKLekLcRelqkqnkklkeeskqrareeeekrkelaekfqakLkdiqa 117
                                        +k+KL++L R  qk  + + e    ++  e+e  +e+ +  ++ L+di++
  gi|298675139|ref|YP_003726889.1|  10 RTKEKLDSLRRFPQKSYNSIIERLIIMSVDEDELSDEAIQGIEEALEDIKK 60 
                                       69***********************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 464.19
//
Query:       gi|298675140|ref|YP_003726890.1|  [L=92]
Description: RelE/StbE family addiction module toxin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-12   47.2   0.2      3e-12   47.0   0.2    1.1  1  ParE_toxin       ParE toxin of type II toxin-antitoxin system
    0.00037   20.6   0.0    0.00039   20.5   0.0    1.1  1  Gp49             Phage derived protein Gp49-like (DUF891)
  ------ inclusion threshold ------
      0.017   15.0   0.2       0.03   14.3   0.2    1.4  1  ParE-like_toxin  ParE-like toxin of type II bacterial toxin-a
      0.048   14.0   0.0      0.073   13.5   0.0    1.2  1  SPOR             Sporulation related domain


Domain annotation for each model (and alignments):
>> ParE_toxin  ParE toxin of type II toxin-antitoxin system, parDE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.2   6.6e-16     3e-12       1      88 [.       5      87 ..       5      89 .. 0.85

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 6.6e-16
                                      EEEEHHHHHHHHHHHHHHHCC-HHHHHHHHHHHHHHHHHHHHTTTSEECTSTC.......CTTEEEEEECTEEEEEEEE CS
                        ParE_toxin  1 vrltprAlkdlkkiadyiardgpaakrfldaleealellaenpalgrprrelg.......lkglrririgdyriiYrid 72
                                      ++l+p + k lk +++++          +++++e +e+l + p +  pr +++        k ++r+r+g+yr+iY+i+
  gi|298675140|ref|YP_003726890.1|  5 IKLHPGVAKYLKSLDSNT----------KARIKESIETLSDKPYPENPRTDIKklkgtkgRKSFYRLRVGNYRVIYTIE 73
                                      689999999999998866..........6777777788888888888877777889999999****************7 PP

                                      TSTTEEEEEEEEEHHH CS
                        ParE_toxin 73 deelvvvilrvlhrse 88
                                       +e+++ i ++ hr++
  gi|298675140|ref|YP_003726890.1| 74 -DETIL-ITDIIHREK 87
                                      .66888.*******86 PP

>> Gp49  Phage derived protein Gp49-like (DUF891)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   8.6e-08   0.00039       1      64 [.      13      78 ..      13      91 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 8.6e-08
                              Gp49  1 eeldalpkkarakilaaldlleegg.pdlgkplvkkle.....dglwElrpksaggiiRvlyafdpgrkv 64
                                      ++l++l+ +++a+i + ++ l ++  p++++  +kkl+     +  + lr+    g +Rv+y+   +  +
  gi|298675140|ref|YP_003726890.1| 13 KYLKSLDSNTKARIKESIETLSDKPyPENPRTDIKKLKgtkgrKSFYRLRV----GNYRVIYTIEDETIL 78
                                      589**********************999**************99*******....99*****99877654 PP

>> ParE-like_toxin  ParE-like toxin of type II bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   6.8e-06      0.03       4      73 ..       8      79 ..       5      91 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.8e-06
                   ParE-like_toxin  4 trrfkkalkklkeklkadldkavkeiiedPelGeeKkGDLsgvfvyk.....fklnkqltllaYeldekkrvlvl 73
                                       + ++k+lk l ++ ka++++ ++++ ++P+  ++++ D++ +   k     ++l+  ++++ Y++++++++  +
  gi|298675140|ref|YP_003726890.1|  8 HPGVAKYLKSLDSNTKARIKESIETLSDKPYPENPRT-DIKKLKGTKgrksfYRLRVGNYRVIYTIEDETIL--I 79
                                      56789*************************9866654.7766655543335467888889999999888865..3 PP

>> SPOR  Sporulation related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.6e-05     0.073      13      51 ..      21      66 ..      18      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.6e-05
                                      S-HHHHHHHHHHCCHH.T--.........EEECCSSSCEEEEESSB CS
                              SPOR 13 sseanAerlaakLrak.gfaaav......avvsgggglyrVrvGpf 51
                                      +++a+ ++ ++ L++k +++++       + ++g++++yr+rvG++
  gi|298675140|ref|YP_003726890.1| 21 NTKARIKESIETLSDKpYPENPRtdikklKGTKGRKSFYRLRVGNY 66
                                      677888888888888855555558889999**************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 538.57
//
Query:       gi|298675141|ref|YP_003726891.1|  [L=63]
Description: hypothetical protein Metev_1222 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.065   13.1   0.1      0.072   12.9   0.1    1.0  1  DUF4158   Domain of unknown function (DUF4158)


Domain annotation for each model (and alignments):
>> DUF4158  Domain of unknown function (DUF4158)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1     4e-06     0.072      85     123 ..      15      53 ..       5      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4e-06
                           DUF4158  85 salakyasreqtrrehlaeIrellgyrpfteadlrelee 123
                                       + l++y+s+ +t ++ l+++++ ++y++f e+++++le+
  gi|298675141|ref|YP_003726891.1|  15 DRLKSYGSKGETYSQILTRLMDEIDYESFMERQYKRLED 53 
                                       77999*****************************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 471.35
//
Query:       gi|298675142|ref|YP_003726892.1|  [L=245]
Description: restriction endonuclease [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.6e-22   79.7   0.3    3.5e-22   78.6   0.3    1.6  1  Mrr_cat    Restriction endonuclease
    3.1e-05   23.9   1.2    6.2e-05   22.9   0.4    1.9  2  Mrr_cat_2  Restriction endonuclease
     0.0092   16.2   0.9       0.61   10.3   0.0    2.7  3  BTB        BTB/POZ domain
  ------ inclusion threshold ------
      0.048   13.7   0.3       0.11   12.6   0.3    1.5  1  DUF1676    Protein of unknown function (DUF1676)
      0.091   13.7   0.4      0.091   13.7   0.4    2.0  2  DUF4284    Immunity protein 22
        1.2    9.5   3.9       0.81   10.1   1.4    2.0  2  CpxA_peri  Two-component sensor protein CpxA, periplasmic dom


Domain annotation for each model (and alignments):
>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.6   0.3   1.2e-25   3.5e-22       1     114 [.     132     242 ..     132     243 .. 0.92

  Alignments for each domain:
  == domain 1  score: 78.6 bits;  conditional E-value: 1.2e-25
                                       HTTT-TTCHHHHHHHHHHHHSSSEEE---B-TTSSB--EEEETTEEEEEEEEEEE--..TS-B-HHHHHHHHHHCTT CS
                           Mrr_cat   1 ldkmspkeFeklvaellealGykeveltgrsgDggiDliakkdplgserilvqaKry..knkvgvkeVqeligalkk 75 
                                       ld+ms+ke+e++++++++ +Gy  ve+tg   D g+Dli+++ +   er++v +K+   ++kv +++Vqe ++a+++
  gi|298675142|ref|YP_003726892.1| 132 LDEMSWKELEDFLESMYKDKGYL-VERTG-ITDMGADLIITSYG--VERTAVVIKHLnsDQKVTRNAVQEAAAAMNY 204
                                       689*******************9.****8.99*********965..567777777764369**************** PP

                                       S..SEEEEEESS-B-HHHHHHHHTT--EEEE-HHHHHHH CS
                           Mrr_cat  76 rgadkgifvttsdftkaAreeaeelnkieLldgdeLael 114
                                       ++++ +i+v++++ft++A + ae+ n + L+d+++L e+
  gi|298675142|ref|YP_003726892.1| 205 YHCNGAIVVSNQEFTEQAVKLAES-NDVSLIDRKQLEEM 242
                                       ************************.***********998 PP

>> Mrr_cat_2  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.3   3.8e+03      91     114 ..     101     124 ..      97     137 .. 0.70
   2 !   22.9   0.4   2.1e-08   6.2e-05      23     113 ..     156     242 ..     138     244 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.3
                         Mrr_cat_2  91 aeealknqkipvkridledLeese 114
                                       +ee+++nq+ p +r + ++++ s 
  gi|298675142|ref|YP_003726892.1| 101 IEENIENQDSPDSRNQNQRIQTSG 124
                                       677888888887777777776664 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 2.1e-08
                         Mrr_cat_2  23 krlgkkDtGIDlVakerkegeywAIQcKfYaedekiqkedidsFlsasgkkkftkrliisTtdkwsknaeealknqk 99 
                                       +r+g +D+G Dl++++    e +A+  K  ++d+k++++ +++  +a++  +   ++++s  ++++++a +   +++
  gi|298675142|ref|YP_003726892.1| 156 ERTGITDMGADLIITS-YGVERTAVVIKHLNSDQKVTRNAVQEAAAAMNYYHCNGAIVVS-NQEFTEQAVKL--AES 228
                                       567889**********.8889999*******************99998888877777775.566*****999..566 PP

                         Mrr_cat_2 100 ipvkridledLees 113
                                        +v++id ++Lee 
  gi|298675142|ref|YP_003726892.1| 229 NDVSLIDRKQLEEM 242
                                       68*****9999985 PP

>> BTB  BTB/POZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.026        77      33     102 ..      15      52 ..       7      86 .. 0.55
   2 !   10.3   0.0    0.0002      0.61      47      77 ..     123     153 ..     112     164 .. 0.80
   3 ?   -2.4   0.0       1.9   5.6e+03      83     105 ..     194     216 ..     186     222 .. 0.60

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.026
                                       H-HHHHHHHTSTTTTTCCCEEEEETTSGHHHHHHHHHHHHHSEEEC-CGGGHHHHHHHHHHHT-HHHHHH CS
                               BTB  33 rSpyFkalftskeieessvseielddvepeafealLefiYtgeleitseenleelLaaadllqiprlkka 102
                                         +++++++t +                                  t ++++e+ L   ++l  + ++++
  gi|298675142|ref|YP_003726892.1|  15 VESMLEVMLTTD-------------------------------SHCT-KKEIEDCLIRMEHLAADTIIEH 52 
                                       334455555555...............................4443.4444444444444444444333 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0002
                                       TTCCCEEEEETTSGHHHHHHHHHHHHHSEEE CS
                               BTB  47 eessvseielddvepeafealLefiYtgele 77 
                                       + +s+++ +ld+++ +++e +Le +Y ++  
  gi|298675142|ref|YP_003726892.1| 123 SGNSQQNNNLDEMSWKELEDFLESMYKDKGY 153
                                       4455667889*****************9865 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.9
                                       GHHHHHHHHHHHT-HHHHHHHHH CS
                               BTB  83 nleelLaaadllqiprlkkacee 105
                                        ++e  aa ++++++  + +  +
  gi|298675142|ref|YP_003726892.1| 194 AVQEAAAAMNYYHCNGAIVVSNQ 216
                                       45555555677777766655444 PP

>> DUF1676  Protein of unknown function (DUF1676)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   3.5e-05      0.11       5      80 ..      71     146 ..      68     148 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.5e-05
                           DUF1676   5 sdlvsClkkkalrfldrlldkdeielv.dgvslvrneeaasassk.eeeeelsreeeeareeelekllleklerflk 79 
                                       +  v+Cl +k+ ++ +r  d+ +++l+ d+++   n e+++++++ +++++ +++ +++++++l+++ +++le+fl+
  gi|298675142|ref|YP_003726892.1|  71 QPAVDCLSEKIKQYQNRYGDTHQLQLIlDRIE--ENIENQDSPDSrNQNQRIQTSGNSQQNNNLDEMSWKELEDFLE 145
                                       56789*******************99834443..2222222222233334444444445558**************9 PP

                           DUF1676  80 s 80 
                                       s
  gi|298675142|ref|YP_003726892.1| 146 S 146
                                       8 PP

>> DUF4284  Immunity protein 22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       1.1   3.3e+03      68      96 ..      50      79 ..       3      98 .. 0.55
   2 ?   13.7   0.4   3.1e-05     0.091      11     114 ..     137     233 ..     133     238 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.1
                           DUF4284 68 ldseiieklkeklkekkln.kanavillyd 96
                                      +++   + +++ l++  l+ k +av +l++
  gi|298675142|ref|YP_003726892.1| 50 IEHLYHDGYNQDLENVLLQiKQPAVDCLSE 79
                                      333333333333333333344555555554 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 3.1e-05
                           DUF4284  11 ekefeeYldqsydedgkelssqFckdlgleeyDeDfleikfleteaedieellekvsldseiieklkek.lkekkln 86 
                                        ke+e++l++ y+++g +l    ++  g+ +   D++++ +     e+ + +++ +  d+++  ++ ++ +++++ +
  gi|298675142|ref|YP_003726892.1| 137 WKELEDFLESMYKDKG-YL----VERTGITDMGADLIITSY---GVERTAVVIKHLNSDQKVTRNAVQEaAAAMNYY 205
                                       689*************.44....6999**************...777778899999999999666555505555555 PP

                           DUF4284  87 kanavillydkeyseitekkaednelkf 114
                                       + n +i+++++e +e + k ae+n +++
  gi|298675142|ref|YP_003726892.1| 206 HCNGAIVVSNQEFTEQAVKLAESNDVSL 233
                                       **********996666666666666555 PP

>> CpxA_peri  Two-component sensor protein CpxA, periplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.4   0.00027      0.81       8      85 ..      70     147 ..      64     153 .. 0.84
   2 ?   -1.6   0.0       1.1   3.3e+03      49      89 ..     196     238 ..     171     242 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00027
                                       -HHHHHHHHHHHHHHHHHTSS---HHHHHHHHHH..T---TT--S-EEEEE-TTS-EE----S-HHHHHHHHHHHHH CS
                         CpxA_peri   8 paeelerlleirdkiekrfseeedlkkilkrleerknrkkkkderlrlfltdldgeilttkkradfklkalrnfvts 84 
                                        +   + l e  ++ ++r+ ++++l+ il r+ee+ ++++  d+r++    ++ g+  ++++  +++ k l++f+ s
  gi|298675142|ref|YP_003726892.1|  70 KQPAVDCLSEKIKQYQNRYGDTHQLQLILDRIEENIENQDSPDSRNQNQRIQTSGNSQQNNNLDEMSWKELEDFLES 146
                                       566677788899999*******************9998888888888888888899888888889999999999877 PP

                                       - CS
                         CpxA_peri  85 i 85 
                                       +
  gi|298675142|ref|YP_003726892.1| 147 M 147
                                       5 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.1
                                       T--S-EEEEE-TTS-EE----S-HHH.HH.HHHHHHHH-S-TT CS
                         CpxA_peri  49 kderlrlfltdldgeilttkkradfk.lk.alrnfvtsiespe 89 
                                       ++  + +     +g+i+ ++++   + +k a  n v++i++++
  gi|298675142|ref|YP_003726892.1| 196 QEAAAAMNYYHCNGAIVVSNQEFTEQaVKlAESNDVSLIDRKQ 238
                                       3445555555666777666554222202213456677777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1523  (0.0849462); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 1619.94
//
Query:       gi|298675143|ref|YP_003726893.1|  [L=373]
Description: restriction endonuclease [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-22   80.1   0.0    2.4e-22   79.1   0.0    1.6  1  Mrr_cat   Restriction endonuclease


Domain annotation for each model (and alignments):
>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.1   0.0   1.3e-26   2.4e-22       2     112 ..     259     365 ..     258     368 .. 0.96

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 1.3e-26
                                       TTT-TTCHHHHHHHHHHHHSSSEEE---B-TTSSB--EEEETTEEEEEEEEEEE--TS-B-HHHHHHHHHHCTTS.. CS
                           Mrr_cat   2 dkmspkeFeklvaellealGykeveltgrsgDggiDliakkdplgserilvqaKryknkvgvkeVqeligalkkrga 78 
                                       +++s++e+e  + +l+e++Gyk ve t++ +D+g+D+ia++   gseri+vq+K+ +n+++  +Vqe+++a +++ +
  gi|298675143|ref|YP_003726893.1| 259 YNISWEELELGLMNLYEKMGYK-VEKTPKNSDYGADFIATQ--WGSERIAVQVKHLNNTTSPSAVQEVVAAKMYYIC 332
                                       6899*****************9.****************97..6899****************************** PP

                                       SEEEEEESS-B-HHHHHHHHTT--EEEE-HHHHH CS
                           Mrr_cat  79 dkgifvttsdftkaAreeaeelnkieLldgdeLa 112
                                       +k+ +v+t+ f+k+A++ a+   ++ L+d+d+L 
  gi|298675143|ref|YP_003726893.1| 333 SKAEVVSTNNFSKQAKNLADI-TGVNLIDRDKLK 365
                                       ********************9.9*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2648.40
//
Query:       gi|298675144|ref|YP_003726894.1|  [L=142]
Description: hypothetical protein Metev_1226 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   12.5   1.2       0.18   12.1   1.2    1.1  1  zf-C4H2   Zinc finger-containing protein


Domain annotation for each model (and alignments):
>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.2   9.8e-06      0.18      13      66 ..      88     141 ..      79     142 .] 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.8e-06
                           zf-C4H2  13 eklknklakevealekeekcleeykkelelLeqEkmaHveeLrlIhaDinalEs 66 
                                       ++  n+ + +v++ +  ek+l e+k+    L++E+++ ++ +r I++ +++l++
  gi|298675144|ref|YP_003726894.1|  88 DQQCNNQSWAVDMWDVIEKHLPEFKSHEVILKEERKQLSDRIREIDEELKNLDD 141
                                       5555666778999**********************************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1028  (0.0573373); expected 358.6 (0.02)
Passed bias filter:                      640  (0.0356964); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1008.75
//
Query:       gi|298675145|ref|YP_003726895.1|  [L=168]
Description: hypothetical protein Metev_1227 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1291.04
//
Query:       gi|298675146|ref|YP_003726896.1|  [L=448]
Description: orc1/cdc6 family replication initiation protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-09   37.9   0.0    4.1e-09   37.0   0.0    1.5  1  AAA              ATPase family associated with various cellul
    1.5e-08   35.0   0.2      1e-07   32.3   0.0    2.3  3  AAA_22           AAA domain
    2.1e-08   34.0   0.1    9.1e-08   32.0   0.1    2.2  1  Cdc6_C           CDC6, C terminal winged helix domain
    5.6e-08   33.4   0.0    1.8e-07   31.7   0.0    1.8  1  AAA_16           AAA ATPase domain
    1.8e-07   31.3   1.0    3.2e-07   30.5   0.3    1.6  2  ATPase_2         ATPase domain predominantly from Archaea
    0.00049   20.0   0.0    0.00092   19.2   0.0    1.5  1  NACHT            NACHT domain
     0.0013   18.9   0.2     0.0029   17.7   0.2    1.6  1  AAA_2            AAA domain (Cdc48 subfamily)
     0.0032   16.7   0.3     0.0064   15.7   0.3    1.5  1  NB-ARC           NB-ARC domain
      0.005   16.3   0.0     0.0096   15.3   0.0    1.4  1  TniB             Bacterial TniB protein
     0.0051   17.2   0.3        0.7   10.3   0.0    2.7  2  RNA_helicase     RNA helicase
     0.0062   16.1   1.1      0.028   13.9   0.1    2.3  2  AAA_7            P-loop containing dynein motor region
     0.0068   15.7   0.4      0.022   14.0   0.4    1.8  1  KAP_NTPase       KAP family P-loop domain
     0.0085   16.1   0.1       0.05   13.6   0.0    2.0  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
  ------ inclusion threshold ------
      0.012   15.3   1.3       0.18   11.6   1.3    2.4  1  DEAD             DEAD/DEAH box helicase
      0.015   15.0   0.0      0.037   13.8   0.0    1.6  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.026   14.3   0.0      0.045   13.4   0.0    1.4  1  Sigma54_activat  Sigma-54 interaction domain
      0.035   14.2   0.0      0.081   13.1   0.0    1.6  1  TIP49_C          TIP49 AAA-lid domain
      0.044   13.5   0.1       0.43   10.2   0.0    2.3  2  Ribosomal_L4     Ribosomal protein L4/L1 family
      0.084   12.0   0.1       0.28   10.3   0.0    1.8  2  DUF815           Protein of unknown function (DUF815)
       0.22   11.9   0.7        1.1    9.5   0.4    2.3  1  AAA_19           AAA domain
        1.3    9.5   8.1          1    9.9   0.2    3.4  2  AAA_18           AAA domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.0   4.8e-12   4.1e-09       1     112 [.      64     195 ..      64     209 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 4.8e-12
                                       EEEESSTTSSHHHHHHHHHHHH..........THEEEEEETTTCSSS.....................STTHHHHHH CS
                               AAA   1 vllyGppGtGKTllakavakel..........gvefleisgsellsk.....................yvgesekki 46 
                                       vl+ G+ GtGKTll + v+++l          +v+ l +++s+   k                     +v    + i
  gi|298675146|ref|YP_003726896.1|  64 VLIDGNHGTGKTLLTRIVMENLenltksdvytDVYTLHVNCSQTGTKfsivktlisdlekkgnvssqtLVNSYDSYI 140
                                       6788*****************8555554444446777788887777778888888888888******999999**** PP

                                       HHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSG CS
                               AAA  47 relfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrp 112
                                       + +f+ +    + +i+++DE+d++ +          ++vvn +l+ ++++k++++ ++v+g+tn+ 
  gi|298675146|ref|YP_003726896.1| 141 ERFFDLVNVLDGVVIVVFDELDQIQE----------DTVVNDILRSVENMKTYRG-ICVVGITNDH 195
                                       *****99999877***********44..........46**************977.********85 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0   1.2e-10     1e-07       7     117 ..      63     179 ..      57     193 .. 0.78
   2 ?   -1.9   0.0       4.5   3.8e+03      98     135 ..     281     315 ..     246     317 .. 0.71
   3 ?   -1.2   0.0       2.6   2.2e+03      54      76 ..     324     346 ..     291     364 .. 0.68

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 1.2e-10
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee.erpevvfvtlpsstsskdllrellralglelkaerlsseelleal 82 
                                        +++ G  GtGKT+l r ++e+l++  k +   ++ +++v++++ ++  ++ + l ++l+ +++    ss+ l++  
  gi|298675146|ref|YP_003726896.1|  63 NVLIDGNHGTGKTLLTRIVMENLENLTKSDVyTDVYTLHVNCSQTGTKFSIVKTLISDLEKKGNV---SSQTLVNSY 136
                                       57999******************776655559999999**********************98888...555555555 PP

                            AAA_22  83 eqalrarav.......ielliiDEaqhlrs.eealeeL.rslln 117
                                         ++++ ++       +++++ DE + + + +++++++ rs  n
  gi|298675146|ref|YP_003726896.1| 137 DSYIERFFDlvnvldgVVIVVFDELDQI-QeDTVVNDIlRSVEN 179
                                       5555554445555999************.559999999444444 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.5
                            AAA_22  98 DEaqhlrseealeeLrsllnlsrkgvqliLvGtpelrk 135
                                       ++ +++   + ++e +++l+   k+++ +L+  p  +k
  gi|298675146|ref|YP_003726896.1| 281 ENSDYI-DSDFVSEAKEILD--NKNIKKVLIQLPRTDK 315
                                       566777.7888888888899..8888888887666555 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 2.6
                            AAA_22  54 kdl.lrellralglelkaerlsse 76 
                                        ++ + +++++l++++k+ + + +
  gi|298675146|ref|YP_003726896.1| 324 LSFvYPKICEQLERRGKD-TERFD 346
                                       445588999999988888.44444 PP

>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.1   1.1e-10   9.1e-08      15      70 ..     347     402 ..     334     414 .. 0.91

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 1.1e-10
                                       -EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEE CS
                            Cdc6_C  15 evttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtr 70 
                                        +++++vy+ Y+++C++ +++p+   + ++ ++ L+ l ++++ k s Gr +g  +
  gi|298675146|ref|YP_003726896.1| 347 RIRSRDVYNIYEKVCRDNEIEPVGDHRKWESIRHLSELDVIDTIKTSLGRNQGVDT 402
                                       57999*********************************************999876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   2.1e-10   1.8e-07       2     151 ..      38     168 ..      37     179 .. 0.75

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 2.1e-10
                            AAA_16   2 lvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellr...alekdggif.lrgkcdqlesaipysala 73 
                                        ++Re+ le+L++ l ++ +g++  +vl+ G+ G+GK+ l r +++    l+k+++++ +++  + +          
  gi|298675146|ref|YP_003726896.1|  38 IYYREDVLEELKDSLMPALRGETpDNVLIDGNHGTGKTLLTRIVMEnleNLTKSDVYTdVYTLHVNC---------S 105
                                       599*************99999999*****************99998333455555555444444444.........4 PP

                            AAA_16  74 qalareellrqlldeaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqwadea 150
                                       q+ ++ ++++ l +++e+ + +  +++l               ++    + r+++l    +  +++v+D+l++++e+
  gi|298675146|ref|YP_003726896.1| 106 QTGTKFSIVKTLISDLEK-KGNVSSQTLV--------------NSYDSYIERFFDLVNVLDGVVIVVFDELDQIQED 167
                                       444455999999999555.3333333333..............577788888888888878889999*****99987 PP

                            AAA_16 151 s 151
                                       +
  gi|298675146|ref|YP_003726896.1| 168 T 168
                                       6 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.3   3.7e-10   3.2e-07      11     161 ..      52     189 ..      41     198 .. 0.77
   2 ?   -2.4   0.0       4.4   3.8e+03      71     112 ..     217     256 ..     189     292 .. 0.53

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 3.7e-10
                          ATPase_2  11 leeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialr..eesiskldefieeeeekkklekalgia 85 
                                       l   l+ e+ + ++i G  g GKt L + ++enle++ k  +y +        +++ +        k ++ k+l ++
  gi|298675146|ref|YP_003726896.1|  52 LMPALRGETPDNVLIDGNHGTGKTLLTRIVMENLENLTKSDVYTDVYTlhVNCSQTGT--------KFSIVKTLISD 120
                                       4456788999999*****************************9765440033333334........44677888788 PP

                          ATPase_2  86 vpkaeleeilk.eksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnliesltkekhlcvv 161
                                       ++k+    +++ +  +  +++ie++++ ++     +i+++Del ++       +  +v+++l+ +e+    + +cvv
  gi|298675146|ref|YP_003726896.1| 121 LEKKGN--VSSqTLVNSYDSYIERFFDLVNVLDGVVIVVFDELDQIQ------EDTVVNDILRSVENMKTYRGICVV 189
                                       888665..4555889999****************9***********9......368888888888885555555554 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.4
                          ATPase_2  71 eeeekkklekalgiavpkaeleeilkeksklvfkaielllek 112
                                       +++ ++++++ l+ + + a  +e+   +++++ + i++  + 
  gi|298675146|ref|YP_003726896.1| 217 TTYTSNQMKQILSRRAKLAFTDEM--IENTDLSSVINECCKY 256
                                       555555555555555555554444..2334444444444444 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.1e-06   0.00092       3      98 ..      64     169 ..      62     233 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.1e-06
                                       EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-C........ CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfsqlpepaapvse........ 71 
                                       v++ G  G GKT L + +++ +   +   + +  v+ l++ + ++ +++ s+ ++l s+l +++  +s+        
  gi|298675146|ref|YP_003726896.1|  64 VLIDGNHGTGKTLLTRIVMENLENLTKSDV-YTDVYTLHVNCSQTGTKF-SIVKTLISDLEKKGNVSSQtlvnsyds 138
                                       89**********999999999998887776.688888888888888888.888999999888888888889998888 PP

                                       ....CHHHHCCSCCCEEEEEE-STT-SS-TC CS
                             NACHT  72 ....vwavllelperlLlilDglDelvtdlg 98 
                                           ++ ++  l   +  ++D lD++++d  
  gi|298675146|ref|YP_003726896.1| 139 yierFFDLVNVLDGVVIVVFDELDQIQEDTV 169
                                       7777777777777777799*****9998654 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.2   3.4e-06    0.0029       5     105 ..      63     179 ..      59     185 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.4e-06
                                       -EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS........... CS
                             AAA_2   5 silllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG........... 70 
                                       ++l+ g+ g+Gkt+l++ ++e l+ + +k+ +  d  +l    + +++ +++ + ++ +   e++G           
  gi|298675146|ref|YP_003726896.1|  63 NVLIDGNHGTGKTLLTRIVMENLE-NLTKSDVYTDVYTLHV--NCSQTGTKFSIVKTLISDLEKKGnvssqtlvnsy 136
                                       68999*******************.8999999999999999..99999999999999999999999999999***** PP

                                       ..................EEEEETGGG-------------HHHHHHHHHHHH- CS
                             AAA_2  71 ..................ivllDEidKihpkessgadvSregVqrdLLqileg 105
                                                         iv +DE+d i++          + V++d+L+ +e+
  gi|298675146|ref|YP_003726896.1| 137 dsyierffdlvnvldgvvIVVFDELDQIQE----------DTVVNDILRSVEN 179
                                       ******************************..........7888888877775 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.3   7.5e-06    0.0064       2     110 ..      42     159 ..      41     189 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7.5e-06
                                       HHHHHHHHHHHHC...TTTSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCC..CBT..EEEEEEEESXXHHHHHHHX CS
                            NB-ARC   2 eksvekviekLle...kdelqslvvalvGmgGvGKttlakqilnksdeveg..rFd..svawvvvsktdkseeilet 71 
                                       e+ +e++++ L+     + ++   v + G  G GKt l + ++++++++++   +       v  s+t ++ +i++t
  gi|298675146|ref|YP_003726896.1|  42 EDVLEELKDSLMPalrGETPD--NVLIDGNHGTGKTLLTRIVMENLENLTKsdVYTdvYTLHVNCSQTGTKFSIVKT 116
                                       666777777777543155555..999*******************99998866676333456789************ PP

                                       XHHHHHCCCTTSSSS-STTS......HHHHHHHHCCCTTEEEEEE CS
                            NB-ARC  72 ilkeLslseddleekeeves......lkrklvrlLltkrfllvlD 110
                                       ++ +L+++  + ++++ v+s      +  +lv++L    +++v+D
  gi|298675146|ref|YP_003726896.1| 117 LISDLEKK-GNVSSQTLVNSydsyieRFFDLVNVLD-GVVIVVFD 159
                                       *****877.444444444443344445555555553.34555555 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.1e-05    0.0096      17     135 ..      42     168 ..      31     198 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.1e-05
                              TniB  17 keilerL.eeLleypkrkrmpnlllvGdsnnGKtmivekFarlhppekded.aekvpvlvvqappkpdekrlyaaiL 91 
                                       +++le+L ++L+ + + + + n+l+ G+  +GKt + +  +++ ++ +++d  + v  l+v++ ++ ++  + + ++
  gi|298675146|ref|YP_003726896.1|  42 EDVLEELkDSLMPALRGETPDNVLIDGNHGTGKTLLTRIVMENLENLTKSDvYTDVYTLHVNCSQTGTKFSIVKTLI 118
                                       57899995568888999999****************9999988777666552678999******************* PP

                              TniB  92 ealgaplkararvs.kleqqvl.rllrel....kvrvLiiDEihnllags 135
                                         l+++ + + ++  + ++  + r+++ +    +v ++++DE++++ + +
  gi|298675146|ref|YP_003726896.1| 119 SDLEKKGNVSSQTLvNSYDSYIeRFFDLVnvldGVVIVVFDELDQIQEDT 168
                                       *****988776443255554441444444223346789999999998544 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00082       0.7       1      36 [.      64      99 ..      64     107 .. 0.80
   2 ?    4.1   0.1     0.069        59      13      80 ..     112     180 ..     105     184 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00082
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklklkkkdsvys 36
                                      +++ G++g+GK++l++ ++++l++  k++   +vy+
  gi|298675146|ref|YP_003726896.1| 64 VLIDGNHGTGKTLLTRIVMENLENLTKSDVYTDVYT 99
                                      5789*************9999997777777777776 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.069
                      RNA_helicase  13 tlakeLakallkklklkkkdsvys.rnpeddfwdgYt...gqevvvidDfgqvkdeenpsdlaelirlvsst 80 
                                       +++k+L+++l+kk +  ++  v s  +  + f+d  +   g  +vv+d++ q++++     +++++r v++ 
  gi|298675146|ref|YP_003726896.1| 112 SIVKTLISDLEKKGNVSSQTLVNSyDSYIERFFDLVNvldGVVIVVFDELDQIQED---TVVNDILRSVENM 180
                                       5678888888888888887777777777778887766555888999*******988...6777777777664 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1   3.3e-05     0.028      34      90 ..      62     125 ..      52     135 .. 0.79
   2 ?   -0.4   0.1       0.8   6.8e+02      53      81 ..     200     227 ..     191     234 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.3e-05
                             AAA_7  34 kpvllvGptGtGKtviikdllkkld...k....ekylsltinfsaqtsanqlqdiiesklekrr 90 
                                        +vl+ G+ GtGKt++++ ++++l+   k    +++ +l++n+s++ +  ++ +++ s lek+ 
  gi|298675146|ref|YP_003726896.1|  62 DNVLIDGNHGTGKTLLTRIVMENLEnltKsdvyTDVYTLHVNCSQTGTKFSIVKTLISDLEKKG 125
                                       589***********99887777766222322223456789999999999999999999999985 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.8
                             AAA_7  53 llkkldkekylsltinfsaqtsanqlqdi 81 
                                       +l++   + +++++i+f+ +ts + +++i
  gi|298675146|ref|YP_003726896.1| 200 YLNRKTLDVFNPVKIKFTTYTSNQ-MKQI 227
                                       566666688999999999998755.4444 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.4   2.6e-05     0.022      92     216 ..      55     196 ..      42     222 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.6e-05
                        KAP_NTPase  92 llrakklkalkikgkiklrkacaiplvlilevalflliegasllavls............raaklkeeaplkklqte 156
                                        lr++++  + i+g  +++k+ ++ +v+  +    +l + ++ ++v++              +k + ++  kk   +
  gi|298675146|ref|YP_003726896.1|  55 ALRGETPDNVLIDGNHGTGKTLLTRIVMENL---ENLTKSDVYTDVYTlhvncsqtgtkfSIVKTLISDLEKKGNVS 128
                                       5666677777777777777777777664443...3445666677777788888888888855555555555555555 PP

                        KAP_NTPase 157 veelladmektLda.......lqkrlVvviDdLDrceteevlq.lleavkllfslkpvvfilavDphv 216
                                        ++l ++ ++++++       l+  ++vv D+LD ++ ++v++ +l+ v+ +   +++ ++ ++++h+
  gi|298675146|ref|YP_003726896.1| 129 SQTLVNSYDSYIERffdlvnvLDGVVIVVFDELDQIQEDTVVNdILRSVENMKTYRGICVVGITNDHR 196
                                       555555555555555557888999**************998754999999999999999999999986 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   5.9e-05      0.05       9      50 ..      47      91 ..      40     108 .. 0.69
   2 ?   -0.5   0.0       1.3   1.2e+03      33      62 ..     111     139 ..     106     182 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.9e-05
                                      HHHHHHHHCH....TEEEEEEESTTSSHHHHHHHHHHHTT------ CS
                              TsaE  9 algkklakal....gdvilLeGdLGaGKTtlvrglakalgveevkS 50
                                      +l  +l  al     d +l++G+ G+GKT l+r ++++l+    kS
  gi|298675146|ref|YP_003726896.1| 47 ELKDSLMPALrgetPDNVLIDGNHGTGKTLLTRIVMENLEN-LTKS 91
                                      45555555555433456********************9964.3333 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHTT--.----TTTTSEEEEEE. CS
                              TsaE  33 Ttlvrglakalgve.evkSPTFtlveeYele 62 
                                         +v+ l++ l+ + +v+S T  lv++Y++ 
  gi|298675146|ref|YP_003726896.1| 111 FSIVKTLISDLEKKgNVSSQT--LVNSYDSY 139
                                       567899999999989999986..88998764 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.3   0.00021      0.18      15     150 ..      62     181 ..      48     189 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00021
                                       CEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEE.ETTSSHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                              DEAD  15 gdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlli.iggvaardq 90 
                                       ++vl+ ++ G+GKTl   i +  ++ e + ++      v  ++  + qt ++++ +k  i+    l   g+v+    
  gi|298675146|ref|YP_003726896.1|  62 DNVLIDGNHGTGKTLLTRIVME-NL-E-NLTKSDVYTDVYTLHVNCSQTGTKFSIVKTLIS---DLEkKGNVS---- 128
                                       5778888888888887666554.33.2.122222333345555556666666655555322...111012222.... PP

                                       HHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  91 lskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlp 150
                                        ++l n++d ++   +r++dl++     l+ v ++V+DE d+++++   ++i r +++++
  gi|298675146|ref|YP_003726896.1| 129 SQTLVNSYDSYI---ERFFDLVN----VLDGVVIVVFDELDQIQEDTVVNDILRSVENMK 181
                                       233324445554...89999987....59*****************88888888888874 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.3e-05     0.037      28      60 ..      56      88 ..      36      95 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.3e-05
                            RuvB_N 28 kreealdhvllyGpPGlGkttlakiiakelgvk 60
                                       r+e+ d vl+ G  G Gkt l++i+ ++l+  
  gi|298675146|ref|YP_003726896.1| 56 LRGETPDNVLIDGNHGTGKTLLTRIVMENLENL 88
                                      599************************999865 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.3e-05     0.045      20      51 ..      59      90 ..      38     116 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.3e-05
                                      TSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS CS
                   Sigma54_activat 20 ktdlsvlitGesGtGKellaraiheaskrkek 51
                                      +t+ +vli G+ GtGK+ll r + e+ ++ +k
  gi|298675146|ref|YP_003726896.1| 59 ETPDNVLIDGNHGTGKTLLTRIVMENLENLTK 90
                                      45689****************99984443322 PP

>> TIP49_C  TIP49 AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   9.5e-05     0.081      25      63 ..     259     297 ..     250     299 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.5e-05
                           TIP49_C  25 gtetSLRYaiqLltpasilakkrkkkevevedveeveeL 63 
                                       + + S RYa+ Ll  +  la +++++ ++ + v e++e+
  gi|298675146|ref|YP_003726896.1| 259 QDRNSIRYALDLLLEVGDLAYRENSDYIDSDFVSEAKEI 297
                                       5689********************************987 PP

>> Ribosomal_L4  Ribosomal protein L4/L1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.29   2.4e+02      66      89 ..     181     204 ..     114     245 .. 0.75
   2 ?   10.2   0.0    0.0005      0.43      91     160 ..     260     327 ..     174     338 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.29
                                       TSTT---SS---S.EEHHHHHHHH CS
                      Ribosomal_L4  66 iargGgvahgpkperdystklnkK 89 
                                        ++ G  + g++ +++ys+ ln+K
  gi|298675146|ref|YP_003726896.1| 181 KTYRGICVVGITNDHRYSYYLNRK 204
                                       445566666666666777777766 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0005
                                       HHHHHHHHHHHHHHTT-EEEES---.-SS--HHHHHHHHHHTT-TTSSEEEEESSSSCHHHHHHTT-TTE CS
                      Ribosomal_L4  91 rrlAlrsaLsakakqglllvvdnlepleesktkelvellkklglksksvLivvsekdenlvlaarnlpgv 160
                                        r  +r aL   ++ g+l  ++n + +++   +e++e+l+++++  k+vLi ++++d+ ++l+   l+ v
  gi|298675146|ref|YP_003726896.1| 260 DRNSIRYALDLLLEVGDLAYRENSDYIDSDFVSEAKEILDNKNI--KKVLIQLPRTDKMILLSLSYLSFV 327
                                       5778999***************987899999*************..**************9998877665 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00033      0.28      29      78 ..      37      86 ..      21      95 .. 0.83
   2 ?   -2.2   0.1       2.1   1.8e+03      66     116 ..     110     161 ..     104     177 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00033
                            DUF815 29 dLvgidkqkealventeqfleglpannvLLwGarGtGKSslvkallneya 78
                                      ++   ++  e+l++     l+g++  nvL+ G+ GtGK  l + ++++++
  gi|298675146|ref|YP_003726896.1| 37 NIYYREDVLEELKDSLMPALRGETPDNVLIDGNHGTGKTLLTRIVMENLE 86
                                      55556667778888888899*********************999988765 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.1
                            DUF815  66 KSslvkallneyaeeg....LrlievekedlkelpklvellrerperfilfvDDL 116
                                       K s+vk+l+++++++g      l++   + ++ + +lv++l      +i++ D L
  gi|298675146|ref|YP_003726896.1| 110 KFSIVKTLISDLEKKGnvssQTLVNSYDSYIERFFDLVNVLD---GVVIVVFDEL 161
                                       778889988888888876656666666666666555555554...4466666666 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.4    0.0013       1.1      11     136 ..      62     190 ..      55     199 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0013
                            AAA_19  11 kvllvtaGpGtGKTrvlkhivallvelggvkp.....eeillvaftgrAakelrerlaalgaeatTiHrlalldfdd 82 
                                       +++l+ +  GtGKT +++ +++ l++l++ ++        + ++ tg   +        ++  ++ + + +++  ++
  gi|298675146|ref|YP_003726896.1|  62 DNVLIDGNHGTGKTLLTRIVMENLENLTKSDVytdvyTLHVNCSQTGTKFSI-------VKTLISDLEKKGNVSSQT 131
                                       67899999***************99999776533322222223333333333.......334444444444444444 PP

                            AAA_19  83 lltealelle.eaeeekklqeee.llivDEfqdvd..elqyrLlkallgekkk..lllvG 136
                                       l++   +++e   +  + l ++  +++ DE  +++   + + +l+ + + k++  +++vG
  gi|298675146|ref|YP_003726896.1| 132 LVNSYDSYIErFFDLVNVL-DGVvIVVFDELDQIQedTVVNDILRSVENMKTYrgICVVG 190
                                       4444444444222233344.6665677788888876566777888877555334577777 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.2    0.0012         1       1      25 [.      64     101 ..      64     189 .. 0.76
   2 ?    1.0   2.4      0.69   5.9e+02      24      70 ..     256     309 ..     226     370 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0012
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf............g 25 
                                       +l+ G +G+GKt l++ + + l ++            +
  gi|298675146|ref|YP_003726896.1|  64 VLIDGNHGTGKTLLTRIVMENLeNLtksdvytdvytlH 101
                                       6889****************995559955555544443 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.69
                            AAA_18  24 f...gvnlrdvakenglllevdpealdeskrldedkldklldaleenss.....a 70 
                                       +    +n++ +a +  l+ ++ ++  ++s+ +d d++ ++ ++l++ +       
  gi|298675146|ref|YP_003726896.1| 256 YtlqDRNSIRYALDLLLEVGDLAY-RENSDYIDSDFVSEAKEILDNKNIkkvliQ 309
                                       366677888888888888888888.888888888888888888888776333331 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 3102.51
//
Query:       gi|298675147|ref|YP_003726897.1|  [L=73]
Description: hypothetical protein Metev_1229 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.092   12.6   1.4       0.38   10.6   0.4    2.0  2  HTH_30    PucR C-terminal helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0     0.021   3.8e+02      24      48 ..       9      33 ..       6      37 .. 0.79
   2 ?   10.6   0.4   2.1e-05      0.38      23      40 ..      46      63 ..      43      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.021
                                      S-HHHHHHHHHHHHHHHS--TTSHH CS
                            HTH_30 24 vHrnTlryRLrrieellgldlddpd 48
                                      + r T + R++  ++l+++  + + 
  gi|298675147|ref|YP_003726897.1|  9 IKRKTKKSRVNNKKQLTKIKTSKTK 33
                                      6788999999999999998876665 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 2.1e-05
                                      TS-HHHHHHHHHHHHHHH CS
                            HTH_30 23 hvHrnTlryRLrrieell 40
                                      + H n++++R+++i ++ 
  gi|298675147|ref|YP_003726897.1| 46 YHHINSVTKRIKKITQII 63
                                      77*************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2628  (0.146578); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 552.79
//
Query:       gi|298675148|ref|YP_003726898.1|  [L=803]
Description: hypothetical protein Metev_1230 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.5e-55  178.5  37.4    1.2e-05   25.0   0.0   19.2 19  TPR_2            Tetratricopeptide repeat
    9.1e-47  155.1  55.9    1.3e-05   24.8   0.0   19.2 20  TPR_1            Tetratricopeptide repeat
    4.6e-45  148.1  51.2    0.00013   21.9   0.0   18.9 19  TPR_8            Tetratricopeptide repeat
    2.1e-38  127.7   6.7    0.00051   20.6   0.0   15.6 17  TPR_14           Tetratricopeptide repeat
    2.9e-38  130.2  22.6    1.1e-05   25.9   0.1   12.8 15  TPR_19           Tetratricopeptide repeat
    2.5e-34  117.6   0.0     0.0005   20.7   0.0   10.7 10  TPR_16           Tetratricopeptide repeat
    2.8e-29  101.2  16.3     0.0028   17.9   0.1   12.9 12  TPR_12           Tetratricopeptide repeat
    1.5e-25   89.1   0.0    0.00056   20.0   0.0   10.5 11  TPR_9            Tetratricopeptide repeat
    4.6e-24   83.8  34.7     0.0011   18.6   0.2   14.7 16  TPR_11           TPR repeat
    6.2e-24   84.8  18.3    0.00021   20.3   0.0    9.3  9  NARP1            NMDA receptor-regulated protein 1
    8.2e-24   83.6  21.5    0.00013   22.1   0.1    9.0 10  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    1.2e-19   68.8  10.2      0.005   16.8   0.0   12.7 12  TPR_7            Tetratricopeptide repeat
    5.2e-17   62.0  14.2     0.0041   16.4   0.1    8.1  8  TPR_15           Tetratricopeptide repeat
    5.4e-16   57.7  29.2       0.21   12.1   0.1   15.1 15  TPR_17           Tetratricopeptide repeat
    1.7e-15   56.5   8.5        1.1   10.0   0.0   13.2 12  TPR_6            Tetratricopeptide repeat
    5.4e-10   39.3  23.4     0.0009   19.2   0.2    7.7  7  SRP_TPR_like     Putative TPR-like repeat
    6.4e-10   39.0  12.2      0.067   13.3   0.0   10.9 12  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
    1.1e-09   38.1   0.0      0.035   13.5   0.0    5.4  5  TPR_MalT         MalT-like TPR region
    3.7e-08   33.5   7.6        2.6    8.1   0.0    8.5  8  DUF3856          Domain of Unknown Function (DUF3856)
    1.1e-06   28.3   9.8        5.7    7.0   0.0   10.4 12  TPR_10           Tetratricopeptide repeat
      5e-05   23.1   1.3       0.55   10.1   0.0    5.4  5  ATP13            Mitochondrial ATPase expression
    0.00023   20.3  14.9          1    8.3   0.3    5.4  6  ChAPs            ChAPs (Chs5p-Arf1p-binding proteins)
    0.00035   20.3   8.0       0.24   11.1   0.0    4.9  5  TPR_21           Tetratricopeptide repeat-like domain
    0.00064   20.0  17.0         11    6.5   0.0    8.1  9  TPR_20           Tetratricopeptide repeat
    0.00065   19.7   0.0        5.5    6.9   0.0    4.0  3  Wzy_C_2          Virulence factor membrane-bound polymerase, 
     0.0011   19.4   0.0        5.8    7.8   0.1    5.1  3  TPR_4            Tetratricopeptide repeat
     0.0014   18.7  10.9         62    4.2   0.1    9.2  9  PPR              PPR repeat
      0.003   18.0   0.3        4.6    7.7   0.1    4.3  4  BTAD             Bacterial transcriptional activator domain
     0.0092   16.4   7.0         30    5.1   0.1    6.1  5  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
  ------ inclusion threshold ------
      0.014   15.4  10.7          7    6.7   0.0    6.8  7  DUF627           Protein of unknown function (DUF627)
      0.025   14.8   0.3         29    4.9   0.0    4.9  4  TPR_5            Tetratrico peptide repeat
      0.028   14.0   0.1         62    3.3   0.0    5.7  6  HTH_Bact         Helix-turn-helix bacterial domain
      0.083   12.7   0.0        9.8    6.1   0.0    2.6  2  PDEase_I_N       3'5'-cyclic nucleotide phosphodiesterase N-t
       0.11   12.6  14.1         13    6.0   0.2    8.0  7  MIT              MIT (microtubule interacting and transport) 
       0.11   12.4   1.0       0.47   10.4   0.2    2.5  1  PUB              PUB domain
       0.32   10.5   9.6        2.2    7.8   1.3    4.0  5  Hormone_recep    Ligand-binding domain of nuclear hormone rec
        4.4    7.2  31.2       0.76    9.6   1.0    8.0  8  Clathrin         Region in Clathrin and VPS


Domain annotation for each model (and alignments):
>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.15        72       3      29 ..      72      98 ..      70     102 .. 0.87
   2 !   14.4   0.2   6.2e-05      0.03       3      31 ..     105     133 ..     104     136 .. 0.83
   3 !   10.9   0.3   0.00082       0.4       6      31 ..     141     166 ..     137     168 .. 0.90
   4 ?    6.7   0.1     0.018       8.6       3      31 ..     174     202 ..     172     203 .. 0.87
   5 !   10.0   0.0    0.0016      0.77       2      34 .]     207     239 ..     206     239 .. 0.94
   6 ?   -1.4   0.0       7.2   3.5e+03      11      22 ..     250     261 ..     248     264 .. 0.81
   7 ?    7.0   0.2     0.015       7.1       4      32 ..     277     305 ..     274     305 .. 0.93
   8 !   13.7   0.0    0.0001     0.051       8      33 ..     315     340 ..     312     341 .. 0.92
   9 !   12.0   0.1   0.00037      0.18       4      32 ..     344     372 ..     341     374 .. 0.90
  10 !   25.0   0.0   2.5e-08   1.2e-05       3      34 .]     377     408 ..     375     408 .. 0.95
  11 ?    6.0   0.0      0.03        15      10      34 .]     418     442 ..     416     442 .. 0.91
  12 ?    3.1   0.0      0.27   1.3e+02       6      33 ..     448     475 ..     443     476 .. 0.81
  13 ?    3.3   0.0      0.22   1.1e+02       2      34 .]     478     510 ..     477     510 .. 0.92
  14 !   15.3   0.0   3.4e-05     0.016       1      28 [.     511     538 ..     511     541 .. 0.95
  15 !   14.0   0.0   8.6e-05     0.042       6      33 ..     549     576 ..     545     577 .. 0.88
  16 ?    6.8   0.0     0.017       8.3      10      24 ..     620     634 ..     614     636 .. 0.90
  17 ?    4.3   0.0      0.11        53      16      34 .]     701     719 ..     699     719 .. 0.93
  18 !   14.3   0.0     7e-05     0.034       2      34 .]     721     753 ..     720     753 .. 0.92
  19 !   15.1   0.0   3.8e-05     0.018       1      34 []     754     787 ..     754     787 .. 0.96

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.15
                             TPR_2  3 alynlGlayyklgdyeeAleafekAle 29
                                       +y+++ ++  +g++   le+++  ++
  gi|298675148|ref|YP_003726898.1| 72 TWYYRAFIASLMGNHVTSLEYLNNIVK 98
                                      6******************99987776 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 6.2e-05
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleld 31 
                                       ++   +  +   g+y+eA+e+++kAl+l 
  gi|298675148|ref|YP_003726898.1| 105 YWLLKAANLDFIGHYKEAVECCNKALKLK 133
                                       566777777778***************96 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00082
                             TPR_2   6 nlGlayyklgdyeeAleafekAleld 31 
                                         G+++ k+g +++A+ a+ kAle d
  gi|298675148|ref|YP_003726898.1| 141 KKGELLKKQGLFKKARIAYGKALEND 166
                                       5799*******************976 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.018
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleld 31 
                                       +l     ay   g+ +eAl+  ++A  l+
  gi|298675148|ref|YP_003726898.1| 174 LLKDYSHAYQMEGKVNEALKVIKRAKNLN 202
                                       5667789******************8876 PP

  == domain 5  score: 10.0 bits;  conditional E-value: 0.0016
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       e l+++++ ++++g+ +eA+e  +  le++P++
  gi|298675148|ref|YP_003726898.1| 207 ETLHMQADMLAESGHRKEAVEVINMILEINPDD 239
                                       578999*************************97 PP

  == domain 6  score: -1.4 bits;  conditional E-value: 7.2
                             TPR_2  11 yyklgdyeeAle 22 
                                       ++ +++y+eA++
  gi|298675148|ref|YP_003726898.1| 250 LLIMKRYKEAEN 261
                                       66789*****86 PP

  == domain 7  score: 7.0 bits;  conditional E-value: 0.015
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleldP 32 
                                       + + ++++   g y eA ea ++A +l+P
  gi|298675148|ref|YP_003726898.1| 277 WLYKAKILSTYGYYTEADEAINEAEKLNP 305
                                       88899999999*****************9 PP

  == domain 8  score: 13.7 bits;  conditional E-value: 0.0001
                             TPR_2   8 GlayyklgdyeeAleafekAleldPn 33 
                                       ++ y +lg+y++A++ + +Ale d++
  gi|298675148|ref|YP_003726898.1| 315 ANHYSNLGEYDKAIDICSRALEVDED 340
                                       899*******************9875 PP

  == domain 9  score: 12.0 bits;  conditional E-value: 0.00037
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleldP 32 
                                       +  + +ay+k+gd++ Al++ + A+ l+ 
  gi|298675148|ref|YP_003726898.1| 344 YSSRSEAYAKKGDLKNALRDINNAINLND 372
                                       778999*********************96 PP

  == domain 10  score: 25.0 bits;  conditional E-value: 2.5e-08
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                        ++++G+++++lgd+  Ale f+kAl++d n+
  gi|298675148|ref|YP_003726898.1| 377 FWNQRGEILWALGDLRGALESFRKALKIDDND 408
                                       69***************************986 PP

  == domain 11  score: 6.0 bits;  conditional E-value: 0.03
                             TPR_2  10 ayyklgdyeeAleafekAleldPnn 34 
                                       ++ +lgd+ eA+++++k l+ +P++
  gi|298675148|ref|YP_003726898.1| 418 LLHNLGDHSEAVNLMDKYLSNYPED 442
                                       6889****************99986 PP

  == domain 12  score: 3.1 bits;  conditional E-value: 0.27
                             TPR_2   6 nlGlayyklgdyeeAleafekAleldPn 33 
                                         G + +k g+ ee l++ +kAl+l +n
  gi|298675148|ref|YP_003726898.1| 448 LKGSSKAKTGNCEEGLKWVNKALKLKEN 475
                                       5667778889999************987 PP

  == domain 13  score: 3.3 bits;  conditional E-value: 0.22
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       +a+     +y ++g++e  l+a e  l +dP+n
  gi|298675148|ref|YP_003726898.1| 478 DAWDIKSAIYTEMGKHEASLDAAEYGLFYDPEN 510
                                       78999999*****************99999987 PP

  == domain 14  score: 15.3 bits;  conditional E-value: 3.4e-05
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAl 28 
                                       +e+ y  G+ +++l++yeeA ++ ++Al
  gi|298675148|ref|YP_003726898.1| 511 PELMYKKGCTLINLQRYEEAFDCINQAL 538
                                       6889***********************8 PP

  == domain 15  score: 14.0 bits;  conditional E-value: 8.6e-05
                             TPR_2   6 nlGlayyklgdyeeAleafekAleldPn 33 
                                       n +++   lg+ e+A++ +++A+el+P+
  gi|298675148|ref|YP_003726898.1| 549 NKARLESLLGKIEDAVKTYNRAIELEPR 576
                                       77888889*******************7 PP

  == domain 16  score: 6.8 bits;  conditional E-value: 0.017
                             TPR_2  10 ayyklgdyeeAleaf 24 
                                       + +kl++y+eAle+ 
  gi|298675148|ref|YP_003726898.1| 620 CFIKLNRYDEALECI 634
                                       7899*********96 PP

  == domain 17  score: 4.3 bits;  conditional E-value: 0.11
                             TPR_2  16 dyeeAleafekAleldPnn 34 
                                       ++++Ale +++ l+++P++
  gi|298675148|ref|YP_003726898.1| 701 NPKDALESLNRTLSINPDD 719
                                       6899*************97 PP

  == domain 18  score: 14.3 bits;  conditional E-value: 7e-05
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       +al + ++++y+l dy++ l+  +kAle++ +n
  gi|298675148|ref|YP_003726898.1| 721 DALRMKADLHYNLSDYKKSLKTIDKALEIEGDN 753
                                       68999***********************98765 PP

  == domain 19  score: 15.1 bits;  conditional E-value: 3.8e-05
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a+++ ++ +++  lg+  +Ale +ekA  l P++
  gi|298675148|ref|YP_003726898.1| 754 ARLWLMRSYVLDSLGKTSDALESLEKAHNLSPDD 787
                                       689*****************************97 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.032        15       3      29 ..      72      98 ..      71     102 .. 0.88
   2 !   15.7   0.4     2e-05    0.0095      14      31 ..     116     133 ..     104     136 .. 0.80
   3 !    9.8   0.8    0.0014       0.7       7      31 ..     142     166 ..     139     167 .. 0.93
   4 ?    3.0   0.1       0.2        99       9      30 ..     180     201 ..     180     202 .. 0.87
   5 ?    3.0   0.0       0.2        96      15      34 .]     220     239 ..     208     239 .. 0.83
   6 ?   -1.1   0.1         4     2e+03      11      21 ..     250     260 ..     248     261 .. 0.84
   7 ?    0.7   0.4       1.1   5.3e+02       4      32 ..     277     305 ..     275     305 .. 0.86
   8 !   22.7   0.0   1.2e-07   5.9e-05       7      33 ..     314     340 ..     312     341 .. 0.94
   9 !    9.7   0.1    0.0015      0.74      10      31 ..     350     371 ..     342     373 .. 0.92
  10 !   24.8   0.0   2.7e-08   1.3e-05       3      34 .]     377     408 ..     375     408 .. 0.94
  11 ?   -0.5   0.0       2.6   1.2e+03      10      22 ..     418     430 ..     417     442 .. 0.78
  12 ?    1.6   0.0      0.55   2.7e+02       5      34 .]     447     476 ..     443     476 .. 0.77
  13 ?    2.4   0.1      0.32   1.6e+02      10      34 .]     486     510 ..     485     510 .. 0.83
  14 !   13.2   0.1   0.00013     0.062       3      28 ..     513     538 ..     511     543 .. 0.91
  15 !   19.8   0.0     1e-06   0.00049       4      34 .]     547     577 ..     544     577 .. 0.91
  16 ?   -1.9   0.0       7.1   3.4e+03      10      22 ..     586     598 ..     585     599 .. 0.83
  17 !   16.6   0.1     1e-05     0.005       2      24 ..     612     634 ..     611     636 .. 0.91
  18 ?    7.1   0.0      0.01       4.9      16      34 .]     701     719 ..     700     719 .. 0.93
  19 !   13.0   0.1   0.00014     0.068       2      34 .]     721     753 ..     720     753 .. 0.91
  20 !    9.1   0.0    0.0025       1.2      10      34 .]     763     787 ..     754     787 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.032
                                      HHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_1  3 alynlGnayfklgkydeAleyyekALe 29
                                      ++y ++ +   +g++   ley +  ++
  gi|298675148|ref|YP_003726898.1| 72 TWYYRAFIASLMGNHVTSLEYLNNIVK 98
                                      7********************987666 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 2e-05
                                       TT-HHHHHHHHHHHHHHS CS
                             TPR_1  14 lgkydeAleyyekALeln 31 
                                        g y+eA+e+++kAL+l 
  gi|298675148|ref|YP_003726898.1| 116 IGHYKEAVECCNKALKLK 133
                                       689*************96 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0014
                                       HHHHHHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1   7 lGnayfklgkydeAleyyekALeln 31 
                                       +G ++ k+g +++A  +y kALe +
  gi|298675148|ref|YP_003726898.1| 142 KGELLKKQGLFKKARIAYGKALEND 166
                                       799*******************965 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.2
                                       HHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   9 nayfklgkydeAleyyekALel 30 
                                       +ay+  gk +eAl+  ++A  l
  gi|298675148|ref|YP_003726898.1| 180 HAYQMEGKVNEALKVIKRAKNL 201
                                       69************99999665 PP

  == domain 5  score: 3.0 bits;  conditional E-value: 0.2
                                       T-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  15 gkydeAleyyekALelnPnn 34 
                                       g  +eA+e  +  Le+nP++
  gi|298675148|ref|YP_003726898.1| 220 GHRKEAVEVINMILEINPDD 239
                                       66689*************96 PP

  == domain 6  score: -1.1 bits;  conditional E-value: 4
                                       HHHTT-HHHHH CS
                             TPR_1  11 yfklgkydeAl 21 
                                       ++ +++y+eA+
  gi|298675148|ref|YP_003726898.1| 250 LLIMKRYKEAE 260
                                       6789******7 PP

  == domain 7  score: 0.7 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   4 lynlGnayfklgkydeAleyyekALelnP 32 
                                       +  ++ ++   g y eA e+ ++A +lnP
  gi|298675148|ref|YP_003726898.1| 277 WLYKAKILSTYGYYTEADEAINEAEKLNP 305
                                       777788888888899*************9 PP

  == domain 8  score: 22.7 bits;  conditional E-value: 1.2e-07
                                       HHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   7 lGnayfklgkydeAleyyekALelnPn 33 
                                       ++n y +lg+yd+A++ +++ALe++++
  gi|298675148|ref|YP_003726898.1| 314 KANHYSNLGEYDKAIDICSRALEVDED 340
                                       6899********************986 PP

  == domain 9  score: 9.7 bits;  conditional E-value: 0.0015
                                       HHHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1  10 ayfklgkydeAleyyekALeln 31 
                                       ay k+g+++ Al + + A+ ln
  gi|298675148|ref|YP_003726898.1| 350 AYAKKGDLKNALRDINNAINLN 371
                                       8******************999 PP

  == domain 10  score: 24.8 bits;  conditional E-value: 2.7e-08
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                        ++++G ++  lg++  Ale ++kAL+++ n+
  gi|298675148|ref|YP_003726898.1| 377 FWNQRGEILWALGDLRGALESFRKALKIDDND 408
                                       6****************************886 PP

  == domain 11  score: -0.5 bits;  conditional E-value: 2.6
                                       HHHHTT-HHHHHH CS
                             TPR_1  10 ayfklgkydeAle 22 
                                       ++++lg++ eA+ 
  gi|298675148|ref|YP_003726898.1| 418 LLHNLGDHSEAVN 430
                                       5789*******86 PP

  == domain 12  score: 1.6 bits;  conditional E-value: 0.55
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   5 ynlGnayfklgkydeAleyyekALelnPnn 34 
                                         +G    k g+ +e l+  +kAL+l +n+
  gi|298675148|ref|YP_003726898.1| 447 GLKGSSKAKTGNCEEGLKWVNKALKLKENY 476
                                       55666667777778889999******9997 PP

  == domain 13  score: 2.4 bits;  conditional E-value: 0.32
                                       HHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  10 ayfklgkydeAleyyekALelnPnn 34 
                                       +y ++gk++  l++ e  L  +P+n
  gi|298675148|ref|YP_003726898.1| 486 IYTEMGKHEASLDAAEYGLFYDPEN 510
                                       8***********9988777777765 PP

  == domain 14  score: 13.2 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHHHTT-HHHHHHHHHHHH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekAL 28 
                                         y +G ++ +l++y+eA ++ ++AL
  gi|298675148|ref|YP_003726898.1| 513 LMYKKGCTLINLQRYEEAFDCINQAL 538
                                       6799*********************9 PP

  == domain 15  score: 19.8 bits;  conditional E-value: 1e-06
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   4 lynlGnayfklgkydeAleyyekALelnPnn 34 
                                       l n++ +   lgk ++A++ y++A+el+P +
  gi|298675148|ref|YP_003726898.1| 547 LVNKARLESLLGKIEDAVKTYNRAIELEPRY 577
                                       679999999********************76 PP

  == domain 16  score: -1.9 bits;  conditional E-value: 7.1
                                       HHHHTT-HHHHHH CS
                             TPR_1  10 ayfklgkydeAle 22 
                                       ++  l++++eA +
  gi|298675148|ref|YP_003726898.1| 586 CLITLERFEEAMD 598
                                       777899*****75 PP

  == domain 17  score: 16.6 bits;  conditional E-value: 1e-05
                                       HHHHHHHHHHHHTT-HHHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyy 24 
                                       + + n+ +++ kl++ydeAle+ 
  gi|298675148|ref|YP_003726898.1| 612 EFWMNKIMCFIKLNRYDEALECI 634
                                       57*******************95 PP

  == domain 18  score: 7.1 bits;  conditional E-value: 0.01
                                       -HHHHHHHHHHHHHHSTTH CS
                             TPR_1  16 kydeAleyyekALelnPnn 34 
                                       ++++Ale  ++ L++nP++
  gi|298675148|ref|YP_003726898.1| 701 NPKDALESLNRTLSINPDD 719
                                       789**************96 PP

  == domain 19  score: 13.0 bits;  conditional E-value: 0.00014
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       +al  ++ ++++l +y++ l+  +kALe++ +n
  gi|298675148|ref|YP_003726898.1| 721 DALRMKADLHYNLSDYKKSLKTIDKALEIEGDN 753
                                       78888999*********************8765 PP

  == domain 20  score: 9.1 bits;  conditional E-value: 0.0025
                                       HHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  10 ayfklgkydeAleyyekALelnPnn 34 
                                       ++ +lgk  +Ale  ekA  l P++
  gi|298675148|ref|YP_003726898.1| 763 VLDSLGKTSDALESLEKAHNLSPDD 787
                                       6789*******************96 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.2   1.3e-05    0.0064       3      33 ..     105     135 ..     104     136 .. 0.92
   2 !    9.4   0.6    0.0026       1.3       5      31 ..     140     166 ..     137     168 .. 0.91
   3 ?    0.8   0.1       1.5   7.3e+02       8      31 ..     179     202 ..     177     205 .. 0.86
   4 ?    6.2   0.0      0.03        14       3      34 .]     208     239 ..     207     239 .. 0.93
   5 ?    2.1   0.1       0.6   2.9e+02       2      21 ..     241     260 ..     240     262 .. 0.89
   6 ?    6.7   0.2     0.019       9.4       7      32 ..     280     305 ..     277     306 .. 0.91
   7 !   13.1   0.1   0.00017     0.083       8      33 ..     315     340 ..     308     341 .. 0.89
   8 !    7.8   0.2    0.0086       4.1       4      31 ..     344     371 ..     341     373 .. 0.81
   9 !   21.9   0.0   2.6e-07   0.00013       3      33 ..     377     407 ..     375     408 .. 0.93
  10 !    8.3   0.0    0.0062         3       9      33 ..     417     441 ..     413     442 .. 0.90
  11 ?    6.5   0.1     0.022        11       2      33 ..     444     475 ..     443     476 .. 0.93
  12 ?    2.4   0.0      0.49   2.4e+02       2      22 ..     478     498 ..     477     508 .. 0.86
  13 !   17.1   0.0   9.4e-06    0.0045       2      28 ..     512     538 ..     511     540 .. 0.94
  14 !   17.7   0.0   5.7e-06    0.0028       2      33 ..     545     576 ..     544     577 .. 0.93
  15 ?    1.9   0.0       0.7   3.4e+02       2      25 ..     578     601 ..     577     603 .. 0.81
  16 ?    4.1   0.0      0.13        64       6      24 ..     616     634 ..     611     635 .. 0.79
  17 ?   -1.2   0.0       6.6   3.2e+03      18      34 .]     703     719 ..     701     719 .. 0.86
  18 !   11.0   0.2   0.00083       0.4       6      33 ..     725     752 ..     720     753 .. 0.90
  19 !   14.4   0.0     7e-05     0.034       1      34 []     754     787 ..     754     787 .. 0.96

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.3e-05
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       ++++++  ++  g y+eA+e+++kal+l+ d
  gi|298675148|ref|YP_003726898.1| 105 YWLLKAANLDFIGHYKEAVECCNKALKLKND 135
                                       7999999999******************986 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0026
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   5 ynlgsiylklgdyeeAkeyyekaleld 31 
                                        ++g +++k+g +++A  +y kale d
  gi|298675148|ref|YP_003726898.1| 140 IKKGELLKKQGLFKKARIAYGKALEND 166
                                       579*********************976 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 1.5
                                       HHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   8 gsiylklgdyeeAkeyyekaleld 31 
                                       +++y+  g+ +eA +++++a  l+
  gi|298675148|ref|YP_003726898.1| 179 SHAYQMEGKVNEALKVIKRAKNLN 202
                                       68899999**********998876 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.03
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                        +++ ++ + + g  +eA+e+++  le++pd+
  gi|298675148|ref|YP_003726898.1| 208 TLHMQADMLAESGHRKEAVEVINMILEINPDD 239
                                       689999************************96 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.6
                                       CHHHHHHHHHHHTT-HHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAk 21 
                                       ea +++  ++l +++y+eA+
  gi|298675148|ref|YP_003726898.1| 241 EAAFMKLELLLIMKRYKEAE 260
                                       6779999************7 PP

  == domain 6  score: 6.7 bits;  conditional E-value: 0.019
                                       HHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   7 lgsiylklgdyeeAkeyyekaleldp 32 
                                       +++i+++ g y eA e++++a +l+p
  gi|298675148|ref|YP_003726898.1| 280 KAKILSTYGYYTEADEAINEAEKLNP 305
                                       67888999*****************9 PP

  == domain 7  score: 13.1 bits;  conditional E-value: 0.00017
                                       HHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   8 gsiylklgdyeeAkeyyekaleldpd 33 
                                       ++ y++lg+y++A+  + +ale d+d
  gi|298675148|ref|YP_003726898.1| 315 ANHYSNLGEYDKAIDICSRALEVDED 340
                                       6669*******************986 PP

  == domain 8  score: 7.8 bits;  conditional E-value: 0.0086
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleld 31 
                                       y   + +y k+gd+++A   ++ a+ l+
  gi|298675148|ref|YP_003726898.1| 344 YSSRSEAYAKKGDLKNALRDINNAINLN 371
                                       5567789999999999999999999887 PP

  == domain 9  score: 21.9 bits;  conditional E-value: 2.6e-07
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                        +++ g i++ lgd+  A e+++kal++d +
  gi|298675148|ref|YP_003726898.1| 377 FWNQRGEILWALGDLRGALESFRKALKIDDN 407
                                       79**************************987 PP

  == domain 10  score: 8.3 bits;  conditional E-value: 0.0062
                                       HHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   9 siylklgdyeeAkeyyekaleldpd 33 
                                       +++++lgd+ eA+  + k+l+  p+
  gi|298675148|ref|YP_003726898.1| 417 KLLHNLGDHSEAVNLMDKYLSNYPE 441
                                       6899****************98887 PP

  == domain 11  score: 6.5 bits;  conditional E-value: 0.022
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       e++ ++gs   k+g+ ee  ++ +kal+l+++
  gi|298675148|ref|YP_003726898.1| 444 EILGLKGSSKAKTGNCEEGLKWVNKALKLKEN 475
                                       78899************************997 PP

  == domain 12  score: 2.4 bits;  conditional E-value: 0.49
                                       CHHHHHHHHHHHTT-HHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAke 22 
                                       +a+  ++ iy ++g++e++  
  gi|298675148|ref|YP_003726898.1| 478 DAWDIKSAIYTEMGKHEASLD 498
                                       57888899*********9865 PP

  == domain 13  score: 17.1 bits;  conditional E-value: 9.4e-06
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekal 28 
                                       e++y++g+++++l++yeeA  ++++al
  gi|298675148|ref|YP_003726898.1| 512 ELMYKKGCTLINLQRYEEAFDCINQAL 538
                                       689***********************8 PP

  == domain 14  score: 17.7 bits;  conditional E-value: 5.7e-06
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       ++++n++++ + lg++e A+++y++a+el+p 
  gi|298675148|ref|YP_003726898.1| 545 DMLVNKARLESLLGKIEDAVKTYNRAIELEPR 576
                                       6899**************************95 PP

  == domain 15  score: 1.9 bits;  conditional E-value: 0.7
                                       CHHHHHHHHHHHTT-HHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyye 25 
                                       ea++ +  ++++l+++eeA+  + 
  gi|298675148|ref|YP_003726898.1| 578 EALNAKVACLITLERFEEAMDIID 601
                                       67778888999********98765 PP

  == domain 16  score: 4.1 bits;  conditional E-value: 0.13
                                       HHHHHHHHTT-HHHHHHHH CS
                             TPR_8   6 nlgsiylklgdyeeAkeyy 24 
                                       n+ ++ +kl++y+eA e++
  gi|298675148|ref|YP_003726898.1| 616 NKIMCFIKLNRYDEALECI 634
                                       5557889********9986 PP

  == domain 17  score: -1.2 bits;  conditional E-value: 6.6
                                       HHHHHHHHHHHHHHHH. CS
                             TPR_8  18 eeAkeyyekaleldpdn 34 
                                       + A e++++ l+++pd+
  gi|298675148|ref|YP_003726898.1| 703 KDALESLNRTLSINPDD 719
                                       568999*********96 PP

  == domain 18  score: 11.0 bits;  conditional E-value: 0.00083
                                       HHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   6 nlgsiylklgdyeeAkeyyekaleldpd 33 
                                       ++++++ +l dy+++ +++ kale++ d
  gi|298675148|ref|YP_003726898.1| 725 MKADLHYNLSDYKKSLKTIDKALEIEGD 752
                                       79***********************876 PP

  == domain 19  score: 14.4 bits;  conditional E-value: 7e-05
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       a+++++ ++++++lg+   A e++eka  l+pd+
  gi|298675148|ref|YP_003726898.1| 754 ARLWLMRSYVLDSLGKTSDALESLEKAHNLSPDD 787
                                       799************************9999986 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0       1.7   8.4e+02       3      42 ..      72     110 ..      70     113 .. 0.84
   2 ?    2.8   0.0      0.55   2.7e+02      15      37 ..     117     138 ..     103     145 .. 0.71
   3 ?    1.3   0.0       1.8   8.6e+02       7      30 ..     142     165 ..     136     171 .. 0.85
   4 ?    1.7   0.0       1.3   6.1e+02       2      27 ..     173     198 ..     172     202 .. 0.93
   5 !   16.1   0.0     3e-05     0.015       3      43 ..     208     248 ..     206     249 .. 0.91
   6 ?    1.8   0.0       1.1   5.6e+02       4      32 ..     277     305 ..     275     310 .. 0.92
   7 !   11.3   0.0    0.0011      0.52       8      33 ..     315     340 ..     308     352 .. 0.90
   8 ?   -1.0   0.0       9.1   4.4e+03       6      27 ..     346     367 ..     341     373 .. 0.75
   9 !   20.6   0.0   1.1e-06   0.00051       3      39 ..     377     413 ..     375     418 .. 0.90
  10 !   12.0   0.0   0.00064      0.31      10      41 ..     418     449 ..     416     452 .. 0.90
  11 ?    0.1   0.0       4.1     2e+03      13      38 ..     455     480 ..     448     493 .. 0.85
  12 ?    1.0   0.0       2.1     1e+03      11      33 ..     521     543 ..     511     553 .. 0.81
  13 !   10.7   0.0    0.0016      0.78       8      38 ..     551     581 ..     544     585 .. 0.87
  14 ?   -0.3   0.0       5.7   2.8e+03       8      27 ..     584     603 ..     578     616 .. 0.76
  15 !   13.0   0.0    0.0003      0.15      15      44 .]     700     729 ..     693     729 .. 0.92
  16 !   14.9   0.0   7.2e-05     0.035       2      41 ..     721     760 ..     720     763 .. 0.94
  17 !   13.5   0.0    0.0002     0.097       2      36 ..     755     789 ..     754     795 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 1.7
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                        ++ +a +    G++ +++++l+ +++ + d+  +wll a
  gi|298675148|ref|YP_003726898.1|  72 TWYYRAFIASLMGNHVTSLEYLNNIVK-NNDEMKYWLLKA 110
                                       69999999999**************77.667778887766 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.55
                            TPR_14  15 GdpdeAiallrralalaPddaea 37 
                                       G ++eA++++++al+l  +d+ +
  gi|298675148|ref|YP_003726898.1| 117 GHYKEAVECCNKALKL-KNDPGI 138
                                       899**********994.444555 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 1.8
                            TPR_14   7 laeallalGdpdeAiallrralal 30 
                                        +e+l  +G +++A+ ++ +al+ 
  gi|298675148|ref|YP_003726898.1| 142 KGELLKKQGLFKKARIAYGKALEN 165
                                       5889999***********999985 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 1.3
                            TPR_14   2 eallalaeallalGdpdeAiallrra 27 
                                       e+l+++ +a+   G+  eA+++ +ra
  gi|298675148|ref|YP_003726898.1| 173 ELLKDYSHAYQMEGKVNEALKVIKRA 198
                                       78999******************998 PP

  == domain 5  score: 16.1 bits;  conditional E-value: 3e-05
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                        l + a+ l+++G  +eA+++ + +l+ +Pdd ea ++  +
  gi|298675148|ref|YP_003726898.1| 208 TLHMQADMLAESGHRKEAVEVINMILEINPDDFEAAFMKLE 248
                                       5678899****************************999766 PP

  == domain 6  score: 1.8 bits;  conditional E-value: 1.1
                            TPR_14   4 llalaeallalGdpdeAiallrralalaP 32 
                                       +l  a++l + G + eA ++ ++a +l+P
  gi|298675148|ref|YP_003726898.1| 277 WLYKAKILSTYGYYTEADEAINEAEKLNP 305
                                       8999********************99998 PP

  == domain 7  score: 11.3 bits;  conditional E-value: 0.0011
                            TPR_14   8 aeallalGdpdeAiallrralalaPd 33 
                                       a  + +lG++d+Ai+++ ral+ + d
  gi|298675148|ref|YP_003726898.1| 315 ANHYSNLGEYDKAIDICSRALEVDED 340
                                       77899****************98876 PP

  == domain 8  score: -1.0 bits;  conditional E-value: 9.1
                            TPR_14   6 alaeallalGdpdeAiallrra 27 
                                        + ea++  Gd++ A++  + a
  gi|298675148|ref|YP_003726898.1| 346 SRSEAYAKKGDLKNALRDINNA 367
                                       6779999999999998866655 PP

  == domain 9  score: 20.6 bits;  conditional E-value: 1.1e-06
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawl 39 
                                        + +++e+l+alGd+++A++ +r+al+ + +d +a+ 
  gi|298675148|ref|YP_003726898.1| 377 FWNQRGEILWALGDLRGALESFRKALKIDDNDSTALK 413
                                       6889*************************99999876 PP

  == domain 10  score: 12.0 bits;  conditional E-value: 0.00064
                            TPR_14  10 allalGdpdeAiallrralalaPddaeawlll 41 
                                       +l +lGd+ eA++l +++l+ +P+d e++ l 
  gi|298675148|ref|YP_003726898.1| 418 LLHNLGDHSEAVNLMDKYLSNYPEDVEILGLK 449
                                       6889**********************998765 PP

  == domain 11  score: 0.1 bits;  conditional E-value: 4.1
                            TPR_14  13 alGdpdeAiallrralalaPddaeaw 38 
                                         G+ +e ++  ++al+l  + ++aw
  gi|298675148|ref|YP_003726898.1| 455 KTGNCEEGLKWVNKALKLKENYPDAW 480
                                       56888999*********988888888 PP

  == domain 12  score: 1.0 bits;  conditional E-value: 2.1
                            TPR_14  11 llalGdpdeAiallrralalaPd 33 
                                       l +l++++eA ++ ++al +  d
  gi|298675148|ref|YP_003726898.1| 521 LINLQRYEEAFDCINQALGKKED 543
                                       67899************976554 PP

  == domain 13  score: 10.7 bits;  conditional E-value: 0.0016
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeaw 38 
                                       a+++  lG+ ++A++ ++ra++l P  ++++
  gi|298675148|ref|YP_003726898.1| 551 ARLESLLGKIEDAVKTYNRAIELEPRYEALN 581
                                       6777889******************988765 PP

  == domain 14  score: -0.3 bits;  conditional E-value: 5.7
                            TPR_14   8 aeallalGdpdeAiallrra 27 
                                       ++ l +l++++eA+++ +++
  gi|298675148|ref|YP_003726898.1| 584 VACLITLERFEEAMDIIDQV 603
                                       56678999******998876 PP

  == domain 15  score: 13.0 bits;  conditional E-value: 0.0003
                            TPR_14  15 GdpdeAiallrralalaPddaeawlllaql 44 
                                        +p++A++ l+r l+ +Pdd +a+++ a+l
  gi|298675148|ref|YP_003726898.1| 700 SNPKDALESLNRTLSINPDDVDALRMKADL 729
                                       589***********************9986 PP

  == domain 16  score: 14.9 bits;  conditional E-value: 7.2e-05
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawlll 41 
                                       +al++ a+++++l d++++++  ++al+   d+a++wl+ 
  gi|298675148|ref|YP_003726898.1| 721 DALRMKADLHYNLSDYKKSLKTIDKALEIEGDNARLWLMR 760
                                       79999********************************996 PP

  == domain 17  score: 13.5 bits;  conditional E-value: 0.0002
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddae 36 
                                       +++l++  +l  lG++ +A++ l++a  l Pdd +
  gi|298675148|ref|YP_003726898.1| 755 RLWLMRSYVLDSLGKTSDALESLEKAHNLSPDDND 789
                                       79*****************************9855 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.2      0.41     2e+02      15      61 ..      23      73 ..      19      82 .. 0.76
   2 ?    5.1   0.0     0.066        32       4      57 ..      83     135 ..      80     145 .. 0.82
   3 ?    5.5   0.0     0.051        25       5      52 ..     117     163 ..     116     167 .. 0.83
   4 ?    5.7   0.2     0.044        21       4      53 ..     149     200 ..     146     211 .. 0.83
   5 !   11.7   0.0    0.0006      0.29       4      61 ..     185     243 ..     184     250 .. 0.76
   6 !   13.5   0.0   0.00016     0.079       1      63 [.     250     312 ..     250     316 .. 0.90
   7 !   11.5   0.1   0.00068      0.33      12      61 ..     298     344 ..     293     348 .. 0.78
   8 !    7.9   0.1    0.0092       4.5       4      60 ..     354     410 ..     351     414 .. 0.77
   9 !   19.2   0.0   2.6e-06    0.0013       1      64 [.     385     448 ..     385     455 .. 0.92
  10 !   10.2   0.0    0.0017      0.84       5      66 ..     423     484 ..     419     486 .. 0.93
  11 !   10.6   0.0    0.0013      0.62       3      57 ..     489     543 ..     487     560 .. 0.85
  12 !   19.1   0.0   2.9e-06    0.0014       5      54 ..     558     606 ..     556     615 .. 0.92
  13 !    8.6   0.0    0.0054       2.6      26      57 ..     612     643 ..     602     649 .. 0.79
  14 !   25.9   0.1   2.2e-08   1.1e-05       5      63 ..     700     758 ..     696     762 .. 0.93
  15 !   15.7   0.1   3.4e-05     0.016       6      61 ..     735     790 ..     735     795 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.41
                            TPR_19 15 eqalqedpknaearllL....AeallalgqldeAealLdalpeedpddary 61
                                      e+al+ ++ +++++ +L    +e++ ++++++ A ++ + l  ++ d+a +
  gi|298675148|ref|YP_003726898.1| 23 ENALEMENLDDDLKQRLlyfkIELYKSANDFQTANQIENSLSMSFDDEATW 73
                                      567777666666666665677****************99999999996554 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.066
                            TPR_19   4 egdyaeAlalleqalqedpknaearllL..AeallalgqldeAealLdalpeedpd 57 
                                       +g++   l++l ++     +n+e +++L  A  l   g+++eA ++++++++ + d
  gi|298675148|ref|YP_003726898.1|  83 MGNHVTSLEYLNNI---VKNNDEMKYWLlkAANLDFIGHYKEAVECCNKALKLKND 135
                                       57777778888888...78888888888777788888*************999988 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.051
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalp 52 
                                       g y eA++   +al+   +++ +++   e+l ++g +++A+ +  +++
  gi|298675148|ref|YP_003726898.1| 117 GHYKEAVECCNKALKL-KNDPGIQIKKGELLKKQGLFKKARIAYGKAL 163
                                       6799999999999888.7799****99************996666555 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.044
                            TPR_19   4 egdyaeAlalleqalqe..dpknaearllLAeallalgqldeAealLdalpe 53 
                                       +g +  A  ++ +al+   + ++ e++ ++  a+   g ++eA ++++++ +
  gi|298675148|ref|YP_003726898.1| 149 QGLFKKARIAYGKALENdnYKHDIELLKDYSHAYQMEGKVNEALKVIKRAKN 200
                                       6666777777788885544888*************************99876 PP

  == domain 5  score: 11.7 bits;  conditional E-value: 0.0006
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd.ary 61 
                                       eg+  eAl+  ++a   +  + e +   A+ l ++g+ +eA ++++ ++e +pdd +++
  gi|298675148|ref|YP_003726898.1| 185 EGKVNEALKVIKRAKNLNLFDKETLHMQADMLAESGHRKEAVEVINMILEINPDDfEAA 243
                                       67778888888887333333666666569*************************95555 PP

  == domain 6  score: 13.5 bits;  conditional E-value: 0.00016
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryas 63 
                                       ll +++y eA +l ++++  +p+ ++ +l+ A++l   g ++eA ++++++ + +p  a+++ 
  gi|298675148|ref|YP_003726898.1| 250 LLIMKRYKEAENLVSYIFNSNPDTGDQWLYKAKILSTYGYYTEADEAINEAEKLNPVLANISL 312
                                       7899*********************************************99999887666655 PP

  == domain 7  score: 11.5 bits;  conditional E-value: 0.00068
                            TPR_19  12 alleqalqedpknaearllLAeallalgqldeAealLdalpeedpddary 61 
                                       +  e++   +p  a++ l  A+ + +lg++d+A++++++++e d d   y
  gi|298675148|ref|YP_003726898.1| 298 NEAEKL---NPVLANISLIKANHYSNLGEYDKAIDICSRALEVDEDVNTY 344
                                       555555...666677778889*********************99985555 PP

  == domain 8  score: 7.9 bits;  conditional E-value: 0.0092
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddar 60 
                                        gd+ +Al+   +a+  + +  + + +  e+l+alg+l  A +   ++++ d +d+ 
  gi|298675148|ref|YP_003726898.1| 354 KGDLKNALRDINNAINLNDDVINFWNQRGEILWALGDLRGALESFRKALKIDDNDST 410
                                       578888888888888888888888888888888888888888888888888888754 PP

  == domain 9  score: 19.2 bits;  conditional E-value: 2.6e-06
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasL 64 
                                       l+a gd+  Al+ +++al+ d +++ a+    ++l +lg+  eA +l+d+++  +p d ++ +L
  gi|298675148|ref|YP_003726898.1| 385 LWALGDLRGALESFRKALKIDDNDSTALKHGSKLLHNLGDHSEAVNLMDKYLSNYPEDVEILGL 448
                                       5788*************************99************************998666555 PP

  == domain 10  score: 10.2 bits;  conditional E-value: 0.0017
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasLlA 66 
                                       gd+ eA++l+ + l+ +p++ e++ l      ++g+ +e  + ++++++ + + +++++ + 
  gi|298675148|ref|YP_003726898.1| 423 GDHSEAVNLMDKYLSNYPEDVEILGLKGSSKAKTGNCEEGLKWVNKALKLKENYPDAWDIKS 484
                                       9**************************************************99999988765 PP

  == domain 11  score: 10.6 bits;  conditional E-value: 0.0013
                            TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       ++g++++ l++ e+ l +dp+n+e+ +     l++l +++eA +++++++ ++ d
  gi|298675148|ref|YP_003726898.1| 489 EMGKHEASLDAAEYGLFYDPENPELMYKKGCTLINLQRYEEAFDCINQALGKKED 543
                                       78999999999999999*************************9999999988777 PP

  == domain 12  score: 19.1 bits;  conditional E-value: 2.9e-06
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpee 54 
                                       g+ ++A++ + +a++ +p ++++ +  + +l+ l +++eA++++d++ + 
  gi|298675148|ref|YP_003726898.1| 558 GKIEDAVKTYNRAIELEPRYEALNA-KVACLITLERFEEAMDIIDQVDPN 606
                                       7899**************9999999.*******************98765 PP

  == domain 13  score: 8.6 bits;  conditional E-value: 0.0054
                            TPR_19  26 earllLAeallalgqldeAealLdalpeedpd 57 
                                       e +++ + + ++l+++deA +++d  ++  pd
  gi|298675148|ref|YP_003726898.1| 612 EFWMNKIMCFIKLNRYDEALECIDNFGNNVPD 643
                                       56677788**************9987777777 PP

  == domain 14  score: 25.9 bits;  conditional E-value: 2.2e-08
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryas 63 
                                        ++ +Al+ l + l+ +p++ +a+   A+++++l ++++  +++d+++e + d+ar++ 
  gi|298675148|ref|YP_003726898.1| 700 SNPKDALESLNRTLSINPDDVDALRMKADLHYNLSDYKKSLKTIDKALEIEGDNARLWL 758
                                       6899*************************************************999985 PP

  == domain 15  score: 15.7 bits;  conditional E-value: 3.4e-05
                            TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddary 61 
                                       dy   l+   +al+ + +na+++l    +l +lg + +A + L+++ +  pdd ++
  gi|298675148|ref|YP_003726898.1| 735 DYKKSLKTIDKALEIEGDNARLWLMRSYVLDSLGKTSDALESLEKAHNLSPDDNDV 790
                                       56667788899*****************************************9776 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.069        33      11      64 ..     117     166 ..     107     170 .. 0.78
   2 !    9.0   0.0    0.0047       2.3       2      54 ..     211     260 ..     210     266 .. 0.94
   3 !   16.1   0.0   2.7e-05     0.013      13      63 ..     290     337 ..     288     341 .. 0.93
   4 !   14.1   0.0   0.00011     0.054       6      67 ..     350     408 ..     346     409 .. 0.90
   5 !   13.6   0.0   0.00017     0.082       9      66 ..     421     478 ..     417     479 .. 0.93
   6 ?    6.6   0.0     0.025        12       9      62 ..     489     539 ..     485     544 .. 0.88
   7 !   13.7   0.0   0.00015     0.075      10      58 ..     557     601 ..     549     607 .. 0.89
   8 ?    1.3   0.0       1.2   5.6e+02      34      54 ..     611     631 ..     604     635 .. 0.83
   9 !   20.7   0.0     1e-06    0.0005      12      62 ..     701     748 ..     697     754 .. 0.92
  10 ?    2.3   0.0      0.55   2.6e+02      22      60 ..     745     780 ..     740     788 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.069
                            TPR_16  11 gdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAa.alyraalraa 64 
                                       g+y +A++  + alk+   +P     +  +g+++ +qg +++A+ a+  +al+++
  gi|298675148|ref|YP_003726898.1| 117 GHYKEAVECCNKALKLK-NDPG---IQIKKGELLKKQGLFKKARiAYG-KALEND 166
                                       78888888888888888.5555...99999**************5555.555665 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0047
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAa 54 
                                       ++a+ ++++g+  +A+++ +  l+ +   Pd+ eA++ + +++l  +r++eA+
  gi|298675148|ref|YP_003726898.1| 211 MQADMLAESGHRKEAVEVINMILEIN---PDDFEAAFMKLELLLIMKRYKEAE 260
                                       7899999*******************...***********************8 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 2.7e-05
                            TPR_16  13 yddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalra 63 
                                       y++A +a ++a k++   P+ a  +l +++ +  +g++++A++ + +al+ 
  gi|298675148|ref|YP_003726898.1| 290 YTEADEAINEAEKLN---PVLANISLIKANHYSNLGEYDKAIDICSRALEV 337
                                       89999**********...*****************************9975 PP

  == domain 4  score: 14.1 bits;  conditional E-value: 0.00011
                            TPR_16   6 aalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       a+++ gd   A++  + a+ ++    d   +++ +g++++++g+l +A++ +r+al+ + ++
  gi|298675148|ref|YP_003726898.1| 350 AYAKKGDLKNALRDINNAINLN---DDVINFWNQRGEILWALGDLRGALESFRKALKIDDND 408
                                       7889999999999999999999...999999*************************998877 PP

  == domain 5  score: 13.6 bits;  conditional E-value: 0.00017
                            TPR_16   9 ragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal...raapd 66 
                                       ++gd  +A+++ + +l ++   P+++e l l+g + ++ g+ +e + ++++al   +++pd
  gi|298675148|ref|YP_003726898.1| 421 NLGDHSEAVNLMDKYLSNY---PEDVEILGLKGSSKAKTGNCEEGLKWVNKALklkENYPD 478
                                       5799***************...*******************************77777776 PP

  == domain 6  score: 6.6 bits;  conditional E-value: 0.025
                            TPR_16   9 ragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalr 62 
                                       + g+ ++ + a+e  l +d   P+++e ++ +g  +  ++r++eA + ++ al+
  gi|298675148|ref|YP_003726898.1| 489 EMGKHEASLDAAEYGLFYD---PENPELMYKKGCTLINLQRYEEAFDCINQALG 539
                                       67999**************...99999******************877777665 PP

  == domain 7  score: 13.7 bits;  conditional E-value: 0.00015
                            TPR_16  10 agdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyr 58 
                                       +g+ +dA++ +++a+++    P ++eAl+++  ++  + r++eA + ++
  gi|298675148|ref|YP_003726898.1| 557 LGKIEDAVKTYNRAIELE---P-RYEALNAKVACLITLERFEEAMDIID 601
                                       699***************...9.8********************86655 PP

  == domain 8  score: 1.3 bits;  conditional E-value: 1.2
                            TPR_16  34 aeAllllgdaalrqgrlaeAa 54 
                                        e+++++  ++ +++r++eA+
  gi|298675148|ref|YP_003726898.1| 611 FEFWMNKIMCFIKLNRYDEAL 631
                                       678999999999999999997 PP

  == domain 9  score: 20.7 bits;  conditional E-value: 1e-06
                            TPR_16  12 dyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalr 62 
                                       ++ dA++ l+++l  +   Pd+++Al  ++d+++ ++++++ +  +++al+
  gi|298675148|ref|YP_003726898.1| 701 NPKDALESLNRTLSIN---PDDVDALRMKADLHYNLSDYKKSLKTIDKALE 748
                                       789*************...************************99999985 PP

  == domain 10  score: 2.3 bits;  conditional E-value: 0.55
                            TPR_16  22 aalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraa 60 
                                        al+      d+a+ +l +  ++  +g   +A++ +++a
  gi|298675148|ref|YP_003726898.1| 745 KALEIE---GDNARLWLMRSYVLDSLGKTSDALESLEKA 780
                                       566666...7899********************776665 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.077        37       8      74 ..      75     132 ..      68     135 .. 0.55
   2 !   12.0   0.3   0.00041       0.2       7      71 ..     140     198 ..     137     203 .. 0.90
   3 ?    4.8   0.0     0.072        35      28      74 ..     190     235 ..     189     238 .. 0.80
   4 ?   -1.7   0.0       7.5   3.6e+03      14      66 ..     251     261 ..     248     263 .. 0.50
   5 !   17.9   0.1   5.7e-06    0.0028       9      67 ..     314     370 ..     306     377 .. 0.80
   6 !   17.1   0.0     1e-05    0.0049       5      75 ..     343     405 ..     340     407 .. 0.88
   7 !   16.5   0.0   1.5e-05    0.0074       2      76 ..     374     440 ..     373     441 .. 0.85
   8 !    9.5   0.0    0.0025       1.2       5      52 ..     445     491 ..     443     501 .. 0.76
   9 !   13.7   0.1   0.00012     0.056      24      74 ..     525     573 ..     513     576 .. 0.85
  10 ?    4.2   0.0      0.11        53      24      66 ..     591     632 ..     578     635 .. 0.74
  11 ?   -1.1   0.0       4.9   2.4e+03      59      74 ..     700     715 ..     692     718 .. 0.81
  12 !   15.0   0.0   4.8e-05     0.023       9      74 ..     726     783 ..     720     786 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.077
                            TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                        +a +   +g++  +le+l+  +        +++ ++  +    +  ++  g+y+eA+e  ++al++
  gi|298675148|ref|YP_003726898.1|  75 YRAFIASLMGNHVTSLEYLNNIV--------KNN-DEMKYWLLKAANLDFIGHYKEAVECCNKALKL 132
                                       56666666666666666666662........222.23333334444456667777777777777766 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00041
                            TPR_12   7 nnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleea 71 
                                        + +++l ++g + +A+  + kale  +     +h   ++ l +++ +y++ g+  eAl+  ++a
  gi|298675148|ref|YP_003726898.1| 140 IKKGELLKKQGLFKKARIAYGKALENDN----YKH--DIELLKDYSHAYQMEGKVNEALKVIKRA 198
                                       56799**********************3....568..89********************998887 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.072
                            TPR_12  28 kaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       +al +++r+ +  ++   +tl+  ++++ ++g+ +eA+e  +  l+i
  gi|298675148|ref|YP_003726898.1| 190 EALKVIKRAKNL-NLFDKETLHMQADMLAESGHRKEAVEVINMILEI 235
                                       566666666554.457779********************99988887 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 7.5
                            TPR_12  14 rrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAle 66 
                                       +                                           ++ry+eA++
  gi|298675148|ref|YP_003726898.1| 251 L------------------------------------------IMKRYKEAEN 261
                                       3..........................................4455555554 PP

  == domain 5  score: 17.9 bits;  conditional E-value: 5.7e-06
                            TPR_12   9 laavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlel 67 
                                        a+ +  lg+yd+A++++ +ale+ + +   ++   ++++   g+l  al +   A++l
  gi|298675148|ref|YP_003726898.1| 314 KANHYSNLGEYDKAIDICSRALEVDEDV--NTYSSRSEAYAKKGDLKNALRDINNAINL 370
                                       799**********************999..55558888888888888887777777766 PP

  == domain 6  score: 17.1 bits;  conditional E-value: 1e-05
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       +++ + +++++ g++  Al+  + a+++      +d   +++  +  g++++alg+++ Ale +++al+i+
  gi|298675148|ref|YP_003726898.1| 343 TYSSRSEAYAKKGDLKNALRDINNAINLN-----DD---VINFWNQRGEILWALGDLRGALESFRKALKID 405
                                       67778899999999999999999997777.....54...9****************************997 PP

  == domain 7  score: 16.5 bits;  conditional E-value: 1.5e-05
                            TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       v + +n+++++l++lg++  Ale ++kal i      ++    +t+l   + l++ lg++ eA++l  + l  ++
  gi|298675148|ref|YP_003726898.1| 374 VINFWNQRGEILWALGDLRGALESFRKALKID-----DN---DSTALKHGSKLLHNLGDHSEAVNLMDKYLSNYP 440
                                       5667889*********************9999.....44...578899999999999999999999999888775 PP

  == domain 8  score: 9.5 bits;  conditional E-value: 0.0025
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLg 52 
                                       +l   ++  ++ g+++e l++ +kal + +++++  ++  ++++  +g
  gi|298675148|ref|YP_003726898.1| 445 ILGLKGSSKAKTGNCEEGLKWVNKALKLKENYPD-AWDIKSAIYTEMG 491
                                       566789999********************99843.3455555555555 PP

  == domain 9  score: 13.7 bits;  conditional E-value: 0.00012
                            TPR_12  24 ellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       + +e+a + ++++lG++    +  l n +rl ++lg+ e+A++ +++a+++
  gi|298675148|ref|YP_003726898.1| 525 QRYEEAFDCINQALGKKE--DVDMLVNKARLESLLGKIEDAVKTYNRAIEL 573
                                       456777777766688776..899*************************986 PP

  == domain 10  score: 4.2 bits;  conditional E-value: 0.11
                            TPR_12  24 ellekaleiarrllGpdhpltattlrnLgrlyralgryeeAle 66 
                                       e +e+a++i+ ++ +p++++  +   n  +++ +l+ry+eAle
  gi|298675148|ref|YP_003726898.1| 591 ERFEEAMDIIDQV-DPNYLNRFEFWMNKIMCFIKLNRYDEALE 632
                                       6677777777766.57777777777777777777777777776 PP

  == domain 11  score: -1.1 bits;  conditional E-value: 4.9
                            TPR_12  59 gryeeAlelleealai 74 
                                        ++++Ale l+++l i
  gi|298675148|ref|YP_003726898.1| 700 SNPKDALESLNRTLSI 715
                                       6889999999999987 PP

  == domain 12  score: 15.0 bits;  conditional E-value: 4.8e-05
                            TPR_12   9 laavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                        a++++ l +y ++l+  +kalei      +d+   a+     + +++ lg++ +Ale le+a ++
  gi|298675148|ref|YP_003726898.1| 726 KADLHYNLSDYKKSLKTIDKALEIE-----GDN---ARLWLMRSYVLDSLGKTSDALESLEKAHNL 783
                                       79999********************.....887...888899999999***************987 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       1.7   8.5e+02      11      57 ..      53      98 ..      45     103 .. 0.77
   2 ?    2.8   0.0      0.28   1.3e+02      10      69 ..     118     176 ..     117     178 .. 0.87
   3 ?    5.6   0.0     0.037        18       6      30 ..     217     241 ..     180     250 .. 0.72
   4 ?    6.6   0.0     0.018       8.5       5      59 ..     318     371 ..     313     373 .. 0.87
   5 !   20.0   0.0   1.2e-06   0.00056       4      65 ..     350     411 ..     348     413 .. 0.95
   6 ?    3.8   0.0      0.14        66      38      64 ..     418     444 ..     417     450 .. 0.90
   7 !   12.6   0.0   0.00023      0.11       3      60 ..     485     542 ..     483     553 .. 0.90
   8 ?    2.2   0.0      0.42     2e+02      28      61 ..     543     576 ..     540     585 .. 0.82
   9 ?   -1.1   0.0       4.6   2.2e+03       6      20 ..     622     636 ..     617     648 .. 0.69
  10 !   14.6   0.0   5.8e-05     0.028      13      61 ..     704     752 ..     700     753 .. 0.92
  11 !   17.4   0.0   7.4e-06    0.0036       7      65 ..     732     790 ..     729     794 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.7
                             TPR_9 11 weralavverllllaPddpeerrdRGlllaqlGclsaAladLeayla 57
                                      ++ a   +e  l +  dd   ++ R+++   +G+  + l+ L+  + 
  gi|298675148|ref|YP_003726898.1| 53 FQTA-NQIENSLSMSFDDEATWYYRAFIASLMGNHVTSLEYLNNIVK 98
                                      5544.3478889999999999************99999999887665 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.28
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaeair 69 
                                       ++ +a ++++  l l+  dp+     G ll ++G +++A+ +   +l+++   +d+e+++
  gi|298675148|ref|YP_003726898.1| 118 HYKEAVECCNKALKLKN-DPGIQIKKGELLKKQGLFKKARIAYGKALENDNYKHDIELLK 176
                                       56788899999999885.56888899************************9999999986 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.037
                             TPR_9   6 ireedweralavverllllaPddpe 30 
                                       +++ +  +a +v++++l ++Pdd e
  gi|298675148|ref|YP_003726898.1| 217 AESGHRKEAVEVINMILEINPDDFE 241
                                       4555666777777777777777754 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.018
                             TPR_9   5 aireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylala 59 
                                       + +  ++++a+ ++ r l ++ +d+  +  R  ++a+ G+l+ Al+d + ++ l+
  gi|298675148|ref|YP_003726898.1| 318 YSNLGEYDKAIDICSRALEVD-EDVNTYSSRSEAYAKKGDLKNALRDINNAINLN 371
                                       46778899************9.567**********************99988765 PP

  == domain 5  score: 20.0 bits;  conditional E-value: 1.2e-06
                             TPR_9   4 iaireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                       +++ + d   al+ ++  + l+ d +  +  RG +l  lG+l++Al+ +  +l +++++ +a
  gi|298675148|ref|YP_003726898.1| 350 AYAKKGDLKNALRDINNAINLNDDVINFWNQRGEILWALGDLRGALESFRKALKIDDNDSTA 411
                                       689999**************************************************999887 PP

  == domain 6  score: 3.8 bits;  conditional E-value: 0.14
                             TPR_9  38 llaqlGclsaAladLeaylalapdapd 64 
                                       ll+ lG+ s+A++ ++ yl++ p++ +
  gi|298675148|ref|YP_003726898.1| 418 LLHNLGDHSEAVNLMDKYLSNYPEDVE 444
                                       6899*******************9865 PP

  == domain 7  score: 12.6 bits;  conditional E-value: 0.00023
                             TPR_9   3 aiaireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                       ai+ +  ++e+ l ++e  l  +P+ pe+ +  G  l  l ++++A ++ +++l + +
  gi|298675148|ref|YP_003726898.1| 485 AIYTEMGKHEASLDAAEYGLFYDPENPELMYKKGCTLINLQRYEEAFDCINQALGKKE 542
                                       678888999*****************************************99996654 PP

  == domain 8  score: 2.2 bits;  conditional E-value: 0.42
                             TPR_9  28 dpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       d++ +   ++l+  lG ++ A++  +++++l+p 
  gi|298675148|ref|YP_003726898.1| 543 DVDMLVNKARLESLLGKIEDAVKTYNRAIELEPR 576
                                       66667788999999*****************995 PP

  == domain 9  score: -1.1 bits;  conditional E-value: 4.6
                             TPR_9   6 ireedweralavver 20 
                                       i  +++++al++++ 
  gi|298675148|ref|YP_003726898.1| 622 IKLNRYDEALECIDN 636
                                       445677777777764 PP

  == domain 10  score: 14.6 bits;  conditional E-value: 5.8e-05
                             TPR_9  13 ralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                        al+ ++r l ++Pdd++ +r  + l++ l ++++ l+  + +l++++d
  gi|298675148|ref|YP_003726898.1| 704 DALESLNRTLSINPDDVDALRMKADLHYNLSDYKKSLKTIDKALEIEGD 752
                                       699**********************************999999998765 PP

  == domain 11  score: 17.4 bits;  conditional E-value: 7.4e-06
                             TPR_9   7 reedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                       +  d+ + l++++  l +  d +++++ R  +l  lG +s Al+ Le +  l+pd+ d+
  gi|298675148|ref|YP_003726898.1| 732 NLSDYKKSLKTIDKALEIEGDNARLWLMRSYVLDSLGKTSDALESLEKAHNLSPDDNDV 790
                                       6679999*************************************************987 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.1    0.0015      0.71       8      42 .]     117     150 ..     116     150 .. 0.89
   2 ?    1.2   0.1      0.63     3e+02       1      22 [.     143     164 ..     143     167 .. 0.87
   3 ?   -1.1   0.1       3.2   1.5e+03       7      22 ..     185     200 ..     180     202 .. 0.76
   4 ?   -0.1   0.0       1.6   7.6e+02       4      30 ..     216     242 ..     213     244 .. 0.71
   5 ?   -1.5   0.3       4.2     2e+03      10      30 ..     290     310 ..     288     312 .. 0.78
   6 ?    3.8   0.1     0.096        46       5      26 ..     319     340 ..     315     344 .. 0.84
   7 !   17.3   0.1   5.6e-06    0.0027       3      42 .]     350     389 ..     349     389 .. 0.97
   8 !   13.8   0.0     7e-05     0.034       1      28 [.     382     409 ..     382     414 .. 0.89
   9 !    8.3   0.0    0.0038       1.8       6      31 ..     455     480 ..     450     480 .. 0.85
  10 ?    4.7   0.1     0.049        24       3      35 ..     486     518 ..     485     525 .. 0.89
  11 ?   -1.5   0.0       4.2   2.1e+03       7      21 ..     524     538 ..     518     541 .. 0.81
  12 !   18.6   0.2   2.4e-06    0.0011       7      28 ..     557     578 ..     554     583 .. 0.91
  13 ?    1.7   0.0      0.42     2e+02       5      16 ..     622     633 ..     621     633 .. 0.85
  14 !    8.7   0.0    0.0028       1.3      12      40 ..     704     732 ..     703     734 .. 0.88
  15 ?    4.4   0.1     0.062        30       2      32 ..     728     758 ..     727     764 .. 0.89
  16 !    9.9   0.0    0.0012      0.56       6      31 ..     766     791 ..     762     793 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0015
                            TPR_11   8 GkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G y+eA+e+ +kAlkl+ +++ +  + G+++ kqG
  gi|298675148|ref|YP_003726898.1| 117 GHYKEAVECCNKALKLK-NDPGIQIKKGELLKKQG 150
                                       78**************8.57999999999999998 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.63
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlk 22 
                                       G ++ +qG +++A  aY kAl+
  gi|298675148|ref|YP_003726898.1| 143 GELLKKQGLFKKARIAYGKALE 164
                                       6778899*************98 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 3.2
                            TPR_11   7 qGkyeeAieaYkkAlk 22 
                                        Gk +eA+++ k+A +
  gi|298675148|ref|YP_003726898.1| 185 EGKVNEALKVIKRAKN 200
                                       79******99887755 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 1.6
                            TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaea 30 
                                       + e G  +eA+e+ +  l+++Pd+ ea
  gi|298675148|ref|YP_003726898.1| 216 LAESGHRKEAVEVINMILEINPDDFEA 242
                                       5555666666666666699*****997 PP

  == domain 5  score: -1.5 bits;  conditional E-value: 4.2
                            TPR_11  10 yeeAieaYkkAlkldPdnaea 30 
                                       y+eA ea ++A kl+P  a++
  gi|298675148|ref|YP_003726898.1| 290 YTEADEAINEAEKLNPVLANI 310
                                       777777779999999987776 PP

  == domain 6  score: 3.8 bits;  conditional E-value: 0.096
                            TPR_11   5 yeqGkyeeAieaYkkAlkldPd 26 
                                         +G+y++Ai   ++Al+ d+d
  gi|298675148|ref|YP_003726898.1| 319 SNLGEYDKAIDICSRALEVDED 340
                                       5689******999999999876 PP

  == domain 7  score: 17.3 bits;  conditional E-value: 5.6e-06
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       ay ++G++++A+ + ++A++l+ d  ++++ +G++++++G
  gi|298675148|ref|YP_003726898.1| 350 AYAKKGDLKNALRDINNAINLNDDVINFWNQRGEILWALG 389
                                       89***********************************998 PP

  == domain 8  score: 13.8 bits;  conditional E-value: 7e-05
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdna 28 
                                       G ++ ++G++ +A+e+++kAlk+d ++ 
  gi|298675148|ref|YP_003726898.1| 382 GEILWALGDLRGALESFRKALKIDDNDS 409
                                       778899******************9875 PP

  == domain 9  score: 8.3 bits;  conditional E-value: 0.0038
                            TPR_11   6 eqGkyeeAieaYkkAlkldPdnaeay 31 
                                       + G+ ee +++ +kAlkl++++++a+
  gi|298675148|ref|YP_003726898.1| 455 KTGNCEEGLKWVNKALKLKENYPDAW 480
                                       568888888888************97 PP

  == domain 10  score: 4.7 bits;  conditional E-value: 0.049
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLG 35 
                                       +y+e Gk e+++ a +  l +dP+n+e+ y+ G
  gi|298675148|ref|YP_003726898.1| 486 IYTEMGKHEASLDAAEYGLFYDPENPELMYKKG 518
                                       79999999999999999999********99988 PP

  == domain 11  score: -1.5 bits;  conditional E-value: 4.2
                            TPR_11   7 qGkyeeAieaYkkAl 21 
                                       +++yeeA  + ++Al
  gi|298675148|ref|YP_003726898.1| 524 LQRYEEAFDCINQAL 538
                                       689999988877776 PP

  == domain 12  score: 18.6 bits;  conditional E-value: 2.4e-06
                            TPR_11   7 qGkyeeAieaYkkAlkldPdna 28 
                                       +Gk+e+A++ Y++A++l P + 
  gi|298675148|ref|YP_003726898.1| 557 LGKIEDAVKTYNRAIELEPRYE 578
                                       7******************986 PP

  == domain 13  score: 1.7 bits;  conditional E-value: 0.42
                            TPR_11   5 yeqGkyeeAiea 16 
                                        ++++y+eA+e+
  gi|298675148|ref|YP_003726898.1| 622 IKLNRYDEALEC 633
                                       6899*****996 PP

  == domain 14  score: 8.7 bits;  conditional E-value: 0.0028
                            TPR_11  12 eAieaYkkAlkldPdnaeayynLGlayyk 40 
                                       +A+e++++ l ++Pd+++a+   ++++y+
  gi|298675148|ref|YP_003726898.1| 704 DALESLNRTLSINPDDVDALRMKADLHYN 732
                                       7******************9888888886 PP

  == domain 15  score: 4.4 bits;  conditional E-value: 0.062
                            TPR_11   2 dayyeqGkyeeAieaYkkAlkldPdnaeayy 32 
                                       d+ y + +y+++++   kAl++  dna++++
  gi|298675148|ref|YP_003726898.1| 728 DLHYNLSDYKKSLKTIDKALEIEGDNARLWL 758
                                       67888999*******************9875 PP

  == domain 16  score: 9.9 bits;  conditional E-value: 0.0012
                            TPR_11   6 eqGkyeeAieaYkkAlkldPdnaeay 31 
                                       ++Gk  +A+e+++kA +l+Pd+ +++
  gi|298675148|ref|YP_003726898.1| 766 SLGKTSDALESLEKAHNLSPDDNDVL 791
                                       68*******************97765 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.2    0.0079       3.8     210     255 ..      88     132 ..      33     168 .. 0.58
   2 !   11.0   0.3    0.0003      0.15      16      71 ..     184     239 ..     175     251 .. 0.89
   3 !   10.1   0.0   0.00056      0.27     205     255 ..     253     303 ..     248     306 .. 0.94
   4 !   10.4   0.1   0.00045      0.22     198     245 ..     314     360 ..     304     361 .. 0.89
   5 !   20.3   0.0   4.3e-07   0.00021     201     259 ..     350     408 ..     343     410 .. 0.95
   6 !    7.4   0.0    0.0037       1.8     204     256 ..     421     473 ..     413     478 .. 0.93
   7 !   10.2   0.1   0.00052      0.25     205     265 ..     524     583 ..     521     586 .. 0.86
   8 !    8.2   0.0    0.0021         1      16      89 ..     589     664 ..     578     675 .. 0.82
   9 !   11.3   0.1   0.00025      0.12     201     259 ..     730     787 ..     696     795 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0079
                                       HHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHC CS
                             NARP1 210 kAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearkl 255
                                        +ley+++ ++++++ + ++l Ka  l   G  k+A+e+ ++a kl
  gi|298675148|ref|YP_003726898.1|  88 TSLEYLNNIVKNNDE-MKYWLLKAANLDFIGHYKEAVECCNKALKL 132
                                       555555554444443.345555555555555555555555555444 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0003
                                       HHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT- CS
                             NARP1  16 eagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpen 71 
                                         gk++eAl+ ++++++  +   + + ++a++l + g+++eA ++++ +le np++
  gi|298675148|ref|YP_003726898.1| 184 MEGKVNEALKVIKRAKNLNLFDKETLHMQADMLAESGHRKEAVEVINMILEINPDD 239
                                       5799**********8887766668899***************************97 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00056
                                       HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHC CS
                             NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearkl 255
                                       ++++++A ++++   +++p   + +l Ka+il  +G  ++A e+++ea kl
  gi|298675148|ref|YP_003726898.1| 253 MKRYKEAENLVSYIFNSNPDTGDQWLYKAKILSTYGYYTEADEAINEAEKL 303
                                       56789999****************************************998 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.00045
                                       HHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHH CS
                             NARP1 198 lAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkA 245
                                        A hy +lg+++kA+++ ++a+e +   v+ y  +++ + ++Gdlk+A
  gi|298675148|ref|YP_003726898.1| 314 KANHYSNLGEYDKAIDICSRALEVDE-DVNTYSSRSEAYAKKGDLKNA 360
                                       599*******************9865.5899**************998 PP

  == domain 5  score: 20.3 bits;  conditional E-value: 4.3e-07
                                       HHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT- CS
                             NARP1 201 hydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaD 259
                                        y k g+ ++Al+ i++ai+ ++ +++++ ++++il   Gdl++A e   +a k+D +D
  gi|298675148|ref|YP_003726898.1| 350 AYAKKGDLKNALRDINNAINLNDDVINFWNQRGEILWALGDLRGALESFRKALKIDDND 408
                                       5889999*************************************************998 PP

  == domain 6  score: 7.4 bits;  conditional E-value: 0.0037
                                       HHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                             NARP1 204 klgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                       +lg+ ++A++++dk +++ p+ ve+   K+    ++G+ ++  +++++a kl 
  gi|298675148|ref|YP_003726898.1| 421 NLGDHSEAVNLMDKYLSNYPEDVEILGLKGSSKAKTGNCEEGLKWVNKALKLK 473
                                       678999*******************************************9885 PP

  == domain 7  score: 10.2 bits;  conditional E-value: 0.00052
                                       HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT-HHHHHH CS
                             NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaDRyiNsk 265
                                       l+++e+A ++i++a+ ++   v++ ++Kar+    G +++A+++ ++a +l  +   +N+k
  gi|298675148|ref|YP_003726898.1| 524 LQRYEEAFDCINQALGKKED-VDMLVNKARLESLLGKIEDAVKTYNRAIELEPRYEALNAK 583
                                       67899**********99865.8************************998887665556666 PP

  == domain 8  score: 8.2 bits;  conditional E-value: 0.0021
                                       HHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CH.H.HHHHHHHT..SSS-H CS
                             NARP1  16 eagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpensk.Y.yeglekakklskede 89 
                                         ++ eeA++ +++++ + +++ ++  +k    +kL+r++eA + + +  +  p++ k Y ++ l +++++++ d+
  gi|298675148|ref|YP_003726898.1| 589 TLERFEEAMDIIDQVDPNYLNRFEFWMNKIMCFIKLNRYDEALECIDNFGNNVPDEIKeYmFQTLSETLDTDNVDQ 664
                                       56899*************************************************9976243567777775444433 PP

  == domain 9  score: 11.3 bits;  conditional E-value: 0.00025
                                       HHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT- CS
                             NARP1 201 hydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaD 259
                                       hy+ l +++k+l++idka+e +     l+l+++ +l   G  ++A e +e+a +l   D
  gi|298675148|ref|YP_003726898.1| 730 HYN-LSDYKKSLKTIDKALEIEGDNARLWLMRSYVLDSLGKTSDALESLEKAHNLSPDD 787
                                       665.789999************9999***********************9999986555 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.4    0.0084       4.1      16      78 ..      64     125 ..      49     129 .. 0.77
   2 !   11.3   0.4   0.00065      0.32       2      79 ..     149     229 ..     148     232 .. 0.89
   3 !   11.3   0.0   0.00062       0.3      23      78 ..     206     262 ..     202     266 .. 0.93
   4 !   12.5   0.1   0.00027      0.13       6      80 ..     223     298 ..     218     300 .. 0.91
   5 !   15.3   0.6   3.6e-05     0.018       3      78 ..     254     330 ..     253     334 .. 0.94
   6 !    9.9   0.0    0.0017      0.82       3      81 ..     322     400 ..     320     401 .. 0.86
   7 ?    6.4   0.0     0.022        11       3      77 ..     423     498 ..     407     501 .. 0.82
   8 !    8.5   0.1    0.0049       2.4      18      80 ..     506     568 ..     500     570 .. 0.79
   9 !   22.1   0.1   2.8e-07   0.00013       4      81 ..     559     636 ..     556     637 .. 0.93
  10 !   18.1   0.0   4.7e-06    0.0023       6      82 .]     703     780 ..     698     780 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0084
                                       H.HHH--HHHHHHH.HHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3  16 laaetespedayll.AlclylngqykrAyellrkaklnskslgcrylfAqcllkLkkyeeAiaa 78 
                                          ++ ++e++ ++ A    l+g++ + +e+l++  +n+  +++++l+A  l  +++y+eA+ +
  gi|298675148|ref|YP_003726898.1|  64 S--MSFDDEATWYYrAFIASLMGNHVTSLEYLNNIVKNNDEMKYWLLKAANLDFIGHYKEAVEC 125
                                       4..3444444444459999999*************88888889******************987 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00065
                                       TT-HHHHHHHHHHHH.HHH--HHHHHH..HHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHH CS
                            ANAPC3   2 qnnyknAiflaerllaaetespedayl..lAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeA 75 
                                       q+ +k+A + + ++l+ +++ ++  +l  ++ ++   g+ ++A++++++a +ln  +++ +   A  l + ++ +eA
  gi|298675148|ref|YP_003726898.1| 149 QGLFKKARIAYGKALENDNYKHDIELLkdYSHAYQMEGKVNEALKVIKRAkNLNLFDKETLHMQADMLAESGHRKEA 225
                                       778999999999999888888888888666********************9**999999999999999999999999 PP

                                       HHHH CS
                            ANAPC3  76 iaaL 79 
                                       + ++
  gi|298675148|ref|YP_003726898.1| 226 VEVI 229
                                       9887 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00062
                                       HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3  23 pedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                        e +++ A  l ++g  k+A e+++   ++n+ + ++++ + + ll +k+y+eA+++
  gi|298675148|ref|YP_003726898.1| 206 KETLHMQADMLAESGHRKEAVEVINMIlEINPDDFEAAFMKLELLLIMKRYKEAENL 262
                                       5778999***********************************************987 PP

  == domain 4  score: 12.5 bits;  conditional E-value: 0.00027
                                       HHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3   6 knAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                       k+A+ +++ +l+ ++++ e+a+++ + l+ +++yk+A +l++   ++n+ +   ++ +A+ l  ++ y eA  a+ 
  gi|298675148|ref|YP_003726898.1| 223 KEAVEVINMILEINPDDFEAAFMKLELLLIMKRYKEAENLVSYIfNSNPDTGDQWLYKAKILSTYGYYTEADEAIN 298
                                       78889999999999******************************************************99977765 PP

  == domain 5  score: 15.3 bits;  conditional E-value: 3.6e-05
                                       T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                       ++yk+A+ l + +++++++  +  +++A+ l   g y++A e +++a kln+   ++ +++A  +  L++y++Ai++
  gi|298675148|ref|YP_003726898.1| 254 KRYKEAENLVSYIFNSNPDTGDQWLYKAKILSTYGYYTEADEAINEAeKLNPVLANISLIKANHYSNLGEYDKAIDI 330
                                       68************8889888888889************************************************97 PP

  == domain 6  score: 9.9 bits;  conditional E-value: 0.0017
                                       T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                       + y++Ai +++r+l    e+ +     ++++ + g+ k A++ +++a +ln+  ++ +   ++ l +L+ +  A+  
  gi|298675148|ref|YP_003726898.1| 322 GEYDKAIDICSRAL-EVDEDVNTYSSRSEAYAKKGDLKNALRDINNAiNLNDDVINFWNQRGEILWALGDLRGALES 397
                                       579***********.555555555556***************************99999999999999999999888 PP

                                       H-S CS
                            ANAPC3  79 Lek 81 
                                       + k
  gi|298675148|ref|YP_003726898.1| 398 FRK 400
                                       766 PP

  == domain 7  score: 6.4 bits;  conditional E-value: 0.022
                                       T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHH CS
                            ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAia 77 
                                       +++ +A+ l +++l+  +e+ e + l++ +  ++g+ ++ +++++ka kl+++ + ++ ++   + +++k+e  ++
  gi|298675148|ref|YP_003726898.1| 423 GDHSEAVNLMDKYLSNYPEDVEILGLKGSSKAKTGNCEEGLKWVNKAlKLKENYPDAWDIKSAIYTEMGKHEASLD 498
                                       5688899999999955566666677779999999999999999999999999999999999988888888876655 PP

  == domain 8  score: 8.5 bits;  conditional E-value: 0.0049
                                       HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3  18 aetespedayllAlclylngqykrAyellrkaklnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                       +++e+pe  y ++ +l ++++y++A++ +++a  ++++   ++ +A+    L+k+e+A++++ 
  gi|298675148|ref|YP_003726898.1| 506 YDPENPELMYKKGCTLINLQRYEEAFDCINQALGKKEDVDMLVNKARLESLLGKIEDAVKTYN 568
                                       68899999999999******************5555555566666666666799999998876 PP

  == domain 9  score: 22.1 bits;  conditional E-value: 2.8e-07
                                       -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
                            ANAPC3   4 nyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaL 79 
                                       ++++A+  ++r+      ++e++ ++  cl  ++++++A++++++    + +  + ++ +  c +kL++y+eA+ ++
  gi|298675148|ref|YP_003726898.1| 559 KIEDAVKTYNRAI-ELEPRYEALNAKVACLITLERFEEAMDIIDQVdPNYLNRFEFWMNKIMCFIKLNRYDEALECI 634
                                       6899*********.66779***************************99999999********************999 PP

                                       -S CS
                            ANAPC3  80 ek 81 
                                       ++
  gi|298675148|ref|YP_003726898.1| 635 DN 636
                                       86 PP

  == domain 10  score: 18.1 bits;  conditional E-value: 4.7e-06
                                       HHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHH..HTT-HHHHHHHH- CS
                            ANAPC3   6 knAiflaerllaaetespedayllAlclylngqykrAyellrkaklnskslgcrylfAqcll..kLkkyeeAiaaLe 80 
                                       k+A+  ++r l+ ++++ +++ ++A  +y++++yk+ ++ ++ka l+ +  ++r+ + ++++   L+k  +A+  Le
  gi|298675148|ref|YP_003726898.1| 703 KDALESLNRTLSINPDDVDALRMKADLHYNLSDYKKSLKTIDKA-LEIEGDNARLWLMRSYVldSLGKTSDALESLE 778
                                       7899999999999999999*************************.666777777777777754699**********9 PP

                                       SS CS
                            ANAPC3  81 kl 82 
                                       k+
  gi|298675148|ref|YP_003726898.1| 779 KA 780
                                       85 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0    0.0012      0.57      13      34 ..     117     138 ..     114     140 .. 0.93
   2 ?    1.8   0.0      0.62     3e+02       6      33 ..     143     168 ..     142     170 .. 0.87
   3 ?    4.5   0.0     0.088        43       1      35 [.     208     242 ..     208     243 .. 0.86
   4 !   16.8   0.0     1e-05     0.005       6      32 ..     315     341 ..     314     345 .. 0.85
   5 !    8.1   0.0    0.0062         3       3      32 ..     379     408 ..     378     411 .. 0.81
   6 ?    1.6   0.0      0.73   3.6e+02       8      23 ..     418     433 ..     417     444 .. 0.82
   7 ?   -1.1   0.0       5.5   2.7e+03       8      35 ..     486     511 ..     485     512 .. 0.80
   8 ?    0.9   0.0       1.2     6e+02       7      27 ..     519     539 ..     516     545 .. 0.77
   9 ?    3.4   0.1       0.2        96       4      29 ..     549     574 ..     547     582 .. 0.77
  10 ?    2.7   0.0      0.34   1.6e+02       9      21 ..     621     633 ..     619     636 .. 0.85
  11 ?    5.1   0.1     0.055        27       5      29 ..     726     750 ..     722     755 .. 0.85
  12 ?    2.7   0.0      0.32   1.6e+02      10      34 ..     765     787 ..     761     790 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0012
                             TPR_7  13 GdyeeAielyeqsLaltkdped 34 
                                       G+y+eA+e++ ++L l +dp++
  gi|298675148|ref|YP_003726898.1| 117 GHYKEAVECCNKALKLKNDPGI 138
                                       99******************97 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.62
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkdpe 33 
                                       ++l  ++G +++A   y +  al++d +
  gi|298675148|ref|YP_003726898.1| 143 GELLKKQGLFKKARIAYGK--ALENDNY 168
                                       678889*************..9988876 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.088
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                       +L+  a++  + G+++eA+e+    L++  d+++a
  gi|298675148|ref|YP_003726898.1| 208 TLHMQADMLAESGHRKEAVEVINMILEINPDDFEA 242
                                       68888999************999988888888765 PP

  == domain 4  score: 16.8 bits;  conditional E-value: 1e-05
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkdp 32 
                                       a+ ys+lG+y++Ai+++ ++L++++d 
  gi|298675148|ref|YP_003726898.1| 315 ANHYSNLGEYDKAIDICSRALEVDEDV 341
                                       788****************77777665 PP

  == domain 5  score: 8.1 bits;  conditional E-value: 0.0062
                             TPR_7   3 lnLarlysrlGdyeeAielyeqsLaltkdp 32 
                                       ++ +++  +lGd + A+e ++++L +++ +
  gi|298675148|ref|YP_003726898.1| 379 NQRGEILWALGDLRGALESFRKALKIDDND 408
                                       66799*****************66666544 PP

  == domain 6  score: 1.6 bits;  conditional E-value: 0.73
                             TPR_7   8 lysrlGdyeeAielye 23 
                                       l ++lGd++eA+ l  
  gi|298675148|ref|YP_003726898.1| 418 LLHNLGDHSEAVNLMD 433
                                       5689*******99865 PP

  == domain 7  score: -1.1 bits;  conditional E-value: 5.5
                             TPR_7   8 lysrlGdyeeAielyeqsLaltkdpeda 35 
                                       +y ++G++e  ++  e   +l +dpe++
  gi|298675148|ref|YP_003726898.1| 486 IYTEMGKHEASLDAAEY--GLFYDPENP 511
                                       79999999998888888..888888876 PP

  == domain 8  score: 0.9 bits;  conditional E-value: 1.2
                             TPR_7   7 rlysrlGdyeeAielyeqsLa 27 
                                        +  +l++yeeA ++  q+L+
  gi|298675148|ref|YP_003726898.1| 519 CTLINLQRYEEAFDCINQALG 539
                                       567799******999999554 PP

  == domain 9  score: 3.4 bits;  conditional E-value: 0.2
                             TPR_7   4 nLarlysrlGdyeeAielyeqsLalt 29 
                                       n arl s lG+ e+A++ y ++++l+
  gi|298675148|ref|YP_003726898.1| 549 NKARLESLLGKIEDAVKTYNRAIELE 574
                                       666666679************55554 PP

  == domain 10  score: 2.7 bits;  conditional E-value: 0.34
                             TPR_7   9 ysrlGdyeeAiel 21 
                                       + +l++y+eA+e+
  gi|298675148|ref|YP_003726898.1| 621 FIKLNRYDEALEC 633
                                       5689*******99 PP

  == domain 11  score: 5.1 bits;  conditional E-value: 0.055
                             TPR_7   5 LarlysrlGdyeeAielyeqsLalt 29 
                                        a+l+ +l dy++ ++   ++L+++
  gi|298675148|ref|YP_003726898.1| 726 KADLHYNLSDYKKSLKTIDKALEIE 750
                                       599*****************98887 PP

  == domain 12  score: 2.7 bits;  conditional E-value: 0.32
                             TPR_7  10 srlGdyeeAielyeqsLaltkdped 34 
                                        +lG++++A+e +e+  a   +p+d
  gi|298675148|ref|YP_003726898.1| 765 DSLGKTSDALESLEK--AHNLSPDD 787
                                       589************..76666654 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.9   6.2e-05      0.03     166     255 ..      19     111 ..      15     134 .. 0.86
   2 !    9.3   0.4    0.0012      0.58     134     270 ..      91     228 ..      81     234 .. 0.80
   3 !    7.5   0.2    0.0042       2.1     100     185 ..     162     245 ..     152     272 .. 0.70
   4 !   16.4   0.1   8.5e-06    0.0041      93     242 ..     324     471 ..     316     481 .. 0.64
   5 !   14.4   0.0   3.4e-05     0.017      21     184 ..     354     515 ..     351     544 .. 0.50
   6 ?    6.2   0.0     0.011       5.1     144     239 ..     542     636 ..     534     648 .. 0.84
   7 ?    4.8   0.0     0.029        14      10      35 ..     721     747 ..     708     754 .. 0.81
   8 !   13.2   0.1   8.1e-05     0.039     113     183 ..     723     791 ..     718     795 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.2e-05
                            TPR_15 166 lrdyreAlalapdsselraallWlliDlgrrae...LrellkawkaraesdasLwgplaaAlllLgrpkkALeylrk 239
                                       l+d+++Al+++  +++l+++ll++ i+l + a+     + +++    +  d++ w   a+  +l+g+    Leyl++
  gi|298675148|ref|YP_003726898.1|  19 LEDIENALEMENLDDDLKQRLLYFKIELYKSANdfqTANQIENSLSMSFDDEATWYYRAFIASLMGNHVTSLEYLNN 95 
                                       899************************99888755566667777777799******99******************* PP

                            TPR_15 240 qakenrkdplwllaYA 255
                                         k+n +   wll+ A
  gi|298675148|ref|YP_003726898.1|  96 IVKNNDEMKYWLLKAA 111
                                       ***9999888988755 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0012
                            TPR_15 134 ksleeeeaaeqsaafllaraelyrqegqtdaAlrdyreAlalapd.sselraallWlliDlgrraeLrellkawkar 209
                                       ++l +  + +++  ++l+ a+     g+ ++A+++  +Al+l+ d   +++++ l     l ++a   ++ ka++++
  gi|298675148|ref|YP_003726898.1|  91 EYLNNIVKNNDEMKYWLLKAANLDFIGHYKEAVECCNKALKLKNDpGIQIKKGELLKKQGLFKKAR-IAYGKALEND 166
                                       444444556788999*************************99887336788887755544444443.2334566666 PP

                            TPR_15 210 a.esdasLwgplaaAlllLgrpkkALeylrkqakenrkdplwllaYADaleqagradeAwrl 270
                                         + d +L + +  A+++ g+ ++AL+ +++  + n  d   l   AD l  +g + eA ++
  gi|298675148|ref|YP_003726898.1| 167 NyKHDIELLKDYSHAYQMEGKVNEALKVIKRAKNLNLFDKETLHMQADMLAESGHRKEAVEV 228
                                       6899999************************9999*******************99999765 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0042
                            TPR_15 100 aekgwrrfrsprlLssalellerakdydriaellksleeeeaaeqsaafllaraelyrqegqtdaAlrdyreAlala 176
                                       a++  +  ++ +lL+ + ++++  +++++  +++k++++++ + ++   l + a +  + g+ ++A++++   l+ +
  gi|298675148|ref|YP_003726898.1| 162 ALENDNYKHDIELLKDYSHAYQMEGKVNEALKVIKRAKNLNLFDKE--TLHMQADMLAESGHRKEAVEVINMILEIN 236
                                       5555555677888888888888887777777777776666666555..67788899999999999999999999999 PP

                            TPR_15 177 pdsselraa 185
                                       pd+ e+   
  gi|298675148|ref|YP_003726898.1| 237 PDDFEAAFM 245
                                       998776544 PP

  == domain 4  score: 16.4 bits;  conditional E-value: 8.5e-06
                            TPR_15  93 pkeaarlaekgwrrfrsprlLssalellerakdydriaellksleeeeaaeqsa.afllaraelyrqegqtdaAlrd 168
                                       +++a+++   + + + +++ +ss  e++ + +d++   + l+ + +  +++++   f+  r+e+  + g+   Al+ 
  gi|298675148|ref|YP_003726898.1| 324 YDKAIDICSRALEVDEDVNTYSSRSEAYAKKGDLK---NALRDINNAINLNDDViNFWNQRGEILWALGDLRGALES 397
                                       66666666666667777777777777776666654...455555556666655325788888888888888888888 PP

                            TPR_15 169 yreAlalapdsselra...allWlliDlgrraeLrellkawkaraesdasLwgplaaAlllLgrpkkALeylrkqak 242
                                       +r+Al+ ++++s++ +   +ll +l D +   e+ +l+ ++  +  +d ++ g  ++  ++ g+ ++ L++++k +k
  gi|298675148|ref|YP_003726898.1| 398 FRKALKIDDNDSTALKhgsKLLHNLGDHS---EAVNLMDKYLSNYPEDVEILGLKGSSKAKTGNCEEGLKWVNKALK 471
                                       88888887777776641113444444444...444677777777777777777777777777777777777777554 PP

  == domain 5  score: 14.4 bits;  conditional E-value: 3.4e-05
                            TPR_15  21 qgdvkkAlevLkeaaqkaapskdteyWrtladLAwalqqedearkAyrqLlasgkaraedyerliel.lydaepkea 96 
                                       +gd+k+Al+ +++a++ +  ++  ++W ++++  wal + + a +  r+ l++++ ++  +++  +l  +  +  ea
  gi|298675148|ref|YP_003726898.1| 354 KGDLKNALRDINNAINLN--DDVINFWNQRGEILWALGDLRGALESFRKALKIDDNDSTALKHGSKLlHNLGDHSEA 428
                                       566666666663332222..444566666666666666666666666666666666665555555553344444454 PP

                            TPR_15  97 arlaekgwrrfrsprlLssalellerakdydriaellkslee.eeaaeqsaafllaraelyrqegqtdaAlrdyreA 172
                                       ++l  + +      ++    l+   +a +  + +e lk + + ++  e+ +  + + +++y++ g+++a+l +++ +
  gi|298675148|ref|YP_003726898.1| 429 VNLM-DKYLSNYPEDVEILGLKGSSKA-KTGNCEEGLKWVNKaLKLKENYPDAWDIKSAIYTEMGKHEASLDAAEYG 503
                                       4442.3333322222222222222222.2233344444443312223345555666666666666666666666666 PP

                            TPR_15 173 lalapdsselra 184
                                       l ++p++ el  
  gi|298675148|ref|YP_003726898.1| 504 LFYDPENPELMY 515
                                       666666666555 PP

  == domain 6  score: 6.2 bits;  conditional E-value: 0.011
                            TPR_15 144 qsaafllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkaraesdasLwgpl 220
                                       ++  +l+  a+l++  g+ ++A++ y +A++l+p  ++l a  +  li l+r +e+  ++ +   +  +  + w   
  gi|298675148|ref|YP_003726898.1| 542 EDVDMLVNKARLESLLGKIEDAVKTYNRAIELEPRYEALNA-KVACLITLERFEEAMDIIDQVDPNYLNRFEFWMNK 617
                                       5567899999*************************666555.56789999999999999999998889999999999 PP

                            TPR_15 221 aaAlllLgrpkkALeylrk 239
                                            +L+r+++ALe + +
  gi|298675148|ref|YP_003726898.1| 618 IMCFIKLNRYDEALECIDN 636
                                       9999999999999987765 PP

  == domain 7  score: 4.8 bits;  conditional E-value: 0.029
                            TPR_15  10 ealkl.atllykqgdvkkAlevLkeaa 35 
                                       +al++ a l+y+ +d+kk+l+ +++a+
  gi|298675148|ref|YP_003726898.1| 721 DALRMkADLHYNLSDYKKSLKTIDKAL 747
                                       778778*****************7765 PP

  == domain 8  score: 13.2 bits;  conditional E-value: 8.1e-05
                            TPR_15 113 Lssalellerakdydriaellksleeeeaae.qsaafllaraelyrqegqtdaAlrdyreAlalapdsselr 183
                                       L    +l +++ dy++    lk++ +  + e ++a+ +l+r+ +    g+t +Al+ +++A +l+pd++++ 
  gi|298675148|ref|YP_003726898.1| 723 LRMKADLHYNLSDYKK---SLKTIDKALEIEgDNARLWLMRSYVLDSLGKTSDALESLEKAHNLSPDDNDVL 791
                                       5555666666666665...45554445555558899********************************9985 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       2.5   1.2e+03      15      32 ..      72      89 ..      68      91 .. 0.85
   2 ?    1.5   0.0         1     5e+02       2      33 ..     119     156 ..     118     157 .. 0.79
   3 !    8.4   0.0    0.0063       3.1       6      33 ..     233     260 ..     231     261 .. 0.95
   4 ?   -0.5   0.0       4.4   2.2e+03      23      33 ..     318     328 ..     306     329 .. 0.77
   5 ?    3.3   0.1      0.27   1.3e+02      11      33 ..     339     361 ..     323     362 .. 0.76
   6 ?    2.8   0.1      0.38   1.9e+02       4      33 ..     366     395 ..     364     396 .. 0.84
   7 ?    5.3   0.0     0.062        30       2      32 ..     398     428 ..     397     429 .. 0.92
   8 ?   -1.6   0.0       9.9   4.8e+03       3      20 ..     433     450 ..     431     458 .. 0.79
   9 ?   -0.2   0.0       3.6   1.7e+03       4      29 ..     468     493 ..     467     501 .. 0.81
  10 !   10.4   0.0    0.0014       0.7       8      32 ..     506     530 ..     497     532 .. 0.93
  11 ?    2.2   0.0       0.6   2.9e+02      11      33 ..     542     564 ..     536     565 .. 0.89
  12 ?    0.7   0.1       1.8   8.6e+02       1      12 [.     566     577 ..     566     586 .. 0.87
  13 ?    1.7   0.0      0.86   4.2e+02       9      34 .]     604     632 ..     593     632 .. 0.86
  14 !   12.1   0.1   0.00042      0.21       4      32 ..     711     739 ..     709     741 .. 0.90
  15 !   12.0   0.0   0.00044      0.21       3      34 .]     744     775 ..     742     775 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 2.5
                            TPR_17 15 aynnLAelllknGdlmtA 32
                                       ++++A + +  G++ t 
  gi|298675148|ref|YP_003726898.1| 72 TWYYRAFIASLMGNHVTS 89
                                      6*********99998876 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 1
                            TPR_17   2 ylkaleld......PnnadaynnLAelllknGdlmtAr 33 
                                       y++a+e++      +n++     ++ell+k+G +++Ar
  gi|298675148|ref|YP_003726898.1| 119 YKEAVECCnkalklKNDPGIQIKKGELLKKQGLFKKAR 156
                                       77788886677777888888889999999999888886 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0063
                            TPR_17   6 leldPnnadaynnLAelllknGdlmtAr 33 
                                       le++P++++a +++ elll  +++++A+
  gi|298675148|ref|YP_003726898.1| 233 LEINPDDFEAAFMKLELLLIMKRYKEAE 260
                                       89***********************997 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 4.4
                            TPR_17  23 llknGdlmtAr 33 
                                       ++++G++++A+
  gi|298675148|ref|YP_003726898.1| 318 YSNLGEYDKAI 328
                                       67999999986 PP

  == domain 5  score: 3.3 bits;  conditional E-value: 0.27
                            TPR_17  11 nnadaynnLAelllknGdlmtAr 33 
                                        +++ y  + e+++k+Gdl+ A+
  gi|298675148|ref|YP_003726898.1| 339 EDVNTYSSRSEAYAKKGDLKNAL 361
                                       5799999***********99885 PP

  == domain 6  score: 2.8 bits;  conditional E-value: 0.38
                            TPR_17   4 kaleldPnnadaynnLAelllknGdlmtAr 33 
                                       +a+ l+ +  +++n+++e+l  +Gdl+ A+
  gi|298675148|ref|YP_003726898.1| 366 NAINLNDDVINFWNQRGEILWALGDLRGAL 395
                                       67777888889*********9999999886 PP

  == domain 7  score: 5.3 bits;  conditional E-value: 0.062
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       ++kal++d n++ a+    +ll+++Gd+ +A
  gi|298675148|ref|YP_003726898.1| 398 FRKALKIDDNDSTALKHGSKLLHNLGDHSEA 428
                                       78**************9999***99999887 PP

  == domain 8  score: -1.6 bits;  conditional E-value: 9.9
                            TPR_17   3 lkaleldPnnadaynnLA 20 
                                        k l ++P +++ + +++
  gi|298675148|ref|YP_003726898.1| 433 DKYLSNYPEDVEILGLKG 450
                                       68899******9987776 PP

  == domain 9  score: -0.2 bits;  conditional E-value: 3.6
                            TPR_17   4 kaleldPnnadaynnLAelllknGdl 29 
                                       kal+l  n++da+  +  ++ + G++
  gi|298675148|ref|YP_003726898.1| 468 KALKLKENYPDAWDIKSAIYTEMGKH 493
                                       89***********7777777777765 PP

  == domain 10  score: 10.4 bits;  conditional E-value: 0.0014
                            TPR_17   8 ldPnnadaynnLAelllknGdlmtA 32 
                                       +dP n+++++ ++ +l ++ ++++A
  gi|298675148|ref|YP_003726898.1| 506 YDPENPELMYKKGCTLINLQRYEEA 530
                                       59********************998 PP

  == domain 11  score: 2.2 bits;  conditional E-value: 0.6
                            TPR_17  11 nnadaynnLAelllknGdlmtAr 33 
                                        ++d + n+A+l + +G+ ++A+
  gi|298675148|ref|YP_003726898.1| 542 EDVDMLVNKARLESLLGKIEDAV 564
                                       689999************99997 PP

  == domain 12  score: 0.7 bits;  conditional E-value: 1.8
                            TPR_17   1 lylkaleldPnn 12 
                                       +y +a+el+P +
  gi|298675148|ref|YP_003726898.1| 566 TYNRAIELEPRY 577
                                       69*******975 PP

  == domain 13  score: 1.7 bits;  conditional E-value: 0.86
                            TPR_17   9 dPnn...adaynnLAelllknGdlmtArq 34 
                                       dPn+   ++++ n+  ++ k++++++A++
  gi|298675148|ref|YP_003726898.1| 604 DPNYlnrFEFWMNKIMCFIKLNRYDEALE 632
                                       8888888999****************985 PP

  == domain 14  score: 12.1 bits;  conditional E-value: 0.00042
                            TPR_17   4 kaleldPnnadaynnLAelllknGdlmtA 32 
                                       + l ++P+++da+ ++A l++++ d+++ 
  gi|298675148|ref|YP_003726898.1| 711 RTLSINPDDVDALRMKADLHYNLSDYKKS 739
                                       7799*********************9976 PP

  == domain 15  score: 12.0 bits;  conditional E-value: 0.00044
                            TPR_17   3 lkaleldPnnadaynnLAelllknGdlmtArq 34 
                                        kale++ +na ++ ++ ++l ++G++ +A++
  gi|298675148|ref|YP_003726898.1| 744 DKALEIEGDNARLWLMRSYVLDSLGKTSDALE 775
                                       79*************************99975 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0       1.4   6.8e+02       4      29 ..      74      99 ..      71     101 .. 0.83
   2 ?    2.9   0.2      0.44   2.1e+02       6      29 ..     142     165 ..     139     166 .. 0.89
   3 ?    0.7   0.0       2.1     1e+03       3      32 ..     209     238 ..     207     239 .. 0.84
   4 ?    1.6   0.0       1.1   5.3e+02      11      27 ..     318     335 ..     315     337 .. 0.79
   5 ?    4.2   0.0      0.16        79       6      28 ..     381     403 ..     380     407 .. 0.89
   6 !   10.0   0.0    0.0023       1.1      10      32 ..     419     441 ..     412     442 .. 0.87
   7 ?    0.4   0.0       2.6   1.3e+03       3      25 ..     514     536 ..     512     540 .. 0.82
   8 ?    6.7   0.0     0.026        13       5      31 ..     549     575 ..     545     577 .. 0.83
   9 ?    6.0   0.0     0.045        22       8      32 ..     619     643 ..     615     644 .. 0.93
  10 ?   -1.0   0.0       7.3   3.5e+03      15      32 ..     701     718 ..     675     719 .. 0.82
  11 ?   -0.4   0.0       4.8   2.3e+03       1      27 [.     721     747 ..     721     750 .. 0.83
  12 ?    8.0   0.0      0.01       4.9       2      32 ..     754     786 ..     753     787 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 1.4
                                      HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6  4 yklalsyrklgdtdkAlealerlike 29
                                      y++a     +g++ ++le+l++++k+
  gi|298675148|ref|YP_003726898.1| 74 YYRAFIASLMGNHVTSLEYLNNIVKN 99
                                      77777777779************997 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.44
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtdkAlealerlike 29 
                                        +++++k+g   kA+ a+ + +++
  gi|298675148|ref|YP_003726898.1| 142 KGELLKKQGLFKKARIAYGKALEN 165
                                       6899999************99986 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 2.1
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   3 lyklalsyrklgdtdkAlealerlikeYPd 32 
                                       l ++a  + + g   +A+e  + +++  Pd
  gi|298675148|ref|YP_003726898.1| 209 LHMQADMLAESGHRKEAVEVINMILEINPD 238
                                       66788777886699************9998 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 1.1
                                       HH.HHHHHHHHHHHHHHH CS
                             TPR_6  11 rk.lgdtdkAlealerli 27 
                                       ++ lg++dkA+++  r +
  gi|298675148|ref|YP_003726898.1| 318 YSnLGEYDKAIDICSRAL 335
                                       44499******9987766 PP

  == domain 5  score: 4.2 bits;  conditional E-value: 0.16
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtdkAlealerlik 28 
                                       +++ + +lgd + Ale +++ +k
  gi|298675148|ref|YP_003726898.1| 381 RGEILWALGDLRGALESFRKALK 403
                                       689999999***********987 PP

  == domain 6  score: 10.0 bits;  conditional E-value: 0.0023
                                       HHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6  10 yrklgdtdkAlealerlikeYPd 32 
                                       + +lgd+++A+ ++++ +++YP+
  gi|298675148|ref|YP_003726898.1| 419 LHNLGDHSEAVNLMDKYLSNYPE 441
                                       55689*****************7 PP

  == domain 7  score: 0.4 bits;  conditional E-value: 2.6
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   3 lyklalsyrklgdtdkAlealer 25 
                                       +yk +  +++l+++++A +  ++
  gi|298675148|ref|YP_003726898.1| 514 MYKKGCTLINLQRYEEAFDCINQ 536
                                       99********77*****887665 PP

  == domain 8  score: 6.7 bits;  conditional E-value: 0.026
                                       HHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   5 klalsyrklgdtdkAlealerlikeYP 31 
                                       + a++   lg+ ++A+++++r i+  P
  gi|298675148|ref|YP_003726898.1| 549 NKARLESLLGKIEDAVKTYNRAIELEP 575
                                       5677777889*************9887 PP

  == domain 9  score: 6.0 bits;  conditional E-value: 0.045
                                       HHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   8 lsyrklgdtdkAlealerlikeYPd 32 
                                       ++++kl+++d+Ale  +++ ++ Pd
  gi|298675148|ref|YP_003726898.1| 619 MCFIKLNRYDEALECIDNFGNNVPD 643
                                       89***99************999997 PP

  == domain 10  score: -1.0 bits;  conditional E-value: 7.3
                                       HHHHHHHHHHHHHHH-TT CS
                             TPR_6  15 dtdkAlealerlikeYPd 32 
                                       ++ +Ale l+r ++  Pd
  gi|298675148|ref|YP_003726898.1| 701 NPKDALESLNRTLSINPD 718
                                       667899999999988887 PP

  == domain 11  score: -0.4 bits;  conditional E-value: 4.8
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerli 27 
                                       dAl + a ++++l d+ k+l++ ++ +
  gi|298675148|ref|YP_003726898.1| 721 DALRMKADLHYNLSDYKKSLKTIDKAL 747
                                       577788999***99***9999988776 PP

  == domain 12  score: 8.0 bits;  conditional E-value: 0.01
                                       HHHHHHHHHH.H.HHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   2 Alyklalsyr.k.lgdtdkAlealerlikeYPd 32 
                                       A ++l +sy    lg+t++Ale le+  +  Pd
  gi|298675148|ref|YP_003726898.1| 754 ARLWLMRSYVlDsLGKTSDALESLEKAHNLSPD 786
                                       78999999995556*************999998 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.6      0.46   2.2e+02      30      99 ..      47     127 ..      18     142 .. 0.66
   2 ?    1.1   3.1      0.82     4e+02      48     116 ..     239     315 ..     139     316 .. 0.68
   3 ?    4.0   0.9       0.1        49      20     102 ..     246     335 ..     224     349 .. 0.57
   4 ?   -0.3   0.0       2.1     1e+03      30      98 ..     357     432 ..     322     446 .. 0.54
   5 !   19.2   0.2   1.9e-06    0.0009      12     102 ..     509     604 ..     492     606 .. 0.81
   6 !   13.7   0.0   9.7e-05     0.047      10      41 ..     602     638 ..     599     682 .. 0.81
   7 !    8.9   0.0     0.003       1.4      51     102 ..     726     781 ..     699     797 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.46
                      SRP_TPR_like  30 yeeaLkllkkgs........alsedvrfEkaYvlYklkkykkalkilkkveaee...kvkvlksqvlYrlgsyekAY 95 
                                       y+ a  + + ++          +e + + +a++   + +   +l+ l+++ +++   k   lk+  l ++g+y++A 
  gi|298675148|ref|YP_003726898.1|  47 YKSANDFQTANQienslsmsFDDEATWYYRAFIASLMGNHVTSLEYLNNIVKNNdemKYWLLKAANLDFIGHYKEAV 123
                                       44444444444444444332334567788888888888888888888775433223477789999999999999998 PP

                      SRP_TPR_like  96 klLs 99 
                                       ++  
  gi|298675148|ref|YP_003726898.1| 124 ECCN 127
                                       7764 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.82
                      SRP_TPR_like  48 rfEkaYvlYkl....kkykkalkilkkveaee...kvk.vlksqvlYrlgsyekAYklLskekkedelvvNllAvds 116
                                        fE a++   l    k+yk+a ++++ + +++   + +   k+++l   g+y +A + + + +k + + +N+  +++
  gi|298675148|ref|YP_003726898.1| 239 DFEAAFMKLELllimKRYKEAENLVSYIFNSNpdtGDQwLYKAKILSTYGYYTEADEAINEAEKLNPVLANISLIKA 315
                                       46666654443233388999988777665543333333145899999999999999999888888888888877665 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.1
                      SRP_TPR_like  20 kvvaliklekyeeaLkllk...kgsalsedvrfEkaYvlYklkkykkalkilkkveaee....kvkvlksqvlYrlg 89 
                                       k   l+ + +y+ea +l++   + +  ++d    ka +l     y++a + ++++e+ +    +++ +k+  +  lg
  gi|298675148|ref|YP_003726898.1| 246 KLELLLIMKRYKEAENLVSyifNSNPDTGDQWLYKAKILSTYGYYTEADEAINEAEKLNpvlaNISLIKANHYSNLG 322
                                       55556667777777444331113333445555567777777777777777777776654332344556677777777 PP

                      SRP_TPR_like  90 syekAYklLskek 102
                                       +y+kA ++ s+  
  gi|298675148|ref|YP_003726898.1| 323 EYDKAIDICSRAL 335
                                       7777777766544 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 2.1
                      SRP_TPR_like  30 yeeaLkllkkgsalsedvr.f..EkaYvlYklkkykkalkilkkveaee..kvkvlk..sqvlYrlgsyekAYklL 98 
                                        ++aL+ ++++ +l++dv+ f   +  +l+ l  ++ al+ ++k+ + +   ++ lk  s++l  lg++++A +l+
  gi|298675148|ref|YP_003726898.1| 357 LKNALRDINNAINLNDDVInFwnQRGEILWALGDLRGALESFRKALKIDdnDSTALKhgSKLLHNLGDHSEAVNLM 432
                                       4555555555555555543212244555555555555555555443322123333433377777777777776554 PP

  == domain 5  score: 19.2 bits;  conditional E-value: 1.9e-06
                      SRP_TPR_like  12 egkelkkfkvvaliklekyeeaLkllkkgs..alsedvrfEkaYvlYklkkykkalkilkkveaee.kvkvlksqv. 84 
                                       e++el   k  +li+l++yeea   ++++   + + d+ + ka  +  l k ++a+k+ +++ + e + + l+++v 
  gi|298675148|ref|YP_003726898.1| 509 ENPELMYKKGCTLINLQRYEEAFDCINQALgkKEDVDMLVNKARLESLLGKIEDAVKTYNRAIELEpRYEALNAKVa 585
                                       566666669999*************999762244557889*******************99888777*****99862 PP

                      SRP_TPR_like  85 .lYrlgsyekAYklLskek 102
                                        l  l+ +e+A +++ +++
  gi|298675148|ref|YP_003726898.1| 586 cLITLERFEEAMDIIDQVD 604
                                       267899*****99987765 PP

  == domain 6  score: 13.7 bits;  conditional E-value: 9.7e-05
                      SRP_TPR_like  10 rlegkelkkf.....kvvaliklekyeeaLkllkkgs 41 
                                       +++ + l++f     k++++ikl++y+eaL+ +++ +
  gi|298675148|ref|YP_003726898.1| 602 QVDPNYLNRFefwmnKIMCFIKLNRYDEALECIDNFG 638
                                       666777889999999****************999866 PP

  == domain 7  score: 8.9 bits;  conditional E-value: 0.003
                      SRP_TPR_like  51 kaYvlYklkkykkalkilkkv...eaee.kvkvlksqvlYrlgsyekAYklLskek 102
                                       ka  +Y l  ykk+lk+++k+   e+++ ++  ++s vl  lg+ ++A + L k +
  gi|298675148|ref|YP_003726898.1| 726 KADLHYNLSDYKKSLKTIDKAleiEGDNaRLWLMRSYVLDSLGKTSDALESLEKAH 781
                                       78899************997522255556778899999999999999999995443 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       3.8   1.8e+03       5      29 ..      74      98 ..      72     103 .. 0.83
   2 ?    2.0   0.0      0.46   2.3e+02      14      30 ..     116     132 ..     116     136 .. 0.88
   3 ?    1.4   0.0      0.69   3.4e+02      18      37 ..     223     242 ..     220     247 .. 0.86
   4 ?   -1.3   0.0       4.9   2.4e+03      14      33 ..     253     272 ..     252     273 .. 0.85
   5 !    7.4   0.0    0.0098       4.7      13      33 ..     320     340 ..     317     344 .. 0.89
   6 ?   -0.4   0.0       2.5   1.2e+03       8      27 ..     348     367 ..     347     373 .. 0.83
   7 ?    3.4   0.0      0.17        84      14      45 ..     422     453 ..     420     463 .. 0.89
   8 ?    0.0   0.0       1.9   9.1e+02      12      49 ..     454     491 ..     452     495 .. 0.87
   9 ?   -0.3   0.0       2.5   1.2e+03      13      29 ..     523     539 ..     514     544 .. 0.86
  10 ?    3.4   0.0      0.17        82      12      27 ..     622     637 ..     621     643 .. 0.90
  11 ?   -1.9   0.0       7.8   3.8e+03      19      39 ..     704     724 ..     703     727 .. 0.83
  12 !   13.3   0.0   0.00014     0.067      11      35 ..     730     754 ..     730     766 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 3.8
                                      HHHHHHHHHHT-HHHHHHHHHHHHH CS
                        Fis1_TPR_C  5 YylAlGhyklgeYseArryvdalLe 29
                                      Yy A+    +g++ ++++y++ + +
  gi|298675148|ref|YP_003726898.1| 74 YYRAFIASLMGNHVTSLEYLNNIVK 98
                                      7777777779*********998876 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.46
                                       HT-HHHHHHHHHHHHHH CS
                        Fis1_TPR_C  14 lgeYseArryvdalLei 30 
                                       +g Y+eA ++++  L++
  gi|298675148|ref|YP_003726898.1| 116 IGHYKEAVECCNKALKL 132
                                       589**********9986 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.69
                                       HHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C  18 seArryvdalLeiEPenrQa 37 
                                       +eA + ++++Lei P+   a
  gi|298675148|ref|YP_003726898.1| 223 KEAVEVINMILEINPDDFEA 242
                                       58999**********98666 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 4.9
                                       HT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPe 33 
                                       +++Y+eA ++v  + +  P+
  gi|298675148|ref|YP_003726898.1| 253 MKRYKEAENLVSYIFNSNPD 272
                                       799*****999988887776 PP

  == domain 5  score: 7.4 bits;  conditional E-value: 0.0098
                                       HHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  13 klgeYseArryvdalLeiEPe 33 
                                        lgeY++A   + + Le++ +
  gi|298675148|ref|YP_003726898.1| 320 NLGEYDKAIDICSRALEVDED 340
                                       79***************9976 PP

  == domain 6  score: -0.4 bits;  conditional E-value: 2.5
                                       HHHHHHHT-HHHHHHHHHHH CS
                        Fis1_TPR_C   8 AlGhyklgeYseArryvdal 27 
                                       + +++k g+ ++A+r ++  
  gi|298675148|ref|YP_003726898.1| 348 SEAYAKKGDLKNALRDINNA 367
                                       5699**********987765 PP

  == domain 7  score: 3.4 bits;  conditional E-value: 0.17
                                       HT-HHHHHHHHHHHHHHTTS-HHHHHHHHHHH CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPenrQaqsLkelie 45 
                                       lg++seA +++d  L+  Pe    + Lk   +
  gi|298675148|ref|YP_003726898.1| 422 LGDHSEAVNLMDKYLSNYPEDVEILGLKGSSK 453
                                       8*******************999999997666 PP

  == domain 8  score: 0.0 bits;  conditional E-value: 1.9
                                       HHHT-HHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHH CS
                        Fis1_TPR_C  12 yklgeYseArryvdalLeiEPenrQaqsLkeliedkik 49 
                                       +k g+ +e ++ v+  L++  +   a + k++i  ++ 
  gi|298675148|ref|YP_003726898.1| 454 AKTGNCEEGLKWVNKALKLKENYPDAWDIKSAIYTEMG 491
                                       799999*************9999999999999877775 PP

  == domain 9  score: -0.3 bits;  conditional E-value: 2.5
                                       HHT-HHHHHHHHHHHHH CS
                        Fis1_TPR_C  13 klgeYseArryvdalLe 29 
                                        l++Y+eA  ++++ L 
  gi|298675148|ref|YP_003726898.1| 523 NLQRYEEAFDCINQALG 539
                                       799********999885 PP

  == domain 10  score: 3.4 bits;  conditional E-value: 0.17
                                       HHHT-HHHHHHHHHHH CS
                        Fis1_TPR_C  12 yklgeYseArryvdal 27 
                                       +kl +Y+eA++++d +
  gi|298675148|ref|YP_003726898.1| 622 IKLNRYDEALECIDNF 637
                                       59***********986 PP

  == domain 11  score: -1.9 bits;  conditional E-value: 7.8
                                       HHHHHHHHHHHHTTS-HHHHH CS
                        Fis1_TPR_C  19 eArryvdalLeiEPenrQaqs 39 
                                       +A++ +++ L+i P+   a+ 
  gi|298675148|ref|YP_003726898.1| 704 DALESLNRTLSINPDDVDALR 724
                                       799999********9887765 PP

  == domain 12  score: 13.3 bits;  conditional E-value: 0.00014
                                       HHHHT-HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C  11 hyklgeYseArryvdalLeiEPenr 35 
                                       hy l +Y+++++ +d  LeiE +n 
  gi|298675148|ref|YP_003726898.1| 730 HYNLSDYKKSLKTIDKALEIEGDNA 754
                                       8********************9995 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       2.1     1e+03      85     114 ..     109     137 ..      87     142 .. 0.71
   2 !    7.0   0.0    0.0069       3.3      31     119 ..     163     245 ..     161     254 .. 0.71
   3 !   13.5   0.0   7.2e-05     0.035       2     112 ..     309     406 ..     308     424 .. 0.83
   4 ?    4.4   0.0     0.043        21     146     265 ..     528     636 ..     524     641 .. 0.65
   5 ?    5.6   0.0     0.019         9     267     309 ..     741     783 ..     718     788 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.1
                          TPR_MalT  85 qqaeilvaqGrLheAletyeqalqlateqg 114
                                       + a++ +  G+ +eA+e +++al+l  ++g
  gi|298675148|ref|YP_003726898.1| 109 KAANLDFI-GHYKEAVECCNKALKLKNDPG 137
                                       44555555.788888888888888877765 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0069
                          TPR_MalT  31 lpeddllariaatavlGeasllqGdleaAlqalqeaeklarqadslhvallallqqaeilvaqGrLheAletyeqal 107
                                       l++d++ + i  +  + +a++++G++++Al++ + a  l      ++    +l  qa++l + G+ +eA+e+ +++l
  gi|298675148|ref|YP_003726898.1| 163 LENDNYKHDIELLKDYSHAYQMEGKVNEALKVIKRAKNLN----LFD--KETLHMQADMLAESGHRKEAVEVINMIL 233
                                       5666666677777777788888888888877665555543....333..4455678********************* PP

                          TPR_MalT 108 qlateqglqqlp 119
                                       +  ++  ++++ 
  gi|298675148|ref|YP_003726898.1| 234 EINPDDFEAAFM 245
                                       988877666655 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 7.2e-05
                          TPR_MalT   2 eiaalrAllaiasgdaeralelArqALallpeddllariaatavlGeasllqGdleaAlqalqeaeklarqadslhv 78 
                                        i+ ++A  + + g+ ++a++++ +AL+  ++ +      ++++  ea+  +Gdl++Al+  + a+ l    d ++ 
  gi|298675148|ref|YP_003726898.1| 309 NISLIKANHYSNLGEYDKAIDICSRALEVDEDVN------TYSSRSEAYAKKGDLKNALRDINNAINLN--DDVIN- 376
                                       688899**********************977766......6677789999************9999987..44444. PP

                          TPR_MalT  79 allallqqaeilvaqGrLheAletyeqalqlate 112
                                         +   q +eil a G+L+ Ale +++al+  ++
  gi|298675148|ref|YP_003726898.1| 377 -FW--NQRGEILWALGDLRGALESFRKALKI-DD 406
                                       .34..467*********************94.44 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.043
                          TPR_MalT 146 qeGielleql.epeaaldayvllarialaqGdleeAetllekaeelaresnfhvdwlanaeevrvrlwlaqgdlaaa 221
                                       +e+ +++ q  +++  +d++v  ar+    G++e+A ++ ++a el  + +           ++v+ +     l+++
  gi|298675148|ref|YP_003726898.1| 528 EEAFDCINQAlGKKEDVDMLVNKARLESLLGKIEDAVKTYNRAIELEPRYEA--------LNAKVACLI---TLERF 593
                                       5666766665578888888888888888888888888888888888664433........223333222...34555 PP

                          TPR_MalT 222 erwleaaelpsdddnhflelel.rnlarvllalgrydeAleller 265
                                       e++++ + +   d n+++++e+ +n + + ++l+rydeAle +++
  gi|298675148|ref|YP_003726898.1| 594 EEAMDIIDQV--DPNYLNRFEFwMNKIMCFIKLNRYDEALECIDN 636
                                       5555555433..346777777658888888888999999887765 PP

  == domain 5  score: 5.6 bits;  conditional E-value: 0.019
                          TPR_MalT 267 lkaaeelgrvrslieiliLqalalqaqgreeeAlaaLeqALeL 309
                                        +  ++l++ ++  + +++++++l+ +g++ +Al++Le+A +L
  gi|298675148|ref|YP_003726898.1| 741 KTIDKALEIEGDNARLWLMRSYVLDSLGKTSDALESLEKAHNL 783
                                       55556678889999************************99666 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0       0.1        48      80     140 ..      88     148 ..      62     151 .. 0.66
   2 ?    1.2   0.0      0.74   3.6e+02      91     128 ..     163     200 ..     158     212 .. 0.88
   3 ?   -0.9   0.0       3.2   1.5e+03     104     128 ..     210     234 ..     187     237 .. 0.84
   4 !    7.7   0.1    0.0069       3.4      23      97 ..     315     390 ..     306     414 .. 0.76
   5 ?    1.9   0.0      0.45   2.2e+02      62      97 ..     484     519 ..     479     525 .. 0.82
   6 ?    2.9   0.0      0.22     1e+02      99     129 ..     543     573 ..     519     581 .. 0.77
   7 ?    0.4   0.0       1.3   6.1e+02      64      80 ..     620     636 ..     614     639 .. 0.88
   8 !    8.1   0.0    0.0053       2.6      65     129 ..     730     783 ..     710     792 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.1
                                       HHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH.....HHH--S--TTH CS
                           DUF3856  80 kalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem.....iaerkGelkgk 140
                                       ++l+y+n   + ++de k W+     +a+ l+ +G+++ea++  ++a  +     i+ +kGel +k
  gi|298675148|ref|YP_003726898.1|  88 TSLEYLNNIVK-NNDEMKYWL----LKAANLDFIGHYKEAVECCNKALKLkndpgIQIKKGELLKK 148
                                       46777776554.678888886....48888999999999998888887653333355666666555 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.74
                                       TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  91 leqdeGklWiaavfsravaleelGrkdealkafrmage 128
                                       le+d+ k  i  + + ++a++  G+ +ealk  + a++
  gi|298675148|ref|YP_003726898.1| 163 LENDNYKHDIELLKDYSHAYQMEGKVNEALKVIKRAKN 200
                                       788999999999999999*************9999876 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 3.2
                                       HHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856 104 fsravaleelGrkdealkafrmage 128
                                         +a  l+e G+++ea++  +m+ e
  gi|298675148|ref|YP_003726898.1| 210 HMQADMLAESGHRKEAVEVINMILE 234
                                       5578889999999999999999887 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0069
                                       T-HHHHHHHHHHHHHH.HTTS-TTS---HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHH CS
                           DUF3856  23 gayeeaaasyrkalev.srtipaeeafdheGfdalchaglsealaklgrydealesadkalryfnrrGeleqdeGk 97 
                                       +++     +y ka+++ sr++  +e  +     + ++a   +    l++ ++a++  d  ++++n+rGe+  + G 
  gi|298675148|ref|YP_003726898.1| 315 ANHYSNLGEYDKAIDIcSRALEVDEDVNTYSSRSEAYAKKGDLKNALRDINNAINLNDDVINFWNQRGEILWALGD 390
                                       4444455677888886467888888777777777888988899999999999999999999*******98766665 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 0.45
                                       HHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHH CS
                           DUF3856  62 sealaklgrydealesadkalryfnrrGeleqdeGk 97 
                                       s  ++++g+++++l +a+ +l y     el   +G 
  gi|298675148|ref|YP_003726898.1| 484 SAIYTEMGKHEASLDAAEYGLFYDPENPELMYKKGC 519
                                       566899*****************8888888777665 PP

  == domain 6  score: 2.9 bits;  conditional E-value: 0.22
                                       HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  99 WiaavfsravaleelGrkdealkafrmagem 129
                                        + +++++a+  + lG+ ++a+k+++ a e+
  gi|298675148|ref|YP_003726898.1| 543 DVDMLVNKARLESLLGKIEDAVKTYNRAIEL 573
                                       4677888888777889999999999999885 PP

  == domain 7  score: 0.4 bits;  conditional E-value: 1.3
                                       HHHHTT-HHHHHHHHHH CS
                           DUF3856  64 alaklgrydealesadk 80 
                                        ++kl rydeale++d+
  gi|298675148|ref|YP_003726898.1| 620 CFIKLNRYDEALECIDN 636
                                       5899********99875 PP

  == domain 8  score: 8.1 bits;  conditional E-value: 0.0053
                                       HHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  65 laklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                         +l +y+++l+++dkal       e+e d+ +lW+     r+  l++lG++++al+++++a ++
  gi|298675148|ref|YP_003726898.1| 730 HYNLSDYKKSLKTIDKAL-------EIEGDNARLWL----MRSYVLDSLGKTSDALESLEKAHNL 783
                                       556777777777777777.......8999******7....5999***************999765 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       2.1     1e+03      25      37 ..     119     131 ..     116     136 .. 0.69
   2 ?   -1.7   0.0         6   2.9e+03      10      27 ..     180     197 ..     177     200 .. 0.77
   3 ?   -0.2   0.0         2   9.9e+02      15      24 ..     253     262 ..     249     263 .. 0.85
   4 ?    7.0   0.0     0.012       5.7       9      31 ..     315     337 ..     315     342 .. 0.89
   5 ?   -0.8   0.0       3.3   1.6e+03       4      28 ..     343     367 ..     341     371 .. 0.80
   6 ?    5.7   0.0     0.029        14       8      31 ..     381     404 ..     379     404 .. 0.90
   7 ?    4.7   0.0     0.062        30      11      27 ..     418     434 ..     416     436 .. 0.90
   8 ?   -0.7   0.0       2.9   1.4e+03      10      24 ..     485     499 ..     484     501 .. 0.82
   9 ?    1.2   0.0      0.76   3.7e+02       9      29 ..     518     538 ..     516     544 .. 0.73
  10 ?   -2.3   0.0       9.5   4.6e+03       9      30 ..     551     572 ..     547     573 .. 0.64
  11 ?   -1.3   0.0       4.5   2.2e+03      15      23 ..     624     632 ..     623     634 .. 0.82
  12 ?   -1.0   0.0       3.6   1.8e+03      11      30 ..     763     782 ..     761     784 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 2.1
                            TPR_10  25 leealairrrllG 37 
                                       ++ea++++ ++l 
  gi|298675148|ref|YP_003726898.1| 119 YKEAVECCNKALK 131
                                       6777777777775 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 6
                            TPR_10  10 nalrqrgrydeAeallee 27 
                                       +a++  g+ +eA++  ++
  gi|298675148|ref|YP_003726898.1| 180 HAYQMEGKVNEALKVIKR 197
                                       689999999999986555 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 2
                            TPR_10  15 rgrydeAeal 24 
                                       ++ry+eAe+l
  gi|298675148|ref|YP_003726898.1| 253 MKRYKEAENL 262
                                       79******98 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.012
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       an ++++g+yd+A +++ +al++
  gi|298675148|ref|YP_003726898.1| 315 ANHYSNLGEYDKAIDICSRALEV 337
                                       788*****************997 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 3.3
                            TPR_10   4 slnNLanalrqrgrydeAealleea 28 
                                       +++  + a+ + g+++ A+++   a
  gi|298675148|ref|YP_003726898.1| 343 TYSSRSEAYAKKGDLKNALRDINNA 367
                                       77778899**********9986555 PP

  == domain 6  score: 5.7 bits;  conditional E-value: 0.029
                            TPR_10   8 LanalrqrgrydeAealleealai 31 
                                        + +l+++g++ +A++ +++al i
  gi|298675148|ref|YP_003726898.1| 381 RGEILWALGDLRGALESFRKALKI 404
                                       5889*****************986 PP

  == domain 7  score: 4.7 bits;  conditional E-value: 0.062
                            TPR_10  11 alrqrgrydeAeallee 27 
                                       +l+++g++ eA++l+++
  gi|298675148|ref|YP_003726898.1| 418 LLHNLGDHSEAVNLMDK 434
                                       689***********975 PP

  == domain 8  score: -0.7 bits;  conditional E-value: 2.9
                            TPR_10  10 nalrqrgrydeAeal 24 
                                       ++++++g+++++++ 
  gi|298675148|ref|YP_003726898.1| 485 AIYTEMGKHEASLDA 499
                                       68********99876 PP

  == domain 9  score: 1.2 bits;  conditional E-value: 0.76
                            TPR_10   9 analrqrgrydeAealleeal 29 
                                       +++l +++ry+eA +   +al
  gi|298675148|ref|YP_003726898.1| 518 GCTLINLQRYEEAFDCINQAL 538
                                       667888888888877666665 PP

  == domain 10  score: -2.3 bits;  conditional E-value: 9.5
                            TPR_10   9 analrqrgrydeAealleeala 30 
                                       a++ + +g+ ++A++ + +a++
  gi|298675148|ref|YP_003726898.1| 551 ARLESLLGKIEDAVKTYNRAIE 572
                                       5556667777777776666665 PP

  == domain 11  score: -1.3 bits;  conditional E-value: 4.5
                            TPR_10  15 rgrydeAea 23 
                                       ++rydeA++
  gi|298675148|ref|YP_003726898.1| 624 LNRYDEALE 632
                                       689999987 PP

  == domain 12  score: -1.0 bits;  conditional E-value: 3.6
                            TPR_10  11 alrqrgrydeAealleeala 30 
                                       +l ++g+  +A++ le+a +
  gi|298675148|ref|YP_003726898.1| 763 VLDSLGKTSDALESLEKAHN 782
                                       567899999*******9976 PP

>> ATP13  Mitochondrial ATPase expression
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.35   1.7e+02      48      79 ..     166     197 ..     145     200 .. 0.84
   2 ?   -2.0   0.0       6.6   3.2e+03      62      82 ..     349     369 ..     347     380 .. 0.74
   3 ?   -1.1   0.0       3.3   1.6e+03      68      86 ..     423     441 ..     416     448 .. 0.80
   4 !   10.1   0.0    0.0011      0.55      36      85 ..     559     608 ..     531     618 .. 0.82
   5 ?    3.8   0.0       0.1        51      62      98 ..     619     654 ..     616     669 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.35
                             ATP13  48 splyPtselLkaivssfsynneiesAlklvdk 79 
                                       +    + elLk   +++  ++++++Alk++++
  gi|298675148|ref|YP_003726898.1| 166 DNYKHDIELLKDYSHAYQMEGKVNEALKVIKR 197
                                       44456899*********************975 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 6.6
                             ATP13  62 ssfsynneiesAlklvdkfsk 82 
                                       +++++++++++Al+ +++ ++
  gi|298675148|ref|YP_003726898.1| 349 EAYAKKGDLKNALRDINNAIN 369
                                       589999999999998887665 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 3.3
                             ATP13  68 neiesAlklvdkfskkYpe 86 
                                       ++ ++A++l+dk  + Ype
  gi|298675148|ref|YP_003726898.1| 423 GDHSEAVNLMDKYLSNYPE 441
                                       37889************96 PP

  == domain 4  score: 10.1 bits;  conditional E-value: 0.0011
                             ATP13  36 kleeketkvksdsplyPtselLkaivssfsynneiesAlklvdkfskkYp 85 
                                       k+e+  +++++  +l P +e L a v +++  +++e+A++++d++   Y 
  gi|298675148|ref|YP_003726898.1| 559 KIEDAVKTYNRAIELEPRYEALNAKVACLITLERFEEAMDIIDQVDPNYL 608
                                       4445455666677899*****************************99887 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.1
                             ATP13  62 ssfsynneiesAlklvdkfskkYpeielkkefWeell 98 
                                       ++f++ n++++Al+ +d+f +  p  e+k+ ++++l 
  gi|298675148|ref|YP_003726898.1| 619 MCFIKLNRYDEALECIDNFGNNVP-DEIKEYMFQTLS 654
                                       689999******************.899998888875 PP

>> ChAPs  ChAPs (Chs5p-Arf1p-binding proteins)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       7.5   3.6e+03     276     305 ..      45      74 ..      38     108 .. 0.67
   2 ?    5.5   0.2     0.015       7.3     218     281 ..     190     253 ..     178     273 .. 0.80
   3 ?    5.2   0.2     0.018       8.6     178     293 ..     249     366 ..     242     372 .. 0.82
   4 ?    3.5   0.0     0.059        29     218     288 ..     427     497 ..     403     500 .. 0.92
   5 !    8.3   0.3    0.0021         1     183     291 ..     525     634 ..     519     661 .. 0.85
   6 ?    5.4   0.1     0.016       7.8     217     294 ..     703     780 ..     639     800 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 7.5
                                       HHHHHTT-HHHHHHHHHT----SS------ CS
                             ChAPs 276 kvYikledienALltLNscPmftykekdvl 305
                                       + Y + +d++ A  + Ns+ m+   e   +
  gi|298675148|ref|YP_003726898.1|  45 ELYKSANDFQTANQIENSLSMSFDDEATWY 74 
                                       667788888888888888888865554433 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.015
                                       HHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHT CS
                             ChAPs 218 davkllneeleeeekdaelLllqaefllskkkeelAlevakravksaPsefktWalLvkvYikl 281
                                       +a+k+++++ + +  d e L++qa+ l +  + + A+ev +   ++ P +f+  ++  +  + +
  gi|298675148|ref|YP_003726898.1| 190 EALKVIKRAKNLNLFDKETLHMQADMLAESGHRKEAVEVINMILEINPDDFEAAFMKLELLLIM 253
                                       689999999999999************************************9766555544444 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.018
                                       HHHHHT-HHHHHHHHHHHHTT-GGG...HHHHHHHHHHTT-HHHHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--H CS
                             ChAPs 178 lvrltkrydralellekLkeeepev...villarvllladeEvdavkllneeleeeekdaelLllqaefllskkkee 251
                                       l+ + kry++a +l++ + +++p+        a++l +     +a + +ne+ + ++  a++ l++a++  +  +++
  gi|298675148|ref|YP_003726898.1| 249 LLLIMKRYKEAENLVSYIFNSNPDTgdqWLYKAKILSTYGYYTEADEAINEAEKLNPVLANISLIKANHYSNLGEYD 325
                                       5556778888888888888888876221233467777777778888888888888888899999************* PP

                                       HHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHT CS
                             ChAPs 252 lAlevakravksaPsefktWalLvkvYikledienALltLNs 293
                                        A+++ +ra ++   + +t+   ++ Y k +d++nAL  +N 
  gi|298675148|ref|YP_003726898.1| 326 KAIDICSRALEVD-EDVNTYSSRSEAYAKKGDLKNALRDINN 366
                                       **********985.899********************98885 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.059
                                       HHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHH CS
                             ChAPs 218 davkllneeleeeekdaelLllqaefllskkkeelAlevakravksaPsefktWalLvkvYikledienAL 288
                                       +av+l+ + l++ ++d+e+L l+     +  + e  l+  ++a k+  +    W + + +Y++++  e  L
  gi|298675148|ref|YP_003726898.1| 427 EAVNLMDKYLSNYPEDVEILGLKGSSKAKTGNCEEGLKWVNKALKLKENYPDAWDIKSAIYTEMGKHEASL 497
                                       8************************99999999*******************************9998876 PP

  == domain 5  score: 8.3 bits;  conditional E-value: 0.0021
                                       T-HHHHHHHHHHHHTT-GGGHHHHHHHHH..HTT-HHHHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHH CS
                             ChAPs 183 krydralellekLkeeepevvillarvll..ladeEvdavkllneeleeeekdaelLllqaefllskkkeelAleva 257
                                       +ry++a + +++   ++ +v +l+ +  l  l  +  davk+ n+++e  e  +e L +++  l+  ++ e A+++ 
  gi|298675148|ref|YP_003726898.1| 525 QRYEEAFDCINQALGKKEDVDMLVNKARLesLLGKIEDAVKTYNRAIEL-EPRYEALNAKVACLITLERFEEAMDII 600
                                       67888888888888888888888876655224555569*********55.556999********************* PP

                                       HHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHH CS
                             ChAPs 258 kravksaPsefktWalLvkvYikledienALltL 291
                                       ++      + f+ W+    ++ikl+ +++AL  +
  gi|298675148|ref|YP_003726898.1| 601 DQVDPNYLNRFEFWMNKIMCFIKLNRYDEALECI 634
                                       **999999**********************9765 PP

  == domain 6  score: 5.4 bits;  conditional E-value: 0.016
                                       HHHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHT CS
                             ChAPs 217 vdavkllneeleeeekdaelLllqaefllskkkeelAlevakravksaPsefktWalLvkvYikledienALltLNs 293
                                        da++ ln++l+ +++d++ L ++a+   + ++++  l++ ++a ++   + + W + + v  +l+ +++AL +L  
  gi|298675148|ref|YP_003726898.1| 703 KDALESLNRTLSINPDDVDALRMKADLHYNLSDYKKSLKTIDKALEIEGDNARLWLMRSYVLDSLGKTSDALESLEK 779
                                       489999*************************************************9999999999******999976 PP

                                       - CS
                             ChAPs 294 c 294
                                        
  gi|298675148|ref|YP_003726898.1| 780 A 780
                                       5 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0    0.0005      0.24     144     179 ..     134     169 ..      86     177 .. 0.80
   2 ?    3.4   0.1      0.12        56     125     166 ..     184     226 ..     179     248 .. 0.89
   3 ?    6.5   0.0     0.013       6.1     124     180 ..     352     409 ..     295     421 .. 0.79
   4 ?   -1.8   0.1       4.5   2.2e+03     157     175 ..     555     573 ..     521     585 .. 0.68
   5 ?   -0.8   0.1       2.1     1e+03      93     175 ..     703     783 ..     649     800 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0005
                            TPR_21 144 faalvaelrGDilvaqgkldeAraaYqaAlaaleek 179
                                        +  ++  +G++l +qg +++Ar aY +Al++ + k
  gi|298675148|ref|YP_003726898.1| 134 NDPGIQIKKGELLKKQGLFKKARIAYGKALENDNYK 169
                                       555566679*********************998765 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.12
                            TPR_21 125 aekkydeAlktLeakke.eafaalvaelrGDilvaqgkldeAr 166
                                        e+k++eAlk ++++k+ + f+ +   ++ D+l++ g+++eA 
  gi|298675148|ref|YP_003726898.1| 184 MEGKVNEALKVIKRAKNlNLFDKETLHMQADMLAESGHRKEAV 226
                                       6899********87665378********************995 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.013
                            TPR_21 124 laekkydeAlktLeakkeea.faalvaelrGDilvaqgkldeAraaYqaAlaaleeka 180
                                       ++++++++Al+ ++++ + +     + + rG+il a g+l  A + +++Al+  ++++
  gi|298675148|ref|YP_003726898.1| 352 AKKGDLKNALRDINNAINLNdDVINFWNQRGEILWALGDLRGALESFRKALKIDDNDS 409
                                       56677777777775554433034467899**********************9888775 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 4.5
                            TPR_21 157 vaqgkldeAraaYqaAlaa 175
                                       +  gk+++A + Y++A++ 
  gi|298675148|ref|YP_003726898.1| 555 SLLGKIEDAVKTYNRAIEL 573
                                       5568999999999999875 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 2.1
                            TPR_21  93 aaAkaqLewvlekakdeelkalarlRL.arvllaekkydeAlktLeakke.eafaalvaelrGDilvaqgkldeAra 167
                                       ++A ++L++ l+ ++d+    +  lR+ a +  +  +y++ lkt++++ e e+ +a+   +r  +l + gk+ +A +
  gi|298675148|ref|YP_003726898.1| 703 KDALESLNRTLSINPDD----VDALRMkADLHYNLSDYKKSLKTIDKALEiEGDNARLWLMRSYVLDSLGKTSDALE 775
                                       45555555555555444....44445445666666677777777755533244555555556666666666666666 PP

                            TPR_21 168 aYqaAlaa 175
                                         ++A + 
  gi|298675148|ref|YP_003726898.1| 776 SLEKAHNL 783
                                       66666554 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       3.8   1.8e+03       4      55 ..      52     103 ..      49     124 .. 0.80
   2 ?   -0.1   0.0       2.4   1.2e+03      19      43 ..     169     193 ..     160     203 .. 0.71
   3 ?    5.8   0.1     0.037        18      21      78 ..     205     263 ..     185     266 .. 0.72
   4 ?    5.5   0.0     0.044        21      10      57 ..     228     275 ..     221     307 .. 0.79
   5 ?    0.8   0.1       1.3   6.4e+02      28      67 ..     314     364 ..     290     378 .. 0.63
   6 ?    3.0   0.0      0.26   1.3e+02       7      46 ..     394     433 ..     391     443 .. 0.88
   7 ?    6.5   0.0     0.022        11       5      62 ..     494     551 ..     490     571 .. 0.80
   8 ?    6.4   0.2     0.024        11       6      55 ..     704     749 ..     699     780 .. 0.77
   9 ?   -1.4   0.0       6.4   3.1e+03       5      23 ..     771     789 ..     767     791 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 3.8
                            TPR_20   4 dapelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkw 55 
                                       d ++  ++e+ l  + dd ++ +  A      g++  +le L +i+k++ + 
  gi|298675148|ref|YP_003726898.1|  52 DFQTANQIENSLSMSFDDEATWYYRAFIASLMGNHVTSLEYLNNIVKNNDEM 103
                                       5566778888888888898888999999999999999999999999988765 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2.4
                            TPR_20  19 pddldarldlAlallaagryeeAle 43 
                                       + d+++  d++ a+ ++g++ eAl+
  gi|298675148|ref|YP_003726898.1| 169 KHDIELLKDYSHAYQMEGKVNEALK 193
                                       4567777788888888888888875 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.037
                            TPR_20  21 dldarldlAlallaagryeeAleqLleilkrdrkw.eddaarkqllkifealgsqdplv 78 
                                       d ++ +  A+ l++ g+++eA+e + +il+ + ++ e   ++ +ll i++   ++++lv
  gi|298675148|ref|YP_003726898.1| 205 DKETLHMQADMLAESGHRKEAVEVINMILEINPDDfEAAFMKLELLLIMKRYKEAENLV 263
                                       66777778999999999999999999999988765244446666776666666666555 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.044
                            TPR_20  10 eleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkwed 57 
                                        +   l+ npdd +a++   ++ll  +ry+eA ++   i+ ++ +  d
  gi|298675148|ref|YP_003726898.1| 228 VINMILEINPDDFEAAFMKLELLLIMKRYKEAENLVSYIFNSNPDTGD 275
                                       55666889************************9998888888877755 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 1.3
                            TPR_20  28 lAlallaagryeeAleqLleilkrdrkw...........eddaarkqllki 67 
                                        A+++   g+y++A++   + l+ d +            ++++ +++l +i
  gi|298675148|ref|YP_003726898.1| 314 KANHYSNLGEYDKAIDICSRALEVDEDVntyssrseayaKKGDLKNALRDI 364
                                       577777777777777777777777777744444444444455555555444 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.26
                            TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAleqLl 46 
                                        l+++++al+ + +d  a    +++l+  g++ eA++++ 
  gi|298675148|ref|YP_003726898.1| 394 ALESFRKALKIDDNDSTALKHGSKLLHNLGDHSEAVNLMD 433
                                       578999******************************9875 PP

  == domain 7  score: 6.5 bits;  conditional E-value: 0.022
                            TPR_20   5 apelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkweddaark 62 
                                       +++l++ e  l  +p++ +++++    l+  +ryeeA++ + + l ++ + +    + 
  gi|298675148|ref|YP_003726898.1| 494 EASLDAAEYGLFYDPENPELMYKKGCTLINLQRYEEAFDCINQALGKKEDVDMLVNKA 551
                                       56777777788889*************************9999998888876555544 PP

  == domain 8  score: 6.4 bits;  conditional E-value: 0.024
                            TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkw 55 
                                         l++l ++l  npdd+da    A++ +  ++y+++l+ +     + ++ 
  gi|298675148|ref|YP_003726898.1| 704 DALESLNRTLSINPDDVDALRMKADLHYNLSDYKKSLKTID----KALEI 749
                                       578999***************************99987543....33344 PP

  == domain 9  score: -1.4 bits;  conditional E-value: 6.4
                            TPR_20   5 apelaeleaalaanpddld 23 
                                       +  l++le+a++ +pdd+d
  gi|298675148|ref|YP_003726898.1| 771 SDALESLEKAHNLSPDDND 789
                                       567899999***9**9987 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.098        47     146     172 ..     175     201 ..     171     214 .. 0.85
   2 ?    3.7   0.0      0.11        51     152     176 ..     418     442 ..     410     446 .. 0.90
   3 ?    6.9   0.0     0.011       5.5     125     180 ..     559     614 ..     545     618 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.098
                           Wzy_C_2 146 ierlilslallGdedeAeqilararal 172
                                       ++ +  ++++ G+  eA+++++ra++l
  gi|298675148|ref|YP_003726898.1| 175 LKDYSHAYQMEGKVNEALKVIKRAKNL 201
                                       667899******************975 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.11
                           Wzy_C_2 152 slallGdedeAeqilararalfpee 176
                                       +l  lGd++eA   ++++   +pe+
  gi|298675148|ref|YP_003726898.1| 418 LLHNLGDHSEAVNLMDKYLSNYPED 442
                                       67889******************98 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.011
                           Wzy_C_2 125 nlaaklalarklihlsPepavierlilslallGdedeAeqilararalfpeedakw 180
                                       ++++ ++ ++++i+l P+   ++    +l  l + +eA +i++++   + +  + w
  gi|298675148|ref|YP_003726898.1| 559 KIEDAVKTYNRAIELEPRYEALNAKVACLITLERFEEAMDIIDQVDPNYLNRFEFW 614
                                       68899999*****************************************9999999 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.52   2.5e+02       3      23 ..     208     228 ..     207     230 .. 0.89
   2 ?    7.8   0.1     0.012       5.8       7      25 ..     381     399 ..     378     400 .. 0.88
   3 ?    1.2   0.0       1.6   7.9e+02      10      25 ..     418     433 ..     417     434 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.52
                             TPR_4   3 allaLArallalGdldeAral 23 
                                       +l+++A  l++ G+  eA ++
  gi|298675148|ref|YP_003726898.1| 208 TLHMQADMLAESGHRKEAVEV 228
                                       68899*************986 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.012
                             TPR_4   7 LArallalGdldeAralle 25 
                                       +++ l+alGdl  A++ ++
  gi|298675148|ref|YP_003726898.1| 381 RGEILWALGDLRGALESFR 399
                                       799***********98766 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 1.6
                             TPR_4  10 allalGdldeAralle 25 
                                       +l+ lGd+ eA  l++
  gi|298675148|ref|YP_003726898.1| 418 LLHNLGDHSEAVNLMD 433
                                       6999*******98876 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0      0.13        64       9      28 ..     181     200 ..     180     203 .. 0.83
   2 ?   -1.4   0.0       7.4   3.6e+03      10      28 ..     216     234 ..     214     236 .. 0.80
   3 ?    1.1   0.0       1.2   5.7e+02      10      24 ..     318     332 ..     316     336 .. 0.85
   4 ?    3.6   0.0      0.19        94       2      20 ..     343     361 ..     343     362 .. 0.87
   5 ?   -1.4   0.0       7.5   3.7e+03      13      25 ..     422     434 ..     420     438 .. 0.85
   6 ?    0.4   0.0       2.1     1e+03      11      25 ..     454     468 ..     451     472 .. 0.84
   7 ?   -0.8   0.0         5   2.4e+03      13      26 ..     557     570 ..     555     573 .. 0.83
   8 ?   -1.4   0.0       7.5   3.6e+03      14      24 ..     591     601 ..     586     603 .. 0.83
   9 ?    4.2   0.1      0.13        62       7      24 ..     618     635 ..     618     637 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.13
                               PPR   9 gycknGkleeAlelfkeMke 28 
                                       +y  +Gk+ eAl+++k+ k 
  gi|298675148|ref|YP_003726898.1| 181 AYQMEGKVNEALKVIKRAKN 200
                                       77889**********99776 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 7.4
                               PPR  10 ycknGkleeAlelfkeMke 28 
                                       ++ +G  +eA+e+++ ++e
  gi|298675148|ref|YP_003726898.1| 216 LAESGHRKEAVEVINMILE 234
                                       67788889*****998876 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 1.2
                               PPR  10 ycknGkleeAlelfk 24 
                                       y+  G++++A+++  
  gi|298675148|ref|YP_003726898.1| 318 YSNLGEYDKAIDICS 332
                                       999********9865 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.19
                               PPR   2 tynslIsgycknGkleeAl 20 
                                       ty+s   +y+k+G+l+ Al
  gi|298675148|ref|YP_003726898.1| 343 TYSSRSEAYAKKGDLKNAL 361
                                       7888889*********998 PP

  == domain 5  score: -1.4 bits;  conditional E-value: 7.5
                               PPR  13 nGkleeAlelfke 25 
                                        G+++eA+ l+++
  gi|298675148|ref|YP_003726898.1| 422 LGDHSEAVNLMDK 434
                                       699******9987 PP

  == domain 6  score: 0.4 bits;  conditional E-value: 2.1
                               PPR  11 cknGkleeAlelfke 25 
                                       +k G++ee l++ ++
  gi|298675148|ref|YP_003726898.1| 454 AKTGNCEEGLKWVNK 468
                                       799*******99886 PP

  == domain 7  score: -0.8 bits;  conditional E-value: 5
                               PPR  13 nGkleeAlelfkeM 26 
                                        Gk+e+A++ +++ 
  gi|298675148|ref|YP_003726898.1| 557 LGKIEDAVKTYNRA 570
                                       699******99875 PP

  == domain 8  score: -1.4 bits;  conditional E-value: 7.5
                               PPR  14 GkleeAlelfk 24 
                                        ++eeA+++++
  gi|298675148|ref|YP_003726898.1| 591 ERFEEAMDIID 601
                                       589*****987 PP

  == domain 9  score: 4.2 bits;  conditional E-value: 0.13
                               PPR   7 IsgycknGkleeAlelfk 24 
                                       I+++ k ++++eAle+++
  gi|298675148|ref|YP_003726898.1| 618 IMCFIKLNRYDEALECID 635
                                       899***********9875 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.89   4.3e+02      62     122 ..     341     401 ..     293     405 .. 0.70
   2 ?    3.5   0.0      0.18        87      23      87 ..     365     434 ..     337     463 .. 0.53
   3 !    7.7   0.1    0.0095       4.6      60     116 ..     542     597 ..     518     603 .. 0.84
   4 ?    0.6   0.0       1.4   6.9e+02      62     123 ..     720     781 ..     697     789 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.89
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  62 lealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                       +  + ++ ea ++ G+ ++al++ ++++++++   +++ q  + l ++G+   ALe ++++
  gi|298675148|ref|YP_003726898.1| 341 VNTYSSRSEAYAKKGDLKNALRDINNAINLNDDVINFWNQRGEILWALGDLRGALESFRKA 401
                                       5566666677777777777777777777777766666666666666666666666666655 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHHTT-..-SSTTGGGTT.STTHHHHHHHHH..HHHHHHHHHHHHHHHHTT-HHHHHHHHHH CS
                              BTAD  23 eeaaelleaAlalw..rGpaladlea.gewleaererle..elrlealealaeaelrlGraeealaelea 87 
                                       ++a++l ++ +++w  rG+ l  l + +  le++r++l+  +   +al+   +++  lG+++ea+  +++
  gi|298675148|ref|YP_003726898.1| 365 NNAINLNDDVINFWnqRGEILWALGDlRGALESFRKALKidDNDSTALKHGSKLLHNLGDHSEAVNLMDK 434
                                       3333333333444433344333333333444444444431133344444444444455555555555555 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0095
                                       HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHH CS
                              BTAD  60 lrlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeAL 116
                                       + +++l   a++e+ lG++e+a+++++++++++P  E+l +++ ++l  ++r +eA+
  gi|298675148|ref|YP_003726898.1| 542 EDVDMLVNKARLESLLGKIEDAVKTYNRAIELEPRYEALNAKV-ACLITLERFEEAM 597
                                       55667777788889***********************998764.7888888877776 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD  62 lealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                       ++al+  a+++  l ++++ l++ +++++ +  + rl+      l  +G++++ALe  e++ 
  gi|298675148|ref|YP_003726898.1| 720 VDALRMKADLHYNLSDYKKSLKTIDKALEIEGDNARLWLMRSYVLDSLGKTSDALESLEKAH 781
                                       67777777777778899999999999999999999998777777889999999999887765 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.062        30      68     125 ..     205     262 ..     171     299 .. 0.76
   2 ?   -1.4   0.0       6.2     3e+03      75     102 ..     314     341 ..     296     364 .. 0.74
   3 ?    3.2   0.0      0.22   1.1e+02      81     132 ..     387     438 ..     340     442 .. 0.91
   4 ?    2.4   0.0       0.4   1.9e+02      77     126 ..     451     500 ..     442     506 .. 0.86
   5 ?    2.9   0.0      0.28   1.4e+02      55     120 ..     702     771 ..     690     777 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.062
                                       SHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHHH CS
                   Alkyl_sulf_dimr  68 gaekvlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesatw 125
                                       ++e++  +a   +++g  + a+e++n++++ +p++ ea  +k + l  + + +e+ + 
  gi|298675148|ref|YP_003726898.1| 205 DKETLHMQADMLAESGHRKEAVEVINMILEINPDDFEAAFMKLELLLIMKRYKEAENL 262
                                       5666666677777888888888888888888888888888777777777766666554 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 6.2
                                       HHHHHHHTT-HHHHHHHHHHHHHHSTT- CS
                   Alkyl_sulf_dimr  75 kakealkegdyrwaaellnhlvfadpen 102
                                       ka+++ + g+y  a+ +++ +++ d++ 
  gi|298675148|ref|YP_003726898.1| 314 KANHYSNLGEYDKAIDICSRALEVDEDV 341
                                       6777778899999999999999998873 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.22
                                       HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHHHHHHHHHH CS
                   Alkyl_sulf_dimr  81 kegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesatwRniYlsg 132
                                       + gd+r a+e   +++  d+++++a +   + l +lg ++e+ +    Yls 
  gi|298675148|ref|YP_003726898.1| 387 ALGDLRGALESFRKALKIDDNDSTALKHGSKLLHNLGDHSEAVNLMDKYLSN 438
                                       568999999***********************************99999986 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.4
                                       HHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHHHH CS
                   Alkyl_sulf_dimr  77 kealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesatwR 126
                                       ++++k g+ +  ++ +n+++  +++  +a ++k ++++++g+++ s  + 
  gi|298675148|ref|YP_003726898.1| 451 SSKAKTGNCEEGLKWVNKALKLKENYPDAWDIKSAIYTEMGKHEASLDAA 500
                                       667788999999999***************************99998765 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.28
                                       HHHHHHHHHHHTT....SHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH- CS
                   Alkyl_sulf_dimr  55 peekakrlvelmG....gaekvlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqa 120
                                       p+++ + l++ ++    +++++  ka  +++  dy+ +++ ++++++ + +na+   ++  +l++lg+ +
  gi|298675148|ref|YP_003726898.1| 702 PKDALESLNRTLSinpdDVDALRMKADLHYNLSDYKKSLKTIDKALEIEGDNARLWLMRSYVLDSLGKTS 771
                                       5555555556666666678888889999999999999999****99999999999999999999999876 PP

>> DUF627  Protein of unknown function (DUF627)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       5.1   2.5e+03       9      31 ..      84     105 ..      80     110 .. 0.79
   2 ?    4.2   0.1     0.088        43      80     107 ..     107     133 ..     103     134 .. 0.85
   3 ?   -1.4   0.1       4.8   2.3e+03      12      89 ..     189     218 ..     177     228 .. 0.50
   4 ?   -1.8   0.0       6.6   3.2e+03       2      33 ..     213     244 ..     212     248 .. 0.78
   5 ?    6.7   0.0     0.014         7      58     107 ..     289     338 ..     285     339 .. 0.80
   6 ?    2.8   0.1      0.24   1.2e+02      59      89 ..     391     428 ..     347     439 .. 0.64
   7 ?    0.1   0.0       1.6   7.9e+02      79     106 ..     722     749 ..     688     751 .. 0.53

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 5.1
                            DUF627   9 gnhikALeiiedlisrhgedeks 31 
                                       gnh+  Le ++++++++ e  k 
  gi|298675148|ref|YP_003726898.1|  84 GNHVTSLEYLNNIVKNNDEM-KY 105
                                       9**********999888773.45 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.088
                            DUF627  80 LfelasqlgsklyYkkavkkakraLsve 107
                                       L+++a+ l+   +Yk+av+ +++aL+++
  gi|298675148|ref|YP_003726898.1| 107 LLKAAN-LDFIGHYKEAVECCNKALKLK 133
                                       667777.888899************876 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 4.8
                            DUF627  12 ikALeiiedlisrhgedeksallhrlqGtifvklakktedpdvkfayllasvecfseavelsrfyArsLfelasqlg 88 
                                        +AL++i+                                                 a +l  f  ++L++ a+ l 
  gi|298675148|ref|YP_003726898.1| 189 NEALKVIKR------------------------------------------------AKNLNLFDKETLHMQADMLA 217
                                       455555554................................................44444444444444444333 PP

                            DUF627  89 s 89 
                                        
  gi|298675148|ref|YP_003726898.1| 218 E 218
                                       3 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 6.6
                            DUF627   2 AkdllargnhikALeiiedlisrhgedeksal 33 
                                       A  l ++g++ +A e+i+ ++  + +d ++a+
  gi|298675148|ref|YP_003726898.1| 213 ADMLAESGHRKEAVEVINMILEINPDDFEAAF 244
                                       667888999999****9998888877766655 PP

  == domain 5  score: 6.7 bits;  conditional E-value: 0.014
                            DUF627  58 yllasvecfseavelsrfyAr.sLfelasqlgsklyYkkavkkakraLsve 107
                                       y   + e+++ea++l  + A+ sL++ a+++ +  +Y ka+  + raL v 
  gi|298675148|ref|YP_003726898.1| 289 YYTEADEAINEAEKLNPVLANiSLIK-ANHYSNLGEYDKAIDICSRALEVD 338
                                       55666789999*****8888725665.66688888*************985 PP

  == domain 6  score: 2.8 bits;  conditional E-value: 0.24
                            DUF627  59 llasvecfseavels.......rfyArsLfelasqlgs 89 
                                       l++++e+f++a ++        +   ++L++l+++ + 
  gi|298675148|ref|YP_003726898.1| 391 LRGALESFRKALKIDdndstalKHGSKLLHNLGDHSEA 428
                                       56666666666666666666655555666666665554 PP

  == domain 7  score: 0.1 bits;  conditional E-value: 1.6
                            DUF627  79 sLfelasqlgsklyYkkavkkakraLsv 106
                                        L + a+   + ++Ykk++k   +aL +
  gi|298675148|ref|YP_003726898.1| 722 ALRMKADLHYNLSDYKKSLKTIDKALEI 749
                                       3444444334445677777666666665 PP

>> TPR_5  Tetratrico peptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.68   3.3e+02       7      29 ..     109     131 ..     105     142 .. 0.89
   2 ?    4.9   0.0      0.06        29      42      95 ..     211     263 ..     178     271 .. 0.76
   3 ?    0.6   0.0       1.3   6.5e+02      46      69 ..     417     440 ..     381     479 .. 0.74
   4 ?   -0.5   0.0       2.9   1.4e+03      11      29 ..     554     572 ..     524     601 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.68
                             TPR_5   7 ragarDstGhedkavplYrraLa 29 
                                       +a+  D++Gh ++av+  ++aL+
  gi|298675148|ref|YP_003726898.1| 109 KAANLDFIGHYKEAVECCNKALK 131
                                       68889************999996 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.06
                             TPR_5  42 iqLassLRnlGeaeealaLLraeleapsdelddalaaflaLvLsdlgrereavs 95 
                                       +q a  L   G+ +ea+++++  le ++d++++a   +  L +++  +e+e + 
  gi|298675148|ref|YP_003726898.1| 211 MQ-ADMLAESGHRKEAVEVINMILEINPDDFEAAFMKLELLLIMKRYKEAENLV 263
                                       44.66788889**************************99999999999999875 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 1.3
                             TPR_5  46 ssLRnlGeaeealaLLraeleaps 69 
                                         L nlG+  ea++L+++ l++ +
  gi|298675148|ref|YP_003726898.1| 417 KLLHNLGDHSEAVNLMDKYLSNYP 440
                                       347899999999999988777644 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 2.9
                             TPR_5  11 rDstGhedkavplYrraLa 29 
                                       +   G+ + av+ Y+ra++
  gi|298675148|ref|YP_003726898.1| 554 ESLLGKIEDAVKTYNRAIE 572
                                       4455666666666666654 PP

>> HTH_Bact  Helix-turn-helix bacterial domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       3.3   1.6e+03       2      14 ..     119     131 ..     118     133 .. 0.89
   2 ?   -1.4   0.0       3.7   1.8e+03       1      15 [.     323     337 ..     323     339 .. 0.89
   3 ?   -2.6   0.0       8.7   4.2e+03       3      14 ..     460     471 ..     459     472 .. 0.86
   4 ?    1.8   0.0      0.37   1.8e+02       1      13 [.     526     538 ..     526     540 .. 0.93
   5 ?   -2.1   0.0       6.2     3e+03       1      10 [.     626     635 ..     626     636 .. 0.86
   6 ?    3.3   0.0      0.13        62       2      15 ..     736     749 ..     735     758 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3.3
                                       HHHHHHHHHHHHH CS
                          HTH_Bact   2 YeeaLeqvnkAie 14 
                                       Y ea e  nkA++
  gi|298675148|ref|YP_003726898.1| 119 YKEAVECCNKALK 131
                                       99*********98 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.7
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       +Y++a+    +A+e+
  gi|298675148|ref|YP_003726898.1| 323 EYDKAIDICSRALEV 337
                                       69******9999985 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 8.7
                                       HHHHHHHHHHHH CS
                          HTH_Bact   3 eeaLeqvnkAie 14 
                                       ee L+ vnkA++
  gi|298675148|ref|YP_003726898.1| 460 EEGLKWVNKALK 471
                                       68899*****97 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.37
                                       -HHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAi 13 
                                       rYeea+  +n+A+
  gi|298675148|ref|YP_003726898.1| 526 RYEEAFDCINQAL 538
                                       7**********97 PP

  == domain 5  score: -2.1 bits;  conditional E-value: 6.2
                                       -HHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvn 10 
                                       rY+eaLe ++
  gi|298675148|ref|YP_003726898.1| 626 RYDEALECID 635
                                       7*****9886 PP

  == domain 6  score: 3.3 bits;  conditional E-value: 0.13
                                       HHHHHHHHHHHHHH CS
                          HTH_Bact   2 YeeaLeqvnkAiei 15 
                                       Y ++L+ ++kA+ei
  gi|298675148|ref|YP_003726898.1| 736 YKKSLKTIDKALEI 749
                                       9***********98 PP

>> PDEase_I_N  3'5'-cyclic nucleotide phosphodiesterase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.13        63      28      54 ..     343     369 ..     341     370 .. 0.91
   2 ?    6.1   0.0      0.02       9.8      15      52 ..     639     676 ..     627     678 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.13
                        PDEase_I_N  28 tFtrqqeakkrrseekpkfrsvanair 54 
                                       t++ ++ea+ ++ + k+ +r + nai+
  gi|298675148|ref|YP_003726898.1| 343 TYSSRSEAYAKKGDLKNALRDINNAIN 369
                                       7888899999***************97 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.02
                        PDEase_I_N  15 daVPseVrdWLastFtrqqeakkrrseekpkfrsvana 52 
                                       ++VP+e+++ +  t++ +  + +  +e++pk++    a
  gi|298675148|ref|YP_003726898.1| 639 NNVPDEIKEYMFQTLSETLDTDNVDQEDEPKLMLLKGA 676
                                       58*****************************9976655 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       4.3   2.1e+03      30      46 ..      89     105 ..      86     116 .. 0.77
   2 ?    6.0   0.2     0.026        13      26      51 ..     118     148 ..     108     159 .. 0.75
   3 ?    1.7   0.1      0.58   2.8e+02      27      45 ..     324     340 ..     315     355 .. 0.58
   4 ?   -1.6   0.0       6.1     3e+03      30      40 ..     394     405 ..     389     417 .. 0.62
   5 ?    1.2   0.0      0.79   3.8e+02      25      39 ..     525     539 ..     520     552 .. 0.67
   6 ?    4.6   0.0     0.072        35       7      33 ..     547     573 ..     545     573 .. 0.91
   7 ?   -1.5   0.0       5.7   2.8e+03      27      42 ..     736     753 ..     733     767 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 4.3
                               MIT  30 alelLlqalkekneerr 46 
                                       +le+L+ ++k+++e + 
  gi|298675148|ref|YP_003726898.1|  89 SLEYLNNIVKNNDEMKY 105
                                       89*******97665554 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.026
                               MIT  26 lYkealelLlqalk.ekne....errellre 51 
                                        Ykea+e +++alk  +++    ++ ell++
  gi|298675148|ref|YP_003726898.1| 118 HYKEAVECCNKALKlKNDPgiqiKKGELLKK 148
                                       6999999999999944665776666666655 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.58
                               MIT  27 YkealelLlqalkekneer 45 
                                       Y +a+++++ al    +e+
  gi|298675148|ref|YP_003726898.1| 324 YDKAIDICSRALE--VDED 340
                                       5555555555554..2233 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 6.1
                               MIT  30 alelLlqalk.e 40 
                                       ale + +alk  
  gi|298675148|ref|YP_003726898.1| 394 ALESFRKALKiD 405
                                       566666666633 PP

  == domain 5  score: 1.2 bits;  conditional E-value: 0.79
                               MIT  25 elYkealelLlqalk 39 
                                       + Y+ea + ++qal 
  gi|298675148|ref|YP_003726898.1| 525 QRYEEAFDCINQALG 539
                                       567777777777776 PP

  == domain 6  score: 4.6 bits;  conditional E-value: 0.072
                               MIT   7 lvkkAveeDnagnyeeAlelYkealel 33 
                                       lv+kA  e   g++e+A++ Y  a+el
  gi|298675148|ref|YP_003726898.1| 547 LVNKARLESLLGKIEDAVKTYNRAIEL 573
                                       78899889999**************96 PP

  == domain 7  score: -1.5 bits;  conditional E-value: 5.7
                               MIT  27 YkealelLlqalk.e.kn 42 
                                       Yk++l+ + +al  e +n
  gi|298675148|ref|YP_003726898.1| 736 YKKSLKTIDKALEiEgDN 753
                                       999999999999877444 PP

>> PUB  PUB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   0.00097      0.47      13      37 ..      91     115 ..      88     133 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00097
                               PUB  13 kylnNilehpteekyrrIrleNkaf 37 
                                        ylnNi+++ +e ky  ++ +N  f
  gi|298675148|ref|YP_003726898.1|  91 EYLNNIVKNNDEMKYWLLKAANLDF 115
                                       69****************9999655 PP

>> Hormone_recep  Ligand-binding domain of nuclear hormone receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.2     0.051        25      90     134 ..      47      93 ..      22      94 .. 0.68
   2 ?    1.8   0.1      0.31   1.5e+02      86     141 ..     162     216 ..     144     227 .. 0.79
   3 ?    7.8   1.3    0.0046       2.2     110     149 ..     220     256 ..     170     268 .. 0.70
   4 ?   -1.0   0.1       2.2   1.1e+03     130     174 ..     610     651 ..     586     718 .. 0.76
   5 ?   -2.4   0.0       6.1     3e+03      87     143 ..     688     732 ..     650     748 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.051
                                       .HHHHCCTTHHHHHHHHH............HHHHHHHHCT--HHHHH CS
                     Hormone_recep  90 kiedskvskssekeqlll..fgpkiiklfdeliqplqelkltetEfa 134
                                       ++++ ++++ ++ e  l   f+++ +++++ +i +l+  ++t+ E++
  gi|298675148|ref|YP_003726898.1|  47 YKSANDFQTANQIENSLSmsFDDEATWYYRAFIASLMGNHVTSLEYL 93 
                                       33333344444444444478*************************95 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.31
                                       .......HHHHCCTTHHHHHHHHH..........HHHHHHHHCT--HHHHHHHHHHHH CS
                     Hormone_recep  86 a..nkekiedskvskssekeqlllfgpkiiklfdeliqplqelkltetEfafllaill 141
                                       a  n+++++d +  k++++ +++   +k+++ + ++i++ ++l+l + E + + a +l
  gi|298675148|ref|YP_003726898.1| 162 AleNDNYKHDIELLKDYSHAYQME--GKVNEAL-KVIKRAKNLNLFDKETLHMQADML 216
                                       345678888999999999999888..99*****.***************999998887 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0046
                                       ........HHHHHHHHCT--HHHHHHHHHHHHCTSSS--S CS
                     Hormone_recep 110 pkiiklfdeliqplqelkltetEfafllaillfnfagdrl 149
                                       ++ ++   e+i+ + e++++++E af+++ ll+    +r+
  gi|298675148|ref|YP_003726898.1| 220 GHRKEAV-EVINMILEINPDDFEAAFMKLELLLI--MKRY 256
                                       3344444.99*******************99943..4554 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 2.2
                                       HHHHHHHHHHHHCTSSS--STTH..HHHHHHHHHHHHHHHHHHHH CS
                     Hormone_recep 130 etEfafllaillfnfagdrlqgetqeiveklqeklsneLheYyss 174
                                       ++Ef   +++++++   +r+ +e +e ++++ +++ +e++eY+ +
  gi|298675148|ref|YP_003726898.1| 610 RFEFWMNKIMCFIK--LNRY-DEALECIDNFGNNVPDEIKEYMFQ 651
                                       55666666666655..6666.444788888888888888888754 PP

  == domain 5  score: -2.4 bits;  conditional E-value: 6.1
                                       ....HHHHCCTTHHHHHHHHH..........HHHHHHHHCT--HHHHHHHHHHHHCT CS
                     Hormone_recep  87 nkekiedskvskssekeqlllfgpkiiklfdeliqplqelkltetEfafllaillfn 143
                                       + ++  ++k+++s++k+ l               ++  +++++++  + ++a l +n
  gi|298675148|ref|YP_003726898.1| 688 EVFYSVAEKWMDSNPKDALES------------LNRTLSINPDDVDALRMKADLHYN 732
                                       566666677777777666655............777778888888888888777666 PP

>> Clathrin  Region in Clathrin and VPS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1       1.4     7e+02      81     107 ..      36      61 ..       5      75 .. 0.66
   2 ?    6.0   2.5     0.021        10      76     124 ..     142     190 ..      90     208 .. 0.83
   3 ?   -2.0   0.0       6.2     3e+03      16      63 ..     215     264 ..     201     273 .. 0.55
   4 ?    9.6   1.0    0.0016      0.76      64     123 ..     283     348 ..     280     374 .. 0.82
   5 ?    4.0   0.0     0.088        43      92     125 ..     418     452 ..     411     455 .. 0.86
   6 ?    1.0   0.4      0.72   3.5e+02      79     108 ..     607     636 ..     544     657 .. 0.69
   7 ?   -0.3   0.1       1.8   8.7e+02      44     103 ..     689     747 ..     683     757 .. 0.72
   8 ?   -1.1   0.0       3.2   1.6e+03      82     112 ..     753     783 ..     743     794 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.4
                                       HT-SSHHHHHHHHHTTXTHSSHSSXSS CS
                          Clathrin  81 ekadlyeeavilykkinefkkaisllk 107
                                       +++ ly + ++lyk  n+f+ a ++ +
  gi|298675148|ref|YP_003726898.1|  36 KQRLLY-FKIELYKSANDFQTANQIEN 61 
                                       444444.66667777777777666544 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.021
                                       HHHHHHT-SSHHHHHHHHHT...TXTHSSHSSXSSSSHCSCHHHHTTTTTXX CS
                          Clathrin  76 vaklcekadlyeeavilykk...inefkkaisllkklkdfddaieyaakvsn 124
                                        ++l++k++l++ a+i y k   ++++k+ i+    lkd+ +a +  +kv+ 
  gi|298675148|ref|YP_003726898.1| 142 KGELLKKQGLFKKARIAYGKaleNDNYKHDIE---LLKDYSHAYQMEGKVNE 190
                                       5899****************888888888555...45678888888888775 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 6.2
                                       HHHCTT-HHHHCHHHCCHHHCHTS..--HHHHHHHHHHHHHTT-HHHHHH CS
                          Clathrin  16 lfeeaglleelleyLekvlkedsk..enpalqtallelyakyddpqelee 63 
                                       ++ e g+ +e+ e+  ++l+ ++   e   +  +ll ++ +y++ ++l +
  gi|298675148|ref|YP_003726898.1| 215 MLAESGHRKEAVEVINMILEINPDdfEAAFMKLELLLIMKRYKEAENLVS 264
                                       55555666666666666664443333444444455555555555444444 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.0016
                                       TTSS---.S-TTHHHHHHHT-SSHHHHHH......HHHTTXTHSSHSSXSSSSHCSCHHHHTTTTTX CS
                          Clathrin  64 flkknnn.ydlekvaklcekadlyeeavi......lykkinefkkaisllkklkdfddaieyaakvs 123
                                       +l+++ +   ++++++ +ek +++ +a i      +y++++e++kai+++ +  + d++++++  +s
  gi|298675148|ref|YP_003726898.1| 283 ILSTYGYyTEADEAINEAEKLNPV-LANIslikanHYSNLGEYDKAIDICSRALEVDEDVNTYSSRS 348
                                       566666655678889999999966.5555566999**************9999*******9987765 PP

  == domain 5  score: 4.0 bits;  conditional E-value: 0.088
                                       HHHTTXTHSSHSSX.SSSSHCSCHHHHTTTTTXXS CS
                          Clathrin  92 lykkinefkkaisl.lkklkdfddaieyaakvsnp 125
                                       l+ +++++++a++l  k+l+++++++e+++   ++
  gi|298675148|ref|YP_003726898.1| 418 LLHNLGDHSEAVNLmDKYLSNYPEDVEILGLKGSS 452
                                       455699*******88************99877766 PP

  == domain 6  score: 1.0 bits;  conditional E-value: 0.72
                                       HHHT-SSHHHHHHHHHTTXTHSSHSSXSSS CS
                          Clathrin  79 lcekadlyeeavilykkinefkkaisllkk 108
                                       ++  ++ +   + ++ k+n++++a++++++
  gi|298675148|ref|YP_003726898.1| 607 YLNRFEFWMNKIMCFIKLNRYDEALECIDN 636
                                       455555555556666677777777776433 PP

  == domain 7  score: -0.3 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHHTT-HHHHHHTTSS---S-TTHHHHHHHT-SSHHHHHHHHHT.TXTHSSHS CS
                          Clathrin  44 lqtallelyakyddpqeleeflkknnnydlekvaklcekadlyeeavilykk.inefkkai 103
                                       ++ +++e   ++++ ++++e+l+++ +++++ v  l +kadl+   +  ykk ++ ++ka+
  gi|298675148|ref|YP_003726898.1| 689 VFYSVAEKWMDSNP-KDALESLNRTLSINPDDVDALRMKADLH-YNLSDYKKsLKTIDKAL 747
                                       66666666777885.9999999999999999999999999998.33334444455555554 PP

  == domain 8  score: -1.1 bits;  conditional E-value: 3.2
                                       T-SSHHHHHHHHHTTXTHSSHSS.XSSSSHCS CS
                          Clathrin  82 kadlyeeavilykkinefkkais.llkklkdf 112
                                       +a+l+ ++ ++++ ++++++a++ l k  +++
  gi|298675148|ref|YP_003726898.1| 753 NARLWLMRSYVLDSLGKTSDALEsLEKA-HNL 783
                                       688999999************9954333.333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (803 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       889  (0.0495845); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        37  (0.0020637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              37  [number of targets reported over threshold]
# CPU time: 0.88u 0.24s 00:00:01.12 Elapsed: 00:00:00.53
# Mc/sec: 4535.15
//
Query:       gi|298675149|ref|YP_003726899.1|  [L=105]
Description: hypothetical protein Metev_1231 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 832.98
//
Query:       gi|298675150|ref|YP_003726900.1|  [L=240]
Description: hypothetical protein Metev_1232 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-15   54.8   0.3      0.013   15.5   0.2    5.1  5  TPR_2          Tetratricopeptide repeat
    3.6e-14   51.9   0.2     0.0017   18.1   0.2    4.9  5  TPR_1          Tetratricopeptide repeat
    3.6e-13   48.6   0.7      0.022   15.0   0.0    5.2  5  TPR_8          Tetratricopeptide repeat
    1.1e-09   38.7   0.7    4.3e-05   23.9   0.0    3.9  4  TPR_19         Tetratricopeptide repeat
    6.3e-09   36.3   0.0     0.0011   19.6   0.0    3.0  3  TPR_16         Tetratricopeptide repeat
    8.5e-09   35.5   0.1      0.016   16.0   0.1    5.0  5  TPR_14         Tetratricopeptide repeat
    2.8e-08   33.9   0.0     0.0062   16.7   0.2    2.4  3  ANAPC3         Anaphase-promoting complex, cyclosome, subunit
    3.1e-07   29.7   0.1    0.00052   19.1   0.0    2.1  2  NARP1          NMDA receptor-regulated protein 1
    3.7e-07   30.2   0.2     0.0021   18.2   0.2    2.8  3  TPR_9          Tetratricopeptide repeat
    4.4e-07   29.5   0.6      0.028   14.4   0.0    4.7  6  TPR_7          Tetratricopeptide repeat
      6e-07   29.7   1.2       0.19   12.0   0.0    4.0  4  TPR_12         Tetratricopeptide repeat
    2.7e-05   24.5   0.3         12    6.7   0.0    5.0  5  TPR_6          Tetratricopeptide repeat
    0.00017   21.7   0.1          1    9.9   0.0    3.9  3  TPR_17         Tetratricopeptide repeat
    0.00023   20.8   0.7       0.88    9.3   0.0    3.9  4  TPR_11         TPR repeat
     0.0003   21.1   0.0         25    5.9   0.0    4.3  4  TPR_4          Tetratricopeptide repeat
     0.0003   20.8   0.5       0.21   11.9   0.1    4.5  5  PPR            PPR repeat
    0.00093   19.0   4.1       0.21   11.5   0.1    3.8  3  TPR_10         Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.023   14.9   0.0        1.2    9.3   0.0    2.6  2  PPR_2          PPR repeat family
      0.073   12.5   0.1        1.2    8.5   0.0    2.5  3  Coatomer_E     Coatomer epsilon subunit
      0.073   13.1   0.0       0.16   12.0   0.0    1.4  1  Type_III_YscG  Bacterial type II secretion system chaperone p


Domain annotation for each model (and alignments):
>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.88   7.9e+02      11      25 ..      73      87 ..      71      92 .. 0.74
   2 !   15.0   0.0   2.2e-05     0.019       4      31 ..     100     127 ..      98     130 .. 0.86
   3 ?    3.4   0.0      0.11     1e+02       8      29 ..     137     158 ..     134     160 .. 0.85
   4 !   15.5   0.2   1.5e-05     0.013       2      30 ..     164     192 ..     163     195 .. 0.92
   5 !   13.3   0.0   7.5e-05     0.067       3      33 ..     199     229 ..     197     230 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.88
                             TPR_2 11 yyklgdyeeAleafe 25
                                      ++ lg+++eA e  e
  gi|298675150|ref|YP_003726900.1| 73 LELLGRPDEADEIAE 87
                                      6789******77655 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.2e-05
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleld 31 
                                       l+  ++++  +g+ye+A+e+fe+A + d
  gi|298675150|ref|YP_003726900.1| 100 LMFKAEVLSSKGRYEDAVELFEEAEKRD 127
                                       5667899999**************8876 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.11
                             TPR_2   8 GlayyklgdyeeAleafekAle 29 
                                       +  +++ g++e+A+e ++  l+
  gi|298675150|ref|YP_003726900.1| 137 AVHHIRYGEPEQAIEVCNDLLK 158
                                       7789999********9998876 PP

  == domain 4  score: 15.5 bits;  conditional E-value: 1.5e-05
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAlel 30 
                                       e++y ++++y+  g++e+Ale+ + Al +
  gi|298675150|ref|YP_003726900.1| 164 EVYYVRAYVYAVIGNLEQALEDIDTALYI 192
                                       89************************965 PP

  == domain 5  score: 13.3 bits;  conditional E-value: 7.5e-05
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                        ++ +Gl+ +k+gd + A+e f+ Al +d +
  gi|298675150|ref|YP_003726900.1| 199 SWNFRGLIMEKMGDRKGAVESFKYALGIDSE 229
                                       699**********************977765 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.4   1.2e+03      11      20 ..      73      82 ..      71      84 .. 0.84
   2 !   13.8   0.0   4.5e-05      0.04       7      31 ..     103     127 ..      98     128 .. 0.86
   3 ?    2.3   0.0      0.18   1.6e+02      11      25 ..     140     154 ..     135     157 .. 0.80
   4 !   18.1   0.2   1.9e-06    0.0017       2      30 ..     164     192 ..     163     195 .. 0.93
   5 !   10.6   0.0   0.00045       0.4       3      34 .]     199     230 ..     197     230 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.4
                                      HHHTT-HHHH CS
                             TPR_1 11 yfklgkydeA 20
                                      +  lg++deA
  gi|298675150|ref|YP_003726900.1| 73 LELLGRPDEA 82
                                      7789*****9 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 4.5e-05
                                       HHHHHHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1   7 lGnayfklgkydeAleyyekALeln 31 
                                       ++ ++ ++g+y++A+e +e+A + +
  gi|298675150|ref|YP_003726900.1| 103 KAEVLSSKGRYEDAVELFEEAEKRD 127
                                       788999***************7765 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.18
                                       HHHTT-HHHHHHHHH CS
                             TPR_1  11 yfklgkydeAleyye 25 
                                       + + g++++A+e ++
  gi|298675150|ref|YP_003726900.1| 140 HIRYGEPEQAIEVCN 154
                                       66789******9775 PP

  == domain 4  score: 18.1 bits;  conditional E-value: 1.9e-06
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALel 30 
                                       +++y ++++y   g++++Ale+ + AL +
  gi|298675150|ref|YP_003726900.1| 164 EVYYVRAYVYAVIGNLEQALEDIDTALYI 192
                                       78*************************87 PP

  == domain 5  score: 10.6 bits;  conditional E-value: 0.00045
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                       +++ +G++  k+g+ + A+e ++ AL ++ +n
  gi|298675150|ref|YP_003726900.1| 199 SWNFRGLIMEKMGDRKGAVESFKYALGIDSEN 230
                                       7999**********************999876 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.12     1e+02      10      30 ..      72      92 ..      63      92 .. 0.82
   2 !   15.0   0.0   2.4e-05     0.022       4      31 ..     100     127 ..      98     130 .. 0.88
   3 ?    1.0   0.0      0.73   6.5e+02      15      30 ..     144     159 ..     140     159 .. 0.86
   4 !   11.4   0.1   0.00033       0.3       2      31 ..     164     193 ..     163     195 .. 0.94
   5 !   11.2   0.0    0.0004      0.36       3      34 .]     199     230 ..     198     230 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.12
                                      HHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8 10 iylklgdyeeAkeyyekalel 30
                                      +++ lg+ +eA e  e  +el
  gi|298675150|ref|YP_003726900.1| 72 TLELLGRPDEADEIAELIIEL 92
                                      67889********99988886 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.4e-05
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleld 31 
                                       ++ ++ +++++g+ye A+e +e+a + d
  gi|298675150|ref|YP_003726900.1| 100 LMFKAEVLSSKGRYEDAVELFEEAEKRD 127
                                       678999******************9887 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.73
                                       T-HHHHHHHHHHHHHH CS
                             TPR_8  15 gdyeeAkeyyekalel 30 
                                       g+ e+A+e+++  l++
  gi|298675150|ref|YP_003726900.1| 144 GEPEQAIEVCNDLLKW 159
                                       7889*****9998885 PP

  == domain 4  score: 11.4 bits;  conditional E-value: 0.00033
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleld 31 
                                       e+yy  +++y   g++e+A e +  al+++
  gi|298675150|ref|YP_003726900.1| 164 EVYYVRAYVYAVIGNLEQALEDIDTALYIR 193
                                       89*************************986 PP

  == domain 5  score: 11.2 bits;  conditional E-value: 0.0004
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       +++  g+i +k+gd + A+e+++ al +d +n
  gi|298675150|ref|YP_003726900.1| 199 SWNFRGLIMEKMGDRKGAVESFKYALGIDSEN 230
                                       7999************************9875 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0      0.04        36      18      53 ..      56      91 ..      48     106 .. 0.85
   2 !   23.9   0.0   4.8e-08   4.3e-05       5      57 ..     111     162 ..     107     172 .. 0.89
   3 ?    0.9   0.1      0.73   6.5e+02      26      46 ..     164     184 ..     161     191 .. 0.80
   4 ?    4.9   0.0     0.042        38       3      33 ..     209     239 ..     208     240 .] 0.91

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.04
                            TPR_19 18 lqedpknaearllLAeallalgqldeAealLdalpe 53
                                      l+++p n e ++  +  l  lg++deA ++ + + e
  gi|298675150|ref|YP_003726900.1| 56 LEYEPYNIESLYKKMVTLELLGRPDEADEIAELIIE 91
                                      78899999999999*************999887765 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 4.8e-08
                            TPR_19   5 gdyaeAlalleqa.lqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       g+y++A++l+e+a   ++p++a ++   A  ++  g++++A++++++l+++ + 
  gi|298675150|ref|YP_003726900.1| 111 GRYEDAVELFEEAeKRDSPDDAPLAK--AVHHIRYGEPEQAIEVCNDLLKWHQC 162
                                       9************6677999999999..*********************99885 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.73
                            TPR_19  26 earllLAeallalgqldeAea 46 
                                       e+ +  A ++   g+l++A +
  gi|298675150|ref|YP_003726900.1| 164 EVYYVRAYVYAVIGNLEQALE 184
                                       567778899999999999987 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.042
                            TPR_19   3 aegdyaeAlalleqalqedpknaearllLAe 33 
                                       ++gd   A++ +++al  d +n  a   LA+
  gi|298675150|ref|YP_003726900.1| 209 KMGDRKGAVESFKYALGIDSENTMATSHLAK 239
                                       589*******************999888886 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.2e-06    0.0011      12      67 ..      78     131 ..      76     132 .. 0.76
   2 !   12.5   0.0    0.0002      0.18       2      61 ..     135     190 ..     134     195 .. 0.86
   3 ?    0.1   0.0       1.5   1.3e+03      37      65 ..     200     228 ..     198     234 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.2e-06
                            TPR_16  12 dyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal.raapda 67 
                                       ++d+A + +e  ++++     ++++l+++++++  +gr+++A++l+++a  r +pd+
  gi|298675150|ref|YP_003726900.1|  78 RPDEADEIAELIIELG---TMNRRFLMFKAEVLSSKGRYEDAVELFEEAEkRDSPDD 131
                                       5555555555566666...668899**********************9995555554 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.0002
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal 61 
                                       a+a  ++r g++++A+++ + +lk +     ++e ++ ++ ++++ g+l+ A++ ++ al
  gi|298675150|ref|YP_003726900.1| 135 AKAVHHIRYGEPEQAIEVCNDLLKWH---Q-CHEVYYVRAYVYAVIGNLEQALEDIDTAL 190
                                       56667777899***************...5.**********************7776665 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.5
                            TPR_16  37 llllgdaalrqgrlaeAaalyraalraap 65 
                                       ++++g++  + g+ ++A++ ++ al+ ++
  gi|298675150|ref|YP_003726900.1| 200 WNFRGLIMEKMGDRKGAVESFKYALGIDS 228
                                       77777777778888888888888887665 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.48   4.3e+02       9      29 ..      71      91 ..      63      95 .. 0.77
   2 !   16.0   0.1   1.8e-05     0.016       7      36 ..     103     133 ..      97     138 .. 0.83
   3 ?    7.2   0.0     0.012        10       8      29 ..     137     158 ..     134     162 .. 0.84
   4 ?    2.4   0.1      0.41   3.7e+02       2      23 ..     164     185 ..     163     190 .. 0.82
   5 ?    1.4   0.0      0.87   7.8e+02       7      43 ..     203     239 ..     198     240 .] 0.82

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.48
                            TPR_14  9 eallalGdpdeAiallrrala 29
                                        l+ lG+pdeA ++++ +++
  gi|298675150|ref|YP_003726900.1| 71 VTLELLGRPDEADEIAELIIE 91
                                      568899******888887776 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.8e-05
                            TPR_14   7 laeallalGdpdeAiallrralala.Pddae 36 
                                        ae+l   G++++A++l+++a +++ Pdda 
  gi|298675150|ref|YP_003726900.1| 103 KAEVLSSKGRYEDAVELFEEAEKRDsPDDAP 133
                                       599********************74499975 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.012
                            TPR_14   8 aeallalGdpdeAiallrrala 29 
                                       a  + + G+p++Ai++++++l+
  gi|298675150|ref|YP_003726900.1| 137 AVHHIRYGEPEQAIEVCNDLLK 158
                                       5568999************986 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.41
                            TPR_14   2 eallalaeallalGdpdeAial 23 
                                       e+++ +a +++  G++++A++ 
  gi|298675150|ref|YP_003726900.1| 164 EVYYVRAYVYAVIGNLEQALED 185
                                       6789999999999****99975 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.87
                            TPR_14   7 laeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                       ++ +++  Gd ++A++ ++ al  + ++  a  +la+
  gi|298675150|ref|YP_003726900.1| 203 RGLIMEKMGDRKGAVESFKYALGIDSENTMATSHLAK 239
                                       67788999*********99888888888888888887 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00039      0.35      16      81 ..      56     122 ..      46     123 .. 0.80
   2 !   15.9   0.0   1.2e-05     0.011       9      77 ..      83     151 ..      76     152 .. 0.88
   3 !   16.7   0.2   6.9e-06    0.0062       3      77 ..     111     184 ..     110     189 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00039
                                       H.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  16 laaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       l++e+++ e++y +  +l l+g+ ++A e+++   +l   + + ++ +A++l   ++ye+A+ ++e+
  gi|298675150|ref|YP_003726900.1|  56 LEYEPYNIESLYKKMVTLELLGRPDEADEIAELIiELGTMNRRFLMFKAEVLSSKGRYEDAVELFEE 122
                                       5688888888888888888899999999998888888888888888888888888999999888876 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.2e-05
                                       HHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHH CS
                            ANAPC3   9 iflaerllaaetespedayllAlclylngqykrAyellrkaklnskslgcrylfAqcllkLkkyeeAia 77 
                                         +ae++ +  t +   ++++A++l + g+y+ A el+++a+++++   + + +A   + +++ e+Ai 
  gi|298675150|ref|YP_003726900.1|  83 DEIAELIIELGTMNRRFLMFKAEVLSSKGRYEDAVELFEEAEKRDSPDDAPLAKAVHHIRYGEPEQAIE 151
                                       56899999999999999************************7777777899999999999999999997 PP

  == domain 3  score: 16.7 bits;  conditional E-value: 6.9e-06
                                       T-HHHHHHHHHHHH.HHH--HHHHHH.HHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHH CS
                            ANAPC3   3 nnyknAiflaerllaaetespedayl.lAlclylngqykrAyellrkaklnskslgcrylfAqcllkLkkyeeAia 77 
                                       ++y++A+ l+e +   +++sp+da l +A  + + g+ ++A+e+++++ + ++ +++ y+ A ++  ++++e+A+ 
  gi|298675150|ref|YP_003726900.1| 111 GRYEDAVELFEEAE--KRDSPDDAPLaKAVHHIRYGEPEQAIEVCNDLLKWHQCHEVYYVRAYVYAVIGNLEQALE 184
                                       79**********99..788888877747********************8889999999****************85 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0   0.00072      0.65     207     281 ..      78     151 ..      53     158 .. 0.77
   2 !   19.1   0.0   5.8e-07   0.00052     194     258 ..     165     229 ..     154     239 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00072
                                       -SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT-HHHHHHHHHHHHHTT-HHHHHH CS
                             NARP1 207 srekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaDRyiNskcakymLradeveeAee 281
                                       + ++A e+ +  ie       + + Ka++l  +G  ++A+e+ eea k D  D    +k+++ ++r +e e+A e
  gi|298675150|ref|YP_003726900.1|  78 RPDEADEIAELIIELGTMNRRFLMFKAEVLSSKGRYEDAVELFEEAEKRDSPDDAPLAKAVH-HIRYGEPEQAIE 151
                                       55667777777777777777889999*******************99999988665555553.345555555555 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 5.8e-07
                                       HHHHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT CS
                             NARP1 194 vlyflAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDla 258
                                       v+y  A+ y  +g+ e+Ale id+a+   ++l + +  ++ i++++Gd k+A+e  + a  +D +
  gi|298675150|ref|YP_003726900.1| 165 VYYVRAYVYAVIGNLEQALEDIDTALYIRDELCNSWNFRGLIMEKMGDRKGAVESFKYALGIDSE 229
                                       57778999**********************************************99999888865 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0         2   1.8e+03      36      56 ..     104     124 ..      76     140 .. 0.63
   2 !   18.2   0.2   2.3e-06    0.0021       2      56 ..     136     190 ..     135     199 .. 0.88
   3 !    9.6   0.0    0.0011      0.99      29      60 ..     197     228 ..     189     239 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2
                             TPR_9  36 GlllaqlGclsaAladLeayl 56 
                                       + +l   G+++ A++ +e + 
  gi|298675150|ref|YP_003726900.1| 104 AEVLSSKGRYEDAVELFEEAE 124
                                       566666778888887777665 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 2.3e-06
                             TPR_9   2 kaia.ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeayl 56 
                                       ka++ ir  + e+a++v++ ll ++   +e ++ R+ ++a  G+l++Al+d +++l
  gi|298675150|ref|YP_003726900.1| 136 KAVHhIRYGEPEQAIEVCNDLLKWHQ-CHEVYYVRAYVYAVIGNLEQALEDIDTAL 190
                                       67777*******************86.5599**********************998 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0011
                             TPR_9  29 peerrdRGlllaqlGclsaAladLeaylalap 60 
                                       +  +  RGl+ +++G+ ++A++ + ++l ++ 
  gi|298675150|ref|YP_003726900.1| 197 CNSWNFRGLIMEKMGDRKGAVESFKYALGIDS 228
                                       556777*********************96665 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       5.3   4.8e+03      22      35 ..      52      63 ..      51      64 .. 0.82
   2 ?   -0.8   0.0       2.3     2e+03       9      20 ..      73      84 ..      61      92 .. 0.62
   3 !   14.4   0.0   3.1e-05     0.028       6      31 ..     104     127 ..     100     132 .. 0.80
   4 ?    1.0   0.0      0.62   5.6e+02       6      22 ..     137     153 ..     134     157 .. 0.79
   5 ?   -1.4   0.0       3.7   3.3e+03      13      20 ..     177     184 ..     169     194 .. 0.60
   6 !    7.4   0.0    0.0055         5       4      31 ..     202     229 ..     199     231 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5.3
                             TPR_7 22 yeqsLaltkdpeda 35
                                      +e+  +l+++p+++
  gi|298675150|ref|YP_003726900.1| 52 NEE--ELEYEPYNI 63
                                      688..99***9986 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.3
                             TPR_7  9 ysrlGdyeeAie 20
                                       + lG+ +eA e
  gi|298675150|ref|YP_003726900.1| 73 LELLGRPDEADE 84
                                      333777777765 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 3.1e-05
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkd 31 
                                       a++ s+ G+ye+A+el+e+  a  +d
  gi|298675150|ref|YP_003726900.1| 104 AEVLSSKGRYEDAVELFEE--AEKRD 127
                                       78899*************9..65544 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.62
                             TPR_7   6 arlysrlGdyeeAiely 22 
                                       a+ + r G+ e+Aie++
  gi|298675150|ref|YP_003726900.1| 137 AVHHIRYGEPEQAIEVC 153
                                       556777799*****986 PP

  == domain 5  score: -1.4 bits;  conditional E-value: 3.7
                             TPR_7  13 GdyeeAie 20 
                                       G+ e+A+e
  gi|298675150|ref|YP_003726900.1| 177 GNLEQALE 184
                                       44444444 PP

  == domain 6  score: 7.4 bits;  conditional E-value: 0.0055
                             TPR_7   4 nLarlysrlGdyeeAielyeqsLaltkd 31 
                                         + + +++Gd++ A+e ++ +L+++++
  gi|298675150|ref|YP_003726900.1| 202 FRGLIMEKMGDRKGAVESFKYALGIDSE 229
                                       55677789*************9998865 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0       0.2   1.8e+02      54      69 ..      72      87 ..      47      94 .. 0.70
   2 !   12.0   0.0   0.00022      0.19      10      71 ..     104     123 ..      98     141 .. 0.67
   3 ?    4.8   0.2     0.037        33       6      30 ..     166     190 ..     128     191 .. 0.66
   4 !   11.2   0.0   0.00039      0.35       6      72 ..     166     224 ..     161     229 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.2
                            TPR_12 54 lyralgryeeAlelle 69
                                      ++++lgr++eA e+ e
  gi|298675150|ref|YP_003726900.1| 72 TLELLGRPDEADEIAE 87
                                      4455666666655554 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00022
                            TPR_12  10 aavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleea 71 
                                       a+vl   gry++A el+e+                                          a
  gi|298675150|ref|YP_003726900.1| 104 AEVLSSKGRYEDAVELFEE------------------------------------------A 123
                                       5555555555555555555..........................................5 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.037
                            TPR_12   6 lnnlaavlrrlgrydeAlellekal 30 
                                       ++ +a v++  g++++Ale  ++al
  gi|298675150|ref|YP_003726900.1| 166 YYVRAYVYAVIGNLEQALEDIDTAL 190
                                       4345666666666666666666554 PP

  == domain 4  score: 11.2 bits;  conditional E-value: 0.00039
                            TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeal 72 
                                       ++ +a v++  g++++Ale  ++al i+ +        ++++ +  g + +++g+ + A+e ++ al
  gi|298675150|ref|YP_003726900.1| 166 YYVRAYVYAVIGNLEQALEDIDTALYIRDE--------LCNSWNFRGLIMEKMGDRKGAVESFKYAL 224
                                       656899*********************933........67778888888888888888888887666 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.014        12       1      28 [.      64      91 ..      64      92 .. 0.90
   2 ?    5.2   0.0     0.042        38      10      28 ..     107     125 ..      99     130 .. 0.75
   3 ?    0.8   0.0       1.1   9.5e+02      13      28 ..     143     158 ..     136     158 .. 0.82
   4 ?    1.6   0.0      0.61   5.5e+02       2      21 ..     165     184 ..     164     190 .. 0.84
   5 ?    3.0   0.0      0.22   1.9e+02       7      24 ..     204     221 ..     203     224 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.014
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6  1 dAlyklalsyrklgdtdkAlealerlik 28
                                      ++lyk    ++ lg++d+A e+ e +i+
  gi|298675150|ref|YP_003726900.1| 64 ESLYKKMVTLELLGRPDEADEIAELIIE 91
                                      689999999***99********998876 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.042
                                       HHHHHHHHHHHHHHHHHHH CS
                             TPR_6  10 yrklgdtdkAlealerlik 28 
                                       + + g++++A+e++e+  k
  gi|298675150|ref|YP_003726900.1| 107 LSSKGRYEDAVELFEEAEK 125
                                       44448**********8755 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHH CS
                             TPR_6  13 lgdtdkAlealerlik 28 
                                        g++++A+e  ++l+k
  gi|298675150|ref|YP_003726900.1| 143 YGEPEQAIEVCNDLLK 158
                                       4799*****9999875 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.61
                                       HHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   2 AlyklalsyrklgdtdkAle 21 
                                       ++y +a+ y   g+ ++Ale
  gi|298675150|ref|YP_003726900.1| 165 VYYVRAYVYAVIGNLEQALE 184
                                       7888999999988*****97 PP

  == domain 5  score: 3.0 bits;  conditional E-value: 0.22
                                       HHHHHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrklgdtdkAleale 24 
                                       +l ++k+gd   A+e ++
  gi|298675150|ref|YP_003726900.1| 204 GLIMEKMGDRKGAVESFK 221
                                       899***********9985 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.045        40       5      32 ..      55      82 ..      53      84 .. 0.90
   2 ?    2.1   0.0      0.34   3.1e+02      20      34 .]     104     118 ..     103     118 .. 0.89
   3 !    9.9   0.0    0.0011         1      14      34 .]     164     184 ..     147     184 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.045
                            TPR_17  5 aleldPnnadaynnLAelllknGdlmtA 32
                                       le++P n ++++ + ++l+ +G++++A
  gi|298675150|ref|YP_003726900.1| 55 ELEYEPYNIESLYKKMVTLELLGRPDEA 82
                                      599********************99998 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.34
                            TPR_17  20 AelllknGdlmtArq 34 
                                       Ae+l+++G++++A++
  gi|298675150|ref|YP_003726900.1| 104 AEVLSSKGRYEDAVE 118
                                       99**********975 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0011
                            TPR_17  14 daynnLAelllknGdlmtArq 34 
                                       ++y+ +A++++ +G+l++A++
  gi|298675150|ref|YP_003726900.1| 164 EVYYVRAYVYAVIGNLEQALE 184
                                       79*****************85 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00098      0.88       6      22 ..     109     125 ..     104     132 .. 0.84
   2 ?   -2.9   0.0       6.4   5.7e+03      18      26 ..     147     155 ..     147     156 .. 0.70
   3 ?    5.3   0.0     0.017        15       4      42 .]     173     211 ..     170     211 .. 0.89
   4 ?    3.1   0.0     0.084        76       8      29 ..     211     232 ..     209     240 .] 0.79

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00098
                            TPR_11   6 eqGkyeeAieaYkkAlk 22 
                                       ++G+ye+A+e +++A k
  gi|298675150|ref|YP_003726900.1| 109 SKGRYEDAVELFEEAEK 125
                                       89*************87 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.4
                            TPR_11  18 kkAlkldPd 26 
                                       ++A++ ++d
  gi|298675150|ref|YP_003726900.1| 147 EQAIEVCND 155
                                       478888776 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.017
                            TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       y   G++e+A+e+  +Al ++ +  + ++ +Gl++ k+G
  gi|298675150|ref|YP_003726900.1| 173 YAVIGNLEQALEDIDTALYIRDELCNSWNFRGLIMEKMG 211
                                       66679****************999999999999999998 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.084
                            TPR_11   8 GkyeeAieaYkkAlkldPdnae 29 
                                       G+ ++A+e++k Al +d++n  
  gi|298675150|ref|YP_003726900.1| 211 GDRKGAVESFKYALGIDSENTM 232
                                       77789************99965 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.028        25      11      25 ..      73      87 ..      69      87 .. 0.85
   2 ?    5.3   0.0     0.043        38       3      26 .]      99     122 ..      97     122 .. 0.85
   3 ?    0.1   0.0         2   1.8e+03       7      20 ..     136     149 ..     134     153 .. 0.79
   4 ?    3.8   0.0      0.13   1.2e+02       3      22 ..     165     184 ..     163     184 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.028
                             TPR_4 11 llalGdldeAralle 25
                                      l +lG++deA +++e
  gi|298675150|ref|YP_003726900.1| 73 LELLGRPDEADEIAE 87
                                      6689******99886 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.043
                             TPR_4   3 allaLArallalGdldeAraller 26 
                                       +l + A++l   G++++A +l+e+
  gi|298675150|ref|YP_003726900.1|  99 FLMFKAEVLSSKGRYEDAVELFEE 122
                                       566778999999*********996 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 2
                             TPR_4   7 LArallalGdldeA 20 
                                        A  + + G++++A
  gi|298675150|ref|YP_003726900.1| 136 KAVHHIRYGEPEQA 149
                                       57788888*****9 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.13
                             TPR_4   3 allaLArallalGdldeAra 22 
                                       +++++A +++  G+l++A++
  gi|298675150|ref|YP_003726900.1| 165 VYYVRAYVYAVIGNLEQALE 184
                                       67899*************85 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       2.2   1.9e+03      20      28 ..      64      72 ..      61      75 .. 0.83
   2 ?    1.2   0.0      0.61   5.4e+02      13      30 ..      76      93 ..      73      94 .. 0.81
   3 !   11.9   0.1   0.00024      0.21      10      29 ..     107     126 ..     105     128 .. 0.88
   4 ?    0.9   0.0      0.77   6.9e+02      12      28 ..     142     158 ..     140     160 .. 0.83
   5 ?   -1.1   0.0       3.3   2.9e+03      10      21 ..     173     184 ..     171     184 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2.2
                               PPR 20 lelfkeMke 28
                                      ++l+k+M+ 
  gi|298675150|ref|YP_003726900.1| 64 ESLYKKMVT 72
                                      689****85 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.61
                               PPR 13 nGkleeAlelfkeMkekG 30
                                       G+++eA e+ + ++e G
  gi|298675150|ref|YP_003726900.1| 76 LGRPDEADEIAELIIELG 93
                                      59******9977777765 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00024
                               PPR  10 ycknGkleeAlelfkeMkek 29 
                                       ++++G++e+A+elf+e +++
  gi|298675150|ref|YP_003726900.1| 107 LSSKGRYEDAVELFEEAEKR 126
                                       7899************8876 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.77
                               PPR  12 knGkleeAlelfkeMke 28 
                                       + G++e A+e+ +++++
  gi|298675150|ref|YP_003726900.1| 142 RYGEPEQAIEVCNDLLK 158
                                       6799*******998765 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 3.3
                               PPR  10 ycknGkleeAle 21 
                                       y+  G+le Ale
  gi|298675150|ref|YP_003726900.1| 173 YAVIGNLEQALE 184
                                       8999******97 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.21   1.8e+02      15      30 ..      76      91 ..      71      93 .. 0.81
   2 !   11.5   0.1   0.00023      0.21       9      28 ..     104     123 ..     104     123 .. 0.93
   3 ?    4.3   0.1     0.044        39       9      36 ..     170     197 ..     166     199 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.21
                            TPR_10 15 rgrydeAealleeala 30
                                      +gr deA +++e  ++
  gi|298675150|ref|YP_003726900.1| 76 LGRPDEADEIAELIIE 91
                                      79********997665 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00023
                            TPR_10   9 analrqrgrydeAealleea 28 
                                       a +l++ gry++A++l+eea
  gi|298675150|ref|YP_003726900.1| 104 AEVLSSKGRYEDAVELFEEA 123
                                       67899**************8 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.044
                            TPR_10   9 analrqrgrydeAealleealairrrll 36 
                                       a ++   g++++A+++ + al ir +l+
  gi|298675150|ref|YP_003726900.1| 170 AYVYAVIGNLEQALEDIDTALYIRDELC 197
                                       56778889*************9998876 PP

>> PPR_2  PPR repeat family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0014       1.2      13      34 ..     107     128 ..     105     132 .. 0.84
   2 ?    2.7   0.0      0.16   1.4e+02      13      32 ..     140     159 ..     138     163 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0014
                             PPR_2  13 lckkgkveeAfklfneMkkrgl 34 
                                       l  kg++e+A++lf+e +kr  
  gi|298675150|ref|YP_003726900.1| 107 LSSKGRYEDAVELFEEAEKRDS 128
                                       6689************999875 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.16
                             PPR_2  13 lckkgkveeAfklfneMkkr 32 
                                       + + g++e+A+++ n+  k+
  gi|298675150|ref|YP_003726900.1| 140 HIRYGEPEQAIEVCNDLLKW 159
                                       678899**********9997 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.1   9.9e+02     226     255 ..      54      83 ..      50      92 .. 0.83
   2 ?    8.5   0.0    0.0013       1.2     199     253 ..      95     148 ..      87     166 .. 0.73
   3 ?    0.4   0.0      0.39   3.5e+02     176     203 ..     179     206 ..     155     226 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.1
                                       HHHHH-TT-HHHHHHHHHHHHHTT--HHHH CS
                        Coatomer_E 226 eaLdkdakdeetLiNlvvaaqhlgkdaevs 255
                                       e L+ ++ + e L   +v+ ++lg+++e+ 
  gi|298675150|ref|YP_003726900.1|  54 EELEYEPYNIESLYKKMVTLELLGRPDEAD 83 
                                       667888888899999999999999998875 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0013
                                       --HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HH CS
                        Coatomer_E 199 stplllngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdae 253
                                       ++   l+ kA v    grye+A +l +ea ++d+ d   L+  v ++   +++ +
  gi|298675150|ref|YP_003726900.1|  95 MNRRFLMFKAEVLSSKGRYEDAVELFEEAEKRDSPDDAPLAKAVHHIRYGEPE-Q 148
                                       56667788888888888888888888888888888888888776666544433.3 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.39
                                       HHH-TTHHHHHHHHHHHHHHHS---HHH CS
                        Coatomer_E 176 lavggekiqdAyyifqelsekykstpll 203
                                       l ++ e i  A+yi +el++ ++   l+
  gi|298675150|ref|YP_003726900.1| 179 LEQALEDIDTALYIRDELCNSWNFRGLI 206
                                       4455577888888888888877666555 PP

>> Type_III_YscG  Bacterial type II secretion system chaperone protein (type_III_yscG)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00018      0.16      23      66 ..      80     123 ..      73     148 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00018
                                       HHHHHHHHHHHHTT-H.HHHHHHHHHHHHHTT-HHHHHHHHTTS CS
                     Type_III_YscG  23 eeaniiadwLeekeeeeeavrlirlssLmnkGkyeealalaekl 66 
                                       +ea  ia+ + e +  +    + ++  L  kG+ye+a +l e+ 
  gi|298675150|ref|YP_003726900.1|  80 DEADEIAELIIELGTMNRRFLMFKAEVLSSKGRYEDAVELFEEA 123
                                       8***************9********************9987664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1700.86
//
Query:       gi|298675151|ref|YP_003726901.1|  [L=269]
Description: hypothetical protein Metev_1233 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.3e-11   42.3   1.8    2.1e-05   24.9   0.2    3.0  3  TPR_19         Tetratricopeptide repeat
    1.6e-09   37.1   6.6       0.19   11.9   0.0    5.6  5  TPR_2          Tetratricopeptide repeat
    4.8e-09   35.7   9.9       0.25   11.7   0.2    5.5  5  TPR_8          Tetratricopeptide repeat
    3.1e-07   29.9  11.0     0.0054   16.5   0.1    5.2  5  TPR_1          Tetratricopeptide repeat
    1.1e-06   28.8   0.1      0.064   13.5   0.0    2.5  2  ANAPC3         Anaphase-promoting complex, cyclosome, subunit
    1.7e-06   28.3   0.7        1.7    9.6   0.2    4.5  5  TPR_14         Tetratricopeptide repeat
    1.2e-05   25.8   0.0    0.00082   20.0   0.0    2.9  3  TPR_16         Tetratricopeptide repeat
    1.9e-05   23.8   0.7      0.041   12.8   0.0    2.4  2  NARP1          NMDA receptor-regulated protein 1
    7.2e-05   23.0   2.5        1.6    9.1   0.0    4.0  4  TPR_12         Tetratricopeptide repeat
    8.2e-05   22.7   0.1       0.13   12.4   0.0    2.7  3  TPR_9          Tetratricopeptide repeat
     0.0018   18.5   2.2       0.38   11.2   0.0    4.2  4  TPR_17         Tetratricopeptide repeat
      0.007   16.4   0.4        1.4    9.0   0.2    2.4  2  SRP_TPR_like   Putative TPR-like repeat
  ------ inclusion threshold ------
      0.011   15.8   4.4      0.052   13.6   0.1    3.5  3  Fis1_TPR_C     Fis1 C-terminal tetratricopeptide repeat
      0.013   14.9   0.0        0.4   10.0   0.0    2.3  2  TPR_MalT       MalT-like TPR region
      0.017   15.2   0.3        3.1    7.9   0.0    2.3  2  Type_III_YscG  Bacterial type II secretion system chaperone p
      0.022   14.4   0.1      0.037   13.7   0.1    1.4  1  HrpB1_HrpK     Bacterial type III secretion protein (HrpB1_Hr
      0.024   14.7   0.3         20    5.5   0.0    3.9  4  TPR_7          Tetratricopeptide repeat
      0.053   13.2   6.6        2.2    8.0   0.1    4.1  4  TPR_11         TPR repeat


Domain annotation for each model (and alignments):
>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.2   3.5e-05     0.035      20      67 ..      78     136 ..      61     137 .. 0.77
   2 !   24.9   0.2   2.1e-08   2.1e-05       4      66 ..     141     201 ..     138     203 .. 0.92
   3 !   15.6   0.0   1.7e-05     0.017       4      53 ..     174     222 ..     172     237 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.5e-05
                            TPR_19  20 e...........dpknaearllLAeallalgqldeAealLdalpeedpddaryasLlAk 67 
                                       e           dp+n e +++ +  l  l +ldeA ++ ++++  +p+d r  +L+A 
  gi|298675151|ref|YP_003726901.1|  78 EgietadeelesDPNNIETLYRKMTNLELLERLDEADKVAEDILSLNPKDRRQMMLKAD 136
                                       333333344444**************************************999999985 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 2.1e-08
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasLlA 66 
                                        g+y +A++l+++a ++   +a+a l+ +  +l  g+ d+A ++++ l+e +++ + +  ++A
  gi|298675151|ref|YP_003726901.1| 141 KGQYNDAVELFKEA-EKMKSYADAPLAKVVHHLRYGEHDQALEICNNLLEIEQN-PKVYYVRA 201
                                       69***********8.99999**********************************.77766665 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 1.7e-05
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpe 53 
                                        g +++Al++  ++l+   +n+ + +  A ++   g++++A + ++ + +
  gi|298675151|ref|YP_003726901.1| 174 YGEHDQALEICNNLLEI-EQNPKVYYVRAYIYTVIGNFEQALENINSAIN 222
                                       699**********7766.77*********************998877665 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.013        13      11      34 .]     104     127 ..     102     127 .. 0.90
   2 !    9.9   0.0   0.00083      0.83       7      28 ..     134     155 ..     131     158 .. 0.87
   3 ?    3.2   0.0      0.12   1.2e+02      11      31 ..     171     191 ..     169     193 .. 0.86
   4 !   11.9   0.0   0.00019      0.19       1      28 [.     194     221 ..     194     224 .. 0.90
   5 ?    4.6   0.1     0.041        41       3      24 ..     230     251 ..     228     252 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.013
                             TPR_2  11 yyklgdyeeAleafekAleldPnn 34 
                                       ++ l +++eA +  e  l+l+P++
  gi|298675151|ref|YP_003726901.1| 104 LELLERLDEADKVAEDILSLNPKD 127
                                       56789*****************86 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00083
                             TPR_2   7 lGlayyklgdyeeAleafekAl 28 
                                        ++++  +g+y++A+e+f++A 
  gi|298675151|ref|YP_003726901.1| 134 KADVLSGKGQYNDAVELFKEAE 155
                                       68889999************96 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.12
                             TPR_2  11 yyklgdyeeAleafekAleld 31 
                                       +++ g++++Ale ++  le++
  gi|298675151|ref|YP_003726901.1| 171 HLRYGEHDQALEICNNLLEIE 191
                                       67889***********99987 PP

  == domain 4  score: 11.9 bits;  conditional E-value: 0.00019
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAl 28 
                                       ++++y ++++y   g++e+Ale  + A+
  gi|298675151|ref|YP_003726901.1| 194 PKVYYVRAYIYTVIGNFEQALENINSAI 221
                                       589*******************988776 PP

  == domain 5  score: 4.6 bits;  conditional E-value: 0.041
                             TPR_2   3 alynlGlayyklgdyeeAleaf 24 
                                       +++  Gl+++++g   eA+ +f
  gi|298675151|ref|YP_003726901.1| 230 YWNLKGLILENMGYRLEAKGCF 251
                                       89****************9998 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0087       8.7      14      34 .]     107     127 ..     102     127 .. 0.91
   2 !   11.7   0.2   0.00025      0.25       5      31 ..     132     158 ..     131     160 .. 0.91
   3 ?    1.6   0.0      0.43   4.3e+02      15      33 ..     175     193 ..     172     194 .. 0.89
   4 !   10.0   0.1   0.00083      0.83       2      29 ..     195     222 ..     194     225 .. 0.91
   5 !    7.9   0.1    0.0041       4.1       2      24 ..     229     251 ..     228     252 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0087
                                       TT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8  14 lgdyeeAkeyyekaleldpdn 34 
                                       l++++eA ++ e  l+l+p++
  gi|298675151|ref|YP_003726901.1| 107 LERLDEADKVAEDILSLNPKD 127
                                       899****************96 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00025
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   5 ynlgsiylklgdyeeAkeyyekaleld 31 
                                       ++++++++ +g+y+ A+e +++a +++
  gi|298675151|ref|YP_003726901.1| 132 MLKADVLSGKGQYNDAVELFKEAEKMK 158
                                       5799*******************9886 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.43
                                       T-HHHHHHHHHHHHHHHHH CS
                             TPR_8  15 gdyeeAkeyyekaleldpd 33 
                                       g++++A e ++  le++++
  gi|298675151|ref|YP_003726901.1| 175 GEHDQALEICNNLLEIEQN 193
                                       789********99999876 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.00083
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekale 29 
                                       ++yy  ++iy   g++e+A e ++ a+ 
  gi|298675151|ref|YP_003726901.1| 195 KVYYVRAYIYTVIGNFEQALENINSAIN 222
                                       79*******************9999885 PP

  == domain 5  score: 7.9 bits;  conditional E-value: 0.0041
                                       CHHHHHHHHHHHTT-HHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyy 24 
                                       ++++++g+i++++g   eAk ++
  gi|298675151|ref|YP_003726901.1| 229 SYWNLKGLILENMGYRLEAKGCF 251
                                       68**************9999666 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.62   6.2e+02      13      34 .]     106     127 ..     104     127 .. 0.83
   2 !    9.1   0.0    0.0012       1.2       7      27 ..     134     154 ..     131     159 .. 0.85
   3 !    6.2   0.1    0.0096       9.6      12      33 ..     172     193 ..     170     194 .. 0.88
   4 !   16.5   0.1   5.5e-06    0.0054       1      28 [.     194     221 ..     194     224 .. 0.92
   5 ?    0.7   0.1      0.52   5.2e+02       3      15 ..     230     242 ..     228     242 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.62
                                       HTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  13 klgkydeAleyyekALelnPnn 34 
                                        l+++deA +  e  L+lnP++
  gi|298675151|ref|YP_003726901.1| 106 LLERLDEADKVAEDILSLNPKD 127
                                       6889999999999999999986 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0012
                                       HHHHHHHTT-HHHHHHHHHHH CS
                             TPR_1   7 lGnayfklgkydeAleyyekA 27 
                                       ++ ++  +g+y++A+e +++A
  gi|298675151|ref|YP_003726901.1| 134 KADVLSGKGQYNDAVELFKEA 154
                                       56778889************9 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0096
                                       HHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1  12 fklgkydeAleyyekALelnPn 33 
                                       ++ g++d+Ale ++  Le++ n
  gi|298675151|ref|YP_003726901.1| 172 LRYGEHDQALEICNNLLEIEQN 193
                                       6789***********9999887 PP

  == domain 4  score: 16.5 bits;  conditional E-value: 5.5e-06
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekAL 28 
                                       +k++y ++++y   g++++Ale  + A+
  gi|298675151|ref|YP_003726901.1| 194 PKVYYVRAYIYTVIGNFEQALENINSAI 221
                                       589*******************998887 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 0.52
                                       HHHHHHHHHHHTT CS
                             TPR_1   3 alynlGnayfklg 15 
                                        ++ +G+++ ++g
  gi|298675151|ref|YP_003726901.1| 230 YWNLKGLILENMG 242
                                       69********998 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   6.5e-05     0.064       4      51 ..     109     155 ..     107     169 .. 0.88
   2 !   12.9   0.1    0.0001       0.1      33      80 ..     171     218 ..     162     220 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.5e-05
                                       -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCTSH CS
                            ANAPC3   4 nyknAiflaerllaaetespedayllAlclylngqykrAyellrkakl 51 
                                       ++++A  +ae +l+ ++++    +l+A +l   gqy+ A el+++a +
  gi|298675151|ref|YP_003726901.1| 109 RLDEADKVAEDILSLNPKDRRQMMLKADVLSGKGQYNDAVELFKEA-E 155
                                       678888999****9*******************************9.3 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.0001
                                       HHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3  33 lylngqykrAyellrkaklnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                       +++ g++++A+e+++++ + ++++++ y+ A  +  ++++e+A+  + 
  gi|298675151|ref|YP_003726901.1| 171 HLRYGEHDQALEICNNLLEIEQNPKVYYVRAYIYTVIGNFEQALENIN 218
                                       78899************9999**********************98875 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       4.4   4.4e+03      17      39 ..      76      98 ..      71     104 .. 0.63
   2 !    9.6   0.2    0.0017       1.7      11      36 ..     104     129 ..      94     135 .. 0.84
   3 ?    5.7   0.0     0.031        31       7      29 ..     134     156 ..     128     170 .. 0.81
   4 !    7.5   0.0    0.0087       8.7      10      33 ..     170     195 ..     165     203 .. 0.74
   5 ?    1.4   0.0      0.77   7.7e+02       2      24 ..     195     217 ..     194     225 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 4.4
                            TPR_14 17 pdeAiallrralalaPddaeawl 39
                                      ++e i+ +++ l+ +P++ e+++
  gi|298675151|ref|YP_003726901.1| 76 LEEGIETADEELESDPNNIETLY 98
                                      45556666666666777766554 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0017
                            TPR_14  11 llalGdpdeAiallrralalaPddae 36 
                                       l+ l+++deA ++++++l+l+P+d++
  gi|298675151|ref|YP_003726901.1| 104 LELLERLDEADKVAEDILSLNPKDRR 129
                                       677899*****************975 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.031
                            TPR_14   7 laeallalGdpdeAiallrrala 29 
                                        a++l   G++ +A++l+++a +
  gi|298675151|ref|YP_003726901.1| 134 KADVLSGKGQYNDAVELFKEAEK 156
                                       48899999************976 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.0087
                            TPR_14  10 allalGdpdeAiallrrala..laPd 33 
                                        +l+ G++d+A+++++ +l+  ++P+
  gi|298675151|ref|YP_003726901.1| 170 HHLRYGEHDQALEICNNLLEieQNPK 195
                                       47999*************99334554 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.77
                            TPR_14   2 eallalaeallalGdpdeAiall 24 
                                       ++++ +a ++   G++++A++  
  gi|298675151|ref|YP_003726901.1| 195 KVYYVRAYIYTVIGNFEQALENI 217
                                       6789999999999******9855 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       3.4   3.4e+03      48      67 ..      74      93 ..      68      94 .. 0.84
   2 !   20.0   0.0   8.3e-07   0.00082      11      66 ..     108     160 ..     107     164 .. 0.89
   3 ?    2.3   0.0      0.28   2.8e+02      33      55 ..     193     215 ..     165     225 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3.4
                            TPR_16 48 grlaeAaalyraalraapda 67
                                      + l+e ++  +++l+ +p++
  gi|298675151|ref|YP_003726901.1| 74 QLLEEGIETADEELESDPNN 93
                                      67999999999999999986 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 8.3e-07
                            TPR_16  11 gdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                        + d+A +++e  l ++   P +++ ++l++d++  +g + +A++l+++a +  ++
  gi|298675151|ref|YP_003726901.1| 108 ERLDEADKVAEDILSLN---PKDRRQMMLKADVLSGKGQYNDAVELFKEAEKMKSY 160
                                       5899*************...*****************************9955444 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.28
                            TPR_16  33 aaeAllllgdaalrqgrlaeAaa 55 
                                       ++  ++ ++ ++ + g+++ A++
  gi|298675151|ref|YP_003726901.1| 193 NPKVYYVRAYIYTVIGNFEQALE 215
                                       66677777777777777777764 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.6   0.00078      0.78     204     283 ..     106     184 ..      67     195 .. 0.77
   2 !   12.8   0.0   4.1e-05     0.041     194     248 ..     196     250 ..     189     261 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00078
                                       HHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT-HHHHHHHHH..HHHHTT-HHH CS
                             NARP1 204 klgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaDRyiNskcak..ymLradevee 278
                                        l++ ++A ++ +  ++ +p+    ++ Ka +l  +G+ ++A+e+ +ea k+     y  +  ak  ++Lr +e ++
  gi|298675151|ref|YP_003726901.1| 106 LLERLDEADKVAEDILSLNPKDRRQMMLKADVLSGKGQYNDAVELFKEAEKMKS---YADAPLAKvvHHLRYGEHDQ 179
                                       566778888999999999999999999999999999999999999999999964...33333333225677777777 PP

                                       HHHHH CS
                             NARP1 279 Aeetv 283
                                       A e++
  gi|298675151|ref|YP_003726901.1| 180 ALEIC 184
                                       77666 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 4.1e-05
                                       HHHHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHH CS
                             NARP1 194 vlyflAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaev 248
                                       v+y  A+ y  +g+ e+Ale i++ai+  + +  ++  K+ il+ +G   +A  +
  gi|298675151|ref|YP_003726901.1| 196 VYYVRAYIYTVIGNFEQALENINSAINFRDGISSYWNLKGLILENMGYRLEAKGC 250
                                       57888999***************************************88887655 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.52   5.2e+02      26      73 ..      76     122 ..      72     126 .. 0.57
   2 !    9.1   0.0    0.0016       1.6      52      74 ..     135     157 ..     128     159 .. 0.82
   3 !    7.6   0.2    0.0047       4.7      17      61 ..     175     217 ..     161     225 .. 0.59
   4 ?    4.5   0.0     0.043        43       6      34 ..     197     225 ..     192     249 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.52
                            TPR_12  26 lekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                       le+ +e a + l+   p+ ++tl+   + +++l+r++eA +  e+ l 
  gi|298675151|ref|YP_003726901.1|  76 LEEGIETADEELES-DPNNIETLYRKMTNLELLERLDEADKVAEDILS 122
                                       55556666444443.344444444444445678888888887777665 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0016
                            TPR_12  52 grlyralgryeeAlelleealai 74 
                                       +++++  g+y +A+el++ea ++
  gi|298675151|ref|YP_003726901.1| 135 ADVLSGKGQYNDAVELFKEAEKM 157
                                       78888889999999999998776 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0047
                            TPR_12  17 grydeAlellekaleiarrllGpdhpltattlrnLgrlyralgry 61 
                                       g++d+Ale+++  lei ++   + ++  a ++  +g   +al++ 
  gi|298675151|ref|YP_003726901.1| 175 GEHDQALEICNNLLEIEQNP--KVYYVRAYIYTVIGNFEQALENI 217
                                       78888888888888887432..33334444444444444444444 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.043
                            TPR_12   6 lnnlaavlrrlgrydeAlellekaleiar 34 
                                       ++ +a +++  g++++Ale+ + a++ + 
  gi|298675151|ref|YP_003726901.1| 197 YYVRAYIYTVIGNFEQALENINSAINFRD 225
                                       55578899999999999999998887665 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0     0.005         5       9      52 ..     108     151 ..     106     170 .. 0.88
   2 !   12.4   0.0   0.00013      0.13       5      55 ..     171     220 ..     166     225 .. 0.88
   3 ?   -1.9   0.0       3.8   3.8e+03      35      52 ..     234     251 ..     230     253 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.005
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladL 52 
                                       e+ ++a +v+e +l l+P+d +  +  + +l   G+++ A++ +
  gi|298675151|ref|YP_003726901.1| 108 ERLDEADKVAEDILSLNPKDRRQMMLKADVLSGKGQYNDAVELF 151
                                       67888999*******************************99855 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00013
                             TPR_9   5 aireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeay 55 
                                       ++r  ++++al++++ ll +  ++   ++ R+ ++   G++++Al+  + +
  gi|298675151|ref|YP_003726901.1| 171 HLRYGEHDQALEICNNLLEIEQNP-KVYYVRAYIYTVIGNFEQALENINSA 220
                                       59999***************9875.99******************987765 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3.8
                             TPR_9  35 RGlllaqlGclsaAladL 52 
                                        Gl+l+ +G   +A  ++
  gi|298675151|ref|YP_003726901.1| 234 KGLILENMGYRLEAKGCF 251
                                       79*******999987766 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.19   1.9e+02       5      17 ..      86      98 ..      82     113 .. 0.86
   2 ?    0.5   0.0      0.99   9.8e+02      18      33 ..     133     148 ..     117     149 .. 0.78
   3 !   11.2   0.0   0.00038      0.38      11      34 .]     192     215 ..     176     215 .. 0.86
   4 ?   -1.1   0.1       3.3   3.2e+03      15      27 ..     230     242 ..     226     247 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.19
                            TPR_17  5 aleldPnnadayn 17
                                       le dPnn + ++
  gi|298675151|ref|YP_003726901.1| 86 ELESDPNNIETLY 98
                                      5899****99988 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.99
                            TPR_17  18 nLAelllknGdlmtAr 33 
                                       ++A +l+ +G++ +A+
  gi|298675151|ref|YP_003726901.1| 133 LKADVLSGKGQYNDAV 148
                                       6788999999999987 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00038
                            TPR_17  11 nnadaynnLAelllknGdlmtArq 34 
                                        n+++y+ +A+++  +G++++A++
  gi|298675151|ref|YP_003726901.1| 192 QNPKVYYVRAYIYTVIGNFEQALE 215
                                       58*******************985 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 3.3
                            TPR_17  15 aynnLAelllknG 27 
                                        +n+++ +l++ G
  gi|298675151|ref|YP_003726901.1| 230 YWNLKGLILENMG 242
                                       69*******9987 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.012        12      60     103 ..     109     156 ..      88     166 .. 0.71
   2 !    9.0   0.2    0.0014       1.4      18      70 ..     159     219 ..     151     229 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.012
                      SRP_TPR_like  60 kykkalkilkkv...eaee.kvkvlksqvlYrlgsyekAYklLskekk 103
                                       ++ +a k+ + +   + ++ +  +lk+ vl  +g+y++A +l  + +k
  gi|298675151|ref|YP_003726901.1| 109 RLDEADKVAEDIlslNPKDrRQMMLKADVLSGKGQYNDAVELFKEAEK 156
                                       5555555544331113444488899**************888766554 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0014
                      SRP_TPR_like  18 kf......kvvaliklekyeeaLkllkkgs..alsedvrfEkaYvlYklkkykkalkilkk 70 
                                        +      kvv  ++ + +++aL+++++    + + +v + +aY++  + ++++al+ +++
  gi|298675151|ref|YP_003726901.1| 159 SYadaplaKVVHHLRYGEHDQALEICNNLLeiEQNPKVYYVRAYIYTVIGNFEQALENINS 219
                                       4455566699999************99987334566899****************987765 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.65   6.4e+02      16      41 ..     109     134 ..     107     137 .. 0.83
   2 ?   13.6   0.1   5.2e-05     0.052      11      32 ..     171     192 ..     169     196 .. 0.91
   3 ?    0.5   0.0      0.64   6.4e+02       5      30 ..     198     223 ..     194     241 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.65
                                       -HHHHHHHHHHHHHHTTS-HHHHHHH CS
                        Fis1_TPR_C  16 eYseArryvdalLeiEPenrQaqsLk 41 
                                       + +eA + ++ +L++ P+ r    Lk
  gi|298675151|ref|YP_003726901.1| 109 RLDEADKVAEDILSLNPKDRRQMMLK 134
                                       678999***********998777766 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 5.2e-05
                                       HHHHT-HHHHHHHHHHHHHHTT CS
                        Fis1_TPR_C  11 hyklgeYseArryvdalLeiEP 32 
                                       h++ ge+++A++ ++ lLeiE 
  gi|298675151|ref|YP_003726901.1| 171 HLRYGEHDQALEICNNLLEIEQ 192
                                       89******************94 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.64
                                       HHHHHHHHHHT-HHHHHHHHHHHHHH CS
                        Fis1_TPR_C   5 YylAlGhyklgeYseArryvdalLei 30 
                                       Y  A+ ++ +g++++A++ ++  ++ 
  gi|298675151|ref|YP_003726901.1| 198 YVRAYIYTVIGNFEQALENINSAINF 223
                                       44567777799*****9988877665 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0    0.0004       0.4      16      88 ..     109     176 ..     106     196 .. 0.88
   2 ?    1.9   0.0      0.12   1.2e+02       6      53 ..     199     248 ..     195     252 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0004
                          TPR_MalT  16 daeralelArqALallpeddllariaatavlGeasllqGdleaAlqalqeaeklarqadslhvallallqqae 88 
                                       + ++a + A+ +L+l p+d+  + + a  + G     +G+ ++A++ ++eaek+   ad++ + +++ l+ +e
  gi|298675151|ref|YP_003726901.1| 109 RLDEADKVAEDILSLNPKDRRQMMLKADVLSG-----KGQYNDAVELFKEAEKMKSYADAPLAKVVHHLRYGE 176
                                       5678999****************999999999.....*****************9999999998888876666 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.12
                          TPR_MalT   6 lrAllaiasgdaeralelArqALallpeddllar..iaatavlGeasllq 53 
                                       +rA++++  g++e+ale  + A+++ +    ++   ++++ ++G++   +
  gi|298675151|ref|YP_003726901.1| 199 VRAYIYTVIGNFEQALENINSAINFRDGISSYWNlkGLILENMGYRLEAK 248
                                       68888888888888888888888887765544433377777777765555 PP

>> Type_III_YscG  Bacterial type II secretion system chaperone protein (type_III_yscG)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0031       3.1      23      65 ..     111     153 ..     107     172 .. 0.85
   2 ?    5.3   0.1     0.019        19      21      65 ..     176     219 ..     153     233 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0031
                                       HHHHHHHHHHHHTT-H.HHHHHHHHHHHHHTT-HHHHHHHHTT CS
                     Type_III_YscG  23 eeaniiadwLeekeeeeeavrlirlssLmnkGkyeealalaek 65 
                                       +ea  +a+ + + + ++    ++++  L  kG+y++a +l ++
  gi|298675151|ref|YP_003726901.1| 111 DEADKVAEDILSLNPKDRRQMMLKADVLSGKGQYNDAVELFKE 153
                                       899999998888888879999****************998765 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.019
                                       -HHHHHHHHHHHHHTT-H.HHHHHHHHHHHHHTT-HHHHHHHHTT CS
                     Type_III_YscG  21 rheeaniiadwLeekeeeeeavrlirlssLmnkGkyeealalaek 65 
                                        h++a+ i + L e e++   v  +r+   +  G++e+al+  ++
  gi|298675151|ref|YP_003726901.1| 176 EHDQALEICNNLLEIEQN-PKVYYVRAYIYTVIGNFEQALENINS 219
                                       59**********999999.88999***************987665 PP

>> HrpB1_HrpK  Bacterial type III secretion protein (HrpB1_HrpK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   3.7e-05     0.037       7      86 ..      90     166 ..      84     202 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.7e-05
                        HrpB1_HrpK   7 skelvggLievlslalasedtedaellLdalrvLrPevaeldllegvlliergrweeAlrlLreveaeasgtpyaka 83 
                                       + + +++L + ++     e+ ++a+++ + +  L P+     +l + +l  +g++++A+ l++e e+ +    ya a
  gi|298675151|ref|YP_003726901.1|  90 DPNNIETLYRKMTNLELLERLDEADKVAEDILSLNPKDRRQMMLKADVLSGKGQYNDAVELFKEAEKMK---SYADA 163
                                       555566666666666678999********************************************9544...44444 PP

                        HrpB1_HrpK  84 LlA 86 
                                        lA
  gi|298675151|ref|YP_003726901.1| 164 PLA 166
                                       444 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       3.1   3.1e+03       4      19 ..      93     108 ..      86     117 .. 0.63
   2 ?    5.5   0.0      0.02        20       6      24 ..     135     153 ..     133     159 .. 0.87
   3 ?    3.1   0.0      0.12   1.2e+02      11      32 ..     173     194 ..     168     198 .. 0.83
   4 ?    0.3   0.0      0.89   8.9e+02       8      20 ..     203     215 ..     196     219 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3.1
                             TPR_7   4 nLarlysrlGdyeeAi 19 
                                       n+  ly+++ + e ++
  gi|298675151|ref|YP_003726901.1|  93 NIETLYRKMTNLELLE 108
                                       5556666655555444 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.02
                             TPR_7   6 arlysrlGdyeeAielyeq 24 
                                       a++ s  G+y +A+el+++
  gi|298675151|ref|YP_003726901.1| 135 ADVLSGKGQYNDAVELFKE 153
                                       6777889**********98 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.12
                             TPR_7  11 rlGdyeeAielyeqsLaltkdp 32 
                                       r G++++A+e++  +L+++  p
  gi|298675151|ref|YP_003726901.1| 173 RYGEHDQALEICNNLLEIEQNP 194
                                       559*********9999988766 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.89
                             TPR_7   8 lysrlGdyeeAie 20 
                                       +y   G++e+A+e
  gi|298675151|ref|YP_003726901.1| 203 IYTVIGNFEQALE 215
                                       5555789999986 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.7   1.6e+03      22      32 ..      88      98 ..      87      99 .. 0.82
   2 ?    8.0   0.1    0.0022       2.2       7      22 ..     141     156 ..     135     162 .. 0.87
   3 ?    1.4   0.2      0.26   2.6e+02      25      38 ..     191     204 ..     175     208 .. 0.68
   4 ?    5.4   0.2     0.014        14       2      24 ..     202     224 ..     201     242 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.7
                            TPR_11 22 kldPdnaeayy 32
                                      + dP+n e +y
  gi|298675151|ref|YP_003726901.1| 88 ESDPNNIETLY 98
                                      569****9988 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0022
                            TPR_11   7 qGkyeeAieaYkkAlk 22 
                                       +G+y++A+e +k+A k
  gi|298675151|ref|YP_003726901.1| 141 KGQYNDAVELFKEAEK 156
                                       8*************87 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.26
                            TPR_11  25 PdnaeayynLGlay 38 
                                       ++n+ +yy ++++y
  gi|298675151|ref|YP_003726901.1| 191 EQNPKVYYVRAYIY 204
                                       36888888888877 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.014
                            TPR_11   2 dayyeqGkyeeAieaYkkAlkld 24 
                                       ++y+  G++e+A+e+ + A++++
  gi|298675151|ref|YP_003726901.1| 202 YIYTVIGNFEQALENINSAINFR 224
                                       578888*************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1623.97
//
Query:       gi|298675152|ref|YP_003726902.1|  [L=43]
Description: hypothetical protein Metev_1234 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.28s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 324.71
//
Query:       gi|298675153|ref|YP_003726903.1|  [L=480]
Description: polysaccharide biosynthesis protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-21   76.4  11.4    2.1e-21   76.4  11.4    2.3  2  Polysacc_synt_3  Polysaccharide biosynthesis protein
    5.1e-21   75.3  21.5    5.1e-21   75.3  21.5    2.1  2  Polysacc_synt    Polysaccharide biosynthesis protein
    1.3e-16   60.9  29.5    1.3e-16   60.9  29.5    3.7  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
    4.1e-10   39.5   6.5    4.1e-10   39.5   6.5    4.2  3  MatE             MatE
    5.2e-05   22.0  36.6    0.00076   18.2  36.5    2.4  1  MurJ             Lipid II flippase MurJ


Domain annotation for each model (and alignments):
>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.4  11.4   5.9e-25   2.1e-21       6     283 ..      36     320 ..      31     327 .. 0.90
   2 ?   -4.3  12.5       2.3   8.3e+03      60     157 ..     367     464 ..     358     474 .. 0.81

  Alignments for each domain:
  == domain 1  score: 76.4 bits;  conditional E-value: 5.9e-25
                   Polysacc_synt_3   6 LspedFGvvaialvvislanlfvdmGlssaliqke..dlteedlstvft....fnlvlgllialvlfllapliasfy 76 
                                       L  +d+G+ a ++v i+++  ++++Gl  a+ +       +e+++ +f+    +  v+g+++a++++l++  ia+++
  gi|298675153|ref|YP_003726903.1|  36 LPIQDYGIWAQVMVTIGIVPGIMSLGLPGAMARFMpsVKVKEKFQDMFYsflsVAAVTGMFAAFLIYLASGPIADLL 112
                                       6679************************99998765345566899999833224678999***************98 PP

                   Polysacc_synt_3  77 nqpelvtvlrvlalvlilsglssvqeallrrelkFkklfkitlvssvvgvivaivlAllglgvwALvigtllsslls 153
                                        +   + ++++l++v++++++ +v  +++r   + kk ++ ++  ++++v++  + +l g g+   + g l++s++ 
  gi|298675153|ref|YP_003726903.1| 113 FD-GNAFIVKLLSIVVFFETIEKVLFNYFRATEQIKKDSILRFSKNFLMVVLVSIFVLQGGGLLGAIAGLLAKSVVV 188
                                       65.55689*****************************************99888999******************** PP

                   Polysacc_synt_3 154 lvllwlaskwrprlkf.slkslkelfsfglklllsnllnylarnldnlliGkvlssaaLGlYsvakrlaslpvaeit 229
                                       +++ ++++  ++ +k+ ++  lk ++++g+ l+ s +  +++r++d  +iG +l+++a+G+Ys +++l ++ v+++ 
  gi|298675153|ref|YP_003726903.1| 189 FLMAFVIIVSQLGFKLpKFGGLKGYLKYGIPLVPSRMSSWIVRSSDRYVIGGYLGTSAVGYYSPGYTLGNI-VQMFV 264
                                       *9999999999999874689***********************************************9986.79999 PP

                   Polysacc_synt_3 230 sviakVlfPalSrlqd..dkkklrelylkvlrlialivlPiavglavvaellvkvl 283
                                       ++++ +l  +lSr  d  + +++++++  +l+    +++P+++gl +++++++ +l
  gi|298675153|ref|YP_003726903.1| 265 APLNFILPMVLSRHYDgdNLDEVKKYLGYSLKYFLAVAIPAVFGLSLLSKPMLVIL 320
                                       *************975227789*****************************98776 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 2.3
                   Polysacc_synt_3  60 lialvlfllapliasfynqpelvtvlrvlalvlilsglssvqeallrrelkFkklfkitlvssvvgvivaivlAllg 136
                                       lia+vl l  +li   y   +++  +++l++ ++l+ +   +  +++ +++F  ++k  ++s ++++i+ ++     
  gi|298675153|ref|YP_003726903.1| 367 LIAAVLNLGLNLILVPYIGIIAAATTTLLSFIVVLAFMAYYSLRFFQFDMNFRFIVKSLVASLLMSGIILMWSPTGV 443
                                       5555666666666666666677889999****************************************999999999 PP

                   Polysacc_synt_3 137 lgvwALvigtllssllslvll 157
                                       l+  A++    +s +  lvll
  gi|298675153|ref|YP_003726903.1| 444 LSTLAIIGVCAVSYFAVLVLL 464
                                       999998887777777666665 PP

>> Polysacc_synt  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3  21.5   1.4e-24   5.1e-21       4     268 ..      10     272 ..       7     277 .. 0.91
   2 ?   -2.3  20.5      0.62   2.2e+03      93     218 ..     298     440 ..     291     460 .. 0.70

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 1.4e-24
                     Polysacc_synt   4 gvivlllsqlitkllafvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrekkelvslilln 80 
                                        +i   l +++++  + + l++l+  l+  ++G+ a+++ ++++   + +lGl+ a  r++   + k e+++ ++ +
  gi|298675153|ref|YP_003726903.1|  10 RIILVGLTRFVNNFKGVILLPVLTKNLPIQDYGIWAQVMVTIGIVPGIMSLGLPGAMARFMPSVKVK-EKFQDMFYS 85 
                                       567777889999999************************************************9996.********* PP

                     Polysacc_synt  81 vllvllvlvllfllllliaa......flglpelavlylilalmllllvgvasfrrglfqglermkyaavsqvveqls 151
                                        l+v  v+ +++++l ++a       +++    a+++ +l++++  + ++  +  ++f++ e  k  ++ +++++  
  gi|298675153|ref|YP_003726903.1|  86 FLSVAAVTGMFAAFLIYLASgpiadlLFD--GNAFIVKLLSIVVF-FETIEKVLFNYFRATEQIKKDSILRFSKNFL 159
                                       ******************98998744444..44556666666555.89***************************** PP

                     Polysacc_synt 152 rvilvliavflfldivaavlgavlaalvggivslavlrkkfrprfvilslklvrellsfsapltisslaillytyid 228
                                        v+lv i+v+ ++ +++a++g+++ ++v  +++++++   ++++  ++     +  l++++pl+ s++++ +   +d
  gi|298675153|ref|YP_003726903.1| 160 MVVLVSIFVLQGGGLLGAIAGLLAKSVVVFLMAFVIIVSQLGFKLPKF--GGLKGYLKYGIPLVPSRMSSWIVRSSD 234
                                       **************************************7776555555..8999*********************** PP

                     Polysacc_synt 229 sillglllgaeavGiYnaayqllvaisgllapivtaalfP 268
                                       ++++g +lg++avG+Y+ +y+l +++++++ap +   + P
  gi|298675153|ref|YP_003726903.1| 235 RYVIGGYLGTSAVGYYSPGYTLGNIVQMFVAPLNF--ILP 272
                                       *******************************9876..555 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.62
                     Polysacc_synt  93 llllliaaflglpelavlylilalmll......llvgvasfrrglfqglermkyaavs.qvveqlsrvilvliavfl 162
                                       +l+  i a++gl+ l+ ++l++ ++        ++++++++ + lf  +  ++ +a+     ++++++ l+++++ l
  gi|298675153|ref|YP_003726903.1| 298 FLAVAIPAVFGLSLLSKPMLVILSTPEiaeqsyIITPFVALSALLFGVFAVFNKVAMLvKKTQVIGIIWLIAAVLNL 374
                                       45555555677777777777777765322333378888999999999998555555550555666667777777778 PP

                     Polysacc_synt 163 fld........ivaavlgavlaalvggivslavlrkkfr..prfvilslklvrellsfsapltiss 218
                                       +l         i aa+ +++l+ +v + + ++++ ++f    +f ++ ++lv  ll  ++ l+ s 
  gi|298675153|ref|YP_003726903.1| 375 GLNlilvpyigIIAAATTTLLSFIVVLAFMAYYSLRFFQfdMNFRFIVKSLVASLLMSGIILMWSP 440
                                       888888888778888888888888888887777777774577777777799999999999999775 PP

>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   1.9       0.3   1.1e+03      92     134 ..      53     102 ..      26     108 .. 0.51
   2 !   13.8   5.6   1.3e-05     0.046       2      88 ..     120     207 ..     119     249 .. 0.87
   3 ?   -0.9   0.1      0.44   1.6e+03      77     104 ..     287     307 ..     258     325 .. 0.62
   4 !   60.9  29.5   3.7e-20   1.3e-16       4     142 ..     335     465 ..     332     466 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.3
                   Polysacc_synt_C  92 lkpllaalvmgivvylllllllglllla..........alalllavlvgalvY 134
                                       ++p +++l++ ++   ++++++++   +          ++a + +++++ l+Y
  gi|298675153|ref|YP_003726903.1|  53 IVPGIMSLGLPGA---MARFMPSVKVKEkfqdmfysflSVAAVTGMFAAFLIY 102
                                       3555555555555...5555555555555555332211113333333333333 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.3e-05
                   Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplf.givGaaiatvlallvvavlnlyal 77 
                                       + +l+++++f ++  vl +++ ++ + k+  +  +   ++ ++l  +++ +  g++Ga+++ ++  +vv+++ ++++
  gi|298675153|ref|YP_003726903.1| 120 VKLLSIVVFFETIEKVLFNYFRATEQIKKDSILRFSKNFLMVVLVSIFVLQGgGLLGAIAGLLAKSVVVFLMAFVII 196
                                       579**********************************************666379********************** PP

                   Polysacc_synt_C  78 rrllgikl.ell 88 
                                         +lg+kl + +
  gi|298675153|ref|YP_003726903.1| 197 VSQLGFKLpK-F 207
                                       *******952.3 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.44
                   Polysacc_synt_C  77 lrrllgiklellrrllkpllaalvmgiv 104
                                       ++++lg++l       k++la+++ ++ 
  gi|298675153|ref|YP_003726903.1| 287 VKKYLGYSL-------KYFLAVAIPAVF 307
                                       344444444.......555555555555 PP

  == domain 4  score: 60.9 bits;  conditional E-value: 3.7e-20
                   Polysacc_synt_C   4 ilalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyalrrl 80 
                                       ++als+++++++ v++ +   +++++ + ++ +i+a+++l+lnl+l+p++gi+ aa  t+l+++vv++++ y+  r 
  gi|298675153|ref|YP_003726903.1| 335 FVALSALLFGVFAVFNKVAMLVKKTQVIGIIWLIAAVLNLGLNLILVPYIGIIAAATTTLLSFIVVLAFMAYYSLRF 411
                                       679************************************************************************** PP

                   Polysacc_synt_C  81 lgiklellrrllkpllaalvmgivvylllllllgllllaalalllavlvgalvYlllllllr 142
                                       +++++  +r ++k l+a+l+m+++   +l++ ++  l    ++l+ ++v+a+ Y+++l+ll+
  gi|298675153|ref|YP_003726903.1| 412 FQFDM-NFRFIVKSLVASLLMSGI---ILMWSPTGVL----STLAIIGVCAVSYFAVLVLLK 465
                                       *****.6*****************...8899988765....66777779**********998 PP

>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7  10.3       1.1     4e+03      66     144 ..      77     149 ..      41     203 .. 0.72
   2 !   39.5   6.5   1.1e-13   4.1e-10       7     160 ..     225     378 ..     219     379 .. 0.93
   3 ?   -2.9   2.3       1.3   4.7e+03      92      96 ..     403     407 ..     383     441 .. 0.50

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.1
                              MatE  66 krakealrqglilllllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktk 142
                                       ++++  ++  l ++++ + ++a+l++l s +i+ l+ + ++   ++ ++l+i+++++ +     vl +++r+++  k
  gi|298675153|ref|YP_003726903.1|  77 EKFQDMFYSFLSVAAVTGMFAAFLIYLASGPIADLLFDGNA---FIVKLLSIVVFFETIE---KVLFNYFRATEQIK 147
                                       56667777778888888999999999999999998877774...6677777777776665...55555555555555 PP

                              MatE 143 vp 144
                                         
  gi|298675153|ref|YP_003726903.1| 148 KD 149
                                       44 PP

  == domain 2  score: 39.5 bits;  conditional E-value: 1.1e-13
                              MatE   7 llesllslidtllvgrl.gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglilllll 82 
                                       +  +++   d +++g++ g++a++ +s + ++ +++ +f+  l+  l  + ++ +   n +++k++l ++l+  l++
  gi|298675153|ref|YP_003726903.1| 225 MSSWIVRSSDRYVIGGYlGTSAVGYYSPGYTLGNIVQMFVAPLNFILPMVLSRHYDGDNLDEVKKYLGYSLKYFLAV 301
                                       556666677888999999*********************************************************** PP

                              MatE  83 sliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislllnipln 159
                                       ++++++ + l+s+++l ++ +++e++e++  + ++++l++++++++ v++++   ++kt v+ +i li+++ln+ ln
  gi|298675153|ref|YP_003726903.1| 302 AIPAVFGLSLLSKPMLVIL-STPEIAEQSYIITPFVALSALLFGVFAVFNKVAMLVKKTQVIGIIWLIAAVLNLGLN 377
                                       ****************999.5666**************************************************999 PP

                              MatE 160 y 160
                                        
  gi|298675153|ref|YP_003726903.1| 378 L 378
                                       6 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.3
                              MatE  92 lfseq 96 
                                       + + +
  gi|298675153|ref|YP_003726903.1| 403 FMAYY 407
                                       22223 PP

>> MurJ  Lipid II flippase MurJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2  36.5   2.1e-07   0.00076      63     433 ..      82     438 ..      75     451 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.1e-07
                              MurJ  63 lilvlllvtligilaapllirllatgfdeetlelavsllrillpylllvslsavfgavLnarkkFfapafsPvllNv 139
                                       ++++ l+v++++ ++a +li+l + +++   +   + ++++l   +++ ++  v++    a ++    ++     N+
  gi|298675153|ref|YP_003726903.1|  82 MFYSFLSVAAVTGMFAAFLIYLASGPIADLLFDGNAFIVKLLSIVVFFETIEKVLFNYFRATEQIKKDSILRFSKNF 158
                                       66778888888888999999999999988888888888999999999999999999999999999999999999999 PP

                              MurJ 140 svIltllllanklgeeailaLaiGvliGgvlqllvqlpalkkaglllkprfafrdeglkkflklllptllgvsvsql 216
                                        +++ + ++  + g    l+  +G+l+  v+ +l+ ++ ++     + p+f+    glk  lk  +p + +  +s +
  gi|298675153|ref|YP_003726903.1| 159 LMVVLVSIFVLQGG--GLLGAIAGLLAKSVVVFLMAFVIIVSQLGFKLPKFG----GLKGYLKYGIPLVPSRMSSWI 229
                                       99999999988888..444544566666666666666665555555566666....777777777777766544444 PP

                              MurJ 217 .nllvdtalAsflaegsvsilayadrilqlPlglfgvsistvlLP.rlSrsakekdedevrdllsqairltllllip 291
                                         +    ++  +l +++v +++ +  + ++ +  + v+ ++ +LP  lSr+++ ++ dev++ l  +++  l+++ip
  gi|298675153|ref|YP_003726903.1| 230 vRSSDRYVIGGYLGTSAVGYYSPGYTLGNI-VQ-MFVAPLNFILPmVLSRHYDGDNLDEVKKYLGYSLKYFLAVAIP 304
                                       045555677777777666666555555444.33.45899999999559***************************** PP

                              MurJ 292 vsfgllvlskpivsllferGnFseedveataevLaay.algLipyalvklllrvfYAredtktPvkislislvlnil 367
                                       ++fgl +lskp++ +l       + ++++ ++++  + al+ + + ++ ++ +v    + t+   +i li++vln++
  gi|298675153|ref|YP_003726903.1| 305 AVFGLSLLSKPMLVILS------TPEIAEQSYIITPFvALSALLFGVFAVFNKVAMLVKKTQVIGIIWLIAAVLNLG 375
                                       *************9996......77788888888877689999***********999999999999*********** PP

                              MurJ 368 lsllllpplgvvglalatslsaliglvllyvllrkrlkltearg.iktflaklvvllalaavvilll 433
                                       l+l+l+p++g ++ a  t ls+++ l+++ ++  +    +++ + +++ +++ +v+ +l++++il+ 
  gi|298675153|ref|YP_003726903.1| 376 LNLILVPYIGIIAAATTTLLSFIVVLAFMAYYSLRF---FQFDMnFRFIVKS-LVASLLMSGIILMW 438
                                       **********************66666666665555...4444405555555.77788888887754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1068  (0.0595683); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.45
# Mc/sec: 3193.11
//
Query:       gi|298675154|ref|YP_003726904.1|  [L=474]
Description: mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-62  208.3   1.6    7.8e-62  207.6   1.6    1.3  1  MannoseP_isomer  Mannose-6-phosphate isomerase
    8.3e-54  182.8   0.0    1.9e-53  181.6   0.0    1.6  2  NTP_transferase  Nucleotidyl transferase
    1.8e-12   46.7   0.1    3.7e-12   45.8   0.1    1.6  1  Cupin_2          Cupin domain
    5.2e-06   26.9   0.0    8.5e-06   26.2   0.0    1.3  1  NTP_transf_3     MobA-like NTP transferase domain
     0.0076   16.2   0.1      0.014   15.2   0.1    1.4  1  AraC_binding     AraC-like ligand binding domain
  ------ inclusion threshold ------
      0.016   14.9   0.0       0.03   14.1   0.0    1.4  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
      0.076   13.1   1.5       0.35   10.9   0.1    2.6  2  ID               Intracellular delivery domain


Domain annotation for each model (and alignments):
>> MannoseP_isomer  Mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.6   1.6   3.1e-65   7.8e-62       2     151 .]     304     453 ..     303     453 .. 0.99

  Alignments for each domain:
  == domain 1  score: 207.6 bits;  conditional E-value: 3.1e-65
                   MannoseP_isomer   2 GvedlvvvetkdavlvadkdkvqdvkkvveelkaegreeaelhrevyrPWGsyevldegeryqvkritvkPgeklsl 78 
                                        v+++vvv+t+da+lv  k++ q+vk++v+ lk++++e+a lh+ vyrPWGsy+v++++e++++k+itv P++ ls+
  gi|298675154|ref|YP_003726904.1| 304 DVNNMVVVDTSDALLVCPKESSQKVKEIVNGLKERNDERAYLHKYVYRPWGSYTVMESSETHKIKNITVIPQKSLSM 380
                                       589************************************************************************** PP

                   MannoseP_isomer  79 qkhhhraehWvvvkGtakvtvddevlllkenestyiplgaihrlenpGkiplelievqsGsylgeddivrled 151
                                       q hhhr+ehWvvvkG+a+v+vd +++ l++ est+i++g+ hrl npGk+ple+ievq G+y+geddivr++d
  gi|298675154|ref|YP_003726904.1| 381 QLHHHRSEHWVVVKGMASVKVDGQEYFLRQGESTFIRAGVKHRLSNPGKVPLEIIEVQLGEYVGEDDIVRFDD 453
                                       ***********************************************************************98 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.6   0.0   7.6e-57   1.9e-53       1     245 [.       2     271 ..       2     274 .. 0.92
   2 ?   -2.8   0.0       1.5   3.7e+03      50     129 ..     317     338 ..     294     384 .. 0.52

  Alignments for each domain:
  == domain 1  score: 181.6 bits;  conditional E-value: 7.6e-57
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHH.TT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEE CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlan.sgieeiivvltqehsflveeqlkegskfgvevl 76 
                                       k +ILaGGsGtRLwPL+r++++k++++lg+ +l+q t+ r+++ s+i ei vv+ + ++f v  q++e      e +
  gi|298675154|ref|YP_003726904.1|   2 KSIILAGGSGTRLWPLSREQYPKQFLKLGETSLFQDTVIRCFKvSDISEIFVVTKKSQKFFVLGQINELGYEIPEDN 78 
                                       67*****************************************9**********************9987433699* PP

                                       EEEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEE CS
                   NTP_transferase  77 ialepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGviea 153
                                        ++epegk+t +A++ +a+ +e+++ + +v v+++Dh+ +d  ++++ + +   +++++tfgivp++++t+yG+i++
  gi|298675154|ref|YP_003726904.1|  79 LLIEPEGKNTLPAIYYGAQEIERKFGKSIVGVFPSDHILDDGAMQTISDVQVLTSDYLLTFGIVPDSPQTGYGYIKP 155
                                       *******************************************************99******************** PP

                                       C.......TTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHH.CCHHHTTSSCHHHHHHHHHHHTT..EEEEE CS
                   NTP_transferase 154 d.......eegrverfvEKPkeakaselassGiYvfnsevllflak.dleelkrgedeitdilpkaleeg..kvala 220
                                       +       +++rv +f EKP+ + a+ ++++G  ++ns+++lf  + + +e  ++++ei+d+++  ++ +  ++++ 
  gi|298675154|ref|YP_003726904.1| 156 EeeidsrvSGFRVSEFREKPDIEYAQRYMNEG-CLWNSGIFLFDTAvFFDEVIKHAPEISDTFESNIDLEviYQQVP 231
                                       *8887766666*********************.8******************************9876531145555 PP

                                       ECSTTEE...............-EEEXSSHHHHHHHHHHH CS
                   NTP_transferase 221 flfkdae...............yWsDvGtldslleanekl 245
                                        +  d+e               +W+D+G+++s+++  ek+
  gi|298675154|ref|YP_003726904.1| 232 SVSIDYEimeksnkvavvklnkKWNDLGDFNSIYNEFEKD 271
                                       5555555999************************999887 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.5
                                       EEEEETTTHHHHHHHHTTSGGGTSEEEEEEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHH CS
                   NTP_transferase  50 ivvltqehsflveeqlkegskfgvevlialepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkka 126
                                       ++v+ +e s+ v                                                          +e+v+  
  gi|298675154|ref|YP_003726904.1| 317 LLVCPKESSQKV----------------------------------------------------------KEIVNGL 335
                                       333333333333..........................................................3333333 PP

                                       HTH CS
                   NTP_transferase 127 iek 129
                                       +e+
  gi|298675154|ref|YP_003726904.1| 336 KER 338
                                       333 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.1   1.4e-15   3.7e-12       5      70 ..     372     437 ..     354     438 .. 0.89

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 1.4e-15
                                       EETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEE CS
                           Cupin_2   5 lppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllvv 70 
                                       + p+ s  +  H++  e  +V++G + ++vdg+e+ l++G+s ++ ag+ Hr+ N+g+ p++++ v
  gi|298675154|ref|YP_003726904.1| 372 VIPQKSLSMQLHHHRSEHWVVVKGMASVKVDGQEYFLRQGESTFIRAGVKHRLSNPGKVPLEIIEV 437
                                       55666666666555559*********************************************9876 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   3.3e-09   8.5e-06       2      98 ..       4     117 ..       3     128 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 3.3e-09
                                       EEEEESS-TTT.....TT.THHHHCCCCCCHHHHHHHHHCTT..-CEEEEECSHCH...HHHHHTTCTS-EEE-... CS
                      NTP_transf_3   2 viLAGGrSsRm.....gg.dKallplggkpllervldalraa.gvdevvvvggdee...vlaalarlgvrvved... 65 
                                       +iLAGG ++R+      + +K++l+lg+++l++ ++ +  ++  ++e++vv++ ++   vl ++++lg+++ ed   
  gi|298675154|ref|YP_003726904.1|   4 IILAGGSGTRLwplsrEQyPKQFLKLGETSLFQDTVIRCFKVsDISEIFVVTKKSQkffVLGQINELGYEIPEDnll 80 
                                       8**********88876347**************999999888469*******9974344777889999999777677 PP

                                       .TTSS-SHHHHHHHHHHHH....SSSCEEEEETT-TT CS
                      NTP_transf_3  66 .edpgkgplaslaaalraaa...dadavlvlacDmPl 98 
                                        e++gk++l +++ ++++++   +++ v v++ D++l
  gi|298675154|ref|YP_003726904.1|  81 iEPEGKNTLPAIYYGAQEIErkfGKSIVGVFPSDHIL 117
                                       6777999999999999998766677778888888865 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   5.7e-06     0.014      16      65 ..     380     428 ..     375     442 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.7e-06
                                       EEEETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-T CS
                      AraC_binding  16 fpphvhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesds 65 
                                       ++ h+h   ++ +v++G ++++++g++y l++G+  +++ g+ H++   +
  gi|298675154|ref|YP_003726904.1| 380 MQLHHHRSEHW-VVVKGMASVKVDGQEYFLRQGESTFIRAGVKHRLSNPG 428
                                       56677776666.578******************************98877 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.2e-05      0.03       3      55 ..       3      59 ..       1      68 [. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.2e-05
                                      EEEECTTSSCTT....-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGG CS
                              IspD  3 vvipAAGsGkRm....kaglpKqflelkgqtllehtvdallaskavdkivvvvsedd 55
                                       +i A GsG+R+    +++ pKqfl+l   +l + tv    + + +++i vv ++ +
  gi|298675154|ref|YP_003726904.1|  3 SIILAGGSGTRLwplsREQYPKQFLKLGETSLFQDTVIRCFKVSDISEIFVVTKKSQ 59
                                      699********865556899*****************999999*******9998865 PP

>> ID  Intracellular delivery domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.53   1.4e+03      17      36 ..     279     298 ..     269     301 .. 0.77
   2 ?   10.9   0.1   0.00014      0.35      18      36 ..     306     324 ..     302     337 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.53
                                ID  17 gdesfaIntkddlVickkee 36 
                                        ++ f I + d+l+ ++k++
  gi|298675154|ref|YP_003726904.1| 279 ECDDFSIGSTDNLIYSEKNK 298
                                       57889999******999987 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00014
                                ID  18 desfaIntkddlVickkee 36 
                                       +++++++t+d+l +c+ke 
  gi|298675154|ref|YP_003726904.1| 306 NNMVVVDTSDALLVCPKES 324
                                       89***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 3366.45
//
Query:       gi|298675155|ref|YP_003726905.1|  [L=304]
Description: transposase IS4 family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.6e-21   75.0   0.1    7.3e-21   74.0   0.1    1.5  1  DUF772       Transposase domain (DUF772)
    2.7e-10   40.3   3.7    5.3e-09   36.0   3.7    2.2  1  DDE_Tnp_1    Transposase DDE domain
      0.003   17.6   0.3     0.0073   16.3   0.1    1.8  2  DDE_Tnp_1_3  Transposase DDE domain
  ------ inclusion threshold ------
      0.016   14.8   0.3      0.066   12.9   0.3    1.9  1  DDE_Tnp_4    DDE superfamily endonuclease
      0.087   13.0   0.1       0.17   12.1   0.1    1.5  1  DDE_Tnp_1_6  Transposase DDE domain


Domain annotation for each model (and alignments):
>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.0   0.1     2e-24   7.3e-21       1      70 [.      51     120 ..      51     126 .. 0.92

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 2e-24
                            DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlf 70 
                                       Grp +++ +mlk+l+lq+++glSd e+e+++ +++sfr fl +    + +pd +t + fRkr+++    ++++
  gi|298675155|ref|YP_003726905.1|  51 GRPEADVIVMLKMLILQQWHGLSDQEIEKQCIDRISFRHFLKFP---EYIPDSTTVWLFRKRIIDtnkEKEVW 120
                                       9*****************************************96...88**************9988766555 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   3.7   1.5e-12   5.3e-09       6      89 ..     137     229 ..     133     292 .. 0.88

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 1.5e-12
                         DDE_Tnp_1   6 vlivDattvrvpgtk................edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglk 66 
                                       + i Dat++     +                +d+ w +k gk+++gyklh+++dt   li ++++t++ vhd+k+  
  gi|298675155|ref|YP_003726905.1| 137 GMIQDATFIHSDPGHagadkprgneaktrrsKDGTWAKKSGKSHFGYKLHTIIDTDYQLIRRFETTTATVHDNKVDL 213
                                       566788888865555888888888888888999*****************************************743 PP

                         DDE_Tnp_1  67 qlldelrprkgklvlaDaGYasa 89 
                                             r  ++ +v++D+GY+++
  gi|298675155|ref|YP_003726905.1| 214 S-----R--EDEVVYRDKGYFGT 229
                                       3.....4..99*********974 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1     2e-06    0.0073      35      94 ..     172     229 ..     136     247 .. 0.79
   2 ?   -1.7   0.0      0.72   2.6e+03      96     113 ..     261     278 ..     234     289 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2e-06
                       DDE_Tnp_1_3  35 rGkssmGWfyGfkLhliindkGeila.vkltpgnvdDrepveelakellgklfaDkgyisk 94 
                                       + k s    +G+kLh ii+   ++++ ++ t++ v+D++    l++e  + ++ Dkgy + 
  gi|298675155|ref|YP_003726905.1| 172 WAKKSGKSHFGYKLHTIIDTDYQLIRrFETTTATVHDNKVD--LSRE-DEVVYRDKGYFGT 229
                                       4455556689*********9999985389999999998763..5555.7899******976 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.72
                       DDE_Tnp_1_3  96 laeelleegielitklrk 113
                                       +++ +++ g +l+t++++
  gi|298675155|ref|YP_003726905.1| 261 VTKGVFKAGTTLVTTMKR 278
                                       556677888888887654 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   1.8e-05     0.066      25     133 ..     178     268 ..     156     287 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.8e-05
                         DDE_Tnp_4  25 kkkntlkvlivvdpngkiifvskgypGsvsDkeilensgllkalkeavkpgdvilaDkgFklsekllvpykkkkkkq 101
                                       k++ ++k+  ++d +++ i   +  ++ v+D+++    +l++       +++v+  Dkg+ ++     p+   + + 
  gi|298675155|ref|YP_003726905.1| 178 KSHFGYKLHTIIDTDYQLIRRFETTTATVHDNKV----DLSR-------EDEVVYRDKGYFGTN----PQ---GYDA 236
                                       6677888888888888888888888888888776....3333.......457899999999999....66...5677 PP

                         DDE_Tnp_4 102 lseeevefnraiasarihvErvigrlkgrfri 133
                                         ++e  +n++i+ +r++ Erv +  kg f+ 
  gi|298675155|ref|YP_003726905.1| 237 TMQREILRNSRISAIRVTGERVYAVTKGVFKA 268
                                       789*************************9986 PP

>> DDE_Tnp_1_6  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   4.7e-05      0.17      80     124 ..     252     295 ..     228     296 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.7e-05
                       DDE_Tnp_1_6  80 RaitvEgvfaqikrnlglrrfrlrGlkkvklqfllvalalNlkkl 124
                                       R  t E+v a +k   ++  + ++ +k+v+l++l++a+++Nl +l
  gi|298675155|ref|YP_003726905.1| 252 RV-TGERVYAVTKGVFKAGTTLVTTMKRVNLKMLFTAFGFNLYQL 295
                                       43.669************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2195.13
//
Query:       gi|298675156|ref|YP_003726906.1|  [L=296]
Description: hypothetical protein Metev_1241 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-08   34.9   0.0    0.00097   19.6   0.0    2.5  2  Sulfotransfer_3  Sulfotransferase family
     0.0047   16.4   1.1      0.059   12.9   1.1    2.4  1  Sulfotransfer_1  Sulfotransferase domain
  ------ inclusion threshold ------
      0.021   14.4   0.0       0.27   10.7   0.0    2.3  2  Sulphotransf     Stf0 sulphotransferase
      0.041   14.1   1.5        0.3   11.4   1.5    2.1  1  ESCRT-II         ESCRT-II complex subunit


Domain annotation for each model (and alignments):
>> Sulfotransfer_3  Sulfotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   3.3e-05      0.15       2      31 ..      11      40 ..      11      55 .. 0.88
   2 !   19.6   0.0   2.2e-07   0.00097     128     216 ..     157     231 ..     144     232 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.3e-05
                                      EEEE--TTSSHHHHHHHHHTSTTEE--S-- CS
                   Sulfotransfer_3  2 ifivGlpRSGTTlLhrlLaahpdvripeet 31
                                      i i+G   +G+TlL    +ahp++++ +e 
  gi|298675156|ref|YP_003726906.1| 11 IYIMGSGHTGSTLLDLCIGAHPKIQSCGEF 40
                                      789********************9998886 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 2.2e-07
                                       EEEEE--H.HHHHHHHHHTT----------..-HHHHHHHHHHHHHHHHHHHHHHS-TTSEEEEEHHHHHH-HHHHH CS
                   Sulfotransfer_3 128 fihlvRdpvdtvlssyvslfgkkresysedsldeledaleewarayerllaararlppdrfldvrYedLvadpegtl 204
                                       +ihlvR++ + ++s++++     r+  s         + + w  +  r +  ++++ + + l++rYed++++p +tl
  gi|298675156|ref|YP_003726906.1| 157 LIHLVRNGNAVTWSNMKKD----RSVKS---------SSKNWLISNLRSEIVYHKI-KTKKLRIRYEDFINNPTDTL 219
                                       5788888855555554444....32222.........2244555444444444554.5788**************** PP

                                       HHHHHHHT---- CS
                   Sulfotransfer_3 205 rriyeflglpwd 216
                                       ++i + lgl+++
  gi|298675156|ref|YP_003726906.1| 220 NSIGNLLGLDFS 231
                                       *********986 PP

>> Sulfotransfer_1  Sulfotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   1.1   1.3e-05     0.059      31     222 ..      91     261 ..       8     283 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.3e-05
                                       HHHTSSGHCT-HHHSCBTTHECCTSG.CCGTTECCCHHHTTTEEHHHHHHHS.TSS.EEEE...GGGS.CHHHHTT- CS
                   Sulfotransfer_1  31 ekaeepalfnardrspfLelydlyfp.nslkppdhlrsyshvaekvvrlral.esprllktHlplkllpkslldsnl 105
                                       +k+e++ +   ++r   L+ y   f    +++++ l+s+s +  k+  +++  +s r+l     l+l+     +  l
  gi|298675156|ref|YP_003726906.1|  91 DKFENISI---NQR-INLDSYETEFYsYLIYNQELLYSISYISDKPILVDSTkNSIRALN----LSLM----PNIEL 155
                                       44444444...222.234555444554444555555777777777777766513455555....3333....36678 PP

                                       EEEEEE--HHHHHHHHHHHHHHBTTSTTT-S-HHHHHHHHHTTHSTTC-HHHHHHHHHHHTTTTTEEEEEHHHHHHH CS
                   Sulfotransfer_1 106 KiiylvRnpkdvavSryhfsrslkklkepetpfeeffdlflegrvvcgsyfdhvkswlklrkkgnvlflrYEdlkkd 182
                                        +i+lvRn  +v  S++   rs+k ++               ++ ++++ ++ +     ++ k + l +rYEd + +
  gi|298675156|ref|YP_003726906.1| 156 ILIHLVRNGNAVTWSNMKKDRSVKSSS---------------KNWLISNLRSEIV---YHKIKTKKLRIRYEDFINN 214
                                       8999****************9999533...............3334444444443...34445788999******** PP

                                       HHHHHHHHHHHTT--.........HHHHHHHHHHTSHHHHHTETTTS CS
                   Sulfotransfer_1 183 pakeikkiaeFlGiplt.......eeelekivkhlsfenmksnpvsn 222
                                       p  +++ i   lG++++       +++  +i  hl   n k + +sn
  gi|298675156|ref|YP_003726906.1| 215 PTDTLNSIGNLLGLDFSnisknliNGTGIEINSHLLAGNRKVFSSSN 261
                                       ***************87666656555555555555555555555555 PP

>> Sulphotransf  Stf0 sulphotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0     0.058   2.6e+02      58      88 ..      63      93 ..      11     102 .. 0.61
   2 ?   10.7   0.0   6.1e-05      0.27     186     220 ..     200     234 ..     189     240 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.058
                      Sulphotransf 58 aeayleaaltaGrtengvfGlklmreqlgll 88
                                      +  + +++++  ++++g++ l +m+++ +++
  gi|298675156|ref|YP_003726906.1| 63 SCPFWSQVINDWKSKTGIYDLNVMKNSQDKF 93
                                      4445567777788888888888888887766 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 6.1e-05
                      Sulphotransf 186 giepldisyealvaapvavvaavlealgldpelak 220
                                       + ++l+i ye+++++p+++++++ + lgld +++ 
  gi|298675156|ref|YP_003726906.1| 200 KTKKLRIRYEDFINNPTDTLNSIGNLLGLDFSNIS 234
                                       5679*************************988765 PP

>> ESCRT-II  ESCRT-II complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.5   6.6e-05       0.3      22      83 ..      65     122 ..      58     206 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.6e-05
                          ESCRT-II  22 ekWsslilaycrhhrifklslseaeeeeeeselFknkkinRrlsledir.evleelvkkgrae 83 
                                         Ws++i ++  ++ i+ l++      +++++ F+n +in+r++l++ + e +++l+ ++++ 
  gi|298675156|ref|YP_003726906.1|  65 PFWSQVINDWKSKTGIYDLNVM-----KNSQDKFENISINQRINLDSYEtEFYSYLIYNQELL 122
                                       56********************.....345689***********9887525667777666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1906.81
//
Query:       gi|298675157|ref|YP_003726907.1|  [L=373]
Description: group 1 glycosyl transferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.8e-40  136.4   0.0    1.3e-39  135.5   0.0    1.5  1  Glycos_transf_1  Glycosyl transferases group 1
    9.2e-26   90.9   0.0    1.5e-25   90.2   0.0    1.3  1  Glyco_trans_1_4  Glycosyl transferases group 1
    2.1e-10   40.9   0.0      4e-10   39.9   0.0    1.5  1  Glyco_transf_4   Glycosyltransferase Family 4
    0.00023   21.5   0.0     0.0004   20.7   0.0    1.3  1  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
       0.13   12.5   0.0       0.26   11.5   0.0    1.4  1  CaMBD            Calmodulin binding domain


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.5   0.0   3.7e-43   1.3e-39       3     169 ..     186     351 ..     184     354 .. 0.96

  Alignments for each domain:
  == domain 1  score: 135.5 bits;  conditional E-value: 3.7e-43
                                       HHHHHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEE CS
                   Glycos_transf_1   3 ekkrkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflg 79 
                                       ++ r++l++ + + i+l+v+rl ++Kg+ l+ +a+ +      +nv+++i+G+g ee+ lk+ a +l+++d+v flg
  gi|298675157|ref|YP_003726907.1| 186 NNLRNELNICKSDTILLTVSRLHPRKGHRLVMDAISK-----MDNVHYLIIGKGYEEDLLKQYASSLNINDKVDFLG 257
                                       56788999999*************************6.....59********************************* PP

                                       CCHSSSHHHHHHCESEEEEEESS.....BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHH CS
                   Glycos_transf_1  80 evsredleellknadifvlpsis.....EgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaea 151
                                       +v+++dl+++++ +dif+++ +      EgfGi+ lEA aag+pvi ++++g+a  vkd+etGllv+p+ +++++++
  gi|298675157|ref|YP_003726907.1| 258 YVNDDDLPNYYQTCDIFIMTGQPsekdvEGFGIAYLEANAAGKPVIGTDIYGVASAVKDNETGLLVEPT-VKSIKNG 333
                                       *******************9998999*******************************************.******* PP

                                       HHHHHHSHHHHHHHHHHH CS
                   Glycos_transf_1 152 irklledeelrerlgena 169
                                       i+ l++++ +re +++n+
  gi|298675157|ref|YP_003726907.1| 334 IEILMNNNIKREYISKNS 351
                                       ***************997 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.2   0.0   4.1e-29   1.5e-25       3     133 ..     200     339 ..     198     340 .. 0.87

  Alignments for each domain:
  == domain 1  score: 90.2 bits;  conditional E-value: 4.1e-29
                                       EEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---..HHHHHHHT..T-T.TEEEE---..THHHHHHHH-SE CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkkdvrlvivGdgprpeeleelaa..gleerveftGfv..edlaellaaadv 75 
                                       ++l+v+rl+ ++kg++l+++a+ ++   +v+ +i+G+g +++ l+++a+  +++++v f+G+v  +dl+++++ +d+
  gi|298675157|ref|YP_003726907.1| 200 ILLTVSRLH-PRKGHRLVMDAISKMD--NVHYLIIGKGYEEDLLKQYASslNINDKVDFLGYVndDDLPNYYQTCDI 273
                                       789*****5.66**************..89******997445677777578999*********9777********** PP

                                       EEE...--....---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH CS
                   Glyco_trans_1_4  76 fva...Ps....egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLle 133
                                       f++   Ps    egfg++ lEa aag+pv+ td+ g+a +v  +e+gllv+p  ++++ + i+ L++
  gi|298675157|ref|YP_003726907.1| 274 FIMtgqPSekdvEGFGIAYLEANAAGKPVIGTDIYGVASAVkdNETGLLVEP-TVKSIKNGIEILMN 339
                                       ***6666688888***********************99999988******97.47777777777766 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.0   1.1e-13     4e-10      66     167 ..      73     176 ..      15     177 .. 0.73

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 1.1e-13
                    Glyco_transf_4  66 rllkrekpDvvHahspaalgaallalrrrlgiplVltvHglye....krllkarlkplsrllralerrl....lrra 134
                                        l+ r k+Dv+        + +l+a    lg++++ ++Hg++         k   +++ +l+  +e+      l+ +
  gi|298675157|ref|YP_003726907.1|  73 LLINRKKYDVIYLSRLNDSIIGLVAYI--LGKKVISHAHGSELikngL---KTTGGKFPILRTFWENLKfklnLNLT 144
                                       357778*********************..7************995542...4444455555554444445568**** PP

                    Glyco_transf_4 135 drviavSeatadelrerygvppekitVipnGvD 167
                                        ++iavSe+ ++ l+e  g +++k++++++G+D
  gi|298675157|ref|YP_003726907.1| 145 YKLIAVSEWSKNKLIE-NGANENKVHIVHPGID 176
                                       ****************.***************9 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   1.1e-07    0.0004       8      87 ..     283     364 ..     259     369 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.1e-07
                   Glyco_trans_1_2   8 s..espnlrlfEaaacGafaltddaegleelftpgkevilfe.dleelaekiryllanpeerraiaeaarervlaeh 81 
                                       +  e++   ++Ea a+G +++ +d+ g++  ++++++++l+e +++++   i+ l++n  +r+ i+++ + +  ++h
  gi|298675157|ref|YP_003726907.1| 283 KdvEGFGIAYLEANAAGKPVIGTDIYGVASAVKDNETGLLVEpTVKSIKNGIEILMNNNIKREYISKNSIYW-AKKH 358
                                       3557788889**************************************************************.8999 PP

                   Glyco_trans_1_2  82 tydhra 87 
                                       ++ + +
  gi|298675157|ref|YP_003726907.1| 359 DWSQII 364
                                       **9976 PP

>> CaMBD  Calmodulin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   7.1e-05      0.26      11      54 ..     183     226 ..     180     228 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.1e-05
                             CaMBD  11 aAanVLretwliykltklvkkvdqsrvrkhqRklLqAihrlRkv 54 
                                        ++n+Lr+   i+k  +++ +v++  +rk +R + +Ai+++ +v
  gi|298675157|ref|YP_003726907.1| 183 YVNNNLRNELNICKSDTILLTVSRLHPRKGHRLVMDAISKMDNV 226
                                       689************************************99665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2682.69
//
Query:       gi|298675158|ref|YP_003726908.1|  [L=231]
Description: hypothetical protein Metev_1243 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1759.08
//
Query:       gi|298675159|ref|YP_003726909.1|  [L=530]
Description: hypothetical protein Metev_1244 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.8e-14   52.2  17.7    7.8e-14   52.2  17.7    2.9  3  PMT_2     Dolichyl-phosphate-mannose-protein mannosyltransfer


Domain annotation for each model (and alignments):
>> PMT_2  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.2       0.6   1.1e+04      57      83 ..      21      47 ..      17      58 .. 0.51
   2 !   52.2  17.7   4.3e-18   7.8e-14      22     159 .]     102     243 ..      78     243 .. 0.83
   3 ?    1.6   6.1     0.016   2.8e+02       6      65 ..     336     393 ..     333     401 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 0.6
                             PMT_2 57 lllavvplfvalsalftpdaplvllwa 83
                                      l+++++++f  l+    ++++l  ++a
  gi|298675159|ref|YP_003726909.1| 21 LIISISFIFKLLLIHQDINTILNKFLA 47
                                      444444445455555555555555555 PP

  == domain 2  score: 52.2 bits;  conditional E-value: 4.3e-18
                             PMT_2  22 lairlvsalagvltilllyllarrlfgkraallaalllavvplfvalsalftpdaplvllwalalylllrale..kn 96 
                                       +a  ++ +++++ t++++yl+++++++k+a+llaa+++ + p+++++++      +++++++l++y+++      k 
  gi|298675159|ref|YP_003726909.1| 102 YASLILMIIFSIGTSIIIYLIMKNVLNKKAGLLAAFIWLFNPNILFVTLSAMETPIQIFFISLLTYYIVSKSNipKL 178
                                       56678999********************************9988888884444556667776666666655443477 PP

                             PMT_2  97 klkywllagvlfGlgflsKytaallliaallyllis..arrilkekkpylalllalllfspvliw 159
                                       ++k  +++g+l+Gl+fls++  ++++i+++ +l+++  ++ +l +k +++++  a l ++p+l+w
  gi|298675159|ref|YP_003726909.1| 179 SIKESAIIGLLIGLIFLSRMDGVFIGIGVISALVLRnfKQNKLETKSLIAIISTASLTVVPWLMW 243
                                       7**************************99888888888888****999999999999999***** PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.016
                             PMT_2   6 iawllalftklfgfselairlvsalagvltilllyllarrlfgkraallaalllavvplf 65 
                                       i++l   f+++ gf  +  +   +l+++l ++++ +l+++l   +   la +l+ ++++f
  gi|298675159|ref|YP_003726909.1| 336 IYFLFYWFYEI-GFRSWYTIYTYFLLTILFSAIIVKLIQELKP-KKRQLAYILVIFILIF 393
                                       67788888999.9999999999999999999999999999754.5555555555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (530 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1295  (0.0722293); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3789.29
//
Query:       gi|298675160|ref|YP_003726910.1|  [L=327]
Description: hypothetical protein Metev_1245 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-44  151.9  28.1    3.1e-44  151.7  28.1    1.0  1  LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
  ------ inclusion threshold ------
      0.043   13.9   0.5      0.043   13.9   0.5    3.4  4  NS3_envE         Non-structural protein NS3/Small envelope pr


Domain annotation for each model (and alignments):
>> LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.7  28.1   3.4e-48   3.1e-44       2     301 .]      28     312 ..      23     312 .. 0.94

  Alignments for each domain:
  == domain 1  score: 151.7 bits;  conditional E-value: 3.4e-48
                   LPG_synthase_TM   2 llglalsalllalllrgvdlaalaaalrsldpwwlllalllallsvllralrWrlllrslgarislrrllrayligl 78 
                                       + + +++++ll ++    d++++++a+  +++ +l  +l+l+ + +++r ++W + l+++g+ i+  ++  +++ g 
  gi|298675160|ref|YP_003726910.1|  28 IFAAVVVLGLLIYA----DFNSIISAFVDFGWIYLPIILILTVFNYIVRFYKWDFYLSTIGVDIGKKNSAIVFFSG- 99 
                                       55666667777788....**********************************************************. PP

                   LPG_synthase_TM  79 fvnnvtPgalgGevvrayllkrkegvslskalasvvverlldllalvllgllallllggllaegaavllllalalll 155
                                       ++ ++tPg+l Gev++ yllk++++vs s+ + +v++erl d+++l++l  +++++ +          ++ +++++l
  gi|298675160|ref|YP_003726910.1| 100 LIMSITPGKL-GEVLKSYLLKQTNDVSISRTAPVVFAERLTDIVGLIILSSVGVVIYQ---------YGISVMVVTL 166
                                       **********.*******************************************8666.........3677888888 PP

                   LPG_synthase_TM 156 lavlalllllllrrrlarlarvlkrlarllarfarklasakr.klvlasprrlllafllslliwllealtlylllra 231
                                       l + a++ ++ +r+  ++l  + ++l +++++fa +l+   +   +l ++r l++++lls++ w +e+ +++ ++++
  gi|298675160|ref|YP_003726910.1| 167 LIISAVVSIIQSRKLSLKLIEFGEKL-PFISKFAHHLHELYEsAYILLKFRPLSITILLSIVSWFFECIAMWYVFKG 242
                                       888889999*****************.6678888888766558999999**************************** PP

                   LPG_synthase_TM 232 lgvdvslallllillaltlvgalpplPgGlGvrEaalalllallGvsaaealaaallyrlitlylllllG 301
                                       +g+d+s++++ +++++++++ga++ lPgGlGv+E++ + ll  ++vs+a+a+  al++r++tl++ +++G
  gi|298675160|ref|YP_003726910.1| 243 FGLDLSMLVATFVFAFSSVAGAVSMLPGGLGVAEGSIVGLLLTMDVSKATATGSALIIRFCTLWFGVVVG 312
                                       ********************************************************************98 PP

>> NS3_envE  Non-structural protein NS3/Small envelope protein E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.9       0.2   1.8e+03       4      27 ..      14      39 ..      11      47 .. 0.66
   2 ?   -2.2   0.3      0.51   4.6e+03      11      21 ..      56      66 ..      46      74 .. 0.54
   3 ?   13.9   0.5   4.8e-06     0.043      17      69 ..     160     214 ..     142     221 .. 0.75
   4 ?   -2.3   1.1      0.54   4.9e+03      17      28 ..     307     318 ..     298     326 .. 0.60

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.2
                          NS3_envE  4 klvDd..halvvqvlfilvvlivvll 27
                                       l+D+    +  +++f  vv++ +l+
  gi|298675160|ref|YP_003726910.1| 14 SLIDKlkKRILYSIIFAAVVVLGLLI 39
                                      56665113466788888888876665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.51
                          NS3_envE 11 lvvqvlfilvv 21
                                      +   +++il v
  gi|298675160|ref|YP_003726910.1| 56 IYLPIILILTV 66
                                      33333333333 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 4.8e-06
                          NS3_envE  17 filvvlivvlliviallkvikLClvlcglcntlvlsP..akqvYkiYkeemrlda 69 
                                        ++vv ++++  v++++++ kL l+l +++++l +    a+++ ++Y++   l  
  gi|298675160|ref|YP_003726910.1| 160 SVMVVTLLIISAVVSIIQSRKLSLKLIEFGEKLPFISkfAHHLHELYESAYILLK 214
                                       3567778888889******************984443459999999998655544 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 0.54
                          NS3_envE  17 filvvlivvlli 28 
                                       f +vv i+v+l+
  gi|298675160|ref|YP_003726910.1| 307 FGVVVGIIVVLF 318
                                       333444555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1193  (0.0665402); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2314.74
//
Query:       gi|298675161|ref|YP_003726911.1|  [L=221]
Description: phosphoresterase PHP domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-14   53.3   0.0    8.2e-14   51.1   0.0    2.1  2  PHP_C     PHP-associated
    1.5e-12   48.2   0.0    1.6e-12   48.1   0.0    1.2  1  PHP       PHP domain


Domain annotation for each model (and alignments):
>> PHP_C  PHP-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.15   1.4e+03      41      53 ..      83      95 ..      75      96 .. 0.76
   2 !   51.1   0.0   9.1e-18   8.2e-14       3      53 ..     139     190 ..     137     193 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.15
                             PHP_C 41 iatpdelleaire 53
                                      + +p++++e i++
  gi|298675161|ref|YP_003726911.1| 83 STSPEDVIEDIHN 95
                                      4588*****9986 PP

  == domain 2  score: 51.1 bits;  conditional E-value: 9.1e-18
                             PHP_C   3 aNrrArrfAeklglpgtgGSDAHrleeVGrayTef.eepiatpdelleaire 53 
                                       +N+ ArrfA k++l ++gGSDAH+l eVG +yT+f   +  t d ++ a+ +
  gi|298675161|ref|YP_003726911.1| 139 SNEAARRFANKNNLLMVGGSDAHYLNEVGLGYTDFfWVDDLTRDNMMYALEK 190
                                       7**********************************84444444777777665 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.0   1.8e-16   1.6e-12       1      74 [.       4     144 ..       4     214 .. 0.70

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 1.8e-16
                                       EEEE--CCC--.S-H..HHHHHHHHHCT-SEEEEEEEEBTTHHHHHHHHHHHHTTTTSEEEEEEE............ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
                               PHP   1 dlHvHteyslldgalsieelvkkakelglkaiaiTDhgnlfgyvefykaakkkykagikpiiGleayvaddse.... 73 
                                       dlH+Ht+ys   g+ ++++lv++a+++gl+ ia+TDh+ + g++e+ k+    +  ++ +iiG+e++  +++     
  gi|298675161|ref|YP_003726911.1|   4 DLHTHTKYSPRCGVTEPKKLVNTAIKKGLDGIAVTDHDTIKGALEA-KKF---ETPDFGVIIGCEVSTDKGELiglf 76 
                                       89*******555******************************9986.455...5566********555554447777 PP

                                       .................................................................... CS
                                       ...................................................................x RF
                               PHP  74 ...................................................................k 74 
                                                                                                          +
  gi|298675161|ref|YP_003726911.1|  77 lqdeitstspedviedihnqggivvvphpfdeyrskrfsslseyykqidaievfnsrcikeksneaaR 144
                                       77777766666666666666666666666665555555555555555555555555555444444442 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1609.45
//
Query:       gi|298675162|ref|YP_003726912.1|  [L=299]
Description: prenyltransferase UbiA [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-28   97.8  15.2    6.2e-28   97.8  15.2    1.6  1  UbiA      UbiA prenyltransferase family
  ------ inclusion threshold ------
      0.016   15.1   3.7        3.2    7.7   0.6    3.4  2  PsbN      Photosystem II reaction centre N protein (psbN)


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.8  15.2   6.9e-32   6.2e-28      17     238 ..      34     251 ..      18     270 .. 0.84

  Alignments for each domain:
  == domain 1  score: 97.8 bits;  conditional E-value: 6.9e-32
                              UbiA  17 pdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilgllllalllnplta 93 
                                         +   +++++++++++++ +++Nd+ D+e D++++ + +RP++sG++++ +a++++ivll  +l ++  ++n  ++
  gi|298675162|ref|YP_003726912.1|  34 MAWMDSITAFVIFCMLSGSLYLMNDIMDAEDDKKHPVKCKRPIASGELKKSHAFFIFIVLLSGSLYIS-SIVNYAFL 109
                                       45566677888888******************************************************.******** PP

                              UbiA  94 llgllalllyvvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavflltwaialan.dlrdre 169
                                       l+++l+++l+++Y+ l lK++ l++ +++++ f+l +++g++a t s+s+++++++++ ++l++a+      l  + 
  gi|298675162|ref|YP_003726912.1| 110 LISVLYFVLLFAYN-LKLKYIVLVDVLTISAGFVLRAIAGAVALTVSISPWLIICTFL-LALFLAFGKRRhELVLLG 184
                                       **************.9********************************9999999999.555666665555999999 PP

                              UbiA 170 gDrkagikt...lpvvlGrkaarillalllavlllallllllalllllylllalllaalallraarlvrrrd 238
                                       +D+k ++k     +v l ++ ++i ++++l+v     +ll+++  ++ y+ +++++++++l+r + lv+++d
  gi|298675162|ref|YP_003726912.1| 185 DDAKNHRKIldeYTVPLLEQMTLI-VTSALIVS----YLLYTFFASTHYMMVTIPFLVYGLFRYLLLVHSQD 251
                                       99******9666555555666666.33333333....45688899999999999999999999998888776 PP

>> PsbN  Photosystem II reaction centre N protein (psbN)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.6   0.00036       3.2       4      34 ..     149     180 ..     134     181 .. 0.88
   2 ?    6.4   0.1   0.00087       7.8       4      19 ..     264     279 ..     261     283 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00036
                              PsbN   4 AtvlsisiaavlvaiT.gfsiYtaFGPPskeL 34 
                                       A++l++si+  l+  T  +++++aFG    eL
  gi|298675162|ref|YP_003726912.1| 149 AVALTVSISPWLIICTfLLALFLAFGKRRHEL 180
                                       89999****9999888458*******877776 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.00087
                              PsbN   4 AtvlsisiaavlvaiT 19 
                                       ++++sisi+a+lva+ 
  gi|298675162|ref|YP_003726912.1| 264 GMLFSISIWAILVAVV 279
                                       6789*********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1016  (0.056668); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2020.18
//
Query:       gi|298675163|ref|YP_003726913.1|  [L=354]
Description: hypothetical protein Metev_1248 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-26   94.0   0.0    2.3e-26   93.3   0.0    1.3  1  DUF362    Domain of unknown function (DUF362)


Domain annotation for each model (and alignments):
>> DUF362  Domain of unknown function (DUF362)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.3   0.0   1.3e-30   2.3e-26       2     203 .]      38     241 ..      37     241 .. 0.81

  Alignments for each domain:
  == domain 1  score: 93.3 bits;  conditional E-value: 1.3e-30
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                            DUF362   2 aiKpNlgeagnpegatthpevvravvellkeagagkiivgdspglyvsrgkahrevaeeagydelae..gadiadgl 76 
                                       +iK+Nl ++   +++ t p  ++av+++lke+g ++i+ +++ ++     ++  + a+++ + ++++  ++d++   
  gi|298675163|ref|YP_003726913.1|  38 IIKLNLSWSLYYPACSTEPWQLEAVLKTLKEDGYKDIVAMENKTV----VTNPIKGAKQNKWLSILDkyDVDFVPLT 110
                                       69*****877777899*****************999********5....2336677777777776665544444444 PP

                                       xxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DUF362  77 egedevvvpvk.....gkhlkkelkiakavleaDviInlpklKgHalagvtgalKnlfGcisgsgkaeiHskrdsek 148
                                       + ++  ++p +     +k + + ++i++++  a  ++ lp  K+H  +++tga+Kn+fG + ++++++ H     + 
  gi|298675163|ref|YP_003726913.1| 111 DVKWLDYNPSTemvgmDKVFPDGFQIPEPFIGAN-VLHLPTQKTHGHTTITGAMKNAFGGLLNERRHHSH-----KY 181
                                       44444444222334557777778*******9995.68***********************9999899999.....56 PP

                                       xxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                            DUF362 149 faekiadlakalkpd....lnvvdgikamegegpsggs.kelglvlaStDpvalDaaaad 203
                                       ++e ++dl+k+ k +    ++v+dg+ ++ g gp+  + k  + +laS D+v +Da++a+
  gi|298675163|ref|YP_003726913.1| 182 IHEVLVDLLKIQKEIhpgiFAVMDGTVCGDGAGPRTMTpKIKDYILASYDQVSIDAVSAK 241
                                       9**********532224558**************999999999**************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2729.63
//
Query:       gi|298675164|ref|YP_003726914.1|  [L=397]
Description: group 1 glycosyl transferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-36  126.0   2.0    7.9e-36  123.2   1.2    2.5  2  Glycos_transf_1  Glycosyl transferases group 1
    3.5e-26   92.2   0.0    1.3e-24   87.1   0.0    2.2  2  Glyco_trans_1_4  Glycosyl transferases group 1
    1.6e-10   41.2   0.0    3.3e-10   40.2   0.0    1.6  1  Glyco_transf_4   Glycosyltransferase Family 4
    0.00036   21.0   0.0     0.0005   20.5   0.0    1.2  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
     0.0047   17.3   0.0       0.01   16.2   0.0    1.6  1  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
      0.034   15.2   0.5       0.15   13.1   0.2    2.4  2  DUF3298          Protein of unknown function (DUF3298)


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.5   4.4e+03      84     100 ..     138     154 ..     131     156 .. 0.76
   2 !  123.2   1.2   2.6e-39   7.9e-36      15     171 ..     202     379 ..     197     380 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.5
                                       SSHHHHHHCESEEEEEE CS
                   Glycos_transf_1  84 edleellknadifvlps 100
                                         ++ ++++ad++v+ s
  gi|298675164|ref|YP_003726914.1| 138 VLIKLFYNRADLVVAVS 154
                                       557889999**999876 PP

  == domain 2  score: 123.2 bits;  conditional E-value: 2.6e-39
                                       -EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHH CS
                   Glycos_transf_1  15 kkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellk 91 
                                        ++i+ v+rl+++Kg+++likaf ++kk+   n+klvi G+ge e+ l+ +a+e++l+++++f+g+++  +  +++k
  gi|298675164|ref|YP_003726914.1| 202 SPVIINVARLVEQKGQKNLIKAFSQVKKE-IVNAKLVILGKGELEDDLRTMAKEYKLENDIFFIGFQK--NPFKFIK 275
                                       689***********************987.**************************************..9****** PP

                                       CESEEEEEESSBSS-HHHHHHHHTT--EEEET.TTTHCHHCHTTT.........................SEEEE-T CS
                   Glycos_transf_1  92 nadifvlpsisEgfGivllEAmaaglpviasn.aggpaevvkdge.........................tGllvkp 142
                                       ++++fvl+s++Egf+ +l+EAm++g+pvi+++  +gp+e++++                           +  l k+
  gi|298675164|ref|YP_003726914.1| 276 KSSVFVLSSYNEGFPNTLVEAMSCGTPVISTDcKSGPREILAPDTdinfetksieysrygiltpvcninnSNNLTKN 352
                                       ******************************************99988888888888887777776666543333333 PP

                                       T-HHHHHHHHHHHHHSHHHHHHHHHHHHH CS
                   Glycos_transf_1 143 nnaealaeairklledeelrerlgenark 171
                                           +l+e i+++l+d+el++++g  a+k
  gi|298675164|ref|YP_003726914.1| 353 --EYMLSESITRILKDNELNKKYGALAKK 379
                                       ..368888888888888888888877776 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.051   1.5e+02      66      88 ..     140     162 ..     130     166 .. 0.81
   2 !   87.1   0.0   4.3e-28   1.3e-24       2     112 ..     203     320 ..     202     332 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.051
                                       HHHHHHH-SEEEE-----SHHHH CS
                   Glyco_trans_1_4  66 laellaaadvfvaPsegfglkll 88 
                                       ++ ++++ad++va seg++  l+
  gi|298675164|ref|YP_003726914.1| 140 IKLFYNRADLVVAVSEGVKRDLI 162
                                       5668*************987665 PP

  == domain 2  score: 87.1 bits;  conditional E-value: 4.3e-28
                                       EEEEEES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---...HHHHHHHT..T-T.TEEEE---THHHHHHHH- CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk..dvrlvivGdgp.rpeeleelaa..gleerveftGfvedlaellaaa 73 
                                       pvi+ v rl+ ++kg++ l++a+ +++k+  +++lvi G+g+ + ++l+ +a+  +le+++ f Gf ++  ++++++
  gi|298675164|ref|YP_003726914.1| 203 PVIINVARLV-EQKGQKNLIKAFSQVKKEivNAKLVILGKGElE-DDLRTMAKeyKLENDIFFIGFQKNPFKFIKKS 277
                                       899******5.56**************88766*********965.69*998877999999***************** PP

                                       SEEEE--..---SHHHHHHHHTT-EEEE-TGG.GTTT--.TTS CS
                   Glyco_trans_1_4  74 dvfvaPs..egfglkllEamaaglpvVatdvg.giaevv.gen 112
                                       +vfv+ s  egf+++l+Eam++g+pv++td++ g++e++  ++
  gi|298675164|ref|YP_003726914.1| 278 SVFVLSSynEGFPNTLVEAMSCGTPVISTDCKsGPREILaPDT 320
                                       *******************************879898765344 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   1.1e-13   3.3e-10       2     168 ..      15     181 ..      14     183 .. 0.67

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 1.1e-13
                    Glyco_transf_4   2 GGverhvleLaraLarrGheVtvvtpgddgpleeev.......elvvrvprvplpllkrllrslaflrrlrrllkre 71 
                                       GG+er++ +L+ +L  +  +  ++  +d+ + ++         +    v+     ++ + +r l  +++l+++ k++
  gi|298675164|ref|YP_003726914.1|  15 GGAERVTSNLSLNLSNDYNKKLILYNKDQIDYPYDGdiidlniDQSNPVKITVNNIFLKTYRFLKVMLKLKKVKKEH 91 
                                       67777777777777777444444444443333333356665554444444444455566666666777777777777 PP

                    Glyco_transf_4  72 kpDvvHahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadel 148
                                       ++    +    + ++ l+    +++ +++++v +       k  +++  +++  l + +++rad v+avSe ++++l
  gi|298675164|ref|YP_003726914.1|  92 NISTTISFLNNPNILNLF---SKYDDKTIISVRNYN----SKLLSGFDGKIYSVLIKLFYNRADLVVAVSEGVKRDL 161
                                       777776666666655544...335666666666666....4566777778888888999****************** PP

                    Glyco_transf_4 149 rerygvppekitVipnGvDl 168
                                       +++++++p+ki Vi+n+  +
  gi|298675164|ref|YP_003726914.1| 162 IDNFKINPDKIKVIYNPYEI 181
                                       ****************9876 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.7e-07    0.0005     110     159 ..     127     177 ..     106     178 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.7e-07
                   Glyco_trans_4_4 110 rgsgavrrlyralerrllrradavlvvseaeaeelra.lgvpadrvvvvpn 159
                                         sg+++ +y  l ++ ++rad+v++vse++ ++l++ + + +d++ v+ n
  gi|298675164|ref|YP_003726914.1| 127 LLSGFDGKIYSVLIKLFYNRADLVVAVSEGVKRDLIDnFKINPDKIKVIYN 177
                                       458999999****************************899*********99 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.4e-06      0.01       5      43 ..     283     322 ..     278     381 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.4e-06
                   Glyco_trans_1_2   5 psrsespnlrlfEaaacGafaltdda.egleelftpgkev 43 
                                        s +e++   l+Ea+ cG++++++d  +g++e++ p++++
  gi|298675164|ref|YP_003726914.1| 283 SSYNEGFPNTLVEAMSCGTPVISTDCkSGPREILAPDTDI 322
                                       4555889999**************99**********9865 PP

>> DUF3298  Protein of unknown function (DUF3298)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   5.1e-05      0.15      44      68 ..     157     181 ..      83     188 .. 0.84
   2 ?   -1.1   0.0       1.4   4.1e+03      21      49 ..     183     217 ..     182     265 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.1e-05
                                       SS-TTTSSEEEETTEEEEEE-TTSS CS
                           DUF3298  44 edilgyqnfyltddglviyfppYei 68 
                                       ++ +  +nf +++d + ++++pYei
  gi|298675164|ref|YP_003726914.1| 157 VKRDLIDNFKINPDKIKVIYNPYEI 181
                                       5566679*****************9 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.4
                                       HHHHHTCH-TTS-HCCCCTT......TTTSS-TTT CS
                           DUF3298  21 qikkenekqqedeyaglper......rdkedilgy 49 
                                       +i++++++ +e ey  l ++      +  ++++g+
  gi|298675164|ref|YP_003726914.1| 183 KIQEMMNESIEVEYRDLFNSpviinvARLVEQKGQ 217
                                       56777777777776666665555555333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       889  (0.0495845); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.22s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2861.99
//
Query:       gi|298675165|ref|YP_003726915.1|  [L=351]
Description: NAD-dependent epimerase/dehydratase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.8e-51  173.1   0.0    8.9e-51  172.7   0.0    1.2  1  Epimerase        NAD dependent epimerase/dehydratase family
    2.3e-50  171.9   0.0    3.8e-50  171.2   0.0    1.3  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    1.8e-17   63.2   0.2    3.8e-17   62.2   0.2    1.5  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    1.3e-14   54.0   0.0    2.7e-14   52.9   0.0    1.5  1  RmlD_sub_bind    RmlD substrate binding domain
      4e-10   39.3   0.1    1.4e-09   37.5   0.1    2.0  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    3.4e-07   29.7   0.1    7.1e-07   28.6   0.1    1.4  1  NAD_binding_4    Male sterility protein
    0.00029   20.8   0.0      0.012   15.5   0.0    2.2  2  NAD_binding_10   NAD(P)H-binding


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.7   0.0   3.5e-54   8.9e-51       1     228 [.       3     249 ..       3     278 .. 0.93

  Alignments for each domain:
  == domain 1  score: 172.7 bits;  conditional E-value: 3.5e-54
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.........................EEEE--TT- CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl.........................elveldltd 52 
                                       il+tG +GfiG +lvk+l +  +e+igld+ ++    +++                            ++++l+l d
  gi|298675165|ref|YP_003726915.1|   3 ILITGTAGFIGFHLVKKLVNSEHEIIGLDNINDYYDVNLKYGRleetginskkieynkfvqsdlypnySFIKLNLED 79 
                                       8*****************************98888877777668999****************************** PP

                                       HHHHHHHHHHHT-SEEEE--S---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBST CS
                         Epimerase  53 rsalerlfkeeqpdavihlAavggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkee 129
                                       +++++ lf++e++ +v hlAa++gv+ s+++p  +i++n++g ln+le +r +++k l+++sSs+vYG ++++p + 
  gi|298675165|ref|YP_003726915.1|  80 KENIKFLFENEKFVVVCHLAAQAGVRYSITHPYSYIQSNIVGFLNILESCRYNNIKHLVYASSSSVYGLNKKMPFST 156
                                       ************************************************************************99777 PP

                                       CSTTS--.--SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETT CS
                         Epimerase 130 ttltgpl.kpnspYaaaKlageklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgd 205
                                       +    ++ +p s Ya +K   e +++ y   y+++++ lr f++yGp    g+++  ++++ ++il+ + ++ +++ 
  gi|298675165|ref|YP_003726915.1| 157 QD---NVdHPISLYASSKKSNELMAHTYSYLYNIPTTGLRFFTVYGPW---GRPDMAYFKFTKSILDDR-PINVYNY 226
                                       77...777****************************************...99****************.******* PP

                                       ST-EEEEEEHHHHHHHHHHHHHH CS
                         Epimerase 206 gtalRdflyveDvaeaillvleh 228
                                       g+ +Rdf yv+Dv+++++ +l++
  gi|298675165|ref|YP_003726915.1| 227 GDMQRDFTYVDDVVDGLIKILDN 249
                                       *********************99 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.2   0.0   1.5e-53   3.8e-50       1     331 [.       4     340 ..       4     341 .. 0.83

  Alignments for each domain:
  == domain 1  score: 171.2 bits;  conditional E-value: 1.5e-53
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEE....EESS-TTHHHH.........HCTTT...TTGCCEEEEE--TT-H CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivr....rsssfntgrie.........hlakdpkeeleenlklhkgDltDs 64 
                                       LiTG aGfiG +l+++L++ ++e++g+++    ++ +++ gr+e         +  k  +++l +n++++k +l+D+
  gi|298675165|ref|YP_003726915.1|   4 LITGTAGFIGFHLVKKLVNSEHEIIGLDNindyYDVNLKYGRLEetginskkiEYNKFVQSDLYPNYSFIKLNLEDK 80 
                                       9**************************993333333445677773333222111112233455569*********** PP

                                       HHHHHHHHHHT-SEEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB CS
                     GDP_Man_Dehyd  65 sslerllaevqpdevynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpq 141
                                       ++++ l+++ ++  v +LAAq  V++s+++P  +++ n++G l++Le +r  +++   +++ aS+s vYG  ++ p+
  gi|298675165|ref|YP_003726915.1|  81 ENIKFLFENEKFVVVCHLAAQAGVRYSITHPYSYIQSNIVGFLNILESCRYNNIK---HLVYASSSSVYGLNKKMPF 154
                                       **************************************************98764...899***************8 PP

                                       .-TTS-----SHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTT CS
                     GDP_Man_Dehyd 142 .tEttpfyPrsPYaaaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnl 217
                                        t ++  +P s Ya +K + + +++ y   y+++++  ++f  ++p   +++   k+t+ +        +v+++G++
  gi|298675165|ref|YP_003726915.1| 155 sTQDNVDHPISLYASSKKSNELMAHTYSYLYNIPTTGLRFFTVYGPWGRPDMAYFKFTKSILD--DRPINVYNYGDM 229
                                       45677789****************************************999999999998864..444567777777 PP

                                       T-EEEEEEHHHHHHHHHHHHHCSS---EEE-TT-EEEC.HHCHHCCHHCCCHHHHHH............TTGGCCCE CS
                     GDP_Man_Dehyd 218 dakRdwghvkDyveamwlmlqqdkpedyviatgethsv.refvelaflelgktiewegkgeeevgrakesgkvvvev 293
                                         +Rd+++v+D+v+++ ++l ++ p+     +ge+     + +   + ++g++   +    + ++++++   ++ + 
  gi|298675165|ref|YP_003726915.1| 230 --QRDFTYVDDVVDGLIKILDNEPPSGNSDWSGEKPDPsSSTAPYRVYNIGNNNPVN--LIDFINAIEKATGKEAKK 302
                                       ..6*********************988888888776651455667777777754333..344455555555568999 PP

                                       ECGG--SS--SB--B-THHHHHHH----SS-HHHHHHH CS
                     GDP_Man_Dehyd 294 dpkyfrpgevdlllgdaskakeeLgWkpkvsfeelvre 331
                                       ++k+ +pg+v  +++d++ + ++ +++p++ +e+++++
  gi|298675165|ref|YP_003726915.1| 303 NYKPLQPGDVISTWADIDNLIKDFNYEPNTPVEKGIKK 340
                                       ***********************************997 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2   0.2   1.5e-20   3.8e-17       1     274 [.       4     302 ..       4     307 .. 0.74

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 1.5e-20
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlD...................lrespelleelskvnvkk.....viegD 53 
                                       ++tG aGF+G +lvk+Lv+ e+  e+  lD                   ++ ++   +++ +++        +i+  
  gi|298675165|ref|YP_003726915.1|   4 LITGTAGFIGFHLVKKLVNSEH--EIIGLDnindyydvnlkygrleetgINSKKIEYNKFVQSD--LypnysFIKLN 76 
                                       69*****************995..8888888888999999988877755333333333333333..14467799*** PP

                         3Beta_HSD  54 vtdkdkleealegvd..vvihlaslvdvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslge 127
                                       + dk++++   e+ +  vv hla+   v+   ++  ++ + n+ G  n+le+c++++++ lvY Ss +v g n ++ 
  gi|298675165|ref|YP_003726915.1|  77 LEDKENIKFLFENEKfvVVCHLAAQAGVRYsITHPYSYIQSNIVGFLNILESCRYNNIKHLVYASSSSVYGLN-KKM 152
                                       *********9988763266688888888764778899**********************************95.456 PP

                         3Beta_HSD 128 eilngdEeleyeslhqdaypesKalaEklvlkaNgrtlknggrlyTcaLRpagiyGeg...dkllvpllkqlaklg. 200
                                       ++     ++     + + y++sK+  E +      + l n+    T  LR  ++yG+    d   +++ k ++  + 
  gi|298675165|ref|YP_003726915.1| 153 PFS----TQDNVDHPISLYASSKKSNELMAHTY--SYLYNI---PTTGLRFFTVYGPWgrpDMAYFKFTKSILDDRp 220
                                       777....44445567799******998665443..357776...9***********962224456677777776661 PP

                         3Beta_HSD 201 lalfkigdeevlsdrvYvgNvawahilAaralqdpkk...............kssvagqayfisddsPvesyddfnl 262
                                        +++++gd  +  d++Yv+ v++  i    +   + +               +s++  ++y i +++Pv+   df  
  gi|298675165|ref|YP_003726915.1| 221 INVYNYGD--MQRDFTYVDDVVDGLIKILDN---E-PpsgnsdwsgekpdpsSSTAPYRVYNIGNNNPVN-LIDFIN 290
                                       34555555..556********9976633222...1.2233345667777776777778888888999999.899999 PP

                         3Beta_HSD 263 tllkelglelks 274
                                        + k+ g e k+
  gi|298675165|ref|YP_003726915.1| 291 AIEKATGKEAKK 302
                                       999998888776 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.0   1.1e-17   2.7e-14       1     201 [.       1     251 [.       1     312 [. 0.84

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 1.1e-17
                                       EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT........................................T--T CS
                     RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre........................................eldl 37 
                                       mkil+tG  G +G +L+k+l ++++e+++l++                                         +l+l
  gi|298675165|ref|YP_003726915.1|   1 MKILITGTAGFIGFHLVKKLVNSEHEIIGLDNIndyydvnlkygrleetginskkieynkfvqsdlypnysfiKLNL 77 
                                       89****************************77789****************************************** PP

                                       TSHHHHHHHHHHH--SEEEE------HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-.EEEEEEEGGGS-S-TTS-B CS
                     RmlD_sub_bind  38 tdaeavaellkeakpdvvvnaAAytavDkaEseeeaayavnaeavealAeaaaavga.lLihvStDyVFdGekkrpY 113
                                       +d+e+++ l+++ k  vv ++AA   v    +++ +  + n  +  ++ e ++  ++ +L++ S+  V+  +kk+p+
  gi|298675165|ref|YP_003726915.1|  78 EDKENIKFLFENEKFVVVCHLAAQAGVRYSITHPYSYIQSNIVGFLNILESCRYNNIkHLVYASSSSVYGLNKKMPF 154
                                       *****************************************************999847****************** PP

                                       -TTS--.--SSHHHHHHHHHHHHHHHH-SSEEE....EEE-SEESS..SSS-HHHHHHHHHHH-SEEEEES..S-EE CS
                     RmlD_sub_bind 114 eeddet.sPlnvYGrtKlaGEqavlaagkkali....vRtswvyge..kgknfvktmlrlakereelkvva..Dqlg 181
                                       +++d++ +P+++Y+ +K   E +   ++  + i    +R+  vyg   +     +++ +   ++ +++v +  D ++
  gi|298675165|ref|YP_003726915.1| 155 STQDNVdHPISLYASSKKSNELMAHTYSYLYNIpttgLRFFTVYGPwgRPDMAYFKFTKSILDDRPINVYNygDMQR 231
                                       99998647**************9999666555544559******994333445667778888888899876559999 PP

                                       --EEHHHHHHHHHHHHHHCH CS
                     RmlD_sub_bind 182 sPTsardlAevllqllekaa 201
                                         T+++d+ + l+++l+++ 
  gi|298675165|ref|YP_003726915.1| 232 DFTYVDDVVDGLIKILDNEP 251
                                       99************998764 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.1   5.6e-13   1.4e-09       1     128 [.       3     142 ..       3     241 .. 0.83

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 5.6e-13
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH..................-TTEEEE....E--TT- CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeieke............leeelkkkklkveivpvigdvrd 65 
                                       +l+tG +G iG +lv+++++++ + i l + +++   +++                +++ +++l  ++  +  +++d
  gi|298675165|ref|YP_003726915.1|   3 ILITGTAGFIGFHLVKKLVNSEHEIIGLDNINDYYDVNLKYGrleetginskkiEYNKFVQSDLYPNYSFIKLNLED 79 
                                       89******************9999888877777666655544432335533232223333444444445566799** PP

                                       HHHHHHHTT..T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE CS
                   Polysacc_synt_2  66 kerlekaleelkvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliSt 128
                                       ke+++ ++e+ k  vv h AA   V    ++p++ i+ N++g  n++e +  +++k++v+ S+
  gi|298675165|ref|YP_003726915.1|  80 KENIKFLFENEKFVVVCHLAAQAGVRYSITHPYSYIQSNIVGFLNILESCRYNNIKHLVYASS 142
                                       ***********************************************************9986 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.1   2.8e-10   7.1e-07       1     197 [.       5     188 ..       5     215 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 2.8e-10
                                       EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGG.... CS
                     NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlsepr.... 73 
                                       +TG  GF+G +L++kL++++   +i+ l   ++  +++ +    le++++ s+ +    e  k+v+ Dl  ++    
  gi|298675165|ref|YP_003726915.1|   5 ITGTAGFIGFHLVKKLVNSEH--EIIGLDNINDYYDVNLKY-GRLEETGINSKKI----EYNKFVQSDLYPNYsfik 74 
                                       8******************98..8*****************.999*****99995....777888888876655544 PP

                                       GG--H.HHHHHH..HHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-T CS
                     NAD_binding_4  74 lGLse.edlqel..aeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngere 144
                                       l L++ e+++ l   e+  v++h aA+  + +++      ++ N+ G  ++le ++  + + +l++ S++ v+g ++
  gi|298675165|ref|YP_003726915.1|  75 LNLEDkENIKFLfeNEKFVVVCHLAAQAGVRYSITHpysYIQSNIVGFLNILESCRYNNIK-HLVYASSSSVYGLNK 150
                                       888761456666556788999*****98888877664457899*************66555.99*****77777777 PP

                                       TT--SSS-H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH--- CS
                     NAD_binding_4 145 geveekvyeegekeekldederaklkglpntYeqsKalaEklvrearrrsglp 197
                                       +               +   ++++ +     Y  sK   E + ++++   ++p
  gi|298675165|ref|YP_003726915.1| 151 K---------------MPFSTQDNVDHPISLYASSKKSNELMAHTYSYLYNIP 188
                                       3...............2333444444444556666666665555555555555 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.033        85       1      22 [.       7      27 ..       7      33 .. 0.86
   2 !   15.5   0.0   4.7e-06     0.012      39     114 ..      68     157 ..      57     188 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.033
                                      TTTSHHHHHHHHHHHHC-T-EE CS
                    NAD_binding_10  1 GAtGkvGrllvkellargghev 22
                                      G  G +G +lvk+l++++ he+
  gi|298675165|ref|YP_003726915.1|  7 GTAGFIGFHLVKKLVNSE-HEI 27
                                      6689*************5.987 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 4.7e-06
                                       TTCEEEE--TT-CCHHHHHHTT-S.EEEES---TCC.....HHHH...........HHHHHHHHHHCT--EEEEEEE CS
                    NAD_binding_10  39 eglevvegdvtdvedlaealkgad.aVvsalggggk.....deeg...........aknivdaakeagvkRfvlvsa 98 
                                       ++ + ++++++d+e ++  +++   +Vv+ l+++++     +                ni++ ++ +++k++v+ s+
  gi|298675165|ref|YP_003726915.1|  68 PNYSFIKLNLEDKENIKFLFENEKfVVVCHLAAQAGvrysiT--HpysyiqsnivgFLNILESCRYNNIKHLVYASS 142
                                       677899******************556666677766555551..045666666788999****************** PP

                                       TTTTSGCGCHHHHHHH CS
                    NAD_binding_10  99 igvgdevpgefgewnk 114
                                         v+    ++ +  ++
  gi|298675165|ref|YP_003726915.1| 143 SSVYGLN-KKMPFSTQ 157
                                       9999632.22222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 2626.88
//
Query:       gi|298675166|ref|YP_003726916.1|  [L=400]
Description: group 1 glycosyl transferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-35  121.8   0.9    5.4e-35  120.5   0.2    2.1  2  Glycos_transf_1  Glycosyl transferases group 1
    3.7e-25   88.9   0.0    1.2e-24   87.3   0.0    2.0  2  Glyco_trans_1_4  Glycosyl transferases group 1
    3.1e-09   37.1   0.0    7.3e-09   35.8   0.0    1.6  2  Glyco_transf_4   Glycosyltransferase Family 4
    0.00018   21.8   0.0    0.00054   20.3   0.0    1.8  1  Glyco_trans_1_2  Glycosyl transferases group 1
    0.00099   19.6   0.0     0.0014   19.1   0.0    1.2  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
  ------ inclusion threshold ------
      0.073   14.1   0.5       0.26   12.3   0.2    2.3  2  DUF3298          Protein of unknown function (DUF3298)


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       2.3     7e+03      84     100 ..     138     154 ..     131     155 .. 0.74
   2 !  120.5   0.2   1.8e-38   5.4e-35      15     134 ..     202     319 ..     197     377 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.3
                                       SSHHHHHHCESEEEEEE CS
                   Glycos_transf_1  84 edleellknadifvlps 100
                                         ++ ++++ad++v+ s
  gi|298675166|ref|YP_003726916.1| 138 VLIKLFYNRADAIVAVS 154
                                       55788999999999866 PP

  == domain 2  score: 120.5 bits;  conditional E-value: 1.8e-38
                                       -EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHH CS
                   Glycos_transf_1  15 kkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellk 91 
                                        ++i+ v+rl+++Kg+++likaf ++k++   ++klvi G+ge e+ l+ +a+e++l+++++f+g+++  +  +++k
  gi|298675166|ref|YP_003726916.1| 202 SPVIINVARLVEQKGQKHLIKAFSQVKEE-IVDAKLVILGKGELEDDLRTMAKEYKLENDIFFIGFQK--NPFKFIK 275
                                       689***********************997.**************************************..9****** PP

                                       CESEEEEEESSBSS-HHHHHHHHTT--EEEET.TTTHCHHCHTT CS
                   Glycos_transf_1  92 nadifvlpsisEgfGivllEAmaaglpviasn.aggpaevvkdg 134
                                       ++++fvl+s++Egf+ +l+EAm++g+pvi+++  +gp+e++++ 
  gi|298675166|ref|YP_003726916.1| 276 KSSVFVLSSYNEGFPNTLVEAMSCGTPVISTDcKSGPREILAPD 319
                                       ****************************************9875 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.8   8.3e+03      67      83 ..     141     157 ..     133     163 .. 0.78
   2 !   87.3   0.0     4e-28   1.2e-24       2     112 ..     203     320 ..     202     369 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.8
                                       HHHHHH-SEEEE----- CS
                   Glyco_trans_1_4  67 aellaaadvfvaPsegf 83 
                                       + ++++ad  va s+g+
  gi|298675166|ref|YP_003726916.1| 141 KLFYNRADAIVAVSKGV 157
                                       55899999999998765 PP

  == domain 2  score: 87.3 bits;  conditional E-value: 4e-28
                                       EEEEEES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---...HHHHHHHT..T-T.TEEEE---THHHHHHHH- CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk..dvrlvivGdgp.rpeeleelaa..gleerveftGfvedlaellaaa 73 
                                       pvi+ v rl+ ++kg++ l++a+ +++++  d++lvi G+g+ + ++l+ +a+  +le+++ f Gf ++  ++++++
  gi|298675166|ref|YP_003726916.1| 203 PVIINVARLV-EQKGQKHLIKAFSQVKEEivDAKLVILGKGElE-DDLRTMAKeyKLENDIFFIGFQKNPFKFIKKS 277
                                       899******5.56**************98766*********965.69*998877999999***************** PP

                                       SEEEE--..---SHHHHHHHHTT-EEEE-TGG.GTTT--.TTS CS
                   Glyco_trans_1_4  74 dvfvaPs..egfglkllEamaaglpvVatdvg.giaevv.gen 112
                                       +vfv+ s  egf+++l+Eam++g+pv++td++ g++e++  ++
  gi|298675166|ref|YP_003726916.1| 278 SVFVLSSynEGFPNTLVEAMSCGTPVISTDCKsGPREILaPDT 320
                                       *******************************879999775444 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0         1   3.1e+03       2      25 ..      15      38 ..      14      89 .. 0.73
   2 !   35.8   0.0   2.4e-12   7.3e-09     118     168 ..     131     181 ..     103     183 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1
                    Glyco_transf_4  2 GGverhvleLaraLarrGheVtvv 25
                                      GG+e ++ +L+ +L     ++ ++
  gi|298675166|ref|YP_003726916.1| 15 GGAEKVISNLSLNLSHEYDKIILL 38
                                      899999999998888765555544 PP

  == domain 2  score: 35.8 bits;  conditional E-value: 2.4e-12
                    Glyco_transf_4 118 plsrllralerrllrradrviavSeatadelrerygvppekitVipnGvDl 168
                                       +  +++  l + +++rad+++avS+ + ++l+++++++p+ki Vi+n+  +
  gi|298675166|ref|YP_003726916.1| 131 FDGKIYSVLIKLFYNRADAIVAVSKGVEKDLVDNFKIDPDKIKVIYNPYEI 181
                                       5556667788899**********************************9876 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.8e-07   0.00054       5      90 ..     283     396 ..     278     398 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.8e-07
                   Glyco_trans_1_2   5 psrsespnlrlfEaaacGafaltdda.egleelftpgk............................evilfedleel 52 
                                        s +e++   l+Ea+ cG++++++d  +g++e++ p++                              +l e+++ l
  gi|298675166|ref|YP_003726916.1| 283 SSYNEGFPNTLVEAMSCGTPVISTDCkSGPREILAPDTdinfetesieysrygiltpvfdkckfnkNDLLTENEKLL 359
                                       4555889999**************99************999999999999999999999999999844445799999 PP

                   Glyco_trans_1_2  53 aekiryllanpeerraiaeaarervlaehtydhraeql 90 
                                       a  + +ll+n ++r+  a  a +r  +++  ++ + q+
  gi|298675166|ref|YP_003726916.1| 360 ASSLVELLKNNKLREDYALLALQR-AQDFEIKNIMSQW 396
                                       999999999999999999999999.6777777766665 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   4.8e-07    0.0014     104     159 ..     121     177 ..     106     178 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 4.8e-07
                   Glyco_trans_4_4 104 hglllrrgsgavrrlyralerrllrradavlvvseaeaeelra.lgvpadrvvvvpn 159
                                       ++      sg+++ +y  l ++ ++rada+++vs ++ ++l++ + +++d++ v+ n
  gi|298675166|ref|YP_003726916.1| 121 RNYNSKLLSGFDGKIYSVLIKLFYNRADAIVAVSKGVEKDLVDnFKIDPDKIKVIYN 177
                                       55444555899999*****************************899*********99 PP

>> DUF3298  Protein of unknown function (DUF3298)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   8.8e-05      0.26      46      68 ..     159     181 ..      45     183 .. 0.86
   2 ?   -1.5   0.0       1.9   5.6e+03      22      41 ..     184     209 ..     182     273 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.8e-05
                                       -TTTSSEEEETTEEEEEE-TTSS CS
                           DUF3298  46 ilgyqnfyltddglviyfppYei 68 
                                        +  +nf +++d + ++++pYei
  gi|298675166|ref|YP_003726916.1| 159 KDLVDNFKIDPDKIKVIYNPYEI 181
                                       55668*****************9 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.9
                                       HHHHTCH-TTS-HCCCCTT......T CS
                           DUF3298  22 ikkenekqqedeyaglper......r 41 
                                       i++++++ +e ey  l ++      +
  gi|298675166|ref|YP_003726916.1| 184 IQEMMNESIEVEYRDLFNSpviinvA 209
                                       66666666655555555444444431 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       997  (0.0556082); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2828.60
//
Query:       gi|298675167|ref|YP_003726917.1|  [L=320]
Description: NAD-dependent epimerase/dehydratase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-48  165.8   0.0    1.3e-48  165.5   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    8.8e-45  153.5   0.2    3.7e-44  151.5   0.2    1.7  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    6.1e-20   71.4   0.1    7.7e-20   71.0   0.1    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    9.6e-18   64.3   0.1    1.1e-16   60.9   0.1    1.9  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    9.7e-13   47.9   0.0    1.2e-12   47.6   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    3.3e-09   36.3   0.1    1.6e-06   27.5   0.1    2.8  1  NAD_binding_4    Male sterility protein
    5.9e-07   29.6   0.0    9.3e-07   28.9   0.0    1.3  1  NAD_binding_10   NAD(P)H-binding
    0.00061   19.3   0.0     0.0088   15.5   0.0    2.3  1  adh_short        short chain dehydrogenase
     0.0031   17.8   0.0     0.0055   17.0   0.0    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
      0.011   15.3   0.1        1.1    8.7   0.0    2.2  2  NmrA             NmrA-like family
       0.97    9.5   3.7          4    7.5   1.3    2.5  2  Lipase_GDSL_3    GDSL-like Lipase/Acylhydrolase family


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.5   0.0   8.2e-52   1.3e-48       1     241 []      14     249 ..      14     249 .. 0.97

  Alignments for each domain:
  == domain 1  score: 165.5 bits;  conditional E-value: 8.2e-52
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.....EEEE--TT-HHHHHHHHHHHT-SEEEE-- CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl.....elveldltdrsalerlfkeeqpdavihlA 72 
                                       il+tG++GfiGs++++ l+e + e++ +d+lss++++  ++++     ++++++l++ ++++ +++  + d v+h+A
  gi|298675167|ref|YP_003726917.1|  14 ILITGGAGFIGSHILDLLMEYDNEILIFDNLSSGNENFIKHHInknnfKFIDGNLLNFKEIDSACE--ETDFVFHIA 88 
                                       8******************************999999999999***********************..79******* PP

                                       S---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHH CS
                         Epimerase  73 avggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlag 149
                                       a  +v+  se+ +  +++n++ t+nlle +rk++vk++ f s+s++YG+ + +p+ e+   gpl p s Y+a+Kl  
  gi|298675167|ref|YP_003726917.1|  89 ANPDVKLGSENTKVHFDQNIKATYNLLESMRKNNVKKIAFTSTSTIYGEADIIPTPENY--GPLVPISLYGASKLSC 163
                                       ************************************************99999977777..9*************** PP

                                       HHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHH CS
                         Epimerase 150 eklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvl 226
                                       e l+ ++ ++++++  i+r  n++G r    ++++vi+ +i+k++ + +++ +lgdg+++  +l+v D+++ail+ +
  gi|298675167|ref|YP_003726917.1| 164 EGLISSFCHTFDMQSWIFRFANIVGNR----SNHGVIFDFIKKLKINPNQLEILGDGQQRKSYLHVHDCVNAILYSI 236
                                       ***************************....***************99***************************** PP

                                       HHHTT-STTEEEEES CS
                         Epimerase 227 ehvdagdkgeiyniG 241
                                       ++ +  ++ +iyniG
  gi|298675167|ref|YP_003726917.1| 237 NKSN--NTVNIYNIG 249
                                       **44..5678****9 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.5   0.2   2.2e-47   3.7e-44       1     332 []      15     315 ..      15     315 .. 0.88

  Alignments for each domain:
  == domain 1  score: 151.5 bits;  conditional E-value: 2.2e-47
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       LiTG+aGfiGs++++lL+e + e+ +++++ss  n + i+h        +++n+k++ g+l + ++++++ +e+  d
  gi|298675167|ref|YP_003726917.1|  15 LITGGAGFIGSHILDLLMEYDNEILIFDNLSSG-NENFIKHHI------NKNNFKFIDGNLLNFKEIDSACEET--D 82 
                                       9*******************9999988877665.767777654......3579********************9..8 PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TT.S-----SHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEt.tpfyPrsPY 153
                                        v++ AA   V+   e+ +  ++ n+ +t++LLe +r+ +++   ++ ++Sts++YG+++ +p  E+  p+ P s Y
  gi|298675167|ref|YP_003726917.1|  83 FVFHIAANPDVKLGSENTKVHFDQNIKATYNLLESMRKNNVK---KIAFTSTSTIYGEADIIPTPENyGPLVPISLY 156
                                       9*************************************9875...8899**************998868******** PP

                                       HHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHH CS
                     GDP_Man_Dehyd 154 aaaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyv 230
                                       +a+Kl+++ ++ ++ ++++++  + ++ n  + r  ++     i +++ + + + ++  +lG+++++++++hv+D v
  gi|298675167|ref|YP_003726917.1| 157 GASKLSCEGLISSFCHTFDMQSWIFRFANIVGNRS-NH---GVIFDFIKKLKINPNQLEILGDGQQRKSYLHVHDCV 229
                                       *********************************95.44...5699********99999999**************** PP

                                       HHHHHHHHC..SS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB CS
                     GDP_Man_Dehyd 231 eamwlmlqq..dkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdl 305
                                       +a+   +++  ++ + y+i++ +t +v e++e+ + e+g + +         +          +   ++  +g+v +
  gi|298675167|ref|YP_003726917.1| 230 NAILYSINKsnNTVNIYNIGSEDTINVTEIAEIVVDEMGLKNV---------EF-------NYT-GGSRGWKGDVPK 289
                                       ***9999873355688999999999999999999999997422.........11.......111.1233446999** PP

                                       --B-THHHHHHH----SS-HHHHHHHH CS
                     GDP_Man_Dehyd 306 llgdaskakeeLgWkpkvsfeelvrem 332
                                       ++  ++k+k +LgW+p+++ e+ +r++
  gi|298675167|ref|YP_003726917.1| 290 MMLSIDKLK-NLGWEPTYNSEKSIRDT 315
                                       ********9.8********99999986 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.0   0.1   4.7e-23   7.7e-20       1     225 [.      15     232 ..      15     250 .. 0.80

  Alignments for each domain:
  == domain 1  score: 71.0 bits;  conditional E-value: 4.7e-23
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespel..leelskvnvkkviegDvtdkdkleealegvdvvihlas 75 
                                       ++tGgaGF+G+++   L++ ++  e+ ++D   s +    ++  + n+ k+i g +++ ++++ a+e+ d v+h+a+
  gi|298675167|ref|YP_003726917.1|  15 LITGGAGFIGSHILDLLMEYDN--EILIFDNLSSGNEnfIKHHINKNNFKFIDGNLLNFKEIDSACEETDFVFHIAA 89 
                                       69*******************6..******55444330133333333344*************************** PP

                         3Beta_HSD  76 lvdvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKa 151
                                         dv+    +++   + n+k T n+le+ +k++v+++ +tS+  + g+   +++i    E  + + ++ + y  sK 
  gi|298675167|ref|YP_003726917.1|  90 NPDVKLgSENTKVHFDQNIKATYNLLESMRKNNVKKIAFTSTSTIYGE---ADIIP-TPE-NYGPLVPISLYGASKL 161
                                       ***9853777788899***************************99999...55555.554.567899********** PP

                         3Beta_HSD 152 laEklvlkaNgrtlknggrlyTcaLRpagiyGegdk..llvpllkqlaklglalfkigdeevlsdrvYvgNvawah 225
                                         E l+ +          ++     R a i G++++  +++ ++k+l+ + ++l  +gd ++ +++  v   + a+
  gi|298675167|ref|YP_003726917.1| 162 SCEGLISSFCH-----TFDMQSWIFRFANIVGNRSNhgVIFDFIKKLKINPNQLEILGDGQQRKSYLHVHDCVNAI 232
                                       ****9977655.....557888888888888888762246777888888888888888888888877777766665 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.1   6.5e-20   1.1e-16       1     263 [.      14     278 ..      14     299 .. 0.79

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 6.5e-20
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77 
                                       +l+tG++G iGs++++ +++ + ++i+++++      ++ k++   ++k+++k+    + g++ + +++++a+e  +
  gi|298675167|ref|YP_003726917.1|  14 ILITGGAGFIGSHILDLLMEYD-NEILIFDNLSSGNENFIKHH---INKNNFKF----IDGNLLNFKEIDSACE--E 80 
                                       89*************9888876.67889998777666655554...34444443....479*************..* PP

                                       -SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGG...............SS--SHHH CS
                   Polysacc_synt_2  78 vdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDKA...............vnPtnvmG 139
                                        d+vfh AA   V l  en+   +++N+ +t n++e   +++vkk+ + St                    P++++G
  gi|298675167|ref|YP_003726917.1|  81 TDFVFHIAANPDVKLGSENTKVHFDQNIKATYNLLESMRKNNVKKIAFTSTSTIygeadiiptpenygpLVPISLYG 157
                                       **************************************************965322212222222222246899*** PP

                                       HHHHHHHHHHHHGGG--SSS--EEEEEEE-EETT..GTTSSHHHHHHHHHTT.SSEEE.S-TT-EEEEE-HHHHHHH CS
                   Polysacc_synt_2 140 atKrlaekllqalakeseekktkfvvvRfGNVlg..SrGSviplFkkqikeg.gpvtv.TdpemtRyfmtieeavqL 212
                                       a+K+ +e l+ ++ ++    +++  + Rf N++g  S+  vi  F k++k + +++ +  d +  + ++ +++ v+ 
  gi|298675167|ref|YP_003726917.1| 158 ASKLSCEGLISSFCHTF---DMQSWIFRFANIVGnrSNHGVIFDFIKKLKINpNQLEIlGDGQQRKSYLHVHDCVNA 231
                                       ***********999988...7889999******94456679999999888776888872567777789********* PP

                                       HHHHHHH--SS-EEEE--...-EEEHHHHHHHH..........SSSS-EEE-- CS
                   Polysacc_synt_2 213 vlqalalakggeifvldmG..epvkivdlakalielsgleekkeedieikitG 263
                                       +l++++++++  + + ++G  ++++++++a+ +++ +gl+     ++e ++tG
  gi|298675167|ref|YP_003726917.1| 232 ILYSINKSNN-TVNIYNIGseDTINVTEIAEIVVDEMGLK-----NVEFNYTG 278
                                       ****987655.4555555522689999******9999974.....45555555 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.0   7.1e-16   1.2e-12       2     235 ..      13     271 ..      12     316 .. 0.87

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 7.1e-16
                                       EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT....................T--TTSHHHHHHHHHHH--SEEEE- CS
                     RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre....................eldltdaeavaellkeakpdvvvna 58 
                                       kil+tG+ G +Gs++ ++l e + e+l +++                     + +l + ++++++ +e   d+v + 
  gi|298675167|ref|YP_003726917.1|  13 KILITGGAGFIGSHILDLLMEYDNEILIFDNLssgnenfikhhinknnfkfiDGNLLNFKEIDSACEE--TDFVFHI 87 
                                       89*******************999999997667899*************99999999********999..789**** PP

                                       -----HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-E.EEEEEEGGGS-S-TTS-.B-TTS----SSHHHHHHHHHH CS
                     RmlD_sub_bind  59 AAytavDkaEseeeaayavnaeavealAeaaaavgal.LihvStDyVFdGekkrp.YeeddetsPlnvYGrtKlaGE 133
                                       AA  +v    ++ +  +  n +a+ +l e  ++ +++ + + St  ++  +   p  e+  +  P+++YG++Kl  E
  gi|298675167|ref|YP_003726917.1|  88 AANPDVKLGSENTKVHFDQNIKATYNLLESMRKNNVKkIAFTSTSTIYGEADIIPtPENYGPLVPISLYGASKLSCE 164
                                       **********************************99636789******9887777345567899************* PP

                                       HHHHH....H-SSEEEEEE-SEESS.SSS-HHHHHHHHH.HH-SEEEEESS-EE--EEHHHHHHHHHHHHHHCHH.G CS
                     RmlD_sub_bind 134 qavla....agkkalivRtswvyge.kgknfvktmlrla.kereelkvvaDqlgsPTsardlAevllqllekaaeek 204
                                         + +       + +i+R++ + g+ +++  ++ +++++  + ++l++  D + + ++   + +++ ++l  + +++
  gi|298675167|ref|YP_003726917.1| 165 GLISSfchtFDMQSWIFRFANIVGNrSNHGVIFDFIKKLkINPNQLEILGDGQQRKSYL-HVHDCVNAILYSINKSN 240
                                       ****9444333489*********984455566666655528999*******87776654.57788888888888888 PP

                                       GG-EEEE---BS-EEHHHHHHHHHHHHCHTT CS
                     RmlD_sub_bind 205 elagvyHlanegetswlefArailkeagads 235
                                       ++  +y +++e++++  e+A+ +++e+g ++
  gi|298675167|ref|YP_003726917.1| 241 NTVNIYNIGSEDTINVTEIAEIVVDEMGLKN 271
                                       89************************99865 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.1   9.8e-10   1.6e-06       1     215 [.      16     196 ..      16     232 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 9.8e-10
                                       EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG-- CS
                     NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLs 77 
                                       +TG+ GF+G+++l  L++ ++  +i +    +sg   +    e++ k+ +        +++ k++ G+l      L+
  gi|298675167|ref|YP_003726917.1|  16 ITGGAGFIGSHILDLLMEYDN--EILIFDNLSSG---N----ENFIKHHIN-------KNNFKFIDGNL------LN 70 
                                       899999999999999998888..45555444433...3....333444444.......45579999999......66 PP

                                       HHHHHHHHHH--EEEE--SS-S.S...TTSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS CS
                     NAD_binding_4  78 eedlqelaeevdviihsaAtvnfd...epykellrvNveGtrevlelakklkklkvllhvSTayvngeregeveekv 151
                                        ++++  +ee+d ++h+aA+ +++   e++k+ ++ N+++t ++le  +k + +  + + ST++++ge    +    
  gi|298675167|ref|YP_003726917.1|  71 FKEIDSACEETDFVFHIAANPDVKlgsENTKVHFDQNIKATYNLLESMRKNNVK-KIAFTSTSTIYGEAD--I---- 140
                                       779****************9776522258999**************99987777.9************99..3.... PP

                                       -H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-.-SSST-- CS
                     NAD_binding_4 152 yeegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg.esktGwi 215
                                                  + e          Y  sK   E l+ +  +  +++  i+R  +i+g +s  G+i
  gi|298675167|ref|YP_003726917.1| 141 ---------IPTPENYGPLVPISLYGASKLSCEGLISSFCHTFDMQSWIFRFANIVGnRSNHGVI 196
                                       .........567777777777789****************99999***********955555654 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   5.7e-10   9.3e-07       1     105 [.      18     138 ..      18     157 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 5.7e-10
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCH.....HHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TC CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpekla.....eleaeeglevvegdvtdvedlaealkgadaVvsalgggg 72 
                                       G+ G +G+++++ l +  + e  ++  n ++ +     +  ++++ + ++g++++ +++ +a++ +d V+  +++ +
  gi|298675167|ref|YP_003726917.1|  18 GGAGFIGSHILDLLMEY-DNE-ILIFDNLSSGNenfikHHINKNNFKFIDGNLLNFKEIDSACEETDFVFHIAANPD 92 
                                       999*********99999.456.5777775544311111444679*************************99996655 PP

                                       C...........HHHH..HHHHHHHHHHCT--EEEEEEETTTTSGC CS
                    NAD_binding_10  73 k...........deeg..aknivdaakeagvkRfvlvsaigvgdev 105
                                                   d+++  + n+++ +++++vk++ + s+  ++ e+
  gi|298675167|ref|YP_003726917.1|  93 VklgsentkvhfDQNIkaTYNLLESMRKNNVKKIAFTSTSTIYGEA 138
                                       556544335555444388*********************9999654 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   5.4e-06    0.0088       2      71 ..      13      81 ..      12     180 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.4e-06
                                      EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHH CS
                         adh_short  2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealveka 71
                                       +l+tG+++ IG  i + l++ + +++++d+ ++  e+ +k+  + ++++ +i +++ + +e++ + e+ 
  gi|298675167|ref|YP_003726917.1| 13 KILITGGAGFIGSHILDLLMEYDNEILIFDNLSSGNENFIKHHIN-KNNFKFIDGNLLNFKEIDSACEET 81
                                      59******************************9999999998776.578*******99999999988876 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   3.4e-06    0.0055       2      78 ..      15      89 ..      14      95 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.4e-06
                                      EEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH.TTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SS CS
                   Sacchrp_dh_NADP  2 liiGa.GsvGqavaellarhfdvdaeitvadrskeklealaaka.lgvrfeaialdaenyeavLaallkegdlvvnlsp 78
                                      li G+ G++G+ +++ll + ++   ei + d   ++ e+ +++  ++ +f++i  +  n ++ ++++++e+d+v + + 
  gi|298675167|ref|YP_003726917.1| 15 LITGGaGFIGSHILDLLMEYDN---EILIFDNLSSGNENFIKHHiNKNNFKFIDGNLLNFKE-IDSACEETDFVFHIAA 89
                                      556655***********99765...7*********9999988778*****************.***********98775 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0007       1.1       1      73 [.      14      89 ..      14     134 .. 0.78
   2 ?    4.4   0.0     0.014        23     164     230 ..     207     273 ..     193     276 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0007
                                      EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S.....-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE--- CS
                              NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdt.....kselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtg 73
                                      Il++G++G +G+++ + l++ ++++ +   d      ++   ++++++  +++ g+l + + +++a ++ d vf   +
  gi|298675167|ref|YP_003726917.1| 14 ILITGGAGFIGSHILDLLMEYDNEILI--FDNlssgnENFIKHHINKNNFKFIDGNLLNFKEIDSACEETDFVFHIAA 89
                                      89*****************98888754..444456644445567889999999***999999*****99999998766 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.014
                                       S.-EEEEESS-TTS-EE-HHHHHHHHHHHHHHHHHHHTTEEEEE-SEEE-HHHHHHHHHHHHT.S-EE CS
                              NmrA 164 edkvtllgpgnpkavlldaeeDiGafvikilkdprklkgkriklagntlsgneivelfekkig.ktvk 230
                                        +++++lg+g+    +l +++D  ++++  +++ +++ + +   +++t+ ++ei+e+   ++g k+v+
  gi|298675167|ref|YP_003726917.1| 207 PNQLEILGDGQQRKSYL-HVHDCVNAILYSINKSNNTVNIYNIGSEDTINVTEIAEIVVDEMGlKNVE 273
                                       34699******999999.****99999999999888866677789************99888844455 PP

>> Lipase_GDSL_3  GDSL-like Lipase/Acylhydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   1.3    0.0024         4      41     150 ..      17     137 ..      10     141 .. 0.72
   2 ?    1.1   0.0      0.24   3.9e+02     112     152 ..     217     258 ..     205     271 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0024
                     Lipase_GDSL_3  41 fsGnalleaeladvlaevdasvfvldllpN.........asaeeirerleyfv.......ktlrkahPktpillved 101
                                       + G++ + ++++d+l e d ++ ++d l+                ++   +f+       k + +a  +t  ++   
  gi|298675167|ref|YP_003726917.1|  17 TGGAGFIGSHILDLLMEYDNEILIFDNLSSgnenfikhhI-----NKNNFKFIdgnllnfKEIDSACEETDFVFHIA 88 
                                       679999**********************984455444441.....33333333111112267888888888888887 PP

                     Lipase_GDSL_3 102 lsttkglvdeklekeveaknkaleelvkklkkekekklylisskellgk 150
                                       ++   +l  e+++ +  ++ ka ++l++++ k+++kk+ + s+  ++g+
  gi|298675167|ref|YP_003726917.1|  89 ANPDVKLGSENTKVHFDQNIKATYNLLESMRKNNVKKIAFTSTSTIYGE 137
                                       7777777788888888888888888888888888888888888777765 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.24
                     Lipase_GDSL_3 112 klekeveaknkaleelvkk.lkkekekklylisskellgkde 152
                                       + +k + + ++ ++ ++ + +k++++ ++y i s++ ++ +e
  gi|298675167|ref|YP_003726917.1| 217 QQRKSYLHVHDCVNAILYSiNKSNNTVNIYNIGSEDTINVTE 258
                                       556777788888888776636777899*****9999776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       771  (0.043003); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.69u 0.33s 00:00:01.02 Elapsed: 00:00:00.53
# Mc/sec: 1824.53
//
Query:       gi|298675168|ref|YP_003726918.1|  [L=394]
Description: group 1 glycosyl transferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-37  128.1   0.3    3.9e-37  127.4   0.3    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    4.2e-32  111.4   0.0    6.3e-32  110.8   0.0    1.3  1  Glyco_trans_1_4  Glycosyl transferases group 1
    2.5e-08   34.1   0.0    5.2e-08   33.1   0.0    1.6  1  Glyco_transf_4   Glycosyltransferase Family 4
    1.2e-07   32.0   0.0    2.9e-07   30.8   0.0    1.6  1  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
      0.012   16.2   1.2      0.023   15.2   1.2    1.5  1  DUF5626          Domain of unknown function (DUF5626)


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.4   0.3   1.1e-40   3.9e-37       9     171 ..     200     367 ..     192     368 .. 0.95

  Alignments for each domain:
  == domain 1  score: 127.4 bits;  conditional E-value: 1.1e-40
                                       TTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSS CS
                   Glycos_transf_1   9 lgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsred 85 
                                       ++ n+ +  ilsv+rl ++Kg+ +li++++++ k    n+ ++i+G+ge e+elkkl+eel++++ v+f+g v + +
  gi|298675168|ref|YP_003726918.1| 200 KQNNSSRVKILSVSRLIEKKGHIYLIRSIPEVIKH-CTNCEFIIVGSGELENELKKLVEELNIKEYVNFVGDVTDYE 275
                                       456678899***********************776.***************************************** PP

                                       HHHHHHCESEEEEEESS......BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHH CS
                   Glycos_transf_1  86 leellknadifvlpsis......EgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairkll 156
                                       l+e+++ adifvlp+        +g +++ +EAm+  lpvi++n++g++e+v+++ tGl+++++n+++l +ai++l 
  gi|298675168|ref|YP_003726918.1| 276 LIEYYNTADIFVLPCVIdkngdrDGIPVAMMEAMSMELPVISTNVSGIPELVENENTGLIIPEKNVKQLTNAIIRLC 352
                                       **************9999*********************************************************** PP

                                       HSHHHHHHHHHHHHH CS
                   Glycos_transf_1 157 edeelrerlgenark 171
                                       +++++r+++g ++r+
  gi|298675168|ref|YP_003726918.1| 353 KNPDERKKMGIKGRQ 367
                                       **********99986 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.8   0.0   1.8e-35   6.3e-32       3     134 .]     208     354 ..     206     354 .. 0.90

  Alignments for each domain:
  == domain 1  score: 110.8 bits;  conditional E-value: 1.8e-35
                                       EEEEES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---...HHHHHHHT..T-T.TEEEE---TH..HHHHHHH CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkk..dvrlvivGdgp.rpeeleelaa..gleerveftGfved..laellaa 72 
                                       +il v+rl e+ kg+ +l++ +p++ k+  +++++ivG+g+ + +el++l++  +++e v f+G v+d  l e+++ 
  gi|298675168|ref|YP_003726918.1| 208 KILSVSRLIEK-KGHIYLIRSIPEVIKHctNCEFIIVGSGElE-NELKKLVEelNIKEYVNFVGDVTDyeLIEYYNT 282
                                       799*****655.*************988755*********955.69*999976899999*******6666******* PP

                                       -SEEEE--........---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
                   Glyco_trans_1_4  73 advfvaPs........egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLled 134
                                       ad+fv+P          g++++++Eam+++lpv++t+v+gi+e+v  +++gl++p++++++l++ai+rL ++
  gi|298675168|ref|YP_003726918.1| 283 ADIFVLPCvidkngdrDGIPVAMMEAMSMELPVISTNVSGIPELVenENTGLIIPEKNVKQLTNAIIRLCKN 354
                                       **********9877644****************************977899******************876 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0   1.4e-11   5.2e-08       6     169 ..      17     193 ..      15     194 .. 0.70

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 1.4e-11
                    Glyco_transf_4   6 rhvleLaraLarrGheVtvv.....tpgddgpleeev.........................elvvrvprvplpllk 52 
                                        ++l+ + +L r+G++++++     +     ++  ++                         + ++    +  +l+k
  gi|298675168|ref|YP_003726918.1|  17 SFILNEIFNLKRKGFDIYIFsiykpS-----ESIVHDeldnellnktyyfdityvlknlpkfIKYYLKYIIKELLDK 88 
                                       56777777899999999999654442.....2222222445567777776666666555444333333333334555 PP

                    Glyco_transf_4  53 rllrslaflrrlrrllkrekpDvvHahspaalgaallalrr.rlgiplVltvHglyekrllkarlkplsrllraler 128
                                       rl++  + + ++  +++  k+D+ H+h ++a  aa+++ +    g+ + lt+H  +          ++++ +   ++
  gi|298675168|ref|YP_003726918.1|  89 RLPLHATKMAYFSIIIE--KIDINHIHAHFATKAAHARVLSnIFGLSYTLTAHAYD----------LYRNPNISHLK 153
                                       55555555555555555..7777777777776666666665789************..........899999999** PP

                    Glyco_transf_4 129 rllrradrviavSeatadelrerygvppekitVipnGvDle 169
                                       r+l+ a   i++Se+ +++++   g ++++i Vi +G+D e
  gi|298675168|ref|YP_003726918.1| 154 RTLDDAEYNITISEYNKNYMKNVIG-SNNNINVIRCGIDYE 193
                                       *************************.559**********76 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   8.2e-11   2.9e-07       9      85 ..     299     377 ..     285     382 .. 0.90

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 8.2e-11
                   Glyco_trans_1_2   9 espnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervlaehty 83 
                                       +++ + + Ea+ +  +++++  +g++el++++++++++   ++++l  +i +l +np+er+++++++r+ + ++++ 
  gi|298675168|ref|YP_003726918.1| 299 DGIPVAMMEAMSMELPVISTNVSGIPELVENENTGLIIPekNVKQLTNAIIRLCKNPDERKKMGIKGRQIIVNKFNI 375
                                       56667799*******************************9****************************999888876 PP

                   Glyco_trans_1_2  84 dh 85 
                                       d+
  gi|298675168|ref|YP_003726918.1| 376 DK 377
                                       65 PP

>> DUF5626  Domain of unknown function (DUF5626)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   1.2   6.4e-06     0.023      36     104 ..     138     216 ..      99     225 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.4e-06
                                       EEEEEEEE.EESSE......EEEEEEEEE..TEEEEEEEEE..EEEEEE-TT-EEEEEEEEE-TSSEEEEEEEEE-S CS
                           DUF5626  36 ngtykikyntavrw......nasFkvkve..sknkItsahs..lsykaiagsisssklkvtstatakatyvfktkas 102
                                         +y+ + n +++        a+++++++  +kn+++++ +   ++++i++ i+ +k+k t++ + + +++   ++ 
  gi|298675168|ref|YP_003726918.1| 138 AHAYDLYRNPNISHlkrtldDAEYNITISeyNKNYMKNVIGsnNNINVIRCGIDYEKFKPTNKQNNSSRVKILSVSR 214
                                       4555555554444455566689*********99******7611689***************9955555555555555 PP

                                       SE CS
                           DUF5626 103 li 104
                                       li
  gi|298675168|ref|YP_003726918.1| 215 LI 216
                                       55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       936  (0.0522059); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 2266.19
//
Query:       gi|298675169|ref|YP_003726919.1|  [L=277]
Description: hypothetical protein Metev_1256 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0077   16.3   0.1      0.085   13.0   0.0    2.6  2  PMBR             Pseudomurein-binding repeat
     0.0098   16.3   0.0        3.1    8.1   0.0    2.3  2  Sulfotransfer_3  Sulfotransferase family
  ------ inclusion threshold ------
      0.018   14.5   2.8       0.32   10.4   2.8    2.2  1  Sulfotransfer_1  Sulfotransferase domain
       0.02   14.7   0.1       0.34   10.7   0.0    2.4  2  Sulfotransfer_4  Sulfotransferase domain


Domain annotation for each model (and alignments):
>> PMBR  Pseudomurein-binding repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.36   1.6e+03      12      21 ..      86      95 ..      85      97 .. 0.81
   2 !   13.0   0.0   1.9e-05     0.085       2      24 ..     204     226 ..     203     226 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.36
                              PMBR 12 dmasrvlafi 21
                                      ++ sr++++i
  gi|298675169|ref|YP_003726919.1| 86 WVTSRYKQYI 95
                                      5779****98 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 1.9e-05
                              PMBR   2 sgkisyeeyldmasrvlafiesn 24 
                                       sg i y++y++  ++v+++i +n
  gi|298675169|ref|YP_003726919.1| 204 SGIIPYNQYTWFVRKVIRYILQN 226
                                       799****************9877 PP

>> Sulfotransfer_3  Sulfotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0    0.0033        15       5      16 ..       6      17 ..       4      18 .. 0.92
   2 !    8.1   0.0   0.00069       3.1     116     175 ..      64     127 ..      35     166 .. 0.58

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0033
                                      E--TTSSHHHHH CS
                   Sulfotransfer_3  5 vGlpRSGTTlLh 16
                                      +Glp++GTT+L+
  gi|298675169|ref|YP_003726919.1|  6 IGLPKTGTTFLQ 17
                                      8*********98 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00069
                                       HHHHHHHBSSEEEEEEE--H.HHHHHHHHHTT--.------.--..-.HHH.HHHHHHHHHHHH CS
                   Sulfotransfer_3 116 ldlllelfPdAkfihlvRdpvdtvlssyvslfgk.kresys.edsld.ele.daleewarayer 175
                                       +  l++lfP+Ak+ +  R   + v s+y++ +++ + +++s ++++d e + +  ++ +  y++
  gi|298675169|ref|YP_003726919.1|  64 IVNLAKLFPEAKIMVSFRKHDKWVTSRYKQYIQDiNCSTLSfKEFFDiENNnGYFKKENLNYRK 127
                                       66799*************9733344446665443133444444666655443444444444444 PP

>> Sulfotransfer_1  Sulfotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   2.8   7.1e-05      0.32       8     197 ..       7     166 ..       3     176 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 7.1e-05
                                       ESTTSSHHHHHHHHHHHHTTTCC..HHHTSSGHCT-HHHSCBTTHECCTSGCCGTTECCCHHHTTTEEHHHHHHHST CS
                   Sulfotransfer_1   8 typKSGTtwlqellslitsegdf..ekaeepalfnardrspfLelydlyfpnslkppdhlrsyshvaekvvrlrale 82 
                                       ++pK+GTt+lq  ++ + +  ++   + +e+ l    +++  ++  + y +         ++y   + k+v+l++l 
  gi|298675169|ref|YP_003726919.1|   7 GLPKTGTTFLQVEIFPKWNGIKYlgGRKKEITL----KELVEIDDNQTYLIS--------KEYLAGEPKIVNLAKL- 70 
                                       667777777776555555555554322233333....223334442222211........3344455666666666. PP

                                       SS.EEEE...GGGS.CHHHHTT-EEEEEE--HHHHHHHHHHHHHHBTTSTTT-S.-HHHHHHHHHT.THSTTC..-H CS
                   Sulfotransfer_1  83 sprllktHlplkllpkslldsnlKiiylvRnpkdvavSryhfsrslkklkepet.pfeeffdlfle.grvvcg..sy 155
                                                           + +Ki++  R     + Sry +   +++ +  +t +f+effd  ++ g    +  +y
  gi|298675169|ref|YP_003726919.1|  71 -------------------FPEAKIMVSFRKHDKWVTSRYKQY--IQDIN-CSTlSFKEFFDIENNnGYFKKEnlNY 125
                                       ...................899*******************99..44433.4445899***9877543333333379 PP

                                       HHHHHHHHHHTTTTTEEEEEHHHHHHHHHHHHHHHHHHTT-- CS
                   Sulfotransfer_1 156 fdhvkswlklrkkgnvlflrYEdlkkdpakeikkiaeFlGip 197
                                       ++ +k+  ++++++ + fl+ E+l+ ++++++k +  F+G  
  gi|298675169|ref|YP_003726919.1| 126 RKKIKTIEESFNQKPFVFLQ-EELTDNLDGVLKDMEYFMGGR 166
                                       *******************9.******************976 PP

>> Sulfotransfer_4  Sulfotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.086   3.8e+02       3      15 ..       4      16 ..       3      19 .. 0.86
   2 ?   10.7   0.0   7.6e-05      0.34      83     114 ..      66      98 ..      63     125 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.086
                   Sulfotransfer_4  3 iglGlpRtGTkSl 15
                                      i++Glp+tGT+ l
  gi|298675169|ref|YP_003726919.1|  4 IHIGLPKTGTTFL 16
                                      789*******865 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 7.6e-05
                   Sulfotransfer_4  83 elleayPdakvIlteRdpekWlks.mkktllal 114
                                        l++ +P+ak+ +  R+ +kW++s +k++++ +
  gi|298675169|ref|YP_003726919.1|  66 NLAKLFPEAKIMVSFRKHDKWVTSrYKQYIQDI 98 
                                       6899******************99344555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1915.60
//
Query:       gi|298675170|ref|YP_003726920.1|  [L=828]
Description: oligosaccharyl transferase subunit STT3 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-27   96.3   5.0      1e-27   96.3   5.0    2.0  2  AglB_L1          Archaeal glycosylation protein B long periph
      3e-25   89.1  26.6      3e-25   89.1  26.6    2.2  2  STT3             Oligosaccharyl transferase STT3 subunit
  ------ inclusion threshold ------
       0.27   11.7   1.0         14    6.2   0.1    3.6  3  DUF4179          Domain of unknown function (DUF4179)
        0.6   10.8   4.9         29    5.4   1.0    4.3  3  NADH-u_ox-rdase  NADH-ubiquinone oxidoreductase complex I, 21


Domain annotation for each model (and alignments):
>> AglB_L1  Archaeal glycosylation protein B long peripheral domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       1.4   6.4e+03      26      43 ..     533     550 ..     526     551 .. 0.81
   2 !   96.3   5.0   2.2e-31     1e-27       1      92 []     736     825 ..     736     825 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.4
                                       -EEEEEEEEE.-BTTEEE CS
                           AglB_L1  26 rtftYrqeaeadedGefe 43 
                                       +  +Y+++ e  edG++ 
  gi|298675170|ref|YP_003726920.1| 533 PGLDYYESYEIPEDGSYD 550
                                       5578999999*****995 PP

  == domain 2  score: 96.3 bits;  conditional E-value: 2.2e-31
                                       -EEEEEEBSSSSEEEEEEEEE-TTS-EEEEEEEEE.-BTTEEEEEE---SS......-SSSSEESS-EEEEETTEEE CS
                           AglB_L1   1 GAtitGsaeagatvtasveletnqgrtftYrqeaeadedGefeltvPYstegeedgetnssveaagpYevtagnvta 77 
                                       GA+++G+a+++++vt+sv+++t+qgrtf+Y+q+++  +dG++++tvPYsteg  +get++++ +++pY+++++nvt+
  gi|298675170|ref|YP_003726920.1| 736 GAKVQGTAPEDTKVTISVPIRTSQGRTFEYSQTTT--SDGTYSFTVPYSTEGPIQGETQFDTMPTEPYTISYNNVTE 810
                                       9********************************95..9*************************************** PP

                                       EE---HHHHHHT-EE CS
                           AglB_L1  78 eveVpEeaVlsgetv 92 
                                       +v+V+E++Vl+g+tv
  gi|298675170|ref|YP_003726920.1| 811 QVSVTERDVLDGNTV 825
                                       ************998 PP

>> STT3  Oligosaccharyl transferase STT3 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.1  26.6   6.7e-29     3e-25      20     377 ..      38     446 ..      16     453 .. 0.79
   2 ?    1.2   0.1     0.031   1.4e+02     463     478 ..     557     572 ..     549     575 .. 0.83

  Alignments for each domain:
  == domain 1  score: 89.1 bits;  conditional E-value: 6.7e-29
                                       CCCCCCT--S--SSCHHHHHHHCCCHHHT-C.....CCHHSSEETTSSTTT-EEESTTCCHCCC.CHHHHHHCCHHC CS
                              STT3  20 lFtdedglsylsefDpYYnyRltenllnnGfpGdvvikkknwfdhsqyyPpGsrvdygplivlLamlasaiinhsld 96 
                                       +F  e+++     +Dp+Y +R +en+l+n       ++   wfd ++ +P G    + pl  ++ ++++  i    d
  gi|298675170|ref|YP_003726920.1|  38 VFISENFVRF-GGNDPWYHLRNVENILHN-------FPDMLWFDAYTQFPNGTEQVFAPLFDMI-LAFILWIIGLGD 105
                                       5777777765.789***************.......8***********************9999.555555555555 PP

                                       ...HHHHHHHHCCHHHHHHHHCHHHHHHHHHHS-CCCHHHHHHHCCC-CC.CCCTTSTT--STCCCCHHHHHHHHHH CS
                              STT3  97 ...vsirevclwlpallgsLlaIpiyflvrelksdiaGllAAlllaiaPg.YlsrtvaGfyDtdmfeivlllfvlff 169
                                            i     + p++lg L++Ip+yf  + l + + Gll+A+l+aiaPg +lsr++ Gf+D+++ e +++ +v  +
  gi|298675170|ref|YP_003726920.1| 106 psqSLIHTFSAYYPTILGALVVIPTYFAGKWLYDRRVGLLSAILVAIAPGqFLSRSMIGFNDHHIAETLFSTIVAAL 182
                                       8854555666799**************************************************************99 PP

                                       HHHHHHCCS..................TTCHHHHHHHHHHHHHHTTSCCGGHHHHCCHHHHHHHHHCTTT..S-CCH CS
                              STT3 170 flkaiktks..................nkislaviaaliiflivlaWggyailiyallllfilalLiigr..felkl 226
                                       ++ ai +                    + i+++  +++++ l+ l+W g   ++  ++ ++i +  ii      +  
  gi|298675170|ref|YP_003726920.1| 183 LIIAIVKARqhnisfenlknknfsefkQAIPYFIFTGIALGLYTLSWKGA-LFFSFIIGVYITIQHIIDHlhGRSTD 258
                                       99999888889****************9*********************8.99999999999888888773433444 PP

                                       HHHH...HHHHHHHHHH..CCCCCCCTTCHHH....STTTCHHCCCCHHHHHHHHCCCHHC..CCCCCHHCC..... CS
                              STT3 227 kiav...tfsviiaflviaiivllflgfqvva....vseiigalgifgllqlvafgsvvvlvaelkfyqfis..... 291
                                       ++a+   t++ +++++v   i   + g++++      ++i++  +  g ++ +  +++ + ++  ++  f       
  gi|298675170|ref|YP_003726920.1| 259 YLAIggiTIFFVTLIMV--LITPELGGSKSLNikglLGGILAFPILTGISIALKNKDLKRYYYPFAVAAFFIagigl 333
                                       55654444444444444..5555566666665655445555555556666666677777778888887777789999 PP

                                       ..CHHTT.HHHHTT--GGGHHHHHHHHHHHHC...................CCCCCTS---.....--TTHHHHHHH CS
                              STT3 292 ..lfqpgilsevlgligevvtalavlglialw...................lgilyslldl.....eyaklkikiii 342
                                         lf p+ +  v+ ++g  + + ++l +   +                   +  l s+l l     +  k + +   
  gi|298675170|ref|YP_003726920.1| 334 arLFSPSAYQLVTNVGGYFMRTGGALTIAEASpllnmggqfsfaplwfnfgTLALISFLALaflayKSTKENTPERT 410
                                       99999998888888876666555555544444668999999999*****9955566666556667788999999*** PP

                                       HHS---S--CCHHHCCSSST.TTTCCCHHHCHHCCH CS
                              STT3 343 lvsvwlpvgllaltkglrfl.iftvPlgiifvglll 377
                                       ++ +w ++ + a+++  rf+  ++v++++ ++++  
  gi|298675170|ref|YP_003726920.1| 411 FLIIWSIMVIWAMLQQNRFAyYYSVNASLLSAFIGI 446
                                       ********************99*****995555443 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.031
                                       HHHHHHHHHHHHHHHH CS
                              STT3 463 vvitwwdyghilavea 478
                                        v++wwdygh + v+ 
  gi|298675170|ref|YP_003726920.1| 557 GVMSWWDYGHWIEVIG 572
                                       69********998875 PP

>> DUF4179  Domain of unknown function (DUF4179)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.29   1.3e+03       8      19 ..     176     187 ..     140     223 .. 0.60
   2 ?    6.2   0.1    0.0031        14       3      46 ..     315     356 ..     312     365 .. 0.80
   3 ?    0.1   0.0      0.26   1.2e+03      10      31 ..     486     507 ..     479     523 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.29
                                       XXXXXXXXXXXX CS
                           DUF4179   8 kvaaaaaalvll 19 
                                       ++++aa +++++
  gi|298675170|ref|YP_003726920.1| 176 STIVAALLIIAI 187
                                       344444444444 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0031
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.--SS-HHHHT- CS
                           DUF4179   3 krrikkvaaaaaalvllllssrllspalAsalnpvigslfekls 46 
                                       kr ++ +a+aa  ++ + + +rl sp+  + + + +g++f  ++
  gi|298675170|ref|YP_003726920.1| 315 KRYYYPFAVAAFFIAGI-GLARLFSPSAYQLV-TNVGGYFMRTG 356
                                       45555677777777777.***********999.99999997665 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.26
                                       XXXXXXXXXXXXXXXXXXXXXX CS
                           DUF4179  10 aaaaaalvllllssrllspalA 31 
                                        ++a ++v+l+l++ ++++++ 
  gi|298675170|ref|YP_003726920.1| 486 HIIAFVIVILVLIVPTANETMN 507
                                       4566666666567777777665 PP

>> NADH-u_ox-rdase  NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.14   6.4e+02      55      70 ..      13      28 ..       3      32 .. 0.82
   2 ?    5.4   1.0    0.0066        29      21      64 ..     255     297 ..     251     404 .. 0.84
   3 ?   -4.0   0.0         4   1.8e+04      20      31 ..     559     570 ..     556     572 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.14
                   NADH-u_ox-rdase 55 tlagligflggfllay 70
                                       l+++ig++++fl+a+
  gi|298675170|ref|YP_003726920.1| 13 SLSYFIGVIASFLVAF 28
                                      689*********9986 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0066
                   NADH-u_ox-rdase  21 rpsDYvkaaaitaafplallaleklsPsvagka.mtlagligflg 64 
                                       r +DY+++ +it++f  ++++l  ++P  +g++ + + gl+g + 
  gi|298675170|ref|YP_003726920.1| 255 RSTDYLAIGGITIFFVTLIMVL--ITPELGGSKsLNIKGLLGGIL 297
                                       7899999999999777777776..578887766777777777654 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 4
                   NADH-u_ox-rdase  20 frpsDYvkaaai 31 
                                       + + DY++++ +
  gi|298675170|ref|YP_003726920.1| 559 MSWWDYGHWIEV 570
                                       6788*****965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (828 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1004  (0.0559987); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.44
# Mc/sec: 5650.35
//
Query:       gi|298675171|ref|YP_003726921.1|  [L=103]
Description: DNA polymerase beta domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.1e-13   48.9   0.5      7e-13   48.7   0.5    1.1  1  NTP_transf_2  Nucleotidyltransferase domain
    2.6e-10   40.3   0.2    3.3e-10   39.9   0.2    1.1  1  Polbeta       Polymerase beta, Nucleotidyltransferase


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.5   7.8e-17     7e-13       3      82 ..      19      93 ..      17     103 .] 0.87

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 7.8e-17
                                      HHHHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECCC CS
                      NTP_transf_2  3 klleelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekled 81
                                      ++l +lk+++p++ + +fGSy+r++ +++SD D+l+ ++++        +l++ a  + +l+  l ++vdlv +++l++
  gi|298675171|ref|YP_003726921.1| 19 RILPDLKKRYPIKYLGIFGSYVRDEQTPDSDFDVLIDFNKP-------ISLLDFAGLELELSDTLSVKVDLVSKTSLKS 90
                                      89999************************************.......778*********************8888884 PP

                                      ..C CS
                      NTP_transf_2 82 ..p 82
                                         
  gi|298675171|ref|YP_003726921.1| 91 iiG 93
                                      332 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.2   3.7e-14   3.3e-10       7      82 ..      24      98 ..      15     102 .. 0.88

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 3.7e-14
                                      HHHHHHHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEEEETTTS-HHHHHHHHH CS
                           Polbeta  7 lekekeielaylFGSrakgkareeSDiDlavllkekldleeelelaaelediklgkkvDlvdlneapplllyeilk 82
                                      l+k+  i+ + +FGS+++++++++SD+D+ + +++  +l + + l+ el+d  l+ kvDlv   + ++ + ++i+ 
  gi|298675171|ref|YP_003726921.1| 24 LKKRYPIKYLGIFGSYVRDEQTPDSDFDVLIDFNKPISLLDFAGLELELSDT-LSVKVDLVSKTSLKSIIGKRIMD 98
                                      566669**********************************************.99******988877777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 795.44
//
Query:       gi|298675172|ref|YP_003726922.1|  [L=112]
Description: hypothetical protein Metev_1259 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-13   50.9   0.2    1.7e-13   50.5   0.2    1.1  1  DUF86     Protein of unknown function DUF86


Domain annotation for each model (and alignments):
>> DUF86  Protein of unknown function DUF86
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   0.2   9.4e-18   1.7e-13       1     118 [.      12     106 ..      12     107 .. 0.95

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 9.4e-18
                                       HHHHHHHHCCHH...TSTSCCGSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----SSCHHHHHHHTTSS-HHHHH CS
                             DUF86   1 ikealeklkefteeldeeeflsdeleydavernlqvigEaaidiakhlakklgikkpgdyifeilaekgviaeepee 77 
                                       i++a+e  ++ft+++++++f++de++++ave +l +igE    i ++                      +++++p++
  gi|298675172|ref|YP_003726922.1|  12 ILKAMENSQDFTADYTFNDFKEDEKTQYAVEWALKMIGEMSRIITEE----------------------TKSKYPDI 66 
                                       57889999***************************************......................******** PP

                                       HHHHHHCCHHHHHT-CCCTTHHHHHHHHHHTCHHHHHHHHH CS
                             DUF86  78 pwrkmiglRNrLvHgYlgidpeivwsiikenlpdleefles 118
                                       pw+++  l ++L  +Y + d+  +w+++++++p l +  ++
  gi|298675172|ref|YP_003726922.1|  67 PWNELENLGDILT-NYHKTDLHLIWNTVQKDIPPLIPEFRR 106
                                       ************7.7999****************9987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 775.44
//
Query:       gi|298675173|ref|YP_003726923.1|  [L=438]
Description: HNH endonuclease [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-69  232.4   3.1    4.3e-69  231.8   3.1    1.3  1  RRXRR     RRXRR protein
    8.6e-14   51.1   0.4    1.7e-13   50.2   0.4    1.5  1  HNH_5     HNH endonuclease
    6.2e-12   45.3   0.0    1.6e-11   43.9   0.0    1.7  1  HNH_4     HNH endonuclease
    4.1e-11   42.9   1.7    4.1e-11   42.9   1.7    2.1  2  HNH       HNH endonuclease
     0.0065   16.1   0.3      0.065   12.9   0.2    2.3  2  SH3_2     Variant SH3 domain


Domain annotation for each model (and alignments):
>> RRXRR  RRXRR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.8   3.1   1.2e-72   4.3e-69       1     174 []       2     175 ..       2     175 .. 0.98

  Alignments for each domain:
  == domain 1  score: 231.8 bits;  conditional E-value: 1.2e-72
                             RRXRR   1 VfVldkegkplmPtkpkrarklLkqgkAkvvrrkpftiqLkeesseesvqpvelklDpGskvtGiavvsek.kvllk 76 
                                       VfVl+k++k l+P++p++ar+lLk +kA++++++pfti+Lke +s++  ++++lk+D Gsk+tG+a+ +++ +v++ 
  gi|298675173|ref|YP_003726923.1|   2 VFVLNKNKKFLTPCHPAKARILLKARKATIHKKYPFTIRLKELKSDDIKDDFRLKIDYGSKHTGLAILKNNkDVIWL 78 
                                       9**********************************************99******************965549**** PP

                             RRXRR  77 aelelrgkdikkkleeRrelRraRRsrktryrqaRfdnRkkkegwLapslqhrvqthlrvvkrlakllpitkivvel 153
                                       a++++r+ dikkkl++Rr++Rr+RRs+++ryr++RfdnRkk++gwL+pslq+rv+++ ++v++l+kl+pi++i++e 
  gi|298675173|ref|YP_003726923.1|  79 AQIHHRT-DIKKKLDDRRSFRRRRRSKNLRYRKPRFDNRKKPKGWLPPSLQSRVDNIQTWVRKLMKLIPINSISYEN 154
                                       ******9.********************************************************************* PP

                             RRXRR 154 vkfDiqklenpeisgaeyqqG 174
                                       +kfD+q ++npei+g+eyqqG
  gi|298675173|ref|YP_003726923.1| 155 IKFDTQLMQNPEIKGVEYQQG 175
                                       ********************9 PP

>> HNH_5  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.4   4.7e-17   1.7e-13       1      51 [.     194     242 ..     194     245 .. 0.93

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 4.7e-17
                             HNH_5   1 CiyCgkeiaekelseeHIiPeslGGkltisnlvtlCkkCNqkkgqkvdaal 51 
                                       C+yC+k+  + +l+ eHI+P+s+GG+  +snl+ +C +CNq+k + + +++
  gi|298675173|ref|YP_003726923.1| 194 CAYCDKQ--NVQLEVEHIVPRSRGGSDRVSNLTIACHDCNQRKSNLTAEEF 242
                                       *******..888*******************************98887776 PP

>> HNH_4  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   4.4e-15   1.6e-11      17      53 ..     202     238 ..     194     240 .. 0.90

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 4.4e-15
                                       ..SEEEESSTTTT---BSGGGEEEES-GGGGTSSSSS CS
                             HNH_4  17 keydiDHilPrsrskdDsvsNkVLvlrdaNqeKsnrt 53 
                                        +++++Hi+Prsr+  D vsN++++++d+Nq Ksn t
  gi|298675173|ref|YP_003726923.1| 202 VQLEVEHIVPRSRGGSDRVSNLTIACHDCNQRKSNLT 238
                                       479********************************87 PP

>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       1.2   4.4e+03      15      26 ..      80      91 ..      75      96 .. 0.76
   2 !   42.9   1.7   1.1e-14   4.1e-11       1      46 [.     194     236 ..     194     237 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.2
                               HNH 15 evdHiipisqgg 26
                                      +++H   i+++ 
  gi|298675173|ref|YP_003726923.1| 80 QIHHRTDIKKKL 91
                                      799999998754 PP

  == domain 2  score: 42.9 bits;  conditional E-value: 1.1e-14
                               HNH   1 CeyCgrkfhksealevdHiipisqggaddieNlqllCksCHnkkhd 46 
                                       C yC+++     +lev Hi+p+s+gg+d  +Nl+ +C +C+++k++
  gi|298675173|ref|YP_003726923.1| 194 CAYCDKQN---VQLEVEHIVPRSRGGSDRVSNLTIACHDCNQRKSN 236
                                       9******6...679******************************87 PP

>> SH3_2  Variant SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.15   5.3e+02      10      27 ..     309     326 ..     304     343 .. 0.73
   2 !   12.9   0.2   1.8e-05     0.065      17      51 ..     356     390 ..     338     392 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.15
                                       SCGCCB--B-TTEEEEEE CS
                             SH3_2  10 gedkseLsfkkGdvikvl 27 
                                        + ++eL+fk + v+++ 
  gi|298675173|ref|YP_003726923.1| 309 ESTPDELRFKTNSVLHIH 326
                                       356777****99999986 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 1.8e-05
                                       -B-TTEEEEEE..EEEECTTEEEEEE.CCCEEEEEG CS
                             SH3_2  17 sfkkGdvikvlslgskdsdgwwegev.gGrvGlfPs 51 
                                        f+ Gd+ik++ + + +  g w+g+v  + +G+f +
  gi|298675173|ref|YP_003726923.1| 356 GFQSGDIIKAI-VENGKYKGTWKGAVtCRSKGYFDI 390
                                       69*********.555555577*****89*****966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 3181.42
//
Query:       gi|298675174|ref|YP_003726924.1|  [L=526]
Description: phosphoenolpyruvate carboxylase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   2.5e-125  418.8   0.3   2.9e-125  418.6   0.3    1.0  1  PEPcase_2   Phosphoenolpyruvate carboxylase
    1.8e-07   29.7   0.0      3e-07   28.9   0.0    1.3  1  PEPcase     Phosphoenolpyruvate carboxylase
     0.0039   17.2   0.2        0.1   12.6   0.0    2.5  2  PLC-beta_C  PLC-beta C terminal


Domain annotation for each model (and alignments):
>> PEPcase_2  Phosphoenolpyruvate carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  418.6   0.3  4.8e-129  2.9e-125       2     494 .]       8     526 .]       7     526 .] 0.94

  Alignments for each domain:
  == domain 1  score: 418.6 bits;  conditional E-value: 4.8e-129
                                       -SEEEE--ST-.......SS--B-TTTHHHHHHHHHSS----EEEEE-SSB---TTHHHHHHHHHHC..TT--TTTS CS
                         PEPcase_2   2 prtmsTQHPDnakvPefaeeevisgedEveEAykalselgvdEvMwDfEGKevdehvvrkllseyeeffkekvlGed 78 
                                       p++m+TQHPD       + +++is+++E++EA++a++++g+dE+M D+EGK +++h+  +++s++ +  ++ ++G+d
  gi|298675174|ref|YP_003726924.1|   8 PKVMCTQHPD-------SVSKYISTKEEINEALEAVVKFGCDEYMPDYEGKTTPYHQNVQIVSKFID-ETDIIPGKD 76 
                                       99********.......79**********************************************99.899****** PP

                                       SEEEEE---TTTS-HHHHHHHHHHHHHHHHH.HHHHH.SS-S-SEEEESS--SHHHHHHHHHHHHHHHH........ CS
                         PEPcase_2  79 vfltlRvPnpkvEkaerkvlaetlesipnsydlaekfeetkpifevilPmttsaeelievakyyekvvagkeelela 155
                                       vf+t+R  ++  E+  r+++  +++ ++n   + ++  ++++i e ++Pmt++ +e+++ ++ +++v +        
  gi|298675174|ref|YP_003726924.1|  77 VFITPRATSALHENRFRQLMVMMSIAEANYN-AYQYS-KSQAITEFVHPMTSNIQEIVAAQQHMQDVSE-------- 143
                                       ********************99999999877.44444.8****************************99........ PP

                                       .HHHHH-SS---TTSSEEEEEE-SHHHHHTHHHHHHHHHHHT......--SEEEEEEESHHHHHHH-HHHHHHHHHH CS
                         PEPcase_2 156 dlkvkelvgelkpesievIPLiEdkesllnideiveeyvkek......klkelRvflarSDpAlnyGlisavllvkv 226
                                        l+ ke++ +++  + ++IPL+Ed++ lln+ +i++e++k+       +++  Rvf+++SD+Al++G++++ l++k+
  gi|298675174|ref|YP_003726924.1| 144 -LAKKEFNFKME--TPRIIPLLEDVQGLLNAGKIINELIKANqdlldiDENRYRVFIGKSDSALSFGHVASNLSCKY 217
                                       .78888876665..7899*********************5544567669999************************* PP

                                       HHHHHHHHHHHHT-EEEEEEE-BSSGGGT---TTGHHHHHHHTTT-SEEEE-HHHHHTTHHHHHHHHHHHHHHGGG- CS
                         PEPcase_2 227 AlselykleeelgvkiyPilGvGslpfRGhlspenveevleeYagvkTfTvQSafkYdyeeeevkeairkineaevk 303
                                       A+sel +l+ ++g +i  ilG+GslpfRGh+s +n++++ eeY+g+ T+T+QSa++Y++ e+++++ ++  +++  k
  gi|298675174|ref|YP_003726924.1| 218 AISELNQLGMDTGTDIGIILGAGSLPFRGHMSLKNADNFFEEYRGIDTITLQSALRYNHAESDAEKLVNIAKSELSK 294
                                       *************************************************************************999* PP

                                       ------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS---S-B----------EEE--H............. CS
                         PEPcase_2 304 kprelseeeeelllevieklseaYqekiekladvinevaklipkrRaRklhiglfgYsReieev............. 367
                                       ++r++++ e+e ++++i ++  +Y++ i+++   in++a+l+p++R+R+ + g  gY+R++ ++             
  gi|298675174|ref|YP_003726924.1| 295 TARIFNSSEKEEIINIIGIFGARYNKSIQQISSSINRIADLLPPQRDRLVRGGGTGYARDVPDItgvscacrsdikk 371
                                       ***************************************************************9************* PP

                                       ...........E---HHHHHHHHHHTT--GGGTTHHHHHHHHHHHH......HHHHHHSTTHHHHHHHHHTT--SST CS
                         PEPcase_2 368 ...........elPRAIsftgalYsiGlPpellgissllelaeeel......evllevykalkedlaeaarylnlek 427
                                                  elPRAI+ftgalYs+G+Ppe++g++++le+  e++      + l+e ++ lk+dl++a  yl+l+ 
  gi|298675174|ref|YP_003726924.1| 372 eledsmpkesmELPRAIKFTGALYSMGIPPEIIGTGTALEKVREKMgedvhdRLLSEYFPSLKSDLEFAFDYLDLDA 448
                                       **************************************999999999999988999********************* PP

                                       TTTTS-HHHHHHHHHHHHHHHHHTT--HHHHHHH-HHHHHHHHHHHHHHHH..............HHHHHHHHHHHH CS
                         PEPcase_2 428 sklkldeetvkkikedleiveeildlkyeeeeheeltsellkalkekkdee..............lkelilemaklR 490
                                       + + l +  +++i++d++i++e+++l   e++ +  ++ ll+ l+++  ++              +++++++mak+R
  gi|298675174|ref|YP_003726924.1| 449 ASRFLPAPLMEDIQKDVKILSETFGL---EKKCNPSYKMLLDMLQPHMLDAkytgdlmdeeisqlVRSTLIQMAKMR 522
                                       **************************...667777777777777777777777788888888888************ PP

                                       TS-- CS
                         PEPcase_2 491 kflG 494
                                       k+lG
  gi|298675174|ref|YP_003726924.1| 523 KALG 526
                                       ***9 PP

>> PEPcase  Phosphoenolpyruvate carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   5.1e-11     3e-07     359     488 ..     110     240 ..      81     253 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 5.1e-11
                                       -...TTSEEEEEEET--SHHHHHHHHHHHHHTT-..-.......S---EEEEE-SHHHHHHHHHHHHHHHHSHHHHH CS
                           PEPcase 359 eefgkeiietyviSmaeeasdvLevllLakeaglldkaega...aelrvvPLfEtvedLknapevleellslplyre 432
                                       +   +++i+++v  m++++ ++++    ++++  l k+e +   ++ r++PL+E v+ L na ++++el++ +  ++
  gi|298675174|ref|YP_003726924.1| 110 QYSKSQAITEFVHPMTSNIQEIVAAQQHMQDVSELAKKEFNfkmETPRIIPLLEDVQGLLNAGKIINELIKAN--QD 184
                                       44456899999**********999987777666656655554657789*********************9877..56 PP

                                       HTTT...EEEEEE-HHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHT-EEEEEE-SS CS
                           PEPcase 433 lvkksgelqevMlGYSDSnKdaGfltsnWelykaqealvkvaeeagvklrlFHGrG 488
                                       l++  +++  v +G SDS+   G ++sn +   a ++l ++  ++g ++ +  G G
  gi|298675174|ref|YP_003726924.1| 185 LLDIDENRYRVFIGKSDSALSFGHVASNLSCKYAISELNQLGMDTGTDIGIILGAG 240
                                       777777***********************************999998888877776 PP

>> PLC-beta_C  PLC-beta C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   1.7e-05       0.1      10      75 ..      94     158 ..      85     167 .. 0.88
   2 ?    1.8   0.0     0.036   2.1e+02      29      82 ..     273     326 ..     265     334 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.7e-05
                        PLC-beta_C  10 leqeLlelreeqyesikkkkeqhlkeqiqkllelarekqaaelKkLkeisekekKelkKkleakrl 75 
                                       + + ++   e+ y++ ++ k q ++e ++ ++   +e  aa+ ++++++se  kKe   k+e+ r+
  gi|298675174|ref|YP_003726924.1|  94 QLMVMMSIAEANYNAYQYSKSQAITEFVHPMTSNIQEIVAAQ-QHMQDVSELAKKEFNFKMETPRI 158
                                       4555677899****************************9998.68*****************9886 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.036
                        PLC-beta_C  29 keqhlkeqiqkllelarekqaaelKkLkeisekekKelkKkleakrleriqeak 82 
                                       + +h++   +kl ++a++  +   + +  +  +e+ ++  ++ a ++ +iq+ +
  gi|298675174|ref|YP_003726924.1| 273 RYNHAESDAEKLVNIAKSELSKTARIFNSSEKEEIINIIGIFGARYNKSIQQIS 326
                                       5689**************999999999888888888888888888888888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (526 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       849  (0.0473534); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 3431.07
//
Query:       gi|298675175|ref|YP_003726925.1|  [L=49]
Description: hypothetical protein Metev_1263 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-11   42.7   0.0    5.2e-11   42.7   0.0    1.0  1  CGGC      CGGC domain


Domain annotation for each model (and alignments):
>> CGGC  CGGC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.0   2.9e-15   5.2e-11      13      58 ..       1      46 [.       1      49 [] 0.94

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 2.9e-15
                              CGGC 13 vCpgvkClkalkerkgaFeeyeeevelvgfvtCggCpgkkvveklk 58
                                      +Cpg+ ++k +ke+k aFe ++ +++++g+v+CggCpgkk++ +l 
  gi|298675175|ref|YP_003726925.1|  1 MCPGTMDFKIIKEKKFAFEGITGDIDIIGMVSCGGCPGKKAIYRLV 46
                                      6***************************************998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 376.56
//
Query:       gi|298675176|ref|YP_003726926.1|  [L=229]
Description: hypothetical protein Metev_1264 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-68  230.9  25.2    1.4e-68  230.7  25.2    1.0  1  DUF2162          Predicted transporter (DUF2162)
  ------ inclusion threshold ------
      0.017   15.3   2.7      0.017   15.3   2.7    2.8  3  YrvL             Regulatory protein YrvL
        9.7    6.3   7.7        1.6    8.8   0.4    2.6  2  Phage_holin_2_1  Bacteriophage P21 holin S


Domain annotation for each model (and alignments):
>> DUF2162  Predicted transporter (DUF2162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.7  25.2   2.3e-72   1.4e-68       3     222 ..       8     219 ..       6     220 .. 0.99

  Alignments for each domain:
  == domain 1  score: 230.7 bits;  conditional E-value: 2.3e-72
                           DUF2162   3 vlGiLfailifgiKtGlglglsnlsrkklllilllYlllflllalllssldekllesllrygmvlhllmAlllialG 79 
                                       v+GiL++i++fg+KtG+g+g+sn++++++++++++Y+l++l+++  ++++d+++l+s++ +gm+lh+l+Allli++G
  gi|298675176|ref|YP_003726926.1|   8 VIGILTGIFVFGLKTGIGCGFSNIKKQNIIILAGVYFLISLIIGTSMDYIDMSYLQSITDMGMMLHVLVALLLIGAG 84 
                                       89*************************************************************************** PP

                           DUF2162  80 lytlkkwkkskkdvssrtflalvlPCPvCltailfsiillasslglspvevglvlglvflilvlvtyllsrkivklt 156
                                       +yt kkw  +++dvs+++fla++lPCPvClta+++s+++lassl++s++++g+++g+vf+++++v++l++++++k  
  gi|298675176|ref|YP_003726926.1|  85 IYTRKKWF-CGHDVSKHSFLAISLPCPVCLTALFISCTMLASSLDWSGLSIGVLTGFVFFVSIIVSSLTFKRMGK-- 158
                                       ********.**************************************************************8888.. PP

                           DUF2162 157 ktnypiiLGnlmlfiGlyfLlsaliipniaqakaiylspltessieslllvlvlllallllGfllr 222
                                          +p++LG++m+f+G++++l+a+i+p+++++k++ l+p++   +e ++++++l+++l+l Gf+l+
  gi|298675176|ref|YP_003726926.1| 159 ---TPETLGSVMMFLGIFYVLGAMIAPAYMEVKQMDLAPIAA--GEFEIGPYLLFFVLILGGFILN 219
                                       ...**************************************9..8*******************98 PP

>> YrvL  Regulatory protein YrvL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   9.5      0.13   7.6e+02       9      84 ..       5      80 ..       2     107 .. 0.62
   2 ?   15.3   2.7   2.8e-06     0.017       6      57 ..     131     182 ..     127     193 .. 0.90
   3 ?   -2.7   0.3         1   6.1e+03      42      49 ..     206     213 ..     201     221 .. 0.55

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.13
                              YrvL  9 lllvliivfaifflvvvglfkllGieYeSvgslllFfliflvlglllellakillkvlle.lkklskslakllalil 84
                                      +++v+ i  +if+++ ++ +   G++    + +++ ++++++++l+++  +  + +  l+ +  + ++l++l+al+l
  gi|298675176|ref|YP_003726926.1|  5 YIAVIGILTGIFVFGLKTGI-GCGFSNIKKQNIIILAGVYFLISLIIGTSMDYIDMSYLQsITDMGMMLHVLVALLL 80
                                      44555555555555544433.24555555677888888888888888888777766555335555555555555544 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.8e-06
                              YrvL   6 llilllvliivfaifflvvvglfkllGieYeSvgslllFfliflvlglllel 57 
                                       +l +++++ +vf + ++v+  +fk +G + e +gs+++F +if vlg+++ +
  gi|298675176|ref|YP_003726926.1| 131 GLSIGVLTGFVFFVSIIVSSLTFKRMGKTPETLGSVMMFLGIFYVLGAMIAP 182
                                       5678899999*************************************99876 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1
                              YrvL  42 llFflifl 49 
                                       llFf+++l
  gi|298675176|ref|YP_003726926.1| 206 LLFFVLIL 213
                                       34444433 PP

>> Phage_holin_2_1  Bacteriophage P21 holin S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   1.3       0.1   6.1e+02      33      47 ..       7      22 ..       5      36 .. 0.79
   2 ?    8.8   0.4   0.00026       1.6      27      56 ..     124     155 ..     113     159 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.1
                   Phage_holin_2_1 33 saigvlgglv.igllT 47
                                      ++ig+l g++ +gl T
  gi|298675176|ref|YP_003726926.1|  7 AVIGILTGIFvFGLKT 22
                                      6899**9995267777 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00026
                   Phage_holin_2_1  27 lspeeWs..aigvlgglvigllTyltnlYFKr 56 
                                        s+ +Ws   igvl g v+ +  ++++l FKr
  gi|298675176|ref|YP_003726926.1| 124 ASSLDWSglSIGVLTGFVFFVSIIVSSLTFKR 155
                                       58899*95569********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       927  (0.0517039); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1696.95
//
Query:       gi|298675177|ref|YP_003726927.1|  [L=207]
Description: MotA/TolQ/ExbB proton channel [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-11   43.3   1.8    4.3e-11   42.7   1.8    1.4  1  MotA_ExbB       MotA/TolQ/ExbB proton channel family
    0.00015   21.7   0.0    0.00024   21.0   0.0    1.3  1  VIT1            VIT family
  ------ inclusion threshold ------
      0.041   14.2   0.1      0.086   13.2   0.1    1.5  1  HHH_8           Helix-hairpin-helix domain
      0.046   13.8   0.7      0.069   13.3   0.0    1.6  2  Spore_III_AB    Stage III sporulation protein AB (spore_III_A
       0.14   12.1   0.0        0.2   11.6   0.0    1.2  1  HisG            ATP phosphoribosyltransferase
       0.15   12.1   4.5       0.63   10.0   0.6    2.3  2  Colicin_V       Colicin V production protein
       0.16   11.3   3.3        1.4    8.2   1.3    2.0  2  DUF1574         Protein of unknown function (DUF1574)
       0.27   11.5   3.8        6.7    7.0   0.2    2.4  2  DUF3925         Protein of unknown function (DUF3925)
       0.32   11.1   5.2        6.1    7.0   0.1    2.2  2  Fumarate_red_D  Fumarate reductase subunit D
        1.9    8.4   5.7        1.8    8.4   0.8    2.2  2  DUF2975         Protein of unknown function (DUF2975)


Domain annotation for each model (and alignments):
>> MotA_ExbB  MotA/TolQ/ExbB proton channel family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   1.8   2.4e-14   4.3e-11      21     107 ..      96     178 ..      52     194 .. 0.79

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 2.4e-14
                                       HHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSSSGGCTHHHHHHHHHHH CS
                         MotA_ExbB  21 gaepeelrraleealsreeerlekglsilatigslaPllGLlGTVlGlieafqaladagsadlakvapgiaeALiaT 97 
                                       + e++++ + +e+   + e r+ k+l+  ++i+ +aP+lGL+GT++ l  a+  l++    ++ ++a+++ +A+ +T
  gi|298675177|ref|YP_003726927.1|  96 HLENQRIPS-IERISGEYEIRMAKQLEHTKIIAVVAPMLGLMGTLIPLGPALIGLTE---GNIVQLANNLMVAFATT 168
                                       334444443.45555667889999********************************9...5679************* PP

                                       HHHHHHHHHH CS
                         MotA_ExbB  98 alGlvvAipa 107
                                       ++Gl++  + 
  gi|298675177|ref|YP_003726927.1| 169 VVGLFAGSIG 178
                                       *****99444 PP

>> VIT1  VIT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.3e-07   0.00024      50     194 ..      37     188 ..      31     194 .. 0.65

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.3e-07
                              VIT1  50 iGeYlsvkserdlekaerkreeeeleedpe.ege..aeelaeilearglseelaqevaaellknpdalle.lmlree 122
                                       iGe+ls  s+r+   ++++++ +++e++ + ++   a+e  + l++  +  + +++ a++l +++    e +  + e
  gi|298675177|ref|YP_003726927.1|  37 IGEFLSEYSKRSRDVNNLEHTCNHVEDNIKdSAYekAAEALRNLKQNHIVTSFSRDAADHLENQRIPSIErISGEYE 113
                                       8*****99999999999999999998887533312334444445555566666666666666654443331444444 PP

                              VIT1 123 lgpsaseelasplkaAlssalsfliGgliPllpylf.ve.....svglalvvsiavtllalllfGavkalltgsskl 193
                                         + ++  l++    A++  ++ l+G liPl p+l+ ++     +  + l+v++a t++ l+  G ++ +lt+++++
  gi|298675177|ref|YP_003726927.1| 114 IRMAKQ--LEHTKIIAVVAPMLGLMGTLIPLGPALIgLTegnivQLANNLMVAFATTVVGLF-AGSIGHVLTQVRRR 187
                                       444432..223344899999999***********9865557655566677777666666665.68888888876664 PP

                              VIT1 194 v 194
                                       +
  gi|298675177|ref|YP_003726927.1| 188 W 188
                                       4 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   4.8e-05     0.086      15      41 ..      58      84 ..      51     107 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.8e-05
                                      HHHCT--CCCHHHHHHHHCCCCC-SS.- CS
                             HHH_8 15 lelkgedpfrvraYrrAaraiealpe.e 41
                                      + +  ed+ +  aY +Aa+a+++l++  
  gi|298675177|ref|YP_003726927.1| 58 CNHV-EDNIKDSAYEKAAEALRNLKQnH 84
                                      5555.8999**************99753 PP

>> Spore_III_AB  Stage III sporulation protein AB (spore_III_AB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.8e-05     0.069       2      88 ..      24     108 ..      23     125 .. 0.85
   2 ?   -3.7   0.2       6.4   1.2e+04       6      19 ..     161     174 ..     160     176 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.8e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXHHHHHHHHHHHHHHHHHHHHHH.-SS-HHHHHHHHHHCS-TTHHHHHHHHHHHH CS
                      Spore_III_AB   2 ligallillactgiGfalakrlkrrlkeleelkralellegeiry.gatpLpealeklaeksesplseffeevaerl 77 
                                       ++ +l+i+++ ++iG  l+ ++++r +  + l++  + +e  i+  +++   eal++l+   +  + +f +++a++l
  gi|298675177|ref|YP_003726927.1|  24 ILLILFIVASLVLIGEFLS-EYSKRSRDVNNLEHTCNHVEDNIKDsAYEKAAEALRNLK--QNHIVTSFSRDAADHL 97 
                                       5678899999999998775.79*********************98677779*******9..555679999******* PP

                                       H.STSS-HHHH CS
                      Spore_III_AB  78 eekegesfeea 88 
                                       e+++  s+e++
  gi|298675177|ref|YP_003726927.1|  98 ENQRIPSIERI 108
                                       99988887766 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 6.4
                                       XXXXXXXXXXXXXX CS
                      Spore_III_AB   6 llillactgiGfal 19 
                                       l++++a+t +G+ +
  gi|298675177|ref|YP_003726927.1| 161 LMVAFATTVVGLFA 174
                                       68999999999865 PP

>> HisG  ATP phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00011       0.2      52     105 ..      66     119 ..      39     129 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                                       TTSS--SGCGG.TT.-.EEEEES-HHHHHHHHHHTT-EEEEEE-SS-CTHHHHTT CS
                              HisG  52 eesevkslkdlved.kgkriaTsypnlakkyfeekglkveiiklsGsvEaapalg 105
                                       ++s ++++++  ++ k++ i+Ts+ + a++++e++++  +i ++sG  E+ +a +
  gi|298675177|ref|YP_003726927.1|  66 KDSAYEKAAEALRNlKQNHIVTSFSRDAADHLENQRIP-SIERISGEYEIRMAKQ 119
                                       4566666666534468899****************986.7999*****9988765 PP

>> Colicin_V  Colicin V production protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.2     0.031        56      52      75 ..      13      36 ..       2      55 .. 0.60
   2 ?   10.0   0.6   0.00035      0.63       7      52 ..     139     184 ..     124     200 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.031
                         Colicin_V 52 lilspalaaiiaflllfllvlliv 75
                                       ++s+ l+ +i  l+lf+++ l++
  gi|298675177|ref|YP_003726927.1| 13 TFSSALLYPVIILLILFIVASLVL 36
                                      345666666666666666665553 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00035
                         Colicin_V   7 lilllsallGlrrGfvrevlsllgwvvafvvasllypslaellael 52 
                                       li l+ al+Gl  G + ++++ l++++a+ v  l++ s+++ l+++
  gi|298675177|ref|YP_003726927.1| 139 LIPLGPALIGLTEGNIVQLANNLMVAFATTVVGLFAGSIGHVLTQV 184
                                       6778889************************************994 PP

>> DUF1574  Protein of unknown function (DUF1574)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   1.3   0.00078       1.4       7      38 ..      18      49 ..      14      56 .. 0.80
   2 ?    3.9   0.0     0.015        28     217     268 ..      54     105 ..      45     134 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00078
                           DUF1574  7 LlyPlllllllFllDklllleiiatyveksle 38
                                      LlyP+++ll+lF + +l l+  +  +++k   
  gi|298675177|ref|YP_003726927.1| 18 LLYPVIILLILFIVASLVLIGEFLSEYSKRSR 49
                                      99****************99999555555444 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.015
                           DUF1574 217 neaqvekpqekleekairtyneylrsfalsplqleflekilklakeknikvl 268
                                        e++ ++ ++ ++ +a++   e lr+ + + +  +f +++ + ++++ i+++
  gi|298675177|ref|YP_003726927.1|  54 LEHTCNHVEDNIKDSAYEKAAEALRNLKQNHIVTSFSRDAADHLENQRIPSI 105
                                       56778888999**************************************997 PP

>> DUF3925  Protein of unknown function (DUF3925)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.3     0.013        24      10      41 ..      15      45 ..      11      51 .. 0.82
   2 ?    7.0   0.2    0.0037       6.7      40      64 ..     154     178 ..     144     179 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.013
                           DUF3925 10 snrefyfvlymmllfvvGWvldvnGlflskyf 41
                                      s   +y v+ +++lf+v  ++ + G fls+y 
  gi|298675177|ref|YP_003726927.1| 15 SSALLYPVIILLILFIVASLVLI-GEFLSEYS 45
                                      56668999********9988755.99***995 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0037
                           DUF3925  40 yftlagmimlPlvGGivGlfimsvs 64 
                                         +la+ +m+     +vGlf  s++
  gi|298675177|ref|YP_003726927.1| 154 IVQLANNLMVAFATTVVGLFAGSIG 178
                                       578*****************99987 PP

>> Fumarate_red_D  Fumarate reductase subunit D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0034       6.1      20      38 ..      15      33 ..       4      53 .. 0.80
   2 ?    5.2   1.9     0.012        22      20      67 ..     125     170 ..     123     183 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0034
                    Fumarate_red_D 20 vaAlvlpvlililglllpl 38
                                       +Al+ pv+il++ ++++ 
  gi|298675177|ref|YP_003726927.1| 15 SSALLYPVIILLILFIVAS 33
                                      69*********99888765 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.012
                    Fumarate_red_D  20 vaAlvlpvlililglllplGlldsdalsyekvlafaqswigklvllvv 67 
                                       + A+v+p+l l+ g l+plG +    l+  +++++a++ +++++  vv
  gi|298675177|ref|YP_003726927.1| 125 IIAVVAPMLGLM-GTLIPLGPALIG-LTEGNIVQLANNLMVAFATTVV 170
                                       569999988776.*******96655.7778999999999988776554 PP

>> DUF2975  Protein of unknown function (DUF2975)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.4     0.085   1.5e+02      16      38 ..      18      37 ..       4      48 .. 0.49
   2 ?    8.4   0.8     0.001       1.8      57     119 ..     118     183 ..     113     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.085
                           DUF2975 16 lrvpvlllgvlallafvvalvql 38
                                      l +pv++l +l+++a    lv++
  gi|298675177|ref|YP_003726927.1| 18 LLYPVIILLILFIVA---SLVLI 37
                                      333333333333333...33333 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.001
                           DUF2975  57 rrLrriglaliaa.....alllaagivalallaelelapgvvllllgvafaslvigllvlvlaellae 119
                                       + L   + ++++a     + +l+++++al +l e   +  ++  +l+vafa+ v+gl++  + ++l +
  gi|298675177|ref|YP_003726927.1| 118 KQLEHTKIIAVVApmlglMGTLIPLGPALIGLTE--GNIVQLANNLMVAFATTVVGLFAGSIGHVLTQ 183
                                       5666666777777778888889999999999999..8999******************9999988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1529  (0.0852808); expected 358.6 (0.02)
Passed bias filter:                     1022  (0.0570026); expected 358.6 (0.02)
Passed Vit filter:                       111  (0.00619109); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.38
# Mc/sec: 1614.05
//
Query:       gi|298675178|ref|YP_003726928.1|  [L=118]
Description: hypothetical protein Metev_1266 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.7e-35  119.0   0.2      9e-35  118.8   0.2    1.0  1  DUF2149   Uncharacterized conserved protein (DUF2149)
  ------ inclusion threshold ------
       0.12   12.2   0.6       0.44   10.5   0.1    2.0  3  DUF5049   Domain of unknown function (DUF5049)


Domain annotation for each model (and alignments):
>> DUF2149  Uncharacterized conserved protein (DUF2149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.8   0.2     1e-38     9e-35       1      92 []      21     112 ..      21     112 .. 0.99

  Alignments for each domain:
  == domain 1  score: 118.8 bits;  conditional E-value: 1e-38
                           DUF2149   1 lsgvaNLfDvalVlavallvalvsslnlqellsseedvtvvkkpgkekmeiivkegeelkkakesaekasgkGerlG 77 
                                       ++gvaNLfD+a+V++vallvalv+s n+ ell+++edvt+vk+pg+++m+ii k+g+++k  + ++e+++g+Ge lG
  gi|298675178|ref|YP_003726928.1|  21 MTGVANLFDIAMVFSVALLVALVMSHNIPELLNPTEDVTIVKNPGEKNMQIIEKKGQDIKVLNRTDEVGGGTGEALG 97 
                                       89*************************************************************************** PP

                           DUF2149  78 tayrlkdGkliyVPe 92 
                                       tayrl+dG+++yVPe
  gi|298675178|ref|YP_003726928.1|  98 TAYRLSDGRVVYVPE 112
                                       **************8 PP

>> DUF5049  Domain of unknown function (DUF5049)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   4.9e-05      0.44      15      31 ..      22      38 ..      21      43 .. 0.90
   2 ?   -2.5   0.0      0.55   4.9e+03      11      20 ..      60      69 ..      56      73 .. 0.72
   3 ?   -2.5   0.0      0.56     5e+03      39      48 ..     107     116 ..     105     116 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.9e-05
                           DUF5049 15 tGltNMfdvaaVqriAe 31
                                      tG++N+fd+a+V ++A 
  gi|298675178|ref|YP_003726928.1| 22 TGVANLFDIAMVFSVAL 38
                                      9***********99995 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.55
                           DUF5049 11 aiRdtGltNM 20
                                       +++ G+ NM
  gi|298675178|ref|YP_003726928.1| 60 IVKNPGEKNM 69
                                      5677788888 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.56
                           DUF5049  39 vvyleehkke 48 
                                       vvy+ e+k+e
  gi|298675178|ref|YP_003726928.1| 107 VVYVPENKSE 116
                                       8999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 962.03
//
Query:       gi|298675179|ref|YP_003726929.1|  [L=1543]
Description: magnesium chelatase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
          0 1144.3  10.1          0 1143.2   2.1    2.3  3  CobN-Mg_chel  CobN/Magnesium Chelatase
  ------ inclusion threshold ------
      0.054   13.0   1.4        0.1   12.1   1.4    1.3  1  TRM13         Methyltransferase TRM13


Domain annotation for each model (and alignments):
>> CobN-Mg_chel  CobN/Magnesium Chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0   0.00013       1.1       2      47 ..     137     185 ..     136     249 .. 0.71
   2 ! 1143.2   2.1         0         0       2    1087 ..     282    1371 ..     281    1373 .. 0.94
   3 ?   -4.2   0.3      0.27   2.5e+03     563     658 ..    1379    1466 ..    1375    1495 .. 0.45

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.00013
                                       xxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel   2 aYlkeggveNlknllryladkllg...kkeeeveppvelpeegiyhpda 47 
                                       +Y+ +gg+ N+kn+l+++ +k+++   +++ + +++++  ++  y  ++
  gi|298675179|ref|YP_003726929.1| 137 RYWIQGGKTNMKNMLKTMGQKFCEqwvGENITGPEVTHSETNITYILNS 185
                                       8**********************97654444444444555555554333 PP

  == domain 2  score: 1143.2 bits;  conditional E-value: 0
                                        xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx.xxxxxxxxxxx RF
                      CobN-Mg_chel    2 aYlkeggveNlknllryladkllg.kkeeeveppvelpeegiyhpdake.lfesleeylewyk.kakkekaptvg 73  
                                        +Yl +++ +N+++++ry+ ++l +   e ++++p  +p++giyhpda   +fe++++y ewyk + ++e+apt+g
  gi|298675179|ref|YP_003726929.1|  282 EYLYNSSFSNMEHWIRYIGAELEDdYIEYKPSQPPAVPDHGIYHPDAFPrIFENSTTYFEWYKdHGYEESAPTIG 356 
                                        7****************999999987777889**************9655************************* PP

                                        xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel   74 ilfyrahllag.ntavidaliraleerglnvlpvfvssldseaqealeelftkegeekvdalinttsfalvkgpa 147 
                                        i+   +   ++ + ++ d +i++le++g+nv+ ++++     ++e+++ +ft++g++ vd++i+  +f l+ g +
  gi|298675179|ref|YP_003726929.1|  357 IIGGGSLGKNElDYNADDVIIEELESKGCNVIYTTSKV----CEEDVD-YFTNNGSVLVDTIISQKGFYLNYGDQ 426 
                                        **9776655442667778899***********775444....667776.8889999**************87765 PP

                                        xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  148 eeeeeeaeeealkelnvPvlqa.ilssqsreeWeessqGlspldlamsvalpEldGriepvvisfkeeeeeetev 221 
                                        e+       + l+e nvPv++a + +++s +++++s++G++p++la++v++pE+dG++e ++++++ +++++ + 
  gi|298675179|ref|YP_003726929.1|  427 EKG-----VNYLEEYNVPVIKAvFDYYNSPADYNASTHGVNPQSLAFQVTQPEIDGATEYIWVAGRVQDPDNPDK 496 
                                        444.....4568**********999****************************************999999999* PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                      CobN-Mg_chel  222 ekyepipervervadlaarwarLrrkpnaekkvaiilanyppgegrlgnavgLdvpaSlvnlLkalkeeGYdv.e 295 
                                          y++++++v++++d+a +w +L r++n++k + ii++n+  g++++g a++Ld+ +S   lL+++++ GYd+ e
  gi|298675179|ref|YP_003726929.1|  497 YYYKAHDQQVDWLTDRAISWSELGRTDNSDKNISIIYYNHGGGKSNIG-ASYLDIASSFELLLQNMNNTGYDTgE 570 
                                        ************************************************.55**********************65 PP

                                        xxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                      CobN-Mg_chel  296 elpesgdeLiellleggtndpew......eelkvgaaallpaeeYeewfeeLpeelreeveerWgeppge.mvee 363 
                                         +  +++++i+l++e+++   +w      + ++ g+++l+p++eY ew+++Lp+++re+ve+rWgeppg+ mv+ 
  gi|298675179|ref|YP_003726929.1|  571 RDIPNASQFIDLFIESRN-VGSWapgeleKVVESGNVTLVPKDEYMEWYNDLPNSVREDVEDRWGEPPGDiMVY- 643 
                                        55569*******998887.566667666333344***********************************75555. PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  364 eksgekklvipglqlGnvfvgvQPargyeedpsklyhdpdlpPthqYlAfYlWlreefgadavvHvGkHGtlEwl 438 
                                            e+++vip++q+Gnv  ++QP+rg  +d+s++yhd++lpPth+YlA+Y+W++++++ada++H+G+HGt+Ewl
  gi|298675179|ref|YP_003726929.1|  644 ----EDNFVIPAIQMGNVNFVPQPMRGDLSDESTIYHDKELPPTHHYLATYFWINQVYDADAMIHFGTHGTQEWL 714 
                                        ....79********************************************************************* PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  439 PGKqvglseecyPdillgdlPhlYpYivnnpgEGtqAKRRsyAviidHltPpmtraelygelaeLeelideYeea 513 
                                        PGK+vgl +++yP i++ d+P++YpYi++n+gEGtqAKRR++AviidHltPp+ + +lyg+l++L+++i++Ye+a
  gi|298675179|ref|YP_003726929.1|  715 PGKEVGLWKYDYPSIMVSDTPVIYPYIMDNVGEGTQAKRRGNAVIIDHLTPPISSGGLYGNLTQLHDKIHSYETA 789 
                                        **************************************************************************9 PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  514 esldperlkalreqilelveelnldkdlg..leeakeeeeeefeelle.kldgyleelkeaqirdglhilGeape 585 
                                        e+     +++ re+i+el+ +ln+++dlg  ++e k+++++ef+e+++ +++++l++lk+++++ glh++G ape
  gi|298675179|ref|YP_003726929.1|  790 ENG---TKSEYRETIIELYSSLNMEADLGvtSDELKNMNTSEFSEFVNtDIHDHLHKLKNTLMPLGLHTFGVAPE 861 
                                        888...7889999****************887778999********8879************************* PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  586 geqlvdlvvailrleneegesltealaealgldldeleeksekelrtagdalealeeeaeelveelleeeaeeee 660 
                                        ge+lv +v+++l      g+++ e++++ l ++              ++d+  a++e+a +l+++++ +++e ++
  gi|298675179|ref|YP_003726929.1|  862 GEELVYMVKSML------GQDFIEHVMDVLPHQS------------DEEDMEIAADENATKLLNATILNGTEVTK 918 
                                        ************......9*********963322............22233345678999999999999999999 PP

                                        xxxxxxxxxxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  661 aeaeeleeeeeeeee.............eteeEitallraLdGeyippgpsGdptrgraevLPTGrNfysvDpra 722 
                                        a++++l++++++ +e             +t +Ei+++l+a+d+++i+pgp++dp+r+++ +LPTGrNfys+Dpr+
  gi|298675179|ref|YP_003726929.1|  919 AQEDILNTTDTNITEdlntalnyskklqQTGREINQTLKAMDAGFIEPGPGNDPIRNPE-ALPTGRNFYSFDPRK 992 
                                        9999999999988889999999999998888**************************66.*************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  723 iPteaAwevGkklaeellerylqehgeyPekvglslwgtetmrteGediAqiLallGvrPvwdaagrvvdlelip 797 
                                         P ++  e+G  la+++l++y++ehg+yP+kv ++lw++etmr+eG ++Aqi  llGv+Pv+d  gr+v++++ip
  gi|298675179|ref|YP_003726929.1|  993 FPDKETEERGAVLADQMLDKYKSEHGDYPKKVNYVLWSVETMRHEGLMEAQIYSLLGVEPVRDW-GRIVGFDVIP 1066
                                        **************************************************************98.********** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxx RF
                      CobN-Mg_chel  798 leeLgRPRiDVtvriSGffRDafpnlielldkavelvaeldEpeedNfvrkhvleeeaeleeke....eaeerat 868 
                                         e++ +PRiDVtv+ SG++RD+fp +++l+d+av++va+l+E++e+N+vr ++l+ e+el++ +    +a + ++
  gi|298675179|ref|YP_003726929.1| 1067 AENITHPRIDVTVTPSGLYRDTFPYQLKLIDNAVRTVAALNESNETNYVRMNSLKMEEELKDMGynnsTAVNLSR 1141
                                        **************************************************************554322444**** PP

                                        xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  869 yRvFgskpGaYgagvqelies.snWedeedLaeaYlnwssyaYgkgaegeeaeeafearLkrvdvvvqnqdsreh 942 
                                         R+F+++pG+Yg+g+ +++++ ++W++e++La++Y++++s++Yg+++ ge+ e++f+ +L++v+v+ ++ +s+ +
  gi|298675179|ref|YP_003726929.1| 1142 SRIFSEPPGSYGTGLPGAVTAsDTWDSEDELADLYMSRMSNIYGQNNWGENYEDVFRLNLRDVEVAQHSDSSNLY 1216
                                        *********************9***************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  943 dlldsddyyqflGGltaavrslsgkkpeayfgdssnpenpkvrtlkeeiarelrsrvlNPkWiegmmrhGykGaf 1017
                                        +l+d dd+yq+lGG+ +avrsl+g++pe+y++d ++ +np+++tl+e+++ elr+r++NP+Wi+gmm+h+y+Ga+
  gi|298675179|ref|YP_003726929.1| 1217 GLIDNDDFYQYLGGVGLAVRSLTGENPEMYVADFKDADNPQINTLNEAFRTELRARYFNPTWISGMMEHDYAGAR 1291
                                        *************************************************************************** PP

                                        xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxx......xxx RF
                      CobN-Mg_chel 1018 elaatvdnlfgwdata.dvvddwvyeevaetYvlDee...vrefleekNpwAlreiaerLlEaarr......glW 1082
                                        e+ ++ ++++gwda++ ++v+d  ++e+++ Yv+D++   ++ef++++Np+ +++ ++r+lE++r+       +W
  gi|298675179|ref|YP_003726929.1| 1292 EFMKFTEHMWGWDAVSpELVKDSDWNEMYDIYVRDKYdlgMNEFMKSENPYQYQSTTARMLETTRKmgpdgnAYW 1366
                                        ******************************************************************888887899 PP

                                        xxxxx RF
                      CobN-Mg_chel 1083 easee 1087
                                        +as+e
  gi|298675179|ref|YP_003726929.1| 1367 KASDE 1371
                                        99987 PP

  == domain 3  score: -4.2 bits;  conditional E-value: 0.27
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  563 gyleelkeaqirdglhilGeapegeqlvdlvvailrleneegesltealaealgldldeleeksekelrtagdal 637 
                                        +y+  + e+ +++  h+ G++  +e  v+  ++++ ++ e++e +++ + ea g + ++++e       ++++ +
  gi|298675179|ref|YP_003726929.1| 1379 EYVDSVVENGVTCCHHTCGNPTLNE-YVEGQMSVAGISPEKQEAYKKLMDEATGSEKQSTSE-------KETSST 1445
                                        5555555555555666666554333.333333333333344444444444443333322222.......222233 PP

                                        xxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  638 ealeeeaeelveelleeeaee 658 
                                        ++l++ ++e+v++  + ++++
  gi|298675179|ref|YP_003726929.1| 1446 DSLNSVQREMVNSSNTATSNQ 1466
                                        333444444444333332222 PP

>> TRM13  Methyltransferase TRM13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.4   1.2e-05       0.1     137     218 ..    1390    1473 ..    1375    1479 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.2e-05
                             TRM13  137 lCChhvCswkeyvn..keyleelgitkeefqiltkmvSWavsgkrkseaeeedekeekekeekkeeeeseeekks 209 
                                        +CChh+C   ++ +  +  ++  gi+ e+ ++ +k++  a+ ++++s++e+e++++++ ++ ++e  +s+++ +s
  gi|298675179|ref|YP_003726929.1| 1390 TCCHHTCGNPTLNEyvEGQMSVAGISPEKQEAYKKLMDEATGSEKQSTSEKETSSTDSLNSVQREMVNSSNTATS 1464
                                        8******877766665566799********************999888776666666666555555555555555 PP

                             TRM13  210 klsseeree 218 
                                        + ++++ +e
  gi|298675179|ref|YP_003726929.1| 1465 NQTQNSNSE 1473
                                        555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1543 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1398  (0.0779742); expected 358.6 (0.02)
Passed bias filter:                      676  (0.0377043); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.89u 0.32s 00:00:01.21 Elapsed: 00:00:00.45
# Mc/sec: 10206.21
//
Query:       gi|298675180|ref|YP_003726930.1|  [L=1273]
Description: peptidase S8 and S53 subtilisin kexin sedolisin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-50  170.7   8.7    4.3e-50  170.7   8.7    2.8  3  Peptidase_S8  Subtilase family
      2e-13   50.1  47.5    1.1e-07   31.6   6.1    6.4  7  Big_2         Bacterial Ig-like domain (group 2)
  ------ inclusion threshold ------
       0.63   10.0   7.2       0.12   12.3   2.6    2.2  2  Serglycin     Serglycin


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.7   8.7   7.1e-54   4.3e-50       1     298 []     237     525 ..     237     525 .. 0.87
   2 ?   -7.6   6.9         3   1.8e+04     251     251 ..     737     737 ..     613     824 .. 0.53
   3 ?   -3.8   1.5      0.99   5.9e+03     150     182 ..     963     984 ..     868    1039 .. 0.44

  Alignments for each domain:
  == domain 1  score: 170.7 bits;  conditional E-value: 7.1e-54
                                       -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG.GGEETT-SS-TT-SC-SSS....HHHHHHHHHH-B.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegagfngadsettstnwarddngnsieHGthvAGiaaanap 77 
                                       g+g ++av+D+G+d+++    +t++++         +g+ f  +d  ++  ++a+d ng    HGthv G++ +n  
  gi|298675180|ref|YP_003726930.1| 237 GDGQVIAVADSGIDSGADN--ETMHPDL--------NGS-F--KDIINYAGSDAADHNG----HGTHVTGTVTGN-- 294
                                       789**********998776..4444433........333.4..5555666666666666....************.. PP

                                       SSSSSB-SSTTSEEEEEE-SSTTSB-HH..HHHHHHHHHHHHCT-SEEEE-EESCETTCHHCHHHHHHHHHHHH.CC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8  78 eegekngvapgakilsvkvldtsggsmetgteliraieeaaedkvdvinmslgestslpktgrsiealainravnkk 154
                                         g++ g ap+ +i  +++l++++g+ +   +++r ++ea ++ ++++ +s+g  ++l+++g+  +   ++++++++
  gi|298675180|ref|YP_003726930.1| 295 --GSARGAAPKSDIV-FQALGDDDGNLTADINIYRLFSEAYNKSARIHTNSWGFVSELNDYGEHAK--SVDEFMWDH 366
                                       ..*************.66666666677777*********************************999..********* PP

                                       .T-EEEEE--SS-T-HHEEE-TTCEECTTTSTTCEEEEEES...........TTSSB-TT--B-TT.......-EEE CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 155 .gvlvviSaGNngktgsslqagspvgtpstsknvitvgayt...........tegkiapfSsrGpssdgklkpdiva 219
                                        ++l+ ++aGN+g    ++ ++++++ pst+kn +tvga++           + ++ia+fSsrGp+ d ++kpd+va
  gi|298675180|ref|YP_003726930.1| 367 kDMLILFAAGNEG----DTEDNESISRPSTAKNCLTVGATEnnrssmgyssdDVDEIAYFSSRGPTNDSRIKPDVVA 439
                                       *************....5567*******************************9999********************* PP

                                       E-S-CCCCCCCCCHHHTTTHHEEEE-SHHHCHHHHHHHHHHHHHHHTT...--HHH..HHHHHHCCS-EE....... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxx..xxxxxxxxxxxx.....xx RF
                      Peptidase_S8 220 pGgnivstwsrqsnnsaglssyqsmsGTSmAsPnaagaaAlllsalpk...ltpet..vraallntAqdl.....gk 286
                                       pG+ni+st  + ++    + +y++msGTSmA+P++ag a l+++++ +    tp    ++++l+n A d+     g+
  gi|298675180|ref|YP_003726930.1| 440 PGTNILSTKANITS---AENDYTYMSGTSMATPHVAGTASLVRQYYMDnlsVTPSAslIKTTLINGAYDItpvryGD 513
                                       ****7777666663...334599*********************55555664554489*********999*****99 PP

                                       ....SSSSSSTT CS
                                       xxxxxxxxxxxx RF
                      Peptidase_S8 287 adniesfaqGaG 298
                                        ++  ++ qG+G
  gi|298675180|ref|YP_003726930.1| 514 LQTQPNYVQGWG 525
                                       9999*******9 PP

  == domain 2  score: -7.6 bits;  conditional E-value: 3
                                       H CS
                                       x RF
                      Peptidase_S8 251 s 251
                                       +
  gi|298675180|ref|YP_003726930.1| 737 T 737
                                       2 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 0.99
                                       HH.CCT-EEEEE--SS-T-HHEEE-TTCEECTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 150 avnkkgvlvviSaGNngktgsslqagspvgtps 182
                                       + + ++v+v + +           ++ +vgt  
  gi|298675180|ref|YP_003726930.1| 963 FGDGYEVIVNWTS-----------SNLDVGTIN 984
                                       3333333333332...........222222222 PP

>> Big_2  Bacterial Ig-like domain (group 2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.47   2.8e+03      40      53 ..     144     157 ..     140     160 .. 0.86
   2 ?   -3.4   0.7       1.6   9.3e+03      48      62 ..     287     301 ..     281     302 .. 0.63
   3 !   31.6   6.1   1.9e-11   1.1e-07       3      79 .]     663     741 ..     661     741 .. 0.95
   4 !   20.4   3.9   5.9e-08   0.00035       3      78 ..     749     826 ..     747     827 .. 0.87
   5 !    5.7   0.1    0.0022        13      37      72 ..     879     914 ..     868     920 .. 0.85
   6 !   19.0   1.2   1.6e-07   0.00098      36      70 ..     971    1006 ..     935    1015 .. 0.85
   7 ?   -0.9   0.3      0.27   1.6e+03      10      36 ..    1216    1242 ..    1214    1243 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.47
                                       ECC-SSEEEETCCE CS
                             Big_2  40 ssngsvAtVsatGl 53 
                                       +sn+++A+V+ t++
  gi|298675180|ref|YP_003726930.1| 144 ISNSEKASVNVTIN 157
                                       89*******98876 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.6
                                       EETCCEECCCSSEEE CS
                             Big_2  48 VsatGlVtavaaGka 62 
                                       V++t +++++a G+a
  gi|298675180|ref|YP_003726930.1| 287 VTGTVTGNGSARGAA 301
                                       555555577777765 PP

  == domain 3  score: 31.6 bits;  conditional E-value: 1.9e-11
                                       SEEEEEEC-CEEETT-EEEEEEEEESTT-S-..--EEEEECC-SSEEEETCCEECCCSSEEEEEEEEETTTSSEEEE CS
                             Big_2   3 tsvtvsptevtvkkgatqqltvevtpssasd..kkvtwtssngsvAtVsatGlVtavaaGkatitatskdgndkatl 77 
                                        s+++sp+++t+   +t+ + + ++ ++ ++   +v w+s n++v+t+++tG  ta+  G+a+ita ++ ++ ++t+
  gi|298675180|ref|YP_003726930.1| 663 SSIEISPQNPTIYDNQTVLFNADIYDKNGNKinETVYWSSNNTTVGTINSTGYFTANVSGTANITANKDGTSNSTTV 739
                                       689*************************999999999999**************************99999999999 PP

                                       EE CS
                             Big_2  78 tv 79 
                                       tv
  gi|298675180|ref|YP_003726930.1| 740 TV 741
                                       87 PP

  == domain 4  score: 20.4 bits;  conditional E-value: 5.9e-08
                                       SEEEEEEC-CEEETT-EEEEEEEEESTT-S-..--EEEEECC-SSEEEETCCEECCCSSEEEEEEEEETTTSSEEEE CS
                             Big_2   3 tsvtvsptevtvkkgatqqltvevtpssasd..kkvtwtssngsvAtVsatGlVtavaaGkatitatskdgndkatl 77 
                                       t+++v+p  +++   +t+++ + +t +  +     v w++ n+sv+ ++ tG+ t +++G ++ita  +   d + +
  gi|298675180|ref|YP_003726930.1| 749 TNINVTPLDPIIYTNQTLDFDANTTDQYGNEvdVNVNWSVGNDSVGNINDTGTFTPNKTGITNITAKNGSIKDVTNI 825
                                       89*******************9887665555449********************************98887777666 PP

                                       E CS
                             Big_2  78 t 78 
                                       t
  gi|298675180|ref|YP_003726930.1| 826 T 826
                                       6 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.0022
                                       EEEECC-SSEEEE.TCCEECCCSSEEEEEEEEETTTS CS
                             Big_2  37 twtssngsvAtVs.atGlVtavaaGkatitatskdgn 72 
                                       +w+s n++v+t++ +tG    + +G ++i  t  + n
  gi|298675180|ref|YP_003726930.1| 879 EWYSNNTTVGTINqSTGVFEINDTGLTKIYWTNST-N 914
                                       8************9999989999999998877666.5 PP

  == domain 6  score: 19.0 bits;  conditional E-value: 1.6e-07
                                        EEEEECC-SSEEEE.TCCEECCCSSEEEEEEEEETT CS
                             Big_2   36 vtwtssngsvAtVs.atGlVtavaaGkatitatskd 70  
                                        v wtssn +v+t++ +tG  +av +G+++ita  + 
  gi|298675180|ref|YP_003726930.1|  971 VNWTSSNLDVGTINnSTGVFNAVNTGSTNITAKNGS 1006
                                        89************99***************97666 PP

  == domain 7  score: -0.9 bits;  conditional E-value: 0.27
                                        C-CEEETT-EEEEEEEEESTT-S---E CS
                             Big_2   10 tevtvkkgatqqltvevtpssasdkkv 36  
                                        ++++++  +t++    +t++s+++++v
  gi|298675180|ref|YP_003726930.1| 1216 NHTSINDNQTTKTANNTTMQSSGNGDV 1242
                                        7999999************99999887 PP

>> Serglycin  Serglycin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.2       0.9   5.3e+03     106     133 ..      65      92 ..      63      97 .. 0.83
   2 ?   12.3   2.6     2e-05      0.12      47     138 ..     982    1077 ..     966    1086 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.9
                         Serglycin 106 sgsgflteieqeYqpvdendafyynfrp 133
                                       s s+f t+  q Y  v+ + ++  +++ 
  gi|298675180|ref|YP_003726930.1|  65 STSKFYTDSTQKYYIVQFDGIIKQKWKQ 92 
                                       8899***********9999888777665 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 2e-05
                         Serglycin   47 Cidekgpvfdllpdesnrilpprtdpflmeksqnlndvfplsedysgsg.sGsGsGsGsgs.gsgflteieqeYq 119 
                                         i++   vf+ ++  s +i+     +  + ++  ++d +  s d s sg sGsG G+G g  g+++ +  e+  q
  gi|298675180|ref|YP_003726930.1|  982 TINNSTGVFNAVNTGSTNITAKNGSINNTFTIDVVKDEVESSTDSSSSGsSGSGGGAGGGNtGEEYENIKEELVQ 1056
                                        577788899999999999999888888888888888899999998777635788877765415556554333333 PP

                         Serglycin  120 p..vdendafyynfrplkrnl 138 
                                           v+  +++ y+fr++++++
  gi|298675180|ref|YP_003726930.1| 1057 QeyVNYGEQVSYEFRTKENKI 1077
                                        334888889999999977655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1156  (0.0644765); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.75u 0.28s 00:00:01.03 Elapsed: 00:00:00.44
# Mc/sec: 8647.75
//
Query:       gi|298675181|ref|YP_003726931.1|  [L=45]
Description: hypothetical protein Metev_1269 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 354.86
//
Query:       gi|298675182|ref|YP_003726932.1|  [L=171]
Description: hypothetical protein Metev_1270 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-11   44.1   2.8    4.2e-11   43.6   2.8    1.4  1  Pilin_N   Archaeal Type IV pilin, N-terminal


Domain annotation for each model (and alignments):
>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   2.8   2.3e-15   4.2e-11       1      39 [.      12      50 ..      12     111 .. 0.81

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 2.3e-15
                           Pilin_N  1 eAVSpViGviLmvaitvIlaAviaafvlglasneekapq 39
                                      e+V pV+G+iLmvaitvI+aAvi+a+v+ + s+ ++ p+
  gi|298675182|ref|YP_003726932.1| 12 EGVAPVVGIILMVAITVIAAAVIGASVFDITSKLKEPPE 50
                                      69****************************655555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1246.03
//
Query:       gi|298675183|ref|YP_003726933.1|  [L=272]
Description: metal dependent hydrolase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-12   47.0   0.2    3.9e-12   46.6   0.2    1.4  1  Lactamase_B    Metallo-beta-lactamase superfamily
    5.5e-05   22.8   0.1    8.4e-05   22.2   0.1    1.3  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.014   15.3   0.0      0.039   13.8   0.0    1.7  2  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.2   6.5e-16   3.9e-12       5      68 ..      15      75 ..      13     193 .. 0.91

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 6.5e-16
                                      SSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHH CS
                       Lactamase_B  5 pvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveat 68
                                      p+ s++ie+ +  iL+DtG+s+ +   a   ++ g+++ d+d+++++H+HlDH++g   l++ +
  gi|298675183|ref|YP_003726933.1| 15 PGLSFYIEDRNNKILFDTGYSNIFIENA---RKMGIDLQDLDYLVISHGHLDHTWGIVPLIRLY 75
                                      6789***********************9...6************************98887765 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.1   1.4e-08   8.4e-05       2      52 ..      27      73 ..      26     119 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.4e-08
                                      EEEES--TT..HHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC CS
                     Lactamase_B_2  2 riLiDagpd..lrqqalralqPvelrdelppidaVllthaHyDHlaglltlre 52
                                       iL+D+g +  + ++ +r++       +l+++d ++++h+H DH+ g+  l +
  gi|298675183|ref|YP_003726933.1| 27 KILFDTGYSniFIEN-ARKM-----GIDLQDLDYLVISHGHLDHTWGIVPLIR 73
                                      69*******977766.6666.....7899****************99988877 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   6.6e-06     0.039       9      50 ..      18      65 ..      16     128 .. 0.86
   2 ?   -1.5   0.0      0.33     2e+03      82     119 ..     213     253 ..     190     263 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.6e-06
                     Lactamase_B_3  9 sflletagarilvDPf......kanlgyeppaeeaDlvlisqaledHa 50
                                      sf +e+++ +il D +      ++  +++++ ++ D ++is+++ dH 
  gi|298675183|ref|YP_003726933.1| 18 SFYIEDRNNKILFDTGysnifiENARKMGIDLQDLDYLVISHGHLDHT 65
                                      899***********886666653355666667***************5 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.33
                     Lactamase_B_3  82 atshdavggs.erge..nngflleqdgltiyhlGhlahels 119
                                        + h + + + + ++  +++  l+ ++   +h  +l+ +++
  gi|298675183|ref|YP_003726933.1| 213 GGFHLQNPSKkQLKGtvEYMMKLNPKETHACHCTDLYSKIE 253
                                       44554443331333312444444446777888877777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2100.71
//
Query:       gi|298675184|ref|YP_003726934.1|  [L=145]
Description: DtxR family iron (metal) dependent repressor [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.8e-23   80.9   0.3      8e-23   80.4   0.3    1.2  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      1e-15   57.5   0.1    3.5e-15   55.8   0.1    1.9  2  Fe_dep_repr_C   Iron dependent repressor, metal binding and d
    3.1e-05   23.8   0.0      5e-05   23.1   0.0    1.3  1  MarR_2          MarR family
    7.3e-05   22.2   0.0    0.00012   21.5   0.0    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
    0.00015   21.6   0.0    0.00025   20.9   0.0    1.3  1  MarR            MarR family
    0.00083   19.8   0.1     0.0018   18.7   0.1    1.6  2  HTH_27          Winged helix DNA-binding domain
     0.0091   15.9   0.1      0.015   15.2   0.1    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.049   13.3   0.0       0.28   10.9   0.0    2.0  2  HrcA_DNA-bdg    Winged helix-turn-helix transcription repress
        0.1   13.0   0.0       0.15   12.4   0.0    1.3  1  Rrf2            Transcriptional regulator
       0.19   11.7   0.0       0.32   11.0   0.0    1.4  1  HTH_Crp_2       Crp-like helix-turn-helix domain
        0.2   11.5   0.0        0.3   10.9   0.0    1.3  1  HTH_IclR        IclR helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.4   0.3   4.9e-26     8e-23       1      59 [.       1      59 [.       1      60 [. 0.98

  Alignments for each domain:
  == domain 1  score: 80.4 bits;  conditional E-value: 4.9e-26
                                      X--HHHHHHHHHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTE CS
                    Fe_dep_repress  1 dLvestEdYLetIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyveyekykg 59
                                      +L++++EdYLe+I+ l e+k++++ kd+a +Ln +p+sV+em+k+L+++Gyv+y ky g
  gi|298675184|ref|YP_003726934.1|  1 MLSSKAEDYLEAILNLTEDKGYARIKDIAVALNRRPPSVTEMVKRLDEMGYVVYRKYEG 59
                                      89*******************************************************99 PP

>> Fe_dep_repr_C  Iron dependent repressor, metal binding and dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.7   2.8e+03      19      30 ..       7      18 ..       2      28 .. 0.58
   2 !   55.8   0.1   2.1e-18   3.5e-15       1      64 [.      63     125 ..      63     141 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.7
                                      HHHHHHHCT--C CS
                     Fe_dep_repr_C 19 erfLvdvlgvdw 30
                                      e++L  +l++ +
  gi|298675184|ref|YP_003726934.1|  7 EDYLEAILNLTE 18
                                      444444444444 PP

  == domain 2  score: 55.8 bits;  conditional E-value: 2.1e-18
                                       -HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHCT-.SB-TT CS
                     Fe_dep_repr_C   1 TekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldellgfpeecPh 64 
                                       TekG+e A  +++rh +l++fL  +++v++++a+++A+ +Eh l+  +i++++++++f ++ P+
  gi|298675184|ref|YP_003726934.1|  63 TEKGKERAHVIKDRHDTLKDFL-MMINVPENIADKDACTMEHELDATTIKNVRNFVDFVNTAPD 125
                                       9*********************.77***********************************9996 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   3.1e-08     5e-05      11      55 ..      13      56 ..       9      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 3.1e-08
                                      HHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2 11 LaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                      +++L    g+  +++++a +l+  +++v+ ++krL + G+v++r+
  gi|298675184|ref|YP_003726934.1| 13 ILNLTEDKGY-ARIKDIAVALNRRPPSVTEMVKRLDEMGYVVYRK 56
                                      5667777777.69****************************9985 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   7.5e-08   0.00012       7      47 ..      12      52 ..       7      53 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 7.5e-08
                            HTH_24  7 kILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      +IL+l ++++   ++++A +l+  p+ v++ +krL e+G++
  gi|298675184|ref|YP_003726934.1| 12 AILNLTEDKGYARIKDIAVALNRRPPSVTEMVKRLDEMGYV 52
                                      7***************************************9 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.6e-07   0.00025      13      47 ..      18      52 ..      12      56 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.6e-07
                                      HHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              MarR 13 yeqgplsvseLakklgvskstvtrvldrLekkGli 47
                                      +++g ++++++a +l+  +++vt++++rL + G++
  gi|298675184|ref|YP_003726934.1| 18 EDKGYARIKDIAVALNRRPPSVTEMVKRLDEMGYV 52
                                      6678899**************************98 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   1.1e-06    0.0018       8      68 .]      13      66 ..      10      66 .. 0.86
   2 ?   -3.1   0.0       7.4   1.2e+04      13      28 ..     102     117 ..      99     122 .. 0.61

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.1e-06
                            HTH_27  8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      +L+l +   + ++++d++ +ln+   ++ +++k+L e+G+v+  ++e       ++lT+kG
  gi|298675184|ref|YP_003726934.1| 13 ILNLTE-DKGYARIKDIAVALNRRPPSVTEMVKRLDEMGYVVYRKYE------GITLTEKG 66
                                      677777.889999****************************655555......88888888 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.4
                            HTH_27  13 rhrrrrkkladlcgrl 28 
                                       +h+++  +++ ++ ++
  gi|298675184|ref|YP_003726934.1| 102 EHELDATTIKNVRNFV 117
                                       5666666666666555 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   9.1e-06     0.015      20      55 ..      20      55 ..       9      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.1e-06
                                      HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                              TrmB 20 lgpatadeiaeelgvprskvYevLrsLedkGlVere 55
                                      +g a++++ia +l++  ++v e++++L ++G+V  +
  gi|298675184|ref|YP_003726934.1| 20 KGYARIKDIAVALNRRPPSVTEMVKRLDEMGYVVYR 55
                                      677899**************************9765 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00017      0.28       1      53 [.       1      52 [.       1      59 [. 0.88
   2 ?    0.2   0.0      0.35   5.8e+02      24      47 ..      64      87 ..      53      94 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00017
                      HrcA_DNA-bdg  1 eLtsvqkeilqaLielyrkkkravKgeeiAevlkrneGtvRNqlqsLkalgLv 53
                                      +L+s  ++ l+a+++l + k+   + ++iA +l+r +  v  +++ L  +g v
  gi|298675184|ref|YP_003726934.1|  1 MLSSKAEDYLEAILNLTEDKGY-ARIKDIAVALNRRPPSVTEMVKRLDEMGYV 52
                                      689999999*******988754.4677********************999987 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.35
                      HrcA_DNA-bdg 24 vKgeeiAevlkrneGtvRNqlqsL 47
                                       Kg+e A+v+k    t++  l+++
  gi|298675184|ref|YP_003726934.1| 64 EKGKERAHVIKDRHDTLKDFLMMI 87
                                      599999999999999988877765 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   9.2e-05      0.15       1      59 [.       1      56 [.       1      69 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.2e-05
                                      X---HHHHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                              Rrf2  1 MklsskteyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvr 59
                                      M lssk e  l a+l L++ ++   +++++ia   n  p+ +  ++++L + g+v  ++
  gi|298675184|ref|YP_003726934.1|  1 M-LSSKAEDYLEAILNLTEDKGY--ARIKDIAVALNRRPPSVTEMVKRLDEMGYVVYRK 56
                                      5.889999999999999988885..7****************************97665 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0002      0.32      25      60 ..      26      63 ..      11      67 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0002
                                      HHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEE.EEES CS
                         HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglis.rgrr.iril 60
                                      +++A  l+ ++ +v+ + ++L + g++  r+++ i+++
  gi|298675184|ref|YP_003726934.1| 26 KDIAVALNRRPPSVTEMVKRLDEMGYVVyRKYEgITLT 63
                                      79**************************6554458876 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00018       0.3      15      50 ..      19      54 ..       8      56 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00018
                                      TBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 15 apqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                        +  +++++A ++   +++v  +++ L e+Gyv +
  gi|298675184|ref|YP_003726934.1| 19 DKGYARIKDIAVALNRRPPSVTEMVKRLDEMGYVVY 54
                                      3333699***************************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 974.64
//
Query:       gi|298675185|ref|YP_003726935.1|  [L=87]
Description: hypothetical protein Metev_1274 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-05   24.9   1.5      2e-05   24.6   1.5    1.2  1  FeoC           FeoC like transcriptional regulator
    8.5e-05   22.3   0.0    0.00012   21.8   0.0    1.2  1  HTH_IclR       IclR helix-turn-helix domain
    0.00069   19.5   0.1     0.0044   17.0   0.1    2.0  1  PadR           Transcriptional regulator PadR-like family
  ------ inclusion threshold ------
      0.012   15.9   0.1      0.017   15.5   0.1    1.2  1  Rrf2           Transcriptional regulator
      0.016   15.4   0.1       0.02   15.1   0.1    1.2  1  YjcQ           YjcQ protein
      0.018   15.3   0.0      0.021   15.1   0.0    1.1  1  DUF2513        Hypothetical protein (DUF2513)
      0.018   15.7   0.1      0.024   15.3   0.1    1.2  1  RPA_C          Replication protein A C terminal
      0.022   14.6   0.0      0.029   14.3   0.0    1.1  1  MarR_2         MarR family
      0.023   14.6   0.1      0.031   14.2   0.1    1.3  1  MarR           MarR family
      0.026   14.6   0.5      0.056   13.5   0.4    1.6  2  Baculo_LEF5    Baculoviridae late expression factor 5
      0.027   14.0   0.0      0.034   13.7   0.0    1.2  1  HTH_24         Winged helix-turn-helix DNA-binding
      0.041   14.0   0.4       0.29   11.3   0.4    2.0  1  HTH_34         Winged helix DNA-binding domain
      0.093   13.1   0.2        1.6    9.1   0.1    2.0  2  ANT            Phage antirepressor protein KilAC domain
      0.099   12.6   0.8       0.13   12.2   0.8    1.2  1  RseC_MucC      Positive regulator of sigma(E), RseC/MucC
       0.18   11.5   5.9       0.61    9.8   0.2    2.3  2  zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain


Domain annotation for each model (and alignments):
>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   1.5   1.6e-08     2e-05      13      69 .]      17      74 ..       3      74 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.6e-08
                              FeoC 13 grvslkeLsrhfkaspealeamLeqwvrkGrvekvaataccsgsCkkCg..gkeeeiYe 69
                                       +  ++ L+++++ ++++l a+ e+++  G +e ++++++c +sC++C   g+e+++Y+
  gi|298675185|ref|YP_003726935.1| 17 SSMTMDMLAKELDLNKSTLLAITEFMEHEGYIETTKTQSFC-SSCSGCSkcGSETKMYR 74
                                      4556788*********************************9.55555554445567775 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   9.7e-08   0.00012       7      50 ..       6      50 ..       2      52 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 9.7e-08
                                      HHHCT-CTTBSS.-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  7 aiLdalaeapqe.ltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      ++L +++ ++   +t   lA++++l+kSt   ++  ++++Gy+e+
  gi|298675185|ref|YP_003726935.1|  6 QVLSQFTNRNTSsMTMDMLAKELDLNKSTLLAITEFMEHEGYIET 50
                                      78999987776659*****************************96 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   3.6e-06    0.0044      26      72 ..      27      82 ..       7      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.6e-06
                                      -CCTTHHHHHHHHHHHHHTTSEEEEEE-S..TS.......SS-EEEEEESHCCCHH CS
                              PadR 26 llelseGslYpaLkrLekeglvesewees..ge.......gpprkyYrlTdaGrre 72
                                      +l+l++++l  + + +e eg++e+++++s  ++       g ++k+YrlT +G++ 
  gi|298675185|ref|YP_003726935.1| 27 ELDLNKSTLLAITEFMEHEGYIETTKTQSfcSScsgcskcGSETKMYRLTLKGKNF 82
                                      478999********************9966422233333389***********976 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.1   1.4e-05     0.017      15      58 ..       9      51 ..       3      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.4e-05
                                      HHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              Rrf2 15 lyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksv 58
                                         +++++++ ++++ +a++ ++++s l  i++ ++++g+++++
  gi|298675185|ref|YP_003726935.1|  9 SQFTNRNTSS-MTMDMLAKELDLNKSTLLAITEFMEHEGYIETT 51
                                      5555555554.******************************997 PP

>> YjcQ  YjcQ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1   1.7e-05      0.02       9      81 ..      10      87 .]       3      87 .] 0.78

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.7e-05
                                      HH........-S---HHHHTS-HHHHHHHHHHHHHHTSEE--EESSS........SEE--SS--EE-HHHHHHHHHHT CS
                              YjcQ  9 ealdegeevdnkelsaekldisesrfndiiemlveegyikGvkvkktkk.....geivisidnvritlkGleyLkeNs 81
                                      +  ++++ +   ++ a++ld+++s   +i e++++egyi+  k ++  +     ++     +  r+tlkG ++ ++ s
  gi|298675185|ref|YP_003726935.1| 10 QFTNRNTSSMTMDMLAKELDLNKSTLLAITEFMEHEGYIETTKTQSFCSscsgcSKCGSETKMYRLTLKGKNFVNNDS 87
                                      555666677777788899**********************99999877666643355667778899******998765 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   1.8e-05     0.021       8      84 ..       5      85 ..       1      86 [. 0.75

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.8e-05
                           DUF2513  8 RdiLltleeletkeeslddeeeklsaidgyskeeiiyhlkllaeagLieaekkkakss........iislvvkrLtweG 78
                                      +++L ++ + +t+ + +d   +   ++ + +k ++    + ++ +g+ie++k+++  s         ++++++rLt +G
  gi|298675185|ref|YP_003726935.1|  5 KQVLSQFTNRNTSSMTMDMLAK---EL-DLNKSTLLAITEFMEHEGYIETTKTQSFCSscsgcskcGSETKMYRLTLKG 79
                                      5555555555555555555322...22.3455577788899***************999*****9999*********** PP

                           DUF2513 79 hdFLds 84
                                        F+ +
  gi|298675185|ref|YP_003726935.1| 80 KNFVNN 85
                                      ***975 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.1     2e-05     0.024      52     100 ..       5      51 ..       1      54 [. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2e-05
                                       HHHHHHHHH.SXSTTTEEHHHHHHHSTSXHHHHHHHHHHHHHTTSEEES CS
                             RPA_C  52 qqvlnlikqspeseeGvhvdeiaqklrlsvndvkqavdeLsneGiiYsT 100
                                       +qvl+ +++  +++  + +d +a++l l+++++  ++++++ eG+i +T
  gi|298675185|ref|YP_003726935.1|   5 KQVLSQFTN--RNTSSMTMDMLAKELDLNKSTLLAITEFMEHEGYIETT 51 
                                       466666666..78999******************************777 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.4e-05     0.029      15      55 ..      12      52 ..       6      55 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.4e-05
                                      HCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2 15 grrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                       +r    +t+  la++l+l ks++  i + ++  G++e+++
  gi|298675185|ref|YP_003726935.1| 12 TNRNTSSMTMDMLAKELDLNKSTLLAITEFMEHEGYIETTK 52
                                      55555579******************************986 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   2.6e-05     0.031      15      51 ..      16      52 ..      11      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.6e-05
                                      STTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR 15 qgplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                        ++++  Lak l ++kst+  ++  +e++G+ie +k
  gi|298675185|ref|YP_003726935.1| 16 TSSMTMDMLAKELDLNKSTLLAITEFMEHEGYIETTK 52
                                      56799999*************************9665 PP

>> Baculo_LEF5  Baculoviridae late expression factor 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.46   5.5e+02       3      27 ..       4      28 ..       2      35 .. 0.80
   2 ?   13.5   0.4   4.7e-05     0.056      74     126 ..      31      83 ..       9      87 .] 0.76

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.46
                       Baculo_LEF5  3 lfkvfkkfrrnndysklidylkenf 27
                                      + +v+++f + n  s  +d l ++ 
  gi|298675185|ref|YP_003726935.1|  4 MKQVLSQFTNRNTSSMTMDMLAKEL 28
                                      6789999999999999999988775 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 4.7e-05
                       Baculo_LEF5  74 aentkndfklytelleliekseiddyicPceliskslleiksykealksknfd 126
                                        + t   +  + e  ++ie ++++ ++  c   sk   e+k y+ +lk knf 
  gi|298675185|ref|YP_003726935.1|  31 NKSTLLAITEFMEHEGYIETTKTQSFCSSCSGCSKCGSETKMYRLTLKGKNFV 83 
                                       34444444455566689**********************************95 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.9e-05     0.034      16      48 .]      17      49 ..       5      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.9e-05
                            HTH_24 16 prisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +++++  LA++l+l +st+++  + +e eG+I+
  gi|298675185|ref|YP_003726935.1| 17 SSMTMDMLAKELDLNKSTLLAITEFMEHEGYIE 49
                                      6788888*************************7 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.4   0.00024      0.29      13      51 ..      17      55 ..       6      86 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00024
                            HTH_34 13 deadfvelkealeatdgnLsvhlkkLekagYievdkefk 51
                                      +++++  l ++l ++++ L + ++ +e  gYie +k+ +
  gi|298675185|ref|YP_003726935.1| 17 SSMTMDMLAKELDLNKSTLLAITEFMEHEGYIETTKTQS 55
                                      5677888999************************99854 PP

>> ANT  Phage antirepressor protein KilAC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1    0.0013       1.6      19      53 ..      14      51 ..       6      57 .. 0.77
   2 ?    2.1   0.0       0.2   2.3e+02      88     103 ..      70      85 ..      59      87 .] 0.83

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0013
                               ANT 19 esdgsititeiAkllgigenrlf...elLrekgilyrq 53
                                       +++s+t+  +Ak+l +++  l    e+++++g++   
  gi|298675185|ref|YP_003726935.1| 14 RNTSSMTMDMLAKELDLNKSTLLaitEFMEHEGYIETT 51
                                      6899************8888875222688888888665 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.2
                               ANT  88 ktqtrvTqkGqeflae 103
                                       +++ r+T kG+ f+ +
  gi|298675185|ref|YP_003726935.1|  70 TKMYRLTLKGKNFVNN 85 
                                       57889******99876 PP

>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.8   0.00011      0.13      13      40 ..      51      75 ..      40      86 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                         RseC_MucC 13 ierksaCgsCaakssCklsaleskekrl 40
                                      ++ +s C+sC+ +s+C   ++e+k  rl
  gi|298675185|ref|YP_003726935.1| 51 TKTQSFCSSCSGCSKC---GSETKMYRL 75
                                      67899******88888...244444444 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   1.2      0.03        36       1       9 [.      52      60 ..      52      62 .. 0.88
   2 ?    9.8   0.2   0.00051      0.61       6      15 ..      63      72 ..      63      74 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.03
                     zf-NADH-PPase  1 rthrFCgrC 9 
                                      +t+ FC+ C
  gi|298675185|ref|YP_003726935.1| 52 KTQSFCSSC 60
                                      5899***** PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00051
                     zf-NADH-PPase  6 CgrCGaptep 15
                                      C++CG++t++
  gi|298675185|ref|YP_003726935.1| 63 CSKCGSETKM 72
                                      ********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1069  (0.0596241); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 632.92
//
Query:       gi|298675186|ref|YP_003726936.1|  [L=155]
Description: hypothetical protein Metev_1275 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1268.50
//
Query:       gi|298675187|ref|YP_003726937.1|  [L=99]
Description: FeoA family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.5e-12   45.3   1.0    9.6e-12   45.0   1.0    1.1  1  FeoA      FeoA domain


Domain annotation for each model (and alignments):
>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   1.0   5.3e-16   9.6e-12       6      73 ..      32      96 ..      28      97 .. 0.93

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 5.3e-16
                                      --TT-EEEEEEE-TT.SSHHHHHHHHT--TT-EEEEEEE-TTS-SEEEEETTEEEEE-HHHHTTEEEE CS
                              FeoA  6 lkeGergeiarisdedpellrrLremGlvpGarievvarapfggplvvrvgdtrvaLgreeAqaIlVe 73
                                      ++ Ge gei+ i   d  l+ r + mG+++ ++++++ ++p +gp+vv v++++++Lg ++A++I Ve
  gi|298675187|ref|YP_003726937.1| 32 MDFGEYGEIVDI---DNSLRGRVAGMGIRVRKTLKMITKQPVKGPVVVVVDESQISLGLDMAEKIKVE 96
                                      5669999****9...578*************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 786.49
//
Query:       gi|298675188|ref|YP_003726938.1|  [L=71]
Description: FeoA family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-12   46.4   0.7    3.7e-12   46.3   0.7    1.0  1  FeoA           FeoA domain
     0.0017   18.2   0.1       0.11   12.4   0.0    2.2  2  DUF1967        Domain of unknown function (DUF1967)
  ------ inclusion threshold ------
       0.07   12.5   0.0       0.07   12.5   0.0    1.2  1  Orn_Arg_deC_N  Pyridoxal-dependent decarboxylase, pyridoxal b


Domain annotation for each model (and alignments):
>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.7   6.2e-16   3.7e-12       1      73 [.       1      69 [.       1      70 [. 0.94

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 6.2e-16
                                      EEGGG--TT-EEEEEEE-TT.SSHHHHHHHHT--TT-EEEEEEE-TTS-SEEEEETTEEEEE-HHHHTTEEEE CS
                              FeoA  1 vpLsdlkeGergeiarisdedpellrrLremGlvpGarievvarapfggplvvrvgdtrvaLgreeAqaIlVe 73
                                      ++Ls++k Ge+++i+ i      ++++Lr  G+ +G +++v++    + p++++vg +++++g ++Aq++ V 
  gi|298675188|ref|YP_003726938.1|  1 MNLSQVKSGETVRIVDIGGG-YGIRNKLRLRGIDEGRTVRVLST---RCPVTIEVGRNTISIGCGMAQKVRVS 69
                                      89***************765.99*******************75...68*********************997 PP

>> DUF1967  Domain of unknown function (DUF1967)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.0   0.0     0.008        48      55      66 ..       6      17 ..       3      18 .. 0.88
   2 !   12.4   0.0   1.9e-05      0.11      44      64 ..      21      41 ..      19      45 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.008
                                      --TT-EEEETTE CS
                           DUF1967 55 akeGdtVrIgdv 66
                                      +k G+tVrI d+
  gi|298675188|ref|YP_003726938.1|  6 VKSGETVRIVDI 17
                                      799******985 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 1.9e-05
                                      TTHHHHHHTTT--TT-EEEET CS
                           DUF1967 44 lGvedaLrkaGakeGdtVrIg 64
                                      +G+ ++Lr +G+ eG tVr+ 
  gi|298675188|ref|YP_003726938.1| 21 YGIRNKLRLRGIDEGRTVRVL 41
                                      69*****************86 PP

>> Orn_Arg_deC_N  Pyridoxal-dependent decarboxylase, pyridoxal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.2e-05      0.07     186     206 ..       6      26 ..       1      63 [. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.2e-05
                                       HHHT---SEEE--S-BS-HCS CS
                     Orn_Arg_deC_N 186 aelGvklkiLdvGGGfgveye 206
                                       ++ G +++i+d+GGG+g++ +
  gi|298675188|ref|YP_003726938.1|   6 VKSGETVRIVDIGGGYGIRNK 26 
                                       578999************977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 547.66
//
Query:       gi|298675189|ref|YP_003726939.1|  [L=250]
Description: ABC-2 type transporter [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-22   79.5  20.3    2.3e-22   79.5  20.3    1.7  2  ABC2_membrane    ABC-2 type transporter
    2.6e-12   46.5  29.9    2.6e-12   46.5  29.9    1.8  2  ABC2_membrane_3  ABC-2 family transporter protein
    1.2e-06   28.0  23.2    1.7e-05   24.3  19.2    2.3  2  ABC2_membrane_2  ABC-2 family transporter protein
    2.9e-06   27.0   9.7    2.9e-06   27.0   9.7    1.3  1  CcmB             CcmB protein


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.5  20.3   5.2e-26   2.3e-22       4     209 ..      13     212 ..      10     213 .. 0.90
   2 ?   -1.0   1.2      0.21   9.5e+02      50      64 ..     222     236 ..     207     246 .. 0.40

  Alignments for each domain:
  == domain 1  score: 79.5 bits;  conditional E-value: 5.2e-26
                     ABC2_membrane   4 kallkreflqrwrdpslgllwrliqplllalvfgtvfgnlgnsedgl.nrpgllffsvlflafsaltsvapvferer 79 
                                       +++  ++++ +++    + ++ li+p++++l f           d    +pg++ ++++f+a s++  +++ +e+++
  gi|298675189|ref|YP_003726939.1|  13 LTVAEKDIRIYYKKAPVI-IFGLIFPFFMFLAFYIGRD-----MDLStLFPGFISMALFFTA-SSVGPLITPWEKQQ 82 
                                       567788888899999888.8899999999888887777.....2333356************.************** PP

                     ABC2_membrane  80 gvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldlsrfflflllllltalaasslgllisalap 156
                                       g++er+l++p+    +++l+ +l+ +++++l++++ ++ +++l+g+ +++++ ++l l+l +l++ slg+l+++ ++
  gi|298675189|ref|YP_003726939.1|  83 GTYERLLSYPV-NINTILLGDILAGAAFGFLISTVAIVASVVLLGIVIEQIMVLILSLILGSLCFASLGVLLASPSS 158
                                       ***********.******************************99****988999******************99776 PP

                     ABC2_membrane 157 sf.edasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsnl 209
                                        +  ++++l+slv +pl++ sG+fipi+ +++  + +++++Plty+v+++ +++
  gi|298675189|ref|YP_003726939.1| 159 QApSNIMMLSSLVRFPLIFISGIFIPIQELEGAGRILSQISPLTYLVDIFNAGF 212
                                       5427999999********************88999*************998876 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.21
                     ABC2_membrane  50 lnrpgllffsvlfla 64 
                                       +n++ l +f++lf+ 
  gi|298675189|ref|YP_003726939.1| 222 INILILSAFTLLFVY 236
                                       222333333333322 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   2.8      0.38   1.7e+03       5      18 ..      31      44 ..      26      54 .. 0.46
   2 !   46.5  29.9   5.9e-16   2.6e-12     162     343 ..      54     238 ..      48     240 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.38
                   ABC2_membrane_3  5 iitlllPiilvlll 18
                                      i+ l++P++++l +
  gi|298675189|ref|YP_003726939.1| 31 IFGLIFPFFMFLAF 44
                                      22222222222222 PP

  == domain 2  score: 46.5 bits;  conditional E-value: 5.9e-16
                   ABC2_membrane_3 162 flvgliliilifitasfiavsi.veEkesrikelqlvsgvsplqywlskilgdflvyllqlllill...lafglgip 234
                                       +l++ ++ +++f+tas++   i   Ek++++ e++l+ +v+  +++l+ il+ ++ ++l++ ++++   +++g  i 
  gi|298675189|ref|YP_003726939.1|  54 TLFPGFISMALFFTASSVGPLItPWEKQQGTYERLLSYPVNINTILLGDILAGAAFGFLISTVAIVasvVLLG--IV 128
                                       56665666666666665554331589************************************99985634999..*9 PP

                   ABC2_membrane_3 235 fgnlglllllfllfglayialgyllsslfkns.etaqilifivilllsgffgglfpledlpsalkwifsiiPffapg 310
                                       ++++++l+l ++l++l++++lg ll s ++++ ++ + l ++v ++l++++g+++p++ l++a ++++ i P++++ 
  gi|298675189|ref|YP_003726939.1| 129 IEQIMVLILSLILGSLCFASLGVLLASPSSQApSNIMMLSSLVRFPLIFISGIFIPIQELEGAGRILSQISPLTYLV 205
                                       *************************999776648888889999999999999999********************** PP

                   ABC2_membrane_3 311 lgllrlitgdplweillsliilalfavvyllla 343
                                       + +    +g++ + + ++++il +f+++++ +a
  gi|298675189|ref|YP_003726939.1| 206 DIFNAGFYGTSVFATSINILILSAFTLLFVYVA 238
                                       ***7777999999999*********99998776 PP

>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.2    0.0014       6.1       1      44 [.      13      55 ..      13      73 .. 0.84
   2 !   24.3  19.2   3.8e-09   1.7e-05      87     286 ..      66     244 ..      48     246 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0014
                   ABC2_membrane_2  1 laiakkEfrdlvrsrrfllltvllplidvalaylkdlgsslqse 44
                                      l++a+k++r   ++  ++++++++p++ ++la++   + +l++ 
  gi|298675189|ref|YP_003726939.1| 13 LTVAEKDIRIYYKKAPVIIFGLIFPFF-MFLAFYIGRDMDLSTL 55
                                      589************************.*****98877776665 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 3.8e-09
                   ABC2_membrane_2  87 viaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaigla.iavallatvllalaiilalgivlaledll 162
                                       + a   g  +   Ek +gT ++lLs+Pv   +illg +++g+a g +   va++a+v+l       lgiv++  +++
  gi|298675189|ref|YP_003726939.1|  66 FTASSVGPLITPWEKQQGTYERLLSYPVNINTILLGDILAGAAFGFLiSTVAIVASVVL-------LGIVIE--QIM 133
                                       44555555555569******************************776666666666555.......565554..444 PP

                   ABC2_membrane_2 163 llvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeindflsllspt 239
                                       + +++s++l+  ++f++lg+ll+s + ++ + + +  +l+ + +i+++++  ++ el+           +ls +sp 
  gi|298675189|ref|YP_003726939.1| 134 V-LILSLILGS-LCFASLGVLLASPSSQAPSNIMMLSSLVRFPLIFISGIFIPIQELEGAGR-------ILSQISPL 201
                                       3.344555555.489*********99955555555556666777888888877777776555.......59999999 PP

                   ABC2_membrane_2 240 sayntllneilagsdlnalgstatnllilllllavllvlgyvlFkrk 286
                                        +   ++n+ + g++    ++t  n+lil + ++ ++  ++ lF ++
  gi|298675189|ref|YP_003726939.1| 202 TYLVDIFNAGFYGTS---VFATSINILILSAFTLLFV-YVASLFHKR 244
                                       999999999999995...4556666666666555544.444666655 PP

>> CcmB  CcmB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   9.7   6.4e-10   2.9e-06       3     167 ..      14     176 ..      12     226 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 6.4e-10
                              CcmB   3 alllrdlrlalRakgelllgllFfllvvtllplavGPdtallsriapgilWvaallaslLsldrlfaadfedGsLel 79 
                                       ++ ++d+r+  ++  ++  gl+F     + l + +G d + ls++ pg + +a+ +++      +   ++++G+ e 
  gi|298675189|ref|YP_003726939.1|  14 TVAEKDIRIYYKKAPVIIFGLIFPFF--MFLAFYIGRDMD-LSTLFPGFISMALFFTASSVGPLITPWEKQQGTYER 87 
                                       6789******************9775..568999**9986.89**********99988766666777899******* PP

                              CcmB  80 lllapvplellvlaKalAhwlltglplvllapllalllnleaaalgllaltLllGtpalsllgavgaAltvgLkrgg 156
                                       ll +pv +++++l+ +lA + +  l  +++     +ll++ ++ +++l+l+L+lG++ ++ lg++ a  + +     
  gi|298675189|ref|YP_003726939.1|  88 LLSYPVNINTILLGDILAGAAFGFLISTVAIVASVVLLGIVIEQIMVLILSLILGSLCFASLGVLLASPSSQAPSNI 164
                                       **********************99999999988999****************************9999888888877 PP

                              CcmB 157 lLlslLv.lPli 167
                                       ++ls Lv +Pli
  gi|298675189|ref|YP_003726939.1| 165 MMLSSLVrFPLI 176
                                       777655438876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       976  (0.0544369); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1877.18
//
Query:       gi|298675190|ref|YP_003726940.1|  [L=306]
Description: ABC transporter-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.8e-32  110.8   0.0    1.2e-31  110.1   0.0    1.4  1  ABC_tran         ABC transporter
    4.8e-13   49.6   0.9    3.8e-07   30.2   0.0    2.4  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    4.3e-07   30.0   0.6      0.012   15.3   0.0    2.4  3  AAA_15           AAA ATPase domain
    0.00048   20.7   5.4     0.0016   19.0   5.4    2.2  1  AAA_23           AAA domain
    0.00084   19.0   0.0     0.0022   17.7   0.0    1.7  1  AAA_29           P-loop containing region of AAA domain
    0.00088   18.8   1.5      0.015   14.7   0.6    2.6  2  SMC_N            RecF/RecN/SMC N terminal domain
     0.0009   19.9   0.4      0.026   15.2   0.0    2.5  2  DUF4162          Domain of unknown function (DUF4162)
     0.0014   19.1   1.2      0.019   15.4   1.2    2.4  1  AAA              ATPase family associated with various cellul
     0.0025   17.7   0.5        1.7    8.5   0.0    2.4  2  NTPase_1         NTPase
  ------ inclusion threshold ------
      0.037   13.6   0.3      0.079   12.5   0.1    1.6  2  AAA_27           AAA domain
      0.069   12.9   0.1       0.15   11.8   0.0    1.7  1  AAA_30           AAA domain
        0.1   12.3   0.0        1.7    8.3   0.0    2.3  2  Thymidylate_kin  Thymidylate kinase
       0.12   11.8   0.0       0.33   10.3   0.0    1.7  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
       0.13   12.6   0.6       0.34   11.2   0.5    2.0  1  AAA_19           AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.1   0.0   9.2e-35   1.2e-31       1     136 [.      19     162 ..      19     163 .. 0.97

  Alignments for each domain:
  == domain 1  score: 110.1 bits;  conditional E-value: 9.2e-35
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       ++n+s+++ +ge  +++G+nGaGK+t+++++ gll+p+ G+il++g d+ + +  s++ +++++p++ ++  +l++r
  gi|298675190|ref|YP_003726940.1|  19 VDNISFEVANGEFFGLLGPNGAGKTTIIRMIVGLLTPNDGSILIQGLDIIK-DVISAKMKLSTVPETGNVYTDLSAR 94 
                                       58**********************************************999.89999******************** PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       en             e  e+ +++l++lgl + +d++v     ++S+G++qrv++a+a++++p++l+lDEpt
  gi|298675190|ref|YP_003726940.1|  95 ENiqlagkfyglskkEIAEKSDELLNELGLFDRRDDPV----INFSKGMRQRVSIACAVINEPDILILDEPT 162
                                       ***********999888899******************....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.5   2.2e-06    0.0028       1      24 [.      31      54 ..      31      89 .. 0.77
   2 !   30.2   0.0     3e-10   3.8e-07     232     299 ..     130     194 ..      90     198 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.2e-06
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllar 24
                                      + +l GpNg+GK+++++ + +l  
  gi|298675190|ref|YP_003726940.1| 31 FFGLLGPNGAGKTTIIRMIVGLLT 54
                                      6789***************99964 PP

  == domain 2  score: 30.2 bits;  conditional E-value: 3e-10
                            AAA_21 232 lparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                        p+ ++S G+++   +  a++  +++ ++l++DEp  gL+ +  r l+  +k+ ++ng+ viltTH+ 
  gi|298675190|ref|YP_003726940.1| 130 DPVINFSKGMRQR--VSIACAVINEP-DILILDEPTEGLDVQSRRLLINKMKQMNENGTTVILTTHNI 194
                                       3455679999997..55666666666.***************************************95 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   9.7e-06     0.012      28      92 ..      34     112 ..      19     137 .. 0.78
   2 !   12.7   0.1   5.9e-05     0.075     322     365 ..     151     193 ..     131     195 .. 0.91
   3 ?   -3.0   0.1       3.6   4.6e+03     250     276 ..     229     255 ..     208     284 .. 0.51

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9.7e-06
                            AAA_15  28 liGkNnsGKSsilealdlFlnnkekkn...............kkvikiekedleifeniseskdikIdvefaek.ek 88 
                                       l G+N++GK++i++++  +l+ + + +               k+++ +  e  +++ + s   +i+++ +f +  +k
  gi|298675190|ref|YP_003726940.1|  34 LLGPNGAGKTTIIRMIVGLLTPN-DGSiliqgldiikdvisaKMKLSTVPETGNVYTDLSARENIQLAGKF-YGlSK 108
                                       78*******************88.33368899999999999999999999999999999999999999999.33222 PP

                            AAA_15  89 akey 92 
                                       +++ 
  gi|298675190|ref|YP_003726940.1| 109 KEIA 112
                                       2222 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 5.9e-05
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                       ++++il+++EP   L  q  + li+++k + +++   vi+tTH+
  gi|298675190|ref|YP_003726940.1| 151 NEPDILILDEPTEGLDVQSRRLLINKMKQMNENGT-TVILTTHN 193
                                       6789**************************99996.9******7 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 3.6
                            AAA_15 250 keidkklaeelkkilkkkidkikkfny 276
                                       + i+  ++ + +++++++++    +ny
  gi|298675190|ref|YP_003726940.1| 229 QSIEISFNRSVTQDFFEPVSVYRIENY 255
                                       333333333333444444444444444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   5.4   1.3e-06    0.0016      14      44 ..      21      54 ..       4     297 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.3e-06
                            AAA_23 14 eidF...skgltlItGpNGaGKTTildAiklaLy 44
                                      +i F   +  ++ + GpNGaGKTTi++ i   L+
  gi|298675190|ref|YP_003726940.1| 21 NISFevaNGEFFGLLGPNGAGKTTIIRMIVGLLT 54
                                      3667778889*****************9988777 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.7e-06    0.0022      16      50 ..      23      57 ..      13      60 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.7e-06
                            AAA_29 16 tieidlkg.atlltGpsGsGKSTllDAiqalLvpak 50
                                      ++e+   g ++ l Gp+G+GK+T++  i  lL+p+ 
  gi|298675190|ref|YP_003726940.1| 23 SFEVAN-GeFFGLLGPNGAGKTTIIRMIVGLLTPND 57
                                      445553.358889********************986 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.6   1.2e-05     0.015      25     205 ..      30     200 ..      12     213 .. 0.71
   2 ?   -1.8   0.0       1.3   1.7e+03     183     214 ..     221     252 ..     218     255 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-05
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisr 101
                                       +f  ++GpNG+GK+ ++  i  +L          ++ s li+  +  + v +a++++    e  +     +++s + 
  gi|298675190|ref|YP_003726940.1|  30 EFFGLLGPNGAGKTTIIRMIVGLLT--------PNDGSILIQGLDIIKDVISAKMKLSTVPETGN---VYTDLSARE 95 
                                       577899***********99954444........56666677766666677777777765444444...355667777 PP

                                       EEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 102 rvkrkgeseykingkevtkkevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLD 172
                                       +++  g+  y + +ke+ +k   ell++ g+         ++S G ++ v++a       ++   + +lDe    LD
  gi|298675190|ref|YP_003726940.1|  96 NIQLAGK-FYGLSKKEIAEK-SDELLNELGLFDRrddpviNFSKGMRQRVSIACA----VINEPDILILDEPTEGLD 166
                                       7777776.566666666544.35677777766666667779****9988877654....456667899********* PP

                                       HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC- CS
                                       xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                             SMC_N 173 eknvkkvaellkekskn.aQfivislreemleka 205
                                        + ++ + + +k+ ++n + +i ++++ e  ++ 
  gi|298675190|ref|YP_003726940.1| 167 VQSRRLLINKMKQMNENgTTVILTTHNIEEANQL 200
                                       ***********99998868888888876655544 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.3
                                       HHHHCTTSEEEEE-SSHHHCCC-SCEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 183 lkeksknaQfivislreemlekadklvgvtkv 214
                                       l ++ +++Q i is+++ ++++  + v v+  
  gi|298675190|ref|YP_003726940.1| 221 LTTTFDKTQSIEISFNRSVTQDFFEPVSVYRI 252
                                       66778899999999999999988888888765 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.21   2.7e+02      28      65 ..     175     214 ..     154     221 .. 0.80
   2 !   15.2   0.0     2e-05     0.026      12      80 ..     228     301 ..     218     302 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.21
                                       ---EEEE-TTS-EEEEE-------------.-.---EEEE CS
                           DUF4162  28 pgveeveeeggelelkledeeaanellkal.t.sgveirs 65 
                                       ++ ++++e+g++++l+  + e an+l +++   ++++i  
  gi|298675190|ref|YP_003726940.1| 175 NKMKQMNENGTTVILTTHNIEEANQLCERVcIiNKGKIAA 214
                                       45788899999999*****9999*9999997568888765 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 2e-05
                                       SSEEEEE..--.-----..---EEEE-TTS-EEEEE--.-----------.----EEEEEEEE---HHHHHHHH CS
                           DUF4162  12 knrieve..ad.aeelleepgveeveeeggelelkled.eeaanellkal.tsgveirsFeeeePsLndIFiek 80 
                                       ++ ie++       +++e  +v  +e+ g++++l  ++ + + ++l k + ++++ei+s++   PsL++ F+ +
  gi|298675190|ref|YP_003726940.1| 228 TQSIEISfnRSvTQDFFEPVSVYRIENYGDKWRLYTSSpDRTIKHLSKIAeNQDLEIVSLRTLGPSLEEAFVSL 301
                                       55666775422345555556699999999********99***********88*******************976 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   1.2   1.5e-05     0.019       3     115 ..      34     197 ..      32     209 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.5e-05
                                       EESSTTSSHHHHHHHHHHHHTHE..EEEEETTTCSSS........................................ CS
                               AAA   3 lyGppGtGKTllakavakelgve..fleisgsellsk........................................ 37 
                                       l Gp G GKT++++ ++  l  +   + i+g +++++                                        
  gi|298675190|ref|YP_003726940.1|  34 LLGPNGAGKTTIIRMIVGLLTPNdgSILIQGLDIIKDvisakmklstvpetgnvytdlsareniqlagkfyglskke 110
                                       78*****************9533334444555554334444444444444455555555555555555555555555 PP

                                       ....................STTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHH CS
                               AAA  38 ....................yvgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLltel 93 
                                                            v + +k +r+ ++ a +   +p il++DE  +    +              L++++
  gi|298675190|ref|YP_003726940.1| 111 iaeksdellnelglfdrrddPVINFSKGMRQRVSIACAVInEPDILILDEPTEGLDVQ----------SRRLLINKM 177
                                       5555888888888777777755555555555555554433467788888866665555..........456788888 PP

                                       HHTTTSSSTEEEEEEESSGGGS CS
                               AAA  94 dgvkkkeskvivigatnrpdkl 115
                                       +++++  + ++vi++t+++++ 
  gi|298675190|ref|YP_003726940.1| 178 KQMNE--NGTTVILTTHNIEEA 197
                                       88887..357888888887665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0013       1.7       4      26 ..      34      56 ..      32      66 .. 0.84
   2 !    7.3   0.1    0.0031         4      89     156 ..     145     216 ..      92     226 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0013
                                      EE--TTSSHHHHHHHHHHHH... CS
                          NTPase_1  4 iTGppGvGKtTlvkkvlellkss 26
                                      + Gp G GKtT+++ ++ ll  +
  gi|298675190|ref|YP_003726940.1| 34 LLGPNGAGKTTIIRMIVGLLTPN 56
                                      569*************9999654 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0031
                                       HHHHH.HHH-EEEE---ST.TGGG-HH.HHHHHHHHHTTTSEEEEE--SS-.-SHHHHHHHT-TT-EEEE-- CS
                          NTPase_1  89 lrkal.seadviviDEiGk.mElkskk.fkeaveevLksekpvlavihrrk.dlalveeirerkdvkvfevt 156
                                       + +a+ +e+d++++DE  + + ++s++ ++++++++ ++++ v+ + h+ +  ++l e++   +++k+  ++
  gi|298675190|ref|YP_003726940.1| 145 IACAViNEPDILILDEPTEgLDVQSRRlLINKMKQMNENGTTVILTTHNIEeANQLCERVCIINKGKIAAID 216
                                       33333499********64338888876268999999999999999999988789999998888888877765 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   6.2e-05     0.079      10      50 ..      12      53 ..       5      54 .. 0.85
   2 ?   -3.2   0.0         4   5.1e+03     122     140 ..     103     121 ..     101     123 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.2e-05
                            AAA_27 10 ryGkftd.rsldfsaeeadlhliyGpNEAGKstalrAisdll 50
                                       +G f    +++f+ ++ ++  ++GpN AGK+t++r i  ll
  gi|298675190|ref|YP_003726940.1| 12 TFGDFVAvDNISFEVANGEFFGLLGPNGAGKTTIIRMIVGLL 53
                                      688886525899***9*******************9988776 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4
                            AAA_27 122 lFgLdherLreGGeallea 140
                                        +gL+++++ e  ++ll++
  gi|298675190|ref|YP_003726940.1| 103 FYGLSKKEIAEKSDELLNE 121
                                       6999999999999999986 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00011      0.15      20      48 ..      31      59 ..      25     190 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                            AAA_30 20 vavltGpAGtGKttalkalreaweaaggr 48
                                      +  l Gp G+GKtt+++ ++ +++ + g+
  gi|298675190|ref|YP_003726940.1| 31 FFGLLGPNGAGKTTIIRMIVGLLTPNDGS 59
                                      56789**************9999877544 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0013       1.7       3      24 ..      36      57 ..      35      63 .. 0.85
   2 ?    1.5   0.0      0.16     2e+02      44     117 ..     172     245 ..     108     253 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0013
                                      ESTTSSHHHHHHHHHHHHHHTT CS
                   Thymidylate_kin  3 GlDGaGKttqaellkerlkeeg 24
                                      G +GaGKtt++++++  l+ + 
  gi|298675190|ref|YP_003726940.1| 36 GPNGAGKTTIIRMIVGLLTPND 57
                                      889***********99998776 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.16
                                       HHHHTCS---HHHHHHHHHHHHHHTTHHHHHHH..HHTT-EEEEES-HHHHHHHHHTTTTTTCHHHHHHGGGTTSE CS
                   Thymidylate_kin  44 elllkeeeleeqteallfaadriehleekikpa..lkqgktvivdRylfSslaYqgakegvdldlvlslnedvllk 117
                                        l++k+++++e      ++ + ie++ ++ ++   +++gk+  +dR    +  +++ ++ +++++ +s+++d++ +
  gi|298675190|ref|YP_003726940.1| 172 LLINKMKQMNENGTTVILTTHNIEEANQLCERVciINKGKIAAIDRPETLTTTFDKTQS-IEISFNRSVTQDFF-E 245
                                       33345556666555555555555666655555422456666666666666666666444.66666666666666.5 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00026      0.33      23      50 ..      30      57 ..       9      81 .. 0.81
   2 ?   -2.7   0.0       2.5   3.3e+03      34      65 ..     210     241 ..     208     249 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00026
                      Mg_chelatase 23 HnlllvGppGsGKtmlakrlpsllppls 50
                                        + l+Gp G+GKt +++ + +ll+p +
  gi|298675190|ref|YP_003726940.1| 30 EFFGLLGPNGAGKTTIIRMIVGLLTPND 57
                                      455689******************9876 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.5
                      Mg_chelatase  34 GKtmlakrlpsllpplseeealevakiasvag 65 
                                       GK   + r ++l +  ++++++e++  +sv++
  gi|298675190|ref|YP_003726940.1| 210 GKIAAIDRPETLTTTFDKTQSIEISFNRSVTQ 241
                                       66666778888888999999999999999987 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.5   0.00027      0.34       8      37 ..      27      56 ..      21     215 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00027
                            AAA_19  8 lkekvllvtaGpGtGKTrvlkhivallvel 37
                                      ++ + + ++++ G GKT+++++iv ll  +
  gi|298675190|ref|YP_003726940.1| 27 ANGEFFGLLGPNGAGKTTIIRMIVGLLTPN 56
                                      56677889***************9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 2185.74
//
Query:       gi|298675191|ref|YP_003726941.1|  [L=67]
Description: hypothetical protein Metev_1281 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00027   22.0   0.1    0.00028   21.9   0.1    1.2  1  DUF5320         Family of unknown function (DUF5320)
      0.009   16.5   0.1      0.013   16.0   0.1    1.3  1  Arg_decarbox_C  Arginine decarboxylase C-terminal helical ext
  ------ inclusion threshold ------
      0.098   11.9   0.3       0.12   11.6   0.3    1.1  1  Closter_coat    Closterovirus coat protein


Domain annotation for each model (and alignments):
>> DUF5320  Family of unknown function (DUF5320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.1   4.8e-08   0.00028      63      99 .]      29      65 ..       2      65 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 4.8e-08
                           DUF5320 63 aaetaeaskeeekelLeeqaeaLeeeleaikkrlkel 99
                                       +  +  +++e++e+Lee+++ L+eel+a+++ l++l
  gi|298675191|ref|YP_003726941.1| 29 HSFRDYLTAKEKQEFLEEYKSQLKEELKAVDEHLQNL 65
                                      4556777999************************986 PP

>> Arg_decarbox_C  Arginine decarboxylase C-terminal helical extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   2.3e-06     0.013      28      47 ..      34      53 ..      25      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.3e-06
                    Arg_decarbox_C 28 rLtpeerqalleeleagLkg 47
                                       Lt++e+q++lee+++ Lk+
  gi|298675191|ref|YP_003726941.1| 34 YLTAKEKQEFLEEYKSQLKE 53
                                      69****************85 PP

>> Closter_coat  Closterovirus coat protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3     2e-05      0.12      11      42 ..      32      63 ..      26      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2e-05
                      Closter_coat 11 asklneeevkellekfkealktklklsdedil 42
                                      ++ l+++e++e+le+ k +lk++lk+ de++ 
  gi|298675191|ref|YP_003726941.1| 32 RDYLTAKEKQEFLEEYKSQLKEELKAVDEHLQ 63
                                      67899***********************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1666  (0.0929221); expected 358.6 (0.02)
Passed bias filter:                      825  (0.0460148); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 508.12
//
Query:       gi|298675192|ref|YP_003726942.1|  [L=121]
Description: HxlR family transcriptional regulator [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-22   79.4   0.1    1.5e-22   79.2   0.1    1.1  1  HxlR            HxlR-like helix-turn-helix
    0.00081   19.4   0.0     0.0012   18.8   0.0    1.2  1  HTH_20          Helix-turn-helix domain
    0.00097   19.1   0.0     0.0016   18.4   0.0    1.4  1  HTH_45          Winged helix-turn-helix
     0.0016   18.4   0.0     0.0024   17.8   0.0    1.2  1  PadR            Transcriptional regulator PadR-like family
     0.0021   18.1   0.0     0.0034   17.5   0.0    1.4  1  DUF2250         Uncharacterized protein conserved in archaea 
      0.009   15.9   0.0      0.014   15.3   0.0    1.2  1  MarR            MarR family
  ------ inclusion threshold ------
      0.032   14.4   0.0      0.058   13.6   0.0    1.4  2  HTH_34          Winged helix DNA-binding domain
      0.052   13.1   0.1       0.11   12.1   0.1    1.6  1  HTH_24          Winged helix-turn-helix DNA-binding
      0.077   12.8   0.0       0.12   12.1   0.0    1.2  1  LexA_DNA_bind   LexA DNA binding domain
       0.11   12.8   3.5        0.2   12.0   3.1    1.6  2  FXa_inhibition  Coagulation Factor Xa inhibitory site
       0.14   12.3   0.0       0.21   11.8   0.0    1.3  1  B-block_TFIIIC  B-block binding subunit of TFIIIC


Domain annotation for each model (and alignments):
>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.2   0.1   9.4e-26   1.5e-22       1      85 [.      33     118 ..      33     121 .] 0.96

  Alignments for each domain:
  == domain 1  score: 79.2 bits;  conditional E-value: 9.4e-26
                                       HHHSTTHHHHHHHHTT.S-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHH CS
                              HxlR   1 liggkWkllilvellk.gkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvl 76 
                                       ++++kW lli+ ++ +  k R++++ ++l +is k+La rL+eLe+ gliere+ +e+Pp+veYslt+ G +l++ +
  gi|298675192|ref|YP_003726942.1|  33 VVSKKWALLIIATIGNnEKIRYTKIMKNLADISPKTLADRLKELENFGLIERETFDEIPPRVEYSLTQDGIELRDSM 109
                                       689***********996778********************************************************* PP

                                       HHHHHHHHH CS
                              HxlR  77 qelkkwgee 85 
                                         l++w+++
  gi|298675192|ref|YP_003726942.1| 110 IPLMEWASK 118
                                       ******987 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   7.4e-07    0.0012      30      58 ..      57      86 ..      50      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 7.4e-07
                                      HHHHH.TS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20 30 laerl.dlskntlsyHLrvLeeagLvevvr 58
                                      +++ l d+s++tl ++L++Le  gL+e+++
  gi|298675192|ref|YP_003726942.1| 57 IMKNLaDISPKTLADRLKELENFGLIERET 86
                                      6777779********************987 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   9.6e-07    0.0016      17      69 ..      49     109 ..      39     117 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 9.6e-07
                            HTH_45  17 egeakkTkimyk.anLsykllnkYLdmLvekgli.......kkskekYvlTekGlellekl 69 
                                       +++ + Tkim++ a++s k+l   L+ L + gli            +Y+lT+ G el +++
  gi|298675192|ref|YP_003726942.1|  49 NEKIRYTKIMKNlADISPKTLADRLKELENFGLIeretfdeIPPRVEYSLTQDGIELRDSM 109
                                       566778*****978********************888775333789***********9987 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.5e-06    0.0024      22      69 ..      57     102 ..      51     107 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.5e-06
                                       CSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCC CS
                              PadR  22 lsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaG 69 
                                        +++l ++s+ +l + Lk+Le+ gl+e+e  +  e ppr  Y lT++G
  gi|298675192|ref|YP_003726942.1|  57 IMKNLADISPKTLADRLKELENFGLIERETFD--EIPPRVEYSLTQDG 102
                                       56788899999999***************998..59***********9 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.1e-06    0.0034      13      56 ..      43      86 ..      31      95 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.1e-06
                           DUF2250 13 vlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerve 56
                                      +  + ++ +  Y k + +  +i+ +   + lk+Le+ GL+er +
  gi|298675192|ref|YP_003726942.1| 43 IATIGNNEKIRYTKIMKNLADISPKTLADRLKELENFGLIERET 86
                                      33444666788*******************************87 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   8.8e-06     0.014       7      50 ..      41      85 ..      39      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8.8e-06
                                      HHHHHHHHSTTEEHHHHHHHH.TS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  7 viLrilyeqgplsvseLakkl.gvskstvtrvldrLekkGlieRs 50
                                      +i++++ +++ ++ +++ k l  +s+ t+   l++Le  GlieR+
  gi|298675192|ref|YP_003726942.1| 41 LIIATIGNNEKIRYTKIMKNLaDISPKTLADRLKELENFGLIERE 85
                                      78999**********98775438*********************7 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       8.4   1.4e+04      56      65 ..       9      18 ..       4      21 .. 0.67
   2 ?   13.6   0.0   3.6e-05     0.058       5      68 ..      42     105 ..      39     114 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 8.4
                            HTH_34 56 rtllriTpeG 65
                                      +  ++ T++G
  gi|298675192|ref|YP_003726942.1|  9 CKNVNCTQKG 18
                                      5567788888 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 3.6e-05
                            HTH_34   5 vlsyLasvdeadfvel.kealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGrea 68 
                                       ++++   ++++ ++++ k+   ++   L+  lk Le+ g ie++ +f++  pr  +++T++G e 
  gi|298675192|ref|YP_003726942.1|  42 IIATIGNNEKIRYTKImKNLADISPKTLADRLKELENFGLIERE-TFDEIPPRVEYSLTQDGIEL 105
                                       66777778888888763777789*******************87.788999***********875 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   6.7e-05      0.11       8      48 .]      42      83 ..      40      83 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.7e-05
                            HTH_24  8 ILelLqknprisqreLAerl.glSpstvnrrlkrLeeeGlIk 48
                                      I+ ++  n +i ++ + + l ++Sp t+  rlk+Le+ GlI+
  gi|298675192|ref|YP_003726942.1| 42 IIATIGNNEKIRYTKIMKNLaDISPKTLADRLKELENFGLIE 83
                                      6666666666666666666547***************99996 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.5e-05      0.12      30      59 ..      56      85 ..      53      88 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.5e-05
                                      HHHHHHTS-.HHHHHHHHHHHHHTTSEE-G CS
                     LexA_DNA_bind 30 eiaralglkSpsaveehLkaLerKGyierd 59
                                       i+++l   Sp++ + +Lk Le+ G+ier+
  gi|298675192|ref|YP_003726942.1| 56 KIMKNLADISPKTLADRLKELENFGLIERE 85
                                      588888889*******************96 PP

>> FXa_inhibition  Coagulation Factor Xa inhibitory site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   3.1   0.00012       0.2       3      26 ..       4      28 ..       3      35 .. 0.90
   2 ?   -2.4   0.0       3.8   6.2e+03      26      33 ..      95     102 ..      93     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                                      TCCCCSSSE.EEEETTCEEEE--TT CS
                    FXa_inhibition  3 dnNggCshl.ClptpggytCsCpeg 26
                                      +nN  C    C++  g   C Cp g
  gi|298675192|ref|YP_003726942.1|  4 ENNAHCKNVnCTQKGGNEVCLCPVG 28
                                      79****9866*************88 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.8
                                       TEEE-TTS CS
                    FXa_inhibition  26 gykLaeDg 33 
                                       +y+L +Dg
  gi|298675192|ref|YP_003726942.1|  95 EYSLTQDG 102
                                       79999997 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00013      0.21      26      53 ..      60      87 ..      52     108 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                    B-block_TFIIIC 26 keskqdprslfyrlksLekkgLIvkqsi 53
                                      ++ +++p+ l  rlk Le+ gLI++ + 
  gi|298675192|ref|YP_003726942.1| 60 NLADISPKTLADRLKELENFGLIERETF 87
                                      6778********************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 885.60
//
Query:       gi|298675193|ref|YP_003726943.1|  [L=132]
Description: transcriptional regulator TrmB [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00065   19.5   0.0    0.00098   19.0   0.0    1.3  1  TrmB      Sugar-specific transcriptional regulator TrmB
     0.0021   17.9   0.0     0.0029   17.5   0.0    1.2  1  MarR_2    MarR family
     0.0029   17.5   0.1     0.0047   16.8   0.1    1.4  1  MarR      MarR family
     0.0091   15.9   0.0      0.017   15.1   0.0    1.5  1  HTH_36    Helix-turn-helix domain
  ------ inclusion threshold ------
      0.019   14.9   0.0      0.033   14.1   0.0    1.4  1  HTH_11    HTH domain


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   2.7e-07   0.00098       3      64 ..      18      87 ..      15      91 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.7e-07
                                      HCHHHHHCCCHCHHHHHHCC..CHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST......TTEEEE CS
                              TrmB  3 klGLseyEakvYlaLlklgp..atadeiaeelgvprskvYevLrsLedkGlVerekgr......pklYra 64
                                      +l+L+  E k+  + l+++    t d+ia   g++ s+v++++++L   ++ +r++++       ++Y+a
  gi|298675193|ref|YP_003726943.1| 18 ALNLTRSELKIMNKFLENDDtwFTSDDIAVTMGLDLSTVQKAVKKLYTSDVLNRSQKNldnggyVYIYKA 87
                                      689999999999999977653379**********************************999998889988 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0     8e-07    0.0029       2      49 ..      20      67 ..      19      79 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 8e-07
                                      T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTT CS
                            MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaG 49
                                       lt++++ +++    +++  +t  ++a ++gl+ s+v++++k+L    
  gi|298675193|ref|YP_003726943.1| 20 NLTRSELKIMNKFLENDDTWFTSDDIAVTMGLDLSTVQKAVKKLYTSD 67
                                      58889999999988999999***********************97655 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   1.3e-06    0.0047       1      55 [.      21      77 ..      21      78 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.3e-06
                                      --HHHHHHHHHHHHSTTEEHH..HHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTS CS
                              MarR  1 ltltqfviLrilyeqgplsvs..eLakklgvskstvtrvldrLekkGlieRskspeD 55
                                      lt+++++i+ +  e+++   +  ++a  +g++ stv +++++L+  + ++Rs++  D
  gi|298675193|ref|YP_003726943.1| 21 LTRSELKIMNKFLENDDTWFTsdDIAVTMGLDLSTVQKAVKKLYTSDVLNRSQKNLD 77
                                      56677777777666666555555******************************9755 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   4.7e-06     0.017      21      49 ..      35      63 ..      26      67 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.7e-06
                            HTH_36 21 nggcfpsqetlakrlglsknTvsraikeL 49
                                      n   +++ +++a  +gl+ +Tv++a+k+L
  gi|298675193|ref|YP_003726943.1| 35 NDDTWFTSDDIAVTMGLDLSTVQKAVKKL 63
                                      455899**********************9 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   9.2e-06     0.033       3      39 ..      26      63 ..      24      72 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.2e-06
                            HTH_11  3 lqilelLleargp.isgeeLAeeLnvSrrtvrrdIkaL 39
                                      l+i+  +le++++ ++++++A  +++  +tv++ +k+L
  gi|298675193|ref|YP_003726943.1| 26 LKIMNKFLENDDTwFTSDDIAVTMGLDLSTVQKAVKKL 63
                                      78999999****************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1114  (0.062134); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1007.06
//
Query:       gi|298675194|ref|YP_003726944.1|  [L=207]
Description: 4Fe-4S ferredoxin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-12   45.5  11.1      2e-10   40.4   1.9    3.7  5  Fer4_5    4Fe-4S binding domain
    4.1e-10   39.0  17.5    2.2e-05   24.1   2.1    3.7  4  Fer4      4Fe-4S binding domain
    1.8e-08   34.9  14.6     0.0013   19.2   1.8    3.2  3  Fer4_7    4Fe-4S dicluster domain
    2.3e-08   34.1  15.6    5.6e-05   23.2  15.0    3.0  3  Fer4_9    4Fe-4S dicluster domain
      2e-07   31.2  11.4      2e-07   31.2  11.4    2.2  2  Fer4_18   4Fe-4S dicluster domain
    2.5e-07   30.7  19.1    3.1e-06   27.2   4.7    2.8  3  Fer4_21   4Fe-4S dicluster domain
    5.6e-07   29.4  14.4    1.3e-05   25.1   2.7    3.4  4  Fer4_6    4Fe-4S binding domain
    2.2e-06   27.6  21.0    3.8e-05   23.7  17.2    3.2  3  Fer4_10   4Fe-4S dicluster domain
      4e-05   24.1  17.2     0.0099   16.4   6.5    3.0  3  Fer4_17   4Fe-4S dicluster domain
    5.3e-05   24.1  15.9     0.0056   17.6   2.3    3.2  3  Fer4_16   4Fe-4S double cluster binding domain
    5.6e-05   23.0   1.8    5.6e-05   23.0   1.8    3.1  3  Fer4_2    4Fe-4S binding domain
     0.0024   18.4   1.9     0.0024   18.4   1.9    2.8  3  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
     0.0034   18.2  22.8       0.03   15.3   3.0    3.8  3  Fer4_3    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.064   13.7  20.7       0.22   12.0   4.2    2.9  4  Fer4_8    4Fe-4S dicluster domain
       0.56   11.1  13.9        2.2    9.2   3.2    2.5  3  Fer4_22   4Fe-4S dicluster domain
          1   10.1   8.9        2.9    8.7   0.7    2.3  2  Fer4_15   4Fe-4S single cluster domain
        7.2    7.4  27.1       0.96   10.1   4.5    3.7  4  Fer4_4    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4_5  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.3       3.1   3.2e+03       9      18 ..      11      20 ..       5      22 .. 0.51
   2 !   40.4   1.9   1.9e-13     2e-10       2      39 ..      26      63 ..      25      72 .. 0.84
   3 ?   -2.4   0.6       4.6   4.8e+03       9      20 ..      82      93 ..      77      97 .. 0.60
   4 !   17.0   2.1   3.9e-06    0.0041      10      38 ..     123     150 ..     111     156 .. 0.86
   5 ?   -1.8   0.2         3   3.2e+03      24      30 ..     169     175 ..     169     176 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.1
                            Fer4_5  9 flaivlvtll 18
                                       ++iv++++l
  gi|298675194|ref|YP_003726944.1| 11 IVLIVATAGL 20
                                      3445555554 PP

  == domain 2  score: 40.4 bits;  conditional E-value: 1.9e-13
                            Fer4_5  2 allllilflaivlvtllfGRafCgWiCPfGalqellak 39
                                      +++++++++++++++ + GR+fCg+iCP+G+l +++  
  gi|298675194|ref|YP_003726944.1| 26 GYFMVLMLATLMIISPFRGRWFCGNICPRGSLYDFWVG 63
                                      789999999*************************7644 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 4.6
                            Fer4_5  9 flaivlvtllfG 20
                                      ++++v+++++ G
  gi|298675194|ref|YP_003726944.1| 82 VPVFVAMMGFMG 93
                                      446777776643 PP

  == domain 4  score: 17.0 bits;  conditional E-value: 3.9e-06
                            Fer4_5  10 laivlvtllfGRafCgWiCPfGalqella 38 
                                       +a++l  ++  R +C  iCP G++q +++
  gi|298675194|ref|YP_003726944.1| 123 VAVILGVFVSPRTWCT-ICPMGTVQRVIG 150
                                       678888888*******.********9886 PP

  == domain 5  score: -1.8 bits;  conditional E-value: 3
                            Fer4_5  24 CgWiCPf 30 
                                       C+ +CP 
  gi|298675194|ref|YP_003726944.1| 169 CSKVCPM 175
                                       999***6 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.19     2e+02      14      22 ..      48      56 ..      47      58 .. 0.82
   2 ?   -1.9   0.0       3.3   3.5e+03      17      21 ..     139     143 ..     138     145 .. 0.79
   3 !   24.1   2.1   2.1e-08   2.2e-05       2      20 ..     157     175 ..     156     176 .. 0.91
   4 !   21.0   2.5     2e-07   0.00021       7      23 ..     187     203 ..     184     204 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.19
                                      HHHHSTTTE CS
                              Fer4 14 CvevCPvgA 22
                                      C ++CP g 
  gi|298675194|ref|YP_003726944.1| 48 CGNICPRGS 56
                                      999***986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.3
                                       HSTTT CS
                              Fer4  17 vCPvg 21 
                                       +CP g
  gi|298675194|ref|YP_003726944.1| 139 ICPMG 143
                                       7**87 PP

  == domain 3  score: 24.1 bits;  conditional E-value: 2.1e-08
                                       EEETTTSSS-THHHHHSTT CS
                              Fer4   2 videekCigCGaCvevCPv 20 
                                        ++ +kCi C++C +vCP 
  gi|298675194|ref|YP_003726944.1| 157 HVNDDKCISCNKCSKVCPM 175
                                       5899**************5 PP

  == domain 4  score: 21.0 bits;  conditional E-value: 2e-07
                                       TSSS-THHHHHSTTTEE CS
                              Fer4   7 kCigCGaCvevCPvgAI 23 
                                       +Ci+C +Cv+ CP +A+
  gi|298675194|ref|YP_003726944.1| 187 DCIKCERCVDNCPKDAL 203
                                       5**************97 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.38     4e+02       7      17 ..      47      57 ..      44      83 .. 0.82
   2 !   18.0   4.8     3e-06    0.0032      12      50 ..     140     175 ..     135     177 .. 0.70
   3 !   19.2   1.8   1.3e-06    0.0013       2      19 ..     188     205 ..     187     207 .] 0.91

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.38
                            Fer4_7  7 aCvaaCpvkai 17
                                      +C + Cp + +
  gi|298675194|ref|YP_003726944.1| 47 FCGNICPRGSL 57
                                      79999997765 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 3e-06
                            Fer4_7  12 CpvkaieldeeenekgtekveidpekClgCgaCvavCPt 50 
                                       Cp+++++     ++    +++++ +kC++C++C +vCP 
  gi|298675194|ref|YP_003726944.1| 140 CPMGTVQRVIGGDK---YQLHVNDDKCISCNKCSKVCPM 175
                                       55555554443222...3467889**************6 PP

  == domain 3  score: 19.2 bits;  conditional E-value: 1.3e-06
                            Fer4_7   2 CigCgaCvaaCpvkaiel 19 
                                       Ci+C++Cv++Cp +a+++
  gi|298675194|ref|YP_003726944.1| 188 CIKCERCVDNCPKDALNF 205
                                       **************9987 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.98     1e+03      42      49 ..      48      55 ..      45      71 .. 0.66
   2 !   22.1   3.5   1.2e-07   0.00012       9      49 ..     138     176 ..     135     177 .. 0.89
   3 !   23.2  15.0   5.3e-08   5.6e-05       1      50 [.     162     202 ..     162     203 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.98
                            Fer4_9 42 CveaCpkg 49
                                      C ++Cp+g
  gi|298675194|ref|YP_003726944.1| 48 CGNICPRG 55
                                      44555554 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 1.2e-07
                            Fer4_9   9 veaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                       +  Cp+g+v++  ++ k +l+  ++ +Ci+C++C ++Cp +
  gi|298675194|ref|YP_003726944.1| 138 T-ICPMGTVQRVIGGDKYQLHVNDD-KCISCNKCSKVCPMH 176
                                       4.4****************998777.9************86 PP

  == domain 3  score: 23.2 bits;  conditional E-value: 5.3e-08
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                       kC++C++C ++Cp+++ v+  +++          +Ci+C++Cv+ Cpk+a
  gi|298675194|ref|YP_003726944.1| 162 KCISCNKCSKVCPMHLDVKNVSTNP---------DCIKCERCVDNCPKDA 202
                                       7**************9887766554.........5*************97 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.52   5.4e+02       8      22 ..     138     152 ..     134     161 .. 0.74
   2 !   31.2  11.4   1.9e-10     2e-07      56      97 ..     158     200 ..     147     206 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.52
                           Fer4_18   8 yvcPyarvqsvlyde 22 
                                        +cP + vq v+  +
  gi|298675194|ref|YP_003726944.1| 138 TICPMGTVQRVIGGD 152
                                       58*******998654 PP

  == domain 2  score: 31.2 bits;  conditional E-value: 1.9e-10
                           Fer4_18  56 kgagdcidcescvkvcPtgidirk.Glqleciscllcidacdk 97 
                                        ++ +ci+c++c kvcP+++d+++     +ci+c +c+d c k
  gi|298675194|ref|YP_003726944.1| 158 VNDDKCISCNKCSKVCPMHLDVKNvSTNPDCIKCERCVDNCPK 200
                                       45678******************934678************65 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.9     3e+03      46      52 ..      47      53 ..      44      57 .. 0.80
   2 !   27.2   4.7   2.9e-09   3.1e-06      16      53 ..     138     175 ..     135     180 .. 0.90
   3 !   10.9   3.9   0.00037      0.39      39      56 ..     186     202 ..     177     205 .. 0.59

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.9
                           Fer4_21 46 lCssvCP 52
                                       C ++CP
  gi|298675194|ref|YP_003726944.1| 47 FCGNICP 53
                                      5999999 PP

  == domain 2  score: 27.2 bits;  conditional E-value: 2.9e-09
                           Fer4_21  16 iaCedtshqaieidaktvlkvvedeCvGCnlCssvCPv 53 
                                       + C+ +++q + + +k +l+v +d+C+ Cn Cs+vCP+
  gi|298675194|ref|YP_003726944.1| 138 TICPMGTVQRVIGGDKYQLHVNDDKCISCNKCSKVCPM 175
                                       4699999999999999999******************8 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00037
                           Fer4_21  39 deCvGCnlCssvCPvedc 56 
                                        +C+ C+ C++ CP +d+
  gi|298675194|ref|YP_003726944.1| 186 PDCIKCERCVDNCP-KDA 202
                                       45666666666666.344 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       4.4   4.6e+03      17      21 ..      50      54 ..      48      57 .. 0.69
   2 ?   -0.8   0.2       1.8   1.9e+03      17      22 ..     138     143 ..     137     146 .. 0.82
   3 !   25.1   2.7   1.2e-08   1.3e-05       3      21 ..     157     175 ..     156     178 .. 0.93
   4 !   16.8   4.0   4.9e-06    0.0052       9      24 .]     188     203 ..     185     203 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 4.4
                            Fer4_6 17 rvCPe 21
                                      ++CP 
  gi|298675194|ref|YP_003726944.1| 50 NICPR 54
                                      58996 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.8
                            Fer4_6  17 rvCPeg 22 
                                       ++CP+g
  gi|298675194|ref|YP_003726944.1| 138 TICPMG 143
                                       699986 PP

  == domain 3  score: 25.1 bits;  conditional E-value: 1.2e-08
                            Fer4_6   3 eidpdkCigCgdCvrvCPe 21 
                                       ++++dkCi+C++C +vCP+
  gi|298675194|ref|YP_003726944.1| 157 HVNDDKCISCNKCSKVCPM 175
                                       69****************7 PP

  == domain 4  score: 16.8 bits;  conditional E-value: 4.9e-06
                            Fer4_6   9 CigCgdCvrvCPegai 24 
                                       Ci C++Cv++CP +a+
  gi|298675194|ref|YP_003726944.1| 188 CIKCERCVDNCPKDAL 203
                                       ************9986 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.9   3.1e+03      15      21 ..      48      54 ..      47      76 .. 0.72
   2 ?   -1.6   0.0         3   3.1e+03      18      21 ..     139     142 ..     136     154 .. 0.66
   3 !   23.7  17.2   3.6e-08   3.8e-05       3      56 .]     157     199 ..     155     199 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.9
                           Fer4_10 15 CvkaCPa 21
                                      C + CP 
  gi|298675194|ref|YP_003726944.1| 48 CGNICPR 54
                                      6777876 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3
                           Fer4_10  18 aCPa 21 
                                        CP+
  gi|298675194|ref|YP_003726944.1| 139 ICPM 142
                                       5998 PP

  == domain 3  score: 23.7 bits;  conditional E-value: 3.6e-08
                           Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +++dd+Ci C+kC k+CP+             + ++     +C++c+ Cv+ CP
  gi|298675194|ref|YP_003726944.1| 157 HVNDDKCISCNKCSKVCPM-----------HLDVKNVSTNPDCIKCERCVDNCP 199
                                       5799***************...........333333334568***********9 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       2.7   2.8e+03       8      19 ..      48      59 ..      46      76 .. 0.77
   2 !   16.4   6.5   9.4e-06    0.0099      44      61 .]     161     178 ..     136     178 .. 0.84
   3 !   12.2   2.3    0.0002      0.21      45      59 ..     187     201 ..     180     203 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.7
                           Fer4_17  8 ClpeCpsyeayd 19
                                      C + Cp++  yd
  gi|298675194|ref|YP_003726944.1| 48 CGNICPRGSLYD 59
                                      777788877665 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 9.4e-06
                           Fer4_17  44 slCieCgeCerkCPqgld 61 
                                       ++Ci+C++C+++CP++ld
  gi|298675194|ref|YP_003726944.1| 161 DKCISCNKCSKVCPMHLD 178
                                       79**************98 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 0.0002
                           Fer4_17  45 lCieCgeCerkCPqg 59 
                                       +Ci+C++C+  CP++
  gi|298675194|ref|YP_003726944.1| 187 DCIKCERCVDNCPKD 201
                                       799999999999986 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0         3   3.2e+03       8      16 ..      48      56 ..      47      71 .. 0.76
   2 !   14.9   1.0   3.7e-05     0.039       1      14 [.     162     175 ..     151     180 .. 0.78
   3 !   17.6   2.3   5.3e-06    0.0056       2      20 ..     188     206 ..     187     207 .] 0.92

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 3
                           Fer4_16  8 CaevCPtna 16
                                      C ++CP + 
  gi|298675194|ref|YP_003726944.1| 48 CGNICPRGS 56
                                      667777665 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 3.7e-05
                           Fer4_16   1 rCgtCgkCaevCPt 14 
                                       +C++C+kC +vCP 
  gi|298675194|ref|YP_003726944.1| 162 KCISCNKCSKVCPM 175
                                       47777777777774 PP

  == domain 3  score: 17.6 bits;  conditional E-value: 5.3e-06
                           Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                       C++C++C++ CP +a++ +
  gi|298675194|ref|YP_003726944.1| 188 CIKCERCVDNCPKDALNFP 206
                                       ***************9876 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.7       7.7   8.1e+03      16      21 ..     137     141 ..     137     142 .. 0.74
   2 !   23.0   1.8   5.3e-08   5.6e-05       3      21 ..     156     174 ..     154     175 .. 0.93
   3 !   11.9   4.9   0.00018      0.19       6      21 ..     185     199 ..     181     200 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 7.7
                            Fer4_2  16 CvsaCP 21 
                                       C + CP
  gi|298675194|ref|YP_003726944.1| 137 C-TICP 141
                                       6.7888 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 5.3e-08
                            Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                        +v+ d+Ci+C++C ++CP
  gi|298675194|ref|YP_003726944.1| 156 LHVNDDKCISCNKCSKVCP 174
                                       589**************** PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00018
                            Fer4_2   6 dtdrCigCgaCvsaCP 21 
                                       ++d Ci C+ Cv++CP
  gi|298675194|ref|YP_003726944.1| 185 NPD-CIKCERCVDNCP 199
                                       788.***********9 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       4.6   4.9e+03      12      17 ..      48      53 ..      47      55 .. 0.87
   2 !   18.4   1.9   2.2e-06    0.0024       1      21 [.     158     178 ..     158     183 .. 0.89
   3 ?    6.7   4.0      0.01        11       5      18 ..     187     200 ..     184     200 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.6
                           Fer4_13 12 CvelaP 17
                                      C++++P
  gi|298675194|ref|YP_003726944.1| 48 CGNICP 53
                                      99***9 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 2.2e-06
                           Fer4_13   1 VDrdtCiacgaCvelaPdvFe 21 
                                       V+ d+Ci+c++C +++P + +
  gi|298675194|ref|YP_003726944.1| 158 VNDDKCISCNKCSKVCPMHLD 178
                                       788**************9876 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.01
                           Fer4_13   5 tCiacgaCvelaPd 18 
                                        Ci c+ Cv+ +P+
  gi|298675194|ref|YP_003726944.1| 187 DCIKCERCVDNCPK 200
                                       6************5 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.49   5.2e+02       7      14 ..      48      55 ..      46      56 .. 0.87
   2 !   10.4   5.3     0.001       1.1       1      12 [.     163     174 ..     163     176 .. 0.93
   3 !   15.3   3.0   2.8e-05      0.03       1      15 []     188     202 ..     188     202 .. 0.98

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.49
                            Fer4_3  7 CvevCPvg 14
                                      C + CP g
  gi|298675194|ref|YP_003726944.1| 48 CGNICPRG 55
                                      8899**98 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.001
                            Fer4_3   1 CtgCgaCvevCP 12 
                                       C+ C+ C +vCP
  gi|298675194|ref|YP_003726944.1| 163 CISCNKCSKVCP 174
                                       ************ PP

  == domain 3  score: 15.3 bits;  conditional E-value: 2.8e-05
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+ C++Cv+ CP++A
  gi|298675194|ref|YP_003726944.1| 188 CIKCERCVDNCPKDA 202
                                       *************98 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       4.5   4.7e+03      11      63 ..      48      54 ..      47      76 .. 0.69
   2 ?    8.5   7.9    0.0026       2.8      49      64 ..     161     176 ..     134     177 .. 0.82
   3 ?   12.0   4.2   0.00021      0.22       4      19 ..     162     177 ..     160     187 .. 0.60
   4 ?   10.0   4.3   0.00087      0.92       4      16 ..     187     199 ..     184     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4.5
                            Fer4_8 11 CqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63
                                      C + Cp                                               
  gi|298675194|ref|YP_003726944.1| 48 CGNICP----------------------------------------------R 54
                                      556665..............................................3 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0026
                            Fer4_8  49 wsCttcgaCtevCpvg 64 
                                       ++C +c++C++vCp++
  gi|298675194|ref|YP_003726944.1| 161 DKCISCNKCSKVCPMH 176
                                       6899999999999987 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00021
                            Fer4_8   4 kCieCgaCqsaCpvlr 19 
                                       kCi C  C + Cp+  
  gi|298675194|ref|YP_003726944.1| 162 KCISCNKCSKVCPMHL 177
                                       5555555555555544 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.00087
                            Fer4_8   4 kCieCgaCqsaCp 16 
                                       +Ci+C++C ++Cp
  gi|298675194|ref|YP_003726944.1| 187 DCIKCERCVDNCP 199
                                       5888888888887 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   3.2    0.0021       2.2      79      94 ..     160     175 ..     143     177 .. 0.68
   2 ?    8.0   3.4    0.0049       5.1       1      14 [.     162     175 ..     162     185 .. 0.86
   3 ?    8.8   1.6    0.0028         3      77      94 ..     183     200 ..     175     202 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0021
                           Fer4_22  79 esgCvGCgRCieacpv 94 
                                         +C+ C++C+++cp+
  gi|298675194|ref|YP_003726944.1| 160 DDKCISCNKCSKVCPM 175
                                       5566666666666665 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0049
                           Fer4_22   1 rClsCgaCtlvCpt 14 
                                       +C+sC++C+ vCp 
  gi|298675194|ref|YP_003726944.1| 162 KCISCNKCSKVCPM 175
                                       69999999999995 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0028
                           Fer4_22  77 fgesgCvGCgRCieacpv 94 
                                         +  C+ C RC+++cp+
  gi|298675194|ref|YP_003726944.1| 183 STNPDCIKCERCVDNCPK 200
                                       46678***********97 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.7    0.0027       2.9       3      19 ..     158     174 ..     156     183 .. 0.88
   2 ?    5.3   1.9     0.031        33       7      20 ..     187     200 ..     185     202 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0027
                           Fer4_15   3 vDrdaCigcglCvaeap 19 
                                       v+ d+Ci+c+ C +++p
  gi|298675194|ref|YP_003726944.1| 158 VNDDKCISCNKCSKVCP 174
                                       789************98 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.031
                           Fer4_15   7 aCigcglCvaeape 20 
                                        Ci c++Cv+++p+
  gi|298675194|ref|YP_003726944.1| 187 DCIKCERCVDNCPK 200
                                       6***********96 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1       1.9     2e+03      10      16 ..      48      54 ..      47      59 .. 0.80
   2 ?   -0.7   0.2       2.7   2.8e+03      13      16 ..     139     142 ..     135     143 .. 0.63
   3 ?    8.8   5.3    0.0025       2.6       2      16 ..     161     175 ..     160     185 .. 0.92
   4 ?   10.1   4.5   0.00091      0.96       4      16 ..     188     200 ..     180     201 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.9
                            Fer4_4 10 CvaaCPq 16
                                      C ++CP 
  gi|298675194|ref|YP_003726944.1| 48 CGNICPR 54
                                      6689*96 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.7
                            Fer4_4  13 aCPq 16 
                                       +CP+
  gi|298675194|ref|YP_003726944.1| 139 ICPM 142
                                       4776 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0025
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       ++Ci C +C  +CP+
  gi|298675194|ref|YP_003726944.1| 161 DKCISCNKCSKVCPM 175
                                       79************5 PP

  == domain 4  score: 10.1 bits;  conditional E-value: 0.00091
                            Fer4_4   4 CigCgsCvaaCPq 16 
                                       Ci C +Cv+ CP 
  gi|298675194|ref|YP_003726944.1| 188 CIKCERCVDNCPK 200
                                       ************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1327  (0.0740142); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1546.95
//
Query:       gi|298675195|ref|YP_003726945.1|  [L=65]
Description: hypothetical protein Metev_1286 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.035   14.3   0.4       0.12   12.6   0.3    1.7  2  K-box     K-box region
      0.094   12.7   1.4        1.1    9.2   0.2    2.0  2  Borealin  Cell division cycle-associated protein 8
        1.4    8.9   4.8        1.6    8.8   0.1    2.1  2  RHH_1     Ribbon-helix-helix protein, copG family


Domain annotation for each model (and alignments):
>> K-box  K-box region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.11   6.4e+02      37      52 ..       8      23 ..       6      29 .. 0.73
   2 ?   12.6   0.3     2e-05      0.12      24      60 ..      27      63 ..      16      65 .] 0.85

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.11
                             K-box 37 leslslkeLqqLEqqL 52
                                      l++ s+k  ++LE+++
  gi|298675195|ref|YP_003726945.1|  8 LDEDSIKAINELEKKM 23
                                      6666788888888877 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 2e-05
                             K-box 24 klqrsqRkllGedleslslkeLqqLEqqLekslkkiR 60
                                       l  s R +   dl++ +lk  ++LE++L++sl  + 
  gi|298675195|ref|YP_003726945.1| 27 LLAFSDRDIKAADLDEDQLKSIKDLEDKLDMSLVAVT 63
                                      56678899999**********************8875 PP

>> Borealin  Cell division cycle-associated protein 8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1     0.012        72      98     117 ..       5      24 ..       2      29 .. 0.86
   2 ?    9.2   0.2   0.00019       1.1      98     118 ..      37      57 ..      24      61 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.012
                          Borealin  98 lekLdeetlkqlkkLqsnLa 117
                                       ++kLde+ +k +++L++++ 
  gi|298675195|ref|YP_003726945.1|   5 FSKLDEDSIKAINELEKKMG 24 
                                       689************99875 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00019
                          Borealin  98 lekLdeetlkqlkkLqsnLak 118
                                        ++Lde+ lk++k L+++L++
  gi|298675195|ref|YP_003726945.1|  37 AADLDEDQLKSIKDLEDKLDM 57 
                                       468****************97 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1   0.00026       1.6       5      22 ..       7      24 ..       7      26 .. 0.92
   2 ?    1.7   1.3     0.047   2.8e+02       6      24 ..      40      58 ..      38      59 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00026
                                      EEEHHHHHHHHHHHHHHT CS
                             RHH_1  5 rldeellerLdelarrrg 22
                                      +lde+ +++++el +++g
  gi|298675195|ref|YP_003726945.1|  7 KLDEDSIKAINELEKKMG 24
                                      69***********99998 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.047
                                      EEHHHHHHHHHHHHHHTSS CS
                             RHH_1  6 ldeellerLdelarrrgrS 24
                                      lde+ l+ +  l +++++S
  gi|298675195|ref|YP_003726945.1| 40 LDEDQLKSIKDLEDKLDMS 58
                                      89******99999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.20s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 507.01
//
Query:       gi|298675196|ref|YP_003726946.1|  [L=358]
Description: uroporphyrinogen decarboxylase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-62  210.0   0.0      6e-62  209.8   0.0    1.0  1  URO-D     Uroporphyrinogen decarboxylase (URO-D)
  ------ inclusion threshold ------
      0.039   13.1   0.0      0.058   12.6   0.0    1.2  1  RtcB      tRNA-splicing ligase RtcB


Domain annotation for each model (and alignments):
>> URO-D  Uroporphyrinogen decarboxylase (URO-D)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.8   0.0   6.7e-66     6e-62       1     344 [.       6     352 ..       6     354 .. 0.93

  Alignments for each domain:
  == domain 1  score: 209.8 bits;  conditional E-value: 6.7e-66
                                       ----HHHHHHTT---SS--B--TT-SSTTSHHHHHHHTSSSHHHHHH-HHHHHHHHHHHHHHH--S-EE-S--TTGG CS
                             URO-D   1 tknerllralrgekvdrvPvwlmRqaGrylpeyraeragvsflelcknpelaaevtlqpvrrfglDaailfsdilve 77 
                                       t+ er+ ++++g+k+drvPv++      ++  y+  ++g+s+ +++++ +++++++++ +r +g++   ++ + ++ 
  gi|298675196|ref|YP_003726946.1|   6 TSPERMAAVMSGQKPDRVPVVP------FIEGYATNITGISLGDFYADGDMCFDAQFASMRLHGYEQTPMYGYASCG 76 
                                       5789******************......************************************************* PP

                                       GGGGT-EEEEETTTE...EEEE--S-.....GGGS----GGG.G..HHHHHHHHHHHHH..--SS-EEEEEE-HHHH CS
                             URO-D  78 aealGlevefeegeg...Pvvekpvr.taedveklevpddveegrlpyvleaikllkkel.ggevpligfvgaPftl 149
                                       a+ +G ++ f+  +g   P+ve++++ ++edve+l+vpd  + ++lp  ++  + + ++  ++ +p+++ +g+ ft 
  gi|298675196|ref|YP_003726946.1|  77 AWEFGGKIGFPYRKGqgaPYVEEHPVnKVEDVENLKVPDF-R-DELPGAYKEADKVAAKCaERGMPVTVQIGSVFTA 151
                                       ***********9666669****99999***********86.4.579999988888888775789************* PP

                                       HHHHHCTT-SS-HHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHH.HTT-SEEEEEE....TTGGGS-HHHHHHHTH CS
                             URO-D 150 asylveGgskgfekllkllykdpeevhklldkltdvvieylkaqi.eagAdaiqifD....swagllspedfeefvl 221
                                       as +      +++k++++ +++p++vh++ldk++d++i+ ++ ++ + g + +  fD     +++++s ++feef++
  gi|298675196|ref|YP_003726946.1| 152 ASVIA-----ETSKFFNWVVTKPDVVHQILDKVSDMFINAVDYFAdKYGPKNLLPFDggpsESNTMISAKMFEEFAY 223
                                       *****.....***********************************99999**********99*************** PP

                                       HHHHHHHHHHHH.H--S-EEEEESSHH.HHHHHHTT.......S--SEEE--TTS-HHHHHHSS....EEE--B-G. CS
                             URO-D 222 pylkrivdevkaegpkvpvilfikgagaeiledlae.......lgadvlsldwtvdlkeaarevgdkvalqGnldPi 291
                                       py+k+i d+v+++g    v+++++++ +  +++  +       +g  v+ + +++++k ++ ++gd+ +++Gn++P+
  gi|298675196|ref|YP_003726946.1| 224 PYVKKIHDHVRERGI-PAVLMHPCADQNGNIPYYVKmreendwSGKYVWLFGPETSIKTQIDAFGDHDVICGNINPP 299
                                       ************986.6899*****9665333333324478889999*****************************6 PP

                                       GGGG.S-HHHHHHHHHHHHT.T---SSSEEB-BSS---TTS-HHHHHHHHHHHH CS
                             URO-D 292 alLl.gspeeiekevkeilekgaggkkgyilnlGhgippetppenvkalveavk 344
                                        l   +s +e+ + ++e +e+g+++++gyil+ G++ pp++ p +v a+v+a++
  gi|298675196|ref|YP_003726946.1| 300 -LFQsSSYDEVLELCRENIEEGMNSPSGYILAAGCEFPPNAAPIKVMAMVDAAE 352
                                       .5557***********************************************97 PP

>> RtcB  tRNA-splicing ligase RtcB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.4e-06     0.058     361     399 ..     103     141 ..      90     149 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.4e-06
                                       CCT-EEEE------------------HHHHHHHHCTS-E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB 361 eqgigvearkkegvleEapeaYKdideVveaqaeaglve 399
                                       ++   ve  k  ++ +E p+aYK+ d+V++++ae g+  
  gi|298675196|ref|YP_003726946.1| 103 NKVEDVENLKVPDFRDELPGAYKEADKVAAKCAERGMPV 141
                                       56677888899999*******************988755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2664.91
//
Query:       gi|298675197|ref|YP_003726947.1|  [L=532]
Description: copper-binding protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.2e-65  219.1 103.9    3.3e-35  121.5  37.5    3.2  3  NosD             Periplasmic copper-binding protein (NosD)
    2.2e-33  115.4 126.2    3.4e-19   69.2  38.9    3.8  4  Beta_helix       Right handed beta helix region
    4.6e-06   26.2  68.9     0.0082   15.5  18.4    5.0  3  DUF1565          Protein of unknown function (DUF1565)
     0.0072   16.2  11.1     0.0072   16.2  11.1    4.5  5  Pectate_lyase_3  Pectate lyase superfamily protein


Domain annotation for each model (and alignments):
>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2  23.5   2.1e-17   9.5e-14       1     135 [.      48     195 ..      48     198 .. 0.82
   2 !   59.1  26.8   8.1e-20   3.7e-16      46     154 ..     199     314 ..     195     318 .. 0.86
   3 !  121.5  37.5   7.4e-39   3.3e-35      84     238 ..     318     478 ..     314     481 .. 0.93

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 2.1e-17
                              NosD   1 vnnaisgdevlvsa........rgngiqlens........egseisnneisnsrdgilldnssnntitgntienl.. 59 
                                       +nna+sgd++lv++                 +        +g+++++     s+d++++ +++++ti g  ++    
  gi|298675197|ref|YP_003726947.1|  48 INNASSGDTILVDSgnyydnvdV--------TiplnitsiNGASVTSVIAAVSSDNVFHITAEGVTINGFDVSGAts 116
                                       5899999**99996555554332........1444444458888888888888888999999999998885555555 PP

                              NosD  60 ..ryGihlensesntiedntlssnesGialmsssnntlenNtisnnenyGillsdssnntisnNtis.nnnkGifle 133
                                          +Gi++e+s++++i +n +s+n+ Gi+l +s nn +++Nt+ +n+++Gi+l++s+nn++++N +s nn++Gi+l+
  gi|298675197|ref|YP_003726947.1| 117 tsCSGIRIESSNHSNIFNNMVSNNKLGISLINSDNNNITGNTAPGNDYAGIYLQQSDNNDLNDNIVSdNNQYGIYLT 193
                                       5589***********************************************************************98 PP

                              NosD 134 ns 135
                                       ++
  gi|298675197|ref|YP_003726947.1| 194 SA 195
                                       76 PP

  == domain 2  score: 59.1 bits;  conditional E-value: 8.1e-20
                              NosD  46 ssnntitgntienlryGihlensesntiedntlssne.sGialmsss......nntlenNtisnnenyGillsdssn 115
                                       ss+n++t+nt++++++Gi+l++ +++t+ dn +++n+ +Gi+l+ss       nntl  Nt+ nn n Gi+++d+++
  gi|298675197|ref|YP_003726947.1| 199 SSDNNFTNNTVHQNSKGIFLQSPNDSTLIDNNVFNNTnNGITLDSSGdpfdteNNTLISNTVLNNYN-GIIIDDINY 274
                                       7899999*************9999977766666666669****999977777666888888888888.********* PP

                              NosD 116 ntisnNtis.nnnkGiflensssntitgNriesnqkiGil 154
                                       n++++N++s n+nkGi+l  s++n++ +N i +n++iG+l
  gi|298675197|ref|YP_003726947.1| 275 NKLNENNVSnNTNKGIHLFYSHYNKLIDNAILDNNNIGFL 314
                                       *******9999999*****************999999987 PP

  == domain 3  score: 121.5 bits;  conditional E-value: 7.4e-39
                              NosD  84 GialmsssnntlenNtisnnenyGillsdssnntisnNtis.nnnkGiflensssntit.gNriesnqkiGilllss 158
                                       G+ l+ ssnn++ nN+isnn ++Gi +++s+ n++s+Nt s n +++i++++ s++ +  +N+i++n+  Gi    s
  gi|298675197|ref|YP_003726947.1| 318 GLDLHTSSNNFIGNNNISNNGYNGIEIDFSELNDLSGNTLSnNVEYAIYFDGPSYEHYIyNNTISNNERGGIS--LS 392
                                       88899************************************999*******996655444999****666666..66 PP

                              NosD 159 segntiynNyFinnsenvkydgsnnneWnttktsgtniiggpylgGNyWsdydg.......eDadgDGigDtpYein 228
                                       + +n+iynNyF nns+n++  ++++n+Wntt+t+g ni++g+y+gGN+W  +dg       eD++gDG++D +Y+i+
  gi|298675197|ref|YP_003726947.1| 393 GLRNHIYNNYF-NNSNNADFYAGSDNQWNTTNTTGPNIVNGSYVGGNFWVHPDGtgfsvenEDSNGDGFCDNSYNIS 468
                                       669********.***************************************************************** PP

                              NosD 229 dgviDylplv 238
                                       +++iDylpl+
  gi|298675197|ref|YP_003726947.1| 469 SNNIDYLPLA 478
                                       ********96 PP

>> Beta_helix  Right handed beta helix region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.7      0.68     3e+03     136     136 ..      49      49 ..      16      99 .. 0.48
   2 !   69.2  38.9   7.7e-23   3.4e-19       7     157 ..     101     254 ..      87     255 .. 0.91
   3 !   45.2  34.3   1.8e-15   8.2e-12      31     146 ..     251     369 ..     248     374 .. 0.89
   4 !   29.3  36.9   1.5e-10   6.9e-07      25     153 ..     318     450 ..     317     472 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.68
                                       S CS
                        Beta_helix 136 n 136
                                       n
  gi|298675197|ref|YP_003726947.1|  49 N 49 
                                       1 PP

  == domain 2  score: 69.2 bits;  conditional E-value: 7.7e-23
                                       SS-E.EEESEEEES-...SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S-- CS
                        Beta_helix   7 gssnvtiknntisns...ggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnn 80 
                                        ++ vti+++++s++   + +Gi +++s++  i nn ++n +  Gi++ +s+nn+i++nt  +n + gi+l++++nn
  gi|298675197|ref|YP_003726947.1| 101 AEG-VTINGFDVSGAtstSCSGIRIESSNHSNIFNNMVSN-NKLGISLINSDNNNITGNTAPGNDYAGIYLQQSDNN 175
                                       333.58888888888999999*********9999888888.************************************ PP

                                       EEES-EEES-SS-SEE-TT....-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EE CS
                        Beta_helix  81 lienneitdnggsGiylny....ssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtv 153
                                        +++n ++dn+++Giyl++    ss+n ++nN+++ n+  Gi++++ + + t  +N+++nn ++Gi++ +s++ +  
  gi|298675197|ref|YP_003726947.1| 176 DLNDNIVSDNNQYGIYLTSaggfSSDNNFTNNTVHQNS-KGIFLQSPN-DSTLIDNNVFNNTNNGITLDSSGDPFDT 250
                                       ******************99******************.*********.88889999999999************** PP

                                       ES-E CS
                        Beta_helix 154 rnNt 157
                                       +nNt
  gi|298675197|ref|YP_003726947.1| 251 ENNT 254
                                       ***8 PP

  == domain 3  score: 45.2 bits;  conditional E-value: 1.8e-15
                                       SS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-......SEE-TT-S CS
                        Beta_helix  31 ssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnlienneitdnggs......Giylnyss 101
                                        +n++i+ n++ n +++Gi i   ++n++ +n++s+n++ gi+lf++++n + +n i dn++       G+ l++ss
  gi|298675197|ref|YP_003726947.1| 251 ENNTLIS-NTVLN-NYNGIIIDDINYNKLNENNVSNNTNKGIHLFYSHYNKLIDNAILDNNNIgflsigGLDLHTSS 325
                                       3444555.77777.8*********************************************887777777999999** PP

                                       --EEES-EEESTT--SEE---TT.---EEES-EEES-SSEEEE-TT CS
                        Beta_helix 102 nntienNiidnnagsGividdss.snvtvtnNtitnnkgaGiavvg 146
                                       nn i nN+i+nn+ +Gi+id s+ +++  ++Nt++nn+ ++i++ g
  gi|298675197|ref|YP_003726947.1| 326 NNFIGNNNISNNGYNGIEIDFSElNDL--SGNTLSNNVEYAIYFDG 369
                                       ***********************7777..*************8766 PP

  == domain 4  score: 29.3 bits;  conditional E-value: 1.5e-10
                                       SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT.--S--EEES-EEES-SS-SEE-TT- CS
                        Beta_helix  25 GiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialf.gasnnlienneitdnggsGiylnys 100
                                       G+ l +ssn+ i nn+i+nn+++Gi+i  s+ n +s+nt s+n +++i+++  +    i+nn+i++n++ Gi+l+  
  gi|298675197|ref|YP_003726947.1| 318 GLDLHTSSNNFIGNNNISNNGYNGIEIDFSELNDLSGNTLSNNVEYAIYFDgPSYEHYIYNNTISNNERGGISLS-G 393
                                       7889999********************************************999999*****************8.6 PP

                                       S--EEES-EEESTT--SEE---TT..---EEES-EEES-S..SEEEE-TT-SS--EE CS
                        Beta_helix 101 snntienNiidnnagsGividdss..snvtvtnNtitnnk..gaGiavvgsssnvtv 153
                                        +n i nN+++n +++ ++  + +  ++++ t+ +i+n +  g  ++v  +++++ v
  gi|298675197|ref|YP_003726947.1| 394 LRNHIYNNYFNNSNNADFYAGSDNqwNTTNTTGPNIVNGSyvGGNFWVHPDGTGFSV 450
                                       89********99995555555555998888999999999945222334444444444 PP

>> DUF1565  Protein of unknown function (DUF1565)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5  18.4   1.8e-06    0.0082      78     219 ..      87     213 ..      32     215 .. 0.73
   2 !   11.9  34.5   2.3e-05       0.1     109     225 ..     207     344 ..     197     361 .. 0.79
   3 ?    2.5   6.6     0.018        79     104     150 ..     354     406 ..     346     473 .. 0.51

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.8e-06
                           DUF1565  78 lisgggddlsgvqnvtivlaneatiaGvtitNpnilkgtgvliesa.sakianNtitgniadGievsiyeaktgagg 153
                                       +i          +nv  ++a+ +ti G+ +   + ++  g+ ies+  ++i nN +++n + Gi+  + + +++++g
  gi|298675197|ref|YP_003726947.1|  87 VIAAV-----SSDNVFHITAEGVTINGFDVSGATSTSCSGIRIESSnHSNIFNNMVSNN-KLGISLINSD-NNNITG 156
                                       22222.....245778889999**********999999*******9889********97.99***99996.889999 PP

                           DUF1565 154 niisGnsilfeknGiaisgasaavenkienNiivkNli.GvvanalalDlGsgsegsaGnNifsnna 219
                                       n++ Gn     ++Gi  +++    +n +++Ni++ N++ G+  +  +   G  s++   nN++  n+
  gi|298675197|ref|YP_003726947.1| 157 NTAPGND----YAGIYLQQSD---NNDLNDNIVSDNNQyGIYLTSAG---GFSSDNNFTNNTVHQNS 213
                                       9999985....6788776554...56899999998777799988777...77777778888887776 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 2.3e-05
                           DUF1565 109 Npnilkgtgvliesa..sakianNtitgniadGievsiyeaktgaggniisGnsilfeknGiaisgasaa..venki 181
                                       N+   +++g++++s   s+ i nN +++ +++Gi+ +      ++ +n+   n++l+++nGi+i++++     en +
  gi|298675197|ref|YP_003726947.1| 207 NTVHQNSKGIFLQSPndSTLIDNNVFNN-TNNGITLDSSGDPFDTENNTLISNTVLNNYNGIIIDDINYNklNENNV 282
                                       34447889*****987677788888877.79*****99988889999******************998874345777 PP

                           DUF1565 182 en..................N.iivkNliGvvanalalDlGsgsegsaGnNifsnnaeaDini 225
                                        n                  N i+ +N+iG   +  +lDl + s++ +GnN +snn+++ i+i
  gi|298675197|ref|YP_003726947.1| 283 SNntnkgihlfyshynklidNaILDNNNIGFL-SIGGLDLHTSSNNFIGNNNISNNGYNGIEI 344
                                       66788888888888877777534455778988.45569********************99988 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.018
                           DUF1565 104 GvtitNpnilkgtgvliesa..sakianNtitgniadGiev........siyeaktg 150
                                       G t+ N     +++++  +      i nNti++n + Gi+         ++y+ +++
  gi|298675197|ref|YP_003726947.1| 354 GNTLSNN---VEYAIYFDGPsyEHYIYNNTISNNERGGISLsglrnhiyNNYF-NNS 406
                                       5555555...2445555433225667777777777777776444444432221.111 PP

>> Pectate_lyase_3  Pectate lyase superfamily protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3  13.2      0.12   5.3e+02      85     201 ..      23     155 ..       9     166 .. 0.60
   2 !   16.2  11.1   1.6e-06    0.0072     131     214 ..     150     239 ..     147     240 .. 0.90
   3 !   11.7  16.4   3.9e-05      0.18     114     214 ..     184     290 ..     167     291 .. 0.79
   4 ?    1.6  16.3     0.048   2.2e+02     100     214 ..     268     389 ..     243     390 .. 0.65
   5 ?    1.8   7.5      0.04   1.8e+02     135     195 ..     376     436 ..     366     457 .. 0.67

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.12
                                       TTT-..-EEEEEEEEEEEGGGG-SS---SSEEEES-EEEEEEEEEEES-SS....EEE-SSS---TT---SS--EEE CS
                   Pectate_lyase_3  85 yvsggsealiatnnfyrqirnlkiditavapgatgihwqtaqatslenvef....emseasgtkhqgifiengsggf 157
                                       ++ ++s +++ t++f  + + +k  i+++++g t     ++++   +nv++    ++++ +g   ++ +i   s++ 
  gi|298675197|ref|YP_003726947.1|  23 INVNESGWWEDTSSFNISSTPIKAAINNASSGDTI---LVDSGNYYDNVDVtiplNITSINGA-SVTSVIAAVSSDN 95 
                                       33222358888888888888888888887777766...5666666666665334455555543.3344455556656 PP

                                       EES-EEES-SS-SEEES..............-EEEEEES-EEE-S--SEEE-T.T-E.EE CS
                   Pectate_lyase_3 158 lndlvfsglgdigiavg..............nqqftvrnitfnnattgievlw.gwg.wt 201
                                       + +++++g+   g+ v+              ++++++ n+ ++n++ gi++   +++ +t
  gi|298675197|ref|YP_003726947.1|  96 VFHITAEGVTINGFDVSgatstscsgiriesSNHSNIFNNMVSNNKLGISLINsDNNnIT 155
                                       666666664444444422444456666666777777777777777999999874443233 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.6e-06
                                       ES-SSEEE-SSS---TT---SS--EEEEES-EEES-SS-SEEES.....-EEEEEES-EEE-S--SEEE-T.T-EEE CS
                   Pectate_lyase_3 131 envefemseasgtkhqgifiengsggflndlvfsglgdigiavg.....nqqftvrnitfnnattgievlw.gwgwt 201
                                       +n++++ ++a g+   gi+++++ ++ lnd ++s + ++gi ++     + + +++n+t+++++ gi +++ + +  
  gi|298675197|ref|YP_003726947.1| 150 DNNNITGNTAPGNDYAGIYLQQSDNNDLNDNIVSDNNQYGIYLTsaggfSSDNNFTNNTVHQNSKGIFLQSpNDSTL 226
                                       6889999999999999************99999999*******5599999999999***************666699 PP

                                       EEEEEEESSSEEE CS
                   Pectate_lyase_3 202 lknvkinncegGi 214
                                       + n+ +nn+++Gi
  gi|298675197|ref|YP_003726947.1| 227 IDNNVFNNTNNGI 239
                                       999999******9 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 3.9e-05
                                       SEEEES-EEEEEEEEEEES-SSEEE-SSS---TT---SS--EEEE.ES-EEES-SS-SEEE.S.......-EEEEEE CS
                   Pectate_lyase_3 114 apgatgihwqtaqatslenvefemseasgtkhqgifiengsggfl.ndlvfsglgdigiav.g.......nqqftvr 181
                                       +++ +gi  ++a + s +n+ f++++ + ++ +gif+++++ ++l ++ vf++  + gi++ +       +++  ++
  gi|298675197|ref|YP_003726947.1| 184 DNNQYGIYLTSAGGFSSDNN-FTNNTVH-QNSKGIFLQSPNDSTLiDNNVFNN-TNNGITLdSsgdpfdtENNTLIS 257
                                       45558999999999999998.7777777.5899***********99*******.*******6598888844444445 PP

                                       S-EEE-S--SEEE-T.T-EEEEEEEEEESSSEEE CS
                   Pectate_lyase_3 182 nitfnnattgievlw.gwgwtlknvkinncegGi 214
                                       n + n + +gi +++ + +   +n+  nn+++Gi
  gi|298675197|ref|YP_003726947.1| 258 NTVLN-NYNGIIIDDiNYNKLNENNVSNNTNKGI 290
                                       54444.5******987777777788889999998 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.048
                                       EEE.GGGG-SS---S.SEEE.ES-E.EEEEEEEEEES-SSEEE-SSS---T.T---SS--EEEE..ES-EEES-SS- CS
                   Pectate_lyase_3 100 yrq.irnlkiditav.apga.tgih.wqtaqatslenvefemseasgtkhq.gifiengsggfl..ndlvfsglgdi 169
                                       + + i   k++ ++v ++ + +gih   ++ ++ ++n ++++++        g+ ++ +s++f+  n++  +g+ +i
  gi|298675197|ref|YP_003726947.1| 268 IIDdINYNKLNENNVsNN-TnKGIHlFYSHYNKLIDNAILDNNNIGF-LSIgGLDLHTSSNNFIgnNNISNNGYNGI 342
                                       222233334444444333.3699**7779999999**9999998884.4445999*********7556666666666 PP

                                       SEEES-EEEEEES-EEE-S--SEEE-T.T-E.EEEEEEEEESSSEEE CS
                   Pectate_lyase_3 170 giavgnqqftvrnitfnnattgievlw.gwg.wtlknvkinncegGi 214
                                        i +++ +    n   nn + +i+++  + + ++++n   nn  gGi
  gi|298675197|ref|YP_003726947.1| 343 EIDFSELNDLSGNTLSNNVEYAIYFDGpSYEhYIYNNTISNNERGGI 389
                                       6666788888888888899*******999997777555556665577 PP

  == domain 5  score: 1.8 bits;  conditional E-value: 0.04
                                       SEEE-SSS---TT---SS--EEEEES-EEES-SS-SEEES-EEEEEES-EEE-S--SEEE- CS
                   Pectate_lyase_3 135 femseasgtkhqgifiengsggflndlvfsglgdigiavgnqqftvrnitfnnattgievl 195
                                       +++++ s+++  gi ++   ++++n+ + + + ++ +a + +q++++n t  n  +g +v+
  gi|298675197|ref|YP_003726947.1| 376 IYNNTISNNERGGISLSGLRNHIYNNYFNNSNNADFYAGSDNQWNTTNTTGPNIVNGSYVG 436
                                       4444444333446766666666667777777777777778888888888888877776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (532 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       827  (0.0461264); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 3508.46
//
Query:       gi|298675198|ref|YP_003726948.1|  [L=2140]
Description: ricin B lectin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.7e-21   74.3  14.6      4e-12   46.7   2.0    4.3  4  RicinB_lectin_2  Ricin-type beta-trefoil lectin domain-like
    1.5e-12   47.7   1.4    2.6e-07   30.9   0.0    4.0  4  Fascin           Fascin domain
    2.7e-11   43.8   8.2    8.5e-11   42.2   8.2    1.9  1  Ricin_B_lectin   Ricin-type beta-trefoil lectin domain
    4.7e-10   39.5   2.2    9.1e-06   25.5   0.1    3.0  3  FRG1             FRG1-like domain


Domain annotation for each model (and alignments):
>> RicinB_lectin_2  Ricin-type beta-trefoil lectin domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   2.0     9e-16     4e-12      16      83 ..     281     347 ..     274     353 .. 0.91
   2 !   33.0   0.2   1.6e-11   7.3e-08       1      58 [.     360     414 ..     360     432 .. 0.89
   3 ?   -0.3   0.3      0.42   1.9e+03      15      89 .]     485     557 ..     470     557 .. 0.74
   4 ?   -0.6   0.2      0.49   2.2e+03      23      76 ..     534     583 ..     506     596 .. 0.69

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 9e-16
                                       EEECTSSSEEEECGCCTBCTTEEEEEE-TTT-GGCEEEEECCESSEEEEEETTTTEEEEECGCS-STT CS
                   RicinB_lectin_2  16 tiknvasgkvLdvaggstanganvqqwtcsgaanqqWrledtgdgtyrivnkasgkvLdvaggstanG 83 
                                       +i ++ +gk+L+ +++ ++n +nv + +c+g +nq+W+le++++++y+i+ k+++k+L v + ++++G
  gi|298675198|ref|YP_003726948.1| 281 NIISAVDGKCLQTQNNTNKNVTNVTTGNCTGEDNQLWKLEPADENHYSIILKNTSKCLQVGN-ASQDG 347
                                       6999*********************************************************5.55666 PP

  == domain 2  score: 33.0 bits;  conditional E-value: 1.6e-11
                                       CCGEEEECETTTTEEEEECTSSSEEEECGCCTBCTTEEEEEE-TTT-GGCEEEEECCE CS
                   RicinB_lectin_2   1 anQqWtlgsggdgyytiknvasgkvLdvaggstanganvqqwtcsgaanqqWrledtg 58 
                                       ++Q W+l+s+++ yy++ +++sgk+L++++  ++   ++ q++++g++ q+W +e  g
  gi|298675198|ref|YP_003726948.1| 360 DHQLWKLESENERYYKLAAKHSGKYLEIDNTTNK---TLIQNASQGNNRQLWEIEIVG 414
                                       58*****878889*****************9998...69999999********97766 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.42
                                       EEEECTSSSEEEECGCCTBCTTEEEEEE-TTT-GGCEEEEECCESSEEEEEETTTTEEEEECGCS-...STTEEEEE CS
                   RicinB_lectin_2  15 ytiknvasgkvLdvaggstanganvqqwtcsgaanqqWrledtgdgtyrivnkasgkvLdvaggst...anGtnvqq 88 
                                       +++   ++g++++v++   +    ++ ++++ ++   + ++ ++++   +++  + +v   +gg+    an t ++ 
  gi|298675198|ref|YP_003726948.1| 485 VSL-KTHKGQYVSVDSTTSE----LVARSNTITNDSIFEIVYLDNNKAALKTSGNKYVYAANGGGEeliANSTEIGE 556
                                       556.4578999999998888....77777788889999999999999999998888777777676678888888876 PP

                                       E CS
                   RicinB_lectin_2  89 w 89 
                                       w
  gi|298675198|ref|YP_003726948.1| 557 W 557
                                       6 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 0.49
                                       SEEEECGCCTBCTTEEEEEE-TTT-GGCEEEEECCESSEEEEEETTTTEEEEEC CS
                   RicinB_lectin_2  23 gkvLdvaggstanganvqqwtcsgaanqqWrledtgdgtyrivnkasgkvLdva 76 
                                       +k++ +a+g+ +    +  ++   ++   + l+++ +g   +++++s+ ++  +
  gi|298675198|ref|YP_003726948.1| 534 NKYVYAANGGGE---ELIANSTEIGEWEIFELVQLENGKIALKANNSQ-YVSAE 583
                                       566655555444...356666567777788888888888888888887.44444 PP

>> Fascin  Fascin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.41   1.9e+03      18      42 ..     308     333 ..     285     351 .. 0.72
   2 !   11.3   0.1   6.7e-05       0.3      22      75 ..     359     414 ..     342     418 .. 0.74
   3 !   30.9   0.0   5.7e-11   2.6e-07      26     111 .]     472     562 ..     459     562 .. 0.84
   4 !    7.2   0.0    0.0013       5.6      13      56 ..     546     588 ..     543     606 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.41
                                       ESSSSGGGEEEEEEETT.SEEEEEEE CS
                            Fascin  18 aesekkkqlftLefdee.syavaLrs 42 
                                       + + ++ ql++Le  +e  y++ L+ 
  gi|298675198|ref|YP_003726948.1| 308 NCTGEDNQLWKLEPADEnHYSIILKN 333
                                       4444567******9999788877774 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 6.7e-05
                                       SGGGEEEEEEETTSEEEEEEETTSEEEEE-T..TSBEEEEESS--GGGEEEEEEET CS
                            Fascin  22 kkkqlftLefdeesyavaLrshngkYlsldk..dGrvvaeaetkeedtlFelefrg 75 
                                       +++ql++Le ++e+y      h+gkYl++d+  + ++  +a++ +++ l+e+e+ g
  gi|298675198|ref|YP_003726948.1| 359 QDHQLWKLESENERYYKLAAKHSGKYLEIDNttNKTLIQNASQGNNRQLWEIEIVG 414
                                       578**********99856669*******9861145577777777777777777765 PP

  == domain 3  score: 30.9 bits;  conditional E-value: 5.7e-11
                                       EEEEEEETT.SEEEEEEETTSEEEEE-T.TSBEEEEESS--GGGEEEEEEE.TCEEEEEETTSCEEE..ECTTTEEE CS
                            Fascin  26 lftLefdee.syavaLrshngkYlsldk.dGrvvaeaetkeedtlFelefr.grwallresngryLg..igkeglLk 97 
                                       ++ ++ + +  ++v L++h+g+Y+s+d+ ++++va+++t  +d+ Fe+ +  + +a+l+ s  +y+    g+ + L 
  gi|298675198|ref|YP_003726948.1| 472 TWMVTGQTDrPKKVSLKTHKGQYVSVDStTSELVARSNTITNDSIFEIVYLdNNKAALKTSGNKYVYaaNGGGEELI 548
                                       56666555567889************962689******************998899999999999976678899*** PP

                                       EEESSSSGGGEEEE CS
                            Fascin  98 asastvgkdelftl 111
                                       a+++++g+ e f+l
  gi|298675198|ref|YP_003726948.1| 549 ANSTEIGEWEIFEL 562
                                       ***********986 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.0013
                                       BEEEEESSSSGGGEEEEEEETTSEEEEEEETTSEEEEE-TTSBE CS
                            Fascin  13 klsasaesekkkqlftLefdeesyavaLrshngkYlsldkdGrv 56 
                                       +l a++ +  + ++f+L++ e++++ aL++ n++Y+s+++ G+ 
  gi|298675198|ref|YP_003726948.1| 546 ELIANSTEIGEWEIFELVQLENGKI-ALKANNSQYVSAENGGGA 588
                                       677888888888******9999888.9**********9988864 PP

>> Ricin_B_lectin  Ricin-type beta-trefoil lectin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   8.2   1.9e-14   8.5e-11       5     127 .]     282     408 ..     279     408 .. 0.79

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 1.9e-14
                                       EEETTTGEEEEETTCTTS.TEBEEEEE-TSCCGGGEEEEE....TTSEEEETT.TTEEEEES..SSSTTSBEEEEET CS
                    Ricin_B_lectin   5 irnvasgkCLdvegeska.gapvglydChgskgkQlwtlt....kdgeirskaqselCldvs..staegakvvlakC 74 
                                       i ++ +gkCL+++++ ++  ++v++ +C+g+++ Qlw+l+    ++ +i +k ++++Cl+v+  s++   +v++ + 
  gi|298675198|ref|YP_003726948.1| 282 IISAVDGKCLQTQNNTNKnVTNVTTGNCTGEDN-QLWKLEpadeNHYSIILK-NTSKCLQVGnaSQDGVVNVTIGDY 356
                                       777789*********9999************99.******654333555555.5*******7533333345555555 PP

                                       TTTSGGGCEEEETTTTE...EEETTTSEEEEESTTSSTTTBEEEEEE.TSSGGGBE CS
                    Ricin_B_lectin  75 hkgkgnqrWefdkdgtq...irhkksgkCLdvkgasksneklilkkcdsgsdsQkW 127
                                       + g+++q+W++++++++   +  k+sgk L++++ +++   li++   +g+++Q W
  gi|298675198|ref|YP_003726948.1| 357 T-GQDHQLWKLESENERyykLAAKHSGKYLEIDNTTNK--TLIQN-ASQGNNRQLW 408
                                       5.999*******9999977788888*******988763..57777.67******99 PP

>> FRG1  FRG1-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       0.5   2.3e+03     144     171 ..     373     400 ..     358     410 .. 0.55
   2 !   25.5   0.1     2e-09   9.1e-06      38      94 ..     482     539 ..     470     543 .. 0.85
   3 !   18.7   0.1   2.4e-07    0.0011      38      99 ..     524     587 ..     522     616 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.5
                              FRG1 144 yvkkfqkiqdkklrldkedvkrlkkark 171
                                       y k  +k + k l +d+  +k+l +   
  gi|298675198|ref|YP_003726948.1| 373 YYKLAAKHSGKYLEIDNTTNKTLIQNAS 400
                                       4444444444444444444444444444 PP

  == domain 2  score: 25.5 bits;  conditional E-value: 2e-09
                              FRG1  38 dekislKsgyGkYlgvd.kegilsaraeAisseEqfevvfeegktallalaketflsv 94 
                                        +k+slK++ G+Y++vd ++  l+ar++ i +  +fe+v+ ++++a+l ++ ++++ +
  gi|298675198|ref|YP_003726948.1| 482 PKKVSLKTHKGQYVSVDsTTSELVARSNTITNDSIFEIVYLDNNKAALKTSGNKYVYA 539
                                       589**************45678******************999888888788888765 PP

  == domain 3  score: 18.7 bits;  conditional E-value: 2.4e-07
                              FRG1  38 dekislKsgyGkYlgvdkeg..ilsaraeAisseEqfevv.feegktallalaketflsvdeekd 99 
                                       ++k +lK++  kY+   + g   l+a+++ i++ E+fe+v  e+gk al a ++++++s+++ + 
  gi|298675198|ref|YP_003726948.1| 524 NNKAALKTSGNKYVYAANGGgeELIANSTEIGEWEIFELVqLENGKIALKA-NNSQYVSAENGGG 587
                                       6899**********988765347****************95589*******.*******998654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (2140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       921  (0.0513693); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.89u 0.31s 00:00:01.20 Elapsed: 00:00:00.45
# Mc/sec: 14367.45
//
Query:       gi|298675199|ref|YP_003726949.1|  [L=244]
Description: hypothetical protein Metev_1290 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       962  (0.0536561); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1777.16
//
Query:       gi|298675200|ref|YP_003726950.1|  [L=729]
Description: signal transduction histidine kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.2e-44  148.2   0.0    1.2e-18   67.3   0.0    4.5  4  PAS_4            PAS fold
    3.6e-40  136.4   8.5    5.7e-13   49.0   0.2    5.3  6  PAS_9            PAS domain
    1.5e-34  118.4   0.0    6.8e-11   42.2   0.0    4.5  4  PAS              PAS fold
    1.6e-28   98.6   1.4    1.6e-28   98.6   1.4    2.5  2  HisKA_2          Histidine kinase
    4.9e-19   67.9   0.0    1.7e-05   24.7   0.0    4.5  4  PAS_8            PAS domain
      5e-09   36.6   0.2    6.6e-07   29.8   0.0    3.5  2  HATPase_c        Histidine kinase-, DNA gyrase B-, and HSP90-
    4.8e-06   26.8   0.2       0.12   12.7   0.0    4.5  5  PAS_3            PAS fold
      1e-05   25.7   0.0      0.006   16.7   0.0    3.2  2  sCache_3_2       Single cache domain 3
    1.7e-05   25.2   0.5       0.17   12.3   0.0    3.9  4  sCache_3_3       Single cache domain 3
    2.8e-05   24.7   0.0    2.8e-05   24.7   0.0    2.4  2  HWE_HK           HWE histidine kinase
    0.00021   21.9   1.4       0.51   11.0   0.0    4.1  4  PAS_10           PAS domain
    0.00047   20.1   0.0     0.0012   18.8   0.0    1.6  1  HATPase_c_2      Histidine kinase-like ATPase domain
     0.0012   18.2   3.2      0.088   12.1   0.0    3.3  3  Cache_3-Cache_2  Cache 3/Cache 2 fusion domain
     0.0085   15.7   0.5       0.57    9.8   0.0    3.1  3  PAS_12           UPF0242 C-terminal PAS-like domain
  ------ inclusion threshold ------
      0.017   15.3   7.1        3.9    7.7   0.0    5.1  5  PAS_7            PAS fold
      0.033   14.5   0.6       0.15   12.4   0.6    2.2  1  Peptidase_M3_N   Oligopeptidase F
      0.045   13.8   0.1       0.91    9.6   0.0    2.8  2  DnaB             DnaB-like helicase N terminal domain


Domain annotation for each model (and alignments):
>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   4.9e-08   5.2e-05      14     107 ..      40     125 ..      39     128 .. 0.89
   2 !   14.9   0.0   2.2e-05     0.024       1     109 [.     144     250 ..     144     251 .. 0.88
   3 !   67.3   0.0   1.2e-21   1.2e-18       1     110 []     267     378 ..     267     378 .. 0.97
   4 !   37.1   0.0   2.8e-12     3e-09       1     108 [.     394     497 ..     394     499 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 4.9e-08
                             PAS_4  14 dgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgeerhyelrllPlrd 90 
                                       d+ ++++N+a+++ +g+  +e+lGk+  e++ + d +++ + +++v+e++e  +f+++  +   ++++ ++++    
  gi|298675200|ref|YP_003726950.1|  40 DYLIIDCNPAYESTIGLKKDEVLGKKASEVYGT-DEPPHLSTYAKVAETGEQTYFETYFPP--FDKYFKISAISP-- 111
                                       56689*************************999.********************9997666..899999999777.. PP

                             PAS_4  91 esGevigvlvisrDiTe 107
                                       e+G+   ++ i+ DiTe
  gi|298675200|ref|YP_003726950.1| 112 EKGK---FVTIFNDITE 125
                                       6788...9999999998 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 2.2e-05
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       +ds+ dal+v d +g++l++N++a + +g++ +e+l +++ ++       ++ + l  + e ++  ++  +++ +g 
  gi|298675200|ref|YP_003726950.1| 144 FDSMEDALFVGDLEGNILDVNETAVKRLGYSKKEILSMHVKDIDGLYNENGVKTKLMNLPENGKQRFESVHVTNNGN 220
                                       7999*************************************964444778999999999999987777777777999 PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerr 109
                                         ++e++ + +   +G+  +vl ++r iT+r+
  gi|298675200|ref|YP_003726950.1| 221 KIPVEINSNLI-SYRGK-TAVLSVVRNITDRK 250
                                       99999999999.57899.99999999999997 PP

  == domain 3  score: 67.3 bits;  conditional E-value: 1.2e-21
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll..p 75 
                                       l+s+p++++ +d+ +++l aN a+++ +g+p e + Gk +++l++  da+ ++++++ v+ +++pi+  ee+ +   
  gi|298675200|ref|YP_003726950.1| 267 LSSTPAYVYLKDSKLNYLTANDAFCKGVGLPVENIKGKNDFDLFSGNDAEKFRSDDASVMNSGKPIYNFEETYTtsK 343
                                       6799**************************************************************98888888899 PP

                             PAS_4  76 geerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                        e r+ +++++P +d +G vig+++ s DiTer+r
  gi|298675200|ref|YP_003726950.1| 344 CEKRWALTSKVPYFDVEGNVIGIVGSSLDITERKR 378
                                       9********************************97 PP

  == domain 4  score: 37.1 bits;  conditional E-value: 2.8e-12
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       lds+++++++ d +gr+l++N+aa +  g+ + +l+G+ ++ ll   +     + +++ l++++++e++ + ++   
  gi|298675200|ref|YP_003726950.1| 394 LDSTSEIVVYHDLEGRILWCNKAATKFTGLNGSDLIGQYCYKLLYNKSEICDNCLINEILKTGKHQEETVTFTD--- 467
                                       799999***********************************99887555555679**********999997777... PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTer 108
                                        r++++ + P+rd+sG++ig++ ++ DiT+ 
  gi|298675200|ref|YP_003726950.1| 468 -RILNIKKDPVRDTSGDIIGIISVGNDITDK 497
                                       .****************************86 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.9e-06     0.002      13     104 .]      43     125 ..      26     125 .. 0.84
   2 !   37.3   0.2   2.5e-12   2.6e-09       2     104 .]     149     248 ..     148     248 .. 0.87
   3 !   32.8   0.0     6e-11   6.3e-08       6     104 .]     276     375 ..     271     375 .. 0.91
   4 !   49.0   0.2   5.4e-16   5.7e-13       6     104 .]     403     496 ..     398     496 .. 0.94
   5 ?   -3.2   0.1       9.7     1e+04      50      71 ..     526     545 ..     501     558 .. 0.54
   6 ?   -1.4   0.0       2.7   2.8e+03      60      82 ..     707     729 .]     681     729 .] 0.75

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.9e-06
                             PAS_9  13 ilyaNeaalrllGyspeevlgksitdlf.vtdpeanerlraaleqgrkkerevevvlirkngetfwvlltaspvkdd 88 
                                       i+++N+a +  +G +++evlgk+ ++++  ++p + ++ +++ e+g+  +  +e+ +   +    +  +++s++  +
  gi|298675200|ref|YP_003726950.1|  43 IIDCNPAYESTIGLKKDEVLGKKASEVYgTDEPPHLSTYAKVAETGE--QTYFETYFPPFDK---Y--FKISAISPE 112
                                       78***************************99***************9..9999999998887...6..455556445 PP

                             PAS_9  89 dgelvgiivilrDite 104
                                       +g++v    i++Dite
  gi|298675200|ref|YP_003726950.1| 113 KGKFV---TIFNDITE 125
                                       66655...59999997 PP

  == domain 2  score: 37.3 bits;  conditional E-value: 2.5e-12
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetf 76 
                                       d+ ++ + +g+il++Ne+a + lGys++e+l  +++d+   +++   + +l ++ e+g+   +++e v++++ng+++
  gi|298675200|ref|YP_003726950.1| 149 DALFVGDLEGNILDVNETAVKRLGYSKKEILSMHVKDIDglYNENGVKTKLMNLPENGK---QRFESVHVTNNGNKI 222
                                       56777669************************998888866677777777777777777...*************** PP

                             PAS_9  77 wvlltaspvkdddgelvgiivilrDite 104
                                       +v+++   +   +++ v+  +++r+it+
  gi|298675200|ref|YP_003726950.1| 223 PVEINSNLISYRGKTAVL--SVVRNITD 248
                                       *********888888888..******96 PP

  == domain 3  score: 32.8 bits;  conditional E-value: 6e-11
                             PAS_9   6 idnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwvll 80 
                                       + +++ + l aN+a+++  G   e + gk+ +dlf   ++++ +++ + ++++g+ + +++e ++++++ e+ w+l 
  gi|298675200|ref|YP_003726950.1| 276 LKDSKLNYLTANDAFCKGVGLPVENIKGKNDFDLFsgNDAEKFRSDDASVMNSGK-PIYNFEETYTTSKCEKRWALT 351
                                       5567888999*************************88888888888888888888.9******************** PP

                             PAS_9  81 taspvkdddgelvgiivilrDite 104
                                       + +p +d +g+++gi++ + Dite
  gi|298675200|ref|YP_003726950.1| 352 SKVPYFDVEGNVIGIVGSSLDITE 375
                                       ***********************8 PP

  == domain 4  score: 49.0 bits;  conditional E-value: 5.4e-16
                             PAS_9   6 idnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwvll 80 
                                         + +gril++N+aa +++G +  +++g+++  l+  +++  +n+ ++++l++g+   +e++v+++++       ++
  gi|298675200|ref|YP_003726950.1| 403 YHDLEGRILWCNKAATKFTGLNGSDLIGQYCYKLLynKSEICDNCLINEILKTGK--HQEETVTFTDR-----ILNI 472
                                       356899*************************************************..9**********.....778* PP

                             PAS_9  81 taspvkdddgelvgiivilrDite 104
                                       +  pv+d++g ++gii++ +Dit+
  gi|298675200|ref|YP_003726950.1| 473 KKDPVRDTSGDIIGIISVGNDITD 496
                                       ***********************6 PP

  == domain 5  score: -3.2 bits;  conditional E-value: 9.7
                             PAS_9  50 lraaleqgrkkerevevvlirk 71 
                                        ++++++ r   re e++++ k
  gi|298675200|ref|YP_003726950.1| 526 TEEIINAER--TRELELHHRIK 545
                                       233333333..55555555555 PP

  == domain 6  score: -1.4 bits;  conditional E-value: 2.7
                             PAS_9  60 kerevevvlirkngetfwvllta 82 
                                        + +++++  + ng++f +++t+
  gi|298675200|ref|YP_003726950.1| 707 DQINGDLEVETINGTKFVIKFTC 729
                                       4788999999*******998875 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   5.9e-05     0.062      23      71 ..      43      87 ..      39      95 .. 0.84
   2 !   23.0   0.0   5.7e-08     6e-05       6     111 ..     143     244 ..     138     246 .. 0.86
   3 !   34.4   0.0   1.7e-11   1.7e-08       4     111 ..     264     371 ..     261     373 .. 0.96
   4 !   42.2   0.0   6.5e-14   6.8e-11       2     113 .]     389     494 ..     388     494 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.9e-05
                                      EEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT- CS
                               PAS 23 ilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgee 71
                                      i+ +N+a+e+  Gl+ +evlgk+ ++++ ++     + +l+++++++e 
  gi|298675200|ref|YP_003726950.1| 43 IIDCNPAYESTIGLKKDEVLGKKASEVYGTD----EPPHLSTYAKVAET 87
                                      899************************9887....77777777766655 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 5.7e-08
                                       HHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECT CS
                               PAS   6 ileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfklr 82 
                                       +++s+ d+ fv D  g+il vN++a + lG+s +e+l+ ++  +i   +++  ++  + +l ++ ++r + + ++  
  gi|298675200|ref|YP_003726950.1| 143 LFDSMEDALFVGDLEGNILDVNETAVKRLGYSKKEILSMHVK-DIDGLYNENGVKTKLMNLPENGKQRFESVHVTN- 217
                                       7899**********************************9888.666666665999999999999999999999999. PP

                                       TSSEEEEEEEEEEEEETTEEEEEEEEEEE CS
                               PAS  83 dgrpihlevraspvrdaggeilgflgvlr 111
                                       +g +i++e++ + +  +g++   +l v+r
  gi|298675200|ref|YP_003726950.1| 218 NGNKIPVEINSNLISYRGKT--AVLSVVR 244
                                       **********9999999876..6766666 PP

  == domain 3  score: 34.4 bits;  conditional E-value: 1.7e-11
                                       HHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEE CS
                               PAS   4 raileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfk 80 
                                       +a+l+s+p+ + + D + + l +N+a+++  Gl+ e + gk+ +dl++ +d +++++    ++++g++  ++e + +
  gi|298675200|ref|YP_003726950.1| 264 KALLSSTPAYVYLKDSKLNYLTANDAFCKGVGLPVENIKGKNDFDLFSGNDAEKFRSDDASVMNSGKPIYNFEETYT 340
                                       789************************************************99************************ PP

                                       CTTSSEEEEEEEEEEEEETTEEEEEEEEEEE CS
                               PAS  81 lrdgrpihlevraspvrdaggeilgflgvlr 111
                                       + + +++++++  +p++d +g+++g++g   
  gi|298675200|ref|YP_003726950.1| 341 TSKCEKRWALTSKVPYFDVEGNVIGIVGSSL 371
                                       **************************99655 PP

  == domain 4  score: 42.2 bits;  conditional E-value: 6.5e-14
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       + r il+s+ + ++  D  gril++N+aa++++Gl+ ++++g+  + l+ ++ +++   +l + ++ + + + + ++
  gi|298675200|ref|YP_003726950.1| 389 EKRVILDSTSEIVVYHDLEGRILWCNKAATKFTGLNGSDLIGQYCYKLLYNK-SEICDNCLINEILKTGKHQEETVT 464
                                       5689*********************************************655.557888888888888888999999 PP

                                       EECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  79 fklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       f+      + l +   pvrd +g i+g++ v++di
  gi|298675200|ref|YP_003726950.1| 465 FTD-----RILNIKKDPVRDTSGDIIGIISVGNDI 494
                                       999.....**************************8 PP

>> HisKA_2  Histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       5.8   6.1e+03      24      57 ..     378     390 ..     362     399 .. 0.56
   2 !   98.6   1.4   1.5e-31   1.6e-28       1      75 [.     539     613 ..     539     614 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 5.8
                           HisKA_2  24 akdeevkealresqnRvlsialiheeLyksedle 57 
                                                             +he+L kse  +
  gi|298675200|ref|YP_003726950.1| 378 R---------------------MHERLEKSEYEK 390
                                       3.....................355555554444 PP

  == domain 2  score: 98.6 bits;  conditional E-value: 1.5e-31
                           HisKA_2   1 EihHRvkNnLqvisslLslqarkakdeevkealresqnRvlsialiheeLyksedletvdfseylekLvenlfks 75 
                                       E+hHR+kNnLqvisslLslq+++++d +vk+a+ ++qnRv+s++l+h++Ly++++le+v+ ++y+e+Lv++l+ +
  gi|298675200|ref|YP_003726950.1| 539 ELHHRIKNNLQVISSLLSLQSENFTDGKVKDAFIDTQNRVISMSLVHNKLYQTNGLENVNSKDYIEDLVDHLVGL 613
                                       99*********************************************************************9876 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0     5e-05     0.053      10      58 ..      21      80 ..      14      90 .. 0.70
   2 !   24.7   0.0   1.6e-08   1.7e-05       4      51 ..     141     188 ..     138     198 .. 0.84
   3 ?    3.8   0.0     0.059        62       7      57 ..     267     315 ..     263     325 .. 0.64
   4 !   19.8   0.0   5.7e-07    0.0006       4      48 ..     391     436 ..     387     451 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5e-05
                             PAS_8 10 spdgiav....vdlgd.......rivdvNqaalellGys.adlkgellg.qllpvlrplled 58
                                      +++g++     +d  +       +i+d+N+a++   G++ ++++g++   +++++ +p l +
  gi|298675200|ref|YP_003726950.1| 21 MNEGVCFheiiYD--KkgypvdyLIIDCNPAYESTIGLKkDEVLGKKASeVYGTDEPPHLST 80
                                      6777774444334..223455567*********************99976666666665555 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 1.6e-08
                             PAS_8   4 ralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellgqllpv 51 
                                         lf+s+ d+++v d +g+ i+dvN++a + lGys ++++ + + +++++
  gi|298675200|ref|YP_003726950.1| 141 NYLFDSMEDALFVGDlEGN-ILDVNETAVKRLGYSkKEILSMHV-KDIDG 188
                                       679*********9785666.***************999998777.55555 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.059
                             PAS_8   7 fesspdgiavvdlgd..rivdvNqaalellGys.adlkgellgqllpvlrplle 57 
                                       + s p  + + d     + + +N+a+++  G++ + +k     ++++ + ++ +
  gi|298675200|ref|YP_003726950.1| 267 LSSTPAYVYLKD--SklNYLTANDAFCKGVGLPvENIK---GKNDFDLFSGNDA 315
                                       555566666444..2346899**********9843333...3466666666555 PP

  == domain 4  score: 19.8 bits;  conditional E-value: 5.7e-07
                             PAS_8   4 ralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgql 48 
                                       r +++s ++ ++  dl +ri+++N+aa +++G++  dl+g+ + +l
  gi|298675200|ref|YP_003726950.1| 391 RVILDSTSEIVVYHDLEGRILWCNKAATKFTGLNgSDLIGQYCYKL 436
                                       5689999999997886667*************88888777776544 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0       0.2   2.1e+02      38      86 ..     211     248 ..     168     280 .. 0.73
   2 !   29.8   0.0   6.2e-10   6.6e-07       5     107 ..     637     726 ..     633     728 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.2
                                       EEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHHHHHHH CS
                         HATPase_c  38 lvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsivkklve 86 
                                        ++ v++nG  ip+e+  +l            ++ g    ls+v+++++
  gi|298675200|ref|YP_003726950.1| 211 ESVHVTNNGNKIPVEINSNLI-----------SYRGKTAVLSVVRNITD 248
                                       5789999****9998766333...........35555556666666555 PP

  == domain 2  score: 29.8 bits;  conditional E-value: 6.2e-10
                                       HHHHHHHHHHHHHHHHHS...TTTEEEEEEEE.EETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHH CS
                         HATPase_c   5 rLrqiisnlvdNavkfat...kageieveika.seddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlG 77 
                                        L  ii +l++N++k+a    ++ge+ v + + +e+++++ v DnG+G ++e+                  + + lG
  gi|298675200|ref|YP_003726950.1| 637 PLGMIITELLSNSLKYAFfddEQGEVYVGLYQnDEEYYKLIVADNGKGFSEEIDI---------------EEPNTLG 698
                                       67789***********54545888999999975449**************98766...............24778** PP

                                       HHHHHHHHHHTTTEEEEEEETTTEEEEEEE CS
                         HATPase_c  78 lsivkklvelmgGeiwvesepgrGttftft 107
                                       l +v++lv++++G+++ve+    Gt+f+++
  gi|298675200|ref|YP_003726950.1| 699 LQLVNSLVDQINGDLEVETIN--GTKFVIK 726
                                       *****************8888..***9986 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.023        24       1      50 [.      43      89 ..      43      97 .. 0.72
   2 ?    3.1   0.0      0.11   1.1e+02       2      28 ..     161     185 ..     160     239 .. 0.76
   3 !   12.7   0.0   0.00011      0.12       2      87 ..     284     368 ..     283     370 .. 0.96
   4 ?   -3.0   0.0       8.6   9.1e+03       2      25 ..     411     432 ..     410     439 .. 0.81
   5 ?   -2.5   0.2       6.2   6.6e+03      38      66 ..     500     530 ..     496     543 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.023
                             PAS_3  1 iiyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge 50
                                      ii +++++e ++G+ ++e+lgk  + ++ v+  D +   +++++++++ge
  gi|298675200|ref|YP_003726950.1| 43 IIDCNPAYESTIGLKKDEVLGK--K-ASEVYGTDEPPHLSTYAKVAETGE 89
                                      589*******************..4.444555555666666666777776 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.11
                             PAS_3   2 iyvserveeilGyspeellgkveswld 28 
                                       + v+e+  + lGys+ e+l+   +++d
  gi|298675200|ref|YP_003726950.1| 161 LDVNETAVKRLGYSKKEILSM--HVKD 185
                                       67999999***********99..4444 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 0.00011
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvird 77 
                                       +++++++++ +G+  e ++gk  +  dl    D e++r++ + ++++g+  y++e  + +   e rw  ++ ++++d
  gi|298675200|ref|YP_003726950.1| 284 LTANDAFCKGVGLPVENIKGK--NDFDLFSGNDAEKFRSDDASVMNSGKpIYNFEETYTTSKCEKRWALTSKVPYFD 358
                                       689******************..99************************777************************* PP

                             PAS_3  78 engkpvrvig 87 
                                        +g+++ ++g
  gi|298675200|ref|YP_003726950.1| 359 VEGNVIGIVG 368
                                       ********99 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 8.6
                             PAS_3   2 iyvserveeilGyspeellgkves 25 
                                       + ++++  + +G+  ++l+g+   
  gi|298675200|ref|YP_003726950.1| 411 LWCNKAATKFTGLNGSDLIGQ--Y 432
                                       679999999****99999998..4 PP

  == domain 5  score: -2.5 bits;  conditional E-value: 6.2
                             PAS_3  38 vrealqealkkgepy..egeyRirrkdGeyr 66 
                                       ++e++q+++++ e++  e e+R+r++  e++
  gi|298675200|ref|YP_003726950.1| 500 TEEKIQRYAEELEKMnrELEHRVRKQTEEII 530
                                       5566666665555442255677777766665 PP

>> sCache_3_2  Single cache domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.023        24     103     122 ..     348     367 ..     317     379 .. 0.83
   2 !   16.7   0.0   5.7e-06     0.006      85     127 ..     451     493 ..     448     506 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.023
                        sCache_3_2 103 pslrvklPvfdadgrviGiv 122
                                        +l+ k+P+fd +g viGiv
  gi|298675200|ref|YP_003726950.1| 348 WALTSKVPYFDVEGNVIGIV 367
                                       57899**************8 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 5.7e-06
                        sCache_3_2  85 aalkagrayvgtvtgtlgpslrvklPvfdadgrviGivsvGvk 127
                                       ++lk g+++ +tvt+t+      k Pv+d +g++iGi+svG +
  gi|298675200|ref|YP_003726950.1| 451 EILKTGKHQEETVTFTDRILNIKKDPVRDTSGDIIGIISVGND 493
                                       78999************99999*******************65 PP

>> sCache_3_3  Single cache domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       2.7   2.8e+03      61      82 ..      80     101 ..      57     110 .. 0.79
   2 !    7.8   0.0    0.0041       4.3      57     102 ..     327     378 ..     312     382 .. 0.78
   3 !   12.3   0.0   0.00017      0.17      51      99 ..     448     496 ..     417     503 .. 0.88
   4 ?   -1.9   0.0       4.1   4.3e+03      36      69 ..     657     692 ..     649     697 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.7
                        sCache_3_3  61 tysgraeilgkkyltaYePlkd 82 
                                       ty + ae   + y+  Y P +d
  gi|298675200|ref|YP_003726950.1|  80 TYAKVAETGEQTYFETYFPPFD 101
                                       6888888889999999998777 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0041
                        sCache_3_3  57 kkGet.ys.....graeilgkkyltaYePlkdadgkviGmlfvGlpeeevqa 102
                                       ++G++ y+      + +   ++ lt  +P +d +g+viG++  +l+++e + 
  gi|298675200|ref|YP_003726950.1| 327 NSGKPiYNfeetyTTSKCEKRWALTSKVPYFDVEGNVIGIVGSSLDITERKR 378
                                       555553334444478888999********************99999887655 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00017
                        sCache_3_3  51 vaeavlkkGetysgraeilgkkyltaYePlkdadgkviGmlfvGlpeee 99 
                                        ++++lk G+  +++++  ++      +P++d +g++iG++ vG ++++
  gi|298675200|ref|YP_003726950.1| 448 LINEILKTGKHQEETVTFTDRILNIKKDPVRDTSGDIIGIISVGNDITD 496
                                       567889999999999999999999999*****************99876 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 4.1
                        sCache_3_3  36 kedgeravGtklseevaea..vlkkGetysgraeil 69 
                                       +e+ge  vG + ++e +++  v  +G+ +s++++i 
  gi|298675200|ref|YP_003726950.1| 657 DEQGEVYVGLYQNDEEYYKliVADNGKGFSEEIDIE 692
                                       677888888888888666522556777788887775 PP

>> HWE_HK  HWE histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.2       7.3   7.7e+03       1       7 [.     517     523 ..     504     525 .. 0.67
   2 !   24.7   0.0   2.7e-08   2.8e-05       1      53 [.     539     593 ..     539     625 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 7.3
                                       HHHHHHH CS
                            HWE_HK   1 ElnHRvK 7  
                                       El+HRv+
  gi|298675200|ref|YP_003726950.1| 517 ELEHRVR 523
                                       5666664 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 2.7e-08
                                       HHHHHHHHHHHHHHHHHHHHSSSXS-..HHHHHHHHHHHHHHHHHHHHHHHHCTT CS
                            HWE_HK   1 ElnHRvKNlLavvqsiarqtlrsaes..leefaeklsgRLqALsaahdllsreew 53 
                                       El+HR+KN L v++s+ +  +++ ++  ++++  + ++R+ ++s +h+ l +++ 
  gi|298675200|ref|YP_003726950.1| 539 ELHHRIKNNLQVISSLLSLQSENFTDgkVKDAFIDTQNRVISMSLVHNKLYQTNG 593
                                       9****************988776544126777778899***********988774 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       2.9   3.1e+03      37      83 ..      60     106 ..      47     124 .. 0.76
   2 ?   -2.0   0.0       5.3   5.6e+03      38      81 ..     178     222 ..     141     228 .. 0.58
   3 ?    6.6   0.0     0.011        12      72     106 .]     338     374 ..     294     374 .. 0.84
   4 !   11.0   0.0   0.00048      0.51       4     106 .]     393     495 ..     391     495 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.9
                            PAS_10  37 advGrpladihpkkavknveeviealrtgekdevevvvpkngkwvlv 83 
                                       + +G + +++  +++ +++    +   tge+ + e++ p  +k++ +
  gi|298675200|ref|YP_003726950.1|  60 EVLGKKASEVYGTDEPPHLSTYAKVAETGEQTYFETYFPPFDKYFKI 106
                                       45688888888889999999999999999999999999988888754 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.3
                            PAS_10  38 dvGrpladihpkkavknveevieal.rtgekdevevvvpkngkwv 81 
                                        +  +++di    +++ v+  + +l  +g++  ++v+v++ng+ +
  gi|298675200|ref|YP_003726950.1| 178 ILSMHVKDIDGLYNENGVKTKLMNLpENGKQRFESVHVTNNGNKI 222
                                       455566666666666666655544425666777788888887655 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.011
                            PAS_10  72 vvvp..kngkwvlvrylpyrdedgeiaGvvetfvDit 106
                                       ++ +   +++w l    py d +g++ G+v   +Dit
  gi|298675200|ref|YP_003726950.1| 338 TYTTskCEKRWALTSKVPYFDVEGNVIGIVGSSLDIT 374
                                       444333679***********************99997 PP

  == domain 4  score: 11.0 bits;  conditional E-value: 0.00048
                            PAS_10   4 lLnstpieltflDdnlqirrFtpaakklfklipad.vGrpladihpkkavknveeviealrtgekdevevvvpkngk 79 
                                       +L+st   +++ D + +i++ ++aa+k+  l+ +d +G    ++  +k++   + +i+++ ++ k+++e  v+  ++
  gi|298675200|ref|YP_003726950.1| 393 ILDSTSEIVVYHDLEGRILWCNKAATKFTGLNGSDlIGQYCYKLLYNKSEICDNCLINEILKTGKHQEE-TVTFTDR 468
                                       6888888999**********************9995699999997665444445555555555544444.45678** PP

                            PAS_10  80 wvlvrylpyrdedgeiaGvvetfvDit 106
                                       +  ++  p+rd+ g+i G++ +  Dit
  gi|298675200|ref|YP_003726950.1| 469 ILNIKKDPVRDTSGDIIGIISVGNDIT 495
                                       ********************9999996 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.1e-06    0.0012      32     113 ..     638     710 ..     628     727 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.1e-06
                       HATPase_c_2  32 irlaveEactNavehayleapegpvevrlesdeea.ltvevaDsGpgfdpetlpdpteeepkeslkegGrGlalikg 107
                                       + + ++E+++N  ++a  ++++g+v v l +++e+  ++ vaD+G+gf  e           + ++++ +Gl l+++
  gi|298675200|ref|YP_003726950.1| 638 LGMIITELLSNSLKYAFFDDEQGEVYVGLYQNDEEyYKLIVADNGKGFSEEI----------DIEEPNTLGLQLVNS 704
                                       67899***********************66555555*************985..........6778999******** PP

                       HATPase_c_2 108 lvDeve 113
                                       lvD+++
  gi|298675200|ref|YP_003726950.1| 705 LVDQIN 710
                                       ***984 PP

>> Cache_3-Cache_2  Cache 3/Cache 2 fusion domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.45   4.7e+02     147     179 ..     343     374 ..     331     408 .. 0.79
   2 !   12.1   0.0   8.3e-05     0.088     158     183 ..     475     500 ..     451     506 .. 0.88
   3 ?    3.8   0.7     0.027        29       6      52 ..     512     569 ..     510     606 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.45
                   Cache_3-Cache_2 147 kvfgkwYvTaYePikdadgkViGilyVgvdqse 179
                                       k   +w +T   P  d +g+ViGi+   +d+  
  gi|298675200|ref|YP_003726950.1| 343 KCEKRWALTSKVPYFDVEGNVIGIVGSSLDI-T 374
                                       56678999999*************9555555.3 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 8.3e-05
                   Cache_3-Cache_2 158 ePikdadgkViGilyVgvdqsealks 183
                                       +P++d +g++iGi+ Vg d+++ +k+
  gi|298675200|ref|YP_003726950.1| 475 DPVRDTSGDIIGIISVGNDITDKVKT 500
                                       7*******************999875 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.027
                   Cache_3-Cache_2   6 eevnklieeelekevedlaetletqdellrekverdlnvfakllsn...........e 52 
                                       e++n++ e++++k++e + +  +t++  l+ +++++l+v+++lls            +
  gi|298675200|ref|YP_003726950.1| 512 EKMNRELEHRVRKQTEEIINAERTRELELHHRIKNNLQVISSLLSLqsenftdgkvkD 569
                                       5789999************************************998444444333332 PP

>> PAS_12  UPF0242 C-terminal PAS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1      0.13   1.4e+02      63     133 ..     154     226 ..     123     234 .. 0.71
   2 ?   -1.1   0.0       1.3   1.3e+03      79     122 ..     310     353 ..     304     358 .. 0.85
   3 !    9.8   0.0   0.00054      0.57      55      89 ..     396     430 ..     387     440 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.13
                            PAS_12  63 sqkenkllfaNaqirallGwssdkflqdfseivqegleeW..kralaklsskteskirlvlKtKagqevllnc 133
                                          e  +l +N+   + lG+s+ ++l+   + ++  ++e   k++l +l  +  ++ + v  t +g+++++++
  gi|298675200|ref|YP_003726950.1| 154 GDLEGNILDVNETAVKRLGYSKKEILSMHVKDIDGLYNENgvKTKLMNLPENGKQRFESVHVTNNGNKIPVEI 226
                                       566888999***************9998888888777775113444444444444444455667777776665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.3
                            PAS_12  79 llGwssdkflqdfseivqegleeWkralaklsskteskirlvlK 122
                                       + G  ++kf +d +++++ g+  ++ + + ++sk e++  l+ K
  gi|298675200|ref|YP_003726950.1| 310 FSGNDAEKFRSDDASVMNSGKPIYNFEETYTTSKCEKRWALTSK 353
                                       568899***************99999999999999988887766 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00054
                            PAS_12  55 nlgailvysqkenkllfaNaqirallGwssdkflq 89 
                                        ++ i+vy   e ++l+ N+   +++G++  +++ 
  gi|298675200|ref|YP_003726950.1| 396 STSEIVVYHDLEGRILWCNKAATKFTGLNGSDLIG 430
                                       5789************************9988875 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0037       3.9      65     112 ..      80     128 ..      60     131 .. 0.70
   2 ?    2.9   0.0      0.11   1.2e+02       2      52 ..     145     194 ..     144     254 .. 0.60
   3 ?   -1.4   0.0       2.4   2.5e+03      99     113 ..     365     379 ..     361     381 .. 0.84
   4 ?    4.5   0.1     0.035        37      68     115 .]     450     502 ..     394     502 .. 0.81
   5 ?   -3.0   0.4       7.6   8.1e+03      57      69 ..     520     532 ..     503     553 .. 0.40

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0037
                             PAS_7  65 rrlaaaragkphsfererpd.grvievrgnplpdgGfVttytDiTerrr 112
                                       +  + a++g++++fe   p   +  ++ +   ++g fVt+++DiTe+++
  gi|298675200|ref|YP_003726950.1|  80 TYAKVAETGEQTYFETYFPPfDKYFKISAISPEKGKFVTIFNDITEYKK 128
                                       555556666666666655432667777777778888**********987 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.11
                             PAS_7   2 enmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaerg 52 
                                       ++m++++ v D +++++ +N+  ++ l+++++ +   ++++++     e+g
  gi|298675200|ref|YP_003726950.1| 145 DSMEDALFVGDLEGNILDVNETAVKRLGYSKKEI-LSMHVKDIDGLYNENG 194
                                       7899999999999999999999999999988877.6777766644444443 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.4
                             PAS_7  99 GfVttytDiTerrra 113
                                       G+V +  DiTer+r 
  gi|298675200|ref|YP_003726950.1| 365 GIVGSSLDITERKRM 379
                                       8888899*****996 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.035
                             PAS_7  68 aaaragkphsfererpdgrvievrgnpl.....pdgGfVttytDiTerrraee 115
                                       +++ +  +h+ e  + + r++++++ p+     +  G++++ +DiT+++++ee
  gi|298675200|ref|YP_003726950.1| 450 NEILKTGKHQEETVTFTDRILNIKKDPVrdtsgDIIGIISVGNDITDKVKTEE 502
                                       5556677888888899999999999999443333369***********99986 PP

  == domain 5  score: -3.0 bits;  conditional E-value: 7.6
                             PAS_7  57 gdveaeverrlaa 69 
                                       ++v+++ e++++a
  gi|298675200|ref|YP_003726950.1| 520 HRVRKQTEEIINA 532
                                       1222222222222 PP

>> Peptidase_M3_N  Oligopeptidase F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.6   0.00014      0.15       8      47 ..     493     531 ..     487     534 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                    Peptidase_M3_N   8 ekleellkeepelaeyrfyleeilrqkphtLseeeEklLa 47 
                                       +  +++ + e+++++y+  le++ r+ +h+  ++ E++++
  gi|298675200|ref|YP_003726950.1| 493 DITDKVKT-EEKIQRYAEELEKMNRELEHRVRKQTEEIIN 531
                                       44555556.5****************************97 PP

>> DnaB  DnaB-like helicase N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.47     5e+02      73     102 ..     483     512 ..     437     513 .. 0.85
   2 ?    9.6   0.0   0.00086      0.91      51      88 ..     573     610 ..     545     616 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.47
                                       GHGT.HHHHHHHHHC-S-CCCHHHHHHHHH CS
                              DnaB  73 edvggaaylaelvaavpsaanieeyaeivk 102
                                       + +g ++   +++++v + ++i++yae ++
  gi|298675200|ref|YP_003726950.1| 483 DIIGIISVGNDITDKVKTEEKIQRYAEELE 512
                                       4567777788999*************9875 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00086
                                       HHTTTS-SHHHHHHHSCSSS-GGHGT.HHHHHHHHHC- CS
                              DnaB  51 yekgepiDlvtvkeelekkgkledvggaaylaelvaav 88 
                                        ++++ i + +v+++l +++ le+v+ ++y+++lv+  
  gi|298675200|ref|YP_003726950.1| 573 DTQNRVISMSLVHNKLYQTNGLENVNSKDYIEDLVDHL 610
                                       568899****************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (729 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1372  (0.0765241); expected 358.6 (0.02)
Passed bias filter:                      637  (0.035529); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.42
# Mc/sec: 5198.96
//
Query:       gi|298675201|ref|YP_003726951.1|  [L=119]
Description: hypothetical protein Metev_1292 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-08   32.8   0.0    6.6e-08   32.6   0.0    1.1  1  Mrr_cat   Restriction endonuclease
  ------ inclusion threshold ------
      0.032   14.0   0.0       0.04   13.7   0.0    1.2  1  DUF2840   Protein of unknown function (DUF2840)


Domain annotation for each model (and alignments):
>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.0   7.3e-12   6.6e-08       3     114 ..      10     115 ..       8     116 .. 0.89

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 7.3e-12
                                       TT-TTCHHHHHHHHHHHHSSSEEE---B-TTSSB--EEEETTEEEEEEEEEEE--TS-B-HHHHHHHHHHCTTS..S CS
                           Mrr_cat   3 kmspkeFeklvaellealGykeveltgrsgDggiDliakkdplgserilvqaKryknkvgvkeVqeligalkkrgad 79 
                                       +m +ke+ + v++++++ Gy+ v++ + + D g+Dl+a+ ++   e++ + +   +   +v  V+e+ +a  ++++d
  gi|298675201|ref|YP_003726951.1|  10 SMLWKELLQEVENYYKNRGYH-VQRIP-GIDTGADLLATLEG--VEKVSIKICS-REFASVSTVHEVSSAKIYYRCD 81 
                                       7889999999**********9.****8.88*********976..5677776644.5667899*************** PP

                                       EEEEEESS-B-HHHHHHHHTT--EEEE-HHHHHHH CS
                           Mrr_cat  80 kgifvttsdftkaAreeaeelnkieLldgdeLael 114
                                       ++ ++ t  f+k+ +  a+    ++L++++eL ++
  gi|298675201|ref|YP_003726951.1|  82 RAEIINTEPFSKEVELLADV-IDVKLINRNELGNI 115
                                       *******************9.9*********9775 PP

>> DUF2840  Protein of unknown function (DUF2840)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.5e-06      0.04      68      95 ..      27      54 ..      20      86 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.5e-06
                           DUF2840 68 pgeavqtlpfvrpGgeiLLrvegwpkVe 95
                                      +g +vq++p++++G+++L  +eg +kV 
  gi|298675201|ref|YP_003726951.1| 27 RGYHVQRIPGIDTGADLLATLEGVEKVS 54
                                      67799*********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 876.44
//
Query:       gi|298675202|ref|YP_003726952.1|  [L=128]
Description: hypothetical protein Metev_1293 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-05   24.5   0.0    3.2e-05   24.2   0.0    1.2  1  PTH2      Peptidyl-tRNA hydrolase PTH2
  ------ inclusion threshold ------
       0.12   12.5   0.1        0.2   11.7   0.1    1.4  1  Mhr1      Transcriptional regulation of mitochondrial recombi


Domain annotation for each model (and alignments):
>> PTH2  Peptidyl-tRNA hydrolase PTH2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   3.6e-09   3.2e-05      21     115 ..      20     126 ..      12     128 .] 0.77

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3.6e-09
                                       HHHHHHHHHHHHHHHH..................CHHHHHHHHHHT.TTSEEEEEESSHHHHHHHHHHHH.HTT-SE CS
                              PTH2  21 qcahAavalvkkllkes.................nekellkeWeee.gqkkivlkveseeeLlelaakak.alglpa 78 
                                       qc +  v +++++l+++                 n +  ++ W     q  + l +++ +e++el++ka    g+pa
  gi|298675202|ref|YP_003726952.1|  20 QCRQVIVYCTQSYLSHEdyvdkidhvakasinkaN-EMDYDIWCCYcYQDTVLLMCNDFSEMDELYEKAVyGVGVPA 95 
                                       55555556666666655555555554444443323.356899*9888******************999862689*** PP

                                       EEEEETSSSSSSTTCEEEEEEEEEEHHHHHHHHTTSE CS
                              PTH2  79 alirDagrtqiepgtkTvlaigPapksivdkvtgkLk 115
                                       + i +      + +   ++aigPa+++i+d++++++ 
  gi|298675202|ref|YP_003726952.1|  96 SFICN------KNNNMIMMAIGPAKAQIIDNLVKNFD 126
                                       *****......9999******************9986 PP

>> Mhr1  Transcriptional regulation of mitochondrial recombination
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   2.3e-05       0.2       9      54 ..      19      66 ..      16      86 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.3e-05
                              Mhr1  9 nletgqVvYSltrvleknkalkqlpfvgkkqvp..aklRkDlWkplav 54
                                      +  ++ +vY +++ l++++ + ++ +v k +++  +++  D+W +++ 
  gi|298675202|ref|YP_003726952.1| 19 HQCRQVIVYCTQSYLSHEDYVDKIDHVAKASINkaNEMDYDIWCCYCY 66
                                      55667789************************65589999******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       975  (0.0543812); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 960.74
//
Query:       gi|298675203|ref|YP_003726953.1|  [L=434]
Description: putative PAS/PAC sensor protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-34  116.9   0.3    4.4e-19   68.6   0.2    2.4  2  PAS_3     PAS fold
    1.4e-11   44.8   0.0    2.1e-11   44.3   0.0    1.3  1  GAF_2     GAF domain
    4.7e-07   30.0   0.7    9.5e-05   22.6   0.1    2.4  2  PAS_9     PAS domain
    0.00065   19.7   0.3      0.031   14.3   0.1    3.3  3  PAS       PAS fold
    0.00079   19.5   0.0      0.067   13.3   0.0    2.3  2  PAS_11    PAS domain
     0.0011   19.3   0.0     0.0017   18.7   0.0    1.3  1  GAF_3     GAF domain
  ------ inclusion threshold ------
      0.026   15.1   0.0      0.045   14.4   0.0    1.4  1  GAF       GAF domain
      0.039   14.2   3.4       0.11   12.7   0.5    3.1  4  CdiA_C    Contact-dependent growth inhibition CdiA C-terminal
       0.05   13.9   0.0       0.49   10.7   0.0    2.4  3  PAS_4     PAS fold
        0.1   12.6   0.1       0.71    9.9   0.0    2.1  2  SpoVT_C   Stage V sporulation protein T C-terminal, transcrip


Domain annotation for each model (and alignments):
>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.0   2.2e-15   3.9e-12      12      79 ..      25      93 ..      20     103 .. 0.89
   2 !   68.6   0.2   2.4e-22   4.4e-19       3      89 .]     153     239 ..     151     239 .. 0.94

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 2.2e-15
                             PAS_3 12 lGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvirden 79
                                      +Gy +++l++   ++ld+vhp D++ v ++++ + k+g+ +++ +yR+++ +G++rwv +++  + + +
  gi|298675203|ref|YP_003726953.1| 25 FGYARDDLTSGNINYLDIVHPKDIDDVTKNFASCSKSGSdDISLQYRVITNSGDIRWVNEKVISHANTD 93
                                      8***********************************************************988884444 PP

  == domain 2  score: 68.6 bits;  conditional E-value: 2.4e-22
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvirde 78 
                                       +vs+++ + +Gy+p+e+     ++ d+++p+D+erv+ +l +  +kg+ ++++eyRi++k+G++rwv++r+++ rd+
  gi|298675203|ref|YP_003726953.1| 153 FVSDNINR-FGYTPDEFVTGELQYGDIIYPDDLERVQYELCKRREKGHnDFSQEYRIVTKSGKIRWVDERTFIQRDK 228
                                       67777755.5**********999************************99**************************** PP

                             PAS_3  79 ngkpvrvigva 89 
                                       +g+pv ++g++
  gi|298675203|ref|YP_003726953.1| 229 DGNPVSYQGII 239
                                       *********96 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.0   1.2e-14   2.1e-11       3     136 ..     267     401 ..     266     403 .. 0.90

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 1.2e-14
                                       HHHHHHHHHHHHHHHSS...EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B---TT.HHHHHHHHTS-EEES-GGG- CS
                             GAF_2   3 dleelldlvldelvelg.aalgyillvdddgglrlaawgeaeeefgaaldrplgeg.lvgealrtgrpvilndleed 77 
                                       ++ee+l++vld  +++g +++g+i+++d+ g+l l ++ +   ef   + + lg+  ++ ++++tg+pv+  d+ e 
  gi|298675203|ref|YP_003726953.1| 267 EPEEILNQVLDLTINIGiIDCGCIHFIDEYGNLNLMVYKGLSHEFVNNI-SYLGSNsILNRIIMTGQPVY-KDYSEI 341
                                       689*****************************99999999999999999.45677779************.99***9 PP

                                       S-HHHHH.HHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHH CS
                             GAF_2  78 pdkkglp.aghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaia 136
                                       p k+ l     ++lr+ + +Pl+ +g+v+G lnl+++  ++   + ++ +e++a+q++  
  gi|298675203|ref|YP_003726953.1| 342 PFKSDLFaNKNERLRAVALIPLVCNGEVLGSLNLSSHLYDEIPVDIRTAIETIAAQLGGF 401
                                       *9999997778888888*****8899********888778899999999*******9865 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.011        20      24     104 .]      25     107 ..      21     107 .. 0.73
   2 !   22.6   0.1   5.3e-08   9.5e-05      13     104 .]     151     244 ..     143     244 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.011
                             PAS_9  24 lGyspeevlgksitdlf.vtdpeanerlraaleqgrk..kerevevvlirkngetfwvlltaspvkdddgelvgiiv 97 
                                       +Gy ++++   +i  l  v++++ ++  +++    ++     + ++  i+++g   wv+ +++   +  +  + +++
  gi|298675203|ref|YP_003726953.1|  25 FGYARDDLTSGNINYLDiVHPKDIDDVTKNFASCSKSgsDDISLQYRVITNSGDIRWVNEKVISHAN-TDSSQQYLS 100
                                       7888888888886666554666666666666666666778999**************9955544433.445666789 PP

                             PAS_9  98 ilrDite 104
                                       i++Dit+
  gi|298675203|ref|YP_003726953.1| 101 IVIDITD 107
                                       *****96 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 5.3e-08
                             PAS_9  13 ilyaNeaalrllGyspeevlgks..itdlfvtdpeanerlraaleqgrk...kerevevvlirkngetfwvlltasp 84 
                                       ++++++  +r+ Gy+p+e++     + d++   p++ er++  l   r+   + +++e+ +++k+g+  wv+ + + 
  gi|298675203|ref|YP_003726953.1| 151 VEFVSDNINRF-GYTPDEFVTGElqYGDII--YPDDLERVQYELCKRREkghNDFSQEYRIVTKSGKIRWVDERTFI 224
                                       56888888888.******998877789999..44444444444444444489********************77766 PP

                             PAS_9  85 vkdddgelvgiivilrDite 104
                                        +d+dg+ v++ +i++Dit+
  gi|298675203|ref|YP_003726953.1| 225 QRDKDGNPVSYQGIIVDITD 244
                                       6799***************6 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0       0.3   5.4e+02      34      97 ..      25      90 ..      23     106 .. 0.55
   2 !   14.3   0.1   1.7e-05     0.031      34     113 .]     161     242 ..     123     242 .. 0.84
   3 ?   -3.2   0.0       4.7   8.4e+03       2      18 ..     247     263 ..     246     264 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.3
                                      HSSTHHHCTTSBG..GGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEEEEEEEE CS
                               PAS 34 lGlsreevlgksl..ldliheeddaelaelleqlleqgeesrageisfklrdgrpihlevraspvr 97
                                      +G++r+++ + ++  ld +h++d +++ + +  + ++g++  + + ++ +  g ++++   + +  
  gi|298675203|ref|YP_003726953.1| 25 FGYARDDLTSGNInyLDIVHPKDIDDVTKNFASCSKSGSDDISLQYRVITNSGDIRWVNEKVISHA 90
                                      566666665433310444444443366666777777777777777666666666666655554444 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.7e-05
                                       HSSTH.HHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEEEEEEEEETTEEEEEEEE CS
                               PAS  34 lGlsr.eevlgkslldliheedda.elaelleqlleqgeesrageisfklrdgrpihlevraspvrdaggeilgflg 108
                                       +G+++ e v g+  +++i+ +dd   ++ +l +++e g++  ++e ++ ++ g++++++ r+   rd++g++  + g
  gi|298675203|ref|YP_003726953.1| 161 FGYTPdEFVTGELQYGDIIYPDDLeRVQYELCKRREKGHNDFSQEYRIVTKSGKIRWVDERTFIQRDKDGNPVSYQG 237
                                       89999899***************98888899999999999999****************************999999 PP

                                       EEEES CS
                               PAS 109 vlrdi 113
                                       ++ di
  gi|298675203|ref|YP_003726953.1| 238 IIVDI 242
                                       98776 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 4.7
                                       HHHHHHHHSSSEEEEEE CS
                               PAS   2 dlraileslpdpifvvD 18 
                                       + ++il++ +d  +v++
  gi|298675203|ref|YP_003726953.1| 247 HTENILHTEHDIALVIN 263
                                       678999**999999987 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   3.7e-05     0.067      38     103 ..      37     102 ..      20     112 .. 0.81
   2 ?    3.8   0.0     0.034        61      40      92 ..     175     227 ..     160     242 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.7e-05
                            PAS_11  38 rsiydLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvkvktksklfknqksneqdfima 103
                                       + + d++hp+d  ++++ +     s  +  s+ yR +++++++ +v+ k     n++s++q   + 
  gi|298675203|ref|YP_003726953.1|  37 INYLDIVHPKDIDDVTKNFASCSKSGSDDISLQYRVITNSGDIRWVNEKVISHANTDSSQQYLSIV 102
                                       556799*****************7777788888****************99999999988865554 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.034
                            PAS_11  40 iydLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvkvktksklfkn 92 
                                       + d++ p+dl+++++ l +  ++  +  s+ yR+ ++++k+ +v  ++ + ++
  gi|298675203|ref|YP_003726953.1| 175 YGDIIYPDDLERVQYELCKRREKGHNDFSQEYRIVTKSGKIRWVDERTFIQRD 227
                                       458999**************97777778899*****99998777655555554 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   9.3e-07    0.0017       1     129 []     267     404 ..     267     404 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 9.3e-07
                             GAF_3   1 sldellekllkllvkllgaevgalllldedgn.klqvaagwdgkpalsesld..edsalarralssgevvse..... 69 
                                       +++e+l+++l+l+ ++   + g ++  de+gn +l v +g   ++ ++ ++     ++   r +++g++v++     
  gi|298675203|ref|YP_003726953.1| 267 EPEEILNQVLDLTINIGIIDCGCIHFIDEYGNlNLMVYKGL--SHEFVNNISylGSNSILNRIIMTGQPVYKdysei 341
                                       689****************************9999888998..7778888888666666668888899997767666 PP

                             GAF_3  70 ...psfaeedglpdraalavPLvagrqviGvlalastkprafdaedlelleslArqiataier 129
                                           +  +  + ++ra+ ++PLv   +v+G l l s+ + ++  + +  +e++A+q++  i+r
  gi|298675203|ref|YP_003726953.1| 342 pfkSDLFANKNERLRAVALIPLVCNGEVLGSLNLSSHLYDEIPVDIRTAIETIAAQLGGFIAR 404
                                       6654444567899***********66*********************************9987 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.5e-05     0.045       3     129 ..     269     398 ..     267     402 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.5e-05
                                       HHHHHHHHHHHHHHHTESEEEE.EEEEETTEEECEEEEECCEEEET.....TSHHHHHHHHHSSSEEESTGG...TS CS
                               GAF   3 eelldtvveelrellgadrval.ylpdydGlhydipqasrwlfmkn.....grgicgqvlatgqplvipdst...pd 70 
                                       ee+l++v++    +   d +++ ++++y  l+  ++ +++  f  n       +i ++++ tgqp+  + s    ++
  gi|298675203|ref|YP_003726953.1| 269 EEILNQVLDLTINIGIIDCGCIhFIDEYGNLNLMVYKGLSHEFVNNisylgSNSILNRIIMTGQPVYKDYSEipfKS 345
                                       67777777777777777777773343344443336667776555555445344588899999***999975576777 PP

                                       TTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEE..SSSCSHHHHHHHH.HHHHHHH CS
                               GAF  71 prfaqynrrdllenmgirsslvvPlvndgelwGllvlhn..psppftreelell.qvladqv 129
                                       + fa+       +n   r+++ +Plv +ge++G l l +   ++   + +++ + +++a+q+
  gi|298675203|ref|YP_003726953.1| 346 DLFAN-------KNERLRAVALIPLVCNGEVLGSLNLSShlYDE--IPVDIRTAiETIAAQL 398
                                       77888.......78999********************9943222..3333444446666665 PP

>> CdiA_C  Contact-dependent growth inhibition CdiA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.76   1.4e+03      38      81 .]      35      79 ..      32      79 .. 0.85
   2 ?   12.7   0.5   6.3e-05      0.11      23      60 ..      84     121 ..      70     132 .. 0.83
   3 ?   -1.7   0.0         2   3.6e+03      67      81 .]     201     215 ..     183     215 .. 0.74
   4 ?   -1.9   0.0       2.3   4.1e+03      39      52 ..     237     250 ..     235     256 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.76
                            CdiA_C 38 kni.vlnlrdsdlsieeikegieralkwpk.kglkeliiikkdgki 81
                                      +ni  l++   + +i++++++++ + k+   ++ +++ +i+++g+i
  gi|298675203|ref|YP_003726953.1| 35 GNInYLDIV-HPKDIDDVTKNFASCSKSGSdDISLQYRVITNSGDI 79
                                      567778888.788999999999999999999999999999999986 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 6.3e-05
                            CdiA_C  23 kniisnilkkakkQaknivlnlrdsdlsieeikegier 60 
                                       +++is++   + +Q  +iv++++ds++++e+++e ++ 
  gi|298675203|ref|YP_003726953.1|  84 EKVISHANTDSSQQYLSIVIDITDSKMEEEKLQETLAI 121
                                       499****************************9998875 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2
                            CdiA_C  67 kglkeliiikkdgki 81 
                                       +  +e+ i++k+gki
  gi|298675203|ref|YP_003726953.1| 201 DFSQEYRIVTKSGKI 215
                                       667899999999997 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 2.3
                            CdiA_C  39 nivlnlrdsdlsie 52 
                                        i+++++d++++++
  gi|298675203|ref|YP_003726953.1| 237 GIIVDITDRKHTEN 250
                                       58999999999854 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.68   1.2e+03      72     107 ..      72     107 ..      60     109 .. 0.65
   2 ?   10.7   0.0   0.00027      0.49      69     109 ..     205     246 ..     151     247 .. 0.82
   3 ?   -2.5   0.0       3.3   5.9e+03      75     102 ..     350     376 ..     321     379 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.68
                             PAS_4  72 lll.pgeerhyelrllPlrdesGevigvlvisrDiTe 107
                                       + + +g+ r+++  ++   +++   + +l i++DiT+
  gi|298675203|ref|YP_003726953.1|  72 VITnSGDIRWVNEKVISHANTDSS-QQYLSIVIDITD 107
                                       444567777777777666555555.778888888887 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00027
                             PAS_4  69 leelll.pgeerhyelrllPlrdesGevigvlvisrDiTerr 109
                                       +   ++ +g+ r+++ r +  rd +G ++ + +i++DiT+r+
  gi|298675203|ref|YP_003726953.1| 205 EYRIVTkSGKIRWVDERTFIQRDKDGNPVSYQGIIVDITDRK 246
                                       33344469**********999*******************97 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 3.3
                             PAS_4  75 pgeerhyelrllPlrdesGevigvlvis 102
                                       ++ er   + l+Pl   +Gev+g l +s
  gi|298675203|ref|YP_003726953.1| 350 NKNERLRAVALIPL-VCNGEVLGSLNLS 376
                                       66677777778888.6889998888766 PP

>> SpoVT_C  Stage V sporulation protein T C-terminal, transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1      0.62   1.1e+03      43      64 ..     118     140 ..     100     156 .. 0.72
   2 ?    9.9   0.0    0.0004      0.71      69     118 ..     344     396 ..     319     404 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.62
                           SpoVT_C  43 k.eiskeleklmeerktvlakke 64 
                                          i++ele+++++   ++++ +
  gi|298675203|ref|YP_003726953.1| 118 TlAIKDELESIINNSPAIVFQWK 140
                                       3379999***9999888777654 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0004
                           SpoVT_C  69 v...veeekeeysaqviaPIiaeGdviGaVillskeekkklgelekklaetaA 118
                                             +++e+++a +++P++++G+v+G+  l s+  ++   ++ + +  +aA
  gi|298675203|ref|YP_003726953.1| 344 KsdlFANKNERLRAVALIPLVCNGEVLGSLNLSSHLYDEIPVDIRTAIETIAA 396
                                       2333367778999*****************99988777766666655555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 2982.72
//
Query:       gi|298675204|ref|YP_003726954.1|  [L=179]
Description: hypothetical protein Metev_1296 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.3   10.5   4.2        9.1    5.7   0.4    2.9  3  DUF2608   Protein of unknown function (DUF2608)


Domain annotation for each model (and alignments):
>> DUF2608  Protein of unknown function (DUF2608)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.4   0.00051       9.1      21      35 ..      24      38 ..       7      51 .. 0.86
   2 ?    1.9   0.0    0.0072   1.3e+02      87     115 ..      57      84 ..      39     129 .. 0.67
   3 ?    4.0   0.1    0.0017        30     172     191 ..     128     147 ..     126     161 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.00051
                           DUF2608 21 vvfDiDdtLltstea 35
                                       vfD+DdtL t++++
  gi|298675204|ref|YP_003726954.1| 24 YVFDLDDTLATPDKE 38
                                      59********99875 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.0072
                           DUF2608  87 vpslvnnlqnqgttvlaLTarsptlrtat 115
                                       + ++ n+  +  + +++LT+r p l+ + 
  gi|298675204|ref|YP_003726954.1|  57 MIQFFNET-KSRHPTMILTTRHPDLKPKI 84 
                                       44566666.7788899*****99987654 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.0017
                           DUF2608 172 lLdkigrepksviFiDDkkk 191
                                       +L+++ +++ +viF DD  +
  gi|298675204|ref|YP_003726954.1| 128 VLNQLSEQYRKVIFFDDLVH 147
                                       689999***********765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1170.32
//
Query:       gi|298675205|ref|YP_003726955.1|  [L=195]
Description: resolvase domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      3e-19   69.6   0.1    3.5e-19   69.3   0.1    1.1  1  Resolvase  Resolvase, N terminal domain
  ------ inclusion threshold ------
      0.065   13.4   0.0       0.12   12.6   0.0    1.5  1  HTH_17     Helix-turn-helix domain
      0.069   12.0   0.0      0.093   11.6   0.0    1.2  1  Trp_syntA  Tryptophan synthase alpha chain


Domain annotation for each model (and alignments):
>> Resolvase  Resolvase, N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.3   0.1   5.9e-23   3.5e-19       2     134 ..      56     186 ..      55     195 .] 0.83

  Alignments for each domain:
  == domain 1  score: 69.3 bits;  conditional E-value: 5.9e-23
                                       EEEEEES-----THHHHHHHHHHHH-S--..SE...EEEE.S-TT-TT.-HHHHHHHHHHTT-EE.EEEESSCCCC- CS
                         Resolvase   2 igYaRvSteeqddslerQkealrayakenglkivkefeDkgvSGakle.RpglkrllaalregkgdvlvvekldRLa 77 
                                       ++YaRvSt++q+++le+Q+++l+ +a + g+++  +++D   SG + e R+++ ++l+++++ k++ +++   dRL+
  gi|298675205|ref|YP_003726955.1|  56 VIYARVSTSKQKKDLENQVQMLKTWAFNSGYQVNHIYSDV-SSGISFEkRKDFFKMLDEITNYKVENVIISYKDRLS 131
                                       89*******************************9******.*****555**************************** PP

                                       S...S-HHHHHHHHHTT-EEEESS..SS----H.HHHHHHHHHHHHHHHHHHHHCT-T CS
                         Resolvase  78 Rsvrdlltlleelrekgvslvsldegidtstpm.grlllqilaalaeferelirertk 134
                                       R  ++l+  ++ +++ g +++++++ i  ++    +++ +i + l  +  +l ++  +
  gi|298675205|ref|YP_003726955.1| 132 RVGFELF--YHLFSKYGTNIIVVSD-IGSKKLDdEEVFSEITSLLHCYSVNLYSKTRA 186
                                       *999998..789************9.43333332566777766666555555555554 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     2e-05      0.12       5      50 ..       4      50 ..       1      51 [. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2e-05
                            HTH_17  5 eEaAelLgvsrstvyrlirrgelpaak.iGrrwriprsdleewlekr 50
                                       ++ + L++ r t+yr + +g ++ +   ++++ ++ +++ ++l+k+
  gi|298675205|ref|YP_003726955.1|  4 GDVLKTLRITRPTLYRCVENGYIKRTLlPNGQYEYDDESVYAFLNKD 50
                                      577788*****************888345666999999999999985 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.6e-05     0.093      72     128 ..     105     159 ..      95     187 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHHHHHHHCSSS-EEEEE-CHHHCCC-HHHHCHHHHHCTEEEEEETTSBCCC CS
                         Trp_syntA  72 ekvlelveevrkkevevPivlltylnlvlsygeerflaelkeagvdglivpDlPlee 128
                                       ++++++++e++  + +v  v+++y + + ++g e f++ + + g + ++v D+  ++
  gi|298675205|ref|YP_003726955.1| 105 KDFFKMLDEIT--NYKVENVIISYKDRLSRVGFELFYHLFSKYGTNIIVVSDIGSKK 159
                                       67999*****9..667777999******************************97654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1040  (0.0580066); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1280.05
//
Query:       gi|298675206|ref|YP_003726956.1|  [L=400]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.1e-24   85.1   0.1    1.1e-23   83.8   0.1    1.7  1  OrfB_IS605      Probable transposase
    1.9e-12   46.9   0.0    4.9e-12   45.6   0.0    1.8  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    0.00017   21.0   0.8    0.00026   20.4   0.8    1.3  1  Glyco_hydro_97  Glycoside hydrolase 97
  ------ inclusion threshold ------
      0.065   13.3   0.5       0.14   12.2   0.1    1.8  2  Dynamin_N       Dynamin family
       0.18   12.2   0.9        1.6    9.1   0.1    2.3  2  HEPN_Swt1       Swt1-like HEPN
       0.33   11.4   2.6        1.1    9.7   0.4    2.8  3  ACP_PD          Acyl carrier protein phosphodiesterase


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.8   0.1   3.6e-27   1.1e-23       3     117 ..     168     281 ..     166     284 .. 0.92

  Alignments for each domain:
  == domain 1  score: 83.8 bits;  conditional E-value: 3.6e-27
                        OrfB_IS605   3 pvevevelpkpkgnkaagiDlGinnLatvvtedgtw.flykgrrlksdykylakeiaelqsklkksknykkasrkla 78 
                                       +++++ e+   ++n+ a+iDlGinn++t+v++ g+  +++kg  +ks ++y++k++ +  s+++k +     +++l 
  gi|298675206|ref|YP_003726956.1| 168 VYKQKIEHINLNENNIASIDLGINNIITMVNNIGEKpIVIKGGGVKSINQYYNKKKSQWKSFYDKRG--FDETKRLE 242
                                       5555555667789**********************99*****************************9..78888999 PP

                        OrfB_IS605  79 rlhrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       +l++kr++++++++hk+++++i+++ e++++tL++g+  
  gi|298675206|ref|YP_003726956.1| 243 KLYQKRNNKINDFFHKVSKKIINYCIENNIGTLVIGYNE 281
                                       ************************************986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.0   1.6e-15   4.9e-12       1      69 []     302     376 ..     302     376 .. 0.91

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 1.6e-15
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke......alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f klk+q+eyk +++Gikv+  +++yTSk +    +  ++      ++ +r +  +n g ++++Dvn+a+Nilk+
  gi|298675206|ref|YP_003726956.1| 302 FFKLKKQIEYKSEDAGIKVVFQEESYTSKCSFLDDEPIEKrtsylgKRIKRGLFKSNTGKVINADVNGAYNILKK 376
                                       789*************************97777777777689999988999999999****************96 PP

>> Glyco_hydro_97  Glycoside hydrolase 97
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.8   8.8e-08   0.00026      28     110 ..     251     332 ..     211     366 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 8.8e-08
                    Glyco_hydro_97  28 fkhgantetvkryiDfAaengleyvlvegwdegWee..kkkkekefdftkpypdfdleelvaYakekgvgvelwlhs 102
                                       + + +  +  k+ i+++ en++ ++++ g++egW++  +  k+ +++ + ++p f+l++ ++Y  e   g++++ ++
  gi|298675206|ref|YP_003726956.1| 251 KINDFFHKVSKKIINYCIENNIGTLVI-GYNEGWKQecNIGKK-NNQNFVQIPFFKLKKQIEYKSEDA-GIKVVFQE 324
                                       44555567789****************.*******98655544.55555689***********66554.88888888 PP

                    Glyco_hydro_97 103 etsgnvan 110
                                       e ++++ +
  gi|298675206|ref|YP_003726956.1| 325 ESYTSKCS 332
                                       87665544 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.7   4.9e+03      77      77 ..      60      60 ..       8     100 .. 0.58
   2 ?   12.2   0.1   4.6e-05      0.14      35      97 ..     204     270 ..     188     276 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.7
                                      H CS
                         Dynamin_N 77 e 77
                                      +
  gi|298675206|ref|YP_003726956.1| 60 N 60
                                      1 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 4.6e-05
                                       -EEEEECCT---C..CS...SSEEEE..T-EB--CHHHHHHHHHHHHHHHTSSSS--SS-EEEEEEE CS
                         Dynamin_N  35 plelqlgeeeeas..eravkeelkek..ekkledfsevreeieketekiagankgiskkvillkils 97 
                                       p++++ g  ++++   ++ k ++k++  ++ +++ +++++ ++k+++ki++   ++skk+i+++i +
  gi|298675206|ref|YP_003726956.1| 204 PIVIKGGGVKSINqyYNKKKSQWKSFydKRGFDETKRLEKLYQKRNNKINDFFHKVSKKIINYCIEN 270
                                       55565554444443345678889999999**********************************9875 PP

>> HEPN_Swt1  Swt1-like HEPN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1   0.00055       1.6      35      70 ..      49      86 ..      21      92 .. 0.66
   2 ?    1.0   0.1      0.17   5.2e+02      62      89 ..     224     250 ..     177     255 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00055
                         HEPN_Swt1 35 e.kdeeekkesekei.skldvqdllrvitenWkevFkk 70
                                      +  +ee k+ ++++i  ++++q+ l+++++nWk++F++
  gi|298675206|ref|YP_003726956.1| 49 QkVNEELKGTENYSIlPSQTAQQTLKMVDRNWKSFFNS 86
                                      224455554555555157889999**********7764 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.17
                         HEPN_Swt1  62 enWkevFkkklsraerslaseLrevRNk 89 
                                        +Wk+ F +k + +e +  ++L + RN+
  gi|298675206|ref|YP_003726956.1| 224 SQWKS-FYDKRGFDETKRLEKLYQKRNN 250
                                       39*99.9999999999999999999996 PP

>> ACP_PD  Acyl carrier protein phosphodiesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.4   0.00038       1.1      34      91 ..      22      82 ..      15      90 .. 0.68
   2 ?   -2.3   0.0         2   5.8e+03      81     101 ..     211     231 ..     192     234 .. 0.83
   3 ?   -1.7   0.1       1.3   3.9e+03      84     101 ..     240     257 ..     214     265 .. 0.52

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00038
                            ACP_PD 34 alPerlqrllprmieedwLesY..aelegieralqrma.rrlkrasklaeaieeleenyae 91
                                      +++++l + ++++i+++wL+ Y   + + +++ l++ + + +  ++  +++++ +++n + 
  gi|298675206|ref|YP_003726956.1| 22 HISKNLYNQANYIIRQNWLNGYgyTKYQKVNEELKGTEnYSILPSQTAQQTLKMVDRNWKS 82
                                      5677888999*********986115677899999998844444444455555555555544 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2
                            ACP_PD  81 aieeleenyaeleadFleffp 101
                                        ++ +++ y++ ++++++f+ 
  gi|298675206|ref|YP_003726956.1| 211 GVKSINQYYNKKKSQWKSFYD 231
                                       677889999999999999996 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.3
                            ACP_PD  84 eleenyaeleadFleffp 101
                                        le+ y++ +++ ++ff 
  gi|298675206|ref|YP_003726956.1| 240 RLEKLYQKRNNKINDFFH 257
                                       233333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1223  (0.0682135); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3020.90
//
Query:       gi|298675207|ref|YP_003726957.1|  [L=139]
Description: hypothetical protein Metev_1300 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-37  126.7   0.2    3.3e-37  126.4   0.2    1.1  1  DUF22     Domain of unknown function DUF22


Domain annotation for each model (and alignments):
>> DUF22  Domain of unknown function DUF22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.4   0.2   1.9e-41   3.3e-37       2     106 .]       6     110 ..       5     110 .. 0.99

  Alignments for each domain:
  == domain 1  score: 126.4 bits;  conditional E-value: 1.9e-41
                             DUF22   2 vkivyrkdgeivrekvevepfgytrstvakwelliAdedvevkkGevkkikikeielpentivvplsimrhalgtvl 78 
                                       v+iv+rk+ge++++kv+++p+++t++t+akwe+++Ad dv++++Ge+kki +ke+ ++++++++p+ +++ha+++vl
  gi|298675207|ref|YP_003726957.1|   6 VQIVSRKNGELKSTKVKASPYEFTMATRAKWETIVADGDVDIRAGEYKKIPVKELYIEPDMVAMPCIFSQHAVASVL 82 
                                       89*************************************************************************** PP

                             DUF22  79 dvvekgkpkkveeereiteavflpvedG 106
                                       ++++kg++k+veeer +++a+++++e+G
  gi|298675207|ref|YP_003726957.1|  83 RIGTKGGCKPVEEERLVNTAYVIGQETG 110
                                       **************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1022.26
//
Query:       gi|298675208|ref|YP_003726958.1|  [L=172]
Description: hypothetical protein Metev_1301 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.24   11.5   0.2       0.24   11.5   0.2    2.4  2  DZR            Double zinc ribbon
       0.54   10.2   0.0       0.54   10.2   0.0    2.8  2  DUF4428        Domain of unknown function (DUF4428)
       0.94    9.5   3.6          5    7.2   0.4    2.7  2  PriA_CRR       PriA DNA helicase Cys-rich region (CRR) domain
          2    7.9   6.7        4.7    6.8   0.1    2.8  3  zf-ribbon_3    zinc-ribbon domain
        6.6    6.7   8.9         49    3.9   0.1    3.2  3  PHD            PHD-finger


Domain annotation for each model (and alignments):
>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   1.6      0.44   1.6e+03      24      34 ..      20      30 ..       6      37 .. 0.45
   2 ?   11.5   0.2   6.7e-05      0.24      11      39 ..     128     164 ..     124     168 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.44
                               DZR 24 avaaedrCpsC 34
                                      ++++ + C  C
  gi|298675208|ref|YP_003726958.1| 20 QYESYNICTGC 30
                                      22224444444 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 6.7e-05
                               DZR  11 darfCseCgtklkavaa........edrCpsCgekvd 39 
                                       d+ +C++C ++l +  +           C++C++ ++
  gi|298675208|ref|YP_003726958.1| 128 DNYVCPNCSASLFEKYTtnsigewfVVSCSNCDTLLK 164
                                       6789*******97666689*************98765 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   5.0       2.8     1e+04       2       7 ..       9      14 ..       8      47 .. 0.72
   2 ?   10.2   0.0   0.00015      0.54      17      30 ..     126     139 ..     120     153 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.8
                           DUF4428  2 CaiCgk 7 
                                      CaiC++
  gi|298675208|ref|YP_003726958.1|  9 CAICDD 14
                                      888865 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00015
                           DUF4428  17 leDgyvCkdClkKl 30 
                                       ++D+yvC++C   l
  gi|298675208|ref|YP_003726958.1| 126 FKDNYVCPNCSASL 139
                                       79********8765 PP

>> PriA_CRR  PriA DNA helicase Cys-rich region (CRR) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.4    0.0014         5       1       8 [.     132     139 ..     132     140 .. 0.95
   2 ?    2.3   0.2     0.048   1.7e+02       1       9 [.     156     164 ..     156     171 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0014
                          PriA_CRR   1 CpnCdvsl 8  
                                       CpnC++sl
  gi|298675208|ref|YP_003726958.1| 132 CPNCSASL 139
                                       ******98 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.048
                          PriA_CRR   1 CpnCdvslt 9  
                                       C nCd  l+
  gi|298675208|ref|YP_003726958.1| 156 CSNCDTLLK 164
                                       *****8665 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.3       1.6   5.7e+03      19      22 ..       9      12 ..       8      13 .. 0.74
   2 ?    4.4   0.3    0.0071        25       4       8 ..     131     135 ..     127     139 .. 0.66
   3 ?    6.8   0.1    0.0013       4.7       3      13 ..     154     164 ..     152     165 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.6
                       zf-ribbon_3 19 CpyC 22
                                      C+ C
  gi|298675208|ref|YP_003726958.1|  9 CAIC 12
                                      8888 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0071
                       zf-ribbon_3   4 rCPnC 8  
                                        CPnC
  gi|298675208|ref|YP_003726958.1| 131 VCPNC 135
                                       46666 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0013
                       zf-ribbon_3   3 vrCPnCGapls 13 
                                       v+C+nC+++l+
  gi|298675208|ref|YP_003726958.1| 154 VSCSNCDTLLK 164
                                       89****99766 PP

>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   2.0     0.027        95       2      22 ..       9      31 ..       8      34 .. 0.83
   2 ?    3.9   0.1     0.014        49      42      51 ..     128     137 ..     117     138 .. 0.84
   3 ?    2.6   0.0     0.036   1.3e+02      14      23 ..     152     161 ..     143     164 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.027
                                      BTTTTS..TTSTTSCEEEETTTS CS
                               PHD  2 CavCkk..ksdeeeelvqCdgCk 22
                                      Ca+C++  +s++ e    C gC 
  gi|298675208|ref|YP_003726958.1|  9 CAICDDvqDSKQYESYNICTGCV 31
                                      ******98777888899999996 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.014
                                       STBSSTTTHT CS
                               PHD  42 gewlCekCke 51 
                                       ++++C++C+ 
  gi|298675208|ref|YP_003726958.1| 128 DNYVCPNCSA 137
                                       48******85 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.036
                                       CEEEETTTSC CS
                               PHD  14 elvqCdgCkr 23 
                                       ++v+C +C++
  gi|298675208|ref|YP_003726958.1| 152 FVVSCSNCDT 161
                                       6799999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1054  (0.0587874); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.35
# Mc/sec: 1453.06
//
Query:       gi|298675209|ref|YP_003726959.1|  [L=87]
Description: alkylhydroperoxidase-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-14   53.5   0.0    2.2e-14   53.3   0.0    1.1  1  CMD       Carboxymuconolactone decarboxylase family
  ------ inclusion threshold ------
      0.039   14.0   0.0      0.044   13.9   0.0    1.2  1  OS-D      Insect pheromone-binding family, A10/OS-D


Domain annotation for each model (and alignments):
>> CMD  Carboxymuconolactone decarboxylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3   0.0   2.5e-18   2.2e-14       9      77 ..      17      84 ..      14      87 .] 0.91

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 2.5e-18
                                      HHHHHHCCGSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHSHHHHH CS
                               CMD  9 alreallareggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaqaaayagwpaar 77
                                      ++ ++++  +g+++ +++ L+++a ++a+gc++Cv  H ++A++aG +++ei e++ +a    ++  ++
  gi|298675209|ref|YP_003726959.1| 17 NIKGNIMG-DGAVSSRTKKLLTIASAVATGCDECVEKHKKEAKDAGINDDEISEAILVASLIRFGSGIK 84
                                      56788998.9*************************************************9998877665 PP

>> OS-D  Insect pheromone-binding family, A10/OS-D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.9e-06     0.044      39      65 ..      34      59 ..       4      63 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.9e-06
                                      HHHHHHHHHHTTS-TTS-HHHHHHHHH CS
                              OS-D 39 elkkvlpealetkCakCtekqkeklkk 65
                                      +l  ++  a++t C++C ek+k+++k 
  gi|298675209|ref|YP_003726959.1| 34 KLL-TIASAVATGCDECVEKHKKEAKD 59
                                      333.68899**************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 637.83
//
Query:       gi|298675210|ref|YP_003726960.1|  [L=110]
Description: putative ArsR family transcriptional regulator [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-05   25.4   0.0    1.6e-05   24.9   0.0    1.1  1  HTH_20    Helix-turn-helix domain
    2.8e-05   23.9   0.0    4.2e-05   23.3   0.0    1.3  1  HTH_5     Bacterial regulatory protein, arsR family
    0.00063   19.7   0.8      0.001   19.0   0.8    1.3  1  HTH_45    Winged helix-turn-helix
  ------ inclusion threshold ------
      0.018   15.2   0.0      0.031   14.5   0.0    1.3  1  HTH_34    Winged helix DNA-binding domain
       0.02   14.7   0.1       0.04   13.7   0.1    1.7  1  DUF4364   Domain of unknown function (DUF4364)
      0.057   13.3   1.0       0.12   12.3   1.0    1.7  1  DUF3116   Protein of unknown function (DUF3116)
      0.065   11.6   1.0      0.069   11.5   1.0    1.2  1  DUF505    Protein of unknown function (DUF505)


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   6.2e-09   1.6e-05       4      57 ..      34      86 ..      34      88 .. 0.95

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 6.2e-09
                                      HHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20  4 aeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                      ++AL +P+Rr il+    ++ +  s+l+e ++l++ ++  HL+ Leea ++e +
  gi|298675210|ref|YP_003726960.1| 34 LKALQNPTRRNILKSM-LNGSMNYSDLKEKFGLDDVQAKLHLNFLEEALYIEKE 86
                                      69***********999.9******************************999976 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   1.6e-08   4.2e-05       1      46 [.      39      84 ..      39      85 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.6e-08
                                      SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      +ptR+ ILk++ +g++  ++l e++gl       HL++L+ea ++e
  gi|298675210|ref|YP_003726960.1| 39 NPTRRNILKSMLNGSMNYSDLKEKFGLDDVQAKLHLNFLEEALYIE 84
                                      69***************************************96665 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.8   3.9e-07     0.001      10      68 ..      44     106 ..      42     109 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 3.9e-07
                            HTH_45  10 dILeaisegeakkTkimykanLsykllnkYLdmLvekgli....kkskekYvlTekGlellek 68 
                                       +IL+++ +g+ + + +  k  L+  +++  L++L e  +i    ++++  Y+lT +G+ +le+
  gi|298675210|ref|YP_003726960.1|  44 NILKSMLNGSMNYSDLKEKFGLDDVQAKLHLNFLEEALYIekeeNNNDYLYYLTPRGEAYLEN 106
                                       69**************************************8886678889**********997 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.2e-05     0.031      12      67 ..      51     102 ..      43     107 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.2e-05
                            HTH_34  12 vdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGre 67 
                                       + ++++++lke+ ++ d +   hl+ Le+a Yie + +  +     l+ +Tp G +
  gi|298675210|ref|YP_003726960.1|  51 NGSMNYSDLKEKFGLDDVQAKLHLNFLEEALYIEKEEN--N--NDYLYYLTPRGEA 102
                                       78999***************************975433..3..3668999999876 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.6e-05      0.04      39      72 ..      73     106 ..      32     110 .] 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.6e-05
                           DUF4364  39 alseLvesglieeeekenktlykiTekGketlel 72 
                                        l+ L+e+ +ie+ee++n+ ly +T++G+  le 
  gi|298675210|ref|YP_003726960.1|  73 HLNFLEEALYIEKEENNNDYLYYLTPRGEAYLEN 106
                                       6889*************************99986 PP

>> DUF3116  Protein of unknown function (DUF3116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.0   4.6e-05      0.12      50      81 ..      76     105 ..      23     108 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.6e-05
                           DUF3116  50 WLElkgyilRkeekannkkrYelTekGellyk 81 
                                        LE+  yi ++e+  nn   Y+lT++Ge  ++
  gi|298675210|ref|YP_003726960.1|  76 FLEEALYIEKEEN--NNDYLYYLTPRGEAYLE 105
                                       69*********99..8***********98775 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.0   2.7e-05     0.069     332     404 ..      32     107 ..       9     110 .] 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.7e-05
                            DUF505 332 YGRkleempkkkeeia...kkfeeakdle.kWyednfdlreaLysLesfeLieseveekgkevyvlTeyGekvledq 404
                                       +G k  ++p +++ ++   +  +++ dl+ k+  d+++ +  L  Le    ie+e e++++  y+lT+ Ge  le+ 
  gi|298675210|ref|YP_003726960.1|  32 FGLKALQNPTRRNILKsmlNGSMNYSDLKeKFGLDDVQAKLHLNFLEEALYIEKE-ENNNDYLYYLTPRGEAYLENA 107
                                       555555555555544411133456666652445677888899999**********.6799************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 879.01
//
Query:       gi|298675211|ref|YP_003726961.1|  [L=163]
Description: hypothetical protein Metev_1305 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0038   16.7   1.1       0.78    9.2   0.1    2.8  3  DUF2608     Protein of unknown function (DUF2608)
  ------ inclusion threshold ------
       0.05   13.5   2.6       0.71    9.7   2.6    2.0  1  Acid_PPase  Acid Phosphatase


Domain annotation for each model (and alignments):
>> DUF2608  Protein of unknown function (DUF2608)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.1   8.7e-05      0.78      22      41 ..       3      22 ..       1      32 [. 0.85
   2 !    4.7   0.0    0.0021        19      87     157 ..      35     106 ..      24     110 .. 0.66
   3 ?    1.4   0.1     0.021   1.9e+02     172     191 ..     106     125 ..     104     134 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 8.7e-05
                           DUF2608 22 vfDiDdtLltstealgsdaw 41
                                      vfD+DdtL t+++++  +++
  gi|298675211|ref|YP_003726961.1|  3 VFDLDDTLATPNKEIDRKHY 22
                                      9*************988877 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0021
                           DUF2608  87 vpslvnnlqnqgttvlaLTarsptlrtatlre....LkslgidfskkaltqekveyrftltldkaerevsykkGv 157
                                       + +l n++ +  + +++LT+r p l++  + +     + +++++   ++++      +++  d   + vs+k Gv
  gi|298675211|ref|YP_003726961.1|  35 MVELFNDI-KSRHPTMILTTRHPDLKKEIMDKfnceVECRNFCLTWDKIFEA--LRTDDNLKDFMLQMVSWKTGV 106
                                       45566777.677889***********99999855555556666666666654..233333344445556666666 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.021
                           DUF2608 172 lLdkigrepksviFiDDkkk 191
                                       +L+++  ++++viF DD  +
  gi|298675211|ref|YP_003726961.1| 106 VLNQLADNYQTVIFYDDLVH 125
                                       58889999*********866 PP

>> Acid_PPase  Acid Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   2.6   7.9e-05      0.71       7     133 ..       3     123 ..       1     139 [. 0.77

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 7.9e-05
                                       EE-STTTSSSS-TTTSS-S-EEE-TTS.-EEETT--EE---TTHHHHHHHHHHTT--EEEEE--S-HHHHHHHHHHT CS
                        Acid_PPase   7 vFDLDyTLWpfevdtlvsaplkkeskksevvDrrgeelklypdveeileelkskevklavaSrtdepdlarelLkll 83 
                                       vFDLD+TL          +p k+ ++k   +  +  +l+ +p   e+++++ks++ ++++  +t +pdl +e+++ +
  gi|298675211|ref|YP_003726961.1|   3 VFDLDDTLA---------TPNKEIDRKH-YF-MTIDHLEPIPSMVELFNDIKSRHPTMIL--TTRHPDLKKEIMDKF 66 
                                       556665554.........3444444442.22.2345677888888888888886666655..5889*********** PP

                                       T-G...........GGESEEEESSS-HHHHHHHHHHHH--......-GGGEEEEES- CS
                        Acid_PPase  84 ein.dakekekklldvfddveiykgsktkhfeklkkktgi......eyedmlfFDde 133
                                       + + ++++   ++ ++f+ +   +  k   ++ ++ ktg+      +y+ ++f+Dd 
  gi|298675211|ref|YP_003726961.1|  67 NCEvECRNFCLTWDKIFEALRTDDNLKDFMLQMVSWKTGVlnqladNYQTVIFYDDL 123
                                       **988899999*************************999998888899*******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1224.90
//
Query:       gi|298675212|ref|YP_003726962.1|  [L=92]
Description: putative AsnC family transcriptional regulator [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-06   27.1   0.3    4.5e-06   26.7   0.3    1.2  1  FeoC           FeoC like transcriptional regulator
    0.00015   21.2   0.1    0.00025   20.5   0.1    1.4  1  HTH_24         Winged helix-turn-helix DNA-binding
    0.00016   21.6   0.0    0.00021   21.3   0.0    1.1  1  HTH_20         Helix-turn-helix domain
    0.00037   20.0   0.0    0.00064   19.2   0.0    1.3  1  Sigma70_r4     Sigma-70, region 4
      0.001   19.0   0.0     0.0015   18.4   0.0    1.3  1  HTH_11         HTH domain
     0.0026   17.7   1.5      0.023   14.7   1.5    1.9  1  HTH_45         Winged helix-turn-helix
     0.0047   16.9   0.2     0.0066   16.5   0.2    1.3  1  HTH_Mga        M protein trans-acting positive regulator (MGA
     0.0055   16.5   0.5      0.013   15.4   0.1    1.8  2  HTH_5          Bacterial regulatory protein, arsR family
     0.0074   16.4   0.1       0.66   10.2   0.0    2.0  2  HTH_34         Winged helix DNA-binding domain
     0.0075   16.1   0.0      0.013   15.3   0.0    1.4  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
  ------ inclusion threshold ------
      0.016   15.6   0.0       0.02   15.2   0.0    1.2  1  FaeA           FaeA-like protein
      0.024   14.7   0.2      0.042   13.9   0.2    1.5  1  HTH_19         Helix-turn-helix domain
      0.058   13.3   0.0      0.067   13.1   0.0    1.2  1  TrmB           Sugar-specific transcriptional regulator TrmB
      0.064   13.0   0.0        0.1   12.4   0.0    1.3  1  HTH_38         Helix-turn-helix domain
      0.074   13.1   0.0       0.15   12.1   0.0    1.4  1  HTH_29         Winged helix-turn helix
      0.085   12.7   0.0       0.13   12.1   0.0    1.3  1  HTH_23         Homeodomain-like domain
      0.086   13.0   0.0       0.14   12.3   0.0    1.3  1  HTH_AraC       Bacterial regulatory helix-turn-helix proteins
      0.088   12.4   0.8       0.11   12.1   0.8    1.1  1  DDRGK          DDRGK domain
        0.1   12.4   0.0       0.19   11.5   0.0    1.4  1  HTH_10         HTH DNA binding domain
       0.14   12.2   0.0       0.21   11.7   0.0    1.3  1  HTH_3          Helix-turn-helix
       0.15   12.2   0.0       0.23   11.6   0.0    1.4  1  HTH_28         Helix-turn-helix domain
       0.17   12.0   0.0       0.34   11.0   0.0    1.5  1  HTH_7          Helix-turn-helix domain of resolvase
       0.18   11.9   0.0       0.23   11.5   0.0    1.2  1  HTH_35         Winged helix-turn-helix DNA-binding


Domain annotation for each model (and alignments):
>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.3   5.7e-09   4.5e-06      12      64 ..      21      70 ..      12      81 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 5.7e-09
                              FeoC 12 rgrvslkeLsrhfkaspealeamLeqwvrkGrvekvaataccsgsCkkCggke 64
                                      ++   l+e++ ++  s + l+  Le+++ +G +e v+++    ++C++C g++
  gi|298675212|ref|YP_003726962.1| 21 KNNMTLNEIADELGLSRDELKFRLEMMEHMGEIESVKNNQ---SGCSGCSGSK 70
                                      67789*****************************999844...4666665433 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   3.2e-07   0.00025       6      45 ..      13      51 ..      11      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.2e-07
                            HTH_24  6 rkILelLqknprisqreLAerlglSpstvnrrlkrLeeeG 45
                                      +kIL+l+ k  +++ +e+A++lglS+  ++ rl+ +e +G
  gi|298675212|ref|YP_003726962.1| 13 KKILQLIDK-NNMTLNEIADELGLSRDELKFRLEMMEHMG 51
                                      799999999.89**************99999999998666 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   2.7e-07   0.00021      14      58 ..      14      57 ..      13      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.7e-07
                                      HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20 14 rilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                      +il+++ ++  +t++e+a++l+ls+ +l ++L+ +e  g +e+v+
  gi|298675212|ref|YP_003726962.1| 14 KILQLI-DKNNMTLNEIADELGLSRDELKFRLEMMEHMGEIESVK 57
                                      699999.999**************************999888876 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   8.3e-07   0.00064      10      34 ..      13      37 ..      12      41 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 8.3e-07
                                      HHHHHHHHTTT--HHHHHHHHTS-H CS
                        Sigma70_r4 10 revlelrfgeglTleEIgerlgiSr 34
                                      +++l+l    ++Tl EI+++lg+Sr
  gi|298675212|ref|YP_003726962.1| 13 KKILQLIDKNNMTLNEIADELGLSR 37
                                      689*********************9 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0     2e-06    0.0015       3      51 ..      13      58 ..      11      63 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2e-06
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepg 51
                                      ++il+l+   +++++ +e+A+eL++Sr     +++ +e +g +Ies+++
  gi|298675212|ref|YP_003726962.1| 13 KKILQLI--DKNNMTLNEIADELGLSRDELKFRLEMMEHMG-EIESVKN 58
                                      5788888..4445**************87777777777777.7777665 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   1.5   2.9e-05     0.023       8      67 ..      12      91 ..       7      92 .] 0.93

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.9e-05
                            HTH_45  8 iadILeaisegeakkTkimykanLsykllnkYLdmLvekgli....................kkskekYvlTekGlell 66
                                      i  IL+ i++++ +  +i  +  Ls + l+  L+m+ + g i                    +++   Y+lTekG+++ 
  gi|298675212|ref|YP_003726962.1| 12 IKKILQLIDKNNMTLNEIADELGLSRDELKFRLEMMEHMGEIesvknnqsgcsgcsgskclgDNKLVVYQLTEKGRKIC 90
                                      789*****99999**************************999999**************9999999***********98 PP

                            HTH_45 67 e 67
                                      +
  gi|298675212|ref|YP_003726962.1| 91 N 91
                                      6 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2   8.5e-06    0.0066      14      45 ..      18      48 ..      13      61 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8.5e-06
                           HTH_Mga 14 LteneksltldelakeLglseltlqsdiseLn 45
                                      L++ ++ +tl e+a eLgls+ +l+ +++ + 
  gi|298675212|ref|YP_003726962.1| 18 LID-KNNMTLNEIADELGLSRDELKFRLEMME 48
                                      688.9*******************98888776 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.6e-05     0.013       6      43 ..      14      51 ..      13      55 .. 0.83
   2 ?   -1.2   0.0       2.5   1.9e+03      14      23 ..      75      84 ..      70      90 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.6e-05
                                      HHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTT CS
                             HTH_5  6 kILklLaegelcvcelaeelglsqstvShHLkkLreaG 43
                                      kIL+l  +++++  e+a+elgls+  +   L +++ +G
  gi|298675212|ref|YP_003726962.1| 14 KILQLIDKNNMTLNEIADELGLSRDELKFRLEMMEHMG 51
                                      89999999***************977766666666665 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.5
                                      SSEEHHHHHH CS
                             HTH_5 14 gelcvcelae 23
                                      ++l v +l+e
  gi|298675212|ref|YP_003726962.1| 75 NKLVVYQLTE 84
                                      5566666655 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   0.00084      0.66       8      52 ..      17      61 ..      12      65 .. 0.91
   2 ?    4.6   0.0     0.048        38      55      68 ..      76      89 ..      69      92 .] 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00084
                            HTH_34  8 yLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkg 52
                                       L+++++++ +e+ ++l+++  +L   l+++e  g ie  k+ ++
  gi|298675212|ref|YP_003726962.1| 17 QLIDKNNMTLNEIADELGLSRDELKFRLEMMEHMGEIESVKNNQS 61
                                      5889999******************************99988765 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.048
                            HTH_34 55 prtllriTpeGrea 68
                                      +  ++++T++Gr+ 
  gi|298675212|ref|YP_003726962.1| 76 KLVVYQLTEKGRKI 89
                                      6789********85 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.6e-05     0.013       7      42 .]      14      48 ..      11      48 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-05
                     HTH_AsnC-type  7 kILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      kIL+++ ++  ++  e+A+++GlS+++   R++ +e
  gi|298675212|ref|YP_003726962.1| 14 KILQLIDKN-NMTLNEIADELGLSRDELKFRLEMME 48
                                      666666555.6899*************999988775 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   2.6e-05      0.02       5      49 ..      15      57 ..       9      66 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.6e-05
                                      HHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE- CS
                              FaeA  5 IleylnsikapckTreiAdalglsaYQaRyYLeqLekegkikrsp 49
                                      Il+ +   k+  + +eiAd lgls    ++ Le++e+ g i+ + 
  gi|298675212|ref|YP_003726962.1| 15 ILQLID--KNNMTLNEIADELGLSRDELKFRLEMMEHMGEIESVK 57
                                      555554..589999***************************9874 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   5.4e-05     0.042       2      28 ..      13      39 ..      12      49 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.4e-05
                            HTH_19  2 erLkeaReelgltqeelaerlgisrsk 28
                                      +++ +++ ++++t+ e+a++lg sr  
  gi|298675212|ref|YP_003726962.1| 13 KKILQLIDKNNMTLNEIADELGLSRDE 39
                                      5788999****************9855 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   8.6e-05     0.067      16      58 ..      17      59 ..      13      84 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.6e-05
                                      HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                       L+ + ++t +eia elg++r      L+ +e +G +e +k +
  gi|298675212|ref|YP_003726962.1| 17 QLIDKNNMTLNEIADELGLSRDELKFRLEMMEHMGEIESVKNN 59
                                      688999*******************************999876 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00013       0.1      12      34 ..      14      37 ..      12      38 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                            HTH_38 12 eIerllaeG.lslreIArrLgrsp 34
                                      +I +l++++ ++l eIA +Lg s+
  gi|298675212|ref|YP_003726962.1| 14 KILQLIDKNnMTLNEIADELGLSR 37
                                      6999997666***********886 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00019      0.15       2      27 ..      13      38 ..      13      40 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                            HTH_29  2 aqallllaeGvstvsqiAkllglsrr 27
                                      +++l+l+++  +t  +iA  lglsr+
  gi|298675212|ref|YP_003726962.1| 13 KKILQLIDKNNMTLNEIADELGLSRD 38
                                      79***********************8 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00017      0.13       9      31 ..      14      37 ..      13      38 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00017
                            HTH_23  9 rillllae.GlsvreIAreLgvsr 31
                                      +il+l ++  ++  eIA+eLg sr
  gi|298675212|ref|YP_003726962.1| 14 KILQLIDKnNMTLNEIADELGLSR 37
                                      599999*99**************8 PP

>> HTH_AraC  Bacterial regulatory helix-turn-helix proteins, AraC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00018      0.14       6      22 ..      21      37 ..      19      41 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00018
                                      SCT--HHHHHHHTTSSH CS
                          HTH_AraC  6 stnltiediAdelgfSr 22
                                      ++n+t+++iAdelg+Sr
  gi|298675212|ref|YP_003726962.1| 21 KNNMTLNEIADELGLSR 37
                                      679************98 PP

>> DDRGK  DDRGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.8   0.00014      0.11      94     146 ..       6      56 ..       1      60 [. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                                       XXXXXX.HHHHHHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EE CS
                             DDRGK  94 aeeeek.lleefinyikekKvvlleelavkfklktqevierikeLeeqgsltGv 146
                                       +++    l++++++ i ++ + +l+e+a +++l+ +e   r++ +e+ g+++ v
  gi|298675212|ref|YP_003726962.1|   6 SDD--TfLIKKILQLIDKNNM-TLNEIADELGLSRDELKFRLEMMEHMGEIESV 56 
                                       222..3499*******99886.69*************************99865 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00025      0.19      23      45 ..      23      45 ..      20      49 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00025
                            HTH_10 23 rvtlkeLAkelGIskstlsehLr 45
                                      ++tl+e+A+elG+s+  l+ +L+
  gi|298675212|ref|YP_003726962.1| 23 NMTLNEIADELGLSRDELKFRLE 45
                                      579*************9999987 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00026      0.21       3      23 ..      17      37 ..      12      41 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00026
                                      HHHHHTTHHHHHHHHHHTSSH CS
                             HTH_3  3 elRkqlglsqeeLAeklGvsr 23
                                      +l +++++++ e+A++lG+sr
  gi|298675212|ref|YP_003726962.1| 17 QLIDKNNMTLNEIADELGLSR 37
                                      44459***************8 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0003      0.23       4      27 ..      14      38 ..      13      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0003
                            HTH_28  4 eiikllaaGh.svreaArelgisrr 27
                                      +i++l+ + + + +e+A elg+sr+
  gi|298675212|ref|YP_003726962.1| 14 KILQLIDKNNmTLNEIADELGLSRD 38
                                      79999996655************97 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00043      0.34      11      35 ..      12      37 ..       3      41 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00043
                                      HGGGGSSTTTT.--STTTSSSS---S CS
                             HTH_7 11 inrvvkLleeG.isiskIAkevnisR 35
                                      i  +++L+++  ++ ++IA+e+++sR
  gi|298675212|ref|YP_003726962.1| 12 IKKILQLIDKNnMTLNEIADELGLSR 37
                                      77899********************9 PP

>> HTH_35  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00029      0.23       9      38 ..      17      46 ..      12      54 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00029
                            HTH_35  9 AaLrkrgttLaalsreaglssstlsnaltr 38
                                        + k+++tL +++ e+gls+ +l+  l+ 
  gi|298675212|ref|YP_003726962.1| 17 QLIDKNNMTLNEIADELGLSRDELKFRLEM 46
                                      56789****************999876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       973  (0.0542696); expected 358.6 (0.02)
Passed bias filter:                      625  (0.0348597); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 649.05
//
Query:       gi|298675213|ref|YP_003726963.1|  [L=139]
Description: hypothetical protein Metev_1307 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1056.35
//
Query:       gi|298675214|ref|YP_003726964.1|  [L=662]
Description: ferrous iron transport protein B [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-68  228.0   2.8    5.3e-68  227.4   2.8    1.3  1  FeoB_N           Ferrous iron transport protein B
    1.1e-44  151.3  13.6    7.6e-29  100.3   2.4    2.7  2  Gate             Nucleoside recognition
    4.5e-22   77.5   1.1    4.5e-22   77.5   1.1    3.9  4  FeoB_C           Ferrous iron transport protein B C terminus
    4.8e-19   68.5   0.3    9.5e-19   67.6   0.3    1.5  1  MMR_HSR1         50S ribosome-binding GTPase
    4.9e-18   65.5   0.7    8.6e-18   64.7   0.7    1.4  1  FeoB_Cyto        FeoB cytosolic helical domain
    6.3e-05   22.5   0.1    0.00011   21.7   0.1    1.4  1  SRPRB            Signal recognition particle receptor beta su
     0.0015   18.5   3.0       0.95    9.4   0.1    2.3  2  RsgA_GTPase      RsgA GTPase
  ------ inclusion threshold ------
       0.03   13.9   1.5      0.097   12.2   1.1    2.0  2  GTP_EFTU         Elongation factor Tu GTP binding domain
      0.046   13.3   0.3       0.38   10.3   0.3    2.4  1  Ras              Ras family
       0.12   12.6   0.0       0.25   11.6   0.0    1.5  1  Roc              Ras of Complex, Roc, domain of DAPkinase
       0.22   11.7   2.1       0.79    9.9   0.1    2.7  2  Myco_arth_vir_N  Mycoplasma virulence signal region (Myco_art
       0.27   10.2   1.2       0.73    8.8   0.1    2.1  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 


Domain annotation for each model (and alignments):
>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.4   2.8   3.6e-71   5.3e-68       2     154 ..       5     157 ..       4     159 .. 0.99

  Alignments for each domain:
  == domain 1  score: 227.4 bits;  conditional E-value: 3.6e-71
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHHCTS CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardflleee 78 
                                       +val+GnpnvGkt+lfn ltg++q+vgNwpGvtvekk g+++++++e+ei+DlPG+Ysl+ays++e vard++++e+
  gi|298675214|ref|YP_003726964.1|   5 KVALAGNPNVGKTSLFNVLTGTRQHVGNWPGVTVEKKVGETTYNSEEIEITDLPGTYSLTAYSIDEIVARDYIVDEK 81 
                                       79*************************************************************************** PP

                                       SSEEEEEEEGGGHHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHHHH CS
                            FeoB_N  79 pdvvvnvvdatnlernLyLtlqllelgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieellk 154
                                       pdvvv+vvdatn+ernLyLt+ql+elg++vv+alnm+d ae++gi  d+++++e L++pvvkt+akk++g++ell+
  gi|298675214|ref|YP_003726964.1|  82 PDVVVQVVDATNIERNLYLTTQLMELGTKVVIALNMSDIAESQGIVTDINRMREFLEIPVVKTVAKKGQGLNELLD 157
                                       *************************************************************************987 PP

>> Gate  Nucleoside recognition
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.0   3.7   2.9e-18   4.3e-15       2     111 ..     346     440 ..     345     441 .. 0.96
   2 !  100.3   2.4   5.1e-32   7.6e-29       1     112 []     507     632 ..     507     632 .. 0.90

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 2.9e-18
                              Gate   2 lkagpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqg 78 
                                       l ++p i+++++l+++l++s++l+r+++++++v+  +g  l +k+++++l+gf+   ++v++++ ++         +
  gi|298675214|ref|YP_003726964.1| 346 LVFVPNIFILFFLLSILEDSGYLARAAFIMDKVMYSIG--LQGKSFIPMLMGFG---CNVPAIMATR---------T 408
                                       66899*********************************..**************...*********9.........* PP

                              Gate  79 fdtpksalafllfvllytpcvatlavivrelgs 111
                                       +++ k++l++++++ +++ c a+l+v+v   g+
  gi|298675214|ref|YP_003726964.1| 409 IEDHKDRLVTIMITPFMS-CSARLPVYVLLGGA 440
                                       ****************98.********987775 PP

  == domain 2  score: 100.3 bits;  conditional E-value: 5.1e-32
                              Gate   1 llkagpiillasiliwflss..........ssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtl 67 
                                       ++kag iil++++++w+l s          +sl+g ig llep++aplg  +dwk++vsl++gf+ake+v+g+lgtl
  gi|298675214|ref|YP_003726964.1| 507 IKKAGSIILVGVVVVWLLASlpfgveygsaNSLVGTIGHLLEPLVAPLG--FDWKIAVSLVLGFVAKEIVIGSLGTL 581
                                       68***********************************************..************************** PP

                              Gate  68 y.....tsalgellqgfdtpks.alafllfvllytpcvatlavivrelgsk 112
                                       y     ++ +  l++  + ++   l +++f+lly+pc+at++v+++e+gs+
  gi|298675214|ref|YP_003726964.1| 582 YgtgegSGLMERLQADPELFALnSLGLMVFILLYMPCIATVGVVKQETGSW 632
                                       **988544444455554444444889***********************98 PP

>> FeoB_C  Ferrous iron transport protein B C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.5   1.1     3e-25   4.5e-22       1      53 []     450     502 ..     450     502 .. 0.98
   2 ?   -0.6   0.4      0.74   1.1e+03       9      20 ..     514     525 ..     511     532 .. 0.61
   3 ?   -2.9   0.3       3.7   5.5e+03       9      22 ..     560     573 ..     559     576 .. 0.82
   4 ?    0.8   0.9      0.26   3.9e+02       6      21 ..     636     651 ..     634     657 .. 0.63

  Alignments for each domain:
  == domain 1  score: 77.5 bits;  conditional E-value: 3e-25
                            FeoB_C   1 lfslYllgilvallvalllkktt.lkgepspfvmELPpYrlPslknvliktweR 53 
                                       +f+lY+lgilva+l+a+l+++ t lkg+p+pf+mELPpYr+P+l + l+++w++
  gi|298675214|ref|YP_003726964.1| 450 IFGLYVLGILVAVLTAKLFRS-TiLKGDPAPFIMELPPYRIPHLTTSLMHMWDK 502
                                       69*******************.99****************************98 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.74
                            FeoB_C   9 ilvallvalllk 20 
                                       ilv ++v +ll 
  gi|298675214|ref|YP_003726964.1| 514 ILVGVVVVWLLA 525
                                       556666666654 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 3.7
                            FeoB_C   9 ilvallvalllkkt 22 
                                       i+v l++++++k +
  gi|298675214|ref|YP_003726964.1| 560 IAVSLVLGFVAKEI 573
                                       78999999999875 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.26
                            FeoB_C   6 llgilvallvalllkk 21 
                                       l++++  ++va+++  
  gi|298675214|ref|YP_003726964.1| 636 LFSVVYGIAVAWIFAF 651
                                       5666666777776643 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.6   0.3   6.4e-22   9.5e-19       1     112 [.       5     115 ..       5     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 67.6 bits;  conditional E-value: 6.4e-22
                                       EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS..HHHHHHHHHHHHHHHHC CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGlie..gaseekglgkaflalee 75 
                                       +va++G+pNvGK++L+n ltg++ +v+++pg+T + + g+ +++ +eie++D+pG ++    s ++ +++++   e+
  gi|298675214|ref|YP_003726964.1|   5 KVALAGNPNVGKTSLFNVLTGTRQHVGNWPGVTVEKKVGETTYNSEEIEITDLPGTYSltAYSIDEIVARDYIVDEK 81 
                                       69****************************************999**********876556778889******9999 PP

                                       TSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEE CS
                          MMR_HSR1  76 adlillvvdaseeklkpldeeleelleeakkplilvl 112
                                        d+++ vvda+ + ++++   l   l e + +++++l
  gi|298675214|ref|YP_003726964.1|  82 PDVVVQVVDAT-N-IERN-LYLTTQLMELGTKVVIAL 115
                                       9********77.3.4443.333333334445555555 PP

>> FeoB_Cyto  FeoB cytosolic helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.7   0.7   5.8e-21   8.6e-18       1      91 []     175     262 ..     175     262 .. 0.95

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 5.8e-21
                         FeoB_Cyto   1 YgeeiEkaiekleellkes.nlkaklppRwlAlklLegDeelleelkedpelraeveearkeleaelgedledvIvd 76 
                                       Yg++iEk i++le ll+++ nl +++p Rwl++k+LegD ++l ++++  ++++ev+e  k++ +++    e  ++d
  gi|298675214|ref|YP_003726964.1| 175 YGNDIEKDISELEFLLEKDeNLYKHYPLRWLSIKILEGDNNVLAKIQN-SQVKDEVDEYLKKIDTDY---YEALMAD 247
                                       9***********************************************.899999999988888876...6899*** PP

                         FeoB_Cyto  77 arykfiegilrevvk 91 
                                        ry+ i++++++v++
  gi|298675214|ref|YP_003726964.1| 248 RRYGTISSVVSQVCT 262
                                       *************96 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   7.3e-08   0.00011       4      99 ..       4     105 ..       2     181 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 7.3e-08
                                       -EEEEE-STTSSHHHHHHHHHHS..S---.B---SS-EEETTG...GGTT-SEEEETT-GCCSHHHHHHHHHHGGE. CS
                             SRPRB   4 pavllvGlsdsGKTslftrLttd..svkk.tvtSqessaalkvksekgskltliDfPGheklrqklleklkakssl. 76 
                                        +v l+G  + GKTslf+ Lt    +v +   + +e+++ + +   + +++++ D+PG  +l    +++++a++ + 
  gi|298675214|ref|YP_003726964.1|   4 TKVALAGNPNVGKTSLFNVLTGTrqHVGNwPGVTVEKKVGETT--YNSEEIEITDLPGTYSLTAYSIDEIVARDYIv 78 
                                       57899***************97733222212344466666555..578899***********999999988887642 PP

                                       ....EEEEEEEETTS-HHHHHHHHHHH CS
                             SRPRB  77 ....kglvfvvDStidpkevkevAEll 99 
                                             +v vvD+t  ++++  +  l+
  gi|298675214|ref|YP_003726964.1|  79 dekpDVVVQVVDATNIERNLYLTTQLM 105
                                       222246899999999999886665443 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.1   0.00063      0.95     101     137 ..       5      43 ..       1      63 [. 0.68
   2 !    9.3   0.4   0.00067         1      33      97 ..      92     159 ..      83     168 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00063
                                       EEEEECSTTSSHHHHHHHHCTT-----S-...-------- CS
                       RsgA_GTPase 101 tsvlvGqSGvGKStLinallpelelktge...vseklgrG 137
                                        ++l+G+  vGK++L n+l+++ ++++g+   v  +++ G
  gi|298675214|ref|YP_003726964.1|   5 KVALAGNPNVGKTSLFNVLTGT-RQHVGNwpgVTVEKKVG 43 
                                       4689****************97.45554311144444444 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00067
                                       HHHHHHHH...HHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHC CS
                       RsgA_GTPase  33 nlldrfLv...laeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkell 97 
                                         ++r L    ++ e g ++vi+ln  D++e++  +++++   e l+++v+++ ak+++gl+el +++
  gi|298675214|ref|YP_003726964.1|  92 TNIERNLYlttQLMELGTKVVIALNMSDIAESQGIVTDINRMREFLEIPVVKTVAKKGQGLNELLDVV 159
                                       456665541114567899****************888888888889*****************98876 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.1   1.6e+03       6      25 ..       6      25 ..       4      33 .. 0.81
   2 ?   12.2   1.1   6.5e-05     0.097      53     191 ..      35     162 ..      28     165 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.1
                                      EEEEESTTSSHHHHHHHHHH CS
                          GTP_EFTU  6 igiighvDhGKtTLtdrLly 25
                                      ++++g  + GKt+L   L+ 
  gi|298675214|ref|YP_003726964.1|  6 VALAGNPNVGKTSLFNVLTG 25
                                      7789999*******998874 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 6.5e-05
                                       TSCSSCEEEEEETTCSSEEEEEEEESSSGG...GHHHHHHH.....HHT-SEEEEEEETTTBSTHHHHHHHHHHHHT CS
                          GTP_EFTU  53 giTiksaaisleketkkylinliDtPGHvd...Fskevirg.....lrvlDgavlvvdaveGvepqteevlrlalke 121
                                       g+T++ ++ ++   +++ +i + D PG  +   +s + i +      ++ D++v vvda+  +e +   +  ++ ++
  gi|298675214|ref|YP_003726964.1|  35 GVTVEKKVGETT--YNSEEIEITDLPGTYSltaYSIDEIVArdyivDEKPDVVVQVVDAT-NIERN-LYLTTQLMEL 107
                                       788999999999..9999999999999987344665555554555456778888888887.44444.4566788899 PP

                                       TTEEEEEEESCGSTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHH CS
                          GTP_EFTU 122 gvpiivfiNKmDrlkaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvel 191
                                       g+++++++N  D +  e + iv++++ ++       +++      e+pvv + a+kg+g+++ll+++ve 
  gi|298675214|ref|YP_003726964.1| 108 GTKVVIALNMSDIA--ESQGIVTDIN-RM-------REF-----LEIPVVKTVAKKGQGLNELLDVVVEE 162
                                       **********9965..5667777777.33.......111.....369*******************9985 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.3   0.00026      0.38       1     159 [.       5     162 ..       5     165 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00026
                                       EEEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHH......HHHHHHTT CS
                               Ras   1 KlvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqeefks......lrelyyrd 71 
                                       K+ l G+ +vGKtsl +  +  + +    + + v++++ e++++++e++  i D  G    ++      +++ y+ d
  gi|298675214|ref|YP_003726964.1|   5 KVALAGNPNVGKTSLFNVLTGTRQHVGNWPGVTVEKKVGETTYNSEEIE--ITDLPGTYSLTAysideiVARDYIVD 79 
                                       89999***************99999999999999*********999875..66666665544411111133344444 PP

                                       ESEEEEEEETTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGGG-SS-HHHHHHHHHHHTSEEEEEBTTTTCT CS
                               Ras  72 aegillvyditsresfenvkkwveeikrvaeenvpivLvGnKvDleekravsteegeelakelglkfletSAktnen 148
                                        +  ++  ++ +++  e+   +++++ +  +   ++v+  n +D++e++ + t+  +++ + l+++ ++t Ak+ ++
  gi|298675214|ref|YP_003726964.1|  80 EKPDVV-VQVVDATNIERNLYLTTQLMELGT---KVVIALNMSDIAESQGIVTDI-NRMREFLEIPVVKTVAKKGQG 151
                                       444444.345555555554455555555444...466666788888877776655.447777778888888888888 PP

                                       HHHHHHHHHHH CS
                               Ras 149 veeafeellre 159
                                       ++e+++ +++e
  gi|298675214|ref|YP_003726964.1| 152 LNELLDVVVEE 162
                                       88877777665 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00016      0.25       1      27 [.       5      31 ..       5      64 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                                      EEEEESSTTSSHHHHHHCHCT-CCC-E CS
                               Roc  1 KvvlvGdsgvGKtsllkrfvedkfsek 27
                                      Kv l G+ +vGKtsl++ ++  + +  
  gi|298675214|ref|YP_003726964.1|  5 KVALAGNPNVGKTSLFNVLTGTRQHVG 31
                                      899**************9987665544 PP

>> Myco_arth_vir_N  Mycoplasma virulence signal region (Myco_arth_vir_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.2      0.78   1.2e+03      11      21 ..     458     468 ..     457     471 .. 0.88
   2 ?    9.9   0.1   0.00053      0.79      10      27 ..     513     530 ..     507     533 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.78
                   Myco_arth_vir_N  11 IltlalvaaLl 21 
                                       Il+ +l+a L+
  gi|298675214|ref|YP_003726964.1| 458 ILVAVLTAKLF 468
                                       9*******998 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00053
                   Myco_arth_vir_N  10 kIltlalvaaLlaaltfg 27 
                                        Il++++v+ Lla+l fg
  gi|298675214|ref|YP_003726964.1| 513 IILVGVVVVWLLASLPFG 530
                                       59*************998 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.57   8.6e+02      30      51 ..       4      25 ..       2      36 .. 0.81
   2 ?    8.8   0.1   0.00049      0.73     199     229 ..     133     163 ..      80     185 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.57
                                      EEEEEEE-TTSSHHHHHHHHHH CS
                              MeaB 30 qvvGltGvPGaGkstlvealgl 51
                                      ++v l G P +Gk  l + l+ 
  gi|298675214|ref|YP_003726964.1|  4 TKVALAGNPNVGKTSLFNVLTG 25
                                      46899*********99988875 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00049
                                       TBTTB--EEEEEBCCCTBSHHHHHHHHHHHH CS
                              MeaB 199 kekeWrpkvlktsavegeGidelvdaieehr 229
                                        ++  + +v+kt+a++g+G++el+d + e  
  gi|298675214|ref|YP_003726964.1| 133 MREFLEIPVVKTVAKKGQGLNELLDVVVEES 163
                                       34555679*****************987654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (662 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       966  (0.0538792); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.41
# Mc/sec: 4823.73
//
Query:       gi|298675215|ref|YP_003726965.1|  [L=77]
Description: FeoA family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.7e-20   70.9   0.0    8.4e-20   70.8   0.0    1.0  1  FeoA      FeoA domain


Domain annotation for each model (and alignments):
>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.8   0.0   4.7e-24   8.4e-20       2      74 .]       5      76 ..       4      76 .. 0.97

  Alignments for each domain:
  == domain 1  score: 70.8 bits;  conditional E-value: 4.7e-24
                                      EGGG--TT-EEEEEEE-TT.SSHHHHHHHHT--TT-EEEEEEE-TTS-SEEEEETTEEEEE-HHHHTTEEEEE CS
                              FeoA  2 pLsdlkeGergeiarisdedpellrrLremGlvpGarievvarapfggplvvrvgdtrvaLgreeAqaIlVea 74
                                      +L+ l+e+ rg+i++i+   ++l++r+ emGlvpG+++ev++rap+g+p+ +++++ ++a ++ eAq +lVe+
  gi|298675215|ref|YP_003726965.1|  5 TLNLLDENSRGRIKQIQGK-GKLRKRFFEMGLVPGSEVEVIKRAPLGDPIELKIKGYNIAFRKNEAQYVLVEP 76
                                      89**************876.99*************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 645.65
//
Query:       gi|298675216|ref|YP_003726966.1|  [L=164]
Description: DtxR family iron (metal) dependent repressor [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.8e-18   64.6   0.5      1e-17   64.0   0.5    1.3  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    1.1e-15   57.4   0.0    2.7e-15   56.2   0.0    1.5  2  Fe_dep_repr_C   Iron dependent repressor, metal binding and d
    0.00018   21.4   0.0     0.0003   20.7   0.0    1.3  1  HTH_Crp_2       Crp-like helix-turn-helix domain
    0.00028   20.6   0.0    0.00054   19.7   0.0    1.5  1  LexA_DNA_bind   LexA DNA binding domain
     0.0016   17.9   0.0     0.0025   17.3   0.0    1.3  1  HTH_24          Winged helix-turn-helix DNA-binding
     0.0019   18.2   0.0     0.0032   17.5   0.0    1.4  1  FeoC            FeoC like transcriptional regulator
     0.0048   16.7   0.1     0.0074   16.2   0.1    1.3  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0068   16.7   0.0      0.011   16.1   0.0    1.4  1  Rrf2            Transcriptional regulator
     0.0098   15.8   0.0      0.016   15.0   0.0    1.3  1  MarR_2          MarR family
  ------ inclusion threshold ------
      0.037   14.2   0.0       0.06   13.5   0.0    1.4  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
      0.038   13.7   0.0      0.078   12.7   0.0    1.5  1  HTH_DeoR        DeoR-like helix-turn-helix domain
      0.039   13.8   0.0      0.057   13.2   0.0    1.3  1  HTH_IclR        IclR helix-turn-helix domain
      0.054   13.8   0.1       0.78   10.1   0.0    2.6  2  Mnd1            Mnd1 HTH domain
      0.063   13.4   0.0       0.14   12.3   0.0    1.6  1  Mrr_N           Mrr N-terminal domain
       0.07   13.1   0.0       0.12   12.3   0.0    1.3  1  MarR            MarR family


Domain annotation for each model (and alignments):
>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.0   0.5   8.7e-21     1e-17       1      60 []       1      60 [.       1      60 [. 0.98

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 8.7e-21
                                      X--HHHHHHHHHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTEE CS
                    Fe_dep_repress  1 dLvestEdYLetIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyveyekykgl 60
                                      +++e+tEdYL+tI  +  +k+++++kd++++L+ spssV+ m +kL++dGy++yeky+g+
  gi|298675216|ref|YP_003726966.1|  1 MTTERTEDYLKTIEAVVSKKGYAQVKDVSSALGTSPSSVTGMFQKLKNDGYINYEKYGGV 60
                                      799*******************************************************97 PP

>> Fe_dep_repr_C  Iron dependent repressor, metal binding and dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       5.3   6.3e+03      34      47 ..       7      20 ..       2      36 .. 0.61
   2 !   56.2   0.0   2.2e-18   2.7e-15       1      62 [.      63     123 ..      63     128 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 5.3
                                      HHHCCCCGGGS-HH CS
                     Fe_dep_repr_C 34 heeAerlEhalsee 47
                                      ++  + +E ++s++
  gi|298675216|ref|YP_003726966.1|  7 EDYLKTIEAVVSKK 20
                                      44445566666655 PP

  == domain 2  score: 56.2 bits;  conditional E-value: 2.2e-18
                                       -HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHCT-.SB- CS
                     Fe_dep_repr_C   1 TekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldellgfpeec 62 
                                       T kG+ +A++++ ++ ++ +fL  vlg+d+e a+e+A+r+Eh+l++++ie l ++++f+ ++
  gi|298675216|ref|YP_003726966.1|  63 TNKGKNVAQNTKAKYGVVRDFL-TVLGIDDETADEDACRIEHVLTDDTIEVLTKFMEFIHKN 123
                                       99********************.88*********************************9886 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   2.5e-07    0.0003      25      61 ..      26      64 ..      23      67 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.5e-07
                                      HHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEE.EEES- CS
                         HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglis.rgrr.irild 61
                                      ++ +s lG+++++v+ ++++Lk++g+i   +++ +++++
  gi|298675216|ref|YP_003726966.1| 26 KDVSSALGTSPSSVTGMFQKLKNDGYINyEKYGgVTLTN 64
                                      58899***********************64434499887 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   4.5e-07   0.00054       5      58 ..       3      54 ..       1      57 [. 0.94

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 4.5e-07
                                      -HHHHHHHHHHHHHHHHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE- CS
                     LexA_DNA_bind  5 TerQrevldlikasieetgypPsireiaralglkSpsaveehLkaLerKGyier 58
                                      Ter ++ l+ i+a ++++gy+  +++++ alg +Sps+v    ++L++ Gyi+ 
  gi|298675216|ref|YP_003726966.1|  3 TERTEDYLKTIEAVVSKKGYA-QVKDVSSALG-TSPSSVTGMFQKLKNDGYINY 54
                                      899999**************9.79********.67*****************86 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.1e-06    0.0025      12      47 ..      17      52 ..      11      53 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.1e-06
                            HTH_24 12 LqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      + k++    ++++ +lg Sps v+   ++L+++G+I
  gi|298675216|ref|YP_003726966.1| 17 VSKKGYAQVKDVSSALGTSPSSVTGMFQKLKNDGYI 52
                                      568899999**************************9 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.7e-06    0.0032       2      45 ..      10      53 ..       9      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.7e-06
                              FeoC  2 LtelkeyleergrvslkeLsrhfkaspealeamLeqwvrkGrve 45
                                      L+ +++ + ++g +++k+ s ++ +sp+ + +m   +   G ++
  gi|298675216|ref|YP_003726966.1| 10 LKTIEAVVSKKGYAQVKDVSSALGTSPSSVTGMFQKLKNDGYIN 53
                                      899*******************************9998888776 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   6.2e-06    0.0074      16      56 ..      15      56 ..       8      80 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.2e-06
                                      HHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB 16 aLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                      a++ k+g a++++++++lg + s+v  + ++L++ G+++ ek
  gi|298675216|ref|YP_003726966.1| 15 AVVsKKGYAQVKDVSSALGTSPSSVTGMFQKLKNDGYINYEK 56
                                      56668999******************************9886 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   9.3e-06     0.011      22      73 ..      19      68 ..       2      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 9.3e-06
                                      TCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEEESSHCCC CS
                              Rrf2 22 eeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyrLakppee 73
                                      +++ ++++++++  ++sps +  +++kL++ g+++ ++   GG++L+ + ++
  gi|298675216|ref|YP_003726966.1| 19 KKGYAQVKDVSSALGTSPSSVTGMFQKLKNDGYINYEK--YGGVTLTNKGKN 68
                                      445589*****************************995..899999887665 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.4e-05     0.016      23      54 ..      24      55 ..      13      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.4e-05
                                      EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 23 tvgelarrlglsksavsrilkrLvaaGLverr 54
                                       v+++  +lg s+s+v+ + ++L   G++ ++
  gi|298675216|ref|YP_003726966.1| 24 QVKDVSSALGTSPSSVTGMFQKLKNDGYINYE 55
                                      699**************************876 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     5e-05      0.06      17      53 ..      20      57 ..       7      76 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5e-05
                    B-block_TFIIIC 17 sGitq.sdLakeskqdprslfyrlksLekkgLIvkqsi 53
                                      +G++q +d++++++ +p+s+++  ++L++ g+I   ++
  gi|298675216|ref|YP_003726966.1| 20 KGYAQvKDVSSALGTSPSSVTGMFQKLKNDGYINYEKY 57
                                      6888845899***********************76655 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.5e-05     0.078       4      54 ..      12      63 ..      10      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.5e-05
                          HTH_DeoR  4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqgllt.RthGGavsi 54
                                       i   + ++g+ +v++++  lg+S+  +   +++L+++g +    +GG+++ 
  gi|298675216|ref|YP_003726966.1| 12 TIEAVVSKKGYAQVKDVSSALGTSPSSVTGMFQKLKNDGYINyEKYGGVTLT 63
                                      688899********************************99752678988775 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.8e-05     0.057      20      49 ..      24      53 ..      13      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.8e-05
                                      BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR 20 tlselArrtglpkStvhRlLqtLvelGyve 49
                                       +++++ ++g ++S+v ++ q L + Gy+ 
  gi|298675216|ref|YP_003726966.1| 24 QVKDVSSALGTSPSSVTGMFQKLKNDGYIN 53
                                      5899************************86 PP

>> Mnd1  Mnd1 HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00065      0.78      21      53 ..      28      60 ..      13      62 .. 0.85
   2 ?   -2.0   0.0       3.8   4.5e+03      29      43 ..      77      92 ..      67      99 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00065
                              Mnd1 21 apkekgivsqsVkdvlqsLvdDglveveKiGss 53
                                      ++++ g ++ sV  + q+L +Dg ++ eK G  
  gi|298675216|ref|YP_003726966.1| 28 VSSALGTSPSSVTGMFQKLKNDGYINYEKYGGV 60
                                      4555677899*******************9965 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.8
                              Mnd1 29 sqsVkdvlqsL.vdDg 43
                                         V+d l+ L +dD+
  gi|298675216|ref|YP_003726966.1| 77 YGVVRDFLTVLgIDDE 92
                                      5578999988845555 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00012      0.14      59      86 ..      44      71 ..      42      72 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                             Mrr_N 59 tyLkkagllespkrgvwkiTekGrevlk 86
                                      ++Lk+ g+++++k g +++T+kG++v +
  gi|298675216|ref|YP_003726966.1| 44 QKLKNDGYINYEKYGGVTLTNKGKNVAQ 71
                                      689*********************9975 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   9.9e-05      0.12      17      48 ..      22      53 ..      16      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.9e-05
                                      TEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR 17 plsvseLakklgvskstvtrvldrLekkGlie 48
                                       + v++  ++lg+s+s+vt +  +L  +G+i+
  gi|298675216|ref|YP_003726966.1| 22 YAQVKDVSSALGTSPSSVTGMFQKLKNDGYIN 53
                                      56788999**********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       847  (0.0472419); expected 358.6 (0.02)
Passed bias filter:                      688  (0.0383736); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1250.60
//
Query:       gi|298675217|ref|YP_003726967.1|  [L=117]
Description: hypothetical protein Metev_1311 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-28   98.4  12.3    1.9e-27   96.2  12.3    1.8  1  DUF5320          Family of unknown function (DUF5320)
  ------ inclusion threshold ------
      0.011   16.1   1.6      0.014   15.8   1.6    1.1  1  Snapin_Pallidin  Snapin/Pallidin
      0.021   14.7   0.6      0.027   14.4   0.6    1.1  1  Lipoprotein_20   YfhG lipoprotein
       0.05   13.5   0.4      0.069   13.0   0.4    1.1  1  Matrilin_ccoil   Trimeric coiled-coil oligomerisation domain 
       0.63   10.3   2.5       0.81    9.9   2.5    1.1  1  XhlA             Haemolysin XhlA


Domain annotation for each model (and alignments):
>> DUF5320  Family of unknown function (DUF5320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.2  12.3   5.2e-31   1.9e-27       1      99 []       1     114 [.       1     114 [. 0.94

  Alignments for each domain:
  == domain 1  score: 96.2 bits;  conditional E-value: 5.2e-31
                           DUF5320   1 MPrgdgtGpmGlGpmtGrglGyCagadapgyans........agfGr.....grg.grglgrgfgrrrraggarla. 62 
                                       MP+gd+tGp+G+GpmtGrg+GyCag+d pg+an+        +g+G+     g+g gr +grgfg+r+++ + +++ 
  gi|298675217|ref|YP_003726967.1|   1 MPGGDRTGPIGAGPMTGRGAGYCAGFDLPGFANNvpvgrglaRGRGFafyrkGMGlGRARGRGFGFRSYPDVPTTYn 77 
                                       **********************************9988777766666999998889***************999999 PP

                           DUF5320  63 aaetaeaskeeekelLeeqaeaLeeeleaikkrlkel 99 
                                       +++  e + e++++ Le+++++L+eel++i+k+l++l
  gi|298675217|ref|YP_003726967.1|  78 ENTGFERDVETSIRSLEQEQRILREELDNINKKLDNL 114
                                       99999*****************************986 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   1.6   3.9e-06     0.014      17      47 ..      85     115 ..      84     117 .] 0.92

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.9e-06
                   Snapin_Pallidin  17 eldeklkelrqsQeeLleqldrlnekLkele 47 
                                       ++++++++l+q+Q+ L+e+ld+ n+kL++le
  gi|298675217|ref|YP_003726967.1|  85 DVETSIRSLEQEQRILREELDNINKKLDNLE 115
                                       6899************************987 PP

>> Lipoprotein_20  YfhG lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.6   7.6e-06     0.027     123     155 ..      82     114 ..      75     116 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.6e-06
                    Lipoprotein_20 123 lqeesdskldslreqqaaLeaeLeettrKLenL 155
                                       ++++ ++ + sl ++q+ L++eL+++++KL+nL
  gi|298675217|ref|YP_003726967.1|  82 FERDVETSIRSLEQEQRILREELDNINKKLDNL 114
                                       56778999************************9 PP

>> Matrilin_ccoil  Trimeric coiled-coil oligomerisation domain of matrilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.4   1.9e-05     0.069      16      44 ..      82     117 .]      80     117 .] 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.9e-05
                                       HHHHHHHHHHHHHHH.......HHHHHHHHHHHHHH CS
                    Matrilin_ccoil  16 FQtkVeseiqaLtqk.......LeavtkRlealEnk 44 
                                       F + Ve++i++L q        L+++ k+l  lE+k
  gi|298675217|ref|YP_003726967.1|  82 FERDVETSIRSLEQEqrilreeLDNINKKLDNLESK 117
                                       7899**********55678888************87 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   2.5   0.00023      0.81      17      46 ..      87     116 ..      84     117 .] 0.90

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00023
                              XhlA  17 eervdkleekaaeaeekiknleedlkkles 46 
                                       e+ +  le+ ++  +e+++n++++l++les
  gi|298675217|ref|YP_003726967.1|  87 ETSIRSLEQEQRILREELDNINKKLDNLES 116
                                       567889**********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); expected 358.6 (0.02)
Passed bias filter:                      690  (0.0384851); expected 358.6 (0.02)
Passed Vit filter:                       125  (0.00697194); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 855.42
//
Query:       gi|298675218|ref|YP_003726968.1|  [L=164]
Description: 3-isopropylmalate dehydratase small subunit [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.1e-20   72.1   0.0    8.7e-20   71.4   0.0    1.4  1  Aconitase_C    Aconitase C-terminal domain
    0.00038   20.1   0.2     0.0099   15.5   0.2    2.1  1  Aconitase_2_N  Aconitate hydratase 2 N-terminus


Domain annotation for each model (and alignments):
>> Aconitase_C  Aconitase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.4   0.0   9.7e-24   8.7e-20      58     123 ..      35      99 ..      11     106 .. 0.83

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 9.7e-24
                                       EEEEHHHHHHHHHHTT--EEEE--SSBTBS---THHHHHHHHTTEEEEEES-B-HHHHHHHHHTT- CS
                       Aconitase_C  58 ekedvvdaaerykkegaklvviagknfGeGSSRehAAkalrllGikaviaeSFerIfennlikngl 123
                                         ++ +d ++  k+++ +++v++ +nfG+GSSRe+A++al++ G+  v+a+SF+rIf +n+i+ gl
  gi|298675218|ref|YP_003726968.1|  35 HAMEGIDPEFSSKVQKGDVIVAG-NNFGCGSSREQAPLALKHAGVACVVAKSFARIFFRNAINVGL 99 
                                       45578899999999999999888.***************************************997 PP

>> Aconitase_2_N  Aconitate hydratase 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   1.1e-06    0.0099      90     166 ..      74     148 ..       7     162 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.1e-06
                                       EEE--EEEEEE.E-HHHHHHHHHTT-EEEE---TT--TT-EEEEETTTTEEEETT--EEEE---S-TCHHHHHHHTS CS
                     Aconitase_2_N  90 kraggvvlGgk.iaPiFfntvedsGalpieadvskletGdvieikpkegkikkeegevvsefklkpetlldevragg 165
                                       k+ag  ++ +k  a iFf  + + G lp+ +   + ++Gd+++i+ k+g+++  ++++ +  kl p+ ll+ +  gg
  gi|298675218|ref|YP_003726968.1|  74 KHAGVACVVAKsFARIFFRNAINVG-LPVMEADVECSEGDIVKIDLKNGSVEV-NNKTFKGNKL-PDFLLEILTDGG 147
                                       4555444444449*****9998887.77777667899**************99.5555555555.666667777776 PP

                                       H CS
                     Aconitase_2_N 166 r 166
                                        
  gi|298675218|ref|YP_003726968.1| 148 L 148
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1286.34
//
Query:       gi|298675219|ref|YP_003726969.1|  [L=284]
Description: hypothetical protein Metev_1313 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1849.13
//
Query:       gi|298675220|ref|YP_003726970.1|  [L=336]
Description: isopropylmalate/isohomocitrate dehydrogenase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   7.4e-100  334.5   0.1   9.1e-100  334.2   0.1    1.0  1  Iso_dh    Isocitrate/isopropylmalate dehydrogenase


Domain annotation for each model (and alignments):
>> Iso_dh  Isocitrate/isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  334.2   0.1  5.1e-104  9.1e-100       1     348 []       2     323 ..       2     324 .. 0.95

  Alignments for each domain:
  == domain 1  score: 334.2 bits;  conditional E-value: 5.1e-104
                                       EEEEEEESTTHHHHHHHHHHHHHHHHHHHT-EEEEEE---THHHHHHHSSSS-HHHHHHHHHSSEEEEEE---CSSS CS
                            Iso_dh   1 kiallegdgiGpevveaalkvlkaakekaglelefeevdvGgaaidetgeplpeetleaikeadvvllgavgtpkek 77 
                                       k+a++egdgiG+ev+++a+kvl+a++    l +e   v++G    ++tg ++++e +e +k+ d +l+gav+tp + 
  gi|298675220|ref|YP_003726970.1|   2 KLAVVEGDGIGKEVIPEAVKVLDALS----LPIEKVPVEIGYGKWKKTGYAITDEDIETLKNCDCILFGAVTTPPDP 74 
                                       5799********************99....66899999*************************************77 PP

                                       SSSHHHHHHHHHHHTTEEEEEEEEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEETTG.GGGEEEEE CS
                            Iso_dh  78 evrpengLlaLrkeldlfanlrpvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkgsifteevavdt 154
                                       e ++   Ll++rkeld++an+rpvk +       + k    ++++ vivRe+t+g+Y+g+e+ +++      va++t
  gi|298675220|ref|YP_003726970.1|  75 EYKSV--LLTIRKELDMYANIRPVKPLA-GITGVTGK----SDFNYVIVRENTEGLYSGIEEIHDD------VAYTT 138
                                       77775..599****************93.33344445....4799****************99999......69*** PP

                                       EEEEHHHHHHHHHHHHHHHHHTTTSEEEEEESTTTTHHHHHHHHHHHHHHCCTTTTSEEEEEEHHHHHHHHHHSGGG CS
                            Iso_dh 155 klyseeeieriaraafelAlkrgkkkvtlvdKanvlksselwrkiveevaeeeypdielehqlvDsaamqlvkspkq 231
                                        ++s+++++ria++a++lA+ r +++vt+v+K+nv+ks +l+ ++++++ae   +d+++++ lvD++a++l++ p++
  gi|298675220|ref|YP_003726970.1| 139 RVVSRKGSKRIAEYACKLAKMR-NNNVTIVHKSNVMKSDKLFLDVCQQTAE--SGDVNYSDTLVDAMAYYLITYPEK 212
                                       **********************.*************************998..9*********************** PP

                                       GSEEEE-HHHHHHHHHHHHHHTTSGCC-EEEEEETSS-EEEEESS---CCCTTSS-S-THHHHHHHHHHHHHTTT-H CS
                            Iso_dh 232 fdVivtkNlfGDilSDeaaalvGslGllpSaslgekkvaifEavHGsapdiagkdkaNpiavilSaalmLryslgle 308
                                       +dV+vt+NlfGDilSD+ aa +Gs+Gl+pSa++g +++a fE+vHGsapdiag ++aNp+a+ilS+ ++L+   g +
  gi|298675220|ref|YP_003726970.1| 213 YDVVVTTNLFGDILSDMSAAHIGSMGLMPSANIG-EEHAFFEPVHGSAPDIAGEKIANPVAAILSIKMLLQW-YGYN 287
                                       **********************************.68***********************************.**** PP

                                       HHHHHHHHHHHHHHHHTSCCHHHCTTSTCCCHHHHHHHHH CS
                            Iso_dh 309 eaAdkiekAvekvleagivTkDlageaakevstsefgdav 348
                                       ++A+ +e++v+ +l++gi+T Dl+ge     +t+e+g+av
  gi|298675220|ref|YP_003726970.1| 288 NEASLVERSVNYTLNKGIKTPDLGGEY----TTEELGQAV 323
                                       *************************99....999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2392.90
//
Query:       gi|298675221|ref|YP_003726971.1|  [L=550]
Description: type II secretion system F domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-14   53.2   0.0    2.3e-10   40.5   0.0    4.1  5  T2SSF     Type II secretion system (T2SS), protein F


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -7.1   5.4         1   1.8e+04     103     124 ..      32      53 ..      25      64 .. 0.67
   2 !   40.5   0.0   1.3e-14   2.3e-10       2     121 ..      86     210 ..      85     214 .. 0.97
   3 ?   -3.0   3.1      0.38   6.8e+03     105     123 ..     217     235 ..     211     238 .. 0.55
   4 !   18.9   0.0   6.2e-08    0.0011       1     119 [.     330     452 ..     330     458 .. 0.87
   5 ?   -5.2   2.0         1   1.8e+04     115     122 ..     493     500 ..     489     510 .. 0.47

  Alignments for each domain:
  == domain 1  score: -7.1 bits;  conditional E-value: 1
                                       HTTXXXXXXXXXXXXXXXXXXX CS
                             T2SSF 103 lepllllvvallvllillaill 124
                                       +++l++l+v +l+ +++++il+
  gi|298675221|ref|YP_003726971.1|  32 TSVLIYLIVPWLFTGPFISILI 53 
                                       5566666666666666666654 PP

  == domain 2  score: 40.5 bits;  conditional E-value: 1.3e-14
                                       HHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTS.SHHHHHC....T-TT.TS-HHHHHHHHHHHH CS
                             T2SSF   2 lrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGg.slseale....rtpssefpelvvqliragee 73 
                                       ++q++    a  p  +++++++++ +++ laee ++i++ ++ +  +l +a +    rtps  f ++++++ +a  +
  gi|298675221|ref|YP_003726971.1|  86 ITQMGAVATANTPRIDVIRIVSKNEDFQDLAEENREIYNLVSVWNlNLGDACKfvskRTPSVIFEDFLDRFAHALHS 162
                                       789999***************************************999*************999************* PP

                                       HT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXX CS
                             T2SSF  74 ggnLaevLerlaeyleeerelrrkllaallepllllvvallvllilla 121
                                       g n+ e+L+  +  +++e+e+ + + + ++ ++ +l+v l++++i+la
  gi|298675221|ref|YP_003726971.1| 163 GENVNEFLSTEQNVVMNEYESMYYSSLYMIDVIKELFVSLVISMIFLA 210
                                       **********************************************97 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 0.38
                                       TXXXXXXXXXXXXXXXXXX CS
                             T2SSF 105 pllllvvallvllillail 123
                                       p+l+ + a+++++++++++
  gi|298675221|ref|YP_003726971.1| 217 PILTGMSAVVLMAVVVIVF 235
                                       5555555555555555554 PP

  == domain 4  score: 18.9 bits;  conditional E-value: 6.2e-08
                                       HHHHHHHHHH.TT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHC....T-TT.TS-HHHHHHHHHHH CS
                             T2SSF   1 flrqlatlls.aGvplveaLellaeeaengplaeelkriarrlraGgslseale....rtpssefpelvvqlirage 72 
                                       f+r+l++  +  G  +++aL++l  ++ +gpl+  ++++++rl   ++  +++     +t+s+ +  +++++++a  
  gi|298675221|ref|YP_003726971.1| 330 FIRSLGSSAGaKGNMIDDALKSLRLHD-FGPLTNDVNELYKRLILRINKIKSWYwfaaSTGSNLIQHFCSMFVEATN 405
                                       77888877774677899**********.*******************888888888989999888************ PP

                                       HHT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXX CS
                             T2SSF  73 eggnLaevLerlaeyleeerelrrkllaallepllllvvallvllil 119
                                        gg+ + + + +a+++ ++  lr+k+     + + +l+ + + +++ 
  gi|298675221|ref|YP_003726971.1| 406 LGGKPDTIGNIIATNFHRMVTLRKKRYQTASSFVGVLYGLTAGIGFT 452
                                       ***********************999988888888887776666655 PP

  == domain 5  score: -5.2 bits;  conditional E-value: 1
                                       XXXXXXXX CS
                             T2SSF 115 vllillai 122
                                        +l+++++
  gi|298675221|ref|YP_003726971.1| 493 TMLVMVIM 500
                                       22222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (550 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1116  (0.0622455); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.26s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 3632.24
//
Query:       gi|298675222|ref|YP_003726972.1|  [L=553]
Description: type II secretion system protein E [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-41  141.8   0.0    2.7e-41  141.4   0.0    1.1  1  T2SSE        Type II/IV secretion system protein
     0.0043   16.8   0.0     0.0088   15.8   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.021   15.2   0.0      0.049   14.0   0.0    1.6  1  AAA_16       AAA ATPase domain
      0.042   14.3   1.0      0.072   13.6   0.2    1.7  2  AAA_23       AAA domain
      0.098   12.6   0.2        1.6    8.7   0.1    2.4  2  Microtub_bd  Microtubule binding
        0.1   12.1   0.0       0.23   10.9   0.0    1.5  1  AAA_7        P-loop containing dynein motor region
       0.12   12.7   0.0       0.57   10.4   0.0    2.1  2  AAA_22       AAA domain


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.4   0.0   1.1e-44   2.7e-41       3     255 ..     173     429 ..     171     445 .. 0.90

  Alignments for each domain:
  == domain 1  score: 141.4 bits;  conditional E-value: 1.1e-44
                             T2SSE   3 illeallddekvsdihvekper.vkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpekgv 78 
                                        +le++++d+   dih    +  ++v++ +d     ++++ +++ l    + +    ++ +++ +p+ d++lp +g 
  gi|298675222|ref|YP_003726972.1| 173 GPLEPVIRDPYLEDIHSVGVNGvYIVHKILDM-IKTNIHFGDDSRLDDWFRSMSERIGRPVNDASPISDGALP-DGS 247
                                       578999999*******9998886888777777.9999************************************.999 PP

                             T2SSE  79 rlrvvllP..vvagealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkei 153
                                       r++++     +++g ++++Rk s   +++ +l+  ++ + ++a+ +    ++ +++ +sG T sGKtt+l+a+l++i
  gi|298675222|ref|YP_003726972.1| 248 RINMIYSTdiSLQGSSFTMRKFSDTPISIIQLMNFGSINTEMAAYIWMCFENGMSVFFSGETASGKTTMLNACLAFI 324
                                       9888765511455599************************************************************* PP

                             T2SSE 154 nksderivtvEDpvEiqleganqvqlnak.....kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGHl 225
                                       n    ++  +ED+ E+q+ ++   ql ++     + +v++ +ll+aaLR rP  i+vGEiR+ e   + +A++TGH+
  gi|298675222|ref|YP_003726972.1| 325 NPW-SKVYSAEDTSEVQPPQDVWQQLLTReegpeESRVELYTLLKAALRSRPNYIIVGEIRGVEGSVAFQAMQTGHP 400
                                       ***.*****************9999999999**99****************************************** PP

                             T2SSE 226 gslsTlHansaagalerLeqlgaeveaael 255
                                       + +sT Ha s+++ ++rL     +v+ + +
  gi|298675222|ref|YP_003726972.1| 401 V-VSTFHAASVKKLIQRLTGHPINVPITFI 429
                                       *.****************876655555555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   3.4e-06    0.0088       4      49 ..     277     327 ..     274     332 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.4e-06
                            AAA_29   4 lqlvNWgtfdght....ieidlkg.atlltGpsGsGKSTllDAiqalLvpa 49 
                                       +ql+N g+++ +     ++  ++g +++++G++ sGK+T+l A  a + p 
  gi|298675222|ref|YP_003726972.1| 277 IQLMNFGSINTEMaayiWMCFENGmSVFFSGETASGKTTMLNACLAFINPW 327
                                       677777777764312224455688899****************99987775 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.9e-05     0.049      25      88 ..     301     352 ..     293     443 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.9e-05
                            AAA_16  25 elvllsGesGvGKsslvrellralekdg.giflrgkcdqlesaipysalaqalareellrqllde 88 
                                        +v++sGe ++GK+++++++l  ++    ++ ++ + +      p + ++q+l         l++
  gi|298675222|ref|YP_003726972.1| 301 MSVFFSGETASGKTTMLNACLAFINPWSkVYSAEDTSEVQ----PPQDVWQQL---------LTR 352
                                       589******************9888873233344433333....323333333.........333 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.3   5.9e+03     149     149 ..      82      82 ..       9     121 .. 0.52
   2 ?   13.6   0.2   2.8e-05     0.072       2      39 ..     277     320 ..     277     325 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.3
                            AAA_23 149 k 149
                                       +
  gi|298675222|ref|YP_003726972.1|  82 S 82 
                                       2 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2.8e-05
                            AAA_23   2 Lkienfrsfrdqe...i..dFskgltl.ItGpNGaGKTTildAi 39 
                                       +++ nf+s++ +    i   F++g+ + ++G++ +GKTT l+A+
  gi|298675222|ref|YP_003726972.1| 277 IQLMNFGSINTEMaayIwmCFENGMSVfFSGETASGKTTMLNAC 320
                                       678899999554333444488998875167************97 PP

>> Microtub_bd  Microtubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.17   4.3e+02      91     145 ..      67     123 ..      36     125 .. 0.85
   2 ?    8.7   0.1   0.00062       1.6      67      99 ..     285     316 ..     276     332 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.17
                                       S..................ST-HCHHHHHHHHHHCCTSCCCCEEEEEEEEEEESS-E CS
                       Microtub_bd  91 qTGsGKtyTmeg..eeeeagmipraveeifetiselkekgwkyeielqfveiynekv 145
                                       q G  + y +e   +++e+++ + ++++i+e+++++   + + e++  ++e+ ne+v
  gi|298675222|ref|YP_003726972.1|  67 QMGQARYYAIEPtlTSSERKKYDAVMNAILEKSAKKPVPESESELKDLIIELLNESV 123
                                       456677788888777889999999**********99999999999999999999965 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00062
                                       CCCCCHHHHHHHHTT--EEEEEEES........ CS
                       Microtub_bd  67 vfeeisqlvqsaldgynvcifaygqTGsGKtyT 99 
                                       +  e+++++ +++++  +++f+ g+T sGKt  
  gi|298675222|ref|YP_003726972.1| 285 INTEMAAYIWMCFEN-GMSVFFSGETASGKTTM 316
                                       77899*******954.4799***********44 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   9.2e-05      0.23      22      57 ..     289     324 ..     278     347 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 9.2e-05
                             AAA_7  22 ysyllelllknkkpvllvGptGtGKtviikdllkkl 57 
                                       +   + ++++n+++v++ G+t +GKt++++ +l  +
  gi|298675222|ref|YP_003726972.1| 289 MAAYIWMCFENGMSVFFSGETASGKTTMLNACLAFI 324
                                       556677899********************9987655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.4   3.5e+03      48      87 ..      81     120 ..      37     125 .. 0.62
   2 ?   10.4   0.0   0.00022      0.57       7     100 ..     302     383 ..     298     397 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.4
                            AAA_22  48 psst..sskdllrellralglelkaerlsseellealeqalr 87 
                                       +ss+  + + +++++l++   +    + s++el +++ + l+
  gi|298675222|ref|YP_003726972.1|  81 TSSErkKYDAVMNAILEKSAKKP--VPESESELKDLIIELLN 120
                                       33333233333444444444333..34677777776666665 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00022
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelkaerlsseelleal 82 
                                       +++  Ge+ +GKTt l+  l   + +       ++v++ + +s+   ++d++++ll   + + +    s+ el+++l
  gi|298675222|ref|YP_003726972.1| 302 SVFFSGETASGKTTMLNACLAFINPW-------SKVYSAEDTSEVqPPQDVWQQLLTREEGPEE----SRVELYTLL 367
                                       56778*****************9754.......788888888888999*******999886555....599999999 PP

                            AAA_22  83 eqalraravielliiDEa 100
                                         alr+r     +i+ E+
  gi|298675222|ref|YP_003726972.1| 368 KAALRSRPN--YIIVGEI 383
                                       999999988..7777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 3698.10
//
Query:       gi|298675223|ref|YP_003726973.1|  [L=231]
Description: AAA ATPase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-19   70.3   1.5    1.9e-19   69.9   1.5    1.0  1  ATPase           KaiC
    6.9e-06   25.6   0.3    1.6e-05   24.4   0.1    1.6  2  DnaB_C           DnaB-like helicase C terminal domain
    4.9e-05   23.0   0.0     0.0001   21.9   0.0    1.4  1  AAA_25           AAA domain
    6.6e-05   22.9   0.0    9.6e-05   22.4   0.0    1.3  1  NACHT            NACHT domain
    0.00056   20.5   0.0    0.00077   20.0   0.0    1.3  1  AAA_18           AAA domain
     0.0011   18.7   0.0     0.0018   17.9   0.0    1.6  1  SRP54            SRP54-type protein, GTPase domain
     0.0017   18.8   0.2     0.0032   17.9   0.2    1.5  1  AAA              ATPase family associated with various cellul
     0.0029   17.9   0.1     0.0055   17.0   0.1    1.5  1  AAA_22           AAA domain
     0.0036   17.3   0.0     0.0071   16.3   0.0    1.5  1  AAA_5            AAA domain (dynein-related subfamily)
     0.0047   16.2   0.2     0.0067   15.7   0.2    1.4  1  DUF2075          Uncharacterized conserved protein (DUF2075)
     0.0057   16.6   0.1        2.3    8.2   0.0    2.4  2  P-mevalo_kinase  Phosphomevalonate kinase
     0.0069   15.9   0.9       0.01   15.3   0.0    1.7  2  KTI12            Chromatin associated protein KTI12
  ------ inclusion threshold ------
      0.012   15.4   0.2       0.33   10.7   0.0    2.2  2  IstB_IS21        IstB-like ATP binding protein
      0.012   15.2   0.3       0.45   10.1   0.1    2.1  2  CobU             Cobinamide kinase / cobinamide phosphate gua
       0.02   14.9   1.2       0.18   11.9   1.1    2.1  1  AAA_14           AAA domain
      0.027   14.6   0.0      0.032   14.4   0.0    1.3  1  AAA_33           AAA domain
      0.039   14.0   0.1       0.14   12.3   0.0    1.8  2  Torsin           Torsin
      0.052   13.2   0.0      0.095   12.4   0.0    1.4  1  Sigma54_activat  Sigma-54 interaction domain
      0.069   13.5   0.0       0.11   12.8   0.0    1.3  1  AAA_16           AAA ATPase domain
      0.086   12.5   0.1       0.25   11.0   0.0    1.8  2  Thymidylate_kin  Thymidylate kinase
       0.16   11.9   0.2       0.33   10.8   0.0    1.6  2  APS_kinase       Adenylylsulphate kinase


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9   1.5   2.2e-22   1.9e-19       8     207 ..      14     204 ..      10     225 .. 0.91

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 2.2e-22
                            ATPase   8 lDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeegkla 84 
                                       + e l  G+pe++ vli G++G+GK+i++++ ++  ae+ +  + ++++  + + +++++ sl+  +     +g++ 
  gi|298675223|ref|YP_003726973.1|  14 FNEKLGSGFPEDSLVLIEGVSGSGKSIVSQRIAYGLAEN-ETSVTYISTQMTTKGFINQMYSLDYQISSHLLNGNML 89 
                                       7888999************************99999888.9*****************************9999999 PP

                            ATPase  85 iidasesaeesaeekdkedleelieelaeaikeikakrvviDsitglayeekeavaReilrqlvrvlkklgvTailv 161
                                       +i +    ++      + + + +i++l++a + ++   ++iD+i++l +++ +++    l  ++++l++++ T i++
  gi|298675223|ref|YP_003726973.1|  90 YIPVIPLVKN------TRQSMDFIQKLMNAEDLFEKDVIIIDTISSLIKNSVNSEKGFDLVSFFKRLNGMDKTIIMT 160
                                       9999998765......7788899************************8888999999******************** PP

                            ATPase 162 sekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRg 207
                                        e + s ++     +   ++d ++ L++k+++++++R+l + k  g
  gi|298675223|ref|YP_003726973.1| 161 LE-PGSLDEEIVTMLRS-SSDINLSLNVKQMSNQVRRMLTVNKFIG 204
                                       **.55556666677788.9**********************99755 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.1   1.8e-08   1.6e-05      11     109 ..      17     126 ..      12     150 .. 0.71
   2 ?   -2.3   0.0       2.5   2.2e+03     110     125 ..     182     197 ..     166     206 .. 0.73

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.8e-08
                                       HHCTSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHHHHHTXXHHHHHHTTSXH. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                            DnaB_C  11 kltsGlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRllsseaeidskklrtgklke. 86 
                                       kl sG+ +  l++i + ++ Gk+ +   ia   a+ ++++v+++s  m+++  ++++ s + +i+s+ l+   l   
  gi|298675223|ref|YP_003726973.1|  17 KLGSGFPEDSLVLIEGVSGSGKSIVSQRIAYGLAE-NETSVTYISTQMTTKGFINQMYSLDYQISSHLLNGNMLYIp 92 
                                       6779***************************9996.6779************************9998854222212 PP

                                       ............HHHHHHHHHHHHHHHSEEEEEEX CS
                                       ............xxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  87 ............edweklteaieelseaklfiddt 109
                                                   + ++kl++a e+l e +++i dt
  gi|298675223|ref|YP_003726973.1|  93 viplvkntrqsmDFIQKLMNA-EDLFEKDVIIIDT 126
                                       333332222221334444444.3444444444333 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.5
                                       SSXCHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxx RF
                            DnaB_C 110 paltvseirskarrlk 125
                                        +l+v+++ +++rr+ 
  gi|298675223|ref|YP_003726973.1| 182 LSLNVKQMSNQVRRML 197
                                       4677888888888874 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   1.2e-07    0.0001      24     165 ..      17     141 ..       6     157 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.2e-07
                            AAA_25  24 wlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal... 97 
                                       +l  g+ p+++l+l+ G +g+GK+ +   +a+ +a+ +            V y+s+ ++ +++ + ++ +  ++   
  gi|298675223|ref|YP_003726973.1|  17 KLGSGF-PEDSLVLIEGVSGSGKSIVSQRIAYGLAENE----------TSVTYISTQMTTKGFINQMYSLDYQIssh 82 
                                       566778.9***************************977..........38******************999888533 PP

                            AAA_25  98 rddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralggdensnsdv 165
                                        ++++ l +       +pL++++r++     ++++l++a e+  + ++++iD++s++  ++ ns++  
  gi|298675223|ref|YP_003726973.1|  83 LLNGNMLYIP-----VIPLVKNTRQS---MDFIQKLMNA-EDLFEKDVIIIDTISSLIKNSVNSEKGF 141
                                       2334443333.....49999876555...3455555544.444558*****************99875 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.1e-07   9.6e-05       2     151 ..      27     190 ..      26     205 .. 0.64

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.1e-07
                                       CEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-....-HCHHHCCCCTS--SSS-CCHHHHC CS
                             NACHT   2 lvilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna.rsladllfsqlpepaapvsevwavll 77 
                                       lv+++G +GsGK++  q++a  +ae++      ++ +  ++ +++   n  +sl++++ s+l+  ++   + ++ l+
  gi|298675223|ref|YP_003726973.1|  27 LVLIEGVSGSGKSIVSQRIAYGLAENE-----TSVTYISTQMTTKGFINQmYSLDYQISSHLLNGNMLYIP-VIPLV 97 
                                       79***********************99.....4666666666666654445***********999998888.44445 PP

                                       CSCCCEE.................EEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCCHHH.HC CS
                             NACHT  78 elperlL.................lilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpralrd.le 136
                                       ++ ++ +                 +i+D +  l +   +   ++  +l  + +++      ++++t+ p++l + + 
  gi|298675223|ref|YP_003726973.1|  98 KNTRQSMdfiqklmnaedlfekdvIIIDTISSLIKNSVN--SEKGFDL-VSFFKRLNGMDKTIIMTLEPGSLDEeIV 171
                                       555555555555566666666666888888877764444..2222222.2444443334555666666666654544 PP

                                       TTSSCE......EEEE--T CS
                             NACHT 137 eqleea....ivlevegfs 151
                                        +l+++     +l v+ +s
  gi|298675223|ref|YP_003726973.1| 172 TMLRSSsdinLSLNVKQMS 190
                                       4444444545555555555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0     9e-07   0.00077       1      84 [.      28     129 ..      28     172 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 9e-07
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf........................gvnlrdvakenglllevdpealdeskrl 52 
                                       +l+ G++G+GK+ ++++++  l ++                         +++++++  n+l+++v p    ++ r 
  gi|298675223|ref|YP_003726973.1|  28 VLIEGVSGSGKSIVSQRIAYGLaENetsvtyistqmttkgfinqmysldYQISSHLLNGNMLYIPVIPL--VKNTRQ 102
                                       79****************66665556778999999999999****************************..777777 PP

                            AAA_18  53 dedkldklldaleenssaleegknlvidghla 84 
                                        +d+ +kl++a +   +     ++++id + +
  gi|298675223|ref|YP_003726973.1| 103 SMDFIQKLMNAEDLFEK-----DVIIIDTISS 129
                                       77777777776666644.....8999998765 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.1e-06    0.0018       3      92 ..      27     127 ..      25     207 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.1e-06
                                       EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEE...........SSTTSCH CS
                             SRP54   3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvik...........kkeeadp 68 
                                       ++l+ G+ G+GK     ++a  l +++++v  +++ +   + ++Q+  l  ++  ++++            k+++++
  gi|298675223|ref|YP_003726973.1|  27 LVLIEGVSGSGKSIVSQRIAYGLAENETSVTYISTQMTTKGFINQMYSLDYQISSHLLNgnmlyipviplVKNTRQS 103
                                       68999*****************************************9877775544444444444444476677789 PP

                                       HHHHHHHHHHHHHTTSSEEEEEE- CS
                             SRP54  69 aavakeavekakeekidvvlvDTa 92 
                                       ++++++ +++++  + dv+++DT 
  gi|298675223|ref|YP_003726973.1| 104 MDFIQKLMNAEDLFEKDVIIIDTI 127
                                       ***********************6 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.2   3.8e-06    0.0032       1     130 [.      28     182 ..      28     184 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.8e-06
                                       EEEESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSS.............................STTHHH CS
                               AAA   1 vllyGppGtGKTllakavakel.....gvefleisgsellsk.............................yvgese 43 
                                       vl+ G  G GK+++ + +a  l     +v+++  s    + k                             +v+++ 
  gi|298675223|ref|YP_003726973.1|  28 VLIEGVSGSGKSIVSQRIAYGLaenetSVTYI--STQMTT-KgfinqmysldyqisshllngnmlyipvipLVKNTR 101
                                       6899**************99985442223333..332222.234445888888888888888899998888555555 PP

                                       HHHHHHHHHHHHTS..TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHH CS
                               AAA  44 kkirelfkeakeka..kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpa 118
                                       +++  + k + ++   ++ +++iD i +l+k++   +se++ ++v  +++ l+g++k       i++t +p +ld++
  gi|298675223|ref|YP_003726973.1| 102 QSMDFIQKLMNAEDlfEKDVIIIDTISSLIKNS--VNSEKGFDLV-SFFKRLNGMDK------TIIMTLEPGSLDEE 169
                                       555444444444446788**************9..3333333333.34455555555......79999********9 PP

                                       HHS.TTSSEEEET CS
                               AAA 119 llr.gRfdrkiei 130
                                       ++   R ++ i++
  gi|298675223|ref|YP_003726973.1| 170 IVTmLRSSSDINL 182
                                       9977777776665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   6.4e-06    0.0055       6     105 ..      26     137 ..      23     169 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.4e-06
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdl.lrellralglelka........... 70 
                                       +++++ G sG+GK+ + +r+++ l e         e+   +++ +++ k +  ++   +++ + +            
  gi|298675223|ref|YP_003726973.1|  26 SLVLIEGVSGSGKSIVSQRIAYGLAE--------NETSVTYISTQMTTKGFiNQMYSLDYQISSHLlngnmlyipvi 94 
                                       78899*******************64........3333222333333333313333333332222244566777777 PP

                            AAA_22  71 .erlsseellealeqalrarav..ielliiDEaqhlr.....s 105
                                          +++++ ++ +++ ++a +   + ++iiD +  l+     s
  gi|298675223|ref|YP_003726973.1|  95 pLVKNTRQSMDFIQKLMNAEDLfeKDVIIIDTISSLIknsvnS 137
                                       7556778888888888888888888999999998887653321 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   8.4e-06    0.0071       2      73 ..      28     126 ..      27     137 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.4e-06
                                       EEEE--SSSSHHHHHHHGGGGB..S--EEEEE--TT--HHHHH--B--..................--------... CS
                             AAA_5   2 vlLvGppGtgKselaerlaaal..nreveyvqltrdtteedlkgrreik........ngttslvd.splvraar... 64 
                                       vl+ G +G+gKs +++r+a  l  n + +++  t+ tt+  + + ++++        ng+  + +  plv++ r   
  gi|298675223|ref|YP_003726973.1|  28 VLIEGVSGSGKSIVSQRIAYGLaeNETSVTYISTQMTTKGFINQMYSLDyqisshllNGNMLYIPvIPLVKNTRqsm 104
                                       7999*******************655555555555555555555555545455555555544444234555555666 PP

                                       .............G-SEEEEES CS
                             AAA_5  65 .............egeilvlDE 73 
                                                    e++++++D 
  gi|298675223|ref|YP_003726973.1| 105 dfiqklmnaedlfEKDVIIIDT 126
                                       6666666666666666666665 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   7.8e-06    0.0067       2      38 ..      26      60 ..      25     126 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7.8e-06
                           DUF2075  2 avvlVtGvaGtGKtvvllnllaeleddeeertavyls 38
                                      ++vl++Gv+G+GK++v  ++++ l   e+e +++y+s
  gi|298675223|ref|YP_003726973.1| 26 SLVLIEGVSGSGKSIVSQRIAYGL--AENETSVTYIS 60
                                      589*********************..55555555555 PP

>> P-mevalo_kinase  Phosphomevalonate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.013        11       2      47 ..      31      78 ..      30      84 .. 0.81
   2 !    8.2   0.0    0.0027       2.3       9      48 ..     104     145 ..      99     154 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.013
                   P-mevalo_kinase  2 sGkrksGKdyvtellkerlgeekvavirlSepi..Keeyakekgldle 47
                                       G   sGK  v+++++  l e++ +v+ +S ++  K    +++ ld++
  gi|298675223|ref|YP_003726973.1| 31 EGVSGSGKSIVSQRIAYGLAENETSVTYISTQMttKGFINQMYSLDYQ 78
                                      67889************************9875226667777777765 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0027
                   P-mevalo_kinase   9 Kdyvtellker.lgeekvavi.rlSepiKeeyakekgldlee 48 
                                        d++ +l++ + l e++v +i ++S  iK+++ +ekg dl  
  gi|298675223|ref|YP_003726973.1| 104 MDFIQKLMNAEdLFEKDVIIIdTISSLIKNSVNSEKGFDLVS 145
                                       58888887654155555555549****************865 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.2e-05      0.01       3      40 ..      27      64 ..      26      81 .. 0.88
   2 ?   -1.6   0.2       1.8   1.5e+03     186     186 ..     141     141 ..      98     208 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-05
                                      EEEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHH CS
                             KTI12  3 LvvltGlPssGKstrakeLakaleeekrsvvviddesl 40
                                      Lv++ G+  sGKs +++++a  l+e++ sv++i+++  
  gi|298675223|ref|YP_003726973.1| 27 LVLIEGVSGSGKSIVSQRIAYGLAENETSVTYISTQMT 64
                                      9********************************98765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.8
                                       - CS
                             KTI12 186 l 186
                                        
  gi|298675223|ref|YP_003726973.1| 141 F 141
                                       1 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00038      0.33      50      84 ..      28      62 ..      19      78 .. 0.89
   2 ?    2.3   0.1      0.14   1.2e+02      79     134 ..      89     144 ..      83     160 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00038
                         IstB_IS21 50 ivllGpsGvGKshlaialgveavraglsvlfvrve 84
                                      +++ G sG GKs ++  +++  +++++sv++++++
  gi|298675223|ref|YP_003726973.1| 28 VLIEGVSGSGKSIVSQRIAYGLAENETSVTYISTQ 62
                                      6788***************************9986 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.14
                         IstB_IS21  79 lfvrvedLveelkrarrdgklaralkrllkvdllilDdlgllpldqaeaellfevi 134
                                       l++ v  Lv++ ++  +  +   +++ l + d++i+D ++ l  ++ ++e+ f+++
  gi|298675223|ref|YP_003726973.1|  89 LYIPVIPLVKNTRQSMDFIQKLMNAEDLFEKDVIIIDTISSLIKNSVNSEKGFDLV 144
                                       5666666666666666666666667889999*******998877776666666666 PP

>> CobU  Cobinamide kinase / cobinamide phosphate guanyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00052      0.45       1      34 [.      28      64 ..      28      83 .. 0.89
   2 ?    3.6   0.0      0.05        43      63      93 ..     106     139 ..      96     196 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00052
                              CobU  1 ilvtGgarSGKSefAekla...eeskekvvYiATaea 34
                                      +l+ G + SGKS + +++a   +e++ +v+Yi T  +
  gi|298675223|ref|YP_003726973.1| 28 VLIEGVSGSGKSIVSQRIAyglAENETSVTYISTQMT 64
                                      6999**************999888899******9865 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.05
                              CobU  63 laealkeeek...kevvLvDcltlwltnllleee 93 
                                       + ++l ++e+   k+v+++D ++ +++n + +e+
  gi|298675223|ref|YP_003726973.1| 106 FIQKLMNAEDlfeKDVIIIDTISSLIKNSVNSEK 139
                                       444444444447789*************998755 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.1   0.00021      0.18       4      90 ..      27     114 ..      24     188 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00021
                            AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelilek.lkeekkty.lflDEiqevpe 78 
                                       +++i+G+  +GK+ + +++++ l  ++ s+ yi+ +  ++  +++  +l+  i ++ l++ ++ y  ++  +++ ++
  gi|298675223|ref|YP_003726973.1|  27 LVLIEGVSGSGKSIVSQRIAYGLAENETSVTYISTQMTTKGFINQMYSLDYQISSHlLNG-NMLYiPVIPLVKNTRQ 102
                                       789*************99999988999999***999877733333324444455442223.2322134444555555 PP

                            AAA_14  79 wekalkslvdeg 90 
                                         +++++l++ +
  gi|298675223|ref|YP_003726973.1| 103 SMDFIQKLMNAE 114
                                       555555555533 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.8e-05     0.032       1      23 [.      27      49 ..      27     163 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.8e-05
                            AAA_33  1 lvllvGlpGsGKstlaerllkkl 23
                                      lvl+ G++GsGKs +++r++  l
  gi|298675223|ref|YP_003726973.1| 27 LVLIEGVSGSGKSIVSQRIAYGL 49
                                      799***************85333 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00016      0.14      51     106 ..      24      78 ..      15      87 .. 0.89
   2 ?   -1.9   0.0         4   3.4e+03      36      54 ..     122     141 ..     100     162 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                                       SS-EEEEEEE-TTSSHHHHHHHHHHHHSTTGGGSTTEEEEEHHHHS--GGGHHHHH CS
                            Torsin  51 kkpLvlsfhGwtGtGknfvaeiiaenlyrdGlrsdyvkkfvatadfPkkkkveeyk 106
                                       + +Lvl + G +G+Gk+ v++ ia  l ++    +y+ + ++t+ f ++ +  +y+
  gi|298675223|ref|YP_003726973.1|  24 EDSLVL-IEGVSGSGKSIVSQRIAYGLAENETSVTYISTQMTTKGFINQMYSLDYQ 78 
                                       566776.79*************************************9999988887 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4
                                       HHHHHHHHHHT-S.S-SS-E CS
                            Torsin  36 lvvksvkaylene.kpkkpL 54 
                                       +++ ++ + ++n  +++k +
  gi|298675223|ref|YP_003726973.1| 122 IIIDTISSLIKNSvNSEKGF 141
                                       45677777777765666654 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00011     0.095      18      53 ..      21      56 ..       8      73 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                                      HCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-E CS
                   Sigma54_activat 18 vaktdlsvlitGesGtGKellaraiheaskrkekpf 53
                                        + d+ vli+G sG+GK+++++ i     ++e+++
  gi|298675223|ref|YP_003726973.1| 21 GFPEDSLVLIEGVSGSGKSIVSQRIAYGLAENETSV 56
                                      5667889****************9987555554444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00013      0.11      19      52 ..      18      53 ..       8      89 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                            AAA_16 19 vrsgrp..elvllsGesGvGKsslvrellralekdg 52
                                      + sg p  +lvl+ G sG+GKs + ++++  l +++
  gi|298675223|ref|YP_003726973.1| 18 LGSGFPedSLVLIEGVSGSGKSIVSQRIAYGLAENE 53
                                      556667789***************999987666664 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0003      0.25       1      27 [.      30      57 ..      30      85 .. 0.85
   2 ?   -2.0   0.0       2.8   2.4e+03     149     178 ..     104     131 ..      98     137 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0003
                                      EEESTTSSHHHHHHHHHHHHHHTTE..E CS
                   Thymidylate_kin  1 iEGlDGaGKttqaellkerlkeegik.v 27
                                      iEG+ G+GK+ +++ ++  l e+  + +
  gi|298675223|ref|YP_003726973.1| 30 IEGVSGSGKSIVSQRIAYGLAENETSvT 57
                                      8*******************99998743 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.8
                                       HHHHHHHHHHHHHHHHTTSTEEEEETTS-.H CS
                   Thymidylate_kin 149 ldflrkvrerylelakederiliidasks.i 178
                                        df +k++  + +l+  ++ ++iid+ +s i
  gi|298675223|ref|YP_003726973.1| 104 MDFIQKLMN-AEDLF--EKDVIIIDTISSlI 131
                                       556666665.66777..78888888866644 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00039      0.33       4      37 ..      27      60 ..      24      74 .. 0.86
   2 ?   -3.1   0.0       7.5   6.4e+03      48      71 ..     181     204 ..     173     210 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00039
                                      EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEE CS
                        APS_kinase  4 vvwltGlsgsGKstianalekkLvekgisvylLd 37
                                       v++ G+sgsGKs ++++++  L e+ +sv+ + 
  gi|298675223|ref|YP_003726973.1| 27 LVLIEGVSGSGKSIVSQRIAYGLAENETSVTYIS 60
                                      6899********************9999988765 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.5
                                       T--SSHHHHHHHHHHHHHHHHHHH CS
                        APS_kinase  48 dLgfseedRkenirrvaevaklla 71 
                                       +L+ + ++ ++++rr+  v k + 
  gi|298675223|ref|YP_003726973.1| 181 NLSLNVKQMSNQVRRMLTVNKFIG 204
                                       566666666677777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 1671.76
//
Query:       gi|298675224|ref|YP_003726974.1|  [L=166]
Description: flagellin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-22   80.5   6.0    1.7e-22   80.3   6.0    1.0  1  Arch_flagellin  Archaebacterial flagellin
  ------ inclusion threshold ------
      0.064   13.2   0.1       0.26   11.3   0.0    1.9  2  DUF4313         Domain of unknown function (DUF4313)


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.3   6.0   1.9e-26   1.7e-22       1     164 []      17     164 ..      17     164 .. 0.94

  Alignments for each domain:
  == domain 1  score: 80.3 bits;  conditional E-value: 1.9e-26
                                       X--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSEEEEEEE--T CS
                    Arch_flagellin   1 GfvgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvgdsatngtineitiyvklna 77 
                                       G + ++++I fIA+V++A  +agvl  ++  +  +a++  +  ++q++++++i++d+  +++n+t +++t+yvk n+
  gi|298675224|ref|YP_003726974.1|  17 GDTAVSHMIFFIAAVIIAVGVAGVLSVNVESIMGAASTNSDVVSDQLKTDITIISDPEVIPYNSTSDYYTFYVK-NT 92 
                                       67899*********************************************************************.** PP

                                       TS--EEGGG-EEEEEESS--EE--E..................T-EE-TT-EEEEEEE--TTT---TT-EEEEEEE- CS
                    Arch_flagellin  78 Gsspidlnkttisvtddgqetlltadefgivvisdtdgsltngdevlekgekvelevnvneddgitagdevsvevvp 154
                                       G+s+i l+ +   v+ dg          +++  ++ + sl+++ e++++  ++ ++v++    g  +++++ ++vv+
  gi|298675224|ref|YP_003726974.1|  93 GKSDIALEYVN--VILDG----------EYIQDKNLNLSLQDSGETWKPLGVLIVNVTT---GGELNSGDHGLKVVS 154
                                       ***77777655..56888..........89*******************9999999997...79999********** PP

                                       SSS--EEEEE CS
                    Arch_flagellin 155 enGasttief 164
                                       +nG s+ti+f
  gi|298675224|ref|YP_003726974.1| 155 DNGISDTIDF 164
                                       *******987 PP

>> DUF4313  Domain of unknown function (DUF4313)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.16   1.4e+03      29      79 ..      40      87 ..      36      91 .. 0.51
   2 ?   11.3   0.0   2.9e-05      0.26       6      40 ..     109     144 ..     106     164 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.16
                           DUF4313 29 dltVnlpgvslepneayidtnnlskdvleflkenklgevlgetakSGyceY 79
                                       l+Vn+  + + +     + + +s ++ + ++ +   ev++++  S y ++
  gi|298675224|ref|YP_003726974.1| 40 VLSVNVE-SIMGAAS--TNSDVVSDQLKTDITIISDPEVIPYNSTSDYYTF 87
                                      6777773.2222222..2222333444444555566666677766666655 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 2.9e-05
                           DUF4313   6 sYasngnlyigLvtkedgleefgdltVnlp.gvsle 40 
                                       +Y++++nl + L ++ + + + g l Vn+  g +l+
  gi|298675224|ref|YP_003726974.1| 109 EYIQDKNLNLSLQDSGETWKPLGVLIVNVTtGGELN 144
                                       7****************************7555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1182.77
//
Query:       gi|298675225|ref|YP_003726975.1|  [L=144]
Description: flagellin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-08   35.4   5.2    1.6e-08   34.9   5.2    1.2  1  Arch_flagellin  Archaebacterial flagellin
     0.0025   18.0   5.4     0.0042   17.3   4.5    1.8  1  CARDB           CARDB
  ------ inclusion threshold ------
      0.033   14.2   0.7        1.2    9.2   0.2    2.1  2  I-set           Immunoglobulin I-set domain
       0.45   10.5   3.9        3.9    7.5   3.9    2.0  1  DUF2393         Protein of unknown function (DUF2393)


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   5.2   3.6e-12   1.6e-08       8     160 ..      10     138 ..       2     142 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 3.6e-12
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSEEEEEEE--TTS--EEG CS
                    Arch_flagellin   8 lIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvgdsatngtineitiyvklnaGsspidl 84 
                                       +I f+++++  + a++v+  +  ++ ++ + + e  ++ ++++l+it+ + d+++++   ++t++v  n G  ++ l
  gi|298675225|ref|YP_003726975.1|  10 AIFFVSAIILGTSAYTVISASEERIDEATDLKHEMQVKRLQTDLNITNTTTDNSSDT--YNLTVTVS-NSG--SVTL 81 
                                       8*************************************************9666665..56999999.999..679* PP

                                       GG-EEEEEESS--EE--E..................T-EE-TT-EEEEEEE--TTT---TT-EEEEEEE-SSS--E CS
                    Arch_flagellin  85 nkttisvtddgqetlltadefgivvisdtdgsltngdevlekgekvelevnvneddgitagdevsvevvpenGast 160
                                       ++ +++v+++g                +  +++t++ +++ ++++   ++n+    + +  +e++v+v++enG s+
  gi|298675225|ref|YP_003726975.1|  82 DSGKLDVLING----------------TLMSYSTSSPDTWTPDKIRNFTINN---ISKGSASEHRVKVTTENGISD 138
                                       ***********................333356677799************8...5899**************875 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   4.5   9.4e-07    0.0042       3      72 ..      52     133 ..      48     142 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 9.4e-07
                                       -EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE...............EEEEESEE-CTEEEE CS
                             CARDB   3 DLtvtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv...............gtvtvpsLaagestt 64 
                                       DL +   +n ++ +  +++++tvtv+N+G+ +  + k+++ ++g+l                 ++t+++++ g+ ++
  gi|298675225|ref|YP_003726975.1|  52 DLNI---TNTTTDNSSDTYNLTVTVSNSGSVTLDSGKLDVLINGTLMsystsspdtwtpdkiRNFTINNISKGSASE 125
                                       6666...666777788999***************************9774444444444333334446666666666 PP

                                       EEEEEE-S CS
                             CARDB  65 vsftwtte 72 
                                        ++++tte
  gi|298675225|ref|YP_003726975.1| 126 HRVKVTTE 133
                                       66665554 PP

>> I-set  Immunoglobulin I-set domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.2   0.00027       1.2      44      83 ..      39      80 ..      26      88 .. 0.82
   2 ?    3.7   0.0     0.015        66      54      80 ..     109     135 ..      95     141 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00027
                                      SSSEEEEEETTEEEEEESSB-GGGG.EEEEEEEEET.SEEEE CS
                             I-set 44 sqrvkvtveeaeytLtIsnvevsDe.GkYtckatns.agkae 83
                                      + +++++v+  ++ L I+n +++++ ++Y++++t+s +g+++
  gi|298675225|ref|YP_003726975.1| 39 DLKHEMQVKRLQTDLNITNTTTDNSsDTYNLTVTVSnSGSVT 80
                                      667889999999********99985379******99899887 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.015
                                       TEEEEEESSB-GGGGEEEEEEEEETSE CS
                             I-set  54 aeytLtIsnvevsDeGkYtckatnsag 80 
                                       ++  +tI+n+++  + + ++k+t + g
  gi|298675225|ref|YP_003726975.1| 109 KIRNFTINNISKGSASEHRVKVTTENG 135
                                       6789***************99998865 PP

>> DUF2393  Protein of unknown function (DUF2393)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   3.9   0.00088       3.9      46     126 ..      50     128 ..       3     142 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00088
                           DUF2393  46 kaeltilsqkrllyteafvvdgtitNeGkftikeCkleiklvnkshnkkskellkklkplvsksevikedlkpgesk 122
                                       +++l+i+  +  ++++++ +++t+ N G+ t+   kl + +        s+   ++++p +  +++i  ++++g+  
  gi|298675225|ref|YP_003726975.1|  50 QTDLNITNTTTDNSSDTYNLTVTVSNSGSVTLDSGKLDVLINGTLMSY-STSSPDTWTPDKIRNFTIN-NISKGSAS 124
                                       678999999999999999999999999999999999988655444444.7888888888888888887.88888887 PP

                           DUF2393 123 eFrv 126
                                       e rv
  gi|298675225|ref|YP_003726975.1| 125 EHRV 128
                                       7776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1036  (0.0577835); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1113.61
//
Query:       gi|298675226|ref|YP_003726976.1|  [L=374]
Description: flagella protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-28   97.6   0.1    7.5e-28   96.2   0.1    1.8  1  Arch_fla_DE      Archaeal flagella protein
    1.2e-21   76.9  18.4    8.1e-21   74.2   4.8    4.0  2  FlaC_arch        Flagella accessory protein C (FlaC)
    8.3e-05   22.2   1.5       0.22   11.1   0.6    2.5  2  PI3K_P85_iSH2    Phosphatidylinositol 3-kinase regulatory sub
    0.00069   19.5  11.6      0.025   14.4   3.2    2.6  2  Sec34            Sec34-like family
      0.001   17.3  18.6     0.0074   14.5   7.9    2.2  2  EzrA             Septation ring formation regulator, EzrA
     0.0012   19.1  16.7       0.27   11.5   4.4    3.3  3  BLOC1_2          Biogenesis of lysosome-related organelles co
     0.0019   18.4   6.6      0.028   14.7   0.5    2.6  2  ABC_tran_CTD     ABC transporter C-terminal domain
     0.0024   18.3   0.6     0.0024   18.3   0.6    3.4  2  ZapB             Cell division protein ZapB
     0.0033   17.8   4.1     0.0033   17.8   4.1    2.5  2  Syntaxin_2       Syntaxin-like protein
     0.0035   17.4  11.1       0.05   13.6   0.6    2.7  2  DUF1664          Protein of unknown function (DUF1664)
     0.0056   16.5  15.7     0.0099   15.7   4.2    3.2  3  Nsp1_C           Nsp1-like C-terminal region
     0.0057   15.6  10.9       0.14   11.0   1.2    2.2  2  Spc7             Spc7 kinetochore protein
     0.0063   16.3   4.0      0.074   12.9   1.7    2.5  2  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
     0.0091   15.7  14.5      0.054   13.2  14.5    2.0  1  SHE3             SWI5-dependent HO expression protein 3
     0.0094   15.7  11.5       0.52   10.1   3.6    2.9  2  DivIC            Septum formation initiator
  ------ inclusion threshold ------
      0.012   14.4   9.4      0.026   13.3   0.9    2.1  2  Tektin           Tektin family
      0.014   14.5   4.6       0.54    9.3   0.1    2.2  2  Atg14            Vacuolar sorting 38 and autophagy-related su
      0.015   15.7  11.8       0.35   11.3   0.9    3.6  4  Snapin_Pallidin  Snapin/Pallidin
      0.019   15.4   3.9      0.019   15.4   3.9    2.6  2  DUF16            Protein of unknown function DUF16
      0.035   14.6  12.0       0.33   11.4   1.6    2.8  2  NPV_P10          Nucleopolyhedrovirus P10 protein
      0.036   14.1  14.8       0.21   11.6   1.8    2.5  2  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
      0.036   14.0   5.9        2.1    8.2   0.2    3.0  2  CagA             CagA exotoxin
      0.072   12.2  10.4        1.2    8.3   0.7    2.2  2  Taxilin          Myosin-like coiled-coil protein
      0.076   13.2  15.6       0.18   12.0   3.7    2.8  2  Tropomyosin_1    Tropomyosin like
       0.11   12.0   5.9        0.2   11.1   0.8    2.1  2  Allexi_40kDa     Allexivirus 40kDa protein
       0.11   12.8   7.4        2.7    8.3   0.5    3.5  3  DUF4164          Domain of unknown function (DUF4164)
       0.12   13.0  16.3       0.08   13.5   2.9    2.8  2  Syntaxin-6_N     Syntaxin 6, N-terminal
       0.14   12.8  11.5        2.4    8.8   2.1    2.7  2  YabA             Initiation control protein YabA
       0.14   11.7   7.9       0.89    9.1   2.5    2.3  2  PTRF_SDPR        PTRF/SDPR family
       0.16   11.3   5.1       0.37   10.1   5.1    1.5  1  DUF4407          Domain of unknown function (DUF4407)
       0.17   12.0   6.7       0.58   10.3   0.4    2.7  2  DUF2959          Protein of unknown function (DUF2959)
       0.18   11.2  12.8        3.3    7.0   2.3    2.4  2  GAS              Growth-arrest specific micro-tubule binding
       0.21   11.7   6.6        7.3    6.7   6.6    2.3  1  Nup54            Nucleoporin complex subunit 54
       0.21   11.6   6.9        5.1    7.1   0.2    2.3  2  LOH1CR12         Tumour suppressor protein
       0.28   11.9  10.7        2.3    9.0   1.1    3.3  2  Occludin_ELL     Occludin homology domain
       0.29   11.2   2.1         18    5.4   0.1    2.5  2  DUF1515          Protein of unknown function (DUF1515)
       0.29   10.4  11.9       0.76    9.0   0.5    2.3  2  DUF3450          Protein of unknown function (DUF3450)
       0.33    9.5  18.4        1.3    7.5  18.4    1.7  1  AAA_13           AAA domain
       0.34   10.6  10.7        1.6    8.4   1.6    2.4  2  DUF4201          Domain of unknown function (DUF4201)
       0.37    8.7  15.2      0.054   11.4   4.2    2.1  2  V_ATPase_I       V-type ATPase 116kDa subunit family
       0.39   11.1   9.7          3    8.2   2.1    2.6  2  LPP20            LPP20 lipoprotein
       0.45   10.7   5.5        7.6    6.7   0.7    2.5  2  CREPT            Cell-cycle alteration and expression-elevate
       0.46   10.8   8.9        1.4    9.2   0.5    3.4  2  DUF948           Bacterial protein of unknown function (DUF94
       0.46   11.0  14.0        2.8    8.5   0.4    2.4  2  APG6_N           Apg6 coiled-coil region
       0.51   10.8  12.2        1.9    8.9   4.4    2.6  2  CENP-H           Centromere protein H (CENP-H)
       0.53   10.2  10.2        1.8    8.5   1.6    2.5  2  Ax_dynein_light  Axonemal dynein light chain
       0.56   10.1   6.5        1.6    8.6   0.5    2.5  2  EMP24_GP25L      emp24/gp25L/p24 family/GOLD
       0.59    9.7   5.5        1.1    8.8   1.5    2.2  2  PspA_IM30        PspA/IM30 family
       0.64   10.1  11.8        0.6   10.2   3.0    2.4  2  Mod_r            Modifier of rudimentary (Mod(r)) protein
        0.7    9.6   4.3       0.72    9.6   0.4    2.3  2  Lectin_N         Hepatic lectin, N-terminal domain
       0.72    9.4  12.0       0.88    9.1   1.5    2.5  2  4HB_MCP_1        Four helix bundle sensory module for signal 
       0.79   10.0  13.2        2.8    8.2   5.9    2.6  2  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
       0.81    9.4  12.9        3.5    7.4   0.9    2.6  2  TACC_C           Transforming acidic coiled-coil-containing p
       0.81    9.3  12.9        3.5    7.3   5.1    2.3  2  Laminin_I        Laminin Domain I
       0.81   10.1   6.7        1.2    9.6   0.4    3.3  3  DASH_Dad2        DASH complex subunit Dad2
       0.91    8.9   7.1       0.44    9.9   0.9    2.1  2  HBM              Helical bimodular sensor domain
       0.96   10.1   4.8         10    6.8   0.3    2.6  2  AKNA             AT-hook-containing transcription factor
       0.97    9.4  10.5        5.5    6.9   1.4    3.3  3  Prefoldin        Prefoldin subunit
          1    9.5  10.4        1.5    8.9   2.1    2.4  2  DHR10            Designed helical repeat protein 10 domain
        1.1    9.3   6.0        1.7    8.8   0.3    2.7  2  TolA_bind_tri    TolA binding protein trimerisation
        1.1    9.2   7.4        1.4    8.9   1.3    2.3  2  Blo-t-5          Mite allergen Blo t 5
        1.2    8.6   7.1        6.4    6.3   7.1    1.9  1  Exonuc_VII_L     Exonuclease VII, large subunit
        1.2    9.3   8.9        1.1    9.5   1.5    3.3  2  JIP_LZII         JNK-interacting protein  leucine zipper II
        1.3    9.5   8.9        5.8    7.3   0.3    3.7  3  CLZ              C-terminal leucine zipper domain of cyclic n
        1.4    9.2   6.2        0.6   10.4   0.7    2.3  2  DUF641           Plant protein of unknown function (DUF641)
        1.6    9.0  13.0          5    7.3   2.3    2.4  2  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
        1.8    9.0   8.5        2.4    8.6   0.3    2.5  2  T3SSipB          Type III cell invasion protein SipB
          2    8.6  11.6        5.6    7.1   4.9    2.3  2  ATG16            Autophagy protein 16 (ATG16)
          2    8.6   8.8          8    6.7   2.9    2.9  3  GCN5L1           GCN5-like protein 1 (GCN5L1)
          2    8.5  12.5        4.2    7.5   1.7    2.8  2  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
        2.1    8.8   8.4       0.59   10.6   1.5    2.8  2  UPF0184          Uncharacterised protein family (UPF0184)
        2.1    8.4  17.3        2.2    8.3   8.2    2.3  2  UPF0242          Uncharacterised protein family (UPF0242) N-t
        2.2    8.4  12.4       0.77    9.9   3.3    2.8  2  BRE1             BRE1 E3 ubiquitin ligase
        2.4    8.1  15.2       0.43   10.5   0.9    3.0  2  SIKE             SIKE family
        2.4    7.9   4.6        4.9    6.9   1.5    2.2  2  USP8_interact    USP8 interacting
        2.5    7.9  12.3        8.1    6.3  12.3    1.8  1  FTA4             Kinetochore complex Fta4 of Sim4 subunit, or
        2.6    7.3  10.5        8.6    5.5   0.3    2.4  2  HemX             HemX, putative uroporphyrinogen-III C-methyl
        2.7    8.1   8.0       0.77    9.9   1.4    3.0  3  DASH_Dad3        DASH complex subunit Dad3
        2.9    8.4   7.4        8.3    7.0   0.9    2.5  2  UPF0449          Uncharacterised protein family UPF0449
        2.9    7.8  10.7         10    6.1   1.8    3.0  3  DUF4446          Protein of unknown function (DUF4446)
        3.2    7.9   8.4         14    5.8   1.1    2.8  2  Swi5             Swi5
        3.4    7.7  13.4          2    8.4   2.8    3.0  3  Prefoldin_2      Prefoldin subunit
        3.6    7.8  13.1        1.3    9.2   1.5    3.1  2  bZIP_1           bZIP transcription factor
        4.4    6.9  14.2        0.7    9.5   2.8    2.4  2  DUF4795          Domain of unknown function (DUF4795)
        4.6    7.5  12.2        0.5   10.6   2.9    3.0  3  THOC7            Tho complex subunit 7
        4.8    7.2  17.7       0.93    9.5   1.1    2.6  2  Laminin_II       Laminin Domain II
          5    7.6  11.4         15    6.1   0.2    4.1  3  LPP              Lipoprotein leucine-zipper
        5.5    6.8  15.7       0.34   10.7   4.6    2.7  2  DUF724           Protein of unknown function (DUF724)
        6.6    6.8  13.5        6.7    6.8   2.3    2.5  2  ADIP             Afadin- and alpha -actinin-Binding
        7.6    6.8   7.7         30    4.9   0.5    3.1  3  PI_PP_I          Phosphoinositide phosphatase insertion domai
        7.8    4.3  10.9        3.8    5.3   2.1    1.7  2  Prominin         Prominin
        8.4    6.4   8.8         56    3.8   1.2    3.8  3  SOAR             STIM1 Orai1-activating region
        9.9    6.6  14.0         56    4.2   7.4    3.0  2  DUF4200          Domain of unknown function (DUF4200)
         10    6.2  15.1          2    8.5   2.3    3.2  3  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding


Domain annotation for each model (and alignments):
>> Arch_fla_DE  Archaeal flagella protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.2   0.1   3.9e-30   7.5e-28       4      95 .]     264     351 ..     261     351 .. 0.96

  Alignments for each domain:
  == domain 1  score: 96.2 bits;  conditional E-value: 3.9e-30
                       Arch_fla_DE   4 pyLeelpedyaaelvvleWlefLvervgvenaaealdyYeeigWiseevreeLlkylkgikledeekeelkkseltv 80 
                                       + L ++++++++++++++W+e+L+ervg ++++eal+yY +igWiseev +++l+y+kg+++ ++ek++++   lt+
  gi|298675226|ref|YP_003726976.1| 264 VILGSIEKEPTTMIAIFNWIEYLIERVGGNHLQEALRYYVNIGWISEEVFSDILNYAKGMDY-YTEKDDWE---LTP 336
                                       6799*********************************************************9.99999997...*** PP

                       Arch_fla_DE  81 edHvkSllyieklag 95 
                                       +dH+kSl++iek++g
  gi|298675226|ref|YP_003726976.1| 337 DDHTKSLMFIEKMSG 351
                                       ************975 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.2   4.8   4.3e-23   8.1e-21       1      55 []      87     141 ..      87     141 .. 0.99
   2 ?    8.3   2.5     0.016       3.1       1      34 [.     200     233 ..     152     247 .. 0.88

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 4.3e-23
                         FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelkenVkdllsLYEvVsnqvNPFv 55 
                                       +i+++E+++sk++ +++tv++en+el+k++++++++V +llsLYE+VsnqvNPFv
  gi|298675226|ref|YP_003726976.1|  87 KIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVELLSLYEIVSNQVNPFV 141
                                       89****************************************************8 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.016
                         FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelk 34 
                                       +++el +k ++l  +l+t+k++ +e+s+ v+ l+
  gi|298675226|ref|YP_003726976.1| 200 KTNELFEKYDELNENLSTLKQSTDEISDRVDILE 233
                                       5677777788888888888888888888888766 PP

>> PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0042       0.8      87     135 ..      78     126 ..      27     132 .. 0.84
   2 !   11.1   0.6    0.0011      0.22      71     119 ..     151     223 ..     147     232 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0042
                     PI3K_P85_iSH2  87 qenleqlksrlkelhsskekLeedlkqqkeeereleReinalkpellqL 135
                                       +e++e+  +++k+++s ++k++ ++ +   e++el + i ++   +++L
  gi|298675226|ref|YP_003726976.1|  78 NEQVENNAQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVEL 126
                                       4455566789999**************************9998888877 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0011
                     PI3K_P85_iSH2  71 qekfskeaq........................ehEieklqenleqlksrlkelhsskekLeedlkqqkeeer 119
                                       +e+f+k+ +                         + i+kl++ +++l+s+ +el ++ ++L+e+l + k++  
  gi|298675226|ref|YP_003726976.1| 151 IERFEKNEErineignyatmlkndldalyqkfdTQGINKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTD 223
                                       566666663333333444444444444444555999*****************************99887665 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   1.3    0.0043      0.82       8      69 ..      77     138 ..      72     145 .. 0.57
   2 !   14.4   3.2   0.00013     0.025       1      73 [.     150     220 ..     150     248 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0043
                             Sec34   8 keeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLk 69 
                                       ++e++++  ++++++++ ++++  + ++v+ + ++l+++ +++ ++  +l +l+e ++++++
  gi|298675226|ref|YP_003726976.1|  77 NNEQVENNAQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVELLSLYEIVSNQVN 138
                                       44555555555555555556666666666666666666555555555555555555555555 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 0.00013
                             Sec34   1 yldqLeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFee 73 
                                       y++++e++ee+++e+ + ++ ++++L+ l +kf++  +  ++lh++ ++l++++++l e ++e++e+L+  ++
  gi|298675226|ref|YP_003726976.1| 150 YIERFEKNEERINEIGNYATMLKNDLDALYQKFDT--QGINKLHSKIDDLTSKTNELFEKYDELNENLSTLKQ 220
                                       67889999999999999999999999999999995..88999**********************999987654 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   2.9    0.0027      0.52      95     149 ..      80     134 ..      73     139 .. 0.54
   2 !   14.5   7.9   3.9e-05    0.0074      59     168 ..     151     257 ..     144     266 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0027
                                       HHHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHH CS
                              EzrA  95 kfkkakkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelr 149
                                       ++ +  +k++++e+++++v+++i +++ e +el++   k  + + +l + Y+ ++
  gi|298675226|ref|YP_003726976.1|  80 QVENNAQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVELLSLYEIVS 134
                                       3444445555555555555555555555555555555555555555555555555 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3.9e-05
                                       HHHHHHHHHHHHHHHHHHTHHHHHT-GGGT--S-SHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTH CS
                              EzrA  59 eekfeewkkkwdeiktkklpeieellfeaeelldkykfkkakkklaeleeeldeveekikkileelkelteseeknr 135
                                        e+fe+ +++ +ei +     +++ l  + + +d+  ++k+++k+++l+++ +e+ ek+++++e l+ l++s  + +
  gi|298675226|ref|YP_003726976.1| 151 IERFEKNEERINEIGN-YATMLKNDLDALYQKFDTQGINKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEIS 226
                                       589***********99.999********************************************************* PP

                                       HHHHHHHHHHHHHHHT--TTTTHHHHHHHHHHH CS
                              EzrA 136 eeieklkekYrelrkkllanrfsygealeelek 168
                                       ++++ l++   +l+k+++  +++y  +++  e+
  gi|298675226|ref|YP_003726976.1| 227 DRVDILEKI--DLSKTYEPSENQYNVIYQDEEE 257
                                       ****99996..8999999999999998876665 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   4.4    0.0014      0.27      27      78 ..      79     127 ..      72     135 .. 0.69
   2 !   10.4   2.6    0.0033      0.62      32      92 ..     157     219 ..     148     221 .. 0.81
   3 !   11.5   3.6    0.0015      0.29      37      79 ..     192     234 ..     166     236 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0014
                           BLOC1_2  27 klNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLe 78 
                                       +  e+ ++k+k ++++++++ ++++ +++   e q++++ id+i+++v eL 
  gi|298675226|ref|YP_003726976.1|  79 EQVENNAQKIKTVESRMSKVDANISTVQR---ENQELKKTIDKIDQSVVELL 127
                                       44567778888888888888888888888...55666666666666666654 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0033
                           BLOC1_2  32 asekykklkdvaaslekkleklnekye..elqpylqqidqiekqvteLeeavseLDeyskeLE 92 
                                        +e+++++ + a  l+++l++l +k +   ++++ ++id++  +++eL e  +eL+e  + L+
  gi|298675226|ref|YP_003726976.1| 157 NEERINEIGNYATMLKNDLDALYQKFDtqGINKLHSKIDDLTSKTNELFEKYDELNENLSTLK 219
                                       567888888999999999999988876557889999999999999999998888888887775 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.0015
                           BLOC1_2  37 kklkdvaaslekkleklnekyeelqpylqqidqiekqvteLee 79 
                                        k++d ++++++ +ek++e++e+l+ ++q+ d+i ++v+ Le+
  gi|298675226|ref|YP_003726976.1| 192 SKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISDRVDILEK 234
                                       2334444444444444444444666666666778888888886 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.9     0.067        13      21      58 ..      85     120 ..      76     131 .. 0.56
   2 !   14.7   0.5   0.00015     0.028       9      69 .]     153     213 ..     150     213 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.067
                      ABC_tran_CTD  21 EeeiaeleaeladpelysdpeklaelsaeleeleaeLe 58 
                                        ++i+++e ++++ +  ++  ++++ ++el++  ++++
  gi|298675226|ref|YP_003726976.1|  85 AQKIKTVESRMSKVD--ANISTVQRENQELKKTIDKID 120
                                       467777777777776..455555555555554444444 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 0.00015
                      ABC_tran_CTD   9 eleeleaeIeaLEeeiaeleaeladpelysdp..eklaelsaeleeleaeLeelyerWeeLee 69 
                                       ++e+ e++I+++ +  + l + l   +ly+++  + +++l+ ++++l ++ +el+e++ eL+e
  gi|298675226|ref|YP_003726976.1| 153 RFEKNEERINEIGNYATMLKNDLD--ALYQKFdtQGINKLHSKIDDLTSKTNELFEKYDELNE 213
                                       578889999999999999999999..8898887566*************************87 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   5.1      0.78   1.5e+02       7      45 ..      89     127 ..      72     163 .. 0.71
   2 !   18.3   0.6   1.3e-05    0.0024      18      66 ..     185     232 ..     173     236 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.78
                              ZapB   7 eqLEskiqkaidtitlLqmeieeLkeeneelkeenrele 45 
                                       +  Es+ +k   +i++ q e++eLk+   +  +   el 
  gi|298675226|ref|YP_003726976.1|  89 KTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVELL 127
                                       455677777777777777777777777666666665555 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 1.3e-05
                              ZapB  18 dtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkkLL 66 
                                       + i +L  +i++L  + +el e+ +el+e ++ lk+   ++ +r++ +L
  gi|298675226|ref|YP_003726976.1| 185 QGINKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISDRVD-IL 232
                                       5699*************************************99997.44 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   1.7      0.26        49       3      83 ..      83     127 ..      69     143 .. 0.46
   2 !   17.8   4.1   1.7e-05    0.0033       3      91 ..     159     253 ..     157     260 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.26
                        Syntaxin_2   3 snlqkinsnvstleklvkqLgtk.kdteelreklhelieeinelikktnellkklsqldnsssdsqqklqkekLkkd 78 
                                       +n qki +  s + k    ++t  ++++el++ +                                     +k+ ++
  gi|298675226|ref|YP_003726976.1|  83 NNAQKIKTVESRMSKVDANISTVqRENQELKKTI-------------------------------------DKIDQS 122
                                       2333333333333333333333322344444333.....................................344444 PP

                        Syntaxin_2  79 fkeal 83 
                                       + e+l
  gi|298675226|ref|YP_003726976.1| 123 VVELL 127
                                       44433 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 1.7e-05
                        Syntaxin_2   3 snlqkinsnvstleklvkqLgtkkd...teelreklhelieeinelikktnellkklsqldnsssds...qqklqke 73 
                                       + + +i +  + l++ ++ L  k d     +l++k+++l++++nel++k  el ++ls+l++s++       +l+k 
  gi|298675226|ref|YP_003726976.1| 159 ERINEIGNYATMLKNDLDALYQKFDtqgINKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEIsdrVDILEKI 235
                                       568889899999999999999997744466788***************99777777777777763334437777999 PP

                        Syntaxin_2  74 kLkkdfkealqeFqkiqr 91 
                                        L+k ++ + ++++ i +
  gi|298675226|ref|YP_003726976.1| 236 DLSKTYEPSENQYNVIYQ 253
                                       999999999999998766 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   1.8     0.005      0.96      74     119 ..      80     125 ..      72     145 .. 0.59
   2 !   13.6   0.6   0.00026      0.05      44     107 ..     169     233 ..     149     238 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.005
                           DUF1664  74 kldeqkeiskeikeevtevredlseigedvesvkeavegleskler 119
                                       +++++++ +k +++ +++v  ++s+++++ +++k+++ ++++++ +
  gi|298675226|ref|YP_003726976.1|  80 QVENNAQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVE 125
                                       4455555555555555555555555555555555555555555443 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.00026
                           DUF1664  44 esvskqleqvseslaat.krhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvk 107
                                       + + ++l+ ++++  ++  ++L s+id + +k +e  e   e++e+++++++ ++ei++ v+ ++
  gi|298675226|ref|YP_003726976.1| 169 TMLKNDLDALYQKFDTQgINKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISDRVDILE 233
                                       45566677777777655246777777777777777777777777777777777777777776655 PP

>> Nsp1_C  Nsp1-like C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   4.2   5.2e-05    0.0099      55     108 ..      77     130 ..      74     138 .. 0.90
   2 ?    6.2   1.6     0.044       8.4      57      99 ..     192     234 ..     184     251 .. 0.89
   3 ?   -0.5   0.0       5.5     1e+03      59      84 ..     346     371 ..     342     373 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.2e-05
                            Nsp1_C  55 ngekIskLysevleaeqeqnkidqeLeyiesqqdeLeslLdnyEkeleellskl 108
                                       n+e++++  +++ ++e+  +k+d +++ ++++ +eL++ +d++ +++ ells  
  gi|298675226|ref|YP_003726976.1|  77 NNEQVENNAQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVELLSLY 130
                                       89999999***************************************9999654 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.044
                            Nsp1_C  57 ekIskLysevleaeqeqnkidqeLeyiesqqdeLeslLdnyEk 99 
                                       +kI +L s++ e  ++  +++++L+ ++++ de+++ +d +Ek
  gi|298675226|ref|YP_003726976.1| 192 SKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISDRVDILEK 234
                                       699***********************************99997 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 5.5
                            Nsp1_C  59 IskLysevleaeqeqnkidqeLeyie 84 
                                       I+k+  + +e  q++ +id eL+ i+
  gi|298675226|ref|YP_003726976.1| 346 IEKMSGHRVENSQTSDNIDSELSKIK 371
                                       6777888888999999******9887 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   2.8    0.0022      0.42     196     246 ..      76     126 ..      68     139 .. 0.65
   2 !   11.0   1.2   0.00073      0.14     174     244 ..     159     230 ..     141     248 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0022
                              Spc7 196 idkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqksel 246
                                        ++e++e+  ++++++++ +++  ++++++q++ +el+++i++++++  el
  gi|298675226|ref|YP_003726976.1|  76 ANNEQVENNAQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVEL 126
                                       455666666666666666666666666666666666666666666666555 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00073
                              Spc7 174 eekaeleeeleklqeaaeel.esidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqks 244
                                       e+ +e+ + +++l++  + l ++ d + +++l++++++l ++ +e+ ++++el+e+l +l+++ +e++++ +
  gi|298675226|ref|YP_003726976.1| 159 ERINEIGNYATMLKNDLDALyQKFDTQGINKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISDRVD 230
                                       444455556666666444441447888888888888888888888888888888888888888888865543 PP

>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   1.7   0.00039     0.074     116     168 ..      74     126 ..      65     130 .. 0.87
   2 ?    3.2   0.0      0.35        67     102     143 ..     187     228 ..     150     242 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00039
                                       HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 116 veegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqaveev 168
                                        +   e+ve+ ++++k++ +++++v++ ++ +++  +e+ ++i+++ q+v e+
  gi|298675226|ref|YP_003726976.1|  74 GQANNEQVENNAQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVEL 126
                                       566778999***************************************99765 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.35
                                       ........HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHH CS
                         MCPsignal 102 indsvesleetrqrveegselveetgealkeiveavaevadl 143
                                       in+  + +++ +++++e  e+ +e +e+l+++ ++++e++d 
  gi|298675226|ref|YP_003726976.1| 187 INKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISDR 228
                                       333334444444444444444444444444444444444443 PP

>> SHE3  SWI5-dependent HO expression protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2  14.5   0.00028     0.054      26     189 ..      81     240 ..      73     253 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00028
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCH CS
                              SHE3  26 sqeLleklelaqkkeskflenlaslkhENdnLsslLkRKerrlkdlekelselkesveelklekkqlkkrlenssas 102
                                        ++  +k ++++++ sk+  n+++++ EN+ L+  +++ ++ + +l + ++  +++v+    +++  ++ +e+ +++
  gi|298675226|ref|YP_003726976.1|  81 VENNAQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVELLSLYEIVSNQVNPFVGDNEGGSEYIERFEKN 157
                                       55666788888888888888888888888888888888888888888888888888888877776655544444444 PP

                                       H...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSSXXXXXXXXXXX.XXXXXXXXXXX CS
                              SHE3 103 e...teleeelerlkvqYdalvdsqkeYkehYqqeieeLkesleklklenekqleelqerissndkdidtkldsynn 176
                                       e   +e  +   +lk++ dal      Y++   q i++L+ ++++l+   ++ +e++ +++++n  +++++ d+ ++
  gi|298675226|ref|YP_003726976.1| 158 EeriNEIGNYATMLKNDLDAL------YQKFDTQGINKLHSKIDDLTSKTNELFEKY-DELNENLSTLKQSTDEISD 227
                                       411145556677777777776......666667778888888888887777666665.4577888888888888888 PP

                                       XXXXXXXXXXXXX CS
                              SHE3 177 kkknlesieeekn 189
                                       ++  le+i+ +k+
  gi|298675226|ref|YP_003726976.1| 228 RVDILEKIDLSKT 240
                                       8888888876665 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   3.6    0.0027      0.52      17      50 ..      93     126 ..      75     136 .. 0.68
   2 !    9.4   1.0    0.0044      0.85      18      59 ..     186     227 ..     172     233 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0027
                                       XHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC- CS
                             DivIC  17 laykqlkqeiaalqaelaklkaeneeLeaevkdL 50 
                                       +++++++++i + q+e+++lk+++++ ++ v +L
  gi|298675226|ref|YP_003726976.1|  93 SRMSKVDANISTVQRENQELKKTIDKIDQSVVEL 126
                                       4566666677777777777777776666666555 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0044
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXX CS
                             DivIC  18 aykqlkqeiaalqaelaklkaeneeLeaevkdLksdedyiee 59 
                                        + +l+++i++l+ + ++l ++ +eL+++++ Lk++ d i  
  gi|298675226|ref|YP_003726976.1| 186 GINKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISD 227
                                       578999****************************99999975 PP

>> Tektin  Tektin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   1.9     0.032       6.2      41      91 ..      77     127 ..      68     138 .. 0.57
   2 ?   13.3   0.9   0.00014     0.026       9      91 ..     151     233 ..     146     236 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.032
                            Tektin  41 qadsnkrLeeRiediefwkeeLekeleelkeeieaLeeekrrlekaleale 91 
                                       +++  ++  ++i+ +e   ++++ +++ +++e ++L+++ +++++++ +l 
  gi|298675226|ref|YP_003726976.1|  77 NNEQVENNAQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVELL 127
                                       333344445666666666666666666666666666666666666655555 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00014
                            Tektin   9 lkeaeaerneaerlrnesrrlideteektkktqadsnkrLeeRiediefwkeeLekeleelkeeieaLeeekrrlek 85 
                                       +++ e+++++ +++ n +  l +++++  +k +++  ++L+ +i+d++   +eL ++ +el+e   +L+++ +++ +
  gi|298675226|ref|YP_003726976.1| 151 IERFEKNEERINEIGNYATMLKNDLDALYQKFDTQGINKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISD 227
                                       56778889999999999999****************************************************99999 PP

                            Tektin  86 aleale 91 
                                        ++ le
  gi|298675226|ref|YP_003726976.1| 228 RVDILE 233
                                       988877 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1    0.0028      0.54      62     117 ..      74     129 ..      64     141 .. 0.79
   2 ?    6.5   1.1      0.02       3.8      22      97 ..     159     229 ..     144     247 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0028
                             Atg14  62 iknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsd 117
                                        + +++++e+  ++i   ++r++++ + +s+ ++e++e kk++ k ++++ +  s 
  gi|298675226|ref|YP_003726976.1|  74 GQANNEQVENNAQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVELLSL 129
                                       46677888888899999999999999999999999999999999988887655555 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.02
                             Atg14  22 erlyelrerlaklksekeslkkkie.kalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkei 97 
                                       er++e     ++lk + ++l++k++ + +++        +ki+ ++ k +el  +  +l+e+l++lk++ ++  +++
  gi|298675226|ref|YP_003726976.1| 159 ERINEIGNYATMLKNDLDALYQKFDtQGINKL------HSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISDRV 229
                                       55555555666666667777776662222222......355555555555555555555555555555555554444 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   1.7     0.027       5.1      55      88 ..      78     111 ..      69     120 .. 0.60
   2 ?    7.1   1.7     0.038       7.2      10      48 ..      90     128 ..      85     138 .. 0.83
   3 ?    0.0   0.0       6.1   1.2e+03      16      44 ..     155     183 ..     148     189 .. 0.75
   4 ?   11.3   0.9    0.0019      0.35      11      58 ..     190     235 ..     184     240 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.027
                   Snapin_Pallidin  55 lpdlkeyakKLvnikkrmsslnerlqklkkRaek 88 
                                        +++++ a+K+++++ rms++   ++++++  ++
  gi|298675226|ref|YP_003726976.1|  78 NEQVENNAQKIKTVESRMSKVDANISTVQRENQE 111
                                       4566666666666666666666666666654433 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.038
                   Snapin_Pallidin  10 llepkldeldeklkelrqsQeeLleqldrlnekLkelee 48 
                                       ++e+ + ++d++++ ++++ +eL++++d+  +++ el  
  gi|298675226|ref|YP_003726976.1|  90 TVESRMSKVDANISTVQRENQELKKTIDKIDQSVVELLS 128
                                       678889999*****************9998888776665 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 6.1
                   Snapin_Pallidin  16 deldeklkelrqsQeeLleqldrlnekLk 44 
                                       ++ +e+++e+ +  + L+++ld l +k++
  gi|298675226|ref|YP_003726976.1| 155 EKNEERINEIGNYATMLKNDLDALYQKFD 183
                                       45567788888888888888888888887 PP

  == domain 4  score: 11.3 bits;  conditional E-value: 0.0019
                   Snapin_Pallidin  11 lepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdl 58 
                                       l++k+d+l++k +el ++ +eL+e+l++l+++ +e+++  +  +l+++
  gi|298675226|ref|YP_003726976.1| 190 LHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISDRVD--ILEKI 235
                                       55666666666666666666666666666666666666666..55555 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   5.6      0.26        50      41      82 ..      79     120 ..      67     136 .. 0.47
   2 ?   15.4   3.9    0.0001     0.019      31     103 ..     156     233 ..     132     234 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.26
                                       HHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH...... CS
                             DUF16  41 akvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvd 82 
                                       ++v+ + ++i+ +e  ++k +++i+  + e +  ++ ++k+d
  gi|298675226|ref|YP_003726976.1|  79 EQVENNAQKIKTVESRMSKVDANISTVQRENQELKKTIDKID 120
                                       233333333333333333333333333333333333333333 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 0.0001
                                       .BHHHHHHHHHHHH...HHHHHHHHHHHHHH.....HHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHHH CS
                             DUF16  31 snkqrLkkieakvdklgeqinkleqkvekqg.....ekikelkveqkaqgeelnkvdetleliletLqkinkRlDsi 102
                                        n++r+++i +  ++l++ +++l qk ++qg      ki++l+ + +   e+ ++++e l  + ++ ++i++R+D +
  gi|298675226|ref|YP_003726976.1| 156 KNEERINEIGNYATMLKNDLDALYQKFDTQGinklhSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISDRVDIL 232
                                       267777777777777777777777665555422222789999999999999999*********************99 PP

                                       C CS
                             DUF16 103 e 103
                                       e
  gi|298675226|ref|YP_003726976.1| 233 E 233
                                       8 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   3.2     0.035       6.6      11      59 ..      86     134 ..      79     140 .. 0.78
   2 ?   11.4   1.6    0.0018      0.33      20      63 ..     187     227 ..     166     244 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.035
                           NPV_P10  11 adikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkve 59 
                                       + ik v+++++ +++++  vq + +++++  +k+d+   +L +l + v+
  gi|298675226|ref|YP_003726976.1|  86 QKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVELLSLYEIVS 134
                                       5789999999999999999999888877777777777777766666665 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0018
                           NPV_P10  20 VdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqd 63 
                                       ++ l +++dd++++ ++   l ek d+++++L +l+++ ++I+d
  gi|298675226|ref|YP_003726976.1| 187 INKLHSKIDDLTSKTNE---LFEKYDELNENLSTLKQSTDEISD 227
                                       55677788888876555...888888888888888888877775 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.8    0.0011      0.21      52     108 ..      79     135 ..      72     140 .. 0.88
   2 ?    7.3   5.6     0.023       4.5      53     116 ..     186     247 ..     149     263 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0011
                    CENP-F_leu_zip  52 aevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnsslen 108
                                       ++ve+  ++i++ ++++++  ++++++++e++eL+k + k  + v eL sl + ++n
  gi|298675226|ref|YP_003726976.1|  79 EQVENNAQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVELLSLYEIVSN 135
                                       67888999*************************************999887766655 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.023
                    CENP-F_leu_zip  53 evetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnsslenlleekEqe 116
                                        +++l+++i+ l+++++el  + ++l ++  +L+++  +  +rv+ Le++  +l+++ e +E++
  gi|298675226|ref|YP_003726976.1| 186 GINKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISDRVDILEKI--DLSKTYEPSENQ 247
                                       46788899999999999999999999999999999999999999999976..445555555555 PP

>> CagA  CagA exotoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.2     0.026       4.9     118     149 ..      94     125 ..      84     136 .. 0.83
   2 ?    8.2   0.2     0.011       2.1       6      39 ..     201     234 ..     196     254 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.026
                                       XXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXX CS
                              CagA 118 rhdkvdd.lskvgrsrnqelaqkidnlnqavse 149
                                       r  kvd  +s v r  nqel + id+++q+v e
  gi|298675226|ref|YP_003726976.1|  94 RMSKVDAnISTVQR-ENQELKKTIDKIDQSVVE 125
                                       77899952566655.7**************988 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.011
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              CagA   6 kkelnekfknfnnnnnglknstepiyakvnkkkt 39 
                                        +el ek+ ++n+n   lk+st+ i  +v+    
  gi|298675226|ref|YP_003726976.1| 201 TNELFEKYDELNENLSTLKQSTDEISDRVDILEK 234
                                       47999********************999875444 PP

>> Taxilin  Myosin-like coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   3.1    0.0061       1.2     215     298 ..      78     161 ..      69     173 .. 0.76
   2 ?    8.3   0.7    0.0061       1.2       3      53 ..     184     234 ..     182     244 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0061
                           Taxilin 215 keqlnlYaeKfeefqdtLakSnelFatFkkEmekmtkktkklEketnlwkskfektnkallemaeertekkkeiekl 291
                                        eq++  a+K + +++ ++k +  ++t ++E ++++k + k+++   ++ s +e + +++   + +++   + ie++
  gi|298675226|ref|YP_003726976.1|  78 NEQVENNAQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVELLSLYEIVSNQVNPFVGDNEGGSEYIERF 154
                                       57888888888888888888888888888888888888888888888888888888888877777777777777777 PP

                           Taxilin 292 kkkiqkL 298
                                       +k  ++ 
  gi|298675226|ref|YP_003726976.1| 155 EKNEERI 161
                                       7766665 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0061
                           Taxilin   3 aeqlkeslsklespeekleaLvkkyaelleerkrlqkqlkklkkkleqlqk 53 
                                       ++ ++++ sk+++  +k ++L++ky el e+ ++l+++  + + +++ l k
  gi|298675226|ref|YP_003726976.1| 184 TQGINKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISDRVDILEK 234
                                       566788888999999999999999999999999999988888888887765 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   3.7   0.00093      0.18      13      61 ..      78     126 ..      73     138 .. 0.89
   2 ?    5.9   3.7     0.069        13      31      69 ..     188     226 ..     149     240 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00093
                     Tropomyosin_1  13 qekaeeleekvKeleqenlekeqeiksLtkknqqleeevekleeklkea 61 
                                        e++e+  +k+K+ e++  + + +i+  ++ nq+l + ++k+++++ e 
  gi|298675226|ref|YP_003726976.1|  78 NEQVENNAQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVEL 126
                                       57899999************************************99886 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.069
                     Tropomyosin_1  31 lekeqeiksLtkknqqleeevekleeklkeakekaeese 69 
                                        +  ++i +Lt k ++l e+ ++l+e+l++ k++ +e +
  gi|298675226|ref|YP_003726976.1| 188 NKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEIS 226
                                       455678888888888888888888888888888887754 PP

>> Allexi_40kDa  Allexivirus 40kDa protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.4      0.23        44      86     126 ..      84     122 ..      68     142 .. 0.43
   2 ?   11.1   0.8     0.001       0.2      54     159 ..     168     273 ..     162     282 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.23
                      Allexi_40kDa  86 alrtltklldklksvekklelsaetasdskllkklesiets 126
                                       + ++++++  ++++v    ++s+ + ++++l k+++ i++s
  gi|298675226|ref|YP_003726976.1|  84 NAQKIKTVESRMSKVDA--NISTVQRENQELKKTIDKIDQS 122
                                       22222222222222111..1122222233333344444443 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.001
                      Allexi_40kDa  54 LthishdvdsiinklnpvsllsqttlLselrdalrtltklldklksvekklelsaetasds.kllkklesietslee 129
                                        t +++d+d + +k+++  +    +++ +l ++ ++l ++ d+l+++ ++l++s++++sd+ ++l+k++  +t  e 
  gi|298675226|ref|YP_003726976.1| 168 ATMLKNDLDALYQKFDTQGINKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISDRvDILEKIDLSKT-YEP 243
                                       5889999***********9999999*****************************9999987356677765554.888 PP

                      Allexi_40kDa 130 lhakldelsssetsesegPsssptkassae 159
                                         ++ +++ + e+++ e+Ps+   + ++++
  gi|298675226|ref|YP_003726976.1| 244 SENQYNVIYQDEEESAENPSVILGSIEKEP 273
                                       899999999999999999998766666555 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.5      0.25        47      36      84 ..      80     124 ..      67     128 .. 0.53
   2 ?    8.3   0.5     0.014       2.7      11      77 ..     169     230 ..     155     235 .. 0.76
   3 ?    2.0   0.0       1.3   2.5e+02      17      45 ..     343     371 ..     337     373 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.25
                           DUF4164  36 eleaeiealgedrsRLaeeLdqaearaarleevnrEvsrrLkaaietir 84 
                                       ++e++ ++++  +sR    + ++ a  +++++ n+E+++ ++  ++++ 
  gi|298675226|ref|YP_003726976.1|  80 QVENNAQKIKTVESR----MSKVDANISTVQRENQELKKTIDKIDQSVV 124
                                       444444444443333....344555555556666666666655555555 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.014
                           DUF4164  11 trLeaaldsLEkavdrrleaerkrdeleaeiealgedrsRLaeeLdqaearaarleevnrEvsrrLk 77 
                                       t L++ ld+L     +++++ +  ++l ++i  l++  + L e+ d+ +  +++l++ ++E+s+r +
  gi|298675226|ref|YP_003726976.1| 169 TMLKNDLDALY----QKFDT-QGINKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISDRVD 230
                                       44444444443....33333.45689999***********************************987 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 1.3
                           DUF4164  17 ldsLEkavdrrleaerkrdeleaeiealg 45 
                                       l  +Ek + +r+e+ ++ d++++e+++++
  gi|298675226|ref|YP_003726976.1| 343 LMFIEKMSGHRVENSQTSDNIDSELSKIK 371
                                       556799999****************9987 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   3.3     0.054        10       8      71 ..      79     137 ..      75     165 .. 0.77
   2 ?   13.5   2.9   0.00042      0.08      20      70 ..     178     242 ..     152     265 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.054
                      Syntaxin-6_N   8 eeVqkslnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLeetvriveknp 71 
                                       e+V+++++k++++ +r++++  +      + +++ ++eL+k++++i++ + +L    +iv+++ 
  gi|298675226|ref|YP_003726976.1|  79 EQVENNAQKIKTVESRMSKVDAN-----ISTVQRENQELKKTIDKIDQSVVELLSLYEIVSNQV 137
                                       67888888888888888874333.....667899999999999999999999999888888754 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00042
                      Syntaxin-6_N  20 lyrrw..erlledtsss......tseeldetrteLrkalrsiewdledLeetvrivek.......n 70 
                                       ly+++  + + ++ s +      +++el e  +eL+++l+++++  +++ + v+i+ek       +
  gi|298675226|ref|YP_003726976.1| 178 LYQKFdtQGINKLHS-KiddltsKTNELFEKYDELNENLSTLKQSTDEISDRVDILEKidlsktyE 242
                                       555554312222222.1223444799******************************9954444441 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   3.6     0.034       6.4       8      53 ..      79     135 ..      74     181 .. 0.63
   2 ?    8.8   2.1     0.013       2.4      10      53 ..     179     228 ..     170     261 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.034
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...........X CS
                              YabA   8 dkleeleeqleelleeleelkeelaelleenaeLeleneklrerl...........e 53 
                                       +++e+  ++++++ ++++++ ++++++  en+eL+   +k+ + +           +
  gi|298675226|ref|YP_003726976.1|  79 EQVENNAQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVvellslyeivsN 135
                                       466666777777777777777777777777777777777766665555555555550 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.013
                                       HHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.....X CS
                              YabA  10 leeleeq.leelleeleelkeelaelleenaeLeleneklrerl.....e 53 
                                        +++++q +++l++++++l ++++el+e+ +eL+ + ++l++       +
  gi|298675226|ref|YP_003726976.1| 179 YQKFDTQgINKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTdeisdR 228
                                       45554433788888888888888888888888888888888877433331 PP

>> PTRF_SDPR  PTRF/SDPR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   2.5    0.0047      0.89      22      98 ..      85     161 ..      77     181 .. 0.84
   2 ?    5.3   0.3      0.07        13      47     117 ..     188     260 ..     184     284 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0047
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         PTRF_SDPR  22 qesqkrlEerqaelenavksiqgdllkLakshssTsntvnklleksrkvsvnvkevrerlekqavqvkklEaneael 98 
                                        ++ k +E+r ++++ +++++q +   L k+  +  ++v  ll     vs++v       e  +  + + E+ne+ +
  gi|298675226|ref|YP_003726976.1|  85 AQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVELLSLYEIVSNQVNPFVGDNEGGSEYIERFEKNEERI 161
                                       344456899999**************************************999999999999999999999998876 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.07
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHCHXXXXXXXXXXXXXXXXX CS
                         PTRF_SDPR  47 lkLakshssTsntvnklleksrkvsvnvkevrerlekqavqvkklEane...aelLkrnkFkVliyqeenevps 117
                                        kL  +    ++  n l+ek    + n+ ++++  +  + +v  lE+ +   +     n++  +iyq+e+e   
  gi|298675226|ref|YP_003726976.1| 188 NKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISDRVDILEKIDlskTYEPSENQYN-VIYQDEEESAE 260
                                       5665444455556699*************************998887541103334556666.58999988544 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   5.1    0.0019      0.37     115     252 ..      79     234 ..      68     246 .. 0.46

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0019
                           DUF4407 115 eqqeeakelkeqlaaa...ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk................g 172
                                       eq e++++  +++++     +a +++ ++++++l+++id+ ++ + +l   +                        +
  gi|298675226|ref|YP_003726976.1|  79 EQVENNAQKIKTVESRmskVDANISTVQRENQELKKTIDKIDQSVVELLSLY-------EivsnqvnpfvgdneggS 148
                                       2222222233333322444444444444444455555555555444444333.......233333456666644441 PP

                           DUF4407 173 tgttgvaGkgpaakekkaqldaaqaelaelkakld.............atarlaalraelaeleaerakeraasqaa 236
                                               + ++++++++ ++++ +  + lk++ld               +++++l ++ +el +++++ +++  + 
  gi|298675226|ref|YP_003726976.1| 149 -------EYIERFEKNEERINEIGNYATMLKNDLDalyqkfdtqginkLHSKIDDLTSKTNELFEKYDELNENLSTL 218
                                       .......3444444444444444444444444444555555455555644455555555555555555555555555 PP

                           DUF4407 237 aaaddGllarlealdr 252
                                       +++ d + +r ++l++
  gi|298675226|ref|YP_003726976.1| 219 KQSTDEISDRVDILEK 234
                                       5555555555555544 PP

>> DUF2959  Protein of unknown function (DUF2959)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.8      0.21        40     150     184 ..      83     120 ..      78     129 .. 0.71
   2 ?   10.3   0.4    0.0031      0.58      47      83 ..     199     235 ..     184     259 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.21
                           DUF2959 150 lNaqaiaalkgelselekdvsklik...emeksiaead 184
                                        Naq i+++++++s++++++s++ +   e++k+i++ d
  gi|298675226|ref|YP_003726976.1|  83 NNAQKIKTVESRMSKVDANISTVQRenqELKKTIDKID 120
                                       69999999999999999999887641114455555555 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0031
                           DUF2959  47 fdggeLekeyeklnkeyeesekaaeevrerieaveev 83 
                                        +  eL ++y++ln+++ + +++++e+++r++ +e++
  gi|298675226|ref|YP_003726976.1| 199 SKTNELFEKYDELNENLSTLKQSTDEISDRVDILEKI 235
                                       46789999************************99986 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   6.4     0.036       6.8      78     129 ..      79     130 ..      74     181 .. 0.74
   2 ?    7.0   2.3     0.017       3.3      63     129 ..     161     229 ..     145     237 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.036
                               GAS  78 knyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdelykkf 129
                                       ++ e+  q++k +++r+++++ ++++++ e++ l++ ++k+ ++  el + +
  gi|298675226|ref|YP_003726976.1|  79 EQVENNAQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVELLSLY 130
                                       5666677777777777777777777777777777777777777666665544 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.017
                               GAS  63 LkkaeeeveeLrkqlkn.yek.dkqslknlkarlkelekelkdlkwehevleqrfekvekerdelykkf 129
                                       +++  +    L+++l   y+k d q +++l++++ +l+++ ++l ++++ l++ +++++++ de++++ 
  gi|298675226|ref|YP_003726976.1| 161 INEIGNYATMLKNDLDAlYQKfDTQGINKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISDRV 229
                                       555555555566655431333367888999999999999999999999999999999999999998875 PP

>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   6.6     0.038       7.3      40     134 ..      76     195 ..      72     257 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.038
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SS............. CS
                             Nup54  40 aQqkevaqhrerlkeisdrleeleqkhqletsvrlekakkrhvelshRllrllrkleilrsrgy............. 103
                                       a +++v++  +++k++++r++++  ++  +++ + +++kk+  ++ + +++ll+  ei++++               
  gi|298675226|ref|YP_003726976.1|  76 ANNEQVENNAQKIKTVESRMSKVD-ANISTVQRENQELKKTIDKIDQSVVELLSLYEIVSNQVNpfvgdneggseyi 151
                                       567899999999999999999999.8888889999999999999999999999999999888664555555555666 PP

                                       ...........---SSHHHHHHHHHHHHHHHS-H..HH.HHHHH CS
                             Nup54 104 ...........aldaeEeelrarletleaqlndp..aqlkgrvn 134
                                                   + +    l++ l++l ++ + +  ++l ++++
  gi|298675226|ref|YP_003726976.1| 152 erfekneerinEIGNYATMLKNDLDALYQKFDTQgiNKLHSKID 195
                                       66666666666333333333334443333333323333333333 PP

>> LOH1CR12  Tumour suppressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   2.1     0.041       7.7      56     107 ..      86     137 ..      73     164 .. 0.53
   2 ?    7.1   0.2     0.027       5.1      55     105 ..     184     234 ..     165     240 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.041
                          LOH1CR12  56 erikevdakiitllaelrekqkqyasyaealskvnelsdqlsriqiilediv 107
                                       ++ik+v+ +++++ a++   q++ ++  +++ k+ +   +l ++  i+ ++v
  gi|298675226|ref|YP_003726976.1|  86 QKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVELLSLYEIVSNQV 137
                                       4555555555555555555555555555555555554444444444444443 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.027
                          LOH1CR12  55 verikevdakiitllaelrekqkqyasyaealskvnelsdqlsriqiiled 105
                                       ++ i ++  ki  l ++++e  ++y++  e+ls +++  d++s   +ile+
  gi|298675226|ref|YP_003726976.1| 184 TQGINKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISDRVDILEK 234
                                       556788899999999**********************99999988888876 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   1.0      0.06        11      28      65 ..      85     122 ..      75     136 .. 0.77
   2 ?    9.0   1.1     0.012       2.3      25      80 ..     188     246 ..     179     254 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.06
                      Occludin_ELL  28 haeleevskkfseLerelkelkegskeykkieeeilqe 65 
                                        +++++v++++s++++++++ +++++e kk++++i q+
  gi|298675226|ref|YP_003726976.1|  85 AQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQS 122
                                       46778888888888888888888888888888887655 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.012
                      Occludin_ELL  25 kelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkk...dpeyqekkk 80 
                                       ++lh++++++++k +eL ++ +el+e+ ++ k+ ++ei ++   l+k   +++y   ++
  gi|298675226|ref|YP_003726976.1| 188 NKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISDRVDILEKidlSKTYEPSEN 246
                                       58999999999999999999999999999999999999888665554433566655555 PP

>> DUF1515  Protein of unknown function (DUF1515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2      0.13        25      42      75 ..      81     114 ..      69     121 .. 0.82
   2 ?    5.4   0.1     0.092        18      36      73 ..     188     225 ..     155     236 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.13
                           DUF1515  42 mdelvervtalegsvvklkaditsvkevtedvkk 75 
                                       +++  ++++++e+ ++k++a+i++v+   +++kk
  gi|298675226|ref|YP_003726976.1|  81 VENNAQKIKTVESRMSKVDANISTVQRENQELKK 114
                                       455567899**************99988888776 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.092
                           DUF1515  36 akmyrkmdelvervtalegsvvklkaditsvkevtedv 73 
                                        k++ k+d+l  + + l     +l+++++++k+ t+++
  gi|298675226|ref|YP_003726976.1| 188 NKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEI 225
                                       46777777777777777777777777777777777776 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   4.9     0.062        12      30      84 ..      72     126 ..      66     141 .. 0.59
   2 ?    9.0   0.5     0.004      0.76      34      76 ..     189     231 ..     173     235 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.062
                           DUF3450  30 aaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasl 84 
                                       ++ ++ ++++++ +++ +++++++ ++ + ++  + +n++l++ +++ +q++ +l
  gi|298675226|ref|YP_003726976.1|  72 QTGQANNEQVENNAQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVEL 126
                                       4455555555555555555566666666666666666666666665555555544 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.004
                           DUF3450  34 qsqkkidklddekqellaeyralkeeleslevyneqlerlvas 76 
                                       + ++kid+l+ +++el ++y +l+e l+ l+   ++ ++ v+ 
  gi|298675226|ref|YP_003726976.1| 189 KLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISDRVDI 231
                                       6789***************************999999988875 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5  18.4     0.007       1.3     315     501 ..      80     263 ..      69     264 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.007
                            AAA_13 315 ensafeedkeelkaeaealeeqLkglqraleaKrkepfksvelesvkakiesikklva.eineliakhN...ekvan 387
                                       + ++ ++++++++++++++++++ ++qr+ ++ +k + k +  +++  ++ s+ ++v+ ++n  + ++    e++++
  gi|298675226|ref|YP_003726976.1|  80 QVENNAQKIKTVESRMSKVDANISTVQRENQELKKTIDK-I--DQSVVELLSLYEIVSnQVNPFVGDNEggsEYIER 153
                                       233345556666667777777777777766555555444.3..3333333444444441455566555411145555 PP

                            AAA_13 388 leeekeeakkklelhlveeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeein 464
                                       +e+++e++++ +   ++  l+++ld++ +k++   + i+kl  ++++ ++++++l e+  eL ++l++ k++ +ei 
  gi|298675226|ref|YP_003726976.1| 154 FEKNEERINE-IGN-YATMLKNDLDALYQKFDT--QGINKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEIS 226
                                       5555554443.333.356688999999988887..89**************************************** PP

                            AAA_13 465 keLkafGlgeleLkfeee..kkgYrivrkggsqaaetLS 501
                                       + +     ++  L+++ e  ++ Y+++ +++++ ae+ S
  gi|298675226|ref|YP_003726976.1| 227 DRVDIL--EKIDLSKTYEpsENQYNVIYQDEEESAENPS 263
                                       998877..555555544444**************99988 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.6    0.0084       1.6      88     134 ..      76     122 ..      72     130 .. 0.84
   2 ?    6.9   1.4     0.025       4.7      65     112 ..     187     234 ..     170     242 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0084
                           DUF4201  88 mleselselkkelkekeerlaklrkelykvklerdklrkqneklkqq 134
                                       ++++++++  +++k+ e r  k++++++ v+ e++ l+k  +k+ q+
  gi|298675226|ref|YP_003726976.1|  76 ANNEQVENNAQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQS 122
                                       67788899999999999999999999999999999999999998876 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.025
                           DUF4201  65 Lkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrk 112
                                       +++l++k+ +   ++++l ek ++l+++ls+lk++++e+ +r + l+k
  gi|298675226|ref|YP_003726976.1| 187 INKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISDRVDILEK 234
                                       567777777777777888888888888888888888887777776665 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   3.2     0.094        18      60     103 ..      77     120 ..      65     146 .. 0.59
   2 ?   11.4   4.2   0.00028     0.054      21     131 ..     150     254 ..     134     300 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.094
                        V_ATPase_I  60 eesleapeekeldeleeelekleeelkelnenleklkkelnelv 103
                                       ++++ ++++++++++e++++k++++++++++++++lkk+  ++ 
  gi|298675226|ref|YP_003726976.1|  77 NNEQVENNAQKIKTVESRMSKVDANISTVQRENQELKKTIDKID 120
                                       34455555566666666666666666666666666666555443 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00028
                        V_ATPase_I  21 fqrkfvkevrrcdemerklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnenleklkk 97 
                                       +  +f k+  r++e+ +  ++l++ ++        +++ +++  ++ ++++d+l++++++l e+  elnenl++lk+
  gi|298675226|ref|YP_003726976.1| 150 YIERFEKNEERINEIGNYATMLKNDLDA------LYQKFDTQGINKLHSKIDDLTSKTNELFEKYDELNENLSTLKQ 220
                                       3334444444444444444444444444......2233345556778999*************************** PP

                        V_ATPase_I  98 elnelvelkavlekakefleee.eeeeeeeeseee 131
                                       ++ e+ +   +lek++   + e +e++ +    ++
  gi|298675226|ref|YP_003726976.1| 221 STDEISDRVDILEKIDLSKTYEpSENQYN-VIYQD 254
                                       ************99986554442222222.22222 PP

>> LPP20  LPP20 lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   2.1     0.016         3      25      84 ..      74     137 ..      63     151 .. 0.80
   2 ?    6.6   1.0     0.052        10      36      94 ..     191     252 ..     183     253 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.016
                             LPP20  25 raAkqnAlrdiaeqiqvqvksssstqets......aavqnsettnesvsqvvesvlrgieivevee 84 
                                        +A ++ + + a++i+++ +  s+  ++        ++q+ ++t+++++q+v   l+ +eiv+ ++
  gi|298675226|ref|YP_003726976.1|  74 GQANNEQVENNAQKIKTVESRMSK--VDAnistvqRENQELKKTIDKIDQSVVELLSLYEIVSNQV 137
                                       689999999999999999844443..3334578888899999**********99999*99998765 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.052
                             LPP20  36 aeqiqvqvksssstqets....aavqnsettnesvsqvvesvlrgieiveveeledgkyyvlv 94 
                                        ++i    +++++++e+     ++ ++ +++++++s +v+  l++i + +++e + + y v +
  gi|298675226|ref|YP_003726976.1| 191 HSKIDDLTSKTNELFEKYdelnENLSTLKQSTDEISDRVD-ILEKIDLSKTYEPSENQYNVIY 252
                                       4444445555555555447445566666666666666665.369*******999999988765 PP

>> CREPT  Cell-cycle alteration and expression-elevated protein in tumour
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.7      0.04       7.6      86     123 ..      75     112 ..      71     132 .. 0.79
   2 ?    5.8   0.4     0.073        14      62     130 ..     149     219 ..     143     237 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.04
                             CREPT  86 eaqkellakaeekleelkeklekvksvrkelkshiqsL 123
                                       +a +e+++++++k++ ++++++kv+++ +++++  q L
  gi|298675226|ref|YP_003726976.1|  75 QANNEQVENNAQKIKTVESRMSKVDANISTVQRENQEL 112
                                       56778888888888888888888888888888776665 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.073
                             CREPT  62 eYnkrLeaeleeRkklakmledfleaqkellaka.eekleelkeklekvksvrkelkshiqsLPd.Ltelp 130
                                       eY +r e++ e  +++ ++ +++++ + +l +k   + +++l++k++ ++s+ +el ++++ L + L++l 
  gi|298675226|ref|YP_003726976.1| 149 EYIERFEKNEERINEIGNYATMLKNDLDALYQKFdTQGINKLHSKIDDLTSKTNELFEKYDELNEnLSTLK 219
                                       67777777766666666666666666666666641455777788888888888887777777643244444 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   2.7       0.6   1.2e+02      24      67 ..      91     134 ..      68     157 .. 0.57
   2 ?    9.2   0.5    0.0074       1.4      35      88 ..     161     212 ..     151     235 .. 0.44

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.6
                            DUF948  24 lkktldeaaatieelekqvdpilkevedllakvnelledvnekl 67 
                                       +++ ++++ a i +++++ +++ k ++++ + v ell+  +  +
  gi|298675226|ref|YP_003726976.1|  91 VESRMSKVDANISTVQRENQELKKTIDKIDQSVVELLSLYEIVS 134
                                       44444444444444444444444444444444444444333333 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0074
                            DUF948  35 ieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                       i+e+++ ++ + +++++l +k  +  +++n+   k+d lt++ ++l e+  eln
  gi|298675226|ref|YP_003726976.1| 161 INEIGNYATMLKNDLDALYQKFDT--QGINKLHSKIDDLTSKTNELFEKYDELN 212
                                       555554444444444444444444..3333333333333333333322222222 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.4     0.014       2.8      47      97 ..      79     115 ..      60     132 .. 0.56
   2 ?    6.0   7.5     0.087        17      21     118 ..     160     256 ..     148     263 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.014
                            APG6_N  47 eeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeee 97 
                                       e++e+                +++k +e+  ++++a +++ ++e ++l++ 
  gi|298675226|ref|YP_003726976.1|  79 EQVENNA--------------QKIKTVESRMSKVDANISTVQRENQELKKT 115
                                       3344444..............444444444444444444444444444432 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.087
                            APG6_N  21 aekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeee 97 
                                         +e+ +Y + lk+  +   ++  + + +++l+ ++++l ++ +el+e+ +el ++ + l++   +++   + le+ 
  gi|298675226|ref|YP_003726976.1| 160 RINEIGNYATMLKNDLDALYQKF-DTQGINKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISDRVDILEKI 235
                                       34555566666655443334444.689999****************************************9999999 PP

                            APG6_N  98 eerfwreynelqlelleleee 118
                                          +  e +e q +++  +ee
  gi|298675226|ref|YP_003726976.1| 236 DLSKTYEPSENQYNVIYQDEE 256
                                       999999999999888876655 PP

>> CENP-H  Centromere protein H (CENP-H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   4.4      0.01       1.9      11      51 ..      77     117 ..      69     178 .. 0.88
   2 ?    6.3   0.9     0.067        13       9      59 ..     188     238 ..     177     264 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.01
                            CENP-H  11 lssellklsqelrelqeeltevekenlrlkrknrelaaell 51 
                                        ++++++ +q+++++++++++v +++  ++r+n+el +++ 
  gi|298675226|ref|YP_003726976.1|  77 NNEQVENNAQKIKTVESRMSKVDANISTVQRENQELKKTID 117
                                       568999******************************99994 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.067
                            CENP-H   9 delssellklsqelrelqeeltevekenlrlkrknrelaaellelakekes 59 
                                       ++l s++ +l+++++el e+ +e++++   lk+ + e+  ++  l+k + s
  gi|298675226|ref|YP_003726976.1| 188 NKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISDRVDILEKIDLS 238
                                       455666666666666666666666666666666666666666555444444 PP

>> Ax_dynein_light  Axonemal dynein light chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   1.6     0.047         9     110     147 ..      84     121 ..      70     136 .. 0.54
   2 ?    8.5   1.6    0.0095       1.8     118     161 ..     184     227 ..     147     250 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.047
                   Ax_dynein_light 110 gmrkalqaeqgkselekkikeLeeekeelekqvaelka 147
                                       + +k    e ++s+++++i+ +++e++el+k + ++++
  gi|298675226|ref|YP_003726976.1|  84 NAQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQ 121
                                       33333344444444445555555555555554444443 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0095
                   Ax_dynein_light 118 eqgkselekkikeLeeekeelekqvaelkaklealekrekerrq 161
                                        qg ++l++ki +L+++ +el ++  el+++l++l+++  e  +
  gi|298675226|ref|YP_003726976.1| 184 TQGINKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISD 227
                                       35556666666666666666666666666666666666555444 PP

>> EMP24_GP25L  emp24/gp25L/p24 family/GOLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.5    0.0084       1.6     102     139 ..      77     114 ..      61     132 .. 0.73
   2 ?    4.1   0.9       0.2        38     108     147 ..     188     228 ..     151     235 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0084
                       EMP24_GP25L 102 sdykdsakkekletleselkkleekldsikreqkylre 139
                                       ++++ ++  +k++t+es++ k++ +++ ++re + l++
  gi|298675226|ref|YP_003726976.1|  77 NNEQVENNAQKIKTVESRMSKVDANISTVQRENQELKK 114
                                       34455566888888888888888888888888766654 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.2
                       EMP24_GP25L 108 ak.kekletleselkkleekldsikreqkylrereerlrdt 147
                                       +k  +k+++l+s+ ++l ek d++ +++  l+++ ++  d 
  gi|298675226|ref|YP_003726976.1| 188 NKlHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISDR 228
                                       33478888888888888888888888888888877766655 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.5    0.0059       1.1     119     160 ..      79     121 ..      70     132 .. 0.87
   2 ?    2.4   0.1      0.52        99      93     129 ..     187     223 ..     148     236 .. 0.48

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0059
                         PspA_IM30 119 kqlealetkieelkakkellkar.ekaakaqeavqkslgklst 160
                                       +q+e++++ki+ +++ + ++ a+ + +++ +++++k+++k++ 
  gi|298675226|ref|YP_003726976.1|  79 EQVENNAQKIKTVESRMSKVDANiSTVQRENQELKKTIDKIDQ 121
                                       79999***************9994457999999**99999984 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.52
                         PspA_IM30  93 ikslekqaealetqlaqqrsaveqlrkqlealetkie 129
                                       i +l +++ +l  + +++ +  ++l ++l+ l++  +
  gi|298675226|ref|YP_003726976.1| 187 INKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTD 223
                                       3344444444444444444444444444444444444 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   1.6      0.15        29      22      71 ..      81     131 ..      68     140 .. 0.44
   2 ?   10.2   3.0    0.0031       0.6      35      90 ..     175     228 ..     147     257 .. 0.63

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.15
                             Mod_r  22 vktl.pevkqlkeekeellaeneslaeknlslepeleelrselqekleelk 71 
                                       v++  +++k+++++ +++ a +  + ++n +l++++++  +++ e l+ ++
  gi|298675226|ref|YP_003726976.1|  81 VENNaQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVELLSLYE 131
                                       222213444444444444333333444444444444444444444444443 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0031
                             Mod_r  35 keellaeneslaeknlsl.epeleelrselqekleelkelekefeekeqeldellqk 90 
                                       ++ l    +++  + +++ + ++++l s+++e +e+++el++++  ++q  de++++
  gi|298675226|ref|YP_003726976.1| 175 LDAL---YQKFDTQGINKlHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISDR 228
                                       2222...22233444444466777777777777777777777777777777777754 PP

>> Lectin_N  Hepatic lectin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.3       1.6   3.1e+02      84     104 ..      93     113 ..      71     132 .. 0.50
   2 ?    9.6   0.4    0.0038      0.72      46     104 ..     164     223 ..     160     238 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 1.6
                          Lectin_N  84 slsekvtsleaklekkqqdlk 104
                                       s   kv    +++++++q+lk
  gi|298675226|ref|YP_003726976.1|  93 SRMSKVDANISTVQRENQELK 113
                                       222233333344444444444 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0038
                          Lectin_N  46 igsqnsqLqreLetLketfsnfsss.tlaeiqalssqggslsekvtsleaklekkqqdlk 104
                                       ig   + L+++L +L ++f+    +   ++i +l+s++++l ek   l+ +l   +q+ +
  gi|298675226|ref|YP_003726976.1| 164 IGNYATMLKNDLDALYQKFDTQGINkLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTD 223
                                       8889999************99876516789**************9999998876555443 PP

>> 4HB_MCP_1  Four helix bundle sensory module for signal transduction
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   1.5    0.0046      0.88      56      99 ..      88     131 ..      81     136 .. 0.90
   2 ?    4.9   3.3      0.09        17      51     102 ..     161     212 ..     156     234 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0046
                         4HB_MCP_1  56 anlrelradlleliltkdkaekdellkdieeleaeidkllekye 99 
                                       +++ e r++ ++  +++ ++e++el+k+i+++++++ +ll+ ye
  gi|298675226|ref|YP_003726976.1|  88 IKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVELLSLYE 131
                                       567788999999999999*************************9 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.09
                         4HB_MCP_1  51 lgeikanlrelradlleliltkdkaekdellkdieeleaeidkllekyekti 102
                                       ++ei ++++ l+ dl  l  + d++  ++l ++i++l  ++++l eky++++
  gi|298675226|ref|YP_003726976.1| 161 INEIGNYATMLKNDLDALYQKFDTQGINKLHSKIDDLTSKTNELFEKYDELN 212
                                       6677777777777777777778999999999999999999999999999874 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   5.9     0.015       2.8       4      64 ..      78     138 ..      75     185 .. 0.79
   2 ?    4.0   2.0       0.3        57      60      98 ..     188     219 ..     149     234 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.015
                       TMF_TATA_bd   4 tssagpsvqlverlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkk 64 
                                       + + ++++q ++  +s+  + ++ ++++++e+++l++  d++ + +v+l++  e ++++ +
  gi|298675226|ref|YP_003726976.1|  78 NEQVENNAQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVELLSLYEIVSNQVN 138
                                       56678999*****************************************998887776655 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.3
                       TMF_TATA_bd  60 kelkkeleelekeleelqeryetlLellGeksEeveELr 98 
                                       ++l++++++l+++ +el e+       + e +E+   L+
  gi|298675226|ref|YP_003726976.1| 188 NKLHSKIDDLTSKTNELFEK-------YDELNENLSTLK 219
                                       23333333333333333333.......333333333332 PP

>> TACC_C  Transforming acidic coiled-coil-containing protein (TACC), C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1  12.3       1.5   2.9e+02       9      60 ..      94     145 ..      73     236 .. 0.37
   2 ?    7.4   0.9     0.018       3.5       4      54 ..     173     224 ..     170     257 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 1.5
                            TACC_C   9 alekvkeeveekeeeiqelkkkveelkkenqemkkivaefektiaqlieekq 60 
                                        + kv++++ + ++e qelkk++++ ++ + e+  + +   + ++ ++ +++
  gi|298675226|ref|YP_003726976.1|  94 RMSKVDANISTVQRENQELKKTIDKIDQSVVELLSLYEIVSNQVNPFVGDNE 145
                                       3333333333333333334444444444433333333222222222222222 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.018
                            TACC_C   4 kdldaalekvkee.veekeeeiqelkkkveelkkenqemkkivaefektiaq 54 
                                       +dlda+ +k++ + +++  ++i +l++k +el +++ e+++ ++   + + +
  gi|298675226|ref|YP_003726976.1| 173 NDLDALYQKFDTQgINKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDE 224
                                       6777777776655244446677777777777777777777666555554444 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   5.1     0.018       3.5      53     104 ..      78     129 ..      70     161 .. 0.89
   2 ?    6.0   0.9     0.043       8.2      82     118 ..     185     221 ..     168     253 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.018
                         Laminin_I  53 aqeteeLqkkatqvlakaqkvnaesertlnnakeLaekikkladnikeilek 104
                                       ++++e+ ++k + v  + +kv a++++   + +eL++ i k+++++ e+l+ 
  gi|298675226|ref|YP_003726976.1|  78 NEQVENNAQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVELLSL 129
                                       6899999****************************************99875 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.043
                         Laminin_I  82 nnakeLaekikkladnikeilekvatlneneealpss 118
                                       + +++L  ki +l  + +e+ ek  +lnen + l +s
  gi|298675226|ref|YP_003726976.1| 185 QGINKLHSKIDDLTSKTNELFEKYDELNENLSTLKQS 221
                                       5667777777777777777777777777766554332 PP

>> DASH_Dad2  DASH complex subunit Dad2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.5       4.8   9.2e+02      39      63 ..      82     106 ..      71     136 .. 0.53
   2 ?    1.5   0.0       2.1     4e+02      12      37 ..     159     184 ..     151     190 .. 0.86
   3 ?    9.6   0.4    0.0064       1.2      13      50 ..     193     230 ..     189     279 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 4.8
                         DASH_Dad2  39 adgteavasVlanWqnvlraismas 63 
                                       +++++ +++V +   +v  +is  +
  gi|298675226|ref|YP_003726976.1|  82 ENNAQKIKTVESRMSKVDANISTVQ 106
                                       4444444444444444433333332 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 2.1
                         DASH_Dad2  12 eaLkqlrdlsdslakqleeLeeklst 37 
                                       e ++++ +++  l++ l++L +k++t
  gi|298675226|ref|YP_003726976.1| 159 ERINEIGNYATMLKNDLDALYQKFDT 184
                                       678999999**************987 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0064
                         DASH_Dad2  13 aLkqlrdlsdslakqleeLeeklstladgteavasVla 50 
                                       ++  l++ +++l ++ +eL+e+lstl++ t+ +++ ++
  gi|298675226|ref|YP_003726976.1| 193 KIDDLTSKTNELFEKYDELNENLSTLKQSTDEISDRVD 230
                                       57789999**********************99987665 PP

>> HBM  Helical bimodular sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.7      0.52        99      89     125 ..      90     126 ..      69     139 .. 0.51
   2 ?    9.9   0.9    0.0023      0.44      47     126 ..     161     240 ..     153     257 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.52
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCS CS
                               HBM  89 elraayesrnaaRqeldsaaeraleaideleaevlqt 125
                                        +++ + + +a  + ++++ +++++ id+++++v+++
  gi|298675226|ref|YP_003726976.1|  90 TVESRMSKVDANISTVQRENQELKKTIDKIDQSVVEL 126
                                       2222333333333444455555556666666666554 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0023
                                       HHHHHHHHHHHHHHHHH--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               HBM  47 qkkldelkaqlqklkakfkspenvrlLqeqlalvqeyrksfnelraayesrnaaRqeldsaaeraleaideleaevl 123
                                        +++++++++l++  + + +  + + +++   +++ +  + nel + y++ n+  + l+++ +++++++d le+  l
  gi|298675226|ref|YP_003726976.1| 161 INEIGNYATMLKNDLDALYQKFDTQGINKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISDRVDILEKIDL 237
                                       578999999999999999999**************************************************998655 PP

                                       CS- CS
                               HBM 124 qtp 126
                                        + 
  gi|298675226|ref|YP_003726976.1| 238 SKT 240
                                       444 PP

>> AKNA  AT-hook-containing transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.6      0.31        60      39      69 ..      93     123 ..      69     129 .. 0.74
   2 ?    6.8   0.3     0.054        10      28      65 ..     197     232 ..     173     246 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.31
                              AKNA  39 dpsreleaeIyqlgqrleeLkdqtdqlkqkv 69 
                                       +  +++ a+I+  +   +eLk  +d++ q v
  gi|298675226|ref|YP_003726976.1|  93 SRMSKVDANISTVQRENQELKKTIDKIDQSV 123
                                       3457899999999999999999999988776 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.054
                              AKNA  28 lssskgqpgkfdpsreleaeIyqlgqrleeLkdqtdql 65 
                                       l+s   + + f+   el ++++ l+q  +e++d++d l
  gi|298675226|ref|YP_003726976.1| 197 LTS--KTNELFEKYDELNENLSTLKQSTDEISDRVDIL 232
                                       333..377788888888899999999999999988855 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   1.4     0.029       5.5      79     111 ..      88     120 ..      78     133 .. 0.72
   2 ?   -0.0   0.1       4.1   7.8e+02      93     119 ..     154     180 ..     148     188 .. 0.57
   3 ?    6.0   0.6     0.056        11      86     118 ..     187     219 ..     180     221 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.029
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  79 iellkkkleelekqlekleeeleklkdqittle 111
                                       i++++ +++++++++ +++ e ++lk++i+++ 
  gi|298675226|ref|YP_003726976.1|  88 IKTVESRMSKVDANISTVQRENQELKKTIDKID 120
                                       566677777777777777777777777777765 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 4.1
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  93 lekleeeleklkdqittleanlaqlyq 119
                                       +ek ee ++++ + +t+l + l++lyq
  gi|298675226|ref|YP_003726976.1| 154 FEKNEERINEIGNYATMLKNDLDALYQ 180
                                       444455555555555555555555554 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.056
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  86 leelekqlekleeeleklkdqittleanlaqly 118
                                       +++l + +++l+ + ++l +++++l++nl++l 
  gi|298675226|ref|YP_003726976.1| 187 INKLHSKIDDLTSKTNELFEKYDELNENLSTLK 219
                                       677888888888888888888888888888765 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   2.1    0.0078       1.5       2      50 ..      79     127 ..      78     139 .. 0.76
   2 ?    4.8   1.4      0.15        29      34      79 ..     183     228 ..     151     235 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0078
                             DHR10   2 eslaeekeelaelErkarelqakidalqvvekdlrsciklleeieaela 50 
                                       e++++  ++++  E +  ++ a i ++q+  ++l+++i+ +++  +el 
  gi|298675226|ref|YP_003726976.1|  79 EQVENNAQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVELL 127
                                       6788888888888888888888888888888888888887777766665 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.15
                             DHR10  34 dlrsciklleeieaelakleeakkklkelrdaleekeielrelerk 79 
                                       d + + kl  +i + + k++e  +k +el+++l+++++ + e++ +
  gi|298675226|ref|YP_003726976.1| 183 DTQGINKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISDR 228
                                       4444555555555555555555555555555555555555555555 PP

>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.9      0.89   1.7e+02       3      43 ..      92     118 ..      76     138 .. 0.55
   2 ?    8.8   0.3    0.0087       1.7       3      59 ..     172     226 ..     170     239 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.89
                     TolA_bind_tri   3 edrvarLErilearsqlllelqqqlealqqelreLRGqiEe 43 
                                       e              + + ++  ++++ q+e +eL+  i++
  gi|298675226|ref|YP_003726976.1|  92 E--------------SRMSKVDANISTVQRENQELKKTIDK 118
                                       3..............33334444444444444444433333 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0087
                     TolA_bind_tri   3 edrvarLErilearsqlllelqqqlealqqelreLRGqiEelqyqleqleerQrdlY 59 
                                       ++ ++ L ++++   q++ +l++++++l +  +eL  + +el+ +l++l++   ++ 
  gi|298675226|ref|YP_003726976.1| 172 KNDLDALYQKFDT--QGINKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEIS 226
                                       5678889999998..**********************************99877665 PP

>> Blo-t-5  Mite allergen Blo t 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.5      0.34        65      21      52 ..      88     119 ..      73     137 .. 0.84
   2 ?    8.9   1.3    0.0074       1.4       4      61 ..     170     229 ..     167     247 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.34
                                       X-HHHHHHHHHHHHHHHHHHHHHHHHHH--SS CS
                           Blo-t-5  21 ieeleekleklekallklseqvkelektkske 52 
                                       i+++e+++ k++  + +++ + +el+kt  k 
  gi|298675226|ref|YP_003726976.1|  88 IKTVESRMSKVDANISTVQRENQELKKTIDKI 119
                                       7899999******************9998874 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0074
                                       XXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHH--..SSHHHHHHHHH CS
                           Blo-t-5   4 vskkkkDefReefDrllieeleekleklekallklseqvkelektks..kelkeqilrel 61 
                                       + k++ D + ++fD   i++l++k+++l  +  +l e+++el+++ s  k+  ++i   +
  gi|298675226|ref|YP_003726976.1| 170 MLKNDLDALYQKFDTQGINKLHSKIDDLTSKTNELFEKYDELNENLStlKQSTDEISDRV 229
                                       5677889999*********************************98773355555555444 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   7.1     0.033       6.4     159     247 ..      76     223 ..      61     259 .. 0.40

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.033
                      Exonuc_VII_L 159 aikrlleekkqrleklasrlkspee...llerkrqrldeleerler............................... 201
                                       a ++++e+++q++++++sr+++ ++    ++r++q+l+++ +++++                               
  gi|298675226|ref|YP_003726976.1|  76 ANNEQVENNAQKIKTVESRMSKVDAnisTVQRENQELKKTIDKIDQsvvellslyeivsnqvnpfvgdneggseyie 152
                                       55556666666666666666443331114444444444444444443333444444433333333333333332222 PP

                      Exonuc_VII_L 202 ..........alkkqlkkkrerleelkerl.k..............ekleekkerlkklkerlelleekke 247
                                                 ++ + ++  +++l+ l +++ +              +k++e  e++++l+e+l++l+++++
  gi|298675226|ref|YP_003726976.1| 153 rfekneerinEIGNYATMLKNDLDALYQKFdTqginklhskiddltSKTNELFEKYDELNENLSTLKQSTD 223
                                       22222111111111122222222222222211111111111101111111111222333333333333333 PP

>> JIP_LZII  JNK-interacting protein  leucine zipper II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.3      0.91   1.7e+02       9      60 ..     104     120 ..      96     136 .. 0.66
   2 ?    9.5   1.5    0.0058       1.1      28      67 ..     194     233 ..     185     235 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.91
                          JIP_LZII   9 nLikENteLletknaLnvvkddLIarvdeLtsereiLreEleslqkakerle 60 
                                       ++ +EN+eL++t  ++                                    
  gi|298675226|ref|YP_003726976.1| 104 TVQRENQELKKTIDKI-----------------------------------D 120
                                       4556666666664444...................................3 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0058
                          JIP_LZII  28 kddLIarvdeLtsereiLreEleslqkakerlesrikelE 67 
                                        ddL +++ eL + ++ L+e l++l+++ +++ +r+  lE
  gi|298675226|ref|YP_003726976.1| 194 IDDLTSKTNELFEKYDELNENLSTLKQSTDEISDRVDILE 233
                                       4788888888888888888888888888888888888877 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   1.4       0.7   1.3e+02      27      67 ..      89     118 ..      67     125 .. 0.41
   2 ?    0.7   0.0       3.6   6.9e+02      20      47 ..     155     182 ..     150     184 .. 0.75
   3 ?    7.3   0.3     0.031       5.8      32      61 ..     186     215 ..     180     234 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.7
                               CLZ  27 keleekverLessLeaLqtrlarLlaeyessqrkLkqRitk 67 
                                       k++e++++           ++   ++ ++  +++Lk+ i k
  gi|298675226|ref|YP_003726976.1|  89 KTVESRMS-----------KVDANISTVQRENQELKKTIDK 118
                                       22222222...........2222233333333444444444 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 3.6
                               CLZ  20 akagaeqkeleekverLessLeaLqtrl 47 
                                       +k ++  +e+ + ++ L++ L+aL +++
  gi|298675226|ref|YP_003726976.1| 155 EKNEERINEIGNYATMLKNDLDALYQKF 182
                                       5566666778888889999999999888 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.031
                               CLZ  32 kverLessLeaLqtrlarLlaeyessqrkL 61 
                                        +++L s+++ L+ + + L ++y++ ++ L
  gi|298675226|ref|YP_003726976.1| 186 GINKLHSKIDDLTSKTNELFEKYDELNENL 215
                                       588999999999999999999888877766 PP

>> DUF641  Plant protein of unknown function (DUF641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.7    0.0031       0.6      72     121 ..      73     122 ..      62     128 .. 0.87
   2 ?    1.2   0.5       2.3   4.3e+02      80     117 ..     187     224 ..     148     234 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0031
                            DUF641  72 eeseleaeiqeqrsllktyeitvkkleaelkakdseieeLkekLeeaeks 121
                                       + ++ + +++++ +++kt e +++k++a++++ + e +eLk++++++ +s
  gi|298675226|ref|YP_003726976.1|  73 TGQANNEQVENNAQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQS 122
                                       55667788999999******************************998776 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 2.3
                            DUF641  80 iqeqrsllktyeitvkkleaelkakdseieeLkekLee 117
                                       i++++s+++ +   +++l ++ ++ +++++ Lk++ +e
  gi|298675226|ref|YP_003726976.1| 187 INKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDE 224
                                       33344444444444444444444444444444444444 PP

>> Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   3.2     0.037       7.1      92     147 ..      75     130 ..      68     138 .. 0.83
   2 ?    7.3   2.3     0.026         5      92     131 ..     188     227 ..     148     259 .. 0.56

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.037
                     Jnk-SapK_ap_N  92 kelqekveqleeenrelelkaknaadqlsrleekeaelkkeysklheretellkkl 147
                                       ++ +e+ve++ ++++ +e ++++++  +s+++++++elkk  +k  ++  ell  +
  gi|298675226|ref|YP_003726976.1|  75 QANNEQVENNAQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVELLSLY 130
                                       67789999999999999999999999999999999999999999988888887544 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.026
                     Jnk-SapK_ap_N  92 kelqekveqleeenrelelkaknaadqlsrleekeaelkk 131
                                       ++l++k+ +l+++++el  k +++++ ls+l+++ +e + 
  gi|298675226|ref|YP_003726976.1| 188 NKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISD 227
                                       3444455555554444444555555555555544444433 PP

>> T3SSipB  Type III cell invasion protein SipB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.9      0.18        34      57      93 ..      76     112 ..      70     126 .. 0.82
   2 ?    8.6   0.3     0.012       2.4      39      87 ..     185     233 ..     159     261 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT- CS
                           T3SSipB  57 gatddleaaiekadqaksaadaatkkvdeaqkrlkeL 93 
                                       +  +++e+ ++k+++++s + ++++ ++ +q+  +eL
  gi|298675226|ref|YP_003726976.1|  76 ANNEQVENNAQKIKTVESRMSKVDANISTVQRENQEL 112
                                       5568899999999999999999999999999999999 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.012
                                       TTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           T3SSipB  39 eaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaq 87 
                                       +   kl  ++ +++s+++++ +++++  e++ ++k+  d+   +vd   
  gi|298675226|ref|YP_003726976.1| 185 QGINKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISDRVDILE 233
                                       3445677778888888888888888888888888888888777776433 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   4.9     0.029       5.6      61     163 ..      75     178 ..      59     185 .. 0.57
   2 ?    4.7   1.7      0.16        31      86     144 ..     171     230 ..     153     255 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.029
                             ATG16  61 keasasqsnskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaera...a 134
                                       ++ + + + +++++ki++ e++++++ +  ++++++++el++ + +  +++ +l +  +  +++++    +++   +
  gi|298675226|ref|YP_003726976.1|  75 QANN-E-QVENNAQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVELLSLYEIVSNQVNPFVGDNEggsE 149
                                       2222.2.2355566677777777777777777777777777777766666666666666666666666555541113 PP

                             ATG16 135 letklkdreeelrekeklvqdlqDElsaL 163
                                         ++ +++ee+++e  +   +l+ +l+aL
  gi|298675226|ref|YP_003726976.1| 150 YIERFEKNEERINEIGNYATMLKNDLDAL 178
                                       44455555666666666666666655555 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.16
                             ATG16  86 lreelaelyks.rgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdree 144
                                       l+++l +ly++  ++  ++l ++ + l  + ++l e+  +l+e  ++ ++ +++++dr +
  gi|298675226|ref|YP_003726976.1| 171 LKNDLDALYQKfDTQGINKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISDRVD 230
                                       556666555431233333334444444444444444444444444444444455555544 PP

>> GCN5L1  GCN5-like protein 1 (GCN5L1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   2.9     0.042         8      38      87 ..      77     126 ..      70     131 .. 0.89
   2 ?   -0.1   0.0       5.2     1e+03      74     107 ..     151     181 ..     133     185 .. 0.67
   3 ?    3.4   0.4      0.43        82      56      86 ..     187     217 ..     151     229 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.042
                            GCN5L1  38 lnsgvaeayanqkklekeakalqanvakfakqtdqWlalvesfnsalkei 87 
                                        n++v++  ++ k +e+ + ++ an++++++++++  ++++++++++ e+
  gi|298675226|ref|YP_003726976.1|  77 NNEQVENNAQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVEL 126
                                       58889999999999*******************************99887 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 5.2
                            GCN5L1  74 lalvesfnsalkeiGDvenWaktienDlksitea 107
                                       ++ +e+ ++++ eiG   n a ++ nDl ++ ++
  gi|298675226|ref|YP_003726976.1| 151 IERFEKNEERINEIG---NYATMLKNDLDALYQK 181
                                       444444455555555...7788888888777665 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.43
                            GCN5L1  56 akalqanvakfakqtdqWlalvesfnsalke 86 
                                       + +l+++++ ++ +t++  + ++++n++l  
  gi|298675226|ref|YP_003726976.1| 187 INKLHSKIDDLTSKTNELFEKYDELNENLST 217
                                       4556666666666666666666666666543 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   3.4       0.1        20      65     114 ..      80     125 ..      68     138 .. 0.46
   2 ?    7.5   1.7     0.022       4.2      55      96 ..     183     224 ..     148     253 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.1
                        TPR_MLP1_2  65 elnelkaeiaelkaeaesakaeleeseesweeqkeelekelselekried 114
                                       ++++  ++i++++++  +    ++++ +  +++ +el+k ++++ + + +
  gi|298675226|ref|YP_003726976.1|  80 QVENNAQKIKTVESRMSK----VDANISTVQRENQELKKTIDKIDQSVVE 125
                                       444444444443333333....3333334444444444444444444444 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.022
                        TPR_MLP1_2  55 dvkelqalreelnelkaeiaelkaeaesakaeleeseeswee 96 
                                       d++ +++l +++++l+++ +el ++ ++++++l++ ++s +e
  gi|298675226|ref|YP_003726976.1| 183 DTQGINKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDE 224
                                       788899999999999999999999999999999999999876 PP

>> UPF0184  Uncharacterised protein family (UPF0184)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.8       2.2   4.3e+02      15      54 ..      75     114 ..      45     127 .. 0.76
   2 ?   10.6   1.5    0.0031      0.59      20      66 ..     179     225 ..     157     244 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 2.2
                           UPF0184  15 gaeteedefgeeEyeainsmLDqinsaLDalEernDdlns 54 
                                        a++e+ e + + ++ + s + ++++ +  +   n +l+ 
  gi|298675226|ref|YP_003726976.1|  75 QANNEQVENNAQKIKTVESRMSKVDANISTVQRENQELKK 114
                                       2345555777888999999999999999888888888765 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0031
                           UPF0184  20 edefgeeEyeainsmLDqinsaLDalEernDdlnskLrELlesnRqi 66 
                                        ++f+ + ++ + s +D + s  ++l e+ D+ln  L  L +s  +i
  gi|298675226|ref|YP_003726976.1| 179 YQKFDTQGINKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEI 225
                                       5899**********************************999998776 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   8.2     0.012       2.2      66     183 ..      77     198 ..      62     198 .. 0.59
   2 ?    6.5   5.8     0.041       7.8      81     127 ..     179     230 ..     148     260 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.012
                           UPF0242  66 ekskleekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelklelee 142
                                       +++++e++ +k++  +  +++ + ++  +q e++eLk+ +d+ ++ + +l    + ++ + +  + d+e  + e+ e
  gi|298675226|ref|YP_003726976.1|  77 NNEQVENNAQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVELLSLYEIVSNQVNPFVGDNEGGS-EYIE 152
                                       333344444444444444566666666666666666666666666666666666666666666666887655.5666 PP

                           UPF0242 143 qLaekqellqeyqetieeqrsvle...kr..qdqieqLeskVrDln 183
                                       + ++ +e+++e  +  + +++ l+   ++   + i++L sk+ Dl+
  gi|298675226|ref|YP_003726976.1| 153 RFEKNEERINEIGNYATMLKNDLDalyQKfdTQGINKLHSKIDDLT 198
                                       788888888875555555554444111452234599********95 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.041
                           UPF0242  81 d.....eglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekle 127
                                             +g+++ + ++ +l+++++eL e++d+ +e+l  lk+   +++ +  
  gi|298675226|ref|YP_003726976.1| 179 YqkfdtQGINKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISDRVD 230
                                       13344567888889****************************9999986654 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   3.3     0.004      0.77      13      67 ..      75     129 ..      72     133 .. 0.91
   2 ?    2.7   1.8      0.69   1.3e+02       8      37 ..     190     219 ..     152     234 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.004
                              BRE1  13 eelseqlskkvkeltileekklrleaekakadqkyfaamrskdalenelkkLnkl 67 
                                       ++ +eq+++  ++++  e+++++++a+++  +++  ++++ +d++++ ++ L +l
  gi|298675226|ref|YP_003726976.1|  75 QANNEQVENNAQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVELLSL 129
                                       5678999999999**********************************99998776 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.69
                              BRE1   8 lekafeelseqlskkvkeltileekklrle 37 
                                       l+  +++l ++++++ +++  l e+++ l+
  gi|298675226|ref|YP_003726976.1| 190 LHSKIDDLTSKTNELFEKYDELNENLSTLK 219
                                       333333333333333333333333333332 PP

>> SIKE  SIKE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   3.1     0.082        16      66     102 ..      93     129 ..      68     173 .. 0.65
   2 ?   10.5   0.9    0.0022      0.43      12      57 ..     188     233 ..     184     260 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.082
                              SIKE  66 agiqqenrqireLqqENreLrasleehqsaLelImsK 102
                                       +++++ +++i+ +q+EN+eL+ +++   + +  ++s 
  gi|298675226|ref|YP_003726976.1|  93 SRMSKVDANISTVQRENQELKKTIDKIDQSVVELLSL 129
                                       3456677888888888888888888776655555555 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0022
                              SIKE  12 kkLverLkehdtaAdsLleqaqalnkkiesmkqyqeevkelneiak 57 
                                        kL +++++  +++++L e++  ln+++++ kq ++e+++  +i +
  gi|298675226|ref|YP_003726976.1| 188 NKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISDRVDILE 233
                                       6899****************************99999877665554 PP

>> USP8_interact  USP8 interacting
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   1.5     0.026       4.9       4      51 ..      79     126 ..      77     141 .. 0.84
   2 ?    1.7   0.1       1.1     2e+02      12      58 ..     186     232 ..     174     250 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.026
                     USP8_interact   4 elvqkqqqkiaelkkevaeqkqqlseqkrelellkeyiralrstnpvl 51 
                                       e+v++ +qki+++++++++   ++s+ +re + lk++i  + ++  +l
  gi|298675226|ref|YP_003726976.1|  79 EQVENNAQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVEL 126
                                       7899********************************999887665544 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 1.1
                     USP8_interact  12 kiaelkkevaeqkqqlseqkrelellkeyiralrstnpvlraladql 58 
                                        i++l++++++ +++ +e  ++ + l+e + +l++++ ++    d l
  gi|298675226|ref|YP_003726976.1| 186 GINKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISDRVDIL 232
                                       45666666666666666666666666666666665555554444444 PP

>> FTA4  Kinetochore complex Fta4 of Sim4 subunit, or CENP-50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3  12.3     0.042       8.1      44     184 ..      89     269 ..      66     293 .. 0.49

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.042
                              FTA4  44 kavddvLaklNhrlkqhnrrvyspqairhvaeQidklYlea............................edekleie 92 
                                       k v++ + k+ +++   +r+   +q  ++ + +id++ +e                             e       
  gi|298675226|ref|YP_003726976.1|  89 KTVESRMSKVDANISTVQRE---NQELKKTIDKIDQSVVELlslyeivsnqvnpfvgdneggseyierfE------- 155
                                       34444444444444333332...22222223333332222233334444444444444333322222221....... PP

                              FTA4  93 vnedltk.....................eelIkeLPesweveekeaeeepleallerYaelrarLielserrqqlqa 148
                                       +ne+  +                      + I++L  + +        +++++l e+Y+el ++L  l+++ ++  +
  gi|298675226|ref|YP_003726976.1| 156 KNEERINeignyatmlkndldalyqkfdTQGINKLHSKID-----DLTSKTNELFEKYDELNENLSTLKQSTDEISD 227
                                       2222222333333333334444444444444555444444.....3444568899********************** PP

                              FTA4 149 rlarlrklk..allepflgsedpqesvqenlvtrdge............l 184
                                       r++ l+k+   ++ ep        ++ q n++++d+e            +
  gi|298675226|ref|YP_003726976.1| 228 RVDILEKIDlsKTYEP--------SENQYNVIYQDEEesaenpsvilgsI 269
                                       ******9741133333........44455555555554444444444442 PP

>> HemX  HemX, putative uroporphyrinogen-III C-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   4.6     0.092        18      48      99 ..      75     126 ..      67     131 .. 0.71
   2 ?    5.5   0.3     0.045       8.6      38      97 ..     169     230 ..     145     241 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.092
                              HemX  48 eqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlskv 99 
                                       +++ +qve+++++ +++e+r+ + + ++++ ++e+++l+k ++++ q + ++
  gi|298675226|ref|YP_003726976.1|  75 QANNEQVENNAQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVEL 126
                                       4445566677788888888888888888888888888888888877777655 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.045
                              HemX  38 aelqqqlaaleqqlaq..veaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqls 97 
                                       + l+++l al q+ ++  +++++++ ++l+++ ++l ek ++l+++l++l+++ +e+++++ 
  gi|298675226|ref|YP_003726976.1| 169 TMLKNDLDALYQKFDTqgINKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISDRVD 230
                                       45566666666665555566666666666666666666666666666666666666666664 PP

>> DASH_Dad3  DASH complex subunit Dad3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.3       6.7   1.3e+03      11      29 ..     108     126 ..      79     139 .. 0.65
   2 ?    1.3   0.0       1.9   3.7e+02      12      34 ..     179     202 ..     168     205 .. 0.75
   3 ?    9.9   1.4    0.0041      0.77       5      32 ..     201     228 ..     197     253 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 6.7
                         DASH_Dad3  11 eYerLaenlktLaselkeL 29 
                                       e ++L+++++++++++ eL
  gi|298675226|ref|YP_003726976.1| 108 ENQELKKTIDKIDQSVVEL 126
                                       3445555555555555444 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 1.9
                         DASH_Dad3  12 YerLaen.lktLaselkeLasnst 34 
                                       Y++ +++ +++L s++++L+s+++
  gi|298675226|ref|YP_003726976.1| 179 YQKFDTQgINKLHSKIDDLTSKTN 202
                                       66665443899********99864 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0041
                         DASH_Dad3   5 eqevLdeYerLaenlktLaselkeLasn 32 
                                        +e+ ++Y +L+enl tL+++ +e++++
  gi|298675226|ref|YP_003726976.1| 201 TNELFEKYDELNENLSTLKQSTDEISDR 228
                                       578899******************9987 PP

>> UPF0449  Uncharacterised protein family UPF0449
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.8      0.26        49      44      87 ..      82     125 ..      63     138 .. 0.47
   2 ?    7.0   0.9     0.043       8.3      51      87 ..     188     224 ..     152     235 .. 0.54

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.26
                           UPF0449  44 kassseeedleaeveelYeqvrtylelnerLeeakeeLkqkcee 87 
                                       ++++++ +  e+ ++++   + t    n++L+++ +++ q + e
  gi|298675226|ref|YP_003726976.1|  82 ENNAQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVE 125
                                       11122333333334444444444444455555555555555555 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.043
                           UPF0449  51 edleaeveelYeqvrtylelnerLeeakeeLkqkcee 87 
                                       ++l++++++l  +++++ e  ++L+e+ ++Lkq ++e
  gi|298675226|ref|YP_003726976.1| 188 NKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDE 224
                                       3333334444444444444444444444444444444 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   1.8     0.054        10      38      85 ..      86     133 ..      70     147 .. 0.77
   2 ?    0.8   0.1       2.3   4.4e+02      49      82 ..     149     182 ..     131     185 .. 0.75
   3 ?    6.0   0.8     0.057        11      31      83 ..     179     230 ..     168     242 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.054
                           DUF4446  38 kdgksleellkekleeveelkeeseelekeieeleeklkkslqkvglv 85 
                                       ++ k++e+ +++  +++ ++++e++el+k+i+++++++ + l+ +++v
  gi|298675226|ref|YP_003726976.1|  86 QKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVELLSLYEIV 133
                                       366788888888888888899999999999999888887777666665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 2.3
                           DUF4446  49 ekleeveelkeeseelekeieeleeklkkslqkv 82 
                                       e++e+ e+ +e+ +e+ +  + l+++l++ +qk+
  gi|298675226|ref|YP_003726976.1| 149 EYIERFEKNEERINEIGNYATMLKNDLDALYQKF 182
                                       5677777777777777777777777777777775 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.057
                           DUF4446  31 ykklmkgkdgksleellkekleeveelkeeseelekeieeleeklkkslqkvg 83 
                                       y+k+ + +  ++l +++ + +++++el e+ +el++++++l+++ ++  ++v 
  gi|298675226|ref|YP_003726976.1| 179 YQKFDT-QGINKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISDRVD 230
                                       444433.3445555556666666666666666666666666665555555554 PP

>> Swi5  Swi5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   1.1     0.074        14       3      43 ..      86     127 ..      79     133 .. 0.73
   2 ?    5.5   0.9     0.098        19       8      42 ..     190     224 ..     183     241 .. 0.51

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.074
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHH CS
                              Swi5   3 aeikeleeqleelekelaelkeelkekk.dpeetvkrhIklL 43 
                                       ++ik++e++++++++++++++ e +e k + +++ ++ ++lL
  gi|298675226|ref|YP_003726976.1|  86 QKIKTVESRMSKVDANISTVQRENQELKkTIDKIDQSVVELL 127
                                       789999999999999999998887654435555555555555 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.098
                                       HHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHH CS
                              Swi5   8 leeqleelekelaelkeelkekkdpeetvkrhIkl 42 
                                       l+++++ l ++ +el e+++e ++   t+k+  + 
  gi|298675226|ref|YP_003726976.1| 190 LHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDE 224
                                       55555555555555555544444444444433332 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   2.8     0.011         2       3      40 ..      84     121 ..      78     133 .. 0.81
   2 ?    3.2   2.8      0.43        82      65      97 ..     188     220 ..     148     225 .. 0.61
   3 ?    4.8   1.0      0.14        27      67      98 ..     190     221 ..     183     240 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2   3 linkfqqlqqqlqqlaqqikqletqlkelelvleelel 40 
                                       ++ k +  ++++++++++i +++++ +el+++++ +++
  gi|298675226|ref|YP_003726976.1|  84 NAQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQ 121
                                       56677788888888888888888888888888888875 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.43
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  65 eeLeerketlekeiktlekqleklekeleelke 97 
                                       ++L  ++++l+ + ++l +++++l+++l+ lk+
  gi|298675226|ref|YP_003726976.1| 188 NKLHSKIDDLTSKTNELFEKYDELNENLSTLKQ 220
                                       344444444555555555555555555544444 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  67 Leerketlekeiktlekqleklekeleelkee 98 
                                       L  ++++l+ + ++l +++++l+++l+ lk++
  gi|298675226|ref|YP_003726976.1| 190 LHSKIDDLTSKTNELFEKYDELNENLSTLKQS 221
                                       33334444444444444444444444444433 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   1.1     0.093        18      30      59 ..      90     119 ..      78     130 .. 0.59
   2 ?    9.2   1.5    0.0069       1.3      28      62 ..     187     221 ..     184     223 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.093
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  30 eLerrvkaLekeNksLkseleelkkevekL 59 
                                         e+r+++ ++  ++ + e++elkk+++k 
  gi|298675226|ref|YP_003726976.1|  90 TVESRMSKVDANISTVQRENQELKKTIDKI 119
                                       455555555555555555555555555554 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0069
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  28 ieeLerrvkaLekeNksLkseleelkkevekLksk 62 
                                       i++L ++ + L+++  +L ++ +el+++ ++Lk+ 
  gi|298675226|ref|YP_003726976.1| 187 INKLHSKIDDLTSKTNELFEKYDELNENLSTLKQS 221
                                       789******************************86 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   4.9         1   1.9e+02      13      52 ..      85     124 ..      73     185 .. 0.70
   2 ?    9.5   2.8    0.0036       0.7       5      62 ..     183     240 ..     173     250 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 1
                           DUF4795  13 qeaieklqeelekleekvkelekrledkekklealkkqie 52 
                                        ++i+ ++ +++k++   + ++ + ++++k ++ + +++ 
  gi|298675226|ref|YP_003726976.1|  85 AQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVV 124
                                       3444444444444444444444444444444444444443 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0036
                           DUF4795   5 saellkklqeaieklqeelekleekvkelekrledkekklealkkqieelekvkadke 62 
                                       +++ ++kl+++i +l  + ++l ek  el+++l++++++++ + + ++ lek    k+
  gi|298675226|ref|YP_003726976.1| 183 DTQGINKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISDRVDILEKIDLSKT 240
                                       556799********************************************99766655 PP

>> THOC7  Tho complex subunit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   2.9    0.0026       0.5      64     105 ..      75     116 ..      70     122 .. 0.92
   2 ?    0.5   1.5       3.6   6.8e+02      82     103 ..     199     220 ..     148     247 .. 0.53
   3 ?   -0.6   0.0       7.6   1.4e+03      57      88 ..     341     371 ..     332     373 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0026
                             THOC7  64 kanerereryeaekeeieseieavreeieelkaqLeearatr 105
                                       +an +++e+ +++ +++es +++v ++i+  + +++e ++t 
  gi|298675226|ref|YP_003726976.1|  75 QANNEQVENNAQKIKTVESRMSKVDANISTVQRENQELKKTI 116
                                       89***********************************99985 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 3.6
                             THOC7  82 seieavreeieelkaqLeeara 103
                                       s++ ++ e+ +el++ L+  ++
  gi|298675226|ref|YP_003726976.1| 199 SKTNELFEKYDELNENLSTLKQ 220
                                       3333333333333333333333 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 7.6
                             THOC7  57 erlqllakanerereryeaekeeieseieavr 88 
                                       + l++++k+    +e+ +  +++i+se+++++
  gi|298675226|ref|YP_003726976.1| 341 KSLMFIEKMSGHRVENSQ-TSDNIDSELSKIK 371
                                       678999999999999966.7899999999887 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   5.8     0.069        13       3      51 ..      79     127 ..      72     164 .. 0.75
   2 ?    9.5   1.1    0.0049      0.93      51      92 ..     184     229 ..     148     237 .. 0.50

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.069
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II   3 elaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdan 51 
                                       e +++  +++k v++ + ++++n++ ++ + +e++++++++++ v ++ 
  gi|298675226|ref|YP_003726976.1|  79 EQVENNAQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVELL 127
                                       5566666777778888888888888888888888888888777776544 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0049
                                       XXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH.......HHHHH CS
                        Laminin_II  51 nkairdArrsvkkLeklapqLldklkelkqleeasss....lsdni 92 
                                       +++i+   +++ +L+ + ++L++k  el++  +  +     +sd +
  gi|298675226|ref|YP_003726976.1| 184 TQGINKLHSKIDDLTSKTNELFEKYDELNENLSTLKQstdeISDRV 229
                                       3334444444444444444444444444443333111122255554 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   1.8       2.7   5.1e+02       7      36 ..      79     108 ..      77     122 .. 0.81
   2 ?    4.0   0.1      0.36        68       9      25 ..     187     203 ..     184     206 .. 0.85
   3 ?    6.1   0.2     0.078        15       1      24 [.     207     230 ..     207     242 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 2.7
                               LPP   7 sqVsqLkskvdqlssdvnsakaaaqaakeE 36 
                                       +qV++  +k++ ++s ++++ a++ +++ E
  gi|298675226|ref|YP_003726976.1|  79 EQVENNAQKIKTVESRMSKVDANISTVQRE 108
                                       677788888999999999998888888877 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.36
                               LPP   9 VsqLkskvdqlssdvns 25 
                                       +++L sk+d l+s++n+
  gi|298675226|ref|YP_003726976.1| 187 INKLHSKIDDLTSKTNE 203
                                       899*********99986 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.078
                               LPP   1 kldeLssqVsqLkskvdqlssdvn 24 
                                       k deL++++s+Lk+  d++s+ v+
  gi|298675226|ref|YP_003726976.1| 207 KYDELNENLSTLKQSTDEISDRVD 230
                                       679*****************9886 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   4.6    0.0018      0.34     115     173 ..      78     136 ..      68     185 .. 0.67
   2 ?    3.3   1.3      0.33        64     111     169 ..     187     224 ..     148     260 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0018
                            DUF724 115 ekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleee 173
                                       ++++e+++++ + +e+ +++++ +i++++r+++ lk+  ++ d+++++l s  e ++++
  gi|298675226|ref|YP_003726976.1|  78 NEQVENNAQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVELLSLYEIVSNQ 136
                                       56677777777777777777777777777777777777777777766666555544443 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.33
                            DUF724 111 rkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaek 169
                                       ++kl++ki + +s+ ++l e+ del+++ ++l++  +                     +
  gi|298675226|ref|YP_003726976.1| 187 INKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTD---------------------E 224
                                       3344444444444444444444444444444444333.....................3 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   2.9     0.086        16      52     120 ..      78     118 ..      69     136 .. 0.47
   2 ?    6.8   2.3     0.035       6.7      43     104 ..     168     229 ..     148     236 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.086
                              ADIP  52 leqreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqr 120
                                        e                            q+e  ++++++v+++  +  +++ t ++ ++++k  + +
  gi|298675226|ref|YP_003726976.1|  78 NE----------------------------QVENNAQKIKTVESRMSKVDANISTVQRENQELKKTIDK 118
                                       33............................333333333333333333333333333333333333333 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.035
                              ADIP  43 sLlqardrdleqreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekkl 104
                                       + + ++d d+ +++  ++ i+kl + i+ l+sk++ l +++ +l   l+++++ + ++  ++
  gi|298675226|ref|YP_003726976.1| 168 ATMLKNDLDALYQKFDTQGINKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEISDRV 229
                                       55667777888888888888888888888888888888888888888888777776666555 PP

>> PI_PP_I  Phosphoinositide phosphatase insertion domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.5      0.16        30      18      64 ..      80     126 ..      72     139 .. 0.84
   2 ?    4.2   0.5      0.25        48      16      58 ..     184     226 ..     169     233 .. 0.76
   3 ?    0.1   0.0         5   9.6e+02      41      60 ..     354     373 ..     322     374 .] 0.73

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.16
                                       C--TT--SHHHHHHHHHHHHHHHHHHHHH-SSHHHHHHHHHCT-SS- CS
                           PI_PP_I  18 nleskeaslkklkqdlnqfllkWeeikktslsLeedLnkiannktpl 64 
                                       ++e +++++k++++ + +   + +++++++ +L++ + ki++    l
  gi|298675226|ref|YP_003726976.1|  80 QVENNAQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVEL 126
                                       57899999********************************9876665 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.25
                                       HHC--TT--SHHHHHHHHHHHHHHHHHHHHH-SSHHHHHHHHH CS
                           PI_PP_I  16 flnleskeaslkklkqdlnqfllkWeeikktslsLeedLnkia 58 
                                          +++ + ++ +l++++n+++ k++e++++ ++L++   +i+
  gi|298675226|ref|YP_003726976.1| 184 TQGINKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTDEIS 226
                                       3447777788889999999999999999999889988877776 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 5
                                       HHHHHH-SSHHHHHHHHHCT CS
                           PI_PP_I  41 eeikktslsLeedLnkiann 60 
                                        e  +ts ++ ++L+ki+n+
  gi|298675226|ref|YP_003726976.1| 354 VENSQTSDNIDSELSKIKNG 373
                                       455688999********986 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   2.1      0.02       3.8     662     703 ..      84     125 ..      67     155 .. 0.77
   2 ?    3.5   1.5     0.073        14     657     703 ..     186     231 ..     148     241 .. 0.49

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.02
                          Prominin 662 qqelvlplessvkklkksvkkldeensdlqesikkllaaver 703
                                       ++++++++es ++k+  ++ ++++en++l+++i+k+ ++v +
  gi|298675226|ref|YP_003726976.1|  84 NAQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQSVVE 125
                                       456677788899999999999999999999999999888865 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.073
                          Prominin 657 dlraiqqelvlplessvkklkksvkkldeensdlqesikkllaaver 703
                                        ++++++ +++ l+s++++l ++  +l+e+ s+l++s++++ ++v+ 
  gi|298675226|ref|YP_003726976.1| 186 GINKLHS-KIDDLTSKTNELFEKYDELNENLSTLKQSTDEISDRVDI 231
                                       2222222.223344444444444444444445555555555555544 PP

>> SOAR  STIM1 Orai1-activating region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   1.2      0.29        56      59      95 ..      85     121 ..      76     126 .. 0.82
   2 ?    1.0   0.1       2.1     4e+02      68      81 ..     207     220 ..     180     238 .. 0.50
   3 ?    3.2   0.1      0.45        85      52      74 ..     350     372 ..     346     374 .] 0.87

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.29
                              SOAR  59 ssslddvdkkileakqaleevtkelkerqeRWqqiek 95 
                                        +++  v++++ ++ ++++ v++e +e ++   +i++
  gi|298675226|ref|YP_003726976.1|  85 AQKIKTVESRMSKVDANISTVQRENQELKKTIDKIDQ 121
                                       5678889999999999999999999998888888876 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 2.1
                              SOAR  68 kileakqaleevtk 81 
                                       k  e+ ++l+ +++
  gi|298675226|ref|YP_003726976.1| 207 KYDELNENLSTLKQ 220
                                       22233333333333 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.45
                              SOAR  52 gslrlahssslddvdkkileakq 74 
                                       +  r+ +s+++d++d+++ ++k+
  gi|298675226|ref|YP_003726976.1| 350 SGHRVENSQTSDNIDSELSKIKN 372
                                       666899*************9997 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   7.4      0.29        56      44     106 ..      78     119 ..      71     177 .. 0.51
   2 ?    2.7   1.7      0.84   1.6e+02      80     106 ..     185     211 ..     136     223 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.29
                           DUF4200  44 eedllkfdkflkendakraralkkaeeerklkkekeaeikklkaeietlkseiekleekleey 106
                                       +                     +++e+ ++++k  e+ + k  a+i+t++ e+++l++++++ 
  gi|298675226|ref|YP_003726976.1|  78 N---------------------EQVENNAQKIKTVESRMSKVDANISTVQRENQELKKTIDKI 119
                                       2.....................33333333344444444444444444443333333333332 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.84
                           DUF4200  80 aeikklkaeietlkseiekleekleey 106
                                       + i+kl+++i++l s+ ++l ek++e+
  gi|298675226|ref|YP_003726976.1| 185 QGINKLHSKIDDLTSKTNELFEKYDEL 211
                                       345555555555555555555555444 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.3       2.5   4.8e+02      45      65 ..      77      97 ..      72     106 .. 0.62
   2 ?    3.2   1.3      0.47        89      11      37 ..      99     125 ..      89     128 .. 0.76
   3 ?    8.5   2.3     0.011         2      35      71 ..     187     223 ..     180     226 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 2.5
                        TMF_DNA_bd 45 lekeikelkkkleklekelee 65
                                      +++++++  +k++++e+ +++
  gi|298675226|ref|YP_003726976.1| 77 NNEQVENNAQKIKTVESRMSK 97
                                      556666666666666665544 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.47
                        TMF_DNA_bd  11 DeqIaqLmeEGekLskkelklnntikk 37 
                                       D+ I  ++ E ++L+k+ +k  +++ +
  gi|298675226|ref|YP_003726976.1|  99 DANISTVQRENQELKKTIDKIDQSVVE 125
                                       888999999999999999888777655 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.011
                        TMF_DNA_bd  35 ikkLrkknkelekeikelkkkleklekeleeleerlk 71 
                                       i kL +k+ +l+++ +el +k ++l+++l++l+++ +
  gi|298675226|ref|YP_003726976.1| 187 INKLHSKIDDLTSKTNELFEKYDELNENLSTLKQSTD 223
                                       7889999999999999999999999999999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1933  (0.107814); expected 358.6 (0.02)
Passed bias filter:                      866  (0.0483016); expected 358.6 (0.02)
Passed Vit filter:                       179  (0.00998383); expected 17.9 (0.001)
Passed Fwd filter:                       109  (0.00607954); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              94  [number of targets reported over threshold]
# CPU time: 1.18u 0.35s 00:00:01.52 Elapsed: 00:00:00.58
# Mc/sec: 1926.73
//
Query:       gi|298675227|ref|YP_003726977.1|  [L=352]
Description: response regulator receiver protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-27   96.5   1.3      1e-27   96.5   1.3    2.0  3  Response_reg  Response regulator receiver domain
      0.004   16.9   0.4      0.013   15.2   0.1    2.0  2  DUF835        Protein of unknown function (DUF835)


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1      0.85   7.6e+03       1      12 [.     125     136 ..     125     156 .. 0.65
   2 ?   -2.9   0.1      0.86   7.7e+03      96     107 ..     216     227 ..     215     228 .. 0.86
   3 !   96.5   1.3   1.2e-31     1e-27       1     112 []     229     341 ..     229     341 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.85
                                       EEEESSSHHHHH CS
                      Response_reg   1 vlivdDdplvre 12 
                                       +l++dD  ++ +
  gi|298675227|ref|YP_003726977.1| 125 ILVIDDMNILTK 136
                                       677888666544 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.86
                                       EEEESSG-HHHH CS
                      Response_reg  96 dflsKpfdpeeL 107
                                       ++++K++++++L
  gi|298675227|ref|YP_003726977.1| 216 EYIQKKIKRDRL 227
                                       79******9998 PP

  == domain 3  score: 96.5 bits;  conditional E-value: 1.2e-31
                                       EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCT..TTSEEE CS
                      Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireed..pelpvi 75 
                                       +livdD+p++ el++  l +e y +  +a +g++a++++ +e +dlillDi+mp+mdG+e+++e+++++  +++ +i
  gi|298675227|ref|YP_003726977.1| 229 ILIVDDEPDIPELIKLSLSNEPY-DFIVAYSGEQAVDMTLQELPDLILLDIMMPDMDGYEVVEELNKDKstRDIAII 304
                                       8**********************.9999*************************************88886788**** PP

                                       EEESSTSHHHHHHHHHCTESEEEESSG-HHHHHHHHH CS
                      Response_reg  76 iltahseeedavealkagaddflsKpfdpeeLlkale 112
                                       +++a++  ed+ +++++g+dd++sKpfd++eL ++++
  gi|298675227|ref|YP_003726977.1| 305 MVSAKTRVEDKLKGMELGIDDYISKPFDERELNARIK 341
                                       ********************************99985 PP

>> DUF835  Protein of unknown function (DUF835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0         1   9.3e+03      39      54 ..      47      62 ..      42      65 .. 0.69
   2 !   15.2   0.1   1.5e-06     0.013      59     136 .]     105     181 ..      80     181 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1
                            DUF835 39 ienvkviwltkveeen 54
                                       ++ +v+wl+ ++  n
  gi|298675227|ref|YP_003726977.1| 47 DPEQTVVWLSLKKPRN 62
                                      5567899999777555 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.5e-06
                            DUF835  59 tnlekltetivkflkeaekgvvliDgleyLvlengFesvlkflltlkDavllkngtlilvidkealeekelalLkre 135
                                       t+ +k+  +i+k +++    + +iD +  L ++ + + v  f++ +  +v ++ngt++  + ke+l+ +  +l+k+ 
  gi|298675227|ref|YP_003726977.1| 105 TDYTKMGSHISKLFNDYPGAILVIDDMNIL-TKDSLQVVENFIKFVEKTVTNSNGTIVTLLGKEVLSSENEGLIKSF 180
                                       677899999*******9999*******977.6999***************************************986 PP

                            DUF835 136 f 136
                                       f
  gi|298675227|ref|YP_003726977.1| 181 F 181
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2536.59
//
Query:       gi|298675228|ref|YP_003726978.1|  [L=922]
Description: alanyl-tRNA synthetase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   4.4e-138  461.2   0.0   5.7e-138  460.8   0.0    1.1  1  tRNA-synt_2c  tRNA synthetases class II (A)
    2.6e-26   92.7   2.8    2.6e-26   92.7   2.8    2.0  2  DHHA1         DHHA1 domain
    3.2e-12   46.3   0.2    8.7e-12   44.9   0.2    1.8  1  tRNA_SAD      Threonyl and Alanyl tRNA synthetase second addi
  ------ inclusion threshold ------
       0.44   10.8   6.4        9.8    6.4   0.3    3.7  3  DUF4047       Domain of unknown function (DUF4047)
       0.63   10.0   7.4        3.1    7.7   1.3    2.8  2  RRF           Ribosome recycling factor
        1.4    9.5   4.9          6    7.4   0.5    2.8  2  ZapB          Cell division protein ZapB
        2.5    8.4   4.4        4.3    7.6   0.6    3.0  3  WXG100        Proteins of 100 residues with WXG


Domain annotation for each model (and alignments):
>> tRNA-synt_2c  tRNA synthetases class II (A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  460.8   0.0  2.2e-141  5.7e-138       1     552 []      62     603 ..      62     603 .. 0.95

  Alignments for each domain:
  == domain 1  score: 460.8 bits;  conditional E-value: 2.2e-141
                                       HHHHHHHHHHHCTT-EEE----SS-SSSTTCSS--SGGGGGHHHHTTSSCGGSSSEEEEEEEEE-EETTEEGGGGTT CS
                      tRNA-synt_2c   1 eirekFldfFekkgHtvvksssvvpendptllfvnAgmaqfkpiflgkeakpklkravnsQkciRagGkhnDlenVG 77 
                                       e+re+Fl+fFek++H++v++++v + +++++ +++A++a+f+p++++++  p+++++++sQ+c+R++    Dl+ VG
  gi|298675228|ref|YP_003726978.1|  62 EMREQFLKFFEKRDHARVNRYPVTAVWREDIHLTIASIANFQPFVTSGQVPPPANPLTISQPCVRLS----DLDAVG 134
                                       89*****************************************************************....****** PP

                                       TSSS--SEEEEEEEEESS.....SS-HHHHHHHHHHHHHTTTT--GGGEEEEEETTEH..HHHHHHHHTTTTEGGGE CS
                      tRNA-synt_2c  78 ktarHhTfFeMlGnfsfg.....dYfkeeaiefawelltkelgldkerlyvtvfeedd..eaveiweklvgvpeeri 147
                                       + +rH+T+FeM+++++f+      Y+kee+++++ e+l+ +lg+d+  ++++++++++  +a+++ e lvg+ e ++
  gi|298675228|ref|YP_003726978.1| 135 RSGRHLTLFEMMAHHAFNttdneVYWKEETVALCDEFLN-SLGVDPLAVTYKEEPWAGggNAGPCLETLVGGLEVAT 210
                                       **********************99**************9.*****************999***************** PP

                                       EEE-HHHHEEESSSS........EEEEEEEEEEEECETTSHHCHCCCCTTCTCCHEEEEEEEEEEEEEEST....TS CS
                      tRNA-synt_2c 148 lrfgekdnfwemgdt........gpcgpcseiyydrgeeigkrkaaseveadddrvleiwnlvfmqfnree....dg 212
                                       l+f   +n ++  d         +++++++++++++g e+ +++++++++++d+++  i+n +++ ++ e+    ++
  gi|298675228|ref|YP_003726978.1| 211 LVF---MNLKQSKDGdiiidgepYEKMNNYIVDTGYGLERLVWASKGTPTIYDAIFPSIVNELMEYAGLEHeledSE 284
                                       ***...88888777777899888*****************************************9998887666466 PP

                                       HEEEEEEEEEEEEEEHHHHHHHHTTHSSGGGSCCTHHHHHHHHHHHT--TCSTCCHHHHHHHHHHHHHHHHHHHHTT CS
                      tRNA-synt_2c 213 tlkpLpkksidtGmglerlvavLqevrsnydtdlfvpvieaieeisgatyedkdetdealrviaDHvralafaladG 289
                                         + L ++++ +G+++    a L+e+r++++++++++++++++ + +          e++++iaDH+r+l+f+l+dG
  gi|298675228|ref|YP_003726978.1| 285 YSELLSQNARFAGLMDVSEKANLKELRKQVAESIGTSIEKLTSIMEP---------VEKVYAIADHTRCLTFMLGDG 352
                                       677889999***********************************999.........689****************** PP

                                       --SSSSHHHHHHHHHHHHHHHHHHHTT-SSTHHHHHHHHHHHHHTTTGCCHHCCHHHHHHHHHHHHHHHHCCHHHHH CS
                      tRNA-synt_2c 290 vvpsnegrgYvlRrllRravrhakkLglkekflaklvavvvevlgdvypelkekeekveeiieeEeerFakTlerGl 366
                                       vvpsn+++gY++R++ Rr+ r++++Lg++ + +++++ ++++ l+  ype++++ + +e+ii++Ee +F++Tl+rG 
  gi|298675228|ref|YP_003726978.1| 353 VVPSNVKAGYLARLVFRRTTRMMRELGMDIS-ISDIIRMHIDKLQ-EYPEFEDRFDLIEDIIQHEEDKFEETLNRGI 427
                                       *******************************.************9.7****************************** PP

                                       HHHHHHHHHCCC.CSEEXHHHHHHHHHCHXXXHHHHHHHHHCTTXEEXHHHHHHHHHHHHHHHCCHHSXSSXXXXXX CS
                      tRNA-synt_2c 367 klleelikklkk.kkelsgedafkLydtyGfPvdltkeiaeekglkvdiegfekameeqrerskkekkekklikkdv 442
                                       k++++++k+ kk ++++++++++++yd++G+P+++ +++a + g++v+ ++++++ +++r++  kek++ +      
  gi|298675228|ref|YP_003726978.1| 428 KMIQKMAKQYKKqNEKIPLDKLIEMYDSHGIPPEIAEDVASDMGVEVELPDNFYSIVAERHSMAKEKEKPS--FPFE 502
                                       *********999899**********************************************9976666665..4556 PP

                                       XXTTSHCHHCCTSTTTXXXXXXTSXXXXXXSEEEEEEEEEETTEEEESEEXXXXSSSSCSXXXEEEEESSEEEEESE CS
                      tRNA-synt_2c 443 ealkelkkteeflgyeeleaeakvlallkdkefveeveegeevgvvLdrTpfYaesGGqigDeGliekegaefrvkd 519
                                       e +++l++t+  l+y+e           ++ ef++ v  + ++++vLdrT fY+e+GGq +D+G+i +++++++v+d
  gi|298675228|ref|YP_003726978.1| 503 ERISKLPQTKL-LFYNE----------PNRMEFEAVVLDVFDNYIVLDRTLFYPEGGGQPADKGVIIADDETAKVVD 568
                                       67778888777.9****..........7889********************************************** PP

                                       EEEETTEEEEEXSS...XSXXXTTSEEEEEEXHHH CS
                      tRNA-synt_2c 520 vqkakgvvlhkgkl..eegklkvgdkvkaevdeer 552
                                       v+++k+vvlh+++   +e +l++gd v++++d+er
  gi|298675228|ref|YP_003726978.1| 569 VKNIKNVVLHEIDSvgNEISLRKGDLVTCKIDSER 603
                                       ***********987556789************986 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       4.3   1.1e+04      85     107 ..     297     318 ..     290     322 .. 0.61
   2 !   92.7   2.8     1e-29   2.6e-26       2     132 ..     781     912 ..     780     918 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4.3
                                       EEEEESSHSS-HHHHHHHHHHHT CS
                             DHHA1  85 vsarskkdgvdagelakeaaakl 107
                                       + + +++ + ++ el k++a+ +
  gi|298675228|ref|YP_003726978.1| 297 GLMDVSE-KANLKELRKQVAESI 318
                                       5555666.666666666666655 PP

  == domain 2  score: 92.7 bits;  conditional E-value: 1e-29
                                       HHHCHHHHHHHHHHHCHHHHHHHHHHHHHHHTCEEECTCEEEEEECHCCHHHHHHHHHHHHHHTHGBTTCEEEEEEE CS
                             DHHA1   2 eslneerkelekeleelkealaklkaeellekaeevkgvkvlvaevgeewdagalgiaadklksklkkpvivfvake 78 
                                       e++ ee+k+ +ke e+lke+la++  +++ ++a + +g  +++++v ++ d + l+ +a++l +  ++ +i++++++
  gi|298675228|ref|YP_003726978.1| 781 ERFFEEWKQFKKENEKLKEELADIRVQQMMQDAITHDGNHIIAQKV-PDSDSKELQKMAGELVK--NNSTIALLISD 854
                                       6789******************************999*********.*****************..99999999999 PP

                                       ECTEEEEEEEESSH....SS-HHHHHHHHHHHTTCCEEEE.TCEEEEEEEHCHHHHHHH CS
                             DHHA1  79 egdkvkvsarskkd....gvdagelakeaaaklgggGGGH.dlAaGagipaekleeale 132
                                        +  vk+ a+++kd    g+++g+++ke+++++gggGGG+ d+A+G+g++ ++++eal+
  gi|298675228|ref|YP_003726978.1| 855 YN-GVKIAAAASKDavnnGINVGDVVKEISSIVGGGGGGRpDMAQGGGTETSRIDEALN 912
                                       88.9********99*******************************************97 PP

>> tRNA_SAD  Threonyl and Alanyl tRNA synthetase second additional domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   0.2   3.4e-15   8.7e-12       1      44 []     702     744 ..     702     744 .. 0.96

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 3.4e-15
                                       EEEEEETT.EEEEESS---SBGGGC-SEEEECCECCCTCEEEEE CS
                          tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIgafkilseesiakglrRIy 44 
                                       +r+ ++Gd ++e+CgGtH++ Tg++g +kil+ e+i++g+ R++
  gi|298675228|ref|YP_003726978.1| 702 LRILKVGD-DIEACGGTHCSYTGYVGPIKILKSERIQDGVERLE 744
                                       6999***9.*********************************86 PP

>> DUF4047  Domain of unknown function (DUF4047)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.011        28      23      95 ..     261     337 ..     247     347 .. 0.76
   2 ?    6.4   0.3    0.0038       9.8      40      80 ..     409     448 ..     377     457 .. 0.78
   3 ?   -1.0   0.3      0.73   1.9e+03      26      64 ..     777     811 ..     771     826 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.011
                           DUF4047  23 iifPktvdtlveqakqhkelilheyeemksk.lkvdsveeieqal...svwkqgrekikaerealqkvyteieepyn 95 
                                        ifP  v++l+e a   +el   ey e+ s+  +   + ++  ++   ++ kq  e i +  e l  + + +e+ y 
  gi|298675228|ref|YP_003726978.1| 261 AIFPSIVNELMEYAGLEHELEDSEYSELLSQnARFAGLMDVSEKAnlkELRKQVAESIGTSIEKLTSIMEPVEKVYA 337
                                       48***********************9986541555666555555411135677789999999999999999999885 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0038
                           DUF4047  40 kelilheyeemksklkvdsveeieqalsvwkqgrekikaer 80 
                                       +++i+he ++ +  l+ + ++ i++ ++++k++ eki  ++
  gi|298675228|ref|YP_003726978.1| 409 EDIIQHEEDKFEETLN-RGIKMIQKMAKQYKKQNEKIPLDK 448
                                       6789999998887665.89*****************97665 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.73
                           DUF4047  26 Pktvdtlveqakqhkelilheyeemksklkvdsveeieq 64 
                                       P t++++ e+ kq k+    e e++k +l    v+++ q
  gi|298675228|ref|YP_003726978.1| 777 PNTIERFFEEWKQFKK----ENEKLKEELADIRVQQMMQ 811
                                       7888888888888775....4555555555544554444 PP

>> RRF  Ribosome recycling factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   1.3    0.0012       3.1     107     159 ..     382     439 ..     374     440 .. 0.85
   2 ?    4.6   0.5     0.011        29      84     145 ..     777     840 ..     743     849 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHHHHHHHHHH.C....S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               RRF 107 vairniRrdankklkklek.k....iseDdvkkaekeiqkltdkyikeidellkakek 159
                                       ++i +i r + +kl++  + +    + eD +++ e+++++  ++ ik i+++ k+ +k
  gi|298675228|ref|YP_003726978.1| 382 ISISDIIRMHIDKLQEYPEfEdrfdLIEDIIQHEEDKFEETLNRGIKMIQKMAKQYKK 439
                                       577778888888888666655678899***************************9988 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.011
                                       -SSSHHHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHC.S-HHHHHHHHHHHHHHHHH CS
                               RRF  84 pplTeErrkelvkeakkaaekakvairniRrd..ankklkklekk.iseDdvkkaekeiqkltdk 145
                                       p  T Er  e  k+ kk+ ek k+++ +iR +  +++++    ++ i++    +  ke+qk+  +
  gi|298675228|ref|YP_003726978.1| 777 P-NTIERFFEEWKQFKKENEKLKEELADIRVQqmMQDAITHDGNHiIAQKVPDSDSKELQKMAGE 840
                                       3.4889999999****************9955113444433333344444444455555555544 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.4     0.059   1.5e+02      32      69 ..     283     325 ..     270     327 .. 0.76
   2 ?    7.4   0.5    0.0023         6      18      45 ..     778     805 ..     774     840 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.059
                              ZapB  32 eeneelkeenrele.....eeneqlkeereawqerlkkLLgkl 69 
                                        e +el ++n++       +e  +lke r+++ e + + ++kl
  gi|298675228|ref|YP_003726978.1| 283 SEYSELLSQNARFAglmdvSEKANLKELRKQVAESIGTSIEKL 325
                                       345677777777779999999**************99999998 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0023
                              ZapB  18 dtitlLqmeieeLkeeneelkeenrele 45 
                                       +ti++  +e ++ k+ene+lkee + ++
  gi|298675228|ref|YP_003726978.1| 778 NTIERFFEEWKQFKKENEKLKEELADIR 805
                                       4666666777777777777777766655 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       1.5   3.7e+03       8      21 ..     429     442 ..     416     444 .. 0.59
   2 ?   -0.2   0.0      0.46   1.2e+03      58      74 ..     753     769 ..     742     776 .. 0.62
   3 ?    7.6   0.6    0.0017       4.3      47      71 ..     781     805 ..     778     813 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHHHHH CS
                            WXG100   8 elrqaaarfqkqae 21 
                                       +++++a++++kq+e
  gi|298675228|ref|YP_003726978.1| 429 MIQKMAKQYKKQNE 442
                                       45566666666655 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.46
                                       HHHHHHHHHHHHHHHHH CS
                            WXG100  58 qaaqklvdaLeeiseal 74 
                                       +++q++ d L++ s al
  gi|298675228|ref|YP_003726978.1| 753 KSMQEIEDTLQDSSGAL 769
                                       34555555555555544 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0017
                                       HHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  47 dafqaefeewkqaaqklvdaLeeis 71 
                                       ++f++e++++k++ +kl+++L++i+
  gi|298675228|ref|YP_003726978.1| 781 ERFFEEWKQFKKENEKLKEELADIR 805
                                       68*********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (922 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1274  (0.0710581); expected 358.6 (0.02)
Passed bias filter:                      811  (0.045234); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.73u 0.23s 00:00:00.96 Elapsed: 00:00:00.43
# Mc/sec: 6390.24
//
Query:       gi|298675229|ref|YP_003726979.1|  [L=247]
Description: hypothetical protein Metev_1323 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0046   15.9   0.2     0.0077   15.2   0.2    1.3  1  Not1            CCR4-Not complex component, Not1
  ------ inclusion threshold ------
       0.07   13.2   0.3       0.15   12.1   0.1    1.6  2  Glyco_hydro_4C  Family 4 glycosyl hydrolase C-terminal domain


Domain annotation for each model (and alignments):
>> Not1  CCR4-Not complex component, Not1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.2   8.6e-07    0.0077      45      86 ..     145     186 ..     143     196 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.6e-07
                              Not1  45 LisHRlflpklLelkdqkgwealakLlvdllkfleellkkae 86 
                                       Li+HR fl +lLe ++   +e++++Ll ++++++eel++++e
  gi|298675229|ref|YP_003726979.1| 145 LIEHRDFLVRLLENPNLLEHETFTELLRAVFHMTEELISRTE 186
                                       9***********************************998655 PP

>> Glyco_hydro_4C  Family 4 glycosyl hydrolase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.18   1.7e+03      53      90 ..      81     119 ..      30     175 .. 0.60
   2 ?   12.1   0.1   1.7e-05      0.15      24      70 ..     178     227 ..     146     243 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.18
                                       HSSEEECGGHHCTTSS....HCHHHHSHHHHHHHHHHHHHH CS
                    Glyco_hydro_4C  53 lgllpteysrhyaEYvp...ylkreapeliekektraevvk 90 
                                       +  + t  + +++++ p    +k+  +  i ke+t   ++k
  gi|298675229|ref|YP_003726979.1|  81 FSEVGTRLLTYFSDWDPnldDIKS--NLVITKEWTDSDFMK 119
                                       444445555666666664442222..333333333333333 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 1.7e-05
                                       HHHHHHHHHHHHHCTGGGTSHHHHHHHHHHSSEEECGGHHCTTSS.....H CS
                    Glyco_hydro_4C  24 lrelveedewleeiaekkaervridllrrlgllpteysrhyaEYvp....y 70 
                                        +el+++ e l++  e++++  rid+ r +g l+ e++ ++ EY++    y
  gi|298675229|ref|YP_003726979.1| 178 TEELISRTEDLDNLPESDLDHLRIDIERVYGKLVVEWLDYM-EYMKdnypY 227
                                       223333345566666666999********************.*99877662 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       918  (0.051202); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1652.32
//
Query:       gi|298675230|ref|YP_003726980.1|  [L=372]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-26   93.1   2.1    1.4e-26   93.1   2.1    1.8  2  OrfB_IS605      Probable transposase
    4.8e-24   84.1   0.4    1.1e-23   83.0   0.4    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    1.1e-20   72.8   1.7    2.6e-20   71.6   1.7    1.7  1  HTH_OrfB_IS605  Helix-turn-helix domain
     0.0083   16.3   0.3      0.019   15.1   0.3    1.6  1  zf-piccolo      Piccolo Zn-finger
  ------ inclusion threshold ------
      0.041   14.1   7.8       0.28   11.4   3.0    2.4  2  MapZ_EC1        MapZ extracellular domain 1
      0.084   13.1   2.2       0.48   10.6   0.2    2.5  2  DDE_Tnp_IS240   DDE domain
      0.086   12.6   7.7       0.26   11.1   2.8    2.4  2  Phage_GP20      Phage minor structural protein GP20
       0.22   11.5   0.7       0.66   10.0   0.1    2.1  3  HypA            Hydrogenase/urease nickel incorporation, meta
       0.33   11.1   1.6        1.7    8.8   1.6    2.1  1  zf-UDP          Zinc-binding RING-finger
        1.7    9.1   6.6        6.1    7.4   3.0    2.5  2  ZapB            Cell division protein ZapB
        2.6    7.9   6.9         20    5.0   0.2    3.0  2  DivIC           Septum formation initiator


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       5.4   8.8e+03      41      54 ..      54      68 ..      41      74 .. 0.59
   2 !   93.1   2.1   8.5e-30   1.4e-26      10     117 ..     172     276 ..     159     278 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 5.4
                        OrfB_IS605 41 ykg.rrlksdykyla 54
                                      +k  r lk dy++l+
  gi|298675230|ref|YP_003726980.1| 54 NKQiRALKDDYEWLK 68
                                      333255566666654 PP

  == domain 2  score: 93.1 bits;  conditional E-value: 8.5e-30
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsr 86 
                                       +++  + +++g+D+Gi+++a++++++   ++ ++r lk+  ++l+  +++l++k+k+s+nykk + ++a++h+k+++
  gi|298675230|ref|YP_003726980.1| 172 KQTFYEVNTVGVDVGIKDFAVTSDGE---KIDNPRYLKNSIERLKVLQKRLSRKKKGSNNYKKLKHQIAKYHEKIAN 245
                                       45555789******************...************************************************ PP

                        OrfB_IS605  87 rrkhllhklathliktlkevgvetLnvgnmk 117
                                       +r +++hkl+++li ++++v++e Lnv+++ 
  gi|298675230|ref|YP_003726980.1| 246 QREDFQHKLSNKLISENQAVALECLNVKGLL 276
                                       ****************************986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.0   0.4   6.5e-27   1.1e-23       1      68 [.     290     359 ..     290     360 .. 0.98

  Alignments for each domain:
  == domain 1  score: 83.0 bits;  conditional E-value: 6.5e-27
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpay.TSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       ++++ ++leyka++yG++++++ ++  +Sk C++Cg+ +++ +l++r+++Cp+C++e+drD+nA++Ni k
  gi|298675230|ref|YP_003726980.1| 290 WSSFVQKLEYKAEWYGKNIIKIGRFDpSSKICHVCGYYHQDlELKDREWECPDCKTEHDRDINASVNIKK 359
                                       99******************************************************************87 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.6   1.7   1.6e-23   2.6e-20       1      47 []       1      46 [.       1      46 [. 0.98

  Alignments for each domain:
  == domain 1  score: 71.6 bits;  conditional E-value: 1.6e-23
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeegk 47
                                      M lkaykyr yP+++Q+e++a+++G++Rf+YN+aL+ +++ ye+ gk
  gi|298675230|ref|YP_003726980.1|  1 M-LKAYKYRMYPNQTQQELIAKHIGACRFIYNWALENKIKSYEQDGK 46
                                      8.******************************************997 PP

>> zf-piccolo  Piccolo Zn-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.3   1.2e-05     0.019      28      56 ..     318     346 ..     314     348 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.2e-05
                        zf-piccolo  28 kqvCnlCGFnptphltekkeWlclnCQtq 56 
                                       +++C +CG+  ++   + +eW c  C t+
  gi|298675230|ref|YP_003726980.1| 318 SKICHVCGYYHQDLELKDREWECPDCKTE 346
                                       79***********999**********985 PP

>> MapZ_EC1  MapZ extracellular domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2     0.017        28      48      84 ..      34      73 ..      27      92 .. 0.79
   2 ?   11.4   3.0   0.00017      0.28      37      78 ..     205     246 ..     165     268 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.017
                          MapZ_EC1 48 LekkLeklk.gskeYk..klkkkldslkkqisaieavNsq 84
                                      Le+k++ ++ + k  +  +l+k++ +lk+ ++ ++++Nsq
  gi|298675230|ref|YP_003726980.1| 34 LENKIKSYEqDGKAVSrfELNKQIRALKDDYEWLKEINSQ 73
                                      66666666643333322279******************98 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00017
                          MapZ_EC1  37 lknsefaklseLekkLeklk.gskeYkklkkkldslkkqisai 78 
                                       lkns ++ l+ L+k L   k gs++Ykklk+++++  ++i+ +
  gi|298675230|ref|YP_003726980.1| 205 LKNS-IERLKVLQKRLSRKKkGSNNYKKLKHQIAKYHEKIANQ 246
                                       4443.688999*****98777*****************99865 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.16   2.6e+02      74     131 ..      57     111 ..      34     117 .. 0.70
   2 ?   10.6   0.2   0.00029      0.48      88     131 ..     197     241 ..     161     250 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.16
                     DDE_Tnp_IS240  74 lkelkregelfdevshvqvkylnnriEsdhrtlKkrlrptrgfkslksaaktlagfea 131
                                       ++ lk++ e+++e++    +     +E+   ++ k++r ++gf ++ks ++ ++ f++
  gi|298675230|ref|YP_003726980.1|  57 IRALKDDYEWLKEINSQSLQGATLNLEN---AFTKFFREKSGFSKFKSKKNPVQSFSV 111
                                       4555555555555555554444444444...456779999999999999998888876 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00029
                     DDE_Tnp_IS240  88 shvqvk.ylnnriEsdhrtlKkrlrptrgfkslksaaktlagfea 131
                                       ++++ + yl+n iE+     K++ r+++g ++ k++++ +a +  
  gi|298675230|ref|YP_003726980.1| 197 EKIDNPrYLKNSIERLKVLQKRLSRKKKGSNNYKKLKHQIAKYHE 241
                                       5556655*********************************99864 PP

>> Phage_GP20  Phage minor structural protein GP20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.2     0.032        52      54      89 ..      34      70 ..      28      86 .. 0.57
   2 ?   11.1   2.8   0.00016      0.26      32      90 ..     210     268 ..     197     275 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.032
                        Phage_GP20 54 Lqkqieelqaknkkaka.eyeakiadlkldnaielaL 89
                                      L+++i++++++ k+ +  e +++i++lk d+   +++
  gi|298675230|ref|YP_003726980.1| 34 LENKIKSYEQDGKAVSRfELNKQIRALKDDYEWLKEI 70
                                      5555555555555543325555555555555444333 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00016
                        Phage_GP20  32 eqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeyeakiadlkldnaielaLk 90 
                                       e+lk  +k L+  kk +++ ++L+ qi+++ +k++++ ++ + k+++  +++    aL+
  gi|298675230|ref|YP_003726980.1| 210 ERLKVLQKRLSRKKKGSNNYKKLKHQIAKYHEKIANQREDFQHKLSNKLISENQAVALE 268
                                       6788889999999********************************99877766555555 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       4.4   7.1e+03      43      66 ..      59      84 ..      54      90 .. 0.66
   2 ?   -4.0   0.0       9.2   1.5e+04      19      34 ..     171     186 ..     166     187 .. 0.76
   3 ?   10.0   0.1   0.00041      0.66      68      96 ..     316     347 ..     291     361 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4.4
                                      HHHHHHHHHH..CC.TTTT-EEEEEE CS
                              HypA 43 aLefafella..egtvlegaeLeiee 66
                                      aL+  +e+l+  +++ l+ga+L++e+
  gi|298675230|ref|YP_003726980.1| 59 ALKDDYEWLKeiNSQSLQGATLNLEN 84
                                      56666777762234558889888876 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 9.2
                                       CCTT..EEEEEEEEEE CS
                              HypA  19 keaaarkvtkvkvevG 34 
                                       +++++ +v++v v+vG
  gi|298675230|ref|YP_003726980.1| 171 QKQTFYEVNTVGVDVG 186
                                       4567789999999998 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00041
                                       --EEEETTTS-EEE.CHH.H.HHS-TTTSSS- CS
                              HypA  68 pvkvrCreCgkefe.lee.k.alrCpkCgsad 96 
                                       p +  C++Cg+  + le  + + +Cp+C++++
  gi|298675230|ref|YP_003726980.1| 316 PSSKICHVCGYYHQdLELkDrEWECPDCKTEH 347
                                       56678*****8887444333588*****9874 PP

>> zf-UDP  Zinc-binding RING-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.6    0.0011       1.7      36      63 ..     319     350 ..     314     359 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0011
                            zf-UDP  36 pvcrpc....yeyerkdgnqsCPqCktrykrl 63 
                                        +c+ c     + e kd +  CP Ckt+  r 
  gi|298675230|ref|YP_003726980.1| 319 KICHVCgyyhQDLELKDREWECPDCKTEHDRD 350
                                       56666622112457789999*******99984 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.12     2e+02      19      37 ..      56      74 ..      46     102 .. 0.68
   2 ?    7.4   3.0    0.0037       6.1      15      64 ..     207     256 ..     202     261 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.12
                              ZapB 19 titlLqmeieeLkeeneel 37
                                      +i++L+  +e Lke n++ 
  gi|298675230|ref|YP_003726980.1| 56 QIRALKDDYEWLKEINSQS 74
                                      4555555555555555443 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0037
                              ZapB  15 kaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkk 64 
                                       + i++++ Lq+++++ k+ ++++k+ + ++ +  e+  ++re +q +l++
  gi|298675230|ref|YP_003726980.1| 207 NSIERLKVLQKRLSRKKKGSNNYKKLKHQIAKYHEKIANQREDFQHKLSN 256
                                       67999****************************************99975 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2     0.012        20      17      42 ..      48      73 ..      33      98 .. 0.83
   2 ?    4.9   1.5     0.014        22      13      39 ..     223     249 ..     212     257 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.012
                                      XHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             DivIC 17 laykqlkqeiaalqaelaklkaenee 42
                                      +++++l+++i al+++++ lk+ n +
  gi|298675230|ref|YP_003726980.1| 48 VSRFELNKQIRALKDDYEWLKEINSQ 73
                                      66788999999999999999998876 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.014
                                       XXXXXHHHHHHHHHHHHHHHHHHHHHH CS
                             DivIC  13 kkgllaykqlkqeiaalqaelaklkae 39 
                                       kkg ++yk+lk +ia+  +++a+++++
  gi|298675230|ref|YP_003726980.1| 223 KKGSNNYKKLKHQIAKYHEKIANQRED 249
                                       68999******************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1686  (0.0940376); expected 358.6 (0.02)
Passed bias filter:                      678  (0.0378158); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 2422.05
//
Query:       gi|298675231|ref|YP_003726981.1|  [L=655]
Description: glycogen debranching protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     8e-132  439.8   0.0   1.1e-131  439.3   0.0    1.1  1  GDE_C            Amylo-alpha-1,6-glucosidase
    2.2e-75  252.8   0.7    3.2e-75  252.3   0.7    1.2  1  GDE_N            Glycogen debranching enzyme N terminal
    3.7e-07   29.2   0.0     0.0027   16.4   0.0    2.3  2  Glyco_hydro_100  Alkaline and neutral invertase
      0.005   16.2   0.0     0.0073   15.6   0.0    1.2  1  Bac_rhamnosid6H  Bacterial alpha-L-rhamnosidase 6 hairpin gly


Domain annotation for each model (and alignments):
>> GDE_C  Amylo-alpha-1,6-glucosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  439.3   0.0  2.6e-135  1.1e-131       2     383 .]     279     645 ..     277     645 .. 0.96

  Alignments for each domain:
  == domain 1  score: 439.3 bits;  conditional E-value: 2.6e-135
                             GDE_C   2 asdqflvrrkseslkeeekgvsliAGlpwFsdWGRDtfIaLsGllLvtgrfeeAreilltFaktlrhGliPNllde. 77 
                                       ++d+f+v+rk      +++  s++AG++wFsdWGRD++I+L+Gl+Lvtgrf+eA +il+ Fa  +++GliPN++++ 
  gi|298675231|ref|YP_003726981.1| 279 TADSFIVNRK------STNSESIVAGYHWFSDWGRDAMISLPGLTLVTGRFNEASRILKGFAANCQDGLIPNRFADt 349
                                       5789999998......56799*****************************************************987 PP

                             GDE_C  78 .gqealyntvdaslwlieaiekYleyagdaeilrriypvlqeilqkyvqGtkykigldeedglisagerlnqlTWmD 153
                                        + ++ yntvdaslw+i+a  kY+ey+ d   +r+++++++ei+++y++Gt ++i++d +d+li+ ++   qlTWmD
  gi|298675231|ref|YP_003726981.1| 350 dNDNPDYNTVDASLWFIHAAGKYFEYTSDLGTIRDVWNTIREIIHHYIRGTYFNIQMD-KDSLIKYDS---QLTWMD 422
                                       7889******************************************************.9********...****** PP

                             GDE_C 154 akvkgepvtPRdGkaveinaLwyaaLkileelaekalgeakkssykelaekikesfekkFwdeaaaavakreilaDv 230
                                       akv+g+ vtPR Gk +einaLwy+aLk+++ lae +lg   +++y++ a+++k+sf  +Fw+       ++++l+D+
  gi|298675231|ref|YP_003726981.1| 423 AKVDGIEVTPRRGKTCEINALWYNALKTASLLAE-NLGL-LHEEYDKTADRVKSSFVDTFWN------DNNGCLFDC 491
                                       **********************************.7777.79********************......99******* PP

                             GDE_C 231 lkssee....kdlslRpNflialslapellseekakkvlekaeeeLltplGlktLdpedpeYkgnYdgsedsrdaaY 303
                                       ++  +     kd s+RpN+++a+sl++++ls++k+k +++k++ +Llt+ Gl+tL+ped +Y+g+Y+g  ++rd+aY
  gi|298675231|ref|YP_003726981.1| 492 ISIGDDgeiyKDPSIRPNQIFAVSLPYTMLSHDKEKMIVDKVKDKLLTSKGLRTLSPEDEKYRGIYSGGPYERDFAY 568
                                       9876655589******************************************************************* PP

                             GDE_C 304 HqGtvWvwllgsyveallkfgeklgkskealeevkalLeglekhleeaglgslsElfdgdaellpkgciaQAWSvae 380
                                       H+GtvW+wl+g +++a+lk++++   s e+ e +++lL g+e+h +eag+g++sE+fdgd ++ p gc+ QAWSvae
  gi|298675231|ref|YP_003726981.1| 569 HNGTVWPWLMGPFIDAYLKVNND---SVENREYARSLLLGFENHFKEAGIGTISEVFDGDYPHNPGGCVSQAWSVAE 642
                                       **********************8...7778888999***************************************** PP

                             GDE_C 381 llr 383
                                       +lr
  gi|298675231|ref|YP_003726981.1| 643 ILR 645
                                       *97 PP

>> GDE_N  Glycogen debranching enzyme N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  252.3   0.7   7.2e-79   3.2e-75       1     216 [.      18     230 ..      18     232 .. 0.95

  Alignments for each domain:
  == domain 1  score: 252.3 bits;  conditional E-value: 7.2e-79
                             GDE_N   1 REwllTNglGGYasgtvagantRryhGlLvaalnppsgRtlllskldeslevsgkvfeLstneypgeiepeGyeyLe 77 
                                       +Ewl+TNglGGYas+t++gantR+yhGlLv alnpp++Rtl+ls++de++ v+g+ ++L+t++yp +++peGy+yL+
  gi|298675231|ref|YP_003726981.1|  18 KEWLVTNGLGGYASSTIIGANTRTYHGLLVSALNPPVDRTLMLSSVDEEIYVNGSLYRLATHKYPMTVHPEGYKYLN 94 
                                       7**************************************************************************** PP

                             GDE_N  78 sFelepvptwtyrvgdvllekqivmpkgentvliaYrlenadepatLrlrpllafRdfheltkanellqksqeeglv 154
                                       + +++p+p ++y+v+++++ kqi+m++gent++i+Y+++ +d+++ +rl pl++ R+fh +t++n+ +++++   ++
  gi|298675231|ref|YP_003726981.1|  95 EVSFKPFPAFVYQVENTEIIKQIFMQYGENTTIISYQVNCSDNNTVFRLIPLVNLRNFHYTTRSNDIKFEQSPV-KY 170
                                       ****************************************999********************99988888663.56 PP

                             GDE_N 155 eiqaseaepslrlqaskegefqeepvwyynveypeEaerGlddredlyspgyfevelkpges 216
                                        +++  +++ ++l++  + ++++e+vwyyn+ey+ E+ rGl+++ed y+pg fe++l +ge+
  gi|298675231|ref|YP_003726981.1| 171 GTKIVGKNQFFHLHS--NIKYTPEDVWYYNLEYDMERYRGLEYQEDNYNPGFFELNLGKGEN 230
                                       667777777777777..589**************************************9986 PP

>> Glyco_hydro_100  Alkaline and neutral invertase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   4.2e-05      0.19     113     232 ..     358     483 ..     355     488 .. 0.70
   2 !   16.4   0.0   6.1e-07    0.0027     318     388 ..     532     600 ..     513     646 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 4.2e-05
                                       -HHHHHHHHHHHHHHHHHH---HHHHSHHHHHHHHHHHHHHT---S....SSSSS--B-SS-.SSS-S-SS.--... CS
                   Glyco_hydro_100 113 pvDsslWWiillraYvkatgdlslaeeeevqkgiklilelvlaerf....deaPtllvpdga.fmidRrlg.vy... 180
                                       +vD+slW+i  +  Y + t dl     ++v ++i+ i++ +++ ++     +   l+  d+  + +d +++ +    
  gi|298675231|ref|YP_003726981.1| 358 TVDASLWFIHAAGKYFEYTSDLGT--IRDVWNTIREIIHHYIRGTYfniqMDKDSLIKYDSQlTWMDAKVDgIEvtp 432
                                       79*****************99765..568899999999888876541221123456666654145777765342223 PP

                                       ..BSBHHHHHHHHHHHHHHHHHS-STTTHHHHHHHHHHHHHHHHHHHHHHTEE- CS
                   Glyco_hydro_100 181 ..gapleiqaLlyaalrsakelleeeeeekelleaiekrlkaLrsylreyyWld 232
                                         g+  ei+aL+y+al++a +ll+e+     l+e+ +k +++++s   + +W d
  gi|298675231|ref|YP_003726981.1| 433 rrGKTCEINALWYNALKTA-SLLAENL--GLLHEEYDKTADRVKSSFVDTFWND 483
                                       338889***********99.5666654..4667777777777777777777766 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 6.1e-07
                                       HTHHHHTTTSS-BSEES---HHHHHHHHTS-GGG-TTBTTBT-B-GGGHHHHHHHHHHTT-HHHHHHHHHH CS
                   Glyco_hydro_100 318 erwedlvgemPlkicfPaleeeewrivtGsDpkntpwsYhngGsWpvllWllvaaalkterkelaekaiel 388
                                       + +++l+++  l+   P  e+e++r +    p  + ++Yhng  Wp l+  ++ a lk++++++ ++ ++ 
  gi|298675231|ref|YP_003726981.1| 532 KVKDKLLTSKGLRTLSP--EDEKYRGIYSGGPYERDFAYHNGTVWPWLMGPFIDAYLKVNNDSVENREYAR 600
                                       44556667777777666..68889988888999***************************98887776654 PP

>> Bac_rhamnosid6H  Bacterial alpha-L-rhamnosidase 6 hairpin glycosidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.6e-06    0.0073     103     220 ..     365     493 ..     304     541 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.6e-06
                                       HHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHTSBT......TB.--S-S--STT.......-SS----HHHHHH CS
                   Bac_rhamnosid6H 103 ivivpwelyetygDkeilkkqYesmkryldylkqrsdd.....gleelskfqlgDWldpe..ardgaaktekalvat 172
                                        + ++ +++e++ D  ++++ ++++++ + ++ + +       ++  ++ +    W+d +    ++  +  k+   +
  gi|298675231|ref|YP_003726981.1| 365 FIHAAGKYFEYTSDLGTIRDVWNTIREIIHHYIRGTYFniqmdKDSLIKYDSQLTWMDAKvdGIEVTPRRGKTCEIN 441
                                       45567899******************999887765433354424445666677789988854334444445555689 PP

                                       HHHHHHHHHHHHHHHHTTS..--HHHHHHHHHHHHHHHHHHB.-TTS......- CS
                   Bac_rhamnosid6H 173 aylvrslklvakiaellgkeedakkyaalaeelkaafnkkyldsetg......s 220
                                       a  + +lk+++ +ae lg     ++y++ a+++k+ f ++++++++g      s
  gi|298675231|ref|YP_003726981.1| 442 ALWYNALKTASLLAENLGL--LHEEYDKTADRVKSSFVDTFWNDNNGclfdciS 493
                                       ******************7..5689*****************999996666551 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (655 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 4610.05
//
Query:       gi|298675232|ref|YP_003726982.1|  [L=649]
Description: glycoside hydrolase 15-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-14   53.9   0.2    3.1e-08   32.8   0.8    3.6  4  Glyco_hydro_15  Glycosyl hydrolases family 15
  ------ inclusion threshold ------
      0.013   15.7   0.0       0.03   14.6   0.0    1.6  1  DUF3938         Protein of unknown function (DUF3938)
        0.2   11.0   0.5       0.39   10.1   0.5    1.4  1  APCDDC          Adenomatosis polyposis coli down-regulated 1


Domain annotation for each model (and alignments):
>> Glyco_hydro_15  Glycosyl hydrolases family 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.17     1e+03     199     228 ..     225     254 ..     198     257 .. 0.76
   2 !   13.3   0.0   4.5e-06     0.027       4      58 ..     272     330 ..     269     346 .. 0.87
   3 !   32.8   0.8   5.2e-12   3.1e-08     123     370 ..     371     594 ..     365     598 .. 0.82
   4 !    2.5   0.0    0.0084        50     411     444 ..     601     634 ..     591     637 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.17
                                       HHHHHCT-HHHHCCHHHHHHHHHHHHHSTT CS
                    Glyco_hydro_15 199 deadlfgakgdaqlvektkdeilnklqgky 228
                                       + ++++  ++ ++++ektk+++ ++l+gk 
  gi|298675232|ref|YP_003726982.1| 225 KRMHEIYPHSIDDMYEKTKNNCFTWLSGKR 254
                                       55666666778899************9985 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 4.5e-06
                                       HHHHHHCBCSTTSSBTTS-TT-B-S-S-BSSS.....B--SEEHHHHHHHHHHHH..... CS
                    Glyco_hydro_15   4 ldlylrnvktlilleqnpvtGlliASpstsdp.....DYrytWvRDsvyvilavwglgyr 58 
                                       ld y r++ tl ll ++   G ++A+p+ ++      +Y ++W RD++ v+  +++ gy 
  gi|298675232|ref|YP_003726982.1| 272 LDTYNRSLLTLNLLNDSK-HGSFVAAPEFDSNfemcgGYGFCWNRDASEVATSLLNSGYY 330
                                       78999*****99999999.**********999***********************99964 PP

  == domain 3  score: 32.8 bits;  conditional E-value: 5.2e-12
                                       -BTTHHHHHHHHHHHHHCTT.....HCHCCCCHHHHTHHHHHHHHHHHTTS....-EE-TTS--ECEEHH..HHHHH CS
                    Glyco_hydro_15 123 lQlDatslyllalaqmtasg.....lqiistldevafvqnlvdYieaaykt....pdfglWEenqgeselnassvgm 190
                                        Q+D t+  l++   +++s        + ++++    v    +Y+ +  ++    p+ +lWE+ +g   +  + +  
  gi|298675232|ref|YP_003726982.1| 371 TQIDETGSTLQLANLYYQSIggirkADFLYQIWVT--VLHGAEYLMKRSSEglhdPCIDLWETYKGVFSY--TNASI 443
                                       69999999999999997776678878888888887..6666666666554422228***********999..***** PP

                                       HHHHHHHHHHHHHCT-HHHHCCHHHHHHHHHHHHHSTTT..GGGEETTCCECECSCH.....HHHTTS--S-BCHHH CS
                    Glyco_hydro_15 191 akAlleaideadlfgakgdaqlvektkdeilnklqgkygckrgfwplfntylildgsfaedkeqvqeyrealdasll 267
                                        ++ll a+ +a++  + g a+ +++ ++++ +            w +++++ +   +            ++ld  ++
  gi|298675232|ref|YP_003726982.1| 444 YAGLLSAAHLAEEYNELGLAKRWSERAEQVKRNT-----L-DKLWLDEGYFAKGIID------------NNLDTTVD 502
                                       ******************************9888.....4.4588888888876666............89999998 PP

                                       HHHHHCS-TTS-TT-TT-TTTSHHHHHHHHHHHHHHHHHSGGGTT-STTS--SBTT--CGSSSBSCT--BHHHHHHH CS
                    Glyco_hydro_15 268 llpelyfvpaddvdeeyqnpqsprllaqslyildsllsegflavgeldplvrRysedvkpdklglsGrpyylctlwt 344
                                       +    +fvp++       np+ p   + ++  +++++++  l+v+e  + ++Ry++d++       G+p+ ++tlw 
  gi|298675232|ref|YP_003726982.1| 503 VSILGTFVPFNM-----LNPKNPDEKQMIDSMIAKVEEKLALNVNEYYG-IKRYENDNYI-----GGNPWIVATLWL 568
                                       888889999999.....66666666666666678888888999**9888.9********7.....***********9 PP

                                       HHHHHHHHHHHHHHTE-EEEECCCHH CS
                    Glyco_hydro_15 345 vetlldelyekagkgrlwglvryalg 370
                                        + +l+ ++  ++k +  +l+++al+
  gi|298675232|ref|YP_003726982.1| 569 SKSILTLATSINKKTEQQQLIDKALE 594
                                       99999999988888888888888775 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.0084
                                       HHS-TTS---SEE-TTT--EESSTT-HHHHHHHH CS
                    Glyco_hydro_15 411 eednslgvLteevdvylgeliraqpllfsealll 444
                                       + + s g+L e+vd+y+g +    pl +s  l++
  gi|298675232|ref|YP_003726982.1| 601 RGTTSAGLLPEQVDKYTGNPAWVIPLGWSCSLMI 634
                                       448999*************999999999877665 PP

>> DUF3938  Protein of unknown function (DUF3938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0     5e-06      0.03       5      79 ..     489     564 ..     486     580 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5e-06
                           DUF3938   5 nkhivlnsieslvsalllgrlvlf.lldseesaqktvlltmigivggclsysitnyalvlqlssaffhglwawfia 79 
                                       +k i+ n++++ v  ++lg +v f +l++++  +k ++ +mi  v   l+  + +y  + +     + g   w++a
  gi|298675232|ref|YP_003726982.1| 489 AKGIIDNNLDTTVDVSILGTFVPFnMLNPKNPDEKQMIDSMIAKVEEKLALNVNEYYGIKRYENDNYIGGNPWIVA 564
                                       577999****************87589********************99999999876666666556665666655 PP

>> APCDDC  Adenomatosis polyposis coli down-regulated 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.5   6.6e-05      0.39      39      61 ..      95     117 ..      87     123 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 6.6e-05
                            APCDDC  39 efllRkytffknrtFkllqyyYe 61 
                                        fl+Rky++++++ F+   +yY 
  gi|298675232|ref|YP_003726982.1|  95 PFLIRKYRIYSDEDFHGKFFYYL 117
                                       5*********************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (649 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 4780.96
//
Query:       gi|298675233|ref|YP_003726983.1|  [L=269]
Description: 4-vinyl reductase 4VR [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-14   53.2   0.3    3.8e-14   52.4   0.3    1.3  1  V4R       V4R domain
  ------ inclusion threshold ------
      0.013   16.1   0.0      0.029   15.0   0.0    1.5  1  ACT_4     ACT domain
      0.054   13.3   0.0       0.11   12.3   0.0    1.6  1  ACT       ACT domain
       0.13   12.1   0.0       0.26   11.1   0.0    1.5  1  DUF1421   UBA-like domain (DUF1421)


Domain annotation for each model (and alignments):
>> V4R  V4R domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.3   8.5e-18   3.8e-14       7      61 ..     198     252 ..     194     253 .. 0.96

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 8.5e-18
                                       EES-S-TT---SS---HHHHHHHHHHHHHHHSSEEEEEEEE-GGGT-SSEEEEEE CS
                               V4R   7 espelaglpgkeePvCyleaGllagalsellgkrveveEveCaaeGhdhCeFeve 61 
                                       +++ ++ ++++e PvC+++ G+++g+ +e l+++v+v+E++C ++ hd Ce++++
  gi|298675233|ref|YP_003726983.1| 198 NCFIAEYYGKSEIPVCEYVSGFFSGFITEALNEPVHVREIRCKSMNHDVCEHIIS 252
                                       79**************************************************997 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   6.4e-06     0.029       7      79 ..      18      90 ..      14      90 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.4e-06
                             ACT_4  7 vrleveaedrkglLaditqviseekanivsvnaktrkkdglaeikitveVkdvehLsrviakLraipgVisVe 79
                                      v+ ++  +d ++  adi++++++e+++++   +++++ +   +  +   Vk + ++++ ++kL++++ V +Ve
  gi|298675233|ref|YP_003726983.1| 18 VWFKIHHSDTPKSQADIANLFASENVDVRYGYIDNTEYSDRGKYVLFALVKQSVDINSFLDKLKKLDVVLNVE 90
                                      78899******************************98888999999999********************9996 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.4e-05      0.11       5      66 ..      22      84 ..      18      85 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.4e-05
                                      EEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTT.ECEEEEEEEEEEHHHHHHHHHHHHTTC CS
                               ACT  5 vgvpDrPGlLarvfgaladrgiNidsieqrssedk.vagivfvvivvdeedleevlealkkle 66
                                      ++  D P   a++++++a  ++ ++   +  +e++  +++v + +v    d+ + l++lkkl 
  gi|298675233|ref|YP_003726983.1| 22 IHHSDTPKSQADIANLFASENVDVRYGYIDNTEYSdRGKYVLFALVKQSVDINSFLDKLKKLD 84
                                      56668888889**************************************************96 PP

>> DUF1421  UBA-like domain (DUF1421)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   5.9e-05      0.26      30      42 ..      69      81 ..      67      83 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.9e-05
                           DUF1421 30 qpvDfNvvlDkLs 42
                                      q+vD N++lDkL+
  gi|298675233|ref|YP_003726983.1| 69 QSVDINSFLDKLK 81
                                      9***********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1861.39
//
Query:       gi|298675234|ref|YP_003726984.1|  [L=400]
Description: alpha-amylase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-64  216.4   0.0    7.6e-64  216.0   0.0    1.1  1  Glyco_hydro_57   Glycosyl hydrolase family 57
    6.2e-07   29.3   0.0    1.2e-06   28.4   0.0    1.5  1  Polysacc_deac_1  Polysaccharide deacetylase
  ------ inclusion threshold ------
       0.01   15.6   0.0      0.028   14.2   0.0    1.7  1  DUF2733          Protein of unknown function (DUF2733)
      0.032   13.9   0.0      0.055   13.1   0.0    1.3  1  DUF1241          Protein of unknown function (DUF1241)


Domain annotation for each model (and alignments):
>> Glyco_hydro_57  Glycosyl hydrolase family 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.0   0.0   1.7e-67   7.6e-64       4     323 ..       8     289 ..       5     291 .. 0.94

  Alignments for each domain:
  == domain 1  score: 216.0 bits;  conditional E-value: 1.7e-67
                                       EEE-----TTS-SSSSSHHHHHHH.HHHTHHHHHHHHHHHHHTT----EEEEE-HHHHHHHT-HHHHHHHHHHHHHH CS
                    Glyco_hydro_57   4 fhqHqplykkpgkgeytlpwvreh.aaedYiklalilekfpkvhvtfeLsgsLiaqLeeylngekksylpateelle 79 
                                       f+ Hqp++ +         w + + +  +Y++  +++e+f+kv+                    +k+y+p++++lle
  gi|298675234|ref|YP_003726984.1|   8 FQIHQPYRLRWF-------WPDDTsGFYRYFDYTANKEIFEKVA--------------------DKCYRPTNNLLLE 57 
                                       455666665554.......555444899****************....................************* PP

                                       HHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHT.TT-HHHHHHHHHHCTSEEEEEE-TT-B-GGG-S-HHHHHHH CS
                    Glyco_hydro_57  80 lieeglerctelkldlavlfnlaisgplleqiqkwlnkevlelfrelqesgqvElltspyyHpllpllpdsedieaq 156
                                       li    e  +++k      f+++++g+ll q++ w   +vl+ f+++++sg vE+l ++ yH+l+ l++d+++++++
  gi|298675234|ref|YP_003726984.1|  58 LI---DEYNGDFK------FSVSVTGTLLNQCEHW-GDDVLDTFKQMADSGCVEFLDETNYHSLAGLFEDRSEFIEE 124
                                       *9...66667888......****************.***************************************** PP

                                       HHHHHHHHHHHHSS--SBEE-GGG-B--SHHHHHHHTT--EEEE-C------------TTS-EE-TTS.-EEEE--C CS
                    Glyco_hydro_57 157 vkkarelyeeyfgqePrgfwlpElavspeileilaelGfeylftdelaeiledkskespyrpyllknggiavffRdr 233
                                       +k++++++++++g++P++f+++El++++ i++++ +lG++ +++++++++l ++   sp ++y+++ +g+ +++R++
  gi|298675234|ref|YP_003726984.1| 125 IKEHHNVIKDLLGVKPKVFRNTELIYNNNIAKTVSDLGYNAILAEGVDNLLGWR---SPDYVYRAEGSGLPLLLRNY 198
                                       ******************************************************...******************** PP

                                       HH-TTTSGGG-................TTSB..........-TT---TTT-..-BB-TT-S---HHHHHHHHHHHHH CS
                    Glyco_hydro_57 234 eLsddigFrys....eqypleavddfinwlkkvkkaksevvtialdgEnwg..hypetgkkeFleklyeeleengli 304
                                        Lsddig+r+s    + ypl ++d+++ w + v   ++++++i++d+E++g  +++etg+++F+++l+ e+  +g +
  gi|298675234|ref|YP_003726984.1| 199 PLSDDIGYRFSarwwGEYPL-TADKWASWASDV---EGDILNIFMDYETFGehQWEETGIFDFIRALPGEVLDQG-L 270
                                       ***************99***.***********9...***************************************.* PP

                                       HHHHHHHHHHHHSS-EEEE CS
                    Glyco_hydro_57 305 elvtpsefikklkpkglik 323
                                        + tpse+++ + p g i+
  gi|298675234|ref|YP_003726984.1| 271 AFNTPSEVVDMYSPVGNID 289
                                       ********99888877665 PP

>> Polysacc_deac_1  Polysaccharide deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   2.8e-10   1.2e-06      13     123 ..      44     165 ..      35     166 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 2.8e-10
                                       EEESSCSCHHHHHHHHHHCT..--EEEEE-HHHHCH-.......HHHHHHHHHTT.EEEEE--SS--EG.GGSHHHH CS
                   Polysacc_deac_1  13 fDdgprdntteilpvLkkyk..vkatffvigglvedy.......pdevremaasG.veignHtinhsnl.krlseee 78 
                                       +D ++r + + +l++ ++y+  +k  + v+g+l ++         d  ++ma+sG ve+   t  hs     + ++e
  gi|298675234|ref|YP_003726984.1|  44 ADKCYRPTNNLLLELIDEYNgdFKFSVSVTGTLLNQCehwgddvLDTFKQMADSGcVEFLDETNYHSLAgLFEDRSE 120
                                       577888888888888888862256666667776444455566669******************9999876778888* PP

                                       HHHHHHHHHHHHHHHHS----EEE-GGGEE-HHHHHHHHHTT.EE CS
                   Polysacc_deac_1  79 vrreierakdalrkalgreprlfryPygsasatvlevarelgfay 123
                                       + +ei++   ++++ lg +p++fr   + +++++ + +++lg+++
  gi|298675234|ref|YP_003726984.1| 121 FIEEIKEHHNVIKDLLGVKPKVFRNTELIYNNNIAKTVSDLGYNA 165
                                       ******************************************986 PP

>> DUF2733  Protein of unknown function (DUF2733)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   6.2e-06     0.028      17      32 .]     229     244 ..     224     244 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.2e-06
                           DUF2733  17 DVdGepINvveDfEef 32 
                                       DV+G ++N+  D+E f
  gi|298675234|ref|YP_003726984.1| 229 DVEGDILNIFMDYETF 244
                                       **************98 PP

>> DUF1241  Protein of unknown function (DUF1241)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.2e-05     0.055     110     142 ..     116     148 ..     113     156 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.2e-05
                           DUF1241 110 ndRktfLetIkeiAsaIkklLdavnevlkkiqe 142
                                       +dR++f+e Ike  + Ik+lL +  +v+++++ 
  gi|298675234|ref|YP_003726984.1| 116 EDRSEFIEEIKEHHNVIKDLLGVKPKVFRNTEL 148
                                       7***********************9*9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2983.88
//
Query:       gi|298675235|ref|YP_003726985.1|  [L=387]
Description: glycoside hydrolase family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.8e-46  156.8   2.6    1.2e-45  156.1   2.6    1.3  1  Glyco_hydro_57  Glycosyl hydrolase family 57


Domain annotation for each model (and alignments):
>> Glyco_hydro_57  Glycosyl hydrolase family 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.1   2.6   6.9e-50   1.2e-45      93     320 ..      61     282 ..      12     289 .. 0.90

  Alignments for each domain:
  == domain 1  score: 156.1 bits;  conditional E-value: 6.9e-50
                                       HHHHHHHHHHHHHHHHHHHHHT.TT-HHHHHHHHHHCTSEEEEEE-TT-B-GGG-S-HHHHHHHHHHHHHHHHHHHS CS
                    Glyco_hydro_57  93 ldlavlfnlaisgplleqiqkwlnkevlelfrelqesgqvElltspyyHpllpllpdsedieaqvkkarelyeeyfg 169
                                       ++    ++++isg+++  ++kw n +v+++f+el  +++vE+++s+yyH+l +l++ds +++ q+kk+r+ + ++f+
  gi|298675235|ref|YP_003726985.1|  61 IENGGKYSFNISGTFIDICKKW-NFDVIKSFKELSNTEKVEFTSSSYYHSLSSLYNDSFEFRDQIKKHRNEINNLFE 136
                                       33444599**************.****************************************************** PP

                                       S--SBEE-GGG-B--SHHHHHHHTT--EEEE-C------------TTS-EE-TTS.-EEEE--CHH-TTTSGGG-.. CS
                    Glyco_hydro_57 170 qePrgfwlpElavspeileilaelGfeylftdelaeiledkskespyrpyllknggiavffRdreLsddigFrys.. 244
                                       q+P++f  +El+++ ++  il+++Gfe++++++++++l++    +p+++y   n+ + +++R+ +Ls+di+ r+s  
  gi|298675235|ref|YP_003726985.1| 137 QNPQTFIDSELILTTHTGSILQDQGFECIISEGSSNLLDGT---DPVYVYN--NQ-LPILLRHINLSEDIETRFSdr 207
                                       *****************************************...***9998..45.9******************** PP

                                       ..............TTSB..........-TT---TTT-..-BB-TT-S---HHHHHHHHHHHHHHHHHHHHHHHHHS CS
                    Glyco_hydro_57 245 ..eqypleavddfinwlkkvkkaksevvtialdgEnwg..hypetgkkeFleklyeeleenglielvtpsefikklk 317
                                         + ypl  +d+f+ w++++   +++vv+i+ +++++   h + + +++Fl++l+e+l++   i++ tpse++kk++
  gi|298675235|ref|YP_003726985.1| 208 swTGYPL-IPDKFASWINNM---EGDVVVIYFNYDTLArhHENGSNIFQFLKELPESLKKYD-IKMETPSEAVKKHQ 279
                                       **99***.**********99...*************8856666667778*************.***********998 PP

                                       S-E CS
                    Glyco_hydro_57 318 pkg 320
                                       + +
  gi|298675235|ref|YP_003726985.1| 280 KVK 282
                                       765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       834  (0.0465168); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 3010.42
//
Query:       gi|298675236|ref|YP_003726986.1|  [L=157]
Description: CheD protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-32  112.2   0.1    1.6e-32  111.9   0.1    1.1  1  CheD          CheD chemotactic sensory transduction
     0.0084   15.7   0.0      0.015   14.9   0.0    1.5  2  Cu-oxidase_4  Multi-copper polyphenol oxidoreductase laccase


Domain annotation for each model (and alignments):
>> CheD  CheD chemotactic sensory transduction
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.9   0.1   1.8e-36   1.6e-32       1     108 [.      45     148 ..      45     149 .. 0.95

  Alignments for each domain:
  == domain 1  score: 111.9 bits;  conditional E-value: 1.8e-36
                                       -BS--....SS-TTSCCCBHHHHHHHHHHHHHTTT--GGG-EEEEEE----S.....---SS-HHHHHHHHHHHHHH CS
                              CheD   1 mLPdskeskeksasnpakyadtaielLinellklgakkerleaklaGGAqmfafessksdvlniGerNveavkelLk 77 
                                       mLP+s  ++++sa+n+ak++dt i+ L++el+k g+ k+rleakl+GGA+mf++   ++ ++n+G++Nv+ +ke+L+
  gi|298675236|ref|YP_003726986.1|  45 MLPSS--ENARSANNKAKFVDTSIPYLVDELVKYGVAKRRLEAKLVGGADMFSM--GNNGTINVGRNNVKKAKEVLS 117
                                       9****..5666667**************************************99..6799***************** PP

                                       HTT--EEEEEE-SSS-EEEEEETTTTEEEEE CS
                              CheD  78 eegipivaedvggnygRtvlfdpatgkvlvk 108
                                       + +ip+vae++ggnygRt ++d+++g+v+++
  gi|298675236|ref|YP_003726986.1| 118 NLDIPLVAEETGGNYGRTTTLDTSDGTVFIR 148
                                       *****************************98 PP

>> Cu-oxidase_4  Multi-copper polyphenol oxidoreductase laccase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.7e-06     0.015      73     111 ..       5      44 ..       1      61 [. 0.94
   2 ?   -3.2   0.0      0.56     5e+03       8      32 ..      95     119 ..      90     129 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.7e-06
                                       ..-SEEEESSTTSEEEEEESSSEEEEEEETTSSEEEEEEE CS
                      Cu-oxidase_4  73 e.aDalvtdepgvalavltADCvPvlladpkgkvvaaaHa 111
                                       + aD +v++ p+ + ++    Cv + l+dp++kv +++Ha
  gi|298675236|ref|YP_003726986.1|   5 KmADCAVAKSPDNLKTMSLGSCVGITLYDPSKKVGGLIHA 44 
                                       559************************************9 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.56
                                       B-GGG-B----SSSSS-HHHHHHHH CS
                      Cu-oxidase_4   8 segpyaslNlglhvgDdpeaVaenr 32 
                                       s g+ +++N+g +   ++++V  n 
  gi|298675236|ref|YP_003726986.1|  95 SMGNNGTINVGRNNVKKAKEVLSNL 119
                                       5556666777777767777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1230.42
//
Query:       gi|298675237|ref|YP_003726987.1|  [L=210]
Description: inhibitor of MCP methylation CheC [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-18   66.5   0.7      1e-11   44.5   0.0    2.9  3  CheC      CheC-like family
    5.6e-15   55.3   3.5    4.6e-10   39.5   0.4    2.4  3  CheX      Chemotaxis phosphatase CheX


Domain annotation for each model (and alignments):
>> CheC  CheC-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.0   1.2e-15     1e-11       1      37 [.      16      52 ..      16      53 .. 0.95
   2 !   19.4   0.2     8e-08   0.00072       1      34 [.     113     146 ..     113     150 .. 0.88
   3 ?   -1.7   0.0      0.33   2.9e+03      15      25 ..     188     198 ..     187     202 .. 0.83

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 1.2e-15
                                      HHHHHHHHHHHHHHHHHHHHHHTCCTS-EEE---EEE CS
                              CheC  1 melSAlgEigNIlaGsaatalatllnfkidisPPtvv 37
                                      ++++Al+E++NI++G+ +t+l++l n++++i +P+++
  gi|298675237|ref|YP_003726987.1| 16 FQRDALKEVANIGMGNSITSLSKLINRQVNIHVPDLK 52
                                      689*******************************997 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 8e-08
                                       HHHHHHHHHHHHHHHHHHHHHHTCCTS-EEE--- CS
                              CheC   1 melSAlgEigNIlaGsaatalatllnfkidisPP 34 
                                       m lS+ gE+g IlaGs+++a++++++++  i+ P
  gi|298675237|ref|YP_003726987.1| 113 MTLSMMGEVGQILAGSYSSAISDFFGINTSITIP 146
                                       779**********************998888866 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.33
                                       HHHHHHHHTCC CS
                              CheC  15 Gsaatalatll 25 
                                       Gs++t++ ++l
  gi|298675237|ref|YP_003726987.1| 188 GSFLTMFDKSL 198
                                       99***998877 PP

>> CheX  Chemotaxis phosphatase CheX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.2   9.5e-07    0.0085      31      71 ..       5      50 ..       1      65 [. 0.77
   2 !   39.5   0.4   5.2e-14   4.6e-10       1      73 [.      71     149 ..      71     160 .. 0.89
   3 ?   -3.3   0.0       1.2   1.1e+04      10      28 ..     185     203 ..     179     207 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.5e-07
                              CheX 31 l.gedeeeieedvndavgEltNmiaGnakskl....geevklspPl 71
                                      +  e+  + +e  +da+ E++N+ +Gn  + l    + +v++++P 
  gi|298675237|ref|YP_003726987.1|  5 MeNEEILNLNEFQRDALKEVANIGMGNSITSLskliNRQVNIHVPD 50
                                      53444445799******************88843355599999996 PP

  == domain 2  score: 39.5 bits;  conditional E-value: 5.2e-14
                              CheX   1 vtgiiglaGdisGliilsadeelalkiasa.lgedeee.ieedvndavgEltNmiaGnakskl....geevklspPl 71 
                                       v  i+gl+G++ G+i++ ++ee+a+ki +  ++ d+ +   e+  + +gE+  ++aG++ s +    g + ++++P+
  gi|298675237|ref|YP_003726987.1|  71 VGTIVGLRGNFMGYIAIIFPEESAEKISQIvMDSDDADlQSEMTLSMMGEVGQILAGSYSSAIsdffGINTSITIPY 147
                                       5689*************************7699999998999******************888555777*******9 PP

                              CheX  72 vi 73 
                                       + 
  gi|298675237|ref|YP_003726987.1| 148 TN 149
                                       75 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 1.2
                              CheX  10 disGliilsadeelalkia 28 
                                       +++G+++ ++d++l+ +++
  gi|298675237|ref|YP_003726987.1| 185 KVRGSFLTMFDKSLLDDFL 203
                                       5688888888888876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1561.76
//
Query:       gi|298675238|ref|YP_003726988.1|  [L=319]
Description: tyrosyl-tRNA synthetase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.9e-55  187.2   0.0    4.6e-55  187.0   0.0    1.0  1  tRNA-synt_1b  tRNA synthetases class I (W and Y)
  ------ inclusion threshold ------
      0.065   12.0   0.1       0.16   10.7   0.0    1.6  2  tRNA-synt_1g  tRNA synthetases class I (M)
      0.086   11.7   0.0        3.5    6.4   0.0    2.2  2  tRNA-synt_1f  tRNA synthetases class I (K)


Domain annotation for each model (and alignments):
>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.0   0.0   7.8e-59   4.6e-55       4     293 .]      28     310 ..      25     310 .. 0.94

  Alignments for each domain:
  == domain 1  score: 187.0 bits;  conditional E-value: 7.8e-59
                                       S--EEEEEEETSSS-BGGGHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHHTC CS
                      tRNA-synt_1b   4 rplrvysGidPTgklHlGylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkreevlenaikaqlakgl 80 
                                       ++ ++y+G +P+gk+H G+++ ++kl++lq++g ++++l+aD hA+++++   +++++r+ +e+ +      la gl
  gi|298675238|ref|YP_003726988.1|  28 NRPTAYVGYEPSGKIHMGHVLTVNKLIDLQRSGFDIIVLLADIHAYLNQKG--SLEEVRELAEQNKRC---FLALGL 99 
                                       67899*******************************************999..888998888888888...****** PP

                                       HTTTEEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHH.CCHHCSSSC--BHHHHHHHHHHHHHHHHTCHSEEEE CS
                      tRNA-synt_1b  81 dpekaevvlqsewlehlelaellrdlgklgslnrmlqfks.vkkrleegegislgeftYplLqaaDilllkadlvpg 156
                                       dp+k+++v++s+ + + +++  + +l++ +slnr  +  + v +++   +  +++++ Yp++qa Di++l++d+ + 
  gi|298675238|ref|YP_003726988.1| 100 DPDKTKFVFGSDFQLNHDYMLNVLKLTQETSLNRAKRSMDeVGRKMDD-P--KVSQMVYPIMQAVDIAMLEVDVAVS 173
                                       ***********************************8765538888888.4..7************************ PP

                                       EGGGHHHHHHHHHHHHHHHHHSTTSS-EEEEET-BBSTTSSSBTTCETTCGC-BTTCCHHHHHHHHHHCHCSTTC.. CS
                      tRNA-synt_1b 157 GsDQkqnielgrdlarrfnkkevfkkpegltvplltgldGekKmSKSagnsaIfLddekesvkkkiqkavtdsde.. 231
                                       G DQ+++  l+r+ +++++++     p ++ +p++ gldG  KmS+S++n +I  dd ++++k k++ka++  +   
  gi|298675238|ref|YP_003726988.1| 174 GIDQRKIHMLAREELPDVGYR----SPTCIHTPIMLGLDGV-KMSSSKEN-YISVDDTEDDIKRKMKKAYCPAETve 244
                                       ********************9....****************.********.********************999988 PP

                                       SHHHHHHHHHTHHH....CHHHHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1b 232 evekllklktelsn....elierleavsgkkpkreaeellaeevtklvhggdlkkalaealnelle 293
                                       ++  l+  k+ +++     +++r e+++g+ + + ++el+++++++++h++dlk+a++e +n ll+
  gi|298675238|ref|YP_003726988.1| 245 DNPVLEIFKYHVFPrydeITLKRPEKFGGNLEISGYQELEEQFASGEIHPMDLKNAATEYMNDLLK 310
                                       8887777777777777668999**********99****************************9985 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1      0.32   1.9e+03      11      21 ..      39      49 ..      34      51 .. 0.84
   2 ?   10.7   0.0   2.7e-05      0.16     306     349 ..     190     233 ..     177     247 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.32
                                      SS---HHHHHH CS
                      tRNA-synt_1g 11 ngklHlGhlle 21
                                      +gk+H+Gh+l+
  gi|298675238|ref|YP_003726988.1| 39 SGKIHMGHVLT 49
                                      799*****986 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 2.7e-05
                                       HTT----S-EEEE--EEE--------------HHHHHHHH-HHH CS
                      tRNA-synt_1g 306 gaelklpkkvvaheyltvegkKlSkSrgvvvkakealerldadl 349
                                       + +++ p+ +++  +l ++g K+S+S+++ + ++++ + ++  +
  gi|298675238|ref|YP_003726988.1| 190 DVGYRSPTCIHTPIMLGLDGVKMSSSKENYISVDDTEDDIKRKM 233
                                       47899*****************************9999887665 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0   0.00059       3.5      14      43 ..      18      48 ..       7      58 .. 0.73
   2 ?    3.2   0.0    0.0058        34     276     296 ..     207     226 ..     161     242 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00059
                      tRNA-synt_1f 14 erkkkka.ekdevvvesGispSGliHiGnlr 43
                                      e+ ++   +k+  +   G+ pSG+iH+G + 
  gi|298675238|ref|YP_003726988.1| 18 EELDELVaTKNRPTAYVGYEPSGKIHMGHVL 48
                                      44444445677788889***********865 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.0058
                      tRNA-synt_1f 276 lkggekmssSkGnvltledwl 296
                                       l+ g kmssSk n+++++d  
  gi|298675238|ref|YP_003726988.1| 207 LD-GVKMSSSKENYISVDDTE 226
                                       33.44************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2395.00
//
Query:       gi|298675239|ref|YP_003726989.1|  [L=385]
Description: hypothetical protein Metev_1334 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0065   16.7   0.9      0.017   15.3   0.9    1.7  1  DUF3654        Protein of unknown function (DUF3654)
  ------ inclusion threshold ------
      0.052   13.9   0.9       0.48   10.8   0.0    2.7  3  YlqD           YlqD protein
      0.057   12.7   0.7        3.9    6.7   0.2    2.5  3  DUF3450        Protein of unknown function (DUF3450)
      0.072   12.0   2.0       0.21   10.4   0.5    2.0  2  DUF3375        Protein of unknown function (DUF3375)
       0.13   12.1   1.6       0.27   11.1   1.6    1.5  1  PCRF           PCRF domain
       0.17   12.1   5.2       0.46   10.7   5.2    1.8  1  Fib_alpha      Fibrinogen alpha/beta chain family
       0.35   10.9   4.9         10    6.2   0.3    3.1  3  DUF1664        Protein of unknown function (DUF1664)
       0.39   10.7   6.3       0.11   12.5   1.4    2.3  2  DUF327         Protein of unknown function (DUF327)
        1.3    9.4   9.4       0.47   10.8   0.8    3.3  3  BLOC1_2        Biogenesis of lysosome-related organelles comp
          2    8.4   7.5        6.4    6.8   0.7    2.5  2  Prefoldin_2    Prefoldin subunit
          3    8.0   8.4         18    5.5   8.6    2.0  1  Tropomyosin_1  Tropomyosin like


Domain annotation for each model (and alignments):
>> DUF3654  Protein of unknown function (DUF3654)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.9     1e-05     0.017      15      61 ..      59     108 ..      47     164 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1e-05
                           DUF3654  15 keeevlqkikeygesLctkekqeeiveaqkivcdaCkei...werleedr 61 
                                       + e++ ++ik y+e+L +    eei+e +  v+d+C      w +  e++
  gi|298675239|ref|YP_003726989.1|  59 ELERFEKNIKGYVEKLADDTDSEEIIEFKDAVVDTCSSYtnkWTQYLEEE 108
                                       45677889****************************87511144333333 PP

>> YlqD  YlqD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2       0.9   1.5e+03      22      41 ..      43      62 ..      19      85 .. 0.53
   2 ?   10.8   0.0    0.0003      0.48      14      43 ..      98     127 ..      91     141 .. 0.92
   3 ?   -1.2   0.0       1.5   2.4e+03      58      89 ..     331     362 ..     303     370 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.9
                              YlqD 22 qqqlqaqieqldkelqqLef 41
                                       ++ +++i+ l+k +++Le 
  gi|298675239|ref|YP_003726989.1| 43 YNDTETRIKSLNKRINELER 62
                                      33333334444433333332 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0003
                              YlqD  14 TeklKeelqqqlqaqieqldkelqqLefqa 43 
                                       T+k+ + l++++++q++q ++e++++e q 
  gi|298675239|ref|YP_003726989.1|  98 TNKWTQYLEEEIKSQKKQCENEIENIESQV 127
                                       99*************************997 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.5
                              YlqD  58 ieeiqeqvekekserlekkkqllqqleqvqkL 89 
                                       ++ei+ +++k   +r+ek +++++  +q+++L
  gi|298675239|ref|YP_003726989.1| 331 KNEITIKIHKSDGNRTEKYANINEIFNQLSSL 362
                                       45677777777778888888888888887776 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.2    0.0024       3.9      74     108 ..      43      77 ..      15      85 .. 0.73
   2 ?    3.8   0.0     0.019        31      71     103 ..      99     132 ..      89     137 .. 0.80
   3 ?   -3.4   0.0       2.8   4.6e+03     137     160 ..     340     363 ..     334     365 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0024
                           DUF3450  74 vasqeqeiasleeqieeieeierelvpllekmidr 108
                                        ++ e++i+sl+++i+e+e+ e++++ + ek+ d+
  gi|298675239|ref|YP_003726989.1|  43 YNDTETRIKSLNKRINELERFEKNIKGYVEKLADD 77 
                                       45677788888888888888888887777776664 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.019
                           DUF3450  71 erlvasqeqeiasleeqie.eieeierelvplle 103
                                       +++ + +e+ei+s ++q e eie+ie+++ p l+
  gi|298675239|ref|YP_003726989.1|  99 NKWTQYLEEEIKSQKKQCEnEIENIESQVYPALD 132
                                       5677778999999999975379*****9999987 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 2.8
                           DUF3450 137 radvslaekyrrvleayqiEaeYg 160
                                       ++d + +eky ++ e++++  ++g
  gi|298675239|ref|YP_003726989.1| 340 KSDGNRTEKYANINEIFNQLSSLG 363
                                       566677888988888888877776 PP

>> DUF3375  Protein of unknown function (DUF3375)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.5   0.00013      0.21     125     174 ..      35      84 ..      32      95 .. 0.77
   2 ?    0.6   0.0      0.13   2.1e+02     141     167 ..     107     133 ..      91     134 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00013
                           DUF3375 125 leqlaeetepDpeeRlaeLeaeiaeidaeidrlrageveelddeqvleri 174
                                       le+ a et +D+e+R+++L+++i+e+++  ++++    ++ dd++ +e i
  gi|298675239|ref|YP_003726989.1|  35 LEKSAIETYNDTETRIKSLNKRINELERFEKNIKGYVEKLADDTDSEEII 84 
                                       7888999********************98888875444444555544443 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.13
                           DUF3375 141 aeLeaeiaeidaeidrlrageveeldd 167
                                       +e+++++++ ++ei++++++  + ld+
  gi|298675239|ref|YP_003726989.1| 107 EEIKSQKKQCENEIENIESQVYPALDP 133
                                       57899**************99999985 PP

>> PCRF  PCRF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.6   0.00017      0.27      15      82 ..      41     123 ..      28     134 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00017
                                       GGGTTTGGGSSSTTHHHHHTHHHHHHHHHHHHHTTTHHH...HT.....-S-..-GG...........G....THHH CS
                              PCRF  15 pevwedqekakklskelaeleeivealeeleealedleeakelle.edeelaelaee...........e....leel 75 
                                       ++  + ++++k+l+k+++ele+  ++++ + e+l+d ++ +e++e +d+ +     +           e     +++
  gi|298675239|ref|YP_003726989.1|  41 ETYNDTETRIKSLNKRINELERFEKNIKGYVEKLADDTDSEEIIEfKDAVVDTCS-SytnkwtqyleeEiksqKKQC 116
                                       3456678999**************************9999***955553333222.123333333332222224444 PP

                                       HHHHHHH CS
                              PCRF  76 ekeleel 82 
                                       e+e+e++
  gi|298675239|ref|YP_003726989.1| 117 ENEIENI 123
                                       4444444 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   5.2   0.00028      0.46      29     105 ..      42     124 ..      35     128 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00028
                                       CCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHHHHHHHHHHCCCHHHHHHHC CS
                         Fib_alpha  29 yekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn......dnvikksskeleeeilrlketida 99 
                                       + +d+++++++l+++++e+++ +k+++ +v+++ d + +++  + +       +++++k ++ leeei   k++  +
  gi|298675239|ref|YP_003726989.1|  42 TYNDTETRIKSLNKRINELERFEKNIKGYVEKLADDTDSEEIIEFKDavvdtcSSYTNKWTQYLEEEIKSQKKQCEN 118
                                       557899***************************99998887666531122234666667777777666666666666 PP

                                       CHHHHH CS
                         Fib_alpha 100 qesnir 105
                                       +++ni+
  gi|298675239|ref|YP_003726989.1| 119 EIENIE 124
                                       666664 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.3    0.0063        10      46      97 ..      28      79 ..      19      91 .. 0.83
   2 ?    4.9   0.1     0.015        25      40      75 ..      91     127 ..      86     132 .. 0.82
   3 ?    0.1   0.1      0.49   8.1e+02      42      92 ..     309     362 ..     272     372 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0063
                           DUF1664 46 vskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredls 97
                                      v++++  + +s  +t ++ + ri++++k+++e ++  k+ik  v+++ +d++
  gi|298675239|ref|YP_003726989.1| 28 VTQKVIPLEKSAIETYNDTETRIKSLNKRINELERFEKNIKGYVEKLADDTD 79
                                      566666667777778888899************************9999886 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.015
                           DUF1664  40 sdavesvskqleq.vseslaatkrhLssridrvdkkl 75 
                                        d ++s +++ +q + e+++++k++ +++i+++++++
  gi|298675239|ref|YP_003726989.1|  91 VDTCSSYTNKWTQyLEEEIKSQKKQCENEIENIESQV 127
                                       578888888887725689**************99875 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.49
                           DUF1664  42 avesvskqleqvseslaa...tkrhLssridrvdkkldeqkeiskeikeevtev 92 
                                        ++++++q   + ++  +   +k++++ +i++ d +  e  + ++ei ++++++
  gi|298675239|ref|YP_003726989.1| 309 CLKNIAQQYGYIVTECLErgyVKNEITIKIHKSDGNRTEKYANINEIFNQLSSL 362
                                       455555555554433322122688888888888888888888888888877766 PP

>> DUF327  Protein of unknown function (DUF327)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.4   6.8e-05      0.11      37     110 ..      55     126 ..      22     134 .. 0.81
   2 ?   -0.5   0.1      0.67   1.1e+03      79     116 ..     329     364 ..     286     368 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.8e-05
                                       HHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHT..-----HHHHHHHHHHHHHHH CS
                            DUF327  37 eseeelkelleeidkqgerLaesrtiedlkkYkklvkeflkevvknslklkkersldrkgrsrvykivkeiDek 110
                                       ++ +el+++ ++i+   e+La++ + e++ ++k++v +  ++++++  ++ +e+  +  +++++ + +++i+++
  gi|298675239|ref|YP_003726989.1|  55 KRINELERFEKNIKGYVEKLADDTDSEEIIEFKDAVVDTCSSYTNKWTQYLEEEIKS--QKKQCENEIENIESQ 126
                                       455679999************************************999998876654..366777777777665 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.67
                                       HHHHHHHHHT..-----H.HHHHHHHHHHHHHHHHHHHH CS
                            DUF327  79 vvknslklkkersldrkg.rsrvykivkeiDekldeLte 116
                                       +vkn +++k  +s    g r+++y  ++ei ++l +L +
  gi|298675239|ref|YP_003726989.1| 329 YVKNEITIKIHKS---DGnRTEKYANINEIFNQLSSLGS 364
                                       4555555554443...23388999999999888888865 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.8   0.00029      0.47      28      68 ..      35      75 ..      19      90 .. 0.87
   2 ?    0.7   0.5       0.4   6.4e+02      48      78 ..      95     124 ..      76     132 .. 0.46
   3 ?    1.3   0.1      0.26   4.3e+02      44      73 ..     336     365 ..     330     373 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00029
                           BLOC1_2 28 lNeaasekykklkdvaaslekkleklnekyeelqpylqqid 68
                                      l ++a+e y++ +++++sl+k +++l++ +++++ y++++ 
  gi|298675239|ref|YP_003726989.1| 35 LEKSAIETYNDTETRIKSLNKRINELERFEKNIKGYVEKLA 75
                                      668999******************************99986 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.4
                           BLOC1_2  48 kkleklnekye..elqpylqqidqiekqvteLe 78 
                                       ++  + + +y   e+++++   +q e++++ +e
  gi|298675239|ref|YP_003726989.1|  95 SSYTNKWTQYLeeEIKSQK---KQCENEIENIE 124
                                       4444444444311333333...33333333333 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.26
                           BLOC1_2  44 aslekkleklnekyeelqpylqqidqiekq 73 
                                        +++k+  +  eky+++++ ++q+  +  +
  gi|298675239|ref|YP_003726989.1| 336 IKIHKSDGNRTEKYANINEIFNQLSSLGSE 365
                                       556666666777888888888888777655 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.7    0.0039       6.4      64      95 ..      43      74 ..      35      79 .. 0.83
   2 ?    4.5   1.2      0.02        33      63      84 ..     105     126 ..     100     128 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0039
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2 64 keeLeerketlekeiktlekqleklekeleel 95
                                       ++ e+r+++l+k+i++le+ +++++  +e+l
  gi|298675239|ref|YP_003726989.1| 43 YNDTETRIKSLNKRINELERFEKNIKGYVEKL 74
                                      56789999***********9999998888776 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.02
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  63 vkeeLeerketlekeiktlekq 84 
                                       ++ee + +k+++e ei+++e+q
  gi|298675239|ref|YP_003726989.1| 105 LEEEIKSQKKQCENEIENIESQ 126
                                       5555666666666666666655 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   8.6     0.011        18      28     100 ..      41     120 ..      21     126 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.011
                     Tropomyosin_1  28 qenlekeqeiksLtkknqqle...eevekleeklkeakekaeesekkktnne....altrkiqlLEeeleesdkkLk 97 
                                       ++  + e  iksL+k++++le   +++  + ekl + +++ e  e k++  +      ++  q LEee+ +  k+ +
  gi|298675239|ref|YP_003726989.1|  41 ETYNDTETRIKSLNKRINELErfeKNIKGYVEKLADDTDSEEIIEFKDAVVDtcssYTNKWTQYLEEEIKSQKKQCE 117
                                       55567899999999999766422145666666666666666666655555558884556778999999998888766 PP

                     Tropomyosin_1  98 ett 100
                                       + +
  gi|298675239|ref|YP_003726989.1| 118 NEI 120
                                       655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1691  (0.0943165); expected 358.6 (0.02)
Passed bias filter:                      764  (0.0426125); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 2468.97
//
Query:       gi|298675240|ref|YP_003726990.1|  [L=356]
Description: hypothetical protein Metev_1335 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-49  169.0  44.6    1.6e-49  168.8  44.6    1.0  1  AI-2E_transport  AI-2E family transporter


Domain annotation for each model (and alignments):
>> AI-2E_transport  AI-2E family transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.8  44.6   8.9e-54   1.6e-49       2     325 ..      10     342 ..       9     344 .. 0.92

  Alignments for each domain:
  == domain 1  score: 168.8 bits;  conditional E-value: 8.9e-54
                   AI-2E_transport   2 llilvllllllalypfiselllplliAlvlayllnpvvkfLkkrgvkrvlavllvlllllvllvllvlllvplliaq 78 
                                       ++i++lll++++++++++e++  ++++++l y+l pv+ +L+k   + ++a ++ +l++l +l l ++ll+++++  
  gi|298675240|ref|YP_003726990.1|  10 FIISLLLLVSIIAIYLTKEFVPVVVFSIFLTYVLYPVYSYLEKVTKSERIASSISVLSALFILGLCIYLLLSSAVRE 86 
                                       789999************9**********************6666666677778888999999************** PP

                   AI-2E_transport  79 ltqlvkslpayidslqnilnelpslleele.n.......liqalkqslskilsnilssilnsllsllasllglilsl 147
                                       +++l++s  ++ + + ++ +el +                 + l q + ++++ + +++ ++l+s++ +++ +++s+
  gi|298675240|ref|YP_003726990.1|  87 ISKLITSPDQIREPIIALEKELLDFISSTDyLsfiaesyISNGLSQPVVTVINWVSPYVKTFLTSFITNTPLYLISF 163
                                       *******997777777776666655544433356677789999********************************** PP

                   AI-2E_transport 148 vlvllllffllldgeklrqgilkllpervrervkailrelektlsgylrgqvlvaliigvlvfigllilgvpyalll 224
                                       vl+ll+++++l d +++r  i+ ++pe++++ v+ +++el+ ++ +++++ +++++++gv++ +g+ +lg+py+ +l
  gi|298675240|ref|YP_003726990.1| 164 VLTLLFTYYFLIDARRIRAQIMDVIPEKNKHVVSLFINELNVIYYNLFNIFFVTSFLTGVIASVGFFLLGIPYPVIL 240
                                       ***************************************************************************** PP

                   AI-2E_transport 225 ailvglanliPyiGavivlipiaiialltgg.ikevlivlivvllvqliegnilePklmgkrlglhplvillsllag 300
                                       ++ v+l+ l+P++Ga +++ip +i+ l++++  ++++i+l+++++++++ +++++P+l ++++++hp+++lls+ a 
  gi|298675240|ref|YP_003726990.1| 241 GMAVFLLTLLPLVGAPVIYIPFFIYYLIIQDyATAIIILLFGIFILSIFPDSFIRPRLAKNKASIHPVITLLSFTAP 317
                                       *******************************888888899999999******************************* PP

                   AI-2E_transport 301 gklfGlvGlilavpltavikailea 325
                                       + + G+ G+i+++++++++ a++++
  gi|298675240|ref|YP_003726990.1| 318 IFVIGFTGFIVGPLVYGFLLAFYRT 342
                                       *********************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1029  (0.0573931); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2309.89
//
Query:       gi|298675241|ref|YP_003726991.1|  [L=113]
Description: nitrogen regulatory protein P-II [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-05   23.7   0.3    7.2e-05   23.3   0.3    1.1  1  P-II      Nitrogen regulatory protein P-II


Domain annotation for each model (and alignments):
>> P-II  Nitrogen regulatory protein P-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.3     4e-09   7.2e-05       1      99 [.      10     103 ..      10     105 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 4e-09
                                       EEEEEEGGGHHHHHHHHHHTTGGCEEEEEEEEEESTCCEEEECTTEEEEEEEEEEEEEEEEEEGGGHHHHHHHHHHH CS
                              P-II   1 ieaiirpekleevkeaLekagvkgltvtevkGrGkqkghtelyrgaeyevellpkvkleivvsdedvekvveaiika 77 
                                       i +i+++   ++v +a +kag +g tv+  +G+G  ++  +++ g  +e e   k  +  +v+ +  e+v + ii+a
  gi|298675241|ref|YP_003726991.1|  10 IVTIVKKGWGDTVVQASKKAGAQGGTVIFGRGTGIHED--QTFMGFIVEPE---KEIVLTIVPSSISERVSKRIIDA 81 
                                       678999999******************98777777774..44566666544...66666667*************** PP

                                       H-SSSTTSEEEEEEEESEEEET CS
                              P-II  78 aktgeiGDGkiFvlpveeviri 99 
                                       +  +++G G  F+lpv++v  i
  gi|298675241|ref|YP_003726991.1|  82 VDLEKPGNGMGFMLPVDRVFGI 103
                                       *****************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 840.54
//
Query:       gi|298675242|ref|YP_003726992.1|  [L=242]
Description: hypothetical protein Metev_1337 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-71  239.6  21.9    2.5e-71  239.4  21.9    1.0  1  DUF1538   Protein of unknown function (DUF1538)
  ------ inclusion threshold ------
        3.4    7.7  12.8        1.3    9.0   0.5    3.0  3  DUF1304   Protein of unknown function (DUF1304)


Domain annotation for each model (and alignments):
>> DUF1538  Protein of unknown function (DUF1538)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  239.4  21.9   2.8e-75   2.5e-71       2     210 ..      23     231 ..      22     232 .. 0.99

  Alignments for each domain:
  == domain 1  score: 239.4 bits;  conditional E-value: 2.8e-75
                           DUF1538   2 vlvlllfqllvlklslkelaeillGlllvvlGlalFllGvelgllplGeqvgsklakkkklllvllvafllGflvtl 78 
                                       ++++++fq+l+lk +  el++++ G++l+ +G++lFl Gv  g+lp+G+++g+ l + ++ +++++++f++Gfl+t+
  gi|298675242|ref|YP_003726992.1|  23 LIFFAIFQILYLKFPRLELVKLIRGIILTAIGMILFLYGVYNGFLPVGQEIGEILGNFEHKWILMPFGFIMGFLATF 99 
                                       689************************************************************************** PP

                           DUF1538  79 AEPalsvlakqveevsagaikkkvlilavaiGvglaialgvlrillgislkylllpgyllvllltllvpkefvaiaf 155
                                       AEPa++vl  q+ee s+g ik++++i++++iGvg+++a++++++++gi+++y+++pgy+l++ll +l++k+f+aiaf
  gi|298675242|ref|YP_003726992.1| 100 AEPAVRVLCYQIEESSSGFIKSNLMIYTLSIGVGVFVAIAMAKLVYGIPFQYIIIPGYILAILLLWLSDKDFIAIAF 176
                                       ***************************************************************************** PP

                           DUF1538 156 DsgGvttgpitvplilalglGvasalegknalvdgFGlvalaslgPilavlllgl 210
                                       D+gGv+tgp++v++++++++Gvas+++g+n+++dgFGlva+++l+Pi++v++lg+
  gi|298675242|ref|YP_003726992.1| 177 DAGGVATGPMAVTFLMSMAIGVASSIDGRNPVIDGFGLVAMIALAPIIFVMILGV 231
                                       ******************************************************8 PP

>> DUF1304  Protein of unknown function (DUF1304)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.5   0.00015       1.3      40      79 ..      55      94 ..      22     110 .. 0.80
   2 ?    5.0   2.9    0.0027        24      43     100 ..     121     180 ..     109     194 .. 0.83
   3 ?   -1.0   0.3      0.18   1.7e+03     100     106 ..     214     220 ..     175     235 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00015
                           DUF1304 40 vlaanqGlYNgfLAagliwglllgseavglalvlfflgcv 79
                                      ++ +  G+YNgfL +g  +g +lg+ + +  l+ f+ ++ 
  gi|298675242|ref|YP_003726992.1| 55 MILFLYGVYNGFLPVGQEIGEILGNFEHKWILMPFGFIMG 94
                                      567788**************99987755555555554444 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0027
                           DUF1304  43 anqGlYNgfLAagliwglllgseavglalvlfflgcvvvaglygaltask..killvQgl 100
                                        n  +Y + +++g+++++++ + ++g  ++ +++   ++a l ++l++++   i++  g 
  gi|298675242|ref|YP_003726992.1| 121 SNLMIYTLSIGVGVFVAIAMAKLVYGIPFQYIIIPGYILAILLLWLSDKDfiAIAFDAGG 180
                                       67789*************999999***********************9996556555554 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.18
                           DUF1304 100 lpallAl 106
                                       l+a++Al
  gi|298675242|ref|YP_003726992.1| 214 LVAMIAL 220
                                       3333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       846  (0.0471861); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1696.55
//
Query:       gi|298675243|ref|YP_003726993.1|  [L=229]
Description: hypothetical protein Metev_1338 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-66  223.5  31.9      2e-66  223.3  31.9    1.0  1  DUF1538   Protein of unknown function (DUF1538)


Domain annotation for each model (and alignments):
>> DUF1538  Protein of unknown function (DUF1538)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.3  31.9   1.1e-70     2e-66       1     211 []      19     228 ..      19     228 .. 0.98

  Alignments for each domain:
  == domain 1  score: 223.3 bits;  conditional E-value: 1.1e-70
                           DUF1538   1 ivlvlllfqllvlklslkelaeillGlllvvlGlalFllGvelgllplGeqvgsklakkkklllvllvafllGflvt 77 
                                       i++++llf l+++  +l+ +  +l G+++v+lG+ lFl+Gv+lg+lp+Ge++gs+l+k+++ll++++++fll flvt
  gi|298675243|ref|YP_003726993.1|  19 IIVTVLLFILFFVGPDLELILPFLSGAVMVILGMGLFLMGVKLGMLPMGESIGSELPKHGSLLFIIVITFLLAFLVT 95 
                                       67889999999****************************************************************** PP

                           DUF1538  78 lAEPalsvlakqveevsagaikkkvlilavaiGvglaialgvlrillgislkylllpgyllvllltllvpkefvaia 154
                                       +AEP+++vl++  + vs+  +++ +li+++a+G g+++a+++lri +gi++kyl+++gyl+v++l++++p+ef+ai+
  gi|298675243|ref|YP_003726993.1|  96 IAEPDVRVLSSMFAMVSE-GVSRIALIISIALGLGVFVAISMLRIAYGIPIKYLFTVGYLFVIILSFFTPPEFLAIS 171
                                       ****************77.6999****************************************************** PP

                           DUF1538 155 fDsgGvttgpitvplilalglGvasalegknalvdgFGlvalaslgPilavlllgll 211
                                       fD+gGvttgp++vp+ilalg+G+as+l+gk++l+dgFGl++las+gPi++v+l+g++
  gi|298675243|ref|YP_003726993.1| 172 FDAGGVTTGPLAVPVILALGIGIASMLGGKSQLSDGFGLIGLASIGPIITVMLMGVF 228
                                       *******************************************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       894  (0.0498633); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 1755.60
//
Query:       gi|298675244|ref|YP_003726994.1|  [L=678]
Description: sodium/hydrogen exchanger [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.5e-69  233.1  54.4    5.8e-69  232.7  54.4    1.1  1  Na_H_Exchanger  Sodium/hydrogen exchanger family
    4.1e-25   88.3   0.1    1.5e-24   86.5   0.1    2.0  2  TrkA_N          TrkA-N domain
    2.8e-17   62.3   0.0    8.3e-17   60.8   0.0    1.9  1  TrkA_C          TrkA-C domain
  ------ inclusion threshold ------
        4.1    7.3  10.7        4.9    7.0   0.1    4.2  3  CAAD            CAAD domains of cyanobacterial aminoacyl-tRNA


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  232.7  54.4   1.3e-72   5.8e-69       3     369 ..      11     368 ..       9     376 .. 0.96

  Alignments for each domain:
  == domain 1  score: 232.7 bits;  conditional E-value: 1.3e-72
                                       HHHHHHHHHHH.HHHHTTSXHHHHHHHHHHHHTTTTTS.....HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHH CS
                    Na_H_Exchanger   3 llillallvgl.larrlklpeivgliiaGlllGpsglgliepseedlevlselglilllFlaGleldlrelrknlks 78 
                                       ++i  ++++ l +++rl++++ivg++++Gl++Gp+gl+lie+  ++++ lse+g+illlF +G+el+l+el++++k 
  gi|298675244|ref|YP_003726994.1|  11 IIIG-LSIAALyICNRLGISVIVGFLLTGLIVGPHGLKLIENI-HQVDSLSEIGIILLLFTIGVELSLQELWSVRKG 85 
                                       3333.44444426******************************.********************************* PP

                                       HHHHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHHHC CS
                    Na_H_Exchanger  79 illlallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDava 155
                                       + +++ l+vl t+++++ ++y+   lgi+++eal++g+++s++++++vl+il+ ++++++  g + l++++++D++ 
  gi|298675244|ref|YP_003726994.1|  86 VAIGGSLQVLSTILVTTGIVYY---LGISITEALFVGFLISLSSTAIVLKILQGKNEINTPHGKMSLAILIFQDVII 159
                                       ***************9999997...789************************************************* PP

                                       CCCCHHHHHHTX.XXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTHHHHHHHHHHHHHHHHHHHHH CS
                    Na_H_Exchanger 156 vvllavllalak.eeaggetslllllliflvvavgglllglvigwllrlitrftdddrelevllvlllallaallae 231
                                       v++  v + la+ e + g +sll +++ + +++++++ ++++++ +l  + r+  ++rel++l v+ +++++a+l+ 
  gi|298675244|ref|YP_003726994.1| 160 VPMMLVTPLLAGgELNLGSSSLLIIAKGLGIILLIIVSAKWIVPGILYQVART--RNRELFLLSVIFICFSIAWLTA 234
                                       ************999**************************************..9********************* PP

                                       TSXXXHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHSXHHHHHXXHHHHHHHHHHHHHHHTHHH CS
                    Na_H_Exchanger 232 llgvsgilgaflaGlvlseyefsnklseklesfreglfnplfFvlvGlsldlkvlnnhlsvlilvllilvaillgri 308
                                       ++g+s  lgaflaGl++se+e+s+++  k+ +fr ++f++lfFv+vG+ ld +++   l+ +i+ lli+v +++ + 
  gi|298675244|ref|YP_003726994.1| 235 SVGLSLSLGAFLAGLIISESEYSHQALSKILPFR-DIFLGLFFVSVGMLLDYTFI---LQYPIIFLLIVVGVIVFKS 307
                                       **********************************.9******************9...999999999999999**** PP

                                       HHHHHHTTTXSSXHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTTSSTTTCSTSXHHH CS
                    Na_H_Exchanger 309 lavflllrllglslrealiigfgglqrgavalalaalgpalgllarelyallivvvlftvl 369
                                       l + +++ ++g+++r+++++g++++q+g+++l+l  +g ++++++  +y +++ v ++t+ 
  gi|298675244|ref|YP_003726994.1| 308 LIAGTVTFIMGYPIRTSILVGLALCQVGEFSLILSKVGLDANVISDSVYQIFLSVSVVTMA 368
                                       ***********************************************************98 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.5   0.1   3.3e-28   1.5e-24       2     115 ..     419     532 ..     418     533 .. 0.98
   2 ?   -3.5   0.0       2.8   1.2e+04      18      34 ..     615     632 ..     613     639 .. 0.71

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 3.3e-28
                                       EEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHH CS
                            TrkA_N   2 iiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeanil 78 
                                       ii+G+G  Gr++a+  + +g++++vi++++++v++ r +g ++++gdat+e vLe+a+i++a++++ a++d  a+  
  gi|298675244|ref|YP_003726994.1| 419 IILGYGFNGRTIAKAAKVAGIPYIVIETNPDTVKSERSKGEPIIYGDATHELVLEKANIKSARIMVLAISDFFATRQ 495
                                       9***************998888******************************************************* PP

                                       HHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEEE CS
                            TrkA_N  79 avllakelnpkkkiiaraqdpehaellkklgadvvis 115
                                       ++ +ak+lnpk++ii+r+ + ++++ll++ gad+vis
  gi|298675244|ref|YP_003726994.1| 496 VIDIAKSLNPKLYIITRTPYMKDIDLLYESGADEVIS 532
                                       ************************************8 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.8
                                       HH.TTEEEEEEESSHHHH CS
                            TrkA_N  18 se.ggkdvvvidkdeerv 34 
                                       ++ +g  v++i++d e++
  gi|298675244|ref|YP_003726994.1| 615 RQkYGVTVLAIERDSETI 632
                                       553444599999999876 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.8   0.0   1.9e-20   8.3e-17       4      69 ..     596     663 ..     593     664 .. 0.96

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 1.9e-20
                                       EEEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHHHHHHH CS
                            TrkA_C   4 vtvpagsplvGktlkelnlrar.gvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlaelrell 69 
                                       +++++ sp ++k l+el+lr++ gv+v+ai R+ + +++p gdt+L +GD+++v+g+p++lae+++++
  gi|298675244|ref|YP_003726994.1| 596 FKLNKRSPSANKCLSELGLRQKyGVTVLAIERDsETITNPHGDTKLFPGDIVIVLGKPDHLAEAQAFF 663
                                       78999**********************************************************99987 PP

>> CAAD  CAAD domains of cyanobacterial aminoacyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0011       4.9      39      63 ..       2      26 ..       1      30 [. 0.93
   2 ?    1.8   3.2     0.048   2.2e+02      11      47 ..     290     326 ..     279     334 .. 0.86
   3 ?   -0.3   0.1      0.22   9.9e+02      17      42 ..     364     389 ..     353     393 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0011
                              CAAD 39 diPllpplleLvGlgytgwFvyryL 63
                                      diPl++ ++ ++Gl  ++ ++ ++L
  gi|298675244|ref|YP_003726994.1|  2 DIPLFNDFIIIIGLSIAALYICNRL 26
                                      7********************9887 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.048
                              CAAD  11 erklkviglilaaivalklalavldaiddiPllppll 47 
                                       + +++ + +++++iv+  l+++++  i   P+  ++l
  gi|298675244|ref|YP_003726994.1| 290 QYPIIFLLIVVGVIVFKSLIAGTVTFIMGYPIRTSIL 326
                                       6688999999*****************9999977764 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.22
                              CAAD  17 iglilaaivalklalavldaiddiPl 42 
                                       ++ ++a+ +++ ++ +v+d + ++Pl
  gi|298675244|ref|YP_003726994.1| 364 VVTMAATSFIVDFSPKVVDSVSKLPL 389
                                       4455666677889999*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (678 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       995  (0.0554967); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.44
# Mc/sec: 4587.38
//
Query:       gi|298675245|ref|YP_003726995.1|  [L=494]
Description: sodium/proline symporter [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-98  330.0  23.9      3e-98  329.4  23.9    1.3  1  SSF       Sodium:solute symporter family


Domain annotation for each model (and alignments):
>> SSF  Sodium:solute symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  329.4  23.9  1.7e-102     3e-98       1     406 []      38     440 ..      38     440 .. 0.96

  Alignments for each domain:
  == domain 1  score: 329.4 bits;  conditional E-value: 1.7e-102
                               SSF   1 yflagrsltgfvlglslaasnisaasfvGlaGavaasGlavvllelgalllvlllllllaerlr.....nagalTlp 72 
                                       y+l+gr+l ++v++ls  as++s+++++Gl+Ga+++sGl+ ++++lg+ ++ +++++++a+rlr       + lT+p
  gi|298675245|ref|YP_003726995.1|  38 YILGGRRLNSWVTALSSQASDMSGWLLLGLPGAAYLSGLEAGWIALGLGIGTYFNWKFIAKRLRkytkmAGNSLTIP 114
                                       9***************************************************************888877799**** PP

                               SSF  73 dylskRfkgkr.ilvylsalslllvitlklsvdlvggaklielalGlnyetavlllaaltalYtviGGllAvvytdt 148
                                        ++++Rfk++  +l+ +sa+ +l+++ ++ s++lv+g+kl+ +++ l+y ta+ +++++++ Yt++GG++Av +td 
  gi|298675245|ref|YP_003726995.1| 115 VFFENRFKDNTkMLRSISAIFILIFFLFYTSSGLVAGGKLFSTVFELDYFTALTIGVVVVISYTFLGGFMAVCWTDF 191
                                       ********9988***************************************************************** PP

                               SSF 149 iqavlmlvgalilliivllevGgleslveklkeaapkvvdllt.pdslkllrdpltalslwlglvlGvaglphilvR 224
                                        q++lm+++   ++i+  +++Gg+ s ++ l +++p++v+ l+  d+   ++  ++++s+  +++lG++g+philvR
  gi|298675245|ref|YP_003726995.1| 192 FQGMLMVLAITAVPILGAIDMGGIGSTIDILNNIDPHLVNPLReLDG--SVLPLISIISM-SAWGLGYFGQPHILVR 265
                                       ************************************88777763344..46777777777.9*************** PP

                               SSF 225 flaakdakailkgvlkltivlilvligmisiilfaiklagavpkavgtevgvsniaypeLvvkllpnllaGlllavm 301
                                       f+a+++ + i ++++++++++ + l+ +++++l + ++          e  +s+ +++ +v++l+ +++aG+lla++
  gi|298675245|ref|YP_003726995.1| 266 FMAIDNPEHIKRSRIIAMVWVTISLAFAVFVGLVGRAYLPQ---F--LEGSASETVFMVMVNNLFHPVIAGVLLAAI 337
                                       ***********************************999755...4..567899************************ PP

                               SSF 302 lAaimstltslllsassaftkDlYkkirrkasakekelvgvsriivlvvislaillavqeeqkgvlklvelafagla 378
                                       lAaimst +s+ll+++saft+D+Y  +++   a++kelv+++r +v+ ++ +a l a+++e++ vl+lv++a+ag++
  gi|298675245|ref|YP_003726995.1| 338 LAAIMSTADSQLLVSASAFTEDIYRFVFKTD-ASDKELVWMGRFTVITISIIAYLFALDPESS-VLDLVSYAWAGFG 412
                                       ******************************9.*******************************.************* PP

                               SSF 379 savlavillalfwkrvneqGAlagliiG 406
                                       +a+++ i+++lf k+++++ Al g++ G
  gi|298675245|ref|YP_003726995.1| 413 AAFGPPIIFSLFSKKMTKNAALGGMMSG 440
                                       **************************88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (494 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       911  (0.0508115); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 3210.06
//
Query:       gi|298675246|ref|YP_003726996.1|  [L=417]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-21   75.8   0.3    1.5e-20   73.6   0.0    2.3  2  OrfB_IS605      Probable transposase
    2.8e-10   40.0   0.3      1e-09   38.2   0.1    2.1  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.005   16.6   0.5      0.012   15.4   0.5    1.6  1  DUF919          Nucleopolyhedrovirus protein of unknown funct
  ------ inclusion threshold ------
       0.12   12.8   0.0       0.27   11.6   0.0    1.6  1  RuvX            Holliday junction resolvase


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.68     3e+03      37      60 ..      39      62 ..      27      77 .. 0.75
   2 !   73.6   0.0   3.3e-24   1.5e-20      10     119 ..     185     299 ..     176     300 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.68
                        OrfB_IS605 37 twflykgrrlksdykylakeiael 60
                                      + f+++g+ l++d  y + +  e 
  gi|298675246|ref|YP_003726996.1| 39 QYFFNHGKYLDKDTAYHTVKENEN 62
                                      568889999999999988877665 PP

  == domain 2  score: 73.6 bits;  conditional E-value: 3.3e-24
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkkskn.....ykkasrklarlh 81 
                                        ++ + n++++iDlG+ n+at+vt+ gt+f+ +gr +ks +++++ke+ +lqs ++k+             k+ r +
  gi|298675246|ref|YP_003726996.1| 185 IAELDYNSHLSIDLGVDNFATCVTTGGTAFILDGRVIKSYNRWWNKEKSRLQSVYDKQDVdngikDVDNGIKMDRFS 261
                                       56677899*************************************************98777866667778****** PP

                        OrfB_IS605  82 rkrsrrrkhllhklathliktlkevgvetLnvgnmkdi 119
                                       +kr  ++++++++ ++h++k++ e+ ++++++g+mk+i
  gi|298675246|ref|YP_003726996.1| 262 NKRFWKINDYMNQCVNHVVKHCLENRIGNIVIGEMKEI 299
                                       ************************************87 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.4   6.1e+03       9      21 ..     167     179 ..     164     181 .. 0.88
   2 !   38.2   0.1   2.3e-13     1e-09       1      69 []     318     392 ..     318     392 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.4
                    OrfB_Zn_ribbon   9 eykakeyGikvee 21 
                                       +yk +++ i++++
  gi|298675246|ref|YP_003726996.1| 167 KYKGRWFEIEFVY 179
                                       79*******9987 PP

  == domain 2  score: 38.2 bits;  conditional E-value: 2.3e-13
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke......alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f++++++l+ k++ +Gik+ evn+ayTSk  +   +  ++      ++s+r    ++ g  +++D+n+a+Nil++
  gi|298675246|ref|YP_003726996.1| 318 FARFRHKLASKCEYHGIKYNEVNEAYTSKVDALALEPIRKhknylgKRSKRGIFQSSTGRLINADINGALNILRK 392
                                       899**************************9766655555555677*99************************986 PP

>> DUF919  Nucleopolyhedrovirus protein of unknown function (DUF919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.5   2.7e-06     0.012      15      58 ..       4      45 ..       2      47 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.7e-06
                            DUF919 15 qaKrkltiksqHfErlkkitKnpkElqdlekklnklRqeFLnfg 58
                                       +K  l+ + q +E lk++tK +k l +   +l ++Rq+F+n g
  gi|298675246|ref|YP_003726996.1|  4 TQKNHLRADKQTYETLKRLTKLSKNLYNF--TLYTIRQYFFNHG 45
                                      58999******************888765..8**********98 PP

>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.1e-05      0.27      37     106 ..     273     352 ..     259     374 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.1e-05
                                       HHHHHHHHHHHHHTT--EEEEE--........----SSS---SSTTHHHHHHHHHT....T-EEEEE--S----XXX CS
                              RuvX  37 ekdleelkelvkeeeveeiVvGlP........lnldgsegesakkvrkfaeeLakrl..kklpvelvDErlttveae 103
                                       ++ ++++ + + e+++ +iV+G          +  +++++ ++  +++f ++La+++  ++++   v+E +t++  +
  gi|298675246|ref|YP_003726996.1| 273 NQCVNHVVKHCLENRIGNIVIGEMkeikqeqnIGKENTQNFQTIPFARFRHKLASKCeyHGIKYNEVNEAYTSKVDA 349
                                       789999****************99777776656666777777888899999999998778999**********8755 PP

                                       XXX CS
                              RuvX 104 ril 106
                                        +l
  gi|298675246|ref|YP_003726996.1| 350 LAL 352
                                       544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       915  (0.0510346); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2856.55
//
Query:       gi|298675247|ref|YP_003726997.1|  [L=231]
Description: hypothetical protein Metev_1343 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00029   20.0   3.8    0.00038   19.6   3.8    1.0  1  Acyl_transf_3  Acyltransferase family
  ------ inclusion threshold ------
      0.017   14.9   5.3       0.29   10.9   2.5    2.2  2  DUF2427        Domain of unknown function (DUF2427)
       0.04   12.8   1.9       0.15   10.9   0.0    2.0  2  LMBR1          LMBR1-like membrane protein
       0.07   11.9   4.0       0.15   10.8   4.0    1.5  1  O-antigen_lig  O-antigen ligase like membrane protein
      0.072   12.9   1.2       0.14   12.0   1.2    1.5  1  Amastin        Amastin surface glycoprotein
      0.078   12.3   0.6       0.35   10.2   0.0    1.8  2  Urate_ox_N     Urate oxidase N-terminal
       0.19   11.4   7.4       0.39   10.3   7.4    1.4  1  TauE           Sulfite exporter TauE/SafE
       0.33   11.2   3.5       0.44   10.8   3.5    1.1  1  EI24           Etoposide-induced protein 2.4 (EI24)
       0.35   10.3   4.7        1.5    8.2   4.0    2.3  3  DUF1129        Protein of unknown function (DUF1129)
       0.92    9.8   8.1          2    8.7   8.1    1.5  1  TctB           Tripartite tricarboxylate transporter TctB fam
        1.1   10.0   4.3         24    5.7   1.1    2.3  2  PrgI           PrgI family protein
        1.2    9.1   4.2        9.3    6.3   0.1    2.5  2  DUF485         Protein of unknown function, DUF485
        1.5    9.4   4.5        7.2    7.2   0.0    2.3  2  GTA_holin_3TM  Holin of 3TMs, for gene-transfer release
        1.9    8.3  12.3       0.48   10.2   4.8    2.2  2  DUF4118        Domain of unknown function (DUF4118)
        3.7    7.8  11.9         34    4.6  11.8    2.0  1  DUF3792        Protein of unknown function (DUF3792)


Domain annotation for each model (and alignments):
>> Acyl_transf_3  Acyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   3.8   3.2e-07   0.00038     155     278 ..       4     125 ..       3     130 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.2e-07
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Acyl_transf_3 155 rkvrkshlllllilllllslvfirhelfgpatsvgllplpsvlallfflfGalladaddrdrnlsrglkislllsll 231
                                       +k+r +++l++++++++l+l +  ++  +++ +v+l +l  v +l++ +fG+l++  ++ d  l+ g  ++++++ +
  gi|298675247|ref|YP_003726997.1|   4 KKIRVWGILAIIVFAAYLILPVASAVDGNNNVPVYLIAL--VTILIVSVFGGLMYAGYKADADLNKGEMRRAIAGTF 78 
                                       79999*******************999888777776544..444********************************* PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Acyl_transf_3 232 llalillalfgqtdggglvasvliqsaslllvslgimllllllfalp 278
                                       ++ +i+l +++ ++  + ++   ++   l+ v++g+++  ++++  p
  gi|298675247|ref|YP_003726997.1|  79 SVGFIILMVLSLHYSFDENKEIVTTFIQLVGVVIGFYFGTRTALSVP 125
                                       *************9999999999999999999999999999887766 PP

>> DUF2427  Domain of unknown function (DUF2427)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.5   0.00024      0.29      19      94 ..       9      88 ..       3      94 .. 0.71
   2 ?    4.3   0.1     0.028        34      52      82 ..     100     130 ..      97     136 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00024
                           DUF2427 19 wvHiilmtlalvvvyPvalvL.slaksrwylpvqivnlvlavlglllghiykgstPelypn....niyaklswillill 92
                                      w   +++++a+ +++Pva +  ++ +  +yl +++  l++ v g l+++ yk+ + +l ++    +i +++s+ ++il+
  gi|298675247|ref|YP_003726997.1|  9 WGILAIIVFAAYLILPVASAVdGNNNVPVYLIALVTILIVSVFGGLMYAGYKADA-DLNKGemrrAIAGTFSVGFIILM 86
                                      556688999********97663677789999999999999999999999999987.76555111156666666555555 PP

                           DUF2427 93 av 94
                                      ++
  gi|298675247|ref|YP_003726997.1| 87 VL 88
                                      43 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.028
                           DUF2427  52 ivnlvlavlglllghiykgstPelypnniya 82 
                                       iv + + ++g+++g+ ++++t    p+n+ +
  gi|298675247|ref|YP_003726997.1| 100 IVTTFIQLVGVVIGFYFGTRTALSVPKNMTG 130
                                       899999*************997677888765 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   2.1      0.29   3.4e+02     126     169 ..       5      45 ..       3      58 .. 0.80
   2 ?   10.9   0.0   0.00013      0.15     133     213 ..      75     151 ..      67     210 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.29
                             LMBR1 126 naiiyllllvivlglliyvliilqklsllsiksllpilislant 169
                                       +++++++l++iv++  +++ ++ + ++ ++  +++++li+l+++
  gi|298675247|ref|YP_003726997.1|   5 KIRVWGILAIIVFAAYLILPVA-SAVDGNN--NVPVYLIALVTI 45 
                                       5789999999999999998888.7777665..899999998875 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00013
                             LMBR1 133 llvivlglliyvliilqklsllsiksllpilislantwGlvllilllGyGlvelPrslwreiksdldeelkklyfea 209
                                        +++ +g++i+ ++    +s++   ++++i+ + ++ +G+v+  +++     ++P+++  + +s  + ++++++fe 
  gi|298675247|ref|YP_003726997.1|  75 AGTFSVGFIILMVLS-LHYSFD---ENKEIVTTFIQLVGVVIGFYFGTRTALSVPKNMTGTTESGMSLDIENVKFET 147
                                       456667777777777.79****...**********************************955555555666666666 PP

                             LMBR1 210 akln 213
                                       ++l 
  gi|298675247|ref|YP_003726997.1| 148 DELG 151
                                       6554 PP

>> O-antigen_lig  O-antigen ligase like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   4.0   0.00013      0.15     135     217 ..      38     122 ..      11     123 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00013
                     O-antigen_lig 135 sliysvlili.slitgtslktY.......eseskiGykGwfysaNelssilllllpivllyllkkkksikfiiilll 203
                                       +li +v+ili s+  g  +  Y       ++e+  ++ G f ++      +++l+++ l y+  ++k i++ +i l+
  gi|298675247|ref|YP_003726997.1|  38 YLIALVTILIvSVFGGLMYAGYkadadlnKGEMRRAIAGTFSVG------FIILMVLSLHYSFDENKEIVTTFIQLV 108
                                       45555555541555567777889988888888888888888665......55666667778999999999999**** PP

                     O-antigen_lig 204 lillllllGTKval 217
                                       ++++ ++ GT++al
  gi|298675247|ref|YP_003726997.1| 109 GVVIGFYFGTRTAL 122
                                       ***********997 PP

>> Amastin  Amastin surface glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.2   0.00012      0.14      62     143 ..       3      87 ..       1      95 [. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                           Amastin  62 fraaqafsiisilvlaaalllsvllllccsslkwvclllnivsvvtllivwalmvavyy..krfCd.alk.sttaky 134
                                       f+ + +  i++i+v+aa l+l v+ ++   + ++ + l+++v+++++ +   lm a y+   +  + +++     ++
  gi|298675247|ref|YP_003726997.1|   3 FKKIRVWGILAIIVFAAYLILPVASAVD-GNNNVPVYLIALVTILIVSVFGGLMYAGYKadADLNKgEMRrAIAGTF 78 
                                       67788999********************.9*****************************763333234441444589 PP

                           Amastin 135 gaGFgLlvv 143
                                       ++GF++l+v
  gi|298675247|ref|YP_003726997.1|  79 SVGFIILMV 87 
                                       999987654 PP

>> Urate_ox_N  Urate oxidase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.2      0.27   3.2e+02     246     292 ..       3      49 ..       1      54 [. 0.77
   2 ?   10.2   0.0   0.00029      0.35     206     276 ..      56     123 ..      51     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.27
                        Urate_ox_N 246 ysseanwlvlallllagalirhffnlrhkgkkklallvaaaalllav 292
                                       +++   w +la++++a+ li  +  + + +++ + +l+a +++l++ 
  gi|298675247|ref|YP_003726997.1|   3 FKKIRVWGILAIIVFAAYLILPVASAVDGNNNVPVYLIALVTILIVS 49 
                                       66677899999999999999999888888887777777776666654 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00029
                        Urate_ox_N 206 kagekpdpklgkrakqrsvhnnYltlPvlflmlsnHypltysseanwlvlallllagalirhffnlrhkgk 276
                                        ag k d++l k   +r++  ++    +++++ls Hy++      + +v + + l+g++i  +f +r + +
  gi|298675247|ref|YP_003726997.1|  56 YAGYKADADLNKGEMRRAIAGTFSVGFIILMVLSLHYSFDE---NKEIVTTFIQLVGVVIGFYFGTRTALS 123
                                       678889999999999999999988888899999****9854...455899999***********9997755 PP

>> TauE  Sulfite exporter TauE/SafE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   7.4   0.00033      0.39      98     218 ..      12     126 ..       4     130 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00033
                              TauE  98 vlllllallmllrkkrsrakgrerrptaillvligglvGllsGllGiGgGfllvpllllllglplkkavatslllil 174
                                       ++++++a++++l    s+ +g+++ p +++++++ ++v +++Gl+ +G  +    +   l + ++++a+a +  + +
  gi|298675247|ref|YP_003726997.1|  12 LAIIVFAAYLILPVA-SAVDGNNNVPVYLIALVTILIVSVFGGLMYAGYKA---DA--DLNKGEMRRAIAGTFSVGF 82 
                                       455666666666444.45555566666666666667899999999999777...33..3469999999998888899 PP

                              TauE 175 vislagalgyalagavdwpllllllpgallGallGarlarrlse 218
                                       +i ++  l+y +  +  + + ++ l+g+++G ++G+r+a  +++
  gi|298675247|ref|YP_003726997.1|  83 IILMVLSLHYSFDENKEIVTTFIQLVGVVIGFYFGTRTALSVPK 126
                                       9999999999887777788888999************9999887 PP

>> EI24  Etoposide-induced protein 2.4 (EI24)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   3.5   0.00036      0.44      39     128 ..       9     119 ..       3     130 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00036
                                       -TTHHHHHHHHHHHHH............HHHHHHHHHHHHHHHHHHHHHHHHH.HH.....CCTTSHHHHHHHHHHH CS
                              EI24  39 wvllasllvllllllp............lwlfplvalllaapfygllaekvekrhl.....glvkslaeslksllll 98 
                                       w +la++++ ++l+lp            ++l+ lv++l++++f gl+++  ++ +      ++ +++a ++   +++
  gi|298675247|ref|YP_003726997.1|   9 WGILAIIVFAAYLILPvasavdgnnnvpVYLIALVTILIVSVFGGLMYAGYKA-DAdlnkgEMRRAIAGTFSVGFII 84 
                                       56778888888888889999999***9999999**********6666666643.21223445667787444444444 PP

                                       HHHHHHHHHH.....HHTTHHH....HHHHHHHHH CS
                              EI24  99 lllllvllpl.....liPvvglilsplllswltay 128
                                       l++l + + +     +++ + +++ +++++++  +
  gi|298675247|ref|YP_003726997.1|  85 LMVLSLHYSFdenkeIVTTFIQLVGVVIGFYFGTR 119
                                       44444555556799988666799999999998776 PP

>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   4.0    0.0013       1.5     103     165 ..      31      93 ..       9     115 .. 0.71
   2 ?    0.8   0.3      0.24   2.8e+02      91     129 ..      83     118 ..      69     131 .. 0.57
   3 ?   -1.0   0.0      0.85     1e+03      43      56 ..     216     229 ..     204     231 .] 0.88

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0013
                           DUF1129 103 skkkqtas.iGlitlllvalvgGlamvlvyrlltrekkkkkrpplwkrllilllllvvwlvlft 165
                                       ++++   + i l+t+l+v++ gGl++  +    +  +k + r+ +  ++ + +++l+v+ + ++
  gi|298675247|ref|YP_003726997.1|  31 GNNNVPVYlIALVTILIVSVFGGLMYAGYKADADL-NKGEMRRAIAGTFSVGFIILMVLSLHYS 93 
                                       4455555689**************99988887775.7777788888777777777777666554 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.24
                           DUF1129  91 lfallfgilalfskkkqtasiGlitlllvalvgGlamvl 129
                                       ++ ++  + + f+++k+  +   + + lv++v G+++ +
  gi|298675247|ref|YP_003726997.1|  83 IILMVLSLHYSFDENKEIVT---TFIQLVGVVIGFYFGT 118
                                       34444455555555444444...5555666666666655 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.85
                           DUF1129  43 kkGktArqLygtpt 56 
                                        +G++A+++y +pt
  gi|298675247|ref|YP_003726997.1| 216 TTGIVAEKIYSSPT 229
                                       589*******9998 PP

>> TctB  Tripartite tricarboxylate transporter TctB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   8.1    0.0016         2      38     133 ..      13     125 ..       5     126 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0016
                              TctB  38 llallgllllvaadgekeekearedwrkllklvlallaalllyalllep......................lGfila 92 
                                       +++++++ l+++     ++  +  ++ ++  + l++++++ +++ l+                        +Gfi+ 
  gi|298675247|ref|YP_003726997.1|  13 AIIVFAAYLILP----VASAVDGNNNVPVYLIALVTILIVSVFGGLMYAgykadadlnkgemrraiagtfsVGFIIL 85 
                                       333443444441....1222222233444434444444444455555554444444444444444433333588888 PP

                              TctB  93 talflllllgreerkwlkalilavvlallvyllFtklLgvp 133
                                       ++l l + +  e++ +++++i  v++++++y+  +++L+vp
  gi|298675247|ref|YP_003726997.1|  86 MVLSLHYSF-DENKEIVTTFIQLVGVVIGFYFGTRTALSVP 125
                                       888886666.77999*****************999999997 PP

>> PrgI  PrgI family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   1.1      0.02        24      23      71 ..      10      61 ..       5      67 .. 0.48
   2 ?    5.2   0.1      0.03        36      27      65 ..      76     119 ..      70     141 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.02
                              PrgI 23 iflvlallvaiglylllrafl.....eelasvlvillavP.vaalgfykkdglpl 71
                                      ++l+++   ++++yl+l+++      ++++++l+ l+++  v ++g   + g+++
  gi|298675247|ref|YP_003726997.1| 10 GILAII---VFAAYLILPVASavdgnNNVPVYLIALVTILiVSVFGGLMYAGYKA 61
                                      444444...5566666666555556544444444444222122223223555554 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.03
                              PrgI  27 lallvaiglylllrafl..eelasvlvillavPvaalgfy...k 65 
                                       +++ v+++++++l+  +  +e+  ++ +++ +  +++gfy   +
  gi|298675247|ref|YP_003726997.1|  76 GTFSVGFIILMVLSLHYsfDENKEIVTTFIQLVGVVIGFYfgtR 119
                                       44555555555555555568888888888888888888885540 PP

>> DUF485  Protein of unknown function, DUF485
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   2.8      0.18   2.1e+02      15      38 ..       7      30 ..       2      51 .. 0.78
   2 ?    6.3   0.1    0.0077       9.3      17      60 ..      45      87 ..      41      92 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.18
                            DUF485 15 rfafpltaiflvvYfgfvllvafa 38
                                      r+  +l++i++++Y+ +++++a++
  gi|298675247|ref|YP_003726997.1|  7 RVWGILAIIVFAAYLILPVASAVD 30
                                      566689999*********999987 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0077
                            DUF485 17 afpltaiflvvYfgfvllvafapdllatkvgegnitvglllgll 60
                                      +++++++  ++Y g+ + + ++++ + + ++ g+++vg+++ ++
  gi|298675247|ref|YP_003726997.1| 45 ILIVSVFGGLMYAGYKADADLNKGEMRRAIA-GTFSVGFIILMV 87
                                      5678889999*********************.******998776 PP

>> GTA_holin_3TM  Holin of 3TMs, for gene-transfer release
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   2.0      0.17   2.1e+02      75     117 ..       8      50 ..       6      58 .. 0.71
   2 ?    7.2   0.0     0.006       7.2     105     123 .]     102     120 ..      79     120 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.17
                     GTA_holin_3TM  75 gyvtlalllwai.vldPllaaaialglalvPepLwwllgg.vvgf 117
                                       ++++la++++a+ ++ P+  a++  g + vP+ L +l++  +v++
  gi|298675247|ref|YP_003726997.1|   8 VWGILAIIVFAAyLILPV--ASAVDGNNNVPVYLIALVTIlIVSV 50 
                                       699999998876488899..677778899***6665554313555 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.006
                     GTA_holin_3TM 105 epLwwllggvvgfyfvaRs 123
                                        ++ +l+g+v+gfyf+ R+
  gi|298675247|ref|YP_003726997.1| 102 TTFIQLVGVVIGFYFGTRT 120
                                       4899*************96 PP

>> DUF4118  Domain of unknown function (DUF4118)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   4.8    0.0004      0.48       1      47 [.       9      57 ..       9      61 .. 0.79
   2 ?    2.7   0.8     0.088   1.1e+02      10      48 ..      82     122 ..      73     124 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0004
                           DUF4118  1 yllavlllalatllallldklls..lanivllfllavllvallgglgpg 47
                                      +++ ++++++a l++ + + +++  +  ++l+ l+ +l+v+++ggl+++
  gi|298675247|ref|YP_003726997.1|  9 WGILAIIVFAAYLILPVASAVDGnnNVPVYLIALVTILIVSVFGGLMYA 57
                                      6677778888888877776764432589999***************997 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.088
                           DUF4118  10 latllalll.dkllslanivllfllav.llvallgglgpgl 48 
                                        ++l+ l l +++++++ iv++f+ +v +++ +++g + +l
  gi|298675247|ref|YP_003726997.1|  82 FIILMVLSLhYSFDENKEIVTTFIQLVgVVIGFYFGTRTAL 122
                                       22222233313444467888877655525566666776665 PP

>> DUF3792  Protein of unknown function (DUF3792)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6  11.8     0.028        34       7     111 ..       9     113 ..       4     117 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.028
                           DUF3792   7 kgllialvitlilllilalllyftslsekvlsililiililsvfigGflagkkak...kkgllnGllvGllyflill 80 
                                        g+l+++v+++ l+l +a ++  ++ +  v+ i+++ ili+svf g ++ag+ka+   +kg +  +++G + + +++
  gi|298675247|ref|YP_003726997.1|   9 WGILAIIVFAAYLILPVASAV-DGNNNVPVYLIALVTILIVSVFGGLMYAGYKADadlNKGEMRRAIAGTFSVGFII 84 
                                       566777777777777666664.5667778888899999999999999999999975556899999999999666644 PP

                           DUF3792  81 llsllikksgsafslkllikllllllagaiG 111
                                       l+ l ++ s+   + k +++ ++ l++ +iG
  gi|298675247|ref|YP_003726997.1|  85 LMVLSLHYSFD--ENKEIVTTFIQLVGVVIG 113
                                       33333333333..344444444445544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       918  (0.051202); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 1566.35
//
Query:       gi|298675248|ref|YP_003726998.1|  [L=194]
Description: ferric reductase domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-05   23.8   7.7    3.8e-05   23.8   7.7    2.2  3  Ferric_reduct    Ferric reductase like transmembrane componen
  ------ inclusion threshold ------
        1.9    7.8   8.1       0.22   10.9   3.5    1.6  2  ThrE             Putative threonine/serine exporter
          2    7.7  23.2         15    4.8  23.9    2.0  1  Glucos_trans_II  Glucosyl transferase GtrII
        4.1    6.8  13.6        5.4    6.4  13.6    1.2  1  DUF373           Domain of unknown function (DUF373)
        9.5    6.7   8.5       0.61   10.5   0.5    2.8  3  FeoB_associated  FeoB-associated Cys-rich membrane protein


Domain annotation for each model (and alignments):
>> Ferric_reduct  Ferric reductase like transmembrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   1.4     0.036   1.3e+02      69     102 ..      29      61 ..       8      76 .. 0.66
   2 !   23.8   7.7   1.1e-08   3.8e-05      11     124 ..      47     156 ..      41     157 .. 0.79
   3 ?   -2.3   0.1       1.3   4.5e+03      82      94 ..     170     182 ..     157     188 .. 0.53

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.036
                     Ferric_reduct  69 rlldsllkkpynllGvlalllliilaitSlkfir 102
                                       ++ +s +k  y + G++++l+++  +i+S +++ 
  gi|298675248|ref|YP_003726998.1|  29 QNPESPIKLIYRTAGIFSYLFIFSAIISS-EYMS 61 
                                       45567777788889999999999888888.4444 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 1.1e-08
                     Ferric_reduct  11 lallla..lRnnflepltglsldklllfHkwlgvlafllallHvilyllnflrfsaldeerlldsllkkpynllGvl 85 
                                        +++++  +++  ++++ +l    +l fH  l  la++l++lH + ++l  +  +       +     ++ +l G  
  gi|298675248|ref|YP_003726998.1|  47 YLFIFSaiISSEYMSKIKKLFGLPFLKFHHNLIKLALILMVLHPLSFALDIQSLQ---VFLPVFYPPVTFLELAGRP 120
                                       444444334456666666666677788*********************9888765...566666667777789**** PP

                     Ferric_reduct  86 alllliilaitSlkfirrrlsyelFyylHhllyvaylll 124
                                       a++l+ii +it+  + r +  ++ ++ +H + y+a++l+
  gi|298675248|ref|YP_003726998.1| 121 AFYLFIIAIITA--VYR-KKIPKDWKKIHLFNYLAFFLV 156
                                       ************..666.8889**************986 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.3
                     Ferric_reduct  82 lGvlalllliila 94 
                                       +G+ +l ++++++
  gi|298675248|ref|YP_003726998.1| 170 TGMQILSVAMMII 182
                                       5544443333333 PP

>> ThrE  Putative threonine/serine exporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1      0.44   1.6e+03     161     172 ..      14      25 ..       4      61 .. 0.52
   2 ?   10.9   3.5   6.1e-05      0.22     133     200 ..     121     187 ..     111     188 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.44
                              ThrE 161 eavaaflaslla 172
                                       ++v a+   +++
  gi|298675248|ref|YP_003726998.1|  14 TIVIAIALFVIY 25 
                                       333333333333 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 6.1e-05
                              ThrE 133 flvaflagllggllrlllakrglnsfvleavaaflasllallavslglglnpdaiiigsillLvPGlp 200
                                       ++  f++++++ + r +++k      +++ +a fl+s+ all++  +++++  +i+  +++++v+G+ 
  gi|298675248|ref|YP_003726998.1| 121 AFYLFIIAIITAVYRKKIPKDWKKIHLFNYLAFFLVSIHALLIGT-DFSSTGMQILSVAMMIIVAGVF 187
                                       57789**************9999999**************99999.677778999***********96 PP

>> Glucos_trans_II  Glucosyl transferase GtrII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8  23.9    0.0043        15     142     290 ..      10     182 ..       8     188 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0043
                   Glucos_trans_II 142 YQaylnvyia.lllilllrdlldekkklkeilkkllllllvliisfvlylllykiilklfglelsy........... 206
                                       Y  y  v+++ l++i++l  +++ ++ +k+i +++ ++ +++i s ++++  ++ i klfgl               
  gi|298675248|ref|YP_003726998.1|  10 YLIYTIVIAIaLFVIYTL--YQNPESPIKLIYRTAGIFSYLFIFSAIISSEYMSKIKKLFGLPFLKfhhnliklali 84 
                                       445555555546666666..578999999999999999999998888888888888999999987788888888887 PP

                   Glucos_trans_II 207 ........isellqnlkryysisnygvkpkklllililliliilllalllkkkkkkkksll.llllllllllpfaln 274
                                               ++  +q+l+ ++  ++  v +  l +  ++ ++ii+++  +++kk++k ++ + l+ +l++ l ++ + 
  gi|298675248|ref|YP_003726998.1|  85 lmvlhplsFALDIQSLQVFLPVFYPPVTFLELAGRPAFYLFIIAIITAVYRKKIPKDWKKIhLFNYLAFFLVSIHAL 161
                                       7777776532225555555558889999**********************************9*9****99999999 PP

                   Glucos_trans_II 275 lil.....lkssllrprtlmp 290
                                       li        +++l++++++ 
  gi|298675248|ref|YP_003726998.1| 162 LIGtdfssTGMQILSVAMMII 182
                                       999444443344444444444 PP

>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4  13.6    0.0015       5.4     164     329 ..      15     184 ..       2     189 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0015
                            DUF373 164 llliyallll...lglpelalaiillllGl...ylllrGfgldelleelleklkesleegritfvtyvvalllllig 234
                                       +++ +al+++   ++ pe+ +++i    G+   ++++ ++       e+++k+k+ +    + f  +++ l+l+l+ 
  gi|298675248|ref|YP_003726998.1|  15 IVIAIALFVIytlYQNPESPIKLIYRTAGIfsyLFIFSAIISS----EYMSKIKKLFGLPFLKFHHNLIKLALILMV 87 
                                       2223333333333555566666665555551105555555444....5778******************99999887 PP

                            DUF373 235 iisgyislesvssasvssglltlilafiygavewlalailtaslgkiideylkreekdiarllllpflvlaiglvly 311
                                       +    + + +++s +v   ++   ++f+  a       +++a+++ +  + + +++k+i  + +l f++++i ++l+
  gi|298675248|ref|YP_003726998.1|  88 LHPL-SFALDIQSLQVFLPVFYPPVTFLELAGRPAFYLFIIAIITAVYRKKIPKDWKKIHLFNYLAFFLVSIHALLI 163
                                       7555.5568888889999**********************************9999999988899999999999996 PP

                            DUF373 312 ga..saylls.lsilalslvv 329
                                       g+  s+  ++ ls  ++++v+
  gi|298675248|ref|YP_003726998.1| 164 GTdfSSTGMQiLSVAMMIIVA 184
                                       640043333333444444444 PP

>> FeoB_associated  FeoB-associated Cys-rich membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.5   0.00017      0.61       4      23 ..      11      30 ..       8      34 .. 0.88
   2 ?   -0.2   0.2      0.37   1.3e+03       9      19 ..     126     136 ..     123     144 .. 0.55
   3 ?   -1.6   0.2       1.1   3.9e+03       3       8 ..     181     186 ..     175     192 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00017
                   FeoB_associated  4 IVgliiaaavafvirrlikk 23
                                      ++  i++a+++fvi+ l+++
  gi|298675248|ref|YP_003726998.1| 11 LIYTIVIAIALFVIYTLYQN 30
                                      7999************9986 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.37
                   FeoB_associated   9 iaaavafvirr 19 
                                       i+a++ +v r+
  gi|298675248|ref|YP_003726998.1| 126 IIAIITAVYRK 136
                                       44555555554 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.1
                   FeoB_associated   3 iIVgli 8  
                                       iIV+++
  gi|298675248|ref|YP_003726998.1| 181 IIVAGV 186
                                       444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1071  (0.0597356); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1349.10
//
Query:       gi|298675249|ref|YP_003726999.1|  [L=602]
Description: putative PAS/PAC sensor protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-50  170.0   5.7    2.4e-18   66.2   0.2    3.6  3  PAS_3     PAS fold
    1.1e-14   54.5   2.6    5.7e-05   23.3   0.4    3.6  3  PAS_9     PAS domain
    6.2e-10   39.1   0.1    4.3e-05   23.5   0.0    3.6  4  PAS       PAS fold
    2.4e-06   27.9   0.0    4.8e-06   26.9   0.0    1.5  1  GAF_2     GAF domain
    0.00014   21.9   0.0     0.0019   18.3   0.0    2.5  2  PAS_11    PAS domain
     0.0025   18.1   0.0        3.6    7.9   0.0    3.1  3  PAS_4     PAS fold
     0.0085   16.4   0.6        1.1    9.6   0.1    3.4  3  DUF3823   Protein of unknown function (DUF3823) N-terminal do
  ------ inclusion threshold ------
      0.013   15.4   0.0      0.032   14.2   0.0    1.6  1  Raptor_N  Raptor N-terminal CASPase like domain
       0.02   14.8   0.1        2.4    8.1   0.0    2.8  2  LPD15     Large polyvalent-protein-associated domain 15
      0.021   14.5   0.1       0.44   10.3   0.0    2.7  2  TUDOR_5   Histone methyltransferase Tudor domain 1


Domain annotation for each model (and alignments):
>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.2   0.2   1.3e-21   2.4e-18       5      89 .]      66     150 ..      62     150 .. 0.89
   2 !   46.2   0.0   2.3e-15   4.2e-12       3      88 ..     197     282 ..     195     283 .. 0.95
   3 !   58.9   0.3   2.6e-19   4.7e-16       3      89 .]     336     422 ..     334     422 .. 0.96

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 1.3e-21
                             PAS_3   5 serveeilGyspeellgkveswldlvhpeDrervrealqeal.kkgepyegeyRirrkdGeyrwveararvirdeng 80 
                                        +++e+ +Gys++e++    ++ d++hp+D+++v+++l++   k+ + ++ eyRi++k+Ge+ w++++ +++rde+g
  gi|298675249|ref|YP_003726999.1|  66 TNNIEN-FGYSADEFITGELKYEDIIHPDDLKEVKNKLNNTYfKNESTFSKEYRIITKSGEVKWIDETSYIHRDEEG 141
                                       555555.5**********99*******************66626666****************************** PP

                             PAS_3  81 kpvrvigva 89 
                                       +++++ g++
  gi|298675249|ref|YP_003726999.1| 142 NVTFYKGII 150
                                       *****9985 PP

  == domain 2  score: 46.2 bits;  conditional E-value: 2.3e-15
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvirde 78 
                                       yvs++v++  Gy pe++++   ++  l++ +D++r+r ++ ++ + g  ++++eyRi++k+G+ rwv + + v+++ 
  gi|298675249|ref|YP_003726999.1| 197 YVSNNVSQF-GYVPEDFTSGSIRHDCLIYSDDLDRIRFEFSKLCQLGYtDFTQEYRILTKSGKLRWVNEEVIVHYNG 272
                                       788899887.**********************************99999**************************** PP

                             PAS_3  79 ngkpvrvigv 88 
                                       +g pv ++++
  gi|298675249|ref|YP_003726999.1| 273 HGSPVAYQSI 282
                                       *****99987 PP

  == domain 3  score: 58.9 bits;  conditional E-value: 2.6e-19
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvirde 78 
                                       yvs+++ +  Gy+p+e+ + + ++ d+++ eD+++v++ l+e  k+g  ++++eyRi++k+G  rwv++r+++ r++
  gi|298675249|ref|YP_003726999.1| 336 YVSDNIAQF-GYTPDEFVKGKIQYGDIIYSEDLDKVQTGLHEQRKNGYsDFSQEYRIVTKSGYLRWVDERTFIQRND 411
                                       788888877.*************************************99**************************** PP

                             PAS_3  79 ngkpvrvigva 89 
                                        g+p++++g++
  gi|298675249|ref|YP_003726999.1| 412 AGEPLYYQGII 422
                                       *********96 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.4   3.2e-08   5.7e-05       4     103 ..      51     154 ..      47     155 .. 0.79
   2 !   14.0   0.0   2.6e-05     0.046      15     104 .]     197     288 ..     183     288 .. 0.78
   3 !   15.1   0.0   1.1e-05      0.02       8     103 ..     327     426 ..     322     427 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 3.2e-08
                             PAS_9   4 ili.dnpdgril.yaNeaalrllGyspeevlgks..itdlf...vtdpeanerlraaleqgrkkerevevvlirkng 73 
                                       +++   +dg  + y+ +  +++ Gys++e++     ++d++   + ++  n+  + ++++   + +++e+ +i+k+g
  gi|298675249|ref|YP_003726999.1|  51 VFLwKSEDGWPVeYVTNNIENF-GYSADEFITGElkYEDIIhpdDLKEVKNKLNNTYFKNE--STFSKEYRIITKSG 124
                                       3347779996665999999988.******99877778888866444444444444555555..5************* PP

                             PAS_9  74 etfwvlltaspvkdddgelvgiivilrDit 103
                                       e  w++ t +  +d++g+++++ +i++Dit
  gi|298675249|ref|YP_003726999.1| 125 EVKWIDETSYIHRDEEGNVTFYKGIITDIT 154
                                       ******9999999****************9 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 2.6e-05
                             PAS_9  15 yaNeaalrllGyspeevlgksitdlf...vtdpeanerlraaleqgrk...kerevevvlirkngetfwvlltaspv 85 
                                       y+++ + ++ Gy pe++   si+  +   +   ++ +r+r  +  + +   + +++e+ + +k+g+  wv+  ++  
  gi|298675249|ref|YP_003726999.1| 197 YVSNNVSQF-GYVPEDFTSGSIRHDCliyS---DDLDRIRFEFSKLCQlgyTDFTQEYRILTKSGKLRWVNEEVIVH 269
                                       777777777.***********998885442...333333322222222455********************999999 PP

                             PAS_9  86 kdddgelvgiivilrDite 104
                                       ++++g  v++ +i+ Dit+
  gi|298675249|ref|YP_003726999.1| 270 YNGHGSPVAYQSIMYDITD 288
                                       9****************96 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 1.1e-05
                             PAS_9   8 npdg..rilyaNeaalrllGyspeevlgks..itdlfvtdpeanerlraaleqgrk...kerevevvlirkngetfw 77 
                                       npd   +++y+++  +++ Gy+p+e++  +  + d++   +e+ ++++  l + rk   + +++e+ +++k+g   w
  gi|298675249|ref|YP_003726999.1| 327 NPDEmwPVEYVSDNIAQF-GYTPDEFVKGKiqYGDII--YSEDLDKVQTGLHEQRKngySDFSQEYRIVTKSGYLRW 400
                                       5555657789******99.******999987788999..88888888888888888888****************** PP

                             PAS_9  78 vlltaspvkdddgelvgiivilrDit 103
                                       v+ + +  ++d ge   + +i++D t
  gi|298675249|ref|YP_003726999.1| 401 VDERTFIQRNDAGEPLYYQGIIVDNT 426
                                       *9666666688888888999999988 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   2.4e-08   4.3e-05      10     113 .]      47     153 ..      35     153 .. 0.91
   2 ?    1.3   0.0      0.19   3.4e+02      59     110 ..     232     283 ..     173     286 .. 0.73
   3 ?   -3.0   0.0       4.1   7.3e+03       4      17 ..     307     320 ..     305     323 .. 0.83
   4 !    9.8   0.0   0.00044      0.79      33     110 ..     343     422 ..     336     424 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.4e-08
                                       SSSEEEEEE.TTSBEEEECHHHHHHHSSTH.HHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEEECTT CS
                               PAS  10 lpdpifvvD.edgrilyvNaaaeellGlsr.eevlgkslldliheedda.elaelleqlleqgeesrageisfklrd 83 
                                         + +f++  edg+ ++  ++  e +G+s+ e + g+  +++i+++dd  e++ +l + +  +e+  ++e ++ ++ 
  gi|298675249|ref|YP_003726999.1|  47 NNSIVFLWKsEDGWPVEYVTNNIENFGYSAdEFITGELKYEDIIHPDDLkEVKNKLNNTYFKNESTFSKEYRIITKS 123
                                       56778888889999999999999*******99999****************************************** PP

                                       SSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  84 grpihlevraspvrdaggeilgflgvlrdi 113
                                       g++++++ +    rd++g+++ + g++ di
  gi|298675249|ref|YP_003726999.1| 124 GEVKWIDETSYIHRDEEGNVTFYKGIITDI 153
                                       *********************999999997 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.19
                                       HHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEEEEEEEEETTEEEEEEEEEE CS
                               PAS  59 aelleqlleqgeesrageisfklrdgrpihlevraspvrdaggeilgflgvl 110
                                       + ++++l++ g    ++e ++ ++ g+ +++  ++   +++ g +  +  ++
  gi|298675249|ref|YP_003726999.1| 232 RFEFSKLCQLGYTDFTQEYRILTKSGKLRWVNEEVIVHYNGHGSPVAYQSIM 283
                                       445667777777778888889999************9999999876666555 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 4.1
                                       HHHHHHSSSEEEEE CS
                               PAS   4 raileslpdpifvv 17 
                                       + i++++p+ +f +
  gi|298675249|ref|YP_003726999.1| 307 EYIINNSPVVVFQW 320
                                       6699********99 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.00044
                                       HHSSTH.HHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEEEEEEEEETTEEEEEEE CS
                               PAS  33 llGlsr.eevlgkslldliheedda.elaelleqlleqgeesrageisfklrdgrpihlevraspvrdaggeilgfl 107
                                       ++G+++ e v gk  +++i+  +d  +++  l++++++g +  ++e ++ ++ g  ++++ r+   r+  ge+l++ 
  gi|298675249|ref|YP_003726999.1| 343 QFGYTPdEFVKGKIQYGDIIYSEDLdKVQTGLHEQRKNGYSDFSQEYRIVTKSGYLRWVDERTFIQRNDAGEPLYYQ 419
                                       79****999***********9998899999999999999999999999999********999999999999998888 PP

                                       EEE CS
                               PAS 108 gvl 110
                                       g++
  gi|298675249|ref|YP_003726999.1| 420 GII 422
                                       876 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   2.7e-09   4.8e-06       2     134 ..     449     580 ..     448     583 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 2.7e-09
                                       HHHHHHHHHHHHHHHHSS...EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B---TTHHHHHHHHTS-EEES-GGG- CS
                             GAF_2   2 adleelldlvldelvelg.aalgyillvdddgglrlaawgeaeeefgaaldrplgeglvgealrtgrpvilndleed 77 
                                        d++ +++ v+++++e++ +++g+i++v++ ggl+l++  +   ++   +++  +++ +   l tg pv+  d+ e 
  gi|298675249|ref|YP_003726999.1| 449 EDVDKTVEKVVEHVLEINtIDCGCIHFVNESGGLDLVVHKGLSSSLVYDISHINANSFITNLLNTGNPVY-KDYSEI 524
                                       6899*************66******************9999999999999776677799***********.999998 PP

                                       S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHH CS
                             GAF_2  78 pdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqia 134
                                        + + ++  ++ +++  ++P+  +g +v++l+++++  ++  +e +  +e +a++++
  gi|298675249|ref|YP_003726999.1| 525 FYNSDYN-TKHEYKALGIIPIKFKGDIVAALSVSSHTYDDIPQEVRIAVENIADLLG 580
                                       8777777.*************99889*******877777776666666888888775 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0     1e-06    0.0019      40      96 ..      86     142 ..      73     158 .. 0.88
   2 ?    0.2   0.0      0.44   7.9e+02      40      79 ..     358     397 ..     342     416 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1e-06
                            PAS_11  40 iydLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvkvktksklfknqksn 96 
                                       + d++hp+dl+++k++l +++ +n+ + s  yR++++++++ ++  +s++ ++++ n
  gi|298675249|ref|YP_003726999.1|  86 YEDIIHPDDLKEVKNKLNNTYFKNESTFSKEYRIITKSGEVKWIDETSYIHRDEEGN 142
                                       679******************9*****************999999988888876655 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.44
                            PAS_11  40 iydLchpqdlstlkshlrevissngea.tsslyRLrlsqdk 79 
                                       + d++  +dl ++++ l+e   +ng +  s+ yR+ ++++ 
  gi|298675249|ref|YP_003726999.1| 358 YGDIIYSEDLDKVQTGLHEQR-KNGYSdFSQEYRIVTKSGY 397
                                       34889999**********999.6665415667999998775 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0     0.005         9      74     109 ..     120     157 ..      46     158 .. 0.82
   2 !    7.9   0.0     0.002       3.6      67     109 ..     246     290 ..     177     291 .. 0.72
   3 ?   -0.8   0.0      0.97   1.7e+03      74     106 ..     393     426 ..     333     429 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.005
                             PAS_4  74 l..pgeerhyelrllPlrdesGevigvlvisrDiTerr 109
                                          +ge ++++ + +  rde+G v ++ +i++DiT ++
  gi|298675249|ref|YP_003726999.1| 120 ItkSGEVKWIDETSYIHRDEEGNVTFYKGIITDITGQK 157
                                       34689999**9999999******************876 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.002
                             PAS_4  67 efleelll..pgeerhyelrllPlrdesGevigvlvisrDiTerr 109
                                       +++e++ l  +g+ r+++ +++   + +G ++++  i++DiT+r+
  gi|298675249|ref|YP_003726999.1| 246 FTQEYRILtkSGKLRWVNEEVIVHYNGHGSPVAYQSIMYDITDRK 290
                                       34444444679********************************98 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.97
                             PAS_4  74 l.pgeerhyelrllPlrdesGevigvlvisrDiT 106
                                       + +g  r+++ r +  r++ Ge++ + +i++D T
  gi|298675249|ref|YP_003726999.1| 393 TkSGYLRWVDERTFIQRNDAGEPLYYQGIIVDNT 426
                                       2477788888888888888888888888888866 PP

>> DUF3823  Protein of unknown function (DUF3823) N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.1   0.00063       1.1      49      71 ..     107     144 ..      84     164 .. 0.74
   2 ?    2.0   0.0      0.14   2.5e+02      54      81 ..     246     271 ..     245     296 .. 0.73
   3 ?    0.0   0.0      0.61   1.1e+03      54      73 ..     385     403 ..     383     414 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00063
                                       E.EEEE-SEEEEEEE-TT-SSB-..............T CS
                           DUF3823  49 f.ntllFdGeYklvlkegegpfv..............k 71 
                                       f n+  F+ eY++++k+ge  ++              +
  gi|298675249|ref|YP_003726999.1| 107 FkNESTFSKEYRIITKSGEVKWIdetsyihrdeegnvT 144
                                       59999******************666666544444443 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.14
                                       -SEEEEEEE-TT-SSB-TT---EEEEES CS
                           DUF3823  54 FdGeYklvlkegegpfvkavdtievelk 81 
                                       F  eY++++k+g+  +v+  +++ v+ +
  gi|298675249|ref|YP_003726999.1| 246 FTQEYRILTKSGKLRWVN--EEVIVHYN 271
                                       8899*************2..33444333 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.61
                                       -SEEEEEEE-TT-SSB-TT- CS
                           DUF3823  54 FdGeYklvlkegegpfvkav 73 
                                       F+ eY++v+k+g   +v ++
  gi|298675249|ref|YP_003726999.1| 385 FSQEYRIVTKSGYLRWV-DE 403
                                       899*******9999999.33 PP

>> Raptor_N  Raptor N-terminal CASPase like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.8e-05     0.032      74     107 ..     253     284 ..     239     309 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.8e-05
                          Raptor_N  74 lcqslrrnakdervlfHYnGhgvprptengeiwv 107
                                       l++s + +  +e v++HYnGhg p   + ++i++
  gi|298675249|ref|YP_003726999.1| 253 LTKSGKLRWVNEEVIVHYNGHGSP--VAYQSIMY 284
                                       56666777889************9..55555553 PP

>> LPD15  Large polyvalent-protein-associated domain 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.037        66      18      47 ..      48      77 ..      34     102 .. 0.77
   2 ?    8.1   0.0    0.0014       2.4       8      39 ..     171     202 ..     166     214 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.037
                             LPD15 18 iawviiykegrsWkaeaiwldeddtleeed 47
                                      ++ v ++k++  W +e++ ++ ++  +++d
  gi|298675249|ref|YP_003726999.1| 48 NSIVFLWKSEDGWPVEYVTNNIENFGYSAD 77
                                      456789************999888744444 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0014
                             LPD15   8 kelqeelrdgiawviiykegrsWkaeaiwlde 39 
                                         lq+ + +  + v ++k +r+W ae++ ++ 
  gi|298675249|ref|YP_003726999.1| 171 DILQNVIDNSPLVVFLWKFDRNWPAEYVSNNV 202
                                       45788899999999************998765 PP

>> TUDOR_5  Histone methyltransferase Tudor domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00024      0.44      11      34 ..     134     159 ..     117     161 .. 0.75
   2 ?    0.9   0.0      0.21   3.8e+02      16      30 ..     413     427 ..     390     431 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00024
                           TUDOR_5  11 y..kdekkkskyyaGiiAEppkktNr 34 
                                       y  +de+++ ++y+Gii+ + +++N+
  gi|298675249|ref|YP_003726999.1| 134 YihRDEEGNVTFYKGIITDITGQKNK 159
                                       43367799****************98 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.21
                           TUDOR_5  16 kkskyyaGiiAEppk 30 
                                       ++  yy+Gii    k
  gi|298675249|ref|YP_003726999.1| 413 GEPLYYQGIIVDNTK 427
                                       6678******97655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (602 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 4384.59
//
Query:       gi|298675250|ref|YP_003727000.1|  [L=163]
Description: desulfoferrodoxin ferrous iron-binding region [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-28   99.6   5.0    3.8e-27   94.7   5.0    2.1  1  Desulfoferrodox  Desulfoferrodoxin


Domain annotation for each model (and alignments):
>> Desulfoferrodox  Desulfoferrodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.7   5.0   2.1e-31   3.8e-27       3      95 ..      20     140 ..      18     141 .. 0.97

  Alignments for each domain:
  == domain 1  score: 94.7 bits;  conditional E-value: 2.1e-31
                                       HTTTHTTSEEEEEESEEEETTEEEEEEEESSSS--BSSSS-EEEEEEEEEETTSSEEEE-TBSE.SEEEEEEEESSS CS
                   Desulfoferrodox   3 dekeekHvPvieadevvkagelfevkvkvgkipHpneeeHyIewielyleeegekrvelsaede.pevtftvklkke 78 
                                       +e e+ H P+i+a+++v +g+ fev+v+vg+ pHp++eeHyIewi+ly++ e  ++++++++de +e++f+v +k++
  gi|298675250|ref|YP_003727000.1|  20 TEDEKEHLPLIKAPDEVVEGNEFEVTVNVGHKPHPMKEEHYIEWIQLYFNGELVEEKTFTPNDEkAEAKFKVYAKED 96 
                                       788999*********************************************************77************ PP

                                       ...........................EEEEEEEEETTTEEEEE CS
                   Desulfoferrodox  79 ...........................kklvalsyCnlHGlWes 95 
                                                                  + l+al yCn HGlWe+
  gi|298675250|ref|YP_003727000.1|  97 iiaayqfencyihgynvcgecdgkvvaTSLTALGYCNTHGLWEE 140
                                       ******************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.52
# Mc/sec: 948.51
//
Query:       gi|298675251|ref|YP_003727001.1|  [L=80]
Description: hypothetical protein Metev_1347 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.27   11.7   6.6        2.4    8.7   6.3    1.9  2  FtsX      FtsX-like permease family


Domain annotation for each model (and alignments):
>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   1.8    0.0013        24      62      83 ..       9      30 ..       3      36 .. 0.83
   2 ?    8.7   6.3   0.00013       2.4      25      89 ..      19      76 ..      13      80 .] 0.69

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0013
                              FtsX 62 isidlitvliiivlllllalla 83
                                        i+ ++vl+i+vl+++++++ 
  gi|298675251|ref|YP_003727001.1|  9 NIIKAFDVLFIFVLAFVCVVMP 30
                                      5688999*********999875 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00013
                              FtsX 25 illitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlllllallagllsis 89
                                      i+++++v+ v+     +++  ++  ++++    +el +++d+ t++ +++ +l ++ ++++ s+ 
  gi|298675251|ref|YP_003727001.1| 19 IFVLAFVCVVMP----TVLKGAVLVGWEKG---GELGYTFDPVTFIGFVAAILGFFFVILFHSVK 76
                                      344444444444....77777777777777...9***********99999888888888554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       940  (0.052429); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 589.81
//
Query:       gi|298675252|ref|YP_003727002.1|  [L=94]
Description: monomethylamine permease [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0067   15.9   1.1     0.0079   15.7   1.1    1.1  1  Tmemb_40  Predicted membrane protein


Domain annotation for each model (and alignments):
>> Tmemb_40  Predicted membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   1.1   4.4e-07    0.0079     159     212 ..      30      84 ..      21      90 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.4e-07
                          Tmemb_40 159 llltlvYglilllpktklrer.LParpsFynYvvillvlnavqllgsalvgagas 212
                                       ++l++v  +++++ +t+++ + +   p F +Y+v++ +l  +++lg+a v+  ++
  gi|298675252|ref|YP_003727002.1|  30 TVLIAVELFVFIMITTTTQAWtMMPLPMFGVYIVVIGLLIGIETLGCAQVYRSIK 84 
                                       578899999999999999999966689*********************9998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1098  (0.0612416); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 624.03
//
Query:       gi|298675253|ref|YP_003727003.1|  [L=466]
Description: amino acid permease [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-42  144.8  37.2    4.1e-42  144.4  37.2    1.1  1  AA_permease    Amino acid permease
    6.9e-22   77.9  42.5    8.3e-22   77.6  42.5    1.0  1  AA_permease_2  Amino acid permease
  ------ inclusion threshold ------
        2.2    7.4  11.8       0.79    8.9   1.2    2.8  3  Herpes_LMP1    Herpesvirus latent membrane protein 1 (LMP1)


Domain annotation for each model (and alignments):
>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.4  37.2   6.9e-46   4.1e-42       9     434 ..      28     419 ..      21     447 .. 0.89

  Alignments for each domain:
  == domain 1  score: 144.4 bits;  conditional E-value: 6.9e-46
                       AA_permease   9 gviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGlnylfs 85 
                                       g++ +g ++g  ++++++G+lgal+a+ lagv ++++ l+ +e+  +  ++gg y +a+ f+gp +++++Gl   + 
  gi|298675253|ref|YP_003727003.1|  28 GIVLVGEYMGWNFTVAKGGILGALIAMTLAGVLYIIISLCASELGAATQSAGGPYEWARLFVGPGAAGSVGLAVYME 104
                                       444577889999*************************************************************5555 PP

                       AA_permease  86 witvlaleltaasiliqfwelvtdlpkawvtgavflvvlliinlvgvkvygeaefilalikiiaiiafiivgiilla 162
                                       +i+  a++ ++++ l q +  ++++   + + ++++++l+++n+ gv +     f++++i+++aii f+  +  + +
  gi|298675253|ref|YP_003727003.1| 105 YIALEAADAIVVAQLAQSI--FPEIA-VFPMTLLVIGALTFVNYRGVVGALTLNFVITMIAFLAIIVFFFSSTLGGI 178
                                       6666666777777777777..99999.888899***************************************54444 PP

                       AA_permease 163 ggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPkailqv 239
                                        + ++++     l+++g+     +p+g        + + ++++++    + Gie  a+ a+E++ P++s+P +    
  gi|298675253|ref|YP_003727003.1| 179 VELNSAE-----LWSQGA-----MPQG--------LIGLFAALQFGPWFYLGIEGAAMSAEECAKPSRSVPLGQQAG 237
                                       4444555.....9*****.....****........****************************************** PP

                       AA_permease 240 viritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssansslysasRvly 316
                                       +i ++++  + l+ +++++p +dlg+         p+  + +esgv +l +l+ +++l+++l san+ +  +sR  y
  gi|298675253|ref|YP_003727003.1| 238 MISLLVVAAMTLFYCSSILPASDLGVSV------YPQWEAARESGVTFLIVLMGIGTLLTCLASANGTICDSSRSWY 308
                                       ***********************88877......38***************************************** PP

                       AA_permease 317 slakdglaP.kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliilsylrfRk 392
                                       +lakd++ + ++ +++  +++P+r+++++m i+ ++ +  +l           +++s ++gl++++li +s++rfRk
  gi|298675253|ref|YP_003727003.1| 309 ALAKDDYVAkWFSAVHPYYRSPYRSVIFTMPIAIAFAFSGYLDQV--------ITFSIISGLLCYVLIPFSLIRFRK 377
                                       *********5666788999******************99999888........8999******************** PP

                       AA_permease 393 alkyqgrsieelgfkaallplgvilvlaaliiillilalyay 434
                                        +  +  + +  +fk +l+p+++++ +++ i il++l + ++
  gi|298675253|ref|YP_003727003.1| 378 MFPDRIANDKVRPFKGPLQPYIAWFSIIVAIVILTTLYWGYF 419
                                       *99888888889************998887777777655544 PP

>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.6  42.5   1.4e-25   8.3e-22       6     405 ..      22     420 ..      17     436 .. 0.79

  Alignments for each domain:
  == domain 1  score: 77.6 bits;  conditional E-value: 1.4e-25
                     AA_permease_2   6 afalvigsvigsgifvkn.laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvaflsa 81 
                                       + al +g+v+   ++  n  +a+gg++ +l+ ++ ++++ ++ +l+  El++a  + gG y +++ + g+ +a  ++
  gi|298675253|ref|YP_003727003.1|  22 VWALGVGIVLVGEYMGWNfTVAKGGILGALIAMTLAGVLYIIISLCASELGAATQSAGGPYEWARLFVGPGAAGSVG 98 
                                       5566666665555554447799***********9999999**********888************************ PP

                     AA_permease_2  82 wfnwfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkillplii 158
                                        +  + y++  a+ ++v+a+  +++ +p++     +++ +  +++  ++++n+rg+ +  +++++++ + +l  +i+
  gi|298675253|ref|YP_003727003.1|  99 LAVYMEYIALEAADAIVVAQLAQSI-FPEI-----AVFPMTLLVIGALTFVNYRGVVGALTLNFVITMIAFL-AIIV 168
                                       *********8888888888888885.5765.....78888899********************999999995.5555 PP

                     AA_permease_2 159 liilglitvdgggfsslstetdt.ffpngwpgvllgllivlwsfdGfesaanvsee.vkk.kdvpkaifigllivlv 232
                                       ++    + +    +s +   +++  +p+g  g +++l    w + G+e+aa  +ee +k  + vp++   g++  lv
  gi|298675253|ref|YP_003727003.1| 169 FFFSSTLGGIVELNSAE--LWSQgAMPQGLIGLFAALQFGPWFYLGIEGAAMSAEEcAKPsRSVPLGQQAGMISLLV 243
                                       55444444444444421..2322356666666788888899***************8665699***99888887777 PP

                     AA_permease_2 233 lyllvniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealardgvlP 309
                                       +   +   +++++++   + l+ ++++    ++ +g +++ +++ i++ l +l ++n+ +  ssr  +ala+d++  
  gi|298675253|ref|YP_003727003.1| 244 VAAMT---LFYCSSILPASDLGVSVYPQWEAARESGVTFLIVLMGIGTLLTCLASANGTICDSSRSWYALAKDDYVA 317
                                       66555...444555544444444443433455555777777777799999*************************** PP

                     AA_permease_2 310 rffakvn.kfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigalilrkkrphl...kr. 381
                                       ++f+ v+  + sp+r++i+t+ ++++    f++  s  ++ + + s ++ +++y l+ ++++  rk  p++    + 
  gi|298675253|ref|YP_003727003.1| 318 KWFSAVHpYYRSPYRSVIFTMPIAIA----FAF--SGYLDQVITFSIISGLLCYVLIPFSLIRFRKMFPDRianDKv 388
                                       *******77**************933....334..3469****************************9988654226 PP

                     AA_permease_2 382 ........pgkilvaiigalfllfllvalffp 405
                                               p++++++ii a+++l +l++++f+
  gi|298675253|ref|YP_003727003.1| 389 rpfkgplqPYIAWFSIIVAIVILTTLYWGYFY 420
                                       77777788777788899999999999888887 PP

>> Herpes_LMP1  Herpesvirus latent membrane protein 1 (LMP1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.2   0.00013      0.79       8      98 ..      80     169 ..      75     183 .. 0.86
   2 ?   -2.2   0.0       0.3   1.8e+03      13      39 ..     224     251 ..     220     266 .. 0.76
   3 ?    4.1   1.6    0.0037        22     154     191 ..     404     444 ..     394     464 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00013
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       Herpes_LMP1   8 gppgprrpprgpplssslglallllllallfwlyivmsdwtggallvlysfallliiiiliififrrdllcplgalc 84 
                                       gp    r   gp  + s+gla+ +  +al     iv+++ +   +  +  f + l++i  + f+  r ++  l  l 
  gi|298675253|ref|YP_003727003.1|  80 GPYEWARLFVGPGAAGSVGLAVYMEYIALEAADAIVVAQLAQSIFPEIAVFPMTLLVIGALTFVNYRGVVGALT-LN 155
                                       55555677789********************************************************9988774.66 PP

                                       XXXXXXXXXXXXXX CS
                       Herpes_LMP1  85 llllmitlllialw 98 
                                       +++ mi++l i ++
  gi|298675253|ref|YP_003727003.1| 156 FVITMIAFLAIIVF 169
                                       77888888887765 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.3
                                       XXXXXXXXXXXXXXXXXXXXXXXX.XXX CS
                       Herpes_LMP1  13 rrpprgpplssslglallllllal.lfw 39 
                                        +p r  pl    g+  ll++ a+ lf+
  gi|298675253|ref|YP_003727003.1| 224 AKPSRSVPLGQQAGMISLLVVAAMtLFY 251
                                       5799999999999998888877762444 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.0037
                                       XXXX.XXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXX CS
                       Herpes_LMP1 154 liia.lylqqnwwtllvdllwlllflailiw..myyhgqrh 191
                                       +i+a + l   +w  + +ll+ llf +i  +   y h +r 
  gi|298675253|ref|YP_003727003.1| 404 IIVAiVILTTLYWGYFYNLLFGLLFYTIAYFyfHYKHTERP 444
                                       333313567789*************9885430034444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       879  (0.0490267); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3262.76
//
Query:       gi|298675254|ref|YP_003727004.1|  [L=458]
Description: monomethylamine methyltransferase MtmB [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   6.7e-225  747.0   0.7   7.5e-225  746.8   0.7    1.0  1  MtmB      Monomethylamine methyltransferase MtmB


Domain annotation for each model (and alignments):
>> MtmB  Monomethylamine methyltransferase MtmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  746.8   0.7  4.2e-229  7.5e-225       2     450 .]       8     456 ..       7     456 .. 1.00

  Alignments for each domain:
  == domain 1  score: 746.8 bits;  conditional E-value: 4.2e-229
                              MtmB   2 dvydaykrakkGekveedewdyveipqkaeelkekydikfenefiPededladrlfqaGlelLvetGvycidtervi 78 
                                       +vyd+y+rak+Gek+++d+wd ++ip+ka elk+ky ++f++ef+P+d+d++++lf+aG+e+L+e+G+yc+dt+r++
  gi|298675254|ref|YP_003727004.1|   8 TVYDFYDRAKTGEKTTQDDWDLMTIPMKAGELKQKYGLDFGDEFVPTDKDMMENLFNAGFEMLLECGIYCTDTKRIV 84 
                                       8**************************************************************************** PP

                              MtmB  79 kvteeeilegikkapkklelGegkdaveleerksndskkPiiqgGPtGapvsedvfleviqsyaqeplvdtivsGvl 155
                                       k+te+ei+++i++++k+++lG+g+dav++++r++ d++kP+iqgGPtGapvsedvf++v++sya e   d iv+Gv+
  gi|298675254|ref|YP_003727004.1|  85 KYTEDEIWDAINNVDKEFTLGTGRDAVTVRKREVGDKRKPLIQGGPTGAPVSEDVFVPVHMSYAMERECDLIVNGVM 161
                                       ***************************************************************************** PP

                              MtmB 156 etvegkeaktksPfeikatlaearlvkeatslagrpglalkGpetplsaagrlaadlaeglresdshevsqLnelki 232
                                       ++++gk+++++sP+e+ a+++e rl+kea++++grpg++l+Gpet+lsa g+++ad+ +gl++ dshevsqLnelki
  gi|298675254|ref|YP_003727004.1| 162 TSIRGKSPVPGSPYEVLAAKSESRLIKEACAMCGRPGMGLOGPETSLSAPGNISADAVGGLNPADSHEVSQLNELKI 238
                                       ***************************************************************************** PP

                              MtmB 233 dvealnliagykangdvilveqmPifGGyaggieetaivdvattlasfvltdasfhldGpihirwgstttretlqia 309
                                       d++a++++a+y+an+dvi+ eqmPifGGyaggieetaivdvatt+++f++ +a++hldGp+hirwgst+tre+l+ia
  gi|298675254|ref|YP_003727004.1| 239 DLDAIAVVAHYQANSDVIMDEQMPIFGGYAGGIEETAIVDVATTINAFLMNNATWHLDGPVHIRWGSTNTREALKIA 315
                                       ***************************************************************************** PP

                              MtmB 310 ahaaaaidantdlllanqyytlaGpctemclletaaqaiadtasGrellsGvaaakGvvkdkttGlearlmgevaia 386
                                       ++++a+i+++td++l+nqyy++aGpctemclle+aaq+++dtasGre+lsGva+akGv +dkttG+ear+mge a+a
  gi|298675254|ref|YP_003727004.1| 316 GWTSATIKEHTDMILGNQYYPCAGPCTEMCLLEAAAQSMTDTASGREILSGVASAKGVGQDKTTGMEARMMGETARA 392
                                       ***************************************************************************** PP

                              MtmB 387 aaglevsevneildklvskyeknyakaPaGkrfqeCydvktvePtdeyldvydkalkkleelGl 450
                                       +ag++++evn+ildklv +ye+++ + P+ k+fqeCyd++t++P dey++vyd a kkle+lGl
  gi|298675254|ref|YP_003727004.1| 393 TAGMDINEVNKILDKLVGMYENDFGNLPEDKTFQECYDISTITPIDEYVNVYDGAKKKLEDLGL 456
                                       **************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2922.13
//
Query:       gi|298675255|ref|YP_003727005.1|  [L=219]
Description: methyltransferase cognate corrinoid protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-23   81.4   0.0    8.9e-23   80.5   0.0    1.5  1  B12-binding_2  B12 binding domain
    2.2e-15   56.8   0.2    3.9e-15   55.9   0.2    1.4  1  B12-binding    B12 binding domain


Domain annotation for each model (and alignments):
>> B12-binding_2  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.5   0.0     1e-26   8.9e-23       3      75 .]       9      81 ..       7      81 .. 0.97

  Alignments for each domain:
  == domain 1  score: 80.5 bits;  conditional E-value: 1e-26
                     B12-binding_2  3 erlhwaivhgdkegieelidealaqgsaavdvlndvllpamkeVGdlfgagelflpqvllsaevmkkavahLe 75
                                      e+l++ai++ d eg++ l++eal++g ++ +++n++l p+mk+VGd+f++ge flpq +++a++m+ a++++e
  gi|298675255|ref|YP_003727005.1|  9 EKLKNAIINQDIEGCKNLTKEALDAGLSPIEIVNKGLTPGMKVVGDRFENGEAFLPQIMMAAKAMQGAMEYIE 81
                                      89********************************************************************986 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.9   0.2   4.4e-19   3.9e-15       5     119 ..      99     209 ..      95     211 .. 0.85

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 4.4e-19
                       B12-binding   5 latvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvgl..Salltsqleavkelvel..lkr 77 
                                         + +gd+h++G +++  +l+++gf++++lg +v++++++++i+++k   ++l  Sal+t+++ + kel++l  + +
  gi|298675255|ref|YP_003727005.1|  99 TFVQEGDIHDIGHRLVTTMLQANGFDIVDLGTDVPDDTVLEEIEKNKDKKLLLvgSALMTTSMLGQKELMNLirESG 175
                                       566789****************************************655533335999**************99999 PP

                       B12-binding  78 irprvkvvvGGahpsldpeetleaklgiddvvvgegedalea 119
                                       +r+ vk+++GGa+++  + +   + +g +d    ++e+a+ea
  gi|298675255|ref|YP_003727005.1| 176 VRDYVKIMLGGAPVTQKWID---E-IG-AD---ATAENAAEA 209
                                       99**********96666666...6.99.55...588877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1735.64
//
Query:       gi|298675256|ref|YP_003727006.1|  [L=459]
Description: hypothetical protein Metev_1352 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00079   19.2   0.0     0.0026   17.6   0.0    1.8  2  Abhydrolase_5    Alpha/beta hydrolase family
     0.0015   17.8   0.0      0.018   14.3   0.0    2.2  1  Hydrolase_4      Serine aminopeptidase, S33
     0.0037   16.9   0.0     0.0061   16.1   0.0    1.2  1  DLH              Dienelactone hydrolase family
     0.0054   15.7   0.0      0.013   14.4   0.0    1.6  1  Chlorophyllase2  Chlorophyllase enzyme
  ------ inclusion threshold ------
      0.052   14.1   0.0      0.078   13.6   0.0    1.3  1  Abhydrolase_6    Alpha/beta hydrolase family
      0.087   12.3   0.0        3.7    7.0   0.0    2.3  2  Peptidase_S9     Prolyl oligopeptidase family
       0.13   12.0   0.0       0.21   11.4   0.0    1.3  1  Abhydrolase_2    Phospholipase/Carboxylesterase
        1.4    9.5   0.0        1.4    9.5   0.0    3.3  3  DUF2627          Protein of unknown function (DUF2627)
        3.2    8.1  18.5       0.84    9.9   4.1    3.0  3  DUF2842          Protein of unknown function (DUF2842)


Domain annotation for each model (and alignments):
>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.5   2.9e+03       4      31 ..      72      99 ..      69     102 .. 0.80
   2 !   17.6   0.0   1.3e-06    0.0026      54     121 ..     145     212 ..     132     236 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.5
                     Abhydrolase_5  4 fYpGakveaesYaelaeklaksGyevvl 31
                                      f  G+  ++  Y++++e   ++G+ +++
  gi|298675256|ref|YP_003727006.1| 72 FGAGSGADPIQYSHYGEGFSRQGFLTFI 99
                                      44567789999************99876 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 1.3e-06
                     Abhydrolase_5  54 pklekfvvgGhslGGvvasrfaaeeekiegvvflas.YPekdelselskkvlsivgteDgvlnvkslek 121
                                        + ++ vvgGhs G   a r+a e+  + g++ +a  +P  +++ el++++l  +g +D +++ ++le 
  gi|298675256|ref|YP_003727006.1| 145 TDSDRIVVGGHSGGANGAYRIALEKPDVSGIIAIAGrFPP-ENIDELETNLLLATGGKDTLVPPEKLED 212
                                       456789******9999999*************99863786.67********************999875 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   9.1e-06     0.018      60     180 ..     131     273 ..     119     291 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9.1e-06
                       Hydrolase_4  60 dDlaafvekvkeehpel..plfllGhSmGGliallyllrypdkvaglilsaPalkikakl................. 117
                                       +D+   +++++++h +   ++++ GhS G+  a +++l++pd v+g+i +a  + ++ ++                 
  gi|298675256|ref|YP_003727006.1| 131 EDIIV-LSQLESRHDTDsdRIVVGGHSGGANGAYRIALEKPD-VSGIIAIAGRFPPE-NIdeletnlllatggkdtl 204
                                       45544.46777777766679999*******************.********998665.4444455555555555444 PP

                       Hydrolase_4 118 .kappllklllkllgkllpklqv.....snnlkadslsrdpevvaayeadplvhgkitvrlllelldam 180
                                        ++ +l  ++ +++gk l + ++      nn  + ++s+   ++ +  +d+l+ + +++ l+    da 
  gi|298675256|ref|YP_003727006.1| 205 vPPEKLEDIAFNVTGKHLNRNKFdgdfeGNNATKIFVSESSGHLTEAFDDKLIEESVRWALYSAGKDAS 273
                                       224444444555555555555557777766666777777777777777777777777776666655555 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   3.1e-06    0.0061      86     173 ..     136     220 ..     125     227 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.1e-06
                               DLH  86 vaylksvpevstkkvgvvGfCmGGalalllaaevpevdaavafYGlspekeleeaakikapilalfgeeDefipade 162
                                       +  l+s+ ++++++++v G   G++ a+ +a e+p v + +a  G +p    e+++++++ +l   g++D+ +p ++
  gi|298675256|ref|YP_003727006.1| 136 LSQLESRHDTDSDRIVVGGHSGGANGAYRIALEKPDVSGIIAIAGRFP---PENIDELETNLLLATGGKDTLVPPEK 209
                                       677999999************************************444...456788999***************** PP

                               DLH 163 vekleealkaa 173
                                       +e+++ +++ +
  gi|298675256|ref|YP_003727006.1| 210 LEDIAFNVTGK 220
                                       **998776655 PP

>> Chlorophyllase2  Chlorophyllase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   6.6e-06     0.013       7     114 ..      57     172 ..      52     183 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.6e-06
                   Chlorophyllase2   7 lvvaPteageYpvllflhGylllnslYsqlLkhiashgfivv..apqlykvaeada..keiksaakvl..nWlakg. 76 
                                       l + P  +g +pv+ f  G    +  Ys+  +  ++ gf+ +  +p  + ++ +++   ei + ++ l    l ++ 
  gi|298675256|ref|YP_003727006.1|  57 LLYIPDGEGPFPVVYFGAGSGADPIQYSHYGEGFSRQGFLTFihGPSRSFTSFPSTihWEIVHGNEFLfnRSLREDi 133
                                       6789***********************************85523776555555554345665555543113344443 PP

                   Chlorophyllase2  77 .LesvlpeevepdlsklalsgHSrGgktafalalgkakt 114
                                        + s+l++    d +++++ gHS G++ a  +al+k ++
  gi|298675256|ref|YP_003727006.1| 134 iVLSQLESRHDTDSDRIVVGGHSGGANGAYRIALEKPDV 172
                                       333455699999**********************99874 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.9e-05     0.078      54     105 ..     137     187 ..      78     255 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.9e-05
                                       HHHHCCTT......TTSEEEEEETCHHH....HHHHHHHCC..EE.EEES-..----TTTS CS
                     Abhydrolase_6  54 aalldelaa....gggpvvlvGHSlGGa....lalaaaplalvvg.vlldppptalpagll 105
                                       ++l     +    + +++v+ GHS G+     +al+    ++v+g +++++    +p+ ++
  gi|298675256|ref|YP_003727006.1| 137 SQLE----SrhdtDSDRIVVGGHSGGANgayrIALE---KPDVSGiIAIAG---RFPPENI 187
                                       2222....234458999*******996544667777...8899999****9...6665553 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0019       3.7      51      88 ..     135     172 ..     126     180 .. 0.83
   2 ?    3.0   0.0      0.03        60     139     186 ..     186     247 ..     177     270 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0019
                                       HHHHHHHTTS--GGGEEEEEETHHHHHHHHHHHH-GGG CS
                      Peptidase_S9  51 aaealakegyvdserlaitGgSyGGyltgaalnqrpdl 88 
                                       ++  l +++ +ds+r+++ G+S G   +  ++ ++pd+
  gi|298675256|ref|YP_003727006.1| 135 VLSQLESRHDTDSDRIVVGGHSGGANGAYRIALEKPDV 172
                                       667788999***************98888877777775 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.03
                                       G--.---EEEEEEETT-SSS-THHHHHHHHHHH............--S-S.EEEEEETTS-S CS
                      Peptidase_S9 139 nvk.aypplLlihGlaDdrvppaealklvaaLq............kkgkn.vlllifpdegH 186
                                       n+   +++lLl +G +D+ vpp++ + ++ +++             +g+n +++ +   +gH
  gi|298675256|ref|YP_003727006.1| 186 NIDeLETNLLLATGGKDTLVPPEKLEDIAFNVTgkhlnrnkfdgdFEGNNaTKIFVSESSGH 247
                                       4444899***************9988777666555555555555544444455555555555 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00011      0.21     102     145 ..     145     187 ..     105     223 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                                       --GGGEEEEEETHHHHHHHHHHHT-SS--SEEEEES---TTGGG CS
                     Abhydrolase_2 102 ipssriiigGFSqGaalalylaltlpkklggivafsgalplsqk 145
                                        +s+ri++gG S Ga  a y +  ++  ++gi+a+ g++p++  
  gi|298675256|ref|YP_003727006.1| 145 TDSDRIVVGGHSGGANGA-YRIALEKPDVSGIIAIAGRFPPENI 187
                                       799*********888766.5555566689**********99865 PP

>> DUF2627  Protein of unknown function (DUF2627)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.4       2.7   5.3e+03       2      11 ..      11      20 ..      10      31 .. 0.75
   2 ?    9.5   0.0    0.0007       1.4      32      61 ..     280     309 ..     273     316 .. 0.83
   3 ?    2.5   1.5      0.11   2.3e+02       9      56 ..     355     405 ..     352     407 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.7
                           DUF2627  2 rlialliLvi 11
                                      ++ia+liL+ 
  gi|298675256|ref|YP_003727006.1| 11 QIIAVLILLA 20
                                      6899999875 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0007
                           DUF2627  32 sspfsslwlqflaGlllfaiglgfiaGfil 61 
                                       ++ f++++lqfl+G+++f+ ++++ + + +
  gi|298675256|ref|YP_003727006.1| 280 TKSFRTVLLQFLSGMVMFISAVWLSGSYNY 309
                                       5778999****************9888765 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.11
                           DUF2627   9 LvipgllaayGiklmrda.lfgilsspfssl..wlqflaGlllfaiglgfi 56 
                                       Lvi ++++++G+ + + + +f+il+++  +l  +  +++G  +++i+ +f+
  gi|298675256|ref|YP_003727006.1| 355 LVIGIIASTIGVVVTKSSnIFKILNKKEFALdlFFLLITGASFVLISTQFV 405
                                       899999********9975389988877666544666778999998888886 PP

>> DUF2842  Protein of unknown function (DUF2842)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.1         9   1.8e+04       3      13 ..      12      22 ..      10      23 .. 0.65
   2 ?    9.9   4.1   0.00042      0.84       9      46 ..     323     360 ..     319     360 .. 0.94
   3 ?    7.0   2.0    0.0036       7.1      18      51 ..     421     454 ..     404     456 .. 0.75

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 9
                           DUF2842  3 liglvlllvll 13
                                       i++++ll++l
  gi|298675256|ref|YP_003727006.1| 12 IIAVLILLAGL 22
                                      56777777765 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00042
                           DUF2842   9 llvllvvYavvavslaelllgrapalvqllvYvvlGll 46 
                                        +v++++Y+v+  ++a  +++ +pa +q   Y+v+G++
  gi|298675256|ref|YP_003727006.1| 323 VIVFVIFYIVLLSTIARQFIQLEPAGYQWFQYLVIGII 360
                                       589*********************************97 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0036
                           DUF2842  18 vvavslaelllgrapalvqllvYvvlGllWvlPl 51 
                                       ++   ++ ll+++   l q l++ +l ++W+lP+
  gi|298675256|ref|YP_003727006.1| 421 LFLSFISLLLWKSGMDLRQRLIFNILAVIWLLPV 454
                                       333444555589999******************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1027  (0.0572815); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2977.61
//
Query:       gi|298675257|ref|YP_003727007.1|  [L=215]
Description: hypothetical protein Metev_1353 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.1e-22   79.3   8.0    3.1e-22   79.3   8.0    1.8  3  SNARE_assoc  SNARE associated Golgi protein
  ------ inclusion threshold ------
          6    6.9  28.0      0.044   13.9   9.0    2.8  3  ECF_trnsprt  ECF transporter, substrate-specific component


Domain annotation for each model (and alignments):
>> SNARE_assoc  SNARE associated Golgi protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.2       1.4   1.2e+04      81      85 ..      17      21 ..       8      35 .. 0.51
   2 !   79.3   8.0   3.4e-26   3.1e-22       1     119 [.      66     182 ..      66     183 .. 0.96
   3 ?   -3.1   0.1       1.2     1e+04     103     116 ..     194     207 ..     187     209 .. 0.53

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.4
                       SNARE_assoc 81 Prdlv 85
                                       +++ 
  gi|298675257|ref|YP_003727007.1| 17 LFTVF 21
                                      22222 PP

  == domain 2  score: 79.3 bits;  conditional E-value: 3.4e-26
                       SNARE_assoc   1 lPsevllvaaGvlfglllgtlvtslgallGaslayllgrylgrkalrrkllsekrvkalerlverygflallllrll 77 
                                       +Ps+vl+++aG l+g+++g+l+  lg+ll++++++ l ry+g++++   +++e   k  ++++ + g  +l+l+r++
  gi|298675257|ref|YP_003727007.1|  66 VPSSVLMTLAGSLYGFFWGVLIGTLGSLLASITGFCLTRYIGKRKALT-FIDESEQKLMNKWFTQWGEGILILSRMV 141
                                       7*****************************************665555.999999999******************* PP

                       SNARE_assoc  78 pivPrdlvnyvaGltrvsfkrFflatfiGsipwalvyaylGs 119
                                       p++ +  ++++aGlt++sf rF+   +iG+ip ++ y+y+Gs
  gi|298675257|ref|YP_003727007.1| 142 PML-TETMSCFAGLTGISFLRFLSIIIIGTIPVTVYYSYFGS 182
                                       **9.*************************************8 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 1.2
                       SNARE_assoc 103 tfiGsipwalvyay 116
                                        ++G i++ +++++
  gi|298675257|ref|YP_003727007.1| 194 LAVGVIIPGILWIF 207
                                       34455555555444 PP

>> ECF_trnsprt  ECF transporter, substrate-specific component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.6      0.34   3.1e+03     110     114 ..      19      23 ..       7      37 .. 0.46
   2 ?   13.9   9.0   4.9e-06     0.044       9      62 ..      49      98 ..      49     115 .. 0.81
   3 ?    4.7   4.1    0.0031        28      53     119 ..     143     207 ..     130     213 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.34
                                       HCCCC CS
                       ECF_trnsprt 110 gvlgt 114
                                       +v+  
  gi|298675257|ref|YP_003727007.1|  19 TVFLM 23 
                                       11111 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 4.9e-06
                                      HHHHHHHHHHHHEEE.STSEEESHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHC CS
                       ECF_trnsprt  9 liAisivlsllgyiplpnikitiihipvllggllfGpikGailgiitsvlkail 62
                                      l++++i+l+   +i l+ i++ ++ +++ l+g l+G ++G+++g+++s+l+ i+
  gi|298675257|ref|YP_003727007.1| 49 LAGLIIILM--LIIDLV-IPV-PSSVLMTLAGSLYGFFWGVLIGTLGSLLASIT 98
                                      6899*****..444444.444.37788888**********************99 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.0031
                                       HHHHHHHHHCHT-SSTTHHHH.HHHHHHHHCHHHHHHHHHHCCCHTTHHHHHHHHHHHHCCCCCHHHH CS
                       ECF_trnsprt  53 iitsvlkailtggtgalssfv.piaflsriligliagllykkgkkknlkeivvsfilagvlgtivatl 119
                                       ++t +++++ + +++++   + + ++++ + i++ +++ y ++   + +e  +++++++++  i++ +
  gi|298675257|ref|YP_003727007.1| 143 MLTETMSCFAGLTGISF---LrFLSIIIIGTIPVTVYYSYFGSYLHSVSEWSFPLAVGVIIPGILWIF 207
                                       45666666663333322...237777777777777778888888888888888888888877666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1634.13
//
Query:       gi|298675258|ref|YP_003727008.1|  [L=489]
Description: homoserine O-acetyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-33  116.9   0.0    1.5e-33  116.5   0.0    1.1  1  Abhydrolase_1  alpha/beta hydrolase fold
    1.5e-27   95.8   4.8    7.3e-16   58.4   0.6    2.8  2  CBS            CBS domain
     0.0039   16.5   0.0     0.0078   15.5   0.0    1.5  1  Hydrolase_4    Serine aminopeptidase, S33
  ------ inclusion threshold ------
      0.074   12.7   0.0       0.11   12.2   0.0    1.2  1  Esterase       Putative esterase


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.5   0.0   3.4e-37   1.5e-33       1     256 [.      47     354 ..      47     355 .. 0.87

  Alignments for each domain:
  == domain 1  score: 116.5 bits;  conditional E-value: 3.4e-37
                                       SEEEEE-STTTCGGG...........GTTGHHHHHHHHT..TSEEEEEEETTSTTSSSTTTGB.........CHHSH CS
                     Abhydrolase_1   1 pvlvilhGlpgssdv...........waerglapaLakd..gfdvillDlrGvgySspapacin........ddygt 56 
                                       ++++++h+l+g ++            w+   ++p+ a d  ++++i+ ++ G +++s++p++in         d++ 
  gi|298675258|ref|YP_003727008.1|  47 NAILVCHALTGDAHAagwhegdrkpgWWDIIIGPGKALDtrKYFIICSNVIGGCKGSTGPSSINpdtgesygLDFPV 123
                                       689********77777777899999****999999999999***************************9999889** PP

                                       HHHHHHHH...HHHHHCTTSSEE.EEEETHHHHHHHHHHHHHGGGEEEEEEESE....CSSCCHHHHHHHHHHHHHH CS
                     Abhydrolase_1  57 asvaddld...rildalgddklt.lvGhSmGGmialayaaeyperVkalvllga....idpaaslieaqrqqaksfp 125
                                       +++ d+++   ++ d lg+ kl  ++G+SmGG+++l++   yp+ Vk+ + +++     +  ++++e  r ++ s+p
  gi|298675258|ref|YP_003727008.1| 124 VTIKDMVNaqkKLIDYLGISKLLaVIGGSMGGLQVLQWSVSYPDMVKKAIPIATagysTPQQIAFNEVGRIAIVSDP 200
                                       ********87777********************************************9999**************** PP

                                       CHHCHHHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHH.............HCHHHCCHHHHHHHCHHHHHHHHHHH CS
                     Abhydrolase_1 126 dffdgyaadcarnpagplladelaaleqrhrlvdalkf.............pdkskrfpssgsdnasslatgalksi 189
                                       +++ g+++ ++++++g+ la++ +++++ ++  d++++              d+s+     ++  +s+l +++l + 
  gi|298675258|ref|YP_003727008.1| 201 NWNSGNYYGEKEPTHGLALARMIGHITYLSD--DSMHQkfgrrlqdkneyeFDFSR-----EFEVESYLHYQGLTFT 270
                                       *****************************88..67777779999886444444444.....4455555555555555 PP

                                       HHHHHCCHHHHHHHHHC............THHHHSEEEEEEETTCSSSCHHHHHHHHHCHTS.....EEEEEEETCS CS
                     Abhydrolase_1 190 eqwpttdsaklllrlre............lknvlaptlvisgtsDplvppkaledlaqllpk.....krlvvisdag 249
                                       e+++++ + +l   ++             lknv a+ lvis tsD+l pp +l+++  +l+       +++++s++g
  gi|298675258|ref|YP_003727008.1| 271 ERFDANSYLYLTKAIDYfdltennslaegLKNVEAKFLVISFTSDWLYPPYQLREIVMALSAnnadvTYREIESNYG 347
                                       5555555555555555566677****************************9999999885555699*********** PP

                                       SSHHHHS CS
                     Abhydrolase_1 250 Hlafleg 256
                                       H++fl++
  gi|298675258|ref|YP_003727008.1| 348 HDSFLLE 354
                                       ****986 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.3   2.8e-13   1.3e-09       1      54 [.     371     424 ..     371     427 .. 0.92
   2 !   58.4   0.6   1.6e-19   7.3e-16       2      55 ..     433     486 ..     432     488 .. 0.94

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 2.8e-13
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                       V+dim +d+ t+++  ++ ea++ m ek++++lP V +d klvG+vt  D+ + 
  gi|298675258|ref|YP_003727008.1| 371 VSDIMIEDIATIKEGISIDEAARVMFEKEITHLPLVSSDSKLVGLVTSWDISKS 424
                                       89**********************66999*******88889*********9765 PP

  == domain 2  score: 58.4 bits;  conditional E-value: 1.6e-19
                                       HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       ++imt++vvt++pd+++e+a+e+m++k++s+lPV+d+d +++G+vt +D+ r++
  gi|298675258|ref|YP_003727008.1| 433 EEIMTKNVVTARPDEPIEKAAEKMESKDISALPVIDKDRRVIGMVTSEDISRLI 486
                                       69**********************9999**********************9887 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.7e-06    0.0078      75     116 ..     143     184 ..     113     220 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.7e-06
                       Hydrolase_4  75 elplfllGhSmGGliallyllrypdkvaglilsaPalkikak 116
                                        + l ++G SmGGl +l++   ypd v+++i +a+a    ++
  gi|298675258|ref|YP_003727008.1| 143 SKLLAVIGGSMGGLQVLQWSVSYPDMVKKAIPIATAGYSTPQ 184
                                       44689***************************9999766655 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.4e-05      0.11     117     165 ..     146     202 ..     126     267 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.4e-05
                                       EEEEEETHHHHHHHHHHHCSTTTCCEEE..EES--S-CCHCHHHC......TTCCHH CS
                          Esterase 117 ravaGqSmGGlgALilalkhpdrFgsvs..sfSpivnpsnamWgq......eekeaw 165
                                        av+G SmGGl  L   + +pd+ + ++  + +++  p +    +      +++++w
  gi|298675258|ref|YP_003727008.1| 146 LAVIGGSMGGLQVLQWSVSYPDMVKKAIpiATAGYSTPQQIAFNEvgriaiVSDPNW 202
                                       59***********************99622556666666444333444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3475.66
//
Query:       gi|298675259|ref|YP_003727009.1|  [L=428]
Description: O-acetylhomoserine/O-acetylserine sulfhydrylase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   4.2e-141  469.9   0.0   4.8e-141  469.7   0.0    1.0  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    4.4e-11   42.7   0.0    6.7e-11   42.1   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
      5e-07   29.2   0.0    7.3e-07   28.7   0.0    1.2  1  Aminotran_1_2    Aminotransferase class I and II
    1.6e-06   27.3   0.1    2.6e-06   26.7   0.1    1.2  1  Aminotran_5      Aminotransferase class-V
  ------ inclusion threshold ------
      0.037   13.3   0.0       0.16   11.2   0.0    1.8  1  Beta_elim_lyase  Beta-eliminating lyase
      0.043   12.4   0.8       0.27    9.7   0.8    2.0  1  Met_gamma_lyase  Methionine gamma-lyase


Domain annotation for each model (and alignments):
>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  469.7   0.0  1.6e-144  4.8e-141       2     382 .]      10     423 ..       9     423 .. 0.98

  Alignments for each domain:
  == domain 1  score: 469.7 bits;  conditional E-value: 1.6e-144
                                       HHHHHTTTTCHTTTTBSS--B---SBBBESSHHHH...CTTCSSS-SBTTT--HHHHHHHHHHHHHHT-SEEEEESS CS
                   Cys_Met_Meta_PP   2 Tllvhagqekdeqtgavavpiyltstykfkdvdea...fageekgyeYsRsgnptrsvleeriaaLeggeaalavss 75 
                                       T +vhagq +d++tg++avpiy+t++y+fkd+d+a   f+ +e g++Y+R++npt++vle+r+a Legg+ alavss
  gi|298675259|ref|YP_003727009.1|  10 TRAVHAGQVPDPTTGSRAVPIYQTTSYNFKDTDHAarlFGLKEFGNIYTRITNPTNEVLEQRVASLEGGAGALAVSS 86 
                                       99*********************************9***************************************** PP

                                       HHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCTTEEEEEEESS-TTTT- CS
                   Cys_Met_Meta_PP  76 GmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdtsdleelekaikentklvylEtptnpllk 152
                                       Gm+Ai++a+l + + Gdeiv+ d+lYggt++l++++l+ lg +vkfvd +++ e++++i+entk++y+E ++np+l+
  gi|298675259|ref|YP_003727009.1|  87 GMSAITLAVLGITQPGDEIVSADNLYGGTYQLFNNTLPDLGRKVKFVDSTKPGEFKEQINENTKAIYTEIIGNPKLD 163
                                       ***************************************************************************** PP

                                       ---HHHHHHHHHHTT-EEEEEGTTTHTTTS-GGGGT-SEEEEETTTTTTCSSS--EEEEEESSCHHHHHHHHHHH.. CS
                   Cys_Met_Meta_PP 153 vvDiekiaklakkagvlvvvDntfaspllqrplklgaDivvhSaTKylgGhsdvvaGvivvkgkeelkkelkflq.. 227
                                       v+D+e+i+++a++ag++++vDnt   ++ ++p+++gaDi v SaTK+lgGh++ ++G+iv++g++++++  kf +  
  gi|298675259|ref|YP_003727009.1| 164 VPDFEQITDIAHSAGIPLIVDNTTGIGI-SQPISFGADIEVLSATKFLGGHGTSIGGLIVDSGNFNWNNG-KFPElt 238
                                       ***********************98885.79************************************996.666688 PP

                                       .............................HHHT-B--HHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHTSTTEEE CS
                   Cys_Met_Meta_PP 228 .............................nalGavlspfdawlllrGlkTLslRlerhqenAlkvAefLekhpkvek 275
                                                                    ++lG +lspf+a+l+l+Gl+TL lR+e+h  nA+kvA+fLekh+ ve+
  gi|298675259|ref|YP_003727009.1| 239 epdpgyhglkyweefgkiafivkmrvqllRDLGTALSPFNAFLFLQGLETLPLRMEKHCDNAFKVAKFLEKHQDVEW 315
                                       9**************************************************************************** PP

                                       EE-TTSTTSTTHHHHHHHSSSG-S.EEEEEESSHHHHHHHHHHC-SSSEECSS-SSSS-EEEETTTTTTTTSCHHHH CS
                   Cys_Met_Meta_PP 276 vyYpglpshpqhelakkqlkgagg.vlsFelkseeekakkfvdnlklfslaeslGgveslielpasmthasipkeer 351
                                       v+Ypgl++hp he a k+l+g+ g +++F +k+++e+ kkf++n++l+s+++++G+++sl+ +pas+th+++++ee+
  gi|298675259|ref|YP_003727009.1| 316 VNYPGLETHPTHERAGKYLNGKYGaLIGFGIKGGLESGKKFIENVQLLSHLANIGDAKSLVVHPASTTHQQLTEEEK 392
                                       *******************998666**************************************************** PP

                                       HHTTS-TTEEEEE--SS-HHHHHHHHHHHHH CS
                   Cys_Met_Meta_PP 352 eaagvtddliRlsvGiEdvdDliaDlkqale 382
                                       +++gvtdd+iRls+GiEd++D+i+D++qale
  gi|298675259|ref|YP_003727009.1| 393 KSTGVTDDFIRLSIGIEDAEDIIQDIDQALE 423
                                       *****************************96 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.0   2.2e-14   6.7e-11      20     151 ..      60     191 ..      49     217 .. 0.86

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 2.2e-14
                                       SSSHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTT.TT-EEEEESSS-THHH....HHHHHTT-EEEEE- CS
                   DegT_DnrJ_EryC1  20 tsgpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvg.pgdeVIvpsltFvata....navlelgakpvfvD 91 
                                       +++p++e +E+++a   g + a+avssG +A+   L +lg++ pgde++ + + + +t     n+   lg k+ fvD
  gi|298675259|ref|YP_003727009.1|  60 ITNPTNEVLEQRVASLEGGAGALAVSSGMSAIT--LAVLGITqPGDEIVSADNLYGGTYqlfnNTLPDLGRKVKFVD 134
                                       4599**************************976..567999889*********9999972222466789******** PP

                                       B-TTTSSB-GGGCGGG--TTEEEEEEB-GGGB--....-HHHHHHHHHHCT-EEEEE-TT-TT- CS
                   DegT_DnrJ_EryC1  92 vdpdtynidpaaieaaitertkaIlpVhlyGqva....dmdalkaiaakhglkvieDaAhAlGa 151
                                        +      +p + ++ i+e+tkaI   ++ G++     d++++++ia++ g+++i D   ++G 
  gi|298675259|ref|YP_003727009.1| 135 ST------KPGEFKEQINENTKAIY-TEIIGNPKldvpDFEQITDIAHSAGIPLIVDNTTGIGI 191
                                       99......8**************96.69999875545599*****************9999985 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   2.4e-10   7.3e-07      26     197 ..      44     194 ..      30     228 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 2.4e-10
                                       HHHH.HHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEES CS
                     Aminotran_1_2  26 aeke.galaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdp 101
                                       a++  g+ ++g++    ++     le+++a++ g          +a+ v+sG +a+  a+  +++  pgdei++ d 
  gi|298675259|ref|YP_003727009.1|  44 AARLfGLKEFGNIYTRITNPTNEVLEQRVASLEG--------GAGALAVSSGMSAITLAVLGITQ--PGDEIVSADN 110
                                       44446666666666556666689999******99........777*******************9..*******997 PP

                                       ....S-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHH CS
                     Aminotran_1_2 102 ....tyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleelekll 174
                                           ty  ++n l   g +v  +        +    +++e+++e       tk i++e + NP  +v++ e+++++ 
  gi|298675259|ref|YP_003727009.1| 111 lyggTYQLFNNTLPDLGRKVKFVD-------STKPGEFKEQINE------NTKAIYTEIIGNPKLDVPDFEQITDI- 173
                                       222245556666667899999999.......899**********......99************************. PP

                                       HHHHHTTEEEEEEETTTTCBSSS CS
                     Aminotran_1_2 175 dlakkynlllfvDeaYagfvfgs 197
                                         a++ ++ l+vD + +++ +++
  gi|298675259|ref|YP_003727009.1| 174 --AHSAGIPLIVDNTTGIGISQP 194
                                       ..***********9877777773 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.1   8.6e-10   2.6e-06      65     210 ..      82     217 ..      51     223 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 8.6e-10
                                       EEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEE CS
                       Aminotran_5  65 iftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektk 141
                                       + +s++ +ai+l++l++    +pgdeiv  ++ + ++    ++   + g kvk++  ++       e+++++ne+tk
  gi|298675259|ref|YP_003727009.1|  82 LAVSSGMSAITLAVLGI---TQPGDEIVSADNLYGGTYQLFNNTLPDLGRKVKFVDSTKP-----GEFKEQINENTK 150
                                       56788888999999999...99****************99999999********999655.....56779******* PP

                                       EEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTT.TS---HHHHTESEEEEETTTTTSSTT-EE CS
                       Aminotran_5 142 lvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavg.hipidvkklgvDflafsghKllgPtGiGv 210
                                       +++   + n    + ++e+i+++a+ +g+ ++vD ++++g ++pi    +g+D+ ++s+ K+lg  G+++
  gi|298675259|ref|YP_003727009.1| 151 AIYTEIIGNPKLDVPDFEQITDIAHSAGIPLIVDNTTGIGiSQPI---SFGADIEVLSATKFLGGHGTSI 217
                                       ***************************************834444...69*****************875 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   5.4e-05      0.16      31     132 ..      62     183 ..      57     196 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.4e-05
                                       -HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT.........-HHHHSSTTHHHHCC--EE CS
                   Beta_elim_lyase  31 dktvnrLedavaelfgkeaalfvpqGtaAnsillkillqrgeevivtep.........ahihfdetgaiaelagvkl 98 
                                       ++t ++Le++va l g ++al v +G  A  +++  ++q+g+e++  ++         +++  d  + ++++ + k+
  gi|298675259|ref|YP_003727009.1|  62 NPTNEVLEQRVASLEGGAGALAVSSGMSAITLAVLGITQPGDEIVSADNlyggtyqlfNNTLPDLGRKVKFVDSTKP 138
                                       788899***************************************99998888888877777777788888888877 PP

                                       EEE-EBTT.............TBE-HHHHHHHS--S-TTS-EEEEEE CS
                   Beta_elim_lyase  99 rdlknkea.............Gkmdlekleaaikevgaheekiklis 132
                                        ++k + +              k+d+ ++e++ +   ah++ i+li+
  gi|298675259|ref|YP_003727009.1| 139 GEFKEQINentkaiyteiignPKLDVPDFEQITDI--AHSAGIPLIV 183
                                       77775554556777777776666677777776666..5667777764 PP

>> Met_gamma_lyase  Methionine gamma-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.8   8.9e-05      0.27      78     239 ..      83     224 ..      54     245 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 8.9e-05
                   Met_gamma_lyase  78 qlvsGthaiatalfgvlrpgdellaitGkPydtleeviGlrgegqgslkdfgikykevdlleegkvdieavkeaike 154
                                        + sG  ai++a+ g+ +pgde++++     d l    G+ +  +++l d g k k vd ++ g+      ke+i+e
  gi|298675259|ref|YP_003727009.1|  83 AVSSGMSAITLAVLGITQPGDEIVSA-----DNLYG--GTYQLFNNTLPDLGRKVKFVDSTKPGE-----FKEQINE 147
                                       56799999*************99986.....33322..444447889999998888888777554.....6788999 PP

                   Met_gamma_lyase 155 ktkliliqrskGyserkslsieeieeiiklvkeinedvivfvdncyGefveekePtevGadliaGsliknpGGgiak 231
                                       +tk i           + l + + e+i ++ ++    + + vdn  G  +   +P++ Gad+   s  k  GG  ++
  gi|298675259|ref|YP_003727009.1| 148 NTKAIYTE----IIGNPKLDVPDFEQITDIAHSAG--IPLIVDNTTG--IGISQPISFGADIEVLSATKFLGGHGTS 216
                                       99998754....34468899999999988877655..55668**999..67789*********************** PP

                   Met_gamma_lyase 232 tGGyiaGk 239
                                       +GG i+  
  gi|298675259|ref|YP_003727009.1| 217 IGGLIVDS 224
                                       ***99854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 3127.06
//
Query:       gi|298675260|ref|YP_003727010.1|  [L=384]
Description: Sep-tRNA [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-50  170.8   0.0    6.3e-50  170.0   0.0    1.4  1  SepSecS          O-phosphoseryl-tRNA(Sec) selenium transferas
    1.5e-15   57.0   0.0    2.3e-15   56.5   0.0    1.2  1  Aminotran_5      Aminotransferase class-V
    5.4e-10   39.0   0.0    6.1e-10   38.8   0.0    1.2  1  Aminotran_1_2    Aminotransferase class I and II
    0.00075   18.3   0.0     0.0019   17.0   0.0    1.5  1  OKR_DC_1         Orn/Lys/Arg decarboxylase, major domain
  ------ inclusion threshold ------
      0.093   11.7   0.0       0.64    8.9   0.0    2.2  3  HSL_N            Hormone-sensitive lipase (HSL) N-terminus
       0.18   11.0   0.0       0.46    9.7   0.0    1.6  2  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family


Domain annotation for each model (and alignments):
>> SepSecS  O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.0   0.0   2.1e-53   6.3e-50      21     388 ..      59     380 ..      45     381 .. 0.87

  Alignments for each domain:
  == domain 1  score: 170.0 bits;  conditional E-value: 2.1e-53
                                       -HHHHHCCCCHHCTBSBTTBTTS-CCCCCCCCCHCCCCCHHHHHHHHHTTHCCHHEECCCSS-HHHHHHHHHHHHHH CS
                           SepSecS  21 selkeesvfdfiHgvGrsGnlvdvqPKalGasvlakltNklvkdilkllGlrevknafvvPlatGlslaLClsalrk 97 
                                       +++k++++ df+H            P + Ga+   ++tN          G+re k  f+v                +
  gi|298675260|ref|YP_003727010.1|  59 DQIKKPKIKDFVHE---------ALPEFIGADE-VRVTN----------GARESK--FAV----------------M 97 
                                       55666666666665.........4466666665.56666..........666444..666................5 PP

                                       HCC--CCEEEEEETC...HHHHHHHCTT-EEEEE-EEECTTEEEEHH...HHHHHHHHCCTCCCEEEEEECSSTTTT CS
                           SepSecS  98 rskakkviwvridek...SslkavelaGleialvekvlegDelitdv...edveeiiekkreevilavlstlsffap 168
                                       +s a++  w+++d+    Ss +a+++a l+   v  + ++D+ i ++   +++e++i++ ++   +a+l++++++++
  gi|298675260|ref|YP_003727010.1|  98 HSVANEGDWIVLDNLahySSHVAAQRARLNTETVSSTGHPDYWIDPEgyaKAIENVIDESGKPPSMALLTYPDGNYG 174
                                       555666555555543333**************************997333577888899999999************ PP

                                       B----HHHHHHHHHCCT--EEEEGCCCCT-HHHHHHHHHHHHHTTC-EECCCHCHCCCEECCHCCCCESSCHCCCCC CS
                           SepSecS 169 rspDdvkeiakiCaeydvPhlvNgAYaiqsekyieklkkalkvGRvdvvvksldknllvpvGgaiiaasdesfikei 245
                                       ++p   k++a +C+eydvP+l+N AY+i               GR+++  ++++++++v++G++++a+s+++++ ++
  gi|298675260|ref|YP_003727010.1| 175 NLPN-AKKVASVCHEYDVPLLLNCAYSI---------------GRMPIDANDIGADFVVGSGHKSMASSGPIGVLGV 235
                                       ***9.9**********************...............********************************** PP

                                       HCCCHCHCTSCHCCCCCCCHHHCCHHHCCHHHHHHHHHHHHHHHHHHHHHHCCC..............EEESSSTT- CS
                           SepSecS 246 skeypgrasaapskdvlisllllGskaykkllkeqkesfkllreklkklaeeve..............ekllevpeN 308
                                       s+ey++++ +++ +++ ++++llG++a++++l +  +sf+ + ++ +++++eve              ++++++p+N
  gi|298675260|ref|YP_003727010.1| 236 SEEYSDIVFRKSPTHKKKEVELLGCTARGATLMTMIASFPNVVKRTREWDREVEnarwfseklenlgmNQVGDKPHN 312
                                       ***************************************************************************** PP

                                       SSEEEEE-CCCHCCCC...THHHHHHHHHHHTTECSSE.EE-SSTCECTTSSS-SSSEEEEEE-TT--HHHHHHHHH CS
                           SepSecS 309 pissaltletldeikk...karldlaseLfsrkvtGargvrasdsklTshlkeyhsrYlkiasaiGlkdedvdkvle 382
                                       ++++++ +  ++ei++    +r +l++eL+sr+++G++       +lT        +++k+ s++ +  e++ +v++
  gi|298675260|ref|YP_003727010.1| 313 HDLMFFEAPNIYEISQkakSGRYFLYKELKSRNIHGIK------AGLT--------KFFKL-STFRVGRENLSTVVD 374
                                       ***************96666899***************......8889........99999.999999999999999 PP

                                       HHHHHH CS
                           SepSecS 383 rldeil 388
                                       ++dei+
  gi|298675260|ref|YP_003727010.1| 375 AFDEII 380
                                       999998 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   0.0   7.6e-19   2.3e-15      48     218 ..      70     240 ..      64     268 .. 0.86

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 7.6e-19
                                       HHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETT CS
                       Aminotran_5  48 arekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldee 124
                                       ++e + e+i+a+   e+ +t G+ e+  +v++s+    ++gd iv+ ++ h + +v++q+++   + + +  +  ++
  gi|298675260|ref|YP_003727010.1|  70 VHEALPEFIGAD---EVRVTNGARESKFAVMHSV---ANEGDWIVLDNLAHYSSHVAAQRAR--LNTETVSSTGHPD 138
                                       567788999998...5999***************...89********************997..4455556666688 PP

                                       SCBEGGGHHHH-.......-TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESE CS
                       Aminotran_5 125 geldldelekll.......nektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipidvkklgvDf 194
                                         +d++ ++k++        + +++  +t      G++   ++++++++++++ +l+  a ++g +pid +++g+Df
  gi|298675260|ref|YP_003727010.1| 139 YWIDPEGYAKAIenvidesGKPPSMALLTYPDGNYGNLPNAKKVASVCHEYDVPLLLNCAYSIGRMPIDANDIGADF 215
                                       8888777777776666765566788888999999******************************************* PP

                                       EEEETTTTTSSTT.-EEEEEEHHHH CS
                       Aminotran_5 195 lafsghKllgPtG.iGvlyvrkell 218
                                       ++ sghK ++ +G iGvl v++e+ 
  gi|298675260|ref|YP_003727010.1| 216 VVGSGHKSMASSGpIGVLGVSEEYS 240
                                       *******9999999****9999865 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.0   2.1e-13   6.1e-10      44     239 ..      65     239 ..      35     351 .. 0.87

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 2.1e-13
                                       THHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEE CS
                     Aminotran_1_2  44 dglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvry 120
                                       ++ + + eal +f+g        ++ +v v++Ga +   a++    +n gd i+++++ + s + +++ +++   ++
  gi|298675260|ref|YP_003727010.1|  65 KIKDFVHEALPEFIG--------AD-EVRVTNGARESKFAVMHSV-ANEGDWIVLDNLAHYSSHVAAQRARLNTETV 131
                                       555667788889999........77.*******************.9****************************** PP

                                       EBEETTTTEE-HHHHHHHHTTHHCTTE.TEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSS CS
                     Aminotran_1_2 121 plyseedfhldlealeealkeapegnk.ktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfg 196
                                       + +  +d+ +d e++ +a+++   ++  ++ + l++ p  + G +++ +++  +   +++y + l++  aY+++ + 
  gi|298675260|ref|YP_003727010.1| 132 SSTGHPDYWIDPEGYAKAIENVIDESGkPPSMALLTYPDGNYGNLPNAKKVASV---CHEYDVPLLLNCAYSIGRMP 205
                                       *9999***************975444349999999*999999999999998888...*****************997 PP

                                       SSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHH CS
                     Aminotran_1_2 197 sldavatranveeepnllivgslsKafGlaGeRvGyilgnaav 239
                                                ++++  ++++vgs  K++++ G  +G + +++++
  gi|298675260|ref|YP_003727010.1| 206 --------IDANDIGADFVVGSGHKSMASSG-PIGVLGVSEEY 239
                                       ........666666678**************.99999888844 PP

>> OKR_DC_1  Orn/Lys/Arg decarboxylase, major domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   6.4e-07    0.0019      86     244 ..      84     226 ..      70     273 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.4e-07
                                       EESSHHHHHHHHHHHHH--TTEEEEEESS--HHHHHHHHHS-EEEEEE--E.B-TTS-BE---GGGGSHHHHHHHHH CS
                          OKR_DC_1  86 fvvnGTsssnkvvlnavltpgdlvlvdRNcHKSiehalvlsgatPvylepe.rnalgiiggidlkefeeetlkekik 161
                                        v+nG   s  +v+++v+++gd +++d  +H S + a   +      l++e  +    ++g +   +++e  +++i+
  gi|298675260|ref|YP_003727010.1|  84 RVTNGARESKFAVMHSVANEGDWIVLDNLAHYSSHVAAQRAR-----LNTEtVS----STGHPDYWIDPEGYAKAIE 151
                                       699******************************998765554.....4444222....2333333556688888888 PP

                                       HSTTTGS..ESEEEEESS.-TTSEEE-HHHHHHHHTTSESEEEEE-TT-TTGGGSGGGTTSSSSSSS-BTTBEEEEE CS
                          OKR_DC_1 162 evpdaka..prlavitns.TYdGvlynakeivdkleklsdrilfDeAwvgyeqfiplyadaskllaenendpgilvt 235
                                       +v d+ +  p++a++t +   +G l nak++    +++++++l+  A+     +  ++ da +++a+       +v+
  gi|298675260|ref|YP_003727010.1| 152 NVIDESGkpPSMALLTYPdGNYGNLPNAKKVASVCHEYDVPLLLNCAYS----IGRMPIDANDIGAD-------FVV 217
                                       8888877779999999983479***********************9985....67899999999999.......999 PP

                                       EEHCCCCS- CS
                          OKR_DC_1 236 qSvHKllaa 244
                                        S HK  a+
  gi|298675260|ref|YP_003727010.1| 218 GSGHKSMAS 226
                                       999998876 PP

>> HSL_N  Hormone-sensitive lipase (HSL) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00021      0.64     181     225 ..     112     156 ..     106     158 .. 0.92
   2 ?   -3.8   0.0       1.7     5e+03      44      56 ..     178     190 ..     177     191 .. 0.84
   3 ?   -0.8   0.0      0.19   5.7e+02     203     223 ..     330     350 ..     322     361 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00021
                             HSL_N 181 masfsesykkeksklakaasslltsgkYvldpElRarrivkitqn 225
                                       +a +s +   +  +l++ + s +  + Y +dpE  a+ i++++++
  gi|298675260|ref|YP_003727010.1| 112 LAHYSSHVAAQRARLNTETVSSTGHPDYWIDPEGYAKAIENVIDE 156
                                       899**************************************9876 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 1.7
                             HSL_N  44 lvkelaavahefD 56 
                                       + k++a+v+he+D
  gi|298675260|ref|YP_003727010.1| 178 NAKKVASVCHEYD 190
                                       678999******9 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.19
                             HSL_N 203 ltsgkYvldpElRarrivkit 223
                                       ++sg+Y+l  El+ r+i  i 
  gi|298675260|ref|YP_003727010.1| 330 AKSGRYFLYKELKSRNIHGIK 350
                                       589**************9885 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00015      0.46      23     150 ..      64     202 ..      56     214 .. 0.77
   2 ?   -2.9   0.0       1.1   3.2e+03     244     302 ..     287     346 ..     280     348 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00015
                                       HHHHHH.HHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-.TTTS CS
                   DegT_DnrJ_EryC1  23 peveeF.EkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvd.pdty 97 
                                       p++++F  +a+ +++g++ +  v++G      a +   +++gd ++   l   ++  a++++ +++  v  +   +y
  gi|298675260|ref|YP_003727010.1|  64 PKIKDFvHEALPEFIGADEV-RVTNGARESKFAVMHSVANEGDWIVLDNLAHYSSHVAAQRARLNTETVSSTgHPDY 139
                                       56666634678999999885.66777777777777777788*******************99999988876625799 PP

                                       SB-GGGCGGG--TTE........EEEE..EB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT CS
                   DegT_DnrJ_EryC1  98 nidpaaieaaitert........kaIl..pVhlyGqvadmdalkaiaakhglkvieDaAhAlG 150
                                        idp+  ++ai++           a l  p   yG+  + +++  ++++++++++  +A ++G
  gi|298675260|ref|YP_003727010.1| 140 WIDPEGYAKAIENVIdesgkppsMALLtyPDGNYGNLPNAKKVASVCHEYDVPLLLNCAYSIG 202
                                       9**986666665544444577765554224568999999999*****************9999 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHTCCCCEESCGGTTSSSEEESCEEEEEHCCHHHC..HHHHHHHHHHCCE CS
                   DegT_DnrJ_EryC1 244 RreiaelykeeLaelegtaelttpketkkhawhlyavlveeeaevk..rdelvealkeegi 302
                                         e+a  ++e+L++l+++++   p++++   ++  + + e ++++k  r  l ++lk+++i
  gi|298675260|ref|YP_003727010.1| 287 EVENARWFSEKLENLGMNQVGDKPHNHD-LMFFEAPNIYEISQKAKsgRYFLYKELKSRNI 346
                                       5578888999999999876655555555.66666665555444422246667777776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2850.43
//
Query:       gi|298675261|ref|YP_003727011.1|  [L=93]
Description: RNA polymerase dimerization [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-20   72.7   0.2    1.9e-20   72.4   0.2    1.1  1  RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
    2.4e-07   30.1   0.1    4.4e-07   29.2   0.0    1.5  2  RNA_pol_L    RNA polymerase Rpb3/Rpb11 dimerisation domain


Domain annotation for each model (and alignments):
>> RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.4   0.2   2.1e-24   1.9e-20       2      74 ..      13      84 ..      12      85 .. 0.96

  Alignments for each domain:
  == domain 1  score: 72.4 bits;  conditional E-value: 2.1e-24
                                      EEEEEES--HHHHHHHHHHHTTSTTEEEEEEECSSTTTSEEEEEEEESTSS-HHHHHHHHHHHHHHHHHHHHH CS
                       RNA_pol_L_2  2 ltfeingEDhTLgnlLrhlllknpsVefagYkipHPlepkmnlriqtkssnnpleaLkkalkdlldicdelee 74
                                      +++ei+gEDhTL+n+L+ +ll++ +Ve+a+Y+++H   ++  l ++t+ +++ ++++k+al++l++ cde+ e
  gi|298675261|ref|YP_003727011.1| 13 INMEIQGEDHTLLNVLKSILLEDSRVEIASYDMKHVNVSEPILYVKTD-GTDQITVIKEALSKLISRCDEFNE 84
                                      789********************************************8.59*******************976 PP

>> RNA_pol_L  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   4.9e-11   4.4e-07       3      69 .]      16      79 ..      14      79 .. 0.88
   2 ?   -3.2   0.0      0.65   5.8e+03      56      63 ..      84      91 ..      83      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 4.9e-11
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         RNA_pol_L  3 llrgvdhtlgNaLRrillsevpgvaiea......pvvkvntdkdklilevetdgslkPeealkeAlkiLkekl 69
                                      +++g+dhtl N L+ ill e   v+i++       v       ++ il v+tdg+ +   ++keAl +L++++
  gi|298675261|ref|YP_003727011.1| 16 EIQGEDHTLLNVLKSILL-EDSRVEIASydmkhvNV-------SEPILYVKTDGT-DQITVIKEALSKLISRC 79
                                      79****************.*********98764433.......5689****9998.899**********9988 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.65
                                      xxxxxxxx RF
                         RNA_pol_L 56 ealkeAlk 63
                                      e+++eA+k
  gi|298675261|ref|YP_003727011.1| 84 EVFSEAVK 91
                                      79999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 653.08
//
Query:       gi|298675262|ref|YP_003727012.1|  [L=199]
Description: RNA-binding protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-13   49.8   0.9    3.2e-13   49.2   0.9    1.3  1  ECR1_N          Exosome complex exonuclease RRP4 N-terminal r
    0.00059   19.8   0.0    0.00076   19.5   0.0    1.3  1  HypA            Hydrogenase/urease nickel incorporation, meta
    0.00069   20.2   0.3     0.0017   18.9   0.3    1.7  1  EXOSC1          Exosome component EXOSC1/CSL4
  ------ inclusion threshold ------
      0.011   15.7   1.5      0.018   15.0   1.5    1.2  1  DZR             Double zinc ribbon
      0.028   14.1   5.3      0.066   13.0   5.3    1.7  1  zinc_ribbon_2   zinc-ribbon domain
      0.033   14.2   0.2      0.051   13.6   0.2    1.3  1  Zn_Tnp_IS91     Transposase zinc-binding domain
      0.039   14.2   1.6      0.065   13.5   1.6    1.3  1  IBR             IBR domain, a half RING-finger domain
      0.047   13.9   0.1       0.09   13.0   0.1    1.5  1  DUF3006         Protein of unknown function (DUF3006)
      0.051   13.5   0.6      0.051   13.5   0.6    1.6  1  Prok-RING_1     Prokaryotic RING finger family 1
       0.06   13.3   2.7       0.09   12.8   2.7    1.2  1  zinc-ribbons_6  zinc-ribbons
       0.06   13.3   2.6       0.12   12.3   2.6    1.5  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.078   13.1   3.0       0.09   12.9   1.9    1.6  1  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
       0.24   11.5   3.5       0.66   10.1   3.6    1.7  1  Zn-ribbon_8     Zinc ribbon domain
       0.64   10.3   2.5        4.9    7.5   0.1    2.3  2  zf-LITAF-like   LITAF-like zinc ribbon domain
        1.1    9.3   6.5         14    5.7   4.9    2.6  2  zinc_ribbon_4   zinc-ribbon domain
        1.1    9.2   5.0        1.8    8.5   5.0    1.3  1  zf-C3HC4        Zinc finger, C3HC4 type (RING finger)
        1.3    8.6   5.4        1.6    8.3   0.9    2.6  2  TF_Zn_Ribbon    TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> ECR1_N  Exosome complex exonuclease RRP4 N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.9     3e-16   3.2e-13       1      37 [.      18      54 ..      18      55 .. 0.96

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 3e-16
                                      EE-TT-EEEETTTSEE-TTEEEETTEEEESSSEEEEE CS
                            ECR1_N  1 iVtPGevlttdeefmrGhGTYvrggtiyAsvaGtvev 37
                                      +V+PG+ ++t+ee+++G+GTY ++g+iy+ vaG v v
  gi|298675262|ref|YP_003727012.1| 18 FVMPGDFVGTTEEYIPGEGTYMYHGNIYSLVAGDVVV 54
                                      7********************************9976 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   7.2e-07   0.00076      69      97 ..     159     187 ..      79     195 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 7.2e-07
                                       -EEEETTTS-EEECHHHHHS-TTTSSS-E CS
                              HypA  69 vkvrCreCgkefeleekalrCpkCgsadv 97 
                                       +k++C++C++ +e+++++l+Cp+Cg+++ 
  gi|298675262|ref|YP_003727012.1| 159 MKAYCTNCRSAMEKDNNKLKCPNCGKTEK 187
                                       6889*********998799******9865 PP

>> EXOSC1  Exosome component EXOSC1/CSL4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.3   1.7e-06    0.0017       3      50 ..      74     127 ..      71     157 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.7e-06
                                       -TT-EEEEEEEEEESSEEEEEEEEECTB......SBCCCEEECCCTTSS--STS CS
                            EXOSC1   3 kegdvVLarvtrlrkkqalveilsvege......nnvlsdsgvgangegavkei 50 
                                       kegd+V++ +t++r + a+v + +++++      +  ++  +v+++++++vk++
  gi|298675262|ref|YP_003727012.1|  74 KEGDIVIGGITDVRDSVAIVGLEAIKDKgerefqESRPAAIHVSNVKDAYVKKL 127
                                       68************************9999999888999************986 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   1.5   1.7e-05     0.018      13      37 ..     161     185 ..     155     190 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.7e-05
                               DZR  13 rfCseCgtklkavaaedrCpsCgek 37 
                                        +C +C++++++ +++ +Cp+Cg+ 
  gi|298675262|ref|YP_003727012.1| 161 AYCTNCRSAMEKDNNKLKCPNCGKT 185
                                       69********99999*******975 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   5.3   6.2e-05     0.066       1      21 [.     162     184 ..     162     185 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.2e-05
                     zinc_ribbon_2   1 fCpnCGaelq.dnakF.CpyCGt 21 
                                       +C+nC    + dn+k  Cp+CG 
  gi|298675262|ref|YP_003727012.1| 162 YCTNCRSAMEkDNNKLkCPNCGK 184
                                       8********6489999******5 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   4.8e-05     0.051      28      72 ..     149     191 ..     119     195 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.8e-05
                       Zn_Tnp_IS91  28 lrCrtaalGfaryeCeeCghekivyfsCksrhCpsCqkkateewl 72 
                                       l+ ++ +lG+++  C++C++   +    ++  Cp+C+k ++++  
  gi|298675262|ref|YP_003727012.1| 149 LSTSEDSLGVMKAYCTNCRS--AMEKDNNKLKCPNCGKTEKRKIS 191
                                       55667789**********85..4444444555******9998865 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.6   6.1e-05     0.065      18      46 ..     160     184 ..     140     185 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.1e-05
                               IBR  18 lkwCprpdCeaiieksegcksvtCskCgf 46 
                                       + +C+  +C +++ek+++  +++C++Cg+
  gi|298675262|ref|YP_003727012.1| 160 KAYCT--NCRSAMEKDNN--KLKCPNCGK 184
                                       78**9..******99999..667****96 PP

>> DUF3006  Protein of unknown function (DUF3006)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   8.5e-05      0.09      12      39 ..      52      80 ..      51     104 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.5e-05
                           DUF3006 12 Vleled.getidiprsdLpegakeGdvLe 39
                                      V+++++ + +  ip ++ p+++keGd+++
  gi|298675262|ref|YP_003727012.1| 52 VVVDDNsRSVSVIPNTKTPPSIKEGDIVI 80
                                      677888666777***************85 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.6   4.8e-05     0.051       4      32 ..     160     188 ..     158     197 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.8e-05
                       Prok-RING_1   4 gkkCpvCgkelkeedDiVvCpeCgtpyHr 32 
                                       +  C+ C+ ++++++    Cp+Cg    r
  gi|298675262|ref|YP_003727012.1| 160 KAYCTNCRSAMEKDNNKLKCPNCGKTEKR 188
                                       678*********************77665 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   2.7   8.6e-05      0.09       2      28 ..     162     188 ..     161     193 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.6e-05
                                       --SSS-S--EE-SSEEE-TTT--EEEE CS
                    zinc-ribbons_6   2 kCpeCqqelekrgeqyhCeaCqedlkk 28 
                                       +C +C +++ek++++++C +C +  k+
  gi|298675262|ref|YP_003727012.1| 162 YCTNCRSAMEKDNNKLKCPNCGKTEKR 188
                                       8********************986554 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.6   0.00012      0.12      30      58 ..     162     188 ..     161     193 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                    OrfB_Zn_ribbon  30 tCseCgsknkealsgrtfkCpnCgfeadr 58 
                                        C +C s +++  +++++kCpnCg +  r
  gi|298675262|ref|YP_003727012.1| 162 YCTNCRSAMEK--DNNKLKCPNCGKTEKR 188
                                       5**********..***********99887 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.9   8.6e-05      0.09      10      38 ..     162     191 ..     158     196 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.6e-05
                      NOB1_Zn_bind  10 rChaCfkvt.kdmtkkFCpkCGnktLkrva 38 
                                        C+ C + + kd++k  Cp+CG+   ++++
  gi|298675262|ref|YP_003727012.1| 162 YCTNCRSAMeKDNNKLKCPNCGKTEKRKIS 191
                                       599999877477**********99877776 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   3.6   0.00063      0.66       8      39 ..     163     189 ..     160     190 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00063
                       Zn-ribbon_8   8 CeeCghefevlqsisdapltaCPeCgsevrrv 39 
                                       C++C +  e+     d+++ +CP+Cg++ +r 
  gi|298675262|ref|YP_003727012.1| 163 CTNCRSAMEK-----DNNKLKCPNCGKTEKRK 189
                                       8899877662.....555777*****955554 PP

>> zf-LITAF-like  LITAF-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.3      0.14   1.4e+02      55      66 ..     159     170 ..     152     174 .. 0.76
   2 ?    7.5   0.1    0.0046       4.9       5      25 ..     176     196 ..     172     199 .] 0.77

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.14
                     zf-LITAF-like  55 vehyCpnCgall 66 
                                       ++ yC+nC++ +
  gi|298675262|ref|YP_003727012.1| 159 MKAYCTNCRSAM 170
                                       677999998765 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0046
                     zf-LITAF-like   5 qvdCpaCqqrvvTsveyksgk 25 
                                       +++Cp+C++++  ++++  g+
  gi|298675262|ref|YP_003727012.1| 176 KLKCPNCGKTEKRKISSDYGT 196
                                       688999999988888877765 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       6.6     7e+03      14      23 ..      64      73 ..      61      75 .. 0.80
   2 ?    5.7   4.9     0.014        14       1      33 [.     159     184 ..     159     185 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6.6
                     zinc_ribbon_4 14 iddeklpakg 23
                                      i++ k p+++
  gi|298675262|ref|YP_003727012.1| 64 IPNTKTPPSI 73
                                      8999999986 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.014
                     zinc_ribbon_4   1 MkitCpsCkakyeiddeklpakgvkvrCskCgh 33 
                                       Mk  C +C +        + ++  k++C++Cg+
  gi|298675262|ref|YP_003727012.1| 159 MKAYCTNCRS-------AMEKDNNKLKCPNCGK 184
                                       5666666654.......4566667999****97 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   5.0    0.0017       1.8      21      41 .]     162     182 ..     160     182 .. 0.95

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0017
                                       B-CHHHHHHHHCTSSB--TTT CS
                          zf-C3HC4  21 fCskCirkilksrkkvkCPlC 41 
                                       +C++C + + k+++k kCP+C
  gi|298675262|ref|YP_003727012.1| 162 YCTNCRSAMEKDNNKLKCPNC 182
                                       8**********9********* PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   5.5     0.028        29       3      26 ..     163     183 ..     161     187 .. 0.58
   2 ?    8.3   0.9    0.0015       1.6       2      10 ..     178     186 ..     177     197 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.028
                                       ETTTTCEECHEETSTTCEEESSSS CS
                      TF_Zn_Ribbon   3 CPnCgstnlveDpergelvCtdCG 26 
                                       C nC s + + D  ++ l C++CG
  gi|298675262|ref|YP_003727012.1| 163 CTNCRSAM-EKD--NNKLKCPNCG 183
                                       66666653.444..4466666666 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0015
                                       EETTTTCEE CS
                      TF_Zn_Ribbon   2 kCPnCgstn 10 
                                       kCPnCg t+
  gi|298675262|ref|YP_003727012.1| 178 KCPNCGKTE 186
                                       9*****976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       859  (0.0479112); expected 358.6 (0.02)
Passed bias filter:                      621  (0.0346366); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1323.89
//
Query:       gi|298675263|ref|YP_003727013.1|  [L=197]
Description: ribosomal L11 methyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-14   52.9   0.0    4.5e-14   52.3   0.0    1.2  1  MTS              Methyltransferase small domain
    1.6e-13   50.7   0.3    2.1e-13   50.3   0.3    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    3.5e-09   37.2   0.0    9.9e-09   35.8   0.0    1.8  2  Methyltransf_25  Methyltransferase domain
    2.4e-07   30.7   0.4    1.2e-06   28.4   0.4    1.9  1  UPF0020          Putative RNA methylase family UPF0020
    3.1e-07   30.3   0.2    6.1e-07   29.3   0.0    1.5  2  Methyltransf_31  Methyltransferase domain
      6e-06   26.8   0.1    1.8e-05   25.3   0.0    1.8  2  Methyltransf_11  Methyltransferase domain
     0.0051   16.5   0.0      0.007   16.0   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
     0.0073   16.2   0.0      0.008   16.0   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
  ------ inclusion threshold ------
      0.019   14.2   0.0      0.079   12.2   0.0    1.8  1  N6_Mtase         N-6 DNA Methylase
       0.04   13.4   0.1      0.099   12.1   0.1    1.6  2  AviRa            RRNA methyltransferase AviRa
      0.041   13.5   0.1      0.055   13.0   0.1    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
      0.053   14.3   0.0      0.098   13.4   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
       0.12   12.0   0.1       0.15   11.6   0.1    1.3  1  FmrO             Ribosomal RNA methyltransferase (FmrO)
       0.15   12.1   0.0       0.18   11.7   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
       0.15   12.0   0.2       0.24   11.3   0.2    1.2  1  Methyltransf_18  Methyltransferase domain


Domain annotation for each model (and alignments):
>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.3   0.0   3.8e-17   4.5e-14      25     111 ..      40     123 ..      32     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 3.8e-17
                                       HHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEE CS
                               MTS  25 etlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdli 101
                                        +++ +++++v D+GcG+Gvl++ ++    e  vt +d d++Al++a +n+++ +++v+++ +d+  +++ ++ +++
  gi|298675263|ref|YP_003727013.1|  40 AYMKGDIRDTVYDIGCGTGVLAIGAKLLGAE-IVTGFDTDHYALQIADKNARSMNVDVDFICKDIS-NIS-GEAQTV 113
                                       5678889999*************98887777.6*******************************85.566.799*** PP

                                       EE---STTTC CS
                               MTS 102 vsNPPfhagk 111
                                       v+NPPf ++ 
  gi|298675263|ref|YP_003727013.1| 114 VMNPPFGSQV 123
                                       ******8775 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3   0.3   1.8e-16   2.1e-13     162     233 ..      47     116 ..      32     117 .. 0.83

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 1.8e-16
                              PrmA 162 geevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk.eekadvivaN 233
                                       +++v D+G+G+G+Lai+a++Lga+ v++ D+D+ A+++a +Na+  +v+  +     +++ + +++a  +v N
  gi|298675263|ref|YP_003727013.1|  47 RDTVYDIGCGTGVLAIGAKLLGAEIVTGFDTDHYALQIADKNARSMNVDVDFIC---KDISNiSGEAQTVVMN 116
                                       469*****************************************9999988833...4444334567777766 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.0   8.3e-12   9.9e-09       1      64 [.      50     112 ..      50     136 .. 0.91
   2 ?   -1.9   0.0       4.9   5.9e+03      47      59 ..     175     187 ..     157     191 .. 0.71

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 8.3e-12
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTT CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgs 64 
                                       v d+GcGtG l++ +    g++ vtg+D ++ +l++a ++a++ +++v+f+++d+++++ e+++
  gi|298675263|ref|YP_003727013.1|  50 VYDIGCGTGVLAIGAKLL-GAEIVTGFDTDHYALQIADKNARSMNVDVDFICKDISNISGEAQT 112
                                       78*******999998766.79************************************9877654 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.9
                                       TEEEEESBCCGBS CS
                   Methyltransf_25  47 nvefvqgdaedlp 59 
                                        ++f+++d+e+++
  gi|298675263|ref|YP_003727013.1| 175 TFKFHKKDVEQIE 187
                                       6789999999876 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.4   9.8e-10   1.2e-06      16     135 ..      32     123 ..      25     129 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 9.8e-10
                                       HHHHHHHHTT--TT..S-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHH CS
                           UPF0020  16 LAaalvrlagwkpg..epllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvvq 90 
                                       +Aa l+  a +k +  ++ +D  CG+G ++I a llga+i+                          g+D d+ ++q
  gi|298675263|ref|YP_003727013.1|  32 IAAELLHFAYMKGDirDTVYDIGCGTGVLAIGAKLLGAEIV-------------------------TGFDTDHYALQ 83 
                                       56666666666665447788888*****************9.........................6********** PP

                                       HHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE-------- CS
                           UPF0020  91 gareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerl 135
                                        a +Na++++v+  ++f ++d+ ++    ge  ++v npP+G  +
  gi|298675263|ref|YP_003727013.1|  84 IADKNARSMNVD--VDFICKDISNIS---GEAQTVVMNPPFGSQV 123
                                       *******99886..89*******999...77899********876 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   5.1e-10   6.1e-07       6      67 ..      49     107 ..      46     128 .. 0.90
   2 ?   -3.0   0.0       4.6   5.5e+03      56      67 ..     176     187 ..     173     191 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 5.1e-10
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkae.vvGiDiseeaielArenaqklgldnveFeqgdieele 67 
                                       +v+D+GCGtG l++ +  +lg  ae v+G+D +  a++ A +na++ ++d v F   di +++
  gi|298675263|ref|YP_003727013.1|  49 TVYDIGCGTGVLAIGAK-LLG--AEiVTGFDTDHYALQIADKNARSMNVD-VDFICKDISNIS 107
                                       79************999.775..5559**********************8.*******99875 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.6
                   Methyltransf_31  56 veFeqgdieele 67 
                                       ++F++ d+e++e
  gi|298675263|ref|YP_003727013.1| 176 FKFHKKDVEQIE 187
                                       689999999987 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   1.5e-08   1.8e-05       2      56 ..      52     107 ..      51     115 .. 0.93
   2 ?   -1.9   0.0       4.7   5.6e+03      46      83 ..     177     189 ..     157     194 .. 0.59

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.5e-08
                                       EET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTS CS
                   Methyltransf_11   2 dvGcGtGrlaealakrg.arvvgvDlskemlklakekaseeglkvefvvadaeklp 56 
                                       d+GcGtG la   +  g + v+g+D+++++l++a ++a+  ++ v+f++ d++++ 
  gi|298675263|ref|YP_003727013.1|  52 DIGCGTGVLAIGAKLLGaEIVTGFDTDHYALQIADKNARSMNVDVDFICKDISNIS 107
                                       9*************999999*********************99*********9874 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.7
                                       EETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHHHHH CS
                   Methyltransf_11  46 efvvadaeklpfednsfDlvvssevlhhvedpekalke 83 
                                       +f++                          d+e++  e
  gi|298675263|ref|YP_003727013.1| 177 KFHKK-------------------------DVEQIEVE 189
                                       44444.........................44444445 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   5.9e-06     0.007      33     126 ..      39     122 ..      28     154 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.9e-06
                                       HHHHCCCHCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS-- CS
                     Cons_hypoth95  33 FnilaaeiegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklak 109
                                       F  ++ +i++  v D+ +G+G+l++ A   ga+ ++ +++d+ a++i  +n ++++++     ++ ++ ++++ +  
  gi|298675263|ref|YP_003727013.1|  39 FAYMKGDIRDT-VYDIGCGTGVLAIGAKLLGAEIVTGFDTDHYALQIADKNARSMNVD---VDFICKDISNISGE-- 109
                                       55556666666.89******************************************77...45555555566555.. PP

                                       SS-EEEEEEE--SSSTT CS
                     Cons_hypoth95 110 kkeefdivflDPPyake 126
                                            + v ++PP+ ++
  gi|298675263|ref|YP_003727013.1| 110 ----AQTVVMNPPFGSQ 122
                                       ....3568899999876 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   6.7e-06     0.008      23      71 ..      47      94 ..       4     159 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.7e-06
                   Methyltransf_23 23 ggrvLdiGcGtGillevlrengfsvt.gvDlspeaveiaekakkaqkdqf 71
                                      +  v diGcGtG l+  ++  g++++ g+D +  a +ia   k+a++ ++
  gi|298675263|ref|YP_003727013.1| 47 RDTVYDIGCGTGVLAIGAKLLGAEIVtGFDTDHYALQIAD--KNARSMNV 94
                                      55788******************7555*****99999984..33333333 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   6.6e-05     0.079      26     139 ..      24     123 ..       7     161 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.6e-05
                          N6_Mtase  26 GeffTPrevsklivell..epksgesvyDpacGsggllvqaekvlkeedgktkelsiyGqeknettyrLakmNlllh 100
                                        ++ TP  +   + + +  +   + +vyD  cG+g l + a+  l        +  + G ++++ + ++a  N    
  gi|298675263|ref|YP_003727013.1|  24 EQYTTPAPIAAELLHFAymKGDIRDTVYDIGCGTGVLAIGAKL-L-------GAEIVTGFDTDHYALQIADKNARSM 92 
                                       48999**9999998888665556678********998888765.4.......3455679999999999999999877 PP

                          N6_Mtase 101 gieykkvkirlgdtlekpkfekdkkfdvvvaNppfnqke 139
                                       +++++         + k+ ++   ++++vv Nppf+++ 
  gi|298675263|ref|YP_003727013.1|  93 NVDVD--------FICKDISNISGEAQTVVMNPPFGSQV 123
                                       77777........345555666677889999****9983 PP

>> AviRa  RRNA methyltransferase AviRa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   8.3e-05     0.099      53     100 ..      46      90 ..      24      96 .. 0.76
   2 ?   -1.7   0.0       1.3   1.6e+03     161     181 ..     104     124 ..      89     144 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.3e-05
                             AviRa  53 apltlyDpCCGgayLltvlgllhgkkikkvlasDvdeevlelakkNLs 100
                                          t+yD  CG++ L+    ll ++ i  v++ D+d+ +l++a+kN +
  gi|298675263|ref|YP_003727013.1|  46 IRDTVYDIGCGTGVLAIGAKLLGAE-I--VTGFDTDHYALQIADKNAR 90 
                                       3458*********999888887654.4..7899*************75 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.3
                             AviRa 161 eeaekevdivitDlPYGelvs 181
                                       ++ + e++ v++  P+G++v+
  gi|298675263|ref|YP_003727013.1| 104 SNISGEAQTVVMNPPFGSQVR 124
                                       345556888999999999886 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   4.6e-05     0.055       3      82 ..      49     120 ..      47     157 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.6e-05
                   Methyltransf_15   3 vilDlfsGaGGnviqfalv.fekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflS 78 
                                       ++ D+ +G+G  +i  +l   e v + ++++  l++a +Na++   +  +++++ d+ ++  + +        v++ 
  gi|298675263|ref|YP_003727013.1|  49 TVYDIGCGTGVLAIGAKLLgAEIVTGFDTDHYALQIADKNARSM--NVDVDFICKDISNISGEAQ-------TVVMN 116
                                       67899************994455789*****************9..5578999988877544322.......34445 PP

                   Methyltransf_15  79 pPwG 82 
                                       pP G
  gi|298675263|ref|YP_003727013.1| 117 PPFG 120
                                       5544 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   8.2e-05     0.098       2      53 ..      52      98 ..      51     123 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.2e-05
                   Methyltransf_12  2 eiGcGtGsllralleklpdieyt.gvDispsaiedakeklakrennnnnnvel 53
                                      +iGcGtG l+        ++e++ g D +  a+ + + k a+  n     v++
  gi|298675263|ref|YP_003727013.1| 52 DIGCGTGVLAIGAKLL--GAEIVtGFDTDHYAL-QIADKNARSMNV---DVDF 98
                                      9******998777666..999999*********.555554444443...3444 PP

>> FmrO  Ribosomal RNA methyltransferase (FmrO)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00012      0.15     108     163 ..      48     102 ..      38     165 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                              FmrO 108 asvlDvaCgLnpLavpwlllaadatylasDidsdlvefldrflalvevegrvevrD 163
                                       ++v D++Cg  +La++  ll a+ + +++D d   + + d+    ++v+     +D
  gi|298675263|ref|YP_003727013.1|  48 DTVYDIGCGTGVLAIGAKLLGAEIV-TGFDTDHYALQIADKNARSMNVDVDFICKD 102
                                       79***************99999865.899999999999888776666666655555 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00015      0.18      26      85 ..      47      99 ..      30     159 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00015
                   Methyltransf_32 26 altvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfa 85
                                      + tv D+G+G g L+   +l        v+g+d+ +   + a k a+ ++ ++     f+
  gi|298675263|ref|YP_003727013.1| 47 RDTVYDIGCGTGVLAIGAKL---LGAEIVTGFDTDHYALQIADKNARSMNVDV----DFI 99
                                      679*************9999...5566789****9999999999888888333....333 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2    0.0002      0.24      16      87 ..      48     114 ..      38     116 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0002
                   Methyltransf_18  16 srvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeeevdtvv 87 
                                       ++v DiG+  g+l+i +     a+ v+  D  + +l+ a++n+++ ++  ++++++ d +++++ +e++tvv
  gi|298675263|ref|YP_003727013.1|  48 DTVYDIGCGTGVLAIGAKLL-GAEIVTGFDTDHYALQIADKNARSMNV--DVDFICKD-ISNIS-GEAQTVV 114
                                       689***********988654.57799******************9888..68888877.45663.5677776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1389.48
//
Query:       gi|298675264|ref|YP_003727014.1|  [L=333]
Description: diphthamide biosynthesis protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-84  283.5   0.8    2.6e-84  283.2   0.8    1.0  1  Diphthamide_syn  Putative diphthamide synthesis protein
  ------ inclusion threshold ------
       0.16   12.3   0.3       0.39   11.1   0.0    1.7  2  DUF1104          Protein of unknown function (DUF1104)


Domain annotation for each model (and alignments):
>> Diphthamide_syn  Putative diphthamide synthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  283.2   0.8   2.9e-88   2.6e-84       1     299 [.      31     322 ..      31     325 .. 0.95

  Alignments for each domain:
  == domain 1  score: 283.2 bits;  conditional E-value: 2.9e-88
                   Diphthamide_syn   1 fPegllpdsaeiadil.eefgaevvilgDttYGaCcvdevaaehlgadllvHyGhsclspvd.rlpvlYvfveield 75 
                                       +Pegl++ s +ia++l +++ +ev+++++++YGaC++d+  ++   +d+l H+Ghs+l  ++ + +++Y+ + +e++
  gi|298675264|ref|YP_003727014.1|  31 LPEGLKRKSIDIASKLeQSTCVEVIVSANPCYGACDIDTDILDD--VDILFHFGHSELDDCKyNEKIYYIKAASEIN 105
                                       6***************77889*********************99..9*************999************** PP

                   Diphthamide_syn  76 vehlvetlkknfkekkkivlvstiqyahaleevkeeleeegyevv.kvpqsekplspgevlgctspklkeeeeevda 151
                                       ++++v+++ +n+ +  ++++++t+q++h+leev++++e+   e + +++++ ++ +pg+vlgc++++++   +e+d+
  gi|298675264|ref|YP_003727014.1| 106 ISEIVKQAMENI-KAYRVGVLTTVQHVHKLEEVRKIIESCSRECIiQKGDT-RIAYPGQVLGCNFSSAE--IDECDE 178
                                       ************.6778*********************6555666455566.9***************8..679*** PP

                   Diphthamide_syn 152 ilyigdgrfhllslmlsnpklpvyrydpyskklteesydakkllrrRyaaiekakdakkvGiivgtlgvqgrlelve 228
                                       +lyig+g+fh+ ++++++ k pv+ +dp+ +  ++   d +++lr+R a+i+k+ d++++Gi+v+++ +q+r+el++
  gi|298675264|ref|YP_003727014.1| 179 YLYIGSGEFHPVGVAVATGK-PVMVADPFMD--KTYYVDPSRILRQRSAVIAKSLDSSTFGILVSSKIGQYRMELAK 252
                                       ******************87.*********8..577899************************************** PP

                   Diphthamide_syn 229 rlkkllkeagkksylvlvgelnpakLanfaeidafVlvaCprlsiddgkeFekPvltpyElevalgerewt 299
                                        lk+l+k++gkk+y++++++++ ++L +f ++dafV++aCpr++idd   F+ P+ltp+E+e++lger+w+
  gi|298675264|ref|YP_003727014.1| 253 YLKNLAKKHGKKAYILTMDRVTSDQLLQF-KVDAFVNTACPRIAIDDVGHFPSPMLTPQEFEIVLGERKWE 322
                                       *****************************.9***************************************6 PP

>> DUF1104  Protein of unknown function (DUF1104)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.89     8e+03      27      63 ..     114     116 ..      97     142 .. 0.55
   2 ?   11.1   0.0   4.3e-05      0.39      15      64 ..     236     286 ..     232     290 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.89
                                       HHHHHHHHHS-HHHHHHHHHHHHHHHHHHHTTS-HHH CS
                           DUF1104  27 mevaKrlkslkekekkkfkkklkeaaeknlekmtvke 63 
                                       me                                  +
  gi|298675264|ref|YP_003727014.1| 114 ME----------------------------------N 116
                                       22..................................2 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 4.3e-05
                                       TTS-GGGHHHHHHHHHHHHHHS-HHH.HHHHHHHHHHHHHHHHTTS-HHHH CS
                           DUF1104  15 GkvapeevldykmevaKrlkslkeke.kkkfkkklkeaaeknlekmtvkef 64 
                                       G +  +++  y+me+aK lk+l +k+ kk++   +++    +l + +v  f
  gi|298675264|ref|YP_003727014.1| 236 GILVSSKIGQYRMELAKYLKNLAKKHgKKAYILTMDRVTSDQLLQFKVDAF 286
                                       6777889999************99653788999999998888877776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       963  (0.0537119); expected 358.6 (0.02)
Passed bias filter:                      717  (0.0399911); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2422.29
//
Query:       gi|298675265|ref|YP_003727015.1|  [L=190]
Description: phosphoribosyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.6e-18   65.6   0.9    4.9e-18   65.2   0.9    1.1  1  Pribosyltran  Phosphoribosyl transferase domain
    0.00019   21.0   0.2    0.00028   20.4   0.2    1.3  1  UPRTase       Uracil phosphoribosyltransferase
       0.01   15.4   0.1      0.015   14.8   0.1    1.3  1  PRTase_2      Phosphoribosyl transferase
  ------ inclusion threshold ------
      0.033   14.5   0.2      0.088   13.1   0.2    1.7  1  PDZ_2         PDZ domain
      0.056   13.6   1.0        6.5    6.9   0.1    2.9  3  STT3_PglB_C   STT3/PglB C-terminal beta-barrel domain
       0.48    9.7   5.8      0.096   12.0   1.3    1.8  2  DUF1235       Protein of unknown function (DUF1235)


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.2   0.9   1.6e-21   4.9e-18      15     150 ..      39     178 ..      34     184 .. 0.88

  Alignments for each domain:
  == domain 1  score: 65.2 bits;  conditional E-value: 1.6e-21
                                       EEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE...........EE----TTS CS
                      Pribosyltran  15 varlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes...rlledpagk 88 
                                        +++a  i+e+ + + d +v i+  G+p+a+ l+ + +vpl ++rk+ky  +g   ++++   +       ++  g 
  gi|298675265|ref|YP_003727015.1|  39 LQEIANHIVENTKMNVDKIVSIEAMGIPIATSLSLKSGVPLSIIRKRKYGLNGEIAVSQSTGYSKgqlYINGIESGD 115
                                       56788889999999******************************************9976655449999999***** PP

                                       EEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHHHHH-TTS......EEEEE CS
                      Pribosyltran  89 kVliVDDildtGgTllaalelLkekgpeevriavlvdkpateeevdknakrvfsls.pdnfva 150
                                       ++liVDD+++tGgTl+ ++++L ++g  + +++v+v++++++ + +   + v+sl+ +  +++
  gi|298675265|ref|YP_003727015.1| 116 RILIVDDVVSTGGTLQSVIKALIDAGSIIDEVVVIVERGEGVSKLKEMNIPVKSLIkINVDEK 178
                                       ***************************999999999******999988888888884544444 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.2   9.5e-08   0.00028     120     176 ..     113     167 ..      92     183 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 9.5e-08
                           UPRTase 120 aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrlaeefpkv 176
                                       + +++l++D v++TGg+++++i+ L+++g   ++++v  ++   egv++l e    v
  gi|298675265|ref|YP_003727015.1| 113 SGDRILIVDDVVSTGGTLQSVIKALIDAGSIIDEVVV--IVERGEGVSKLKEMNIPV 167
                                       5678***********************8876666554..577888888887755444 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   5.1e-06     0.015     119     155 ..     112     149 ..     102     170 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.1e-06
                          PRTase_2 119 aaakelvLvDDEistGktalnliralqeklpr.kryvv 155
                                       ++ +++++vDD +stG t+  +i+al ++    +++vv
  gi|298675265|ref|YP_003727015.1| 112 ESGDRILIVDDVVSTGGTLQSVIKALIDAGSIiDEVVV 149
                                       667899*******************9988555455555 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   2.9e-05     0.088      31      73 ..     110     155 ..     101     167 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.9e-05
                                       .--TT-EEEEETTB--..SSHHHHHHHHH.TS-TT-EEEEEEEETT CS
                             PDZ_2  31 glkagDvilkvdgkkv..ksledlislll.kkkpGdtVkltvlRdg 73 
                                       g+++gD+il vd+++    +l+++i++l  ++++ d+V + v+R+ 
  gi|298675265|ref|YP_003727015.1| 110 GIESGDRILIVDDVVStgGTLQSVIKALIdAGSIIDEVVVIVERGE 155
                                       899**********998667788888888779************964 PP

>> STT3_PglB_C  STT3/PglB C-terminal beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.73   2.2e+03      32      46 ..      47      61 ..      38      65 .. 0.81
   2 ?    3.8   0.0      0.02        60      37      79 ..      77     119 ..      69     120 .. 0.81
   3 ?    6.9   0.1    0.0022       6.5      31      51 ..     159     179 ..     143     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.73
                                      ETTEEEEEEEEEEEE CS
                       STT3_PglB_C 32 iggqkvpvktfvete 46
                                      +++ k++v+++v +e
  gi|298675265|ref|YP_003727015.1| 47 VENTKMNVDKIVSIE 61
                                      678899999999886 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.02
                                       EEEEEEEEEEETTTTEEEE..EE--TT--EEEEEETTTTEEEE CS
                       STT3_PglB_C  37 vpvktfveteydkngklkvketeidskaqlyvifmkdYgrFli 79 
                                       vp+  + + +y  ng+++v +++  sk+qly+  +++ +r+li
  gi|298675265|ref|YP_003727015.1|  77 VPLSIIRKRKYGLNGEIAVSQSTGYSKGQLYINGIESGDRILI 119
                                       6666677778999******************977666666666 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0022
                                       EETTEEEEEEEEEEEEETTTT CS
                       STT3_PglB_C  31 kiggqkvpvktfveteydkng 51 
                                       k++++++pvk++++++ d++g
  gi|298675265|ref|YP_003727015.1| 159 KLKEMNIPVKSLIKINVDEKG 179
                                       78999**************98 PP

>> DUF1235  Protein of unknown function (DUF1235)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2      0.27     8e+02      36      54 ..      40      60 ..       9      75 .. 0.62
   2 ?   12.0   1.3   3.2e-05     0.096      66     146 ..      96     176 ..      76     182 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.27
                           DUF1235 36 seikkyi..dekilvknlisi 54
                                      +ei ++i  + k+ v++++si
  gi|298675265|ref|YP_003727015.1| 40 QEIANHIveNTKMNVDKIVSI 60
                                      444433333334444444444 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 3.2e-05
                           DUF1235  66 linsnlskiivCiqsakkGGliividkelnekkilklnvdkivilspLseytvskvvkGsliiivldidiPsmrlvk 142
                                       + ++ +sk  + i+ +  G  i+++d ++++   l+  +  ++   ++++ +v  v +G+ +    +++iP + l+k
  gi|298675265|ref|YP_003727015.1|  96 SQSTGYSKGQLYINGIESGDRILIVDDVVSTGGTLQSVIKALIDAGSIIDEVVVIVERGEGVSKLKEMNIPVKSLIK 172
                                       334556999999***************************************************************** PP

                           DUF1235 143 skie 146
                                       ++++
  gi|298675265|ref|YP_003727015.1| 173 INVD 176
                                       9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1299.54
//
Query:       gi|298675266|ref|YP_003727016.1|  [L=396]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-22   79.1   0.0    6.3e-22   78.1   0.0    1.5  1  OrfB_IS605      Probable transposase
    2.4e-12   46.6   0.0    4.9e-12   45.6   0.0    1.5  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    5.2e-05   22.7   0.2    9.8e-05   21.8   0.2    1.5  1  Glyco_hydro_97  Glycoside hydrolase 97
  ------ inclusion threshold ------
       0.05   14.0   1.1       0.14   12.5   1.1    1.7  1  HEPN_Swt1       Swt1-like HEPN


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.1   0.0   1.4e-25   6.3e-22       2     117 ..     164     278 ..     163     281 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.1 bits;  conditional E-value: 1.4e-25
                        OrfB_IS605   2 ipvevevelpkpkgnkaagiDlGinnLatvvtedgtw.flykgrrlksdykylakeiaelqsklkksknykkasrkl 77 
                                       i++e + e+p p++++ a+iDlGinn++t+v++ g+  +++kg  +ks ++ ++k+  +l s+++k +   k s+kl
  gi|298675266|ref|YP_003727016.1| 164 IVYEKDLETPDPNEENIASIDLGINNIVTMVNNIGEKpIVIKGGVAKSINQFYNKKAGKLKSIYDKLG--IKNSKKL 238
                                       88999999****************************99*****************************9..9****** PP

                        OrfB_IS605  78 arlhrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       ++l++k + ++++++hk+++++i+ + + +++tL++g+  
  gi|298675266|ref|YP_003727016.1| 239 KKLYHKYKMKINDFFHKASKRVIDFCVKHNIGTLVIGYNE 278
                                       *************************************986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.0   1.1e-15   4.9e-12       1      69 []     299     373 ..     299     373 .. 0.96

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 1.1e-15
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke......alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f++l eql+yka++ G kv+e +++yTSk +   g+ +++      ++ +r + +++ g+ +++Dvn+a+Ni+k+
  gi|298675266|ref|YP_003727016.1| 299 FHRLLEQLKYKAEDVGLKVIEQEESYTSKCSFLDGEPVERrtsylgKRIKRGLFRSSNGTIINADVNGAYNIMKK 373
                                       899**************************999******999*****99999999999****************96 PP

>> Glyco_hydro_97  Glycoside hydrolase 97
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.2   2.2e-08   9.8e-05      34     106 ..     254     325 ..     210     343 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.2e-08
                    Glyco_hydro_97  34 tetvkryiDfAaengleyvlvegwdegWee..kkkkekefdftkpypdfdleelvaYakekgvgvelwlhsetsg 106
                                        +  kr iDf+ ++++ ++++ g++egW++   + k ++++ ++++p  +l e ++Y k+ +vg++++ ++e ++
  gi|298675266|ref|YP_003727016.1| 254 HKASKRVIDFCVKHNIGTLVI-GYNEGWKQevYMGK-RNNQKFTQIPFHRLLEQLKY-KAEDVGLKVIEQEESYT 325
                                       56789****************.*******9965554.45555667788888888888.44466788887777654 PP

>> HEPN_Swt1  Swt1-like HEPN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.1     3e-05      0.14      10      70 ..      26      85 ..      18      97 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3e-05
                         HEPN_Swt1 10 Lrpfverelskayged..wweeveaslekdeeekkesekeiskldvqdllrvitenWkevFkk 70
                                      L++  + +++++++++  w++  e    +++ ++ e+++ +  +++q+ l+++++nWk++F++
  gi|298675266|ref|YP_003727016.1| 26 LYNQANFIVKQSLNDEgdWVRYEEL---NKQLKGTENHSVLPTQTAQQTLKLMDKNWKSFFQS 85
                                      5555555566666555545555554...55666667888899999**************7775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1105  (0.061632); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 2370.65
//
Query:       gi|298675267|ref|YP_003727017.1|  [L=163]
Description: rubrerythrin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-25   90.0  11.3    2.5e-24   86.2  11.3    2.0  1  Rubrerythrin     Rubrerythrin
     0.0021   18.1   0.6     0.0033   17.4   0.6    1.3  1  DZR              Double zinc ribbon
     0.0034   16.9   0.8     0.0076   15.8   0.8    1.6  1  RecR             RecR protein
     0.0059   16.7   0.1      0.008   16.3   0.1    1.2  1  PI3K_rbd         PI3-kinase family, ras-binding domain
     0.0077   15.9   2.6      0.014   15.1   2.6    1.4  1  zinc_ribbon_2    zinc-ribbon domain
  ------ inclusion threshold ------
      0.011   15.9   1.7       0.03   14.5   1.7    1.8  1  Zn-ribbon_8      Zinc ribbon domain
      0.017   15.8   0.6      0.027   15.2   0.6    1.4  1  zinc_ribbon_15   zinc-ribbon family
      0.028   14.4   1.5      0.066   13.2   1.4    1.7  1  HypA             Hydrogenase/urease nickel incorporation, met
      0.033   14.1   0.4      0.049   13.5   0.4    1.2  1  zf-C3HC4_3       Zinc finger, C3HC4 type (RING finger)
      0.039   13.9   1.8      0.073   13.0   1.8    1.4  1  Prok-RING_1      Prokaryotic RING finger family 1
      0.077   13.3   0.6       0.55   10.5   0.2    2.2  2  DUF2492          Protein of unknown function (DUF2492)
      0.087   12.6   2.3       0.28   10.9   0.5    2.2  2  A2L_zn_ribbon    A2L zinc ribbon domain
       0.12   12.3   1.1        0.2   11.6   1.1    1.3  1  zf-RING_5        zinc-RING finger domain
       0.18   11.1   1.6       0.24   10.7   1.5    1.5  1  SLATT_5          SMODS and SLOG-associating 2TM effector doma
       0.24   11.0   5.4        1.4    8.5   0.7    2.4  2  TF_Zn_Ribbon     TFIIB zinc-binding
       0.52   10.1   3.7        6.6    6.5   0.1    2.3  2  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
        0.7   10.0   6.0       0.64   10.1   0.6    2.4  2  Rubredoxin       Rubredoxin
          2    8.1   8.1       0.18   11.4   2.6    1.9  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
        3.9    7.8   5.3         19    5.6   0.2    2.4  2  zf-Di19          Drought induced 19 protein (Di19), zinc-bind


Domain annotation for each model (and alignments):
>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.2  11.3   2.6e-27   2.5e-24       1     136 [.       5     119 ..       5     120 .. 0.98

  Alignments for each domain:
  == domain 1  score: 86.2 bits;  conditional E-value: 2.6e-27
                                       HHHHHHHHHHHHHHHHHHHHHHCHH.TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS------- CS
                      Rubrerythrin   1 eiLekAiagEssarrlYkelaekak.egypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakp 76 
                                       ++L+ A++gEs+a r Y ++a+ka+ +gy qia+lF++ A++E  Ha+++ ++l++++ ++e               
  gi|298675267|ref|YP_003727017.1|   5 DNLKDAFSGESMANRKYLAFAKKAEkDGYNQIAKLFRAAAAAETVHAHNHLDILDEVKSTNE--------------- 66 
                                       79******************************************************999999............... PP

                                       TTGGHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  77 kflttaknLeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlrkl 136
                                              nL+eai+g++ e e+my+ y e+a++e++ +a+++f+ + + Ek H+++++k+
  gi|298675267|ref|YP_003727017.1|  67 -------NLQEAINGETFEFEQMYPGYIEEAKEEEQTKAEWSFDVANKVEKIHADLYQKA 119
                                       .......**************************************************997 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.6   3.5e-06    0.0033      11      39 ..     130     157 ..     124     162 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.5e-06
                               DZR  11 darfCseCgtklkavaaedrCpsCgekvd 39 
                                       d  +C+ Cg++++  +a+d+Cp Cg++ +
  gi|298675267|ref|YP_003727017.1| 130 DYYVCQVCGNTVE-NEAPDVCPICGAPKS 157
                                       6679********7.789********9855 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.8     8e-06    0.0076      19      37 ..     134     155 ..     131     156 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8e-06
                                       -TTT--EESSS...S-CCCCST CS
                              RecR  19 CsrCgnlteed...lCaICsdp 37 
                                       C++Cgn  e++   +C+IC  p
  gi|298675267|ref|YP_003727017.1| 134 CQVCGNTVENEapdVCPICGAP 155
                                       *******99987779****877 PP

>> PI3K_rbd  PI3-kinase family, ras-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   8.4e-06     0.008      25      72 ..      92     139 ..      61     141 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.4e-06
                                       SS-SEEEEEEEETTS-HHHHHHHHHHCHH----------GEEEEETTC CS
                          PI3K_rbd  25 enkqqkvtlkvnpnstpesllaealrkklsvldqedvtddyvLkvcGr 72 
                                       e++q+k   ++++ + +e++ a + +k l+++ ++++ d yv +vcG 
  gi|298675267|ref|YP_003727017.1|  92 EEEQTKAEWSFDVANKVEKIHADLYQKALDNMGNNEEVDYYVCQVCGN 139
                                       478889999999999********************************6 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   2.6   1.4e-05     0.014       2      22 ..     134     155 ..     133     156 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.4e-05
                     zinc_ribbon_2   2 CpnCGaelqdnakF.CpyCGtp 22 
                                       C  CG++++++a+  Cp CG+p
  gi|298675267|ref|YP_003727017.1| 134 CQVCGNTVENEAPDvCPICGAP 155
                                       9*******************98 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.7   3.1e-05      0.03       6      35 ..     132     155 ..     131     159 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.1e-05
                       Zn-ribbon_8   6 YrCeeCghefevlqsisdapltaCPeCgse 35 
                                       Y C+ Cg++ e  +      + +CP Cg++
  gi|298675267|ref|YP_003727017.1| 132 YVCQVCGNTVENEA------PDVCPICGAP 155
                                       99*********443......456*****94 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.6   2.9e-05     0.027      53      86 .]     119     153 ..      88     153 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.9e-05
                    zinc_ribbon_15  53 lgkeiekkessekkeCknCgkeveee.fkyCpkCg 86 
                                         +++ ++e++++++C+ Cg++ve+e  + Cp Cg
  gi|298675267|ref|YP_003727017.1| 119 ALDNMGNNEEVDYYVCQVCGNTVENEaPDVCPICG 153
                                       345666777888************99569*****9 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.4   6.9e-05     0.066      70      98 ..     131     158 ..      92     162 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.9e-05
                                       EEEETTTS-EEECHHHHHS-TTTSSS-EE CS
                              HypA  70 kvrCreCgkefeleekalrCpkCgsadve 98 
                                        + C++Cg+++e e+ +  Cp Cg+ + +
  gi|298675267|ref|YP_003727017.1| 131 YYVCQVCGNTVENEAPD-VCPICGAPKSK 158
                                       468*********88643.6*****98766 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.4   5.2e-05     0.049      24      49 ..     132     158 ..     130     159 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.2e-05
                                       EE-HHHHHHHHH.TT-B-TTT--B--E CS
                        zf-C3HC4_3  24 vlCeeCaekllk.rkkkCpiCrrpiek 49 
                                       ++C+ C +++++   + CpiC +p +k
  gi|298675267|ref|YP_003727017.1| 132 YVCQVCGNTVENeAPDVCPICGAPKSK 158
                                       58********99999******998765 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.8   7.7e-05     0.073       6      30 ..     133     156 ..     128     159 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.7e-05
                       Prok-RING_1   6 kCpvCgkelkee.dDiVvCpeCgtpy 30 
                                        C+vCg+++++e  D  vCp Cg+p 
  gi|298675267|ref|YP_003727017.1| 133 VCQVCGNTVENEaPD--VCPICGAPK 156
                                       6********998445..7******96 PP

>> DUF2492  Protein of unknown function (DUF2492)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   0.00058      0.55       2      30 ..      48      74 ..      47      83 .. 0.86
   2 ?    0.5   0.0      0.81   7.6e+02      21      45 ..     112     138 ..     104     143 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00058
                           DUF2492  2 siHgHevLelllasgesytkasLkeaiee 30
                                       +H+H+ L++l   + + t+++L+eai+ 
  gi|298675267|ref|YP_003727017.1| 48 TVHAHNHLDIL--DEVKSTNENLQEAING 74
                                      69*********..99999********984 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.81
                           DUF2492  21 kasLkeaieekFGe..earFhtCsaed 45 
                                       +a+L ++  ++ G+  e+ ++ C+  +
  gi|298675267|ref|YP_003727017.1| 112 HADLYQKALDNMGNneEVDYYVCQVCG 138
                                       567777777777751156799998755 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.5    0.0003      0.28      18      30 ..     128     140 ..     124     142 .. 0.83
   2 ?    0.8   0.1      0.44   4.2e+02      23      29 ..     148     154 ..     145     156 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0003
                     A2L_zn_ribbon  18 eqgylvCieCgas 30 
                                       e +y+vC+ Cg++
  gi|298675267|ref|YP_003727017.1| 128 EVDYYVCQVCGNT 140
                                       569*******986 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.44
                     A2L_zn_ribbon  23 vCieCga 29 
                                       vC+ Cga
  gi|298675267|ref|YP_003727017.1| 148 VCPICGA 154
                                       8999997 PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.1   0.00022       0.2      24      43 ..     133     153 ..     131     154 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00022
                         zf-RING_5  24 fCekClkkll.ekeavCpiCr 43 
                                       +C+ C ++   e+++vCpiC+
  gi|298675267|ref|YP_003727017.1| 133 VCQVCGNTVEnEAPDVCPICG 153
                                       8********99*********7 PP

>> SLATT_5  SMODS and SLOG-associating 2TM effector domain family 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.5   0.00026      0.24     114     149 ..     101     136 ..      27     147 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00026
                           SLATT_5 114 seedlkekykeiskeYeeiLdkyeNHdeiDyklfra 149
                                       s + +++  k   + Y+++Ld++ N +e+Dy++ ++
  gi|298675267|ref|YP_003727017.1| 101 SFDVANKVEKIHADLYQKALDNMGNNEEVDYYVCQV 136
                                       556666666655678*****************9876 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.7    0.0015       1.4      19      33 ..     131     145 ..     122     147 .. 0.75
   2 ?    4.3   0.3     0.029        28       2       9 ..     148     155 ..     148     160 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0015
                                       CEEESSSSBEEEECC CS
                      TF_Zn_Ribbon  19 elvCtdCGlVledns 33 
                                        +vC  CG+ +e++ 
  gi|298675267|ref|YP_003727017.1| 131 YYVCQVCGNTVENEA 145
                                       35*******999875 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.029
                                       EETTTTCE CS
                      TF_Zn_Ribbon   2 kCPnCgst 9  
                                       +CP+Cg +
  gi|298675267|ref|YP_003727017.1| 148 VCPICGAP 155
                                       7****975 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   1.0     0.041        39       6      12 ..     133     139 ..     131     142 .. 0.63
   2 ?    6.5   0.1     0.007       6.6       5      13 ..     147     156 ..     144     163 .] 0.75

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.041
                           zf-RRN7   6 pCgvCgc 12 
                                       +C vCg+
  gi|298675267|ref|YP_003727017.1| 133 VCQVCGN 139
                                       5677766 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.007
                           zf-RRN7   5 ppCgvCgc.r 13 
                                        +C++Cg+ +
  gi|298675267|ref|YP_003727017.1| 147 DVCPICGApK 156
                                       69*****974 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.5      0.16   1.5e+02       2       9 ..     132     139 ..     131     147 .. 0.80
   2 ?   10.1   0.6   0.00068      0.64      36      47 .]     148     159 ..     140     159 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.16
                                       EEETTT-B CS
                        Rubredoxin   2 yeCkvCgy 9  
                                       y C+vCg 
  gi|298675267|ref|YP_003727017.1| 132 YVCQVCGN 139
                                       89****95 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00068
                                       BBTTTB-BGGGE CS
                        Rubredoxin  36 vCPdCgvekeqF 47 
                                       vCP Cg++k++F
  gi|298675267|ref|YP_003727017.1| 148 VCPICGAPKSKF 159
                                       7*********99 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   2.6   0.00019      0.18       2      17 ..     127     142 ..     126     143 .. 0.89
   2 ?   -1.1   0.3       1.6   1.5e+03       9      13 ..     149     153 ..     148     155 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                                       -TT-EEE-TTT--EEE CS
                   Desulfoferrod_N   2 eklevYkCevCGniVe 17 
                                       e+ + Y C+vCGn Ve
  gi|298675267|ref|YP_003727017.1| 127 EEVDYYVCQVCGNTVE 142
                                       67899*********98 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.6
                                       -TTT- CS
                   Desulfoferrod_N   9 CevCG 13 
                                       C +CG
  gi|298675267|ref|YP_003727017.1| 149 CPICG 153
                                       99999 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.2      0.02        19      28      44 ..     128     144 ..     125     147 .. 0.82
   2 ?    4.6   0.8     0.043        40      31      39 ..     146     154 ..     142     162 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.02
                           zf-Di19  28 eskevvCPvCaekvtkd 44 
                                       e  ++vC vC ++v+++
  gi|298675267|ref|YP_003727017.1| 128 EVDYYVCQVCGNTVENE 144
                                       56789*******99876 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.043
                           zf-Di19  31 evvCPvCae 39 
                                       + vCP+C +
  gi|298675267|ref|YP_003727017.1| 146 PDVCPICGA 154
                                       569****64 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1605  (0.0895198); expected 358.6 (0.02)
Passed bias filter:                      880  (0.0490825); expected 358.6 (0.02)
Passed Vit filter:                       113  (0.00630264); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1007.35
//
Query:       gi|298675268|ref|YP_003727018.1|  [L=143]
Description: hypothetical protein Metev_1364 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 897.02
//
Query:       gi|298675269|ref|YP_003727019.1|  [L=211]
Description: multiple antibiotic resistance (MarC)-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-58  197.5  19.2    1.7e-58  197.3  19.2    1.0  1  MarC      MarC family integral membrane protein
  ------ inclusion threshold ------
       0.18   11.8   3.6       0.51   10.3   3.6    1.7  1  SH        Viral small hydrophobic protein
        1.7    7.9  10.9       0.46    9.8   1.8    2.5  2  DUF4191   Domain of unknown function (DUF4191)


Domain annotation for each model (and alignments):
>> MarC  MarC family integral membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.3  19.2   2.9e-62   1.7e-58       4     203 .]       7     206 ..       4     206 .. 0.99

  Alignments for each domain:
  == domain 1  score: 197.3 bits;  conditional E-value: 2.9e-62
                              MarC   4 iikafvsLlaiinplgnvpvflslleevskeerkrialkasilallillvfllfGelilklfgisidalkiaGgill 80 
                                       ++ afvs+++i++pl++v  f+sl+++++++ ++ +a++a++la +i l+f+l+G+ +l++fgi +d+l+iaGgill
  gi|298675269|ref|YP_003727019.1|   7 FVFAFVSIFVIVDPLAAVVTFISLTNKMDDKTKNMVAKRAVLLACVIALAFALTGNFVLNIFGIGVDSLRIAGGILL 83 
                                       7889************************************************************************* PP

                              MarC  81 fliaidmlkakqkkekkkkseeeeseekdeiavvPLAlPliaGPgaittvlvlaseassivekvavvlaillaalit 157
                                       f++a+dm++ak ++e+  k+e +e ++++++ ++P+AlPl++GPgaittv+vl+ +  +i +k++v+lai++  +it
  gi|298675269|ref|YP_003727019.1|  84 FTVALDMMHAKISRESITKNEISEYIDREDVWIFPIALPLLTGPGAITTVIVLMGNSDTILNKLVVILAIIATFIIT 160
                                       ***************************************************************************** PP

                              MarC 158 llilllsslilrllgktginaleRlmGllLvalavqlivdGikeil 203
                                       l +++ s  +++ +g tg+ +++R+mGllL+a+++++i +Gi +++
  gi|298675269|ref|YP_003727019.1| 161 LYVFIFSRRLYKIMGYTGMLVFTRIMGLLLAAISIEFITTGILNMF 206
                                       ******************************************9986 PP

>> SH  Viral small hydrophobic protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   3.6   8.5e-05      0.51      13      35 ..     150     172 ..     146     177 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 8.5e-05
                                SH  13 lllillsliitlyvwiistityk 35 
                                       +l i+ ++iitlyv+i s   yk
  gi|298675269|ref|YP_003727019.1| 150 ILAIIATFIITLYVFIFSRRLYK 172
                                       6789999***********99998 PP

>> DUF4191  Domain of unknown function (DUF4191)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.8    0.0042        25      12      60 ..      25      72 ..      18     104 .. 0.64
   2 ?    9.8   1.8   7.7e-05      0.46      16      75 ..     107     172 ..      96     180 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0042
                           DUF4191 12 aqvfkltrkedkkllwlllaaflvvvvvfvvlglllgslilllilgill 60
                                      ++  +lt+k d k+  +++  +++ + v+ ++  l ++ ++l i+gi +
  gi|298675269|ref|YP_003727019.1| 25 VTFISLTNKMDDKTKNMVAKRAVLLACVIALAFAL-TGNFVLNIFGIGV 72
                                      55667899999998877776666666555555555.4566666677653 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 7.7e-05
                           DUF4191  16 kltrkedkkllwlllaaflvvvvvfvvlglllg....slilllilgillgll..valivltrraek 75 
                                       ++  +ed ++ +++l ++ ++ ++++v++l+ +       l++il+i++ ++  + +++++rr+ k
  gi|298675269|ref|YP_003727019.1| 107 EYIDREDVWIFPIALPLLTGPGAITTVIVLMGNsdtiLNKLVVILAIIATFIitLYVFIFSRRLYK 172
                                       677899**********************99964322123356778887665511556778898765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1432  (0.0798706); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 1319.28
//
Query:       gi|298675270|ref|YP_003727020.1|  [L=417]
Description: 3-hydroxy-3-methylglutaryl-CoA reductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   5.2e-136  453.5   3.0   5.9e-136  453.3   3.0    1.0  1  HMG-CoA_red  Hydroxymethylglutaryl-coenzyme A reductase


Domain annotation for each model (and alignments):
>> HMG-CoA_red  Hydroxymethylglutaryl-coenzyme A reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  453.3   3.0  3.3e-140  5.9e-136       1     367 []      37     414 ..      37     414 .. 0.99

  Alignments for each domain:
  == domain 1  score: 453.3 bits;  conditional E-value: 3.3e-140
                                       -HHHHHHHHHHS-HHHHHHHTT----.HHHHHHHSSS---------EEEEEEEETTE....EEEEEE---STTHHHH CS
                       HMG-CoA_red   1 aveeRrklleelteeeleelkeesld.eevadkmiEnviGyvqlPlGvagpllingk....eylvPmAteEgslvAs 72 
                                       av+ Rr+++ee+++ ++++++++++d eeva+k+iEn+iG+vq+PlGvagpl++ng+    +y++P+At+Eg+lvAs
  gi|298675270|ref|YP_003727020.1|  37 AVKLRRQAVEEMSDISFKNIQNHNIDaEEVARKNIENMIGAVQIPLGVAGPLKVNGEyadgDYHIPLATTEGALVAS 113
                                       5789************************************************************************* PP

                                       HHHHHHHHHHTT-B.EEEE----EEEEEEEE.--S-HHHHHHHHHTHHHHHHHHHHCSHHCCT-EEEEEEEEE-SSE CS
                       HMG-CoA_red  73 asrgakainesgGvkttvlkdgmtraqvvllesvedaaelkkwiekkeeleelanaaestsrggglkdievvlagrl 149
                                       ++rg+++i++s+G+++++++d mtra+++ +e+v++a+e+ +wi+k + +++++++++  +++g+l d+++++ g++
  gi|298675270|ref|YP_003727020.1| 114 INRGCSVITRSDGANVRIFQDVMTRAPAFKVENVARAQEFVEWIKKPDTIKHMQDKISDITSHGELVDVDPYVLGNT 190
                                       ***************************************************************************** PP

                                       EEEEEEEE-TTC--HHHHHHHHHHHHHHHHHHHTSEEEEEEE-S--GGGEEEEEEEEEHHHH..-SSTTHHHHHHHH CS
                       HMG-CoA_red 150 vvlrlkvdtgDAmGaNmvnkateaaaelieeefgeeellsilsNlctdkkasainaiegrgksvvaeatigeevvek 226
                                       v+lr+++dt+DAmG+Nmv++at+ +++lie+efg ++ +s+++N+ctdkk++ain i+grgk+vvae+ i+++v+e+
  gi|298675270|ref|YP_003727020.1| 191 VYLRFSYDTKDAMGMNMVTIATNTLVDLIEDEFG-ADPISLSGNMCTDKKPAAINSIQGRGKTVVAETEIPKKVIED 266
                                       **********************************.999*************************************** PP

                                       HHHHHHHHHH-HHHH....HHHHHHH.......HHHHHHHHHHTT--HHHHHHHHHHHTTSEEETTTEEEEEEEEE. CS
                       HMG-CoA_red 227 ilkasaealvdlnra.n.igtankGiggfnahaaNgiaAvflAtGqDlaaveesshaiaaleevedgdlygsvtlPs 301
                                        lk ++e+++++n + n +g+a++G++g+nahaaN+iaA+ +A+GqD+a+v+e+s++i+++e ++ gdly+svtlPs
  gi|298675270|ref|YP_003727020.1| 267 RLKSTPEEMAEVNYRkNlLGSARAGSLGYNAHAANVIAAMNIACGQDTAHVVEGSNTITTMEVTKYGDLYCSVTLPS 343
                                       ***************************************************************************** PP

                                       ----SBSHHHHH-HHHHHHHHTT---HH........HHHHHHHHHHHHHHHHHHHHHT-----HHHHHHHH CS
                       HMG-CoA_red 302 leVGtvGGgtklppqaellkllgvkgak.....nakeLaeiiaavgLAqelsalrALaaeglqkgHmklhr 367
                                       l VGtvGGgt++ +q+ +l+llgv+g++     nak+Laeiia+ +LA+e+s++ A aa++l+++H +l+r
  gi|298675270|ref|YP_003727020.1| 344 LLVGTVGGGTGIGTQKDCLDLLGVAGSGhppgsNAKKLAEIIASSVLAGEISLIGAQAAGHLARAHAELGR 414
                                       ********************************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       827  (0.0461264); expected 358.6 (0.02)
Passed bias filter:                      617  (0.0344135); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 2625.87
//
Query:       gi|298675271|ref|YP_003727021.1|  [L=356]
Description: magnesium and cobalt transport protein CorA [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-78  263.6   7.0    2.7e-78  263.2   7.0    1.0  1  CorA      CorA-like Mg2+ transporter protein
  ------ inclusion threshold ------
      0.068   13.0   0.1        1.3    8.8   0.0    2.7  3  RhoGAP    RhoGAP domain


Domain annotation for each model (and alignments):
>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  263.2   7.0     3e-82   2.7e-78       3     292 .]      61     352 ..      59     352 .. 0.97

  Alignments for each domain:
  == domain 1  score: 263.2 bits;  conditional E-value: 3e-82
                              CorA   3 gfvWldlssptee.eleeLaeelgldelaledlldseerprvedyddylllvlpsveldkseeeeeevplsillgdn 78 
                                       +++W++++  ++   +e++ e+++l++l+led+l+ ++rp++ed+++y++ vl+ ++++k+e+e+   ++si++g n
  gi|298675271|ref|YP_003727021.1|  61 SVTWINIDGLHKVdIIEKIGEHFDLHPLVLEDILNISQRPKTEDFENYIYTVLKMFTYNKQENETNIEQVSIVIGSN 137
                                       689********98578************************************************9999********* PP

                              CorA  79 flitvrreplealdevikrlk..deggkpkspgellyrlldeivdrlfellekleeeldeledel..edstkkeilr 151
                                       f+i++++++ +++d v++r++  + + ++ ++  l y l+d++vd++f +le++ e+++ +edel  + + + e l+
  gi|298675271|ref|YP_003727021.1| 138 FVISFQEKEGDIFDPVRDRIRfnKGHIRKMKSDYLAYSLIDTVVDNYFIVLEEIGEQIESVEDELskNPDPEPETLQ 214
                                       *********************9988999999999*******************************9999999***** PP

                              CorA 152 elaqlrrrlvklrralapnrevlkrllakaddkllddedkeylrdlldelerllemlealrerleslqdtyssllse 228
                                       ++  l+r++  lr++++p+rev+ + l++++  l+ ++ ++ l+d++d++ + +e+l+++re+l+s+ d+y s +++
  gi|298675271|ref|YP_003727021.1| 215 TIHGLKRDVLFLRKSIWPLREVI-NTLNRNESRLIYKTTQLFLKDVYDHVIQTIETLDTYREMLTSMLDLYLSSINN 290
                                       ***********************.66666************************************************ PP

                              CorA 229 rlNrvmkvLTvltaiflPlTlitGiyGmNfkglPelewsygypfvlllglmallailllfwfkr 292
                                       r+N+vmkvLT+++++f+PlT+i+GiyGmNf+++Pel w++ yp+   +++m+ ++++++++fk+
  gi|298675271|ref|YP_003727021.1| 291 RMNEVMKVLTIIATVFIPLTFIAGIYGMNFEYMPELYWKWSYPIL--WMIMVSASLFMFAYFKK 352
                                       ****************************************99999..9999999*******997 PP

>> RhoGAP  RhoGAP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00015       1.3     112     149 ..     107     144 ..      99     148 .. 0.90
   2 ?   -0.4   0.0       0.1   9.3e+02      62     114 ..     162     216 ..     157     223 .. 0.75
   3 ?   -0.2   0.1     0.088   7.9e+02      70     101 ..     253     282 ..     233     310 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00015
                                       HHHHHHHHHHHHTHHHH---HHHHHHHHHHHHHT-TSS CS
                            RhoGAP 112 ryLlehLkrvaenskenkMtaknLaivfaPtLlrpkse 149
                                       +y+  +Lk ++ n++en+ +++ ++iv++ +++ + +e
  gi|298675271|ref|YP_003727021.1| 107 NYIYTVLKMFTYNKQENETNIEQVSIVIGSNFVISFQE 144
                                       589999**************************999876 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.1
                                       HHHHHSSSTTTTGGHHHHHHH..HHTSSSHHHHHHHHHHHHTTS-HHHHHHHHHH CS
                            RhoGAP  62 rfLrelpepLltkelyeelie..aaksedeeerlealkellekLPkenrdtLryL 114
                                         +r+++   l ++l++++++      e+  e++e++++ l+k P+++ +tL+++
  gi|298675271|ref|YP_003727021.1| 162 GHIRKMKSDYLAYSLIDTVVDnyFIVLEEIGEQIESVEDELSKNPDPEPETLQTI 216
                                       5677777788888888888853433346667889999999999999999999876 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.088
                                       TTTTGGHHHHHHHHHTSSSHHHHHHHHHHHHT CS
                            RhoGAP  70 pLltkelyeelieaaksedeeerlealkelle 101
                                       +L+ k+ y+++i++ ++ d  +  e+l ++l+
  gi|298675271|ref|YP_003727021.1| 253 QLFLKDVYDHVIQTIETLD--TYREMLTSMLD 282
                                       5677777777774433322..22222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       996  (0.0555525); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2186.01
//
Query:       gi|298675272|ref|YP_003727022.1|  [L=188]
Description: UspA domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-34  119.6   0.0      2e-34  119.1   0.0    1.2  1  Usp              Universal stress protein family
      0.002   18.9   0.1     0.0037   18.0   0.1    1.5  1  DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomer
  ------ inclusion threshold ------
      0.015   15.4   1.1       0.33   11.1   0.1    2.5  3  DUF3782          Protein of unknown function (DUF3782)


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.1   0.0   3.3e-38     2e-34       2     141 .]       6     146 ..       5     146 .. 0.99

  Alignments for each domain:
  == domain 1  score: 119.1 bits;  conditional E-value: 3.3e-38
                                       -SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH.HHHHHHC CS
                               Usp   2 ykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada.akaaaea 77 
                                       y++Il+a+Dgs +s+ A++ +le a+ +ga++++l+v  p  ++ +++ +  ++e   el+++ +ea++  k++ e+
  gi|298675272|ref|YP_003727022.1|   6 YDKILIATDGSINSEGAIDSGLEIARLSGAKVYALYVMAPTGFTLRGTQEAWVKEVYNELSKEGKEATEyIKQLGED 82 
                                       99***************************************************************999999****** PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                        g +ve v +eg+p e+i+++a+e+++dli +G++g++gl+++l+GSv+e+v+r++++ VlvVr
  gi|298675272|ref|YP_003727022.1|  83 YGLEVEAVMLEGNPNEMIIDFADENEIDLIAMGTHGKTGLQKFLIGSVAEKVVRNSNKEVLVVR 146
                                       ***************************************************************8 PP

>> DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   6.1e-07    0.0037      74     129 .]      90     147 ..      36     147 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 6.1e-07
                                       EEEES..HHHHHHHHCHTT-SEEEE--SSGGGHHHHHHHHHTTSEEEE--SHHHHHHH CS
                   DXP_reductoisom  74 evlvG..eealkelaeeeeadvvvaaivGaaGLkptlaaikagkriaLANKEsLVvaG 129
                                        +l G  +e +++ a e+e+d++  +  G +GL+  l    a+k +  +NKE LVv G
  gi|298675272|ref|YP_003727022.1|  90 VMLEGnpNEMIIDFADENEIDLIAMGTHGKTGLQKFLIGSVAEKVVRNSNKEVLVVRG 147
                                       44445224778999*****************************************977 PP

>> DUF3782  Protein of unknown function (DUF3782)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   5.5e-05      0.33      10      49 ..      55      94 ..      49      99 .. 0.90
   2 ?    2.1   0.0     0.036   2.1e+02      39      54 ..     128     143 ..     127     148 .. 0.90
   3 ?   -2.2   0.1      0.82   4.9e+03      13      22 ..     158     167 ..     151     173 .. 0.49

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.5e-05
                           DUF3782 10 eeetkedleelekeieklertigaLGaRWGlvsEeafReg 49
                                      e+ +ke+ +el+ke ++ ++ i+ LG  +Gl  E+++ eg
  gi|298675272|ref|YP_003727022.1| 55 EAWVKEVYNELSKEGKEATEYIKQLGEDYGLEVEAVMLEG 94
                                      56689999***************************99887 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.036
                           DUF3782  39 GlvsEeafReglkeiL 54 
                                       G v+E+++R++ ke+L
  gi|298675272|ref|YP_003727022.1| 128 GSVAEKVVRNSNKEVL 143
                                       7899**********99 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.82
                           DUF3782  13 tkedleelek 22 
                                        ke+++e+ +
  gi|298675272|ref|YP_003727022.1| 158 KKEKIKEMVR 167
                                       3333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       899  (0.0501422); expected 358.6 (0.02)
Passed bias filter:                      588  (0.032796); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1130.81
//
Query:       gi|298675273|ref|YP_003727023.1|  [L=138]
Description: UspA domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.2e-33  114.5   0.0    5.8e-33  114.4   0.0    1.0  1  Usp             Universal stress protein family
     0.0024   18.1   0.6          4    7.7   0.0    3.3  3  GAD             GAD domain
  ------ inclusion threshold ------
      0.034   13.5   0.1      0.034   13.5   0.1    1.1  1  Exotox-A_bind   Exotoxin A binding
      0.061   12.9   0.1       0.33   10.5   0.1    1.8  2  SRP54           SRP54-type protein, GTPase domain
      0.062   12.6   0.6       0.46    9.7   0.6    1.9  1  Glyco_hydro_97  Glycoside hydrolase 97


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.4   0.0   1.6e-36   5.8e-33       2     140 ..       7     136 ..       6     137 .. 0.97

  Alignments for each domain:
  == domain 1  score: 114.4 bits;  conditional E-value: 1.6e-36
                                       -SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                               Usp   2 ykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeag 78 
                                       y  Il+a+Dgse+sk A+  ++++ak++ga++++++vi  r   +v ++ ++ +e++  + ++  +         + 
  gi|298675273|ref|YP_003727023.1|   7 YADILIATDGSEYSKMAVNSGIKFAKSFGAKVHAIYVINVRWEREVYNYLRKKGEQATNEVKQLGD---------KN 74 
                                       778***********************************************************9886.........57 PP

                                       TCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEE CS
                               Usp  79 gvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvV 140
                                        v+v+++++egdpae i+++ae++d+dliV+G++g+sg+sr+l+GSv+++v+r+++  Vl+ 
  gi|298675273|ref|YP_003727023.1|  75 NVEVKTQLLEGDPAEQIIDYAENNDIDLIVMGTHGESGISRFLMGSVAQKVVRKSSTEVLIS 136
                                       9***********************************************************95 PP

>> GAD  GAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0011         4      14      44 ..      11      40 ..       2      46 .. 0.81
   2 !    5.6   0.1    0.0052        19      21      47 ..      53      79 ..      39     117 .. 0.62
   3 ?    1.0   0.0      0.14     5e+02      53      74 ..     109     130 ..     104     133 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0011
                                      EEETTG-TTTSHHHHHHHHHHHHHTTHSHCE CS
                               GAD 14 lrvpggaaklsrkeideleefakelgakgla 44
                                      l++ +g +++s+++++ + +fak++gak  a
  gi|298675273|ref|YP_003727023.1| 11 LIATDG-SEYSKMAVNSGIKFAKSFGAKVHA 40
                                      566665.99******************9655 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0052
                                      TTTSHHHHHHHHHHHHHTTHSHCEEEE CS
                               GAD 21 aklsrkeideleefakelgakglawik 47
                                       ++ rk+ ++ ++++k+lg+k  + +k
  gi|298675273|ref|YP_003727023.1| 53 YNYLRKKGEQATNEVKQLGDKNNVEVK 79
                                      466777777777777777777655444 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.14
                                       EETTTCCCS-HHHHHHHHHHCT CS
                               GAD  53 ltgpiakflteeevkklleavg 74 
                                        +++i++fl + + +k++++ +
  gi|298675273|ref|YP_003727023.1| 109 GESGISRFLMGSVAQKVVRKSS 130
                                       5799*******99999988765 PP

>> Exotox-A_bind  Exotoxin A binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   9.6e-06     0.034      94     150 ..      46     102 ..       6     135 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.6e-06
                                       ETTCEEEEEEE-SSSEEEEEEEEEECTTS-SEEEEEEEEE-TTSEEECE-EEEEEE- CS
                     Exotox-A_bind  94 eenktkrysytrkeGefalnwlvpiGeekpasikvsvdeldaqrnlievsklysiel 150
                                          +   y y rk+Ge a n +  +G+++  ++k  + e d  +++i+ ++   i+l
  gi|298675273|ref|YP_003727023.1|  46 VRWEREVYNYLRKKGEQATNEVKQLGDKNNVEVKTQLLEGDPAEQIIDYAENNDIDL 102
                                       4445678****************************************9988777776 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0       0.1   3.6e+02      81     131 ..       4      54 ..       1      63 [. 0.79
   2 ?   10.5   0.1   9.3e-05      0.33      44     107 ..      63     123 ..      60     136 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.1
                                       HTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHH CS
                             SRP54  81 eekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavk 131
                                       ++++  +l+ T G   ++ ++ + +k  k++ ++ + ++v++   ++e+++
  gi|298675273|ref|YP_003727023.1|   4 NKHYADILIATDGSEYSKMAVNSGIKFAKSFGAKVHAIYVINVRWEREVYN 54 
                                       455666888899999999999999999999999999999998887777666 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 9.3e-05
                                       HHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHHHHHTTSSEEEEEE--SSTTHHHHHHHHHH CS
                             SRP54  44 AveQLktlaeklgvpvikkkeeadpaavakeavekakeekidvvlvDTaGrlqndkelmeelkk 107
                                       A++ +k+l++k +v+v ++  e dpa   ++ ++ a++++id++++ T G + + + lm  +++
  gi|298675273|ref|YP_003727023.1|  63 ATNEVKQLGDKNNVEVKTQLLEGDPA---EQIIDYAENNDIDLIVMGTHGESGISRFLMGSVAQ 123
                                       78889********9988888777776...56788999999**********99999988877654 PP

>> Glyco_hydro_97  Glycoside hydrolase 97
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.6   0.00013      0.46      37     126 ..      24     109 ..      12     131 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00013
                    Glyco_hydro_97  37 vkryiDfAaengleyvlvegwdegWeekkkkekefdftkpypdfdleelvaYakekgvgvelwlhs.etsgnvanle 112
                                       v   i fA+ +g + + ++  +  We+     + ++++++  ++  +e+ + + +++v+v+  l +   + ++ ++ 
  gi|298675273|ref|YP_003727023.1|  24 VNSGIKFAKSFGAKVHAIYVINVRWER-----EVYNYLRKKGEQATNEVKQLGDKNNVEVKTQLLEgDPAEQIIDYA 95 
                                       556699999999999999999999995.....456667777777777777777777766654332202333444444 PP

                    Glyco_hydro_97 113 kqldkafklyeklG 126
                                       ++ d  +  + ++G
  gi|298675273|ref|YP_003727023.1|  96 ENNDIDLIVMGTHG 109
                                       44444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 864.04
//
Query:       gi|298675274|ref|YP_003727024.1|  [L=71]
Description: hypothetical protein Metev_1370 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1435  (0.0800379); expected 358.6 (0.02)
Passed bias filter:                      629  (0.0350828); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 495.93
//
Query:       gi|298675275|ref|YP_003727025.1|  [L=413]
Description: 3-isopropylmalate dehydratase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   1.1e-103  347.8   6.1   1.9e-101  340.4   6.1    2.5  1  Aconitase  Aconitase family (aconitate hydratase)
  ------ inclusion threshold ------
      0.015   14.0   0.0      0.023   13.4   0.0    1.2  1  DUF521     Protein of unknown function (DUF521)


Domain annotation for each model (and alignments):
>> Aconitase  Aconitase family (aconitate hydratase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  340.4   6.1  2.1e-105  1.9e-101       2     461 .]       7     405 ..       6     405 .. 0.89

  Alignments for each domain:
  == domain 1  score: 340.4 bits;  conditional E-value: 2.1e-105
                         Aconitase   2 kiwdahlvee.egiayv...pdrvllqdvtgvqalvdlaaareav.rrlggtlatidhlvpvdlvidhsvgaeeale 73 
                                       ki+++   e+ +  ++v   +d  + +d t+  a++ ++ ++ ++ +++++ +   dhl+p+++ i  s       +
  gi|298675275|ref|YP_003727025.1|   7 KIFSRASGEQvKADEFViadVDYAMAHDGTSILAVKSFRDMGVEKvWNPERIVIPFDHLAPANTEITASL------Q 77 
                                       66554433332223444456899***************99986554*****************4444333......2 PP

                         Aconitase  74 knledefernkeryefLksaakafgirvvppgqGIvHqvnlEyglalpgktvvgtDSHTtmigglGvlaiGvGgiea 150
                                       +++++             +   +   +++++g G++Hqv +E+g+a+pgk++vg DSHT+++g++G +a+GvG +++
  gi|298675275|ref|YP_003727025.1|  78 NDIRN-------------WINDQQIEHFYEIGYGVCHQVLPENGFAMPGKLLVGADSHTCTYGAFGSFATGVGATDM 141
                                       33332.............33333333689************************************************ PP

                         Aconitase 151 eavllgqplelkipkvvgvkltGklkegvtakDlvlavigklrkkgvvgkvvEffGegvesLsledraTiaNMaaEv 227
                                       +++++  +l++k+p++++++++G+lk++v akDl l++igk++ +g++ k+vEf+G+ +e+Ls+ +r+T++NMa+E+
  gi|298675275|ref|YP_003727025.1| 142 AEIFASGKLWFKVPESIKITVDGTLKNHVYAKDLTLYIIGKMGSAGATYKAVEFYGDVIENLSMSGRMTLCNMAIEM 218
                                       ***************************************************************************** PP

                         Aconitase 228 GAttglfpvdektleYLkatgreeaavlveaydkaqalfelaadedaeydkvleldlstlepsvagpkrPqdavpls 304
                                       GA+tg++p+d+kt+eYLk  +r   a  ve+y+       +++deda y++++++++++lep+va p++++++ ++ 
  gi|298675275|ref|YP_003727025.1| 219 GAKTGIVPPDDKTFEYLK--NR---A--VEDYEP------VYSDEDAIYSEEYHINADELEPQVAKPHSVDNVANV- 281
                                       ******************..77...2..566766......668*****************************9999. PP

                         Aconitase 305 elvkkefkeelekeaaekaleyklkegtklkdgkvdiaaigSCTNssnedvraaagllakavekglkvkpgvktsva 381
                                       ++v                           + +kvd+++ig CTN+++ed++ aa++l+     g+kv+   +t+++
  gi|298675275|ref|YP_003727025.1| 282 TDV---------------------------SGTKVDQVFIGTCTNGRLEDLEVAAEILK-----GKKVSV--RTIIV 324
                                       333...........................34579************************.....999977..***** PP

                         Aconitase 382 PGSevvkayleaeGlleiLekaGfevvgagCstCig.nsdrleegeaivsssNRNFegRqgpntrayLaSPelvvaa 457
                                       P+S+    ++ ++G+ eiL +aG+++ ++gC++C+g   + + ege++vs+ NRNF+gR+g+++  yLaSP+ ++a+
  gi|298675275|ref|YP_003727025.1| 325 PASRSTMIEAVNNGTAEILLDAGATFGTPGCGPCLGgHMGVIGEGEVCVSTANRNFKGRMGKGGYIYLASPATAAAS 401
                                       ************************************999************************************** PP

                         Aconitase 458 AlaG 461
                                       A++G
  gi|298675275|ref|YP_003727025.1| 402 AITG 405
                                       **98 PP

>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.6e-06     0.023     281     357 ..     280     355 ..     249     365 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.6e-06
                            DUF521 281 eelskakeekvdlvalG.cPhlsleElrelaellkgkkkkvkvelwvttsrevkeeaerlglveklekaGvkvlsdt 356
                                       + +++ + +kvd v++G c    le+l+  ae+lkgkk+ + ++++v +sr+++ ea + g++e+l +aG+++ +  
  gi|298675275|ref|YP_003727025.1| 280 N-VTDVSGTKVDQVFIGtCTNGRLEDLEVAAEILKGKKV-SVRTIIVPASRSTMIEAVNNGTAEILLDAGATFGTPG 354
                                       3.44667889******97888899**********55555.445567789**********************998777 PP

                            DUF521 357 C 357
                                       C
  gi|298675275|ref|YP_003727025.1| 355 C 355
                                       7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 2472.88
//
Query:       gi|298675276|ref|YP_003727026.1|  [L=124]
Description: hypothetical protein Metev_1372 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0018   18.1   0.1     0.0037   17.1   0.0    1.5  2  TrmB      Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.088   12.7   0.0       0.13   12.2   0.0    1.3  1  MarR_2    MarR family


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.72   6.4e+03      40      46 ..      14      20 ..       9      29 .. 0.54
   2 !   17.1   0.0   4.1e-07    0.0037      22      65 ..      41      92 ..      31      95 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.72
                                      HHHHHHH CS
                              TrmB 40 YevLrsL 46
                                      Ye+++ L
  gi|298675276|ref|YP_003727026.1| 14 YEMVEIL 20
                                      3333333 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 4.1e-07
                                      CCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST........TTEEEE- CS
                              TrmB 22 patadeiaeelgvprskvYevLrsLedkGlVerekgr........pklYrav 65
                                      ++t + i +++g+ ++ v  ++r L+d  +Ve+++++         klYr v
  gi|298675276|ref|YP_003727026.1| 41 ELTSRSIEKATGLRQPEVSIAMRYLLDNEWVEIREEKknegkgrpIKLYRLV 92
                                      68999******************************99888888855588776 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.4e-05      0.13       4      55 ..      26      75 ..      23      84 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.4e-05
                                      -HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2  4 tpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                      t+  a  La L ++   +lt + +++++gl ++ vs + + L +  +ve r+
  gi|298675276|ref|YP_003727026.1| 26 TRPVALTLACLSDGY--ELTSRSIEKATGLRQPEVSIAMRYLLDNEWVEIRE 75
                                      555555555555554..5******************************8873 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 792.70
//
Query:       gi|298675277|ref|YP_003727027.1|  [L=107]
Description: heat shock protein DnaJ domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-13   48.9   1.5    1.4e-12   47.5   1.3    1.8  1  DnaJ             DnaJ domain
     0.0074   16.2   0.7      0.011   15.6   0.6    1.3  1  P-mevalo_kinase  Phosphomevalonate kinase
  ------ inclusion threshold ------
      0.051   13.6   0.5      0.078   13.1   0.2    1.6  2  Sin3_corepress   Sin3 family co-repressor


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   1.3   2.3e-16   1.4e-12       4      54 ..      16      67 ..      12      76 .. 0.91

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 2.3e-16
                                      HHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHH.HHHHHHHHHHHHHHHHT CS
                              DnaJ  4 eiLgvskdasedeIkkaYrklalkyHPDknpkdp.eaeekFkeineAyevLs 54
                                      ++L+++++a+ +eIk++Yr+l++k+HPDk++++p   + k +ei +Ay +  
  gi|298675277|ref|YP_003727027.1| 16 KVLNLNEKATMKEIKESYRRLIKKWHPDKCQQNPdICKAKTEEIINAYRIII 67
                                      79********************************7678899*******9975 PP

>> P-mevalo_kinase  Phosphomevalonate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.6   1.9e-06     0.011      37      88 ..      11      60 ..       9      75 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.9e-06
                   P-mevalo_kinase 37 eyakekgldleellsdseykekyRkemikwgeekrkkdpglFcraaiekiea 88
                                       y ++k l+l+e  + +e ke+yR+ + kw  +k +++p + c+a +e+i +
  gi|298675277|ref|YP_003727027.1| 11 IYEASKVLNLNEKATMKEIKESYRRLIKKWHPDKCQQNPDI-CKAKTEEI-I 60
                                      5888999*******************************987.88877765.2 PP

>> Sin3_corepress  Sin3 family co-repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.5     9e+03      67      79 ..      11      23 ..       9      26 .. 0.57
   2 ?   13.1   0.2   1.3e-05     0.078       1      27 [.      27      53 ..      27      84 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.5
                    Sin3_corepress 67 ryelDmvieanrs 79
                                       ye   v++ n++
  gi|298675277|ref|YP_003727027.1| 11 IYEASKVLNLNEK 23
                                      5666666666654 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1.3e-05
                    Sin3_corepress  1 krlgpsYrlLpksyqqpkcsgrdelek 27
                                      k+++ sYr+L k++   kc++  +++k
  gi|298675277|ref|YP_003727027.1| 27 KEIKESYRRLIKKWHPDKCQQNPDICK 53
                                      57899*****************99994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       975  (0.0543812); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 677.82
//
Query:       gi|298675278|ref|YP_003727028.1|  [L=230]
Description: peroxiredoxin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.9e-34  116.4   0.0    9.2e-34  116.0   0.0    1.2  1  AhpC-TSA       AhpC/TSA family
      7e-15   55.0   0.0      9e-15   54.7   0.0    1.2  1  Redoxin        Redoxin
    2.1e-13   49.9   0.8    5.6e-13   48.5   0.4    1.9  2  1-cysPrx_C     C-terminal domain of 1-Cys peroxiredoxin
     0.0073   16.4   0.0      0.013   15.5   0.0    1.5  1  P_C10          Protein C10
  ------ inclusion threshold ------
      0.091   12.7   0.0       0.12   12.3   0.0    1.2  1  PAP_fibrillin  PAP_fibrillin
      0.098   12.5   0.5        1.3    8.9   0.0    2.4  2  zf-C2H2_9      C2H2 type zinc-finger (1 copy)


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.0   0.0   3.1e-37   9.2e-34       1     123 [.      15     151 ..      15     152 .. 0.96

  Alignments for each domain:
  == domain 1  score: 116.0 bits;  conditional E-value: 3.1e-37
                                       TTSB----EEESTTCEEEEC.HHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHH CS
                          AhpC-TSA   1 vgdkapdfelknadgetvsl.sdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkf 76 
                                       +gd ap+f++++++ +++++ +dy+gk+v+lf +p+d++pvCtte   +a++ eef+e++ e+ig+s+ds +sh ++
  gi|298675278|ref|YP_003727028.1|  15 IGDDAPKFTVNTTQ-GKINFpDDYNGKWVILFSHPADFTPVCTTEFMTFANMQEEFRELNTELIGLSIDSNFSHIAW 90 
                                       89*********998.666666******************************************************** PP

                                       HHH-H.............SSEEEE-TTSHHHHHTT-EETT..TTECSCEEEEE-TTSBEEE CS
                          AhpC-TSA  77 iekes............lnfpllsDeegkvakaygvlkee..kglalratfvidkegkiry 123
                                        ++++            + fp++ D + +vak+yg+++++  ++ a+ratf+id++ kir+
  gi|298675278|ref|YP_003727028.1|  91 LRTIKekmeykgmknvrVGFPVIEDLKMEVAKKYGMIQPNasTTQAVRATFIIDPHAKIRA 151
                                       ***************************************999999**************97 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.7   0.0     3e-18     9e-15       3     138 ..      16     160 ..      14     170 .. 0.83

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 3e-18
                                       TSBB---ECCEETTCEEEEEHHH.HTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH... CS
                           Redoxin   3 gdkaPdftlplaatdgnsvslse.fkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf... 75 
                                       gd aP+ft   ++t + +++  + ++gk v++++ p+ f+P+C++e   +++ +e+++e + + +++++d++     
  gi|298675278|ref|YP_003727028.1|  16 GDDAPKFT---VNTTQGKINFPDdYNGKWVILFSHPADFTPVCTTEFMTFANMQEEFRELNTELIGLSIDSNFShia 89 
                                       899*****...5567777777777**********************************************9988666 PP

                                       ....HHHHHHH.........TT-TSEEEE-TTSHHHHHTT-TTEEE.GGG.EEE-EEEEEEETTEEEEEEESSSCHT CS
                           Redoxin  76 ....vkefwgk.........eglkfpvlsDgsaaftkalGlrleedaseg.lrtpryavidedgkvvylevepepet 138
                                                ++           + fpv+ D + +++k++G  + ++++++  + +++++id + k++++ + p +++
  gi|298675278|ref|YP_003727028.1|  90 wlrtI----KEkmeykgmknVRVGFPVIEDLKMEVAKKYG--MIQPNASTtQAVRATFIIDPHAKIRAILYYPQSTG 160
                                       54431....225666788777778****************..6677777778***************9988887744 PP

>> 1-cysPrx_C  C-terminal domain of 1-Cys peroxiredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.99     3e+03      23      34 ..     126     137 ..     123     140 .. 0.72
   2 !   48.5   0.4   1.9e-16   5.6e-13       1      39 [.     172     210 ..     172     211 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.99
                                       EE---SSHHHHH CS
                        1-cysPrx_C  23 ivpPpateedav 34 
                                       +++P a+  +av
  gi|298675278|ref|YP_003727028.1| 126 MIQPNASTTQAV 137
                                       677777776686 PP

  == domain 2  score: 48.5 bits;  conditional E-value: 1.9e-16
                                       HHHHHHHHT-BB-TTT.TBT-EEE---SSHHHHHHHHHH CS
                        1-cysPrx_C   1 ALQladkhgvatPAnWkpGdkvivpPpateedavkryle 39 
                                       A+Q +dk+ +atPAnW+pG++vi+pP+ +++ a++r ++
  gi|298675278|ref|YP_003727028.1| 172 AMQKTDKEHIATPANWNPGEDVIIPPAGDYDTAEQRAES 210
                                       89*******************************999765 PP

>> P_C10  Protein C10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   4.5e-06     0.013      24      63 ..      89     128 ..      65     148 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.5e-06
                             P_C10  24 akleeakesagndmlkvmqlvlPvvvqiqmevikkyGFae 63 
                                       a l  +ke+++   +k +++ +Pv+ +++mev kkyG  +
  gi|298675278|ref|YP_003727028.1|  89 AWLRTIKEKMEYKGMKNVRVGFPVIEDLKMEVAKKYGMIQ 128
                                       5578899******************************865 PP

>> PAP_fibrillin  PAP_fibrillin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.1e-05      0.12      38     137 ..      24     132 ..      22     198 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.1e-05
                     PAP_fibrillin  38 lnptpaplesldlLdGkWrLlYttskellpllarkklpllkvgeiyQtIdvenksvqNsve.........lsglpll 105
                                       +n t+  ++ +d  +GkW+ l++  ++  p+ +++++ + +++e +   ++e   ++   +         +++    
  gi|298675278|ref|YP_003727028.1|  24 VNTTQGKINFPDDYNGKWVILFSHPADFTPVCTTEFMTFANMQEEFRELNTELIGLSIDSNfshiawlrtIKEKMEY 100
                                       67888888889999*****************99999999*****999996665544433330000000003332224 PP

                     PAP_fibrillin 106 egsvsvaakfevaspkrvelkFeravlklkkl 137
                                       +g+  v++ f v ++ ++e+  + ++++++  
  gi|298675278|ref|YP_003727028.1| 101 KGMKNVRVGFPVIEDLKMEVAKKYGMIQPNAS 132
                                       45555555555555555555555555544333 PP

>> zf-C2H2_9  C2H2 type zinc-finger (1 copy)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00045       1.3       5      39 ..      53      93 ..      50     105 .. 0.64
   2 ?    1.1   0.1      0.12   3.7e+02      20      33 ..     168     181 ..     161     183 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00045
                                      TTT--B-S.......SHHHHHHHHHHHTSSS--HHHHHHHHH CS
                         zf-C2H2_9  5 PvCevkfn.......swkdlseHilsaasksdaeHvmWLNRn 39
                                      PvC+ +f        ++++l   ++     s+ +H+ WL R 
  gi|298675278|ref|YP_003727028.1| 53 PVCTTEFMtfanmqeEFRELNTELIGLSIDSNFSHIAWL-RT 93
                                      889888871111222334444555555668********9.44 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.12
                                       HHHHHTSSS--HHH CS
                         zf-C2H2_9  20 HilsaasksdaeHv 33 
                                        +++a +k d+eH+
  gi|298675278|ref|YP_003727028.1| 168 RMIIAMQKTDKEHI 181
                                       57888999*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1442.53
//
Query:       gi|298675279|ref|YP_003727029.1|  [L=204]
Description: FKBP-type peptidylprolyl isomerase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-20   71.4   0.2    8.1e-20   70.9   0.2    1.2  1  FKBP_C    FKBP-type peptidyl-prolyl cis-trans isomerase


Domain annotation for each model (and alignments):
>> FKBP_C  FKBP-type peptidyl-prolyl cis-trans isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.9   0.2   4.5e-24   8.1e-20       5      93 ..      41     186 ..      37     187 .. 0.80

  Alignments for each domain:
  == domain 1  score: 70.9 bits;  conditional E-value: 4.5e-24
                                       B-TTCEEEEEEEEEETTSSEEEEH...........CCHTSEEEEETTSSSSCHHHHHHHTTSBTT-EEEEEEEGGGT CS
                            FKBP_C   5 akegdtVtvhykgkledgkvfdss...........rsrakplefkvGsgqvikGfeealegmkvGekrtltippela 70 
                                       +++gd+Vt++y++++e+g+v+++s            +  +plef+vGs+q+i G+ e++ gm+ Ge++tlt ppe+a
  gi|298675279|ref|YP_003727029.1|  41 VENGDIVTLDYTLMYENGTVVETSvddiaeendniEQSREPLEFEVGSQQMIAGINEGVLGMSEGEQKTLTLPPEEA 117
                                       789*********************888877776644499************************************** PP

                                       TTT...............................TTBCTTTB.TT........................SEEEEEEE CS
                            FKBP_C  71 Yge...............................kglaggvippn........................atLvFeve 92 
                                       +g                                +         +                        +t+vF+++
  gi|298675279|ref|YP_003727029.1| 118 FGPyredlvqsmtieeyqnatnsnttpeqgeqimT---------QmgpitvsdvnethitldanspfagKTVVFDIT 185
                                       ***99999999999888766655555544444440.........155555555555566666667777799999998 PP

                                       E CS
                            FKBP_C  93 L 93 
                                       +
  gi|298675279|ref|YP_003727029.1| 186 I 186
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1330.05
//
Query:       gi|298675280|ref|YP_003727030.1|  [L=128]
Description: nucleic acid-binding OB-fold tRNA/helicase-type protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00012   22.0   0.1    0.00025   21.0   0.1    1.5  2  tRNA_anti-codon  OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
       0.12   12.0   0.5       0.19   11.3   0.1    1.5  2  tRNA_anti-like   tRNA_anti-like


Domain annotation for each model (and alignments):
>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.21   1.9e+03      34      58 ..      26      52 ..      24      61 .. 0.75
   2 !   21.0   0.1   2.8e-08   0.00025       3      72 ..      48     117 ..      46     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.21
                                      EET..HHHHHHHTTS-TTSEEEEEEEE CS
                   tRNA_anti-codon 34 lfr..eeatklaenlkeGdvvrvtGrv 58
                                      +f+  ++ +++ ++  +G  v+ +G+v
  gi|298675280|ref|YP_003727030.1| 26 FFPanNGLQEYSDSSNIGEEVYLEGTV 52
                                      555556777777778888888888887 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 2.8e-08
                                       EEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET.HHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEE CS
                   tRNA_anti-codon   3 vaGrvtsisdrsggkvifidlrDgtgriqvvlfr.eeatklaenlkeGdvvrvtGrvkrrpggelelkvee 72 
                                       ++G v  +  + +g ++ + l+ ++g ++v++ + ++a+ l +++ +G ++ v+G v +++g+  e+++++
  gi|298675280|ref|YP_003727030.1|  48 LEGTVLGKHVTYNGDHLILNLKWNSGLVKVFVPNsNGAETLDKKINKGFYIHVEGAVDKYKGK-REIIIQQ 117
                                       567777776566778899999999**********999999999*******************9.9998875 PP

>> tRNA_anti-like  tRNA_anti-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.16   1.4e+03       6      23 ..       6      23 ..       1      41 [. 0.55
   2 ?   11.3   0.1   2.2e-05      0.19      81     155 ..      38     113 ..      27     119 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.16
                                      XXXXXXXXXXXXXXXXXX CS
                    tRNA_anti-like  6 kkilviilivilllfvia 23
                                      k i+v+i + +++l++++
  gi|298675280|ref|YP_003727030.1|  6 KIIVVLIAMALSSLSIAY 23
                                      334444444444455544 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 2.2e-05
                                       HHHHTT-EEEEEEEEEEEEE.-STT-EEEEEE-TT-S-S--EEEEEEGGHHHHHH--TTSEEEEEEE-----.SS-E CS
                    tRNA_anti-like  81 dkkYkGkiieVeGvvsdikk.ieassvvvlardddgltnVrclledeateasaakiskGqkvtivGqvngvs.idnv 155
                                       d+   G+ +  eG+v ++    +++  ++ ++ + gl++V    ++ a+ ++  ki kG  + ++G v+ +  + ++
  gi|298675280|ref|YP_003727030.1|  38 DSSNIGEEVYLEGTVLGKHVtYNGDHLILNLKWNSGLVKVFVPNSNGAETLDK-KINKGFYIHVEGAVDKYKgKREI 113
                                       6666799999********8889***********99999999988888877776.**************998764444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.33s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 780.74
//
Query:       gi|298675281|ref|YP_003727031.1|  [L=389]
Description: nucleotidyl transferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-52  179.2   0.0    1.6e-52  178.6   0.0    1.2  1  NTP_transferase  Nucleotidyl transferase
    2.9e-18   64.8  21.6    9.4e-07   28.3   0.7    4.6  4  Hexapep          Bacterial transferase hexapeptide (six repea
    1.1e-10   42.1   0.0    1.5e-10   41.7   0.0    1.4  1  NTP_transf_3     MobA-like NTP transferase domain
    6.2e-09   35.5  19.7      0.003   17.3   5.0    4.8  4  Hexapep_2        Hexapeptide repeat of succinyl-transferase
  ------ inclusion threshold ------
      0.086   12.8   0.0       0.21   11.5   0.0    1.7  1  DUF4934          Domain of unknown function (DUF4934)
       0.11   11.4   2.4       0.71    8.8   0.5    2.2  2  Fucokinase       L-fucokinase
       0.97    7.5   6.2        1.7    6.6   6.1    1.5  1  DUF4954          Domain of unknown function (DUF4954)


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.6   0.0   6.1e-56   1.6e-52       1     243 [.       2     231 ..       2     235 .. 0.97

  Alignments for each domain:
  == domain 1  score: 178.6 bits;  conditional E-value: 6.1e-56
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEE CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevli 77 
                                       ka I++GG+GtRL+PLt +++k+ +pvl+k +++ + ++ l+++g++e ivv+  +  +++eeql++g  fgv++++
  gi|298675281|ref|YP_003727031.1|   2 KACIMCGGKGTRLHPLTFERPKPSIPVLNK-PILTHLIEHLSKEGFTE-IVVTLGYMGHMIEEQLGDGRMFGVHINY 76 
                                       688***************************.*****************.**************************** PP

                                       EEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEEC CS
                   NTP_transferase  78 alepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGviead 154
                                       ++e ++ gtA++v+ a+ ll++e     ++vL+gDh+ + +++e++++++ ++   ++t+g+   ++++e+G++ +d
  gi|298675281|ref|YP_003727031.1|  77 VYEHKKLGTAGSVKNAEHLLGNEP----FIVLSGDHVLNLNLREMFRFHETTGD-SMITIGLLSIDDPREFGIADMD 148
                                       *********************999....8**********************999.79******************** PP

                                       TTSBEEEEECS-SSHSH.CSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EE CS
                   NTP_transferase 155 eegrverfvEKPkeaka.selassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWs 230
                                        +++v+rf EKP+  +  s+las+GiYv ++e++ ++     + +++ d+ +d++pk++++gk+   fl  +   W 
  gi|298675281|ref|YP_003727031.1| 149 VNNKVHRFLEKPDSGEIfSNLASTGIYVCDPEIFNYI-----PEDTQYDFAKDVFPKLMSSGKDISGFLVYG--EWT 218
                                       *************98888*******************.....8899**************************..5** PP

                                       EXSSHHHHHHHHH CS
                   NTP_transferase 231 DvGtldslleane 243
                                       DvG++ ++  a++
  gi|298675281|ref|YP_003727031.1| 219 DVGNPAAYRAAQR 231
                                       ********98875 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   2.7   3.8e-09   9.8e-06       2      34 ..     257     289 ..     256     290 .. 0.95
   2 !   28.2   1.4     4e-10     1e-06       1      28 [.     280     307 ..     280     307 .. 0.96
   3 !   20.1   1.3   1.4e-07   0.00036       2      35 ..     310     348 ..     309     349 .. 0.93
   4 !   28.3   0.7   3.7e-10   9.4e-07       2      34 ..     333     365 ..     332     365 .. 0.95

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 3.8e-09
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                       ++I +nv+Ig+++ + g+++IG+n+ Ig +v i
  gi|298675281|ref|YP_003727031.1| 257 LKIDNNVTIGSNSSLVGPIVIGENTEIGDNVLI 289
                                       6899***************************98 PP

  == domain 2  score: 28.2 bits;  conditional E-value: 4e-10
                                       TEEEETTEEE-TTEEEETTEEE-TTEEE CS
                           Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkI 28 
                                       +t IG+nvlI p++vig+n++I +n++I
  gi|298675281|ref|YP_003727031.1| 280 NTEIGDNVLISPYTVIGSNCVIENNARI 307
                                       689***********************98 PP

  == domain 3  score: 20.1 bits;  conditional E-value: 1.4e-07
                                       EEEETTEEE-T.....TEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   2 tvIGsnvlIgp.....faviggnVkIGdnvkIgagvvig 35 
                                       + I +nv+Ig      +avi ++V +G n+ +++g+v+g
  gi|298675281|ref|YP_003727031.1| 310 SYIFNNVKIGQntnasGAVIDNDVSVGQNTSLENGTVLG 348
                                       6789999999999999*********************98 PP

  == domain 4  score: 28.3 bits;  conditional E-value: 3.7e-10
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                       + +G+n+ + +++v+g+ V+IGdn++I+++v i
  gi|298675281|ref|YP_003727031.1| 333 VSVGQNTSLENGTVLGAKVTIGDNATIHSNVKI 365
                                       789***************************987 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.0   5.8e-14   1.5e-10       1      98 [.       3     110 ..       3     245 .. 0.86

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 5.8e-14
                                       EEEEEESS-TTTT.....TTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTC...TS-EEE-.T CS
                      NTP_transf_3   1 aviLAGGrSsRmg.....gdKallplggkpllervldalraagvdevvvvggd..eevlaalarl...gvrvved.e 66 
                                       a+i++GG+++R+      ++K+ +p+ +kp+l +++++l++ g+ e+vv  g+  + ++++l +    gv++ +  e
  gi|298675281|ref|YP_003727031.1|   3 ACIMCGGKGTRLHpltfeRPKPSIPVLNKPILTHLIEHLSKEGFTEIVVTLGYmgHMIEEQLGDGrmfGVHINYVyE 79 
                                       68**********6444436********************************99988888887555333666644423 PP

                                       TSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT CS
                      NTP_transf_3  67 dpgkgplaslaaalraaadadavlvlacDmPl 98 
                                       ++  g+++s++ a + + ++++++vl++D++l
  gi|298675281|ref|YP_003727031.1|  80 HKKLGTAGSVKNAEHLL-GNEPFIVLSGDHVL 110
                                       4589*********9877.9***********98 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   3.4   1.8e-06    0.0046       1      33 [.     256     290 ..     256     291 .. 0.88
   2 !   17.3   5.0   1.2e-06     0.003       1      29 [.     274     304 ..     274     308 .. 0.92
   3 !    8.9   1.1   0.00048       1.2       2      34 .]     316     349 ..     315     349 .. 0.83
   4 !    9.6   0.0   0.00029      0.74       2      14 ..     351     363 ..     350     373 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.8e-06
                                       .EEE-TT-EE-TT-E.ES.EEE-TT-EE-TT-EE- CS
                         Hexapep_2   1 pviIGdnCliGanag.iG.vslGdncvvgaGvvit 33 
                                       p++I +n+ iG+n+  +G + +G+n  +g +v i 
  gi|298675281|ref|YP_003727031.1| 256 PLKIDNNVTIGSNSSlVGpIVIGENTEIGDNVLIS 290
                                       799**********997866******9999999885 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 1.2e-06
                                       .EEE-TT-EE-TT-EES..EEE-TT-EE-TT CS
                         Hexapep_2   1 pviIGdnCliGanagiG..vslGdncvvgaG 29 
                                       p+ IG+n+ iG n  i   + +G ncv++++
  gi|298675281|ref|YP_003727031.1| 274 PIVIGENTEIGDNVLISpyTVIGSNCVIENN 304
                                       899*************559***********9 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.00048
                                       EEE-TT-EE-TT.-EE..SEEE-TT-EE-TT-EE-S CS
                         Hexapep_2   2 viIGdnCliGan.agi..GvslGdncvvgaGvvita 34 
                                       v+IG+n++  a+ a+i   vs+G n  +++G v+ a
  gi|298675281|ref|YP_003727031.1| 316 VKIGQNTN--ASgAVIdnDVSVGQNTSLENGTVLGA 349
                                       78888888..444889888**************975 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.00029
                                       EEE-TT-EE-TT- CS
                         Hexapep_2   2 viIGdnCliGana 14 
                                       v+IGdn  i++n 
  gi|298675281|ref|YP_003727031.1| 351 VTIGDNATIHSNV 363
                                       7888888888886 PP

>> DUF4934  Domain of unknown function (DUF4934)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   8.3e-05      0.21      21      70 ..      94     144 ..      71     168 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.3e-05
                           DUF4934  21 vLvGnspkikllkdkivvsskkqCllfdketGkflasvGhiG.edPegyse 70 
                                        L+Gn+p i l+ d+++  +  + + f+  tG  + ++G +  +dP  +  
  gi|298675281|ref|YP_003727031.1|  94 HLLGNEPFIVLSGDHVLNLNLREMFRFHETTGDSMITIGLLSiDDPREFGI 144
                                       699************************************875488876654 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.3      0.02        50     297     335 ..     258     294 ..     235     301 .. 0.75
   2 ?    8.8   0.5   0.00028      0.71     268     330 ..     299     359 ..     288     368 .. 0.53

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.02
                        Fucokinase 297 slkgnvsigsnsivsglelesseeslelpddtilqtlsl 335
                                       ++++nv+igsns ++g  +  ++   e+ d++++    +
  gi|298675281|ref|YP_003727031.1| 258 KIDNNVTIGSNSSLVGPIVIGEN--TEIGDNVLISPYTV 294
                                       56789999999999998888774..48888888766555 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00028
                        Fucokinase 268 ekkkesavvinSvlessvsvgegsviehsslkgnvsigsnsivsglelesseeslelpddtil 330
                                         ++++a + +S + ++v++g+++      ++++vs+g+n+ + +  +     ++++ d+  +
  gi|298675281|ref|YP_003727031.1| 299 CVIENNARIFSSYIFNNVKIGQNTNASGAVIDNDVSVGQNTSLENGTVLGA--KVTIGDNATI 359
                                       223455555555555555555555555555555555555555555544443..4555555555 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   6.1   0.00068       1.7     217     272 ..     262     319 ..     238     378 .. 0.57

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.00068
                           DUF4954 217 pveiGegViled.fiissGskikdgavisr.cfvGqavklkkqfsaedsllfaNcqge 272
                                        v+iG++  l    +i + ++i d ++is  +++G ++ +++++++  s +f+N ++ 
  gi|298675281|ref|YP_003727031.1| 262 NVTIGSNSSLVGpIVIGENTEIGDNVLISPyTVIGSNCVIENNARIFSSYIFNNVKIG 319
                                       4555554444331334445555555555531345555555555555555555555432 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 2365.63
//
Query:       gi|298675282|ref|YP_003727032.1|  [L=342]
Description: hypothetical protein Metev_1380 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-46  159.1  18.9    2.6e-46  158.5  18.9    1.2  1  LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region


Domain annotation for each model (and alignments):
>> LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.5  18.9   1.5e-50   2.6e-46       8     301 .]      15     323 ..       9     323 .. 0.87

  Alignments for each domain:
  == domain 1  score: 158.5 bits;  conditional E-value: 1.5e-50
                   LPG_synthase_TM   8 s...alllalllrgvdlaalaaalrsldpwwlllalllallsvllralrWrlllrslgarislrrllrayliglfvn 81 
                                       s   +lll+++   +  +++++++ ++ + +++la+++++++++ +alr + ++++++++i+++++++++++g f+ 
  gi|298675282|ref|YP_003727032.1|  15 SgisILLLLIV---TVNSETIETVLKIKYEYIVLAVIMHIVAYFMWALRTKSMCQGIDYKIKFLSCVKIVTAGKFAA 88 
                                       43323333333...225999********************************************************* PP

                   LPG_synthase_TM  82 nvtPgalgGevvrayllkrkegvslskalasvvverlldllalvllgllallllggllaegaavllllalallllav 158
                                       ++tP+++gGe++r+ ll++ + ++ ++a a+v+ er++d + +++  ++al++l   +   +  ++++++ ++l  v
  gi|298675282|ref|YP_003727032.1|  89 SITPSSIGGEPLRIELLHQ-NELPIGRASAIVLGERFMDAFLILFSAPVALYILRDGFSDSSLDIVFIMGEFILMSV 164
                                       *******************.*******************************99999987777777777777777777 PP

                   LPG_synthase_TM 159 lalllllllrrrlarlarvlkrlarllarfarklasakr...................klvlasprrlllafllsll 216
                                       l++ l+ llr+    l+r+++ +a +l ++ +k++   +                    l+++ +++l+   l++++
  gi|298675282|ref|YP_003727032.1| 165 LLIMLYGLLRPEN--LKRIIRFIAIKLTKLLGKKREDQIyhvlkkidsefynfhaslrMLLREGRTSLACGMLFTVF 239
                                       7766665555544..4444444444555566666555558999**************9888888889********** PP

                   LPG_synthase_TM 217 iwllealtlylllralgvdvslallllillaltlvgalpplPgGlGvrEaalalllallGvsaaealaaallyrlit 293
                                       +wl+ +++l ++l++l++++++   ++++++l++++a+p++Pg +Gv+E ++++l++ + v +++++++++ +r++t
  gi|298675282|ref|YP_003727032.1| 240 YWLFLFSILPVILMGLNLNPPVIITFAAQILLLIITAVPITPGASGVAELGATTLFSVF-VVPSLIGITVITWRVLT 315
                                       ***********************************************************.***************** PP

                   LPG_synthase_TM 294 lylllllG 301
                                       +y+ ll+G
  gi|298675282|ref|YP_003727032.1| 316 YYMNLLVG 323
                                       ******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       815  (0.0454571); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2052.96
//
Query:       gi|298675283|ref|YP_003727033.1|  [L=560]
Description: radical SAM domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-17   64.4   0.0    4.8e-17   62.8   0.0    1.9  2  Radical_SAM  Radical SAM superfamily
     0.0001   22.4   0.1      0.001   19.3   0.0    2.4  2  HHH_3        Helix-hairpin-helix motif
  ------ inclusion threshold ------
       0.05   13.5   0.1       0.36   10.8   0.0    2.5  2  HHH          Helix-hairpin-helix motif
      0.095   12.2   0.1       0.19   11.2   0.1    1.4  1  C_LFY_FLO    DNA Binding Domain (C-terminal) Leafy/Floricaula


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       2.9   1.3e+04      23      40 ..     155     172 ..     149     177 .. 0.75
   2 !   62.8   0.0   1.1e-20   4.8e-17       2     167 .]     191     386 ..     190     386 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.9
                                       HHHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  23 egrgrslsveeileevke 40 
                                       + ++r ++veei + +  
  gi|298675283|ref|YP_003727033.1| 155 NITHRQRTVEEIGRWAIN 172
                                       567889999999887765 PP

  == domain 2  score: 62.8 bits;  conditional E-value: 1.1e-20
                                       EEESEESS-..-TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS................ CS
                                       xxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................ RF
                       Radical_SAM   2 vvtrgCnlr..CsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly................ 60 
                                       +++rgC ++  CsfC+ p+    ++ +++++ve+++ ev el ++ g++++ +g + p+l                 
  gi|298675283|ref|YP_003727033.1| 191 ETYRGCGRNthCSFCTEPF----YKESKYRPVEDVIFEVSEL-YNSGARYFRIGRQ-PDLFtyqsientndisepnp 261
                                       5789**************7....9******************.8**********55.44444556666666666663 PP

                                       TTHHHHHHHHHHTC........CCTEEEEEEECSSCHGHHHHHHHHHTT..-SEEEEEEBSSSHHHHHHHHTCTSHH CS
                                       xxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  61 pdfvellerlakla........vpgiritvetngtlpdeeklerllelg..vdrvslgleaaddekvlklmnrghtf 127
                                         +++l++ ++  +         ++++ + ++ ++  ++++l+ +l+++   d+ +lg e+ad++ v   +n + t+
  gi|298675283|ref|YP_003727033.1| 262 EAIEKLYRGIRD-KapdlqvlhMDNVNPATIARYPDKSRKILDIILKYHttGDVCALGMESADPD-VVSANNLKATP 336
                                       224444444444.3488555333355555555555544***************************.88888899*** PP

                                       HHHHHHHHHHHHTTSET..........EEEEEEEBTTTSHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 128 eevlealeklreagikr..........vvdrivglpGendeeleellell 167
                                       eevlea+++++e+g+k             ++++gl+Ge+++++++ +++l
  gi|298675283|ref|YP_003727033.1| 337 EEVLEAIKIINEKGGKCgynglpeilpGLNFVYGLKGETKKTFKNNYDFL 386
                                       **************7777777777888****************9999986 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.27   1.2e+03      35      54 ..      43      62 ..      40      67 .. 0.79
   2 !   19.3   0.0   2.2e-07     0.001       8      48 ..     510     546 ..     507     558 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.27
                             HHH_3 35 eknGpfksreeLlkvkglgp 54
                                      ++n +++++++L k + +++
  gi|298675283|ref|YP_003727033.1| 43 KQNIHYTTIDQLRKLSSMKE 62
                                      67889999999999887765 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 2.2e-07
                             HHH_3   8 iNtAsaeeLqklpGlgpklAknIvayReknGpfksreeLlk 48 
                                       iN As+e+++ +pG+g+++A +I +      pfk+ +++++
  gi|298675283|ref|YP_003727033.1| 510 INEASLELISEIPGVGKNQAAEIYKNI----PFKDKNDFME 546
                                       9**********************9999....****999986 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.1   4.8e+03       3      10 ..     284     291 ..     283     292 .. 0.86
   2 ?   10.8   0.0   7.9e-05      0.36       4      21 ..     509     526 ..     508     534 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.1
                                       HHHHTSSH CS
                               HHH   3 eglipasr 10 
                                       ++++pa++
  gi|298675283|ref|YP_003727033.1| 284 DNVNPATI 291
                                       799****8 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 7.9e-05
                                       HHHTSSHHHHHTSTT-SH CS
                               HHH   4 glipasreeLlalPGVGp 21 
                                       ++++as+e + ++PGVG+
  gi|298675283|ref|YP_003727033.1| 509 RINEASLELISEIPGVGK 526
                                       589**************7 PP

>> C_LFY_FLO  DNA Binding Domain (C-terminal) Leafy/Floricaula
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   4.2e-05      0.19      15      88 ..     367     446 ..     363     452 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.2e-05
                         C_LFY_FLO  15 fivtepgevargkkngldylfhlyeqc....rkfliqvqal..akekgekcptkvtnqvfryakkagasyinkpkmr 85 
                                       f+    ge+ ++ kn  d+l ++++      r  l qv ++  +   g+ + tk  n++f   k+   +yi+kp +r
  gi|298675283|ref|YP_003727033.1| 367 FVYGLKGETKKTFKNNYDFLKKVFDSGllvrRINLRQVVTFpgTPIYGKDTVTKKHNKLFLNHKEKVREYIDKPMLR 443
                                       66777899****************985333255688888883335689***************************** PP

                         C_LFY_FLO  86 hyv 88 
                                       + v
  gi|298675283|ref|YP_003727033.1| 444 KLV 446
                                       877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (560 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 3469.75
//
Query:       gi|298675284|ref|YP_003727034.1|  [L=57]
Description: hypothetical protein Metev_1382 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 355.40
//
Query:       gi|298675285|ref|YP_003727035.1|  [L=553]
Description: dihydroxy-acid dehydratase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   4.7e-218  725.0   0.6   5.3e-218  724.8   0.6    1.0  1  ILVD_EDD  Dehydratase family


Domain annotation for each model (and alignments):
>> ILVD_EDD  Dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  724.8   0.6    3e-222  5.3e-218       1     516 [.      31     549 ..      31     550 .. 0.97

  Alignments for each domain:
  == domain 1  score: 724.8 bits;  conditional E-value: 3e-222
                          ILVD_EDD   1 kpiigiansyselvpchvhlkelaeavkegveeaggvpaefntigvsDgiamgeegmrysLpsReliadsvetmlea 77 
                                       kp+i+++ns++e+vp+h +l++l+e vk+g+++aggvp+efntigv+Dgiamg+egm+ysLpsRe iad++e m++a
  gi|298675285|ref|YP_003727035.1|  31 KPFIAVVNSWNEIVPGHINLDKLGESVKAGIRNAGGVPFEFNTIGVCDGIAMGHEGMKYSLPSREAIADTIELMVQA 107
                                       8**************************************************************************** PP

                          ILVD_EDD  78 qllDalvlisgCDKivPgllmaaarlniPaifvsgGpmeagkkk..kldlssvfeavgalaagkiseeeleeleeaa 152
                                       ++lD++vli+ CDKi+Pg+lmaa rlniPai+v+gGpm++g +    +dl+svfe +g++++++ise++l+ +e+++
  gi|298675285|ref|YP_003727035.1| 108 HQLDGMVLIAACDKILPGHLMAAGRLNIPAIVVTGGPMLPGYVGdeYCDLVSVFEGIGSCRNDNISESQLKMIEDQS 184
                                       ****************************************88444578***************************** PP

                          ILVD_EDD 153 cpgaGsCsgmgTAntmaclaealGlslpgsasipatsaerkelaeeagkrivelvekdlkprdiltkeafeNAivvl 229
                                       c gaGsC+g++TAntm+cl+ea+G+slpg+++++a +a+++++a+++g+riv+++++dl+pr+i+t e+++NAi v+
  gi|298675285|ref|YP_003727035.1| 185 CSGAGSCAGLFTANTMSCLTEAMGMSLPGCGTAHAADAKKARIAKDSGERIVQMTKEDLTPRQIVTDETLNNAIRVD 261
                                       ***************************************************************************** PP

                          ILVD_EDD 230 lalGGStNavlHllAiAreagveltlddfdelsrkvpllaklkPsgkydmedlhraGGvpavlkeLlkagllhgdvl 306
                                       +a+GGStN+vlHl+AiA+e+g+el +++fdelsr++p+l++l+P g  +m d++raGGv+a+l++++   +l  dv+
  gi|298675285|ref|YP_003727035.1| 262 MAIGGSTNTVLHLPAIANEFGLELPIEKFDELSRQTPHLINLRPGGYNHMLDFDRAGGVQAILERIK--PMLFLDVK 336
                                       *******************************************************************..67****** PP

                          ILVD_EDD 307 tvtgktlaenleeaev....keqdvirplekplskegglavLkGnLapeGavvKtsaveeellkfegpArvfdseee 379
                                       tvtgktl+enle+  v    +++d+i ++++p+++egg+a+LkG+LapeG+v+K+sav+e++l+++gpArv+dsee+
  gi|298675285|ref|YP_003727035.1| 337 TVTGKTLGENLEDFVVinpkTNKDIIATIDNPVHPEGGIAILKGSLAPEGSVIKQSAVNEDMLEHKGPARVYDSEED 413
                                       ***********9933345669******************************************************** PP

                          ILVD_EDD 380 aveailkgkikagdvvviryeGPkGgpGmpEmlkptsallgkglgkkvalitDGRfSGaskglvighvsPEAaegGp 456
                                       a+  il g++k++dvvviryeGPkGgpGm+Eml+ptsa++g+gl ++val+tDGRfSG+++g++igh+sPEA + Gp
  gi|298675285|ref|YP_003727035.1| 414 AMCGILGGDVKSDDVVVIRYEGPKGGPGMREMLSPTSAIAGMGL-DTVALVTDGRFSGGTRGPCIGHISPEAIDSGP 489
                                       ********************************************.99****************************** PP

                          ILVD_EDD 457 ialvedGDiieidiekrtlelevseeelaaRraawkp.ekkvktrgllakyaklvssaseG 516
                                       ia+++dGD iei+i++rtl+l++seee+++R+++++  ek+v  +++l+ky+k+v sas+G
  gi|298675285|ref|YP_003727035.1| 490 IAYIQDGDEIEINIPERTLNLNISEEEMKKRKESFELsEKEV-DSKYLTKYRKSVGSASKG 549
                                       *********************************999944444.5****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 3266.14
//
Query:       gi|298675286|ref|YP_003727036.1|  [L=149]
Description: 4Fe-4S ferredoxin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-12   44.6  33.8     0.0012   18.6   2.3    5.0  5  Fer4      4Fe-4S binding domain
    2.6e-11   43.9  24.4     0.0014   19.1   0.8    3.7  3  Fer4_7    4Fe-4S dicluster domain
    1.9e-09   37.5  27.4    8.1e-05   22.7  11.2    3.1  4  Fer4_9    4Fe-4S dicluster domain
    3.9e-09   37.3  22.5     0.0041   18.0   0.4    4.3  4  Fer4_16   4Fe-4S double cluster binding domain
    2.1e-07   30.7  36.6     0.0019   18.2   1.3    4.3  4  Fer4_6    4Fe-4S binding domain
    2.8e-07   30.5  26.6     0.0014   18.7   9.2    3.3  3  Fer4_21   4Fe-4S dicluster domain
      1e-06   28.7  30.9      0.065   13.4  13.3    3.8  4  Fer4_10   4Fe-4S dicluster domain
    2.5e-06   27.2  36.1     0.0075   16.3   2.3    4.5  4  Fer4_2    4Fe-4S binding domain
    1.8e-05   24.9  32.5     0.0042   17.5   1.6    4.6  4  Fer4_4    4Fe-4S binding domain
    2.2e-05   24.5  11.2    2.2e-05   24.5  11.2    2.2  3  Fer4_11   4Fe-4S dicluster domain
    0.00077   19.9  28.5       0.14   12.7   1.5    3.6  4  Fer4_17   4Fe-4S dicluster domain
     0.0025   18.5  21.1       0.15   12.9   2.1    3.5  3  Fer4_15   4Fe-4S single cluster domain
     0.0031   18.4  42.6        1.1   10.3   4.6    4.3  4  Fer4_3    4Fe-4S binding domain
  ------ inclusion threshold ------
       0.07   13.6  28.0       0.93   10.0   7.9    3.7  3  Fer4_8    4Fe-4S dicluster domain
        4.3    7.6  26.5        1.5    9.0   1.5    3.3  3  Fer4_18   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   3.1   1.5e-05     0.018       4      18 ..      14      28 ..      11      28 .. 0.91
   2 ?    0.2   0.3      0.63   7.5e+02       9      16 ..      58      65 ..      58      65 .. 0.76
   3 !   10.8   0.1   0.00028      0.33      14      24 .]      68      78 ..      68      78 .. 0.93
   4 !   18.6   2.3     1e-06    0.0012       3      19 ..      87     103 ..      85     108 .. 0.81
   5 !   18.5   2.8     1e-06    0.0012       8      23 ..     118     133 ..     117     134 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.5e-05
                                      ETTTSSS-THHHHHS CS
                              Fer4  4 deekCigCGaCvevC 18
                                      ++ +CigC  C+ +C
  gi|298675286|ref|YP_003727036.1| 14 NQARCIGCYSCMLAC 28
                                      7889*********** PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.63
                                      SS-THHHH CS
                              Fer4  9 igCGaCve 16
                                      i C aC++
  gi|298675286|ref|YP_003727036.1| 58 IVCHACID 65
                                      56999985 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00028
                                      HHHHSTTTEEE CS
                              Fer4 14 CvevCPvgAIt 24
                                      C  +CP+gA+t
  gi|298675286|ref|YP_003727036.1| 68 CSRACPTGALT 78
                                      99*******96 PP

  == domain 4  score: 18.6 bits;  conditional E-value: 1e-06
                                       EETTTSSS-THHHHHST CS
                              Fer4   3 ideekCigCGaCvevCP 19 
                                        + ++C gC +Cv++C 
  gi|298675286|ref|YP_003727036.1|  87 LHNDLCEGCRYCVDACL 103
                                       6789************5 PP

  == domain 5  score: 18.5 bits;  conditional E-value: 1e-06
                                       SSS-THHHHHSTTTEE CS
                              Fer4   8 CigCGaCvevCPvgAI 23 
                                       C +CG C++ CP +++
  gi|298675286|ref|YP_003727036.1| 118 CKHCGVCASYCPRDVL 133
                                       *************987 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   8.7   5.1e-06     0.006       1      52 []      17      76 ..      17      76 .. 0.69
   2 !   17.3   1.2   4.6e-06    0.0055       2      22 ..      92     112 ..      91     116 .. 0.88
   3 !   19.1   0.8   1.2e-06    0.0014       2      25 ..     118     141 ..     117     149 .] 0.83

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.1e-06
                            Fer4_7  1 rCigCgaCvaaCp...vkaielde...eenekgtekveidpekClgCga..CvavCPtga 52
                                      rCigC  C+ aC    +++++l++   + + kg  +  +++  C  C    C ++CPtga
  gi|298675286|ref|YP_003727036.1| 17 RCIGCYSCMLACArtyYDTVSLKNsaiDIQTKGGIEEGFVSIVCHACIDppCSRACPTGA 76
                                      8***********6444444444431111222355666778889****9889*******98 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 4.6e-06
                            Fer4_7   2 CigCgaCvaaCpvkaieldee 22 
                                       C gC++Cv+aC  +ai +d +
  gi|298675286|ref|YP_003727036.1|  92 CEGCRYCVDACLIGAIHMDAY 112
                                       ***************999865 PP

  == domain 3  score: 19.1 bits;  conditional E-value: 1.2e-06
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeene 25 
                                       C +Cg C+++Cp +++el+++ ++
  gi|298675286|ref|YP_003727036.1| 118 CKHCGVCASYCPRDVLELRKVGDN 141
                                       9****************9998554 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   2.4   5.6e-05     0.067      31      49 ..      13      31 ..       4      33 .. 0.74
   2 !   16.9  10.0   4.5e-06    0.0054       1      50 [.      17      76 ..      17      77 .. 0.78
   3 !   19.1   9.3   9.2e-07    0.0011       2      50 ..      60     106 ..      58     107 .. 0.87
   4 !   22.7  11.2   6.8e-08   8.1e-05       2      50 ..      92     132 ..      91     133 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.6e-05
                            Fer4_9 31 aseeaCigCgaCveaCpkg 49
                                      a++ +CigC +C+ aC ++
  gi|298675286|ref|YP_003727036.1| 13 ANQARCIGCYSCMLACART 31
                                      4446899999999999875 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 4.5e-06
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase........eaCigCga..CveaCpkga 50
                                      +C+gC +C+ aC  + +   + ++ a   +++           C+ C +  C  aCp+ga
  gi|298675286|ref|YP_003727036.1| 17 RCIGCYSCMLACARTYYDTVSLKNSAIDIQTKGgieegfvsIVCHACIDppCSRACPTGA 76
                                      6***********7777766555555554444446888999878***************97 PP

  == domain 3  score: 19.1 bits;  conditional E-value: 9.2e-07
                            Fer4_9   2 CtgCga..CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                       C  C    C +aCp+g+ + +++++ + ++      C gC+ Cv+aC  ga
  gi|298675286|ref|YP_003727036.1|  60 CHACIDppCSRACPTGALTVRKGGGVILHND----LCEGCRYCVDACLIGA 106
                                       88886556******************99976....6***********7666 PP

  == domain 4  score: 22.7 bits;  conditional E-value: 6.8e-08
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                       C gC++Cv+aC  g++ +da ++ +         C +Cg C+  Cp+++
  gi|298675286|ref|YP_003727036.1|  92 CEGCRYCVDACLIGAIHMDAYGKAVV--------CKHCGVCASYCPRDV 132
                                       ******************99999988........9***********985 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.8    0.0014       1.7      41      64 ..       5      28 ..       1      31 [. 0.80
   2 !    8.5   1.9    0.0033         4       2      20 ..      60      80 ..      58      85 .. 0.86
   3 !   15.1   0.6   2.8e-05     0.033       2      21 ..      92     111 ..      91     116 .. 0.88
   4 !   18.0   0.4   3.4e-06    0.0041       2      30 ..     118     144 ..     117     149 .] 0.82

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0014
                           Fer4_16 41 laedeekckkqeaitgCdiCqdvC 64
                                      +++++ k  +q +++gC  C+ +C
  gi|298675286|ref|YP_003727036.1|  5 IIPKRIKVANQARCIGCYSCMLAC 28
                                      667777788899999999999999 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0033
                           Fer4_16  2 CgtCgk..CaevCPtnaikek 20
                                      C+ C    C  +CPt+a++ +
  gi|298675286|ref|YP_003727036.1| 60 CHACIDppCSRACPTGALTVR 80
                                      88888778*********9865 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 2.8e-05
                           Fer4_16   2 CgtCgkCaevCPtnaikekk 21 
                                       C +C+ C+++C  +ai++++
  gi|298675286|ref|YP_003727036.1|  92 CEGCRYCVDACLIGAIHMDA 111
                                       ****************9985 PP

  == domain 4  score: 18.0 bits;  conditional E-value: 3.4e-06
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearec 30 
                                       C+ Cg Ca+ CP ++++ +  k+ ++ e+
  gi|298675286|ref|YP_003727036.1| 118 CKHCGVCASYCPRDVLELR--KVGDNGEE 144
                                       ****************998..66666555 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   1.3   1.6e-06    0.0019       3      19 ..      12      28 ..      10      33 .. 0.90
   2 !    7.4   4.8     0.004       4.7       9      24 .]      60      77 ..      59      77 .. 0.83
   3 !   13.4   3.4   5.2e-05     0.062       7      24 .]      90     107 ..      88     107 .. 0.86
   4 !    9.5   4.1   0.00088         1       9      23 ..     118     132 ..     117     133 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.6e-06
                            Fer4_6  3 eidpdkCigCgdCvrvC 19
                                      + ++ +CigC+ C+ +C
  gi|298675286|ref|YP_003727036.1| 12 VANQARCIGCYSCMLAC 28
                                      57899************ PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.004
                            Fer4_6  9 CigC.gd.CvrvCPegai 24
                                      C  C ++ C r+CP+ga+
  gi|298675286|ref|YP_003727036.1| 60 CHACiDPpCSRACPTGAL 77
                                      66776667********97 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 5.2e-05
                            Fer4_6   7 dkCigCgdCvrvCPegai 24 
                                       d+C gC+ Cv++C  gai
  gi|298675286|ref|YP_003727036.1|  90 DLCEGCRYCVDACLIGAI 107
                                       9************77665 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.00088
                            Fer4_6   9 CigCgdCvrvCPega 23 
                                       C +Cg C++ CP ++
  gi|298675286|ref|YP_003727036.1| 118 CKHCGVCASYCPRDV 132
                                       ************765 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   9.2   1.2e-06    0.0014       4      58 ..      14      78 ..      11      79 .. 0.70
   2 !   11.1  10.4   0.00027      0.33       7      59 .]      62     109 ..      56     109 .. 0.80
   3 !    8.2   1.5    0.0023       2.8      41      56 ..     118     132 ..     111     135 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.2e-06
                           Fer4_21  4 dedkCigCgkCliaCedtshqaieidaktvl.........kvvedeCvGC..nlCssvCPvedcie 58
                                      ++++CigC +C++aC  t ++ ++++++++            v+  C +C    Cs  CP+ ++++
  gi|298675286|ref|YP_003727036.1| 14 NQARCIGCYSCMLACARTYYDTVSLKNSAIDiqtkggieeGFVSIVCHACidPPCSRACPT-GALT 78
                                      789******************9955544322223333343456778888843469*****6.7665 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00027
                           Fer4_21   7 kCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59 
                                        Ci+   C  aC+   + a+++ +   + + +d C GC  C++ C + ++i+m
  gi|298675286|ref|YP_003727036.1|  62 ACID-PPCSRACP---TGALTVRKGGGVILHNDLCEGCRYCVDACLI-GAIHM 109
                                       4444.35889999...577888888888899**************98.99998 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0023
                           Fer4_21  41 CvGCnlCssvCPvedc 56 
                                       C  C +C+s CP  d+
  gi|298675286|ref|YP_003727036.1| 118 CKHCGVCASYCP-RDV 132
                                       888999999999.455 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5  12.4   9.9e-05      0.12       3      56 .]      12      73 ..      10      73 .. 0.73
   2 !    8.5  13.2    0.0018       2.2       8      55 ..      59     102 ..      55     103 .. 0.86
   3 !   13.4  13.3   5.4e-05     0.065       3      56 .]      86     129 ..      84     129 .. 0.87
   4 !   12.3   1.8   0.00012      0.14       8      24 ..     117     136 ..     111     148 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.9e-05
                           Fer4_10  3 vidddtCirCgkCvkaCPadl.......tsvgakgeaseeeavrk.kvekCtgcg..aCveaCP 56
                                      v ++ +Ci+C  C+ aC a          +++a++++++++ +++ ++  C++c    C +aCP
  gi|298675286|ref|YP_003727036.1| 12 VANQARCIGCYSCMLAC-A-RtyydtvsLKNSAIDIQTKGGIEEGfVSIVCHACIdpPCSRACP 73
                                      67899************.5.459**999455555555555555554777788886569999999 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0018
                           Fer4_10   8 tCirCg..kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                        C  C    C +aCP+     ga   +++++++ +  + C+gc +Cv+aC
  gi|298675286|ref|YP_003727036.1|  59 VCHACIdpPCSRACPT-----GALTVRKGGGVILH-NDLCEGCRYCVDAC 102
                                       588888779*******.....88888888888888.677*********** PP

  == domain 3  score: 13.4 bits;  conditional E-value: 5.4e-05
                           Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       ++  d C +C+ Cv+aC           +  ++    +k   C +cg C++ CP
  gi|298675286|ref|YP_003727036.1|  86 ILHNDLCEGCRYCVDAC----------LIGAIHMDAYGKAVVCKHCGVCASYCP 129
                                       67889************..........577777777778899***********9 PP

  == domain 4  score: 12.3 bits;  conditional E-value: 0.00012
                           Fer4_10   8 tCirCgkCvkaCPadl...t 24 
                                        C +Cg C + CP d+   +
  gi|298675286|ref|YP_003727036.1| 117 VCKHCGVCASYCPRDVlelR 136
                                       7************9554442 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   2.3   6.2e-06    0.0075       4      20 ..      12      28 ..       9      30 .. 0.90
   2 ?    1.1   6.0      0.42     5e+02      13      22 .]      63      74 ..      56      74 .. 0.72
   3 !   12.4   3.0   0.00011      0.13       8      20 ..      90     102 ..      85     102 .. 0.91
   4 !   14.8   1.8   1.8e-05     0.022       9      21 ..     117     129 ..     107     130 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.2e-06
                            Fer4_2  4 vvdtdrCigCgaCvsaC 20
                                      v++ +rCigC +C  aC
  gi|298675286|ref|YP_003727036.1| 12 VANQARCIGCYSCMLAC 28
                                      7899************* PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.42
                            Fer4_2 13 C..gaCvsaCPa 22
                                      C   +C  aCP+
  gi|298675286|ref|YP_003727036.1| 63 CidPPCSRACPT 74
                                      43249******7 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00011
                            Fer4_2   8 drCigCgaCvsaC 20 
                                       d C gC+ Cv+aC
  gi|298675286|ref|YP_003727036.1|  90 DLCEGCRYCVDAC 102
                                       78*********** PP

  == domain 4  score: 14.8 bits;  conditional E-value: 1.8e-05
                            Fer4_2   9 rCigCgaCvsaCP 21 
                                        C +Cg C s CP
  gi|298675286|ref|YP_003727036.1| 117 VCKHCGVCASYCP 129
                                       6************ PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   3.1   6.3e-05     0.075       1      14 [.      15      28 ..      15      32 .. 0.92
   2 ?    1.1   1.9       0.6   7.2e+02      10      17 .]      68      75 ..      59      75 .. 0.76
   3 !    9.2   3.3    0.0016       1.9       2      14 ..      90     102 ..      89     103 .. 0.92
   4 !   17.5   1.6   3.5e-06    0.0042       4      16 ..     118     130 ..     114     139 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.3e-05
                            Fer4_4  1 qerCigCgsCvaaC 14
                                      q rCigC sC+ aC
  gi|298675286|ref|YP_003727036.1| 15 QARCIGCYSCMLAC 28
                                      579*********** PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.6
                            Fer4_4 10 CvaaCPqg 17
                                      C +aCP+g
  gi|298675286|ref|YP_003727036.1| 68 CSRACPTG 75
                                      88999985 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0016
                            Fer4_4   2 erCigCgsCvaaC 14 
                                       + C gC+ Cv+aC
  gi|298675286|ref|YP_003727036.1|  90 DLCEGCRYCVDAC 102
                                       679********** PP

  == domain 4  score: 17.5 bits;  conditional E-value: 3.5e-06
                            Fer4_4   4 CigCgsCvaaCPq 16 
                                       C +Cg+C ++CP 
  gi|298675286|ref|YP_003727036.1| 118 CKHCGVCASYCPR 130
                                       9***********5 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.4       2.7   3.3e+03      69      76 ..      16      23 ..       7      35 .. 0.65
   2 !   24.5  11.2   1.9e-08   2.2e-05       5      75 ..      55     125 ..      51     133 .. 0.83
   3 ?    2.3   1.1      0.15   1.8e+02       9      27 ..     117     135 ..     109     148 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.7
                           Fer4_11 69 ekCdmcld 76
                                      ++C +c++
  gi|298675286|ref|YP_003727036.1| 16 ARCIGCYS 23
                                      45666654 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 1.9e-08
                           Fer4_11   5 flpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneetg..kvekCdmcl 75 
                                       f++  C+ C++ppC +++p++a++ ++  G V+l+++ ++ ++r +v+ac   ++ +++  +  +++ C +c+
  gi|298675286|ref|YP_003727036.1|  55 FVSIVCHACIDPPCSRACPTGALTVRK-GGGVILHNDLCE-GCRYCVDACLIGAIHMDAYGKavVCKHCGVCA 125
                                       78999*******************999.8889999999*8.***********999998754411445566665 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.15
                           Fer4_11   9 qCrhCleppCvasapse..ai 27 
                                        C+hC    C++ +p++   +
  gi|298675286|ref|YP_003727036.1| 117 VCKHCG--VCASYCPRDvlEL 135
                                       799*96..6999998874444 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   8.7    0.0039       4.6       1      59 [.      17      75 ..      17      77 .. 0.76
   2 !   12.6   1.3   0.00013      0.15       2      18 ..      92     108 ..      91     117 .. 0.83
   3 !   12.7   1.5   0.00012      0.14      42      60 ..     114     132 ..     104     133 .. 0.76
   4 !    9.9   3.2    0.0009       1.1      46      59 ..     118     131 ..     117     140 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0039
                           Fer4_17  1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCge..CerkCPqg 59
                                      rCi+C  C+ +C + +      k+ + +++   ++++e+  +   C+ C    C+r+CP g
  gi|298675286|ref|YP_003727036.1| 17 RCIGCYSCMLACARTYYDTVSLKNSAIDIQT--KGGIEEGFVSIVCHACIDppCSRACPTG 75
                                      7************988877777776666555..46666677777777775444******76 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00013
                           Fer4_17   2 CiqCgyClpeCpsyeay 18 
                                       C +C+yC+++C  ++++
  gi|298675286|ref|YP_003727036.1|  92 CEGCRYCVDACLIGAIH 108
                                       ***********988775 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 0.00012
                           Fer4_17  42 kaslCieCgeCerkCPqgl 60 
                                       ka  C +Cg C+++CP ++
  gi|298675286|ref|YP_003727036.1| 114 KAVVCKHCGVCASYCPRDV 132
                                       5667888888888888775 PP

  == domain 4  score: 9.9 bits;  conditional E-value: 0.0009
                           Fer4_17  46 CieCgeCerkCPqg 59 
                                       C +Cg C+++CP +
  gi|298675286|ref|YP_003727036.1| 118 CKHCGVCASYCPRD 131
                                       55555555555554 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   4.9   0.00064      0.76       5      66 .]      15      79 ..      12      79 .. 0.81
   2 !   12.9   2.1   0.00012      0.15       2      32 ..      86     117 ..      85     118 .. 0.88
   3 ?    5.4   1.0     0.026        31       8      20 ..     118     130 ..     116     145 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00064
                           Fer4_15  5 rdaCigcglCvaea....pevfeldedglasvllddgeiaegevpddeeeaaqe.AaraCPvdAIrv 66
                                      + +Cigc  C+ ++     + + l++  ++ + + +g i+eg+v    +++++    raCP++A++v
  gi|298675286|ref|YP_003727036.1| 15 QARCIGCYSCMLACartyYDTVSLKNSAID-IQT-KGGIEEGFVSIVCHACIDPpCSRACPTGALTV 79
                                      789***********7777666777777776.555.5889999**********973679******987 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00012
                           Fer4_15   2 vvDrdaCigcglCvaea.pevfeldedglasv 32 
                                        +  d+C+gc  Cv+++    + +d +g+a+v
  gi|298675286|ref|YP_003727036.1|  86 ILHNDLCEGCRYCVDAClIGAIHMDAYGKAVV 117
                                       56689************88899*******977 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.026
                           Fer4_15   8 CigcglCvaeape 20 
                                       C  cg+C+  +p+
  gi|298675286|ref|YP_003727036.1| 118 CKHCGVCASYCPR 130
                                       9**********74 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   4.6   0.00094       1.1       1      11 [.      18      28 ..      18      30 .. 0.96
   2 !    7.9   5.6    0.0054       6.5       1      15 []      60      76 ..      60      76 .. 0.83
   3 !    9.9   3.6    0.0013       1.5       1      15 []      92     106 ..      92     106 .. 0.93
   4 !    8.8   5.1    0.0028       3.3       1      14 [.     118     131 ..     118     132 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00094
                            Fer4_3  1 CtgCgaCvevC 11
                                      C+gC+ C+ +C
  gi|298675286|ref|YP_003727036.1| 18 CIGCYSCMLAC 28
                                      *********** PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0054
                            Fer4_3  1 CtgCg..aCvevCPvgA 15
                                      C+ C   +C ++CP+gA
  gi|298675286|ref|YP_003727036.1| 60 CHACIdpPCSRACPTGA 76
                                      88884468********9 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0013
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C gC+ Cv++C  gA
  gi|298675286|ref|YP_003727036.1|  92 CEGCRYCVDACLIGA 106
                                       99**99*****9887 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.0028
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       C +Cg C   CP +
  gi|298675286|ref|YP_003727036.1| 118 CKHCGVCASYCPRD 131
                                       9***********76 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   7.9   0.00078      0.93       3      64 ..      16      75 ..      14      76 .. 0.60
   2 ?    6.1   2.0     0.013        16       5      16 ..      92     103 ..      88     117 .. 0.75
   3 ?    8.7   2.6    0.0019       2.3       5      63 ..     118     130 ..     114     146 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00078
                            Fer4_8  3 ekCieCgaCqsaCp.....vlrrtk.khlldargeaaedvqeeqvleeeealwsCttcga..CtevCpvg 64
                                       +Ci+C  C+ aC      +++ ++     +++g+ +e                C++c    C+++Cp+g
  gi|298675286|ref|YP_003727036.1| 16 ARCIGCYSCMLACArtyydTVSLKNsAIDIQTKGGIEE-GF---------VSIVCHACIDppCSRACPTG 75
                                      58***********5433332222222333333333333.23.........34569999888899999986 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.013
                            Fer4_8   5 CieCgaCqsaCp 16 
                                       C +C +C +aC 
  gi|298675286|ref|YP_003727036.1|  92 CEGCRYCVDACL 103
                                       888888888884 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0019
                            Fer4_8   5 CieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63 
                                       C +Cg C s Cp                                               
  gi|298675286|ref|YP_003727036.1| 118 CKHCGVCASYCP----------------------------------------------R 130
                                       555566655555..............................................4 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.5    0.0013       1.5      77     109 ..      10      43 ..       5      48 .. 0.71
   2 ?    5.8   8.5     0.012        15      61      95 ..      63     102 ..      45     114 .. 0.73
   3 ?    3.8   1.8     0.052        62      60      75 ..     117     132 ..     106     140 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0013
                           Fer4_18  77 irkGlqleciscllcidacdkv.meklgkpkgli 109
                                       i+   q  ci c  c+ ac +   ++++++++ i
  gi|298675286|ref|YP_003727036.1|  10 IKVANQARCIGCYSCMLACARTyYDTVSLKNSAI 43 
                                       45567999***********864146666666655 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.012
                           Fer4_18  61 cidcescvkvcPtg.idirkG..lqle...ciscllcidac 95 
                                       cid   c + cPtg + +rkG  + l+   c  c  c+dac
  gi|298675286|ref|YP_003727036.1|  63 CID-PPCSRACPTGaLTVRKGggVILHndlCEGCRYCVDAC 102
                                       333.24889****8579**9844223234599********* PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.052
                           Fer4_18  60 dcidcescvkvcPtgi 75 
                                        c +c++c + cP ++
  gi|298675286|ref|YP_003727036.1| 117 VCKHCGVCASYCPRDV 132
                                       5999999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 927.82
//
Query:       gi|298675287|ref|YP_003727037.1|  [L=585]
Description: aldehyde ferredoxin oxidoreductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-66  224.4   0.0    2.7e-66  224.1   0.0    1.1  1  AFOR_C    Aldehyde ferredoxin oxidoreductase, domains 2 & 3
    7.9e-65  218.4   0.0    1.3e-64  217.8   0.0    1.3  1  AFOR_N    Aldehyde ferredoxin oxidoreductase, N-terminal doma


Domain annotation for each model (and alignments):
>> AFOR_C  Aldehyde ferredoxin oxidoreductase, domains 2 & 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.1   0.0     3e-70   2.7e-66       4     365 ..     226     584 ..     223     585 .] 0.91

  Alignments for each domain:
  == domain 1  score: 224.1 bits;  conditional E-value: 3e-70
                                       HHHHHHHHHSH.HHHHHHHH-GGGHHHHHHHTT---BTTTTBS--TTGGGGSHHHHHHHTEEEE.E-TT-SS--EEE CS
                            AFOR_C   4 kkiqkeiksspqvtaelrkyGTaelvnianetgalptknfqegtfekaekisgealeekylvknegCfsCpiaCgre 80 
                                       k++++++ +++  +++++++GT+  vn++ne +alpt+nfq+++fe ae+isge+l ++yl+++ +C++Cpi C ++
  gi|298675287|ref|YP_003727037.1| 226 KQLYHKVVNTD-LMEKYHDLGTTINVNVLNEINALPTRNFQQTYFEYAENISGENLGDNYLIRKLSCAGCPIGCIHV 301
                                       77889999999.667*************************************************99*********** PP

                                       EE.......ET....EE--.-HHHHHHHTGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHHHHHHHHHTTSS-HHH CS
                            AFOR_C  81 vkveegkk.vk....vegp.eyetlaalGsnlgiddleailklnelcdelGlDtisaGntiafamelyekGllkked 151
                                        + ++  +  +    ++ p +ye ++alG+nlg +++e +l+l ++c++ G+D is+G ++a+a e++ k+ ++ ++
  gi|298675287|ref|YP_003727037.1| 302 AMLKTLFSnSHdvevSDIPyDYELVYALGTNLGLKEPEDVLELIDTCERQGVDIISMGVILAWATEMSMKEKISTDE 378
                                       **9988875448887333359******************************************************** PP

                                       HTS----TT-THHHHHHHHHHHTT-T.THHHHTT-HHHHHHCTT-GGG--EETTEE--SS-GGG-HHHHHHHHH-TT CS
                            AFOR_C 152 tdglelefgdaeallellekiAkreg.igdllAeGvkrlaeklgaeelamhvkGlelpaydprgakgmalaYatsnr 227
                                       t g+ l++gd +++l++++ i k  + +   lAeGv  ++ek+g++++amh   le+p y      g  ++ +   r
  gi|298675287|ref|YP_003727037.1| 379 TMGVTLKWGDLNNFLRAVDLITKSPNeFYSALAEGVAVASEKYGGQDFAMHLGRLEVPGYHTGL--GNVVGLTAGVR 453
                                       ************************************************************9886..66666666666 PP

                                       SS-SGG.G-THHHHS---TT--HHHHHHHHHHHHHHHHHHHHT--GGGG-HHH......HHHHHHHHHT----HHHH CS
                            AFOR_C 228 GacHlr.aylialeekvdpletegkaelvkwfqdltalvdslglCkftseaeerldlelyakllsavtGidvteeel 303
                                         +H + +y +  +  +  l+ e+    ++   d++ +++sl++C+f++   + ++++ ++++l+   Gi+ +eeel
  gi|298675287|ref|YP_003727037.1| 454 HSHHDNaGYSADQKAFKSDLSDEEIIDQLIAEDDVRGVLNSLVICLFAR---KVYTPDVIVDALKP-LGIEKSEEEL 526
                                       66999988888888878889899**************************...789**********9.9********* PP

                                       HHHHHHHHHHHHHHHHHHT--HHHS---HHHHHS---SSTTTT---..-HHHHHHHHHHHHT CS
                            AFOR_C 304 lkaGeRiynleRlfnlreGltrkddtlperlleeplkegpakgkvledeleemldeyYelrG 365
                                       +++G  i+  +  +  + G++ ++ +lp+r++e + ++g  +    ++++e +l+ y + rG
  gi|298675287|ref|YP_003727037.1| 527 DRIGTEIFMKKYELKQKFGFNLDNVKLPKRFFETASTNGIID----KERVENALEIYKNKRG 584
                                       ********************************7777777666....4558888887766666 PP

>> AFOR_N  Aldehyde ferredoxin oxidoreductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.8   0.0   1.4e-68   1.3e-64       2     197 ..      11     209 ..      10     210 .. 0.96

  Alignments for each domain:
  == domain 1  score: 217.8 bits;  conditional E-value: 1.4e-68
                                       EEEEEETTTTEEEEEE--HHHHHHH-SCHHHHHHHHHHHS-TTS-TTSTTS-EEEEE-TTTTSSSTTB-EEEEEEE- CS
                            AFOR_N   2 kilrvdLstgkieveelpeelaekylGgrglaakllldevppgvdplspenplvfatGpltgtpapgsgrlvvvaks 78 
                                       ++l++dL++++ +  + p +l+++y+Gg+g+a++ll +  +++ d+l+ e p+vf++Gp++g+ +p+++++v++++s
  gi|298675287|ref|YP_003727037.1|  11 NVLYIDLTNETSKLVQRP-DLFDRYIGGTGVATQLLDEGFREDKDALDTEAPIVFSIGPFSGI-YPCCTKAVAMFRS 85 
                                       69**************99.79*****************************************9.************* PP

                                       TTTSSEEEEEEETCHHHHHHHCT-SEEEEES--SS-EEEEEETTEEEEEE-TTTTTS.-HHHHHHHHHH....HHTS CS
                            AFOR_N  79 PltgtlgesnaGgrfgaelkraGydaivieGkaekpvylvieddkveiedaedlwgl.dtyettealke....elgd 150
                                       Pltg+lges+aGgr+++++++aGyd ivi+Gka++pvyl+++d++++++da+++wgl +t ++ + l++    +  +
  gi|298675287|ref|YP_003727037.1|  86 PLTGELGESYAGGRIATAMRFAGYDSIVITGKAKRPVYLSLHDGNITFKDATSIWGLsSTVDVGKILRDaepySG-R 161
                                       ********************************************************99999*******9766333.3 PP

                                       .EEEEE-HHHHTT-TTB-E.EETTEEE-SSSHHHHHHHTTEEEEEEE- CS
                            AFOR_N 151 .kvaviGpaGenlvrfAsisvddgraagrgGlGavmgsKnlkaivvrg 197
                                        +++ iGpaGe++v++A+++vd++r++gr GlGav+gsKnlkaiv++g
  gi|298675287|ref|YP_003727037.1| 162 rSIIRIGPAGEKGVKYANVNVDTYRHFGRLGLGAVFGSKNLKAIVLSG 209
                                       5999*****************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (585 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 3701.03
//
Query:       gi|298675288|ref|YP_003727038.1|  [L=312]
Description: tetrahydromethanopterin S-methyltransferase subunit MtrH [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   9.1e-123  409.1   0.5   1.1e-122  408.8   0.5    1.0  1  MtrH         Tetrahydromethanopterin S-methyltransferase MtrH
  ------ inclusion threshold ------
      0.012   14.4   0.0       0.22   10.2   0.0    2.0  2  CdhD         CO dehydrogenase/acetyl-CoA synthase delta subun
      0.041   13.5   0.1      0.076   12.7   0.1    1.3  1  Pterin_bind  Pterin binding enzyme


Domain annotation for each model (and alignments):
>> MtrH  Tetrahydromethanopterin S-methyltransferase MtrH subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  408.8   0.5  1.9e-126  1.1e-122       1     296 [.       6     298 ..       6     300 .. 0.98

  Alignments for each domain:
  == domain 1  score: 408.8 bits;  conditional E-value: 1.9e-126
                              MtrH   1 keqkvleiaGvkiGGqpGeyPtvlvgtifyakhkivedekkGifdkeaaealikkqeelsdktGnPalvqvvGetee 77 
                                       keq++++iaGvk+GGqpGe Ptvl+gtify +hki+++e +G fdk+aae+l++ qe  sd+tGnP+++++ G+t+e
  gi|298675288|ref|YP_003727038.1|   6 KEQEIVNIAGVKVGGQPGELPTVLAGTIFYRGHKIIKNESRGTFDKNAAETLVNIQETNSDETGNPHMLHIYGTTPE 82 
                                       79*************************************************************************** PP

                              MtrH  78 aivkyidfvadvtdaPllidstsaevklaaakyatevGladrviynsinasiedaeiealkesdveaaivlafnpmd 154
                                        + +yidf++++tdaP++ids+++ev+  a +y+tevGl+d++iyns+n+si ++e +alk+sdv ++i+l+fn+ d
  gi|298675288|ref|YP_003727038.1|  83 NVCNYIDFISEITDAPFIIDSSETEVRKKALEYVTEVGLSDKTIYNSVNMSISKDEEQALKNSDVFSSIILGFNAID 159
                                       ***************************************************************************** PP

                              MtrH 155 ptvegklkileegegtaekgllelaeeaGiekplidvavtplgsgagaavkaslavkaklGlPvGsgihnvpsaWdw 231
                                        ++eg++kile+g+g++++glle+ae++Gi++ ++d  +tp+g+gag+a++ + +vkak+G+P+Gsgihn+ps+W+w
  gi|298675288|ref|YP_003727038.1| 160 SSMEGRMKILENGGGAIDRGLLEIAEDCGISNIMVDPSITPMGNGAGIALRMTANVKAKWGYPTGSGIHNAPSSWNW 236
                                       ***************************************************************************** PP

                              MtrH 232 lrefkkkekekaaeyevadvganlvqvilgsdfvlyGPienakkvfPavamvdilikeaakelgv 296
                                       l+e  kk   +   y+++d+++  +q+++++dfvlyGPiena  +fP+ am di+++ea+  +g+
  gi|298675288|ref|YP_003727038.1| 237 LKEQGKKD--PLV-YRMCDISSTCMQQMATGDFVLYGPIENAPYTFPVAAMGDIMVSEASAGIGT 298
                                       **987764..444.78*******************************************998887 PP

>> CdhD  CO dehydrogenase/acetyl-CoA synthase delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   3.7e-05      0.22      74     119 ..      73     117 ..      46     128 .. 0.89
   2 ?    2.0   0.0     0.011        67     166     192 ..     185     211 ..     177     218 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 3.7e-05
                                       EEE--SSST.HHHHHHHHHHHCC--SEEEEE-SSHHHHHHHHTTTC CS
                              CdhD  74 airlistdPakkfakavekvakavkvplvlggsdpevlkaalevve 119
                                        ++  +t P +++ + ++ +++ ++ p+++ +s+ ev k+ale v 
  gi|298675288|ref|YP_003727038.1|  73 MLHIYGTTP-ENVCNYIDFISEITDAPFIIDSSETEVRKKALEYVT 117
                                       578889999.9********************************986 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.011
                                       HCTT---EEEE---SH.....HHHHHH CS
                              CdhD 166 lkagvkdivldPttaalGegleetidn 192
                                        ++g+ +i++dP  +++G+g   ++  
  gi|298675288|ref|YP_003727038.1| 185 EDCGISNIMVDPSITPMGNGAGIALRM 211
                                       4599***********999987666554 PP

>> Pterin_bind  Pterin binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   1.3e-05     0.076      60     175 ..      83     200 ..      78     217 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.3e-05
                                       HHHHHHHHHHHHCTSEEEEE-S-HHHHHHHHHT.......TSEEEEETTTTS.SSTTHHHHHHHHT-EEEEESECSS CS
                       Pterin_bind  60 rvvpvlealrdeadvpisiDttkaevaeaAlka.......gadivNdvsgee.rdpkmlelvaeagaavvvmhmrgt 128
                                        v++ ++ +++ +d p  iD++++ev ++Al+         ++i N+v++   +d++ +    +    +++ ++   
  gi|298675288|ref|YP_003727038.1|  83 NVCNYIDFISEITDAPFIIDSSETEVRKKALEYvtevglsDKTIYNSVNMSIsKDEEQALKNSDVFSSIILGFNA-- 157
                                       6899999999999*******************9888877667899999998755555554444444455555555.. PP

                                       TTTHCCCCCCCSSHHHHHHHHHHHHHHHHHHTT--GGGEEEETTTTS CS
                       Pterin_bind 129 pktmqeeegqyedvveeveaflearveaaeeaGvaperillDpgigf 175
                                           +  eg+ + +++   a  +  +e ae  G+   +i++Dp i +
  gi|298675288|ref|YP_003727038.1| 158 --IDSSMEGRMKILENGGGAIDRGLLEIAEDCGIS--NIMVDPSITP 200
                                       ..333334555555566666666666777777774..4777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 1880.24
//
Query:       gi|298675289|ref|YP_003727039.1|  [L=224]
Description: hypothetical protein Metev_1387 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-32  111.5  10.4    4.6e-32  111.0  10.4    1.3  1  PrsW-protease    PrsW family intramembrane metalloprotease


Domain annotation for each model (and alignments):
>> PrsW-protease  PrsW family intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.0  10.4   2.6e-36   4.6e-32       1     191 [.      31     199 ..      31     218 .. 0.85

  Alignments for each domain:
  == domain 1  score: 111.0 bits;  conditional E-value: 2.6e-36
                     PrsW-protease   1 eplwlllaaflwgalvavllalllntvlqallraelgkfiaeflaaflvaglvEEllKalgvllllllrrrefdepl 77 
                                       ep+++++++f+ gal +v++a++++++l +++         ++++ ++vag+vEE++K++ + + +  + +++d+++
  gi|298675289|ref|YP_003727039.1|  31 EPKRYVILTFIYGALNSVIIAMFFEQLLFQFI-------PRTIFSIAIVAGVVEEITKGYIIRIPY--KAKQMDGIM 98 
                                       79***********************9999766.......567999*****************9987..9******** PP

                     PrsW-protease  78 dGivygaavglGFavlEnllYyvqalpsaanegqlgglqllilRillsvagHalftallGiglglaksrrraarrvq 154
                                       dG+vyg+a+glGFa++EnllY +             g+++ + R+ll + +H ++ta++G+g+gl ++++      +
  gi|298675289|ref|YP_003727039.1|  99 DGVVYGVAAGLGFAATENLLYGF-----------GFGVGISVQRALLTPIAHGVWTATIGVGYGLKAENKL----KL 160
                                       **********************7...........258999*************************994443....35 PP

                     PrsW-protease 155 illlglllavllHalwNllasl.aelllav.vgvllyvp 191
                                        l+  +++a+ lH+lwN+ a l  ++   + v +ll+++
  gi|298675289|ref|YP_003727039.1| 161 PLIYFFFAAISLHFLWNYFALLsRDIPILFsVVILLILF 199
                                       55566788999********99944443333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1442.88
//
Query:       gi|298675290|ref|YP_003727040.1|  [L=199]
Description: tetrahydromethanopterin S-methyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-56  189.4   0.1    4.9e-56  189.1   0.1    1.0  1  MtrA      Tetrahydromethanopterin S-methyltransferase, subuni


Domain annotation for each model (and alignments):
>> MtrA  Tetrahydromethanopterin S-methyltransferase, subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.1   0.1   2.7e-60   4.9e-56       2     169 ..       5     167 ..       4     170 .. 0.93

  Alignments for each domain:
  == domain 1  score: 189.1 bits;  conditional E-value: 2.7e-60
                                       ----TTSS-S--S-EE--TT-SEEEE-TT-SS-HHHHHHCT-SEEE----TTHHHHHHHHHHHT-TT--EEEEEE-- CS
                              MtrA   2 kepaegWPvvkGdyevGdaespvavvtlgshleeeavleaGaaiaGplktenlGiekvvanvisnpnirflivtGae 78 
                                       k+ a++WPvvkGdy+vG++es + vvtl+s +e+++     a++ G++ktenlG ek+++n++sn+nirf++++G e
  gi|298675290|ref|YP_003727040.1|   5 KRIADDWPVVKGDYTVGNPESRIVVVTLASSIESNPE----ACLWGTCKTENLGAEKLITNIVSNSNIRFVLLCGGE 77 
                                       56799*****************************998....9*********************************** PP

                                       -TTT-HHHHHHHHHHH-B-TTSBBTT--SSS-B-SSS-HHHHHHHHHH-EEEEEET---HHHHHHHHHHHHHT---- CS
                              MtrA  79 vkGhitGqalkalhenGvdkekkivgakGaiPfienlteeaverfqeqvelvdlidtedvgaikakikelvakdpga 155
                                        +Gh++G+++ +lh+nGvd +++i+g++GaiPf+en+++ a++rf++qve++d i+  d + +  +i +  +   +a
  gi|298675290|ref|YP_003727040.1|  78 SRGHLSGHTILKLHKNGVDGKGRIIGSEGAIPFVENIPRIAIQRFRNQVEVIDCIGETDSEVL-GNIVDTYKDKRDA 153
                                       *******************************************************98887655.566667777789* PP

                                       -SS-------XXXX CS
                              MtrA 156 feeeplvievkeee 169
                                       ++eep++++ k ++
  gi|298675290|ref|YP_003727040.1| 154 YNEEPVLVTSKSRK 167
                                       ******99877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1328.03
//
Query:       gi|298675291|ref|YP_003727041.1|  [L=280]
Description: methanogen marker protein 4 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0002   20.8   0.2      0.095   12.0   0.0    2.3  3  PTA_PTB   Phosphate acetyl/butaryl transferase
  ------ inclusion threshold ------
       0.15   11.9   1.3        0.3   11.0   1.3    1.4  1  DUF2972   Protein of unknown function (DUF2972)


Domain annotation for each model (and alignments):
>> PTA_PTB  Phosphate acetyl/butaryl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.2   0.00056         5       5      71 ..      11      73 ..       7      79 .. 0.66
   2 !   12.0   0.0   1.1e-05     0.095     110     205 ..      81     171 ..      73     191 .. 0.88
   3 ?   -3.3   0.0      0.49   4.4e+03     270     315 ..     225     270 ..     221     274 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.00056
                                      HHHHHHCTS--EEEES.-TTSHHHHHHHHHHHHTTSSEEEEES-HHHHHHHHHHCTB--TT.-EEE-TT CS
                           PTA_PTB  5 rivekakkekkrivlp.egedervlkAakelleegiadviLigdeaeikakaleldldlsg.ieivdpe 71
                                       + +ka ++k+r+++  +  + ++l + k+++++g a+++++g +++i++  +e        ieivd  
  gi|298675291|ref|YP_003727041.1| 11 IVEKKAIENKARVAIGiNFLSTEILDSLKKAQDRGYANIVIVGCKKDIENLDSE------SnIEIVDTD 73
                                      45555557777777652446889********************55555542232......225555544 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 1.1e-05
                                       HHHHTTSSSEEEE-TTS-HHHHHHHHHHCT-B-TT----EEEEEEEET.TEEEEEESSSS-SS--HHHHHHHHHHHH CS
                           PTA_PTB 110 mlvklgeaDglvsGavnttadtlrpalqiiktkpgvklvSsvfimlle.drlllfaDcavnvnPtaeelaeialesa 185
                                       +l++++++D+ v G++++++     +l+ +kt+  ++ +  +++++++ +r ++fa + + +  +   ++e + +s+
  gi|298675291|ref|YP_003727041.1|  81 ELLASNDVDAAVRGNIKASK-----VLDYLKTLMDAEKLYRIALLQTNmGRPFFFAPVGIDEGNDLASKIEHVKKSI 152
                                       688999********998764.....57889999999999999*****99999************************* PP

                                       HHHHHCCSS--EEEEE-SSS CS
                           PTA_PTB 186 ktakalgeeeprvAlLSySt 205
                                       + ++++  ++p+v +LS   
  gi|298675291|ref|YP_003727041.1| 153 EHIRRFD-IDPEVGILSGGR 171
                                       *******.********9654 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 0.49
                                       HHHHHHHHHHHHCCTEEEEEEEEESBSS-EEE--TT--HHHHHHHH CS
                           PTA_PTB 270 eagnigykivqrlakaeaiGPilqGlakPvndlSrgasvedivnva 315
                                        +gn  ++++ +l + e iG  ++  +  + d+Sr+ ++ ++  ++
  gi|298675291|ref|YP_003727041.1| 225 ITGNLIFRTLVYLCGGEGIGAPVLTDEYVFVDTSRARKDFTKAIMI 270
                                       5788888888888888888877777777888888887765555554 PP

>> DUF2972  Protein of unknown function (DUF2972)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.3   3.3e-05       0.3      68     160 ..      22     111 ..       2     120 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.3e-05
                           DUF2972  68 rvyikkqaleedinltditkelfnkqkcfyeriiiyikkkdfeilkeneklleqvkeyllelieeLkkqkeiekkk. 143
                                       rv i +++l      t+i  +l ++q+  y +i+i+  kkd+e l  ++++     ++  + i eL + ++++ +  
  gi|298675291|ref|YP_003727041.1|  22 RVAIGINFLS-----TEILDSLKKAQDRGYANIVIVGCKKDIENLDSESNIEIVDTDNPEKSICELLASNDVDAAVr 93 
                                       3333344444.....78899999999***********************9888888999999****99999998752 PP

                           DUF2972 144 .klsekdvLeylkkhkkv 160
                                        +++ + vL+ylk+  ++
  gi|298675291|ref|YP_003727041.1|  94 gNIKASKVLDYLKTLMDA 111
                                       269999******997766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1953.15
//
Query:       gi|298675292|ref|YP_003727042.1|  [L=33]
Description: hypothetical protein Metev_1390 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (33 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       141  (0.00786435); expected 358.6 (0.02)
Passed bias filter:                      127  (0.0070835); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.40
# Mc/sec: 246.76
//
Query:       gi|298675293|ref|YP_003727043.1|  [L=383]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-28   98.1   2.4    8.8e-28   96.9   2.4    1.6  1  OrfB_IS605      Probable transposase
      6e-24   83.8   0.4    1.2e-23   82.7   0.4    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    4.8e-21   74.0   2.1    9.3e-20   69.8   1.4    2.5  2  HTH_OrfB_IS605  Helix-turn-helix domain
  ------ inclusion threshold ------
      0.015   15.1   4.7       0.37   10.6   2.1    2.4  2  Phage_GP20      Phage minor structural protein GP20
      0.024   14.8   0.3      0.066   13.4   0.3    1.7  1  zf-piccolo      Piccolo Zn-finger
      0.098   12.5   2.8       0.49   10.2   0.6    2.3  2  LemA            LemA family
        1.7    8.4   8.1      0.067   13.0   1.2    2.1  3  DASH_Spc34      DASH complex subunit Spc34


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.9   2.4   3.4e-31   8.8e-28       9     117 ..     176     284 ..     166     286 .. 0.93

  Alignments for each domain:
  == domain 1  score: 96.9 bits;  conditional E-value: 3.4e-31
                        OrfB_IS605   9 e...lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhr 82 
                                       +   +++ ++n+++g+D+Gi+++a++++++   ++ ++r lk+  ++l+  +++l++k+k+s+ny+k + ++a++h+
  gi|298675293|ref|YP_003727043.1| 176 QlpqKQTFDQNNTVGVDVGIKDFAVTSDGE---KIDNPRYLKNSIERLKVLQKRLSRKKKGSNNYRKLKHQIAKYHE 249
                                       3444788899********************...******************************************** PP

                        OrfB_IS605  83 krsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       k++++r +++hkl+++li ++++v++e Lnv+++ 
  gi|298675293|ref|YP_003727043.1| 250 KIANQREDFQHKLSNKLISENQAVALECLNVKGLL 284
                                       ********************************986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.7   0.4   4.8e-27   1.2e-23       1      68 [.     298     367 ..     298     368 .. 0.98

  Alignments for each domain:
  == domain 1  score: 82.7 bits;  conditional E-value: 4.8e-27
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpay.TSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       ++++ ++leyka++yG++++++ ++  +Sk C++Cg+ nk  +l++r+++Cp+C++e+drD+nA++Ni k
  gi|298675293|ref|YP_003727043.1| 298 WSSFVQKLEYKAEWYGKNIIKIGRFDpSSKICHVCGYYNKGlELKDREWECPDCKTEHDRDINASVNIKK 367
                                       99******************************************************************87 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.8   1.4   3.7e-23   9.3e-20       1      47 []       9      54 ..       9      54 .. 0.98
   2 ?    2.0   0.0     0.059   1.5e+02      31      43 ..     335     347 ..     332     350 .. 0.90

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 3.7e-23
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeegk 47
                                      M lkaykyr yP++ Q+e++a+++G++Rf+YN+aL+ +++ ye+ gk
  gi|298675293|ref|YP_003727043.1|  9 M-LKAYKYRMYPNQIQQELIAKHIGACRFIYNWALENKIKSYEQDGK 54
                                      8.******************************************997 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.059
                    HTH_OrfB_IS605  31 YNkaLaerkeaye 43 
                                       YNk+L+ + + +e
  gi|298675293|ref|YP_003727043.1| 335 YNKGLELKDREWE 347
                                       ********99998 PP

>> Phage_GP20  Phage minor structural protein GP20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.011        27     113     137 ..      51      78 ..      22      87 .. 0.77
   2 ?   10.6   2.1   0.00014      0.37      32      90 ..     218     276 ..     205     283 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.011
                        Phage_GP20 113 edgelkg...LdeqikkLkesdkyLFee 137
                                       +dg+ +    L++qi  Lke++++L e 
  gi|298675293|ref|YP_003727043.1|  51 QDGKAISrfeLNKQIRVLKEDHEWLNEI 78 
                                       566665444499**********999873 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00014
                        Phage_GP20  32 eqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeyeakiadlkldnaielaLk 90 
                                       e+lk  +k L+  kk +++  +L+ qi+++ +k++++ ++ + k+++  +++    aL+
  gi|298675293|ref|YP_003727043.1| 218 ERLKVLQKRLSRKKKGSNNYRKLKHQIAKYHEKIANQREDFQHKLSNKLISENQAVALE 276
                                       6788889999999********************************99877766555555 PP

>> zf-piccolo  Piccolo Zn-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   2.6e-05     0.066      28      56 ..     326     354 ..     322     356 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.6e-05
                        zf-piccolo  28 kqvCnlCGFnptphltekkeWlclnCQtq 56 
                                       +++C +CG+  +    + +eW c  C t+
  gi|298675293|ref|YP_003727043.1| 326 SKICHVCGYYNKGLELKDREWECPDCKTE 354
                                       79*******999999999********985 PP

>> LemA  LemA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1     0.086   2.2e+02      36      82 ..      66     112 ..      44     116 .. 0.81
   2 ?   10.2   0.6   0.00019      0.49      58     108 ..     211     262 ..     199     271 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.086
                              LemA  36 evteaRakaaeaesveekaeaenqlssalsrllavaEnYPdLkanen 82 
                                       +v +  ++  ++ + ++ + a  +l++a+ +++     +P++k+++n
  gi|298675293|ref|YP_003727043.1|  66 RVLKEDHEWLNEINSQSLQGATLNLENAFTKFFREKSGFPKFKSKKN 112
                                       55555566678888999999************************987 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00019
                              LemA  58 nqlssalsrllavaEnY.PdLkanenfleLqeelegtEnriavaRrrYneav 108
                                       + l+++++rl +++ +   + k ++n+++L++++++  ++ia++R++++++ 
  gi|298675293|ref|YP_003727043.1| 211 RYLKNSIERLKVLQKRLsRKKKGSNNYRKLKHQIAKYHEKIANQREDFQHKL 262
                                       5667777777777666414557899**********************98765 PP

>> DASH_Spc34  DASH complex subunit Spc34
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.2       1.4   3.5e+03     170     199 ..      17      51 ..      15      84 .. 0.58
   2 ?   -1.9   0.0      0.91   2.3e+03      55      70 ..     136     155 ..     115     192 .. 0.63
   3 ?   13.0   1.2   2.6e-05     0.067     182     219 ..     232     269 ..     216     288 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.4
                        DASH_Spc34 170 kyplleake....kieelreeYe.elseeieelea 199
                                       +yp+++++e    +i + r  Y+  l+++i+++e+
  gi|298675293|ref|YP_003727043.1|  17 MYPNQIQQEliakHIGACRFIYNwALENKIKSYEQ 51 
                                       67777777755553333344443234444444443 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.91
                        DASH_Spc34  55 k....vekkpeRkDGkkgvl 70 
                                       k    +++ ++R DGk+   
  gi|298675293|ref|YP_003727043.1| 136 KigwiKTRLHRRFDGKQRTA 155
                                       15555667788999998654 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 2.6e-05
                        DASH_Spc34 182 elreeYeelseeieeleaeiaeQkkqLeaqnknesess 219
                                       + +++Y++l+++i++++++ia Q+++++++ +n+  s+
  gi|298675293|ref|YP_003727043.1| 232 KGSNNYRKLKHQIAKYHEKIANQREDFQHKLSNKLISE 269
                                       55789************************998876554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1573  (0.087735); expected 358.6 (0.02)
Passed bias filter:                      656  (0.0365888); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2930.60
//
Query:       gi|298675294|ref|YP_003727044.1|  [L=499]
Description: AAA ATPase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-10   41.0   0.7    9.7e-10   39.0   0.0    2.4  3  AAA              ATPase family associated with various cellul
    6.9e-07   29.4   0.0    3.2e-06   27.2   0.0    2.2  2  Rad17            Rad17 P-loop domain
    7.7e-05   23.0   0.1    0.00023   21.4   0.1    1.8  1  AAA_assoc_2      AAA C-terminal domain
    0.00023   21.5   0.0       0.54   10.5   0.0    2.9  2  AAA_22           AAA domain
    0.00028   19.9   0.1      0.017   14.1   0.0    2.3  2  AAA_6            Hydrolytic ATP binding site of dynein motor 
    0.00072   19.3   0.3      0.004   16.9   0.0    2.4  4  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0022   17.7   0.1     0.0041   16.9   0.1    1.4  1  AAA_30           AAA domain
     0.0028   18.0   0.0      0.024   15.0   0.0    2.4  2  AAA_16           AAA ATPase domain
     0.0045   17.0   0.3       0.04   14.0   0.0    2.5  3  AAA_14           AAA domain
     0.0088   16.3   0.4      0.017   15.4   0.4    1.5  1  Helitron_like_N  Helitron helicase-like domain at N-terminus
  ------ inclusion threshold ------
      0.023   13.9   0.0      0.067   12.3   0.0    1.7  2  DUF815           Protein of unknown function (DUF815)
      0.025   14.1   0.0      0.065   12.7   0.0    1.9  1  AAA_7            P-loop containing dynein motor region
       0.03   14.1   0.0        2.6    7.8   0.0    2.7  2  DEAD             DEAD/DEAH box helicase
      0.038   13.9   0.1       0.47   10.3   0.0    2.4  2  NACHT            NACHT domain
      0.048   13.0   0.0       0.14   11.5   0.0    1.8  1  IPT              Isopentenyl transferase
      0.063   13.0   0.1       0.67    9.6   0.1    2.4  3  TPP_enzyme_M_2   Middle domain of thiamine pyrophosphate
      0.074   13.0   0.1       0.39   10.7   0.0    2.2  2  AAA_5            AAA domain (dynein-related subfamily)
       0.12   12.0   0.1       0.67    9.5   0.0    2.1  2  AAA_25           AAA domain
        1.3    9.3  10.6        2.2    8.5   0.0    2.5  2  Hydin_ADK        Hydin Adenylate kinase-like domain
        2.7    8.6  10.7        6.3    7.4  10.7    1.6  1  Striatin         Striatin family


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.0   1.1e-12   9.7e-10       1      86 [.      46     127 ..      46     162 .. 0.78
   2 ?   -1.2   0.0       2.9   2.6e+03      64      94 ..     218     241 ..     148     264 .. 0.57
   3 ?   -2.6   0.0       7.8     7e+03      15      39 ..     414     438 ..     396     447 .. 0.60

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 1.1e-12
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS......TSEEEEEETGGGHH CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakeka......kpsilfiDEidala 71 
                                       v+l+G  G+GKT++a a+a+++g e++e+++s+ +      +++ i+++  +a++        ++  +++DE+d+l+
  gi|298675294|ref|YP_003727044.1|  46 VILHGRAGIGKTSTAYALANDFGWEVIELNASDQR------TAEVINKIAGSASKTGslfgsgGKRLIVLDEADNLH 116
                                       69*********************************......778888888777666668888778************ PP

                                       HHHTTCCCHHHHHHH CS
                               AAA  72 ksrsgseseeeervv 86 
                                       +++    ++ + r++
  gi|298675294|ref|YP_003727044.1| 117 GTN----DRGGARAI 127
                                       *99....22222222 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.9
                                       EETGGGHHHHHTTCCCHHHHHHHHHHHHHHH CS
                               AAA  64 iDEidalaksrsgseseeeervvnqLlteld 94 
                                       i+    +a+s+    ++ ee++ ++L + ++
  gi|298675294|ref|YP_003727044.1| 218 IE---DIATSQ----RDTEESIFKVLTKIFK 241
                                       22...222222....3445555555555555 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 7.8
                                       HHHHHHHHTHEEEEEETTTCSSSST CS
                               AAA  15 akavakelgvefleisgsellskyv 39 
                                        k + +++++ + ++s+++ +s y 
  gi|298675294|ref|YP_003727044.1| 414 LKNIHQKAESMVENFSAPDSFSTYS 438
                                       3555555566666666666665555 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   3.6e-09   3.2e-06       8      78 ..       6      75 ..       1     121 [. 0.86
   2 ?   -2.0   0.0       3.3     3e+03     100     150 ..     231     279 ..     189     283 .. 0.62

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 3.6e-09
                             Rad17  8 lWfekykPekaeelavhkkkieevkewlkadvLesrk.kriLLisGPsGCgkstvvkvLskelgiklrewln 78
                                      +W eky+P ++ ++   kk +e +k+w +   L++ + kr +++ G +G gk+ +   L+  +g +++e  n
  gi|298675294|ref|YP_003727044.1|  6 EWAEKYRPSTLSDVVGNKKALESLKKWAEE-WLDNVPeKRAVILHGRAGIGKTSTAYALANDFGWEVIEL-N 75
                                      7**************************875.566655167999***********************9984.3 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.3
                             Rad17 100 srflsqiesfkeleLkdakylklqklGddlrtdkklilv.edlPnkfyrdsd 150
                                       s f  + + fk   ++da +      G d   +  +  + e+lP +f+ + d
  gi|298675294|ref|YP_003727044.1| 231 SIFKVLTKIFKGHDINDALN---ATYGIDESPEDMVHWIdENLPAQFKHEID 279
                                       44555666666666666655...33444444444444441468888877765 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.1   2.5e-07   0.00023       2      55 ..     179     232 ..     178     245 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.5e-07
                                       XX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXX CS
                       AAA_assoc_2   2 ekklkleddalealaeladGDaRkaLnlLElaaeaaeakegkieitledleeal 55 
                                       +++++++d+ +e la+ +dGD+R+a+n L++a++ +e + ++i  ++ d ee++
  gi|298675294|ref|YP_003727044.1| 179 KEDINCDDESIEKLAQDSDGDVRSAINDLQAAVSGNELHIEDIATSQRDTEESI 232
                                       57899****************************999887666666666665554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0    0.0006      0.54       5      49 ..      43      78 ..      41      95 .. 0.76
   2 !    8.7   0.0    0.0022         2      73     105 ..      79     118 ..      70     144 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0006
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlps 49
                                      ++ ++++G +G+GKT ++  l++ +         + ev++ +++ 
  gi|298675294|ref|YP_003727044.1| 43 KRAVILHGRAGIGKTSTAYALANDF---------GWEVIELNASD 78
                                      67899*************9999988.........55555555544 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0022
                            AAA_22  73 lsseellealeqalrarav......ielliiDEaqhlr.s 105
                                       +++ e++++++  +++++       ++l+++DEa++l  +
  gi|298675294|ref|YP_003727044.1|  79 QRTAEVINKIAGSASKTGSlfgsggKRLIVLDEADNLHgT 118
                                       66777777777777777777888888***********541 PP

>> AAA_6  Hydrolytic ATP binding site of dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   1.9e-05     0.017      37      85 ..      48      96 ..      40      99 .. 0.89
   2 ?    3.4   0.0     0.035        31     238     305 ..     126     194 ..     106     203 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.9e-05
                             AAA_6 37 paGpagtGKtEtvkdLakalakqvvvfncsdqldykslgkifkGlaqsG 85
                                      ++G ag GKt t   La+ ++  v+ +n sdq +++ ++ki    +++G
  gi|298675294|ref|YP_003727044.1| 48 LHGRAGIGKTSTAYALANDFGWEVIELNASDQRTAEVINKIAGSASKTG 96
                                      68************************************99977666666 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.035
                             AAA_6 238 lllralrdvnlpk.lvaeDvplfkglisdlFpgvelpesdyeeleeaieevlkekklqleekfvekviq 305
                                        + ++++++  p  l+a+Dv   ++ i++   ++++++++++++ + +++++k+++++  ++ +ek+ q
  gi|298675294|ref|YP_003727044.1| 126 AISETIKKTDQPVvLIANDVYGVASSIRNQCLEIKFNNVQTRSIAASLKKICKKEDINCDDESIEKLAQ 194
                                       5556666666664277899999999999999999********************************988 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   4.5e-06     0.004       2      61 ..      12      71 ..      11      95 .. 0.92
   2 ?   -2.0   0.0         3   2.7e+03      56      84 ..     126     154 ..     124     160 .. 0.83
   3 ?   -2.8   0.0       5.3   4.8e+03      72     105 ..     197     233 ..     166     237 .. 0.55
   4 ?   -3.3   0.0       7.2   6.5e+03      73     105 ..     371     403 ..     353     405 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.5e-06
                            RuvB_N  2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvkl 61
                                      rP++l++ +g +k  e+lk   e       +   v+l+G  G+Gkt+ a  +a+++g ++
  gi|298675294|ref|YP_003727044.1| 12 RPSTLSDVVGNKKALESLKKWAEEWLDNVPEKRAVILHGRAGIGKTSTAYALANDFGWEV 71
                                      9*********************99999999999*********************998765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3
                            RuvB_N  56 elgvklkitsgPvlekagdlaalltnlee 84 
                                        +  ++k t  Pv+  a+d+ ++ +++++
  gi|298675294|ref|YP_003727044.1| 126 AISETIKKTDQPVVLIANDVYGVASSIRN 154
                                       56778999***********9999988876 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 5.3
                            RuvB_N  72 agdlaalltnlee...kdvlfideihrlsraveevly 105
                                        gd+ + +++l++   ++ l i++i   +r +ee ++
  gi|298675294|ref|YP_003727044.1| 197 DGDVRSAINDLQAavsGNELHIEDIATSQRDTEESIF 233
                                       3444444444442111455666666666666666655 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 7.2
                            RuvB_N  73 gdlaalltnleekdvlfideihrlsraveevly 105
                                       ++l+ + t+l ++d   +d    l+ +++e++y
  gi|298675294|ref|YP_003727044.1| 371 SNLTPVYTKLLKDDDYAVDITADLNLSLDELVY 403
                                       467777777777777777777777777777777 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   4.6e-06    0.0041      18     122 ..      43     141 ..      37     212 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.6e-06
                            AAA_30  18 drvavltGpAGtGKttalkalreaweaaggrvi.glAptgkaAkvLaeelgieastiakllkrlkgrarlepgtlli 93 
                                       +r ++l+G+AG GKt +  al++ +   g +vi + A+ ++ A+v+++ +g  as + +l  + +       ++l++
  gi|298675294|ref|YP_003727044.1|  43 KRAVILHGRAGIGKTSTAYALANDF---GWEVIeLNASDQRTAEVINKIAG-SASKTGSLFGSGG-------KRLIV 108
                                       5689***********9977765543...67777477999999999996666.6666667774443.......49*** PP

                            AAA_30  94 vDEagmv....dtkqlaallkaaekagakvilv 122
                                        DEa  +    d   ++a+ + ++k++  v+l+
  gi|298675294|ref|YP_003727044.1| 109 LDEADNLhgtnDRGGARAISETIKKTDQPVVLI 141
                                       ***977765557777888888888887777765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.7e-05     0.024       7      49 ..      24      68 ..      18     144 .. 0.76
   2 ?   -2.9   0.0       8.5   7.6e+03      95      95 ..     202     202 ..     153     250 .. 0.51

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.7e-05
                            AAA_16  7 eeleqLlsalervrsgrp..elvllsGesGvGKsslvrellrale 49
                                      + le L+   e + ++ p  ++v+l+G +G+GK+s + +l++ + 
  gi|298675294|ref|YP_003727044.1| 24 KALESLKKWAEEWLDNVPekRAVILHGRAGIGKTSTAYALANDFG 68
                                      556666666666667767779***************988887554 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 8.5
                            AAA_16  95 e 95 
                                       +
  gi|298675294|ref|YP_003727044.1| 202 S 202
                                       1 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   4.4e-05      0.04       2      78 ..      43     117 ..      42     144 .. 0.79
   2 ?   -2.6   0.0       5.9   5.3e+03      36      43 ..     182     189 ..     145     213 .. 0.62
   3 ?   -0.3   0.1       1.2     1e+03      68      88 ..     396     416 ..     351     463 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.4e-05
                            AAA_14   2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelilek...lke.ekktylflDEiq 74 
                                       ++++++ G   +GKT  ++ l+++      +++++n  d+r+++  ++  +     +    + +  +k++++lDE+ 
  gi|298675294|ref|YP_003727044.1|  43 KRAVILHGRAGIGKTSTAYALANDFG---WEVIELNASDQRTAEVINK--IAGSASKTgslF-GsGGKRLIVLDEAD 113
                                       6899******************9988...99********999876654..443333332323.1479********99 PP

                            AAA_14  75 evpe 78 
                                       ++ +
  gi|298675294|ref|YP_003727044.1| 114 NLHG 117
                                       9855 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.9
                            AAA_14  36 inldderd 43 
                                       in+dde+ 
  gi|298675294|ref|YP_003727044.1| 182 INCDDESI 189
                                       44455444 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.2
                            AAA_14  68 lflDEiqevpewekalkslvd 88 
                                       l lDE  ++++ +k+ k+l +
  gi|298675294|ref|YP_003727044.1| 396 LSLDELVYLTGSKKTTKRLKN 416
                                       555555555444444444333 PP

>> Helitron_like_N  Helitron helicase-like domain at N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.4   1.9e-05     0.017      34     130 ..     357     459 ..     299     478 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.9e-05
                   Helitron_like_N  34 kveeerlsflrknqkelraesltgeeLkealeeetedee.lkllgklvilpssvpgsprymqekrqdlmaivrelgk 109
                                       k+ +++ + +r+ +++l +  +t+  Lk+   + + +++ +  l++lv+l  s + + +  ++  q++ ++v ++ +
  gi|298675294|ref|YP_003727044.1| 357 KIAQHNYKSIRHVRSNL-TPVYTK-LLKDDDYAVDITADlNLSLDELVYLTGS-KKTTKRLKNIHQKAESMVENFSA 430
                                       44455555555555555.233333.4554444446667778999999999999.6777778999************* PP

                   Helitron_like_N 110 PdlFiTltcndkwpeikeel........r 130
                                       Pd F T++ + k ++ k++         +
  gi|298675294|ref|YP_003727044.1| 431 PDSFSTYSSSTKKTSSKKKNskldeskfN 459
                                       **********9976666655355544332 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   7.5e-05     0.067      20      87 ..       9      74 ..       2      95 .. 0.78
   2 ?   -3.2   0.0       4.2   3.7e+03     189     224 ..     158     193 ..     156     196 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.5e-05
                            DUF815 20 eevdevklddLvgidkqkealventeqfleglpan.nvLLwGarGtGKSslvkallneyaeegLrliev 87
                                      e++++ +l+d+vg +k  e+l++ +e++l++ p +  v+L G  G GK s+  al n++  e    ie+
  gi|298675294|ref|YP_003727044.1|  9 EKYRPSTLSDVVGNKKALESLKKWAEEWLDNVPEKrAVILHGRAGIGKTSTAYALANDFGWEV---IEL 74
                                      667788999999******************999762689****************99886554...444 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.2
                            DUF815 189 wlgFykldqeeYleiveklakklglelekeeleeeA 224
                                        + F++++ ++  + ++k++kk+++++++e++e+ A
  gi|298675294|ref|YP_003727044.1| 158 EIKFNNVQTRSIAASLKKICKKEDINCDDESIEKLA 193
                                       566777777777777777777777777777776655 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   7.3e-05     0.065      31     104 ..      41     108 ..      29     169 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.3e-05
                             AAA_7  31 knkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklekrrkgvygPpggkklvv 104
                                        +k+ v+l G +G GKt+++  l + +    + ++ +n s q +a+ + +i  s    ++++++g  ggk+l+v
  gi|298675294|ref|YP_003727044.1|  41 PEKRAVILHGRAGIGKTSTAYALANDFG---WEVIELNASDQRTAEVINKIAGSA--SKTGSLFGS-GGKRLIV 108
                                       67899********************999...**************9999987664..566677775.4555554 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.063        57       7      32 ..      36      61 ..      30      85 .. 0.83
   2 ?    7.8   0.0    0.0029       2.6     121     151 ..     103     133 ..      74     143 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.063
                                      HHHHHHTTCEEEEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  7 aiplilgggdvlvaaeTGsGKTlafl 32
                                       ++++ +++ v+++++ G GKT  + 
  gi|298675294|ref|YP_003727044.1| 36 WLDNVPEKRAVILHGRAGIGKTSTAY 61
                                      556677899*************8754 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0029
                                       TEEEEEEETHHHHHHTTTHHHHHHHHHHSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 121 qvrflVlDEadrlldqgfsdfinrilnqlpq 151
                                         r++VlDEad+l   + +   ++i +++++
  gi|298675294|ref|YP_003727044.1| 103 GKRLIVLDEADNLHGTNDRGGARAISETIKK 133
                                       4599**********99888888888888842 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00053      0.47       1      23 [.      44      66 ..      44      79 .. 0.86
   2 ?    0.4   0.0      0.59   5.2e+02      83     116 ..     105     134 ..      88     160 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00053
                                      SCEEEEC-TTTCHHHHHHHHHHH CS
                             NACHT  1 rlvilqGeaGsGKTtLlqklala 23
                                      r vil+G+aG+GKT  +  la +
  gi|298675294|ref|YP_003727044.1| 44 RAVILHGRAGIGKTSTAYALAND 66
                                      679***********999888765 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.59
                                       EEEEEE-STT-SS-TCH.........HHHHHCTT CS
                             NACHT  83 lLlilDglDelvtdlgqkekqpvrtlLselirkk 116
                                        L++lD +D l+  ++        + +se i+k+
  gi|298675294|ref|YP_003727044.1| 105 RLIVLDEADNLHGTNDR----GGARAISETIKKT 134
                                       589*********98877....6677777777774 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00016      0.14       4      32 ..      46      74 ..      43      82 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00016
                               IPT  4 ylifGatttGKtaeaiklaketgapvivl 32
                                       +++G  ++GKt++a +la++ g+ vi l
  gi|298675294|ref|YP_003727044.1| 46 VILHGRAGIGKTSTAYALANDFGWEVIEL 74
                                      5789***********************87 PP

>> TPP_enzyme_M_2  Middle domain of thiamine pyrophosphate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00075      0.67      29      69 ..      33      73 ..       6      87 .. 0.83
   2 ?   -0.1   0.0       0.7   6.2e+02      69     127 ..     279     339 ..     277     371 .. 0.69
   3 ?   -2.8   0.0       4.9   4.4e+03      95     119 ..     396     420 ..     388     443 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00075
                                      --TTHHHHTTSSEEEEE-B--HHHHHHHHHHHHHHT--EEE CS
                    TPP_enzyme_M_2 29 tkedwdrwrqkrGvvvaGrlsaeegkqvaawaeklGWpllt 69
                                      ++e +d++ +kr v++ Gr    +++   a+a+  GW ++ 
  gi|298675294|ref|YP_003727044.1| 33 AEEWLDNVPEKRAVILHGRAGIGKTSTAYALANDFGWEVIE 73
                                      4555688999***************************9986 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.7
                                       E-TTT-S--SSTTHHHHTTSHHHHH..HHTT-SEEEEESB---SHHHHHH..HHH---SEEEE CS
                    TPP_enzyme_M_2  69 tDvqsqlgqalpyaDlwLanpkvke..eLaqadiviqfGsrlvsKrllqf..laelkpeeyWl 127
                                        D++s+ g  l++aD++L   + ++  +L +   ++ +G+ +vs+   ++    +++p +yW 
  gi|298675294|ref|YP_003727044.1| 279 DDIKSGYG-YLSKADIYLGRVRNRQnyRLWRYANILMIGGMVVSRSQ-NYkgFIKFSPPSYWR 339
                                       57777665.58999999987666552257788888999999998653.331123566668884 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 4.9
                                       HTT-SEEEEESB---SHHHHHHHHH CS
                    TPP_enzyme_M_2  95 LaqadiviqfGsrlvsKrllqflae 119
                                       L+  ++v   Gs+ + Krl +  ++
  gi|298675294|ref|YP_003727044.1| 396 LSLDELVYLTGSKKTTKRLKNIHQK 420
                                       5556778888888888888765444 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00044      0.39       2      46 ..      46      89 ..      45     119 .. 0.68
   2 ?   -1.0   0.0       1.8   1.6e+03      49      79 ..     163     194 ..     132     244 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00044
                                      EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B- CS
                             AAA_5  2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrre 46
                                      v+L G  G+gK++ a  la  +++ev + + +++ t+e ++ ++ 
  gi|298675294|ref|YP_003727044.1| 46 VILHGRAGIGKTSTAYALANDFGWEVIELNASDQRTAE-VINKIA 89
                                      89***********************9998887766655.444444 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.8
                                       ........--------G-SEEEEES.GGG--H CS
                             AAA_5  49 ngttslvdsplvraaregeilvlDE.veraes 79 
                                       n +t+    +l++ +++ +i ++DE +e++ +
  gi|298675294|ref|YP_003727044.1| 163 NVQTRSIAASLKKICKKEDINCDDEsIEKLAQ 194
                                       66777777777777777777777774555544 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00074      0.67      25      54 ..      36      64 ..      10      67 .. 0.73
   2 ?   -0.9   0.0       1.1     1e+03     143     172 ..     104     134 ..      74     139 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00074
                            AAA_25 25 lvkgllpagelallaGapgtGKttlaldla 54
                                      +++++ p++  ++l G+ g GKt  a+ la
  gi|298675294|ref|YP_003727044.1| 36 WLDNV-PEKRAVILHGRAGIGKTSTAYALA 64
                                      33444.9*******************9998 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.1
                            AAA_25 143 vrlvviDplsralgg.densnsdvgalveal 172
                                        rl+v+D  + ++g  d   ++++++ +++ 
  gi|298675294|ref|YP_003727044.1| 104 KRLIVLDEADNLHGTnDRGGARAISETIKKT 134
                                       58999**999999997777777777777765 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0024       2.2       1      25 [.      45      69 ..      45      94 .. 0.90
   2 ?    1.3   7.5      0.41   3.7e+02      86     149 ..     416     482 ..     392     496 .. 0.36

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0024
                         Hydin_ADK  1 aiivhGaPlsGKtatavtLakkYea 25
                                      a+i+hG    GKt+ta +La  ++ 
  gi|298675294|ref|YP_003727044.1| 45 AVILHGRAGIGKTSTAYALANDFGW 69
                                      89******************99875 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.41
                         Hydin_ADK  86 kktselssaaeekaas....skiskkkktsvvsgkkkaesegaksqkqkekktsetaqissspplaap 149
                                       +  ++++s+ e+ +a+    +  s++kkts  ++++k + ++ + +++++++ts+t+   s+p  ++ 
  gi|298675294|ref|YP_003727044.1| 416 NIHQKAESMVENFSAPdsfsTYSSSTKKTSSKKKNSKLDESKFN-KNENTQTTSKTEDEPSQPVDQSE 482
                                       22222222222222223332222222223222222222222222.12222222223333444433333 PP

>> Striatin  Striatin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4  10.7     0.007       6.3      36     128 ..     403     492 ..     399     497 .. 0.50

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.007
                          Striatin  36 kLegerrgaenlkkdlvrrikmLEyalkqerakylkl.kegtsaakenkkkekeeeeaeeeekseeeskskekksak 111
                                        L g+++++++lk+ + +   m E+         +++ +++ts++k+n+k   +e + +++e++  +++sk+++  +
  gi|298675294|ref|YP_003727044.1| 403 YLTGSKKTTKRLKNIHQKAESMVENFSAPDSFSTYSSsTKKTSSKKKNSK--LDESKFNKNENT--QTTSKTEDEPS 475
                                       599**********************9998875433321333333332222..222222222222..22223333333 PP

                          Striatin 112 eslkkseaeeesesekr 128
                                       + +++se +e+++++k+
  gi|298675294|ref|YP_003727044.1| 476 QPVDQSEYNEKKSQDKS 492
                                       33333222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (499 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2327  (0.12979); expected 358.6 (0.02)
Passed bias filter:                      801  (0.0446762); expected 358.6 (0.02)
Passed Vit filter:                       120  (0.00669307); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.74u 0.30s 00:00:01.04 Elapsed: 00:00:00.46
# Mc/sec: 3238.57
//
Query:       gi|298675295|ref|YP_003727045.1|  [L=622]
Description: DNA topoisomerase VI subunit B [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-67  226.9   0.0    1.9e-67  226.0   0.0    1.4  1  Topo-VIb_trans  Topoisomerase VI B subunit, transducer
    8.4e-43  145.2   2.5    2.6e-42  143.6   1.0    2.3  2  Top6b_C         Type 2 DNA topoisomerase 6 subunit B C-termin
      9e-11   42.3   0.0    4.8e-10   39.9   0.0    2.1  2  HATPase_c       Histidine kinase-, DNA gyrase B-, and HSP90-l
      1e-07   31.9   0.0    2.3e-07   30.7   0.0    1.5  1  HATPase_c_3     Histidine kinase-, DNA gyrase B-, and HSP90-l
  ------ inclusion threshold ------
      0.012   14.4   0.0      0.023   13.5   0.0    1.4  1  FbpA            Fibronectin-binding protein A N-terminus (Fbp
      0.078   13.4   0.0        0.5   10.8   0.0    2.3  2  Ribosomal_S13   Ribosomal protein S13/S18


Domain annotation for each model (and alignments):
>> Topo-VIb_trans  Topoisomerase VI B subunit, transducer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  226.0   0.0   6.4e-71   1.9e-67       1     159 []     312     475 ..     312     475 .. 0.99

  Alignments for each domain:
  == domain 1  score: 226.0 bits;  conditional E-value: 6.4e-71
                    Topo-VIb_trans   1 PstdclspigeeliekglkkelkpefvaavtrkpkvyeghpfivEvgiayGGelekeekaeilRfaNrvPLlydega 77 
                                       P+t+clspige+l  kgl+ke++++f+a++tr+p+vy+g+pfivEvgiayGG+l+k++k++i+RfaNrvPLly++g+
  gi|298675295|ref|YP_003727045.1| 312 PPTNCLSPIGEKLTYKGLNKEFNVDFIATTTRSPSVYSGNPFIVEVGIAYGGDLPKDDKIDIMRFANRVPLLYQQGG 388
                                       99*************************************************************************** PP

                    Topo-VIb_trans  78 dvitkavksinwkrYkleq.....pedpvvvlvhvastkvPfksegKeaiadveeiekeiklalqevarkLkkylsk 149
                                       +v+t+av+si+wk+Y+l+q     p++p+v+lvhvast+vPf+se+K+aiad++ei++ei+l +++varkL++y+++
  gi|298675295|ref|YP_003727045.1| 389 CVTTHAVESIKWKQYGLNQpgggiPTGPAVILVHVASTNVPFTSESKDAIADIPEIKDEIELGIKDVARKLNRYINR 465
                                       ***************************************************************************** PP

                    Topo-VIb_trans 150 kekekeekek 159
                                       +   k+++ek
  gi|298675295|ref|YP_003727045.1| 466 QGTLKKRREK 475
                                       *999998876 PP

>> Top6b_C  Type 2 DNA topoisomerase 6 subunit B C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.32   9.7e+02      48      71 ..     222     245 ..     211     250 .. 0.89
   2 !  143.6   1.0   8.7e-46   2.6e-42       1     114 []     495     613 ..     495     613 .. 0.99

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.32
                                       EE--EES-----------EEE-SS CS
                           Top6b_C  48 elheilpaeieeaspeakvvemdn 71 
                                       ++++ lp  ++e+ p+++ +em+ 
  gi|298675295|ref|YP_003727045.1| 222 RVTDKLPKAPDEILPHPHGIEMGT 245
                                       699*******************95 PP

  == domain 2  score: 143.6 bits;  conditional E-value: 8.7e-46
                                       SSS---SHHHHHHHTT-EEEEEEE--SSS-.EEEEEEE---------EEE--EES-----------EEE-SSSEEE- CS
                           Top6b_C   1 dreepdidpvvArimgnvlvereveengdg.vevslkvkNfsdkkeefelheilpaeieeaspeakvvemdneydlk 76 
                                       dreepdi+pvvA+imgnvlv+r++++n+d+ vevs+++ N+++k++ef+lhe++p+ei++a+p++k++++++++d+k
  gi|298675295|ref|YP_003727045.1| 495 DREEPDINPVVAKIMGNVLVNRQFKRNEDNsVEVSIRIVNYANKSHEFDLHEMFPYEIKNANPDPKTTSLGDDFDYK 571
                                       8**************************************************************************** PP

                                       EEE---TT-EEEE----SS-GGGS--....B----------- CS
                           Top6b_C  77 WelsvsageskvleYsvdseaeeels....liveGveeekvT 114
                                       W+l++s+++skv++Ys+ s +++els    +++eG+e+e+vT
  gi|298675295|ref|YP_003727045.1| 572 WTLNISSNSSKVINYSIVSITDDELSrlpsVTIEGIEDELVT 613
                                       *****************************9***********9 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.0   1.6e-13   4.8e-10       4      88 ..      36     130 ..      33     182 .. 0.77
   2 ?   -1.0   0.0      0.84   2.5e+03      24      86 ..     203     279 ..     189     300 .. 0.55

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 1.6e-13
                                       HHHHHHHHHHHHHHHHHHSTTT...EEEEEEEEEE.TEEEEEEEESSSSSTTHHHTGTCS.TTCH.....HCSTCHT CS
                         HATPase_c   4 krLrqiisnlvdNavkfatkag...eieveikase.ddlvisveDnGiGipkedlkklfe.kfsq.....ddstkrg 70 
                                       + L   ++++vdNa+++a ++g   +i ++i+++  d+l + +eDnG+Gi +e+++k+f+          + +++rg
  gi|298675295|ref|YP_003727045.1|  36 RSLITTVKEAVDNALDAAEESGilpDILLQIERTGkDTLAVIIEDNGPGIVREQIPKVFAkL-LYgsrfhALKQSRG 111
                                       678899**********955555666778888863258*******************999953.33368877888888 PP

                                       STSSSHHHHHHHH.HHHHT CS
                         HATPase_c  71 gggtGlGlsivkk.lvelm 88 
                                       ++g G+++++  + l++ +
  gi|298675295|ref|YP_003727045.1| 112 QQGIGISAAVLYSqLTTGL 130
                                       9999998888877666633 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.84
                                       TTEEEEEEEEEE.TEEEE.EEEESSSSSTTHHHT.....GTCSTTCH.......HCSTCHT....STSSSHHHHHHH CS
                         HATPase_c  24 ageieveikase.ddlvi.sveDnGiGipkedlk.....klfekfsq.......ddstkrg....gggtGlGlsivk 82 
                                       +++ ++++  ++ +++v+ +v+D  +  p e+l+     +    + +        + +k+g    ++ + +Gl  ++
  gi|298675295|ref|YP_003727045.1| 203 NPHARLTLIEPDgNEIVFeRVTDKLPKAPDEILPhphgiE----MGTlmkmlryTERQKVGaflrYSFSKIGLNTAD 275
                                       4566677774334555556699999999999999555552....333222321222222222222444445555555 PP

                                       HHHH CS
                         HATPase_c  83 klve 86 
                                       ++++
  gi|298675295|ref|YP_003727045.1| 276 EICK 279
                                       5555 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   7.6e-11   2.3e-07       6      92 ..      41     132 ..      37     175 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 7.6e-11
                       HATPase_c_3   6 AlaelvdNsldAdaen.....vkievnknrgktgeivieDdGkGmseeelknal.rlatsskeakrkstslGkkGiG 76 
                                        + e vdN+ldA  e+     + +++++  ++t  + ieD+G G+ +e++ +++ +l   s+  +  ++s+G+ GiG
  gi|298675295|ref|YP_003727045.1|  41 TVKEAVDNALDAAEESgilpdILLQIERTGKDTLAVIIEDNGPGIVREQIPKVFaKLLYGSRF-HALKQSRGQQGIG 116
                                       689****************99777777766789*******************77589999988.5789********* PP

                       HATPase_c_3  77 lklAslslgkkltvit 92 
                                       +  A+l +  +  + t
  gi|298675295|ref|YP_003727045.1| 117 ISAAVLYSQLTTGLQT 132
                                       8888776555444444 PP

>> FbpA  Fibronectin-binding protein A N-terminus (FbpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   7.7e-06     0.023     179     238 ..     247     307 ..     225     341 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.7e-06
                                       HHHHHH.S.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH...............HHHHHHH CS
                              FbpA 179 kellsk.kekdlvkaLvkafqGlspllaeelleragldketsakelseedlerlyealqel 238
                                        + l+  + +++  +L  +f+ ++  +a e+++ agld e++ +e++  ++++l ea++++
  gi|298675295|ref|YP_003727045.1| 247 MKMLRYtERQKVGAFLRYSFSKIGLNTADEICKTAGLDFEKEPREITRLEAKKLLEAFSKV 307
                                       333333366899999******************************************9975 PP

>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00017       0.5      21      65 ..     267     311 ..     250     318 .. 0.84
   2 ?   -1.5   0.1         1     3e+03      61      87 ..     454     480 ..     433     498 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00017
                     Ribosomal_S13  21 kGiGrrkakiilkkadvdedkrigelteeeiekieeivenkaqyk 65 
                                       + iG ++a +i+k a++d +k  +e+t  e +k+ e  ++ + + 
  gi|298675295|ref|YP_003727045.1| 267 SKIGLNTADEICKTAGLDFEKEPREITRLEAKKLLEAFSKVKIMS 311
                                       569*******************************99999866555 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1
                     Ribosomal_S13  61 kaqykipnwinrqkdikdGkdshvven 87 
                                        +  k + +inrq  +k+ +++ v+ +
  gi|298675295|ref|YP_003727045.1| 454 DVARKLNRYINRQGTLKKRREKEVIIT 480
                                       244567788899988887777666544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (622 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.71u 0.35s 00:00:01.06 Elapsed: 00:00:00.53
# Mc/sec: 3542.13
//
Query:       gi|298675296|ref|YP_003727046.1|  [L=370]
Description: DNA topoisomerase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-13   49.1   0.1    8.9e-13   48.0   0.1    1.6  1  TP6A_N    Type IIB DNA topoisomerase


Domain annotation for each model (and alignments):
>> TP6A_N  Type IIB DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   0.1   4.9e-17   8.9e-13       5      61 ..      81     142 ..      77     143 .. 0.87

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 4.9e-17
                                       HHHHHHHHH.HHHHHTT--EEHHHHHHH....GGGS-SSHHHHHHHHHHHHHHHTS-GGGGT CS
                            TP6A_N   5 qllkvleli.helleegkvvTkRdiYYr....dvelFksQaesdrliddievllgvsReeLn 61 
                                       ++ k+++++ +++l +++ +T+R++YY      v++F++Q esd+l++d+e +++++Re ++
  gi|298675296|ref|YP_003727046.1|  81 KTSKTIDFVmNNHLGQNRGSTLRELYYIsenwGVAKFREQPESDKLVEDLEIITNLQREYFH 142
                                       566666666478999*************88777**************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 2177.32
//
Query:       gi|298675297|ref|YP_003727047.1|  [L=416]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.6e-26   90.7   0.6    2.4e-25   89.1   0.0    2.1  2  OrfB_IS605      Probable transposase
    2.9e-12   46.3   0.1    1.2e-11   44.4   0.0    2.1  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.011   16.2   0.0      0.022   15.1   0.0    1.5  1  RuvX            Holliday junction resolvase
      0.075   13.0   0.0       0.34   10.9   0.0    2.0  2  Bac_rhamnosid   Bacterial alpha-L-rhamnosidase concanavalin-l


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.2      0.55   2.5e+03      71      86 ..      16      31 ..       4      69 .. 0.67
   2 !   89.1   0.0   5.4e-29   2.4e-25      15     119 ..     192     294 ..     177     295 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.55
                        OrfB_IS605 71 kkasrklarlhrkrsr 86
                                       ++ +++++l++++++
  gi|298675297|ref|YP_003727047.1| 16 YEVLKRITKLSKNLYN 31
                                      3444444444444444 PP

  == domain 2  score: 89.1 bits;  conditional E-value: 5.4e-29
                        OrfB_IS605  15 gnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsrrrkhl 91 
                                        nk+++iDlG+nn+at+v+++gt+f+++gr lks +++++k +  lqs ++k++   k  +kl  l++kr+++++++
  gi|298675297|ref|YP_003727047.1| 192 YNKHLSIDLGVNNFATCVDTNGTAFIIEGRGLKSYNRWWNKVKSGLQSVYDKQG--IKSGQKLNWLFEKRKNKLNDF 266
                                       699**************************************************9..9******************** PP

                        OrfB_IS605  92 lhklathliktlkevgvetLnvgnmkdi 119
                                       +++ +++++k++ +++++++++g++kdi
  gi|298675297|ref|YP_003727047.1| 267 MNQSVNYIVKHCIDNNIGNIIIGELKDI 294
                                       *************************998 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       2.2   9.7e+03       9      23 ..     167     181 ..     166     182 .. 0.84
   2 !   44.4   0.0   2.7e-15   1.2e-11       1      69 []     313     387 ..     313     387 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.2
                    OrfB_Zn_ribbon   9 eykakeyGikveevn 23 
                                       +y  +++ i++++ +
  gi|298675297|ref|YP_003727047.1| 167 KYNGQWFEIEYVYRD 181
                                       688999999999876 PP

  == domain 2  score: 44.4 bits;  conditional E-value: 2.7e-15
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke......alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f+k+k++l+ k++ yGik++ev++ayTSkt +   +   +      ++ +r +  ++ g  +++Dvn+a+Nil++
  gi|298675297|ref|YP_003727047.1| 313 FGKFKQKLRSKCEYYGIKYIEVDEAYTSKTDALALEPIGKhrkymgKRVKRGLFQFSTGKLLNADVNGALNILRK 387
                                       89****************************876655444445568989999999999***************986 PP

>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   4.9e-06     0.022      36     111 ..     265     352 ..     243     363 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.9e-06
                                       H..HHHHHHHHHHHHHTT--EEEEE--......---..-SSS---SSTTHHHHHHHHHT....T-EEEEE--S---- CS
                              RuvX  36 k..ekdleelkelvkeeeveeiVvGlP......lnl..dgsegesakkvrkfaeeLakrl..kklpvelvDErlttv 100
                                       +  +++++ + + + ++++ +i++G         n+  +++++ ++  + kf ++L++++  ++++ + vDE +t++
  gi|298675297|ref|YP_003727047.1| 265 DfmNQSVNYIVKHCIDNNIGNIIIGELkdikqnSNMgkKNNQTFQTIPFGKFKQKLRSKCeyYGIKYIEVDEAYTSK 341
                                       14479999*****************88677777444114455555556699*******9977899***********9 PP

                                       XXXXXXXXXXX CS
                              RuvX 101 eaerilresgl 111
                                       + + +l+  g+
  gi|298675297|ref|YP_003727047.1| 342 TDALALEPIGK 352
                                       98777765554 PP

>> Bac_rhamnosid  Bacterial alpha-L-rhamnosidase concanavalin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       0.6   2.7e+03      28      69 ..     184     225 ..     172     232 .. 0.72
   2 ?   10.9   0.0   7.6e-05      0.34      51      90 ..     300     340 ..     280     350 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.6
                                       TT-EEEEEEESEE-TTS-EE-GGGTT---EEEEE----SSEE CS
                     Bac_rhamnosid  28 eGtevklrfgEvLeddgevdtrnlrkakatdeyilkGreeea 69 
                                       +G++v+l +   L  d  v++       +   +i++Gr+ ++
  gi|298675297|ref|YP_003727047.1| 184 NGEKVDLDYNKHLSIDLGVNNFATCVDTNGTAFIIEGRGLKS 225
                                       688888888888887766666656666677777888876655 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 7.6e-05
                                       G.TT---EEEEE----SSEEE--SS--EEEEEEEEES-SS- CS
                     Bac_rhamnosid  51 l.rkakatdeyilkGreeeawqpsftfhGfrYveieglade 90 
                                       + +k+++t + i  G+ +++ + + +++G +Y+e++++  +
  gi|298675297|ref|YP_003727047.1| 300 MgKKNNQTFQTIPFGKFKQKLRSKCEYYGIKYIEVDEAYTS 340
                                       34788999999************************998444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1075  (0.0599587); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 2410.23
//
Query:       gi|298675298|ref|YP_003727048.1|  [L=634]
Description: DNA gyrase subunit B [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-62  209.5   0.1    4.5e-62  208.6   0.1    1.5  1  DNA_gyraseB    DNA gyrase B
    1.1e-31  108.8   0.2    2.1e-31  107.9   0.2    1.5  1  DNA_gyraseB_C  DNA gyrase B subunit, carboxyl terminus
    3.4e-21   75.9   0.0    1.1e-20   74.2   0.0    2.0  1  HATPase_c      Histidine kinase-, DNA gyrase B-, and HSP90-li
    3.1e-17   62.7   0.0    9.2e-17   61.2   0.0    1.9  1  Toprim         Toprim domain
     0.0059   16.4   0.4      0.018   14.8   0.0    2.0  2  HATPase_c_3    Histidine kinase-, DNA gyrase B-, and HSP90-li


Domain annotation for each model (and alignments):
>> DNA_gyraseB  DNA gyrase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.6   0.1   1.3e-65   4.5e-62       1     173 [.     223     391 ..     223     392 .. 0.98

  Alignments for each domain:
  == domain 1  score: 208.6 bits;  conditional E-value: 1.3e-65
                       DNA_gyraseB   1 GlkdfveelnkdkkelikevlsvegekaveevievevalqwtssysenilsFvNniatpeGGtHvdgfksaltktln 77 
                                       G+ +fv++lnk+++++++e++++ege+  +    ve++lq+t+sy e ++sF+Nni+t+eGGtHv gfk+alt++ n
  gi|298675298|ref|YP_003727048.1| 223 GIVSFVKHLNKNRSPIHEEPIYFEGES--DG-TIVEISLQYTDSYGEYVYSFANNINTHEGGTHVIGFKTALTRVAN 296
                                       89*************************..77.99******************************************* PP

                       DNA_gyraseB  78 eyakkkkllkkkeekisgediregltavvsvkipepqFeGQTKekLgnsevksivekvvseeleafleenkeeakki 154
                                       +y++k+++ +k++ +++gedireglta++s kip+pqFeGQTK++Lgns+vk++ve++v+eel+++leen+++a++i
  gi|298675298|ref|YP_003727048.1| 297 DYIRKNEI-EKGNVRLTGEDIREGLTAIISAKIPDPQFEGQTKTRLGNSDVKGVVESLVTEELSRYLEENPKIANSI 372
                                       ******97.66666*************************************************************** PP

                       DNA_gyraseB 155 lekaveaakareaarkare 173
                                       ++ka++a++areaa++are
  gi|298675298|ref|YP_003727048.1| 373 IKKALSAKRAREAAKRARE 391
                                       *****************98 PP

>> DNA_gyraseB_C  DNA gyrase B subunit, carboxyl terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.9   0.2   5.7e-35   2.1e-31       2      63 .]     562     623 ..     561     623 .. 0.98

  Alignments for each domain:
  == domain 1  score: 107.9 bits;  conditional E-value: 5.7e-35
                     DNA_gyraseB_C   2 kkveiqRfKGLGEmnpeqLweTTmdpetRrLlqvtiedaeeadelfstLmGkkvepRrefie 63 
                                       k+v+iqR+KGLGEmnpeqLw TTm+pe+R+L qvt+eda++ade+fs+LmG++vepRr+fie
  gi|298675298|ref|YP_003727048.1| 562 KGVSIQRYKGLGEMNPEQLWATTMNPESRKLTQVTMEDAAAADEMFSILMGEEVEPRRQFIE 623
                                       789**********************************************************8 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.2   0.0   3.1e-24   1.1e-20       2     111 ..      33     175 ..      32     176 .. 0.89

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 3.1e-24
                                       HHHHHHHHHHHHHHHHHHH..HSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHT..............GTCSTTC CS
                         HATPase_c   2 dekrLrqiisnlvdNavkf..atkageieveikaseddlvisveDnGiGipkedlk..............klfekfs 62 
                                       d+++L++++ ++vdN++++  a++++ei   ++  + d +++ eD+G+Gip++ +               + ++kf+
  gi|298675298|ref|YP_003727048.1|  33 DSRGLHHLVYEVVDNSIDEalAGYCSEINTILN--S-DGSVTLEDDGRGIPVDTHAkynksalevvmtllHAGGKFD 106
                                       899****************76669999999999..6.9******************************777777*** PP

                                       HHCSTCHTSTSSSHHHHHHHHHHHHTTTEEEE.....................EEETTTEEEEEEEEESS CS
                         HATPase_c  63 qddstkrggggtGlGlsivkklvelmgGeiwv.....................esepgrGttftftlple 111
                                       + +s+k++gg +G+G+s+v+ l+e ++ e+++                      +++g Gt+ftf+++ e
  gi|298675298|ref|YP_003727048.1| 107 K-NSYKVSGGLHGVGVSVVNGLSEWLDVEVKRddkryyqhyekgypktevqvlGESEGNGTKFTFKPDSE 175
                                       *.**********************98888888888888888777777666666666688*******9976 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2   0.0   2.6e-20   9.2e-17       1     102 [.     420     531 ..     420     532 .. 0.88

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 2.6e-20
                                       EEEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHS.TTEEEEE..ECTTTHHHHHH.....HHHHHHHHSEEEEE CS
                            Toprim   1 elvivEgpsdaktiakalgsgfqavtaslGhildlet.efkpvye..eiedkkkvlka.....lkelakradeiila 69 
                                       e+++vEg+s+ ++++  +++ fqa+++ +G+i+++e+ ++++v++  ei + ++++++     ++ ++ r++++i++
  gi|298675298|ref|YP_003727048.1| 420 EIFLVEGDSAGGSAKMGRDRRFQAILPFRGKIINVEKaRLSKVLKnnEILSLITAMGTgigedFDINKARYHKVIIM 496
                                       699**********************************8777777788777777888779999*************** PP

                                       CSSSHHHHHHHHHHHHHHTHHHTT..TEEEEEESS CS
                            Toprim  70 tDpDreGeaiawellevlkellen..kigrvefse 102
                                       tD+D++G +i++++l+++ ++ ++  + g+v++++
  gi|298675298|ref|YP_003727048.1| 497 TDADVDGAHIRTLILTFFFRYMNEmvDNGYVYIAQ 531
                                       *****************996555544448887775 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   5.1e-06     0.018       7      50 ..      41      84 ..      36     146 .. 0.81
   2 ?   -2.6   0.1       1.3   4.6e+03      58      75 ..     547     564 ..     541     567 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.1e-06
                       HATPase_c_3  7 laelvdNsld.AdaenvkievnknrgktgeivieDdGkGmseeel 50
                                      + e+vdNs+d A a +++ e+n+  +++g+++ eDdG G++ ++ 
  gi|298675298|ref|YP_003727048.1| 41 VYEVVDNSIDeALAGYCS-EINTILNSDGSVTLEDDGRGIPVDTH 84
                                      89********87777765.6666667789***********97754 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.3
                       HATPase_c_3  58 tsskeakrkstslGkkGi 75 
                                       +++ke++ k + lG+kG+
  gi|298675298|ref|YP_003727048.1| 547 HTEKEKNAKLKELGEKGV 564
                                       344555678899999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (634 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.75u 0.31s 00:00:01.06 Elapsed: 00:00:00.52
# Mc/sec: 3693.66
//
Query:       gi|298675299|ref|YP_003727049.1|  [L=830]
Description: DNA gyrase subunit A [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   4.6e-160  533.2   1.5   6.7e-160  532.6   1.5    1.2  1  DNA_topoisoIV  DNA gyrase/topoisomerase IV, subunit A
    1.1e-77  255.3  18.4    4.8e-14   51.6   0.8    6.9  7  DNA_gyraseA_C  DNA gyrase C-terminal domain, beta-propeller


Domain annotation for each model (and alignments):
>> DNA_topoisoIV  DNA gyrase/topoisomerase IV, subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  532.6   1.5  7.5e-164  6.7e-160       1     425 [.      50     489 ..      50     490 .. 0.98

  Alignments for each domain:
  == domain 1  score: 532.6 bits;  conditional E-value: 7.5e-164
                     DNA_topoisoIV   1 RaiPsvrDGlKPvqRriLyamfkl.lnldkkekKvaqlvGevlgkYhPHGdaslydaivrlaqdfvgniplldpqGn 76 
                                       Ra+P++rDGlKPv+RriLy+m++   + dk++kK+a++vG+vlgk+hPHGd+++yd++vr+ q+f++++pl+d+qGn
  gi|298675299|ref|YP_003727049.1|  50 RALPDARDGLKPVHRRILYSMKEAgITYDKPYKKSARVVGDVLGKFHPHGDMAVYDSLVRMVQEFSMRYPLVDGQGN 126
                                       9**************************************************************************** PP

                     DNA_topoisoIV  77 fGsildgdkdAaaRYietrLskiarellkeidketvdyqenyDgsekEPevlppiiPnlLvnGaeGIavGmatkipp 153
                                       fGsi dgd++Aa+RY+e+r++ki++e+l +idketv +q+nyDg  +EP+vlp+++Pnl+vnG++GIavGmat+ipp
  gi|298675299|ref|YP_003727049.1| 127 FGSI-DGDSAAAMRYTEVRMEKISEEMLVDIDKETVPFQPNYDGALTEPTVLPAKLPNLIVNGSTGIAVGMATNIPP 202
                                       ****.************************************************************************ PP

                     DNA_topoisoIV 154 hnlkeiidaliallkgeea...ellelvlgPdfptgggiigkeeikeayetgrGkikvrakveie....e.ktivit 222
                                       hnlke+ d l  +++++++   el + ++gPdfpt g+i+g+e+ik+ayetgrG+ik+r+ ++ie    + ++iv++
  gi|298675299|ref|YP_003727049.1| 203 HNLKEVADGLLMMIDNPDVsipELRTAIKGPDFPTAGTILGTEGIKSAYETGRGRIKIRSVADIEemknDkHRIVVS 279
                                       *****************9999999999************************************999999559***** PP

                     DNA_topoisoIV 223 ElPigvntskliekieelvkkkkik.isdirdesdr.gvrivielkrgaseekvleklykktkLessisvnnlvlfd 297
                                       ElP++vn+++lie+i++lv++kki+ isd+rdesdr g+riviel+r+++++++l++lyk+t+L+ ++ + nl+l+d
  gi|298675299|ref|YP_003727049.1| 280 ELPYQVNKANLIESIASLVRDKKIQgISDLRDESDReGIRIVIELARNTNPNVILNQLYKHTQLQVTYGIINLALVD 356
                                       *********************************9999**************************************** PP

                     DNA_topoisoIV 298 kkpkylslkeilkeflevrlevyerrkeyllekleerleilegllkalnkidevievirkskkekkakkeLiee..l 372
                                       + pk+l+l e+l+ +l++r++v+++r++y+l+k+eer++il+gl++ l ++devi++ir+sk++ +ak+ Lie+  l
  gi|298675299|ref|YP_003727049.1| 357 GVPKVLNLYELLQIYLNHRMDVIQKRSQYQLRKAEERAHILDGLKICLGNLDEVISFIRNSKTTPEAKEGLIEKfqL 433
                                       **************************************************************************99* PP

                     DNA_topoisoIV 373 seeqaeyllemrlrrLtkeeveklekeieelekeikelekllak...lkklikeel 425
                                       +e+qa+++l+mrl++Lt+ e++k+e+e++el ++i++l++++a+     ++ik+el
  gi|298675299|ref|YP_003727049.1| 434 DEAQAKAILDMRLQNLTAIEQDKIESEYNELVEKIADLKEIIASdsrKYNIIKDEL 489
                                       ******************************************99877677777776 PP

>> DNA_gyraseA_C  DNA gyrase C-terminal domain, beta-propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.18   1.6e+03       8      24 ..     254     270 ..     253     272 .. 0.87
   2 !   50.7   0.1     1e-17   9.2e-14       1      47 [.     521     567 ..     521     568 .. 0.96
   3 !   24.3   0.0   1.7e-09   1.6e-05       1      47 [.     571     620 ..     571     621 .. 0.97
   4 !   38.4   0.0   6.9e-14   6.2e-10       2      47 ..     628     671 ..     626     672 .. 0.90
   5 !   51.3   0.1   6.3e-18   5.7e-14       2      47 ..     676     721 ..     675     722 .. 0.96
   6 !   46.7   0.3   1.8e-16   1.6e-12       2      47 ..     728     774 ..     727     775 .. 0.94
   7 !   51.6   0.8   5.4e-18   4.8e-14       1      47 [.     778     824 ..     778     825 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.18
                                       TTSEEEEEEGGGS-BT- CS
                     DNA_gyraseA_C   8 snGyvkrfplselpeqg 24 
                                        +G++k  +++++ e++
  gi|298675299|ref|YP_003727049.1| 254 GRGRIKIRSVADIEEMK 270
                                       58***********9986 PP

  == domain 2  score: 50.7 bits;  conditional E-value: 1e-17
                                       SEEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEEE CS
                     DNA_gyraseA_C   1 dellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlvv 47 
                                       d l++iT+ Gy+kr+p+ +++ q+Rg++Gv gi+ k++d++ +v+v+
  gi|298675299|ref|YP_003727049.1| 521 DVLITITNSGYIKRLPVTTYSKQHRGGRGVAGINVKDDDFVEDVFVA 567
                                       679*****************************************997 PP

  == domain 3  score: 24.3 bits;  conditional E-value: 1.7e-09
                                       SEEEEEETTSEEEEEEGGGS-BT-TTSCTEEGS...ETTTTSSEEEEEEE CS
                     DNA_gyraseA_C   1 dellliTsnGyvkrfplselpeqgRgakGvkgi...klkegdklvsvlvv 47 
                                       d+lll+T++G+v + +++e+p+ ++ ++G+ ++    l++++ + s++ v
  gi|298675299|ref|YP_003727049.1| 571 DYLLLFTNKGRVNCKKVYEIPQGSKQSRGKALVnlfELENDEAVSSMITV 620
                                       8**********************************************988 PP

  == domain 4  score: 38.4 bits;  conditional E-value: 6.9e-14
                                       EEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEEE CS
                     DNA_gyraseA_C   2 ellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlvv 47 
                                       +ll++T+ G vk++pls+++  +   +G ++i+l+e+d+lv+v+++
  gi|298675299|ref|YP_003727049.1| 628 NLLMATKYGTVKKTPLSSFKTRK--KSGLIAINLNENDELVNVILT 671
                                       69*****************6655..56****************987 PP

  == domain 5  score: 51.3 bits;  conditional E-value: 6.3e-18
                                       EEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEEE CS
                     DNA_gyraseA_C   2 ellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlvv 47 
                                       +++l++s G+++rf +  ++++gR+a+Gv+gi+l+++d+++s+  +
  gi|298675299|ref|YP_003727049.1| 676 DIILVSSTGKAIRFAETNVRPMGRAAQGVRGIRLNPDDRIISMDTI 721
                                       89*****************************************877 PP

  == domain 6  score: 46.7 bits;  conditional E-value: 1.8e-16
                                       EEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTT.SSEEEEEEE CS
                     DNA_gyraseA_C   2 ellliTsnGyvkrfplselpeqgRgakGvkgiklkeg.dklvsvlvv 47 
                                       +ll+iT+nGy+kr++ +e+++++Rg++Gv+ i+++++ + +v+v  v
  gi|298675299|ref|YP_003727049.1| 728 KLLTITQNGYGKRTKFEEYRRMNRGGRGVTTIQMTPRnGPVVNVKTV 774
                                       69*********************************999999999876 PP

  == domain 7  score: 51.6 bits;  conditional E-value: 5.4e-18
                                       SEEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEEE CS
                     DNA_gyraseA_C   1 dellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlvv 47 
                                       d++++ + +G v+r+p+ ++++qgR+++Gvk+++++e+dk+++v+ +
  gi|298675299|ref|YP_003727049.1| 778 DDIVVTSYQGLVIRIPVKDIRVQGRNTQGVKIMNMRENDKVIGVARI 824
                                       89999999************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (830 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1066  (0.0594567); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.78u 0.34s 00:00:01.12 Elapsed: 00:00:00.51
# Mc/sec: 4876.24
//
Query:       gi|298675300|ref|YP_003727050.1|  [L=298]
Description: pyridoxine biosynthesis protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   7.8e-105  349.2   6.9   1.2e-104  348.6   6.9    1.3  1  SOR_SNZ   SOR/SNZ family
      1e-08   34.8   7.8    1.6e-07   30.9   0.4    2.4  2  ThiG      Thiazole biosynthesis protein ThiG
    0.00036   19.8   2.6      0.013   14.7   0.1    2.6  2  NanE      Putative N-acetylmannosamine-6-phosphate epimerase
    0.00068   19.1   3.9     0.0038   16.7   0.1    2.2  2  NMO       Nitronate monooxygenase
    0.00073   18.8   0.2      0.022   13.9   0.0    2.4  2  DUF561    Protein of unknown function (DUF561)
     0.0011   18.1   0.3       0.64    9.1   0.0    2.4  2  Dus       Dihydrouridine synthase (Dus)
      0.002   17.3   0.0      0.059   12.5   0.0    2.2  2  IGPS      Indole-3-glycerol phosphate synthase


Domain annotation for each model (and alignments):
>> SOR_SNZ  SOR/SNZ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  348.6   6.9  4.7e-108  1.2e-104       3     207 .]      12     216 ..      10     216 .. 0.99

  Alignments for each domain:
  == domain 1  score: 348.6 bits;  conditional E-value: 4.7e-108
                                       HHHHHHHHTTTSSEEEEESSHHHHHHHHHHT-SEEEE-SS-HHHHHHH-S------HHHHHHHHHH-SS-EEEEEET CS
                           SOR_SNZ   3 kvkaglaemlkgGvimdvvnaeqakiaeeaGavavmalervpadirkeggvarmsdpklikeikeavsipvmakvri 79 
                                        +k+g+a+m+kgGvimdv+++eqa+iae+aGava+male vpadir++ggvarm+dp+++++i+++v+ipvmak+ri
  gi|298675300|ref|YP_003727050.1|  12 LIKRGFAKMQKGGVIMDVTTPEQAEIAERAGAVAIMALESVPADIREAGGVARMADPAIVSQIVDSVTIPVMAKSRI 88 
                                       68*************************************************************************** PP

                                       T-HHHHHHHHHTT-SEEEEETTS--S-SS----GGG-SS-EEEEESSHHHHHHHHHHT-SEEEEES-TTS--THHHH CS
                           SOR_SNZ  80 GhfveaqilealgvdyiDesevltpadeeahidkkkfkvpfvcGarnlgealrriaeGaamirtkGeagtGdvveav 156
                                       Gh+vea+ile++gvd+iDesevltpad+++hidk++f+vpfvcGarnlgealrri+eGaamirtkGeagtGdv++av
  gi|298675300|ref|YP_003727050.1|  89 GHTVEAEILESIGVDMIDESEVLTPADTRYHIDKTQFTVPFVCGARNLGEALRRINEGAAMIRTKGEAGTGDVSQAV 165
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHTTS-HHHHHHHHHHHHGGGHHHHHHHHHTTS-S---T. CS
                           SOR_SNZ 157 rhvrkikeeirklkslseeelvalakelkaplelvkevaelgrlpvvnfaa 207
                                       +h+++i+ eir+ +  s+eel+ +a++++ap+elv+e+ +lgrlpvvnfaa
  gi|298675300|ref|YP_003727050.1| 166 HHMKQIMGEIREYSGKSKEELMMVARDIEAPYELVEETVNLGRLPVVNFAA 216
                                       *************************************************98 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   2.0    0.0014       3.6     117     200 ..      10     104 ..       2     116 .. 0.69
   2 !   30.9   0.4   6.1e-11   1.6e-07     175     225 ..     208     260 ..     190     265 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0014
                                       HHHHHTT-EEEEE..E-S-HH...HHHHHHHTT-SEBEEBS...SSTTS----...S-HHHHHHHHHH-SS-BEEES CS
                              ThiG 117 eiLvkeGFevlpY..vsdDlv...larrleevGcaavmPla...apiGsglGl...lnkealkiiieeakvPvivDA 182
                                         L+k GF+ +    v  D+     a+  e +G+ a+m l    a i  + G+   ++++ ++ i++++++Pv+   
  gi|298675300|ref|YP_003727050.1|  10 TELIKRGFAKMQKggVIMDVTtpeQAEIAERAGAVAIMALEsvpADIREAGGVarmADPAIVSQIVDSVTIPVMAKS 86 
                                       55666666666432234444311146666789999999886222567777775111568899*************** PP

                                       ---SHHHHHHHHHTT-SE CS
                              ThiG 183 GigspsdaaqamelGada 200
                                        ig++ +a     +G+d 
  gi|298675300|ref|YP_003727050.1|  87 RIGHTVEAEILESIGVDM 104
                                       ******999888889886 PP

  == domain 2  score: 30.9 bits;  conditional E-value: 6.1e-11
                                       SS-BEEES..---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHHH CS
                              ThiG 175 kvPvivDA..GigspsdaaqamelGadavllntavaeakdpvamArafklave 225
                                       ++Pv+  A  Gi +p daa  m+lGad++++ + + +a++p +mA a+  av+
  gi|298675300|ref|YP_003727050.1| 208 RLPVVNFAagGIATPADAALMMKLGADGIFVGSGIFKAENPEKMAGAIVEAVN 260
                                       67887543349***************************************997 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.5   0.4    0.0067        17      96     170 ..      26     105 ..       7     119 .. 0.69
   2 !   14.7   0.1   4.9e-06     0.013     131     180 ..     194     246 ..     143     261 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0067
                                       EEE-SSHHHHHHHHHTT-SEEE-TTTTSSTTS-.....SS--HHHHHHHHHT.T--EEEES---SHHHHHHHHTT-- CS
                              NanE  96 maDistleeglvakklGvdivGttlsGytkeeek....aepDfalvkalsea.glkviaeGrintPekakkaieiGv 167
                                       + D+ t e++ +a+++G+  + +  s  ++  e        D a+v +++++  + v+a  ri    +a+    iGv
  gi|298675300|ref|YP_003727050.1|  26 IMDVTTPEQAEIAERAGAVAIMALESVPADIREAggvaRMADPAIVSQIVDSvTIPVMAKSRIGHTVEAEILESIGV 102
                                       44888888888888888766654333333322223455678889999988763567999999999999999999999 PP

                                       SEE CS
                              NanE 168 dav 170
                                       d++
  gi|298675300|ref|YP_003727050.1| 103 DMI 105
                                       887 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 4.9e-06
                                       S--HHHHHHHHHTT.--..EEEES---SHHHHHHHHTT--SEEEE-HHHH-HH CS
                              NanE 131 epDfalvkalseag.lk..viaeGrintPekakkaieiGvdavvvGsaitrle 180
                                       e  ++lv++ ++ g l     a G i tP+ a+ ++++G+d + vGs i + e
  gi|298675300|ref|YP_003727050.1| 194 EAPYELVEETVNLGrLPvvNFAAGGIATPADAALMMKLGADGIFVGSGIFKAE 246
                                       55577777766655233224699*************************98754 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   1.1     0.021        53     142     198 ..      28      84 ..      17      93 .. 0.65
   2 !   16.7   0.1   1.5e-06    0.0038     183     269 ..     198     288 ..     175     294 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.021
                               NMO 142 tissvkearkvearG......aDalivqGpeaGGhqGtpevgdkglfaLvpqvldavdiPviA 198
                                        +++ ++a ++e++G        ++ ++  eaGG             a+v q++d v iPv+A
  gi|298675300|ref|YP_003727050.1|  28 DVTTPEQAEIAERAGavaimaLESVPADIREAGGVARM------ADPAIVSQIVDSVTIPVMA 84 
                                       55666666666666633333223333344566666552......24579*************9 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1.5e-06
                               NMO 183 aLvpqvldavdiPvi..AaGGiidrrgvaaaLalGAsgvqigtrfLltkesdakdahkkklleaklddtelt..sav 255
                                       +Lv++ ++   +Pv+  AaGGi +  + a ++ lGA g+ +g+    +++ +  + +    +++  + t+l   s+ 
  gi|298675300|ref|YP_003727050.1| 198 ELVEETVNLGRLPVVnfAAGGIATPADAALMMKLGADGIFVGSGIFKAENPEKMAGAIVEAVNNYDNPTKLYeiSKG 274
                                       45555555555999777**************************9888765443333333333333333443300333 PP

                               NMO 256 sGrpaRalatelle 269
                                        G  +R++ t+ +e
  gi|298675300|ref|YP_003727050.1| 275 IGSGMRGISTDTIE 288
                                       34566666666666 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1     0.043   1.1e+02     122     150 ..      77     106 ..      68     126 .. 0.65
   2 !   13.9   0.0   8.6e-06     0.022     150     232 ..     170     257 ..     125     266 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.043
                            DUF561 122 svtiPyiLkleeq.vkLakkLeslgvdliq 150
                                       svtiP + k        a+ Les+gvd+i 
  gi|298675300|ref|YP_003727050.1|  77 SVTIPVMAKSRIGhTVEAEILESIGVDMID 106
                                       566666665443202236667777777775 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 8.6e-06
                            DUF561 150 qteGkitsiskakkvndliekslstlastyeiskkv....slPvi..casGlsd.vtvplalslgasGiGigsavsk 219
                                       q  G+i + s   k ++ + + +  + + ye+++++    +lPv+  +a G+++   + l ++lga Gi +gs + k
  gi|298675300|ref|YP_003727050.1| 170 QIMGEIREYS--GKSKEELMMVARDIEAPYELVEETvnlgRLPVVnfAAGGIATpADAALMMKLGADGIFVGSGIFK 244
                                       5555555555..233344445555666777766543333379*985579999762568999**************** PP

                            DUF561 220 lndeeemvallse 232
                                        ++ e+m  ++ e
  gi|298675300|ref|YP_003727050.1| 245 AENPEKMAGAIVE 257
                                       *******988766 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0     0.001       2.5      98     134 ..      59      91 ..      52     105 .. 0.73
   2 !    9.1   0.0   0.00025      0.64     182     224 ..     209     252 ..     180     275 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.001
                                       EEGGGGGGSHHHHHHHHHHHHCCSSS-EEEEEESESS CS
                               Dus  98 gaGaaLlrkpdlvaqivkavvkaveiPvtvkirigid 134
                                        +G a +++p+    iv+++v+ v iPv +k rig  
  gi|298675300|ref|YP_003727050.1|  59 AGGVARMADPA----IVSQIVDSVTIPVMAKSRIGHT 91 
                                       55666666665....667778899**********976 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00025
                                       -SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHC..CSTTHHH CS
                               Dus 182 vsipviaNGdIkdaedaqaileetGadgvmigrgal..gnPwlfa 224
                                       ++++ +a G+I ++ da  +++  Gadg+ +g g    +nP  +a
  gi|298675300|ref|YP_003727050.1| 209 LPVVNFAAGGIATPADAALMMKL-GADGIFVGSGIFkaENPEKMA 252
                                       45666899*********999998.********9974115666555 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.022        55      61      88 ..      22      49 ..      15     105 .. 0.87
   2 !   12.5   0.0   2.3e-05     0.059     210     250 ..     211     251 ..     189     255 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.022
                                      TEESBSS--HHHHHHHHTTT.-SEEEEE CS
                              IGPS 61 kgliredfdpaeiAkkyeeagAsaiSVL 88
                                      kg + +d+  +e+A+  e+agA ai  L
  gi|298675300|ref|YP_003727050.1| 22 KGGVIMDVTTPEQAEIAERAGAVAIMAL 49
                                      889999*****************99655 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.3e-05
                                       SEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHHHH CS
                              IGPS 210 vllvaeSGiktredveklkeegvnafLvGeslmrqedveka 250
                                       v+  a  Gi+t++d+  + + g++++ vG+ + ++e+ ek+
  gi|298675300|ref|YP_003727050.1| 211 VVNFAAGGIATPADAALMMKLGADGIFVGSGIFKAENPEKM 251
                                       5667899****************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1976.86
//
Query:       gi|298675301|ref|YP_003727051.1|  [L=197]
Description: SNO glutamine amidotransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-52  176.6   0.0    5.2e-52  176.4   0.0    1.0  1  SNO            SNO glutamine amidotransferase family
    6.2e-11   42.2   0.0    8.6e-11   41.8   0.0    1.2  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    2.2e-07   30.8   0.2    9.7e-07   28.7   0.2    1.8  1  GATase         Glutamine amidotransferase class-I
    3.7e-05   23.5   0.1    5.1e-05   23.0   0.1    1.3  1  Peptidase_S51  Peptidase family S51
     0.0035   17.2   0.1     0.0051   16.6   0.1    1.3  1  DJ-1_PfpI      DJ-1/PfpI family
  ------ inclusion threshold ------
      0.027   14.2   0.2       0.13   12.0   0.0    2.2  2  Peptidase_C26  Peptidase C26


Domain annotation for each model (and alignments):
>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.4   0.0   1.7e-55   5.2e-52       1     186 [.       5     196 ..       5     197 .] 0.93

  Alignments for each domain:
  == domain 1  score: 176.4 bits;  conditional E-value: 1.7e-55
                                       EESSSSSHHHHHHHHHHTTSEE......EEE-SGGGGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--E CS
                               SNO   1 vlalqGaveehveaikkclaen......ktvkrkedlaevdaliiPGGestamskliertglyedllefvknsekvv 71 
                                       v+alqG+v ehv+a+kk++ e        t+k+      +dali+PGGest++++l+   g+ +++++ + ++  ++
  gi|298675301|ref|YP_003727051.1|   5 VVALQGDVSEHVDALKKAISERgekgevVTIKHSGITPTCDALILPGGESTTLGHLLVYEGIADEIKKAASDG-VPI 80 
                                       79*******************9999999999**********************************99999888.9** PP

                                       EEETHHHHHHCCEETTB....SS-SS--CCEEEETTTT-SCCGEEEEEEEETTTCSEEEEEESS--EEEEE-.TTTC CS
                               SNO  72 lGtCaGlillskelene....lvktlellkvkvkrnafGrqvdsfekeldfknliekftavfiraPvieeilddeav 144
                                       +GtCaGlil++k  e++        l +++ +v+rnafGrq +sfe +ld++ ++ ++ a+firaP i + +  e+v
  gi|298675301|ref|YP_003727051.1|  81 MGTCAGLILMAKSGEGQvqktRQYLLSIMDTTVNRNAFGRQRESFETKLDVSVFDSPYIAIFIRAPAIVKCG--ESV 155
                                       ************877774333444599********************************************9..99* PP

                                       EEEEECTTEEEEEEETTEEEESS-GGGSTTHCHHHHHHHHHH CS
                               SNO 145 kvlyeldgeivvakqkkilatsfhPelaeddirvhdyfveev 186
                                       k l + d  +v+a+q++++a++fhPel++d  r+h++f++++
  gi|298675301|ref|YP_003727051.1| 156 KTLAKIDDYVVAAEQGNLMALAFHPELTDD-LRFHHHFLDKI 196
                                       *******9999999**************98.*******9875 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.0   2.9e-14   8.6e-11      23     117 ..      26     115 ..      11     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 2.9e-14
                          GATase_3  23 pevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeeiedpegve 99 
                                         +++++v++k++ +++ +d++ilpGg++t+    l  e g++++ik+aa++g+p++g C+Gl+++ ++ e + ++ 
  gi|298675301|ref|YP_003727051.1|  26 RGEKGEVVTIKHSGITPTCDALILPGGESTTLGHLLVYE-GIADEIKKAASDGVPIMGTCAGLILMAKSGEGQVQK- 100
                                       446788999********************9987766666.**************************9997665443. PP

                          GATase_3 100 geageveglglLdietef 117
                                          ++   l ++d++++ 
  gi|298675301|ref|YP_003727051.1| 101 ---TRQYLLSIMDTTVNR 115
                                       ...577777777777655 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.2   3.3e-10   9.7e-07      11     176 ..      17     185 ..      12     196 .. 0.64

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 3.3e-10
                                       HHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.....TTTHHHHHHHHCTSTS-EEEETHHHH CS
                            GATase  11 enlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.....vegkieaikearenkiPiLGICLGmQ 82 
                                        +l++a+ e+g k evv i++s  +      ++d+++++gG  +       +eg  + ik+a++ ++Pi+G C G+ 
  gi|298675301|ref|YP_003727051.1|  17 DALKKAISERGEKGEVVTIKHSGITP-----TCDALILPGGESTTLghllvYEGIADEIKKAASDGVPIMGTCAGLI 88 
                                       58999999999999****99877666.....79********988888999*************************** PP

                                       HHHHHTTTEEEEEECEEEEEEEEEEEETTT......CGGTTTTSEEEEEEEEEEEEESG.........CHHHTT..E CS
                            GATase  83 llaiefgrkvvkekekehhggtmrlgddet......allyglknevierhrHryevnpk.........elepag..l 142
                                       l+a++  ++v k +++  +   m  + +++      +     + +++++   +               ++++ g  +
  gi|298675301|ref|YP_003727051.1|  89 LMAKSGEGQVQKTRQY--LLSIMDTTVNRNafgrqrE---SFETKLDVSVFDS-----PyiaifirapAIVKCGesV 155
                                       ********99977743..2222222222222443321...2222222222222.....1111112233444444114 PP

                                       EEEEEEETTEEEEEEEEETTTEEEESSBTTSTTS CS
                            GATase 143 evtakseddeelmeiiekknpfvgvQFHPEstst 176
                                       + +ak  dd  ++++ e+ n ++++ FHPE t  
  gi|298675301|ref|YP_003727051.1| 156 KTLAKI-DD-YVVAA-EQGN-LMALAFHPELTDD 185
                                       444444.33.34443.3333.6888888888765 PP

>> Peptidase_S51  Peptidase family S51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.1   1.7e-08   5.1e-05      83     136 ..      44      97 ..       9     119 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.7e-08
                                       SSEEEE--S-HHHHHHHHHHTTHHHHHHHHHHTT-EEEEETHHHHTTSSB-GGG CS
                     Peptidase_S51  83 adviyvgGGntfrLlkllketgldkllreavqqglvyiGvSAGaivagesiett 136
                                        d++++ GG+   L +ll  +g+++ +++a ++g++++G+ AG i +++s+e +
  gi|298675301|ref|YP_003727051.1|  44 CDALILPGGESTTLGHLLVYEGIADEIKKAASDGVPIMGTCAGLILMAKSGEGQ 97 
                                       689999******************************************999865 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   1.7e-06    0.0051      57     112 ..      40      95 ..       2     115 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.7e-06
                                       CTCCG-SEEEE--BHHHH.HHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHTTT CS
                         DJ-1_PfpI  57 vkaaeyDalvlpGGragp.erlrenekvvelvkefaekgklvaaICagpqlLaaagv 112
                                       +++   Dal+lpGG++    +l   e + + +k++a++g ++   Cag +l+a+ g 
  gi|298675301|ref|YP_003727051.1|  40 ITPT-CDALILPGGESTTlGHLLVYEGIADEIKKAASDGVPIMGTCAGLILMAKSGE 95 
                                       4444.8********984324566678999*******************999988775 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       0.3     9e+02      56      68 ..      41      53 ..       6      61 .. 0.82
   2 ?   12.0   0.0   4.3e-05      0.13      98     144 ..      70     116 ..      67     181 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.3
                     Peptidase_C26 56 ldkldgllltGgq 68
                                        ++d+l+l+Gg+
  gi|298675301|ref|YP_003727051.1| 41 TPTCDALILPGGE 53
                                      5578999999987 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 4.3e-05
                     Peptidase_C26  98 iraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheq 144
                                       i++a + gvPi+g+C Gl l++    G++ +  +   +++d + +++
  gi|298675301|ref|YP_003727051.1|  70 IKKAASDGVPIMGTCAGLILMAKSGEGQVQKTRQYLLSIMDTTVNRN 116
                                       688999***************88878888777666666666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1453.46
//
Query:       gi|298675302|ref|YP_003727052.1|  [L=146]
Description: pyridoxamine 5'-phosphate oxidase-like FMN-binding protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-18   66.7   0.0    1.9e-18   66.4   0.0    1.1  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
    0.00028   20.5   0.2    0.00033   20.3   0.2    1.1  1  Pyrid_ox_like   Pyridoxamine 5'-phosphate oxidase like
  ------ inclusion threshold ------
       0.02   14.7   0.0      0.025   14.4   0.0    1.3  1  DUF447          Protein of unknown function (DUF447)


Domain annotation for each model (and alignments):
>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.4   0.0   3.2e-22   1.9e-18       1      88 []      16     103 ..      16     103 .. 0.97

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 3.2e-22
                                       HHHHHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETTGSEEEEE CS
                    Putative_PNPOx   1 ldeelreflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallflddelgrgvri 77 
                                       lde+++e +++ k++  AT+++dG Pnv+p++++++ ++++i++a n+  ++l nl+enp++++ +++ e+   ++i
  gi|298675302|ref|YP_003727052.1|  16 LDEKMKEDFSKIKIFPFATASKDGVPNVVPIGFCKLMDDETIWVADNYFDKTLSNLQENPKASIFVWNTETSGCYQI 92 
                                       799************************************************************************** PP

                                       EEEEEEESCHH CS
                    Putative_PNPOx  78 eGtaelvsdge 88 
                                       +G +e+ s ge
  gi|298675302|ref|YP_003727052.1|  93 KGDVEIKSSGE 103
                                       *****988765 PP

>> Pyrid_ox_like  Pyridoxamine 5'-phosphate oxidase like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.2   5.5e-08   0.00033       4      98 ..      18     112 ..      15     132 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 5.5e-08
                     Pyrid_ox_like   4 kklkelvkdiktamLttteadgklksrPMatqkveedgdlwfltkkdsdkvkeirkdsqvnlafsdeskkkyvsvsG 80 
                                       +k+ke  ++ik+  ++t ++dg  ++ P    k  +d+++w   +   +  +++++++++++++ +++ +   +++G
  gi|298675302|ref|YP_003727052.1|  18 EKMKEDFSKIKIFPFATASKDGVPNVVPIGFCKLMDDETIWVADNYFDKTLSNLQENPKASIFVWNTETSGCYQIKG 94 
                                       6899999********************************************************************** PP

                     Pyrid_ox_like  81 taevvedrakieelWspv 98 
                                        +e+    +  + +++ v
  gi|298675302|ref|YP_003727052.1|  95 DVEIKSSGEDYNRMYNMV 112
                                       ****99888877777765 PP

>> DUF447  Protein of unknown function (DUF447)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   4.2e-06     0.025       7      51 ..      34      81 ..      32     118 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.2e-06
                                      EE-TT.-EEEEEEEEEE..SSSE.EEEEEETTSHHHHHHHHHSEEEEEE CS
                            DUF447  7 Tksek.rpnaaPiGviv..kgdk.vvlrlfkgsrTleNllengelvinv 51
                                      T s++ +pn+ PiG  +  ++++ +v+  + + +Tl+Nl+en++++i v
  gi|298675302|ref|YP_003727052.1| 34 TASKDgVPNVVPIGFCKlmDDETiWVADNYFD-KTLSNLQENPKASIFV 81
                                      778888*********99865555677777886.9***********9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 888.22
//
Query:       gi|298675303|ref|YP_003727053.1|  [L=133]
Description: 30S ribosomal protein S6e [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.2e-42  142.3   0.6    8.1e-42  142.2   0.6    1.0  1  Ribosomal_S6e  Ribosomal protein S6e


Domain annotation for each model (and alignments):
>> Ribosomal_S6e  Ribosomal protein S6e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.2   0.6   4.5e-46   8.1e-42       1     124 [.       4     123 ..       4     124 .. 0.98

  Alignments for each domain:
  == domain 1  score: 142.2 bits;  conditional E-value: 4.5e-46
                                       -EEEEEETTTTEEEEEE-CHHHCTTCTT-BSSEEEECCTTTSSSTS-EEEEEEEEETTC-BB-TTS-SSSEEEEEEE CS
                     Ribosomal_S6e   1 mklnisdpatgkqklievdekklrtligkrigeevdgdalGeelkgyvlkitggsdkqGfpmkqgvltpgrvrlLls 77 
                                       +k+++sdp+t k+++++v++ +++++igk+ige++dg+++G  l+gy+lkitgg+dk+Gf m+ ++++++r r+L+s
  gi|298675303|ref|YP_003727053.1|   4 FKVVVSDPKT-KSYQFDVTGDEVNNIIGKSIGETLDGNLVG--LPGYKLKITGGNDKDGFTMRGDLPGAKRHRILMS 77 
                                       79*******8.99****************************..********************************** PP

                                       TTSSSS-SSSSS-EEEEEEE-SB--SSEEEEEEEEEE--SS--TTTS CS
                     Ribosomal_S6e  78 kggvgyrprrkGerkrksvrGcivsadisqlnlvivkkgekdieglt 124
                                       + gvg +p++kGerkrk vrG+++s+d++q+n+++v++g+k+i+ ++
  gi|298675303|ref|YP_003727053.1|  78 G-GVGDEPKSKGERKRKFVRGKEISSDTVQINTKVVEYGDKSIDAIL 123
                                       9.*****************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1019.08
//
Query:       gi|298675304|ref|YP_003727054.1|  [L=590]
Description: translation initiation factor aIF-2 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-33  114.6   1.1      3e-32  111.7   0.2    2.6  2  GTP_EFTU         Elongation factor Tu GTP binding domain
    5.9e-30  103.0   6.4    2.4e-29  101.0   5.8    2.4  2  GTP_EFTU_D4      Elongation factor Tu domain 4
    5.6e-23   81.1   4.1      2e-22   79.3   4.1    2.0  1  IF-2             Translation-initiation factor 2
      5e-09   36.4   0.1      5e-09   36.4   0.1    3.2  3  GTP_EFTU_D2      Elongation factor Tu domain 2
    4.5e-08   33.2   0.8    1.3e-07   31.7   0.1    2.2  2  MMR_HSR1         50S ribosome-binding GTPase
     0.0027   17.5   0.0      0.012   15.4   0.0    2.0  2  ATP_bind_1       Conserved hypothetical ATP binding protein
  ------ inclusion threshold ------
      0.017   14.7   0.5        2.7    7.5   0.0    2.7  3  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.047   13.4   0.5       0.47   10.2   0.0    2.8  3  PduV-EutP        Ethanolamine utilisation - propanediol utili
      0.053   13.3   0.0       0.15   11.9   0.0    1.8  1  NOG1             Nucleolar GTP-binding protein 1 (NOG1)
      0.061   13.4   0.5        2.2    8.3   0.1    2.8  3  Dynamin_N        Dynamin family
      0.081   13.3   0.1       0.21   12.0   0.1    1.6  1  Phage_int_SAM_5  Phage integrase SAM-like domain
       0.11   12.4   0.4       0.42   10.6   0.4    2.0  1  BPL_C            Biotin protein ligase C terminal domain


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.7   0.2     2e-35     3e-32       4     191 ..      10     217 ..       7     220 .. 0.79
   2 ?   -1.0   0.0      0.72   1.1e+03     133     179 ..     333     401 ..     325     461 .. 0.62

  Alignments for each domain:
  == domain 1  score: 111.7 bits;  conditional E-value: 2e-35
                                       EEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSS CS
                          GTP_EFTU   4 rnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisleketkkylinliDtPGH 80 
                                         ++++ghvDhGKtTL+d++  +t +  ++g+ ++       + e     i+ k    +l ++     + +iDtPGH
  gi|298675304|ref|YP_003727054.1|  10 PIVSVMGHVDHGKTTLLDKIRGTTITSGEAGAITQ----HIGATEVPIDLISKKCGDSNLANKFIVPGLLFIDTPGH 82 
                                       5789*****************77777666555443....22233333456777777777777777889********* PP

                                       GGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST...........HHHHHHHHHHH CS
                          GTP_EFTU  81 vdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl...........kaelkeiveev 146
                                         F++  +rg + +D+++++vd++eG +pqt+e l+++++ ++p++v+ NKmDr+            a+++++ + v
  gi|298675304|ref|YP_003727054.1|  83 HAFTSLRSRGGALADLVIVIVDINEGFMPQTKESLEILKRFKTPFVVVANKMDRIhgwnptqdapfSATYQNQSQRV 159
                                       **************************************************************777766666666666 PP

                                       HHHHHHH....HHHHHHHHHTTT.........TTEEEEEEBTTTTBTHHHHHHHHHHH CS
                          GTP_EFTU 147 kqklsrk....eeklekygekge.........kevpvvfgSalkgegvktllealvel 191
                                       k+ l++k     ++l ++g++++         +++ vv++Sa +geg+ +ll +l+ l
  gi|298675304|ref|YP_003727054.1| 160 KDILDQKvyeiVGELYEAGFNSNrydrvtdfqRNIGVVPISASTGEGIPDLLMVLMGL 217
                                       6666444555534444444443377777777789*****************9988765 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.72
                                       GSTHHHHHHHHHHHHHHHHHH.....................HHHHHHHHHTTT...........TTEEEEEEBTTT CS
                          GTP_EFTU 133 Drlkaelkeiveevkqklsrk.....................eeklekygekge...........kevpvvfgSalk 177
                                       Dr+ +e+k+  e++k + +++                     e          e           ++  ++ +Sa++
  gi|298675304|ref|YP_003727054.1| 333 DRVVDEVKKELEDIKISTENTgltikadtigslealanelaeE----------EipirkaevgdiSQRDIIEVSAIE 399
                                       5555555555555554443335666666666644443333320..........133333344444555666666665 PP

                                       TB CS
                          GTP_EFTU 178 ge 179
                                        +
  gi|298675304|ref|YP_003727054.1| 400 DQ 401
                                       55 PP

>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       3.4   5.1e+03      39      54 ..     230     245 ..     226     247 .. 0.85
   2 !  101.0   5.8   1.6e-32   2.4e-29       1      86 []     462     547 ..     462     547 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.4
                                       TTE.EEEEEEEEEETT CS
                       GTP_EFTU_D4  39 edGrevGeilqiqdkg 54 
                                       +dG  vG++l++++++
  gi|298675304|ref|YP_003727054.1| 230 ADGPGVGTVLEVKEEK 245
                                       78999*****999875 PP

  == domain 2  score: 101.0 bits;  conditional E-value: 1.6e-32
                                       S-CEEEEEEEEEEETCCCEEEEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-TTT CS
                       GTP_EFTU_D4   1 rPgkikilpgvvfrrsdpaivGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegkivGr 77 
                                       +Pg+++ilp++vfr+s+pa+vGv+v gG+ik++v++ k+dG+ vG+i+ iq++g+++ eak G+eva++ieg++vGr
  gi|298675304|ref|YP_003727054.1| 462 KPGRFTILPDYVFRQSKPAVVGVKVNGGIIKTNVNVAKKDGTVVGKIKGIQSEGENVGEAKVGMEVAVAIEGPVVGR 538
                                       7**************************************************************************** PP

                                       S--TT-EEE CS
                       GTP_EFTU_D4  78 qikegdily 86 
                                       qike+++ly
  gi|298675304|ref|YP_003727054.1| 539 QIKENEMLY 547
                                       *******99 PP

>> IF-2  Translation-initiation factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.3   4.1   1.3e-25     2e-22       3     105 .]     341     442 ..     339     442 .. 0.93

  Alignments for each domain:
  == domain 1  score: 79.3 bits;  conditional E-value: 1.3e-25
                                       CHHHCCCSCSSCCEEEEEESSHHHHHHHHHHHHCTT.SSTEEEECEEEESSB-HHHHHHHHHST....EEEEEESSS CS
                              IF-2   3 elfeeikeegkelnviikaDvqGsleAlkeaLekleseevkvkvihsgvGaitesDvelasasn....aiiigFnvk 75 
                                       +++e+ik ++++ ++ ikaD+ GsleAl++ L++      ++++ +++vG+i+++D+  +sa +    ++iigFnvk
  gi|298675304|ref|YP_003727054.1| 341 KELEDIKISTENTGLTIKADTIGSLEALANELAEE-----EIPIRKAEVGDISQRDIIEVSAIEdqyySVIIGFNVK 412
                                       6778899999***********************97.....5*********************444688********* PP

                                       CTHHHHHCCCCCTSEEEEESSHHHHHHHHH CS
                              IF-2  76 vskkakklaekegvkirlynvIYkliddvk 105
                                       v ++ak++a+ +++k++ ++vIYklidd+k
  gi|298675304|ref|YP_003727054.1| 413 VLPDAKEKAQFSDIKLFVNDVIYKLIDDYK 442
                                       ****************************86 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.1   3.4e-12     5e-09       1      73 [.     248     325 ..     248     326 .. 0.90
   2 ?   -2.2   0.1       3.7   5.5e+03      43      65 ..     342     364 ..     337     387 .. 0.65
   3 ?    2.8   5.6      0.11   1.6e+02       3      60 ..     481     533 ..     480     541 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 3.4e-12
                                       EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEE.........ETTSEEEEEEEESSCCSGSS CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededea.........vaganaGvivaikgledaii 68 
                                       G +++ ++y+G+l+kGd+++i   + s+++i+t++++l++++   ++          ++ a+ Gv+v +++le+ ++
  gi|298675304|ref|YP_003727054.1| 248 GATIDLILYDGKLRKGDTIVI--GS-SGEPIKTKVRALLKPNYLSEIRtedkfrqvnEVTAATGVKVSAPDLEN-VL 320
                                       789999***************..44.4678***********986666699************************.9* PP

                                       TTCEE CS
                       GTP_EFTU_D2  69 vGdtl 73 
                                       +G+++
  gi|298675304|ref|YP_003727054.1| 321 AGSPI 325
                                       **986 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.7
                                       EEESEEETTSEEEEEEEESSCCS CS
                       GTP_EFTU_D2  43 ededeavaganaGvivaikgled 65 
                                       e ed+ +  +n G+ ++++ + +
  gi|298675304|ref|YP_003727054.1| 342 ELEDIKISTENTGLTIKADTIGS 364
                                       55666666666666666665544 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.11
                                       EEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEE CS
                       GTP_EFTU_D2   3 valgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivai 60 
                                       v++++v  G++k++ +v    +d  ++  v++i++++ + e++ ea +g  + v + +
  gi|298675304|ref|YP_003727054.1| 481 VVGVKVNGGIIKTNVNVAK--KD--GT-VVGKIKGIQSEGENVGEAKVGMEVAVAIEG 533
                                       8999999999999988887..55..33.89********************99998866 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.1   8.4e-11   1.3e-07       2     114 .]      12     133 ..      11     133 .. 0.74
   2 ?   -2.0   0.1       2.5   3.8e+03      69      84 ..     422     439 ..     359     462 .. 0.62

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 8.4e-11
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE................EEEEECGGCSSHHHH CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke................ielvDtpGliegase 62 
                                       v ++G+   GK+tL+ ++ g++   ++    T++i   +v ++  +                + ++DtpG  +    
  gi|298675304|ref|YP_003727054.1|  12 VSVMGHVDHGKTTLLDKIRGTTITSGEAGAITQHIGATEVPIDLISkkcgdsnlankfivpgLLFIDTPG-HH---- 83 
                                       789***************997777777777777776666664421123444567777777779*******.44.... PP

                                       HH.HHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  63 ek.glgkaflalee.adlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                          +l+ +       adl++++vd++ e++ p+ +e  e+l++ k p+++v+nk
  gi|298675304|ref|YP_003727054.1|  84 AFtSLRSRGG---AlADLVIVIVDIN-EGFMPQTKESLEILKRFKTPFVVVANK 133
                                       2212222222...247********99.7799**********99**********8 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.5
                                       HHHHHHC..TSEEEEEEE CS
                          MMR_HSR1  69 aflalee..adlillvvd 84 
                                       +f +++    d+i  ++d
  gi|298675304|ref|YP_003727054.1| 422 QFSDIKLfvNDVIYKLID 439
                                       222222221244444554 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.3   1.9e+03       1      18 [.      14      31 ..      14      42 .. 0.81
   2 !   15.4   0.0   7.8e-06     0.012      92     234 ..      73     213 ..      33     219 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.3
                        ATP_bind_1  1 vvGpaGsGKttfvgalse 18
                                      v+G++  GKtt+  ++  
  gi|298675304|ref|YP_003727054.1| 14 VMGHVDHGKTTLLDKIRG 31
                                      899999******988765 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 7.8e-06
                        ATP_bind_1  92 dyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsalsamlrlelPhvvvlnkfDl 168
                                        +l +DtPG   +  +++ +           a  v+++vD +       f+ ++  +l ++ r ++P+vvv nk+D 
  gi|298675304|ref|YP_003727054.1|  73 GLLFIDTPGHHAFTSLRSRGG--------ALADLVIVIVDIN-----EGFMPQTKESLEILKRFKTPFVVVANKMDR 136
                                       677788888888888888887........4556778888865.....5799999999*******************9 PP

                        ATP_bind_1 169 lkek.....lekeleffedvealslllekee......ekykklaeaiaelleefalvlrflplssekeesiedllsl 234
                                       +        + +   + ++ ++++ +l+++        + +  +++  + +++f++++ ++p+s++++e+i dll +
  gi|298675304|ref|YP_003727054.1| 137 IHGWnptqdAPFSATYQNQSQRVKDILDQKVyeivgeLYEAGFNSNRYDRVTDFQRNIGVVPISASTGEGIPDLLMV 213
                                       88555444555666666666666666666558888844444555666789999999999999999999999999865 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.3     0.016        24       2      49 ..      11      59 ..      10      71 .. 0.79
   2 ?    7.5   0.0    0.0018       2.7     100     154 ..      84     138 ..      71     159 .. 0.85
   3 ?   -3.9   0.0       5.8   8.6e+03      81      92 ..     261     272 ..     242     296 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.016
                                      EEEEEESTTCCHHHHHHHHH.CT--SS-EEEEESS-SSCHCCCCCCHCC CS
                              cobW  2 vtvltGflGsGKTtLlnhll.enraglklavivNefgevsiDaellret 49
                                      ++ + G +  GKTtLl ++  +   + +   i+  +g +++  +l++++
  gi|298675304|ref|YP_003727054.1| 11 IVSVMGHVDHGKTTLLDKIRgTTITSGEAGAITQHIGATEVPIDLISKK 59
                                      6778999999********9986667777788888888888877777665 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0018
                                       HTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHC CS
                              cobW 100 afteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDlld 154
                                       aft+ + +  + +d v+++vD ++    ++k++ ++ + +++  ++v nK+D + 
  gi|298675304|ref|YP_003727054.1|  84 AFTSLRSRGGALADLVIVIVDINEGFMPQTKESLEILKRFKTPFVVVANKMDRIH 138
                                       4555567788999**********99999************************986 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 5.8
                                       TT-SEEEEEECT CS
                              cobW  81 erldviliEttG 92 
                                       ++ d i+i ++G
  gi|298675304|ref|YP_003727054.1| 261 RKGDTIVIGSSG 272
                                       568999999998 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00032      0.47       4      46 ..      12      54 ..      10      68 .. 0.74
   2 ?   -1.0   0.0      0.88   1.3e+03      40      75 ..      76     107 ..      74     140 .. 0.53
   3 ?   -2.2   0.1       2.1   3.1e+03      84     131 ..     353     400 ..     325     406 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00032
                         PduV-EutP  4 illiGkvgsGKttLtqalkgeelkYkktqaiefsdeviDtPGe 46
                                      + ++G+v+ GKttL  +++g +++     ai  +  + + P +
  gi|298675304|ref|YP_003727054.1| 12 VSVMGHVDHGKTTLLDKIRGTTITSGEAGAITQHIGATEVPID 54
                                      568******************9987766555555444444444 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.88
                         PduV-EutP  40 viDtPGeylenrklysalivtsaeadvialvqdate 75 
                                       +iDtPG ++      s      a ad++ +++d++e
  gi|298675304|ref|YP_003727054.1|  76 FIDTPGHHAF----TSLRSRGGALADLVIVIVDINE 107
                                       6999997542....2222233344555555555554 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.1
                         PduV-EutP  84 fasvfnkeviGiitkidlaedeenieaveelLksaGaekifevsavek 131
                                          +++ ++iG +  +     ee+i + + ++     + i+evsa+e+
  gi|298675304|ref|YP_003727054.1| 353 TGLTIKADTIGSLEALANELAEEEIPIRKAEVGDISQRDIIEVSAIED 400
                                       445556666776666666666788888888888888888888888876 PP

>> NOG1  Nucleolar GTP-binding protein 1 (NOG1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0001      0.15      13      58 .]      95     135 ..      84     135 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0001
                              NOG1  13 ladavlFllDpseecgysleeQlsLleeikelfankpvivvlnKiD 58 
                                       lad+v+ ++D+ e    +++e      ei ++f+  p++vv+nK+D
  gi|298675304|ref|YP_003727054.1|  95 LADLVIVIVDINEGFMPQTKES----LEILKRFK-TPFVVVANKMD 135
                                       8999999999999876555554....56677888.8999******9 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1    0.0015       2.2       1      33 [.      12      44 ..      12      51 .. 0.89
   2 ?    2.0   0.0      0.12   1.9e+02      98     114 ..      69      85 ..      63     134 .. 0.66
   3 ?   -2.5   0.0       3.2   4.7e+03      15      48 ..     369     416 ..     364     469 .. 0.49

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0015
                                      EEEEEBTTTTHHHHHHHHHTS--S---SSS--- CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnptTr 33
                                      + v+G++ +GK+++l+++ g  i   +++ +T+
  gi|298675304|ref|YP_003727054.1| 12 VSVMGHVDHGKTTLLDKIRGTTITSGEAGAITQ 44
                                      689******************999888888886 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.12
                                       TTS-SEEEEE---B-SS CS
                         Dynamin_N  98 llvkgltlvDlPGldsv 114
                                       + v+gl ++D+PG +  
  gi|298675304|ref|YP_003727054.1|  69 FIVPGLLFIDTPGHHAF 85 
                                       6689999******8764 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 3.2
                                       HHHHHTS--S---SS...S---S-EEEEECCT---C...........C CS
                         Dynamin_N  15 lnaLlgedilprgpn...ptTrrplelqlgeeeeas...........e 48 
                                       +n L +e+i  r+++   +  r ++e++  e+++ s           +
  gi|298675304|ref|YP_003727054.1| 369 ANELAEEEIPIRKAEvgdISQRDIIEVSAIEDQYYSviigfnvkvlpD 416
                                       566666665555544333445556666666665555444443333332 PP

>> Phage_int_SAM_5  Phage integrase SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00014      0.21      41      73 ..     428     460 ..     417     462 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                                       --TTT--HHHHHHHHHHHHHTS---HHHHHHHH CS
                   Phage_int_SAM_5  41 itfeeidkefleeFedYLkkkkglsentiskyf 73 
                                       + ++++ ++++ +++++ ++kk ls+ntis ++
  gi|298675304|ref|YP_003727054.1| 428 LFVNDVIYKLIDDYKEWVEEKKALSQNTISEMI 460
                                       55689999*********************9876 PP

>> BPL_C  Biotin protein ligase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.4   0.00028      0.42       5      26 ..     494     515 ..     493     516 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00028
                                       EEEEEETSCEEEEEEEEE-TTS CS
                             BPL_C   5 eVtlededgkveGiavGIdddG 26 
                                       +V++  +dg+v+G+++GI ++G
  gi|298675304|ref|YP_003727054.1| 494 NVNVAKKDGTVVGKIKGIQSEG 515
                                       69****************6666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (590 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 4220.92
//
Query:       gi|298675305|ref|YP_003727055.1|  [L=149]
Description: nucleoside-diphosphate kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-56  189.7   0.5    2.3e-56  189.5   0.5    1.0  1  NDK       Nucleoside diphosphate kinase
  ------ inclusion threshold ------
      0.029   14.5   0.1       0.05   13.7   0.1    1.3  1  GHL6      Hypothetical glycosyl hydrolase 6


Domain annotation for each model (and alignments):
>> NDK  Nucleoside diphosphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.5   0.5   2.6e-60   2.3e-56       1     134 [.       2     135 ..       2     136 .. 0.99

  Alignments for each domain:
  == domain 1  score: 189.5 bits;  conditional E-value: 2.6e-60
                                       EEEEEEE-HHHHHTT-HHHHHHHHHHHT-EEEEEEEECE-HHHHHHHTGGGTTSTTHHHHHHHHTSSEEEEEEEEST CS
                               NDK   1 ertlvliKPdavkrgligeiisrleekglkivalkmlrlteeqaeehYaehkgkpffeelvefmtsgpvvalvlege 77 
                                       e+t+v++KPd+v+rgligei+sr+e++glki+a+km +++ee+a+ehY+eh++kpffe lve++ts+p v +++ege
  gi|298675305|ref|YP_003727055.1|   2 EQTYVMVKPDGVQRGLIGEIVSRIEKRGLKITAMKMHQIDEETAREHYKEHSDKPFFEPLVEYITSSPSVSMIVEGE 78 
                                       89*************************************************************************** PP

                                       THHHHHHHHH--SSTTTSSTTSHHHHH-SSSTT-SEEE-SSHHHHHHHHHHHSTGGG CS
                               NDK  78 daiekvreliGatnpaeaapgtiRadfgvslgeNlvHgSdseesaereiklfFkeee 134
                                       +ai+ +r++ Gat+p ea+pgtiR+df++++g+N+vH+Sds+e+ae+ei+l F+e+e
  gi|298675305|ref|YP_003727055.1|  79 NAITIMRSMNGATKPIEAQPGTIRGDFAIETGRNVVHASDSKETAEKEIALHFSESE 135
                                       ******************************************************987 PP

>> GHL6  Hypothetical glycosyl hydrolase 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   5.6e-06      0.05      42      79 ..      12      48 ..       3      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.6e-06
                              GHL6 42 klkrdllkelvkachregikvvvrvdfskaderiyeqh 79
                                       ++r l++e+v   +++g+k+ ++  ++ +de+ +++h
  gi|298675305|ref|YP_003727055.1| 12 GVQRGLIGEIVSRIEKRGLKITAMKMHQ-IDEETAREH 48
                                      457899**********************.***999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1118.85
//
Query:       gi|298675306|ref|YP_003727056.1|  [L=61]
Description: 50S ribosomal protein L24 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-21   75.9   0.7    2.2e-21   75.8   0.7    1.0  1  Ribosomal_L24e  Ribosomal protein L24e
    3.5e-06   27.0   1.5      5e-06   26.5   1.5    1.2  1  YHS             YHS domain
    2.3e-05   24.2   3.7    2.9e-05   23.9   3.7    1.1  1  zf-FCS          MYM-type Zinc finger with FCS sequence motif
  ------ inclusion threshold ------
      0.015   15.6   0.5      0.016   15.5   0.5    1.2  1  DUF3268         zinc-finger-containing domain
      0.018   15.0   0.3       0.17   11.9   0.1    2.0  2  DUF2116         Uncharacterized protein containing a Zn-ribbo
      0.026   14.6   2.0      0.037   14.1   2.0    1.2  1  zf-MYND         MYND finger
       0.03   14.2   6.3       0.06   13.2   6.3    1.5  1  VATC            Vms1-associating treble clef domain
      0.088   12.3   3.3       0.15   11.5   3.3    1.3  1  zf-FLZ          zinc-finger of the FCS-type, C2-C2


Domain annotation for each model (and alignments):
>> Ribosomal_L24e  Ribosomal protein L24e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.8   0.7   9.8e-25   2.2e-21       1      61 [.       1      61 []       1      61 [] 0.95

  Alignments for each domain:
  == domain 1  score: 75.8 bits;  conditional E-value: 9.8e-25
                                      XXX-B-TTT-SB--SS--EEEE-TTS-EEEESSHHHHHHHHTT--GGGSTTSTTT-XXXXX CS
                    Ribosomal_L24e  1 mktekCsFsgykiyPGhGkrfvrnDgkvfrFlssKceklfkqkrnPrklkWTkayRrahkk 61
                                      m+ +kCsF+g+  +PG+Gk++vr+Dg+++ F+ssKc+++++  r Pr++ WT++ R   kk
  gi|298675306|ref|YP_003727056.1|  1 MEQRKCSFCGEMLEPGTGKLYVRKDGTSYYFCSSKCQSNYNLGRLPRRTIWTEQGRIYLKK 61
                                      7889**************************************************9987665 PP

>> YHS  YHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   1.5   2.2e-09     5e-06       6      36 ..       9      39 ..       8      42 .. 0.93

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 2.2e-09
                               YHS  6 cgmkvdkekaeekseYkGkeYyFcSegCkdk 36
                                      cg  +++++ + +++ +G+ YyFcS +C + 
  gi|298675306|ref|YP_003727056.1|  9 CGEMLEPGTGKLYVRKDGTSYYFCSSKCQSN 39
                                      9999************************875 PP

>> zf-FCS  MYM-type Zinc finger with FCS sequence motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   3.7   1.3e-08   2.9e-05       3      39 ..       3      38 ..       2      40 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.3e-08
                            zf-FCS  3 kkrCwfCkkyikgkpeftyvlendgvvgqFCStsCld 39
                                      +++C+fC++ ++ ++    ++ +dg  ++FCS+ C +
  gi|298675306|ref|YP_003727056.1|  3 QRKCSFCGEMLEPGT-GKLYVRKDGTSYYFCSSKCQS 38
                                      589********9999.79*****************66 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.5   7.2e-06     0.016       3      39 ..       4      39 ..       2      58 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.2e-06
                           DUF3268  3 trCpyCGekvilvsaseiYkerskgkllylC.pkCday 39
                                       +C++CGe        ++Y  r+ g+ +y C  kC++ 
  gi|298675306|ref|YP_003727056.1|  4 RKCSFCGEMLEPG-TGKLY-VRKDGTSYYFCsSKCQSN 39
                                      68*****988765.5689*.9999*******999*985 PP

>> DUF2116  Uncharacterized protein containing a Zn-ribbon (DUF2116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.14   3.1e+02       4      15 ..       4      15 ..       2      18 .. 0.78
   2 ?   11.9   0.1   7.4e-05      0.17      18      32 ..      30      44 ..      26      54 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.14
                           DUF2116  4 kHCivCGkaIpl 15
                                      + C  CG+  ++
  gi|298675306|ref|YP_003727056.1|  4 RKCSFCGEMLEP 15
                                      679999987765 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 7.4e-05
                           DUF2116 18 sfCsekCqeeyekkr 32
                                       fCs kCq++y+  r
  gi|298675306|ref|YP_003727056.1| 30 YFCSSKCQSNYNLGR 44
                                      59*********9765 PP

>> zf-MYND  MYND finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   2.0   1.7e-05     0.037      10      28 ..       3      38 ..       1      41 [. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.7e-05
                                      SCE-TTT.................S-SEESSHHHHH CS
                           zf-MYND 10 lkkCagC.................ksvfYCskeCqr 28
                                      ++kC+ C                  s ++Cs++Cq+
  gi|298675306|ref|YP_003727056.1|  3 QRKCSFCgemlepgtgklyvrkdgTSYYFCSSKCQS 38
                                      569*************99999998899********7 PP

>> VATC  Vms1-associating treble clef domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   6.3   2.7e-05      0.06       4      31 ..       4      36 ..       1      39 [. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.7e-05
                              VATC  4 lrCsiCgesleg...kvyFek..fdfrYCstkC 31
                                      ++Cs+Cge le+   k y +k   ++ +Cs kC
  gi|298675306|ref|YP_003727056.1|  4 RKCSFCGEMLEPgtgKLYVRKdgTSYYFCSSKC 36
                                      79*********8444559999667999****** PP

>> zf-FLZ  zinc-finger of the FCS-type, C2-C2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   3.3   6.8e-05      0.15      14      45 ..       4      38 ..       3      40 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.8e-05
                            zf-FLZ 14 saCflCkkkLgegk.DiymYrGdka..FCSeeCRq 45
                                      ++C++C + L++g    y+ +  +   FCS+ C +
  gi|298675306|ref|YP_003727056.1|  4 RKCSFCGEMLEPGTgKLYVRKDGTSyyFCSSKCQS 38
                                      58***********98899988666556******86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 441.60
//
Query:       gi|298675307|ref|YP_003727057.1|  [L=71]
Description: 30S ribosomal protein S28e [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-29  101.8   0.5    1.6e-29  101.7   0.5    1.0  1  Ribosomal_S28e  Ribosomal protein S28e


Domain annotation for each model (and alignments):
>> Ribosomal_S28e  Ribosomal protein S28e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.7   0.5     9e-34   1.6e-29       3      64 .]       7      68 ..       5      68 .. 0.97

  Alignments for each domain:
  == domain 1  score: 101.7 bits;  conditional E-value: 9e-34
                                      -EEEEEEEEEE---SSSSEEEEEEEE-S-SS-S-EEEEEEES---TT-EEEES--S--TT-- CS
                    Ribosomal_S28e  3 aklAeVikvlgrtGsrGevtqVrvellegkdkgriiiRnVkGPvreGDiLtLlEterEArrL 64
                                       ++AeVi+v+g+tG++Ge+ q+++++leg+dkgr+i+Rn++GPvr+GDi++L+Et rEA++L
  gi|298675307|ref|YP_003727057.1|  7 GYAAEVIDVIGNTGMHGEASQIQCRILEGRDKGRVITRNCMGPVRVGDIIVLMETSREAKKL 68
                                      689*********************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 551.05
//
Query:       gi|298675308|ref|YP_003727058.1|  [L=117]
Description: 50S ribosomal protein L7Ae/L30e/S12e/Gadd45 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-28   97.6   0.2    3.1e-28   97.3   0.2    1.1  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
     0.0067   16.3   0.0     0.0099   15.7   0.0    1.2  1  PELOTA_1        PELOTA RNA binding domain
  ------ inclusion threshold ------
      0.012   15.9   0.1          3    8.2   0.0    2.1  2  DUF1269         Protein of unknown function (DUF1269)


Domain annotation for each model (and alignments):
>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.3   0.2   5.3e-32   3.1e-28       2      92 ..      13     103 ..      12     106 .. 0.95

  Alignments for each domain:
  == domain 1  score: 97.3 bits;  conditional E-value: 5.3e-32
                                       HHHHHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEESCHHHHHHHTTSSS CS
                    Ribosomal_L7Ae   2 aieevlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvkskkeLGelvgkkr 78 
                                       ++ e++++a+++gk+++G++e+tka+erg+ kl ++Aed++pee+ ++l+ lc+ek++py++v+ +keLG ++g+++
  gi|298675308|ref|YP_003727058.1|  13 KALEAVELARDTGKIKKGTNESTKAVERGTSKLAVIAEDIDPEEIIAHLPPLCEEKSIPYIFVSQQKELGSACGLEV 89 
                                       5678999********************************************************************** PP

                                       ECSEEEEEESTTTH CS
                    Ribosomal_L7Ae  79 pvsalaikdegdsk 92 
                                        +s++ai+d g+ +
  gi|298675308|ref|YP_003727058.1|  90 GCSSVAITDSGKGN 103
                                       *********99755 PP

>> PELOTA_1  PELOTA RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.7e-06    0.0099      17      71 ..      22      78 ..      10      87 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.7e-06
                          PELOTA_1 17 edinliKPgigEaTRvlLRRvPekvlvrdeee..pdlahlllLakekgvpveevpdl 71
                                      +d+  iK g  E+T+++ R + +  +++++ +  + +ahl  L++ek++p+  v+++
  gi|298675308|ref|YP_003727058.1| 22 RDTGKIKKGTNESTKAVERGTSKLAVIAEDIDpeEIIAHLPPLCEEKSIPYIFVSQQ 78
                                      68899**************999988888866633568************98776554 PP

>> DUF1269  Protein of unknown function (DUF1269)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0005         3      43      77 ..      29      63 ..      14      69 .. 0.82
   2 ?    6.1   0.0    0.0023        13      20      53 ..      81     114 ..      70     116 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0005
                           DUF1269 43 dflkelgeklkpgtsalfllvekatvdkvlealak 77
                                      +  +e  +++++gts l +++e++++++++++l +
  gi|298675308|ref|YP_003727058.1| 29 KGTNESTKAVERGTSKLAVIAEDIDPEEIIAHLPP 63
                                      445677899*********************99865 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0023
                           DUF1269  20 lGaavGAaaGAlvgalsdvgidddflkelgeklk 53 
                                       lG a G  +G  + a++d g  ++++k+++ek++
  gi|298675308|ref|YP_003727058.1|  81 LGSACGLEVGCSSVAITDSGKGNEIIKDIAEKVE 114
                                       7899***************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 802.36
//
Query:       gi|298675309|ref|YP_003727059.1|  [L=289]
Description: hypothetical protein Metev_1407 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.20s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2218.86
//
Query:       gi|298675310|ref|YP_003727060.1|  [L=337]
Description: radical SAM domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.5e-21   75.0   0.0    4.2e-20   72.8   0.0    2.1  2  Radical_SAM     Radical SAM superfamily
     0.0048   16.9   0.2     0.0048   16.9   0.2    2.9  2  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.023   14.9   0.1      0.023   14.9   0.1    1.9  2  Fer4_12         4Fe-4S single cluster domain
      0.029   13.8   0.1        1.2    8.4   0.0    2.1  2  Pkinase         Protein kinase domain
      0.052   13.0   0.0      0.052   13.0   0.0    3.1  3  zf-ribbon_3     zinc-ribbon domain
      0.065   13.3   0.1       0.23   11.6   0.1    1.9  1  DUF2614         Zinc-ribbon containing domain
       0.13   12.1   0.2       0.13   12.1   0.2    4.0  4  zinc_ribbon_2   zinc-ribbon domain
       0.22   11.6  10.7        2.9    8.0   0.3    3.5  3  zf-BED          BED zinc finger
        3.3    7.9   9.0        1.3    9.2   0.4    3.2  3  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
        4.6    7.4  12.0        2.2    8.5   0.1    3.8  4  DUF1272         Protein of unknown function (DUF1272)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.8   0.0   2.3e-23   4.2e-20       5     164 ..      81     234 ..      79     237 .. 0.93
   2 ?   -1.7   0.0       1.9   3.3e+03     127     156 ..     266     295 ..     242     296 .. 0.77

  Alignments for each domain:
  == domain 1  score: 72.8 bits;  conditional E-value: 2.3e-23
                                       SEESS--TTTSCCTT...HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTE CS
                                       xxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   5 rgCnlrCsfCarpet...vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgi 78 
                                        gCn+rC++C+++     + ++    ++++e+ ++ + ++     ++ + ++  ep  + +++ + ++lak+  +g+
  gi|298675310|ref|YP_003727060.1|  81 IGCNFRCKHCQNWVIsqcELDTSQTIEITPEQAIDRALSYN----ADSISWTYNEPAIWFEYTYDSAKLAKE--NGL 151
                                       59************999999999999999999999999998....9**************************..8** PP

                                       EEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  79 ritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGe 155
                                       +++++tng+   +e l+ + ++  d +s++++a+++e + k +     ++ vle++++++e+gi+ v ++++++p  
  gi|298675310|ref|YP_003727060.1| 152 STVYVTNGYIT-PEALKMISPYL-DAYSVDIKAFNEE-FYKDI-ASAKLQPVLESTKLAKELGIH-VEVTYLVIPEL 223
                                       **********8.*********99.*************.*****.88*******************.**********9 PP

                                       SH..HHHHHHH CS
                                       xx..xxxxxxx RF
                       Radical_SAM 156 nd..eeleell 164
                                       nd  ee++++ 
  gi|298675310|ref|YP_003727060.1| 224 NDtrEEIQQFS 234
                                       99556666665 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHHHTTSETEEEEEEEBTTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 127 feevlealeklreagikrvvdrivglpGen 156
                                       +e + +a  ++ e gik v+ + v+++ +n
  gi|298675310|ref|YP_003727060.1| 266 IETLEKAYNTAIEEGIKYVYLGNVMHRQVN 295
                                       577778888888999998888888877665 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -5.1   7.7        10   1.8e+04      27      38 ..      55      94 ..       9     100 .. 0.44
   2 !   16.9   0.2   2.7e-06    0.0048      11      39 ..     294     331 ..     288     336 .. 0.86

  Alignments for each domain:
  == domain 1  score: -5.1 bits;  conditional E-value: 10
                               DZR 27 a............................edrCpsCgekv 38
                                      +                            + rC +C+  v
  gi|298675310|ref|YP_003727060.1| 55 SeaidsiekkplyhfypgslsyslgtigcNFRCKHCQNWV 94
                                      0444444444444444444444444444445566666555 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 2.7e-06
                               DZR  11 darfCseCgtklkavaa.........edrCpsCgekvd 39 
                                        + fC++Cg+ l +            ++ C+ Cge ++
  gi|298675310|ref|YP_003727060.1| 294 VNTFCPNCGKMLIKRGMgveqynisnNNECMYCGENIP 331
                                       567*********9777799***************9876 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.2       4.9   8.7e+03      19      28 ..      18      27 ..      15      63 .. 0.64
   2 ?   14.9   0.1   1.3e-05     0.023       8     106 ..      76     171 ..      71     194 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.9
                           Fer4_12 19 CkgCfnketw 28
                                      Ck C  + t 
  gi|298675310|ref|YP_003727060.1| 18 CKICSHRCTI 27
                                      5555444433 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.3e-05
                           Fer4_12   8 lslfvsgCnlsCkgCfnketwsfksgkeft.kelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeek 83 
                                       +sl + gCn++Ck C n  + + +  +  t + + e++i+++  ++ + ++ +  EP      e  ++ +k  ke++
  gi|298675310|ref|YP_003727060.1|  76 YSLGTIGCNFRCKHCQNWVISQCELDTSQTiEITPEQAIDRALSYNADSISWTYNEPAI--WFEYTYDSAKLAKENG 150
                                       566678***********999977766666645556677777778889999999999999..6677888888888888 PP

                           Fer4_12  84 pekdiwlytgytleelskkekee 106
                                       +  ++ +++gy+  e +k   ++
  gi|298675310|ref|YP_003727060.1| 151 L-STVYVTNGYITPEALKM-ISP 171
                                       8.58999999998877653.444 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00068       1.2     145     188 ..     143     183 ..     140     244 .. 0.66
   2 ?    3.3   0.0     0.025        45     101     123 ..     271     293 ..     247     296 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00068
                                       SEESSSSCSBCTTTSCGGGS-HHHHTTSCBSHHHHHHHHHHHHH CS
                           Pkinase 145 akelessskltsfvgtseYlAPEvlkeneyskkvDvWslGvily 188
                                       ak ++++  l+++ +t  Y+ PE l  +++s+  D +s+ +  +
  gi|298675310|ref|YP_003727060.1| 143 AKLAKEN-GLSTVYVTNGYITPEAL--KMISPYLDAYSVDIKAF 183
                                       5555554.49***************..89999999999877555 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.025
                                       HHHHHHHHHHHHHHHHTTEE-SS CS
                           Pkinase 101 kkiakqilegleylHskgiiHrD 123
                                       k + + i eg++y++  +++Hr 
  gi|298675310|ref|YP_003727060.1| 271 KAYNTAIEEGIKYVYLGNVMHRQ 293
                                       67888999*************95 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.5      0.84   1.5e+03      19      23 ..      87      91 ..      86      92 .. 0.84
   2 ?   13.0   0.0   2.9e-05     0.052       3      15 ..     296     309 ..     294     311 .. 0.83
   3 ?    1.9   0.4     0.092   1.6e+02      19      25 ..     323     329 ..     319     331 .. 0.57

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.84
                       zf-ribbon_3 19 CpyCG 23
                                      C++C+
  gi|298675310|ref|YP_003727060.1| 87 CKHCQ 91
                                      99996 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 2.9e-05
                       zf-ribbon_3   3 vrCPnCGa.plssd 15 
                                       ++CPnCG+ +++ +
  gi|298675310|ref|YP_003727060.1| 296 TFCPNCGKmLIKRG 309
                                       68999999999887 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.092
                       zf-ribbon_3  19 CpyCGtk 25 
                                       C yCG+ 
  gi|298675310|ref|YP_003727060.1| 323 CMYCGEN 329
                                       5555554 PP

>> DUF2614  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00013      0.23      52      77 ..     280     305 ..     273     333 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                           DUF2614  52 tvvyfwiGllstkavqvvcpeceket 77 
                                        + y+++G +  + v+  cp+c+k+ 
  gi|298675310|ref|YP_003727060.1| 280 GIKYVYLGNVMHRQVNTFCPNCGKML 305
                                       577********************974 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.61   1.1e+03       8      19 ..      10      21 ..       9      24 .. 0.83
   2 ?   -0.9   1.3      0.85   1.5e+03       1       6 [.      86      91 ..      86      92 .. 0.80
   3 ?   12.1   0.2     7e-05      0.13      13      21 ..     295     303 ..     291     305 .. 0.75
   4 ?    7.7   0.3    0.0017         3      11      22 ..     318     329 ..     315     330 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.61
                     zinc_ribbon_2  8 elqdnakFCpyC 19
                                      +l+dn + C  C
  gi|298675310|ref|YP_003727060.1| 10 KLDDNKVQCKIC 21
                                      789999999888 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.85
                     zinc_ribbon_2  1 fCpnCG 6 
                                      +C++C 
  gi|298675310|ref|YP_003727060.1| 86 RCKHCQ 91
                                      6****6 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 7e-05
                     zinc_ribbon_2  13 akFCpyCGt 21 
                                       ++FCp+CG 
  gi|298675310|ref|YP_003727060.1| 295 NTFCPNCGK 303
                                       688999986 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0017
                     zinc_ribbon_2  11 dnakFCpyCGtp 22 
                                        n++ C yCG++
  gi|298675310|ref|YP_003727060.1| 318 SNNNECMYCGEN 329
                                       58999*****97 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.4    0.0047       8.4      11      23 ..      10      22 ..       7      30 .. 0.82
   2 ?    2.0   0.5      0.12   2.1e+02      16      24 ..      84      92 ..      68     103 .. 0.84
   3 ?    8.0   0.3    0.0016       2.9      14      26 ..     318     330 ..     314     331 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0047
                                      -GGSS--EETTTT CS
                            zf-BED 11 slkeqkavCryCg 23
                                      +l+++k++C++C 
  gi|298675310|ref|YP_003727060.1| 10 KLDDNKVQCKICS 22
                                      4569********7 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.12
                                      --EETTTTE CS
                            zf-BED 16 kavCryCgk 24
                                      + +C++C +
  gi|298675310|ref|YP_003727060.1| 84 NFRCKHCQN 92
                                      569****75 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0016
                                       SS--EETTTTEE- CS
                            zf-BED  14 eqkavCryCgkil 26 
                                       +++ +C+yCg+++
  gi|298675310|ref|YP_003727060.1| 318 SNNNECMYCGENI 330
                                       6899******987 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.2      0.12   2.1e+02       9      28 ..      16      37 ..      10      66 .. 0.75
   2 ?   -0.0   0.2      0.57     1e+03      26      44 ..      87     105 ..      83     121 .. 0.77
   3 ?    9.2   0.4   0.00072       1.3      18      36 ..     290     308 ..     287     329 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.12
                      NOB1_Zn_bind  9 lrChaCfkvtkd..mtkkFCpk 28
                                      ++C  C + ++    +k FC+ 
  gi|298675310|ref|YP_003727060.1| 16 VQCKICSHRCTIapGKKGFCQV 37
                                      579999997755449999**85 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.57
                      NOB1_Zn_bind  26 CpkCGnktLkrvavsvden 44 
                                       C++C n  + ++++ ++++
  gi|298675310|ref|YP_003727060.1|  87 CKHCQNWVISQCELDTSQT 105
                                       8888888888887777665 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00072
                      NOB1_Zn_bind  18 tkdmtkkFCpkCGnktLkr 36 
                                       ++++   FCp+CG+  +kr
  gi|298675310|ref|YP_003727060.1| 290 MHRQVNTFCPNCGKMLIKR 308
                                       5667789******988877 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.028        51      15      30 ..      11      26 ..       8      41 .. 0.85
   2 ?    0.2   0.9      0.47   8.4e+02      25      34 ..      83      92 ..      76      99 .. 0.70
   3 ?    8.5   0.1    0.0012       2.2      39      54 ..     293     308 ..     285     310 .. 0.82
   4 ?   -1.7   0.1       1.8   3.3e+03      28      33 ..     322     327 ..     318     332 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.028
                           DUF1272 15 lppdseearicsyEct 30
                                      l+ ++ + +ics+ ct
  gi|298675310|ref|YP_003727060.1| 11 LDDNKVQCKICSHRCT 26
                                      677788999******9 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.47
                           DUF1272 25 csyEctFCae 34
                                      c + c +C++
  gi|298675310|ref|YP_003727060.1| 83 CNFRCKHCQN 92
                                      7777777765 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0012
                           DUF1272  39 vlenvCPncgGelvkR 54 
                                        ++  CPncg  l+kR
  gi|298675310|ref|YP_003727060.1| 293 QVNTFCPNCGKMLIKR 308
                                       56889*****999998 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 1.8
                           DUF1272  28 EctFCa 33 
                                       Ec +C 
  gi|298675310|ref|YP_003727060.1| 322 ECMYCG 327
                                       666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1053  (0.0587317); expected 358.6 (0.02)
Passed bias filter:                      640  (0.0356964); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2391.02
//
Query:       gi|298675311|ref|YP_003727061.1|  [L=290]
Description: hypothetical protein Metev_1409 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.017   15.7   5.5       0.13   12.8   0.5    2.8  2  NEAT           Iron Transport-associated domain


Domain annotation for each model (and alignments):
>> NEAT  Iron Transport-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.5    0.0025        46      32      83 ..      95     159 ..      89     236 .. 0.75
   2 ?   12.8   0.5   7.5e-06      0.13       4      47 ..     241     284 ..     238     288 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0025
                                       SEEEEEETTEEEEEEEEE........SGGGEEEEEEEETTTEEEEEEEEEEET....TTT.EEEE CS
                              NEAT  32 paklevknGkyyvtltlk........nsdwiknfkvekvnGykvkttvvseda....gkd.trvv 83 
                                         +l v++  yy+t++ +        +s+++ +++++++n+y+v++  + e+     ++d  +v+
  gi|298675311|ref|YP_003727061.1|  95 SGTLAVNDYNYYLTVKASnssgeiynSSNYLGSISYRSNNNYYVDKVFGYENGalivAQDnRSVI 159
                                       56788888888888888855555555566799999999889988887776666566633323444 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 7.5e-06
                                       -SEEEEEEEEEEETTSSSB-GGGGGB-SSEEEEEETTEEEEEEE CS
                              NEAT   4 adgtYtidfkvlkdnsdeaSmankyidkpaklevknGkyyvtlt 47 
                                       +  tY+i++k+ ++n+++     + +++++ l+v+n+  +++lt
  gi|298675311|ref|YP_003727061.1| 241 EGLTYNINYKLKNTNRNTVNFTVNSTNNKIDLTVTNDSFIARLT 284
                                       5669*********************************9998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1006  (0.0561102); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2212.82
//
Query:       gi|298675312|ref|YP_003727062.1|  [L=306]
Description: hypothetical protein Metev_1410 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-18   65.7   1.4    5.3e-18   65.7   1.4    2.0  2  Pilin_N   Archaeal Type IV pilin, N-terminal


Domain annotation for each model (and alignments):
>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.7   1.4     3e-22   5.3e-18       1      80 [.      15      89 ..      15      90 .. 0.96
   2 ?   -1.4   0.1      0.26   4.6e+03      39      68 ..     213     243 ..     201     265 .. 0.60

  Alignments for each domain:
  == domain 1  score: 65.7 bits;  conditional E-value: 3e-22
                           Pilin_N  1 eAVSpViGviLmvaitvIlaAviaafvlglasneekapqasievkidssastgknavslehkgGdsidtkdlkivlnse 79
                                      +AV++V+G+iLm+ai+v++++v+++f++++  + +++p+++++ +++ +++     ++l+h+gG+++dtkd+ki+++ +
  gi|298675312|ref|YP_003727062.1| 15 DAVTEVVGEILMTAIVVLAFSVLSVFAFSY-LDITEKPHVDVDGWVNVESDV----INLRHSGGEVVDTKDMKIIISLN 88
                                      69****************************.99*****************97....*******************9987 PP

                           Pilin_N 80 g 80
                                      +
  gi|298675312|ref|YP_003727062.1| 89 N 89
                                      6 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.26
                           Pilin_N  39 qasievk.idssastgknavslehkgGdsid 68 
                                       + +i+ + i+ +++ ++  +s++ kg   i+
  gi|298675312|ref|YP_003727062.1| 213 ELKIQDNgIKVEGQGNYSDISITGKGNKKIN 243
                                       4444433333333333334777777755555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       796  (0.0443973); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2309.91
//
Query:       gi|298675313|ref|YP_003727063.1|  [L=652]
Description: type II secretion system F domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.6e-33  112.8   0.6    8.5e-18   64.5   0.0    3.0  3  T2SSF     Type II secretion system (T2SS), protein F
  ------ inclusion threshold ------
       0.38   11.4   5.5       0.58   10.8   1.5    2.7  2  Renin_r   Renin receptor-like protein
       0.48    9.4  13.6       0.71    8.8   2.8    2.3  2  Pex24p    Integral peroxisomal membrane peroxin


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.5   0.0   1.4e-21   8.5e-18       4     124 ..     141     268 ..     138     269 .. 0.92
   2 ?   -7.5   5.5         3   1.8e+04     106     123 ..     282     299 ..     278     301 .. 0.57
   3 !   55.2   0.1   1.1e-18   6.5e-15       1     123 [.     448     573 ..     448     575 .. 0.94

  Alignments for each domain:
  == domain 1  score: 64.5 bits;  conditional E-value: 1.4e-21
                                       HHHHHHH.TT--HHHHHHHHHHHHS.SHHHHHHHHHHHHHHHTTS.SHHHHHC....T-TT.TS-HHHHHHHHHHHH CS
                             T2SSF   4 qlatlls.aGvplveaLellaeeae.ngplaeelkriarrlraGg.slseale....rtpssefpelvvqliragee 73 
                                       +l+ +++ +G++l +++++l+++++ +g  aee+ +i+r+++  g ++ +al+    rtps  f+el++ li++ ++
  gi|298675313|ref|YP_003727063.1| 141 YLYAMTRgGGLSLFDIFKSLSNHKHiYGTAAEEFGYIVRDMEFFGhDIITALQnaklRTPSQNFRELIDGLISILSS 217
                                       566666669*********************************988766666667777******************** PP

                                       HT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXXX CS
                             T2SSF  74 ggnLaevLerlaeyleeerelrrkllaallepllllvvallvllillaill 124
                                       gg+++++L++  e+++  ++++++ ++++l+ l++ +v ++v+++l+++++
  gi|298675313|ref|YP_003727063.1| 218 GGDITAYLKNKTEQYRSVAKTEQQTFLETLGILAESYVSVFVVAPLFLMTI 268
                                       ************************************************986 PP

  == domain 2  score: -7.5 bits;  conditional E-value: 3
                                       XXXXXXXXXXXXXXXXXX CS
                             T2SSF 106 llllvvallvllillail 123
                                       +++l++ ++v++  +++l
  gi|298675313|ref|YP_003727063.1| 282 IMYLLIYIAVPFGTMVFL 299
                                       455555566666666555 PP

  == domain 3  score: 55.2 bits;  conditional E-value: 1.1e-18
                                       HHHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHC....T-TT.TS-HHHHHHHHHHHH CS
                             T2SSF   1 flrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGgslseale....rtpssefpelvvqliragee 73 
                                       f   la+  +aG+ l +a+++ a+++  g +  e+ ++++++++G++l +al+    r  ++  ++ v+++i a e+
  gi|298675313|ref|YP_003727063.1| 448 FFKKLASINEAGIMLMDAISMTAQSK-VGIIHTEIGKMKEDINWGTNLTQALKkfeyRVRTDLTRRIVTTIIKASES 523
                                       67789*********************.**************************88874444566************* PP

                                       HT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXX CS
                             T2SSF  74 ggnLaevLerlaeyleeerelrrkllaallepllllvvallvllillail 123
                                       + +++ vL+ +a + e + ++++++ +++  +++++++a++v l+++ il
  gi|298675313|ref|YP_003727063.1| 524 TNDVTSVLNIAANDAEVQKQMKNQRSTEMYVYVFIIYMAFFVYLFIVYIL 573
                                       **********************************************9887 PP

>> Renin_r  Renin receptor-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1     0.096   5.8e+02      34      68 ..     236     272 ..     209     291 .. 0.62
   2 ?   10.8   1.5   9.7e-05      0.58      21      79 ..     524     581 ..     505     593 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.096
                           Renin_r  34 kdkke.kklnlakkyssdYpaiFnii.Lwlvvvlvla 68 
                                       +++++ + l+      ++Y ++F +  L+l+ +lv+ 
  gi|298675313|ref|YP_003727063.1| 236 AKTEQqTFLETLGILAESYVSVFVVApLFLMTILVVL 272
                                       3333312455555667788888877547777777653 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 9.7e-05
                           Renin_r  21 krkkrsileakeakdkkekklnlakkyssdYpaiFniiLwlvvvlvlaliaivvalasm 79 
                                       + ++ s+l+ ++++++  +k   +++ +++Y  +F i++ + v l++  i++v  l sm
  gi|298675313|ref|YP_003727063.1| 524 TNDVTSVLNIAANDAEV-QKQMKNQRSTEMYVYVFIIYMAFFVYLFIVYILTVHFLSSM 581
                                       33444444444433333.35566788999*********************999999998 PP

>> Pex24p  Integral peroxisomal membrane peroxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   2.8   0.00012      0.71     110     185 ..     144     289 ..      44     355 .. 0.66
   2 ?    6.0   3.2   0.00087       5.2      69     175 ..     417     576 ..     396     588 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00012
                            Pex24p 110 a........................................skeivlnLr........................... 119
                                       a                                          +i++ L+                           
  gi|298675313|ref|YP_003727063.1| 144 AmtrggglslfdifkslsnhkhiygtaaeefgyivrdmeffGHDIITALQnaklrtpsqnfrelidglisilssggd 220
                                       14444444444444444444444444555555555555555555555555555666666666666666677777777 PP

                            Pex24p 120 ...dlqnkmedllnpidalekflkelagfkdenlstllfltllltpililllsrlipwrlillvlgail 185
                                           l+nk+e+++++ +  ++ + e+ g+ +e++ +++++  l ++ ++++l+ l p++ +++ l +++
  gi|298675313|ref|YP_003727063.1| 221 itaYLKNKTEQYRSVAKTEQQTFLETLGILAESYVSVFVVAPLFLMTILVVLGLLNPTSILIMYLLIYI 289
                                       77789***********99999999999977777777777776666666666666666666655554333 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.00087
                            Pex24p  69 lllfvvmvpaylyrhplrksslik...........................................keesknests 102
                                       + ++ +m++ ++ +h lr + + +                                           ++e+ n  t+
  gi|298675313|ref|YP_003727063.1| 417 FYSVLIMIVPFIVFHELRAKRISQieeqipeffkklasineagimlmdaismtaqskvgiihteigkMKEDINWGTN 493
                                       44566678888888866666554456777788888888888888777777777777777777777665665666666 PP

                            Pex24p 103 egptldea........skeivlnLrdlqnkmedllnpidalekflkelagfkdenlstllfltllltp.ililll.s 169
                                         ++l++         ++ iv++  +    ++d+ ++++ + +  + + ++k+++ + + ++++++ + +++ l+ +
  gi|298675313|ref|YP_003727063.1| 494 LTQALKKFeyrvrtdlTRRIVTTIIKASESTNDVTSVLNIAANDAEVQKQMKNQRSTEMYVYVFIIYMaFFVYLFiV 570
                                       666665449999999999************************99999999*******99988776654044444423 PP

                            Pex24p 170 rlipwr 175
                                       +++++ 
  gi|298675313|ref|YP_003727063.1| 571 YILTVH 576
                                       444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (652 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1563  (0.0871772); expected 358.6 (0.02)
Passed bias filter:                      634  (0.0353617); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.69u 0.29s 00:00:00.98 Elapsed: 00:00:00.44
# Mc/sec: 4455.75
//
Query:       gi|298675314|ref|YP_003727064.1|  [L=539]
Description: type II secretion system protein E [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      8e-43  146.4   0.0    1.3e-42  145.8   0.0    1.2  1  T2SSE     Type II/IV secretion system protein
  ------ inclusion threshold ------
       0.11   12.3   0.0       0.29   10.9   0.0    1.7  1  AAA_29    P-loop containing region of AAA domain


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.8   0.0   1.4e-46   1.3e-42      11     256 ..     152     403 ..     144     415 .. 0.87

  Alignments for each domain:
  == domain 1  score: 145.8 bits;  conditional E-value: 1.4e-46
                             T2SSE  11 dekvsdihvekper.vkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpekgvrlrvvllP 86 
                                       d+ + di     +  v +   +   ++ +  + ++++l+ l+ ++ + ++++is  +pl+da+++ +g rl++ l  
  gi|298675314|ref|YP_003727064.1| 152 DPYIEDISCDGIDVpVYL-YHIKYHNIMTNISFSEEQLNSLVIKLCQKSGKQISIGEPLVDATMS-DGSRLQATLGK 226
                                       556666666666666666.3333336666677888999999999*********************.******99977 PP

                             T2SSE  87 vvag..ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderiv 161
                                        v +   +++iR+ +++ lt  dl+  ++ + +i +     +++ ++ +++GgT sGKt +l+a+  +i+    +i+
  gi|298675314|ref|YP_003727064.1| 227 EVTTrgSSFSIRRFRSNPLTPIDLIRFNTSSLEIMAYFWMVIENGKNAIFAGGTASGKTSMLNAVSLFIPPL-TKII 302
                                       65555699***********99999999988888888889999******************************.**** PP

                             T2SSE 162 tvEDpvEiqleganqvqlnak.......kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGHlgslsTl 231
                                        +ED++E+ l+++n ++ +++       + ++ + dll+aa+R+rP  i+vGE+R+ke+l++ +A++TGH    sT+
  gi|298675314|ref|YP_003727064.1| 303 SIEDTRELTLHHDNWIAGVTRksftedgTSEISMYDLLKAAMRQRPEYILVGEVRGKEALTLFQAMSTGHTT-YSTM 378
                                       ****************988888****9999******************************************.**** PP

                             T2SSE 232 HansaagalerLeqlgaeveaaelk 256
                                       Ha++a+ +++rLe+   +v++ +l+
  gi|298675314|ref|YP_003727064.1| 379 HAGDAQTVVNRLENDPINVPRVMLR 403
                                       ************9866555555555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   3.2e-05      0.29      21      48 ..     269     297 ..     263     302 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.2e-05
                            AAA_29  21 lkg.atlltGpsGsGKSTllDAiqalLvp 48 
                                       ++g + +++G + sGK+++l A++  + p
  gi|298675314|ref|YP_003727064.1| 269 ENGkNAIFAGGTASGKTSMLNAVSLFIPP 297
                                       467799****************9876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (539 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3855.93
//
Query:       gi|298675315|ref|YP_003727065.1|  [L=298]
Description: PfkB domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-45  154.2   0.0    6.2e-45  153.8   0.0    1.2  1  PfkB      pfkB family carbohydrate kinase


Domain annotation for each model (and alignments):
>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.8   0.0   3.5e-49   6.2e-45       3     300 ..       4     279 ..       2     281 .. 0.91

  Alignments for each domain:
  == domain 1  score: 153.8 bits;  conditional E-value: 3.5e-49
                                       EEEEEEEEEEEEEEECSSH.TTSEE.EESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTE CS
                              PfkB   3 kvvviGealidliavsekl.egelv.evktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegv 77 
                                        + ++G++  d   ++ek+  ++ +    ++e s+GG +aN+A  +a lg++ ++i+ vG+D+ ++ ++++l + gv
  gi|298675315|ref|YP_003727065.1|   4 TISIVGHTALDHLFNVEKIaGPNESfPILDYEISYGGGAANIAATIATLGGKCQLISGVGNDFKSSGYEDYLTSTGV 80 
                                       6889****************555555*************************************************** PP

                                       EETTEEEESSSEEEEEEEEETTTSEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEESEECTTSHHHHHHHHHHH CS
                              PfkB  78 dtdyvkidedtrtglalivvdedgertivfnrgaaadltkeeleededlleeadllyisgllsselpeavleelaea 154
                                       d +++++ ed++ ++a++++d+++++  +f++g++a l+k+       +  + d++++++      p+ +     ++
  gi|298675315|ref|YP_003727065.1|  81 DLSHLYRMEDEKSTKAFVFTDKNHNQCTYFHWGPSARLKKT-------DPPSLDFVHLAT----SEPVFNS----KV 142
                                       ****************************************7.......889********9....3344444....45 PP

                                       HHHTTE..EEEEECESSSHHHHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGG CS
                              PfkB 155 aknggt..fdpnlldplgaqfkeallellaladllkpneeElealtgekledieealaalhklkakgaktvvvtlGk 229
                                       a+++g+  fdp +   +     e l+++l  ++++++n +E+++++++ ++  ++++++l        ++vvvt  +
  gi|298675315|ref|YP_003727065.1| 143 AQKAGFvsFDPGQDLVTYT--SELLETILYNTNIMFANKHEIKRVCDMINQPFDKLKDML--------DVVVVTYDE 209
                                       555555567*********5..79999999*******************988888888886........58******* PP

                                       GEEEEEETTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTSSSSSTCSC CS
                              PfkB 230 eGalvvekdgelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvqkkgaiaslp 300
                                       eG+ +++ d  + +pa+ +v++vD+tGAGD + +gfl ++ +  +l e+ +++++vA+++v+k g++++lp
  gi|298675315|ref|YP_003727065.1| 210 EGSRIYTDDIDYWIPAI-PVNAVDPTGAGDGYRAGFLLGYIQRYPLNECGKIGSTVASFIVEKAGCQTNLP 279
                                       ****************5.5************************************************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:01.47
# Mc/sec: 615.77
//
Query:       gi|298675316|ref|YP_003727066.1|  [L=113]
Description: hypothetical protein Metev_1414 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.3e-49  164.1   0.1    9.6e-49  163.9   0.1    1.0  1  DUF555    Protein of unknown function (DUF555)
  ------ inclusion threshold ------
      0.024   15.0   0.0       0.03   14.7   0.0    1.1  1  RuvX      Holliday junction resolvase


Domain annotation for each model (and alignments):
>> DUF555  Protein of unknown function (DUF555)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.9   0.1   1.1e-52   9.6e-49       1     101 []       3     103 ..       3     103 .. 1.00

  Alignments for each domain:
  == domain 1  score: 163.9 bits;  conditional E-value: 1.1e-52
                            DUF555   1 dyevvleaawivrdvksvddAigiAiseagkrlnpeldfveievgetecPkcgeelesalvvadtalvglllemkvf 77 
                                       +y+v+leaaw+vrdvk++ddAig+Aiseagkrlnp+ldfve++vg+t+cP+c+e+++s++++adta+vgl+l+mkvf
  gi|298675316|ref|YP_003727066.1|   3 NYHVTLEAAWLVRDVKTADDAIGVAISEAGKRLNPKLDFVEVDVGTTSCPACEESFSSVFLAADTAIVGLILDMKVF 79 
                                       8**************************************************************************** PP

                            DUF555  78 naeseEhaeriakseigkaledvP 101
                                       +aeseEha+riaks+ig++l+dvP
  gi|298675316|ref|YP_003727066.1|  80 DAESEEHASRIAKSVIGRTLRDVP 103
                                       ***********************9 PP

>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   3.4e-06      0.03      12      93 ..      23     109 ..      19     112 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.4e-06
                                       EEEEEEE-S--SS---EEEEE---HHHHHHHHHHHHHHT..T--EEEEE------SSS---SSTTHHHHHHHHHT.. CS
                              RuvX  12 riGvAvsdplgilaspletierkskekdleelkelvkee..eveeiVvGlPlnldgsegesakkvrkfaeeLakrl. 85 
                                        iGvA+s+  ++l  +l+ +e + +++++ + +e +++    +++ +vGl l+++  ++es ++++++a+ +  r+ 
  gi|298675316|ref|YP_003727066.1|  23 AIGVAISEAGKRLNPKLDFVEVDVGTTSCPACEESFSSVflAADTAIVGLILDMKVFDAESEEHASRIAKSVIGRTl 99 
                                       69*******************99899999999999998744689*************************99988876 PP

                                       ...T-EEEEE CS
                              RuvX  86 ..kklpvelv 93 
                                          +l+v+ v
  gi|298675316|ref|YP_003727066.1| 100 rdVPLKVIEV 109
                                       4444455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 799.69
//
Query:       gi|298675317|ref|YP_003727067.1|  [L=93]
Description: hypothetical protein Metev_1415 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-32  110.6   0.6    3.3e-32  110.4   0.6    1.0  1  DUF357    Protein of unknown function (DUF357)
  ------ inclusion threshold ------
      0.011   15.6   1.7      0.026   14.3   0.1    2.3  3  TPR_1     Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> DUF357  Protein of unknown function (DUF357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.4   0.6   3.7e-36   3.3e-32       1      73 []      11      83 ..      11      83 .. 0.99

  Alignments for each domain:
  == domain 1  score: 110.4 bits;  conditional E-value: 3.7e-36
                                      HHHHHHHHHHHHHH.....TS---HHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTSTS CS
                            DUF357  1 rYirlleealekvkiapdeesplgeaaeevlemaesYleDakyflekgdlvnAlasfsYaeGwLDagarlgll 73
                                      rY+rlle+alek+++ p e+s++++aa+++++ma++Y+eD+ +fl+ +d+vnAla+fsY+++wLDaga lg++
  gi|298675317|ref|YP_003727067.1| 11 RYQRLLEKALEKAEFIPIENSHMYTAASDFYTMAKAYYEDGMHFLKMNDPVNALACFSYGHAWLDAGAKLGVF 83
                                      8**********************************************************************98 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.16   1.4e+03      25      29 ..      17      21 ..      12      24 .. 0.66
   2 ?   -1.2   0.0      0.23   2.1e+03      16      27 ..      33      44 ..      31      44 .. 0.81
   3 ?   14.3   0.1   2.9e-06     0.026       1      25 [.      44      68 ..      44      69 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.16
                                      HHHHH CS
                             TPR_1 25 ekALe 29
                                      ekALe
  gi|298675317|ref|YP_003727067.1| 17 EKALE 21
                                      56665 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.23
                                      -HHHHHHHHHHH CS
                             TPR_1 16 kydeAleyyekA 27
                                      +y  A ++y  A
  gi|298675317|ref|YP_003727067.1| 33 MYTAASDFYTMA 44
                                      588999999877 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 2.9e-06
                                      HHHHHHHHHHHHHTT-HHHHHHHHH CS
                             TPR_1  1 akalynlGnayfklgkydeAleyye 25
                                      aka+y  G+ ++k++++  Al++++
  gi|298675317|ref|YP_003727067.1| 44 AKAYYEDGMHFLKMNDPVNALACFS 68
                                      89*********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 731.51
//
Query:       gi|298675318|ref|YP_003727068.1|  [L=551]
Description: hypothetical protein Metev_1416 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      6e-39  134.5   0.1      1e-38  133.7   0.1    1.4  1  DUF87          Helicase HerA, central domain
    1.3e-06   28.5   0.1    3.3e-06   27.2   0.1    1.7  1  HAS-barrel     HAS barrel domain
      7e-05   21.6   0.0       0.17   10.5   0.0    2.3  2  DUF853         Bacterial protein of unknown function (DUF853)
     0.0039   16.2   0.0       0.11   11.4   0.0    2.5  2  AAA_10         AAA-like domain
  ------ inclusion threshold ------
      0.026   14.8   0.1         17    5.7   0.0    3.0  3  AAA_22         AAA domain
       0.06   12.2   0.0          3    6.6   0.0    2.2  2  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
      0.066   12.9   0.0       0.16   11.6   0.0    1.6  1  Zot            Zonular occludens toxin (Zot)
        2.9    7.6   7.9        4.7    6.9   7.9    1.2  1  ATP11          ATP11 protein


Domain annotation for each model (and alignments):
>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.7   0.1   4.5e-42     1e-38       2     225 ..     126     345 ..     125     347 .. 0.95

  Alignments for each domain:
  == domain 1  score: 133.7 bits;  conditional E-value: 4.5e-42
                             DUF87   2 eiGrllsgsevpvyldlnklvtrHlAilgsTGsGKSntvavLleellekkgatililDpHGEYgkal.......... 68 
                                       +iG l +g+++pv l +n+lv+rH+ il++TGsGKS+t++v leell ++++++li+DpH+EY++++          
  gi|298675318|ref|YP_003727068.1| 126 NIGLL-EGTDIPVNLSVNSLVQRHCSILAKTGSGKSYTAGVVLEELL-DNNVPLLIIDPHSEYASLKdpgsekqgdl 200
                                       68977.9****************************************.***************************** PP

                             DUF87  69 ......ekllsekvkvitpspsa....kdkelkinpwsldpeelldlleeddkpaaavqrsvleealdqakakeeke 135
                                             +k++ +++ ++tp+++a     d+ +++n ++l+++el ++++e   + ++++  +l+ea+++++   e  
  gi|298675318|ref|YP_003727068.1| 201 dkynisPKGYGSDITIYTPANKAinpvADEAFRLNGNNLTVKELTSIFPE---SYTSTHVGILYEAVQKLR--SEMD 272
                                       ******9************9999***************************...77777************9..9999 PP

                             DUF87 136 klssdepveklleelkkekeelrklknqaiarlldkledllrkggsfsnsstdliallleklekegkitiidlsgvd 212
                                        +++d+++            e+ ++k++a++++++ le++ +++++  +++t +++ll     ++gk ++idl+gv+
  gi|298675318|ref|YP_003727068.1| 273 TYTIDDIIF-----------EVGNDKSKAKWNVINLLESVRDSEILS-TTPTPIEDLL-----QKGKASVIDLKGVS 332
                                       999999999...........5668999********************.9999999999.....999*********** PP

                             DUF87 213 elaqqlvvsvilr 225
                                        + q+++v+ ++ 
  gi|298675318|ref|YP_003727068.1| 333 PDLQRMIVAEVCS 345
                                       ******9998886 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.1   1.5e-09   3.3e-06       1      79 [.       6      81 ..       6      88 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 1.5e-09
                        HAS-barrel  1 iGevigestssslifrvegskdvkvGeyVeielpdgeivlGmvtdirrgn.selsndlalvlsleeleeangddevala 78
                                      +G++ ge++  ++ f v +s++v  GeyV+++++ ++++l +v  i+r++ +    ++ ++     ++ + gd+ va a
  gi|298675318|ref|YP_003727068.1|  6 VGVIFGETGTLEFKFLVSESTPVHRGEYVKAWHESDGWILAQVILIKRYSeK----YTLKEAKNGLRKDKSGDNIVAEA 80
                                      7999********************************************6443....33333333333444444444444 PP

                        HAS-barrel 79 t 79
                                      t
  gi|298675318|ref|YP_003727068.1| 81 T 81
                                      4 PP

>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   7.4e-05      0.17      18      72 ..     143     197 ..     131     206 .. 0.88
   2 !    8.8   0.0   0.00024      0.55     289     334 ..     392     435 ..     338     457 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 7.4e-05
                            DUF853  18 klanrhGliaGatGtGktvtLqvlaeslseaGvpvfladvkGdLsgiakaGevkd 72 
                                       +l+ rh  i   tG Gk  t  v+ e+l +  vp ++ d   + +++  +G+ k+
  gi|298675318|ref|YP_003727068.1| 143 SLVQRHCSILAKTGSGKSYTAGVVLEELLDNNVPLLIIDPHSEYASLKDPGSEKQ 197
                                       5789****************************************99999998664 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00024
                            DUF853 289 rskGvGvyfvtqnPldlPdtvLaqLGnrvqhalraftpkdqkavka 334
                                       r  G G+  ++q P+ + ++vL+q G+++   ++   p+d k++ +
  gi|298675318|ref|YP_003727068.1| 392 RKFGLGMMVISQRPARVDKNVLSQCGTQI--IMKVTNPNDLKSISK 435
                                       45589*********************977..466777888777765 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   4.8e-05      0.11      22      65 ..     147     190 ..     142     310 .. 0.67
   2 ?    1.7   0.0     0.045     1e+02     259     314 ..     381     438 ..     338     458 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.8e-05
                            AAA_10  22 sasliiGdlGnGKSvlakllvlyisllggkaliiDpkkerekfk 65 
                                        ++ i+ ++G GKS++a ++   ++  +  +liiDp  e    k
  gi|298675318|ref|YP_003727068.1| 147 RHCSILAKTGSGKSYTAGVVLEELLDNNVPLLIIDPHSEYASLK 190
                                       5889999*****************99************966664 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.045
                            AAA_10 259 kkllkelvRiGRsynaavylvtqsadDvlkeelknniglklaFr...etdkeeikkvLe 314
                                        ++l+++   GR++   ++ ++q +  v+k+ l++  g++++ +   ++d + i k+Le
  gi|298675318|ref|YP_003727068.1| 381 SEVLRNIASEGRKFGLGMMVISQRPARVDKNVLSQ-CGTQIIMKvtnPNDLKSISKGLE 438
                                       678999999******************99987653.34444443000344445555555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       1.1   2.4e+03       4      16 ..       3      15 ..       1      15 [. 0.86
   2 ?    5.4   0.0    0.0092        21       5      49 ..     146     184 ..     144     202 .. 0.73
   3 ?    5.7   0.0    0.0076        17      83     113 ..     344     388 ..     304     426 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.1
                            AAA_22  4 tagilvvtGesGt 16
                                      + +++v++Ge+Gt
  gi|298675318|ref|YP_003727068.1|  3 RGSVGVIFGETGT 15
                                      5789********7 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0092
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlps 49 
                                       ++++ + + +G+GK++++  +le+l         +++++ +++ s
  gi|298675318|ref|YP_003727068.1| 146 QRHCSILAKTGSGKSYTAGVVLEELLDN------NVPLLIIDPHS 184
                                       67889999*********99999988533......44444444444 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0076
                            AAA_22  83 eqalrarav.....ielliiDEaqhlr.....s....eealeeLr 113
                                          l ++++     +++l+i+Ea+++      s     e+l+++ 
  gi|298675318|ref|YP_003727068.1| 344 CSSLFEARKmdnvpPGMLVIEEAHNFApekgfSkspsSEVLRNIA 388
                                       4444444444788899**********8766551434466666663 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0014         3      12      56 ..     143     187 ..     134     193 .. 0.90
   2 ?    3.2   0.0     0.015        34     261     322 ..     384     437 ..     380     449 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0014
                     TrwB_AAD_bind  12 eretqhilivGttGsGKtqalekllrairargdraivlDltGafv 56 
                                       +  ++h  i+  tGsGK+ ++   l+++   +   +++D++ ++ 
  gi|298675318|ref|YP_003727068.1| 143 SLVQRHCSILAKTGSGKSYTAGVVLEELLDNNVPLLIIDPHSEYA 187
                                       56799**********************************998876 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.015
                     TrwB_AAD_bind 261 lksllaegRkfGgavvlglqsiaqlrevYGedaaqsilslvntklilrvsdaetAeelsell 322
                                       l +++ egRkfG  + +  q  a++         +++ls ++t++i++v++ +  + +s+ l
  gi|298675318|ref|YP_003727068.1| 384 LRNIASEGRKFGLGMMVISQRPARVD--------KNVLSQCGTQIIMKVTNPNDLKSISKGL 437
                                       67888999999998888889888886........4678888888888888777777777655 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   7.1e-05      0.16      70     139 ..     345     417 ..     315     426 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.1e-05
                               Zot  70 kefakwatid..kgallviDEcqeifpvrakegrkdpevi.naftehRhlgwDivlltqdiskihkevralae 139
                                       ++++  +++d    ++lvi E++++ p++   + +  ev+ n   e R++g  ++ + q +++++k+v   ++
  gi|298675318|ref|YP_003727068.1| 345 SSLFEARKMDnvPPGMLVIEEAHNFAPEKGFSKSPSSEVLrNIASEGRKFGLGMMVISQRPARVDKNVLSQCG 417
                                       4555555556566789********888887777778899999999*********************9977665 PP

>> ATP11  ATP11 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   7.9    0.0021       4.7      13      76 ..     474     535 ..     470     545 .. 0.57

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0021
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--- CS
                             ATP11  13 kakeeglesieeLkeaykdkieekrkeaaaidleesksesekekeakasssektekkesaaksk 76 
                                       ++ ++g +s++ Lk + k++ ++++k+++++ ++++  + e++++++ + s++++k+++a++++
  gi|298675318|ref|YP_003727068.1| 474 RKSQHGGKSVNVLKGKQKKQKSKETKQKQSPPPKKT--PPEPSQPSADTGSTSAPKQSEASEQN 535
                                       6678999*********98887777777734333332..33333333333344444444433332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (551 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       948  (0.0528752); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.61u 0.24s 00:00:00.85 Elapsed: 00:00:00.40
# Mc/sec: 4164.83
//
Query:       gi|298675319|ref|YP_003727069.1|  [L=263]
Description: diphthine synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.7e-16   58.5   0.0      1e-15   58.3   0.0    1.1  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
     0.0033   16.9   0.0     0.0058   16.1   0.0    1.3  1  DUF1248       Protein of unknown function (DUF1248)


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   0.0   1.2e-19     1e-15       1     167 [.       1     169 [.       1     215 [. 0.74

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 1.2e-19
                      TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaeal.aeal 76 
                                       +l ++G+G+ d ++++v++l+++k+ad v+ +  ++++++   +++     + +++ k+ +  + e+++++  + + 
  gi|298675319|ref|YP_003727069.1|   1 MLNFIGLGLYDEKDISVKGLETIKNADKVYLEF-YTSHLFGTDIKK-----MEQFYGKKIHVLKREDVEQHPdWIDE 71 
                                       5789*************************9888.888888877765.....67777778888888888888885555 PP

                      TP_methylase  77 ragkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl........... 142
                                       ++ k++v+l++GD +v++t+  l   +ra ++gi++ vi G s+++a++  +g+  + + +++++            
  gi|298675319|ref|YP_003727069.1|  72 AKEKNIVFLTGGDSMVATTHVDLR--IRAIDKGIKTSVIHGASIASAVCGLTGLQNYRFSKSTTIPfpyttgrgkti 146
                                       55578******************7..777779**********************99999999888877766433322 PP

                      TP_methylase 143 .lpglakeeereleallan....gdtlvll 167
                                                e  ++ + +n     +tlv l
  gi|298675319|ref|YP_003727069.1| 147 vS-------EVPYDTIKSNfeqgLHTLVYL 169
                                       22.......333333333333334555555 PP

>> DUF1248  Protein of unknown function (DUF1248)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   6.5e-07    0.0058      17      77 ..      45     106 ..      40     112 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.5e-07
                           DUF1248  17 afmkvhGneRldfkkeDiakwkesfkddYrlklvllkgterviatsht.itfkplkeskdkn 77 
                                       ++ + +G++  ++k+eD+++  +  +++ + ++v+l+g ++++at+h+ +  +++++  +++
  gi|298675319|ref|YP_003727069.1|  45 KMEQFYGKKIHVLKREDVEQHPDWIDEAKEKNIVFLTGGDSMVATTHVdLRIRAIDKGIKTS 106
                                       566889*****************9999999*****************756777777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1820.04
//
Query:       gi|298675320|ref|YP_003727070.1|  [L=548]
Description: thermosome [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   7.1e-160  532.8  15.1   8.1e-160  532.7  15.1    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  532.7  15.1  4.5e-164  8.1e-160       1     490 [.      35     520 ..      35     521 .. 0.97

  Alignments for each domain:
  == domain 1  score: 532.7 bits;  conditional E-value: 4.5e-164
                                       HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHH CS
                        Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleea 77 
                                       +a++v++tlGPkGmdKmlvn+ g++++TnDGatil e++iehP+akl+ve+a++qd+ +GDGTt++v+++geL+++a
  gi|298675320|ref|YP_003727070.1|  35 VANVVRSTLGPKGMDKMLVNDVGDIILTNDGATILDEMDIEHPTAKLIVEVASTQDDIAGDGTTSAVVMTGELMDKA 111
                                       689************************************************************************** PP

                                       HHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHCHC CS
                        Cpn60_TCP1  78 ekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvklie 154
                                       e+l+++gvhpt i +gy++a++ka e+L++   +i++++ dr++L k+a+ts+++k +++  ++l k++vdAv++ie
  gi|298675320|ref|YP_003727070.1| 112 EELVHKGVHPTIIAKGYRMAANKAQEILENF--AIDVDKGDRKILEKIAKTSITGKASESYGDYLPKICVDAVTAIE 186
                                       *******************************..8888889**********************************9*8 PP

                                       CCSEECSCCC.EECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHH CS
                        Cpn60_TCP1 155 enekeldlgr.ikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdaeel 230
                                       +n +e++++  i + +  gg+ +d+el++G++l+kg l+p+mpk++++ak+ l+d ++e ekt+++++v++++++e+
  gi|298675320|ref|YP_003727070.1| 187 DN-GEVNIEDkILINQEVGGKASDTELIRGIALNKGKLHPSMPKTIQDAKITLVDAPIEVEKTQIDSKVEINSPDEM 262
                                       88.57777666****************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGGCG CS
                        Cpn60_TCP1 231 eklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledltpe 307
                                        +++++ee+ql+++ e++i+sg+nv++c kg dd a h+l+ +gi a+rrv +++++ l++atGa++v+++ +l+ +
  gi|298675320|ref|YP_003727070.1| 263 SAYTEREEAQLKKMAESVIASGANVLFCSKGLDDRAVHYLQNKGIYAARRVGNSEMKSLSQATGARIVQDVNELEAT 339
                                       ***************************************************************************** PP

                                       C-EEEEEEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHH CS
                        Cpn60_TCP1 308 elGtakkveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelela 384
                                       +lGta+ +e+    ++  t+i++++ + ++ti + g t++v d ierai+dA +vvk+++ed+k+vpGGG++e+e+a
  gi|298675320|ref|YP_003727070.1| 340 DLGTAGMLEQVGEFDDAKTYIKDCPYK-TVTITIHGGTEHVTDNIERAIDDAFKVVKSVVEDGKIVPGGGSSEIEVA 415
                                       ********66666668999****9876.99*********************************************** PP

                                       HHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTXEE CS
                        Cpn60_TCP1 385 kklkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveagvvD 461
                                         l++ya s+ g++qlai afa+A e+ipk+La+NaG+d+i+ l +lr +h++ + ++g+++++ge+id+ e+++vD
  gi|298675320|ref|YP_003727070.1| 416 LGLRDYAVSIGGRQQLAISAFADAVEAIPKSLATNAGYDSIDSLLELRTKHSSIK-NAGFNLNTGEVIDMYENNIVD 491
                                       ***************************************************9999.********************* PP

                                       EHHHHHHHHHHHHHHHHHHHCEEEEEXXX CS
                        Cpn60_TCP1 462 plkvkrqalksAteaastiLrideiikak 490
                                       pl+vk+qa+ksA+ea  ++Lrid++++ +
  gi|298675320|ref|YP_003727070.1| 492 PLRVKTQAIKSASEASVMVLRIDDVLRSQ 520
                                       *************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (548 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 4275.44
//
Query:       gi|298675321|ref|YP_003727071.1|  [L=193]
Description: hypothetical protein Metev_1419 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.8e-74  247.3   0.7    7.7e-74  247.2   0.7    1.0  1  DUF2119        Uncharacterized protein conserved in archaea (
  ------ inclusion threshold ------
      0.044   13.6   0.0        2.3    7.9   0.1    2.2  2  Peptidase_M14  Zinc carboxypeptidase


Domain annotation for each model (and alignments):
>> DUF2119  Uncharacterized protein conserved in archaea (DUF2119)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  247.2   0.7   8.6e-78   7.7e-74       2     188 .]       9     192 ..       8     192 .. 0.99

  Alignments for each domain:
  == domain 1  score: 247.2 bits;  conditional E-value: 8.6e-78
                           DUF2119   2 egpvrlfvgGlHGdEgkdtskileklkeedlsegllvipnlekskYiSTldkeyyeseegkklidlveklkpeiYvE 78 
                                       ++pvrlfv+GlHGdE+kdts+il +lk ++++++l++ip++++++Y+STld++yy++ +gk +id v k++p+iYvE
  gi|298675321|ref|YP_003727071.1|   9 GDPVRLFVAGLHGDEWKDTSDILYNLK-TPIHGTLITIPVVNSGEYVSTLDESYYKN-KGKIIIDTVIKYQPSIYVE 83 
                                       579************************.****************************9.9****************** PP

                           DUF2119  79 lHsYskenykkLtdedRlkktgvPplvdlengvLigSvsplirkkyfkkealcltlEipklkskesleevlkileli 155
                                       lHsYs en+  Ltd++RlkktgvP++++l+n+vL+gSv+p+ir++yf+k+alcl++Ei+k++ ++s+++++k+ +++
  gi|298675321|ref|YP_003727071.1|  84 LHSYSGENIVYLTDKNRLKKTGVPAYSKLDNNVLLGSVAPYIRRNYFSKKALCLSFEIKKSD-EKSKQFAAKMADIV 159
                                       *************************************************************9.9************* PP

                           DUF2119 156 aesksreelieklkkkYpeqvekakeyakkfyg 188
                                       +e++sr+++i  lk+kYpeq+eka+e++kkfyg
  gi|298675321|ref|YP_003727071.1| 160 KECNSRDDFILFLKQKYPEQAEKAIENYKKFYG 192
                                       *******************************97 PP

>> Peptidase_M14  Zinc carboxypeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0    0.0053        47      45      61 ..       9      25 ..       4      36 .. 0.80
   2 ?    7.9   0.1   0.00026       2.3     164     228 ..      67     129 ..      49     187 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0053
                                      T-CEEEEEE-SSTT-HH CS
                     Peptidase_M14 45 gkpvvlidggiHarEwi 61
                                      g pv l+ +g+H++Ew 
  gi|298675321|ref|YP_003727071.1|  9 GDPVRLFVAGLHGDEWK 25
                                      678999**********5 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00026
                                       HHHHHHHHHTTEEEEEEEEESSS.EEEESHSSSS---SS-TTHHHHHHHHHHHHHHHCHTTTTEEE CS
                     Peptidase_M14 164 ravlefiqkknivlfidlhsysq.vilypygstrdeispppddeelkslarkyaealqkmvrgtey 228
                                       + +++++ k++ + +++lhsys   i+y  +++r +++++p + +l++    ++ a+  +++   y
  gi|298675321|ref|YP_003727071.1|  67 KIIIDTVIKYQPSIYVELHSYSGeNIVYLTDKNRLKKTGVPAYSKLDNNVLLGSVAPYIRRN---Y 129
                                       66778888899**********96156699999999999999999998888877777755333...3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       833  (0.046461); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1559.46
//
Query:       gi|298675322|ref|YP_003727072.1|  [L=220]
Description: RNA-binding S4 domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-11   41.9   0.2    1.1e-10   41.1   0.2    1.5  1  S4               S4 domain
    1.1e-08   35.4   0.0    1.8e-08   34.7   0.0    1.4  1  FtsJ             FtsJ-like methyltransferase
    4.1e-08   33.1   0.1    6.2e-08   32.6   0.1    1.4  1  Methyltransf_31  Methyltransferase domain
    2.8e-05   23.3   0.1    4.5e-05   22.7   0.1    1.3  1  Fibrillarin      Fibrillarin
      6e-05   23.7   0.0    9.7e-05   23.0   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    8.1e-05   23.2   0.0    0.00013   22.5   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
     0.0014   18.5   0.0     0.0024   17.7   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
     0.0074   17.0   0.0      0.015   16.0   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
  ------ inclusion threshold ------
       0.04   14.1   0.7       0.09   13.0   0.1    2.0  2  Response_reg     Response regulator receiver domain
      0.057   13.2   0.2      0.098   12.5   0.2    1.4  1  S4_2             S4 domain
       0.15   13.0   0.0        0.3   12.1   0.0    1.6  1  Methyltransf_24  Methyltransferase domain


Domain annotation for each model (and alignments):
>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.2   6.5e-14   1.1e-10       1      46 [.       1      46 [.       1      48 [. 0.96

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 6.5e-14
                                      EEHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTC CS
                                S4  1 rRLdkvlarlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgD 46
                                      +RLd++l++ g+  sr   + +I  G+V+++G++vk++s  Vkp+ 
  gi|298675322|ref|YP_003727072.1|  1 MRLDVYLVENGYFTSRGRSKTAIASGKVKIDGRIVKKASKDVKPEN 46
                                      8******************************************986 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.0   1.1e-11   1.8e-08       3     101 ..      57     157 ..      56     216 .. 0.78

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 1.1e-11
                                       CCHHHHHHHHHHHHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS.........HHHTTEEEECS-C CS
                              FtsJ   3 sRsayKLleidekfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm.........aplpgvttiqgdi 70 
                                        ++ +KL+ i+ek +l+++++ v+D+g++ Gg+  ++++     + v ++    +         +   +v+++  di
  gi|298675322|ref|YP_003727072.1|  57 PQGYFKLQYIQEKTGLINKNDYVLDIGSSAGGFLLYASEIA---AYVRGIEFSRYfeselekisSEYGNVSFVIDDI 130
                                       5789*********************************9994...578888887776766643333337********* PP

                                       CCSSHHHHHCHCHHHSSEEEEEE--S.-SS-C CS
                              FtsJ  71 tdpetiekikealserkvdlvvsDga.pdvsg 101
                                       ++ +  ++ +     rkvd+++sD+  + +  
  gi|298675322|ref|YP_003727072.1| 131 FTVTMDKLSS-----RKVDVILSDLTlEPMDS 157
                                       *996555444.....69*******97333444 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.1   3.8e-11   6.2e-08       2     109 ..      74     176 ..      73     219 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 3.8e-11
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieelekl.ledekfDl 77 
                                       +k+ +vlD+G+ +G +++ +  e+   a v Gi++s    +  +++  + ++ nv+F + di++  ++ l+ +k+D+
  gi|298675322|ref|YP_003727072.1|  74 NKNDYVLDIGSSAGGFLLYAS-EI--AAYVRGIEFSRYFESELEKI--SSEYGNVSFVIDDIFTVTMDkLSSRKVDV 145
                                       7999*********99999888.44..47799*****9988888887..5699************999999******* PP

                   Methyltransf_31  78 ilsnevlnaladpdkileeiervlkpggilli 109
                                       ils+ +l    d+ +ile++  +lk++g ll 
  gi|298675322|ref|YP_003727072.1| 146 ILSDLTL-EPMDSVQILERVLPLLKQNGKLLQ 176
                                       ****999.666999**************9984 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1   2.8e-08   4.5e-05      67     182 ..      72     185 ..      65     216 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 2.8e-08
                                       S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHTTSTTEEEEES-TTSGGGGTTTS--EEE CS
                       Fibrillarin  67 pikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlrelievakkRknivPileDArkPekYralvekvDv 143
                                        i+k++ vL +G+++G    + s+i      v ++efs     el +++++  n+  +++D  + +  +   +kvDv
  gi|298675322|ref|YP_003727072.1|  72 LINKNDYVLDIGSSAGGFLLYASEIAA---YVRGIEFSRYFESELEKISSEYGNVSFVIDDIFTVTMDKLSSRKVDV 145
                                       689999*******************98...9********************************9999999999**** PP

                                       EEEESS.STTHHHHHHHHHHHHEEEEEEEEEEEEHHHHHS CS
                       Fibrillarin 144 ifaDva.qpdqarilaknaklflkeggyllisikarsidv 182
                                       i +D++ +p     + + +   lk++g+ll + k++ i++
  gi|298675322|ref|YP_003727072.1| 146 ILSDLTlEPMDSVQILERVLPLLKQNGKLLQVTKTKDINT 185
                                       ****984566666666778889********9999998875 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0     6e-08   9.7e-05       1      97 []      79     172 ..      79     172 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 6e-08
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBS...SSTTTEEEEEEESTG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlp...fedgsfDlvvssgal 74 
                                       vLd+G   G ++l++++    a v g+++s  +  + ++  +e g nv+fv  d+ ++    + ++++D+++s  + 
  gi|298675322|ref|YP_003727072.1|  79 VLDIGSSAGGFLLYASEIA--AYVRGIEFSRYFESELEKISSEYG-NVSFVIDDIFTVTmdkLSSRKVDVILSDLT- 151
                                       9**************9885..*********999888877665554.*********77643336999*******533. PP

                                       GGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  75 hhlsdedlekalkeiarvLkpgG 97 
                                         l++ d  ++l+++  +Lk++G
  gi|298675322|ref|YP_003727072.1| 152 --LEPMDSVQILERVLPLLKQNG 172
                                       ..45678899**********998 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   8.3e-08   0.00013       1      95 [.      80     175 ..      80     176 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 8.3e-08
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCC..T.SS-TT-EEEEEEES-CCC- CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaek..l.pfednsfDlvvssevlhhv 74 
                                       Ld+G+ +G ++ +  + +a v g+++s ++    ++ +se g +v+fv  d+ +  + ++ + ++D+++s  +l+ +
  gi|298675322|ref|YP_003727072.1|  80 LDIGSSAGGFLLYASEIAAYVRGIEFSRYFESELEKISSEYG-NVSFVIDDIFTvtMdKLSSRKVDVILSDLTLEPM 155
                                       8*****************************988866666666.69********744666999*************** PP

                                       CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  75 edpekalkeiaRvLkpgGllv 95 
                                        d  ++l+ +  +Lk++G+l+
  gi|298675322|ref|YP_003727072.1| 156 -DSVQILERVLPLLKQNGKLL 175
                                       .799**************985 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.5e-06    0.0024      20     121 ..      73     180 ..      51     198 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.5e-06
                   Methyltransf_23  20 lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.......kakkaqkdqfdeqeaaepqgkfdlIvlr 89 
                                        +++  vLdiG   G +l +++e  + v g++ s+   +++e       + ++ ++d f    ++ +++k d+I + 
  gi|298675322|ref|YP_003727072.1|  73 INKNDYVLDIGSSAGGFLLYASEIAAYVRGIEFSRYFESELEkisseygNVSFVIDDIFTVTMDKLSSRKVDVILSD 149
                                       578999******************99999*****999999999999999999999999988888899********** PP

                   Methyltransf_23  90 evlehvpdppellrqiatllkpgGylllsepl 121
                                        +le +++    l ++  llk +G ll  + +
  gi|298675322|ref|YP_003727072.1| 150 LTLEPMDS-VQILERVLPLLKQNGKLLQVTKT 180
                                       ******99.56699999999999999877755 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   9.2e-06     0.015       1      99 []      80     174 ..      80     174 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9.2e-06
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieyt.gvDispsaiedakeklakren.nnnnnvelealdlldldggssfDlvvasnv 75 
                                       L+iG+  G +l +  e    + y+ g+++s+ +     ek++++ +  ++   ++++   ++l ++ ++D++++  +
  gi|298675322|ref|YP_003727072.1|  80 LDIGSSAGGFLLYASEI---AAYVrGIEFSRYFE-SELEKISSEYGnVSFVIDDIFTVTMDKL-SSRKVDVILSDLT 151
                                       89*********999888...77777*********.5566655555505555555555555555.456********** PP

                   Methyltransf_12  76 lhhlkdirevldnirklLkpgGrl 99 
                                       l+ + d  ++l+++  lLk++G+l
  gi|298675322|ref|YP_003727072.1| 152 LEPM-DSVQILERVLPLLKQNGKL 174
                                       ***8.9999*************97 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.5   2.5e+03      77     104 ..      13      40 ..      12      43 .. 0.85
   2 ?   13.0   0.1   5.5e-05      0.09      34      88 ..     133     188 ..     105     214 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.5
                                       EESSTSHHHHHHHHHCTESEEEESSG-H CS
                      Response_reg  77 ltahseeedavealkagaddflsKpfdp 104
                                       +t+++ +++a++  k+ +d+ ++K+ ++
  gi|298675322|ref|YP_003727072.1|  13 FTSRGRSKTAIASGKVKIDGRIVKKASK 40 
                                       68889999999999999***99999765 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 5.5e-05
                                       HHHHHHHHHHESEEEEESSCSSSEHHHHHHHH.HHCTTTSEEEEEESSTSHHHHHH CS
                      Response_reg  34 ealellkeekvdlillDinmpgmdGlellkei.reedpelpviiltahseeedave 88 
                                         +++l ++kvd+il D+ ++ md +++l+++    +++ + + +t +++ ++++ 
  gi|298675322|ref|YP_003727072.1| 133 VTMDKLSSRKVDVILSDLTLEPMDSVQILERVlPLLKQNGKLLQVTKTKDINTRNI 188
                                       46789999**********************98566678999999999988877665 PP

>> S4_2  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2     6e-05     0.098      16      59 ..       9      52 ..       1      55 [. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6e-05
                              S4_2 16 laglvesGgeaKafiaegeVkvNGevetrRgkKlraGdvVeidg 59
                                      + g+  s g  K+ ia+g+Vk++G + ++  k + ++  V++++
  gi|298675322|ref|YP_003727072.1|  9 ENGYFTSRGRSKTAIASGKVKIDGRIVKKASKDVKPENKVQVEE 52
                                      55666677999***************************999965 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00019       0.3      45     101 ..     118     174 ..      65     176 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                   Methyltransf_24  45 aglddrvrlikadseealaslaagsiDllfiDgghaaeavledleallprlapggvv 101
                                       +++ ++  +i + +  ++ +l+++++D+++ D   +  +  + le +lp+l+++g +
  gi|298675322|ref|YP_003727072.1| 118 SEYGNVSFVIDDIFTVTMDKLSSRKVDVILSDLTLEPMDSVQILERVLPLLKQNGKL 174
                                       5666666677777777889999*******************************9966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.41u 0.20s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1849.26
//
Query:       gi|298675323|ref|YP_003727073.1|  [L=371]
Description: NADH:flavin oxidoreductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-73  247.5   0.1    2.5e-73  247.3   0.1    1.0  1  Oxidored_FMN  NADH:flavin oxidoreductase / NADH oxidase famil
    0.00033   19.9   0.1     0.0016   17.6   0.1    1.9  1  Dus           Dihydrouridine synthase (Dus)
     0.0042   16.7   0.1      0.037   13.6   0.0    2.2  2  HMGL-like     HMGL-like
     0.0055   16.2   0.1      0.012   15.0   0.1    1.6  1  His_biosynth  Histidine biosynthesis protein
  ------ inclusion threshold ------
      0.014   14.6   0.4      0.032   13.4   0.3    1.6  2  DUF561        Protein of unknown function (DUF561)
      0.087   12.4   0.0       0.14   11.6   0.0    1.2  1  DUF4908       Domain of unknown function (DUF4908)


Domain annotation for each model (and alignments):
>> Oxidored_FMN  NADH:flavin oxidoreductase / NADH oxidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  247.3   0.1   8.4e-77   2.5e-73       2     341 ..       2     339 ..       1     340 [. 0.90

  Alignments for each domain:
  == domain 1  score: 247.3 bits;  conditional E-value: 8.4e-77
                                       CCS-EEETTEEESSSEEE----S-TTTTTCS.HHHHHHHHHHHHHHTT-SEEEEEEEESSCCC-SCTTSEE-SSGGG CS
                      Oxidored_FMN   2 LFkPikignmtLknRivmapmtrlraldkgnvledlaaeyysqraeipvtliiteaafvnpksggfdnapgiwdeeq 78 
                                       LF+Pi+i + ++ nR+v ++     a+++g +++  +ae y++ a+ +v+liit+++ vnp ++  +n+ gi++++ 
  gi|298675323|ref|YP_003727073.1|   2 LFEPINISQLEIPNRFVRSATHEWLAENNG-KPTYKLAEMYEELARNEVGLIITGYSYVNPRGKSANNQQGIYTDDF 77 
                                       9****************9998888888888.99999***************************************** PP

                                       HHHHHHHHHHHHHTT-EEEEEEE--GGGS..SCSTCEC..SS.ESSSSSTTT-.S...CS-EE--HHHHHHHHHHHH CS
                      Oxidored_FMN  79 ieewrklteavhengskvvvqlwhlGreakseyladqevdspsdpvaldaqeeesaeevykkeltkeeikqliqefv 155
                                       ie + +++ +vh ++sk+++q+ h+Gr++ + ++  +   +ps++++         ++v   e+++++i q+i++f+
  gi|298675323|ref|YP_003727073.1|  78 IEPYSQVVSKVHRYNSKIMLQIVHGGRQSLVSKDYPAL--APSAVTDEATG----ITPV---EMSESQILQTIEDFA 145
                                       *****************************654444444..56644444333....5677...*************** PP

                                       HHHHHHHHTT-SEEEEEE-CTSHHHHHH-TTT----STTSSSHHHHHHHHHHHHHHHHHHH-SSS...EEEEEECE- CS
                      Oxidored_FMN 156 eAAkraieAgfDgVeihganGYLlnqFlspksnkrtDeygGslenRarFllevvdaVkeavgeer...vgyRlSped 229
                                       +AA+ra++AgfDgV+ h a+G+Ll +F+sp++n+rtD++gGs+enR r + e+++ ++     ++   + ++l   d
  gi|298675323|ref|YP_003727073.1| 146 NAARRAKAAGFDGVQLHCAHGFLLSNFISPYTNQRTDKWGGSVENRTRIITEIIKRIRGM-TLDMdypITVKLNSTD 221
                                       **********************************************************87.334446*******999 PP

                                       -ST.....TS--HHHHHHHHHHHCHCCEEEEEEETT-SS.SSSTTS-TTTTHHHCCTTHHHHHHCCCHSSEEEE-SS CS
                      Oxidored_FMN 230 vve.....kgldfaetaqkivllkelekrlkdgkklalv.haaeprkrgagsvrteqekntefvkevwkkplitvgr 300
                                        ++     +gld+ +t+q +++l++ ++++++++ + +  h+ ++++ ++ +++ + +kn++ +k+ ++ p+i vg+
  gi|298675323|ref|YP_003727073.1| 222 GFGsdsdkPGLDINDTIQIAKILQQNGVNAIEVSGGIFEtHLMSQQNIDSVEKEAYFKKNAKLIKNAVDIPVILVGG 298
                                       9871111145677888***************999888766999999999999999999******************* PP

                                       --SHHHHHHHHHTTS-SEEEESTHHHH-TTHHHHHHCCTCG CS
                      Oxidored_FMN 301 iadeekaaeivaegeadLvamgRefladpdlveklkkglpl 341
                                         ++  +++i + ++ad+++m R+f+ +pd+v k+k+g+ +
  gi|298675323|ref|YP_003727073.1| 299 VRSKYIMEKIISADNADMISMSRPFICEPDFVAKIKEGISE 339
                                       *************************************9976 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   5.5e-07    0.0016     105     238 ..     190     342 ..     137     351 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.5e-07
                                       GSHHHHHHHHHHHHCCSS...S-EEEEEESESS.........TTTC.HHHHHHHHHHCT-SEEEEESS......... CS
                               Dus 105 rkpdlvaqivkavvkave...iPvtvkirigid.........deeenalelakiveaaGaqaltvHgR......... 160
                                       +  + + +i+k ++  +     P+tvk                + ++++++aki++++G++a+ v g          
  gi|298675323|ref|YP_003727073.1| 190 NRTRIITEIIKRIRGMTLdmdYPITVKLNSTDGfgsdsdkpgLDINDTIQIAKILQQNGVNAIEVSGGifethlmsq 266
                                       555666666666555433333788888775433333243333124579********************999999633 PP

                                       ECCCTT-CG--CHHHHH.HHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHHHHHHHHSC--- CS
                               Dus 161 traqnyegtadweaIke.vkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfaestavktgeaep 236
                                        + +  e++a++++ ++ +k+av ipvi  G++++   +++i++   ad + ++r    +P ++a   ++k+g+ e+
  gi|298675323|ref|YP_003727073.1| 267 QNIDSVEKEAYFKKNAKlIKNAVDIPVILVGGVRSKYIMEKIISADNADMISMSRPFICEPDFVA---KIKEGISEE 340
                                       333445559999876651677777****************************************9...888888777 PP

                                       -- CS
                               Dus 237 ap 238
                                       ++
  gi|298675323|ref|YP_003727073.1| 341 SQ 342
                                       65 PP

>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.13     4e+02      76     133 ..     142     209 ..     135     229 .. 0.56
   2 !   13.6   0.0   1.2e-05     0.037      17      67 ..     229     284 ..     221     302 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.13
                                       HHHHHHHH....TT-SEEEEEEE..........S-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ET CS
                         HMGL-like  76 kdikaavealkgagakrvhvfia..........tselhlkaklkkdreevakkaeeavkaarslgkdv 133
                                       +d++ a++++k ag + v++  a            + ++  k + + e+  ++++e++k++r ++ d+
  gi|298675323|ref|YP_003727073.1| 142 EDFANAARRAKAAGFDGVQLHCAhgfllsnfisPYTNQRTDKWGGSVENRTRIITEIIKRIRGMTLDM 209
                                       55566666666666666554433111100000011225566667777777777777777777777774 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 1.2e-05
                                       SS---HHHHHHHHHHHHHHT-SEE--.....TSGGGT.THHHHHHHS---TT-B.. CS
                         HMGL-like  17 kaalsveeklaiakaLdeagvdeiEv.....gfpaaseddfevvraiakavkkari 67 
                                       k  l++++ ++iak L++ gv++iEv         +s++++++v++ a + k+a++
  gi|298675323|ref|YP_003727073.1| 229 KPGLDINDTIQIAKILQQNGVNAIEVsggifETHLMSQQNIDSVEKEAYFKKNAKL 284
                                       5668999*******************998777788999999999998888888764 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   4.1e-06     0.012      65     127 ..     282     345 ..     233     368 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.1e-06
                                       HHHHHHH-SSEEEEESSSSSHHHHHHHHHCT.-SEEEESHHHHH-THHHHHHHHHHCGGGEEEE CS
                      His_biosynth  65 veeiaeevfipvqvGGGIrsledveelleag.adkviigtaavknpelikelaekfgsqkivva 127
                                        + i ++v+ipv + GG+rs   +e++++a  ad ++++   + +p+++ ++ e + +++ +v+
  gi|298675323|ref|YP_003727073.1| 282 AKLIKNAVDIPVILVGGVRSKYIMEKIISADnADMISMSRPFICEPDFVAKIKEGISEESQCVS 345
                                       455889999********************98799******************999987776666 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0         1     3e+03      16      34 ..      83     101 ..      54     112 .. 0.56
   2 ?   13.4   0.3   1.1e-05     0.032     129     197 ..     232     301 ..     231     318 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1
                            DUF561  16 kvisGlnnfnveqvlkiar 34 
                                       +v+s +  +n++ +l+i++
  gi|298675323|ref|YP_003727073.1|  83 QVVSKVHRYNSKIMLQIVH 101
                                       2444444444444444444 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.1e-05
                            DUF561 129 LkleeqvkLakkLeslgvdliqteGkitsis.kakkvndliekslstlastyeiskkvslPvicasGlsd 197
                                       L++++ +++ak L++ gv+ i   G+i +    +++  d +ek +     +  i ++v++Pvi   G+ +
  gi|298675323|ref|YP_003727073.1| 232 LDINDTIQIAKILQQNGVNAIEVSGGIFETHlMSQQNIDSVEKEAYFKKNAKLIKNAVDIPVILVGGVRS 301
                                       7899*********************9987765667777889999999999*************9999865 PP

>> DUF4908  Domain of unknown function (DUF4908)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.8e-05      0.14      79     132 ..      99     152 ..      92     164 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.8e-05
                           DUF4908  79 atklGGlilftddrPtGdavalaGraeslqpallsvnallqrlvqasarasraa 132
                                       + + G   l ++d P  ++ a++ +a+ + p  +s +++lq +   ++ a ra 
  gi|298675323|ref|YP_003727073.1|  99 IVHGGRQSLVSKDYPALAPSAVTDEATGITPVEMSESQILQTIEDFANAARRAK 152
                                       5555667899******************************99876555555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2885.50
//
Query:       gi|298675324|ref|YP_003727074.1|  [L=589]
Description: hypothetical protein Metev_1422 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (589 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 4070.31
//
Query:       gi|298675325|ref|YP_003727075.1|  [L=165]
Description: hypothetical protein Metev_1423 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-17   62.2   0.0    5.4e-17   62.0   0.0    1.1  1  DUF111    Protein of unknown function DUF111


Domain annotation for each model (and alignments):
>> DUF111  Protein of unknown function DUF111
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.0   0.0     3e-21   5.4e-17     247     363 ..       2     132 ..       1     141 [. 0.90

  Alignments for each domain:
  == domain 1  score: 62.0 bits;  conditional E-value: 3e-21
                            DUF111 247 vletniDDlspevlgyvlerLleaGAlDvfltpilmKKgRpavllsvlckeedaeeleellfretttlGvResever 323
                                       +l tn+D +s  +++y++++L+++ A +v+++p ++KKgR  ++  + ++++++e+++e ++ et+ lG+R+ e+e 
  gi|298675325|ref|YP_003727075.1|   2 LLMTNVDSVSCDQIPYIIDELYKKSAKNVHVVPSFTKKGRQEYIFFIDVSKDNMENVAEFMALETGILGIRKIETEH 78 
                                       689************************************************************************** PP

                            DUF111 324 lvlereietvetelg..........evrvKva...ee.vvkvkpEyedvkkiAe 363
                                       +v + +i++v+++++            + K++   ++  +++++E+e++k++ e
  gi|298675325|ref|YP_003727075.1|  79 YVFDFDIQKVNLSFDdndgellwkgCLDAKIVknkQGiPLSARAEFEQLKSATE 132
                                       ***********9998888866666655666666533379999******998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       935  (0.0521501); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1241.78
//
Query:       gi|298675326|ref|YP_003727076.1|  [L=446]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-26   93.5   0.1    2.5e-26   92.2   0.1    1.6  1  OrfB_IS605      Probable transposase
    4.1e-24   84.3   1.3      1e-23   83.0   1.3    1.7  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    3.9e-14   51.9   0.1    1.2e-13   50.3   0.1    1.7  1  HTH_OrfB_IS605  Helix-turn-helix domain
     0.0038   16.9   1.4        1.1    9.1   0.2    2.7  2  zinc_ribbon_2   zinc-ribbon domain
     0.0093   15.9   1.4      0.022   14.7   1.4    1.6  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
  ------ inclusion threshold ------
       0.02   14.9   0.7      0.052   13.6   0.7    1.7  1  DZR             Double zinc ribbon
      0.024   14.8   1.0        5.2    7.2   0.1    2.9  3  ASFV_p27        IAP-like protein p27 C-terminus
      0.037   14.3   1.4       0.51   10.6   0.2    2.6  2  MapZ_EC1        MapZ extracellular domain 1
      0.048   13.2   2.9       0.35   10.4   2.6    2.4  2  TF_Zn_Ribbon    TFIIB zinc-binding
      0.094   12.6   3.0        0.2   11.6   3.0    1.5  1  Remorin_C       Remorin, C-terminal region
       0.12   11.8   6.2        3.5    7.1   0.3    3.4  3  zf-ribbon_3     zinc-ribbon domain
       0.18   11.5   1.0        6.3    6.6   0.1    2.4  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.2   0.1   1.7e-29   2.5e-26       3     117 ..     204     315 ..     202     317 .. 0.97

  Alignments for each domain:
  == domain 1  score: 92.2 bits;  conditional E-value: 1.7e-29
                        OrfB_IS605   3 pvevevelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklar 79 
                                        ve+++++ + ++++a+giDlG++ ++t+++ d   f+  +++l++++ +lake+++l++ + +s+ny k+++k+ r
  gi|298675326|ref|YP_003727076.1| 204 TVELPDNPVPSTPENAVGIDLGLKSFITTSDDD---FVEPPKFLRKAENRLAKEQRKLSRMKFRSNNYNKQKQKVNR 277
                                       689999999************************...***************************************** PP

                        OrfB_IS605  80 lhrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       +hrk++  r+h+ h l++ l+++++ ++ e+L+++n+ 
  gi|298675326|ref|YP_003727076.1| 278 IHRKVAAARNHFSHCLSKLLVNKYDLIVFEELKIKNLI 315
                                       ***********************************986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.0   1.3   6.7e-27     1e-23       1      68 [.     329     398 ..     329     399 .. 0.98

  Alignments for each domain:
  == domain 1  score: 83.0 bits;  conditional E-value: 6.7e-27
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke..alsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       ++kl + + yka e+G+ v +vnp +TS+ Cs+Cg k+ke  +l++rtf+C+nCg+e+drD+nA++N+l 
  gi|298675326|ref|YP_003727076.1| 329 WNKLVQHVTYKAAEKGKIVDKVNPDNTSQVCSHCGTKKKEklRLENRTFYCSNCGLEMDRDLNASVNVLT 398
                                       99*****************************************************************987 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3   0.1     8e-17   1.2e-13       5      44 ..      11      50 ..       9      52 .. 0.94

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 8e-17
                    HTH_OrfB_IS605  5 aykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayee 44
                                        ++r+ PTpeQe kl++t++c+R+++N+ L+ + + ye+
  gi|298675326|ref|YP_003727076.1| 11 NLRFRIHPTPEQEKKLNETLECCRLIWNHLLSLQVDLYER 50
                                      679***********************************98 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.2   0.00073       1.1      11      22 ..     354     365 ..     349     366 .. 0.72
   2 !    6.1   0.1    0.0065       9.7       1      20 [.     378     383 ..     368     387 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00073
                     zinc_ribbon_2  11 dnakFCpyCGtp 22 
                                       ++++ C++CGt+
  gi|298675326|ref|YP_003727076.1| 354 NTSQVCSHCGTK 365
                                       477779999997 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0065
                     zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCG 20 
                                       +              C++CG
  gi|298675326|ref|YP_003727076.1| 378 Y--------------CSNCG 383
                                       3..............66666 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   1.4   1.5e-05     0.022      19      44 ..     357     383 ..     351     385 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.5e-05
                     Zn_Tnp_IS1595  19 fvCPhCgsr..kayriktrglfqCkeCr 44 
                                       +vC hCg +  +  r+++ + f C+ C+
  gi|298675326|ref|YP_003727076.1| 357 QVCSHCGTKkkEKLRLEN-RTFYCSNCG 383
                                       89*******999999998.********7 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.7   3.5e-05     0.052      10      40 ..     354     388 ..     349     394 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.5e-05
                               DZR  10 pdarfCseCgtklkavaa....edrCpsCgekvdp 40 
                                       + +++Cs+Cgtk k+  +       C++Cg ++d 
  gi|298675326|ref|YP_003727076.1| 354 NTSQVCSHCGTKKKEKLRlenrTFYCSNCGLEMDR 388
                                       66788888888865444455557778888877665 PP

>> ASFV_p27  IAP-like protein p27 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       2.1   3.1e+03       6      42 ..     224     263 ..     219     276 .. 0.63
   2 ?    5.3   0.0     0.013        19      71     102 ..     334     365 ..     314     369 .. 0.85
   3 ?    7.2   0.1    0.0035       5.2      86     106 ..     369     389 ..     365     406 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.1
                          ASFV_p27   6 iglkkmidsyn.dyynnevfv.khknrvythkr.ledmgf 42 
                                       +glk +i + + d+ +   f+ k +nr+   +r l  m f
  gi|298675326|ref|YP_003727076.1| 224 LGLKSFITTSDdDFVEPPKFLrKAENRLAKEQRkLSRMKF 263
                                       6889888755405555555552667887655432666766 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.013
                          ASFV_p27  71 ryftfkfaahllsfhkvnldnqttycmtcgie 102
                                       +++t+k a +   + kvn dn +  c  cg +
  gi|298675326|ref|YP_003727076.1| 334 QHVTYKAAEKGKIVDKVNPDNTSQVCSHCGTK 365
                                       46899999999999****************76 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0035
                          ASFV_p27  86 kvnldnqttycmtcgiepikk 106
                                       k+ l+n+t yc  cg+e  + 
  gi|298675326|ref|YP_003727076.1| 369 KLRLENRTFYCSNCGLEMDRD 389
                                       889*************96443 PP

>> MapZ_EC1  MapZ extracellular domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1      0.23   3.4e+02      24      41 ..      86     103 ..      77     110 .. 0.86
   2 ?   10.6   0.2   0.00034      0.51      25      78 ..     226     285 ..     217     290 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.23
                          MapZ_EC1  24 eyaafftddketflknse 41 
                                       +y++ff d ++  lkn++
  gi|298675326|ref|YP_003727076.1|  86 AYDKFFDDLEKGRLKNTK 103
                                       79**************98 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00034
                          MapZ_EC1  25 yaafftddketflknsef.ak....lseLekkLeklk.gskeYkklkkkldslkkqisai 78 
                                       +++f t++++ f+ + +f  k    l + + kL  +k  s++Y+k k+k++++ ++++a 
  gi|298675326|ref|YP_003727076.1| 226 LKSFITTSDDDFVEPPKFlRKaenrLAKEQRKLSRMKfRSNNYNKQKQKVNRIHRKVAAA 285
                                       78999**********999976222244557789999999*****************9885 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.2     0.015        22      13      27 ..     350     364 ..     347     370 .. 0.87
   2 ?   10.4   2.6   0.00023      0.35       2      32 ..     358     389 ..     357     393 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.015
                                       EETSTTCEEESSSSB CS
                      TF_Zn_Ribbon  13 eDpergelvCtdCGl 27 
                                       ++p+++  vC+ CG+
  gi|298675326|ref|YP_003727076.1| 350 VNPDNTSQVCSHCGT 364
                                       68999999******7 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00023
                                       EETTTTCEE.CHEETSTTCEEESSSSBEEEEC CS
                      TF_Zn_Ribbon   2 kCPnCgstn.lveDpergelvCtdCGlVledn 32 
                                       +C  Cg+++   +  e+ +++C++CGl ++ +
  gi|298675326|ref|YP_003727076.1| 358 VCSHCGTKKkEKLRLENRTFYCSNCGLEMDRD 389
                                       899****8878899999**********98765 PP

>> Remorin_C  Remorin, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   3.0   0.00013       0.2      38      79 ..     245     288 ..     242     294 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                         Remorin_C  38 akaeaelrkleeklEkkr..akaleklknklariekkAeekRas 79 
                                       +kae++l+k ++kl +++  +++ +k k+k++ri++k + +R +
  gi|298675326|ref|YP_003727076.1| 245 RKAENRLAKEQRKLSRMKfrSNNYNKQKQKVNRIHRKVAAARNH 288
                                       59*************997226667899*************9986 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.33   4.9e+02      13      21 ..       3      11 ..       2      11 .. 0.84
   2 ?    7.1   0.3    0.0024       3.5      13      25 ..     353     365 ..     349     365 .. 0.79
   3 ?    5.1   0.1     0.011        16       2       9 ..     376     383 ..     375     386 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.33
                       zf-ribbon_3 13 ssddnvCpy 21
                                      ++dd++C +
  gi|298675326|ref|YP_003727076.1|  3 RKDDQNCRN 11
                                      79*****86 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0024
                       zf-ribbon_3  13 ssddnvCpyCGtk 25 
                                       +   +vC +CGtk
  gi|298675326|ref|YP_003727076.1| 353 DNTSQVCSHCGTK 365
                                       556789*****96 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.011
                       zf-ribbon_3   2 tvrCPnCG 9  
                                       t +C+nCG
  gi|298675326|ref|YP_003727076.1| 376 TFYCSNCG 383
                                       67999998 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1    0.0042       6.3       2      12 ..     355     365 ..     354     368 .. 0.87
   2 ?    3.1   0.1      0.05        75       5      12 ..     378     385 ..     374     389 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0042
                     zf-NADH-PPase   2 thrFCgrCGap 12 
                                       t++ C++CG++
  gi|298675326|ref|YP_003727076.1| 355 TSQVCSHCGTK 365
                                       7899*****97 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.05
                     zf-NADH-PPase   5 FCgrCGap 12 
                                       +C+ CG +
  gi|298675326|ref|YP_003727076.1| 378 YCSNCGLE 385
                                       67777744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1161  (0.0647554); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3346.24
//
Query:       gi|298675327|ref|YP_003727077.1|  [L=166]
Description: hypothetical protein Metev_1426 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-53  180.5   4.5    3.9e-53  180.3   4.5    1.0  1  DUF2115        Uncharacterized protein conserved in archaea (
     0.0011   19.1   1.5     0.0051   16.9   0.3    2.1  2  Erf4           Golgin subfamily A member 7/ERF4 family
  ------ inclusion threshold ------
      0.068   12.8   1.8      0.099   12.2   0.3    1.7  2  Peptidase_M85  NFkB-p65-degrading zinc protease


Domain annotation for each model (and alignments):
>> DUF2115  Uncharacterized protein conserved in archaea (DUF2115)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.3   4.5   6.6e-57   3.9e-53       2     163 ..       3     159 ..       2     160 .. 0.96

  Alignments for each domain:
  == domain 1  score: 180.3 bits;  conditional E-value: 6.6e-57
                           DUF2115   2 kgeLleilkkeaskisieDlmkisarlekeikklpekyrkelseslteylfeaykelknkrsgdkseykeevideee 78 
                                       +++L+++lkk+a kisi+Dlmk++a++e + ++lpeky+k+++++l+ey+f+++ e+kn    ++s ++ e+ide+ 
  gi|298675327|ref|YP_003727077.1|   3 TSQLFQCLKKNALKISIHDLMKAKAYIEYNNRNLPEKYQKDYTQNLFEYIFNTLIEIKN----KNSVDSVEHIDENV 75 
                                       579********************************************************....5555566789**** PP

                           DUF2115  79 lkeflemleeqceeekeekeerlrklyylvslYliFvleePlHpvgtpfPGgfkveekdgeyYCPvkdkqkdvekal 155
                                       +k+++e++++  e++++e ++ +++l+++vslYl+F++++P+Hp g+ fPGgfk++++ g+yYCPvk+kq+ +e+al
  gi|298675327|ref|YP_003727077.1|  76 FKDLVEKINRLNENYSPE-QKIFNRLIKIVSLYLVFIAKKPIHPEGMIFPGGFKITKESGVYYCPVKNKQSGIEFAL 151
                                       *****************9.********************************************************** PP

                           DUF2115 156 CkfCiakq 163
                                       C+fC++++
  gi|298675327|ref|YP_003727077.1| 152 CDFCVCRD 159
                                       ******98 PP

>> Erf4  Golgin subfamily A member 7/ERF4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1     0.061   3.7e+02      80      97 ..      20      39 ..       3      54 .. 0.69
   2 !   16.9   0.3   8.5e-07    0.0051      27      73 ..      69     112 ..      39     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.061
                              Erf4 80 kklkklekyieelNeel..f 97
                                      + l k ++yie  N++l  +
  gi|298675327|ref|YP_003727077.1| 20 HDLMKAKAYIEYNNRNLpeK 39
                                      45777899999999988541 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 8.5e-07
                              Erf4  27 gyiseeefeeiinkiNeilaeafspysvrnildnvlglltlylwslv 73 
                                       + i+e+ f+++++kiN  l e++sp   ++i++ ++++++lyl+ + 
  gi|298675327|ref|YP_003727077.1|  69 EHIDENVFKDLVEKIN-RLNENYSP--EQKIFNRLIKIVSLYLVFIA 112
                                       4599************.89******..9**************99775 PP

>> Peptidase_M85  NFkB-p65-degrading zinc protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.3     0.059   3.5e+02      68     113 ..      12      57 ..       2      63 .. 0.79
   2 ?   12.2   0.3   1.7e-05     0.099     200     244 ..      58     105 ..      45     109 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.059
                     Peptidase_M85  68 rkavafsireerenlgfikyrNeYelneesevrledldelsldeil 113
                                       ++a++ si++  +   +i+y N  + ++++++  ++l e+ ++++ 
  gi|298675327|ref|YP_003727077.1|  12 KNALKISIHDLMKAKAYIEYNNRNLPEKYQKDYTQNLFEYIFNTLI 57 
                                       5789999999999999999999999999988888888887777665 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 1.7e-05
                     Peptidase_M85 200 eFkgYadpeRveairerefqaLletitRheee...eeelleRLleise 244
                                       e k+ ++++ ve+i e  f+ L+e i+R +e+   e+++++RL++i +
  gi|298675327|ref|YP_003727077.1|  58 EIKNKNSVDSVEHIDENVFKDLVEKINRLNENyspEQKIFNRLIKIVS 105
                                       567889**********************9987444689*******976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1506  (0.083998); expected 358.6 (0.02)
Passed bias filter:                      683  (0.0380947); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1178.53
//
Query:       gi|298675328|ref|YP_003727078.1|  [L=237]
Description: cytochrome c assembly protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-29  103.8  14.7    1.1e-29  103.8  14.7    2.0  2  Cytochrom_C_asm  Cytochrome C assembly protein
     0.0039   16.2   4.9      0.012   14.7   4.9    1.7  1  PalH             PalH/RIM21
  ------ inclusion threshold ------
       0.13   12.4   0.5       0.13   12.4   0.5    3.7  4  DUF2304          Uncharacterized conserved protein (DUF2304)
        1.6    7.7   8.2       0.44    9.6   4.4    1.9  2  DUF973           Protein of unknown function (DUF973)
        2.5    8.4   5.4        7.4    6.8   0.4    2.3  2  PRCH             Photosynthetic reaction centre, H-chain N-te
        4.5    7.1  12.5        1.8    8.4   1.6    3.5  4  DUF1461          Protein of unknown function (DUF1461)


Domain annotation for each model (and alignments):
>> Cytochrom_C_asm  Cytochrome C assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.8  14.7   3.6e-33   1.1e-29      27     211 ..       5     174 ..       1     176 [. 0.91
   2 ?    2.0   0.1      0.05   1.5e+02      38      67 ..     200     229 ..     195     235 .. 0.72

  Alignments for each domain:
  == domain 1  score: 103.8 bits;  conditional E-value: 3.6e-33
                   Cytochrom_C_asm  27 rklnlsllaavaliaalillgfalflllaelqesadlnpalqspilmiHvplallsYatliigallsialliierql 103
                                       ++ +++lla ++ ia+++++g+++f l+ ++  ++  + +++ +i++iH p+a++sY ++ i++++ i++l      
  gi|298675328|ref|YP_003727078.1|   5 ESKKVNLLAVLTTIAIIVATGMIFFYLP-QMTGGSSEVLGESFKIFYIHLPIAFTSYLAFFIVFVAGIMYL------ 74 
                                       5567999*****************9555.56666677899*******************************...... PP

                   Cytochrom_C_asm 104 kkkkklklsanlkllkqldrlsyriiliGfvlltigiilGsvWaeeaWGsywsWDpketaslitWlvfaallhsri. 179
                                                    ++k++d l+++ + +G+ + ++ i +Gs+Wa+ +WG yw+W p++t sl+++lv++a+++ r  
  gi|298675328|ref|YP_003727078.1|  75 -----------RSSNKKWDILARSSAEVGIGFAFLVIATGSIWAKAVWGWYWIWEPRLTTSLVLLLVYLAYFMVRQs 140
                                       ...........56788889999*****************************************************99 PP

                   Cytochrom_C_asm 180 .ek.gwrgkkaailailgflllllayfgvrllge 211
                                         + + r++ ++i+ i+gf  ++l +++vrl+++
  gi|298675328|ref|YP_003727078.1| 141 iDEpETRARLSSIFGIVGFAAVPLSFLSVRLWRS 174
                                       8667***************************984 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.05
                   Cytochrom_C_asm  38 aliaalillgfalflllaelqesadlnpal 67 
                                       +l+++ i++++++++l++  +++++l+   
  gi|298675328|ref|YP_003727078.1| 200 TLLVNFIAFFMLFATLFVYKIQNEELKEQV 229
                                       566677777777778888888888887655 PP

>> PalH  PalH/RIM21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   4.9   3.8e-06     0.012     180     277 ..      10     226 ..       1     234 [. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.8e-06
                              PalH 180 riiilvGlaliildt..ilsalllfskkfldalpalsylfelalvtlyaalviyYliskrkyilspkrm........ 246
                                        +  +++++ ii+ t  i++ l++++  + ++l   +++f + l +++ + ++++++  +++++  +++        
  gi|298675328|ref|YP_003727078.1|  10 NLLAVLTTIAIIVATgmIFFYLPQMTGGSSEVLGESFKIFYIHLPIAFTSYLAFFIVFVAGIMYLRSSNkkwdilar 86 
                                       34444555555544422777888887799************************************8888******** PP

                              PalH 247 ............................................................................. 246
                                                                                                                    
  gi|298675328|ref|YP_003727078.1|  87 ssaevgigfaflviatgsiwakavwgwywiweprlttslvlllvylayfmvrqsidepetrarlssifgivgfaavp 163
                                       ***************************************************************************** PP

                              PalH 247 ...............................ketilllilnllvi.llpvvffildisnadva 277
                                                                       ++il+l++n++++ +l+ ++f+ +i+n ++ 
  gi|298675328|ref|YP_003727078.1| 164 lsflsvrlwrsvhplmfgesiyggsggglegPSLILTLLVNFIAFfMLFATLFVYKIQNEELK 226
                                       *********************************************99999*******998765 PP

>> DUF2304  Uncharacterized conserved protein (DUF2304)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   4.2      0.66     2e+03      43      68 ..      27      52 ..       3      89 .. 0.48
   2 ?   -3.2   6.2       3.2   9.6e+03       7      46 ..      62     102 ..      55     141 .. 0.48
   3 ?    1.4   0.2      0.12   3.6e+02       7      39 ..     126     159 ..     120     170 .. 0.41
   4 ?   12.4   0.5   4.5e-05      0.13      66      99 ..     202     235 ..     194     236 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.66
                           DUF2304 43 vlslfpqiltvlanllGvgrgtnllf 68
                                      ++   pq++   +++lG ++++  + 
  gi|298675328|ref|YP_003727078.1| 27 IFFYLPQMTGGSSEVLGESFKIFYIH 52
                                      33344555555555555444432222 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.2
                           DUF2304   7 iivsvllllliirlvrkkklkl.eysllwlllalilivlsl 46 
                                        +++v+++ +++ +  +kk ++  +s + + ++++ +v++ 
  gi|298675328|ref|YP_003727078.1|  62 AFFIVFVAGIMYLRSSNKKWDIlARSSAEVGIGFAFLVIAT 102
                                       44555555555555555555441344444444444444443 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.12
                           DUF2304   7 iivsvllllliir.lvrkkklkleysllwlllal 39 
                                       ++++v+l+++++r ++ + +++++ s ++ ++++
  gi|298675328|ref|YP_003727078.1| 126 VLLLVYLAYFMVRqSIDEPETRARLSSIFGIVGF 159
                                       3333333333333123333333333333333333 PP

  == domain 4  score: 12.4 bits;  conditional E-value: 4.5e-05
                           DUF2304  66 llfllgivfllvilfslslklskleekikeLaqe 99 
                                       l+ ++++++l+ +lf   ++ ++l+e++++L q 
  gi|298675328|ref|YP_003727078.1| 202 LVNFIAFFMLFATLFVYKIQNEELKEQVNDLKQS 235
                                       6779***************************996 PP

>> DUF973  Protein of unknown function (DUF973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   4.4   0.00015      0.44      18     103 ..      12     100 ..       4     169 .. 0.85
   2 ?   -0.6   0.1      0.18   5.3e+02      16      39 ..     198     222 ..     194     236 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00015
                            DUF973  18 asllaliliilvlvvlftaissgl...sqliqssasilssvlllliaaiiliiiasvllilgllkirsgfsiLsstg 91 
                                        ++l+ i+ii+   ++f ++ + +   s++  +s +i+ + l +++ + +   i+ v  i++l +  + + iL+  +
  gi|298675328|ref|YP_003727078.1|  12 LAVLTTIAIIVATGMIFFYLPQMTggsSEVLGESFKIFYIHLPIAFTSYLAFFIVFVAGIMYLRSSNKKWDILARSS 88 
                                       4677888888877777775555556669**********************9999999******************** PP

                            DUF973  92 rdvgiGitgltl 103
                                        +vgiG + l++
  gi|298675328|ref|YP_003727078.1|  89 AEVGIGFAFLVI 100
                                       ******875544 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.18
                            DUF973  16 iiasllaliliilvlvvlft.aiss 39 
                                       i++ l+++i+ ++ +++lf   i++
  gi|298675328|ref|YP_003727078.1| 198 ILTLLVNFIAFFMLFATLFVyKIQN 222
                                       5555777777777777777654443 PP

>> PRCH  Photosynthetic reaction centre, H-chain N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.4    0.0025       7.4       7      34 ..      53      80 ..      47      82 .. 0.84
   2 ?    3.6   0.6     0.024        72      12      35 ..     203     227 ..     199     230 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0025
                                      X-HHHHHHHHHHHHHHHHHHHHHHHTTS CS
                              PRCH  7 ldvAqlvlyaFwiFfagLifYlrrEdkR 34
                                      l +A  +  aF+i f++ i+Ylr  +k+
  gi|298675328|ref|YP_003727078.1| 53 LPIAFTSYLAFFIVFVAGIMYLRSSNKK 80
                                      5677888899*************99985 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.024
                                       HHHHHHHHHHHHHHHH.HHHHTTSS CS
                              PRCH  12 lvlyaFwiFfagLifY.lrrEdkRE 35 
                                       + ++aF++ fa+L +Y +++E+ +E
  gi|298675328|ref|YP_003727078.1| 203 VNFIAFFMLFATLFVYkIQNEELKE 227
                                       5678999999999777478887666 PP

>> DUF1461  Protein of unknown function (DUF1461)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       0.6   1.8e+03     136     148 ..      14      26 ..       4      37 .. 0.47
   2 ?    8.4   1.6    0.0006       1.8      98     154 ..      55     111 ..      44     118 .. 0.68
   3 ?    1.4   0.0     0.088   2.6e+02     103     166 ..     124     180 ..     119     185 .. 0.49
   4 ?    3.4   0.1     0.021        63       7      40 ..     197     229 ..     192     237 .] 0.64

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.6
                           DUF1461 136 villlliliilgl 148
                                       v+++++i++++g+
  gi|298675328|ref|YP_003727078.1|  14 VLTTIAIIVATGM 26 
                                       2222222222222 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0006
                           DUF1461  98 ivrlvtlillvllllllivlkkkkkkirllkskslllavilllliliilgllalidF 154
                                       i +   l++++++++ +++l+ ++kk+ +l+ +s  +++++ +l+++ + ++a   +
  gi|298675328|ref|YP_003727078.1|  55 IAFTSYLAFFIVFVAGIMYLRSSNKKWDILARSSAEVGIGFAFLVIATGSIWAKAVW 111
                                       44445566666777777777778888***9977888888887888777777765555 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.088
                           DUF1461 103 tlillvllllllivlkkkkkkirllkskslllavilllliliilgllalidFdkaFtlFHkifF 166
                                       +l+ll+++l++++v++  ++  +  + +s++  v++ +++l +l +       +++   H ++F
  gi|298675328|ref|YP_003727078.1| 124 SLVLLLVYLAYFMVRQSIDEPETRARLSSIFGIVGFAAVPLSFLSV-------RLWRSVHPLMF 180
                                       4555555566666655554444444434444444444444444433.......45555555555 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.021
                           DUF1461   7 lilvllvlsvelvinskkplyekeikklnvkest 40 
                                       lil+llv  +++ ++++  l+ ++i++ ++ke++
  gi|298675328|ref|YP_003727078.1| 197 LILTLLVNFIAFFMLFA-TLFVYKIQNEELKEQV 229
                                       56666666666666663.6777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1134  (0.0632495); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 1743.98
//
Query:       gi|298675329|ref|YP_003727079.1|  [L=224]
Description: cytochrome c-type biogenesis protein CcmB [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.2e-37  127.2  12.4    6.9e-37  127.0  12.4    1.0  1  CcmB             CcmB protein
    9.9e-14   51.2  18.3    9.9e-14   51.2  18.3    1.5  2  ABC2_membrane    ABC-2 type transporter
     0.0091   15.1  32.8     0.0081   15.3  28.8    2.2  2  ABC2_membrane_3  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> CcmB  CcmB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.0  12.4   1.2e-40   6.9e-37       3     213 ..       6     222 ..       4     224 .] 0.95

  Alignments for each domain:
  == domain 1  score: 127.0 bits;  conditional E-value: 1.2e-40
                              CcmB   3 alllrdlrlalRakgelllgllFfllvvtllplavGP...dtallsriapgilWvaallaslLsldrlfaadfedGs 76 
                                       ++ l+dl+ ++R+k+ l   l+F l+v++++ +++G     ++++ ++apg+lW++  +a  L+l r faa+ e+G 
  gi|298675329|ref|YP_003727079.1|   6 RIALKDLKSEFRTKQMLNSMLVFSLIVIVIFSISFGNllnRSQIIGQLAPGVLWISFTFAGTLGLSRSFAAELENGC 82 
                                       6789********************************733367999******************************** PP

                              CcmB  77 LellllapvplellvlaKalAhwlltglplvllapllalllnleaaalgllaltLllGtpalsllgavgaAltvgLk 153
                                       L+ l l     + ++++K+l   +l+ +  +++ pl+ +++n++++++    + L+lGt +   +g++ +Altv+++
  gi|298675329|ref|YP_003727079.1|  83 LDGLKLCSFNWNSIYIGKMLSSTILMIIIELIIIPLFVVFFNFNIQGIYGFFIILVLGTIGYISVGTLLSALTVNIR 159
                                       ***************************************************************************** PP

                              CcmB 154 rgglLlslLvlPliiPvlifaveaveaaaeg...ldveaalalllaltvvtlvlapfAaaaal 213
                                         ++Ll++L lPliiPvl+ av a+ ++  g   +dv   ++ll+  ++++ v+a + +  a+
  gi|298675329|ref|YP_003727079.1| 160 TREILLPVLLLPLIIPVLLPAVLATGKLFSGgniTDVFQEIRLLIVYDIIFFVIAQLVFEYAI 222
                                       ************************99988887888999999**********999998887776 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2  18.3   1.7e-17   9.9e-14       6     174 ..       7     174 ..       3     179 .. 0.89
   2 ?   -1.9   0.2      0.31   1.9e+03      26      41 ..     196     211 ..     180     222 .. 0.53

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 1.7e-17
                     ABC2_membrane   6 llkreflqrwrdpslgllwrliqplllalvfgtvfgnlgnsedgl.nr.pgllffsvlflafsaltsvapvfererg 80 
                                       +  +++++ +r+++++  ++l++ l+++++f   fgnl n+++++ +  pg+l +s++f ++++l+ + +  e e+g
  gi|298675329|ref|YP_003727079.1|   7 IALKDLKSEFRTKQML-NSMLVFSLIVIVIFSISFGNLLNRSQIIgQLaPGVLWISFTFAGTLGLSRS-FAAELENG 81 
                                       567889999****888.9*******************886666665557************5555555.******** PP

                     ABC2_membrane  81 vlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldlsrf.flflllllltalaasslgllisalap 156
                                        l+ +    +  + +++++k+l++ ++++++ li++ +++++++++++ +   f+++l+l ++  +s+g l+sal++
  gi|298675329|ref|YP_003727079.1|  82 CLDGLKLCSF-NWNSIYIGKMLSSTILMIIIELIIIPLFVVFFNFNIQ-GiYGFFIILVLGTIGYISVGTLLSALTV 156
                                       **********.*************9999999999988777778****8.55888999999***************** PP

                     ABC2_membrane 157 sfedasqlaslvllplll 174
                                       ++++  +l +++llpl++
  gi|298675329|ref|YP_003727079.1| 157 NIRTREILLPVLLLPLII 174
                                       ***************975 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.31
                     ABC2_membrane  26 liqplllalvfgtvfg 41 
                                       ++q + l++v+  +f+
  gi|298675329|ref|YP_003727079.1| 196 VFQEIRLLIVYDIIFF 211
                                       4444444444444444 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3  28.8   1.4e-06    0.0081     135     282 ..      28     174 ..       3     185 .. 0.74
   2 ?    0.1   0.8     0.058   3.4e+02     307     343 ..     173     214 ..     168     216 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.4e-06
                   ABC2_membrane_3 135 qseatstsaninvestqleeelsnvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskil 211
                                       +s + +  ++i++ +  l + ++ + + + g++ i + f + + +++s++ E e++ + +++++  +  +++++k+l
  gi|298675329|ref|YP_003727079.1|  28 FSLIVIVIFSISFGN--LLNRSQIIGQLAPGVLWISFTFAGTLGLSRSFAAELENGCLDGLKLCSFNWNSIYIGKML 102
                                       444444444444443..355555666666668888888888999999****************************** PP

                   ABC2_membrane_3 212 gdflvyllqlllil.ll..afglgipfgnlglllllfllfglayialgyllsslfknsetaqilifivilllsg 282
                                       ++ ++++++ l+i+ l+  +f+  +++ ++  +++ ++l+ + yi++g+lls+l+ n +t  il+++++l+l++
  gi|298675329|ref|YP_003727079.1| 103 SSTILMIIIELIIIpLFvvFFN--FNIQGIYGFFIILVLGTIGYISVGTLLSALTVNIRTREILLPVLLLPLII 174
                                       *********9988844444566..8888999999*********************9998877777776664443 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.058
                   ABC2_membrane_3 307 fapglgllrli.....tgdplweillsliilalfavvyllla 343
                                         p l+   l+     +g ++ ++++ + +l++  ++++++a
  gi|298675329|ref|YP_003727079.1| 173 IIPVLLPAVLAtgklfSGGNITDVFQEIRLLIVYDIIFFVIA 214
                                       444444444443344456678889999999999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1571.29
//
Query:       gi|298675330|ref|YP_003727080.1|  [L=246]
Description: ABC transporter-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-34  119.9   0.0    1.8e-34  119.2   0.0    1.3  1  ABC_tran      ABC transporter
    2.7e-10   40.5   1.1    9.5e-06   25.6   0.3    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    4.8e-06   25.5   1.0    7.2e-05   21.7   0.1    2.0  2  AAA_13        AAA domain
    3.8e-05   24.3   3.4    6.5e-05   23.5   3.4    1.5  1  AAA_23        AAA domain
    4.1e-05   24.0   0.1    0.00016   22.1   0.1    1.9  1  AAA           ATPase family associated with various cellular 
    4.8e-05   22.9   1.7      0.011   15.1   1.7    2.2  1  SMC_N         RecF/RecN/SMC N terminal domain
    0.00014   21.5   0.1    0.00025   20.7   0.1    1.3  1  AAA_29        P-loop containing region of AAA domain
    0.00047   19.9   1.1     0.0014   18.4   1.1    1.9  1  AAA_24        AAA domain
      0.001   19.3   1.0      0.028   14.7   0.9    2.3  2  AAA_22        AAA domain
     0.0011   19.4   0.0     0.0017   18.8   0.0    1.4  1  AAA_16        AAA ATPase domain
     0.0056   16.3   0.0       0.17   11.5   0.0    2.1  2  AAA_27        AAA domain
     0.0071   16.1   0.0      0.016   14.9   0.0    1.6  2  AAA_30        AAA domain
     0.0094   15.9   0.3      0.045   13.7   0.2    1.9  2  RsgA_GTPase   RsgA GTPase
  ------ inclusion threshold ------
      0.013   15.5   0.0      0.021   14.7   0.0    1.4  1  NACHT         NACHT domain
      0.024   14.4   0.5        4.2    7.1   0.1    2.2  2  IstB_IS21     IstB-like ATP binding protein
      0.028   14.0   0.0      0.072   12.7   0.0    1.7  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
      0.028   13.8   0.0      0.053   13.0   0.0    1.5  1  SRPRB         Signal recognition particle receptor beta subun
      0.033   14.2   0.1        0.6   10.2   0.0    2.4  2  AAA_14        AAA domain
      0.034   13.6   0.6      0.055   13.0   0.1    1.5  1  AAA_7         P-loop containing dynein motor region
      0.035   14.7   0.4       0.11   13.0   0.4    2.1  1  AAA_18        AAA domain
      0.043   13.1   0.2      0.065   12.5   0.2    1.6  1  KAP_NTPase    KAP family P-loop domain
       0.06   13.8   0.1       0.31   11.4   0.0    2.2  2  RNA_helicase  RNA helicase
      0.062   12.7   0.0       0.13   11.6   0.0    1.5  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
       0.07   13.1   0.0       0.12   12.3   0.0    1.4  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
      0.076   12.8   0.0       0.12   12.1   0.0    1.3  1  DEAD          DEAD/DEAH box helicase
      0.083   13.1   0.2       0.22   11.8   0.1    1.7  2  AAA_28        AAA domain
       0.09   12.9   0.1       0.62   10.2   0.0    2.2  2  MMR_HSR1      50S ribosome-binding GTPase
       0.11   12.4   3.0       0.48   10.3   3.0    2.1  1  ATPase_2      ATPase domain predominantly from Archaea
       0.19   10.9   1.5       0.56    9.3   0.0    2.1  2  NB-ARC        NB-ARC domain
        0.2   11.2   0.1       0.39   10.3   0.1    1.4  1  AAA_25        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.2   0.0     3e-37   1.8e-34       1     136 [.      28     171 ..      28     172 .. 0.98

  Alignments for each domain:
  == domain 1  score: 119.2 bits;  conditional E-value: 3e-37
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       lkn+ +++k+g++vai G+nGaGK+tL+k+l+ l +pteG++ +++ d+++ + +  rk+ig+l++e++l ++lt++
  gi|298675330|ref|YP_003727080.1|  28 LKNICFSVKKGSTVAIYGPNGAGKTTLFKILSTLWTPTEGSVAINKFDVST-DSSNIRKSIGILSHETFLYNDLTAE 103
                                       79************************************************9.99*********************** PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       en               d++ie +l+k g+++ ++++v    s+LS G+kqr+++ar+l+ +p++l+lDEp 
  gi|298675330|ref|YP_003727080.1| 104 ENlrfygqmygidndILDKRIEYLLEKTGITYRATDRV----SELSRGMKQRLSIARTLIHEPQVLFLDEPY 171
                                       *************9999999************9****9....*****************************5 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.3   1.6e-08   9.5e-06       3      37 ..      42      85 ..      41     126 .. 0.69
   2 !   13.7   0.0   6.8e-05     0.041     233     297 ..     140     201 ..     114     204 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.6e-08
                            AAA_21  3 vliGpNgsGKSnLLdaldllarl.........drdvegltdels 37
                                      +++GpNg+GK++L+++l+ l+           ++ ++++ +++ 
  gi|298675330|ref|YP_003727080.1| 42 AIYGPNGAGKTTLFKILSTLWTPtegsvainkFDVSTDSSNIRK 85
                                      79****************99766775555333333333333333 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 6.8e-05
                            AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                        ++elS G+k+ l ++  l+  +    +l++DEp +gL+  ++  +  +lkel ++++  ++++H
  gi|298675330|ref|YP_003727080.1| 140 RVSELSRGMKQRLSIARTLIHEP---QVLFLDEPYTGLDQNAVNVFENILKELDSKKTTKLIVSH 201
                                       46789999999988888888777...9*************8885555555555553444455555 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   1.2e-07   7.2e-05      21      80 ..      43     111 ..      39     117 .. 0.79
   2 ?    2.6   0.1      0.07        42     523     572 ..     158     204 ..     150     220 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.2e-07
                            AAA_13  21 iYGwNGaGKTtLSrllrslelgetepkfangsieitnge..........eldirVfNrdFveenlseqge 80 
                                       iYG NGaGKTtL ++l+ l +  te   a  ++ ++ ++          +++++ +N+   eenl+  g+
  gi|298675330|ref|YP_003727080.1|  43 IYGPNGAGKTTLFKILSTLWT-PTEGSVAINKFDVSTDSsnirksigilSHETFLYNDLTAEENLRFYGQ 111
                                       9*****************965.45666677777666665567778888899******9999999984454 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.07
                            AAA_13 523 eigkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnle 572
                                        i + ++ ++D P   LD+n++++  + +k+   ++kk  +l+++ Hn+e
  gi|298675330|ref|YP_003727080.1| 158 LIHEPQVLFLDEPYTGLDQNAVNVFENILKEL--DSKKTTKLIVS-HNIE 204
                                       567899***************98655555555..68888888886.8875 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   3.4   1.1e-07   6.5e-05      14     115 ..      30     135 ..      13     244 .. 0.51

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.1e-07
                            AAA_23  14 eidF...skgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiese.....gkvkayveltfenk 82 
                                       +i F   +   ++I+GpNGaGKTT++  +    +  t++    ++ +  +++ +i ++     +  +++    +++ 
  gi|298675330|ref|YP_003727080.1|  30 NICFsvkKGSTVAIYGPNGAGKTTLFKILSTLWTP-TEGSVAINKFDVSTDSSNIRKSigilsH--ETF---LYNDL 100
                                       4777773334668**************88865554.5555555544555555555554333321..222...22222 PP

                            AAA_23  83 dgrytrsiererelskkkgkttkkaklellei....d 115
                                       + +  +++++  + +  +++  +k ++ lle+     
  gi|298675330|ref|YP_003727080.1| 101 TAE--ENLRFYGQMYGIDNDILDKRIEYLLEKtgitY 135
                                       221..23444444444444444444444444433331 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   2.7e-07   0.00016       2     105 ..      42     197 ..      41     221 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.7e-07
                                       EEESSTTSSHHHHHHHHHHHH.....T...HEE.EEEETTTCSSS................................ CS
                               AAA   2 llyGppGtGKTllakavakel.....g...vef.leisgsellsk................................ 37 
                                        +yGp G GKT+l k + + +     +    +f ++++ s+++++                                
  gi|298675330|ref|YP_003727080.1|  42 AIYGPNGAGKTTLFKILSTLWtptegSvaiNKFdVSTDSSNIRKSigilshetflyndltaeenlrfygqmygidnd 118
                                       68*****************9744433122223345556666664488888888888889999999999999999999 PP

                                       .....................STTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHH CS
                               AAA  38 .....................yvgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlte 92 
                                                             v+e ++ +++ ++ a++   +p +lf+DE +    ++       + +v + +l+e
  gi|298675330|ref|YP_003727080.1| 119 ildkrieyllektgityratdRVSELSRGMKQRLSIARTLIhEPQVLFLDEPYTGLDQN-------AVNVFENILKE 188
                                       99999999999999999998999999999999999999998999********9999888.......77788888888 PP

                                       HHHTTTSSSTEEE CS
                               AAA  93 ldgvkkkeskviv 105
                                       ld  k+      +
  gi|298675330|ref|YP_003727080.1| 189 LDSKKTT----KL 197
                                       8888773....23 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   1.7   1.9e-05     0.011      25     207 ..      39     212 ..      13     220 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.9e-05
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisr 101
                                       s  ai+GpNG+GK+ l+  ++ +           ++ s  i+k     s+++ ++   +   +++ +   ++++ + 
  gi|298675330|ref|YP_003727080.1|  39 STVAIYGPNGAGKTTLFKILSTLWT--------PTEGSVAINK--FDVSTDSSNIRKSIGILSHE-TFLYNDLTAEE 104
                                       456899*******999987733333........3333444444..34444444555444445555.33345566666 PP

                                       EEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 102 rvkrkgeseykingkevtkkevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLD 172
                                       ++   g+  y i++     k ++ lle++gi+        +LS+G k+ +++a  +     +p+ l +lDe    LD
  gi|298675330|ref|YP_003727080.1| 105 NLRFYGQ-MYGIDNDIL-DKRIEYLLEKTGITYRatdrvsELSRGMKQRLSIARTL---IHEPQVL-FLDEPYTGLD 175
                                       6666666.899988655.56899999999999887788889****99988887553...3456655.58******** PP

                                       HHHHHHHHHHHHHH.CTTSEEEEE-SS.HHHCCC-SC CS
                                       xxxxxxxxxxxxxx.xxxxxxxxxxxx.xxxxxxxxx RF
                             SMC_N 173 eknvkkvaellkek.sknaQfivislr.eemlekadk 207
                                       ++ v+ + ++lke  sk++  +++s++ e+ ++ +d+
  gi|298675330|ref|YP_003727080.1| 176 QNAVNVFENILKELdSKKTTKLIVSHNiEQSFKLCDR 212
                                       ***********97524556666667662455555565 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.1   4.1e-07   0.00025      16      56 ..      32      73 ..      21      76 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 4.1e-07
                            AAA_29 16 tieidlkg.atlltGpsGsGKSTllDAiqalLvpak.kvrfNk 56
                                       ++++ kg ++ + Gp+G+GK+Tl+  +++l +p++ +v+ Nk
  gi|298675330|ref|YP_003727080.1| 32 CFSVK-KGsTVAIYGPNGAGKTTLFKILSTLWTPTEgSVAINK 73
                                      45666.44599***********************998888886 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   1.1   2.3e-06    0.0014       4      41 ..      40      72 ..      37     243 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.3e-06
                            AAA_24  4 kiliyGpsgiGKTtlakelgpkplfidtekGlksldad 41
                                       ++iyGp+g+GKTtl k l  ++l   te++++    +
  gi|298675330|ref|YP_003727080.1| 40 TVAIYGPNGAGKTTLFKIL--STLWTPTEGSVA---IN 72
                                      799****************..777777777542...22 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.9   4.6e-05     0.028       5     126 ..      38     198 ..      35     205 .. 0.65
   2 ?    5.9   0.1     0.024        15      35      98 ..     154     217 ..     131     228 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.6e-05
                            AAA_22   5 agilvvtGesGtGKTtllrrlle.qldeeakaee...................erpevvfvtlpsstsskdllrell 61 
                                        + ++++G+ G+GKTtl + l   + + e + +                     + ++++ +l++++    ++ ++ 
  gi|298675330|ref|YP_003727080.1|  38 GSTVAIYGPNGAGKTTLFKILSTlWTPTEGSVAInkfdvstdssnirksigilSHETFLYNDLTAEE-NLRFYGQMY 113
                                       56789**************986514444333333677777777666666666544444444444444.344444444 PP

                            AAA_22  62 ralglelka..............erlsseellealeqalrarav....ielliiDEaqh.lr.s.eealeeL.rsll 116
                                        + ++ l++              ++++ +el + + q l+ +++    +++l +DE    l+ +  +++e++ ++l 
  gi|298675330|ref|YP_003727080.1| 114 GIDNDILDKrieyllektgityrATDRVSELSRGMKQRLSIARTlihePQVLFLDEPYTgLDqNaVNVFENIlKELD 190
                                       44444444477788888888888899999999888888888888899999999999888786524666666623333 PP

                            AAA_22 117 nlsrkgvqli 126
                                          +k ++li
  gi|298675330|ref|YP_003727080.1| 191 S--KKTTKLI 198
                                       3..6666665 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.024
                            AAA_22  35 aee...erpevvfvtlpsst...sskdllrellralglelkaerlsseellealeqalraravielliiD 98 
                                       +++   ++p+v+f + p  +   +  ++++++l++l++++     ++  + + +eq ++ +++  ++i+D
  gi|298675330|ref|YP_003727080.1| 154 IARtliHEPQVLFLDEPYTGldqNAVNVFENILKELDSKKT----TKLIVSHNIEQSFKLCDR--AIILD 217
                                       22256788888899998888877777888888888885333....355555888888888887..77776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   2.8e-06    0.0017      18      88 ..      34     103 ..      25     199 .. 0.60

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.8e-06
                            AAA_16  18 rvrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdql..esaipysa.laqalareellrqllde 88 
                                       +v++g  + v ++G+ G GK++l + l + ++ ++g ++  k+d +  +s+i+ s+ +++   +  l+++l +e
  gi|298675330|ref|YP_003727080.1|  34 SVKKG--STVAIYGPNGAGKTTLFKILSTLWTPTEGSVAINKFDVStdSSNIRKSIgILSHE-T-FLYNDLTAE 103
                                       45566..67***********************************995444444343333333.2.244444444 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00028      0.17      21      49 ..      33      61 ..      28      64 .. 0.79
   2 ?    2.8   0.0      0.12        74     112     142 ..     102     132 ..      81     196 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00028
                            AAA_27 21 fsaeeadlhliyGpNEAGKstalrAisdl 49
                                      fs ++ +   iyGpN AGK+t+++ +s l
  gi|298675330|ref|YP_003727080.1| 33 FSVKKGSTVAIYGPNGAGKTTLFKILSTL 61
                                      6666666778***********99877765 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.12
                            AAA_27 112 ggldretFealFgLdherLreGGealleaeg 142
                                       ++ + +++ +++g+d++ L +  e lle++g
  gi|298675330|ref|YP_003727080.1| 102 AEENLRFYGQMYGIDNDILDKRIEYLLEKTG 132
                                       555667899**********999999998877 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.7e-05     0.016      19      50 ..      39      70 ..      26     116 .. 0.87
   2 ?   -1.8   0.0       3.7   2.2e+03      64      96 ..     129     169 ..     119     198 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.7e-05
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrvi 50
                                       ++++ Gp G+GKtt+ k l  +w+  +g+v+
  gi|298675330|ref|YP_003727080.1| 39 STVAIYGPNGAGKTTLFKILSTLWTPTEGSVA 70
                                      478999******************99876665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.7
                            AAA_30  64 eelgi...eastiakllkrlk........grarlepgtllivDE 96 
                                       e++gi   +++++ +l    +        +r+ +++ ++l  DE
  gi|298675330|ref|YP_003727080.1| 129 EKTGItyrATDRVSELS---RgmkqrlsiARTLIHEPQVLFLDE 169
                                       56666333333333333...344477777556666778888887 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.2   7.5e-05     0.045      78     120 ..      16      59 ..       5      65 .. 0.85
   2 ?   -0.9   0.0       2.3   1.4e+03      50      68 ..      68      86 ..      60     105 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.5e-05
                                       EEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  78 evllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinall 120
                                       + l  s  +++ l+++   +k+ +t+++ G+ G+GK+tL + l 
  gi|298675330|ref|YP_003727080.1|  16 KNLSKSIGNHQVLKNICFSVKKgSTVAIYGPNGAGKTTLFKILS 59 
                                       5566677888999999999998899**************98875 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.3
                                      EEEEE-GGG--HHHHHHHH CS
                       RsgA_GTPase 50 vivlnKiDlleeeeeleel 68
                                       +++nK D+ ++++++++ 
  gi|298675330|ref|YP_003727080.1| 68 SVAINKFDVSTDSSNIRKS 86
                                      6899999999998866654 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   3.6e-05     0.021       2      25 ..      40      63 ..      39     101 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.6e-05
                                      CEEEEC-TTTCHHHHHHHHHHHHC CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawa 25
                                      +v++ G++G GKTtL + l ++w 
  gi|298675330|ref|YP_003727080.1| 40 TVAIYGPNGAGKTTLFKILSTLWT 63
                                      89**************99999986 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1     0.007       4.2      44      63 ..      35      54 ..      15      69 .. 0.85
   2 ?    5.6   0.1      0.02        12      82     143 ..     136     195 ..     126     211 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.007
                         IstB_IS21 44 iekkenivllGpsGvGKshl 63
                                      ++k   +++ Gp G+GK+ l
  gi|298675330|ref|YP_003727080.1| 35 VKKGSTVAIYGPNGAGKTTL 54
                                      678899************88 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.02
                         IstB_IS21  82 rvedLveelkra.rrdgklaralkrllkvdllilDdlgllpldqaeaellfeviekryerrsi 143
                                       r++d v+el+r  ++  ++ar  + + ++++l lD+  ++ ldq++ +++ +++++   ++++
  gi|298675330|ref|YP_003727080.1| 136 RATDRVSELSRGmKQRLSIAR--TLIHEPQVLFLDE-PYTGLDQNAVNVFENILKELDSKKTT 195
                                       445555555554044444444..457889******9.699********999999988776654 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00012     0.072       3      49 ..      41      86 ..      39      97 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                                      EEEEESTTCCHHHHHHHHHCT--SS-EEEEESS-SSCHCCCCCCHCC CS
                              cobW  3 tvltGflGsGKTtLlnhllenraglklavivNefgevsiDaellret 49
                                      + + G+ G+GKTtL + l +     +  v +N f  vs D++ +r++
  gi|298675330|ref|YP_003727080.1| 41 VAIYGPNGAGKTTLFKILSTLWTPTEGSVAINKFD-VSTDSSNIRKS 86
                                      6789***********9999999999999999**99.99**9999887 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.8e-05     0.053       4      62 ..      39      95 ..      36     161 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.8e-05
                                      -EEEEE-STTSSHHHHHHHHHHSS---B---S.S-EEETTG...GGTT-SEEEETT-GCC CS
                             SRPRB  4 pavllvGlsdsGKTslftrLttdsvkktvtSq.essaalkvksekgskltliDfPGhekl 62
                                       +v + G+  +GKT+lf+ L+t   ++t  S+  +++  ++  +  +  + i +  he +
  gi|298675330|ref|YP_003727080.1| 39 STVAIYGPNGAGKTTLFKILST-LWTPTEGSVaINKFDVST--DSSNIRKSIGILSHETF 95
                                      6899*************99987.566777777566665554..33333334444455554 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0     0.001       0.6       4      45 ..      40      80 ..      37     111 .. 0.69
   2 ?    1.7   0.0      0.41   2.4e+02      29      73 ..     129     170 ..     117     201 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.001
                            AAA_14  4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkk 45
                                       ++i G+  +GKTtl  +++++l ++ e  + in  d ++++
  gi|298675330|ref|YP_003727080.1| 40 TVAIYGPNGAGKTTLF-KILSTLWTPTEGSVAINKFDVSTDS 80
                                      689************5.6666666677777777655544433 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.41
                            AAA_14  29 kkesilyinldderdkkladpekllelileklkeekktylflDEi 73 
                                       +k  i y + d+ ++ ++  + + l++ + ++  ++ ++lflDE 
  gi|298675330|ref|YP_003727080.1| 129 EKTGITYRATDRVSELSRGMK-QRLSIARTLI--HEPQVLFLDEP 170
                                       666666666666666443322.2233333333..36789999995 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   9.2e-05     0.055      30      82 ..      35      87 ..      22      89 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.2e-05
                             AAA_7 30 lknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdii 82
                                      +k++  v ++Gp G GKt++ k l +   +++ ++++ +f  +t+++++++ i
  gi|298675330|ref|YP_003727080.1| 35 VKKGSTVAIYGPNGAGKTTLFKILSTLWTPTEGSVAINKFDVSTDSSNIRKSI 87
                                      789999****************99999999999999999*******9999876 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.4   0.00019      0.11       1      21 [.      41      61 ..      41     230 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00019
                            AAA_18  1 IlltGtpGvGKttlakeLskr 21
                                      +++ G+ G+GKttl k Ls +
  gi|298675330|ref|YP_003727080.1| 41 VAIYGPNGAGKTTLFKILSTL 61
                                      689***************876 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   0.00011     0.065      11      56 ..      30      72 ..      15     205 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                        KAP_NTPase 11 ilseptlatpivvgLygkWGsGKssllnkledelkefakpvrflfa 56
                                       ++  +++++++v++yg+ G+GK++l + l   +     + ++++ 
  gi|298675330|ref|YP_003727080.1| 30 NIC-FSVKKGSTVAIYGPNGAGKTTLFKILSTLWTPT--EGSVAIN 72
                                      444.23599********************99988776..4555554 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00052      0.31       2      23 ..      42      63 ..      41     112 .. 0.69
   2 ?   -0.8   0.0       3.2   1.9e+03      22      62 ..     185     230 ..     176     245 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00052
                      RNA_helicase  2 wlyGpsgeGKStlakeLakall 23
                                       +yGp+g GK+tl k L++ ++
  gi|298675330|ref|YP_003727080.1| 42 AIYGPNGAGKTTLFKILSTLWT 63
                                      69*************9877655 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 3.2
                      RNA_helicase  22 llkklklkkkdsvys.rnpeddfw..dgYt..gqevvvidDfgqvk 62 
                                       +lk+l++kk+ ++++ +n e++f   d     ++  +v+dD++++ 
  gi|298675330|ref|YP_003727080.1| 185 ILKELDSKKTTKLIVsHNIEQSFKlcDRAIilDKGKIVFDDLKKDI 230
                                       5555544444444443665555532222222355556677776665 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00022      0.13       6      59 ..      22      75 ..      17      98 .. 0.79
   2 ?   -2.7   0.0       5.3   3.1e+03     109     115 ..     164     170 ..     149     195 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00022
                      Mg_chelatase  6 kGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeealevak 59
                                      +G+++  + +  ++  g  + ++Gp G+GKt l k l++l +p + + a++   
  gi|298675330|ref|YP_003727080.1| 22 IGNHQVLKNICFSVKKGSTVAIYGPNGAGKTTLFKILSTLWTPTEGSVAINKFD 75
                                      677777777778888888999*******************99988777766554 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.3
                      Mg_chelatase 109 vLfLDEl 115
                                       vLfLDE 
  gi|298675330|ref|YP_003727080.1| 164 VLFLDEP 170
                                       8999983 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0    0.0002      0.12      18      40 ..      32      59 ..      11      71 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0002
                                      H.....TEEEEEEESTTSSHHHHHHHHH CS
                              TsaE 18 l.....gdvilLeGdLGaGKTtlvrgla 40
                                      +     g++++++G+ GaGKTtl + l 
  gi|298675330|ref|YP_003727080.1| 32 CfsvkkGSTVAIYGPNGAGKTTLFKILS 59
                                      133334667**************99775 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0    0.0002      0.12      11      87 ..      35     203 ..      24     233 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0002
                                       HHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS........................................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................................ RF
                              DEAD  11 ilgggdvlvaaeTGsGKTlaflipvlqivyetkgktg........................................ 47 
                                       + +g  v + ++ G+GKT+ f i     +++  ++ g                                        
  gi|298675330|ref|YP_003727080.1|  35 VKKGSTVAIYGPNGAGKTTLFKILST--LWT-PTE-Gsvainkfdvstdssnirksigilshetflyndltaeenlr 107
                                       3388999*************988766..443.222.2355677777888899999999******************* PP

                                       ......................................................-EEEEE.ESSHHHHHHHHHHHHH CS
                                       ......................................................xxxxxx.xxxxxxxxxxxxxxxx RF
                              DEAD  48 ......................................................pkaliv.ePtreLaeqtlnnlkk 69 
                                                                                             p++l++ eP + L ++ +n +++
  gi|298675330|ref|YP_003727080.1| 108 fygqmygidndildkrieyllektgityratdrvselsrgmkqrlsiartlihePQVLFLdEPYTGLDQNAVNVFEN 184
                                       ******************************************************99998878*************** PP

                                       HTTTST.SEEEEEETTSSH CS
                                       xxxxxx.xxxxxxxxxxxx RF
                              DEAD  70 fkkyid.lrvlliiggvaa 87 
                                       ++k++d  ++  +i +++ 
  gi|298675330|ref|YP_003727080.1| 185 ILKELDsKKTTKLIVSHNI 203
                                       **99885333333444444 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00037      0.22       2      21 ..      41      60 ..      40      74 .. 0.86
   2 ?   -2.3   0.0       7.8   4.6e+03      47      79 ..     136     168 ..     119     171 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00037
                            AAA_28  2 ivitGgestGKTtlleaLaa 21
                                      ++i G+ ++GKTtl + L+ 
  gi|298675330|ref|YP_003727080.1| 41 VAIYGPNGAGKTTLFKILST 60
                                      89**************9986 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7.8
                            AAA_28  47 pwvedllafaervleeqleeeaaa.aankvlfcD 79 
                                       ++++++ ++ +++ + +l+ ++   ++++vlf+D
  gi|298675330|ref|YP_003727080.1| 136 RATDRVSELSRGMKQ-RLSIARTLiHEPQVLFLD 168
                                       444455555555443.444444435777777777 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0     0.001      0.62       2      21 ..      41      60 ..      40     108 .. 0.75
   2 ?    0.4   0.0       1.1   6.5e+02      28      55 ..     190     214 ..     152     242 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.001
                                      EEEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                                      vai+G   +GK+tL++ l+ 
  gi|298675330|ref|YP_003727080.1| 41 VAIYGPNGAGKTTLFKILST 60
                                      9***************9975 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.1
                                       SSTTSSSSEEEEEEEETTEEEEEEECGG CS
                          MMR_HSR1  28 dkpgtTrdinegrvklkgkeielvDtpG 55 
                                       d + tT+ i+ ++++   ++++l+D + 
  gi|298675330|ref|YP_003727080.1| 190 DSKKTTKLIVSHNIE---QSFKLCDRAI 214
                                       456788888888887...6788888665 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   3.0    0.0008      0.48      21      38 ..      39      56 ..      27     245 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0008
                          ATPase_2 21 eiyfiYGpegsGKtaLlk 38
                                      + + iYGp g GKt+L+k
  gi|298675330|ref|YP_003727080.1| 39 STVAIYGPNGAGKTTLFK 56
                                      5678************98 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00095      0.56      21      38 ..      39      56 ..      24      67 .. 0.84
   2 ?   -0.0   0.4      0.68     4e+02      67     112 ..     180     226 ..     174     242 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00095
                                      EEEEEEESTTSSHHHHHH CS
                            NB-ARC 21 lvvalvGmgGvGKttlak 38
                                        va++G  G GKttl+k
  gi|298675330|ref|YP_003727080.1| 39 STVAIYGPNGAGKTTLFK 56
                                      469*************97 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.68
                                       HHHHXXHHHHHCCCTTSSSS-STTSHHHHHH.HHCCCTTEEEEEEEE CS
                            NB-ARC  67 eiletilkeLslseddleekeeveslkrklv.rlLltkrfllvlDDV 112
                                       +++e+ilkeL  ++    + +++ +   kl+ r+++  +  +v+DD 
  gi|298675330|ref|YP_003727080.1| 180 NVFENILKELDSKKTTKLIVSHNIEQSFKLCdRAIILDKGKIVFDDL 226
                                       68888999998888888888877777777773455555666778886 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00065      0.39      31      50 ..      36      55 ..      22      78 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00065
                            AAA_25 31 pagelallaGapgtGKttla 50
                                       +g++++++G+ g+GKttl 
  gi|298675330|ref|YP_003727080.1| 36 KKGSTVAIYGPNGAGKTTLF 55
                                      689***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 1751.86
//
Query:       gi|298675331|ref|YP_003727081.1|  [L=414]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.4e-25   87.9   0.8    1.5e-24   86.6   0.0    2.0  2  OrfB_IS605      Probable transposase
    3.2e-12   46.2   0.3    9.4e-12   44.7   0.1    2.0  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.018   15.4   0.0      0.037   14.4   0.0    1.5  1  RuvX            Holliday junction resolvase


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.2      0.35   2.1e+03      48      85 ..      11      30 ..       2      64 .. 0.66
   2 !   86.6   0.0   2.4e-28   1.5e-24      14     119 ..     189     292 ..     176     293 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.35
                        OrfB_IS605 48 sdykylakeiaelqsklkksknykkasrklarlhrkrs 85
                                      +d+++                   ++ +++++l+++++
  gi|298675331|ref|YP_003727081.1| 11 ADKQK------------------YEVLKRITKLSKNLY 30
                                      33333..................334444444444444 PP

  == domain 2  score: 86.6 bits;  conditional E-value: 2.4e-28
                        OrfB_IS605  14 kgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsrrrkh 90 
                                       + nk+++iDlG+nn+at v+++gt+f+++gr lks +++++k +  lqs+++k++   k  +kl  l++kr++++++
  gi|298675331|ref|YP_003727081.1| 189 DYNKHLSIDLGVNNFATSVDTNGTAFIIEGRGLKSYNRWWNKVKSGLQSIYDKQG--IKSGQKLNWLFEKRKNKIND 263
                                       679***************************************************9..9******************* PP

                        OrfB_IS605  91 llhklathliktlkevgvetLnvgnmkdi 119
                                       ++++ ++++ik++ +++++++++g++k+i
  gi|298675331|ref|YP_003727081.1| 264 FMNQSVNYIIKHCIDNNIGNIIIGELKNI 292
                                       **************************987 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.7     1e+04       9      23 ..     167     181 ..     167     182 .. 0.83
   2 !   44.7   0.1   1.6e-15   9.4e-12       1      69 []     311     385 ..     311     385 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.7
                    OrfB_Zn_ribbon   9 eykakeyGikveevn 23 
                                       +y  +++ i++++ +
  gi|298675331|ref|YP_003727081.1| 167 KYNGQWFEIEYVYRD 181
                                       688999999999876 PP

  == domain 2  score: 44.7 bits;  conditional E-value: 1.6e-15
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke......alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f+k+k++l+ k++ yGik +ev++ayTSkt +   +  ++      ++ +r +  ++ g  +++Dvn+a+Nil++
  gi|298675331|ref|YP_003727081.1| 311 FGKFKQKLRSKCEYYGIKCIEVDEAYTSKTDALALEPIEKhqkymgKRVKRGLFQSSTGKLLNADVNGALNILRK 385
                                       89****************************887776666666688977788888888***************986 PP

>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   6.2e-06     0.037      36     107 ..     263     346 ..     240     362 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.2e-06
                                       H..HHHHHHHHHHHHHTT--EEEEE--......---..-SSS---SSTTHHHHHHHHHT....T-EEEEE--S---- CS
                              RuvX  36 k..ekdleelkelvkeeeveeiVvGlP......lnl..dgsegesakkvrkfaeeLakrl..kklpvelvDErlttv 100
                                       +  +++++ + + + ++++ +i++G         n+  +++++ ++  + kf ++L++++  ++++ + vDE +t++
  gi|298675331|ref|YP_003727081.1| 263 DfmNQSVNYIIKHCIDNNIGNIIIGELknikqnSNMgkKNNQTFQTIPFGKFKQKLRSKCeyYGIKCIEVDEAYTSK 339
                                       13479999999**************885666653341134444455556899*****99977899***********9 PP

                                       XXXXXXX CS
                              RuvX 101 eaerilr 107
                                       + + +l+
  gi|298675331|ref|YP_003727081.1| 340 TDALALE 346
                                       8776664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1114  (0.062134); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2743.84
//
Query:       gi|298675332|ref|YP_003727082.1|  [L=103]
Description: transposase IS200-family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-27   95.1   1.7    3.7e-27   94.8   1.7    1.0  1  Y1_Tnp    Transposase IS200 like
  ------ inclusion threshold ------
      0.019   14.9   0.2      0.026   14.5   0.2    1.2  1  DUF4768   Domain of unknown function (DUF4768)


Domain annotation for each model (and alignments):
>> Y1_Tnp  Transposase IS200 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.8   1.7   4.2e-31   3.7e-27      24     121 .]       4     102 ..       2     102 .. 0.98

  Alignments for each domain:
  == domain 1  score: 94.8 bits;  conditional E-value: 4.2e-31
                            Y1_Tnp  24 eerlkeiikeiaekkevkilelelmpDHvHllvelppklsiskivkalkgassrlinkefpelkkkklkk.eslWqr 99 
                                       e++lk+i+ +ia+k +++i+e+e+++DH+H+lv+ +pk+si +++++lk++s +li+k+++++ k ++++ ++lW++
  gi|298675332|ref|YP_003727082.1|   4 EDSLKDILITIASKSDFDIVEMECDKDHIHILVKSKPKISILSFIRKLKQESIYLIWKNHKKYLKIYYWNeNTLWSD 80 
                                       6899******************************************************************99***** PP

                            Y1_Tnp 100 gYfvstvgeasletvkrYIenq 121
                                       gYf++t+g+ s++t+ +YI++q
  gi|298675332|ref|YP_003727082.1|  81 GYFCCTIGNISKKTITEYIRSQ 102
                                       *******************988 PP

>> DUF4768  Domain of unknown function (DUF4768)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2   2.9e-06     0.026      14      63 ..      16      63 ..       7      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.9e-06
                           DUF4768 14 lpfdfetshlpCDldssgreklieafpnhCiwaynnkyasegeyrvykiy 63
                                       + df++  + CD d    + l+++ p+  i ++  k ++e+ y ++k +
  gi|298675332|ref|YP_003727082.1| 16 SKSDFDIVEMECDKDHI--HILVKSKPKISILSFIRKLKQESIYLIWKNH 63
                                      5689********99875..889*************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       944  (0.0526521); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 777.13
//
Query:       gi|298675333|ref|YP_003727083.1|  [L=138]
Description: molybdopterin dinucleotide-binding region [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-12   46.8   0.0    3.9e-12   46.2   0.0    1.3  1  Molydop_binding  Molydopterin dinucleotide binding domain
    0.00045   20.3   0.0    0.00068   19.8   0.0    1.2  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
      0.004   17.6   0.1      0.009   16.4   0.1    1.5  1  SAM_1            SAM domain (Sterile alpha motif)


Domain annotation for each model (and alignments):
>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.0   6.5e-16   3.9e-12       4     108 ..      17     113 ..      14     116 .. 0.85

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 6.5e-16
                                       EEE-BTTBSTTTTTCGCCHHHHCSSS-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESS..B-TTEEEEES CS
                   Molydop_binding   4 itgrsldqlhsqtrtrpvlrlakpepevveinpedAaalGikdGdlVevesrrGsvevrakvter..vrpGvvfmpf 78 
                                       it+r   q  +   +    ++++ +   + +  +d++++Gik G +V +++++Gsv+v+a+ +++   ++G ++mp 
  gi|298675333|ref|YP_003727083.1|  17 ITYRDIFQSEALESSLFGDEYKDLSA-IIKLDSNDMEKMGIKSGNTVYLKNKYGSVVVKAVESDSenPHRGYAYMPN 92 
                                       78888888888888888888888888.*********************************7665444********** PP

                                       SHCC.....S-GHCTS--SCSTTT--CSTT CS
                   Molydop_binding  79 gwweagekggnaNaltddatdplsgtpefk 108
                                         w+        Nal+ ++ +  +g p++k
  gi|298675333|ref|YP_003727083.1|  93 SPWS--------NALV-SDETGNTGVPNYK 113
                                       ****........****.5555667777777 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.1e-07   0.00068      14      64 ..      41      92 ..      32     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.1e-07
                                      TTEEEE-HHHHHHHTS-TTSEEEEECCCC.EEEEEEEBSTTSTTTTEEEE-H CS
                           CDC48_N 14 rgivridpedmeelglepgdvveiegkrk.TvaivwpaepedegkgiIrmdg 64
                                        i+ +d++dme++g+++g++v +++k    v+++++++ e +++g+  m +
  gi|298675333|ref|YP_003727083.1| 41 SAIIKLDSNDMEKMGIKSGNTVYLKNKYGsVVVKAVESDSENPHRGYAYMPN 92
                                      57899*********************665599*******9999999887765 PP

>> SAM_1  SAM domain (Sterile alpha motif)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   1.5e-06     0.009      23      49 ..      32      58 ..      29      61 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.5e-06
                                      HHHTTTSSHHHHTTSCHHHHHHCTTTS CS
                             SAM_1 23 lFrageidgdaLlllteddLeklgvtl 49
                                      lF +++ d+ a+ +l+++d+ek+g+++
  gi|298675333|ref|YP_003727083.1| 32 LFGDEYKDLSAIIKLDSNDMEKMGIKS 58
                                      799**********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1005.38
//
Query:       gi|298675334|ref|YP_003727084.1|  [L=417]
Description: formylmethanofuran dehydrogenase subunit B [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-05   23.4   0.2      0.083   12.6   0.0    2.7  2  TPP_enzyme_M     Thiamine pyrophosphate enzyme, central domai
  ------ inclusion threshold ------
      0.041   13.3   0.0        5.4    6.4   0.0    2.9  3  Diphthamide_syn  Putative diphthamide synthesis protein


Domain annotation for each model (and alignments):
>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   9.2e-06     0.083       1      42 [.      65     105 ..      65     190 .. 0.77
   2 !    8.0   0.0   0.00024       2.2       3      39 ..     233     270 ..     231     271 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.2e-06
                                       HHHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EE CS
                      TPP_enzyme_M   1 iekaaellkaakrpvilvGggvarsgaseelrelaeklgiPv 42 
                                       i++ a++lk++++p+i+ G g +++ga++++ ela++l++  
  gi|298675334|ref|YP_003727084.1|  65 ISETANILKKSENPLIF-GLGNSTEGAQKKAIELAKQLNANL 105
                                       67899*********986.7777788**************976 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00024
                                       HHHHHHHH-SSEEEEE-CHHCHT.TGHHHHHHHHHHHT CS
                      TPP_enzyme_M   3 kaaellkaakrpvilvGggvars.gaseelrelaeklg 39 
                                       ++a++lk+ak  vi++G g  +s +  e +++l +kl+
  gi|298675334|ref|YP_003727084.1| 233 ELANILKKAKYGVIFAGLGLVYSlDNLEPIKRLMDKLN 270
                                       789*******************9999999999999986 PP

>> Diphthamide_syn  Putative diphthamide synthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.02   1.8e+02       3      56 ..      88     148 ..      60     164 .. 0.75
   2 ?    6.4   0.0   0.00061       5.4     193     238 ..     225     270 ..     212     290 .. 0.87
   3 ?    1.6   0.0     0.017   1.5e+02     136     186 ..     313     365 ..     280     373 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.02
                   Diphthamide_syn   3 egllpdsaeiadil.eef..........gaevvilgDttYGaCcvdevaaehlgadllvHyGhsc 56 
                                       eg ++ + e+a++l +++           +e ++ g++ Y  C +d+v  +   ad++v  G  +
  gi|298675334|ref|YP_003727084.1|  88 EGAQKKAIELAKQLnANLddtssfcqgpVVEAILNGEINY-TCTLDDVRNN---ADVIVYWGADP 148
                                       5666677777777755555555545444455788888888.5888888644...59999888765 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.00061
                   Diphthamide_syn 193 kllrrRyaaiekakdakkvGiivgtlgvqgrlelverlkkllkeag 238
                                       ++ ++R   ++++ ++ k+G+i+  lg  ++l+ +e +k+l+++ +
  gi|298675334|ref|YP_003727084.1| 225 EMNKKRILELANILKKAKYGVIFAGLGLVYSLDNLEPIKRLMDKLN 270
                                       78999*****************************999999998876 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.017
                   Diphthamide_syn 136 gctspklkee.eeevdailyigdgrf.hllslmlsn.pklpvyrydpyskklte 186
                                       g++++ ++   +++vd+ l+ig+++  +l + +  n +++p++++dp +  lt+
  gi|298675334|ref|YP_003727084.1| 313 GYKYSVVELLkNKSVDSALIIGSDPMcSLPGSIARNlNEIPIITIDPCET-LTS 365
                                       5555555333467899999999888735555555557999*******985.433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 3006.32
//
Query:       gi|298675335|ref|YP_003727085.1|  [L=152]
Description: Fe-S cluster domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.2e-15   54.0   2.2    9.2e-15   54.0   2.2    3.0  3  FeS       Putative Fe-S cluster
    4.7e-11   42.0  21.9    2.6e-08   33.4   5.1    3.3  3  Fer4      4Fe-4S binding domain
    1.4e-09   38.0   6.9    1.4e-09   38.0   6.9    2.5  2  Fer4_10   4Fe-4S dicluster domain
    1.9e-08   34.7  40.9    4.7e-06   27.1  13.1    3.0  4  Fer4_7    4Fe-4S dicluster domain
    1.2e-06   28.4  12.5    5.4e-06   26.2   3.7    3.5  3  Fer4_6    4Fe-4S binding domain
    2.9e-06   27.4   9.5    2.9e-06   27.4   9.5    3.0  2  Fer4_9    4Fe-4S dicluster domain
    9.2e-06   25.5  18.3    2.1e-05   24.4   2.6    3.5  3  Fer4_2    4Fe-4S binding domain
    1.4e-05   25.1  15.0    9.1e-05   22.5   2.0    3.1  3  Fer4_21   4Fe-4S dicluster domain
    3.3e-05   24.2  12.1    0.00057   20.3   6.3    2.4  2  Fer4_8    4Fe-4S dicluster domain
    0.00015   22.5  23.1      0.016   16.1   8.0    3.5  3  Fer4_3    4Fe-4S binding domain
    0.00029   21.3  11.7     0.0013   19.2   5.6    2.5  2  Fer4_17   4Fe-4S dicluster domain
    0.00052   20.9  11.6      0.011   16.6   3.4    3.2  3  Fer4_16   4Fe-4S double cluster binding domain
     0.0016   18.8   3.4     0.0016   18.8   3.4    3.6  3  Fer4_4    4Fe-4S binding domain
     0.0016   19.1   6.8      0.047   14.4   6.8    2.6  1  Fer4_15   4Fe-4S single cluster domain
     0.0028   18.2   9.1     0.0028   18.2   9.1    3.2  3  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
     0.0047   16.9   1.4     0.0047   16.9   1.4    2.6  2  YhfH      YhfH-like protein
  ------ inclusion threshold ------
      0.049   14.5   2.1      0.049   14.5   2.1    2.9  3  Fer4_22   4Fe-4S dicluster domain
        1.8    8.8  14.0        1.5    9.0   3.5    2.6  3  Fer4_18   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> FeS  Putative Fe-S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   2.2   9.2e-18   9.2e-15       1      32 [.      11      42 ..      11      43 .. 0.99
   2 ?   -2.8   3.2       5.3   5.3e+03       4       9 ..      79      84 ..      77      86 .. 0.60
   3 ?   -2.4   1.8         4     4e+03      14      32 ..     127     145 ..     124     146 .. 0.56

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 9.2e-18
                               FeS  1 LPgtNCgaCGypgCmafAealvegeaqledCp 32
                                      LP+tNC++CG  +CmafA+al++ge +l+dCp
  gi|298675335|ref|YP_003727085.1| 11 LPKTNCKKCGKSTCMAFATALLSGELRLDDCP 42
                                      9******************************9 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.3
                               FeS  4 tNCgaC 9 
                                      t Cg C
  gi|298675335|ref|YP_003727085.1| 79 TGCGNC 84
                                      345555 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 4
                               FeS  14 CmafAealvegeaqledCp 32 
                                       C+ f e  +   a +e Cp
  gi|298675335|ref|YP_003727085.1| 127 CRRFGENKILCNACIETCP 145
                                       6655555555555566665 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.7      0.58   5.8e+02       7      12 ..      15      20 ..      13      21 .. 0.73
   2 !   33.4   5.1   2.6e-11   2.6e-08       2      22 ..      72      92 ..      71      94 .. 0.93
   3 !   18.3   1.9   1.5e-06    0.0015       9      24 .]     135     150 ..     135     150 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.58
                                      TSSS-T CS
                              Fer4  7 kCigCG 12
                                       C +CG
  gi|298675335|ref|YP_003727085.1| 15 NCKKCG 20
                                      688888 PP

  == domain 2  score: 33.4 bits;  conditional E-value: 2.6e-11
                                      EEETTTSSS-THHHHHSTTTE CS
                              Fer4  2 videekCigCGaCvevCPvgA 22
                                      +i+eekC+gCG+Cv +CPv++
  gi|298675335|ref|YP_003727085.1| 72 IIHEEKCTGCGNCVVACPVNV 92
                                      799****************96 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 1.5e-06
                                       SS-THHHHHSTTTEEE CS
                              Fer4   9 igCGaCvevCPvgAIt 24 
                                       i C+aC+e CP+ AI+
  gi|298675335|ref|YP_003727085.1| 135 ILCNACIETCPTKAIE 150
                                       78*************6 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   3.0      0.23   2.3e+02       7      17 ..      14      26 ..      10      64 .. 0.59
   2 !   38.0   6.9   1.4e-12   1.4e-09       2      56 .]      71     145 ..      70     147 .. 0.97

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.23
                           Fer4_10  7 dtCirCg..kCvk 17
                                        C +Cg  +C++
  gi|298675335|ref|YP_003727085.1| 14 TNCKKCGksTCMA 26
                                      4566666555665 PP

  == domain 2  score: 38.0 bits;  conditional E-value: 1.4e-12
                           Fer4_10   2 vvidddtCirCgkCvkaCPadl.............tsvgakgeaseeeavrkkvekCtg.......cgaCveaCP 56 
                                       ++i +++C++Cg+Cv aCP+++             ++++++ +  ++ ++++++ +C +       c aC+e CP
  gi|298675335|ref|YP_003727085.1|  71 MIIHEEKCTGCGNCVVACPVNVaedpegtgiglapKNDRVILKVVNGVVQKGNIHNCRRfgenkilCNACIETCP 145
                                       68999***************99*************************************99999999*******9 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   2.2      0.94   9.3e+02      36      45 ..      14      25 ..       3      43 .. 0.73
   2 !   17.7  11.8     4e-06    0.0039       4      52 .]      15      92 ..      14      92 .. 0.48
   3 !   27.1  13.1   4.7e-09   4.7e-06       1      52 []      77     148 ..      77     148 .. 0.65
   4 !   13.7   1.0   7.1e-05     0.071       4      19 ..     136     151 ..     134     152 .] 0.87

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.94
                            Fer4_7 36 ekClgCga..Cv 45
                                      ++C  Cg+  C+
  gi|298675335|ref|YP_003727085.1| 14 TNCKKCGKstCM 25
                                      456666665565 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 4e-06
                            Fer4_7  4 gCgaCv.aaC.........................pvkaieldeeenek...............gtekveidpekClgC 41
                                      +C++C  ++C                         +            +                   + i++ekC+gC
  gi|298675335|ref|YP_003727085.1| 15 NCKKCGkSTCmafatallsgelrlddcpeiledkyK------------QnyeklselvapienaSETGMIIHEEKCTGC 81
                                      566665345633333333333333332222222220............111223333333322222446899******* PP

                            Fer4_7 42 gaCvavCPtga 52
                                      g+Cv +CP+++
  gi|298675335|ref|YP_003727085.1| 82 GNCVVACPVNV 92
                                      ********986 PP

  == domain 3  score: 27.1 bits;  conditional E-value: 4.7e-09
                            Fer4_7   1 rCigCgaCvaaCpvkaielde........eenekgtekv..........eidpekClg.......CgaCvavCPtga 52 
                                       +C+gCg+Cv+aCpv++ e +e        + n++    v          +++  +C         C+aC+++CPt+a
  gi|298675335|ref|YP_003727085.1|  77 KCTGCGNCVVACPVNVAEDPEgtgiglapK-NDR----VilkvvngvvqKGNIHNCRRfgenkilCNACIETCPTKA 148
                                       7*****************765333333212.222....112223444445677889855566666**********87 PP

  == domain 4  score: 13.7 bits;  conditional E-value: 7.1e-05
                            Fer4_7   4 gCgaCvaaCpvkaiel 19 
                                        C+aC ++Cp+kaie+
  gi|298675335|ref|YP_003727085.1| 136 LCNACIETCPTKAIEF 151
                                       6999999999999987 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   1.5       0.2     2e+02       8      16 ..      15      25 ..      13      26 .. 0.82
   2 !   26.2   3.7   5.4e-09   5.4e-06       4      23 ..      73      92 ..      71      93 .. 0.90
   3 !   13.8   1.5   4.7e-05     0.047      10      24 .]     135     149 ..     125     149 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.2
                            Fer4_6  8 kCigCgd..Cv 16
                                      +C  Cg+  C+
  gi|298675335|ref|YP_003727085.1| 15 NCKKCGKstCM 25
                                      8****998887 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 5.4e-09
                            Fer4_6  4 idpdkCigCgdCvrvCPega 23
                                      i ++kC+gCg+Cv++CP ++
  gi|298675335|ref|YP_003727085.1| 73 IHEEKCTGCGNCVVACPVNV 92
                                      679**************975 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 4.7e-05
                            Fer4_6  10 igCgdCvrvCPegai 24 
                                       i C++C+  CP++ai
  gi|298675335|ref|YP_003727085.1| 135 ILCNACIETCPTKAI 149
                                       58***********98 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2  11.9   3.6e-05     0.036       3      49 ..      14      91 ..       2      93 .. 0.66
   2 !   27.4   9.5   2.9e-09   2.9e-06       1      51 []      77     149 ..      77     149 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.6e-05
                            Fer4_9  3 tgCgaCvea.C.......................pagvvvedaaerkarlraase.......................e 34
                                      t+C++C ++ C                       +++                 +                       e
  gi|298675335|ref|YP_003727085.1| 14 TNCKKCGKStCmafatallsgelrlddcpeiledKYKQ----------------NyeklselvapienasetgmiiheE 76
                                      57777744448777777754444433333332222222................1455555666677777799999999 PP

                            Fer4_9 35 aCigCgaCveaCpkg 49
                                      +C+gCg Cv aCp +
  gi|298675335|ref|YP_003727085.1| 77 KCTGCGNCVVACPVN 91
                                      9************87 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 2.9e-09
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase......................eaCigCgaCveaCpkgai 51 
                                       kCtgCg+Cv aCp +v+++ +++++    + +                       e+ i C+aC+e Cp++ai
  gi|298675335|ref|YP_003727085.1|  77 KCTGCGNCVVACPVNVAEDPEGTGIGLAPKNDRvilkvvngvvqkgnihncrrfgENKILCNACIETCPTKAI 149
                                       7******************999999988666559**************999999977799**********987 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.4      0.15   1.5e+02       9      16 ..      15      24 ..       9      27 .. 0.64
   2 !   24.4   2.6   2.1e-08   2.1e-05       5      21 ..      73      89 ..      70      90 .. 0.89
   3 !    7.4   2.2     0.005       4.9      12      22 .]     136     146 ..     126     146 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.15
                            Fer4_2  9 rCigCg..aC 16
                                      +C  Cg  +C
  gi|298675335|ref|YP_003727085.1| 15 NCKKCGksTC 24
                                      4566654455 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 2.1e-08
                            Fer4_2  5 vdtdrCigCgaCvsaCP 21
                                      + +++C+gCg Cv aCP
  gi|298675335|ref|YP_003727085.1| 73 IHEEKCTGCGNCVVACP 89
                                      6799************* PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.005
                            Fer4_2  12 gCgaCvsaCPa 22 
                                        C+aC+  CP+
  gi|298675335|ref|YP_003727085.1| 136 LCNACIETCPT 146
                                       4*********7 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.4      0.64   6.4e+02      10      16 ..      15      21 ..      11      43 .. 0.67
   2 !   22.5   2.0   9.2e-08   9.1e-05      26      54 ..      63      91 ..      57      94 .. 0.82
   3 !   10.1   0.7   0.00071       0.7      42      58 ..     135     150 ..     115     151 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.64
                           Fer4_21 10 gCgkCli 16
                                      +C+kC +
  gi|298675335|ref|YP_003727085.1| 15 NCKKCGK 21
                                      4555533 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 9.2e-08
                           Fer4_21 26 ieidaktvlkvvedeCvGCnlCssvCPve 54
                                      ie +++t + + e++C+GC  C+  CPv+
  gi|298675335|ref|YP_003727085.1| 63 IENASETGMIIHEEKCTGCGNCVVACPVN 91
                                      566677777888999***********994 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00071
                           Fer4_21  42 vGCnlCssvCPvedcie 58 
                                       + Cn C++ CP+ ++ie
  gi|298675335|ref|YP_003727085.1| 135 ILCNACIETCPT-KAIE 150
                                       558888888885.6665 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   6.3   5.7e-07   0.00057       4      65 .]      15      92 ..      13      92 .. 0.77
   2 !    7.2   0.3    0.0068       6.7      53      64 ..     136     147 ..     102     148 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 5.7e-07
                            Fer4_8  4 kCieCg..aCq.............saCpvlrrtk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvgi 65
                                      +C +Cg   C+             + Cp + + k k ++++  e  +  ++  ++      ++Ct+cg+C+++Cpv++
  gi|298675335|ref|YP_003727085.1| 15 NCKKCGksTCMafatallsgelrlDDCPEILEDKyKQNYEKLSELVAPIENASETGMIIHEEKCTGCGNCVVACPVNV 92
                                      79999877899999999999999999997777775777777777777444444444477889*************996 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0068
                            Fer4_8  53 tcgaCtevCpvg 64 
                                        c+aC e Cp++
  gi|298675335|ref|YP_003727085.1| 136 LCNACIETCPTK 147
                                       577788888765 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   1.1       0.9     9e+02       1       8 [.      16      25 ..      15      27 .. 0.80
   2 !   16.1   8.0   1.6e-05     0.016       1      14 [.      78      91 ..      78      92 .. 0.95
   3 !   14.4   0.6   5.7e-05     0.057       3      15 .]     136     148 ..     135     148 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.9
                            Fer4_3  1 CtgCg..aCv 8 
                                      C  Cg  +C+
  gi|298675335|ref|YP_003727085.1| 16 CKKCGksTCM 25
                                      8899866798 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.6e-05
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      CtgCg Cv++CPv+
  gi|298675335|ref|YP_003727085.1| 78 CTGCGNCVVACPVN 91
                                      ************98 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 5.7e-05
                            Fer4_3   3 gCgaCvevCPvgA 15 
                                        C+aC e CP++A
  gi|298675335|ref|YP_003727085.1| 136 LCNACIETCPTKA 148
                                       7**********98 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   5.6   1.3e-06    0.0013       1      60 [.      15      92 ..      15      93 .. 0.69
   2 ?    5.4   0.4     0.027        27      48      58 ..     136     146 ..     112     149 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.3e-06
                           Fer4_17  1 rCiqCgy..Clp.............eCpsyea..ydnepkkllraaklglleeaeke.ekaslCieCgeCerkCPqgl 60
                                      +C +Cg   C++              Cp   +  y+++ +kl + +++ ++  +  +    ++C++Cg+C+ +CP ++
  gi|298675335|ref|YP_003727085.1| 15 NCKKCGKstCMAfatallsgelrldDCPEILEdkYKQNYEKLSELVAPIENASETGMiIHEEKCTGCGNCVVACPVNV 92
                                      699999666999999999999999999987764455544455555444222222222235699************886 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.027
                           Fer4_17  48 eCgeCerkCPq 58 
                                        C+ C + CP 
  gi|298675335|ref|YP_003727085.1| 136 LCNACIETCPT 146
                                       45555555553 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9  14.1     0.012        12      39      67 .]      64      91 ..      14      91 .. 0.49
   2 !   16.6   3.4   1.1e-05     0.011       1      20 [.      77      96 ..      77     128 .. 0.86
   3 !   15.7   1.2   2.1e-05     0.021       5      18 ..     137     150 ..     135     152 .] 0.91

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.012
                           Fer4_16 39 kdlaedeekckkqeaitgCdiCqdvCPan 67
                                      ++++e+    + +e++tgC++C+ +CP+n
  gi|298675335|ref|YP_003727085.1| 64 ENASETGMIIH-EEKCTGCGNCVVACPVN 91
                                      22222222222.47889*********998 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.1e-05
                           Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                      +C++Cg+C+ +CP+n+ + +
  gi|298675335|ref|YP_003727085.1| 77 KCTGCGNCVVACPVNVAEDP 96
                                      59************998877 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 2.1e-05
                           Fer4_16   5 CgkCaevCPtnaik 18 
                                       C++C+e+CPt+ai+
  gi|298675335|ref|YP_003727085.1| 137 CNACIETCPTKAIE 150
                                       *************7 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   1.4      0.22   2.2e+02       3      12 ..      15      26 ..      13      27 .. 0.68
   2 !   18.8   3.4   1.6e-06    0.0016       2      17 .]      76      91 ..      75      94 .. 0.93
   3 ?    6.7   1.6     0.012        12       5      16 ..     135     146 ..     125     147 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.22
                            Fer4_4  3 rCigCgs..Cva 12
                                      +C  Cg+  C+a
  gi|298675335|ref|YP_003727085.1| 15 NCKKCGKstCMA 26
                                      688888656876 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 1.6e-06
                            Fer4_4  2 erCigCgsCvaaCPqg 17
                                      e+C+gCg Cv aCP++
  gi|298675335|ref|YP_003727085.1| 76 EKCTGCGNCVVACPVN 91
                                      89************75 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.012
                            Fer4_4   5 igCgsCvaaCPq 16 
                                       i C +C+ +CP+
  gi|298675335|ref|YP_003727085.1| 135 ILCNACIETCPT 146
                                       57*********8 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   6.8   4.7e-05     0.047       5      65 ..      75     150 ..      72     151 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.7e-05
                           Fer4_15   5 rdaCigcglCvaeapevfeldedglasvl...........lddgeiaeg......evpddeeeaaqeAaraCPvdAI 64 
                                       +++C+gcg+Cv ++p  + +d +g   +            + +g +++g      +++++++ +     ++CP++AI
  gi|298675335|ref|YP_003727085.1|  75 EEKCTGCGNCVVACPVNVAEDPEGTG-IGlapkndrvilkVVNGVVQKGnihncrRFGENKILC-NACIETCPTKAI 149
                                       789******************99987.4457777777777444444455555566777766666.446777777777 PP

                           Fer4_15  65 r 65 
                                       +
  gi|298675335|ref|YP_003727085.1| 150 E 150
                                       5 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.5       2.9   2.9e+03       8      20 ..      15      27 ..      14      31 .. 0.63
   2 ?   -0.7   0.0       2.1   2.1e+03      12      25 ..      41      54 ..      36      68 .. 0.59
   3 !   18.2   9.1   2.8e-06    0.0028       3      57 ..      75     150 ..      73     151 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.9
                           Fer4_13  8 acgaCvelaPdvF 20
                                      +c++C++     F
  gi|298675335|ref|YP_003727085.1| 15 NCKKCGKSTCMAF 27
                                      6777776555555 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.1
                           Fer4_13 12 CvelaPdvFeedde 25
                                      C e+  d ++ + e
  gi|298675335|ref|YP_003727085.1| 41 CPEILEDKYKQNYE 54
                                      44444444444444 PP

  == domain 3  score: 18.2 bits;  conditional E-value: 2.8e-06
                           Fer4_13   3 rdtCiacgaCvelaPdvFeeddeggasvvaeqpts.....................eeekadaeeAadaCPvesIg 57 
                                       +++C++cg+Cv ++P   +ed+eg     a ++                        e k ++++ +++CP+++I+
  gi|298675335|ref|YP_003727085.1|  75 EEKCTGCGNCVVACPVNVAEDPEGTGIGLAPKNDRvilkvvngvvqkgnihncrrfGENKILCNACIETCPTKAIE 150
                                       69*********************988777765444677777777777889999999889****************6 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   1.4   4.7e-06    0.0047       1      22 [.       1      22 [.       1      25 [. 0.94
   2 ?    0.0   2.5      0.87   8.7e+02      15      21 ..      77      83 ..      73      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.7e-06
                              YhfH  1 lekiveFfrnLPkKkCteCGke 22
                                      + + +e+++ LPk  C +CGk 
  gi|298675335|ref|YP_003727085.1|  1 MANAMEIYQLLPKTNCKKCGKS 22
                                      7899****************95 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.87
                              YhfH 15 kCteCGk 21
                                      kCt CG+
  gi|298675335|ref|YP_003727085.1| 77 KCTGCGN 83
                                      8*****7 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.8         4     4e+03       2      16 ..      16      25 ..      13      37 .. 0.57
   2 ?   14.5   2.1   4.9e-05     0.049      77      95 ..      73      91 ..      42      92 .. 0.79
   3 ?    3.5   0.4      0.13   1.3e+02       4      14 ..     136     146 ..     109     149 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 4
                           Fer4_22  2 ClsCgaCtlvCptCs 16
                                      C +Cg+      tC+
  gi|298675335|ref|YP_003727085.1| 16 CKKCGKS-----TCM 25
                                      3333332.....333 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 4.9e-05
                           Fer4_22 77 fgesgCvGCgRCieacpvk 95
                                      ++e++C+GCg C+ acpv+
  gi|298675335|ref|YP_003727085.1| 73 IHEEKCTGCGNCVVACPVN 91
                                      47899************97 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.13
                           Fer4_22   4 sCgaCtlvCpt 14 
                                        C+aC  +Cpt
  gi|298675335|ref|YP_003727085.1| 136 LCNACIETCPT 146
                                       45556555655 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1         6   5.9e+03      60      65 ..      15      20 ..       6      31 .. 0.62
   2 ?    9.0   3.5    0.0015       1.5      56      75 ..      73      92 ..      39      95 .. 0.80
   3 ?    7.1   0.5    0.0059       5.9      60      74 ..     133     147 ..     108     150 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 6
                           Fer4_18 60 dcidce 65
                                      +c +c+
  gi|298675335|ref|YP_003727085.1| 15 NCKKCG 20
                                      344443 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0015
                           Fer4_18 56 kgagdcidcescvkvcPtgi 75
                                        + +c+ c+ cv  cP+++
  gi|298675335|ref|YP_003727085.1| 73 IHEEKCTGCGNCVVACPVNV 92
                                      45779************987 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0059
                           Fer4_18  60 dcidcescvkvcPtg 74 
                                       + i c++c++ cPt+
  gi|298675335|ref|YP_003727085.1| 133 NKILCNACIETCPTK 147
                                       5689*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       859  (0.0479112); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1053.65
//
Query:       gi|298675336|ref|YP_003727086.1|  [L=98]
Description: ferredoxin thioredoxin reductase subunit beta [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.8e-27   93.8   1.1    6.9e-27   93.5   1.1    1.1  1  FeThRed_B  Ferredoxin thioredoxin reductase catalytic beta ch


Domain annotation for each model (and alignments):
>> FeThRed_B  Ferredoxin thioredoxin reductase catalytic beta chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.5   1.1   3.9e-31   6.9e-27       4      88 ..      13      95 ..      10      98 .] 0.95

  Alignments for each domain:
  == domain 1  score: 93.5 bits;  conditional E-value: 3.9e-31
                                      HHHHHHHHHHHHTT-B-BSSHHHHHHHHHHHHHHHHHHSS-B-SSC--S-HHHHHHH-TTBSS-HHHHHH....---TT CS
                         FeThRed_B  4 ktrkflekvakklgtkfnpdeevtevvieglarnkeeyGkrlCPCrlvedkeeeekkavwnCPCvplreeldeekeChC 82
                                      ++ + + ++a+++g+k+npd+e+ + v+egla+nk + G r+CPCr+++++ee++kk +  CPCv++++e+d+++ ChC
  gi|298675336|ref|YP_003727086.1| 13 QMYRWTYRYASRVGYKLNPDDEMLDLVLEGLAKNKIKHGRRYCPCRIITGDEEQDKKVI--CPCVYHKDEIDNDGMCHC 89
                                      6778899****************************************************..****************** PP

                                      SSSB-T CS
                         FeThRed_B 83 glfvtk 88
                                       lf  +
  gi|298675336|ref|YP_003727086.1| 90 ALFFYD 95
                                      ***865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 686.07
//
Query:       gi|298675337|ref|YP_003727087.1|  [L=153]
Description: UspA domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-35  121.1   0.1    5.7e-35  120.9   0.1    1.0  1  Usp       Universal stress protein family
     0.0047   17.2   0.8      0.011   15.9   0.1    1.9  2  Dodecin   Dodecin


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.9   0.1   6.4e-39   5.7e-35       2     141 .]      10     152 ..       9     152 .. 0.99

  Alignments for each domain:
  == domain 1  score: 120.9 bits;  conditional E-value: 6.4e-39
                                       -SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH...HHHHH CS
                               Usp   2 ykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada...akaaa 75 
                                       yk+Il+a+Dgse+skkA++ ++ela  +ga++++++v+++r+       +     +  ++ ++e+ ++a   ak+ a
  gi|298675337|ref|YP_003727087.1|  10 YKKILIATDGSENSKKAVQSGIELASCTGADVYAVYVVSTRSRFGGIPQRGGDWIQTIKSDLEEEGKKAlddAKKDA 86 
                                       9*************************************************************999999999****** PP

                                       HCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  76 eaggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       e++gv+ e+ + eg+pa ei+++a++++adliV+G+ g++g+ ++llGSv+++v++ha+  VlvVr
  gi|298675337|ref|YP_003727087.1|  87 EEKGVNIETAIIEGHPANEIIDYADKNGADLIVIGTLGKTGVNKFLLGSVAQNVVAHANSKVLVVR 152
                                       *****************************************************************8 PP

>> Dodecin  Dodecin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.2e-06     0.011       1      42 [.       9      50 ..       9      54 .. 0.96
   2 ?   -1.9   0.1      0.46   4.2e+03      18      28 ..      78      88 ..      74      99 .. 0.52

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.2e-06
                                      EEEEEEEEEEESS-HHHHHHHHHHHHHHH-SSEEEEEEEEEE CS
                           Dodecin  1 VyKvielvGsSpkSwedAiqnAiaeAsktlrnirwveVketr 42
                                      +yK+i +    ++  ++A+q++i+ As t  ++  v+V+ tr
  gi|298675337|ref|YP_003727087.1|  9 IYKKILIATDGSENSKKAVQSGIELASCTGADVYAVYVVSTR 50
                                      79*************************************998 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.46
                                      HHHHHHHHHHH CS
                           Dodecin 18 AiqnAiaeAsk 28
                                      A ++A + A++
  gi|298675337|ref|YP_003727087.1| 78 ALDDAKKDAEE 88
                                      33344444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 1007.53
//
Query:       gi|298675338|ref|YP_003727088.1|  [L=472]
Description: amino acid permease [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-60  205.5  44.6    1.6e-60  205.2  44.6    1.0  1  AA_permease_2  Amino acid permease
    6.6e-11   41.5  36.1    9.7e-11   40.9  36.1    1.2  1  AA_permease    Amino acid permease


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.2  44.6   1.7e-64   1.6e-60       1     423 [.      13     446 ..      13     448 .. 0.89

  Alignments for each domain:
  == domain 1  score: 205.2 bits;  conditional E-value: 1.7e-64
                     AA_permease_2   1 lsllsafalvigsv....igsgifvknlaasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaaf. 72 
                                       +++ + +a+++g++     ++g+f    a++  + +i+++ ++v+ g + + ++y El+ ++p+  G+ ++++++f 
  gi|298675338|ref|YP_003727088.1|  13 IDWKQGLAIALGVPllvlPSIGYF----AGYLWAFAIMVWALSVIQG-FFQNFAYGELAVMFPKASGLPGFAQNVFa 84 
                                       789999*******96443334444....5666666777888999999.68*************************** PP

                     AA_permease_2  73 ........gkkvaflsawfnwfayvpvlasilsvaasyllnalgpdlqgntw.ltyliaiaililvalinirgikes 140
                                               gk+++ +saw +wfa+ pv+a+++++++ yl ++l pd+  +++ l+++ +i+ +  + lin+rg + +
  gi|298675338|ref|YP_003727088.1|  85 gkggkfdrGKLIGGFSAWGYWFAWNPVMAIMAILIGTYLHQML-PDIGISQYvLSIIAGIVMYGALLLINSRGLSSG 160
                                       *99999999********************************99.999999884667778****************** PP

                     AA_permease_2 141 akiqnilgilkillpliiliilglitvdgggfsslstetdtffpngwpgv.......llgllivlwsfdGfesaanv 210
                                       a + +il+il++  pl+i+ +++++t+d++ ++    +t++++p+ w++        l+ ++++ ws +++e+aa++
  gi|298675338|ref|YP_003727088.1| 161 ALVGMILAILSL-APLVIISAAPFATGDFQLAN----ITGSWLPTDWTWDlhhililLGIFAMAEWSACAWETAAVY 232
                                       ************.6******************9....799*****8887445556656677889************* PP

                     AA_permease_2 211 see..vkkkdvpkaifigllivlvlyllvniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsll 285
                                         e   ++ d+pka f+++ ++l++++lv+ a++g ++++ + ++    s++ ++ +a++g+v+++i++++++++++
  gi|298675338|ref|YP_003727088.1| 233 GPEynKPNSDLPKAVFVCGFVCLIIFVLVQTAVTGTLGIERLLEVP--FSPLLPVSQAAFGQVGSYIAIFVLIFAMV 307
                                       ***855569*********************************8765..45799************************ PP

                     AA_permease_2 286 gaintavigssrvlealardgvlPrffakvnkfgspiraiiltaivslillllfllassaaynfllsvsslgliisy 362
                                       ++  ta++gssr ++++a++g lP  + kvn  g+pi+a+ilta+++l+l+ l          ++l++s++g+ + +
  gi|298675338|ref|YP_003727088.1| 308 LITQTAFLGSSRAMHSMAKEGNLPPILGKVNSAGTPINAMILTALFNLVLIGLQNP------AAVLAASAIGYSVAN 378
                                       ***********************************************888766643......7************** PP

                     AA_permease_2 363 llliigalilrkkrp..hlkr....pgki.lvaiigalfllfllvalffppkgpatqssliytiiltv 423
                                       ++ ++++++ + +++  +l+r    p+ +  va+i+ ++++ l+ ++ ++++ ++++ ++ y  i+++
  gi|298675338|ref|YP_003727088.1| 379 GISLFSYVKAKTDPElsQLERpfkaPAGWkYVALIFGILNIPLFLIGLIYLNSLEVGWTSTYIGIGVL 446
                                       *******999998665555665444444668************************9999998877665 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9  36.1   1.1e-14   9.7e-11      30     433 ..      43     430 ..      17     463 .. 0.71

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 1.1e-14
                       AA_permease  30 gallayllagvviflvmlslgeiatngpksggfytyasrfl.........gpelGfviGlnylfswitvlaleltaa 97 
                                        a+ +++l+++  f+   + ge+a+++pk++g   +a+++          g+  G++ ++ y+f w  v+a+  + +
  gi|298675338|ref|YP_003727088.1|  43 FAIMVWALSVIQGFFQNFAYGELAVMFPKASGLPGFAQNVFagkggkfdrGKLIGGFSAWGYWFAWNPVMAIMAILI 119
                                       348999999***********************999999875444444444677999***************999999 PP

                       AA_permease  98 siliqfwelvtdlpkawvt.....gavflvvlliinlvgvkvygeaefilalikiiaiiafiivgiillaggkpnkg 169
                                       + +++ +  ++d+    ++     g+v++++ll+in  g+   +    + ++++i++++ ++i+++ + a g+ + +
  gi|298675338|ref|YP_003727088.1| 120 GTYLHQM--LPDIGISQYVlsiiaGIVMYGALLLINSRGLSSGAL---VGMILAILSLAPLVIISAAPFATGDFQLA 191
                                       9999999..88887444447888999**********999998888...66677778888889999888887775555 PP

                       AA_permease 170 agfrflgdngsifknnlppgfa.keeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPkailqvviriti 245
                                             +  gs    +lp +++ +     ++  +++f+ +  ++   e  a+ + E   P  ++Pka+    +  +i
  gi|298675338|ref|YP_003727088.1| 192 ------NITGS----WLPTDWTwDLHH--ILILLGIFAMAEWSACAWETAAVYGPEYNKPNSDLPKAVFVCGFVCLI 256
                                       ......34445....999999988888..999999999999999*************************99999999 PP

                       AA_permease 246 fYvlsllligllvprndlgllndsasaaspfv.ifikesgvsvlaplinaviltaalssansslysasRvlyslakd 321
                                       ++vl+  +++ +++     ll+   ++ sp+  + +   g  +    i ++i++ +l +   +   +sR+++s+ak+
  gi|298675338|ref|YP_003727088.1| 257 IFVLVQTAVTGTLGIER--LLE---VPFSPLLpVSQAAFGQVGSYIAIFVLIFAMVLITQ-TAFLGSSRAMHSMAKE 327
                                       99999888888888877..555...23334440333444444444444444444444444.4455889********* PP

                       AA_permease 322 glaPkvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliilsylrfRkalkyqg 398
                                       g +P +l+kv+  g P++a++l++++ l+++     n+a       +la+sa+   +  +++++sy++ ++  ++++
  gi|298675338|ref|YP_003727088.1| 328 GNLPPILGKVNSAGTPINAMILTALFNLVLI--GLQNPA------AVLAASAIGYSVANGISLFSYVKAKTDPELSQ 396
                                       ***************************9999..444444......66777777777778888888886666655555 PP

                       AA_permease 399 rsieelgfkaallp..lgvilvlaaliiillilalya 433
                                           e +fka+ +     +i++++ + ++l+ l +  
  gi|298675338|ref|YP_003727088.1| 397 L---ERPFKAPAGWkyVALIFGILNIPLFLIGLIYLN 430
                                       5...334444444300222333333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 3353.14
//
Query:       gi|298675339|ref|YP_003727089.1|  [L=467]
Description: dimethylamine methyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   3.1e-266  883.2   4.9   3.5e-266  883.0   4.9    1.0  1  Dimeth_Pyl       Dimethylamine methyltransferase (Dimeth_PyL)
  ------ inclusion threshold ------
      0.045   14.0   0.0      0.093   13.0   0.0    1.5  1  Antimicrobial_7  Scorpion antimicrobial peptide


Domain annotation for each model (and alignments):
>> Dimeth_Pyl  Dimethylamine methyltransferase (Dimeth_PyL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  883.0   4.9  3.9e-270  3.5e-266       2     463 .]       4     465 ..       3     465 .. 1.00

  Alignments for each domain:
  == domain 1  score: 883.0 bits;  conditional E-value: 3.9e-270
                        Dimeth_Pyl   2 eyklrlGdgkrvyltkekiledieaGiadaadlaevpalsedeiekladilvskeklvsveaGkevvltydiGtlkl 78 
                                       +y++r+Gd+++ y++k++i+edieaG++daa+l+++pals+d++ek+adil+s++k+vsv+aG+ev++t+diGtl++
  gi|298675339|ref|YP_003727089.1|   4 GYRIRMGDSTTEYHSKDRIMEDIEAGTNDAAELGGIPALSDDDKEKIADILMSPQKMVSVDAGNEVPVTHDIGTLRI 80 
                                       79*************************************************************************** PP

                        Dimeth_Pyl  79 egdqgnsglgieisrlegvliheralgadtlelahidysikpvkpvvaeeaqameviqqnlvvpllyGampnlglyy 155
                                       +gdqgnsg+gi++srl+gv++hera+g+dt+el+hidys+kpvkpvv++e+q+mev+qqn++vpl+yGampn+glyy
  gi|298675339|ref|YP_003727089.1|  81 DGDQGNSGTGIPASRLTGVMTHERAFGTDTMELGHIDYSFKPVKPVVSQECQTMEVCQQNMTVPLMYGAMPNMGLYY 157
                                       ***************************************************************************** PP

                        Dimeth_Pyl 156 apdGpfenpadllrefkieeakesiekaadhlardivyvvskllkagadGvnfdttasaGdadfvatlkavealrkk 232
                                       +pdGpf+np+dl+refk++eak++ie aad+l++d+v++v+kl+k++adGvnfdt+a+aGd+df+atl+a+ealrk+
  gi|298675339|ref|YP_003727089.1| 158 QPDGPFKNPSDLMREFKLQEAKKEIEGAADELTNDMVWTVDKLYKSAADGVNFDTIAAAGDGDFYATLNAIEALRKR 234
                                       ***************************************************************************** PP

                        Dimeth_Pyl 233 fpniyielGmagelvlGihGeleydGktlaGlyphqqvklvekaGanvfGpvvntntskslawnlaravtlvkeavk 309
                                       fpn+yie+Gma+e++lG+hGe+eydG+tlaGl+ph+q++l+ kaGan+fGpv+nt+ts+s++wnlaravt+vk+av+
  gi|298675339|ref|YP_003727089.1| 235 FPNMYIEAGMASESILGMHGEFEYDGTTLAGLWPHEQAPLLGKAGANLFGPVCNTSTSHSTSWNLARAVTFVKSAVD 311
                                       ***************************************************************************** PP

                        Dimeth_Pyl 310 asdipvhvnlGmGvGGiplletppidavsraskalveiakvdGikvGvGdpvGmaiahvlasGmgGirtaGdlvarm 386
                                       +s+ip+hvn+GmGvGGip++etpp+dav+r+ska+ve+a+vdGi+vGvGdpvGm+iahv+asGm+G+r++Gdlvarm
  gi|298675339|ref|YP_003727089.1| 312 KSPIPCHVNMGMGVGGIPMFETPPVDAVTRCSKAMVEVAGVDGIOVGVGDPVGMPIAHVSASGMTGMRAGGDLVARM 388
                                       ***************************************************************************** PP

                        Dimeth_Pyl 387 elsknmkideakeyvakklgveeldladevvmrdlreelgiGvvtsvaGaakGiaaklnieklldikinscekfrnk 463
                                       +lsknm+i+eak+yv+kklgve++dl+de+vmrdlreelgiGv+tsv+Ga+kGi+ak+nie+lldikinscekfrn+
  gi|298675339|ref|YP_003727089.1| 389 QLSKNMRINEAKDYVSKKLGVEPMDLSDEYVMRDLREELGIGVLTSVEGAPKGISAKMNIEELLDIKINSCEKFRNQ 465
                                       ***************************************************************************96 PP

>> Antimicrobial_7  Scorpion antimicrobial peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     1e-05     0.093      24      43 .]     392     411 ..     387     411 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1e-05
                   Antimicrobial_7  24 KnkalNAAKNfVAeKiGatP 43 
                                       Kn  +N AK +V  K+G+ P
  gi|298675339|ref|YP_003727089.1| 392 KNMRINEAKDYVSKKLGVEP 411
                                       8999**************88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 3270.94
//
Query:       gi|298675340|ref|YP_003727090.1|  [L=217]
Description: methyltransferase cognate corrinoid protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.4e-26   90.4   0.8    1.5e-25   89.5   0.8    1.4  1  B12-binding    B12 binding domain
    1.8e-20   73.1   0.4    4.4e-20   71.9   0.4    1.7  1  B12-binding_2  B12 binding domain


Domain annotation for each model (and alignments):
>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.5   0.8   1.7e-29   1.5e-25       2     116 ..      94     202 ..      93     206 .. 0.93

  Alignments for each domain:
  == domain 1  score: 89.5 bits;  conditional E-value: 1.7e-29
                       B12-binding   2 kvllatvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvel..lk 76 
                                        v+ +tv+gd+h++G+ ++  +l+++gfeV+++g +v+++d++++i++ ++ vvg+Sal+t++l++ k+++el  ++
  gi|298675340|ref|YP_003727090.1|  94 VVVNGTVEGDVHDIGKSIVSTMLQASGFEVYDIGRDVPAQDFIDKIKEVNANVVGISALMTTTLPGQKDIIELlkEA 170
                                       68999********************************************************************9999 PP

                       B12-binding  77 rirprvkvvvGGahpsldpeetleaklgiddvvvgegeda 116
                                       ++r+++ v+vGGa+++ ++++   + +g+d+    ++e+a
  gi|298675340|ref|YP_003727090.1| 171 GMRDDTVVMVGGAPATQAWAD---K-IGADI----YAENA 202
                                       99************9999999...7.99554....66665 PP

>> B12-binding_2  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.9   0.4     5e-24   4.4e-20       2      75 .]       8      80 ..       7      80 .. 0.94

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 5e-24
                     B12-binding_2  2 aerlhwaivhgdkegieelidealaqgsa..avdvlndvllpamkeVGdlfgagelflpqvllsaevmkkavahLe 75
                                      ++++++ai+  +k+++ e++++a+    +  a d+++++l+++m+eVG +f++g+lflp+v+++ae+m  av+ Le
  gi|298675340|ref|YP_003727090.1|  8 LKEIADAIISCKKDSVTEAVNKAR---GDleASDIIENGLAAGMNEVGMKFERGKLFLPHVMMAAEAMTDAVKTLE 80
                                      5799********************...2346*****************************************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1543.37
//
Query:       gi|298675341|ref|YP_003727091.1|  [L=789]
Description: methyl-viologen-reducing hydrogenase delta subunit [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-59  199.9   3.7    1.1e-53  180.4   0.3    4.4  4  FlpD             Methyl-viologen-reducing hydrogenase, delta 
    8.1e-23   81.1   0.3    2.9e-22   79.3   0.3    1.9  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
    2.1e-15   55.8  53.6    1.6e-06   27.7   4.4    6.2  5  Fer4             4Fe-4S binding domain
    1.4e-14   54.7  21.7     0.0017   19.3   4.8    5.9  5  Fer4_16          4Fe-4S double cluster binding domain
    4.8e-13   49.5  39.6    5.4e-06   26.9  12.3    6.0  6  Fer4_7           4Fe-4S dicluster domain
    1.2e-12   47.7  35.8      2e-05   24.6   0.5    5.3  5  Fer4_10          4Fe-4S dicluster domain
    3.3e-12   46.4  46.7    8.4e-06   25.8  10.8    6.8  7  Fer4_21          4Fe-4S dicluster domain
    1.3e-10   40.8  51.8    4.7e-05   23.3   2.3    6.0  5  Fer4_6           4Fe-4S binding domain
    7.5e-10   38.3  53.3    1.2e-05   25.1   2.0    6.2  6  Fer4_2           4Fe-4S binding domain
    3.6e-08   33.9   0.9      2e-05   25.0   0.2    3.1  3  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
    5.2e-08   32.5   0.6    2.1e-06   27.2   0.0    2.9  3  Pyr_redox_3      Pyridine nucleotide-disulphide oxidoreductas
    9.3e-08   32.0   0.2     0.0008   19.1   0.4    2.9  4  DAO              FAD dependent oxidoreductase
    1.1e-07   31.9  40.8    8.3e-07   29.1  10.7    4.9  6  Fer4_9           4Fe-4S dicluster domain
    1.9e-07   30.5   0.8    6.5e-07   28.8   0.6    1.8  2  FAD_binding_2    FAD binding domain
    2.6e-07   30.4   0.3    6.7e-07   29.0   0.2    1.7  2  FAD_oxidored     FAD dependent oxidoreductase
    1.3e-06   28.7  30.5      0.031   14.7   0.0    5.2  4  Fer4_8           4Fe-4S dicluster domain
    2.4e-06   26.9   0.8    9.2e-06   25.0   0.1    2.2  2  GIDA             Glucose inhibited division protein A
    1.2e-05   25.4   0.0      3e-05   24.1   0.0    1.7  1  NAD_binding_8    NAD(P)-binding Rossmann-like domain
    2.3e-05   23.3   0.8    6.2e-05   21.9   0.7    1.8  2  HI0933_like      HI0933-like protein
    5.5e-05   23.4  33.7      0.097   13.2   1.4    5.1  4  Fer4_4           4Fe-4S binding domain
    0.00077   18.8   0.0     0.0016   17.8   0.0    1.5  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
      0.002   17.4   0.2     0.0037   16.6   0.2    1.4  1  FAD_binding_3    FAD binding domain
     0.0024   18.7  31.9      0.064   14.1   0.8    5.2  4  Fer4_22          4Fe-4S dicluster domain
      0.005   16.1   0.9     0.0086   15.3   0.1    1.7  2  Thi4             Thi4 family
     0.0078   15.4   0.5        5.5    6.0   0.0    3.2  3  K_oxygenase      L-lysine 6-monooxygenase (NADPH-requiring)
  ------ inclusion threshold ------
      0.019   15.4   0.6       0.12   12.8   0.1    2.6  1  NAD_binding_7    Putative NAD(P)-binding
       0.02   14.0   0.5       0.23   10.5   0.4    2.4  3  Lycopene_cycl    Lycopene cyclase protein
      0.052   13.5   0.1         15    5.5   0.1    3.0  2  NAD_binding_9    FAD-NAD(P)-binding
      0.058   13.9  30.7       0.14   12.7   1.0    4.6  4  Fer4_13          4Fe-4S single cluster domain of Ferredoxin I
      0.066   13.2   0.1       0.33   10.9   0.0    2.2  2  Glyco_tran_WecB  Glycosyl transferase WecB/TagA/CpsF family
       0.12   11.6   0.1       0.92    8.7   0.0    2.4  3  Amino_oxidase    Flavin containing amine oxidoreductase
       0.16   10.8   0.5        1.3    7.8   0.3    2.0  2  Trp_halogenase   Tryptophan halogenase
       0.16   11.9   0.1       0.36   10.8   0.1    1.5  1  MinC_N           Septum formation inhibitor MinC, N-terminal 
       0.32   11.6  43.1       0.55   10.8   2.8    5.3  6  Fer4_17          4Fe-4S dicluster domain
       0.48   10.3   3.7       0.38   10.6   0.6    2.2  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
        1.4    9.7  27.2          2    9.2   4.5    4.6  4  Fer4_15          4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> FlpD  Methyl-viologen-reducing hydrogenase, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0022       1.1      28      63 ..      37      72 ..      18     118 .. 0.87
   2 ?    1.9   0.1      0.43   2.1e+02       5      53 ..     398     449 ..     396     452 .. 0.82
   3 ?    5.7   0.0     0.028        14      46      81 ..     522     561 ..     520     568 .. 0.73
   4 !  180.4   0.3   2.3e-56   1.1e-53       1     123 []     651     773 ..     651     773 .. 0.99

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0022
                              FlpD 28 vriirvpCsgrvdpefilkalekGadgVlvlgChpg 63
                                      vr i+ +Cs++ ++++i +  e+++d Vl+++C p+
  gi|298675341|ref|YP_003727091.1| 37 VRDIQFMCSDTGQEAIIEDIKEHNIDRVLIAACSPK 72
                                      7889*****************************975 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.43
                              FlpD   5 lCnwcayaaadlagvsrlqypp...nvriirvpCsgrvdpefilkalekGad 53 
                                       + + c+  a+++a++ + +yp+   +++ i ++ sg++ +e+ ++a + G++
  gi|298675341|ref|YP_003727091.1| 398 CSKVCCMSAIKNAQLLKERYPEmdiRLHYIDIRASGEMYEEYYTNAQSMGIQ 449
                                       6778999999****99999999544578899999999999998888887776 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.028
                              FlpD  46 kalekGadgVlvlgChpgd....ChyvkGnekaerrvekl 81 
                                       +  e+++dgV+++gC  g         +G+  a++ +++l
  gi|298675341|ref|YP_003727091.1| 522 RPVESNIDGVYIAGCASGPkeiqISIAQGSAVASKAMQLL 561
                                       667899*********9876445444556777776666655 PP

  == domain 4  score: 180.4 bits;  conditional E-value: 2.3e-56
                              FlpD   1 ilaFlCnwcayaaadlagvsrlqyppnvriirvpCsgrvdpefilkalekGadgVlvlgChpgdChyvkGnekaerr 77 
                                       i+ FlCnwc+ya adlag+sr+qyp+nvriirv+C+grvdpef+l+a+ekGadgV+v+gC+ g+Chyv Gn++a++r
  gi|298675341|ref|YP_003727091.1| 651 IVSFLCNWCSYACADLAGTSRIQYPTNVRIIRVMCAGRVDPEFVLTAFEKGADGVMVSGCRLGECHYVYGNYNAKQR 727
                                       899************************************************************************** PP

                              FlpD  78 veklkelleelgiepeRvrleevsaaegekfaevikefvekikeLG 123
                                       ++ lk++lee++i+p+R+++e++sa+e ++fae i++fve+++++G
  gi|298675341|ref|YP_003727091.1| 728 MDVLKDVLEEIDINPNRLNVEWISASECNRFAESIENFVEELEKIG 773
                                       *******************************************998 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.3   0.3   5.8e-25   2.9e-22       2     294 .]     143     550 ..     142     550 .. 0.72

  Alignments for each domain:
  == domain 1  score: 79.3 bits;  conditional E-value: 5.8e-25
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEE...........TTHCHHHCSHHH...HCHHHHHHHHHHHHH....... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxx...xxxxxxxxxxxxxxx....... RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve...........legtclnggcll...skallgvaedaeias....... 57 
                                       +v+viGgG+AG++aal+la ag+ v++ve           l++ +++++c++   ++++++v+ +++i++       
  gi|298675341|ref|YP_003727091.1| 143 NVLVIGGGVAGIEAALNLADAGYHVYMVEkepsiggkmalLNEVFPTNDCSIcvlAPKMTEVSNHPNIELytnseit 219
                                       79**************************88899999*************987777******************9999 PP

                                       ................................................HHHHCHHHHCCCCHCCTCEEEEESCEEEE CS
                                       ................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 ................................................evvkklnqgielllgeevvkidpgkkkvk 86 
                                                                                                                    
  gi|298675341|ref|YP_003727091.1| 220 eitgsvgnftvkglkkpryvsedkckgcieecssvcpveisnpfdygiG---------------------------- 268
                                       7777777666666666666666666666666666666644444444440............................ PP

                                       ETEEEC...........................................TCEEEEEESEEEE---EEE-BCTCTTC. CS
                                       xxxxxx...........................................xxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       Pyr_redox_2  87 lekkke...........................................gdeekiaydklvlAtGssprdlgipGv. 119
                                            +                                           ++e++++++++++AtG + +d   + + 
  gi|298675341|ref|YP_003727091.1| 269 -----KikaismpfpqavpqcayindeycvgcglcrqvcpadavdyeqkEEEFSFDAGAVIVATGYNVFDASRKEEy 340
                                       .....0334444444444444444444444444445566666666776678999999*********99999777665 PP

                                       ......................TTBEECCSECHHHHHHCCSS-T.....SEEEEES-SHHHHHHHHHHHHHT-.... CS
                                       .....................xxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxx.... RF
                       Pyr_redox_2 120 .....................aenvgklvrtldsaealklkllp.....krivvvGgGyiGvElAaalaklgk.... 166
                                                            +   +++   + s++++ +k         r   vG+ y++ ++++ + k ++    
  gi|298675341|ref|YP_003727091.1| 341 gyskypdvitnmelerminasG--PTHGKVVVPSTKEIPQKVAFihcvgSRDETVGNPYCSKVCCMSAIKNAQllke 415
                                       6677777777777777776433..333333555555555555555555555589*************7444333444 PP

                                       EEEEEESSSSSS..TTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE...EEEEEETTSCE...EEESEEEE-S CS
                                       xxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxx...xxxxxxxxxx RF
                       Pyr_redox_2 167 evtlveardrll..raldkelsaaleealekeGvevklgtsvkeidgnge...klevvledgee...idadlvvvav 235
                                       + + ++ r +    ra +++ ++++++a + +G++++ g+++ ei+++++    l+++++ +++   + +dlvv++v
  gi|298675341|ref|YP_003727091.1| 416 RYPEMDIRLHYIdiRASGEMYEEYYTNA-QSMGIQFVRGKVA-EIQEDNSgkpVLRYEDTLENKifeETYDLVVLSV 490
                                       3444444444445566677777776655.667*****66666.9999999898777777777777779********* PP

                                       -EEES-HHCS.HCCT-EEEETTEEE--T.TS...BESSTTEEE-GGGCTECCSS--HHHHHHHH CS
                                       xxxxxxxxxx.xxxxxxxxxxxxxxxxx.xx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 236 Gvrpstelle.eklglelderggivvde.fl...rtnvpgiyaiGDvaggkggpelaqaAvqqG 294
                                       G++++++ +    l+l + ++g+  v + ++   ++n++g+y +G +a   +gp+ +q +++qG
  gi|298675341|ref|YP_003727091.1| 491 GLEANKDEKIsSMLNLSTRSDGFYTVSHpKMrpvESNIDGVYIAG-CA---SGPKEIQISIAQG 550
                                       ********989999*********96655166666789********.78...8999999998887 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   5.9     0.055        27       2      21 ..     238     258 ..     237     259 .. 0.92
   2 !   27.7   4.4   3.1e-09   1.6e-06       2      23 ..     286     307 ..     285     308 .. 0.93
   3 !   24.2   3.5     4e-08     2e-05       2      21 ..     574     593 ..     573     593 .. 0.91
   4 !   27.3   2.5   4.2e-09   2.1e-06       2      24 .]     603     625 ..     602     625 .. 0.94
   5 ?   -1.3   1.2       4.6   2.3e+03      11      18 ..     656     663 ..     655     663 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.055
                                       EEETTTSSS-.THHHHHSTTT CS
                              Fer4   2 videekCigC.GaCvevCPvg 21 
                                       ++ e+kC gC  +C +vCPv+
  gi|298675341|ref|YP_003727091.1| 238 YVSEDKCKGCiEECSSVCPVE 258
                                       689****************97 PP

  == domain 2  score: 27.7 bits;  conditional E-value: 3.1e-09
                                       EEETTTSSS-THHHHHSTTTEE CS
                              Fer4   2 videekCigCGaCvevCPvgAI 23 
                                       +i+ e C+gCG+C +vCP +A 
  gi|298675341|ref|YP_003727091.1| 286 YINDEYCVGCGLCRQVCPADAV 307
                                       89******************96 PP

  == domain 3  score: 24.2 bits;  conditional E-value: 4e-08
                                       EEETTTSSS-THHHHHSTTT CS
                              Fer4   2 videekCigCGaCvevCPvg 21 
                                        +d++kC+gCG+C +vC +g
  gi|298675341|ref|YP_003727091.1| 574 FVDTDKCTGCGICQDVCKFG 593
                                       59***************875 PP

  == domain 4  score: 27.3 bits;  conditional E-value: 4.2e-09
                                       EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                       ++de  C gCG C  +CP +AI+
  gi|298675341|ref|YP_003727091.1| 603 EVDELSCHGCGSCSAACPEDAIY 625
                                       79********************6 PP

  == domain 5  score: -1.3 bits;  conditional E-value: 4.6
                                       -THHHHHS CS
                              Fer4  11 CGaCvevC 18 
                                       C+ C  +C
  gi|298675341|ref|YP_003727091.1| 656 CNWCSYAC 663
                                       ******** PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.2     0.021        10      51      66 ..     241     257 ..     201     262 .. 0.78
   2 !   19.0   0.1   4.2e-06    0.0021       2      28 ..     292     321 ..     291     350 .. 0.71
   3 ?    1.1   0.0       1.6   7.8e+02       8      20 ..     398     410 ..     395     448 .. 0.73
   4 !   16.2   0.2   3.1e-05     0.015      49      66 ..     575     592 ..     547     593 .. 0.80
   5 !   19.3   4.8   3.4e-06    0.0017       2      43 ..     609     650 ..     608     665 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.021
                           Fer4_16  51 qeaitgCd.iCqdvCPa 66 
                                       + +++gC   C  vCP+
  gi|298675341|ref|YP_003727091.1| 241 EDKCKGCIeECSSVCPV 257
                                       46677775477777775 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 4.2e-06
                           Fer4_16   2 CgtCgkCaevCPtnaikek...kekeiear 28 
                                       C++Cg C +vCP++a++ +   +e++++a 
  gi|298675341|ref|YP_003727091.1| 292 CVGCGLCRQVCPADAVDYEqkeEEFSFDAG 321
                                       ****************96632244444544 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 1.6
                           Fer4_16   8 CaevCPtnaikek 20 
                                       C +vC  +aik+ 
  gi|298675341|ref|YP_003727091.1| 398 CSKVCCMSAIKNA 410
                                       99*******9976 PP

  == domain 4  score: 16.2 bits;  conditional E-value: 3.1e-05
                           Fer4_16  49 kkqeaitgCdiCqdvCPa 66 
                                           ++tgC+iCqdvC +
  gi|298675341|ref|YP_003727091.1| 575 VDTDKCTGCGICQDVCKF 592
                                       34689***********77 PP

  == domain 5  score: 19.3 bits;  conditional E-value: 3.4e-06
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisyntaekkdlae 43 
                                       C++Cg C  +CP++ai +++++ ++++ +i+++ + k++++ 
  gi|298675341|ref|YP_003727091.1| 609 CHGCGSCSAACPEDAIYMRNQTDAQIHSQIEAALEVKDEFPL 650
                                       *******************99999999999987666666653 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   1.5   0.00021       0.1      27      51 ..     232     258 ..     190     259 .. 0.61
   2 !   20.7   0.9   9.1e-07   0.00045      32      52 .]     286     306 ..     269     327 .. 0.71
   3 ?    1.7   0.2      0.82   4.1e+02       7      26 ..     397     416 ..     384     444 .. 0.72
   4 !   15.5   2.3     4e-05      0.02      30      51 ..     572     593 ..     552     594 .. 0.80
   5 !   26.9  12.3   1.1e-08   5.4e-06       1      52 []     579     623 ..     579     623 .. 0.93
   6 !   15.1   8.5   5.2e-05     0.026       1      27 [.     608     637 ..     608     715 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00021
                            Fer4_7  27 gtekv.eidpekClgCga.CvavCPtg 51 
                                       g +k+ +++++kC gC + C +vCP++
  gi|298675341|ref|YP_003727091.1| 232 GLKKPrYVSEDKCKGCIEeCSSVCPVE 258
                                       33555345799*****777******97 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 9.1e-07
                            Fer4_7  32 eidpekClgCgaCvavCPtga 52 
                                       +i+ e+C+gCg C +vCP++a
  gi|298675341|ref|YP_003727091.1| 286 YINDEYCVGCGLCRQVCPADA 306
                                       566677777777777777665 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.82
                            Fer4_7   7 aCvaaCpvkaieldeeenek 26 
                                       +C ++C ++ai+  +  +e+
  gi|298675341|ref|YP_003727091.1| 397 YCSKVCCMSAIKNAQLLKER 416
                                       9*****99999877654443 PP

  == domain 4  score: 15.5 bits;  conditional E-value: 4e-05
                            Fer4_7  30 kveidpekClgCgaCvavCPtg 51 
                                       ++ +d +kC+gCg C++vC +g
  gi|298675341|ref|YP_003727091.1| 572 SAFVDTDKCTGCGICQDVCKFG 593
                                       4567899999999999999886 PP

  == domain 5  score: 26.9 bits;  conditional E-value: 1.1e-08
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       +C+gCg C+++C+ + i+l +       +k+e+d+ +C gCg+C a+CP +a
  gi|298675341|ref|YP_003727091.1| 579 KCTGCGICQDVCKFGKIKLYN-------HKAEVDELSCHGCGSCSAACPEDA 623
                                       7******************55.......4789*****************986 PP

  == domain 6  score: 15.1 bits;  conditional E-value: 5.2e-05
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenek...g 27 
                                       +C gCg C aaCp +ai+++++++++   +
  gi|298675341|ref|YP_003727091.1| 608 SCHGCGSCSAACPEDAIYMRNQTDAQihsQ 637
                                       5******************98766552221 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.4   0.00026      0.13       5      23 ..     240     259 ..     237     281 .. 0.76
   2 !   24.6   0.5   4.1e-08     2e-05       2      29 ..     285     312 ..     284     340 .. 0.78
   3 ?   -1.3   0.1       4.9   2.5e+03      14      22 ..     397     405 ..     385     440 .. 0.76
   4 !   23.0  13.4   1.3e-07   6.4e-05       4      56 .]     575     620 ..     572     620 .. 0.84
   5 !   15.8   6.4   2.3e-05     0.011       2      48 ..     602     659 ..     601     666 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00026
                           Fer4_10   5 dddtCirCg.kCvkaCPadl 23 
                                        +d+C +C  +C ++CP+ +
  gi|298675341|ref|YP_003727091.1| 240 SEDKCKGCIeECSSVCPVEI 259
                                       689*****87*******954 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 4.1e-08
                           Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgak 29 
                                       ++i+d+ C++Cg C+++CPad+  +++k
  gi|298675341|ref|YP_003727091.1| 285 AYINDEYCVGCGLCRQVCPADAVDYEQK 312
                                       589*****************44222222 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 4.9
                           Fer4_10  14 kCvkaCPad 22 
                                        C k+C ++
  gi|298675341|ref|YP_003727091.1| 397 YCSKVCCMS 405
                                       799999553 PP

  == domain 4  score: 23.0 bits;  conditional E-value: 1.3e-07
                           Fer4_10   4 idddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +d+d+C++Cg C+++C       +  +++ ++ + +++  +C+gcg+C +aCP
  gi|298675341|ref|YP_003727091.1| 575 VDTDKCTGCGICQDVC-------KFGKIKLYNHKAEVDELSCHGCGSCSAACP 620
                                       799*************.......44666666777777779************9 PP

  == domain 5  score: 15.8 bits;  conditional E-value: 2.3e-05
                           Fer4_10   2 vvidddtCirCgkCvkaCPadl...........tsvgakgeaseeeavrkkvekCtgc 48 
                                       +++d+ +C +Cg C +aCP d+           +s+   + + ++e   +++  C  c
  gi|298675341|ref|YP_003727091.1| 602 AEVDELSCHGCGSCSAACPEDAiymrnqtdaqiHSQIEAALEVKDEFPLIVSFLCNWC 659
                                       5678999*************88666555555444444444444444444444444444 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.2         1   5.1e+02      17      33 ..      43      59 ..      40      70 .. 0.66
   2 !   16.3   0.7   1.5e-05    0.0077      35      54 ..     238     258 ..     218     260 .. 0.83
   3 !   20.6   2.3   7.1e-07   0.00036      34      57 ..     285     307 ..     270     309 .. 0.79
   4 ?    1.3   0.9      0.74   3.7e+02      37      57 ..     388     407 ..     371     409 .. 0.77
   5 !   14.7   1.9   5.2e-05     0.026      35      52 ..     574     591 ..     556     597 .. 0.78
   6 !   25.8  10.8   1.7e-08   8.4e-06       1      59 []     573     626 ..     573     626 .. 0.90
   7 ?    2.1   0.4      0.43   2.1e+02      11      22 ..     656     667 ..     653     687 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 1
                           Fer4_21 17 aCedtshqaieidaktv 33
                                      +C+dt+ +ai  d k++
  gi|298675341|ref|YP_003727091.1| 43 MCSDTGQEAIIEDIKEH 59
                                      7*********6554443 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1.5e-05
                           Fer4_21  35 kvvedeCvGC.nlCssvCPve 54 
                                        v ed+C GC + CssvCPve
  gi|298675341|ref|YP_003727091.1| 238 YVSEDKCKGCiEECSSVCPVE 258
                                       4779******789******94 PP

  == domain 3  score: 20.6 bits;  conditional E-value: 7.1e-07
                           Fer4_21  34 lkvvedeCvGCnlCssvCPvedci 57 
                                       + + ++ CvGC lC +vCP  d++
  gi|298675341|ref|YP_003727091.1| 285 AYINDEYCVGCGLCRQVCPA-DAV 307
                                       4456899************6.665 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.74
                           Fer4_21  37 vedeCvGCnlCssvCPvedci 57 
                                         de vG   Cs+vC +  +i
  gi|298675341|ref|YP_003727091.1| 388 SRDETVGNPYCSKVCCM-SAI 407
                                       47899999*******86.555 PP

  == domain 5  score: 14.7 bits;  conditional E-value: 5.2e-05
                           Fer4_21  35 kvvedeCvGCnlCssvCP 52 
                                        v +d+C+GC +C +vC 
  gi|298675341|ref|YP_003727091.1| 574 FVDTDKCTGCGICQDVCK 591
                                       46799************6 PP

  == domain 6  score: 25.8 bits;  conditional E-value: 1.7e-08
                           Fer4_21   1 AridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59 
                                       A++d dkC gCg C  +C+      i++  +++++v e +C GC  Cs+ CP ed+i m
  gi|298675341|ref|YP_003727091.1| 573 AFVDTDKCTGCGICQDVCK---FGKIKLY-NHKAEVDELSCHGCGSCSAACP-EDAIYM 626
                                       789****************...7888886.556699****************.8*9987 PP

  == domain 7  score: 2.1 bits;  conditional E-value: 0.43
                           Fer4_21  11 CgkCliaCedts 22 
                                       C+ C  aC d +
  gi|298675341|ref|YP_003727091.1| 656 CNWCSYACADLA 667
                                       999*****9954 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   2.7   4.7e-05     0.024       4      22 ..     239     258 ..     238     260 .. 0.90
   2 !   11.0   7.1   0.00073      0.36       2      23 ..     285     306 ..     284     307 .. 0.92
   3 ?   -1.3   1.7       5.4   2.7e+03      15      24 .]     398     407 ..     395     407 .. 0.89
   4 !   20.3   2.1     8e-07    0.0004       2      22 ..     573     593 ..     572     595 .. 0.90
   5 !   23.3   2.3   9.5e-08   4.7e-05       1      24 []     601     624 ..     601     624 .. 0.96

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.7e-05
                            Fer4_6   4 idpdkCigC.gdCvrvCPeg 22 
                                       + +dkC gC ++C +vCP  
  gi|298675341|ref|YP_003727091.1| 239 VSEDKCKGCiEECSSVCPVE 258
                                       679***************75 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00073
                            Fer4_6   2 veidpdkCigCgdCvrvCPega 23 
                                       + i+++ C+gCg C  vCP++a
  gi|298675341|ref|YP_003727091.1| 285 AYINDEYCVGCGLCRQVCPADA 306
                                       679****************998 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 5.4
                            Fer4_6  15 CvrvCPegai 24 
                                       C +vC + ai
  gi|298675341|ref|YP_003727091.1| 398 CSKVCCMSAI 407
                                       *****99997 PP

  == domain 4  score: 20.3 bits;  conditional E-value: 8e-07
                            Fer4_6   2 veidpdkCigCgdCvrvCPeg 22 
                                       + +d dkC+gCg C +vC +g
  gi|298675341|ref|YP_003727091.1| 573 AFVDTDKCTGCGICQDVCKFG 593
                                       679***************986 PP

  == domain 5  score: 23.3 bits;  conditional E-value: 9.5e-08
                            Fer4_6   1 vveidpdkCigCgdCvrvCPegai 24 
                                       ++e+d+ +C gCg C ++CPe+ai
  gi|298675341|ref|YP_003727091.1| 601 KAEVDELSCHGCGSCSAACPEDAI 624
                                       689*******************98 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.2       5.1   2.5e+03      12      18 ..     191     197 ..     190     198 .. 0.77
   2 !   12.5   2.5   0.00025      0.13       4      21 ..     238     256 ..     235     257 .. 0.88
   3 !   19.5   2.8   1.5e-06   0.00074       4      22 .]     286     304 ..     285     304 .. 0.90
   4 !   25.1   2.0   2.5e-08   1.2e-05       3      20 ..     573     590 ..     571     592 .. 0.92
   5 !   15.9   2.0     2e-05      0.01       3      22 .]     602     621 ..     600     621 .. 0.90
   6 ?   -0.8   0.2       4.1     2e+03       9      17 ..     655     664 ..     648     665 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 5.1
                            Fer4_2  12 gCgaCvs 18 
                                        C++Cv 
  gi|298675341|ref|YP_003727091.1| 191 DCSICVL 197
                                       79***86 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00025
                            Fer4_2   4 vvdtdrCigC.gaCvsaCP 21 
                                       +v +d+C gC + C s+CP
  gi|298675341|ref|YP_003727091.1| 238 YVSEDKCKGCiEECSSVCP 256
                                       6779*******99****** PP

  == domain 3  score: 19.5 bits;  conditional E-value: 1.5e-06
                            Fer4_2   4 vvdtdrCigCgaCvsaCPa 22 
                                       +++ + C+gCg C+++CPa
  gi|298675341|ref|YP_003727091.1| 286 YINDEYCVGCGLCRQVCPA 304
                                       678889************8 PP

  == domain 4  score: 25.1 bits;  conditional E-value: 2.5e-08
                            Fer4_2   3 vvvdtdrCigCgaCvsaC 20 
                                       ++vdtd+C+gCg+C+++C
  gi|298675341|ref|YP_003727091.1| 573 AFVDTDKCTGCGICQDVC 590
                                       589*************** PP

  == domain 5  score: 15.9 bits;  conditional E-value: 2e-05
                            Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                       ++vd+ +C gCg+C  aCP+
  gi|298675341|ref|YP_003727091.1| 602 AEVDELSCHGCGSCSAACPE 621
                                       689****************5 PP

  == domain 6  score: -0.8 bits;  conditional E-value: 4.1
                            Fer4_2   9 rCigCg.aCv 17 
                                        C+ C+ aC 
  gi|298675341|ref|YP_003727091.1| 655 LCNWCSyACA 664
                                       5888866885 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.2     4e-08     2e-05       1      35 [.     143     177 ..     143     189 .. 0.92
   2 ?    5.6   0.0     0.047        23      51      72 ..     205     227 ..     193     234 .. 0.79
   3 ?   -1.8   0.0       9.5   4.7e+03      48      72 ..     441     464 ..     423     471 .. 0.66

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 4e-08
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkll 35 
                                       +v+v+GgG+ g+E+A +la+ g +V++ve ++ + 
  gi|298675341|ref|YP_003727091.1| 143 NVLVIGGGVAGIEAALNLADAGYHVYMVEKEPSIG 177
                                       599****************************9998 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.047
                                       HHT.TEEEECSEEEEEEEEETTS CS
                         Pyr_redox  51 ekn.gievllntkveeiegsedg 72 
                                       +++ +ie+++n++++ei+gs  +
  gi|298675341|ref|YP_003727091.1| 205 SNHpNIELYTNSEITEITGSVGN 227
                                       44459*************99876 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 9.5
                                       HHHHHTTEEEECSEEEEEEEEETTS CS
                         Pyr_redox  48 eklekngievllntkveeiegsedg 72 
                                       ++ + +gi+++ ++++e i+++++g
  gi|298675341|ref|YP_003727091.1| 441 TNAQSMGIQFVRGKVAE-IQEDNSG 464
                                       44566799999987655.4444443 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   4.2e-09   2.1e-06     164     248 ..     141     231 ..     120     243 .. 0.79
   2 ?   -0.5   0.0       1.2     6e+02     122     137 ..     317     334 ..     305     356 .. 0.70
   3 ?    1.4   0.0      0.31   1.5e+02     234     305 .]     454     535 ..     425     535 .. 0.56

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 4.2e-09
                       Pyr_redox_3 164 gqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdie.......nrleelvkeekikvlfna 233
                                       +++v+ViGg+  +++aAl+l+++g +V +v ++ +i  +      ++ p++        +++ e++++ +i++++n+
  gi|298675341|ref|YP_003727091.1| 141 NRNVLVIGGGVAGIEAALNLADAGYHVYMVEKEPSIGGKM-ALLNEVFPTNDcsicvlaPKMTEVSNHPNIELYTNS 216
                                       789*******************************999874.56667877765111111266777777788******* PP

                       Pyr_redox_3 234 evkeikekeeeykvk 248
                                       e++ei+ +  +++vk
  gi|298675341|ref|YP_003727091.1| 217 EITEITGSVGNFTVK 231
                                       ******998888876 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.2
                       Pyr_redox_3 122 tyeAkkviiAtGe..fdk 137
                                       ++ A  vi+AtG+  fd 
  gi|298675341|ref|YP_003727091.1| 317 SFDAGAVIVATGYnvFDA 334
                                       577889999999744555 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.31
                       Pyr_redox_3 234 evkeikekeee.....ykvktedgkkvevkddvvlatGykpdlsf.lkk.slfeldedgrpvlteete...etnvpg 300
                                       +v ei+e+++      y+ + e++   e++d vvl +G + + +  +++   +++++dg+ ++   ++   e+n++g
  gi|298675341|ref|YP_003727091.1| 454 KVAEIQEDNSGkpvlrYEDTLENKIFEETYDLVVLSVGLEANKDEkISSmLNLSTRSDGFYTVSHPKMrpvESNIDG 530
                                       55555554443111112333333333344666667788888875535544555666777777766554444899999 PP

                       Pyr_redox_3 301 lflaG 305
                                       +++aG
  gi|298675341|ref|YP_003727091.1| 531 VYIAG 535
                                       99988 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.4   1.6e-06    0.0008       2      35 ..     144     178 ..     143     181 .. 0.93
   2 ?   -3.1   0.0       9.1   4.5e+03     190     203 ..     315     330 ..     305     371 .. 0.75
   3 !    9.2   0.0    0.0016       0.8     151     206 ..     438     499 ..     407     540 .. 0.69
   4 ?   -2.7   0.0       6.7   3.3e+03      96     124 ..     728     758 ..     710     766 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.6e-06
                                       EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSS CS
                               DAO   2 vviiGGGiiGlstAyeLarrg..Vtllekgdiagsg 35 
                                       v++iGGG++G+ +A+ La +g  V  +ek++ +g g
  gi|298675341|ref|YP_003727091.1| 144 VLVIGGGVAGIEAALNLADAGyhVYMVEKEPSIG-G 178
                                       9*****************99**********9998.5 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 9.1
                                       EEEEEE..EEE--GGG CS
                               DAO 190 ndaada..vVnaaGaw 203
                                       ++++da  v++a+G  
  gi|298675341|ref|YP_003727091.1| 315 EFSFDAgaVIVATGYN 330
                                       3233444499999976 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0016
                                       HHHHHHHHTT-EEEESECEEEEEEEETCEEEEE......EECTEEEE..EEEEEEE--GGGHH...H CS
                               DAO 151 alaraaealGveilegtevtgleeedgkvwgve......rttpgend..aadavVnaaGawsd...l 206
                                        ++  a++ G+++++g +v +++e++  ++ v       +   + ++  ++d vV++ G+ ++   +
  gi|298675341|ref|YP_003727091.1| 438 EYYTNAQSMGIQFVRG-KVAEIQEDN-SGKPVLryedtlE---NKIFeeTYDLVVLSVGLEANkdeK 499
                                       577889**********.*****7755.3445555644322...2222336788*******9875332 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 6.7
                                       HHHHHHHHHHH..HHTTTTEEEEEHHHHHHH CS
                               DAO  96 lealdkllall..leagldaelldaeevrel 124
                                       ++ l++ l++   +++ l +e+++a+e+++ 
  gi|298675341|ref|YP_003727091.1| 728 MDVLKDVLEEIdiNPNRLNVEWISASECNRF 758
                                       444545555547788999999****999875 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   4.8      0.13        64      33      49 ..     230     258 ..     190     260 .. 0.61
   2 !   15.9  12.4   2.1e-05     0.011       1      50 [.     243     306 ..     243     307 .. 0.83
   3 !   16.0   2.1   2.1e-05      0.01       1      26 [.     291     316 ..     291     320 .. 0.85
   4 ?   -1.2   0.4       4.9   2.4e+03       7      19 ..     397     409 ..     383     422 .. 0.75
   5 !   29.1  10.7   1.7e-09   8.3e-07       1      51 []     579     624 ..     579     624 .. 0.92
   6 ?    0.1   0.4       1.9   9.3e+02       5      14 ..     656     665 ..     654     688 .. 0.64

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.13
                            Fer4_9  33 e...........eaCigCga.CveaCpkg 49 
                                                   ++C gC + C  +Cp +
  gi|298675341|ref|YP_003727091.1| 230 VkglkkpryvseDKCKGCIEeCSSVCPVE 258
                                       04444455555578888865599999876 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 2.1e-05
                            Fer4_9   1 kCtgC.gaCveaCpagvvvedaaerkarlraase..............eaCigCgaCveaCpkga 50 
                                       kC gC  +C ++Cp ++ ++ + +      + s+              e C+gCg C ++Cp +a
  gi|298675341|ref|YP_003727091.1| 243 KCKGCiEECSSVCPVEISNPFDYGIGKIKAI-SMpfpqavpqcayindEYCVGCGLCRQVCPADA 306
                                       7****557*****999999988777665444.445889999999999999************987 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 2.1e-05
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerka 26 
                                       +C+gCg C ++Cpa++v ++++e++ 
  gi|298675341|ref|YP_003727091.1| 291 YCVGCGLCRQVCPADAVDYEQKEEEF 316
                                       69*************99999888765 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 4.9
                            Fer4_9   7 aCveaCpagvvve 19 
                                       +C ++C + ++++
  gi|298675341|ref|YP_003727091.1| 397 YCSKVCCMSAIKN 409
                                       6888887776654 PP

  == domain 5  score: 29.1 bits;  conditional E-value: 1.7e-09
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       kCtgCg C+++C++g ++  + + ++        +C+gCg+C +aCp++ai
  gi|298675341|ref|YP_003727091.1| 579 KCTGCGICQDVCKFGKIKLYNHKAEVDEL-----SCHGCGSCSAACPEDAI 624
                                       7****************999999998863.....6*************997 PP

  == domain 6  score: 0.1 bits;  conditional E-value: 1.9
                            Fer4_9   5 CgaCveaCpa 14 
                                       C+ C +aC  
  gi|298675341|ref|YP_003727091.1| 656 CNWCSYACAD 665
                                       8999999943 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.6   1.3e-09   6.5e-07       2      39 ..     144     181 ..     143     182 .. 0.94
   2 ?   -1.5   0.0         2     1e+03     177     200 ..     305     328 ..     296     342 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1.3e-09
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGG CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefggata 39 
                                       v+ViG+G+AG  AAl++a+aG  v +veke++ gg  a
  gi|298675341|ref|YP_003727091.1| 144 VLVIGGGVAGIEAALNLADAGYHVYMVEKEPSIGGKMA 181
                                       9*******************************999765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2
                                       EEEEETTTTCEEEEEESEEEE--- CS
                     FAD_binding_2 177 avvenpesgrevrirakavvlatg 200
                                       + v  +++++e+ + a av++atg
  gi|298675341|ref|YP_003727091.1| 305 DAVDYEQKEEEFSFDAGAVIVATG 328
                                       55555689999************8 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.2   1.3e-09   6.7e-07       2      39 ..     144     181 ..     143     189 .. 0.96
   2 ?   -2.5   0.0       4.9   2.5e+03     315     387 ..     466     540 ..     463     547 .. 0.71

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 1.3e-09
                      FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGllt 39 
                                       v+V+GGg+aG+ AA+  a aG  v +ve+++ +GG ++
  gi|298675341|ref|YP_003727091.1| 144 VLVIGGGVAGIEAALNLADAGYHVYMVEKEPSIGGKMA 181
                                       9**********************************985 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.9
                      FAD_oxidored 315 yvlteedvlearrfeD..siaigsypiDlHaaqgeksneggveveakgpYqIPyrsLvPkr..veNLlvagRciSat 387
                                        vl+ ed le++ fe+     + s  ++  + ++  s+  +    ++g Y+++   + P +  ++++ +ag c+S+ 
  gi|298675341|ref|YP_003727091.1| 466 PVLRYEDTLENKIFEEtyDLVVLSVGLEANKDEKI-SSMLNLSTRSDGFYTVSHPKMRPVEsnIDGVYIAG-CASGP 540
                                       56677777777777753344455555555555555.66677788888899999999999999999****99.99975 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   1.0      0.05        25      49      65 .]     242     259 ..     191     263 .. 0.80
   2 !   14.7   0.0   6.2e-05     0.031       4      17 ..     291     308 ..     286     365 .. 0.75
   3 !   12.4  12.4   0.00032      0.16       2      64 ..     577     622 ..     576     623 .. 0.74
   4 !    8.6   6.9     0.005       2.5       4      60 ..     608     662 ..     605     667 .. 0.55

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.05
                            Fer4_8  49 wsCttc.gaCtevCpvgi 65 
                                       ++C +c ++C++vCpv+i
  gi|298675341|ref|YP_003727091.1| 242 DKCKGCiEECSSVCPVEI 259
                                       567777345999999876 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 6.2e-05
                            Fer4_8   4 kCieCgaCqsaCp....v 17 
                                       +C++Cg+C++ Cp     
  gi|298675341|ref|YP_003727091.1| 291 YCVGCGLCRQVCPadavD 308
                                       788888888888855441 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00032
                            Fer4_8   2 lekCieCgaCqsaCpvlrrtk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                        +kC++Cg Cq+ C + + +  +h        ++ +++e          sC++cg+C+ +Cp++
  gi|298675341|ref|YP_003727091.1| 577 TDKCTGCGICQDVCKFGKIKLyNH--------KA-EVDE---------LSCHGCGSCSAACPED 622
                                       589***********8777765233........22.2222.........37************85 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.005
                            Fer4_8   4 kCieCgaCqsaCp....vlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtev 60 
                                       +C++Cg C +aCp     +r++ +   +++ eaa  +++++       l     c+ C+ +
  gi|298675341|ref|YP_003727091.1| 608 SCHGCGSCSAACPedaiYMRNQTDAQIHSQIEAAL-EVKDEF-----PLIVSFLCNWCSYA 662
                                       69999999999987774333333444444444333.222222.....24445555555555 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.1   1.8e-08   9.2e-06       2      31 ..     144     173 ..     143     193 .. 0.86
   2 ?   -1.0   0.1       1.4   6.9e+02     213     279 ..     416     480 ..     401     508 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.8e-08
                                       EEEE-SSHHHHHHHHHHHHTT--EEEEES- CS
                              GIDA   2 viViGgGhAGceAAlaaarlGakvlLithk 31 
                                       v ViGgG AG+eAAl++a +G++v ++ ++
  gi|298675341|ref|YP_003727091.1| 144 VLVIGGGVAGIEAALNLADAGYHVYMVEKE 173
                                       99************************9544 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.4
                                       --.SS-B-SSSSSSSTCG----EEEEE--HHHHHHHHCTCCC-T.T----B--S-CCC-SSTCCCCCC CS
                              GIDA 213 gd.kegeefsylnkplnkeqvecfltatneathkiikenlkksaklfegcieelgprycpsiedkivr 279
                                       ++ +  +   y++ + + e +e+++t+ ++   ++++ ++ +   + e+   +   ry++++e+ki++
  gi|298675341|ref|YP_003727091.1| 416 RYpEMDIRLHYIDIRASGEMYEEYYTNAQSMGIQFVRGKVAE---IQEDNSGKPVLRYEDTLENKIFE 480
                                       444666777888888888889999998888888888888887...55666666778999999999875 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   6.1e-08     3e-05       1      36 [.     146     181 ..     146     210 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 6.1e-08
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG- CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraa 36 
                                       ++G+G++G  aA  La+ag++v  +ek +++GG++a
  gi|298675341|ref|YP_003727091.1| 146 VIGGGVAGIEAALNLADAGYHVYMVEKEPSIGGKMA 181
                                       8********************************997 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.7   1.2e-07   6.2e-05       2      40 ..     143     181 ..     142     185 .. 0.95
   2 ?   -2.4   0.0         3   1.5e+03     101     145 ..     186     230 ..     182     239 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.2e-07
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHH CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKil 40 
                                       +v+viGgG AG+ aA+++a++g +V ++ek++++g K++
  gi|298675341|ref|YP_003727091.1| 143 NVLVIGGGVAGIEAALNLADAGYHVYMVEKEPSIGGKMA 181
                                       799*********************************986 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3
                                       EEETT.-CHHHHHHHHHHHHH.HT-EEE-S--EEEEECETTE.EEE CS
                       HI0933_like 101 lFpvsdkaedivdallkelke.agvklrletevksvekeedgkfrv 145
                                       +Fp++d +  ++   ++e+++  +++l++++e+++++ + ++ f+v
  gi|298675341|ref|YP_003727091.1| 186 VFPTNDCSICVLAPKMTEVSNhPNIELYTNSEITEITGSVGN-FTV 230
                                       788888888888776666654278999999999998654444.555 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   3.3       1.6   7.9e+02       2      16 ..     242     257 ..     241     261 .. 0.83
   2 !   13.0   2.3   0.00023      0.11       2      16 ..     290     304 ..     289     312 .. 0.90
   3 !   11.9   3.9   0.00052      0.26       2      17 .]     578     593 ..     577     593 .. 0.91
   4 !   13.2   1.4    0.0002     0.097       3      16 ..     608     621 ..     606     631 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 1.6
                            Fer4_4   2 erCigCgs.CvaaCPq 16 
                                       ++C gC   C ++CP+
  gi|298675341|ref|YP_003727091.1| 242 DKCKGCIEeCSSVCPV 257
                                       78999985599***96 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00023
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       e C+gCg C+ +CP 
  gi|298675341|ref|YP_003727091.1| 290 EYCVGCGLCRQVCPA 304
                                       67************5 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00052
                            Fer4_4   2 erCigCgsCvaaCPqg 17 
                                       ++C+gCg C ++C++g
  gi|298675341|ref|YP_003727091.1| 578 DKCTGCGICQDVCKFG 593
                                       89***********975 PP

  == domain 4  score: 13.2 bits;  conditional E-value: 0.0002
                            Fer4_4   3 rCigCgsCvaaCPq 16 
                                       +C gCgsC aaCP 
  gi|298675341|ref|YP_003727091.1| 608 SCHGCGSCSAACPE 621
                                       6************4 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   3.2e-06    0.0016      30      67 ..     143     180 ..     133     246 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.2e-06
                                       EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHH CS
                       AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleql 67 
                                       +vlviGgGvaG++A+ + +  g +V++++++p+   ++
  gi|298675341|ref|YP_003727091.1| 143 NVLVIGGGVAGIEAALNLADAGYHVYMVEKEPSIGGKM 180
                                       79***************************999765555 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.2   7.5e-06    0.0037       3      33 ..     143     173 ..     141     177 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 7.5e-06
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekr 33 
                                       +Vl++G+G aG+ +al L+ aG  v +vek 
  gi|298675341|ref|YP_003727091.1| 143 NVLVIGGGVAGIEAALNLADAGYHVYMVEKE 173
                                       69***************************96 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.3      0.25   1.2e+02      74      96 .]     236     259 ..     215     259 .. 0.79
   2 !   11.8   1.8   0.00069      0.34      77      94 ..     287     304 ..     277     306 .. 0.85
   3 !    8.6   2.5    0.0067       3.4      75      93 ..     573     591 ..     547     594 .. 0.81
   4 !   14.1   0.8   0.00013     0.064      69      94 ..     596     621 ..     592     623 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.25
                           Fer4_22  74 kekfgesgCvGC.gRCieacpvki 96 
                                        + ++e +C GC   C+++cpv+i
  gi|298675341|ref|YP_003727091.1| 236 PRYVSEDKCKGCiEECSSVCPVEI 259
                                       55568899999955799***9986 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00069
                           Fer4_22  77 fgesgCvGCgRCieacpv 94 
                                       ++ + CvGCg C ++cp+
  gi|298675341|ref|YP_003727091.1| 287 INDEYCVGCGLCRQVCPA 304
                                       47789***********97 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0067
                           Fer4_22  75 ekfgesgCvGCgRCieacp 93 
                                       + +++ +C+GCg C+++c+
  gi|298675341|ref|YP_003727091.1| 573 AFVDTDKCTGCGICQDVCK 591
                                       445899************7 PP

  == domain 4  score: 14.1 bits;  conditional E-value: 0.00013
                           Fer4_22  69 klsefkekfgesgCvGCgRCieacpv 94 
                                       kl+++k++++e +C GCg C++acp+
  gi|298675341|ref|YP_003727091.1| 596 KLYNHKAEVDELSCHGCGSCSAACPE 621
                                       788889999***************97 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       7.7   3.8e+03     181     210 ..      29      58 ..      16      67 .. 0.72
   2 !   15.3   0.1   1.7e-05    0.0086      17      63 ..     141     186 ..     134     190 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 7.7
                                       HHCTTTS-----ECB-HHHHHHHHHHHECE CS
                              Thi4 181 kleakiekvkgeksldaekaedaivkktre 210
                                       k+ + ie v++ + + ++++ +ai+++ +e
  gi|298675341|ref|YP_003727091.1|  29 KEFKDIEIVRDIQFMCSDTGQEAIIEDIKE 58 
                                       444556778899999999999999987765 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.7e-05
                                       EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTT CS
                              Thi4  17 esDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGql 63 
                                       + +v+++G+G +G+ aa  la + + +v ++e++ s+GG + l   +
  gi|298675341|ref|YP_003727091.1| 141 NRNVLVIGGGVAGIEAALNLADA-GYHVYMVEKEPSIGGKMALLNEV 186
                                       5689*******************.***************98776555 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.073        36     189     215 ..     139     165 ..     109     188 .. 0.84
   2 ?    2.3   0.0      0.15        75     321     341 ..     310     330 ..     305     331 .. 0.85
   3 ?    6.0   0.0     0.011       5.5     283     340 ..     434     492 ..     419     494 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.073
                       K_oxygenase 189 lakkriaVvGsGqSaaeifedllrrqk 215
                                         +++++V+G+G  + e + +l++   
  gi|298675341|ref|YP_003727091.1| 139 SINRNVLVIGGGVAGIEAALNLADAGY 165
                                       55789***************9998743 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.15
                       K_oxygenase 321 eesgeeetlevdavvlATGYr 341
                                       e+++ee++ ++ av++ATGY+
  gi|298675341|ref|YP_003727091.1| 310 EQKEEEFSFDAGAVIVATGYN 330
                                       6788999999**********7 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.011
                       K_oxygenase 283 elyeqkvkgeerlrllp.nrevesaeaegkgeveltlrneesgeeetlevdavvlATGY 340
                                       e+ye+ +++++++ ++  + +v +++++++g+  l ++++ +++ +++++d vvl+ G 
  gi|298675341|ref|YP_003727091.1| 434 EMYEEYYTNAQSMGIQFvRGKVAEIQEDNSGKPVLRYEDTLENKIFEETYDLVVLSVGL 492
                                       456666666555555431458**********************************9985 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   0.00025      0.12       7      53 ..     141     185 ..     139     207 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00025
                     NAD_binding_7   7 gkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaee 53 
                                       +++vlv+GgG  + + + +l++ag +v +v +e  + + +++ l +e
  gi|298675341|ref|YP_003727091.1| 141 NRNVLVIGGGVAGIEAALNLADAGYHVYMVEKE--PSIGGKMALLNE 185
                                       689***************************999..455555555555 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.4   0.00046      0.23       2      36 ..     144     176 ..     143     181 .. 0.89
   2 ?   -0.5   0.0      0.96   4.8e+02     254     282 ..     309     337 ..     302     352 .. 0.84
   3 ?   -1.4   0.0       1.9   9.4e+02      86     122 ..     432     468 ..     417     478 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00046
                     Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieaspsl 36 
                                       v+viG+G Ag+  A +l  a +g +v ++e  ps+
  gi|298675341|ref|YP_003727091.1| 144 VLVIGGGVAGIEAALNL--ADAGYHVYMVEKEPSI 176
                                       89***************..8889999999988876 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.96
                     Lycopene_cycl 254 leqkvlaiGaaaglvhPaTGYsvarslae 282
                                        eqk  ++   ag+v  aTGY v ++ ++
  gi|298675341|ref|YP_003727091.1| 309 YEQKEEEFSFDAGAVIVATGYNVFDASRK 337
                                       5677777888999**********999876 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.9
                     Lycopene_cycl  86 skrlkeellerlvengvklleakvesveeeeageslv 122
                                       s ++ ee   +  + g++++++kv++++e++ g+ + 
  gi|298675341|ref|YP_003727091.1| 432 SGEMYEEYYTNAQSMGIQFVRGKVAEIQEDNSGKPVL 468
                                       45666777777778899999******99999876655 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.031        15       2      40 ..     146     179 ..     145     189 .. 0.84
   2 ?    4.5   0.0     0.062        31     105     154 ..     437     491 ..     431     493 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.031
                     NAD_binding_9   2 ivGaGprGlavlerLlarakkkspleitlfdpsep.gagr 40 
                                       ++G+G++G+ ++ +L++        ++ +++++++ g g+
  gi|298675341|ref|YP_003727091.1| 146 VIGGGVAGIEAALNLADA-----GYHVYMVEKEPSiG-GK 179
                                       8**************999.....59999999987745.44 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.062
                     NAD_binding_9 105 eellarlpegvtvevhraevvdleeradgq.avlladg..as...laadaVvLAlG 154
                                       ee   ++ +++ ++++r++v +++e+++g   ++ +d   ++    ++d VvL +G
  gi|298675341|ref|YP_003727091.1| 437 EEYYTNA-QSMGIQFVRGKVAEIQEDNSGKpVLRYEDTleNKifeETYDLVVLSVG 491
                                       5555555.4579****************9745555554222233369999999998 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   2.2       7.9   3.9e+03       3      17 ..     241     256 ..     239     259 .. 0.70
   2 ?   11.2   0.9   0.00083      0.41       1      18 [.     287     304 ..     287     318 .. 0.88
   3 ?    6.5   5.1     0.025        12       1      16 [.     575     590 ..     575     591 .. 0.95
   4 ?   12.7   1.0   0.00028      0.14       1      32 [.     604     635 ..     604     647 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 7.9
                           Fer4_13   3 rdtCiac.gaCvelaP 17 
                                       +d+C +c + C +++P
  gi|298675341|ref|YP_003727091.1| 241 EDKCKGCiEECSSVCP 256
                                       5777777567888887 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00083
                           Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                       ++ + C++cg+C++++P 
  gi|298675341|ref|YP_003727091.1| 287 INDEYCVGCGLCRQVCPA 304
                                       56799************5 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.025
                           Fer4_13   1 VDrdtCiacgaCvela 16 
                                       VD d+C++cg+C +++
  gi|298675341|ref|YP_003727091.1| 575 VDTDKCTGCGICQDVC 590
                                       9************999 PP

  == domain 4  score: 12.7 bits;  conditional E-value: 0.00028
                           Fer4_13   1 VDrdtCiacgaCvelaPd..vFeeddeggasvva 32 
                                       VD+ +C +cg+C +++P+  ++ +++    ++++
  gi|298675341|ref|YP_003727091.1| 604 VDELSCHGCGSCSAACPEdaIYMRNQT--DAQIH 635
                                       8999*************8445555554..34555 PP

>> Glyco_tran_WecB  Glycosyl transferase WecB/TagA/CpsF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00065      0.33      58     108 ..      21      72 ..      18      92 .. 0.84
   2 ?   -2.0   0.0         6     3e+03      83     101 ..     469     487 ..     405     505 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00065
                   Glyco_tran_WecB  58 ekaaerlrekypglriagthdgy.keeeeeaiieainaskpdlllvglGapk 108
                                       +++++++++++++++i+   +   +++ +eaiie+i++++ d +l++  +pk
  gi|298675341|ref|YP_003727091.1|  21 DTLQDKIKKEFKDIEIVRDIQFMcSDTGQEAIIEDIKEHNIDRVLIAACSPK 72 
                                       678999**********975555566899********************9998 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 6
                   Glyco_tran_WecB  83 eeeeaiieainaskpdlll 101
                                         e+ + ++i +   dl++
  gi|298675341|ref|YP_003727091.1| 469 RYEDTLENKIFEETYDLVV 487
                                       3344445555555555555 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0018      0.92       1      30 [.     151     180 ..     151     184 .. 0.95
   2 ?   -2.9   0.0       6.2   3.1e+03     230     266 ..     454     496 ..     451     504 .. 0.82
   3 ?   -1.2   0.0       1.9   9.6e+02     403     429 ..     514     538 ..     507     554 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0018
                                       HHHHHHHHHHHHTTEEEEEEESSSSSBTTS CS
                     Amino_oxidase   1 laGLaaArqLlsaGfdVtvlEardrvGGRi 30 
                                       +aG+ aA  L++aG+ V  +E ++ +GG++
  gi|298675341|ref|YP_003727091.1| 151 VAGIEAALNLADAGYHVYMVEKEPSIGGKM 180
                                       59**************************98 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.2
                                       EEEEEEE.ETTCEEEEETTSTEE.....EESEEEE-S-HHHHH CS
                     Amino_oxidase 230 rVkeikr.egdgvtvtledgevv.....eaDaVvvTvplgvlk 266
                                       +V ei+  ++++  +++ed  ++     ++D Vv+ v l + k
  gi|298675341|ref|YP_003727091.1| 454 KVAEIQEdNSGKPVLRYEDTLENkifeeTYDLVVLSVGLEANK 496
                                       7999999555559999999999999999*******99998776 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.9
                                       TTHHHHHHHHHHCHHCSTTEEE.SGGG CS
                     Amino_oxidase 403 vgpghedydplakpegdprlffAGeht 429
                                       ++++h  ++p+ ++  ++++++AG++ 
  gi|298675341|ref|YP_003727091.1| 514 YTVSHPKMRPVESN--IDGVYIAGCAS 538
                                       67788888888888..*********95 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.3    0.0026       1.3       1      34 [.     143     173 ..     143     179 .. 0.91
   2 ?    0.7   0.0      0.37   1.9e+02     162     186 ..     441     465 ..     397     493 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0026
                                       EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S CS
                    Trp_halogenase   1 kivivGGGtaGwlaAaalakalkgklevtlvese 34 
                                       +++++GGG aG  aA  la a+   ++v +ve+e
  gi|298675341|ref|YP_003727091.1| 143 NVLVIGGGVAGIEAALNLADAG---YHVYMVEKE 173
                                       599******************9...899999987 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.37
                                       HHHHHCT-EEEE--EEEEEE-TTS- CS
                    Trp_halogenase 162 rvaearGvtrvegkvvevqldedgr 186
                                       ++a++ G++ v+gkv+e+q d++g+
  gi|298675341|ref|YP_003727091.1| 441 TNAQSMGIQFVRGKVAEIQEDNSGK 465
                                       6899****************99875 PP

>> MinC_N  Septum formation inhibitor MinC, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00072      0.36      30      91 ..      21      79 ..       5      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00072
                            MinC_N 30 qkLsdkiaeaPklfknapvvldvskleekvdlkaLkelisraglrivgvsgckdkaskeeim 91
                                        L+dki++    fk++ +v d++ ++ ++  +a+ e i+++++  v ++ c  k  ++  +
  gi|298675341|ref|YP_003727091.1| 21 DTLQDKIKK---EFKDIEIVRDIQFMCSDTGQEAIIEDIKEHNIDRVLIAACSPKLHEKTFQ 79
                                      469999996...48**************************************9998887744 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   3.4      0.76   3.8e+02      44      60 ..     242     259 ..     190     260 .. 0.67
   2 ?    8.3  11.6    0.0068       3.4       1      59 [.     243     305 ..     243     307 .. 0.68
   3 ?   -1.8   0.1       9.9   4.9e+03       7      18 ..     397     408 ..     394     438 .. 0.72
   4 ?   10.0   1.7     0.002      0.98       1      17 [.     579     595 ..     579     607 .. 0.79
   5 ?   10.8   2.8    0.0011      0.55      45      59 ..     608     622 ..     599     626 .. 0.88
   6 ?    6.9   8.3     0.018         9       2      32 ..     609     641 ..     608     667 .. 0.53

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.76
                           Fer4_17  44 slCieC.geCerkCPqgl 60 
                                       ++C +C +eC+++CP ++
  gi|298675341|ref|YP_003727091.1| 242 DKCKGCiEECSSVCPVEI 259
                                       556666467888888765 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0068
                           Fer4_17   1 rCiqCgy.ClpeCpsyeaydnepk.kllraaklglleeaeke..ekaslCieCgeCerkCPqg 59 
                                       +C +C   C  +Cp  + ++++     ++a+++   +++ +    + + C++Cg+C+++CP++
  gi|298675341|ref|YP_003727091.1| 243 KCKGCIEeCSSVCPVEISNPFDYGiGKIKAISMPFPQAVPQCayINDEYCVGCGLCRQVCPAD 305
                                       6999975599999999999985332455555553333333321145588************86 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 9.9
                           Fer4_17   7 yClpeCpsyeay 18 
                                       yC ++C + ++ 
  gi|298675341|ref|YP_003727091.1| 397 YCSKVCCMSAIK 408
                                       899988776553 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.002
                           Fer4_17   1 rCiqCgyClpeCpsyea 17 
                                       +C++Cg C ++C ++++
  gi|298675341|ref|YP_003727091.1| 579 KCTGCGICQDVCKFGKI 595
                                       6***********99776 PP

  == domain 5  score: 10.8 bits;  conditional E-value: 0.0011
                           Fer4_17  45 lCieCgeCerkCPqg 59 
                                       +C++Cg C+++CP++
  gi|298675341|ref|YP_003727091.1| 608 SCHGCGSCSAACPED 622
                                       799*********986 PP

  == domain 6  score: 6.9 bits;  conditional E-value: 0.018
                           Fer4_17   2 CiqCgyClpeCpsyeaydne..pkkllraaklg 32 
                                       C++Cg C ++Cp  ++y  +   +++  +++++
  gi|298675341|ref|YP_003727091.1| 609 CHGCGSCSAACPEDAIYMRNqtDAQIHSQIEAA 641
                                       888888888888766644431134566666554 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       2.1     1e+03      57      91 ..      24      57 ..      12      69 .. 0.80
   2 ?   10.6   0.6   0.00076      0.38       1      33 [.     143     175 ..     143     182 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.1
                                      HHHHCCCHHCEEEES-HHHHHC-SEEEE-S-SSHH CS
                           3HCDH_N 57 eeeveaalarisfttdleeavdadlviEavvEnle 91
                                      ++++++ ++ i++  d++ +   d  +Ea++E+++
  gi|298675341|ref|YP_003727091.1| 24 QDKIKKEFKDIEIVRDIQFM-CSDTGQEAIIEDIK 57
                                      48889999999999999887.56888999999875 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00076
                                       EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HH CS
                           3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdisee 33 
                                       +v viG G+ G + a  +a ag++V +v+ +++
  gi|298675341|ref|YP_003727091.1| 143 NVLVIGGGVAGIEAALNLADAGYHVYMVEKEPS 175
                                       588*************************98775 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.6       5.9   2.9e+03       5      19 ..     241     256 ..     238     261 .. 0.55
   2 ?    6.0   0.6     0.039        19       3      19 ..     287     303 ..     286     324 .. 0.88
   3 ?    9.2   4.5     0.004         2       3      19 ..     575     591 ..     574     605 .. 0.79
   4 ?    8.3   2.0     0.008         4       2      20 ..     603     621 ..     602     654 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 5.9
                           Fer4_15   5 rdaCigc.glCvaeap 19 
                                       +d+C gc + C  ++p
  gi|298675341|ref|YP_003727091.1| 241 EDKCKGCiEECSSVCP 256
                                       5666665234554444 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.039
                           Fer4_15   3 vDrdaCigcglCvaeap 19 
                                       ++ + C gcglC +++p
  gi|298675341|ref|YP_003727091.1| 287 INDEYCVGCGLCRQVCP 303
                                       77889**********98 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.004
                           Fer4_15   3 vDrdaCigcglCvaeap 19 
                                       vD d+C+gcg C ++++
  gi|298675341|ref|YP_003727091.1| 575 VDTDKCTGCGICQDVCK 591
                                       9*************996 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.008
                           Fer4_15   2 vvDrdaCigcglCvaeape 20 
                                       +vD+  C gcg C a++pe
  gi|298675341|ref|YP_003727091.1| 603 EVDELSCHGCGSCSAACPE 621
                                       58999************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (789 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       855  (0.0476881); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        38  (0.00211947); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              36  [number of targets reported over threshold]
# CPU time: 0.72u 0.28s 00:00:01.00 Elapsed: 00:00:00.45
# Mc/sec: 5318.52
//
Query:       gi|298675342|ref|YP_003727092.1|  [L=447]
Description: 4Fe-4S ferredoxin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-44  148.3  71.1    1.4e-08   34.2   3.4    8.3  8  Fer4             4Fe-4S binding domain
    3.8e-32  110.6  60.6    9.3e-12   45.4   8.5    5.2  4  Fer4_7           4Fe-4S dicluster domain
    4.4e-27   94.0  56.1      2e-07   31.1  10.1    5.7  8  Fer4_9           4Fe-4S dicluster domain
    1.8e-25   87.9  76.1      1e-06   28.5   1.6    8.4  8  Fer4_6           4Fe-4S binding domain
    9.7e-25   86.5  55.9    5.4e-05   23.2   8.6    6.7  6  Fer4_21          4Fe-4S dicluster domain
    1.2e-24   86.2  69.0    5.8e-08   32.7   9.8    7.0  8  Fer4_10          4Fe-4S dicluster domain
    1.9e-22   80.0  64.6    0.00037   21.4   0.8    8.1  8  Fer4_16          4Fe-4S double cluster binding domain
    1.2e-20   72.2  69.4    7.9e-05   22.5   2.5    8.3  8  Fer4_2           4Fe-4S binding domain
      6e-18   65.1  59.0    1.1e-06   29.0   5.6    6.3  7  Fer4_8           4Fe-4S dicluster domain
    1.9e-10   40.4  75.0    0.00067   20.0   3.6    8.3  8  Fer4_4           4Fe-4S binding domain
    2.5e-10   40.5  88.6     0.0094   16.8   5.1    8.3  8  Fer4_3           4Fe-4S binding domain
    5.4e-09   36.5  70.7      0.011   16.2  11.0    7.7  8  Fer4_17          4Fe-4S dicluster domain
    1.1e-08   35.7  52.4      0.061   14.1   0.8    8.4  8  Fer4_15          4Fe-4S single cluster domain
    9.5e-07   29.3  69.6        0.3   11.6   3.4    8.6  8  Fer4_13          4Fe-4S single cluster domain of Ferredoxin I
  ------ inclusion threshold ------
      0.021   15.0   0.4      0.021   15.0   0.4    7.3  7  Fer4_18          4Fe-4S dicluster domain
      0.021   15.6   0.5      0.021   15.6   0.5    8.4 10  Fer4_22          4Fe-4S dicluster domain
      0.048   13.8   0.1      0.079   13.1   0.1    1.3  1  Pox_A22          Poxvirus A22 protein
       0.17   12.0   0.4       0.62   10.2   0.3    1.9  2  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   1.0   2.9e-11   2.9e-08       3      24 .]      44      65 ..      42      65 .. 0.92
   2 !   30.1   1.6   2.7e-10   2.7e-07       2      23 ..      82     103 ..      81     104 .. 0.90
   3 !   12.3   1.8   0.00011      0.11       6      24 .]     128     146 ..     123     146 .. 0.82
   4 !   16.9   2.3     4e-06     0.004       1      18 [.     168     185 ..     168     187 .. 0.92
   5 !   26.9   3.3   2.9e-09   2.9e-06       3      24 .]     208     229 ..     206     229 .. 0.95
   6 !   34.2   3.4   1.4e-11   1.4e-08       2      23 ..     246     267 ..     245     268 .. 0.93
   7 !    9.6   1.0   0.00082      0.82      10      20 ..     291     301 ..     290     303 .. 0.91
   8 !   26.5   4.5   3.8e-09   3.7e-06       3      22 ..     314     333 ..     312     335 .. 0.89

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 2.9e-11
                                      EETTTSSS-THHHHHSTTTEEE CS
                              Fer4  3 ideekCigCGaCvevCPvgAIt 24
                                      +d+ +C+gCG+Cv++CP+ A++
  gi|298675342|ref|YP_003727092.1| 44 YDYKRCTGCGLCVKICPTQALE 65
                                      799*****************85 PP

  == domain 2  score: 30.1 bits;  conditional E-value: 2.7e-10
                                       EEETTTSSS-THHHHHSTTTEE CS
                              Fer4   2 videekCigCGaCvevCPvgAI 23 
                                       + d ekC++CG C++ CPv+A 
  gi|298675342|ref|YP_003727092.1|  82 TLDIEKCTFCGMCAKFCPVNAF 103
                                       6789*****************7 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00011
                                       TTSSS-THHHHHSTTTEEE CS
                              Fer4   6 ekCigCGaCvevCPvgAIt 24 
                                       + C  C +C++ CP +AI+
  gi|298675342|ref|YP_003727092.1| 128 NNCLPCLLCESSCPEDAIE 146
                                       56677*************6 PP

  == domain 4  score: 16.9 bits;  conditional E-value: 4e-06
                                       EEEETTTSSS-THHHHHS CS
                              Fer4   1 vvideekCigCGaCvevC 18 
                                       ++id+ekC  CG+C   C
  gi|298675342|ref|YP_003727092.1| 168 IEIDTEKCNLCGLCSHFC 185
                                       68************9999 PP

  == domain 5  score: 26.9 bits;  conditional E-value: 2.9e-09
                                       EETTTSSS-THHHHHSTTTEEE CS
                              Fer4   3 ideekCigCGaCvevCPvgAIt 24 
                                       +de+ C +C++C ++CP +AI+
  gi|298675342|ref|YP_003727092.1| 208 VDEDECDYCMLCQDICPEDAIK 229
                                       9********************6 PP

  == domain 6  score: 34.2 bits;  conditional E-value: 1.4e-11
                                       EEETTTSSS-THHHHHSTTTEE CS
                              Fer4   2 videekCigCGaCvevCPvgAI 23 
                                        ide+kC++CG C evCP++A 
  gi|298675342|ref|YP_003727092.1| 246 HIDEDKCTRCGWCREVCPYDAV 267
                                       79*******************7 PP

  == domain 7  score: 9.6 bits;  conditional E-value: 0.00082
                                       S-THHHHHSTT CS
                              Fer4  10 gCGaCvevCPv 20 
                                       gC aC +vCP 
  gi|298675342|ref|YP_003727092.1| 291 GCQACFNVCPA 301
                                       9*********6 PP

  == domain 8  score: 26.5 bits;  conditional E-value: 3.8e-09
                                       EETTTSSS-THHHHHSTTTE CS
                              Fer4   3 ideekCigCGaCvevCPvgA 22 
                                       i e+ Ci+CGaC+++CP ++
  gi|298675342|ref|YP_003727092.1| 314 IKEDYCIYCGACENACPENV 333
                                       789**************997 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   8.5   9.3e-15   9.3e-12       1      52 []      48     102 ..      48     102 .. 0.89
   2 !   25.6   4.5   1.4e-08   1.4e-05       2      48 ..     130     185 ..     121     189 .. 0.81
   3 !   29.9  12.7   6.4e-10   6.4e-07       2      52 .]     213     266 ..     212     266 .. 0.82
   4 !   27.2  11.1   4.4e-09   4.4e-06       4      52 .]     291     333 ..     286     333 .. 0.90

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 9.3e-15
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgt...ekveidpekClgCgaCvavCPtga 52 
                                       rC+gCg Cv+ Cp++a+el + ++ ++    + v++d ekC++Cg+C++ CP++a
  gi|298675342|ref|YP_003727092.1|  48 RCTGCGLCVKICPTQALELGPMHEIATGmdaPPVTLDIEKCTFCGMCAKFCPVNA 102
                                       8*******************99877643355778*******************97 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 1.4e-08
                            Fer4_7   2 CigCgaCvaaCpvkaield..........eeenekgtekveidpekClgCgaCvavC 48 
                                       C  C  C++ Cp +aie++          ++ +e+   ++eid ekC  Cg C   C
  gi|298675342|ref|YP_003727092.1| 130 CLPCLLCESSCPEDAIEVKlnipkkeditPF-DENAEGEIEIDTEKCNLCGLCSHFC 185
                                       999**************88555544444322.33344899**************999 PP

  == domain 3  score: 29.9 bits;  conditional E-value: 6.4e-10
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgt....ekveidpekClgCgaCvavCPtga 52 
                                       C  C  C++ Cp +ai+++ ++  +       +v+id++kC+ Cg C +vCP++a
  gi|298675342|ref|YP_003727092.1| 213 CDYCMLCQDICPEDAIKVKGKKPCE-PpaieGEVHIDEDKCTRCGWCREVCPYDA 266
                                       99***************99652222.12344899******************997 PP

  == domain 4  score: 27.2 bits;  conditional E-value: 4.4e-09
                            Fer4_7   4 gCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       gC+aC ++Cp++  +++e+      + ++i++++C++CgaC+++CP ++
  gi|298675342|ref|YP_003727092.1| 291 GCQACFNVCPAHLWYVPED------KNIAIKEDYCIYCGACENACPENV 333
                                       9***************987......569******************885 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   1.2   2.3e-07   0.00023      24      50 ..      36      63 ..      22      64 .. 0.69
   2 !   31.1  10.1     2e-10     2e-07       1      50 [.      48     102 ..      48     103 .. 0.91
   3 !   26.5   6.9   5.4e-09   5.4e-06       1      51 []      87     145 ..      87     145 .. 0.93
   4 !   23.9   5.6   3.3e-08   3.3e-05       1      51 []     174     228 ..     163     228 .. 0.91
   5 !   14.2   2.9   3.7e-05     0.037      32      50 ..     249     266 ..     236     267 .. 0.74
   6 !   24.6  10.8     2e-08     2e-05       1      49 [.     251     302 ..     251     304 .. 0.91
   7 !   25.0  12.3   1.5e-08   1.5e-05       4      50 ..     291     333 ..     286     334 .. 0.90
   8 !   15.8   3.5   1.1e-05     0.011       1      21 [.     318     338 ..     318     343 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.3e-07
                            Fer4_9 24 rkarlraase....eaCigCgaCveaCpkga 50
                                      +k r +        ++C+gCg Cv++Cp++a
  gi|298675342|ref|YP_003727092.1| 36 EKSRKE---LdydyKRCTGCGLCVKICPTQA 63
                                      333332...0334689*************97 PP

  == domain 2  score: 31.1 bits;  conditional E-value: 2e-10
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase.....eaCigCgaCveaCpkga 50 
                                       +CtgCg Cv+ Cp+++ +    +++a    a       e+C++Cg C++ Cp +a
  gi|298675342|ref|YP_003727092.1|  48 RCTGCGLCVKICPTQALELGPMHEIATGMDAPPvtldiEKCTFCGMCAKFCPVNA 102
                                       6************************998655559******************986 PP

  == domain 3  score: 26.5 bits;  conditional E-value: 5.4e-09
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase........eaCigCgaCveaCpkgai 51 
                                       kCt Cg C + Cp ++++++ +++  + + + e        ++C+ C  C+  Cp++ai
  gi|298675342|ref|YP_003727092.1|  87 KCTFCGMCAKFCPVNAFKMEISGEVPSEDSYPEfdsyvkinNNCLPCLLCESSCPEDAI 145
                                       7****************9999999999887777999*****9**************997 PP

  == domain 4  score: 23.9 bits;  conditional E-value: 3.3e-08
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase....eaCigCgaCveaCpkgai 51 
                                       kC+ Cg C + C a ++ e++   ++    ++     ++C  C+ C ++Cp++ai
  gi|298675342|ref|YP_003727092.1| 174 KCNLCGLCSHFCDAFIMLEKEPSPTDPSPFEQLmvdeDECDYCMLCQDICPEDAI 228
                                       7***********999999999998888766555899999*************997 PP

  == domain 5  score: 14.2 bits;  conditional E-value: 3.7e-05
                            Fer4_9  32 seeaCigCgaCveaCpkga 50 
                                       + ++C+ Cg C e+Cp +a
  gi|298675342|ref|YP_003727092.1| 249 E-DKCTRCGWCREVCPYDA 266
                                       3.48999999999999986 PP

  == domain 6  score: 24.6 bits;  conditional E-value: 2e-08
                            Fer4_9   1 kCtgCgaCveaCpagvv.vedaaerkarlraaseeaC..igCgaCveaCpkg 49 
                                       kCt+Cg C e+Cp+++v +++ +e+++ l++ + ++C  +gC+aC+++Cp +
  gi|298675342|ref|YP_003727092.1| 251 KCTRCGWCREVCPYDAVeIKKPFEGEITLKENNIKRCdpHGCQACFNVCPAH 302
                                       7****************77788999999998888***8889*********86 PP

  == domain 7  score: 25.0 bits;  conditional E-value: 1.5e-08
                            Fer4_9   4 gCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                       gC+aC ++Cpa+++   + +++a  + +    Ci CgaC++aCp+++
  gi|298675342|ref|YP_003727092.1| 291 GCQACFNVCPAHLWYVPEDKNIAIKEDY----CIYCGACENACPENV 333
                                       8*************99999999997765....************985 PP

  == domain 8  score: 15.8 bits;  conditional E-value: 1.1e-05
                            Fer4_9   1 kCtgCgaCveaCpagvvveda 21 
                                       +C+ CgaC++aCp +v++ ++
  gi|298675342|ref|YP_003727092.1| 318 YCIYCGACENACPENVMSVKR 338
                                       6***************98876 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   1.6     1e-09     1e-06       4      24 .]      44      64 ..      43      64 .. 0.93
   2 !   13.1   1.6   7.5e-05     0.075       5      24 .]      84     103 ..      80     103 .. 0.89
   3 !   13.7   2.7   4.9e-05     0.049       6      24 .]     127     145 ..     124     145 .. 0.93
   4 !   13.4   1.7   6.1e-05     0.061       2      19 ..     168     185 ..     167     189 .. 0.89
   5 !   12.3   5.9   0.00014      0.14       4      24 .]     208     228 ..     208     228 .. 0.95
   6 !   17.7   3.3   2.6e-06    0.0026       2      23 ..     245     266 ..     244     267 .. 0.94
   7 !   11.8   1.7    0.0002       0.2       7      22 ..     285     302 ..     281     304 .. 0.86
   8 !   19.0   4.4     1e-06     0.001       2      23 ..     312     333 ..     311     334 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1e-09
                            Fer4_6  4 idpdkCigCgdCvrvCPegai 24
                                      +d+ +C+gCg Cv++CP++a+
  gi|298675342|ref|YP_003727092.1| 44 YDYKRCTGCGLCVKICPTQAL 64
                                      6899***************97 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 7.5e-05
                            Fer4_6   5 dpdkCigCgdCvrvCPegai 24 
                                       d +kC+ Cg C++ CP +a+
  gi|298675342|ref|YP_003727092.1|  84 DIEKCTFCGMCAKFCPVNAF 103
                                       789**************995 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 4.9e-05
                            Fer4_6   6 pdkCigCgdCvrvCPegai 24 
                                        ++C+ C  C++ CPe+ai
  gi|298675342|ref|YP_003727092.1| 127 NNNCLPCLLCESSCPEDAI 145
                                       699**************98 PP

  == domain 4  score: 13.4 bits;  conditional E-value: 6.1e-05
                            Fer4_6   2 veidpdkCigCgdCvrvC 19 
                                       +eid +kC+ Cg C   C
  gi|298675342|ref|YP_003727092.1| 168 IEIDTEKCNLCGLCSHFC 185
                                       89************8777 PP

  == domain 5  score: 12.3 bits;  conditional E-value: 0.00014
                            Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                                       +d+d C+ C+ C ++CPe+ai
  gi|298675342|ref|YP_003727092.1| 208 VDEDECDYCMLCQDICPEDAI 228
                                       79999**************98 PP

  == domain 6  score: 17.7 bits;  conditional E-value: 2.6e-06
                            Fer4_6   2 veidpdkCigCgdCvrvCPega 23 
                                       v+id+dkC+ Cg C  vCP++a
  gi|298675342|ref|YP_003727092.1| 245 VHIDEDKCTRCGWCREVCPYDA 266
                                       89******************98 PP

  == domain 7  score: 11.8 bits;  conditional E-value: 0.0002
                            Fer4_6   7 dkCi..gCgdCvrvCPeg 22 
                                        +C+  gC +C++vCP+ 
  gi|298675342|ref|YP_003727092.1| 285 KRCDphGCQACFNVCPAH 302
                                       68**999*********85 PP

  == domain 8  score: 19.0 bits;  conditional E-value: 1e-06
                            Fer4_6   2 veidpdkCigCgdCvrvCPega 23 
                                       ++i++d Ci Cg+C+++CPe++
  gi|298675342|ref|YP_003727092.1| 312 IAIKEDYCIYCGACENACPENV 333
                                       689*****************96 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.1   1.4e-07   0.00014      32      56 ..      40      63 ..      24      66 .. 0.76
   2 !   15.4   1.0   1.5e-05     0.015      35      59 .]      82     105 ..      69     105 .. 0.80
   3 !   13.5   0.8   5.8e-05     0.058      36      58 ..     125     146 ..     114     148 .. 0.85
   4 !   23.2   8.6   5.4e-08   5.4e-05       2      58 ..     169     229 ..     168     230 .. 0.76
   5 !   20.7  10.0   3.3e-07   0.00033       2      53 ..     246     301 ..     245     303 .. 0.69
   6 !   15.7   1.9   1.2e-05     0.012       3      23 ..     314     334 ..     312     349 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.4e-07
                           Fer4_21 32 tvlkvvedeCvGCnlCssvCPvedc 56
                                      + l +  ++C+GC lC+++CP+ ++
  gi|298675342|ref|YP_003727092.1| 40 KELDYDYKRCTGCGLCVKICPT-QA 63
                                      445666789************7.55 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.5e-05
                           Fer4_21  35 kvvedeCvGCnlCssvCPvedciem 59 
                                       ++  ++C+ C +C++ CPv ++ +m
  gi|298675342|ref|YP_003727092.1|  82 TLDIEKCTFCGMCAKFCPV-NAFKM 105
                                       45569*************9.77666 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 5.8e-05
                           Fer4_21  36 vvedeCvGCnlCssvCPvedcie 58 
                                        ++++C  C lC s CP ed+ie
  gi|298675342|ref|YP_003727092.1| 125 KINNNCLPCLLCESSCP-EDAIE 146
                                       46899************.89997 PP

  == domain 4  score: 23.2 bits;  conditional E-value: 5.4e-08
                           Fer4_21   2 ridedkCigCgkCliaCedtshqaieidakt.......vlkvvedeCvGCnlCssvCPvedcie 58 
                                        id +kC  Cg+C   C+  +   +e++++        +l v edeC  C lC ++CP ed+i+
  gi|298675342|ref|YP_003727092.1| 169 EIDTEKCNLCGLCSHFCD--AFIMLEKEPSPtdpspfeQLMVDEDECDYCMLCQDICP-EDAIK 229
                                       59****************..45555444332222222277999***************.89997 PP

  == domain 5  score: 20.7 bits;  conditional E-value: 3.3e-07
                           Fer4_21   2 ridedkCigCgkCliaCedtshqaieidak....tvl.kvvedeC..vGCnlCssvCPv 53 
                                       +idedkC  Cg C  +C+   ++a+ei++      +l +   ++C   GC+ C +vCP 
  gi|298675342|ref|YP_003727092.1| 246 HIDEDKCTRCGWCREVCP---YDAVEIKKPfegeITLkENNIKRCdpHGCQACFNVCPA 301
                                       69****************...677765533111122222223455448**********5 PP

  == domain 6  score: 15.7 bits;  conditional E-value: 1.2e-05
                           Fer4_21   3 idedkCigCgkCliaCedtsh 23 
                                       i+ed Ci Cg C  aC+++ +
  gi|298675342|ref|YP_003727092.1| 314 IKEDYCIYCGACENACPENVM 334
                                       99***************8543 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   9.8   5.8e-11   5.8e-08       4      56 .]      44      99 ..      41      99 .. 0.86
   2 !   17.5   1.6   3.4e-06    0.0034       3      23 ..      82     102 ..      80     119 .. 0.73
   3 !   17.8   9.7   2.7e-06    0.0027       5      55 ..     126     185 ..     122     186 .. 0.83
   4 !   10.4   1.9   0.00053      0.53       2      19 ..     168     185 ..     167     196 .. 0.87
   5 !   10.2   4.4   0.00065      0.65       4      27 ..     208     231 ..     205     239 .. 0.81
   6 !   24.9  13.4   1.7e-08   1.6e-05       2      56 .]     245     300 ..     244     300 .. 0.77
   7 !   17.7  13.4   2.9e-06    0.0029       7      56 .]     285     330 ..     280     330 .. 0.81
   8 !   19.4   2.1   8.3e-07   0.00083       2      29 ..     312     339 ..     311     384 .. 0.77

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 5.8e-11
                           Fer4_10  4 idddtCirCgkCvkaCPadl...tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      +d ++C++Cg Cvk CP+++     +  ++  ++  +v  ++ekCt+cg+C++ CP
  gi|298675342|ref|YP_003727092.1| 44 YDYKRCTGCGLCVKICPTQAlelGPMHEIATGMDAPPVTLDIEKCTFCGMCAKFCP 99
                                      6899**************99987666777777777777779**************9 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 3.4e-06
                           Fer4_10   3 vidddtCirCgkCvkaCPadl 23 
                                        +d ++C+ Cg C k+CP+++
  gi|298675342|ref|YP_003727092.1|  82 TLDIEKCTFCGMCAKFCPVNA 102
                                       578899************944 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 2.7e-06
                           Fer4_10   5 dddtCirCgkCvkaCPadl........tsvgakgea.seeeavrkkvekCtgcgaCveaC 55 
                                         + C+ C  C ++CP d+        ++ + ++++ + e++++++ ekC  cg C   C
  gi|298675342|ref|YP_003727092.1| 126 INNNCLPCLLCESSCPEDAievklnipKKEDITPFDeNAEGEIEIDTEKCNLCGLCSHFC 185
                                       4589***********************666666555156778899***********9999 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.00053
                           Fer4_10   2 vvidddtCirCgkCvkaC 19 
                                       ++id+++C  Cg C  +C
  gi|298675342|ref|YP_003727092.1| 168 IEIDTEKCNLCGLCSHFC 185
                                       689*************** PP

  == domain 5  score: 10.2 bits;  conditional E-value: 0.00065
                           Fer4_10   4 idddtCirCgkCvkaCPadltsvg 27 
                                       +d+d C  C  C++ CP d+ +v+
  gi|298675342|ref|YP_003727092.1| 208 VDEDECDYCMLCQDICPEDAIKVK 231
                                       699**************9665554 PP

  == domain 6  score: 24.9 bits;  conditional E-value: 1.7e-08
                           Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrk.kvekCtg..cgaCveaCP 56 
                                       v+id+d+C+rCg C+++CP+  ++v+ k+  ++e + ++ ++++C+   c aC  +CP
  gi|298675342|ref|YP_003727092.1| 245 VHIDEDKCTRCGWCREVCPY--DAVEIKKPFEGEITLKEnNIKRCDPhgCQACFNVCP 300
                                       789*****************..55555554444444444589999865588******9 PP

  == domain 7  score: 17.7 bits;  conditional E-value: 2.9e-06
                           Fer4_10   7 dtC..irCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       ++C   +C++C ++CPa         +  e++ + +k + C+ cgaC  aCP
  gi|298675342|ref|YP_003727092.1| 285 KRCdpHGCQACFNVCPA------HLWYVPEDKNIAIKEDYCIYCGACENACP 330
                                       6786679**********......55556666777777899***********9 PP

  == domain 8  score: 19.4 bits;  conditional E-value: 8.3e-07
                           Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgak 29 
                                       + i +d Ci Cg+C +aCP ++ sv+ +
  gi|298675342|ref|YP_003727092.1| 312 IAIKEDYCIYCGACENACPENVMSVKRT 339
                                       56899***************66333332 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.8   3.7e-07   0.00037       1      23 [.      48      70 ..      48      82 .. 0.82
   2 !   18.5   0.3     3e-06     0.003       1      25 [.      87     111 ..      87     127 .. 0.77
   3 !   15.7   6.9   2.2e-05     0.022       1      64 [.     129     185 ..     129     188 .. 0.71
   4 !   14.5   3.3   5.1e-05     0.051       2      28 ..     213     239 ..     212     250 .. 0.81
   5 !   17.2   1.2   7.7e-06    0.0076       1      26 [.     251     276 ..     251     286 .. 0.74
   6 !   10.4   2.9   0.00097      0.97      49      66 ..     282     301 ..     273     302 .. 0.73
   7 !   20.2   0.7   8.5e-07   0.00085       2      29 ..     319     345 ..     318     391 .. 0.72
   8 ?   -1.8   0.3       6.2   6.2e+03      37      49 ..     418     430 ..     398     445 .. 0.48

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 3.7e-07
                           Fer4_16  1 rCgtCgkCaevCPtnaikekkek 23
                                      rC++Cg C+++CPt+a++     
  gi|298675342|ref|YP_003727092.1| 48 RCTGCGLCVKICPTQALELGPMH 70
                                      6****************987444 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 3e-06
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekei 25 
                                       +C+ Cg Ca+ CP+na+k++ + e+
  gi|298675342|ref|YP_003727092.1|  87 KCTFCGMCAKFCPVNAFKMEISGEV 111
                                       59***************99944443 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 2.2e-05
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvC 64 
                                       +C  C  C ++CP++ai+ k    ++++++++  t+ +++++ ++e ++  e++  C+ C   C
  gi|298675342|ref|YP_003727092.1| 129 NCLPCLLCESSCPEDAIEVK----LNIPKKEDI-TPFDENAEGEIEIDT--EKCNLCGLCSHFC 185
                                       5999****************....555555544.334444444444444..5677******999 PP

  == domain 4  score: 14.5 bits;  conditional E-value: 5.1e-05
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeiear 28 
                                       C  C  C ++CP++aik k +k  e++
  gi|298675342|ref|YP_003727092.1| 213 CDYCMLCQDICPEDAIKVKGKKPCEPP 239
                                       *****************9966666655 PP

  == domain 5  score: 17.2 bits;  conditional E-value: 7.7e-06
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekeie 26 
                                       +C++Cg C evCP +a++ kk +e e
  gi|298675342|ref|YP_003727092.1| 251 KCTRCGWCREVCPYDAVEIKKPFEGE 276
                                       5***************8877444444 PP

  == domain 6  score: 10.4 bits;  conditional E-value: 0.00097
                           Fer4_16  49 kkqeai..tgCdiCqdvCPa 66 
                                       ++ +++  +gC++C +vCPa
  gi|298675342|ref|YP_003727092.1| 282 NNIKRCdpHGCQACFNVCPA 301
                                       33455566***********7 PP

  == domain 7  score: 20.2 bits;  conditional E-value: 8.5e-07
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeieare 29 
                                       C+ Cg+C ++CP+n+++ k ++++   +
  gi|298675342|ref|YP_003727092.1| 319 CIYCGACENACPENVMSVK-RTQVHHTK 345
                                       *****************99.44544444 PP

  == domain 8  score: -1.8 bits;  conditional E-value: 6.2
                           Fer4_16  37 ekkdlaedeekck 49 
                                        ++++++++ +++
  gi|298675342|ref|YP_003727092.1| 418 VRRKWEKESSEET 430
                                       3333333322222 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   1.4   8.9e-08   8.9e-05       5      22 .]      44      61 ..      40      61 .. 0.92
   2 !   11.0   2.7   0.00035      0.35       1      21 [.      79      99 ..      79     100 .. 0.90
   3 ?    5.3   2.0     0.023        23       8      22 .]     128     142 ..     122     142 .. 0.78
   4 !   16.8   1.4   5.2e-06    0.0052       3      20 ..     168     185 ..     166     187 .. 0.93
   5 !   12.7   1.2   0.00011      0.11       4      22 .]     207     225 ..     204     225 .. 0.91
   6 !   22.5   2.5   7.9e-08   7.9e-05       3      22 .]     245     264 ..     243     264 .. 0.93
   7 ?    5.9   3.6     0.015        15      12      22 .]     291     301 ..     282     301 .. 0.84
   8 !   16.4   2.2   6.8e-06    0.0068       3      22 .]     312     331 ..     310     331 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 8.9e-08
                            Fer4_2  5 vdtdrCigCgaCvsaCPa 22
                                      +d  rC+gCg Cv+ CP+
  gi|298675342|ref|YP_003727092.1| 44 YDYKRCTGCGLCVKICPT 61
                                      7899*************7 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00035
                            Fer4_2  1 apvvvdtdrCigCgaCvsaCP 21
                                      +pv  d ++C+ Cg C + CP
  gi|298675342|ref|YP_003727092.1| 79 PPVTLDIEKCTFCGMCAKFCP 99
                                      5788999************** PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.023
                            Fer4_2   8 drCigCgaCvsaCPa 22 
                                       ++C+ C  C s+CP+
  gi|298675342|ref|YP_003727092.1| 128 NNCLPCLLCESSCPE 142
                                       4588899999****5 PP

  == domain 4  score: 16.8 bits;  conditional E-value: 5.2e-06
                            Fer4_2   3 vvvdtdrCigCgaCvsaC 20 
                                       +++dt++C+ Cg C + C
  gi|298675342|ref|YP_003727092.1| 168 IEIDTEKCNLCGLCSHFC 185
                                       789*************99 PP

  == domain 5  score: 12.7 bits;  conditional E-value: 0.00011
                            Fer4_2   4 vvdtdrCigCgaCvsaCPa 22 
                                        vd+d C  C  C++ CP+
  gi|298675342|ref|YP_003727092.1| 207 MVDEDECDYCMLCQDICPE 225
                                       589***************5 PP

  == domain 6  score: 22.5 bits;  conditional E-value: 7.9e-08
                            Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                       v++d+d+C++Cg C+ +CP+
  gi|298675342|ref|YP_003727092.1| 245 VHIDEDKCTRCGWCREVCPY 264
                                       89*****************5 PP

  == domain 7  score: 5.9 bits;  conditional E-value: 0.015
                            Fer4_2  12 gCgaCvsaCPa 22 
                                       gC aC ++CPa
  gi|298675342|ref|YP_003727092.1| 291 GCQACFNVCPA 301
                                       7*********8 PP

  == domain 8  score: 16.4 bits;  conditional E-value: 6.8e-06
                            Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                       +++ +d Ci CgaC +aCP+
  gi|298675342|ref|YP_003727092.1| 312 IAIKEDYCIYCGACENACPE 331
                                       6788999************5 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   5.6   1.1e-09   1.1e-06       3      64 ..      47     101 ..      45     102 .. 0.85
   2 ?    5.4   2.7     0.025        25      49      63 ..     128     142 ..     113     145 .. 0.71
   3 !   10.9  10.0    0.0005      0.49       3      63 ..     128     187 ..     126     189 .. 0.62
   4 !   15.3   9.2     2e-05      0.02       2      64 ..     172     226 ..     171     227 .. 0.82
   5 !   14.1  14.2   4.8e-05     0.048       4      63 ..     212     264 ..     209     267 .. 0.85
   6 !    9.6  12.8    0.0012       1.2       3      64 ..     250     302 ..     248     303 .. 0.72
   7 !   21.6   0.3   2.3e-07   0.00022       4      38 ..     318     355 ..     316     390 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 1.1e-09
                            Fer4_8   3 ekCieCgaCqsaCpvlrrtk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                       ++C++Cg+C + Cp+   +   ++  a g+ a   ++ +        ++Ct cg+C++ Cpv+
  gi|298675342|ref|YP_003727092.1|  47 KRCTGCGLCVKICPTQALELgPMHEIATGMDAP-PVTLDI-------EKCTFCGMCAKFCPVN 101
                                       79************8887776888888888777.777776.......9*************97 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.025
                            Fer4_8  49 wsCttcgaCtevCpv 63 
                                       ++C+ c  C++ Cp+
  gi|298675342|ref|YP_003727092.1| 128 NNCLPCLLCESSCPE 142
                                       456666666666655 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.0005
                            Fer4_8   3 ekCieCgaCqsaCp......vlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63 
                                       ++C  C +C+s+Cp       l+  kk+  ++ +e+ae +        e   ++C+ cg C+  C  
  gi|298675342|ref|YP_003727092.1| 128 NNCLPCLLCESSCPedaievKLNIPKKEDITPFDENAEGEI-------EIDTEKCNLCGLCSHFCDA 187
                                       68***********9664432222222222333333232122.......44579************86 PP

  == domain 4  score: 15.3 bits;  conditional E-value: 2e-05
                            Fer4_8   2 lekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                        ekC+ Cg+C + C ++    k++  +     e +   ++       ++C  c+ C++ Cp++
  gi|298675342|ref|YP_003727092.1| 172 TEKCNLCGLCSHFCDAFIMLEKEPSPTDPSPFE-QLMVDE-------DECDYCMLCQDICPED 226
                                       589***********9999998887777777777.444455.......68************85 PP

  == domain 5  score: 14.1 bits;  conditional E-value: 4.8e-05
                            Fer4_8   4 kCieCgaCqsaCp..vlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63 
                                       +C  C++Cq+ Cp  +++ ++k + +++    e v+ + +       ++Ct cg C+evCp 
  gi|298675342|ref|YP_003727092.1| 212 ECDYCMLCQDICPedAIKVKGKKPCEPPAIEGE-VHID-E-------DKCTRCGWCREVCPY 264
                                       7999********999999999999999999666.5444.4.......59************7 PP

  == domain 6  score: 9.6 bits;  conditional E-value: 0.0012
                            Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsC..ttcgaCtevCpvg 64 
                                       +kC++Cg C++ Cp    + k +++ +   +e      +      +++C  ++c+aC +vCp +
  gi|298675342|ref|YP_003727092.1| 250 DKCTRCGWCREVCPYDAVEIKKPFEGEITLKE-----NN------IKRCdpHGCQACFNVCPAH 302
                                       69************544443444444444333.....33......7889889**********98 PP

  == domain 7  score: 21.6 bits;  conditional E-value: 2.3e-07
                            Fer4_8   4 kCieCgaCqsaCp....vlrrtkkhlldargeaaedvqe 38 
                                       +Ci CgaC++aCp    +++rt+ h+ + ++   +  q+
  gi|298675342|ref|YP_003727092.1| 318 YCIYCGACENACPenvmSVKRTQVHHTKIPDAPWA-SQW 355
                                       7***********99988888888788777777666.333 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   3.6   6.7e-07   0.00067       2      17 .]      47      62 ..      46      62 .. 0.92
   2 !   10.7   2.5   0.00063      0.63       2      17 .]      86     101 ..      85     104 .. 0.92
   3 !    7.2   1.6    0.0082       8.1       2      16 ..     128     142 ..     127     148 .. 0.90
   4 ?    4.3   3.2     0.071        71       2      14 ..     173     185 ..     172     186 .. 0.92
   5 !    7.4   2.2    0.0069       6.9       2      16 ..     211     225 ..     210     230 .. 0.87
   6 !    9.6   4.6    0.0014       1.4       2      16 ..     250     264 ..     249     265 .. 0.92
   7 !    8.0   1.6    0.0045       4.5       2      15 ..     285     300 ..     284     306 .. 0.85
   8 !   14.8   2.1   3.1e-05     0.031       2      16 ..     317     331 ..     316     340 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 6.7e-07
                            Fer4_4  2 erCigCgsCvaaCPqg 17
                                      +rC+gCg Cv +CP++
  gi|298675342|ref|YP_003727092.1| 47 KRCTGCGLCVKICPTQ 62
                                      8*************86 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00063
                            Fer4_4   2 erCigCgsCvaaCPqg 17 
                                       e+C+ Cg C  +CP++
  gi|298675342|ref|YP_003727092.1|  86 EKCTFCGMCAKFCPVN 101
                                       89************75 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0082
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       ++C+ C  C+++CP 
  gi|298675342|ref|YP_003727092.1| 128 NNCLPCLLCESSCPE 142
                                       68999*********5 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.071
                            Fer4_4   2 erCigCgsCvaaC 14 
                                       e+C+ Cg C  +C
  gi|298675342|ref|YP_003727092.1| 173 EKCNLCGLCSHFC 185
                                       89*******9998 PP

  == domain 5  score: 7.4 bits;  conditional E-value: 0.0069
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       + C  C+ C ++CP 
  gi|298675342|ref|YP_003727092.1| 211 DECDYCMLCQDICPE 225
                                       56888*********5 PP

  == domain 6  score: 9.6 bits;  conditional E-value: 0.0014
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       ++C++Cg C+ +CP+
  gi|298675342|ref|YP_003727092.1| 250 DKCTRCGWCREVCPY 264
                                       89************8 PP

  == domain 7  score: 8.0 bits;  conditional E-value: 0.0045
                            Fer4_4   2 erC..igCgsCvaaCP 15 
                                       +rC   gC +C ++CP
  gi|298675342|ref|YP_003727092.1| 285 KRCdpHGCQACFNVCP 300
                                       688445********** PP

  == domain 8  score: 14.8 bits;  conditional E-value: 3.1e-05
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       + Ci Cg+C++aCP 
  gi|298675342|ref|YP_003727092.1| 317 DYCIYCGACENACPE 331
                                       78************5 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   5.1   9.4e-06    0.0094       1      15 []      49      63 ..      49      63 .. 0.93
   2 !   11.1   5.5   0.00065      0.64       1      15 []      88     102 ..      88     102 .. 0.98
   3 ?    5.9   2.6     0.029        29       4      15 .]     133     144 ..     128     144 .. 0.82
   4 ?    2.8   4.8      0.28   2.8e+02       1      11 [.     175     185 ..     175     186 .. 0.95
   5 !   11.7   2.1    0.0004       0.4       1      15 []     213     227 ..     213     227 .. 0.96
   6 !   14.6   3.0   4.7e-05     0.047       1      15 []     252     266 ..     252     266 .. 0.97
   7 !    8.5   5.9    0.0042       4.2       1      12 [.     287     300 ..     287     302 .. 0.82
   8 !   12.9   4.6   0.00017      0.17       1      14 [.     319     332 ..     319     333 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 9.4e-06
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      CtgCg+Cv+ CP+ A
  gi|298675342|ref|YP_003727092.1| 49 CTGCGLCVKICPTQA 63
                                      ************866 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00065
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       Ct Cg C + CPv+A
  gi|298675342|ref|YP_003727092.1|  88 CTFCGMCAKFCPVNA 102
                                       *************99 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.029
                            Fer4_3   4 CgaCvevCPvgA 15 
                                       C +C+ +CP++A
  gi|298675342|ref|YP_003727092.1| 133 CLLCESSCPEDA 144
                                       779******998 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.28
                            Fer4_3   1 CtgCgaCvevC 11 
                                       C+ Cg+C   C
  gi|298675342|ref|YP_003727092.1| 175 CNLCGLCSHFC 185
                                       *******9999 PP

  == domain 5  score: 11.7 bits;  conditional E-value: 0.0004
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+ C++C + CP++A
  gi|298675342|ref|YP_003727092.1| 213 CDYCMLCQDICPEDA 227
                                       9***********998 PP

  == domain 6  score: 14.6 bits;  conditional E-value: 4.7e-05
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       Ct Cg C evCP++A
  gi|298675342|ref|YP_003727092.1| 252 CTRCGWCREVCPYDA 266
                                       *************98 PP

  == domain 7  score: 8.5 bits;  conditional E-value: 0.0042
                            Fer4_3   1 Ct..gCgaCvevCP 12 
                                       C+  gC+aC++vCP
  gi|298675342|ref|YP_003727092.1| 287 CDphGCQACFNVCP 300
                                       55559********* PP

  == domain 8  score: 12.9 bits;  conditional E-value: 0.00017
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       C+ CgaC+++CP++
  gi|298675342|ref|YP_003727092.1| 319 CIYCGACENACPEN 332
                                       9***********87 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   1.4   3.1e-05     0.031      37      58 ..      40      61 ..       8      64 .. 0.72
   2 !   16.2  11.0   1.1e-05     0.011       1      58 [.      48     100 ..      48     102 .. 0.81
   3 !   13.8  11.1   6.7e-05     0.066       1      59 [.      87     143 ..      87     144 .. 0.71
   4 !    7.0   2.2    0.0084       8.4      42      57 ..     171     186 ..     154     190 .. 0.77
   5 ?    1.3  12.8       0.5     5e+02       1      59 [.     174     226 ..     174     228 .. 0.74
   6 ?    5.0  14.7     0.037        37       1      59 [.     212     265 ..     212     267 .. 0.72
   7 !    8.1  11.8    0.0038       3.7       1      60 [.     251     303 ..     251     304 .. 0.76
   8 !   11.8   2.9   0.00026      0.26      44      60 ..     317     333 ..     304     334 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.1e-05
                           Fer4_17 37 aekeekaslCieCgeCerkCPq 58
                                       e +   ++C++Cg+C++ CP 
  gi|298675342|ref|YP_003727092.1| 40 KELDYDYKRCTGCGLCVKICPT 61
                                      3334688999999999999996 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.1e-05
                           Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPq 58 
                                       rC++Cg C++ Cp+ +      ++++  + +           +++C+ Cg+C++ CP 
  gi|298675342|ref|YP_003727092.1|  48 RCTGCGLCVKICPTQALELGPMHEIATGMDAPP-----VTLDIEKCTFCGMCAKFCPV 100
                                       7****************9996666666644432.....23589**************6 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 6.7e-05
                           Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaeke..ekaslCieCgeCerkCPqg 59 
                                       +C+ Cg+C++ Cp ++   +    +  ++ +++   + ++  +  ++C+ C +Ce++CP++
  gi|298675342|ref|YP_003727092.1|  87 KCTFCGMCAKFCPVNAFKME----ISGEVPSEDSYPEFDSyvKINNNCLPCLLCESSCPED 143
                                       6*************998554....4444444322222222236789*************86 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.0084
                           Fer4_17  42 kaslCieCgeCerkCP 57 
                                         ++C+ Cg+C++ C 
  gi|298675342|ref|YP_003727092.1| 171 DTEKCNLCGLCSHFCD 186
                                       6789999999999995 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.5
                           Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqg 59 
                                       +C+ Cg C   C  ++  ++ep  +      + +e+   +   ++C  C +C+  CP++
  gi|298675342|ref|YP_003727092.1| 174 KCNLCGLCSHFCDAFIMLEKEPS-PTDP---SPFEQL--MVDEDECDYCMLCQDICPED 226
                                       6**************99888776.3333...223332..33347999999999999986 PP

  == domain 6  score: 5.0 bits;  conditional E-value: 0.037
                           Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqg 59 
                                       +C  C  C + Cp  ++ + + kk+ +  +++  +e+      ++C+ Cg C+++CP++
  gi|298675342|ref|YP_003727092.1| 212 ECDYCMLCQDICPEDAI-KVKGKKPCEPPAIE--GEV--HIDEDKCTRCGWCREVCPYD 265
                                       5999999******8766.44466677664442..222..234589************97 PP

  == domain 7  score: 8.1 bits;  conditional E-value: 0.0038
                           Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslC..ieCgeCerkCPqgl 60 
                                       +C++Cg C+++Cp+ +   +   k+ +       e + ke+++++C  ++C+ C  +CP++l
  gi|298675342|ref|YP_003727092.1| 251 KCTRCGWCREVCPYDAVEIK---KPFEG------EITLKENNIKRCdpHGCQACFNVCPAHL 303
                                       6************9887444...44443......2233456889997789*********998 PP

  == domain 8  score: 11.8 bits;  conditional E-value: 0.00026
                           Fer4_17  44 slCieCgeCerkCPqgl 60 
                                       + Ci Cg Ce +CP+++
  gi|298675342|ref|YP_003727092.1| 317 DYCIYCGACENACPENV 333
                                       67************986 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.8   6.2e-05     0.061       3      20 ..      44      61 ..      43      67 .. 0.90
   2 !   11.7   0.7   0.00034      0.34       1      19 [.      81      99 ..      81     111 .. 0.84
   3 ?    2.8   0.2       0.2   1.9e+02      57      66 .]     138     147 ..     135     147 .. 0.89
   4 !   13.0   0.4   0.00013      0.13       1      26 [.     168     193 ..     168     198 .. 0.92
   5 !    8.0   2.9    0.0049       4.8       3      20 ..     208     225 ..     206     231 .. 0.92
   6 !   10.9   1.1   0.00061      0.61       1      19 [.     245     263 ..     245     276 .. 0.89
   7 ?   -1.2   0.5       3.5   3.5e+03      10      19 ..     291     300 ..     284     308 .. 0.77
   8 !    7.9   1.2    0.0052       5.2       2      25 ..     313     336 ..     312     403 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.2e-05
                           Fer4_15  3 vDrdaCigcglCvaeape 20
                                      +D ++C+gcglCv+ +p+
  gi|298675342|ref|YP_003727092.1| 44 YDYKRCTGCGLCVKICPT 61
                                      5999************96 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00034
                           Fer4_15  1 VvvDrdaCigcglCvaeap 19
                                      V++D ++C+ cg+C++ +p
  gi|298675342|ref|YP_003727092.1| 81 VTLDIEKCTFCGMCAKFCP 99
                                      89**************997 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.2
                           Fer4_15  57 raCPvdAIrv 66 
                                       ++CP+dAI+v
  gi|298675342|ref|YP_003727092.1| 138 SSCPEDAIEV 147
                                       58******97 PP

  == domain 4  score: 13.0 bits;  conditional E-value: 0.00013
                           Fer4_15   1 VvvDrdaCigcglCvaeapevfelde 26 
                                       +++D ++C  cglC   ++ ++ l++
  gi|298675342|ref|YP_003727092.1| 168 IEIDTEKCNLCGLCSHFCDAFIMLEK 193
                                       79*****************9999886 PP

  == domain 5  score: 8.0 bits;  conditional E-value: 0.0049
                           Fer4_15   3 vDrdaCigcglCvaeape 20 
                                       vD+d+C+ c lC + +pe
  gi|298675342|ref|YP_003727092.1| 208 VDEDECDYCMLCQDICPE 225
                                       9***************96 PP

  == domain 6  score: 10.9 bits;  conditional E-value: 0.00061
                           Fer4_15   1 VvvDrdaCigcglCvaeap 19 
                                       V++D+d+C+ cg C +++p
  gi|298675342|ref|YP_003727092.1| 245 VHIDEDKCTRCGWCREVCP 263
                                       89***************97 PP

  == domain 7  score: -1.2 bits;  conditional E-value: 3.5
                           Fer4_15  10 gcglCvaeap 19 
                                       gc +C  ++p
  gi|298675342|ref|YP_003727092.1| 291 GCQACFNVCP 300
                                       7888988887 PP

  == domain 8  score: 7.9 bits;  conditional E-value: 0.0052
                           Fer4_15   2 vvDrdaCigcglCvaeapevfeld 25 
                                        + +d Ci cg+C  ++pe +   
  gi|298675342|ref|YP_003727092.1| 313 AIKEDYCIYCGACENACPENVMSV 336
                                       677899************987655 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   1.6   0.00032      0.32       3      18 ..      46      61 ..      45      62 .. 0.89
   2 !    9.7   0.9    0.0012       1.2       2      22 ..      84     105 ..      83     111 .. 0.81
   3 ?    3.2   2.2      0.13   1.3e+02       2      18 ..     127     142 ..     126     147 .. 0.86
   4 ?    6.2   0.9     0.016        16       1      17 [.     170     186 ..     170     194 .. 0.90
   5 !    8.2   5.4    0.0037       3.7       1      18 [.     208     225 ..     208     226 .. 0.97
   6 !   11.6   3.4    0.0003       0.3       1      17 [.     247     263 ..     247     265 .. 0.96
   7 !    9.6   0.4    0.0014       1.4       8      33 ..     291     316 ..     286     318 .. 0.91
   8 !    9.2   3.9    0.0018       1.8       3      18 ..     316     331 ..     314     360 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00032
                           Fer4_13  3 rdtCiacgaCvelaPd 18
                                       ++C++cg+Cv+++P 
  gi|298675342|ref|YP_003727092.1| 46 YKRCTGCGLCVKICPT 61
                                      579************5 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0012
                           Fer4_13   2 DrdtCiacgaCvelaP.dvFee 22 
                                       D ++C+ cg C++++P + F++
  gi|298675342|ref|YP_003727092.1|  84 DIEKCTFCGMCAKFCPvNAFKM 105
                                       6689************445666 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.13
                           Fer4_13   2 DrdtCiacgaCvelaPd 18 
                                       + ++C  c +C + +P+
  gi|298675342|ref|YP_003727092.1| 127 N-NNCLPCLLCESSCPE 142
                                       5.899999999999997 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.016
                           Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                       +D ++C  cg+C +++ 
  gi|298675342|ref|YP_003727092.1| 170 IDTEKCNLCGLCSHFCD 186
                                       899************95 PP

  == domain 5  score: 8.2 bits;  conditional E-value: 0.0037
                           Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                       VD+d+C  c++C +++P+
  gi|298675342|ref|YP_003727092.1| 208 VDEDECDYCMLCQDICPE 225
                                       9****************7 PP

  == domain 6  score: 11.6 bits;  conditional E-value: 0.0003
                           Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                       +D+d+C+ cg C+e++P
  gi|298675342|ref|YP_003727092.1| 247 IDEDKCTRCGWCREVCP 263
                                       89**************9 PP

  == domain 7  score: 9.6 bits;  conditional E-value: 0.0014
                           Fer4_13   8 acgaCvelaPdvFeeddeggasvvae 33 
                                       +c+aC +++P +  + +e++  +++e
  gi|298675342|ref|YP_003727092.1| 291 GCQACFNVCPAHLWYVPEDKNIAIKE 316
                                       7*****************99988876 PP

  == domain 8  score: 9.2 bits;  conditional E-value: 0.0018
                           Fer4_13   3 rdtCiacgaCvelaPd 18 
                                       +d Ci cgaC +++P+
  gi|298675342|ref|YP_003727092.1| 316 EDYCIYCGACENACPE 331
                                       588************8 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.4   2.1e-05     0.021      21      74 ..      12      62 ..       9      66 .. 0.70
   2 ?    4.4   1.5     0.041        41      59      74 ..      86     101 ..      77     111 .. 0.89
   3 ?    1.7   1.0      0.29   2.8e+02      56      73 ..     125     142 ..     105     151 .. 0.78
   4 ?    1.1   0.6      0.43   4.3e+02      55      75 ..     169     189 ..     150     195 .. 0.70
   5 ?    1.8   2.4      0.26   2.6e+02      57      74 ..     209     226 ..     201     235 .. 0.79
   6 ?    7.3   3.0    0.0051       5.1      57      81 ..     248     273 ..     228     288 .. 0.79
   7 ?   10.9   6.3    0.0004       0.4      58     100 ..     286     335 ..     276     345 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.1e-05
                           Fer4_18 21 deetllvvyda.krGekiagrkkekkalkekeerkekgagdcidcescvkvcPtg 74
                                      d++t++v+ d+ ++G + + ++ ++k+ ke +     +   c+ c+ cvk+cPt+
  gi|298675342|ref|YP_003727092.1| 12 DKNTIKVTKDMdVQGSHFIYKQFTEKSRKELDY----DYKRCTGCGLCVKICPTQ 62
                                      677777777752456666665555555555544....5778************96 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.041
                           Fer4_18  59 gdcidcescvkvcPtg 74 
                                        +c+ c++c k cP++
  gi|298675342|ref|YP_003727092.1|  86 EKCTFCGMCAKFCPVN 101
                                       68************85 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.29
                           Fer4_18  56 kgagdcidcescvkvcPt 73 
                                       k +++c+ c  c + cP 
  gi|298675342|ref|YP_003727092.1| 125 KINNNCLPCLLCESSCPE 142
                                       556788888888888885 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.43
                           Fer4_18  55 ekgagdcidcescvkvcPtgi 75 
                                       e ++ +c  c+ c + c   i
  gi|298675342|ref|YP_003727092.1| 169 EIDTEKCNLCGLCSHFCDAFI 189
                                       455677888888888887655 PP

  == domain 5  score: 1.8 bits;  conditional E-value: 0.26
                           Fer4_18  57 gagdcidcescvkvcPtg 74 
                                       ++ +c  c  c ++cP +
  gi|298675342|ref|YP_003727092.1| 209 DEDECDYCMLCQDICPED 226
                                       567999999999999964 PP

  == domain 6  score: 7.3 bits;  conditional E-value: 0.0051
                           Fer4_18  57 gagdcidcescvkvcPtg.idirkGl 81 
                                       ++ +c+ c+ c +vcP + ++i+k +
  gi|298675342|ref|YP_003727092.1| 248 DEDKCTRCGWCREVCPYDaVEIKKPF 273
                                       5678************7438888866 PP

  == domain 7  score: 10.9 bits;  conditional E-value: 0.0004
                           Fer4_18  58 agdcidcescvkvcPtgi...dirkGlqle...ciscllcidac.dkvme 100
                                         d   c++c +vcP ++      k + ++   ci c+ c +ac ++vm 
  gi|298675342|ref|YP_003727092.1| 286 RCDPHGCQACFNVCPAHLwyvPEDKNIAIKedyCIYCGACENACpENVMS 335
                                       456678**********97322223444443456***********445664 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.5   2.1e-05     0.021      65      95 ..      29      62 ..       8      63 .. 0.66
   2 ?    7.6   0.3    0.0071         7      77      95 ..      83     101 ..      69     102 .. 0.80
   3 ?    1.4   0.8      0.61   6.1e+02       1      13 [.     129     141 ..     123     146 .. 0.76
   4 ?    3.8   0.2      0.11   1.1e+02      77      94 ..     170     187 ..     159     189 .. 0.78
   5 ?    1.0   0.2      0.81   8.1e+02      78      94 ..     209     225 ..     202     227 .. 0.70
   6 ?    6.8   1.0     0.012        12      78      94 ..     248     264 ..     241     266 .. 0.75
   7 ?    1.0   1.8      0.81   8.1e+02      83      94 ..     290     301 ..     276     303 .. 0.65
   8 ?    1.1   1.5      0.73   7.3e+02       4      15 ..     291     302 ..     286     316 .. 0.71
   9 ?    7.6   1.7    0.0069       6.9      78      95 ..     315     332 ..     306     333 .. 0.77
  10 ?   -2.1   0.2       7.2   7.1e+03      53      72 ..     421     440 ..     396     445 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.1e-05
                           Fer4_22 65 rllhklsefkekf...gesgCvGCgRCieacpvk 95
                                       ++++++e  +k    + + C+GCg C++ cp++
  gi|298675342|ref|YP_003727092.1| 29 FIYKQFTEKSRKEldyDYKRCTGCGLCVKICPTQ 62
                                      4444444333322233999************986 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0071
                           Fer4_22  77 fgesgCvGCgRCieacpvk 95 
                                        + ++C+ Cg C + cpv+
  gi|298675342|ref|YP_003727092.1|  83 LDIEKCTFCGMCAKFCPVN 101
                                       5678899999999999875 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.61
                           Fer4_22   1 rClsCgaCtlvCp 13 
                                       +Cl C  C   Cp
  gi|298675342|ref|YP_003727092.1| 129 NCLPCLLCESSCP 141
                                       4777777777776 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.11
                           Fer4_22  77 fgesgCvGCgRCieacpv 94 
                                       +++++C  Cg C++ c +
  gi|298675342|ref|YP_003727092.1| 170 IDTEKCNLCGLCSHFCDA 187
                                       578889999999999875 PP

  == domain 5  score: 1.0 bits;  conditional E-value: 0.81
                           Fer4_22  78 gesgCvGCgRCieacpv 94 
                                       +e  C  C  C++ cp+
  gi|298675342|ref|YP_003727092.1| 209 DEDECDYCMLCQDICPE 225
                                       56667777777777775 PP

  == domain 6  score: 6.8 bits;  conditional E-value: 0.012
                           Fer4_22  78 gesgCvGCgRCieacpv 94 
                                       +e +C+ Cg C e+cp 
  gi|298675342|ref|YP_003727092.1| 248 DEDKCTRCGWCREVCPY 264
                                       67778888888888875 PP

  == domain 7  score: 1.0 bits;  conditional E-value: 0.81
                           Fer4_22  83 vGCgRCieacpv 94 
                                        GC  C ++cp+
  gi|298675342|ref|YP_003727092.1| 290 HGCQACFNVCPA 301
                                       577777777776 PP

  == domain 8  score: 1.1 bits;  conditional E-value: 0.73
                           Fer4_22   4 sCgaCtlvCptC 15 
                                       +C+aC  vCp+ 
  gi|298675342|ref|YP_003727092.1| 291 GCQACFNVCPAH 302
                                       577777777764 PP

  == domain 9  score: 7.6 bits;  conditional E-value: 0.0069
                           Fer4_22  78 gesgCvGCgRCieacpvk 95 
                                       +e  C+ Cg C++acp++
  gi|298675342|ref|YP_003727092.1| 315 KEDYCIYCGACENACPEN 332
                                       667888999999999876 PP

  == domain 10  score: -2.1 bits;  conditional E-value: 7.2
                           Fer4_22  53 nvrkekkerlrqrllhklse 72 
                                       +  ke++e +r+ + +k+++
  gi|298675342|ref|YP_003727092.1| 421 KWEKESSEETRKEFREKFKN 440
                                       44444555555555555543 PP

>> Pox_A22  Poxvirus A22 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   7.9e-05     0.079      17      99 ..     333     419 ..     323     442 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.9e-05
                           Pox_A22  17 llevkdnkarikvldiekldwssdwerrvardils.....ynvdvvllEkqgrrs.knvkfiyfikgllyskktkvl 87 
                                       +++vk+++  ++  +i  ++w+s+we ++   i+s      +  +v +Ek + +  + v+f    ++ll   + ++ 
  gi|298675342|ref|YP_003727092.1| 333 VMSVKRTQ--VHHTKIPDAPWASQWEDAIESMITSkrkhpDTSRTVEVEKEPSKEhEEVEFPEIDESLLKAARERIN 407
                                       67777777..9999********************98876556678999*99876516789999999*********** PP

                           Pox_A22  88 vvkPvlkggsYr 99 
                                       ++kP+lk  + r
  gi|298675342|ref|YP_003727092.1| 408 STKPALKNINVR 419
                                       *****9865544 PP

>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       3.3   3.3e+03      48      80 ..     190     222 ..     187     232 .. 0.80
   2 ?   10.2   0.3   0.00062      0.62      45      99 ..     359     413 ..     352     437 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.3
                   HicB_lk_antitox  48 liedgeeipepssieellanpeyaggiwalvdv 80 
                                       ++e++ + + ps+ e+l+ +++  ++ ++  d+
  gi|298675342|ref|YP_003727092.1| 190 MLEKEPSPTDPSPFEQLMVDEDECDYCMLCQDI 222
                                       567777778999*****9999999988877776 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00062
                   HicB_lk_antitox  45 legliedgeeipepssieellanpeyaggiwalvdvdlskldgkaeriNitlper 99 
                                       +e++i++ ++ p +s   e+ ++p  +   + + ++d s l++  eriN t p+ 
  gi|298675342|ref|YP_003727092.1| 359 IESMITSKRKHPDTSRTVEVEKEPSKEHEEVEFPEIDESLLKAARERINSTKPAL 413
                                       89*************************************************9974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1108  (0.0617993); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.61u 0.22s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 3240.62
//
Query:       gi|298675343|ref|YP_003727093.1|  [L=634]
Description: aspartyl-tRNA(Asn) amidotransferase subunit B [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.7e-72  241.6   0.1    5.9e-71  239.0   0.1    1.9  2  GatB_N     GatB/GatE catalytic domain
    1.2e-22   80.4   1.2      1e-21   77.4   0.3    2.5  2  GatB_Yqey  GatB domain
    5.8e-17   61.7   0.0    3.2e-16   59.3   0.0    2.2  2  GAD        GAD domain
    9.5e-06   25.7   1.2    1.6e-05   25.0   0.2    2.0  2  YqeY       Yqey-like protein


Domain annotation for each model (and alignments):
>> GatB_N  GatB/GatE catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  239.0   0.1   1.3e-74   5.9e-71       2     272 ..      13     444 ..      12     445 .. 0.96
   2 ?   -0.1   0.0      0.11   4.9e+02      25      55 ..     489     519 ..     476     523 .. 0.84

  Alignments for each domain:
  == domain 1  score: 239.0 bits;  conditional E-value: 1.3e-74
                                       EEEEEEEEEB--SB-SSSSSBSS...SSCE...........STTSS--TTTTTS....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxx...xxxx...........xxxxxxxxxxxxx....................... RF
                            GatB_N   2 viGlEiHaqlktksKlFssaste...eege...........epnsevsevdlal....................... 41 
                                       ++GlEiH+ql+tk+KlF++++t+   +  e            + se++e+dla+                       
  gi|298675343|ref|YP_003727093.1|  13 KCGLEIHQQLDTKEKLFCRCPTKlrdT--EesnleffryirPAASEMGETDLAAleqsklnrkyiykaydstclvey 87 
                                       89*******************885431..2356778888844889999999999*********************** PP

                                       ...TT..--.EEHHHHHHHHHHHHHTTEEE-SEE-EEEEE-TCTTCTTSEEEEESSS.SEEEEEEEE.TEEEEEEEE CS
                                       ...xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                            GatB_N  42 ...PGtlPv.lnkeavelaikaalalnceiaeeskfdRKnyfypdlpkgyQitqkeeplakeGslel.ekkvrieri 113
                                          P   P+ ++kea+++++++++ ln++  ++++++RK+++++++++g+Q+t+    la++G+le+ +  v++e++
  gi|298675343|ref|YP_003727093.1|  88 deeP---PNeIDKEALNTSLTITKLLNMQPVDQMHVMRKIVVDGSNTTGFQRTA---FLASGGYLETsKGYVGMESL 158
                                       9998...989********************************************...788******967789***** PP

                                       EEEE---EEEEEETTEEEEETTSTT-EEEEEEE-STB-SHHHHHHHHHHHHHHHHHHTSB--SGGGTTEEEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 114 hlEeDaaksvheekeeslvdlnRaGvpLiEivtepdlrspeearavveklrellralgvsdgnmeeGslRcDvNvSv 190
                                       +lEe++a+ +++++++++++l+R+G+pL+Ei t+pd+r+p++ar++++ +++llr++g++++++  G++R+DvN+S+
  gi|298675343|ref|YP_003727093.1| 159 CLEEESARIIEQNTDSTIYSLDRLGIPLVEIGTAPDIRTPQQARETAQLIGMLLRSTGKVKRGL--GTIRQDVNISI 233
                                       ************999*************************************************..*********** PP

                                       CTSETTSSS.--EEEEEE-SHHHHHHHHHHHHHHHHHHH...................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................................... RF
                            GatB_N 191 reeekgeeegtrvEiKnlnslksiekaieyeierqiell...................................... 229
                                       ++       g+r+EiK+++sl++ie+++e+e+erqi+l+                                      
  gi|298675343|ref|YP_003727093.1| 234 AK-------GARIEIKGVQSLEQIESIVENEVERQINLIkirdellqkgahinenmydvsevfadtqskiikkalkk 303
                                       *4.......59****************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                            GatB_N 230 ............................................................................. 229
                                                                                                                    
  gi|298675343|ref|YP_003727093.1| 304 gkviagvlpgfagyigkeiqpgrrlgtefsdraktsgvggifhtdelpnygitedeieslceyvnagdndavvlvsd 380
                                       ***************************************************************************** PP

                                       ........................-EEEEEETTTTEEEEECC----...-EEE-TTS--EE--HHHH CS
                                       ........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 230 ........................qeTrkfdedkgetvslRskeeaedYryfpepdlppleiseeli 272
                                                               +eTrk+ +d g+t+++R+ + a   r++pe+d+p++eis+e++
  gi|298675343|ref|YP_003727093.1| 381 nekrsfsamesviqrakealegvpEETRKALPD-GNTSYMRPLPGA--ARMYPETDVPQVEISREYF 444
                                       *********************************.**********77..5**************9987 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.11
                                       SSCESTTSS--TTTTTSTT..--EEHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N  25 eegeepnsevsevdlalPGtlPvlnkeavel 55 
                                       ++++++n + + v   l Gt+P l +e ve+
  gi|298675343|ref|YP_003727093.1| 489 TFKDSSNINATMVARTLTGTVPELRREGVEV 519
                                       47788999*****************999875 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.085   3.8e+02      91     121 ..     357     387 ..     351     402 .. 0.84
   2 !   77.4   0.3   2.2e-25     1e-21       3     148 .]     483     627 ..     481     627 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.085
                                       SSXHHHHHHHHHHTXHHHHHHHTTXXTTSTH CS
                         GatB_Yqey  91 eeeleklveeviaenpkavedyksgkekalk 121
                                       e+e+e+l+e v a  ++av  + + +++++ 
  gi|298675343|ref|YP_003727093.1| 357 EDEIESLCEYVNAGDNDAVVLVSDNEKRSFS 387
                                       48************99999888888877765 PP

  == domain 2  score: 77.4 bits;  conditional E-value: 2.2e-25
                                       HHHHHHHSS.....HHHHHHHHHTCHHHHHHHHTXXTTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHH.TX CS
                         GatB_Yqey   3 feevvkegad....aklaanwllnellgelnkegleieelkltpeqlaellkliaegkIskkiakevleellee.gk 74 
                                       fe +++  +d    ++++++ +l+ ++ el++eg+e+++  +t+e++ +l++l++ gk +k+ ++e+l++l+++ + 
  gi|298675343|ref|YP_003727093.1| 483 FEDIIRTFKDssniNATMVARTLTGTVPELRREGVEVDS--ITDEHFFQLFELVEGGKTAKEGIEEILKKLADNpEL 557
                                       56666555554334566667777888889**********..9*********************************** PP

                                       XHHHHHHHCTXXXXXXSSXHHHHHHHHHHTXHHHHHHHTTXXT.TSTHHHHHHHHHTTSSXSXHHHHHHHHHHHS CS
                         GatB_Yqey  75 speeiieekgLkqisdeeeleklveeviaenpkavedyksgke.kalkflvGqvMkktkGkadpklvnellkekL 148
                                       s+e++ +e gL+ + d++e+ek+v+evi++     e++ + k   a++ l+G vM + +Gkad+k+v+ +lk+k+
  gi|298675343|ref|YP_003727093.1| 558 SAENAASELGLTGV-DTSEIEKFVDEVIDNR----EEFVQEKGlDAVGPLMGVVMGEFRGKADGKQVSSILKQKI 627
                                       **************.67**************....5555555559***************************996 PP

>> GAD  GAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.3   0.0   7.2e-20   3.2e-16       2      92 ..     298     386 ..     297     389 .. 0.90
   2 ?   -1.8   0.0      0.85   3.8e+03      21      40 ..     577     596 ..     567     600 .. 0.71

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 7.2e-20
                                       HHHHHSTEEEEEEEETTG-TTTSHHHHHHHHHHHHHTTHSHCEEEEESSGGEETTTCCC.S-HHHHHHHHHHCT--T CS
                               GAD   2 sealksggsvkalrvpggaaklsrkeideleefakelgakglawikvegegltgpiakf.lteeevkklleavgaee 77 
                                       ++alk+ g+v a ++pg +a++++kei++++++++e+++++++  +v+g ++t++++ + +te+e++ l e v+a +
  gi|298675343|ref|YP_003727093.1| 298 KKALKK-GKVIAGVLPG-FAGYIGKEIQPGRRLGTEFSDRAKTS-GVGGIFHTDELPNYgITEDEIESLCEYVNAGD 371
                                       556555.56666679**.8************************9.******************************** PP

                                       TEEEEEEEEEHHHHH CS
                               GAD  78 gDillfvAdkkktvn 92 
                                       +D++++v+d++k   
  gi|298675343|ref|YP_003727093.1| 372 NDAVVLVSDNEKRSF 386
                                       **********88755 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.85
                                       TTTSHHHHHHHHHHHHHTTH CS
                               GAD  21 aklsrkeideleefakelga 40 
                                       +k++ + id+ eef++e+g 
  gi|298675343|ref|YP_003727093.1| 577 EKFVDEVIDNREEFVQEKGL 596
                                       45666777777777777765 PP

>> YqeY  Yqey-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.1       2.8   1.2e+04      39      56 ..     286     303 ..     274     305 .. 0.68
   2 !   25.0   0.2   3.7e-09   1.6e-05      92     142 ..     572     626 ..     569     627 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.8
                                       SS--HHHHHHHHHHHHHH CS
                              YqeY  39 kelsdeevlkvlakevkq 56 
                                       +e+  +   k+++k++k+
  gi|298675343|ref|YP_003727093.1| 286 SEVFADTQSKIIKKALKK 303
                                       466667778888888887 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 3.7e-09
                                       -HHHHHHHHHHHHHHT....T--BGGGHHHHHHHHHHHHTTTS-HHHHHHHHHHH CS
                              YqeY  92 seeeiealvkeaiaev....gaesmkdmGkvmkalkpkvkGkaDgkkvsalvkek 142
                                       + +eie++v+e+i++     ++++  ++G +m++++ +++GkaDgk+vs+++k+k
  gi|298675343|ref|YP_003727093.1| 572 DTSEIEKFVDEVIDNReefvQEKGLDAVGPLMGVVMGEFRGKADGKQVSSILKQK 626
                                       578999******98753333888******************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (634 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 4303.64
//
Query:       gi|298675344|ref|YP_003727094.1|  [L=365]
Description: carbamoyl-phosphate synthase small subunit [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.2e-47  158.2   0.1    1.4e-46  157.5   0.1    1.3  1  CPSase_sm_chain  Carbamoyl-phosphate synthase small chain, CP
    1.1e-40  139.4   0.0    1.7e-40  138.9   0.0    1.2  1  GATase           Glutamine amidotransferase class-I
    4.6e-07   29.8   0.5    5.9e-05   22.9   0.5    2.3  1  Peptidase_C26    Peptidase C26


Domain annotation for each model (and alignments):
>> CPSase_sm_chain  Carbamoyl-phosphate synthase small chain, CPSase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.5   0.1   2.3e-50   1.4e-46       2     127 ..       3     129 ..       2     130 .. 0.98

  Alignments for each domain:
  == domain 1  score: 157.5 bits;  conditional E-value: 2.3e-50
                   CPSase_sm_chain   2 avLvLedGtvfeGksfg.akeavGEvvfnTgmtGYqeiltDpsYagqilvltypliGnyGvneedvesekikvaglv 77 
                                       avL LedGt+++G+++g +++++GE+vf+T  tGY+e++tDpsY+gqil++typliGnyGv+ e+++s++i++ g+v
  gi|298675344|ref|YP_003727094.1|   3 AVLGLEDGTIVKGTGIGsEGAVSGELVFTTLYTGYEEAMTDPSYKGQILMFTYPLIGNYGVSGENFQSDNIQTDGIV 79 
                                       7899*************88999******************************************************* PP

                   CPSase_sm_chain  78 vrelseepsnwraeesLsewlkeekipgisgvDTRaLtkklrekgamkgv 127
                                       vre++++p +++++++ +++l++e+ipgi+gvDTR+Lt k re+gam+++
  gi|298675344|ref|YP_003727094.1|  80 VREACSSPYHYKSTRNYNQLLQDEGIPGIAGVDTRMLTIKTRETGAMRAA 129
                                       ***********************************************997 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.9   0.0   2.8e-44   1.7e-40       2     184 ..     182     353 ..     181     359 .. 0.96

  Alignments for each domain:
  == domain 1  score: 138.9 bits;  conditional E-value: 2.8e-44
                                       EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.TTTHHHHHHHHCTSTS-EEEE CS
                            GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.vegkieaikearenkiPiLGI 77 
                                       +iD +  +++n++ +l+++g++v+vvp ++s + i  ++ +pd i++ +Gpg+p  ++g+i+a++e+++ k+Pi+GI
  gi|298675344|ref|YP_003727094.1| 182 VIDLG--LKRNILSSLLSRGIDVTVVPANTSTSMI--EAYEPDFIFLTNGPGDPLqAKGAISAVNEFAG-KLPIIGI 253
                                       78999..**********************999999..489***************9*************.******* PP

                                       THHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEE CS
                            GATase  78 CLGmQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeel 154
                                       C+G+Q++ +++g++++k k ++h+g++++++d       ++++++i++++H+++v+ ++l  ++l vt  +++d+++
  gi|298675344|ref|YP_003727094.1| 254 CFGNQIISLALGAETYKLK-FGHRGANQPVKD------LETGKVYITSQNHGFAVDGQSLDTTDLSVTQINANDNTV 323
                                       *******************.************......8888***************999999************** PP

                                       EEEEEETTTEEEESSBTTSTTSTTHHHHHH CS
                            GATase 155 meiiekknpfvgvQFHPEststpegpellf 184
                                       +++ ++   +++vQ+HPE+ ++p ++e lf
  gi|298675344|ref|YP_003727094.1| 324 EGVAHEYLDIYSVQYHPEANPGPWDTEKLF 353
                                       **************************9988 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.5   9.9e-09   5.9e-05     101     216 .]     243     341 ..     238     341 .. 0.68

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 9.9e-09
                     Peptidase_C26 101 alergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavk.vekgsllaellgseeievnslHhq 176
                                       + + ++Pi+giC G q++  alG ++y+  +       hr ++     + vk +e+g+++    +++ ++v     q
  gi|298675344|ref|YP_003727094.1| 243 EFAGKLPIIGICFGNQIISLALGAETYKL-K-----FGHRGAN-----QPVKdLETGKVYI-TSQNHGFAV---DGQ 304
                                       566799*****************999964.4.....2454443.....3443033333322.222233443...356 PP

                     Peptidase_C26 177 aikelaeelrveAvae.DgviEaieseeakafvlgvQwHPE 216
                                       ++++  ++l v+ + + D+++E + +e  +  +++vQ+HPE
  gi|298675344|ref|YP_003727094.1| 305 SLDT--TDLSVTQINAnDNTVEGVAHEYLD--IYSVQYHPE 341
                                       6665..56788877666***********88..********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2766.79
//
Query:       gi|298675345|ref|YP_003727095.1|  [L=1076]
Description: carbamoyl-phosphate synthase large subunit [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.6e-108  360.4   0.2    3.6e-70  235.8   0.0    2.3  2  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    5.6e-38  130.0   0.3    1.4e-37  128.7   0.3    1.8  1  CPSase_L_D3      Carbamoyl-phosphate synthetase large chain, 
    7.6e-23   80.5   0.7      9e-21   73.9   0.1    4.2  4  MGS              MGS-like domain
      2e-17   63.4   0.1    7.4e-08   32.2   0.0    2.4  2  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
      6e-17   61.7   0.1    2.8e-08   33.5   0.0    2.4  2  ATP-grasp        ATP-grasp domain
    2.3e-16   59.7   0.0    5.5e-08   32.6   0.0    2.8  2  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
    6.2e-15   55.6   1.8    8.4e-08   32.4   0.0    3.1  4  ATP-grasp_3      ATP-grasp domain
    6.7e-09   35.8   0.1    0.00054   19.8   0.0    2.6  2  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
     0.0017   17.9   0.0      0.052   13.0   0.0    2.7  3  ATP-grasp_5      ATP-grasp domain
  ------ inclusion threshold ------
        0.1   12.0   0.0       0.34   10.3   0.0    1.8  2  Epimerase        NAD dependent epimerase/dehydratase family


Domain annotation for each model (and alignments):
>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.8   0.0     2e-73   3.6e-70       1     210 [.     129     332 ..     129     333 .. 0.99
   2 !  122.7   0.0     8e-39   1.4e-35       1     209 [.     671     872 ..     671     874 .. 0.96

  Alignments for each domain:
  == domain 1  score: 235.8 bits;  conditional E-value: 2e-73
                                       SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaa 77 
                                       D+e +ke++ +i+++v +s+a   ++l+ea ++ +e+g P i+++a++lGG G+++a+++e+l e+v+++l+ ++  
  gi|298675345|ref|YP_003727095.1| 129 DRELFKEKMGDIGEKVPQSKAI--SSLKEAEEMIDELGLPLIVRPAYTLGGAGGGIAHTKEQLFEIVERGLRRSR-- 201
                                       9*******************99..**************************************************7.. PP

                                       HSTS-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCEC..TCCCCEEEES-SS--HHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2  78 fgnkqvlvekslkgpkeiEvevlrDakgnvitvcerenslql..rtqkvievAPsqtLtdeerqalreaavkvvrev 152
                                          +qvlve+s+ g+ke E+ev+rD++++++++c++en++++  +t+++i+v PsqtL+dee+q+lr++a++++r+ 
  gi|298675345|ref|YP_003727095.1| 202 --IHQVLVEESVLGWKEFEYEVMRDSNDTCVIICNMENFDPMgiHTGESIVVTPSQTLSDEEHQMLRSSAINIIRSF 276
                                       ..9************************************************************************** PP

                                       T-EEEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GCG CS
                       CPSase_L_D2 153 gvvgagtveflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLee 210
                                       g++g+++++f+++  +++y v+EvN+R+s++sala+kaTG++++ ++akia g++L+e
  gi|298675345|ref|YP_003727095.1| 277 GIEGGCNIQFAVK--DGDYRVVEVNPRVSRSSALASKATGYPIARVTAKIAIGMTLDE 332
                                       ************9..6****************************************97 PP

  == domain 2  score: 122.7 bits;  conditional E-value: 8e-39
                                       SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaa 77 
                                       D++++ +++k+++++  ++  a   ++ ea+++a eigyPv++++++ lGG+ m ++++eeel+  +++++  +k  
  gi|298675345|ref|YP_003727095.1| 671 DRDKFYALMKELGINQPDGRYA--LSQGEAINFATEIGYPVLVRPSYVLGGRAMEIVYDEEELKRYLRESVCVSK-- 743
                                       9*******************99..999***********************************************6.. PP

                                       HSTS-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCEC..TCCCCEEEES-SS--HHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2  78 fgnkqvlvekslkgpkeiEvevlrDakgnvitvcerenslql..rtqkvievAPsqtLtdeerqalreaavkvvrev 152
                                         ++ +l++ +l+g  ei+v+ + D + nv++ + +e + +   + +++  v P q Lt+e+ +++r  + k++ ++
  gi|298675345|ref|YP_003727095.1| 744 --DNPILIDDFLEGAVEIDVDAVCDGE-NVLIGAIMEHIEEAgvHSGDSACVIPPQSLTEETMEIVRDYTRKIALSL 817
                                       ..9**********************85.7777788999988888********************************* PP

                                       T-EEEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GC CS
                       CPSase_L_D2 153 gvvgagtveflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLe 209
                                       +v+g  +++ +    ++e yv+E N+R s+  +  +ka G++l+k+aa++ +g+kL+
  gi|298675345|ref|YP_003727095.1| 818 DVKGLINIQMAKR--DGEVYVLEANPRSSRTIPFVSKAVGIPLAKIAAQVIMGHKLK 872
                                       *********9876..7***************************************98 PP

>> CPSase_L_D3  Carbamoyl-phosphate synthetase large chain, oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.7   0.3     8e-41   1.4e-37       3     122 .]     418     538 ..     416     538 .. 0.96

  Alignments for each domain:
  == domain 1  score: 128.7 bits;  conditional E-value: 8e-41
                       CPSase_L_D3   3 lkeptdeRifaiaealrrglsveeiheltkidpwFLekleelvelekelkkkkk..eldeellreakklGfsDkqia 77 
                                       l++pt++R+f+i++alr+g++ve i++ t +  +FL+k++++v++ek+l+++ +  e++ + l + k+lG++D++ia
  gi|298675345|ref|YP_003727095.1| 418 LRTPTSNRLFVIFQALRNGFTVEAINQFTGVSTFFLWKIKNIVDMEKSLQEYAEssEVPLNYLCDSKRLGITDSRIA 494
                                       899************************************************99988999999*************** PP

                       CPSase_L_D3  78 elleeeeeeevrelrkklgilpvykrvDtcAaeFeaetpYlYstY 122
                                       el+  ++eee+ ++r++ +i+ +yk+vDtcAaeF+a tpY+Ys+Y
  gi|298675345|ref|YP_003727095.1| 495 ELTD-KTEEEIGDTRRDNQIKTTYKMVDTCAAEFAAVTPYYYSSY 538
                                       **65.78888**********************************9 PP

>> MGS  MGS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.48   8.6e+02      51      72 ..      33      54 ..       7      68 .. 0.73
   2 ?   -0.1   0.0      0.59   1.1e+03      47      93 ..     279     328 ..     255     330 .. 0.75
   3 ?   -2.1   0.0       2.6   4.6e+03      51      70 ..     574     593 ..     543     604 .. 0.73
   4 !   73.9   0.1     5e-24     9e-21       2      95 .]     956    1041 ..     955    1041 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.48
                                      HHHHHHHTTSCCEEEEE--THH CS
                               MGS 51 eildaikngeidlvintlypfk 72
                                      +   a+++++i++v ++ +p +
  gi|298675345|ref|YP_003727095.1| 33 QACRALREEGIEVVLVNSNPAT 54
                                      6677899999999999988876 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.59
                                       THCHHHHHHHHTTSCCEEEEE--THHHHHH...CHHHHHHHHHHHTTSHE CS
                               MGS  47 ggrveildaikngeidlvintlypfkatva...kdgykirraaenidIpl 93 
                                       +g ++i+ a+k+g++ +v +++   ++        gy i+r+  +i I++
  gi|298675345|ref|YP_003727095.1| 279 EGGCNIQFAVKDGDYRVVEVNPRVSRSSALaskATGYPIARVTAKIAIGM 328
                                       34568999999999999999988777766556778999***999999997 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.6
                                       HHHHHHHTTSCC.EEEEE--T CS
                               MGS  51 eildaikngeid.lvintlyp 70 
                                       + + ai++++i+  +in  +p
  gi|298675345|ref|YP_003727095.1| 574 HAVSAISEENIEsHIIN-NNP 593
                                       77889999999954444.333 PP

  == domain 4  score: 73.9 bits;  conditional E-value: 5e-24
                                        HHHHHHHHHHTTCEEEEEHHHHHHHHHTT--EEECCCCHSTGSGGTHCHHHHHHHHTTSCCEEEEE--THHHHHH CS
                               MGS    2 lvelakklkelgfellATgGTakllkeagipvtevvektgegerlggrveildaikngeidlvintlypfkatva 76  
                                        +v++a+k++++g+el+ T+GTa +l+e+gi  +e v+k+++g +++    + d+++  e++l+int++++++++ 
  gi|298675345|ref|YP_003727095.1|  956 IVNVARKMQDAGIELMGTHGTASYLAEHGII-VESVKKVHDG-SPN----VIDMMRRDEVSLIINTPTSKQSRK- 1023
                                        89*****************************.9999******.999....********************9986. PP

                                        CHHHHHHHHHHHTTSHEES CS
                               MGS   77 kdgykirraaenidIplpt 95  
                                         dgy+irraa+++++p++t
  gi|298675345|ref|YP_003727095.1| 1024 -DGYQIRRAAVDFKVPYIT 1041
                                        .****************98 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   4.9e-10   8.7e-07      26     174 ..     154     300 ..     143     304 .. 0.85
   2 !   32.2   0.0   4.1e-11   7.4e-08      30     174 ..     700     841 ..     678     866 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 4.9e-10
                                       HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT-..SCEEEEE--.ESEEEEEEEEETSSCEEE CS
                   Dala_Dala_lig_C  26 ellekveeelgypvfVKpareGSSvGvskveseeelkeaieeafkyd..ekvlvEeai.egreievavlgneklevs 99 
                                       +  e++++elg+p++V+pa +    G   ++++e+l e +e+ +++   ++vlvEe +   +e+e  v+ + + ++ 
  gi|298675345|ref|YP_003727095.1| 154 KEAEEMIDELGLPLIVRPAYTLGGAGGGIAHTKEQLFEIVERGLRRSriHQVLVEESVlGWKEFEYEVMRDSNDTCV 230
                                       4578999************987778888899***********998763369******9899*********6655544 PP

                                       EEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEES CS
                   Dala_Dala_lig_C 100 evgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNt 174
                                           i+ + + +d    ++++++ ++   +l++e+++ ++  a+++ +  +++G + + f ++ +g+  + EvN+
  gi|298675345|ref|YP_003727095.1| 231 ----IICNMENFDPMGIHTGESIVVTPSQTLSDEEHQMLRSSAINIIRSFGIEGGCNIQFAVK-DGDYRVVEVNP 300
                                       ....45555667777778888999999999*******************************98.9*********6 PP

  == domain 2  score: 32.2 bits;  conditional E-value: 4.1e-11
                                       HHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHH..HTT-SCEEEEE--.ESEEEEE.EEEETSSCEEEEEE CS
                   Dala_Dala_lig_C  30 kveeelgypvfVKpareGSSvGvskveseeelkeaieea..fkydekvlvEeai.egreiev.avlgneklevsevg 102
                                       +  +e+gypv+V+p+       ++ v  eeelk++++e+  +++d+ +l++ ++  + ei+v av + e++ +  + 
  gi|298675345|ref|YP_003727095.1| 700 NFATEIGYPVLVRPSYVLGGRAMEIVYDEEELKRYLRESvcVSKDNPILIDDFLeGAVEIDVdAVCDGENVLIGAIM 776
                                       457899*********9888889**************99733589**********7789****78999999******* PP

                                       EEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEES CS
                   Dala_Dala_lig_C 103 eivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNt 174
                                       e++ + g+       s+d+a +  p +l++e+ e ++++  k+   ld++Gl  + +  +++ge+++ E N+
  gi|298675345|ref|YP_003727095.1| 777 EHIEEAGVH------SGDSACVIPPQSLTEETMEIVRDYTRKIALSLDVKGLINIQM-AKRDGEVYVLEANP 841
                                       ***999986......678999999****************************99985.577**********7 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   4.5e-09     8e-06       6     161 ..     142     303 ..     138     311 .. 0.87
   2 !   33.5   0.0   1.6e-11   2.8e-08       2     160 ..     680     843 ..     679     846 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 4.5e-09
                                       --B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC....GTTCEEEEE----SEEE CS
                         ATP-grasp   6 lpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal....keekvivEefvpfekEl 78 
                                        +vp+  a++s +e+ee+++elglp++v+ +     G G  + + +e+l +++e      + ++v+vEe v   kE 
  gi|298675345|ref|YP_003727095.1| 142 EKVPQSKAISSLKEAEEMIDELGLPLIVR-PAYTLGGAGGGIAHTKEQLFEIVERGlrrsRIHQVLVEESVLGWKEF 217
                                       5899*************************.999999************9999988778778899*******999999 PP

                                       EEEEEEETTC-EEE--EEEEEEETTEEE...EEEECEE-SCH.HHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTE CS
                         ATP-grasp  79 svlvvrsaeGetafypvvetvqedgilr...lsvapaevsek.aqkkaeeiakkiveeLggvGvfavElFvledgel 151
                                          v+r+ + + +++  +e+    gi     ++v p++  ++ +++  ++ a +i++++g+ G   + + v+ dg+ 
  gi|298675345|ref|YP_003727095.1| 218 EYEVMRDSNDTCVIICNMENFDPMGIHTgesIVVTPSQTLSDeEHQMLRSSAINIIRSFGIEGGCNIQFAVK-DGDY 293
                                       9999******9999999****99999753337888887766615555667777**************86666.**** PP

                                       EEEEEESS-- CS
                         ATP-grasp 152 lvnElapRpH 161
                                        v E+ pR+ 
  gi|298675345|ref|YP_003727095.1| 294 RVVEVNPRVS 303
                                       ********85 PP

  == domain 2  score: 33.5 bits;  conditional E-value: 1.6e-11
                                       HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC....GTTCEEEEE---- CS
                         ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal....keekvivEefvpf 74 
                                       ++lg++ p+  ++ s+ e+ ++a+e+g+pv+v+ +     G+   +v +ee+l++ l++     k++++++ +f + 
  gi|298675345|ref|YP_003727095.1| 680 KELGINQPDGRYALSQGEAINFATEIGYPVLVR-PSYVLGGRAMEIVYDEEELKRYLRESvcvsKDNPILIDDFLEG 755
                                       68899999999999999****************.99999******************9999999************* PP

                                       SEEEEEEEEEETTC-EEE--EEEEEEETTEE....EEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEET CS
                         ATP-grasp  75 ekElsvlvvrsaeGetafypvvetvqedgil....rlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvle 147
                                        +E+ v +v + e  + + +++e+++e g+       ++ p++++e+  + ++++++ki+ +L++ G++ + +    
  gi|298675345|ref|YP_003727095.1| 756 AVEIDVDAVCDGEN-VLIGAIMEHIEEAGVHsgdsACVIPPQSLTEETMEIVRDYTRKIALSLDVKGLINIQMAKR- 830
                                       ******99987776.778888899887765411117889999*******************************888. PP

                                       TCTEEEEEEESS- CS
                         ATP-grasp 148 dgellvnElapRp 160
                                       dge++v E  pR 
  gi|298675345|ref|YP_003727095.1| 831 DGEVYVLEANPRS 843
                                       ***********96 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   1.4e-08   2.5e-05      44     118 ..     260     335 ..     253     348 .. 0.80
   2 !   32.6   0.0   3.1e-11   5.5e-08       3     114 ..     745     872 ..     743     892 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.4e-08
                      ATPgrasp_Ter  44 ekdeelielaerlaeefgldglvnvQvrededgpkLLEiNpRasGGlg.ysalaGvnlpylalklllgleteevee 118
                                       e+++ l + a +++++fg++g  n+Q+  +++ +++ E+NpR+s      s ++G  ++++ +k + g+  +e+++
  gi|298675345|ref|YP_003727095.1| 260 EEHQMLRSSAINIIRSFGIEGGCNIQFAVKDGDYRVVEVNPRVSRSSAlASKATGYPIARVTAKIAIGMTLDEIPN 335
                                       45677788999********************************96555156677*999999999999985444433 PP

  == domain 2  score: 32.6 bits;  conditional E-value: 3.1e-11
                      ATPgrasp_Ter   3 pallvmeyLegp.EySvDvlae.kgevlaavpRrKekgglq.............elekdeelielaerlaeefgldg 64 
                                       +++l+ ++Leg+ E+ vD +++ ++ ++ a+    e+ g++             + e+ e + ++++++a ++ ++g
  gi|298675345|ref|YP_003727095.1| 745 NPILIDDFLEGAvEIDVDAVCDgENVLIGAIMEHIEEAGVHsgdsacvippqslTEETMEIVRDYTRKIALSLDVKG 821
                                       5789999**9966********9777777788877775555556677888888533334445568999999999**** PP

                      ATPgrasp_Ter  65 lvnvQvrededgpkLLEiNpRasGGlgy.salaGvnlpylalklllglete 114
                                       l+n+Q+ +++++ ++LE NpR s ++   s + G+ l+++a++ ++g++ +
  gi|298675345|ref|YP_003727095.1| 822 LINIQMAKRDGEVYVLEANPRSSRTIPFvSKAVGIPLAKIAAQVIMGHKLK 872
                                       **************************9625566*************97444 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.1   1.2e-07   0.00021       9     158 ..     135     302 ..     127     305 .. 0.72
   2 ?   -4.0   0.0       7.6   1.4e+04      64      85 ..     464     485 ..     455     494 .. 0.77
   3 !   32.4   0.0   4.7e-11   8.4e-08       2     157 ..     670     842 ..     669     846 .. 0.83
   4 ?   -2.7   0.0       2.9   5.2e+03     112     146 ..     948     982 ..     942     988 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.2e-07
                                       HHHTTT.S---...........-EESS--SSSEEEEESS-------B--SS--TTE...............EEEE-- CS
                       ATP-grasp_3   9 kkLkeagvkvP.......tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve........lvqefi 70 
                                       +k+ + g kvP        k  +e ++e   +l+v p++  gg +  +++ ke++++++e           lv e +
  gi|298675345|ref|YP_003727095.1| 135 EKMGDIGEKVPqskaissLKEAEEMIDELGLPLIVRPAYTLGGAGGGIAHTKEQLFEIVERGLrrsrihqvLVEESV 211
                                       55556666777544442112222334444899********************9999888876578887888777777 PP

                                       -S.EEEEEEEEE.SSSEEEEEEEEEEEET....TEEEEE...EES----H...HHHHHHHHHHHHTTSTT--EEEEE CS
                       ATP-grasp_3  71 eG.kplSvsllsdgekvlvlavnrqliekaekefvyaGn...vtpietel...keevvelaeevvekleglaGyvGv 140
                                        G k++  +++ d ++  v+ +n +  +  +     +G+   vtp++t     ++ +++ a ++++++ g+ G   +
  gi|298675345|ref|YP_003727095.1| 212 LGwKEFEYEVMRDSNDTCVIICNMENFDPMGI---HTGEsivVTPSQTLSdeeHQMLRSSAINIIRSF-GIEGGCNI 284
                                       77678999999999999999999999987444...445422257777655111555667777777788.******** PP

                                       EEEESS.SEEEEEEESS- CS
                       ATP-grasp_3 141 DlvlkdeepyviEvNPRl 158
                                        + +kd++  v+EvNPR+
  gi|298675345|ref|YP_003727095.1| 285 QFAVKDGDYRVVEVNPRV 302
                                       *****************8 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 7.6
                                       .EEEE---SEEEEEEEEE.SSS CS
                       ATP-grasp_3  64 elvqefieGkplSvsllsdgek 85 
                                       + +qe+ e++++ ++ l+d ++
  gi|298675345|ref|YP_003727095.1| 464 KSLQEYAESSEVPLNYLCDSKR 485
                                       4579999999999999998765 PP

  == domain 3  score: 32.4 bits;  conditional E-value: 4.7e-11
                                       TSHHHHHHHHTTT.S---...........-EESS--SSSEEEEESS-------B--SS--TTE.............. CS
                       ATP-grasp_3   2 sdKlktykkLkeagvkvP.......tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve....... 64 
                                       +d  k+y  +ke g++ P       +    + ++e  +++ v p++  gg ++ +v ++ee+++ + e         
  gi|298675345|ref|YP_003727095.1| 670 EDRDKFYALMKELGINQPdgryalsQGEAINFATEIGYPVLVRPSYVLGGRAMEIVYDEEELKRYLRESVcvskdnp 746
                                       6778899999999*****988766433444445666***************************9998877899**** PP

                                       .EEEE---SE.EEEEEEEE.SSSEEEEEEEEEEEET....TEEEEEEES-..---HHHHHHHHHHHHHTTST...T- CS
                       ATP-grasp_3  65 .lvqefieGk.plSvsllsdgekvlvlavnrqliekaekefvyaGnvtpi..etelkeevvelaeevvekle...gl 134
                                        l+ +f+eG  ++ v++++dge+vl+ a+ + + e      v +G ++ +  +++l+ee++e++++ ++k+    ++
  gi|298675345|ref|YP_003727095.1| 747 iLIDDFLEGAvEIDVDAVCDGENVLIGAIMEHIEEA----GVHSGDSACVipPQSLTEETMEIVRDYTRKIAlslDV 819
                                       *********6599********999888887766655....6667765544113367999999999999999887899 PP

                                       -EEEEEEEEESS.SEEEEEEESS CS
                       ATP-grasp_3 135 aGyvGvDlvlkdeepyviEvNPR 157
                                       +G+  + +  +d+e yv+E NPR
  gi|298675345|ref|YP_003727095.1| 820 KGLINIQMAKRDGEVYVLEANPR 842
                                       *********************** PP

  == domain 4  score: -2.7 bits;  conditional E-value: 2.9
                                       ----HHHHHHHHHHHHHTTSTT--EEEEEEEEESS CS
                       ATP-grasp_3 112 ietelkeevvelaeevvekleglaGyvGvDlvlkd 146
                                       i+ e+ke++v++a+++  +  +l+G  G    l++
  gi|298675345|ref|YP_003727095.1| 948 IRDEDKEKIVNVARKMQDAGIELMGTHGTASYLAE 982
                                       67889999999999998876688888886655555 PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   2.7e-05     0.049       6     106 ..     133     229 ..     128     275 .. 0.82
   2 !   19.8   0.0     3e-07   0.00054       8     107 ..     677     772 ..     672     842 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.7e-05
                                       HHHHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSS CS
                            GARS_A   6 akdllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkfGeagek 82 
                                        k+ + ++g + ++ +a+++ +ea+e+i+e++ +  +v+++   +g g  +a+++e+ +++v+  l++ +     ++
  gi|298675345|ref|YP_003727095.1| 133 FKEKMGDIGEKVPQSKAISSLKEAEEMIDELGLPL-IVRPAYTLGGAGGGIAHTKEQLFEIVERGLRRSR----IHQ 204
                                       5777888999999**********************.8898888899999***********9999998544....579 PP

                                       EEEEE---S.EEEEEEEEECTTEEE CS
                            GARS_A  83 vviEelleG.eEvsllalvdgktvk 106
                                       v++Ee + G +E+   ++ d +++ 
  gi|298675345|ref|YP_003727095.1| 205 VLVEESVLGwKEFEYEVMRDSNDTC 229
                                       9999998885799999999976544 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 3e-07
                                       HHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSSEE CS
                            GARS_A   8 dllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkfGeagekvv 84 
                                       +l+k+ gi+ ++ +   ++ ea ++ +e + ++  v+++ + +g+ + ++ +eee  ++++e +      +  + ++
  gi|298675345|ref|YP_003727095.1| 677 ALMKELGINQPDGRYALSQGEAINFATEIGYPV-LVRPSYVLGGRAMEIVYDEEELKRYLRESVC----VSKDNPIL 748
                                       599********999999****************.99**********************9999875....45689*** PP

                                       EEE---S.EEEEEEEEECTTEEEE CS
                            GARS_A  85 iEelleG.eEvsllalvdgktvkp 107
                                       i+++leG  E+ + a++dg++v  
  gi|298675345|ref|YP_003727095.1| 749 IDDFLEGaVEIDVDAVCDGENVLI 772
                                       *******55***********9864 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0       0.1   1.8e+02      19      51 ..     137     169 ..     122     173 .. 0.85
   2 ?   -3.5   0.0       3.3   5.9e+03      80     119 ..     185     223 ..     181     226 .. 0.71
   3 !   13.0   0.0   2.9e-05     0.052      13      51 ..     673     711 ..     664     714 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.1
                       ATP-grasp_5  19 leaygipvvetrlassaeeaveaaeeigypvvl 51 
                                       + ++g +v++++ +ss +ea e+++e+g p  +
  gi|298675345|ref|YP_003727095.1| 137 MGDIGEKVPQSKAISSLKEAEEMIDELGLPLIV 169
                                       5678999**********************9766 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.3
                       ATP-grasp_5  80 aaeeilervkekspeariegvlVqemakrggrElivgvte 119
                                       + e++ e v++   ++ri++vlV+e +  g  E+   v +
  gi|298675345|ref|YP_003727095.1| 185 TKEQLFEIVERGLRRSRIHQVLVEESVL-GWKEFEYEVMR 223
                                       5567777888888899999999999977.55555555555 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 2.9e-05
                       ATP-grasp_5  13 aeakelleaygipvvetrlassaeeaveaaeeigypvvl 51 
                                        + ++l++ +gi+ ++ r+a s+ ea++ a eigypv +
  gi|298675345|ref|YP_003727095.1| 673 DKFYALMKELGINQPDGRYALSQGEAINFATEIGYPVLV 711
                                       56789*******************************976 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00019      0.34       9      71 ..      29      90 ..      28     107 .. 0.81
   2 ?   -2.8   0.0         2   3.6e+03      17      71 ..     578     631 ..     574     643 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00019
                                      HHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.EEEE--TT-HHHHHHHHHHHT-SEEEE- CS
                         Epimerase  9 fiGsalvkallekgyevigldrlssasntarledl.elveldltdrsalerlfkeeqpdavihl 71
                                      f Gs+ ++al e+g+ev+ +++++ +  t   e   + v+++ +++  +e+++++e+pd +i  
  gi|298675345|ref|YP_003727095.1| 29 FSGSQACRALREEGIEVVLVNSNPATIMTDP-E-MaDSVYIEPLEPRVVEKIIERERPDGIIAG 90
                                      67******************99955555433.2.2599*********************99864 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2
                                       HHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE- CS
                         Epimerase  17 allekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihl 71 
                                       a+ e+++e + +++++++  t  +   +l    lt  +++ +++++eqpd v+  
  gi|298675345|ref|YP_003727095.1| 578 AISEENIESHIINNNPETVSTDYDTSDKLFFEPLT-LEDVMNVIEKEQPDGVLVQ 631
                                       55666666666666666555555444433333333.4568889999999999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1076 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      649  (0.0361983); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.94u 0.30s 00:00:01.24 Elapsed: 00:00:00.53
# Mc/sec: 6114.52
//
Query:       gi|298675346|ref|YP_003727096.1|  [L=395]
Description: argininosuccinate synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.7e-175  583.9   0.1     2e-175  583.7   0.1    1.0  1  Arginosuc_synth  Arginosuccinate synthase
    0.00027   20.1   0.0     0.0006   19.0   0.0    1.5  1  NAD_synthase     NAD synthase
    0.00029   20.4   0.0     0.0012   18.4   0.0    1.9  2  QueC             Queuosine biosynthesis protein QueC
     0.0053   15.6   0.0     0.0089   14.9   0.0    1.3  1  tRNA_Me_trans    tRNA methyl transferase


Domain annotation for each model (and alignments):
>> Arginosuc_synth  Arginosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  583.7   0.1  4.4e-179    2e-175       1     387 [.       8     389 ..       8     390 .. 0.99

  Alignments for each domain:
  == domain 1  score: 583.7 bits;  conditional E-value: 4.4e-179
                   Arginosuc_synth   1 vLaysGGlDtsviikllkeklg.eeviavavdvGqeeedldevkekalklgavksvvvDakeefvedyifpaikana 76 
                                       vLaysGGlDtsv+i+llke++g +evi+vav+vGq+ee+++e++eka+k+++ k++++Da++efv+dyifp ikan+
  gi|298675346|ref|YP_003727096.1|   8 VLAYSGGLDTSVCIPLLKEEYGyDEVITVAVNVGQPEEEIKEADEKAEKISD-KHYTIDARKEFVNDYIFPLIKANG 83 
                                       8*********************899**************************9.************************ PP

                   Arginosuc_synth  77 lYedrYllgtalaRPliakklvevakkegaeavahGctGkGnDqvRfevsirslaPdlkviaPvReleltReeeiey 153
                                        Ye+ Y++gt++aRPliakk+veva+ke a+a++hGctGkGnDq+Rfe+++r ++  l+viaP+R+++ltRe+eiey
  gi|298675346|ref|YP_003727096.1|  84 DYEG-YVMGTSVARPLIAKKVVEVAEKEKASALSHGCTGKGNDQLRFEAVFRLTD--LEVIAPMRDMNLTREWEIEY 157
                                       ****.**********************************************9987..******************** PP

                   Arginosuc_synth 154 akekgipvevtkkkpysiDenllgrsieagiLedpknappediyeltkdpakapdepeeveiefekGvPvaldgeel 230
                                       ak++gipv+vt+ +p+siDen+++rsie+g Ledp  app++iy++t +p +ap e++ + i+f++GvPv+ldg+e+
  gi|298675346|ref|YP_003727096.1| 158 AKKHGIPVSVTTGEPWSIDENIWSRSIEGGELEDPACAPPQEIYSWTVSPDDAP-EAQAMVIGFDNGVPVSLDGKEM 233
                                       ******************************************************.788899**************** PP

                   Arginosuc_synth 231 svlelieklneiagkhGvGRiDivedRlvglksReiYeapaalvLikahkdlekltlerevakfkkiveekyaelvY 307
                                       + +eli++ln+iag hG+GR+D++edR++glk+Re+Ye+paa+vL++ah+dlekl+l+r++ +fk  v+++++el Y
  gi|298675346|ref|YP_003727096.1| 234 DGVELIQQLNNIAGSHGIGRTDMIEDRVLGLKARENYEHPAATVLLTAHQDLEKLVLTRSEIRFKADVDAQWSELAY 310
                                       ***************************************************************************** PP

                   Arginosuc_synth 308 kGlwfsPlkealdafiektqervtGtvrvklfkGsvvvlgReseeslYdeelasydeedefdqkeaeGfikihglqa 384
                                       +Gl+ +Pl+ +l++fi+ktqervtG+v vkl+kG+v vl+R+s+++lY+ee +s+d +++++qk+aeGf+k++g+q+
  gi|298675346|ref|YP_003727096.1| 311 YGLVDEPLYTDLNEFINKTQERVTGKVTVKLHKGNVSVLARSSPYALYSEEFVSFD-SKTINQKDAEGFAKYYGFQS 386
                                       ********************************************************.9******************* PP

                   Arginosuc_synth 385 kly 387
                                       +ly
  gi|298675346|ref|YP_003727096.1| 387 RLY 389
                                       998 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.3e-07    0.0006      19      81 ..       5      66 ..       2      81 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.3e-07
                                      SEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE--- CS
                      NAD_synthase 19 kgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidi 81
                                      k+vvl  SGG+D s+   l ++  g ++v+++ + ++ ++ee++++a + ae+++++  tid 
  gi|298675346|ref|YP_003727096.1|  5 KKVVLAYSGGLDTSVCIPLLKEEYGYDEVITVAV-NVGQPEEEIKEADEKAEKISDKHYTIDA 66
                                      89********************************.9999**************9999999885 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.7e-07    0.0012       1      60 [.       6      65 ..       6      75 .. 0.77
   2 ?   -1.5   0.0      0.34   1.5e+03     150     180 ..     136     168 ..     125     170 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.7e-07
                                      EEEEE--SSHHHHHHHHHHHHH-..SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE CS
                              QueC  1 kavvllSGGlDSttvlalakkeg..kevealtfdYgqrhkkeleaakkiakelgveehkild 60
                                      k+v+  SGGlD ++++ l k+e+  +ev+++ ++ gq + +e++ a++ a+++   +h ++d
  gi|298675346|ref|YP_003727096.1|  6 KVVLAYSGGLDTSVCIPLLKEEYgyDEVITVAVNVGQPE-EEIKEADEKAEKISD-KHYTID 65
                                      578889**************997669**********985.466666666666554.555555 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.34
                                       S--EEE-TTTT--..HHHHHHHHHHTTHHHHH- CS
                              QueC 150 kkieieaPlidls..Kaeivklgkelgvpleet 180
                                       +++e+ aP+ d++  ++  ++ +k+ g+p++ t
  gi|298675346|ref|YP_003727096.1| 136 TDLEVIAPMRDMNltREWEIEYAKKHGIPVSVT 168
                                       568999999666500555556788888877666 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0     2e-06    0.0089       1      83 [.       5      79 ..       5      86 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2e-06
                     tRNA_Me_trans  1 kkvvvalSgGVDSsvaaallkeqg..yevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfekeykek 77
                                      kkvv a SgG D sv   llke++   evi v +++ +           ee++k+a + aek++ +++++d +ke+ ++
  gi|298675346|ref|YP_003727096.1|  5 KKVVLAYSGGLDTSVCIPLLKEEYgyDEVITVAVNVGQ----------PEEEIKEADEKAEKISDKHYTIDARKEFVND 73
                                      69*******************99732344444443322..........3466788888888888889999999999888 PP

                     tRNA_Me_trans 78 vfeefl 83
                                       + +++
  gi|298675346|ref|YP_003727096.1| 74 YIFPLI 79
                                      776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2957.80
//
Query:       gi|298675347|ref|YP_003727097.1|  [L=192]
Description: phosphatidate cytidylyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.04   14.4   4.0       0.04   14.4   4.0    2.7  3  DUF2061       Predicted membrane protein (DUF2061)
      0.079   12.7  18.2       0.11   12.2   5.3    2.2  2  CTP_transf_1  Cytidylyltransferase family


Domain annotation for each model (and alignments):
>> DUF2061  Predicted membrane protein (DUF2061)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.4      0.07   6.3e+02      10      25 ..      15      31 ..       7      49 .. 0.71
   2 ?   -2.3   0.1      0.73   6.5e+03      42      42 ..      95      95 ..      80     112 .. 0.57
   3 ?   14.4   4.0   4.5e-06      0.04      12      42 ..     136     166 ..     133     168 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.07
                           DUF2061 10 ihtv.vtflvaylltgs 25
                                      +h++ v ++v y++ g+
  gi|298675347|ref|YP_003727097.1| 15 FHLIsVLIIVIYAFLGK 31
                                      56551456677888876 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.73
                           DUF2061 42 v 42
                                      +
  gi|298675347|ref|YP_003727097.1| 95 I 95
                                      2 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 4.5e-06
                           DUF2061  12 tvvtflvaylltgslalAgaialvEpvvktv 42 
                                       +vv +++++++tg++ +A+ +a+v +vv t 
  gi|298675347|ref|YP_003727097.1| 136 FVVDLAIGFVFTGNWIIAVGMAFVATVVETT 166
                                       677889**********************986 PP

>> CTP_transf_1  Cytidylyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   5.5    0.0011       9.5       3      46 ..      12      56 ..      10      65 .. 0.87
   2 ?   12.2   5.3   1.3e-05      0.11     120     192 ..      79     148 ..      56     171 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0011
                                      HHHHHHHHHHHHHHTTTSH..HHHHHHHHHHHHHHHHHHHHTT-- CS
                      CTP_transf_1  3 Rvitalvlilivliilllgg.lvflllvavvvilalkElirlvrl 46
                                      R i++l+ +li++i  +lg+ +v++ll++ ++++++ E+irl r 
  gi|298675347|ref|YP_003727097.1| 12 RKIFHLISVLIIVIYAFLGKqIVLILLFVSLIFFLVLEYIRLERS 56
                                      889999999999999999997888888888999999*****9875 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 1.3e-05
                                       HH.TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCH---B-S-TTS---BHHHHHHHHHHHHHHHHHHHH CS
                      CTP_transf_1 120 llqslllienikeglllvllllalvvaaDigaYffGklfGktkllpkiSPkKTveGfigGlvaavvvglllal 192
                                       +l++ ++i+    +  ++++ ++++ + D +a ++Gk+fG tkl+ +    K++eG+   +v+ +++g++++ 
  gi|298675347|ref|YP_003727097.1|  79 FLTIGAIISIAMFSKQIAFACILMTTLGDLFAAIVGKTFGNTKLAYN---DKSLEGSASEFVVDLAIGFVFTG 148
                                       44556666666667777889999**********************98...8*********9999999999864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1135  (0.0633053); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.20s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 1508.10
//
Query:       gi|298675348|ref|YP_003727098.1|  [L=887]
Description: HAD superfamily ATPase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.9e-54  181.8   1.6    8.9e-54  181.8   1.6    3.6  4  E1-E2_ATPase     E1-E2 ATPase
    1.8e-37  128.8   9.5    1.8e-37  128.8   9.5    2.6  3  Cation_ATPase_C  Cation transporting ATPase, C-terminus
    1.8e-23   83.9   2.1    1.9e-22   80.6   2.1    2.4  1  Hydrolase        haloacid dehalogenase-like hydrolase
    2.3e-20   72.1   0.1    8.4e-19   67.0   0.0    2.7  2  Cation_ATPase_N  Cation transporter/ATPase, N-terminus
    1.6e-10   40.9   0.0    4.2e-10   39.6   0.0    1.8  1  Cation_ATPase    Cation transport ATPase (P-type)
    8.5e-08   32.2   5.7     0.0038   17.0   0.6    3.2  3  Hydrolase_3      haloacid dehalogenase-like hydrolase
      5e-05   23.8   0.0    9.7e-05   22.8   0.0    1.5  1  HAD              haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.2   0.2    0.0054        14     103     145 ..      44      86 ..      40      98 .. 0.76
   2 !  181.8   1.6   3.5e-57   8.9e-54       2     180 ..     114     306 ..     113     307 .. 0.98
   3 ?   -2.1   0.1      0.91   2.3e+03     119     160 ..     693     734 ..     659     736 .. 0.59
   4 ?   -0.6   0.2      0.32   8.2e+02     111     156 ..     752     797 ..     744     802 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0054
                                       -------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT CS
                      E1-E2_ATPase 103 eakskktplqkkldklgkvlvpvvlliallvflialllgksla 145
                                       eak++ +++ k+l+++++ l+ + +++a+++f++  ++   ++
  gi|298675348|ref|YP_003727098.1|  44 EAKKEHSEIYKFLKQFASPLIYILMAAAIITFFLEKYIDTAVI 86 
                                       5678899999999999999999999999999998766655554 PP

  == domain 2  score: 181.8 bits;  conditional E-value: 3.5e-57
                                       SS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-S.EEE-TTTS---S-EE-............. CS
                      E1-E2_ATPase   2 llpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsa.evdesaLTGEslpvek............. 64 
                                       +l p+a+virdg+ + i++kelv+GD+v+l++g+r+paD+r++  ++ +vdes LTGEs+pvek             
  gi|298675348|ref|YP_003727098.1| 114 MLVPEATVIRDGQRKVIPSKELVVGDVVILESGSRIPADIRLFYVKNlRVDESPLTGESVPVEKktraidedsiplg 190
                                       67899***********************************************************************9 PP

                                       G-TTEE-TT-EEEE-EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTT CS
                      E1-E2_ATPase  65 ekgdmvfsGtvvvsgeakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllg 141
                                       ++ +  f+Gt+v +g  ++vV+atgedte+gki ++++e+++  tpl++k+ ++g +l++++l+i+++vf+i ll+g
  gi|298675348|ref|YP_003727098.1| 191 DQINLSFAGTFVSEGLGRGVVIATGEDTEIGKISQSIRESEEISTPLVRKIARFGVFLSVAILAISVFVFFIGLLRG 267
                                       9**************************************************************************** PP

                                       SSTTHHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHHHHH CS
                      E1-E2_ATPase 142 kslaeallralallvaaiPcaLplavplalalgarrlak 180
                                        +++e++l a++l+vaaiP++Lp+++++++a+g++++a 
  gi|298675348|ref|YP_003727098.1| 268 FDAVETFLAAVSLAVAAIPEGLPATITISFAIGIKAMAS 306
                                       *************************************96 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.91
                                       HHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS- CS
                      E1-E2_ATPase 119 gkvlvpvvlliallvflialllgkslaeallralallvaaiP 160
                                       g+ l++v+ +i+ +++ +++l+  +++++ + +l++ ++a P
  gi|298675348|ref|YP_003727098.1| 693 GQALTVVSAIILGITLPLLPLHILWINTITTIGLGVTISAEP 734
                                       445666777777777777777666666666668888887776 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 0.32
                                       HHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHH CS
                      E1-E2_ATPase 111 lqkkldklgkvlvpvvlliallvflialllgkslaeallralallv 156
                                       l+++++k +++++++++ +a+++f + ++  ++l  a + al ++v
  gi|298675348|ref|YP_003727098.1| 752 LTQFIKKRIGFVSILMVSAAFFLFTLEMFSSNELPAARTTALNTIV 797
                                       6777888888888888888888888887777776655555555444 PP

>> Cation_ATPase_C  Cation transporting ATPase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       1.3   3.2e+03     110     141 ..      46      77 ..      41      93 .. 0.64
   2 ?    1.7   0.1     0.069   1.8e+02      53      74 ..     243     265 ..     215     331 .. 0.68
   3 !  128.8   9.5   7.1e-41   1.8e-37       2     182 .]     708     878 ..     707     878 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.3
                   Cation_ATPase_C 110 rsrreslfkfsglfsnkllllaillslllqvl 141
                                       ++++ ++ kf + f ++l+++ ++++++  +l
  gi|298675348|ref|YP_003727098.1|  46 KKEHSEIYKFLKQFASPLIYILMAAAIITFFL 77 
                                       56667777777777776666666555554444 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.069
                   Cation_ATPase_C  53 ri.liqgllqalvtllvffltll 74 
                                       r+ ++ ++ +++++++vff++ll
  gi|298675348|ref|YP_003727098.1| 243 RFgVFLSVAILAISVFVFFIGLL 265
                                       22244444444444445555554 PP

  == domain 3  score: 128.8 bits;  conditional E-value: 7.1e-41
                   Cation_ATPase_C   2 lplsaiqiLwinLvtDllpalaLaleppekdimkrpPrkkkepliskkmlrriliqgllqalvtllvffltlllfgi 78 
                                       lpl +++iLwin +t + ++++++ ep  k+++++pPr+++epl++  + +ri+++++l++ +++++f l ++  ++
  gi|298675348|ref|YP_003727098.1| 708 LPLLPLHILWINTITTIGLGVTISAEPRAKGLLDNPPRPTEEPLLTQFIKKRIGFVSILMVSAAFFLFTLEMF--SS 782
                                       8*******************************************************************88887..66 PP

                   Cation_ATPase_C  79 sekenklssnyaqtmaFitlvlsqifnalnlrsrreslfkfsglfsnkllllaillslllqvlivyvpglnavfgta 155
                                       +e        +a+t+a++t+v++qi +++n++s++  +f    lfsnk++l++i + ++lq+l++y p++n +f+ta
  gi|298675348|ref|YP_003727098.1| 783 NELP------AARTTALNTIVFIQISYLFNIKSLHGYVFD--ELFSNKYMLIGIGGVIGLQMLLTYHPFMNLIFDTA 851
                                       6644......4**********************8887766..9********************************** PP

                   Cation_ATPase_C 156 plsleewlialllalvvllvdelvKll 182
                                       p++l++w +++ +a+vv+++ el K++
  gi|298675348|ref|YP_003727098.1| 852 PIGLYNWSWIITVAIVVFFIIELEKYV 878
                                       *************************85 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.6   2.1   7.4e-26   1.9e-22       3     210 .]     325     637 ..     323     637 .. 0.73

  Alignments for each domain:
  == domain 1  score: 80.6 bits;  conditional E-value: 7.4e-26
                                       EEEEESBTTTBCHHHHHHHHHHHH..................................CHHHHHHHHHH.......H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx..................................xxxxxxxxxxx.......x RF
                         Hydrolase   3 tvvfDkdGTLttgepsvedvivsa..................................alalaaaletg.......s 38 
                                       +++ Dk+GTLt+ ++ v++++                                     +l+ +   + +        
  gi|298675348|ref|YP_003727098.1| 325 VICSDKTGTLTKNQMTVTEIYTATgttynvtgsgysskgnfildnetidpkndpvlleTLKAGYLCNDAsfkdgdvV 401
                                       7999***************9999988888888888888888888888887777777765555555555566666776 PP

                                       HCHHHHHH.HHHHHHH..............HHHHHHHHHETTTE...............HHHHTHHHHHHHH..... CS
                                       xxxxxxxx.xxxxxxx..............xxxxxxxxxxxxxx...............xxxxxxxxxxxxx..... RF
                         Hydrolase  39 ehpigkal.vaaakar..............sgaltgfatfigrg...............ayaigkpewltal..... 80 
                                         p   al v a ka               +                             y +g+pe + +l     
  gi|298675348|ref|YP_003727098.1| 402 GDPTEGALmVSALKAGkfyiprldiipfesE------------KrimatlnedsegnkiIYVKGSPEKIMELsqhkf 466
                                       6666666666666666554454444443320............1333444444444558888888886666644444 PP

                                       ....HCHHHHHHHHHHHHHHCHHHHHH.....................................TTHHHHHHHHHHT CS
                                       ....xxxxxxxxxxxxxxxxxxxxxxx.....................................xxxxxxxxxxxxx RF
                         Hydrolase  81 ....dippdlgaaigsaqsqgrtvall.....................................qaralavftiadp 116
                                           +i  d++a                                                    +   l++  i dp
  gi|298675348|ref|YP_003727098.1| 467 dgenEIDIDVNAL-------------SeikksseematqglrvigmaymkvendreridysdldNLVFLGLQGIIDP 530
                                       4434444444444.............03444444444455889999**************99998899********* PP

                                       HHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT....GGGE.SEEEEHHCES...........STTTSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxx.xxxxxxxxxx...........xxxxxxx RF
                         Hydrolase 117 lkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG....ddyf.daviasdiet...........vakpspe 177
                                         +++e++e +++ k agi+v+++tgd+  ta+++a+qlG    +    +++++ ++ +           +a  spe
  gi|298675348|ref|YP_003727098.1| 531 --PREEVKESINKCKTAGIRVIMITGDHTLTAHSIARQLGieteKAVAgSNIDDMTD-EqlkdtlksvsvFARTSPE 604
                                       ..**************************************98753333233333333.2577778889999999*** PP

                                       HHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 178 gkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                       +k ++++ L+ ++  va+ GDg+nDa+al++A+
  gi|298675348|ref|YP_003727098.1| 605 HKSRIVKLLKSEGDIVAVTGDGINDAPALKNAD 637
                                       **********88888****************98 PP

>> Cation_ATPase_N  Cation transporter/ATPase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.0   0.0   3.3e-22   8.4e-19       1      68 [.       7      73 ..       7      74 .. 0.98
   2 ?    1.8   0.0     0.074   1.9e+02      39      67 ..     744     772 ..     742     773 .. 0.85

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 3.3e-22
                   Cation_ATPase_N  1 ehalsleevlekLetdlenGLtqaeaaerlkkyGpNelkekkkkslwvkllkqftnplvilLlvaalv 68
                                      +++l+  +v+ekL+ ++ +GL q+ea++rl++ G Ne+++kk+ s + k+lkqf +pl+++L++aa++
  gi|298675348|ref|YP_003727098.1|  7 WYQLDYADVFEKLK-SSRDGLEQSEAEKRLSTDGYNEVEAKKEHSEIYKFLKQFASPLIYILMAAAII 73
                                      8999999******9.9***************************************************8 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.074
                   Cation_ATPase_N  39 kekkkkslwvkllkqftnplvilLlvaal 67 
                                       + + +++l+ +++k+   ++ il++ aa 
  gi|298675348|ref|YP_003727098.1| 744 PRPTEEPLLTQFIKKRIGFVSILMVSAAF 772
                                       57899**********99999988888875 PP

>> Cation_ATPase  Cation transport ATPase (P-type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.0   1.7e-13   4.2e-10       2      90 ..     389     464 ..     388     465 .. 0.90

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 1.7e-13
                     Cation_ATPase   2 lcNsaafsensekdevkllGnktEsALlvlaeklgldteelreetkkvqeipFnssrKrmsvvlklepekkvrlyvK 78 
                                       lcN+a+f      ++ +++G++tE AL+v a k+g      +   +++ +ipF+s++++m+++ +  +e++ ++yvK
  gi|298675348|ref|YP_003727098.1| 389 LCNDASF------KDGDVVGDPTEGALMVSALKAG------KFYIPRLDIIPFESEKRIMATLNED-SEGNKIIYVK 452
                                       8999999......88899**************995......455799******************8.7********* PP

                     Cation_ATPase  79 GApeiilkrCth 90 
                                       G+pe i++ ++h
  gi|298675348|ref|YP_003727098.1| 453 GSPEKIMELSQH 464
                                       ******997766 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.37   9.4e+02      42     111 ..      49     119 ..      45     137 .. 0.77
   2 !   15.8   0.0   3.4e-06    0.0086      18      77 ..     533     590 ..     528     601 .. 0.86
   3 !   17.0   0.6   1.5e-06    0.0038     194     251 ..     608     666 ..     605     670 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.37
                                       HHHHHHHHHHCCCCSEEEEGGGTEEECTTTEEEEE--.B-HHHHHHHHHHHHHTTCEEEEEESSEEEESTT CS
                       Hydrolase_3  42 lravlpvleelgldlpvialNGaliddekgkilykst.iskedvkeiikllkennveillytedkvyvlnk 111
                                       ++++ ++l+++   l++i +  a+i++  +k++++   +s   +++ii +++e + e +l++ +k++v ++
  gi|298675348|ref|YP_003727098.1|  49 HSEIYKFLKQFASPLIYILMAAAIITFFLEKYIDTAViLSVVIANSIIGYIQESKAEHALESLSKMLVPEA 119
                                       67788888888888888888888997777777755551567889999********9999999999999887 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 3.4e-06
                                       HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEEECTTTEEEEE- CS
                       Hydrolase_3  18 ektkeaikklkekgikvviATGRslravlpvleelgldlpvialNGaliddekgkilyks 77 
                                       e+ ke i+k+k +gi v+  TG ++ ++++++++lg+++   a+ G+ idd +++ l+ +
  gi|298675348|ref|YP_003727098.1| 533 EEVKESINKCKTAGIRVIMITGDHTLTAHSIARQLGIET-EKAVAGSNIDDMTDEQLK-D 590
                                       789***********************************4.44578****999998884.4 PP

  == domain 3  score: 17.0 bits;  conditional E-value: 1.5e-06
                                       HHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHH.HHSSEEE--GGGTHH CS
                       Hydrolase_3 194 klakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevk.kaAdyvtksnnedGV 251
                                       +++k l+ + + v++ GDg ND + L+ a++g+ mg +  ev  +a+d+v  + n  ++
  gi|298675348|ref|YP_003727098.1| 608 RIVKLLKSEGDIVAVTGDGINDAPALKNADIGISMGASGTEVArEASDMVLVDDNFASI 666
                                       578889999999***********************977666650555566555554555 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   3.8e-08   9.7e-05      87     188 .]     532     634 ..     509     634 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 3.8e-08
                               HAD  87 dpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevdd....rltge..........lglegkpv 149
                                       +++++e +++++ aG+rv++++g +   ++ ++++lg    + te +v +    ++t e          ++ + +p 
  gi|298675348|ref|YP_003727098.1| 532 REEVKESINKCKTAGIRVIMITGDHTLTAHSIARQLG----IETEKAVAGsnidDMTDEqlkdtlksvsVFARTSPE 604
                                       3599*********************************....666544444534434443444333334444555555 PP

                               HAD 150 rgegkvaalrewlaaegegidleevvay.GDspsDlpllr 188
                                       ++    +++ +    ++eg+    +va+ GD+++D p+l+
  gi|298675348|ref|YP_003727098.1| 605 HK----SRIVK--LLKSEGD----IVAVtGDGINDAPALK 634
                                       55....44444..2222333....67777*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (887 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.43
# Mc/sec: 6251.29
//
Query:       gi|298675349|ref|YP_003727099.1|  [L=250]
Description: succinate dehydrogenase and fumarate reductase iron-sulfur protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-30  104.2   0.2    1.3e-29  102.3   0.1    1.9  2  Fer2_3         2Fe-2S iron-sulfur cluster binding domain
    4.1e-08   33.6   1.0    4.1e-08   33.6   1.0    1.9  2  Fer4_8         4Fe-4S dicluster domain
    1.6e-07   31.4   1.4    1.6e-07   31.4   1.4    2.0  2  Fer4_10        4Fe-4S dicluster domain
    1.6e-05   24.7   1.2    0.00016   21.5   0.2    2.3  2  Fer2           2Fe-2S iron-sulfur cluster binding domain
    9.7e-05   22.8   0.7    9.7e-05   22.8   0.7    2.1  2  Fer4_17        4Fe-4S dicluster domain
    0.00019   22.0   1.9    0.00019   22.0   1.9    2.5  3  Fer4_7         4Fe-4S dicluster domain
     0.0025   17.9  10.4     0.0036   17.4   5.4    2.9  4  Fer4_9         4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.04   13.4   0.0      0.071   12.6   0.0    1.4  1  Peptidase_C74  Pestivirus NS2 peptidase
       0.05   14.1   1.1       0.05   14.1   1.1    3.4  3  Fer4_4         4Fe-4S binding domain
      0.072   14.0   0.7      0.072   14.0   0.7    3.2  4  Fer4_16        4Fe-4S double cluster binding domain
      0.089   13.0   6.0       0.33   11.1   0.1    2.6  3  Fer4_18        4Fe-4S dicluster domain
        1.5    9.6   6.0        7.1    7.4   0.2    3.1  3  Fer4_15        4Fe-4S single cluster domain
          3    7.8  18.9       0.22   11.4   3.6    3.5  3  Fer4           4Fe-4S binding domain
        4.8    7.4  12.2       0.27   11.4   0.6    2.8  3  Fer4_21        4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer2_3  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.3   0.1   1.1e-32   1.3e-29       1     108 [.       3     126 ..       3     127 .. 0.95
   2 ?   -1.4   0.0       1.8   2.3e+03       5      23 ..     191     210 ..     188     216 .. 0.69

  Alignments for each domain:
  == domain 1  score: 102.3 bits;  conditional E-value: 1.1e-32
                            Fer2_3   1 tlkvkRfdprrdrgkqkvqeyeveaeeedtvldaLlkikeevdptlafrasCregiCGscavainGkptlaCtatik 77 
                                       tl++kR+++    +k ++++++v+ +++++vl+aL +i+e++d +l fr  Cr ++CGsca+ in  p+laC++ + 
  gi|298675349|ref|YP_003727099.1|   3 TLNIKRQED----DKIWYDTFQVDEKPGMNVLEALFEIQEKQDGSLCFRFACRGAVCGSCAMLINKVPRLACKKLVG 75 
                                       578999988....689************************************************************* PP

                            Fer2_3  78 dlakqkse....................ieleplpkfpvirDLvvDideml 108
                                       d++k++ +                    i +eplp++ virDLvvD+++++
  gi|298675349|ref|YP_003727099.1|  76 DVKKEDISslksdqiltspqfskesndrILIEPLPNLGVIRDLVVDMEHFY 126
                                       ***99864689************************************9986 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.8
                            Fer2_3   5 kRfdp.rrdrgkqkvqeyev 23 
                                       +Rf+   rd++k+k+q y++
  gi|298675349|ref|YP_003727099.1| 191 WRFQLdPRDSEKSKLQRYNI 210
                                       66654135667999999998 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.3       3.1     4e+03       8      12 ..      55      59 ..      45      95 .. 0.73
   2 !   33.6   1.0   3.2e-11   4.1e-08       3      65 .]     160     234 ..     158     234 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3.1
                            Fer4_8  8 CgaCq 12
                                      Cg C 
  gi|298675349|ref|YP_003727099.1| 55 CGSCA 59
                                      44443 PP

  == domain 2  score: 33.6 bits;  conditional E-value: 3.2e-11
                            Fer4_8   3 ekCieCgaCqsaCpvlrr...........tk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvgi 65 
                                        +Ci C  C   Cp++ r           ++ ++ ld+r+  + + q+   +++  ++w C    +C+ vCp+++
  gi|298675349|ref|YP_003727099.1| 160 TNCILCAVCHGICPAAARddkylspaglaRAwRFQLDPRDSEKSKLQRYNIVDSLSGVWGCDLVYKCVAVCPKKV 234
                                       69***********9555533333333333555777777777777777777777799****************986 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   1.3       5.4   6.9e+03      45      51 ..      50      58 ..      38      60 .. 0.68
   2 !   31.4   1.4   1.2e-10   1.6e-07       7      56 .]     160     231 ..     154     231 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 5.4
                           Fer4_10 45 Ctg..cgaC 51
                                      C g  cg+C
  gi|298675349|ref|YP_003727099.1| 50 CRGavCGSC 58
                                      444445555 PP

  == domain 2  score: 31.4 bits;  conditional E-value: 1.2e-10
                           Fer4_10   7 dtCirCgkCvkaCPadl......................tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                         Ci C+ C   CPa +                      +s + k ++ ++     +v+ C+ + +Cv++CP
  gi|298675349|ref|YP_003727099.1| 160 TNCILCAVCHGICPAAArddkylspaglarawrfqldprDSEKSKLQRYNIVDSLSGVWGCDLVYKCVAVCP 231
                                       67*************88*********************655555666666666666***************9 PP

>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.2   1.3e-07   0.00016       7      73 ..      18      70 ..      11      81 .. 0.81
   2 ?    1.6   0.1      0.21   2.7e+02      30      47 ..     157     172 ..     132     192 .. 0.64

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.3e-07
                                      EEEEEEETTTHBHHHHHH.....HTTTTTSTTSSSSSSSSTTEEEEEESCECTTSSSSTHHHHHTTEEEEGG CS
                              Fer2  7 evevevadgettlldaae.....enggidipysCggggCgtClvevlegevqsdetelegeeldegklrlaC 73
                                      +++v++++g + +l+a+      ++g + ++++C+g+ Cg+C+  ++            + +      rlaC
  gi|298675349|ref|YP_003727099.1| 18 TFQVDEKPGMN-VLEALFeiqekQDGSLCFRFACRGAVCGSCAMLIN------------KVP------RLAC 70
                                      57889988888.999998788766889********999*****9999............343......3444 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.21
                                       TSTTSSSSSSSSTTEEEE CS
                              Fer2  30 dipysCggggCgtClvev 47 
                                       +  ++C    C++C+  +
  gi|298675349|ref|YP_003727099.1| 157 EKYTNCI--LCAVCHGIC 172
                                       5544554..599999864 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.3       2.4   3.1e+03      49      53 ..      55      59 ..      32      84 .. 0.75
   2 !   22.8   0.7   7.6e-08   9.7e-05       1      60 [.     161     234 ..     161     235 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.4
                           Fer4_17 49 CgeCe 53
                                      Cg C+
  gi|298675349|ref|YP_003727099.1| 55 CGSCA 59
                                      33333 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 7.6e-08
                           Fer4_17   1 rCiqCgyClpeCpsyeaydne..pkkllraakl.........glleeaeke........ekaslCieCgeCerkCPq 58 
                                       +Ci C+ C   Cp  ++ d++  p+ l+ra+++         +   +   +        + +  C    +C+++CP+
  gi|298675349|ref|YP_003727099.1| 161 NCILCAVCHGICPAAARDDKYlsPAGLARAWRFqldprdsekS---KL--QrynivdslSGVWGCDLVYKCVAVCPK 232
                                       6*************99988744499******997777663331...22..13356666779999************9 PP

                           Fer4_17  59 gl 60 
                                       ++
  gi|298675349|ref|YP_003727099.1| 233 KV 234
                                       87 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.3       1.8   2.3e+03      41      45 ..      55      59 ..      17      71 .. 0.75
   2 !    9.8   1.6   0.00092       1.2      34      52 .]     158     176 ..     137     176 .. 0.75
   3 !   22.0   1.9   1.5e-07   0.00019       2      51 ..     162     233 ..     161     234 .. 0.59

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.8
                            Fer4_7 41 CgaCv 45
                                      Cg+C+
  gi|298675349|ref|YP_003727099.1| 55 CGSCA 59
                                      55554 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00092
                            Fer4_7  34 dpekClgCgaCvavCPtga 52 
                                       ++++C+ C +C   CP+ a
  gi|298675349|ref|YP_003727099.1| 158 KYTNCILCAVCHGICPAAA 176
                                       5678999999999999765 PP

  == domain 3  score: 22.0 bits;  conditional E-value: 1.5e-07
                            Fer4_7   2 CigCgaCvaaCpvkaie................ldeeenek.gtekveidpek.....ClgCgaCvavCPtg 51 
                                       Ci C  C   Cp+ a++                ld++++ek + ++++i+ +      C   ++CvavCP++
  gi|298675349|ref|YP_003727099.1| 162 CILCAVCHGICPAAARDdkylspaglarawrfqLDPRDSEKsKLQRYNIVDSLsgvwgCDLVYKCVAVCPKK 233
                                       ************9999944444444444433332234333324477777554222222555567******97 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.2       0.5   6.4e+02      33      43 ..      41      59 ..      16      61 .. 0.59
   2 !   12.2   1.6   0.00012      0.16      33      49 ..     155     175 ..     137     177 .. 0.70
   3 !   17.4   5.4   2.8e-06    0.0036       1      49 [.     161     233 ..     161     235 .. 0.94
   4 !    7.3   0.6    0.0041       5.3       6      25 ..     224     243 ..     218     247 .. 0.61

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.5
                            Fer4_9 33 e......eaCig..CgaCv 43
                                      +       aC g  Cg+C+
  gi|298675349|ref|YP_003727099.1| 41 DgslcfrFACRGavCGSCA 59
                                      1555555567444488885 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00012
                            Fer4_9  33 e....eaCigCgaCveaCpkg 49 
                                       +    ++Ci C  C  +Cp  
  gi|298675349|ref|YP_003727099.1| 155 KlekyTNCILCAVCHGICPAA 175
                                       1233478***********976 PP

  == domain 3  score: 17.4 bits;  conditional E-value: 2.8e-06
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase........................eaCigCgaCveaCpkg 49 
                                       +C+ C  C+  Cpa +  ++        ra++                         + C    +Cv++Cpk+
  gi|298675349|ref|YP_003727099.1| 161 NCILCAVCHGICPAAARDDKYLSPAGLARAWRFqldprdseksklqrynivdslsgvWGCDLVYKCVAVCPKK 233
                                       6****************999999999999998899*********************999999999******97 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.0041
                            Fer4_9   6 gaCveaCpagvvvedaaerk 25 
                                        +Cv++Cp++v   +a +++
  gi|298675349|ref|YP_003727099.1| 224 YKCVAVCPKKVPPTKAIKQM 243
                                       35888888877777666665 PP

>> Peptidase_C74  Pestivirus NS2 peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.6e-05     0.071     128     178 ..     128     172 ..      96     189 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.6e-05
                     Peptidase_C74 128 rnetvaswygeeevygmpkimtiikastlsksrhciictvcegrewkggtc 178
                                         ++v  w   ee y   +++       l k   ci+c+vc g       c
  gi|298675349|ref|YP_003727099.1| 128 LVDSVQPWITAEENYDDQHLIEPATQKKLEKYTNCILCAVCHG------IC 172
                                       3577889**********************************87......44 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   1.9         4   5.1e+03       7      10 ..      55      58 ..      43      60 .. 0.80
   2 ?   14.1   1.1   3.9e-05      0.05       3      16 ..     161     174 ..     158     184 .. 0.90
   3 ?    7.9   0.6    0.0038       4.9       6      16 ..     219     232 ..     218     239 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 4
                            Fer4_4  7 CgsC 10
                                      CgsC
  gi|298675349|ref|YP_003727099.1| 55 CGSC 58
                                      8888 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 3.9e-05
                            Fer4_4   3 rCigCgsCvaaCPq 16 
                                       +Ci C +C+ +CP 
  gi|298675349|ref|YP_003727099.1| 161 NCILCAVCHGICPA 174
                                       8************4 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0038
                            Fer4_4   6 gCg...sCvaaCPq 16 
                                       gC+   +Cva+CP 
  gi|298675349|ref|YP_003727099.1| 219 GCDlvyKCVAVCPK 232
                                       7886667******5 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.5       3.3   4.2e+03      55      61 ..      53      59 ..      33      61 .. 0.70
   2 ?   14.0   0.7   5.6e-05     0.072      36      66 ..     143     174 ..     129     175 .. 0.69
   3 ?    6.6   0.5     0.011        15      52      66 ..     215     232 ..     188     233 .. 0.69
   4 ?    4.9   1.3      0.04        51       7      16 ..     225     234 ..     218     249 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3.3
                           Fer4_16 55 tgCdiCq 61
                                      + C+ C+
  gi|298675349|ref|YP_003727099.1| 53 AVCGSCA 59
                                      5566664 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 5.6e-05
                           Fer4_16  36 aekkdlaedeekck.kqeaitgCdiCqdvCPa 66 
                                       ++++ +++ ++k+  k+++++ C++C  +CPa
  gi|298675349|ref|YP_003727099.1| 143 DDQHLIEPATQKKLeKYTNCILCAVCHGICPA 174
                                       3444444445554436899************7 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.011
                           Fer4_16  52 eaitgCd...iCqdvCPa 66 
                                         + gCd   +C++vCP 
  gi|298675349|ref|YP_003727099.1| 215 SGVWGCDlvyKCVAVCPK 232
                                       455788877799999995 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.04
                           Fer4_16   7 kCaevCPtna 16 
                                       kC+ vCP ++
  gi|298675349|ref|YP_003727099.1| 225 KCVAVCPKKV 234
                                       6777777665 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.4       8.2   1.1e+04      87     100 ..      57      75 ..      49      81 .. 0.49
   2 ?   11.1   0.1   0.00026      0.33      44      73 ..     145     174 ..     113     180 .. 0.76
   3 ?    4.9   0.1     0.022        29      57      75 ..     216     234 ..     193     243 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 8.2
                           Fer4_18  87 scllcid.....acdkvme 100
                                       sc+  i+     ac+k+++
  gi|298675349|ref|YP_003727099.1|  57 SCAMLINkvprlACKKLVG 75 
                                       4443333222225555555 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00026
                           Fer4_18  44 kkalkekeerkekgagdcidcescvkvcPt 73 
                                       ++ ++   ++k ++ ++ci c +c  +cP 
  gi|298675349|ref|YP_003727099.1| 145 QHLIEPATQKKLEKYTNCILCAVCHGICPA 174
                                       444555667778899**************7 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.022
                           Fer4_18  57 gagdcidcescvkvcPtgi 75 
                                       g+  c    +cv+vcP ++
  gi|298675349|ref|YP_003727099.1| 216 GVWGCDLVYKCVAVCPKKV 234
                                       5556778889******987 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       3.7   4.7e+03      11      21 ..      55      65 ..      48      87 .. 0.77
   2 ?    7.4   0.2    0.0056       7.1       6      26 ..     160     180 ..     157     202 .. 0.89
   3 ?    4.1   0.1     0.061        79       7      20 ..     219     232 ..     217     244 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3.7
                           Fer4_15 11 cglCvaeapev 21
                                      cg C+ +  +v
  gi|298675349|ref|YP_003727099.1| 55 CGSCAMLINKV 65
                                      88888887665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0056
                           Fer4_15   6 daCigcglCvaeapevfelde 26 
                                       ++Ci c++C   +p   + d+
  gi|298675349|ref|YP_003727099.1| 160 TNCILCAVCHGICPAAARDDK 180
                                       79************8887776 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.061
                           Fer4_15   7 aCigcglCvaeape 20 
                                        C+ +  Cva++p+
  gi|298675349|ref|YP_003727099.1| 219 GCDLVYKCVAVCPK 232
                                       5***********97 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.6      0.47     6e+02      11      16 ..      55      60 ..      54      61 .. 0.87
   2 ?   11.4   3.6   0.00017      0.22       6      22 ..     160     176 ..     158     178 .. 0.89
   3 ?    5.1   1.2     0.017        22      13      20 ..     225     232 ..     224     235 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.47
                                      -THHHH CS
                              Fer4 11 CGaCve 16
                                      CG C++
  gi|298675349|ref|YP_003727099.1| 55 CGSCAM 60
                                      ****85 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00017
                                       TTSSS-THHHHHSTTTE CS
                              Fer4   6 ekCigCGaCvevCPvgA 22 
                                         Ci C  C  +CP  A
  gi|298675349|ref|YP_003727099.1| 160 TNCILCAVCHGICPAAA 176
                                       57************988 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.017
                                       HHHHHSTT CS
                              Fer4  13 aCvevCPv 20 
                                       +Cv vCP 
  gi|298675349|ref|YP_003727099.1| 225 KCVAVCPK 232
                                       6******7 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   1.2       7.6   9.7e+03      11      16 ..      55      60 ..      49      71 .. 0.74
   2 ?   11.4   0.6   0.00021      0.27      39      53 ..     160     174 ..     140     179 .. 0.68
   3 ?    4.2   0.2     0.037        47      43      52 ..     219     231 ..     202     239 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 7.6
                           Fer4_21 11 CgkCli 16
                                      Cg+C++
  gi|298675349|ref|YP_003727099.1| 55 CGSCAM 60
                                      777765 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00021
                           Fer4_21  39 deCvGCnlCssvCPv 53 
                                        +C+ C++C+ +CP 
  gi|298675349|ref|YP_003727099.1| 160 TNCILCAVCHGICPA 174
                                       467777777777774 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.037
                           Fer4_21  43 GCnl...CssvCP 52 
                                       GC+l   C++vCP
  gi|298675349|ref|YP_003727099.1| 219 GCDLvykCVAVCP 231
                                       7876666*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1458.05
//
Query:       gi|298675350|ref|YP_003727100.1|  [L=558]
Description: succinate dehydrogenase or fumarate reductase flavoprotein subunit [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     1e-114  383.9   0.0   1.3e-114  383.6   0.0    1.1  1  FAD_binding_2   FAD binding domain
    2.6e-41  140.6   0.8    4.3e-41  139.9   0.8    1.4  1  Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
      4e-09   36.1   2.0    0.00018   20.8   0.1    3.8  4  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    2.5e-06   27.3   1.7    9.5e-06   25.4   1.6    1.9  1  DAO             FAD dependent oxidoreductase
    3.1e-06   26.1   0.3    0.00017   20.4   0.5    2.7  3  HI0933_like     HI0933-like protein
    1.1e-05   24.8   4.5      5e-05   22.5   2.9    2.6  2  GIDA            Glucose inhibited division protein A
    1.8e-05   24.3   0.7    4.9e-05   22.9   0.4    1.8  2  FAD_oxidored    FAD dependent oxidoreductase
     0.0012   19.3   1.3      0.017   15.7   0.1    2.8  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0015   17.9   0.3     0.0044   16.3   0.1    1.8  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
     0.0016   18.6   0.1     0.0057   16.8   0.1    2.0  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
     0.0034   16.7   0.3     0.0053   16.0   0.3    1.3  1  FAD_binding_3   FAD binding domain
     0.0053   16.1   0.1     0.0092   15.3   0.1    1.4  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
      0.019   15.3   0.4        1.5    9.2   0.0    3.1  3  GARS_C          Phosphoribosylglycinamide synthetase, C domai
      0.024   14.2   0.0        1.8    8.2   0.1    2.6  2  DUF374          Domain of unknown function (DUF374)
      0.029   13.6   1.5      0.089   12.0   0.2    2.4  3  Thi4            Thi4 family
      0.088   11.8   0.3       0.14   11.2   0.3    1.2  1  Lycopene_cycl   Lycopene cyclase protein


Domain annotation for each model (and alignments):
>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  383.6   0.0  1.1e-117  1.3e-114       1     417 []       5     378 ..       5     378 .. 0.99

  Alignments for each domain:
  == domain 1  score: 383.6 bits;  conditional E-value: 1.1e-117
                                       SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHTTT-S CS
                     FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidavlspeqkkagikdspelhrtdtlkaldela 77 
                                       DviViG+Gl+GL+AAlea+++G++va+++k+++ +++++++qGgi+a+l       g++ds+e+h++dt+k++d+la
  gi|298675350|ref|YP_003727100.1|   5 DVIVIGGGLSGLRAALEAHKKGADVAIISKVPPIRSHSVAAQGGINASL-------GDDDSWEAHAWDTVKGSDYLA 74 
                                       9************************************************.......778****************** PP

                                       -HHHHHHHHHTHHHHHHHHHHTT----BCCTSSB-EEE-TT-SSTEEEE-.STT-......HHHHHHHHHHHHHHTC CS
                     FAD_binding_2  78 dqplveafveaapeavdeLeelgvpfsrtedgpvdvrelGglsatartlhdaadarretlvtghallarlvesarka 154
                                       dq++ve+++++a e v e+ ++g  fsrt+dg++++r++Gg   + rt++ a+d+      tgh+ll++l e+++ka
  gi|298675350|ref|YP_003727100.1|  75 DQDAVEILCKEATEIVLEMDNWGTSFSRTQDGKIAQRPFGGAGFP-RTCY-AGDK------TGHNLLYTLQEQVLKA 143
                                       *********************************************.****.****......**************** PP

                                       TEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG..........GSSSBSSGTT-S-HHHH CS
                     FAD_binding_2 155 gvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgrallkellgaaaeaettnapavtGdgla 231
                                       g+++++++ +++L++++gr+tG v+ n  +++   ++ k +v+atgG+gr           ++ +tn  ++ G g++
  gi|298675350|ref|YP_003727100.1| 144 GIKVHPEWMVTRLVTDGGRCTGFVAINIFNSEPDVFKVKITVIATGGYGR----------IYKRSTNSIINRGFGIG 210
                                       ****************************9999999***************..........***************** PP

                                       HHHCTTSSEES..TT-EEEEEEEET....TTTBB--THHHHTT-EEE-TTSSBTH.......GGGS-HHHHHHHHH. CS
                     FAD_binding_2 232 lalragaalnddrmeevqfhPtslvpirdgsgiLitealrgeGgilvdkdGrrFm.......nelasrdvvsraile 301
                                       la+rag++l+d  me+vqfhPt l      s+iLite++rgeGg+l++k+ +rFm        ela+rd+v+rai  
  gi|298675350|ref|YP_003727100.1| 211 LAYRAGVPLQD--MEFVQFHPTTLW----DSNILITEGVRGEGGYLYNKNHQRFMksyapesIELAPRDIVARAIQ- 280
                                       ***********..************....9**********************************************. PP

                                       HHHHTTTS..CCBEEEE-TT.SSHHHHHHHSHHHHHHHHHCCT......S-TTTSEEE.......EEEEEEEES-EE CS
                     FAD_binding_2 302 keiaeggs..eanvyldashgldaegleatleaineeaangldkdfgrgidpadrpipgpfyavkvvpaqhytmgGv 376
                                       +ei+eg++  +++v ld++h ld++ ++++l +i+e+ +++++      +dp ++pip       v p+qhy+mgG+
  gi|298675350|ref|YP_003727100.1| 281 TEINEGRGisNEYVHLDITH-LDPQLIKERLSGIREISMDFAG------VDPIKEPIP-------VQPGQHYSMGGI 343
                                       **********99********.**********************......*********.......************ PP

                                       EBETTSBESTTEEESSBTEEE-STCEESSSSTTS--TTHHH CS
                     FAD_binding_2 377 etdengrvldadgqpipGLYAaGevaaggvhganrlgGnsl 417
                                           ng++      pi+GLYA+Ge+a+ +vhganrlgGnsl
  gi|298675350|ref|YP_003727100.1| 344 LSSINGKT------PIDGLYAVGECACISVHGANRLGGNSL 378
                                       ********......*************************98 PP

>> Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.9   0.8   3.9e-44   4.3e-41       1     128 []     433     558 .]     433     558 .] 0.98

  Alignments for each domain:
  == domain 1  score: 139.9 bits;  conditional E-value: 3.9e-44
                                       .HHHHHHHHHHSSSSB-HHHHHHHHHHHHHHHHHHTTB--S---SSS-HHHHHHHHHHHHHHHHHHHHHHHHH--S- CS
                    Succ_DH_flav_C   1 rkeLgkimqkkvgvfRteegLkealkelkelrerlknvkvtdkskvaNqelvealelanllelAeaiaksAlaRkES 77 
                                       r+eL++imq+kvgvfR++e+L++a++++k+l+ r++++kv+++ k +N el++a+el+ ++++A +ia++AlaR+ES
  gi|298675350|ref|YP_003727100.1| 433 RNELKNIMQEKVGVFRNHENLEHAIEDIKNLKYRAQKIKVKSRAKSFNLELLDAIELKGMVDIAHVIATGALARQES 509
                                       79*************************************************************************** PP

                                       BTTBEBTTS-SEETTT-SEEEEE...TT-SS-EEEEEE--GGG--S---SS CS
                    Succ_DH_flav_C  78 rGaHaredfperdDenwlkhtlasldaakeeveleyepveletlkpkeRsY 128
                                       rGaH+r+df+erdD+nw kht+a+++++   ++ley++v+++ +  ++R+Y
  gi|298675350|ref|YP_003727100.1| 510 RGAHYRTDFTERDDNNWTKHTIAYYTPQ--GPRLEYRDVTITSFYSEKREY 558
                                       ***********************88866..9*************9999999 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   1.6e-07   0.00018       1      30 [.       4      33 ..       4      86 .. 0.90
   2 !    6.8   0.0     0.003       3.4     182     236 ..     129     189 ..     120     201 .. 0.88
   3 !    5.3   0.0    0.0087       9.8     254     279 ..     339     368 ..     319     397 .. 0.77
   4 ?   -0.9   0.1      0.68   7.6e+02      48     110 ..     424     504 ..     385     509 .. 0.52

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.6e-07
                                      CSEEEE--SHHHHHHHHHHHHHTS-EEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlve 30
                                      +dv+viGgG  Gl+aal++ ++ga+v++++
  gi|298675350|ref|YP_003727100.1|  4 HDVIVIGGGLSGLRAALEAHKKGADVAIIS 33
                                      59**************************94 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.003
                                       -HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE......EEEEEETTSCEEEESEEEE-S- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 182 dkelsaaleealekeGvevklgtsvkeidgnge......klevvledgeeidadlvvvavG 236
                                       +++l  +l+e++ k G++v+ + +v+++  +g        +   +++ ++++++  v+a+G
  gi|298675350|ref|YP_003727100.1| 129 GHNLLYTLQEQVLKAGIKVHPEWMVTRLVTDGGrctgfvAINIFNSEPDVFKVKITVIATG 189
                                       566677899*********************99989987666699****************9 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.0087
                                       ETTEEE--TTSBESSTTEEE-GGGC....T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx....x RF
                       Pyr_redox_2 254 erggivvdeflrtnvpgiyaiGDva....g 279
                                       + ggi+   +++t ++g+ya+G +a    +
  gi|298675350|ref|YP_003727100.1| 339 SMGGILSSINGKTPIDGLYAVGECAcisvH 368
                                       56888888899**************55551 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 0.68
                                       HHHHHHHHHH....................HHHHCHHHHCCCCHC.CTCEEEEESCEEEEETEEECTCEEEEEESEE CS
                                       xxxxxxxxxx....................xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  48 gvaedaeias....................evvkklnqgielllg.eevvkidpgkkkvklekkkegdeekiaydkl 103
                                       +++ed  +++                    e      ++i++l+  ++++k+   +k + le ++  + + + + + 
  gi|298675350|ref|YP_003727100.1| 424 ESGEDFATVRnelknimqekvgvfrnhenlE---HAIEDIKNLKYrAQKIKVKSRAKSFNLELLDAIELKGMVDIAH 497
                                       4444444333444444444444443332221...1112222222223366665555666664444444444555667 PP

                                       EE---EE CS
                                       xxxxxxx RF
                       Pyr_redox_2 104 vlAtGss 110
                                       v+AtG+ 
  gi|298675350|ref|YP_003727100.1| 498 VIATGAL 504
                                       7888875 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   1.6   8.5e-09   9.5e-06       1     182 [.       5     166 ..       5     207 .. 0.58

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 8.5e-09
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSS.STHHSTHHHHHHHHHHHHHHHHHHHH CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsgl.rylpeaselarlslealeelreleee 74 
                                       dv++iGGG  Gl +A+e+ ++g  V+++ k + +    S +++g + ++l ++  +       + ++++  + l+++
  gi|298675350|ref|YP_003727100.1|   5 DVIVIGGGLSGLRAALEAHKKGadVAIISKVPPIR-SHSVAAQGGINASLgDDDSWE----AHAWDTVKGSDYLADQ 76 
                                       8*****************9999*********7777.999999999999883323322....5555555555666666 PP

                                       HSSTTSEEEEEEEEEESSHHHHHHHHHHHHHHHHTTTTEEEEEHHHHHHHSTTSTTTSEEEEETTEEEEEHHHHHHH CS
                               DAO  75 lgididyrrtGllslaadeeelealdkllallleagldaelldaeevrelepalpgllgalfypdtgqvdpakltaa 151
                                        +++i  ++ + ++l+     ++++  ++ + ++  +  + + +    + +p        ++  d  +   + l+  
  gi|298675350|ref|YP_003727100.1|  77 DAVEILCKEATEIVLE-----MDNWGTSFSRTQDGKIAQRPFGG----AGFP------RTCYAGD-KT--GHNLLYT 135
                                       6777777777777774.....55554444443211111122222....1222......2222112.22..3355555 PP

                                       HHHHHHHTT-EEEESECEEEEEEEETCEEEE CS
                               DAO 152 laraaealGveilegtevtgleeedgkvwgv 182
                                       l++++ ++G++++ +  vt+l  ++g+ +g 
  gi|298675350|ref|YP_003727100.1| 136 LQEQVLKAGIKVHPEWMVTRLVTDGGRCTGF 166
                                       6666666666666666666654444555555 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.5   1.5e-07   0.00017       1      34 [.       4      37 ..       4      53 .. 0.83
   2 ?    2.1   0.0     0.054        61     105     165 ..     126     191 ..     120     227 .. 0.79
   3 ?   -1.7   0.0      0.78   8.8e+02     363     408 ..     345     390 ..     267     391 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.5e-07
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSS CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakk 34
                                      +dviviGgG +Gl aA++a+k+g++V+++ k + 
  gi|298675350|ref|YP_003727100.1|  4 HDVIVIGGGLSGLRAALEAHKKGADVAIISKVPP 37
                                      59***************************98754 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.054
                                       T.-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE....EEEEE...TTEEEEESEEEE----S CS
                       HI0933_like 105 sdkaedivdallkelkeagvklrletevksvekeedg...kfrvkt..kseeeleadklvlAtGGl 165
                                       +++ ++++ +l++++ +ag+k++ e  v+++ ++ ++   ++ +++  ++ + ++ + +v+AtGG 
  gi|298675350|ref|YP_003727100.1| 126 DKTGHNLLYTLQEQVLKAGIKVHPEWMVTRLVTDGGRctgFVAINIfnSEPDVFKVKITVIATGGY 191
                                       5667889999********************9776654111456666533667899999******95 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.78
                                       GGB-TTT-BBTTSTTEEE-GGG..BSEEE-..TTTHHHHHHHHHHHHHHH CS
                       HI0933_like 363 kevssktmeskkvpgLffaGEv..lDvegv..tGGynlqaAwasgyaAGk 408
                                       ++++ kt     + gL+ +GE+  + v+g   +GG  l   ++ g  AG+
  gi|298675350|ref|YP_003727100.1| 345 SSINGKTP----IDGLYAVGECacISVHGAnrLGGNSLLDTLVFGKRAGQ 390
                                       45555554....89999999963367777433788777777777777776 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   2.9   4.5e-08     5e-05       1     152 [.       5     192 ..       5     211 .. 0.57
   2 ?   -1.4   0.0      0.82   9.2e+02      91     152 ..     430     505 ..     416     538 .. 0.61

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 4.5e-08
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEE............................ES-GGGTT--SSSSEEE-T.. CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGakvlLi............................thkldtiaelsCnpsiggi.. 47 
                                       dviViGgG++G+ AAl+a ++Ga+v++i                            +h  dt+              
  gi|298675350|ref|YP_003727100.1|   5 DVIVIGGGLSGLRAALEAHKKGADVAIIskvppirshsvaaqgginaslgdddsweAHAWDTVKG---------Sdy 72 
                                       8***************************9999877666666666666555555555333333333.........122 PP

                                       ............THHHHHHHHHHHT-SHHHHHHHHEEEEEEESTTS-CCC-EEEEEE-HHHHHHHHHHHHHT...ST CS
                              GIDA  48 ............akgllvrEidalggliikaadkagiqfrilNrskGpavralraqvdrelyskevteklen...ep 109
                                                    + ++v E+d+ g    ++ d +  q        G     +  + d+    +++  +l++   + 
  gi|298675350|ref|YP_003727100.1|  73 ladqdaveilckEATEIVLEMDNWGTSFSRTQDGKIAQRPFG----GAGFPRTCYAGDKTG--HNLLYTLQEqvlKA 143
                                       222222233455566677777777777777666665544442....222222222444433..33333333322225 PP

                                       TEEEE.ES-EEEEEECTTEEEE.....EEETTS-EEEECEEEE--TT-B CS
                              GIDA 110 nleii.eeeveeliveekkvkg.....vvtedgetikakavviatGtfl 152
                                        +++  e +v++l+++ ++++g     +  ++  ++k k++viatG + 
  gi|298675350|ref|YP_003727100.1| 144 GIKVHpEWMVTRLVTDGGRCTGfvainIFNSEPDVFKVKITVIATGGYG 192
                                       6777623467777666655555322224456667777777777777754 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.82
                                       EE-HHHHHHHHHHHH...HTSTTEEEEES-EEEEEECT......TEEEEEEETTS-EEEEC.........EEEE--T CS
                              GIDA  91 qvdrelyskevtekl...enepnleiieeeveelivee......kkvkgvvtedgetikak.........avviatG 149
                                       ++ r++ ++ ++ek+   +n++nle   e +++l+ +       ++ k   +e                 a viatG
  gi|298675350|ref|YP_003727100.1| 430 ATVRNELKNIMQEKVgvfRNHENLEHAIEDIKNLKYRAqkikvkSRAKSFNLELLD----AielkgmvdiAHVIATG 502
                                       55666677777776533356777777777777776655332222112222222222....12222445557777777 PP

                                       T-B CS
                              GIDA 150 tfl 152
                                       +  
  gi|298675350|ref|YP_003727100.1| 503 ALA 505
                                       744 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.4   4.4e-08   4.9e-05       1      30 [.       5      34 ..       5      38 .. 0.95
   2 ?   -1.9   0.0       1.4   1.6e+03      92     126 ..     135     169 ..     128     189 .. 0.67

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 4.4e-08
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLvee 30
                                      Dv+V+GGg++G+ AA+ A ++Ga v+++++
  gi|298675350|ref|YP_003727100.1|  5 DVIVIGGGLSGLRAALEAHKKGADVAIISK 34
                                      9**************************987 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.4
                      FAD_oxidored  92 vleemlaeagvtvllntrlvevekegkriesvtve 126
                                       +l+e + +ag++v  + ++++ +++g+r+++ ++ 
  gi|298675350|ref|YP_003727100.1| 135 TLQEQVLKAGIKVHPEWMVTRLVTDGGRCTGFVAI 169
                                       567777788****************9886654433 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   1.5e-05     0.017       2      33 ..       6      37 ..       5      44 .. 0.89
   2 ?    1.2   0.0      0.48   5.4e+02      46      71 ..     136     161 ..     126     169 .. 0.85
   3 ?   -2.9   0.1       9.4   1.1e+04      23      57 ..     442     472 ..     428     478 .. 0.55

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.5e-05
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdk 33
                                      v+v+GgG++gl +A ++++ g++V ++   + 
  gi|298675350|ref|YP_003727100.1|  6 VIVIGGGLSGLRAALEAHKKGADVAIISKVPP 37
                                      89************************987665 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.48
                                       HHHHHHHTTEEEECSEEEEEEEEETT CS
                         Pyr_redox  46 lqeklekngievllntkveeiegsed 71 
                                       lqe++ k gi+v+ +  v+++++++ 
  gi|298675350|ref|YP_003727100.1| 136 LQEQVLKAGIKVHPEWMVTRLVTDGG 161
                                       7999999********99999998875 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 9.4
                                       SEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEE CS
                         Pyr_redox  23 kkVtvversdkllrllDeeaskilqeklekngiev 57 
                                        kV v+ ++++l     +++++i   k ++++i+v
  gi|298675350|ref|YP_003727100.1| 442 EKVGVFRNHENLE----HAIEDIKNLKYRAQKIKV 472
                                       4455555554444....555555555555555555 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   3.9e-06    0.0044     165     203 ..       4      42 ..       2      53 .. 0.87
   2 ?   -3.5   0.0       4.2   4.7e+03     121     136 ..     177     192 ..     130     197 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.9e-06
                       Pyr_redox_3 165 qkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekee 203
                                       ++v+ViGg+ S+  aAle  +kga+V ++ +  +i++++
  gi|298675350|ref|YP_003727100.1|   4 HDVIVIGGGLSGLRAALEAHKKGADVAIISKVPPIRSHS 42 
                                       589*************************99988887764 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.2
                       Pyr_redox_3 121 etyeAkkviiAtGefd 136
                                       ++++ k  +iAtG ++
  gi|298675350|ref|YP_003727100.1| 177 DVFKVKITVIATGGYG 192
                                       4666777788888887 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   5.1e-06    0.0057       1      31 [.       8      38 ..       8      71 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.1e-06
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrl 31
                                      ++G+GlsGl aA +++k+g+dv ++ k + +
  gi|298675350|ref|YP_003727100.1|  8 VIGGGLSGLRAALEAHKKGADVAIISKVPPI 38
                                      8***********************9886655 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.3   4.7e-06    0.0053       2      34 ..       4      36 ..       3      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.7e-06
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrs 34
                                       dV+++G+G++Gl +al+ +++G +v ++ k  
  gi|298675350|ref|YP_003727100.1|  4 HDVIVIGGGLSGLRAALEAHKKGADVAIISKVP 36
                                      59***************************9975 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   8.2e-06    0.0092      30      60 ..       5      35 ..       3      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8.2e-06
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESS CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvr 60
                                       v+viGgG  Gl A+  a++ ga+V ++ + 
  gi|298675350|ref|YP_003727100.1|  5 DVIVIGGGLSGLRAALEAHKKGADVAIISKV 35
                                      599**********************998654 PP

>> GARS_C  Phosphoribosylglycinamide synthetase, C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0013       1.5      10      48 ..     117     169 ..     115     175 .. 0.80
   2 ?   -1.5   0.0       2.9   3.2e+03       5      21 ..     185     203 ..     183     245 .. 0.56
   3 ?    2.3   0.1      0.19   2.1e+02      55      77 ..     496     518 ..     484     521 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0013
                                       TTTSS--ST-EEBS.......TTEEEEESSEE.........EEE-SSEEEEEEEE CS
                            GARS_C  10 GYPgsyekgkeitg.......egvkvfhagtk.........lvtsGGRvlavvav 48 
                                       G+P +   g++  g       +  +v+ ag k         lvt+GGR+ + va+
  gi|298675350|ref|YP_003727100.1| 117 GFPRTCYAGDKT-GhnllytlQ-EQVLKAGIKvhpewmvtrLVTDGGRCTGFVAI 169
                                       778887777777.557778854.569****888888888889*******999986 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.9
                                       EEEETTTTSS--..ST-EE CS
                            GARS_C   5 vlaskGYPgsye..kgkei 21 
                                       v+a +GY   y+  +++ i
  gi|298675350|ref|YP_003727100.1| 185 VIATGGYGRIYKrsTNSII 203
                                       8899999888773223333 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.19
                                       HHHHHHHHHTTCB-TTEE--STT CS
                            GARS_C  55 ArakayeavkkikfeglfyRkDI 77 
                                       A+  a  a+++ +  g++yR+D 
  gi|298675350|ref|YP_003727100.1| 496 AHVIATGALARQESRGAHYRTDF 518
                                       66778889999999********6 PP

>> DUF374  Domain of unknown function (DUF374)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1    0.0016       1.8      40      65 ..      11      36 ..       9      38 .. 0.91
   2 ?    3.0   0.0     0.068        76      12      56 ..     100     145 ..      94     148 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0016
                            DUF374 40 ggaealremlralkegesvaitpDgP 65
                                      gg ++lr++l+a k+g +vai+  +P
  gi|298675350|ref|YP_003727100.1| 11 GGLSGLRAALEAHKKGADVAIISKVP 36
                                      899******************97776 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.068
                            DUF374  12 iSrsrDGeliarvlerlGiktirGSsskggaealremlral.kege 56 
                                        Sr +DG+++ r +   G+     +++k g++ l  + +++ k+g 
  gi|298675350|ref|YP_003727100.1| 100 FSRTQDGKIAQRPFGGAGFPRTCYAGDKTGHNLLYTLQEQVlKAGI 145
                                       69**************999999999999999999888877656665 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   7.9e-05     0.089      18      48 ..       4      33 ..       1      51 [. 0.85
   2 ?   -2.0   0.0       1.5   1.7e+03     109     167 ..     142     189 ..     131     201 .. 0.50
   3 ?   -2.1   0.0       1.6   1.8e+03     212     232 ..     353     374 ..     348     376 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.9e-05
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEE CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvaile 48
                                       Dv+++G+G sGL aa    kk +  vai+ 
  gi|298675350|ref|YP_003727100.1|  4 HDVIVIGGGLSGLRAALEAHKK-GADVAIIS 33
                                      7*****************9999.88999886 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.5
                                       TSTTEEEEESEEEEEEEEETBTEEEEEEEEEHHHHTCTTTSS.-B-EEEEEEEEEE--G CS
                              Thi4 109 qlanvkllnavaveDlivregegvaGvvinwtlvelahdtqscvDPlvirakvvvdatG 167
                                       + a++k+    +v  l++       G ++ + ++++        +P v + k+ v atG
  gi|298675350|ref|YP_003727100.1| 142 K-AGIKVHPEWMVTRLVTDG-----GRCTGFVAINIFN-----SEPDVFKVKITVIATG 189
                                       4.555555444444444433.....3333333333332.....3445555555555554 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.6
                                       ETTEEE-T.HHHHHHHT-EB-- CS
                              Thi4 212 vpnlyvaG.mevaevdganRmG 232
                                       +++ly+ G  +   v+ganR+G
  gi|298675350|ref|YP_003727100.1| 353 IDGLYAVGeCACISVHGANRLG 374
                                       68999887357789******99 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   0.00012      0.14       1      32 [.       5      34 ..       5      46 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvliea 32
                                      Dv+viG+G+ gl+ A +    k+g  v +i  
  gi|298675350|ref|YP_003727100.1|  5 DVIVIGGGLSGLRAALEA--HKKGADVAIISK 34
                                      9*****************..999999999943 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (558 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.73u 0.35s 00:00:01.08 Elapsed: 00:00:00.52
# Mc/sec: 3248.40
//
Query:       gi|298675351|ref|YP_003727101.1|  [L=462]
Description: fumarate lyase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.2e-99  331.9   0.0    5.3e-99  331.5   0.0    1.1  1  Lyase_1      Lyase
    4.9e-20   71.7   0.7    4.9e-20   71.7   0.7    2.0  2  FumaraseC_C  Fumarase C C-terminus


Domain annotation for each model (and alignments):
>> Lyase_1  Lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  331.5   0.0    6e-103   5.3e-99       1     312 []      10     340 ..      10     340 .. 0.98

  Alignments for each domain:
  == domain 1  score: 331.5 bits;  conditional E-value: 6e-103
                                       CEEEEETCHHHHHHHHHHHHHGGGHHHHHC.....HHHHHHHHHHHTTSST....HHHHHHHHHHHHHHHCHCHHCG CS
                           Lyase_1   1 grftvkadklmgiftersrenfrlseedik.....alaalkkaaakanvdl....keeaaaiikaldevleegkldd 68 
                                       g ++v+ d ++g +t+r+  nf++s+++       a a++k a ak n+++     e+ + ii+a++ev++ gk +d
  gi|298675351|ref|YP_003727101.1|  10 GDVEVPDDVYYGPQTARAVINFKISNHQLPvefirAQAVIKWASAKSNIRTgklnPEIGNTIISAASEVRD-GKFND 85 
                                       67899********************77666889999***********************************.***** PP

                                       GHHHBSSSSSHHHHHHHHHHHHHH....HHTT......HSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHH CS
                           Lyase_1  69 qfvlkviqegsgtavnmnlnevig....ellg......ekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpal 135
                                       qfv++ +q g+gt+ nmn+nevi+    e+lg        ++pnd+v+++qSsnD+  Ta+++a+ ++l+ +L+p l
  gi|298675351|ref|YP_003727101.1|  86 QFVVDAFQSGAGTSQNMNANEVIAnralEILGyekgryDIIHPNDHVNMSQSSNDTTHTAIHIAAMESLNSRLIPIL 162
                                       *************************9999999****9999************************************* PP

                                       HHHHHHHHHHHHHTTT-EEEEEETTEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCC CS
                           Lyase_1 136 eqLidalkekakefkdvvkiGrThlqdAtPvtlgqelsayaealerdrerlkellkrllvellgggtavgtglnadp 212
                                       +qL + +k k+ ef++vvk+GrThlqdA+P+tlgqe+s+y ++le+ +erl ++    l+el++ggtavgtglna  
  gi|298675351|ref|YP_003727101.1| 163 KQLYNDFKTKSAEFNNVVKPGRTHLQDAVPITLGQEFSGYTRMLEMGIERLYNSI-DRLAELNMGGTAVGTGLNAPE 238
                                       *******************************************************.888999999************ PP

                                       THHHHHHHHHHHHHCST.EESSSHHHHHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHHTSTT.TSSEEEEGCCTSSC CS
                           Lyase_1 213 efaelvakelakvtglp.vkapnsfeavsdrDavvellgalkllatsLskfaeDlrllssge.aglvelslaesepG 287
                                        f    ++e++++tgl    a+n fea+++   ++el+++l+ la+sL+k+a D rl+ssg+ + l+e++l++ +pG
  gi|298675351|ref|YP_003727101.1| 239 GFGYIAVEEVNRITGLDfKLADNYFEATQSAESILELSSVLRGLAVSLIKIADDFRLFSSGPrTALGEIQLPAVQPG 315
                                       ***************************************************************************** PP

                                       -TTSTTTEBTHHHHHHHHHHHHHHH CS
                           Lyase_1 288 SSiMPgKvNPvqlElltgvagrvvG 312
                                       SSiMPgKvNPv++E+l++v+ +v+G
  gi|298675351|ref|YP_003727101.1| 316 SSIMPGKVNPVMAEMLNMVCYQVMG 340
                                       ************************9 PP

>> FumaraseC_C  Fumarase C C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.1         2   1.8e+04       8      13 ..     115     120 ..     114     121 .. 0.81
   2 !   71.7   0.7   5.5e-24   4.9e-20       1      54 []     406     459 ..     406     459 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2
                                       HHHHHH CS
                       FumaraseC_C   8 hIGYek 13 
                                       ++GYek
  gi|298675351|ref|YP_003727101.1| 115 ILGYEK 120
                                       68***8 PP

  == domain 2  score: 71.7 bits;  conditional E-value: 5.5e-24
                                       GGGGGHHHHHHHHHHHHHHHHHHHT--HHHHHHHTT-.-HHHHHHHT-HHHHH. CS
                       FumaraseC_C   1 LVTaLnphIGYekAakIAkeAlkegktlreavlelgllteeeldelldpekMtg 54 
                                       L+TaL+p+IGYekAa++A +A++egkt+r+++le+ ll e e+delld  kMtg
  gi|298675351|ref|YP_003727101.1| 406 LATALAPKIGYEKAAEVAYQAYNEGKTVRQVILEKDLLVESEVDELLDLIKMTG 459
                                       79**************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2784.79
//
Query:       gi|298675352|ref|YP_003727102.1|  [L=116]
Description: hypothetical protein Metev_1452 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-06   28.2   0.0    1.6e-06   27.7   0.0    1.2  1  Cupin_2          Cupin domain
  ------ inclusion threshold ------
      0.027   14.4   0.0      0.029   14.3   0.0    1.1  1  MannoseP_isomer  Mannose-6-phosphate isomerase


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   1.8e-10   1.6e-06       2      69 ..      32      99 ..      31     101 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.8e-10
                                      EEEEETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEE CS
                           Cupin_2  2 lvelppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllv 69
                                      l  ++ G+s p h+H + + ++ V++Ge+++ vdge+v +++ +++ ++  ++  + Ntg+  + l+v
  gi|298675352|ref|YP_003727102.1| 32 LLNIASGQSLPNHTHFDCTVLLQVIKGEAVVNVDGEPVSMNESELLQIDGSEEMSVDNTGQNVLILYV 99
                                      678999******************************************************88777765 PP

>> MannoseP_isomer  Mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.2e-06     0.029      66     132 ..      31      97 ..       3     114 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.2e-06
                   MannoseP_isomer  66 kritvkPgeklslqkhhhraehWvvvkGtakvtvddevlllkenestyiplgaihrlenpGkiplel 132
                                         + +  g+ l  + h+  +    v+kG a v+vd e + ++e+e   i  ++  +++n G+  l l
  gi|298675352|ref|YP_003727102.1|  31 FLLNIASGQSLPNHTHFDCTVLLQVIKGEAVVNVDGEPVSMNESELLQIDGSEEMSVDNTGQNVLIL 97 
                                       5577888999999999999999***************************************988866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 730.62
//
Query:       gi|298675353|ref|YP_003727103.1|  [L=334]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-23   81.6   0.1    1.3e-22   79.4   0.0    2.3  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0012   19.0   0.8     0.0027   17.9   0.8    1.5  1  OrfB_IS605      Probable transposase
  ------ inclusion threshold ------
      0.027   14.1   0.2      0.054   13.1   0.2    1.5  1  Zn_ribbon_17    Zinc-ribbon, C4HC2 type
      0.071   13.3   0.1        0.2   11.9   0.1    1.7  1  zf-RING_7       C4-type zinc ribbon domain
       0.15   12.2   1.6       0.33   11.1   1.6    1.6  1  UPF0547         Uncharacterised protein family UPF0547


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       1.5   5.4e+03      33      49 ..     214     231 ..     209     235 .. 0.56
   2 !   79.4   0.0   3.8e-26   1.3e-22       1      68 [.     244     309 ..     244     310 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.5
                    OrfB_Zn_ribbon  33 eCgsknke.alsgrtfkC 49 
                                       +Cg ++++ +  ++  kC
  gi|298675353|ref|YP_003727103.1| 214 NCGIRMENlKGIRDSAKC 231
                                       566666664444444444 PP

  == domain 2  score: 79.4 bits;  conditional E-value: 3.8e-26
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       f++l+ +leyka+  G+k+e v+p+yTS++Cs+ g+ + +  +g++fkCp+Cg++ ++D nAa+Ni+ 
  gi|298675353|ref|YP_003727103.1| 244 FYQLQFMLEYKARLLGVKIEFVDPEYTSQDCSRYGYLDIR--NGELFKCPHCGHVDHADANAAFNIAM 309
                                       899*************************************..************************96 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.8   7.6e-07    0.0027       4     107 ..     119     214 ..     108     225 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 7.6e-07
                        OrfB_IS605   4 vevevelpkpkgnkaagiDlGin.nLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklar 79 
                                       v+v +  ++ ++++ +g+Dl+   ++a++++ ++  + + g++++    ++++ +++lq k k         +k++ 
  gi|298675353|ref|YP_003727103.1| 119 VTVHE-REQIEPENYLGVDLNTTgHIAVMSNPKTGKIWKLGKKAQHIHLKYKNDRRKLQVKGKY--------KKVKQ 186
                                       33333.88999**********87367777777766677889******************98443........47999 PP

                        OrfB_IS605  80 lhrkrsrrrkhllhklathliktlkevg 107
                                       + ++ sr++++l +k+++++++t  +++
  gi|298675353|ref|YP_003727103.1| 187 VNDRESRIVRDLNQKISSRIVETAAANN 214
                                       **********************988775 PP

>> Zn_ribbon_17  Zinc-ribbon, C4HC2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   1.5e-05     0.054      15      33 ..     284     302 ..     270     316 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.5e-05
                      Zn_ribbon_17  15 kgrvvlcgvCeHvlHasCa 33 
                                       +g ++ c+ C+Hv Ha+  
  gi|298675353|ref|YP_003727103.1| 284 NGELFKCPHCGHVDHADAN 302
                                       4789************965 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   5.4e-05       0.2      15      30 ..     280     294 ..     278     294 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.4e-05
                                       HHHCCSTB-EE-TTT- CS
                         zf-RING_7  15 selragdevvtCpeCG 30 
                                        ++r+g e+++Cp+CG
  gi|298675353|ref|YP_003727103.1| 280 LDIRNG-ELFKCPHCG 294
                                       578888.8*******9 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.6   9.3e-05      0.33      16      25 ..     289     298 ..     288     299 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.3e-05
                           UPF0547  16 fCphCGyvFq 25 
                                       +CphCG+v+ 
  gi|298675353|ref|YP_003727103.1| 289 KCPHCGHVDH 298
                                       7******985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1410  (0.0786435); expected 358.6 (0.02)
Passed bias filter:                      648  (0.0361426); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2269.64
//
Query:       gi|298675354|ref|YP_003727104.1|  [L=712]
Description: signal transduction histidine kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-39  134.3   2.0    3.8e-18   65.6   0.0    3.7  3  PAS_3        PAS fold
    2.9e-29  101.0   3.9    8.4e-29   99.5   3.9    1.9  1  HisKA_2      Histidine kinase
    8.8e-25   87.0   5.2    5.3e-12   45.9   0.0    5.3  6  PAS_9        PAS domain
    7.2e-20   71.1   0.0    1.4e-10   41.2   0.0    5.0  5  PAS          PAS fold
    3.6e-18   65.8   0.0    5.5e-09   36.3   0.0    4.5  5  PAS_4        PAS fold
    2.8e-14   53.2   0.0    1.1e-06   28.8   0.1    2.8  2  PAS_11       PAS domain
    9.6e-10   38.3   0.0      0.008   16.2   0.0    4.2  4  PAS_8        PAS domain
    1.3e-07   32.1   0.0    6.8e-07   29.8   0.0    2.2  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    3.9e-06   27.5   0.2      8e-06   26.5   0.2    1.5  1  HWE_HK       HWE histidine kinase
     0.0091   15.8   0.0      0.024   14.4   0.0    1.6  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
  ------ inclusion threshold ------
      0.022   14.7   0.0      0.047   13.7   0.0    1.5  1  HATPase_c_2  Histidine kinase-like ATPase domain
       0.03   14.4   0.7       0.58   10.3   0.1    2.8  2  DnaB         DnaB-like helicase N terminal domain
       0.25   11.8   2.8       0.78   10.2   2.7    1.8  1  MitMem_reg   Maintenance of mitochondrial structure and funct


Domain annotation for each model (and alignments):
>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0057       7.8       2      41 ..      24      61 ..      23      83 .. 0.75
   2 !   59.3   0.2   2.5e-19   3.5e-16       2      85 ..     277     358 ..     276     360 .. 0.97
   3 !   65.6   0.0   2.7e-21   3.8e-18       2      89 .]     403     492 ..     402     492 .. 0.98

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0057
                             PAS_3  2 iyvserveeilGyspeellgkveswldlvhpeDrervrea 41
                                      i  + ++e i+Gy++e+l g+  +  d+   e ++++++ 
  gi|298675354|ref|YP_003727104.1| 24 IDSNSAYESIIGYRKEDLAGS--KASDIFGTEYIPHLYTY 61
                                      67799***************9..77777766666666655 PP

  == domain 2  score: 59.3 bits;  conditional E-value: 2.5e-19
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       +yvs++ e+ lGy+ e+l +k  ++ +++hp+D++++++ + e l++  p+  e R+r+  G+y+w+e++++v++d+
  gi|298675354|ref|YP_003727104.1| 277 VYVSPSHEHHLGYHFEDLVDK--NIFEFIHPDDLKHIEKLYFEFLQTLNPIRSECRFRHSKGHYVWLETSVNVVYDD 351
                                       8********************..****************************************************** PP

                             PAS_3  79 ngkpvrv 85 
                                        g + ++
  gi|298675354|ref|YP_003727104.1| 352 YGDIKYF 358
                                       9998776 PP

  == domain 3  score: 65.6 bits;  conditional E-value: 2.7e-21
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvi.r 76 
                                       +y se+++++l+    el  + ++w +l+hp+D +rv +al+++ ++++ ++e eyRi+  +G++ w+ ++++++ r
  gi|298675354|ref|YP_003727104.1| 403 LYFSEQFSKLLDCGNKELVLDTQTWWNLIHPDDVNRVSKALNDYYAGRTtVFESEYRIKDNSGKWLWLLDKGKITkR 479
                                       799**********************************************999************************* PP

                             PAS_3  77 dengkpvrvigva 89 
                                       d++g+  r+ gv+
  gi|298675354|ref|YP_003727104.1| 480 DNSGNSERLTGVI 492
                                       **********986 PP

>> HisKA_2  Histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.5   3.9   6.1e-32   8.4e-29       1      76 []     522     597 ..     522     597 .. 0.98

  Alignments for each domain:
  == domain 1  score: 99.5 bits;  conditional E-value: 6.1e-32
                           HisKA_2   1 EihHRvkNnLqvisslLslqarkakdeevkealresqnRvlsialiheeLyksedletvdfseylekLvenlfksy 76 
                                       E+hHR+kNnLqvisslL+lq++k++de+v ea++++qnRv+s++ +h++Ly++++l++++ ++y+++Lv+ l ++y
  gi|298675354|ref|YP_003727104.1| 522 ELHHRIKNNLQVISSLLNLQSEKFEDEDVVEAFKDTQNRVISMSFVHQKLYQTNNLDNLNSKDYIKELVSYLTNLY 597
                                       99********************************************************************998876 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   9.7e-06     0.013       7     103 ..      12     104 ..       4     105 .. 0.74
   2 !    8.1   0.0    0.0022         3       2     103 ..     122     240 ..     120     241 .. 0.56
   3 !   45.9   0.0   3.8e-15   5.3e-12       3     104 .]     266     367 ..     265     367 .. 0.88
   4 !   15.1   0.0   1.5e-05      0.02      13     104 .]     402     497 ..     392     497 .. 0.83
   5 ?   -2.9   0.1       6.1   8.4e+03      51      77 ..     509     534 ..     500     558 .. 0.55
   6 ?   -2.1   0.0       3.4   4.7e+03      49      79 ..     673     709 ..     624     711 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.7e-06
                             PAS_9   7 dnpdg.....rilyaNeaalrllGyspeevlgksitdlf.vtdpeanerlraaleqgrkkerevevvlirkngetfw 77 
                                       ++++g     +i++ N a + ++Gy +e++ g + +d+f  +   +  + +++ e+g+  + ++e+ + +      +
  gi|298675354|ref|YP_003727104.1|  12 YDSNGyptdyMIIDSNSAYESIIGYRKEDLAGSKASDIFgTEYIPHLYTYAKIAETGK--QTNFETYCPYIGK---H 83 
                                       5566666666999**************************6666666667777777777..9999999999966...5 PP

                             PAS_9  78 vlltaspvkdddgelvgiivilrDit 103
                                       ++++++    ++g+   +i il+Dit
  gi|298675354|ref|YP_003727104.1|  84 YRVSIISP--EKGK---FITILTDIT 104
                                       55555333..2444...556888887 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0022
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlf..............vtdpeanerlraaleqgrk..... 59 
                                       + i+++++d ril+ N+ a+ + G+s++ + g +  d +                            ++ +      
  gi|298675354|ref|YP_003727104.1| 122 VVIMLVDSDRRILKLNKNAELFAGSSAKNLKGLRGGDALgclhslddpegcgfG----------PHCKNCKVrntvl 188
                                       5677799*************************9977777666654444444331..........3333333112222 PP

                             PAS_9  60 .........kerevevvlirkngetfwvlltaspvkdddgelvgiivilrDit 103
                                                +  ev++ +i +  e+ ++ll  + ++++d+  + ++v ++Dit
  gi|298675354|ref|YP_003727104.1| 189 dtfntgtnyNNVEVNLPFIVNGYEKHLTLLLSTSFINTDNQPK-VLVSIQDIT 240
                                       2222233355555555555555555555555555555544444.345555555 PP

  == domain 3  score: 45.9 bits;  conditional E-value: 3.8e-15
                             PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfwv 78 
                                       ++++ +++++ +y++++ +  lGy++e+++ k+i++++ ++++ ++ ++ ++e +++ ++ + e  +++++g ++w 
  gi|298675354|ref|YP_003727104.1| 266 MVCLADKNCNFVYVSPSHEHHLGYHFEDLVDKNIFEFI-HPDDLKHIEKLYFEFLQTlNPIRSECRFRHSKGHYVWL 341
                                       577888********************************.55555555555555555588****************** PP

                             PAS_9  79 lltaspvkdddgelvgiivilrDite 104
                                       + ++  v+dd g ++ +++ +rDite
  gi|298675354|ref|YP_003727104.1| 342 ETSVNVVYDDYGDIKYFVFNSRDITE 367
                                       *************************8 PP

  == domain 4  score: 15.1 bits;  conditional E-value: 1.5e-05
                             PAS_9  13 ilyaNeaalrllG.yspeevlgks.itdlfvtdpeanerlraaleqgrk...kerevevvlirkngetfwvlltasp 84 
                                        ly++e++ +ll   ++e vl ++ +++l+  +p++ +r+++al++      +++e e+ + +++g+ +w l     
  gi|298675354|ref|YP_003727104.1| 402 ELYFSEQFSKLLDcGNKELVLDTQtWWNLI--HPDDVNRVSKALNDYYAgrtTVFESEYRIKDNSGKWLWLL-DKGK 475
                                       5799*******9987788888777588888..88888888888888777777******************55.5545 PP

                             PAS_9  85 v..kdddgelvgiivilrDite 104
                                       +  +d++g+  ++ +++ Dit+
  gi|298675354|ref|YP_003727104.1| 476 ItkRDNSGNSERLTGVILDITD 497
                                       555888**************96 PP

  == domain 5  score: -2.9 bits;  conditional E-value: 6.1
                             PAS_9  51 raaleqgrkkerevevvlirkngetfw 77 
                                       ++ +++ + + re+e++++ kn+ ++ 
  gi|298675354|ref|YP_003727104.1| 509 ANKIKESK-ITREKELHHRIKNNLQVI 534
                                       34444444.677888888777774444 PP

  == domain 6  score: -2.1 bits;  conditional E-value: 3.4
                             PAS_9  49 rlraaleqgrk......kerevevvlirkngetfwvl 79 
                                       ++r+a   g +      ++ +++ +++  ng+ f ++
  gi|298675354|ref|YP_003727104.1| 673 DIRDAETLGFQlvsslvNQVNGDFEIYSGNGTMFIIE 709
                                       3334444444455556667777777777777777765 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0074        10      23      48 ..      23      48 ..      19      74 .. 0.84
   2 !   14.7   0.0   1.6e-05     0.022       2      43 ..     112     153 ..     111     155 .. 0.93
   3 ?    1.4   0.0      0.23   3.1e+02      53     113 .]     178     239 ..     174     239 .. 0.78
   4 !   41.2   0.0     1e-13   1.4e-10       4     113 .]     257     365 ..     254     365 .. 0.93
   5 ?    0.3   0.0      0.51     7e+02       4      81 ..     383     462 ..     380     495 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0074
                                      EEEECHHHHHHHSSTHHHCTTSBGGG CS
                               PAS 23 ilyvNaaaeellGlsreevlgkslld 48
                                      i+  N+a+e++ G++ e++ g++ +d
  gi|298675354|ref|YP_003727104.1| 23 IIDSNSAYESIIGYRKEDLAGSKASD 48
                                      7889*****************98775 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTT CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlg 43 
                                       +l+a+ e+ p+ i++vD d ril  N++ae + G s++ + g
  gi|298675354|ref|YP_003727104.1| 112 ELKAVYENVPVVIMLVDSDRRILKLNKNAELFAGSSAKNLKG 153
                                       6899******************************99998766 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.23
                                       THHHHHHHHHHHHHHHTT-ECCCCEEEEC.TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  53 eddaelaelleqlleqgeesrageisfkl.rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       +++ +++  ++   ++g++ +++e+++++ ++g ++hl +  s+ +   ++   +l+ ++di
  gi|298675354|ref|YP_003727104.1| 178 CKNCKVRNTVLDTFNTGTNYNNVEVNLPFiVNGYEKHLTLLLSTSFINTDNQPKVLVSIQDI 239
                                       5555677788888999**************9**99999888777655555544888888876 PP

  == domain 4  score: 41.2 bits;  conditional E-value: 1e-13
                                       HHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEE CS
                               PAS   4 raileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfk 80 
                                       + i e++ d++++ D++ +++yv+++ e  lG+  e+++ k+++++ih++d     +l+ + l++ ++ r++++ + 
  gi|298675354|ref|YP_003727104.1| 257 KDITENIWDMVCLADKNCNFVYVSPSHEHHLGYHFEDLVDKNIFEFIHPDDLKHIEKLYFEFLQTLNPIRSECRFRH 333
                                       56789999******************************************999999999999999999999888555 PP

                                       CTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  81 lrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                         +g +++le+ ++ v+d  g i++f++  rdi
  gi|298675354|ref|YP_003727104.1| 334 S-KGHYVWLETSVNVVYDDYGDIKYFVFNSRDI 365
                                       5.**************************99997 PP

  == domain 5  score: 0.3 bits;  conditional E-value: 0.51
                                       HHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTT..SBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   4 raileslpdpifvvDedgrilyvNaaaeellGlsreevlg..kslldliheeddaelaelleqlleqgeesrageis 78 
                                       +  l+s+  +++  D +   ly+++ + +ll    +e++   ++   lih++d   + ++l  +++ ++     e +
  gi|298675354|ref|YP_003727104.1| 383 ELALNSTSLAVWDCDIKKGELYFSEQFSKLLDCGNKELVLdtQTWWNLIHPDDVNRVSKALNDYYAGRTTVFESEYR 459
                                       56677777888888899999999999999998888776642234445555554447777777777777777777777 PP

                                       EEC CS
                               PAS  79 fkl 81 
                                       +k 
  gi|298675354|ref|YP_003727104.1| 460 IKD 462
                                       776 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00036       0.5      13     107 ..      19     105 ..      18     108 .. 0.83
   2 !   10.9   0.0   0.00031      0.42       2      39 ..     118     155 ..     117     172 .. 0.86
   3 ?   -2.4   0.0       4.1   5.6e+03      75     109 ..     209     243 ..     184     244 .. 0.66
   4 !   36.3   0.0     4e-12   5.5e-09       2     110 .]     261     370 ..     260     370 .. 0.95
   5 ?    2.0   0.0      0.18   2.4e+02      39     109 ..     426     499 ..     420     500 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00036
                             PAS_4  13 pdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgeerhyelrllPlr 89 
                                       +d+ +++ N a+++++g++ e+l G++  +++ +    ++   +++ +e+++   f+++      ++hy ++++   
  gi|298675354|ref|YP_003727104.1|  19 TDYMIIDSNSAYESIIGYRKEDLAGSKASDIFGT-EYIPHLYTYAKIAETGKQTNFETYCPY--IGKHYRVSIISP- 91 
                                       5888999**************************9.555566678999999999999997777..778888888776. PP

                             PAS_4  90 desGevigvlvisrDiTe 107
                                        e+G+   ++ i++DiT 
  gi|298675354|ref|YP_003727104.1|  92 -EKGK---FITILTDITG 105
                                       .6677...8888888885 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00031
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGkt 39 
                                       +++p+++  +d+d r+l +N++a+  +g +++ l G +
  gi|298675354|ref|YP_003727104.1| 118 ENVPVVIMLVDSDRRILKLNKNAELFAGSSAKNLKGLR 155
                                       899*******************8888888888887766 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 4.1
                             PAS_4  75 pgeerhyelrl.lPlrdesGevigvlvisrDiTerr 109
                                       +g e+h+ l l + + +++ +   vlv ++DiT+ +
  gi|298675354|ref|YP_003727104.1| 209 NGYEKHLTLLLsTSFINTDNQ-PKVLVSIQDITDKK 243
                                       555555555554444455555.78999999999875 PP

  == domain 4  score: 36.3 bits;  conditional E-value: 4e-12
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pge 77 
                                       +++ d+++  d++ +++y++++ ++++g+++e+l++k  +e+  ++d   +e  + + l++  pi+++   ++  g 
  gi|298675354|ref|YP_003727104.1| 261 ENIWDMVCLADKNCNFVYVSPSHEHHLGYHFEDLVDKNIFEFIHPDDLKHIEKLYFEFLQTLNPIRSECRFRHsKGH 337
                                       677799****************999****************99999*******************999988887999 PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerrr 110
                                        +++e++++ + d+ G++  +++ srDiTer++
  gi|298675354|ref|YP_003727104.1| 338 YVWLETSVNVVYDDYGDIKYFVFNSRDITERKE 370
                                       99999**************************85 PP

  == domain 5  score: 2.0 bits;  conditional E-value: 0.18
                             PAS_4  39 tlaellpeedaarleralrrvlegeepiefleelll.pgeerhyelrl..lPlrdesGevigvlvisrDiTerr 109
                                       t++ l  ++d  r++ al+   +g++++++ e++   + +   ++l +  +  rd sG    + +++ DiT+ +
  gi|298675354|ref|YP_003727104.1| 426 TWWNLIHPDDVNRVSKALNDYYAGRTTVFESEYRIKdNSGKWLWLLDKgkITKRDNSGNSERLTGVILDITDKV 499
                                       67777778899999999*******99999999888875555556666678888999999999999999999875 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.1   7.8e-10   1.1e-06      11      92 ..     273     350 ..     266     368 .. 0.89
   2 !   21.2   0.0   1.8e-07   0.00025      38      98 ..     425     485 ..     416     493 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 7.8e-10
                            PAS_11  11 dgkIisvDtsaLrasfslglekeelvgrsiydLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvkvktks 87 
                                       + +++ v +   +++++lg+  e+lv++ i++++hp+dl+++++ + e + ++ +   s  R+r s++++v++ t  
  gi|298675354|ref|YP_003727104.1| 273 NCNFVYVSP---SHEHHLGYHFEDLVDKNIFEFIHPDDLKHIEKLYFEFL-QTLNPIRSECRFRHSKGHYVWLETSV 345
                                       667888888...99************************************.8888899999**************99 PP

                            PAS_11  88 klfkn 92 
                                        + ++
  gi|298675354|ref|YP_003727104.1| 346 NVVYD 350
                                       98876 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 1.8e-07
                            PAS_11  38 rsiydLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvkvktksklfknqksneq 98 
                                         +++L+hp+d+ ++ ++l + +  + +  +s yR++ +++k++++  k+k+ k  +s ++
  gi|298675354|ref|YP_003727104.1| 425 QTWWNLIHPDDVNRVSKALNDYYAGRTTVFESEYRIKDNSGKWLWLLDKGKITKRDNSGNS 485
                                       57*********************8888889999*************999999998887765 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   0.00079       1.1      10      46 ..       1      47 [.       1      71 [. 0.66
   2 !   16.2   0.0   5.8e-06     0.008       3      45 ..     113     156 ..     112     173 .. 0.77
   3 !    6.9   0.0    0.0047       6.5       6      55 ..     259     306 ..     254     323 .. 0.67
   4 ?   -0.7   0.0       1.2   1.6e+03       3      55 ..     382     434 ..     380     442 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00079
                             PAS_8 10 spdgiav....vd.lgd.....rivdvNqaalellGys.adlkgellg 46
                                      +++g+++    +d + +      i+d N a++ + Gy+ +dl g++  
  gi|298675354|ref|YP_003727104.1|  1 MSEGVCIfeiiYDsN-GyptdyMIIDSNSAYESIIGYRkEDLAGSKAS 47
                                      678888855544432.2465666***************9666666554 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 5.8e-06
                             PAS_8   3 lralfesspdgiavvdlgdrivdvNqaalellGys.adlkgell 45 
                                       l+a++e++p+ i++vd ++ri+  N+ a+ + G s + lkg   
  gi|298675354|ref|YP_003727104.1| 113 LKAVYENVPVVIMLVDSDRRILKLNKNAELFAGSSaKNLKGLRG 156
                                       789*************9999*************44444444433 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0047
                             PAS_8   6 lfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellgqllpvlrpl 55 
                                       + e++ d ++++d + + +v+v ++ ++ lGy  +dl +    ++++ ++p 
  gi|298675354|ref|YP_003727104.1| 259 ITENIWDMVCLADkNCN-FVYVSPSHEHHLGYHfEDLVD---KNIFEFIHPD 306
                                       55566678889996666.*************98444333...3554444444 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 1.2
                             PAS_8   3 lralfesspdgiavvd.lgdrivdvNqaalellGysadlkgellg..qllpvlrpl 55 
                                       l+ +++s + +++ +d   +  ++  +++ +ll      k+ +l+  ++++ ++p 
  gi|298675354|ref|YP_003727104.1| 382 LELALNSTSLAVWDCDiKKG-ELYFSEQFSKLLDCG--NKELVLDtqTWWNLIHPD 434
                                       67789999999997777666.788888888888755..666665444777776665 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   4.9e-10   6.8e-07       5     107 ..     620     709 ..     617     711 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 4.9e-10
                                       HHHHHHHHHHHHHHHHHS...TTTEEEEEEEEEE...TEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSS CS
                         HATPase_c   5 rLrqiisnlvdNavkfat...kageieveikase...ddlvisveDnGiGipkedlkklfekfsqddstkrggggtG 75 
                                        L  +i++lv+N++k+a    ++g++++++   +   + +++ + DnG+Gip+++         +          + 
  gi|298675354|ref|YP_003727104.1| 620 PLGMLINELVSNSLKYAFpegESGKVDIQLY--KnykECYTLIIADNGRGIPENIDI-------R--------DAET 679
                                       57789***********554225555555555..2245699************96655.......2........3677 PP

                                       HHHHHHHHHHHHTTTEEEEEEETTTEEEEEEE CS
                         HATPase_c  76 lGlsivkklvelmgGeiwvesepgrGttftft 107
                                       lG+ +v +lv++++G++++ s    Gt f+++
  gi|298675354|ref|YP_003727104.1| 680 LGFQLVSSLVNQVNGDFEIYSGN--GTMFIIE 709
                                       9*******9999*******8888..9999875 PP

>> HWE_HK  HWE histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.2   5.8e-09     8e-06       1      53 [.     522     576 ..     522     605 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 5.8e-09
                                       HHHHHHHHHHHHHHHHHHHHSSSXS-HH..HHHHHHHHHHHHHHHHHHHHHHCTT CS
                            HWE_HK   1 ElnHRvKNlLavvqsiarqtlrsaesle..efaeklsgRLqALsaahdllsreew 53 
                                       El+HR+KN L v++s+ +  +++ e+ +  e+ ++ ++R+ ++s +h+ l ++++
  gi|298675354|ref|YP_003727104.1| 522 ELHHRIKNNLQVISSLLNLQSEKFEDEDvvEAFKDTQNRVISMSFVHQKLYQTNN 576
                                       9*****************99775544331155566678**********9988874 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   1.8e-05     0.024       8      54 ..     626     678 ..     623     688 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.8e-05
                       HATPase_c_3   8 aelvdNsld.....AdaenvkievnknrgktgeivieDdGkGmsee.elknal 54 
                                        elv Nsl      +++ +v+i++ kn ++  ++ i D+G G++e+ ++++a 
  gi|298675354|ref|YP_003727104.1| 626 NELVSNSLKyafpeGESGKVDIQLYKNYKECYTLIIADNGRGIPENiDIRDAE 678
                                       69*****998888889999********9999**************98888764 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.4e-05     0.047      32     112 ..     621     692 ..     583     709 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.4e-05
                       HATPase_c_2  32 irlaveEactNavehayleapegpvevr.lesdeealtvevaDsGpgfdpetlpdpteeepkeslkegGrGlalikg 107
                                       + + ++E+++N  ++a +e+++g+v ++ ++  +e  t+ +aD+G+g +             + ++ + +G  l+ +
  gi|298675354|ref|YP_003727104.1| 621 LGMLINELVSNSLKYAFPEGESGKVDIQlYKNYKECYTLIIADNGRGIPENI----------DIRDAETLGFQLVSS 687
                                       66789***********************445556669*********965542..........333344455555555 PP

                       HATPase_c_2 108 lvDev 112
                                       lv++v
  gi|298675354|ref|YP_003727104.1| 688 LVNQV 692
                                       55555 PP

>> DnaB  DnaB-like helicase N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.27   3.7e+02      80     103 .]     491     514 ..     475     514 .. 0.83
   2 ?   10.3   0.1   0.00042      0.58      52      91 ..     557     596 ..     532     603 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.27
                                       HHHHHHHC-S-CCCHHHHHHHHHH CS
                              DnaB  80 ylaelvaavpsaanieeyaeivke 103
                                        + +++++v   ++i+eya+ +ke
  gi|298675354|ref|YP_003727104.1| 491 VILDITDKVEREEKIREYANKIKE 514
                                       68899*****************97 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00042
                                       HTTTS-SHHHHHHHSCSSS-GGHGT.HHHHHHHHHC-S-C CS
                              DnaB  52 ekgepiDlvtvkeelekkgkledvggaaylaelvaavpsa 91 
                                       ++++ i + +v+++l ++++l++++ ++y++elv+  ++ 
  gi|298675354|ref|YP_003727104.1| 557 TQNRVISMSFVHQKLYQTNNLDNLNSKDYIKELVSYLTNL 596
                                       46799*****************************988765 PP

>> MitMem_reg  Maintenance of mitochondrial structure and function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   2.7   0.00057      0.78      21     109 ..     483     579 ..     470     598 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00057
                        MitMem_reg  21 tlstglnrqyyslkilqerldlikdYlkkveege....lpvnheilrnlqkllnllPhleteeleke.....fnvet 88 
                                         s++l+     ++   er ++i++Y +k++e +     + +h+i +nlq +  +l +l++e++e+e     f++  
  gi|298675354|ref|YP_003727104.1| 483 GNSERLTGVILDITDKVEREEKIREYANKIKESKitreKELHHRIKNNLQVIS-SLLNLQSEKFEDEdvveaFKDTQ 558
                                       556677777777777789999**********7765544555666777777666.55566665555444333388888 PP

                        MitMem_reg  89 nDvllvvyLasltrsilalne 109
                                       n v  ++++ + +  +++l++
  gi|298675354|ref|YP_003727104.1| 559 NRVISMSFVHQKLYQTNNLDN 579
                                       888777777766666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (712 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1079  (0.0601818); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.78u 0.35s 00:00:01.12 Elapsed: 00:00:00.55
# Mc/sec: 3871.33
//
Query:       gi|298675355|ref|YP_003727105.1|  [L=244]
Description: adenylylsulfate reductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.8e-52  176.8   0.0      5e-52  176.4   0.0    1.1  1  PAPS_reduct  Phosphoadenosine phosphosulfate reductase family


Domain annotation for each model (and alignments):
>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.4   0.0   2.8e-56     5e-52       2     174 .]      39     213 ..      38     213 .. 0.98

  Alignments for each domain:
  == domain 1  score: 176.4 bits;  conditional E-value: 2.8e-56
                                       EEEE--SSCTCHHHHHHHHHHCTTHEEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-THH CS
                       PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpvpvvfvdtghefpetiefvdeleeryglrlkvyepeeevaekinaekhgssly 78 
                                       + +s+s G++++Vl+++a k+ +++ v+ +dtg+ +pet++f++e+ + y++++ vy p++e++ek+++ek  +s+y
  gi|298675355|ref|YP_003727105.1|  39 ISISFS-GAEDVVLIDMAKKIRDDISVFTLDTGRLYPETYRFIEEICDYYNIDIDVYMPDRESTEKLVKEKGLFSFY 114
                                       778999.********************************************************************** PP

                                       HC...HHHHHHTHHHHHHHHHCTTECEEE----CCCTTTTTTSSSEEECTTT-S..CEEE-CCCT--HHHHHHHHHH CS
                       PAPS_reduct  79 ee...aaeriaKveplkkaLekldedalltGaRrdesksraklpiveidedfek..slrvfPllnWteedvwqyilr 150
                                       ++   ++++++K+ plk+aL++ld  a++tG+R+d+s+sr+ lp+v+id++f     ++++Pl+nWt ++vwqyi +
  gi|298675355|ref|YP_003727105.1| 115 NDghnECCSVRKIAPLKRALDGLD--AWVTGQRKDQSPSRSDLPVVQIDSAFGGgeLVKFNPLANWTLKQVWQYIFE 189
                                       ************************..**************************97779******************** PP

                                       CT--B-CCCCTT-SS--BCTTB-S CS
                       PAPS_reduct 151 enipynpLydqgfrsiGcvpctga 174
                                       +++pyn+L+++g+ siGc pct++
  gi|298675355|ref|YP_003727105.1| 190 NDVPYNKLHEKGYISIGCEPCTRP 213
                                       **********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1466.60
//
Query:       gi|298675356|ref|YP_003727106.1|  [L=127]
Description: hypothetical protein Metev_1456 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-07   30.6   0.0    3.8e-07   30.4   0.0    1.1  1  PTH2             Peptidyl-tRNA hydrolase PTH2
     0.0031   17.7   0.0     0.0046   17.1   0.0    1.2  1  Par3_HAL_N_term  N-terminal of Par3 and HAL proteins


Domain annotation for each model (and alignments):
>> PTH2  Peptidyl-tRNA hydrolase PTH2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   4.2e-11   3.8e-07      12     115 ..      32     125 ..      21     127 .] 0.78

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 4.2e-11
                                       SS-HHHHHHHHHHHHHHHHHHHHHH.CHHHHHHHHHHT.TTSEEEEEESSHHHHHHHHHHHHHTT-SEEEEEETSSS CS
                              PTH2  12 kmskGkiaaqcahAavalvkkllkesnekellkeWeee.gqkkivlkveseeeLlelaakakalglpaalirDagrt 87 
                                        +s G +  ++++ + +  +k+      ++ l+ W+ + +  k  lk+++ +e++e+ ++a+  g+pa+ i +    
  gi|298675356|ref|YP_003727106.1|  32 DLSSGDLSKKICDVSKKSSNKAP-----EKNLDIWNFNnNRDKQLLKCDDFSEMEEIFEEAEYGGVPASSICN---- 99 
                                       45555555555554444443333.....45799**988899*******************************9.... PP

                                       SSSTTCEEEEEEEEEEHHHHHHHHTTSE CS
                              PTH2  88 qiepgtkTvlaigPapksivdkvtgkLk 115
                                           +  + +aigP + + + ++t +L+
  gi|298675356|ref|YP_003727106.1| 100 --VDNNIVLIAIGPDKTERISELTTNLE 125
                                       ..668899****************9986 PP

>> Par3_HAL_N_term  N-terminal of Par3 and HAL proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   5.1e-07    0.0046      10      64 ..      22      77 ..      18      88 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.1e-07
                   Par3_HAL_N_term 10 vrvvvPCgdgellvrdLikqavqRykkatekdsdslvkvhsles.kdggiLDpDDl 64
                                      ++v+v C +++l+  dL k+  +  kk ++k +++ + + + ++ +d  +L  DD 
  gi|298675356|ref|YP_003727106.1| 22 IQVIVYCTKADLSSGDLSKKICDVSKKSSNKAPEKNLDIWNFNNnRDKQLLKCDDF 77
                                      78****************************************9989********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 816.51
//
Query:       gi|298675357|ref|YP_003727107.1|  [L=430]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.7e-23   80.8   0.5    2.9e-22   79.1   0.5    1.9  1  OrfB_IS605      Probable transposase
    1.9e-08   34.1   0.0    5.5e-08   32.6   0.0    1.9  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.017   15.0   2.9      0.037   14.0   2.9    1.5  1  PhaP_Bmeg       Polyhydroxyalkanoic acid inclusion protein (P
      0.022   15.1   0.1      0.049   14.0   0.1    1.5  1  CRF1            Transcription factor CRF1
        0.1   12.7   3.3       0.17   12.0   0.0    2.2  2  DUF986          Protein of unknown function (DUF986)


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.1   0.5   8.1e-26   2.9e-22       1     119 [.     178     297 ..     178     298 .. 0.95

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 8.1e-26
                        OrfB_IS605   1 sipvevevelpkpkgnkaagiDlGinnLatvv.tedgtwflykgrrlksdykylakeiaelqsklkksknykkasrk 76 
                                       +++++ +++    ++n+ ++iDlG+ n+at v t++gt+++++g+++ks ++ ++ke+a+lq  ++k+   +k +++
  gi|298675357|ref|YP_003727107.1| 178 QYVYDKKPQDMNLDKNQYLSIDLGLDNFATFVeTSTGTAEIIDGKHIKSINQFYNKEKAKLQGVKDKQSMEHKFTKR 254
                                       57888888899999****************773678999************************************** PP

                        OrfB_IS605  77 larlhrkrsrrrkhllhklathliktlkevgvetLnvgnmkdi 119
                                       l+rl +kr ++++++l+  + +++kt+ ++ ++++++g++k+i
  gi|298675357|ref|YP_003727107.1| 255 LSRLTNKRDNKVDEFLNRSVDYIVKTCIDKDIGNIVIGELKEI 297
                                       ****************************************987 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.0   1.5e-11   5.5e-08       4      69 .]     319     390 ..     316     390 .. 0.87

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 1.5e-11
                    OrfB_Zn_ribbon   4 lkeqleykakeyGikveevnpayTSktCseCgsknke......alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       +k +l+ k+  yGi+++e +++yTSkt +   +  ++      ++ +r +  ++ g  +++Dvn+a+Nil++
  gi|298675357|ref|YP_003727107.1| 319 FKSKLQSKCDLYGINYIEEDESYTSKTDALALEPIRKheeymgRRIKRGLFKSSTGQLINADVNGALNILRK 390
                                       899************************887776666556699978888888888***************986 PP

>> PhaP_Bmeg  Polyhydroxyalkanoic acid inclusion protein (PhaP_Bmeg)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   2.9     1e-05     0.037      22      94 ..     225     298 ..     221     314 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1e-05
                         PhaP_Bmeg  22 erfaslskqvEqltLkalkqqqdlvkeltkalselekeskqltaeledqlqktven..lrskaGnkvednieEwt 94 
                                       + ++++ +  E++ L+ +k++q + +++tk ls+l ++  +   e++++ ++++ +  + ++ Gn v  +++E +
  gi|298675357|ref|YP_003727107.1| 225 KSINQFYN-KEKAKLQGVKDKQSMEHKFTKRLSRLTNKRDNKVDEFLNRSVDYIVKtcIDKDIGNIVIGELKEIK 298
                                       55666654.599**************************99999*********99773357888888777777765 PP

>> CRF1  Transcription factor CRF1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.4e-05     0.049      43     108 ..     207     273 ..     199     275 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.4e-05
                              CRF1  43 tWakednkpfgiiDGlstkSLqekd.kedactkgentanngagaqtlnetsesdkdelsLddlLntS 108
                                       t++++ +    iiDG++ kS+++   ke+a  +g + +++ +++ t++ ++ ++k +  +d++Ln S
  gi|298675357|ref|YP_003727107.1| 207 TFVETSTGTAEIIDGKHIKSINQFYnKEKAKLQGVKDKQSMEHKFTKRLSRLTNKRDNKVDEFLNRS 273
                                       78888888999**********743303333444444444444444444444478999999**99987 PP

>> DUF986  Protein of unknown function (DUF986)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   1.1       0.2   7.1e+02      96     118 ..      41      63 ..      36      83 .. 0.70
   2 ?   12.0   0.0   4.6e-05      0.17      88     140 ..     165     217 ..     161     221 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.2
                            DUF986  96 ffyanifieYkkikainlsedgi 118
                                       +fy+n f++Y++  +   ++d++
  gi|298675357|ref|YP_003727107.1|  41 YFYNNKFLPYTNNYHYCKNNDNY 63 
                                       8*********9876665555554 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 4.6e-05
                            DUF986  88 klllKeeGffyanifieYkkikainlsedgilvidlekrrllikvkklddlek 140
                                       +++ K++G fy+  ++  kk +++nl  +++l idl   ++   v++   + +
  gi|298675357|ref|YP_003727107.1| 165 RIVPKHDGKFYQIQYVYDKKPQDMNLDKNQYLSIDLGLDNFATFVETSTGTAE 217
                                       6788************99*****************988777777776665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       859  (0.0479112); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2639.76
//
Query:       gi|298675358|ref|YP_003727108.1|  [L=933]
Description: aconitate hydratase 1 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   7.3e-178  592.3   0.0     1e-177  591.8   0.0    1.1  1  Aconitase    Aconitase family (aconitate hydratase)
    1.8e-44  151.2   0.2    7.2e-44  149.3   0.0    2.1  2  Aconitase_C  Aconitase C-terminal domain


Domain annotation for each model (and alignments):
>> Aconitase  Aconitase family (aconitate hydratase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  591.8   0.0  1.1e-181    1e-177       8     461 .]      75     595 ..      63     595 .. 0.94

  Alignments for each domain:
  == domain 1  score: 591.8 bits;  conditional E-value: 1.1e-181
                         Aconitase   8 lveeegiayvpdrvllqdvtgvqalvdlaaareavrrlggtlatidhlvpvdlvidhsv.....gaeealeknlede 79 
                                        v e++i+++p+rvl+qd+tgv+a+vd+aa+r+a++r gg+ + i++ vp+dlvidhs      g++ + + n e+e
  gi|298675358|ref|YP_003727108.1|  75 KVPEHEIPFIPSRVLMQDFTGVPAVVDIAAMRSAMQREGGDSSRINPEVPADLVIDHSLqidyfGTAYSKKYNEEKE 151
                                       3434449****************************************************9***9999999******* PP

                         Aconitase  80 fernkeryefLksaakaf.girvvppgqGIvHqvnlEy...............glalpgktvvgtDSHTtmigglGv 140
                                       fernkery+ L++a+++f +++vvppg+GI+HqvnlE+                +a+p+ t+vgtDSHTtmi+glGv
  gi|298675358|ref|YP_003727108.1| 152 FERNKERYSLLRWAQESFdNFQVVPPGKGIIHQVNLEHlaplvhfknsknkneKIAYPD-TLVGTDSHTTMINGLGV 227
                                       ***********************************************9999877*****.***************** PP

                         Aconitase 141 laiGvGgieaeavllgqplelkipkvvgvkltGklkegvtakDlvlavigklrkkgvvgkvvEffGegvesLsledr 217
                                       l++GvGgieaeav++gqp++++ip+vvg+kl+G+l+egvta+Dlvl+v+++lrk+gvvgk+vEf+G+g+e+Lsl dr
  gi|298675358|ref|YP_003727108.1| 228 LGWGVGGIEAEAVMMGQPYYMSIPEVVGFKLDGELQEGVTATDLVLTVTQMLRKHGVVGKFVEFYGPGLEKLSLPDR 304
                                       ***************************************************************************** PP

                         Aconitase 218 aTiaNMaaEvGAttglfpvdektleYLkatgreeaav.lveaydkaqalfelaadedaeydkvleldlstlepsvag 293
                                       aT+aNMa+E+GAt+g+fp+de+tleYLk+tgr+e++v +v++y+k+q+l+  ++++++ y++ leld+s++eps+ag
  gi|298675358|ref|YP_003727108.1| 305 ATLANMAPEYGATMGYFPIDEETLEYLKLTGRSEKHVnMVREYTKEQGLLFDSQNDEPMYNDKLELDMSNVEPSIAG 381
                                       *************************************9**********9966777789******************* PP

                         Aconitase 294 pkrPqdavplselvkkefkeele................................keaaekaley..klkegtklkd 336
                                       pkrP d+++++++  ++f++ ++                                +++  ++++y    ++ t++++
  gi|298675358|ref|YP_003727108.1| 382 PKRPYDRISIENMS-EHFHNLMKqtfaekrgekdiqendpdynrwleeggnisnvHTQSAHHTSYikCRDSFTTITH 457
                                       **********5555.4677766678899************************998444444444454566799**** PP

                         Aconitase 337 gkvdiaaigSCTNssnedvraaaglla.kavekglkvkpgvktsvaPGSevvkayleaeGlleiLekaGfevvgagC 412
                                       g+v ia i+SCTN+sn++v + aglla +ave gl vkp+vkts+aPGS+vv++yl+++ ll++Le++Gf++vg+gC
  gi|298675358|ref|YP_003727108.1| 458 GAVAIASITSCTNTSNPSVLIGAGLLAkNAVEMGLDVKPYVKTSLAPGSRVVTDYLDKSELLPYLEALGFHLVGYGC 534
                                       ***************************************************************************** PP

                         Aconitase 413 stCignsdrle........ege....aivsssNRNFegRqgpntra.yLaSPelvvaaAlaG 461
                                        tCigns++++        e +    a+v+s+NRNFegR++p  +a yL+SP lvva+AlaG
  gi|298675358|ref|YP_003727108.1| 535 ATCIGNSGPINesveneikE-KdltvAAVLSGNRNFEGRINPYIKAnYLTSPMLVVAYALAG 595
                                       *********99788665543.16999***********************************9 PP

>> Aconitase_C  Aconitase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.69   6.2e+03      16      55 ..     627     666 ..     622     681 .. 0.68
   2 !  149.3   0.0     8e-48   7.2e-44       3     130 ..     725     851 ..     723     852 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.69
                                       HSTGGGCCGHCCHHHCCCGGTTTCCCCTTTSBBSEEEETT CS
                       Aconitase_C  16 ksnvdtdlkipkqfegtianiglgnelveekrankttdld 55 
                                       ++++  d ++  +fe++   ++ g el +++ ++++++ +
  gi|298675358|ref|YP_003727108.1| 627 INQIIKDTIDSDMFENEYSHVMEGTELWDDMDVPQDDQYH 666
                                       5555566777778888888888887777777777766655 PP

  == domain 2  score: 149.3 bits;  conditional E-value: 8e-48
                                       CCCCCTT--CHHHHSTGGGCCGHCCHHHCCCGGTTTCCCCTTTSBBSEEEETTTTEEEEHHHHHHHHHHTT--EEEE CS
                       Aconitase_C   3 kllklkGlttedeksnvdtdlkipkqfegtianiglgnelveekrankttdlddgekedvvdaaerykkegaklvvi 79 
                                       ++l ++G+++ed++ +++++++++++++gt+ ni+l+n+lv+  + + t + ++g++++++daa++y++++++l+v+
  gi|298675358|ref|YP_003727108.1| 725 QYLLNQGVKEEDFNTYGSRRGNHEVMMRGTFGNIRLNNKLVD-RNGGWTLYHPTGKEMSIYDAAMNYQDNNIPLIVM 800
                                       68899*************************************.7788888889************************ PP

                                       --SSBTBS---THHHHHHHHTTEEEEEES-B-HHHHHHHHHTT-EEEEEST CS
                       Aconitase_C  80 agknfGeGSSRehAAkalrllGikaviaeSFerIfennliknglLplefke 130
                                       agk++G+GSSR++AAk+++llG+kaviaeSFerI+++nl+++g+Lpl+fk+
  gi|298675358|ref|YP_003727108.1| 801 AGKEYGTGSSRDWAAKGTQLLGVKAVIAESFERIHRSNLVGMGVLPLQFKK 851
                                       *************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (933 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.76u 0.30s 00:00:01.06 Elapsed: 00:00:00.49
# Mc/sec: 5697.53
//
Query:       gi|298675359|ref|YP_003727109.1|  [L=173]
Description: hypothetical protein Metev_1460 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.5e-20   71.4   4.2    9.5e-20   71.0   4.2    1.1  1  LTD       Lamin Tail Domain
     0.0001   23.2   8.7    0.00013   22.8   4.0    2.8  2  Pilin_N   Archaeal Type IV pilin, N-terminal
  ------ inclusion threshold ------
      0.048   13.3   0.4      0.065   12.9   0.4    1.1  1  DUF3341   Protein of unknown function (DUF3341)


Domain annotation for each model (and alignments):
>> LTD  Lamin Tail Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.0   4.2   1.6e-23   9.5e-20       3     107 ..      63     169 ..      61     172 .. 0.89

  Alignments for each domain:
  == domain 1  score: 71.0 bits;  conditional E-value: 1.6e-23
                               LTD   3 aaagdvvIsevmedgagnnanefvelyNtsskavdLsgwkledasge....ytfpngtgtlaageyvvvwsgsgtts 75 
                                       + ++ + I+e+  ++++n ++e+v ++N+  +av+L++w ++d+ +     y++ +  + l  ge+v+v++g+gt++
  gi|298675359|ref|YP_003727109.1|  63 SGNPGIYINEFKLGADNNPNKEWVSIKNSKKSAVNLKNWIIKDYEQIynysYKLNS--FNLGTGETVTVHTGKGTNT 137
                                       56889********99776666************************88996666644..48************99998 PP

                               LTD  76 asngskasssavwnnggdavaLydasgevvds 107
                                       +s+ + +  + +wnn+gd+v+Ly+++g++vd+
  gi|298675359|ref|YP_003727109.1| 138 SSDIYLGLDKCIWNNTGDKVYLYNSNGNLVDT 169
                                       88887777**********************97 PP

>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   4.0   2.2e-08   0.00013       2      38 ..       7      43 ..       6      90 .. 0.90
   2 ?    2.1   0.2     0.063   3.8e+02      56      68 ..     153     168 ..      85     172 .. 0.57

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2.2e-08
                           Pilin_N  2 AVSpViGviLmvaitvIlaAviaafvlglasneekap 38
                                      A SpV+G+++m  +tv +aA + ++++g+a++  k p
  gi|298675359|ref|YP_003727109.1|  7 AASPVVGIVIMFILTVTMAATVVTIAFGFAEPLPKNP 43
                                      78***************************76665555 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.063
                           Pilin_N  56 a...vslehkgGdsid 68 
                                       +   v+l +++G+ +d
  gi|298675359|ref|YP_003727109.1| 153 TgdkVYLYNSNGNLVD 168
                                       0222666666666555 PP

>> DUF3341  Protein of unknown function (DUF3341)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.4   1.1e-05     0.065      82     130 ..       3      49 ..       1      56 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.1e-05
                                       TT--SS-HHHHHHHHTHHHHHHHHHHHHHTTTTTT-S-----TTTT-TT CS
                           DUF3341  82 gGkPlfslpafipitFEltvLfaalatvlgllllnglprlyhpvfkaen 130
                                       g k   s +  i+i+F ltv +aa  + +++ +   l  +++p+f++ n
  gi|298675359|ref|YP_003727109.1|   3 GDKTAASPVVGIVIMFILTVTMAATVVTIAFGFAEPL--PKNPFFESGN 49 
                                       67888899999************************99..6788988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1052.48
//
Query:       gi|298675360|ref|YP_003727110.1|  [L=397]
Description: amidohydrolase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-29  101.4   0.0    6.4e-29  101.1   0.0    1.1  1  Peptidase_M20  Peptidase family M20/M25/M40
    2.5e-07   30.6   0.0    6.7e-07   29.2   0.0    1.7  1  M20_dimer      Peptidase dimerisation domain
  ------ inclusion threshold ------
       0.17   11.6   0.0       0.27   10.9   0.0    1.4  1  Peptidase_M28  Peptidase family M28


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.1   0.0   1.1e-32   6.4e-29       1     204 [.      65     385 ..      65     388 .. 0.91

  Alignments for each domain:
  == domain 1  score: 101.1 bits;  conditional E-value: 1.1e-32
                                       EEEEES-BSS.TTCGGGSSSTTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTT CS
                                       xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20   1 llgsHlDvVp.eeetdgwttpfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrg 76 
                                       +l++++D++  +ee+++ ++ + +++e G ++++G+d+++++vl+a+ +l +++ +    +g+i+l+fqp+EE   g
  gi|298675360|ref|YP_003727110.1|  65 ALRADMDALRvAEEQTELNKDYISQNE-GIMHACGHDGHMAIVLGAARLLNEMRNQI---PGSIKLIFQPAEEQPPG 137
                                       69********9888877766*****88.************************99998...*************888* PP

                                       HHHHHHH..HHHTTTCESEEEEEEEESSSBTCHSTETEEEE.................................... CS
                                       xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................... RF
                     Peptidase_M20  77 Gakalle..gleerekvdavfelhieepgileagklaigvv.................................... 115
                                       Ga ++++  g    ++vda+++lhi   g ++ gk++++ +                                    
  gi|298675360|ref|YP_003727110.1| 138 GASKIIKegG---IDDVDAIVGLHIF--GDMDFGKIKFKSGcfmassnrlnlsifgkgghhsnphdcidpvfiasdf 209
                                       *******433...669**********..666669966666699********************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Peptidase_M20 116 ............................................................................. 115
                                                                                                                    
  gi|298675360|ref|YP_003727110.1| 210 lssihdeiqkiispsryvlgigkteggeqfnrsmdrldivgsfrtfhdediniiesvikqkldnlmyaysiegisdv 286
                                       ***************************************************************************** PP

                                       .EEEEEEEEEESHEEECCHHHHHHHHHHHHHHH.TSCEEEEEES.SSBHTHHHH.TTTEEEEE.EE.SS.G....GC CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx.xxxxxxxxx.xxxxxxxx.xx.xx.x....xx RF
                     Peptidase_M20 116 .kvevelleggapvtlndsplvkalaeaaeelf.gekvelivsg.pggtdarff.agiptvmi.fg.pg.s....gl 181
                                        k++++ + +++pv  n+++++ a+ + +++ +  ++ +  +++  g++d++f+ ++ip +++ +g  + +    ++
  gi|298675360|ref|YP_003727110.1| 287 pKYNLD-IIRAYPVLNNNDKFASAVYKLLKDKHpEVEIDKNAKPlFGSEDFAFYvKNIPGFYFtIGtKNiQknvvEI 362
                                       88***9.889999**99**************8754445555888**********9999*885559966652678888 PP

                                       TTSTTTEEEHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 182 aHspnEyvdledlekgikvlarl 204
                                        Hs + ++d+e l  g+++l+ +
  gi|298675360|ref|YP_003727110.1| 363 NHSSKFDIDEEVLIIGVRILKTI 385
                                       888888888**********9876 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   1.1e-10   6.7e-07       9     106 ..     182     276 ..     177     279 .. 0.94

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 1.1e-10
                                       EEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC.....TCCTCCCCCEECCE-CCCCEESSEEEEEEEEEHH CS
                         M20_dimer   9 gkitvkgkagHsgapgagaNAieklarllaeledeegdiaeerslprttlnvtgiegGsaknvipdeaeakidiRll 85 
                                        ++++ gk+gH ++p++ ++++ +++++l++++de ++i    s++r+ l ++  egG + n   d+     ++R+ 
  gi|298675360|ref|YP_003727110.1| 182 LNLSIFGKGGHHSNPHDCIDPVFIASDFLSSIHDEIQKII---SPSRYVLGIGKTEGGEQFNRSMDRLDIVGSFRTF 255
                                       57889******************************99999...********************************** PP

                                       HHHHHHHHHHHHHHHHTSCCS CS
                         M20_dimer  86 pgedpeevleeieeilekeap 106
                                         ed   ++  i++ l+++  
  gi|298675360|ref|YP_003727110.1| 256 HDEDINIIESVIKQKLDNLMY 276
                                       *************99998765 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   4.5e-05      0.27      42     101 ..     103     161 ..      51     222 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.5e-05
                                       HHHHHHHHHHCHHGGCCSSEEEEEEEESSCSGSSHHHHHHHHHHCCCTTEEEEEEECS-S CS
                     Peptidase_M28  42 vaalLelarvlaasgsrpkrgvrflffdaEEagllGSkafakakpelkkiaavlnlDmvg 101
                                       +a++L  ar+l+++ ++   +++++f  aEE+   G+++ + ++  +++++a + l ++g
  gi|298675360|ref|YP_003727110.1| 103 MAIVLGAARLLNEMRNQIPGSIKLIFQPAEEQPPGGASKII-KEGGIDDVDAIVGLHIFG 161
                                       699**********99899*******************9999.666777777776666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2646.43
//
Query:       gi|298675361|ref|YP_003727111.1|  [L=148]
Description: N-acetyltransferase GCN5 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.2e-13   48.8   0.1    8.6e-13   48.5   0.1    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
      5e-12   46.1   0.3    8.5e-12   45.3   0.3    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    8.1e-12   45.2   0.1    9.5e-12   45.0   0.1    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    4.7e-06   26.5   0.1    6.3e-06   26.1   0.1    1.2  1  FR47             FR47-like protein
      9e-06   25.9   0.5    1.1e-05   25.7   0.5    1.2  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    1.9e-05   25.3   0.0    2.2e-05   25.1   0.0    1.1  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    7.4e-05   22.8   0.0    0.00013   22.0   0.0    1.4  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
    0.00079   18.9   1.3     0.0011   18.5   1.3    1.5  1  Acetyltransf_15  Putative acetyl-transferase
  ------ inclusion threshold ------
      0.025   14.6   0.1      0.051   13.6   0.1    1.6  1  Thioredoxin_3    Thioredoxin domain
       0.03   14.3   0.0      0.055   13.5   0.0    1.4  1  Acetyltransf_13  ESCO1/2 acetyl-transferase
      0.064   13.0   0.0      0.073   12.8   0.0    1.3  1  PanZ             Acetyltransferase (GNAT) domain, PanZ


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.1   5.3e-16   8.6e-13       6     117 .]      20     129 ..      15     129 .. 0.82

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 5.3e-16
                                       HHHHHHTH..HHHHHHHHHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHH CS
                    Acetyltransf_1   6 ellvesff..ppnedaseeefeesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsa 80 
                                       e+l+e  f   p++d ++++ e++   + + ++++  dg+++G+  l+ i++   ++++i +++V++++r++G+G +
  gi|298675361|ref|YP_003727111.1|  20 EILNEHGFeyDPEKDYDLDDIEKYYLTDGSVFYIGIADGQIVGTGALKRIDN---NRCEIKRMYVKKSFRNRGYGLK 93 
                                       4455444522455666666677776666669999******************...********************** PP

                                       HHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  81 LlealeerareegikkivlaveedndaairlYeklGF 117
                                       L +a +e+a ++ +k   + +    ++ai+lY k GF
  gi|298675361|ref|YP_003727111.1|  94 LFDATLEFAQKH-YKTATIKTNIKLKRAINLYLKNGF 129
                                       *******99999.44448899999********99999 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.3   5.2e-15   8.5e-12       4      74 ..      50     129 ..      41     130 .. 0.76

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 5.2e-15
                                       EEEEEEETTEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHHHH......TTSEEE...EE.EEEETHH..HH CS
                    Acetyltransf_7   4 evfVaeddgkivGfialslld...aeitrlaVdpeyrgkGiGraLlea......aekgii...le.qlelnae..ka 65 
                                        +++   dg+ivG+ al+++d   +ei+r++V++++r++G+G +L +a      +  +++   ++ +     +  +a
  gi|298675361|ref|YP_003727111.1|  50 VFYIGIADGQIVGTGALKRIDnnrCEIKRMYVKKSFRNRGYGLKLFDAtlefaqK--HYKtatIKtNI----KlkRA 120
                                       46666668***************999999*****************975544321..22222122223....1448* PP

                                       HHHHHHTTE CS
                    Acetyltransf_7  66 ikfYeklGF 74 
                                       i++Y k+GF
  gi|298675361|ref|YP_003727111.1| 121 INLYLKNGF 129
                                       ********9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.1   5.9e-15   9.5e-12      20     113 ..      38     136 ..       7     145 .. 0.78

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 5.9e-15
                   Acetyltransf_10  20 ealreri.eegealllvaeeggkivGviel.rdgs...hisllfVdpeyrgqGigkaLleaveeeaekdgikl.elt 90 
                                       + ++++  ++g++++++   +g+ivG+++l r ++   +i +++V++++r +G+g +L++a +e a+k ++k+ +++
  gi|298675361|ref|YP_003727111.1|  38 DDIEKYYlTDGSVFYIGIA-DGQIVGTGALkRIDNnrcEIKRMYVKKSFRNRGYGLKLFDATLEFAQK-HYKTaTIK 112
                                       5566666357777777775.66***9997743333568****************************55.57777*** PP

                   Acetyltransf_10  91 vnasp.yavpfYeklGFkavgeeq 113
                                        n +   a+++Y k GF  +   +
  gi|298675361|ref|YP_003727111.1| 113 TNIKLkRAINLYLKNGFLITALDT 136
                                       *99999***********7654444 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.1   3.9e-09   6.3e-06       2      77 ..      53     129 ..      52     138 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 3.9e-09
                                       EEEEET.TT--EEEEEEE-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT- CS
                              FR47   2 lGlyrk.elgelaawilrkdggelgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGf 77 
                                       +G+ ++  +g  a  ++ ++  e+  ++v++++r+rG+g +l  a  +   +  kt+++ ++++ +++i+ly k Gf
  gi|298675361|ref|YP_003727111.1|  53 IGIADGqIVGTGALKRIDNNRCEIKRMYVKKSFRNRGYGLKLFDATLEFAQKHYKTATIKTNIKLKRAINLYLKNGF 129
                                       677777556666778999999************************9999999**********************999 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.5   6.6e-09   1.1e-05      40     134 ..      39     129 ..       4     141 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 6.6e-09
                    Acetyltransf_4  40 fleal.dsekeyvflvaesdrivGyaylgqfkkrakdwkaels.vylaerdnnkeglgrelidaleqvl.keqnien 113
                                        +e++  ++++ ++  + +++ivG+ +l+ ++     + +e++ +y++ +  +++g+g +l da  +++ k +   +
  gi|298675361|ref|YP_003727111.1|  39 DIEKYyLTDGSVFYIGIADGQIVGTGALKRIDN----NRCEIKrMYVK-KSFRNRGYGLKLFDATLEFAqKHYKTAT 110
                                       4666658**********************9999....66666538997.89******************99999999 PP

                    Acetyltransf_4 114 llaeiaspnensiqfhkalGF 134
                                       + + i    + +i+++ + GF
  gi|298675361|ref|YP_003727111.1| 111 IKTNIKL--KRAINLYLKNGF 129
                                       9999974..446666666666 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   1.4e-08   2.2e-05      27     137 ..      29     129 ..       7     130 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.4e-08
                    Acetyltransf_3  27 ylpe.pltleeaeewlerawaeeseeegygwaivlkdtgviGsvglrdleeedeeaelgym.lapsfwgkGyateav 101
                                       y pe +++l++ e+++ +        +g  + i   d++++G+  l ++++++  +e+  m +++sf+++Gy+    
  gi|298675361|ref|YP_003727111.1|  29 YDPEkDYDLDDIEKYYLT--------DGSVFYIGIADGQIVGTGALKRIDNNR--CEIKRMyVKKSFRNRGYGLKLF 95 
                                       544447777777777772........45445552356646***********97..****6615577*********** PP

                    Acetyltransf_3 102 ralleyafeelglerlvavidkeNeaSirvleklGf 137
                                        a le+a +++ +++  ++++ + ++ i+++ k Gf
  gi|298675361|ref|YP_003727111.1|  96 DATLEFA-QKH-YKTATIKTNIKLKRAINLYLKNGF 129
                                       *******.444.7999*******************9 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   8.1e-08   0.00013       2      58 ..      51     107 ..      44     112 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 8.1e-08
                   Acetyltransf_CG   2 feltldegeevafleYevrkegvldfthTeVpeelrGkGiAkkLvkaalddareegl 58 
                                       f++ + +g+ v++   ++ ++++ ++   +V++++r +G++ kL +a l++a+++ +
  gi|298675361|ref|YP_003727111.1|  51 FYIGIADGQIVGTGALKRIDNNRCEIKRMYVKKSFRNRGYGLKLFDATLEFAQKHYK 107
                                       666666788899999999999********************************9976 PP

>> Acetyltransf_15  Putative acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   1.3   6.7e-07    0.0011      66     109 ..      67     110 ..       2     131 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 6.7e-07
                   Acetyltransf_15  66 ilieknvleiYtlyvsekyrgkGlakklLeeslkelkknYkvdn 109
                                        +i +n  ei  +yv++ +r++G+  kl   +l+  +k+Yk   
  gi|298675361|ref|YP_003727111.1|  67 KRIDNNRCEIKRMYVKKSFRNRGYGLKLFDATLEFAQKHYKTAT 110
                                       56788999*********************************876 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   3.1e-05     0.051       9      46 ..       5      44 ..       2      70 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.1e-05
                                      SSTTCH..HHHHHHHHHCHCCTCECEEECCTTHHHHHHCT CS
                     Thioredoxin_3  9 gCakCp..klekavkeaaaekgikaevekvtdfeeiekyg 46
                                       C+k +  +++++v e+++e g++++ ek +d+++ieky 
  gi|298675361|ref|YP_003727111.1|  5 ECKKYQntQVKNLVLEILNEHGFEYDPEKDYDLDDIEKYY 44
                                      465555789****************************995 PP

>> Acetyltransf_13  ESCO1/2 acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.4e-05     0.055       5      31 ..      74     100 ..      71     115 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.4e-05
                   Acetyltransf_13   5 cGisriWvssshRrkgiAtkLldaare 31 
                                       c i+r++v++s+R++g   kL da  e
  gi|298675361|ref|YP_003727111.1|  74 CEIKRMYVKKSFRNRGYGLKLFDATLE 100
                                       779********************9765 PP

>> PanZ  Acetyltransferase (GNAT) domain, PanZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.5e-05     0.073      34      99 ..      45     111 ..       7     137 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.5e-05
                              PanZ  34 lteegalfaarFNdRlLgAvkvel.edkeaelsdlcVRevTRrRGVgsyLleearrqaPevkswvla 99 
                                       lt++  ++++       g  ++++ +++  e++ + V++  R+RG g++L + +++ a +  ++   
  gi|298675361|ref|YP_003727111.1|  45 LTDGSVFYIGIADGQIVGTGALKRiDNNRCEIKRMYVKKSFRNRGYGLKLFDATLEFAQKHYKTATI 111
                                       555566666666677777777765155689**********************999877444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 943.00
//
Query:       gi|298675362|ref|YP_003727112.1|  [L=652]
Description: glycoside hydrolase 15-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-10   39.8   4.6      1e-06   27.8   4.0    3.1  2  Glyco_hydro_15   Glycosyl hydrolases family 15
    0.00021   20.6   0.9    0.00021   20.6   0.9    1.7  2  DUF608           Glycosyl-hydrolase family 116, catalytic reg
  ------ inclusion threshold ------
      0.013   14.8   0.0      0.024   13.9   0.0    1.3  1  Bac_rhamnosid6H  Bacterial alpha-L-rhamnosidase 6 hairpin gly


Domain annotation for each model (and alignments):
>> Glyco_hydro_15  Glycosyl hydrolases family 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   4.0   1.7e-10     1e-06       9     345 ..     301     580 ..     294     586 .. 0.76
   2 !    2.6   0.0    0.0076        46     412     444 ..     601     634 ..     591     638 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.7e-10
                                       HCBCSTTSSBTTS-TT-B-S-S-BSSS.....B--SEEHHHHHHHHHHHH.......HHHHHTTT-HCCHHHHHHHH CS
                    Glyco_hydro_15   9 rnvktlilleqnpvtGlliASpstsdp.....DYrytWvRDsvyvilavwglgyrdedrakayeleqslvklmrgll 80 
                                       r++ ++i + +  + G liAS +t+        Y+y+W RD++  + a+          ak ++l+ ++ +    ++
  gi|298675362|ref|YP_003727112.1| 301 RSLLATISHMD--INGSLIASCDTDIKqfgadYYTYCWPRDASWAVVALD--------SAKYHNLSLEVFD----FY 363
                                       55555544444..3588888888777777784456888888888777776........5555565555555....45 PP

                                       HHHHHHCTS-BTTB-TTSCGGGG--EE-TTS-B--S-..-S--BTTHHHHHHHHHHHH...HCTTHCHCCCCHHHHT CS
                    Glyco_hydro_15  81 eamvrqagkvekfketqstkgLhakyftktgstvvGddewghlQlDatslyllalaqm...tasglqiistldevaf 154
                                       + +++ +g    f +   +      +++++  + v+      +Q+D t+l+l+al+       +  +i ++  ++  
  gi|298675362|ref|YP_003727112.1| 364 SKVISEKGY---FLHKYTP-----AGDFGSTWHPVPM-----IQIDETGLPLYALYNNwlmSRNVWTIGRYFMSI-- 425
                                       555555554...3333333.....3444444454555.....9************99874233335555665555.. PP

                                       HHHHHHHHHHHTTS-.....EE-TTS--ECEEHH..HHHHHHHHHHHHHHHHHHCT-HHHHCCHHHHHHHHHHHHHS CS
                    Glyco_hydro_15 155 vqnlvdYieaayktp.....dfglWEenqgeselnassvgmakAlleaideadlfgakgdaqlvektkdeilnklqg 226
                                       v     Y+++ +++      +f+lWEe++g + +  s     ++l  a+++a+++g + + + + k ++++ n +  
  gi|298675362|ref|YP_003727112.1| 426 VVPAANYLASSIDSDglpisSFDLWEERKGVHTY--SACTIYAGLYGAAEIAKALGHDVEFEYWLKSAKKVKNAI-- 498
                                       999999999999876555669*************..9999***********************999999999999.. PP

                                       TTT..GGGEETTCCECECSCH.....HHHTTS--S-BCHHHHHHHHCS-TTS-TT-TT-TTTSHHHHHHHHHHHHHH CS
                    Glyco_hydro_15 227 kygckrgfwplfntylildgsfaedkeqvqeyrealdasllllpelyfvpaddvdeeyqnpqsprllaqslyildsl 303
                                          ++  ++++++ + +  ++            +  d+sl  +   +  p dd          +r+++++++i+ +l
  gi|298675362|ref|YP_003727112.1| 499 ---IEYLYDEQKQRFKRSLHD------------STIDSSLFGVWYFGILPSDD----------ERVVNTMKAIEYEL 550
                                       ...77889**********999............*******99999********..........*************9 PP

                                       HHHSGGGTT-STTS--SBTT--CGSSSBSCT--BHHHHHHHH CS
                    Glyco_hydro_15 304 lsegflavgeldplvrRysedvkpdklglsGrpyylctlwtv 345
                                       ++            + Ry  d++     +  +++ +ctlw +
  gi|298675362|ref|YP_003727112.1| 551 SRPSG--------GIARYMDDNYM----GYMNSWIICTLWVA 580
                                       98633........499******97....67799999999955 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.0076
                                       H..S-TTS---SEE-TTT--EESSTT-HHHHHHHH CS
                    Glyco_hydro_15 412 e..dnslgvLteevdvylgeliraqpllfsealll 444
                                       +   + +g+++e+v   +g l +  pl++s+ +++
  gi|298675362|ref|YP_003727112.1| 601 DnsHPTTGLMAEQVAN-DGSLKSVLPLMWSHSAFV 634
                                       3356778999999987.9*************9987 PP

>> DUF608  Glycosyl-hydrolase family 116, catalytic region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1      0.43   2.6e+03      59     106 ..     161     207 ..     143     208 .. 0.72
   2 !   20.6   0.9   3.5e-08   0.00021     143     250 ..     434     542 ..     403     596 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.43
                            DUF608  59 dgkvlprkvknavpHdlgdpeeepweevnayllhdtseWkDlnlkfvL 106
                                       +  ++++k +++  H+   p+ + w   +a       +WkD++ +  L
  gi|298675362|ref|YP_003727112.1| 161 RDFLIHYKRNRYFLHSSS-PQFDQWAVGDAEWNGFEGTWKDMEDDGLL 207
                                       444567788888888887.99999998888877778899999887765 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 3.5e-08
                            DUF608 143 dglienegfadqtYDaws.vkGvsaycgglwlaaLeaaiemaellgdkkdaeeykellekakkvyekkLwnGeYfky 218
                                        ++i+++g +  ++D w+  kGv +y++   +a L  a+e+a+ lg++ + e++ +  +k k++  + L+  +  ++
  gi|298675362|ref|YP_003727112.1| 434 ASSIDSDGLPISSFDLWEeRKGVHTYSACTIYAGLYGAAEIAKALGHDVEFEYWLKSAKKVKNAIIEYLYDEQKQRF 510
                                       57899************7368************************99999888888888888899999999999999 PP

                            DUF608 219 desssesesimadqlaGqwylracglee..ivpk 250
                                       ++s   ++s +   l G wy  ++  ++  +v++
  gi|298675362|ref|YP_003727112.1| 511 KRSL--HDSTIDSSLFGVWYFGILPSDDerVVNT 542
                                       9644..45555569******99876665555554 PP

>> Bac_rhamnosid6H  Bacterial alpha-L-rhamnosidase 6 hairpin glycosidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.9e-06     0.024     168     248 ..     457     540 ..     442     558 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.9e-06
                                       HHHHHHHHHHHHHHHHHHHHHTTS..--HHHHHHHHHHHHHHHHHHB.-TTS....-BTT--HHHHHH.HHHTT-S- CS
                   Bac_rhamnosid6H 168 alvataylvrslklvakiaellgkeedakkyaalaeelkaafnkkyldsetg....svandtqtanal.pLafglvp 239
                                       ++ + + ++  l  +a+ia++lg++ + +++ + a+++k+a+ + ++d+++     s++++t  + ++   +fg++p
  gi|298675362|ref|YP_003727112.1| 457 HTYSACTIYAGLYGAAEIAKALGHDVEFEYWLKSAKKVKNAIIEYLYDEQKQrfkrSLHDSTIDSSLFgVWYFGILP 533
                                       555677888888899********************************999887777777777766665245889998 PP

                                       GGGH.HHHH CS
                   Bac_rhamnosid6H 240 eaeraakva 248
                                        + +  +v+
  gi|298675362|ref|YP_003727112.1| 534 SDDE--RVV 540
                                       8776..333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (652 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.72u 0.29s 00:00:01.01 Elapsed: 00:00:00.48
# Mc/sec: 4089.28
//
Query:       gi|298675363|ref|YP_003727113.1|  [L=150]
Description: N-acetyltransferase GCN5 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-12   46.7   0.0    4.1e-12   46.4   0.0    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.1e-11   44.9   0.0    1.7e-11   44.4   0.0    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    1.4e-07   31.5   0.0    1.8e-07   31.1   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
     0.0036   17.4   0.0      0.056   13.5   0.0    2.1  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
     0.0096   16.1   0.1      0.036   14.2   0.1    1.8  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.031   14.4   0.0      0.045   13.9   0.0    1.3  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
       0.08   13.6   0.0        0.1   13.3   0.0    1.3  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
       0.21   11.3   0.0       0.53   10.0   0.0    1.6  2  Acetyltransf_16  GNAT acetyltransferase, Mec-17


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.0   1.8e-15   4.1e-12      34      87 ..      40      90 ..      17     115 .. 0.85

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 1.8e-15
                                      EEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHH CS
                    Acetyltransf_1 34 gllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealee 87
                                       ++v+e dge+iG++ l+  ++   + a+i s+aV+pey+++G+Gs+Ll++++e
  gi|298675363|ref|YP_003727113.1| 40 DFYVYETDGEVIGCCALHVMWE---DLAEILSFAVKPEYQNNGIGSELLNTCLE 90
                                      48999*****************...9*************************995 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.0   7.6e-15   1.7e-11       4      74 ..      40     115 ..      37     117 .. 0.71

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 7.6e-15
                                       EEEEEEETTEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHHHH....TT...SEEEEEEEEETHHHHHH.HH CS
                    Acetyltransf_7   4 evfVaeddgkivGfialslld...aeitrlaVdpeyrgkGiGraLlea....ae...kgiileqlelnaekaik.fY 69 
                                        ++V+e dg+++G++al++ +   aei  +aV+pey+++GiG++Ll+     ++    g +++  +l   + i+ f+
  gi|298675363|ref|YP_003727113.1|  40 DFYVYETDGEVIGCCALHVMWedlAEILSFAVKPEYQNNGIGSELLNTcledEHaldVG-TVF--TL---TCIPeFF 110
                                       69**************9999998888888******************633321122222.111..22...1233477 PP

                                       HHTTE CS
                    Acetyltransf_7  70 eklGF 74 
                                       ek  F
  gi|298675363|ref|YP_003727113.1| 111 EKREF 115
                                       77666 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   8.1e-11   1.8e-07      28     111 ..      36     120 ..      18     128 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 8.1e-11
                   Acetyltransf_10  28 egealllvaeeggkivGvielrdgs....hisllfVdpeyrgqGigkaLleaveeeaekdgikleltvnaspyavpf 100
                                       e+   ++v+e +g+++G+++l   +    +i  ++V+pey+ +Gig++Ll++++e    + +    tv   +   +f
  gi|298675363|ref|YP_003727113.1|  36 ESIRDFYVYETDGEVIGCCALHVMWedlaEILSFAVKPEYQNNGIGSELLNTCLEDE--HALD-VGTVFTLTCIPEF 109
                                       4556799************8755555677************************9994..4344.7788888888999 PP

                   Acetyltransf_10 101 YeklGFkavge 111
                                       +ek  F +v++
  gi|298675363|ref|YP_003727113.1| 110 FEKREFNRVEK 120
                                       99999988865 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   2.5e-05     0.056      33     105 ..      29      95 ..       1     118 [. 0.65

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.5e-05
                                       HHHHHHHTT.SEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHT CS
                    Acetyltransf_9  33 eyfrkllee.srvlgaedngelvgqlallplelnvpGktlkaagvtgVavapehrgrgvlskLlaraleemree 105
                                       +++++l+e+  ++++ e +ge++g++al+ +         + a + + av+pe++++g+ s+Ll++ le+ ++ 
  gi|298675363|ref|YP_003727113.1|  29 RSYSELYESiRDFYVYETDGEVIGCCALHVMW-------EDLAEILSFAVKPEYQNNGIGSELLNTCLEDEHAL 95 
                                       44555555425777777777777777766553.......356789999*******************9987665 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   1.6e-05     0.036      52     104 ..      41      90 ..       2     114 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.6e-05
                    Acetyltransf_4  52 flvae.sdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleq 104
                                       f v+e +++++G ++l  + +  +d + +ls+ ++    +++g+g+el++ + +
  gi|298675363|ref|YP_003727113.1|  41 FYVYEtDGEVIGCCALH-VMW--EDLAEILSFAVK-PEYQNNGIGSELLNTCLE 90 
                                       555566***********.777..89*********8.689**********99975 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0     2e-05     0.045       8      53 ..      47      92 ..      40     114 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2e-05
                   Acetyltransf_CG  8 egeevafleYevrkegvldfthTeVpeelrGkGiAkkLvkaaldda 53
                                      +ge ++ +  +v  e+  ++    V++e++  Gi+++L +++l+d 
  gi|298675363|ref|YP_003727113.1| 47 DGEVIGCCALHVMWEDLAEILSFAVKPEYQNNGIGSELLNTCLEDE 92
                                      466677777766667788999999*******************974 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.4e-05       0.1      55     106 ..      40      90 ..       4     107 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.4e-05
                    Acetyltransf_3  55 gwaivlkdtgviGsvglrdleeedeeaelgymlapsfwgkGyateavralle 106
                                        + + + d++viG++ l+ + e+  +  l++ ++p+++++G+++e ++ +le
  gi|298675363|ref|YP_003727113.1|  40 DFYVYETDGEVIGCCALHVMWED-LAEILSFAVKPEYQNNGIGSELLNTCLE 90 
                                       36676777767*******66555.4345679999***********9998776 PP

>> Acetyltransf_16  GNAT acetyltransferase, Mec-17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.59   1.3e+03     105     115 ..      37      47 ..      29      59 .. 0.80
   2 ?   10.0   0.0   0.00024      0.53     104     133 ..      64      93 ..      38     100 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.59
                                       EEEEEEE-GGG CS
                   Acetyltransf_16 105 cvldFyvhese 115
                                       ++ dFyv e+ 
  gi|298675363|ref|YP_003727113.1|  37 SIRDFYVYETD 47 
                                       57799999874 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00024
                                       EEEEEEEE-GGGTTSSHHHHHHHHHHHHHT CS
                   Acetyltransf_16 104 lcvldFyvheseqrkGlGkklfeamlkeek 133
                                         +l F v+ + q +G+G++l+++ l++e+
  gi|298675363|ref|YP_003727113.1|  64 AEILSFAVKPEYQNNGIGSELLNTCLEDEH 93 
                                       4589***********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.33s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 917.84
//
Query:       gi|298675364|ref|YP_003727114.1|  [L=151]
Description: hypothetical protein Metev_1465 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1014  (0.0565564); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1010.13
//
Query:       gi|298675365|ref|YP_003727115.1|  [L=230]
Description: type 11 methyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-17   62.2   0.0    9.1e-17   61.6   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    3.5e-14   53.2   0.0    5.6e-14   52.6   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    1.9e-08   34.3   0.0    3.1e-08   33.6   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    3.3e-08   33.1   0.0    7.8e-08   31.9   0.0    1.6  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    5.5e-08   32.8   0.0    8.2e-08   32.2   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
    2.5e-07   30.3   0.3    8.3e-07   28.6   0.2    1.9  2  TehB             Tellurite resistance protein TehB
      2e-05   24.6   0.0    0.00052   19.9   0.0    2.2  1  Methyltransf_8   Hypothetical methyltransferase
      2e-05   25.3   0.0    4.5e-05   24.1   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
     0.0057   16.2   0.0     0.0063   16.1   0.0    1.2  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
  ------ inclusion threshold ------
      0.038   13.8   0.0      0.047   13.5   0.0    1.1  1  DUF938           Protein of unknown function (DUF938)
      0.085   12.4   0.0       0.14   11.7   0.0    1.3  1  MTS              Methyltransferase small domain


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.6   0.0   5.6e-20   9.1e-17       1      97 []      52     150 ..      52     150 .. 0.96

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 5.6e-20
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCG.BSSSTTTEEEEEEEST. CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaed.lpfedgsfDlvvssga. 73 
                                       +L+lG G+Gr+t+++a+++   kv  vD++++ +e+++e+ + +gl   ++ vq+d+++ lpfed++fD ++s +  
  gi|298675365|ref|YP_003727115.1|  52 ILELGGGQGRDTINFAQNG--FKVDVVDYTKKGIEIIKEKSRYQGLaeYINPVQHDVRNpLPFEDETFDGCYSHMLy 126
                                       8*****************5..**************************9*********888*************9886 PP

                                       GGGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  74 lhhlsdedlekalkeiarvLkpgG 97 
                                        + l+ ++l+ + +ei+rvLkpgG
  gi|298675365|ref|YP_003727115.1| 127 CMALTTSELQFITDEIWRVLKPGG 150
                                       667999*****************9 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.0   3.4e-17   5.6e-14       1      93 [.      53     151 ..      53     154 .. 0.94

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 3.4e-17
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCC.TSS-TT-EEEEEEES-CCC- CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl..kvefvvadaek.lpfednsfDlvvssevlhhv 74 
                                       L++G G+Gr +  +a++g +v  vD++k+ +++ kek++ +gl   ++ v+ d+++ lpfed++fD ++s++  +  
  gi|298675365|ref|YP_003727115.1|  53 LELGGGQGRDTINFAQNGFKVDVVDYTKKGIEIIKEKSRYQGLaeYINPVQHDVRNpLPFEDETFDGCYSHMLYCMA 129
                                       89****************************************9876667******988**************88888 PP

                                       ...CCHHHHHHHHHHHEEEEEE CS
                   Methyltransf_11  75 ...edpekalkeiaRvLkpgGl 93 
                                           +++ + +ei+RvLkpgGl
  gi|298675365|ref|YP_003727115.1| 130 lttSELQFITDEIWRVLKPGGL 151
                                       88899****************8 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.0   1.9e-11   3.1e-08      16     162 ..      43     200 ..      31     203 .. 0.75

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 1.9e-11
                   Methyltransf_23  16 llpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.........kakkaqkdqfdeq.eaaepqgk 82 
                                       ll+ ++ ++r+L++G G G+ +  +++ngf+v++vD   + +ei++         +    +++q+d     ++++++
  gi|298675365|ref|YP_003727115.1|  43 LLK-KENKNRILELGGGQGRDTINFAQNGFKVDVVDYTKKGIEIIKeksryqglaE--YINPVQHDVRnPLPFEDET 116
                                       553.78999***********************************998888887541..333333333313334888* PP

                   Methyltransf_23  83 fdlIvlrevlehvp...dppellrqiatllkpgGylllseplasl....kedrllldwlylvpagrhisffsarslk 152
                                       fd  ++ ++ +       +    + i++ lkpgG+ + ++ ++++       ++  + ly+ ++g  ++ff+ + +k
  gi|298675365|ref|YP_003727115.1| 117 FDGCYSHMLYCMALttsELQFITDEIWRVLKPGGLNIYTVRNKNDirygTGINR-GEDLYEIKDGFIVHFFDKDKIK 192
                                       ***9999999998843225556688999**************999876424444.3457777776666999999999 PP

                   Methyltransf_23 153 elleeaGlev 162
                                       +l +  G+e+
  gi|298675365|ref|YP_003727115.1| 193 HLSR--GFEI 200
                                       9865..5555 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   4.8e-11   7.8e-08      38     148 ..      39     151 ..       9     162 .. 0.81
   2 ?   -2.2   0.0       1.2     2e+03     195     226 ..     182     211 ..     169     214 .. 0.77

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 4.8e-11
                                       HHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT.-TT CS
                   Ubie_methyltran  38 fveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqanaee.Lpf 112
                                        ++kl  + + +++l++ gG g  +++++   ++ +kv+v+D+ ++ +++ ++k + +g    i+ +q +  + Lpf
  gi|298675365|ref|YP_003727115.1|  39 ETIKLLKKENKNRILELGGGQGRDTINFA---QNGFKVDVVDYTKKGIEIIKEKSRYQGLAeYINPVQHDVRNpLPF 112
                                       5667777788899**********999986...5789***********************997799999887544*** PP

                                       S-T-EE..EEEEES-GGG-S-H.HHHHHHHHHHEEEEEE CS
                   Ubie_methyltran 113 eddsfD..vvtvsfGlrnvtDk.lkaLkeayrvlkpGGr 148
                                       ed++fD  +  + + +  +t   +    e++rvlkpGG 
  gi|298675365|ref|YP_003727115.1| 113 EDETFDgcYSHMLYCMALTTSElQFITDEIWRVLKPGGL 151
                                       ******63345778887666550556689********95 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.2
                                       HHHS--HHHHHHHHHHTTEEEEEEEEEGGGTE CS
                   Ubie_methyltran 195 irafPdqetlkeliedaGfksveyesltgGvv 226
                                       i +f d++++k+l +  Gf+ v+ +++  G++
  gi|298675365|ref|YP_003727115.1| 182 IVHFFDKDKIKHLSR--GFEIVDIDEFEEGIL 211
                                       667888888888865..899999999888885 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0     5e-11   8.2e-08       3     108 ..      48     153 ..      46     194 .. 0.86

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 5e-11
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee.leklledekfDl 77 
                                       +++r+l+lG G+G++t+++a++ g+k  v  +D++++ ie  +e+++ +gl   ++  q d+ + l+  +ede+fD 
  gi|298675365|ref|YP_003727115.1|  48 NKNRILELGGGQGRDTINFAQN-GFK--VDVVDYTKKGIEIIKEKSRYQGLAeYINPVQHDVRNpLP--FEDETFDG 119
                                       6789****************54.554..5579*******************978999**********..******** PP

                   Methyltransf_31  78 ilsnevl...naladpdkileeiervlkpggill 108
                                         s+ +     ++++++ i  ei rvlkpgg  +
  gi|298675365|ref|YP_003727115.1| 120 CYSHMLYcmaLTTSELQFITDEIWRVLKPGGLNI 153
                                       888833344367777777777*********9755 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.77   1.3e+03     154     172 ..       9      29 ..       4      35 .. 0.67
   2 !   28.6   0.2   5.1e-10   8.3e-07      23     132 ..      41     154 ..      15     169 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.77
                                       THHHHHTTTSEEE..EEE--E CS
                              TehB 154 gelkeyykdwell..kynedv 172
                                       + l++ y++we +  ++ e+ 
  gi|298675365|ref|YP_003727115.1|   9 ELLNKQYEQWENVytEHSEKF 29 
                                       457889999*98722444555 PP

  == domain 2  score: 28.6 bits;  conditional E-value: 5.1e-10
                                       HHHCCCS-S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TT.EEEEE--GGG.---.-S-E CS
                              TehB  23 veavkivkpgkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlkn.istalydine.akl.dery 96 
                                       ++  k  +  ++l+lg gqgr+++ ++ +g++v+ +d  ++ i+ ++e    + l + i+    d+ + + + de +
  gi|298675365|ref|YP_003727115.1|  41 IKLLKKENKNRILELGGGQGRDTINFAQNGFKVDVVDYTKKGIEIIKEKSRYQGLAEyINPVQHDVRNpLPFeDETF 117
                                       333444446789***********************************999999986537888889855256636889 PP

                                       EEEEEESSG.GGS-GGGHHHHHHHHHHTEEEEEEEEE CS
                              TehB  97 dfilstvvl.mfleaeripsiienmqectkvggynli 132
                                       d   s +++ m l +  +  i +++ +  k+gg n+ 
  gi|298675365|ref|YP_003727115.1| 118 DGCYSHMLYcMALTTSELQFITDEIWRVLKPGGLNIY 154
                                       9999987754999********************9975 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   3.2e-07   0.00052     109     153 ..     102     151 ..       7     164 .. 0.62

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.2e-07
                                       EES-T.TS-S--TT-EE....EEEEES---SS-HHHHHHHHHHHEEEEEE CS
                    Methyltransf_8 109 vacdl.akvPledesvd....vavfclslmgtnladflkeanrvlkvGGl 153
                                       v  d+ + +P ede+ d      ++c++l + +l+  + e+ rvlk+GGl
  gi|298675365|ref|YP_003727115.1| 102 VQHDVrNPLPFEDETFDgcysHMLYCMALTTSELQFITDEIWRVLKPGGL 151
                                       345774459******994443469*************************7 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   2.8e-08   4.5e-05       1      97 [.      53     150 ..      53     151 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2.8e-08
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg..ssfDlvvasnv 75 
                                       Le+G+G G+ +  ++++  + ++ +vD+ ++ ie  kek + ++   ++ ++  + d+ +  +   ++fD  +++ +
  gi|298675365|ref|YP_003727115.1|  53 LELGGGQGRDTINFAQN--GFKVDVVDYTKKGIEIIKEKSRYQGL--AEYINPVQHDVRNPLPFedETFDGCYSHML 125
                                       8****************..**************777777655554..33344444443333333457***9886644 PP

                   Methyltransf_12  76 lhhl...kdirevldnirklLkpgG 97 
                                        +      +++++ d+i ++LkpgG
  gi|298675365|ref|YP_003727115.1| 126 YCMAlttSELQFITDEIWRVLKPGG 150
                                       4444569*****************9 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   3.9e-06    0.0063       3      61 ..      51     129 ..      49     223 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.9e-06
                   Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfe................... 60 
                                        il l +G G ++i+fa+++ kv  +++ ++ ++++++  +  g ++ i +v+ dv +                   
  gi|298675365|ref|YP_003727115.1|  51 RILELGGGQGRDTINFAQNGFKVDVVDYTKKGIEIIKEKSRYQGLAEYINPVQHDVRNplpfedetfdgcyshmlyc 127
                                       689999*************99**********************************9986666666666666665554 PP

                   Methyltransf_15  61 .l 61 
                                        +
  gi|298675365|ref|YP_003727115.1| 128 mA 129
                                       32 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.9e-05     0.047      24      93 ..      47     113 ..      31     153 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.9e-05
                            DUF938  24 kttervLEiasGtGqHAvffApalpnlkwqpsdqdeelresiaawadelalsnlkpPleldvtaevapve 93 
                                       ++++r+LE++ G G+  + fA++    k    d+ ++  e i+   + ++l+    P++ dv ++  p e
  gi|298675365|ref|YP_003727115.1|  47 ENKNRILELGGGQGRDTINFAQNG--FKVDVVDYTKKGIEIIKEKSRYQGLAEYINPVQHDVRNP-LPFE 113
                                       33449****************985..455678999999999********************9887.5555 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   8.5e-05      0.14      25      94 ..      42     111 ..      37     122 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.5e-05
                                       HHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTST CS
                               MTS  25 etlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvleeve 94 
                                       + l+ke ++++l lG G G  ++++a++  +  v++vd  ++ +e+ ke  + ++l+  ++ v++dv + ++
  gi|298675365|ref|YP_003727115.1|  42 KLLKKENKNRILELGGGQGRDTINFAQNGFK--VDVVDYTKKGIEIIKEKSRYQGLAeyINPVQHDVRNPLP 111
                                       6788999999****************97666..9****************9999998888889999887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1463.42
//
Query:       gi|298675366|ref|YP_003727116.1|  [L=455]
Description: monomethylamine methyltransferase MtmB [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.6e-199  662.6   0.2     3e-199  662.5   0.2    1.0  1  MtmB      Monomethylamine methyltransferase MtmB


Domain annotation for each model (and alignments):
>> MtmB  Monomethylamine methyltransferase MtmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  662.5   0.2  1.7e-203    3e-199       3     448 ..       4     452 ..       2     455 .] 0.99

  Alignments for each domain:
  == domain 1  score: 662.5 bits;  conditional E-value: 1.7e-203
                              MtmB   3 vydaykrakkGekveedewdyveipqkaeelkekydikfene.fiPededladrlfqaGlelLvetGvycidtervi 78 
                                       +y+++k+a++Ge+++e+++d +e++qkaeel+e+ydik++ne f+P+d++lad++f+aG++lL++tGvycidter+i
  gi|298675366|ref|YP_003727116.1|   4 LYNYLKAATEGEQKKEKKHD-MEVFQKAEELAEEYDIKYDNEsFVPDDDELADSVFEAGIDLLSSTGVYCIDTERII 79 
                                       79******************.9*****************9988********************************** PP

                              MtmB  79 kvteeeilegikkapkklelGegkdaveleerksndskkPiiqgGPtGapvsedvfleviqsyaqeplvdtivsGvl 155
                                        v++++il++i+++ k+le+G+++++v + er+ +ds++P+i+gGP+G++vse++fl+v+ s+a+eplv++i++Gv+
  gi|298675366|ref|YP_003727116.1|  80 PVDKDDILKSIYSL-KELEIGKYREKVPVPERCPVDSTPPVIIGGPMGGTVSEENFLNVHLSSAREPLVQGIYAGVI 155
                                       **************.************************************************************** PP

                              MtmB 156 etvegkeaktksPfeikatlaearlvkeatslagrpglalkGpetplsaagrlaadlaeglresdshevsqLnelki 232
                                       +++egk +k+ksPfe++a+l+earl+k +t++agr+glal+Gp+tp++++++++++++e+++esd++evsqL+elk+
  gi|298675366|ref|YP_003727116.1| 156 DKLEGKGIKPKSPFEMYAALKEARLEKLSTRIAGREGLALMGPGTPTISQAYMLVSADELYSESDPQEVSQLDELKT 232
                                       ***************************************************************************** PP

                              MtmB 233 dvealnliagykangdvilveqmPifGGya.ggieetaivdvattlasfvltdasfhldGpihirwgstttretlqi 308
                                       d+e+++++++++++g+++l++q+PifGG++ ++++++aivdva+t++++++t+asfh++G+ih++++s++t+e++++
  gi|298675366|ref|YP_003727116.1| 233 DYETFYKSIYHQEHGNHYLSGQCPIFGGTSiASAPGLAIVDVAETIQAKIVTGASFHVSGAIHVNTNSSSTKEVIWA 309
                                       *****************************99********************************************** PP

                              MtmB 309 aahaaaaidantdlllanqyytlaGpctemclletaaqaiadtasGrellsGvaaakGvvkdkttGlearlmgevai 385
                                       ++++++a+++n+++++a++y+++aG+ct+m+++etaaqaiadt+sGr++l+G+a+a+G+++d++tGle+r+m+e+a+
  gi|298675366|ref|YP_003727116.1| 310 SSLSSIALSRNMNYYKARYYWNQAGCCTDMMFYETAAQAIADTVSGRDILIGPAGARGGTADHSTGLESRFMAEIAH 386
                                       ***************************************************************************** PP

                              MtmB 386 aaaglevsevneildklvskyeknyakaPaGkrfqeCydvkt...vePtdeyldvydkalkkleel 448
                                       +a++l++se+n+i++k++sky+++++++P+Gk+f+eCy+v++   +ePtdey+++y+++l+++e++
  gi|298675366|ref|YP_003727116.1| 387 MATDLNLSEANDIVSKIYSKYKDRFTNPPTGKPFDECYVVNSeydMEPTDEYINLYKSILSEIEDY 452
                                       *****************************************9999******************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 2731.40
//
Query:       gi|298675367|ref|YP_003727117.1|  [L=370]
Description: periplasmic-binding protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-24   85.8   0.1    6.4e-24   84.8   0.1    1.4  2  Peripla_BP_2  Periplasmic binding protein
  ------ inclusion threshold ------
       0.07   11.8   0.1       0.11   11.1   0.1    1.2  1  AAA_13        AAA domain


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.8   0.1   7.2e-28   6.4e-24      17     234 ..      73     302 ..      58     305 .. 0.87
   2 ?   -3.3   0.0       0.6   5.4e+03     203     223 ..     336     356 ..     326     357 .. 0.75

  Alignments for each domain:
  == domain 1  score: 84.8 bits;  conditional E-value: 7.2e-28
                                       -GGGEEEB-GGG--GGGGGGT.........TS-BS.BESSSB-HHHHHHH--SEEEE-GGG...GGGHHHHHHHS-E CS
                      Peripla_BP_2  17 atdkvvgvdtttsdpldadklee.......aivev.gadgeidvEklaalkPDlvilskglgltdedeellksgipt 85 
                                       a dkvvgv+    ++ + ++          +++ +  ++g+ d Ek++ + P +++  +  ++ d+d+ ++k g+p+
  gi|298675367|ref|YP_003727117.1|  73 AQDKVVGVESIELREDENRRPYRianpqlkNKPLIgEYRGNTDPEKIVSVNPEVIFWTYVTSPDDADKLQQKTGVPV 149
                                       56777777777777777765554777777755555056677888***************99**************** PP

                                       EE----TTS...HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT..-EEEEEEEETTE..EEEE-TTS CS
                      Peripla_BP_2  86 vivessntg...eslkeqiralgellgledeaeklvaeidsklaaaksaidse.kpkpvlvfggadeggyvvagsns 158
                                       v+ +++  g   ++  +++r  g +l++e++ e++++++++++ +++++++++  +++  v++g+ ++  +  + ++
  gi|298675367|ref|YP_003727117.1| 150 VALNYGTLGvhrDEMFKSLRIMGDVLNKEERSEDVIQFFNKTIKDLNKRTNNIpEDEKRSVYIGGIAYKGSHGYQST 226
                                       ******777*********************************************88888888888887777777777 PP

                                       TTTH.HHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEHHHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE CS
                      Peripla_BP_2 159 yigd.lldalgieniaaeskkseyeeisaEqilasdpdvifvsgraeadnktgleflkenpllaelpAvkngrVyal 234
                                       +  +  +d ++++n+a++  + + ++ s E+i ++dpd++fv+ +  + +   +e+lk++p + +l+Av++g Vy++
  gi|298675367|ref|YP_003727117.1| 227 EPAYpPFDFINAKNVASDM-GTDHADASKEAIIEWDPDILFVDLSTYDAQPSAVEQLKTDPSYRSLTAVEEGEVYGV 302
                                       776524677*********9.*************************88889999**********************86 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.6
                                       HHHT-S--HHHHT-SHHHHTS CS
                      Peripla_BP_2 203 aeadnktgleflkenpllael 223
                                       +e+++++++efl + p++++l
  gi|298675367|ref|YP_003727117.1| 336 PEEKANKIYEFLVSEPVYEDL 356
                                       567888888888888888765 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   1.2e-05      0.11     340     393 ..     153     207 ..     136     210 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 1.2e-05
                            AAA_13 340 lqraleaKrkepfksve.lesvkakiesikklvaeineliakhNekvanleeeke 393
                                       ++  l   r+e+fks+  + +v +k e+ ++ ++ +n++i++ N++++n+ e+++
  gi|298675367|ref|YP_003727117.1| 153 NYGTLGVHRDEMFKSLRiMGDVLNKEERSEDVIQFFNKTIKDLNKRTNNIPEDEK 207
                                       566788889******99559*****************************988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 2167.02
//
Query:       gi|298675368|ref|YP_003727118.1|  [L=364]
Description: transporter permease [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.8e-91  304.0  29.5    1.2e-90  303.7  29.5    1.0  1  FecCD     FecCD transport family


Domain annotation for each model (and alignments):
>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  303.7  29.5   6.7e-95   1.2e-90       2     312 .]      39     360 ..      37     360 .. 0.98

  Alignments for each domain:
  == domain 1  score: 303.7 bits;  conditional E-value: 6.7e-95
                             FecCD   2 lllllllslllgavkispsevfeallgkadsleaeivlelrlprvlaallvGaaLavaGallQtvtrNpLadPsilG 78 
                                       l+ ++++s+++g++++++ +vf++llg++ +++++i++++rlpr+laa+ +G++L+v+G+ lQ+++rNpL +P++lG
  gi|298675368|ref|YP_003727118.1|  39 LITIFFYSISVGNANVPLNDVFRVLLGQNIENSSTIIWNIRLPRALAAISAGVGLSVSGVALQSILRNPLGSPYTLG 115
                                       677899***********************99999******************************************* PP

                             FecCD  79 issgaalgavlallll............lgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsal 143
                                       is++aa+ga++++++l            +   + + ++++afl +l+a++++l+++ k kgasp+ +iL+G+a+s+l
  gi|298675368|ref|YP_003727118.1| 116 ISNAAAFGAAFSVIILgagsmhstgagaVIINNPYITTIVAFLWSLVATFMLLAIS-KYKGASPEVMILIGVALSSL 191
                                       *************9999*******999878889999********************.******************** PP

                             FecCD 144 lsaltsllllllneealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnverv 220
                                       ++a t++l++++++ +l++++fw++G++++a+w ++ ++ ++++ ++++++ ++ +++++  gdetA+ lGvnver+
  gi|298675368|ref|YP_003727118.1| 192 FTAGTMFLQYFADDVELAAVVFWTFGDVGRADWGELGIITAVVVPAMIYFIHNRWNYNAIDAGDETARGLGVNVERI 268
                                       ***************************************************************************** PP

                             FecCD 221 rllllllvalltavavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgiv 297
                                       rl+ +ll++++ta+++++ G+igF+GL+ Phiar+++g++ r l+p+s+++G+llll++d++arl+lsp  lpv i+
  gi|298675368|ref|YP_003727118.1| 269 RLWGMLLASFVTAIIISFLGVIGFIGLVCPHIARRFIGDEQRFLIPASCITGGLLLLASDTAARLMLSPHVLPVAIL 345
                                       ***************************************************************************** PP

                             FecCD 298 taliGapffiylllr 312
                                       t+++Gap+fiyll+r
  gi|298675368|ref|YP_003727118.1| 346 TSFMGAPLFIYLLVR 360
                                       *************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       837  (0.0466841); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.36s 00:00:01.00 Elapsed: 00:00:00.52
# Mc/sec: 2087.76
//
Query:       gi|298675369|ref|YP_003727119.1|  [L=250]
Description: ABC transporter-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-30  105.6   0.0    4.1e-30  105.1   0.0    1.3  1  ABC_tran      ABC transporter
    2.5e-09   37.4   2.4    0.00052   19.9   0.3    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.7e-05   24.4   0.4    0.00018   21.0   0.4    2.0  1  SMC_N         RecF/RecN/SMC N terminal domain
    1.8e-05   25.3   0.2    3.4e-05   24.4   0.2    1.7  1  AAA_23        AAA domain
    4.9e-05   23.6   0.4    0.00057   20.2   0.4    2.0  1  AAA_22        AAA domain
    0.00027   21.0   0.1      0.014   15.4   0.0    2.2  2  AAA_14        AAA domain
    0.00051   20.5   0.0    0.00097   19.6   0.0    1.6  1  AAA_16        AAA ATPase domain
     0.0006   19.5   0.0      0.002   17.8   0.0    1.8  2  AAA_29        P-loop containing region of AAA domain
    0.00073   19.0   0.0     0.0016   17.9   0.0    1.5  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
    0.00089   18.5   0.6     0.0093   15.2   0.6    2.0  1  NB-ARC        NB-ARC domain
    0.00097   19.1   0.0     0.0024   17.8   0.0    1.7  1  RsgA_GTPase   RsgA GTPase
     0.0015   18.5   0.8       0.83    9.5   0.1    2.8  2  NTPase_1      NTPase
     0.0027   17.5   0.4     0.0062   16.3   0.1    1.7  2  AAA_15        AAA ATPase domain
     0.0028   18.1   0.0      0.026   15.0   0.0    2.1  1  AAA           ATPase family associated with various cellular 
     0.0033   16.2   0.0        1.1    7.8   0.0    2.1  2  AAA_13        AAA domain
     0.0076   15.3   0.0      0.018   14.1   0.0    1.6  2  T2SSE         Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.016   14.1   0.1        1.1    8.0   0.0    2.8  2  ABC_ATPase    Predicted ATPase of the ABC class
      0.019   15.3   0.7       0.22   11.8   0.7    2.1  1  AAA_19        AAA domain
      0.023   14.1   0.2      0.038   13.4   0.2    1.4  1  HSM3_N        DNA mismatch repair protein HSM3, N terminal do
      0.033   14.1   0.0      0.059   13.3   0.0    1.4  1  ATPase_2      ATPase domain predominantly from Archaea
      0.054   13.2   0.0      0.094   12.4   0.0    1.3  1  AAA_24        AAA domain
      0.061   13.2   0.0       0.12   12.3   0.0    1.5  1  NACHT         NACHT domain
      0.089   12.6   0.1       0.76    9.6   0.0    2.5  3  IF2_N         Translation initiation factor IF-2, N-terminal 
       0.12   12.0   0.0       0.23   11.1   0.0    1.7  1  AAA_30        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.1   0.0   5.4e-33   4.1e-30       1     137 []      17     163 ..      17     163 .. 0.92

  Alignments for each domain:
  == domain 1  score: 105.1 bits;  conditional E-value: 5.4e-33
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       lk++ ++l++ge++ai+G+nG GK+tLl+++ + l p++G i+++++++ + +  +  +++g++pq +++ + + + 
  gi|298675369|ref|YP_003727119.1|  17 LKDIGFELYHGEILAILGPNGVGKTTLLRCINNILPPKKGIIKVEDEEILSMKNDEIARRLGYVPQRSEVGRLT-AF 92 
                                       799************************************************99**************7666655.77 PP

                                       HH...............HHHTC...HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx...............xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en...............esdee...iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +                +   +   ++ +++kl+l+el  +++    ++LSgG+ q+v+ aral+++pk+lllDEpt
  gi|298675369|ref|YP_003727119.1|  93 DAillgrkphmgfhvkdK---DikiVNFVINKLELEELSLRNI----NELSGGELQKVMFARALVQEPKVLLLDEPT 162
                                       77899999***9986533...2456999***********9*99....*****************************9 PP

                                       T CS
                                       x RF
                          ABC_tran 137 a 137
                                       +
  gi|298675369|ref|YP_003727119.1| 163 S 163
                                       6 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.3     7e-07   0.00052       2      22 ..      30      50 ..      29      77 .. 0.74
   2 !   18.3   0.4   2.2e-06    0.0016     196     300 ..      57     196 ..      49     200 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 7e-07
                            AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                       ++ GpNg+GK++LL+++  +
  gi|298675369|ref|YP_003727119.1| 30 LAILGPNGVGKTTLLRCINNI 50
                                      589***************544 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 2.2e-06
                            AAA_21 196 eielsdlgegeeliasvderlrer.....................................gvvflengdgqelpar 235
                                        i+++d+++ + +++++++rl ++                                      +  le +    ++++
  gi|298675369|ref|YP_003727119.1|  57 IIKVEDEEILSMKNDEIARRLGYVpqrsevgrltafdaillgrkphmgfhvkdkdikivnfVINKLELEELSLRNIN 133
                                       5556666666666666666666666666666666666666667777777777777776666666677777778999* PP

                            AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSpl 300
                                       elS G ++   ++ al + +   ++ll+DEp ++L+ k +  +l+ ++++ + n +  ++t H+  
  gi|298675369|ref|YP_003727119.1| 134 ELSGGELQKVMFARALVQEP---KVLLLDEPTSSLDLKNQLGILKTVRQTVDeNQISAVFTMHDLN 196
                                       *********66666666555...8*************99999998887777755666677777655 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.4   2.4e-07   0.00018      23     192 ..      26     186 ..      18     210 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.4e-07
                                       TSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  23 sksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsi 99 
                                       + ++ ai+GpNG GK+ ll  i  +L  ++   ++ e+ + +++ ++++ +   ++v    ++ ++   +  + + +
  gi|298675369|ref|YP_003727119.1|  26 HGEILAILGPNGVGKTTLLRCINNILPPKKG-IIKVEDEE-ILSMKNDEIARRLGYVPQR-SEVGRL--TAFDAILL 97 
                                       556789*********************7666.66666655.5555588888899999884.444444..56666777 PP

                                       EEEEETT...SEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-H CS
                                       xxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 100 srrvkrk...geseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDe 173
                                        r+   +   ++ ++ki +  ++k e++el +    ++++LSgGe + v    +fA   v+   + llDe  + LD 
  gi|298675369|ref|YP_003727119.1|  98 GRKPHMGfhvKDKDIKIVNFVINKLELEEL-SLR--NINELSGGELQKV----MFARALVQEPKVLLLDEPTSSLDL 167
                                       766443311144555555555555555443.223..4568****98754....56666777778899********** PP

                                       HHHHHHHHHHHHHCTTSEE CS
                                       xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 174 knvkkvaellkeksknaQf 192
                                       kn   + + ++++ ++ Q+
  gi|298675369|ref|YP_003727119.1| 168 KNQLGILKTVRQTVDENQI 186
                                       *************999997 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.2   4.6e-08   3.4e-05      17      54 ..      24      62 ..      10     188 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 4.6e-08
                            AAA_23 17 F.skgltlItGpNGaGKTTildAiklaLygetprlsrks 54
                                      + +  + +I GpNG GKTT+l++i  +L  +++  + ++
  gi|298675369|ref|YP_003727119.1| 24 LyHGEILAILGPNGVGKTTLLRCINNILPPKKGIIKVED 62
                                      34556889****************988866666555555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.4   7.6e-07   0.00057       4     130 ..      26     193 ..      23     201 .. 0.62

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 7.6e-07
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee................................erpevvfvtlp 48 
                                       +  il++ G+ G+GKTtllr + + l+  + + +                                           
  gi|298675369|ref|YP_003727119.1|  26 HGEILAILGPNGVGKTTLLRCINNILPPKKGIIKvedeeilsmkndeiarrlgyvpqrsevgrltaF---------- 92 
                                       6789**********************98777776877777777444333333333333333333221.......... PP

                            AAA_22  49 sstsskdllrellralglelka....................................erlsseell.ealeqalra 88 
                                                 ++                                              ++ls  el   ++++al +
  gi|298675369|ref|YP_003727119.1|  93 ---------DAI---------LlgrkphmgfhvkdkdikivnfvinkleleelslrniNELSGGELQkVMFARALVQ 151
                                       .........222.........02222223455666666666666655555555455555555555554555555555 PP

                            AAA_22  89 ravielliiDEaqh.lr...seealeeLrsllnlsrkgvqliLvGt 130
                                          +++l++DE    l+   +  +l+++r+ ++  + +++ ++  +
  gi|298675369|ref|YP_003727119.1| 152 E--PKVLLLDEPTSsLDlknQLGILKTVRQTVD--ENQISAVFTMH 193
                                       5..459999999998988655999999999999..99998888765 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.9e-05     0.014       2      47 ..      27      69 ..      26      95 .. 0.66
   2 ?    3.7   0.0     0.079        59      34      83 ..     120     171 ..     101     205 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.9e-05
                            AAA_14  2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkla 47
                                      ++il+i G+  vGKTtll ++i++ l +k+ i+ +  +de+  +++
  gi|298675369|ref|YP_003727119.1| 27 GEILAILGPNGVGKTTLL-RCINNILPPKKGIIKV--EDEEILSMK 69
                                      5799*************8.5566666344444444..333333333 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.079
                            AAA_14  34 lyinldderdkkladpe..kllelilek.lkeekktylflDEiqevpewekal 83 
                                         ++l++ +++++++ +  +l ++++++ l  ++ ++l+lDE   + ++++ l
  gi|298675369|ref|YP_003727119.1| 120 NKLELEELSLRNINELSggELQKVMFARaLV-QEPKVLLLDEPTSSLDLKNQL 171
                                       3444555555555544455666666666344.4899******98885554444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.3e-06   0.00097      25      56 ..      28      60 ..      22     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.3e-06
                            AAA_16 25 elvllsGesGvGKsslvrellralekdggif.l 56
                                      e++ + G+ GvGK++l+r++ + l  ++gi  +
  gi|298675369|ref|YP_003727119.1| 28 EILAILGPNGVGKTTLLRCINNILPPKKGIIkV 60
                                      7999*****************999988766543 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.7e-06     0.002      23      50 ..      27      55 ..      16      59 .. 0.86
   2 ?   -2.4   0.0       5.5   4.1e+03      31      43 ..      84      96 ..      83      97 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.7e-06
                            AAA_29 23 g.atlltGpsGsGKSTllDAiqalLvpak 50
                                      g +  + Gp+G+GK+Tll  i+ +L p+k
  gi|298675369|ref|YP_003727119.1| 27 GeILAILGPNGVGKTTLLRCINNILPPKK 55
                                      44889*******************99987 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.5
                            AAA_29 31 sGsGKSTllDAiq 43
                                      s++G  T +DAi 
  gi|298675369|ref|YP_003727119.1| 84 SEVGRLTAFDAIL 96
                                      77899999**985 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.1e-06    0.0016      25      68 ..      30      73 ..      25      98 .. 0.87
   2 ?   -2.9   0.0       4.8   3.6e+03     109     136 ..     155     187 ..     152     202 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.1e-06
                      Mg_chelatase 25 lllvGppGsGKtmlakrlpsllpplseeealevakiasvagkke 68
                                      l ++Gp G GKt l ++++++lpp +    +e ++i s+++ + 
  gi|298675369|ref|YP_003727119.1| 30 LAILGPNGVGKTTLLRCINNILPPKKGIIKVEDEEILSMKNDEI 73
                                      5689**********************999999999999988554 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.8
                      Mg_chelatase 109 vLfLDElp...efkrk..vlevLRePledgevt 136
                                       vL+LDE +   ++k++  +l+++R+ +++++++
  gi|298675369|ref|YP_003727119.1| 155 VLLLDEPTsslDLKNQlgILKTVRQTVDENQIS 187
                                       566666431113333222788888888888776 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.6   1.2e-05    0.0093      22     115 ..      29     164 ..      17     210 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-05
                                       EEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEE......................................... CS
                            NB-ARC  22 vvalvGmgGvGKttlakqilnksdevegrFdsvawv......................................... 57 
                                       ++a+ G  GvGKttl++ i+n +   +g    ++ v                                         
  gi|298675369|ref|YP_003727119.1|  29 ILAILGPNGVGKTTLLRCINNILPPKKG----IIKVedeeilsmkndeiarrlgyvpqrsevgrltafdaillgrkp 101
                                       89*****************998766654....444445555567889999999999999999999999999999999 PP

                                       ..EEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTS...HHHHHHHHCCCTTEEEEEEEE-SH CS
                            NB-ARC  58 ..vvsktdkseeiletilkeLslseddleekeeves...lkrklvrlLltkrfllvlDDVwee 115
                                             +dk  +i+++++++L+l+e  l + +e       k +  r+L +   +l+lD    +
  gi|298675369|ref|YP_003727119.1| 102 hmGFHVKDKDIKIVNFVINKLELEELSLRNINELSGgelQKVMFARALVQEPKVLLLDEPTSS 164
                                       663333455567888899999888888888887776776788888888888888888865554 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   3.1e-06    0.0024      77     122 ..       4      50 ..       1      97 [. 0.77

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.1e-06
                                       SEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  77 yevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                       ++ l  + k+++ l+++  +l + ++ +++G+ GvGK+tL+  +++ 
  gi|298675369|ref|YP_003727119.1|   4 VDNLEFNYKSGNVLKDIGFELYHgEILAILGPNGVGKTTLLRCINNI 50 
                                       566778888999999999988777****************8776653 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.1    0.0011      0.83       3      23 ..      31      51 ..      29      61 .. 0.84
   2 ?    6.0   0.1     0.014        11      40     162 ..      85     229 ..      75     233 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0011
                                      EEE--TTSSHHHHHHHHHHHH CS
                          NTPase_1  3 fiTGppGvGKtTlvkkvlell 23
                                      +i Gp GvGKtTl++ + + l
  gi|298675369|ref|YP_003727119.1| 31 AILGPNGVGKTTLLRCINNIL 51
                                      688***********9998877 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.014
                                       ------EEEEEET.T--EEEEEETT---SSEETTEEE-HHHHHHHHHHHHHHHH...HHH-.............EEE CS
                          NTPase_1  40 eggrrigFkivdlasgeegiLarveakreprvgkyvvdvesfeelalealrkal...sead.............viv 100
                                       e gr ++F+ + l  g++  +    + + +++ ++v++  ++eel l+++++        +             v++
  gi|298675369|ref|YP_003727119.1|  85 EVGRLTAFDAILL--GRKPHMGFHVKDKDIKIVNFVINKLELEELSLRNINELSggeL--QkvmfaralvqepkVLL 157
                                       5566666666666..4444444444456677777777776777776666665433220..12233333333333888 PP

                                       E--.-STTGGG-H.HHHHHHHHHHT.TTSEEEEE--SS-.-SHHHHHHHT-TT-EEEE......--TTTTTT CS
                          NTPase_1 101 iDE.iGkmElksk.kfkeaveevLk.sekpvlavihrrk.dlalveeirerkdvkvfe......vteenrda 162
                                       +DE   ++ lk +  + ++v+++++ ++   ++++h  +  l++ ++    k+++vf+      +t+en ++
  gi|298675369|ref|YP_003727119.1| 158 LDEpTSSLDLKNQlGILKTVRQTVDeNQISAVFTMHDLNlALRFADRYVLVKNGRVFKhggsdiITPENIEQ 229
                                       888556788887734779999999978888999999988888899998888888888877777777777665 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   8.4e-06    0.0062      23      72 ..      28      72 ..      10      78 .. 0.82
   2 ?   -2.5   0.0       4.1   3.1e+03     323     358 ..     152     185 ..     141     198 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.4e-06
                            AAA_15 23 eeltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifenis 72
                                      e +  + G+N++GK+++l+ ++ +l  k    k  ik+e+e++  ++n++
  gi|298675369|ref|YP_003727119.1| 28 E-ILAILGPNGVGKTTLLRCINNILPPK----KGIIKVEDEEILSMKNDE 72
                                      4.8899***************9999999....899999999999988876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.1
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQ 358
                                       ++++ll++EP  +L  ++q  + k+ +  +++n  Q
  gi|298675369|ref|YP_003727119.1| 152 EPKVLLLDEPTSSLDLKNQLGILKTVRQTVDEN--Q 185
                                       567888899988888888888888888888888..4 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   3.4e-05     0.026       3      47 ..      32      78 ..      30     192 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.4e-05
                                      EESSTTSSHHHHHHHHHHHH..THEEEEEETTTCSSSSTTHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavakel..gvefleisgsellskyvgesekkir 47
                                      + Gp G+GKT+l + + + l  +  +++++  e+ls+   e ++++ 
  gi|298675369|ref|YP_003727119.1| 32 ILGPNGVGKTTLLRCINNILppKKGIIKVEDEEILSMKNDEIARRLG 78
                                      68****************99665667777777777663333333333 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0    0.0039       2.9      21      39 ..      32      50 ..      26      76 .. 0.84
   2 !    7.8   0.0    0.0015       1.1     524     565 ..     150     190 ..     140     206 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0039
                            AAA_13 21 iYGwNGaGKTtLSrllrsl 39
                                      i G NG GKTtL r ++++
  gi|298675369|ref|YP_003727119.1| 32 ILGPNGVGKTTLLRCINNI 50
                                      88***********999886 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0015
                            AAA_13 524 igkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlf 565
                                       +++ k+  +D P SSLD + +  +   +++ + ++++++ +f
  gi|298675369|ref|YP_003727119.1| 150 VQEPKVLLLDEPTSSLDLKNQLGILKTVRQTV-DENQISAVF 190
                                       67899*************************98.899999888 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   2.4e-05     0.018     131     168 ..      29      65 ..       2      77 .. 0.82
   2 ?   -2.5   0.0       2.8   2.1e+03      94     140 ..     118     164 ..     111     165 .. 0.51

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.4e-05
                             T2SSE 131 lilvsGgTgsGKttllyallkeinksderivtvEDpvE 168
                                       ++ + G+ g GKttll  + ++++ + + i+ vED   
  gi|298675369|ref|YP_003727119.1|  29 ILAILGPNGVGKTTLLRCINNILPPK-KGIIKVEDEEI 65 
                                       44588*******************99.9*******754 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.8
                             T2SSE  94 viRkksakel...tlddlgaeealkekiaevlrkavrerglilvsGgTgs 140
                                       vi k + +el   ++++l+  e +k  +    r+ v+e +++l+  +T+s
  gi|298675369|ref|YP_003727119.1| 118 VINKLELEELslrNINELSGGELQKVMF---ARALVQEPKVLLLDEPTSS 164
                                       5554445555111233333333333333...3444555788888888876 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0015       1.1     239     265 ..      21      48 ..       5      51 .. 0.81
   2 ?    2.7   0.0     0.057        43     324     353 ..     136     165 ..     106     217 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0015
                                       EEEE-SS.EEEEEE-TTSSHHHHHHHHH CS
                        ABC_ATPase 239 GmgipkG.vtlIvGggfhGKsTLLeAle 265
                                       G  + +G + +I G++  GK+TLL+ ++
  gi|298675369|ref|YP_003727119.1|  21 GFELYHGeILAILGPNGVGKTTLLRCIN 48 
                                       66678999*****************996 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.057
                                       -HHHHHHHHHHHHHHTT-SEEEEEGGGS-H CS
                        ABC_ATPase 324 SGStsqAanimealeagakllLiDEDtsAt 353
                                       SG   q +  ++al  + k+lL+DE ts  
  gi|298675369|ref|YP_003727119.1| 136 SGGELQKVMFARALVQEPKVLLLDEPTSSL 165
                                       666666777777777777777777777754 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.7    0.0003      0.22       9      40 ..      26      57 ..      20     191 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0003
                            AAA_19  9 kekvllvtaGpGtGKTrvlkhivallvelggv 40
                                      + ++l+++++ G GKT++l++i ++l   +g+
  gi|298675369|ref|YP_003727119.1| 26 HGEILAILGPNGVGKTTLLRCINNILPPKKGI 57
                                      567899****************9998766654 PP

>> HSM3_N  DNA mismatch repair protein HSM3, N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   5.1e-05     0.038      32     112 ..     135     215 ..     110     230 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.1e-05
                            HSM3_N  32 lstvaklkedakrllanikrllvenksedkldydlllelldklvkvssfedvlevysvddlvkalkseidslvvaac 108
                                       ls     k    r l++  ++l+ ++++++ld +  l +l+ + ++++ + + +v++++dl  al+     + v   
  gi|298675369|ref|YP_003727119.1| 135 LSGGELQKVMFARALVQEPKVLLLDEPTSSLDLKNQLGILKTVRQTVDENQISAVFTMHDLNLALRFADRYVLVKNG 211
                                       444444444566777888888999999**************************************988777776666 PP

                            HSM3_N 109 kvie 112
                                       +v +
  gi|298675369|ref|YP_003727119.1| 212 RVFK 215
                                       6655 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   7.9e-05     0.059      20      44 ..      27      51 ..      21     123 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.9e-05
                          ATPase_2 20 neiyfiYGpegsGKtaLlkeiienl 44
                                       ei+ i Gp g+GKt+Ll+ i + l
  gi|298675369|ref|YP_003727119.1| 27 GEILAILGPNGVGKTTLLRCINNIL 51
                                      57999*************9776655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00013     0.094       5      33 ..      30      62 ..      27      84 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                            AAA_24  5 iliyGpsgiGKTtlakel....gpkplfidtek 33
                                      ++i Gp+g+GKTtl++ +    +pk  +i +e+
  gi|298675369|ref|YP_003727119.1| 30 LAILGPNGVGKTTLLRCInnilPPKKGIIKVED 62
                                      689************999777766666666665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00016      0.12       2      20 ..      29      47 ..      28      55 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                                      CEEEEC-TTTCHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqkl 20
                                      ++++ G++G+GKTtLl+ +
  gi|298675369|ref|YP_003727119.1| 29 ILAILGPNGVGKTTLLRCI 47
                                      5789************977 PP

>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0         6   4.5e+03      13      24 ..      66      77 ..      64      79 .. 0.70
   2 ?    9.6   0.0     0.001      0.76      24      48 ..     167     190 ..     166     194 .. 0.88
   3 ?   -1.4   0.0       2.8   2.1e+03      36      49 ..     219     232 ..     218     232 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 6
                             IF2_N 13 LgvkskevikkL 24
                                      L +k+ e+ ++L
  gi|298675369|ref|YP_003727119.1| 66 LSMKNDEIARRL 77
                                      667888887766 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.001
                             IF2_N  24 LfkelGievkshsssLDeetaelia 48 
                                       L+++lGi  k++ +++De+++ ++ 
  gi|298675369|ref|YP_003727119.1| 167 LKNQLGIL-KTVRQTVDENQISAVF 190
                                       6678****.***********99885 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.8
                             IF2_N  36 sssLDeetaeliae 49 
                                       s++++ e +e+++e
  gi|298675369|ref|YP_003727119.1| 219 SDIITPENIEQVYE 232
                                       789********986 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00031      0.23      20      45 ..      29      54 ..      23     191 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00031
                            AAA_30 20 vavltGpAGtGKttalkalreaweaa 45
                                      + ++ Gp G GKtt+l+ +++++  +
  gi|298675369|ref|YP_003727119.1| 29 ILAILGPNGVGKTTLLRCINNILPPK 54
                                      67899*************99987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.62u 0.36s 00:00:00.98 Elapsed: 00:00:00.51
# Mc/sec: 1467.95
//
Query:       gi|298675370|ref|YP_003727120.1|  [L=166]
Description: DtxR family iron (metal) dependent repressor [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-17   63.9   0.4    2.2e-17   63.0   0.4    1.5  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    2.5e-15   56.3   0.0    5.3e-15   55.3   0.0    1.5  2  Fe_dep_repr_C   Iron dependent repressor, metal binding and d
    0.00039   20.1   0.0    0.00068   19.4   0.0    1.4  1  LexA_DNA_bind   LexA DNA binding domain
    0.00067   19.6   0.0     0.0011   18.9   0.0    1.3  1  HTH_Crp_2       Crp-like helix-turn-helix domain
    0.00096   18.7   0.0     0.0015   18.1   0.0    1.3  1  HTH_24          Winged helix-turn-helix DNA-binding
      0.002   18.2   0.0     0.0031   17.5   0.0    1.4  1  FeoC            FeoC like transcriptional regulator
     0.0027   18.0   0.0     0.0042   17.4   0.0    1.4  1  Rrf2            Transcriptional regulator
     0.0034   17.2   0.0     0.0058   16.5   0.0    1.3  1  MarR_2          MarR family
  ------ inclusion threshold ------
       0.01   15.6   0.0       0.02   14.6   0.0    1.5  1  HTH_DeoR        DeoR-like helix-turn-helix domain
      0.013   15.3   0.0      0.019   14.8   0.0    1.2  1  HTH_IclR        IclR helix-turn-helix domain
      0.013   15.4   0.1       0.02   14.8   0.1    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.038   14.3   0.1        1.7    9.0   0.0    2.9  3  Mnd1            Mnd1 HTH domain
        0.1   12.8   0.0       0.16   12.2   0.0    1.3  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
       0.15   12.2   0.1       0.81    9.9   0.0    2.2  2  HTH_34          Winged helix DNA-binding domain
       0.17   11.8   0.0        0.3   11.0   0.0    1.4  1  MarR            MarR family


Domain annotation for each model (and alignments):
>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.0   0.4   1.8e-20   2.2e-17       1      60 []       1      60 [.       1      60 [. 0.98

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 1.8e-20
                                      X--HHHHHHHHHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTEE CS
                    Fe_dep_repress  1 dLvestEdYLetIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyveyekykgl 60
                                      +++e+tEdYL+tI  +  +k+++++kd++ +L+ spssV+ m +kL++dGy++yeky+g+
  gi|298675370|ref|YP_003727120.1|  1 MTTERTEDYLKTIEAVVSKKGYAQVKDVSAALGTSPSSVTGMFQKLKNDGYINYEKYGGV 60
                                      799*******************************************************97 PP

>> Fe_dep_repr_C  Iron dependent repressor, metal binding and dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       6.9   8.3e+03      35      46 ..       8      19 ..       2      32 .. 0.61
   2 !   55.3   0.0   4.4e-18   5.3e-15       1      62 [.      63     123 ..      63     129 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 6.9
                                      HHCCCCGGGS-H CS
                     Fe_dep_repr_C 35 eeAerlEhalse 46
                                      +  + +E ++s+
  gi|298675370|ref|YP_003727120.1|  8 DYLKTIEAVVSK 19
                                      444455555555 PP

  == domain 2  score: 55.3 bits;  conditional E-value: 4.4e-18
                                       -HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHCT-.SB- CS
                     Fe_dep_repr_C   1 TekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldellgfpeec 62 
                                       T kG+ +A++++ ++ ++++fL  vlgvd + a+e+A+r+Eh+l++++i+ l ++++f+ ++
  gi|298675370|ref|YP_003727120.1|  63 TSKGKNIAQNTKAKYGVVKDFL-TVLGVDSNTADEDACRIEHVLTDDTIDVLTKFVDFIHHS 123
                                       99********************.88*********************************9885 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   5.7e-07   0.00068       5      58 ..       3      54 ..       1      57 [. 0.94

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 5.7e-07
                                      -HHHHHHHHHHHHHHHHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE- CS
                     LexA_DNA_bind  5 TerQrevldlikasieetgypPsireiaralglkSpsaveehLkaLerKGyier 58
                                      Ter ++ l+ i+a ++++gy+  +++++ alg +Sps+v    ++L++ Gyi+ 
  gi|298675370|ref|YP_003727120.1|  3 TERTEDYLKTIEAVVSKKGYA-QVKDVSAALG-TSPSSVTGMFQKLKNDGYINY 54
                                      899999**************9.79********.67*****************86 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   9.1e-07    0.0011      25      60 ..      26      63 ..      23      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 9.1e-07
                                      HHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEE.EEES CS
                         HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglis.rgrr.iril 60
                                      ++ ++ lG+++++v+ ++++Lk++g+i   +++ ++++
  gi|298675370|ref|YP_003727120.1| 26 KDVSAALGTSPSSVTGMFQKLKNDGYINyEKYGgVTLT 63
                                      578899**********************6443347776 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.2e-06    0.0015      12      47 ..      17      52 ..      11      53 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.2e-06
                            HTH_24 12 LqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      + k++    ++++ +lg Sps v+   ++L+++G+I
  gi|298675370|ref|YP_003727120.1| 17 VSKKGYAQVKDVSAALGTSPSSVTGMFQKLKNDGYI 52
                                      568899999**************************9 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.6e-06    0.0031       2      46 ..      10      54 ..       9      76 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.6e-06
                              FeoC  2 LtelkeyleergrvslkeLsrhfkaspealeamLeqwvrkGrvek 46
                                      L+ +++ + ++g +++k+ s ++ +sp+ + +m   +   G ++ 
  gi|298675370|ref|YP_003727120.1| 10 LKTIEAVVSKKGYAQVKDVSAALGTSPSSVTGMFQKLKNDGYINY 54
                                      899*******************************99988887765 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   3.5e-06    0.0042      22      74 ..      19      69 ..       2      77 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.5e-06
                                      TCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEEESSHCCCS CS
                              Rrf2 22 eeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyrLakppeeI 74
                                      +++ ++++++++  ++sps +  +++kL++ g+++ ++   GG++L+ + ++I
  gi|298675370|ref|YP_003727120.1| 19 KKGYAQVKDVSAALGTSPSSVTGMFQKLKNDGYINYEK--YGGVTLTSKGKNI 69
                                      445589*****************************995..9999999988877 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   4.8e-06    0.0058      23      54 ..      24      55 ..      13      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.8e-06
                                      EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 23 tvgelarrlglsksavsrilkrLvaaGLverr 54
                                       v+++ ++lg s+s+v+ + ++L   G++ ++
  gi|298675370|ref|YP_003727120.1| 24 QVKDVSAALGTSPSSVTGMFQKLKNDGYINYE 55
                                      699**************************876 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.7e-05      0.02       4      55 ..      12      64 ..      10      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.7e-05
                          HTH_DeoR  4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqgllt.RthGGavsis 55
                                       i   + ++g+ +v+++++ lg+S+  +   +++L+++g +    +GG+++ s
  gi|298675370|ref|YP_003727120.1| 12 TIEAVVSKKGYAQVKDVSAALGTSPSSVTGMFQKLKNDGYINyEKYGGVTLTS 64
                                      688899*********************************97526799998766 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.6e-05     0.019      20      49 ..      24      53 ..      13      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.6e-05
                                      BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR 20 tlselArrtglpkStvhRlLqtLvelGyve 49
                                       ++++++++g ++S+v ++ q L + Gy+ 
  gi|298675370|ref|YP_003727120.1| 24 QVKDVSAALGTSPSSVTGMFQKLKNDGYIN 53
                                      589*************************86 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   1.7e-05      0.02      16      56 ..      15      56 ..       8      81 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.7e-05
                                      HHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB 16 aLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                      a++ k+g a++++++ +lg + s+v  + ++L++ G+++ ek
  gi|298675370|ref|YP_003727120.1| 15 AVVsKKGYAQVKDVSAALGTSPSSVTGMFQKLKNDGYINYEK 56
                                      56668999******************************9887 PP

>> Mnd1  Mnd1 HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.25     3e+02      14      39 ..      10      32 ..       9      35 .. 0.86
   2 ?    9.0   0.0    0.0014       1.7      26      53 ..      33      60 ..      26      62 .. 0.84
   3 ?   -0.5   0.0       1.3   1.6e+03      25      41 ..      73      89 ..      66      99 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.25
                              Mnd1 14 lKeleklapkekgivsqsVkdvlqsL 39
                                      lK +e  ++k kg    +Vkdv  +L
  gi|298675370|ref|YP_003727120.1| 10 LKTIEAVVSK-KG--YAQVKDVSAAL 32
                                      7899999999.89..899**997666 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0014
                              Mnd1 26 givsqsVkdvlqsLvdDglveveKiGss 53
                                      g ++ sV  + q+L +Dg ++ eK G  
  gi|298675370|ref|YP_003727120.1| 33 GTSPSSVTGMFQKLKNDGYINYEKYGGV 60
                                      66789999****************9965 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.3
                              Mnd1 25 kgivsqsVkdvlqsLvd 41
                                      ++ +   Vkd l+ L  
  gi|298675370|ref|YP_003727120.1| 73 TKAKYGVVKDFLTVLGV 89
                                      55566789999998854 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00013      0.16      17      53 ..      20      57 ..       7      81 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                    B-block_TFIIIC 17 sGitq.sdLakeskqdprslfyrlksLekkgLIvkqsi 53
                                      +G++q +d++ +++ +p+s+++  ++L++ g+I   ++
  gi|298675370|ref|YP_003727120.1| 20 KGYAQvKDVSAALGTSPSSVTGMFQKLKNDGYINYEKY 57
                                      6888845888999********************76655 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00067      0.81      12      49 ..      20      57 ..      10      77 .. 0.83
   2 ?   -1.4   0.0       2.2   2.7e+03      39      55 ..     138     154 ..     132     156 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00067
                            HTH_34 12 vdeadfvelkealeatdgnLsvhlkkLekagYievdke 49
                                      +  a+ +++++al+++ +      +kL++ gYi+++k 
  gi|298675370|ref|YP_003727120.1| 20 KGYAQVKDVSAALGTSPSSVTGMFQKLKNDGYINYEKY 57
                                      667899999**************************984 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.2
                            HTH_34  39 ekagYievdkefkgkkp 55 
                                       e+ +Yi+++ + k++ p
  gi|298675370|ref|YP_003727120.1| 138 ETGEYINCSPATKKNCP 154
                                       6779****988877665 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00025       0.3      18      48 ..      23      53 ..      16      56 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00025
                                      EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR 18 lsvseLakklgvskstvtrvldrLekkGlie 48
                                      + v++   +lg+s+s+vt +  +L  +G+i+
  gi|298675370|ref|YP_003727120.1| 23 AQVKDVSAALGTSPSSVTGMFQKLKNDGYIN 53
                                      667888899********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1017.83
//
Query:       gi|298675371|ref|YP_003727121.1|  [L=301]
Description: CoB/CoM heterodisulfide reductase subunit B [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-34  116.1   0.3    4.9e-19   68.3   0.2    2.4  2  CCG              Cysteine-rich domain
  ------ inclusion threshold ------
       0.14   12.1   0.1       0.32   10.9   0.1    1.6  1  DUF2024          Domain of unknown function (DUF2024)
       0.17   12.6   0.2       0.45   11.2   0.0    1.7  2  Phage_int_SAM_2  Phage integrase, N-terminal


Domain annotation for each model (and alignments):
>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.0   9.3e-16   5.5e-12       3      84 ..       8      88 ..       6      89 .. 0.94
   2 !   68.3   0.2   8.2e-23   4.9e-19       1      85 []     150     242 ..     150     242 .. 0.96

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 9.3e-16
                               CCG  3 yfdgChllraaypevrkalkkllealgveleelekesCCGagggrsgkee.laealakrnvetaeetgadaivtacpgC 80
                                      +f gC ++ ++yp  +ka+k  l +l ++  +l ++sCC+a+g++++++  + +a+a rn++  ee++ d i+t+c+gC
  gi|298675371|ref|YP_003727121.1|  8 LFLGC-IIPNRYPGIEKATKLCLDKLEIDWIDLPNASCCPAPGVFRSFDMnTWLAIAGRNISISEELERD-ILTICNGC 84
                                      699**.******************************************995777************9888.******** PP

                               CCG 81 llql 84
                                      +++l
  gi|298675371|ref|YP_003727121.1| 85 YGSL 88
                                      *987 PP

  == domain 2  score: 68.3 bits;  conditional E-value: 8.2e-23
                               CCG   1 vayfdgChllraa......ypevrkalkkllealgveleel.ekesCCGagggrsgkee.laealakrnvetaeetg 69 
                                       va+++gChl++++      + e ++ + +l+e +g+   ++ +k +CCGaggg+++  + +a+++++++++++++ g
  gi|298675371|ref|YP_003727121.1| 150 VALHYGCHLVKPSgernlgNVERPEFFDELIESTGASSLDYpDKMECCGAGGGVRSALHdKALEITNHKLSQIKNRG 226
                                       799************************************999***********9999666***************** PP

                               CCG  70 adaivtacpgCllqlk 85 
                                       +d+iv+acp+C++ql+
  gi|298675371|ref|YP_003727121.1| 227 VDCIVNACPFCHMQLD 242
                                       **************96 PP

>> DUF2024  Domain of unknown function (DUF2024)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   5.3e-05      0.32      29      64 ..     208     243 ..     203     254 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.3e-05
                                       HHHHHHHHHHHHHHHT---S---TTTEEEEEEEE-- CS
                           DUF2024  29 eekaleyakeyLkskgeeeakvtskeCkfCHseeae 64 
                                       ++kale +++ L+++ +++ +   + C fCH++  +
  gi|298675371|ref|YP_003727121.1| 208 HDKALEITNHKLSQIKNRGVDCIVNACPFCHMQLDS 243
                                       78999999***********************99544 PP

>> Phage_int_SAM_2  Phage integrase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   7.6e-05      0.45       3      69 ..      72     141 ..      70     143 .. 0.70
   2 ?   -2.8   0.0       1.7     1e+04      38      58 ..     211     231 ..     205     233 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.6e-05
                   Phage_int_SAM_2   3 kLskdlkrlakqagGsykTvndrerilqrlar....eLlalniqvrdvkslKarHieayi.eerlaeeiskr 69 
                                       +L +d+ ++++ + Gs    n++    ++l +    +L+++n + r    +K+rHi +y+ +e   e+is+r
  gi|298675371|ref|YP_003727121.1|  72 ELERDILTICNGCYGSLADANNKLINSEKLKEetnnHLKQINKEFR--GTIKIRHIIEYLyREFGPEDISER 141
                                       7999*************99999866666665511115666665555..469****97776255666777766 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.7
                   Phage_int_SAM_2  38 alniqvrdvkslKarHieayi 58 
                                       al+i  ++ +++K r ++  +
  gi|298675371|ref|YP_003727121.1| 211 ALEITNHKLSQIKNRGVDCIV 231
                                       566666677788888777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       785  (0.0437838); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1883.75
//
Query:       gi|298675372|ref|YP_003727122.1|  [L=164]
Description: CoB/CoM heterodisulfide reductase subunit C [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.5e-11   42.5   7.8    1.1e-10   41.8   7.4    1.6  2  Fer4_8    4Fe-4S dicluster domain
    1.9e-09   37.5   7.4    3.5e-09   36.6   7.4    1.5  1  Fer4_10   4Fe-4S dicluster domain
    1.2e-08   35.4   9.6      2e-08   34.7   9.6    1.4  1  Fer4_17   4Fe-4S dicluster domain
    2.6e-08   33.9   8.6    5.1e-08   33.0   8.6    1.5  1  Fer4_9    4Fe-4S dicluster domain
    1.3e-07   32.0  10.3    3.9e-06   27.3  11.9    2.3  2  Fer4_7    4Fe-4S dicluster domain
      8e-05   22.5  10.7     0.0088   16.1   1.9    2.4  2  Fer4_2    4Fe-4S binding domain
    0.00019   21.5   6.4    0.00036   20.6   6.4    1.4  1  Fer4_21   4Fe-4S dicluster domain
    0.00029   20.5  13.7      0.019   14.8   3.4    2.4  2  Fer4      4Fe-4S binding domain
    0.00052   19.8   3.5       0.26   11.1   0.2    2.2  2  Fer4_20   Dihydroprymidine dehydrogenase domain II, 4Fe-4S cl
     0.0054   17.6  12.0      0.019   15.9  11.2    2.2  1  Fer4_16   4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
      0.012   15.7   7.9      0.084   13.1   1.0    2.3  2  Fer4_18   4Fe-4S dicluster domain
      0.022   15.3   4.1        2.2    8.9   0.3    2.5  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
      0.037   14.8   3.6       0.33   11.7   0.1    2.3  2  Fer4_15   4Fe-4S single cluster domain
      0.055   14.0  11.7       0.27   11.9   3.5    2.5  2  Fer4_4    4Fe-4S binding domain
       0.15   13.1   3.2       0.15   13.1   3.2    2.4  2  Fer4_3    4Fe-4S binding domain
        1.4    9.8  12.4        2.3    9.1   1.0    2.4  2  Fer4_22   4Fe-4S dicluster domain
        5.6    7.2  12.1        1.2    9.4   1.6    2.3  2  Fer4_6    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   7.4     1e-13   1.1e-10       2      65 .]      17      77 ..      16      77 .. 0.77
   2 ?   -2.4   0.0       6.4   6.8e+03      41      41 ..     128     128 ..     101     154 .. 0.50

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 1e-13
                            Fer4_8  2 lekCieCgaCqsaCpvlrrtk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvgi 65
                                      + kC++Cg C  +Cp+ r++  + ++  ++  ++ +++      ++ lw Cttc  C+e+Cp gi
  gi|298675372|ref|YP_003727122.1| 17 ILKCMQCGVCSGSCPSGRHMSlNIRKIIKKAYSN-DRNILT---DKDLWMCTTCYTCQERCPRGI 77
                                      579************9999875555555555444.333333...678***************997 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.4
                            Fer4_8  41 v 41 
                                       +
  gi|298675372|ref|YP_003727122.1| 128 G 128
                                       1 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   7.4   3.3e-12   3.5e-09       6      56 .]      17      74 ..      12      74 .. 0.92

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 3.3e-12
                           Fer4_10  6 ddtCirCgkCvkaCPadl.......tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                        +C++Cg C  +CP+         +  ++ + ++++   +k+++ Ct+c  C+e CP
  gi|298675372|ref|YP_003727122.1| 17 ILKCMQCGVCSGSCPSGRhmslnirKIIKKAYSNDRNILTDKDLWMCTTCYTCQERCP 74
                                      568*************88*****999999999999999999****************9 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   9.6   1.9e-11     2e-08       1      60 [.      19      77 ..      19      78 .. 0.91

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 1.9e-11
                           Fer4_17  1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqgl 60
                                      +C+qCg C  +Cps++ ++ + +k++++a++++  ++ +++    C++C  C+++CP g+
  gi|298675372|ref|YP_003727122.1| 19 KCMQCGVCSGSCPSGRHMSLNIRKIIKKAYSNDR-NILTDKDLWMCTTCYTCQERCPRGI 77
                                      6***************************999755.5667888889************997 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   8.6   4.8e-11   5.1e-08       1      49 [.      19      76 ..      19      77 .. 0.93

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 4.8e-11
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase.........eaCigCgaCveaCpkg 49
                                      kC++Cg C  +Cp+g ++  + +++++    ++         + C++C +C e+Cp+g
  gi|298675372|ref|YP_003727122.1| 19 KCMQCGVCSGSCPSGRHMSLNIRKIIKKAYSNDrniltdkdlWMCTTCYTCQERCPRG 76
                                      7****************999999999987777799*********************98 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.9   1.1e-05     0.012      29      51 ..      11      33 ..       2      34 .. 0.83
   2 !   27.3  11.9   3.7e-09   3.9e-06       1      52 []      19      77 ..      19      77 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.1e-05
                            Fer4_7 29 ekveidpekClgCgaCvavCPtg 51
                                      +k+ +d  kC++Cg+C   CP+g
  gi|298675372|ref|YP_003727122.1| 11 KKTGVDILKCMQCGVCSGSCPSG 33
                                      66778999*************97 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 3.7e-09
                            Fer4_7  1 rCigCgaCvaaCpvkaie.......ldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      +C++Cg C   Cp++  +       ++++ +++++  ++ d ++C++C+ C+++CP g+
  gi|298675372|ref|YP_003727122.1| 19 KCMQCGVCSGSCPSGRHMslnirkiIKKAYSNDRNILTDKDLWMCTTCYTCQERCPRGI 77
                                      7************7766644443333345555566777999***************986 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   1.9   8.3e-06    0.0088       5      21 ..      15      31 ..      12      32 .. 0.88
   2 !   11.2   1.7   0.00031      0.32       7      21 ..      60      74 ..      53      75 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.3e-06
                            Fer4_2  5 vdtdrCigCgaCvsaCP 21
                                      vd  +C++Cg C  +CP
  gi|298675372|ref|YP_003727122.1| 15 VDILKCMQCGVCSGSCP 31
                                      56679************ PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00031
                            Fer4_2  7 tdrCigCgaCvsaCP 21
                                        +C+ C +C+  CP
  gi|298675372|ref|YP_003727122.1| 60 LWMCTTCYTCQERCP 74
                                      449*********9*9 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   6.4   3.4e-07   0.00036       4      52 ..      16      74 ..      13      79 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.4e-07
                           Fer4_21  4 dedkCigCgkCliaCedtshqai........eidaktvlkvved..eCvGCnlCssvCP 52
                                      d  kC++Cg C  +C+ + h  +         +++++ + + +d   C+ C  C + CP
  gi|298675372|ref|YP_003727122.1| 16 DILKCMQCGVCSGSCPSGRHMSLnirkiikkAYSNDRNILTDKDlwMCTTCYTCQERCP 74
                                      5569*************999998666433322223333344444457************ PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   3.4   1.8e-05     0.019       4      21 ..      16      33 ..      14      33 .. 0.87
   2 !   11.0   2.6   0.00029       0.3       7      21 ..      62      76 ..      62      78 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.8e-05
                                      ETTTSSS-THHHHHSTTT CS
                              Fer4  4 deekCigCGaCvevCPvg 21
                                      d  kC+ CG C   CP g
  gi|298675372|ref|YP_003727122.1| 16 DILKCMQCGVCSGSCPSG 33
                                      6669************76 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00029
                                      TSSS-THHHHHSTTT CS
                              Fer4  7 kCigCGaCvevCPvg 21
                                      +C+ C +C e CP g
  gi|298675372|ref|YP_003727122.1| 62 MCTTCYTCQERCPRG 76
                                      5************98 PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.2   0.00053      0.56      23      63 ..      19      57 ..       5      62 .. 0.83
   2 !   11.1   0.2   0.00024      0.26      24      62 ..      63      99 ..      56     121 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00053
                                      T----TT-HHHHCSTT---HHHHHHHHHTT-HHHHHHHHHH CS
                           Fer4_20 23 RClqCkkapcvkgCPveidipefikkiaegnleeaakiike 63
                                      +C+qC    c+ +CP   ++   i+ki ++ +++  +i+++
  gi|298675372|ref|YP_003727122.1| 19 KCMQC--GVCSGSCPSGRHMSLNIRKIIKKAYSNDRNILTD 57
                                      79***..78*******9999999999999988877776665 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00024
                                      ----TT-HHHHCSTT---HHHHHHHHHTT-HHHHHHHHH CS
                           Fer4_20 24 ClqCkkapcvkgCPveidipefikkiaegnleeaakiik 62
                                      C +C   +c++ CP  i+i + + ki++  ++e + + +
  gi|298675372|ref|YP_003727122.1| 63 CTTC--YTCQERCPRGIKIVDGVYKIRNVAVREGTMLSE 99
                                      8888..78******************9999988876654 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9  11.2   1.8e-05     0.019       1      65 [.      19      74 ..      19      76 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.8e-05
                           Fer4_16  1 rCgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCP 65
                                      +C +Cg C  +CP++      + ++++r+ i+++  +++++ +d+      + +t C +Cq+ CP
  gi|298675372|ref|YP_003727122.1| 19 KCMQCGVCSGSCPSGR-----HMSLNIRKIIKKAYSNDRNILTDKD--L--WMCTTCYTCQERCP 74
                                      5************974.....3456789998885555555554443..3..77************ PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   1.1    0.0079       8.4      55      74 ..      14      33 ..       2      47 .. 0.70
   2 ?   13.1   1.0     8e-05     0.084      50      81 ..      52      83 ..      39      93 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0079
                           Fer4_18 55 ekgagdcidcescvkvcPtg 74
                                        +  +c++c++c   cP g
  gi|298675372|ref|YP_003727122.1| 14 GVDILKCMQCGVCSGSCPSG 33
                                      44556899999999999976 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 8e-05
                           Fer4_18 50 keerkekgagdcidcescvkvcPtgidirkGl 81
                                      ++  ++k+   c++c +c + cP gi i +G+
  gi|298675372|ref|YP_003727122.1| 52 RNILTDKDLWMCTTCYTCQERCPRGIKIVDGV 83
                                      44455666778*******************97 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.3    0.0021       2.2       1      18 [.      15      32 ..      15      47 .. 0.90
   2 ?    7.5   0.3    0.0056       5.9       6      18 ..      63      75 ..      59      95 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0021
                           Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                      VD  +C+ cg+C   +P 
  gi|298675372|ref|YP_003727122.1| 15 VDILKCMQCGVCSGSCPS 32
                                      66679***********96 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0056
                           Fer4_13  6 CiacgaCvelaPd 18
                                      C+ c +C e +P 
  gi|298675372|ref|YP_003727122.1| 63 CTTCYTCQERCPR 75
                                      ************6 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.8      0.11   1.1e+02       3      19 ..      15      31 ..      14      37 .. 0.85
   2 ?   11.7   0.1   0.00031      0.33       4      41 ..      59      93 ..      57     126 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.11
                           Fer4_15  3 vDrdaCigcglCvaeap 19
                                      vD  +C+ cg+C   +p
  gi|298675372|ref|YP_003727122.1| 15 VDILKCMQCGVCSGSCP 31
                                      56679*******99988 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00031
                           Fer4_15  4 DrdaCigcglCvaeapevfeldedglasvllddgeiae 41
                                      D + C+ c  C +++p+ +++  dg+ +++  +  + e
  gi|298675372|ref|YP_003727122.1| 59 DLWMCTTCYTCQERCPRGIKIV-DGVYKIR--NVAVRE 93
                                      6678***************999.7776666..233333 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   3.5   0.00025      0.27       3      17 .]      19      33 ..      17      33 .. 0.93
   2 ?    6.4   1.2     0.014        15       4      16 ..      63      75 ..      56      83 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00025
                            Fer4_4  3 rCigCgsCvaaCPqg 17
                                      +C +Cg+C  +CP+g
  gi|298675372|ref|YP_003727122.1| 19 KCMQCGVCSGSCPSG 33
                                      7************86 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.014
                            Fer4_4  4 CigCgsCvaaCPq 16
                                      C+ C  C   CP 
  gi|298675372|ref|YP_003727122.1| 63 CTTCYTCQERCPR 75
                                      *******999995 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   7.0     0.053        56       1      14 [.      20      33 ..      20      33 .. 0.96
   2 ?   13.1   3.2   0.00014      0.15       1      14 [.      63      76 ..      63      77 .. 0.94

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.053
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      C++Cg C  +CP+g
  gi|298675372|ref|YP_003727122.1| 20 CMQCGVCSGSCPSG 33
                                      99**********97 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00014
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      Ct C++C e CP g
  gi|298675372|ref|YP_003727122.1| 63 CTTCYTCQERCPRG 76
                                      ************98 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   3.4      0.01        11       1      16 [.      19      34 ..      19      55 .. 0.78
   2 ?    9.1   1.0    0.0022       2.3      65      96 .]      46      77 ..      33      77 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.01
                           Fer4_22  1 rClsCgaCtlvCptCs 16
                                      +C++Cg C+  Cp+  
  gi|298675372|ref|YP_003727122.1| 19 KCMQCGVCSGSCPSGR 34
                                      7***********9865 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0022
                           Fer4_22 65 rllhklsefkekfgesgCvGCgRCieacpvki 96
                                      + +   +++ +  +  +C+ C  C+e+cp +i
  gi|298675372|ref|YP_003727122.1| 46 KAYSNDRNILTDKDLWMCTTCYTCQERCPRGI 77
                                      3333444555556899*************876 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   1.6    0.0011       1.2       5      22 ..      16      33 ..      14      36 .. 0.86
   2 ?    2.7   3.3      0.14   1.5e+02       9      22 ..      63      76 ..      62      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0011
                            Fer4_6  5 dpdkCigCgdCvrvCPeg 22
                                      d  kC +Cg C   CP g
  gi|298675372|ref|YP_003727122.1| 16 DILKCMQCGVCSGSCPSG 33
                                      5569************86 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.14
                            Fer4_6  9 CigCgdCvrvCPeg 22
                                      C+ C+ C   CP g
  gi|298675372|ref|YP_003727122.1| 63 CTTCYTCQERCPRG 76
                                      99999999999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       882  (0.049194); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 979.28
//
Query:       gi|298675373|ref|YP_003727123.1|  [L=251]
Description: NADPH-dependent F420 reductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      7e-18   65.0   0.1    1.3e-17   64.2   0.1    1.4  1  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
       0.14   11.1   0.0       0.23   10.5   0.0    1.4  1  PDH            Prephenate dehydrogenase
       0.16   11.9   0.0        0.3   11.0   0.0    1.4  1  KR             KR domain


Domain annotation for each model (and alignments):
>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.2   0.1   2.1e-21   1.3e-17       1      96 [.      32     134 ..      32     135 .. 0.96

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 2.1e-21
                                       EEEEE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC............-EEECECHHHHHHH-SE CS
                     F420_oxidored   1 kigii.GaGnmgealasgllaagaqpheivvansrnpekaeelaeelg............vkvtavdneeaaeeadv 64 
                                       ki+ii G+G++ge+l  ++++++    ei+++ sr+peka e+ae++             v++ ++ n++a + ad 
  gi|298675373|ref|YP_003727123.1|  32 KIAIIgGTGHLGEGLSIRWAQKN----EIIIG-SRKPEKAVEAAERYLsemksigcdtskVEIRGMGNKDASNVADL 103
                                       7*********************7....99988.**************9***************************** PP

                                       EEE-S-HHHHHHHHHHCGHHHHTTSEEEEESS CS
                     F420_oxidored  65 vvlavkpedveevlselakdalkgklvisvla 96 
                                       +vlav++++v ++l+ +  ++l++k++++  +
  gi|298675373|ref|YP_003727123.1| 104 IVLAVPYKHVFKTLEPI-YSELENKILVTPIV 134
                                       *****************.999*******8766 PP

>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   3.8e-05      0.23      41      81 ..      96     136 ..      47     140 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 3.8e-05
                                       GGGCCGSEEEE-S-GGGHHHHHHHHHHHS-TT-EEEE--S- CS
                               PDH  41 eavkeadivvlavPvevilevlkelaphlkedalitDvgsv 81 
                                       +a + ad++vlavP + + ++l+ + + l+++ l+t +  +
  gi|298675373|ref|YP_003727123.1|  96 DASNVADLIVLAVPYKHVFKTLEPIYSELENKILVTPIVPM 136
                                       455679***************************99976655 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0     5e-05       0.3       4      55 ..      34      87 ..      32     113 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5e-05
                                      EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS...--HHHHHHHHHHHHTT-...EE CS
                                KR  4 litGGlGgLGlelarwlaekgarhlvllsRsa.aadedskaliaelealga...ev 55
                                       i+GG+G+LG  l+   a+k  +++++ sR++ +a e++++ ++e+++ g+   +v
  gi|298675373|ref|YP_003727123.1| 34 AIIGGTGHLGEGLSIRWAQK--NEIIIGSRKPeKAVEAAERYLSEMKSIGCdtsKV 87
                                      599********998877775..79*******6345566667899999999843334 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1517.65
//
Query:       gi|298675374|ref|YP_003727124.1|  [L=407]
Description: HNH endonuclease [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-61  207.4   3.9    2.3e-61  206.6   3.9    1.4  1  RRXRR     RRXRR protein
    1.8e-11   44.0   8.8    4.3e-11   42.8   8.8    1.7  1  HNH       HNH endonuclease
    1.9e-07   30.8   5.7      5e-07   29.5   5.7    1.7  1  HNH_5     HNH endonuclease
    8.6e-05   22.6   0.4     0.0004   20.5   0.4    2.1  1  HNH_2     HNH endonuclease
  ------ inclusion threshold ------
      0.032   14.1   0.9        4.7    7.2   0.1    2.7  2  PHD       PHD-finger
        6.6    6.4   7.6        3.6    7.3   3.4    2.3  2  zf_UBZ    Ubiquitin-Binding Zinc Finger


Domain annotation for each model (and alignments):
>> RRXRR  RRXRR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.6   3.9   7.9e-65   2.3e-61       1     174 []       3     176 ..       3     176 .. 0.99

  Alignments for each domain:
  == domain 1  score: 206.6 bits;  conditional E-value: 7.9e-65
                             RRXRR   1 VfVldkegkplmPtkpkrarklLkqgkAkvvrrkpftiqLkeesseesvqpvelklDpGskvtGiavvsekkvllka 77 
                                       V+Vl+k++kplmPt+p++ar+lLk+gkAkvvrr+pf i+L++e++e++ qpv  ++D+Gsk++G+a+v +++v++++
  gi|298675374|ref|YP_003727124.1|   3 VYVLSKNKKPLMPTRPAKARRLLKSGKAKVVRRTPFSIKLLYETTEYT-QPVIAGMDSGSKYIGCAAVANDEVMYQS 78 
                                       9***********************************************.**************************** PP

                             RRXRR  78 elelrgkdikkkleeRrelRraRRsrktryrqaRfdnR..kkkegwLapslqhrvqthlrvvkrlakllpitkivve 152
                                       e++lr  d++kk+++R+ +R++RR+rktryr++Rf+nR  +kke+++aps++++vq+h r  + ++++lp++k+ ve
  gi|298675374|ref|YP_003727124.1|  79 EIKLRD-DVSKKMKDRADHRMNRRYRKTRYRKPRFNNRgnSKKENRIAPSIKSKVQSHERERRFVESILPVKKWIVE 154
                                       *****9.********************************99************************************ PP

                             RRXRR 153 lvkfDiqklenpeisgaeyqqG 174
                                       + +fDi+k++np++sg+ yq+G
  gi|298675374|ref|YP_003727124.1| 155 TTSFDIHKITNPNVSGTGYQNG 176
                                       ********************98 PP

>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   8.8   1.4e-14   4.3e-11       1      46 [.     196     240 ..     196     241 .. 0.96

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 1.4e-14
                               HNH   1 CeyCgrkfhksealevdHiipisqggaddieNlqllCksCHnkkhd 46 
                                       C+ C++k ++ + le++Hii +s+gg+d  +Nl++lC++CH+k+h+
  gi|298675374|ref|YP_003727124.1| 196 CQKCKNKSKD-PKLECHHIIFRSKGGTDRPNNLITLCETCHSKLHK 240
                                       *******777.7********************************97 PP

>> HNH_5  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   5.7   1.7e-10     5e-07       1      43 [.     196     238 ..     196     245 .. 0.96

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 1.7e-10
                             HNH_5   1 CiyCgkeiaekelseeHIiPeslGGkltisnlvtlCkkCNqkk 43 
                                       C+ C+++ ++ +l+  HIi +s+GG+  ++nl tlC++C++k+
  gi|298675374|ref|YP_003727124.1| 196 CQKCKNKSKDPKLECHHIIFRSKGGTDRPNNLITLCETCHSKL 238
                                       9****************************************98 PP

>> HNH_2  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.4   1.3e-07    0.0004       8      72 .]     205     246 ..     196     246 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.3e-07
                             HNH_2   8 dpslleaAHIiPwslssffndlilnrfeigrillekgstidspsNgllLspdiHklFdqflfafe 72 
                                       dp  le++HIi           +++            +++d+p+N+++L+ ++H   +++ f+++
  gi|298675374|ref|YP_003727124.1| 205 DP-KLECHHIIF----------RSK------------GGTDRPNNLITLCETCHSKLHKGEFSIN 246
                                       44.566666666..........334............469**********************996 PP

>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1    0.0096        29      40      52 .]     190     202 ..     182     202 .. 0.78
   2 ?    7.2   0.1    0.0016       4.7      10      35 ..     223     248 ..     216     256 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0096
                                       HSSTBSSTTTHTT CS
                               PHD  40 pegewlCekCkek 52 
                                       + ++++C+kCk+k
  gi|298675374|ref|YP_003727124.1| 190 HRDDYTCQKCKNK 202
                                       4568******985 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0016
                                       STTSCEEEETTTSCEEETTTSSSTHS CS
                               PHD  10 deeeelvqCdgCkrwfHqkClkpple 35 
                                         ++ + +C++C++  H+   +++++
  gi|298675374|ref|YP_003727124.1| 223 RPNNLITLCETCHSKLHKGEFSINKN 248
                                       44667779*********876666655 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   3.4    0.0012       3.6       1      20 [.     192     211 ..     192     212 .. 0.93
   2 ?    0.6   0.1      0.15   4.5e+02       4      13 ..     230     239 ..     229     243 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0012
                            zf_UBZ   1 dtylCerCgkeipeselqEH 20 
                                       d y+C++C+ +  +++l++H
  gi|298675374|ref|YP_003727124.1| 192 DDYTCQKCKNKSKDPKLECH 211
                                       68****************99 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.15
                            zf_UBZ   4 lCerCgkeip 13 
                                       lCe C++++ 
  gi|298675374|ref|YP_003727124.1| 230 LCETCHSKLH 239
                                       7*****9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1137  (0.0634168); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.68u 0.27s 00:00:00.95 Elapsed: 00:00:00.51
# Mc/sec: 2399.81
//
Query:       gi|298675375|ref|YP_003727125.1|  [L=245]
Description: glutamate synthase subunit alpha domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-38  130.9  10.3    5.2e-38  130.6  10.3    1.1  1  GXGXG     GXGXG motif


Domain annotation for each model (and alignments):
>> GXGXG  GXGXG motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.6  10.3   2.9e-42   5.2e-38      10     184 ..      19     198 ..      10     204 .. 0.86

  Alignments for each domain:
  == domain 1  score: 130.6 bits;  conditional E-value: 2.9e-42
                                       TTH.........HHHHHHHHHHTTT---.-EEEEEEEEEE-TTTTTT--TTEEEEEEEEE-STTTTT-ESSEEEEE- CS
                             GXGXG  10 vgt.........ilsneiakrygeeglpedtikiklkGsaGqslgaflakGltleleGdandyvGkglsgGkivikp 77 
                                       ++          il+n  ++ry  +g++ ++++i+++G++G++ ++f+ +G++l+++G+a+d+++++++ Gki++++
  gi|298675375|ref|YP_003727125.1|  19 IQDeaesgetefILDNLNGQRYLGTGIN-KNVNITVNGTPGNDCAVFM-NGPSLTINGNAQDMIANTMNMGKITVHG 93 
                                       544555555666999*************.9******************.**************************** PP

                                       -TT-SS-GGGSB-S-SSTTTT--SEEEEESSB--SSTTTT-.....SS-EEEESEB.-SSTTTT-EEEEEEE-S-B. CS
                             GXGXG  78 skeskfkaeeniivGnvvlygatgGklfirgkageRfavrn.....sgatavvegv.gdhgceYmtGGvvvvLgkt. 147
                                       +             G+vv yg++gGklfi+g++g+R+++++     + ++++ +g+  d+++eYm+GG+ ++Lg   
  gi|298675375|ref|YP_003727125.1|  94 NV------------GDVVGYGMRGGKLFIKGNVGYRAGIHMkeyksQIPVIISGGTaRDFLGEYMAGGIFILLGIDn 158
                                       99............***************************99984444455566689****************999 PP

                                       ......-SSBTTT--EEEEEEE.-SSSTHHHHB-TTT-EEEES- CS
                             GXGXG 148 ......grnfaaGmsgGiayvl.dedekfekklnkelvelekve 184
                                             g+++++Gm+gG++y++ d++++   +l+ke+ +l+  +
  gi|298675375|ref|YP_003727125.1| 159 dseiitGDYLGTGMHGGVIYIRgDVEND---TLGKEVKKLDI-D 198
                                       999*******************888877...77777666654.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1494.62
//
Query:       gi|298675376|ref|YP_003727126.1|  [L=503]
Description: glutamate synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   6.6e-139  463.1   0.0   9.7e-139  462.6   0.0    1.2  1  Glu_synthase     Conserved region in glutamate synthase
    7.6e-15   55.1   0.0    2.3e-07   30.6   0.0    2.3  2  Glu_syn_central  Glutamate synthase central domain
      9e-08   31.6  22.1    1.1e-05   25.0   4.2    3.0  3  Fer4             4Fe-4S binding domain
    1.3e-07   31.0   6.1    8.5e-05   21.7   4.7    2.7  3  IMPDH            IMP dehydrogenase / GMP reductase domain
      2e-07   30.4   1.4      2e-07   30.4   1.4    2.9  4  FMN_dh           FMN-dependent dehydrogenase
    6.5e-07   29.9  16.1    3.6e-06   27.4  11.5    2.9  3  Fer4_7           4Fe-4S dicluster domain
    3.1e-06   28.0  11.1    0.00039   21.3   0.8    3.3  3  Fer4_16          4Fe-4S double cluster binding domain
    4.5e-06   26.5  14.3    9.2e-05   22.4   1.6    3.1  2  Fer4_6           4Fe-4S binding domain
    2.9e-05   24.1  15.4    9.1e-05   22.5  10.6    2.7  2  Fer4_9           4Fe-4S dicluster domain
    3.1e-05   24.0   9.1    3.1e-05   24.0   9.1    2.2  2  Fer4_21          4Fe-4S dicluster domain
    5.4e-05   22.7   3.0    0.00012   21.6   3.0    1.5  1  NMO              Nitronate monooxygenase
    0.00018   21.9   8.5       0.19   12.2   0.2    3.6  3  Fer4_8           4Fe-4S dicluster domain
    0.00074   19.6  19.7     0.0058   16.7   2.7    3.2  3  Fer4_10          4Fe-4S dicluster domain
       0.01   15.9  23.3       0.01   15.9   2.1    3.4  3  Fer4_2           4Fe-4S binding domain
  ------ inclusion threshold ------
      0.085   11.9   0.1       0.15   11.1   0.1    1.4  1  Dus              Dihydrouridine synthase (Dus)
      0.097   12.1   1.0       0.11   11.9   0.1    1.5  2  His_biosynth     Histidine biosynthesis protein
       0.21   12.1  18.5        3.6    8.2   3.9    3.5  3  Fer4_17          4Fe-4S dicluster domain
        5.5    7.2  13.0      0.055   13.7   4.9    1.8  1  Fer4_18          4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  462.6   0.0  9.7e-142  9.7e-139       3     368 .]     104     469 ..     102     469 .. 0.98

  Alignments for each domain:
  == domain 1  score: 462.6 bits;  conditional E-value: 9.7e-142
                                       S-HHHHHHHHHHHHH---HHHHHHHHHHHTS.-S-SGGGGEEE--SS--..--GGGS--HHHHHTTEE---B-TTTS CS
                      Glu_synthase   3 neievikllqkavqveskesidkyrekleerevlkakrdlleldaaeeal.ikleevepalkikkriltsamSyGal 78 
                                       ++i +++ll +a+qv +++sid +re++e r++l++k+d le+ +++e + +  +e++p++k++ +++++amSyGa+
  gi|298675376|ref|YP_003727126.1| 104 HKIIWDHLLIDACQV-TNPSIDPLREPMELRTYLGKKPDNLEFVENKEGEiELATELQPQVKLDVPVVFAAMSYGAV 179
                                       577899*********.***************************8777766256789********************* PP

                                       -HHHHHHHHHHHHHHT-B-EETTS---GGGGS-----SEEEE-TT-TT--HHHHHH-SEEEEE---TTSTTS--EE- CS
                      Glu_synthase  79 seeahealakamnrlgtksntGEGGedeerlktakdvaikQvasgrFGvteeyLnnakaleikiaQGakpgeGgqlp 155
                                       s ++h+ala a+ + gt +ntGEGG++e  +++ +++ ++QvasgrFGv++eyLn+++ +eiki+QGakpg+Gg+lp
  gi|298675376|ref|YP_003727126.1| 180 SLNTHKALALAARKSGTLMNTGEGGLHEDLYRYSDNI-MVQVASGRFGVHNEYLNTCSMIEIKIGQGAKPGIGGHLP 255
                                       *************************************.*************************************** PP

                                       GGG--HHHHHHHTS-TT--EE--SS-TT-SSHHHHHHHHHHHHHH-.TTSEEEEEEE-STTHHHHHHHHHHTT-SEE CS
                      Glu_synthase 156 geKvseeiakiRkikpgvdliSPaphhdiysiedlaqliedLkevn.keakvsvKlvaeagvetiaagvakanadii 231
                                       geKv e+i+k+R+i+ g+d++SPaphhdiysiedl+qli++Lke++ +e++v+vK+ a ++v +ia+gv++a+ad++
  gi|298675376|ref|YP_003727126.1| 256 GEKVGEDISKTRMIPLGTDVLSPAPHHDIYSIEDLSQLIYALKEATnYEKPVGVKISAVHNVAAIASGVVRAGADVL 332
                                       *********************************************99****************************** PP

                                       EEE-TT---SSEEHHHHHHB---HHHHHHHHHHHHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-SHHHHH CS
                      Glu_synthase 232 lidGleGGTGAspkssikhaGlPlelalaevdqtlkeeglrdrvsliadGglktgadvvkalalGAdavgigtaali 308
                                       +idG++GG GAsp ++++++G+P+elala vdq+l++eg+r+r s+  +G ++++adv+ka+alGAdav igtaali
  gi|298675376|ref|YP_003727126.1| 333 TIDGYRGGSGASPMVIRDNVGIPIELALATVDQRLRDEGIRNRASILCAGSIRSSADVAKAVALGADAVVIGTAALI 409
                                       ***************************************************************************** PP

                                       HTT--S---GGGT--TTSSS---HHHH..TT----HHHHHHHHHHHHHHHHHHHHHHT-S CS
                      Glu_synthase 309 algCimarvChtntCpvGvatqdpeLrkrlkveekaervvnyikalaeevrellaalgin 368
                                       a+gC ++++C+t++C++G+atq+peL +rl+ e +a++++n++  ++ e++e+l++lg+n
  gi|298675376|ref|YP_003727126.1| 410 AMGCSVCQRCYTGNCAWGIATQKPELVNRLDPEIAAQKLTNLLSGWSFELKEILGSLGVN 469
                                       *********************************************************986 PP

>> Glu_syn_central  Glutamate synthase central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   7.4e-08   7.3e-05      56      98 ..     116     156 ..     101     222 .. 0.85
   2 !   30.6   0.0   2.3e-10   2.3e-07      91     269 ..     265     476 ..     255     479 .. 0.66

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 7.4e-08
                                       --SSS----TTTTGGG-B--EEES----SSS--GGGG-EEEES CS
                   Glu_syn_central  56 AqVTNPpiDpiREelvmsletllGkegnlleeeeeqakrlkle 98 
                                        qVTNP+iDp+RE   m l+t+lGk+++ le  e++  +++l+
  gi|298675376|ref|YP_003727126.1| 116 CQVTNPSIDPLREP--MELRTYLGKKPDNLEFVENKEGEIELA 156
                                       7************6..89**********999666666666554 PP

  == domain 2  score: 30.6 bits;  conditional E-value: 2.3e-10
                                       GG-EEEESSSB--HHHHHHH....HHSSS-EEEEESEE......S.HHHHHHHHHHHHHHHHHTT-SEEEEESS... CS
                   Glu_syn_central  91 qakrlklesPiLteeeleklkklkekkefkaktlditfeae...a.leealerlceeaeeavregaeilvLsDr... 160
                                       +++++ l + +L+ +  +++ ++++ +++  +  ++t   e   +   +a++++++ a+  vr+ga++l ++     
  gi|298675376|ref|YP_003727126.1| 265 KTRMIPLGTDVLSPAPHHDIYSIEDLSQLIYALKEATN-YEkpvGvKISAVHNVAAIASGVVRAGADVLTIDGYrgg 340
                                       55666677777777777777666444333333333322.122342356899999*****************987677 PP

                                       .....--STTEEE--HHHHHHHHHHHHHHTT-GGG-EEEEEESS--SHHHHHHHHHTT-SEEEEHHHHHHH...... CS
                   Glu_syn_central 161 .....kvseervpipslLavgavhhhLvrkglrtkvslvvesgearevhhfavllgyGadavnPylaleti...... 226
                                             v +++v ip  La+++v+++L ++g r+++s+++ +g++r+  ++a  +++Gadav    a  ++      
  gi|298675376|ref|YP_003727126.1| 341 sgaspMVIRDNVGIPIELALATVDQRLRDEGIRNRASILC-AGSIRSSADVAKAVALGADAVVIGTAALIAmgcsvc 416
                                       777666788****************************865.8*******************9755544444233332 PP

                                       HHHHTTT...............S-.......----HH..HHHHHHHHHHHHHHHHHTT--BHHHHHH CS
                   Glu_syn_central 227 eklveeg...............al.......aeeele..knyrkavekGllKimskmGistlqSYkg 269
                                       +     +               +l        ++  +  +n+ ++ +  l  i+  +G+  ++S +g
  gi|298675376|ref|YP_003727126.1| 417 Q-----RcytgncawgiatqkpELvnrldpeIAA--QklTNLLSGWSFELKEILGSLGVNSIESLRG 476
                                       1.....1233334333333333113333322122..1347777777777777777777777777766 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   1.4     6e-07    0.0006       2      24 .]      11      33 ..      10      33 .. 0.92
   2 !   25.0   4.2   1.1e-08   1.1e-05       2      24 .]      40      62 ..      39      62 .. 0.92
   3 ?   -2.7   1.8       6.4   6.4e+03       8      14 ..     413     419 ..     411     421 .. 0.63

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 6e-07
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                       id  +C +CG+Cv+ C +gA++
  gi|298675376|ref|YP_003727126.1| 11 SIDSARCRKCGICVNNCSFGALE 33
                                      69******************985 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 1.1e-08
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                      + d +kC++C +Cv+ CP +AIt
  gi|298675376|ref|YP_003727126.1| 40 IPDDSKCVACYRCVSKCPDNAIT 62
                                      5699******************7 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 6.4
                                       SSS-THH CS
                              Fer4   8 CigCGaC 14 
                                       C  C +C
  gi|298675376|ref|YP_003727126.1| 413 CSVCQRC 419
                                       6666666 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.3   0.00014      0.14      18     129 ..     150     341 ..     140     350 .. 0.82
   2 !   21.7   4.7   8.5e-08   8.5e-05     159     237 ..     321     405 ..     292     414 .. 0.81
   3 ?   -2.5   0.0       1.9   1.9e+03     299     328 ..     448     477 ..     444     482 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
                                       GGGSB--EESSTTEEESSSEEE-SST..TT...-SHHHHHHHHHTTSE.....EEE-SSS-HHHHHHHHHHHHTS.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx..xx...xxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxx.. RF
                             IMPDH  18 pkevdlktkltkkiklniPlvsaamd..tv...tesemAialareGgi.....gvihknlsieeqaeevkkvkrs.. 82 
                                         e++l+t+l  ++kl +P+v aam   +v   t + +A a  ++G +     g +h++l   +   +v+       
  gi|298675376|ref|YP_003727126.1| 150 EGEIELATELQPQVKLDVPVVFAAMSygAVslnTHKALALAARKSGTLmntgeGGLHEDLYRYSDNIMVQVASGRfg 226
                                       45899********************7333433377888888888886644444778888887777777765554489 PP

                                       ...................................................................TTSXBX.TTS CS
                                       ...................................................................xxxxxx.xxx RF
                             IMPDH  83 ...................................................................pnaakd.ekg 91 
                                                                                                            a k+ ++ 
  gi|298675376|ref|YP_003727126.1| 227 vhneylntcsmieikigqgakpgigghlpgekvgedisktrmiplgtdvlspaphhdiysiedlsqlIYALKEaTNY 303
                                       9999**********************************************************999994444442667 PP

                                       XB-EEEEE-SSTTHHHHHHHHHHTT-SEEEEE-STSSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH  92 rllvgaavgvkedalervkalveagvdvlvvdsahghs 129
                                       +  vg  +++ ++  + ++ +v+ag+dvl++d   g s
  gi|298675376|ref|YP_003727126.1| 304 EKPVGVKISAVHNVAAIASGVVRAGADVLTIDGYRGGS 341
                                       7889999999999999999************9877765 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 8.5e-08
                                       HHHHHHTT-SEEEE.-SS-STTBHHHHH.CSB---HHHHHHHHHHHHCTCT....-EEEEES---SHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxx.xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 159 akaLieagadavkv.GiGpGsiCttrvv.agvGvpqltAvaevaeaakkag....vpviaDGGikysgdivkAlaaG 229
                                       a+ +++agad++ + G   Gs     v+   vG+p   A+a+v +  ++ g      ++  G i++s d++kA+a+G
  gi|298675376|ref|YP_003727126.1| 321 ASGVVRAGADVLTIdGYRGGSGASPMVIrDNVGIPIELALATVDQRLRDEGirnrASILCAGSIRSSADVAKAVALG 397
                                       5668899999999977777777666655258*****************999445557999***************** PP

                                       -SEEEESC CS
                                       xxxxxxxx RF
                             IMPDH 230 adavmlGs 237
                                       adav++G 
  gi|298675376|ref|YP_003727126.1| 398 ADAVVIGT 405
                                       *******7 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHHHHHHHHHT-SSHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 299 vkevveqlvgglrsgmgylGaktieelkek 328
                                       ++++++    +l++ +g lG+++ie+l+ +
  gi|298675376|ref|YP_003727126.1| 448 LTNLLSGWSFELKEILGSLGVNSIESLRGN 477
                                       556666677789999***********9976 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.16   1.6e+02      56      92 ..     164     199 ..     146     206 .. 0.79
   2 ?   -4.0   0.1       5.5   5.5e+03     272     287 ..     317     332 ..     311     333 .. 0.77
   3 !   30.4   1.4     2e-10     2e-07     268     308 ..     372     412 ..     348     417 .. 0.82
   4 ?   -0.8   0.0      0.59   5.8e+02     315     342 ..     448     475 ..     444     480 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.16
                                       EESSSEEE--BSTGGGTSTTHHHHHHHHHHHHTS-EE CS
                            FMN_dh  56 klslPvliaPvglaklahpdgelalaraaakagipfv 92 
                                       kl++Pv++a++++  +   +   ala aa+k g+++ 
  gi|298675376|ref|YP_003727126.1| 164 KLDVPVVFAAMSYGAVSL-NTHKALALAARKSGTLMN 199
                                       799********9987765.788899999999999885 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 5.5
                                       S-EEEESS--SHHHHH CS
                            FMN_dh 272 ievlvDgGirrGsDvl 287
                                       +  +++g +r G+Dvl
  gi|298675376|ref|YP_003727126.1| 317 VAAIASGVVRAGADVL 332
                                       5667889999999997 PP

  == domain 3  score: 30.4 bits;  conditional E-value: 2e-10
                                       H..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHHHH CS
                            FMN_dh 268 vggrievlvDgGirrGsDvlkAlalGAdavllGRpflygla 308
                                       +++r+ +l+ g ir+ +Dv+kA+alGAdav++G ++l ++ 
  gi|298675376|ref|YP_003727126.1| 372 IRNRASILCAGSIRSSADVAKAVALGADAVVIGTAALIAMG 412
                                       3569*******************************999876 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 0.59
                                       HHHHHHHHHHHHHHHHHHHT-SBHHHHH CS
                            FMN_dh 315 vervleilraelertmallGvksvaeld 342
                                       ++++l+ ++ el++ +  lGv+s+++l+
  gi|298675376|ref|YP_003727126.1| 448 LTNLLSGWSFELKEILGSLGVNSIESLR 475
                                       5678888999**************9986 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4  11.5   3.7e-09   3.6e-06       1      52 []      16      60 ..      16      60 .. 0.92
   2 !   13.7   4.1   7.1e-05     0.071       1      25 [.      45      69 ..      45      83 .. 0.79
   3 ?    3.5   0.2      0.11   1.1e+02      35      51 ..     410     427 ..     385     446 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 3.7e-09
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      rC +Cg Cv++C+ +a+e+++        +v  d +kC+ C++Cv+ CP +a
  gi|298675376|ref|YP_003727126.1| 16 RCRKCGICVNNCSFGALEFRDG-------RVIPDDSKCVACYRCVSKCPDNA 60
                                      8******************874.......677899**************886 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 7.1e-05
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeene 25
                                      +C+ C +Cv+ Cp +ai++ +++ +
  gi|298675376|ref|YP_003727126.1| 45 KCVACYRCVSKCPDNAITISNYQWA 69
                                      7****************99876544 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.11
                            Fer4_7  35 pekClgCgaCva.vCPtg 51 
                                       ++ C+ C++C +  C +g
  gi|298675376|ref|YP_003727126.1| 410 AMGCSVCQRCYTgNCAWG 427
                                       566777777766445554 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.5   0.00063      0.63       1      20 [.      16      35 ..      16      43 .. 0.86
   2 !   21.3   0.8   3.9e-07   0.00039       1      38 [.      45      81 ..      45      92 .. 0.78
   3 ?    1.0   0.2      0.83   8.3e+02      56      62 ..     412     418 ..     389     445 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00063
                           Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                      rC +Cg C++ C  +a++ +
  gi|298675376|ref|YP_003727126.1| 16 RCRKCGICVNNCSFGALEFR 35
                                      6*************999876 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 3.9e-07
                           Fer4_16  1 rCgtCgkCaevCPtnaikekkekeiearecisyntaek 38
                                      +C+ C +C++ CP nai+   ++++++r + +++ +  
  gi|298675376|ref|YP_003727126.1| 45 KCVACYRCVSKCPDNAITIS-NYQWANRGNANWTPEVA 81
                                      5*****************99.79999999888843333 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.83
                           Fer4_16  56 gCdiCqd 62 
                                       gC +Cq+
  gi|298675376|ref|YP_003727126.1| 412 GCSVCQR 418
                                       5555543 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   1.6   9.2e-08   9.2e-05       1      24 []       9      32 ..       9      32 .. 0.95
   2 !   17.6   5.3   2.9e-06    0.0029       5      24 .]      42      61 ..      42      61 .. 0.96

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 9.2e-08
                            Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                      +v id  +C  Cg Cv++C +ga+
  gi|298675376|ref|YP_003727126.1|  9 KVSIDSARCRKCGICVNNCSFGAL 32
                                      689*******************97 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 2.9e-06
                            Fer4_6  5 dpdkCigCgdCvrvCPegai 24
                                      d++kC+ C++Cv+ CP +ai
  gi|298675376|ref|YP_003727126.1| 42 DDSKCVACYRCVSKCPDNAI 61
                                      899***************98 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5  10.6   9.2e-08   9.1e-05       1      51 []      16      61 ..      16      61 .. 0.91
   2 ?    3.2   0.2     0.099        99       2      15 ..     413     427 ..     392     445 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 9.2e-08
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      +C +Cg Cv+ C +g+ + ++++ +         +C+ C +Cv +Cp +ai
  gi|298675376|ref|YP_003727126.1| 16 RCRKCGICVNNCSFGALEFRDGRVIPDDS-----KCVACYRCVSKCPDNAI 61
                                      5****************999988888763.....6*************987 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.099
                            Fer4_9   2 CtgCgaCvea.Cpag 15 
                                       C  C++C +  C  g
  gi|298675376|ref|YP_003727126.1| 413 CSVCQRCYTGnCAWG 427
                                       777777754436444 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   9.1   3.1e-08   3.1e-05       2      58 ..      11      62 ..      10      63 .. 0.90
   2 ?   -0.1   1.2       1.1   1.1e+03      38      48 ..     410     420 ..     372     425 .. 0.64

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 3.1e-08
                           Fer4_21  2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58
                                       id+++C +Cg C+  C+     a+e+ + +v++  +++Cv+C  C+s CP +++i+
  gi|298675376|ref|YP_003727126.1| 11 SIDSARCRKCGICVNNCS---FGALEFRDGRVIP-DDSKCVACYRCVSKCP-DNAIT 62
                                      59***************9...899***9888865.689*************.89998 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.1
                           Fer4_21  38 edeCvGCnlCs 48 
                                       +  C  C+ C+
  gi|298675376|ref|YP_003727126.1| 410 AMGCSVCQRCY 420
                                       44455555554 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   3.0   1.2e-07   0.00012     139     233 ..     311     415 ..     291     419 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.2e-07
                               NMO 139 liptissvkearkvearGaDalivqGpeaG.GhqGtpevgd.kglfaLvpqvldavd...........iPviAaGGi 202
                                       ++ +   +  a  v ++GaD+l ++G+ +G G  + + + d +g    ++ +l  vd             ++ aG i
  gi|298675376|ref|YP_003727126.1| 311 ISAVHNVAAIASGVVRAGADVLTIDGYRGGsGASP-MVIRDnVG--IPIELALATVDqrlrdegirnrASILCAGSI 384
                                       333333344455677899**********9956666.55554322..223333333334445788899999******* PP

                               NMO 203 idrrgvaaaLalGAsgvqigtrfLltkesda 233
                                           +va a alGA +v igt+ L++  + +
  gi|298675376|ref|YP_003727126.1| 385 RSSADVAKAVALGADAVVIGTAALIAMGCSV 415
                                       ************************9988765 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   1.1    0.0016       1.6       3      17 ..      15      29 ..      13      40 .. 0.83
   2 !   12.2   0.2   0.00019      0.19       3      17 ..      44      62 ..      42     119 .. 0.64
   3 ?    3.3   0.0      0.12   1.2e+02       4      21 ..     412     430 ..     390     462 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0016
                            Fer4_8  3 ekCieCgaCqsaCpv 17
                                       +C +Cg C ++C +
  gi|298675376|ref|YP_003727126.1| 15 ARCRKCGICVNNCSF 29
                                      68***********64 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00019
                            Fer4_8  3 ekCieCgaCqsaCp....v 17
                                      +kC+ C +C s+Cp    +
  gi|298675376|ref|YP_003727126.1| 44 SKCVACYRCVSKCPdnaiT 62
                                      5788888888888755431 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.12
                            Fer4_8   4 kCieCgaCq.saCpvlrrt 21 
                                        C  C++C   +C    +t
  gi|298675376|ref|YP_003727126.1| 412 GCSVCQRCYtGNCAWGIAT 430
                                       4666666665567554444 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4  14.1   7.6e-06    0.0076       1      56 []       9      57 ..       9      57 .. 0.82
   2 !   16.7   2.7   5.8e-06    0.0058       2      34 ..      39      71 ..      38      89 .. 0.75
   3 ?    2.9   0.4      0.12   1.2e+02       8      19 ..     412     424 ..     406     450 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.6e-06
                           Fer4_10  1 kvvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      kv id+ +C +Cg Cv+ C       ga +++++    ++  +kC +c  Cv++CP
  gi|298675376|ref|YP_003727126.1|  9 KVSIDSARCRKCGICVNNCS-----FGALEFRDGRVIPDD--SKCVACYRCVSKCP 57
                                      5889***************3.....466666655555555..*************9 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 5.8e-06
                           Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgease 34
                                      v+ dd++C+ C +Cv+ CP ++ + ++++ a++
  gi|298675376|ref|YP_003727126.1| 39 VIPDDSKCVACYRCVSKCPDNAITISNYQWANR 71
                                      5668999************97755555544443 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.12
                           Fer4_10   8 tCirCgkCvka.C 19 
                                        C  C++C +  C
  gi|298675376|ref|YP_003727126.1| 412 GCSVCQRCYTGnC 424
                                       5888999988667 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   2.1     1e-05      0.01       3      20 ..      10      27 ..       8      29 .. 0.91
   2 !   11.6   3.6   0.00023      0.23       6      21 ..      42      57 ..      37      58 .. 0.86
   3 ?   -0.5   2.4       1.6   1.6e+03       7      13 ..     413     419 ..     407     426 .. 0.51

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1e-05
                            Fer4_2  3 vvvdtdrCigCgaCvsaC 20
                                      v +d++rC  Cg+Cv++C
  gi|298675376|ref|YP_003727126.1| 10 VSIDSARCRKCGICVNNC 27
                                      679*************** PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00023
                            Fer4_2  6 dtdrCigCgaCvsaCP 21
                                      d  +C++C  Cvs CP
  gi|298675376|ref|YP_003727126.1| 42 DDSKCVACYRCVSKCP 57
                                      5569***********9 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.6
                            Fer4_2   7 tdrCigC 13 
                                       +  C +C
  gi|298675376|ref|YP_003727126.1| 413 CSVCQRC 419
                                       3344444 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00015      0.15     110     218 ..     290     409 ..     284     460 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
                                       HHHHHHHHHCCSS..S-EEEEEESESSTTTC.HHHHHHHHHHCT-SEEEEESS.........ECCCTT-C..G--CH CS
                               Dus 110 vaqivkavvkave..iPvtvkirigiddeeenalelakiveaaGaqaltvHgR.........traqnyeg..tadwe 173
                                       + q++ a+++a++   Pv vki+       +n   +a  v +aGa+ lt+ g          + ++n  +  ++ ++
  gi|298675376|ref|YP_003727126.1| 290 LSQLIYALKEATNyeKPVGVKISA-----VHNVAAIASGVVRAGADVLTIDGYrggsgaspmVIRDNVGIpiELALA 361
                                       678899999998877999999875.....567999*****************66**999665444455453455556 PP

                                       HHHH.HHHH.-S..S-EEEESS--SHHHHHHHHHHH--SEEEESCHHCC CS
                               Dus 174 aIke.vkqa.vs..ipviaNGdIkdaedaqaileetGadgvmigrgalg 218
                                       ++ + ++++ ++   +++  G I++  d+ ++++  Gad+v+ig +al 
  gi|298675376|ref|YP_003727126.1| 362 TVDQrLRDEgIRnrASILCAGSIRSSADVAKAVAL-GADAVVIGTAALI 409
                                       66543444322256899****************99.*********9985 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.1       9.2   9.1e+03     186     208 ..     311     333 ..     308     340 .. 0.71
   2 ?   11.9   0.1   0.00011      0.11      76     106 ..     378     408 ..     370     436 .. 0.88

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 9.2
                                       HHHHHSSEEEEESS--SHHHHHH CS
                      His_biosynth 186 laeavkipviasGGvgsledlke 208
                                       +++  ++  iasG v+  +d+ +
  gi|298675376|ref|YP_003727126.1| 311 ISAVHNVAAIASGVVRAGADVLT 333
                                       55666788888888877777765 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00011
                                       EEEESSSSSHHHHHHHHHCT-SEEEESHHHH CS
                      His_biosynth  76 vqvGGGIrsledveelleagadkviigtaav 106
                                       +   G Irs  dv++++ +gad v+igtaa+
  gi|298675376|ref|YP_003727126.1| 378 ILCAGSIRSSADVAKAVALGADAVVIGTAAL 408
                                       666788***********************97 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   3.0    0.0044       4.4       1      15 [.      16      30 ..      16      42 .. 0.87
   2 ?    8.2   3.9    0.0036       3.6      44      59 ..      44      59 ..      41      61 .. 0.90
   3 ?    3.1   0.1      0.15   1.5e+02      44      56 ..     411     424 ..     388     448 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0044
                           Fer4_17  1 rCiqCgyClpeCpsy 15
                                      rC++Cg C+++C+++
  gi|298675376|ref|YP_003727126.1| 16 RCRKCGICVNNCSFG 30
                                      7***********986 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0036
                           Fer4_17 44 slCieCgeCerkCPqg 59
                                      s+C+ C +C++kCP +
  gi|298675376|ref|YP_003727126.1| 44 SKCVACYRCVSKCPDN 59
                                      58************86 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.15
                           Fer4_17  44 slCieCgeCe.rkC 56 
                                         C+ C++C    C
  gi|298675376|ref|YP_003727126.1| 411 MGCSVCQRCYtGNC 424
                                       55666666653344 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   4.9   5.6e-05     0.055      57      96 ..      13      57 ..       6      70 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.6e-05
                           Fer4_18 57 gagdcidcescvkvcPtg.idirkGlql....eciscllcidacd 96
                                      +++ c +c+ cv+ c  g ++ r+G  +    +c++c +c+  c 
  gi|298675376|ref|YP_003727126.1| 13 DSARCRKCGICVNNCSFGaLEFRDGRVIpddsKCVACYRCVSKCP 57
                                      6789***********98758*****86544448*********995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.68u 0.34s 00:00:01.02 Elapsed: 00:00:00.52
# Mc/sec: 2894.67
//
Query:       gi|298675377|ref|YP_003727127.1|  [L=375]
Description: glutamine amidotransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-13   50.2   0.0    3.9e-11   42.3   0.0    2.1  1  GATase_2  Glutamine amidotransferases class-II
      1e-07   32.2   0.0    1.6e-06   28.3   0.0    2.5  3  GATase_6  Glutamine amidotransferase domain
    1.9e-05   24.6   0.0      0.061   13.2   0.0    2.4  2  GATase_7  Glutamine amidotransferase domain


Domain annotation for each model (and alignments):
>> GATase_2  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.0   6.4e-15   3.9e-11     120     376 ..     113     351 ..     107     357 .. 0.79

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 6.4e-15
                                       HHHHH--EEEEEEEE-TT---HHHHHHHHHHHHHHHGGG.....-BTTBEEEEEESSEEEEEESS-GGGHHHHBHGG CS
                          GATase_2 120 aakesePsieqvfvekkedlseeelerklyviRkriekeiakkkaekefYicslssrtivYkglltseqlkefykdl 196
                                       +  ++ P++ + fv+ +  ++++ + ++ yv  k +e +     + +  +++s  ++  ++kgl  +e++ +fy+  
  gi|298675377|ref|YP_003727127.1| 113 NPITESPVLWRYFVDVPG-NRTQFVSESEYVFEKVMEINS----KIEGAFVASSGKNMGIFKGLGYPEDIAAFYN-- 182
                                       556677888888888876.667777777788887776654....567899************************6.. PP

                                       GSTT--BSEEEEEE---SSSS--GGGSSS-SSE....EEEE--TTHHHHHHHHHHHCTT--BT-HH.HHHTC--S-- CS
                          GATase_2 197 kdeelesalalvHsRfstntfPsWelaqPlRll....aHnGEintlrGnknwmkareaelksellgdelekllPivn 269
                                         +e+++++   H Rf tnt   W  a+P+ ll     HnGEi     nk++ +    +++                
  gi|298675377|ref|YP_003727127.1| 183 -LDEYKAYIWTAHGRFPTNTPGWWGGAHPFGLLdwsiVHNGEISSYGINKRYLEPFGYRMEL--------------- 243
                                       .4689*************************87533338******999999887765555543............... PP

                                       TTS-HHHHHHHHHHHHHHTT.--HHHHHHHHS----TT-GGGTHHHHHHHHHHTTT-..----SSEEEEEE-SSEEE CS
                          GATase_2 270 eegsDsasldnvlellvlsg.rslaealmlliPeawennksldkekkafyeyasalm..epWDGPalivftdGkvvg 343
                                         + D++ +   ++llv+   + ++ a+  l  + w+n +++ ++ ++      ++      +GP +iv+   + + 
  gi|298675377|ref|YP_003727127.1| 244 --KTDTEVVAYLFDLLVRRHnMPIKTAISALSAPFWKNIDKMPERERKIITAIRQVYgsALLNGPYSIVLGHSRGIV 318
                                       ..4688999999999998764899999***************977777665444433113469************** PP

                                       EEE-TT--S--EEEEETT--EEEESST.TSS--- CS
                          GATase_2 344 avLDRnGLRPaRylvtkddlvvlasEv.Gvldle 376
                                          DR  LRP   +  kdd+++++sE   + ++e
  gi|298675377|ref|YP_003727127.1| 319 GFNDRIKLRPMT-CARKDDMLYMSSEEsAIREIE 351
                                       **********86.677899999999751455555 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.71   4.2e+03       9      24 ..      28      43 ..      22      65 .. 0.77
   2 !   28.3   0.0   2.7e-10   1.6e-06      14      93 ..     190     273 ..     175     303 .. 0.77
   3 ?    0.8   0.0     0.084     5e+02      13      36 ..     308     330 ..     285     343 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.71
                          GATase_6  9 lvedevalaHvRlaiv 24
                                      ++++++al H R+   
  gi|298675377|ref|YP_003727127.1| 28 AITKSIALMHDRSNGL 43
                                      5678899999997654 PP

  == domain 2  score: 28.3 bits;  conditional E-value: 2.7e-10
                          GATase_6  14 valaHvRlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall......eel 84 
                                       ++ aH R  ++      ga+Pf      +++vhNGei+ y+ +++++ +  g++++ ++Dtev++ l+      +++
  gi|298675377|ref|YP_003727127.1| 190 IWTAHGRFPTNTPGWWGGAHPF--GLLDWSIVHNGEISSYG-INKRYLEPFGYRMELKTDTEVVAYLFdllvrrHNM 263
                                       5567777777777767789***..9999************8.77777777****************99777766666 PP

                          GATase_6  85 G.eevlerlr 93 
                                       + + ++++l 
  gi|298675377|ref|YP_003727127.1| 264 PiKTAISALS 273
                                       6555556665 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.084
                          GATase_6  13 evalaHvRlaivglaeeegaqPfp 36 
                                       +++l+H R  ivg +++ +  P++
  gi|298675377|ref|YP_003727127.1| 308 SIVLGHSR-GIVGFNDRIKLRPMT 330
                                       37888888.788887666668882 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0     1e-05     0.061      24      63 ..     216     255 ..     206     272 .. 0.89
   2 !    8.9   0.0   0.00022       1.3      74     122 ..     303     348 ..     288     349 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1e-05
                          GATase_7  24 lvivfnGeiyNykelreeLeakghrfrtksDtevllalle 63 
                                         iv+nGei  y   ++ Le  g+r++ k+Dtev++ l++
  gi|298675377|ref|YP_003727127.1| 216 WSIVHNGEISSYGINKRYLEPFGYRMELKTDTEVVAYLFD 255
                                       579********************************88876 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00022
                          GATase_7  74 lnGmfAfaiwdeeekrlllaRDrlGikPLyygedkgdallfaSelkall 122
                                       lnG +++++ +++   ++   Dr+  +P+  ++++ d l+++Se +a++
  gi|298675377|ref|YP_003727127.1| 303 LNGPYSIVLGHSRG--IVGFNDRIKLRPMTCARKD-DMLYMSSEESAIR 348
                                       89*******99999..******************6.8*******99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2496.23
//
Query:       gi|298675378|ref|YP_003727128.1|  [L=61]
Description: hypothetical protein Metev_1479 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 461.88
//
Query:       gi|298675379|ref|YP_003727129.1|  [L=71]
Description: hypothetical protein Metev_1480 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.059   12.7   0.0      0.063   12.6   0.0    1.0  1  UbiA      UbiA prenyltransferase family


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.5e-06     0.063      17      67 ..       9      56 ..       3      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.5e-06
                              UbiA 17 pdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispk 67
                                      +  ++++l+++ ++l+ + +  +Ndy+  ++ ad  r+ +    + +i+pk
  gi|298675379|ref|YP_003727129.1|  9 IK-WIIILFTISVVLVDSIGRYINDYYASKSSAD--RHYDIVAQKSEITPK 56
                                      44.5999************************999..887776668888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 589.84
//
Query:       gi|298675380|ref|YP_003727130.1|  [L=115]
Description: hypothetical protein Metev_1481 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 885.80
//
Query:       gi|298675381|ref|YP_003727131.1|  [L=181]
Description: hypothetical protein Metev_1482 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-26   92.9   9.8    1.5e-26   92.6   9.3    1.3  1  UPF0228   Uncharacterised protein family (UPF0228)
  ------ inclusion threshold ------
      0.041   13.8   0.7      0.069   13.1   0.2    1.6  2  DUF1980   Domain of unknown function (DUF1980)
       0.23   11.8   3.0       0.52   10.7   0.4    2.2  2  DUF3221   Protein of unknown function (DUF3221)


Domain annotation for each model (and alignments):
>> UPF0228  Uncharacterised protein family (UPF0228)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.6   9.3   2.6e-30   1.5e-26       6     120 ..      63     176 ..      58     179 .. 0.96

  Alignments for each domain:
  == domain 1  score: 92.6 bits;  conditional E-value: 2.6e-30
                           UPF0228   6 tieydsniveekyYivvdkdnitdvrkelekeknwtssipaikkgdeyiievseqaiedeevlaiLekydlqvkkfv 82 
                                       +++y+ ++ +++yY+vv++d+ + +++el k + w+   ++ikkgd+y+i vs+ + +++++l iL+k dlq+kkfv
  gi|298675381|ref|YP_003727131.1|  63 KLDYNIDHLHNQYYLVVNQDKKSVLYNELMKANIWIRDEEVIKKGDNYLIVVSKSIANNKDFLDILSKQDLQLKKFV 139
                                       79*************************************************************************** PP

                           UPF0228  83 wCyiefgdgsekywineedairikneLeknekilsvsl 120
                                        Cyi f++ ++++ +  +   +ik+eL +++ki+ v l
  gi|298675381|ref|YP_003727131.1| 140 NCYIYFSKQPKDW-VGYDKGQKIKKELLEKDKIIRVAL 176
                                       ***********65.99999***************9976 PP

>> DUF1980  Domain of unknown function (DUF1980)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   1.1e-05     0.069      70     169 ..       6     116 ..       2     140 .. 0.66
   2 ?   -1.9   0.0      0.46   2.8e+03     136     158 ..     150     174 ..     130     175 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.1e-05
                           DUF1980  70 kkllsylilviPlllglllptkvldssiakak.....Gfnfslak....eskseqkedegtqeqslkpdtssyvtkd 137
                                       kk+l+y++++i +ll+ l+ +++ d  i + +     G++ ++a     +s+ ++  + + + + l++++  +v++d
  gi|298675381|ref|YP_003727131.1|   6 KKVLIYFVFSIFVLLAVLINPSSHDMRIGGLYisfeeGTTEKYARsvidDSNLREDIKLDYNIDHLHNQYYLVVNQD 82 
                                       89**************************9888766666666666666543333333344444555666688889999 PP

                           DUF1980 138 gydkemkkeakk...lskkkkItvtdenYlevmee 169
                                       + +  +++ +k+   + ++++I+ + +nYl v+++
  gi|298675381|ref|YP_003727131.1|  83 KKSVLYNELMKAniwIRDEEVIK-KGDNYLIVVSK 116
                                       99999999888888744444444.34444444332 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.46
                           DUF1980 136 kd..gydkemkkeakklskkkkItv 158
                                       kd  gydk +k +++ l+k+k+I+v
  gi|298675381|ref|YP_003727131.1| 150 KDwvGYDKGQKIKKELLEKDKIIRV 174
                                       3344555555555555777777776 PP

>> DUF3221  Protein of unknown function (DUF3221)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1     0.075   4.5e+02      18      62 ..      56      99 ..      46     101 .. 0.65
   2 ?   10.7   0.4   8.7e-05      0.52       4      58 ..     103     162 ..     102     165 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.075
                           DUF3221 18 iekeeaenlseeeiekykgeaiwvlidsdkvsnlevGqkVrVwfd 62
                                       +  e+++l+++ i+  +++ ++v+++++k   + + +k ++w+ 
  gi|298675381|ref|YP_003727131.1| 56 SNLREDIKLDYN-IDHLHNQYYLVVNQDKKSVLYNELMKANIWIR 99
                                      555555555555.57777777777777777767777777777765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 8.7e-05
                           DUF3221   4 vieksdnriLvvse...iekeeaenlseee..iekykgeaiwvlidsdkvsnlevGqkVr 58 
                                       vi+k dn ++vvs+   ++k+  + ls+++  ++k+ +  i+++ + ++  ++ +Gqk++
  gi|298675381|ref|YP_003727131.1| 103 VIKKGDNYLIVVSKsiaNNKDFLDILSKQDlqLKKFVNCYIYFSKQPKDWVGYDKGQKIK 162
                                       899*********9854469999999999999999999999999***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1414.41
//
Query:       gi|298675382|ref|YP_003727132.1|  [L=391]
Description: hypothetical protein Metev_1483 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.1   12.0   0.0       0.16   11.4   0.0    1.2  1  DUF92     Integral membrane protein DUF92


Domain annotation for each model (and alignments):
>> DUF92  Integral membrane protein DUF92
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   8.9e-06      0.16     171     226 ..      22     119 ..       8     123 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.9e-06
                             DUF92 171 llillltlaGllGsllDSlLGatlqasvvdkrtgkvvegegge.................................. 213
                                       l ++ +t+++ +G+++DS +G  l+ +v d+++  ++ +  ++                                  
  gi|298675382|ref|YP_003727132.1|  22 LTLFTGTVSASAGCTIDSNMGENLDTKVCDAQNYTIMIEG-KSldnqnimqqrsmfidkflnetndekeprhigkvk 97 
                                       245679999******************9999887776552.223577777777777777777777777777777777 PP

                             DUF92 214 .........kvvsGldlLdNna 226
                                                 v  G+++++N  
  gi|298675382|ref|YP_003727132.1|  98 nlkspknteLVAYGFKIFSNGV 119
                                       7777777765556777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 3284.11
//
Query:       gi|298675383|ref|YP_003727133.1|  [L=326]
Description: ABC transporter-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.1e-25   88.9   0.0      1e-24   87.6   0.0    1.6  1  ABC_tran     ABC transporter
    1.1e-12   48.4   0.1    1.1e-08   35.3   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    2.2e-05   24.4   0.0       0.13   12.0   0.0    2.3  2  AAA_15       AAA ATPase domain
    0.00027   21.6   0.1    0.00086   20.0   0.0    1.9  1  DUF4162      Domain of unknown function (DUF4162)
    0.00043   20.8   0.6      0.002   18.6   0.5    2.1  1  AAA_23       AAA domain
     0.0068   15.7   0.0      0.011   15.0   0.0    1.3  1  Zeta_toxin   Zeta toxin
     0.0091   16.4   0.7       0.15   12.5   0.7    2.4  1  AAA          ATPase family associated with various cellular a
  ------ inclusion threshold ------
      0.019   14.9   0.1      0.039   13.9   0.1    1.5  1  RsgA_GTPase  RsgA GTPase
      0.033   14.4   0.2       0.31   11.3   0.2    2.2  1  AAA_22       AAA domain
      0.034   13.9   0.2      0.091   12.5   0.1    1.9  2  AAA_30       AAA domain
      0.061   13.0   0.1       0.17   11.5   0.1    1.7  1  SRP54        SRP54-type protein, GTPase domain
      0.064   13.0   0.2       0.15   11.8   0.2    1.5  1  AAA_29       P-loop containing region of AAA domain
      0.089   12.7   0.0       0.19   11.7   0.0    1.5  1  MobB         Molybdopterin guanine dinucleotide synthesis pro


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.6   0.0   7.2e-28     1e-24       2     137 .]      37     180 ..      36     180 .. 0.90

  Alignments for each domain:
  == domain 1  score: 87.6 bits;  conditional E-value: 7.2e-28
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       + +++++k+g + ++vG+nGaGK+t +k+l+gll+p  G  ++ g d+ + e    r+  gvlp+ + +  +lt+r+
  gi|298675383|ref|YP_003727133.1|  37 DSLTFNVKKGDVFGFVGQNGAGKTTTMKMLIGLLEPSDGYAKVAGYDSVR-EVINIREVTGVLPEPAGFYGNLTARQ 112
                                       7899****************************************999999.889999******************** PP

                                       H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       n             +++++i ++l+ +gl++  d+++      +S G+ +r  la+al+++p++l+lDEpt+
  gi|298675383|ref|YP_003727133.1| 113 NlrfyaklydmdseTRENRIVELLEMVGLDDAIDQKI----GGFSTGMLKRFGLAQALINDPEILFLDEPTS 180
                                       *********9965555555666666666666666666....*****************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.1   0.00016      0.22       2      23 ..      49      70 ..      48     126 .. 0.77
   2 !   35.3   0.0   7.7e-12   1.1e-08     231     300 ..     146     213 ..     110     216 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                            AAA_21  2 nvliGpNgsGKSnLLdaldlla 23
                                       +++G Ng+GK++ ++ l +l 
  gi|298675383|ref|YP_003727133.1| 49 FGFVGQNGAGKTTTMKMLIGLL 70
                                      679*************998875 PP

  == domain 2  score: 35.3 bits;  conditional E-value: 7.7e-12
                            AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHP...kllrrllellkelsrngaQviltTHSpl 300
                                       +  +  +S G+++ ++l+ al+ ++    +l++DEp +g++P   +++r l++ l+++++  + ++l++HS +
  gi|298675383|ref|YP_003727133.1| 146 DQKIGGFSTGMLKRFGLAQALINDP---EILFLDEPTSGIDPkgaQMMRDLIKQLSREKD--VTIFLSSHSMS 213
                                       5567789****************99...9*************777777777766666655..*********76 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   9.1e-05      0.13      27      50 ..      50      73 ..      36     133 .. 0.83
   2 !   10.3   0.0    0.0003      0.42     321     365 ..     167     211 ..     156     213 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.1e-05
                            AAA_15 27 vliGkNnsGKSsilealdlFlnnk 50
                                       ++G N++GK++ +++l  +l+ +
  gi|298675383|ref|YP_003727133.1| 50 GFVGQNGAGKTTTMKMLIGLLEPS 73
                                      59***************9998877 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0003
                            AAA_15 321 eeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                        +++ il+++EP   + p+  +++ +l+k l+++++  +++++HS
  gi|298675383|ref|YP_003727133.1| 167 INDPEILFLDEPTSGIDPKGAQMMRDLIKQLSREKDVTIFLSSHS 211
                                       57899***************************************9 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   6.2e-07   0.00086       9      80 ..     245     323 ..     234     324 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 6.2e-07
                                       TS-SSEEEEE......-------...---EEEE-TTS-EEEEE-------------.----EEEEEEEE---HHHHH CS
                           DUF4162   9 sygknrieve......adaeellee.pgveeveeeggelelkledeeaanellkal.tsgveirsFeeeePsLndIF 77 
                                       +  + ++ +e      +d  e l++ +gv++v++ +g+l+++ +++  + e+ k++ +sg++i ++eee+  L+ +F
  gi|298675383|ref|YP_003727133.1| 245 EREGVNYLLEvwdisyNDMIEKLNLmDGVHDVKTLDGTLQVHADSG-MRAEIAKTIsKSGGTISRLEEERMDLQSVF 320
                                       3344566677888878665555555266*********9****9985.9********77******************* PP

                                       HHH CS
                           DUF4162  78 iek 80 
                                       +++
  gi|298675383|ref|YP_003727133.1| 321 LKL 323
                                       986 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.5   1.5e-06     0.002      14     130 ..      40     154 ..      18     254 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.5e-06
                            AAA_23  14 eidF.skgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkay.veltfenkdgrytr 88 
                                       +++  +  ++ ++G+NGaGKTT +  +   L    +   +  g +++++ ++i   + v +  + +  + + +   +
  gi|298675383|ref|YP_003727133.1|  40 TFNVkKGDVFGFVGQNGAGKTTTMKMLIGLLEPSDG-YAKVAGYDSVREVINIREVTGVLPEpAGFYGNLTAR---Q 112
                                       445544479***************988776655433.333345566666666555534333333333322223...4 PP

                            AAA_23  89 siererelskkkgkttkkaklelleideleqfisellgskki 130
                                       ++++  +l++ +++t+ + + elle+  l++ i++++g +  
  gi|298675383|ref|YP_003727133.1| 113 NLRFYAKLYDMDSETRENRIVELLEMVGLDDAIDQKIGGFST 154
                                       577888888888888888888888888888888887776655 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   8.2e-06     0.011      22     101 ..      52     134 ..      34     135 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.2e-06
                        Zeta_toxin  22 gGqpGAGKselaellkdelerqgnvvrldp.DdlRelhPeyeeilk...adpkkaseltqkdaselvekllqeaien 94 
                                       +Gq GAGK++++++l   le+ +++ ++ + D++Re + + +e+     +    + +lt ++  ++ +kl +   e 
  gi|298675383|ref|YP_003727133.1|  52 VGQNGAGKTTTMKMLIGLLEPSDGYAKVAGyDSVREVI-NIREVTGvlpEPAGFYGNLTARQNLRFYAKLYDMDSET 127
                                       7*******************999999987559999987.44554442115555566667777777777777766666 PP

                        Zeta_toxin  95 gyniive 101
                                       + n ive
  gi|298675383|ref|YP_003727133.1| 128 RENRIVE 134
                                       6666665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.7   0.00011      0.15       3     122 ..      51     223 ..      49     230 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                                       EESSTTSSHHHHHHHHHHHHTHE...................................................... CS
                               AAA   3 lyGppGtGKTllakavakelgve...................................................... 25 
                                       ++G  G GKT+++k ++  l+ +                                                      
  gi|298675383|ref|YP_003727133.1|  51 FVGQNGAGKTTTMKMLIGLLEPSdgyakvagydsvrevinirevtgvlpepagfygnltarqnlrfyaklydmdset 127
                                       789****************8522232233344455455555555555555555555555555555555555555555 PP

                                       .......EEEEETTTCSSS...........STTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHH CS
                               AAA  26 .......fleisgsellsk...........yvgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeee 83 
                                              +                       +g  +  + + f  a++   +p ilf+DE  + +  +       + 
  gi|298675383|ref|YP_003727133.1| 128 renriveL----------LemvglddaidqKIGGFSTGMLKRFGLAQALInDPEILFLDEPTSGIDPK-------GA 187
                                       55555554..........04444444444488989999999999888777889*******99988877.......88 PP

                                       HHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.T CS
                               AAA  84 rvvnqLlteldgvkkkeskvivigatnrpdkldpallr.g 122
                                       +++  L+++l+++k+    v++ + +++++++++   r g
  gi|298675383|ref|YP_003727133.1| 188 QMMRDLIKQLSREKD----VTIFLSSHSMSEVEEICSRiG 223
                                       999999999999988....999999999999888766555 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   2.8e-05     0.039      69     121 ..      15      68 ..       2      87 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.8e-05
                                       HHHHHHTTSEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  69 keelealgyevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                       ++ +e  +++  + +++t +++++l+ ++k+ ++  +vGq G+GK+t +++l++
  gi|298675383|ref|YP_003727133.1|  15 ENVIEIQNLTKRFGKQNTITAVDSLTFNVKKgDVFGFVGQNGAGKTTTMKMLIG 68 
                                       44444445555566677778999****999989**************9999876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00022      0.31      11      38 ..      52      84 ..      44     269 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00022
                            AAA_22 11 tGesGtGKTtllrrlleqldeeakaee.....e 38
                                      +G+ G+GKTt++++l   l+     ++      
  gi|298675383|ref|YP_003727133.1| 52 VGQNGAGKTTTMKMLIGLLEPSDGYAKvagydS 84
                                      8*************9988853333222555551 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   6.6e-05     0.091      17      47 ..      46      76 ..      38     208 .. 0.84
   2 ?   -2.8   0.0       3.2   4.4e+03     117     140 ..     228     242 ..     205     261 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.6e-05
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaweaa.gg 47
                                      gd v   +G  G+GKtt++k l  ++e + g+
  gi|298675383|ref|YP_003727133.1| 46 GD-VFGFVGQNGAGKTTTMKMLIGLLEPSdGY 76
                                      44.77889**************9999988663 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.2
                            AAA_30 117 akvilvGDerQlasVeaGgvlrdl 140
                                        k++ +G  +Ql           +
  gi|298675383|ref|YP_003727133.1| 228 GKLLAIGTVDQLRD---------I 242
                                       44444444444443.........3 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00012      0.17       5      41 ..      50      86 ..      47      88 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                                      EEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSS CS
                             SRP54  5 llvGlqGaGKTttlaKLaallkkegkkvllvaaDtfR 41
                                       +vG +GaGKTtt+  L  ll+ +   + ++  D  R
  gi|298675383|ref|YP_003727133.1| 50 GFVGQNGAGKTTTMKMLIGLLEPSDGYAKVAGYDSVR 86
                                      59************99988877776666666666665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   0.00011      0.15      16      49 ..      40      73 ..      32      80 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                            AAA_29 16 tieidlkgatlltGpsGsGKSTllDAiqalLvpa 49
                                      t++++  +++ ++G++G+GK+T +  ++ lL p+
  gi|298675383|ref|YP_003727133.1| 40 TFNVKKGDVFGFVGQNGAGKTTTMKMLIGLLEPS 73
                                      56676555999***********998777777776 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00013      0.19       1      24 [.      48      71 ..      48      80 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                              MobB  1 vlgivgksgsGKTtLleklipelk 24
                                      v+g+vg++g+GKTt ++ li  l+
  gi|298675383|ref|YP_003727133.1| 48 VFGFVGQNGAGKTTTMKMLIGLLE 71
                                      689*****************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       803  (0.0447878); expected 358.6 (0.02)
Passed bias filter:                      698  (0.0389313); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 2520.76
//
Query:       gi|298675384|ref|YP_003727134.1|  [L=302]
Description: hypothetical protein Metev_1486 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-31  110.1  21.6    1.4e-30  106.5  21.6    1.9  1  ABC2_membrane_2  ABC-2 family transporter protein
  ------ inclusion threshold ------
       0.04   13.9  24.9      0.018   15.0  19.1    2.4  2  ABC2_membrane_4  ABC-2 family transporter protein
       0.08   12.5  37.2       0.03   13.9  28.3    2.9  2  ABC2_membrane_5  ABC-2 family transporter protein
        2.1    7.4  40.9       0.13   11.4  33.2    2.4  2  ABC2_membrane_3  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.5  21.6   3.2e-34   1.4e-30       2     288 .]      18     300 ..      17     300 .. 0.83

  Alignments for each domain:
  == domain 1  score: 106.5 bits;  conditional E-value: 3.2e-34
                   ABC2_membrane_2   2 aiakkEfrdlvrsrrfllltvllplidvalaylkdlgsslqseakaikeatlaleyveaasasdeaedtdqdlkvvs 78 
                                       ++a+kEf+d +++ +flllt+ ++li   +  ++  +  +++     +e+tl + ++  +                 
  gi|298675384|ref|YP_003727134.1|  18 VVAQKEFADNITNSMFLLLTATYLLI---IFTFSYRSVIHGTN-IGGGELTLIFGFSGLIE---------------- 74 
                                       799***********************...44444444444443.33455555555554433................ PP

                   ABC2_membrane_2  79 timavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvll.alaiilalgi 154
                                         +  +ip+i++++g++ + +E+ +g+l +lL++Pv+Rd i++gK++g + +   ia  ++ tv++ +  +i+ lgi
  gi|298675384|ref|YP_003727134.1|  75 -EIGWFIPLIGITLGFNTVIKERKSGSLNVLLTHPVFRDNIITGKLLGIIGV---IAFVIMSTVVIsSGTLIAMLGI 147
                                       .4789***********************************************...7777777766647789999*** PP

                   ABC2_membrane_2 155 vlaledllllvvasvlllllv.vflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqein 230
                                       +++l+++++++++sv++l++   ++++++l+S+v+ ++++++ + +++++++ i+ + +  ++++ll+ + +     
  gi|298675384|ref|YP_003727134.1| 148 QVSLMEITRIALFSVFTLFYAlIYAGIAVLISTVVYEAANSLIYNVAIWILTCIFTGPIMETLSDLLTKAGI----G 220
                                       *******************999**********************************************7777....5 PP

                   ABC2_membrane_2 231 dflsllsptsayntllneilagsdlna.......................lgstatnllilllllavllvlgyvlFk 284
                                       ++ s l  +s+ ++  + +   +d ++                          ++t + ++l+++++ll  ++ +F+
  gi|298675384|ref|YP_003727134.1| 221 LKASELIMISPLHYYSKIVHGVDD-MSigkvgvqyeidgildaqftlaqwFNTFWTDITAILIIPIILLFASFIMFM 296
                                       555555555555554443333333.3336689999999999******9999999*********************** PP

                   ABC2_membrane_2 285 rkDl 288
                                       r+D+
  gi|298675384|ref|YP_003727134.1| 297 RQDI 300
                                       **96 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0  19.1     4e-06     0.018      15     172 ..      32     196 ..      21     204 .. 0.66
   2 ?    1.8   0.3     0.047   2.1e+02      48      73 ..     271     295 ..     251     299 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4e-06
                   ABC2_membrane_4  15 vwllvlaallvpllallyfnllgktgldpaefys...lsvfgftlllllplilgiiasylifrEeqndtlknLltiP 88 
                                       ++ll++a+ l+ ++++ y   +  t++   e+++   +s +   +  ++pli + ++   + +E++++ l+ Llt P
  gi|298675384|ref|YP_003727134.1|  32 MFLLLTATYLLIIFTFSYRSVIHGTNIGGGELTLifgFSGLIEEIGWFIPLIGITLGFNTVIKERKSGSLNVLLTHP 108
                                       44555555556566666666677777777666663334555555557888888889999****************** PP

                   ABC2_membrane_4  89 vsrtklllaKlivllllsvllmlvtflit..vlfallsgfvg.fsvklvlellkkclelgllvffavlpii.alvl. 160
                                       v r +++ +Kl+ ++ +++++++ t++i+   l+a+l   v+ ++++  + l+  ++++ +l+++ ++++i  +v+ 
  gi|298675384|ref|YP_003727134.1| 109 VFRDNIITGKLLGIIGVIAFVIMSTVVISsgTLIAMLGIQVSlMEITR-IALFSVFTLFYALIYAGIAVLIsTVVYe 184
                                       ***********9888877777666665541145566666555345444.4455566667777777666655256665 PP

                   ABC2_membrane_4 161 lkksyvlplilt 172
                                       + +s ++ +++ 
  gi|298675384|ref|YP_003727134.1| 185 AANSLIYNVAIW 196
                                       666666666654 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.047
                   ABC2_membrane_4  48 slsvfgftlllllplilgiiasylif 73 
                                           + +t++l++p+il ++as+++f
  gi|298675384|ref|YP_003727134.1| 271 NTFWTDITAILIIPIIL-LFASFIMF 295
                                       22233344555555555.56776665 PP

>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9  28.3   6.7e-06      0.03      40     167 ..      76     209 ..      13     236 .. 0.80
   2 ?    1.6   1.5     0.039   1.8e+02      15      31 ..     279     295 ..     256     302 .] 0.51

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.7e-06
                   ABC2_membrane_5  40 fsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitlllli..iavlikgn...v 111
                                       +++++++i i+l ++t+ +++ks++  +llt Pv r +i+  K l+++ +i+++i+ t++++   ++ ++  +   +
  gi|298675384|ref|YP_003727134.1|  76 IGWFIPLIGITLGFNTVIKERKSGSLNVLLTHPVFRDNIITGKLLGIIGVIAFVIMSTVVISSgtLIAMLGIQvslM 152
                                       5678888888899999999**********************************999999998511344444444566 PP

                   ABC2_membrane_5 112 tisevllsiliglvialif.laivlPlyfkfgvekgrivliiiifgiifllvaifsl 167
                                        i  + l++++ l++ali+ ++ vl  +  +++ ++ i++++i+++ +++   i+++
  gi|298675384|ref|YP_003727134.1| 153 EITRIALFSVFTLFYALIYaGIAVLISTVVYEAANSLIYNVAIWILTCIFTGPIMET 209
                                       6666667777777777777566688889999999999*9999999988877766664 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.039
                   ABC2_membrane_5  15 killivllllaiiilif 31 
                                        il+i ++ll+ ++++f
  gi|298675384|ref|YP_003727134.1| 279 AILIIPIILLFASFIMF 295
                                       22222233333333333 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   1.4      0.44     2e+03     217     240 ..      33      65 ..      27      74 .. 0.42
   2 ?   11.4  33.2   2.8e-05      0.13     170     344 ..      79     292 ..      69     296 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.44
                   ABC2_membrane_3 217 yllqlllilllafgl.........gipfgnlgl 240
                                       +ll ++ +ll++f +         +i  g+l l
  gi|298675384|ref|YP_003727134.1|  33 FLLLTATYLLIIFTFsyrsvihgtNIGGGELTL 65 
                                       233333333333332234434433444444444 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 2.8e-05
                   ABC2_membrane_3 170 ilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll.......afglgipfg..n 237
                                       ++ +i+++   + +++E++s+ + ++l+ +v +  ++++k+lg+  v +++++ ++++       ++g++++ +   
  gi|298675384|ref|YP_003727134.1|  79 FIPLIGITLGFNTVIKERKSGSLNVLLTHPVFRDNIITGKLLGIIGVIAFVIMSTVVIssgtliaMLGIQVSLMeiT 155
                                       33344444455589*****************************9999998888777754444457888655555344 PP

                   ABC2_membrane_3 238 lglll.llfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwi.........fsii 304
                                        ++l+ ++ l+++l+y+ ++ l+s+++  +++  i  +++++l+++f g+++  e+l++ l ++          +i 
  gi|298675384|ref|YP_003727134.1| 156 RIALFsVFTLFYALIYAGIAVLISTVVYEAANSLIYNVAIWILTCIFTGPIM--ETLSDLLTKAgiglkaselIMIS 230
                                       477778******************************9999999*******99..77886666654444522226666 PP

                   ABC2_membrane_3 305 Pffapglg...llrlitgdplwe...................illsliilalfavvylllal 344
                                       P++++++      +++ g  +++                   +++++++ +++ +++l +++
  gi|298675384|ref|YP_003727134.1| 231 PLHYYSKIvhgVDDMSIGKVGVQyeidgildaqftlaqwfntFWTDITAILIIPIILLFASF 292
                                       66666554111333333333333778888888888888888866666666666666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1054  (0.0587874); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.38
# Mc/sec: 2353.68
//
Query:       gi|298675385|ref|YP_003727135.1|  [L=302]
Description: putative ABC-2 type transporter permease [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.4e-34  117.0  13.3    5.3e-33  114.5  13.3    1.8  1  ABC2_membrane_2  ABC-2 family transporter protein
    2.1e-06   27.1  21.3    2.1e-06   27.1  21.3    1.4  1  ABC2_membrane_3  ABC-2 family transporter protein
    0.00011   22.2  17.5    0.00011   22.2  17.5    2.2  3  ABC2_membrane_4  ABC-2 family transporter protein
  ------ inclusion threshold ------
          1    8.9  32.2        2.1    7.9  28.9    2.6  2  ABC2_membrane_5  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.5  13.3   1.2e-36   5.3e-33       2     288 .]      10     299 ..       9     299 .. 0.89

  Alignments for each domain:
  == domain 1  score: 114.5 bits;  conditional E-value: 1.2e-36
                   ABC2_membrane_2   2 aiakkEfrdlvrsrrfllltvllplidvalaylkdlgsslqseakaikeatlaleyveaasasdeaedtdqdlkvvs 78 
                                       +ia+kEf+d + s+rf+l+++++ l+     +++d+++s  +   ++++ ++ + +v +                  
  gi|298675385|ref|YP_003727135.1|  10 VIAQKEFADNLWSPRFILMVIVFTLV-----VFSDSYNSVIN--DSNFSFLTGFLNVTQ------------------ 61 
                                       69************************.....77777666655..467888888888877.................. PP

                   ABC2_membrane_2  79 timavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaigla.iavallatvllalaiilalgi 154
                                         +a+++p+++ ++g+d++ +Ek + +l + L++Pv+Rd i++gK++g ++  l+ + ++++ +v +   +i ++g+
  gi|298675385|ref|YP_003727135.1|  62 -TIAIFLPLLGFALGFDSVIKEKKSASLNIFLTHPVYRDNIITGKISGAMITLLFvVFISVVSSVGT---VIIISGM 134
                                       .9**************************************************888888888888555...6667888 PP

                   ABC2_membrane_2 155 vlaledllllvvasvlllllv.vflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavp.... 226
                                       ++ + +l +++++++l+ l++  flalg+++S+ + s  +++ + +  ++vl ++++ ++  +a++ +g ++     
  gi|298675385|ref|YP_003727135.1| 135 QVGWFELERTLIFAILTYLYMsIFLALGIFISTSVNSEIKSLVYGICTWLVLCVIYSAIVMMIASAATGQSPFdlnn 211
                                       888888888888888888888899********************************************99999**** PP

                   ABC2_membrane_2 227 ....qeindflsllsptsayntllneilagsdlna........................lgstatnllilllllavl 275
                                             +n  l+ lsp  +y   ++  +  s  +                         l   ++n+l+l + +++l
  gi|298675385|ref|YP_003727135.1| 212 ndevLDLNEQLTKLSPVYHYAEPVQDQPGLS--WGgvsrgkivkntlklfdtrytliqwLEEYWENILVLTVTPLIL 286
                                       *888888888888888766666666665555..778999*****************9999999************** PP

                   ABC2_membrane_2 276 lvlgyvlFkrkDl 288
                                       l+++y +F r+D+
  gi|298675385|ref|YP_003727135.1| 287 LIMSYIRFLRQDI 299
                                       ***********96 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1  21.3   4.7e-10   2.1e-06     150     344 ..      47     291 ..      33     292 .. 0.74

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 4.7e-10
                   ABC2_membrane_3 150 tqleeelsnvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllill 226
                                        ++++ l+++ +   +++++++++  a+    s+++Ek+s  + + l+ +v +  ++++ki g ++  l+++++ ++
  gi|298675385|ref|YP_003727135.1|  47 DSNFSFLTGFLNVTQTIAIFLPLLGFAL-GFDSVIKEKKSASLNIFLTHPVYRDNIITGKISGAMITLLFVVFISVV 122
                                       3457777888888888888888876665.7779***************************76666666666666665 PP

                   ABC2_membrane_3 227 lafgl..........gipfgnlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfp.led 292
                                         +g+          +++ +  +++ +l  l++ +++alg ++s+ ++++ +  +  ++++l+l++++ ++++ + +
  gi|298675385|ref|YP_003727135.1| 123 SSVGTviiisgmqvgWFELERTLIFAILTYLYMSIFLALGIFISTSVNSEIKSLVYGICTWLVLCVIYSAIVMmIAS 199
                                       3333333334344444444444444488888999*************************************884333 PP

                   ABC2_membrane_3 293 lp...............salkwifsiiPffapglgllrli......tgdplwe........................ 324
                                        +               +   +++ + P +++++   + +            +                        
  gi|298675385|ref|YP_003727135.1| 200 AAtgqspfdlnnndevlDLNEQLTKLSPVYHYAEPVQDQPglswggV-----Srgkivkntlklfdtrytliqwlee 271
                                       33666666666777776666789999999999999999986655440.....1455555666666677778889999 PP

                   ABC2_membrane_3 325 illsliilalfavvylllal 344
                                       ++ ++++l ++ +++l++++
  gi|298675385|ref|YP_003727135.1| 272 YWENILVLTVTPLILLIMSY 291
                                       99999999999999998876 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2  17.5   2.5e-08   0.00011      23     178 ..      27     181 ..      18     182 .. 0.73
   2 ?    0.1   0.4      0.15   6.7e+02     101     130 ..     182     208 ..     180     218 .. 0.56
   3 ?   -2.6   0.1         1   4.5e+03      57     158 ..     279     287 ..     259     294 .. 0.47

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.5e-08
                   ABC2_membrane_4  23 llvpllallyfnllgktgldpaefys...lsvfgftlllllplilgiiasylifrEeqndtlknLltiPvsrtklll 96 
                                       l+v +++l++f    ++ +++++f     + ++  t+ ++lpl+   ++  ++ +E+++  l+  lt Pv r +++ 
  gi|298675385|ref|YP_003727135.1|  27 LMVIVFTLVVFSDSYNSVINDSNFSFltgFLNVTQTIAIFLPLLGFALGFDSVIKEKKSASLNIFLTHPVYRDNIIT 103
                                       22333344444433334444333333112445566677889998888999*************************** PP

                   ABC2_membrane_4  97 aKlivllllsvllmlvtflitvlfallsgfvgfsvklvlellkkclelgllvffavlpiialvllkksyvlpliltl 173
                                       +K++  +++ +++++++++++v + +++ ++++ +    + l ++l++++l+++ ++  +al ++ +++v + i +l
  gi|298675385|ref|YP_003727135.1| 104 GKISGAMITLLFVVFISVVSSVGTVIIISGMQVGW----FELERTLIFAILTYLYMSIFLALGIFISTSVNSEIKSL 176
                                       ***99999888888888887776655555555554....67899999999999999998999999999999999999 PP

                   ABC2_membrane_4 174 vytia 178
                                       vy+i+
  gi|298675385|ref|YP_003727135.1| 177 VYGIC 181
                                       99886 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.15
                   ABC2_membrane_4 101 vllllsvllmlvtflitvlfallsgfvgfs 130
                                       ++l+l v+++ +   ++++++   g ++f+
  gi|298675385|ref|YP_003727135.1| 182 TWLVLCVIYSAI---VMMIASAATGQSPFD 208
                                       444444444443...555555555655555 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1
                   ABC2_membrane_4  57 llllplilgiiasylifrEeqndtlknLltiPvsrtklllaKlivllllsvllmlvtflitvlfallsgfvgfsvkl 133
                                       l                                                                            
  gi|298675385|ref|YP_003727135.1| 279 L---------------------------------------------------------------------------- 279
                                       1............................................................................ PP

                   ABC2_membrane_4 134 vlellkkclelgllvffavlpiial 158
                                                        +v+p+i+l
  gi|298675385|ref|YP_003727135.1| 280 -----------------TVTPLILL 287
                                       .................22222222 PP

>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9  28.9   0.00047       2.1      35     167 ..      58     196 ..      20     216 .. 0.78
   2 ?   -1.3   0.1      0.29   1.3e+03     184     199 ..     277     292 ..     255     298 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00047
                   ABC2_membrane_5  35 svllifsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitlllliiavlikgn. 110
                                       +v+ +++i+ +++ + l + ++ +++ks +  ++lt Pv r +i+  K +++++++l+ ++++++++ ++++i  + 
  gi|298675385|ref|YP_003727135.1|  58 NVTQTIAIFLPLLGFALGFDSVIKEKKSASLNIFLTHPVYRDNIITGK-ISGAMITLLFVVFISVVSSVGTVIIISg 133
                                       345667788888888889999999************************.8888888888888888888877766666 PP

                   ABC2_membrane_5 111 .....vtisevllsiliglvialiflaivlPlyfkfgvekgr.ivliiiifgiifllvaifsl 167
                                            + ++ +l+++++  ++++ifla+ + +      e    ++ i  +++++++++ai+++
  gi|298675385|ref|YP_003727135.1| 134 mqvgwFELERTLIFAILTYLYMSIFLALGIFISTSVNSEIKSlVYGICTWLVLCVIYSAIVMM 196
                                       798888888888888888888888888877777777766555267777777888888888775 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.29
                   ABC2_membrane_5 184 iillviillliivSyf 199
                                       ++l+v  l+l+i+Sy+
  gi|298675385|ref|YP_003727135.1| 277 LVLTVTPLILLIMSYI 292
                                       2223333445555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1116  (0.0622455); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.39
# Mc/sec: 2309.66
//
Query:       gi|298675386|ref|YP_003727136.1|  [L=616]
Description: WD40 domain-containing protein beta Propeller [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.2e-19   68.0   4.2    0.00016   21.5   0.0    5.8  5  PD40            WD40-like Beta Propeller Repeat
    1.2e-07   31.8   0.3      0.018   14.9   0.0    4.5  4  eIF2A           Eukaryotic translation initiation factor eIF2
    1.5e-07   30.6   4.8      0.036   12.8   0.1    5.9  6  DPPIV_N         Dipeptidyl peptidase IV (DPP IV) N-terminal r
     0.0021   18.3   0.2         14    6.0   0.0    4.5  5  ANAPC4_WD40     Anaphase-promoting complex subunit 4 WD40 dom
  ------ inclusion threshold ------
      0.013   15.4   0.5      0.013   15.4   0.5    2.2  2  PEGA            PEGA domain
      0.039   13.2   0.1        2.7    7.2   0.0    2.9  3  Lactonase       Lactonase, 7-bladed beta-propeller
       0.11   12.3   0.0         59    3.3   0.0    3.5  4  Gmad1           Lipoprotein LpqB beta-propeller domain
       0.13   11.0   2.3       0.39    9.5   0.1    2.7  4  Peptidase_S9_N  Prolyl oligopeptidase, N-terminal beta-propel


Domain annotation for each model (and alignments):
>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1      0.01        23      11      23 ..      65      77 ..      61      78 .. 0.76
   2 !   16.9   0.0     2e-06    0.0045      11      28 ..     133     150 ..     128     157 .. 0.89
   3 !    8.8   0.1   0.00068       1.5      16      30 ..     189     203 ..     188     207 .. 0.84
   4 !   11.8   0.0   8.2e-05      0.18      12      32 ..     230     249 ..     225     252 .. 0.87
   5 !   21.5   0.0   7.1e-08   0.00016       9      30 ..     271     293 ..     263     301 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.01
                                      EEEEEE-TTSSEE CS
                              PD40 11 egaPsfSPDGkrl 23
                                       + + +SPDG+r 
  gi|298675386|ref|YP_003727136.1| 65 AMYIHWSPDGTRA 77
                                      56666*****985 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 2e-06
                                       EEEEEE-TTSSEEEEEEE CS
                              PD40  11 egaPsfSPDGkrlaFsSd 28 
                                       +g Ps+SPDG  ++++S+
  gi|298675386|ref|YP_003727136.1| 133 IGLPSWSPDGDVFTYTSE 150
                                       678**************7 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00068
                                       E-TTSSEEEEEEECT CS
                              PD40  16 fSPDGkrlaFsSdRg 30 
                                       +SPDG++l +  +++
  gi|298675386|ref|YP_003727136.1| 189 WSPDGSYLLYRGYKK 203
                                       *********988877 PP

  == domain 4  score: 11.8 bits;  conditional E-value: 8.2e-05
                                       EEEEE-TTSSEEEEEEECT.T CS
                              PD40  12 gaPsfSPDGkrlaFsSdRgsG 32 
                                       +++++SP G+++aF  + + G
  gi|298675386|ref|YP_003727136.1| 230 EDITWSPKGNKIAFLGEEK-G 249
                                       679***********98877.6 PP

  == domain 5  score: 21.5 bits;  conditional E-value: 7.1e-08
                                       S..EEEEEE-TTSSEEEEEEECT CS
                              PD40   9 g.negaPsfSPDGkrlaFsSdRg 30 
                                          +++P +SPDG++laFs   +
  gi|298675386|ref|YP_003727136.1| 271 NsSIHNPLWSPDGRKLAFSKIED 293
                                       3469**************97655 PP

>> eIF2A  Eukaryotic translation initiation factor eIF2A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.016        36      10      54 ..      67     115 ..      60     126 .. 0.72
   2 ?    3.7   0.0     0.021        48     117     159 ..     152     197 ..     136     200 .. 0.76
   3 !   14.9   0.0   8.1e-06     0.018      40     121 ..     208     292 ..     198     337 .. 0.79
   4 ?    3.3   0.0      0.03        66     140     160 ..     454     474 ..     398     482 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.016
                                       EEEE-TTTTEEEEEEE.E--TT-CE.EEEEE...EEEESSSTT--EEEC CS
                             eIF2A  10 klkWnkkGtsllvlvstevdktnks.yyget...elyliklkkkksevv 54 
                                        ++W+  Gt  lvl++  v  +nk   ++ +   +ly++++++ +++++
  gi|298675386|ref|YP_003727136.1|  67 YIHWSPDGTRALVLTKLTVHAKNKPeATTRSeirALYIMNADGFDIKRI 115
                                       689************9666655554033333122589999888888776 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.021
                                       EE-TTSSS-EEEEEETTTTEEEEE...EE-TT--EEEE-TTSSEEE CS
                             eIF2A 117 laGfgnlaGeleiwdvkkkkkiak...aeaanatlvewspdgryvl 159
                                       la  gn+ Ge  i+d +++++i+k   + ++     +wspdg+y+l
  gi|298675386|ref|YP_003727136.1| 152 LAKNGNILGEFLIVDADNLNTIEKgsfISNKIDFIKKWSPDGSYLL 197
                                       567799***********99999882223344455679******986 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 8.1e-06
                                       EEEESSSTT--EEECCEESSS.EEEEEE-TTSS-EEEEES.SSSCEEEEEEC...SCEEEEEEEEES--EEEE-TTS CS
                             eIF2A  40 elyliklkkkksevvelkkegpihdvaWspkskefaviyG.kmpakvslfdl...kvkviskleeqkrNtiffspkg 112
                                       ++yl++l+ + + ++++++ +   d++Wspk++++a +   k ++++ +++l   ++k i+++++++    ++sp g
  gi|298675386|ref|YP_003727136.1| 208 KCYLLDLTRNITRRFPITQYN-PEDITWSPKGNKIAFLGEeKGNESAFVYNLdngNLKNIFSTKNSSIHNPLWSPDG 283
                                       79***************9887.69************996624455788888854459999999999999999***** PP

                                       SEEEEE-TT CS
                             eIF2A 113 klvllaGfg 121
                                       + ++++ + 
  gi|298675386|ref|YP_003727136.1| 284 RKLAFSKIE 292
                                       998877665 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.03
                                       EEE-TT--EEEE-TTSSEEEE CS
                             eIF2A 140 kaeaanatlvewspdgryvlT 160
                                       +++ ++  +++w+p+gry+ T
  gi|298675386|ref|YP_003727136.1| 454 SVNGSHIEKINWNPTGRYLFT 474
                                       444455556778888888877 PP

>> DPPIV_N  Dipeptidyl peptidase IV (DPP IV) N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0     0.085   1.9e+02      42      59 ..      62      79 ..      44     100 .. 0.74
   2 !    5.4   0.0     0.003       6.7      23      61 ..     108     149 ..      71     151 .. 0.76
   3 ?    0.1   0.0      0.12   2.6e+02     107     117 ..     188     198 ..     182     205 .. 0.85
   4 !   12.8   0.1   1.6e-05     0.036     107     132 ..     278     303 ..     190     314 .. 0.77
   5 ?    1.9   0.2     0.034        76     303     339 ..     335     371 ..     329     377 .. 0.79
   6 ?   -3.1   0.0       1.1   2.5e+03      23      57 ..     438     472 ..     430     476 .. 0.67

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.085
                                      TT.BSEEEEESSTTEEEE CS
                           DPPIV_N 42 eeklqlakwSPagdklaf 59
                                       +++++++wSP+g++  +
  gi|298675386|ref|YP_003727136.1| 62 GGPAMYIHWSPDGTRALV 79
                                      578999999999987655 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.003
                                       TEEEEEETTTEECEEEETT...TT.BSEEEEESSTTEEEEEE CS
                           DPPIV_N  23 aeyyiydletneveelspg...eeklqlakwSPagdklafvr 61 
                                       ++++i+ ++++e ++ +++   ++ + l+ wSP+gd + ++ 
  gi|298675386|ref|YP_003727136.1| 108 DGFDIKRIAWGEYTPYTRKvgnDKLIGLPSWSPDGDVFTYTS 149
                                       45667777779999999999999999***********99986 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.12
                                       EE-TTSSEEEE CS
                           DPPIV_N 107 wWspdgsrlay 117
                                        Wspdgs+l+y
  gi|298675386|ref|YP_003727136.1| 188 KWSPDGSYLLY 198
                                       59999999998 PP

  == domain 4  score: 12.8 bits;  conditional E-value: 1.6e-05
                                       EE-TTSSEEEEEEEECTTS-EEEEEE CS
                           DPPIV_N 107 wWspdgsrlaylrfdeseVpeitlps 132
                                        Wspdg++la+ ++ +++V+++ + +
  gi|298675386|ref|YP_003727136.1| 278 LWSPDGRKLAFSKIEDNNVKDVYVID 303
                                       59999999999999999999988876 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 0.034
                                       SETTEBEEEEEESSCTTEEEESSTTTSEE.EEEEE-TT CS
                           DPPIV_N 303 dsPlerhlYsvslesggeltrltdeegdh.ysasfsps 339
                                       + + e +lYs+s++ ++++t l ++++++  ++s+s++
  gi|298675386|ref|YP_003727136.1| 335 EYSPEDNLYSISVN-SRNKTLLYNSTNESgIDYSYSDH 371
                                       567899********.99999998888888666666654 PP

  == domain 6  score: -3.1 bits;  conditional E-value: 1.1
                                       TEEEEEETTTEECEEEETTTT.BSEEEEESSTTEE CS
                           DPPIV_N  23 aeyyiydletneveelspgeeklqlakwSPagdkl 57 
                                       +++++++ +t++ +++s + + ++ ++w+P+g++l
  gi|298675386|ref|YP_003727136.1| 438 NKLVMVNASTKSESNISVNGSHIEKINWNPTGRYL 472
                                       45566666666666666666777777777777665 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.6   5.8e+03      39      53 ..      63      77 ..      56      84 .. 0.74
   2 ?   -0.9   0.0      0.91     2e+03      36      55 ..     128     147 ..     101     186 .. 0.71
   3 ?   -2.3   0.0       2.5   5.6e+03      45      59 ..     188     203 ..     180     215 .. 0.75
   4 !    6.0   0.0    0.0063        14      25      72 ..     262     306 ..     232     326 .. 0.67
   5 ?    5.3   0.1     0.011        25       3      53 ..     422     472 ..     420     480 .. 0.59

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.6
                       ANAPC4_WD40 39 sevrsLaWkpdgklL 53
                                      +    ++W+pdg+  
  gi|298675386|ref|YP_003727136.1| 63 GPAMYIHWSPDGTRA 77
                                      5566799****9754 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.91
                       ANAPC4_WD40  36 kedsevrsLaWkpdgklLav 55 
                                       ++d+ +   +W+pdg ++  
  gi|298675386|ref|YP_003727136.1| 128 GNDKLIGLPSWSPDGDVFTY 147
                                       44555555578888888765 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.5
                       ANAPC4_WD40  45 aWkpdgklLav.aysd 59 
                                       +W+pdg+ L   +y++
  gi|298675386|ref|YP_003727136.1| 188 KWSPDGSYLLYrGYKK 203
                                       6*****9765315555 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.0063
                       ANAPC4_WD40  25 ngqrvwtleedkedsevrsLaWkpdgklLava.ysdgevrlldaesgkv 72 
                                       n ++++++    ++s++++  W+pdg+ La++ ++d++v+ + + + +v
  gi|298675386|ref|YP_003727136.1| 262 NLKNIFST----KNSSIHNPLWSPDGRKLAFSkIEDNNVKDVYVIDINV 306
                                       34666666....88999999**********8736788887665555555 PP

  == domain 5  score: 5.3 bits;  conditional E-value: 0.011
                       ANAPC4_WD40   3 wcptmDLiAlatedgellvfRlngqrvwtleedkedsevrsLaWkpdgklL 53 
                                       wc    L+ ++te++   +  +n     + + + ++s++++++W+p g+ L
  gi|298675386|ref|YP_003727136.1| 422 WCGDDLLLEVVTENDTNKLVMVNASTKSESNISVNGSHIEKINWNPTGRYL 472
                                       555555555555544444444444444444446677888888888888777 PP

>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       2.7     6e+03       8      20 ..     446     458 ..     442     460 .. 0.84
   2 ?   15.4   0.5   5.7e-06     0.013       6      55 ..     509     563 ..     504     571 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.7
                              PEGA   8 SnpeGatVyidGk 20 
                                       S+ ++++++++G+
  gi|298675386|ref|YP_003727136.1| 446 STKSESNISVNGS 458
                                       8889999****97 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 5.7e-06
                              PEGA   6 irSnpeGatVyidGkylGkTP....vtls.leaGnyslrvekeGYedlektvtvt 55 
                                       ++ +  +atVy +G+ +G+T+    ++     +G+y+l+ +k GY +++ +v++ 
  gi|298675386|ref|YP_003727136.1| 509 VSGSVGNATVYSNGEHIGRTNpegvLSHQfKNNGSYRLKAVKVGYINASHKVSIG 563
                                       777889**************9444445566789*******************986 PP

>> Lactonase  Lactonase, 7-bladed beta-propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0012       2.7     284     332 ..     220     268 ..     214     279 .. 0.87
   2 ?    1.8   0.1      0.05   1.1e+02       5     102 ..     289     383 ..     285     400 .. 0.79
   3 ?   -0.4   0.0      0.24   5.3e+02     283     310 ..     450     477 ..     436     502 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0012
                                       EEEE-SSS.--EEEE-TTSSEEEEEETTTTEEEEEEEETTTTEEEEESE CS
                         Lactonase 284 eevstegkfPRdfaldpsgklllvanqksdnvtvferdaetGkLtelgk 332
                                        +++++  +P d++++p+g+ +++ +++ +n + f  + ++G+L+++ +
  gi|298675386|ref|YP_003727136.1| 220 RRFPITQYNPEDITWSPKGNKIAFLGEEKGNESAFVYNLDNGNLKNIFS 268
                                       57889999*************************************9855 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.05
                                       EEGGSSS.TEEEEEEEETTTS-EEEEEEEEESS---SEEE-TTSSEEEEEET.STTTEEEEEEEETTTTEEEEEEEE CS
                         Lactonase   5 GtytkgeskgiytlkldtetgkltplelvaelenPsyLalspdgktlYavnetgeeggvsafaidkdsgeltllnkv 81 
                                       +  ++++ k +y+++++  +g+  +l++   +  +++L     +k lY+     +e ++++ ++++++++l l n++
  gi|298675386|ref|YP_003727136.1| 289 SKIEDNNVKDVYVIDINVVNGRPYKLTTLHGGILVEWLDS---EKLLYTEYS--PEDNLYSISVNSRNKTL-LYNST 359
                                       5566788899999999999999999999999999999999...999998655..78899999999986555.55665 PP

                                       E....SSS-EEEEEE-TTSSEEEE CS
                         Lactonase  82 ss...egaspchlsvdedgkllav 102
                                       ++   + + + h  vd++g++++v
  gi|298675386|ref|YP_003727136.1| 360 NEsgiDYSYSDHSFVDPTGEFVFV 383
                                       552335566667789999999987 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.24
                                       EEEEE-SSS.--EEEE-TTSSEEEEEET CS
                         Lactonase 283 veevstegkfPRdfaldpsgklllvanq 310
                                         ++s++g +  +++++p+g++l+  nq
  gi|298675386|ref|YP_003727136.1| 450 ESNISVNGSHIEKINWNPTGRYLFTRNQ 477
                                       4566666666667777777777777776 PP

>> Gmad1  Lipoprotein LpqB beta-propeller domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.037        82     112     130 ..      63      81 ..      32      88 .. 0.75
   2 ?    3.3   0.0     0.026        59      46      82 ..     112     148 ..      86     156 .. 0.80
   3 ?    0.9   0.0      0.15   3.3e+02      23      76 ..     227     283 ..     221     307 .. 0.66
   4 ?   -2.6   0.0       1.6   3.6e+03     178     203 ..     440     463 ..     421     476 .. 0.57

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.037
                             Gmad1 112 gpvtelrvSrDGtRaAviv 130
                                       gp   +  S+DGtRa+v++
  gi|298675386|ref|YP_003727136.1|  63 GPAMYIHWSPDGTRALVLT 81 
                                       666666779********99 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.026
                             Gmad1  46 grtLvvgsyggeasevleggsltrpSwdrdgalWvve 82 
                                        ++++ g+y   +++v +++ +  pSw++dg++++  
  gi|298675386|ref|YP_003727136.1| 112 IKRIAWGEYTPYTRKVGNDKLIGLPSWSPDGDVFTYT 148
                                       56778888888899999999*************9965 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.15
                             Gmad1  23 vdlrsaAvSrdgqqvaavtapdggrtLvvg.syggeasevl..eggsltrpSwdrdg 76 
                                        +++    S++g+++a++ +++g+++  v    +g+ ++++  + +s+ +p w++dg
  gi|298675386|ref|YP_003727136.1| 227 YNPEDITWSPKGNKIAFLGEEKGNESAFVYnLDNGNLKNIFstKNSSIHNPLWSPDG 283
                                       567777888888888888866666665555134455555554455577777777774 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 1.6
                             Gmad1 178 LvVlrsseggpvqalVsldgseseal 203
                                       L V+ ++++++ ++ +s++gs++e++
  gi|298675386|ref|YP_003727136.1| 440 L-VMVNASTKSESN-ISVNGSHIEKI 463
                                       2.233333333444.55666655554 PP

>> Peptidase_S9_N  Prolyl oligopeptidase, N-terminal beta-propeller domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.24   5.4e+02     175     191 ..     187     203 ..     133     222 .. 0.60
   2 ?   -0.7   0.0      0.21   4.7e+02     177     193 ..     189     205 ..     159     260 .. 0.61
   3 ?    9.5   0.1   0.00017      0.39     120     203 ..     270     350 ..     263     362 .. 0.68
   4 ?   -2.3   0.0      0.65   1.4e+03     147     185 ..     435     473 ..     433     476 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.24
                                       EEECTTSSEEEEEESS- CS
                    Peptidase_S9_N 175 ivWaadekgffYtrydk 191
                                        +W +d+++++Y  y+k
  gi|298675386|ref|YP_003727136.1| 187 KKWSPDGSYLLYRGYKK 203
                                       46777777777777764 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.21
                                       ECTTSSEEEEEESS-SS CS
                    Peptidase_S9_N 177 WaadekgffYtrydked 193
                                       W +d+++++Y  y+k +
  gi|298675386|ref|YP_003727136.1| 189 WSPDGSYLLYRGYKKGE 205
                                       44444444444444222 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00017
                                       TS-.EEEEEEEE-TTSSEEEEE..EEETTSSEEEEEEEETTTTEEEEEEEEEEESEE.EEECTTSSEEEEEESS-SS CS
                    Peptidase_S9_N 120 dgtfvalgefavsedgkllAys..lsksGsdwytirvkdietgedlpdeledvkfsg.ivWaadekgffYtrydked 193
                                       + +  ++++   s+dg+ lA+s  ++ + +d+y i +    +g+  p +l+   +   ++W++  + ++Yt+y +ed
  gi|298675386|ref|YP_003727136.1| 270 KNS--SIHNPLWSPDGRKLAFSkiEDNNVKDVYVIDINV-VNGR--PYKLTTLHGGIlVEWLDS-EKLLYTEYSPED 340
                                       555..6677778**********44466677777776543.3444..5566666666669***99.9999****9888 PP

                                       S-TSTSB-S- CS
                    Peptidase_S9_N 194 ersdtdtnln 203
                                       +  + + n  
  gi|298675386|ref|YP_003727136.1| 341 NLYSISVNSR 350
                                       7776444433 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 0.65
                                       SSEEEEEEEETTTTEEEEEEEEEEESEEEEECTTSSEEE CS
                    Peptidase_S9_N 147 sdwytirvkdietgedlpdeledvkfsgivWaadekgff 185
                                       +d +++ +++++t+ + + ++++  +++i W + ++++f
  gi|298675386|ref|YP_003727136.1| 435 NDTNKLVMVNASTKSESNISVNGSHIEKINWNPTGRYLF 473
                                       688889999999999999999999********9999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (616 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.46
# Mc/sec: 4057.89
//
Query:       gi|298675387|ref|YP_003727137.1|  [L=102]
Description: hypothetical protein Metev_1489 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       917  (0.0511462); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 800.95
//
Query:       gi|298675388|ref|YP_003727138.1|  [L=142]
Description: hypothetical protein Metev_1490 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1020.00
//
Query:       gi|298675389|ref|YP_003727139.1|  [L=188]
Description: hypothetical protein Metev_1491 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00011   22.7   0.0    0.00017   22.1   0.0    1.2  1  Reprolysin_3   Metallo-peptidase family M12B Reprolysin-like
    0.00096   19.4   0.3     0.0013   18.9   0.3    1.3  1  Reprolysin_5   Metallo-peptidase family M12
  ------ inclusion threshold ------
       0.13   11.9   0.1       0.16   11.6   0.1    1.1  1  Peptidase_M90  Glucose-regulated metallo-peptidase M90


Domain annotation for each model (and alignments):
>> Reprolysin_3  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   2.8e-08   0.00017       7     121 ..      40     147 ..      37     148 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.8e-08
                      Reprolysin_3   7 lvnranqiyerdlg.irlqlvaiiitdkas..dpytkkdatealdelaevtaeaergqagyDlvhlftardesgvgG 80 
                                       +vn  ++++   ++  ++++ ++ +++  +  d ++  d++ al+ l e+t  +    +  D+v    + d+ +  G
  gi|298675389|ref|YP_003727139.1|  40 IVNPTDEALA-RFEqFNINVDRTWYWNGWDasDVSPADDSSNALEDLIEDTNVR---DDANDIVIGWAH-DM-DHNG 110
                                       6777777777.3333777899999999876114444445566666666666666...788899998888.45.799* PP

                      Reprolysin_3  81 lAyv...gsvcnsskkagvnsgssvlgkvgadtvaHEiGHnfga 121
                                       +A +   ++vc+ s + +v + +       ++ v+HE+ Hnf+a
  gi|298675389|ref|YP_003727139.1| 111 IAKIggpYCVCSDSANLKVDWPH-------DSIVQHEVSHNFDA 147
                                       ***999999*******9999999.......689*********98 PP

>> Reprolysin_5  Metallo-peptidase family M12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.3   2.1e-07    0.0013      68     159 ..      73     149 ..      37     183 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.1e-07
                      Reprolysin_5  68 sstgdaselLnefqsassalrgqqnddlailflmtnfsggvGlAwlgqlcnsgsagsvstrveksnsvvvstatevq 144
                                       s  +d+s+ L+++  ++++ r+ + +d++i + + +++++ G+A  g++        v+++   s++  v ++  + 
  gi|298675389|ref|YP_003727139.1|  73 SPADDSSNALEDL-IEDTNVRD-DANDIVIGWAH-DMDHN-GIAKIGGPYC------VCSD---SANLKV-DWPHDS 135
                                       4468899999999.45555555.55579999999.78888.8999977622......2222...133335.677899 PP

                      Reprolysin_5 145 vvaHElGHnfGavHD 159
                                       +v+HE++Hnf a+ D
  gi|298675389|ref|YP_003727139.1| 136 IVQHEVSHNFDAE-D 149
                                       ***********98.4 PP

>> Peptidase_M90  Glucose-regulated metallo-peptidase M90
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   2.6e-05      0.16     110     168 ..      99     155 ..      83     182 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.6e-05
                     Peptidase_M90 110 gvvheeeeellGeawergpviLswedveaggeneedkenvviHEfaHkLDmedgeadGv 168
                                        + + ++    G a  +gp  ++ ++++ + ++++   ++v HE++H++D ed    G+
  gi|298675389|ref|YP_003727139.1|  99 VIGWAHDMDHNGIAKIGGPYCVCSDSANLKVDWPH--DSIVQHEVSHNFDAEDQGYWGY 155
                                       44456677788999999999999999999999999..99*************9887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1413.28
//
Query:       gi|298675390|ref|YP_003727140.1|  [L=173]
Description: hypothetical protein Metev_1492 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.036   14.0   0.0      0.046   13.7   0.0    1.2  1  Thioredoxin_14  Thioredoxin-like domain
      0.077   13.9   0.0       0.32   11.9   0.0    1.9  2  Pilin_N         Archaeal Type IV pilin, N-terminal
        0.2   10.4   0.4        0.2   10.4   0.4    1.0  1  O-antigen_lig   O-antigen ligase like membrane protein


Domain annotation for each model (and alignments):
>> Thioredoxin_14  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   7.7e-06     0.046      83     206 ..      19     150 ..       7     168 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.7e-06
                                       EEEEEEEE-..SSH.H.HHHHHHHHHHHHH................TT-HHHHHHHHHHHH..HT-SSS--..HHHH CS
                    Thioredoxin_14  83 iRfGlVplvssese.d.skklaklfyylae................nygakaalefltaleakakkskepdltkevv 141
                                       i +++Vp+ s +++ + +kk  + +yy ++                +++                        k+ +
  gi|298675390|ref|YP_003727140.1|  19 ISIAVVPAASGNENtNsDKKTLNELYYTKSelqslydkynisendiKFS------------------------KDKL 71 
                                       5578888885555433222222223333222322222221111112122........................2333 PP

                                       HHHHHHH.........................SS----TT...........TTHHHHHHHHHHHHHTT--SSS-EEE CS
                    Thioredoxin_14 142 esafkea.........................ldealkseveeileaeitseydealkasrefikrlglkeaqepvf 193
                                        +++k +                         ++++++++       + +s +d   +a +e++++ g++ a++ v 
  gi|298675390|ref|YP_003727140.1|  72 PHYLKGTilnsdkrviatedgtppeglvkgeyYEKVISHD-------KMNSIID---QARQEYVNKYGVDPANPKVE 138
                                       3333333333333444444556665554444455555555.......3444445...4669***********98898 PP

                                       E.TTEEEESSSSH CS
                    Thioredoxin_14 194 llNGvvlpfdekw 206
                                       ++NG++lp++e +
  gi|298675390|ref|YP_003727140.1| 139 MVNGQPLPKEE-V 150
                                       99******998.5 PP

>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   5.4e-05      0.32      10      42 ..      11      43 ..      10      69 .. 0.72
   2 ?   -0.9   0.0      0.53   3.2e+03      57      75 ..     135     153 ..     110     158 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.4e-05
                           Pilin_N 10 iLmvaitvIlaAviaafvlglasneekapqasi 42
                                      iL++a+++I +Av+ a  ++ + n++k++  ++
  gi|298675390|ref|YP_003727140.1| 11 ILLIALVIISIAVVPAASGNENTNSDKKTLNEL 43
                                      8**************999988666666655444 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.53
                           Pilin_N  57 vslehkgGdsidtkdlkiv 75 
                                        ++e+ +G++++++++k +
  gi|298675390|ref|YP_003727140.1| 135 PKVEMVNGQPLPKEEVKRL 153
                                       5788999999999888755 PP

>> O-antigen_lig  O-antigen ligase like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.4   3.3e-05       0.2     242     319 ..       4     123 ..       1     156 [. 0.70

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 3.3e-05
                     O-antigen_lig 242 lkkkklllaiillvligill..aiypyspiyrrkelkekeieiksekk...eeeeikne.................. 295
                                       +k k+l + +i+lv+i i++  a+ + +++ + k++ ++ + +kse +   ++++i ++                  
  gi|298675390|ref|YP_003727140.1|   4 IKGKQLGILLIALVIISIAVvpAASGNENTNSDKKTLNELYYTKSELQslyDKYNISENdikfskdklphylkgtil 80 
                                       678889777888888888777899999*****9999999**999999988855555444466666666666666666 PP

                     O-antigen_lig 296 ..................ikenykseglk.eavleqyeyandk 319
                                                         +k +y  + +  +++ ++ ++a ++
  gi|298675390|ref|YP_003727140.1|  81 nsdkrviatedgtppeglVKGEYYEKVIShDKMNSIIDQARQE 123
                                       6667777766777777775555555555554444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       820  (0.045736); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1347.49
//
Query:       gi|298675391|ref|YP_003727141.1|  [L=303]
Description: hypothetical protein Metev_1493 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-30  106.5  18.1    1.9e-30  106.2  18.1    1.1  1  ABC2_membrane_2  ABC-2 family transporter protein
     0.0013   18.3   7.8      0.003   17.1   7.5    1.7  1  CcmB             CcmB protein
     0.0016   18.0  20.3     0.0016   18.0  20.3    3.7  3  ABC2_membrane_5  ABC-2 family transporter protein
     0.0039   17.2  14.7     0.0039   17.2  14.7    3.0  3  ABC2_membrane_4  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.064   13.2   1.2       0.71    9.9   0.0    2.8  2  SafA             Two-component-system connector protein


Domain annotation for each model (and alignments):
>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.2  18.1   5.2e-34   1.9e-30       3     288 .]      11     301 ..       9     301 .. 0.89

  Alignments for each domain:
  == domain 1  score: 106.2 bits;  conditional E-value: 5.2e-34
                   ABC2_membrane_2   3 iakkEfrdlvrsrrfllltvllplidvalaylkdlgsslqseakaikeatlaleyveaasasdeaedtdqdlkvvst 79 
                                       i +kEf+d++ s++flll + + l+   + + +  +++l++  + i +  +++ ++ + +                 
  gi|298675391|ref|YP_003727141.1|  11 IGQKEFADSLWSPVFLLLLLTFTLV---IFFASYWQGMLGEHLGRITAGPSSVLMLGFKNL--------------AD 70 
                                       678**********************...99***********************99999665..............56 PP

                   ABC2_membrane_2  80 imavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvll.alaiilalgiv 155
                                       ima + p+i+++++++a+  E  +g+l +lL +Pv+Rd i+lgK+ g l+    +a+ l++++ + a  + + +g+ 
  gi|298675391|ref|YP_003727141.1|  71 IMAWFTPLIGIALSFNAVINEQKSGSLNVLLGHPVFRDNIILGKVFGALLT---TAIVLFISTAVsAGTLLMFFGVT 144
                                       *************************************************99...6665555554427778999**** PP

                   ABC2_membrane_2 156 laledllllvvasvlllllv.vflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavp..... 226
                                       +++++l+++++ +++++l++ vf+++g+  S+ +++++ ++ + +++++ l+i++++++ ++ +ll +++       
  gi|298675391|ref|YP_003727141.1| 145 VTAAELVRIALYVIITFLYTsVFIGIGFISSIKLKDASDSLIYNIVIWLCLSIVFTVIVNAI-YLLIEHTLVgnpds 220
                                       ***********************************************************883.33333443344444 PP

                   ABC2_membrane_2 227 qeindflsllsptsayntllneilagsdlna.....................lgstatnllilllllavllvlgyvl 282
                                        ++   +s +sp ++y  l+    + +  ++                     l  ++tnl++l++ +++l+v+++ +
  gi|298675391|ref|YP_003727141.1| 221 WNVIGGISNISPMHHYAELITGRANLG--WSgpgvestikgvidtrftlfqwLNEFWTNLVVLIATPVILFVISFIS 295
                                       344455888888888888888888888..66889******************************************* PP

                   ABC2_membrane_2 283 FkrkDl 288
                                       F r+D+
  gi|298675391|ref|YP_003727141.1| 296 FLRRDI 301
                                       ****96 PP

>> CcmB  CcmB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   7.5   8.3e-07     0.003      45     133 ..      66     157 ..      50     208 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 8.3e-07
                              CcmB  45 sriapgilWvaallaslLsldrlfaadfedGsLellllapvplellvlaKalAhwlltglplvllaplla....lll 117
                                       +++a  + W + l+   Ls++ +  +++++GsL+ ll +pv  + ++l+K++   l+t + l + +++ a    +++
  gi|298675391|ref|YP_003727141.1|  66 KNLADIMAWFTPLIGIALSFNAVI-NEQKSGSLNVLLGHPVFRDNIILGKVFGALLTTAIVLFISTAVSAgtllMFF 141
                                       67899999*************986.6899*********************************999999765544677 PP

                              CcmB 118 nleaaalgllaltLll 133
                                       ++ ++a +l+ ++L +
  gi|298675391|ref|YP_003727141.1| 142 GVTVTAAELVRIALYV 157
                                       8888888888777755 PP

>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.3     0.056     2e+02     180     199 ..      23      42 ..       8      45 .. 0.75
   2 !   18.0  20.3   4.5e-07    0.0016      33     175 ..      65     213 ..      53     231 .. 0.74
   3 ?    1.6   0.3     0.049   1.8e+02     103     140 ..     257     294 ..     249     299 .. 0.61

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.056
                   ABC2_membrane_5 180 yilliillviillliivSyf 199
                                       +++l++ll ++l+++++Sy+
  gi|298675391|ref|YP_003727141.1|  23 PVFLLLLLTFTLVIFFASYW 42 
                                       45666777888888988885 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 4.5e-07
                   ABC2_membrane_5  33 ndsvllifsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitlllli..iavli 107
                                        ++++ i+++++++i i l ++++ +++ks++  +ll  Pv r +i+  K +++l+ ++i+++i++++++  + +++
  gi|298675391|ref|YP_003727141.1|  65 FKNLADIMAWFTPLIGIALSFNAVINEQKSGSLNVLLGHPVFRDNIILGKVFGALLTTAIVLFISTAVSAgtLLMFF 141
                                       3456667788999999999***********************************************99862145555 PP

                   ABC2_membrane_5 108 kgnvtisevllsiliglvialiflaivlPlyfkfgvekgri.....vliiiifgiifllvaifslsklelsli 175
                                         +vt  e++  i+++++i+++++++++ + f+ + +         ++i+i++++ ++++ i++  +l ++++
  gi|298675391|ref|YP_003727141.1| 142 GVTVTAAELVR-IALYVIITFLYTSVFIGIGFISSIKLKDAsdsliYNIVIWLCLSIVFTVIVNAIYLLIEHT 213
                                       56688777655.5777778888888887777766532222233344999999999999999999988865533 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.049
                   ABC2_membrane_5 103 iavlikgnvtisevllsiliglvialiflaivlPlyfk 140
                                       i+++i  ++t+ ++l+ +   lv+ ++  +i++++ f+
  gi|298675391|ref|YP_003727141.1| 257 IKGVIDTRFTLFQWLNEFWTNLVVLIATPVILFVISFI 294
                                       55556666666666666666666666665665555554 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2  14.7   1.1e-06    0.0039      20     158 ..      25     170 ..      17     180 .. 0.61
   2 ?   -0.6   1.6      0.32   1.1e+03     100     121 ..     190     211 ..     185     225 .. 0.63
   3 ?   -0.1   0.4      0.21   7.5e+02     144     162 ..     276     293 ..     253     299 .. 0.45

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.1e-06
                   ABC2_membrane_4  20 laallvpllallyfn.........llgktgldpaefys..lsvfgftlllllplilgi.iasylifrEeqndtlknL 84 
                                       +++ll+ +++++ f+          lg+ ++ p+++ +  ++++   ++  ++ ++gi ++   + +E++++ l+ L
  gi|298675391|ref|YP_003727141.1|  25 FLLLLLTFTLVIFFAsywqgmlgeHLGRITAGPSSVLMlgFKNLA-DIMAWFTPLIGIaLSFNAVINEQKSGSLNVL 100
                                       333333333333332222244444344444445444442233333.34455666666637778999*********** PP

                   ABC2_membrane_4  85 ltiPvsrtklllaKlivllllsvllmlvtflitvlfallsgfvgfsvklvlellkkclelgllvffavlpiial 158
                                       l  Pv r +++l+K++  ll+++++++++++++  ++ l++f+g++v++    l+++ ++++++f+ +++ i +
  gi|298675391|ref|YP_003727141.1| 101 LGHPVFRDNIILGKVFGALLTTAIVLFISTAVS--AGTLLMFFGVTVTA--AELVRIALYVIITFLYTSVFIGI 170
                                       *************************99988765..55566666555433..45555556666666666655544 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.32
                   ABC2_membrane_4 100 ivllllsvllmlvtflitvlfa 121
                                       +++l+ls++++++  +i +l++
  gi|298675391|ref|YP_003727141.1| 190 VIWLCLSIVFTVIVNAIYLLIE 211
                                       4566666666666665555553 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.21
                   ABC2_membrane_4 144 lgllvffavlpiialvllk 162
                                       ++l+v+ + +p+i++v+ +
  gi|298675391|ref|YP_003727141.1| 276 TNLVVL-IATPVILFVISF 293
                                       223233.333333333332 PP

>> SafA  Two-component-system connector protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0    0.0002      0.71      10      52 ..      11      54 ..       6      58 .. 0.82
   2 ?   -0.5   1.2      0.34   1.2e+03      13      41 ..     179     207 ..     173     212 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0002
                              SafA 10 itqrdnykeimsvivvvllltltliaifsaidqlsise.mGria 52
                                      i q++    + s + ++lllt+tl+  f++  q  + e +Gri+
  gi|298675391|ref|YP_003727141.1| 11 IGQKEFADSLWSPVFLLLLLTFTLVIFFASYWQGMLGEhLGRIT 54
                                      5677777778899999************9999877776478885 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.34
                              SafA  13 rdnykeimsvivvvllltltliaifsaid 41 
                                       +d    ++  iv+ l l++ +  i  ai 
  gi|298675391|ref|YP_003727141.1| 179 KDASDSLIYNIVIWLCLSIVFTVIVNAIY 207
                                       66667778889999999999999988885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1050  (0.0585643); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 2369.49
//
Query:       gi|298675392|ref|YP_003727142.1|  [L=300]
Description: hypothetical protein Metev_1494 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-32  113.0  20.9    3.1e-31  108.7  20.9    2.0  1  ABC2_membrane_2  ABC-2 family transporter protein
    5.7e-06   26.4  20.7    5.7e-06   26.4  20.7    2.0  2  ABC2_membrane_4  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.018   14.6  34.2      0.015   14.9  30.1    2.5  2  ABC2_membrane_5  ABC-2 family transporter protein
      0.058   12.5  38.6       0.18   10.9  37.8    2.1  1  ABC2_membrane_3  ABC-2 family transporter protein
       0.26   11.0  23.9       0.82    9.4  23.9    1.9  1  PhoLip_ATPase_C  Phospholipid-translocating P-type ATPase C-t
       0.33   10.4  31.3      0.065   12.6  25.4    2.2  2  ABC2_membrane    ABC-2 type transporter
       0.73    9.9   4.2         14    5.8   0.4    2.8  2  UPF0370          Uncharacterised protein family (UPF0370)
          6    6.5   8.6        1.1    8.8   3.3    2.4  2  DUF3687          D-Ala-teichoic acid biosynthesis protein


Domain annotation for each model (and alignments):
>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.7  20.9   1.4e-34   3.1e-31       2     288 .]      10     298 ..       9     298 .. 0.88

  Alignments for each domain:
  == domain 1  score: 108.7 bits;  conditional E-value: 1.4e-34
                   ABC2_membrane_2   2 aiakkEfrdlvrsrrfllltvllplidvalaylkdlgsslqseakaikeatlaleyveaasasdeaedtdqdlkvvs 78 
                                       +ia+kE+ d + s rf +l +++ li   +  ++  +++++s   +++ +++a+                       
  gi|298675392|ref|YP_003727142.1|  10 VIAQKEIEDNLQSSRFKVLLFIFTLI---VFSFSVREGMSGSNIFEQGFLDVAQ----------------------- 60 
                                       58999999999999999999999999...4445555555555555555555554....................... PP

                   ABC2_membrane_2  79 timavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiila.lgi 154
                                        im +++p++++++g+da+++E+ + +l + L++Pv++d i++gK+++gl+    +a+ ++++v+++++ +l+  g+
  gi|298675392|ref|YP_003727142.1|  61 -IMGIFLPIVGIAIGFDAVVKERKSSSLTIFLTHPVFKDNIITGKMVAGLVT---LAMVIVISVIFSVGTVLIlTGV 133
                                       .***************************************************...7777777777777666551578 PP

                   ABC2_membrane_2 155 vlaledllllvvasvlllllv.vflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavp.... 226
                                       ++ l++l +++++ +++++++ vfla+g+llS+++ +++++  + ++++++l ++++ ++++ a++ +g++++    
  gi|298675392|ref|YP_003727142.1| 134 PVGLMELNRIFLFGIITFVYLsVFLAMGILLSIFSSNQTNSFIYGIVIWIILILMFGTISSATASIATGESIIdmen 210
                                       889999999999999999999*****************************************999999999999*** PP

                   ABC2_membrane_2 227 ....qeindflsllsptsayntllneilagsdlna.......................lgstatnllilllllavll 276
                                           +++n +++ l+p+++y  ++  ++  s + +                           + n+++ll++   l+
  gi|298675392|ref|YP_003727142.1| 211 nqeaAKLNSDMQKLTPIHHYAEAVTGFSGIS-VGSvnfnsdqkassgvfdlshtlgkwFNDYWMNIVTLLVMQFLLF 286
                                       *999****************99998888777.45567889***************9999999*************** PP

                   ABC2_membrane_2 277 vlgyvlFkrkDl 288
                                       + ++ +F+ kD+
  gi|298675392|ref|YP_003727142.1| 287 AASFAMFMHKDV 298
                                       **********96 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4  20.7   2.5e-09   5.7e-06      17     177 ..      29     187 ..      21     190 .. 0.70
   2 ?    0.1   0.1       0.3   6.8e+02      52      69 ..     271     288 ..     238     297 .. 0.62

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 2.5e-09
                   ABC2_membrane_4  17 llvlaallvpllallyfnllgktgldpaefyslsvfgftlllllplilgiiasylifrEeqndtlknLltiPvsrtk 93 
                                       l+++ ++++ +    + + ++ +++++++f + ++++ +  ++lp++ + i+   + +E+++  l   lt Pv + +
  gi|298675392|ref|YP_003727142.1|  29 LFIFTLIVFSF---SVREGMSGSNIFEQGFLDVAQIM-G--IFLPIVGIAIGFDAVVKERKSSSLTIFLTHPVFKDN 99 
                                       22222222222...22233455566666665554444.3..689999999*************************** PP

                   ABC2_membrane_4  94 lllaKlivllllsvllmlvtflitvlfallsgfvgfsvkl....vlellkkclelgllvffavlpiialvllkksyv 166
                                       ++ +K+++ l++ +++++++++++v + l++++v++  +     +l+ +  ++ l +++++ +l  i+ ++ ++s++
  gi|298675392|ref|YP_003727142.1| 100 IITGKMVAGLVTLAMVIVISVIFSVGTVLILTGVPVGLMElnriFLFGIITFVYLSVFLAMGILLSIFSSNQTNSFI 176
                                       *********************999999999999887766522112233334444455555556666777889999** PP

                   ABC2_membrane_4 167 lpliltlvyti 177
                                       +++++ +++++
  gi|298675392|ref|YP_003727142.1| 177 YGIVIWIILIL 187
                                       ****9888765 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.3
                   ABC2_membrane_4  52 fgftlllllplilgiias 69 
                                       +++++++ll++ + ++a+
  gi|298675392|ref|YP_003727142.1| 271 YWMNIVTLLVMQFLLFAA 288
                                       344444444444444433 PP

>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9  30.1   6.7e-06     0.015      36     170 ..      58     197 ..      14     215 .. 0.74
   2 ?    0.3   0.1      0.19   4.2e+02     115     137 ..     270     292 ..     239     298 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.7e-06
                   ABC2_membrane_5  36 vllifsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitlllliiavlikgn.. 110
                                       v+ i++i+ +++ i + + ++ +++ks + +++lt Pv + +i+  K + +l+  +++i+i++++++  vli     
  gi|298675392|ref|YP_003727142.1|  58 VAQIMGIFLPIVGIAIGFDAVVKERKSSSLTIFLTHPVFKDNIITGKMVAGLVTLAMVIVISVIFSVGTVLILTGvp 134
                                       334455666666666699********************************************999977666665579 PP

                   ABC2_membrane_5 111 ...vtisevllsiliglvialiflaivlPlyfkfgvekgrivliiiifgiifllvaifslskl 170
                                          + ++ ++l+ +i +v+ ++fla+ + l +  ++++  +++ i+i +i +l++ ++s+ + 
  gi|298675392|ref|YP_003727142.1| 135 vglMELNRIFLFGIITFVYLSVFLAMGILLSIFSSNQTNSFIYGIVIWIILILMFGTISSATA 197
                                       787888888888888888889999999999988888888887777777777777777665433 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.19
                   ABC2_membrane_5 115 evllsiliglvialiflaivlPl 137
                                       + ++ i+  lv+ ++++a ++ +
  gi|298675392|ref|YP_003727142.1| 270 DYWMNIVTLLVMQFLLFAASFAM 292
                                       33444444444444444444433 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9  37.8     8e-05      0.18     156     344 ..      48     290 ..       4     291 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8e-05
                   ABC2_membrane_3 156 lsnvasflvgliliilifitasfiav...siveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilllaf 229
                                       ++ +++ ++ ++ i+ if++++ ia    ++v+E++s  + + l+ +v +  ++++k+++ ++  + ++++ +++ +
  gi|298675392|ref|YP_003727142.1|  48 SNIFEQGFLDVAQIMGIFLPIVGIAIgfdAVVKERKSSSLTIFLTHPVFKDNIITGKMVAGLVTLAMVIVISVIFSV 124
                                       4445555555444444444444444422288*****************99999999987777776666666666644 PP

                   ABC2_membrane_3 230 gl.....gipfg....nlglll.llfllfglayialgyllsslfknsetaqilifivilllsgffgglfp.....le 291
                                       g+     g+p+g    n ++l+ +  ++++ +++a+g lls +++n+++ +i  +++++ ++++++g+++     + 
  gi|298675392|ref|YP_003727142.1| 125 GTvliltGVPVGlmelNRIFLFgIITFVYLSVFLAMGILLSIFSSNQTNSFIYGIVIWI-ILILMFGTISsatasI- 199
                                       54555563555544448899999************************999998888888.5555555554363331. PP

                   ABC2_membrane_3 292 dlp...............salkwifsiiPffapglgllrli........tgdplwe..................... 324
                                         +               +  +    + P+++++++ +  +        +     +                     
  gi|298675392|ref|YP_003727142.1| 200 --AtgesiidmennqeaaKLNSDMQKLTPIHHYAEAVTGFSgisvgsvnF-----Nsdqkassgvfdlshtlgkwfn 269
                                       ..344445445566655433445799999999999988887777443331.....2466777788888888888888 PP

                   ABC2_membrane_3 325 .illsliilalfavvylllal 344
                                        ++++++ l+++ ++++++++
  gi|298675392|ref|YP_003727142.1| 270 dYWMNIVTLLVMQFLLFAASF 290
                                       899999999999999998875 PP

>> PhoLip_ATPase_C  Phospholipid-translocating P-type ATPase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4  23.9   0.00037      0.82      41     200 ..      30     197 ..      20     298 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00037
                   PhoLip_ATPase_C  41 vvftlvqfwfqfyngfsgqslyeswlltlynllftslpvivlgi.fdqdvsaelllkyPelYk.lgqknklfnlktf 115
                                       ++ftl+ f f++  g+sg++++e+ +l + +++  +lp++ ++i fd  v+++ + +   + +    k+++++ k +
  gi|298675392|ref|YP_003727142.1|  30 FIFTLIVFSFSVREGMSGSNIFEQGFLDVAQIMGIFLPIVGIAIgFDAVVKERKSSSLTIFLThPVFKDNIITGKMV 106
                                       56666666677779***************************99989******9999998766645556777776666 PP

                   PhoLip_ATPase_C 116 llw..ileglyqsliifflsylvlddssfsdgktndlqlfgtlvftalvlvvnlkvaletktwt....liliililg 186
                                        +   ++  ++ s+i  + ++l+l+   +   + n ++lfg+++f++l +   + ++l + + +    +i  i+i++
  gi|298675392|ref|YP_003727142.1| 107 AGLvtLAMVIVISVIFSVGTVLILTGVPVGLMELNRIFLFGIITFVYLSVFLAMGILLSIFSSNqtnsFIYGIVIWI 183
                                       65421333344444444445555666555577888888888888888888888777776554441123566666666 PP

                   PhoLip_ATPase_C 187 sillyflflllyss 200
                                        ++l+f  +   ++
  gi|298675392|ref|YP_003727142.1| 184 ILILMFGTISSATA 197
                                       55555555433222 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6  25.4   2.9e-05     0.065      14     179 ..      19     192 ..       7     199 .. 0.71
   2 ?    0.9   0.3      0.11   2.5e+02     133     149 ..     276     292 ..     231     297 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.9e-05
                     ABC2_membrane  14 rwrdpslgllwrliqplllalvfgtvfgn..lg...nsedglnrpgllffsvlflafsaltsvapvferergvlere 85 
                                        ++++      +++  +++++vf +       g    ++++l+ + ++++++  ++ +a+   a+v er+ ++l   
  gi|298675392|ref|YP_003727142.1|  19 NLQSSRF----KVLLFIFTLIVFSFSVREgmSGsniFEQGFLDVAQIMGIFLPIVG-IAIGFDAVVKERKSSSLTIF 90 
                                       5555533....444444445555555442211121223344444444444444444.5555555999999******* PP

                     ABC2_membrane  86 lvsplyslsayvlakv...lvelpvsllqalifll.ivyflvgldls.....rfflflllllltalaasslgllisa 153
                                       l++p+     ++++k+   lv l++ +++++if++ +v++l+g+++      r+flf +++++++ +++++g+l+s+
  gi|298675392|ref|YP_003727142.1|  91 LTHPV-FKDNIITGKMvagLVTLAMVIVISVIFSVgTVLILTGVPVGlmelnRIFLFGIITFVYLSVFLAMGILLSI 166
                                       *****.889999999945555567778888888887777788****99988888*********************** PP

                     ABC2_membrane 154 lapsfedasqlaslvllpllllsGff 179
                                       +++++ +  +++ ++ ++l+l+ G +
  gi|298675392|ref|YP_003727142.1| 167 FSSNQTNSFIYGIVIWIILILMFGTI 192
                                       ***************99999998865 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.11
                     ABC2_membrane 133 flllllltalaasslgl 149
                                       + ll++ ++l+a s+++
  gi|298675392|ref|YP_003727142.1| 276 VTLLVMQFLLFAASFAM 292
                                       22223333333333333 PP

>> UPF0370  Uncharacterised protein family (UPF0370)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.3     0.018        41       9      22 ..     182     195 ..     180     203 .. 0.85
   2 ?    5.8   0.4    0.0064        14       2      16 ..     266     280 ..     265     290 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.018
                           UPF0370   9 WvillllvGillng 22 
                                       W+il+l+ G +  +
  gi|298675392|ref|YP_003727142.1| 182 WIILILMFGTISSA 195
                                       *********98765 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0064
                           UPF0370   2 eWLadYWWvillllv 16 
                                       +W +dYW  i+ llv
  gi|298675392|ref|YP_003727142.1| 266 KWFNDYWMNIVTLLV 280
                                       6******98877776 PP

>> DUF3687  D-Ala-teichoic acid biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   3.3    0.0005       1.1       6      40 ..     142     177 ..     138     178 .. 0.87
   2 ?   -0.9   0.2      0.52   1.2e+03      19      29 ..     180     190 ..     179     195 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0005
                           DUF3687   6 pavkfvlkTlfYfaIllaL.iYLYgYsginqgtFIY 40 
                                        ++ f + T++Y+ ++la  i+L  +s  ++++FIY
  gi|298675392|ref|YP_003727142.1| 142 RIFLFGIITFVYLSVFLAMgILLSIFSSNQTNSFIY 177
                                       56778899*********9878888999********* PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.52
                           DUF3687  19 aIllaLiYLYg 29 
                                       +I ++Li+++g
  gi|298675392|ref|YP_003727142.1| 180 VIWIILILMFG 190
                                       68889999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1282  (0.0715043); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 2030.42
//
Query:       gi|298675393|ref|YP_003727143.1|  [L=597]
Description: peptidase S9B dipeptidylpeptidase IV domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-11   42.7   3.2    0.00011   21.1   0.1    6.0  6  DPPIV_N          Dipeptidyl peptidase IV (DPP IV) N-terminal 
      1e-10   41.3   2.6      7e-10   38.6   2.5    2.5  1  DUF5050          Domain of unknown function (DUF5050)
    6.8e-06   25.9   3.0        1.7    8.7   0.3    5.9  5  PD40             WD40-like Beta Propeller Repeat
    4.9e-05   23.2   1.5    0.00012   21.9   0.4    2.3  2  PEGA             PEGA domain
    8.4e-05   22.5   1.9     0.0015   18.5   0.4    2.7  2  CarbopepD_reg_2  CarboxypepD_reg-like domain
    0.00069   19.8   1.0      0.018   15.3   0.1    2.5  2  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
  ------ inclusion threshold ------
      0.026   13.6   1.1      0.069   12.2   0.3    1.9  2  Coatomer_WDAD    Coatomer WD associated region
       0.38   11.4   2.2          5    7.8   0.3    2.8  2  DUF3139          Protein of unknown function (DUF3139)


Domain annotation for each model (and alignments):
>> DPPIV_N  Dipeptidyl peptidase IV (DPP IV) N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.16   3.6e+02      28      64 ..      50      86 ..      34      88 .. 0.75
   2 ?    0.9   0.0     0.069   1.5e+02       2      57 ..      74     135 ..      73     137 .. 0.83
   3 !    8.0   0.1   0.00048       1.1      16      83 ..     199     266 ..     188     331 .. 0.89
   4 ?    0.3   0.0       0.1   2.3e+02      25      73 ..     290     340 ..     275     349 .. 0.64
   5 !   21.1   0.1   5.1e-08   0.00011      43      82 ..     354     393 ..     331     438 .. 0.88
   6 ?    2.0   0.0     0.031        69     108     121 ..     446     459 ..     441     474 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.16
                                      EETTTEECEEEETTTT.BSEEEEESSTTEEEEEETTE CS
                           DPPIV_N 28 ydletneveelspgeeklqlakwSPagdklafvrnnn 64
                                      y+l++n+  e+ ++++ +++ +w P+g++l +  ++n
  gi|298675393|ref|YP_003727143.1| 50 YELAENANMEVKDSRDIVMVGRWGPDGNRLLVNSKHN 86
                                      5566666666666688999999999999998766655 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.069
                                       TTSSEEEEEECEEEESSSEETTEEEEEETTT..EECEEEETT....TT.BSEEEEESSTTEE CS
                           DPPIV_N   2 pdgkflllatnaeknwRhsytaeyyiydlet..neveelspg....eeklqlakwSPagdkl 57 
                                       pdg++ll+ ++++     ++ a y++++  t  +e+++++++    +  ++ ++w+P+g+++
  gi|298675393|ref|YP_003727143.1|  74 PDGNRLLVNSKHNPLNGVELHALYMVSPNGTgvKEIVSTPNNtkdkSLSISPPDWNPNGNRI 135
                                       68888999999999999999999999999998877777777777767788999999999987 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.00048
                                       ESSSEETTEEEEEETTTEECEEEETT.TT.BSEEEEESSTTEEEEEETTEEEEESTTTSEEEECES-ST CS
                           DPPIV_N  16 nwRhsytaeyyiydletneveelspg.eeklqlakwSPagdklafvrnnnLyvrelatgkeiqlTsdgs 83 
                                       + + +++ ++y++d+    +++l ++  +++++a wS +g+k+a ++   ++v +  +++ +q+T+ gs
  gi|298675393|ref|YP_003727143.1| 199 DKKSQMEYQLYLVDMDGSILRKLGNKsIDDVSDAFWSNDGEKIA-IQGDGIWVVNRNNSNLRQVTQKGS 266
                                       5567788999999999999999999988899************9.68889******999******9994 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.1
                                       EEEEETTTEECEEEETTTT.BSEEEEESSTTEEEEE..ETTEEEEESTTTS CS
                           DPPIV_N  25 yyiydletneveelspgeeklqlakwSPagdklafv..rnnnLyvrelatg 73 
                                        y+++++    +++s++  k  ++ +SP+ +k+ f+  + + Ly++++  g
  gi|298675393|ref|YP_003727143.1| 290 IYMVNINGTGNRKISEKCYKDDVFSLSPDEEKILFTtfHRSKLYISDSDGG 340
                                       344444444444555555567788888888888886446777777776555 PP

  == domain 5  score: 21.1 bits;  conditional E-value: 5.1e-08
                                       T.BSEEEEESSTTEEEEEETTEEEEESTTTSEEEECES-S CS
                           DPPIV_N  43 eklqlakwSPagdklafvrnnnLyvrelatgkeiqlTsdg 82 
                                        + q a+wSP+g+k++++ n +Ly  ++   ++ ++Tsd 
  gi|298675393|ref|YP_003727143.1| 354 IPDQGATWSPTGNKVSYIENGDLYTINTDGTNRSKITSDV 393
                                       467899**********************999*******96 PP

  == domain 6  score: 2.0 bits;  conditional E-value: 0.031
                                       E-TTSSEEEEEEEE CS
                           DPPIV_N 108 Wspdgsrlaylrfd 121
                                       Wspdgsrl++ ++d
  gi|298675393|ref|YP_003727143.1| 446 WSPDGSRLLFGSID 459
                                       **********9998 PP

>> DUF5050  Domain of unknown function (DUF5050)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   2.5   3.1e-13     7e-10      68     256 ..     236     435 ..     200     441 .. 0.75

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 3.1e-13
                                       ------SS-SEEEEEEETTS---EE.EE-S-EEEEEEETTEEEEEEESSSS-EEEEEEETTS---EEEESS---... CS
                           DUF5050  68 stsksllslltglyriktdGtertk.lsddkslevslvgnwiYYqhydekdglklykikidgkektklsdeaie... 140
                                       ++++++  + +g+  +++++++  +  ++ + le    ++ +YY + + ++g+++y ++i+g+ ++k+s+++++   
  gi|298675393|ref|YP_003727143.1| 236 NDGEKIAIQGDGIWVVNRNNSNLRQvTQKGSFLEWGKEDERLYYKTGSVSTGYSIYMVNINGTGNRKISEKCYKddv 312
                                       333446677899999******9999345567788**********************************887654222 PP

                                       .-SEEETTEEEEE-T.TT--EEEEETTTTEEEEEE-..S-EEE......EEEEETTEEEEEGGGTT-EEEE-SSS-- CS
                           DUF5050 141 .plsvkdgwiYytgesedhslykldtdgksiskvse..enlyl......lvvegdyiYyidlsknyaLyrvklsgse 208
                                        +ls ++++i +t+  ++++ly  d dg++++ +++  ++ ++       +  g+++ yi+   n  Ly ++++g++
  gi|298675393|ref|YP_003727143.1| 313 fSLSPDEEKILFTTF-HRSKLYISDSDGGNKRLFLNitKERHIpdqgatWSPTGNKVSYIE---NGDLYTINTDGTN 385
                                       279999*******99.888999999999999888774333333111111345677777755...9************ PP

                                       -EE-S-S-EEE.EEEETTEE.EEEE-SSS-E.EEEEETTS---EEEEES- CS
                           DUF5050 209 kevltedkvdn.yNvtgnwi.YyqkesdeekalyrikldGsekeklaegn 256
                                        +++t+d  +   N +g++i Y  ++++++  +   + +G++k+ ++ g+
  gi|298675393|ref|YP_003727143.1| 386 RSKITSDVGQYkWNPSGDYIaYITVNGSDKRPILVATPEGNKKTRISPGR 435
                                       *****9998555********455555555556*************99876 PP

>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.13     3e+02      15      27 ..      71      83 ..      70      91 .. 0.80
   2 !    7.0   0.0    0.0026       5.8      13      28 ..     231     246 ..     219     255 .. 0.88
   3 ?    1.0   0.0       0.2   4.4e+02      15      29 ..     314     328 ..     312     335 .. 0.83
   4 ?    0.8   0.0      0.22     5e+02      13      22 ..     358     367 ..     348     371 .. 0.85
   5 !    8.7   0.3   0.00074       1.7      16      25 ..     446     455 ..     443     458 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.13
                                      EE-TTSSEEEEEE CS
                              PD40 15 sfSPDGkrlaFsS 27
                                      ++ PDG+rl   S
  gi|298675393|ref|YP_003727143.1| 71 RWGPDGNRLLVNS 83
                                      699*****98666 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0026
                                       EEEE-TTSSEEEEEEE CS
                              PD40  13 aPsfSPDGkrlaFsSd 28 
                                       + ++S+DG ++a+  d
  gi|298675393|ref|YP_003727143.1| 231 DAFWSNDGEKIAIQGD 246
                                       579*********9766 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.2
                                       EE-TTSSEEEEEEEC CS
                              PD40  15 sfSPDGkrlaFsSdR 29 
                                       s+SPD  ++ F+ + 
  gi|298675393|ref|YP_003727143.1| 314 SLSPDEEKILFTTFH 328
                                       89*********9875 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.22
                                       EEEE-TTSSE CS
                              PD40  13 aPsfSPDGkr 22 
                                       + ++SP G++
  gi|298675393|ref|YP_003727143.1| 358 GATWSPTGNK 367
                                       689****987 PP

  == domain 5  score: 8.7 bits;  conditional E-value: 0.00074
                                       E-TTSSEEEE CS
                              PD40  16 fSPDGkrlaF 25 
                                       +SPDG+rl F
  gi|298675393|ref|YP_003727143.1| 446 WSPDGSRLLF 455
                                       ********99 PP

>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.5   3.4e+03      15      45 ..     408     436 ..     399     440 .. 0.68
   2 !   21.9   0.4   5.3e-08   0.00012      12      60 ..     505     558 ..     491     561 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.5
                              PEGA  15 VyidGkylGkTPvtlsleaGnyslrvekeGY 45 
                                       ++++G++  k P+ ++ ++Gn + r++   +
  gi|298675393|ref|YP_003727143.1| 408 ITVNGSD--KRPILVATPEGNKKTRISPGRH 436
                                       6666644..6788888888888888776555 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 5.3e-08
                              PEGA  12 GatVyidGkylGkTPvt....ls.leaGnyslrvekeGYedlektvtvtagetv 60 
                                       + +V++dG+++G T+ t    +    +G+++l   keGY++ +k v ++++  +
  gi|298675393|ref|YP_003727143.1| 505 NVSVSLDGNNIGTTNATghltYKiNRTGKHQLNAAKEGYQPTSKYVLLQSDNST 558
                                       469*********999752221565679*******************99987655 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.078   1.8e+02      18      67 ..     378     425 ..     372     436 .. 0.79
   2 !   18.5   0.4   6.6e-07    0.0015      11      71 ..     500     559 ..     493     572 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.078
                   CarbopepD_reg_2  18 tVyvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvske 67 
                                       t+   gt++  +T + G+++ +  p+g+y   +++ G +++ + v + ++
  gi|298675393|ref|YP_003727143.1| 378 TINTDGTNRSKITSDVGQYKWN--PSGDYIAYITVNGSDKRPILVATPEG 425
                                       678899**************96..99999888888887776666655544 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 6.6e-07
                   CarbopepD_reg_2  11 keplpgatVyvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvskektld 71 
                                        +p+  ++V++ g++ gt T++ G+ + k    gk++L++   Gy++ +k v ++++++++
  gi|298675393|ref|YP_003727143.1| 500 SKPVGNVSVSLDGNNIGT-TNATGHLTYKINRTGKHQLNAAKEGYQPTSKYVLLQSDNSTQ 559
                                       479999**********97.9****999998999*********************9998765 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1     0.082   1.8e+02      25      61 ..     381     415 ..     369     431 .. 0.81
   2 !   15.3   0.1   8.1e-06     0.018      11      74 ..     500     557 ..     493     563 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.082
                   CarboxypepD_reg  25 dtgtvastttdadGafrlrglppgtysvtvsapGyat 61 
                                        +gt++s  t + G+++++  p g+y   ++ +G + 
  gi|298675393|ref|YP_003727143.1| 381 TDGTNRSKITSDVGQYKWN--PSGDYIAYITVNGSDK 415
                                       57999************98..8899988888777765 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 8.1e-06
                   CarboxypepD_reg  11 gapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagqt 74 
                                        +p+ +++V++       +   tt+a+G+ + +   +g++++ + ++Gy+++++  v l+ +++
  gi|298675393|ref|YP_003727143.1| 500 SKPVGNVSVSLD-----GNNIGTTNATGHLTYKINRTGKHQLNAAKEGYQPTSK-YVLLQSDNS 557
                                       579*********.....5667799*****99998899**************995.577776655 PP

>> Coatomer_WDAD  Coatomer WD associated region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3   3.1e-05     0.069     143     266 ..     225     349 ..     203     352 .. 0.87
   2 ?   -1.3   0.0      0.39   8.7e+02      41      83 ..     362     405 ..     354     414 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.1e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..................XXXXXXX.XXXXXXXXXXXXXXXXXX CS
                     Coatomer_WDAD 143 dvkkvknVvwsddgelvalvskdtvyilsynleavee.....edeeegvedafevlhelsesiksgaWvgdvfiYtt 214
                                       ++++v++ +ws+dge +a+   d + ++++n  +  +     +  e g ed      + + s+ +g  +  v i  t
  gi|298675393|ref|YP_003727143.1| 225 SIDDVSDAFWSNDGEKIAIQ-GDGIWVVNRNNSNLRQvtqkgSFLEWGKEDERLYY-K-TGSVSTGYSIYMVNINGT 298
                                       47899*************98.89999999999988888877766777888765444.4.6***************** PP

                                       XX.XXXX.XXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXX CS
                     Coatomer_WDAD 215 snnrlky.lvngevgiikhldktlyilgykgkenklylldkdgnvvsleidls 266
                                        n +++  + +++v  ++  ++++  +  +   +kly+ d dg  ++l+++++
  gi|298675393|ref|YP_003727143.1| 299 GNRKISEkCYKDDVFSLSPDEEKILFTTFHR--SKLYISDSDGGNKRLFLNIT 349
                                       ******99***********999999999999..*********99999999986 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.39
                                       XXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                     Coatomer_WDAD  41 npngrfvlV.cgdgeyiiytalalrnkaygkgldfvwvssnrfa 83 
                                       +p+g+ v    + + y+i t   +r+k +    +  w++s+++ 
  gi|298675393|ref|YP_003727143.1| 362 SPTGNKVSYiENGDLYTINTDGTNRSKITSDVGQYKWNPSGDYI 405
                                       66666665424445577777777777777777777777777754 PP

>> DUF3139  Protein of unknown function (DUF3139)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.3    0.0022         5       1      42 [.       1      38 [.       1      61 [. 0.75
   2 ?    2.0   0.1      0.15   3.5e+02      33      72 ..     370     409 ..     361     412 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0022
                           DUF3139  1 mkkiiiililliillvivkvflglvgskpikk.ylankkldky 42
                                      mkk  i+++++i+ll++     +++ s ++++   +  k++k 
  gi|298675393|ref|YP_003727143.1|  1 MKKTMILFLIIISLLAS-----NCNASANLQEnTNGSIKVEKV 38
                                      8****************.....999999997622333444444 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.15
                           DUF3139  33 ylankkldkylqekgykeddIksikpkydskkg.syyakVv 72 
                                       y+ n +l+ +++++g+++++I s   +y+++ +  y a+++
  gi|298675393|ref|YP_003727143.1| 370 YIENGDLY-TINTDGTNRSKITSDVGQYKWNPSgDYIAYIT 409
                                       55555555.45799***************999867777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (597 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 4075.22
//
Query:       gi|298675394|ref|YP_003727144.1|  [L=231]
Description: hypothetical protein Metev_1496 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-22   79.0   1.1    2.4e-10   39.8   0.2    2.3  2  HTH_24         Winged helix-turn-helix DNA-binding
    2.3e-07   30.6   0.1      0.002   18.0   0.0    2.4  2  MarR           MarR family
    2.3e-07   30.5   0.0    0.00035   20.4   0.0    2.5  2  HTH_5          Bacterial regulatory protein, arsR family
    1.6e-06   28.1   0.0     0.0002   21.3   0.0    2.3  2  HTH_20         Helix-turn-helix domain
    1.6e-06   27.7   0.0      0.048   13.4   0.0    2.3  2  HTH_41         Helix-turn-helix domain
    5.8e-05   23.0   0.2      0.013   15.4   0.1    2.5  2  HTH_11         HTH domain
     0.0011   19.5   0.7       0.49   11.0   0.0    2.3  2  Mga            Mga helix-turn-helix domain
     0.0018   17.4   0.7     0.0023   17.0   0.7    1.1  1  TnsD           Tn7-like transposition protein D
     0.0032   17.2   0.0        0.3   10.9   0.0    2.3  2  HTH_IclR       IclR helix-turn-helix domain
     0.0038   17.0   0.0       0.18   11.6   0.0    2.3  2  HTH_AsnC-type  AsnC-type helix-turn-helix domain
     0.0052   16.9   0.2       0.81    9.9   0.0    2.3  2  HTH_34         Winged helix DNA-binding domain
     0.0053   16.3   1.7       0.19   11.3   0.1    2.6  2  GerE           Bacterial regulatory proteins, luxR family
     0.0065   16.3   0.0       0.25   11.3   0.1    2.3  2  TrmB           Sugar-specific transcriptional regulator TrmB
     0.0097   16.3   0.0      0.025   14.9   0.0    1.7  1  FaeA           FaeA-like protein
  ------ inclusion threshold ------
      0.011   15.6   0.0       0.19   11.6   0.0    2.2  2  MarR_2         MarR family
      0.013   16.0   2.6       0.42   11.1   0.5    2.5  2  HTH_40         Helix-turn-helix domain
      0.016   15.4   0.2       0.69   10.2   0.1    2.3  2  HTH_Tnp_Tc3_2  Transposase
      0.017   15.1   0.3       0.46   10.5   0.0    2.3  2  HTH_6          Helix-turn-helix domain, rpiR family
      0.093   12.5   0.2       0.92    9.3   0.0    2.2  2  HTH_DeoR       DeoR-like helix-turn-helix domain
       0.11   12.2   0.0       0.22   11.2   0.0    1.5  1  Sigma70_r4_2   Sigma-70, region 4
       0.11   12.1   0.0        1.6    8.3   0.0    2.1  2  RP-C           Replication protein C N-terminal domain
       0.16   11.8   0.0       0.29   10.9   0.0    1.4  1  HTH_30         PucR C-terminal helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   0.2     3e-13   2.4e-10       2      48 .]      81     127 ..      80     127 .. 0.96
   2 !   38.1   0.0     1e-12   8.2e-10       2      48 .]     157     203 ..     156     203 .. 0.97

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 3e-13
                            HTH_24   2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                       ++++r+I++++  np++s+++++  l +S++tv+++++ Le ++ I+
  gi|298675394|ref|YP_003727144.1|  81 NKNRRRIYNYIVNNPSCSIADISSNLAISRGTVRYHVRLLETMEKIR 127
                                       899**************************************999886 PP

  == domain 2  score: 38.1 bits;  conditional E-value: 1e-12
                            HTH_24   2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                       +et +++L+ ++++p+i+++eL+ +  l ++t+n+++k++ ++ +I+
  gi|298675394|ref|YP_003727144.1| 157 NETSKQLLKSIKEQPGITNQELSHKHSLNKGTINWHIKKFHNDDIIT 203
                                       89*******************************************96 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00061       0.5      14      47 ..      93     126 ..      90     133 .. 0.88
   2 !   18.0   0.0   2.5e-06     0.002       4      50 ..     159     205 ..     156     209 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00061
                                       HSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              MarR  14 eqgplsvseLakklgvskstvtrvldrLekkGli 47 
                                       +++++s++++ + l +s++tv   ++ Le  + i
  gi|298675394|ref|YP_003727144.1|  93 NNPSCSIADISSNLAISRGTVRYHVRLLETMEKI 126
                                       789**********************999988766 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 2.5e-06
                                       HHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR   4 tqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50 
                                       t   +L +++eq++++++eL  k +++k+t+   +++   ++ i+ +
  gi|298675394|ref|YP_003727144.1| 159 TSKQLLKSIKEQPGITNQELSHKHSLNKGTINWHIKKFHNDDIITFE 205
                                       56679********************************9998888876 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   4.3e-07   0.00035       2      42 ..      82     123 ..      81     127 .. 0.93
   2 !    7.7   0.0    0.0038       3.1       5      45 ..     161     202 ..     157     203 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 4.3e-07
                                       HHHHHHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHHHHT CS
                             HTH_5   2 ptRlkILklLaege.lcvcelaeelglsqstvShHLkkLrea 42 
                                       ++R++I ++  +++ +++ +++  l +s++tv++H + L+ +
  gi|298675394|ref|YP_003727144.1|  82 KNRRRIYNYIVNNPsCSIADISSNLAISRGTVRYHVRLLETM 123
                                       789*********999**********************99865 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0038
                                       HHHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5   5 lkILklLaege.lcvcelaeelglsqstvShHLkkLreaGLV 45 
                                        ++Lk+  e++  +  el+ +  l+++t+  H kk ++ +++
  gi|298675394|ref|YP_003727144.1| 161 KQLLKSIKEQPgITNQELSHKHSLNKGTINWHIKKFHNDDII 202
                                       5899999****99**********************9998887 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   2.5e-07    0.0002       5      49 ..      77     121 ..      73     131 .. 0.92
   2 ?    4.6   0.0     0.042        34      10      55 ..     158     203 ..     150     209 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.5e-07
                                       HHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHH CS
                            HTH_20   5 eALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLe 49 
                                       ++++++ Rrri+ ++  +   + +++   l +s+ t++yH+r Le
  gi|298675394|ref|YP_003727144.1|  77 DLFSNKNRRRIYNYIVNNPSCSIADISSNLAISRGTVRYHVRLLE 121
                                       57899***************************************8 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.042
                                       HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20  10 PvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55 
                                       ++   +l+ +++  g t  el +  +l k t++ H+++    ++++
  gi|298675394|ref|YP_003727144.1| 158 ETSKQLLKSIKEQPGITNQELSHKHSLNKGTINWHIKKFHNDDIIT 203
                                       566666777777788889999999**************98888887 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00016      0.13       8      39 ..      98     129 ..      97     131 .. 0.92
   2 !   13.4   0.0   5.9e-05     0.048      10      43 ..     176     209 ..     173     211 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00016
                            HTH_41   8 tIeelakeleLSvGlvQkALklLeddkaisle 39 
                                       +I +++++l +S+G+v   + lLe +  i l+
  gi|298675394|ref|YP_003727144.1|  98 SIADISSNLAISRGTVRYHVRLLETMEKIRLI 129
                                       6999**********************999886 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 5.9e-05
                            HTH_41  10 eelakeleLSvGlvQkALklLeddkaislerrGr 43 
                                       +el+++ +L  G++   +k+  +d +i+ e+ G+
  gi|298675394|ref|YP_003727144.1| 176 QELSHKHSLNKGTINWHIKKFHNDDIITFESSGK 209
                                       69****************************9996 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.7e-05     0.013       4      43 ..      86     124 ..      83     134 .. 0.80
   2 ?    5.3   0.0     0.023        19       3      38 ..     161     195 ..     159     210 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.7e-05
                            HTH_11   4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43 
                                        i+  + ++ +  s+++++  L +Sr tvr +++ Le++ 
  gi|298675394|ref|YP_003727144.1|  86 RIYNYIVNNPS-CSIADISSNLAISRGTVRYHVRLLETME 124
                                       56666655555.9***********************9986 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.023
                            HTH_11   3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIka 38 
                                       +q+l+ + ++++ i+ +eL+ + ++ + t+  +Ik+
  gi|298675394|ref|YP_003727144.1| 161 KQLLKSI-KEQPGITNQELSHKHSLNKGTINWHIKK 195
                                       6888888.44545*****************999997 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00061      0.49       7      52 ..      73     118 ..      71     140 .. 0.89
   2 ?    6.7   0.2     0.013        11      13      55 ..     155     197 ..     140     206 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00061
                                       HHHHHHHHHSHHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHH CS
                               Mga   7 ellqellkeslkyqllkflfeeeevsieelaqelyiSestlkrkik 52 
                                        ++++l+ + +  ++  +++++ ++si++++ +l iS+ t+  +++
  gi|298675394|ref|YP_003727144.1|  73 SIIKDLFSNKNRRRIYNYIVNNPSCSIADISSNLAISRGTVRYHVR 118
                                       5788999999999***************************987766 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.013
                                       HHHSHHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHH CS
                               Mga  13 lkeslkyqllkflfeeeevsieelaqelyiSestlkrkikeln 55 
                                       lk+ ++ qllk + e+  ++ +el+ ++ + + t++ +ik++ 
  gi|298675394|ref|YP_003727144.1| 155 LKNETSKQLLKSIKEQPGITNQELSHKHSLNKGTINWHIKKFH 197
                                       4558889********************************9974 PP

>> TnsD  Tn7-like transposition protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.7   2.9e-06    0.0023     194     280 ..      91     195 ..      78     198 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.9e-06
                              TnsD 194 LveeeglslkeiAkelgvdiktVlryakklgllkekkkqkkesrelsskd...............rekkrkewleli 255
                                        v++ + s+++i++ l+++ +tV+ + + l+  ++ ++ k ++ +l+ ++               +++  k++l++i
  gi|298675394|ref|YP_003727144.1|  91 IVNNPSCSIADISSNLAISRGTVRYHVRLLETMEKIRLIKSDKYTLAIQNsdtfndiektiiphlKNETSKQLLKSI 167
                                       4555899***********************9999999999888887777789************************* PP

                              TnsD 256 ksypdlgktel...rklnpalyawLyrn 280
                                       k+ p ++++el    +ln+ + +w++++
  gi|298675394|ref|YP_003727144.1| 168 KEQPGITNQELshkHSLNKGTINWHIKK 195
                                       ****999999933346789999999876 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00036       0.3      18      51 ..      96     132 ..      77     133 .. 0.85
   2 ?    4.0   0.0     0.053        43       7      34 ..     162     188 ..     161     193 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00036
                                       S-BHHHHHHHHTS-HHHHH...HHHHHHHHTTSEE.. CS
                          HTH_IclR  18 eltlselArrtglpkStvh...RlLqtLvelGyveqd 51 
                                         ++++++ ++++++ tv+   RlL t+++ ++++ d
  gi|298675394|ref|YP_003727144.1|  96 SCSIADISSNLAISRGTVRyhvRLLETMEKIRLIKSD 132
                                       3799**************9888999999999999876 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.053
                                       HHHCT-CTTBSS-BHHHHHHHHTS-HHH CS
                          HTH_IclR   7 aiLdalaeapqeltlselArrtglpkSt 34 
                                       ++L+ + e+p+  t++el+++  l+k t
  gi|298675394|ref|YP_003727144.1| 162 QLLKSIKEQPG-ITNQELSHKHSLNKGT 188
                                       78999999999.8***********9998 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00023      0.18       6      41 ..      85     120 ..      85     121 .. 0.91
   2 ?    3.2   0.0     0.099        81       3      29 ..     158     184 ..     157     194 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                     HTH_AsnC-type   6 rkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41 
                                       r+I + +  +++ s a+++  + +S+ tv+  vr L
  gi|298675394|ref|YP_003727144.1|  85 RRIYNYIVNNPSCSIADISSNLAISRGTVRYHVRLL 120
                                       8999999**********************9877766 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.099
                     HTH_AsnC-type   3 eiDrkILeaLqedaRisyaeLAervGl 29 
                                       e+ +++L+ + e++ i+++eL+ +  l
  gi|298675394|ref|YP_003727144.1| 158 ETSKQLLKSIKEQPGITNQELSHKHSL 184
                                       67799****************987655 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0     0.001      0.81       5      49 ..      87     131 ..      84     137 .. 0.89
   2 ?    4.8   0.0     0.038        31      12      51 ..     170     209 ..     162     214 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.001
                            HTH_34   5 vlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdke 49 
                                       +  y + + + + +++++ l ++ g    h++ Le+ + i   k+
  gi|298675394|ref|YP_003727144.1|  87 IYNYIVNNPSCSIADISSNLAISRGTVRYHVRLLETMEKIRLIKS 131
                                       56788899999**************************99988776 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.038
                            HTH_34  12 vdeadfvelkealeatdgnLsvhlkkLekagYievdkefk 51 
                                       +  ++ +el+ + ++++g +  h+kk+ + + i+ + + k
  gi|298675394|ref|YP_003727144.1| 170 QPGITNQELSHKHSLNKGTINWHIKKFHNDDIITFESSGK 209
                                       56778899*******************9999998876655 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.1   0.00023      0.19      21      44 ..     100     125 ..      97     130 .. 0.80
   2 ?    3.7   0.2     0.056        45      17      39 ..     172     194 ..     161     197 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00023
                                       HHHHHHHTS-HHHHHHHHH..HHHHH CS
                              GerE  21 keIAeelniSekTVkvhks..nimkK 44 
                                        +I+++l iS  TV++h++  + m+K
  gi|298675394|ref|YP_003727144.1| 100 ADISSNLAISRGTVRYHVRllETMEK 125
                                       68***************983344555 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.056
                                       TS-HHHHHHHHTS-HHHHHHHHH CS
                              GerE  17 GksnkeIAeelniSekTVkvhks 39 
                                       G +n+e + + ++ + T++ h++
  gi|298675394|ref|YP_003727144.1| 172 GITNQELSHKHSLNKGTINWHIK 194
                                       889******************98 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.1    0.0003      0.25      12      60 ..      86     134 ..      81     139 .. 0.90
   2 ?    2.5   0.0      0.16   1.3e+02      20      63 ..     170     214 ..     158     218 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0003
                                       CHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT CS
                              TrmB  12 kvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpk 60 
                                       ++Y +++++ + ++ +i+++l ++r +v   +r Le +  ++ +k+ ++
  gi|298675394|ref|YP_003727144.1|  86 RIYNYIVNNPSCSIADISSNLAISRGTVRYHVRLLETMEKIRLIKSDKY 134
                                       78**********************************9999988887654 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.16
                                       HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.STTTEEE CS
                              TrmB  20 lgpatadeiaeelgvprskvYevLrsLedkGlVerek.grpklYr 63 
                                       +   t +e++++  + + +++  +++  + ++++ e  g++k+Y 
  gi|298675394|ref|YP_003727144.1| 170 QPGITNQELSHKHSLNKGTINWHIKKFHNDDIITFESsGKYKKYF 214
                                       5667899**************************999945577885 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   3.1e-05     0.025       4      46 ..      86     127 ..      71     133 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.1e-05
                                       HHHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEE CS
                              FaeA   4 eIleylnsikapckTreiAdalglsaYQaRyYLeqLekegkik 46 
                                        I +y+ + + +c  ++i   l++s   +Ry    Le   ki+
  gi|298675394|ref|YP_003727144.1|  86 RIYNYIVN-NPSCSIADISSNLAISRGTVRYHVRLLETMEKIR 127
                                       58899999.99***************************99997 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00023      0.19      12      48 ..      89     123 ..      83     133 .. 0.84
   2 ?    1.5   0.0      0.34   2.7e+02       9      55 ..     162     206 ..     159     209 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                                       HHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHT CS
                            MarR_2  12 aaLgrrpgrdltvgelarrlglsksavsrilkrLvaa 48 
                                       +++ ++p   ++++++   l +s+++v ++++ L+  
  gi|298675394|ref|YP_003727144.1|  89 NYIVNNPS--CSIADISSNLAISRGTVRYHVRLLETM 123
                                       57889998..9**********************9976 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.34
                                       HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2   9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55 
                                       ++L  +   pg  +t +el  +  l k++++ ++k++     ++ ++
  gi|298675394|ref|YP_003727144.1| 162 QLLKSIKEQPG--ITNQELSHKHSLNKGTINWHIKKFHNDDIITFES 206
                                       68889999999..9**********************99998888775 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.5   0.00052      0.42      12      75 ..      96     170 ..      90     172 .. 0.66
   2 ?    4.8   0.1     0.048        39      12      39 ..     172     199 ..     170     223 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00052
                            HTH_40  12 glsieeIAkerglkesTIegH..Laelieegeeidlerl...v.seeeekeIeeaiekvgsek.....lkpikea 75 
                                       ++si++I+ +  ++++T+  H  L+e +e+ + i+ +++   + ++++++ Ie++i  + +++     lk ike+
  gi|298675394|ref|YP_003727144.1|  96 SCSIADISSNLAISRGTVRYHvrLLETMEKIRLIKSDKYtlaIqNSDTFNDIEKTIIPHLKNEtskqlLKSIKEQ 170
                                       579******************444555555444444555434344577777776665533222355689999997 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.048
                            HTH_40  12 glsieeIAkerglkesTIegHLaeliee 39 
                                       g + +e +++ +l+++TI  H+ ++ ++
  gi|298675394|ref|YP_003727144.1| 172 GITNQELSHKHSLNKGTINWHIKKFHND 199
                                       77889999**************998776 PP

>> HTH_Tnp_Tc3_2  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00085      0.69       1      36 [.      84     114 ..      84     122 .. 0.91
   2 ?    3.1   0.0      0.14   1.2e+02       3      23 ..     162     182 ..     160     195 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00085
                     HTH_Tnp_Tc3_2   1 krrIvrlvrkdPritlreLanelkeeGksvsreTir 36 
                                       +rrI+ ++ ++P+ +++++++ l      +sr T+r
  gi|298675394|ref|YP_003727144.1|  84 RRRIYNYIVNNPSCSIADISSNL-----AISRGTVR 114
                                       69*******************99.....99999998 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.14
                     HTH_Tnp_Tc3_2   3 rIvrlvrkdPritlreLanel 23 
                                       ++++ ++++P it +eL+ + 
  gi|298675394|ref|YP_003727144.1| 162 QLLKSIKEQPGITNQELSHKH 182
                                       79999************9876 PP

>> HTH_6  Helix-turn-helix domain, rpiR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00056      0.46      15      52 ..      81     114 ..      67     123 .. 0.87
   2 ?    2.2   0.2      0.22   1.8e+02      10      39 ..     140     169 ..     134     171 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00056
                                       -HHHHHHHHHHHH-S---TT--HHHHHHHTT--HHHHH CS
                             HTH_6  15 tksekkiaeyilaspdkaielsikalAkaaavSeativ 52 
                                       +k+ ++i +yi ++p+    +si++++ ++a+S+ t+ 
  gi|298675394|ref|YP_003727144.1|  81 NKNRRRIYNYIVNNPS----CSIADISSNLAISRGTVR 114
                                       7999*********995....9*************9984 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.22
                                       H-----HHHHHHHHHHHH-S---TT--HHH CS
                             HTH_6  10 kkekltksekkiaeyilaspdkaielsika 39 
                                       + + +++ ek+i+  ++++ +k   +sik+
  gi|298675394|ref|YP_003727144.1| 140 NSDTFNDIEKTIIPHLKNETSKQLLKSIKE 169
                                       46789999************9999999985 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0011      0.92       4      38 ..      86     120 ..      84     129 .. 0.83
   2 ?    0.8   0.0      0.52   4.2e+02       3      43 ..     161     201 ..     160     203 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0011
                          HTH_DeoR   4 qilellkqqgklsveelvellgvSeaTiRRDLneL 38 
                                        i  ++ +  ++s+ +++  l +S  T+R   + L
  gi|298675394|ref|YP_003727144.1|  86 RIYNYIVNNPSCSIADISSNLAISRGTVRYHVRLL 120
                                       588999999********************655555 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.52
                          HTH_DeoR   3 eqilellkqqgklsveelvellgvSeaTiRRDLneLeeqgl 43 
                                       +q+l+ +k+q  ++ +el+      + Ti   +++ +++++
  gi|298675394|ref|YP_003727144.1| 161 KQLLKSIKEQPGITNQELSHKHSLNKGTINWHIKKFHNDDI 201
                                       7999******9999999999888888888666666666655 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00027      0.22      27      48 ..      97     118 ..      96     119 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00027
                                       --HHHHHHHHT--HHHHHHHHH CS
                      Sigma70_r4_2  27 lsykEIAellgisegtVksrls 48 
                                       +s+++I++ l is gtV+++++
  gi|298675394|ref|YP_003727144.1|  97 CSIADISSNLAISRGTVRYHVR 118
                                       79*****************985 PP

>> RP-C  Replication protein C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.23   1.9e+02      75      95 ..     100     120 ..      73     130 .. 0.88
   2 ?    8.3   0.0     0.002       1.6      73     112 ..     174     213 ..     156     217 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.23
                              RP-C  75 aqLsralglsestlrrhlaaL 95 
                                       a++s++l +s+ t+r+h++ L
  gi|298675394|ref|YP_003727144.1| 100 ADISSNLAISRGTVRYHVRLL 120
                                       67889999**********988 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.002
                              RP-C  73 sNaqLsralglsestlrrhlaaLveaGliirrDspngkRy 112
                                        N++Ls +++l + t+  h+++  +  +i+   s  +k y
  gi|298675394|ref|YP_003727144.1| 174 TNQELSHKHSLNKGTINWHIKKFHNDDIITFESSGKYKKY 213
                                       69************************************99 PP

>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00036      0.29      12      39 ..      96     123 ..      88     137 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00036
                                       TT-HHHHHHHHTS-HHHHHHHHHHHHHH CS
                            HTH_30  12 ggnisatAkaLhvHrnTlryRLrrieel 39 
                                       +++i++ +  L ++r T+ry +r +e +
  gi|298675394|ref|YP_003727144.1|  96 SCSIADISSNLAISRGTVRYHVRLLETM 123
                                       49*******************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       896  (0.0499749); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1781.22
//
Query:       gi|298675395|ref|YP_003727145.1|  [L=164]
Description: N-acetyltransferase GCN5 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-16   60.2   0.0    2.8e-16   59.8   0.0    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
      7e-10   39.2   0.0    1.1e-09   38.6   0.0    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    6.7e-09   35.8   0.0    9.7e-09   35.2   0.0    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
      7e-07   29.1   0.0    2.1e-06   27.6   0.0    1.7  2  FR47             FR47-like protein
    3.9e-06   27.1   0.2    4.9e-06   26.8   0.2    1.1  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    0.00054   20.0   0.1     0.0093   16.0   0.0    2.1  2  Acetyltransf_9   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.025   14.7   0.0      0.039   14.1   0.0    1.3  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   0.0   1.1e-19   2.8e-16       2     117 .]      19     141 ..      18     141 .. 0.84

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 1.1e-19
                                       HHHHHHHHHHTHHHHHHHHHHH..HHHH.HHSTTCEEEEEEETTE.....EEEEEEEEEEETTSTTEEEEEEEEESG CS
                    Acetyltransf_1   2 rdlvellvesffppnedaseee..fees.fsleaegllvaeedge.....liGfisllkipdekggvayieslaVsp 70 
                                       ++++el +++ffpp  +++  +  + +    ++++ +l+ae + e     ++G i++ k++  +++ ayi++laV+p
  gi|298675395|ref|YP_003727145.1|  19 HRFMELVNDEFFPPLDKREKSIdkRIQQtILNTNSAYLIAESETEnnfcfIAGLIGFEKYWK-SEDDAYINFLAVHP 94 
                                       56789999999988888888887633332445555777777775578********9999999.99************ PP

                                       GGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  71 eyrgkGlGsaLlealeerareegikkivlaveedndaairlYeklGF 117
                                       eyrg+Gl s+L ++le ++++ gi +i + + ++n++  ++Yek+ +
  gi|298675395|ref|YP_003727145.1|  95 EYRGMGLSSKLEKQLELKLKQDGILYINVCTWSTNKPVLNFYEKMNY 141
                                       *****************9******8885569999**********976 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.0   4.2e-13   1.1e-09       3      75 ..      65     142 ..      51     143 .. 0.68

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 4.2e-13
                                       EEEEEEEETTEEEEEEEEEEES..TCTEEEEE-GGGTTSSHHHHHHHH...TT..SEEEEE.EEEE..THHHHHHHH CS
                    Acetyltransf_7   3 gevfVaeddgkivGfialslld..aeitrlaVdpeyrgkGiGraLlea...ae..kgiile.qlel..naekaikfY 69 
                                       + +f+a    + +Gf  ++ ++  a+i++laV+peyrg G+ ++L +    +    gi  + ++ +  ++++ ++fY
  gi|298675395|ref|YP_003727145.1|  65 NFCFIA----GLIGFEKYWKSEddAYINFLAVHPEYRGMGLSSKLEKQlelKLkqDGIL-YiNVCTwsTNKPVLNFY 136
                                       345555....6678777777779999999****************66323311446643.333333433348899** PP

                                       HHTTEE CS
                    Acetyltransf_7  70 eklGFe 75 
                                       ek+ ++
  gi|298675395|ref|YP_003727145.1| 137 EKMNYR 142
                                       ***997 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.0   3.8e-12   9.7e-09      21     115 ..      43     150 ..      33     162 .. 0.67

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 3.8e-12
                   Acetyltransf_10  21 alrerieegealllvaeeggk.....ivGvielrdgs......hisllfVdpeyrgqGigkaLleaveeeaekdgik 86 
                                       ++++ i + +  +l+ae +++     i+G i+ ++ +      +i  l+V+peyrg G++++L +++e ++++dgi 
  gi|298675395|ref|YP_003727145.1|  43 RIQQTILNTNSAYLIAESETEnnfcfIAGLIGFEKYWkseddaYINFLAVHPEYRGMGLSSKLEKQLELKLKQDGIL 119
                                       4555554444445555444322222233666443333344478****************************999999 PP

                   Acetyltransf_10  87 l.eltvnasp.yavpfYeklGFkavgeeqee 115
                                          +   +++    +fYek+ ++  +  +++
  gi|298675395|ref|YP_003727145.1| 120 YiNVCTWSTNkPVLNFYEKMNYRINSVLKND 150
                                       674444455559999*******977555444 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.61   1.6e+03      75      83 ..      73      81 ..      42      83 .. 0.74
   2 !   27.6   0.0   8.1e-10   2.1e-06      20      79 ..      83     143 ..      78     149 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.61
                                      HT-EEEEEE CS
                              FR47 75 lGfekieet 83
                                      +Gfek++++
  gi|298675395|ref|YP_003727145.1| 73 IGFEKYWKS 81
                                      899999876 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 8.1e-10
                                       TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EE.EEEETT-HHHHHHHHHHT-EE CS
                              FR47  20 dggelgalqvlpehrrrGlgsrlvkalakeiaergktvl.lvvvasNtpsirlyeklGfek 79 
                                       d+ ++  l v+pe r++Gl s+l k+l  ++ + g+  + + +  +N+p  ++yek++++ 
  gi|298675395|ref|YP_003727145.1|  83 DDAYINFLAVHPEYRGMGLSSKLEKQLELKLKQDGILYInVCTWSTNKPVLNFYEKMNYRI 143
                                       6789999****************************97542778899*************96 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.2   1.9e-09   4.9e-06       1     139 [.       7     146 ..       7     155 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.9e-09
                    Acetyltransf_4   1 iraateeDakeilaiyaeyvvntaitfeyevssveefekflealdsekeyvflvae...sdrivGyaylgqfkkr.a 73 
                                       ir a ++D+ +i + ++   vn ++ +    +  + ++k++++++   +  +l+ae   + +   +a l +f+k   
  gi|298675395|ref|YP_003727145.1|   7 IREAYQDDFHRIHRFMEL--VNDEFFPPL-DKREKSIDKRIQQTILNTNSAYLIAEsetENNFCFIAGLIGFEKYwK 80 
                                       89999***********97..777766553.45667789999999777788899999444444555666666666444 PP

                    Acetyltransf_4  74 kdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFelvgi 139
                                        +  a + ++ ++   + +gl ++l + le  lk+ +i++++ ++ s+n++  +f++++ +++   
  gi|298675395|ref|YP_003727145.1|  81 SEDDAYINFLAVHPEYRGMGLSSKLEKQLELKLKQDGILYINVCTWSTNKPVLNFYEKMNYRINSV 146
                                       444455555555889999*****************************************9998665 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1     0.084   2.2e+02       2      37 ..       7      42 ..       6      68 .. 0.66
   2 !   16.0   0.0   3.6e-06    0.0093      74     126 ..      85     142 ..      80     143 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.084
                                      EEEE-GGGHHHHHHHHHHHTT----H..HHHHHHHH CS
                    Acetyltransf_9  2 irelteedldevlellkyaFqdeespleeireyfrk 37
                                      ire+ ++d++ ++++ + +  +  +pl++++++ +k
  gi|298675395|ref|YP_003727145.1|  7 IREAYQDDFHRIHRFMELVNDEFFPPLDKREKSIDK 42
                                      899999999999999888877777776323333333 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 3.6e-06
                                       EEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--SSH.....HHHHTTT-E CS
                    Acetyltransf_9  74 agvtgVavapehrgrgvlskLlaraleemreegqplsllfPssi.....piYrrfGye 126
                                       a++   av+pe+rg g+ skL +++  +++++g+  +     s      ++Y+++ y+
  gi|298675395|ref|YP_003727145.1|  85 AYINFLAVHPEYRGMGLSSKLEKQLELKLKQDGILYINVCTWSTnkpvlNFYEKMNYR 142
                                       688899*******************999999998765444422222345777777775 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.5e-05     0.039      12      66 ..      73     126 ..      64     136 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.5e-05
                   Acetyltransf_CG  12 vafleYevrkegvldfthTeVpeelrGkGiAkkLvkaalddareeglkvvptCsy 66 
                                       ++f +Y  + e+   ++   V++e+rG G+ +kL k+   + ++ g   + +C+ 
  gi|298675395|ref|YP_003727145.1|  73 IGFEKYW-KSEDDAYINFLAVHPEYRGMGLSSKLEKQLELKLKQDGILYINVCTW 126
                                       6788884.77778889999******************999999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1326.68
//
Query:       gi|298675396|ref|YP_003727146.1|  [L=442]
Description: glutamine synthetase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   9.6e-130  432.6   0.0   1.1e-129  432.3   0.0    1.0  1  Gln-synt_C    Glutamine synthetase, catalytic domain
      7e-33  112.2   0.1    1.7e-32  111.0   0.1    1.7  1  Gln-synt_N    Glutamine synthetase, beta-Grasp domain
  ------ inclusion threshold ------
      0.033   14.0   0.0      0.067   13.0   0.0    1.6  1  Gln-synt_N_2  Glutamine synthetase N-terminal domain


Domain annotation for each model (and alignments):
>> Gln-synt_C  Glutamine synthetase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  432.3   0.0  1.9e-133  1.1e-129       2     345 .]     106     438 ..     105     438 .. 0.98

  Alignments for each domain:
  == domain 1  score: 432.3 bits;  conditional E-value: 1.9e-133
                                       T-HHHHHHHHHHHHHHTTCEEEEEEEEEEEEESEECCCESSEEEEEEE.TB...B.TSS-TTBHCCCCCTCCHHHHH CS
                        Gln-synt_C   2 rdPRsvlkralarlaeeGltvvvgpElEFflfdkeedkeasksllevdseekgrpaekggyfsvapvdeaedlrrei 78 
                                       +dPR+vlk++l++++e+G++++vgpElEFf+f+ke+ ++            +++p++ g+yf++ap+d aed+rr+i
  gi|298675396|ref|YP_003727146.1| 106 GDPRYVLKKMLREAKEMGYEFNVGPELEFFMFKKENGEA------------TTKPHDFGRYFEFAPADLAEDIRRDI 170
                                       79*******************************987744............678999******************** PP

                                       HHHHHHTT--EECCEEECCCTEEEEEE--EECHHHHHHHHHHHHHHHHHHHHTT-EEE-SSSSSTTS---BEEEEEE CS
                        Gln-synt_C  79 vealealgieveashhEvatgQvEinlkfadalkaaDnvvtfKrvvkevArkhgltatFmpKplegdnGsgmHvhlS 155
                                       v +l++l++++eashhEva gQ+Ei++k++dal++aDnv+tfK+v+++vA+ hgl+atFmpKp++g+nGsgmHv+lS
  gi|298675396|ref|YP_003727146.1| 171 VLTLSDLNFDIEASHHEVAFGQHEIDFKYSDALTTADNVMTFKYVTRTVAKLHGLHATFMPKPIYGENGSGMHVNLS 247
                                       ***************************************************************************** PP

                                       EEECTTEESSB-TTSGGGB-HHHHHHHHHHHHHHHHHHHHHS-SCCHHHHCSSSTTSSSBEEEESS-TTCSEEEE-T CS
                        Gln-synt_C 156 lwdkdgknlfadeddeyalselarhfigGllkhakaltaltaptvnSYkRlvpgyeaPvalawgarNRsallRipas 232
                                       l+  ++ n+f+++++++++s++ar figG+l+h++ +ta+t+p vnSYkRlvpgyeaPv+++w+  NR+ l+Ripa+
  gi|298675396|ref|YP_003727146.1| 248 LF-GNDGNAFYNPNGDMEISDVARWFIGGVLRHIRGITAVTNPIVNSYKRLVPGYEAPVYISWSGANRTSLIRIPAA 323
                                       **.7788********************************************************************** PP

                                       SGGCSTEEEECEBTTS-HHHHHHHHHHHHHHHHHTT--------S-SSSS-TTTH..TSS-B--SSHHHHHHHHHCS CS
                        Gln-synt_C 233 kekakrvElRlpdasaNPYLalAallaAgldGienklepgepvekdlyelspeer..kgieelPasleeAlealeed 307
                                       +++++r+ElR pd+s+NPY+a+Aa+l Agl+Gi++k++pge+ve++++els++er  ++i++lP+ ++e  ++le+d
  gi|298675396|ref|YP_003727146.1| 324 RGNSTRLELRNPDPSCNPYIAFAAILGAGLEGIREKIDPGEKVESNIFELSDQERarLNIDTLPSMINETASHLEND 400
                                       ******************************************************9999******************* PP

                                       HHHCCSS-HHHHHHHHHHHHHCHHHHHCT--HHHHHHH CS
                        Gln-synt_C 308 ellkevlgeevieaylalkraEleeleeevsdwelery 345
                                       ell++vlg +v ++ l++ +aE+e+++ +v+dwe++ry
  gi|298675396|ref|YP_003727146.1| 401 ELLRDVLGPHVHNNILRIAKAEWEDYRIQVHDWEVNRY 438
                                       ***********************************998 PP

>> Gln-synt_N  Glutamine synthetase, beta-Grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.0   0.1   2.8e-36   1.7e-32       1      83 []      17      99 ..      17      99 .. 0.98

  Alignments for each domain:
  == domain 1  score: 111.0 bits;  conditional E-value: 2.8e-36
                                      T--EEEEEEE-SSS-EEEEEEEHHHHHHHTTTT-EEEETTSSTTT------EEEEEEEGGGEEE-SS-SS-..EEEEEE CS
                        Gln-synt_N  1 evkfvdlqFtDikgklkhvtipadelsedaleegvsFDGSsiegfaeieeSDmlLkPdlstavidPfreek.ktarvic 78
                                      +vkf++lqF Di+g +k+v+ip++++ e+al+eg+sFDGSsiegf++i+eSDm+LkPd+st++i+P+++ek  +ar+ic
  gi|298675396|ref|YP_003727146.1| 17 DVKFIRLQFSDIQGIVKDVEIPVTQI-EKALNEGISFDGSSIEGFVRIDESDMVLKPDVSTFAILPWNQEKgVVARMIC 94
                                      69************************.**************************************************** PP

                                      EEE-T CS
                        Gln-synt_N 79 dvydp 83
                                      dv+ p
  gi|298675396|ref|YP_003727146.1| 95 DVHLP 99
                                      **976 PP

>> Gln-synt_N_2  Glutamine synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.1e-05     0.067       4      49 ..       7      52 ..       4     103 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.1e-05
                                      .......------EEEEEEE-TTS-EEEEEEEGGGHHHHHTT-EEE CS
                      Gln-synt_N_2  4 eavveqleekqveLieflyvdlaGvtrGkalplasLeekLasGiGl 49
                                      e v++ +e+ +v++i++ + d +G+++   +p +++e+ L +Gi +
  gi|298675396|ref|YP_003727146.1|  7 EDVIKAIEQYDVKFIRLQFSDIQGIVKDVEIPVTQIEKALNEGISF 52
                                      78999**************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3248.04
//
Query:       gi|298675397|ref|YP_003727147.1|  [L=382]
Description: hypothetical protein Metev_1499 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.028   13.8   0.0      0.047   13.1   0.0    1.2  1  DUF92     Integral membrane protein DUF92


Domain annotation for each model (and alignments):
>> DUF92  Integral membrane protein DUF92
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.6e-06     0.047     171     227 ..      22     120 ..       8     123 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.6e-06
                             DUF92 171 llillltlaGllGsllDSlLGatlqasvvdkrtgkvvegegge.................................. 213
                                       l ++ +t+++ +G+++DS +G  l+ +v d+++  ++ + g++                                  
  gi|298675397|ref|YP_003727147.1|  22 LTLFTGTVSASAGCTIDSNMGENLDTKVCDAQNYTIMIE-GKSldnqnimqqrsmfidkflnetndekeprhigkvk 97 
                                       245679999******************999988877765.3334789999999999999999999999999999999 PP

                             DUF92 214 .........kvvsGldlLdNnaV 227
                                                 v  G+++L+N aV
  gi|298675397|ref|YP_003727147.1|  98 nlkspknteLVAYGFKMLSNGAV 120
                                       99999999877789999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 3002.78
//
Query:       gi|298675398|ref|YP_003727148.1|  [L=326]
Description: ABC transporter-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.1e-25   88.9   0.0      1e-24   87.6   0.0    1.6  1  ABC_tran     ABC transporter
    1.1e-12   48.4   0.1    1.1e-08   35.3   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    2.2e-05   24.3   0.0       0.13   12.0   0.0    2.2  2  AAA_15       AAA ATPase domain
    0.00023   21.8   0.1    0.00075   20.2   0.0    1.9  1  DUF4162      Domain of unknown function (DUF4162)
    0.00046   20.7   0.7     0.0021   18.6   0.6    2.1  1  AAA_23       AAA domain
     0.0068   15.7   0.0      0.011   15.0   0.0    1.3  1  Zeta_toxin   Zeta toxin
     0.0091   16.4   0.7       0.15   12.5   0.7    2.4  1  AAA          ATPase family associated with various cellular a
  ------ inclusion threshold ------
       0.02   14.8   0.1      0.039   13.9   0.1    1.5  1  RsgA_GTPase  RsgA GTPase
      0.033   14.5   0.2       0.36   11.1   0.2    2.2  2  AAA_22       AAA domain
      0.034   13.9   0.3      0.086   12.6   0.2    1.9  2  AAA_30       AAA domain
       0.06   13.0   0.1       0.17   11.5   0.1    1.7  1  SRP54        SRP54-type protein, GTPase domain
      0.064   13.0   0.2       0.15   11.8   0.2    1.5  1  AAA_29       P-loop containing region of AAA domain
      0.089   12.7   0.0       0.19   11.7   0.0    1.5  1  MobB         Molybdopterin guanine dinucleotide synthesis pro


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.6   0.0   7.2e-28     1e-24       2     137 .]      37     180 ..      36     180 .. 0.90

  Alignments for each domain:
  == domain 1  score: 87.6 bits;  conditional E-value: 7.2e-28
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       + +++++k+g + ++vG+nGaGK+t +k+l+gll+p  G  ++ g d+ + e    r+  gvlp+ + +  +lt+r+
  gi|298675398|ref|YP_003727148.1|  37 DSLTFNVKKGDVFGFVGQNGAGKTTTMKMLIGLLEPSDGYAKVAGYDSVR-EVINIREVTGVLPEPAGFYGNLTARQ 112
                                       7899****************************************999999.889999******************** PP

                                       H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       n             +++++i ++l+ +gl++  d+++      +S G+ +r  la+al+++p++l+lDEpt+
  gi|298675398|ref|YP_003727148.1| 113 NlrfyaklydmdseTRENRIVELLEMVGLDDAIDQKI----GGFSTGMLKRFGLAQALINDPEILFLDEPTS 180
                                       *********9965555555666666666666666666....*****************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.1   0.00016      0.22       2      23 ..      49      70 ..      48     126 .. 0.77
   2 !   35.3   0.0   7.7e-12   1.1e-08     231     300 ..     146     213 ..     110     216 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                            AAA_21  2 nvliGpNgsGKSnLLdaldlla 23
                                       +++G Ng+GK++ ++ l +l 
  gi|298675398|ref|YP_003727148.1| 49 FGFVGQNGAGKTTTMKMLIGLL 70
                                      679*************998875 PP

  == domain 2  score: 35.3 bits;  conditional E-value: 7.7e-12
                            AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHP...kllrrllellkelsrngaQviltTHSpl 300
                                       +  +  +S G+++ ++l+ al+ ++    +l++DEp +g++P   +++r l++ l+++++  + ++l++HS +
  gi|298675398|ref|YP_003727148.1| 146 DQKIGGFSTGMLKRFGLAQALINDP---EILFLDEPTSGIDPkgaQMMRDLIKQLSREKD--VTIFLSSHSMS 213
                                       5567789****************99...9*************777777777766666655..*********76 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   9.1e-05      0.13      27      50 ..      50      73 ..      36     133 .. 0.83
   2 !   10.3   0.0    0.0003      0.42     321     365 ..     167     211 ..     156     213 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.1e-05
                            AAA_15 27 vliGkNnsGKSsilealdlFlnnk 50
                                       ++G N++GK++ +++l  +l+ +
  gi|298675398|ref|YP_003727148.1| 50 GFVGQNGAGKTTTMKMLIGLLEPS 73
                                      59***************9998877 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0003
                            AAA_15 321 eeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                        +++ il+++EP   + p+  +++ +l+k l+++++  +++++HS
  gi|298675398|ref|YP_003727148.1| 167 INDPEILFLDEPTSGIDPKGAQMMRDLIKQLSREKDVTIFLSSHS 211
                                       57899***************************************9 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   5.4e-07   0.00075       8      80 ..     244     323 ..     234     324 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 5.4e-07
                                       TTS-SSEEEEE......-------...---EEEE-TTS-EEEEE-------------.----EEEEEEEE---HHHH CS
                           DUF4162   8 rsygknrieve......adaeellee.pgveeveeeggelelkledeeaanellkal.tsgveirsFeeeePsLndI 76 
                                       r+  + ++ +e      +d  e l++ +gv++v++ +g+l+++ +++  + e+ k++ +sg++i ++eee+  L+ +
  gi|298675398|ref|YP_003727148.1| 244 REREGVNYLLEvwdisyNDMVEKLNLmDGVHDVKTLDGTLQVHADSG-MRAEIAKTIsKSGGTISRLEEERMDLQSV 319
                                       33344566677888888665555555266*********9****9985.9********77****************** PP

                                       HHHH CS
                           DUF4162  77 Fiek 80 
                                       F+++
  gi|298675398|ref|YP_003727148.1| 320 FLKL 323
                                       *986 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.6   1.5e-06    0.0021      14     130 ..      40     154 ..      18     254 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.5e-06
                            AAA_23  14 eidF.skgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkay.veltfenkdgrytr 88 
                                       +++  +  ++ ++G+NGaGKTT +  +   L    +   +  g +++++ ++i   + v +  + +  + + +   +
  gi|298675398|ref|YP_003727148.1|  40 TFNVkKGDVFGFVGQNGAGKTTTMKMLIGLLEPSDG-YAKVAGYDSVREVINIREVTGVLPEpAGFYGNLTAR---Q 112
                                       445544479***************988776655433.333345566666666555534333333333322223...4 PP

                            AAA_23  89 siererelskkkgkttkkaklelleideleqfisellgskki 130
                                       ++++  +l++ +++t+ + + elle+  l++ i++++g +  
  gi|298675398|ref|YP_003727148.1| 113 NLRFYAKLYDMDSETRENRIVELLEMVGLDDAIDQKIGGFST 154
                                       577888888888888888888888888888888887776655 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   8.2e-06     0.011      22     101 ..      52     134 ..      34     135 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.2e-06
                        Zeta_toxin  22 gGqpGAGKselaellkdelerqgnvvrldp.DdlRelhPeyeeilk...adpkkaseltqkdaselvekllqeaien 94 
                                       +Gq GAGK++++++l   le+ +++ ++ + D++Re + + +e+     +    + +lt ++  ++ +kl +   e 
  gi|298675398|ref|YP_003727148.1|  52 VGQNGAGKTTTMKMLIGLLEPSDGYAKVAGyDSVREVI-NIREVTGvlpEPAGFYGNLTARQNLRFYAKLYDMDSET 127
                                       7*******************999999987559999987.44554442115555566667777777777777766666 PP

                        Zeta_toxin  95 gyniive 101
                                       + n ive
  gi|298675398|ref|YP_003727148.1| 128 RENRIVE 134
                                       6666665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.7   0.00011      0.15       3     122 ..      51     223 ..      49     230 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                                       EESSTTSSHHHHHHHHHHHHTHE...................................................... CS
                               AAA   3 lyGppGtGKTllakavakelgve...................................................... 25 
                                       ++G  G GKT+++k ++  l+ +                                                      
  gi|298675398|ref|YP_003727148.1|  51 FVGQNGAGKTTTMKMLIGLLEPSdgyakvagydsvrevinirevtgvlpepagfygnltarqnlrfyaklydmdset 127
                                       789****************8522232233344455455555555555555555555555555555555555555555 PP

                                       .......EEEEETTTCSSS...........STTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHH CS
                               AAA  26 .......fleisgsellsk...........yvgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeee 83 
                                              +                       +g  +  + + f  a++   +p ilf+DE  + +  +       + 
  gi|298675398|ref|YP_003727148.1| 128 renriveL----------LemvglddaidqKIGGFSTGMLKRFGLAQALInDPEILFLDEPTSGIDPK-------GA 187
                                       55555554..........04444444444488989999999999888777889*******99988877.......88 PP

                                       HHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.T CS
                               AAA  84 rvvnqLlteldgvkkkeskvivigatnrpdkldpallr.g 122
                                       +++  L+++l+++k+    v++ + +++++++++   r g
  gi|298675398|ref|YP_003727148.1| 188 QMMRDLIKQLSREKD----VTIFLSSHSMSEVEEICSRiG 223
                                       999999999999988....999999999999888766555 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   2.8e-05     0.039      69     121 ..      15      68 ..       2      87 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.8e-05
                                       HHHHHHTTSEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  69 keelealgyevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                       ++ +e  +++  + +++t +++++l+ ++k+ ++  +vGq G+GK+t +++l++
  gi|298675398|ref|YP_003727148.1|  15 ENVIEIQNLTKRFGKQNTITAVDSLTFNVKKgDVFGFVGQNGAGKTTTMKMLIG 68 
                                       44444445555566677778999****999989**************9999876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00026      0.36      11      38 ..      52      84 ..      44     218 .. 0.61
   2 ?    2.5   0.0      0.12   1.6e+02      38     103 ..     168     239 ..     114     269 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00026
                            AAA_22 11 tGesGtGKTtllrrlleqldeeakaee.....e 38
                                      +G+ G+GKTt++++l   l+     ++      
  gi|298675398|ref|YP_003727148.1| 52 VGQNGAGKTTTMKMLIGLLEPSDGYAKvagydS 84
                                      8**************988853333222555551 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.12
                            AAA_22  38 erpevvfvtlpsst...sskdllrellralglelkaerlsseellealeqalrarav...ielliiDEaqhl 103
                                       ++pe++f + p s+   + ++++r+l ++l +e++     s++ ++ +e+ +++ +v    +ll i  ++ l
  gi|298675398|ref|YP_003727148.1| 168 NDPEILFLDEPTSGidpKGAQMMRDLIKQLSREKDVTIFLSSHSMSEVEEICSRIGVidsGKLLAIGTVDQL 239
                                       456666666666666555556666666666666555444455555555555555555555555555555555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   6.2e-05     0.086      17      47 ..      46      76 ..      35     208 .. 0.84
   2 ?   -2.0   0.0       1.8   2.5e+03     128     148 ..     230     249 ..     207     287 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.2e-05
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaweaa.gg 47
                                      gd v   +G  G+GKtt++k l  ++e + g+
  gi|298675398|ref|YP_003727148.1| 46 GD-VFGFVGQNGAGKTTTMKMLIGLLEPSdGY 76
                                      44.77889**************9999988663 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.8
                            AAA_30 128 lasVeaGgvlrdlveaagigt 148
                                       l ++++ ++lrd+++ ++ g+
  gi|298675398|ref|YP_003727148.1| 230 LLAIGTVDQLRDIIR-EREGV 249
                                       344444444444443.44444 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00012      0.17       5      41 ..      50      86 ..      47      88 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                                      EEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSS CS
                             SRP54  5 llvGlqGaGKTttlaKLaallkkegkkvllvaaDtfR 41
                                       +vG +GaGKTtt+  L  ll+ +   + ++  D  R
  gi|298675398|ref|YP_003727148.1| 50 GFVGQNGAGKTTTMKMLIGLLEPSDGYAKVAGYDSVR 86
                                      59************99988877776666666666665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   0.00011      0.15      16      49 ..      40      73 ..      32      80 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                            AAA_29 16 tieidlkgatlltGpsGsGKSTllDAiqalLvpa 49
                                      t++++  +++ ++G++G+GK+T +  ++ lL p+
  gi|298675398|ref|YP_003727148.1| 40 TFNVKKGDVFGFVGQNGAGKTTTMKMLIGLLEPS 73
                                      56676555999***********998777777776 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00013      0.19       1      24 [.      48      71 ..      48      80 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                              MobB  1 vlgivgksgsGKTtLleklipelk 24
                                      v+g+vg++g+GKTt ++ li  l+
  gi|298675398|ref|YP_003727148.1| 48 VFGFVGQNGAGKTTTMKMLIGLLE 71
                                      689*****************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       803  (0.0447878); expected 358.6 (0.02)
Passed bias filter:                      700  (0.0390429); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2388.96
//
Query:       gi|298675399|ref|YP_003727149.1|  [L=407]
Description: hypothetical protein Metev_1501 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      4e-12   46.2   1.4     0.0015   18.7   0.0    4.4  4  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi
    0.00017   21.8   8.4       0.01   16.1   0.8    3.4  3  CARDB        CARDB
     0.0029   18.3   1.9        4.9    7.9   0.0    4.0  4  fn3_5        Fn3-like domain
     0.0099   16.2   7.6       0.16   12.3   0.6    3.9  4  DUF11        Domain of unknown function DUF11
  ------ inclusion threshold ------
      0.027   14.8   0.1       0.11   12.9   0.0    2.0  2  DUF5060      Domain of unknown function (DUF5060)
      0.042   14.1   0.0        0.1   12.9   0.0    1.6  1  AP3B1_C      Clathrin-adaptor complex-3 beta-1 subunit C-term
        0.2   11.8   0.9          2    8.6   0.0    3.0  5  Ig_GlcNase   Exo-beta-D-glucosaminidase Ig-fold domain


Domain annotation for each model (and alignments):
>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.1    0.0029       7.5      33      60 ..      34      62 ..      32      69 .. 0.88
   2 !   18.7   0.0     6e-07    0.0015       3      73 ..      51     128 ..      49     132 .. 0.76
   3 !   10.4   0.0   0.00023       0.6       4      76 ..     169     247 ..     166     248 .. 0.81
   4 !   11.3   0.0   0.00012       0.3       2      74 ..     286     358 ..     285     362 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0029
                       NPCBM_assoc 33 GWt.vvevspasaaslapGetveatvkVt 60
                                      +W  + ++s+ +++ ++pG+t+e+t+++ 
  gi|298675399|ref|YP_003727149.1| 34 DWAsIAATSTVTGKVVCPGDTAEFTLDIE 62
                                      68878899999**************9986 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 6e-07
                       NPCBM_assoc   3 pGetvtltltvtndgtaa.atnvslslsl.PeGWtvvev..spasaa....slapGetveatvkVtppagaaaGdye 71 
                                       pG+t ++tl +  +++ + +   sls+s  Pe+Wt v +    ++++    s   +et e+t++V +p++a  G y 
  gi|298675399|ref|YP_003727149.1|  51 PGDTAEFTLDIEKGCNVSdKAWCSLSVSEkPEDWT-VGFykNNDEVThitfSEGEDETEEVTLRVEVPSDASEGRYS 126
                                       89*************766155689***999*****.44411333344331444578899*****************9 PP

                       NPCBM_assoc  72 vt 73 
                                       v 
  gi|298675399|ref|YP_003727149.1| 127 VW 128
                                       95 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00023
                       NPCBM_assoc   4 GetvtltltvtndgtaaatnvslslslPeGWtvvevspasaa......slapGetveatvkVtppagaaaGdyevta 74 
                                        ++v++++t++nd +  +t    + + Pe+W v+  + ++++      s+ p  t+ + vkV p ++  +G y+v +
  gi|298675399|ref|YP_003727149.1| 169 NDPVEFDVTLKNDYDNRVTVDLYTDKKPENWDVEFLQDENGQyrqnkiSIGPENTQDFIVKVHPDSNSSNGVYPVII 245
                                       577888888888888777644444455*****87777777778888899**************************88 PP

                       NPCBM_assoc  75 ka 76 
                                       +a
  gi|298675399|ref|YP_003727149.1| 246 NA 247
                                       76 PP

  == domain 4  score: 11.3 bits;  conditional E-value: 0.00012
                       NPCBM_assoc   2 epGetvtltltvtndgtaaatnvslslslPeGWtvvevspasaa...slapGetveatvkVtppagaaaGdyevta 74 
                                       +pG + ++t+ + n+g++++ nv+l++++ +G +   ++++s+    +l+ G++ +  v+V++ a+   G  e+ +
  gi|298675399|ref|YP_003727149.1| 286 NPGGSREITVNLRNSGDQTLNNVELRVQTDSGIS---TDVKSFGaidELESGDSESIPVEVSARASVNSGSNEILM 358
                                       69999***************************99...555544444499999999999999998888888777655 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.029        74      36      88 ..      82     135 ..      78     137 .. 0.70
   2 ?    5.0   0.2     0.011        29      17      87 ..     168     235 ..     158     238 .. 0.77
   3 !   16.1   0.8   3.9e-06      0.01      15      86 ..     285     362 ..     272     375 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.029
                                       EEEEEEEEETTEEEEEEEESEE-.CTEEEEEEEEEE-S-S-CEEEEEEEESTT- CS
                             CARDB  36 gatkvalyldgelvgtvtvpsLa.agesttvsftwtteategevtltvvvDpdn 88 
                                       ++++v +y + ++v+ +t ++ +   e++t ++ ++ +a+eg + +   +Dpd+
  gi|298675399|ref|YP_003727149.1|  82 EDWTVGFYKNNDEVTHITFSEGEdETEEVTLRVEVPSDASEGRYSVWSEIDPDD 135
                                       689999999999999888855220233344444444449999999999999985 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.011
                                       TTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-..CTEEEEEEEEEE-S-S-CEEEEEEEESTT CS
                             CARDB  17 vgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLa..agesttvsftwtteategevtltvvvDpd 87 
                                       +++ +++ vt+kN    +   ++v+ly d++  ++++v+ L+  +g++++ ++++ +e ++++  ++v+ D++
  gi|298675399|ref|YP_003727149.1| 168 PNDPVEFDVTLKND---YDNRVTVDLYTDKKP-ENWDVEFLQdeNGQYRQNKISIGPE-NTQDFIVKVHPDSN 235
                                       67778888888886...88999*********9.99***99972256666777777777.77777777777765 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 3.9e-06
                                       EETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE....EEEEESEE-CTEEEEEEEEEE-S..-S-CEEEEEEEES CS
                             CARDB  15 afvgeentitvtvkNqGtaasgatkvalyldgelv....gtvtvpsLaagesttvsftwtte..ategevtltvvvD 85 
                                       +++g + +itv+++N+G+++  ++++++  d        +   + +L++g+s+++ + + ++   ++g+ ++ + + 
  gi|298675399|ref|YP_003727149.1| 285 LNPGGSREITVNLRNSGDQTLNNVELRVQTDSGIStdvkSFGAIDELESGDSESIPVEVSARasVNSGSNEILMRAV 361
                                       66777889********************9987775233344456**********99999998777888887544443 PP

                                       T CS
                             CARDB  86 p 86 
                                       +
  gi|298675399|ref|YP_003727149.1| 362 S 362
                                       3 PP

>> fn3_5  Fn3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.5   3.8e+03      70      85 ..      51      66 ..      29     112 .. 0.59
   2 ?   -0.4   0.0      0.72   1.8e+03      71      88 ..     105     122 ..      50     131 .. 0.75
   3 !    6.3   0.1    0.0059        15      16      85 ..     178     235 ..     166     243 .. 0.63
   4 !    7.9   0.0    0.0019       4.9      62      82 ..     279     299 ..     253     309 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.5
                             fn3_5 70 Anssktvtvtldlpsd 85
                                      ++ ++++t+++  + +
  gi|298675399|ref|YP_003727149.1| 51 PGDTAEFTLDIEKGCN 66
                                      4556555555544333 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.72
                             fn3_5  71 nssktvtvtldlpsdakk 88 
                                       +++++vt+ + +psda++
  gi|298675399|ref|YP_003727149.1| 105 DETEEVTLRVEVPSDASE 122
                                       456777777777777766 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0059
                             fn3_5  16 lkNtsnkaltykvsandvlTdladkeegklilkaaspeikeaaltfetskvtvpAnssktvtvtldlpsd 85 
                                       lkN  ++++t ++     +     ++++   ++ ++++    + +  ++k+ ++++ ++++ v++ ++s+
  gi|298675399|ref|YP_003727149.1| 178 LKNDYDNRVTVDL-----Y-----TDKKPENWDVEFLQD--ENGQYRQNKISIGPENTQDFIVKVHPDSN 235
                                       4444444433322.....2.....233334455566554..599999****************9999663 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.0019
                             fn3_5  62 etskvtvpAnssktvtvtldl 82 
                                       +t+++t+++++s+++tv+l  
  gi|298675399|ref|YP_003727149.1| 279 NTRSITLNPGGSREITVNLRN 299
                                       6899*************9876 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.11   2.9e+02       4      21 ..      43      60 ..      40      62 .. 0.84
   2 ?   -3.4   0.0       4.9   1.2e+04      67      80 ..     103     116 ..      90     123 .. 0.60
   3 ?    3.6   0.1     0.033        84      10      42 ..     166     198 ..     146     239 .. 0.75
   4 !   12.3   0.6   6.1e-05      0.16       8      85 ..     280     352 ..     264     360 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.11
                             DUF11  4 tvdksevrpGdtvtytlt 21
                                      tv+ + v pGdt ++tl 
  gi|298675399|ref|YP_003727149.1| 43 TVTGKVVCPGDTAEFTLD 60
                                      77778999********96 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.9
                             DUF11  67 gesatlsftvrvtr 80 
                                       ge  t ++t+rv +
  gi|298675399|ref|YP_003727149.1| 103 GEDETEEVTLRVEV 116
                                       44555455555443 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.033
                             DUF11  10 vrpGdtvtytltvtNtgpasangvvvtDtlPag 42 
                                        rp d v++ +t++N + +  +    tD  P++
  gi|298675399|ref|YP_003727149.1| 166 TRPNDPVEFDVTLKNDYDNRVTVDLYTDKKPEN 198
                                       6899************98887444446666655 PP

  == domain 4  score: 12.3 bits;  conditional E-value: 6.1e-05
                             DUF11   8 s...evrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsv.gsLeagesatlsftvrvtr 80 
                                       +   +++pG+  + t+ ++N+g +++n+v ++    +g ++   s +         +  +Le g s  + ++v++++
  gi|298675399|ref|YP_003727149.1| 280 TrsiTLNPGGSREITVNLRNSGDQTLNNVELRVQTDSGISTDVKSFG---------AiDELESGDSESIPVEVSARA 347
                                       145689************************98766666665555555.........347888888888888888888 PP

                             DUF11  81 taasg 85 
                                       + +sg
  gi|298675399|ref|YP_003727149.1| 348 SVNSG 352
                                       88776 PP

>> DUF5060  Domain of unknown function (DUF5060)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.8   9.8e+03      43      48 ..      87      92 ..      77     110 .. 0.60
   2 ?   12.9   0.0   4.1e-05      0.11      21      64 ..     168     212 ..     154     215 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.8
                                      -EE-ST CS
                           DUF5060 43 GFYdGd 48
                                      GFY+ +
  gi|298675399|ref|YP_003727149.1| 87 GFYKNN 92
                                      777433 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 4.1e-05
                                       GG.G--EEEEEEET.TEEEEEE-EE-ST.TEEEEEE---S-EEEE CS
                           DUF5060  21 PftdvelsatFtspsgksltvpGFYdGd.gayrvrFaPdeeGeWt 64 
                                       P + ve+++t++++ + ++tv+ + d + +++ v F  de+G+++
  gi|298675399|ref|YP_003727149.1| 168 PNDPVEFDVTLKNDYDNRVTVDLYTDKKpENWDVEFLQDENGQYR 212
                                       66779********************999788************97 PP

>> AP3B1_C  Clathrin-adaptor complex-3 beta-1 subunit C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.9e-05       0.1      91     136 ..     292     338 ..     274     345 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.9e-05
                           AP3B1_C  91 sveltltNtsdseiknihigek.klqagmeihefaeiesLepgastt 136
                                        + ++l N++d++++n+++  + +   +  ++ f  i++Le g+s +
  gi|298675399|ref|YP_003727149.1| 292 EITVNLRNSGDQTLNNVELRVQtDSGISTDVKSFGAIDELESGDSES 338
                                       6999***************99856677799************99866 PP

>> Ig_GlcNase  Exo-beta-D-glucosaminidase Ig-fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.4   3.6e+03      77      92 ..     107     122 ..      97     128 .. 0.73
   2 ?   -2.5   0.0       2.3   5.9e+03      21      39 ..     172     190 ..     164     196 .. 0.60
   3 ?   -2.3   0.0       1.9   4.8e+03      67      92 ..     211     236 ..     209     243 .. 0.79
   4 ?    8.6   0.0   0.00078         2      55      93 ..     265     304 ..     253     314 .. 0.76
   5 ?   -3.0   0.0       3.1   7.9e+03      30      41 ..     367     378 ..     337     382 .. 0.56

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.4
                        Ig_GlcNase  77 gEsltltveypaaalk 92 
                                        E++tl+ve+p++a++
  gi|298675399|ref|YP_003727149.1| 107 TEEVTLRVEVPSDASE 122
                                       4677777777777766 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.3
                        Ig_GlcNase  21 akvsvtakkkeetkvtvtL 39 
                                       ++ +vt k++ +++vtv L
  gi|298675399|ref|YP_003727149.1| 172 VEFDVTLKNDYDNRVTVDL 190
                                       4445555544455555555 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.9
                        Ig_GlcNase  67 wsDNyvtLlPgEsltltveypaaalk 92 
                                       +  N +++ P+ +++  v+++ ++++
  gi|298675399|ref|YP_003727149.1| 211 YRQNKISIGPENTQDFIVKVHPDSNS 236
                                       77899999999999999988666554 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.00078
                        Ig_GlcNase  55 vdaa.geevlPvlwsDNyvtLlPgEsltltveypaaalkg 93 
                                        ++  ++evl v+ +   +tL Pg s+++tv+ +++  ++
  gi|298675399|ref|YP_003727149.1| 265 DRSLeKTEVLSVFPNTRSITLNPGGSREITVNLRNSGDQT 304
                                       4555578999**********************98877664 PP

  == domain 5  score: -3.0 bits;  conditional E-value: 3.1
                        Ig_GlcNase  30 keetkvtvtLen 41 
                                       +++++v+v +e 
  gi|298675399|ref|YP_003727149.1| 367 SDDEQVEVSIEK 378
                                       225555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       837  (0.0466841); expected 358.6 (0.02)
Passed bias filter:                      666  (0.0371465); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2879.86
//
Query:       gi|298675400|ref|YP_003727150.1|  [L=309]
Description: hypothetical protein Metev_1502 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      7e-31  107.6  24.2    5.1e-30  104.8  24.2    1.9  1  ABC2_membrane_2  ABC-2 family transporter protein
    3.9e-05   23.3  20.2    3.9e-05   23.3  20.2    2.9  3  ABC2_membrane_5  ABC-2 family transporter protein
     0.0017   18.3  17.7     0.0017   18.3  17.7    2.3  2  ABC2_membrane_4  ABC-2 family transporter protein
  ------ inclusion threshold ------
        4.5    6.3  40.6         28    3.7  40.4    2.3  1  ABC2_membrane_3  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.8  24.2   1.1e-33   5.1e-30       3     288 .]      23     307 ..      21     307 .. 0.87

  Alignments for each domain:
  == domain 1  score: 104.8 bits;  conditional E-value: 1.1e-33
                   ABC2_membrane_2   3 iakkEfrdlvrsrrfllltvllplidvalaylkdlgsslqseakaikeatlaleyveaasasdeaedtdqdlkvvst 79 
                                       +a+kEf+d v++ +flllt+ ++li  +   + +   + + +++   +  l   ++  + +                
  gi|298675400|ref|YP_003727150.1|  23 VAQKEFADNVTNSMFLLLTATYLLI-IFTFSYRSVILDTSLKYGLYEDFILLSVFGGLIEQ---------------- 82 
                                       89***********************.77777777777777788888888888777777665................ PP

                   ABC2_membrane_2  80 imavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvll.alaiilalgiv 155
                                        +  +ip+i++++g++ + +E+ +g+l +lL++Pv+Rd i++gK++g   +   ia  ++ tv++ +  +i+ lgi+
  gi|298675400|ref|YP_003727150.1|  83 -VGWFIPLIGIALGFNTVIKERKSGSLNVLLTHPVFRDNIIAGKLLGITGV---IAFVIMSTVVIsSGTLIAMLGIQ 155
                                       .899***********************************************...7777777666647789999**** PP

                   ABC2_membrane_2 156 laledllllvvasvlllllv.vflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeind 231
                                       ++l+++++++++sv++l++   ++++++l+S+v+ ++++++ + +++++++ i+ + +  ++++ll+ + +     +
  gi|298675400|ref|YP_003727150.1| 156 VSLMEITRIALFSVFTLFYAlIYAGIAVLISTVVYEATNSLIYNVAIWILTCIFTGSIMETLSDLLTKAGI----DL 228
                                       ******************999**********************************************7777....55 PP

                   ABC2_membrane_2 232 flsllsptsayntllneilagsdlna.......................lgstatnllilllllavllvlgyvlFkr 285
                                       + s l  +s+ ++ ++ i++g++ ++                          ++t + ++l+++++ll  ++ +F+r
  gi|298675400|ref|YP_003727150.1| 229 KASELIMISPLHY-YSKITQGTADMSflgvgvqyeidgildaqftlaqwFNTFWTDITAILIIPIILLFASFIMFMR 304
                                       5555555555555.344555554444566799999999999999999988999************************ PP

                   ABC2_membrane_2 286 kDl 288
                                       +D+
  gi|298675400|ref|YP_003727150.1| 305 QDI 307
                                       *96 PP

>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   1.9      0.17   7.6e+02     114     142 ..      35      52 ..      20      81 .. 0.51
   2 !   23.3  20.2   8.7e-09   3.9e-05      26     170 ..      71     220 ..      69     244 .. 0.73
   3 ?    1.8   1.5     0.033   1.5e+02      15      30 ..     286     301 ..     252     309 .] 0.53

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.17
                   ABC2_membrane_5 114 sevllsiliglvialiflaivlPlyfkfg 142
                                       s++ll  + +l+i+++f           +
  gi|298675400|ref|YP_003727150.1|  35 SMFLLLTATYLLIIFTF-----------S 52 
                                       33333333333333322...........1 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 8.7e-09
                   ABC2_membrane_5  26 iiiliflndsvllifsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitlllli 102
                                       i++++f+   ++ ++ +++++i i l ++t+ +++ks++  +llt Pv r +i++ K l+++ +i+++i+ t++++ 
  gi|298675400|ref|YP_003727150.1|  71 ILLSVFG-GLIEQVG-WFIPLIGIALGFNTVIKERKSGSLNVLLTHPVFRDNIIAGKLLGITGVIAFVIMSTVVISS 145
                                       5556664.3344455.55566666667788888********************************999999999975 PP

                   ABC2_membrane_5 103 ..iavlikgn...vtisevllsiliglvialif.laivlPlyfkfgvekgrivliiiifgiifllvaifsl.skl 170
                                         ++ ++  +   + i  + l++++ l++ali+ ++ vl  +  +++ ++ i++++i+++ +++  +i+++ s l
  gi|298675400|ref|YP_003727150.1| 146 gtLIAMLGIQvslMEITRIALFSVFTLFYALIYaGIAVLISTVVYEATNSLIYNVAIWILTCIFTGSIMETlSDL 220
                                       1134444444556666667777777777778875667889999*****************999999998865444 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.033
                   ABC2_membrane_5  15 killivllllaiiili 30 
                                        il+i ++ll+ ++++
  gi|298675400|ref|YP_003727150.1| 286 AILIIPIILLFASFIM 301
                                       2222222222222222 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3  17.7   3.8e-07    0.0017      15     173 ..      36     204 ..      25     213 .. 0.65
   2 ?    2.0   0.3     0.039   1.7e+02      47      73 ..     277     302 ..     248     306 .. 0.59

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.8e-07
                   ABC2_membrane_4  15 vwllvlaallvpllallyfnllgktgldpaefys...lsvfgftll...lllplilgiiasylifrEeqndtlknLl 85 
                                       ++ll++a+ l+ ++++ y   + +t+l+   + +   lsvfg  +     ++pli + ++   + +E++++ l+ Ll
  gi|298675400|ref|YP_003727150.1|  36 MFLLLTATYLLIIFTFSYRSVILDTSLKYGLYEDfilLSVFGGLIEqvgWFIPLIGIALGFNTVIKERKSGSLNVLL 112
                                       44445555555555555555555566665555542224677633223347788888889999*************** PP

                   ABC2_membrane_4  86 tiPvsrtklllaKlivllllsvllmlvtflit..vlfallsgfvg.fsvklvlellkkclelgllvffavlpii.al 158
                                       t Pv r +++++Kl+ +  +++++++ t++i+   l+a+l   v+ ++++  + l+  ++++ +l+++ ++++i  +
  gi|298675400|ref|YP_003727150.1| 113 THPVFRDNIIAGKLLGITGVIAFVIMSTVVISsgTLIAMLGIQVSlMEITR-IALFSVFTLFYALIYAGIAVLIsTV 188
                                       **************9888887777766666541155666666655355544.4556666677777777776655256 PP

                   ABC2_membrane_4 159 vl.lkksyvlpliltl 173
                                       v+ +++s ++ +++ +
  gi|298675400|ref|YP_003727150.1| 189 VYeATNSLIYNVAIWI 204
                                       6667777777777654 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.039
                   ABC2_membrane_4  47 yslsvfgftlllllplilgiiasylif 73 
                                       +    + +t++l++p+il ++as+++f
  gi|298675400|ref|YP_003727150.1| 277 FNTFWTDITAILIIPIIL-LFASFIMF 302
                                       222223344455555554.56776665 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7  40.4    0.0062        28     166     344 ..      86     299 ..      23     304 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0062
                   ABC2_membrane_3 166 liliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll.......afglgipf 235
                                       +i     +i+++   + +++E++s+ + ++l+ +v +  ++ +k+lg+  v +++++ ++++       ++g++++ 
  gi|298675400|ref|YP_003727150.1|  86 FIP----LIGIALGFNTVIKERKSGSLNVLLTHPVFRDNIIAGKLLGITGVIAFVIMSTVVIssgtliaMLGIQVSL 158
                                       233....33334355589****************************9988888888777764444445788865555 PP

                   ABC2_membrane_3 236 g..nlglll.llfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwi......... 300
                                       +    ++l+ ++ l+++l+y+ ++ l+s+++  +++  i  +++++ l ++f+g++ +e+l++ l ++         
  gi|298675400|ref|YP_003727150.1| 159 MeiTRIALFsVFTLFYALIYAGIAVLISTVVYEATNSLIYNVAIWI-LTCIFTGSI-METLSDLLTKAgidlkasel 233
                                       5344477778**************************9999999999.555555555.36677555554334442222 PP

                   ABC2_membrane_3 301 fsiiPffapglgllrli....tgdplwe...................illsliilalfavvylllal 344
                                        +i P++++++     +     g+ +++                   +++++++ +++ +++l +++
  gi|298675400|ref|YP_003727150.1| 234 IMISPLHYYSKITQGTAdmsfLGV-GVQyeidgildaqftlaqwfntFWTDITAILIIPIILLFASF 299
                                       777777777776655555556333.223667788888888888888866666666666666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1123  (0.062636); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2177.52
//
Query:       gi|298675401|ref|YP_003727151.1|  [L=305]
Description: ABC transporter inner membrane protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-32  112.7  16.5    2.8e-32  112.2  16.5    1.2  1  ABC2_membrane_2  ABC-2 family transporter protein
    3.9e-06   26.2  21.4    3.9e-06   26.2  21.4    1.7  1  ABC2_membrane_3  ABC-2 family transporter protein
    0.00069   19.6  19.7    0.00069   19.6  19.7    2.3  3  ABC2_membrane_4  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.2  16.5   4.6e-36   2.8e-32       2     288 .]      10     302 ..       9     302 .. 0.86

  Alignments for each domain:
  == domain 1  score: 112.2 bits;  conditional E-value: 4.6e-36
                   ABC2_membrane_2   2 aiakkEfrdlvrsrrfllltvllplidvalaylkdlgsslqseakaikeatlaleyveaasasdeaedtdqdlkvvs 78 
                                       +ia+kEf+d + s+rf+l+++++ l+     +++++ s ++  ++++++ +  + +v +                  
  gi|298675401|ref|YP_003727151.1|  10 VIAQKEFADNLWSPRFILMVIVFTLV----VFSSSYNSVNSVINVSNFSFLAGFLTVTQ------------------ 64 
                                       69************************....99999999999999999999999999988.................. PP

                   ABC2_membrane_2  79 timavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaigla.iavallatvllalaiilalgi 154
                                         +a+++p+++ ++g+d++++Ek + +l + L++Pv+Rd i++gK++g ++  l+ + ++++ +v + ++i+     
  gi|298675401|ref|YP_003727151.1|  65 -TIAIFLPLLGFALGFDSVVKEKKSASLNIFLTHPVYRDNIITGKISGAMITLLFvVFISVVSSVGTNIIISGMKVG 140
                                       .9**************************************************9999999999998887777666666 PP

                   ABC2_membrane_2 155 vlaledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavp..... 226
                                        ++le  l++++++ l++    flalg+++S+ + s  +++ + +  ++vl ++++ ++  +a++ +g ++      
  gi|298675401|ref|YP_003727151.1| 141 WFELERTLIFAILTYLYMS--IFLALGIFISTSVNSEIKSLIYGICTWLVLCVIYSAIVVMIASAVTGQSPMylnnn 215
                                       6666666666666666666..88*********************************************9999999** PP

                   ABC2_membrane_2 227 ..........qeindflsllsptsayntllneilagsdlna....................lgstatnllillllla 273
                                                 +++++ +++ +p +    l+    +     +                    l   ++n+l+l + ++
  gi|298675401|ref|YP_003727151.1| 216 devldlneqlTKLSPVYHYAKPVQDQPGLTTGGVS-----RgkivkntlklfdnrytliqwLEEYWENILVLTVTPL 287
                                       99955555555555555555554444333333333.....2555668***********9999999************ PP

                   ABC2_membrane_2 274 vllvlgyvlFkrkDl 288
                                       +ll+++y +F r+D+
  gi|298675401|ref|YP_003727151.1| 288 ILLIMSYISFLRQDI 302
                                       *************96 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2  21.4   6.6e-10   3.9e-06     153     344 ..      53     294 ..      33     295 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 6.6e-10
                   ABC2_membrane_3 153 eeelsnvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilllaf 229
                                       ++ l ++     +++++++++ +++    s+v+Ek+s  + + l+ +v +  ++++ki g ++  l+++++ ++  +
  gi|298675401|ref|YP_003727151.1|  53 FSFLAGFLTVTQTIAIFLPLL-GFALGFDSVVKEKKSASLNIFLTHPVYRDNIITGKISGAMITLLFVVFISVVSSV 128
                                       333333333344455555554.344366699**************************98888888888888887434 PP

                   ABC2_membrane_3 230 gl..........gipfgnlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlp.. 294
                                       g+          +++ +  +++ +l  l++ +++alg ++s+ ++++ +  i  ++++l+l++++ +++++ + +  
  gi|298675401|ref|YP_003727151.1| 129 GTniiisgmkvgWFELERTLIFAILTYLYMSIFLALGIFISTSVNSEIKSLIYGICTWLVLCVIYSAIVVMIASAvt 205
                                       4444666566655555555555599999999**********************************999885443344 PP

                   ABC2_membrane_3 295 ..............salkwifsiiPffapglgllrli...tgdplwe........................illsli 330
                                                     +   +++ + P +++++   + +   tg   ++                        ++ +++
  gi|298675401|ref|YP_003727151.1| 206 gqspmylnnndevlDLNEQLTKLSPVYHYAKPVQDQPgltTGG--VSrgkivkntlklfdnrytliqwleeYWENIL 280
                                       66666677777777666789999******99999998765333..33477777888888888889999999999999 PP

                   ABC2_membrane_3 331 ilalfavvylllal 344
                                       +l ++ +++l++++
  gi|298675401|ref|YP_003727151.1| 281 VLTVTPLILLIMSY 294
                                       99999999999876 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6  19.7   1.2e-07   0.00069      22     178 ..      27     184 ..      18     185 .. 0.74
   2 ?   -0.9   0.5      0.22   1.3e+03     101     122 ..     185     203 ..     183     213 .. 0.47
   3 ?   -2.0   0.1      0.52   3.1e+03      56      66 ..     281     291 ..     262     299 .. 0.48

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.2e-07
                   ABC2_membrane_4  22 allvpl.lallyfnllgk...tgldpaefys.lsvfgftlllllplilgiiasylifrEeqndtlknLltiPvsrtk 93 
                                       ++++++ l+++ + + +     ++++ +f   + ++  t+ ++lpl+   ++  ++ +E+++  l+  lt Pv r +
  gi|298675401|ref|YP_003727151.1|  27 LMVIVFtLVVFSSSYNSVnsvINVSNFSFLAgFLTVTQTIAIFLPLLGFALGFDSVVKEKKSASLNIFLTHPVYRDN 103
                                       2222220222222222220013333333333344555567788999888899************************* PP

                   ABC2_membrane_4  94 lllaKlivllllsvllmlvtflitvlfallsgfvgfsvklvlellkkclelgllvffavlpiialvllkksyvlpli 170
                                       ++ +K++  +++ +++++++++++v + +++ ++++ +    + l ++l++++l+++ ++  +al ++ +++v + i
  gi|298675401|ref|YP_003727151.1| 104 IITGKISGAMITLLFVVFISVVSSVGTNIIISGMKVGW----FELERTLIFAILTYLYMSIFLALGIFISTSVNSEI 176
                                       ************99999999999999998888888876....66899999999999999988999999999999999 PP

                   ABC2_membrane_4 171 ltlvytia 178
                                        +l+y+i+
  gi|298675401|ref|YP_003727151.1| 177 KSLIYGIC 184
                                       99999886 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.22
                   ABC2_membrane_4 101 vllllsvllmlvtflitvlfal 122
                                       ++l+l v+++ + ++   +++ 
  gi|298675401|ref|YP_003727151.1| 185 TWLVLCVIYSAIVVM---IASA 203
                                       444444555444333...3333 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.52
                   ABC2_membrane_4  56 lllllplilgi 66 
                                       +l++ plil i
  gi|298675401|ref|YP_003727151.1| 281 VLTVTPLILLI 291
                                       22222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1162  (0.0648112); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 2194.32
//
Query:       gi|298675402|ref|YP_003727152.1|  [L=628]
Description: WD40 domain-containing protein beta Propeller [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.6e-18   64.0   5.7    0.00017   21.4   0.0    6.0  6  PD40             WD40-like Beta Propeller Repeat
    5.2e-08   33.0   0.4      0.042   13.7   0.0    4.6  4  eIF2A            Eukaryotic translation initiation factor eIF
    2.5e-07   29.8   5.9      0.041   12.6   0.1    5.9  6  DPPIV_N          Dipeptidyl peptidase IV (DPP IV) N-terminal 
    0.00062   20.0   0.2        7.4    6.9   0.1    4.5  5  ANAPC4_WD40      Anaphase-promoting complex subunit 4 WD40 do
    0.00081   18.3   4.2       0.43    9.3   0.1    3.3  4  Peptidase_S9_N   Prolyl oligopeptidase, N-terminal beta-prope
     0.0013   18.5   0.5      0.004   17.0   0.5    1.8  1  PEGA             PEGA domain
  ------ inclusion threshold ------
      0.037   13.3   0.8        3.1    7.0   0.0    3.0  3  Lactonase        Lactonase, 7-bladed beta-propeller
       0.53   10.3   4.9       0.14   12.2   0.6    2.3  2  CarbopepD_reg_2  CarboxypepD_reg-like domain


Domain annotation for each model (and alignments):
>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.3   5.1e+03      31      38 .]      61      68 ..      56      68 .. 0.79
   2 ?    4.1   0.1     0.021        46      16      23 ..      70      77 ..      61      78 .. 0.85
   3 !   16.9   0.0   2.1e-06    0.0046      11      28 ..     133     150 ..     128     157 .. 0.89
   4 !    8.8   0.1    0.0007       1.6      16      30 ..     189     203 ..     188     207 .. 0.84
   5 !   10.1   0.0   0.00028      0.63      12      26 ..     230     244 ..     225     250 .. 0.86
   6 !   21.4   0.0   7.5e-08   0.00017       9      30 ..     271     293 ..     263     301 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.3
                                      .TCEEEEE CS
                              PD40 31 sGkpdIyv 38
                                      +G+pd+yv
  gi|298675402|ref|YP_003727152.1| 61 DGDPDMYV 68
                                      5******8 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.021
                                      E-TTSSEE CS
                              PD40 16 fSPDGkrl 23
                                      +SPDG+r 
  gi|298675402|ref|YP_003727152.1| 70 WSPDGTRA 77
                                      *****985 PP

  == domain 3  score: 16.9 bits;  conditional E-value: 2.1e-06
                                       EEEEEE-TTSSEEEEEEE CS
                              PD40  11 egaPsfSPDGkrlaFsSd 28 
                                       +g Ps+SPDG  ++++S+
  gi|298675402|ref|YP_003727152.1| 133 IGLPSWSPDGDVFTYTSE 150
                                       678**************7 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.0007
                                       E-TTSSEEEEEEECT CS
                              PD40  16 fSPDGkrlaFsSdRg 30 
                                       +SPDG++l +  +++
  gi|298675402|ref|YP_003727152.1| 189 WSPDGSYLLYRGYKK 203
                                       *********988877 PP

  == domain 5  score: 10.1 bits;  conditional E-value: 0.00028
                                       EEEEE-TTSSEEEEE CS
                              PD40  12 gaPsfSPDGkrlaFs 26 
                                       +++++SP G+++aF 
  gi|298675402|ref|YP_003727152.1| 230 EDITWSPKGNKIAFL 244
                                       679***********6 PP

  == domain 6  score: 21.4 bits;  conditional E-value: 7.5e-08
                                       S..EEEEEE-TTSSEEEEEEECT CS
                              PD40   9 g.negaPsfSPDGkrlaFsSdRg 30 
                                          +++P +SPDG++laFs   +
  gi|298675402|ref|YP_003727152.1| 271 NsSIHNPLWSPDGRKLAFSKIED 293
                                       2369**************97655 PP

>> eIF2A  Eukaryotic translation initiation factor eIF2A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.025        56       9      54 ..      66     115 ..      60     126 .. 0.73
   2 ?    3.7   0.0     0.022        49     117     159 ..     152     197 ..     136     200 .. 0.76
   3 !   13.7   0.0   1.9e-05     0.042      40     121 ..     208     292 ..     198     338 .. 0.79
   4 !    5.9   0.1    0.0048        11     137     165 ..     451     479 ..     438     496 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.025
                                       EEEEE-TTTTEEEEEEE.E--TT-CEE.EEE...EEEEESSSTT--EEEC CS
                             eIF2A   9 vklkWnkkGtsllvlvstevdktnksy.yge...telyliklkkkksevv 54 
                                       + ++W+  Gt  l+l+   v  +nk   ++    ++lyl+++++ +++++
  gi|298675402|ref|YP_003727152.1|  66 MYVHWSPDGTRALLLTRLTVHAKNKPEaTTRseiKALYLMEADGFDIKRI 115
                                       6789*******999999665555554303331124699999998888877 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.022
                                       EE-TTSSS-EEEEEETTTTEEEEE...EE-TT--EEEE-TTSSEEE CS
                             eIF2A 117 laGfgnlaGeleiwdvkkkkkiak...aeaanatlvewspdgryvl 159
                                       la  gn+ Ge  i+d +++++i+k   + ++     +wspdg+y+l
  gi|298675402|ref|YP_003727152.1| 152 LAKNGNILGEFLIVDADNLNTIEKgsfISNKIDFIKKWSPDGSYLL 197
                                       567799***********99999882223344455679******986 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 1.9e-05
                                       EEEESSSTT--EEECCEESSS.EEEEEE-TTSS-EEEEES.SSSCEEEEEEC...SCEEEEEEEEES--EEEE-TTS CS
                             eIF2A  40 elyliklkkkksevvelkkegpihdvaWspkskefaviyG.kmpakvslfdl...kvkviskleeqkrNtiffspkg 112
                                       ++yl++l+ + + ++++++ +   d++Wspk++++a +   k ++++ +++l   +++ i+++++++    ++sp g
  gi|298675402|ref|YP_003727152.1| 208 KCYLLDLTRNITRRFPITQYN-PEDITWSPKGNKIAFLGEdKGNESAFVYNLdngNLRNIFSTKNSSIHNPLWSPDG 283
                                       79***************9887.69************996535555888888843459999999999999999***** PP

                                       SEEEEE-TT CS
                             eIF2A 113 klvllaGfg 121
                                       + ++++ + 
  gi|298675402|ref|YP_003727152.1| 284 RKLAFSKIE 292
                                       998877665 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.0048
                                       EEEEEE-TT--EEEE-TTSSEEEEEE-TT CS
                             eIF2A 137 kiakaeaanatlvewspdgryvlTattap 165
                                       + ++++ ++  +++w+p+gry+ T t + 
  gi|298675402|ref|YP_003727152.1| 451 SNTSVNGSHIEKINWNPTGRYLFTRTYSQ 479
                                       44455566667789999999999988764 PP

>> DPPIV_N  Dipeptidyl peptidase IV (DPP IV) N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       0.2   4.6e+02      43      56 ..      63      76 ..      47      99 .. 0.79
   2 !    5.9   0.0    0.0021       4.8      23      61 ..     108     149 ..      92     151 .. 0.89
   3 ?    0.5   0.0     0.087     2e+02     107     118 ..     188     199 ..     182     217 .. 0.82
   4 !   12.6   0.1   1.8e-05     0.041     107     132 ..     278     303 ..     190     313 .. 0.79
   5 ?    1.8   0.3     0.035        78     303     339 ..     335     371 ..     328     377 .. 0.80
   6 ?   -1.9   0.0      0.47     1e+03      30     198 ..     445     472 ..     421     517 .. 0.58

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.2
                                      T.BSEEEEESSTTE CS
                           DPPIV_N 43 eklqlakwSPagdk 56
                                      ++ ++++wSP+g++
  gi|298675402|ref|YP_003727152.1| 63 DPDMYVHWSPDGTR 76
                                      56788888888775 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0021
                                       TEEEEEETTTEECEEEETT...TT.BSEEEEESSTTEEEEEE CS
                           DPPIV_N  23 aeyyiydletneveelspg...eeklqlakwSPagdklafvr 61 
                                       ++++i+ ++++e+++ +++   ++ + l+ wSP+gd + ++ 
  gi|298675402|ref|YP_003727152.1| 108 DGFDIKRIAWGECTPYTRKvgnDKLIGLPSWSPDGDVFTYTS 149
                                       5788999999*********9999999***********99986 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.087
                                       EE-TTSSEEEEE CS
                           DPPIV_N 107 wWspdgsrlayl 118
                                        Wspdgs+l+y 
  gi|298675402|ref|YP_003727152.1| 188 KWSPDGSYLLYR 199
                                       599999999995 PP

  == domain 4  score: 12.6 bits;  conditional E-value: 1.8e-05
                                       EE-TTSSEEEEEEEECTTS-EEEEEE CS
                           DPPIV_N 107 wWspdgsrlaylrfdeseVpeitlps 132
                                        Wspdg++la+ ++ +++V+++ + +
  gi|298675402|ref|YP_003727152.1| 278 LWSPDGRKLAFSKIEDNNVKDVYVID 303
                                       59999999999999999999998876 PP

  == domain 5  score: 1.8 bits;  conditional E-value: 0.035
                                       SETTEBEEEEEESSCTTEEEESSTTTSEE.EEEEE-TT CS
                           DPPIV_N 303 dsPlerhlYsvslesggeltrltdeegdh.ysasfsps 339
                                       + + e +lYs+s++ ++++t l ++++++  ++s+s++
  gi|298675402|ref|YP_003727152.1| 335 EYSPEDNLYSISVN-SRNKTLLYNSTNESgIDYSYSDH 371
                                       567899********.99999998888888666666654 PP

  == domain 6  score: -1.9 bits;  conditional E-value: 0.47
                                       TTTEECEEEETTTT.BSEEEEESSTTEEEEEETTEEEEESTTTSEEEECES-STTTEEESB--HHHHHHTSSSSBEE CS
                           DPPIV_N  30 letneveelspgeeklqlakwSPagdklafvrnnnLyvrelatgkeiqlTsdgsagifnGvadWvyeEEvlgsnsav 106
                                        +t++ +++s + + ++ ++w+P+g++                                                  
  gi|298675402|ref|YP_003727152.1| 445 ASTKSESNTSVNGSHIEKINWNPTGRY-------------------------------------------------- 471
                                       222222222222233333333333332.................................................. PP

                                       EE-TTSSEEEEEEEECTTS-EEEEEESSSSC-SS-EEEEEE--BTTS---EEEEEEEECTTSCEEECS-HHHHCTTC CS
                           DPPIV_N 107 wWspdgsrlaylrfdeseVpeitlpsytdeesqypevksikYPkaGsknpkVelkvvdlasgktvevqlpdslsekd 183
                                                                                                                    
  gi|298675402|ref|YP_003727152.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       EEEEEEEECTTSCCE CS
                           DPPIV_N 184 eyitrvkWtsdeksl 198
                                                     l
  gi|298675402|ref|YP_003727152.1| 472 --------------L 472
                                       ..............2 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.62   1.4e+03      21      55 ..     112     147 ..     101     187 .. 0.71
   2 ?   -2.1   0.0       2.2     5e+03      45      60 ..     188     204 ..     174     217 .. 0.77
   3 !    5.7   0.0    0.0078        18      27      73 ..     264     307 ..     232     327 .. 0.65
   4 !    6.3   0.1    0.0051        11      38      90 ..     412     466 ..     402     468 .. 0.79
   5 !    6.9   0.1    0.0033       7.4       2      54 ..     421     473 ..     420     489 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.62
                       ANAPC4_WD40  21 vfRlngqrvwtl.eedkedsevrsLaWkpdgklLav 55 
                                       ++R+ + +      + ++d+ +   +W+pdg ++  
  gi|298675402|ref|YP_003727152.1| 112 IKRIAWGECTPYtRKVGNDKLIGLPSWSPDGDVFTY 147
                                       566666655555233445555555589999988765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.2
                       ANAPC4_WD40  45 aWkpdgklLav.aysdg 60 
                                       +W+pdg+ L   +y++g
  gi|298675402|ref|YP_003727152.1| 188 KWSPDGSYLLYrGYKKG 204
                                       69***997653155555 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0078
                       ANAPC4_WD40  27 qrvwtleedkedsevrsLaWkpdgklLava.ysdgevrlldaesgkvv 73 
                                       ++++++    ++s++++  W+pdg+ La++ ++d++v+ + + + +vv
  gi|298675402|ref|YP_003727152.1| 264 RNIFST----KNSSIHNPLWSPDGRKLAFSkIEDNNVKDVYVIDINVV 307
                                       455555....889999999********987357888876655555555 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.0051
                       ANAPC4_WD40  38 dsevr..sLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavtclgWg 90 
                                       d +++  +++W  d+ lL v++++ + +l+ ++  +  +s +  + +++ +++W+
  gi|298675402|ref|YP_003727152.1| 412 DWKINpqGFEWCGDDLLLEVVTENDTNKLVMVNASTKSESNTSVNGSHIEKINWN 466
                                       5555444899*************9999998888777777777777778******7 PP

  == domain 5  score: 6.9 bits;  conditional E-value: 0.0033
                       ANAPC4_WD40   2 swcptmDLiAlatedgellvfRlngqrvwtleedkedsevrsLaWkpdgklLa 54 
                                       +wc    L+ ++te++   +  +n     + +++ ++s++++++W+p g+ L 
  gi|298675402|ref|YP_003727152.1| 421 EWCGDDLLLEVVTENDTNKLVMVNASTKSESNTSVNGSHIEKINWNPTGRYLF 473
                                       57766667777777766666666666666667788999999999999999886 PP

>> Peptidase_S9_N  Prolyl oligopeptidase, N-terminal beta-propeller domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.25   5.5e+02     175     191 ..     187     203 ..     133     222 .. 0.60
   2 ?   -0.7   0.0      0.21   4.6e+02     131     178 ..     189     235 ..     171     259 .. 0.56
   3 !    9.3   0.1   0.00019      0.43     125     203 ..     273     350 ..     264     362 .. 0.68
   4 !    8.2   0.2   0.00042      0.93     147     206 ..     435     490 ..     429     494 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.25
                                       EEECTTSSEEEEEESS- CS
                    Peptidase_S9_N 175 ivWaadekgffYtrydk 191
                                        +W +d+++++Y  y+k
  gi|298675402|ref|YP_003727152.1| 187 KKWSPDGSYLLYRGYKK 203
                                       46777777777777764 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.21
                                       E-TTSSEEEEEEEETTSSEEEEEEEETTTTEEEEEEEEEEESEEEEEC CS
                    Peptidase_S9_N 131 vsedgkllAyslsksGsdwytirvkdietgedlpdeledvkfsgivWa 178
                                        s+dg++l y+  k+G+   +  + d++   +    +++ +++ i+W 
  gi|298675402|ref|YP_003727152.1| 189 WSPDGSYLLYRGYKKGE-GPKCYLLDLTRNITRRFPITQYNPEDITWS 235
                                       45555555555444442.233344444444444444444444444444 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00019
                                       EEEEEEE-TTSSEEEEE..EEETTSSEEEEEEEETTTTEEEEEEEEEEESEE.EEECTTSSEEEEEESS-SSS-TST CS
                    Peptidase_S9_N 125 algefavsedgkllAys..lsksGsdwytirvkdietgedlpdeledvkfsg.ivWaadekgffYtrydkedersdt 198
                                       ++++   s+dg+ lA+s  ++ + +d+y i +    +g+  p +l+   +   ++W++  + ++Yt+y +ed+  + 
  gi|298675402|ref|YP_003727152.1| 273 SIHNPLWSPDGRKLAFSkiEDNNVKDVYVIDINV-VNGR--PYKLTTLHGGIlVEWLDS-EKLLYTEYSPEDNLYSI 345
                                       6666678**********44466677777776543.3444..5566666666669***99.9999****988877764 PP

                                       SB-S- CS
                    Peptidase_S9_N 199 dtnln 203
                                       + n  
  gi|298675402|ref|YP_003727152.1| 346 SVNSR 350
                                       44433 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.00042
                                       SSEEEEEEEETTTTEEEEEEEEEEESEEEEECTTSSEEEEEESS-SSS-TSTSB-S-BEE CS
                    Peptidase_S9_N 147 sdwytirvkdietgedlpdeledvkfsgivWaadekgffYtrydkedersdtdtnlnqkv 206
                                       +d +++ +++++t+ + + ++++  +++i W + ++++f  +y ++++++     +++++
  gi|298675402|ref|YP_003727152.1| 435 NDTNKLVMVNASTKSESNTSVNGSHIEKINWNPTGRYLFTRTYSQKRSKQV----YHNQI 490
                                       68999999************************************6655555....66665 PP

>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.5   1.8e-06     0.004       6      55 ..     521     575 ..     514     583 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.8e-06
                              PEGA   6 irSnpeGatVyidGkylGkTPvt....ls.leaGnyslrvekeGYedlektvtvt 55 
                                       ++ +  +atVy +G+++G+T+ +         +G+y+l+ +k GY +++ +v++ 
  gi|298675402|ref|YP_003727152.1| 521 VSGSVGNATVYSNGENIGRTNSEgvlsHQfKNNGSYRLKAVKVGYINASHKVSIG 575
                                       5667889**************762211455679*******************986 PP

>> Lactonase  Lactonase, 7-bladed beta-propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0014       3.1     284     332 ..     220     268 ..     214     279 .. 0.87
   2 ?    2.1   0.1     0.043        96       5     102 ..     289     383 ..     285     412 .. 0.78
   3 ?    0.6   0.0      0.12   2.6e+02      79     106 ..     452     478 ..     426     495 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0014
                                       EEEE-SSS.--EEEE-TTSSEEEEEETTTTEEEEEEEETTTTEEEEESE CS
                         Lactonase 284 eevstegkfPRdfaldpsgklllvanqksdnvtvferdaetGkLtelgk 332
                                        +++++  +P d++++p+g+ +++ +++ +n + f  + ++G+L+++ +
  gi|298675402|ref|YP_003727152.1| 220 RRFPITQYNPEDITWSPKGNKIAFLGEDKGNESAFVYNLDNGNLRNIFS 268
                                       57889999************************************98754 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.043
                                       EEGGSSS.TEEEEEEEETTTS-EEEEEEEEESS---SEEE-TTSSEEEEEET.STTTEEEEEEEETTTTEEEEEEEE CS
                         Lactonase   5 GtytkgeskgiytlkldtetgkltplelvaelenPsyLalspdgktlYavnetgeeggvsafaidkdsgeltllnkv 81 
                                       +  ++++ k +y+++++  +g+  +l++   +  +++L     +k lY+     +e ++++ ++++++++l l n++
  gi|298675402|ref|YP_003727152.1| 289 SKIEDNNVKDVYVIDINVVNGRPYKLTTLHGGILVEWLDS---EKLLYTEYS--PEDNLYSISVNSRNKTL-LYNST 359
                                       5566788889999999999999999999999999999998...999998655..78899999999986555.55655 PP

                                       E....SSS-EEEEEE-TTSSEEEE CS
                         Lactonase  82 ss...egaspchlsvdedgkllav 102
                                       ++   + + + h  vd++g++++v
  gi|298675402|ref|YP_003727152.1| 360 NEsgiDYSYSDHSFVDPTGEFVFV 383
                                       552335566667889999999987 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.12
                                       EEEE.SSS-EEEEEE-TTSSEEEEEETT CS
                         Lactonase  79 nkvssegaspchlsvdedgkllavAnYs 106
                                       n+   +g++   +  +++g++l++  Ys
  gi|298675402|ref|YP_003727152.1| 452 NTS-VNGSHIEKINWNPTGRYLFTRTYS 478
                                       222.255555555555555555555555 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.3       2.3   5.1e+03       5      26 ..     431     452 ..     430     458 .. 0.69
   2 ?   12.2   0.6   6.3e-05      0.14      13      71 ..     524     581 ..     515     594 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.3
                   CarbopepD_reg_2   5 VvdketkeplpgatVyvkgtkk 26 
                                       Vv++++ ++l  ++ + k+ ++
  gi|298675402|ref|YP_003727152.1| 431 VVTENDTNKLVMVNASTKSESN 452
                                       5556666888888888877655 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 6.3e-05
                   CarbopepD_reg_2  13 plpgatVyvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvskektld 71 
                                       ++  atVy +g + g  T+++G  + + +++g y+L++  vGy +++ kv++ +++ +d
  gi|298675402|ref|YP_003727152.1| 524 SVGNATVYSNGENIG-RTNSEGVLSHQFKNNGSYRLKAVKVGYINASHKVSIGGKSIVD 581
                                       566799**9999998.69****999888999*********************8876555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (628 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 4253.94
//
Query:       gi|298675403|ref|YP_003727153.1|  [L=139]
Description: hypothetical protein Metev_1505 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.077   13.4   0.1      0.092   13.1   0.1    1.1  1  CssAB     CS6 fimbrial subunits A and B, Coli surface antigen


Domain annotation for each model (and alignments):
>> CssAB  CS6 fimbrial subunits A and B, Coli surface antigen 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   5.1e-06     0.092      46     123 ..      21      99 ..       4     108 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.1e-06
                             CssAB  46 dsltssgqqigklvnvnnpdqnmnyyirkdsgagk..fmagqkgsfsvkentsytfsaiytggeypnsgyssgtyag 120
                                        s+++ g+     v++n p++ + y+   + g+g   f     g      +  ytf+  y g  y    y  g    
  gi|298675403|ref|YP_003727153.1|  21 TSMAAGGDTYSGAVEINVPEDRLGYFGEYEKGTGDdwFKFDGSGGDCAEIDLDYTFTNDYNGEMYLHDEYE-GDIEA 96 
                                       578889999999**************98888877632666666667788899*************999996.45555 PP

                             CssAB 121 hlt 123
                                       h+t
  gi|298675403|ref|YP_003727153.1|  97 HIT 99 
                                       666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 908.46
//
Query:       gi|298675404|ref|YP_003727154.1|  [L=149]
Description: hypothetical protein Metev_1506 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.18   12.2   1.5       0.76   10.2   0.4    2.4  3  DUF4969   Domain of unknown function (DUF4969)


Domain annotation for each model (and alignments):
>> DUF4969  Domain of unknown function (DUF4969)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.4   4.2e-05      0.76       1      30 [.       1      29 [.       1      49 [. 0.87
   2 ?   -0.0   0.1     0.064   1.2e+03      26      42 ..      43      59 ..      38      98 .. 0.56
   3 ?   -2.0   0.0      0.27   4.8e+03      39      55 ..     117     133 ..     111     143 .. 0.49

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 4.2e-05
                           DUF4969  1 mkkRgllLvsvLvlFillavaCsdsednee 30
                                      m ++  +L+ vL+l + +a+a ++  dne 
  gi|298675404|ref|YP_003727154.1|  1 MFRKICILTLVLLLTVSFATATTN-GDNES 29
                                      778899****************99.88986 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.064
                           DUF4969 26 edneesveiilkeiels 42
                                      ed e+sv i++    +s
  gi|298675404|ref|YP_003727154.1| 43 EDTETSVGIMTVSDSIS 59
                                      66677776665433333 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.27
                           DUF4969  39 ielsvddpiklvdenge 55 
                                       i+l v++p  l   n +
  gi|298675404|ref|YP_003727154.1| 117 INLDVENPNGLASGNWK 133
                                       44444444444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.36s 00:00:00.91 Elapsed: 00:00:00.55
# Mc/sec: 821.56
//
Query:       gi|298675405|ref|YP_003727155.1|  [L=256]
Description: hypothetical protein Metev_1507 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.2e-22   76.5   1.1    1.1e-10   40.9   0.1    2.3  2  HTH_24         Winged helix-turn-helix DNA-binding
    7.6e-07   29.0   0.1     0.0052   16.7   0.0    2.3  2  MarR           MarR family
    1.1e-06   28.6   0.0    5.5e-05   23.1   0.0    2.1  2  HTH_20         Helix-turn-helix domain
    3.7e-06   26.7   0.0    0.00046   20.0   0.0    2.3  2  HTH_5          Bacterial regulatory protein, arsR family
    8.9e-06   25.3   0.0       0.16   11.7   0.0    2.4  2  HTH_41         Helix-turn-helix domain
    0.00067   19.5   0.2      0.014   15.3   0.0    2.4  2  HTH_11         HTH domain
     0.0018   17.4   0.4     0.0024   16.9   0.4    1.1  1  TnsD           Tn7-like transposition protein D
      0.003   18.1   0.3       0.95   10.1   0.0    2.4  2  Mga            Mga helix-turn-helix domain
     0.0052   16.6   0.0      0.041   13.8   0.0    2.0  2  MarR_2         MarR family
  ------ inclusion threshold ------
       0.01   16.2   1.8       0.14   12.6   0.5    2.3  2  HTH_40         Helix-turn-helix domain
      0.015   15.7   0.0      0.036   14.4   0.0    1.7  1  FaeA           FaeA-like protein
      0.016   14.8   0.1      0.076   12.6   0.0    2.1  2  GerE           Bacterial regulatory proteins, luxR family
      0.019   14.7   0.0       0.22   11.4   0.0    2.2  2  HTH_IclR       IclR helix-turn-helix domain
      0.031   13.9   0.0       0.06   13.0   0.0    1.4  1  Sigma70_r4_2   Sigma-70, region 4
       0.05   13.4   0.0      0.094   12.5   0.0    1.4  1  HTH_38         Helix-turn-helix domain
      0.061   13.2   0.0       0.37   10.7   0.0    2.0  2  TrmB           Sugar-specific transcriptional regulator TrmB
      0.075   13.2   0.1        1.8    8.8   0.0    2.2  2  HTH_34         Winged helix DNA-binding domain
      0.086   12.8   0.3        1.9    8.5   0.0    2.2  2  HTH_6          Helix-turn-helix domain, rpiR family
      0.099   12.4   0.1       0.16   11.8   0.1    1.3  1  Sortase        Sortase domain
       0.12   12.7   0.1        2.9    8.2   0.0    2.4  2  HTH_Tnp_Tc3_2  Transposase
       0.14   12.0   0.0       0.25   11.2   0.0    1.3  1  HTH_30         PucR C-terminal helix-turn-helix domain
        1.1    9.4   3.6       0.27   11.3   0.3    1.7  1  DUF997         Protein of unknown function (DUF997)


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.1   1.3e-13   1.1e-10       2      48 .]     106     152 ..     105     152 .. 0.96
   2 !   34.4   0.1   1.4e-11   1.1e-08       2      48 .]     182     228 ..     181     228 .. 0.97

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 1.3e-13
                            HTH_24   2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                       ++++r+I++++  np++s+++++  l +S++tv+++++ Le ++ I+
  gi|298675405|ref|YP_003727155.1| 106 NKNRRRIYNYIVNNPGCSIADISSNLAISRGTVRYHVRLLETMEKIR 152
                                       899**************************************999886 PP

  == domain 2  score: 34.4 bits;  conditional E-value: 1.4e-11
                            HTH_24   2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                       +et +++L+ ++++p+i+++eL  +  l ++t+n+++k++ ++ +I+
  gi|298675405|ref|YP_003727155.1| 182 NETSKQLLKSIKEQPGITNQELLHKHSLNKGTINWHIKKFHNDDIIT 228
                                       89*******************************************96 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   0.00069      0.56      14      47 ..     118     151 ..     115     158 .. 0.88
   2 !   16.7   0.0   6.3e-06    0.0052       4      50 ..     184     230 ..     181     234 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00069
                                       HSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              MarR  14 eqgplsvseLakklgvskstvtrvldrLekkGli 47 
                                       +++++s++++ + l +s++tv   ++ Le  + i
  gi|298675405|ref|YP_003727155.1| 118 NNPGCSIADISSNLAISRGTVRYHVRLLETMEKI 151
                                       789**********************999988766 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 6.3e-06
                                       HHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR   4 tqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50 
                                       t   +L +++eq++++++eL  k +++k+t+   +++   ++ i+ +
  gi|298675405|ref|YP_003727155.1| 184 TSKQLLKSIKEQPGITNQELLHKHSLNKGTINWHIKKFHNDDIITFE 230
                                       56679********************************9998888876 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   6.7e-08   5.5e-05       5      49 ..     102     146 ..      98     156 .. 0.93
   2 ?    3.4   0.0       0.1        82      11      55 ..     184     228 ..     175     234 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 6.7e-08
                                       HHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHH CS
                            HTH_20   5 eALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLe 49 
                                       ++++++ Rrri+ ++  + g + +++   l +s+ t++yH+r Le
  gi|298675405|ref|YP_003727155.1| 102 DLFSNKNRRRIYNYIVNNPGCSIADISSNLAISRGTVRYHVRLLE 146
                                       57899***************************************8 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.1
                                       HHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20  11 vRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55 
                                       +   +l+ +++  g t  el +  +l k t++ H+++    ++++
  gi|298675405|ref|YP_003727155.1| 184 TSKQLLKSIKEQPGITNQELLHKHSLNKGTINWHIKKFHNDDIIT 228
                                       5556666667777788889999999************98888887 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   5.6e-07   0.00046       2      42 ..     107     148 ..     106     152 .. 0.94
   2 ?    4.4   0.0     0.041        33       5      45 ..     186     227 ..     182     228 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 5.6e-07
                                       HHHHHHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHHHHT CS
                             HTH_5   2 ptRlkILklLaege.lcvcelaeelglsqstvShHLkkLrea 42 
                                       ++R++I ++  +++ +++ +++  l +s++tv++H + L+ +
  gi|298675405|ref|YP_003727155.1| 107 KNRRRIYNYIVNNPgCSIADISSNLAISRGTVRYHVRLLETM 148
                                       78***********************************99865 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.041
                                       HHHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5   5 lkILklLaege.lcvcelaeelglsqstvShHLkkLreaGLV 45 
                                        ++Lk+  e++  +  el  +  l+++t+  H kk ++ +++
  gi|298675405|ref|YP_003727155.1| 186 KQLLKSIKEQPgITNQELLHKHSLNKGTINWHIKKFHNDDII 227
                                       58899999999999999999***************9998887 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00019      0.16       8      39 ..     123     154 ..     122     156 .. 0.92
   2 !   11.1   0.0   0.00031      0.25      10      43 ..     201     234 ..     198     236 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00019
                            HTH_41   8 tIeelakeleLSvGlvQkALklLeddkaisle 39 
                                       +I +++++l +S+G+v   + lLe +  i l+
  gi|298675405|ref|YP_003727155.1| 123 SIADISSNLAISRGTVRYHVRLLETMEKIRLI 154
                                       6999**********************999886 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00031
                            HTH_41  10 eelakeleLSvGlvQkALklLeddkaislerrGr 43 
                                       +el ++ +L  G++   +k+  +d +i+ e+ G+
  gi|298675405|ref|YP_003727155.1| 201 QELLHKHSLNKGTINWHIKKFHNDDIITFESSGK 234
                                       6999**************************9996 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.8e-05     0.014       4      43 ..     111     149 ..     108     159 .. 0.80
   2 ?    1.8   0.0      0.29   2.3e+02       3      38 ..     186     220 ..     184     234 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.8e-05
                            HTH_11   4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43 
                                        i+  + ++ g  s+++++  L +Sr tvr +++ Le++ 
  gi|298675405|ref|YP_003727155.1| 111 RIYNYIVNNPG-CSIADISSNLAISRGTVRYHVRLLETME 149
                                       56666655555.9***********************9986 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.29
                            HTH_11   3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIka 38 
                                       +q+l+ + ++++ i+ +eL  + ++ + t+  +Ik+
  gi|298675405|ref|YP_003727155.1| 186 KQLLKSI-KEQPGITNQELLHKHSLNKGTINWHIKK 220
                                       6888888.44445******99999999999999987 PP

>> TnsD  Tn7-like transposition protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.4   2.9e-06    0.0024     194     280 ..     116     220 ..     104     223 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.9e-06
                              TnsD 194 LveeeglslkeiAkelgvdiktVlryakklgllkekkkqkkesrelsskd...............rekkrkewleli 255
                                        v++ g s+++i++ l+++ +tV+ + + l+  ++ ++ k ++ +l+ ++               +++  k++l++i
  gi|298675405|ref|YP_003727155.1| 116 IVNNPGCSIADISSNLAISRGTVRYHVRLLETMEKIRLIKSDKYTLAIQNsdtfndiektiiphlKNETSKQLLKSI 192
                                       4555899***********************9999999999888887777789************************* PP

                              TnsD 256 ksypdlgktel...rklnpalyawLyrn 280
                                       k+ p ++++el    +ln+ + +w++++
  gi|298675405|ref|YP_003727155.1| 193 KEQPGITNQELlhkHSLNKGTINWHIKK 220
                                       *******999944456889999999876 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0    0.0012      0.95       7      52 ..      98     143 ..      96     167 .. 0.89
   2 ?    5.9   0.2     0.025        20      13      55 ..     180     222 ..     165     231 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHSHHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHH CS
                               Mga   7 ellqellkeslkyqllkflfeeeevsieelaqelyiSestlkrkik 52 
                                        ++++l+ + +  ++  +++++  +si++++ +l iS+ t+  +++
  gi|298675405|ref|YP_003727155.1|  98 SIIKDLFSNKNRRRIYNYIVNNPGCSIADISSNLAISRGTVRYHVR 143
                                       5788999999999***************************987766 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.025
                                       HHHSHHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHH CS
                               Mga  13 lkeslkyqllkflfeeeevsieelaqelyiSestlkrkikeln 55 
                                       lk+ ++ qllk + e+  ++ +el  ++ + + t++ +ik++ 
  gi|298675405|ref|YP_003727155.1| 180 LKNETSKQLLKSIKEQPGITNQELLHKHSLNKGTINWHIKKFH 222
                                       4558889********************************9974 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0     5e-05     0.041      12      48 ..     114     148 ..     108     158 .. 0.85
   2 ?    0.4   0.0      0.77   6.3e+02       9      55 ..     187     231 ..     184     234 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5e-05
                                       HHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHT CS
                            MarR_2  12 aaLgrrpgrdltvgelarrlglsksavsrilkrLvaa 48 
                                       +++ ++pg  ++++++   l +s+++v ++++ L+  
  gi|298675405|ref|YP_003727155.1| 114 NYIVNNPG--CSIADISSNLAISRGTVRYHVRLLETM 148
                                       67999***..***********************9975 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.77
                                       HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2   9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55 
                                       ++L  +   pg  +t +el  +  l k++++ ++k++     ++ ++
  gi|298675405|ref|YP_003727155.1| 187 QLLKSIKEQPG--ITNQELLHKHSLNKGTINWHIKKFHNDDIITFES 231
                                       67888999999..9999999999999****99999999988888775 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.5   0.00017      0.14      12      75 ..     121     195 ..     113     199 .. 0.68
   2 ?    2.7   0.0      0.21   1.7e+02      12      39 ..     197     224 ..     195     238 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00017
                            HTH_40  12 glsieeIAkerglkesTIegH..Laelieegeeidlerl...v.seeeekeIeeaiekvgsek.....lkpikea 75 
                                       g+si++I+ +  ++++T+  H  L+e +e+ + i+ +++   + ++++++ Ie++i  + +++     lk ike+
  gi|298675405|ref|YP_003727155.1| 121 GCSIADISSNLAISRGTVRYHvrLLETMEKIRLIKSDKYtlaIqNSDTFNDIEKTIIPHLKNEtskqlLKSIKEQ 195
                                       89*******************444555555444444555434344577777776665533222355689999997 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.21
                            HTH_40  12 glsieeIAkerglkesTIegHLaeliee 39 
                                       g + +e  ++ +l+++TI  H+ ++ ++
  gi|298675405|ref|YP_003727155.1| 197 GITNQELLHKHSLNKGTINWHIKKFHND 224
                                       66778888999**********9988776 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   4.4e-05     0.036       4      46 ..     111     152 ..      95     158 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.4e-05
                                       HHHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEE CS
                              FaeA   4 eIleylnsikapckTreiAdalglsaYQaRyYLeqLekegkik 46 
                                        I +y+ + + +c  ++i   l++s   +Ry    Le   ki+
  gi|298675405|ref|YP_003727155.1| 111 RIYNYIVN-NPGCSIADISSNLAISRGTVRYHVRLLETMEKIR 152
                                       58899999.99**************************999997 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   9.3e-05     0.076      17      44 ..     121     150 ..     118     155 .. 0.81
   2 ?   -1.7   0.0       2.7   2.2e+03      18      39 ..     198     219 ..     196     221 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.3e-05
                                       TS-HHHHHHHHTS-HHHHHHHHH..HHHHH CS
                              GerE  17 GksnkeIAeelniSekTVkvhks..nimkK 44 
                                       G s  +I+++l iS  TV++h++  + m+K
  gi|298675405|ref|YP_003727155.1| 121 GCSIADISSNLAISRGTVRYHVRllETMEK 150
                                       678899***************983344555 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.7
                                       S-HHHHHHHHTS-HHHHHHHHH CS
                              GerE  18 ksnkeIAeelniSekTVkvhks 39 
                                        +n+e   + ++ + T++ h++
  gi|298675405|ref|YP_003727155.1| 198 ITNQELLHKHSLNKGTINWHIK 219
                                       5666666677778889999987 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00027      0.22      17      51 ..     120     157 ..     106     158 .. 0.89
   2 ?    0.8   0.0      0.54   4.4e+02       7      34 ..     187     213 ..     186     216 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00027
                                       SS-BHHHHHHHHTS-HHHHH...HHHHHHHHTTSEE.. CS
                          HTH_IclR  17 qeltlselArrtglpkStvh...RlLqtLvelGyveqd 51 
                                       ++ ++++++ ++++++ tv+   RlL t+++ ++++ d
  gi|298675405|ref|YP_003727155.1| 120 PGCSIADISSNLAISRGTVRyhvRLLETMEKIRLIKSD 157
                                       5679***************9888999999999999876 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.54
                                       HHHCT-CTTBSS-BHHHHHHHHTS-HHH CS
                          HTH_IclR   7 aiLdalaeapqeltlselArrtglpkSt 34 
                                       ++L+ + e+p+  t++el ++  l+k t
  gi|298675405|ref|YP_003727155.1| 187 QLLKSIKEQPG-ITNQELLHKHSLNKGT 213
                                       78999999999.8*****9999999988 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.3e-05      0.06      26      48 ..     121     143 ..     120     144 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.3e-05
                                       ---HHHHHHHHT--HHHHHHHHH CS
                      Sigma70_r4_2  26 glsykEIAellgisegtVksrls 48 
                                       g+s+++I++ l is gtV+++++
  gi|298675405|ref|YP_003727155.1| 121 GCSIADISSNLAISRGTVRYHVR 143
                                       89******************985 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00012     0.094       6      42 ..     105     143 ..     104     143 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                            HTH_38   6 sleeReeIerll..aeGlslreIArrLgrspsTIsRElk 42 
                                       s  +R++I+  +  + G+s+++I   L  s++T+ ++++
  gi|298675405|ref|YP_003727155.1| 105 SNKNRRRIYNYIvnNPGCSIADISSNLAISRGTVRYHVR 143
                                       67899*****9755689******************9997 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00045      0.37      12      60 ..     111     159 ..     106     164 .. 0.90
   2 ?   -0.1   0.0       1.1   8.8e+02      21      63 ..     196     239 ..     183     243 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00045
                                       CHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT CS
                              TrmB  12 kvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpk 60 
                                       ++Y +++++   ++ +i+++l ++r +v   +r Le +  ++ +k+ ++
  gi|298675405|ref|YP_003727155.1| 111 RIYNYIVNNPGCSIADISSNLAISRGTVRYHVRLLETMEKIRLIKSDKY 159
                                       78**********************************9999988887654 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.1
                                       CCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.STTTEEE CS
                              TrmB  21 gpatadeiaeelgvprskvYevLrsLedkGlVerek.grpklYr 63 
                                          t +e+ ++  + + +++  +++  + ++++ e  g++k+Y 
  gi|298675405|ref|YP_003727155.1| 196 PGITNQELLHKHSLNKGTINWHIKKFHNDDIITFESsGKYKKYF 239
                                       56678888899999999999999999999999999844577885 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0023       1.8       5      49 ..     112     156 ..     109     162 .. 0.88
   2 ?    2.2   0.0      0.25     2e+02      13      50 ..     196     233 ..     187     239 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0023
                            HTH_34   5 vlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdke 49 
                                       +  y + +   + +++++ l ++ g    h++ Le+ + i   k+
  gi|298675405|ref|YP_003727155.1| 112 IYNYIVNNPGCSIADISSNLAISRGTVRYHVRLLETMEKIRLIKS 156
                                       5567888899999************************99988776 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.25
                            HTH_34  13 deadfvelkealeatdgnLsvhlkkLekagYievdkef 50 
                                         ++ +el  + ++++g +  h+kk+ + + i+ + + 
  gi|298675405|ref|YP_003727155.1| 196 PGITNQELLHKHSLNKGTINWHIKKFHNDDIITFESSG 233
                                       56677888889999************999998887665 PP

>> HTH_6  Helix-turn-helix domain, rpiR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0024       1.9      15      52 ..     106     139 ..      93     148 .. 0.87
   2 ?    1.8   0.3      0.29   2.4e+02      10      39 ..     165     194 ..     159     195 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0024
                                       -HHHHHHHHHHHH-S---TT--HHHHHHHTT--HHHHH CS
                             HTH_6  15 tksekkiaeyilaspdkaielsikalAkaaavSeativ 52 
                                       +k+ ++i +yi ++p     +si++++ ++a+S+ t+ 
  gi|298675405|ref|YP_003727155.1| 106 NKNRRRIYNYIVNNPG----CSIADISSNLAISRGTVR 139
                                       78999*******9995....9*************9984 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.29
                                       H-----HHHHHHHHHHHH-S---TT--HHH CS
                             HTH_6  10 kkekltksekkiaeyilaspdkaielsika 39 
                                       + + +++ ek+i+  ++++ +k   +sik+
  gi|298675405|ref|YP_003727155.1| 165 NSDTFNDIEKTIIPHLKNETSKQLLKSIKE 194
                                       4678999*************9999999975 PP

>> Sortase  Sortase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00019      0.16      18      77 ..     182     238 ..     161     251 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                                       SCHCTTSEEECSTT-BTTSSSEEEEEEEBSSTTSTTGGGGGGHTT-EEEEEESSSEEEEE CS
                           Sortase  18 eedlkagagfldesakpgeagnfvlaGHrvgkgavFsdLkklekgdaivvetkkgksyvY 77 
                                       +e+ k+    ++e  +pg +++ +l+ H+ +kg++  ++kk++++d i++e+  gk+++Y
  gi|298675405|ref|YP_003727155.1| 182 NETSKQLLKSIKE--QPGITNQELLHKHSLNKGTINWHIKKFHNDDIITFES-SGKYKKY 238
                                       4444444444443..48999999*****************************.8888888 PP

>> HTH_Tnp_Tc3_2  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0035       2.9       1      36 [.     109     139 ..     109     147 .. 0.91
   2 ?    1.9   0.0      0.32   2.6e+02       3      23 ..     187     207 ..     185     220 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0035
                     HTH_Tnp_Tc3_2   1 krrIvrlvrkdPritlreLanelkeeGksvsreTir 36 
                                       +rrI+ ++ ++P  +++++++ l      +sr T+r
  gi|298675405|ref|YP_003727155.1| 109 RRRIYNYIVNNPGCSIADISSNL-----AISRGTVR 139
                                       69*******************99.....99999998 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.32
                     HTH_Tnp_Tc3_2   3 rIvrlvrkdPritlreLanel 23 
                                       ++++ ++++P it +eL  + 
  gi|298675405|ref|YP_003727155.1| 187 QLLKSIKEQPGITNQELLHKH 207
                                       789999*******99998765 PP

>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0003      0.25      12      39 ..     121     148 ..     113     161 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0003
                                       TT-HHHHHHHHTS-HHHHHHHHHHHHHH CS
                            HTH_30  12 ggnisatAkaLhvHrnTlryRLrrieel 39 
                                       g++i++ +  L ++r T+ry +r +e +
  gi|298675405|ref|YP_003727155.1| 121 GCSIADISSNLAISRGTVRYHVRLLETM 148
                                       69*******************9998876 PP

>> DUF997  Protein of unknown function (DUF997)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   0.00033      0.27      31      58 ..      61      88 ..      56     101 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00033
                            DUF997 31 eveeyyilglPlWfflscillpilfivl 58
                                       ++++++++lPlW+ ++ i ++i+ ++ 
  gi|298675405|ref|YP_003727155.1| 61 ADKTITFWDLPLWIQIAHISGIIITFLS 88
                                      556789***************8876654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1018  (0.0567795); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.65u 0.35s 00:00:01.00 Elapsed: 00:00:00.55
# Mc/sec: 1410.05
//
Query:       gi|298675406|ref|YP_003727156.1|  [L=61]
Description: hypothetical protein Metev_1508 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 377.00
//
Query:       gi|298675407|ref|YP_003727157.1|  [L=484]
Description: transposase IS4 family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.4e-15   55.2   0.2      2e-14   53.8   0.2    1.7  1  DDE_Tnp_1  Transposase DDE domain
  ------ inclusion threshold ------
      0.014   15.1   1.5      0.029   14.0   1.5    1.6  1  SWIM       SWIM zinc finger


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.8   0.2   2.2e-18     2e-14       4     213 ..     272     449 ..     270     450 .. 0.86

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 2.2e-18
                         DDE_Tnp_1   4 revlivDattvrvpgtkedarwgyk.ggkykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrpr.kgk 78 
                                       + +++vD++ + +  t+++  ++y+ ++  + ++k+hi+  + s++i+++++t+ +v+d+  + +l+ + ++r +  
  gi|298675407|ref|YP_003727157.1| 272 ENIFAVDSSGFSTSVTDTWYEHKYQvKKDERIWMKCHIMAGLDSKIITAAKVTQHRVNDNIPFSDLIYRTAERfNIE 348
                                       6799*********************7777************************************999999999*** PP

                         DDE_Tnp_1  79 lvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyyvt 155
                                        + aD++Y+s+++++ +++ g+++ i+ k+n +          ++r    + ++ ++ ++++ ++            
  gi|298675407|ref|YP_003727157.1| 349 EISADKAYSSKSNIELIRKLGAEPFIPFKNNLTG---------KSRGVSEWAEEYRKFVNNKAEF------------ 404
                                       ****************************887733.........3445566666666666666666............ PP

                         DDE_Tnp_1 156 ntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllaln 213
                                                        +R  +E+vF  +k+kfg   l++r+ ++  +++l + l++n
  gi|298675407|ref|YP_003727157.1| 405 ------------SKHFGNRNKVESVFNMMKSKFG-VQLKSRDEQALINEVLCKVLCHN 449
                                       ............788899****************.66777777777777777777777 PP

>> SWIM  SWIM zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.5   3.3e-06     0.029      16      35 ..     108     127 ..      97     129 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.3e-06
                              SWIM  16 tCsCpefqkngipCkHalAv 35 
                                       +C Cp+ ++   +CkH++Av
  gi|298675407|ref|YP_003727157.1| 108 SCNCPDSEHRITCCKHVYAV 127
                                       7******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (484 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1205  (0.0672095); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.51
# Mc/sec: 2842.34
//
Query:       gi|298675408|ref|YP_003727158.1|  [L=61]
Description: hypothetical protein Metev_1510 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0058   16.6   0.0     0.0069   16.3   0.0    1.0  1  Spore_coat_CotO  Spore coat protein CotO
  ------ inclusion threshold ------
      0.017   15.4   0.0      0.019   15.3   0.0    1.1  1  Kringle          Kringle domain


Domain annotation for each model (and alignments):
>> Spore_coat_CotO  Spore coat protein CotO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   7.7e-07    0.0069     144     187 ..      14      57 ..       9      59 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.7e-07
                   Spore_coat_CotO 144 kclieteektYrgvilerredivsiktfssmeetelaiddItsi 187
                                       k+ + +e+ktY g + e +++ +s+k   + e t++ ++ It i
  gi|298675408|ref|YP_003727158.1|  14 KVSLDAEGKTYHGTVAECNDGVLSLKWDVEDEYTHIEVEKITAI 57 
                                       57889************************************988 PP

>> Kringle  Kringle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   2.1e-06     0.019       3      35 ..      18      50 ..      16      60 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.1e-06
                                      STTSTTC-S---BBTTS-BBE-TTSCSSSCHSS CS
                           Kringle  3 egnGesYrGtvsttesgaeCqaWdsetphkhkk 35
                                      + +G++Y+Gtv++ + g+  ++Wd e +++h +
  gi|298675408|ref|YP_003727158.1| 18 DAEGKTYHGTVAECNDGVLSLKWDVEDEYTHIE 50
                                      578*********************999988755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 386.10
//
Query:       gi|298675409|ref|YP_003727159.1|  [L=531]
Description: ferredoxin-dependent glutamate synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.8e-13   48.7   0.0    1.7e-11   43.8   0.0    2.1  1  Glu_synthase  Conserved region in glutamate synthase


Domain annotation for each model (and alignments):
>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.0   9.8e-16   1.7e-11      61     308 ..     115     413 ..      95     416 .. 0.70

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 9.8e-16
                                       HHHHHTTEE---B-TTTS-HHHHHHHHHHHHHHT-B-EETT..S---GG.GGS-----................... CS
                      Glu_synthase  61 alkikkriltsamSyGalseeahealakamnrlgtksntGE..GGedee.rlktakdv................... 115
                                       +++++ ++ t+a+    ++++  e +a+++   g++  +GE   G+d+e ++  + +v                   
  gi|298675409|ref|YP_003727159.1| 115 KVRMSVPMFTGALGSTDIARKNWEHFAVGAAISGITLVCGEnvCGVDPElKFDGEGKVkespemdrrieaynryheg 191
                                       55666677777777777777777777777777777777777443666651344444447777777778888888888 PP

                                       ...SEEE..E-TT-TT--HHHH..HH-SEEEEE---TTSTTS--EE-GGG--HHHHHHHT...S-TT--EE--SS-T CS
                      Glu_synthase 116 ...aikQ..vasgrFGvteeyL..nnakaleikiaQGakpgeGgqlpgeKvseeiakiRk...ikpgvdliSPaphh 182
                                          +++Q  v     Gv e+    +n++ +eik +QGak   Gg+++ + +   +   R+   ++p  +l S  + +
  gi|298675409|ref|YP_003727159.1| 192 ygeMLVQlnVEDTNLGVAEYLAskHNMETIEIKWGQGAKCI-GGEIKVKTLDRALELKRRgyiVTPDPELSSVQEAY 267
                                       88755552255678899865542246889**********97.***99998888877666544467777777766544 PP

                                       T..............-SSHHHHHHHHHHHHHH-TTSEEEEEEE-STTHHHHHHH..HHHTT-SEEEEE-TT---SSE CS
                      Glu_synthase 183 d..............iysiedlaqliedLkevnkeakvsvKlvaeagvetiaag..vakanadiilidGleGGTGAs 243
                                                      ++++e++ + i  L++++   +v+ K +a + +e+  a    ++a++d+++ dG  GGTG s
  gi|298675409|ref|YP_003727159.1| 268 KvgaireferhsrlgFVDKEEFLEQIDYLHSIG-FDRVTLKTGAYSMTEAAMAMkyGSEAKVDLLTYDGAPGGTGMS 343
                                       3111111111111226788999999*******9.67899***999888876665346899***************** PP

                                       EHHHHHHB---HHHHHHHHHHHH.HHTT-GGG-.EEEEESS--SHHHHHHHHHHT-...SEEE-SHHHHH CS
                      Glu_synthase 244 pkssikhaGlPlelalaevdqtl.keeglrdrv.sliadGglktgadvvkalalGA...davgigtaali 308
                                       p+ ++++ G+P     + v+    k ++  ++v +l ++Gg+ + + + kala+G     av +g+a +i
  gi|298675409|ref|YP_003727159.1| 344 PWPMMEEWGIPAFYLQSLVNDFAdKLNNKGEKVpDLAMAGGFSSEDGIYKALAMGSpyfKAVCMGRALMI 413
                                       ***********876444444333133444555648********************833335556776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (531 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.50
# Mc/sec: 3192.29
//
Query:       gi|298675410|ref|YP_003727160.1|  [L=133]
Description: hypothetical protein Metev_1512 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-23   81.6   3.0    5.4e-23   81.4   3.0    1.0  1  DUF1284   Protein of unknown function (DUF1284)


Domain annotation for each model (and alignments):
>> DUF1284  Protein of unknown function (DUF1284)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.4   3.0     3e-27   5.4e-23       1     102 []      21     124 ..      21     124 .. 0.96

  Alignments for each domain:
  == domain 1  score: 81.4 bits;  conditional E-value: 3e-27
                           DUF1284   1 GYseeFvenmeeiveklkkeeeekielvegaDdiCsacpnk.kelC..eeeekvkelDrkvlealgleegeelklee 74 
                                       GYs++F++nm+ i++ l+++ +  i++++++D iCs cp + +++C  +++++ k++D+ v+++lglee+ +++ e 
  gi|298675410|ref|YP_003727160.1|  21 GYSQDFIKNMKYIINCLNSHGS-LIDIITDCDVICSFCPYNkNGICklNSASDLKKMDELVIDKLGLEEHMVISPEY 96 
                                       9****************99888.6***************965999*988999************************* PP

                           DUF1284  75 llekvkekileekklkeiCgeCeWkelc 102
                                       +++ v++k++++ + +e+Cg+C Wke c
  gi|298675410|ref|YP_003727160.1|  97 AFSLVNKKLQKTLDADEVCGGCIWKEKC 124
                                       **************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 823.14
//
Query:       gi|298675411|ref|YP_003727161.1|  [L=324]
Description: hypothetical protein Metev_1513 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-95  317.2   4.2    7.8e-95  316.7   4.2    1.2  1  NRD1_2    NrpR regulatory domains NRD1 and 2
    6.9e-31  106.0   1.2    1.3e-30  105.1   1.2    1.5  1  HTH_12    Ribonuclease R winged-helix domain
  ------ inclusion threshold ------
      0.014   15.6   0.1      0.032   14.4   0.1    1.6  1  HTH_21    HTH-like domain
       0.12   12.4   0.0       0.29   11.2   0.0    1.6  1  HTH_20    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> NRD1_2  NrpR regulatory domains NRD1 and 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  316.7   4.2   1.8e-98   7.8e-95       2     237 ..      86     322 ..      85     323 .. 0.99

  Alignments for each domain:
  == domain 1  score: 316.7 bits;  conditional E-value: 1.8e-98
                                       --HHHHHHHHHCC---BTTTTB-EEEEEEEEEEGGGHHHHHHHHHHHHHTT-SSSSEEEEEE-SSE.........EE CS
                            NRD1_2   2 gfviskieelaykvtfdpetgkGkVivNlslidkedleealeilkeviksglsvsdrvkileegek.elevpegkvg 77 
                                       +fv+++ieel+y+++fdpet++G+VivN+sl+d++dle+alei+k v ++g+++s+r++i++e+++ +++vpegk++
  gi|298675411|ref|YP_003727161.1|  86 SFVSTRIEELMYRMNFDPETEEGNVIVNISLVDNNDLEDALEIIKIVTANGITISPRIQIFDENSDsKIDVPEGKTA 162
                                       79*************************************************************************** PP

                                       EEEE-CHHHHHHHHCTT--EEEEEEEEEEE-SS.-EEEEEEEESTT-SS-HHHHCGGG.........--SSSEEEEE CS
                            NRD1_2  78 iatvCSitidgvLlknGIpvkpkyGGlleiedkepvrFtelIsYegtsidPlevfiskklTsvlevietgegkilAn 154
                                       iatvCSitidg+Ll++G+pv+p+yGG+l+i+++epv+F++lIsY+gtsidP+++f+s+k Tsvl+v++tg+gkilAn
  gi|298675411|ref|YP_003727161.1| 163 IATVCSITIDGILLNQGVPVEPAYGGTLNIKNNEPVNFQDLISYSGTSIDPIKIFMSRKTTSVLDVLDTGTGKILAN 239
                                       ***************************************************************************** PP

                                       EEEEETTTHHHHHHHHHHH...T-TTEEEE--TT--BTTB---TTEEEEEEE-TTHHHHHHHHTT---EEEEEEEEE CS
                            NRD1_2 155 lReipvsarekveeileklkkagisgvleigepneevlgvpveeekvgivvvgGlnpiaalkeagikveikalsgli 231
                                       +R+ip+sa ek+ ++++++++++i gv+++ge++e v+g+pv+ ++ g+ v+ G+n+i+a++eagi+v + ++s+++
  gi|298675411|ref|YP_003727161.1| 240 MRTIPASASEKALDVINRINASEIGGVIRTGESGEYVFGAPVDFGMSGVPVYVGTNVICAVEEAGIDVATYPVSTVL 316
                                       ***************************************************************************** PP

                                       EGGGSE CS
                            NRD1_2 232 diselk 237
                                       ++s+++
  gi|298675411|ref|YP_003727161.1| 317 EYSNMS 322
                                       *****7 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.1   1.2   2.9e-34   1.3e-30       1      66 []      11      76 ..      11      76 .. 0.99

  Alignments for each domain:
  == domain 1  score: 105.1 bits;  conditional E-value: 2.9e-34
                            HTH_12  1 veILkilaesdkpigakeiaeeLkkrgydigeravRyrLrkleergltrrvgyagreltEkGleeL 66
                                      +eI++i++esdkp+ga+ ia+eL++rgy igeravRy+Lr+l+erg+t++ gy+gr +tE G++eL
  gi|298675411|ref|YP_003727161.1| 11 IEIMRIISESDKPVGARSIADELNNRGYGIGERAVRYHLRILDERGFTKKEGYSGRVITELGEKEL 76
                                      79**************************************************************98 PP

>> HTH_21  HTH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   7.1e-06     0.032       9      52 ..      12      54 ..       3      61 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.1e-06
                            HTH_21  9 lireifeeskgrYGyrriwaeLrreggvrvnhkrVrRlMrelGL 52
                                      +i +i  es    G+r+i+ eL+++g+  ++++ Vr   r l+ 
  gi|298675411|ref|YP_003727161.1| 12 EIMRIISESDKPVGARSIADELNNRGYG-IGERAVRYHLRILDE 54
                                      4778888888999************875.******977776655 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   6.4e-05      0.29      14      54 ..      12      58 ..       2      62 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.4e-05
                                      HHHHHH.STCTTB-HHHHHHHH.....TS-HHHHHHHHHHHHHCTTE CS
                            HTH_20 14 rilraL.araegltaselaerl.....dlskntlsyHLrvLeeagLv 54
                                      +i+r +  +++++ a  +a++l     ++    ++yHLr+L e g+ 
  gi|298675411|ref|YP_003727161.1| 12 EIMRIIsESDKPVGARSIADELnnrgyGIGERAVRYHLRILDERGFT 58
                                      4555557788899999999999777677*************999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1976.07
//
Query:       gi|298675412|ref|YP_003727162.1|  [L=559]
Description: serine/threonine protein kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-38  130.7   0.1    5.2e-38  129.9   0.1    1.5  1  ABC1      ABC1 family
     0.0023   17.3   0.1     0.0049   16.3   0.1    1.5  1  Pkinase   Protein kinase domain
  ------ inclusion threshold ------
      0.019   14.9   0.2       0.05   13.5   0.2    1.6  1  APH       Phosphotransferase enzyme family
       0.11   13.5   5.1       0.17   12.9   2.4    2.3  2  DUF3986   Protein of unknown function (DUF3986)


Domain annotation for each model (and alignments):
>> ABC1  ABC1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.9   0.1   1.2e-41   5.2e-38       2     118 ..     118     235 ..     117     236 .. 0.98

  Alignments for each domain:
  == domain 1  score: 129.9 bits;  conditional E-value: 1.2e-41
                              ABC1   2 elgkkleeiFaefdeePiAaASiaqVhrAklksgeeVavKvqrpgvkkriksDlellkllakllkkflkelr.ldle 77 
                                       +lgk+++e+F+ef eePiA+ASi+qVh Akl +g+eVavKvqrpg++k i+sDl++++ la  +++ +++ + ++ +
  gi|298675412|ref|YP_003727162.1| 118 DLGKDVSEFFSEFREEPIASASIGQVHYAKLLNGDEVAVKVQRPGIRKVIESDLDIMYSLAGFAEQHIEGAElYKPT 194
                                       79**********************************************************************9**** PP

                              ABC1  78 elvdefskslleEldferEAknaekfrenfaklkevkvPkv 118
                                        +vdefsks+  E+d+ rEA n e+f +n++++++++v kv
  gi|298675412|ref|YP_003727162.1| 195 DIVDEFSKSIHAEMDYVREATNIERFSNNLKDDPNIYVHKV 235
                                       **************************************998 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   1.1e-06    0.0049      57     147 ..     227     316 ..     197     335 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.1e-06
                                       CTTB--EEEEEEESSEEEEEEE--TTEB...HHHHHH...HHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGG CS
                           Pkinase  57 hpnivrlyevfeekdelylvleyvegge...ladlle...rkgslseeeakkiakqilegleylHskgiiHrDlKpe 127
                                        pni   + ++    e++l +ey++g +   ++++ e   ++ +++e+  ++++kq+       ++ g++H D  + 
  gi|298675412|ref|YP_003727162.1| 227 DPNIYVHKVFWDFCGEYVLTTEYIRGIKgddFEKIDEygfNRYKIAENGGQSFMKQV-------FEDGVFHADAHSG 296
                                       566666666666677778888887765522244444466666677777777777777.......579********** PP

                                       GEEEETTTEEEE-SGTTSEE CS
                           Pkinase 128 NiLidekgelKitDFGlake 147
                                       N+Li  +g++ + DFG++  
  gi|298675412|ref|YP_003727162.1| 297 NVLIMWDGKIALLDFGMVGY 316
                                       ****************9866 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   1.1e-05      0.05     167     198 ..     287     316 ..     281     318 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.1e-05
                                       EEE-SS-SGGGEEEC..TTEEEEE---TT-EE CS
                               APH 167 vllHgDlhpgNllvdpddgrvtGviDfedagl 198
                                       ++ H D h+gN+l+   dg++ +++Df+++g+
  gi|298675412|ref|YP_003727162.1| 287 GVFHADAHSGNVLIM-WDGKI-ALLDFGMVGY 316
                                       678**********99.88999.*******998 PP

>> DUF3986  Protein of unknown function (DUF3986)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   2.4   3.8e-05      0.17       2      86 ..     199     286 ..     198     290 .. 0.85
   2 ?    0.4   0.0      0.31   1.4e+03      55      87 ..     363     395 ..     336     398 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.8e-05
                           DUF3986   2 nfdesiHlhlgyykdnldlEaiayKrk...nedvWvvyfdf.edygvekdelslskfdkyalfdkyGykvysikakd 74 
                                       +f +siH  ++y+++ +++E      k   n  v  v+ df  +y   ++ ++  k d+++  d+yG++ y+i a++
  gi|298675412|ref|YP_003727162.1| 199 EFSKSIHAEMDYVREATNIERFSNNLKddpNIYVHKVFWDFcGEYVLTTEYIRGIKGDDFEKIDEYGFNRYKI-AEN 274
                                       6899****************88766551125568899***98999999999999999****************.888 PP

                           DUF3986  75 ldeeeasklfee 86 
                                         +++ +++fe+
  gi|298675412|ref|YP_003727162.1| 275 GGQSFMKQVFED 286
                                       888888888886 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.31
                           DUF3986  55 dkyalfdkyGykvysikakdldeeeasklfeew 87 
                                        +y l + yG  +y+i+   + e+    l ++w
  gi|298675412|ref|YP_003727162.1| 363 IEYILNKYYGRPMYHIDGAAMIEDIVAVLRRNW 395
                                       366544559999999988777666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (559 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 3399.03
//
Query:       gi|298675413|ref|YP_003727163.1|  [L=88]
Description: hypothetical protein Metev_1515 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-08   33.1   0.1    5.7e-08   32.9   0.1    1.1  1  DUF3303   Protein of unknown function (DUF3303)


Domain annotation for each model (and alignments):
>> DUF3303  Protein of unknown function (DUF3303)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.1   3.2e-12   5.7e-08      23      89 ..      16      80 ..       3      81 .. 0.94

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 3.2e-12
                           DUF3303 23 rflesGaledkpegfellgrvhapgegrgfaiveaddakalfkhfapWralfGiefeitPvltdeev 89
                                      +++e +++   p g+++ + ++    gr f+++e+dd++   +  +pW++   +e++  Pv++++e+
  gi|298675413|ref|YP_003727163.1| 16 DIMEHFKELKVPSGITIKNQWVDLTGGRYFILFETDDPESYGAFNLPWSDV--CEIDCVPVMESAEF 80
                                      67899999999****************************************..************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 554.61
//
Query:       gi|298675414|ref|YP_003727164.1|  [L=173]
Description: hypothetical protein Metev_1516 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00034   20.5   0.0       0.66   10.0   0.0    2.7  2  Y_Y_Y     Y_Y_Y domain
  ------ inclusion threshold ------
      0.013   16.1   0.3      0.033   14.8   0.2    1.9  1  MBG       MBG domain
      0.015   16.0   0.2       0.12   13.2   0.1    2.4  2  Big_7     Bacterial Ig domain
       0.08   13.2   0.1       0.45   10.8   0.0    2.2  3  Big_6     Bacterial Ig domain
      0.088   13.1   0.1        2.6    8.3   0.0    3.2  2  Gmad2     Immunoglobulin-like domain of bacterial spore germi


Domain annotation for each model (and alignments):
>> Y_Y_Y  Y_Y_Y domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0   0.00098       3.5      34      55 ..     102     123 ..      87     129 .. 0.83
   2 !   10.0   0.0   0.00018      0.66      23      46 ..     135     161 ..     131     169 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00098
                                       ES--SEEEEEEEEEEETTS-B- CS
                             Y_Y_Y  34 tnlppGdYtlkVkakdndgqwn 55 
                                       +n ppG+Y  k+ +k n+g+++
  gi|298675414|ref|YP_003727164.1| 102 SNVPPGTYDTKIHGKANSGESS 123
                                       79**************999876 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00018
                                       EESSTS....EEEEES--SEEEEEEEE CS
                             Y_Y_Y  23 easdysq...easytnlppGdYtlkVk 46 
                                       +a++ ++   ++  + lppGd+tlkV 
  gi|298675414|ref|YP_003727164.1| 135 KADSDGNfsfSYDTSALPPGDFTLKVN 161
                                       5555555533444479*********96 PP

>> MBG  MBG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.2   9.3e-06     0.033      40      84 ..     108     150 ..      54     162 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 9.3e-06
                               MBG  40 DfewktadgnttaptnvGtYtvkLtaaglaklkaa.npNytf..tdak 84 
                                        +++     ++  + n G   v+L+ + l+k+ka+ ++N++f  +++ 
  gi|298675414|ref|YP_003727164.1| 108 TYDT-----KIHGKANSGESSVRLNIQALQKIKADsDGNFSFsyDTSA 150
                                       3333.....355669********************889***9754444 PP

>> Big_7  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.44   1.6e+03      49      70 .]      47      70 ..      30      70 .. 0.77
   2 ?   13.2   0.1   3.4e-05      0.12      26      70 .]      87     160 ..      56     160 .. 0.63

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.44
                                      SSSEEEEEE--.....SEEEEEEE CS
                             Big_7 49 sapysltwttta..ltagthtltV 70
                                      ++ y++ ++  +   + + +t+t+
  gi|298675414|ref|YP_003727164.1| 47 DGMYEYIFNNVDipSPPNRYTVTA 70
                                      577888888877677788888876 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 3.4e-05
                                       E-S.S-EEEEEEEETTEE.............................EEEE-SSSEEEEEE--...SEEEEEEE CS
                             Big_7  26 sdd.ggvskVefyvdgtl.g...........................lgtdtsapysltwtttaltagthtltV 70 
                                       + +  + s V ++ d ++                             + +d+++++s++++t+al+ g  tl+V
  gi|298675414|ref|YP_003727164.1|  87 TRKrKSSSGVAVFEDSNVpPgtydtkihgkansgessvrlniqalqkIKADSDGNFSFSYDTSALPPGDFTLKV 160
                                       555555555555555444323444555555555666666666666679************************98 PP

>> Big_6  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.68   2.4e+03      13      29 ..      19      35 ..      12      50 .. 0.69
   2 ?   -2.7   0.0         2   7.3e+03      35      50 ..      65      80 ..      55      82 .. 0.51
   3 ?   10.8   0.0   0.00013      0.45      14      73 ..     110     167 ..     102     170 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.68
                             Big_6 13 dgttltGkaeagatVtv 29
                                      d  +++Gk  + ++V++
  gi|298675414|ref|YP_003727164.1| 19 DVLKINGKNIPKSEVNI 35
                                      55678899889998876 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2
                             Big_6 35 tvlgtgtadadGeFsv 50
                                      + + t++  ++ +Fsv
  gi|298675414|ref|YP_003727164.1| 65 RYTVTAKNVENVKFSV 80
                                      4444444445555555 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00013
                             Big_6  14 gttltGkaeag.atVtvkdadgtvlgtgtadadGeFsvtlepaqangetlsvvatDaagnt 73 
                                       +t++ Gka  g ++V++     + l++ +ad+dG+Fs++ +++     ++++ + D+a n+
  gi|298675414|ref|YP_003727164.1| 110 DTKIHGKANSGeSSVRLN---IQALQKIKADSDGNFSFSYDTSALPPGDFTLKVNDSAVNV 167
                                       688899998874666655...4678999*************99999999999999999886 PP

>> Gmad2  Immunoglobulin-like domain of bacterial spore germination
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.46   1.6e+03      12      24 ..      16      28 ..      12      48 .. 0.57
   2 ?    8.3   0.0   0.00074       2.6      46      79 ..     127     161 ..     100     166 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.46
                             Gmad2 12 evtspvkvsGkar 24
                                      +v++ +k+ Gk++
  gi|298675414|ref|YP_003727164.1| 16 VVGDVLKINGKNI 28
                                      5677788888765 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00074
                             Gmad2  46 fvtAdeg..apkfgdFeatvefkapepgkgtlevye 79 
                                       +++A ++  a++ g+F+++ + +a++pg+ tl+v  
  gi|298675414|ref|YP_003727164.1| 127 NIQALQKikADSDGNFSFSYDTSALPPGDFTLKV-N 161
                                       4455554447888*******************99.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1073.43
//
Query:       gi|298675415|ref|YP_003727165.1|  [L=103]
Description: hypothetical protein Metev_1517 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.6e-09   37.1   7.4    3.4e-05   23.8   2.2    2.0  2  Phasin     Poly(hydroxyalcanoate) granule associated protein 
    0.00076   19.9   4.3    0.00076   19.9   4.3    1.8  2  BMFP       Membrane fusogenic activity
  ------ inclusion threshold ------
      0.011   15.8   0.6      0.013   15.6   0.6    1.1  1  Spo0A_C    Sporulation initiation factor Spo0A C terminal
      0.016   15.4   2.6      0.016   15.4   2.6    3.0  3  Osmo_CC    Osmosensory transporter coiled coil
      0.033   15.0   2.6       0.26   12.1   2.6    2.1  1  DUF3349    Protein of unknown function (DUF3349)
      0.058   12.9   9.1      0.065   12.8   9.1    1.1  1  DUF1002    Protein of unknown function (DUF1002)
      0.079   12.8   0.4      0.079   12.8   0.4    2.0  2  sCache_2   Single Cache domain 2
       0.08   13.5  11.2        0.1   13.2  11.2    1.1  1  PRESAN     Plasmodium RESA N-terminal
       0.22   11.7   6.5       0.33   11.1   6.5    1.3  1  Uds1       Up-regulated During Septation
       0.32   11.4  10.1       0.16   12.4   1.6    2.6  3  CLZ        C-terminal leucine zipper domain of cyclic nucleot
       0.48   11.5   8.4        1.6    9.8   4.3    2.3  2  RNase_J_C  Ribonuclease J C-terminal domain
       0.76   10.4   9.1       0.82   10.2   3.1    2.2  2  YtxH       YtxH-like protein
        1.6    9.0  10.4        2.3    8.4  10.4    1.2  1  Fib_alpha  Fibrinogen alpha/beta chain family
        4.6    7.2  10.2       0.45   10.4   0.4    2.9  3  MtrG       Tetrahydromethanopterin S-methyltransferase, subun
        5.3    6.2   9.8        5.9    6.0   9.8    1.0  1  TMPIT      TMPIT-like protein
        6.3    7.1  11.1         20    5.4   5.8    2.5  2  XhlA       Haemolysin XhlA


Domain annotation for each model (and alignments):
>> Phasin  Poly(hydroxyalcanoate) granule associated protein (phasin)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.9     2e-06    0.0023      17      65 ..       7      55 ..       2      58 .. 0.89
   2 !   23.8   2.2   3.1e-08   3.4e-05      78     125 ..      53     100 ..      47     101 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2e-06
                            Phasin 17 qiWLAGLGafakvqeeGsklfeaLvkeGeklekktkkvaeekleevres 65
                                      +  L G+Ga+a ++e+ ++ +e+Lv++Ge  ++++k+ ++e + e r++
  gi|298675415|ref|YP_003727165.1|  7 KLALMGIGAWALTEEKINETVEELVQKGELSREEGKNLVNEMIAERRKQ 55
                                      55688***********************************999887755 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 3.1e-08
                            Phasin  78 eeqwdklekafdervakaLsrlgvpsredveaLsarvdeLtkelekla 125
                                        +q + +e+ + e+v+++ ++ +++++ed ++L++++d+++++le+l+
  gi|298675415|ref|YP_003727165.1|  53 RKQKEDIENKISEKVQETFEQSNIATKEDYNNLEEKIDQIQNTLEELK 100
                                       578899***************************************986 PP

>> BMFP  Membrane fusogenic activity
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.8    0.0068       7.6      28      72 ..      19      63 ..       3      63 .. 0.91
   2 !   19.9   4.3   6.7e-07   0.00076      12      71 ..      43     102 ..      39     103 .] 0.93

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0068
                              BMFP 28 ieknvravlqealsklDLVtREEFdvqrevlartrekleaLearv 72
                                       e+++ + ++e+++k +L + E   ++ e++a+ r++ e  e ++
  gi|298675415|ref|YP_003727165.1| 19 TEEKINETVEELVQKGELSREEGKNLVNEMIAERRKQKEDIENKI 63
                                      5899999***********888889****************99987 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 6.7e-07
                              BMFP  12 kkvgdalpaaagvreeieknvravlqealsklDLVtREEFdvqrevlartrekleaLear 71 
                                       + v++ +++  + +e+ie+++ + +qe++++ ++ t+E++  + e + + +  le+L+++
  gi|298675415|ref|YP_003727165.1|  43 NLVNEMIAERRKQKEDIENKISEKVQETFEQSNIATKEDYNNLEEKIDQIQNTLEELKEK 102
                                       6788888888899********************************************987 PP

>> Spo0A_C  Sporulation initiation factor Spo0A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.6   1.1e-05     0.013       5      81 ..       8      84 ..       5      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                           Spo0A_C  5 LrklGipaklkGykylreaielvledpellesitkelypevAkkykttpsrVeraIrhaIevaWekgnkekleelfg 81
                                      L  +Gi a     + + e +e ++++ el  +  k+l +e+  +  ++++ +e++I + ++ ++e++n+ + e++ +
  gi|298675415|ref|YP_003727165.1|  8 LALMGIGAWALTEEKINETVEELVQKGELSREEGKNLVNEMIAERRKQKEDIENKISEKVQETFEQSNIATKEDYNN 84
                                      6778888888889999****************************************************998887765 PP

>> Osmo_CC  Osmosensory transporter coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.8       1.2   1.4e+03      26      32 ..      25      31 ..      19      56 .. 0.56
   2 ?    0.3   2.0      0.78   8.7e+02      15      21 ..      57      63 ..      36      73 .. 0.56
   3 ?   15.4   2.6   1.4e-05     0.016      11      35 ..      79     103 .]      77     103 .] 0.95

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.2
                                      HHHHHHH CS
                           Osmo_CC 26 eeIaaLe 32
                                      e +++L 
  gi|298675415|ref|YP_003727165.1| 25 ETVEELV 31
                                      3333333 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.78
                                      THHHHHH CS
                           Osmo_CC 15 dnIEqkv 21
                                      ++IE+k+
  gi|298675415|ref|YP_003727165.1| 57 EDIENKI 63
                                      3445444 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 1.4e-05
                                       XXXXTHHHHHHHHHHHHHHHHHHHH CS
                           Osmo_CC  11 qehYdnIEqkvedideeIaaLeekR 35 
                                       +e Y+n E+k+++i + +++L+ek+
  gi|298675415|ref|YP_003727165.1|  79 KEDYNNLEEKIDQIQNTLEELKEKK 103
                                       699********************97 PP

>> DUF3349  Protein of unknown function (DUF3349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.6   0.00023      0.26      24      75 ..       8      72 ..       2     100 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00023
                                      HHHHHHHCTT--HHHHHHHHHHHHHH-............-..SSS.BSHHHCHHHHHHHCTS--- CS
                           DUF3349 24 vpLlalLrrrLsdeevkevaeelvaea............a.eadeavdeedieelitkvteeeps 75
                                      ++L+ + +  L++e+++e +eelv+++            +  a+++ ++edie+ i++ ++e+ +
  gi|298675415|ref|YP_003727165.1|  8 LALMGIGAWALTEEKINETVEELVQKGelsreegknlvnEmIAERRKQKEDIENKISEKVQETFE 72
                                      67888888899999999999999999955444444443312333344444444444444444444 PP

>> DUF1002  Protein of unknown function (DUF1002)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   9.1   5.8e-05     0.065     124     207 ..      17      95 ..       9     103 .] 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.8e-05
                           DUF1002 124 kldeekkeaAneeLvttselaekigsekaaelvaevkeevakeklkteeeikkiveevanelninlsdeqiqqivnl 200
                                       +l+eek++   eeLv+ +el+    +e+ ++lv+e+ +e  k+k++ e++i++ v+e+ ++ ni  + e+ +++ + 
  gi|298675415|ref|YP_003727165.1|  17 ALTEEKINETVEELVQKGELS----REEGKNLVNEMIAERRKQKEDIENKISEKVQETFEQSNIATK-EDYNNLEEK 88 
                                       578899999999999999998....888889999999999999999999999999999999999854.445555555 PP

                           DUF1002 201 lkkiqkl 207
                                       +++iq++
  gi|298675415|ref|YP_003727165.1|  89 IDQIQNT 95 
                                       5555544 PP

>> sCache_2  Single Cache domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.4   7.1e-05     0.079      21      52 ..      25      56 ..      18      58 .. 0.89
   2 ?    1.1   0.9      0.28   3.2e+02      21      50 ..      65      94 ..      54     103 .] 0.57

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.1e-05
                          sCache_2 21 eavykqvesgkiteeeaqeevkelvnglkfgd 52
                                      e v++ v++g++++ee + +v e++ + ++++
  gi|298675415|ref|YP_003727165.1| 25 ETVEELVQKGELSREEGKNLVNEMIAERRKQK 56
                                      78999********************9988765 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.28
                          sCache_2 21 eavykqvesgkiteeeaqeevkelvnglkf 50
                                      e+v++ +e+++i  +e   + +e++ ++++
  gi|298675415|ref|YP_003727165.1| 65 EKVQETFEQSNIATKEDYNNLEEKIDQIQN 94
                                      455555555555555555555555555543 PP

>> PRESAN  Plasmodium RESA N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2  11.2     9e-05       0.1       2      83 ..      18     101 ..      17     103 .] 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9e-05
                                       --HHHHHHHHT-S..-SEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHH CS
                            PRESAN   2 lteeelnklinsl..neviskkdmyiiwnyvmknekkkyknmikkLsnyleelakkynipeeykkklwkeckneitk 76 
                                       ltee++n+ +++l  + ++s+++  ++ n+ +   +k+ +++++k+s++++e+ ++ ni  ++  + ++e  ++i++
  gi|298675415|ref|YP_003727165.1|  18 LTEEKINETVEELvqKGELSREEGKNLVNEMIAERRKQKEDIENKISEKVQETFEQSNIATKEDYNNLEEKIDQIQN 94 
                                       79999999999998889999999999999999999999999999999999999999999888776667777777777 PP

                                       HHHHHHH CS
                            PRESAN  77 elkklek 83 
                                       +l++l++
  gi|298675415|ref|YP_003727165.1|  95 TLEELKE 101
                                       7776654 PP

>> Uds1  Up-regulated During Septation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   6.5    0.0003      0.33      51     111 ..      38     102 ..      17     103 .] 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0003
                              Uds1  51 rdaarsLsrlyssskksak....ssaarsnskssreslakaeeelaeserkvdelaselekleer 111
                                       r+  ++L + ++++++++k    ++ +++ +++ ++s+  ++e+++++e+k+d+++++le+l+e+
  gi|298675415|ref|YP_003727165.1|  38 REEGKNLVNEMIAERRKQKedieNKISEKVQETFEQSNIATKEDYNNLEEKIDQIQNTLEELKEK 102
                                       6667778777777777777788744444555555678999**********************986 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       2.2   2.4e+03      29      36 ..      23      30 ..      17      40 .. 0.53
   2 ?    3.9   1.5      0.06        67      13      34 ..      43      64 ..      30      79 .. 0.79
   3 ?   12.4   1.6   0.00014      0.16      16      46 ..      72     102 ..      67     103 .] 0.83

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.2
                               CLZ 29 leekverL 36
                                      ++e ve+L
  gi|298675415|ref|YP_003727165.1| 23 INETVEEL 30
                                      23333332 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.06
                               CLZ 13 glLDeeaakagaeqkeleekve 34
                                      +l  e  a+++++++++e+k++
  gi|298675415|ref|YP_003727165.1| 43 NLVNEMIAERRKQKEDIENKIS 64
                                      788899999999******9995 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00014
                               CLZ  16 DeeaakagaeqkeleekverLessLeaLqtr 46 
                                       ++++ + +++ ++leek+++++++Le L+ +
  gi|298675415|ref|YP_003727165.1|  72 EQSNIATKEDYNNLEEKIDQIQNTLEELKEK 102
                                       555556678999****************986 PP

>> RNase_J_C  Ribonuclease J C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1       0.1   1.1e+02      44      58 ..      19      33 ..       1      52 [. 0.58
   2 ?    9.8   4.3    0.0014       1.6      13      50 ..      54      91 ..      50     103 .] 0.86

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.1
                         RNase_J_C 44 lkrkirealkkflyk 58
                                       ++ki e+++++++k
  gi|298675415|ref|YP_003727165.1| 19 TEEKINETVEELVQK 33
                                      455555555554443 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0014
                         RNase_J_C 13 keseeLieeakkvvretieealeekesdwnelkrkire 50
                                      k++e++ ++++++v+et e+++  ++ d+n+l++ki +
  gi|298675415|ref|YP_003727165.1| 54 KQKEDIENKISEKVQETFEQSNIATKEDYNNLEEKIDQ 91
                                      78899*****************************9964 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   3.1   0.00074      0.82      24      71 ..      24      71 ..      17      75 .. 0.78
   2 ?    5.8   5.6     0.018        20      35      72 ..      61     101 ..      50     103 .] 0.44

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00074
                              YtxH 24 ketRkdlkekaddlkekakelleeakekakekaedlkekvkekadelk 71
                                      +et ++l++k + ++e  k+l++e+    +++ ed+ +k++ek++e  
  gi|298675415|ref|YP_003727165.1| 24 NETVEELVQKGELSREEGKNLVNEMIAERRKQKEDIENKISEKVQETF 71
                                      688888888888888888888888887778888888888888888754 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.018
                              YtxH  35 ddlkekakelleeakekakek...aedlkekvkekadelke 72 
                                       ++++ek++e+ e+ +  +ke     e+  ++++++ +elke
  gi|298675415|ref|YP_003727165.1|  61 NKISEKVQETFEQSNIATKEDynnLEEKIDQIQNTLEELKE 101
                                       34444444444444444444411144444444444555555 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4  10.4     0.002       2.3      39     116 ..      26     101 ..      17     102 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.002
                                       CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHH CS
                         Fib_alpha  39 kleneleeisnstkeaeelvkeikdslrekqkskkdn.dnvikksskeleeeilrlketidaqesnirvLqnvlesn 114
                                       ++e+ +++ + s +e ++lv+e+      + k+k+d  +++ +k++++ e+  +  ke  ++ e++i ++qn+le++
  gi|298675415|ref|YP_003727165.1|  26 TVEELVQKGELSREEGKNLVNEMIAE---RRKQKEDIeNKISEKVQETFEQSNIATKEDYNNLEEKIDQIQNTLEEL 99 
                                       23444455555555555555555544...444444432556667888888888888888888888888888888777 PP

                                       HH CS
                         Fib_alpha 115 eq 116
                                       ++
  gi|298675415|ref|YP_003727165.1| 100 KE 101
                                       65 PP

>> MtrG  Tetrahydromethanopterin S-methyltransferase, subunit G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.3      0.28   3.2e+02      20      39 ..      21      42 ..      18      48 .. 0.59
   2 ?    1.2   0.5      0.29   3.3e+02      19      33 ..      56      70 ..      45      75 .. 0.61
   3 ?   10.4   0.4    0.0004      0.45       6      28 ..      76      98 ..      73     102 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.28
                              MtrG 20 deieekvefv..nsEiaqriGk 39
                                      ++i+e+ve    ++E+++  Gk
  gi|298675415|ref|YP_003727165.1| 21 EKINETVEELvqKGELSREEGK 42
                                      4566666643114666666666 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.29
                              MtrG 19 LdeieekvefvnsEi 33
                                       ++ie+k+     E 
  gi|298675415|ref|YP_003727165.1| 56 KEDIENKISEKVQET 70
                                      456666665555554 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.0004
                              MtrG  6 vvdpddfnevkkrLdeieekvef 28
                                      ++ ++d+n++++++d+i++++e 
  gi|298675415|ref|YP_003727165.1| 76 IATKEDYNNLEEKIDQIQNTLEE 98
                                      56789**************9985 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   9.8    0.0053       5.9      12      87 ..      25     101 ..      15     103 .] 0.78

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0053
                             TMPIT  12 keleetakeykqkleelsklqskcskeikkqkkrlk.elksslkklkksvkeeeeeeveelkeelkerkkvlkeves 87 
                                       +++ee  ++ + + ee ++l +++  e +kqk++++ +++++++++ ++++  ++e +++l+e++++++++l+e+++
  gi|298675415|ref|YP_003727165.1|  25 ETVEELVQKGELSREEGKNLVNEMIAERRKQKEDIEnKISEKVQETFEQSNIATKEDYNNLEEKIDQIQNTLEELKE 101
                                       344555555566778889999999999999998885268899999999999999*****************999875 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.2     0.038        42      15      40 ..      22      47 ..      19      51 .. 0.87
   2 ?    5.4   5.8     0.018        20      22      48 ..      70      96 ..      49     102 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.038
                              XhlA 15 nleervdkleekaaeaeekiknleed 40
                                      +++e+v++l +k +  +e+ knl ++
  gi|298675415|ref|YP_003727165.1| 22 KINETVEELVQKGELSREEGKNLVNE 47
                                      6789999***************9775 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.018
                              XhlA 22 kleekaaeaeekiknleedlkklesnq 48
                                      + e+ +  ++e   nlee+++++++++
  gi|298675415|ref|YP_003727165.1| 70 TFEQSNIATKEDYNNLEEKIDQIQNTL 96
                                      456666777777777777777777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      4066  (0.226783); expected 358.6 (0.02)
Passed bias filter:                     1168  (0.0651459); expected 358.6 (0.02)
Passed Vit filter:                       164  (0.00914719); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 627.61
//
Query:       gi|298675416|ref|YP_003727166.1|  [L=572]
Description: ABC transporter-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-53  180.2   0.0    6.1e-28   98.1   0.0    2.4  2  ABC_tran       ABC transporter
    2.6e-08   34.0  12.7     0.0029   17.5   0.5    4.4  3  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
    1.9e-07   31.1   1.6    0.00052   20.0   0.2    2.5  2  RsgA_GTPase    RsgA GTPase
    2.5e-07   30.3   2.2     0.0095   15.7   0.1    2.5  2  AAA_29         P-loop containing region of AAA domain
    8.3e-07   29.4   1.6       0.11   12.8   0.0    3.8  4  AAA_22         AAA domain
    1.2e-06   29.0   0.1      0.043   14.2   0.0    2.7  2  AAA_16         AAA ATPase domain
    1.5e-06   28.1   0.0      0.063   13.0   0.0    2.5  2  AAA_30         AAA domain
      1e-05   25.1   1.5      0.017   14.6   0.0    4.0  4  TniB           Bacterial TniB protein
    1.7e-05   24.9   0.5       0.45   10.4   0.0    3.4  3  ATPase_2       ATPase domain predominantly from Archaea
    3.5e-05   23.5   0.3        0.3   10.7   0.0    2.6  2  cobW           CobW/HypB/UreG, nucleotide-binding domain
    7.5e-05   22.9   0.5      0.024   14.8   0.1    3.4  2  SbcCD_C        Putative exonuclease SbcCD, C subunit
    8.8e-05   22.4   0.2       0.38   10.7   0.1    2.4  2  MobB           Molybdopterin guanine dinucleotide synthesis p
    0.00013   21.3   0.2       0.23   10.6   0.1    2.4  2  NB-ARC         NB-ARC domain
    0.00015   22.3  12.6      0.011   16.3   0.3    3.1  3  AAA_23         AAA domain
    0.00015   21.6   5.3    0.00083   19.2   0.2    2.9  2  AAA_15         AAA ATPase domain
    0.00099   18.9   0.2       0.33   10.7   0.2    2.3  2  PRK            Phosphoribulokinase / Uridine kinase family
     0.0011   18.3   0.0       0.73    9.1   0.0    2.3  2  Zeta_toxin     Zeta toxin
     0.0013   19.3   0.3        1.3    9.6   0.1    3.5  3  AAA_18         AAA domain
     0.0025   17.4   0.2        1.6    8.3   0.1    3.4  3  AAA_25         AAA domain
     0.0029   16.7   0.0       0.15   11.1   0.0    2.2  2  T2SSE          Type II/IV secretion system protein
      0.003   16.4   2.2        1.7    7.4   0.1    3.5  4  ABC_ATPase     Predicted ATPase of the ABC class
     0.0031   17.7   0.2        0.8    9.9   0.0    2.7  2  AAA_33         AAA domain
     0.0039   16.4   0.4        2.9    7.0   0.0    3.5  4  PIF1           PIF1-like helicase
     0.0041   16.9   0.2        1.6    8.5   0.0    2.4  2  PduV-EutP      Ethanolamine utilisation - propanediol utilisa
     0.0045   17.0   0.2        1.9    8.5   0.0    2.4  2  TsaE           Threonylcarbamoyl adenosine biosynthesis prote
     0.0059   16.5   4.1       0.91    9.4   0.3    3.0  2  NACHT          NACHT domain
     0.0071   15.5   0.3       0.52    9.4   0.0    2.5  2  G-alpha        G-protein alpha subunit
  ------ inclusion threshold ------
       0.01   15.7   0.7       0.53   10.2   0.1    2.5  2  NTPase_1       NTPase
      0.012   16.0   0.2         38    4.7   0.0    4.0  4  AAA            ATPase family associated with various cellular
      0.012   15.3   0.5          6    6.5   0.0    2.5  2  AAA_24         AAA domain
      0.014   15.4   0.7        8.9    6.4   0.0    2.8  2  MMR_HSR1       50S ribosome-binding GTPase
      0.019   15.2   0.8        4.2    7.6   0.1    2.6  2  AAA_28         AAA domain
      0.025   14.5   0.1        8.7    6.2   0.0    2.3  2  APS_kinase     Adenylylsulphate kinase
      0.026   14.0   0.3         12    5.3   0.0    3.0  3  PhoH           PhoH-like protein
      0.041   13.9   0.3         19    5.3   0.2    3.5  3  AAA_14         AAA domain
      0.071   11.9   0.3          9    5.0   0.1    2.3  2  DLIC           Dynein light intermediate chain (DLIC)
      0.073   13.2   0.8         13    5.8   0.0    2.7  2  DUF87          Helicase HerA, central domain
       0.08   12.9   0.1        4.2    7.2   0.0    2.4  2  Rad17          Rad17 P-loop domain
        0.1   12.1   0.2         15    4.9   0.0    2.5  2  Pox_A32        Poxvirus A32 protein
       0.13   11.2   0.2        4.3    6.1   0.0    2.2  2  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
       0.23   10.1   1.1        6.8    5.2   0.1    2.5  3  AAA_13         AAA domain
       0.23   10.8   1.1         12    5.2   0.2    2.7  2  ATPase         KaiC


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.8   0.0   5.9e-25   2.5e-22       1     136 [.      21     180 ..      21     181 .. 0.87
   2 !   98.1   0.0   1.4e-30   6.1e-28       2     136 ..     285     490 ..     284     491 .. 0.87

  Alignments for each domain:
  == domain 1  score: 79.8 bits;  conditional E-value: 5.9e-25
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS.--S-T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx.xxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqe.pqlfp 72 
                                       l+ ++l ++ ge+++i+G++G+GK+tLl+++ g ++ + G i ldg+ ++     + +++l+ + ++  q    l+ 
  gi|298675416|ref|YP_003727166.1|  21 LDGINLAVNDGEILGITGRSGSGKTTLLRIIRGVENFDGGIIDLDGNVITPesgyEGKRFLNLNTAIHLQRsFGLWA 97 
                                       789**********************************************9977776666666677666666555555 PP

                                       TSBHHHH.....................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSS CS
                                       xxxxxxx.....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  73 eltvren.....................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpk 128
                                       +  + en                     +++e  ++als l+l++l+++ + +s + LSgG+kqr+ lar l  kp+
  gi|298675416|ref|YP_003727166.1|  98 GP-AIENiirklnffysgdeslpsedspYYEELYNTALSYLKLVGLENKAL-HSSNFLSGGEKQRLILARQLSAKPR 172
                                       55.3444799999**9999999888887777779***********999999.66799******************** PP

                                       EEEEESTT CS
                                       xxxxxxxx RF
                          ABC_tran 129 llllDEpt 136
                                        lllDEp 
  gi|298675416|ref|YP_003727166.1| 173 ALLLDEPV 180
                                       *******6 PP

  == domain 2  score: 98.1 bits;  conditional E-value: 1.4e-30
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET.TCEGGG.....B-HHHCCHCEEEE-SS--S-T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx.....xxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilld.gkdlke.....qeleslrkeigvlpqepqlfp 72 
                                       kn+sl+++ege++a+vG++GaGK+tLlk++ gl++p++G+i +  + d+ +      ++ +lr++i+ ++qe  l p
  gi|298675416|ref|YP_003727166.1| 285 KNLSLDINEGEITAFVGSSGAGKTTLLKMIEGLHEPDNGKICYLhNGDWVDishysLQRMELRRKISLMHQEFILPP 361
                                       8****************************************65546666666667778999**************** PP

                                       TSBHHHH......................................HHHTCHHHHHHHSTTGG............... CS
                                       xxxxxxx......................................xxxxxxxxxxxxxxxxx............... RF
                          ABC_tran  73 eltvren......................................esdeeiekalsklglke............... 96 
                                       ++t+re+                                       s++e +++l+klg +e               
  gi|298675416|ref|YP_003727166.1| 362 HSTLREQiafklkikregaigyarkkadelgisdelldliyklpdMSEDEKSDILQKLGVTEniyyelfpeieqedv 438
                                       ********************************************955556666666666666666666666666667 PP

                                       ............TTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  97 ............lkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                   l  +v+++ ++++SgG+ +r  +a ++ + p++l+lDEp+
  gi|298675416|ref|YP_003727166.1| 439 esyareifdaldLSMDVLDKTTYQMSGGEHVRAFIALSMSTSPEILMLDEPF 490
                                       7777777666668889999999*****************************6 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.5   6.8e-06    0.0029       3      52 ..      35      67 ..      33      85 .. 0.67
   2 ?    4.5   0.4     0.062        26     155     301 ..      95     215 ..      75     217 .. 0.77
   3 !   13.2   1.1   0.00013     0.056       1      24 [.     296     319 ..     296     527 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.8e-06
                            AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldly 52
                                      +++G+ gsGK++LL++++++  +                 ++ +  ld++
  gi|298675416|ref|YP_003727166.1| 35 GITGRSGSGKTTLLRIIRGVENF-----------------DGGIIDLDGN 67
                                      79***************998654.................3333333333 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.062
                            AAA_21 155 lllldglrke.rigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgq 230
                                       l+   ++ +  r++++++++d+  +++  ++ ++l++  +     + +++   +   s++++               
  gi|298675416|ref|YP_003727166.1|  95 LWAGPAIENIiRKLNFFYSGDESLPSEDSPYYEELYNTALSYLKLVGLEN---KALHSSNFL--------------- 153
                                       44444445557999999999999999999999999999999999998884...444444444............... PP

                            AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSpll 301
                                              S G k+   +l+  l+a +  + ll+DEp +   P    ++l+++k+l++  ++ +++ +H p++
  gi|298675416|ref|YP_003727166.1| 154 -------SGGEKQR-LILARQLSAKP--RALLLDEPVTMTGPDTKQEILDVIKSLKNrLNIPILVISHLPEI 215
                                       .......*******.88888888887..99******999999999999999988888789999999998876 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 0.00013
                            AAA_21   1 lnvliGpNgsGKSnLLdaldllar 24 
                                       +++++G  g+GK++LL+ +++l+ 
  gi|298675416|ref|YP_003727166.1| 296 ITAFVGSSGAGKTTLLKMIEGLHE 319
                                       799*****************9963 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.1    0.0016      0.68      85     122 ..      16      54 ..       5      64 .. 0.79
   2 !   20.0   0.2   1.2e-06   0.00052      73     122 ..     267     317 ..     206     330 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0016
                                       TTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  85 ktkegleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                       ++k+ l+ ++ +++d ++  + G SG GK+tL+  +++ 
  gi|298675416|ref|YP_003727166.1|  16 EKKRILDGINLAVNDgEILGITGRSGSGKTTLLRIIRGV 54 
                                       55666677777777779999*************999875 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 1.2e-06
                                       HHTTSEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  73 ealgyevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                       ++l  ++ l+++ +  ++++l+  +++ +++++vG+SG+GK+tL++++ + 
  gi|298675416|ref|YP_003727166.1| 267 QNLSRRLSLIRVGEVLSIKNLSLDINEgEITAFVGSSGAGKTTLLKMIEGL 317
                                       5555556666667777888898888888******************99875 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.3   9.2e-05     0.039      23      39 ..      31      48 ..      20      51 .. 0.78
   2 !   15.7   0.1   2.2e-05    0.0095      15      39 ..     287     311 ..     273     325 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.2e-05
                            AAA_29 23 g.atlltGpsGsGKSTll 39
                                      g +  +tG+sGsGK+Tll
  gi|298675416|ref|YP_003727166.1| 31 GeILGITGRSGSGKTTLL 48
                                      34777***********98 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 2.2e-05
                            AAA_29  15 htieidlkgatlltGpsGsGKSTll 39 
                                        +++i++ ++t ++G sG+GK+Tll
  gi|298675416|ref|YP_003727166.1| 287 LSLDINEGEITAFVGSSGAGKTTLL 311
                                       567788666***************8 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.2     0.001      0.45       6      23 ..      32      49 ..      28      54 .. 0.86
   2 ?    2.1   0.0       0.5   2.2e+02      61     128 ..     137     209 ..     124     219 .. 0.76
   3 !   12.8   0.0   0.00025      0.11       5      40 ..     294     320 ..     291     404 .. 0.75
   4 ?   -2.0   0.0       9.1   3.9e+03      86     128 ..     476     519 ..     423     525 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.001
                            AAA_22  6 gilvvtGesGtGKTtllr 23
                                       il +tG sG+GKTtllr
  gi|298675416|ref|YP_003727166.1| 32 EILGITGRSGSGKTTLLR 49
                                      67889***********98 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.5
                            AAA_22  61 lralglelkaerlsseell.ealeqalrarav...ielliiDEaqhlr....seealeeLrsllnlsrkgvqliLv 128
                                       l+ +gle+ka  +ss  l     ++ + ar+    +++l++DE   ++    ++e+l  ++sl n  r +++++++
  gi|298675416|ref|YP_003727166.1| 137 LKLVGLENKA-LHSSNFLSgGEKQRLILARQLsakPRALLLDEPVTMTgpdtKQEILDVIKSLKN--RLNIPILVI 209
                                       5566666666.66666666777777777777788888******9999776544999999999999..998988876 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 0.00025
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerp 40 
                                         i++ +G sG+GKTtll+++   +         +p
  gi|298675416|ref|YP_003727166.1| 294 GEITAFVGSSGAGKTTLLKMIEGLH---------EP 320
                                       568999*************999887.........33 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 9.1
                            AAA_22  86 lrarav..ielliiDEaqh.lr..s.eealeeLrsllnlsrkgvqliLv 128
                                       +       +e+l++DE    l+  +  ++ + L+s+ +   +g++++Lv
  gi|298675416|ref|YP_003727166.1| 476 SM---StsPEILMLDEPFGdLDpiTlRDVTNSLKSINK--NFGTTIVLV 519
                                       22...244477888874333543335666666666666..777777766 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.1   0.00053      0.23      19      44 ..      28      51 ..      15      62 .. 0.82
   2 !   14.2   0.0    0.0001     0.043      22     107 ..     292     403 ..     284     488 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00053
                            AAA_16 19 vrsgrpelvllsGesGvGKsslvrel 44
                                      v++g  e++ ++G sG+GK++l+r +
  gi|298675416|ref|YP_003727166.1| 28 VNDG--EILGITGRSGSGKTTLLRII 51
                                      4444..8999*************865 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 0.0001
                            AAA_16  22 grpelvllsGesGvGKsslvrellralekd..g.giflrgkcdqlesaipysalaqalareellrqlldeaesaele 95 
                                       +++e++ ++G sG GK++l++++    e d  + +++ +g++++     +y   +q     el r++  ++++  l+
  gi|298675416|ref|YP_003727166.1| 292 NEGEITAFVGSSGAGKTTLLKMIEGLHEPDngKiCYLHNGDWVDI---SHY--SLQRM---ELRRKISLMHQEFILP 360
                                       4558999*************9999766666653455588888888...333..44444...6777777775553333 PP

                            AAA_16  96 awrekleeala................................a 107
                                       ++++ l+e++a                                 
  gi|298675416|ref|YP_003727166.1| 361 PHST-LREQIAfklkikregaigyarkkadelgisdelldliyK 403
                                       3333.444444445555555555555444444444444444443 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00024       0.1      14      41 ..      28      54 ..      22      69 .. 0.80
   2 !   13.0   0.0   0.00015     0.063      19      50 ..     295     326 ..     288     330 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00024
                            AAA_30 14 ltsgdrvavltGpAGtGKttalkalrea 41
                                      +++g  +  +tG+ G+GKtt+l+ +r +
  gi|298675416|ref|YP_003727166.1| 28 VNDG-EILGITGRSGSGKTTLLRIIRGV 54
                                      4444.5899**************99876 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00015
                            AAA_30  19 rvavltGpAGtGKttalkalreaweaaggrvi 50 
                                        +++ +G  G+GKtt+lk ++ ++e ++g+++
  gi|298675416|ref|YP_003727166.1| 295 EITAFVGSSGAGKTTLLKMIEGLHEPDNGKIC 326
                                       58999******************999877776 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1       1.5   6.6e+02      39      53 ..      35      49 ..      29      53 .. 0.87
   2 !   14.6   0.0   3.9e-05     0.017     111     159 ..     162     208 ..     121     221 .. 0.76
   3 ?    2.6   0.0      0.18        76      39      63 ..     298     322 ..     292     326 .. 0.87
   4 ?    3.2   0.0      0.12        52     112     160 ..     473     519 ..     434     527 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.5
                              TniB 39 llvGdsnnGKtmive 53
                                       + G+s  GKt++++
  gi|298675416|ref|YP_003727166.1| 35 GITGRSGSGKTTLLR 49
                                      589*********986 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 3.9e-05
                              TniB 111 vlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivl 159
                                       +l+   + k+r L++DE   +     ++++e+l ++ksL+n+l+ipi +
  gi|298675416|ref|YP_003727166.1| 162 ILARQLSAKPRALLLDEPVTMT--GPDTKQEILDVIKSLKNRLNIPILV 208
                                       44444456899******98877..5566678***************976 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.18
                              TniB  39 llvGdsnnGKtmivekFarlhppek 63 
                                        +vG s  GKt++++  + lh+p++
  gi|298675416|ref|YP_003727166.1| 298 AFVGSSGAGKTTLLKMIEGLHEPDN 322
                                       689************9999998875 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.12
                              TniB 112 lrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlv 160
                                       ++l  ++++++L++DE    l     + r ++n+lks++ ++  +ivlv
  gi|298675416|ref|YP_003727166.1| 473 IALSMSTSPEILMLDEPFGDL--DPITLRDVTNSLKSINKNFGTTIVLV 519
                                       555556778899999955544..5778899*****************98 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0037       1.6      19      40 ..      30      51 ..      19      59 .. 0.84
   2 ?    2.3   0.0      0.31   1.3e+02      85     141 ..     170     225 ..     118     251 .. 0.70
   3 !   10.4   0.0    0.0011      0.45      18      73 ..     292     347 ..     277     450 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0037
                          ATPase_2 19 pneiyfiYGpegsGKtaLlkei 40
                                        ei+ i+G+ gsGKt+Ll+ i
  gi|298675416|ref|YP_003727166.1| 30 DGEILGITGRSGSGKTTLLRII 51
                                      567999*************854 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.31
                          ATPase_2  85 avpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaell 141
                                       + +   l+e +  +  + ++ i ++++++k++   +i++i  l+++  ++l     +
  gi|298675416|ref|YP_003727166.1| 170 KPRALLLDEPVTMTGPDTKQEILDVIKSLKNRLNIPILVISHLPEIH-MYLSDRVIY 225
                                       33334445555578889999999*********999*****9999999.666644444 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.0011
                          ATPase_2  18 epneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeee 73 
                                       ++ ei    G+ g GKt+Llk i   +e  + ++ y+ +   ++is+++    e +
  gi|298675416|ref|YP_003727166.1| 292 NEGEITAFVGSSGAGKTTLLKMIEGLHEPDNGKICYLHNGDWVDISHYSLQRMELR 347
                                       556777778***********9988888888889***************98822332 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.2   0.00097      0.42       2      19 ..      33      50 ..      32      62 .. 0.86
   2 !   10.7   0.0   0.00069       0.3       2      23 ..     296     319 ..     295     346 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00097
                                      EEEEEESTTCCHHHHHHH CS
                              cobW  2 vtvltGflGsGKTtLlnh 19
                                      ++++tG  GsGKTtLl+ 
  gi|298675416|ref|YP_003727166.1| 33 ILGITGRSGSGKTTLLRI 50
                                      5789************85 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00069
                                       EEEEEESTTCCHHHHHHHHH..CT CS
                              cobW   2 vtvltGflGsGKTtLlnhll..en 23 
                                       +t ++G+ G+GKTtLl+ +   ++
  gi|298675416|ref|YP_003727166.1| 296 ITAFVGSSGAGKTTLLKMIEglHE 319
                                       57899***********98754444 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1      0.15        65      28      43 ..     148     163 ..     131     196 .. 0.78
   2 !   14.8   0.1   5.7e-05     0.024      26      88 ..     456     505 ..     438     507 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.15
                           SbcCD_C  28 rssgtlSGGekqflay 43 
                                       +ss+ lSGGekq l+ 
  gi|298675416|ref|YP_003727166.1| 148 HSSNFLSGGEKQRLIL 163
                                       677889*****98764 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 5.7e-05
                           SbcCD_C  26 lsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllell 88 
                                       l++ + ++SGGe+ +        a+ al  s     +++++++LDE F+ lD+ +++ + + l
  gi|298675416|ref|YP_003727166.1| 456 LDKTTYQMSGGEH-V-------RAFIALSMS-----TSPEILMLDEPFGDLDPITLRDVTNSL 505
                                       6788889999999.2.......222333333.....5789*************9999988776 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1   0.00088      0.38       1      17 [.      33      49 ..      33      58 .. 0.88
   2 !    9.4   0.0    0.0021      0.91       3      19 ..     298     314 ..     296     336 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00088
                              MobB  1 vlgivgksgsGKTtLle 17
                                      +lgi+g+sgsGKTtLl 
  gi|298675416|ref|YP_003727166.1| 33 ILGITGRSGSGKTTLLR 49
                                      799************95 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0021
                              MobB   3 givgksgsGKTtLlekl 19 
                                       ++vg sg+GKTtLl+ +
  gi|298675416|ref|YP_003727166.1| 298 AFVGSSGAGKTTLLKMI 314
                                       79***********9754 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.1   0.00053      0.23      17      40 ..      30      51 ..      17      59 .. 0.84
   2 !    8.1   0.0    0.0031       1.3      17      41 ..     293     315 ..     280     351 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00053
                                      TSCSEEEEEEESTTSSHHHHHHHH CS
                            NB-ARC 17 elqslvvalvGmgGvGKttlakqi 40
                                      + +  ++++ G+ G+GKttl++ i
  gi|298675416|ref|YP_003727166.1| 30 DGE--ILGITGRSGSGKTTLLRII 51
                                      445..9**************9755 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0031
                                       TSCSEEEEEEESTTSSHHHHHHHHC CS
                            NB-ARC  17 elqslvvalvGmgGvGKttlakqil 41 
                                       e +  + a+vG  G GKttl+k i 
  gi|298675416|ref|YP_003727166.1| 293 EGE--ITAFVGSSGAGKTTLLKMIE 315
                                       334..889*************9884 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.3   0.00012     0.052      20      40 ..      32      52 ..      19      54 .. 0.82
   2 ?   -1.6   0.1       7.3   3.1e+03     132     176 ..     212     264 ..     152     278 .. 0.58
   3 !   16.3   0.3   2.6e-05     0.011       8      39 ..     282     314 ..     275     317 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00012
                            AAA_23 20 gltlItGpNGaGKTTildAik 40
                                       +  ItG  G+GKTT+l+ i+
  gi|298675416|ref|YP_003727166.1| 32 EILGITGRSGSGKTTLLRIIR 52
                                      5678*************9997 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 7.3
                            AAA_23 132 lnlilflgqer......feefelkdkkerleelekeleeledekkllekl..e 176
                                       l+ i ++ ++r      ++ +++ ++++ l+++ k+l+   +  +  +k+  +
  gi|298675416|ref|YP_003727166.1| 212 LPEIHMYLSDRviylenQKIIDEGEPEKVLKNFLKKLQPSIELSDVHNKKpcI 264
                                       33333333444444443444444555566666666666666666655555554 PP

  == domain 3  score: 16.3 bits;  conditional E-value: 2.6e-05
                            AAA_23   8 rsfrdqeidFsk.gltlItGpNGaGKTTildAi 39 
                                        s+++ ++d +   +t+++G  GaGKTT+l  i
  gi|298675416|ref|YP_003727166.1| 282 LSIKNLSLDINEgEITAFVGSSGAGKTTLLKMI 314
                                       58899999995537****************877 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   1.1      0.16        70      28      48 ..      36      56 ..      23     270 .. 0.50
   2 !   19.2   0.2   1.9e-06   0.00083      13     175 ..     283     462 ..     283     521 .. 0.64

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.16
                            AAA_15 28 liGkNnsGKSsilealdlFln 48
                                      + G+ +sGK+++l+++    n
  gi|298675416|ref|YP_003727166.1| 36 ITGRSGSGKTTLLRIIRGVEN 56
                                      568888999999998854444 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1.9e-06
                            AAA_15  13 slkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekkn..........................kkvikiek 62 
                                       s+k+ ++d++e  +t ++G  ++GK+++l++++ + + +   n                          k  +  ++
  gi|298675416|ref|YP_003727166.1| 283 SIKNLSLDINEGeITAFVGSSGAGKTTLLKMIEGLHEPD---NgkicylhngdwvdishyslqrmelrrKISLMHQE 356
                                       6899999*99999********************999988...43346666666665555555555555322222222 PP

                            AAA_15  63 edleifeniseskdikIdvefaekekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisve 139
                                         l       e + +k++++    e a+ y + ++++       +l +++ +l ++++d+k ++ ++   +e+i++e
  gi|298675416|ref|YP_003727166.1| 357 FILPPHSTLREQIAFKLKIKR---EGAIGYARKKADE-L-GISDELLDLIYKLPDMSEDEKSDILQKLGVTENIYYE 428
                                       223333333333444444444...2333333333322.2.2222455566667777777777777777777777777 PP

                            AAA_15 140 kkkskkelpkekeeklekekeelkidkedlkklikk 175
                                          ++ + ++e  +++ +  + l++  + l+k+ ++
  gi|298675416|ref|YP_003727166.1| 429 LFPEIEQEDVE--SYAREIFDALDLSMDVLDKTTYQ 462
                                       76666554433..44444566666666666666665 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.2   0.00078      0.33       1      20 [.      33      52 ..      33      61 .. 0.89
   2 ?    6.0   0.0     0.021         9       3      21 ..     298     316 ..     296     349 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00078
                               PRK  1 vIgvagsSGaGkttvarkle 20
                                      ++g++g SG+Gktt+ r ++
  gi|298675416|ref|YP_003727166.1| 33 ILGITGRSGSGKTTLLRIIR 52
                                      78************999876 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.021
                               PRK   3 gvagsSGaGkttvarklek 21 
                                       +  gsSGaGktt+ + +e 
  gi|298675416|ref|YP_003727166.1| 298 AFVGSSGAGKTTLLKMIEG 316
                                       567**********998875 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0081       3.5      21      52 ..      36      67 ..      26     107 .. 0.87
   2 !    9.1   0.0    0.0017      0.73      21      41 ..     299     319 ..     284     332 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0081
                        Zeta_toxin 21 lgGqpGAGKselaellkdelerqgnvvrldpD 52
                                      + G +G+GK++l++ ++   + +g+++ ld+ 
  gi|298675416|ref|YP_003727166.1| 36 ITGRSGSGKTTLLRIIRGVENFDGGIIDLDGN 67
                                      6799************9988889999999876 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0017
                        Zeta_toxin  21 lgGqpGAGKselaellkdele 41 
                                        +G++GAGK++l+++++  +e
  gi|298675416|ref|YP_003727166.1| 299 FVGSSGAGKTTLLKMIEGLHE 319
                                       579*************98876 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.1     0.003       1.3       2      24 ..      35      57 ..      34      84 .. 0.81
   2 ?    0.5   0.0         2   8.4e+02      15      67 ..     195     247 ..     193     264 .. 0.81
   3 ?    4.4   0.0      0.12        52       4      19 ..     300     315 ..     298     355 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.003
                            AAA_18  2 lltGtpGvGKttlakeLskrlgf 24
                                      ++tG +G+GKttl + ++  ++f
  gi|298675416|ref|YP_003727166.1| 35 GITGRSGSGKTTLLRIIRGVENF 57
                                      59************999654455 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 2
                            AAA_18  15 akeLskrlgfgvnlrdvakenglllevdpealdeskrldedkldklldaleen 67 
                                        k L++rl++ + +++ ++e +++l++    l+++k++de+  +k+l+++ + 
  gi|298675416|ref|YP_003727166.1| 195 IKSLKNRLNIPILVISHLPEIHMYLSDRVIYLENQKIIDEGEPEKVLKNFLKK 247
                                       56777777777788888888899999888899*************99999886 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.12
                            AAA_18   4 tGtpGvGKttlakeLs 19 
                                        G +G+GKttl k ++
  gi|298675416|ref|YP_003727166.1| 300 VGSSGAGKTTLLKMIE 315
                                       6999*******99875 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.099        42      32      50 ..      30      48 ..      14      49 .. 0.85
   2 !    8.3   0.1    0.0037       1.6      30      50 ..     291     311 ..     285     316 .. 0.92
   3 ?    0.6   0.0      0.82   3.5e+02     168     188 ..     501     521 ..     495     523 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.099
                            AAA_25 32 agelallaGapgtGKttla 50
                                       ge+  ++G++g+GKttl+
  gi|298675416|ref|YP_003727166.1| 30 DGEILGITGRSGSGKTTLL 48
                                      57777899*********96 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0037
                            AAA_25  30 lpagelallaGapgtGKttla 50 
                                       + +ge+++++G +g+GKttl+
  gi|298675416|ref|YP_003727166.1| 291 INEGEITAFVGSSGAGKTTLL 311
                                       689****************96 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.82
                            AAA_25 168 lvealeriarrtgaavllvhH 188
                                       + + l++i +++g +++lv H
  gi|298675416|ref|YP_003727166.1| 501 VTNSLKSINKNFGTTIVLVSH 521
                                       678999*********999998 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00034      0.15     113     149 ..      15      51 ..       3      85 .. 0.87
   2 ?    3.2   0.0     0.092        39     134     163 ..     299     328 ..     283     362 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00034
                             T2SSE 113 alkekiaevlrkavrerglilvsGgTgsGKttllyal 149
                                       + k++i + ++ av+   ++ ++G  gsGKttll ++
  gi|298675416|ref|YP_003727166.1|  15 SEKKRILDGINLAVNDGEILGITGRSGSGKTTLLRII 51 
                                       56788999999**99999999************9875 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.092
                             T2SSE 134 vsGgTgsGKttllyallkeinksderivtv 163
                                       + G  g GKttll ++    + ++ +i+ +
  gi|298675416|ref|YP_003727166.1| 299 FVGSSGAGKTTLLKMIEGLHEPDNGKICYL 328
                                       6799*********99877777777777765 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.019       8.1     240     264 ..      26      51 ..      10      59 .. 0.80
   2 ?    0.9   0.0      0.35   1.5e+02     376     420 ..     191     235 ..     154     255 .. 0.84
   3 !    7.4   0.1    0.0039       1.7     241     265 ..     290     315 ..     283     326 .. 0.89
   4 ?   -2.8   0.0       4.9   2.1e+03     377     412 ..     502     537 ..     495     538 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.019
                                       EEE-SS.EEEEEE-TTSSHHHHHHHH CS
                        ABC_ATPase 240 mgipkG.vtlIvGggfhGKsTLLeAl 264
                                       +++  G +  I+G+   GK+TLL+ +
  gi|298675416|ref|YP_003727166.1|  26 LAVNDGeILGITGRSGSGKTTLLRII 51 
                                       5678888999*************966 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.35
                                       HHHCHHHHHHHH--EEEEEESS-GCCTTT-SEEEEEETTEEEE-H CS
                        ABC_ATPase 376 lvdrvrelykklgvstilvvggsgdyldvAdtvilmeeykpkdvt 420
                                       ++d +++l ++l++ +++++   +  + ++d+vi++e+ k+ d  
  gi|298675416|ref|YP_003727166.1| 191 ILDVIKSLKNRLNIPILVISHLPEIHMYLSDRVIYLENQKIIDEG 235
                                       67899999999999988888888999999*******998887765 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0039
                                       EE-SS.EEEEEE-TTSSHHHHHHHHH CS
                        ABC_ATPase 241 gipkG.vtlIvGggfhGKsTLLeAle 265
                                        i +G +t+ vG+   GK+TLL+ +e
  gi|298675416|ref|YP_003727166.1| 290 DINEGeITAFVGSSGAGKTTLLKMIE 315
                                       588999*****************997 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 4.9
                                       HHCHHHHHHHH--EEEEEESS-GCCTTT-SEEEEEE CS
                        ABC_ATPase 377 vdrvrelykklgvstilvvggsgdyldvAdtvilme 412
                                       ++ ++++ k++g +++lv+  ++   +vA++ il++
  gi|298675416|ref|YP_003727166.1| 502 TNSLKSINKNFGTTIVLVSHHMDFVNEVAHRAILVN 537
                                       567788999999999999999999999999999876 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.063        27       5      17 ..      37      49 ..      34      63 .. 0.90
   2 !    9.9   0.0    0.0019       0.8       3      17 ..     298     312 ..     296     333 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.063
                            AAA_33  5 vGlpGsGKstlae 17
                                       G +GsGK+tl++
  gi|298675416|ref|YP_003727166.1| 37 TGRSGSGKTTLLR 49
                                      599*******987 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0019
                            AAA_33   3 llvGlpGsGKstlae 17 
                                        +vG +G+GK+tl++
  gi|298675416|ref|YP_003727166.1| 298 AFVGSSGAGKTTLLK 312
                                       69***********87 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0067       2.9       3      43 ..      14      52 ..      12      61 .. 0.87
   2 ?    2.8   0.0      0.12        52      18      43 ..     290     315 ..     281     326 .. 0.82
   3 ?   -1.9   0.0       3.4   1.4e+03     115     142 ..     442     467 ..     436     472 .. 0.73
   4 ?    2.0   0.0      0.22        92     110     145 ..     482     518 ..     449     526 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0067
                                      -HHHHHHHHHH......HCTS-EEEEESTTSSCHHHHHHHH CS
                              PIF1  3 neeQkkvfdaiieavlnekgklfFvtGsgGtgKtflwkall 43
                                       +e k+++d i   +  + g+++ +tG +G+gKt l++ + 
  gi|298675416|ref|YP_003727166.1| 14 GSEKKRILDGI--NLAVNDGEILGITGRSGSGKTTLLRIIR 52
                                      57899999999..677789******************9875 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.12
                                       ..HCTS-EEEEESTTSSCHHHHHHHH CS
                              PIF1  18 lnekgklfFvtGsgGtgKtflwkall 43 
                                         ++g++  + Gs+G+gKt l+k + 
  gi|298675416|ref|YP_003727166.1| 290 DINEGEITAFVGSSGAGKTTLLKMIE 315
                                       45788999999***********9885 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3.4
                                       BHHHHHHHHHHHHHHCT-...-SCCCC- CS
                              PIF1 115 erecfealdrtlrdilkekeidkpFGGk 142
                                        re+f+ald ++  + k+ +  +  GG 
  gi|298675416|ref|YP_003727166.1| 442 AREIFDALDLSMDVLDKT-T-YQMSGGE 467
                                       699******998655555.3.4666775 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.22
                                       CGGGSBHHHHHHHH.HHHHHHCT-....-SCCCC-EEE CS
                              PIF1 110 Eapmverecfeald.rtlrdilkeke.idkpFGGktvv 145
                                       E+ m++   f  ld  tlrd++++ + i+k FG  +v 
  gi|298675416|ref|YP_003727166.1| 482 EILMLDE-PFGDLDpITLRDVTNSLKsINKNFGTTIVL 518
                                       6667664.577787458*****99888*****987765 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.025        11       6      23 ..      36      53 ..      32      58 .. 0.85
   2 !    8.5   0.0    0.0037       1.6       5      24 ..     298     317 ..     295     327 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.025
                         PduV-EutP  6 liGkvgsGKttLtqalkg 23
                                      + G++gsGKttL + ++g
  gi|298675416|ref|YP_003727166.1| 36 ITGRSGSGKTTLLRIIRG 53
                                      569*********999987 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0037
                         PduV-EutP   5 lliGkvgsGKttLtqalkge 24 
                                        ++G++g+GKttL + ++g 
  gi|298675416|ref|YP_003727166.1| 298 AFVGSSGAGKTTLLKMIEGL 317
                                       599************99985 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.027        12      19      39 ..      31      51 ..      13      58 .. 0.78
   2 !    8.5   0.0    0.0045       1.9      14      39 ..     291     314 ..     273     322 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.027
                                      TEEEEEEESTTSSHHHHHHHH CS
                              TsaE 19 gdvilLeGdLGaGKTtlvrgl 39
                                      g+++ ++G  G+GKTtl r +
  gi|298675416|ref|YP_003727166.1| 31 GEILGITGRSGSGKTTLLRII 51
                                      678999***********9965 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0045
                                       HHHCHTEEEEEEESTTSSHHHHHHHH CS
                              TsaE  14 lakalgdvilLeGdLGaGKTtlvrgl 39 
                                       + +  g++ ++ G  GaGKTtl + +
  gi|298675416|ref|YP_003727166.1| 291 INE--GEITAFVGSSGAGKTTLLKMI 314
                                       333..77899************9976 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.3    0.0021      0.91       5      20 ..      36      51 ..      32      53 .. 0.86
   2 !    7.3   0.1    0.0093         4       4      20 ..     298     314 ..     295     324 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0021
                                      EEC-TTTCHHHHHHHH CS
                             NACHT  5 lqGeaGsGKTtLlqkl 20
                                      ++G++GsGKTtLl+ +
  gi|298675416|ref|YP_003727166.1| 36 ITGRSGSGKTTLLRII 51
                                      89***********865 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0093
                                       EEEC-TTTCHHHHHHHH CS
                             NACHT   4 ilqGeaGsGKTtLlqkl 20 
                                       +  G +G GKTtLl+ +
  gi|298675416|ref|YP_003727166.1| 298 AFVGSSGAGKTTLLKMI 314
                                       678***********976 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.064        28      28      44 ..      36      52 ..      24     217 .. 0.93
   2 !    9.4   0.0    0.0012      0.52      28      50 ..     299     321 ..     290     472 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.064
                                      EEESTTSSHHHHHHHHH CS
                           G-alpha 28 llGqseSGKsTilkqlk 44
                                      + G s+SGK+T+l+ ++
  gi|298675416|ref|YP_003727166.1| 36 ITGRSGSGKTTLLRIIR 52
                                      5799*********9887 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0012
                                       EEESTTSSHHHHHHHHHHHCS-- CS
                           G-alpha  28 llGqseSGKsTilkqlkllykkg 50 
                                       ++G+s+ GK+T+lk ++ l+++ 
  gi|298675416|ref|YP_003727166.1| 299 FVGSSGAGKTTLLKMIEGLHEPD 321
                                       79******************886 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1    0.0012      0.53       3      20 ..      35      52 ..      33      80 .. 0.75
   2 ?    3.5   0.1      0.14        61       6      20 ..     301     315 ..     297     326 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0012
                                      EEE--TTSSHHHHHHHHH CS
                          NTPase_1  3 fiTGppGvGKtTlvkkvl 20
                                       iTG++G+GKtTl++ + 
  gi|298675416|ref|YP_003727166.1| 35 GITGRSGSGKTTLLRIIR 52
                                      69***********98664 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.14
                                       --TTSSHHHHHHHHH CS
                          NTPase_1   6 GppGvGKtTlvkkvl 20 
                                       G++G GKtTl+k + 
  gi|298675416|ref|YP_003727166.1| 301 GSSGAGKTTLLKMIE 315
                                       999*******98775 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.18        77       3      18 ..      36      51 ..      34      89 .. 0.82
   2 ?    0.4   0.0       1.9     8e+02      45     111 ..     158     212 ..     129     251 .. 0.67
   3 ?    4.7   0.0     0.088        38       3      18 ..     299     314 ..     297     349 .. 0.91
   4 ?    1.3   0.0         1   4.4e+02      32      66 ..     456     488 ..     431     510 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.18
                                      EESSTTSSHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakav 18
                                      ++G  G GKT+l + +
  gi|298675416|ref|YP_003727166.1| 36 ITGRSGSGKTTLLRII 51
                                      5799********9988 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS CS
                               AAA  45 kirelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr 111
                                       k r +++  ++ + kp  l++DE   +++ +          + +++l +++ +k++ + + ++++++ 
  gi|298675416|ref|YP_003727166.1| 158 KQRLILA--RQLSaKPRALLLDEPVTMTGPD----------TKQEILDVIKSLKNRLN-IPILVISHL 212
                                       4555553..3333457777777766666555..........56666666666666555.666555554 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.088
                                       EESSTTSSHHHHHHHH CS
                               AAA   3 lyGppGtGKTllakav 18 
                                       ++G  G GKT+l k +
  gi|298675416|ref|YP_003727166.1| 299 FVGSSGAGKTTLLKMI 314
                                       89**********9987 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 1
                                       TTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEET CS
                               AAA  32 sellskyvgesekkirelfkeakekakpsilfiDE 66 
                                        + +  y+  + +++r++++   + + p il++DE
  gi|298675416|ref|YP_003727166.1| 456 LDKT-TYQMSGGEHVRAFIALSMSTS-PEILMLDE 488
                                       3333.5889999999**999877777.9******9 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1     0.016       6.9       6      22 ..      35      51 ..      31      71 .. 0.82
   2 ?    6.5   0.0     0.014         6       7      22 ..     299     314 ..     295     328 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.016
                            AAA_24  6 liyGpsgiGKTtlakel 22
                                       i+G sg+GKTtl++ +
  gi|298675416|ref|YP_003727166.1| 35 GITGRSGSGKTTLLRII 51
                                      699*********99865 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.014
                            AAA_24   7 iyGpsgiGKTtlakel 22 
                                        +G+sg+GKTtl+k++
  gi|298675416|ref|YP_003727166.1| 299 FVGSSGAGKTTLLKMI 314
                                       58***********987 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1     0.022       9.5       3      19 ..      35      51 ..      33      63 .. 0.87
   2 ?    6.4   0.0     0.021       8.9       3      19 ..     298     314 ..     296     324 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.022
                                      EEEESTTSSHHHHHHHH CS
                          MMR_HSR1  3 aivGrpNvGKStLinal 19
                                      +i Gr+ +GK+tL++ +
  gi|298675416|ref|YP_003727166.1| 35 GITGRSGSGKTTLLRII 51
                                      89************976 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.021
                                       EEEESTTSSHHHHHHHH CS
                          MMR_HSR1   3 aivGrpNvGKStLinal 19 
                                       a+vG + +GK+tL++ +
  gi|298675416|ref|YP_003727166.1| 298 AFVGSSGAGKTTLLKMI 314
                                       89***********9876 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.043        18       4      19 ..      36      51 ..      34      76 .. 0.84
   2 ?    7.6   0.1    0.0099       4.2       3      20 ..     298     315 ..     296     331 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.043
                            AAA_28  4 itGgestGKTtlleaL 19
                                      itG +++GKTtll+ +
  gi|298675416|ref|YP_003727166.1| 36 ITGRSGSGKTTLLRII 51
                                      89**********9976 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0099
                            AAA_28   3 vitGgestGKTtlleaLa 20 
                                       +++G +++GKTtll+ ++
  gi|298675416|ref|YP_003727166.1| 298 AFVGSSGAGKTTLLKMIE 315
                                       799***********8765 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.024        10       3      40 ..      32      68 ..      30      72 .. 0.70
   2 ?    6.2   0.0      0.02       8.7       5      41 ..     297     334 ..     293     356 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.024
                                      EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHH CS
                        APS_kinase  3 vvvwltGlsgsGKstianalekkLvekgisvylLdGdn 40
                                       ++ +tG sgsGK+t+ + +   +++    ++ LdG++
  gi|298675416|ref|YP_003727166.1| 32 EILGITGRSGSGKTTLLRIIR-GVENFDGGIIDLDGNV 68
                                      56779**********987765.4444444556666665 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.02
                                       EEEESSTTSSHHHHHHHHHHHHH.HTT--EEEEEHHHH CS
                        APS_kinase   5 vwltGlsgsGKstianalekkLv.ekgisvylLdGdnv 41 
                                         + G sg+GK+t+ +++e   + ++g+ +yl +Gd v
  gi|298675416|ref|YP_003727166.1| 297 TAFVGSSGAGKTTLLKMIEGLHEpDNGKICYLHNGDWV 334
                                       5689**********999995444245688888899876 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.027        12      16      35 ..      28      47 ..      13      63 .. 0.71
   2 ?    5.0   0.0     0.034        15      16      35 ..     291     310 ..     283     328 .. 0.76
   3 ?   -1.4   0.0       3.1   1.3e+03      72      92 ..     434     454 ..     428     471 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.027
                                      HHH-SEEEEE--TTSSTTHH CS
                              PhoH 16 lkkndivfaiGpaGtGKtyl 35
                                      +++ +i+ ++G++G+GKt l
  gi|298675416|ref|YP_003727166.1| 28 VNDGEILGITGRSGSGKTTL 47
                                      346789***********865 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.034
                                       HHH-SEEEEE--TTSSTTHH CS
                              PhoH  16 lkkndivfaiGpaGtGKtyl 35 
                                       +++ +i+  +G++G+GKt l
  gi|298675416|ref|YP_003727166.1| 291 INEGEITAFVGSSGAGKTTL 310
                                       67889************865 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 3.1
                                       ------TTTHHHHHHHTTTS- CS
                              PhoH  72 leekvdpylrplydaLkdllg 92 
                                       ++e v+ y r + daL+  ++
  gi|298675416|ref|YP_003727166.1| 434 EQEDVESYAREIFDALDLSMD 454
                                       68999***********97775 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.2     0.044        19       3      20 ..      32      49 ..      30      62 .. 0.88
   2 ?   -0.8   0.0       3.4   1.5e+03      51      90 ..     157     202 ..     125     227 .. 0.65
   3 ?    4.0   0.0      0.11        47       3      35 ..     295     327 ..     293     356 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.044
                            AAA_14  3 kilvitGaRrvGKTtllk 20
                                      +il itG   +GKTtll+
  gi|298675416|ref|YP_003727166.1| 32 EILGITGRSGSGKTTLLR 49
                                      7999************96 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 3.4
                            AAA_14  51 kllelilek.lkeekktylflDEiqev......pewekalkslvdeg 90 
                                       +  +lil++ l++ k + l+lDE   +      +e+ +++ksl ++ 
  gi|298675416|ref|YP_003727166.1| 157 EKQRLILARqLSA-KPRALLLDEPVTMtgpdtkQEILDVIKSLKNRL 202
                                       4456666653555.788899999766667666666677777766655 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.11
                            AAA_14   3 kilvitGaRrvGKTtllkqlikell.vkkesily 35 
                                       +i + +G   +GKTtllk + + l   ++ +i y
  gi|298675416|ref|YP_003727166.1| 295 EITAFVGSSGAGKTTLLKMI-EGLHePDNGKICY 327
                                       5777889999******9765.3333345555555 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.021         9      30      52 ..      36      58 ..      28      62 .. 0.85
   2 ?    4.7   0.0     0.026        11      30      55 ..     299     324 ..     279     333 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.021
                              DLIC 30 vlGedgsGkttliaklqGveeek 52
                                      + G +gsGkttl+  ++Gve+  
  gi|298675416|ref|YP_003727166.1| 36 ITGRSGSGKTTLLRIIRGVENFD 58
                                      67999***************865 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.026
                              DLIC  30 vlGedgsGkttliaklqGveeekkGr 55 
                                        +G +g+Gkttl+  + G+ e+  G+
  gi|298675416|ref|YP_003727166.1| 299 FVGSSGAGKTTLLKMIEGLHEPDNGK 324
                                       6899****************999986 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.2     0.056        24      26      43 ..      34      51 ..      31      56 .. 0.91
   2 ?    5.8   0.0      0.03        13       2      43 ..     277     314 ..     276     354 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.056
                             DUF87 26 lAilgsTGsGKSntvavL 43
                                      l+i g++GsGK+++ +++
  gi|298675416|ref|YP_003727166.1| 34 LGITGRSGSGKTTLLRII 51
                                      6899**********9987 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.03
                             DUF87   2 eiGrllsgsevpvyldlnklvtrHlAilgsTGsGKSntvavL 43 
                                       ++G++ls ++  ++ld+n+   + +A +gs+G+GK+++ + +
  gi|298675416|ref|YP_003727166.1| 277 RVGEVLSIKN--LSLDINEG--EITAFVGSSGAGKTTLLKMI 314
                                       6777776665..77777776..77999**********99865 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0099       4.2      33      65 ..      19      51 ..      12      56 .. 0.84
   2 ?    2.9   0.0      0.21        89      39      66 ..     288     315 ..     272     328 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0099
                             Rad17 33 ewlkadvLesrkkriLLisGPsGCgkstvvkvL 65
                                      + l+   L  +  +iL i+G sG gk+t ++++
  gi|298675416|ref|YP_003727166.1| 19 RILDGINLAVNDGEILGITGRSGSGKTTLLRII 51
                                      56677777778889***************9986 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.21
                             Rad17  39 vLesrkkriLLisGPsGCgkstvvkvLs 66 
                                       +L+ ++ +i    G sG gk+t +k++ 
  gi|298675416|ref|YP_003727166.1| 288 SLDINEGEITAFVGSSGAGKTTLLKMIE 315
                                       5566666788899***********9876 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.036        15      16      31 ..      34      49 ..       6      55 .. 0.90
   2 ?    4.5   0.0     0.047        20      17      31 ..     298     312 ..     290     319 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.036
                           Pox_A32 16 lalvGgsGsGktvyLl 31
                                      l ++G sGsGkt+ L+
  gi|298675416|ref|YP_003727166.1| 34 LGITGRSGSGKTTLLR 49
                                      5699********9885 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.047
                           Pox_A32  17 alvGgsGsGktvyLl 31 
                                       a+vG sG+Gkt+ L+
  gi|298675416|ref|YP_003727166.1| 298 AFVGSSGAGKTTLLK 312
                                       89**********987 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1      0.11        47      18      43 ..      34      58 ..      19      74 .. 0.74
   2 ?    6.1   0.0      0.01       4.3      14      55 ..     293     333 ..     281     343 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.11
                     TrwB_AAD_bind 18 ilivGttGsGKtqalekllrairarg 43
                                      + i+G  GsGKt+ l+ ++r++++  
  gi|298675416|ref|YP_003727166.1| 34 LGITGRSGSGKTTLLR-IIRGVENFD 58
                                      569*********8765.777776655 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.01
                     TrwB_AAD_bind  14 etqhilivGttGsGKtqalekllrairargdraivlDltGaf 55 
                                       e + +++vG+ G+GKt+   k+++++ +  +  i +  +G+ 
  gi|298675416|ref|YP_003727166.1| 293 EGEITAFVGSSGAGKTTL-LKMIEGLHEPDNGKICYLHNGDW 333
                                       5566899********985.57899888888877777666665 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.016       6.8      23      41 ..      38      56 ..      33      65 .. 0.89
   2 ?    2.6   0.0     0.097        41      23      41 ..     301     319 ..     294     344 .. 0.82
   3 ?   -2.4   0.0       3.2   1.4e+03     528     579 ..     482     531 ..     477     558 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.016
                            AAA_13 23 GwNGaGKTtLSrllrslel 41
                                      G+ G+GKTtL r++r +e+
  gi|298675416|ref|YP_003727166.1| 38 GRSGSGKTTLLRIIRGVEN 56
                                      999************9975 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.097
                            AAA_13  23 GwNGaGKTtLSrllrslel 41 
                                       G+ GaGKTtL ++++ l +
  gi|298675416|ref|YP_003727166.1| 301 GSSGAGKTTLLKMIEGLHE 319
                                       899***********99853 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 3.2
                            AAA_13 528 kivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiL.THnleffkevkk 579
                                       +i ++D P   LD   l  v + +ks     k++   ++L  H+++f +ev  
  gi|298675416|ref|YP_003727166.1| 482 EILMLDEPFGDLDPITLRDVTNSLKSIN---KNFGTTIVLvSHHMDFVNEVAH 531
                                       6777788888888888888888887775...6665544442688888888765 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.2     0.028        12      18      35 ..      30      47 ..      20      61 .. 0.84
   2 ?    3.2   0.1      0.11        49      16      35 ..     291     310 ..     286     318 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.028
                            ATPase 18 egrvvlitGepGtGKtif 35
                                      +g++  itG +G+GKt++
  gi|298675416|ref|YP_003727166.1| 30 DGEILGITGRSGSGKTTL 47
                                      688999**********97 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.11
                            ATPase  16 ipegrvvlitGepGtGKtif 35 
                                       i eg+++  +G++G+GKt++
  gi|298675416|ref|YP_003727166.1| 291 INEGEITAFVGSSGAGKTTL 310
                                       67899*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (572 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                        42  (0.00234257); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              42  [number of targets reported over threshold]
# CPU time: 0.81u 0.34s 00:00:01.15 Elapsed: 00:00:00.52
# Mc/sec: 3283.88
//
Query:       gi|298675417|ref|YP_003727167.1|  [L=248]
Description: geranylgeranylglyceryl phosphate synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.6e-67  225.3   0.8    7.8e-67  225.0   0.8    1.0  1  PcrB            PcrB family
    3.7e-07   29.8   0.1    9.3e-07   28.5   0.0    1.7  2  His_biosynth    Histidine biosynthesis protein
     0.0019   17.4   0.5      0.012   14.8   0.1    2.0  2  NanE            Putative N-acetylmannosamine-6-phosphate epim
  ------ inclusion threshold ------
      0.037   13.4   0.1      0.064   12.6   0.1    1.4  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
      0.046   13.1   0.1      0.087   12.2   0.1    1.4  1  G3P_antiterm    Glycerol-3-phosphate responsive antiterminato
      0.093   12.9   1.5        1.6    8.9   0.2    2.1  2  MlrC_C          MlrC C-terminus
       0.17   11.2   4.8       0.18   11.1   0.9    2.2  2  ThiG            Thiazole biosynthesis protein ThiG


Domain annotation for each model (and alignments):
>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.0   0.8   3.1e-70   7.8e-67       2     224 ..       9     243 ..       8     245 .. 0.94

  Alignments for each domain:
  == domain 1  score: 225.0 bits;  conditional E-value: 3.1e-70
                                       HGGGTS...EEEEE-TTSS-CHHHHHHH...HCTT-SEEEEECST...CHHHHHHHHHHHHHCTSSS-EEEEESSGG CS
                              PcrB   2 dileer...hltklDPeeenpdEiveiv...iesgtDavmigGsq...svtldntvrllkkvsriklPivlepsnve 69 
                                       di + +   hlt++DP  + pdE++ei+   +++g+Da+m+gGs+   ++ ld+t+ ++++   +++P +l+p+n  
  gi|298675417|ref|YP_003727167.1|   9 DISKNQgtvHLTLIDPASQSPDEAAEIAfaaANGGSDAIMVGGSIeagGALLDQTLIKIREK--TSIPTILFPANAG 83 
                                       566666777*****************9988899***********98777889****999999..************* PP

                                       G--TTSSEEEEEEETTBSSTTTTTHHHHHHHHHHHHHHHCTEEEEEEEEEBTTTSHHHHHTTB-.B-TTHHHHHHHH CS
                              PcrB  70 gvvryaDalFvmsllnsanadWivgahalglkkvkklieseeilaegYlvvePdskvaavteak.vdlnkediaaya 145
                                       gv+ y Da+F+msllns + ++i++ +a g+  v k+   +e + ++Yl++eP+++v++v++ak +++nk++ia  +
  gi|298675417|ref|YP_003727167.1|  84 GVSAYSDAIFFMSLLNSRDINYITTNQAMGAPLVYKFG--IESISMAYLIIEPGGTVGWVGDAKlIPKNKPEIAVSY 158
                                       **************************************..************************************* PP

                                       HHHHHHTT-SEEEEE-.TTSSS-H..HHHHHHHHHHSSSEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHH..H CS
                              PcrB 146 llaakllglrliYlEa.sGaledv..eevialkkklekarlivGGGirsaEkAkevvea.ADvivvGnvveekd..e 216
                                        la k+lg+ + YlEa sGa e+   e ++a+kk+l +++livGGGir++E+A+  v+a AD+iv+G+vvee +   
  gi|298675417|ref|YP_003727167.1| 159 SLAGKYLGMHYTYLEAgSGADEPAspEMIKAVKKVLGDNKLIVGGGIRDPETARVCVKAgADMIVTGTVVEETSdvA 235
                                       ********************9987779999******************************************99455 PP

                                       CHHHHHHH CS
                              PcrB 217 rkidaile 224
                                        ki++i+ 
  gi|298675417|ref|YP_003727167.1| 236 AKIEEIVS 243
                                       67777765 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.4   3.6e+03     183     205 ..      64      90 ..      55      93 .. 0.69
   2 !   28.5   0.0   3.6e-10   9.3e-07      58     118 ..     183     241 ..     148     246 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.4
                                       HHHHHHHHSSEEEE....ESS--SHHH CS
                      His_biosynth 183 tkelaeavkipvia....sGGvgsled 205
                                       + +++e+++ip+i     +GGv+  +d
  gi|298675417|ref|YP_003727167.1|  64 LIKIREKTSIPTILfpanAGGVSAYSD 90 
                                       557888888888754444778777665 PP

  == domain 2  score: 28.5 bits;  conditional E-value: 3.6e-10
                                       HHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHH CS
                      His_biosynth  58 reanldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpelikelaek 118
                                       +++++++v++++     ++ vGGGIr+ e+++  ++agad ++ gt++ + +++  ++ e 
  gi|298675417|ref|YP_003727167.1| 183 SPEMIKAVKKVLGD--NKLIVGGGIRDPETARVCVKAGADMIVTGTVVEETSDVAAKIEEI 241
                                       45566677777766..9********************************999999888775 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.12     3e+02     157     176 ..      34      53 ..       9      64 .. 0.74
   2 !   14.8   0.1   4.7e-06     0.012     136     188 ..     189     240 ..     164     245 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.12
                                       HHHHHHHTT--SEEEE-HHH CS
                              NanE 157 ekakkaieiGvdavvvGsai 176
                                       e a  a + G da++vG++i
  gi|298675417|ref|YP_003727167.1|  34 EIAFAAANGGSDAIMVGGSI 53 
                                       22334567899999999987 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 4.7e-06
                                       HHHHHHHTT--EEEES---SHHHHHHHHTT--SEEEE-HHHH-HHHHHHHHHH CS
                              NanE 136 lvkalseaglkviaeGrintPekakkaieiGvdavvvGsaitrleeiakkfve 188
                                        vk+++  + k+i+ G i  Pe a+ +++ G+d++v G+ +   +++a k  e
  gi|298675417|ref|YP_003727167.1| 189 AVKKVLG-DNKLIVGGGIRDPETARVCVKAGADMIVTGTVVEETSDVAAKIEE 240
                                       3343333.45799***************************9999999888765 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   2.5e-05     0.064     153     197 ..     187     228 ..     180     229 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.5e-05
                                       HHHHHHHHHHHT---EEEEESS--T.TTCHHHHHHT--EEEESHHH CS
                    Ribul_P_3_epim 153 ikkvrklidekeldlkievDGGvkl.dnieqiaeagadvlVagsav 197
                                       ik+v+k++     d k+ v GG+++ ++++  ++agad++V+g+ v
  gi|298675417|ref|YP_003727167.1| 187 IKAVKKVLG----DNKLIVGGGIRDpETARVCVKAGADMIVTGTVV 228
                                       566666665....58999*****8636777889**********876 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   3.4e-05     0.087     128     168 ..     184     225 ..     181     228 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.4e-05
                                       HHHHCTSTTS....EEEEESS--SHHHHHHHCTT.SSEEEE- CS
                      G3P_antiterm 128 pkvikeikkel.kipiiaGGLietkedveealkaGaiavsts 168
                                       p++ik++kk l + ++i GG i++ e+ + ++kaGa+ + t+
  gi|298675417|ref|YP_003727167.1| 184 PEMIKAVKKVLgDNKLIVGGGIRDPETARVCVKAGADMIVTG 225
                                       8999****9987899************************997 PP

>> MlrC_C  MlrC C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.037        96      40      64 ..      31      55 ..      12      68 .. 0.88
   2 ?    8.9   0.2   0.00061       1.6      30      64 ..     199     233 ..     174     246 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.037
                                      HHHHHHHHH-TT-EEEEEES-SS-T CS
                            MlrC_C 40 eavaaaaaagvGatveltlGgkvda 64
                                      ea+++a+aa  G++  +++Gg+++a
  gi|298675417|ref|YP_003727167.1| 31 EAAEIAFAAANGGSDAIMVGGSIEA 55
                                      899******************9876 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00061
                                       --EEEEEE-HHHHHHHHHH-TT-EEEEEES-SS-T CS
                            MlrC_C  30 kvlvasivDpeavaaaaaagvGatveltlGgkvda 64 
                                        ++ ++i Dpe+++++++ag++  v+ t+ +++++
  gi|298675417|ref|YP_003727167.1| 199 LIVGGGIRDPETARVCVKAGADMIVTGTVVEETSD 233
                                       567789***************99999988766665 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1     0.062   1.6e+02     142     194 ..      41      95 ..      30     112 .. 0.70
   2 ?   11.1   0.9   6.9e-05      0.18     162     224 ..     182     245 ..     172     247 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.062
                                       HTT-SEBEEBSSSTTS----S-HHHHHHHHHH-SS-BEE...ES.---SHHHHHHHH CS
                              ThiG 142 evGcaavmPlaapiGsglGllnkealkiiieeakvPviv...DA.Gigspsdaaqam 194
                                       + G  a+m  +  i +g  ll+++ l  i+e++++P i+   +A G+   sda+  m
  gi|298675417|ref|YP_003727167.1|  41 NGGSDAIMV-GGSIEAGGALLDQT-LIKIREKTSIPTILfpaNAgGVSAYSDAIFFM 95 
                                       557888885.55577775555555.55589999999887443332566666666655 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 6.9e-05
                                       S-HHHHHHHHHH-.SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHH CS
                              ThiG 162 lnkealkiiieea.kvPvivDAGigspsdaaqamelGadavllntavaeakdpvamArafklav 224
                                       +++e++k + + + +  +iv  Gi+ p+ a   ++ Gad ++  t v e++d +a  + +  a+
  gi|298675417|ref|YP_003727167.1| 182 ASPEMIKAVKKVLgDNKLIVGGGIRDPETARVCVKAGADMIVTGTVVEETSDVAAKIEEIVSAI 245
                                       56788888888888899***********************************998777776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1521.86
//
Query:       gi|298675418|ref|YP_003727168.1|  [L=48]
Description: 50S ribosomal protein L40e [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      8e-05   22.4   5.7    9.7e-05   22.2   5.7    1.1  1  Ribosomal_L40e  Ribosomal L40e family
    0.00044   19.9   3.7     0.0009   18.9   3.7    1.4  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
     0.0011   18.9   1.0     0.0013   18.7   1.0    1.1  1  DZR             Double zinc ribbon
     0.0022   17.6   2.0     0.0028   17.3   2.0    1.2  1  zinc_ribbon_2   zinc-ribbon domain
  ------ inclusion threshold ------
      0.084   12.9   1.5      0.085   12.9   1.5    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta


Domain annotation for each model (and alignments):
>> Ribosomal_L40e  Ribosomal L40e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   5.7   2.7e-08   9.7e-05      14      40 ..      12      36 ..       7      44 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.7e-08
                    Ribosomal_L40e 14 cdKmiCrkCYArlpprAtnCrkkkCgh 40
                                       +K iC  C Ar  p+A  Cr  kCg 
  gi|298675418|ref|YP_003727168.1| 12 LNKTICMDCNARNAPKAERCR--KCGY 36
                                      69*******************..9*96 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   3.7   2.5e-07    0.0009       2      26 ..      16      37 ..      16      39 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.5e-07
                                      B-SSS--B----SSS----SSS--- CS
                    DNA_RNApol_7kD  2 iCgeCgaevslkkgdpiRCkeCGhR 26
                                      iC++C+a++  k++   RC++CG++
  gi|298675418|ref|YP_003727168.1| 16 ICMDCNARNAPKAE---RCRKCGYK 37
                                      8*************...*******8 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   1.0   3.6e-07    0.0013      28      49 .]      14      35 ..       2      39 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 3.6e-07
                               DZR 28 edrCpsCgekvdpearfCpeCG 49
                                      ++ C+ C++ + p+a+ C +CG
  gi|298675418|ref|YP_003727168.1| 14 KTICMDCNARNAPKAERCRKCG 35
                                      7789999999999999999998 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   2.0   7.9e-07    0.0028       2      22 ..      17      37 ..      16      39 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 7.9e-07
                     zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGtp 22
                                      C  C a + ++a  C +CG++
  gi|298675418|ref|YP_003727168.1| 17 CMDCNARNAPKAERCRKCGYK 37
                                      9******************97 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.5   2.4e-05     0.085      69      98 ..      13      40 ..       6      46 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.4e-05
                                      -EEEETTTS-EEECHHHHHS-TTTSSS-EE CS
                              HypA 69 vkvrCreCgkefeleekalrCpkCgsadve 98
                                       k+ C +C+++   +  a+rC kCg ++++
  gi|298675418|ref|YP_003727168.1| 13 NKTICMDCNARNAPK--AERCRKCGYKHLR 40
                                      6789*****999877..459*****98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 313.80
//
Query:       gi|298675419|ref|YP_003727169.1|  [L=380]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.1e-27   94.2   2.1    1.5e-26   93.0   2.1    1.6  1  OrfB_IS605      Probable transposase
    1.7e-23   82.3   0.3    3.6e-23   81.3   0.3    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    1.8e-19   69.0   1.4      4e-19   67.8   1.4    1.6  1  HTH_OrfB_IS605  Helix-turn-helix domain
  ------ inclusion threshold ------
      0.012   15.7   0.3       0.03   14.5   0.3    1.6  1  zf-piccolo      Piccolo Zn-finger
      0.023   14.6   1.3       0.38   10.6   0.3    2.3  2  LemA            LemA family
      0.064   13.1   5.9       0.27   11.0   2.8    2.3  2  Phage_GP20      Phage minor structural protein GP20
        1.2    9.4   9.7       0.29   11.4   3.0    2.3  2  MapZ_EC1        MapZ extracellular domain 1


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.0   2.1   5.7e-30   1.5e-26      10     117 ..     180     284 ..     167     286 .. 0.91

  Alignments for each domain:
  == domain 1  score: 93.0 bits;  conditional E-value: 5.7e-30
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsr 86 
                                       +++  + +++g+D+Gi+++a++++++   ++ ++r lk+  ++l+  +++l++k+k+s+nykk + ++a++h+k+++
  gi|298675419|ref|YP_003727169.1| 180 KQTFYEVNTVGVDVGIKDFAVTSDGE---KIDNPRYLKNSIERLKVLQKRLSRKKKGSNNYKKLKHQIAKYHEKIAN 253
                                       45555789******************...************************************************ PP

                        OrfB_IS605  87 rrkhllhklathliktlkevgvetLnvgnmk 117
                                       +r +++hkl+++li ++++v++e Lnv+++ 
  gi|298675419|ref|YP_003727169.1| 254 QREDFQHKLSNKLISENQAVALECLNVKGLL 284
                                       ****************************986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.3   0.3   1.4e-26   3.6e-23       1      68 [.     298     367 ..     298     368 .. 0.98

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 1.4e-26
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpay.TSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       ++++ ++leyka++yG++++++ ++  +Sk C++Cg+ +++ +l++r+++Cp+C++ +drD+nA++Ni k
  gi|298675419|ref|YP_003727169.1| 298 WSSFVQKLEYKAEWYGKNIIKIGRFDpSSKICHVCGYYHQDlELKDREWECPDCKTIHDRDINASVNIKK 367
                                       99******************************************************************87 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.8   1.4   1.6e-22     4e-19       1      47 []       9      54 ..       9      54 .. 0.98

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 1.6e-22
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeegk 47
                                      M lkaykyr yP++ Q+e++a+++G++Rf+YN+aL+ + + ye+ gk
  gi|298675419|ref|YP_003727169.1|  9 M-LKAYKYRMYPNQIQQELIAKHIGACRFIYNWALENKLKSYEQDGK 54
                                      8.******************************************997 PP

>> zf-piccolo  Piccolo Zn-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.3   1.2e-05      0.03      28      55 ..     326     353 ..     322     356 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.2e-05
                        zf-piccolo  28 kqvCnlCGFnptphltekkeWlclnCQt 55 
                                       +++C +CG+  ++   + +eW c  C t
  gi|298675419|ref|YP_003727169.1| 326 SKICHVCGYYHQDLELKDREWECPDCKT 353
                                       79***********999**********86 PP

>> LemA  LemA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.049   1.2e+02      35      82 ..      65     112 ..      51     116 .. 0.81
   2 ?   10.6   0.3   0.00015      0.38      55     108 ..     208     262 ..     180     271 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.049
                              LemA  35 eevteaRakaaeaesveekaeaenqlssalsrllavaEnYPdLkanen 82 
                                        +v +  ++  ++ + ++ + a  +l++a+ +++     +P++k+++n
  gi|298675419|ref|YP_003727169.1|  65 IRVLKQDHEWLNEINSQSLQGATLNLENAFTKIFREKSGFPKFKSKKN 112
                                       55666666668888999999*************************987 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00015
                              LemA  55 eaenqlssalsrllavaEnY.PdLkanenfleLqeelegtEnriavaRrrYneav 108
                                       ++ + l+++++rl +++ +   + k ++n+++L++++++  ++ia++R++++++ 
  gi|298675419|ref|YP_003727169.1| 208 DNPRYLKNSIERLKVLQKRLsRKKKGSNNYKKLKHQIAKYHEKIANQREDFQHKL 262
                                       5556677777777777776414567899**********************98765 PP

>> Phage_GP20  Phage minor structural protein GP20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.043   1.1e+02     113     137 ..      51      78 ..      22      88 .. 0.74
   2 ?   11.0   2.8   0.00011      0.27      32      90 ..     218     276 ..     205     283 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.043
                        Phage_GP20 113 edgelkg...LdeqikkLkesdkyLFee 137
                                       +dg+ +    L++qi  Lk+++++L e 
  gi|298675419|ref|YP_003727169.1|  51 QDGKAISrfeLNKQIRVLKQDHEWLNEI 78 
                                       5666554444999999999999999863 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00011
                        Phage_GP20  32 eqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeyeakiadlkldnaielaLk 90 
                                       e+lk  +k L+  kk +++ ++L+ qi+++ +k++++ ++ + k+++  +++    aL+
  gi|298675419|ref|YP_003727169.1| 218 ERLKVLQKRLSRKKKGSNNYKKLKHQIAKYHEKIANQREDFQHKLSNKLISENQAVALE 276
                                       6788889999999********************************99877766555555 PP

>> MapZ_EC1  MapZ extracellular domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.6      0.11   2.9e+02      48      84 ..      42      81 ..      38      93 .. 0.78
   2 ?   11.4   3.0   0.00011      0.29      37      78 ..     213     254 ..     173     276 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.11
                          MapZ_EC1 48 LekkLeklk.gskeYk..klkkkldslkkqisaieavNsq 84
                                      Le+kL+ ++ + k  +  +l+k++  lk+  + ++++Nsq
  gi|298675419|ref|YP_003727169.1| 42 LENKLKSYEqDGKAISrfELNKQIRVLKQDHEWLNEINSQ 81
                                      777788777544443323799*****************97 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00011
                          MapZ_EC1  37 lknsefaklseLekkLeklk.gskeYkklkkkldslkkqisai 78 
                                       lkns ++ l+ L+k L   k gs++Ykklk+++++  ++i+ +
  gi|298675419|ref|YP_003727169.1| 213 LKNS-IERLKVLQKRLSRKKkGSNNYKKLKHQIAKYHEKIANQ 254
                                       4443.688999*****98777*****************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1674  (0.0933683); expected 358.6 (0.02)
Passed bias filter:                      699  (0.0389871); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 2263.39
//
Query:       gi|298675420|ref|YP_003727170.1|  [L=432]
Description: hypothetical protein Metev_1522 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-13   49.4   0.5    1.9e-12   47.1   0.5    2.1  1  ATP-grasp_4      ATP-grasp domain
     0.0025   17.9   0.1     0.0054   16.8   0.1    1.7  1  ATP-grasp_3      ATP-grasp domain
     0.0066   16.0   0.0      0.013   15.0   0.0    1.4  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
     0.0092   15.5   0.1        3.8    7.0   0.2    2.4  2  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
  ------ inclusion threshold ------
      0.011   15.4   0.0      0.029   14.1   0.0    1.7  2  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T


Domain annotation for each model (and alignments):
>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.5   5.2e-16   1.9e-12       3     154 ..     132     292 ..     130     299 .. 0.83

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 5.2e-16
                       ATP-grasp_4   3 lPvviKPsvgffSlGVykinneeewkaavaaieeeleqakeey...........keevveeesflvEeyieGeEfav 68 
                                       lP   KP+   +S+  +ki++ +++++ +++  e ++  ++ y           +e+    ++fl Ee+i G+ +  
  gi|298675420|ref|YP_003727170.1| 132 LPAFAKPVRSNVSFAAQKIDTTKDLQQLINDFGEYIKDYNQYYvdslslssydnPENLYTCNKFLCEELIFGTQVTA 208
                                       67888**************************99999988887722222222222344455689************** PP

                       ATP-grasp_4  69 dayfdeeGepvilnilkkefaseedvsdrlyvtsakvieetlealeellkevnallglknfpvHiElrvsedg.kii 144
                                       d y+ ++ ++++ +++k  f + +++s   +  + +v+ et++++ +++++++++l+l n  + +El+++e+  ++ 
  gi|298675420|ref|YP_003727170.1| 209 DCYVYNQ-KAHVFALTKAAFFD-DKISFSHHEFPYQVSPETEQKIYNMIDKLAKNLKLDNTFINVELKIDEKTgNVS 283
                                       ****777.88888888777765.5577889***************************************98644*** PP

                       ATP-grasp_4 145 piEvnplrfa 154
                                        iEvn+ r+a
  gi|298675420|ref|YP_003727170.1| 284 IIEVNA-RIA 292
                                       *****9.554 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   1.5e-06    0.0054      61     158 ..     193     291 ..      97     293 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.5e-06
                                       ....EEEE---SEEEEEEEEE.SSSEEEEEEEEEEEET....TEEEEEEES----H..HHHHHHHHHHHHTTSTT-- CS
                       ATP-grasp_3  61 eevelvqefieGkplSvsllsdgekvlvlavnrqliekaekefvyaGnvtpietel..keevvelaeevveklegla 135
                                       + + l  e i G+++++++ + ++k++v+a+ ++      ++++++    p++++   ++++++++ ++ ++l+  +
  gi|298675420|ref|YP_003727170.1| 193 N-KFLCEELIFGTQVTADCYVYNQKAHVFALTKAAFF--DDKISFSHHEFPYQVSPetEQKIYNMIDKLAKNLKLDN 266
                                       2.23999**************************9984..5779999999999987666999************8779 PP

                                       EEEEEEEEESS...SEEEEEEESS- CS
                       ATP-grasp_3 136 GyvGvDlvlkd..eepyviEvNPRl 158
                                        +  v+l + +  ++  +iEvN+R+
  gi|298675420|ref|YP_003727170.1| 267 TFINVELKIDEktGNVSIIEVNARI 291
                                       999****999988899********8 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   3.6e-06     0.013     134     205 ..     244     317 ..     238     321 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.6e-06
                                       -HHHHHHHHHHHHHHHHHHT-EEEE.EEEEEEETTTTEEEEEEEESS--CCHHHH.HHHHS--HHHHHHHHHTT CS
                       CPSase_L_D2 134 tdeerqalreaavkvvrevgvvgag.tveflldpkskeyyviEvNtRlsvesala.ekaTGldlvkeaakialg 205
                                       ++e+ q++ +   k+++++++ +   +ve  +d+k+++  +iEvN+R+  + a + e++ G+d ++    +a+g
  gi|298675420|ref|YP_003727170.1| 244 SPETEQKIYNMIDKLAKNLKLDNTFiNVELKIDEKTGNVSIIEVNARIAFQFAKTiETVKGFDPLHLICDLASG 317
                                       66778888888889999999988766**********************99988664778888877777777766 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0    0.0022         8      35      71 ..     130     166 ..     120     170 .. 0.88
   2 !    7.0   0.2    0.0011       3.8     115     174 ..     232     289 ..     193     294 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0022
                                       C-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT CS
                   Dala_Dala_lig_C  35 lgypvfVKpareGSSvGvskveseeelkeaieeafky 71 
                                        ++p+f Kp+r+  S+  +k+ ++++l++ i++  +y
  gi|298675420|ref|YP_003727170.1| 130 KSLPAFAKPVRSNVSFAAQKIDTTKDLQQLINDFGEY 166
                                       468***************************9987665 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0011
                                       HHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--S.EEEEEEEE.ETTTEEEEEEEES CS
                   Dala_Dala_lig_C 115 akysddkaqlevpaklekeveekiqelalkaykaldlrG.laRvDffl.teegeivlnEvNt 174
                                              ++ e+p ++++e+e+ki ++  k  k+l+l   +  v + + +++g++ + EvN 
  gi|298675420|ref|YP_003727170.1| 232 IS----FSHHEFPYQVSPETEQKIYNMIDKLAKNLKLDNtFINVELKIdEKTGNVSIIEVNA 289
                                       33....357799************************97626799999967889*******96 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       2.1   7.4e+03      61      72 ..      90     101 ..      86     106 .. 0.80
   2 ?   14.1   0.0   8.1e-06     0.029      44     110 ..     246     317 ..     193     333 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.1
                      ATPgrasp_Ter  61 gldglvnvQvre 72 
                                       +++g+vn Q ++
  gi|298675420|ref|YP_003727170.1|  90 SVEGVVNCQNKY 101
                                       68999****998 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 8.1e-06
                      ATPgrasp_Ter  44 ekdeelielaerlaeefgldg.lvnvQvrededg..pkLLEiNpRasGGlgysala..Gvnlpylalklllg 110
                                       e+++++ ++  +la++++ld   +nv ++ de++    ++E+N+R++  +  ++ +  G +  +l  +l+ g
  gi|298675420|ref|YP_003727170.1| 246 ETEQKIYNMIDKLAKNLKLDNtFINVELKIDEKTgnVSIIEVNARIAFQFAKTIETvkGFDPLHLICDLASG 317
                                       678999*************86167*****999887899*******987776665544466666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 2619.99
//
Query:       gi|298675421|ref|YP_003727171.1|  [L=413]
Description: amidohydrolase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.6e-53  179.8   1.2    1.1e-52  179.5   1.2    1.1  1  Amidohydro_1  Amidohydrolase family
    1.7e-19   70.7   0.1    3.4e-15   56.5   0.0    2.1  2  Amidohydro_3  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.5   1.2   1.2e-56   1.1e-52       1     342 [.      61     403 ..      61     404 .. 0.89

  Alignments for each domain:
  == domain 1  score: 179.5 bits;  conditional E-value: 1.2e-56
                                       EEEE-EEEEEEECETTECSSS...GHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHHHHHHHHT.S CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrga...tledwlvppetaaealesgiktalksGtttvadmgattstgiealleaaee.l 73 
                                       +++PGlID+HvHl   +       t+++ l+++ + a  +++ ++++++sG+ttv+++g ++ + + a+++a+e+ l
  gi|298675421|ref|YP_003727171.1|  61 FIIPGLIDTHVHLD-LH---GfpdTYQENLLDDKYRAIRAAIDMEKTVNSGFTTVRNVGSVN-YIDIAVKKAVEDgL 132
                                       79***********4.33...2467************************************86.68888999****** PP

                                       SSEEEEEEESSEGGS................GCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHH CS
                      Amidohydro_1  74 plglrilggkvsldr................gsaetskasreklkagaaetikgkadgvvkvalapheapafsdeel 134
                                       + g+ril+++ ++ +                g++e++ka re+lk+g+ +++k++a+g+++   + ++ap++  ee+
  gi|298675421|ref|YP_003727171.1| 133 IAGPRILTSGKIICMqsagseyfsgmyreadGVDENRKAAREQLKEGV-DFLKVMATGAIMNPGGIPGAPQLDVEEI 208
                                       *********99988899******************************5.**************************** PP

                                       HHHHHHHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHH.HHHHHHHHH CS
                      Amidohydro_1 135 kealkeakkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpt.eaellkerl 210
                                       +++++e  k +++ a+Ha++++g++ +a++a+++tiehgt+ +         ++k++   +v+l  t ++++   r+
  gi|298675421|ref|YP_003727171.1| 209 SAVVDEGLKLGIYTAAHAHGSEGIK-NAIKAGVRTIEHGTLADE-------QTLKMMKNNNVYLVSTlSSNYFMVRK 277
                                       ******************9999997.******************.......889***********777344433333 PP

                                       HHHCEE...HHHHHHHHSEHHHHHHHHHHHHTSCEEEEEECT.....TSSCCGGHHHHHHHHHHHHHHCCTTTTHCH CS
                      Amidohydro_1 211 keagva...hcpfsnsilrsgrealrkaldeGvkvglgtDga.....asgnslnlleelrlalklqrgllyedeegg 279
                                        +  +    +  +++++ +   + +rkal+ Gvkv++gtD         +ns++l   +r+             e  
  gi|298675421|ref|YP_003727171.1| 278 ENEALIpdfMREKAEEVAQMRKNVIRKALEIGVKVIMGTDAGtpfnyHGNNSMEL---VRYVR-----------ENL 340
                                       344444699999*****9999999****************224444333333333...44444...........666 PP

                                       CHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECCCTCGGGTTTCTSEEEEEEEETTE CS
                      Amidohydro_1 280 lslkealrmaTingAkalglddkvGsievGkdADlvvvdldilaafvglkkdgnvkkvivkGk 342
                                       +++++a+ ++T  +A+a+gl d +G++evGk AD v+++ ++ +++  l +  n++++++ G+
  gi|298675421|ref|YP_003727171.1| 341 MTPEQAIIASTRTAAEAIGLGDVTGTLEVGKSADCVILNKNPMEDISCLLETQNIIMTFKEGN 403
                                       ************************************************************996 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   8.8e-06     0.079       4      25 ..      56      77 ..      54     108 .. 0.80
   2 !   56.5   0.0   3.8e-19   3.4e-15     255     451 ..     198     384 ..     148     404 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.8e-06
                      Amidohydro_3  4 DakGrlvlPGFvDsHtHlaggg 25
                                      D +G + +PG++D H Hl+ +g
  gi|298675421|ref|YP_003727171.1| 56 DVSGQFIIPGLIDTHVHLDLHG 77
                                      889**************99887 PP

  == domain 2  score: 56.5 bits;  conditional E-value: 3.8e-19
                      Amidohydro_3 255 tgwpdfedealaelvaaadergldvaihaigdaavddvldafeaaaekngnqdrrrlehaegvtesqiervaalqva 331
                                        g p ++ e++ ++v++  + g+  a ha+g + +          a k g++   ++eh++  +e++++ ++  +v 
  gi|298675421|ref|YP_003727171.1| 198 PGAPQLDVEEISAVVDEGLKLGIYTAAHAHGSEGIK--------NAIKAGVR---TIEHGTLADEQTLKMMKNNNVY 263
                                       677778888899999999999999999999999999........33455666...*********************9 PP

                      Amidohydro_3 332 agvqpvfnf.....edelldsrlgperargs.....tpvkellnagvkvalgsDapvgpfdpwprigaavmrktrrg 398
                                           + +n+     e+e l+  ++ e+a+ +     + ++  l+ gvkv++g+D  ++pf+ +      +       
  gi|298675421|ref|YP_003727171.1| 264 LVSTLSSNYfmvrkENEALIPDFMREKAEEVaqmrkNVIRKALEIGVKVIMGTD-AGTPFNYHGNNSMELV------ 333
                                       999999999**********************9**********************.4444444443333333...... PP

                      Amidohydro_3 399 gevlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvldadpld 451
                                         ++ +++ ++ e+a+ + Tr++A+a+gl d +GtLevG++AD v+l+++p++
  gi|298675421|ref|YP_003727171.1| 334 --RYVRENLMTPEQAIIASTRTAAEAIGLGDVTGTLEVGKSADCVILNKNPME 384
                                       ..4556889****************************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 2513.87
//
Query:       gi|298675422|ref|YP_003727172.1|  [L=62]
Description: hypothetical protein Metev_1524 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.035   13.4   3.2       0.04   13.2   3.2    1.0  1  UbiA      UbiA prenyltransferase family
       0.75    9.2   4.5        0.8    9.2   4.5    1.0  1  DUF1129   Protein of unknown function (DUF1129)
       0.99    9.4   2.3        1.1    9.3   2.3    1.0  1  DUF3043   Protein of unknown function (DUF3043)
        4.6    7.0   8.9        6.6    6.5   3.8    2.1  2  FixS      Cytochrome oxidase maturation protein cbb3-type


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   3.2   8.9e-06      0.04      66     113 ..       4      60 ..       2      62 .] 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.9e-06
                              UbiA  66 pkealifaivllilgllll..........alllnpltallgllalllyvvYtglrlKr 113
                                       ++++++f+++ +++ ++ll           +ll  l+ ll++++++++ +Y+ l++++
  gi|298675422|ref|YP_003727172.1|   4 VQTGMLFFMIAFAILFGLLmlnnipsmenQVLLPNLAGLLVVAGFIIAGIYN-LFTGK 60 
                                       566777777777777777778********999999*****************.77665 PP

>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   4.5   0.00018       0.8      84     135 ..       7      58 ..       3      62 .] 0.84

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00018
                           DUF1129  84 nsLlllalfallfgilalfskkkqtasiGlitlllvalvgGlamvlvyrllt 135
                                       ++L++++ fa+lfg+l+l +  ++++++ l  l+ + +v+G+++  +y+l+t
  gi|298675422|ref|YP_003727172.1|   7 GMLFFMIAFAILFGLLMLNNIPSMENQVLLPNLAGLLVVAGFIIAGIYNLFT 58 
                                       57999999********999888888887888888888999999998888876 PP

>> DUF3043  Protein of unknown function (DUF3043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   2.3   0.00024       1.1      79     124 ..       7      54 ..       3      60 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00024
                           DUF3043  79 gelflplalvvlvlllv..slvkvpevqavvsllllvllllvvidgil 124
                                       g lf+++a+++l+ ll+  ++ ++++   + +l+ l++++ ++i gi+
  gi|298675422|ref|YP_003727172.1|   7 GMLFFMIAFAILFGLLMlnNIPSMENQVLLPNLAGLLVVAGFIIAGIY 54 
                                       667888889999886653233333333334455666677778887776 PP

>> FixS  Cytochrome oxidase maturation protein cbb3-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   3.8    0.0015       6.6       2      18 ..       8      24 ..       7      25 .. 0.92
   2 ?    3.8   0.2      0.01        46      10      29 ..      41      60 ..      35      62 .] 0.66

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0015
                              FixS  2 iLylLiplSlllgllal 18
                                      +L+++i  ++l+gll l
  gi|298675422|ref|YP_003727172.1|  8 MLFFMIAFAILFGLLML 24
                                      79************976 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.01
                              FixS 10 SlllgllalaaFlWavksGQ 29
                                       ll+++++++a ++ + +G 
  gi|298675422|ref|YP_003727172.1| 41 GLLVVAGFIIAGIYNLFTGK 60
                                      46667777776666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       873  (0.0486921); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 410.90
//
Query:       gi|298675423|ref|YP_003727173.1|  [L=337]
Description: histone deacetylase superfamily protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-87  293.9   0.1    2.2e-87  293.4   0.1    1.2  1  Hist_deacetyl  Histone deacetylase domain


Domain annotation for each model (and alignments):
>> Hist_deacetyl  Histone deacetylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  293.4   0.1   1.2e-91   2.2e-87       1     306 [.      18     301 ..      18     302 .. 0.95

  Alignments for each domain:
  == domain 1  score: 293.4 bits;  conditional E-value: 1.2e-91
                                       SCCGTHHHHHHHHHHHHT.THHHHCCE.EE-----HHHHTTTS-HHHHHHHHCHHHHCHHT.TTHCCHHHCCTSTSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl   1 hpenpkRlsaileslaesvglldelelliqpseatkeellkvHskeYlelleslsnelkkkeeakekeleeiaskll 77 
                                       hpe+  Rls+++e l+++ ++++++  l++p+ a+ ++++++H+++Y++++e  +n+    e         i  + l
  gi|298675423|ref|YP_003727173.1|  18 HPESSIRLSHAVEYLEKQ-DVFKNHP-LVEPNTAEISQIQTIHTPDYIKKVEYHCNN----E---------I--P-L 76 
                                       89***************8.8776644.69**********************976644....3.........1..2.4 PP

                                       SSSTHCTTTCCHHHHHHHHHHHHHHHHHHTTSSSEEEETTSS--TT-BTTB-BTTBSS-HHHHHHHHHHHCC-SS-E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl  78 dddtpvspktlkaallavgavleavdavlsgsvkaafvlvrPpgHHakaseasGFClvNnvaiaikylqakhelkrv 154
                                       d dt+vs+++++aalla+g++++av++ +++  ++af+lvrPpgHHa++++a+GFCl+Nn+aia+ky+q+ +++krv
  gi|298675423|ref|YP_003727173.1|  77 DPDTVVSKDSYRAALLAAGGSIRAVNETYTN--NSAFALVRPPGHHAESDRAKGFCLFNNIAIAAKYAQS-QGMKRV 150
                                       679**************************99..9************************************.789*** PP

                                       EEEE-SSS--HHHHHHCTT-TTEEEEEEEE-CCTSTTSS--TT---SGGGTTSEEEEEE-TT-BHHHHHHHHHHCHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl 155 ailDvDvHhGnGteeafysdpdvltlSiHryegifyPgtgaledlgegkgkgfnlnvpleegtgdeeylkvfeeilr 231
                                       +i+D+DvHhGnGt++ fysd++v+++S+Hry+   +Pgtg ++++g+g+g+g+n+nvpl +g++d+ey++vf++i++
  gi|298675423|ref|YP_003727173.1| 151 LIIDWDVHHGNGTQHSFYSDSTVMYMSTHRYP--WFPGTGWMDETGSGEGEGYNINVPLFAGSTDDEYAYVFDKIFM 225
                                       ******************************75..5****************************************** PP

                                       HHHCCH--SEEEEEE-STTBTTSTT-S-BB-HHHHHHHHHHHCCCHGS-.G.EEEEE-S---HHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl 232 pvleefkPdlilvsaGfDalkgdplgelnlsvegykeltkklaeladkv.kkvvllleGGYnlealaravtavlsa 306
                                       pv+ +f+Pd+i+vsaG+Da ++d lg+++l+ eg++ l  +++++ad + k+++l+leGGY++e+la+++ +v++a
  gi|298675423|ref|YP_003727173.1| 226 PVALQFQPDIIMVSAGMDAQENDMLGGMKLTSEGFATLAGYIKRIADLTcKQFILVLEGGYQHEKLAESIYQVITA 301
                                       ***********************************************9988*****************99998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2041.55
//
Query:       gi|298675424|ref|YP_003727174.1|  [L=413]
Description: hypothetical protein Metev_1526 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-71  237.6   0.0    1.1e-70  237.0   0.0    1.3  1  Lar_N     Lactate racemase N-terminal domain
  ------ inclusion threshold ------
      0.062   13.5   0.0      0.093   13.0   0.0    1.3  1  DUF362    Domain of unknown function (DUF362)


Domain annotation for each model (and alignments):
>> Lar_N  Lactate racemase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.0   0.0   1.2e-74   1.1e-70       1     203 [.       8     206 ..       8     207 .. 0.98

  Alignments for each domain:
  == domain 1  score: 237.0 bits;  conditional E-value: 1.2e-74
                             Lar_N   1 ygkkkleleipeenllgvlepkevkeekdeeeaieeaLenpigsekleelvkekekvvivvsDiTRptpskiilpll 77 
                                       yg+++l+l+ip++nl +v+ p+e + ++de++ +++aLenp++s++l+e+v  +++v++ vsD TRp p++++lp l
  gi|298675424|ref|YP_003727174.1|   8 YGHDSLTLDIPDKNLSRVIVPEEPEITEDESSLMQKALENPVKSKRLSEIVDDESTVAVLVSDTTRPAPTSKMLPPL 84 
                                       9**************************************************************************** PP

                             Lar_N  78 leelkeagvkdeditilvAtGlHrkqteeelkkilGeevvkrikvvnhdaedksslvklGttskGtpveinklvaea 154
                                       l+el ++g+kde+iti++++GlHr+qteee++k++G ++++r+++++h   d++++ ++G+ts+Gtpvei+++v+++
  gi|298675424|ref|YP_003727174.1|  85 LNELYRGGIKDENITIVFGLGLHRNQTEEEMEKLVGSDIYNRVRCIEH---DRERCRHIGDTSNGTPVEIFEEVLDS 158
                                       ************************************************...68************************ PP

                             Lar_N 155 dlviltGfiepHyfaGfsGGrKsilpGvasretimanHkavlaepraal 203
                                       d++++tG+ie+Hy+aG+sGG K+ilp+v+s++t+m+nH+++  +++a++
  gi|298675424|ref|YP_003727174.1| 159 DMIVCTGNIEFHYYAGYSGGGKAILPAVSSEKTVMTNHEMMR-DDKATT 206
                                       ****************************************88.777766 PP

>> DUF362  Domain of unknown function (DUF362)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     1e-05     0.093      36     143 ..      96     224 ..      65     312 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1e-05
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                            DUF362  36 gkiivgdspglyvsrgkahrevaeeagydelaega.diadglegedevvvpvkgkhlkke.lkiakavleaDviInl 110
                                       ++i+++ + gl++   ++++e +e+   +++++++  i +++   +e++  + g++++ + ++i ++vl+ D+i++ 
  gi|298675424|ref|YP_003727174.1|  96 ENITIVFGLGLHR---NQTEEEMEKLVGSDIYNRVrCI-EHD---RERCRHI-GDTSNGTpVEIFEEVLDSDMIVCT 164
                                       5677777777543...2223333333333344444222.222...2233334.333222249*************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx..........................x RF
                            DUF362 111 pklKgHalagvtgalKnlfGcisgs.gkaeiHs..........................k 143
                                            H +ag++g+ K     +s + + +  H                            
  gi|298675424|ref|YP_003727174.1| 165 GNIEFHYYAGYSGGGKAILPAVSSEkTVMTNHEmmrddkattgviespvrtdieeaaqmV 224
                                       ****************97777766624344443555555555555544444444444440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 2482.64
//
Query:       gi|298675425|ref|YP_003727175.1|  [L=531]
Description: SSS sodium solute transporter superfamily protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-61  209.1  41.4    1.4e-61  208.6  41.4    1.2  1  SSF       Sodium:solute symporter family
  ------ inclusion threshold ------
      0.021   14.6   0.2      0.021   14.6   0.2    2.7  3  YniB      YniB-like protein
        3.7    8.0   7.9       0.52   10.7   0.2    3.4  3  ATP19     ATP synthase subunit K


Domain annotation for each model (and alignments):
>> SSF  Sodium:solute symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.6  41.4   2.4e-65   1.4e-61       1     406 []      36     455 ..      36     455 .. 0.86

  Alignments for each domain:
  == domain 1  score: 208.6 bits;  conditional E-value: 2.4e-65
                               SSF   1 yflagrsltgfvlglslaasnisaasfvGlaGavaasGlavvlle.lgalllvlllllllaerlr....nagalTlp 72 
                                       y++agr++ ++ l+ls +a+ is + +vG  Ga+ a+G++ ++l  +++++++ +++++++ r r    n+ a+T+p
  gi|298675425|ref|YP_003727175.1|  36 YMVAGRKINPYILALSYGATFISTSAIVGFGGAAGAYGMGLLWLTfMNIVFGIFIAFVVFGSRTRrmgvNLDAVTFP 112
                                       99****************************************99846889999***********99999999***** PP

                               SSF  73 dylskRfkgkrilvylsalslllvitlklsvdlvggaklielalGlnyetavlllaaltalYtviGGllAvvytdti 149
                                       ++l kRf+++  +  +s   + +++ l+    l+gga+++e+al++ny +avl+la+++a Y+++GGl+Av+ytd +
  gi|298675425|ref|YP_003727175.1| 113 EFLGKRFQSRF-IQGFSGALVGIFMPLYAGIVLIGGARFVETALSINYDVAVLILAIIIAAYVITGGLIAVMYTDAL 188
                                       **********9.6667766666677778888899******************************************* PP

                               SSF 150 qavlmlvgalilliivllevGgleslveklkeaapkv.vdl..........ltpdslkllrdpltalslwlglvlGv 215
                                       q++lm +g  +lli++ +++Gg+ ++ + l+++a  v  +l          + + + ++    +++ +l  g+++Gv
  gi|298675425|ref|YP_003727175.1| 189 QGTLMFIGMGLLLIFTYIKLGGVTEAHQALTNMAYLVpEKLvasghmgwtaMPELGSQIWWTVVSTFIL--GVGIGV 263
                                       ******************************999998865556677777654446666666666666655..9999** PP

                               SSF 216 aglphilvRflaakdakailkgvlkltivlilvligmisiilfaiklagavp.kav.gtevgvsniaypeLvvkllp 290
                                         +p  +vRf+++ +++++ k+vl + ++++++   + +++  ++ +++ +  k++   ++g++++++pe ++  +p
  gi|298675425|ref|YP_003727175.1| 264 LAQPQLAVRFMTVRSSSSLNKAVLVGGPFILMMAGVAYIVGSLSNVYFFDNFgKIAlEVANGNTDLIMPEYINSAMP 340
                                       ***************************9998887777777777777777765555515678999************* PP

                               SSF 291 nllaGlllavmlAaimstltslllsassaftkDlYkkirrkasakekelvgvsriivlvvislaillavqeeqkgvl 367
                                       +l+  l++   l+a mstl+s++ +  +++ +D+Yk++++k++  ++    v +i + v i+++++la   + + ++
  gi|298675425|ref|YP_003727175.1| 341 DLFVVLFMLTLLSAAMSTLSSQFHIMGTSIGHDFYKEFLKKGK-GKTTSDVVTKIGIAVTIVVSVVLAYVLPISIIA 416
                                       *****************************************94.444444455555555555556666655656377 PP

                               SSF 368 klvelafaglasavlavillalfwkrvneqGAlagliiG 406
                                          ++ ++  ++a+l++ + alfwk ++++GA+++liiG
  gi|298675425|ref|YP_003727175.1| 417 RATAIFMGLCTAAFLPMYMGALFWKGMTKEGAISSLIIG 455
                                       77777778889***************************9 PP

>> YniB  YniB-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.6   0.7       2.9   1.7e+04      76      93 ..      80      97 ..      77     103 .. 0.54
   2 ?   14.6   0.2   3.5e-06     0.021      81     159 ..     343     420 ..     332     426 .. 0.89
   3 ?   -0.9   0.0       0.2   1.2e+03       4      37 ..     491     524 ..     489     530 .. 0.78

  Alignments for each domain:
  == domain 1  score: -4.6 bits;  conditional E-value: 2.9
                              YniB 76 aFlliylliFvGlalqas 93
                                      +F+ i + iF+ + +++s
  gi|298675425|ref|YP_003727175.1| 80 TFMNIVFGIFIAFVVFGS 97
                                      455555556655555444 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 3.5e-06
                              YniB  81 ylliFvGlalqasgarlsrqvkeireeiedqlilekakGeegktreeleerivvprhtillqifpLyilPviiavig 157
                                       ++++F+   l+a+ + ls q + +  +i  +   e  k  +gkt +++ ++i +   ti++ ++  y+lP+ i++ +
  gi|298675425|ref|YP_003727175.1| 343 FVVLFMLTLLSAAMSTLSSQFHIMGTSIGHDFYKEFLKKGKGKTTSDVVTKIGIA-VTIVVSVVLAYVLPISIIARA 418
                                       7778888888999999**************************************7.69999**********998765 PP

                              YniB 158 yv 159
                                         
  gi|298675425|ref|YP_003727175.1| 419 TA 420
                                       54 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.2
                              YniB   4 wvifipallstlisllkllyaksekkeginavla 37 
                                       w ++ p l++t isl++ + +++++k   n  l+
  gi|298675425|ref|YP_003727175.1| 491 WTVVDPILVATPISLITAVVVSLKTKPPSNKHLK 524
                                       889999999999**99999998888776665555 PP

>> ATP19  ATP synthase subunit K
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1       0.2   1.2e+03      11      36 ..       2      27 ..       1      34 [. 0.81
   2 ?   10.7   0.2   8.8e-05      0.52       4      29 ..      35      63 ..      32      69 .. 0.78
   3 ?   -3.2   0.5       1.9   1.1e+04      20      35 ..     162     177 ..     161     180 .. 0.63

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.2
                                      SS--S-SHHHHHHHHH--XXXXXXXX CS
                             ATP19 11 avkshyLAlgtLgttglivylamggs 36
                                      av + +LA  +L+ +++i yl   g 
  gi|298675425|ref|YP_003727175.1|  2 AVSTPVLAVVVLIYLIVIFYLGLLGY 27
                                      688889***********999987765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 8.8e-05
                                      X---STTSS--S-SHH...HHHHHHH--X CS
                             ATP19  4 aYtIaGravkshyLAl...gtLgttgliv 29
                                       Y +aGr++++ +LAl   +t+++t +iv
  gi|298675425|ref|YP_003727175.1| 35 DYMVAGRKINPYILALsygATFISTSAIV 63
                                      59**************4444666666665 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 1.9
                                       HHHHHHH--XXXXXXX CS
                             ATP19  20 gtLgttglivylamgg 35 
                                       ++L++++ i+++  +g
  gi|298675425|ref|YP_003727175.1| 162 AVLILAIIIAAYVITG 177
                                       5666666666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (531 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1200  (0.0669307); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.75u 0.35s 00:00:01.10 Elapsed: 00:00:00.52
# Mc/sec: 3074.34
//
Query:       gi|298675426|ref|YP_003727176.1|  [L=36]
Description: hypothetical protein Metev_1528 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (36 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 225.10
//
Query:       gi|298675427|ref|YP_003727177.1|  [L=286]
Description: type 11 methyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-24   85.8   0.0    4.2e-24   85.1   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
      3e-22   79.1   0.0    5.4e-22   78.3   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    1.8e-21   76.6   0.0    3.6e-21   75.7   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
      1e-18   67.9   0.0      2e-18   67.0   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
    9.8e-16   57.8   0.0    3.4e-15   56.0   0.0    1.8  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    1.5e-15   57.4   0.0    2.9e-15   56.5   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
    1.3e-11   44.2   0.1    7.6e-11   41.8   0.1    2.2  3  Methyltransf_4   Putative methyltransferase
    1.1e-08   34.8   0.0    1.8e-08   34.1   0.0    1.3  1  MTS              Methyltransferase small domain
    1.6e-05   24.8   0.0    2.1e-05   24.4   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    1.6e-05   24.9   0.0    0.00034   20.5   0.0    2.1  1  Methyltransf_8   Hypothetical methyltransferase
    1.8e-05   24.2   0.0      3e-05   23.4   0.0    1.3  1  CMAS             Mycolic acid cyclopropane synthetase
    9.3e-05   22.1   0.1    0.00018   21.1   0.1    1.5  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    0.00022   20.2   0.0    0.00038   19.5   0.0    1.3  1  Methyltransf_9   Protein of unknown function (DUF1698)
    0.00028   20.3   0.0    0.00076   18.8   0.0    1.7  2  Methyltransf_2   O-methyltransferase domain
    0.00032   20.7   0.0    0.00053   19.9   0.0    1.3  1  Methyltransf_18  Methyltransferase domain
    0.00051   19.2   0.0    0.00087   18.5   0.0    1.3  1  DREV             DREV methyltransferase
    0.00072   19.6   0.0    0.00099   19.1   0.0    1.3  1  Methyltransf_32  Methyltransferase domain
     0.0016   17.7   0.2      0.062   12.5   0.1    2.2  2  N2227            N2227-like protein
     0.0035   17.0   0.0     0.0052   16.4   0.0    1.2  1  NodS             Nodulation protein S (NodS)
     0.0035   17.0   0.0     0.0069   16.0   0.0    1.5  1  MetW             Methionine biosynthesis protein MetW
     0.0045   16.3   0.1     0.0078   15.5   0.1    1.3  1  N6_Mtase         N-6 DNA Methylase
     0.0047   16.5   0.0      0.009   15.6   0.0    1.5  1  DOT1             Histone methylation protein DOT1
     0.0093   15.1   0.0      0.014   14.4   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
  ------ inclusion threshold ------
      0.012   15.1   0.0       0.02   14.3   0.0    1.4  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.036   13.7   0.0      0.052   13.2   0.0    1.2  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
      0.044   13.5   0.0       0.09   12.4   0.0    1.5  1  UPF0020          Putative RNA methylase family UPF0020
      0.074   11.6   0.0       0.11   11.0   0.0    1.3  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m
       0.22   11.1   0.0        0.3   10.6   0.0    1.1  1  FmrO             Ribosomal RNA methyltransferase (FmrO)


Domain annotation for each model (and alignments):
>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.1   0.0   6.5e-27   4.2e-24       4     125 ..     140     258 ..     138     281 .. 0.90

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 6.5e-27
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlils 80 
                                       g+++lD+GCG G +t  +a e +p++ v+Gi+i+e+ i++++ n++ l+++nv+F+ gdi +l+  +e + +D +++
  gi|298675427|ref|YP_003727177.1| 140 GNYILDIGCGVGSITMDIA-EQNPDSSVYGIEIEENLINQCKMNSEILEISNVNFKTGDIYDLP--FENDAVDTVTC 213
                                       789****************.99******************************************..*********** PP

                   Methyltransf_31  81 nevlnaladpdkileeiervlkpggilliedprllaelpakveee 125
                                       +  l++l d ++ leei+rvl+ gg+l+++dp ++   p++ ee+
  gi|298675427|ref|YP_003727177.1| 214 FFMLHHLDDIPAGLEEIKRVLSGGGHLITTDPFGHHHGPEITEEN 258
                                       *******************************98666666555554 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.3   0.0   8.4e-25   5.4e-22       1      95 [.     144     241 ..     144     242 .. 0.98

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 8.4e-25
                                       EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC- CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhhv 74 
                                       Ld+GcG G+++ ++a++   ++v+g+++ +++++++k++++  ++ +v+f  +d+ +lpfe++ +D v+++++lhh+
  gi|298675427|ref|YP_003727177.1| 144 LDIGCGVGSITMDIAEQNpdSSVYGIEIEENLINQCKMNSEILEIsNVNFKTGDIYDLPFENDAVDTVTCFFMLHHL 220
                                       8**************8889***********************999******************************** PP

                                       CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  75 edpekalkeiaRvLkpgGllv 95 
                                       +d  + l+ei+RvL  gG+l+
  gi|298675427|ref|YP_003727177.1| 221 DDIPAGLEEIKRVLSGGGHLI 241
                                       *******************98 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.7   0.0   5.6e-24   3.6e-21       1      97 []     143     238 ..     143     238 .. 0.96

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 5.6e-24
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalhh 76 
                                       +Ld+GcG G +t+++a++ ++++v+g++i e+++++++ + e  ++ nv+f +gd+ dlpfe++ +D v+++++lhh
  gi|298675427|ref|YP_003727177.1| 143 ILDIGCGVGSITMDIAEQNPDSSVYGIEIEENLINQCKMNSEILEIsNVNFKTGDIYDLPFENDAVDTVTCFFMLHH 219
                                       8*****************879*******************9887789****************************** PP

                                       SSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  77 lsdedlekalkeiarvLkpgG 97 
                                       l+  d+++ l+ei+rvL  gG
  gi|298675427|ref|YP_003727177.1| 220 LD--DIPAGLEEIKRVLSGGG 238
                                       98..9************9998 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.0   0.0   3.1e-21     2e-18       1      99 []     144     240 ..     144     240 .. 0.91

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 3.1e-21
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvvasnvl 76 
                                       L+iGcG+Gs+++ ++e++pd++++g++i ++ i   + k+++++ +  +nv++++ d+ dl+ + +++D+v++++ l
  gi|298675427|ref|YP_003727177.1| 144 LDIGCGVGSITMDIAEQNPDSSVYGIEIEENLI--NQCKMNSEI-LEISNVNFKTGDIYDLPFEnDAVDTVTCFFML 217
                                       8********************************..566666655.578999999999988888789*********** PP

                   Methyltransf_12  77 hhlkdirevldnirklLkpgGrl 99 
                                       hhl+di + l++i+++L+ gG+l
  gi|298675427|ref|YP_003727177.1| 218 HHLDDIPAGLEEIKRVLSGGGHL 240
                                       *********************97 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.6     1e+03      28      47 ..      17      36 ..      11      43 .. 0.79
   2 !   56.0   0.0   5.3e-18   3.4e-15      18     151 ..     109     242 ..      95     268 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.6
                                      HTTTHHHHHHHHHHH--S-- CS
                   Ubie_methyltran 28 slgihrlWkkfveklvavkr 47
                                      sl+i  lWk+ + k+++  +
  gi|298675427|ref|YP_003727177.1| 17 SLHILTLWKDSISKIESYNN 36
                                      899999****9999987655 PP

  == domain 2  score: 56.0 bits;  conditional E-value: 5.3e-18
                                       HHHHHHHHHHHTTTHHHHHH.HHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHH CS
                   Ubie_methyltran  18 skyDlmndvlslgihrlWkk.fveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklk 93 
                                       +++D +n+       +  ++  + ++  +  g+ +lD+ +G g ++++++++      v +++i+en++++ +   +
  gi|298675427|ref|YP_003727177.1| 109 TSFDSLNATYPHPAMKELRTkVLGQILPNIDGNYILDIGCGVGSITMDIAEQN-PDSSVYGIEIEENLINQCKMNSE 184
                                       66777777777666666666245577788899******************985.6678***************9999 PP

                                       HHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEE CS
                   Ubie_methyltran  94 eegkinieflqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvv 151
                                           +n++f +++  +Lpfe+d+ D+vt  f l  + D++ +L+e+ rvl  GG+l+ 
  gi|298675427|ref|YP_003727177.1| 185 ILEISNVNFKTGDIYDLPFENDAVDTVTCFFMLHHLDDIPAGLEEIKRVLSGGGHLIT 242
                                       99999*************************************************9975 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   0.0   4.5e-18   2.9e-15      10     127 ..     124     260 ..     116     277 .. 0.83

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 4.5e-18
                   Methyltransf_23  10 sdklerllpk...lraggrvLdiGcGtG.illevlrengf.svtgvDlspeaveiae......kakkaqkdqfdeqe 75 
                                       ++++ ++l+    +  g+ +LdiGcG+G i+++++++n+  sv+g+++ +++++  +      ++++ +++  d  +
  gi|298675427|ref|YP_003727177.1| 124 KELRTKVLGQilpNIDGNYILDIGCGVGsITMDIAEQNPDsSVYGIEIEENLINQCKmnseilEISNVNFKTGDIYD 200
                                       455555443334389999**********88999888887789***********9999******9999999999999* PP

                   Methyltransf_23  76 aaepqgkfdlIvlrevlehvpdppellrqiatllkpgGylllseplasl........ked 127
                                        +++++  d+++++++l+h++d p+ l  i++ l+ gG+l+ ++p   +         ++
  gi|298675427|ref|YP_003727177.1| 201 LPFENDAVDTVTCFFMLHHLDDIPAGLEEIKRVLSGGGHLITTDPFGHHhgpeiteeNWK 260
                                       ********************************************9777745444433233 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       4.3   2.8e+03      64      91 ..     102     129 ..      94     130 .. 0.77
   2 !   41.8   0.1   1.2e-13   7.6e-11       4      80 ..     142     215 ..     139     221 .. 0.88
   3 ?   -1.4   0.0       2.2   1.4e+03      99     118 ..     226     244 ..     223     272 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.3
                                       HHHCS-TTSEEEEEEES-----SGGGGG CS
                    Methyltransf_4  64 llelledgslekifilFPDPwfKkrhhK 91 
                                       + e+l+  s++ +   +P P +K+ ++K
  gi|298675427|ref|YP_003727177.1| 102 VYEVLPYTSFDSLNATYPHPAMKELRTK 129
                                       5577888899999999999999986665 PP

  == domain 2  score: 41.8 bits;  conditional E-value: 1.2e-13
                                       EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHHHHCS-TTSEEEEEEES CS
                    Methyltransf_4   4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkvllelledgslekifilF 80 
                                        +l+iGcG G++++++A++nPd ++ GiEi++++++++  + e le++N++   gd  + l   +e++ ++ +  +F
  gi|298675427|ref|YP_003727177.1| 142 YILDIGCGVGSITMDIAEQNPDSSVYGIEIEENLINQCKMNSEILEISNVNFKTGDIYD-L--PFENDAVDTVTCFF 215
                                       689****************************************************9844.4..36777777666666 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.2
                                       HHHHHHHHEEEEEEEEEEES CS
                    Methyltransf_4  99 llkelarvLkkgGvlelaTD 118
                                        l+e++rvL  gG l + TD
  gi|298675427|ref|YP_003727177.1| 226 GLEEIKRVLSGGGHLIT-TD 244
                                       58899999999999865.66 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   2.8e-11   1.8e-08      20     102 ..     128     212 ..     121     242 .. 0.90

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 2.8e-11
                                       HHHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTT.TST CS
                               MTS  20 sklLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvle.eve 94 
                                       +k+L + lp+   + +lD+GcG+G +++ +a+++p+ +v  ++++ + ++ +k n e  +++ v++ + d+++  +e
  gi|298675427|ref|YP_003727177.1| 128 TKVLGQILPNIDGNYILDIGCGVGSITMDIAEQNPDSSVYGIEIEENLINQCKMNSEILEISnVNFKTGDIYDlPFE 204
                                       889999****88889*********************************************999********983455 PP

                                       TS-EEEEE CS
                               MTS  95 ekkfdliv 102
                                       ++ +d++ 
  gi|298675427|ref|YP_003727177.1| 205 NDAVDTVT 212
                                       77777775 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   3.3e-08   2.1e-05      21     132 ..      78     197 ..      66     241 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 3.3e-08
                                       HHHHHHHS-GGGGSSCGGGG...GTTSSS-EEE..ETTEEE--HHHHHHHHHHTT....--TT-EEEEES-TTSHHH CS
                              PCMT  21 vaealeevdReefvpesfke...kaYedaplsi..gynatiSaphmvalalelle....lkkgarvLevGsGsGylt 88 
                                       v+e l++ d +++v+  f e   ++Ye  p +   + nat   p m  l ++ l       +g+ +L++G+G G  t
  gi|298675427|ref|YP_003727177.1|  78 VVEFLKSDDNGVYVKGLFAEnnsNVYEVLPYTSfdSLNATYPHPAMKELRTKVLGqilpNIDGNYILDIGCGVGSIT 154
                                       66667777777777766654333677777763222456999999999999999988633246899************ PP

                                       HHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES- CS
                              PCMT  89 avlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgD 132
                                         +a+    +  v +ie  ++l+++ k n + l+++nv +++gD
  gi|298675427|ref|YP_003727177.1| 155 MDIAEQNP-DSSVYGIEIEENLINQCKMNSEILEISNVNFKTGD 197
                                       99999755.556*******************************9 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   5.3e-07   0.00034      92     187 ..     177     277 ..      90     286 .] 0.73

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 5.3e-07
                                       S-..EEEEESS-SSTTEEES-TTS-S--TT-EEEEEEES---..SS-HHHHHHHHHHHEEEEEEEEEEEEGGG-S.. CS
                    Methyltransf_8  92 ekekvrsfdlvavnervvacdlakvPledesvdvavfclslm..gtnladflkeanrvlkvGGllkvaevksrfe.. 164
                                       ++ k++s  l   n +  + d+  +P e+++vd +  c+ ++   +++   l+e++rvl  GG+l  ++     +  
  gi|298675427|ref|YP_003727177.1| 177 NQCKMNSEILEISNVNFKTGDIYDLPFENDAVDTVT-CFFMLhhLDDIPAGLEEIKRVLSGGGHLITTDPFGHHHgp 252
                                       34455555566667778899*************765.555541247999***************9887755554433 PP

                                       ..-HHHHHHHHHCTTEEEEEEE--S CS
                    Methyltransf_8 165 ..svklfaraltklGfevkskdlsn 187
                                           + +++++++ Gf ++  ++ n
  gi|298675427|ref|YP_003727177.1| 253 eiTEENWKNHFENAGFSTNIEKIGN 277
                                       3334455666666666666666555 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   4.8e-08     3e-05      62     164 ..     139     242 ..     122     266 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 4.8e-08
                                       TT-EEEEES-TTSHHHHHHHHH.H--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---...--SEEEEE CS
                              CMAS  62 pGmtlLdiGcGWGslvrraver.ydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde...kvdrvvsv 134
                                       +G+++LdiGcG Gs+++  +e+  d +v g+ + ++  +++k + + l++  +v+ k  d  dl+     vd v  +
  gi|298675427|ref|YP_003727177.1| 139 DGNYILDIGCGVGSITMDIAEQnPDSSVYGIEIEENLINQCKMNSEILEI-SNVNFKTGDIYDLPFendAVDTVTCF 214
                                       79************98887765169***********99999988877774.56788888888887622356666666 PP

                                       S-GGGTSGGGHHHHHHHHHHHS-TT-EEEE CS
                              CMAS 135 gafehvgkenydtffkklkkllkedGllll 164
                                        ++ h+  +  ++  +++k++l  +G l+ 
  gi|298675427|ref|YP_003727177.1| 215 FMLHHL--DDIPAGLEEIKRVLSGGGHLIT 242
                                       666665..5667777777777777777665 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   2.8e-07   0.00018       2      60 ..     141     200 ..     140     232 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.8e-07
                   Methyltransf_15   2 rvilDlfsGaGGnviqfalv..fekviaieinleklacaqhNaevYgvsdkitlvlgdvfe 60 
                                       ++ilD+ +G G  ++ +a++   ++v++iei+++ +++++ N e+ ++s ++ +++gd+ +
  gi|298675427|ref|YP_003727177.1| 141 NYILDIGCGVGSITMDIAEQnpDSSVYGIEIEENLINQCKMNSEILEIS-NVNFKTGDIYD 200
                                       689***************9966679*********************986.69999999987 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0     6e-07   0.00038     110     216 ..     134     241 ..     124     245 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 6e-07
                                       GS.--TT-EEEEET-TTSHHHHHHHHCT-SE.EEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T.---EE CS
                    Methyltransf_9 110 hlsdlkgrtildvGcgnGyhlwrmvgegakl.vvGidPselfliqfeavrkllgedqrahllplgieqlpe.leafd 184
                                        l+++ g  ild+Gcg G   + ++ +++++ v Gi+ +e  + q +   ++l   + +++    i +lp   +a d
  gi|298675427|ref|YP_003727177.1| 134 ILPNIDGNYILDIGCGVGSITMDIAEQNPDSsVYGIEIEENLINQCKMNSEILEISNVNFKT-GDIYDLPFeNDAVD 209
                                       578899*******************999975267*******************888888777.689****8799*** PP

                                       EEEEES-GGG-S-HHHHHHHHHCTEEEEEEEE CS
                    Methyltransf_9 185 tvfsmGvlyhrrsPldhllqlkdqlvkgGelv 216
                                       tv    +l+h       l ++k  l  gG+l+
  gi|298675427|ref|YP_003727177.1| 210 TVTCFFMLHHLDDIPAGLEEIKRVLSGGGHLI 241
                                       **********99988999**********9998 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.2e-06   0.00076      65     167 ..     142     245 ..     112     259 .. 0.83
   2 ?   -1.0   0.0       1.4   9.1e+02     190     210 .]     249     269 ..     245     269 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.2e-06
                                       EEEEET-TTSHHHHHHHHH-TT-EEEEEE-HH.HHHHHHHHS-----TTEEEEES-TTTS---.--SEEEEESSGGG CS
                    Methyltransf_2  65 slvDvGGGtGalakaivsayPtikvivfDlpe.VveaAkehlsageeervefvgGdffkdslP.eaDaillkrvlhD 139
                                        ++D+G G+G +   i+++ P  +v   ++ e  +++ k   +  e ++v+f  Gd++   lP e Da+  +   + 
  gi|298675427|ref|YP_003727177.1| 142 YILDIGCGVGSITMDIAEQNPDSSVYGIEIEEnLINQCKMNSEILEISNVNFKTGDIY--DLPfENDAVDTVTCFFM 216
                                       689***************************75389999999999999***********..89999999877666554 PP

                                       .S-HHHHHHHHHHHHHH--TT-EEEEEE- CS
                    Methyltransf_2 140 .wsdekcvklLkrvkkalpagGkvivvea 167
                                        +  +++   L+++k+ l  gG++i  + 
  gi|298675427|ref|YP_003727177.1| 217 lHHLDDIPAGLEEIKRVLSGGGHLITTDP 245
                                       133466788899****9999999997665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.4
                                       SS-----HHHHHHHHHHCT-E CS
                    Methyltransf_2 190 teGkeRteaeyeellseaGfs 210
                                       ++G e te+++++ +++aGfs
  gi|298675427|ref|YP_003727177.1| 249 HHGPEITEENWKNHFENAGFS 269
                                       579999**************6 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   8.3e-07   0.00053       7      87 ..     133     212 ..     127     217 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 8.3e-07
                   Methyltransf_18   7 aiaslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeee. 82 
                                       +i   ++ g+ ++DiG+  g +++ +++++  ++v+ ++i+e+ ++++k n e  +++ ++++  +d  +   e++ 
  gi|298675427|ref|YP_003727177.1| 133 QILPNID-GNYILDIGCGVGSITMDIAEQNPDSSVYGIEIEENLINQCKMNSEILEIS-NVNFKTGDIYDLPFENDa 207
                                       5555666.899******************************************99995.699999998887766666 PP

                   Methyltransf_18  83 vdtvv 87 
                                       vdtv+
  gi|298675427|ref|YP_003727177.1| 208 VDTVT 212
                                       88876 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.4e-06   0.00087      93     200 ..     138     256 ..     126     281 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.4e-06
                              DREV  93 qedkklldlGaGdGeitkrvaptfee..vyatelsetmrdrlkkkk.ynvlsalelqetdv........kldlilcl 158
                                        + + +ld+G G G it  +a++  +  vy  e+ e+++++ k       +s+++++  d+          d ++c+
  gi|298675427|ref|YP_003727177.1| 138 IDGNYILDIGCGVGSITMDIAEQNPDssVYGIEIEENLINQCKMNSeILEISNVNFKTGDIydlpfendAVDTVTCF 214
                                       566789*************998764445************9875421333445555544432222222246789*** PP

                              DREV 159 nlldrcfdplklledirsalepngrvivalvlPvshyvetnt 200
                                        +l   +d    le+i+ +l   g+ i +  +  +h  e   
  gi|298675427|ref|YP_003727177.1| 215 FMLHHLDDIPAGLEEIKRVLSGGGHLITTDPFGHHHGPEITE 256
                                       *******99999*******99999999876666666555554 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.6e-06   0.00099      25      91 ..     139     200 ..     123     259 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.6e-06
                   Methyltransf_32  25 galtvvDvGaGkgYLsfvlalkeke.yklkvvgidakeelvekaekraeklgkkfnkrlsfaelsiee 91 
                                       + ++++D+G+G g  +  +a    +    +v+gi+++e+l+++++   e l+  + ++++f++++i +
  gi|298675427|ref|YP_003727177.1| 139 DGNYILDIGCGVGSITMDIAE---QnPDSSVYGIEIEENLINQCKMNSEILE--I-SNVNFKTGDIYD 200
                                       56789************9999...4378****************99999998..6.788888887765 PP

>> N2227  N2227-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.053        34      61      87 ..     143     171 ..     120     176 .. 0.81
   2 !   12.5   0.1   9.6e-05     0.062     134     217 ..     178     258 ..     170     283 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.053
                                       EEEET-TT-HHHHHHHHT..T-EEEEEE- CS
                             N2227  61 ilvPGaGlGrlavelatk..gyqvegnEf 87 
                                       il  G+G+G +++++a++  + +v g+E+
  gi|298675427|ref|YP_003727177.1| 143 ILDIGCGVGSITMDIAEQnpDSSVYGIEI 171
                                       6667************9966677777776 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 9.6e-05
                                       SS------TTS--EEEEES-HHHHH--SSHTT-EEEEEEES-TTSSS-HHHHHHHHHHHEEEEEEEEEEE----TTT CS
                             N2227 134 DveplselkrkknlsmaagdflevykeeeaaesydvvvtcfFiDtaeNvleYletiekvlkpgglwiNlGPLlYhfe 210
                                         ++ se+ + +n++  +gd  ++  e+   ++ d+v + f +     +   le i++vl  gg++i   P  +h  
  gi|298675427|ref|YP_003727177.1| 178 QCKMNSEILEISNVNFKTGDIYDLPFEN---DAVDTVTCFFMLHHLDDIPAGLEEIKRVLSGGGHLITTDPFGHHHG 251
                                       5566788888999999999999999999...99999998899999******************************99 PP

                                       TTTSEEE CS
                             N2227 211 dltvade 217
                                       +  ++++
  gi|298675427|ref|YP_003727177.1| 252 PEITEEN 258
                                       8754443 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   8.1e-06    0.0052      45     144 ..     141     242 ..     123     259 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.1e-06
                              NodS  45 adalevGcaaGalterlapyckrltv..vdvveeaiarar..ervkesshiswivsdvqqfst.dekfdlivvaevl 116
                                         +l++Gc  G++t  +a      +v  +++ e+ i++++    + e s++++ + d+  +   ++  d++ +   +
  gi|298675427|ref|YP_003727177.1| 141 NYILDIGCGVGSITMDIAEQNPDSSVygIEIEENLINQCKmnSEILEISNVNFKTGDIYDLPFeNDAVDTVTC---F 214
                                       5589**************99865555449999****98772256889***********999751456777777...5 PP

                              NodS 117 yyiedvaelraavrnlvsllapdgqlvf 144
                                       + ++++ ++ a ++++ ++l+ +g+l+ 
  gi|298675427|ref|YP_003727177.1| 215 FMLHHLDDIPAGLEEIKRVLSGGGHLIT 242
                                       666667778899************9995 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.1e-05    0.0069      13      65 ..     139     194 ..     129     251 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.1e-05
                              MetW  13 pgsrvldlGcGdGel.lellkeekqvdgrGleldeegvaecvakG..lsviqgdld 65 
                                       +g  +ld+GcG G++ +++ +++ + + +G+e++e+ +++c      l++ + +  
  gi|298675427|ref|YP_003727177.1| 139 DGNYILDIGCGVGSItMDIAEQNPDSSVYGIEIEENLINQCKMNSeiLEISNVNFK 194
                                       56789*********93456666779999*************754322444444444 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   1.2e-05    0.0078      36     115 ..     129     199 ..     124     214 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.2e-05
                          N6_Mtase  36 klivellepksgesvyDpacGsggllvqaekvlkeedgktkelsiyGqeknettyrLakmNlllhgieykkvkirlg 112
                                       k++ ++l + +g+ ++D  cG g++ +  ++       ++ + s+yG e++e+ ++ +kmN  + +i + ++  ++g
  gi|298675427|ref|YP_003727177.1| 129 KVLGQILPNIDGNYILDIGCGVGSITMDIAE-------QNPDSSVYGIEIEENLINQCKMNSEILEISNVNF--KTG 196
                                       77888998899999**********9776655.......7899********************9999987754..445 PP

                          N6_Mtase 113 dtl 115
                                       d +
  gi|298675427|ref|YP_003727177.1| 197 DIY 199
                                       554 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.4e-05     0.009      43      89 ..     140     186 ..     108     199 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.4e-05
                                       T-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHHHHHHHHH CS
                              DOT1  43 edvFvDLGSGvGnvvlqaalevgcklsvGvEimdnaselaekqkeel 89 
                                        ++ +D+G GvG +++ +a +      +G+Ei +n  +  + + e+l
  gi|298675427|ref|YP_003727177.1| 140 GNYILDIGCGVGSITMDIAEQNPDSSVYGIEIEENLINQCKMNSEIL 186
                                       57889******************************998888777766 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   2.2e-05     0.014      32      96 ..     141     209 ..     125     234 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.2e-05
                                       SEEEEES-TTTCCHHHHHCC-..SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S-CCGHHHHHHHCT CS
                            RrnaAD  32 ltvleigpGkGilTeeLakra..kqvvvlElderLakllqkkls..kdeklkvvhqDflkfetpeevte 96 
                                         +l+ig G+G  T  +a++    +v  +E+ e+L++  + + +  + ++++    D+++  + +++ +
  gi|298675427|ref|YP_003727177.1| 141 NYILDIGCGVGSITMDIAEQNpdSSVYGIEIEENLINQCKMNSEilEISNVNFKTGDIYDLPFENDAVD 209
                                       579******************9888999*********99886667688999999999999888887654 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.1e-05      0.02     162     258 ..     140     242 ..     126     266 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.1e-05
                              PrmA 162 geevlDvGtGSGiLaiaaakLg.akkvvavDiDevAvkvakeNaelNkvea.klevalseell.keekadvivaNIL 235
                                       g+ +lD+G+G G +++  a  +  ++v+++ i+e  ++  k N e+ ++++ ++++    +l+ ++  +d + +  +
  gi|298675427|ref|YP_003727177.1| 140 GNYILDIGCGVGSITMDIAEQNpDSSVYGIEIEENLINQCKMNSEILEISNvNFKTGDIYDLPfENDAVDTVTCFFM 216
                                       5689******9998887666651578************************9999875556666558899*****999 PP

                              PrmA 236 aevliel...aedikklvkeggllil 258
                                        + l ++   +e+ik+++  gg+li+
  gi|298675427|ref|YP_003727177.1| 217 LHHLDDIpagLEEIKRVLSGGGHLIT 242
                                       99998884445788889999998886 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   8.2e-05     0.052       4      70 ..     135     200 ..     132     212 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.2e-05
                                       H---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTC CS
                   Methyltr_RsmB-F   4 LapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDark 70 
                                       L   +++ ilD+ ++ G+ T  iae  ++ + v+ ++++++ +++ + n + L + n+   ++D+  
  gi|298675427|ref|YP_003727177.1| 135 LPNIDGNYILDIGCGVGSITMDIAEQ-NPDSSVYGIEIEENLINQCKMNSEILEISNVNFKTGDIYD 200
                                       55668899*****************9.88999**************************999999765 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00014      0.09      72     127 ..     159     213 ..     138     214 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                                       HHHHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE CS
                           UPF0020  72 earaelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivt 127
                                       e++++ ++yg++++++++++++ N e  +++  ++f++ d+ +L+ +++ vd++ +
  gi|298675427|ref|YP_003727177.1| 159 EQNPDSSVYGIEIEENLINQCKMNSEILEIS-NVNFKTGDIYDLPFENDAVDTVTC 213
                                       5567888**********************97.59***********88889**9976 PP

>> Methyltransf_29  Putative S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00018      0.11     119     223 ..     141     248 ..     108     269 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00018
                   Methyltransf_29 119 rtvlDvGCgvasfgayllsrdvlt..lslapkDeheaqvqfaLeRgvpailav...lgt.krlpyPsrsfdlihCsr 189
                                         +lD+GCgv s +  + +++  +    +  +++  +q ++  e  +  i +v    g    lp+   + d++ C  
  gi|298675427|ref|YP_003727177.1| 141 NYILDIGCGVGSITMDIAEQNPDSsvYGIEIEENLINQCKMNSE--ILEISNVnfkTGDiYDLPFENDAVDTVTCFF 215
                                       579**************999865511344455555555555555..54444442113322589*********99975 PP

                   Methyltransf_29 190 CridwteedgilllevdRvlRpgGyfvlsappvy 223
                                         +++ ++  + l e++Rvl  gG+++ + p  +
  gi|298675427|ref|YP_003727177.1| 216 -MLHHLDDIPAGLEEIKRVLSGGGHLITTDPFGH 248
                                       .455666667789***********9998766444 PP

>> FmrO  Ribosomal RNA methyltransferase (FmrO)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00046       0.3     102     190 ..     133     225 ..     120     231 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00046
                              FmrO 102 aalPapa..svlDvaCgLnpLavpwlllaadatylasDidsdlvefldrflalvevegrvevrDlvad..vpapraD 174
                                        +lP ++   +lD++Cg+  +++    +  d+  ++ +i+ +l++  +   +++e+ +       + d     + +D
  gi|298675427|ref|YP_003727177.1| 133 QILPNIDgnYILDIGCGVGSITMDIAEQNPDSSVYGIEIEENLINQCKMNSEILEISNVNFKTGDIYDlpFENDAVD 209
                                       47899863369*********************************999999999998765554444455222345566 PP

                              FmrO 175 laLvLktlpvLeqrrr 190
                                           + +l+ L+++ +
  gi|298675427|ref|YP_003727177.1| 210 TVTCFFMLHHLDDIPA 225
                                       6666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 1689.20
//
Query:       gi|298675428|ref|YP_003727178.1|  [L=163]
Description: phosphodiesterase family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-27   95.6   0.1    3.9e-27   95.5   0.1    1.0  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    8.8e-06   26.4   3.7    0.00019   22.0   0.4    2.1  2  Metallophos    Calcineurin-like phosphoesterase
    0.00058   19.3   0.2       0.34   10.2   0.0    2.2  2  Metallophos_3  Metallophosphoesterase, calcineurin superfamil


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.5   0.1   6.5e-31   3.9e-27       3     164 ..       2     155 ..       1     156 [. 0.89

  Alignments for each domain:
  == domain 1  score: 95.5 bits;  conditional E-value: 6.5e-31
                     Metallophos_2   3 laiiSDlHsnldaleavlealkevgvdaiihaGDleeeepevleellela.pvlaVrGNnDeev..veedvlreaae 76 
                                       ++i+SD+H+n+da+ ++++ ++e +v+ i+haGD+  ++p + ++l++l+ ++++V+GNnD+++  +++ + +  ae
  gi|298675428|ref|YP_003727178.1|   2 IGIMSDSHDNMDAIYKAVSVFNEKKVNSILHAGDI--VSPFTGKALKNLEsKLYYVFGNNDGDIltIKKWFDEIGAE 76 
                                       89*********************************..***99999999999**********6666777777777777 PP

                     Metallophos_2  77 lgtdlpeeaelelagekvlliHgdplgvkdalaellkeaeegsd.vvvcGHtHvpevekeggvlvvnPGsvgeprdg 152
                                         +d+    +l++++++++l+Hg     ++++ +++    +g++ vvv GHtH ++ e ++g+l++nPG+ ++  +g
  gi|298675428|ref|YP_003727178.1|  77 NCGDF---GDLTIEDRHIALVHGV----NNSMVKAIAG--SGDYdVVVRGHTHNRGTEYIKGTLIINPGESAGVLTG 144
                                       77777...888889*********7....7888888877..55555****************************9888 PP

                     Metallophos_2 153 dpetyaildtde 164
                                        + ++a+ldtd+
  gi|298675428|ref|YP_003727178.1| 145 NR-SIALLDTDT 155
                                       88.******986 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.4   3.2e-08   0.00019       3     105 ..       2      84 ..       1     101 [. 0.71
   2 !    5.5   0.8    0.0036        21     189     203 ..     107     121 ..      80     122 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 3.2e-08
                                       EEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTSCHHH CS
                       Metallophos   3 ilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHegfee 79 
                                       i +++D H      ++d++ k+++ ++++ k++ +l+aGD+v        + + l+ l +   ++y + GN +  ++
  gi|298675428|ref|YP_003727178.1|   2 IGIMSDSH-----DNMDAIYKAVSVFNEK-KVNSILHAGDIVSPF-----TGKALKNLES---KLYYVFGNND-GDI 63 
                                       6799****.....**********999888.**********99998.....7777777777...7889******.333 PP

                                       .HHHHHHHHHHHHHHHHEHHHCEEETS CS
                       Metallophos  80 .ellnkygylgifsepwrsdaevfnnl 105
                                         ++  +++      +   +++ f+ l
  gi|298675428|ref|YP_003727178.1|  64 lTIKKWFDE------IGAENCGDFGDL 84 
                                       333333222......222334444444 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0036
                                       HHTTESEEEEESSSS CS
                       Metallophos 189 kkygvdlvisGHtHv 203
                                         ++ d+v++GHtH 
  gi|298675428|ref|YP_003727178.1| 107 GSGDYDVVVRGHTHN 121
                                       56789*********6 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0   0.00034         2      11      87 ..       5      75 ..       2      83 .. 0.74
   2 !   10.2   0.0   5.6e-05      0.34     203     237 ..     103     138 ..      81     163 .] 0.73

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00034
                                      EE--TT-GGGHHHHHHHHHHH--SEEEEES-----HHHHHHHHHHHHTT----THHHHHHHHHHHHHHHHHHHHHHT CS
                     Metallophos_3 11 isdlkgevellerlveviedkdpDllvlvGdlvkaeakadeyesaqeerrepdkkeileekneiiklldklfrelge 87
                                      +sd +++++ + + v v ++k+++ ++  Gd+v++ +  +      +++ e +   ++ +++ +i ++ k f+e+g 
  gi|298675428|ref|YP_003727178.1|  5 MSDSHDNMDAIYKAVSVFNEKKVNSILHAGDIVSPFTG-KA-----LKNLESKLYYVFGNNDGDILTIKKWFDEIGA 75
                                      5788999*************************987432.22.....2234555566666666777777777777665 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 5.6e-05
                                       HHHHHHH--SEEEE-SS--EE.EEETTEEEEE--BG CS
                     Metallophos_3 203 aelvktlnPevvvvghavkeh.eelgktlvvnPGal 237
                                         +  + + +vvv gh++ +  e +  tl++nPG+ 
  gi|298675428|ref|YP_003727178.1| 103 KAIAGSGDYDVVVRGHTHNRGtEYIKGTLIINPGES 138
                                       34444445689999***98767************84 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 980.86
//
Query:       gi|298675429|ref|YP_003727179.1|  [L=172]
Description: Appr-1-p processing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-45  152.9   0.2    4.6e-45  152.5   0.2    1.2  1  Macro     Macro domain


Domain annotation for each model (and alignments):
>> Macro  Macro domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.5   0.2   2.6e-49   4.6e-45       1     118 []      22     134 ..      22     134 .. 0.98

  Alignments for each domain:
  == domain 1  score: 152.5 bits;  conditional E-value: 2.6e-49
                                       EEEEETTSS-CSHHHHHHHHHHHHHHHHHHHHHHHHHHS--TTSEEEEE-TTSSSSEEEEEESE-TTTSTSTTHHHH CS
                             Macro   1 VnAaNsrllggggvagaihraagkalkeeckelekkqggcllGeavvtpaynlpakyvihtvgplftsskskeeeel 77 
                                       VnAaN++l ggggv+gaihraag++l+eeck+l    ggc++Gea++t+ay+lpa++vihtvgp+++ ++++ e+el
  gi|298675429|ref|YP_003727179.1|  22 VNAANKSLHGGGGVDGAIHRAAGPQLLEECKNL----GGCETGEAKITNAYKLPANWVIHTVGPVWK-GGGHHEDEL 93 
                                       9********************************....99***************************8.8******** PP

                                       HHHHHHHHHHHHHHTT-SEEEEE-TTSSTTSBTHHHHHHHH CS
                             Macro  78 lakayknalelaeekgiksvafPaistGifgvpweeaarva 118
                                       lak+y n+l la++ +ik++afPaistG++g+p+e+a r+a
  gi|298675429|ref|YP_003727179.1|  94 LAKCYINSLTLAKQYNIKTIAFPAISTGVYGFPVERASRIA 134
                                       *************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1063.55
//
Query:       gi|298675430|ref|YP_003727180.1|  [L=361]
Description: hypothetical protein Metev_1534 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-21   74.6   1.4    7.4e-14   51.7   0.0    2.6  3  CCG       Cysteine-rich domain
      6e-09   36.7   4.8    1.7e-08   35.2   4.8    1.9  1  Fer4_16   4Fe-4S double cluster binding domain
      1e-08   35.5   2.7      1e-08   35.5   2.7    1.9  2  Fer4_8    4Fe-4S dicluster domain
      4e-08   33.2   8.3    0.00047   20.2   0.7    3.8  4  Fer4_10   4Fe-4S dicluster domain
    7.9e-07   29.6   4.2    3.4e-06   27.6   4.2    2.2  1  Fer4_7    4Fe-4S dicluster domain
    5.6e-06   26.8   2.1    5.6e-06   26.8   2.1    2.6  3  Fer4_17   4Fe-4S dicluster domain
    0.00027   20.6  19.5     0.0085   15.9   4.3    3.1  3  Fer4      4Fe-4S binding domain
    0.00067   19.8   9.4       0.11   12.7   0.4    2.6  2  Fer4_18   4Fe-4S dicluster domain
    0.00081   19.5   9.1      0.013   15.6   1.6    3.2  3  Fer4_21   4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.01   16.4   5.2       0.04   14.4   1.5    2.7  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
      0.024   15.1   2.4      0.024   15.1   2.4    4.0  4  Fer4_4    4Fe-4S binding domain
       0.11   12.6  17.3      0.066   13.4  11.0    3.3  5  Fer4_9    4Fe-4S dicluster domain
       0.39   10.9  18.0       0.18   12.0   2.0    3.1  3  Fer4_2    4Fe-4S binding domain
        2.2    8.5  18.9       0.13   12.4   3.6    3.4  3  Fer4_6    4Fe-4S binding domain
        9.3    7.2   9.0         28    5.6   1.4    2.9  3  Fer4_22   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       9.3   1.1e+04      69      80 ..      55      66 ..      46      67 .. 0.69
   2 !   51.7   0.0   6.2e-17   7.4e-14       2      84 ..     135     216 ..     134     217 .. 0.97
   3 !   21.6   0.1   1.6e-07   0.00019       5      84 ..     260     336 ..     256     337 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 9.3
                               CCG 69 gadaivtacpgC 80
                                      ++ ++ t c+ C
  gi|298675430|ref|YP_003727180.1| 55 DNIYLSTRCGAC 66
                                      567888999999 PP

  == domain 2  score: 51.7 bits;  conditional E-value: 6.2e-17
                               CCG   2 ayfdgChllraaypevrkalkkllealgveleelekesCCGagggrsgkeelaealakrnvetaeetgadaivtacp 78 
                                        y  gC ++ +a+pe  +++ ++l+ +g+e  +l++e+CCG   + +g+ +++++ ak+ v+ +e+++ +++++ cp
  gi|298675430|ref|YP_003727180.1| 135 GYMAGC-WISYAQPEIARSTIRVLNSAGIEPRILKDEKCCGIFLVDNGHFDEMKSHAKNYVDYIESLEIKKLIVSCP 210
                                       5889**.********************************************************************** PP

                               CCG  79 gCllql 84 
                                       gC+ +l
  gi|298675430|ref|YP_003727180.1| 211 GCYKTL 216
                                       **9887 PP

  == domain 3  score: 21.6 bits;  conditional E-value: 1.6e-07
                               CCG   5 dgChllraaypevrkalkkllealgveleel..ekesCCGagggrsgkee.laealakrnvetaeetgadaivtacp 78 
                                       d+Ch l+++ + +r+    +l+ +gve+ e   ++  CCGa++g + + + ++ ++a   ++  +++  d +v+ cp
  gi|298675430|ref|YP_003727180.1| 260 DSCH-LKNNIDTPRN----ILNNMGVEVIEIfdRDVVCCGAPAGLKPNFPeTSSNIAGLSLRKSNDV-SDLMVAYCP 330
                                       6774.5566666666....55666777655446799*******99988877999************8.99******* PP

                               CCG  79 gCllql 84 
                                       +C +++
  gi|298675430|ref|YP_003727180.1| 331 FCIYHM 336
                                       **8876 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   4.8   1.5e-11   1.7e-08       2      67 .]      11      73 ..      10      73 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 1.5e-11
                           Fer4_16  2 CgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCPan 67
                                      C++C+kC +vCP+  +k++   e+ ++ +i+   + + + + ++++ ++ +  t C++C dvCP+n
  gi|298675430|ref|YP_003727180.1| 11 CIDCKKCWDVCPVTKVKGE---EYTPQGKIQLLSKVESGETLEKAEFDNIYLSTRCGACDDVCPVN 73
                                      *******************...6777777777666666666666666666888***********98 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   2.7   8.6e-12     1e-08       2      65 .]       8      74 ..       7      74 .. 0.74
   2 ?   -3.0   0.1       8.5     1e+04      45      54 ..     203     212 ..     172     215 .. 0.51

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 8.6e-12
                            Fer4_8  2 lekCieCgaCqsaCpvlrrtkkhlldargeaae....dvqeeqvlee...eealwsCttcgaCtevCpvgi 65
                                      +++Ci C  C + Cpv + ++++   ++g+ +     +   + ++ e    ++++  t cgaC++vCpv+i
  gi|298675430|ref|YP_003727180.1|  8 VDSCIDCKKCWDVCPVTKVKGEEYT-PQGKIQLlskvE---SGETLEkaeFDNIYLSTRCGACDDVCPVNI 74
                                      579****************987744.444434345442...333333455899****************97 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 8.5
                            Fer4_8  45 eealwsCttc 54 
                                       ++ + sC +c
  gi|298675430|ref|YP_003727180.1| 203 KKLIVSCPGC 212
                                       5666666666 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.7   3.9e-07   0.00047       6      34 ..       8      34 ..       4      47 .. 0.75
   2 !   14.2   0.1   2.9e-05     0.034      10      30 ..      61      94 ..      60     109 .. 0.68
   3 ?    0.4   0.1      0.59   7.1e+02      25      49 ..     189     213 ..     162     217 .. 0.76
   4 ?   -1.3   0.0         2   2.4e+03      18      28 ..     328     341 ..     318     353 .. 0.65

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.9e-07
                           Fer4_10  6 ddtCirCgkCvkaCPadltsvgakgease 34
                                       d+Ci C+kC ++CP+  t+v++++++ +
  gi|298675430|ref|YP_003727180.1|  8 VDSCIDCKKCWDVCPV--TKVKGEEYTPQ 34
                                      689*************..55555554444 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 2.9e-05
                           Fer4_10 10 irCgkCvkaCPadl.............tsvgakg 30
                                      +rCg+C ++CP+++              +++ ++
  gi|298675430|ref|YP_003727180.1| 61 TRCGACDDVCPVNIpikdiiqyeryllAEQNREP 94
                                      69**********9987777655544443333333 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.59
                           Fer4_10  25 svgakgeaseeeavrkkvekCtgcg 49 
                                       + +++  + e+ +++k + +C+gc 
  gi|298675430|ref|YP_003727180.1| 189 HAKNYVDYIESLEIKKLIVSCPGCY 213
                                       5566667777788888899999996 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 2
                           Fer4_10  18 aCPadl...tsvga 28 
                                        CP+++   +sv++
  gi|298675430|ref|YP_003727180.1| 328 YCPFCIyhmNSVNN 341
                                       58887765433333 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   4.2   2.8e-09   3.4e-06       1      52 []      10      74 ..      10      74 .. 0.70

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 2.8e-09
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgt.............ekveid.pekClgCgaCvavCPtga 52
                                      +Ci C++C ++Cpv  ++ +e++ +  +             ek+e+d     + CgaC +vCP+++
  gi|298675430|ref|YP_003727180.1| 10 SCIDCKKCWDVCPVTKVKGEEYTPQG-KiqllskvesgetlEKAEFDnIYLSTRCGACDDVCPVNI 74
                                      5************9999998764332.223333333333457778873456899*********986 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   2.1   4.7e-09   5.6e-06       2      60 ..      11      74 ..      10      75 .. 0.73
   2 ?   -1.3   0.0       2.9   3.4e+03      11      20 ..     208     217 ..     181     236 .. 0.72
   3 ?   -2.4   0.0       6.1   7.3e+03      12      20 ..     329     337 ..     326     357 .. 0.58

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 4.7e-09
                           Fer4_17  2 CiqCgyClpeCpsyeaydne..pk...kllraaklglleeaekeekaslCieCgeCerkCPqgl 60
                                      Ci C+ C ++Cp  +  ++e  p+   +ll ++++g++ e  + +++ l + Cg C+ +CP ++
  gi|298675430|ref|YP_003727180.1| 11 CIDCKKCWDVCPVTKVKGEEytPQgkiQLLSKVESGETLEKAEFDNIYLSTRCGACDDVCPVNI 74
                                      *************99966632233333666666665444444448****************987 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.9
                           Fer4_17  11 eCpsyeaydn 20 
                                       +Cp ++++ n
  gi|298675430|ref|YP_003727180.1| 208 SCPGCYKTLN 217
                                       3666666555 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 6.1
                           Fer4_17  12 Cpsyeaydn 20 
                                       Cp+++ + n
  gi|298675430|ref|YP_003727180.1| 329 CPFCIYHMN 337
                                       555554333 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   4.3   7.1e-06    0.0085       6      20 ..       9      23 ..       7      23 .. 0.94
   2 !   13.8   2.6   3.3e-05      0.04       9      22 ..      61      74 ..      61      76 .. 0.90
   3 ?   -3.3   0.2       8.1   9.6e+03      15      20 ..     326     331 ..     326     331 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.1e-06
                                      TTSSS-THHHHHSTT CS
                              Fer4  6 ekCigCGaCvevCPv 20
                                      + Ci C++C +vCPv
  gi|298675430|ref|YP_003727180.1|  9 DSCIDCKKCWDVCPV 23
                                      89************7 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 3.3e-05
                                      SS-THHHHHSTTTE CS
                              Fer4  9 igCGaCvevCPvgA 22
                                      ++CGaC +vCPv+ 
  gi|298675430|ref|YP_003727180.1| 61 TRCGACDDVCPVNI 74
                                      58**********96 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 8.1
                                       HHHSTT CS
                              Fer4  15 vevCPv 20 
                                       v  CP+
  gi|298675430|ref|YP_003727180.1| 326 VAYCPF 331
                                       568**6 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   3.5   0.00061      0.73      55      73 ..       5      23 ..       2      30 .. 0.86
   2 !   12.7   0.4   8.9e-05      0.11      59      84 ..      58      83 ..      24      88 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00061
                           Fer4_18 55 ekgagdcidcescvkvcPt 73
                                      ++++  cidc++c +vcP+
  gi|298675430|ref|YP_003727180.1|  5 KQAVDSCIDCKKCWDVCPV 23
                                      577889************7 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 8.9e-05
                           Fer4_18 59 gdcidcescvkvcPtgidirkGlqle 84
                                         + c++c +vcP++i i++ +q+e
  gi|298675430|ref|YP_003727180.1| 58 YLSTRCGACDDVCPVNIPIKDIIQYE 83
                                      34679****************99987 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   1.6   1.1e-05     0.013      38      54 ..       8      24 ..       2      28 .. 0.81
   2 !    7.1   0.2    0.0048       5.7      42      54 ..      61      73 ..      50      80 .. 0.87
   3 ?   -2.5   0.0       4.9   5.9e+03       9      16 ..     207     214 ..     201     221 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                           Fer4_21 38 edeCvGCnlCssvCPve 54
                                       d+C+ C+ C +vCPv+
  gi|298675430|ref|YP_003727180.1|  8 VDSCIDCKKCWDVCPVT 24
                                      68999999999999996 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0048
                           Fer4_21 42 vGCnlCssvCPve 54
                                      + C  C +vCPv+
  gi|298675430|ref|YP_003727180.1| 61 TRCGACDDVCPVN 73
                                      569********95 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 4.9
                           Fer4_21   9 igCgkCli 16 
                                       ++C  C++
  gi|298675430|ref|YP_003727180.1| 207 VSCPGCYK 214
                                       45555555 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.5   3.4e-05      0.04       4      17 ..       9      22 ..       8      34 .. 0.92
   2 ?    2.3   0.1       0.2   2.5e+02       8      18 ..      62      72 ..      61      98 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.4e-05
                           Fer4_13  4 dtCiacgaCvelaP 17
                                      d+Ci+c++C++++P
  gi|298675430|ref|YP_003727180.1|  9 DSCIDCKKCWDVCP 22
                                      59************ PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.2
                           Fer4_13  8 acgaCvelaPd 18
                                       cgaC +++P 
  gi|298675430|ref|YP_003727180.1| 62 RCGACDDVCPV 72
                                      69*******95 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   2.4     2e-05     0.024       2      16 ..       9      23 ..       9      32 .. 0.92
   2 ?    7.7   1.2    0.0049       5.8       5      17 .]      61      73 ..      61      74 .. 0.90
   3 ?   -0.9   0.3       2.6   3.1e+03       6      11 ..     208     213 ..     207     215 .. 0.74
   4 ?   -1.0   0.4         3   3.6e+03      11      16 ..     326     331 ..     326     334 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2e-05
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      ++Ci+C++C ++CP+
  gi|298675430|ref|YP_003727180.1|  9 DSCIDCKKCWDVCPV 23
                                      79************5 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0049
                            Fer4_4  5 igCgsCvaaCPqg 17
                                      ++Cg+C ++CP++
  gi|298675430|ref|YP_003727180.1| 61 TRCGACDDVCPVN 73
                                      68*********75 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.6
                            Fer4_4   6 gCgsCv 11 
                                        C+ C+
  gi|298675430|ref|YP_003727180.1| 208 SCPGCY 213
                                       699998 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 3
                            Fer4_4  11 vaaCPq 16 
                                       va+CP+
  gi|298675430|ref|YP_003727180.1| 326 VAYCPF 331
                                       577885 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   3.7   0.00019      0.23      34      48 ..       9      23 ..       1      26 [. 0.74
   2 ?   13.4  11.0   5.5e-05     0.066       2      49 ..      11      73 ..      10      74 .. 0.88
   3 ?    9.1   0.5    0.0012       1.4       3      20 ..      61      78 ..      59      92 .. 0.74
   4 ?   -1.8   0.1       3.2   3.8e+03      33      39 ..     199     212 ..     170     214 .. 0.57
   5 ?   -2.2   0.0       3.9   4.7e+03      11      25 ..     328     342 ..     326     347 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00019
                            Fer4_9 34 eaCigCgaCveaCpk 48
                                      ++Ci+C++C ++Cp 
  gi|298675430|ref|YP_003727180.1|  9 DSCIDCKKCWDVCPV 23
                                      579999999999996 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 5.5e-05
                            Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraase...............eaCigCgaCveaCpkg 49
                                      C++C++C ++Cp + v++++ +   +++  s+                  + CgaC ++Cp +
  gi|298675430|ref|YP_003727180.1| 11 CIDCKKCWDVCPVTKVKGEEYTPQGKIQLLSKvesgetlekaefdniYLSTRCGACDDVCPVN 73
                                      ***********99999888888888888887789999999999**9*6679**********87 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0012
                            Fer4_9  3 tgCgaCveaCpagvvved 20
                                      t+CgaC ++Cp ++ ++d
  gi|298675430|ref|YP_003727180.1| 61 TRCGACDDVCPVNIPIKD 78
                                      568888888888777666 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 3.2
                            Fer4_9  33 e.......eaCigC 39 
                                                +C gC
  gi|298675430|ref|YP_003727180.1| 199 SleikkliVSCPGC 212
                                       13444445556666 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 3.9
                            Fer4_9  11 aCpagvvvedaaerk 25 
                                        Cp++++ + +++++
  gi|298675430|ref|YP_003727180.1| 328 YCPFCIYHMNSVNNY 342
                                       599888887777665 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.0   0.00015      0.18       7      21 ..       8      22 ..       2      23 .. 0.87
   2 ?    8.8   2.7    0.0015       1.8      11      21 ..      61      71 ..      61      72 .. 0.91
   3 ?   -3.0   0.3       8.5     1e+04      10      14 ..     209     213 ..     208     214 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
                            Fer4_2  7 tdrCigCgaCvsaCP 21
                                       d+Ci C++C ++CP
  gi|298675430|ref|YP_003727180.1|  8 VDSCIDCKKCWDVCP 22
                                      689************ PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0015
                            Fer4_2 11 igCgaCvsaCP 21
                                      ++CgaC ++CP
  gi|298675430|ref|YP_003727180.1| 61 TRCGACDDVCP 71
                                      69********* PP

  == domain 3  score: -3.0 bits;  conditional E-value: 8.5
                            Fer4_2  10 CigCg 14 
                                       C gC 
  gi|298675430|ref|YP_003727180.1| 209 CPGCY 213
                                       88885 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   3.6   0.00011      0.13       7      20 ..       9      22 ..       8      27 .. 0.92
   2 ?    4.0   2.4     0.048        57      11      23 ..      62      74 ..      61      75 .. 0.87
   3 ?   -0.1   0.2      0.97   1.2e+03       8      14 ..     208     214 ..     207     214 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                            Fer4_6  7 dkCigCgdCvrvCP 20
                                      d+Ci+C +C +vCP
  gi|298675430|ref|YP_003727180.1|  9 DSCIDCKKCWDVCP 22
                                      89************ PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.048
                            Fer4_6 11 gCgdCvrvCPega 23
                                       Cg+C +vCP ++
  gi|298675430|ref|YP_003727180.1| 62 RCGACDDVCPVNI 74
                                      6*********986 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.97
                            Fer4_6   8 kCigCgd 14 
                                       +C gC++
  gi|298675430|ref|YP_003727180.1| 208 SCPGCYK 214
                                       6****86 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   2.0      0.04        47       2      14 ..      11      23 ..       4      26 .. 0.65
   2 ?    5.6   1.4     0.023        28       2      15 ..      11      24 ..      10      56 .. 0.84
   3 ?    4.6   0.4      0.05        59      83      96 .]      61      74 ..      48      74 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.04
                           Fer4_22  2 ClsCgaCtlvCpt 14
                                      C++C +C  vCp 
  gi|298675430|ref|YP_003727180.1| 11 CIDCKKCWDVCPV 23
                                      6666666666654 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.023
                           Fer4_22  2 ClsCgaCtlvCptC 15
                                      C++C +C  vCp  
  gi|298675430|ref|YP_003727180.1| 11 CIDCKKCWDVCPVT 24
                                      99999999999865 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.05
                           Fer4_22 83 vGCgRCieacpvki 96
                                      + Cg C+++cpv+i
  gi|298675430|ref|YP_003727180.1| 61 TRCGACDDVCPVNI 74
                                      56888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 2068.94
//
Query:       gi|298675431|ref|YP_003727181.1|  [L=477]
Description: pyruvate kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   4.2e-121  404.1   4.8   5.9e-121  403.6   4.8    1.2  1  PK         Pyruvate kinase, barrel domain
    1.1e-21   77.2   0.0    4.3e-21   75.3   0.0    2.0  2  PK_C       Pyruvate kinase, alpha/beta domain
    0.00015   21.0   1.3    0.00055   19.1   1.3    1.9  2  HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
  ------ inclusion threshold ------
      0.062   12.7   2.2       0.24   10.8   0.2    2.5  2  PcrB       PcrB family
      0.082   11.9   0.3       0.76    8.7   0.0    2.4  2  IMPDH      IMP dehydrogenase / GMP reductase domain


Domain annotation for each model (and alignments):
>> PK  Pyruvate kinase, barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  403.6   4.8  1.6e-124  5.9e-121       2     339 ..       6     337 ..       5     345 .. 0.98

  Alignments for each domain:
  == domain 1  score: 403.6 bits;  conditional E-value: 1.6e-124
                                       --SEEEEEESCCCTSHHHHHHHHHHTEEEEEEETTSS-HHHHHHHHHHHHHHHHTTTTS-EEEEE---S-EBB--BT CS
                                PK   2 rrtkivctlGPasesvekleklieaGlnvvrlnfshGsheehqerienvreaekklgkkvaillDtkGpeirtgllk 78 
                                       ++tkivct+GPas+s  +l++li  G+nv+rlnfshG+ e h+e+i+++r+   +l   v+i+ D+ Gp+ir+g+lk
  gi|298675431|ref|YP_003727181.1|   6 HKTKIVCTIGPASSSEAMLKDLILYGMNVARLNFSHGDLEGHREVIHKIRKLSSELDVVVSIMADLPGPKIRIGKLK 82 
                                       59*************************************************************************** PP

                                       TCSSSEEE-TTSEEEEE-SCTCTTTBBTTEEEBS-TTHHHHS-TTEEEEETTTTEEEEEEEEETTEEEEEEESS-EE CS
                                PK  79 dgkkdielkegdklkvsldeklkeegdeelialdyknivkdvevGktilvdDGllslkvlevdeekeleveventgv 155
                                       +  + i+lk+ dk+++++++    egde +i ++y+++ + v++G+ ++++DG ++l+ lev++++ + ++v ++g 
  gi|298675431|ref|YP_003727181.1|  83 N--EPIHLKKDDKVTLTTENI---EGDESVIPVNYSKLSESVKPGRPVYLNDGFIQLNCLEVSDKS-VDCTVVVGGP 153
                                       *..68**********998764...4579**********************************9998.********** PP

                                       E-SS-BEE-TTS---S-SS-HHHHHHHHHHHHCT-SEEEETTE-SHHHHHHHHHHHTCCCTTSEEEEEE-SCHHHHT CS
                                PK 156 lgskkgvnlpgtkvdlpalsekDkadlrfgvkqgvdliaasfvrkasDvkevrevleeegkeikiiakienqegven 232
                                       l+s+kg+nlpg++v l+ ++e D + + f++++gvd+  +sf+ ka+D++++r+ ++ +gk++ i++kie++e+v+n
  gi|298675431|ref|YP_003727181.1| 154 LSSNKGMNLPGSRVFLEPVTETDLNIVDFALNEGVDIFSVSFIEKADDIQKIRNHAKVKGKSVFIVSKIEREEAVKN 230
                                       ***************************************************************************** PP

                                       HHHHHHHSSEEEEEHHHHHHHSTCCCHHHHHHHHHHHHHHHT--EEEESSTTGGGGTSSS--HHHHHHHHHHHHHT- CS
                                PK 233 ldeileasDgimvarGDlGieipaekvllvqkklikkcnlagkpvitatqmlesmiknPrptraevsDvanavlDGt 309
                                       ++eil+++Dg+m+arGDlG+eip ++v+ vqk l +k+nl++ pvitatqmlesm++n rptraev+Dvana+lDGt
  gi|298675431|ref|YP_003727181.1| 231 INEILNVTDGLMIARGDLGVEIPIQNVPNVQKELTHKANLLSIPVITATQMLESMTENIRPTRAEVTDVANAILDGT 307
                                       ***************************************************************************** PP

                                       SEEEESHHHHTSS-HHHHHHHHHHHHHHHH CS
                                PK 310 DavmLsgetakGkyPveavkamaevaleae 339
                                       DavmLsgeta+GkyPve+v +m+++a+e e
  gi|298675431|ref|YP_003727181.1| 308 DAVMLSGETAAGKYPVETVSMMTKIAREIE 337
                                       *************************99876 PP

>> PK_C  Pyruvate kinase, alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.99   3.6e+03      62      62 ..     274     274 ..     199     329 .. 0.55
   2 !   75.3   0.0   1.2e-24   4.3e-21       3     117 .]     365     474 ..     363     474 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.99
                                       H CS
                              PK_C  62 p 62 
                                       p
  gi|298675431|ref|YP_003727181.1| 274 P 274
                                       1 PP

  == domain 2  score: 75.3 bits;  conditional E-value: 1.2e-24
                                       HHHHHHHHHHHHT-SEEEEE-SSSHHHHHHHHT-TSSEEEEEESHHHHHHHHHHCTTEEHHH.HHHHH...TTSHHH CS
                              PK_C   3 iakaaveaaeelgakaIvvltesGetArliskyrpkvpiiavtpneltarqlalyrGvypvlvekaktaestdellr 79 
                                       i+  + +a ++l +k++v++t sGe+ r+is+++++ +i+a+++  +t r la++ Gvyp++v +     +td+ ++
  gi|298675431|ref|YP_003727181.1| 365 ISLQVNDALQKLPIKYVVTPTVSGESSRHISRFKSGTWILAFSRYLNTGRNLAFSYGVYPIYVGN-----KTDS-WE 435
                                       777888999****************************************************9753.....3455.44 PP

                                       HH.HHHHHHTTSS-STSEEEEEE-SSSS..SS--EEEEE CS
                              PK_C  80 ea.vkvakeaglvkkgdevvvtaGtpkgesgttNtlrVv 117
                                       ++ v+ +k+ +lv++gd +v+t+G + g++g tN+l+++
  gi|298675431|ref|YP_003727181.1| 436 TIvVEKLKQWELVRNGDYIVLTQGQSPGKPGGTNLLKII 474
                                       4449*********************************97 PP

>> HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   1.3   1.5e-07   0.00055      75     165 ..     174     259 ..     168     313 .. 0.80
   2 ?   -0.6   0.0      0.17   6.1e+02      84     115 ..     267     298 ..     253     333 .. 0.58

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.5e-07
                                       HHHGG....HHHTTSSEEEESS--SHHHHHHHHHHTSHTTTS---HCCC-EEEEEE-SHHHHHTHHHHHTSTTEEEE CS
                         HpcH_HpaI  75 kqdle....vldlgaqvvlvPkvetaeealevvsalrepekgirganketrllaqiEsaegvknaeeIaavegldgv 147
                                       + dl+    +l++g++ + v ++e+a++++++ +  +          k++ ++  iE +e+vkn++eI++v   dg+
  gi|298675431|ref|YP_003727181.1| 174 ETDLNivdfALNEGVDIFSVSFIEKADDIQKIRNHAKVKG-------KSVFIVSKIEREEAVKNINEILNV--TDGL 241
                                       455555567899******************9999887777.......9********************976..4777 PP

                                       EE-HHHHHHHTT-TTSTT CS
                         HpcH_HpaI 148 flGaeDlsadlgtkrspe 165
                                       +++  Dl +++  ++ p+
  gi|298675431|ref|YP_003727181.1| 242 MIARGDLGVEIPIQNVPN 259
                                       888888888777666655 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.17
                                       TSSEEEESS--SHHHHHHHHHHTSHTTTS--- CS
                         HpcH_HpaI  84 gaqvvlvPkvetaeealevvsalrepekgirg 115
                                       +a+ + +P ++  ++++ + + +r   +++  
  gi|298675431|ref|YP_003727181.1| 267 KANLLSIPVITATQMLESMTENIRPTRAEVTD 298
                                       55555666666666665555555544444333 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.2     0.077   2.8e+02      19      63 ..     224     277 ..     219     292 .. 0.63
   2 ?   10.8   0.2   6.7e-05      0.24      14      56 ..     291     334 ..     283     359 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.077
                                       CHHHHHHH..HCTT-SEEEEECST......CHHHHHHHHHHH.HHCTSSS-EEE CS
                              PcrB  19 pdEiveiv..iesgtDavmigGsq......svtldntvrllk.kvsriklPivl 63 
                                        +E+v+++  i + tD++mi+  +      + +  n+++ l  k + +++P++ 
  gi|298675431|ref|YP_003727181.1| 224 REEAVKNIneILNVTDGLMIARGDlgveipIQNVPNVQKELThKANLLSIPVIT 277
                                       58889988777799*****98555422133334455665553144455666665 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 6.7e-05
                                       TTSS-CHHHHHHHHCTT-SEEEEECST..CHHHHHHHHHHHHHCT CS
                              PcrB  14 PeeenpdEiveiviesgtDavmigGsq..svtldntvrllkkvsr 56 
                                       P + ++ +++++ i +gtDavm++G +  +    +tv ++ k+ r
  gi|298675431|ref|YP_003727181.1| 291 PTRAEVTDVANA-ILDGTDAVMLSGETaaGKYPVETVSMMTKIAR 334
                                       555555555555.589*********99633334588999999854 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00021      0.76      93     151 ..       8      66 ..       3      75 .. 0.88
   2 ?   -0.4   0.1      0.12   4.3e+02     219     241 ..     296     319 ..     292     340 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00021
                                       B-EEEEE-SSTTHHHHHHHHHHTT-SEEEEE-STSSSHHHHHHHHHHHHHTTTSEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH  93 llvgaavgvkedalervkalveagvdvlvvdsahghsekvleavkeikkkveeveviaG 151
                                         +  ++g  +++++ +k l+  g++v  ++ +hg  e+  e++++i+k  +e++v++ 
  gi|298675431|ref|YP_003727181.1|   8 TKIVCTIGPASSSEAMLKDLILYGMNVARLNFSHGDLEGHREVIHKIRKLSSELDVVVS 66 
                                       45566899999999************************************999999975 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.12
                                       HHHHHHHHHTT-SEEEE.SCCCTT CS
                                       xxxxxxxxxxxxxxxxx.xxxxxx RF
                             IMPDH 219 sgdivkAlaaGadavml.Gsllag 241
                                         d++ A+  G+davml G+  ag
  gi|298675431|ref|YP_003727181.1| 296 VTDVANAILDGTDAVMLsGETAAG 319
                                       5799************95555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.49
# Mc/sec: 2905.37
//
Query:       gi|298675432|ref|YP_003727182.1|  [L=851]
Description: multi-sensor signal transduction histidine kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.5e-31  106.8   0.0    2.3e-30  105.4   0.0    1.8  1  HATPase_c       Histidine kinase-, DNA gyrase B-, and HSP90-l
    2.3e-27   96.4   3.7    2.3e-27   96.4   3.7    2.3  2  dCache_1        Cache domain
    2.1e-19   69.3   3.0    4.5e-19   68.3   0.1    2.8  2  HisKA           His Kinase A (phospho-acceptor) domain
    2.6e-18   66.1   0.0    6.2e-18   64.9   0.0    1.7  1  PAS_3           PAS fold
      2e-06   27.8   0.0    2.2e-05   24.4   0.0    2.5  2  PAS             PAS fold
    2.8e-06   27.5   0.3    1.1e-05   25.6   0.3    2.1  1  PAS_9           PAS domain
    2.6e-05   24.0   0.0    0.00016   21.5   0.0    2.3  2  HATPase_c_3     Histidine kinase-, DNA gyrase B-, and HSP90-l
    2.9e-05   24.4   0.0       0.29   11.6   0.0    3.5  3  HAMP            HAMP domain
    0.00057   19.9   1.7     0.0039   17.2   0.5    2.7  2  Bromodomain     Bromodomain
     0.0006   19.8   0.0     0.0014   18.6   0.0    1.6  1  HATPase_c_2     Histidine kinase-like ATPase domain
     0.0026   18.0   0.7      0.007   16.6   0.7    1.7  1  DUF3333         Domain of unknown function (DUF3333)
  ------ inclusion threshold ------
      0.012   15.8   0.0      0.022   15.0   0.0    1.4  1  PAS_4           PAS fold
      0.016   14.4   0.1      0.016   14.4   0.1    3.8  5  dCache_2        Cache domain
      0.023   14.6   0.5       0.14   12.1   0.0    2.5  2  HATPase_c_5     GHKL domain
      0.037   12.9   2.1        2.8    6.7   0.2    2.6  2  Spc7            Spc7 kinetochore protein
      0.057   13.3   0.0       0.17   11.7   0.0    1.8  1  sCache_2        Single Cache domain 2
       0.28   11.9   3.2        3.2    8.5   0.2    2.9  2  Occludin_ELL    Occludin homology domain
       0.51   11.0   5.3       0.25   12.0   0.6    3.0  3  DNA_repr_REX1B  DNA repair REX1-B
        1.2    9.3   8.9       0.42   10.8   0.1    3.3  3  CREPT           Cell-cycle alteration and expression-elevated
        6.8    6.9   5.4        5.8    7.1   0.1    3.5  4  PAH             Paired amphipathic helix repeat


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.4   0.0   2.6e-33   2.3e-30       2     110 ..     741     850 ..     740     851 .] 0.95

  Alignments for each domain:
  == domain 1  score: 105.4 bits;  conditional E-value: 2.6e-33
                                       HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTSSSHH CS
                         HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsq.ddstkrggggtGlG 77 
                                       de +L++++ nlv+Na+kf+++ g++++++++ ++++++ v+D+GiGip++++  lf++f+q d s++r++gg GlG
  gi|298675432|ref|YP_003727182.1| 741 DENKLKEALYNLVTNAIKFTPERGKVTLQVNKLDGNIRFAVKDTGIGIPEDKQSDLFKPFTQiDTSASREYGGAGLG 817
                                       899****************8899999999996559****************************************** PP

                                       HHHHHHHHHHTTTEEEEEEETTTEEEEEEEEES CS
                         HATPase_c  78 lsivkklvelmgGeiwvesepgrGttftftlpl 110
                                       l++vkk+ve+++G+iw+ese ++Gt ++ft+p 
  gi|298675432|ref|YP_003727182.1| 818 LALVKKFVEMHNGRIWIESEVNKGTAIYFTIPV 850
                                       ******************************996 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.4   3.7   2.6e-30   2.3e-27       5     247 ..      27     279 ..      23     281 .. 0.84
   2 ?   -1.5   0.1       1.9   1.7e+03      30      94 ..     516     584 ..     452     602 .. 0.62

  Alignments for each domain:
  == domain 1  score: 96.4 bits;  conditional E-value: 2.6e-30
                          dCache_1   5 eqaeeqllglaeqlanniedvldslenlaetlasnpslqdlleepnraneasreslqallksilksnpdisgvylvd 81 
                                       + a++q++ +a+++an+i+++++s+ ++a+tl+ +      +e+++    ++r +++++lk +l  np++ g y+++
  gi|298675432|ref|YP_003727182.1|  27 DLAYKQSSRMAQSYANEIDADMRSYMTIAKTLSKT------MENYE---SSNRTEVNQMLKDTLINNPKLVGTYVAF 94 
                                       66899***************************775......55556...689***********************99 PP

                          dCache_1  82 .....adGqviassdpssppnleg......................tddpadrdwykealaggggkpvisdpyvdqt 131
                                            ++++ ++++++       g                      ++d+   ++y+ ++ ++    v+++py++  
  gi|298675432|ref|YP_003727182.1|  95 epnafDNNDSYYANKT-------GhdstgrfipywnklhgnvtldpLQDYDTLNYYQLPKITK--SEVVTEPYMY-Q 161
                                       6666523333444443.......33334456888888888889**************999999..567******6.5 PP

                          dCache_1 132 ggkpvitiavpiyddsgkfiGvlaadldldnlqdllsniklgetgyvfivdsdGniiahpd.kdllgknlrdelkaq 207
                                        gk ++++++pi  d g+fiG+++ d ++ ++ ++l ++ + ++gy+f+v+++G+i +hpd k++ gk+ + +  + 
  gi|298675432|ref|YP_003727182.1| 162 -GKMIVSFVSPIIED-GEFIGIAGTDATIKYIEKMLGKVEVFDSGYAFMVSRSGTIMTHPDkKEWTGKKNIGVIDSP 236
                                       .79**********86.*********************************************9889888888888777 PP

                          dCache_1 208 ..ealekalakiesgvssvklng..eeylva.yapiptglgWylv 247
                                          ++++++++ ++g  ++   +  ++  v  y pi+t  +  +v
  gi|298675432|ref|YP_003727182.1| 237 rfSKMKNDIQNGTPGHIETLDPStgNKV-VMfYEPIKT-GNFAVV 279
                                       999**********999999855542677.555*****8.666665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.9
                          dCache_1  30 enlaetlasnps..lqdlleepnra.neasreslqallksilksnpdi.sgvylvdadGqviassdpss 94 
                                        n++ +++ +p+  l ++l++ +   + + ++  + ++++i +  + + ++  +++++G+v +++ + s
  gi|298675432|ref|YP_003727182.1| 516 SNNVDQFGYDPDdfLSGSLNYADIIhPDDLENVKEKTVETITNCLEEFnHEYRILTKNGEVRWVDERTS 584
                                       455555555554333334433333363333333333333333333444356677778888877665554 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1         1   8.9e+02      31      56 ..     467     495 ..     454     497 .. 0.78
   2 !   68.3   0.1     5e-22   4.5e-19       2      67 .]     627     694 ..     626     694 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1
                                       .T-HSSCHHHHHHHHHHHH...HHHHHHH CS
                             HisKA  31 gklteelkeyletiesear...rldhlve 56 
                                       +k +e+l+ey + ++++ +    l +++e
  gi|298675432|ref|YP_003727182.1| 467 KKVSEDLREYTKELKKSNQlrnELAKIIE 495
                                       56789999999999999887777777776 PP

  == domain 2  score: 68.3 bits;  conditional E-value: 5e-22
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                             HisKA   2 lgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsrieag 67 
                                       +++fla+v+HELrtPL++i+g++e++  e  g+l+e +k yl+ +++++ +l++l++ +Ld+s+ieag
  gi|298675432|ref|YP_003727182.1| 627 KNEFLANVSHELRTPLNSIIGFSELMLTErrGELNEYQKHYLNNVKNSGYHLLSLINKILDISKIEAG 694
                                       79***********************9444459**********************************97 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.9   0.0   6.9e-21   6.2e-18       3      89 .]     514     600 ..     512     600 .. 0.92

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 6.9e-21
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvirde 78 
                                       yvs++v + +Gy+p+++l+   +++d++hp+D+e+v+e+  e +++   ++++eyRi++k+Ge+rwv++r++  +de
  gi|298675432|ref|YP_003727182.1| 514 YVSNNVDQ-FGYDPDDFLSGSLNYADIIHPDDLENVKEKTVETITNCLeEFNHEYRILTKNGEVRWVDERTSSDFDE 589
                                       67777755.5******************************999977777**************************** PP

                             PAS_3  79 ngkpvrvigva 89 
                                       ng+++++ g++
  gi|298675432|ref|YP_003727182.1| 590 NGNVTYLRGIV 600
                                       ******99985 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.87   7.8e+02      26      75 ..     209     254 ..     202     267 .. 0.82
   2 !   24.4   0.0   2.5e-08   2.2e-05       2     113 .]     489     603 ..     488     603 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.87
                                       ECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCC CS
                               PAS  26 vNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrag 75 
                                       v+++ + +++ + +e+ gk+ +++i  +    + +++++ +++g++++++
  gi|298675432|ref|YP_003727182.1| 209 VSRSGTIMTHPDKKEWTGKKNIGVIDSP----RFSKMKNDIQNGTPGHIE 254
                                       788899999999*************988....888888888888877765 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 2.5e-08
                                       HHHHHHHHSSSEEEEEE..TTSBEEEECHHHHHHHSSTH.HHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECC CS
                               PAS   2 dlraileslpdpifvvD..edgrilyvNaaaeellGlsr.eevlgkslldliheedda.elaelleqlleqgeesra 74 
                                       +l  i+es+p+  f+++   +  ++yv+ +  +++G+++ + ++g+  + +i+++dd   ++e+  + + +  e+ +
  gi|298675432|ref|YP_003727182.1| 489 ELAKIIESSPVIAFLWNkdDSCSVNYVSNNV-DQFGYDPdDFLSGSLNYADIIHPDDLeNVKEKTVETITNCLEEFN 564
                                       6789*************64444567888886.789999977788888889999999987555555555555555666 PP

                                       CCEEEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  75 geisfklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                        e ++ +++g++++++ r+s+ +d+ g+++++ g++ d+
  gi|298675432|ref|YP_003727182.1| 565 HEYRILTKNGEVRWVDERTSSDFDENGNVTYLRGIVIDV 603
                                       66666668***********************99999986 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.3   1.2e-08   1.1e-05       9     104 .]     507     605 ..     498     605 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.2e-08
                             PAS_9   9 pdgril.yaNeaalrllGyspeevlgks..itdlfvtdpeanerlraaleqgrk..kerevevvlirkngetfwvll 80 
                                       +d   + y+++ + ++ Gy+p+++l  s  + d++ ++++ ++ +++ +e++++  +e++ e+ + +knge  wv+ 
  gi|298675432|ref|YP_003727182.1| 507 DDSCSVnYVSNNVDQF-GYDPDDFLSGSlnYADII-HPDDLENVKEKTVETITNclEEFNHEYRILTKNGEVRWVDE 581
                                       3443444788888777.*********999999***.9999999999999999999*********************7 PP

                             PAS_9  81 taspvkdddgelvgiivilrDite 104
                                       + s  +d++g+++ + +i++D+t+
  gi|298675432|ref|YP_003727182.1| 582 RTSSDFDENGNVTYLRGIVIDVTD 605
                                       77777799**************96 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       3.2   2.9e+03      81     114 ..     206     239 ..     186     254 .. 0.83
   2 !   21.5   0.0   1.8e-07   0.00016       3      77 ..     745     818 ..     743     827 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3.2
                       HATPase_c_3  81 slslgkkltvitkkegesstltldvdkidkenek 114
                                       +++++++ t++t+ + +++t + ++ +id+ ++ 
  gi|298675432|ref|YP_003727182.1| 206 AFMVSRSGTIMTHPDKKEWTGKKNIGVIDSPRFS 239
                                       5889999999999999999988888888876654 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 1.8e-07
                       HATPase_c_3   3 lekAlaelvdNsld..AdaenvkievnknrgktgeivieDdGkGmseeelknalrlatsskeakrkstslGkkGiGl 77 
                                       l++Al  lv N++    +  +v+++vnk +  + ++ ++D G G++e++  + +++ t+  +  + s+ +G  G+Gl
  gi|298675432|ref|YP_003727182.1| 745 LKEALYNLVTNAIKftPERGKVTLQVNKLD-GNIRFAVKDTGIGIPEDKQSDLFKPFTQIDT--SASREYGGAGLGL 818
                                       579*********985566777999999987.589*********************9888887..4799999999994 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.026        23       1      30 [.     315     348 ..     315     356 .. 0.85
   2 !   11.6   0.0   0.00032      0.29       2      33 ..     365     398 ..     364     416 .. 0.82
   3 ?    3.3   0.0      0.12   1.1e+02      17      51 ..     425     459 ..     422     461 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.026
                                       HHHHTTHHHHHHHHHHHHHHTT....TBTSSTCC CS
                              HAMP   1 llarrilrPLrrLaraarriaa....Gdldtrlp 30 
                                       l+ar+++ P+ ++++  ++i +    G ldtr +
  gi|298675432|ref|YP_003727182.1| 315 LIARSVSSPIDKIVDDFKNITEdvinGKLDTRAE 348
                                       69*****************997666689999854 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00032
                                       HHHTTHHHHHHHHHHHHHHTTTBTSST..CCTTS CS
                              HAMP   2 larrilrPLrrLaraarriaaGdldtr..lpvsg 33 
                                       ++r+++ P+++ + +++++++G+l +r  l+v+g
  gi|298675432|ref|YP_003727182.1| 365 IMRTVSSPVQETVNVTKQLSNGNLGARynLDVKG 398
                                       89***********************995555544 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.12
                                       HHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHH CS
                              HAMP  17 arriaaGdldtrlpvsgrDEiGeLarafNaMldrL 51 
                                         +i++ d++ r+ v+g+  + +L   +++ +++L
  gi|298675432|ref|YP_003727182.1| 425 LTAIQNEDFTRRVRVYGNGDFKTLTCGIENTRQSL 459
                                       6789999************9999999999999888 PP

>> Bromodomain  Bromodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.89   7.9e+02      28      67 ..     535     573 ..     531     575 .. 0.81
   2 !   17.2   0.5   4.4e-06    0.0039       8      80 ..     696     768 ..     682     772 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.89
                                       THHHH.SS---HHHHHHHHHTT--SSHHHHHHHHHHHHHH CS
                       Bromodomain  28 dyyavikkPldLstIkkklesnkYksladfeadlkllfsN 67 
                                       +y ++i +P dL+ +k+k  +   + l++f ++ + l +N
  gi|298675432|ref|YP_003727182.1| 535 NYADII-HPDDLENVKEKTVETITNCLEEFNHEYRILTKN 573
                                       688877.9*********99888888888888877777666 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 4.4e-06
                                       BHTTTCGGGGCSTT-GCCSTTHHHH.SS---HHHHHHHHHTT--SSHHHHHHHHHHHHHHHHHHSHTTSHHHH CS
                       Bromodomain   8 llehklaepFlepvdpeefpdyyavikkPldLstIkkklesnkYksladfeadlkllfsNarkyngegsviye 80 
                                       +  ++ + p ++ v++ ++   +++ +k + L+tI +k+  n Y    ++++ l  l++Na+k+ +e+  ++ 
  gi|298675432|ref|YP_003727182.1| 696 MDYNPQNLPIIDLVNDVSNTMHPQALNKNIELETITDKYLGNIYADENKLKEALYNLVTNAIKFTPERGKVTL 768
                                       55567788888899999999999*****************************************998766655 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.6e-06    0.0014      36     110 ..     745     826 ..     742     844 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.6e-06
                       HATPase_c_2  36 veEactNavehayleap.egpvevrlesdeealtvevaDsGpgfdpetlpdpteeep......keslkegGrGlali 105
                                       ++Ea++N v+ a +  p  g+v++++   ++ +++ v+D G g +  ++ d  ++        + +    G+Glal+
  gi|298675432|ref|YP_003727182.1| 745 LKEALYNLVTNAIKFTPeRGKVTLQVNKLDGNIRFAVKDTGIGIPEDKQSDLFKPFTqidtsaSREYGGAGLGLALV 821
                                       68***************89***********************9776666555443336788777777888999**** PP

                       HATPase_c_2 106 kglvD 110
                                       k++v+
  gi|298675432|ref|YP_003727182.1| 822 KKFVE 826
                                       *9986 PP

>> DUF3333  Domain of unknown function (DUF3333)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.7   7.8e-06     0.007      65     146 ..      27     110 ..      15     115 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 7.8e-06
                           DUF3333  65 k.aeeskklatanyeklirdalkaklpeveerrekrelae.lissgaayqlrdrvladpsligttvtvwllasddvD 139
                                       + a ++++ + ++y + i++ +++ ++ +++ +++ e +e    ++++  l+d ++++p+l+gt v ++  a d+ D
  gi|298675432|ref|YP_003727182.1|  27 DlAYKQSSRMAQSYANEIDADMRSYMTIAKTLSKTMENYEsSNRTEVNQMLKDTLINNPKLVGTYVAFEPNAFDNND 103
                                       4445556778899**************77765555555553888899999*************************** PP

                           DUF3333 140 sllkGei 146
                                       s++ ++ 
  gi|298675432|ref|YP_003727182.1| 104 SYYANKT 110
                                       **97765 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   2.5e-05     0.022       2     109 ..     495     607 ..     494     608 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.5e-05
                             PAS_4   2 dslpdalavl..dpdgrvlyaNaaaaelfgappeellGktla..ellpeedaarleralrrvlegeepiefleelll 74 
                                       +s+p++ + +  d+   v y++++  + fg++p+++l  +l   ++  ++d +++ +   + ++     + +e++ l
  gi|298675432|ref|YP_003727182.1| 495 ESSPVIAFLWnkDDSCSVNYVSNNVDQ-FGYDPDDFLSGSLNyaDIIHPDDLENVKEKTVETITNCLEEFNHEYRIL 570
                                       7899999999889999999****9555.*********9999989877777777777777777777555566666555 PP

                             PAS_4  75 ..pgeerhyelrllPlrdesGevigvlvisrDiTerr 109
                                         +ge r+++ r +  +de+G v  + +i++D+T+ +
  gi|298675432|ref|YP_003727182.1| 571 tkNGEVRWVDERTSSDFDENGNVTYLRGIVIDVTDKK 607
                                       89********************************987 PP

>> dCache_2  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   1.3     0.026        23      29      86 ..      22      82 ..      11      94 .. 0.80
   2 ?   14.4   0.1   1.8e-05     0.016      81     258 ..     191     254 ..     183     287 .. 0.51
   3 ?   -3.3   0.2       4.3   3.8e+03      20      34 ..     469     483 ..     452     508 .. 0.47
   4 ?   -3.5   0.0       5.2   4.7e+03     216     257 ..     537     576 ..     515     597 .. 0.58
   5 ?   -0.2   0.5      0.52   4.6e+02       5      66 ..     619     687 ..     615     776 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.026
                          dCache_2 29 dsaielie.yeknsleeslkesLksrveeaysiaeeiyekykn.elseee.akklikealr 86
                                       +  e ++ ++ ++  +s+ +++++ +++  +ia+ + ++++n e s+ + + +++k++l 
  gi|298675432|ref|YP_003727182.1| 22 TEQQEDLAyKQSSRMAQSYANEIDADMRSYMTIAKTLSKTMENyESSNRTeVNQMLKDTLI 82
                                      44445555244555999**************************988887779999999985 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 1.8e-05
                          dCache_2  81 ikealrsirydggegyyfiidskgtlilhpdspsleGknlldlkdkdGryiiremiklakkkgeGfveytwpkpdek 157
                                       i                                                                            
  gi|298675432|ref|YP_003727182.1| 191 I---------------------------------------------------------------------------- 191
                                       3............................................................................ PP

                          dCache_2 158 kprkkisyvkyfepldwiIGtgaylddieeelkqellktlksirygnngyifiydtdgniilhplkkelngknll.e 233
                                                                            k l ++ + ++gy+f+ + +g+i  hp+kke  gk+ +  
  gi|298675432|ref|YP_003727182.1| 192 ------------------------------------EKMLGKVEVFDSGYAFMVSRSGTIMTHPDKKEWTGKKNIgV 232
                                       ....................................44455555556666666666666666666666666665534 PP

                          dCache_2 234 vkdkkgkllqelleaakkkgegfve 258
                                       +++++   ++++ + ++++  g +e
  gi|298675432|ref|YP_003727182.1| 233 IDSPR---FSKMKNDIQNGTPGHIE 254
                                       44433...55555544444334444 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 4.3
                          dCache_2  20 rkellksevdsaiel 34 
                                         e l++++++++++
  gi|298675432|ref|YP_003727182.1| 469 VSEDLREYTKELKKS 483
                                       222222222222222 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 5.2
                          dCache_2 216 niilhplkkelngknll.evkdkkgkllqelleaakkkgegfv 257
                                         i+hp++ e ++++++  +++  + ++++  +  +k+ge  v
  gi|298675432|ref|YP_003727182.1| 537 ADIIHPDDLENVKEKTVeTITNCLE-EFNHEYRILTKNGE--V 576
                                       5567775555555555523333222.26666666666665..3 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 0.52
                          dCache_2   5 fkeeiekleeetikerkellksevdsaielie.......yeknsleeslkesLksrveeaysiaeeiye 66 
                                       + e+++++++e++ +   +l+   +s+i + e        e n+ ++ + +++k+  ++ +s++++i +
  gi|298675432|ref|YP_003727182.1| 619 IAESANRTKNEFLANVSHELRTPLNSIIGFSElmlterrGELNEYQKHYLNNVKNSGYHLLSLINKILD 687
                                       667788888888888888888888888887777765333333335555555666666666677776655 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       1.9   1.7e+03      12      53 ..     416     463 ..     405     485 .. 0.57
   2 ?   12.1   0.0   0.00015      0.14       5      90 ..     744     837 ..     740     844 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.9
                       HATPase_c_5  12 nlLd..NAieacskieeekrfIrltvrekkksliisieNsyeg....e 53 
                                       n++d  N +  + + e+ +r +r+  + + k+l+  ieN+ ++    +
  gi|298675432|ref|YP_003727182.1| 416 NIIDdsNTVLTAIQNEDFTRRVRVYGNGDFKTLTCGIENTRQSlyeiT 463
                                       444422333333333446788888888888888888999866544331 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00015
                       HATPase_c_5   5 dlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg.....ek......kkle.sskskkeehGi 69 
                                        l   l nl  NAi    +    + +++l+v++ ++++ + ++ +  g     ++       ++  s +++ +  G+
  gi|298675432|ref|YP_003727182.1| 744 KLKEALYNLVTNAIKFTPE----RGKVTLQVNKLDGNIRFAVKDTGIGipedkQSdlfkpfTQIDtSASREYGGAGL 816
                                       5666778888888865544....668******************96665555411344444444434477788999* PP

                       HATPase_c_5  70 Glksireivkkykgnlsieae 90 
                                       Gl  +++ v+ ++g ++ie e
  gi|298675432|ref|YP_003727182.1| 817 GLALVKKFVEMHNGRIWIESE 837
                                       *****************9986 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.2    0.0031       2.8      65     105 ..      57      97 ..      18     103 .. 0.84
   2 ?    4.9   0.1     0.011        10     201     259 ..     452     489 ..     397     498 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0031
                              Spc7  65 hscreLkkyisegrkiireieeetleenPpLfreYmeadpd 105
                                        +++ +++y s +r  ++++ ++tl +nP+L+  Y++ +p+
  gi|298675432|ref|YP_003727182.1|  57 TLSKTMENYESSNRTEVNQMLKDTLINNPKLVGTYVAFEPN 97 
                                       567788899999***********************998876 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.011
                              Spc7 201 Leelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervlee 259
                                       +e++r++l e+ +++++ +++l e +++l+++++                     +++e
  gi|298675432|ref|YP_003727182.1| 452 IENTRQSLYEITSKYKKVSEDLREYTKELKKSNQ---------------------LRNE 489
                                       4555555555555555555555555555555444.....................4433 PP

>> sCache_2  Single Cache domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00019      0.17      42      86 ..     192     235 ..     180     259 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00019
                          sCache_2  42 kelvnglkfgdGkgYffvldedgtllvhPfnpqleGknasnlkDa 86 
                                       ++++ +    d +gY f++   gt++ hP ++++ Gk+ + + D+
  gi|298675432|ref|YP_003727182.1| 192 EKMLGKVEVFD-SGYAFMVSRSGTIMTHPDKKEWTGKKNIGVIDS 235
                                       45555666667.9************************99988775 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.2      0.23   2.1e+02       6      39 ..      33      66 ..      29      85 .. 0.84
   2 ?    8.5   0.2    0.0036       3.2      45      92 ..     445     493 ..     400     496 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.23
                      Occludin_ELL  6 saeqrerYkaeFnkeYkeYkelhaeleevskkfs 39
                                      s++ +++Y +e +++ ++Y+++ + l++++++ +
  gi|298675432|ref|YP_003727182.1| 33 SSRMAQSYANEIDADMRSYMTIAKTLSKTMENYE 66
                                      6788999**************9999998887655 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0036
                      Occludin_ELL  45 lkelkegskeykkieeeilqeykklkk.dpeyqekkkrceyLkekLshi 92 
                                        k+l+ g +++++   ei ++ykk+++  +ey ++ k+ ++L+++L+ i
  gi|298675432|ref|YP_003727182.1| 445 FKTLTCGIENTRQSLYEITSKYKKVSEdLREYTKELKKSNQLRNELAKI 493
                                       566666677778888999*******996689***************987 PP

>> DNA_repr_REX1B  DNA repair REX1-B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.2       9.2   8.2e+03      17      50 ..      30      65 ..      19      87 .. 0.50
   2 ?   -2.3   0.0       8.4   7.5e+03      46      80 ..     399     431 ..     395     437 .. 0.79
   3 ?   12.0   0.6   0.00028      0.25      32      75 ..     451     495 ..     424     497 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 9.2
                    DNA_repr_REX1B 17 Ykefeegfkaylksgaeee..ykqlvkevTeefsei 50
                                      Yk+ ++  ++y ++ ++    y ++ k+++++++++
  gi|298675432|ref|YP_003727182.1| 30 YKQSSRMAQSYANEIDADMrsYMTIAKTLSKTMENY 65
                                      444444444444433322233555555555555544 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 8.4
                    DNA_repr_REX1B  46 efseiSkevleieaaLreeasredlaelirkvqek 80 
                                       +f++ S+ ++   ++L++    +d  +++ ++q++
  gi|298675432|ref|YP_003727182.1| 399 DFKQFSDSLNMFAESLENI--IDDSNTVLTAIQNE 431
                                       7999999999999999984..67777788888876 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00028
                    DNA_repr_REX1B  32 aeeeykqlvkevTeefseiSkevleieaaLreea.sredlaelir 75 
                                       + e+ +q + e+T++ +++S++++e+ ++L++++  r++la++i+
  gi|298675432|ref|YP_003727182.1| 451 GIENTRQSLYEITSKYKKVSEDLREYTKELKKSNqLRNELAKIIE 495
                                       5566689999*********************998799*****997 PP

>> CREPT  Cell-cycle alteration and expression-elevated protein in tumour
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   1.2      0.27   2.4e+02      37      95 ..      18      76 ..      11      87 .. 0.72
   2 ?   10.8   0.1   0.00047      0.42      89     130 ..     463     504 ..     451     511 .. 0.83
   3 ?   -1.4   0.1       2.6   2.4e+03      77     134 ..     660     714 ..     615     721 .. 0.59

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.27
                             CREPT 37 lekikdkeeaekllkqveealellaeYnkrLeaeleeRkklakmledfleaqkellaka 95
                                      ++ +++++e  ++ ++ + a++  +e  + + + ++  k+l+k++e++ ++ ++++++ 
  gi|298675432|ref|YP_003727182.1| 18 ISTVTEQQEDLAYKQSSRMAQSYANEIDADMRSYMTIAKTLSKTMENYESSNRTEVNQM 76
                                      66777777777777777777777777777777777777788888888877777777664 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00047
                             CREPT  89 kellakaeekleelkeklekvksvrkelkshiqsLPdLtelp 130
                                        ++ +k  e l+e+ + l+k ++ r+el + i+s P ++ l 
  gi|298675432|ref|YP_003727182.1| 463 TSKYKKVSEDLREYTKELKKSNQLRNELAKIIESSPVIAFLW 504
                                       5667889999**************************998765 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.6
                             CREPT  77 lakmledfleaqkellakaeekleelkeklekvks.vrkelkshiqsLPdLtelpdvtg 134
                                       l+++ +++l+++k+    +  +l +l +k+  +++ +  +++   q+LP + ++ dv++
  gi|298675432|ref|YP_003727182.1| 660 LNEYQKHYLNNVKN----SGYHLLSLINKILDISKiEAGKMDYNPQNLPIIDLVNDVSN 714
                                       33333333333333....33333333333333333033455666677777766666665 PP

>> PAH  Paired amphipathic helix repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       6.7     6e+03      10      38 ..      62      88 ..      55      94 .. 0.74
   2 ?   -1.1   0.0       2.4   2.2e+03       8      26 ..     138     156 ..     137     175 .. 0.77
   3 ?   -1.4   0.0       2.9   2.6e+03       3      16 ..     400     413 ..     399     430 .. 0.73
   4 ?    7.1   0.1    0.0064       5.8       2      35 ..     465     498 ..     464     499 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 6.7
                               PAH 10 LhdyqkeqidskeVyeqVskLFhdhpdLl 38
                                      + +y +    ++eV +++++ + ++p L 
  gi|298675432|ref|YP_003727182.1| 62 MENYESSN--RTEVNQMLKDTLINNPKLV 88
                                      55666554..8999999999888888885 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.4
                               PAH   8 diLhdyqkeqidskeVyeq 26 
                                       d+L+ yq  +i++ eV+++
  gi|298675432|ref|YP_003727182.1| 138 DTLNYYQLPKITKSEVVTE 156
                                       689999999999***9997 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.9
                               PAH   3 YkeFLdiLhdyqke 16 
                                       +k+F d L+++ + 
  gi|298675432|ref|YP_003727182.1| 400 FKQFSDSLNMFAES 413
                                       68999999999865 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.0064
                               PAH   2 vYkeFLdiLhdyqkeqidskeVyeqVskLFhdhp 35 
                                       +Yk+  + L++y+ke + s+ +  +++k+++++p
  gi|298675432|ref|YP_003727182.1| 465 KYKKVSEDLREYTKELKKSNQLRNELAKIIESSP 498
                                       799999*********999***********99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (851 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1579  (0.0880696); expected 358.6 (0.02)
Passed bias filter:                      967  (0.053935); expected 358.6 (0.02)
Passed Vit filter:                       114  (0.00635841); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.91u 0.32s 00:00:01.23 Elapsed: 00:00:00.51
# Mc/sec: 5065.11
//
Query:       gi|298675433|ref|YP_003727183.1|  [L=156]
Description: peptide methionine sulfoxide reductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.5e-68  227.7   1.8    7.2e-68  227.6   1.8    1.0  1  PMSR      Peptide methionine sulfoxide reductase


Domain annotation for each model (and alignments):
>> PMSR  Peptide methionine sulfoxide reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.6   1.8     4e-72   7.2e-68       1     152 [.       3     154 ..       3     155 .. 0.98

  Alignments for each domain:
  == domain 1  score: 227.6 bits;  conditional E-value: 4e-72
                                       EEEEE-S-HHHHHHHHCTSTTEEEEEEEEESSS-SS--HHHHHTTTT--EEEEEEEEETTTS-HHHHHHHHHHTS-T CS
                              PMSR   1 eavlagGCFWgveklfeklkGvlstevGYagGktenptYeevcsgktghaEavevvydpekvsleellelffeihDp 77 
                                       +a++a+GCFWgve++f++++G+lst+vGY+gG+ enptY++vc+gktghaEavev+++p+ vs+e+ll++f++ihDp
  gi|298675433|ref|YP_003727183.1|   3 KATFAAGCFWGVEAAFRQIEGLLSTRVGYTGGTWENPTYKDVCTGKTGHAEAVEVTFEPSIVSYEKLLDVFWKIHDP 79 
                                       589************************************************************************** PP

                                       T-SSEETTEESGGG--EEEESSCCHHHHHHHHHHHHHTTHTTSSS---EEEEG-SEEE--CCCTTHHHH-TTS-- CS
                              PMSR  78 tqlnrqgnDvGtqYrsaiyytneeqkevaeevleelqkkkalkkkivteieplkefykaeeyHqqYleknpegyc 152
                                       t+lnrqg D+GtqYrsai+y+neeqk+ a e++++lq++ ++kk+ivt+i p++efy+aeeyHq+Y+ek+  + c
  gi|298675433|ref|YP_003727183.1|  80 TTLNRQGPDIGTQYRSAIFYHNEEQKKKAIESRDKLQQSGKYKKDIVTDIVPASEFYEAEEYHQRYFEKHGYSAC 154
                                       *********************************************************************987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 981.23
//
Query:       gi|298675434|ref|YP_003727184.1|  [L=233]
Description: ATP-binding protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-69  233.2   1.8    2.6e-69  233.1   1.8    1.0  1  Diphthami_syn_2  Diphthamide synthase
  ------ inclusion threshold ------
      0.025   14.7   0.1       0.28   11.3   0.1    2.4  2  PFO_beta_C       Pyruvate ferredoxin oxidoreductase beta subu
      0.088   12.3   0.1       0.23   10.9   0.0    1.7  2  Proteasome       Proteasome subunit
      0.092   11.5   0.0       0.18   10.6   0.0    1.6  1  tRNA_Me_trans    tRNA methyl transferase
       0.11   12.1   0.0        2.3    7.8   0.0    2.1  2  ThiI             Thiamine biosynthesis protein (ThiI)


Domain annotation for each model (and alignments):
>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  233.1   1.8   7.3e-73   2.6e-69       2     215 ..       7     226 ..       6     230 .. 0.96

  Alignments for each domain:
  == domain 1  score: 233.1 bits;  conditional E-value: 7.3e-73
                   Diphthami_syn_2   2 kvavlysGGkDsilaLykalke.sevesLvsvisenkesymfhvvnvhlvellaesvGiplikletaGeeekevedL 77 
                                       k  vlys GkDs++a y   +e + +e L++v s+n++symfh++n+++  +++e++ i li++  +Geee e+ed+
  gi|298675434|ref|YP_003727184.1|   7 KLGVLYSSGKDSNYATYLMQQEgHSIECLITVKSNNQDSYMFHTPNIDFSRMQSEAMDIALIEEISEGEEEVEIEDM 83 
                                       5679*****************99****************************************************** PP

                   Diphthami_syn_2  78 kgtlkkld....veavviGaieseyqksriervCrelGlksvaPLWkkdpeelleeiveekfevivvavkaegldes 150
                                       k  +kk +    +++vv+Ga++s yqk rier+C+elGl  + PLW+ d e  + + +e +fe i  +v+a+gl+++
  gi|298675434|ref|YP_003727184.1|  84 KRAIKKAQerylIDGVVTGALYSSYQKDRIERICNELGLEVFSPLWHIDQEAEMRKLLELGFEFIFSSVAAYGLNKD 160
                                       *****9999999***************************************************************** PP

                   Diphthami_syn_2 151 lLGrridkklidelkklsekygidkagegGeaetlvlDaPlfkkrlevkelekkwderrg.yldie 215
                                       +LG++i+ k id+l +l+ek g++ agegGe+e++v+D+P+++kr+e+k++e+ + +++  +l i+
  gi|298675434|ref|YP_003727184.1| 161 WLGKIITDKQIDKLVRLNEKVGLNVAGEGGEFESFVIDSPMYNKRIEIKDYEIVERDEYTaHLIIK 226
                                       ****************************************************99877665155555 PP

>> PFO_beta_C  Pyruvate ferredoxin oxidoreductase beta subunit C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.18   6.5e+02      43      55 ..       5      18 ..       1      27 [. 0.71
   2 ?   11.3   0.1   7.9e-05      0.28      21      62 ..      75     118 ..      68     121 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.18
                                      -EEEEEEEE.TTS- CS
                        PFO_beta_C 43 kiplGifYk.eekp 55
                                      k+ lG++Y+  + +
  gi|298675434|ref|YP_003727184.1|  5 KLKLGVLYSsGKDS 18
                                      6889****944444 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 7.9e-05
                                       GGST---EEHHHHHHHHT-..----EEEEEEEE.TTS--HHHHHH CS
                        PFO_beta_C  21 eedgyDpsdlekAlekale..wgdkiplGifYk.eekptyeerle 62 
                                       ee + + +d+++A++ka+e    d +++G +Y+  +k   e  ++
  gi|298675434|ref|YP_003727184.1|  75 EE-EVEIEDMKRAIKKAQEryLIDGVVTGALYSsYQKDRIERICN 118
                                       34.58999***********76678*********888877776555 PP

>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.86   3.1e+03     161     177 ..      77      93 ..      67     100 .. 0.72
   2 ?   10.9   0.0   6.5e-05      0.23      29      61 ..     164     196 ..     157     222 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.86
                                       HHHHHHHHHHHHHHHHH CS
                        Proteasome 161 eeavelavkalkealer 177
                                       e  +e +++a+k+a er
  gi|298675434|ref|YP_003727184.1|  77 EVEIEDMKRAIKKAQER 93 
                                       44567788888888876 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 6.5e-05
                                       EEEESSSSTSEEEEETTEEEEEEESHHHHHHHH CS
                        Proteasome  29 kllskstveKifkiddhigvafaGlaaDartlv 61 
                                       k++++++++K+ ++++++g+ +aG+ ++++ +v
  gi|298675434|ref|YP_003727184.1| 164 KIITDKQIDKLVRLNEKVGLNVAGEGGEFESFV 196
                                       5667888********************999875 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   4.9e-05      0.18       3      42 ..       8      47 ..       6      95 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 4.9e-05
                     tRNA_Me_trans  3 vvvalSgGVDSsvaaallkeqgyevigvflklweeedeeg 42
                                      + v+ S+G DS +a +l++++g++++ ++  +++++d+  
  gi|298675434|ref|YP_003727184.1|  8 LGVLYSSGKDSNYATYLMQQEGHSIECLITVKSNNQDSYM 47
                                      56889*******************9988777777666654 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0   0.00063       2.3       9      35 ..      11      37 ..       7      47 .. 0.84
   2 ?    2.5   0.0     0.026        93      70     150 ..      53     134 ..      35     148 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00063
                              ThiI  9 LlSgGiDSpVaaylllkRGcrvvlvhl 35
                                      L S G DS  a+yl+ + G  ++++  
  gi|298675434|ref|YP_003727184.1| 11 LYSSGKDSNYATYLMQQEGHSIECLIT 37
                                      889*******************99754 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.026
                              ThiI  70 vdfkevlkeilekv.....kekltivllkrkmlriAekvaeeegakalvtGesLgqVaSqtleNlrvisavvnllil 141
                                       +df ++++e ++ +      e+   v +   m r+ +k  e++ ++ +vtG      +S   + ++ i +   l ++
  gi|298675434|ref|YP_003727184.1|  53 IDFSRMQSEAMDIAlieeiSEGEEEVEI-EDMKRAIKKAQERYLIDGVVTGAL---YSSYQKDRIERICNELGLEVF 125
                                       5555555554333322222555555544.356777777778899999999954...456677788888888888888 PP

                              ThiI 142 rPLigldKe 150
                                       +PL  +d+e
  gi|298675434|ref|YP_003727184.1| 126 SPLWHIDQE 134
                                       888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1360.55
//
Query:       gi|298675435|ref|YP_003727185.1|  [L=496]
Description: asparagine synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.9e-46  158.3   0.0    3.6e-28   99.2   0.0    2.3  2  Asn_synthase   Asparagine synthase
    3.4e-12   46.3   0.0    6.7e-12   45.4   0.0    1.4  1  GATase_7       Glutamine amidotransferase domain
      2e-05   24.8   0.0    4.1e-05   23.8   0.0    1.5  1  GATase_6       Glutamine amidotransferase domain
    0.00087   18.5   0.2     0.0086   15.2   0.0    2.3  2  NAD_synthase   NAD synthase
      0.004   16.9   0.0     0.0097   15.7   0.0    1.6  1  ATP_bind_3     PP-loop family
      0.009   14.8   0.0      0.015   14.1   0.0    1.2  1  tRNA_Me_trans  tRNA methyl transferase
  ------ inclusion threshold ------
      0.023   14.2   0.0      0.041   13.4   0.0    1.5  1  QueC           Queuosine biosynthesis protein QueC


Domain annotation for each model (and alignments):
>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.2   0.0   1.4e-31   3.6e-28       4     139 ..     232     373 ..     229     377 .. 0.88
   2 !   57.9   0.0   5.3e-19   1.3e-15     203     300 ..     375     472 ..     372     494 .. 0.89

  Alignments for each domain:
  == domain 1  score: 99.2 bits;  conditional E-value: 1.4e-31
                      Asn_synthase   4 elLedaVkrrlradvpvGalLSGGlDSSliaalaarqsksplktFsigf......eekgsdeakyakevaehlgteh 74 
                                         LedaV  r   d p+G+l+SGG+DS++ia++ ++  k+p   F++        ++  s++++yak+va++lg+e 
  gi|298675435|ref|YP_003727185.1| 232 NILEDAVSIRF-PDEPFGILFSGGIDSTIIAYICKKLGKQPGIDFTCYVagfkgnDSGYSPDVSYAKKVADELGLEL 307
                                       579*****998.9**************************66666665554447655599****************** PP

                      Asn_synthase  75 telvlteeelldalpdviyhlee...pfadrsaiplyllsrlakrkgvkvvLsGeGaDElfgGYpyfy 139
                                          ++t +e++d+l+ v++ +e+   p     a+ +y ++ +a+++g++v++sG GaDEl +GY+ ++
  gi|298675435|ref|YP_003727185.1| 308 KIKQITYREVEDYLKTVVSLIEDtsvP-KVGVALTMYAACVAAREDGIRVMFSGSGADELLAGYN-RH 373
                                       **********************98855.5556699******************************.87 PP

  == domain 2  score: 57.9 bits;  conditional E-value: 5.3e-19
                      Asn_synthase 203 gedelhrelyldlktllpgdllrkDrasmahglEaRvPflDhrlvevalrlppelklrg..gieKyiLRealegy.l 276
                                       + ++++ e+y d+ ++++ +  r D  sm + +E+RvP+lD +lv++ l++p++ k+++  g++K  LR + +++ l
  gi|298675435|ref|YP_003727185.1| 375 HSEDVNYECYQDILNIYQKNTYRDDVVSMNNNIELRVPYLDSNLVDYGLKIPAHCKIDNkqGQNKLTLRNVGKKLgL 451
                                       678999*****************************************************999************99* PP

                      Asn_synthase 277 PeeileRpKegfsapvgewklkge 300
                                       ++++++R K++++++++   ++++
  gi|298675435|ref|YP_003727185.1| 452 HDDFVHRNKKAAQYGSR---FDKA 472
                                       ***********998443...3344 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.0   2.6e-15   6.7e-12      14     122 ..      71     180 ..      64     181 .. 0.89

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 2.6e-15
                          GATase_7  14 QPmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea..............ewgeealerlnG 76 
                                       QP++     +  +v+n eiyN k l + +     + + + D+  l++ +e+              + +e+al+++ G
  gi|298675435|ref|YP_003727185.1|  71 QPIAY----TGKMVANCEIYNWKMLSNTY-----NLDAENDSDFLIKFIEYqisktdssnpvrikDNIEKALNKIIG 138
                                       77773....33589********9999885.....567888999999999989999*********99*********** PP

                          GATase_7  77 mfAfaiwdeeekrlllaRDrlGikPLyygedkgdallfaSelkall 122
                                        ++fa++      +++ RD +G+kPL y +++  +++faSe kal+
  gi|298675435|ref|YP_003727185.1| 139 VYSFAYMLGGY--VYVFRDIIGVKPLWYSNSS--GFAFASEKKALM 180
                                       *******9888..******************5..7*********97 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   1.6e-08   4.1e-05      33     134 .]      71     175 ..      47     175 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.6e-08
                          GATase_6  33 qPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall........eelG.........eevlerl 92 
                                       qP+   + +  +v N eiyn+k l++++         +++D+  l++ +        +            e++l+++
  gi|298675435|ref|YP_003727185.1|  71 QPI---AYTGKMVANCEIYNWKMLSNTYNL------DAENDSDFLIKFIeyqisktdS--SnpvrikdniEKALNKI 136
                                       666...33334789*******966665555......5789*******98888866541..155777778899999** PP

                          GATase_6  93 rGmfafaiwdkrentlila.rdrlgvkplyyavdesglafase 134
                                        G+++fa +    ++++ + rd +gvkpl+y+ + sg+afase
  gi|298675435|ref|YP_003727185.1| 137 IGVYSFAYML---GGYVYVfRDIIGVKPLWYS-NSSGFAFASE 175
                                       **99998664...6666666************.6********8 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   3.3e-06    0.0086      25      82 ..     251     313 ..     245     374 .. 0.64
   2 ?   -0.1   0.1      0.16   4.1e+02     192     217 ..     378     403 ..     375     415 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.3e-06
                                       E-SSHHHHHHHHHHHHHHTCGEE..EEEE--....SSSTTHHHHHHHHHHHHHHTSEEEE---H CS
                      NAD_synthase  25 lSGGvDSslvaalavkalgkenv..lalllP....ssvsseedvedalalaenlgievktidik 82 
                                        SGG+DS+++a++++k+  k+    ++ ++     +      dv  a+++a++lg+e k  +i+
  gi|298675435|ref|YP_003727185.1| 251 FSGGIDSTIIAYICKKLG-KQPGidFTCYVAgfkgNDSGYSPDVSYAKKVADELGLELKIKQIT 313
                                       5*************9965.554301334443221133334569999999999999988776664 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.16
                                       SS-HHHHHHHHTHSSSS...HHHHHT CS
                      NAD_synthase 192 gikYdelDeiLklvekkkspeeiike 217
                                       +++Y+   +iL++++k++ ++++++ 
  gi|298675435|ref|YP_003727185.1| 378 DVNYECYQDILNIYQKNTYRDDVVSM 403
                                       57899999999999999999998874 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   3.8e-06    0.0097       5      69 ..     250     315 ..     247     324 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.8e-06
                                       E--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSS.TCHHHHHHHHHHHHHHTT-EEEEEE--HH CS
                        ATP_bind_3   5 AvSgGlDSmaLllllaklkkklgiklvaihvdhglr.eeskeeaelvkelckklnikleiekvdva 69 
                                        +SgG+DS+++ ++ +kl k+ gi++++ +  ++   +    +  + k+++++l+++l+i++++  
  gi|298675435|ref|YP_003727185.1| 250 LFSGGIDSTIIAYICKKLGKQPGIDFTCYVAGFKGNdSGYSPDVSYAKKVADELGLELKIKQITYR 315
                                       59*******************************99945678899******************9963 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   5.8e-06     0.015       6      80 ..     250     326 ..     247     332 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.8e-06
                     tRNA_Me_trans   6 alSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplev..vdfe..keykekv 78 
                                       ++SgG+DS++ a++ k+ g++  g+ + ++   + +g+   ++ d+++a++va++lg++l++  + ++  ++y ++v
  gi|298675435|ref|YP_003727185.1| 250 LFSGGIDSTIIAYICKKLGKQ-PGIDFTCYVA-GFKGNDSGYSPDVSYAKKVADELGLELKIkqITYRevEDYLKTV 324
                                       68**************99987.5788877776.5566688999************9987765114443225666666 PP

                     tRNA_Me_trans  79 fe 80 
                                       ++
  gi|298675435|ref|YP_003727185.1| 325 VS 326
                                       65 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.6e-05     0.041       4      62 ..     249     313 ..     248     414 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.6e-05
                                       EE--SSHHHHHHHHHHHHH-SE......EEEEEEESS-T.TSHHHHHHHHHHHHT--.-EEEEE-G CS
                              QueC   4 vllSGGlDSttvlalakkegke......vealtfdYgqr.hkkeleaakkiakelgveehkildld 62 
                                       +l+SGG+DSt+++++ kk gk+      +++ +f+ +    + ++++akk+a+elg+ e ki +++
  gi|298675435|ref|YP_003727185.1| 249 ILFSGGIDSTIIAYICKKLGKQpgidftCYVAGFKGNDSgYSPDVSYAKKVADELGL-ELKIKQIT 313
                                       69****************997433333378888888888788999999999999998.66665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 2981.48
//
Query:       gi|298675436|ref|YP_003727186.1|  [L=596]
Description: ATP-dependent DNA helicase RecQ [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-32  111.5   0.2    3.3e-32  110.6   0.2    1.4  1  RQC            RQC domain
    1.3e-23   83.4   0.1    3.4e-20   72.4   0.0    2.9  2  Helicase_C     Helicase conserved C-terminal domain
    5.7e-23   81.6   0.0      1e-21   77.5   0.0    2.2  2  DEAD           DEAD/DEAH box helicase
    8.9e-21   73.7   0.0    1.6e-20   72.8   0.0    1.5  1  HRDC           HRDC domain
    1.4e-17   64.2   3.6    1.4e-17   64.2   3.6    3.3  5  RecQ_Zn_bind   RecQ zinc-binding
    1.7e-06   28.1   0.1    1.4e-05   25.2   0.0    2.3  3  ResIII         Type III restriction enzyme, res subunit
    0.00021   20.2   0.0    0.00035   19.4   0.0    1.3  1  SNF2_N         SNF2 family N-terminal domain
    0.00087   19.3   0.0     0.0029   17.6   0.0    1.8  1  Helicase_Sgs1  Sgs1 RecQ helicase
  ------ inclusion threshold ------
      0.012   16.3   2.6      0.074   13.7   0.4    2.9  2  DUF573         Protein of unknown function, DUF573
      0.044   13.7   0.0       0.11   12.4   0.0    1.7  1  HHH            Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> RQC  RQC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.6   0.2   1.9e-35   3.3e-32       1     110 [.     395     503 ..     395     507 .. 0.96

  Alignments for each domain:
  == domain 1  score: 110.6 bits;  conditional E-value: 1.9e-35
                                       ---EEE-HHHHHHHHHHHHHTTS-SBHHHHHHHHHT---CCCCCTTGGGSTTTTTTTTS-HHHHHHHHHHHHHTTSE CS
                               RQC   1 ppetvDvteeaqkilscvyrtgqrfgaghivdvLrGsktkkirqlghdklstfGigkdlskkewrrlirqLiaegyL 77 
                                       p+e+ D+t  a++ lscv +++q++g++h+vdvL+Gsktkki++++hd l+ +G g +++k++w ++ ++L+++gyL
  gi|298675436|ref|YP_003727186.1| 395 PKEMTDGTATAKTFLSCVDELNQKYGLNHVVDVLTGSKTKKITDKQHDLLESYGAGYNYKKNQWLDIGKELLHKGYL 471
                                       6899************************************************************************* PP

                                       EEE..SSSBEEE-CCGHHHHTSSS--EEESHHH CS
                               RQC  78 eedveeygvlkltekarevlkgeekvklreekk 110
                                       e++++ y+vlkl++k++++l+g+e+v+l++ ++
  gi|298675436|ref|YP_003727186.1| 472 EVKGK-YPVLKLNQKSQNILSGQENVQLTKLSE 503
                                       ***77.**********************98766 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0021       3.8      14      73 ..      51     110 ..      41     128 .. 0.82
   2 !   72.4   0.0   1.9e-23   3.4e-20       5     110 ..     214     318 ..     210     319 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0021
                                       TTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEES CS
                        Helicase_C  14 eeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvLiat 73 
                                         +g ++++++ i+ +++ v+ l +++gi++a+l+++l  +e ++i ++   +++dvL  t
  gi|298675436|ref|YP_003727186.1|  51 LMEGVTIVVSPLISLMKDqVDEL-RSNGISAACLNSTLGYQESNQICNDLLYNRIDVLYIT 110
                                       4678899999***9776556777.5779********************9998899988655 PP

  == domain 2  score: 72.4 bits;  conditional E-value: 1.9e-23
                                       HHHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSS CS
                        Helicase_C   5 allellkleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGi 80 
                                       +++++l +++++++ +i++++++ +e+  + l +k+g++v+++h+ lp++ ree  e+f ++++++++at + ++Gi
  gi|298675436|ref|YP_003727186.1| 214 QMVRYL-KTHRKYNGIIYCQSRRAVEDlYNKL-KKEGFRVLPYHAGLPAKIREENQESFIRDDVQIIVATIAFGMGI 288
                                       566667.78999999********998554555.677***************************************** PP

                                       TSTTESEEEESSSSSSHHHHHHHHTTSSST CS
                        Helicase_C  81 dipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                       + p+v++Vi++dlp+n+++y q+ GR gR 
  gi|298675436|ref|YP_003727186.1| 289 NKPNVRFVIHYDLPKNLENYYQQTGRGGRD 318
                                       *****************************6 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.5   0.0   5.7e-25     1e-21       2     173 ..      16     176 ..      15     180 .. 0.85
   2 ?    1.6   0.0      0.11     2e+02      43     105 ..     220     282 ..     205     296 .. 0.76

  Alignments for each domain:
  == domain 1  score: 77.5 bits;  conditional E-value: 5.7e-25
                                       HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrv 78 
                                       + Q+ +i  il+++d +v ++TG GK+l++++p+l  ++      +  +++v+P+ +L+++++++l++ +  +   +
  gi|298675436|ref|YP_003727186.1|  16 SHQKDIITDILDKKDTFVVMPTGGGKSLCYQLPAL--LM------EGVTIVVSPLISLMKDQVDELRSNGISAA-CL 83 
                                       57*********************************..53......3589*****************99999744.33 PP

                                       EEEETTSSHHHHHHHHH.TTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHT..TTHHHHHHHHHHSHHH CS
                                       xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx RF
                              DEAD  79 lliiggvaardqlskld.ngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldq..gfsdfinrilnqlpqi 152
                                       ++++g ++ ++  ++l  n++d+++ tp+rl    +   l+  +++++ +DEa++++++  +f++++ r ln l+++
  gi|298675436|ref|YP_003727186.1|  84 NSTLGYQESNQICNDLLyNRIDVLYITPERLTMSKTLDFLESVNINLFAIDEAHCISEWgqDFRPEYLR-LNMLKKK 159
                                       46788777777777775488************855555567888899***********9989*******.9***999 PP

                                       CTTSTTTSEEEEEESSBSHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 153 tcdgklqrqvivlSATlpkdv 173
                                         d +    +i+l+AT++  v
  gi|298675436|ref|YP_003727186.1| 160 FPDIP----LIALTATATPRV 176
                                       99988....99*****99554 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.11
                                       TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEET.TSSHHHHHHHHHTTCSEEEEEH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  43 kgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliig.gvaardqlskldngvdivvgtp 105
                                       k+ ++   +i + +r  +e+ +n+lkk +  + l +++ +  + ++++q s ++ +v+i+v+t 
  gi|298675436|ref|YP_003727186.1| 220 KTHRKYNGIIYCQSRRAVEDLYNKLKKEGFRV-LPYHAGLPaKIREENQESFIRDDVQIIVATI 282
                                       67777888999999999999999999988853.44443333256667888888888****9995 PP

>> HRDC  HRDC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.8   0.0   9.1e-24   1.6e-20       2      68 .]     519     585 ..     518     585 .. 0.97

  Alignments for each domain:
  == domain 1  score: 72.8 bits;  conditional E-value: 9.1e-24
                                       HHHHHHHHHHHHHHHHHHTS-HHHHS-HHHHHHHHHH---SHHHHHTSTTT-HHHHHHHHHHHHHHH CS
                              HRDC   2 lallkaLrewReelAreedvppyvvfpdktLleiAeklPttleeLlqiegvgkrklekygeeileai 68 
                                       ++l+++Lr +R++lA++e+ +py++f d  L+++A  +P+t +e+l+i+gvg++klekyg+ +l+ i
  gi|298675436|ref|YP_003727186.1| 519 NQLFEKLRRLRKKLADSENKAPYIIFADTSLRQMASICPKTYDEFLKISGVGEYKLEKYGDMFLSEI 585
                                       89*************************************************************9876 PP

>> RecQ_Zn_bind  RecQ zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.1        10   1.8e+04      45      54 ..       4      13 ..       3      16 .. 0.71
   2 ?   -2.3   0.1       4.4   7.9e+03      33      44 ..     182     192 ..     178     210 .. 0.79
   3 ?   -1.2   0.6       1.9   3.4e+03      22      37 ..     206     221 ..     186     224 .. 0.63
   4 !   64.2   3.6   7.6e-21   1.4e-17       2      66 .]     331     393 ..     330     393 .. 0.94
   5 ?   -2.9   0.0       6.5   1.2e+04      24      35 ..     545     556 ..     510     560 .. 0.60

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 10
                      RecQ_Zn_bind 45 llleyFgeea 54
                                      +l +yFg e+
  gi|298675436|ref|YP_003727186.1|  4 ILHKYFGYEE 13
                                      6789**9655 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.4
                      RecQ_Zn_bind  33 aycentteCrrk 44 
                                       ++  + ++Crr 
  gi|298675436|ref|YP_003727186.1| 182 SLL-ELEDCRRY 192
                                       555.45679996 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.9
                      RecQ_Zn_bind  22 eaelekleamlaycen 37 
                                       +++ +  ++m++y ++
  gi|298675436|ref|YP_003727186.1| 206 RHKKDAYKQMVRYLKT 221
                                       4455668999999865 PP

  == domain 4  score: 64.2 bits;  conditional E-value: 7.6e-21
                      RecQ_Zn_bind   2 qDvsrlrrlieqseesekekeaelekleamlaycentteCrrkllleyFgeeaaeeeCgnCDnCl 66 
                                       +D+ +++++i+q++ +++e++ +l+kl+ m++yce+++ Crrklll+yFge+++ ++Cg+CD+Cl
  gi|298675436|ref|YP_003727186.1| 331 GDRYKIEYFINQKS-RKSERDIALSKLNMMIDYCESNV-CRRKLLLNYFGEDFDVQNCGKCDVCL 393
                                       7999******7765.88999*****************9.*************************6 PP

  == domain 5  score: -2.9 bits;  conditional E-value: 6.5
                      RecQ_Zn_bind  24 elekleamlayc 35 
                                       + ++l++m + c
  gi|298675436|ref|YP_003727186.1| 545 ADTSLRQMASIC 556
                                       336778887777 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   7.5e-09   1.4e-05       3     169 ..      13     172 ..      12     175 .. 0.79
   2 ?   -3.2   0.0         4   7.2e+03      84     111 ..     247     282 ..     213     284 .. 0.50
   3 ?   -0.9   0.2      0.78   1.4e+03      89     128 ..     482     521 ..     402     546 .. 0.53

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 7.5e-09
                                       EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTG CS
                            ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkfls 79 
                                       e+r++Q+++i+++l      ++k  +++m+TG GK+l++ +l + l++      ++++ p +sl++   +e+++   
  gi|298675436|ref|YP_003727186.1|  13 EFRSHQKDIITDIL------DKKDTFVVMPTGGGKSLCY-QLPALLMEG----VTIVVSPLISLMKDQVDELRSNGI 78 
                                       689**********8......67889***********986.566666664....79*****************99999 PP

                                       G....GEEEESSS-B--........-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS...T..... CS
                            ResIII  80 eaykeigkkvsgdkkka.kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak..k..... 148
                                       +a+  +++   ++++++ +    + +++l +t ++l+ ++     + + l++ +++++ iDEaH +++   +     
  gi|298675436|ref|YP_003727186.1|  79 SAACLNSTLGYQESNQIcNDLLYNRIDVLYITPERLTMSK-----TLDFLESVNINLFAIDEAHCISEWgqDfrpey 150
                                       98655555544444444577788999**********9999.....55666667778***********9765155534 PP

                                       .TTHHHHHT---SEEEEEESS- CS
                            ResIII 149 .swreilekfkeavllglTATp 169
                                          + +++kf++  l++lTAT 
  gi|298675436|ref|YP_003727186.1| 151 lRLNMLKKKFPDIPLIALTATA 172
                                       4555559999999999999994 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4
                                       ...........GEEEESSS-B--.......-SEEEEEH CS
                            ResIII  84 e..........igkkvsgdkkkakekdstnkkilvtti 111
                                       e             k++++++++    +++ +i+v+ti
  gi|298675436|ref|YP_003727186.1| 247 EgfrvlpyhagLPAKIREENQES--FIRDDVQIIVATI 282
                                       22222222223333333333333..3556666666665 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.78
                                       ESSS-B--.......-SEEEEEHHHHHHTH........HH CS
                            ResIII  89 vsgdkkkakekdstnkkilvttiqsldadseeeeeeseel 128
                                       ++++++++ +++++     ++++ s +++ ++++e++++l
  gi|298675436|ref|YP_003727186.1| 482 LNQKSQNILSGQENVQLTKLSEYPSTSKQDNSANETDNQL 521
                                       3333333333344444444555555555554444444443 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0     2e-07   0.00035      95     273 ..      52     237 ..      17     252 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2e-07
                                       ..S-EEEE--H.HHHHHHHHHHHHH-TTS-EEE--SSHHHH-----------------EEEE-HHHHHHHT...... CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N  95 lagptLivvPa.slldqWeneierhvsssalrvlvyggqkkmkkkntkvapklladydvvittYdvlsreaelqkkr 170
                                       ++g t++v+P  sl++  ++e+++   s a  +l  + ++  +++n+   + l +  dv+ +t ++l   +      
  gi|298675436|ref|YP_003727186.1|  52 MEGVTIVVSPLiSLMKDQVDELRSNGISAA--CLNSTLGY--QESNQICNDLLYNRIDVLYITPERLTMSK----TL 120
                                       4566999***99***999999998666654..45555554..5677888999999*************555....9* PP

                                       TTS-S-S-SEEEES-GGGT--T.T......SHHHHHHHH---S-EEEE-S--SSS-HHHHHHHHHHH-TTTT--HHH CS
                                       xxxxxxxxxxxxxxxxxxxxxx.x......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 171 svlkqvewkrvvlDEghtlkns.t......skaaeavskLstsnrwiltGTPiqnsledlygLlkfLreepfgekqt 240
                                       + l++v+++   +DE+h +    +       ++ +  +k+     + lt+T +++  +d+++Ll++  ++ + +  +
  gi|298675436|ref|YP_003727186.1| 121 DFLESVNINLFAIDEAHCISEWgQdfrpeyLRLNMLKKKFPDIPLIALTATATPRVQNDVISLLELEDCRRYIS-SF 196
                                       *******************9886234444466666666699999**********************99999984.44 PP

                                       HHHHTHHHHHHHHHHHHHHHHTT-ST.........TEE---G CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxx RF
                            SNF2_N 241 fdkllqrpieaqaekgrsrLlqllqr.........lmlrrak 273
                                        ++ l+ +++ ++++  ++++  l+          +  rra 
  gi|298675436|ref|YP_003727186.1| 197 NRDNLYYEVR-HKKDAYKQMVRYLKThrkyngiiyCQSRRAV 237
                                       4556666666.5666666677666644444444445555555 PP

>> Helicase_Sgs1  Sgs1 RecQ helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.6e-06    0.0029       8      73 ..     521     588 ..     516     592 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.6e-06
                                       HHHHHHHHHHHHHHSSSS--S-SS-HHHHHHHHHH---SHHHHGGGS---HHHHHHGGG..THHHHHH CS
                     Helicase_Sgs1   8 ayerlravainlgnrmnlpvdtylpdnilkkiAaiLPatedeFislvgnndkarrkyky..fkatlad 73 
                                        +e+lr +  +l++  n +    + d+ l+++A i P+t deF ++ g+ + +  ky +  +++++  
  gi|298675436|ref|YP_003727186.1| 521 LFEKLRRLRKKLADSENKAPYIIFADTSLRQMASICPKTYDEFLKISGVGEYKLEKYGDmfLSEIIDH 588
                                       589999999999999999999999*****************************999976224666655 PP

>> DUF573  Protein of unknown function, DUF573
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.42   7.6e+02      40      73 ..     190     222 ..     168     229 .. 0.79
   2 ?   13.7   0.4   4.1e-05     0.074      30      69 ..     499     538 ..     481     551 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.42
                            DUF573  40 ksslssdvsksqlseKlrrLkkkyrnavskikkg 73 
                                       ++ +s +++ ++l+  +r+ k  y+++v+  k++
  gi|298675436|ref|YP_003727186.1| 190 RRYIS-SFNRDNLYYEVRHKKDAYKQMVRYLKTH 222
                                       44444.899999*************999876644 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 4.1e-05
                            DUF573  30 sdldafyeavksslssdvsksqlseKlrrLkkkyrnavsk 69 
                                        +l+++  + k+  s++ + +ql eKlrrL+kk     +k
  gi|298675436|ref|YP_003727186.1| 499 TKLSEYPSTSKQDNSANETDNQLFEKLRRLRKKLADSENK 538
                                       45666667777888889999*************8876555 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.3e-05      0.11       7      23 ..     557     573 ..     554     576 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.3e-05
                                       TSSHHHHHTSTT-SHHH CS
                               HHH   7 pasreeLlalPGVGpkt 23 
                                       p +++e l+++GVG+++
  gi|298675436|ref|YP_003727186.1| 557 PKTYDEFLKISGVGEYK 573
                                       88**************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (596 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       940  (0.052429); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.71u 0.35s 00:00:01.06 Elapsed: 00:00:00.52
# Mc/sec: 3465.17
//
Query:       gi|298675437|ref|YP_003727187.1|  [L=304]
Description: GMP synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-31  106.5   0.0    1.5e-30  105.1   0.0    1.8  1  GMP_synt_C       GMP synthase C terminal domain
      2e-10   40.2   0.2    1.3e-09   37.6   0.2    2.0  1  NAD_synthase     NAD synthase
    2.8e-05   23.7   0.0    0.00029   20.4   0.0    2.1  2  QueC             Queuosine biosynthesis protein QueC
    8.4e-05   21.5   0.0     0.0084   14.9   0.0    2.1  2  tRNA_Me_trans    tRNA methyl transferase
     0.0015   18.1   0.0     0.0047   16.5   0.0    1.8  1  ThiI             Thiamine biosynthesis protein (ThiI)
     0.0037   17.0   0.0     0.0057   16.4   0.0    1.4  1  ATP_bind_3       PP-loop family
  ------ inclusion threshold ------
      0.015   14.6   0.2      0.069   12.4   0.0    1.9  2  Arginosuc_synth  Arginosuccinate synthase
      0.036   14.4   0.2       0.13   12.6   0.1    1.9  2  DinI             DinI-like family
       0.04   14.0   0.0       0.14   12.2   0.0    1.8  2  PAPS_reduct      Phosphoadenosine phosphosulfate reductase fa
       0.12   12.6   0.0       0.31   11.3   0.0    1.6  1  DUF5388          Family of unknown function (DUF5388)


Domain annotation for each model (and alignments):
>> GMP_synt_C  GMP synthase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.1   0.0   8.2e-34   1.5e-30      11      92 .]     223     303 ..     211     303 .. 0.94

  Alignments for each domain:
  == domain 1  score: 105.1 bits;  conditional E-value: 8.2e-34
                                       GSSEEEEEEEEEEE----------EEEEEEEEE---------B----HHHHHHHHHHHHHHSTT---EEEE---TTT CS
                        GMP_synt_C  11 kiwQafavllpvksvGvmgdkRtyeyvvalRaveseDamtadvaelpyevLekissrivnevkgvnrvvyditskPp 87 
                                       + wQ+fa+ll  k +Gv+gd R +++++a+Rav+s+D+mta++++lp++vL++i sri +e+k+v+rvvyd+t kPp
  gi|298675437|ref|YP_003727187.1| 223 HPWQTFAALLG-KGTGVKGDVRVHGWIIAVRAVSSRDGMTAEAMQLPWDVLNRIESRINSEIKSVSRVVYDLTPKPP 298
                                       56********9.99*************************************************************** PP

                                       S-S-- CS
                        GMP_synt_C  88 atiEw 92 
                                       atiE+
  gi|298675437|ref|YP_003727187.1| 299 ATIEF 303
                                       ****7 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.2   7.2e-13   1.3e-09      10     177 ..      12     185 ..       1     206 [. 0.77

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 7.2e-13
                                       HHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---HHHHH CS
                      NAD_synthase  10 keyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidikpivr 86 
                                       +e++k++   ++++ lSGGvDSs+  +la +a+  +n + +++ +    + ++e  ++   +  ++  ++++k+   
  gi|298675437|ref|YP_003727187.1|  12 TEKIKEQIDGKAIIALSGGVDSSVCTVLAHNAI-GDNLVPIYIETGLMRKGETERIKETFAD--MNLRVVNMKNRFL 85 
                                       45666777789**********************.678999***9888888888888888877..8999999999888 PP

                                       HHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHTEEEB--..........-BHHHHTTT-S-TTTTT--SBETTTT CS
                      NAD_synthase  87 afeqelkeakedlakgNlkaRiRmailyaianklnllvlgT..........gnksElvvGyfTkyGDgaadlapiae 153
                                          + +++ + + +++  ++ iR     a  ++ ++l+ gT          g ks   vG      D    ++pi +
  gi|298675437|ref|YP_003727187.1|  86 NALEGVEDPE-EKRRAVGETFIRVFEEIAKEEQAEYLIQGTiypdriesdgGIKSHHNVGGLPDVVDFKDIVEPISD 161
                                       8888777766.556666778899999999999********955322222222344444555555556666789**** PP

                                       S-HHHHHHHHHHTT--HHHHCS-- CS
                      NAD_synthase 154 llKtevkeLakelnvPervlkkpP 177
                                       l+K ev+e ak+l  Pe++ ++ P
  gi|298675437|ref|YP_003727187.1| 162 LYKDEVREVAKALDLPEELSERMP 185
                                       *********************998 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.6e-07   0.00029       1      68 [.      22      89 ..      22     130 .. 0.90
   2 ?    1.4   0.0      0.11   1.9e+02     153     180 ..     154     181 ..     112     183 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.6e-07
                                      EEEEE--SSHHHHHHHHHHHHH-.SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGGGGS CS
                              QueC  1 kavvllSGGlDSttvlalakkeg.kevealtfdYgqrhkkeleaakkiakelgveehkildldllkelg 68
                                      ka++ lSGG+DS+++++la++++ +++  + ++ g  +k e+e  k+ ++++++ +   ++ ++l++l 
  gi|298675437|ref|YP_003727187.1| 22 KAIIALSGGVDSSVCTVLAHNAIgDNLVPIYIETGLMRKGETERIKETFADMNL-RVVNMKNRFLNALE 89
                                      79*****************9985499************************9999.88888888888776 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.11
                                       EEE-TTTT--HHHHHHHHHHTTHHHHH- CS
                              QueC 153 eieaPlidlsKaeivklgkelgvpleet 180
                                        i+ P+ dl K e+ +++k l++p e++
  gi|298675437|ref|YP_003727187.1| 154 DIVEPISDLYKDEVREVAKALDLPEELS 181
                                       5899*****************9988765 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   4.7e-06    0.0084       3      52 ..      23      76 ..      21     111 .. 0.67
   2 !    4.6   0.0    0.0063        11     162     186 ..     153     177 ..     149     184 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.7e-06
                     tRNA_Me_trans  3 vvvalSgGVDSsvaaallkeq.gyevigvflklwee.edeeg..keccaeedlk 52
                                       ++alSgGVDSsv  +l +++ g +++ +++++    ++e++  ke  a+ +l+
  gi|298675437|ref|YP_003727187.1| 23 AIIALSGGVDSSVCTVLAHNAiGDNLVPIYIETGLMrKGETEriKETFADMNLR 76
                                      689*************99987368888898887554222222234555555555 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0063
                     tRNA_Me_trans 162 ekllfPlgeltKeevrkiAkeagla 186
                                       ++++ P+ +l K+evr++Ak+ +l+
  gi|298675437|ref|YP_003727187.1| 153 KDIVEPISDLYKDEVREVAKALDLP 177
                                       56788***************99986 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   2.6e-06    0.0047       3     117 ..      20     126 ..      18     185 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.6e-06
                              ThiI   3 qgkvlaLlSgGiDSpVaaylllkR.Gcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlke 78 
                                        gk++  lSgG+DS V + l+ +  G + v ++++    t+   ++  e++ e +a+ +      l+vv+ k+   +
  gi|298675437|ref|YP_003727187.1|  20 DGKAIIALSGGVDSSVCTVLAHNAiGDNLVPIYIE----TGLMRKGETERIKETFADMN------LRVVNMKNRFLN 86 
                                       6999**************99976449999999997....44445566677888777665......899999998888 PP

                              ThiI  79 ilekv..kekltivllkrkmlriAekvaeeegakalvtGes 117
                                        le v  + + +   +  +++r+ e++a+ee+a+ l++G  
  gi|298675437|ref|YP_003727187.1|  87 ALEGVedP-EEKRRAVGETFIRVFEEIAKEEQAEYLIQGTI 126
                                       88888432.33344567899******************964 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   3.2e-06    0.0057       2     111 ..      23     132 ..      22     177 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.2e-06
                                       EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSST..CHHHHHHHHHHHH.HHTT-EEEEEE--HHHCTTST CS
                        ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglre..eskeeaelvkelc.kklnikleiekvdvakkkgkn 75 
                                       +++A+SgG+DS + ++l+++     g +lv i+++ gl    e+++ +e+ ++++ + +n+k +  ++  + +  ++
  gi|298675437|ref|YP_003727187.1|  23 AIIALSGGVDSSVCTVLAHNAI---GDNLVPIYIETGLMRkgETERIKETFADMNlRVVNMKNRFLNALEGVEDPEE 96 
                                       79*********99888887774...4588888888888641133444444444431334455555555545555555 PP

                                       CCCHHHHHHHHHHHHCHHCCT.CEEE---BHHHHHH CS
                        ATP_bind_3  76 leeaARelRYevlkealkkegievlllAhhadDqaE 111
                                          a  e   +v++e++k+e++e+l+ +    D +E
  gi|298675437|ref|YP_003727187.1|  97 KRRAVGETFIRVFEEIAKEEQAEYLIQGTIYPDRIE 132
                                       555666777899*************99988888887 PP

>> Arginosuc_synth  Arginosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.9e-05     0.069       1      64 [.      24      85 ..      24      89 .. 0.77
   2 ?   -0.5   0.1      0.33     6e+02     190     245 ..     156     216 ..     151     221 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.9e-05
                   Arginosuc_synth  1 vLaysGGlDtsviikllkeklgeeviavavdvGqeee.dldevkekalklgavksvvvDakeefv 64
                                      ++a sGG+D sv+  l ++ +g++ + + ++ G  ++ + +++k   + +++++  vv++k+ f 
  gi|298675437|ref|YP_003727187.1| 24 IIALSGGVDSSVCTVLAHNAIGDNLVPIYIETGLMRKgETERIK---ETFADMNLRVVNMKNRFL 85
                                      6899*****************************87431444444...456666777777777775 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.33
                   Arginosuc_synth 190 nappediye.ltkdpakapdepeeve..iefe.kGvPvald.geelsvlelieklneiagk 245
                                       ++p+ d+y+  ++++aka d pee++  + f   G+ v +  + + + le+++++n i  +
  gi|298675437|ref|YP_003727187.1| 156 VEPISDLYKdEVREVAKALDLPEELSerMPFPgPGLAVRIIdEVTEEKLEVVREANAIVEE 216
                                       5788999973578899999999999633667525999987515556669999999988665 PP

>> DinI  DinI-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   7.1e-05      0.13      14      47 ..      64      99 ..      60     111 .. 0.82
   2 ?   -2.2   0.0       3.2   5.7e+03      10      29 ..     178     197 ..     175     218 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.1e-05
                                      HHHHHH-SS-EEEEEEESS-EEEE.ES.--HHHHHH CS
                              DinI 14 kRiqevfPdaevrvrkasanglsv.eG.askedker 47
                                       Ri+e f d+++rv+ +++  l++ eG +++e+k+r
  gi|298675437|ref|YP_003727187.1| 64 ERIKETFADMNLRVVNMKNRFLNAlEGvEDPEEKRR 99
                                      7******************99986268888888876 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.2
                                       HHHHHHHHHH-SS-EEEEEE CS
                              DinI  10 aELskRiqevfPdaevrvrk 29 
                                       +ELs R+    P   vr+  
  gi|298675437|ref|YP_003727187.1| 178 EELSERMPFPGPGLAVRIID 197
                                       56777765444445555543 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.5e-05      0.14       2      90 ..      23     117 ..      22     126 .. 0.67
   2 ?   -1.2   0.0         1   1.8e+03      75      97 ..     160     182 ..     149     221 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.5e-05
                                       EEEE--SSCTCHHHHHHHHHHCTTH.EEEEEE-STB-HHHHHHHHHHHHHTT-E.EEEEE-SCHHHHHHHHHH-S-T CS
                       PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpv.pvvfvdtghefpetiefvdeleeryglr.lkvyepeeevaekinaekhgss 76 
                                        +++ sgG ds+V   La +a  +    ++++tg   +  +e ++e+   ++lr + + ++  +  e+++  +   +
  gi|298675437|ref|YP_003727187.1|  23 AIIALSGGVDSSVCTVLAHNAIGDNlVPIYIETGLMRKGETERIKETFADMNLRvVNMKNRFLNALEGVEDPEEKRR 99 
                                       57899****************99952589******999988889999888877744444443444444333333333 PP

                                       HHHC....HHHHHHTHHH CS
                       PAPS_reduct  77 lyee....aaeriaKvep 90 
                                        + e     +e+iaK e+
  gi|298675437|ref|YP_003727187.1| 100 AVGEtfirVFEEIAKEEQ 117
                                       333344445666666555 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1
                                       -THHHCHHHHHHTHHHHHHHHHC CS
                       PAPS_reduct  75 sslyeeaaeriaKveplkkaLek 97 
                                       s+ly+++++++aK+  l + L++
  gi|298675437|ref|YP_003727187.1| 160 SDLYKDEVREVAKALDLPEELSE 182
                                       46777777777777777775544 PP

>> DUF5388  Family of unknown function (DUF5388)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00017      0.31       8      59 ..      70     122 ..      64     127 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                           DUF5388   8 f.dvnvrvdNHirNklqALaaiGlaksqkeavkklveslidsLsesdkkrfkk 59 
                                       f d+n+rv N    +l+AL  + + + ++ av +    + +++ +++++++  
  gi|298675437|ref|YP_003727187.1|  70 FaDMNLRVVNMKNRFLNALEGVEDPEEKRRAVGETFIRVFEEIAKEEQAEYLI 122
                                       5489******888899********************************99965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 1952.01
//
Query:       gi|298675438|ref|YP_003727188.1|  [L=352]
Description: radical SAM domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0024   18.3   0.1      0.017   15.5   0.1    2.2  1  Radical_SAM    Radical SAM superfamily
  ------ inclusion threshold ------
      0.022   14.8   0.0       0.41   10.7   0.0    2.3  2  Radical_SAM_C  Radical_SAM C-terminal domain
       0.11   12.1   0.5       0.26   10.9   0.2    1.6  2  Snf7           Snf7


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   2.9e-06     0.017      12     155 ..      60     210 ..      48     226 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.9e-06
                                       TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC.............. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............. RF
                       Radical_SAM  12 sfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla.............. 74 
                                       s C                                  +v  ++++p  y d+   l +++++a              
  gi|298675438|ref|YP_003727188.1|  60 SMCG---------------------------------YVYDSSQNPPSYEDLKSQLQKAMEKAssleefmvkiytsg 103
                                       4444.................................4555555666666666666666665566555555555555 PP

                                       .......................CCTEEEEEEECSSCHG...HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTS CS
                                       .......................xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  75 .......................vpgiritvetngtlpd...eeklerllelgvdrvslgleaaddekvlklmnrgh 125
                                                              ++ ++++ et +  ++     k + +l+     +++gle+ +d   ++ +n+g 
  gi|298675438|ref|YP_003727188.1| 104 sfldenevstdvlkyilqalnqdKRVLKVVAETRPEFVTddtIVKCRNMLKDTEFEIAIGLETSSDIIRRDSINKGF 180
                                       555555555555555555576774444444444444444555448888888778*************888889999* PP

                                       HHHHHHHHHHHHHHTTSETEEEEEEEBTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 126 tfeevlealeklreagikrvvdrivglpGe 155
                                        f+++++a +++ e+++    + ++ +p  
  gi|298675438|ref|YP_003727188.1| 181 KFSDFIKAAQIAEENDVTTKAYLLLKPPFI 210
                                       **************9988656666655555 PP

>> Radical_SAM_C  Radical_SAM C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.057   3.4e+02      34      62 ..     112     140 ..      95     158 .. 0.75
   2 ?   10.7   0.0   6.9e-05      0.41       8      47 ..     237     276 ..     231     280 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.057
                     Radical_SAM_C  34 yvdlvadilellppdirvhRltgdipkel 62 
                                        +d++  il+ l++d rv +++ +  +e 
  gi|298675438|ref|YP_003727188.1| 112 STDVLKYILQALNQDKRVLKVVAETRPEF 140
                                       467888888*********99999665554 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 6.9e-05
                     Radical_SAM_C   8 pllvikgTeLaelyksgeykplsleeyvdlvadilellpp 47 
                                       ++ v kgT  + ++++g+y+p  l   vd++ + ++  p+
  gi|298675438|ref|YP_003727188.1| 237 LCNVQKGTFVEWMWQKGQYRPPWLYSIVDVLKKSKQKHPE 276
                                       68899************************99987765555 PP

>> Snf7  Snf7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       0.9   5.4e+03     146     170 ..       3      25 ..       3      26 .. 0.77
   2 ?   10.9   0.2   4.3e-05      0.26     102     157 ..      71     127 ..      67     144 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.9
                                       HHHHHHHHHHCSH.HHHHHHHTXXX CS
                              Snf7 146 LdaLeqelgdeelldesvklpevPs 170
                                       L+++ +e+ + +    + ++p+vP+
  gi|298675438|ref|YP_003727188.1|   3 LNQIISEIRNRQ--RIKPSAPDVPT 25 
                                       788889988888..57778888887 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 4.3e-05
                                       CCHHHHHHHHHHHHHHHHHTCHHHHHHHHHTT-GGTTHHHHH.HHHHHHHHHHHHCS CS
                              Snf7 102 didkidklmdeiedqmekaeeisEalsrslddadeedEeele.aeLdaLeqelgdee 157
                                       +++  ++l  +++++meka+ ++E + + +++++  dE e+  ++L  ++q l++++
  gi|298675438|ref|YP_003727188.1|  71 NPPSYEDLKSQLQKAMEKASSLEEFMVKIYTSGSFLDENEVStDVLKYILQALNQDK 127
                                       678889999***********************9999999975267777888777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       766  (0.0427241); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2128.20
//
Query:       gi|298675439|ref|YP_003727189.1|  [L=298]
Description: acetylglutamate kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.3e-47  160.7   4.9    4.9e-47  160.5   4.9    1.0  1  AA_kinase  Amino acid kinase family
  ------ inclusion threshold ------
       0.14   11.9   1.1       0.18   11.5   0.1    1.6  2  CagD       Pathogenicity island component CagD


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.5   4.9   5.5e-51   4.9e-47       2     241 .]      23     270 ..      22     270 .. 0.98

  Alignments for each domain:
  == domain 1  score: 160.5 bits;  conditional E-value: 5.5e-51
                                       EEEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HHHHHHHH CS
                         AA_kinase   2 rvVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstleeagevat 78 
                                       + V+KlGG+++ d e   +++++++i  l+  g+++v+VhGgg+ + + +++ +g +s+++  g+r t++e++e+a+
  gi|298675439|ref|YP_003727189.1|  23 IMVIKLGGHAMVDSEI--MNDIIRDIVLLRFVGIHPVIVHGGGPEITEKMER-MGKKSEFIG-GIRITDDETLEIAR 95 
                                       68*************9..**********************************.*********.************** PP

                                       HHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE.................HHHTTTCEEECCHHHHHHHTT-E CS
                         AA_kinase  79 rdalaslgerlvaallaaglpavglsaaaldateagr...............degsdgnvesvdaeaieelleagvv 140
                                       +++++ +++++v+ + ++g +avgls+++  ++ a++               d g +g+ e ++ e i+ l ++ ++
  gi|298675439|ref|YP_003727189.1|  96 MVLVGNINTKIVSLIGHHGGHAVGLSGKDGKMILARKkppqkvrikemehdvDLGWVGDTEIINPELIHILTNKSYI 172
                                       ***************************************************************************** PP

                                       EEEESEEEEETTTEEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH.CSSS.TT CS
                         AA_kinase 141 pvltgfigldeegelgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee.saselat 216
                                       pv+++++ +d++g  +++++D++a+ +A+ l+A+kli+ltdV GV+ +  +     +++++i+v+e+e+ +++  ++
  gi|298675439|ref|YP_003727189.1| 173 PVISPIA-MDTKGNTLNINADVVASDIAVSLNAEKLILLTDVTGVLRDKDDPS---TRISQIAVEEVEQlIEEDVIS 245
                                       *****76.******99******************************9988888...********************* PP

                                       THHHHCHHHHHHHHHCTT-EEEEEE CS
                         AA_kinase 217 gGmkvkhpaalaaarrggipvvItn 241
                                        Gm++k+++a+ a+ +g+ +v+I+n
  gi|298675439|ref|YP_003727189.1| 246 SGMIPKVRSAASAVISGVDRVHIIN 270
                                       ***********************98 PP

>> CagD  Pathogenicity island component CagD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1      0.47   4.2e+03      73      86 ..      35      48 ..      15      59 .. 0.64
   2 ?   11.5   0.1   2.1e-05      0.18      69     125 ..     136     193 ..     124     210 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.47
                              CagD 73 fkevnpdiikdevf 86
                                        e+  dii+d v+
  gi|298675439|ref|YP_003727189.1| 35 DSEIMNDIIRDIVL 48
                                      44666667766653 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 2.1e-05
                              CagD  69 kkvtfkevnpdiikdevfdfvivnrvlkkikdlkhydpvieki.fdekgkemglnvel 125
                                       +kv +ke++ d+    v d  i+n  l +i   k y pvi  i +d kg+ + +n ++
  gi|298675439|ref|YP_003727189.1| 136 QKVRIKEMEHDVDLGWVGDTEIINPELIHILTNKSYIPVISPIaMDTKGNTLNINADV 193
                                       79**************************************9985799***99999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1811.87
//
Query:       gi|298675440|ref|YP_003727190.1|  [L=98]
Description: Non-histone chromosomal MC1 family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-40  137.3   2.4    1.8e-40  137.2   2.4    1.0  1  MC1       Non-histone chromosomal protein MC1


Domain annotation for each model (and alignments):
>> MC1  Non-histone chromosomal protein MC1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.2   2.4   9.8e-45   1.8e-40       1      96 []       5      96 ..       4      96 .. 0.97

  Alignments for each domain:
  == domain 1  score: 137.2 bits;  conditional E-value: 9.8e-45
                               MC1  1 dkrnfalrdedGeeisvfsGkqPrqaaLkaarrletadseeeakeeeirLrekGtkkvhiyegkaeeeeaPddkpdWle 79
                                      ++rnf++rd++G+e++vf+GkqPrqaaLk+a+r++++    ++k ++irLre+Gt+kvh+++g++ +++aP++kp+W++
  gi|298675440|ref|YP_003727190.1|  5 ETRNFVVRDKNGKEHGVFTGKQPRQAALKVANRGKGT----KSKPDTIRLRERGTNKVHVFKGWKDKVDAPKNKPEWMP 79
                                      58**********************************9....778899******************************** PP

                               MC1 80 dkitkanvskqgiekle 96
                                      dki k+ v+kqgiekle
  gi|298675440|ref|YP_003727190.1| 80 DKINKPFVKKQGIEKLE 96
                                      ***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 754.97
//
Query:       gi|298675441|ref|YP_003727191.1|  [L=317]
Description: hypothetical protein Metev_1546 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.7e-83  277.6   4.1    1.1e-82  277.5   4.1    1.0  1  GCHY-1    Type I GTP cyclohydrolase folE2
     0.0038   17.1   0.1      0.044   13.7   0.1    2.3  2  DREPP     DREPP plasma membrane polypeptide
  ------ inclusion threshold ------
      0.043   13.7   0.9        8.1    6.3   0.0    2.4  2  DUF577    Family of unknown function (DUF577)
       0.52   10.5   0.0       0.52   10.5   0.0    2.6  3  CDC37_C   Cdc37 C terminal domain


Domain annotation for each model (and alignments):
>> GCHY-1  Type I GTP cyclohydrolase folE2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  277.5   4.1   2.4e-86   1.1e-82       1     259 []       8     301 ..       8     301 .. 0.94

  Alignments for each domain:
  == domain 1  score: 277.5 bits;  conditional E-value: 2.4e-86
                                       .XXXXXXXXXX----SEEEEEEEEEEEEE--TTTS-EEEEEEEEEEEES-SS--GGGGGHHHHHHH.HS-SSEEG.. CS
                            GCHY-1   1 lpDvqsekderkipldrVGvkgvklpvkvkdkekkaqtlvaevdlfvdLpaekkGihmSRlvevle.eaeeelee.. 74 
                                       lpDvq+ k++++i+l+rVGv++vk++v++k+k+k+++ lv+++d+fvdLp++ kG+++SR++e+++   e+++++  
  gi|298675441|ref|YP_003727191.1|   8 LPDVQAGKPKVPINLTRVGVTDVKKLVEIKRKDKRPIVLVSTFDIFVDLPSSLKGANLSRNFEAIDeVLEKVINMpv 84 
                                       79****************************************************************55667777688 PP

                                       GGHHH....HHHHHHHHTT.-SEEEEEEEEEEEEEEE-TTT--EEEEEEEEEEEEEE....TTE...EEEEEEEEEE CS
                            GCHY-1  75 kslee....ileellekleyaeraevelkfeyfiekkapvsgkeglesyevtleaeler..kee...vkltvgvevp 142
                                       +++e+    + ++ll+++eya+raev++k+ey+i++++p+++ e++e +++++e+++ r  + +   vk+ +g+ev+
  gi|298675441|ref|YP_003727191.1|  85 YEIEQlcgdVSKNLLDRHEYARRAEVRMKSEYVIKRQSPATELECQEVVDIFAESTAFRseS-NeinVKKLIGAEVV 160
                                       777777778***********************************************988532.2355********** PP

                                       EEEE-HHHHHHS.........................SS---EEEEEEEEEEEE......--HHHHHHHHHHHSSEE CS
                            GCHY-1 143 vttlCPCskeisrell.....................eagaHnQRsvvtvkvelaeeekeveiedlielvessasse 198
                                       + t+CPC++ei+r+ +                     ++++HnQR++  +++e+ e+e++ ++ed+ie++e+s+ss+
  gi|298675441|ref|YP_003727191.1| 161 GLTACPCAQEIMRDEAhneleslgvdektiakflhevPMATHNQRGRGIISIEV-EDEEDASLEDVIEIIENSMSSS 236
                                       ************9999*************************************5.68999***************** PP

                                       --S---HHHHHHHHHHHHTS---HHHHHHHHHHHHHS-TTEEEE.........EEEEEEE-TTTSSEEEE CS
                            GCHY-1 199 vyellKReDEkavtekayenpkFvEDvvRevaaaleeeerveef.........sveveneESiHnHnavA 259
                                       vyellKR+DE++++++a+++pkFvED+vR++a+++     v++f         ++++ neESiH+Hna+A
  gi|298675441|ref|YP_003727191.1| 237 VYELLKRADEAEIVKNAHKRPKFVEDCVRTMAKNV-----VHKFgylpdnsvvTIKQINEESIHRHNAFA 301
                                       ***********************************.....8888888999999****************8 PP

>> DREPP  DREPP plasma membrane polypeptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.1   9.7e-06     0.044      41      94 ..     211     265 ..     204     268 .. 0.85
   2 ?    0.4   0.0      0.12   5.2e+02       9      41 ..     283     315 ..     276     317 .] 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.7e-06
                             DREPP  41 nkeleekkteLqpkvveiyeaa.saeikaLvkerkeaglkknsaavqkfleeLak 94 
                                       + e+e+        v+ei e + s+++  L+k   ea + kn+ +  kf+e+ ++
  gi|298675441|ref|YP_003727191.1| 211 SIEVEDEEDASLEDVIEIIENSmSSSVYELLKRADEAEIVKNAHKRPKFVEDCVR 265
                                       55777776666778*****9764789*************************9875 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.12
                             DREPP   9 lpkikkvFekngakkaaaaeavksFdeskeein 41 
                                       + +ik++ e +  +  a ae + +  e k ei+
  gi|298675441|ref|YP_003727191.1| 283 VVTIKQINEESIHRHNAFAERIATLGELKSEIS 315
                                       567999*99999999999**********99997 PP

>> DUF577  Family of unknown function (DUF577)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0018       8.1      61      98 ..      48      85 ..      30      95 .. 0.90
   2 ?    5.8   0.2    0.0025        11     125     157 ..     223     255 ..     208     271 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0018
                            DUF577 61 kavyvFidLpmpldeefikkvlenlleeiekvLlppee 98
                                       ++ +F+dLp +l+   + + +e + e  ekv+++p+ 
  gi|298675441|ref|YP_003727191.1| 48 STFDIFVDLPSSLKGANLSRNFEAIDEVLEKVINMPVY 85
                                      5799******************************9976 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0025
                            DUF577 125 adlvkellekivksvkelVerkmeeelvrrglr 157
                                        d+++ + + + +sv el++r  e e+v+++ +
  gi|298675441|ref|YP_003727191.1| 223 EDVIEIIENSMSSSVYELLKRADEAEIVKNAHK 255
                                       4666777777******************99865 PP

>> CDC37_C  Cdc37 C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00012      0.52      13      52 ..      47      89 ..      35      97 .. 0.82
   2 ?   -1.2   0.1      0.49   2.2e+03      48      69 ..     145     166 ..     125     192 .. 0.57
   3 ?   -1.8   0.2      0.76   3.4e+03      34      63 ..     221     250 ..     216     256 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00012
                           CDC37_C 13 qkkvevFeklppelqkAlktksLdevnkvlak...mkveeAee 52
                                      +  +++F  lp+ l+ A  +++ +++++vl+k   m+v e e+
  gi|298675441|ref|YP_003727191.1| 47 VSTFDIFVDLPSSLKGANLSRNFEAIDEVLEKvinMPVYEIEQ 89
                                      56799*************************9733366666665 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.49
                           CDC37_C  48 eeAeeilellgeagilsleell 69 
                                       e  e  +++l+ a++++l +  
  gi|298675441|ref|YP_003727191.1| 145 ESNEINVKKLIGAEVVGLTACP 166
                                       3444456666777776666554 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.76
                           CDC37_C  34 sLdevnkvlakmkveeAeeilellgeagil 63 
                                       sL+ v +++++   +   e+l++ +ea+i+
  gi|298675441|ref|YP_003727191.1| 221 SLEDVIEIIENSMSSSVYELLKRADEAEIV 250
                                       677777777777777777778888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2308.70
//
Query:       gi|298675442|ref|YP_003727192.1|  [L=50]
Description: hypothetical protein Metev_1547 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.7e-05   23.1   1.5    5.7e-05   23.1   1.5    1.9  2  Zn-ribbon_8     Zinc ribbon domain
    0.00018   21.4   3.3    0.00031   20.7   3.3    1.4  1  DZR             Double zinc ribbon
     0.0043   17.1   2.6     0.0043   17.1   2.6    1.4  2  HypA            Hydrogenase/urease nickel incorporation, meta
     0.0054   16.4   5.2     0.0056   16.4   5.2    1.1  1  TackOD1         Thaumarchaeal output domain 1
     0.0061   16.4   0.9     0.0061   16.4   0.9    1.5  2  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
  ------ inclusion threshold ------
       0.01   16.1   1.8        1.8    8.9   0.3    2.2  2  zinc_ribbon_9   zinc-ribbon
       0.02   14.8   8.6       0.23   11.3   0.2    2.6  3  TFIIS_C         Transcription factor S-II (TFIIS)
       0.02   14.9   2.1       0.02   14.9   2.1    1.5  2  zf-RING_5       zinc-RING finger domain
      0.024   14.4   2.4      0.044   13.5   0.2    2.1  2  Zn_Tnp_IS1      InsA N-terminal domain
      0.027   14.1   2.7      0.027   14.1   2.7    1.8  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
      0.033   14.2   2.0        2.3    8.2   0.1    2.1  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
      0.038   13.3   0.3      0.038   13.3   0.3    1.1  1  CcmH            Cytochrome C biogenesis protein
      0.038   14.0   2.8      0.038   14.0   2.8    2.0  2  ADK_lid         Adenylate kinase, active site lid
       0.08   12.4   5.8       0.12   11.8   0.6    2.7  3  zf-ribbon_3     zinc-ribbon domain
       0.15   12.8   3.9       0.17   12.6   3.2    1.5  1  FYDLN_acid      Protein of unknown function (FYDLN_acid)
       0.16   11.9   8.0        2.5    8.1   4.7    2.8  2  zinc_ribbon_4   zinc-ribbon domain
       0.19   11.3  10.3        0.9    9.1   0.8    2.2  2  TF_Zn_Ribbon    TFIIB zinc-binding
       0.28   11.1   6.6        0.7    9.8   2.5    2.5  2  PHD             PHD-finger
       0.33   11.0   7.1         31    4.7   7.1    2.8  1  Rubredoxin      Rubredoxin
       0.56   10.3   5.6        1.4    9.0   0.6    2.2  2  zf-Sec23_Sec24  Sec23/Sec24 zinc finger
          3    7.6   8.8        6.8    6.5   0.2    2.6  3  Rubredoxin_2    Rubredoxin metal binding domain
        8.3    6.8   9.7        7.3    7.0   0.3    2.6  3  Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase


Domain annotation for each model (and alignments):
>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1       1.6   1.3e+03      11      17 ..       4      10 ..       2      15 .. 0.71
   2 !   23.1   1.5     7e-08   5.7e-05       2      37 ..      17      48 ..      17      50 .] 0.89

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.6
                       Zn-ribbon_8 11 Cghefev 17
                                      Cg+ ++v
  gi|298675442|ref|YP_003727192.1|  4 CGESYDV 10
                                      8877775 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 7e-08
                       Zn-ribbon_8  2 PiYeYrCeeCghefevlqsisdapltaCPeCgs.evr 37
                                      P+ +Y C+eC ++f  l +     +++CP+C+s +v+
  gi|298675442|ref|YP_003727192.1| 17 PTKDYICNECENKFKGLGK-----NVKCPSCKSkNVT 48
                                      7889***********9986.....778******9886 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   3.3   3.8e-07   0.00031       4      38 ..       4      46 ..       2      50 .] 0.80

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3.8e-07
                               DZR  4 Cgee........lppdarfCseCgtklkavaaedrCpsCgekv 38
                                      Cge         lp ++  C+eC +k k   ++ +CpsC++k+
  gi|298675442|ref|YP_003727192.1|  4 CGESydvdadedLPTKDYICNECENKFKGLGKNVKCPSCKSKN 46
                                      5555555555559999************************984 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       3.1   2.5e+03      73      84 ..       2      12 ..       1      20 [. 0.65
   2 !   17.1   2.6   5.2e-06    0.0043      71      98 ..      21      48 ..      14      50 .] 0.84

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.1
                                      ETTTS-EEECHH CS
                              HypA 73 CreCgkefelee 84
                                      C +Cg+++++++
  gi|298675442|ref|YP_003727192.1|  2 C-TCGESYDVDA 12
                                      4.4777776554 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 5.2e-06
                                      EEETTTS-EEECHHHHHS-TTTSSS-EE CS
                              HypA 71 vrCreCgkefeleekalrCpkCgsadve 98
                                      + C+eC+++f+   k+++Cp+C+s++v+
  gi|298675442|ref|YP_003727192.1| 21 YICNECENKFKGLGKNVKCPSCKSKNVT 48
                                      68*********5546699******9986 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   5.2   6.9e-06    0.0056     136     174 ..      10      48 ..       2      50 .] 0.88

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.9e-06
                           TackOD1 136 iGvDYdrplevykCnsCkslfsepevkarClsCekeses 174
                                       ++ D d p ++y+Cn+C++ f+    +++C sC++++ +
  gi|298675442|ref|YP_003727192.1|  10 VDADEDLPTKDYICNECENKFKGLGKNVKCPSCKSKNVT 48 
                                       5678889***************************98765 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       4.7   3.8e+03      24      26 ..       2       4 ..       1       9 [. 0.57
   2 !   16.4   0.9   7.4e-06    0.0061      23      46 ..      21      45 ..      16      48 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.7
                                      EE- CS
                        zf-C3HC4_3 24 vlC 26
                                      ++C
  gi|298675442|ref|YP_003727192.1|  2 CTC 4 
                                      444 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 7.4e-06
                                      EEE-HHHHHHHHH..TT-B-TTT--B CS
                        zf-C3HC4_3 23 lvlCeeCaekllk..rkkkCpiCrrp 46
                                        +C+eC +k++   ++ kCp C+++
  gi|298675442|ref|YP_003727192.1| 21 Y-ICNECENKFKGlgKNVKCPSCKSK 45
                                      4.9********8799********986 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.3    0.0022       1.8      18      31 ..      17      30 ..       3      30 .. 0.65
   2 ?    7.0   0.1    0.0089       7.3      22      30 ..      37      45 ..      33      49 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0022
                     zinc_ribbon_9 18 edsdvlCPhCgggF 31
                                       + d +C++C++ F
  gi|298675442|ref|YP_003727192.1| 17 PTKDYICNECENKF 30
                                      233346*****998 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0089
                     zinc_ribbon_9 22 vlCPhCggg 30
                                      v CP+C++ 
  gi|298675442|ref|YP_003727192.1| 37 VKCPSCKSK 45
                                      56****986 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       2.4   1.9e+03      33      37 ..       3       7 ..       1       9 [. 0.60
   2 ?   11.3   0.2   0.00028      0.23      25      39 .]      17      31 ..      11      31 .. 0.79
   3 ?    8.6   0.6     0.002       1.6       2      12 ..      38      48 ..      37      49 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.4
                           TFIIS_C 33 kCghr 37
                                      +Cg+ 
  gi|298675442|ref|YP_003727192.1|  3 TCGES 7 
                                      67665 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00028
                           TFIIS_C 25 mtvfykCtkCghrWr 39
                                      +t  y C++C+++++
  gi|298675442|ref|YP_003727192.1| 17 PTKDYICNECENKFK 31
                                      6888*********97 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.002
                           TFIIS_C  2 kCpkCgsreay 12
                                      kCp+C+s++++
  gi|298675442|ref|YP_003727192.1| 38 KCPSCKSKNVT 48
                                      8******9985 PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       5.6   4.6e+03       5       7 ..       4       6 ..       2      15 .. 0.61
   2 ?   14.9   2.1   2.4e-05      0.02      23      43 ..      21      43 ..      19      44 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 5.6
                         zf-RING_5 5 Cfe 7
                                     C e
  gi|298675442|ref|YP_003727192.1| 4 CGE 6
                                     444 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 2.4e-05
                         zf-RING_5 23 ifCekClkkll..ekeavCpiCr 43
                                      ++C++C +k +  +k+++Cp C+
  gi|298675442|ref|YP_003727192.1| 21 YICNECENKFKglGKNVKCPSCK 43
                                      69********************9 PP

>> Zn_Tnp_IS1  InsA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.69   5.6e+02      29      34 ..      21      26 ..      19      27 .. 0.84
   2 ?   13.5   0.2   5.5e-05     0.044       5      16 ..      36      47 ..      35      49 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.69
                        Zn_Tnp_IS1 29 frCrdC 34
                                      + C +C
  gi|298675442|ref|YP_003727192.1| 21 YICNEC 26
                                      899999 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 5.5e-05
                        Zn_Tnp_IS1  5 sihCPrCsstdV 16
                                      ++ CP+C+s +V
  gi|298675442|ref|YP_003727192.1| 36 NVKCPSCKSKNV 47
                                      79*******998 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       1.9   1.6e+03       6       7 ..       4       5 ..       2      15 .. 0.64
   2 ?   14.1   2.7   3.3e-05     0.027       1      23 [.      21      42 ..      21      47 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.9
                                     S- CS
                    DNA_RNApol_7kD 6 Cg 7
                                     Cg
  gi|298675442|ref|YP_003727192.1| 4 CG 5
                                     33 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 3.3e-05
                                      -B-SSS--B--.--SSS----SSS CS
                    DNA_RNApol_7kD  1 YiCgeCgaevs.lkkgdpiRCkeC 23
                                      YiC eC+++++ l k+  ++C  C
  gi|298675442|ref|YP_003727192.1| 21 YICNECENKFKgLGKN--VKCPSC 42
                                      ***********9*999..****** PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.2     0.014        11      24      44 ..       2      27 ..       1      29 [. 0.81
   2 ?    8.2   0.1    0.0029       2.3      17      28 ..      35      46 ..      31      49 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.014
                     Zn_Tnp_IS1595 24 Cgsrkayrikt.....rglfqCkeCr 44
                                      C + ++y + +      + + C+eC 
  gi|298675442|ref|YP_003727192.1|  2 CTCGESYDVDAdedlpTKDYICNECE 27
                                      5555888888888898999******7 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0029
                     Zn_Tnp_IS1595 17 ngfvCPhCgsrk 28
                                       ++ CP C+s+ 
  gi|298675442|ref|YP_003727192.1| 35 KNVKCPSCKSKN 46
                                      5688*****985 PP

>> CcmH  Cytochrome C biogenesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   4.6e-05     0.038      18      47 ..      19      48 ..       3      50 .] 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.6e-05
                                      S--SSHHHHHHHHHHHHHEE-TTSSS-BTT CS
                              CcmH 18 eelkdpaqeararalseeLRClvCqnqsia 47
                                      +++  ++ e++++ l ++++C+ C+++++ 
  gi|298675442|ref|YP_003727192.1| 19 KDYICNECENKFKGLGKNVKCPSCKSKNVT 48
                                      455556789******************987 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   2.8   4.7e-05     0.038       6      29 ..       3      28 ..       1      31 [. 0.84
   2 ?    1.2   0.3      0.45   3.7e+02       4       8 ..      39      43 ..      35      47 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.7e-05
                                      TT--EEETTT..B--SSTTB-TTT-- CS
                           ADK_lid  6 kCGrsYhvvf..npPkveglCDkCGe 29
                                       CG+sY v      P ++ +C +C  
  gi|298675442|ref|YP_003727192.1|  3 TCGESYDVDAdeDLPTKDYICNECEN 28
                                      4******8855688**********86 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.45
                                      -TTT- CS
                           ADK_lid  4 CpkCG 8 
                                      Cp+C+
  gi|298675442|ref|YP_003727192.1| 39 CPSCK 43
                                      77775 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.2   9.4e+02       8      10 ..       4       6 ..       3      13 .. 0.63
   2 ?    2.4   0.1      0.14   1.1e+02      18      23 ..      22      27 ..      16      30 .. 0.60
   3 ?   11.8   0.6   0.00015      0.12       2      13 ..      36      48 ..      35      50 .] 0.82

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.2
                       zf-ribbon_3  8 CGa 10
                                      CG+
  gi|298675442|ref|YP_003727192.1|  4 CGE 6 
                                      887 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.14
                       zf-ribbon_3 18 vCpyCG 23
                                      +C  C 
  gi|298675442|ref|YP_003727192.1| 22 ICNECE 27
                                      455554 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00015
                       zf-ribbon_3  2 tvrCPnCGa.pls 13
                                       v+CP+C++ +++
  gi|298675442|ref|YP_003727192.1| 36 NVKCPSCKSkNVT 48
                                      589*****98886 PP

>> FYDLN_acid  Protein of unknown function (FYDLN_acid)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   3.2   0.00021      0.17       3      35 ..      13      45 ..      11      50 .] 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00021
                        FYDLN_acid  3 kpelGtKr.iCpscgakFYDLnkdPivcpkcgee 35
                                      +++l tK  iC +c++kF  L+k+ + cp+c+++
  gi|298675442|ref|YP_003727192.1| 13 DEDLPTKDyICNECENKFKGLGKN-VKCPSCKSK 45
                                      6677777538*************9.9*****986 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.9     0.024        20       8      35 ..       4      30 ..       2      31 .. 0.65
   2 ?    8.1   4.7    0.0031       2.5      16      32 ..      27      43 ..      26      45 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.024
                     zinc_ribbon_4  8 Ckakyeiddek.lpakgvkvrCskCghvF 35
                                      C+  y +d++  lp k     C  C ++F
  gi|298675442|ref|YP_003727192.1|  4 CGESYDVDADEdLPTK--DYICNECENKF 30
                                      7777777766656655..45577777777 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0031
                     zinc_ribbon_4 16 deklpakgvkvrCskCg 32
                                      ++k+++ g++v+C+ C+
  gi|298675442|ref|YP_003727192.1| 27 ENKFKGLGKNVKCPSCK 43
                                      678999999*******7 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   3.1    0.0051       4.1       6      27 ..       4      28 ..       2      31 .. 0.78
   2 ?    9.1   0.8    0.0011       0.9       2      12 ..      38      48 ..      37      50 .] 0.82

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0051
                                      TTCEEC...HEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon  6 Cgstnl...veDpergelvCtdCGl 27
                                      Cg +++    eD  + +++C +C++
  gi|298675442|ref|YP_003727192.1|  4 CGESYDvdaDEDLPTKDYICNECEN 28
                                      777774366678899********86 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0011
                                      EETTTTCEECH CS
                      TF_Zn_Ribbon  2 kCPnCgstnlv 12
                                      kCP C+s+n++
  gi|298675442|ref|YP_003727192.1| 38 KCPSCKSKNVT 48
                                      9*******954 PP

>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.5   0.00085       0.7      35      52 .]      12      29 ..       2      29 .. 0.78
   2 ?    2.7   0.1      0.14   1.2e+02      45      51 ..      38      44 ..      31      46 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00085
                                      SHHSHHSSTBSSTTTHTT CS
                               PHD 35 eseekpegewlCekCkek 52
                                       +e+ p+++++C++C++k
  gi|298675442|ref|YP_003727192.1| 12 ADEDLPTKDYICNECENK 29
                                      34677888*******985 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.14
                                      SSTTTHT CS
                               PHD 45 lCekCke 51
                                       C++Ck+
  gi|298675442|ref|YP_003727192.1| 38 KCPSCKS 44
                                      3666654 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   7.1     0.038        31      24      43 ..      26      45 ..       1      48 [. 0.69

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.038
                                      TT--GGGS-TT-BBTTTB-B CS
                        Rubredoxin 24 pgTkFedlPddWvCPdCgve 43
                                         kF+ l ++ +CP+C+ +
  gi|298675442|ref|YP_003727192.1| 26 CENKFKGLGKNVKCPSCKSK 45
                                      4568999999*******975 PP

>> zf-Sec23_Sec24  Sec23/Sec24 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.3     0.036        29      21      32 ..      18      29 ..      10      33 .. 0.82
   2 ?    9.0   0.6    0.0017       1.4      21      35 ..      34      48 ..      29      50 .] 0.83

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.036
                    zf-Sec23_Sec24 21 gkrwiCnfCnhk 32
                                      +k +iCn C++k
  gi|298675442|ref|YP_003727192.1| 18 TKDYICNECENK 29
                                      57799****987 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0017
                    zf-Sec23_Sec24 21 gkrwiCnfCnhknev 35
                                      gk  +C+ C++kn +
  gi|298675442|ref|YP_003727192.1| 34 GKNVKCPSCKSKNVT 48
                                      7899*********75 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       2.7   2.2e+03       6       9 ..       4       7 ..       3       9 .. 0.68
   2 ?    6.5   0.2    0.0083       6.8       1       9 [.      21      29 ..      21      33 .. 0.83
   3 ?    6.0   1.1     0.012       9.8      16      22 ..      38      44 ..      38      46 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.7
                      Rubredoxin_2 6 CGfe 9
                                     CG +
  gi|298675442|ref|YP_003727192.1| 4 CGES 7
                                     8876 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0083
                      Rubredoxin_2  1 YvCsqCGfe 9 
                                      Y+C++C ++
  gi|298675442|ref|YP_003727192.1| 21 YICNECENK 29
                                      99****765 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.012
                      Rubredoxin_2 16 rCpsCgs 22
                                      +CpsC+s
  gi|298675442|ref|YP_003727192.1| 38 KCPSCKS 44
                                      7****97 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2       2.6   2.1e+03      28      33 ..       2       6 ..       1      15 [. 0.64
   2 ?    7.0   0.3     0.009       7.3      25      33 ..      20      28 ..       9      34 .. 0.77
   3 ?    6.3   0.5     0.014        12       1      12 [.      34      45 ..      34      46 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.6
                                      ETTTTB CS
                    Prim_Zn_Ribbon 28 CrqCgg 33
                                      C +Cg 
  gi|298675442|ref|YP_003727192.1|  2 C-TCGE 6 
                                      7.8843 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.009
                                      -EEETTTTB CS
                    Prim_Zn_Ribbon 25 twfCrqCgg 33
                                      +++C++C+ 
  gi|298675442|ref|YP_003727192.1| 20 DYICNECEN 28
                                      79*****65 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.014
                                      EEEE--TTTT-T CS
                    Prim_Zn_Ribbon  1 gkhspCPvCGGr 12
                                      gk + CP C+++
  gi|298675442|ref|YP_003727192.1| 34 GKNVKCPSCKSK 45
                                      58899****987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       905  (0.0504769); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.38
# Mc/sec: 391.63
//
Query:       gi|298675443|ref|YP_003727193.1|  [L=161]
Description: hypothetical protein Metev_1548 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1233.54
//
Query:       gi|298675444|ref|YP_003727194.1|  [L=100]
Description: hypothetical protein Metev_1549 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-20   71.7   0.5    6.3e-20   71.3   0.5    1.3  1  DUF2098   Uncharacterized protein conserved in archaea (DUF20


Domain annotation for each model (and alignments):
>> DUF2098  Uncharacterized protein conserved in archaea (DUF2098)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.3   0.5   3.5e-24   6.3e-20       2      65 ..      20      81 ..      19     100 .] 0.80

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 3.5e-24
                           DUF2098  2 ievGsvVrYinTgTvGkVvdikkeedgevwvkLdstdLyYrvdtLevidekekkkekeekeked 65
                                      ie+Gs+V YinTgTvGkVvdik ++dg  wv++d+ +LyY+ + Le+++  +kk +++ +ek++
  gi|298675444|ref|YP_003727194.1| 20 IEIGSTVGYINTGTVGKVVDIK-DDDGL-WVLIDEKELYYKPELLEITETTTKKSKEKPAEKKK 81
                                      89********************.99**9.********************776444444444332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.62
# Mc/sec: 484.85
//
Query:       gi|298675445|ref|YP_003727195.1|  [L=313]
Description: hypothetical protein Metev_1550 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00022   21.4   0.4    0.00053   20.2   0.1    1.8  2  NTP_transf_2  Nucleotidyltransferase domain
  ------ inclusion threshold ------
      0.057   13.7   0.0       0.11   12.8   0.0    1.4  1  DUF5041       Domain of unknown function (DUF5041)


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.87   7.8e+03      70      83 ..      72      85 ..      51      96 .. 0.71
   2 !   20.2   0.1     6e-08   0.00053       3      48 ..     100     160 ..      98     194 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.87
                                      EEEEECEEECCCCT CS
                      NTP_transf_2 70 evdlvtrekledpl 83
                                       v++v+++kl++ l
  gi|298675445|ref|YP_003727195.1| 72 DVHIVPKNKLKKVL 85
                                      47777888877643 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 6e-08
                                       HHHHHHHHHTT....TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHH...........H CS
                      NTP_transf_2   3 klleelkelep....vakvvlfGSyarGtalkgSDiDllvvlpeevsre...........k 48 
                                       k++ ++++l+       k+ ++GS   G+ + gSDiD++v+++++++              
  gi|298675445|ref|YP_003727195.1| 100 KVASIVETLDEagipRDKMGVTGSLLPGLEKDGSDIDFIVYGSSWFDARdaifrakskggS 160
                                       555666666666678999***************************6654555555444442 PP

>> DUF5041  Domain of unknown function (DUF5041)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.2e-05      0.11     141     178 ..     131     172 ..     125     180 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.2e-05
                           DUF5041 141 dtleiPLvlygsvwfdkkhnliRfCGe....neidpelkaei 178
                                       d  +i  ++ygs wfd++  ++R   +    +ei+ e+  +i
  gi|298675445|ref|YP_003727195.1| 131 DGSDIDFIVYGSSWFDARDAIFRAKSKggsiQEINEEMWLKI 172
                                       566899*****************8644111256666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 2143.82
//
Query:       gi|298675446|ref|YP_003727196.1|  [L=672]
Description: V-type H(+)-translocating pyrophosphatase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.6e-266  885.4  52.3     3e-266  885.2  52.3    1.0  1  H_PPase   Inorganic H+ pyrophosphatase


Domain annotation for each model (and alignments):
>> H_PPase  Inorganic H+ pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  885.2  52.3  1.7e-270    3e-266       1     650 []      13     662 ..      13     662 .. 0.97

  Alignments for each domain:
  == domain 1  score: 885.2 bits;  conditional E-value: 1.7e-270
                                       HHHHHHHHHHHHHHHTS--SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT....HHHHHHHHHHH CS
                           H_PPase   1 vlallfalvllkkvlkedegtekmkeiaeaikegaeaflkrqykviailvvvlavlllllal.lsvltaiaflvGal 76 
                                       +++l+f+++++++++k++ gte+m++ia ai+ega+a+l+rqyk+i+++++vla+l+++l+   s  ++i f++Gal
  gi|298675446|ref|YP_003727196.1|  13 IVSLVFSAFFIQNIMKKSPGTETMQQIAGAIQEGAMAYLNRQYKTITAVAIVLALLIFALLGdDSGKITIGFIAGAL 89 
                                       689******************************************************99766556799********* PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTS-EE-HHHHHHHH CS
                           H_PPase  77 lSalagyigmkvavranvrtakaarkslkkalkvafrsGavmgllvvglallgvsllllllkaaalelekllellvg 153
                                        Sa+agy+gm+v+vranvrt++aa+++lk+a+++afr+Gav+gl+vvglallgvs +++++ +        ++l++g
  gi|298675446|ref|YP_003727196.1|  90 SSAAAGYLGMNVSVRANVRTTNAASQGLKEAMAIAFRGGAVTGLAVVGLALLGVSGFYIIYGD--------VNLVIG 158
                                       ***************************************************************........99**** PP

                                       HHHHHHHHHHHHHHCHHHHHHHHHHHHTCHHHHTS---TT-TT-TTHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHH CS
                           H_PPase 154 fglGaslvalfarvgGGiytKaADvGaDLvGKveagipEDdprnpaviADnvGDnvGDvaGmgADlfesyvasivaa 230
                                       fg+Gasl++lfarvgGGiytKaADvG DLvGK+eagipEDdprn+aviADnvGDnvGD+aGmgADlfe+yv++++aa
  gi|298675446|ref|YP_003727196.1| 159 FGFGASLISLFARVGGGIYTKAADVGGDLVGKIEAGIPEDDPRNAAVIADNVGDNVGDCAGMGADLFETYVVTVLAA 235
                                       ***************************************************************************** PP

                                       HHH......SHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHSS--HHHHHHHHHHHHHHHHHHHHHHHHH-S- CS
                           H_PPase 231 mvlg.....aavklvllpllvaavgilasiigillvktkedasskkkeellkaLkkgllvsavlsvvlvallslllk 302
                                       m+lg     +  +++l+pl++ a+ i+asii+i++vk+ +d       +++kaL+kg+ +sa+ls+v++++++ +l+
  gi|298675446|ref|YP_003727196.1| 236 MLLGsvileTYPNAILYPLVLGATAIFASIISIFFVKVGDD------GKIMKALYKGVALSAILSIVAFYFVTDFLM 306
                                       ****876653789***********************87776......3599**********************9996 PP

                                       TTTTSHHHHHHHHHHHHHHHHHHHHHHHH-TTSHHHHHHHHHGGG-HHHHHHHHHHHHHHHTHHHHHHHHHHHHHHH CS
                           H_PPase 303 eaaalklflavlvGlvagllivllteyytsteykpvkeiaeasetGaatniisGlavgmestvlpvlviavaillsy 379
                                           +++f+a+lvG+v+ +l+v++teyytst+ +pvk+ia++setGa+tn+isGla+g+est+lpv++++++il++y
  gi|298675446|ref|YP_003727196.1| 307 --GDIEFFYAALVGIVIMVLMVVFTEYYTSTSFRPVKTIAKSSETGAGTNVISGLAIGLESTALPVVIVVIGILAAY 381
                                       ..78************************************************************************* PP

                                       HHH........HHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHHHH CS
                           H_PPase 380 lla........glygialaavgmLstlgitlavdayGPiaDNAggiaemseleeevreitdklDavGNttkAitKgf 448
                                        +         glygia+aa +mLst+g+++++d++GP++DNAggiaem++l+e+vr++td+lDavGNttkA+tKg+
  gi|298675446|ref|YP_003727196.1| 382 FVVggvaapaiGLYGIAIAASAMLSTTGMIVTMDSFGPVTDNAGGIAEMADLPENVRNVTDALDAVGNTTKAVTKGY 458
                                       *98667777778***************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHT..HHCS--BTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTT CS
                           H_PPase 449 aigsAalaalaLfaaylee..aklekvdllnpevlvglliGamlvflfsaltmkaVgkaAeevveevrrqfkeipgi 523
                                       aigsAal+alaLfa y ++   ++ +++l np vlvgl+iG++l+f+fsa+tm+aVgkaA evv+evrrqf+eipgi
  gi|298675446|ref|YP_003727196.1| 459 AIGSAALGALALFADYRHKvdLSAGSLSLDNPVVLVGLFIGGLLPFIFSAVTMRAVGKAAFEVVNEVRRQFREIPGI 535
                                       ******************955445689************************************************** PP

                                       TTTSS---HHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           H_PPase 524 legkekpdykkcveistkaalkemilpgllavlapivvglllgaealagllagalvsgvllAifmanaGgawDNAKk 600
                                       leg++kp y++cv+i+t+aa++em +pg++av++p++vgl+lg+ al+gll+g++vsg+llA++m n+GgawDNAKk
  gi|298675446|ref|YP_003727196.1| 536 LEGTAKPGYSECVDIATRAAIREMAIPGAMAVVVPLAVGLVLGPLALGGLLLGIIVSGFLLALTMDNGGGAWDNAKK 612
                                       ***************************************************************************** PP

                                       HHHTTSTT.SSSHHHHHHHHHHHHHHHHHCTHHHHHHHHHHHHHHHHHHH CS
                           H_PPase 601 yiEegelggkgseahkaaVvGDtVGDPfKDtagpslniliklmsivslvi 650
                                       +iE+ge+ggkgs+ahkaaVvGDtVGDPfKDtagp+ln lik++++vs+++
  gi|298675446|ref|YP_003727196.1| 613 LIEDGEHGGKGSDAHKAAVVGDTVGDPFKDTAGPALNALIKVVNMVSILF 662
                                       ***********************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (672 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1204  (0.0671538); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.68u 0.29s 00:00:00.97 Elapsed: 00:00:00.46
# Mc/sec: 4403.42
//
Query:       gi|298675447|ref|YP_003727197.1|  [L=156]
Description: hypothetical protein Metev_1552 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1207  (0.0673211); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1159.75
//
Query:       gi|298675448|ref|YP_003727198.1|  [L=496]
Description: dihydropteroate synthase-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.8e-09   37.0   0.1    1.2e-08   35.0   0.1    2.0  2  DUF4346      Domain of unknown function (DUF4346)
    1.2e-07   31.6   3.0    3.4e-07   30.2   2.9    1.8  1  Pterin_bind  Pterin binding enzyme
    0.00014   20.7   0.7    0.00034   19.5   0.2    1.8  2  CdhD         CO dehydrogenase/acetyl-CoA synthase delta subun
  ------ inclusion threshold ------
      0.013   15.6   0.0      0.031   14.4   0.0    1.6  1  DUF4990      Domain of unknown function
       0.16   12.0   2.6        8.1    6.5   0.1    3.3  3  ACT_6        ACT domain


Domain annotation for each model (and alignments):
>> DUF4346  Domain of unknown function (DUF4346)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.23   8.4e+02      12      37 ..     415     444 ..     410     457 .. 0.69
   2 !   35.0   0.1   3.3e-12   1.2e-08      62     118 .]     440     493 ..     426     493 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.23
                           DUF4346  12 elDpaGYflikvdr....eaklivakhysn 37 
                                       +lDp G f ik+ +    +++ iv++h ++
  gi|298675448|ref|YP_003727198.1| 415 QLDPVGCFRIKIATnlnySERCIVVEHEKT 444
                                       799999999987541111466677777554 PP

  == domain 2  score: 35.0 bits;  conditional E-value: 3.3e-12
                           DUF4346  62 reaekvyrgrtakelcvkileeeeelpvtkldhaaYlGRelqraeaaLlsgkeYiqD 118
                                       ++++++  g+ta e+   il+    + v++l+ha YlGRel++ae+aL+ +++Y qD
  gi|298675448|ref|YP_003727198.1| 440 EHEKTCIVGKTANEILDTILDM---ELVSTLEHAGYLGRELKKAELALKFNRSYSQD 493
                                       556778899******9999987...57*****************************9 PP

>> Pterin_bind  Pterin binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   2.9   9.5e-11   3.4e-07      28     126 ..     168     255 ..     161     297 .. 0.80

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 9.5e-11
                                       HHHHHTT-SEEEEESS-TSTT--CCHHHHHHHHHHHHHHHHHHHCTSEEEEE-S-HHHHHHHHHTTSEEEEETTTTS CS
                       Pterin_bind  28 rkmveeGAdilDiggestrPgaervdeeeelervvpvlealrdeadvpisiDttkaevaeaAlkagadivNdvsgee 104
                                        + +++GAdi+Dig+             +  e v++ +e  ++ + vp+siDt ++e ++ Al++g div +  g +
  gi|298675448|ref|YP_003727198.1| 168 LSFIDKGADIIDIGVSMD----------ATPEEVINAVEIAKGISSVPLSIDTLDSELISSALDSGIDIVLSLDGSN 234
                                       57799********97554..........45567899999444455******************************** PP

                                       SSTTHHHHHHHHT-EEEEESEC CS
                       Pterin_bind 105 rdpkmlelvaeagaavvvmhmr 126
                                         +++   vae+++  vv    
  gi|298675448|ref|YP_003727198.1| 235 -IEDVGYKVAENDVSAVVIPDV 255
                                       .888888888888888876544 PP

>> CdhD  CO dehydrogenase/acetyl-CoA synthase delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.55     2e+03     330     377 ..      38      83 ..      14      87 .. 0.68
   2 !   19.5   0.2   9.4e-08   0.00034      70     195 ..     175     303 ..     165     306 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.55
                                       HHHHHHHHHHTTHHHHSSS-EEEE-GGGGGGHHHHHHHHTSEEEE--S CS
                              CdhD 330 aekvkdlieetgieekvkhrflilPglvavlkgkiedltgwkvlvgpr 377
                                        +k+ +++e+ ++++k    ++ +Pg v     k+e ++g +v  gp+
  gi|298675448|ref|YP_003727198.1|  38 PNKLLQVMEKRKLKDKY--DIVFVPGIVSGDFTKVEMEMGCSVYLGPK 83 
                                       45667788888887765..46666888887777777777777777665 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 9.4e-08
                                       --EEEEE--SSST.HHHHHHHHHHHCC--SEEEEE-SSHHHHHHHHTTTCCC--EEEEE-TTTHHHHHHHHHHTT-- CS
                              CdhD  70 ldaiairlistdPakkfakavekvakavkvplvlggsdpevlkaalevvederpllyaAtkddykeiaelaleykvp 146
                                       +d+i i    +  ++++ +ave  +    vpl + ++d+e +  al+   d   ++ +    + +++     e++v 
  gi|298675448|ref|YP_003727198.1| 175 ADIIDIGVSMDATPEEVINAVEIAKGISSVPLSIDTLDSELISSALDSGID---IVLSLDGSNIEDVGYKVAENDVS 248
                                       66666666555545999999999999999*****************98774...77889999999**9999999999 PP

                                       EEEE-.SSHHHHHHHH......HHHHCTT---EEEE---SH.....HHHHHHHHH CS
                              CdhD 147 vvllsindleelkela......rkllkagvkdivldPttaalGegleetidnvvr 195
                                        v++   +++e + l       + ++++gv++++ dP+  ++G+g++++i++  +
  gi|298675448|ref|YP_003727198.1| 249 AVVIPDVGVDEDRRLEslikniKSVMEMGVTHVIADPVLDSIGYGIDKSINRYKK 303
                                       999988999887777522222234567899********************99876 PP

>> DUF4990  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   8.6e-06     0.031      34     107 ..     393     462 ..     374     471 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.6e-06
                                       S---TTS------BT-B-HHHHHHSTT-STTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                           DUF4990  34 rdrkadGdlPdidflkltadsklrnkGlGcfitkenedldfdWlekaaiavegniasvvgpeaeaftkfyvnge 107
                                       + r++d ++Pd +fl+ + +   +   +Gcf  k +++l+++   + +i+ve +++ +vg  a+      ++ e
  gi|298675448|ref|YP_003727198.1| 393 KRRHPDSTVPD-NFLQAKESGSWQLDPVGCFRIKIATNLNYS---ERCIVVEHEKTCIVGKTANEILDTILDME 462
                                       5689*******.9**************************996...899*************9988766666555 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1    0.0023       8.1       4      36 ..     152     183 ..     152     185 .. 0.91
   2 ?    1.2   0.1       0.1   3.6e+02      27      63 ..     232     271 ..     226     281 .. 0.70
   3 ?    2.0   0.0     0.058   2.1e+02      10      31 ..     326     347 ..     320     348 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0023
                             ACT_6   4 litvtGpdrpGltasLtsvlaefgvnilDieqa 36 
                                       ++++tG+d   l ++++s +   g++i+Di+++
  gi|298675448|ref|YP_003727198.1| 152 VVNATGMDGLTLKNRILSFID-KGADIIDIGVS 183
                                       79****************985.69******986 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.1
                             ACT_6  27 gvnilDieqavihgrlsLgll..vsgped.alarlekaLl 63 
                                       g ni D++  v ++++s ++   v ++ed +l+ l k + 
  gi|298675448|ref|YP_003727198.1| 232 GSNIEDVGYKVAENDVSAVVIpdVGVDEDrRLESLIKNIK 271
                                       679**************99983344444436666666555 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.058
                             ACT_6  10 pdrpGltasLtsvlaefgvnil 31 
                                       +d  G+ asLt++  + g++il
  gi|298675448|ref|YP_003727198.1| 326 ADSVGINASLTGIANDLGASIL 347
                                       6999**************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3522.69
//
Query:       gi|298675449|ref|YP_003727199.1|  [L=388]
Description: cell division protein FtsZ [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.5e-37  129.0   0.2    4.6e-37  128.1   0.2    1.4  1  Tubulin    Tubulin/FtsZ family, GTPase domain
      9e-33  112.4   0.3    3.3e-32  110.6   0.0    2.2  3  FtsZ_C     FtsZ family, C-terminal domain
  ------ inclusion threshold ------
        7.6    5.6   7.5        8.5    5.4   2.9    2.3  2  Tubulin_2  Tubulin like


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.1   0.2   7.7e-41   4.6e-37       1     195 [.      37     195 ..      37     197 .. 0.96

  Alignments for each domain:
  == domain 1  score: 128.1 bits;  conditional E-value: 7.7e-41
                                       EEEEEEEHHHHHHHHHHHHH...HHHCH....HHHT.....TTEEEEE....EEESBHHHHHTS-GS......EEEE CS
                           Tubulin   1 eiivigvGqcGnqignelwellakehgiqsdgdslesfFsesgkveyiprsvaidtdpqvlneikagselfnpnkll 77 
                                       +i ++g+G++Gn+++n+l++      gi             +g +e++    ai+td+q+l++++a+      +k+l
  gi|298675449|ref|YP_003727199.1|  37 RITIVGCGGAGNNTVNRLYN-----IGI-------------EG-AETV----AINTDKQHLDNVHAD------KKIL 84 
                                       5899****************.....599.............88.7777....***************......**** PP

                                       --CCCCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEE CS
                           Tubulin  78 lgkegagnngaggypevgkeaaeeileeirkevekcdslqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvv 154
                                       +gk+ ++++gaggype+gk+aae  +  +++ ++++d+   +f+ta++gGGTG+G++pv+++++ke+  +a+vv++v
  gi|298675449|ref|YP_003727199.1|  85 VGKTLTRGLGAGGYPEMGKKAAELARGTLEEVFKDSDL---VFVTAGMGGGTGTGVAPVVADIAKEQ--GAIVVGMV 156
                                       **************************************...**************************..******** PP

                                       EE--GG.G-HHHHHHHHHHHHHHHHT-SEEEEEEHHHHHCC CS
                           Tubulin 155 vlPsefsevvvepynailalkelieesdavividNdaLlki 195
                                         P++   +  +  +++++l+el++  d+viv+dN++Ll+ 
  gi|298675449|ref|YP_003727199.1| 157 SSPFRV--ERARTVKSEEGLEELRRAGDTVIVLDNNRLLEY 195
                                       ****98..7899**************************986 PP

>> FtsZ_C  FtsZ family, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0         3   1.8e+04      28      42 ..      54      68 ..      51      71 .. 0.78
   2 ?   -2.7   0.0       1.3   7.7e+03      56      74 ..     136     154 ..     109     160 .. 0.62
   3 !  110.6   0.0   5.6e-36   3.3e-32       1      95 []     244     338 ..     244     338 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 3
                                      GGT--GGG-SEEEEE CS
                            FtsZ_C 28 LLdvdlsgAkgvlvn 42
                                      L ++ ++gA++v +n
  gi|298675449|ref|YP_003727199.1| 54 LYNIGIEGAETVAIN 68
                                      667889999998887 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.3
                                       HHHHHHHHHS-TTSEEEEE CS
                            FtsZ_C  56 evaetireevdeeanvivG 74 
                                        va ++++ ++e+  ++vG
  gi|298675449|ref|YP_003727199.1| 136 GVAPVVADIAKEQGAIVVG 154
                                       3444555555566666665 PP

  == domain 3  score: 110.6 bits;  conditional E-value: 5.6e-36
                                       EEEEEEEEEEESTTHHHHHHHHHHTSGGGT--GGG-SEEEEEEEE-TT--HHHHHHHHHHHHHHS-TTSEEEEEEEE CS
                            FtsZ_C   1 GvAmmgvGeasgedraeeaaeaaisspLLdvdlsgAkgvlvnitggsdltlkEveevaetireevdeeanvivGavi 77 
                                       GvA+m +  +++++++++++++a+++pLLdvd++gA+g lv+itgg+dl+lkE+ee+a  ++ e++++anvi+Ga+i
  gi|298675449|ref|YP_003727199.1| 244 GVAVMLFADSKNQNKSDDVVRSALNHPLLDVDYRGATGSLVHITGGPDLSLKEAEEIAGSLTYELSPDANVIWGARI 320
                                       89*************************************************************************** PP

                                       -TT--SEEEEEEEEES-X CS
                            FtsZ_C  78 deeledeirvtvvatglk 95 
                                        +++e+++rv++++tg++
  gi|298675449|ref|YP_003727199.1| 321 RDDFEGKVRVMAIMTGVQ 338
                                       ****************96 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1     0.013        78       2      18 ..      40      56 ..      39      83 .. 0.84
   2 ?    5.4   2.9    0.0014       8.5     157     177 ..     122     142 ..      71     160 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.013
                         Tubulin_2  2 viGLGGtGgkvlaelrr 18
                                      ++G+GG G +++++l +
  gi|298675449|ref|YP_003727199.1| 40 IVGCGGAGNNTVNRLYN 56
                                      7************9975 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0014
                         Tubulin_2 157 nvfVvgSLaGGTGSGiflDva 177
                                        vfV  ++ GGTG G++  va
  gi|298675449|ref|YP_003727199.1| 122 LVFVTAGMGGGTGTGVAPVVA 142
                                       49*************976554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 3048.47
//
Query:       gi|298675450|ref|YP_003727200.1|  [L=128]
Description: JAMM-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-10   38.8   0.0      1e-09   38.2   0.0    1.3  1  Prok-JAB  Prokaryotic homologs of the JAB domain
     0.0003   20.8   0.2    0.00048   20.1   0.2    1.4  1  RadC      RadC-like JAB domain


Domain annotation for each model (and alignments):
>> Prok-JAB  Prokaryotic homologs of the JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.0   1.1e-13     1e-09      12     117 ..      18     108 ..       8     109 .. 0.74

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 1.1e-13
                          Prok-JAB  12 arrahpeEtcGlllgkeseseevivvplvnewsnrfeipdpedslarlkfearerglevvgiwHSHpggsarPSetD 88 
                                        ++++p E +Gll  +  +  evi+ p  +          +    a  k   +  + + vg +HSHp +   PS++D
  gi|298675450|ref|YP_003727200.1|  18 SESTAPLEFAGLLHVDNGIITEVIILPGTE----------SSNRSAIMK-LFMMPNVKSVGSVHSHPSPNIKPSKAD 83 
                                       577899999999999985555555555442..........222222223.678999********************* PP

                          Prok-JAB  89 rrdaaalarvkalliivgdkaeelrawrl 117
                                       +++++++   + ++iivg+ ++e+ +wr+
  gi|298675450|ref|YP_003727200.1|  84 LQMFSKT---GSHHIIVGEPFDED-SWRC 108
                                       ******9...78899999855555.9998 PP

>> RadC  RadC-like JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.2   5.3e-08   0.00048      32      90 ..      34      89 ..      26     103 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.3e-08
                                      SBEEEEEEEEESTT-GGGCSHHHHHHHHHHTT-SEEEEEEE-TTS--S--HHHHHHHHH CS
                              RadC 32 nrliadeelseGtlnstlvdprevfkealklnAaavilaHnhPsgdlepSeeDieltkr 90
                                      n +i++  +  Gt +s       ++k  +  n ++v  +H hPs +++pS++D+++  +
  gi|298675450|ref|YP_003727200.1| 34 NGIITEVIILPGTESSN---RSAIMKLFMMPNVKSVGSVHSHPSPNIKPSKADLQMFSK 89
                                      55666666666665543...34577777888999********************99766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 936.56
//
Query:       gi|298675451|ref|YP_003727201.1|  [L=279]
Description: methanogenesis marker protein 8 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.9e-112  374.6   1.7   2.2e-112  374.4   1.7    1.0  1  DUF2099          Uncharacterized protein conserved in archaea
  ------ inclusion threshold ------
       0.23   11.2   0.2       0.23   11.2   0.2    1.6  2  Ribosom_S30AE_C  Sigma 54 modulation/S30EA ribosomal protein 


Domain annotation for each model (and alignments):
>> DUF2099  Uncharacterized protein conserved in archaea (DUF2099)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  374.4   1.7  2.4e-116  2.2e-112       1     257 []       3     256 ..       3     256 .. 0.99

  Alignments for each domain:
  == domain 1  score: 374.4 bits;  conditional E-value: 2.4e-116
                           DUF2099   1 HiiealgkarvvvkdgkvvevgepkikyCPlfkklrgikeitkeaikkniefrikefGlftkkRkleskedfvsfGa 77 
                                       H +e+lgk++v+vkdgkvv+v+ep i++CP+f+k++gik+it e +kkn+efri++fG+ft+kR++e++  fv+fGa
  gi|298675451|ref|YP_003727201.1|   3 HKMEMLGKTKVTVKDGKVVDVSEPVISWCPIFDKVHGIKKITPEDVKKNMEFRINDFGMFTDKREIEQE-VFVGFGA 78 
                                       99******************************************************************9.******* PP

                           DUF2099  78 sEilstalkeglidaavivcdgaGtvivtnpelvqglggrisGlveTePieevierieeeggivldketaeidqveG 154
                                       sEi++t+l+++++d++v+vcdgaGtvi++np+lvqg+g+risGlveTePie +ieri++++g+vld+ ta+id++eG
  gi|298675451|ref|YP_003727201.1|  79 SEIMMTGLRRNVLDSTVTVCDGAGTVITSNPKLVQGMGARISGLVETEPIEGLIERIQKSDGVVLDPYTAKIDPIEG 155
                                       ***************************************************************************** PP

                           DUF2099 155 vkkAiekgykkiavtvaeaedakklrelekeegvkilifavhttgiskeeaeelveaaDlvtacAskeireivkkka 231
                                       v+kA+e gyk+iavtv   ++akklr+le+e g+++++++vh+tgi++++a +l+e++D++tacAsk+ir+++k  +
  gi|298675451|ref|YP_003727201.1| 156 VRKAHELGYKRIAVTVPGVDEAKKLRDLESELGLELILIGVHITGIERDKALQLIEYLDITTACASKNIRDVIK--P 230
                                       **************************************************************************..9 PP

                           DUF2099 232 llqvgksvpvfaltekGkelilerlk 257
                                       l+qvg++vp+f++t++Gke++ler+k
  gi|298675451|ref|YP_003727201.1| 231 LVQVGTAVPLFGITQRGKEIMLERAK 256
                                       ***********************986 PP

>> Ribosom_S30AE_C  Sigma 54 modulation/S30EA ribosomal protein C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.1       1.7   1.5e+04      25      31 ..       4      10 ..       4      11 .. 0.81
   2 ?   11.2   0.2   2.6e-05      0.23      10      41 ..      36      67 ..      33      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 1.7
                                      HHHHHT- CS
                   Ribosom_S30AE_C 25 qmellgh 31
                                      +me+lg+
  gi|298675451|ref|YP_003727201.1|  4 KMEMLGK 10
                                      6999997 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 2.6e-05
                                      E-S--S-B-HHHHHHHHHHHT-SEEEEEETTT CS
                   Ribosom_S30AE_C 10 krfelkpmsveeAilqmellghdFfvFrnaet 41
                                      k + +k +++e+ +  me   +dF +F+++  
  gi|298675451|ref|YP_003727201.1| 36 KVHGIKKITPEDVKKNMEFRINDFGMFTDKRE 67
                                      78899************************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1952.28
//
Query:       gi|298675452|ref|YP_003727202.1|  [L=433]
Description: phenylacetate--CoA ligase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.9e-29   99.5   0.8    2.9e-28   98.0   0.8    1.8  1  AMP-binding_C_2  AMP-binding enzyme C-terminal domain
    2.2e-16   59.5   0.2    2.5e-15   56.0   0.2    2.0  1  AMP-binding      AMP-binding enzyme
     0.0002   20.4   0.1      0.021   13.7   0.0    2.1  2  GH3              GH3 auxin-responsive promoter
  ------ inclusion threshold ------
      0.012   14.6   0.0       0.14   11.2   0.0    2.1  2  LuxE             Acyl-protein synthetase, LuxE


Domain annotation for each model (and alignments):
>> AMP-binding_C_2  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.0   0.8   6.4e-32   2.9e-28       1      96 []     333     430 ..     333     430 .. 0.97

  Alignments for each domain:
  == domain 1  score: 98.0 bits;  conditional E-value: 6.4e-32
                                       TEEE-HHHHHHHHHT-TTEEEEEEEEEEEE.TTEEEEEEEEEE-T.T----HHHHHHHHHHHHHHHHHHHSS--EEE CS
                   AMP-binding_C_2   1 GvnvfPsqieevlkeieevepeYqivvtre.gelDelevkvEvke.gfsdelkelealekkiakklksklgvsvkve 75 
                                       G+n+fPsqie+v+ +i+e+++++q+v++r+ ++lDe++v+vE+++ +f+ el++l+a++k+++++lks l+++++ve
  gi|298675452|ref|YP_003727202.1| 333 GINIFPSQIENVIADISEITDQFQVVLDRSqNKLDEITVRVELEDdAFTGELQDLSAVRKHVENELKSILNIRTNVE 409
                                       99***************************7358************88999*************************** PP

                                       EE-TT-S---------EEE-S CS
                   AMP-binding_C_2  76 lvepgtlprsegKakrviDkR 96 
                                       lve+g++pr+ gK++r+iD+R
  gi|298675452|ref|YP_003727202.1| 410 LVEKGSIPRTSGKSQRIIDRR 430
                                       *******************99 PP

>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.0   0.2   5.6e-19   2.5e-15     156     422 ..      80     331 ..      51     332 .. 0.76

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 5.6e-19
                                       -BTTSEEEEEEE--SSSS-EEEEEEHHHH..HHHHHHHHHHHC..SCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT CS
                       AMP-binding 156 lkpddlayiiYTSGTTGkPKGVmlshrnl..vanvaslkletr..fklkeddvvlsilplahifglilelllallsG 228
                                       + ++d++ i  +SGT GkP  V ++++ +   +n+ +   +     ++++ddv+   + +   +g     +++   G
  gi|298675452|ref|YP_003727202.1|  80 VPKKDIVRIHASSGTGGKPTVVGYTTNDIdtWSNIMA--RN-LvmAGVRDDDVFQNSVNYGLFTGGLGYHYGIEKLG 153
                                       56789999999***********999999865233222..12.234568889***99****99999867777777777 PP

                                       -EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHH CS
                       AMP-binding 229 atvvllpkdaaldpklllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllggeplspellrffr 304
                                       a   +++++     ++ le++ +++vt i+++P+ + +l+e +++ +      d  sl++  +ggep s+++ r+++
  gi|298675452|ref|YP_003727202.1| 154 AM-TVPSGTGN--TARQLEMMVDYGVTAIHCTPSYALYLAEtAEQMD----MLDKLSLKTGCFGGEPWSSNTRRQLE 223
                                       75.55555555..234589********************99665555....337789***999************** PP

                                       HHHTCEEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-T..TEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBT CS
                       AMP-binding 305 alfgeevlegYGlTEttgvvtvlpleedkkklgsvGkplp..gvevkivDeetgepvpdgeeGellvrgpgvmkgYl 379
                                       + +  + +++YGl+E+ g  + +++ee+       G  ++  +  v+++De+ ge v +ge+Gel++          
  gi|298675452|ref|YP_003727202.1| 224 DALNISAYDSYGLSEMMGPGVAFECEEQ----D--GLHVWgdHFFVEVLDEN-GEQVSEGEKGELVLT--------- 284
                                       ***999*************985665454....2..55554225678999*99.9************86......... PP

                                       T-HHHHHHHEEETCCEEEEEEEEEEET.T.S.......EEEEEEECCCEEEE CS
                       AMP-binding 380 kkpeataeafdsegrwlrTGDlgrlde.d.G.......yleivgRkkdlikl 422
                                          ++t+ea+      +rTGD+ rl e + G         +++gR++d++++
  gi|298675452|ref|YP_003727202.1| 285 ---SLTKEALP-LI-RYRTGDITRLLEsEcGcgrttprISRVLGRADDMLIV 331
                                       ...46888873.23.6888888887541345777777557788888888877 PP

>> GH3  GH3 auxin-responsive promoter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.7   0.0    0.0025        11      74     109 ..      83     117 ..      79     206 .. 0.79
   2 !   13.7   0.0   4.6e-06     0.021     352     475 ..     271     400 ..     249     412 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0025
                                       SS-SEEEEECCEETTEEEEEEESHHHHHHHHHH.HH CS
                               GH3  74 epiklfalsSGTtsgksKliPvteeslkelallvla 109
                                       + i+++  sSGT  gk+ ++ +t++  +++++++++
  gi|298675452|ref|YP_003727202.1|  83 KDIVRIHASSGTG-GKPTVVGYTTNDIDTWSNIMAR 117
                                       679999*******.***************9988554 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 4.6e-06
                                       CCS-TTSEEEEEEESTT....S-SSEEECEEEEE....EEEETTEEEE.EEEECCTEEE-SSSS-CCHHHHHHHHH. CS
                               GH3 352 eevevGkeYelvvTtfa....GLyRYrigDvvrv....tgfynkaPrl.eFvgRknvvlsidgeklteeelqkavee 419
                                       e+v  G++ elv+T+ +     L RYr+gD+ r      g   ++Pr+ +++gR + +l ++g  +  +++++++++
  gi|298675452|ref|YP_003727202.1| 271 EQVSEGEKGELVLTSLTkealPLIRYRTGDITRLleseCGCGRTTPRIsRVLGRADDMLIVRGINIFPSQIENVIAD 347
                                       68999999999999754223379**********93333467789**764799************************5 PP

                                       HHHHHTT-EEEEEEEEE.ESS.SSSEEEEEEEEECS.........SHHHHHHHHHCS-SH CS
                               GH3 420 aakeltglelvdftsfapdtsesepghyvlflElkkk...eepe.eeecckeldesLedn 475
                                        + e+t     +f ++  d s+++    ++ +El+++    e +  ++++k+++++L ++
  gi|298675452|ref|YP_003727202.1| 348 IS-EIT----DQFQVVL-DRSQNKLDEITVRVELEDDaftGELQdLSAVRKHVENEL-KS 400
                                       55.543....4788866.99999***********98887633333499999999999.43 PP

>> LuxE  Acyl-protein synthetase, LuxE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0     0.044     2e+02     111     147 ..      19      54 ..      15      70 .. 0.82
   2 ?   11.2   0.0   3.1e-05      0.14     253     360 ..     220     327 ..     215     340 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.044
                              LuxE 111 lsierllravarvmkevlspkdrqielvdldPdrfna 147
                                       l  +rl r+v++v ++v s kdr +  + ++Pd   +
  gi|298675452|ref|YP_003727202.1|  19 LQFKRLKRTVSQVYNNVPSSKDR-FDQLGIGPDDVKS 54 
                                       6789***************9997.7888999987665 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 3.1e-05
                              LuxE 253 rdladvlnlsiddvvdiygfteqvelntpdfkdelkrkrvysdviir..deetlkvvgdGkvGlleyvdalstsyPa 327
                                       r+l d ln+s     d yg++e ++   ++  +e    +v  d +     +e+ + v++G  G l   + + ++ P 
  gi|298675452|ref|YP_003727202.1| 220 RQLEDALNISA---YDSYGLSEMMGPGVAFECEEQDGLHVWGDHFFVevLDENGEQVSEGEKGELVLTSLTKEALPL 293
                                       66777777765...689*********99999999999999998765546578899********************** PP

                              LuxE 328 fvvltddlGvieeslcegqkaGklv.kvlrrvkk 360
                                           t d+  + es+c ++++  ++ +vl+r++ 
  gi|298675452|ref|YP_003727202.1| 294 IRYRTGDITRLLESECGCGRTTPRIsRVLGRADD 327
                                       *******************9988764799*9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3077.68
//
Query:       gi|298675453|ref|YP_003727203.1|  [L=426]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-18   67.0   0.2    2.4e-18   65.8   0.2    1.6  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
    4.8e-13   49.4   2.1    9.1e-13   48.5   2.1    1.5  1  OrfB_IS605       Probable transposase
    2.5e-06   26.9   0.1    4.9e-06   25.9   0.1    1.5  1  HTH_OrfB_IS605   Helix-turn-helix domain
  ------ inclusion threshold ------
      0.047   13.5   0.3       0.14   12.0   0.3    1.8  1  Exo_endo_phos_2  Endonuclease-reverse transcriptase
       0.12   12.6   2.0        1.6    9.0   0.1    2.7  2  DUF5048          Domain of unknown function (DUF5048)


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.8   0.2   6.7e-22   2.4e-18       2      67 ..     315     379 ..     314     380 .. 0.98

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 6.7e-22
                    OrfB_Zn_ribbon   2 rklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNil 67 
                                       ++++e+l yk + +G+++++++++yTSk C +Cg++++ +l +r++ C+ Cg e+drD n+aiNi+
  gi|298675453|ref|YP_003727203.1| 315 SRFIEFLTYKSEFAGKQLTKIDESYTSKICYVCGKVHDMPLYKRNLSCD-CGNEIDRDRNSAINIM 379
                                       589**********************************************.***************6 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   2.1   2.5e-16   9.1e-13       2     118 ..     173     292 ..     172     294 .. 0.96

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 2.5e-16
                        OrfB_IS605   2 ipvevevelpkpkgnkaagiDlGinnLatvvtedgtw.flykgrrlksdykylakeiaelqsklkksknykkasrkl 77 
                                       +++e  ++++ ++++k  +iD+Gi + +t v++dg+  +++++r+ k   k+ + ++ + + ++k s+++ +    +
  gi|298675453|ref|YP_003727203.1| 173 VVYETFPQTNYKDNEKYQAIDIGITKTITAVNTDGKIlEITNPRFDKYWDKKINHAKSRRDHCKKYSRRWFRINDAI 249
                                       68898899999*************************99*************************************** PP

                        OrfB_IS605  78 arlhrkrsrrrkhllhklathliktlkev..gvetLnvgnmkd 118
                                       + + +k ++++k+ +hkl+++ +++   +   v++L+v+nmk+
  gi|298675453|ref|YP_003727203.1| 250 RVMTKKKNNQIKDWQHKLSRKMAENTRSNtiIVGDLDVKNMKN 292
                                       ************************99887779*********96 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.1   1.4e-09   4.9e-06       1      46 [.       1      45 [.       1      46 [. 0.94

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.4e-09
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeeg 46
                                      M l++ ky ++PT+eQ   l+     + + YN  L+erkea+ + +
  gi|298675453|ref|YP_003727203.1|  1 M-LLTKKYKIKPTNEQLDVLWSLSKQCTLLYNLSLSERKEAWMHKR 45
                                      7.8999************************************7755 PP

>> Exo_endo_phos_2  Endonuclease-reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   3.9e-05      0.14      11      81 ..     257     323 ..     249     342 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.9e-05
                   Exo_endo_phos_2  11 sdelenlestlekllselkspkiiilGDfNakhplWgsedtdssargeeLiefleehslsllnllksgptf 81 
                                       ++++++ +++l++ + e++++++ii+GD+ +k+ + +++  +  +r+++L + ++++++   ++  + +t+
  gi|298675453|ref|YP_003727203.1| 257 NNQIKDWQHKLSRKMAENTRSNTIIVGDLDVKNMKNSKKLPK--SRQKSLNRSTQNNGYI--SRFIEFLTY 323
                                       447899999999999999999**************9997666..9999999999999887..555545555 PP

>> DUF5048  Domain of unknown function (DUF5048)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   0.00045       1.6      37      75 ..      21      59 ..      10      79 .. 0.91
   2 ?    2.1   0.4     0.067   2.4e+02      57      94 ..     242     279 ..     221     282 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00045
                           DUF5048 37 elWknarltdsitlellliPWldvnekikyaakksniav 75
                                       l k++ l ++++l+     W+++ + iky+ +++n+++
  gi|298675453|ref|YP_003727203.1| 21 SLSKQCTLLYNLSLSERKEAWMHKRKSIKYSHQQDNLPS 59
                                      45699******************************9985 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.067
                           DUF5048  57 Wldvnekikyaak.ksniavdwiikslelnlaeGtmtvt 94 
                                       W++ n+ i+  +k k+n  +dw  ++l+ ++ae t + t
  gi|298675453|ref|YP_003727203.1| 242 WFRINDAIRVMTKkKNNQIKDWQ-HKLSRKMAENTRSNT 279
                                       999*****987774667778885.678888888887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1409  (0.0785878); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2906.46
//
Query:       gi|298675454|ref|YP_003727204.1|  [L=431]
Description: hypothetical protein Metev_1561 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-07   30.5   1.8    2.5e-07   30.5   1.8    2.4  3  Peptidase_M1  Peptidase family M1 domain
     0.0028   17.2   2.8      0.033   13.8   0.1    3.2  3  HARP          HepA-related protein (HARP)


Domain annotation for each model (and alignments):
>> Peptidase_M1  Peptidase family M1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.3     0.042   3.7e+02     145     208 ..      32      97 ..      24     113 .. 0.80
   2 ?   -2.6   0.0      0.37   3.3e+03       2      25 ..     229     252 ..     228     261 .. 0.83
   3 !   30.5   1.8   2.8e-11   2.5e-07      70     205 ..     287     417 ..     279     427 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.042
                                       GSHHHHHHTSSHHHHHHHHHHHHHHH..HHCTHHHHHHHHHHHHHHCTTEEE-HHHHHHHHHHCCC CS
                      Peptidase_M1 145 ekpseidevFdsiaYeKGasllrmle..kllgeevFqkglksYlkefkyknaetedlwdaleealn 208
                                       e+++ei+++++  + eK +++ + ++  ++ ++ ++ +g  s l++   +na + d+w++ +++++
  gi|298675454|ref|YP_003727204.1|  32 ETNKEIESFYKLNPDEKIVNVFKKIHftNYDSDTKYWQGYYSHLHHKIPENAINVDMWNSKNQKIK 97 
                                       567889999999999999999988863366678899999999999999999999999998877644 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.37
                                       HHHHHHHHHHHHHHHHTS--SSSE CS
                      Peptidase_M1   2 alevtkkllefleeyfkvpYplpk 25 
                                       +++ + k+l +lee+ ++ Yp ++
  gi|298675454|ref|YP_003727204.1| 229 TMDLAIKALPILEEKWGFTYPKDH 252
                                       58899999*********9999765 PP

  == domain 3  score: 30.5 bits;  conditional E-value: 2.8e-11
                                       HHHHHHHHHHBTTTEEESSGGGGHHHHHHHHHHHHHHHHHHSC..CCHCHHHHHHHCHHHHHHHHTSTTHHHSSGG- CS
                      Peptidase_M1  70 viaHElaHqWfGnlVtmkwWddlwLnEGfatyleylildklep..ewevseqllleeveealsedaldeshpitqev 144
                                       + +HElaH W+      +  + +w++EG+a  ++yl+l++l++    e +e+++ +  ++++s++   ++ ++ +++
  gi|298675454|ref|YP_003727204.1| 287 ILIHELAHYWT----QKCGFEYIWMDEGYADLYTYLVLNRLDSndALERKEDFIKQYKSMKQSKNLKLSEWSVPDSI 359
                                       789*******8....456899********************994444466777333333334444433444443444 PP

                                       GSHHHHHHTSSHHH..HHHHHHHHHHHHHHCTHHHHHHHHHHHHHHCTTEEE-HHHHHHHHHH CS
                      Peptidase_M1 145 ekpseidevFdsia..YeKGasllrmlekllgeevFqkglksYlkefkyknaetedlwdalee 205
                                       +     +e Fd++   Y+K++ ll  + k +g + ++++ +++l++ + +n e +++++++++
  gi|298675454|ref|YP_003727204.1| 360 G-----SENFDRVDygYKKSFVLLYNIYKKIGINSMKQANQRFLNSDNIGNKEFKHIIQTVSD 417
                                       4.....678997652279***************************999888888888777665 PP

>> HARP  HepA-related protein (HARP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   3.6e-06     0.033       9      31 ..      47      69 ..      44      83 .. 0.93
   2 ?   -1.1   0.0      0.17   1.6e+03      32      45 ..     193     206 ..     192     215 .. 0.79
   3 ?    1.4   0.2     0.027   2.4e+02      21      37 ..     337     353 ..     336     355 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.6e-06
                              HARP  9 eelIavFKqipSrnYdpktkkWn 31
                                      e++++vFK+i   nYd++tk W+
  gi|298675454|ref|YP_003727204.1| 47 EKIVNVFKKIHFTNYDSDTKYWQ 69
                                      789*******************6 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.17
                              HARP  32 FsledyskLmekvr 45 
                                       ++l+dy+ L ++v+
  gi|298675454|ref|YP_003727204.1| 193 VNLTDYKVLNKSVS 206
                                       5799***9999886 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.027
                              HARP  21 rnYdpktkkWnFsledy 37 
                                       ++Y++++ ++n++l++ 
  gi|298675454|ref|YP_003727204.1| 337 KQYKSMKQSKNLKLSEW 353
                                       89************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2940.03
//
Query:       gi|298675455|ref|YP_003727205.1|  [L=80]
Description: hypothetical protein Metev_1562 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-23   83.0   3.0    1.3e-23   82.8   3.0    1.0  1  HTH_45    Winged helix-turn-helix


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.8   3.0   7.1e-28   1.3e-23       1      69 [.       7      74 ..       7      79 .. 0.94

  Alignments for each domain:
  == domain 1  score: 82.8 bits;  conditional E-value: 7.1e-28
                            HTH_45  1 rRskleIiadILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlellekl 69
                                      rRs+++I++dIL++  +++akkT+i+y anL+ +++nkYLdmL +k+lik++++ +v+T+kG+e+ e  
  gi|298675455|ref|YP_003727205.1|  7 RRSRIDITLDILKIA-SNGAKKTEIVYGANLNSNITNKYLDMLKQKELIKQQENIFVTTDKGKEYQELA 74
                                      8************77.99*********************************************987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1088  (0.0606838); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 609.25
//
Query:       gi|298675456|ref|YP_003727206.1|  [L=131]
Description: hypothetical protein Metev_1563 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 986.08
//
Query:       gi|298675457|ref|YP_003727207.1|  [L=192]
Description: hypothetical protein Metev_1564 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.4e-13   48.4   9.2    1.1e-12   48.1   9.2    1.1  1  Exosortase_EpsH  Transmembrane exosortase (Exosortase_EpsH)


Domain annotation for each model (and alignments):
>> Exosortase_EpsH  Transmembrane exosortase (Exosortase_EpsH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   9.2     6e-17   1.1e-12     101     254 ..      44     185 ..      36     187 .. 0.75

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 6e-17
                   Exosortase_EpsH 101 rlllfpllll.llalPlpavlvaqlslpLqllvaavagfllsllgipvereGnviqlptgqveVaeaCsGlrsllal 176
                                        l++f + +  ll++ + + l+     ++++++a+  +++l ++gi+ ++ G vi+l+t+++ V ++C+G+  ll  
  gi|298675457|ref|YP_003727207.1|  44 GLYIFYIGIFtLLYITFKDDLE-----FFRNITADGLSAILGMFGIQNSVFGSVIHLETISLKVIDECTGIYELLVY 115
                                       4555556666555555444444.....49*****************************************6666555 PP

                   Exosortase_EpsH 177 lalglllallfrrrlwkrklllllaavpiaflaNlvRilllvllayhygpeaaegllHeiaGwllfgvalllllgll 253
                                         + l++     ++  k+ +  ++++vp ++  N+vR + l++++ +  p+ + +++H  +  + ++++ ++l++ll
  gi|298675457|ref|YP_003727207.1| 116 SGCVLAYS----TTFDKK-IYGIAFGVPAILSINMVRLVCLAFVGVW-YPAIF-DYVHYYLWQVTLILI-IVLVTLL 184
                                       55544444....333335.999**********************775.67788.9***98855666555.4444444 PP

                   Exosortase_EpsH 254 p 254
                                       +
  gi|298675457|ref|YP_003727207.1| 185 W 185
                                       4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1342  (0.0748508); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1310.46
//
Query:       gi|298675458|ref|YP_003727208.1|  [L=558]
Description: hypothetical protein Metev_1565 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0073   16.6  11.3       0.41   11.0   0.7    3.2  2  DUF11        Domain of unknown function DUF11
  ------ inclusion threshold ------
      0.011   16.0   6.6       0.43   10.9   1.0    2.9  2  CARDB        CARDB
      0.076   13.3   1.2         13    6.1   0.1    2.9  2  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi
      0.097   12.7   0.2        9.1    6.4   0.0    3.0  3  DUF1573      Protein of unknown function (DUF1573)


Domain annotation for each model (and alignments):
>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.7   9.1e-05      0.41      12      79 ..     303     365 ..     297     378 .. 0.81
   2 !    8.4   4.0   0.00057       2.6      13      37 ..     429     453 ..     411     522 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.1e-05
                             DUF11  12 pGdtvtytltvtNtgpasa..ngvvvtDtlPaglayvsvsasqgtasaltsv.gsLeagesatlsftvrvt 79 
                                       +G+tv+    vtN+g+++   ++v+vtD    g++ v   +s      + +    L +ge++t +++ +v 
  gi|298675458|ref|YP_003727208.1| 303 AGQTVEWKYEVTNNGTVPFdlANVTVTD--DKGVTPVLDETS------DDGNdDILSPGETWTYTASGTVE 365
                                       799**************98779******..899999999999......33333667888888888776665 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00057
                             DUF11  13 GdtvtytltvtNtgpasangvvvtD 37 
                                         tvt t  v N+g +++++v+vtD
  gi|298675458|ref|YP_003727208.1| 429 ESTVTWTYEVHNNGSDDLQNVQVTD 453
                                       4599********************9 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.5    0.0016       7.3      17      80 ..     303     374 ..     298     393 .. 0.76
   2 ?   10.9   1.0   9.7e-05      0.43      14      72 ..     425     489 ..     418     517 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0016
                                       TTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEE..........SEE-CTEEEEEEEEEE-S.-S-CEEEE CS
                             CARDB  17 vgeentitvtvkNqGtaasgatkvalyldgelvgtvtv..........psLaagesttvsftwtte.ategevtl 80 
                                       +g++++ +++v+N+Gt      +v+++ d+ ++   +v            L++ge+ t +++ t+e   eg+v+ 
  gi|298675458|ref|YP_003727208.1| 303 AGQTVEWKYEVTNNGTVPFDLANVTVTDDKGVT---PVldetsddgndDILSPGETWTYTASGTVEeCPEGSVYT 374
                                       6889999***********999999999888775...333444445666779***********9999555566653 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 9.7e-05
                                       EEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEE......SEE-CTEEEEEEEEEE-S CS
                             CARDB  14 eafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtv......psLaagesttvsftwtte 72 
                                       ++++++++t t++v+N+G+++ ++++v+    g+l +t++v        L+ ge+   ++t t++
  gi|298675458|ref|YP_003727208.1| 425 KVSNESTVTWTYEVHNNGSDDLQNVQVTDDKLGTLPETAIVdkgdgdDILNIGETWVYEMTGTAD 489
                                       67889999******************998888888888888666666666666666666666666 PP

>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1    0.0029        13       2      27 ..     302     327 ..     301     361 .. 0.86
   2 ?    5.1   0.1    0.0062        28       4      27 ..     429     452 ..     426     454 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0029
                       NPCBM_assoc   2 epGetvtltltvtndgtaaatnvsls 27 
                                       ++G+tv+ + +vtn+gt +    +++
  gi|298675458|ref|YP_003727208.1| 302 SAGQTVEWKYEVTNNGTVPFDLANVT 327
                                       68***************997655555 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0062
                       NPCBM_assoc   4 Getvtltltvtndgtaaatnvsls 27 
                                        +tvt t +v n+g++ ++nv+++
  gi|298675458|ref|YP_003727208.1| 429 ESTVTWTYEVHNNGSDDLQNVQVT 452
                                       6899*****************985 PP

>> DUF1573  Protein of unknown function (DUF1573)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.2   9.8e+03       8      31 ..      39      61 ..      35      66 .. 0.71
   2 ?    6.4   0.0     0.002       9.1      15      40 ..     303     328 ..     295     356 .. 0.92
   3 ?    2.7   0.0     0.029   1.3e+02      12      34 ..     425     447 ..     416     456 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.2
                           DUF1573  8 idfgkieegekvtatFeftNtgka 31
                                      + fg+++ ++++  ++ + N g++
  gi|298675458|ref|YP_003727208.1| 39 WAFGQTN-NATAASEYDINNLGDR 61
                                      5677764.6777889999999886 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.002
                           DUF1573  15 egekvtatFeftNtgkaplvitnvkt 40 
                                       +g++v+ ++e+tN+g+ p+ + nv+ 
  gi|298675458|ref|YP_003727208.1| 303 AGQTVEWKYEVTNNGTVPFDLANVTV 328
                                       6899****************999985 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.029
                           DUF1573  12 kieegekvtatFeftNtgkaplv 34 
                                       k++++++vt t+e+ N+g++ l 
  gi|298675458|ref|YP_003727208.1| 425 KVSNESTVTWTYEVHNNGSDDLQ 447
                                       5678999***********99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (558 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 3675.69
//
Query:       gi|298675459|ref|YP_003727209.1|  [L=239]
Description: hypothetical protein Metev_1566 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       746  (0.0416086); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1680.15
//
Query:       gi|298675460|ref|YP_003727210.1|  [L=498]
Description: hypothetical protein Metev_1567 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00039   20.7   0.6       0.39   11.0   0.1    3.5  3  Big_6            Bacterial Ig domain
      0.006   16.7   0.3         31    4.8   0.0    3.6  3  Big_3_5          Bacterial Ig-like domain (group 3)
  ------ inclusion threshold ------
       0.85    9.9   4.7         15    6.0   0.1    3.2  4  CarboxypepD_reg  Carboxypeptidase regulatory-like domain


Domain annotation for each model (and alignments):
>> Big_6  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.0    0.0035        21      26      64 ..      53      91 ..      47     101 .. 0.76
   2 !   11.0   0.1   6.5e-05      0.39      16      64 ..     133     182 ..     122     208 .. 0.75
   3 ?   -0.8   0.0      0.33     2e+03      22      39 ..     232     249 ..     230     257 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0035
                             Big_6 26 tVtvkdadgtvlgtgtadadGeFsvtl.epaqangetlsv 64
                                      ++t k  dg++++++t++++Ge+++ + +    +g t++v
  gi|298675460|ref|YP_003727210.1| 53 QITAK-LDGELIAKSTIEKEGEYELHFlKMDDYTGITFNV 91
                                      55544.59****************9983444456666655 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 6.5e-05
                             Big_6  16 tltGkaeagatVtvkdadgtvlgtgtadadGeFsvtlepaq.angetlsv 64 
                                       +++G+  +  t  + + +++++g++t++ +G ++++l ++   +g  ++v
  gi|298675460|ref|YP_003727210.1| 133 EINGNPAPAGTNILAKLNNSLIGNSTVKTQGDYEIQLLNKDnYEGIIFNV 182
                                       4788766666666788999*****************95433144444444 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.33
                             Big_6  22 eagatVtvkdadgtvlgt 39 
                                       e +atV+v+   ++ + +
  gi|298675460|ref|YP_003727210.1| 232 EFNATVNVTGVRNSSITE 249
                                       7799****9998877655 PP

>> Big_3_5  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.8   0.0    0.0052        31      10      63 ..      21      76 ..      18      78 .. 0.82
   2 ?    3.8   0.2     0.011        67       9      63 ..     114     167 ..     107     171 .. 0.67
   3 ?    3.5   0.0     0.014        83       4      57 ..     227     282 ..     224     291 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0052
                                      EEEEEE--CCCCTT..S--EEEEEETTEE-SS-EE--TTSEEEEEEE-SS-EEEEE CS
                           Big_3_5 10 vtltatVtaasggt..ptGtVtftdggttlgtavllsanGtAtltvsalaaGthsi 63
                                      v++tat  +  +++  + G V++ d+ ++ gt+++ + +G   ++ +  + G++++
  gi|298675460|ref|YP_003727210.1| 21 VSFTATAEQPPEPPliVKGDVEINDEPAPEGTQITAKLDGELIAKSTIEKEGEYEL 76
                                      778888887766433499**************999999999888888888888876 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.011
                                       EEEEEEE--CCCCTTS--EEEEEETTEE-SS-EE--TTSEEEEEEE-SS-EEEEE CS
                           Big_3_5   9 tvtltatVtaasggtptGtVtftdggttlgtavllsanGtAtltvsalaaGthsi 63 
                                       +v ++ +V +    t+ G+V++  + ++ gt++l + n +   + +  ++G ++i
  gi|298675460|ref|YP_003727210.1| 114 AVYVNLSVEQP-PVTVKGNVEINGNPAPAGTNILAKLNNSLIGNSTVKTQGDYEI 167
                                       56666666666.5678888888888888888887776666666666666666665 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.014
                                       EETTSEEEEEEE--CCCCTTS--EEE..EEE.TTEE-SS-EE--TTSEEEEEEE-SS CS
                           Big_3_5   4 vtagqtvtltatVtaasggtptGtVt..ftd.ggttlgtavllsanGtAtltvsala 57 
                                       v   ++++ t++Vt++ + + t tV   f+  g+t   ++v l+   + t++++  +
  gi|298675460|ref|YP_003727210.1| 227 VIIDEEFNATVNVTGVRNSSITETVPddFKYvGSTIPESNVILN-GNKITFKLEKST 282
                                       56678889999999999999***995557752555557777777.467777776655 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0    0.0053        32      10      51 ..      45      85 ..      37     119 .. 0.82
   2 ?    6.0   0.1    0.0025        15       2      51 ..     128     176 ..     127     211 .. 0.78
   3 ?   -3.0   0.4       1.5   9.1e+03      16      35 ..     234     253 ..     234     254 .. 0.75
   4 ?   -3.6   0.0       2.5   1.5e+04      13      23 ..     383     393 ..     380     402 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0053
                   CarboxypepD_reg 10 sgapiagatVtvtnadtgtvastttdadGafrlrglppgtys 51
                                      +  + +g ++t++  d++  a  t +++G++ l +l+ ++y+
  gi|298675460|ref|YP_003727210.1| 45 DEPAPEGTQITAK-LDGELIAKSTIEKEGEYELHFLKMDDYT 85
                                      5555689999999.79999*****************998886 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0025
                   CarboxypepD_reg   2 isGrVtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtys 51 
                                       ++G V    + + ag ++ ++  +++   + t  ++G++ ++ l  ++y+
  gi|298675460|ref|YP_003727210.1| 128 VKGNVEINGNPAPAGTNILAK-LNNSLIGNSTVKTQGDYEIQLLNKDNYE 176
                                       566666544444467777776.78999****************9999997 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.5
                   CarboxypepD_reg  16 gatVtvtnadtgtvastttd 35 
                                       +atV vt  ++++ ++t+ d
  gi|298675460|ref|YP_003727210.1| 234 NATVNVTGVRNSSITETVPD 253
                                       69999997777777777665 PP

  == domain 4  score: -3.6 bits;  conditional E-value: 2.5
                   CarboxypepD_reg  13 piagatVtvtn 23 
                                       p+   +V+v++
  gi|298675460|ref|YP_003727210.1| 383 PLRAYQVVVSD 393
                                       55566666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (498 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 3292.98
//
Query:       gi|298675461|ref|YP_003727211.1|  [L=86]
Description: hypothetical protein Metev_1568 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-24   85.1   0.9    2.7e-24   84.9   0.9    1.0  1  HTH_45          Winged helix-turn-helix
  ------ inclusion threshold ------
      0.015   15.1   0.1      0.016   15.0   0.1    1.1  1  DUF4393         Domain of unknown function (DUF4393)
      0.022   15.2   0.1       0.24   11.9   0.0    2.0  2  HTH_27          Winged helix DNA-binding domain
      0.042   13.6   0.1      0.046   13.5   0.1    1.2  1  DUF4364         Domain of unknown function (DUF4364)
      0.046   13.4   0.1        0.4   10.4   0.0    1.9  2  DUF4423         Domain of unknown function (DUF4423)
      0.048   12.6   0.1       0.36    9.7   0.0    1.8  2  Hyphal_reg_CWP  Hyphally regulated cell wall protein N-termin
      0.085   12.9   0.0       0.15   12.2   0.0    1.4  1  HemN_C          HemN C-terminal domain
      0.085   13.0   0.0       0.12   12.6   0.0    1.4  1  MotA_activ      Transcription factor MotA, activation domain


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.9   0.9   1.2e-27   2.7e-24       1      72 [.      14      84 ..      14      86 .] 0.97

  Alignments for each domain:
  == domain 1  score: 84.9 bits;  conditional E-value: 1.2e-27
                            HTH_45  1 rRskleIiadILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlelleklkel 72
                                      rRs+++I  +IL+a   ++akkT+++y+anL+++++nkYLdmL ekgli+k+++ Yv+TekG+++ e+ ++l
  gi|298675461|ref|YP_003727211.1| 14 RRSRIDISEEILNAA-IDGAKKTHLVYSANLNFDIINKYLDMLEEKGLIEKEGDLYVTTEKGKKFQERARDL 84
                                      8************99.*************************************************9998876 PP

>> DUF4393  Domain of unknown function (DUF4393)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   7.2e-06     0.016      98     145 ..      21      73 ..       3      84 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.2e-06
                           DUF4393  98 kesiknsfsdlhekvvlenpekv.....kasldnLerlgLiklsekqklteek 145
                                       +e+i+n+  d ++k+ l +  ++     +++ld Le  gLi+++++ ++t+ek
  gi|298675461|ref|YP_003727211.1|  21 SEEILNAAIDGAKKTHLVYSANLnfdiiNKYLDMLEEKGLIEKEGDLYVTTEK 73 
                                       4445555555555555555555455666********************99998 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0       0.2   4.6e+02      45      67 ..       1      23 [.       1      23 [. 0.89
   2 ?   11.9   0.0   0.00011      0.24      17      68 .]      30      74 ..      24      74 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.2
                            HTH_27 45 kGLvertgdeadrrekrvrlTdk 67
                                      +G++++ g+ + +r++r+ ++++
  gi|298675461|ref|YP_003727211.1|  1 MGYLKSRGCGTIKRRSRIDISEE 23
                                      89******999999999999875 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00011
                            HTH_27 17 rrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      +++k++ l+   n++   i + l+ L+ekGL+e++gd       ++  T+kG
  gi|298675461|ref|YP_003727211.1| 30 DGAKKTHLVYSANLNFDIINKYLDMLEEKGLIEKEGD-------LYVTTEKG 74
                                      677888888888888888889***********99988.......47777776 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   2.1e-05     0.046      31      69 ..      43      77 ..      20      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.1e-05
                           DUF4364 31 tnYfdlqqalseLvesglieeeekenktlykiTekGket 69
                                      +n+  ++++l+ L+e+glie+    + +ly  TekGk+ 
  gi|298675461|ref|YP_003727211.1| 43 LNFDIINKYLDMLEEKGLIEK----EGDLYVTTEKGKKF 77
                                      6777899*************5....899*********86 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0       0.1   2.2e+02      65     100 ..       1      35 [.       1      45 [. 0.71
   2 ?   10.4   0.0   0.00018       0.4      55      84 ..      48      76 ..      41      84 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.1
                           DUF4423  65 lgllkkdedgkyrqtekslttssevkseavrsyhkq 100
                                       +g lk  + g++++ ++ +++s+e+ ++a+    k 
  gi|298675461|ref|YP_003727211.1|   1 MGYLKSRGCGTIKR-RSRIDISEEILNAAIDGAKKT 35 
                                       57788888855554.458888999999888777665 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00018
                           DUF4423 55 vekalefLlklgllkkdedgkyrqtekslt 84
                                      ++k l+ L++ gl++k++d  y+ tek  +
  gi|298675461|ref|YP_003727211.1| 48 INKYLDMLEEKGLIEKEGD-LYVTTEKGKK 76
                                      7899**************9.9999998765 PP

>> Hyphal_reg_CWP  Hyphally regulated cell wall protein N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.024        55     183     209 ..       7      35 ..       3      41 .. 0.75
   2 ?    9.7   0.0   0.00016      0.36      30      67 ..      37      74 ..      18      81 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.024
                    Hyphal_reg_CWP 183 sGCitvgedssiyisnsll..sissdqti 209
                                        GC t+++ s i is+ +l   i+  ++ 
  gi|298675461|ref|YP_003727211.1|   7 RGCGTIKRRSRIDISEEILnaAIDGAKKT 35 
                                       6*************888864555555554 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00016
                    Hyphal_reg_CWP 30 ltInsgaylsiinnalsafvgdlsvenngglyitstss 67
                                      l  + +  + iin++l  ++++  +e++g+ly+t+++ 
  gi|298675461|ref|YP_003727211.1| 37 LVYSANLNFDIINKYLDMLEEKGLIEKEGDLYVTTEKG 74
                                      5556788999************************9875 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   6.5e-05      0.15      41      64 ..      51      74 ..      40      75 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.5e-05
                            HemN_C 41 aleklqeqGLLeldggrlrltprG 64
                                       l+ l+e+GL+e +g+ +++t++G
  gi|298675461|ref|YP_003727211.1| 51 YLDMLEEKGLIEKEGDLYVTTEKG 74
                                      5889******************99 PP

>> MotA_activ  Transcription factor MotA, activation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.1e-05      0.12      42      74 ..      42      74 ..      12      84 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.1e-05
                                      TS-HHHHHHHHHHHHHTTSEEEETTEEEE-HHH CS
                        MotA_activ 42 dlgnavvnsnigvlikkglveksgdgliitgea 74
                                      +l   ++n  + +l  kgl+ek gd  + t + 
  gi|298675461|ref|YP_003727211.1| 42 NLNFDIINKYLDMLEEKGLIEKEGDLYVTTEKG 74
                                      5677899******************88777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 644.19
//
Query:       gi|298675462|ref|YP_003727212.1|  [L=226]
Description: hypothetical protein Metev_1569 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0014   18.7   1.3     0.0021   18.1   0.6    1.8  2  DUF4366     Domain of unknown function (DUF4366)
  ------ inclusion threshold ------
       0.22   11.7   0.0       0.22   11.7   0.0    2.3  2  DARPP-32    Protein phosphatase inhibitor 1/DARPP-32
       0.39    9.9   1.1       0.56    9.4   1.1    1.2  1  Zip         ZIP Zinc transporter
       0.88    9.7  12.9       0.83    9.7  11.6    1.6  1  Podoplanin  Podoplanin
          2    6.8   3.6        2.1    6.8   3.6    1.1  1  Macoilin    Macoilin family


Domain annotation for each model (and alignments):
>> DUF4366  Domain of unknown function (DUF4366)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.68   2.4e+03      86      86 ..     110     110 ..      59     144 .. 0.53
   2 !   18.1   0.6   5.8e-07    0.0021      66     142 ..     153     226 .]     119     226 .] 0.77

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.68
                           DUF4366  86 g 86 
                                       +
  gi|298675462|ref|YP_003727212.1| 110 K 110
                                       1 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 5.8e-07
                           DUF4366  66 deeaakeeeevcactekcaagkvntdcpveepepekeaepeepeeepekksnnglllvvlavaligggaayyfkvlk 142
                                       +++++++ + + ++t +++ag+ n d++  + +  +++e   +++epe + +n++l+vv a++++g  aa+ +k++k
  gi|298675462|ref|YP_003727212.1| 153 QNDDNTAGTGTDSETRETTAGDNNPDASTGTNDGAESQES--TAPEPEGT-SNISLMVVGAIIIVGIIAAVGYKMKK 226
                                       4444455556667778888888888887766666666554..55566665.68999**********98888888776 PP

>> DARPP-32  Protein phosphatase inhibitor 1/DARPP-32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.2e-05      0.22       8      57 ..      84     133 ..      78     145 .. 0.90
   2 ?   -1.8   4.7      0.89   3.2e+03     105     140 ..     153     187 ..     139     204 .. 0.36

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.2e-05
                          DARPP-32   8 IQFsVpalpsqLDPrqvEmIRrRRPTPAtLfrvsdqsspedeesshqkve 57 
                                       I F+V  ++sq D + ++ +    PT At + +s  +s+ d+++ +q +e
  gi|298675462|ref|YP_003727212.1|  84 ITFTVDGTESQPDSEIADELNNADPTKATYLDLSVTQSSSDQNTENQDTE 133
                                       89********************************9999999998888765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.89
                          DARPP-32 105 qeeedeegeaeasedsadseeeeeeeeeeeeeeeke 140
                                       q+++++ g+   s +++++++ +++ +++++ ++  
  gi|298675462|ref|YP_003727212.1| 153 QNDDNTAGTGTDS-ETRETTAGDNNPDASTGTNDGA 187
                                       2222222222211.1112222222222222221211 PP

>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   1.1   0.00016      0.56     105     195 ..     121     213 ..      96     218 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00016
                               Zip 105 shkektpkkasssssesaakksvsndkveeseekedhvaeadtdadskeelrngkqeksesekeqas..eeedkekl 179
                                       s +++++++++++ s s+ +    +++++++ ++ d+ a+++td ++ e+++ ++ +  + +++  +  +e+  +++
  gi|298675462|ref|YP_003727212.1| 121 SSSDQNTENQDTELSVSGGSMGGTSSSTTNDNQNDDNTAGTGTDSETRETTAGDNNPDASTGTNDGAesQESTAPEP 197
                                       33334444444444444444444444444444445666666666666666665555544444443333366667777 PP

                               Zip 180 aslkvraiilllglil 195
                                       ++ + ++++++ ++i+
  gi|298675462|ref|YP_003727212.1| 198 EGTSNISLMVVGAIII 213
                                       7888888888877776 PP

>> Podoplanin  Podoplanin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7  11.6   0.00023      0.83      39     148 ..     106     220 ..      84     224 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00023
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XX.....XXXX-----GGG-XXXXXXXXXXXXXXXXXXXXX.XXXX CS
                        Podoplanin  39 dekvtpGvednvvttgaseepyesglttlv.pt.....stesvtdlrledlptaestvkakeesqstttlnv.vtsh 108
                                        + +     d  vt+++s +++e++ t l  +         s+t+++ +d  ta +t  + e+ ++t+  n   +s+
  gi|298675462|ref|YP_003727212.1| 106 ADPTKATYLDLSVTQSSSDQNTENQDTELSvSGgsmggTSSSTTNDNQNDDNTA-GTGTDSETRETTAGDNNpDAST 181
                                       444555566889999999999997777653222423434455666666666664.4445555555444433323333 PP

                                       XX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Podoplanin 109 st.ekvgeetettvekdGLatvtLvgiivGvllaigfiggi 148
                                        t + ++ + +t+ e +G + ++L+  +vG ++ +g+i+ +
  gi|298675462|ref|YP_003727212.1| 182 GTnDGAESQESTAPEPEGTSNISLM--VVGAIIIVGIIAAV 220
                                       33144555567788999*9999994..45555555544433 PP

>> Macoilin  Macoilin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   3.6   0.00059       2.1     292     375 ..      94     175 ..      29     204 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.00059
                          Macoilin 292 kskskrlsksessgsesellveesvkskssssssssnknskkasagsagssnssskkhsessksvtsssssknskkq 368
                                       + +s+   + ++ + ++ +  + sv+++ss ++++++ ++ + s+gs+g ++ss+ + +++++  t ++ ++++ ++
  gi|298675462|ref|YP_003727212.1|  94 QPDSEIADELNNADPTKATYLDLSVTQSSSDQNTENQDTELSVSGGSMGGTSSST-TNDNQNDDNTAGTGTDSETRE 169
                                       4444444444455555555566666555555555444444444454444444444.444444444444422222222 PP

                          Macoilin 369 klpaGks 375
                                        ++aG +
  gi|298675462|ref|YP_003727212.1| 170 -TTAGDN 175
                                       .223332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1018  (0.0567795); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 1680.79
//
Query:       gi|298675463|ref|YP_003727213.1|  [L=678]
Description: hypothetical protein Metev_1570 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      5e-21   75.3   2.3    5.5e-05   23.4   0.0    4.5  4  bMG10           Bacterial Alpha-2-macroglobulin MG10 domain
    5.7e-09   36.2  21.8      0.008   16.5   1.1    5.2  4  DUF11           Domain of unknown function DUF11
    1.8e-06   28.0   0.0       0.69    9.9   0.0    3.5  3  CtaG_Cox11      Cytochrome c oxidase assembly protein CtaG/Co
    1.8e-06   27.6   0.0          2    8.3   0.0    3.7  3  CDC48_2         Cell division protein 48 (CDC48), domain 2
    8.3e-06   26.1   7.9        1.5    9.1   0.1    4.8  4  Cohesin         Cohesin domain
      2e-05   25.1   0.2        5.5    7.4   0.0    3.8  3  Arrestin_C      Arrestin (or S-antigen), C-terminal domain
    6.2e-05   22.0  16.3      0.013   14.3   3.9    3.8  4  BatD            Oxygen tolerance
    0.00013   21.5  22.9       0.11   11.9   9.6    3.7  3  Peptidase_A4    Peptidase A4 family
    0.00071   18.6   1.7        3.7    6.4   0.1    3.3  3  DUF4784         Domain of unknown function (DUF4784)
  ------ inclusion threshold ------
       0.01   15.8   0.5         24    5.0   0.0    3.9  4  DUF4334         Domain of unknown function (DUF4334)
      0.011   15.9  10.8          8    6.8   0.4    6.7  7  NPCBM_assoc     NPCBM-associated, NEW3 domain of alpha-galact
      0.011   15.8   8.4        7.3    6.8   0.1    4.5  4  Big_8           Bacterial Ig domain
      0.021   14.9   0.0         11    6.0   0.0    3.7  4  WYL             WYL domain
      0.023   14.8   0.7        1.2    9.3   0.2    3.7  3  Cupredoxin_1    Cupredoxin-like domain
      0.027   13.8   0.0         20    4.4   0.0    3.0  3  MipZ            ATPase MipZ
      0.055   13.9   0.0         35    4.9   0.0    3.3  3  Rtt106          Histone chaperone Rttp106-like
      0.071   13.5   0.3         13    6.3   0.0    4.0  4  MYEOV2          Myeloma-overexpressed-like
       0.18   11.7   0.1       0.18   11.7   0.1    5.3  7  DUF4307         Domain of unknown function (DUF4307)
       0.18   12.1   8.8        9.5    6.6   0.8    4.5  3  Big_3           Bacterial Ig-like domain (group 3)
       0.25   12.1  13.9        6.2    7.6   0.3    4.7  4  fn3_5           Fn3-like domain
        1.7    8.9  13.5        4.9    7.4   0.4    4.3  4  LRR_adjacent    LRR adjacent
        3.3    8.2  15.9          8    6.9   0.3    4.4  4  PilA4           Pilin A4
        8.5    6.3   7.6    1.1e+02    2.8   0.1    4.1  4  PASTA           PASTA domain


Domain annotation for each model (and alignments):
>> bMG10  Bacterial Alpha-2-macroglobulin MG10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   1.7e-07   0.00013      17      85 ..      48     113 ..      36     138 .. 0.75
   2 !   23.4   0.0     7e-08   5.5e-05      19     105 ..     171     249 ..     151     256 .. 0.75
   3 !   21.4   0.0   2.8e-07   0.00022      19      75 ..     289     342 ..     269     376 .. 0.79
   4 ?    4.4   0.0     0.053        41      29      64 ..     413     446 ..     390     473 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.7e-07
                             bMG10  17 sksdaklkvGdkvrvrltvttprdleyvaledplPAGlepvnpslgtesesaeeyewleeltefsyrei 85 
                                       + s+++++ Gd+++v+l+v+ p+d+  +++++++P+Gl+++++  g++ e +  + w+e++   s + +
  gi|298675463|ref|YP_003727213.1|  48 DLSSQTVSPGDTITVTLNVNNPDDR--IIIDEMIPSGLTLTDSGTGNTAEAGHIK-WVEFSGVSSTTYT 113
                                       233348**************99987..9******************999998877.5555444444444 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 7e-08
                             bMG10  19 sdaklkvGdkvrvrltvttprdleyvaledplPAGlepvnpslgtesesaeeyewleeltefsyreirddrvvffad 95 
                                       s+++++ Gd+++v+l+v+ p+d+  +++++++P+G+ ++n++ +t+++++  +     ++efs ++ + + + + + 
  gi|298675463|ref|YP_003727213.1| 171 SSQTVSPGDTITVTLNVNNPDDR--IIIDEMFPSGWSITNTDGNTSETGHV-K-----WVEFSEVSSTTKTYDIEVP 239
                                       3338**************99987..9**************88766665554.3.....4567777777777777777 PP

                             bMG10  96 ylpkgtytfe 105
                                         ++gty f+
  gi|298675463|ref|YP_003727213.1| 240 MSASGTYNFD 249
                                       7777777775 PP

  == domain 3  score: 21.4 bits;  conditional E-value: 2.8e-07
                             bMG10  19 sdaklkvGdkvrvrltvttprdleyvaledplPAGlepvnpslgtesesaeeyewle 75 
                                       s+++++ Gd+++v+l+v+ p+d+  +++++++P+Gl+++++  g++ e +  + w+e
  gi|298675463|ref|YP_003727213.1| 289 SSQTVSPGDTITVTLNVNNPDDR--IIIDEMIPSGLTLTDSGTGNTAEAGHIK-WVE 342
                                       3338**************99987..9*****************9999988776.433 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.053
                             bMG10  29 vrvrltvttprdleyvaledplPAGlepvnpslgte 64 
                                       +  ++++ ++++ ++  + +++P G+e v +sl  e
  gi|298675463|ref|YP_003727213.1| 413 F--TVSIDVSEEAQNGTVTEMIPEGFECVSTSLPAE 446
                                       4..5667778899999*************9998544 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.7   1.6e-05     0.013       3      88 ..      47     128 ..      45     131 .. 0.80
   2 !   10.3   0.9   0.00084      0.66       3      25 ..     168     190 ..     166     249 .. 0.74
   3 !   16.5   1.1     1e-05     0.008       3      88 ..     286     367 ..     284     369 .. 0.81
   4 ?    5.7   0.0     0.023        18      28      75 ..     421     469 ..     396     514 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.6e-05
                             DUF11   3 KtvdksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsv.gsLeagesatlsftvrv 78 
                                       +  ++++v pGdt+t+tl v N+  +    + +  + P+gl++  + ++ +ta+a      +    +s+t ++ v+v
  gi|298675463|ref|YP_003727213.1|  47 RDLSSQTVSPGDTITVTLNVNNPDDR----IIIDEMIPSGLTLTDSGTG-NTAEAGHIKwVEFSGVSSTTYTYDVEV 118
                                       5567889*************997544....56**********9999999.555555444678889999999999999 PP

                             DUF11  79 trtaasgalt 88 
                                       + +a++g+ +
  gi|298675463|ref|YP_003727213.1| 119 PMSATDGTTY 128
                                       9999887644 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00084
                             DUF11   3 KtvdksevrpGdtvtytltvtNt 25 
                                       +  ++++v pGdt+t+tl v N+
  gi|298675463|ref|YP_003727213.1| 168 RDLSSQTVSPGDTITVTLNVNNP 190
                                       5567889**************97 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 1e-05
                             DUF11   3 KtvdksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsv.gsLeagesatlsftvrv 78 
                                       +  ++++v pGdt+t+tl v N+  +    + +  + P+gl++  + ++ +ta+a      +    +s+t ++ v+v
  gi|298675463|ref|YP_003727213.1| 286 RDLSSQTVSPGDTITVTLNVNNPDDR----IIIDEMIPSGLTLTDSGTG-NTAEAGHIKwVEFSGVSSTTYTYDVEV 357
                                       5567889*************997554....56**********9999999.55555554478889999********** PP

                             DUF11  79 trtaasgalt 88 
                                       +++a++g+ +
  gi|298675463|ref|YP_003727213.1| 358 PNSATDGTTY 367
                                       *999988644 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.023
                             DUF11  28 asangvvvtDtlPaglayvsvsas......qgtasaltsvgsLeagesatlsft 75 
                                         a++ +vt + P+g++ vs s        +g +++++     + +e+  +++t
  gi|298675463|ref|YP_003727213.1| 421 EEAQNGTVTEMIPEGFECVSTSLPaeavdmSGDCNVTF-----NLSETSSFEYT 469
                                       5677889****************954444433333333.....34444444444 PP

>> CtaG_Cox11  Cytochrome c oxidase assembly protein CtaG/Cox11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.049        39      53      89 ..      44      80 ..      31      84 .. 0.83
   2 !    9.4   0.0    0.0013         1      29      85 ..     143     197 ..     117     203 .. 0.80
   3 !    9.9   0.0   0.00088      0.69      30      89 ..     262     319 ..     240     323 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.049
                        CtaG_Cox11 53 efkpeqrslevkpGetalafytaknksdkpiigqavy 89
                                      ++++  +s++v pG+t +++ +++n+ d+ ii   ++
  gi|298675463|ref|YP_003727213.1| 44 DVSRDLSSQTVSPGDTITVTLNVNNPDDRIIIDEMIP 80
                                      566777899*******************999877766 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0013
                        CtaG_Cox11  29 vkvdeertevtveFdadvseklpwefkpeqrslevkpGetalafytaknksdkpiig 85 
                                       +++  e+ +vtv+ +++ +e  p+++++  +s++v pG+t +++ +++n+ d+ ii 
  gi|298675463|ref|YP_003727213.1| 143 TSIMGEQ-QVTVTTNGNGAE-EPMNVSRDLSSQTVSPGDTITVTLNVNNPDDRIIID 197
                                       3455667.599999999876.79****************************998875 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00088
                        CtaG_Cox11  30 kvdeertevtveFdadvseklpwefkpeqrslevkpGetalafytaknksdkpiigqavy 89 
                                       ++  e+ +vtv+ +++ +e  p+++++  +s++v pG+t +++ +++n+ d+ ii   ++
  gi|298675463|ref|YP_003727213.1| 262 SIMGEQ-QVTVTTNGNGAE-EPMNVSRDLSSQTVSPGDTITVTLNVNNPDDRIIIDEMIP 319
                                       445666.599999998876.79*****************************999977766 PP

>> CDC48_2  Cell division protein 48 (CDC48), domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0025         2       8      29 ..      42      64 ..      36      86 .. 0.85
   2 !    7.3   0.0     0.005       3.9       9      29 ..     165     185 ..     158     207 .. 0.85
   3 !    7.4   0.0    0.0048       3.7       9      29 ..     283     303 ..     276     325 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0025
                                      H.HHHCCCTTEEE-TTEEEEECC CS
                           CDC48_2  8 a.ylkrqFlgrpvtkGdlvvfef 29
                                      a  + r + ++ v++Gd+++++ 
  gi|298675463|ref|YP_003727213.1| 42 AqDVSRDLSSQTVSPGDTITVTL 64
                                      44799**************9865 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.005
                                       HHHCCCTTEEE-TTEEEEECC CS
                           CDC48_2   9 ylkrqFlgrpvtkGdlvvfef 29 
                                        + r + ++ v++Gd+++++ 
  gi|298675463|ref|YP_003727213.1| 165 NVSRDLSSQTVSPGDTITVTL 185
                                       68999************9865 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0048
                                       HHHCCCTTEEE-TTEEEEECC CS
                           CDC48_2   9 ylkrqFlgrpvtkGdlvvfef 29 
                                        + r + ++ v++Gd+++++ 
  gi|298675463|ref|YP_003727213.1| 283 NVSRDLSSQTVSPGDTITVTL 303
                                       68999************9865 PP

>> Cohesin  Cohesin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.1    0.0019       1.5       5      28 ..      49      72 ..      45      76 .. 0.83
   2 !    9.1   0.1    0.0019       1.5       5      28 ..     170     193 ..     166     197 .. 0.83
   3 !    9.1   0.1    0.0019       1.5       5      28 ..     288     311 ..     284     315 .. 0.83
   4 ?   -1.7   0.1       4.1   3.2e+03      10      28 ..     407     425 ..     404     431 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0019
                                      ESEEEE-TTSEEEEEEEEESECTT CS
                           Cohesin  5 idkvsakvGdtvtvpvtvsnvskk 28
                                      + + ++ +Gdt+tv+++v+n ++ 
  gi|298675463|ref|YP_003727213.1| 49 LSSQTVSPGDTITVTLNVNNPDDR 72
                                      5677889*************8875 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0019
                                       ESEEEE-TTSEEEEEEEEESECTT CS
                           Cohesin   5 idkvsakvGdtvtvpvtvsnvskk 28 
                                       + + ++ +Gdt+tv+++v+n ++ 
  gi|298675463|ref|YP_003727213.1| 170 LSSQTVSPGDTITVTLNVNNPDDR 193
                                       5677889*************8875 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0019
                                       ESEEEE-TTSEEEEEEEEESECTT CS
                           Cohesin   5 idkvsakvGdtvtvpvtvsnvskk 28 
                                       + + ++ +Gdt+tv+++v+n ++ 
  gi|298675463|ref|YP_003727213.1| 288 LSSQTVSPGDTITVTLNVNNPDDR 311
                                       5677889*************8875 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 4.1
                                       E-TTSEEEEEEEEESECTT CS
                           Cohesin  10 akvGdtvtvpvtvsnvskk 28 
                                       a  G+ +tv + vs+ +++
  gi|298675463|ref|YP_003727213.1| 407 ADIGSDFTVSIDVSEEAQN 425
                                       5679999999999998886 PP

>> Arrestin_C  Arrestin (or S-antigen), C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.026        20      11      33 ..      49      72 ..      44      79 .. 0.80
   2 !    7.3   0.0    0.0076       5.9       3      33 ..     162     193 ..     160     199 .. 0.80
   3 !    7.4   0.0    0.0071       5.5       3      33 ..     280     311 ..     278     318 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.026
                                      ES-SEEETT--EEEEEEEEE.-SS CS
                        Arrestin_C 11 lpkkgyvpGetipvtvkidn.dsk 33
                                      l+++ + pG+ti+vt++++n d +
  gi|298675463|ref|YP_003727213.1| 49 LSSQTVSPGDTITVTLNVNNpDDR 72
                                      788999*************73544 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0076
                                       --EEEEEEES-SEEETT--EEEEEEEEE.-SS CS
                        Arrestin_C   3 gkvsleaslpkkgyvpGetipvtvkidn.dsk 33 
                                       ++++++  l+++ + pG+ti+vt++++n d +
  gi|298675463|ref|YP_003727213.1| 162 EPMNVSRDLSSQTVSPGDTITVTLNVNNpDDR 193
                                       5677888899*****************83444 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0071
                                       --EEEEEEES-SEEETT--EEEEEEEEE.-SS CS
                        Arrestin_C   3 gkvsleaslpkkgyvpGetipvtvkidn.dsk 33 
                                       ++++++  l+++ + pG+ti+vt++++n d +
  gi|298675463|ref|YP_003727213.1| 280 EPMNVSRDLSSQTVSPGDTITVTLNVNNpDDR 311
                                       5677888899*****************73544 PP

>> BatD  Oxygen tolerance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.4   0.00042      0.32       3      80 ..      36     115 ..      34     162 .. 0.74
   2 !   14.3   3.9   1.7e-05     0.013      13     152 ..     167     305 ..     159     321 .. 0.87
   3 ?    0.3   0.1       0.3   2.3e+02      28      76 ..     352     395 ..     346     402 .. 0.71
   4 ?    4.4   0.1     0.018        14      18      83 ..     404     472 ..     388     474 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00042
                              BatD   3 lalaaaaaeftasvdknevevgetfrLtftvngasgepdfsap.slekdfevlsg.....sqssstqiinGksssss 73 
                                       l++aaaa++++  +++++v+ g+t+++t+ vn+ ++   + ++  +++++++             ++++ +   ss+
  gi|298675463|ref|YP_003727213.1|  36 LTSAAAAQDVSRDLSSQTVSPGDTITVTLNVNNPDD--RIIIDeMIPSGLTLTDSgtgntAEAGHIKWVEFSGVSST 110
                                       5789999**************************952..222221444566665443444455566667766666655 PP

                              BatD  74 sktwtyt 80 
                                       +  +ty 
  gi|298675463|ref|YP_003727213.1| 111 T--YTYD 115
                                       5..5554 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.7e-05
                              BatD  13 tasvdknevevgetfrLtftvngasgepdfsap.slekdfevlsg....sqssstqiinGkssssssktwtytLapk 84 
                                       +  +++++v+ g+t+++t+ vn+ +  + + ++  ++++  + ++    s    ++++ +   ss++kt+ + +   
  gi|298675463|ref|YP_003727213.1| 167 SRDLSSQTVSPGDTITVTLNVNNPD--DRIIIDeMFPSGWSITNTdgntSETGHVKWVEFSEVSSTTKTYDIEVPMS 241
                                       556789******************4..3333333788999999999988888999********************** PP

                              BatD  85 keGtltIpaatievdgktyksnpitikVlkseasqsssaisdedlflraevskksvYvqeqvlvtlkl 152
                                        +Gt++     i ++g + +s   + +V    + +++ + ++e++ +  ++s+++v  +  ++vtl +
  gi|298675463|ref|YP_003727213.1| 242 ASGTYNFDGTYILTSGASETSIMGEQQV----TVTTNGNGAEEPMNVSRDLSSQTVSPGDTITVTLNV 305
                                       ****************999998877777....346788889999*********************987 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.3
                              BatD  28 rLtftvngasgepdfsapslekdfevlsgsqssstqiinGksssssskt 76 
                                       +++++v +  +++d +  ++ ++  +l ++qs+ +  i G++s++ s t
  gi|298675463|ref|YP_003727213.1| 352 TYDVEVPN--SATDGTTYNF-DGTYILTTGQSETM--IKGDMSATVSET 395
                                       33333333..4677777788.89999999988888..*******98754 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.018
                              BatD  18 knevevgetfrLtftvngasgepdfsapslekdfevlsg.......sqssstqiinGkssssssktwtytLap 83 
                                       +++  +g  f++++ v++++++  ++ + ++++fe +s+         s     + ++ s++ss  ++ytL++
  gi|298675463|ref|YP_003727213.1| 404 PDKADIGSDFTVSIDVSEEAQNGTVT-EMIPEGFECVSTslpaeavDMSGDC-NVTFNLSETSS--FEYTLMA 472
                                       67778999***********6333333.68999*******9998875555555.67789999888..99**998 PP

>> Peptidase_A4  Peptidase A4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   2.7    0.0031       2.4      85     188 ..      45     154 ..      37     162 .. 0.62
   2 !   11.9   9.6   0.00014      0.11      71     192 ..     147     276 ..     122     285 .. 0.76
   3 !    8.2   1.2     0.002       1.5      85     131 ..     284     330 ..     278     417 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0031
                      Peptidase_A4  85 yavdfsglavsaGDsvtvtvtatsatsgtvtieNlstgqsvtktlsapssklcgqsAeWivE......dfe...sgg 152
                                        + d s+ +vs+GD++tvt++ ++++  +++ e   +g + t + ++++      +  W+ E        +   + +
  gi|298675463|ref|YP_003727213.1|  45 VSRDLSSQTVSPGDTITVTLNVNNPDDRIIIDEMIPSGLTLTDSGTGNT--AEAGHIKWV-EfsgvssT-TytyDVE 117
                                       56788899*****************987777788888888888877755..344555664.22233220.1222112 PP

                      Peptidase_A4 153 .lvplanFgtvtFtdasattsdgksvglsgatiidie 188
                                         +  ++ +t +F ++   ts+ +++++ g + + ++
  gi|298675463|ref|YP_003727213.1| 118 vPMSATDGTTYNFDGTYILTSGASETSIMGEQQVTVT 154
                                       2233555556666666666666656666666555555 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00014
                      Peptidase_A4  71 Geqsydawyewy....P.ayavdfsglavsaGDsvtvtvtatsatsgtvtieNlstgqsvtktlsapssklcgqsAe 142
                                       Geq+++          P + + d s+ +vs+GD++tvt++ ++++  +++ e + +g+s+t+t  ++s    + ++ 
  gi|298675463|ref|YP_003727213.1| 147 GEQQVTVTTNGNgaeePmNVSRDLSSQTVSPGDTITVTLNVNNPDDRIIIDEMFPSGWSITNTDGNTS---ETGHVK 220
                                       55555555555433446788999999*******************88888899**********99988...568999 PP

                      Peptidase_A4 143 WivEdfe.......sgg.lvplanFgtvtFtdasattsdgksvglsgatiidieqngt 192
                                       W+    +       + +  vp+ + gt +F ++   ts+ +++++ g + + +++ng+
  gi|298675463|ref|YP_003727213.1| 221 WVEF--SevssttkTYDiEVPMSASGTYNFDGTYILTSGASETSIMGEQQVTVTTNGN 276
                                       9642..1133455555779******************999999999999988887764 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.002
                      Peptidase_A4  85 yavdfsglavsaGDsvtvtvtatsatsgtvtieNlstgqsvtktlsa 131
                                        + d s+ +vs+GD++tvt++ ++++  +++ e   +g + t + ++
  gi|298675463|ref|YP_003727213.1| 284 VSRDLSSQTVSPGDTITVTLNVNNPDDRIIIDEMIPSGLTLTDSGTG 330
                                       67788999****************99777665666666666666655 PP

>> DUF4784  Domain of unknown function (DUF4784)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.012       9.1      11      44 ..      43      76 ..      39     103 .. 0.84
   2 !    6.4   0.1    0.0047       3.7      16      52 ..     169     205 ..     164     243 .. 0.68
   3 ?    4.4   0.0     0.019        15      16      44 ..     287     315 ..     282     344 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.012
                           DUF4784 11 tnvvlpeagqtfkPGdkvtvsakGfqegDeimld 44
                                      ++v  + ++qt++PGd++tv+ +  + +D i++d
  gi|298675463|ref|YP_003727213.1| 43 QDVSRDLSSQTVSPGDTITVTLNVNNPDDRIIID 76
                                      567777789************9999999999987 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0047
                           DUF4784  16 peagqtfkPGdkvtvsakGfqegDeimldirWplgde 52 
                                       + ++qt++PGd++tv+ +  + +D i++d   p g  
  gi|298675463|ref|YP_003727213.1| 169 DLSSQTVSPGDTITVTLNVNNPDDRIIIDEMFPSGWS 205
                                       5679**********************88765554443 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.019
                           DUF4784  16 peagqtfkPGdkvtvsakGfqegDeimld 44 
                                       + ++qt++PGd++tv+ +  + +D i++d
  gi|298675463|ref|YP_003727213.1| 287 DLSSQTVSPGDTITVTLNVNNPDDRIIID 315
                                       5679************9999999999987 PP

>> DUF4334  Domain of unknown function (DUF4334)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0      0.03        24       4      21 ..      98     115 ..      95     121 .. 0.84
   2 ?    0.9   0.0      0.56   4.4e+02       4      21 ..     218     235 ..     215     241 .. 0.84
   3 ?    4.6   0.0     0.041        32       4      21 ..     337     354 ..     334     358 .. 0.88
   4 ?   -1.3   0.0       2.7   2.1e+03      36      54 ..     469     487 ..     467     488 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.03
                                       EEEEEEETTEEEEEEEES CS
                           DUF4334   4 rLrevefrGvvsAtmvYD 21 
                                        ++ vef Gv s+t  YD
  gi|298675463|ref|YP_003727213.1|  98 HIKWVEFSGVSSTTYTYD 115
                                       57889************* PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.56
                                       EEEEEEETTEEEEEEEES CS
                           DUF4334   4 rLrevefrGvvsAtmvYD 21 
                                        ++ vef +v s+t  YD
  gi|298675463|ref|YP_003727213.1| 218 HVKWVEFSEVSSTTKTYD 235
                                       67889************* PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.041
                                       EEEEEEETTEEEEEEEES CS
                           DUF4334   4 rLrevefrGvvsAtmvYD 21 
                                        ++ vef Gv s+t  YD
  gi|298675463|ref|YP_003727213.1| 337 HIKWVEFSGVSSTTYTYD 354
                                       57889************9 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 2.7
                                       EEEEEEEETT..-SS-EEE CS
                           DUF4334  36 tvlGamdgkgledarpyyF 54 
                                       t++  md +  + +++y+F
  gi|298675463|ref|YP_003727213.1| 469 TLMAPMDVRPCDGSQTYMF 487
                                       899*******999999998 PP

>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.092        72      45      64 ..      52      71 ..      42      79 .. 0.85
   2 ?   -2.5   0.0       7.9   6.2e+03      53      69 ..     110     126 ..     108     135 .. 0.80
   3 ?    3.5   0.0      0.11        86      45      64 ..     173     192 ..     164     196 .. 0.85
   4 ?    6.8   0.4      0.01         8       3      45 ..     177     215 ..     175     251 .. 0.73
   5 ?    3.7   0.0     0.092        72      45      64 ..     291     310 ..     266     318 .. 0.89
   6 ?   -1.0   0.0       2.8   2.2e+03      53      69 ..     349     365 ..     347     375 .. 0.83
   7 ?    0.4   0.0         1   7.8e+02      12      44 ..     414     447 ..     391     461 .. 0.58

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.092
                       NPCBM_assoc 45 aslapGetveatvkVtppag 64
                                      +++ pG+t ++t++V  p++
  gi|298675463|ref|YP_003727213.1| 52 QTVSPGDTITVTLNVNNPDD 71
                                      5899***********99976 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7.9
                       NPCBM_assoc  53 veatvkVtppagaaaGd 69 
                                       ++ t +V +p +a  G+
  gi|298675463|ref|YP_003727213.1| 110 TTYTYDVEVPMSATDGT 126
                                       67889999999998886 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.11
                       NPCBM_assoc  45 aslapGetveatvkVtppag 64 
                                       +++ pG+t ++t++V  p++
  gi|298675463|ref|YP_003727213.1| 173 QTVSPGDTITVTLNVNNPDD 192
                                       5899***********99975 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.01
                       NPCBM_assoc   3 pGetvtltltvtndgtaaatnvslslslPeGWtvvevspasaa 45 
                                       pG+t t+tl v      +  ++ ++  +P+GW+++++++++ +
  gi|298675463|ref|YP_003727213.1| 177 PGDTITVTLNVN----NPDDRIIIDEMFPSGWSITNTDGNTSE 215
                                       555555555554....577889999999*********999876 PP

  == domain 5  score: 3.7 bits;  conditional E-value: 0.092
                       NPCBM_assoc  45 aslapGetveatvkVtppag 64 
                                       +++ pG+t ++t++V  p++
  gi|298675463|ref|YP_003727213.1| 291 QTVSPGDTITVTLNVNNPDD 310
                                       5899***********99976 PP

  == domain 6  score: -1.0 bits;  conditional E-value: 2.8
                       NPCBM_assoc  53 veatvkVtppagaaaGd 69 
                                       ++ t +V +p++a  G+
  gi|298675463|ref|YP_003727213.1| 349 TTYTYDVEVPNSATDGT 365
                                       678999******99986 PP

  == domain 7  score: 0.4 bits;  conditional E-value: 1
                       NPCBM_assoc  12 tvtndgtaaatnvslslslPeGWt.vvevspasa 44 
                                       tv+ d ++ a+n+ ++   PeG + v+++ pa+a
  gi|298675463|ref|YP_003727213.1| 414 TVSIDVSEEAQNGTVTEMIPEGFEcVSTSLPAEA 447
                                       3444445555666666666666664444555555 PP

>> Big_8  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.046        36      16      33 ..      49      67 ..      39     128 .. 0.70
   2 ?    6.8   0.1    0.0094       7.3      10      61 ..     164     219 ..     157     265 .. 0.64
   3 ?    6.2   0.2     0.014        11      10      33 ..     282     306 ..     275     370 .. 0.61
   4 ?   -1.5   0.0       3.6   2.8e+03      52      82 ..     467     497 ..     445     507 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.046
                             Big_8 16 v.gksvkeGDyftitlpdn 33
                                      + +++v +GD++t+tl+ n
  gi|298675463|ref|YP_003727213.1| 49 LsSQTVSPGDTITVTLNVN 67
                                      45789***********765 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0094
                             Big_8  10 lkadfsv.gksvkeGDyftitlpdnlkfngi...stsektfdikdsngnviakakv 61 
                                       ++++ ++ +++v +GD++t+tl+ n   + i   ++ ++   i++ +gn+  +++v
  gi|298675463|ref|YP_003727213.1| 164 MNVSRDLsSQTVSPGDTITVTLNVNNPDDRIiidEMFPSGWSITNTDGNTSETGHV 219
                                       55555666899***********8653332221112333334566666777777666 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.014
                             Big_8  10 lkadfsv.gksvkeGDyftitlpdn 33 
                                       ++++ ++ +++v +GD++t+tl+ n
  gi|298675463|ref|YP_003727213.1| 282 MNVSRDLsSQTVSPGDTITVTLNVN 306
                                       55555666899***********865 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 3.6
                             Big_8  52 ngnviakakvdpgtgtirytFTdyvenkenv 82 
                                       + +++a  +v p +g+ +y F   v+n +  
  gi|298675463|ref|YP_003727213.1| 467 EYTLMAPMDVRPCDGSQTYMFDGTVSNSDTA 497
                                       4567788888888888899998888887755 PP

>> WYL  WYL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.7   1.3e+03      87     116 ..      52      80 ..      31     104 .. 0.62
   2 ?    2.9   0.0      0.13     1e+02      87     128 ..     173     214 ..     147     231 .. 0.71
   3 ?   -0.6   0.0       1.5   1.2e+03      87     115 ..     291     318 ..     258     341 .. 0.59
   4 ?    6.0   0.0     0.015        11      26      55 ..     587     615 ..     571     620 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.7
                               WYL  87 ksfgvfkspvevkvrfspeaarrvrerrfp 116
                                       +     + +++v++ ++++  r+++++ +p
  gi|298675463|ref|YP_003727213.1|  52 QTVSPGD-TITVTLNVNNPDDRIIIDEMIP 80 
                                       2222222.7777777777777777666655 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.13
                               WYL  87 ksfgvfkspvevkvrfspeaarrvrerrfp.dqkieeedddgs 128
                                       +     + +++v++ ++++  r+++++ fp  + i+++d++ s
  gi|298675463|ref|YP_003727213.1| 173 QTVSPGD-TITVTLNVNNPDDRIIIDEMFPsGWSITNTDGNTS 214
                                       3333333.9**************99999974788888777655 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.5
                               WYL  87 ksfgvfkspvevkvrfspeaarrvrerrf 115
                                       +     + +++v++ ++++  r+++++ +
  gi|298675463|ref|YP_003727213.1| 291 QTVSPGD-TITVTLNVNNPDDRIIIDEMI 318
                                       2222222.666666666666666666555 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.015
                               WYL  26 egeertvePyglvlkngrwYLvaydekrde 55 
                                       e++e  v+P  + + +g+wY v+y   +++
  gi|298675463|ref|YP_003727213.1| 587 EPSEELVSPASMSVEAGNWYAVGYTG-TQD 615
                                       456889*****************864.444 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.5   1.1e+03      44      52 ..      61      69 ..      25     126 .. 0.59
   2 ?    9.3   0.2    0.0015       1.2      45      94 ..     183     252 ..     136     258 .. 0.70
   3 ?   -0.2   0.0       1.4   1.1e+03      42      84 ..     266     307 ..     257     321 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.5
                      Cupredoxin_1 44 kvklkiknk 52
                                       v+l+++n 
  gi|298675463|ref|YP_003727213.1| 61 TVTLNVNNP 69
                                      233444444 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0015
                      Cupredoxin_1  45 vklkiknkdkt.......peefesed.............lgeekvlapgktttitiaplkpGeYeftcdm 94 
                                       v+l+++n d++       p+ +++++             +++++v  + kt+ i++++   G+Y+f + +
  gi|298675463|ref|YP_003727213.1| 183 VTLNVNNPDDRiiidemfPSGWSITNtdgntsetghvkwVEFSEVSSTTKTYDIEVPMSASGTYNFDGTY 252
                                       445555555555555555233333333333333333335999************************8766 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1.4
                      Cupredoxin_1  42 gekvklkiknkdktpeefesedlgeekvlapgktttitiaplk 84 
                                       +++v+++ + ++++    +s+dl+  +++ pg+t t+t++  +
  gi|298675463|ref|YP_003727213.1| 266 EQQVTVTTNGNGAEEPMNVSRDLSS-QTVSPGDTITVTLNVNN 307
                                       5556666666666655566777776.78888888888876555 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.025        20     215     235 ..      71      91 ..      61     102 .. 0.83
   2 ?    0.7   0.0      0.34   2.6e+02     215     236 ..     192     213 ..     187     228 .. 0.80
   3 ?    4.3   0.0     0.027        21     215     235 ..     310     330 ..     304     341 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.025
                                       --GGGTTTGGGT--GGGSSSS CS
                              MipZ 215 erviyrelfpsGltlldlkel 235
                                       +r+i  e+ psGltl d  + 
  gi|298675463|ref|YP_003727213.1|  71 DRIIIDEMIPSGLTLTDSGTG 91 
                                       8***************98764 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.34
                                       --GGGTTTGGGT--GGGSSSS- CS
                              MipZ 215 erviyrelfpsGltlldlkelg 236
                                       +r+i  e+fpsG  + + + ++
  gi|298675463|ref|YP_003727213.1| 192 DRIIIDEMFPSGWSITNTDGNT 213
                                       8***********9998776655 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.027
                                       --GGGTTTGGGT--GGGSSSS CS
                              MipZ 215 erviyrelfpsGltlldlkel 235
                                       +r+i  e+ psGltl d  + 
  gi|298675463|ref|YP_003727213.1| 310 DRIIIDEMIPSGLTLTDSGTG 330
                                       8***************98764 PP

>> Rtt106  Histone chaperone Rttp106-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.17   1.3e+02      36      65 ..      98     130 ..      82     138 .. 0.82
   2 ?    4.9   0.0     0.044        35      36      65 ..     218     248 ..     205     268 .. 0.85
   3 ?    1.2   0.0      0.63   4.9e+02      36      58 ..     337     359 ..     322     374 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.17
                            Rtt106  36 diesvsfeRvsvtsrtfdlvvelkk...eeveF 65 
                                       +i+ v+f+ vs+t+ t d++v ++    ++++F
  gi|298675463|ref|YP_003727213.1|  98 HIKWVEFSGVSSTTYTYDVEVPMSAtdgTTYNF 130
                                       5999****99**********9994444466666 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.044
                            Rtt106  36 diesvsfeRvsvtsrtfdlvvelkk.eeveF 65 
                                       +++ v+f+ vs+t++t d++v ++   +++F
  gi|298675463|ref|YP_003727213.1| 218 HVKWVEFSEVSSTTKTYDIEVPMSAsGTYNF 248
                                       5889*****************9954455555 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.63
                            Rtt106  36 diesvsfeRvsvtsrtfdlvvel 58 
                                       +i+ v+f+ vs+t+ t d++v  
  gi|298675463|ref|YP_003727213.1| 337 HIKWVEFSGVSSTTYTYDVEVPN 359
                                       5999****999999999998865 PP

>> MYEOV2  Myeloma-overexpressed-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       1.3     1e+03       5      15 ..      73      83 ..      70      95 .. 0.81
   2 ?    6.3   0.0     0.017        13       5      29 ..     194     217 ..     191     228 .. 0.82
   3 ?    0.3   0.0       1.3     1e+03       5      15 ..     312     322 ..     309     334 .. 0.81
   4 ?   -1.4   0.0       4.4   3.4e+03       8      16 ..     429     437 ..     427     455 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.3
                            MYEOV2  5 vaaDeMfpEGa 15
                                      +++DeM+p G 
  gi|298675463|ref|YP_003727213.1| 73 IIIDEMIPSGL 83
                                      789*****996 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.017
                            MYEOV2   5 vaaDeMfpEGagpyvdldeaggssg 29 
                                       +++DeMfp G + + + d +++ +g
  gi|298675463|ref|YP_003727213.1| 194 IIIDEMFPSGWS-ITNTDGNTSETG 217
                                       789*******98.888888888776 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.3
                            MYEOV2   5 vaaDeMfpEGa 15 
                                       +++DeM+p G 
  gi|298675463|ref|YP_003727213.1| 312 IIIDEMIPSGL 322
                                       789*****996 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 4.4
                            MYEOV2   8 DeMfpEGag 16 
                                        eM+pEG +
  gi|298675463|ref|YP_003727213.1| 429 TEMIPEGFE 437
                                       69****965 PP

>> DUF4307  Domain of unknown function (DUF4307)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00023      0.18       8      58 ..      20      71 ..      15      74 .. 0.80
   2 ?   -0.2   0.1       1.1   8.7e+02      35      85 ..     100     156 ..      84     173 .. 0.63
   3 ?    0.1   0.1      0.89   6.9e+02      31      58 ..     165     192 ..     151     194 .. 0.82
   4 ?    1.3   0.5      0.37   2.9e+02      29      88 ..     214     277 ..     202     302 .. 0.74
   5 ?    0.1   0.1      0.89     7e+02      31      58 ..     283     310 ..     269     312 .. 0.82
   6 ?   -2.3   0.0       4.9   3.8e+03      35      57 ..     339     361 ..     327     367 .. 0.64
   7 ?   -2.3   0.1       5.1     4e+03      89     107 ..     410     428 ..     379     430 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00023
                           DUF4307  8 llvvlvvvalalvawigysq.gsadvsaevvgfevvddstvevtfeVtrddg 58
                                      l ++ + ++l+++a  ++s  +++dvs  + + +v   +t++vt++V+ +d+
  gi|298675463|ref|YP_003727213.1| 20 LKIIGITALLLIMAISLTSAaAAQDVSRDLSSQTVSPGDTITVTLNVNNPDD 71
                                      44555666666666677777799*************************9997 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.1
                           DUF4307  35 evvgfevvddstvevtfeVtrddgs......pavCiVrAldedgaevGrrevlvpag 85 
                                       + v+f+ v+ +t + ++eV +++++      +++ i+++ +++ +  G+++v+v  +
  gi|298675463|ref|YP_003727213.1| 100 KWVEFSGVSSTTYTYDVEVPMSATDgttynfDGTYILTSGASETSIMGEQQVTVTTN 156
                                       556777777777777777766554431111223446666667777777777777655 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.89
                           DUF4307  31 dvsaevvgfevvddstvevtfeVtrddg 58 
                                       +vs  + + +v   +t++vt++V+ +d+
  gi|298675463|ref|YP_003727213.1| 165 NVSRDLSSQTVSPGDTITVTLNVNNPDD 192
                                       56777778889999**********9987 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.37
                           DUF4307  29 sadvsaevvgfevvddstvevtfeVtrddgs....pavCiVrAldedgaevGrrevlvpagder 88 
                                       s++ + + v+f+ v+ +t + ++eV ++++     +++ i+++ +++ +  G+++v+v  ++++
  gi|298675463|ref|YP_003727213.1| 214 SETGHVKWVEFSEVSSTTKTYDIEVPMSASGtynfDGTYILTSGASETSIMGEQQVTVTTNGNG 277
                                       5555677789999999999999999888765344668889999999999999999999866433 PP

  == domain 5  score: 0.1 bits;  conditional E-value: 0.89
                           DUF4307  31 dvsaevvgfevvddstvevtfeVtrddg 58 
                                       +vs  + + +v   +t++vt++V+ +d+
  gi|298675463|ref|YP_003727213.1| 283 NVSRDLSSQTVSPGDTITVTLNVNNPDD 310
                                       56777778889999**********9987 PP

  == domain 6  score: -2.3 bits;  conditional E-value: 4.9
                           DUF4307  35 evvgfevvddstvevtfeVtrdd 57 
                                       + v+f+ v+ +t + ++eV  ++
  gi|298675463|ref|YP_003727213.1| 339 KWVEFSGVSSTTYTYDVEVPNSA 361
                                       55667777777777776665544 PP

  == domain 7  score: -2.3 bits;  conditional E-value: 5.1
                           DUF4307  89 tvrvtvtvrTtaravtgev 107
                                         ++tv++  +++a  g+v
  gi|298675463|ref|YP_003727213.1| 410 GSDFTVSIDVSEEAQNGTV 428
                                       4456777777777777776 PP

>> Big_3  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.8     0.012       9.5      39      61 ..     137     161 ..     105     167 .. 0.71
   2 ?    0.9   0.1      0.73   5.7e+02      19      44 ..     208     235 ..     207     253 .. 0.76
   3 ?    6.0   0.2     0.019        15      40      61 ..     256     279 ..     246     285 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.012
                             Big_3  39 vsgsvdstkaGeytvtvtykg..vs 61 
                                        sg+  ++  Ge++vtvt +g  ++
  gi|298675463|ref|YP_003727213.1| 137 TSGASETSIMGEQQVTVTTNGngAE 161
                                       466999999**********995555 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.73
                             Big_3  19 lfvsatykdGdae.vpfddvevsg.svd 44 
                                       +++  t ++G+++ v+f++v+ +  ++d
  gi|298675463|ref|YP_003727213.1| 208 NTDGNTSETGHVKwVEFSEVSSTTkTYD 235
                                       56788999**********9988877554 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.019
                             Big_3  40 sgsvdstkaGeytvtvtykg..vs 61 
                                       sg+  ++  Ge++vtvt +g  ++
  gi|298675463|ref|YP_003727213.1| 256 SGASETSIMGEQQVTVTTNGngAE 279
                                       557789999*********995555 PP

>> fn3_5  Fn3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.81   6.3e+02      58      84 ..      44      70 ..      32      80 .. 0.79
   2 ?    7.5   0.4    0.0083       6.5      20      84 ..     122     191 ..     102     200 .. 0.72
   3 ?    7.6   0.3    0.0079       6.2      24      84 ..     244     309 ..     212     321 .. 0.68
   4 ?    1.7   0.4       0.5   3.9e+02       7      87 ..     348     424 ..     341     436 .. 0.45

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.81
                             fn3_5 58 altfetskvtvpAnssktvtvtldlps 84
                                       ++ + s+ tv ++ + tvt++++ p+
  gi|298675463|ref|YP_003727213.1| 44 DVSRDLSSQTVSPGDTITVTLNVNNPD 70
                                      566677788999999999999988765 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0083
                             fn3_5  20 snkaltykvsandvlTdladkeegklilkaaspeike.......aaltfetskvtvpAnssktvtvtldlps 84 
                                        +   ty+++ +  lT+ a   e++ +++++++  ++        +++ + s+ tv ++ + tvt++++ p+
  gi|298675463|ref|YP_003727213.1| 122 ATDGTTYNFDGTYILTSGA--SETSIMGEQQVTVTTNgngaeepMNVSRDLSSQTVSPGDTITVTLNVNNPD 191
                                       4555677777776666666..666666666665555566777789****************99999998765 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0079
                             fn3_5  24 ltykvsandvlTdladkeegklilkaaspeike.......aaltfetskvtvpAnssktvtvtldlps 84 
                                        ty+++ +  lT+ a   e++ +++++++  ++        +++ + s+ tv ++ + tvt++++ p+
  gi|298675463|ref|YP_003727213.1| 244 GTYNFDGTYILTSGA--SETSIMGEQQVTVTTNgngaeepMNVSRDLSSQTVSPGDTITVTLNVNNPD 309
                                       455555554555554..455555555444444355555679****************99999998765 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.5
                             fn3_5   7 gdkfsftltlkNtsnkaltykvsandvlTdladkeegklilkaaspeikeaaltfetskvtvpAnssktvtvtldlp 83 
                                       +++ + ++++ N  +   ty+++ +  lT+     e+  i+  +s + +e+    +t+ +  +A+   ++tv +d+ 
  gi|298675463|ref|YP_003727213.1| 348 STTYTYDVEVPNSATDGTTYNFDGTYILTTGQ--SETM-IKGDMSATVSETD-VSATRDLPDKADIGSDFTVSIDVS 420
                                       44455556666666666666666664444333..2222.2222222222222.222334444455556677777775 PP

                             fn3_5  84 sdak 87 
                                       ++a+
  gi|298675463|ref|YP_003727213.1| 421 EEAQ 424
                                       4443 PP

>> LRR_adjacent  LRR adjacent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.4    0.0063       4.9      16      51 ..      95     133 ..      84     135 .. 0.76
   2 ?    1.4   0.8      0.47   3.6e+02      16      51 ..     215     251 ..     206     253 .. 0.75
   3 ?    5.8   0.6      0.02        15      16      51 ..     334     372 ..     323     374 .. 0.73
   4 ?   -1.8   0.0       4.8   3.7e+03      23      52 ..     459     491 ..     453     492 .. 0.53

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0063
                                       ETTEEEEE-SST-SEEEEEEEEEEEETTE...EEEEEEE CS
                      LRR_adjacent  16 adpnitWnlesttsevsYtFsqkitigki...tatfsGt 51 
                                       ++++i+W   s  s++ Yt++  +++ ++   t +f+Gt
  gi|298675463|ref|YP_003727213.1|  95 EAGHIKWVEFSGVSSTTYTYDVEVPMSATdgtTYNFDGT 133
                                       5799***99999************998541114456665 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.47
                                       ETTEEEE.E-SST-SEEEEEEEEEEEET.TEEEEEEEE CS
                      LRR_adjacent  16 adpnitW.nlesttsevsYtFsqkitig.kitatfsGt 51 
                                       + ++++W +  +++s ++ t++  +++  ++t +f+Gt
  gi|298675463|ref|YP_003727213.1| 215 ETGHVKWvEFSEVSSTTK-TYDIEVPMSaSGTYNFDGT 251
                                       67899**66666665554.8888888876899999998 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.02
                                       ETTEEEEE-SST-SEEEEEEEEEEEET.TE..EEEEEEE CS
                      LRR_adjacent  16 adpnitWnlesttsevsYtFsqkitig.ki..tatfsGt 51 
                                       ++++i+W   s  s++ Yt++  ++   ++  t +f+Gt
  gi|298675463|ref|YP_003727213.1| 334 EAGHIKWVEFSGVSSTTYTYDVEVPNSaTDgtTYNFDGT 372
                                       5799***99999*********999766333113445665 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 4.8
                                       E-SST-SEEEEEEEEEEEE....TTEEEEEEEEE CS
                      LRR_adjacent  23 nlesttsevsYtFsqkiti....gkitatfsGtV 52 
                                       nl + ts+ +Yt   +  +    g++t  f+GtV
  gi|298675463|ref|YP_003727213.1| 459 NLSE-TSSFEYTLMAPMDVrpcdGSQTYMFDGTV 491
                                       5544.34455555555554222246777788887 PP

>> PilA4  Pilin A4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.5     0.037        29      56      79 ..     109     135 ..      83     138 .. 0.69
   2 ?    6.9   0.3      0.01         8      54      79 ..     228     253 ..     200     256 .. 0.78
   3 ?    4.5   0.8      0.06        47      55      79 ..     347     374 ..     321     377 .. 0.70
   4 ?   -1.2   0.1       3.5   2.7e+03      17      65 ..     422     473 ..     419     493 .. 0.58

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.037
                                       TSS..EEEEE...EESSSSSSEEEEET CS
                             PilA4  56 tnkd.ytvtat..svtGktftydgael 79 
                                        +++ y v+++  + +G+t+++dg+ +
  gi|298675463|ref|YP_003727213.1| 109 STTYtYDVEVPmsATDGTTYNFDGTYI 135
                                       3344477777511579********865 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.01
                                       STTSS.EEEEE.EESSSSSSEEEEET CS
                             PilA4  54 gttnkdytvtatsvtGktftydgael 79 
                                         t+k+y ++++++   t+++dg+ +
  gi|298675463|ref|YP_003727213.1| 228 SSTTKTYDIEVPMSASGTYNFDGTYI 253
                                       345566*****************865 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.06
                                       TTSS..EEEEE...EESSSSSSEEEEET CS
                             PilA4  55 ttnkd.ytvtat..svtGktftydgael 79 
                                         +++ y v+++  + +G+t+++dg+ +
  gi|298675463|ref|YP_003727213.1| 347 SSTTYtYDVEVPnsATDGTTYNFDGTYI 374
                                       34444488888622569********976 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 3.5
                                       HHTS-TTT----TTEEGCCTS..SS--TTEEEEEEEESTTSS....EEEEE. CS
                             PilA4  17 EakRdpvtgaLptetsCtalaektalPasvtsctviygttnkd...ytvtat 65 
                                       Ea+  +vt   p   +C +++  ++      +c+v+++  +++   yt  a+
  gi|298675463|ref|YP_003727213.1| 422 EAQNGTVTEMIPEGFECVSTSLPAEAVDMSGDCNVTFNLSETSsfeYTLMAP 473
                                       6777778888888888888873333333334677766544443324555554 PP

>> PASTA  PASTA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1      0.14   1.1e+02      49      62 ..      52      65 ..      42      66 .. 0.88
   2 ?    2.5   0.2      0.17   1.3e+02      49      62 ..     173     186 ..     171     187 .. 0.86
   3 ?    2.5   0.2      0.17   1.3e+02      49      62 ..     291     304 ..     289     305 .. 0.86
   4 ?   -2.5   0.0       6.1   4.8e+03      31      46 ..     419     434 ..     413     444 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.14
                                      SEECTTS-EEEEEE CS
                             PASTA 49 tevskgskvtltvs 62
                                      ++vs+g+++t+t++
  gi|298675463|ref|YP_003727213.1| 52 QTVSPGDTITVTLN 65
                                      689********985 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.17
                                       SEECTTS-EEEEEE CS
                             PASTA  49 tevskgskvtltvs 62 
                                       ++vs+g+++t+t++
  gi|298675463|ref|YP_003727213.1| 173 QTVSPGDTITVTLN 186
                                       689********985 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.17
                                       SEECTTS-EEEEEE CS
                             PASTA  49 tevskgskvtltvs 62 
                                       ++vs+g+++t+t++
  gi|298675463|ref|YP_003727213.1| 291 QTVSPGDTITVTLN 304
                                       689********985 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 6.1
                                       ECTCCGTTBEEEECS- CS
                             PASTA  31 tsddvpeGtVisQsPe 46 
                                       +s++   GtV++ +Pe
  gi|298675463|ref|YP_003727213.1| 419 VSEEAQNGTVTEMIPE 434
                                       5667778999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (678 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.43
# Mc/sec: 4725.40
//
Query:       gi|298675464|ref|YP_003727214.1|  [L=745]
Description: hypothetical protein Metev_1571 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0017   18.6   1.0         15    6.0   0.0    5.0  6  SporV_AA    Stage V sporulation protein AA
  ------ inclusion threshold ------
      0.031   13.8  13.6       0.15   11.6   0.0    4.9  5  EF-hand_5   EF hand
      0.054   13.9   9.4      0.098   13.1   0.0    4.6  5  EF-hand_7   EF-hand domain pair
       0.29   10.8   0.0       0.29   10.8   0.0    5.6  7  EF-hand_1   EF hand
        1.1    9.3   0.0        1.1    9.3   0.0    6.9  9  EF-hand_6   EF-hand domain


Domain annotation for each model (and alignments):
>> SporV_AA  Stage V sporulation protein AA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.5   5.5e+03      61      81 ..     114     134 ..     113     135 .. 0.89
   2 ?   -1.1   0.0      0.68   2.4e+03       4      25 ..     139     160 ..     137     170 .. 0.86
   3 ?    0.2   0.0      0.27   9.7e+02       2      25 ..     230     253 ..     229     270 .. 0.83
   4 ?    0.7   0.0      0.19     7e+02       3      34 ..     298     329 ..     296     332 .. 0.89
   5 ?    4.1   0.0     0.017        60       3      23 ..     368     388 ..     366     391 .. 0.93
   6 !    6.0   0.0    0.0042        15       2      25 ..     554     577 ..     553     591 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.5
                          SporV_AA  61 vieaIkkeypnvevenlGetd 81 
                                       v+e+I + ++ ++++  G+ d
  gi|298675464|ref|YP_003727214.1| 114 VVEVIDEPFKYMDINDNGQYD 134
                                       89************9999876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.68
                          SporV_AA   4 vYikldqnvevkkkeVtlgdva 25 
                                       vY+ +++  +++  +++l dv 
  gi|298675464|ref|YP_003727214.1| 139 VYVDVNNDSTITTGDIRLTDVP 160
                                       99****************9995 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.27
                          SporV_AA   2 etvYikldqnvevkkkeVtlgdva 25 
                                       +++Yik   n    ++ Vt++dv 
  gi|298675464|ref|YP_003727214.1| 230 DKLYIKDTTNSWWFEDVVTINDVR 253
                                       789*******************95 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.19
                          SporV_AA   3 tvYikldqnvevkkkeVtlgdvaevycsdkkv 34 
                                       ++Y+ +d+  +v+  +V+l  v + y  + kv
  gi|298675464|ref|YP_003727214.1| 298 EIYMDMDNDGKVSVGDVRLTAVSTTYEPNTKV 329
                                       69*******************99999888876 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.017
                          SporV_AA   3 tvYikldqnvevkkkeVtlgd 23 
                                        vYi +d+n ev++ +V+l d
  gi|298675464|ref|YP_003727214.1| 368 PVYIDMDDNGEVSDGDVRLTD 388
                                       59*****************98 PP

  == domain 6  score: 6.0 bits;  conditional E-value: 0.0042
                          SporV_AA   2 etvYikldqnvevkkkeVtlgdva 25 
                                       ++vYi +d + ev+  +V+l dva
  gi|298675464|ref|YP_003727214.1| 554 DNVYIDMDASGEVTIGDVRLTDVA 577
                                       79*********************8 PP

>> EF-hand_5  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1         1   3.6e+03       5      14 ..     122     131 ..     121     132 .. 0.89
   2 ?    7.7   0.6    0.0007       2.5       8      18 ..     301     311 ..     300     313 .. 0.91
   3 ?   -1.4   0.5      0.55     2e+03       8      17 ..     371     380 ..     370     381 .. 0.89
   4 ?   -0.7   0.0      0.33   1.2e+03       8      17 ..     558     567 ..     557     569 .. 0.88
   5 ?   11.6   0.0   4.1e-05      0.15       6      22 ..     698     714 ..     698     717 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1
                                       HHHH-SS-SS CS
                         EF-hand_5   5 FqaiDlNgDG 14 
                                       F+ +D N  G
  gi|298675464|ref|YP_003727214.1| 122 FKYMDINDNG 131
                                       999****998 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0007
                                       H-SS-SSCE-H CS
                         EF-hand_5   8 iDlNgDGkIsk 18 
                                       +D+++DGk+s+
  gi|298675464|ref|YP_003727214.1| 301 MDMDNDGKVSV 311
                                       8********96 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.55
                                       H-SS-SSCE- CS
                         EF-hand_5   8 iDlNgDGkIs 17 
                                       iD++  G +s
  gi|298675464|ref|YP_003727214.1| 371 IDMDDNGEVS 380
                                       8******998 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 0.33
                                       H-SS-SSCE- CS
                         EF-hand_5   8 iDlNgDGkIs 17 
                                       iD++ +G ++
  gi|298675464|ref|YP_003727214.1| 558 IDMDASGEVT 567
                                       9******997 PP

  == domain 5  score: 11.6 bits;  conditional E-value: 4.1e-05
                                       HHH-SS-SSCE-HHHHH CS
                         EF-hand_5   6 qaiDlNgDGkIskeELk 22 
                                       +++D+++ G Is+ EL 
  gi|298675464|ref|YP_003727214.1| 698 NQFDADQNGVISAGELS 714
                                       69*************96 PP

>> EF-hand_7  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1      0.12   4.1e+02      44      60 ..     116     132 ..      69     137 .. 0.69
   2 ?   -2.0   0.1       1.4   5.1e+03      11      25 ..     141     155 ..     140     158 .. 0.79
   3 ?    1.4   0.0      0.13   4.6e+02      11      25 ..     301     315 ..     299     337 .. 0.76
   4 ?   -1.5   0.2         1   3.7e+03      12      23 ..     543     554 ..     530     607 .. 0.74
   5 ?   13.1   0.0   2.7e-05     0.098       8      47 ..     697     735 ..     694     738 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.12
                         EF-hand_7  44 eelellfkefDtdkdGv 60 
                                       e +++ fk +D +++G+
  gi|298675464|ref|YP_003727214.1| 116 EVIDEPFKYMDINDNGQ 132
                                       668999********996 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.4
                         EF-hand_7  11 lDtdgdgyldkeell 25 
                                        D+++d  ++  +++
  gi|298675464|ref|YP_003727214.1| 141 VDVNNDSTITTGDIR 155
                                       588999999888876 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.13
                         EF-hand_7  11 lDtdgdgyldkeell 25 
                                       +D d+dg++++ +++
  gi|298675464|ref|YP_003727214.1| 301 MDMDNDGKVSVGDVR 315
                                       577888888888866 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 1
                         EF-hand_7  12 Dtdgdgyldkee 23 
                                       D++++g+ d e+
  gi|298675464|ref|YP_003727214.1| 543 DRNDNGMFDSED 554
                                       555555555544 PP

  == domain 5  score: 13.1 bits;  conditional E-value: 2.7e-05
                         EF-hand_7   8 FkelDtdgdgyldkeellrllrkifqgagegsklsdeele 47 
                                       ++++D d++g ++  el +++ ++++g+  gs+ls+  ++
  gi|298675464|ref|YP_003727214.1| 697 YNQFDADQNGVISAGELSSAIDAFYAGNLSGSELSE-VID 735
                                       689************************988888764.555 PP

>> EF-hand_1  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.3      0.94   3.4e+03       6      16 ..     122     132 ..     122     132 .. 0.91
   2 ?    0.8   0.1      0.13   4.6e+02       9      21 ..     141     153 ..     140     156 .. 0.83
   3 ?    5.9   0.1     0.003        11       9      21 ..     301     313 ..     300     317 .. 0.85
   4 ?   -3.7   1.0       3.4   1.2e+04       9      18 ..     371     380 ..     370     384 .. 0.83
   5 ?   -3.0   0.7       2.1   7.5e+03       2      20 ..     535     553 ..     534     554 .. 0.77
   6 ?   -1.6   0.0      0.72   2.6e+03       9      21 ..     558     570 ..     557     573 .. 0.83
   7 ?   10.8   0.0   8.2e-05      0.29       7      26 ..     698     717 ..     697     720 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.94
                                       HHHHTTTSSSE CS
                         EF-hand_1   6 FrefDkDgdGk 16 
                                       F+ +D + +G+
  gi|298675464|ref|YP_003727214.1| 122 FKYMDINDNGQ 132
                                       899*****996 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.13
                                       HTTTSSSEEEHHH CS
                         EF-hand_1   9 fDkDgdGkIdfeE 21 
                                       +D+++d +I+  +
  gi|298675464|ref|YP_003727214.1| 141 VDVNNDSTITTGD 153
                                       7********9765 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.003
                                       HTTTSSSEEEHHH CS
                         EF-hand_1   9 fDkDgdGkIdfeE 21 
                                       +D D+dGk++  +
  gi|298675464|ref|YP_003727214.1| 301 MDMDNDGKVSVGD 313
                                       8********9866 PP

  == domain 4  score: -3.7 bits;  conditional E-value: 3.4
                                       HTTTSSSEEE CS
                         EF-hand_1   9 fDkDgdGkId 18 
                                       +D D +G ++
  gi|298675464|ref|YP_003727214.1| 371 IDMDDNGEVS 380
                                       6999999987 PP

  == domain 5  score: -3.0 bits;  conditional E-value: 2.1
                                       HHHHHHHHTTTSSSEEEHH CS
                         EF-hand_1   2 lkeiFrefDkDgdGkIdfe 20 
                                       ++++ +  D++ +G  d e
  gi|298675464|ref|YP_003727214.1| 535 IDQLLAYSDRNDNGMFDSE 553
                                       6777778899999988776 PP

  == domain 6  score: -1.6 bits;  conditional E-value: 0.72
                                       HTTTSSSEEEHHH CS
                         EF-hand_1   9 fDkDgdGkIdfeE 21 
                                       +D D +G +++ +
  gi|298675464|ref|YP_003727214.1| 558 IDMDASGEVTIGD 570
                                       799******9876 PP

  == domain 7  score: 10.8 bits;  conditional E-value: 8.2e-05
                                       HHHTTTSSSEEEHHHHHHHH CS
                         EF-hand_1   7 refDkDgdGkIdfeEfkell 26 
                                       + fD D++G I+  E+ +++
  gi|298675464|ref|YP_003727214.1| 698 NQFDADQNGVISAGELSSAI 717
                                       57*************98876 PP

>> EF-hand_6  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.2       0.5   1.8e+03       6      16 ..     122     132 ..     122     133 .. 0.93
   2 ?    1.4   0.1      0.11   3.9e+02      10      23 ..     142     155 ..     140     156 .. 0.87
   3 ?    2.9   0.0     0.036   1.3e+02       9      23 ..     301     315 ..     299     320 .. 0.87
   4 ?   -3.0   0.3       2.8     1e+04       9      18 ..     371     380 ..     370     385 .. 0.77
   5 ?   -3.0   0.1       2.8     1e+04       8      17 ..     440     449 ..     439     450 .. 0.73
   6 ?   -2.8   0.2       2.4   8.8e+03      10      20 ..     543     553 ..     539     554 .. 0.80
   7 ?   -0.3   0.0      0.38   1.3e+03       9      23 ..     558     572 ..     556     573 .. 0.86
   8 ?   -1.4   0.0      0.85     3e+03       9      18 ..     640     649 ..     638     650 .. 0.89
   9 ?    9.3   0.0   0.00032       1.1       7      26 ..     698     717 ..     697     726 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.5
                         EF-hand_6   6 FklfDkdgdGk 16 
                                       Fk++D +++G+
  gi|298675464|ref|YP_003727214.1| 122 FKYMDINDNGQ 132
                                       9********95 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.11
                         EF-hand_6  10 DkdgdGkidaeElr 23 
                                       D+++d +i++ ++r
  gi|298675464|ref|YP_003727214.1| 142 DVNNDSTITTGDIR 155
                                       9********99876 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.036
                         EF-hand_6   9 fDkdgdGkidaeElr 23 
                                       +D d+dGk++  ++r
  gi|298675464|ref|YP_003727214.1| 301 MDMDNDGKVSVGDVR 315
                                       799*******98876 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 2.8
                         EF-hand_6   9 fDkdgdGkid 18 
                                       +D d++G+++
  gi|298675464|ref|YP_003727214.1| 371 IDMDDNGEVS 380
                                       6889999987 PP

  == domain 5  score: -3.0 bits;  conditional E-value: 2.8
                         EF-hand_6   8 lfDkdgdGki 17 
                                       ++D+d +G +
  gi|298675464|ref|YP_003727214.1| 440 YIDTDATGDW 449
                                       5799998865 PP

  == domain 6  score: -2.8 bits;  conditional E-value: 2.4
                         EF-hand_6  10 DkdgdGkidae 20 
                                       D++++G  d e
  gi|298675464|ref|YP_003727214.1| 543 DRNDNGMFDSE 553
                                       99999988876 PP

  == domain 7  score: -0.3 bits;  conditional E-value: 0.38
                         EF-hand_6   9 fDkdgdGkidaeElr 23 
                                       +D d +G++++ ++r
  gi|298675464|ref|YP_003727214.1| 558 IDMDASGEVTIGDVR 572
                                       799*******98876 PP

  == domain 8  score: -1.4 bits;  conditional E-value: 0.85
                         EF-hand_6   9 fDkdgdGkid 18 
                                       fD d +G+++
  gi|298675464|ref|YP_003727214.1| 640 FDADCSGTWT 649
                                       9******997 PP

  == domain 9  score: 9.3 bits;  conditional E-value: 0.00032
                         EF-hand_6   7 klfDkdgdGkidaeElrkal 26 
                                       ++fD d +G i+a El +a+
  gi|298675464|ref|YP_003727214.1| 698 NQFDADQNGVISAGELSSAI 717
                                       79**************8887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (745 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 5025.29
//
Query:       gi|298675465|ref|YP_003727215.1|  [L=218]
Description: phosphoribosyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-28   98.6   0.0    3.7e-28   98.0   0.0    1.3  1  Pribosyltran  Phosphoribosyl transferase domain
    5.5e-05   22.7   0.0    7.9e-05   22.2   0.0    1.3  1  UPRTase       Uracil phosphoribosyltransferase
  ------ inclusion threshold ------
      0.049   13.1   0.0      0.094   12.2   0.0    1.4  1  PRTase_2      Phosphoribosyl transferase
       0.17   12.1   0.0       0.49   10.7   0.0    1.7  2  Mur_ligase_C  Mur ligase family, glutamate ligase domain


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.0   0.0   8.2e-32   3.7e-28      14     155 ..       9     192 ..       2     196 .. 0.95

  Alignments for each domain:
  == domain 1  score: 98.0 bits;  conditional E-value: 8.2e-32
                                       EEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE................... CS
                      Pribosyltran  14 avarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes........... 79 
                                       a ++la e+ e++n++ +++++ +rgGvp+a+++a++Levp+++ +++k   +g+ee a g++++            
  gi|298675465|ref|YP_003727215.1|   9 AGKKLADELTEYANRNDVIILALPRGGVPVAYEVAKKLEVPMDVFLVRKLGVPGQEELAMGAIASGgvevlnkdivq 85 
                                       6789999999999**********************************************9998877*********** PP

                                       ..............................EE----TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE- CS
                      Pribosyltran  80 ..............................rlledpagkkVliVDDildtGgTllaalelLkekgpeevriavlvdk 126
                                                                     r+ + ++gk+V+++DD+l+tG +++ a++++++ +p+ev++av+   
  gi|298675465|ref|YP_003727215.1|  86 slgisrntidevaekeykelerrersyrgdRPKPGIEGKHVILIDDGLATGASMRSAVKAVRSWNPAEVIVAVPTSA 162
                                       ***************************************************************************** PP

                                       HHHHHHHHHH-TTS......EEEEEEE-SE CS
                      Pribosyltran 127 pateeevdknakrvfsls.pdnfvavvgfe 155
                                       p+t e  +++a+r+++ls p+ f+ v   +
  gi|298675465|ref|YP_003727215.1| 163 PDTCELFEYEADRIICLStPEPFYGVGAWY 192
                                       ********************9999886655 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   1.8e-08   7.9e-05      67     163 ..      24     163 ..       6     177 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.8e-08
                           UPRTase  67 ekialVpilRaGe.................................gmeealrellpearvghlglqreeetlepve 110
                                       +++++ ++ R+G                                  +++++  e+l +  v  lg+ r+  +  ++ 
  gi|298675465|ref|YP_003727215.1|  24 NDVIILALPRGGVpvayevakklevpmdvflvrklgvpgqeelamgAIASGGVEVLNKDIVQSLGISRNTIDEVAEK 100
                                       56666666666666666666666666666666666666666666667777888899999999999999999988888 PP

                           UPRTase 111 yynkLPkkiaert............vlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlase 163
                                        y+ L ++ ++ +            v+l+D  +aTG+s+ +a++ +++  ++  +++v+   +++
  gi|298675465|ref|YP_003727215.1| 101 EYKELERRERSYRgdrpkpgiegkhVILIDDGLATGASMRSAVKAVRS--WNPAEVIVAVPTSAP 163
                                       9999988864444678899999999***********************..888888887655555 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.1e-05     0.094     121     155 ..     123     157 ..     115     164 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.1e-05
                          PRTase_2 121 akelvLvDDEistGktalnliralqeklprkryvv 155
                                        k+++L+DD ++tG ++   ++a+++ +p++ +v 
  gi|298675465|ref|YP_003727215.1| 123 GKHVILIDDGLATGASMRSAVKAVRSWNPAEVIVA 157
                                       578***********************999987775 PP

>> Mur_ligase_C  Mur ligase family, glutamate ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.8     8e+03      60      77 ..      13      29 ..       9      36 .. 0.63
   2 ?   10.7   0.0   0.00011      0.49      11      48 ..     123     160 ..     115     179 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.8
                                      THHHHHHHHCCHSSEEEE CS
                      Mur_ligase_C 60 fhdefgrlasaladslvv 77
                                      + de+ + a++ +d++++
  gi|298675465|ref|YP_003727215.1| 13 LADELTEYANR-NDVIIL 29
                                      55677777777.555444 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00011
                                       TTTEEEEEET--SHHHHHHHHHHHHHHSSSSEEEEEEE CS
                      Mur_ligase_C  11 adgvtvidDyahnpdslsaalkalreiapdkrlilvfg 48 
                                       +++v +idD  ++ +s++ a+ka+r ++p++ +++v +
  gi|298675465|ref|YP_003727215.1| 123 GKHVILIDDGLATGASMRSAVKAVRSWNPAEVIVAVPT 160
                                       57899****9999**************99988888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1370.10
//
Query:       gi|298675466|ref|YP_003727216.1|  [L=218]
Description: dienelactone hydrolase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.9e-12   45.0   0.0    1.2e-11   44.6   0.0    1.2  1  DLH            Dienelactone hydrolase family
    5.9e-09   35.5   0.1      0.031   13.5   0.0    3.0  3  Hydrolase_4    Serine aminopeptidase, S33
    3.8e-08   33.3   0.2    2.8e-05   23.9   0.3    2.7  2  Abhydrolase_1  alpha/beta hydrolase fold
    9.2e-07   29.0   0.0    0.00015   21.7   0.0    2.2  2  BAAT_C         BAAT / Acyl-CoA thioester hydrolase C terminal
      3e-05   23.6   0.0       0.14   11.6   0.1    2.4  2  Peptidase_S9   Prolyl oligopeptidase family
    0.00057   20.6   0.0     0.0034   18.0   0.0    1.8  1  Abhydrolase_6  Alpha/beta hydrolase family
     0.0023   17.6   0.1      0.014   15.0   0.1    1.9  2  Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
  ------ inclusion threshold ------
       0.13   11.7   0.0       0.37   10.2   0.0    1.6  2  DUF3530        Protein of unknown function (DUF3530)
        0.2   10.7   0.0       0.31   10.1   0.0    1.3  1  DUF1749        Protein of unknown function (DUF1749)


Domain annotation for each model (and alignments):
>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   0.0   5.8e-15   1.2e-11       2     194 ..      20     201 ..      19     217 .. 0.84

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 5.8e-15
                               DLH   2 daylatpknakkpvvvviqeifGvn...dnikdiserlaeeGYvalaPdlYarqaldpndeaeaaraldelvskvae 75 
                                       ++ l +p+n+   +++++    G        k +++ l ++G++ l+ dl++ ++      +e  r+   l  +   
  gi|298675466|ref|YP_003727216.1|  20 EGDLTIPNNP--DGIIIFAHGSGSSrhsPRNKYVAQNLQDNGFATLLIDLLTPDE------DETDRLTGRLRFDI-- 86 
                                       5668889999..9**********9988855668*******************999......34444554555455.. PP

                               DLH  76 ekvlddlkaavaylksvpevstkkvgvvGfCmGGalalllaaevpe.vdaavafYGlspekeleeaakikapilalf 151
                                       + + ++l  a +++ ++pe+s+ ++g  G   G+a al  aa+ p+ ++a+v+  G +p+   +  ++++ap l ++
  gi|298675466|ref|YP_003727216.1|  87 DLLSRRLVTATNWVLNNPETSNLNIGYFGASTGAAAALIAAAQHPMyINAVVSR-GGRPDLAEHIFDRVQAPTLLIV 162
                                       788899999********************************9996515555555.55******************** PP

                               DLH 152 geeDefipadevekleealkaanvdlelkvYpgagHaFandsr 194
                                       g++D+ +   +    + a++  n++ +l++ pga+H F ++ +
  gi|298675466|ref|YP_003727216.1| 163 GGNDPKVIELN----KWAMERMNAKKKLEIVPGATHLFEEPGK 201
                                       *****998775....5677777899999999*******98765 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   1.6e-05     0.031       2      38 ..      28      66 ..      27      68 .. 0.90
   2 !    6.0   0.2    0.0031       6.2      74     105 ..     107     138 ..      94     147 .. 0.84
   3 !   12.5   0.0   3.3e-05     0.065     188     233 ..     152     195 ..     144     199 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.6e-05
                       Hydrolase_4  2 epkavvvlvHGlae..hsgryaelaeaLaaqGfavyalD 38
                                      +p+++++++HG ++  hs r + +a++L+++Gfa++ +D
  gi|298675466|ref|YP_003727216.1| 28 NPDGIIIFAHGSGSsrHSPRNKYVAQNLQDNGFATLLID 66
                                      799*******9875449*******************999 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0031
                       Hydrolase_4  74 pelplfllGhSmGGliallyllrypdkvagli 105
                                       ++l++  +G S+G++ al +++++p  +++++
  gi|298675466|ref|YP_003727216.1| 107 SNLNIGYFGASTGAAAALIAAAQHPMYINAVV 138
                                       45577889*****************9888887 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 3.3e-05
                       Hydrolase_4 188 akitlPllllhGeaDkvvdpeasrelyerlgskdktlklypglyHe 233
                                       +++++P+ll+ G++D+ v  e  + ++er+++ +k+l++ pg+ H 
  gi|298675466|ref|YP_003727216.1| 152 DRVQAPTLLIVGGNDPKVI-ELNKWAMERMNA-KKKLEIVPGATHL 195
                                       6899***********9998.667788889986.9***********4 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.3   1.4e-08   2.8e-05       2     110 ..      32     146 ..      31     153 .. 0.80
   2 !    6.2   0.0    0.0035         7     209     251 ..     153     195 ..     148     198 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.4e-08
                                       EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHH....HHHHHCTTSS CS
                     Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddld....rildalgddk 74 
                                        +++ hG + s ++++++ +a++L+++gf ++l+Dl+ +++ ++   +   ++ ++ + + l     ++l+     +
  gi|298675466|ref|YP_003727216.1|  32 IIIFAHGSGSSRHSPRNKYVAQNLQDNGFATLLIDLLTPDEDETDRLTGRLRFDIDLLSRRLVtatnWVLNNPETSN 108
                                       699*****************************************999966444444444444435557766655555 PP

                                       EE..EEEETHHHHHHHHHHHHHGGGEEEEEEESECSSC CS
                     Abhydrolase_1  75 lt..lvGhSmGGmialayaaeyperVkalvllgaidpa 110
                                       l+  + G S G + al +aa++p +++a+v+ g+ ++ 
  gi|298675466|ref|YP_003727216.1| 109 LNigYFGASTGAAAALIAAAQHPMYINAVVSRGGRPDL 146
                                       5555****************************994433 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0035
                                       HHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSS CS
                     Abhydrolase_1 209 nvlaptlvisgtsDplvppkaledlaqllpkkrlvvisdagHl 251
                                        v aptl+i g +Dp v + +++ +++   kk+l+++++a Hl
  gi|298675466|ref|YP_003727216.1| 153 RVQAPTLLIVGGNDPKVIELNKWAMERMNAKKKLEIVPGATHL 195
                                       4778*************99999999999888899999999986 PP

>> BAAT_C  BAAT / Acyl-CoA thioester hydrolase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   7.6e-08   0.00015       9      52 ..      96     140 ..      94     149 .. 0.93
   2 !    5.3   0.0    0.0083        16     112     166 ..     152     199 ..     143     203 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 7.6e-08
                                       HHHHHHCSTTB--SSEEEEEETHHHHHHHHHHHHSS.SEEEEEEE CS
                            BAAT_C   9 ainyllrhpkvkkdkigllGiSkGgelalllasflk.kisavvli 52 
                                       a n++l++p++++ +ig  G S G+  al+ a+ ++  i+avv+ 
  gi|298675466|ref|YP_003727216.1|  96 ATNWVLNNPETSNLNIGYFGASTGAAAALIAAAQHPmYINAVVSR 140
                                       89**********************************999999985 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0083
                                       GG--SEEEEEEETT-SSS-HHHHHHHHHHHHHCTT--.--EEEEETTB-S---ST CS
                            BAAT_C 112 ekakgpillvvgedDknwpSkesaekaserLkkagkkvevqlltYpkaGHliepP 166
                                       ++ ++p ll+vg +D  +   e ++ a+er+++++k    +++  p+a Hl+e P
  gi|298675466|ref|YP_003727216.1| 152 DRVQAPTLLIVGGNDPKV--IELNKWAMERMNAKKKL---EIV--PGATHLFEEP 199
                                       6889999****9999755..56777789999877655...999..9*****9998 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.1   7.1e-05      0.14      49      98 ..      94     143 ..      91     152 .. 0.89
   2 !    9.7   0.0   0.00027      0.54     142     210 ..     154     218 .]     146     218 .] 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.1e-05
                                       HHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHHH-GGG-SEEEEESE- CS
                      Peptidase_S9  49 iaaaealakegyvdserlaitGgSyGGyltgaalnqrpdlFkaavaevpv 98 
                                       ++a+ ++ ++  +++ +++ +G+S G   ++ a++q+p    a+v+  + 
  gi|298675466|ref|YP_003727216.1|  94 VTATNWVLNNPETSNLNIGYFGASTGAAAALIAAAQHPMYINAVVSRGGR 143
                                       78899999999***************************999999987775 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00027
                                       ---EEEEEEETT-SSS-THHHHHHHHHHH--S-SEEEEEETTS-SSTTSSHHHHHHHHHHHHHHHHHCT CS
                      Peptidase_S9 142 aypplLlihGlaDdrvppaealklvaaLqkkgknvlllifpdegHgvgkprakveelarllaFlkealg 210
                                       +++p+Lli+G +D +v   e  k++  +++ + + +l i p++ H + +p +  e  +   +++k++l+
  gi|298675466|ref|YP_003727216.1| 154 VQAPTLLIVGGNDPKV--IELNKWA--MERMNAKKKLEIVPGATHLFEEPGKLEEVSRLAGEWFKQYLK 218
                                       789*************..4555664..5555666789999**************************985 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.7e-06    0.0034      62     217 ..      24     202 ..      14     205 .. 0.56

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.7e-06
                                       .....TTSEEEEEETCHHH........HHHHHHHCC..EEEEES-..----TTTS----TTHHHHHHTT-C...... CS
                     Abhydrolase_6  62 a...gggpvvlvGHSlGGa........lalaaaplalvvgvlldppptalpagllaaalelllallallrl...... 121
                                       +   +++ +++++H  G +        +a+ +++  + +++l+d     +p+ +  ++l+  l++   l +      
  gi|298675466|ref|YP_003727216.1|  24 TipnNPDGIIIFAHGSGSSrhsprnkyVAQNLQDNGF-ATLLIDL---LTPDEDETDRLTGRLRFDIDLLSrrlvta 96 
                                       3455677889999999987777777756666444443.4499999...77788866666666655554444122233 PP

                                       CCCHCCH....S-HSCCCCHHHCCCCHCHCCCGHHHHCC........HHCHTTCCHHTT-TTGC.EEECTT-C...H CS
                     Abhydrolase_6 122 lawlsre....plprlfladedadaawrarlarlaalla........glgllpaaawadlpvpl.lvlggeDp...l 182
                                         w+  +     l+ ++++  +   a +a  a++++ +         g+  l+ + + ++ +p+ l++gg+Dp    
  gi|298675466|ref|YP_003727216.1|  97 TNWVLNNpetsNLNIGYFGAST--GAAAALIAAAQHPMYinavvsrgGRPDLAEHIFDRVQAPTlLIVGGNDPkviE 171
                                       4555333445434447777333..444444444443333223322211112223344444444455569****9886 PP

                                       HHHCHHCCCHSTTEEETCE...SSS-HHHHSHHHH CS
                     Abhydrolase_6 183 vprllerllaqagarlpvvlpgaGHlphleepdev 217
                                       +  ++ +++  a+++l +++pga Hl+  eep ++
  gi|298675466|ref|YP_003727216.1| 172 LNKWAMERMN-AKKKL-EIVPGATHLF--EEPGKL 202
                                       6666667777.9****.*******964..477665 PP

>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   7.1e-06     0.014      91     143 ..      98     151 ..      92     159 .. 0.90
   2 ?    2.2   0.0     0.058   1.1e+02     223     248 ..     149     175 ..     143     196 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.1e-06
                                       HHHHHC.TTEEEEEEEEEECHHHHHHHHHCTT--TTEEEEEEECE-S-TCCCCS CS
                     Peptidase_S15  91 dWlakq.pwsnGkVgmtGiSYlGttqllaaatgvpalkaivpeaaisdlyddyy 143
                                        W+ ++ + sn ++g +G S ++  +l+aaa+++  ++a+v+  +  dl+++++
  gi|298675466|ref|YP_003727216.1|  98 NWVLNNpETSNLNIGYFGASTGAAAALIAAAQHPMYINAVVSRGGRPDLAEHIF 151
                                       7*****8999*******************************9999999998754 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.058
                                       HH.CT--S-EEEEEECCSSTTCCHHHH CS
                     Peptidase_S15 223 da.dkvkapvllvgGwnDwnvkngaik 248
                                       ++ d+v+ap+ll+ G nD  v++ +  
  gi|298675466|ref|YP_003727216.1| 149 HIfDRVQAPTLLIVGGNDPKVIELNKW 175
                                       4449**************666544333 PP

>> DUF3530  Protein of unknown function (DUF3530)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00019      0.37      84     132 ..      27      74 ..      23      84 .. 0.89
   2 ?   -1.5   0.0      0.66   1.3e+03     197     220 ..     109     131 ..      90     162 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00019
                           DUF3530  84 gkpqGavillpgdgetadwpqaiapLRrkLpdaGWatLsitlpdpqeea 132
                                       ++p G +i+ +g+g +  +p++ +++ ++L d G+atL i l +p+e++
  gi|298675466|ref|YP_003727216.1|  27 NNPDGIIIFAHGSGSSRHSPRN-KYVAQNLQDNGFATLLIDLLTPDEDE 74 
                                       5899**************9997.8*****************98887654 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.66
                           DUF3530 197 enivllghgtgAywaarylaekks 220
                                        ni + g  tgA+ a+   a+  +
  gi|298675466|ref|YP_003727216.1| 109 LNIGYFGASTGAAAALIAAAQ-HP 131
                                       488888889999888776666.44 PP

>> DUF1749  Protein of unknown function (DUF1749)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00016      0.31     221     290 ..     148     208 ..     143     218 .] 0.78

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00016
                           DUF1749 221 ektfGkvkepllillsekDefvpesvdkedllerwkeavkkkewseesGiipgAsHnveeesaeeaqkel 290
                                       e++f +v++p+l+++ ++D+ v e       l++w  a+++ + +++  i+pgA+H  ee+++ e+++ l
  gi|298675466|ref|YP_003727216.1| 148 EHIFDRVQAPTLLIVGGNDPKVIE-------LNKW--AMERMNAKKKLEIVPGATHLFEEPGKLEEVSRL 208
                                       568999999*********944433.......5666..566666777888**********99998877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1538.07
//
Query:       gi|298675467|ref|YP_003727217.1|  [L=295]
Description: response regulator receiver protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-32  113.0   0.9    2.1e-32  112.3   0.9    1.3  1  MetOD1         Metanogen output domain 1
    1.1e-24   86.8   0.1    3.2e-24   85.2   0.1    1.8  2  Response_reg   Response regulator receiver domain
  ------ inclusion threshold ------
      0.013   16.3   1.5      0.033   14.9   1.5    1.9  1  ATC_hydrolase  L-2-amino-thiazoline-4-carboxylic acid hydrola


Domain annotation for each model (and alignments):
>> MetOD1  Metanogen output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.3   0.9   3.5e-36   2.1e-32       4     152 ..     137     290 ..     134     292 .. 0.95

  Alignments for each domain:
  == domain 1  score: 112.3 bits;  conditional E-value: 3.5e-36
                            MetOD1   4 kkkvkaelrsfllsaiPtlaskippeekkilikqfadrveknlkpkfkeelk.....eaekeeedaekvlkayiewl 75 
                                       +++ k+++r++ ++++P l+++ +p++k ili+q+ d+ve  + + +++  +       ++++ ++e++   ++e +
  gi|298675467|ref|YP_003727217.1| 137 ELYKKEQIRDIFIEIMPLLLKSHSPDKKRILIQQMLDKVEIFFTNCYQKSGQfcdddGLDSKKINPENIEYGCCELM 213
                                       677899******************************************77779999989999999************ PP

                            MetOD1  76 nqlfanfgiktekkedeknvlleftnCpWge.earknPifCllcraivsrsftwtglkgsveqkktlgngdekCvFe 151
                                         l+++f   +  ++++  +++++t CpWg  +a+ nP++C+l+++i++r++++++ + +v++ kt+gngd++C+Fe
  gi|298675467|ref|YP_003727217.1| 214 GHLGGSFETYKS-DKNDVLFVVNGTVCPWGVqQAKLNPVLCNLTKGIIERITKKAFNNSKVQTIKTMGNGDDCCQFE 289
                                       *******99888.5888899**********99********************************************* PP

                            MetOD1 152 i 152
                                       i
  gi|298675467|ref|YP_003727217.1| 290 I 290
                                       9 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.2   0.1   5.4e-28   3.2e-24       1     112 []       8     119 ..       8     119 .. 0.97
   2 ?   -1.9   0.0       0.6   3.6e+03      12      35 ..     262     285 ..     258     288 .. 0.81

  Alignments for each domain:
  == domain 1  score: 85.2 bits;  conditional E-value: 5.4e-28
                                       EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCT..TTSEEE CS
                      Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireed..pelpvi 75 
                                       +l+vdD+p+ ++ l++ l  egy ++  a dg+  ++ lk++++d+illD++ p +dG+e++ +i++++  + +pvi
  gi|298675467|ref|YP_003727217.1|   8 ILVVDDNPDTITFLKEHLG-EGY-HIFPAYDGSHIIDTLKSNDIDVILLDVMTPYIDGFEICGNIKNDEnlNYIPVI 82 
                                       8*****************9.9**.*****************************************99997888**** PP

                                       EEESSTSHHHHHHHHHCTESEEEESSG-HHHHHHHHH CS
                      Response_reg  76 iltahseeedavealkagaddflsKpfdpeeLlkale 112
                                       ++ta s+ e+++++l+agaddf+sKp+d e L+++++
  gi|298675467|ref|YP_003727217.1|  83 LVTALSDRENVIKGLNAGADDFISKPVDYEVLKARIK 119
                                       ********************************99985 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.6
                                       HHHHHHHHHTTEEEEEEESSHHHH CS
                      Response_reg  12 ellrqlleeegyeevaeaedgkea 35 
                                       ++++++++++++++++++ +g+++
  gi|298675467|ref|YP_003727217.1| 262 RITKKAFNNSKVQTIKTMGNGDDC 285
                                       678899999999999999999876 PP

>> ATC_hydrolase  L-2-amino-thiazoline-4-carboxylic acid hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   1.5   5.6e-06     0.033      90     144 ..     236     289 ..     124     290 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.6e-06
                     ATC_hydrolase  90 vtrCpyceawkkeGlpelgkllCeiDkavaeginpk....vklertktlaeGgdcCdfr 144
                                        t Cp+         ++l ++lC++ k ++e i +k     k +  kt++ G+dcC+f 
  gi|298675467|ref|YP_003727217.1| 236 GTVCPWGVQQ-----AKLNPVLCNLTKGIIERITKKafnnSKVQTIKTMGNGDDCCQFE 289
                                       5555554433.....35779*************9999888778889***********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.76
# Mc/sec: 1164.04
//
Query:       gi|298675468|ref|YP_003727218.1|  [L=86]
Description: hypothetical protein Metev_1576 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.078   12.2   0.2      0.084   12.1   0.2    1.0  1  DUF3404   Domain of unknown function (DUF3404)


Domain annotation for each model (and alignments):
>> DUF3404  Domain of unknown function (DUF3404)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   4.7e-06     0.084     187     251 ..      20      82 ..      13      86 .] 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.7e-06
                                       EEEEEHHHHHHHHHHHT-------TT----EEETTEEE---XXXXXXXXXXXXXXXXXXXXXXXX CS
                           DUF3404 187 ykvlseevwkklaeklklslslataaksCsvrysNlClnveeksklllksliilvllnlllvlgr 251
                                       + v+s++v +k++ + +++l  ++  k  +++  N+ +n +   k l+ +l++l+l+ +++++  
  gi|298675468|ref|YP_003727218.1|  20 HLVFSQVVVHKYTGTKDIKLGNNS--KVIDIKTTNININYNIIRKYLIFTLFFLILISIMILIIN 82 
                                       568999999999999999988775..589******************************998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       945  (0.0527079); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 576.12
//
Query:       gi|298675469|ref|YP_003727219.1|  [L=383]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-26   92.2   1.5    5.9e-26   91.0   1.5    1.5  1  OrfB_IS605      Probable transposase
    5.1e-24   84.0   0.4    1.1e-23   82.9   0.4    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    1.2e-20   72.7   1.7    2.8e-20   71.5   1.7    1.6  1  HTH_OrfB_IS605  Helix-turn-helix domain
     0.0079   16.3   0.3       0.02   15.1   0.3    1.6  1  zf-piccolo      Piccolo Zn-finger
  ------ inclusion threshold ------
      0.022   15.1   0.1      0.041   14.3   0.1    1.4  1  Flagellin_D3    Flagellin D3 domain
      0.027   14.3   1.0       0.44   10.4   0.2    2.4  2  LemA            LemA family
       0.13   12.1   4.0       0.83    9.4   1.2    2.4  2  Phage_GP20      Phage minor structural protein GP20
       0.78   10.0   6.3       0.36   11.1   1.1    2.3  2  MapZ_EC1        MapZ extracellular domain 1


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.0   1.5   2.7e-29   5.9e-26      10     117 ..     180     284 ..     167     286 .. 0.92

  Alignments for each domain:
  == domain 1  score: 91.0 bits;  conditional E-value: 2.7e-29
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsr 86 
                                       ++k  + +++g+D+Gi+++a++++++   ++ ++r lk+  ++l+  +++l++k+k+s+ny+k + ++a++h+k+++
  gi|298675469|ref|YP_003727219.1| 180 KQKFYEVNTIGVDVGIKDFAVTSDGE---KIGNPRYLKNSIERLKVLQKRLSRKQKGSNNYRKLKHQIAKYHEKIAN 253
                                       55566789******************...************************************************ PP

                        OrfB_IS605  87 rrkhllhklathliktlkevgvetLnvgnmk 117
                                       +r +++hkl+++li ++++v++e Lnv+++ 
  gi|298675469|ref|YP_003727219.1| 254 QREDFQHKLSSRLISENQAVALECLNVKGLL 284
                                       ****************************986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.9   0.4     5e-27   1.1e-23       1      68 [.     298     367 ..     298     368 .. 0.98

  Alignments for each domain:
  == domain 1  score: 82.9 bits;  conditional E-value: 5e-27
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpay.TSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       ++++ ++leyka++yG++++++ ++  +Sk C++Cg+ +++ +l++r+++Cp+C++e+drD+nA++Ni k
  gi|298675469|ref|YP_003727219.1| 298 WSSFVQKLEYKAEWYGKNIIKIGRFDpSSKICHVCGYYHQDlELKDREWECPDCKTEHDRDINASVNIKK 367
                                       99******************************************************************87 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.5   1.7   1.2e-23   2.8e-20       1      47 []       9      54 ..       9      54 .. 0.98

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 1.2e-23
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeegk 47
                                      M lkaykyr yP+++Q+e++a+++G++Rf+YN+aL+ +++ ye+ gk
  gi|298675469|ref|YP_003727219.1|  9 M-LKAYKYRMYPNQTQQELIAKHIGACRFIYNWALENKIKSYEQDGK 54
                                      8.******************************************997 PP

>> zf-piccolo  Piccolo Zn-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.3   8.8e-06      0.02      28      56 ..     326     354 ..     322     356 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.8e-06
                        zf-piccolo  28 kqvCnlCGFnptphltekkeWlclnCQtq 56 
                                       +++C +CG+  ++   + +eW c  C t+
  gi|298675469|ref|YP_003727219.1| 326 SKICHVCGYYHQDLELKDREWECPDCKTE 354
                                       79***********999**********985 PP

>> Flagellin_D3  Flagellin D3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   1.8e-05     0.041      23      58 ..     149     187 ..     139     202 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.8e-05
                      Flagellin_D3  23 tgsvkdgkikfddtgkYYvevtgtdk...taknGyYevt 58 
                                        g++++++ik   tgkYY+ +   d+   ++k+++Yev+
  gi|298675469|ref|YP_003727219.1| 149 DGKQRTATIKRTPTGKYYISILVDDDkqlPQKQKFYEVN 187
                                       5778999999999********7777699**********7 PP

>> LemA  LemA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.077   1.7e+02      30      82 ..      60     112 ..      43     115 .. 0.82
   2 ?   10.4   0.2    0.0002      0.44      60     107 ..     213     261 ..     200     268 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.077
                              LemA  30 EketleevteaRakaaeaesveekaeaenqlssalsrllavaEnYPdLkanen 82 
                                       E +   +v +  ++  ++ + ++ + a  +l++a+ +++     +P++k+++n
  gi|298675469|ref|YP_003727219.1|  60 ELNKQIRVLKQDHEWLNEINSQSLQGATLNLENAFTKFFREKSGFPKFKSKKN 112
                                       55555566666667788889999999************************987 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0002
                              LemA  60 lssalsrllavaEn.YPdLkanenfleLqeelegtEnriavaRrrYnea 107
                                       l+++++rl +++ +   + k ++n+++L++++++  ++ia++R++++++
  gi|298675469|ref|YP_003727219.1| 213 LKNSIERLKVLQKRlSRKQKGSNNYRKLKHQIAKYHEKIANQREDFQHK 261
                                       5666666666666523567899***********************9876 PP

>> Phage_GP20  Phage minor structural protein GP20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.047   1.1e+02     113     136 ..      51      77 ..      23      88 .. 0.71
   2 ?    9.4   1.2   0.00037      0.83      32      90 ..     218     276 ..     211     286 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.047
                        Phage_GP20 113 edgelkg...LdeqikkLkesdkyLFe 136
                                       +dg+ +    L++qi  Lk+++++L e
  gi|298675469|ref|YP_003727219.1|  51 QDGKAISrfeLNKQIRVLKQDHEWLNE 77 
                                       455555334488888888888888876 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00037
                        Phage_GP20  32 eqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeyeakiadlkldnaielaLk 90 
                                       e+lk  +k L+  +k +++  +L+ qi+++ +k++++ ++ + k++ + +++    aL+
  gi|298675469|ref|YP_003727219.1| 218 ERLKVLQKRLSRKQKGSNNYRKLKHQIAKYHEKIANQREDFQHKLSSRLISENQAVALE 276
                                       56777788888888899999*************************99888776666666 PP

>> MapZ_EC1  MapZ extracellular domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.3      0.19   4.2e+02      48      84 ..      42      81 ..      36      92 .. 0.75
   2 ?   11.1   1.1   0.00016      0.36      37      78 ..     213     254 ..     173     277 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.19
                          MapZ_EC1 48 LekkLeklk.gskeYk..klkkkldslkkqisaieavNsq 84
                                      Le+k++ ++ + k  +  +l+k++  lk+  + ++++Nsq
  gi|298675469|ref|YP_003727219.1| 42 LENKIKSYEqDGKAISrfELNKQIRVLKQDHEWLNEINSQ 81
                                      5666666664333332227999999999999999999997 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00016
                          MapZ_EC1  37 lknsefaklseLekkLe.klkgskeYkklkkkldslkkqisai 78 
                                       lkns ++ l+ L+k L  k kgs++Y+klk+++++  ++i+ +
  gi|298675469|ref|YP_003727219.1| 213 LKNS-IERLKVLQKRLSrKQKGSNNYRKLKHQIAKYHEKIANQ 254
                                       3443.688999*****72556*****************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1426  (0.0795359); expected 358.6 (0.02)
Passed bias filter:                      666  (0.0371465); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.68u 0.35s 00:00:01.03 Elapsed: 00:00:00.53
# Mc/sec: 2189.21
//
Query:       gi|298675470|ref|YP_003727220.1|  [L=191]
Description: nuclease [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-26   91.5   0.0    5.6e-26   91.1   0.0    1.1  1  SNase     Staphylococcal nuclease homologue
  ------ inclusion threshold ------
      0.069   12.3   0.1        0.1   11.8   0.1    1.2  1  DUF5006   Domain of unknown function (DUF5006)


Domain annotation for each model (and alignments):
>> SNase  Staphylococcal nuclease homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.1   0.0   6.2e-30   5.6e-26       1     107 [.      64     182 ..      64     183 .. 0.95

  Alignments for each domain:
  == domain 1  score: 91.1 bits;  conditional E-value: 6.2e-30
                                       EEEETTEE-STSSBTTT...........TTSTTHHHHHHHHHHHHHHCSSEEEEE-S..SBSTTSEEEEEEEET.TE CS
                             SNase   1 kvrLvgidaPetakpkk...........tvqpfgkeAkeflkklvlqkkvvvleldk..kkDkygrllayvyln.kk 63 
                                       ++rL+g+d+Pet+  ++           +++++g +A++++++ ++++kv+++ +d+  ++++ygrllayv+l+ ++
  gi|298675470|ref|YP_003727220.1|  64 RIRLLGVDTPETHTDNEpedfegidnasYLHEWGLKASDYTSDILKGNKVRLEYDDIsdRRGYYGRLLAYVFLQnDT 140
                                       79***********8888*********************************9999999999*************9899 PP

                                       EHHHHHHHTTSSEE---BTTSTTTHHHHHHHHHHHHHTT-GGGC CS
                             SNase  64 nineeLvkeGlArvyevyekneekkkellkaeeeAkkkrkglWs 107
                                       + n  L+k+G+Arvy     + e+ +e+l++e+eAk k+ glWs
  gi|298675470|ref|YP_003727220.1| 141 MYNRMLIKNGYARVYDEA--EIEYMDEFLELEQEAKVKQIGLWS 182
                                       9************87744..579********************8 PP

>> DUF5006  Domain of unknown function (DUF5006)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   1.2e-05       0.1       7      52 ..      13      55 ..       8      70 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.2e-05
                           DUF5006  7 lLPvcllallltGCeDddkveplpeavpLvleisskslvmGeelev 52
                                      ++ vcll + l+GC D+d+ ++ ++  +Lv     +++v G+++++
  gi|298675470|ref|YP_003727220.1| 13 IITVCLLLINLSGCIDTDNDSAESNDTNLVT---VTKVVDGDTIDI 55
                                      678***************9998888888864...355666776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1127.28
//
Query:       gi|298675471|ref|YP_003727221.1|  [L=131]
Description: hypothetical protein Metev_1580 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-63  211.9   1.1    2.2e-63  211.7   1.1    1.0  1  DUF1699   Protein of unknown function (DUF1699)


Domain annotation for each model (and alignments):
>> DUF1699  Protein of unknown function (DUF1699)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.7   1.1   1.2e-67   2.2e-63       1     130 []       1     130 [.       1     130 [. 0.99

  Alignments for each domain:
  == domain 1  score: 211.7 bits;  conditional E-value: 1.2e-67
                           DUF1699   1 mkirvvsskeeietlnenekivHlafrpsntdilslvkkcpklkaiqvpeSykktlsksakmfleiqgiellegdvw 77 
                                       m+irv+ssk++i++lnene+ivHlafrpsntdi+s+v+kcp++ka ++p+Sy ktls+sakmfl++qgi+l+egdvw
  gi|298675471|ref|YP_003727221.1|   1 MRIRVISSKDDINNLNENEEIVHLAFRPSNTDIFSIVSKCPDIKAFHIPNSYLKTLSQSAKMFLDMQGIDLIEGDVW 77 
                                       9**************************************************************************** PP

                           DUF1699  78 ghrkdineyyevseevierikelkseglseeeiaeklsketklspdlikfllk 130
                                       ghrkdiney+e+s+ ++eri+elk++++s+eeia+k+s+e++l+pd++kfl+k
  gi|298675471|ref|YP_003727221.1|  78 GHRKDINEYSEISNGIYERINELKKDDYSDEEIADKISRESNLEPDFVKFLMK 130
                                       ***************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 803.26
//
Query:       gi|298675472|ref|YP_003727222.1|  [L=81]
Description: hypothetical protein Metev_1581 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 500.98
//
Query:       gi|298675473|ref|YP_003727223.1|  [L=211]
Description: MgtE integral membrane protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-19   69.9  12.7    2.4e-19   69.9  12.7    1.9  2  MgtE      Divalent cation transporter


Domain annotation for each model (and alignments):
>> MgtE  Divalent cation transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1     0.045     8e+02      33      59 ..      31      57 ..      18      72 .. 0.66
   2 !   69.9  12.7   1.3e-23   2.4e-19       2     124 .]      74     203 ..      73     203 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.045
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              MgtE 33 kkvllkelrvvlllgvilgllifllal 59
                                       k +++e++ + +l+++ g++++++  
  gi|298675473|ref|YP_003727223.1| 31 IKSIISEALPFEILATFGGVVAGIILS 57
                                      567777777788888888888887733 PP

  == domain 2  score: 69.9 bits;  conditional E-value: 1.3e-23
                                       HHHHHHHHHHHHHHHHHHHHHHHTTSS-GG.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-......CTSHHHHH CS
                              MgtE   2 PvilglgGnlgaqlasristalhlgelekk.lkkvllkelrvvlllgvilgllifllalllgw.....slllalvvg 72 
                                       P++lgl+Gn+  +l sr+ +a h+g++++   +  l+++++  l+l++il ++++l+ ++++      s+ ++++ +
  gi|298675473|ref|YP_003727223.1|  74 PAVLGLRGNISCTLGSRLGSAVHMGLITRVeRNPELINNIAGSLTLSLILTIILGLMGHYITLlmgldSAGALILTS 150
                                       9************************9965567888888888888888887777777744333345566777777799 PP

                                       HHHHHHHHHHHHH...HHHHHHHHHHTTS-GGGSHHHHHHHHHHHHHHHHHHH CS
                              MgtE  73 lalvlvllaaall.ilgvllplllwklglDPdnaaiPlltalgDllgtlllvl 124
                                       +a++  + + ++l i++vll+l ++++g+DPdn+++P +++lgD++++l+l+l
  gi|298675473|ref|YP_003727223.1| 151 IAVISGVSSGIILsIITVLLALGMFRFGFDPDNVVTPSIATLGDIISMLMLFL 203
                                       9999999999999**************************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       886  (0.0494171); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1263.83
//
Query:       gi|298675474|ref|YP_003727224.1|  [L=185]
Description: MgtE integral membrane protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-19   70.1   9.3    2.1e-19   70.1   9.3    1.5  2  MgtE      Divalent cation transporter


Domain annotation for each model (and alignments):
>> MgtE  Divalent cation transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1      0.27   4.9e+03      42      54 ..      19      31 ..       8      46 .. 0.58
   2 !   70.1   9.3   1.2e-23   2.1e-19       1     121 [.      48     174 ..      48     177 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.27
                                      HHHHHHHHHHHHH CS
                              MgtE 42 vvlllgvilglli 54
                                      v  ++g++ g+++
  gi|298675474|ref|YP_003727224.1| 19 VTSIIGIFSGQIL 31
                                      3334444444444 PP

  == domain 2  score: 70.1 bits;  conditional E-value: 1.2e-23
                                       HHHHHHHHHHHHHHHHHHHHHHHHTT...SS-GGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-.....CTSHHH CS
                              MgtE   1 iPvilglgGnlgaqlasristalhlg...elekklkkvllkelrvvlllgvilgllifllalllgw....slllalv 70 
                                       iP+++ +gG +g++l +r+s+a+hlg   +++   + v+ ++l+ +l++g++ +++++++++ +++     l  +++
  gi|298675474|ref|YP_003727224.1|  48 IPALIKVGGDTGSMLGARLSSAFHLGmggNIH--KNPVVKNSLLGALIVGITACFILSIVVWSVSNlmgiGLEYITF 122
                                       79***********************9555553..4699999999999999999999999988766633334444444 PP

                                       HHHHHHHHHHHHHHH........HHHHHHHHHHTTS-GGGSHHHHHHHHHHHHHHHH CS
                              MgtE  71 vglalvlvllaaall......ilgvllplllwklglDPdnaaiPlltalgDllgtll 121
                                       + + +++ +     l       ++vl++++++++glDPd  +iPl+++lgDl+g++ 
  gi|298675474|ref|YP_003727224.1| 123 FKICMIAGI-----LeliavyAITVLIAFASHRFGLDPDDTVIPLIATLGDLIGVAG 174
                                       444444444.....444444889*******************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       679  (0.0378716); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1182.18
//
Query:       gi|298675475|ref|YP_003727225.1|  [L=403]
Description: TrkA-C domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-28   98.4   0.0    3.2e-14   52.5   0.0    2.5  2  TrkA_C    TrkA-C domain
    6.7e-18   64.9  12.8    9.1e-10   38.9   7.9    2.4  2  PhoU      PhoU domain
  ------ inclusion threshold ------
      0.026   13.8   4.4       0.13   11.6   0.1    2.6  3  PhoU_div  Protein of unknown function DUF47


Domain annotation for each model (and alignments):
>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.5   0.0   5.3e-18   3.2e-14       1      65 [.     122     188 ..     122     192 .. 0.96
   2 !   43.5   0.0   3.5e-15   2.1e-11       4      64 ..     326     388 ..     323     394 .. 0.90

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 5.3e-18
                                       CEEEEEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHHH CS
                            TrkA_C   1 lvevtvpagsplvGktlkelnlrar.gvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlael 65 
                                       +v+ tv++ s++v+ tl++l l ++ g +++a+rR+ ++++ p+++t++++GDvl+  g+++++  +
  gi|298675475|ref|YP_003727225.1| 122 VVRATVNEKSKMVNNTLGDLELDTEtGMTIIALRRNhNWIYDPNENTKIKAGDVLFARGHDEGIPLF 188
                                       6899**********************************************************99876 PP

  == domain 2  score: 43.5 bits;  conditional E-value: 3.5e-15
                                       EEEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHH CS
                            TrkA_C   4 vtvpagsplvGktlkelnlrar.gvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlae 64 
                                       ++v   sp+vGkt k+l+l+++ gv ++a +R+  ++++ps+ t+ ++GDvl+  g+  + ++
  gi|298675475|ref|YP_003727225.1| 326 LEVEDCSPIVGKTFKDLKLETEtGVHIMAMKRNnRWVYSPSDRTTVQSGDVLIARGTHTGEDA 388
                                       5677779***********************************************999776665 PP

>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   7.9   1.5e-13   9.1e-10       1      89 []      17     101 ..      17     101 .. 0.88
   2 !   28.6   0.2   2.4e-10   1.5e-06       2      87 ..     219     300 ..     218     302 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 1.5e-13
                                       HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHH CS
                              PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlER 77 
                                       l +m++i+e m+d+a++a   +d+++a+ev+ ++++++ l ++++  ++  + +r ++    +e++++l++a + E 
  gi|298675475|ref|YP_003727225.1|  17 LIEMKDISELMVDLAYSAMIYDDVDIAEEVLYLEEKMNLLDYQMKITAMLSA-RRIEE---AEEMSGVLQVADSSET 89 
                                       679*****************************************77755554.33332...567899********** PP

                                       HHHHHHHHHHHH CS
                              PhoU  78 igDhavniaerv 89 
                                       i+  a +ia++v
  gi|298675475|ref|YP_003727225.1|  90 IANAAGDIAKIV 101
                                       *********986 PP

  == domain 2  score: 28.6 bits;  conditional E-value: 2.4e-10
                                       HHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HGG-SHHHHHHHHHHHHHHHHHH CS
                              PhoU   2 rrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealak.rqplaedlrellsllriardlER 77 
                                        +m++++e  + ++++a+  +++++a ev  ++ e+d + +e++  +le +++ ++p   +lr    ll++a+  E 
  gi|298675475|ref|YP_003727225.1| 219 VDMKNMAELSVGLSYSAILFDNEDIAHEVKILESEMDSMKYELQHWVLETAKHlNDPS--QLRG---LLHLANASET 290
                                       68***************999999***************************97735554..3555...9********* PP

                                       HHHHHHHHHH CS
                              PhoU  78 igDhavniae 87 
                                       i+D    ia+
  gi|298675475|ref|YP_003727225.1| 291 ISDAGYGIAD 300
                                       ***9888886 PP

>> PhoU_div  Protein of unknown function DUF47
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.4     0.019   1.1e+02     142     205 ..      25      98 ..       6     102 .. 0.65
   2 ?    2.7   0.1     0.011        65      81     135 ..      81     135 ..      75     153 .. 0.71
   3 ?   11.6   0.1   2.2e-05      0.13     132     199 ..     216     293 ..     205     304 .. 0.62

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.019
                          PhoU_div 142 etalskk.........diveeieslEdeiDqlqrk.likklfsredasnplevlllveiieklenvsdraedva 205
                                       e  ++           di+ee+  lE+++ +l  +  i+ ++s    +   e+  + +  +  e ++++a d+a
  gi|298675475|ref|YP_003727225.1|  25 ELMVDLAysamiyddvDIAEEVLYLEEKMNLLDYQmKITAMLSARRIEEAEEMSGVLQVADSSETIANAAGDIA 98 
                                       33333333344455779999999999999999654146777776666777777777777777778888877777 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.011
                          PhoU_div  81 lelveslDeildvlediamlvtlrkvefpeelkdeflallkktvea.iealaevie 135
                                       l+++ s   i++ + dia++v lr++++p elk  +++  +++v a +++  ++++
  gi|298675475|ref|YP_003727225.1|  81 LQVADSSETIANAAGDIAKIV-LRDMGIPLELKYALREAEETVVRAtVNEKSKMVN 135
                                       5667777889********976.8999******999998888777641444444444 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 2.2e-05
                          PhoU_div 132 evieeleklletalskk.........diveeieslEdeiDqlqrklikklfs.redasnplevlllveiieklenvs 198
                                       ++i  ++ + e ++  +         di++e++ lE e+D+++ +l    ++  +    p +   l ++ +  e +s
  gi|298675475|ref|YP_003727225.1| 216 DIIVDMKNMAELSVGLSysailfdneDIAHEVKILESEMDSMKYELQHWVLEtAKHLNDPSQLRGLLHLANASETIS 292
                                       55555555555555555556666667*****************9987655441444444555555555555555555 PP

                          PhoU_div 199 d 199
                                       d
  gi|298675475|ref|YP_003727225.1| 293 D 293
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2666.24
//
Query:       gi|298675476|ref|YP_003727226.1|  [L=232]
Description: ribose 5-phosphate isomerase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.1e-64  214.6   0.2    7.1e-64  214.6   0.2    1.3  2  Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoribois
    3.4e-05   23.8   0.4     0.0011   18.9   0.1    2.3  2  DeoRC           DeoR C terminal sensor domain
  ------ inclusion threshold ------
       0.14   12.6   0.0       0.32   11.4   0.0    1.6  1  RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7


Domain annotation for each model (and alignments):
>> Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoriboisomerase A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.1       1.5   9.2e+03     151     162 ..      21      32 ..      16      35 .. 0.78
   2 !  214.6   0.2   1.2e-67   7.1e-64       2     173 .]      58     226 ..      57     226 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 1.5
                                       TTEEEESEE-S- CS
                    Rib_5-P_isom_A 151 pGVvetGlFlgl 162
                                       +G ve G+++gl
  gi|298675476|ref|YP_003727226.1|  21 AGLVEDGMIIGL 32 
                                       788999988875 PP

  == domain 2  score: 214.6 bits;  conditional E-value: 1.2e-67
                                       EEESSHHHHHHHHHTT--BE-GGCCSSEEEEEE--SEEETTS-EE--TTS-HHHHHHHHHTEEEEEEEEEGGGBESS CS
                    Rib_5-P_isom_A   2 gvptSeqteelaeelgipllsldeveeidlaiDGaDevdedlnliKGgGgallrEKivaaaakkfiviadesKlvek 78 
                                       +v tS+q+e+la ++gipl+sl+e++e+dl iDGaD+vd +ln+iKGgG+a+++EK+va ++k+fi ++desKl++k
  gi|298675476|ref|YP_003727226.1|  58 AVVTSYQSEMLAIDAGIPLTSLSEHPELDLDIDGADQVDFELNAIKGGGAAHTKEKVVACSSKQFIAVIDESKLSDK 134
                                       799************************************************************************** PP

                                       TTSS-EEEEE-GGGHHHHHHHHHHTTT-EEEE-TETTTTEE-B-TTS-EEEEEESSSBSSSHHHHHHHHHTSTTEEE CS
                    Rib_5-P_isom_A  79 lgkfpvPveVlpfaleavarelekllggkpelReakgkdgpvvTdngnlilDvkfeekiedpeelekelksipGVve 155
                                       l+ ++vPveVlp++++ v++++++ +g++pe+R+a +kdgpv+Tdngnli+D++f + ie+p++l++el++ipG+ve
  gi|298675476|ref|YP_003727226.1| 135 LN-HSVPVEVLPYSRNLVLQNMQN-MGAEPEIRQAVHKDGPVITDNGNLIIDADF-DVIENPNNLASELSAIPGIVE 208
                                       *6.9*******************7.5*********99******************.6899***************** PP

                                       ESEE-S--SEEEEEETTC CS
                    Rib_5-P_isom_A 156 tGlFlgladkvlvgkedg 173
                                       +G+F+g+ d++++gk+dg
  gi|298675476|ref|YP_003727226.1| 209 HGIFTGMIDEIYMGKKDG 226
                                       ***************997 PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   1.9e-07    0.0011       5      41 ..      12      48 ..       8      70 .. 0.83
   2 ?    3.0   0.0     0.015        88     118     142 ..     109     134 ..     101     142 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.9e-07
                             DeoRC  5 eKrrIAkaAaeliedgdtifldaGtTtlelaraLaek 41
                                       K+  + aAa l+edg++i l++G+Tt++ ++++ ++
  gi|298675476|ref|YP_003727226.1| 12 GKESAGVAAAGLVEDGMIIGLGTGSTTAYAISEVGKR 48
                                      69999**********************9877766554 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.015
                             DeoRC 118 evkralie.aarrvillaDssKfgkr 142
                                        +k+++++ ++++ i ++D+sK+  +
  gi|298675476|ref|YP_003727226.1| 109 HTKEKVVAcSSKQFIAVIDESKLSDK 134
                                       5666666515678899******9865 PP

>> RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   5.4e-05      0.32      14      84 ..     103     164 ..      96     167 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.4e-05
                                       HHHTBHHHHHHHHTTTTTEEEEEEESSSSSCCCEEEBTTTTCSSSEEEEEEEHHHHHHHHHHHHTTBEEEE CS
                    RNA_pol_Rpb2_7  14 iayGaaalLkerltikSDavevdvcgrckllaaaneCkivkseekiekveipeafklLlqeLqslgialkl 84 
                                       ++ Gaa++ ke+++  S +  + v ++ kl +         +++ + +v +p++ +l+lq++q +g ++++
  gi|298675476|ref|YP_003727226.1| 103 KGGGAAHT-KEKVVACSSKQFIAVIDESKLSDK-------LNHSVPVEV-LPYSRNLVLQNMQNMGAEPEI 164
                                       55555555.444444444444444444444444.......344445555.8***************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1434.31
//
Query:       gi|298675477|ref|YP_003727227.1|  [L=443]
Description: aspartyl-tRNA synthetase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-91  306.3   0.2    2.6e-91  306.0   0.2    1.1  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    4.7e-16   58.5   0.1      8e-16   57.8   0.1    1.4  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
    6.7e-05   22.5   0.9     0.0086   15.6   0.1    2.9  3  tRNA-synt_2d     tRNA synthetases class II core domain (F)
  ------ inclusion threshold ------
      0.013   15.7   0.0      0.025   14.8   0.0    1.4  1  Med30            Mediator complex subunit 30


Domain annotation for each model (and alignments):
>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  306.0   0.2   5.8e-95   2.6e-91       2     313 ..     122     437 ..     121     438 .. 0.93

  Alignments for each domain:
  == domain 1  score: 306.0 bits;  conditional E-value: 5.8e-95
                                       CCHHHHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE....- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x RF
                       tRNA-synt_2   2 eelrlknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeff....a 74 
                                       +++ l+ ry+dlr++++s+++++r++v+kavr+ ++++gfie +tP ++ ++te+g  lF +       ++f    +
  gi|298675477|ref|YP_003727227.1| 122 MDTCLDSRYVDLRKPRTSAIFKIRHEVLKAVRDNFTREGFIETTTPKVVATATEGGTSLFPI-------TYFdreaF 191
                                       578899********************************************************.......56666667 PP

                                       E-S-SHHHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  75 LtqspqlylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessak 151
                                       L+qspql++++l+++g+++vf+i++ FRaE+++t+rhl+E t+i++e sf ++ dim++le+ i +  ++v+e+  +
  gi|298675477|ref|YP_003727227.1| 192 LNQSPQLFKQILMSGGLEKVFEIGPIFRAEEHDTRRHLNEATSIDMESSFSDHFDIMETLENTIAHAYSQVKENASQ 268
                                       ***********************************************************************776655 PP

                                       CCCHTTTTTSEE-SSS-EEEEHHHHHHHHHTS.......-SS--HHHHHHHHH....HS--SEEEEEEEBGGGSTTC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 152 diefvirrnskdlkkpfkrltykeaieklnei.......gkdldkaderalvk....keknepvfvtdfPaelkpFy 217
                                       ++e       + +++pfkrlty+eai+++n+        g+dl++  e  l +    +++ + +f++d+P e+kpFy
  gi|298675477|ref|YP_003727227.1| 269 QLEYL-GIDLEVPETPFKRLTYSEAIDIINQYgkeelewGDDLSTLSEHTLGEhvynETGAHHYFIIDWPTEIKPFY 344
                                       55555.4555677888************99888888888777887777777776666788899************** PP

                                       BBBSTTSTTBBSEEEEEETTEEEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHHCT--SEEEEEEEHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 218 arkeeddkkltesyDllingvElvgGslRiedpeeleeklkskgldeeaeekfswylealeyGapphgGlglGldRl 294
                                       a   ed++++++ +D++   +El +G++Ri+ +++l+++++++gld   +++f++yl+a++yG+pph+G+glG++Rl
  gi|298675477|ref|YP_003727227.1| 345 AMPYEDNPEISKTFDMMHTRLELSSGAQRIHYYDMLKNRIENQGLD---PDSFDFYLDAFRYGMPPHAGWGLGCERL 418
                                       **********************************************...**************************** PP

                                       HHHHCT-SSGGGCSSS-XX CS
                                       xxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 295 vmlllgsesIrdviaFPkl 313
                                       +m++lg+e+Ir+v++FP+ 
  gi|298675477|ref|YP_003727227.1| 419 LMTMLGLENIREVVLFPRD 437
                                       *****************96 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.8   0.1   1.8e-19     8e-16       1      76 []      24     103 ..      24     103 .. 0.98

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 1.8e-19
                                       EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET....HHHHHHHTTS-TTSEEEEEEEEEEC...TTSSEEEEE CS
                   tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfr....eeatklaenlkeGdvvrvtGrvkrr...pggelelkv 70 
                                       Vt+aG+v+ +  r+ g+++f++lrD++g+ qv+l +    +++++ a++l +++v+ vtG+vk     p+g +e+  
  gi|298675477|ref|YP_003727227.1|  24 VTLAGWVHEV--RDLGGICFVVLRDREGMAQVTLVKkkvdSDFFNKAKKLMRESVISVTGTVKPEekaPNG-YEVLP 97 
                                       89********..*****************************************************99999*.***** PP

                                       EEEEEE CS
                   tRNA_anti-codon  71 eeiell 76 
                                       ++i++l
  gi|298675477|ref|YP_003727227.1|  98 DDITVL 103
                                       ***986 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.15   6.9e+02      16      44 ..     142     170 ..     131     175 .. 0.81
   2 !    3.6   0.0    0.0089        40     103     152 ..     210     255 ..     194     272 .. 0.69
   3 !   15.6   0.1   1.9e-06    0.0086     212     235 ..     409     432 ..     402     441 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.15
                                       -SHHHHHHHHHHHHHHCTTCEESSTTSEE CS
                      tRNA-synt_2d  16 lhpltkvleeikeiflelgfeevegpeve 44 
                                        ++ ++vl+ +++ f++ gf e++ p+v 
  gi|298675477|ref|YP_003727227.1| 142 FKIRHEVLKAVRDNFTREGFIETTTPKVV 170
                                       556789999*************9999985 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0089
                                       EEEEEEEEEBSST-SSSB-SEEEEEEEEEEETT--HHHHHHHHHHHHHHH CS
                      tRNA-synt_2d 103 kiisigrvfRrdavDathlaeFhqveglvvdenvsladlkgvleellkkl 152
                                       k++ ig +fR ++ D ++    h  e   +d + s++d   ++e+l + +
  gi|298675477|ref|YP_003727227.1| 210 KVFEIGPIFRAEEHDTRR----HLNEATSIDMESSFSDHFDIMETLENTI 255
                                       89***********66544....3346666666666666666666655555 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 1.9e-06
                                       EEEEEEHHHHHHHHHT-SSGHHHH CS
                      tRNA-synt_2d 212 fafGlGveRlamlkygieDiRelv 235
                                       +++GlG eRl m ++g+e+iRe+v
  gi|298675477|ref|YP_003727227.1| 409 AGWGLGCERLLMTMLGLENIREVV 432
                                       68*******************976 PP

>> Med30  Mediator complex subunit 30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   5.5e-06     0.025      19      83 ..     210     275 ..     205     299 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.5e-06
                             Med30  19 rtqelfqllkavqlpngrtqskhqaqdrkkklqeqlrqlkvlfkkLrliYekckenc.qgleevpi 83 
                                       ++ e+  +++a    ++r  ++ ++ d +  ++++++ ++ l +++ + Y ++ken  q+le++ i
  gi|298675477|ref|YP_003727227.1| 210 KVFEIGPIFRAEEHDTRRHLNEATSIDMESSFSDHFDIMETLENTIAHAYSQVKENAsQQLEYLGI 275
                                       67788889999999999999************************************9888997765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2791.05
//
Query:       gi|298675478|ref|YP_003727228.1|  [L=418]
Description: glutamyl-tRNA(Gln) amidotransferase subunit D [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-59  200.4   1.2    3.5e-59  199.6   1.2    1.4  1  Asparaginase    Asparaginase, N-terminal
    2.5e-32  111.5   0.0    1.9e-30  105.4   0.0    2.4  2  Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
    7.7e-17   60.4   0.3    1.8e-16   59.2   0.3    1.6  1  GatD_N          GatD N-terminal domain
    4.7e-05   23.1   0.0      0.065   12.8   0.0    2.2  2  Peripla_BP_4    Periplasmic binding protein domain
  ------ inclusion threshold ------
       0.02   14.8   0.0      0.043   13.7   0.0    1.6  1  Asp_Glu_race    Asp/Glu/Hydantoin racemase
      0.091   12.6   0.1        0.2   11.5   0.1    1.5  1  zf-primase      Primase zinc finger


Domain annotation for each model (and alignments):
>> Asparaginase  Asparaginase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.6   1.2   1.2e-62   3.5e-59       1     183 [.      79     266 ..      79     275 .. 0.95

  Alignments for each domain:
  == domain 1  score: 199.6 bits;  conditional E-value: 1.2e-62
                                       EEEEEEEESGGGEEECTTS--CCEES-HHHHHCCTTTCCCCSEEEEEEEEEE-GGG--HHHHHHHHHHHHHHCCT.- CS
                      Asparaginase   1 kvlvlatGGTiasekdesggalapalsaeellealpelekiaeleseqlanidSsnmtpadwlklaeaieealee.y 76 
                                       kv +l+tGGTias+ d+++ga++ ++sa+++le++pel++iae++ +++ n+ S+nm+p+ w +la+++ +++e+ +
  gi|298675478|ref|YP_003727228.1|  79 KVSILSTGGTIASKIDYRTGAVTAQFSADDILETIPELSEIAEFTGKVVYNVLSENMKPEYWTELAKTVSKEIENgA 155
                                       799**********************************************************************777* PP

                                       SEEEEE--STTHHHHHHHHHHHEES.SSEEEEE--SS-TTSTT-SHHHHHHHHHHHHHCGGTTSECEEEETTE.... CS
                      Asparaginase  77 dgfVvlhGTDTlaytAsaLslmlknldkpvvltGsqrplselrsDgpeNlldAllvaasseriagvlvvfngk.... 149
                                       dg++++hGTDT+ y+A+aLs+m+++ ++p+v++Gsqr++++++sD ++N + A++va+s+  ia+v+ v++g+    
  gi|298675478|ref|YP_003727228.1| 156 DGIIIAHGTDTMMYSAAALSFMIDT-PVPIVFVGSQRSADRPSSDNAMNAICAATVATSD--IAEVTAVMHGTtsdd 229
                                       ***********************99.********************************87..*************** PP

                                       ...EEETTTEEE-BSSSSS-EEETTT--SEEEETTEE CS
                      Asparaginase 150 ...llranrvtKvhtssldaFespnlgplaevegskv 183
                                          ++r+++v+K+hts++daF+s+n  p++ v+ s+ 
  gi|298675478|ref|YP_003727228.1| 230 yceIHRGTQVRKMHTSRRDAFKSINSDPIGFVDYSNR 266
                                       ******************************9844433 PP

>> Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.023        70      20      85 ..     144     213 ..     116     227 .. 0.58
   2 !  105.4   0.0   6.4e-34   1.9e-30       4     110 ..     294     400 ..     292     404 .. 0.96

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.023
                                       H.......HTT--EEEEEEBTTTB--HHHHHHHHHHHTTT-EEEEE.ESSSBS-----H.....HHHHHTEEE- CS
                    Asparaginase_C  20 l.......kkgakGvvlegtGvGnlpsallealkeakargivvvat.sqcpsgsvsnseyeagkelerlgvisa 85 
                                               ++ga+G++++ +  + + sa   al+ ++++ +++v + sq +  + s +  +a ++++++ v ++
  gi|298675478|ref|YP_003727228.1| 144 AktvskeiENGADGIIIAHGTDTMMYSAA--ALSFMIDTPVPIVFVgSQRSADRPSSD--NAMNAICAATVATS 213
                                       15555555999*******99998888743..444444445444433133333333333..25666666655555 PP

  == domain 2  score: 105.4 bits;  conditional E-value: 6.4e-34
                                       EEE--TT--HHHHHHHHHTT--EEEEEEBTTTB--HHHHHHHHHHHTTT-EEEEEESSSBS-----H.....HHHHH CS
                    Asparaginase_C   4 vlklhpgmdtkvlkallkkgakGvvlegtGvGnlpsallealkeakargivvvatsqcpsgsvsnseyeagkelerl 80 
                                       ++k++pg +++vl +++++g++G+vlegtG G++++++++++++a+++gi+vv++sqc++g+v + +y++g+++ ++
  gi|298675478|ref|YP_003727228.1| 294 LVKFTPGTSPDVLSHYIDSGYRGIVLEGTGLGHVSTDWVPEIERAVDSGIPVVVASQCLNGRVCDRVYDTGRDMLKA 370
                                       7899************************************************************************* PP

                                       TEEE-TT--HHHHHHHHHHHCTT---HHHH CS
                    Asparaginase_C  81 gvisaddmtpeaarikLmlllgkgldpaev 110
                                       g+i+a+dm pe a +kLm++lg+++d ++ 
  gi|298675478|ref|YP_003727228.1| 371 GAIEAEDMLPEVAHVKLMWVLGQTDDFDTA 400
                                       *************************98765 PP

>> GatD_N  GatD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.2   0.3     6e-20   1.8e-16       2      55 .]       4      52 ..       3      52 .. 0.96

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 6e-20
                                      -TT-EEEEE-SS-EEEEEE----TTS-SSEEEEEETTS-EEEEE-TT-.---EE CS
                            GatD_N  2 evGDlikvekkgreyeGilmPrselsdddiivlKLdnGYNiGikieeiekiell 55
                                      e+GD+++++k++++yeGi+ P++    +++ivlK+d+GYN+Gi  e++ +i+++
  gi|298675478|ref|YP_003727228.1|  4 EQGDRVQIVKNDVVYEGIVRPSN----TEHIVLKMDSGYNAGIHPENA-EITVV 52
                                      89*********************....*********************.99875 PP

>> Peripla_BP_4  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   2.2e-05     0.065      42     160 ..     141     273 ..     115     300 .. 0.80
   2 !    8.2   0.0   0.00055       1.7      49     120 ..     307     383 ..     301     406 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.2e-05
                                       HHHHHHHHHHHHTT-SEEEE--SSHHHHH..HHHHHHHHTT-EEEEESTT...GCTTT-CEEEEEC-HHHHHHHHHH CS
                      Peripla_BP_4  42 aeQvaqiedaiakgvdgiivapvdstala..palkkakaaGIpVvafdsd...dapsgerlayvgfdneaaGelqae 113
                                       +e ++ +++ i++g+dgii+a    t ++  +al    +  +p+v++ s+   d ps++ + +     + a   +ae
  gi|298675478|ref|YP_003727228.1| 141 TELAKTVSKEIENGADGIIIAHGTDTMMYsaAALSFMIDTPVPIVFVGSQrsaDRPSSDNAMNAICAATVATSDIAE 217
                                       666778999************999977774577778**************999999999999999999999999999 PP

                                       HHHHHCTTH.EEEEEE.TSCCCHHHHHHHHHHHHHHHHH.......-T.TCEECCE CS
                      Peripla_BP_4 114 ylaeklggkkgkvvil.aGspgdpnaeeriegfrkvlke.......yp.gikivae 160
                                       + a   g+ + +++ + +G++  + ++ r ++f+++  +        + +i+++++
  gi|298675478|ref|YP_003727228.1| 218 VTAVMHGTTSDDYCEIhRGTQVRKMHTSRRDAFKSINSDpigfvdySNrKIETISD 273
                                       98888888866676666*******************98877777753346666653 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00055
                                       HHHHHTT-SEEEE--SSH....HHHHHHHHHHHHTT-EEEEESTT.GCTTT-CEEEEEC-HHHHHHHHHHHHHHHCT CS
                      Peripla_BP_4  49 edaiakgvdgiivapvds....talapalkkakaaGIpVvafdsd.dapsgerlayvgfdneaaGelqaeylaeklg 120
                                       +  i++g+ gi++  +      t   p +++a + GIpVv+  +  +    +r++  g d  +aG++ ae ++  + 
  gi|298675478|ref|YP_003727228.1| 307 SHYIDSGYRGIVLEGTGLghvsTDWVPEIERAVDSGIPVVVASQClNGRVCDRVYDTGRDMLKAGAIEAEDMLPEVA 383
                                       5567777777776655543334777789**********999766666678889999999999999999998876665 PP

>> Asp_Glu_race  Asp/Glu/Hydantoin racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.4e-05     0.043      74     190 ..      22     161 ..      14     186 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.4e-05
                                       EE--CHHHHHHHHHH........HH-SSEEEECHHHH..........HHHHHH.HSS-EEEEEE-HHHHHCTH.... CS
                      Asp_Glu_race  74 viaCnTahavadelq........kkikiPvlgiveat..........aealka.tgvkkvglLgTrgtlksgl.... 127
                                       v + nT h+v++  +        +++ i v+   +++           +++k+  ++ kv +L T gt++s++    
  gi|298675478|ref|YP_003727228.1|  22 VRPSNTEHIVLKMDSgynagihpENAEITVVE-KKEAeektrffkpeSASTKQkSDLPKVSILSTGGTIASKIdyrt 97 
                                       55666666666555555544444444455555.44445555555544334444589999*********998754222 PP

                                       ..HHHHHHHHGT..EEE....T-CCCHHCCHCHHHHTT-TTSH.HHHHHHHHHHHHHTTT-SEEEE- CS
                      Asp_Glu_race 128 ..yqkeleanqg.ievvvpseelqssvnqaiyeelkaGevtee.arrailkllerlaergadaviLG 190
                                           ++++a ++ +e++++ +e+++   +++y  + ++++++e +++  +++ +  +e+gad++i++
  gi|298675478|ref|YP_003727228.1|  98 gaVTAQFSA-DDiLETIPELSEIAEFTGKVVY-NVLSENMKPEyWTELAKTVSK-EIENGADGIIIA 161
                                       226778888.4635556666666666677778.788999999955555555555.559*******98 PP

>> zf-primase  Primase zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   6.6e-05       0.2      27      46 .]     227     246 ..     219     246 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.6e-05
                        zf-primase  27 kgeyCdfHvqsavkkarakR 46 
                                       +++yC++H  ++v+k++ +R
  gi|298675478|ref|YP_003727228.1| 227 SDDYCEIHRGTQVRKMHTSR 246
                                       589*************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 2509.38
//
Query:       gi|298675479|ref|YP_003727229.1|  [L=492]
Description: argininosuccinate lyase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-61  206.6   0.1    1.1e-60  205.6   0.0    1.5  2  Lyase_1   Lyase
    6.4e-14   52.5   0.0    5.4e-13   49.5   0.0    2.3  2  ASL_C2    Argininosuccinate lyase C-terminal


Domain annotation for each model (and alignments):
>> Lyase_1  Lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.6   0.0   1.3e-64   1.1e-60      19     309 ..      26     297 ..      11     300 .. 0.92
   2 ?   -3.3   0.0      0.51   4.5e+03      51      84 ..     335     368 ..     319     387 .. 0.62

  Alignments for each domain:
  == domain 1  score: 205.6 bits;  conditional E-value: 1.3e-64
                                       HHHGGGHHHHHCHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHCHCHHCGGHHHBSSSSSHHHHHHHHHHHHHHHHT CS
                           Lyase_1  19 renfrlseedikalaalkkaaakanvdlkeeaaaiikaldevleegklddqfvlkviqegsgtavnmnlnevigell 95 
                                        ++ ++ ++di + +a +  +++ +++ +ee   i++al ++ e+g +     l  + e+++ +++ +l +++g   
  gi|298675479|ref|YP_003727229.1|  26 ETDRWIFQADILVDMAHTIMLEEQEIIHEEECTRILEALLKIKEDGIES----LSHDYEDIHISLESKLIDMVG--- 95 
                                       5556666666667777777788888888999999999999999977776....*********************... PP

                                       THSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-EEEEEETTEEEEEEEHHHHH CS
                           Lyase_1  96 gekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpaleqLidalkekakefkdvvkiGrThlqdAtPvtlgqel 172
                                           ++ +k h g+S+nD ++T lr+ l+++++  ++++l +L+++l + a  + d+v++G+Thlq+A+P+t+++ l
  gi|298675479|ref|YP_003727229.1|  96 ---EDIGGKMHSGRSRNDEIATCLRIYLRDEIT-GIMSELVNLRTVLLKIASYNVDTVMPGFTHLQHAQPTTFAHHL 168
                                       ...7999*************************5.5****************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCCTHHHHHHHHHHHHHCSTEESSSHHHHHHC-HHHHHHH CS
                           Lyase_1 173 sayaealerdrerlkellkrllvellgggtavgtglnadpefaelvakelakvtglpvkapnsfeavsdrDavvell 249
                                        a+ae l rd  rl ++ kr+++ +lg+++ + tg+n ++    +  + l+ ++g     +ns++avs+rD++ve +
  gi|298675479|ref|YP_003727229.1| 169 VAHAESLSRDFDRLFDAFKRINMCPLGSAAFASTGFNLNRT---RTQELLG-FDG---LIENSMDAVSTRDFLVESA 238
                                       ****************************************9...8888888.***...******************* PP

                                       HHHHHHHHHHHHHHHHHHHHTSTTTSSEEEEGCCTSSC-TTSTTTEBTHHHHHHHHHHHH CS
                           Lyase_1 250 galkllatsLskfaeDlrllssgeaglvelslaesepGSSiMPgKvNPvqlElltgvagr 309
                                       ++l++l+++Ls++ae++++ ss e+++vel + + +  SSiMP+K+NP+++El++g+ g 
  gi|298675479|ref|YP_003727229.1| 239 SVLSNLMINLSRMAEEIIIWSSPEFNFVELGDKYAS-TSSIMPQKKNPDTAELIRGKTGS 297
                                       **********************99**********99.9******************9875 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.51
                                       HHHHHHHHHHHCHCHHCGGHHHBSSSSSHHHHHH CS
                           Lyase_1  51 aaiikaldevleegklddqfvlkviqegsgtavn 84 
                                       ++ +k ++ + e+++++ ++ l  ++eg  ta++
  gi|298675479|ref|YP_003727229.1| 335 SSSVKIMSGMFEDMNINSEVMLSRSKEGFTTATE 368
                                       4445555555555555555555555555555554 PP

>> ASL_C2  Argininosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.22     2e+03      21      31 ..     165     175 ..     163     189 .. 0.81
   2 !   49.5   0.0     6e-17   5.4e-13       1      65 [.     363     432 ..     363     436 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.22
                                       HHHHHHHHHHH CS
                            ASL_C2  21 AHeivgravrl 31 
                                       AH++v++a +l
  gi|298675479|ref|YP_003727229.1| 165 AHHLVAHAESL 175
                                       9****998666 PP

  == domain 2  score: 49.5 bits;  conditional E-value: 6e-17
                                       STTHHHHHHHHHHC.TS-HHHHHHHHHHHHHHHHHTT--.GGG--HHHHH.HH-TT.--.GGGGGGSSHH CS
                            ASL_C2   1 FstATdlADyLvrk.GlpFReAHeivgravrlaeekgke.leeltleelk.eispl.le.edveeaLdpe 65 
                                       F+tAT+lAD Lvr  G+pFR+AH+i+g+++++     +e +++++l+ l  ++s++ l+   v+eaLdp 
  gi|298675479|ref|YP_003727229.1| 363 FTTATELADTLVRVtGIPFRTAHQIIGAIAKEPGTPTIEkIDNVSLDVLGkKLSDIgLTeGLVQEALDPV 432
                                       99***********99****************933333223555555555533345577745678899986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.51
# Mc/sec: 2897.94
//
Query:       gi|298675480|ref|YP_003727230.1|  [L=754]
Description: PAS/PAC sensor signal transduction histidine kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-41  141.3   0.0    4.8e-12   45.9   0.0    4.7  5  PAS          PAS fold
    1.3e-35  121.8   3.4    2.5e-12   46.9   0.1    4.5  4  PAS_9        PAS domain
    3.4e-31  108.0   0.1      6e-30  104.0   0.0    2.6  2  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    8.2e-30  103.0   0.0    2.4e-14   53.4   0.1    4.6  4  PAS_3        PAS fold
    2.8e-28   98.4   0.0    3.8e-07   30.3   0.0    4.2  4  PAS_4        PAS fold
    1.2e-23   82.6   0.2    3.4e-07   30.1   0.0    3.8  3  PAS_8        PAS domain
    2.4e-16   59.5   0.0    7.7e-16   57.9   0.0    2.0  1  HisKA        His Kinase A (phospho-acceptor) domain
    3.2e-07   30.5   5.5      0.039   14.1   0.0    5.3  4  PAS_7        PAS fold
    7.6e-07   29.7   0.2     0.0014   19.2   0.1    3.0  2  PAS_10       PAS domain
    8.4e-06   25.9   0.0     0.0073   16.4   0.0    2.8  2  PAS_11       PAS domain
    7.7e-05   21.8   4.6    0.00012   21.2   2.0    2.1  2  LMBR1        LMBR1-like membrane protein
    9.6e-05   22.3   0.0       0.14   12.1   0.0    2.9  3  MEKHLA       MEKHLA domain
     0.0026   17.6   0.0      0.011   15.6   0.0    2.2  1  HATPase_c_5  GHKL domain
  ------ inclusion threshold ------
      0.031   14.1   0.0       0.11   12.3   0.0    1.9  2  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
      0.039   13.6   1.1       0.23   11.1   0.2    2.6  2  PAS_12       UPF0242 C-terminal PAS-like domain
      0.084   12.8   0.0       0.19   11.7   0.0    1.6  1  HATPase_c_2  Histidine kinase-like ATPase domain


Domain annotation for each model (and alignments):
>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   0.0   4.3e-15   4.8e-12       1     113 []       3     118 ..       3     118 .. 0.95
   2 !   15.8   0.0   9.5e-06     0.011       3     112 ..     138     250 ..     136     251 .. 0.83
   3 !   36.2   0.0   4.3e-12   4.8e-09       2     113 .]     267     374 ..     266     374 .. 0.95
   4 !   37.8   0.0   1.4e-12   1.6e-09       2     113 .]     390     497 ..     389     497 .. 0.79
   5 ?   -3.0   0.0       6.2     7e+03      57      79 ..     645     667 ..     626     688 .. 0.52

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 4.3e-15
                                       HHHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.....HHHHHHHHHHHHTT-E CS
                               PAS   1 edlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda.....elaelleqlleqgees 72 
                                       e++++ile++  +i+vvD+  +++y+++++++++G+s e+v+gk l+ +++e          ++el++++ ++ +++
  gi|298675480|ref|YP_003727230.1|   3 EFYEQILENISQGIWVVDKFDKFIYFSQNMADITGISKEDVIGKYLMSYMPER--TigndvHFRELFLRVKNTLQPE 77 
                                       689***********************************************986..3358889*************** PP

                                       CCCCEEEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  73 rageisfklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       + + i ++ ++g +++   r +p+ d +++  g  +++ di
  gi|298675480|ref|YP_003727230.1|  78 HFKSIPLRNKKGNITYQSGRLVPISDTDSNYNGMACIIEDI 118
                                       *****9999******************************98 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 9.5e-06
                                       HHHHHHHSSSEEEEEE.TTSBEEEECHHHHHHHSSTH.HHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCC CS
                               PAS   3 lraileslpdpifvvD.edgrilyvNaaaeellGlsr.eevlgkslldliheedda.elaelleqlleqgeesrage 76 
                                       l++i  s+p+  f+++ e+ + +++ +    ++G++  +  +g+ ++++i+++dd  +++++++q++  g    ++e
  gi|298675480|ref|YP_003727230.1| 138 LESIYKSSPVIAFLWRaEKDWPVEFVSDNIIQFGYTSeDFTSGRLIFGDIVHPDDLqKVRDAVSQVEIGGYTYFTKE 214
                                       677788888888888876666666666667789999968899*********************************** PP

                                       EEEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEE CS
                               PAS  77 isfklrdgrpihlevraspvrdaggeilgflgvlrd 112
                                        ++ ++ g+ +++  r    r   g + ++ g++ d
  gi|298675480|ref|YP_003727230.1| 215 YRILTKSGEARWVTERSMLGRKYNGVPAYYQGIIID 250
                                       *****9999999998888777777777777777776 PP

  == domain 3  score: 36.2 bits;  conditional E-value: 4.3e-12
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       ++r i+e++p +if  De+g+++  N+++ ++l l+r+e++g  +  ++  ed   ++++l q+ + ++    g  +
  gi|298675480|ref|YP_003727230.1| 267 KYRLIFENSPLGIFDFDENGVVTSGNENMLKILDLTRDELIGFDMPKSLEDED---MKKALYQVFQKKTGHYEGYYR 340
                                       699**********************************************9887...999999999999999999998 PP

                                       EECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  79 fklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                        ++  +++++l v  sp+++++g+i g +g++ di
  gi|298675480|ref|YP_003727230.1| 341 SPT-SNKTVPLKVDFSPIISEEGTIQGGVGIVEDI 374
                                       999.9*************************99998 PP

  == domain 4  score: 37.8 bits;  conditional E-value: 1.4e-12
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       ++r+++e++ d+if+ D +g+il+vN+ a + lG+s +e+ + + +dli++ + + ++ +l +  + g    ++e+ 
  gi|298675480|ref|YP_003727230.1| 390 KFRSLFENANDAIFIHDLKGNILEVNQLASQRLGYSKDELTNIKSMDLISPFYADNMKNRLNTIQKKG--HGIFETV 464
                                       6899**********************************************974433444443333222..2333333 PP

                                       EECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  79 fklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                         +++g+ i++e+  + +  +g++   +l  +rdi
  gi|298675480|ref|YP_003727230.1| 465 QITKNGSSIPVELSSRIIEYEGKT--AILALARDI 497
                                       3337*********99988888876..999999997 PP

  == domain 5  score: -3.0 bits;  conditional E-value: 6.2
                                       HHHHHHHHHHHHTT-ECCCCEEE CS
                               PAS  57 elaelleqlleqgeesrageisf 79 
                                       +l + l++ll +++++++    +
  gi|298675480|ref|YP_003727230.1| 645 KLTDMLTNLLDNATKFTSSGGEI 667
                                       55555555555555544333333 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.1   2.7e-09     3e-06       2     104 .]      14     120 ..      13     120 .. 0.73
   2 !    9.5   0.0   0.00098       1.1      12     104 .]     159     253 ..     147     253 .. 0.80
   3 !   35.6   0.0   7.5e-12   8.4e-09       3     104 .]     278     376 ..     276     376 .. 0.75
   4 !   46.9   0.1   2.3e-15   2.5e-12       2     104 .]     400     499 ..     399     499 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 2.7e-09
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrk..kerevevvlirknge 74 
                                        gi+++++  + +y+++ +++++G s+e+v+gk++   +   t  ++ ++ + +l+ + +  +e+ + + l++k+g+
  gi|298675480|ref|YP_003727230.1|  14 QGIWVVDKFDKFIYFSQNMADITGISKEDVIGKYLMSYMpeRTIGNDVHFRELFLRVKNTlqPEHFKSIPLRNKKGN 90 
                                       589998677799**********************9999986333333333333444444474444445555555555 PP

                             PAS_9  75 tfwvlltaspvkdddgelvgiivilrDite 104
                                         +   +++p+ d+d ++ g+++i++Dite
  gi|298675480|ref|YP_003727230.1|  91 ITYQSGRLVPISDTDSNYNGMACIIEDITE 120
                                       55555************************8 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00098
                             PAS_9  12 rilyaNeaalrllGyspeevlgks..itdlfvtdpeanerlraaleqgrk...kerevevvlirkngetfwvl.lta 82 
                                       +++++++  +++ Gy++e++   +  + d++  +p++ +++r+a+ q +    + +++e+ + +k+ge  wv   ++
  gi|298675480|ref|YP_003727230.1| 159 PVEFVSDNIIQF-GYTSEDFTSGRliFGDIV--HPDDLQKVRDAVSQVEIggyTYFTKEYRILTKSGEARWVTeRSM 232
                                       677999999998.******999998778888..99999999999999999***99****************653333 PP

                             PAS_9  83 spvkdddgelvgiivilrDite 104
                                          +  +g    + +i++D+te
  gi|298675480|ref|YP_003727230.1| 233 LG-RKYNGVPAYYQGIIIDVTE 253
                                       33.3335566667788888887 PP

  == domain 3  score: 35.6 bits;  conditional E-value: 7.5e-12
                             PAS_9   3 gil.idnpdgril.yaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkng.etf 76 
                                       gi+ +d ++g ++ + Ne +l++l  +++e++g ++   + +d++ ++ l ++++ ++   +e+ +   +    +t+
  gi|298675480|ref|YP_003727230.1| 278 GIFdFD-ENG-VVtSGNENMLKILDLTRDELIGFDMPKSL-EDEDMKKALYQVFQKKT-GHYEGYYRSPT--SnKTV 348
                                       666444.999.666*******************9999999.44444444444444444.33333333333..358** PP

                             PAS_9  77 wvlltaspvkdddgelvgiivilrDite 104
                                       + ++ +sp+++++g+++g ++i++Dite
  gi|298675480|ref|YP_003727230.1| 349 PLKVDFSPIISEEGTIQGGVGIVEDITE 376
                                       ***************************8 PP

  == domain 4  score: 46.9 bits;  conditional E-value: 2.3e-15
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfw 77 
                                       d+i+i + +g+il +N+ a + lGys++e+ + +  dl+  +p  ++++++ l++++k     +e+v i+kng+ ++
  gi|298675480|ref|YP_003727230.1| 400 DAIFIHDLKGNILEVNQLASQRLGYSKDELTNIKSMDLI--SPFYADNMKNRLNTIQKkGHGIFETVQITKNGSSIP 474
                                       89***88********************************..88888888888888888879**************** PP

                             PAS_9  78 vlltaspvkdddgelvgiivilrDite 104
                                       v+l+ + +  ++++ ++  ++ rDite
  gi|298675480|ref|YP_003727230.1| 475 VELSSRIIEYEGKTAIL--ALARDITE 499
                                       ********999988888..*******8 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.54     6e+02      37      59 ..     461     483 ..     387     505 .. 0.70
   2 !  104.0   0.0   5.4e-33     6e-30       1     111 [.     641     752 ..     641     753 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.54
                                       EEEEEEEESSSSSTTHHHTGTCS CS
                         HATPase_c  37 dlvisveDnGiGipkedlkklfe 59 
                                         +++++ nG  ip+e   ++ e
  gi|298675480|ref|YP_003727230.1| 461 FETVQITKNGSSIPVELSSRIIE 483
                                       45789999999999998887765 PP

  == domain 2  score: 104.0 bits;  conditional E-value: 5.4e-33
                                       EHHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTSSSH CS
                         HATPase_c   1 gdekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsq.ddstkrggggtGl 76 
                                       gd+ +L+ ++ nl+dNa kf++++gei+ve   ++++++i+v+D+G Gip++ ++ lf++f+q d+s +r++ggtGl
  gi|298675480|ref|YP_003727230.1| 641 GDKAKLTDMLTNLLDNATKFTSSGGEITVEAFEEDEHIHIKVTDTGVGIPEDLIPYLFQRFYQiDSSIRRKYGGTGL 717
                                       68899***************8899999999996558***************************************** PP

                                       HHHHHHHHHHHTTTEEEEEEETTTEEEEEEEEESS CS
                         HATPase_c  77 GlsivkklvelmgGeiwvesepgrGttftftlple 111
                                       Gl+i+k +v+ + G+iw++s +g+Gtt++++lp++
  gi|298675480|ref|YP_003727230.1| 718 GLYICKLIVDAHYGNIWIDSIEGKGTTVHVKLPET 752
                                       **********999*******************987 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00013      0.14       2      88 ..      26     114 ..      25     115 .. 0.76
   2 !   53.4   0.1   2.2e-17   2.4e-14       4      89 .]     163     248 ..     160     248 .. 0.90
   3 !   12.3   0.0   0.00014      0.15       5      88 ..     292     370 ..     288     371 .. 0.80
   4 !   19.2   0.0     1e-06    0.0011       2      81 ..     412     487 ..     411     492 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeD....rervrealqealkkge.pyegeyRirrkdGeyrwvearar 73 
                                       iy s+++ +i+G+s+e+++gk   +l+   pe       ++re + ++ ++ + +    + +r+k G +++ + r +
  gi|298675480|ref|YP_003727230.1|  26 IYFSQNMADITGISKEDVIGK---YLMSYMPERtignDVHFRELFLRVKNTLQpEHFKSIPLRNKKGNITYQSGRLV 99 
                                       9********************...77777777633334556666666667777433455999999999999999999 PP

                             PAS_3  74 virdengkpvrvigv 88 
                                       +i d +++   + ++
  gi|298675480|ref|YP_003727230.1| 100 PISDTDSNYNGMACI 114
                                       999999887777766 PP

  == domain 2  score: 53.4 bits;  conditional E-value: 2.2e-17
                             PAS_3   4 vserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepy.egeyRirrkdGeyrwveararvirden 79 
                                       vs+++ +  Gy++e++++    + d+vhp+D+++vr+a+ ++  +g  y + eyRi++k+Ge rwv +r    r  n
  gi|298675480|ref|YP_003727230.1| 163 VSDNIIQF-GYTSEDFTSGRLIFGDIVHPDDLQKVRDAVSQVEIGGYTYfTKEYRILTKSGEARWVTERSMLGRKYN 238
                                       56666555.**********999********************88888555*******************9999**** PP

                             PAS_3  80 gkpvrvigva 89 
                                       g p +++g++
  gi|298675480|ref|YP_003727230.1| 239 GVPAYYQGII 248
                                       ********85 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00014
                             PAS_3   5 serveeilGyspeellgkveswldlvhpeD.rervrealqealkkgepyegeyRirrkdGeyrwveararvirdeng 80 
                                       +e++ +il+++++el+g   ++ + +  eD  + +++ +q   kk ++yeg+yR  + + ++  ++   ++i +e+g
  gi|298675480|ref|YP_003727230.1| 292 NENMLKILDLTRDELIGF--DMPKSLEDEDmKKALYQVFQ---KKTGHYEGYYRSPTSNKTV-PLKVDFSPIISEEG 362
                                       899***************..**********5555556665...44458*****988887665.88888888888888 PP

                             PAS_3  81 kpvrvigv 88 
                                        ++  +g+
  gi|298675480|ref|YP_003727230.1| 363 TIQGGVGI 370
                                       88877776 PP

  == domain 4  score: 19.2 bits;  conditional E-value: 1e-06
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       + v++  ++ lGys++el++   + +dl+ p   +++++ l+++ kkg+ + +e   ++k+G+ + ve + r+i   
  gi|298675480|ref|YP_003727230.1| 412 LEVNQLASQRLGYSKDELTNI--KSMDLISPFYADNMKNRLNTIQKKGHGI-FETVQITKNGSSIPVELSSRII-EY 484
                                       678899999************..*******************999999954.78888*****************.66 PP

                             PAS_3  79 ngk 81 
                                       +gk
  gi|298675480|ref|YP_003727230.1| 485 EGK 487
                                       665 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   6.9e-10   7.7e-07       1     109 [.       9     122 ..       9     123 .. 0.97
   2 !    8.6   0.0    0.0019       2.2       4     109 ..     145     255 ..     142     256 .. 0.82
   3 !   30.3   0.0   3.4e-10   3.8e-07       1     110 []     272     379 ..     272     379 .. 0.96
   4 !   25.3   0.0   1.3e-08   1.4e-05       1     110 []     395     502 ..     395     502 .. 0.98

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 6.9e-10
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee...daarleralrrvlegeepiefleelll 74 
                                       l+++++++ v+d+  +++y ++++a++ g++ e+++Gk l +++pe+       +++   rv  + +p +f  ++l+
  gi|298675480|ref|YP_003727230.1|   9 LENISQGIWVVDKFDKFIYFSQNMADITGISKEDVIGKYLMSYMPERtigNDVHFRELFLRVKNTLQPEHFKSIPLR 85 
                                       799********************************************98888899********************** PP

                             PAS_4  75 ..pgeerhyelrllPlrdesGevigvlvisrDiTerr 109
                                          g   + + rl+P+ d++    g  +i+ DiTe++
  gi|298675480|ref|YP_003727230.1|  86 nkKGNITYQSGRLVPISDTDSNYNGMACIIEDITEQK 122
                                       99999999999************************96 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0019
                             PAS_4   4 lpdalavl..dpdgrvlyaNaaaaelfgappeell.Gktla.ellpeedaarleralrrvlegeepiefleelll.. 74 
                                       +p++ + +   +d  v++++ ++ + fg++ e+++ G+  + +++ ++d + +++a+ +v  g+ ++++ e++ l  
  gi|298675480|ref|YP_003727230.1| 145 SPVIAFLWraEKDWPVEFVSDNIIQ-FGYTSEDFTsGRLIFgDIVHPDDLQKVRDAVSQVEIGGYTYFTKEYRILtk 220
                                       5555555566666666666666666.6666666651666669999999***********************99999* PP

                             PAS_4  75 pgeerhyelrllPlrdesGevigvlvisrDiTerr 109
                                       +ge r++  r +  r+ +G +  + +i++D+Ter+
  gi|298675480|ref|YP_003727230.1| 221 SGEARWVTERSMLGRKYNGVPAYYQGIIIDVTERK 255
                                       **********************************8 PP

  == domain 3  score: 30.3 bits;  conditional E-value: 3.4e-10
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pg 76 
                                       ++++p +++ +d++g+v+  N+++ +++ ++++el+G  +   l +   ++   al +v + ++ +++  ++ + + 
  gi|298675480|ref|YP_003727230.1| 272 FENSPLGIFDFDENGVVTSGNENMLKILDLTRDELIGFDMPKSLED---EDMKKALYQVFQKKTGHYEGYYRSPtSN 345
                                       79***********************************999975555...99************************** PP

                             PAS_4  77 eerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                       +++++ + ++P+  e+G+++g ++i+ DiTer++
  gi|298675480|ref|YP_003727230.1| 346 KTVPLKVDFSPIISEEGTIQGGVGIVEDITERKQ 379
                                       ********************************85 PP

  == domain 4  score: 25.3 bits;  conditional E-value: 1.3e-08
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       +++ +da+++ d  g++l +N+ a + +g++ +el++ +  +l ++  a++  + l+   + ++ i+++   + +g+
  gi|298675480|ref|YP_003727230.1| 395 FENANDAIFIHDLKGNILEVNQLASQRLGYSKDELTNIKSMDLISPFYADNMKNRLNTIQKKGHGIFETVQITKNGS 471
                                       7999*******************999*************************************************** PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerrr 110
                                         ++el+ + + + +G+  ++l+++rDiTer+r
  gi|298675480|ref|YP_003727230.1| 472 SIPVELSSRII-EYEGK-TAILALARDITERKR 502
                                       **********9.68999.9************97 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   1.1e-09   1.2e-06       1      55 [.       3      58 ..       3      71 .. 0.82
   2 !   19.6   0.0   6.1e-07   0.00068       2      46 ..     267     312 ..     266     330 .. 0.79
   3 !   30.1   0.0     3e-10   3.4e-07       2      41 ..     390     430 ..     389     453 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1.1e-09
                             PAS_8  1 erlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpvlrpl 55
                                      e++++++e++++gi+vvd  d++++  q +++++G s +d++g+ l  ++p+ + +
  gi|298675480|ref|YP_003727230.1|  3 EFYEQILENISQGIWVVDKFDKFIYFSQNMADITGISkEDVIGKYLMSYMPERTIG 58
                                      79****************8889***************9999999887666655544 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 6.1e-07
                             PAS_8   2 rlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellg 46 
                                       ++r +fe+sp gi+ +d +g  ++  N+ +l++l ++ ++l+g ++ 
  gi|298675480|ref|YP_003727230.1| 267 KYRLIFENSPLGIFDFDeNGV-VTSGNENMLKILDLTrDELIGFDMP 312
                                       8*************9996666.************9887777775543 PP

  == domain 3  score: 30.1 bits;  conditional E-value: 3e-10
                             PAS_8   2 rlralfesspdgiavvd.lgdrivdvNqaalellGys.adlk 41 
                                       ++r+lfe+++d+i++ d  g+ i++vNq a + lGys ++l 
  gi|298675480|ref|YP_003727230.1| 390 KFRSLFENANDAIFIHDlKGN-ILEVNQLASQRLGYSkDELT 430
                                       89*************996666.***************66654 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.9   0.0   6.9e-19   7.7e-16       1      67 []     527     595 ..     527     595 .. 0.93

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 6.9e-19
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH.HC...T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                             HisKA   1 slgrflagvaHELrtPLsailgnaeaL.kre.gklteelkeyletiesearrldhlvedlLdlsrieag 67 
                                       ++ +fl++v+HEL+tPL++i+g++ ++ +++ gkl++e+k+  +ti+++++rl++lv+ l  +s  +ag
  gi|298675480|ref|YP_003727230.1| 527 MKDEFLSNVSHELKTPLTSIKGYSNIIyEETlGKLNDEQKKTMNTIVRNSERLRRLVDSLIYMSMSQAG 595
                                       689************************55559****************************999987775 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   3.5e-05     0.039       1     112 [.       9     123 ..       9     126 .. 0.78
   2 ?   -2.0   0.0       3.5     4e+03     106     115 .]     250     259 ..     246     259 .. 0.88
   3 !    6.7   0.3    0.0069       7.7       2     114 ..     273     381 ..     272     382 .. 0.52
   4 ?    6.2   0.0      0.01        12       2     114 ..     396     504 ..     395     505 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.5e-05
                             PAS_7   1 lenmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaeverrl..aaara..g 73 
                                       len+sqGi v+D+ ++ + + +++ ++ ++++e v +g+ l + +  ++  +++  ++    v+++l  ++ ++   
  gi|298675480|ref|YP_003727230.1|   9 LENISQGIWVVDKFDKFIYFSQNMADITGISKEDV-IGKYLMSYMPERTIGNDVHFRELFLRVKNTLqpEHFKSipL 84 
                                       89********************************9.88877666665555555555565555666664444444545 PP

                             PAS_7  74 kphsfererpdgrvievrgnplpdgGfVttytDiTerrr 112
                                       ++++ + + ++gr + +  +     G+  + +DiTe++ 
  gi|298675480|ref|YP_003727230.1|  85 RNKKGNITYQSGRLVPISDTDSNYNGMACIIEDITEQKL 123
                                       6677777888999999999999999**********9986 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.5
                             PAS_7 106 DiTerrraee 115
                                       D+Ter++aee
  gi|298675480|ref|YP_003727230.1| 250 DVTERKKAEE 259
                                       9******996 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0069
                             PAS_7   2 enmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellryn.aergefg.agdveaeverrlaaaragkph 76 
                                       en + Gi  fD+++ ++  N+++l++ldl+++ + +g  + + l+    ++  ++  ++   ++e      r+ +++
  gi|298675480|ref|YP_003727230.1| 273 ENSPLGIFDFDENGVVTSGNENMLKILDLTRDEL-IGFDMPKSLEDEdMKKALYQvFQKKTGHYEGYY---RSPTSN 345
                                       6777789999999999999999999999988777.666655554444122222222222222222222...222222 PP

                             PAS_7  77 sfererpdgrvievrgnplpdgGfVttytDiTerrrae 114
                                       ++     +  +  + +++    G V + +DiTer++ae
  gi|298675480|ref|YP_003727230.1| 346 KTVPL--KVDFSPIISEEGTIQGGVGIVEDITERKQAE 381
                                       22222..2222333333334455577778888888877 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.01
                             PAS_7   2 enmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaeverrlaaaragkphsf 78 
                                       en +++i + D +++++ +N+   + l+++++ +   ++++ +  + a++ + + ++++++ + +++ ++  k+ s 
  gi|298675480|ref|YP_003727230.1| 396 ENANDAIFIHDLKGNILEVNQLASQRLGYSKDELTNIKSMDLISPFYADNMKNRLNTIQKKGHGIFETVQITKNGSS 472
                                       78889999999999999999999999999999998888888888888888888888888888888888888888888 PP

                             PAS_7  79 ererpdgrvievrgnplpdgGfVttytDiTerrrae 114
                                          + + r+ie +g++     +++   DiTer+rae
  gi|298675480|ref|YP_003727230.1| 473 IPVELSSRIIEYEGKT----AILALARDITERKRAE 504
                                       8888888999999875....69999*********99 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   1.2e-06    0.0014       4     106 .]       8     119 ..       6     119 .. 0.83
   2 !    7.1   0.0     0.007       7.8      15     106 .]     282     375 ..     269     375 .. 0.59

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.2e-06
                            PAS_10   4 lLnstpieltflDdnlqirrFtpaakklfklipadv.Grpladihpk.kavknv..eeviealrtgekdevevvvp. 75 
                                       +L+++  ++  +D+ +++++F+++ + +  + ++dv G  l +  p+  + ++v  +e++ +++++ + e+ + +p 
  gi|298675480|ref|YP_003727230.1|   8 ILENISQGIWVVDKFDKFIYFSQNMADITGISKEDViGKYLMSYMPErTIGNDVhfRELFLRVKNTLQPEHFKSIPl 84 
                                       79999999***********************999855********99633344444999999999999888888888 PP

                            PAS_10  76 ..kngkw..vlvrylpyrdedgeiaGvvetfvDit 106
                                         k+g++     r  p+ d+d +++G+  ++ Dit
  gi|298675480|ref|YP_003727230.1|  85 rnKKGNItyQSGRLVPISDTDSNYNGMACIIEDIT 119
                                       664444411456899******************97 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.007
                            PAS_10  15 lDdnlqirrFtpaakklfklipad.vGrpladihpkkavknveeviealrtgekdevevvvp....kngkwvlvryl 86 
                                       +D+n  ++  +++  k+++l++++ +G ++ +     + +++++ + ++ ++++ + e +      ++     v  +
  gi|298675480|ref|YP_003727230.1| 282 FDENGVVTSGNENMLKILDLTRDElIGFDMPKS---LEDEDMKKALYQVFQKKTGHYEGYYRsptsNKTVPLKVDFS 355
                                       555555555555555555555544245444333...344445555555555555444333322332666678999** PP

                            PAS_10  87 pyrdedgeiaGvvetfvDit 106
                                       p+  e+g i+G v ++ Dit
  gi|298675480|ref|YP_003727230.1| 356 PIISEEGTIQGGVGIVEDIT 375
                                       ******************97 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.0    0.0092        10      37      83 ..     180     227 ..     166     242 .. 0.74
   2 !   16.4   0.0   6.5e-06    0.0073       5      87 ..     402     479 ..     398     488 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0092
                            PAS_11  37 grsiy.dLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvkv 83 
                                       gr+i+ d++hp+dl++++++ ++v     +  +  yR+ +++++  +v
  gi|298675480|ref|YP_003727230.1| 180 GRLIFgDIVHPDDLQKVRDAVSQVEIGGYTYFTKEYRILTKSGEARWV 227
                                       4444439****************9855556677779998887766555 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 6.5e-06
                            PAS_11   5 ttrldidgkIisvDtsaLrasfslglekeelvgrsiydLchpqdlstlkshlrevissngeatsslyRLrlsqdkfv 81 
                                       ++++d++g+I++v++    as +lg++k+el+++   dL++p    ++k+ l  ++ ++g++   +++++  ++  +
  gi|298675480|ref|YP_003727230.1| 402 IFIHDLKGNILEVNQ---LASQRLGYSKDELTNIKSMDLISPFYADNMKNRLNTIQ-KKGHGIFETVQITK-NGSSI 473
                                       789************...999***********************************.99999888888776.77777 PP

                            PAS_11  82 kvktks 87 
                                        v   s
  gi|298675480|ref|YP_003727230.1| 474 PVELSS 479
                                       776555 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.18     2e+02     300     348 ..     111     163 ..      60     173 .. 0.77
   2 !   21.2   2.0     1e-07   0.00012     198     304 ..     482     589 ..     457     660 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.18
                             LMBR1 300 kalelediiknksskekefksses.srrgefakqg...klkltptleyywakl 348
                                        a  +edi ++k sk+++  + e  +++++++k++    ++++    ++++++
  gi|298675480|ref|YP_003727230.1| 111 MACIIEDITEQKLSKKTQRDEWEAeNKLESIYKSSpviAFLWRAEKDWPVEFV 163
                                       456689*********99999998889999999997766667777777777665 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 1e-07
                             LMBR1 198 ldeelkklyfeaaklntekeeaereledllkevkklrksisesdplrkyleeilkkvPeeiaeklks....nenk.t 269
                                       +++e k + + +a+  te++ aer+l+++ +e++k+++++++ d   k+ +e l++v +e+++ l s    ++    
  gi|298675480|ref|YP_003727230.1| 482 IEYEGKTAILALARDITERKRAERKLNEYANELAKANEELKSLD---KMKDEFLSNVSHELKTPLTSikgySN-IiY 554
                                       5556666666777777899*********************9999...9****************999987444.359 PP

                             LMBR1 270 eeslaklekqlikalqkrertekqwkrllekalel 304
                                       ee+l kl+ +++k++++ +r++++++rl++  + +
  gi|298675480|ref|YP_003727230.1| 555 EETLGKLNDEQKKTMNTIVRNSERLRRLVDSLIYM 589
                                       9*****************************99433 PP

>> MEKHLA  MEKHLA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       3.2   3.6e+03     113     139 ..      90     116 ..      69     119 .. 0.83
   2 !    6.7   0.0    0.0057       6.3      44      96 ..     281     330 ..     252     347 .. 0.77
   3 !   12.1   0.0   0.00012      0.14      23     116 ..     384     475 ..     372     481 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.2
                            MEKHLA 113 rfsienavvWkvldeegkahGqAamfs 139
                                       +++++ + +  + d++ ++ G+A +++
  gi|298675480|ref|YP_003727230.1|  90 NITYQSGRLVPISDTDSNYNGMACIIE 116
                                       577888889999999******999876 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0057
                            MEKHLA  44 slkadpvfnyaNqaaldllettweeltdlpsrksaepee.keeRealLekvaeq 96 
                                       +++++ v + +N++ l++l++t +el+ + + ks+e+e+ k+     L +v ++
  gi|298675480|ref|YP_003727230.1| 281 DFDENGVVTSGNENMLKILDLTRDELIGFDMPKSLEDEDmKK----ALYQVFQK 330
                                       5667788999**************************666433....44444443 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.00012
                            MEKHLA  23 sesaeelakaLfe.apfavlshslkadpvfnyaNqaaldllettweeltdlpsrksaepeekeeRealLekvaeqgf 98 
                                        +++e++ ++Lfe a++a++ h+lk + ++   Nq a + l ++ +elt+++s   ++p   ++ ++ L++++++g 
  gi|298675480|ref|YP_003727230.1| 384 LKESEKKFRSLFEnANDAIFIHDLKGN-ILE-VNQLASQRLGYSKDELTNIKSMDLISPFYADNMKNRLNTIQKKGH 458
                                       445789999***999*********955.444.6*************************9999999***********9 PP

                            MEKHLA  99 venysGvrisstGrrfsi 116
                                          ++ v+i+++G  + +
  gi|298675480|ref|YP_003727230.1| 459 -GIFETVQITKNGSSIPV 475
                                       .55999****99987755 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0     1e-05     0.011       5      89 ..     645     737 ..     642     750 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1e-05
                       HATPase_c_5   5 dlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg..........ek.kkle.sskskkeehGi 69 
                                        l+ +l nlLdNA    s       +I++++ e+++++ i+++ +  g          +   ++  s  +k +  G+
  gi|298675480|ref|YP_003727230.1| 645 KLTDMLTNLLDNATKFTSSGG----EITVEAFEEDEHIHIKVTDTGVGipedlipylfQRfYQIDsSIRRKYGGTGL 717
                                       678899******988777755....7******************9777666666655422333433557888999** PP

                       HATPase_c_5  70 Glksireivkkykgnlsiea 89 
                                       Gl   + iv+ + gn++i+ 
  gi|298675480|ref|YP_003727230.1| 718 GLYICKLIVDAHYGNIWIDS 737
                                       ****************9976 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       5.2   5.8e+03      76     108 ..     486     517 ..     484     536 .. 0.66
   2 ?   12.3   0.0   9.7e-05      0.11       5      77 ..     648     719 ..     644     747 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5.2
                       HATPase_c_3  76 GlklAslslgkkltvitkkegesstltldvdki 108
                                       G k+A+l l++++t   ++e + +++  ++ k 
  gi|298675480|ref|YP_003727230.1| 486 G-KTAILALARDITERKRAERKLNEYANELAKA 517
                                       6.8888888888887777776666665555444 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 9.7e-05
                       HATPase_c_3   5 kAlaelvdNsld..AdaenvkievnknrgktgeivieDdGkGmseeelknal.rlatsskeakrkstslGkkGiGl 77 
                                       + l+ l+dN++   ++  ++++e+ +++ ++  i+++D G G++e+ +   + r+ + + +    ++++G  G+Gl
  gi|298675480|ref|YP_003727230.1| 648 DMLTNLLDNATKftSSGGEITVEAFEED-EHIHIKVTDTGVGIPEDLIPYLFqRFYQIDSS---IRRKYGGTGLGL 719
                                       5688999**9884466667888877765.789***********998887766346666666...588888888886 PP

>> PAS_12  UPF0242 C-terminal PAS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.1   1.2e+03      64      89 ..      20      45 ..       9      48 .. 0.78
   2 ?   11.1   0.2    0.0002      0.23      48     138 ..     391     482 ..     376     486 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.1
                            PAS_12 64 qkenkllfaNaqirallGwssdkflq 89
                                       k +k ++  +++ +++G s+++++ 
  gi|298675480|ref|YP_003727230.1| 20 DKFDKFIYFSQNMADITGISKEDVIG 45
                                      5668999999***********99875 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0002
                            PAS_12  48 fDsLrsEnlgailvysqkenkllfaNaqirallGwssdkflq.dfseivqegle.eWkralaklsskteskirlvlK 122
                                       f sL +  + ai+++  k n +l +N+   + lG+s+d++++ +  +++++ ++ + k+ l+++++k     + v  
  gi|298675480|ref|YP_003727230.1| 391 FRSLFENANDAIFIHDLKGN-ILEVNQLASQRLGYSKDELTNiKSMDLISPFYAdNMKNRLNTIQKKGHGIFETVQI 466
                                       55666777788888888875.99******************945679999988625788999999999999999999 PP

                            PAS_12 123 tKagqevllncllgii 138
                                       tK+g +++++    ii
  gi|298675480|ref|YP_003727230.1| 467 TKNGSSIPVELSSRII 482
                                       9999999998877776 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00017      0.19      39     123 ..     649     747 ..     645     749 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                       HATPase_c_2  39 actNavehayleap.egpvevrlesdeealtvevaDsGpgfdpetlpdpteeep......keslkegGrGlalikgl 108
                                       ++tN    a++  +  g+++v++  ++e ++++v+D G g +   +p   +  +        +    G+Gl++ k +
  gi|298675480|ref|YP_003727230.1| 649 MLTNLLDNATKFTSsGGEITVEAFEEDEHIHIKVTDTGVGIPEDLIPYLFQRFYqidssiRRKYGGTGLGLYICKLI 725
                                       7899999999999989************************7777666554433378998888999999********* PP

                       HATPase_c_2 109 vDev..ey.....dgegnvvtm 123
                                       vD    ++     +g+g++v++
  gi|298675480|ref|YP_003727230.1| 726 VDAHygNIwidsiEGKGTTVHV 747
                                       *998663355666999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (754 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1157  (0.0645323); expected 358.6 (0.02)
Passed bias filter:                      643  (0.0358637); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.81u 0.34s 00:00:01.15 Elapsed: 00:00:00.52
# Mc/sec: 4373.02
//
Query:       gi|298675481|ref|YP_003727231.1|  [L=362]
Description: PAS/PAC sensor signal transduction histidine kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.2e-20   72.7   0.2      1e-19   71.1   0.0    2.0  2  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    1.3e-05   25.4   0.5    4.8e-05   23.6   0.5    2.0  1  PAS_9        PAS domain
    2.6e-05   24.2   0.0    5.7e-05   23.1   0.0    1.6  1  PAS          PAS fold
    0.00028   20.7   0.9    0.00098   19.0   0.0    2.3  2  HATPase_c_5  GHKL domain
     0.0046   16.9   0.0      0.011   15.7   0.0    1.6  1  HATPase_c_2  Histidine kinase-like ATPase domain
  ------ inclusion threshold ------
      0.071   13.2   0.1       0.19   11.8   0.1    1.8  1  HisKA        His Kinase A (phospho-acceptor) domain
       0.14   12.2   0.0       0.39   10.8   0.0    1.8  1  PAS_8        PAS domain


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       2.5   6.4e+03       8      30 ..     222     243 ..     216     249 .. 0.61
   2 !   71.1   0.0     4e-23     1e-19       6     110 ..     258     361 ..     254     362 .] 0.93

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.5
                                       HHHHHHHHHHHHHHSTTTEEEEE CS
                         HATPase_c   8 qiisnlvdNavkfatkageieve 30 
                                        iisn+vd + +   +++ i+ve
  gi|298675481|ref|YP_003727231.1| 222 PIISNVVDDLKDQ-IDEKGIKVE 243
                                       4777777776663.344445554 PP

  == domain 2  score: 71.1 bits;  conditional E-value: 4e-23
                                       HHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHHH CS
                         HATPase_c   6 LrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsivk 82 
                                       ++ ++ nl++Na+k++++++++++ i+ ++d  +i   D+G G++k+d  +lfe+f +  ++k++ +g GlGl+ivk
  gi|298675481|ref|YP_003727231.1| 258 IEDVFYNLLSNAIKYSPENSRVTIAIQDEKDFWKINFADSGEGVDKKDKSRLFERFER--ADKSDIKGLGLGLAIVK 332
                                       56799**********99**********7669***************************..7788899********** PP

                                       HHHHHTTTEEEEEEET.TTEEEEEEEEES CS
                         HATPase_c  83 klvelmgGeiwvesep.grGttftftlpl 110
                                       +++el+gG++ v ++p g+G  f++tl++
  gi|298675481|ref|YP_003727231.1| 333 RVIELHGGKVGVYDNPeGIGNIFWVTLKK 361
                                       ************8888799*******986 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.5   1.9e-08   4.8e-05       2     104 .]      31     124 ..      30     124 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.9e-08
                             PAS_9   2 dgilidnpdgril.yaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfw 77 
                                       +gi++++++ +++ + N  a + +Gy+++ v+g ++++++v++++a +        ++ k  e e  +++ +g  ++
  gi|298675481|ref|YP_003727231.1|  31 NGIFVVDKETHVVvDTNIYAVDKTGYTKQSVVGNPVSEFIVFPENAGCL-------ID-KNNELECKIRTIDGDNLP 99 
                                       79999778888999**************************333333332.......22.355777788899999999 PP

                             PAS_9  78 vlltaspvkdddgelvgiivilrDite 104
                                       v +t s +  ++ +++   + ++Dit+
  gi|298675481|ref|YP_003727231.1| 100 VFMTSSSITRNGLNYQI--LSFVDITQ 124
                                       99******777755665..99***996 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   2.2e-08   5.7e-05       3      57 ..      22      81 ..      20      95 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2.2e-08
                                      HHHHHHHSSSEEEEEE.TTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH....H CS
                               PAS  3 lraileslpdpifvvD.edgrilyvNaaaeellGlsreevlgkslldliheedda....e 57
                                      l+ai+e+  ++ifvvD e ++++ +N  a + +G++ + v+g +++++i+ +++a    +
  gi|298675481|ref|YP_003727231.1| 22 LKAIFEAQQNGIFVVDkETHVVVDTNIYAVDKTGYTKQSVVGNPVSEFIVFPENAgcliD 81
                                      789**********************************************99887755554 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.3      0.64   1.6e+03      17      25 ..     197     205 ..     168     249 .. 0.57
   2 !   19.0   0.0   3.8e-07   0.00098       9      87 ..     261     344 ..     254     352 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.64
                       HATPase_c_5  17 Aieacskie 25 
                                        ie++sk++
  gi|298675481|ref|YP_003727231.1| 197 VIESASKLS 205
                                       334444333 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 3.8e-07
                       HATPase_c_5   9 ilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg....ek....kkle.sskskkeehGiGlksire 76 
                                       ++ nlL NAi  + +    ++ +++ ++ +k++  i++  s eg    +k    +++e   ks+ +  G+Gl  +++
  gi|298675481|ref|YP_003727231.1| 261 VFYNLLSNAIKYSPE----NSRVTIAIQDEKDFWKINFADSGEGvdkkDKsrlfERFErADKSDIKGLGLGLAIVKR 333
                                       89********87665....668*******************9996644113344344446699999*********** PP

                       HATPase_c_5  77 ivkkykgnlsi 87 
                                       +++ ++g++ +
  gi|298675481|ref|YP_003727231.1| 334 VIELHGGKVGV 344
                                       ****9999875 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   4.4e-06     0.011      40     108 ..     266     334 ..     256     351 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.4e-06
                       HATPase_c_2  40 ctNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlp...dpteeepkeslkegGrGlalikgl 108
                                       ++Na+++  +   + +v+++++++++  ++ +aDsG+g d +++    ++ e ++k + k  G+Gla++k++
  gi|298675481|ref|YP_003727231.1| 266 LSNAIKYSPE---NSRVTIAIQDEKDFWKINFADSGEGVDKKDKSrlfERFERADKSDIKGLGLGLAIVKRV 334
                                       5677777765...478**********************6666443000344444477777777888888765 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   7.6e-05      0.19       4      65 ..     148     208 ..     145     210 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.6e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHH CS
                             HisKA   4 rflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsrie 65 
                                        f+  + H+L +P   + g++++L + ++++ +  + l++i+ + + l +++e    lsr+e
  gi|298675481|ref|YP_003727231.1| 148 LFTDIIRHDLLNPAGLVNGFTQVLLD-IENDSNKIKILKKIKHHNEKLINVIESASKLSRLE 208
                                       578889******************99.577777788*****************999999987 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00015      0.39       2      45 ..      21      66 ..      20      84 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00015
                             PAS_8  2 rlralfesspdgiavvdlgd.rivdvNqaalellGys.adlkgell 45
                                      +l+a+fe+ ++gi+vvd  +  +vd N  a + +Gy+ + + g ++
  gi|298675481|ref|YP_003727231.1| 21 YLKAIFEAQQNGIFVVDKEThVVVDTNIYAVDKTGYTkQSVVGNPV 66
                                      89***************44457999888888888877655555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1061  (0.0591779); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 2202.93
//
Query:       gi|298675482|ref|YP_003727232.1|  [L=390]
Description: LL-diaminopimelate aminotransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-61  207.1   0.0      5e-61  206.9   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    0.00032   19.3   0.0    0.00052   18.7   0.0    1.3  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
      0.082   11.9   0.0       0.15   11.0   0.0    1.3  1  Aminotran_5      Aminotransferase class-V
        0.1   11.5   0.0       0.83    8.5   0.0    2.1  2  Alliinase_C      Allinase


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.9   0.0   1.1e-64     5e-61       2     362 ..      35     384 ..      34     385 .. 0.96

  Alignments for each domain:
  == domain 1  score: 206.9 bits;  conditional E-value: 1.1e-64
                                       EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGag 78 
                                       dvi+Lg++++++     t+++++  + e a  ++++++y+ + g +++++a a++ +++ + +++++++ ++  G +
  gi|298675482|ref|YP_003727232.1|  35 DVIDLGVGDPDQP----TPQHIIDSMSE-AIYNPNYHRYPSYNGMYDFRNAAADWCKENRGFEVDPDTQTLTMIGLK 106
                                       89**********9....***********.****************************999***************** PP

                                       HHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEE CS
                     Aminotran_1_2  79 aliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilve 155
                                       ++i+  + ++ +npgd  lvp+p y+ yk +   +gge +++pl +e++f  dl+a+ + + +      +tk+++++
  gi|298675482|ref|YP_003727232.1| 107 EGIAHSPLAF-INPGDTALVPNPAYPVYKIGTLFAGGEAYTMPLLEENGFLPDLDAIPKEVCD------RTKMMFLN 176
                                       **********.***************************************************9......******** PP

                                       SS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT.EEEEEESSSTTSSGGG-EE CS
                     Aminotran_1_2 156 sphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepn.llivgslsKafGlaGeRvG 231
                                        p+NPtG+va+++  e+++d+a+ + ++++ D aY++ vf+  +  +  +nv+ + +  + ++slsK ++++G+R++
  gi|298675482|ref|YP_003727232.1| 177 YPNNPTGAVADHKFFEEVVDFARDNDIVVVHDNAYSDIVFDGYESPS-FLNVDGAMDvGVELYSLSKTYNMTGWRIA 252
                                       *****************************************654434.9999999998899**************** PP

                                       EEEEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSS CS
                     Aminotran_1_2 232 yilgnaavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgm 306
                                       +++gn+++++ + k+++++ s   +++q+a ++al  +++    +++m + +++rr+ l ++L++lgl+v ++++++
  gi|298675482|ref|YP_003727232.1| 253 FAVGNSDIIKGIGKVKSNVDSgaFEAVQKAGVTALTSSQQ---CVSDMNKIYKDRRDALLKGLNKLGLDVKPQKATF 326
                                       ***************************************8...9********************************* PP

                                       EEEEEETHH.CHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHH CS
                     Aminotran_1_2 307 flltdlsae.takelskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelvea 362
                                       +++  +++  +  e+sk Lle  g++ tpg  f+    g +R+ + + t e ++++v +
  gi|298675482|ref|YP_003727232.1| 327 YTWAPVPEGyNSIEFSKLLLEDAGIVATPGVGFGDygDGYIRFAL-TQTVERINQAVAR 384
                                       ***998877799*****************99999899999***99.9999999999876 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.2e-07   0.00052     126     177 ..     158     212 ..     114     228 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.2e-07
                                       SHHHHHHHCCTTEEEEEEESS-TTTT----...HHHHHHHHHHTT-EEEEEGTTT CS
                   Cys_Met_Meta_PP 126 dleelekaikentklvylEtptnpllkvvD...iekiaklakkagvlvvvDntfa 177
                                       dl+++ k + ++tk+++l  p np+  v+D   +e+++++a++++++vv Dn+++
  gi|298675482|ref|YP_003727232.1| 158 DLDAIPKEVCDRTKMMFLNYPNNPTGAVADhkfFEEVVDFARDNDIVVVHDNAYS 212
                                       678899999*********************88889*****************975 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.4e-05      0.15     126     177 ..     156     210 ..     140     213 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.4e-05
                                       CBEGGGHHHH--TTEEEEEEESBETTTTEB--...HHHHHHHHHHTT-EEEEE-T CS
                       Aminotran_5 126 eldldelekllnektklvaithvsnvtGtiqp...veeigklakkkgalvlvDaa 177
                                       + dld++ k + ++tk+++++  +n tG + +   +ee+++ a++++++v+ D a
  gi|298675482|ref|YP_003727232.1| 156 LPDLDAIPKEVCDRTKMMFLNYPNNPTGAVADhkfFEEVVDFARDNDIVVVHDNA 210
                                       457**************************8763337899************9987 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0   0.00019      0.83     142     207 ..     174     255 ..     123     286 .. 0.80
   2 ?    0.6   0.0     0.045     2e+02     319     362 ..     344     388 ..     320     389 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00019
                                       EEESS-TTT----.....----...-TT-EEEEEE-TT.......-.STTTS---S-B--SEEEEEHHHHHS-GGG- CS
                       Alliinase_C 142 lvtsPnnPdgllr.....eavv...kgseakviyDlay.......Y.WPhytpitskadedimLftlskltGhaGsr 202
                                       +   PnnP g++      e+vv   ++++  v++D ay       Y  P + ++  + d  + L++lsk+   +G r
  gi|298675482|ref|YP_003727232.1| 174 FLNYPNNPTGAVAdhkffEEVVdfaRDNDIVVVHDNAYsdivfdgYeSPSFLNVDGAMDVGVELYSLSKTYNMTGWR 250
                                       5667999988775222336788776666777899999744443332369**************************** PP

                                       EEEEE CS
                       Alliinase_C 203 lGWal 207
                                       + +a+
  gi|298675482|ref|YP_003727232.1| 251 IAFAV 255
                                       *9995 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.045
                                       HHHHTTTEEEEEGGGGTS.-TTEEEEESSS-HHHHHHHHHHHHTS CS
                       Alliinase_C 319 evlrekkiltrsGevfea.esryvrlsllkrdddfdvllerlkkl 362
                                        +l++++i++  G  f++ +  y+r +l ++ +  ++ ++r+++l
  gi|298675482|ref|YP_003727232.1| 344 LLLEDAGIVATPGVGFGDyGDGYIRFALTQTVERINQAVARMEEL 388
                                       3567899********9864789****************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 2269.48
//
Query:       gi|298675483|ref|YP_003727233.1|  [L=364]
Description: chorismate synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   6.1e-143  475.4   0.9   6.9e-143  475.3   0.9    1.0  1  Chorismate_synt  Chorismate synthase


Domain annotation for each model (and alignments):
>> Chorismate_synt  Chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  475.3   0.9  3.8e-147  6.9e-143       1     327 []      10     353 ..      10     353 .. 0.97

  Alignments for each domain:
  == domain 1  score: 475.3 bits;  conditional E-value: 3.8e-147
                                       SEEEEE-SCCSSEEEEEEE---BT-B--HHHHHHHHHHHTCTSSSSSSHHHCS-EEEEESSEETTEE-SS-EEEEEE CS
                   Chorismate_synt   1 lrvttfGeShgkalgavidgvpagleldeediqkeLdrRrpgqsklttqrkEkDeveilsGvfegktlGtpiallie 77 
                                       +++tt+GeShg+a+g+v+dgvpagle+++e +++eL+rRrpgqs+++t+rkE+DeveilsGvf++k++Gtpi++l++
  gi|298675483|ref|YP_003727233.1|  10 FKITTWGESHGRAVGVVVDGVPAGLEINKELVENELKRRRPGQSSVSTPRKETDEVEILSGVFDNKSTGTPISMLVW 86 
                                       89*************************************************************************** PP

                                       -TTS-..SSSSSTSBE-TTSTCHHHHHHC-S.STHCCCCCTHHCHHHHHHHHHHHHHHHHTTTEEEEEEEEEETTE. CS
                   Chorismate_synt  78 NkdqrskdyeeikevpRpgHADltyalkYgirdlrgggrsSaReTaarvaaGavakklLkelgieivayvssigei. 153
                                       Nk+++s++ye++k+ pRpgHAD+ y +kYgird+rgggrsSaReT++rvaaGa+ak+l++++gi+iva+v ++g+i 
  gi|298675483|ref|YP_003727233.1|  87 NKNANSSSYEHLKNLPRPGHADYFYLKKYGIRDYRGGGRSSARETVGRVAAGAIAKALMETYGIKIVAHVLELGGIk 163
                                       **************************************************************************888 PP

                                       ..........CHHHHHTT-BS-CCCHHHHHHHHHHHHHTT--B-EEEEEEEES--TT-SBTTTB-HHHHHHHHHHTS CS
                   Chorismate_synt 154 ..........ekeaenpvrcpdeeaaeemeeaieeakkegdslGgvvevvvkgvpaGlGepvfdkldakLakalmsi 220
                                                 ++ +++p+rc+d +aae+m+e+ e+a++ gds+Gg+ve+vvkg+paG+Gepvfdklda+L+ka+msi
  gi|298675483|ref|YP_003727233.1| 164 akklefdkilNNLEKTPLRCADLDAAEKMREKAEHARDMGDSIGGIVEIVVKGIPAGIGEPVFDKLDADLSKAIMSI 240
                                       8888887765444778************************************************************* PP

                                       TTEEEEEETTGGGGGGSBHHHHS--EE......EESS-TTTTEETTEEBSS-EEEEEEE--SS--SSEEEEEBTTS- CS
                   Chorismate_synt 221 pAvkgveiGsGfeaaelkGseanDeiv......lrktnnaGGieGGisnGepivvrvavKpipsiakeqktvdletk 291
                                       +Avkgve+GsGfe++++ Gse+nD++v       ++tnnaGGi GG+s+G+pi++r+ vKp+psi+k qktvdl+t+
  gi|298675483|ref|YP_003727233.1| 241 GAVKGVEFGSGFESSKMYGSEMNDSFViengevSTETNNAGGIIGGLSTGMPIICRASVKPTPSISKIQKTVDLSTM 317
                                       ***************************66555433****************************************** PP

                                       E-EEEE--S-S-S-THHHHHHHHHHHHHHHHHHHHH CS
                   Chorismate_synt 292 eevelevkgrhDpcvvpravvvveamvalvladall 327
                                       +e+e++vkgrhDp++ pr+v+v+e+mvalv+a++++
  gi|298675483|ref|YP_003727233.1| 318 TETEISVKGRHDPTIPPRMVPVAESMVALVIAEHMI 353
                                       *********************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 2193.80
//
Query:       gi|298675484|ref|YP_003727234.1|  [L=290]
Description: cation diffusion facilitator family transporter [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      7e-47  159.7   8.6    8.3e-47  159.5   8.6    1.1  1  Cation_efflux  Cation efflux family
    1.3e-22   79.7   3.6    2.4e-22   78.8   3.6    1.4  1  ZT_dimer       Dimerisation domain of Zinc Transporter


Domain annotation for each model (and alignments):
>> Cation_efflux  Cation efflux family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.5   8.6   9.3e-51   8.3e-47       3     199 .]      14     205 ..      12     205 .. 0.98

  Alignments for each domain:
  == domain 1  score: 159.5 bits;  conditional E-value: 9.3e-51
                     Cation_efflux   3 lsllanlilalvelivglltnSlalladafhslsdlvsllllllalklsrkppderfpfGygrlevlgalvsgllll 79 
                                         l++n+++al+++i+g +tn l++ +d++hsl+d +s++ +l+++ ++++ppd+++p+Gy ++e+l a++ + +l+
  gi|298675484|ref|YP_003727234.1|  14 QILILNVVVALAKIIYGRITNTLSMESDGYHSLIDGISNITGLVGIQIASRPPDKQHPYGYRKYETLSAIIISFFLI 90 
                                       5789************************************************************************* PP

                     Cation_efflux  80 glavfllleaiqklikegereihaglalvvalvslvvnlalllilrragrklrsaalkaaalhvlgDaltslgvlvs 156
                                       ++++ ++++ai ++   ++  + +++ ++++++ +++n+++ ++ r++g +l+s++l a+++h+ +D++ sl v+v+
  gi|298675484|ref|YP_003727234.1|  91 LIGFEIISNAIGRFR-ADVSPDVTSISFAIMILTMIINFLVTRYERKQGDELNSEVLIADSMHTKSDIFLSLSVIVG 166
                                       ***************.9************************************************************ PP

                     Cation_efflux 157 alvillfnlksgplaDpvaslligliilysalkllkeslseLl 199
                                       ++ i l+     p++Dp++sl+i++ii+ +++++++++   Ll
  gi|298675484|ref|YP_003727234.1| 167 LVAIELG----YPIIDPIISLIIAVIIFRAGYSIIRQNADTLL 205
                                       ******7....367************************99987 PP

>> ZT_dimer  Dimerisation domain of Zinc Transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8   3.6   2.7e-26   2.4e-22       6      79 .]     212     285 ..     209     285 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 2.7e-26
                                       HHHHHHHHTT-SS-EEEEEEEEE-S----EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-TT--EEEEEEEE. CS
                          ZT_dimer   6 eeeireiiksvpgvkgvhdlrtrksGskifvdlhievdgdlsvkeaHeiadevekrikeefpgvadvliHvePe 79 
                                       eeei  ++ksv g+k++h++r+r   + i++dlhi+v +d+ +  aH +a++ve+++k+++pgv+dv+iH+eP+
  gi|298675484|ref|YP_003727234.1| 212 EEEICTLVKSVSGIKECHKIRSRGTNDAIHIDLHIKVRPDMRIDNAHSVAHDVERDLKNKYPGVKDVTIHIEPA 285
                                       79***********************************************************************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       771  (0.043003); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1725.39
//
Query:       gi|298675485|ref|YP_003727235.1|  [L=239]
Description: hypothetical protein Metev_1594 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.035   14.3   0.2      0.077   13.2   0.2    1.5  1  KapB      Kinase associated protein B
       0.14   12.3   1.4       0.22   11.7   1.4    1.5  1  Ntox23    Bacterial toxin 23
       0.27   12.0   2.3       0.68   10.7   0.2    2.4  3  PTS_IIB   PTS system, Lactose/Cellobiose specific IIB subunit


Domain annotation for each model (and alignments):
>> KapB  Kinase associated protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   1.3e-05     0.077      58     101 ..      47      90 ..      35     101 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.3e-05
                              KapB  58 nvpkeavkpyegevpdYeeSlkealeklkekLkeeksefaeksl 101
                                        + +   ++ye++v dY+ S+++a++++++kL +++ + + + l
  gi|298675485|ref|YP_003727235.1|  47 KTGSVDYQSYEQSVADYNVSVNTAITTYQDKLLSNQISGQIQNL 90 
                                       555566789***********************988866555555 PP

>> Ntox23  Bacterial toxin 23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.4   3.6e-05      0.22      28      81 ..      40      94 ..      33     179 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.6e-05
                            Ntox23 28 gaavgwgksgeekrkgwglgfskkegqlgyvestyldkietsQqtGait.lqagd 81
                                      ++  gw+k g + +++++      + +++ +  ty dk + +Q++G+i+ lq+++
  gi|298675485|ref|YP_003727235.1| 40 LSEYGWEKTGSVDYQSYEQSVADYNVSVNTAITTYQDKLLSNQISGQIQnLQINQ 94
                                      5778*****************99999*********************96255533 PP

>> PTS_IIB  PTS system, Lactose/Cellobiose specific IIB subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.29   1.7e+03      18      55 ..      34      70 ..      32      97 .. 0.58
   2 ?   10.7   0.2   0.00011      0.68      13      52 ..     130     171 ..     128     177 .. 0.75
   3 ?   -1.4   0.0      0.68   4.1e+03      65      86 ..     213     233 ..     174     237 .. 0.54

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.29
                                      HHHHHHHHHCTEEEEETTEEGGGHHHHHHT-SEEEEEE CS
                           PTS_IIB 18 eklekaakelgieaegeagveleaeeiaddaDlvllap 55
                                      e+ e+a+ e g e +g+     ++e+  +d+ + + ++
  gi|298675485|ref|YP_003727235.1| 34 EASESALSEYGWEKTGSVDY-QSYEQSVADYNVSVNTA 70
                                      56678888888555555444.33444444444444333 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHHHHHCT...EEEEETTEEGGGHHHHHHT-SEEE CS
                           PTS_IIB  13 Slmaaeklekaakelg...ieaegeagveleaeeiaddaDlvl 52 
                                       S+++ +++ek ak+++   ++ +g++++ +++   a+ aD+++
  gi|298675485|ref|YP_003727235.1| 130 STIVDTQIEKLAKQANienFDKKGSEEINISDGSTAN-ADYYV 171
                                       89999***********555555666666666666666.99887 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.68
                                       HTTSEEEEECTTHHHCCHCHHH CS
                           PTS_IIB  65 fagkpvavinikdalgimdgek 86 
                                       + + +v+ i+i+    ++++++
  gi|298675485|ref|YP_003727235.1| 213 KGE-NVKLITINGEKEMEEVKA 233
                                       333.333333332123355555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       755  (0.0421105); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1374.65
//
Query:       gi|298675486|ref|YP_003727236.1|  [L=255]
Description: cobyrinic acid ac-diamide synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-20   74.0   0.1    1.3e-20   73.7   0.1    1.1  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    7.6e-12   45.5   0.0    6.8e-11   42.4   0.0    2.0  2  AAA_31       AAA domain
    3.4e-11   43.1   0.2    5.2e-06   26.1   0.1    3.0  2  ParA         NUBPL iron-transfer P-loop NTPase
    5.5e-08   32.3   0.2    1.8e-07   30.6   0.0    1.8  2  ArsA_ATPase  Anion-transporting ATPase
    1.9e-06   27.6   0.8     0.0024   17.4   0.1    2.3  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
    3.1e-06   26.8   0.0     0.0002   20.9   0.2    2.1  2  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
    9.4e-05   22.3   0.9     0.0013   18.6   0.0    2.2  2  AAA_26       AAA domain
     0.0004   20.2   0.0     0.0013   18.5   0.0    1.9  2  AAA_24       AAA domain
    0.00055   20.4   0.0     0.0012   19.3   0.0    1.7  1  AAA_16       AAA ATPase domain
    0.00071   19.5   0.0     0.0014   18.6   0.0    1.4  1  NTPase_1     NTPase
     0.0015   18.4   0.2     0.0029   17.5   0.2    1.4  1  NACHT        NACHT domain
     0.0018   18.9   0.0      0.003   18.1   0.0    1.5  1  AAA_18       AAA domain
     0.0021   18.2   0.0     0.0044   17.2   0.0    1.6  1  DUF87        Helicase HerA, central domain
     0.0032   17.1   0.4     0.0058   16.3   0.4    1.4  1  SRP54        SRP54-type protein, GTPase domain
     0.0039   17.7   0.0     0.0077   16.7   0.0    1.7  1  ABC_tran     ABC transporter
     0.0049   16.1   0.6       0.11   11.6   0.2    2.2  2  NB-ARC       NB-ARC domain
     0.0097   15.8   0.1      0.018   15.0   0.1    1.5  1  APS_kinase   Adenylylsulphate kinase
  ------ inclusion threshold ------
      0.014   15.4   0.0       0.14   12.2   0.0    2.2  2  AAA_14       AAA domain
      0.016   15.2   0.0      0.024   14.6   0.0    1.4  1  AAA_5        AAA domain (dynein-related subfamily)
      0.019   15.2   0.0      0.038   14.3   0.0    1.5  1  AAA_22       AAA domain
      0.019   14.7   0.2       0.28   11.0   0.1    2.6  3  CLP1_P       mRNA cleavage and polyadenylation factor CLP1 P-
       0.02   14.6   1.0      0.061   13.0   0.1    1.9  2  AAA_30       AAA domain
      0.024   14.4   0.0      0.042   13.6   0.0    1.3  1  PRK          Phosphoribulokinase / Uridine kinase family
      0.025   13.6   0.0      0.044   12.8   0.0    1.5  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
      0.034   14.0   0.0       0.07   13.0   0.0    1.5  1  MobB         Molybdopterin guanine dinucleotide synthesis pro
      0.045   13.2   0.0       0.07   12.6   0.0    1.3  1  KTI12        Chromatin associated protein KTI12
      0.045   13.5   0.0      0.082   12.6   0.0    1.3  1  IstB_IS21    IstB-like ATP binding protein
      0.047   13.8   0.0       0.11   12.6   0.0    1.6  1  AAA_2        AAA domain (Cdc48 subfamily)
      0.061   13.6   0.0       0.12   12.6   0.0    1.4  1  AAA_28       AAA domain
      0.071   12.8   1.7        0.2   11.3   1.7    1.6  1  ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-bindi
       0.17   12.0   0.0       0.47   10.6   0.0    1.7  2  AAA_33       AAA domain
       0.18   11.3   0.0       0.29   10.6   0.0    1.3  1  AAA_7        P-loop containing dynein motor region
       0.43   10.4   1.7       0.96    9.2   0.2    2.1  2  AAA_29       P-loop containing region of AAA domain


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.7   0.1   2.5e-23   1.3e-20       3     126 ..       5     225 ..       3     227 .. 0.94

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 2.5e-23
                                       EEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH......................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................... RF
                              CbiA   3 iastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep......................... 54 
                                       ++ +kGGvGKTtla +Lar+la++ ++Vl++DaD ++n+++ + g e+  +p                         
  gi|298675486|ref|YP_003727236.1|   5 AITGKGGVGKTTLAGTLARLLAQDDYQVLAIDADSDMNLAS-AIGIEKPPAPlteykdlireragetggafklnpkv 80 
                                       6789***********************************99.7777777777999********************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|298675486|ref|YP_003727236.1|  81 ddvvekygvvgpdgvnmlvmgtieqggsgcmcpasaflraflrhvvlkeksavimdmeagiehlgrgttrgidlmvi 157
                                       ***************************************************************************** PP

                                       ..........CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCC CS
                                       ..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ..........dlkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaea 121
                                                 +++r++el+ +l +k       +  v+n+  +    +  k +le+l    g+ vlg+ip+d ++++a
  gi|298675486|ref|YP_003727236.1| 158 vvepgmrsveTASRIKELADELEIK------HLAAVVNKSSS----ADVKPHLEKL----GISVLGEIPYDPDIVRA 220
                                       ****999999999999999999966......6999****765....5789999998....****************9 PP

                                       CHHTS CS
                                       xxxxx RF
                              CbiA 122 parge 126
                                       + ++ 
  gi|298675486|ref|YP_003727236.1| 221 DFENT 225
                                       98876 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.0   1.3e-13   6.8e-11       8      53 ..       7      52 ..       1      87 [. 0.87
   2 ?    1.0   0.0      0.65   3.5e+02     121     166 ..     133     178 ..     108     189 .. 0.78

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 1.3e-13
                            AAA_31  8 nqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekn 53
                                        KGGvGKTT +  la  la+ +++vL +D+D+  n+++++giek 
  gi|298675486|ref|YP_003727236.1|  7 TGKGGVGKTTLAGTLARLLAQDDYQVLAIDADSDMNLASAIGIEKP 52
                                      57****************************************9875 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.65
                            AAA_31 121 iiiDcpPsLglltenaLvasdsviipvqaeayaleGleqllktiee 166
                                       +i+D+   ++ l +      d ++i+v++  +++e+++++ +  +e
  gi|298675486|ref|YP_003727236.1| 133 VIMDMEAGIEHLGRGTTRGIDLMVIVVEPGMRSVETASRIKELADE 178
                                       66666666666666666667999***********999888766655 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.1   9.6e-09   5.2e-06       9      41 ..       6      38 ..       1      61 [. 0.90
   2 !   10.8   0.0   0.00046      0.25      97     218 ..     115     220 ..     108     251 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 9.6e-09
                              ParA  9 lSgKGGVGKStvavnlAlaLakkglkvgllDaD 41
                                      + gKGGVGK+t+a +lA  La+ +++v  +DaD
  gi|298675486|ref|YP_003727236.1|  6 ITGKGGVGKTTLAGTLARLLAQDDYQVLAIDAD 38
                                      57******************************9 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00046
                              ParA  97 skaikqllkdvewgelDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvkkaiemfkkvkvkvlGvveN 173
                                       s++++ +l++v  +e   +i+D+  G   e+l    +  ++ +viV  p   +++ +++  e+++++++k l+ v N
  gi|298675486|ref|YP_003727236.1| 115 SAFLRAFLRHVVLKEKSAVIMDMEAGI--EHLGRGTTRGIDLMVIVVEPGMRSVETASRIKELADELEIKHLAAVVN 189
                                       567889999999999999999997554..788888888889999999999999999999999999999999998888 PP

                              ParA 174 msgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeirea 218
                                        s  +               ++   e+lg+++lgeip dp+i++a
  gi|298675486|ref|YP_003727236.1| 190 KSSSA--------------DVKPHLEKLGISVLGEIPYDPDIVRA 220
                                       76543..............34455566667777777777766655 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   3.4e-10   1.8e-07       4      49 ..       4      49 ..       1      62 [. 0.90
   2 ?   -0.8   0.0       1.2   6.7e+02     209     244 ..     155     190 ..     117     202 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 3.4e-10
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS CS
                       ArsA_ATPase  4 ilvgGKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdq 49
                                      i ++GKGGVGKtt++ ++a  l++ +++vl i  D   +l+ +   
  gi|298675486|ref|YP_003727236.1|  4 IAITGKGGVGKTTLAGTLARLLAQDDYQVLAIDADSDMNLASAIGI 49
                                      789********************************99999987665 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.2
                                       EEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEE CS
                       ArsA_ATPase 209 frlVvipEklslkEteRaikeLkkygikvdavivNk 244
                                       +++Vv p   s++   R  +   +++ik  a +vNk
  gi|298675486|ref|YP_003727236.1| 155 MVIVVEPGMRSVETASRIKELADELEIKHLAAVVNK 190
                                       567888888887777776666678888888888888 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   4.5e-06    0.0024       2      39 ..       3      40 ..       2     112 .. 0.91
   2 !    9.2   0.1    0.0014      0.74     157     245 ..     168     246 ..     133     254 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.5e-06
                         Fer4_NifH  2 kiaiyGkGGiGksttsqnlsaalaemgkkvlivGCDPk 39
                                      kiai GkGG+Gk+t +  l+  la++  +vl +  D  
  gi|298675486|ref|YP_003727236.1|  3 KIAITGKGGVGKTTLAGTLARLLAQDDYQVLAIDADSD 40
                                      89*****************************9988865 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0014
                         Fer4_NifH 157 aanniakgiekyaksggvrlgGliinsrkvddereliekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseq 233
                                       +a +    i++ a + +++    ++n +   + +  ++ + e+lg+ vl  +P d ++ +a++++ t+ +  ++s  
  gi|298675486|ref|YP_003727236.1| 168 TASR----IKELADELEIKHLAAVVN-K---SSSADVKPHLEKLGISVLGEIPYDPDIVRADFENTTILDIGSSSV- 235
                                       4444....455666666655555666.3...34455778889**************************99876654. PP

                         Fer4_NifH 234 akeyrelarkil 245
                                        +  r++ ++++
  gi|298675486|ref|YP_003727236.1| 236 -DSIRDIKNRMI 246
                                       .55555555555 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.2   3.7e-07    0.0002       1      44 [.       1      43 [.       1      51 [. 0.89
   2 ?    3.8   0.0     0.062        34      97     150 ..     110     164 ..      89     188 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 3.7e-07
                          CBP_BcsQ  1 mkvlalqGvRGGvGttsllaaLawalhelgesvlviDlspdnlL 44
                                      m  +a++G +GGvG+t+l+++La+ l + +++vl+iD+ +d  L
  gi|298675486|ref|YP_003727236.1|  1 MVKIAITG-KGGVGKTTLAGTLARLLAQDDYQVLAIDADSDMNL 43
                                      66788888.8***************************9988655 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.062
                          CBP_BcsQ  97 qlaekaeallaalkelk.eqyrwillDlpagasaltrellaladlvllvvepdan 150
                                       ++++++  l a+l+++  ++ + +++D+ ag ++l r +++  dl++ vvep + 
  gi|298675486|ref|YP_003727236.1| 110 CMCPASAFLRAFLRHVVlKEKSAVIMDMEAGIEHLGRGTTRGIDLMVIVVEPGMR 164
                                       56777788888888877788999***************************99775 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.2      0.25   1.4e+02      11      32 ..      11      32 ..       3      33 .. 0.84
   2 !   18.6   0.0   2.4e-06    0.0013     131     195 ..     155     218 ..     152     221 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.25
                            AAA_26 11 gvGKTvvslgLvralkrkgvkv 32
                                      gvGKT+++  L+r l + +++v
  gi|298675486|ref|YP_003727236.1| 11 GVGKTTLAGTLARLLAQDDYQV 32
                                      8**************9888776 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 2.4e-06
                            AAA_26 131 vilVargglgtinqllltiealrqknvrvlGvilNkvrnpenvetlekksgipvlGvvPylpdle 195
                                       +++V+ +g ++++ +    e++ + +++ l+ ++Nk  + ++v+   +k gi vlG++Py+pd+ 
  gi|298675486|ref|YP_003727236.1| 155 MVIVVEPGMRSVETASRIKELADELEIKHLAAVVNK-SSSADVKPHLEKLGISVLGEIPYDPDIV 218
                                       6899999999999999999999999***********.78888********************986 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.4e-06    0.0013       3      58 ..       2      65 ..       1     108 [. 0.79
   2 ?   -1.5   0.0       3.2   1.7e+03      23      40 ..     129     146 ..     117     183 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.4e-06
                            AAA_24  3 lkiliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdie.swedfldevve 58
                                      +ki+i+G+ g+GKTtla +l        +++l id +  ++   a+ +++++  +++ +d + e
  gi|298675486|ref|YP_003727236.1|  2 VKIAITGKGGVGKTTLAGTLarllaqdDYQVLAIDADSDMNLASAIGIEKPPaPLTEYKDLIRE 65
                                      69******************99999988999999999877666666666666655555555554 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.2
                            AAA_24  23 gpkplfidtekGlkslda 40 
                                       +++++++d+e+G  +l  
  gi|298675486|ref|YP_003727236.1| 129 EKSAVIMDMEAGIEHLGR 146
                                       477888899999887764 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   2.2e-06    0.0012      28      75 ..       5      46 ..       3     136 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.2e-06
                            AAA_16 28 llsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqa 75
                                       ++G  GvGK++l+ +l+r l +d+  +l+ ++d+  ++     la+a
  gi|298675486|ref|YP_003727236.1|  5 AITGKGGVGKTTLAGTLARLLAQDDYQVLAIDADSD-MN-----LASA 46
                                      79*****************99999999988888887.22.....3333 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.5e-06    0.0014       1      30 [.       3      32 ..       3      39 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.5e-06
                                      EEEEE--TTSSHHHHHHHHHHHH...GGGE CS
                          NTPase_1  1 kvfiTGppGvGKtTlvkkvlellkssgvkv 30
                                      k++iTG+ GvGKtTl   +++ll++++++v
  gi|298675486|ref|YP_003727236.1|  3 KIAITGKGGVGKTTLAGTLARLLAQDDYQV 32
                                      689**********************99988 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.2   5.4e-06    0.0029       3      30 ..       4      31 ..       3      37 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.4e-06
                                      EEEEC-TTTCHHHHHHHHHHHHCTS-SC CS
                             NACHT  3 vilqGeaGsGKTtLlqklalawaegklp 30
                                      ++++G+ G+GKTtL+  la+++a+++++
  gi|298675486|ref|YP_003727236.1|  4 IAITGKGGVGKTTLAGTLARLLAQDDYQ 31
                                      689*********************9865 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   5.5e-06     0.003       1      25 [.       4      29 ..       4      90 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 5.5e-06
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgf.g 25
                                      I++tG+ GvGKttla  L+++l+   
  gi|298675486|ref|YP_003727236.1|  4 IAITGKGGVGKTTLAGTLARLLAQdD 29
                                      89*****************9973342 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0     8e-06    0.0044      26      63 ..       4      40 ..       2      79 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 8e-06
                             DUF87 26 lAilgsTGsGKSntvavLleellekkgatililDpHGE 63
                                      +Ai g+ G+GK+++++ L + l+ ++++++l +D++++
  gi|298675486|ref|YP_003727236.1|  4 IAITGKGGVGKTTLAGTLARLLA-QDDYQVLAIDADSD 40
                                      79********************9.**********9987 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.4   1.1e-05    0.0058       4      38 ..       4      38 ..       1      44 [. 0.92

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.1e-05
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                      i++ G  G+GKTt ++ La+ll ++ ++vl + aD
  gi|298675486|ref|YP_003727236.1|  4 IAITGKGGVGKTTLAGTLARLLAQDDYQVLAIDAD 38
                                      7899*************************998888 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.4e-05    0.0077      13      51 ..       3      41 ..       2     196 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.4e-05
                                      EEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 13 kvaivGenGaGKStLlkllagllkpteGeilldgkdlke 51
                                      k+ai+G+ G GK+tL+ +la+ll ++  ++l  ++d+++
  gi|298675486|ref|YP_003727236.1|  3 KIAITGKGGVGKTTLAGTLARLLAQDDYQVLAIDADSDM 41
                                      689********************9988888665666665 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.2   0.00021      0.11      23      39 ..       4      20 ..       1      33 [. 0.85
   2 ?    2.7   0.0      0.11        58     194     249 ..     149     206 ..     120     208 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00021
                                      EEEEESTTSSHHHHHHH CS
                            NB-ARC 23 valvGmgGvGKttlakq 39
                                      +a+ G+gGvGKttla  
  gi|298675486|ref|YP_003727236.1|  4 IAITGKGGVGKTTLAGT 20
                                      89************976 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.11
                                       CTT-HHHHHHHHHHHC-TCSCCHHHHHHHHHHCTGCC..TS--SSSSSSSHHHHHHHH CS
                            NB-ARC 194 ckGlPlalkvlggllstkktveewkkvleklesklle..vekstskslesvasilqls 249
                                        +G  l ++v+   +++ +t ++ k+++++le k+l   v+ks+s +++   + l +s
  gi|298675486|ref|YP_003727236.1| 149 TRGIDLMVIVVEPGMRSVETASRIKELADELEIKHLAavVNKSSSADVKPHLEKLGIS 206
                                       589999999999999999*************988766567888888887777777666 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   3.3e-05     0.018       5      40 ..       4      39 ..       1      52 [. 0.89

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.3e-05
                                      EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHH CS
                        APS_kinase  5 vwltGlsgsGKstianalekkLvekgisvylLdGdn 40
                                      + +tG  g GK+t+a +l++ L ++ ++v  +d d+
  gi|298675486|ref|YP_003727236.1|  4 IAITGKGGVGKTTLAGTLARLLAQDDYQVLAIDADS 39
                                      789*****************************9985 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00026      0.14       5      46 ..       4      45 ..       3      71 .. 0.76
   2 ?    0.4   0.0       1.1   6.1e+02      90     120 ..     222     252 ..     216     254 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00026
                            AAA_14  5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkl 46
                                      ++itG   vGKTtl+ +l++ l  ++ ++l i+ d++ + ++
  gi|298675486|ref|YP_003727236.1|  4 IAITGKGGVGKTTLAGTLARLLAQDDYQVLAIDADSDMNLAS 45
                                      5799**************977667778888888887666444 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.1
                            AAA_14  90 gknldvivtGSnskllskeiatslagrvaei 120
                                        +n  ++  GS+s +  ++i++++ + v++i
  gi|298675486|ref|YP_003727236.1| 222 FENTTILDIGSSSVDSIRDIKNRMIDMVQNI 252
                                       468888899******9999999998887776 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   4.5e-05     0.024       4      35 ..       6      38 ..       3      72 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.5e-05
                                      EE--SSSSHHHHHHHGGGGB.S--EEEEE--TT CS
                             AAA_5  4 LvGppGtgKselaerlaaal.nreveyvqltrd 35
                                      + G+ G+gK++la  la++l ++ +++ ++ +d
  gi|298675486|ref|YP_003727236.1|  6 ITGKGGVGKTTLAGTLARLLaQDDYQVLAIDAD 38
                                      789******************888888887776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     7e-05     0.038       8      53 ..       4      43 ..       3      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7e-05
                            AAA_22  8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstss 53
                                      +++tG  G+GKTtl+ +l++ l ++      + +v+ +++ s++++
  gi|298675486|ref|YP_003727236.1|  4 IAITGKGGVGKTTLAGTLARLLAQD------DYQVLAIDADSDMNL 43
                                      68*******************9776......777778888777754 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00051      0.28       1      32 [.       8      39 ..       8      49 .. 0.90
   2 ?   -1.1   0.0       2.5   1.4e+03       8      38 ..     115     145 ..     114     155 .. 0.86
   3 ?   -0.5   0.0       1.6   8.8e+02     106     151 ..     156     201 ..     149     212 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00051
                            CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDv 32
                                      G+  +GK+Tla +L+  +++  ++++ +D+D 
  gi|298675486|ref|YP_003727236.1|  8 GKGGVGKTTLAGTLARLLAQDDYQVLAIDADS 39
                                      66789*************************95 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.5
                            CLP1_P   8 STlarlLlNyalrkgrkpvyvDlDvGqseis 38 
                                       S++ r  l  ++ k+++ v++D+  G  +++
  gi|298675486|ref|YP_003727236.1| 115 SAFLRAFLRHVVLKEKSAVIMDMEAGIEHLG 145
                                       7899999999999999999***999977765 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.6
                            CLP1_P 106 liIntpGwvkglgaellleliealepdvvvvldqeellnelkrdlp 151
                                       +i+  pG+ + + a+ ++el++ le+++++++ ++ + +++k +l+
  gi|298675486|ref|YP_003727236.1| 156 VIVVEPGMRSVETASRIKELADELEIKHLAAVVNKSSSADVKPHLE 201
                                       5666678888888888899999999999988888777777777776 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   0.00011     0.061      22      54 ..       5      35 ..       2      79 .. 0.84
   2 ?    0.2   0.1      0.99   5.4e+02      90     115 ..     154     179 ..     118     187 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                            AAA_30 22 vltGpAGtGKttalkalreaweaaggrviglAp 54
                                      ++tG  G GKtt+ ++l+++++++ ++v++   
  gi|298675486|ref|YP_003727236.1|  5 AITGKGGVGKTTLAGTLARLLAQDDYQVLA--I 35
                                      689*********************998864..4 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.99
                            AAA_30  90 tllivDEagmvdtkqlaallkaaeka 115
                                        ++iv E gm + +++ ++ + a++ 
  gi|298675486|ref|YP_003727236.1| 154 LMVIVVEPGMRSVETASRIKELADEL 179
                                       57999999999999999999988775 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   7.7e-05     0.042       2      43 ..       4      45 ..       3      52 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.7e-05
                               PRK  2 IgvagsSGaGkttvarklekifgrekvkaaeiegdsflrldr 43
                                      I+++g+ G Gktt+a +l  ++++   +   i+ ds+++l +
  gi|298675486|ref|YP_003727236.1|  4 IAITGKGGVGKTTLAGTLARLLAQDDYQVLAIDADSDMNLAS 45
                                      9*************************9999999999998876 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   8.1e-05     0.044      31      78 ..       3      48 ..       1      90 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.1e-05
                                      EEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE------------- CS
                              MeaB 31 vvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspftGGsilG 78
                                      ++ +tG  G+Gk tl   l+  l++  ++  vla+D  s ++  s +G
  gi|298675486|ref|YP_003727236.1|  3 KIAITGKGGVGKTTLAGTLARLLAQDDYQ--VLAIDADSDMNLASAIG 48
                                      689*********************99887..69999999887666655 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00013      0.07       2      34 ..       4      36 ..       3      44 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00013
                              MobB  2 lgivgksgsGKTtLleklipelkarglrvgtiK 34
                                      ++i+gk g GKTtL   l + l++ +++v +i 
  gi|298675486|ref|YP_003727236.1|  4 IAITGKGGVGKTTLAGTLARLLAQDDYQVLAID 36
                                      6899************************98875 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00013      0.07       4      39 ..       4      39 ..       1      66 [. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                                      EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THH CS
                             KTI12  4 vvltGlPssGKstrakeLakaleeekrsvvviddes 39
                                      + +tG   +GK+t+a +La+ l++ +++v  id +s
  gi|298675486|ref|YP_003727236.1|  4 IAITGKGGVGKTTLAGTLARLLAQDDYQVLAIDADS 39
                                      889****************************99664 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00015     0.082      50      81 ..       4      35 ..       2      47 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00015
                         IstB_IS21 50 ivllGpsGvGKshlaialgveavraglsvlfv 81
                                      i+++G  GvGK+ la +l++  ++++++vl +
  gi|298675486|ref|YP_003727236.1|  4 IAITGKGGVGKTTLAGTLARLLAQDDYQVLAI 35
                                      89*************************99865 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0    0.0002      0.11       4      45 ..       2      42 ..       1      53 [. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0002
                                      --EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG--- CS
                             AAA_2  4 isilllgptgvGktelakalaellfvkkekkliradaselle 45
                                      ++i ++g+ gvGkt la +la+ll  +++ ++  +da + + 
  gi|298675486|ref|YP_003727236.1|  2 VKIAITGKGGVGKTTLAGTLARLLA-QDDYQVLAIDADSDMN 42
                                      68999*******************9.9999999999987665 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00022      0.12       1      27 [.       3      33 ..       3      41 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00022
                            AAA_28  1 kivitGgestGKTtlleaLa....argypvv 27
                                      ki+itG  + GKTtl+  La    +++y+v+
  gi|298675486|ref|YP_003727236.1|  3 KIAITGKGGVGKTTLAGTLArllaQDDYQVL 33
                                      79**************998844423377765 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.7   0.00037       0.2      16      81 ..       3     193 ..       2     200 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00037
                                       EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEE............................................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................ RF
                       ATP-synt_ab  16 rtlipgafgvGktvisqslskqsnsddaiiyvg............................................ 48 
                                       +++i g+ gvGkt+++ +l++   +dd+ +++                                             
  gi|298675486|ref|YP_003727236.1|   3 KIAITGKGGVGKTTLAGTLARLLAQDDYQVLAIdadsdmnlasaigiekppaplteykdlireragetggafklnpk 79 
                                       689*******************99999999999999***************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                       ATP-synt_ab  49 ............................................................................. 48 
                                                                                                                    
  gi|298675486|ref|YP_003727236.1|  80 vddvvekygvvgpdgvnmlvmgtieqggsgcmcpasaflraflrhvvlkeksavimdmeagiehlgrgttrgidlmv 156
                                       ****************************************************************************9 PP

                                       ....ESEEHHHHHHHHHHCHHSSGGGGEEEEEEETTS CS
                                       ....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  49 ....iGergnevaevleefpegtimkrtvlvantsne 81 
                                            G r+ e a+ ++e+ ++  +k+   v+n+s++
  gi|298675486|ref|YP_003727236.1| 157 ivvePGMRSVETASRIKELADELEIKHLAAVVNKSSS 193
                                       9999999999999999999999999999999999876 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00086      0.47       4      32 ..       6      37 ..       4      94 .. 0.76
   2 ?   -1.6   0.0       4.9   2.7e+03      74     104 ..     157     188 ..     115     195 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00086
                            AAA_33  4 lvGlpGsGKstlaerllkklg...avllssdt 32
                                      + G  G+GK+tla  l++ l+   +++l+ d+
  gi|298675486|ref|YP_003727236.1|  6 ITGKGGVGKTTLAGTLARLLAqddYQVLAIDA 37
                                      57999********9998777777799988887 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.9
                            AAA_33  74 il.datnlsrrerarflklarrlgvpvrivvv 104
                                       i+   +++s ++ +r+ +la +l+ ++++ vv
  gi|298675486|ref|YP_003727236.1| 157 IVvEPGMRSVETASRIKELADELEIKHLAAVV 188
                                       33244466667777777777777777666555 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00054      0.29      36      71 ..       4      39 ..       1      46 [. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00054
                             AAA_7 36 vllvGptGtGKtviikdllkkldkekylsltinfsa 71
                                      + ++G+ G+GKt+++ +l + l +++y++l i   +
  gi|298675486|ref|YP_003727236.1|  4 IAITGKGGVGKTTLAGTLARLLAQDDYQVLAIDADS 39
                                      6789*************************9997665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.2    0.0018      0.96      26      46 ..       5      25 ..       2      32 .. 0.83
   2 ?   -0.8   0.1       2.4   1.3e+03      21      36 ..      92     108 ..      88     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0018
                            AAA_29 26 lltGpsGsGKSTllDAiqalL 46
                                       +tG+ G+GK+Tl   ++ lL
  gi|298675486|ref|YP_003727236.1|  5 AITGKGGVGKTTLAGTLARLL 25
                                      79***********87777777 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.4
                            AAA_29  21 lkg.atlltGpsGsGKS 36 
                                       ++g ++l++G+++ G S
  gi|298675486|ref|YP_003727236.1|  92 PDGvNMLVMGTIEQGGS 108
                                       568899****9999866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                       121  (0.00674884); expected 17.9 (0.001)
Passed Fwd filter:                        33  (0.00184059); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              33  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 1738.18
//
Query:       gi|298675487|ref|YP_003727237.1|  [L=64]
Description: hypothetical protein Metev_1596 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.021   14.9   0.0      0.041   13.9   0.0    1.4  1  CCT       CCT motif


Domain annotation for each model (and alignments):
>> CCT  CCT motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.3e-06     0.041      16      38 ..      27      49 ..      25      50 .. 0.96

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.3e-06
                               CCT 16 kfdkkirYevRkalAdkrpRvKG 38
                                       f+++ir++ R+ l ++  R+KG
  gi|298675487|ref|YP_003727237.1| 27 QFKQQIRSDYRRSLGNEHARIKG 49
                                      69********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1111  (0.0619666); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 481.53
//
Query:       gi|298675488|ref|YP_003727238.1|  [L=246]
Description: hypothetical protein Metev_1597 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-53  182.0   0.0    1.7e-53  181.7   0.0    1.0  1  NIF3      NIF3 (NGG1p interacting factor 3)


Domain annotation for each model (and alignments):
>> NIF3  NIF3 (NGG1p interacting factor 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.7   0.0   9.7e-58   1.7e-53       1     243 [.       5     231 ..       5     234 .. 0.93

  Alignments for each domain:
  == domain 1  score: 181.7 bits;  conditional E-value: 9.7e-58
                              NIF3   1 eivevleelaplelaeswDnv..GlqvgdpekevkkvllaldlteevleeAiekgadliithHPlifkplkrltedd 75 
                                       +i+ vle +ap+e+ae++D    G  + + ++++ k++++ld+t+ vl++A + gadl+ithH lif+p++++++  
  gi|298675488|ref|YP_003727238.1|   5 DIIPVLETVAPPEYAEEFDAGriGDII-NLDNDIDKIAVSLDPTDYVLKRAADIGADLLITHHTLIFEPVTKIAKP- 79 
                                       68999*************986225555.7999******************************************99. PP

                              NIF3  76 ykkrllkkliknnislysaHtnlDaapgGvndwlakalglekieplepskeekkeeeeglgrigeleepvsleelak 152
                                         +  lk ++ n+islys+Htn+D++pgGvnd la++lgl++ie+le            +grig+++ p+s+ ++a 
  gi|298675488|ref|YP_003727238.1|  80 -FSDKLKVALDNEISLYSMHTNYDKVPGGVNDILADRLGLTNIEELE------------IGRIGYIS-PCSTGTFAG 142
                                       .99**************************************999775............8******9.6******** PP

                              NIF3 153 klkkklglekvrvagdldkkvkkvaicaGsGa..slieeakakgaDlliTGelkhhealdakekgiavidvgHyatE 227
                                       +++  l+ ++v+++   +k+v+kv++++GsG   ++++ a ++g+D+++++elkh+ + +    +i++id+ HyatE
  gi|298675488|ref|YP_003727238.1| 143 HVSRCLD-THVQYV-GDNKTVEKVMVFGGSGFksQYLDIAHENGVDAFVSSELKHDVIRNR--GDISLIDATHYATE 215
                                       ******5.59****.889*************87799*******************999877..4589********** PP

                              NIF3 228 rvflealaelLkeklk 243
                                       ++++e+l e+L+e lk
  gi|298675488|ref|YP_003727238.1| 216 NPAMEKLCERLEEMLK 231
                                       ************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1830.62
//
Query:       gi|298675489|ref|YP_003727239.1|  [L=76]
Description: hypothetical protein Metev_1598 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.091   11.5   0.5      0.092   11.5   0.5    1.1  1  Adeno_IVa2  Adenovirus IVa2 protein


Domain annotation for each model (and alignments):
>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.5   5.1e-06     0.092     298     336 ..       9      48 ..       5      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.1e-06
                        Adeno_IVa2 298 ifefleqksrysfilynvePvrealrWc.lldqrdsliPl 336
                                       + ++ +q+ + + i+yn   + e l+Wc + +q++  +P 
  gi|298675489|ref|YP_003727239.1|   9 YSRYNKQRYCRECIIYNQLGKCEYLKWCeSDNQENNNMPK 48 
                                       567899999*******************666677777774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 565.58
//
Query:       gi|298675490|ref|YP_003727240.1|  [L=49]
Description: hypothetical protein Metev_1599 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 373.08
//
Query:       gi|298675491|ref|YP_003727241.1|  [L=219]
Description: Di-trans-poly-cis-decaprenylcistransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-42  145.6   0.0    1.8e-42  145.4   0.0    1.0  1  Prenyltransf  Putative undecaprenyl diphosphate synthase
  ------ inclusion threshold ------
       0.07   14.0   0.0       0.18   12.7   0.0    1.7  2  DUF469        Protein with unknown function (DUF469)


Domain annotation for each model (and alignments):
>> Prenyltransf  Putative undecaprenyl diphosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.4   0.0     2e-46   1.8e-42       1     221 [.      10     215 ..      10     218 .. 0.84

  Alignments for each domain:
  == domain 1  score: 145.4 bits;  conditional E-value: 2e-46
                                       EE--HHHHHHHTT.S-HHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEEGGGGGS-HHHHHHHHHHHHHHHHHHHHH CS
                      Prenyltransf   1 imDGNrRwAkkrgleereeGhkaGaealkeilelclelgvkvvtvYafSteNfkRskeevdalmellkeellkeelk 77 
                                       i DGNrRwA krg +++e+G+  G++   e+++lc+++gv+ +t+Y f+++N kR++e+ +a+ + + + ++    +
  gi|298675491|ref|YP_003727241.1|  10 IPDGNRRWALKRG-LSKEKGYDYGVDPGIELIRLCKKMGVEELTFYGFTMDNTKRTSEQTKAFTNACIQ-AA----N 80 
                                       78***********.67777********************************************999833.33....4 PP

                                       HHHHTTEEEEEESSGG..GS-HHHHHHHHHHHHHHT.TTTSEEEEEEEEE-HHHHHHHHHHHHHHTT..SSSGGGHS CS
                      Prenyltransf  78 ellkegvrvrviGdle..llpedvlealekaeeatkknnkklvlniavnYgsrdeiveavrelvkekseekkkeeid 152
                                         ++eg ++ v+Gd+e  ++pe++   +  + ++t  + + +++n+ vnYg+++++ + +++l +++++++     +
  gi|298675491|ref|YP_003727241.1|  81 GAINEGSQFLVVGDTEspMFPEKL---IPYTSRKTFGDGN-IKVNLLVNYGWQWDL-KGLKNLDNKNKSTN-----N 147
                                       57999*********9844566655...5667778885555.**************9.77888865542222.....2 PP

                                       HHHHHCTSTT..TSSS-SEEEEESS--S-TTSSTTTTTT-EEEEESSSGGG--HHHHHHHHHHHHHCHH CS
                      Prenyltransf 153 eetlekhlytakalpdpDlliRtsGeeRlSnFllwqlayselyfldvlWPdfskedllealleyqkrer 221
                                       ++++   +  +k++  +Dl+iR++G++RlS+Fl  q++ys++y++d +WPdf+ ++l +a+  y k++ 
  gi|298675491|ref|YP_003727241.1| 148 KKNIMYLIN-SKEISRIDLIIRWGGRRRLSGFLPVQSVYSDFYVVDNYWPDFKPKHLNDAIDWYDKQDI 215
                                       345544444.4568**************************************************99875 PP

>> DUF469  Protein with unknown function (DUF469)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     2e-05      0.18       2      42 ..      41      78 ..      40      96 .. 0.82
   2 ?   -2.6   0.0       1.1     1e+04      41      64 ..     158     181 ..     135     186 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2e-05
                            DUF469  2 RlrKKlrvdeFqelgFevslklkedlseeeidalvdafiev 42
                                      Rl+KK+ v+e + +gF++  + +    +e+++a+ +a i++
  gi|298675491|ref|YP_003727241.1| 41 RLCKKMGVEELTFYGFTMDNTKRT---SEQTKAFTNACIQA 78
                                      9****************9976665...77888888888764 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.1
                            DUF469  41 evieanglafggsgkeeleglvcl 64 
                                       + i   +l++  +g+++l+g++ +
  gi|298675491|ref|YP_003727241.1| 158 KEISRIDLIIRWGGRRRLSGFLPV 181
                                       456666677777777777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1624.55
//
Query:       gi|298675492|ref|YP_003727242.1|  [L=529]
Description: hypothetical protein Metev_1602 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      1e-08   35.3   6.8    5.2e-06   26.7   0.6    3.1  2  DUF11      Domain of unknown function DUF11
    8.9e-08   31.4   5.3    0.00015   20.7   1.8    2.5  2  BatD       Oxygen tolerance
    2.7e-06   26.9   8.1     0.0016   17.9   1.9    3.3  3  TRAP_beta  Translocon-associated protein beta (TRAPB)
    9.9e-06   25.8  11.6      0.035   14.4   0.8    3.7  3  CARDB      CARDB
     0.0028   17.7   8.0        1.2    9.1   0.0    3.7  3  DUF2393    Protein of unknown function (DUF2393)


Domain annotation for each model (and alignments):
>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.8   0.00016      0.57       1      69 [.     254     331 ..     254     351 .. 0.75
   2 !   26.7   0.6   1.4e-09   5.2e-06       2      83 ..     367     440 ..     366     450 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00016
                             DUF11   1 ltKtvdksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsas.........qgtasaltsv.gsLeag 67 
                                       +tKtv+++ + ++dt  + + v+N g   +n++ v+ ++   l++  + +s         + t +  +++ + Le+g
  gi|298675492|ref|YP_003727242.1| 254 VTKTVTEE-IYMTDTAYVLVNVRNGGLCELNNINVNNPVTDKLELENNITSnktislepdETTKKLYSYSlQPLEPG 329
                                       79***999.*****************************987777766666655555555444444444446677777 PP

                             DUF11  68 es 69 
                                       + 
  gi|298675492|ref|YP_003727242.1| 330 KY 331
                                       65 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 1.4e-09
                             DUF11   2 tKtvdksevrpGdtvtytltvtNtgpasangvvvtDt.lPaglayvsvsasqgtasaltsv.gsLeagesatlsftv 76 
                                        K v+++ + pG+  + t+  +Ntg+++   v v+Dt lP+++++v++s           +   ++ g+s+ +s+tv
  gi|298675492|ref|YP_003727242.1| 367 NKKVNSTSIVPGGHAKITIEIKNTGNKNT-HVNVSDTdLPSNVEFVEGSKH---------FkDVVKSGNSKSFSYTV 433
                                       599*************************9.888888879************.........43667899999999999 PP

                             DUF11  77 rvtrtaa 83 
                                       + +++++
  gi|298675492|ref|YP_003727242.1| 434 KFNNEGN 440
                                       9999887 PP

>> BatD  Oxygen tolerance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.1   2.5e-05     0.089      47      99 ..     291     341 ..     255     360 .. 0.73
   2 !   20.7   1.8   4.2e-08   0.00015     273     450 ..     366     528 ..     363     529 .] 0.65

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.5e-05
                              BatD  47 lekdfevlsgsqssstqiinGkssssssktwtytLapkkeGtltIpaatievd 99 
                                       +++++e+ ++ +s++t  i  +  ++++k ++y+L+p ++G++ +p a+++++
  gi|298675492|ref|YP_003727242.1| 291 VTDKLELENNITSNKT--ISLEPDETTKKLYSYSLQPLEPGKYRLPDASASFK 341
                                       4456666666666666..66667777778899999999999999999988663 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 4.2e-08
                              BatD 273 lsaslskdelkvgepltltvtisGtGN.lkllqlPelnfpegfevYdpkpedntkktgnglsGsrteeyalvPrkaG 348
                                       ++ +++++++  g    +t++i+ tGN  + +++ + ++p+++e  +  +  ++ +++     s++++y++  +++G
  gi|298675492|ref|YP_003727242.1| 366 FNKKVNSTSIVPGGHAKITIEIKNTGNkNTHVNVSDTDLPSNVEFVEGSKHFKDVVKS---GNSKSFSYTVKFNNEG 439
                                       677888888999999999********966777888888*********99999988886...45899*********** PP

                              BatD 349 kytipaiefsyFDtatkkyetatlpeitikVekgaaaasspasstsaspaqkeevkllgkdirfikgeaslkkkgsf 425
                                       ++++pa ++++ D +  + + ++    +i V+  a++++++ ++ +++ + + ++++++   +++k         + 
  gi|298675492|ref|YP_003727242.1| 440 NVKLPAATLTFIDMEGYSGKKTSN-RPEIWVNTSANTEKQTDNPDNSDGSTSGTTNQNKDGSKPVK---------Q- 505
                                       *************99888765443.33566633332222222222222222222222222222222.........1. PP

                              BatD 426 flfwlllllplllfvvllllwrkrr 450
                                          +  ll++++++ ++++++rk++
  gi|298675492|ref|YP_003727242.1| 506 -PGFTGLLAIAVFT-CVYYIYRKQS 528
                                       .3333444444443.5777888775 PP

>> TRAP_beta  Translocon-associated protein beta (TRAPB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.6   0.0    0.0053        19      35      85 ..     154     201 ..     142     211 .. 0.85
   2 !    6.7   0.1    0.0012       4.3      39     122 ..     270     350 ..     241     361 .. 0.71
   3 !   17.9   1.9   4.3e-07    0.0016      18     114 ..     362     455 ..     356     480 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0053
                         TRAP_beta  35 edltveytiyNvGssaAldVslvDdsfpeeaFevvsgslsakwerlapgen 85 
                                       ++++ ++++ N G+++  dV+l+   +++   e+v+g+l+ ++e+++ g++
  gi|298675492|ref|YP_003727242.1| 154 SKIVADLKVENKGDAEINDVNLN---IDTGGLELVEGELNHEIESIKKGKT 201
                                       6678889999***********95...89999***************98876 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0012
                         TRAP_beta  39 veytiyNvGssaAldVslvDdsfpeeaFevvsgslsakwerlapgenvs..hsfvvepkksgsfngtaavvtYrese 113
                                       v +++ N G  +  +++++  +  +++ e+ +  +s k  +l+p e+ +  +s+ ++p  +g++   +a+ ++++++
  gi|298675492|ref|YP_003727242.1| 270 VLVNVRNGGLCELNNINVN--NPVTDKLELENNITSNKTISLEPDETTKklYSYSLQPLEPGKYRLPDASASFKAPN 344
                                       4455555555555555553..34578889999999999999***999875699********************9998 PP

                         TRAP_beta 114 kgaelqlal 122
                                       +++     +
  gi|298675492|ref|YP_003727242.1| 345 SKKY---DT 350
                                       8443...33 PP

  == domain 3  score: 17.9 bits;  conditional E-value: 4.3e-07
                         TRAP_beta  18 arvlvkKkilnrllvegedltveytiyNvGssaAldVslvDdsfpeeaFevvsgslsakwerlapgenvshsfvvep 94 
                                       + ++++Kk+ + + v g    ++++i N G+   + V+++D+++p++  e+v+gs  +k ++++ g + s+s++v+ 
  gi|298675492|ref|YP_003727242.1| 362 PYLVFNKKVNSTSIVPGGHAKITIEIKNTGNKN-THVNVSDTDLPSNV-EFVEGSKHFK-DVVKSGNSKSFSYTVKF 435
                                       6799**************************976.79********9876.*****99998.9**************** PP

                         TRAP_beta  95 kksgsfngtaavvtYresek 114
                                         +g+ +  aa++t+ + e 
  gi|298675492|ref|YP_003727242.1| 436 NNEGNVKLPAATLTFIDMEG 455
                                       ***************55443 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.2   0.00011       0.4       2      69 ..     132     209 ..     131     235 .. 0.77
   2 !    6.1   0.4    0.0037        13       4      79 ..     252     332 ..     249     338 .. 0.80
   3 !   14.4   0.8   9.8e-06     0.035       4      82 ..     364     445 ..     361     450 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                                       --EEE......EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE....EEEEESEE-CTEEE.EEEEE CS
                             CARDB   2 pDLtv.....tntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv....gtvtvpsLaagest.tvsft 68 
                                       pDL +     + t+ p++ ++ +++   ++v+N+G+a+  ++++++   g +      + +++s++ g+++ t +++
  gi|298675492|ref|YP_003727242.1| 132 PDLKIhinteKDTYDPKKSSNPSKIVADLKVENKGDAEINDVNLNIDTGGLELvegeLNHEIESIKKGKTSqTFTVK 208
                                       9****999988999999999999999999*****************9999877677767888999998765134444 PP

                                       E CS
                             CARDB  69 w 69 
                                        
  gi|298675492|ref|YP_003727242.1| 209 L 209
                                       4 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0037
                                       EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE......EEEEESEE-CTEEEEEEEEEE-S.- CS
                             CARDB   4 LtvtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv......gtvtvpsLaagesttvsftwtte.a 73 
                                       L+v +++  +e +  ++  + v+v+N G  +  +++v+  + ++l       ++ t  sL+++e+t+  +++  + +
  gi|298675492|ref|YP_003727242.1| 252 LIV-TKTVTEEIYMTDTAYVLVNVRNGGLCELNNINVNNPVTDKLElennitSNKT-ISLEPDETTKKLYSYSLQpL 326
                                       777.6777788999999999**************9999888888875544434444.59999999999999888888 PP

                                       S-CEEE CS
                             CARDB  74 tegevt 79 
                                       ++g++ 
  gi|298675492|ref|YP_003727242.1| 327 EPGKYR 332
                                       888886 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 9.8e-06
                                       EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-..EEEEEEEEEETTEEE.EEEEE.SEE-CTEEEEEEEEEE-S-S-C CS
                             CARDB   4 LtvtntlnpseafvgeentitvtvkNqGtaa..sgatkvalyldgelv.gtvtv.psLaagesttvsftwtteateg 76 
                                       L+ ++++n ++ ++g + +it+++kN+G+++     + ++l  + e v g+      +++g+s++ s+t++ + +eg
  gi|298675492|ref|YP_003727242.1| 364 LVFNKKVNSTSIVPGGHAKITIEIKNTGNKNthVNVSDTDLPSNVEFVeGSKHFkDVVKSGNSKSFSYTVKFN-NEG 439
                                       677889999*********************9755567788888888886333335889**************9.*** PP

                                       EEEEEE CS
                             CARDB  77 evtltv 82 
                                       +v+l +
  gi|298675492|ref|YP_003727242.1| 440 NVKLPA 445
                                       *99865 PP

>> DUF2393  Protein of unknown function (DUF2393)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0   0.00035       1.2      56      86 ..     149     179 ..     137     229 .. 0.77
   2 !    6.1   0.7    0.0029        10      49     120 ..     254     327 ..     241     352 .. 0.76
   3 !    5.0   0.4    0.0064        23      80     129 ..     381     434 ..     365     447 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00035
                           DUF2393  56 rllyteafvvdgtitNeGkftikeCkleikl 86 
                                       +++  +++v+d+++ N+G+ +i+ + l+i+ 
  gi|298675492|ref|YP_003727242.1| 149 KSSNPSKIVADLKVENKGDAEINDVNLNIDT 179
                                       555667899*******************985 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0029
                           DUF2393  49 ltilsqkrllyteafvvdgtitNeGkftikeCkleiklvnkshnk...kskellkklkplvsksevikedlkpge 120
                                       +t++  + + +t++ +v ++++N G  ++++  ++  + +k + +      + + +l p +++++ ++  l+p e
  gi|298675492|ref|YP_003727242.1| 254 VTKTVTEEIYMTDTAYVLVNVRNGGLCELNNINVNNPVTDKLELEnniT-SNKTISLEPDETTKKLYSYSLQPLE 327
                                       56778888999***********************998888866554432.3444467777777777776666655 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.0064
                           DUF2393  80 Ckleiklvnkshnk....kskellkklkplvsksevikedlkpgeskeFrviid 129
                                        k++i++ n ++++     s+  l + + +v+ s+ +k+ +k g+sk+F++++ 
  gi|298675492|ref|YP_003727242.1| 381 AKITIEIKNTGNKNthvnVSDTDLPSNVEFVEGSKHFKDVVKSGNSKSFSYTVK 434
                                       5788888888888888887888898999999*******************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (529 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       993  (0.0553851); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3809.64
//
Query:       gi|298675493|ref|YP_003727243.1|  [L=465]
Description: hypothetical protein Metev_1603 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-07   30.7   0.1      0.048   13.9   0.1    3.7  4  bMG10         Bacterial Alpha-2-macroglobulin MG10 domain
    9.1e-05   22.7   2.2    0.00023   21.4   0.0    2.5  2  DUF11         Domain of unknown function DUF11
  ------ inclusion threshold ------
       0.02   14.2   0.1      0.037   13.3   0.1    1.4  1  MFP2b         Cytosolic motility protein
      0.024   14.8   4.3       0.66   10.2   0.2    3.6  3  Top6b_C       Type 2 DNA topoisomerase 6 subunit B C-terminal
      0.025   12.6   0.7      0.041   11.8   0.7    1.4  1  Prominin      Prominin
      0.046   13.8   4.8        2.4    8.3   0.1    3.1  3  Cupredoxin_1  Cupredoxin-like domain
      0.055   13.9   0.7       0.18   12.2   0.1    2.3  2  MG1           Macroglobulin domain MG1


Domain annotation for each model (and alignments):
>> bMG10  Bacterial Alpha-2-macroglobulin MG10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.5   3.8e+03      14      51 ..     165     204 ..     154     209 .. 0.62
   2 !   10.7   0.0   0.00017      0.45      87     124 ..     212     249 ..     186     251 .. 0.89
   3 !   13.9   0.1   1.9e-05     0.048      21      60 ..     291     334 ..     275     339 .. 0.78
   4 ?    0.7   0.0      0.23   5.8e+02      98     124 ..     343     369 ..     340     371 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.5
                             bMG10  14 kevsksdaklkvGdkvrvrltvttpr..dleyvaledplP 51 
                                       + ++   + +   ++ r++l+++  +  d e++ ++++lP
  gi|298675493|ref|YP_003727243.1| 165 EVKKWGGQDVYINERARITLQIENLKdiDFENIKINESLP 204
                                       4444444477888899999999965512456666666665 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00017
                             bMG10  87 ddrvvffadylpkgtytfeylvravtpGtfsvppakae 124
                                       d+ v++ +d   k t +f+y+++   +G+f++pp+++ 
  gi|298675493|ref|YP_003727243.1| 212 DKDVNISMDLDGKSTKQFSYHIKSLKAGEFKLPPTHIA 249
                                       6778889999999**********************985 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 1.9e-05
                             bMG10  21 a...klkvGdkvrvrltvttprdl.eyvaledplPAGlepvnps 60 
                                       +    lkv d+v ++++v+   d+   v +ed lPA +e+++ +
  gi|298675493|ref|YP_003727243.1| 291 DapkDLKVDDVVNITVDVQNTGDRsATVNIEDRLPAKAELIEGN 334
                                       13337**************66666599*********99998765 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.23
                             bMG10  98 pkgtytfeylvravtpGtfsvppakae 124
                                       p+++  ++y +++  +G+  vp+a+ae
  gi|298675493|ref|YP_003727243.1| 343 PSQKRILDYSIKMKDKGNVIVPAASAE 369
                                       5678889******************98 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.6       0.6   1.5e+03      17      51 ..      76     111 ..      66     142 .. 0.73
   2 !   21.4   0.0   9.2e-08   0.00023       1      51 [.     286     336 ..     286     390 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.6
                             DUF11  17 tytltvtNtgpasangvvvtDtl.Paglayvsvsas 51 
                                        +++ v+N+ ++ ++ + v+ t   +++ y  ++as
  gi|298675493|ref|YP_003727243.1|  76 HVVVSVKNSTTSWRSILSVNNTTiQPNVDYNNNTAS 111
                                       688899999998888888888653588888888888 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 9.2e-08
                             DUF11   1 ltKtvdks.evrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsas 51 
                                       +tKt d++ +++  d v+ t+ v+Ntg +sa +v ++D lPa  +++++  +
  gi|298675493|ref|YP_003727243.1| 286 ITKTIDAPkDLKVDDVVNITVDVQNTGDRSA-TVNIEDRLPAKAELIEGNIK 336
                                       79999999899********************.**********9999988766 PP

>> MFP2b  Cytosolic motility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   1.5e-05     0.037     263     334 ..      54     128 ..      31     133 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.5e-05
                             MFP2b 263 evrGydykWkpyseaadfgdkefvpvhv...gdispavvkvdgkellgkvdiktekataafdGkekvleggavks 334
                                       +v Gyd +   +s+a +f d ++v v v   ++   ++++v+  ++  +vd +++ a+  f+G+ k+ + + v++
  gi|298675493|ref|YP_003727243.1|  54 KVSGYDIEVEDFSKASEFSDIKHVVVSVknsTTSWRSILSVNNTTIQPNVDYNNNTASEVFNGSLKINSFEIVNN 128
                                       689*************************664445579**************************998877666665 PP

>> Top6b_C  Type 2 DNA topoisomerase 6 subunit B C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.2       1.1   2.9e+03      32      42 ..      76      86 ..      54     129 .. 0.61
   2 ?    4.2   0.0     0.019        48      54     101 ..     196     241 ..     163     249 .. 0.68
   3 ?   10.2   0.2   0.00026      0.66      29      61 ..     299     332 ..     285     363 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.1
                                      EEEEEE----- CS
                           Top6b_C 32 evslkvkNfsd 42
                                      +v ++vkN ++
  gi|298675493|ref|YP_003727243.1| 76 HVVVSVKNSTT 86
                                      33333333333 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.019
                                       S-----------EEE-SSSEEE-EEE---TT-EEEE----SS-GGGS- CS
                           Top6b_C  54 paeieeaspeakvvemdneydlkWelsvsageskvleYsvdseaeeel 101
                                       +++i+e  pe  vv  d + d++ ++ ++++++k+ +Y+++s +  e 
  gi|298675493|ref|YP_003727243.1| 196 NIKINESLPEHFVV--DPDKDVNISMDLDGKSTKQFSYHIKSLKAGEF 241
                                       34444555444444..55556777888888889999998888776665 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00026
                                       S-.EEEEEEE---------EEE--EES------- CS
                           Top6b_C  29 dg.vevslkvkNfsdkkeefelheilpaeieeas 61 
                                       d+ v++++ v+N +d+++++++ + lpa++e ++
  gi|298675493|ref|YP_003727243.1| 299 DDvVNITVDVQNTGDRSATVNIEDRLPAKAELIE 332
                                       4449************************987665 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.7   1.6e-05     0.041     333     406 ..     387     460 ..     356     465 .] 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.6e-05
                          Prominin 333 tnlssivkeglarlneipekvknqtaevvpdlkkalakgreqikklakkiprealdavisdlenterssktfdd 406
                                        n+  ++ ++ ++l++i  k +n+t+++ ++ +k+ +++++ i +  k++p++a d++ s +++++  +++f  
  gi|298675493|ref|YP_003727243.1| 387 LNVGDVPVQESDELKNIGGKTENNTKNTSNSNIKEQNQTEKGIFEKVKSLPNSAYDQMKSMVDRINGIISSFIS 460
                                       57888999*************************************************99999888777776655 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1      0.81   2.1e+03      14      67 ..      68     121 ..      65     153 .. 0.70
   2 ?    6.4   0.2    0.0037       9.4      36      89 ..     173     242 ..     140     244 .. 0.72
   3 ?    8.3   0.1   0.00095       2.4      33     104 .]     292     363 ..     269     363 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.81
                      Cupredoxin_1  14 kaaaaaektveitvkdggfePskievkagekvklkiknkdktpeefesedlgee 67 
                                       +++ ++ k+v++ vk+ + +  +i    ++ ++ +++ + +t++e+   +l+++
  gi|298675493|ref|YP_003727243.1|  68 ASEFSDIKHVVVSVKNSTTSWRSILSVNNTTIQPNVDYNNNTASEVFNGSLKIN 121
                                       455677788888888888887777777777787777777777777766665554 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0037
                      Cupredoxin_1  36 kievkagekvklkiknkdkt...........peefesed...lgeekvlapgktt..titiaplkpGeYe 89 
                                        + +++  +++l+i+n ++            pe+f++++   ++++ +l+ ++t+  + +i+ lk+Ge++
  gi|298675493|ref|YP_003727243.1| 173 DVYINERARITLQIENLKDIdfenikineslPEHFVVDPdkdVNISMDLDGKSTKqfSYHIKSLKAGEFK 242
                                       55666666677777776666666666666668999999889988888887666551156899******97 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.00095
                      Cupredoxin_1  33 ePskievkagekvklkiknkdktpeefesed.lgee.kvlapgktttitiaplkpGeYeftcdmhmdakGkliV 104
                                        P+ ++v    ++++ ++n++++++++ +ed l  + + ++ + + ++ ++p ++   ++  +m+ +  G++iV
  gi|298675493|ref|YP_003727243.1| 292 APKDLKVDDVVNITVDVQNTGDRSATVNIEDrLPAKaELIEGNIKDSLILHPSQKRILDYSIKMKDK--GNVIV 363
                                       6999***************************966551556666677777777777766666666655..77776 PP

>> MG1  Macroglobulin domain MG1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       2.1   5.3e+03      39      66 ..      64      91 ..      53     113 .. 0.49
   2 ?   12.2   0.1   7.2e-05      0.18       4      47 ..     288     331 ..     285     374 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.1
                                      ETTTTTSEEEEEEEEESTTTTTEEEEEE CS
                               MG1 39 dfpqkkkelasesvtLnsdnnfqalvki 66
                                      df++ ++  + ++v ++ +n+ ++  +i
  gi|298675493|ref|YP_003727243.1| 64 DFSKASEFSDIKHVVVSVKNSTTSWRSI 91
                                      4444444334444444444443333333 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 7.2e-05
                                       EEEEEESSEETTSEEEEEEEEES-SS-EEEEEEEE.ETTTTTSEE CS
                               MG1   4 ylltaPnvlrvgseetivveahgltkeveVtitvk.dfpqkkkel 47 
                                        ++ aP+ l+v+   +i+v++++ t++ + t+++    p k++++
  gi|298675493|ref|YP_003727243.1| 288 KTIDAPKDLKVDDVVNITVDVQN-TGDRSATVNIEdRLPAKAELI 331
                                       6788*******************.667777777774555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       975  (0.0543812); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3328.09
//
Query:       gi|298675494|ref|YP_003727244.1|  [L=209]
Description: GTP-binding protein HSR1-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.6e-18   64.9   0.0    9.4e-18   64.4   0.0    1.2  1  MMR_HSR1     50S ribosome-binding GTPase
    3.2e-12   46.3   0.6    5.4e-11   42.3   0.6    2.1  1  FeoB_N       Ferrous iron transport protein B
    4.2e-05   23.5   1.3      0.028   14.3   0.2    2.8  3  RsgA_GTPase  RsgA GTPase
    0.00079   19.0   0.2      0.005   16.4   0.1    2.0  2  GTP_EFTU     Elongation factor Tu GTP binding domain
     0.0017   18.5   0.0     0.0024   18.0   0.0    1.5  1  Dynamin_N    Dynamin family
  ------ inclusion threshold ------
      0.021   14.1   0.2      0.071   12.4   0.0    1.9  2  Septin       Septin
      0.075   13.6   0.0       0.13   12.9   0.0    1.6  1  AAA_18       AAA domain
       0.11   12.7   0.2       0.31   11.3   0.0    1.8  2  Roc          Ras of Complex, Roc, domain of DAPkinase


Domain annotation for each model (and alignments):
>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.4   0.0   4.2e-21   9.4e-18       1     114 []      15     143 ..      15     143 .. 0.80

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 4.2e-21
                                       EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGC.....SSHHHHHH...HHHHH CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGl.....iegaseek...glgka 69 
                                       e++++Gr+NvGKS++i+ ltg+k++v+++pg+T+++  + ++    ++ ++D+pG+     +++ +++    ++ + 
  gi|298675494|ref|YP_003727244.1|  15 EIVFAGRSNVGKSSFIRELTGKKVKVGKRPGVTLKPYNICYS----DMLVTDMPGFgfmsgVKDRKKDIvhdKIVRY 87 
                                       689*********************************998776....69*******5443332333333345578888 PP

                                       HHHHHC.TSEEEEEEETT............TTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  70 flalee.adlillvvdas............eeklkpldeeleelleeakkplilvlnk 114
                                       f+++ +  ++++l++d              ++   p+d e+ e+l+e ++++i+++nk
  gi|298675494|ref|YP_003727244.1|  88 FENNAKrIKVAVLIID-GpafidiadrwnaRD-EIPIDIEMFEFLNELNIDTIVAVNK 143
                                       88776669*******9.558888888877533.358999*****************98 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.6   2.4e-14   5.4e-11       2     136 ..      15     165 ..      14     188 .. 0.72

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 2.4e-14
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSS......SSSSHHHHHHHH CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYsl......sayseeekvard 72 
                                       +++++G  nvGk++++ +ltg+k kvg  pGvt +  +  ++    ++ ++D+PG   +      +     + +++d
  gi|298675494|ref|YP_003727244.1|  15 EIVFAGRSNVGKSSFIRELTGKKVKVGKRPGVTLKPYNICYS----DMLVTDMPGFGFMsgvkdrK-----KDIVHD 82 
                                       6899******************************99999888....9********97663444441.....333333 PP

                                       HHH......CTSSSEE.........EEEEEGGGHHHHHHHHHH....HHHTTSSEEEEEETHHHHHHTTEEE-HHHH CS
                            FeoB_N  73 fll......eeepdvv.........vnvvdatnlernLyLtlq....llelgvpvvlalnmideaekkgieidlkkL 130
                                        ++       ++++v          ++++d  n + ++ + ++    l el++++++a+n+id++++k +e  ++ +
  gi|298675494|ref|YP_003727244.1|  83 KIVryfennAKRIKVAvliidgpafIDIADRWNARDEIPIDIEmfefLNELNIDTIVAVNKIDKIKSKDYEQIMNGI 159
                                       33323332233344440011111115666667777777766661111567899***************999888888 PP

                                       HHHHTS CS
                            FeoB_N 131 sekLgv 136
                                        e+Lg+
  gi|298675494|ref|YP_003727244.1| 160 VERLGM 165
                                       888875 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.2   1.3e-05     0.028     102     127 ..      16      40 ..       6      70 .. 0.87
   2 ?   -3.2   0.0         3   6.7e+03      55      82 ..      76     102 ..      75     107 .. 0.64
   3 !    7.2   0.0    0.0019       4.3      42      70 ..     130     157 ..     124     170 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.3e-05
                                       EEEECSTTSSHHHHHHHHCTT----- CS
                       RsgA_GTPase 102 svlvGqSGvGKStLinallpelelkt 127
                                       +v++G S vGKS++i +l+++ ++k+
  gi|298675494|ref|YP_003727244.1|  16 IVFAGRSNVGKSSFIRELTGK-KVKV 40 
                                       69*****************98.5555 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3
                                       -GGG--HHHHHHHHHHHHHHTTSEEEE- CS
                       RsgA_GTPase  55 KiDlleeeeeleelkeelealgyevllv 82 
                                       K D+++++  ++ ++++ +++ ++vl++
  gi|298675494|ref|YP_003727244.1|  76 KKDIVHDKI-VRYFENNAKRIKVAVLII 102
                                       666666666.666667777776666655 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0019
                                       HHHTT-EEEEEEE-GGG--HHHHHHHHHH CS
                       RsgA_GTPase  42 aeekgiepvivlnKiDlleeeeeleelke 70 
                                       ++e +i+ ++++nKiD +++++ +e++++
  gi|298675494|ref|YP_003727244.1| 130 LNELNIDTIVAVNKIDKIKSKD-YEQIMN 157
                                       67889****************9.776655 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.11   2.4e+02       5      33 ..      15      43 ..      11     105 .. 0.84
   2 !   16.4   0.1   2.2e-06     0.005     113     153 ..     125     166 ..      81     204 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.11
                                      EEEEEESTTSSHHHHHHHHHHHTTSSCHH CS
                          GTP_EFTU  5 nigiighvDhGKtTLtdrLlyktgaiskk 33
                                       i+++g  + GK++++ +L+ k+ ++ k+
  gi|298675494|ref|YP_003727244.1| 15 EIVFAGRSNVGKSSFIRELTGKKVKVGKR 43
                                      68889999999999999998777776665 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 2.2e-06
                                       HHHHHHHHTTTEEEEEEESCGST.HHHHHHHHHHHHHHHHHH CS
                          GTP_EFTU 113 evlrlalkegvpiivfiNKmDrl.kaelkeiveevkqklsrk 153
                                       e+++ ++++++ +iv++NK+D++  +++++i + + ++l ++
  gi|298675494|ref|YP_003727244.1| 125 EMFEFLNELNIDTIVAVNKIDKIkSKDYEQIMNGIVERLGMS 166
                                       67888999***************9899****99999999655 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.1e-06    0.0024       1      41 [.      16      74 ..      16     163 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.1e-06
                                      EEEEEBTTTTHHHHHHHHHTS--S---SSS---S-EEEEE..................C CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrrplelql..................g 41
                                      i++ G  + GKSS++  L+g+++ + +   +T +p  +++                  +
  gi|298675494|ref|YP_003727244.1| 16 IVFAGRSNVGKSSFIRELTGKKVKVGKRPGVTLKPYNICYsdmlvtdmpgfgfmsgvkD 74
                                      7899******************99999999**********5555555555555554431 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.2e-05     0.071       2      81 ..      11     116 ..      10     132 .. 0.75
   2 ?   -0.7   0.1      0.31   6.9e+02     129     170 ..     121     163 ..     115     194 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.2e-05
                                       EEEEEEEEEEBTTSSCCCCCCTTSSSS----............................--------------S-EE CS
                            Septin   2 gieftlmvvGesglGkttlintlfetdliee............................ekleeasekkkktveikk 50 
                                        i++ ++ +G+s +Gk+++i+ l  ++++                              + ++++++++ ++  ++ 
  gi|298675494|ref|YP_003727244.1|  11 NINLEIVFAGRSNVGKSSFIRELTGKKVKVGkrpgvtlkpynicysdmlvtdmpgfgfmSGVKDRKKDIVHDKIVRY 87 
                                       57899*******************99998777899999999999999999999887655445555555544443333 PP

                                       EEEEEEETTCEEEEEEEE---BSSSSSHHCC CS
                            Septin  51 kkvvieedgvklnltviDtpgfGdavdnsks 81 
                                        +   + + +k+ + +iD p f d  d  ++
  gi|298675494|ref|YP_003727244.1|  88 FE--NNAKRIKVAVLIIDGPAFIDIADRWNA 116
                                       22..334467788888999999888876555 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.31
                                       HHHHHHHHHHTT.TS-EEEEESSGGGS-HHHHHHHHHHHHHHH CS
                            Septin 129 pldvelmkklse.kvnliPviaKaDtltkeElkefKkkireel 170
                                       p+d+e++  l+e ++  i  + K D + +++ +++ + i e+l
  gi|298675494|ref|YP_003727244.1| 121 PIDIEMFEFLNElNIDTIVAVNKIDKIKSKDYEQIMNGIVERL 163
                                       6888888777662355677778999999988888888777765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.6e-05      0.13       1      81 [.      16     104 ..      16     166 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.6e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf......gvnlrdvakenglllevdpe..aldeskrldedkldklldaleens 68 
                                       I+ +G + vGK+++ +eL  +  ++        +   +++ ++l+++   +  +   ++r ++ ++dk+++ +e+n+
  gi|298675494|ref|YP_003727244.1|  16 IVFAGRSNVGKSSFIRELTGKKvKVgkrpgvTLKPYNICYSDMLVTDMPGFgfMSGVKDRKKDIVHDKIVRYFENNA 92 
                                       8899**************55533558788553333344555555555544466556777777888888999999998 PP

                            AAA_18  69 saleegknlvidg 81 
                                       + + +  +l+idg
  gi|298675494|ref|YP_003727244.1|  93 K-RIKVAVLIIDG 104
                                       7.88899999997 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00014      0.31       2      28 ..      16      42 ..      15      58 .. 0.84
   2 ?   -2.3   0.0       2.2     5e+03     108     120 .]     134     146 ..     125     146 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                                      EEEESSTTSSHHHHHHCHCT-CCC-EE CS
                               Roc  2 vvlvGdsgvGKtsllkrfvedkfseke 28
                                      +v+ G s+vGK+s++++++ +k++  +
  gi|298675494|ref|YP_003727244.1| 16 IVFAGRSNVGKSSFIRELTGKKVKVGK 42
                                      8999***************99987655 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.2
                                       SS-EEEEEE-TTT CS
                               Roc 108 kspvilvgnkiDl 120
                                       ++  i+ +nkiD+
  gi|298675494|ref|YP_003727244.1| 134 NIDTIVAVNKIDK 146
                                       5567899999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1586.43
//
Query:       gi|298675495|ref|YP_003727245.1|  [L=205]
Description: radical SAM domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      8e-19   68.6   0.1    9.5e-19   68.4   0.1    1.1  1  Radical_SAM  Radical SAM superfamily
      2e-08   34.4   0.0    3.2e-08   33.7   0.0    1.4  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.4   0.1   1.1e-22   9.5e-19       2     156 ..      26     187 ..      25     197 .. 0.91

  Alignments for each domain:
  == domain 1  score: 68.4 bits;  conditional E-value: 1.1e-22
                                       EEESEESS--TTTSCCTT....HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC CS
                                       xxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpet....vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla 74 
                                       ++t+ C+ rC+fC r  +    +++ +  ++ sveei++ ++++ + k  + v+ g gep+++ d    l r  k  
  gi|298675495|ref|YP_003727245.1|  26 NITNRCTARCVFCVRDLSdgvyGYNLRLLYEPSVEEIKQALEKNNFLKYREIVFTGFGEPTVRLDDMLSLIRWLKG- 101
                                       799*****************************************8666699999999******************9. PP

                                       CCTEEEEEEECSSCHG....HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT..CTSHHHHHHHHHHHHHHTTSETE CS
                                       xxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  75 vpgiritvetngtlpd....eeklerllelgvdrvslgleaaddekvlklmn..rghtfeevlealeklreagikrv 145
                                         g  +++ tng+       ++++++l+++g+d +s++l+a +++ + +l+    ++ ++  l+ ++k+ ++g++ +
  gi|298675495|ref|YP_003727245.1| 102 -HGAYVRLDTNGHAQLlypnRDVVKELKDAGLDAISVSLNAESEDIYNRLCQprYKNAYQSMLDFTKKAVNLGMR-T 176
                                       .7************669****************************88888888788889****************.7 PP

                                       EEEEEEBTTTS CS
                                       xxxxxxxxxxx RF
                       Radical_SAM 146 vdrivglpGen 156
                                         ++vg+    
  gi|298675495|ref|YP_003727245.1| 177 RMTVVGFTEID 187
                                       88888776555 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.0   3.6e-12   3.2e-08       3      97 ..      26     120 ..      24     142 .. 0.74

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 3.6e-12
                           Fer4_14   3 vrlsgCnlsCkgCd.....nketwkselgkpqteelleqilkdlkkseikiqglvltG.GePLhyenkkellklvkr 73 
                                       + +++C+  C++C          ++ +l  + + e+++q l   k++  k +++v+tG GeP    + +++l l+++
  gi|298675495|ref|YP_003727245.1|  26 NITNRCTARCVFCVrdlsdGVYGYNLRLLYEPSVEEIKQAL--EKNNFLKYREIVFTGfGEPT--VRLDDMLSLIRW 98 
                                       5689*********9665432334555666666666677777..7788888899**********..89********** PP

                           Fer4_14  74 lkeeypekkiwletngtleielek 97 
                                       lk ++    ++l tng +++   +
  gi|298675495|ref|YP_003727245.1|  99 LKGHG--AYVRLDTNGHAQLLYPN 120
                                       ***99..*********99965543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      666  (0.0371465); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1386.67
//
Query:       gi|298675496|ref|YP_003727246.1|  [L=115]
Description: AIG2 family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-19   68.9   0.0    6.2e-19   68.8   0.0    1.0  1  GGACT     Gamma-glutamyl cyclotransferase, AIG2-like


Domain annotation for each model (and alignments):
>> GGACT  Gamma-glutamyl cyclotransferase, AIG2-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.8   0.0   3.5e-23   6.2e-19       1     120 [.       3     114 ..       3     115 .] 0.87

  Alignments for each domain:
  == domain 1  score: 68.8 bits;  conditional E-value: 3.5e-23
                                       EEESSTTSTTSCCCHHHHCSECEEEEEEEECCTBEEEE.ETTTEEEETTSSE.EEEEEEEE-HHHHHHHHHCT.TTT CS
                             GGACT   1 vFvYGtLkrgepnhqrlllgarflesgpatlkgyrlydlggkypalvpgdgekVkGelyevddeelarLDelEpeep 77 
                                       vFvYGtLk+g  n   ll +a f++s++ t+++y++ d  g +p++v+g+ +k++Ge+y+vd ++l  +De+E   +
  gi|298675496|ref|YP_003727246.1|   3 VFVYGTLKSGCVNSN-LLNDADFISSAS-TIDKYTMLDF-GIFPGVVEGNTSKIYGEVYDVDFNTLVSIDEFE---G 73 
                                       8*********99996.998999**9999.********96.68*******************************...* PP

                                       TSEEEEEEEEEC.TTS-EEEEEEEEETT....GGGCCS.-S-SS-- CS
                             GGACT  78 seYereevkvevledgeqveawvYvyag..eeeegdrl.iesgdWr 120
                                        ++ r+  +v++   ++ + a++Y+  +  +  +++++ +esg+W+
  gi|298675496|ref|YP_003727246.1|  74 VWFCRD--EVRL---DNNIIAYMYFLVQipDAFDNKYEiVESGNWQ 114
                                       ******..9999...45566*****966553333344469****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 804.85
//
Query:       gi|298675497|ref|YP_003727247.1|  [L=396]
Description: geranylgeranyl reductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-12   47.3   0.1      6e-10   38.9   0.0    2.5  2  FAD_binding_3   FAD binding domain
    3.6e-11   43.2   1.2    1.9e-05   24.4   0.1    2.3  2  DAO             FAD dependent oxidoreductase
    2.8e-10   40.1   0.1    3.1e-09   36.7   0.0    2.2  2  FAD_oxidored    FAD dependent oxidoreductase
    9.9e-10   38.1   0.0    1.7e-06   27.5   0.0    2.3  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    2.4e-07   30.2   0.0    4.3e-07   29.4   0.0    1.4  1  GIDA            Glucose inhibited division protein A
    2.5e-07   29.8   0.1    5.6e-07   28.6   0.1    1.5  2  HI0933_like     HI0933-like protein
    3.3e-07   30.4   0.0      1e-06   28.9   0.0    1.9  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    7.3e-07   28.6   0.1    1.2e-05   24.6   0.1    2.3  1  Lycopene_cycl   Lycopene cyclase protein
    1.6e-06   28.6   0.0     0.0073   16.8   0.0    2.7  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      2e-06   27.0   0.0      0.013   14.4   0.0    2.2  2  Trp_halogenase  Tryptophan halogenase
    5.5e-06   25.8   0.0    1.2e-05   24.6   0.0    1.5  1  Thi4            Thi4 family
    2.7e-05   23.4   0.2    4.8e-05   22.6   0.2    1.4  1  FAD_binding_2   FAD binding domain
     0.0021   17.4   0.1      0.024   13.9   0.1    2.1  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
     0.0032   16.9   0.0       0.96    8.7   0.0    2.3  2  ThiF            ThiF family
     0.0065   15.8   0.0      0.015   14.6   0.0    1.6  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
      0.023   14.6   0.0      0.064   13.1   0.0    1.7  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.085   13.1   0.0       0.17   12.1   0.0    1.5  1  TrkA_N          TrkA-N domain


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0   5.7e-13     6e-10       2     177 ..       7     173 ..       6     201 .. 0.74
   2 !    5.7   0.0    0.0072       7.6     283     308 ..     280     305 ..     274     333 .. 0.87

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 5.7e-13
                                       EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EE..EHHHH.HHHHHTT-HHHHHHHSEECCCCEEE CS
                     FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradgl..nqrtm.ellrqlGledrilaegapnelmgea 75 
                                       +d+++VGaGpaG ++a+  ++ G +v+l+++ ++     + +g+  + +t+ el  ++ l  ++  e +p+e ++++
  gi|298675497|ref|YP_003727247.1|   7 YDIVVVGAGPAGSTAANYAARNGKSVLLIDRKKDIGTPLQCGGFlpHYETLrELVPNAELPYTL--EEYPSECIHTT 81 
                                       6899**************************9887665557777623556663344555555444..55569****** PP

                                       EEEECCCCCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEE CS
                     FAD_binding_3  76 lynelsdtpkaradlelesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeet 152
                                       ++++  +   a+   + ++   +  ++   +++++L+++a++  +qv  +t v+ +    +g t e+ +   g   t
  gi|298675497|ref|YP_003727247.1|  82 TSCQ--RF-IAPDGCS-KQFDVTADAIDRRRFDKYLAKEAAKSDVQVMPGTTVTEI----NGSTLELEGVF-G-SFT 148
                                       ****..22.2222222.4444566789999************************33....44444444432.3.358 PP

                                       EEEEEEEE--GTT-HHHHHHTGGEE CS
                     FAD_binding_3 153 vrakYlvGaDGgrStvrktlgiefe 177
                                        +a+ ++GaDG +Stv+k+ g+++e
  gi|298675497|ref|YP_003727247.1| 149 TDADVIIGADGPNSTVAKSKGLSRE 173
                                       99*******************9965 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0072
                                       ETTEEE-GGGTEEE-STTSHHHHHHH CS
                     FAD_binding_3 283 kgrvflaGDAaHihpPtgGqGlNtai 308
                                       +++ ++aGDAa     t+G G+ ta+
  gi|298675497|ref|YP_003727247.1| 280 SDNTLIAGDAAGHIIATNGGGIPTAM 305
                                       5789*******999********9998 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.1   1.8e-08   1.9e-05       1      33 [.       8      42 ..       8      74 .. 0.89
   2 !   17.6   0.1   2.2e-06    0.0023     141     349 ..     102     311 ..      88     314 .. 0.59

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.8e-08
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                      d+v++G+G +G+++A ++ar g  V+l+++++++g
  gi|298675497|ref|YP_003727247.1|  8 DIVVVGAGPAGSTAANYAARNGksVLLIDRKKDIG 42
                                      9*******************999********9887 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 2.2e-06
                                       EEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEE.EEEEEEEE--GGGHHHHHTTCTTTSE CS
                               DAO 141 gqvdpakltaalaraaealGveilegtevtgleeedgkvwgverttpgen.daadavVnaaGawsdllgllkeldlp 216
                                         +d +++ ++la++a++  v++  gt+vt+++     + gv+    g+  + ad ++ a G+ s+           
  gi|298675497|ref|YP_003727247.1| 102 DAIDRRRFDKYLAKEAAKSDVQVMPGTTVTEINGSTLELEGVF----GSFtTDADVIIGADGPNSTV---------- 164
                                       56799***************************43323344443....332223588********862.......... PP

                                       EEEEEEEEEEEEECCTHSTGSGCSEEEEEEEETTTTEEEEEE..TTSEEEEEESSEEETTCSS..TSCSHHHHHHHH CS
                               DAO 217 ispvrgqvlvlkplseklvspaailpvpetdddgrgvyvtpr..kdgrvlvGgtadeesgddd..pevdeedidell 289
                                           +g +  ++p s  + +++ +  v   d+d+  +y+  +  ++g  ++ + + ++++ ++   e+  e+    +
  gi|298675497|ref|YP_003727247.1| 165 -AKSKGLSREYDPMSVGTAFEYELSGVD-VDRDAVEMYFGKDyvPGGYAWIISQGGDTANIGVgiRETLFEKGMCAR 239
                                       .344444445544444444444333333.333333333332223334433322221223333332444444444488 PP

                                       HHHHHHS...GG....G..CGEEEEEEEEEE.......E.TTSSEEEEEEETEEEEEEEEECTTTHHHHHHHHHHHH CS
                               DAO 290 ealrklf...Pq....l..gdvlrkwaGlrp.......l.pdglpligetpgvkglylatGhsghGltlapatGkll 349
                                       ++l+k++   P     l  g+v++  +G+ p       +  d+  + g      g+++at+    G+ +a+++Gk++
  gi|298675497|ref|YP_003727247.1| 240 DYLNKFMyehPIasekLkkGSVVSVVSGIVPvggapkyTvSDNTLIAGD---AAGHIIATNG--GGIPTAMVAGKVA 311
                                       9999998665445554244778889999999665543223355666666...4789999765..8999999999875 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.0     3e-12   3.1e-09       1      48 [.       8      55 ..       8     160 .. 0.58
   2 ?    1.0   0.1       0.2   2.1e+02     397     422 ..     301     326 ..     280     336 .. 0.88

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 3e-12
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdig 48
                                      D+vVvG+gpaG +AA  Aar+G++vlL+++++ +G  l  g+  +  +
  gi|298675497|ref|YP_003727247.1|  8 DIVVVGAGPAGSTAANYAARNGKSVLLIDRKKDIGTPLQCGGFLPHYE 55
                                      9*******************************9996666665555555 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.2
                      FAD_oxidored 397 epvcmalGqAaGvaAalaleegvapr 422
                                        p+ m+ G+ aG  A+ +++ ++++ 
  gi|298675497|ref|YP_003727247.1| 301 IPTAMVAGKVAGETASESIDGKCELD 326
                                       699*****************999765 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   1.6e-09   1.7e-06       1      31 [.       7      41 ..       7      89 .. 0.83
   2 !    8.5   0.0   0.00096         1     183     234 ..     107     157 ..      95     174 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.6e-09
                                      CSEEEE--SHHHHHHHHHHHHHTS-EEEEE....T CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x RF
                       Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlve....l 31
                                      +d+vv+G+GpAG +aa ++a++g  v+l++     
  gi|298675497|ref|YP_003727247.1|  7 YDIVVVGAGPAGSTAANYAARNGKSVLLIDrkkdI 41
                                      69***************************743332 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00096
                                       HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 183 kelsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvva 234
                                       +++ ++l+++  k++v+v+ gt+v+ei+g + +le v ++ ++ dad ++ a
  gi|298675497|ref|YP_003727247.1| 107 RRFDKYLAKEAAKSDVQVMPGTTVTEINGSTLELEGVFGSFTT-DADVIIGA 157
                                       578999**********************999766644444443.55555555 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   4.1e-10   4.3e-07       1     150 [.       8     160 ..       8     182 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 4.1e-10
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SSSSEEE-T.......THHHHHHHHHHHT-SHHHHHHHH CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGakvlLithkldtiaelsCnpsiggi.......akgllvrEidalggliikaadka 70 
                                       d++V+G+G AG+ AA  aar G +vlLi  k d    l C   +           +++l   +++  +++i+++ ++
  gi|298675497|ref|YP_003727247.1|   8 DIVVVGAGPAGSTAANYAARNGKSVLLIDRKKDIGTPLQCGGFLPHYetlrelvPNAELPYTLEEYPSECIHTTTSC 84 
                                       79**************************6666555555554333332334555788999999999999999999999 PP

                                       EEEEEEESTTS-CCC-EEEEEE-HHHHHHHHHHHHHTSTTEEEEES.-EEEEEECTTEEEEEEETTS-EEEECEEEE CS
                              GIDA  71 giqfrilNrskGpavralraqvdrelyskevteklenepnleiiee.eveeliveekkvkgvvtedgetikakavvi 146
                                       +  +     sk + v a   ++dr+++ k++ ++  +  +++++ + +v+e++ ++ +++gv  +      a++++ 
  gi|298675497|ref|YP_003727247.1|  85 QRFIAPDGCSKQFDVTAD--AIDRRRFDKYLAKEAAK-SDVQVMPGtTVTEINGSTLELEGVFGSFT--TDADVIIG 156
                                       998888999999999999..99999999999999888.78888876258888777777777776543..34556666 PP

                                       --TT CS
                              GIDA 147 atGt 150
                                       a G+
  gi|298675497|ref|YP_003727247.1| 157 ADGP 160
                                       6676 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.1   5.3e-10   5.6e-07       1      42 [.       7      48 ..       7      50 .. 0.92
   2 ?   -2.9   0.0       1.9     2e+03     115     138 ..     113     136 ..     111     163 .. 0.62

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 5.3e-10
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHC CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklgrKilis 42
                                      +d++v+G+G+AG  aA  aa++gk+Vll++++k +g  ++  
  gi|298675497|ref|YP_003727247.1|  7 YDIVVVGAGPAGSTAANYAARNGKSVLLIDRKKDIGTPLQCG 48
                                      589********************************9877665 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.9
                                       HHHHHHHHT-EEE-S--EEEEECE CS
                       HI0933_like 115 llkelkeagvklrletevksveke 138
                                       l ke+ +++v+++  t+v++++ +
  gi|298675497|ref|YP_003727247.1| 113 LAKEAAKSDVQVMPGTTVTEINGS 136
                                       777888888888888888888332 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   9.7e-10     1e-06       1      32 [.      11      42 ..      11      80 .. 0.95

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 9.7e-10
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlG 32
                                      +vGaG +G++aA ++a++g++vll+++  ++G
  gi|298675497|ref|YP_003727247.1| 11 VVGAGPAGSTAANYAARNGKSVLLIDRKKDIG 42
                                      8******************************9 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.1   1.1e-08   1.2e-05       1     322 [.       8     349 ..       8     365 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.1e-08
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnny.vWsdefedlga..............leecvehsW 62 
                                       D+vv+GaGpAg   A+    a+ g +v+li+  +++  p +      + e l +                ec++++ 
  gi|298675497|ref|YP_003727247.1|   8 DIVVVGAGPAGSTAANYA--ARNGKSVLLIDRKKDIGTPLQCgGFLPHYETLRElvpnaelpytleeyPSECIHTTT 82 
                                       9**********9988888..****************9998888888888888889999999*997776678****** PP

                     Lycopene_cycl  63 sgtivylddgkkillgraYgrvsskrlkeellerlvengvkllea.kvesveeeeageslvvleggrkirarlvvda 138
                                       s  +  ++dg +++ + +   + ++r+ + l+++ +++ v+ + + +v++++ ++    l  + g  + +a +++ a
  gi|298675497|ref|YP_003727247.1|  83 SCQRFIAPDGCSKQFDVTADAIDRRRFDKYLAKEAAKSDVQVMPGtTVTEINGSTL--ELEGVFGSFTTDADVIIGA 157
                                       ************************************99999987626888888877..3333345559********* PP

                     Lycopene_cycl 139 rglaslk....karrlglQ.tfyGvevevdnppfdldkmvl.MDfrveqklkgltFlYalPldsdrl..lvEeTela 207
                                        g ++++    k++   +  +  G   e + +  d+d+  + M f     ++g++++     d   +   + eT + 
  gi|298675497|ref|YP_003727247.1| 158 DG-PNSTvaksKGLSREYDpMSVGTAFEYELSGVDVDRDAVeMYFGKDYVPGGYAWIISQGGDTANIgvGIRETLFE 233
                                       **.66553555555555542457888888888888887655255555444599999888877776651156789887 PP

                     Lycopene_cycl 208 skpeLpadalkkrlaaylra.lglkvkevveeEqgviPvtlggslprleqk.vlaiGaaaglvhPaTGYsvarslae 282
                                       ++    +d l+k + +   a   lk  +vv+   g++Pv  gg ++ + +  +l +G aag +  + G  ++ ++ +
  gi|298675497|ref|YP_003727247.1| 234 KGM-CARDYLNKFMYEHPIAsEKLKKGSVVSVVSGIVPV--GGAPKYTVSDnTLIAGDAAGHIIATNGGGIPTAMVA 307
                                       776.77777777776554444999999************..999998887747889******************988 PP

                     Lycopene_cycl 283 apllasaiaaalres...slsarawatlwprerkrqreffrll 322
                                        ++  +  ++  + +   + +++ w+++++ e++  +++ r l
  gi|298675497|ref|YP_003727247.1| 308 GKVAGETASESIDGKcelDEYEKRWKAQMGMEIRT-AVYIRKL 349
                                       77666666665554466688888888888888765.4444444 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   6.9e-06    0.0073       2      35 ..       9      42 ..       8      46 .. 0.93
   2 !    8.8   0.0    0.0022       2.3      42      74 ..     109     141 ..     102     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.9e-06
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      +vvvG+G  g  +A+++a+ gk+V +++r++ + 
  gi|298675497|ref|YP_003727247.1|  9 IVVVGAGPAGSTAANYAARNGKSVLLIDRKKDIG 42
                                      8****************************99886 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0022
                                       HHHHHHHHHHHTTEEEECSEEEEEEEEETTSEE CS
                         Pyr_redox  42 askilqeklekngievllntkveeiegsedgve 74 
                                       + k+l+++  k  ++v+ +t+v+ei+gs+ ++e
  gi|298675497|ref|YP_003727247.1| 109 FDKYLAKEAAKSDVQVMPGTTVTEINGSTLELE 141
                                       678999********************9986655 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   1.2e-05     0.013       1      39 [.       8      44 ..       8      62 .. 0.78
   2 !   10.5   0.0   0.00018       0.2     150     372 ..     103     337 ..      71     356 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-05
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE.-SSS--- CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlve.seeigtv 39
                                      +iv+vG+G+aG++aA++ a+ +    +v+l++ +++igt 
  gi|298675497|ref|YP_003727247.1|  8 DIVVVGAGPAGSTAANYAARNG---KSVLLIDrKKDIGTP 44
                                      69*******************9...469999724567765 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00018
                                       EE-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-.EEE-SEEEE-SGGG-IIIII.IT---EEE CS
                    Trp_halogenase 150 hldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrledgr.eveadlfiDcsGfrgllieq.aLktgfed 224
                                        +d+++++k+L + a +  v+++ g+ v+     +g+  +l+   g  + +ad +i + G ++ + ++  L+ +++ 
  gi|298675497|ref|YP_003727247.1| 103 AIDRRRFDKYLAKEAAKSDVQVMPGTTVTE---INGSTLELEGVFGSfTTDADVIIGADGPNSTVAKSkGLSREYDP 176
                                       58**********************998543...355544444444432679*********99998765155555555 PP

                                       -TTT----EEEEEEEE--H....---SSEEEEE-SSEEEEEEEETTEEEE.EEEE-TTTS-HHHHHHHHHHHCT--T CS
                    Trp_halogenase 225 wsdvLltdrAlavqvesee....lvepytrataekaGWtWkiPLqhrlgn.GyvyssahadddeAlaellaeldgkl 296
                                       +s    + +A   ++  ++    +ve y +      G  W i   + + n G+  ++   ++ + +++ l+++  + 
  gi|298675497|ref|YP_003727247.1| 177 MS----VGTAFEYELSGVDvdrdAVEMYFGKDYVPGGYAWIISQGGDTANiGVGIRETLFEKGMCARDYLNKFMYEH 249
                                       55....4555555555544556699999999999*********9999999999999999999998888888777554 PP

                                       TTS-EEEE---EE..............ES-SEETTEEE-CCCTEE--CCCS-HHHHHHHHHHHHHHT--BTT--HHH CS
                    Trp_halogenase 297 eaeprkirfttGr..............rkqawvknvvalGlasgfvePlestsihliqaalrrLlallpdksdepaa 359
                                          ++  ++++G                k + + n++  G+a+g + + ++ +i ++++a +   ++  +  d + +
  gi|298675497|ref|YP_003727247.1| 250 PIASE--KLKKGSvvsvvsgivpvggaPKYTVSDNTLIAGDAAGHIIATNGGGIPTAMVAGKVAGETASESIDGKCE 324
                                       44433..34455555666666999998888999999999****************999998888888888877799* PP

                                       HHHHHHHHHHHHH CS
                    Trp_halogenase 360 iaefnrevarele 372
                                       ++e++++ +++++
  gi|298675497|ref|YP_003727247.1| 325 LDEYEKRWKAQMG 337
                                       ****999988775 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   1.2e-08   1.2e-05      18      65 ..       7      53 ..       2      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.2e-08
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBS CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfs 65
                                       D+v+vGaG++G taa y a++ +  v++++r+  +G     GG l +
  gi|298675497|ref|YP_003727247.1|  7 YDIVVVGAGPAGSTAANYAARN-GKSVLLIDRKKDIGTPLQCGGFLPH 53
                                      69********************.99*************9999998765 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.2   4.5e-08   4.8e-05       1      34 [.       8      41 ..       8      50 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 4.5e-08
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqef 34
                                      D++V+G+G AG +AA  aa++G++v++++ ++  
  gi|298675497|ref|YP_003727247.1|  8 DIVVVGAGPAGSTAANYAARNGKSVLLIDRKKDI 41
                                      99**************************998765 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1   2.2e-05     0.024       1     108 [.      10     134 ..      10     159 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.2e-05
                       Pyr_redox_3   1 iIiGaGPaGlaaaielkkagledylilEkg.nign......siyrypkemtfispsftsekleipdlnaiseets.. 68 
                                       +++GaGPaG +aa  + ++g  ++l ++++  ig+      ++ +y + + ++  ++    le    ++i++ ts  
  gi|298675497|ref|YP_003727247.1|  10 VVVGAGPAGSTAANYAARNGK-SVLLIDRKkDIGTplqcggFLPHYETLRELVPNAELPYTLEEYPSECIHTTTScq 85 
                                       79******************9.7999999866765111221455677766666665555555555555555555555 PP

                       Pyr_redox_3  69 .........pafslkeeklsrkealeYlrevaksfelpiklfeeVesvk 108
                                                 +f +  + + r+ + +Yl++ a++ +++++  ++V++++
  gi|298675497|ref|YP_003727247.1|  86 rfiapdgcsKQFDVTADAIDRRRFDKYLAKEAAKSDVQVMPGTTVTEIN 134
                                       6666555555666667777777777777777777777777777777765 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.0    0.0061       6.4      20      42 ..       8      30 ..       5      39 .. 0.83
   2 !    8.7   0.0   0.00091      0.96     103     153 ..      90     148 ..      55     340 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0061
                                      EEEEE--SHHHHHHHHHHHHHTT CS
                                      xxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 20 kvllvGaGglGsellknLalsGv 42
                                       +++vGaG  Gs ++ + a+ G 
  gi|298675497|ref|YP_003727247.1|  8 DIVVVGAGPAGSTAANYAARNGK 30
                                      699*****************994 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00091
                                       -HHHHTT-SEEEEESSSHHHHHHHHHHHHHHT-EE........EEEEEETTEEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxx RF
                              ThiF 103 leellesvDlVvdalDniearrlvnracvkkgipl........ieagtlgfegqvvvii 153
                                        +   +++D+ +da+D +   +++++ ++k+++++        i+++tl++eg +  + 
  gi|298675497|ref|YP_003727247.1|  90 PDGCSKQFDVTADAIDRRRFDKYLAKEAAKSDVQVmpgttvteINGSTLELEGVFGSFT 148
                                       455689*************************9877555555557777777777766664 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.5e-05     0.015      30      62 ..       8      40 ..       3      59 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.5e-05
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHH CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrpa 62
                                       ++v+G+G aG  A++ a++ g +V ++D +++
  gi|298675497|ref|YP_003727247.1|  8 DIVVVGAGPAGSTAANYAARNGKSVLLIDRKKD 40
                                      589**************************9876 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     6e-05     0.064       2      33 ..       9      40 ..       8      45 .. 0.93
   2 ?   -3.5   0.0       7.7   8.1e+03     108     125 ..     292     309 ..     289     313 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6e-05
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdisee 33
                                      + v+GaG  G+  a+ +a++g +V l+d++++
  gi|298675497|ref|YP_003727247.1|  9 IVVVGAGPAGSTAANYAARNGKSVLLIDRKKD 40
                                      78***************************987 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 7.7
                                       SEEEE--SSS-HHHHCCC CS
                           3HCDH_N 108 ailasnTSslsiselaea 125
                                        i+a+n  +++ + +a +
  gi|298675497|ref|YP_003727247.1| 292 HIIATNGGGIPTAMVAGK 309
                                       699***999998887766 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00016      0.17       1      32 [.       9      40 ..       9      47 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
                                      EEEES-SHHHHHHHHHHHHTTEEEEEEESSHH CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidkdee 32
                                      i+++G+G  G++ a++  ++gk+v++id++++
  gi|298675497|ref|YP_003727247.1|  9 IVVVGAGPAGSTAANYAARNGKSVLLIDRKKD 40
                                      89*****************8878*****9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 2768.26
//
Query:       gi|298675498|ref|YP_003727248.1|  [L=96]
Description: hypothetical protein Metev_1608 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.05   13.7   0.0      0.056   13.6   0.0    1.1  1  SnoaL_4   SnoaL-like domain


Domain annotation for each model (and alignments):
>> SnoaL_4  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.1e-06     0.056      54     117 ..      19      81 ..       2      88 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.1e-06
                                       HHHHHHSHHHHHH..-EEEEE---EEEEETTEEEEEEEEEEEEEETTEEEEEE..EEEEEEEEEEE CS
                           SnoaL_4  54 iraalrealdgfa..ltqHllsnplieldgdtAtgrayllatlvrdgdggrqvlaggryedelvre 117
                                       i++  +++l+++     +H+++n++ e dg+  ++++ +l+++   g+++ +v+++g y+ +lv+ 
  gi|298675498|ref|YP_003727248.1|  19 IKRNKNTRLNRKThsEKHHVTMNMVAEKDGNMLKVICDFLVVE---GKRTVEVIISGYYRTDLVKN 81 
                                       4444444566555556678888888888***********9995...55678899*********995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1135  (0.0633053); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 746.90
//
Query:       gi|298675499|ref|YP_003727249.1|  [L=426]
Description: diaminopimelate decarboxylase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-61  207.0   0.0    1.7e-60  204.5   0.0    1.9  2  Orn_Arg_deC_N    Pyridoxal-dependent decarboxylase, pyridoxal
    6.3e-26   90.5   0.0    6.7e-26   90.4   0.0    1.2  1  Orn_DAP_Arg_deC  Pyridoxal-dependent decarboxylase, C-termina
    6.3e-11   42.3   0.0    1.3e-10   41.3   0.0    1.5  1  Ala_racemase_N   Alanine racemase, N-terminal domain
  ------ inclusion threshold ------
       0.15   11.5   0.0        1.1    8.7   0.0    2.1  2  AP_endonuc_2     Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> Orn_Arg_deC_N  Pyridoxal-dependent decarboxylase, pyridoxal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.5   0.0   3.8e-64   1.7e-60       2     247 .]      39     288 ..      38     288 .. 0.98
   2 ?    0.2   0.0     0.088   3.9e+02     187     206 ..     366     386 ..     361     416 .. 0.75

  Alignments for each domain:
  == domain 1  score: 204.5 bits;  conditional E-value: 3.8e-64
                                       HHHHHHHHHHHHHCTCCEEEEEGGG---HHHHHHHHHTTEEEEESSHHHHHHHHHCTTTGGGEEEEESS--HHHHHH CS
                     Orn_Arg_deC_N   2 asierklkrwkkalprikvfYavKansdlavlellaelGlgldcaSkaElelvlaagvsperiifanpckqreelry 78 
                                       ++i+ +++r+kka+p++ +fYa Kan +l++l++lae+G+g d+ S +El+++l ag++ ++i f ++ k+  el +
  gi|298675499|ref|YP_003727249.1|  39 QRIRDNFRRYKKAFPDADLFYAAKANGNLTILKILAEEGAGADVFSDGELYTALLAGIPRDKILFNGNSKSDRELLM 115
                                       57999************************************************************************ PP

                                       HHHCTHTEEEESSHHHHHHHHHHHCC....EEEEEEEE-SCCSSSSTCCCSSSTTSSSSEEHCHHHHHHHHHHHHTT CS
                     Orn_Arg_deC_N  79 alekgvkvvtvdnveeleklaklape....akvllRiktdvsaatcelistggessKFGaaleeavealleaakeen 151
                                       a++ gv+ v vd+++el+ l+ +a++     ++  R+++dvs +t++ istg + sKFG+  +e v a+++a  + +
  gi|298675499|ref|YP_003727249.1| 116 AVQTGVR-VSVDSFDELNTLSSIAKNegkvVDIAFRVNPDVSPKTHPKISTGLKTSKFGIPHDEVVSAYKQALDKPG 191
                                       *******.9*****************99999********************************************** PP

                                       EEEEEEE---BSSC-SCHHHHHHHHHHHHHHHHHHHHT---SEEE--S-BS-HCSTTSSSSTHHHHHHHHHHHHHHH CS
                     Orn_Arg_deC_N 152 lqlvGvsfHvGSgvsdleafvkavekalklfdelaelGvklkiLdvGGGfgveyeeeeeplkleeiaekirealeea 228
                                       ++ vG+++H+GS++ ++e+fv+ v+k++ l++++  lGv+ +++d+G G+g+ ye++ e    ++ a +i +  +e 
  gi|298675499|ref|YP_003727249.1| 192 VNPVGIHCHIGSQILEVEPFVETVNKMMDLVEQISRLGVEFEFVDIGSGLGIPYEKNIEVPTPNDLADSIVPIFNER 268
                                       *******************************************************99888888************** PP

                                       HH.TSSS-EEEE--SHHHHG CS
                     Orn_Arg_deC_N 229 fp.gdkevtiiaEpGRalva 247
                                       ++ ++ ++++++EpGR+lv+
  gi|298675499|ref|YP_003727249.1| 269 CKaEGINPKLVLEPGRYLVG 288
                                       **99999**********995 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.088
                                       HHT---SEEE--S.-BS-HCS CS
                     Orn_Arg_deC_N 187 elGvklkiLdvGG.Gfgveye 206
                                       e G  + +LdvGG Gf++  +
  gi|298675499|ref|YP_003727249.1| 366 EKGDVIAFLDVGGyGFSMSSQ 386
                                       567788999**9988855444 PP

>> Orn_DAP_Arg_deC  Pyridoxal-dependent decarboxylase, C-terminal sheet domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.4   0.0   1.5e-29   6.7e-26       5      98 .]     256     377 ..      33     377 .. 0.72

  Alignments for each domain:
  == domain 1  score: 90.4 bits;  conditional E-value: 1.5e-29
                                       E................................GGEEEEEEEEEEEEETCEEEEEES--TTTS-HHHHCTT-S-EES CS
                                       x................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Orn_DAP_Arg_deC   5 d................................eagvLvtrViavkesekkkfvivdaGmndllrpalygsfheipv 49 
                                       d                                ++ +L+t+V++ k+  k kfv +daG+n+++rp +y+++h+++v
  gi|298675499|ref|YP_003727249.1| 256 DladsivpifnerckaeginpklvlepgrylvgDSAILLTSVNTMKNAAK-KFVGIDAGFNTMIRPVMYDAYHHAVV 331
                                       055555555555555555555555555555555899**********7765.9***********************44 PP

                                       BTT-SCEEC.EEEEEEEE-SSSSTT-EEEEEEEEEE--TT-EEEESS-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Orn_DAP_Arg_deC  50 keeeaekeeeeeeevdvvGptCesgDvlakdrelpelevGdllafedaG 98 
                                           +++++++e ++++vGp+Ce+gD++a+drelpe+e Gd++af d+G
  gi|298675499|ref|YP_003727249.1| 332 A---NKADKNAEDTYTIVGPICETGDIMATDRELPEIEKGDVIAFLDVG 377
                                       3...2233445679*********************************98 PP

>> Ala_racemase_N  Alanine racemase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.0     3e-14   1.3e-10       2     190 ..      37     235 ..      36     247 .. 0.77

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 3e-14
                                       EHHHHHHHHHHHHHHSCTTSEEEEE-HHHHHTTHHHHHHHHHHHTTESEEEESSHHHHHHHHHTTS.CSEEEEESC. CS
                    Ala_racemase_N   2 dldalrhNlrrlralagpgaklmavvKanayghgavevaralaeggadgfgvatleEalelreagi.tapilvleg. 76 
                                       + +++r+N+rr ++++ p+a l+   Kan+  + +++++   + +gad f    l    +   agi + +i +++g 
  gi|298675499|ref|YP_003727249.1|  37 NEQRIRDNFRRYKKAF-PDADLFYAAKANGN-LTILKILA-EEGAGADVFSDGELY---TALLAGIpRDKI-LFNGn 106
                                       5799************.9999*******664.44445554.333457766555555...444556635577.55554 PP

                                       .STGGGHHHHHHTTEEEEESSHHHHHHHHHHHHH............TTS-EEEEEEBESSSS..SSSBSCHHHHHHH CS
                    Ala_racemase_N  77 .fspeelaalaeydltvtvdsleqlealaaaare............agkplrvhlkidtgmg..RlGftpeeleell 138
                                         s +el  +++ ++ v vds ++l+ l+++a++             +   + h ki tg+   + G++ +e+ +++
  gi|298675499|ref|YP_003727249.1| 107 sKSDRELLMAVQTGVRVSVDSFDELNTLSSIAKNegkvvdiafrvnPDVSPKTHPKISTGLKtsKFGIPHDEVVSAY 183
                                       7688999999999*********************8888888888888888888888888888*************** PP

                                       HHHHHTTTEEEEEEE-S-SSTTSTS.HHHHHHHHHHHHHHHHHHHTTGGGSEE CS
                    Ala_racemase_N 139 ealaalpglrleglmtHfasadepd.eeteaqlarfeealeelekaglrppvv 190
                                       +++ ++pg++++g+  H +s    + e++ + ++++ +++e++++ g++ ++v
  gi|298675499|ref|YP_003727249.1| 184 KQALDKPGVNPVGIHCHIGSQIL-EvEPFVETVNKMMDLVEQISRLGVEFEFV 235
                                       *****************999732.23466666777777777776555666655 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       0.1   4.5e+02     120     156 ..      60     101 ..      19     104 .. 0.71
   2 ?    8.7   0.0   0.00024       1.1      26      92 ..     176     238 ..     147     284 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.1
                                       HHHHT.....SEEEEE--TTTTSSSTCHHHHHHHHHHTTTTE CS
                      AP_endonuc_2 120 aekeg.....vklalEtlagsgvelgdeelarlldavdspnv 156
                                       a+k++      k+++E +ag++v++ +e + +ll  ++++++
  gi|298675499|ref|YP_003727249.1|  60 AAKANgnltiLKILAEEGAGADVFSDGELYTALLAGIPRDKI 101
                                       333334777789999999999999999999999999999875 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00024
                                       HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHHHHHHTBSEEEEEBC CS
                      AP_endonuc_2  26 sdeelrelrkaldelglriaslslftrfgypdederearreesvdalkraielaaaLGapllvlhpG 92 
                                        de + ++++ald+ g++ ++++++++++ ++++   +     v+++ + +e  ++LG+++  + +G
  gi|298675499|ref|YP_003727249.1| 176 HDEVVSAYKQALDKPGVNPVGIHCHIGSQILEVEPFVET----VNKMMDLVEQISRLGVEFEFVDIG 238
                                       5778999***********************988545555....667777777777778776444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3226.21
//
Query:       gi|298675500|ref|YP_003727250.1|  [L=242]
Description: FKBP-type peptidylprolyl isomerase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-12   48.1   1.1    6.3e-11   42.4   0.3    2.5  2  FKBP_C    FKBP-type peptidyl-prolyl cis-trans isomerase
    3.4e-09   36.6   0.0    8.4e-09   35.4   0.0    1.7  1  FKBP26_C  FKBP26_C-terminal


Domain annotation for each model (and alignments):
>> FKBP_C  FKBP-type peptidyl-prolyl cis-trans isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.3   7.1e-15   6.3e-11       5      76 ..       3      87 ..       1     115 [. 0.88
   2 !    4.3   0.0    0.0058        52       8      74 ..     123     191 ..     116     236 .. 0.77

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 7.1e-15
                                      B-TTCEEEEEEEEEETTSSEEEEH..........CC...HTSEEEEETTSSSSCHHHHHHHTTSBTT-EEEEEEEGGGT CS
                            FKBP_C  5 akegdtVtvhykgkledgkvfdss..........rs...rakplefkvGsgqvikGfeealegmkvGekrtltippela 70
                                      ++egd++++ y+gkledg vfd++          ++   ++    ++ G+g+ ikG++e l g + G+  t++ippe a
  gi|298675500|ref|YP_003727250.1|  3 IQEGDFIKLSYNGKLEDGIVFDTTdenvakengiYNeqgMYGGDVVVAGAGHTIKGLDEELIGKEEGDSGTIEIPPEKA 81
                                      79**********************999999999855445677778999******************************* PP

                                      TTTTTB CS
                            FKBP_C 71 Ygekgl 76
                                      +ge++ 
  gi|298675500|ref|YP_003727250.1| 82 FGEHDP 87
                                      **9765 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0058
                                       TCEEEEEEEEEETTSSEEEEHCCHTSEEEEETTSSSSCHHHHHHHTTSBT...T-EEEEEEEGGGTTTTT CS
                            FKBP_C   8 gdtVtvhykgkledgkvfdssrsrakplefkvGsgqvikGfeealegmkv...GekrtltippelaYgek 74 
                                       g +V+v+++  l  gk++  ++s  k++e   ++ q + +++ ++ +m +   + ++ + ip el + ++
  gi|298675500|ref|YP_003727250.1| 123 GRRVRVDFNHPL-AGKTVTYDYSIDKKIEDDDEKLQGLLALYTGMPEMDAkieNNTAIINIPNELTFNQR 191
                                       788999999999.555555555799999988888888889999999987544478899999999999983 PP

>> FKBP26_C  FKBP26_C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.0   9.4e-13   8.4e-09       2      71 ..     153     218 ..     152     219 .. 0.95

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 9.4e-13
                                       HHHHHHHHHHH..-TT--..--EEEEETTEEEEE--TTGGGSTTHHHHHHHHHHHHHHH-TTEEEEEEEEEE CS
                          FKBP26_C   2 kekikelIkry..iPnidlekfkieiedktvtIelpeeakFieniqlaklrIAkdilkrieevekVkFvdef 71 
                                        ek+++l  +y  +P++d      +ie++t+ I++p+e  F +   ++k rIA ++++ + ++e+V++v+ +
  gi|298675500|ref|YP_003727250.1| 153 DEKLQGLLALYtgMPEMD-----AKIENNTAIINIPNELTFNQRWLMVKGRIASELMQHL-GIEEVQYVEKY 218
                                       799999****98889999.....9************************************.*********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1868.85
//
Query:       gi|298675501|ref|YP_003727251.1|  [L=322]
Description: methenyltetrahydromethanopterin cyclohydrolase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   9.1e-134  445.6   0.1     1e-133  445.5   0.1    1.0  1  MCH       Cyclohydrolase (MCH)


Domain annotation for each model (and alignments):
>> MCH  Cyclohydrolase (MCH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  445.5   0.1  5.7e-138    1e-133       1     311 []       3     317 ..       3     317 .. 0.99

  Alignments for each domain:
  == domain 1  score: 445.5 bits;  conditional E-value: 5.7e-138
                                       -HHHHHHHHHHHHHHTHHHHT-EEEE-TTS-EEEESSSSS---HHHHHHHHHHHTTT-EEEEEEEEEETTEEEEEEE CS
                               MCH   1 SvnelalelveellekaeelrieveelengatviDaGveaeGgleAGlllaeiclggLaevslelsevkgaklpave 77 
                                       Svne++l +++e+l+ +eel+ie++elengat+iD+Gv++eGg++AG++l+++c+++Lae+++++++ +g+++pa++
  gi|298675501|ref|YP_003727251.1|   3 SVNEKGLYIIDEMLDWEEELKIESKELENGATIIDCGVNVEGGYDAGMYLSRLCVADLAELTYTKFDLDGVTVPAIQ 79 
                                       8**************************************************************************** PP

                                       EEESSHHHHHTTTTS--EEEEETTEEEEEESTTHHHHTS.HHHHHHHT-----S-EEEEEESSS---HHHHHHHHHH CS
                               MCH  78 vstdhPvlacLasqkAgWelsaekffalgsGPaRalaak.eelfeelgyedeadaavlvlesdklPdeevvekvaee 153
                                       v+td+P +ac+asq+AgW +s++++f++gsGPaRal  k ++l+ee+gy+d+ ++avlvles++lPdeevve++a++
  gi|298675501|ref|YP_003727251.1|  80 VATDQPNIACMASQYAGWMISVGDYFGMGSGPARALGLKpKSLYEEIGYKDDIEVAVLVLESSTLPDEEVVEYIAKH 156
                                       ***************************************************************************** PP

                                       HTS-GGGEEEEEE-SSSHHHHHHHHTTHHHHHHHHHHHTT--GGGEEEEEEEEE-----SSHHHHHHHHHHHHHHH- CS
                               MCH 154 cgvepenvtllvaptaSlaGsvqvaaRvvevalhkleelgfdlekivsavgtaPiapvakdelkamgrtndailYgg 230
                                       cgve++nv+++vapt+S+aGsvqv+aRvve+++hkle++gfd++ki+s++g+aPiapv + ++k+mg+tnd+++Y+g
  gi|298675501|ref|YP_003727251.1| 157 CGVETDNVYIAVAPTSSIAGSVQVSARVVETGIHKLESVGFDINKIKSGFGVAPIAPVVGGDTKCMGSTNDCVIYCG 233
                                       ***************************************************************************** PP

                                       EEEEEES......TTHHHHHHHSSGGGSTTTTS-HHHHHHHTTTTGGGS-GGGSS-SEEEEEETTT--EEEEE---H CS
                               MCH 231 rvhltve...aedeeaedlakklpssaskdygkpFaeifkeaeydfykidkalFspAevtvndletgktfkaGelne 304
                                       ++++tv+   ++ ee ed++kk ps +s+dygkpF+++fkea++dfykid+++F+pA++tvndl+++kt++ G++n+
  gi|298675501|ref|YP_003727251.1| 234 ETYYTVKygsDNVEEFEDFVKKTPSANSRDYGKPFYDTFKEANFDFYKIDANMFAPAKITVNDLTNKKTVTSGRINP 310
                                       *******8655668999************************************************************ PP

                                       HHHHHHT CS
                               MCH 305 ellaesf 311
                                        +l +sf
  gi|298675501|ref|YP_003727251.1| 311 GILLDSF 317
                                       ******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2458.60
//
Query:       gi|298675502|ref|YP_003727252.1|  [L=157]
Description: hypothetical protein Metev_1612 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-55  186.2   0.0      3e-55  186.0   0.0    1.0  1  DUF2124   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2124  Uncharacterized protein conserved in archaea (DUF2124)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.0   0.0   1.7e-59     3e-55       2     140 ..       9     150 ..       8     151 .. 0.98

  Alignments for each domain:
  == domain 1  score: 186.0 bits;  conditional E-value: 1.7e-59
                                       HHHHHHHHHHHHTTT-SEEEEEE-TTTTHHHHHHHHHHTTT..SEEEEEETT-GGG-EEEEEETTEEEEEEE-.-S- CS
                           DUF2124   2 glsgllrefkelvkesekivfvGspgvCtpfaellayaiRdlekelvfvpdldlekarklevtdvGmqleeeaeeek 78 
                                       g++g+l+ f+elvk+s++i+f+Gspg+Ctpfael+a++iR++ ke++f+p+l+ e+a++l+ t+ G+ql++++ + +
  gi|298675502|ref|YP_003727252.1|   9 GIGGQLTGFRELVKNSNSITFIGSPGFCTPFAELFAFVIRESGKEMAFIPSLKYENAKSLISTEDGIQLGDKT-DPS 84 
                                       9************************************************************************.9** PP

                                       EEEEEEEGGGGSTTTS--HHHHHHHHHHH....EEEEEEEEEETTHHHHTTHHHHS--SEEEEEEE CS
                           DUF2124  79 advvvllGGlampkikveaedvkelieki....ekkkviGvcfmsifekagWldkidFdliidakl 140
                                       ad+vvllGGlampk++++++d++e+i+k+    e+k++iG+cf+sif++++W++ idFd+iid++l
  gi|298675502|ref|YP_003727252.1|  85 ADTVVLLGGLAMPKMGIDPADINEIITKLqqnsENKMIIGICFQSIFQEQEWDSYIDFDYIIDSDL 150
                                       ****************************99998999****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 928.31
//
Query:       gi|298675503|ref|YP_003727253.1|  [L=121]
Description: carboxymuconolactone decarboxylase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-11   42.7   0.2    7.4e-11   42.0   0.0    1.4  2  CMD           Carboxymuconolactone decarboxylase family
  ------ inclusion threshold ------
      0.031   14.1   0.1      0.066   13.1   0.0    1.7  2  CwfJ_C_1      Protein similar to CwfJ C-terminus 1
      0.063   12.1   0.0      0.073   11.9   0.0    1.1  1  MreB_Mbl      MreB/Mbl protein
      0.072   14.0   0.0        1.4    9.9   0.0    2.1  2  Trnau1ap      Selenocysteine tRNA 1 associated proteins
      0.075   12.8   0.1       0.29   11.0   0.0    1.9  2  Tho1_MOS11_C  Tho1/MOS11 C-terminal domain


Domain annotation for each model (and alignments):
>> CMD  Carboxymuconolactone decarboxylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.3   8.2e+03      56      63 ..       5      12 ..       3      12 .. 0.85
   2 !   42.0   0.0   2.1e-14   7.4e-11       2      78 ..      29     106 ..      28     112 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.3
                                      -HHHHHHH CS
                               CMD 56 teeeiaev 63
                                      t++ei+ev
  gi|298675503|ref|YP_003727253.1|  5 TKDEIREV 12
                                      899**997 PP

  == domain 2  score: 42.0 bits;  conditional E-value: 2.1e-14
                                       HHHHHHHHHHHHHCC.GSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHSHHHHH CS
                               CMD   2 ellraltalrealla.reggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaqaaayagwpaar 77 
                                       ++++ ++++++a++  re+gL+ ke++++ ++v++a + ++ ++  ++++++ G+t+ ei +++++aa+++g  +++
  gi|298675503|ref|YP_003727253.1|  29 DFAEGIAEFYQAIWDeRENGLSMKEKHILVFTVACASNNVESASKILERLKKFGATRTEIYDAMMMAAWTGGIQNFT 105
                                       7999*********99**************************99*****************************88876 PP

                                       H CS
                               CMD  78 a 78 
                                       +
  gi|298675503|ref|YP_003727253.1| 106 N 106
                                       6 PP

>> CwfJ_C_1  Protein similar to CwfJ C-terminus 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.75   2.7e+03      68      84 ..      23      40 ..       9      46 .. 0.67
   2 ?   13.1   0.0   1.9e-05     0.066      44      89 ..      51      96 ..      34     112 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.75
                                      HHHHH.HHHHHHHHHHHH CS
                          CwfJ_C_1 68 ldeir.kfrkalvkmykk 84
                                       dei+  f +++++ y++
  gi|298675503|ref|YP_003727253.1| 23 ADEINeDFAEGIAEFYQA 40
                                      455542466666666654 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1.9e-05
                                      SSTT-EEEEESS--SSTTSS-HHHHHHHHHHHHHHHHHHHHTT--E CS
                          CwfJ_C_1 44 LssgHvliipieHisallsldeevldeirkfrkalvkmykkqdkda 89
                                      ++++H+l+ +++ +s+ ++   ++l+ ++kf ++ +++y+++ ++a
  gi|298675503|ref|YP_003727253.1| 51 MKEKHILVFTVACASNNVESASKILERLKKFGATRTEIYDAMMMAA 96
                                      489*************************************998876 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     2e-05     0.073      78     142 ..      38     104 ..      20     115 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2e-05
                                       HHHHHHHHHTSS-SS--EE.EEEE-SS--HHHHHH.HHHHHHHTT-SEEEEEEHHHHHHHHTT--TT CS
                          MreB_Mbl  78 lkyfikkvkkkkslskprv.vicvPsgiteverrA.vkeaakkaGarevllieeplaAAiGaglpve 142
                                        + + ++ ++  s++++++ v +v + +++ve    + e  kk Ga++ ++ +  ++AA   g++ +
  gi|298675503|ref|YP_003727253.1|  38 YQAIWDERENGLSMKEKHIlVFTVACASNNVESASkILERLKKFGATRTEIYDAMMMAAWTGGIQNF 104
                                       55566666665566555550557888899999754499*********************98888644 PP

>> Trnau1ap  Selenocysteine tRNA 1 associated proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0       0.1   3.7e+02      70      89 ..      24      43 ..      18      48 .. 0.90
   2 ?    9.9   0.0   0.00038       1.4      74      93 ..      79      98 ..      65     113 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.1
                          Trnau1ap 70 eelNkefmersEeLYdaLms 89
                                      +e+N++f e   e+Y+a+ +
  gi|298675503|ref|YP_003727253.1| 24 DEINEDFAEGIAEFYQAIWD 43
                                      689*************9866 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00038
                          Trnau1ap 74 kefmersEeLYdaLmschWq 93
                                      k+f + ++e+Yda+m   W 
  gi|298675503|ref|YP_003727253.1| 79 KKFGATRTEIYDAMMMAAWT 98
                                      7899999************7 PP

>> Tho1_MOS11_C  Tho1/MOS11 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       0.5   1.8e+03      19      27 ..      19      27 ..       6      32 .. 0.76
   2 ?   11.0   0.0     8e-05      0.29      27      46 ..      66      85 ..      62      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.5
                      Tho1_MOS11_C 19 akKFgqeee 27
                                      a KF++e +
  gi|298675503|ref|YP_003727253.1| 19 AIKFADEIN 27
                                      668888865 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 8e-05
                      Tho1_MOS11_C 27 eaidelekqleRieKFGvdl 46
                                      ++++++ k leR +KFG ++
  gi|298675503|ref|YP_003727253.1| 66 NNVESASKILERLKKFGATR 85
                                      678999***********765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       818  (0.0456244); expected 358.6 (0.02)
Passed bias filter:                      633  (0.0353059); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 730.27
//
Query:       gi|298675504|ref|YP_003727254.1|  [L=342]
Description: hypothetical protein Metev_1614 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-62  210.3   0.0    3.3e-62  209.8   0.0    1.2  1  Met_10           Met-10+ like-protein
    2.2e-18   65.9   3.2    5.3e-18   64.6   3.2    1.7  1  Trm5_N           tRNA methyltransferase 5 N-terminal domain
    1.3e-05   24.9   0.0    2.1e-05   24.2   0.0    1.4  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    0.00075   19.1   0.0     0.0012   18.4   0.0    1.3  1  MTS              Methyltransferase small domain
     0.0017   18.3   0.0       0.11   12.4   0.0    2.3  2  Methyltransf_18  Methyltransferase domain
     0.0026   17.1   0.0     0.0039   16.5   0.0    1.2  1  GidB             rRNA small subunit methyltransferase G
  ------ inclusion threshold ------
      0.033   14.9   0.0      0.058   14.1   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
       0.15   11.0   0.0       0.24   10.3   0.0    1.2  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase


Domain annotation for each model (and alignments):
>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.8   0.0   1.5e-65   3.3e-62       2     199 .]      90     286 ..      89     286 .. 0.95

  Alignments for each domain:
  == domain 1  score: 209.8 bits;  conditional E-value: 1.5e-65
                                       EEEEETTEEEEEB-TTSSHHHHHHHHHHHHHS.S-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEE CS
                            Met_10   2 kfeiiGdvvilnlreelkeykkvigevildkt.kvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklD 77 
                                       ++++ Gdv+i++++eel++ kk+i+ ++l++  k+++v+++ +  eg+fR+++ +++ G++ tetihkEn c fklD
  gi|298675504|ref|YP_003727254.1|  90 GWQVLGDVIIVRIPEELEHRKKTIAYTLLEMYpKCRSVVEDFGI-EGQFRRPKRKLIIGNE-TETIHKENQCYFKLD 164
                                       8***************************************9997.****************.*************** PP

                                       TTTS---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEE CS
                            Met_10  78 vskvyfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvk 154
                                       v+++++s+++ +Er+r+ kl  e+e+Vvd+f GiG+f+ip+a++sk  ++++i++nP s+kyl+eni+lN+v+++v 
  gi|298675504|ref|YP_003727254.1| 165 VADIMYSKGNLDERQRMSKL-GEDELVVDMFSGIGYFSIPMAVHSKRTKLISIEINPISFKYLQENINLNRVDDTVI 240
                                       ****************9886.6789**************************************************** PP

                                       EEES-GGG---TT-EEEEEE--TTTGGGGHHHHHHHEE.EEEEEEE CS
                            Met_10 155 pileDgrevireqladrvvmnlpksaieFldkvlaalk.dggvihy 199
                                       p+++D+  +++e++adrv+m+++++++ +l+  ++alk  gg+ hy
  gi|298675504|ref|YP_003727254.1| 241 PVCGDCSLYTPENTADRVLMGYVRTTHYYLKYGIKALKeSGGMLHY 286
                                       ********************************66655505689998 PP

>> Trm5_N  tRNA methyltransferase 5 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.6   3.2   2.4e-21   5.3e-18       1      47 []       4      54 ..       4      54 .. 0.98

  Alignments for each domain:
  == domain 1  score: 64.6 bits;  conditional E-value: 2.4e-21
                                      EEEEEGGGHHHHHHHHHHTT-B-TTS--EEE....TTEEEEEB-S--HHHH CS
                            Trm5_N  1 cikVpkkegEkvRkkLlekglLdrnyKIksd....ddylyIPvkeepegye 47
                                      +i +pk+++E+vR++L+ek+lLdr++KIk++    d+yl+IPv+++++gy+
  gi|298675504|ref|YP_003727254.1|  4 AILIPKEKVETVRCYLSEKNLLDRTRKIKRSkkypDKYLEIPVNDDVDGYK 54
                                      79***********************************************96 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   9.4e-09   2.1e-05       3      60 ..     189     248 ..     187     279 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 9.4e-09
                   Methyltransf_15   3 vilDlfsGaGGnviqfalv..fekviaieinleklacaqhNaevYgvsdkitlvlgdvfe 60 
                                       +++D+fsG G  +i +a +   +k i+iein+   +  q+N ++  v+d + +v+gd+  
  gi|298675504|ref|YP_003727254.1| 189 LVVDMFSGIGYFSIPMAVHskRTKLISIEINPISFKYLQENINLNRVDDTVIPVCGDCSL 248
                                       79***************98555678********************************975 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   5.5e-07    0.0012      25     102 ..     182     259 ..     163     261 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 5.5e-07
                                       HHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTSTTS-EE CS
                               MTS  25 etlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvleeveekkfd 99 
                                       ++l +  ++ v+D+ +G+G+ ++ +a +s+++++  ++++  + +  +en++ n+++  v  v  d+   ++e+  d
  gi|298675504|ref|YP_003727254.1| 182 SKLGE--DELVVDMFSGIGYFSIPMAVHSKRTKLISIEINPISFKYLQENINLNRVDdtVIPVCGDCSLYTPENTAD 256
                                       44444..5569*********************************************965555566776666666666 PP

                                       EEE CS
                               MTS 100 liv 102
                                        ++
  gi|298675504|ref|YP_003727254.1| 257 RVL 259
                                       665 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.027        60     111     133 ..       2      24 ..       1      37 [. 0.84
   2 !   12.4   0.0   4.9e-05      0.11      14      85 ..     186     257 ..     178     262 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.027
                   Methyltransf_18 111 kklilqpnseaeelRkylvengf 133
                                       +k il p++++e++R yl e++ 
  gi|298675504|ref|YP_003727254.1|   2 NKAILIPKEKVETVRCYLSEKNL 24 
                                       678***************99875 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 4.9e-05
                   Methyltransf_18  14 kgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeeevdt 85 
                                       +++ v+D  +  gy +i ++ ++k +k i ++in+ +++  +eni+ ++++d +  +++d      e+ +d 
  gi|298675504|ref|YP_003727254.1| 186 EDELVVDMFSGIGYFSIPMAVHSKRTKLISIEINPISFKYLQENINLNRVDDTVIPVCGDCSLYTPENTADR 257
                                       567899999999********************************************9999754444444555 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.8e-06    0.0039      42     156 ..     181     295 ..     163     315 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.8e-06
                                       GGCS-CCC-.EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SS.EEEEES-CCCTTTTT-EE CS
                              GidB  42 lellkekrdkviDvGsGaGlPGipLaiarpelkltLleslekkiaFLeevkeelklen.veivearaeekqeeekyd 117
                                       ++ l e++  v+D  sG G  +ip+a+  +  kl+ +e +    ++L+e ++  ++++ v  v+ +   + +e++ d
  gi|298675504|ref|YP_003727254.1| 181 MSKLGEDE-LVVDMFSGIGYFSIPMAVHSKRTKLISIEINPISFKYLQENINLNRVDDtVIPVCGDCSLYTPENTAD 256
                                       45555555.4*************************************9988877777615669************** PP

                                       EEEEC-SSSHHHHHHHHCCCEEEEEEEEEEESS--HHHH CS
                              GidB 118 vvtsRAlaslnelteillkllkegglilalKGksaedel 156
                                        v++  ++  + + ++  k lke g +l++    +e+ l
  gi|298675504|ref|YP_003727254.1| 257 RVLMGYVRTTHYYLKYGIKALKESGGMLHYHETVPENRL 295
                                       ******************************977666655 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.6e-05     0.058       1      76 [.     190     267 ..     190     285 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.6e-05
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEEST.G CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssga.l 74 
                                       v+d+  G G +++ +a + ++ k++ ++i++   ++ +e+++ +++   v  v+gd++ +  ++++ D v++ ++  
  gi|298675504|ref|YP_003727254.1| 190 VVDMFSGIGYFSIPMAVHSKRTKLISIEINPISFKYLQENINLNRVddTVIPVCGDCSLYT-PENTADRVLMGYVrT 265
                                       8999************99879********************99999999999****97665.7789***99965554 PP

                                       GG CS
                   Methyltransf_25  75 hh 76 
                                        h
  gi|298675504|ref|YP_003727254.1| 266 TH 267
                                       44 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00011      0.24     205     251 ..     190     238 ..     175     243 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00011
                   tRNA_U5-meth_tr 205 llelycGnGnfslalarnfe..kvlateiakssveaaqyniaankidnv 251
                                       +++++ G G fs+++a + +  k+++ ei   s +  q ni+ n++d+ 
  gi|298675504|ref|YP_003727254.1| 190 VVDMFSGIGYFSIPMAVHSKrtKLISIEINPISFKYLQENINLNRVDDT 238
                                       5789*********999765422789*********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2095.82
//
Query:       gi|298675505|ref|YP_003727255.1|  [L=86]
Description: 4-vinyl reductase 4VR [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-12   45.8   1.3    5.6e-12   45.5   1.3    1.1  1  V4R       V4R domain


Domain annotation for each model (and alignments):
>> V4R  V4R domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   1.3   3.1e-16   5.6e-12       2      57 ..      26      81 ..      25      84 .. 0.96

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 3.1e-16
                                      -EEEEEES-S-TT---SS---HHHHHHHHHHHHHHHSSEEEEEEEE-GGGT-SSEE CS
                               V4R  2 elsieespelaglpgkeePvCyleaGllagalsellgkrveveEveCaaeGhdhCe 57
                                      e+ i +++e+ + p  ++++C + aGll+g+ ++ +g    ++E+eC++ Gh hC 
  gi|298675505|ref|YP_003727255.1| 26 EIVINNCFECCSVPPVDKKLCSFSAGLLEGIITGNTGIGGTIKETECQGSGHNHCM 81
                                      78899**************************************************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      155  (0.00864521); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 565.76
//
Query:       gi|298675506|ref|YP_003727256.1|  [L=229]
Description: hypothetical protein Metev_1618 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.1e-88  293.6   0.1      1e-87  293.4   0.1    1.0  1  DUF2110   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2110  Uncharacterized protein conserved in archaea (DUF2110)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  293.4   0.1   5.8e-92     1e-87       2     223 .]       7     225 ..       6     225 .. 0.97

  Alignments for each domain:
  == domain 1  score: 293.4 bits;  conditional E-value: 5.8e-92
                           DUF2110   2 atkvYdareralesleslvenelkdLdveleisvreddfvkvtleGedeevaanllreefgeitkeveegevyvGtl 78 
                                       + ++Y+++era++s++ ++ n+lk+L+v++++s++ +++v+v+l+Gedee++an+l+++++++++eve+g+ y+G++
  gi|298675506|ref|YP_003727256.1|   7 LLHIYRNTERAIHSIKDMIYNDLKELEVSVDVSATLEGWVQVDLSGEDEEFSANYLVSKYNTPVDEVEPGKEYRGYI 83 
                                       679************************************************************************** PP

                           DUF2110  79 esldedgfvldigvevripkdelkpLgegspeqiaerFGlvqhlpleveveeveeeekeiearltdeqvdrlyewkk 155
                                       +s++++++++++gve++ip+++lkpLg+g++eqia+rFG++++lp++v+v  ++++e+++ ar+t++q+d +++wkk
  gi|298675506|ref|YP_003727256.1|  84 QSIKSERILVNVGVELSIPQSHLKPLGTGNVEQIASRFGIIPYLPVSVDV--TDNSENPK-ARFTKKQIDLWWDWKK 157
                                       **************************************************..44555555.9*************** PP

                           DUF2110 156 gkedrlivnsatrsevkaalnraGhardivtverlglleqsvvcredtdapGlvaeiGpylpaelkvv 223
                                       +++dr+i+nsatrse+k+a++++Gh++di++verlg++e+++vcredtd+pG+vaeiG++l ++l+vv
  gi|298675506|ref|YP_003727256.1| 158 SSTDRVIANSATRSELKSAIKKKGHGKDIYGVERLGVMEHAIVCREDTDGPGIVAEIGKLLISDLGVV 225
                                       *****************************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1437.03
//
Query:       gi|298675507|ref|YP_003727257.1|  [L=200]
Description: MarR family transcriptional regulator [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00029   21.3   0.0    0.00055   20.4   0.0    1.4  1  HTH_27          Winged helix DNA-binding domain
    0.00076   18.3   7.3    0.00087   18.1   7.3    1.0  1  AAA_13          AAA domain
     0.0038   17.2   0.1     0.0064   16.5   0.1    1.4  1  HTH_45          Winged helix-turn-helix
     0.0054   16.5   1.4     0.0087   15.8   1.4    1.4  1  DUF4364         Domain of unknown function (DUF4364)
  ------ inclusion threshold ------
       0.01   14.0   8.9      0.013   13.7   8.9    1.0  1  HOOK            HOOK protein
      0.014   15.5   0.0      0.031   14.4   0.0    1.6  1  DUF2250         Uncharacterized protein conserved in archaea 
      0.017   15.3   4.3      0.098   12.9   4.3    2.0  1  Med30           Mediator complex subunit 30
      0.034   14.1   0.3       0.12   12.4   0.0    2.0  2  MarR            MarR family
      0.038   13.4   4.2       0.05   13.0   3.9    1.3  1  EURL            EURL protein
       0.04   13.9   2.1      0.083   12.9   2.1    1.4  1  YscO-like       YscO-like protein
      0.043   12.6   0.9      0.052   12.3   0.9    1.1  1  UPF0061         Uncharacterized ACR, YdiU/UPF0061 family
      0.086   11.9   9.3      0.032   13.3   6.4    1.6  2  Atg14           Vacuolar sorting 38 and autophagy-related sub
      0.094   12.8   2.3       0.15   12.1   0.7    2.0  2  DUF1664         Protein of unknown function (DUF1664)
       0.14   12.2   8.6       0.33   11.0   8.6    1.6  1  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
       0.32   11.1   8.1        0.5   10.5   8.1    1.4  1  Tropomyosin_1   Tropomyosin like
        1.2    9.6   8.6        3.7    8.1   1.8    2.8  3  NPV_P10         Nucleopolyhedrovirus P10 protein
        5.1    7.3   9.5         11    6.2   9.4    1.6  1  Fib_alpha       Fibrinogen alpha/beta chain family


Domain annotation for each model (and alignments):
>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   5.2e-07   0.00055      22      68 .]      31      74 ..      24      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 5.2e-07
                            HTH_27 22 adlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      + + +  n + +h+ ++l+k++  GLv   + ++d+r k v+lTd G
  gi|298675507|ref|YP_003727257.1| 31 SVITKEINSTFAHTTKILSKMEDCGLV---QFKMDGRVKYVELTDRG 74
                                      6788889999*****************...556************98 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   7.3   8.2e-07   0.00087     323     464 ..      34     181 ..       4     188 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 8.2e-07
                            AAA_13 323 keelkaeaealeeqLkg..lqraleaKrkepfksvelesvkaki.esikklvaeineliakh...Nekvanleeeke 393
                                       ++e+++ +  +++ L +   +  ++ K +  +k vel++   ++ +++k+l+ ++++  +++   N++++ ++++++
  gi|298675507|ref|YP_003727257.1|  34 TKEINSTFAHTTKILSKmeDCGLVQFKMDGRVKYVELTDRGMDVvNALKNLILKLENETEENspaNNISSTFQNSES 110
                                       56677777777777776223457888888999999987777776578899999999999887777************ PP

                            AAA_13 394 eakkklelhlveeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeein 464
                                       +  ++ e + v++++s++ ++  k++++ +++++++++ ++++++l   + +ik Le q+++ ++++++i+
  gi|298675507|ref|YP_003727257.1| 111 QSSEESESQKVQSINSKVVNLRLKIENIYEELSNNNEDSDAIARKLGPFKRDIKKLEDQIESSQNPVDDIA 181
                                       ********************************************************************996 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   6.1e-06    0.0064      15      73 ..      23      85 ..      16      89 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.1e-06
                            HTH_45 15 isegeakkTkimykanLsykllnkYLdmLvekgli...kkskekYv.lTekGlelleklkele 73
                                       s +++  + i ++ n ++  + k L+++ + gl+    +   kYv lT++G+++++ lk+l+
  gi|298675507|ref|YP_003727257.1| 23 WSFERTYASVITKEINSTFAHTTKILSKMEDCGLVqfkMDGRVKYVeLTDRGMDVVNALKNLI 85
                                      5555666788999**********************775456778855************9986 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   1.4   8.2e-06    0.0087      25     110 ..      33     118 ..      26     141 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.2e-06
                           DUF4364  25 ileneytnYfdlqqalseLvesglieeeekenktlykiTekGketlelfenripksirekideylkenkeelkkese 101
                                       i+++   ++ + +++ls++++ gl++ + +   ++ ++T++G ++++ ++n i k   e  +++ ++n ++  ++se
  gi|298675507|ref|YP_003727257.1|  33 ITKEINSTFAHTTKILSKMEDCGLVQFKMDGRVKYVELTDRGMDVVNALKNLILKLENETEENSPANNISSTFQNSE 109
                                       5556667889999***************99*********************99886666666665555555555555 PP

                           DUF4364 102 vkadyykke 110
                                        ++  + ++
  gi|298675507|ref|YP_003727257.1| 110 SQSSEESES 118
                                       444444444 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   8.9   1.3e-05     0.013     465     576 ..      83     194 ..      75     198 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.3e-05
                              HOOK 465 NKmLklkqegseeekltelqelledanrrk..neLetenrlanqrileLeaqveelqkalqeqgskaedssllkkkl 539
                                       N +Lkl+ e +e+   +++++  ++++ +   ++  ++ ++ n ++ +L+ ++e++ ++l++   ++eds +  +kl
  gi|298675507|ref|YP_003727257.1|  83 NLILKLENETEENSPANNISSTFQNSESQSseESESQKVQSINSKVVNLRLKIENIYEELSN---NNEDSDAIARKL 156
                                       7789999999988888888887776655440044444457789*************999987...6788889***** PP

                              HOOK 540 eehleklkevqeelqkkkeqleelepklssnk.qkiee 576
                                             +k++++++++ ++ +++++  + + + q+ ++
  gi|298675507|ref|YP_003727257.1| 157 GPFKRDIKKLEDQIESSQNPVDDIAIITLNDTrQRLDN 194
                                       ***********************986554444366665 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.9e-05     0.031      21      65 ..      26      70 ..      10      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.9e-05
                           DUF2250 21 nvdYaksiakeleipleevrellkkLeelGLlervegktikrtea 65
                                      +  Ya  i+ke++  + + +++l k+e+ GL++ +    +k+ e 
  gi|298675507|ref|YP_003727257.1| 26 ERTYASVITKEINSTFAHTTKILSKMEDCGLVQFKMDGRVKYVEL 70
                                      667******************************999999998775 PP

>> Med30  Mediator complex subunit 30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   4.3   9.3e-05     0.098      35     105 ..     106     174 ..      56     198 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.3e-05
                             Med30  35 grtqskhqaqdrkkklqeqlrqlkvlfkkLrliYekckencqgleevpiesLipyvdeekskreerkksee 105
                                       +++ s+++++++++k+q  + ++ +l+ k+ +iYe++ +n ++ + +   +L p++ ++ +k e++ +s++
  gi|298675507|ref|YP_003727257.1| 106 QNSESQSSEESESQKVQSINSKVVNLRLKIENIYEELSNNNEDSDAIA-RKLGPFKRDI-KKLEDQIESSQ 174
                                       5566888999999****************************9999666.99*****988.55555554443 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00011      0.12       8      49 ..      18      59 ..      13      63 .. 0.92
   2 ?   -1.4   0.1       2.1   2.2e+03      38      55 ..     163     178 ..     161     179 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                                      HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR  8 iLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                      +L  +++ +  + s + k ++ + +++t++l ++e+ Gl++ 
  gi|298675507|ref|YP_003727257.1| 18 ALLAIWSFERTYASVITKEINSTFAHTTKILSKMEDCGLVQF 59
                                      68889999999****************************986 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.1
                                       HHHHHHTTSEEEEEETTS CS
                              MarR  38 ldrLekkGlieRskspeD 55 
                                       +++Le++  ie+s++p D
  gi|298675507|ref|YP_003727257.1| 163 IKKLEDQ--IESSQNPVD 178
                                       6777776..888888877 PP

>> EURL  EURL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   3.9   4.8e-05      0.05     189     254 ..      91     156 ..      61     170 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.8e-05
                              EURL 189 qkkektesdseasvqrrhphysreelnsmtleelkqlnekllkqiqevfeeltkqvqekdslasel 254
                                       + +e++ +++ +s+ ++    s ee +s++++ ++    +l+ +i++++eel+++ ++ d++a +l
  gi|298675507|ref|YP_003727257.1|  91 ETEENSPANNISSTFQNSESQSSEESESQKVQSINSKVVNLRLKIENIYEELSNNNEDSDAIARKL 156
                                       23334444445555556667899**************************************99877 PP

>> YscO-like  YscO-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   2.1   7.9e-05     0.083      84     146 ..     112     174 ..      81     183 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.9e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         YscO-like  84 eelkqeekkvekQkekVkvAerkvEqareelakkrkeveklekhkeewlkevkkeeekreele 146
                                         ++ e +kv++ + kV   + k+E+  eel +++ + +++  +   + +++kk e+++e  +
  gi|298675507|ref|YP_003727257.1| 112 SSEESESQKVQSINSKVVNLRLKIENIYEELSNNNEDSDAIARKLGPFKRDIKKLEDQIESSQ 174
                                       45677889************************************************9999765 PP

>> UPF0061  Uncharacterized ACR, YdiU/UPF0061 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.9     5e-05     0.052     353     456 ..      46     147 ..      18     160 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5e-05
                           UPF0061 353 elleellel.LqetqvdYneffveLaeskskkwrdeaesileesekeleeekleeWrelYkklleeleedeleerae 428
                                       ++l+++ ++ L + ++d    +veL++   + ++  ++ il+ ++++ e++ +++ ++++++  +   +++ e+ ++
  gi|298675507|ref|YP_003727257.1|  46 KILSKMEDCgLVQFKMDGRVKYVELTDRGMDVVNALKNLILKLENETEENSPANNISSTFQNSES---QSSEESESQ 119
                                       45555544436666777777788888888888888888887777776777778888888877655...456778889 PP

                           UPF0061 429 rlkkvNpktvllrplieeviekiaeedd 456
                                       +++++N k+v lr  ie+++e+++++++
  gi|298675507|ref|YP_003727257.1| 120 KVQSINSKVVNLRLKIENIYEELSNNNE 147
                                       99********************976654 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.1   1.2e+03     204     225 ..      27      48 ..       9      50 .. 0.82
   2 ?   13.3   6.4   3.1e-05     0.032      30     125 ..      82     177 ..      79     181 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.1
                             Atg14 204 rdlnafpaeeIsasLsyiaqLl 225
                                       r++ ++  +eI++++ +++++l
  gi|298675507|ref|YP_003727257.1|  27 RTYASVITKEINSTFAHTTKIL 48 
                                       6788888999*****9999988 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 3.1e-05
                             Atg14  30 rlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklak 106
                                       ++  lk+e+e+ ++     ++++ +++++++ ++++++k++++ s++  lr +++++ + ls++++  ++  +kl  
  gi|298675507|ref|YP_003727257.1|  82 KNLILKLENETEENSPANNISSTFQNSESQSSEESESQKVQSINSKVVNLRLKIENIYEELSNNNEDSDAIARKLGP 158
                                       566799999999999999999999***************************************************** PP

                             Atg14 107 lsdklkkRrsdleslqnel 125
                                        ++++kk   ++es qn +
  gi|298675507|ref|YP_003727257.1| 159 FKRDIKKLEDQIESSQNPV 177
                                       ***************9975 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.4   1.5e+03      82      91 ..      58      67 ..      28      95 .. 0.49
   2 ?   12.1   0.7   0.00014      0.15      54     112 ..     121     179 ..      99     186 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.4
                           DUF1664 82 skeikeevte 91
                                      + +++  v+ 
  gi|298675507|ref|YP_003727257.1| 58 QFKMDGRVKY 67
                                      3333333322 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00014
                           DUF1664  54 seslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveg 112
                                        +s+++   +L  +i+++ ++l +++e s +i++++   ++d++++++++es ++ v +
  gi|298675507|ref|YP_003727257.1| 121 VQSINSKVVNLRLKIENIYEELSNNNEDSDAIARKLGPFKRDIKKLEDQIESSQNPVDD 179
                                       46777777889999999999999999999999999999999999999999998887766 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   8.6   0.00031      0.33      21     108 ..      80     175 ..      75     180 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00031
                    CENP-F_leu_zip  21 sLkdkvenLerelem.seenq.......ekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekel 89 
                                        Lk+ +++Le e e+ s +n+       ++     E++ ++v+++++++ +l+ + +++  +L++  ++ + ++++l
  gi|298675507|ref|YP_003727257.1|  80 ALKNLILKLENETEEnSPANNisstfqnSESQSSEESESQKVQSINSKVVNLRLKIENIYEELSNNNEDSDAIARKL 156
                                       6888888888888752334431000000333334455555566688888888888888888888888********** PP

                    CENP-F_leu_zip  90 qkkqervseLeslnsslen 108
                                          ++ ++ Le   +s +n
  gi|298675507|ref|YP_003727257.1| 157 GPFKRDIKKLEDQIESSQN 175
                                       ***********99998887 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   8.1   0.00048       0.5       5      96 ..      86     177 ..      80     194 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00048
                     Tropomyosin_1   5 Lkleaeeaqe.kaeeleekvKeleqe..nlekeqeiksLtkknqqleeevekleeklkeakekaeesekkktnneal 78 
                                       Lkle+e+  +  a+++ +  ++ e++  ++++ q+++s++ k+ +l  ++e++ e+l++ +   e+s+  + +   +
  gi|298675507|ref|YP_003727257.1|  86 LKLENETEENsPANNISSTFQNSESQssEESESQKVQSINSKVVNLRLKIENIYEELSNNN---EDSDAIARKLGPF 159
                                       56666654331466666666666544114556789******************99998765...566677778889* PP

                     Tropomyosin_1  79 trkiqlLEeeleesdkkL 96 
                                       +r i+ LE+++e+s++ +
  gi|298675507|ref|YP_003727257.1| 160 KRDIKKLEDQIESSQNPV 177
                                       *************99865 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.8     0.014        15      11      36 ..     119     144 ..      73     158 .. 0.74
   2 ?    8.1   1.8    0.0035       3.7      11      57 ..     119     169 ..     110     171 .. 0.65
   3 ?    7.6   0.8     0.005       5.3      10      46 ..     160     194 ..     156     198 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.014
                           NPV_P10  11 adikavddkVdalqqqvddvqenlpd 36 
                                       + ++ +++kV  l  +++++ e+l +
  gi|298675507|ref|YP_003727257.1| 119 QKVQSINSKVVNLRLKIENIYEELSN 144
                                       34555666666666666554444444 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0035
                           NPV_P10  11 adikavddkVdalqqqv....ddvqenlpdvtelnekLdaqsaqLaeletk 57 
                                       + ++ +++kV  l  ++    +++++n +d + +  kL      +++le++
  gi|298675507|ref|YP_003727257.1| 119 QKVQSINSKVVNLRLKIeniyEELSNNNEDSDAIARKLGPFKRDIKKLEDQ 169
                                       567888888888888884444445555555566666666666666666555 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.005
                           NPV_P10  10 radikavddkVdalqqqvddvqenlpdvtelnekLda 46 
                                       + dik+++d++++ q+ vdd++    +  +  ++Ld+
  gi|298675507|ref|YP_003727257.1| 160 KRDIKKLEDQIESSQNPVDDIAIITLN--DTRQRLDN 194
                                       579*****************9753222..34566665 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   9.4      0.01        11      32     128 ..      76     173 ..      68     176 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.01
                                       CCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHH CS
                         Fib_alpha  32 dvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn.dnvikksskeleeeilrlketidaqesnirvL 107
                                       dv + l++l  +le+ +++++ a++++++ ++s  +  ++++ +  + i++   +l+ +i+++ e+++++ +   ++
  gi|298675507|ref|YP_003727257.1|  76 DVVNALKNLILKLENETEENSPANNISSTFQNSESQSSEESESQkVQSINSKVVNLRLKIENIYEELSNNNEDSDAI 152
                                       55666667777777777777778888888887766655555443366777777789999999999******999*** PP

                                       HHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 108 qnvlesneqkiqkLeqdidqk 128
                                          l   +++i+kLe +i++ 
  gi|298675507|ref|YP_003727257.1| 153 ARKLGPFKRDIKKLEDQIESS 173
                                       ***************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2371  (0.132244); expected 358.6 (0.02)
Passed bias filter:                      802  (0.044732); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.63u 0.34s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 1205.07
//
Query:       gi|298675508|ref|YP_003727258.1|  [L=389]
Description: N2,N2-dimethylguanosine tRNA methyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   1.6e-106  356.6   0.0     2e-106  356.4   0.0    1.0  1  TRM          N2,N2-dimethylguanosine tRNA methyltransferase
  ------ inclusion threshold ------
      0.064   13.3   0.0       0.31   11.0   0.0    1.9  2  HTH_6        Helix-turn-helix domain, rpiR family
       0.11   12.1   0.0       0.24   10.9   0.0    1.6  1  DUF2067      Uncharacterized protein conserved in archaea (DU
          5    6.7   7.3        7.4    6.1   0.4    3.3  3  zf-ribbon_3  zinc-ribbon domain


Domain annotation for each model (and alignments):
>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  356.4   0.0  4.4e-110    2e-106      15     375 ..      26     383 ..      11     384 .. 0.94

  Alignments for each domain:
  == domain 1  score: 356.4 bits;  conditional E-value: 4.4e-110
                                       -TT--SS--GGGHHHHHHHHHH...HHHHHHHH-S-.......EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-H CS
                               TRM  15 skkeeVFYNPvqefnRDlsvlvirqlellkkklgek.......ikvldaLsasGlRaiRfalEvpgvkevlaNDise 84 
                                       ++++ VFYNP +e nRD++v++    +++ ++l++k       +k++daL+asG R+iR + E +g  +  +ND +e
  gi|298675508|ref|YP_003727258.1|  26 PSSASVFYNPEMELNRDITVVA---NAVFAQRLSAKyglapsdVKYADALAASGARGIRVSNE-TGLDTT-LNDWNE 97 
                                       56789*****************...666666666666667888********************.666655.5***** PP

                                       HHHHHHHHHHHHTT--GGEEEE-S-HHHHHC--SS-EEEEEE--SS--GGGHHHHHHHEEEEEEEEEEE--HHHHTT CS
                               TRM  85 kAvelikeNvklneveeivvineddAnvllaekkkrfdviDlDPfGspapfldsavqsvkekglLlvTaTDtavLaG 161
                                       +A++li +N++ln+v ++ ++ +++Anvll   ++r+d++DlDPfG+p p+l+sa+ s ++  lL +TaTDta+L+G
  gi|298675508|ref|YP_003727258.1|  98 EAYKLILKNAELNDVLDLTTVFSKNANVLL--FENRYDIVDLDPFGTPIPYLESAIYSTRH--LLEITATDTAPLCG 170
                                       *****************7777777******..789***********************988..************** PP

                                       SSHHHHHHHHSSB---STTHHHHHHHHHHHHHHHHHHTTTEEEEEEEEEEETTEEEEEEEEEE-HHHHHHHHTTEEE CS
                               TRM 162 aspekclrkYgavalkselcHEvalRillkavareaakYekavepllslsadfYvrvfvkvktgaakvkkvleklgl 238
                                       a+ ++++rkY+av+l++e+  E+++Rill++vare akY+ka+ p+ls+++ +Yvr +++vk+ga+++++ l+ +g+
  gi|298675508|ref|YP_003727258.1| 171 AHLKSGIRKYSAVPLNNEYHREMGVRILLGKVAREFAKYDKAMIPILSHATRHYVRTYLHVKKGAKRADDALKYMGF 247
                                       ***************************************************************************** PP

                                       EEEETTT--EEEE--GGG.--SB-TTT-SBEEEEEEEE-S-S--HHHHHHHHHHHCT..-TTS-HHHHHHHHHHHHH CS
                               TRM 239 vlhCsgClseekvkglak.fkaecehcgaklhlaGPlwlgplkdkefveevleeaekekeeelkkrvkklLklikeE 314
                                       + hC +C  +++v+gla  + ++c+ cg+k++++GPlwlg l++++f +e+l+e+++ ++ + +++++k+++l+++E
  gi|298675508|ref|YP_003727258.1| 248 ISHCDKCGFRKTVYGLAVsIDNNCPLCGNKTSIGGPLWLGSLHETDFCNEILQEIDN-HQLNKRENTRKIITLCRDE 323
                                       *******99999999975155**********************************99.78888************** PP

                                       HS--SS-EEHHHHHHHHT-SS---HHHHHHH....TT-EE-TTSTTEEE-SS-HHHHHHHH CS
                               TRM 315 lldaplyydlsqlasvlklsvpplkkvvsalkelgfevsrtHakpkaikTnapleavvevl 375
                                        l+ p+yydl+ ++++  +s+ +++++++ l + g+ +srtH++++++kT+a ++++ +++
  gi|298675508|ref|YP_003727258.1| 324 -LEYPTYYDLHLICKRQGVSAVSMNRLIDLLIANGYSASRTHFSGTSFKTDAGIDVINDIV 383
                                       .9*******************************************************9986 PP

>> HTH_6  Helix-turn-helix domain, rpiR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.35   1.6e+03      10      36 ..      57      83 ..      52      86 .. 0.81
   2 ?   11.0   0.0   6.9e-05      0.31       3      70 ..     298     365 ..     296     370 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.35
                                      H-----HHHHHHHHHHHH-S---TT-- CS
                             HTH_6 10 kkekltksekkiaeyilaspdkaiels 36
                                      +k +l++s+ k a+ + as    i++s
  gi|298675508|ref|YP_003727258.1| 57 AKYGLAPSDVKYADALAASGARGIRVS 83
                                      567899999999999999887777666 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 6.9e-05
                                       HHHHHHHH-----HHHHHHHHHHHH-S---TT--HHHHHHHTT--HHHHHHHH---S-SSHHHH--HH CS
                             HTH_6   3 llekiqskkekltksekkiaeyilaspdkaielsikalAkaaavSeativrfakkLGfkGFselklaL 70 
                                       +l+ i +++ +  ++ +ki+   + + +  ++  ++ + k  +vS  + +r+   L ++G+s+ + + 
  gi|298675508|ref|YP_003727258.1| 298 ILQEIDNHQLNKRENTRKIITLCRDELEYPTYYDLHLICKRQGVSAVSMNRLIDLLIANGYSASRTHF 365
                                       78999****999*************************************************9988766 PP

>> DUF2067  Uncharacterized protein conserved in archaea (DUF2067)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   5.4e-05      0.24      51     121 ..     314     383 ..     295     385 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.4e-05
                           DUF2067  51 rrikellreklkkekrglfkyslsdllreag.apvppdvLvdaLkllGykaelre..envlktnapleevvela 121
                                       r+i +l r+    e +  + y+l  +++  g  +v+++ L+d+L + Gy+a+     +   kt+a ++++++++
  gi|298675508|ref|YP_003727258.1| 314 RKIITLCRD----ELEYPTYYDLHLICKRQGvSAVSMNRLIDLLIANGYSASRTHfsGTSFKTDAGIDVINDIV 383
                                       555555555....333456899*********9******************9988777999**********9987 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.16     7e+02       8      15 ..     169     176 ..     167     177 .. 0.80
   2 ?    2.3   0.3     0.026   1.2e+02      18      24 ..     250     256 ..     249     257 .. 0.70
   3 ?    6.1   0.4    0.0016       7.4      16      25 ..     268     277 ..     266     278 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.16
                       zf-ribbon_3   8 CGaplssd 15 
                                       CGa+l+s+
  gi|298675508|ref|YP_003727258.1| 169 CGAHLKSG 176
                                       ***88986 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.026
                       zf-ribbon_3  18 vCpyCGt 24 
                                       +C +CG 
  gi|298675508|ref|YP_003727258.1| 250 HCDKCGF 256
                                       6888885 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0016
                       zf-ribbon_3  16 dnvCpyCGtk 25 
                                       dn+Cp CG k
  gi|298675508|ref|YP_003727258.1| 268 DNNCPLCGNK 277
                                       899****987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2733.13
//
Query:       gi|298675509|ref|YP_003727259.1|  [L=162]
Description: hypothetical protein Metev_1621 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.1e-08   32.7   0.0    8.9e-08   32.2   0.0    1.2  1  Cupredoxin_1  Cupredoxin-like domain
    0.00031   21.1   0.1       0.01   16.3   0.1    2.2  1  Copper-bind   Copper binding proteins, plastocyanin/azurin fa


Domain annotation for each model (and alignments):
>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0   9.9e-12   8.9e-08      18     104 .]      74     161 ..      63     161 .. 0.88

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 9.9e-12
                      Cupredoxin_1  18 aaektveitvkdggfePskievkagekvk.lkiknkdktpeefesed.lgeekvlapgktttitiaplkpGeYeftc 92 
                                       ++ ++v i +++ +  Ps++e+++g  v   +++n+ k+p +++sed l+e++++ + +t++ t+   + G+Y+f  
  gi|298675509|ref|YP_003727259.1|  74 KDPESVLIRLQNYASLPSEVEINKGDTVVwQNFQNDPKRPFTLVSEDrLWENTTIVYRQTFKYTF--NETGTYNFSV 148
                                       566679999999999**********9998677********99999888*****************..99******99 PP

                      Cupredoxin_1  93 d.mhmdakGkliV 104
                                       + + + + G+++V
  gi|298675509|ref|YP_003727259.1| 149 RpFSQRMSGTITV 161
                                       957777******9 PP

>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   1.1e-06      0.01      17      99 .]      91     162 .]      84     162 .] 0.65

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.1e-06
                                       SEEEEETTEEEEEEEESSSSBE..EEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSEEEEEEETTTTTTT CS
                       Copper-bind  17 keitvkkgekvtfvnlavmgHN..vvldkdgvpagvdkdkvkaedetkliggGekdsvtfdeagtYkffCsPHaaag 91 
                                       +e++++kg++v++ n +  +      +++d +    +++          i   ++++ tf+e+gtY+f   P +   
  gi|298675509|ref|YP_003727259.1|  91 SEVEINKGDTVVWQNFQNDPKRpfTLVSEDRL---WENT---------TIVYRQTFKYTFNETGTYNFSVRPFSQR- 154
                                       66677777777777654333221011222222...2222.........3334489*****************9977. PP

                                       SEEEEEEE CS
                       Copper-bind  92 Mkgkvtve 99 
                                       M g++tv+
  gi|298675509|ref|YP_003727259.1| 155 MSGTITVK 162
                                       ******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1237.39
//
Query:       gi|298675510|ref|YP_003727260.1|  [L=348]
Description: hypothetical protein Metev_1622 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00031   20.8   1.4     0.0035   17.4   1.8    2.3  2  Lactamase_B    Metallo-beta-lactamase superfamily
    0.00038   20.0   0.0       0.15   11.6   0.0    2.2  2  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.013   15.4   0.0      0.026   14.4   0.0    1.6  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   1.8   5.8e-07    0.0035       6      58 ..      20      83 ..      17      85 .. 0.95
   2 ?   -0.1   0.0      0.13   7.9e+02     125     153 ..     217     245 ..     153     305 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.8e-07
                                      SEEEEEEETTCEEEES--SCHHHHHHHH...........HHHHHTSGGGGEEEEE-SBSSHHHH CS
                       Lactamase_B  6 vnsyliegdggviLiDtGtsteaaraal...........elaalglkpkdvdavilTHlHlDHi 58
                                      ++++l++++++ ++iD+G     + +             +  ++ +  k  ++v+++H+H+DH 
  gi|298675510|ref|YP_003727260.1| 20 STCTLVTTPDTSLIIDPGAAIMHKTFPIsefaksdylnqAKESVMKASKYAEHVVISHYHYDHL 83
                                      78***********************************99999999999999************6 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.13
                                       HECTTSTSCCEEEEEETTCCEEEECTTTS CS
                       Lactamase_B 125 vtggpghghghgvveygggkvlftGDall 153
                                       v +  +   ++ +vey++ k+l+t D+  
  gi|298675510|ref|YP_003727260.1| 217 VEYSKTGWLISTIVEYRDTKLLYTSDLQG 245
                                       55555566667789999999999999865 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   2.5e-05      0.15      25      52 ..      64      90 ..      30     117 .. 0.64
   2 !    6.6   0.0   0.00085       5.1      71     200 ..     177     305 ..     145     306 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.5e-05
                                      S--..SEEEEE-SS--HHHHGGGGCCCC CS
                     Lactamase_B_2 25 rdelppidaVllthaHyDHlaglltlre 52
                                       +  +  + V+++h HyDHl  +++  +
  gi|298675510|ref|YP_003727260.1| 64 MKASKYAEHVVISHYHYDHLM-VDDNSR 90
                                      344457789**********94.555444 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.00085
                                       CTTCGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S.-- CS
                     Lactamase_B_2  71 eanfvylaleeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtg.yi 146
                                       +++++ ++ +++   +++ ++ g  f+ gd++  +++   + ++g  + +++g  ++ ++e  + +++y+ D++  i
  gi|298675510|ref|YP_003727260.1| 177 SQWSKTNWINVK--SDAVNFADGSGFQKGDTK--VRFS-EPLFHGV-EYSKTGWLISTIVEYRDTKLLYTSDLQgPI 247
                                       567677777776..788888889999998765..4443.3444444.4488999999999*************8334 PP

                                       -HHHHHHHCT..-SEEEEE-S-SSTTHHHH..HHT---STSHHHHCTTSSSSEEEEES CS
                     Lactamase_B_2 147 peeigerlgg..adllllditayeddemir..hmgHltpeeaveaaadlgakrlvliH 200
                                        e+ ++++ +  +d+l+ld+ a+    ++   ++   ++++av++++ ++  ++++ H
  gi|298675510|ref|YP_003727260.1| 248 IEDYAQWIINenPDILILDGPATYLLGYMLsnTDLKRSVDNAVDIIKNCDLDIMIYDH 305
                                       488888875555*******876655554444577777778888888888877777766 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   4.3e-06     0.026       7      56 ..      20      89 ..      18     166 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.3e-06
                     Lactamase_B_3  7 hnsflletagarilvDPf............kanlgyeppa................eeaDlvlisqaledHahletlk 56
                                      +++ l++t+++++++DP+            +        a                + a+ v+is+ + dH  ++   
  gi|298675510|ref|YP_003727260.1| 20 STCTLVTTPDTSLIIDPGaaimhktfpiseF--------AksdylnqakesvmkasKYAEHVVISHYHYDHLMVDDNS 89
                                      789***************6666666666551........0444444446777777799*************9887554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2532.89
//
Query:       gi|298675511|ref|YP_003727261.1|  [L=430]
Description: MgtC/SapB transporter [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-47  162.2  19.2    1.3e-47  162.2  19.2    2.8  3  DUF4010        Domain of unknown function (DUF4010)
    2.8e-20   72.9   8.6    2.8e-20   72.9   8.6    3.4  3  MgtC           MgtC family
  ------ inclusion threshold ------
        3.6    7.2   6.3        6.8    6.3   6.3    1.5  1  Polyoma_coat2  Polyomavirus coat protein


Domain annotation for each model (and alignments):
>> DUF4010  Domain of unknown function (DUF4010)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   5.5       0.8   4.8e+03      72     142 ..      50     119 ..      40     132 .. 0.72
   2 !  162.2  19.2   2.2e-51   1.3e-47       1     209 [.     185     392 ..     185     393 .. 0.89
   3 ?   -3.6   0.9       1.2   7.2e+03      90     105 ..     407     422 ..     400     426 .. 0.48

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.8
                           DUF4010  72 llivavvnpallvalalpllalallallvaalllrrrekeeeeeelelenPlelksAlkfallfalillla 142
                                       + i++++++ ++  + l +l+++++++++  ++l  +++   +    l++P+ l s   +++l+a   +l 
  gi|298675511|ref|YP_003727261.1|  50 TSITGMLSIYVAEIVGLEFLLITTAFFALLCIFLAYAKNIIFNH-YGLTSPIALFSTYILGILVAKGYFLF 119
                                       45666777777777778888888877777777777777777666.78888888888888888877555554 PP

  == domain 2  score: 162.2 bits;  conditional E-value: 2.2e-51
                           DUF4010   1 VlisaisfagYvalrllgarrGllltgllGGlvSStAvtlslarrskeepelarllaagillAnavmllrvllivav 77 
                                       Vl+saisf++Yv+l+ +g++ G++++g+l+G+v+S+A   ++a+ +k++p+l ++ ++gill+n++ml+r+++i+++
  gi|298675511|ref|YP_003727261.1| 185 VLVSAISFISYVFLKKFGTHGGVYYSGILSGFVNSEASAGAFASIAKHKPALLDVSYIGILLSNTAMLVRNIIIAVI 261
                                       8**************************************************************************** PP

                           DUF4010  78 vnpallv.alalpllalallallvaalllrrrekeeeeeelelenPlelksAlkfallfalilllakaaqeyfGdag 153
                                       v+p+  +  l+lp  ++++ +  +++l+ r++ k+ +e +lel++P+ l++A+kf++ f+++l++ak+a++++G +g
  gi|298675511|ref|YP_003727261.1| 262 VDPSGRTaLLMLPPHLAIIGVSSFTTLSKRKNIKSVDE-HLELSSPFALGPAFKFGAGFTILLIVAKFANDIAGATG 337
                                       ***44441234666654444444444444444444444.6************************************* PP

                           DUF4010 154 lyalaalsGladvdAitlslarlaaegtlsaataalaillavlsntlvKavlalvi 209
                                       +ya+a ++Gl++++A+t+s+++la +g++s +taa + ++a++ +tl+K +l+ ++
  gi|298675511|ref|YP_003727261.1| 338 IYATA-IGGLVSSAAVTVSVTTLAVNGGISFTTAAETAVIASIISTLNKNILINLS 392
                                       ***99.*******************************************9998665 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 1.2
                           DUF4010  90 llalallallvaalll 105
                                       ll+++ +++lv+++++
  gi|298675511|ref|YP_003727261.1| 407 LLVMVGFVALVIWAVY 422
                                       3333334444444444 PP

>> MgtC  MgtC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.9   8.6   4.7e-24   2.8e-20       1     120 [.      17     139 ..      17     140 .. 0.89
   2 ?   -1.4   0.1       0.5     3e+03      98     110 ..     181     193 ..     148     231 .. 0.66
   3 ?   -6.4   9.2         3   1.8e+04      72      85 ..     360     375 ..     312     429 .. 0.54

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 4.7e-24
                              MgtC   1 LllAlllGlliGleRelrek....aaGlRTfaLvalgaalfvllslelaesrvaaq..vvsgigflgagvilkekeg 71 
                                       Lll+ll+G+l+G+eRe+r+k    +aG+RTfa+ ++ ++l++++  e+    v     +++  +f++ ++i+  + +
  gi|298675511|ref|YP_003727261.1|  17 LLLSLLIGILVGIEREHRRKyrevFAGVRTFAITSITGMLSIYV-AEI----VG-LefLLITTAFFALLCIFLAYAK 87 
                                       799**************9888999********************.222....22.2357888888888888888887 PP

                              MgtC  72 a...kvkglTTaaslwvtaaiGllvglglyllavvatvlvllllallreler 120
                                       +   ++ glT+ ++l+ t+++G+lv+ g++l a+v++v++++ll+ +++l++
  gi|298675511|ref|YP_003727261.1|  88 NiifNHYGLTSPIALFSTYILGILVAKGYFLFAIVGAVVITFLLIEKKPLHS 139
                                       8899**********************************************97 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.5
                              MgtC  98 yllavvatvlvll 110
                                       +l+ v++++++++
  gi|298675511|ref|YP_003727261.1| 181 ILIVVLVSAISFI 193
                                       3333333333333 PP

  == domain 3  score: -6.4 bits;  conditional E-value: 3
                              MgtC  72 a..kvkglTTaaslwv 85 
                                       a     ++TTaa   v
  gi|298675511|ref|YP_003727261.1| 360 AvnGGISFTTAAETAV 375
                                       1112233333333322 PP

>> Polyoma_coat2  Polyomavirus coat protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   6.3    0.0011       6.8       1      64 [.     316     382 ..     316     423 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0011
                     Polyoma_coat2   1 GavlsllidliaevselaaatGlsveailageafaaieveiaslvtvegv...levaeAlaaiglte 64 
                                       Ga  ++l+ + + + ++a atG+ + ai   ++ aa+ v +++l++ +g+   + +++A+ a+ +++
  gi|298675511|ref|YP_003727261.1| 316 GAGFTILLIVAKFANDIAGATGIYATAIGGLVSSAAVTVSVTTLAVNGGIsftTAAETAVIASIIST 382
                                       677788877778889********************************99865545556665555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       893  (0.0498076); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2947.57
//
Query:       gi|298675512|ref|YP_003727262.1|  [L=215]
Description: metallophosphoesterase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.9e-22   78.6   0.1    1.5e-21   77.8   0.1    1.4  1  Metallophos    Calcineurin-like phosphoesterase
    7.1e-20   71.9   0.0    9.6e-20   71.4   0.0    1.1  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    9.5e-08   31.7   0.2    2.5e-05   23.7   0.2    2.6  2  Metallophos_3  Metallophosphoesterase, calcineurin superfamil


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.8   0.1   2.6e-25   1.5e-21       1     203 [.       1     172 [.       1     173 [. 0.82

  Alignments for each domain:
  == domain 1  score: 77.8 bits;  conditional E-value: 2.6e-25
                                       EEEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTSCH CS
                       Metallophos   1 lrilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHegf 77 
                                       +ril i+D+H     g++++++ ll++     ++dl+l+aGDl++ g+ ek  +el+  + +   pv +++GN++  
  gi|298675512|ref|YP_003727262.1|   1 MRILAITDPH-----GNYSKIEPLLQKS---GDIDLILIAGDLTNFGPDEK-AEELVGMFEA---PVLAVPGNCD-- 63 
                                       89********.....**********776...788*************9999.9999999999...**********.. PP

                                       HHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTE...EEEEEEESECEEETHHHHHHHHHHHSCHHHHCC.HHH CS
                       Metallophos  78 eeellnkygylgifsepwrsdaevfnnlplaslgsgs...lkvlllhGgspellvsldklgslnleleapepg.dew 150
                                          ++ +               +v++ l ++ + ++    + +++ +Gg        ++ + +n ++e +e++ ++ 
  gi|298675512|ref|YP_003727262.1|  64 --PVSLP---------------DVLDRLDVNLHNTTVtrdDVTFIGFGG--------SNPTPFNTPFELEEEEiEKH 115
                                       ..22222...............233333333322222333356666666........77788999999999889888 PP

                                       HHH..HHHHTTCSEEEEEESSESS.CSSSCSCCHHHHHHH.HHHTTESEEEEESSSS CS
                       Metallophos 151 lkd..lekrekadwvivlgHsply.rgsgylfgdealedl.lkkygvdlvisGHtHv 203
                                       l++  ++++e + ++++l+H p+y +  + + g+  ++ + ++  +vdlv++GH+H+
  gi|298675512|ref|YP_003727262.1| 116 LENlvNSAEESGNITVLLTHAPPYcTLDEVSAGNVGCKSIiKFMDKVDLVVCGHIHE 172
                                       8889999*****************9888889999999988899999**********7 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.4   0.0   1.6e-23   9.6e-20       1     148 [.       1     192 [.       1     201 [. 0.80

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 1.6e-23
                     Metallophos_2   1 MklaiiSDlHsnldaleavlealkevgvdaiihaGDleeeepevleellela.....pvlaVrGNnD.......... 62 
                                       M++++i+D H+n++ +e +l++  +   d+i+ aGDl  +++   e+++el      pvlaV+GN+D          
  gi|298675512|ref|YP_003727262.1|   1 MRILAITDPHGNYSKIEPLLQKSGDI--DLILIAGDL--TNFGPDEKAEELVgmfeaPVLAVPGNCDpvslpdvldr 73 
                                       9*********************7766..********9..777666666666566688******************** PP

                     Metallophos_2  63 ........................eevveedvlreaaelgtdlp...eeaelelagekvlliHgdpl.......gvk 105
                                                               ++ +   +  e++e++++l+   ++ae + ++ +vll+H  p+       +++
  gi|298675512|ref|YP_003727262.1|  74 ldvnlhnttvtrddvtfigfggsnPTPFNTPFELEEEEIEKHLEnlvNSAEES-GNITVLLTHAPPYctldevsAGN 149
                                       *9999999999987777777775433366666666666666663111222222.6667******999**99988888 PP

                     Metallophos_2 106 dalaellkeaeegsdvvvcGHtHvp.evekeggvlvvnPGsvge 148
                                        + ++ +k  ++++d+vvcGH+H++ +v ++g+ ++vnPG ++ 
  gi|298675512|ref|YP_003727262.1| 150 VGCKSIIKF-MDKVDLVVCGHIHEArGVMEHGKSVIVNPGMASD 192
                                       888888888.88999*********989*************8765 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.0    0.0016       9.5       7      44 ..       2      37 ..       1      48 [. 0.83
   2 !   23.7   0.2   4.2e-09   2.5e-05     128     250 ..      82     203 ..      41     212 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0016
                                      EEEEEE--TT-GGGHHHHHHHHHHH--SEEEEES---- CS
                     Metallophos_3  7 kvlaisdlkgevellerlveviedkdpDllvlvGdlvk 44
                                      ++lai+d +g++  +e l+++    d Dl+++ Gdl +
  gi|298675512|ref|YP_003727262.1|  2 RILAITDPHGNYSKIEPLLQKSG--DIDLILIAGDLTN 37
                                      89****************99865..689*******964 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 4.2e-09
                                       EEETTTEEEEEE-SEEESS--BSSSS-EEEHHHHHHHGGG.GGGS---E..EEEEESS--S-SSTBTTBS---S-HH CS
                     Metallophos_3 128 aekeGevliaGmGGeivdgekeeefrLkYPaweveyrLkv.lkelkdrr..kvlllatpPigelvadkglkekgsev 201
                                         ++ +v ++G+GG      ++  f L     e+e  L   ++ + +     vll + pP   l+  +    +g+  
  gi|298675512|ref|YP_003727262.1|  82 TVTRDDVTFIGFGGSN-PTPFNTPFEL--EEEEIEKHLENlVNSAEESGniTVLLTHAPPYCTLD--E--VSAGNVG 151
                                       4555567777777753.2333334444..355566555441344444441156777889944443..2..4678888 PP

                                       HHHHHHHH.--SEEEE-SS--EE..EEETTEEEEE--BGGGTEEEEEETTTT CS
                     Metallophos_3 202 vaelvktl.nPevvvvghavkeh..eelgktlvvnPGaleeGdfavvdleek 250
                                          ++k + + ++vv+gh + ++   e gk+++vnPG  ++G  a++++++k
  gi|298675512|ref|YP_003727262.1| 152 CKSIIKFMdKVDLVVCGHIHEARgvMEHGKSVIVNPGMASDGYGALININKK 203
                                       888999763579********999776779********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1656.04
//
Query:       gi|298675513|ref|YP_003727263.1|  [L=242]
Description: protein serine/threonine phosphatase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-14   54.6   0.2    1.5e-14   54.1   0.2    1.2  1  PP2C_2    Protein phosphatase 2C
    1.3e-12   48.0   0.9    1.9e-09   37.5   0.2    2.1  2  PP2C      Protein phosphatase 2C
    1.2e-06   28.6   0.4    1.9e-06   27.9   0.4    1.3  1  SpoIIE    Stage II sporulation protein E (SpoIIE)


Domain annotation for each model (and alignments):
>> PP2C_2  Protein phosphatase 2C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   0.2   2.6e-18   1.5e-14       8     179 ..      19     202 ..      13     232 .. 0.75

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 2.6e-18
                            PP2C_2   8 rglpcqDalavwtdsggsllaVaDGaGSakrSerGariaveavvealaelleseeee..eeallraleaailadvlk 82 
                                       ++ +++D + + + +++ llaVaDG G ++ +++++ iav  + e+++e+ ++++ +  +++ll +++++i+++v  
  gi|298675513|ref|YP_003727263.1|  19 NRDHNEDNCLMMKIDDAYLLAVADGLGGHAAGDVASGIAVMKLEEFFKEQYSEDMDDeqIKDLLCNCHERINDEV-- 93 
                                       6789******9999999**********************************877777557788888888888666.. PP

                            PP2C_2  83 eeaeaqdaelkdyatTllaavvtpdeivalqiGDGaivvrd.......rdgev.qllge.....pdsgeyanqttfl 146
                                        +a  +  + + ++tTl+ a+v+++++++++ GD+ + v++       +d+++ q+l++     ++++ y  + + +
  gi|298675513|ref|YP_003727263.1|  94 IQA--SVGDKQGLGTTLVSAFVRGNKAIIANTGDSRATVVGtgikfrtKDHSMvQRLLDrgmidEETARYHPMSHIV 168
                                       333..3336788*************************9999555555544433244444555546667777777777 PP

                            PP2C_2 147 tsedaeeelrirrlk..ledgdalllmTDGlansl 179
                                       t + ++ ++ +   +   ++ + l+l++DGl + +
  gi|298675513|ref|YP_003727263.1| 169 THS-MGNQFDVDAYEteIDEEEILVLSSDGLHDHV 202
                                       766.67777777666323445669999***98544 PP

>> PP2C  Protein phosphatase 2C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.2   3.2e-13   1.9e-09      18     141 ..      17     143 ..       2     148 .. 0.70
   2 !    9.2   0.0   0.00014      0.83     203     231 ..     186     214 ..     177     235 .. 0.78

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 3.2e-13
                                       EEECCCCTCTT..CCCCCCEEEEEEEEESSSHHHHHHHHHHH....HHHHHHHHCHTTHHHHHHHHHHHHH.HHHHH CS
                              PP2C  18 ahislanless..sgkssvsffavfdghggseaakyarehle....eilksqksfeelekleqalrksfla.dtdee 87 
                                       a     n  ++   + ++ +++av dg gg+ a ++a+        e+ k+q s + +   ++++++   + +++++
  gi|298675513|ref|YP_003727263.1|  17 AGNRDHNEDNClmMKIDDAYLLAVADGLGGHAAGDVASGIAVmkleEFFKEQYSEDMD---DEQIKDLLCNcHERIN 90 
                                       554444444445555788899****************998874443555555554444...5555555555454444 PP

                                       HHHHHHHC.HCCT-EEEEEEEEEETTEEEEEEESS-EEEEEETTEEEEECS---S CS
                              PP2C  88 lksskant.epsksGstavvalirgtklyvAnvGDSravLcrkgnakkeltedHk 141
                                        +  +a+   ++  G+t v+a++rg+k ++An+GDSra +++ g +  + t+dH 
  gi|298675513|ref|YP_003727263.1|  91 DEVIQASVgDKQGLGTTLVSAFVRGNKAIIANTGDSRATVVGTGIK--FRTKDHS 143
                                       44444455568999************************99987766..5899997 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00014
                                       TTEEEEEEE-HHHHTTSHHHHHHHHHHHH CS
                              PP2C 203 eedefliLacdGlwdvlsdqeavdlvrde 231
                                       +e+e l+L +dGl d++ +  +v+ v ++
  gi|298675513|ref|YP_003727263.1| 186 DEEEILVLSSDGLHDHVGKSVLVESVAYQ 214
                                       3489*******************999876 PP

>> SpoIIE  Stage II sporulation protein E (SpoIIE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.4   3.2e-10   1.9e-06       2     189 ..      33     239 ..      32     241 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 3.2e-10
                                       TTEEEEEEEECSS....SSHHHHHHHHHHHHHHHHHHHTTTS...HHHHHHHHHHHCHCTTSTT......TTCEEEE CS
                            SpoIIE   2 dgrlalvvgDvvG....hGleAalimgllrsalrelatagle...paevlkrlnralardleee.....erfaTavl 66 
                                       d+ ++l+v+D+ G     ++++ + ++ l   ++e  +++++    +++l + ++++++++ ++     + +   +l
  gi|298675513|ref|YP_003727263.1|  33 DDAYLLAVADGLGghaaGDVASGIAVMKLEEFFKEQYSEDMDdeqIKDLLCNCHERINDEVIQAsvgdkQ-GLGTTL 108
                                       67899********766666777777777777777777777779995555555555555555555666644.444444 PP

                                       EEEETTTTEEEEEEESSSSEEEEETTSTEEEEE--SS--.....TTTSSS...................T-EEEEEE CS
                            SpoIIE  67 avydpstgkleyanaGhpppllvrpdggtklllastglp.....lGilpe...................adyetael 119
                                       +  +   +k+ +an G++   +v    g k+++++++++      G+++e                   +d++ +e 
  gi|298675513|ref|YP_003727263.1| 109 VSAFVRGNKAIIANTGDSRATVVGT--GIKFRTKDHSMVqrlldRGMIDEetaryhpmshivthsmgnqFDVDAYET 183
                                       4447899999***************..99999999999988756699999*************************** PP

                                       E--TTEEEEEESCCCCSSSHHHHHHCCCHHCHHHHCT.....HCCHHHHHHHHHHHHTTSSSSS-EEEEE CS
                            SpoIIE 120 elepgdtlllyTDGvtEardsdgelfgkerllallasaegesleelldalveellelgsgeleDDitllv 189
                                       e++++++l+l +DG+ +     +       l++ +a    ++++e+++ l+++ le      +D +t++v
  gi|298675513|ref|YP_003727263.1| 184 EIDEEEILVLSSDGLHDHVG--KS-----VLVESVA---YQKPSEIVKYLYKKSLE----TTTDNVTIVV 239
                                       ****************9762..22.....2344444...23477777777777777....4467777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1670.52
//
Query:       gi|298675514|ref|YP_003727264.1|  [L=96]
Description: hypothetical protein Metev_1626 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0087   16.0   0.0      0.011   15.7   0.0    1.1  1  PBP-Tp47_c  Penicillin-binding protein Tp47 domain C
  ------ inclusion threshold ------
      0.013   15.4   0.0      0.017   15.0   0.0    1.2  1  DUF1236     Protein of unknown function (DUF1236)
      0.057   13.5   0.1      0.088   12.9   0.1    1.3  1  RuvA_N      RuvA N terminal domain


Domain annotation for each model (and alignments):
>> PBP-Tp47_c  Penicillin-binding protein Tp47 domain C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.8e-06     0.011      95     153 ..       9      66 ..       4      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.8e-06
                        PBP-Tp47_c  95 kfaadnwmhksmGiqlGltdslrcqlPegtdGtGywkltvyalGyedvtvevevteeni 153
                                        f  dn m k   i  G  d  r ++ + tdG    +  ++ +Gye v     vt+ +i
  gi|298675514|ref|YP_003727264.1|   9 SFIKDNLMNKKVDIYCGGPDYFRGTIVDCTDGVITLEWNIKEIGYEHVI-PQTVTKYDI 66 
                                       5899****************************9999999******9764.445666555 PP

>> DUF1236  Protein of unknown function (DUF1236)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   2.9e-06     0.017      22      52 ..      56      89 ..      47      95 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.9e-06
                           DUF1236 22 alPetVelrpv.Pdevv.i.peyrYvvvndrtvi 52
                                      ++P+tV+ +++ P+e+    ++y Y++v+    i
  gi|298675514|ref|YP_003727264.1| 56 VIPQTVTKYDIsPSEWEiKeEGYTYIMVDKILAI 89
                                      89***************5556*******976655 PP

>> RuvA_N  RuvA N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   1.5e-05     0.088       4      38 ..      29      72 ..      28      85 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.5e-05
                                      EEEEEEEEESSCEEEEEE..TTEEEEEEE-HHHHCC........- CS
                            RuvA_N  4 ylkGkvvekepdsivvev..ggvGYevfvplstlss........k 38
                                      y +G++v+ +++ i++e     +GYe  +p+ t+++        +
  gi|298675514|ref|YP_003727264.1| 29 YFRGTIVDCTDGVITLEWniKEIGYEHVIPQ-TVTKydispsewE 72
                                      99**************85349*********4.4444466544443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 728.20
//
Query:       gi|298675515|ref|YP_003727265.1|  [L=396]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-21   76.6   0.0    3.4e-21   75.7   0.0    1.5  1  OrfB_IS605      Probable transposase
    6.5e-12   45.2   0.0    1.4e-11   44.1   0.0    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0004   19.8   0.2     0.0007   19.0   0.2    1.4  1  Glyco_hydro_97  Glycoside hydrolase 97
  ------ inclusion threshold ------
       0.11   12.9   1.0       0.28   11.6   1.0    1.7  1  HEPN_Swt1       Swt1-like HEPN
       0.11   11.7   0.0       0.19   11.0   0.0    1.4  1  EAP30           EAP30/Vps36 family
       0.14   12.5   0.0       0.29   11.5   0.0    1.5  1  RuvX            Holliday junction resolvase


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.7   0.0   1.1e-24   3.4e-21       2     117 ..     164     278 ..     163     281 .. 0.97

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 1.1e-24
                        OrfB_IS605   2 ipvevevelpkpkgnkaagiDlGinnLatvvtedgtw.flykgrrlksdykylakeiaelqsklkksknykkasrkl 77 
                                       i++e + e+p  ++++ a+iDlGinn++t+v++ g+  +++kg  +ks ++ ++k+  +l s+++k +   k s+kl
  gi|298675515|ref|YP_003727265.1| 164 IVYEKDLETPDLNEENIASIDLGINNIVTMVNNIGEKpIVIKGGVAKSINQFYNKKAGKLKSIYDKLG--IKNSKKL 238
                                       78999999****************************99*****************************9..9****** PP

                        OrfB_IS605  78 arlhrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       ++l++k + ++++++hk+++++++ + + +++tL++g+  
  gi|298675515|ref|YP_003727265.1| 239 KKLYHKYKMKINDFFHKASKRIVDFCVKYNIGTLVIGYNE 278
                                       *************************************986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.0   4.8e-15   1.4e-11       1      69 []     299     373 ..     299     373 .. 0.95

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 4.8e-15
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke......alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f++l eql+yka++ G kv+e +++yTSk +   g+ + +      ++ +r + +++ g+ +++Dvn+a+Ni+k+
  gi|298675515|ref|YP_003727265.1| 299 FHRLLEQLKYKAEDVGLKVIEQEESYTSKCSFLDGEPVVRrtsylgKRIKRGLFRSSNGTIINADVNGAYNIMKK 373
                                       899**************************999****9999999***99999999999****************96 PP

>> Glyco_hydro_97  Glycoside hydrolase 97
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.2   2.3e-07    0.0007      34     105 ..     254     324 ..     210     339 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.3e-07
                    Glyco_hydro_97  34 tetvkryiDfAaengleyvlvegwdegWee..kkkkekefdftkpypdfdleelvaYakekgvgvelwlhsets 105
                                        +  kr +Df+ ++++ ++++ g++egW++   + k ++++ ++++p  +l e ++Y k+ +vg++++ ++e +
  gi|298675515|ref|YP_003727265.1| 254 HKASKRIVDFCVKYNIGTLVI-GYNEGWKQevYMGK-RNNQKFTQIPFHRLLEQLKY-KAEDVGLKVIEQEESY 324
                                       56789****************.*******9965554.45555667788888888888.4445678887777765 PP

>> HEPN_Swt1  Swt1-like HEPN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.0   9.3e-05      0.28      10      70 ..      26      85 ..      18      97 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.3e-05
                         HEPN_Swt1 10 Lrpfverelskayged..wweeveaslekdeeekkesekeiskldvqdllrvitenWkevFkk 70
                                      L++  + +++++++++  w++  e    +++ ++ e+ + +  +++q+ l+++++nWk++F++
  gi|298675515|ref|YP_003727265.1| 26 LYNQANFIVKQSLNDEgdWVRYEEL---NKQLKGTENYSVLPTQTAQQTLKLMDKNWKSFFQS 85
                                      5555555566666555535544444...444444455666677889999**********7775 PP

>> EAP30  EAP30/Vps36 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   6.4e-05      0.19      64     123 ..     224     280 ..     207     342 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.4e-05
                             EAP30  64 tkmcaslGvdplsskkseslgfl...ellglgdfyyeLavqivevclatraengglisleely 123
                                       +++ ++lG+     k+s++l++l     ++++df+ + +++iv++c + +     +i   e +
  gi|298675515|ref|YP_003727265.1| 224 KSIYDKLGI-----KNSKKLKKLyhkYKMKINDFFHKASKRIVDFCVKYN-IGTLVIGYNEGW 280
                                       448889999.....3344555666666777****************9653.222555555555 PP

>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   9.8e-05      0.29      14     100 ..     231     327 ..     227     332 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.8e-05
                                       EEEEE-S--SS---EEEEE---HHHHHHHHHHHHHHTT--EEEEE--........----SSS---SSTTHHHHHHHH CS
                              RuvX  14 GvAvsdplgilaspletierkskekdleelkelvkeeeveeiVvGlP........lnldgsegesakkvrkfaeeLa 82 
                                       G+  s++l++l +++++  ++  +k+ +++ +++ ++++ ++V+G+         +  +++++ ++  ++++ e+L+
  gi|298675515|ref|YP_003727265.1| 231 GIKNSKKLKKLYHKYKMKINDFFHKASKRIVDFCVKYNIGTLVIGYNegwkqevyMGKRNNQKFTQIPFHRLLEQLK 307
                                       555666666666666666666568999********************999999544444444555555599999999 PP

                                       HT....T-EEEEE--S---- CS
                              RuvX  83 krl..kklpvelvDErlttv 100
                                        +    +l+v+  +E++t++
  gi|298675515|ref|YP_003727265.1| 308 YKAedVGLKVIEQEESYTSK 327
                                       888444569*********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1077  (0.0600703); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2990.49
//
Query:       gi|298675516|ref|YP_003727266.1|  [L=199]
Description: hypothetical protein Metev_1628 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-64  217.1   0.0    2.1e-64  216.9   0.0    1.0  1  Methyltrn_RNA_2  Putative SAM-dependent RNA methyltransferase


Domain annotation for each model (and alignments):
>> Methyltrn_RNA_2  Putative SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.9   0.0   1.2e-68   2.1e-64       1     195 [.       1     195 [.       1     197 [. 0.98

  Alignments for each domain:
  == domain 1  score: 216.9 bits;  conditional E-value: 1.2e-68
                                       -EEEEEEESSEESSSHHHCCCTTTTTTSHHHHHHHHHHHHBESSSB-TTEEEEEEEEESSSS-EEEEEETTT--S-- CS
                   Methyltrn_RNA_2   1 mrefvvlankapTdsdiplddlpGaagrldvlarcvsaalfvshgiRedvvvylvLegtpdpprtikieasevkkvs 77 
                                       mr f+++++ka T+sd++l+dlpG+agr+d+l+rc++ a+f+sh+iR+dv+v+l+L+g+p+p ++i+++++++k+ +
  gi|298675516|ref|YP_003727266.1|   1 MRDFIIIGHKASTSSDFSLNDLPGSAGRMDILCRCINSAFFLSHDIRNDVQVHLLLLGEPEPGKIIRFNGENIKHLN 77 
                                       9**************************************************************************** PP

                                       SSHHHHHHHHHHHHCHCCTGCCSEEEEETTEEEE---HHHHHHHHHCT.SEEEEESTTSEEGGGS---S.SEEEEEE CS
                   Methyltrn_RNA_2  78 pderniailikkalkaveeikkqekkvrpgltVrkegfealleelsek.ksiillkekGedisnakiel.nPvFilg 152
                                       pder+ a likkal++    +++e +++pg+ +r+ ++e l++e  ++ k + +l e G+di+ + + l + vF lg
  gi|298675516|ref|YP_003727266.1|  78 PDERSSAALIKKALEKD--AGESEIQSTPGVWIRQGSLETLINEFYNQgKTLAYLREGGDDIRTTAGSLnDAVFFLG 152
                                       **************777..9*************************9999********************899***** PP

                                       -TT-SHHHHHHHHHCTTSEEEES-SS---HHHHHHHHHHHHHH CS
                   Methyltrn_RNA_2 153 dHidlpeeeekllerlkakrvslgPlsLhadhcvtlihneldk 195
                                       dHi+++e+ee+++ +++ak +s++P s+hadhc+++  neld+
  gi|298675516|ref|YP_003727266.1| 153 DHIGVTEKEEEMIINAGAKLISVSPYSIHADHCILILNNELDR 195
                                       *****************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1473.89
//
Query:       gi|298675517|ref|YP_003727267.1|  [L=430]
Description: THUMP domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-09   38.2   0.3    5.8e-09   36.2   0.0    2.2  3  THUMP     THUMP domain
  ------ inclusion threshold ------
      0.032   14.4   1.3       0.14   12.4   0.1    2.3  2  DUF2703   Domain of unknown function (DUF2703)
      0.044   14.1   0.1       0.91    9.9   0.1    2.4  1  TruB_N    TruB family pseudouridylate synthase (N terminal do


Domain annotation for each model (and alignments):
>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.0   9.7e-13   5.8e-09      10     143 ..      31     186 ..      22     187 .. 0.69
   2 ?   -2.5   0.0      0.81   4.9e+03      57      81 ..     216     240 ..     198     249 .. 0.81
   3 ?   -1.8   0.1      0.49     3e+03      66      86 ..     308     328 ..     281     353 .. 0.59

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 9.7e-13
                                       TT.H-SEEEEETTEEEEECTEE.EEEETHHHHHHHHHTST...TECEEEEE...EEEEESSHHHHHHHHHHHHHHHH CS
                             THUMP  10 gkvnverveagkgrivvelkge.kpeedeellkealekar...giqrvipv...cevceadledileaakeivkkkf 79 
                                       g +n+er+++ k  +++e  +  k e d+ llke+  +++    +  + p+   c vc   ++ ++  a+ +v+++ 
  gi|298675517|ref|YP_003727267.1|  31 GLGNYERGKSIKTYLTMEGDRLlKDENDDSLLKELAPISPiarKLTDIEPEnetCWVCLGLFDNLEQWAERAVSEMD 107
                                       55666666666666666654331122244444444444443334444444498955555555666655555555554 PP

                                       HHCT-EEEEEEEESSSTS...............SSHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEEEEETTEEEEE CS
                             THUMP  80 eeeketFaVrvkrrgkhf...............eftsreinrevGkaivektglkVdlenPdivvrveiikdkayis 141
                                         e   F V++k  g                  e  + e+nre+Gk+i+  tg++V++enPdivv++++ k+ +++ 
  gi|298675517|ref|YP_003727267.1| 108 AFEYDNFLVGTKMSGLLSeneeilwtesgttyaEQLKSELNREIGKRINVMTGKEVEFENPDIVVMLDLTKEDVLLE 184
                                       332239******99987789999*************************************************99987 PP

                                       EE CS
                             THUMP 142 id 143
                                       ++
  gi|298675517|ref|YP_003727267.1| 185 VR 186
                                       65 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.81
                                       EEEEESSHHHHHHHHHHHHHHHHHH CS
                             THUMP  57 cevceadledileaakeivkkkfee 81 
                                       c++ce++ ++ +e++ e+++++ ++
  gi|298675517|ref|YP_003727267.1| 216 CQACEYTGKQYNESVDELISEQVIN 240
                                       8889999999999999999888775 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.49
                                       HHHHHHHHHHHHHHHHCT-EE CS
                             THUMP  66 dileaakeivkkkfeeeketF 86 
                                       d++e+ k+ + +k  + k tF
  gi|298675517|ref|YP_003727267.1| 308 DVIESLKSSNADKVYKLKVTF 328
                                       344444444444444333333 PP

>> DUF2703  Domain of unknown function (DUF2703)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   2.3e-05      0.14      52     117 ..     178     235 ..     137     237 .. 0.75
   2 ?   -0.2   0.1      0.17     1e+03      24      81 ..     301     358 ..     281     364 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.3e-05
                           DUF2703  52 eeelare.flesntilingrpleell.gvevkeelCescgelsGedveCRtlevegkeyealpkelil 117
                                       +e    +  le+ ++ i gr   +l+ g++ +   C sc       + C + e+ gk+y++   eli 
  gi|298675517|ref|YP_003727267.1| 178 KE----DvLLEVRSVYIYGRYR-KLVrGIPQTRWPCRSCR-----GKGCQACEYTGKQYNESVDELIS 235
                                       22....2358889999999886.888899999********.....559**************999996 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.17
                           DUF2703  24 tleeavkelkeaLealgievelekvelseeelareflesntilingrpleellgvevk 81 
                                        l+ + +++ e+L++ + + +++ +   +e +++e l+s    ++g+++e+   ++v+
  gi|298675517|ref|YP_003727267.1| 301 DLQTVSRDVIESLKSSNADKVYKLKVTFKEPVSEEKLKSAINNLKGVDIEQRTPQRVS 358
                                       5778888888888888887776655555667777788899999999999987655555 PP

>> TruB_N  TruB family pseudouridylate synthase (N terminal domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00015      0.91     113     149 .]     363     395 ..     309     395 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00015
                                       ---------EEEEEEEEEEEEEEEEEEEEEESTTTTH CS
                            TruB_N 113 eeverkkrkvtiyelelleveepevelevecskGtYi 149
                                         v    rk +++++el e+ ++++ ++v+c+ G Y+
  gi|298675517|ref|YP_003727267.1| 363 DLV----RKRRVHDIELSELADNHAVITVNCEGGLYV 395
                                       333....8999************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3075.37
//
Query:       gi|298675518|ref|YP_003727268.1|  [L=98]
Description: 50S ribosomal protein L21e [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-35  119.8   0.2    4.1e-35  119.7   0.2    1.0  1  Ribosomal_L21e  Ribosomal protein L21e


Domain annotation for each model (and alignments):
>> Ribosomal_L21e  Ribosomal protein L21e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.7   0.2   2.3e-39   4.1e-35       1     101 []       1      97 [.       1      97 [. 0.99

  Alignments for each domain:
  == domain 1  score: 119.7 bits;  conditional E-value: 2.3e-39
                                       X--S-STTTT-TTTTS--GGG-SS--SHHHH----TT-EEEE---TT--SS---GGGTT-EEEE..EEEETTEEEEE CS
                    Ribosomal_L21e   1 mknskglrrgtrklfskkfrkkgvpplstylreykkGdkVdikidpsvqkgmphkryhGktgrvynvtkravgvivn 77 
                                       m++s+g+r +tr++++k++r+kg++p+s++++++++G++V+i+idpsvqkgmp +r++Gktg+v  +++r+++++++
  gi|298675518|ref|YP_003727268.1|   1 MPKSEGERCSTRSKLRKSVREKGLSPVSKAIQKFENGQMVHIDIDPSVQKGMPNPRFQGKTGKV--IGQRGRAYLLQ 75 
                                       89**************************************************************..*********** PP

                                       EEETTE..EEEEEE-GGGEEE--. CS
                    Ribosomal_L21e  78 kkvggkileKriivriehlkksks 101
                                       +++ +    K++i  +ehlk++k+
  gi|298675518|ref|YP_003727268.1|  76 VRDMDS--LKQVISLPEHLKPQKQ 97 
                                       ******..*************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 759.64
//
Query:       gi|298675519|ref|YP_003727269.1|  [L=117]
Description: RNA polymerase Rpb4 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.4e-11   42.5   7.5    9.6e-11   42.1   7.5    1.2  1  RNA_pol_Rpb4  RNA polymerase Rpb4
     0.0034   17.6   0.4     0.0034   17.6   0.4    2.5  4  FliG_M        FliG middle domain
     0.0055   16.7   0.5       0.61   10.1   0.1    2.1  2  Cbl_N         CBL proto-oncogene N-terminal domain 1
     0.0091   15.8   0.1      0.038   13.8   0.0    2.0  2  EF-hand_8     EF-hand domain pair
  ------ inclusion threshold ------
       0.13   12.5   2.7       0.17   12.2   2.7    1.1  1  SbcD_C        Type 5 capsule protein repressor C-terminal dom
       0.29   11.6   0.1       0.29   11.6   0.1    2.7  3  FumaraseC_C   Fumarase C C-terminus
        1.4    9.4   5.8        1.7    9.2   2.0    2.6  2  CRR7          Protein CHLORORESPIRATORY REDUCTION 7


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb4  RNA polymerase Rpb4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   7.5   3.7e-14   9.6e-11       2     121 ..      12     114 ..       3     116 .. 0.86

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 3.7e-14
                                       E-HHHHHHHHHHHHHHHHCHHHHHTCCCCCHHSHCHTCHHCHHHHHHHHHHHCTHHTTSSHHHHHHHHHHHTTST.S CS
                      RNA_pol_Rpb4   2 LsnsEvllvlkeeleerknkdkkeseddkisekeevkgnlnkilkktleyltnkfsrlkneekfnelvellksfe.L 77 
                                       +++ Ev++ l+e +eer                +e +++l ++l+k++++ +  fs+   +ek +elv+ l + e +
  gi|298675519|ref|YP_003727269.1|  12 MTLAEVKESLNEIMEER----------------SERGEELGYELRKSINHADI-FSKIS-AEKSRELVNNLLELEkM 70 
                                       56666666666555555................456789*************9.****9.89999999998888868 PP

                                       THHHHHHHHHCSTSSHHHHHHHSTTGTTTSTSHHHHHHHHHHHH CS
                      RNA_pol_Rpb4  78 tkaEklqlvnlkPesavelktlieeleerfedeqleeiLdelke 121
                                       ++  ++++ +++Pe+++el+++  ++++ +++++l+eiL++++e
  gi|298675519|ref|YP_003727269.1|  71 KPEIAVKIADILPETRDELRAIYSKERYTLSEQELDEILNTVNE 114
                                       889999***********************************987 PP

>> FliG_M  FliG middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.74   1.9e+03      60      73 ..       2      15 ..       1      18 [. 0.80
   2 ?   -0.7   0.1      0.67   1.7e+03      58      71 ..      14      27 ..       7      31 .. 0.67
   3 !   17.6   0.4   1.3e-06    0.0034      29      67 ..      46      84 ..      41      92 .. 0.92
   4 ?   -2.0   0.1       1.7   4.2e+03      56      64 ..     107     115 ..      99     117 .] 0.46

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.74
                                      HHHHHHHHHCHHHH CS
                            FliG_M 60 eveevLekklssvg 73
                                      +v+evL ++l++++
  gi|298675519|ref|YP_003727269.1|  2 IVKEVLDEELMTLA 15
                                      58899999999875 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.67
                                      HHHHHHHHHHHCHH CS
                            FliG_M 58 lkeveevLekklss 71
                                      l ev+e+L++ +++
  gi|298675519|ref|YP_003727269.1| 14 LAEVKESLNEIMEE 27
                                      56677777666554 PP

  == domain 3  score: 17.6 bits;  conditional E-value: 1.3e-06
                                      HHHHHTS-HHHHHHHHHHHHTCCTCSHHHHHHHHHHHHH CS
                            FliG_M 29 AevLseLpeelraevirriatlekvspevlkeveevLek 67
                                      A+++s+++ e+++e+++ +++lek++pe+  +++++L +
  gi|298675519|ref|YP_003727269.1| 46 ADIFSKISAEKSRELVNNLLELEKMKPEIAVKIADILPE 84
                                      99**********************************966 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 1.7
                                       HHHHHHHHH CS
                            FliG_M  56 evlkeveev 64 
                                       e+l++v+e+
  gi|298675519|ref|YP_003727269.1| 107 EILNTVNES 115
                                       334444444 PP

>> Cbl_N  CBL proto-oncogene N-terminal domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.1    0.0056        14      37      82 ..      13      63 ..      10      76 .. 0.78
   2 !   10.1   0.1   0.00024      0.61      34      59 ..      78     103 ..      61     116 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0056
                                      HHHHHHHHHHHHHHHS..-HHH.....HTT-HHHHHHHHHHHHHHHHHHHH CS
                             Cbl_N 37 llpdtaqlLrevaekrrekeea.....lseaeylriflanllkkskqvakL 82
                                      +l+++++ L+e++e+r+e+ e+      +++++  if +  ++ks+++++ 
  gi|298675519|ref|YP_003727269.1| 13 TLAEVKESLNEIMEERSERGEElgyelRKSINHADIFSKISAEKSRELVNN 63
                                      588999*********999777767776788899999999999999887653 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00024
                                       HHHHHHHHHHHHHHHHHHS..-HHHH CS
                             Cbl_N  34 lldllpdtaqlLrevaekrrekeeal 59 
                                       + d+lp+t++ Lr++++k+r + ++ 
  gi|298675519|ref|YP_003727269.1|  78 IADILPETRDELRAIYSKERYTLSEQ 103
                                       78***************998755443 PP

>> EF-hand_8  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       0.6   1.5e+03      21      33 ..      45      62 ..      38      64 .. 0.67
   2 !   13.8   0.0   1.5e-05     0.038       6      36 ..      85     113 ..      85     116 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.6
                         EF-hand_8 21 k.....glseeevdilfr 33
                                      +     ++s+e+ ++l++
  gi|298675519|ref|YP_003727269.1| 45 HadifsKISAEKSRELVN 62
                                      444666799999999986 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.5e-05
                         EF-hand_8   6 treelrrilrilglkkglseeevdilfrefD 36 
                                       tr+elr i+++  +   lse+e+d++++++ 
  gi|298675519|ref|YP_003727269.1|  85 TRDELRAIYSKERYT--LSEQELDEILNTVN 113
                                       8********443555..**********9875 PP

>> SbcD_C  Type 5 capsule protein repressor C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   2.7   6.7e-05      0.17       4      81 ..      13     108 ..      11     117 .] 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.7e-05
                            SbcD_C   4 pLrrlkgdleeila............l.eepsekpawlevevtdedplpdlrerlrellegipvevlrl.rrtr... 63 
                                        L+++k++l ei++            l ++ ++ + + ++  +    l +   +l+++ ++i+v++  + ++tr   
  gi|298675519|ref|YP_003727269.1|  13 TLAEVKESLNEIMEersergeelgyeLrKSINHADIFSKISAEKSRELVNNLLELEKMKPEIAVKIADIlPETRdel 89 
                                       5999*********************96678899*********999999999999**************977777655 PP

                            SbcD_C  64 .ekasaeleqeaeetlael 81 
                                          +s+e  + +e++l+e+
  gi|298675519|ref|YP_003727269.1|  90 rAIYSKERYTLSEQELDEI 108
                                       4333556666666666654 PP

>> FumaraseC_C  Fumarase C C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.3       0.2   5.2e+02      31      48 ..       5      22 ..       2      26 .. 0.78
   2 ?   -1.3   0.1       1.2   3.1e+03      39      52 ..      57      70 ..      34      71 .. 0.60
   3 ?   11.6   0.1   0.00012      0.29      14      49 ..      75     111 ..      73     113 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.2
                                      HHHHTT-.-HHHHHHHT- CS
                       FumaraseC_C 31 avlelgllteeeldelld 48
                                       vl+++l+t +e++e l+
  gi|298675519|ref|YP_003727269.1|  5 EVLDEELMTLAEVKESLN 22
                                      578899999999888765 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.2
                                      -HHHHHHHT-HHHH CS
                       FumaraseC_C 39 teeeldelldpekM 52
                                      ++e ++ ll  ekM
  gi|298675519|ref|YP_003727269.1| 57 SRELVNNLLELEKM 70
                                      34444555555555 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00012
                                       HHHHHHHHHHHT--HHHHHHHTT-..-HHHHHHHT-H CS
                       FumaraseC_C  14 AakIAkeAlkegktlreavlelgl.lteeeldelldp 49 
                                       A kIA    +++  lr +  ++ + l+e+elde+l+ 
  gi|298675519|ref|YP_003727269.1|  75 AVKIADILPETRDELRAIYSKERYtLSEQELDEILNT 111
                                       889999999*********9987777**********86 PP

>> CRR7  Protein CHLORORESPIRATORY REDUCTION 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   2.0   0.00066       1.7      19      50 ..       7      41 ..       1      78 [. 0.65
   2 ?    0.6   0.1      0.31   7.9e+02       6      28 ..      92     114 ..      86     117 .] 0.63

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00066
                                      S-SEEE-HHHHHHHHHHHHHH...-TTTS-HHHHH CS
                              CRR7 19 qpEqfltaeellekLkelLek...eqdelprdlak 50
                                       +E+++t +e++e L+e++e+   + +el  +l+k
  gi|298675519|ref|YP_003727269.1|  7 LDEELMTLAEVKESLNEIMEErseRGEELGYELRK 41
                                      68*****************9933334566666665 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.31
                                       S-----EEEEESSS-SEEE-HHH CS
                              CRR7   6 myqedtyVvLepnqpEqfltaee 28 
                                       +y+++ y + e++ +E + t +e
  gi|298675519|ref|YP_003727269.1|  92 IYSKERYTLSEQELDEILNTVNE 114
                                       56666666666666665555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1316  (0.0734006); expected 358.6 (0.02)
Passed bias filter:                      630  (0.0351386); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 836.13
//
Query:       gi|298675520|ref|YP_003727270.1|  [L=200]
Description: hypothetical protein Metev_1632 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-69  233.2   0.1    2.2e-69  233.0   0.1    1.0  1  DUF655    Protein of unknown function (DUF655)
     0.0077   16.5   0.0      0.013   15.8   0.0    1.3  1  HHH_6     Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.021   15.0   0.0      0.058   13.7   0.0    1.7  1  HHH_3     Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> DUF655  Protein of unknown function (DUF655)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  233.0   0.1   3.7e-73   2.2e-69       2     180 ..      11     189 ..      10     190 .. 0.99

  Alignments for each domain:
  == domain 1  score: 233.0 bits;  conditional E-value: 3.7e-73
                                       --EEEEEEEETT--TT--S-GGG---EEEEEETTT--EEEEEE-TT----TT-EEE-SSS--SSEEEEEEE--GGGS CS
                            DUF655   2 eeeaivLDylpeGypddkhrehrdkpvvqalgereltLlelvplkevdilkldevaigkgksdkivkikreisyedL 78 
                                       e++a+vLDylp+G+p+d +  h++kp+ q++g r++ L+e+vp++ v  +++++v+ig g+++ ++++k +isy+dL
  gi|298675520|ref|YP_003727270.1|  11 EDYAWVLDYLPYGNPNDTRPAHQKKPLLQGIGDRYFVLMEMVPKEGVSPEIQSRVYIGDGERKIVDHVKHRISYDDL 87 
                                       89*************************************************************************** PP

                                       -HHHHHHHHHHHHHHHHTTHHHHHHHH-----B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHHHSTT-- CS
                            DUF655  79 tdvaraeLpdvvekivkekEdrfveffneaepitiRlHaLelLpgvgkklarkileeRerrrFesFedvkkrvkglk 155
                                       +++a+ eLp+v+ek v+e+Edrfv+ffn+a+pit+RlH LelLpg+gkkl+++i++e+++ +F+ F d+++rv+g++
  gi|298675520|ref|YP_003727270.1|  88 SHGAQLELPYVLEKTVQEQEDRFVKFFNDAHPITTRLHMLELLPGIGKKLMWAIIDEKKKGNFKDFTDLNDRVSGVH 164
                                       ***************************************************************************** PP

                                       -HHHHHHHHHHHHHH-TTSS--SS- CS
                            DUF655 156 dpaeilverileEiedktekYylFv 180
                                       +p++i+++ri eE++d++ kY+lF+
  gi|298675520|ref|YP_003727270.1| 165 HPVRIIAKRIEEELKDDNIKYRLFT 189
                                       ************************8 PP

>> HHH_6  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.1e-06     0.013      30      65 ..     128     162 ..     121     178 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.1e-06
                             HHH_6  30 aaikglgeaaaerivaeRekegpfksledlarrvds 65 
                                       + + g+g++ + +i++e++ +g+fk+++dl +rv+ 
  gi|298675520|ref|YP_003727270.1| 128 ELLPGIGKKLMWAIIDEKK-KGNFKDFTDLNDRVSG 162
                                       55679*************9.8************985 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   9.7e-06     0.058      13      49 ..     124     160 ..     121     165 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.7e-06
                             HHH_3  13 aeeLqklpGlgpklAknIvayReknGpfksreeLl.kv 49 
                                       +  L+ lpG+g+kl  +I++ + k+G+fk++ +L  +v
  gi|298675520|ref|YP_003727270.1| 124 LHMLELLPGIGKKLMWAIIDEK-KKGNFKDFTDLNdRV 160
                                       567999***************9.999********8455 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1587.62
//
Query:       gi|298675521|ref|YP_003727271.1|  [L=136]
Description: PAS sensor protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-08   35.2   0.0    1.4e-08   34.9   0.0    1.2  1  PAS_9        PAS domain
    2.1e-06   27.7   0.0    5.8e-06   26.3   0.0    1.7  1  PAS          PAS fold
    1.6e-05   24.8   0.0    2.5e-05   24.2   0.0    1.3  1  PAS_8        PAS domain
    6.6e-05   23.1   0.0    9.6e-05   22.6   0.0    1.2  1  PAS_3        PAS fold
    0.00082   19.5   0.0      0.001   19.2   0.0    1.2  1  PAS_11       PAS domain
    0.00085   19.5   0.0     0.0011   19.2   0.0    1.1  1  PAS_4        PAS fold
  ------ inclusion threshold ------
      0.017   14.8   0.1      0.021   14.4   0.1    1.1  1  PAS_12       UPF0242 C-terminal PAS-like domain
      0.029   14.9   0.0      0.042   14.3   0.0    1.2  1  Terminase_2  Terminase small subunit
      0.041   13.8   0.4        0.1   12.5   0.1    1.7  2  DUF3877      Domain of unknown function, E. rectale Gene desc


Domain annotation for each model (and alignments):
>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.0   7.1e-12   1.4e-08       2      85 ..      22     104 ..      21     117 .. 0.89

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 7.1e-12
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfw 77 
                                       d++++ + +g+ l +N++a+  lGys++e+l     ++   +pe +e++++ ++ + k ke ++e v+i+knge+++
  gi|298675521|ref|YP_003727271.1|  22 DATFVHDLKGNFLEINDTAASRLGYSKDELLSMGPQNID--SPEYAEKIADKIKKINKhKELTFESVHITKNGERIP 96 
                                       678887799***********************9999988..999999999999999999****************** PP

                             PAS_9  78 vlltaspv 85 
                                       v+++   +
  gi|298675521|ref|YP_003727271.1|  97 VEINSKII 104
                                       ***99877 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   2.9e-09   5.8e-06       2      95 ..      12     103 ..      11     118 .. 0.66

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 2.9e-09
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda.elaelleqlleqgeesragei 77 
                                       d+ ++++s+ d++fv D +g++l++N++a++ lG+s +e+l+      i  ++ a + a+++++  +  +e + + +
  gi|298675521|ref|YP_003727271.1|  12 DFFNLFNSINDATFVHDLKGNFLEINDTAASRLGYSKDELLSMGPQ-NIDSPEYAeKIADKIKKI-NKHKELTFESV 86 
                                       677899*********************************9976443.343333332333333332.22222222334 PP

                                       EEECTTSSEEEEEEEEEE CS
                               PAS  78 sfklrdgrpihlevrasp 95 
                                        +++ +g+ i++e++ + 
  gi|298675521|ref|YP_003727271.1|  87 HITK-NGERIPVEINSKI 103
                                       4444.7777777777665 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   1.2e-08   2.5e-05       4      42 ..      14      53 ..      11      72 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.2e-08
                             PAS_8  4 ralfesspdgiavvd.lgdrivdvNqaalellGys.adlkg 42
                                       +lf+s++d+ +v d  g+ ++++N++a+  lGys ++l+ 
  gi|298675521|ref|YP_003727271.1| 14 FNLFNSINDATFVHDlKGN-FLEINDTAASRLGYSkDELLS 53
                                      689**********996666.***************877766 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   4.8e-08   9.6e-05       2      79 ..      34     108 ..      33     114 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 4.8e-08
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       + ++++    lGys++ell+      ++  pe  e++ ++++++ +k +++++e   ++k+Ge + ve   ++i+++
  gi|298675521|ref|YP_003727271.1|  34 LEINDTAASRLGYSKDELLSM--GPQNIDSPEYAEKIADKIKKI-NKHKELTFESVHITKNGERIPVEINSKIIHYR 107
                                       578999999************..******************966.6666699**********************887 PP

                             PAS_3  79 n 79 
                                       n
  gi|298675521|ref|YP_003727271.1| 108 N 108
                                       6 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   5.1e-07     0.001       3      94 ..      22     108 ..      20     123 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 5.1e-07
                            PAS_11   3 qfttrldidgkIisvDtsaLrasfslglekeelvgrsiydLchpqdlstlkshlrevissngeatsslyRLrlsqdk 79 
                                         t+ +d++g++++++     a  +lg++k+el+ +  +++ +p+  ++++++ +++  +++e t  +++++  +++
  gi|298675521|ref|YP_003727271.1|  22 DATFVHDLKGNFLEIND---TAASRLGYSKDELLSMGPQNIDSPEYAEKIADKIKKIN-KHKELTFESVHITK-NGE 93 
                                       6799*************...9*************************************.99999999999987.999 PP

                            PAS_11  80 fvkvktksklfknqk 94 
                                        + v  +sk+   ++
  gi|298675521|ref|YP_003727271.1|  94 RIPVEINSKIIHYRN 108
                                       999999998876655 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   5.6e-07    0.0011       1      84 [.      17     100 ..      17     108 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 5.6e-07
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pg 76 
                                       ++s++da++v d  g++l +N +aa+ +g++ +ell + ++ + ++e a+ +++ +++  + +e  ++   + + +g
  gi|298675521|ref|YP_003727271.1|  17 FNSINDATFVHDLKGNFLEINDTAASRLGYSKDELLSMGPQNIDSPEYAEKIADKIKKINKHKELTFESV-HITkNG 92 
                                       799**************************************999999***********877765555555.555599 PP

                             PAS_4  77 eerhyelr 84 
                                       e+ ++e++
  gi|298675521|ref|YP_003727271.1|  93 ERIPVEIN 100
                                       99999876 PP

>> PAS_12  UPF0242 C-terminal PAS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   1.1e-05     0.021      69     138 ..      33     104 ..      12     112 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.1e-05
                            PAS_12  69 llfaNaqirallGwssdkflqdfseivq..egleeWkralaklsskteskirlvlKtKagqevllncllgii 138
                                        l +N+   + lG+s+d++l+   + ++  e  e+   +++k+++++e   + v  tK+g+ +++++  +ii
  gi|298675521|ref|YP_003727271.1|  33 FLEINDTAASRLGYSKDELLSMGPQNIDspEYAEKIADKIKKINKHKELTFESVHITKNGERIPVEINSKII 104
                                       57799***************9998877632345678899**************************9999888 PP

>> Terminase_2  Terminase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.1e-05     0.042      20      67 ..      39      86 ..      33      95 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.1e-05
                       Terminase_2 20 qAaikAgyskktArsigselLrkpkIkkaIreakaereertiieadeV 67
                                       Aa + gysk    s+g +++  p+ +++I+ + +++++ ++++ + V
  gi|298675521|ref|YP_003727271.1| 39 TAASRLGYSKDELLSMGPQNIDSPEYAEKIADKIKKINKHKELTFESV 86
                                      479999**********************************99987766 PP

>> DUF3877  Domain of unknown function, E. rectale Gene description (DUF3877)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.47   9.4e+02     108     133 ..       7      32 ..       4      50 .. 0.78
   2 ?   12.5   0.1   5.1e-05       0.1      40      86 ..      60     106 ..      29     112 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.47
                           DUF3877 108 ectledilelFkkyskkvvvekieed 133
                                       +++ +d ++lF++ ++ + v++ + +
  gi|298675521|ref|YP_003727271.1|   7 DQQYNDFFNLFNSINDATFVHDLKGN 32 
                                       67788889999999988888777655 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 5.1e-05
                           DUF3877  40 eaeedaeelkealeefaeeakeklGevevtekkdrfcveipeegaey 86 
                                       ++ e ae++  ++++++++++ ++ +v++t++++r+ vei  +  +y
  gi|298675521|ref|YP_003727271.1|  60 DSPEYAEKIADKIKKINKHKELTFESVHITKNGERIPVEINSKIIHY 106
                                       34446999*********************************998888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1071.57
//
Query:       gi|298675522|ref|YP_003727272.1|  [L=369]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-25   87.6   2.0    1.8e-24   85.5   1.0    2.3  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
    2.9e-10   40.4   1.2    2.9e-10   40.4   1.2    1.7  2  OrfB_IS605       Probable transposase
  ------ inclusion threshold ------
      0.059   13.4   0.1      0.099   12.7   0.1    1.4  1  HypA             Hydrogenase/urease nickel incorporation, met
       0.27   12.1   6.2       0.61   10.9   6.2    1.6  1  Tnp_zf-ribbon_2  DDE_Tnp_1-like zinc-ribbon
       0.43   10.7   2.6       0.89    9.7   0.1    2.2  2  UPF0547          Uncharacterised protein family UPF0547
       0.54   10.0   7.4          2    8.1   7.4    2.0  1  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
       0.77    9.5   4.8        6.4    6.6   0.5    2.4  2  Rubredoxin_2     Rubredoxin metal binding domain
          1    9.6   5.5         13    6.1   1.7    3.0  2  DUF2387          Probable metal-binding protein (DUF2387)
        1.5    8.8   5.2        3.3    7.8   5.2    1.5  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
        2.2    8.5   8.1        4.4    7.5   0.5    2.7  2  Ribosomal_L37e   Ribosomal protein L37e


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.36   6.4e+02      15      30 ..     195     210 ..     185     238 .. 0.85
   2 !   85.5   1.0   9.8e-28   1.8e-24       1      69 []     285     354 ..     285     354 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.36
                    OrfB_Zn_ribbon  15 yGikveevnpayTSkt 30 
                                       +G k  e+ ++yTS +
  gi|298675522|ref|YP_003727272.1| 195 KGTKADEIRERYTSLK 210
                                       68999999*****965 PP

  == domain 2  score: 85.5 bits;  conditional E-value: 9.8e-28
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f++l+ ++ ykak +G++v+ +np yTS++CseCg+++k+ ++++ +f+C++Cg++ ++D+nA+ Ni++r
  gi|298675522|ref|YP_003727272.1| 285 FSELTDFILYKAKLEGVPVVIINPMYTSQQCSECGYIDKNnRQKQSNFRCKRCGHRENADYNASKNIAHR 354
                                       899*************************************99*************************997 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   1.2   1.6e-13   2.9e-10       4     106 ..     162     254 ..     159     264 .. 0.87
   2 ?   -3.4   0.1       6.1   1.1e+04      41      65 ..     322     346 ..     313     354 .. 0.59

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 1.6e-13
                        OrfB_IS605   4 vevevelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarl 80 
                                       +ev++  +++ +  + giDlG+ n+at ++++    +ykg ++++  ++++  + +lqs    s     a++ l++l
  gi|298675522|ref|YP_003727272.1| 162 MEVGE-NEVEYNDDVMGIDLGVVNIATISDNE----VYKGTKADEIRERYTSLKSRLQSAGTWS-----AKKHLKKL 228
                                       56665.6677778899****************....***********************95555.....79999*** PP

                        OrfB_IS605  81 hrkrsrrrkhllhklathliktlkev 106
                                       ++k +r+ ++l h +a++l+k+ k++
  gi|298675522|ref|YP_003727272.1| 229 SKKERRFKRDLNHRVAKQLVKRAKDT 254
                                       ********************998765 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 6.1
                        OrfB_IS605  41 ykgrrlksdykylakeiaelqsklk 65 
                                        k +r k+ +++ +++  +    ++
  gi|298675522|ref|YP_003727272.1| 322 DKNNRQKQSNFRCKRCGHRENADYN 346
                                       5555556666666665555555555 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   5.5e-05     0.099      60      96 ..     296     341 ..     243     351 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.5e-05
                                       -EEE......EEEE--EEEETTTS-EEECHH..H.HHS-TTTSSS- CS
                              HypA  60 aeLe......ieevpvkvrCreCgkefelee..k.alrCpkCgsad 96 
                                       a+Le      i+ +  + +C+eCg+  + ++  + ++rC++Cg+++
  gi|298675522|ref|YP_003727272.1| 296 AKLEgvpvviINPMYTSQQCSECGYIDKNNRqkQsNFRCKRCGHRE 341
                                       5555555555777888999*****9888555333788******874 PP

>> Tnp_zf-ribbon_2  DDE_Tnp_1-like zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   6.2   0.00034      0.61       3      23 ..     315     338 ..     313     343 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00034
                   Tnp_zf-ribbon_2   3 CkvClk...kkikkeTriiCqeCd 23 
                                       C  C +   ++++k+++++C+ C+
  gi|298675522|ref|YP_003727272.1| 315 CSECGYidkNNRQKQSNFRCKRCG 338
                                       999*****8899999********6 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1    0.0005      0.89      15      25 ..     313     323 ..     311     324 .. 0.87
   2 ?    0.5   0.5      0.37   6.7e+02      17      22 ..     334     339 ..     333     340 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0005
                           UPF0547  15 qfCphCGyvFq 25 
                                       q C++CGy+++
  gi|298675522|ref|YP_003727272.1| 313 QQCSECGYIDK 323
                                       89******986 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.37
                           UPF0547  17 CphCGy 22 
                                       C  CG+
  gi|298675522|ref|YP_003727272.1| 334 CKRCGH 339
                                       766777 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   7.4    0.0011         2       3      26 ..     315     340 ..     314     341 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0011
                                       -SSS-..-B----SSS----SSS--- CS
                    DNA_RNApol_7kD   3 CgeCg..aevslkkgdpiRCkeCGhR 26 
                                       C eCg  +++  +k+   RCk CGhR
  gi|298675522|ref|YP_003727272.1| 315 CSECGyiDKNNRQKQSNFRCKRCGHR 340
                                       99998666888899999********9 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.3     0.018        32       2       8 ..     314     320 ..     314     323 .. 0.89
   2 ?    6.6   0.5    0.0036       6.4       1      10 [.     332     341 ..     332     343 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.018
                      Rubredoxin_2   2 vCsqCGf 8  
                                       +Cs+CG+
  gi|298675522|ref|YP_003727272.1| 314 QCSECGY 320
                                       7*****9 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0036
                      Rubredoxin_2   1 YvCsqCGfes 10 
                                       ++C++CG++ 
  gi|298675522|ref|YP_003727272.1| 332 FRCKRCGHRE 341
                                       8******986 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.042        76      38      73 ..     224     259 ..     221     261 .. 0.87
   2 ?    6.1   1.7     0.007        13      31      49 ..     313     331 ..     307     351 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.042
                           DUF2387  38 ftdelsekgqsvakelktrvnkdeekeasakvqtvq 73 
                                       ++ +ls+k++ ++++l+ rv+k+  k+a+++ +++ 
  gi|298675522|ref|YP_003727272.1| 224 HLKKLSKKERRFKRDLNHRVAKQLVKRAKDTSRAIA 259
                                       7889999****************9999988887775 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.007
                           DUF2387  31 rECvsCgftdelsekgqsv 49 
                                         C +Cg++d+ + ++qs 
  gi|298675522|ref|YP_003727272.1| 313 QQCSECGYIDKNNRQKQSN 331
                                       5799*******99997664 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   5.2    0.0018       3.3      19      45 ..     313     339 ..     309     340 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0018
                     Zn_Tnp_IS1595  19 fvCPhCgsr.kayriktrglfqCkeCrk 45 
                                       + C  Cg+  k  r k+   f+Ck+C++
  gi|298675522|ref|YP_003727272.1| 313 QQCSECGYIdKNNRQKQ-SNFRCKRCGH 339
                                       57*******77777777.********98 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.5    0.0025       4.4      30      46 ..     311     327 ..     309     331 .. 0.76
   2 ?    3.8   3.4     0.035        63      10      25 ..     326     340 ..     323     352 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0025
                    Ribosomal_L37e  30 qkktCascGypsaklrk 46 
                                         ++C++cGy ++  r+
  gi|298675522|ref|YP_003727272.1| 311 TSQQCSECGYIDKNNRQ 327
                                       6799******6666654 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.035
                    Ribosomal_L37e  10 rqkkktHilCrrCgkr 25 
                                       r +k++  +C+rCg+r
  gi|298675522|ref|YP_003727272.1| 326 R-QKQSNFRCKRCGHR 340
                                       4.455889******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1058  (0.0590105); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 2838.97
//
Query:       gi|298675523|ref|YP_003727273.1|  [L=269]
Description: dimethyladenosine transferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-61  206.8   0.2    3.9e-61  206.4   0.2    1.0  1  RrnaAD           Ribosomal RNA adenine dimethylase
    2.3e-07   31.4   0.0    4.9e-07   30.4   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
    4.8e-05   23.9   0.0    0.00031   21.3   0.0    2.1  2  Methyltransf_11  Methyltransferase domain
     0.0001   21.5   0.0    0.00017   20.8   0.0    1.4  1  DREV             DREV methyltransferase
    0.00041   20.2   0.1    0.00073   19.3   0.1    1.5  1  Met_10           Met-10+ like-protein
    0.00062   19.6   0.0     0.0012   18.7   0.0    1.6  1  Methyltransf_31  Methyltransferase domain
    0.00067   19.5   0.0    0.00088   19.2   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
     0.0021   17.6   0.0     0.0042   16.7   0.0    1.4  1  DOT1             Histone methylation protein DOT1
     0.0051   17.5   0.0      0.014   16.1   0.0    1.8  2  Methyltransf_12  Methyltransferase domain
  ------ inclusion threshold ------
      0.013   15.1   0.0       0.02   14.4   0.0    1.3  1  Methyltransf_PK  AdoMet dependent proline di-methyltransferas
      0.014   15.2   0.0      0.027   14.2   0.0    1.4  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.016   14.9   0.0      0.024   14.3   0.0    1.2  1  NodS             Nodulation protein S (NodS)
      0.087   12.4   0.0       0.14   11.7   0.0    1.3  1  MTS              Methyltransferase small domain
       0.09   12.1   0.0       0.14   11.4   0.0    1.3  1  CMAS             Mycolic acid cyclopropane synthetase
       0.13   12.3   0.0       0.24   11.4   0.0    1.4  1  Methyltransf_32  Methyltransferase domain


Domain annotation for each model (and alignments):
>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.4   0.2   3.3e-64   3.9e-61       9     251 ..      17     238 ..      14     252 .. 0.92

  Alignments for each domain:
  == domain 1  score: 206.4 bits;  conditional E-value: 3.3e-64
                                       G--EE--HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTTTCCCEEEE-S-C CS
                            RrnaAD   9 gqnflknkkvineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkklskdeklkvvhqDf 85 
                                        q+fl++ + +n+I+d ++l+e++tvleig+G G+lTe++a+ + ++ ++Eld++L+ +l +++ ++ ++++++ D+
  gi|298675523|ref|YP_003727273.1|  17 DQHFLVDDNFLNQIVDSAELTENDTVLEIGAGIGNLTEKIAETVHKLYAVELDPNLCDILIERFADYDNVEIIEGDI 93 
                                       69*************************************************************************** PP

                                       CGHHHHHHHCTTTCCCCEEEEEEE--TTTHHHHHHHHHHGGGGCEEEEEEEEEHHHHHHHH--TTSTT-SHHHHHHH CS
                            RrnaAD  86 lkfetpeevtekdsihqeflvvanlPyeistqlvkqlleesrfglvkmllwlqkefarrllarpgskkrsrlsvlre 162
                                       l+ e+pe+           +vvanlPy is+ + ++ll+ + f  +  +l+ q efarr++++ +sk++srl+v ++
  gi|298675523|ref|YP_003727273.1|  94 LDIELPEFN----------KVVANLPYSISSHITFKLLK-HEF--ELGILMYQYEFARRMVSPKNSKDYSRLTVTTN 157
                                       *******55..........9******************6.777..89****************************** PP

                                       HHEEEEEEEEC-GGCECS--SSSEEEEEEEE-SS-S--S-HHHHHHHHHHHHCTTTSBCCCHCCCTSTCHHHHHCTT CS
                            RrnaAD 163 aftdvklvakveksifsPppkvdsalvelerkdedlpqkdlkkyesvvrkllnrkrktlstslksllpggelqalss 239
                                       +f+d+ +++kv++s+f+P p+v+sa+v+l++++ +++++d + +  +v++++ ++rk+l++++ ++ ++     l  
  gi|298675523|ref|YP_003727273.1| 158 FFADASIIMKVPRSAFKPAPEVKSAVVKLIPRPASFDVVDEDFFLTFVTAVFGQRRKKLRNAILNTNSK-----L-- 227
                                       **************************************************************8843322.....2.. PP

                                       .T--TTTCCCCS CS
                            RrnaAD 240 tgindnalvkkl 251
                                        gi++ ++v+++
  gi|298675523|ref|YP_003727273.1| 228 -GIANVKEVVNK 238
                                       .45555444444 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   4.1e-10   4.9e-07       1      71 [.      42     107 ..      42     124 .. 0.88

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 4.1e-10
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvss 71 
                                       vL++G+G G+lt+++a+ +  +k+++v+++++++++  er+++ + nve+++gd+ d+++++  f+ vv++
  gi|298675523|ref|YP_003727273.1|  42 VLEIGAGIGNLTEKIAETV--HKLYAVELDPNLCDILIERFADYD-NVEIIEGDILDIELPE--FNKVVAN 107
                                       9*****************9..9*******************7654.************9997..9999884 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   2.6e-07   0.00031       1      62 [.      43     101 ..      43     114 .. 0.91
   2 ?   -0.1   0.0       1.3   1.6e+03      48      74 ..     179     205 ..     141     222 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.6e-07
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-E CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsf 62 
                                       L++G+G G l+e++a++++++++v+l++++ ++  e+  + ++ ve++++d+ ++ +++  f
  gi|298675523|ref|YP_003727273.1|  43 LEIGAGIGNLTEKIAETVHKLYAVELDPNLCDILIERFADYDN-VEIIEGDILDIELPE--F 101
                                       89********************************999999885.**********99987..4 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.3
                                       TTEECCCT.SS-TT-EEEEEEES-CCC- CS
                   Methyltransf_11  48 vvadaekl.pfednsfDlvvssevlhhv 74 
                                       v++ + kl p + +sfD+v   ++l++v
  gi|298675523|ref|YP_003727273.1| 179 VKSAVVKLiP-RPASFDVVDEDFFLTFV 205
                                       4445555524.45699999766666666 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   1.4e-07   0.00017      91     133 ..      35      77 ..      15     122 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.4e-07
                              DREV  91 sdqedkklldlGaGdGeitkrvaptfeevyatelsetmrdrlk 133
                                          e+ ++l++GaG G++t+++a+t++++ya el  ++ d l 
  gi|298675523|ref|YP_003727273.1|  35 ELTENDTVLEIGAGIGNLTEKIAETVHKLYAVELDPNLCDILI 77 
                                       3457889***************************988877664 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   6.1e-07   0.00073      98     186 ..      36     118 ..      28     172 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6.1e-07
                                       --TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---TT-EEEEEE CS
                            Met_10  98 veegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevireqladrvvm 174
                                         e+++V+++ AGiG ++  ia     ++++a++l+P+    l e  +     + v+ i++D  ++     +++vv 
  gi|298675523|ref|YP_003727273.1|  36 LTENDTVLEIGAGIGNLTEKIAE--TVHKLYAVELDPNLCDILIERFA---DYDNVEIIEGDILDIE-LPEFNKVVA 106
                                       579*******************9..88899********9999966554...45678889******98.66789**** PP

                                       --TTTGGGGHHH CS
                            Met_10 175 nlpksaieFldk 186
                                       nlp+s  +++  
  gi|298675523|ref|YP_003727273.1| 107 NLPYSISSHITF 118
                                       ***999988875 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0     1e-06    0.0012       2      84 ..      37     110 ..      36     171 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1e-06
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDli 78 
                                       +++ +vl++G+G G+lt ++ae++    +++ ++ +++      e+ +   +dnve  +gdi ++e  l    f+ +
  gi|298675523|ref|YP_003727273.1|  37 TENDTVLEIGAGIGNLTEKIAETV---HKLYAVELDPNLCDILIERFA--DYDNVEIIEGDILDIE--LP--EFNKV 104
                                       57899****************776...46****************988..9*************99..66..59999 PP

                   Methyltransf_31  79 lsnevl 84 
                                       ++n + 
  gi|298675523|ref|YP_003727273.1| 105 VANLPY 110
                                       999543 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   7.3e-07   0.00088      19      59 ..      35      75 ..      16     197 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 7.3e-07
                   Methyltransf_23 19 klraggrvLdiGcGtGillevlrengfsvtgvDlspeavei 59
                                      +l ++  vL+iG+G G+l+e ++e ++++++v+l+p++ +i
  gi|298675523|ref|YP_003727273.1| 35 ELTENDTVLEIGAGIGNLTEKIAETVHKLYAVELDPNLCDI 75
                                      478899*****************************997655 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   3.5e-06    0.0042      29      80 ..      25      74 ..      22      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.5e-06
                                      HHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHH CS
                              DOT1 29 eflsevldkvnlkkedvFvDLGSGvGnvvlqaalevgcklsvGvEimdnase 80
                                      +fl++++d  +l+++d+ +++G G+Gn++ ++a  v  ++ + vE+  n ++
  gi|298675523|ref|YP_003727273.1| 25 NFLNQIVDSAELTENDTVLEIGAGIGNLTEKIAETV--HKLYAVELDPNLCD 74
                                      79***************************9999765..44577777666665 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.2e-05     0.014       1      57 [.      43      95 ..      43     124 .. 0.81
   2 ?   -2.2   0.0       6.1   7.3e+03      79      79 ..     205     205 ..     167     234 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.2e-05
                   Methyltransf_12  1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnveleald 57
                                      LeiG+G G+l++ ++e     ++++v+++p+ ++   e++a+++n  ++ +e + ld
  gi|298675523|ref|YP_003727273.1| 43 LEIGAGIGNLTEKIAET--VHKLYAVELDPNLCDILIERFADYDN--VEIIEGDILD 95
                                      8****************..99************9999***99995..3344444333 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.1
                   Methyltransf_12  79 l 79 
                                       +
  gi|298675523|ref|YP_003727273.1| 205 V 205
                                       2 PP

>> Methyltransf_PK  AdoMet dependent proline di-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.6e-05      0.02      31      76 ..      16      59 ..       2      95 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.6e-05
                   Methyltransf_PK 31 skiDvkgsrkflkklkkeslpgkrevkvaldcGaGiGrvtknlLlk 76
                                      ++      ++fl+++     ++ +e++++l++GaGiG +t+++  +
  gi|298675523|ref|YP_003727273.1| 16 HDQHFLVDDNFLNQIVDS--AELTENDTVLEIGAGIGNLTEKIAET 59
                                      4556667899***99988..67999****************98543 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.3e-05     0.027      65     132 ..      30      92 ..      22      94 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.3e-05
                                       HHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES- CS
                              PCMT  65 alellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgD 132
                                       +++  el++ + vLe+G+G G lt  +a+ v++     ++e  ++l++   ++    d++nv +++gD
  gi|298675523|ref|YP_003727273.1|  30 IVDSAELTENDTVLEIGAGIGNLTEKIAETVHKLY---AVELDPNLCDILIERF--ADYDNVEIIEGD 92 
                                       4556679*********************9999888...99999****9988876..577899999888 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     2e-05     0.024      45     109 ..      40     103 ..      25     120 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2e-05
                              NodS  45 adalevGcaaGalterlapyckrltvvdvveeaiararervkesshiswivsdvqqfstdekfdl 109
                                         +le+G   G lte++a   ++l  v++ ++  +   er  +  ++  i+ d+  +++ e f+ 
  gi|298675523|ref|YP_003727273.1|  40 DTVLEIGAGIGNLTEKIAETVHKLYAVELDPNLCDILIERFADYDNVEIIEGDILDIELPE-FNK 103
                                       469**************************************************99988765.443 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00012      0.14      31     116 ..      38     119 ..      23     126 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                                       TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE---S CS
                               MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivsNPPf 107
                                       ++++vl +G+G+G l+ ++a+   +  + +v+ d +  ++  e +++ + +ve+++ d+l+     +f+ +v N P+
  gi|298675523|ref|YP_003727273.1|  38 ENDTVLEIGAGIGNLTEKIAETVHK--LYAVELDPNLCDILIERFADYD-NVEIIEGDILDIEL-PEFNKVVANLPY 110
                                       6778*****************9988..6666666666666666666655.4899****998666.89*******999 PP

                                       TTTCHCHHH CS
                               MTS 108 hagkatela 116
                                         +++++ +
  gi|298675523|ref|YP_003727273.1| 111 SISSHITFK 119
                                       887776655 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00012      0.14      52     131 ..      28     104 ..      23     119 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                                       HHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---.- CS
                              CMAS  52 dlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde.k 127
                                       + i++ +el + +t+L+iG+G G+l+ + +e    k  ++ l  +      +r+++ d   +ve+   d  d++  +
  gi|298675523|ref|YP_003727273.1|  28 NQIVDSAELTENDTVLEIGAGIGNLTEKIAET-VHKLYAVELDPNLCDILIERFADYD---NVEIIEGDILDIELpE 100
                                       6789999*******************999998.5567777777777777777777766...4444444444444445 PP

                                       -SEE CS
                              CMAS 128 vdrv 131
                                       +++v
  gi|298675523|ref|YP_003727273.1| 101 FNKV 104
                                       5555 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0002      0.24      12      65 ..      26      74 ..      23      97 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                   Methyltransf_32 12 lvakllkelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelve 65
                                      ++++++++ a+ +++ tv+++GaG g L+  +a       +k++++++  +l++
  gi|298675523|ref|YP_003727273.1| 26 FLNQIVDS-AELTENDTVLEIGAGIGNLTEKIAE----TVHKLYAVELDPNLCD 74
                                      66777777.5778899*****************9....4788888888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1941.18
//
Query:       gi|298675524|ref|YP_003727274.1|  [L=200]
Description: methylase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-08   35.0   0.0    1.6e-08   34.5   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    2.6e-08   33.6   0.0      9e-07   28.6   0.0    2.1  2  MTS              Methyltransferase small domain
    2.9e-06   27.2   0.0    0.00012   22.0   0.0    2.5  2  Methyltransf_23  Methyltransferase domain
    4.9e-06   27.2   0.0      7e-05   23.5   0.0    2.2  1  Methyltransf_25  Methyltransferase domain
    0.00015   22.4   0.0     0.0071   17.0   0.0    2.3  2  Methyltransf_11  Methyltransferase domain
    0.00015   21.6   0.0    0.00022   21.0   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0017   19.1   0.0       0.14   12.9   0.0    2.3  2  Methyltransf_12  Methyltransferase domain
     0.0037   16.6   0.0      0.011   15.0   0.0    1.7  2  CMAS             Mycolic acid cyclopropane synthetase
     0.0038   16.3   0.0     0.0052   15.9   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
     0.0063   16.1   0.0     0.0088   15.7   0.0    1.1  1  MetW             Methionine biosynthesis protein MetW
  ------ inclusion threshold ------
       0.03   14.3   0.0       0.12   12.3   0.0    1.8  2  Methyltransf_18  Methyltransferase domain
      0.074   13.2   0.0       0.12   12.4   0.0    1.3  1  FtsJ             FtsJ-like methyltransferase
       0.09   13.8   0.0       0.31   12.1   0.0    1.8  1  Methyltransf_24  Methyltransferase domain
       0.11   11.3   0.1       0.17   10.7   0.1    1.2  1  5_nucleotid      5' nucleotidase family
       0.12   11.8   0.0       0.58    9.5   0.0    1.8  2  PrmA             Ribosomal protein L11 methyltransferase (Prm
       0.12   12.4   0.0       0.17   11.8   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
       0.15   11.8   0.0        0.2   11.3   0.0    1.2  1  Methyltransf_16  Lysine methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.0   1.5e-11   1.6e-08       2     110 ..      36     154 ..      35     179 .. 0.80

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 1.5e-11
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDl 77 
                                       ++g+++l++G+GtG+ + +l    +++ ++v+ +i+++a + Ar+n        ve+ + ++++ l+     ++fDl
  gi|298675524|ref|YP_003727274.1|  36 KDGMNILEIGTGTGFVSAVLK--NNFEVNIVSTEINPDAAQCARSN-------DVEVIRTNMFDgLKPI---QCFDL 100
                                       799*****************9..467899****************8.......8**********99955...89*** PP

                   Methyltransf_31  78 ilsn.................evlnaladpdkile....eiervlkpggillie 110
                                       il n                  + +   d +++++    +++++lkp+g +++ 
  gi|298675524|ref|YP_003727274.1| 101 ILFNppylptsddekvpgwmnYAYDGGVDGCDAIRnfldNVCNYLKPDGSIMLL 154
                                       ****77777777765555544222444444444445555**********99875 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   8.6e-10     9e-07      32     109 ..      38     109 ..      24     120 .. 0.79
   2 ?    3.1   0.0     0.058        61     116     148 ..     132     164 ..     125     184 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 8.6e-10
                                       CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS-EEEEEE---S CS
                               MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeveekkfdlivsNPPf 107
                                         ++l +G+G+G+++a+l++ + e++++ ++++  A ++a+ n    ++e +++   d+l+ ++   fdli+ NPP+
  gi|298675524|ref|YP_003727274.1|  38 GMNILEIGTGTGFVSAVLKN-NFEVNIVSTEINPDAAQCARSN----DVEvIRTNMFDGLKPIQ--CFDLILFNPPY 107
                                       5689************9987.55669***********999865....55556666777777776..9*********8 PP

                                       TT CS
                               MTS 108 ha 109
                                         
  gi|298675524|ref|YP_003727274.1| 108 LP 109
                                       65 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.058
                                       HHHHHHHHHHHHHEEEEEEEEEEEETTSCHHHH CS
                               MTS 116 avaeeliaeAkeaLkegGeLliVanrklgyesl 148
                                       +++++++ +  ++Lk++G++++ ++++ g++ +
  gi|298675524|ref|YP_003727274.1| 132 DAIRNFLDNVCNYLKPDGSIMLLVSSFSGIDYI 164
                                       67889999999***********99999876544 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   1.1e-07   0.00012      16     119 ..      31     155 ..      24     160 .. 0.62
   2 ?    0.1   0.0       0.6   6.4e+02     145     163 ..     158     176 ..     154     178 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.1e-07
                   Methyltransf_23  16 llpklraggrvLdiGcGtGillevlrengf.svtgvDlspeaveiae.....kakkaqkdqfdeqeaaepqgkfdlI 86 
                                       ++ + + g+++L+iG+GtG ++ vl+ n+  +++  +++p a + a+      ++++ +d        +p + fdlI
  gi|298675524|ref|YP_003727274.1|  31 AFNYIKDGMNILEIGTGTGFVSAVLKNNFEvNIVSTEINPDAAQCARsndveVIRTNMFDGL------KPIQCFDLI 101
                                       66778999*****************999767*********9999988866663333333333......344444444 PP

                   Methyltransf_23  87 vlre.vlehvpdpp.....................ellrqiatllkpgGylllse 119
                                         +  +l + +d +                       l+++ ++lkp+G ++l++
  gi|298675524|ref|YP_003727274.1| 102 LFNPpYLPTSDD-EkvpgwmnyaydggvdgcdairNFLDNVCNYLKPDGSIMLLV 155
                                       443212222222.112334444444444444444447777777777777777765 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.6
                   Methyltransf_23 145 ffsarslkelleeaGlevv 163
                                       f   + +k+ +e +G+ev 
  gi|298675524|ref|YP_003727274.1| 158 FSGIDYIKKVMESYGFEVY 176
                                       5566889**********85 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   6.6e-08     7e-05       1      71 [.      41     104 ..      41     149 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 6.6e-08
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvss 71 
                                       +L++G+GtG +++ l +++ + +++ ++i++++ + ar++       ve+++ ++ d   + + fDl++ +
  gi|298675524|ref|YP_003727274.1|  41 ILEIGTGTGFVSAVLKNNF-EVNIVSTEINPDAAQCARSND------VEVIRTNMFDGLKPIQCFDLILFN 104
                                       8*****************9.7*****************998......99999999887778889**99985 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   6.7e-06    0.0071       1      53 [.      42      89 ..      42     113 .. 0.80
   2 ?    3.2   0.0      0.13   1.4e+02      74      95 ..     131     152 ..     121     153 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.7e-06
                                      EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECC CS
                   Methyltransf_11  1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseeglkvefvvadae 53
                                      L++G+GtG +++ l++++  ++v +++++ + ++a+++ +e       ++ ++ 
  gi|298675524|ref|YP_003727274.1| 42 LEIGTGTGFVSAVLKNNFeVNIVSTEINPDAAQCARSNDVEV------IRTNMF 89
                                      89*************9999****************9998775......344444 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.13
                                       -CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  74 vedpekalkeiaRvLkpgGllv 95 
                                       ++  + +l+++   Lkp+G ++
  gi|298675524|ref|YP_003727274.1| 131 CDAIRNFLDNVCNYLKPDGSIM 152
                                       5678899************987 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   2.1e-07   0.00022      71     117 ..      35      79 ..      10     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.1e-07
                                       --TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHH CS
                              PCMT  71 lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrn 117
                                       +k+g+++Le+G+G+G+ +avl + ++ +   vs e  ++ ++ a+ n
  gi|298675524|ref|YP_003727274.1|  35 IKDGMNILEIGTGTGFVSAVLKNNFEVNI--VSTEINPDAAQCARSN 79 
                                       899*******************9987665..8888777766666544 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   0.00013      0.14       1      37 [.      42      77 ..      42     105 .. 0.73
   2 ?    3.9   0.0     0.086        90      80      98 ..     132     150 ..     120     151 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00013
                   Methyltransf_12  1 LeiGcGtGsllralleklpdieytgvDispsaiedak 37
                                      LeiG+GtG ++++l ++  +++++ ++i+p+a + a+
  gi|298675524|ref|YP_003727274.1| 42 LEIGTGTGFVSAVLKNN-FEVNIVSTEINPDAAQCAR 77
                                      8*******999999888.899999****999993333 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.086
                   Methyltransf_12  80 kdirevldnirklLkpgGr 98 
                                       + ir +ldn+ + Lkp+G 
  gi|298675524|ref|YP_003727274.1| 132 DAIRNFLDNVCNYLKPDGS 150
                                       67899************96 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.1e-05     0.011      60     102 ..      35      77 ..      27      88 .. 0.88
   2 ?   -1.5   0.0       1.2   1.2e+03     144     164 ..     133     153 ..     129     175 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-05
                                       --TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHH CS
                              CMAS  60 lkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklak 102
                                       +k+Gm++L+iG+G G +     ++++v++v+  +  + a+ a+
  gi|298675524|ref|YP_003727274.1|  35 IKDGMNILEIGTGTGFVSAVLKNNFEVNIVSTEINPDAAQCAR 77 
                                       799***************************9998877777665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.2
                                       GHHHHHHHHHHHS-TT-EEEE CS
                              CMAS 144 nydtffkklkkllkedGllll 164
                                          +f +++ + lk+dG ++l
  gi|298675524|ref|YP_003727274.1| 133 AIRNFLDNVCNYLKPDGSIML 153
                                       567899999999999997665 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     5e-06    0.0052      28      70 ..      35      78 ..      26      91 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5e-06
                                      GGTTSEEEEES-TTTCCHHHHHCC-.SEEEEE-S-HHHHHHHHC CS
                            RrnaAD 28 leekltvleigpGkGilTeeLakra.kqvvvlElderLakllqk 70
                                      +++ +++leig+G+G+ ++ L + +  + v+ E+ ++ a+  + 
  gi|298675524|ref|YP_003727274.1| 35 IKDGMNILEIGTGTGFVSAVLKNNFeVNIVSTEINPDAAQCARS 78
                                      7789*****************888889*******9987776665 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   8.4e-06    0.0088       9      80 ..      33     102 ..      28     115 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 8.4e-06
                              MetW   9 elikpgsrvldlGcGdGellellkeekqvdgrGleldeegvaecvakGlsviqgdldkdlenfedksfdyvv 80 
                                       ++ik+g ++l++G+G G +  +lk++ +v+    e++ ++ + + +  ++vi+ ++ ++l+    + fd+++
  gi|298675524|ref|YP_003727274.1|  33 NYIKDGMNILEIGTGTGFVSAVLKNNFEVNIVSTEINPDAAQCARSNDVEVIRTNMFDGLKPI--QCFDLIL 102
                                       89*************************************99999999*********9999854..5677766 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00011      0.12       9      79 ..      32      96 ..      29     102 .. 0.82
   2 ?   -0.9   0.0       1.3   1.4e+03      94     135 ..     132     175 ..     129     190 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                   Methyltransf_18  9 aslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklk 79
                                      ++++++g +++ iGt  g++++ l  ++   +++ ++in+ + + a++n  +      i++ + dGl++++
  gi|298675524|ref|YP_003727274.1| 32 FNYIKDGMNILEIGTGTGFVSAVLK-NNFEVNIVSTEINPDAAQCARSNDVE-----VIRTNMFDGLKPIQ 96
                                      6899*****************9987.55556999*******99999987533.....58888888888875 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.3
                   Methyltransf_18  94 elileILeeakeklkkikk..lilqpnseaeelRkylvengfki 135
                                       + i++ L++  ++lk   +  l++++ s ++ ++k++ + gf++
  gi|298675524|ref|YP_003727274.1| 132 DAIRNFLDNVCNYLKPDGSimLLVSSFSGIDYIKKVMESYGFEV 175
                                       56666677665555544433377888889999999999888764 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00012      0.12      13      72 ..      29      90 ..      25     104 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                                      HHHHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS..HHH...TTEEEECS-CCC CS
                              FtsJ 13 dekfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm..apl...pgvttiqgditd 72
                                      d++f+ +k g++++++g ++G  s vl ++++   ++v+  ++p   +     + v++i+++ +d
  gi|298675524|ref|YP_003727274.1| 29 DSAFNYIKDGMNILEIGTGTGFVSAVLKNNFE--VNIVSTEINPDaaQ-CarsNDVEVIRTNMFD 90
                                      7899*9*********************99985..79********9651.145699****999876 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00029      0.31       1     103 [.      42     131 ..      42     153 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00029
                   Methyltransf_24   1 vEiGvysGvstlwllralrrngagrlvavdhdpgaeeaaalareaglddrvrlikadseealaslaagsiDllfiDg 77 
                                       +EiG+  G+ +++l    ++n + ++v+ + +p   +aa+ ar+    + v++i+ ++++ l+  +   +Dl+++  
  gi|298675524|ref|YP_003727274.1|  42 LEIGTGTGFVSAVL----KNNFEVNIVSTEINP---DAAQCARS----NDVEVIRTNMFDGLKPIQ--CFDLILFNP 105
                                       79997777766655....67777889*******...99999997....99************9999..899999998 PP

                   Methyltransf_24  78 ghaaeavledleallprlapggvvlf 103
                                       +   ++  e ++ + ++  +ggv  +
  gi|298675524|ref|YP_003727274.1| 106 PYLPTSDDEKVPGWMNYAYDGGVDGC 131
                                       88888888889999988888887555 PP

>> 5_nucleotid  5' nucleotidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00017      0.17     195     227 ..      11      44 ..       3      68 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00017
                                       HHHHHHHHHTT-EEEEE-SS-HHHHHHHHHHH.H CS
                       5_nucleotid 195 velLerlreagkklfllTNSefdytnkvmkyl.l 227
                                       v++ +++ e  + +fllT S f+y++ +m+ l +
  gi|298675524|ref|YP_003727274.1|  11 VQFVDNVYEPAEDTFLLTDSAFNYIKDGMNILeI 44 
                                       6778888899999****************98743 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00055      0.58     157     203 ..      33      79 ..      25     102 .. 0.90
   2 ?    0.0   0.0      0.42   4.4e+02     237     258 ..     132     153 ..     131     179 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00055
                              PrmA 157 klvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeN 203
                                       +++k g ++l +GtG+G  + + +     ++v + i++ A + a++N
  gi|298675524|ref|YP_003727274.1|  33 NYIKDGMNILEIGTGTGFVSAVLKNNFEVNIVSTEINPDAAQCARSN 79 
                                       5789999************98888888899***************99 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.42
                              PrmA 237 evlielaedikklvkeggllil 258
                                       +++ ++++++++ +k++g+++l
  gi|298675524|ref|YP_003727274.1| 132 DAIRNFLDNVCNYLKPDGSIML 153
                                       67999*************9874 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00016      0.17      25      75 ..      37      84 ..       9      92 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00016
                   Methyltransf_32 25 galtvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklg 75
                                      + ++++++G G g+ s vl+    ++++++v+ +++ + ++ a+  + ++ 
  gi|298675524|ref|YP_003727274.1| 37 DGMNILEIGTGTGFVSAVLKN---NFEVNIVSTEINPDAAQCARSNDVEVI 84
                                      56799****************...99*************999988877765 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00019       0.2      45      86 ..      36      77 ..      18      90 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00019
                   Methyltransf_16 45 lsklsvlELGsGtGlvGlavaellpeakviltDlee.llellk 86
                                        ++++lE+G GtG v  ++++   e++++ t ++  + ++ +
  gi|298675524|ref|YP_003727274.1| 36 KDGMNILEIGTGTGFVSAVLKNN-FEVNIVSTEINPdAAQCAR 77
                                      4679************9999988.5666666666543555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1414.96
//
Query:       gi|298675525|ref|YP_003727275.1|  [L=414]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.2e-26   90.6   0.7    2.2e-25   89.2   0.0    2.0  2  OrfB_IS605      Probable transposase
      9e-12   44.8   0.3    2.4e-11   43.4   0.1    1.9  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.018   15.5   0.0      0.037   14.4   0.0    1.5  1  RuvX            Holliday junction resolvase
       0.96    9.3   4.2       0.29   11.0   0.7    2.0  2  DUF919          Nucleopolyhedrovirus protein of unknown funct


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.2       0.6   2.7e+03      71      86 ..      16      31 ..       4      64 .. 0.67
   2 !   89.2   0.0   4.9e-29   2.2e-25      15     119 ..     190     292 ..     176     293 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.6
                        OrfB_IS605 71 kkasrklarlhrkrsr 86
                                       ++ +++++l++++++
  gi|298675525|ref|YP_003727275.1| 16 YEVLKRITKLSKNLYN 31
                                      3444444444444444 PP

  == domain 2  score: 89.2 bits;  conditional E-value: 4.9e-29
                        OrfB_IS605  15 gnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsrrrkhl 91 
                                        nk+++iDlG+nn+at+v+++gt+f+++gr lks +++++k +  lqs ++k++   k  +kl  l++kr+++++++
  gi|298675525|ref|YP_003727275.1| 190 YNKHLSIDLGVNNFATCVDTNGTAFIIEGRGLKSYNRWWNKVKSGLQSVYDKQG--IKSGQKLNWLFEKRKNKLNDF 264
                                       699**************************************************9..9******************** PP

                        OrfB_IS605  92 lhklathliktlkevgvetLnvgnmkdi 119
                                       +++ +++++k++ +++++++++g++kdi
  gi|298675525|ref|YP_003727275.1| 265 MNQSVNYIVKHCIDNNIGNIIIGELKDI 292
                                       *************************998 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       3.2   1.4e+04       9      22 ..     167     180 ..     167     181 .. 0.81
   2 !   43.4   0.1   5.3e-15   2.4e-11       1      69 []     311     385 ..     311     385 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 3.2
                    OrfB_Zn_ribbon   9 eykakeyGikveev 22 
                                       +y  +++ i++++ 
  gi|298675525|ref|YP_003727275.1| 167 KYNGQWFEIEYVYR 180
                                       68899999999885 PP

  == domain 2  score: 43.4 bits;  conditional E-value: 5.3e-15
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke......alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f+k+k++l+ k++ yGi+ +ev++ayTSkt +   +  ++      ++ +r +  ++ g  +++Dvn+a+Nil++
  gi|298675525|ref|YP_003727275.1| 311 FGKFKQKLRSKCEYYGINCIEVDEAYTSKTDALALEPIEKhqkymgKRVKRGLFQSSTGKLLNADVNGALNILRK 385
                                       89****************************887776666666688977788888888***************986 PP

>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   8.2e-06     0.037      36     107 ..     263     346 ..     241     362 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.2e-06
                                       H..HHHHHHHHHHHHHTT--EEEEE--......---..-SSS---SSTTHHHHHHHHHT....T-EEEEE--S---- CS
                              RuvX  36 k..ekdleelkelvkeeeveeiVvGlP......lnl..dgsegesakkvrkfaeeLakrl..kklpvelvDErlttv 100
                                       +  +++++ + + + ++++ +i++G         n+  +++++ ++  + kf ++L++++  ++++ + vDE +t++
  gi|298675525|ref|YP_003727275.1| 263 DfmNQSVNYIVKHCIDNNIGNIIIGELkdikqnSNMgkKNNQTFQTIPFGKFKQKLRSKCeyYGINCIEVDEAYTSK 339
                                       14479999*****************88677777444114455555556699*******9977899***********9 PP

                                       XXXXXXX CS
                              RuvX 101 eaerilr 107
                                       + + +l+
  gi|298675525|ref|YP_003727275.1| 340 TDALALE 346
                                       8776664 PP

>> DUF919  Nucleopolyhedrovirus protein of unknown function (DUF919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.7   6.6e-05      0.29      15      57 ..       4      44 ..       3      47 .. 0.85
   2 ?   -2.9   0.2       1.4   6.2e+03      45      60 ..     259     274 ..     254     275 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.6e-05
                            DUF919 15 qaKrkltiksqHfErlkkitKnpkElqdlekklnklRqeFLnf 57
                                       +K  ++ + q +E lk+itK +k l +   +l + Rq++++ 
  gi|298675525|ref|YP_003727275.1|  4 TQKNHIKADKQKYEVLKRITKLSKNLYNF--TLYTTRQYYFDN 44
                                      58999******************888665..788999988875 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.4
                            DUF919  45 kklnklRqeFLnfgvk 60 
                                       +kln+  ++  n++vk
  gi|298675525|ref|YP_003727275.1| 259 NKLNDFMNQSVNYIVK 274
                                       5666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1065  (0.059401); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.54
# Mc/sec: 2306.74
//
Query:       gi|298675526|ref|YP_003727276.1|  [L=286]
Description: pyruvate ferredoxin/flavodoxin oxidoreductase subunit beta [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.2e-30  104.1   0.5    5.2e-30  103.4   0.5    1.4  1  PFO_beta_C    Pyruvate ferredoxin oxidoreductase beta subunit
    4.3e-30  104.5   0.2    6.2e-30  104.0   0.2    1.2  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
  ------ inclusion threshold ------
      0.035   13.5   0.1      0.053   12.9   0.1    1.3  1  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator


Domain annotation for each model (and alignments):
>> PFO_beta_C  Pyruvate ferredoxin oxidoreductase beta subunit C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.4   0.5   8.7e-34   5.2e-30       1      65 [.     199     264 ..     199     265 .. 0.98

  Alignments for each domain:
  == domain 1  score: 103.4 bits;  conditional E-value: 8.7e-34
                                       XTTTXSSSXSXXXXX-EEEGGGST---EEHHHHHHHHT-----EEEEEEEE.TTS--HHHHHHT.. CS
                        PFO_beta_C   1 CvtFNkvnTfdwYkervykleedgyDpsdlekAlekalewgdkiplGifYk.eekptyeerleelk 65 
                                       CvtFN++nTf+wY+ervyklee++y+p d+ kA+ek++ewgd+ip+G+fYk e kpt+e++l++l+
  gi|298675526|ref|YP_003727276.1| 199 CVTFNRLNTFKWYNERVYKLEETDYNPDDKTKAFEKSMEWGDNIPIGVFYKrEGKPTFEDNLPVLE 264
                                       **********************89**************************************9985 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.0   0.2     1e-33   6.2e-30       6     153 .]      52     195 ..      43     195 .. 0.92

  Alignments for each domain:
  == domain 1  score: 104.0 bits;  conditional E-value: 1e-33
                                       HHHHHHHHTTSSSSEEEC.ETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEEEEEE CS
                      TPP_enzyme_C   6 tlwaarllkvkrprsylt.sgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpitvvvl 80 
                                       +          + ++yl  + + g +G+++p AiGak+ + d +v+a+ GDG+++   ++++++avrrn +itv+v+
  gi|298675526|ref|YP_003727276.1|  52 S----------KLPHYLRcNVFNGLHGRAIPPAIGAKVSNHDLNVIAVGGDGDMYGEgGNHFIHAVRRNPNITVIVH 118
                                       3..........367888856699***************99999********************************** PP

                                       E-SBCCCHHHH...HHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                      TPP_enzyme_C  81 nNegygmtggq...qepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpaliev 153
                                       +N++yg+t+gq   ++  g+k+k++++g   +p++  + a +l ++ + r    dv++l  ++k+a+e+kg +l++v
  gi|298675526|ref|YP_003727276.1| 119 DNQIYGLTKGQaspTSDIGMKTKVQKHGVMHTPFNSLATAISLDCTfVSRGFAGDVKHLSGIIKQAIEHKGLSLVDV 195
                                       ***********9999999*******999899999999999999***6668889**********************98 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   8.9e-06     0.053      42     123 ..     111     196 ..     101     209 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.9e-06
                                       TT-EEEEEGGGEET--SSHHHHHH...HHH.TT-SEEEES-HHHHHHHHHTT--EEEEEE--SHHHHHHHHHH.HHH CS
                      G3P_antiterm  42 agkkvfvhiDlieGlskdeaavef...lkkeikvdGiistksslikkakklglltiqrlfliDssalekalkq.iek 114
                                        + +v+vh + i Gl+k +a+ +    +k++++ +G++ t  + + +a +l+   + r f  D + l+ ++kq ie+
  gi|298675526|ref|YP_003727276.1| 111 PNITVIVHDNQIYGLTKGQASPTSdigMKTKVQKHGVMHTPFNSLATAISLDCTFVSRGFAGDVKHLSGIIKQaIEH 187
                                       467899*********88776654333488889999*********************************999871455 PP

                                       HT-SEEEEE CS
                      G3P_antiterm 115 skpdavevl 123
                                           +v+vl
  gi|298675526|ref|YP_003727276.1| 188 KGLSLVDVL 196
                                       566777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1743.57
//
Query:       gi|298675527|ref|YP_003727277.1|  [L=575]
Description: pyruvate flavodoxin/ferredoxin oxidoreductase domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-54  185.7   0.0    1.5e-54  185.2   0.0    1.2  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    4.7e-38  131.0   0.1    7.8e-38  130.3   0.1    1.3  1  POR              Pyruvate ferredoxin/flavodoxin oxidoreductas
    1.6e-06   27.8   0.0    2.7e-06   27.1   0.0    1.3  1  TPP_enzyme_N     Thiamine pyrophosphate enzyme, N-terminal TP
     0.0021   18.3   0.0     0.0055   17.0   0.0    1.7  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
     0.0095   15.8   0.0       0.02   14.8   0.0    1.5  1  Transketolase_C  Transketolase, C-terminal domain


Domain annotation for each model (and alignments):
>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.2   0.0   4.1e-58   1.5e-54       2     229 ..     207     445 ..     206     447 .. 0.91

  Alignments for each domain:
  == domain 1  score: 185.2 bits;  conditional E-value: 4.1e-58
                                       HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCC CS
                             POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmien 78 
                                       +a+a g+++i+aYP+TPs+ +++ +++  +k++v    v q+e+Ei+a ++ +GA++aGar++++TSg G++Lm e+
  gi|298675527|ref|YP_003727277.1| 207 GALASGIKFISAYPMTPSTGVLNYISSNSDKFGV---AVEQAEDEISALNMSLGASFAGARSMVTTSGGGFSLMAEA 280
                                       688999***************************8...9*************************************** PP

                                       HHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHH.....S---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEE CS
                             POR_N  79 lglaageelPvvivvvaRalpstglsirtdqsDlmaar.....dtglivlasenvqeafdlalvAfnlAekvrvPvi 150
                                       +gl + +e+Pvvi++ +R +pstgl+++t+q+Dl +a+     +++ +++a+++  +af l+ +Afn+A ++++P+i
  gi|298675527|ref|YP_003727277.1| 281 VGLSGETETPVVIFLGQRPGPSTGLPTMTEQGDLEFALhasqgEFPRCIFAPKTPDDAFYLTSKAFNMADNYQIPAI 357
                                       ***************************************************************************** PP

                                       EEEEHHHH.HEEEEEEC-SGG....GS-----SBXXXXXXXX........SXXXBXXTXXTSSXXEEESBXBXTTSX CS
                             POR_N 151 vlfDgfllshevekvelpdee...delklikekleeyerkey........aldpekpiargtaanpdtglehrekgn 216
                                       +++D++l+ ++  + +  d       ++l +e+++++++key        +++p+  +   +  + + ++eh+e+g+
  gi|298675527|ref|YP_003727277.1| 358 IMSDQYLA-DSEFTCDKFDTSkirINKHLLTENSKAEQDKEYkryefttsGISPRALPGKFGSLVVADSDEHDEYGH 433
                                       ********.66555555554422144556666666666666688899999*************************** PP

                                       BXXXXHHHHHHHH CS
                             POR_N 217 eaedaaekvveev 229
                                       ++   +++++++ 
  gi|298675527|ref|YP_003727277.1| 434 IDQT-IDNRIKMN 445
                                       *998.88888875 PP

>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.3   0.1   2.2e-41   7.8e-38       1     176 [.      13     171 ..      11     172 .. 0.95

  Alignments for each domain:
  == domain 1  score: 130.3 bits;  conditional E-value: 2.2e-41
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEE CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglk 77 
                                       +GqG++t+g+il+k++ + G+yv+++++y s+irGgh y++ r+sd  +v++i  +++++lvald++++++h+d+l 
  gi|298675527|ref|YP_003727277.1|  13 AGQGLQTIGQILSKIFLKGGFYVFGTQFYLSRIRGGHNYYQARVSDN-PVKAIT-EDVNMLVALDKASIDQHFDELS 87 
                                       5*********************************************9.9*****.*********************9 PP

                                       EEEEEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHTS-HHHHHHHH CS
                               POR  78 pggiiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggneraaNtvmlGalaallglplealeeai 154
                                        gg+i+++++e     +++++e            ++ v++tk+a++ gg +++ Ntv++Ga+++ll  +++ l++++
  gi|298675527|ref|YP_003727277.1|  88 -GGVILVDKNE---VKIDNNDE-----------SIFHVPFTKLAEDVGG-KIYSNTVAVGAALGLLCYDFDRLKQVL 148
                                       .********76...55555555...........468*************.*************************** PP

                                       HCCS-CH..HHHHHHHHHHHHHH CS
                               POR 155 kkrfpkkk.eviekNlkafragy 176
                                       +++f kk+ e+++kN++a+  gy
  gi|298675527|ref|YP_003727277.1| 149 NDTFSKKGeEIVNKNIEAASSGY 171
                                       ******99**************9 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   7.6e-10   2.7e-06      12     159 ..     210     360 ..     199     373 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 7.6e-10
                                       HHCT--EEEE---CCCHHHHCCHHCT....TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHHHHH CS
                      TPP_enzyme_N  12 kalgvehvfgvpGsrilplldalseeq...girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnaltalae 85 
                                       +  g++ + ++p + ++ +l+++s +    g+ v +a +E +a ++  g + a   + +v +tsg G+  +  a+  
  gi|298675527|ref|YP_003727277.1| 210 A-SGIKFISAYPMTPSTGVLNYISSNSdkfGVAVEQAEDEISALNMSLGASFAGA-RSMV-TTSGGGFSLMAEAVGL 283
                                       4.49********************9999*********************999965.5555.55777*********** PP

                                       HHHHT--EEEEEEE--CCCHH..S..TC--T..-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEEE CS
                      TPP_enzyme_N  86 AkvdriPllvlsgdrptslrg..qgvlqqel..dqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPvyle 158
                                          + +P++++ g+rp  ++g  + + q+ l     a   ++ ++ + +++p+++  +  +A+  a  + + P+ + 
  gi|298675527|ref|YP_003727277.1| 284 SGETETPVVIFLGQRPGPSTGlpTMTEQGDLefALHASQGEFPRCIFAPKTPDDAFYLTSKAFNMA-DNYQIPAIIM 359
                                       *********************653333333332344445599999*********************.8888888876 PP

                                       E CS
                      TPP_enzyme_N 159 l 159
                                        
  gi|298675527|ref|YP_003727277.1| 360 S 360
                                       5 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.5e-06    0.0055       1      78 [.     470     548 ..     470     562 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.5e-06
                                       -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--H..HHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHH CS
                           PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPe..eelkellkkvkkvvvldrnisfgseGqlveevk 75 
                                       A++ +v+ Gs+ g + + vd lR +g+++ l+    ++P P+  e + e +  +++++ ++ n++  ++++l  e  
  gi|298675527|ref|YP_003727277.1| 470 AKTTLVGWGSTYGPLTETVDILRSRGVDINLVHFNEVYPLPTsiESILENA-TTSNLICVENNATGQFSNILKVEAG 545
                                       77899************************************8334555554.4667777888885444466655555 PP

                                       HHT CS
                           PFOR_II  76 aal 78 
                                        ++
  gi|298675527|ref|YP_003727277.1| 546 VSM 548
                                       555 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   5.7e-06      0.02       8      71 ..     468     532 ..     464     542 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.7e-06
                                       TTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHH..HSEEEEEEEEE CS
                   Transketolase_C   8 egkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkk..tgrlvvveeav 71 
                                       e  + tlv++Gs+    +e ++ L+++g+++ +v    v pl +  i++++++  t  l++ve+++
  gi|298675527|ref|YP_003727277.1| 468 ESAKTTLVGWGSTYGPLTETVDILRSRGVDINLVHFNEVYPLPT-SIESILENatTSNLICVENNA 532
                                       66789*************************************94.455555432277788888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (575 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.51
# Mc/sec: 3369.46
//
Query:       gi|298675528|ref|YP_003727278.1|  [L=166]
Description: hypothetical protein Metev_1642 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.029   13.2   0.4      0.053   12.3   0.1    1.6  2  UDPGT      UDP-glucoronosyl and UDP-glucosyl transferase
       0.12   12.4   0.2       0.22   11.5   0.2    1.4  1  DUF4006    Family of unknown function (DUF4006)
       0.12   13.4   0.1       0.28   12.2   0.1    1.6  1  Conotoxin  Conotoxin


Domain annotation for each model (and alignments):
>> UDPGT  UDP-glucoronosyl and UDP-glucosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   8.9e-06     0.053      71     133 ..      33      95 ..      17     127 .. 0.77
   2 ?   -1.9   0.0      0.18     1e+03     426     437 ..     146     157 ..     143     159 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.9e-06
                             UDPGT  71 vkklfeeasektvlkllealkeasdlleklCkevvsnkkllkklqeskfdvvladpvlpcgel 133
                                       ++++ e++  k++++ ++  ++ +d++    k++v n+++l  +++s+ d +l ++v+  +e+
  gi|298675528|ref|YP_003727278.1|  33 TQEQSEDELYKQLKSNISVFNQHADMIPGFVKSLVGNEEILVIIEKSNNDTLLIEAVTENAEI 95 
                                       2333333444677777778889***********************************997765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.18
                             UDPGT 426 PvkPLDravfWi 437
                                       Pv  + +avfW+
  gi|298675528|ref|YP_003727278.1| 146 PVGGMKKAVFWV 157
                                       888899*****9 PP

>> DUF4006  Family of unknown function (DUF4006)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   3.6e-05      0.22      15      51 ..      10      47 ..       2      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.6e-05
                           DUF4006 15 tGmliavvLLLsilavLtvlaikvqqaeatnyYk.led 51
                                      tG+l + vLLL i +       ++q+++ ++ Yk l++
  gi|298675528|ref|YP_003727278.1| 10 TGLLLILVLLLPISMATAQETTQTQEQSEDELYKqLKS 47
                                      8********************************94333 PP

>> Conotoxin  Conotoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   4.7e-05      0.28       6      33 ..      12      40 ..       9      57 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.7e-05
                                      XXXXXXXXXX.XXXXXXXXXXXXXXXXXX CS
                         Conotoxin  6 vlivavLllt.tlvtadldgdqpadrkak 33
                                      +l+++vLll+  ++ta+  ++++++ + +
  gi|298675528|ref|YP_003727278.1| 12 LLLILVLLLPiSMATAQETTQTQEQSEDE 40
                                      89********7444444333333333222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1489  (0.0830498); expected 358.6 (0.02)
Passed bias filter:                      862  (0.0480785); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1045.68
//
Query:       gi|298675529|ref|YP_003727279.1|  [L=169]
Description: flavodoxin/nitric oxide synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-26   91.4   0.9    5.5e-26   91.2   0.9    1.0  1  Flavodoxin_3     Flavodoxin domain
    9.8e-12   45.3   0.0    1.4e-11   44.8   0.0    1.4  1  Flavodoxin_5     Flavodoxin domain
    5.9e-06   26.5   0.2    1.2e-05   25.5   0.2    1.8  1  Flavodoxin_1     Flavodoxin
     0.0027   17.4   0.1      0.069   12.9   0.0    2.2  2  Flavodoxin_4     Flavodoxin
  ------ inclusion threshold ------
      0.019   13.9   0.1      0.022   13.8   0.1    1.1  1  Glyco_hydro_30   Glycosyl hydrolase family 30 TIM-barrel doma
      0.053   13.2   0.0       0.15   11.8   0.0    1.9  2  Flavodoxin_2     Flavodoxin-like fold
      0.055   13.6   0.2       0.12   12.6   0.1    1.7  1  Flavodoxin_NdrI  NrdI Flavodoxin like


Domain annotation for each model (and alignments):
>> Flavodoxin_3  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.2   0.9   2.1e-29   5.5e-26       1     160 [.       4     157 ..       4     158 .. 0.93

  Alignments for each domain:
  == domain 1  score: 91.2 bits;  conditional E-value: 2.1e-29
                      Flavodoxin_3   1 lilysSltGNTkkvAeaikealeeekeivsikeakekveeadvvfvGfwvdkgtadeealkflet.lknkkillfgT 76 
                                       l++y ++tGNTkk+A+ai+ea+ e k+i +i+e+++ +e +d+ f+Gf +++ +a +e+++fl++  ++k+i+lf T
  gi|298675529|ref|YP_003727279.1|   4 LVTYMTQTGNTKKIADAIYEAVDEDKDIKDINEVDS-LEGYDLAFIGFPIHQFNAPDEVKNFLNNnTNGKDIALFIT 79 
                                       589********************************9.**************************862678******** PP

                      Flavodoxin_3  77 lGagkdseyakkilekvkalleknnevlgeflcqGkisekvrekyeklaksdeehkkldalianfdeAasHPdeeDl 153
                                        Ga  d + +++ ++k k++  k+ ++++ f cqG +s+++ +++++     + + ++++  +   + +  Pde+ +
  gi|298675529|ref|YP_003727279.1|  80 HGAPSDFDQVSDWVSKSKEAA-KDANIIDVFQCQGEVSKEIMDMLQN-----SGDPQMQQFAELVSKGKGQPDETMV 150
                                       ***************999885.67889************99998887.....5788999999999************ PP

                      Flavodoxin_3 154 ekakevv 160
                                       +kak+++
  gi|298675529|ref|YP_003727279.1| 151 QKAKQFA 157
                                       ****996 PP

>> Flavodoxin_5  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.0   5.5e-15   1.4e-11       1      99 [.       4      93 ..       4     154 .. 0.76

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 5.5e-15
                      Flavodoxin_5  1 lilYsSrdGqTkkiaeriaeelreegelvdvedvekesedlesydavvigasvyygkllpelakFvekhreaLstkpva 79
                                      l++Y +++G+Tkkia++i e+++e     d++d+ +e ++le yd   ig ++++ + + e+++F++ +    + k +a
  gi|298675529|ref|YP_003727279.1|  4 LVTYMTQTGNTKKIADAIYEAVDEDK---DIKDI-NEVDSLEGYDLAFIGFPIHQFNAPDEVKNFLNNNT---NGKDIA 75
                                      79*********************775...55666.3668****************************755...99**** PP

                      Flavodoxin_5 80 lfsvsltarkpeksyvrkfl 99
                                      lf++  +  +  +  v++ +
  gi|298675529|ref|YP_003727279.1| 76 LFITHGAPSDFDQ--VSDWV 93
                                      ***9998443333..22222 PP

>> Flavodoxin_1  Flavodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.2   4.7e-09   1.2e-05       1      62 [.       5      59 ..       5     165 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 4.7e-09
                                      EEEETSSSHHHHHHHHHHHHHHHTTTEEEEEEEEGTTSCGGGGGTHSEEEEEEEEETTTBEE CS
                      Flavodoxin_1  1 ilYgSetGnteklAkqlaeelgehgfnadvvslsdydeslseieeealllvvtsTfgnGdpp 62
                                      + Y ++tGnt+k+A ++ e ++e   + d+ +++++d    ++e ++l+ ++ + +    p 
  gi|298675529|ref|YP_003727279.1|  5 VTYMTQTGNTKKIADAIYEAVDE---DKDIKDINEVD----SLEGYDLAFIGFPIHQFNAPD 59
                                      78********************6...34788888888....9*********99965555444 PP

>> Flavodoxin_4  Flavodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.032        81       1      22 [.       2      23 ..       2      39 .. 0.79
   2 !   12.9   0.0   2.7e-05     0.069      72     114 ..      41      82 ..      34     121 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.032
                                      -EEEEE--SSSHHHHHHHHHHH CS
                      Flavodoxin_4  1 kilvayfscsgvtkavaeklaa 22
                                      k+lv+y++ +g tk +a+ +  
  gi|298675529|ref|YP_003727279.1|  2 KVLVTYMTQTGNTKKIADAIYE 23
                                      79**************997643 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 2.7e-05
                                       GG-SEEEEEEE-BTTB--HHHHHHHHTS--TT-EEEEEEE-SS CS
                      Flavodoxin_4  72 ekyevlfvgfpvwwyiaptiintflesydfagkivvpfatsgg 114
                                       e y++ f+gfp+  + ap  ++ fl++ +  gk +  f t g 
  gi|298675529|ref|YP_003727279.1|  41 EGYDLAFIGFPIHQFNAPDEVKNFLNN-NTNGKDIALFITHGA 82 
                                       789**********************87.567888888888875 PP

>> Glyco_hydro_30  Glycosyl hydrolase family 30 TIM-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   8.5e-06     0.022     187     295 ..      62     167 ..      36     169 .] 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.5e-06
                                       HHHHHTSTT.TTSEEEEEEEEGGGTTHHHHHHHTSHHHHTTEEEEEEEETTTS-HHHHHHHHHHH.STTSEEEEEEE CS
                    Glyco_hydro_30 187 GpalaassagknvkllilddnrgnlpkwadvvlndkdaakyvsGiavhayqdaeadkhldethkk.fpnvlllgtea 262
                                          l++ ++gk++ l+i       + + +d v + k+aak  + i v + q + +++ +d   +   p++  ++   
  gi|298675529|ref|YP_003727279.1|  62 KNFLNNNTNGKDIALFITHGAPSDFDQVSDWVSKSKEAAKDANIIDVFQCQGEVSKEIMDMLQNSgDPQMQQFAELV 138
                                       5568999*********************************************99999999887753799999**99* PP

                                       ESS-STTS-SS-TT-HHHHHHHHHHHHHHHHTT CS
                    Glyco_hydro_30 263 seGskskdqsvdyGsfdraadyasdildnlnnw 295
                                       s+G++  d+       ++a+++a+d+l++ + w
  gi|298675529|ref|YP_003727279.1| 139 SKGKGQPDE----TMVQKAKQFANDVLTQKKAW 167
                                       ***999884....45678999999999987776 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.7e-05      0.15      62     101 ..      27      66 ..       3      90 .. 0.78
   2 ?   -1.9   0.0      0.88   2.2e+03      58      71 ..     120     133 ..      76     158 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.7e-05
                                       TTC.HHHHHHHHHHHHCSSEEEEEEE-BTTB--HHHHHHHH CS
                      Flavodoxin_2  62 ekp.adveseqiekllaadaivlqfPlwwfgvPailKgwiD 101
                                       e + ++   e  + l+  d+  ++fP++ f+ P  +K+++ 
  gi|298675529|ref|YP_003727279.1|  27 EDKdIKDINEV-DSLEGYDLAFIGFPIHQFNAPDEVKNFLN 66 
                                       22335555666.**************************986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.88
                                       HHHHTTCHHHHHHH CS
                      Flavodoxin_2  58 layeekpadveseq 71 
                                       +++ + + d +++q
  gi|298675529|ref|YP_003727279.1| 120 MDMLQNSGDPQMQQ 133
                                       33333223333333 PP

>> Flavodoxin_NdrI  NrdI Flavodoxin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   4.6e-05      0.12       1      79 [.       5      81 ..       5     115 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.6e-05
                                      EEE--TT-HHHHHHHHH-S-EEEE-SSTT--.---SS-EEEEEE--TTSSSSTSS-HHHHHHHTSHHHHHCEEEEEEEE CS
                   Flavodoxin_NdrI  1 vvysSlsgntkrFvekleleaqripleekeeelevdepyvlivptygegeekkavpkqvieflnkeknrkllrGviasG 79
                                      v+y++ +gntk+  + + +   + +  ++ +e++  e y l    +   +   + p++v++fln+++n k +   i+ G
  gi|298675529|ref|YP_003727279.1|  5 VTYMTQTGNTKKIADAIYEAVDEDKDIKDINEVDSLEGYDLAFIGFPIHQ--FNAPDEVKNFLNNNTNGKDIALFITHG 81
                                      78*************99985555555555556888888877777666664..568**************9998877777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1023.88
//
Query:       gi|298675530|ref|YP_003727280.1|  [L=130]
Description: phosphoribosylaminoimidazole carboxylase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-47  160.5   1.0    2.1e-47  160.4   1.0    1.0  1  AIRC      AIR carboxylase


Domain annotation for each model (and alignments):
>> AIRC  AIR carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.4   1.0   1.2e-51   2.1e-47       1     129 [.       3     127 ..       3     130 .] 0.97

  Alignments for each domain:
  == domain 1  score: 160.4 bits;  conditional E-value: 1.2e-51
                                       EEEEEESSGGGHHHHHHHHHHHHHTT-EEEEEE--TTTSHHHHHHHHHHCHTTTEEEEEEEEESS--HHHHHHHHSS CS
                              AIRC   1 kVgiimGSdsDlevmkkaaeilkelgveyevrvvSahrtpeelleyaeeaeerglkviIagAGgaahLpgvvasltt 77 
                                       +V+ii GS+sD e++ ka+++l+++g +y+v+v+Sahr+p+el +y+++ +    kv+I++AG +a+Lpgvvas+t+
  gi|298675530|ref|YP_003727280.1|   3 DVAIISGSESDKEIAVKATKVLDDIGYSYDVQVISAHRNPDELDDYVTSSD---AKVFITIAGLSAALPGVVASKTE 76 
                                       69*********************************************9776...58********************* PP

                                       S-EEEEEE--STTCCHHHHHHHHT--TTS--EE-SSTHHHHHHHHHHHHHTT CS
                              AIRC  78 lPVigvPvkskalkgldsllSivqmPsgvpvatvaigkaknAallAaqilal 129
                                        PVigvPv++ +l gld+llS+ qmP+gvpvatv+i+++knAa lA++il +
  gi|298675530|ref|YP_003727280.1|  77 KPVIGVPVNT-KLGGLDALLSTAQMPPGVPVATVGIDNGKNAANLAIRILNM 127
                                       **********.**************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 807.45
//
Query:       gi|298675531|ref|YP_003727281.1|  [L=95]
Description: chorismate mutase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-15   57.7   7.5    1.2e-15   57.5   7.5    1.0  1  CM_2         Chorismate mutase type II
  ------ inclusion threshold ------
       0.17   11.6   3.0       0.19   11.5   3.0    1.0  1  FTCD_C       Formiminotransferase-cyclodeaminase
       0.26   11.5   6.3       0.77   10.0   6.3    1.7  1  TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
       0.38   11.2   2.3       0.44   11.0   2.3    1.0  1  ESM4         Enhancer of split M4 family


Domain annotation for each model (and alignments):
>> CM_2  Chorismate mutase type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.5   7.5   2.8e-19   1.2e-15       1      75 []       8      86 ..       8      86 .. 0.96

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 2.8e-19
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSGSS-HHHHHHHHHHHHHHH....S-HHHHHHHHHHHHHHHHHHHH CS
                              CM_2  1 RkeIdeiDdeileLLaeRaelakevgeyKkeeglpvydpeReaevlerleega....ldeeaierifreiisasralqk 75
                                      R++I +iD+eil+L+++R +la++v  +K++e+l++ d+e+ + v++r  ++a    ld  ai++i++++i++s++ q+
  gi|298675531|ref|YP_003727281.1|  8 RAQIQQIDSEILALIKKRVDLAEKVLDAKRKENLSINDEEQNQVVINRAIDEAtelnLDTAAIKEIYETLIQMSIDKQY 86
                                      99*************************************************667788*******************997 PP

>> FTCD_C  Formiminotransferase-cyclodeaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   3.0   4.3e-05      0.19      52     127 ..       3      77 ..       1      86 [. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.3e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT..........S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            FTCD_C  52 emeellekleelrkellelideDaeaFnevmeayklpketeeekaareeaiqealkkavevPlelarkalellell 127
                                       ++ee  ++++++ +e+l+li++ ++  ++v++a +  + + +++++ +  i++a+ +a+e  l++a  ++e++e+l
  gi|298675531|ref|YP_003727281.1|   3 TIEETRAQIQQIDSEILALIKKRVDLAEKVLDAKRKENLSINDEEQNQVVINRAIDEATELNLDTAA-IKEIYETL 77 
                                       689999********************************9999999*******************986.45555555 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   6.3   0.00017      0.77      35     114 ..       4      80 ..       1      81 [. 0.72

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00017
                       TMF_TATA_bd  35 lerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetlLellGeksEeveELraDvaDlKemykeq 111
                                       +e+  a+ +++ +ei++l+k+  +l+e  k l+  +ke  +++++ e+   ++    +e  EL  D a +Ke+y+++
  gi|298675531|ref|YP_003727281.1|   4 IEETRAQIQQIDSEILALIKKRVDLAE--KVLDAKRKENLSINDE-EQNQVVINRAIDEATELNLDTAAIKEIYETL 77 
                                       667777888899999999976655544..4444444555555554.445677889999999**************** PP

                       TMF_TATA_bd 112 veq 114
                                       +++
  gi|298675531|ref|YP_003727281.1|  78 IQM 80 
                                       996 PP

>> ESM4  Enhancer of split M4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.3   9.8e-05      0.44      27      97 ..       8      76 ..       2      91 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.8e-05
                              ESM4 27 vrrlkkvlkpLrrllkkggkgrkteltlahpnnvdlentqqqqqqqqeeldednssnaeLeqqlveeevek 97
                                        +++++   ++ l+kk+    ++ l  + + n ++++++q+q  +  +   d++++ +L +++++e++e 
  gi|298675531|ref|YP_003727281.1|  8 RAQIQQIDSEILALIKKRVDLAEKVLDAKRKENLSINDEEQNQVVI--NRAIDEATELNLDTAAIKEIYET 76
                                      5678888889999*******9999999***********88655555..67899999999999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1551  (0.0865079); expected 358.6 (0.02)
Passed bias filter:                      624  (0.0348039); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 585.49
//
Query:       gi|298675532|ref|YP_003727282.1|  [L=495]
Description: amine oxidase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-18   66.9   0.0    4.6e-18   65.8   0.0    1.6  1  Amino_oxidase   Flavin containing amine oxidoreductase
    1.3e-16   60.6   0.1    2.4e-16   59.7   0.1    1.4  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    1.4e-07   31.0   0.2    4.5e-07   29.3   0.3    1.7  2  FAD_binding_2   FAD binding domain
    1.6e-07   31.3   0.1    8.3e-06   25.6   0.1    2.4  2  DAO             FAD dependent oxidoreductase
    1.9e-05   23.5   0.1    4.3e-05   22.4   0.1    1.5  1  HI0933_like     HI0933-like protein
    3.3e-05   23.3   0.2    4.9e-05   22.7   0.2    1.2  1  FAD_binding_3   FAD binding domain
    4.3e-05   22.8   1.4       0.12   11.4   0.1    3.0  3  GIDA            Glucose inhibited division protein A
    4.5e-05   22.8   0.1      0.002   17.4   0.0    2.3  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    0.00013   21.4   0.1     0.0003   20.3   0.1    1.5  2  FAD_oxidored    FAD dependent oxidoreductase
    0.00018   22.0   1.3     0.0025   18.4   0.1    2.5  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    0.00024   20.4   0.1    0.00047   19.5   0.1    1.4  1  Thi4            Thi4 family
    0.00048   18.8   0.2    0.00048   18.8   0.2    1.6  2  GDI             GDP dissociation inhibitor
    0.00071   18.9   1.3     0.0053   16.1   0.2    2.5  3  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
     0.0058   15.5   0.2      0.086   11.7   0.2    2.1  2  Trp_halogenase  Tryptophan halogenase
  ------ inclusion threshold ------
      0.097   12.1   0.0       0.16   11.4   0.0    1.2  1  DUF1202         Protein of unknown function (DUF1202)
       0.12   11.9   0.1       0.25   10.9   0.1    1.4  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
       0.19   11.7   0.3       0.96    9.4   0.1    2.0  2  NAD_binding_9   FAD-NAD(P)-binding


Domain annotation for each model (and alignments):
>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.8   0.0   4.3e-21   4.6e-18       1     368 [.      14     414 ..      14     480 .. 0.78

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 4.3e-21
                                       HHHHHHHHHHHHTTEEEEEEESSSSSBTTS-EEEETTEEEESS--EEET.TTHHHHHHHHHTTCCCCEEEESCCGCE CS
                     Amino_oxidase   1 laGLaaArqLlsaGfdVtvlEardrvGGRirtvrsdGylielGamwftg.agnpllellkelgledslslpdpgapk 76 
                                       ++GL  A  L+ +G++V+v+E ++ vGG +++++ dG+ +++G + +t  +  pl  l++   ++  +++ ++g  +
  gi|298675532|ref|YP_003727282.1|  14 ISGLLSALVLSKHGHKVLVIEKEQEVGGNCNSYEVDGFQVDTGVHAITHlCVGPLKMLMDN-YFNYLPVFESYG--H 87 
                                       8************************************************999999999999.566667788999..4 PP

                                       EEEETTEECCTTEECHHHHHHHHHHHHHHHH.CHHHHHHHHHHHHHHHHH.......HHHCCCCHHHHHHHHHCHHH CS
                     Amino_oxidase  77 rvlskggrefpgdlspvpaewealleqgals.aellsleeklrlgleall.......qktldeldldskslaeslee 145
                                       +++ +     + +l ++p+++++++++ + + ++ + + ++l ++l++++          ++  +    ++  ++ +
  gi|298675532|ref|YP_003727282.1|  88 YYVRY-----KNRLVKFPSNLKEFARFDIFPkRDRVAISQSLTRSLTQFTfgsdlskTPVYNAVPKTISKDCYEFID 159
                                       44443.....8888899999999999888888*********************998777778888888888888899 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTSTTTTCBHHHHTCCCCHHHHHTSCCCEE................. CS
                     Amino_oxidase 146 lgrrepgdvevwdrliepelfaklefasglfagdpselsaklalpllwelegfggslllp................. 205
                                       +  + ++++ + +  +e  l+    ++  +     +e +++l +++++  +++++   l+                 
  gi|298675532|ref|YP_003727282.1| 160 TVSYFLSGKSMYETPVERVLMGSDFVCDSTIK---EEIEQSLNHISEDSNNDKKDRNSLLptnvdipfqfnrdgvpf 233
                                       99999999888888888655556666666665...666777777777766666666555569*************** PP

                                       .............................TTHTHHHHHHHHH.TTTTEEEETSEEEEEEEEETTC.EEEEETTSTEE CS
                     Amino_oxidase 206 .............................rgGlsqlpealae.elrgldirlntrVkeikregdg.vtvtledgevv 251
                                                                    rgGl+++ +++      ++di ++++V  i ++++   +v++ +g+v+
  gi|298675532|ref|YP_003727282.1| 234 lfgslnlldsisslsklatnnvnfcqgypRGGLKSILNSVLYsLPDNVDIITGEEVNTIFTGNNVvEGVETANGNVY 310
                                       ********************************9888888777577799*************7777579********* PP

                                       EESEEEE-S-HHHHHSSEEESCCSHHHHHHHHHSEEEEEEEEEEEESSGGSGCSTS.ECE..CECCCEEETTTEEEE CS
                     Amino_oxidase 252 eaDaVvvTvplgvlkailfsPplpdekaeairnlgfgsvnkvilefdrkfwednal.gqg..vlvseltttlgeafi 325
                                       + D Vv T   + l   + +  lp    + ++n++   +  + l   +k  ++++  g +    ++  + ++ ++++
  gi|298675532|ref|YP_003727282.1| 311 RSDVVVYTGMARDLP-RTID-NLPSRYKSKLENIKISKSLTIWLGLSQKM-DELNYcGSEvwFKNKPYWAMPTSNYD 384
                                       ***************.4444.6999999*********************8.66554543346667777777777777 PP

                                       ECCECCCSTTTEEEEEEEEECHHHHHHHTTS-HHHHHHHHHHH CS
                     Amino_oxidase 326 ssdfpsrappgkglvllvyvggdaaneleslsdeelvqavlrd 368
                                       s    s ap+gk++v ++++++++ +          ++ + + 
  gi|298675532|ref|YP_003727282.1| 385 S----SFAPEGKQVVGFSFIMDEYSD---------TKSNIENA 414
                                       7....55*************965533.........33333333 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   0.1   2.3e-19   2.4e-16       1      53 [.       9      61 ..       9      75 .. 0.93

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 2.3e-19
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECETTCEECTS---EE CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyevpgvrvdygahifh 53
                                      IvGaG+sGl+ A  L+k+g++vl++ek + +GG++ syev+g+ vd+g+h+++
  gi|298675532|ref|YP_003727282.1|  9 IVGAGISGLLSALVLSKHGHKVLVIEKEQEVGGNCNSYEVDGFQVDTGVHAIT 61
                                      9*************************************************985 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.3   4.3e-10   4.5e-07       2      37 ..       7      42 ..       6      45 .. 0.94
   2 ?   -2.4   0.0       1.8   1.9e+03     389     402 ..     454     467 ..     445     477 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 4.3e-10
                                      EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSG CS
                     FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefgga 37
                                       i++G+G++GL +Al ++++G+kv+v+ekeqe+gg+
  gi|298675532|ref|YP_003727282.1|  7 SIIVGAGISGLLSALVLSKHGHKVLVIEKEQEVGGN 42
                                      59*******************************996 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.8
                                       EESSBTEEE-STCE CS
                     FAD_binding_2 389 gqpipGLYAaGeva 402
                                       ++pi++LY aG ++
  gi|298675532|ref|YP_003727282.1| 454 KTPIKNLYLAGTDT 467
                                       689********998 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.1   7.9e-09   8.3e-06       3      35 ..       8      41 ..       6      46 .. 0.93
   2 ?    3.3   0.0     0.048        51     160     203 ..     280     321 ..     270     465 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 7.9e-09
                                      EEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSS CS
                               DAO  3 viiGGGiiGlstAyeLarrg..Vtllekgdiagsg 35
                                      +i+G+Gi Gl  A+ L+++g  V+++ek+ ++g g
  gi|298675532|ref|YP_003727282.1|  8 IIVGAGISGLLSALVLSKHGhkVLVIEKEQEVG-G 41
                                      7******************99********9998.4 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.048
                                       T-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEE.EEE--GGG CS
                               DAO 160 Gveilegtevtgleeedgkvwgverttp.gendaada.vVnaaGaw 203
                                        v+i++g+ev  +   ++ v gv  +t+ g++  ++  vV+ +G  
  gi|298675532|ref|YP_003727282.1| 280 NVDIITGEEVNTIFTGNNVVEGV--ETAnGNV--YRSdVVVYTGMA 321
                                       599*********96666789999..6666887..344577777744 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1   4.1e-08   4.3e-05       3      36 ..       7      40 ..       5      44 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 4.1e-08
                                      EEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like  3 viviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                       i++G+G +Gl+ A+ ++k+g++Vl++ek++++g
  gi|298675532|ref|YP_003727282.1|  7 SIIVGAGISGLLSALVLSKHGHKVLVIEKEQEVG 40
                                      69*****************************998 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.2   4.7e-08   4.9e-05       4      35 ..       7      38 ..       4      43 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 4.7e-08
                                      EEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                     FAD_binding_3  4 VlIVGaGpaGlmlallLseaGvrvvlvekrst 35
                                       +IVGaG +Gl++al+Ls++G +v+++ek ++
  gi|298675532|ref|YP_003727282.1|  7 SIIVGAGISGLLSALVLSKHGHKVLVIEKEQE 38
                                      68***************************875 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.1   0.00012      0.12       3      35 ..       8      39 ..       6      54 .. 0.83
   2 !    7.7   0.0    0.0015       1.6     110     149 ..     280     319 ..     266     357 .. 0.77
   3 ?    0.9   0.0      0.18   1.9e+02     133     163 ..     432     461 ..     396     486 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                                      EEE-SSHHHHHHHHHHHHTT--EEEEES-GGGT CS
                              GIDA  3 iViGgGhAGceAAlaaarlGakvlLithkldti 35
                                      i++G+G +G+  Al +++ G+kvl i  k +++
  gi|298675532|ref|YP_003727282.1|  8 IIVGAGISGLLSALVLSKHGHKVLVIE-KEQEV 39
                                      89*********************9994.44443 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0015
                                       TEEEEE.S-EEEEEECTTEEEEEEETTS-EEEECEEEE--T CS
                              GIDA 110 nleiie.eeveeliveekkvkgvvtedgetikakavviatG 149
                                       n++ii+ eev+ + + ++ v+gv t++g+++++++vv + G
  gi|298675532|ref|YP_003727282.1| 280 NVDIITgEEVNTIFTGNNVVEGVETANGNVYRSDVVVYT-G 319
                                       77777625799999999***************9988875.4 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.18
                                       ETTS-EEEECEEEE--TT-BT-EEEETTEEE CS
                              GIDA 133 tedgetikakavviatGtflkgkihigekel 163
                                       ++++ ti +ka + +tG f + k+ i++  +
  gi|298675532|ref|YP_003727282.1| 432 KHEQITIPEKAAITTTGNFADIKTPIKNL-Y 461
                                       45566788889999999998888877543.3 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.9e-06     0.002       3      40 ..       7      43 ..       5     120 .. 0.86
   2 ?    3.2   0.1     0.042        44     197     233 ..     280     317 ..     268     324 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.9e-06
                                      EEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  3 vvviGgGpAGlaaaltlaqagakvtlvelegtclnggc 40
                                       +++G+G+ Gl  al l+++g+kv+++e +++ ++g c
  gi|298675532|ref|YP_003727282.1|  7 SIIVGAGISGLLSALVLSKHGHKVLVIE-KEQEVGGNC 43
                                      68*************************5.333444444 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.042
                                       TEEEEESCEEEEEEETTEEEE.EEETTSCEEEESEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 197 Gvevklgtsvkeidgngekle.vvledgeeidadlvvv 233
                                       +v++ +g++v++i   ++ +e v++ +g+++  d vv+
  gi|298675532|ref|YP_003727282.1| 280 NVDIITGEEVNTIFTGNNVVEgVETANGNVYRSDVVVY 317
                                       79********998666666999***********99886 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   2.8e-07    0.0003       3      39 ..       8      44 ..       7      62 .. 0.93
   2 ?   -3.5   0.0       4.6   4.8e+03      90     137 ..     267     313 ..     261     316 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.8e-07
                      FAD_oxidored  3 vVvGGgpaGvaAAiaAaraGakvlLveergvlGGllt 39
                                      ++vG+g++G+  A+   ++G kvl++e+++ +GG+  
  gi|298675532|ref|YP_003727282.1|  8 IIVGAGISGLLSALVLSKHGHKVLVIEKEQEVGGNCN 44
                                      79********************************975 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.6
                      FAD_oxidored  90 kavleeml..aeagvtvllntrlvevekegkriesvtveskegrktirAk 137
                                       k++l+ +l    ++v++++++++  + + ++ +e+v++++   + ++r++
  gi|298675532|ref|YP_003727282.1| 267 KSILNSVLysLPDNVDIITGEEVNTIFTGNNVVEGVETAN---GNVYRSD 313
                                       6677777766557999999999999998777899999976...5555555 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   2.3e-06    0.0025       3      36 ..       8      41 ..       6      47 .. 0.90
   2 ?    1.8   0.1      0.34   3.6e+02      54      79 ..     280     305 ..     268     307 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.3e-06
                                      EEECSSHHHHHHHHHHHHTTSEEEEEESSSSSST CS
                         Pyr_redox  3 vvvGgGyiglElAgalaelgkkVtvversdkllr 36
                                      ++vG+G +gl  A +l+++g+kV v+e + ++  
  gi|298675532|ref|YP_003727282.1|  8 IIVGAGISGLLSALVLSKHGHKVLVIEKEQEVGG 41
                                      79**************************999875 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.34
                                       TEEEECSEEEEEEEEETTSEEEEEEE CS
                         Pyr_redox  54 gievllntkveeiegsedgvesvklk 79 
                                       +++++++++v+ i + ++ ve+v+++
  gi|298675532|ref|YP_003727282.1| 280 NVDIITGEEVNTIFTGNNVVEGVETA 305
                                       79***********9666659999876 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   4.4e-07   0.00047      21      56 ..       8      42 ..       3      46 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.4e-07
                                      EEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TT CS
                              Thi4 21 vivGaGssGLtaayylakkpdlkvailersvspGGG 56
                                      +ivGaG sGL +a +l+k+ + kv+++e++  +GG 
  gi|298675532|ref|YP_003727282.1|  8 IIVGAGISGLLSALVLSKH-GHKVLVIEKEQEVGGN 42
                                      9******************.**********999995 PP

>> GDI  GDP dissociation inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.2   4.6e-07   0.00048       1      47 [.       1      47 [.       1      52 [. 0.91
   2 ?   -3.8   0.1       3.2   3.4e+03     255     281 ..     289     316 ..     284     317 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 4.6e-07
                                      XXXEECEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSSCGGG-EE- CS
                               GDI  1 mdeeydvivlGtGlkecilsGllsvdgkkvlhldrndyyGgesaslt 47
                                      md +y+ i++G+G+   + + +ls +g+kvl++++++  Gg++ s +
  gi|298675532|ref|YP_003727282.1|  1 MDRDYNSIIVGAGISGLLSALVLSKHGHKVLVIEKEQEVGGNCNSYE 47
                                      99************988777789******************999865 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 3.2
                                       CEEEE-TTS-EEEEEE.TTEEEEECEEE CS
                               GDI 255 devvldedgkvvGvks.eeevakakkvi 281
                                       ++ ++  +++v Gv++ +++v +++ v+
  gi|298675532|ref|YP_003727282.1| 289 VNTIFTGNNVVEGVETaNGNVYRSDVVV 316
                                       5678889999****98677888887765 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.2     5e-06    0.0053       1      38 [.       8      45 ..       8      58 .. 0.87
   2 ?    0.6   0.0      0.25   2.6e+02     226     268 ..     280     321 ..     262     338 .. 0.60
   3 ?   -2.2   0.0       1.9     2e+03     283     305 .]     440     464 ..     403     464 .. 0.58

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5e-06
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg.nignsiyr 38
                                      iI+GaG  Gl +a+ l k+g  ++l++Ek+ ++g     
  gi|298675532|ref|YP_003727282.1|  8 IIVGAGISGLLSALVLSKHGH-KVLVIEKEqEVGGNCNS 45
                                      8*******************9.7******9666665555 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.25
                       Pyr_redox_3 226 kikvlfnaevkeikekeeey.kvktedgkkvevkddvvlatGyk 268
                                       ++++++ +ev+ i + ++ +  v+t++g+  +  +dvv+ tG  
  gi|298675532|ref|YP_003727282.1| 280 NVDIITGEEVNTIFTGNNVVeGVETANGNVYR--SDVVVYTGMA 321
                                       45566666666665444443235555555443..3556666655 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.9
                       Pyr_redox_3 283 edgrpvlte..eteetnvpglflaG 305
                                       e+  ++ t   ++  t +++l+laG
  gi|298675532|ref|YP_003727282.1| 440 EKAAITTTGnfADIKTPIKNLYLAG 464
                                       3333333221256667777777776 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.2   8.2e-05     0.086       3      35 ..       8      37 ..       6      40 .. 0.94
   2 ?    1.5   0.0       0.1   1.1e+02     163     204 ..     275     316 ..     243     334 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.2e-05
                                      EEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SS CS
                    Trp_halogenase  3 vivGGGtaGwlaAaalakalkgklevtlvesee 35
                                      +ivG+G++G l+A +l+k++   ++v+++e+e+
  gi|298675532|ref|YP_003727282.1|  8 IIVGAGISGLLSALVLSKHG---HKVLVIEKEQ 37
                                      79******************...89*****996 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.1
                                       HHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEE CS
                    Trp_halogenase 163 vaearGvtrvegkvvevqldedgrveslrledgreveadlfi 204
                                       ++  ++v+++ g+ v++    ++ ve++++++g+++  d ++
  gi|298675532|ref|YP_003727282.1| 275 YSLPDNVDIITGEEVNTIFTGNNVVEGVETANGNVYRSDVVV 316
                                       466789*******************************99988 PP

>> DUF1202  Protein of unknown function (DUF1202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00015      0.16     134     186 ..     403     455 ..     397     471 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                           DUF1202 134 dfnyrfsqleaalraqkasipalekelkaldkkivvakkeadaywgkdadgkq 186
                                       ++    s++e a+++  ++ip++e+ ++    +i++ +k+a +  g+ ad k 
  gi|298675532|ref|YP_003727282.1| 403 EYSDTKSNIENAYKTIYNAIPGIENYIEMKHEQITIPEKAAITTTGNFADIKT 455
                                       5666779**********************************999999888775 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00023      0.25       5      34 ..       9      38 ..       6      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00023
                                      EE--STTHHHHHHHHHHCTSEEEEE-S-HH CS
                    UDPG_MGDP_dh_N  5 viGlGYvGlvtaavlaeighevigvDidee 34
                                      ++G+G  Gl +a+vl+++gh+v+++ +++e
  gi|298675532|ref|YP_003727282.1|  9 IVGAGISGLLSALVLSKHGHKVLVIEKEQE 38
                                      89***********************99886 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1   0.00091      0.96       2      39 ..       9      41 ..       8      67 .. 0.81
   2 ?   -0.4   0.0      0.98     1e+03     102     151 ..     268     317 ..     266     319 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00091
                     NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdpsep.gag 39
                                      ivGaG++Gl+ +  L ++      +++ ++++++  g g
  gi|298675532|ref|YP_003727282.1|  9 IVGAGISGLLSALVLSKH-----GHKVLVIEKEQEvG-G 41
                                      9********999999888.....59999999965525.4 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.98
                     NAD_binding_9 102 dlfeellarlpegvtvevhra.evvdleeradgq.avlladgaslaadaVvL 151
                                       ++++++l +lp++  v+++++ ev  + + ++ +  v +a+g+ ++ d Vv 
  gi|298675532|ref|YP_003727282.1| 268 SILNSVLYSLPDN--VDIITGeEVNTIFTGNNVVeGVETANGNVYRSDVVVY 317
                                       5667777777775..5555551555555555555569999******999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.70u 0.34s 00:00:01.04 Elapsed: 00:00:00.60
# Mc/sec: 2499.36
//
Query:       gi|298675533|ref|YP_003727283.1|  [L=287]
Description: shikimate kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-11   44.7   2.6    3.1e-11   43.4   2.6    1.8  2  GHMP_kinases_N  GHMP kinases N terminal domain
     0.0043   17.4   0.0      0.012   16.0   0.0    1.7  2  GHMP_kinases_C  GHMP kinases C terminal


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.82   7.4e+03      21      42 ..      16      40 ..      13      48 .. 0.62
   2 !   43.4   2.6   3.4e-15   3.1e-11       2      66 .]      80     148 ..      79     148 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.82
                                      HHHHHHHHHHHTTEHHHH...HHHH CS
                    GHMP_kinases_N 21 avalvaAllallglslee...akla 42
                                      + a+++   +++g++l++   ++l+
  gi|298675533|ref|YP_003727283.1| 16 INAIATLKGSAFGVDLKTfvdVELS 40
                                      5566666666777777555555554 PP

  == domain 2  score: 43.4 bits;  conditional E-value: 3.4e-15
                                       EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHH.HH..HHHHHHHHHHHHHHHHHSHHH.HHHHHSS CS
                    GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglsl.ee..aklaleaerlaqggngsggDv.aasvyGg 66 
                                       +++kseiP+++GL SS+A+a a+v+A l++ g ++ ++  ++ +++a   a++++++ +D+ +as++Gg
  gi|298675533|ref|YP_003727283.1|  80 VSTKSEIPLASGLKSSSAAANATVLATLDAIGERMdSLdaVRTGVQAAVDAGVTVTGAFDDaCASFFGG 148
                                       789****************************999644467*********************77788876 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.3   1.2e+04      38      56 ..     122     137 ..     108     139 .. 0.61
   2 !   16.0   0.0   1.3e-06     0.012      15      79 ..     209     265 ..     203     270 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.3
                    GHMP_kinases_C  38 ellealselGalgaklsGa 56 
                                       + ++a+ ++G   + ++Ga
  gi|298675533|ref|YP_003727283.1| 122 TGVQAAVDAG---VTVTGA 137
                                       4455555566...666666 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.3e-06
                    GHMP_kinases_C  15 ellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvaral 79 
                                       ++++l+    l  ++g l    e + +al e+G+ g++lsG+  Gp++ al+ +k +a++++ ++
  gi|298675533|ref|YP_003727283.1| 209 RAMTLNGF--L--YCGALGFDTELMMRAL-EVGVEGVSLSGT--GPAFTALV-EKGKANELKKSW 265
                                       55555555..5..6666666666666665.************..********.999999999888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1773.17
//
Query:       gi|298675534|ref|YP_003727284.1|  [L=180]
Description: hypothetical protein Metev_1648 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.33s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1122.78
//
Query:       gi|298675535|ref|YP_003727285.1|  [L=265]
Description: hypothetical protein Metev_1649 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-36  126.3   0.0    1.4e-36  126.0   0.0    1.1  1  DUF1638   Protein of unknown function (DUF1638)


Domain annotation for each model (and alignments):
>> DUF1638  Protein of unknown function (DUF1638)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.0   0.0     8e-41   1.4e-36       2     160 ..      77     251 ..      76     252 .. 0.96

  Alignments for each domain:
  == domain 1  score: 126.0 bits;  conditional E-value: 8e-41
                           DUF1638   2 leaglHnrpeeLrealqeeidrakadydqIllgYGlCggalagl....rsdecpveilkg......ddCislllgse 68 
                                       le +l ++pe+L++ +++ei+ +++++d++l++YGlCg+ l ++    +   c v ilk+      ddCi++ lgs+
  gi|298675535|ref|YP_003727285.1|  77 LEFALDASPEKLKNGVYREIETMSEYVDGVLIFYGLCGNVLGQVesdfSDYPCYVGILKDekgeimDDCIAASLGSR 153
                                       899*****************************************8888888999*********************** PP

                           DUF1638  69 eayaeelkdekg..tffltpgwvkewdrlv.lekygeelarmifgk...llkgYkrlvyidtgltddpeleeraeef 139
                                       e y ++ + ++g  ++fltp+ +k w++++   ++ ++  +  ++k    ++gYk+++++dtgl +d ++e+++ ef
  gi|298675535|ref|YP_003727285.1| 154 ETYLDAIMGCRGegIYFLTPMQAKYWRDMLkIAGITPDPDNIEMTKyvfDYSGYKKVAKVDTGLDYDRDFEDKVSEF 230
                                       *******9999999***************9888888999999999999***************************** PP

                           DUF1638 140 aarlglelevipgglgllekl 160
                                        + ++l++ +++ +lgl+ek+
  gi|298675535|ref|YP_003727285.1| 231 SRLFELDVVEMNADLGLIEKC 251
                                       *******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1608.19
//
Query:       gi|298675536|ref|YP_003727286.1|  [L=645]
Description: hydantoinase/oxoprolinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-31  109.9   7.3    5.7e-29  101.1   2.5    3.8  3  Hydant_A_N      Hydantoinase/oxoprolinase N-terminal region
    1.6e-31  109.7   0.8    6.9e-31  107.6   0.0    2.3  2  Hydantoinase_A  Hydantoinase/oxoprolinase
    1.2e-05   24.1   0.9      0.038   12.6   0.1    2.5  2  MutL            MutL protein
     0.0046   16.2   0.2      0.012   14.8   0.0    1.7  2  StbA            StbA protein
     0.0084   15.6   0.1        3.2    7.2   0.1    2.4  2  BcrAD_BadFG     BadF/BadG/BcrA/BcrD ATPase family
  ------ inclusion threshold ------
       0.14   12.6   0.7        2.8    8.4   0.1    2.8  3  FtsA            Cell division protein FtsA


Domain annotation for each model (and alignments):
>> Hydant_A_N  Hydantoinase/oxoprolinase N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.1   2.5   1.9e-32   5.7e-29       2     177 ..       5     159 ..       4     160 .. 0.92
   2 !    6.8   0.1    0.0016       4.8       3      19 ..     258     274 ..     257     304 .. 0.76
   3 ?   -1.5   0.0       0.6   1.8e+03     108     143 ..     455     490 ..     348     493 .. 0.58

  Alignments for each domain:
  == domain 1  score: 101.1 bits;  conditional E-value: 1.9e-32
                        Hydant_A_N   2 igIDvGGTfTDavaldeke.eevavlKllstpdavaegirealeevleesiprtskidvvrmGTTvatNallerkge 77 
                                       +g+D+GGT+TD v++++++  +v + K+l+t  +  egi+++++ + ++     ++i+ v ++TT+atN++le++g 
  gi|298675536|ref|YP_003727286.1|   5 LGVDAGGTYTDSVIMRNTDgAVVSANKALTTYPDLLEGIKNSIDGLDQSY---LEDINIVSVSTTLATNTILEKTGY 78 
                                       69**************9987788899*******************96664...57********************** PP

                        Hydant_A_N  78 rvaLittkgfrdlleigrqnrpdlfelrikkplvlyeevvevderveadgevlkpldeeevrealkalkaagvesia 154
                                       +v+Li    +    + g +     +                v+++++ +g ++  ldee+v+e ++++k++ v+++a
  gi|298675536|ref|YP_003727286.1|  79 PVGLILAGNYDVPANAGID----YY--------------TVVQGGHDTKGLEVATLDEEKVEEFVNKVKDK-VSAFA 136
                                       ******9999888877754....43..............369***************************99.***** PP

                        Hydant_A_N 155 vvllhSylnpehElrvaeiarei 177
                                       v++++S++npehElr++ei++++
  gi|298675536|ref|YP_003727286.1| 137 VSSYFSVRNPEHELRIKEIVNKL 159
                                       *******************9975 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0016
                        Hydant_A_N   3 gIDvGGTfTDavaldek 19 
                                        ID GGT TD+ +++++
  gi|298675536|ref|YP_003727286.1| 258 VIDLGGTSTDVSLMENG 274
                                       69*********999854 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.6
                        Hydant_A_N 108 kplvlyeevvevderveadgevlkpldeeevrealk 143
                                       +  +  ++ v+++  +++   vlk +d+ee+ ++l+
  gi|298675536|ref|YP_003727286.1| 455 ELCNHVKNEVTLNMSLNLMSYVLKGVDKEEIDKILR 490
                                       333344445555555555577788888888877775 PP

>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       0.2   5.9e+02      82     106 ..       5      29 ..       2      81 .. 0.83
   2 !  107.6   0.0   2.3e-34   6.9e-31       1     145 [.     179     320 ..     179     428 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.2
                    Hydantoinase_A  82 ItfDmGGTstDvslikdgevevsle 106
                                       +++D GGT tD   +++   +v+++
  gi|298675536|ref|YP_003727286.1|   5 LGVDAGGTYTDSVIMRNTDGAVVSA 29 
                                       57999*****988888766655554 PP

  == domain 2  score: 107.6 bits;  conditional E-value: 2.3e-34
                    Hydantoinase_A   1 rtetavvnAylspilreylesvekslekrgakarlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaatsklag 77 
                                       r+ ta++nA l pi ++++ s+ ++ + rg+ arl+++++dG++v ++ea +kp+e i SGPaa++vgaa+   l++
  gi|298675536|ref|YP_003727286.1| 179 RGITAYLNAQLIPIANRFIHSIISETDRRGIDARLLMLKCDGSVVGINEALEKPIESIFSGPAASLVGAAY---LEN 252
                                       789********************************************************************...999 PP

                    Hydantoinase_A  78 ekkvItfDmGGTstDvslikdgevevsletei.agvkvrlpaldirtvgagGgsilvvdeggklrvgpe 145
                                        +++ ++D+GGTstDvsl+++g +e +    + +g +++++al+++t ++gG+s ++v + +k+++gp+
  gi|298675536|ref|YP_003727286.1| 253 LDSCAVIDLGGTSTDVSLMENGLPELTETGAVvGGWQTKVKALRMETSAMGGDSHVWVRN-QKVNIGPR 320
                                       999*********************988776655***********************6655.99****98 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   1.3e-05     0.038       2      56 ..       5      55 ..       4      90 .. 0.86
   2 !    9.7   0.1   9.5e-05      0.28     222     273 ..     234     280 ..     221     292 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.3e-05
                              MutL  2 lviDiGSttTkvtlvdlekvderllgqaeapTtveeedvleGleealeeleeklg 56
                                      l +D G t+T  +++++ +  + ++   +a+Tt    d+leG++++++ l ++  
  gi|298675536|ref|YP_003727286.1|  5 LGVDAGGTYTDSVIMRNTD--GAVVSANKALTTYP--DLLEGIKNSIDGLDQSYL 55
                                      569**************55..*************5..***********9999854 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 9.5e-05
                              MutL 222 aeimpTPaAvlkavellaeeeekglgdllvvDvGGaTTdvhsvaegspekek 273
                                       + i   PaA l ++  l++     l+ + v+D+GG++Tdv  + +g pe ++
  gi|298675536|ref|YP_003727286.1| 234 ESIFSGPAASLVGAAYLEN-----LDSCAVIDLGGTSTDVSLMENGLPELTE 280
                                       5678889999999999998.....67899*************9999888665 PP

>> StbA  StbA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       2.1   6.4e+03     253     269 ..     119     135 ..     102     153 .. 0.58
   2 !   14.8   0.0   4.1e-06     0.012     150     190 ..     240     281 ..     233     289 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 2.1
                              StbA 253 ekvkkLkerviravsef 269
                                       ekv++  ++v+++vs f
  gi|298675536|ref|YP_003727286.1| 119 EKVEEFVNKVKDKVSAF 135
                                       34444444444444444 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 4.1e-06
                              StbA 150 Pagfealke.ldeleslLiiDlGGttLDvakvrgklegiskv 190
                                       Pa+  + +  l++l+s  +iDlGGt  Dv+ ++  l +++++
  gi|298675536|ref|YP_003727286.1| 240 PAASLVGAAyLENLDSCAVIDLGGTSTDVSLMENGLPELTET 281
                                       7777666666*********************99999888876 PP

>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.1    0.0011       3.2       1      28 [.       5      33 ..       5     159 .. 0.75
   2 !    6.4   0.0    0.0019       5.6       3      33 ..     259     296 ..     259     453 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0011
                                      EEEEE-SSEEEEEEEET.TTEEEEEEEE- CS
                       BcrAD_BadFG  1 vGiDgGsTttkavlmde.kgevlgrgitn 28
                                      +G+D G+T t  v+m++ +g v+   ++ 
  gi|298675536|ref|YP_003727286.1|  5 LGVDAGGTYTDSVIMRNtDGAVVSANKAL 33
                                      7**************85145566655554 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0019
                                       EEE-SSEEEEEEEE.......TTTEEEEEEEE--TTS- CS
                       BcrAD_BadFG   3 iDgGsTttkavlmd.......ekgevlgrgitnsanle 33 
                                       iD+G+T+t + lm+       e g v+g ++t+ + l+
  gi|298675536|ref|YP_003727286.1| 259 IDLGGTSTDVSLMEnglpeltETGAVVGGWQTKVKALR 296
                                       9*************999999999999999999875544 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.18   5.4e+02       2      18 ..       6      22 ..       5      68 .. 0.84
   2 ?   -0.9   0.0      0.73   2.2e+03      70      82 ..     198     257 ..     109     258 .. 0.63
   3 ?    8.4   0.1   0.00094       2.8       1      24 [.     257     280 ..     257     295 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.18
                                      EEEE-SSSEEEEEEETT CS
                                      xxxxxxxxxxxxxxxxx RF
                              FtsA  2 lvDiGagktdvavaedg 18
                                      +vD G++ td +++++ 
  gi|298675536|ref|YP_003727286.1|  6 GVDAGGTYTDSVIMRNT 22
                                      79************984 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.73
                                       H...............................................GGGGSTTHHHHH CS
                                       x...............................................xxxxxxxxxxxx RF
                              FtsA  70 s...............................................ggsalpnleela 82 
                                       +                                               g+++l+nl+ +a
  gi|298675536|ref|YP_003727286.1| 198 HsiisetdrrgidarllmlkcdgsvvginealekpiesifsgpaaslvGAAYLENLDSCA 257
                                       033333333344444444444444444445555555566677777777888888888886 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.00094
                                       EEEEE-SSSEEEEEEETTEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                              FtsA   1 alvDiGagktdvavaedgalvhlr 24 
                                       a++D+G+++tdv+++e+g +  ++
  gi|298675536|ref|YP_003727286.1| 257 AVIDLGGTSTDVSLMENGLPELTE 280
                                       79***************9765554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (645 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.79u 0.32s 00:00:01.11 Elapsed: 00:00:00.52
# Mc/sec: 3704.13
//
Query:       gi|298675537|ref|YP_003727287.1|  [L=263]
Description: hypothetical protein Metev_1651 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-40  139.0   0.0    1.7e-40  138.7   0.0    1.1  1  DUF1638   Protein of unknown function (DUF1638)
  ------ inclusion threshold ------
       0.07   13.2   0.9       0.39   10.8   0.2    2.4  2  DUF4839   Domain of unknown function (DUF4839)


Domain annotation for each model (and alignments):
>> DUF1638  Protein of unknown function (DUF1638)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.7   0.0   1.9e-44   1.7e-40       3     160 ..      80     252 ..      78     253 .. 0.94

  Alignments for each domain:
  == domain 1  score: 138.7 bits;  conditional E-value: 1.9e-44
                           DUF1638   3 eaglHnrpeeLrealqeeidrakadydqIllgYGlCggalagl....rsdecpveilkg......ddCislllgsee 69 
                                       e glH +p++L+++++e++d+++   d+Il++YGlCg+ l ++    + ++c v+ilk+      ddCi+++lg+++
  gi|298675537|ref|YP_003727287.1|  80 EFGLHVNPSDLKNEVYEKVDEMS-FLDGILVFYGLCGNVLGNIeedfKDKTCSVRILKEnngevvDDCIGAVLGGRN 155
                                       789*******************8.***************************************************** PP

                           DUF1638  70 ayaeelkdekg..tffltpgwvkewdrlv.lekygeelarmifgk...llkgYkrlvyidtgltddpeleeraeefa 140
                                       +y ++l + +g  tffltp+w+++w++++   ++  +  ++ + k    ++gYkr+ +i+tgl++++++++r++efa
  gi|298675537|ref|YP_003727287.1| 156 EYFKALTSSRGvgTFFLTPMWASNWKEMIkDAGFTSDPYDHEMAKfafDYAGYKRAGKIETGLNYEKDFQDRVDEFA 232
                                       ********999*****************9866666666666666666799*************************** PP

                           DUF1638 141 arlglelevipgglgllekl 160
                                       + +++++   +g+l+l+e++
  gi|298675537|ref|YP_003727287.1| 233 EAFNFDIVSFHGDLRLIENC 252
                                       ******************98 PP

>> DUF4839  Domain of unknown function (DUF4839)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0     0.096   8.6e+02      12      29 ..     190     207 ..     182     216 .. 0.89
   2 ?   10.8   0.2   4.3e-05      0.39      10      54 ..     218     261 ..     209     263 .] 0.87

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.096
                           DUF4839  12 vkdeadeavadFAkkykG 29 
                                       + d+ d+ +a+FA +y+G
  gi|298675537|ref|YP_003727287.1| 190 TSDPYDHEMAKFAFDYAG 207
                                       56999***********99 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 4.3e-05
                           DUF4839  10 LevkdeadeavadFAkkykGrtieFdGsiaalvnhgdkktrydil 54 
                                       L+ + ++++ v +FA+ ++ + + F G +  + n   +kt+ di+
  gi|298675537|ref|YP_003727287.1| 218 LNYEKDFQDRVDEFAEAFNFDIVSFHGDLRLIENC-YEKTKSDIM 261
                                       677888999********************999998.568999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1661.18
//
Query:       gi|298675538|ref|YP_003727288.1|  [L=272]
Description: sulfatase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.6e-15   55.3   0.3    1.7e-11   44.0   0.0    2.7  3  Sulfatase        Sulfatase
    1.6e-13   51.0   0.8    3.7e-06   26.8   0.1    2.1  2  Phosphodiest     Type I phosphodiesterase / nucleotide pyroph
    2.4e-07   30.4   0.3    5.9e-06   25.8   0.3    2.2  2  Metalloenzyme    Metalloenzyme superfamily
     0.0063   16.6   0.7       0.53   10.4   0.7    2.4  1  PglZ             PglZ domain
  ------ inclusion threshold ------
      0.014   14.9   0.2      0.066   12.7   0.0    2.0  2  Elong_Iki1       Elongator subunit Iki1
      0.045   12.7   0.2        2.9    6.7   0.0    2.6  3  Alk_phosphatase  Alkaline phosphatase
      0.053   12.7   0.1       0.16   11.1   0.1    1.8  2  DAP3             Mitochondrial ribosomal death-associated pro


Domain annotation for each model (and alignments):
>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.29   7.5e+02     291     308 ..       4      21 ..       2      22 .. 0.83
   2 !   44.0   0.0   6.8e-15   1.7e-11       2     104 ..      46     148 ..      45     155 .. 0.93
   3 !    7.8   0.1   0.00077         2     209     270 ..     201     258 ..     167     269 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.29
                                       CSEEEGGGHHHHHHHHTT CS
                         Sulfatase 291 eelvshiDlfptildlag 308
                                       ++  s++D++pti + ++
  gi|298675538|ref|YP_003727288.1|   4 DKQCSLVDIAPTISEILN 21 
                                       67789********99876 PP

  == domain 2  score: 44.0 bits;  conditional E-value: 6.8e-15
                                       EEEEEEESSE-TTGSGGGTTTSCSSHHHHHHHHTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTTT... CS
                         Sulfatase   2 nvvliladdlgagdlglyggktattpnldrlaeeglrftnfysaaplcspsraalltgryphnsgvasntevgg... 75 
                                        vvli++d+l   ++ ly++ t  + +++++a++g++++   +a  +++p+ a+++tg yp++++ + + ++++   
  gi|298675538|ref|YP_003727288.1|  46 KVVLIIVDSL---GFALYQHLTKLMSTVKKIADSGMVLKCKSTAD-HTTPAIASIFTGYYPEEHHLYYTDDIYKera 118
                                       69********...7799************************7765.***************************9*** PP

                                       .HHCTTTS-HHHHHHHHTT-EEEEEEES-S CS
                         Sulfatase  76 .gglpqteatLpellkeaGYntaaigkwhl 104
                                        ++ +++  t++e+ +++G +++++  +h 
  gi|298675538|ref|YP_003727288.1| 119 kNESNPKIKTIMEWAHDNGLKSGIVIETHG 148
                                       *********************999887775 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.00077
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSSCCCGHHTTSSSCTTCSSSH CS
                         Sulfatase 209 qlleaylnsveyvDdligrvlaaLeenglldntlvvftSDhgasleesngplrggkganaye 270
                                        ++++ ++ ++y  + i++ ++ +  ++ + ntl+++ +Dh  +   s+++l+  ++   ye
  gi|298675538|ref|YP_003727288.1| 201 AHRSKTWDDIKYSAQRIDEYIEMI-YSNADSNTLFIICGDHPIHS--SQKWLQKANK-IDYE 258
                                       455556666666666666666666.6677***************9..7788877777.5554 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.1   1.4e-09   3.7e-06       1      68 [.      47     112 ..      47     166 .. 0.82
   2 !   23.5   0.1   1.5e-08   3.8e-05     155     238 ..     173     246 ..     125     266 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.4e-09
                                       EEEEEETT-BTTHHHHHGSTSHHHHHHHHHSEEESEEE-SSS-SHHHHHHHHHHSS-HHHHS--SSSE CS
                      Phosphodiest   1 vlvislDGlradlldrlaellpnlaaLakegvsapnlrpvfPtlTfpnhaslvTGlyPgeHGivgNtf 68 
                                       v++i++D+l + l ++l +l++  +++a+ g   + +++++  +T p+ as+ TG yP+eH  ++ + 
  gi|298675538|ref|YP_003727288.1|  47 VVLIIVDSLGFALYQHLTKLMSTVKKIADSGMVLK-CKSTA-DHTTPAIASIFTGYYPEEHHLYYTDD 112
                                       89************99989****************.77776.6888*****************98433 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 1.5e-08
                                       HHHHCHTHSHHHHHCTSSESEEEEEECCCHHHHHHH-.TTSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEE CS
                      Phosphodiest 155 twldaafakvvlekelekpdlllvyleetDtvgHkfG.pdspevedalrrvDkaigdLlealderglsaetniilvS 230
                                       ++++++++k +le    +pd ++v+l+++D++ H+   +d+  ++   +r+D++i+ +++ +d +     t +i+ +
  gi|298675538|ref|YP_003727288.1| 173 KYIAENTKK-ALE---SNPDIVAVHLRSIDRFAHRSKtWDD--IKYSAQRIDEYIEMIYSNADSN-----TLFIICG 238
                                       456666654.444...9*****************9942455..778899***************9.....******* PP

                                       S---EEEH CS
                      Phosphodiest 231 DHGmadvs 238
                                       DH + + +
  gi|298675538|ref|YP_003727288.1| 239 DHPIHSSQ 246
                                       **888774 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.027        69       1      33 [.      45      96 ..      45     131 .. 0.65
   2 !   25.8   0.3   2.3e-09   5.9e-06     118     190 ..     174     245 ..     139     269 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.027
                                      -EEEEEEETTBB----GGGTT.....HHHS-..............-HHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxx.....xxxxx..............xxxxxxx RF
                     Metalloenzyme  1 kkvvlvvlDGlGeapadelna.....ihvAk..............tPtldkL 33
                                      kkvvl+++D+lG a  ++l        ++A+              tP + ++
  gi|298675538|ref|YP_003727288.1| 45 KKVVLIIVDSLGFALYQHLTKlmstvKKIADsgmvlkckstadhtTPAIASI 96
                                      799********98877444433222223333444444444444666666665 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 2.3e-09
                                       HHHHHHHHHH.CC.-SEEEEEE-HHHHHHHTT-HHHHHH.HHHHHHHHHHHHHTTS-TTTEEEEEE-SSB--TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 118 evaekaldailsgkfdlvvvniknaDmvGHtgdleatia.aieaaDeavkeildaieqvdgilvvtADHgnaed 190
                                        +ae++ +a++s+  d+v v++   D  +H+ +    i+   +++De +++i ++ +++  ++++++DH+  ++
  gi|298675538|ref|YP_003727288.1| 174 YIAENTKKALESN-PDIVAVHLRSIDRFAHRSKTWDDIKySAQRIDEYIEMIYSNADSNT-LFIICGDHPIHSS 245
                                       5789999***666.*****************9998888735899***********88777.********86554 PP

>> PglZ  PglZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.7   0.00021      0.53       1      89 [.      45     153 ..      45     242 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00021
                              PglZ   1 ekvfvIisDalryeaweelkqlLnkedr.feaelsavlgvlPslTklgraallpgkkllykeks.aldvlvdeesse 75 
                                       +kv++Ii+D l++   + l +l+++ +      +          T+ + a+++ g  ++ ++   ++d++ +  + e
  gi|298675538|ref|YP_003727288.1|  45 KKVVLIIVDSLGFALYQHLTKLMSTVKKiADSGMVLKCKSTADHTTPAIASIFTGYYPEEHHLYyTDDIYKERAKNE 121
                                       69999999999999999999999986550344454444455556888888888887765543320333333333444 PP

                              PglZ  76 glenrekilekkl..................g 89 
                                          + ++i+e +                    
  gi|298675538|ref|YP_003727288.1| 122 SNPKIKTIMEWAHdnglksgiviethgaeslL 153
                                       44444444443333444444444444444440 PP

>> Elong_Iki1  Elongator subunit Iki1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.6e-05     0.066      70     123 ..      27      76 ..       9     145 .. 0.80
   2 ?   -0.0   0.0      0.19   4.9e+02      30      87 ..     175     230 ..     171     250 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.6e-05
                        Elong_Iki1  70 klkelakeiksalspkssekkkkalviiDsln.plaslikeeslaaflssllssp 123
                                       +  ++ ++i+ +++++++  kk +l+i+Dsl  +l  +++ ++l++ ++++++ +
  gi|298675538|ref|YP_003727288.1|  27 PNGSVLTQITDYAQKNNT--KKVVLIIVDSLGfAL--YQHLTKLMSTVKKIAD-S 76 
                                       556778899998866544..489*********444..7677788888888874.3 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.19
                        Elong_Iki1  30 leelirrakssktkvifvsfetlkkpkgvdvfieaterskklkelakeiksalspkss 87 
                                       ++e  ++a  s+  ++ v  + +++ ++ ++  +    + +++++ + i+  +s+++s
  gi|298675538|ref|YP_003727288.1| 175 IAENTKKALESNPDIVAVHLRSIDRFAHRSKTWDD--IKYSAQRIDEYIEMIYSNADS 230
                                       56777888899999999999999998887777777..444467777777766654433 PP

>> Alk_phosphatase  Alkaline phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.24   6.2e+02     302     330 ..      84     115 ..      63     122 .. 0.70
   2 ?    6.7   0.0    0.0011       2.9      85     108 ..     123     146 ..     114     150 .. 0.85
   3 ?    2.8   0.0     0.018        46     261     308 ..     196     242 ..     178     263 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.24
                                       EEESSEE...SEEEESTTSTT..TTSEECCEE CS
                   Alk_phosphatase 302 vTaDHsh...vfsfggyttrgesvlgleplla 330
                                       +TaDH++   ++ f gy ++ ++ +++  + +
  gi|298675538|ref|YP_003727288.1|  84 STADHTTpaiASIFTGYYPEEHHLYYTDDIYK 115
                                       79***985444567888887666666666555 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0011
                                       T-B---HHHHHHHTT-EEEEEEEE CS
                   Alk_phosphatase  85 gkevksvleaAkkaGkstGlVtTt 108
                                       + ++k+++e+A+++G + G+V  t
  gi|298675538|ref|YP_003727288.1| 123 NPKIKTIMEWAHDNGLKSGIVIET 146
                                       5689****************9766 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.018
                                       CHHHHHHTTTHHHHHH.HHHHHHHHHHHHHHHCHHCTTEEEEEEESSEE CS
                   Alk_phosphatase 261 rIDhaaHendavgals.EvvefdeAvkaalefakkeketlvvvTaDHsh 308
                                       +ID+ aH +++   ++  +  +de ++     a+  ++tl +   DH  
  gi|298675538|ref|YP_003727288.1| 196 SIDRFAHRSKTWDDIKySAQRIDEYIEMIYSNAD--SNTLFIICGDHPI 242
                                       79999******99998346789999999988887..9**********64 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   6.3e-05      0.16     181     251 ..      50     118 ..      28     135 .. 0.73
   2 ?   -1.9   0.0      0.58   1.5e+03      51      97 ..     140     186 ..     127     194 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.3e-05
                                       --B-GGGBHHHHTTHHH..HS--SSS-EEEEE---SS-SS--SS---HHHHHTTTTTGGG-S-E........ CS
                              DAP3 181 kpihahdLtlvkhfldllsgksklknggvvvaLaatsssntpksatlevallqeearpqldpYvkk.ydkrv 251
                                         +++  ++l +h+++l+s+ +k++  g+v+  ++t+   tp +a++ +  + ee+      Y+   y++r 
  gi|298675538|ref|YP_003727288.1|  50 IIVDSLGFALYQHLTKLMSTVKKIADSGMVLKCKSTADHTTPAIASIFTGYYPEEHH---LYYTDDiYKERA 118
                                       35789999**********************999999999999999999999998885...333333444444 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.58
                                       --EEEEES-GGGGTSS-S--EEESTTSSEEE-HHHHHHHHHHHTTSS CS
                              DAP3  51 gwvvlhvpeaedlvngtteyapseseeklyvQpeataalLsrilkaN 97 
                                         +v++ + ae+l+n+   ++  +++ + +  + ++a+  ++ l++N
  gi|298675538|ref|YP_003727288.1| 140 SGIVIETHGAESLLNRIDGIFGVPDSDDIIEYDKYIAENTKKALESN 186
                                       56899999999999999988888877777777777777666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1738.84
//
Query:       gi|298675539|ref|YP_003727289.1|  [L=915]
Description: hypothetical protein Metev_1653 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     4e-185  603.5  54.0      2e-40  137.5   5.1    5.6  6  SdrD_B           SdrD B-like domain
    1.7e-37  127.5  20.4    8.9e-09   35.5   0.9    6.0  5  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    9.6e-24   83.4   0.0    0.00079   19.4   0.0    5.4  5  bMG3             Bacterial alpha-2-macroglobulin MG3 domain
    1.6e-14   54.0  45.3    0.00087   19.6   0.6    7.4  6  SpaA             Prealbumin-like fold domain
      1e-10   41.5  19.2      0.037   14.0   0.3    5.6  5  CarbopepD_reg_2  CarboxypepD_reg-like domain
      1e-09   38.5  23.7      0.021   15.0   0.2    6.0  5  MetallophosN     N terminal of Calcineurin-like phosphoestera
    1.9e-07   31.7   0.2        4.8    7.9   0.0    5.7  5  TTR-52           Transthyretin-like family
      2e-05   24.9  12.6       0.82   10.0   0.1    5.6  5  fn3              Fibronectin type III domain
     0.0019   18.1  12.1       0.41   10.6   0.3    4.1  3  Y_Y_Y            Y_Y_Y domain
  ------ inclusion threshold ------
      0.014   15.7   3.5      0.014   15.7   3.5    3.7  3  DUF11            Domain of unknown function DUF11
      0.015   14.9   0.0        3.9    7.0   0.0    3.1  3  DUF2861          Protein of unknown function (DUF2861)
      0.017   15.1   8.5        5.4    6.9   0.0    4.4  5  EMP24_GP25L      emp24/gp25L/p24 family/GOLD
      0.056   13.4   0.0         18    5.3   0.0    3.4  3  MoaF             MoaF N-terminal domain
      0.097   12.6   2.1        2.8    7.9   0.1    4.4  4  FlgD_ig          FlgD Ig-like domain
       0.11   12.6   0.0        4.2    7.6   0.0    2.3  2  DUF1380          Protein of unknown function (DUF1380)
        0.2   11.4   7.8         13    5.7   0.2    5.2  5  fn3_3            Polysaccharide lyase family 4, domain II


Domain annotation for each model (and alignments):
>> SdrD_B  SdrD B-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.6   5.5   2.8e-42   3.2e-39       1     112 []     186     298 ..     186     298 .. 0.96
   2 !  119.6   2.5   6.3e-38   7.1e-35       2     112 .]     309     420 ..     308     420 .. 0.98
   3 !  117.7   5.7   2.5e-37   2.8e-34       1     112 []     424     533 ..     424     533 .. 0.97
   4 !  137.5   5.1   1.8e-43     2e-40       1     112 []     537     649 ..     537     649 .. 0.96
   5 !  122.9   0.3     6e-39   6.8e-36       2     112 .]     660     770 ..     659     770 .. 0.99
   6 ?   -3.2   0.3       8.9     1e+04      26      50 ..     827     856 ..     805     867 .. 0.54

  Alignments for each domain:
  == domain 1  score: 133.6 bits;  conditional E-value: 2.8e-42
                            SdrD_B   1 asiGdfVweDanknGiqdagekgisgvtVtLkdakgevv.atttTdasGkYkFtnltpGeYkVeftapagytvtakk 76 
                                       asiGd+Vw+D ++nG+q++g++gi gv V+L+d +  ++ +tttT+ +G+Y+Ftnl+pG+Y+V+ftap g+++t ++
  gi|298675539|ref|YP_003727289.1| 186 ASIGDYVWNDLDNNGTQNDGNTGIPGVPVELYDCDAGTIiSTTTTNGTGYYSFTNLEPGNYSVNFTAPPGFEFTIQN 262
                                       68*****************************9877666659************************************ PP

                            SdrD_B  77 aGsddaldSdadpatgltktvtlasgesnetidaGl 112
                                       aG+d++ldSd++++tg+t+++ l++ge+n+tidaGl
  gi|298675539|ref|YP_003727289.1| 263 AGNDNELDSDVNNVTGNTSCIMLDEGENNNTIDAGL 298
                                       ***********************************7 PP

  == domain 2  score: 119.6 bits;  conditional E-value: 6.3e-38
                            SdrD_B   2 siGdfVweDanknGiqdagekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGe.YkVeftapagytvtakka 77 
                                       +iGd+VweD ++nGiq  ge+gi++vtV+L++ +g+ vat  T+++G Y+Ft+l+p e Y+V+f+ p+gy++ta++ 
  gi|298675539|ref|YP_003727289.1| 309 AIGDRVWEDLDGNGIQCCGEPGIDNVTVELYYCNGTPVATNNTNEEGFYQFTDLNPNEqYYVNFSLPSGYEFTAQNV 385
                                       7******************************************************9888****************** PP

                            SdrD_B  78 GsddaldSdadpatgltktvtlasgesnetidaGl 112
                                       G+d+++dSda+ +tg+t++++l sge n t+daG+
  gi|298675539|ref|YP_003727289.1| 386 GTDETIDSDANVTTGNTSCISLISGEYNDTVDAGM 420
                                       *********************************96 PP

  == domain 3  score: 117.7 bits;  conditional E-value: 2.5e-37
                            SdrD_B   1 asiGdfVweDanknGiqdagekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapagytvtakka 77 
                                       asiGd+VweD n++G+q++g++gi++vtV+L++ +g++++tt T++sG+Y+Ft+l+pG+Y+++f+ap+gy++t   +
  gi|298675539|ref|YP_003727289.1| 424 ASIGDYVWEDVNGDGVQNDGDTGIDNVTVNLYNCNGDLLETTKTNESGYYNFTGLAPGDYYINFIAPSGYEFTILGK 500
                                       68*************************************************************************** PP

                            SdrD_B  78 GsddaldSdadpatgltktvtlasgesnetidaGl 112
                                       G++ + dSda+p+ g+t++vtl+sg  n+++daGl
  gi|298675539|ref|YP_003727289.1| 501 GANYE-DSDANPS-GNTTCVTLTSGGINNDVDAGL 533
                                       ****9.****995.5999***************97 PP

  == domain 4  score: 137.5 bits;  conditional E-value: 1.8e-43
                            SdrD_B   1 asiGdfVweDanknGiqdagekgisgvtVtLkd.akgevvatttTdasGkYkFtnltpGeYkVeftapagytvtakk 76 
                                       asiGdfVw+D+n nG+qd+ge+gi+gv V+L++ ++g+++a+ttT+ +G+Y+Ftnl+pGeY+V+f+ap ++++t ++
  gi|298675539|ref|YP_003727289.1| 537 ASIGDFVWNDQNVNGTQDNGEPGITGVLVKLYEcDTGDEIANTTTNGTGYYNFTNLAPGEYYVNFIAPPEFEFTLQD 613
                                       68*****************************762667888************************************* PP

                            SdrD_B  77 aGsddaldSdadpatgltktvtlasgesnetidaGl 112
                                       +G+dd+ldSda+++tg+t+++tl+sge+n tidaGl
  gi|298675539|ref|YP_003727289.1| 614 QGVDDTLDSDANNTTGNTSCITLSSGENNVTIDAGL 649
                                       ***********************************7 PP

  == domain 5  score: 122.9 bits;  conditional E-value: 6e-39
                            SdrD_B   2 siGdfVweDanknGiqdagekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapagytvtakkaG 78 
                                       +iGd+Vw D +k+Giqd+ge+ i++v V+L++ +g+ v++ttTd++G Y Ft+l+p +Y+++f  p+gy++t+ ++G
  gi|298675539|ref|YP_003727289.1| 660 AIGDRVWLDLDKDGIQDEGEPSIENVIVELYYCNGTFVNSTTTDSNGFYLFTDLNPNSYYLNFLLPEGYNFTSPNQG 736
                                       7**************************************************************************** PP

                            SdrD_B  79 sddaldSdadpatgltktvtlasgesnetidaGl 112
                                        d++ dSda+ + g+t++v l+sge n+t+daGl
  gi|298675539|ref|YP_003727289.1| 737 GDSSADSDANISLGNTSCVRLKSGEYNNTLDAGL 770
                                       ********************************97 PP

  == domain 6  score: -3.2 bits;  conditional E-value: 8.9
                            SdrD_B  26 gvtVtL....kdakgevvatttTdas.GkY 50 
                                       gvt++      + +++++ t t +a+ G+Y
  gi|298675539|ref|YP_003727289.1| 827 GVTLNCpkttLNVSESMICTATGNAKlGQY 856
                                       444433222223334444444444333555 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.9   7.9e-12   8.9e-09      10      65 ..     205     261 ..     201     277 .. 0.79
   2 !   21.3   0.3   2.1e-07   0.00024      13      79 ..     330     397 ..     319     402 .. 0.87
   3 !   30.5   0.3   2.9e-10   3.2e-07       8      64 ..     441     497 ..     438     533 .. 0.82
   4 !   28.2   0.4   1.6e-09   1.8e-06      12      57 ..     558     604 ..     549     649 .. 0.82
   5 !   22.3   0.0   1.1e-07   0.00012      10      79 ..     678     747 ..     674     750 .. 0.80

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 7.9e-12
                   CarboxypepD_reg  10 sgapiagatVtvtnadtgt.vastttdadGafrlrglppgtysvtvsapGyatatre 65 
                                        +++i+g+ V++++ d gt  ++ttt+ +G++++++l+pg+ysv ++ap   ++t++
  gi|298675539|ref|YP_003727289.1| 205 GNTGIPGVPVELYDCDAGTiISTTTTNGTGYYSFTNLEPGNYSVNFTAPPGFEFTIQ 261
                                       4679**********88877369999*********************99866666654 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 2.1e-07
                   CarboxypepD_reg  13 piagatVtvtnadtgtvastttdadGafrlrglpp.gtysvtvsapGyatatreevtltagqtttldi 79 
                                       +i ++tV+++  +++ va+  t+++G +++++l p  +y v +s p   ++t ++v  ++  +++ ++
  gi|298675539|ref|YP_003727289.1| 330 GIDNVTVELYYCNGTPVATNNTNEEGFYQFTDLNPnEQYYVNFSLPSGYEFTAQNVGTDETIDSDANV 397
                                       5899******8888889*******************************99999888766655555555 PP

  == domain 3  score: 30.5 bits;  conditional E-value: 2.9e-10
                   CarboxypepD_reg   8 dasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatr 64 
                                       +  +++i ++tV ++n +++   +t+t+++G+++++gl+pg+y + + ap   ++t+
  gi|298675539|ref|YP_003727289.1| 441 NDGDTGIDNVTVNLYNCNGDLLETTKTNESGYYNFTGLAPGDYYINFIAPSGYEFTI 497
                                       556789**********99****************************99988777775 PP

  == domain 4  score: 28.2 bits;  conditional E-value: 1.6e-09
                   CarboxypepD_reg  12 apiagatVtvtnadtg.tvastttdadGafrlrglppgtysvtvsap 57 
                                        +i+g+ V ++  dtg + a+ttt+ +G++++++l+pg+y v + ap
  gi|298675539|ref|YP_003727289.1| 558 PGITGVLVKLYECDTGdEIANTTTNGTGYYNFTNLAPGEYYVNFIAP 604
                                       369********97776267***********************99776 PP

  == domain 5  score: 22.3 bits;  conditional E-value: 1.1e-07
                   CarboxypepD_reg  10 sgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagqtttldi 79 
                                           i+++ V+++  ++++v stttd++G + +++l p +y + +  p    +t+++   +   +++ +i
  gi|298675539|ref|YP_003727289.1| 678 GEPSIENVIVELYYCNGTFVNSTTTDSNGFYLFTDLNPNSYYLNFLLPEGYNFTSPNQGGDSSADSDANI 747
                                       455799*******999999************************998888888887655555555555555 PP

>> bMG3  Bacterial alpha-2-macroglobulin MG3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0     4e-05     0.044      27     102 ..     208     280 ..     202     281 .. 0.83
   2 !   17.1   0.0   3.7e-06    0.0042      28      73 ..     331     371 ..     327     402 .. 0.74
   3 !   19.4   0.0     7e-07   0.00079      28      60 ..     447     479 ..     442     504 .. 0.88
   4 !   10.8   0.0   0.00035      0.39      28      60 ..     560     593 ..     552     628 .. 0.86
   5 !   14.9   0.0   1.8e-05     0.021      28      61 ..     682     715 ..     676     741 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4e-05
                              bMG3  27 PvagaeVrlldkk.gevlaegtTDaqGvarfaallargkegaapylvsArkdedlaflkldwergldlsrfdvpgre 102
                                        ++g+ V+l+d++ g  + ++tT+ +G+++f++l    + g+  + ++A  + ++++ +  ++++ld+   +v+g++
  gi|298675539|ref|YP_003727289.1| 208 GIPGVPVELYDCDaGTIISTTTTNGTGYYSFTNL----EPGNYSVNFTAPPGFEFTIQNAGNDNELDSDVNNVTGNT 280
                                       589********65278889999**********99....556888888888999999999999999999888888865 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 3.7e-06
                              bMG3  28 vagaeVrlldkkgevlaegtTDaqGvarfaallargkegaapylvs 73 
                                       + +++V+l+ ++g  +a+ +T+++G ++f++l     ++++ y+v 
  gi|298675539|ref|YP_003727289.1| 331 IDNVTVELYYCNGTPVATNNTNEEGFYQFTDL-----NPNEQYYVN 371
                                       579***************************99.....445555554 PP

  == domain 3  score: 19.4 bits;  conditional E-value: 7e-07
                              bMG3  28 vagaeVrlldkkgevlaegtTDaqGvarfaall 60 
                                       + +++V+l++++g++l +++T+++G+++f++l+
  gi|298675539|ref|YP_003727289.1| 447 IDNVTVNLYNCNGDLLETTKTNESGYYNFTGLA 479
                                       679**************************9884 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 0.00035
                              bMG3  28 vagaeVrlld.kkgevlaegtTDaqGvarfaall 60 
                                       ++g+ V+l++ ++g+++a++tT+ +G+++f++l+
  gi|298675539|ref|YP_003727289.1| 560 ITGVLVKLYEcDTGDEIANTTTNGTGYYNFTNLA 593
                                       79********5579****************9874 PP

  == domain 5  score: 14.9 bits;  conditional E-value: 1.8e-05
                              bMG3  28 vagaeVrlldkkgevlaegtTDaqGvarfaalla 61 
                                       ++++ V+l+ ++g  + ++tTD++G + f++l++
  gi|298675539|ref|YP_003727289.1| 682 IENVIVELYYCNGTFVNSTTTDSNGFYLFTDLNP 715
                                       799**************************98854 PP

>> SpaA  Prealbumin-like fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.6   7.8e-07   0.00087       1      59 [.     204     249 ..     193     259 .. 0.87
   2 !    9.6   3.5   0.00097       1.1       8      71 ..     255     382 ..     249     394 .. 0.56
   3 !   18.9   4.1   1.2e-06    0.0014      21      68 ..     442     494 ..     375     498 .. 0.58
   4 !   17.7   2.9     3e-06    0.0033      28      58 ..     553     599 ..     488     606 .. 0.63
   5 !   11.8   1.8   0.00021      0.23      28      59 ..     679     721 ..     605     733 .. 0.62
   6 ?   -0.9   0.2         2   2.2e+03      36      51 ..     805     820 ..     764     856 .. 0.57

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 7.8e-07
                                       TCCCB-TS-EEEEEETTTSCCCHCHHTT.TTCCEESEEE-BTTSEEEEEEEESEEEEEE CS
                              SpaA   1 dtgkpLaGaeFtlykvdtttdgkdaleakktgtevttlttdenGkatfegLplGtYllv 59 
                                       d+++ ++G+  +ly++d             +gt + t tt+ +G+ +f++L++G+Y + 
  gi|298675539|ref|YP_003727289.1| 204 DGNTGIPGVPVELYDCD-------------AGTIISTTTTNGTGYYSFTNLEPGNYSVN 249
                                       56889999999999999.............7999**********************986 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00097
                                       S-EEEEEET.....................................TTSCCCHCHHTT................... CS
                              SpaA   8 GaeFtlykv.....................................dtttdgkdalea................... 28 
                                       G eFt++++                                     +                              
  gi|298675539|ref|YP_003727289.1| 255 GFEFTIQNAgndneldsdvnnvtgntscimldegennntidaglyeT----------Vipedkaaigdrvwedldgn 321
                                       66777777744444444444443333333333333333333333320..........02222222233333333334 PP

                                       ...................TTCCEESEEE-BTTSEEEEEEEESEEEEEEEEE-STTEEE-S CS
                              SpaA  29 ..................kktgtevttlttdenGkatfegLplGtYllvEtkaPegYvldk 71 
                                                         + +gt v+t  t+e+G  +f++L++ + + v  + P+gY+ ++
  gi|298675539|ref|YP_003727289.1| 322 giqccgepgidnvtvelyYCNGTPVATNNTNEEGFYQFTDLNPNEQYYVNFSLPSGYEFTA 382
                                       4444444455555555666668888******************955555688999998665 PP

  == domain 3  score: 18.9 bits;  conditional E-value: 1.2e-06
                                       CCHCHHTT.......TTCCEESEEE-BTTSEEEEEEEESEEEEEEEEE-STTEE CS
                              SpaA  21 dgkdalea......kktgtevttlttdenGkatfegLplGtYllvEtkaPegYv 68 
                                       dg++ +++      + +g+  +t +t+e G+ +f+gL++G+Y++    aP+gY+
  gi|298675539|ref|YP_003727289.1| 442 DGDTGIDNvtvnlyNCNGDLLETTKTNESGYYNFTGLAPGDYYIN-FIAPSGYE 494
                                       333333334444444447777**********************98.45888887 PP

  == domain 4  score: 17.7 bits;  conditional E-value: 3e-06
                                       T.................TTCCEESEEE-BTTSEEEEEEEESEEEEE CS
                              SpaA  28 a................kktgtevttlttdenGkatfegLplGtYll 58 
                                       +                 +tg+e+++ tt+ +G+ +f++L++G+Y++
  gi|298675539|ref|YP_003727289.1| 553 QdngepgitgvlvklyeCDTGDEIANTTTNGTGYYNFTNLAPGEYYV 599
                                       12223455557777777679999***********************9 PP

  == domain 5  score: 11.8 bits;  conditional E-value: 0.00021
                                       T............TTCCEESEEE-BTTSEEEEEEEESEEEEEE CS
                              SpaA  28 a...........kktgtevttlttdenGkatfegLplGtYllv 59 
                                       +           + +gt v++ ttd+nG   f++L++ +Y+l 
  gi|298675539|ref|YP_003727289.1| 679 EpsienvivelyYCNGTFVNSTTTDSNGFYLFTDLNPNSYYLN 721
                                       0333335666665667778**********************95 PP

  == domain 6  score: -0.9 bits;  conditional E-value: 2
                                       SEEE-BTTSEEEEEEE CS
                              SpaA  36 ttlttdenGkatfegL 51 
                                       +t+   ++G+++ +++
  gi|298675539|ref|YP_003727289.1| 805 WTYNVTNTGNVNLTDV 820
                                       3333223333333322 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.3   3.3e-05     0.037      11      52 ..     206     252 ..     200     282 .. 0.72
   2 !    8.0   0.4    0.0025       2.8      24      71 ..     344     392 ..     329     404 .. 0.71
   3 !    9.6   0.4   0.00081      0.91      13      50 ..     446     487 ..     434     496 .. 0.71
   4 !   11.1   0.2   0.00027       0.3      26      50 ..     577     601 ..     552     627 .. 0.83
   5 !    8.7   0.1    0.0015       1.7      26      50 ..     698     722 ..     676     730 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.3e-05
                   CarbopepD_reg_2  11 keplpgatVyvkgtkkgtv.....TdenGnFelknlpagkytLvvsy 52 
                                       ++ +pg+ V + +  +gt+     T+  G+++++nl++g+y +++++
  gi|298675539|ref|YP_003727289.1| 206 NTGIPGVPVELYDCDAGTIistttTNGTGYYSFTNLEPGNYSVNFTA 252
                                       556677666665544333222223*****************999875 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0025
                   CarbopepD_reg_2  24 tkkgtv.TdenGnFelknlpa.gkytLvvsy.vGyktqekkvtvskektld 71 
                                       t + t  T+e+G +++++l++ ++y +++s   Gy+   ++v ++  +t+d
  gi|298675539|ref|YP_003727289.1| 344 TPVATNnTNEEGFYQFTDLNPnEQYYVNFSLpSGYEFTAQNVGTD--ETID 392
                                       5444434**********887726799****988999987766654..4444 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00081
                   CarbopepD_reg_2  13 plpgatVyvkgtk....kgtvTdenGnFelknlpagkytLvv 50 
                                        +  +tV + + +      t T+e+G+++++ l +g+y +++
  gi|298675539|ref|YP_003727289.1| 446 GIDNVTVNLYNCNgdllETTKTNESGYYNFTGLAPGDYYINF 487
                                       555666655443323336789*****************9887 PP

  == domain 4  score: 11.1 bits;  conditional E-value: 0.00027
                   CarbopepD_reg_2  26 kgtvTdenGnFelknlpagkytLvv 50 
                                       ++t+T+  G+++++nl +g+y +++
  gi|298675539|ref|YP_003727289.1| 577 ANTTTNGTGYYNFTNLAPGEYYVNF 601
                                       78*******************7665 PP

  == domain 5  score: 8.7 bits;  conditional E-value: 0.0015
                   CarbopepD_reg_2  26 kgtvTdenGnFelknlpagkytLvv 50 
                                       + t+Td+nG + +++l+++ y L++
  gi|298675539|ref|YP_003727289.1| 698 NSTTTDSNGFYLFTDLNPNSYYLNF 722
                                       789******************9987 PP

>> MetallophosN  N terminal of Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.2     0.009        10      19      55 ..     225     262 ..     201     267 .. 0.82
   2 !   15.0   0.2   1.9e-05     0.021      20      56 ..     347     385 ..     322     393 .. 0.73
   3 !   13.7   0.3   5.1e-05     0.057       6      53 ..     443     497 ..     438     516 .. 0.82
   4 ?    5.9   0.2     0.014        16      17      56 ..     574     614 ..     552     628 .. 0.84
   5 !   11.5   0.1   0.00024      0.27      19      53 ..     697     732 ..     676     738 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.009
                      MetallophosN  19 vnvtkTdakGrYeLk.sdkkakfVyistPagyevpted 55 
                                       +++t+T+  G Y+++  +  +  V ++ P g+e+  ++
  gi|298675539|ref|YP_003727289.1| 225 ISTTTTNGTGYYSFTnLEPGNYSVNFTAPPGFEFTIQN 262
                                       5789***********88889999*********998776 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.9e-05
                      MetallophosN  20 nvtkTdakGrYeLk..sdkkakfVyistPagyevptedg 56 
                                        + +T+++G Y+++  + +++ +V +s+P+gye+ +++ 
  gi|298675539|ref|YP_003727289.1| 347 ATNNTNEEGFYQFTdlNPNEQYYVNFSLPSGYEFTAQNV 385
                                       3457*********9766678889**********998876 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 5.1e-05
                      MetallophosN   6 kgkgvagVvVs......DGvnvtkTdakGrYeLk.sdkkakfVyistPagyevpt 53 
                                        ++g+ +V+V+      D  ++tkT+++G Y+++  +    ++ ++ P+gye+  
  gi|298675539|ref|YP_003727289.1| 443 GDTGIDNVTVNlyncngDLLETTKTNESGYYNFTgLAPGDYYINFIAPSGYEFTI 497
                                       567888888876666446689*************999***************976 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.014
                      MetallophosN  17 DGvnvtkTdakGrYeLk.sdkkakfVyistPagyevptedg 56 
                                       D +  t+T+  G Y+++  +    +V ++ P ++e+  +d+
  gi|298675539|ref|YP_003727289.1| 574 DEIANTTTNGTGYYNFTnLAPGEYYVNFIAPPEFEFTLQDQ 614
                                       667789***********8899999***********998887 PP

  == domain 5  score: 11.5 bits;  conditional E-value: 0.00024
                      MetallophosN  19 vnvtkTdakGrYeLk.sdkkakfVyistPagyevpt 53 
                                       vn t+Td++G Y ++  + ++ +  + +P+gy++ +
  gi|298675539|ref|YP_003727289.1| 697 VNSTTTDSNGFYLFTdLNPNSYYLNFLLPEGYNFTS 732
                                       5889***********999**************9876 PP

>> TTR-52  Transthyretin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.12   1.3e+02      11      44 ..     209     239 ..     204     269 .. 0.84
   2 ?    6.0   0.0     0.017        19       2      44 ..     322     360 ..     321     374 .. 0.86
   3 !    7.9   0.0    0.0043       4.8      11      45 ..     447     477 ..     443     490 .. 0.86
   4 ?    5.3   0.0     0.029        33      12      44 ..     561     590 ..     555     604 .. 0.85
   5 ?    0.7   0.0      0.77   8.6e+02      11      41 ..     682     708 ..     677     717 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.12
                                       GSS-EEEEEEHHHHTS--EEEEEE--TTSEEEEE CS
                            TTR-52  11 aknvkVkLwekdtldpddlldetkTdedGnFels 44 
                                       + +v V+L++ d     +++++t+T+ +G+++ +
  gi|298675539|ref|YP_003727289.1| 209 IPGVPVELYDCDA---GTIISTTTTNGTGYYSFT 239
                                       56899*****665...99************9987 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.017
                                       EEEE-TT-GGSS-EEEEEEHHHHTS--EEEEEE--TTSEEEEE CS
                            TTR-52   2 GqLlCggkpaknvkVkLwekdtldpddlldetkTdedGnFels 44 
                                       G   Cg+  + nv+V+L+  +     + +++++T+e+G ++ +
  gi|298675539|ref|YP_003727289.1| 322 GIQCCGEPGIDNVTVELYYCNG----TPVATNNTNEEGFYQFT 360
                                       666899999**********754....789*********99976 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0043
                                       GSS-EEEEEEHHHHTS--EEEEEE--TTSEEEEEE CS
                            TTR-52  11 aknvkVkLwekdtldpddlldetkTdedGnFelsg 45 
                                       + nv+V+L++ +     dll++tkT+e+G+++ +g
  gi|298675539|ref|YP_003727289.1| 447 IDNVTVNLYNCN----GDLLETTKTNESGYYNFTG 477
                                       67999****976....59*************9987 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.029
                                       SS-EEEEEEHHHHTS--EEEEEE--TTSEEEEE CS
                            TTR-52  12 knvkVkLwekdtldpddlldetkTdedGnFels 44 
                                        +v VkL+e dt    d++++t+T+ +G+++ +
  gi|298675539|ref|YP_003727289.1| 561 TGVLVKLYECDT---GDEIANTTTNGTGYYNFT 590
                                       6899*****877...999**********99876 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 0.77
                                       GSS-EEEEEEHHHHTS--EEEEEE--TTSEE CS
                            TTR-52  11 aknvkVkLwekdtldpddlldetkTdedGnF 41 
                                       ++nv V+L+  +     + +++t+Td++G +
  gi|298675539|ref|YP_003727289.1| 682 IENVIVELYYCN----GTFVNSTTTDSNGFY 708
                                       588889999865....47999********87 PP

>> fn3  Fibronectin type III domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.063        71      27      70 ..     206     247 ..     201     255 .. 0.80
   2 !    9.8   0.3    0.0009         1      30      72 ..     331     371 ..     327     379 .. 0.86
   3 ?    4.0   0.1     0.056        63      25      69 ..     442     484 ..     439     492 .. 0.82
   4 !   10.0   0.1   0.00074      0.82      29      69 ..     559     598 ..     551     601 .. 0.88
   5 ?    0.8   0.1      0.55   6.2e+02      29      69 ..     681     719 ..     675     720 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.063
                                       SSTEEEEEEEEEETTSTSTEEEEEECSTSSEEEEESSSTTEEEE CS
                               fn3  27 ggpitgYeveyrekgseeewneftvprtttsvtltgLkpgteYe 70 
                                       +  i g  ve+ +++ +   ++ t ++ t  + +t+L+pg +Y+
  gi|298675539|ref|YP_003727289.1| 206 NTGIPGVPVELYDCDAGT-IISTTTTNGTGYYSFTNLEPG-NYS 247
                                       555666778999999998.99999999999*********9.455 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0009
                                       EEEEEEEEEETTSTSTEEEEEECSTSSEEEEESSSTTEEEEEE CS
                               fn3  30 itgYeveyrekgseeewneftvprtttsvtltgLkpgteYevr 72 
                                       i++ +ve+  ++++  ++  ++++ +  +++t+L+p+++Y v+
  gi|298675539|ref|YP_003727289.1| 331 IDNVTVELYYCNGT--PVATNNTNEEGFYQFTDLNPNEQYYVN 371
                                       67788889999888..58888899999*************986 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.056
                                       SSSSTEEEEEEEEEETTSTSTEEEEEECSTSSEEEEESSSTTEEE CS
                               fn3  25 dgggpitgYeveyrekgseeewneftvprtttsvtltgLkpgteY 69 
                                       dg+  i++ +v + ++++     e t ++ +  +++tgL pg  Y
  gi|298675539|ref|YP_003727289.1| 442 DGDTGIDNVTVNLYNCNGD--LLETTKTNESGYYNFTGLAPGDYY 484
                                       5667789999999999777..577777777889********9777 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.00074
                                       TEEEEEEEEEETTSTSTEEEEEECSTSSEEEEESSSTTEEE CS
                               fn3  29 pitgYeveyrekgseeewneftvprtttsvtltgLkpgteY 69 
                                        itg  v++ e+++++ ++  t ++ t  +++t+L pg+ Y
  gi|298675539|ref|YP_003727289.1| 559 GITGVLVKLYECDTGD-EIANTTTNGTGYYNFTNLAPGEYY 598
                                       58999**********9.88888888888**********988 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 0.55
                                       TEEEEEEEEEETTSTSTEEEEEECSTSSEEEEESSSTTEEE CS
                               fn3  29 pitgYeveyrekgseeewneftvprtttsvtltgLkpgteY 69 
                                       +i++  ve+  ++++   n+ t +++   + +t+L+p++ Y
  gi|298675539|ref|YP_003727289.1| 681 SIENVIVELYYCNGTF-VNSTTTDSNG-FYLFTDLNPNSYY 719
                                       5666677777787775.6666666666.9*********988 PP

>> Y_Y_Y  Y_Y_Y domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.3   0.00037      0.41      24      43 ..     228     248 ..     218     250 .. 0.77
   2 ?    5.0   0.5     0.021        24      21      43 ..     464     485 ..     454     487 .. 0.73
   3 !    7.6   0.7    0.0033       3.7      20      41 ..     575     597 ..     568     600 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00037
                                       ESSTS..EEEEES--SEEEEE CS
                             Y_Y_Y  24 asdysq.easytnlppGdYtl 43 
                                       ++ +++  +s+tnl+pG+Y +
  gi|298675539|ref|YP_003727289.1| 228 TTTNGTgYYSFTNLEPGNYSV 248
                                       33444469***********75 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.021
                                       EEEESSTS.EEEEES--SEEEEE CS
                             Y_Y_Y  21 WveasdysqeasytnlppGdYtl 43 
                                        +++++++  +++t l pGdY +
  gi|298675539|ref|YP_003727289.1| 464 TTKTNESG-YYNFTGLAPGDYYI 485
                                       34445555.9***********65 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0033
                                       SEEEESSTS..EEEEES--SEEE CS
                             Y_Y_Y  20 eWveasdysq.easytnlppGdY 41 
                                       e  +++ +++  +++tnl pG+Y
  gi|298675539|ref|YP_003727289.1| 575 EIANTTTNGTgYYNFTNLAPGEY 597
                                       556777777789*********** PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.2       1.5   1.7e+03      44      68 ..     223     245 ..     196     276 .. 0.68
   2 ?   -1.1   0.2       2.1   2.4e+03      23      53 ..     348     377 ..     340     404 .. 0.59
   3 ?   15.7   3.5   1.3e-05     0.014       9      52 ..     796     846 ..     786     871 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.5
                             DUF11  44 ayvsvsasqgtasaltsvgsLeage 68 
                                       +++s ++++gt+   +s+++Le+g+
  gi|298675539|ref|YP_003727289.1| 223 TIISTTTTNGTG--YYSFTNLEPGN 245
                                       556777776666..33445777775 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.1
                             DUF11  23 tNtgpasangvvvtDtlPaglayvsvsasqg 53 
                                       tN+ +     ++ tD+ P    yv +s  +g
  gi|298675539|ref|YP_003727289.1| 348 TNNTNEEG-FYQFTDLNPNEQYYVNFSLPSG 377
                                       45544444.5666666666666666666633 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 1.3e-05
                             DUF11   9 evrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsas.........q 52 
                                        v+ G +vt t  vtNtg++++++v +tD    g+++   +++         +
  gi|298675539|ref|YP_003727289.1| 796 LVQIGTQVTWTYNVTNTGNVNLTDVNITD--SKGVTLNCPKTTlnvsesmicT 846
                                       6899*************************..6666666655553333333342 PP

>> DUF2861  Protein of unknown function (DUF2861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.05        56     101     149 ..     259     306 ..     246     315 .. 0.86
   2 ?    0.1   0.0      0.45   5.1e+02     102     142 ..     382     422 ..     365     431 .. 0.89
   3 ?    7.0   0.0    0.0035       3.9     102     150 ..     611     658 ..     603     673 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.05
                           DUF2861 101 elskwsedkkllisaekvtseaeyielesrellsklesGlYrLtikadd 149
                                       +++ + +d++l  + ++vt +++ i l + e ++++++GlY+  i  +d
  gi|298675539|ref|YP_003727289.1| 259 TIQNAGNDNELDSDVNNVTGNTSCIMLDEGENNNTIDAGLYETVIP-ED 306
                                       6777889999999**********9999999***********97776.44 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.45
                           DUF2861 102 lskwsedkkllisaekvtseaeyielesrellsklesGlYr 142
                                        + +  d+++  +a+ +t +++ i+l s e + ++++G+Y+
  gi|298675539|ref|YP_003727289.1| 382 AQNVGTDETIDSDANVTTGNTSCISLISGEYNDTVDAGMYQ 422
                                       5667789999999***************************8 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0035
                           DUF2861 102 lskwsedkkllisaekvtseaeyielesrellsklesGlYrLtikadde 150
                                       l+   +d +l  +a+++t +++ i+l+s e + ++++GlY++++  +d+
  gi|298675539|ref|YP_003727289.1| 611 LQDQGVDDTLDSDANNTTGNTSCITLSSGENNVTIDAGLYEIELP-NDK 658
                                       5566788999999******************************98.555 PP

>> EMP24_GP25L  emp24/gp25L/p24 family/GOLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.4         8     9e+03     151     172 ..       3      24 ..       2      25 .. 0.87
   2 ?    6.9   0.0    0.0048       5.4      42      82 ..     215     253 ..     190     283 .. 0.78
   3 ?    4.9   0.0     0.019        22      37      84 ..     448     492 ..     427     522 .. 0.79
   4 ?    4.9   0.0      0.02        22      38      81 ..     562     603 ..     539     635 .. 0.76
   5 ?   -0.6   0.0         1   1.1e+03      20      48 ..     798     827 ..     795     852 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 8
                       EMP24_GP25L 151 tnsrvvwwsilqllvlvlvavl 172
                                       +++r++  +i++l+++ +v++l
  gi|298675539|ref|YP_003727289.1|   3 NYQRIICLAIVFLAMIFAVSGL 24 
                                       678999999*****99999976 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0048
                       EMP24_GP25L  42 svkdpdgngerlvkkkdresegdfsftakesgeykvCfdns 82 
                                       +++d d    +++++  +  +g +sft++e+g+y+v f+ +
  gi|298675539|ref|YP_003727289.1| 215 ELYDCDA--GTIISTTTTNGTGYYSFTNLEPGNYSVNFTAP 253
                                       5554444..5667775676779**************99986 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.019
                       EMP24_GP25L  37 ldvdlsvkdpdgngerlvkkkdresegdfsftakesgeykvCfdnsfs 84 
                                        +v ++++  + ng  l ++k +es+  + ft + +g+y++ f  ++ 
  gi|298675539|ref|YP_003727289.1| 448 DNVTVNLY--NCNGDLLETTKTNESG-YYNFTGLAPGDYYINFIAPSG 492
                                       46777778..6667888888888777.**************9988765 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.02
                       EMP24_GP25L  38 dvdlsvkdpdgngerlvkkkdresegdfsftakesgeykvCfdn 81 
                                       +v +++++ d +g ++ ++  +  +g + ft++ +gey+v f  
  gi|298675539|ref|YP_003727289.1| 562 GVLVKLYECD-TGDEIANTTTN-GTGYYNFTNLAPGEYYVNFIA 603
                                       5666667544.48899999555.556*************98866 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 1
                       EMP24_GP25L  20 k.gtlltgsyqvtdggaaldvdlsvkdpdg 48 
                                       + gt++t +y vt+ g+ +  d++++d++g
  gi|298675539|ref|YP_003727289.1| 798 QiGTQVTWTYNVTNTGNVNLTDVNITDSKG 827
                                       5599*********99966777888987665 PP

>> MoaF  MoaF N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.18     2e+02      55      81 ..     227     253 ..     215     257 .. 0.88
   2 ?    1.0   0.0      0.34   3.8e+02      54      82 ..     463     491 ..     443     497 .. 0.82
   3 ?    5.3   0.0     0.016        18      55      81 ..     578     604 ..     566     611 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.18
                                       TTTEEEEEE-EEEECCTTEEEEEEEET CS
                              MoaF  55 ekeesgeaeyeatevregiYfvdflkk 81 
                                       +++++g+  y  t++++g Y v+f+++
  gi|298675539|ref|YP_003727289.1| 227 TTTTNGTGYYSFTNLEPGNYSVNFTAP 253
                                       56899*******************976 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.34
                                       TTTTEEEEEE-EEEECCTTEEEEEEEETT CS
                              MoaF  54 eekeesgeaeyeatevregiYfvdflkke 82 
                                       e+++++ +  y+ t +++g Y+++f++++
  gi|298675539|ref|YP_003727289.1| 463 ETTKTNESGYYNFTGLAPGDYYINFIAPS 491
                                       56778888899**************9986 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.016
                                       TTTEEEEEE-EEEECCTTEEEEEEEET CS
                              MoaF  55 ekeesgeaeyeatevregiYfvdflkk 81 
                                       +++++g+  y+ t++++g Y+v+f+++
  gi|298675539|ref|YP_003727289.1| 578 NTTTNGTGYYNFTNLAPGEYYVNFIAP 604
                                       57799*******************987 PP

>> FlgD_ig  FlgD Ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       3.9   4.3e+03      63      75 ..     240     252 ..     231     253 .. 0.83
   2 ?   -1.0   0.0       1.5   1.7e+03      21      52 ..     330     359 ..     322     360 .. 0.79
   3 ?    7.9   0.1    0.0025       2.8      18      53 ..     443     476 ..     430     476 .. 0.82
   4 ?   -1.5   0.1       2.1   2.3e+03      19      36 ..     812     829 ..     800     836 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.9
                                       B--SEEEEEEEEE CS
                           FlgD_ig  63 kladGaYtvkvta 75 
                                       +l++G+Y+v+ ta
  gi|298675539|ref|YP_003727289.1| 240 NLEPGNYSVNFTA 252
                                       6899999998776 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.5
                                       SSEEEEEEEE-SS--EEEEEEEEESSSEEEEE CS
                           FlgD_ig  21 aadevtvtikDasGevVrtidlgaqsaGvvsf 52 
                                       ++d+vtv+++  +G+ V t +    ++G ++f
  gi|298675539|ref|YP_003727289.1| 330 GIDNVTVELYYCNGTPVATNNT--NEEGFYQF 359
                                       6899999999999999999865..66666666 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0025
                                       .ESSSEEEEEEEE-SS--EEEEEEEEESSSEEEEEE CS
                           FlgD_ig  18 lpeaadevtvtikDasGevVrtidlgaqsaGvvsft 53 
                                        ++++d+vtv++++ +G++ +t   ++ ++G ++ft
  gi|298675539|ref|YP_003727289.1| 443 GDTGIDNVTVNLYNCNGDLLETT--KTNESGYYNFT 476
                                       67899**************9998..55778888775 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 2.1
                                       ESSSEEEEEEEE-SS--E CS
                           FlgD_ig  19 peaadevtvtikDasGev 36 
                                       + ++  + v+i+D++G +
  gi|298675539|ref|YP_003727289.1| 812 TGNVNLTDVNITDSKGVT 829
                                       4555666899***99965 PP

>> DUF1380  Protein of unknown function (DUF1380)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0037       4.2      55     115 ..     260     320 ..     255     326 .. 0.92
   2 ?    2.3   0.0      0.16   1.8e+02      57     115 ..     613     671 ..     609     680 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0037
                           DUF1380  55 lddipeeqrlesGissaavmelieqvkenrktvtvpadllatllrtaeqalwkrewaarda 115
                                       +++++++++l+s +   +       + e++++ t++a+l +t++     a+ +r w   d 
  gi|298675539|ref|YP_003727289.1| 260 IQNAGNDNELDSDVNNVTGNTSCIMLDEGENNNTIDAGLYETVIPEDKAAIGDRVWEDLDG 320
                                       8899************9999999999**************************999987775 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.16
                           DUF1380  57 dipeeqrlesGissaavmelieqvkenrktvtvpadllatllrtaeqalwkrewaarda 115
                                       d + ++ l+s    ++       +++++++vt++a+l +  l     a+ +r w   d+
  gi|298675539|ref|YP_003727289.1| 613 DQGVDDTLDSDANNTTGNTSCITLSSGENNVTIDAGLYEIELPNDKAAIGDRVWLDLDK 671
                                       56667777777777777777778999*************99999999999999977765 PP

>> fn3_3  Polysaccharide lyase family 4, domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.2     0.012        13      29      53 ..     228     252 ..     226     263 .. 0.81
   2 ?   -2.0   0.0       2.8   3.2e+03      35      61 ..     400     430 ..     392     435 .. 0.67
   3 ?    2.6   0.2       0.1   1.1e+02      29      48 ..     465     484 ..     463     493 .. 0.89
   4 ?    2.3   0.1      0.13   1.4e+02      29      49 ..     579     599 ..     578     613 .. 0.89
   5 ?   -1.9   0.0       2.6   2.9e+03      34      51 ..     748     766 ..     742     780 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.012
                             fn3_3  29 teadssgsftipnVkpGtYrltvYa 53 
                                       t+++ +g+++++n  pG+Y++   a
  gi|298675539|ref|YP_003727289.1| 228 TTTNGTGYYSFTNLEPGNYSVNFTA 252
                                       778888*************987655 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.8
                             fn3_3  35 gsftipnVkpGtYrltv....Yadglfgdyk 61 
                                       g+ ++ +   G+Y+ tv    Y++  +gdy+
  gi|298675539|ref|YP_003727289.1| 400 GNTSCISLISGEYNDTVdagmYQPASIGDYV 430
                                       7777777888888877433348888888887 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.1
                             fn3_3  29 teadssgsftipnVkpGtYr 48 
                                       t++++sg++ ++   pG+Y 
  gi|298675539|ref|YP_003727289.1| 465 TKTNESGYYNFTGLAPGDYY 484
                                       899****************6 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.13
                             fn3_3  29 teadssgsftipnVkpGtYrl 49 
                                       t+++ +g++ ++n  pG+Y +
  gi|298675539|ref|YP_003727289.1| 579 TTTNGTGYYNFTNLAPGEYYV 599
                                       788999*************76 PP

  == domain 5  score: -1.9 bits;  conditional E-value: 2.6
                             fn3_3  34 s.gsftipnVkpGtYrltv 51 
                                       s g+ ++ + k G+Y+ t+
  gi|298675539|ref|YP_003727289.1| 748 SlGNTSCVRLKSGEYNNTL 766
                                       5588899999*****9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (915 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.42
# Mc/sec: 6499.15
//
Query:       gi|298675540|ref|YP_003727290.1|  [L=87]
Description: putative small heat shock protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    0.00014   21.9   0.2    0.00038   20.5   0.2    1.7  1  HSP20       Hsp20/alpha crystallin family
     0.0005   20.4   0.3    0.00056   20.3   0.3    1.0  1  PIH1_CS     PIH1 CS-like domain
      0.001   18.6   0.0      0.002   17.6   0.0    1.5  2  ArsA_HSP20  HSP20-like domain found in ArsA
     0.0012   19.8   0.1     0.0015   19.5   0.1    1.2  1  CS          CS domain


Domain annotation for each model (and alignments):
>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.2   8.5e-08   0.00038       5      43 ..      17      55 ..      14      86 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 8.5e-08
                                      SEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--..-- CS
                             HSP20  5 eeeefevkldvpglkkeelkvkvednrvlvkgeheeeee 43
                                      + e+ ++++++pg+kke++++k+e+++ +v++ ++++e 
  gi|298675540|ref|YP_003727290.1| 17 NSEKLNIEIKLPGVKKENINLKLEEDKFSVNARNKNKEY 55
                                      678999**************************9994443 PP

>> PIH1_CS  PIH1 CS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.3   1.3e-07   0.00056      26      89 ..      14      78 ..       3      85 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.3e-07
                           PIH1_CS 26 kenvpkelaieielPllksikevklrvgerrleleskk..akyfLslkLpYpvdedkveAkFvkkt 89
                                       +n  ++l iei+lP++   ++++l+++e+++++++++  ++y+ + +  Y +d d++  k+++++
  gi|298675540|ref|YP_003727290.1| 14 PDNNSEKLNIEIKLPGV-KKENINLKLEEDKFSVNARNknKEYVGTYSTSYLIDPDRAVTKYSNNK 78
                                      6777899**********.6789********99997776679*********************8765 PP

>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   4.6e-07     0.002       4      36 ..      21      53 ..      18      56 .. 0.90
   2 ?   -2.3   0.0      0.76   3.4e+03      52      61 ..      72      81 ..      65      82 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.6e-07
                        ArsA_HSP20  4 yvlkldLPfvdkeeidlsrsgdeLtIkignfrR 36
                                        + ++LP+v+ke+i+l  ++d  ++++ n ++
  gi|298675540|ref|YP_003727290.1| 21 LNIEIKLPGVKKENINLKLEEDKFSVNARNKNK 53
                                      5689***********************999876 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.76
                        ArsA_HSP20 52 AkfedgvLeI 61
                                       k+ ++ L +
  gi|298675540|ref|YP_003727290.1| 72 TKYSNNKLYV 81
                                      6888988877 PP

>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   3.4e-07    0.0015       9      70 ..      18      79 ..      11      83 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3.4e-07
                                      TTEEEEEEE-TTCTTTTTCEEEEEETTEEEEEE.TS.CEEEEECEBSS-BETTTEEEEEETTEE CS
                                CS  9 ldeVvvtiyvkkvnikkkdvkvefkerslkvki.gk.eklliegeLfgpIdpeesswtieskkv 70
                                      +++++++i +++v  kk++++++++e++++v+  +k ++ +   +    Idp+ +  +  ++k+
  gi|298675540|ref|YP_003727290.1| 18 SEKLNIEIKLPGV--KKENINLKLEEDKFSVNArNKnKEYVGTYSTSYLIDPDRAVTKYSNNKL 79
                                      7899********9..******************9776666655556777888887777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 647.85
//
Query:       gi|298675541|ref|YP_003727291.1|  [L=143]
Description: hypothetical protein Metev_1655 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0083   15.9   0.6      0.015   15.1   0.6    1.5  1  UPF0167      Uncharacterised protein family (UPF0167)
  ------ inclusion threshold ------
      0.035   14.1   0.7      0.087   12.8   0.7    1.7  1  DUF1910      Domain of unknown function (DUF1910)
      0.039   13.9   0.2      0.065   13.2   0.2    1.4  1  Mob_synth_C  Molybdenum Cofactor Synthesis C
       0.24   10.7   0.0       0.28   10.5   0.0    1.1  1  BKACE        beta-keto acid cleavage enzyme


Domain annotation for each model (and alignments):
>> UPF0167  Uncharacterised protein family (UPF0167)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.6   3.4e-06     0.015       8      53 ..      96     140 ..      89     142 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.4e-06
                           UPF0167   8 pdpletgaiek.eeekCqcCgkereliyespfysvedvealCpwCia 53 
                                        + +e + i++ e+e C+ C k+  ++y +  ys    e +C +C+ 
  gi|298675541|ref|YP_003727291.1|  96 KNLVERDIITEmEDEFCEWCRKNYAILYVK--YSDGSKEFICRHCLF 140
                                       68899999*9999***************99..9*9**********85 PP

>> DUF1910  Domain of unknown function (DUF1910)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.7   1.9e-05     0.087       8      66 ..      65     130 ..      49     139 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.9e-05
                           DUF1910   8 eyykesiefdkeriaklkekieelsedeeksiqae........................ikilklsifkykleliia 60 
                                       +++ e ++ + e+ +                                            ++ + ++++++++ ++ +
  gi|298675541|ref|YP_003727291.1|  65 ANFIERLNREMEKEKSS-----------------SsievtnktelrdsknlverdiiteMEDEFCEWCRKNYAILYV 124
                                       44433333332211111.................122222333333333334446666699**************** PP

                           DUF1910  61 kYSlGe 66 
                                       kYS G 
  gi|298675541|ref|YP_003727291.1| 125 KYSDGS 130
                                       ****97 PP

>> Mob_synth_C  Molybdenum Cofactor Synthesis C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   1.4e-05     0.065      19      77 ..      58     117 ..      43     118 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                                       -SSB--HHHHHHHHHHHS-EEEE--SST-SSEEEEETTT-..-EEEEE-TTTS--GGG--E CS
                       Mob_synth_C  19 ekkvvsadeilerieerlalleakketkgpakrykikdgk..geiglIapvsepFCasCnR 77 
                                        + +   ++ +er+++++++++++++  + +++ ++ d k  +e  +I+ ++++FC+ C +
  gi|298675541|ref|YP_003727291.1|  58 SETLSDIANFIERLNREMEKEKSSSSI-EVTNKTELRDSKnlVERDIITEMEDEFCEWCRK 117
                                       566667778888999988888886554.444445554444246789*************76 PP

>> BKACE  beta-keto acid cleavage enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   6.2e-05      0.28     101     165 ..      38     105 ..      16     116 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 6.2e-05
                                       --SEEEEE-S-EEEB-...SGCEE---HHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHHHHTTSS- CS
                             BKACE 101 kpemasldlgslnfgl...kdlvfentpedieellrrmaeagvkpeievfdvghlrnvkrlieeGllk 165
                                       + e + +   s+ f+    ++++++   ++ie+l r+m++++   +iev +  +lr  k+l+e+ +++
  gi|298675541|ref|YP_003727291.1|  38 RKEYIFMPYESVMFQStgfDSETLSDIANFIERLNREMEKEKSSSSIEVTNKTELRDSKNLVERDIIT 105
                                       55666666677777555556888899999***********************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1223  (0.0682135); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1139.56
//
Query:       gi|298675542|ref|YP_003727292.1|  [L=67]
Description: deoxyribonuclease/rho motif-like TRAM protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-14   54.2   0.8    1.1e-14   54.1   0.8    1.0  1  TRAM      TRAM domain


Domain annotation for each model (and alignments):
>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   0.8   6.3e-19   1.1e-14       3      61 ..      11      65 ..       9      66 .. 0.95

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 6.3e-19
                                      XXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEE CS
                              TRAM  3 yvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGel 61
                                        G+ ++V++e  + s+g+gi+r++ g+v+fvp+++   Gd+V++ + kv +++++Ge+
  gi|298675542|ref|YP_003727292.1| 11 RSGEKYDVKIENIA-SKGDGIARIN-GFVIFVPDTSV--GDEVTITVNKVLEKFAFGEV 65
                                      579**********9.**********.********999..******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 476.34
//
Query:       gi|298675543|ref|YP_003727293.1|  [L=355]
Description: CaCA family Na+/Ca+ antiporter [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.9e-56  188.6  40.4    4.5e-30  104.6  16.5    2.0  2  Na_Ca_ex    Sodium/calcium exchanger protein
  ------ inclusion threshold ------
      0.012   15.6   0.1       0.24   11.5   0.0    2.8  2  CrgA        Cell division protein CrgA
        4.6    6.9  18.4       0.97    9.1   3.7    3.1  2  Wzy_C       O-Antigen ligase
        7.4    6.6   7.3         28    4.8   0.2    2.5  2  Flg_bb_rod  Flagella basal body rod protein


Domain annotation for each model (and alignments):
>> Na_Ca_ex  Sodium/calcium exchanger protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.6  16.5   9.9e-34   4.5e-30       3     150 ..       5     144 ..       4     144 .. 0.92
   2 !   90.1  15.8     3e-29   1.3e-25       3     150 ..     206     346 ..     204     347 .. 0.83

  Alignments for each domain:
  == domain 1  score: 104.6 bits;  conditional E-value: 9.9e-34
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex   3 fvlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnl 79 
                                       f++f+++l l++ ++df+v+s ++ia+++g+s+ v+Glt+++ g+slpEl+ss++a l++   ++ign+lGsni+n+
  gi|298675543|ref|YP_003727293.1|   5 FIIFLVGLTLLVKGSDFFVESSSSIAEKFGVSKFVIGLTIVSVGTSLPELASSTTASLNQANGIVIGNILGSNIANI 81 
                                       799************************************************************************** PP

                                       HTHHHHHHHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex  80 llviGlialigslkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvllllYalylvlsl 150
                                       +l++G++ali+s+k + + lk+d  ++l++all++  +l l       +++++ ++l++lllY +y+++++
  gi|298675543|ref|YP_003727293.1|  82 CLIVGCAALISSIKTETQMLKRDGYIMLFAALLFF--ILSLD------NTISRIDSLIFLLLYTAYIIFLI 144
                                       **********9998888889999977666666663..35556......*******************9975 PP

  == domain 2  score: 90.1 bits;  conditional E-value: 3e-29
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex   3 fvlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnl 79 
                                       ++++++s+ +++++a ++++    +a+ l+++++++G+ l+A g+slpEl+++i++a++g++++a+gnv+Gsni n+
  gi|298675543|ref|YP_003727293.1| 206 ILILVISIGAVVIGARYFIEESIFFAQALNVPDTLVGISLVAVGTSLPELMVTISSAKKGYGHIALGNVIGSNITNI 282
                                       579999***************99***9************************************************** PP

                                       HTHHHHHHHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHH.TCHHHHHHTEEHHHHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex  80 llviGlialigslkvdseslkldlgllllvallllllvll.lllplfvpgrltvleglvllllYalylvlsl 150
                                       +lv G+++l+ +   d  ++  d  +++++ +++++++ll l++   + ++l++leg++ll++Y++++++++
  gi|298675543|ref|YP_003727293.1| 283 FLVFGVSGLLLP--LDITQT--D--IFFITPFVIFVSLLLlLFIW--THWELKRLEGIILLIIYGIFMYVLF 346
                                       **********44..444332..3..34444444333333303333..46*******************9975 PP

>> CrgA  Cell division protein CrgA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.17   7.5e+02      41      80 ..       7      48 ..       3      52 .. 0.66
   2 ?   11.5   0.0   5.4e-05      0.24      16      81 ..     186     250 ..     171     254 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.17
                              CrgA 41 lmllGllwlvv..yYlageeipfmaelgawNlliGfgliivG 80
                                      ++l+Gl  lv    ++ +++ ++ +++g   ++iG++++ vG
  gi|298675543|ref|YP_003727293.1|  7 IFLVGLTLLVKgsDFFVESSSSIAEKFGVSKFVIGLTIVSVG 48
                                      667777777742224444444455888888899999988887 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 5.4e-05
                              CrgA  16 aaertpvkakaakpsprwyvpvmlglmllGllwlvvyYlageeipfmaelgawNlliGfgliivGl 81 
                                       ++++t+++ +  k + ++++ +++ ++ +G + +   Y+ +e+i f ++l+    l+G++l++vG 
  gi|298675543|ref|YP_003727293.1| 186 TDKNTDNRLE-LKDNYTLVKDILILVISIGAVVIGARYFIEESIFFAQALNVPDTLVGISLVAVGT 250
                                       5666666665.899999***********************************************96 PP

>> Wzy_C  O-Antigen ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   3.7   0.00022      0.97      16      92 ..     103     196 ..     100     264 .. 0.79
   2 ?    2.3   6.8     0.026   1.2e+02      22      64 ..     310     350 ..     282     354 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00022
                             Wzy_C  16 Rsgiigllvalivlliifykrripfllllgilvgvilliilfvlstnletlknitkafgkldkk............. 79 
                                       R g+i l++al+++++ + +     ++ ++i++++ +++i f++++  ++l  + + f+                  
  gi|298675543|ref|YP_003727293.1| 103 RDGYIMLFAALLFFILSLDNTIS--RIDSLIFLLLYTAYIIFLIDEARMHLSMKDSYFKE---Fisyfvkfkylqsl 174
                                       77899887777666666666666..888889999999***99988887777765544443...13346667777777 PP

                             Wzy_C  80 .........kgkdksgssRlyi 92 
                                                +++dk+++ Rl++
  gi|298675543|ref|YP_003727293.1| 175 kekvdngfnNFTDKNTDNRLEL 196
                                       7778888889999999999885 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.026
                             Wzy_C  22 llvalivlliifykrripfllllgilvgvilliilfvlstnle 64 
                                       ++v l++ll+i+  + +  ++l gi++++i +i   vl + ++
  gi|298675543|ref|YP_003727293.1| 310 IFVSLLLLLFIWTHWEL--KRLEGIILLIIYGIFMYVLFNFYN 350
                                       45666666666666666..999999998888887777766655 PP

>> Flg_bb_rod  Flagella basal body rod protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   2.3     0.011        50      16      25 ..      72      81 ..      72      81 .. 0.92
   2 ?    4.8   0.2    0.0062        28      16      26 ..     273     283 ..     273     287 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.011
                        Flg_bb_rod 16 dvianNiANa 25
                                      +++++NiAN+
  gi|298675543|ref|YP_003727293.1| 72 NILGSNIANI 81
                                      899******6 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0062
                        Flg_bb_rod  16 dvianNiANan 26 
                                       +vi++Ni N++
  gi|298675543|ref|YP_003727293.1| 273 NVIGSNITNIF 283
                                       8********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       987  (0.0550505); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2517.55
//
Query:       gi|298675544|ref|YP_003727294.1|  [L=188]
Description: hypothetical protein Metev_1658 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-35  120.5  16.5    4.2e-18   65.4   3.7    2.1  2  UPF0016   Uncharacterized protein family UPF0016
     0.0046   16.6  10.2      0.087   12.4   2.2    2.2  2  TauE      Sulfite exporter TauE/SafE
  ------ inclusion threshold ------
       0.13   12.2   9.7       0.82    9.6   0.5    2.1  2  DsbD_2    Cytochrome C biogenesis protein transmembrane regio


Domain annotation for each model (and alignments):
>> UPF0016  Uncharacterized protein family UPF0016
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.3   5.0   1.4e-20   8.4e-17       4      75 .]       9      81 ..       6      81 .. 0.98
   2 !   65.4   3.7   7.1e-22   4.2e-18       2      75 .]     105     178 ..     104     178 .. 0.98

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 1.4e-20
                           UPF0016  4 flliflaElGDkTqlaaalLaary.kplpVflGavlAlalmtvlsvllGsslakrlperlielvaavlFllfG 75
                                      f+l+ laE+GDkTql +++L++++ k+++ ++G++l ++++++l++++G+ ++++lp ++i+++a+ +F++fG
  gi|298675544|ref|YP_003727294.1|  9 FFLVGLAEFGDKTQLSILVLSTKTgKYVHLIAGILLSFIIVDGLAIFFGNLVTNFLPVDYITILAGSIFIIFG 81
                                      899*********************************************************************9 PP

  == domain 2  score: 65.4 bits;  conditional E-value: 7.1e-22
                           UPF0016   2 aaflliflaElGDkTqlaaalLaarykplpVflGavlAlalmtvlsvllGsslakrlperlielvaavlFllfG 75 
                                       + f+li+l+ElGDk+ +a+ l+a++y+p+ Vf+G++ Al++ +vl v+ G+ +++r++ ++++ +a+ lF+++G
  gi|298675544|ref|YP_003727294.1| 105 SGFTLILLSELGDKSLIAVTLFATKYEPFYVFAGTITALMILSVLTVYSGKVIMSRINSKIVQKFAGSLFFILG 178
                                       679********************************************************************998 PP

>> TauE  Sulfite exporter TauE/SafE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   1.2   0.00014      0.81      64     131 ..      41     105 ..       7     115 .. 0.73
   2 !   12.4   2.2   1.5e-05     0.087     179     235 ..     121     180 ..     118     181 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00014
                              TauE  64 rlllllllgsliGallGallllllpsellkllfgvlllllallmllrkkrsrakgrerrptaillvli 131
                                        +ll ++++  +++++G l+ + lp +++++l g + +++++l+l+  +   +  +e+ p +   +l 
  gi|298675544|ref|YP_003727294.1|  41 GILLSFIIVDGLAIFFGNLVTNFLPVDYITILAGSIFIIFGALTLYHLNG-YE--NEELPELKSPFLS 105
                                       4566677777789999****************************996652.22..2333433333444 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 1.5e-05
                              TauE 179 agalgyal...agavdwpllllllpgallGallGarlarrlsertlrrlfallllvlgvk 235
                                       ++++ +a      +v   ++ +l++ ++l+++ G+ +++r++ + ++++ ++l ++lg+ 
  gi|298675544|ref|YP_003727294.1| 121 IAVTLFATkyePFYVFAGTITALMILSVLTVYSGKVIMSRINSKIVQKFAGSLFFILGIW 180
                                       4444443332234444555566***********************************985 PP

>> DsbD_2  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.5   0.00014      0.82      39      97 ..      39      96 ..      21     123 .. 0.80
   2 ?    6.7   3.3    0.0011       6.3      40      90 ..     137     187 ..     122     188 .] 0.84

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00014
                            DsbD_2 39 nlGRilsYallGalvgllgsvlqlageleglrallgvllgllllllglklllkkkllkl 97
                                       +G +ls++++ +l+ ++g++++ +  ++++++l+g +++++++l + +l  + + ++l
  gi|298675544|ref|YP_003727294.1| 39 IAGILLSFIIVDGLAIFFGNLVTNFLPVDYITILAGSIFIIFGALTLYHLN-GYENEEL 96
                                      578899************************************999665553.4444444 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0011
                            DsbD_2  40 lGRilsYallGalvgllgsvlqlageleglrallgvllgllllllglklll 90 
                                       +G i++ ++l +l ++ g+v+ +  + + +++++g l+ +l++++ l+l++
  gi|298675544|ref|YP_003727294.1| 137 AGTITALMILSVLTVYSGKVIMSRINSKIVQKFAGSLFFILGIWFYLSLFF 187
                                       688899999999999999999999888999999999999999999888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1212.21
//
Query:       gi|298675545|ref|YP_003727295.1|  [L=276]
Description: molybdopterin-guanine dinucleotide biosynthesis protein B [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-25   89.5   0.2    3.3e-25   88.6   0.2    1.5  1  MoaE          MoaE protein
    2.4e-16   59.8   0.2    5.2e-16   58.8   0.2    1.6  1  MobB          Molybdopterin guanine dinucleotide synthesis pr
    0.00013   22.0   0.0    0.00038   20.5   0.0    1.9  1  AAA_14        AAA domain
    0.00094   19.6   0.0     0.0018   18.6   0.0    1.5  2  AAA_16        AAA ATPase domain
     0.0021   17.6   1.7     0.0033   17.0   0.4    1.9  2  GTP_EFTU      Elongation factor Tu GTP binding domain
     0.0038   17.3   2.1     0.0054   16.8   0.6    2.1  2  MMR_HSR1      50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.013   15.8   0.0      0.035   14.4   0.0    1.8  1  AAA_22        AAA domain
      0.027   14.7   2.7       0.33   11.2   0.6    2.8  3  Roc           Ras of Complex, Roc, domain of DAPkinase
      0.028   15.0   0.3      0.053   14.0   0.3    1.7  1  ABC_tran      ABC transporter
      0.028   13.8   0.5       0.11   12.0   0.3    2.0  2  SRPRB         Signal recognition particle receptor beta subun
      0.059   13.8   0.0       0.14   12.5   0.0    1.7  1  RNA_helicase  RNA helicase
      0.059   13.9   0.3        0.6   10.7   0.1    2.3  2  AAA_18        AAA domain
      0.068   13.3   0.1       0.31   11.2   0.1    2.1  1  LAL_C2        L-amino acid ligase C-terminal domain 2
       0.16   12.1   0.0       0.37   10.9   0.0    1.7  1  AAA_33        AAA domain
        1.6    8.8   3.7         68    3.5   3.7    2.6  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain


Domain annotation for each model (and alignments):
>> MoaE  MoaE protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.6   0.2   2.8e-28   3.3e-25      11     112 ..     154     255 ..     144     256 .. 0.92

  Alignments for each domain:
  == domain 1  score: 88.6 bits;  conditional E-value: 2.8e-28
                                       HHHHH--TT--EEEEEEEE------TS-EEEEEECC-HHHHHHHHHHHHHHHHCCCTTSEEEEEEE-EEEETTSEEE CS
                              MoaE  11 iealvaspkaGAvvlFvGtvRdsfdgkkvteLeyeayepmaektleeiaeearerwelervavvHrlGelevgeasv 87 
                                       +++  + +kaGA+ +F+G+vR+ +++ +++ Le+e ye +ae+++++i  e+++++++ +v+++H+ G++++ge +v
  gi|298675545|ref|YP_003727295.1| 154 VKNNPEIKKAGAIGTFTGVVREITSEVQTKMLEFEKYETVAEDKINQISVELKQKPGIVDVLIHHKSGRVNPGEDIV 230
                                       444445678************999999************************************************** PP

                                       EEEEEESSHHHHHHHHHHHHHHHHH CS
                              MoaE  88 vvavssahRkeafeaceylidelKk 112
                                       +++v ++hR e f+  +++i+++K+
  gi|298675545|ref|YP_003727295.1| 231 YIVVVASHRTELFQTLSEAIERVKS 255
                                       ************************7 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   0.2   4.3e-19   5.2e-16       1     109 [.       3     107 ..       3     132 .. 0.87

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 4.3e-19
                              MobB   1 vlgivgksgsGKTtLleklipelkarglrvgtiKha.hhgfdvdkpgkDsyrhrkAGAkevlvaskerlalikelee 76 
                                       v++i+g++++GKTtL+++l ++l++ g +vgt+K    h f+ d  + D+ rh ++GA+ v+  +k+++  i++   
  gi|298675545|ref|YP_003727295.1|   3 VISIIGHKKTGKTTLVSRLTKQLSRTG-KVGTVKSMiYHRFNPD--DTDTSRHFDSGADMVTALTKDEFVTISK--- 73 
                                       799********************9988.9*****9735888877..57***********************999... PP

                              MobB  77 aelsleellarlse..vDlvlvEGfkkealpkiev 109
                                        ++++e+ l++l++  +D  +vEG k+++lpki +
  gi|298675545|ref|YP_003727295.1|  74 -NPDIEKALDTLADngMDYAIVEGDKNSDLPKILL 107
                                       .467888888885457*****************76 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   3.2e-07   0.00038       3      96 ..       2      93 ..       1     119 [. 0.78

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.2e-07
                            AAA_14  3 kilvitGaRrvGKTtllkqlikell.....vkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76
                                      k++ i G +++GKTtl+ +l k+l       + +s++y  ++ +++++++++++  +++ ++    k++++    i++ 
  gi|298675545|ref|YP_003727295.1|  2 KVISIIGHKKTGKTTLVSRLTKQLSrtgkvGTVKSMIYHRFNPDDTDTSRHFDSGADMVTALT---KDEFVT---ISKN 74
                                      7999*****************999999998667889999888888888888875666666652...234443...6888 PP

                            AAA_14 77 pewekalkslvdegknldvi 96
                                      p++ekal  l d+g ++  i
  gi|298675545|ref|YP_003727295.1| 75 PDIEKALDTLADNGMDYA-I 93
                                      999999999999885543.3 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.5e-06    0.0018      27      99 ..       4      86 ..       2     140 .. 0.75
   2 ?   -3.4   0.0         9   1.1e+04       5      18 ..     239     252 ..     221     259 .. 0.60

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.5e-06
                            AAA_16 27 vllsGesGvGKsslvrellralekd...ggif....lrgkcdql..esaipy...salaqalareellrqlldeaesae 93
                                      + ++G++ +GK++lv +l ++l+++   g  +    ++ ++     ++++++   +  ++al+++e+++  ++++ +++
  gi|298675545|ref|YP_003727295.1|  4 ISIIGHKKTGKTTLVSRLTKQLSRTgkvG--TvksmIYHRFNPDdtDTSRHFdsgADMVTALTKDEFVTISKNPDIEKA 80
                                      6799*********************6550..335555555555511555555985559999999888888888876666 PP

                            AAA_16 94 leawre 99
                                      l+  ++
  gi|298675545|ref|YP_003727295.1| 81 LDTLAD 86
                                      655544 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 9
                            AAA_16   5 ReeeleqLlsaler 18 
                                       R e  ++L +a+er
  gi|298675545|ref|YP_003727295.1| 239 RTELFQTLSEAIER 252
                                       33333333333333 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.4   2.8e-06    0.0033       6      38 ..       4      36 ..       1      67 [. 0.83
   2 ?   -0.7   0.0      0.72   8.6e+02     144     188 ..     174     250 ..     147     255 .. 0.52

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.8e-06
                                      EEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHH CS
                          GTP_EFTU  6 igiighvDhGKtTLtdrLlyktgaiskkgekae 38
                                      i+iigh  +GKtTL+ rL+++++++ k g++++
  gi|298675545|ref|YP_003727295.1|  4 ISIIGHKKTGKTTLVSRLTKQLSRTGKVGTVKS 36
                                      89********************99999888773 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.72
                                       HHHHHHHHHHHHHHHHHHHTTT................................TTEEEEEEBTTTTBTHHHHHHHH CS
                          GTP_EFTU 144 eevkqklsrkeeklekygekge................................kevpvvfgSalkgegvktlleal 188
                                       +e+ +++++k+ + eky++ +e                                ++v +v +++ + e ++tl ea+
  gi|298675545|ref|YP_003727295.1| 174 REITSEVQTKMLEFEKYETVAEdkinqisvelkqkpgivdvlihhksgrvnpgeDIVYIVVVASHRTELFQTLSEAI 250
                                       44444444443444444333332333333333333344444444444444444345555555555555555555555 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.6   4.5e-06    0.0054       2      45 ..       4      46 ..       3     141 .. 0.83
   2 ?   -0.1   0.0      0.82   9.8e+02      49      57 ..     204     212 ..     129     266 .. 0.57

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.5e-06
                                      EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETT CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkg 45
                                      + i+G+  +GK+tL+++lt++ +++++  gt + ++++r++ ++
  gi|298675545|ref|YP_003727295.1|  4 ISIIGHKKTGKTTLVSRLTKQLSRTGK-VGTVKSMIYHRFNPDD 46
                                      78******************9998876.5778888888887655 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.82
                                       EEEECGGCS CS
                          MMR_HSR1  49 elvDtpGli 57 
                                       el   pG++
  gi|298675545|ref|YP_003727295.1| 204 ELKQKPGIV 212
                                       444444432 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.9e-05     0.035       7      35 ..       3      31 ..       1      89 [. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.9e-05
                            AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeaka 35
                                      ++ ++G++ tGKTtl+ rl++ql +  k 
  gi|298675545|ref|YP_003727295.1|  3 VISIIGHKKTGKTTLVSRLTKQLSRTGKV 31
                                      789*******************9755443 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.6   0.00027      0.33       2      22 ..       4      24 ..       2      34 .. 0.84
   2 ?    2.6   0.0      0.13   1.5e+02       6      39 ..      29      62 ..      25      81 .. 0.75
   3 ?   -2.6   0.0       5.3   6.3e+03      82     108 ..     230     256 ..     227     264 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00027
                                      EEEESSTTSSHHHHHHCHCT- CS
                               Roc  2 vvlvGdsgvGKtsllkrfved 22
                                      + ++G +++GKt+l++r++++
  gi|298675545|ref|YP_003727295.1|  4 ISIIGHKKTGKTTLVSRLTKQ 24
                                      569***************986 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.13
                                      SSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEE CS
                               Roc  6 GdsgvGKtsllkrfvedkfsekekstigvdfltk 39
                                      G+ g+ K+ + +rf  d+ +++++   g+d++t 
  gi|298675545|ref|YP_003727295.1| 29 GKVGTVKSMIYHRFNPDDTDTSRHFDSGADMVTA 62
                                      4445559999999999999999999999999875 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 5.3
                                       EEEEEEEGHHHHCHHHHHHHHHHHCSS CS
                               Roc  82 lailvydsrssenlkeWlkelkkvagk 108
                                       ++i+v+ s++ e +++  + +++v ++
  gi|298675545|ref|YP_003727295.1| 230 VYIVVVASHRTELFQTLSEAIERVKSE 256
                                       567776655554444444444444444 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   4.4e-05     0.053      13      95 ..       3     126 ..       1     220 [. 0.69

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.4e-05
                                       EEEEEESTTSSHHHHHHHHTTSS--SEEEE....................EET.TCEGGGB-HHHCCHCEEEE-SS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................xxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  13 kvaivGenGaGKStLlkllagllkpteGei....................lld.gkdlkeqeleslrkeigvlpqep 68 
                                       ++ i+G+  +GK+tL++ l+++l+   G++                    ++d g+d+    +  ++ e+ +++++p
  gi|298675545|ref|YP_003727295.1|   3 VISIIGHKKTGKTTLVSRLTKQLSR-TGKVgtvksmiyhrfnpddtdtsrHFDsGADM---VTALTKDEFVTISKNP 75 
                                       789*******************995.67774335555553333222222222222222...2233334444444444 PP

                                       -S-TTSB.HHHH.......................HHHTCHHHHHHHSTTG CS
                                       xxxxxxx.xxxx.......................xxxxxxxxxxxxxxxx RF
                          ABC_tran  69 qlfpelt.vren.......................esdeeiekalsklglk 95 
                                        + + l  +++n                       ++d++i+++++++ ++
  gi|298675545|ref|YP_003727295.1|  76 DIEKALDtLADNgmdyaivegdknsdlpkillgdmDDDRHIKNVVEQVPDV 126
                                       443333323333677777766666666666666665555566666666555 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   8.9e-05      0.11       6      43 ..       4      42 ..       1      55 [. 0.73
   2 ?   -2.3   0.0       2.1   2.5e+03      10      26 ..     233     249 ..     227     266 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.9e-05
                                      EEEE-STTSSHHHHHHHHHHSS---B---S.S-EEETTG CS
                             SRPRB  6 vllvGlsdsGKTslftrLttdsvkktvtSq.essaalkv 43
                                      + ++G +++GKT+l  rLt++  ++  +   +s++ +++
  gi|298675545|ref|YP_003727295.1|  4 ISIIGHKKTGKTTLVSRLTKQLSRTGKVGTvKSMIYHRF 42
                                      669*****************9766666555355444444 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.1
                                       -STTSSHHHHHHHHHHS CS
                             SRPRB  10 GlsdsGKTslftrLttd 26 
                                        +  s +T lf+ L++ 
  gi|298675545|ref|YP_003727295.1| 233 VVVASHRTELFQTLSEA 249
                                       45667777788777654 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00012      0.14       2      37 ..       5      40 ..       4      87 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsvysr 37
                                       + G++ +GK+tl+ +L+k+l+++ k  + +s++++
  gi|298675545|ref|YP_003727295.1|  5 SIIGHKKTGKTTLVSRLTKQLSRTGKVGTVKSMIYH 40
                                      689*******************88866655554442 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1    0.0005       0.6       1      54 [.       4      55 ..       4     160 .. 0.73
   2 ?    1.3   0.0      0.39   4.6e+02      44      88 ..     183     244 ..     148     257 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0005
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgf...gvnlrdvakenglllevdpe.aldeskrlde 54
                                      I + G   +GKttl  +L k l     +       + + + + ++++ ++d s+ +d 
  gi|298675545|ref|YP_003727295.1|  4 ISIIGHKKTGKTTLVSRLTKQLSRtgkV------GTVKSMIYHRFNPdDTDTSRHFDS 55
                                      66889999**********9998334553......333333333333333333333333 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.39
                            AAA_18  44 e..aldeskrldedkldklldaleenss...........aleegknl....vidghlaeles 88 
                                       +  ++++++ + edk ++++ +l++ +            +   g+++    v+ +h+ el++
  gi|298675545|ref|YP_003727295.1| 183 KmlEFEKYETVAEDKINQISVELKQKPGivdvlihhksgRVNPGEDIvyivVVASHRTELFQ 244
                                       34556678888888888888888888766666555555533444444444466666666655 PP

>> LAL_C2  L-amino acid ligase C-terminal domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00026      0.31      19      77 ..     204     257 ..     197     257 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00026
                            LAL_C2  19 earalpgvveveltvkpGdevrpprssgdrlGyviatgdtaeeaeaaaeeaaaeiriev 77 
                                       e+++ pg+v+v ++ k G +       g+ + y++++++ + e+ +++ ea+++++ ev
  gi|298675545|ref|YP_003727295.1| 204 ELKQKPGIVDVLIHHKSGRVN-----PGEDIVYIVVVASHRTELFQTLSEAIERVKSEV 257
                                       68999*************876.....577899***********************9775 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00031      0.37       1      24 [.       3      26 ..       3      82 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00031
                            AAA_33  1 lvllvGlpGsGKstlaerllkklg 24
                                      ++ ++G++ +GK+tl+ rl k+l 
  gi|298675545|ref|YP_003727295.1|  3 VISIIGHKKTGKTTLVSRLTKQLS 26
                                      67789***************9987 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   3.7     0.057        68      10      28 ..      12      30 ..       4     268 .. 0.62

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.057
                                      SSHHHHHHHHHHHHHHTT- CS
                                      xxxxxxxxxxxxxxxxxxx RF
                              CbiA 10 vGKTtlaanLaralarrgl 28
                                      +GKTtl+  L + l+r g+
  gi|298675545|ref|YP_003727295.1| 12 TGKTTLVSRLTKQLSRTGK 30
                                      6788888877777777543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       766  (0.0427241); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 1847.48
//
Query:       gi|298675546|ref|YP_003727296.1|  [L=672]
Description: hypothetical protein Metev_1660 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    0.00011   22.4   8.6      0.052   13.9   0.8    3.1  2  DUF11       Domain of unknown function DUF11
  ------ inclusion threshold ------
      0.012   15.9  14.5       0.48   10.7   1.5    3.2  3  CARDB       CARDB
       0.45   11.3   2.5         23    5.8   0.1    2.9  3  N_BRCA1_IG  Ig-like domain from next to BRCA1 gene
        1.7    8.0   5.0        2.6    7.4   1.0    2.4  2  TRAP_beta   Translocon-associated protein beta (TRAPB)


Domain annotation for each model (and alignments):
>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   1.6    0.0001      0.46      10      38 ..     450     478 ..     441     520 .. 0.77
   2 !   13.9   0.8   1.2e-05     0.052       9      38 ..     556     585 ..     546     630 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0001
                             DUF11  10 vrpGdtvtytltvtNtgpasangvvvtDt 38 
                                       +   dtvt+   vtNtg++++++v+++D 
  gi|298675546|ref|YP_003727296.1| 450 IPVNDTVTFSYNVTNTGNVNLSKVKISDN 478
                                       56789***********************4 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.2e-05
                             DUF11   9 evrpGdtvtytltvtNtgpasangvvvtDt 38 
                                       +++ G +v+ t  v Ntg++++++v++tD 
  gi|298675546|ref|YP_003727296.1| 556 AIQIGSEVKWTYKVNNTGNVNLTNVKITDS 585
                                       7899*************************4 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.7   7.7e+03      62      87 ..     165     192 ..     147     202 .. 0.63
   2 ?    9.1   5.3   0.00034       1.5      16      79 ..     451     510 ..     444     527 .. 0.74
   3 ?   10.7   1.5   0.00011      0.48      17      79 ..     559     616 ..     552     629 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.7
                                       EEEEEEEEE-S-S-CEEEEEEEE...STT CS
                             CARDB  62 sttvsftwtteategevtltvvv...Dpd 87 
                                       +++v+  w+ + t gev ++v++   D++
  gi|298675546|ref|YP_003727296.1| 165 NAEVEQGWWLP-TLGEVNYSVQTsgrDSS 192
                                       55566666666.66777766665333444 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00034
                                       ETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CEEE CS
                             CARDB  16 fvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtteategevt 79 
                                        v++++t++++v+N+G+ +  ++k+    + ++  + t+ +L+ +es +++ t  ++ + + v 
  gi|298675546|ref|YP_003727296.1| 451 PVNDTVTFSYNVTNTGNVNLSKVKI--SDNSSN-FNYTIGELNVSESFNITNTTSAI-KGQYVN 510
                                       57999************99877665..444444.6699*********9999999988.433333 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00011
                                       TTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CEEE CS
                             CARDB  17 vgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtteategevt 79 
                                        g+e++ t++v+N+G+ + +++k++   d  l +  t+  L+ +es+t ++t t++  +g++ 
  gi|298675546|ref|YP_003727296.1| 559 IGSEVKWTYKVNNTGNVNLTNVKIT---DSRLGDICTIDTLNKSESKTCTTTGTAK--KGQYS 616
                                       689999************9999876...444445589****************998..33332 PP

>> N_BRCA1_IG  Ig-like domain from next to BRCA1 gene
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       3.4   1.5e+04       8      31 ..     162     185 ..     160     189 .. 0.81
   2 ?    4.5   0.1     0.013        57       3      34 ..     445     475 ..     443     523 .. 0.71
   3 ?    5.8   0.1    0.0051        23       4      45 ..     553     597 ..     551     621 .. 0.65

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.4
                        N_BRCA1_IG   8 vppgteftktWrlrNtGseaWpag 31 
                                       v++++e ++ W l   G+++++ +
  gi|298675546|ref|YP_003727296.1| 162 VAANAEVEQGWWLPTLGEVNYSVQ 185
                                       7899999999*9998888887655 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.013
                        N_BRCA1_IG   3 pdgtvvppgteftktWrlrNtGseaWpagtkl 34 
                                       p+g ++p + + t ++ ++NtG+++  +++k+
  gi|298675546|ref|YP_003727296.1| 445 PEGPEIPVNDTVTFSYNVTNTGNVNL-SKVKI 475
                                       78999******************986.44444 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0051
                        N_BRCA1_IG   4 dgtvvppgteftktWrlrNtGseaWpagtklvfvg...Gdkmg.s..a 45 
                                        g +++ g+e + t++++NtG+++    t++++++   Gd ++ +  +
  gi|298675546|ref|YP_003727296.1| 553 RGPAIQIGSEVKWTYKVNNTGNVNL---TNVKITDsrlGDICTiDtlN 597
                                       5778999****************97...44443332246666433542 PP

>> TRAP_beta  Translocon-associated protein beta (TRAPB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   1.0   0.00058       2.6      34      60 ..     453     479 ..     449     516 .. 0.90
   2 ?    1.8   0.2     0.031   1.4e+02      34      59 ..     560     585 ..     556     589 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00058
                         TRAP_beta  34 gedltveytiyNvGssaAldVslvDds 60 
                                       +  +t++y+++N G+    +V+++D+s
  gi|298675546|ref|YP_003727296.1| 453 NDTVTFSYNVTNTGNVNLSKVKISDNS 479
                                       5679*********************98 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.031
                         TRAP_beta  34 gedltveytiyNvGssaAldVslvDd 59 
                                       g+++  +y++ N G+   ++V+++D 
  gi|298675546|ref|YP_003727296.1| 560 GSEVKWTYKVNNTGNVNLTNVKITDS 585
                                       688999******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (672 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.38
# Mc/sec: 5360.54
//
Query:       gi|298675547|ref|YP_003727297.1|  [L=61]
Description: hypothetical protein Metev_1661 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.012   15.6   0.0    1.0  1  Spore_coat_CotO  Spore coat protein CotO
      0.064   13.6   0.0      0.075   13.4   0.0    1.1  1  Kringle          Kringle domain
       0.12   12.2   0.0       0.14   12.0   0.0    1.2  1  SH3_19           Myosin X N-terminal SH3 domain


Domain annotation for each model (and alignments):
>> Spore_coat_CotO  Spore coat protein CotO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.0     2e-06     0.012     144     187 ..      14      57 ..       7      59 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2e-06
                   Spore_coat_CotO 144 kclieteektYrgvilerredivsiktfssmeetelaiddItsi 187
                                       k+ + +e+ktY g + e +++ +s+k     e t++ ++ It i
  gi|298675547|ref|YP_003727297.1|  14 KVSLDAEGKTYHGTVAECNDGVLSLKWDIGDEYTHIEVEKITAI 57 
                                       67899************************************988 PP

>> Kringle  Kringle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.3e-05     0.075       3      35 ..      18      50 ..      16      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.3e-05
                                      STTSTTC-S---BBTTS-BBE-TTSCSSSCHSS CS
                           Kringle  3 egnGesYrGtvsttesgaeCqaWdsetphkhkk 35
                                      + +G++Y+Gtv++ + g+  ++Wd   +++h +
  gi|298675547|ref|YP_003727297.1| 18 DAEGKTYHGTVAECNDGVLSLKWDIGDEYTHIE 50
                                      578********************9877777644 PP

>> SH3_19  Myosin X N-terminal SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.4e-05      0.14      10      38 ..      20      48 ..      13      57 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.4e-05
                            SH3_19 10 keqllPstVsscddgsvvlttdYGevitl 38
                                      +++ +  tV  c dg++ l+ d G ++t+
  gi|298675547|ref|YP_003727297.1| 20 EGKTYHGTVAECNDGVLSLKWDIGDEYTH 48
                                      5666668******************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 454.17
//
Query:       gi|298675548|ref|YP_003727298.1|  [L=329]
Description: glycoprotease family metalloendopeptidase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-87  294.2   0.0    1.2e-87  294.0   0.0    1.0  1  Peptidase_M22   Glycoprotease family
    0.00044   20.3   0.1      0.027   14.6   0.0    2.3  2  CheD            CheD chemotactic sensory transduction
     0.0061   16.3   0.0      0.019   14.6   0.0    1.7  2  Carbam_trans_N  Carbamoyltransferase N-terminus


Domain annotation for each model (and alignments):
>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  294.0   0.0   2.1e-91   1.2e-87       2     271 .]      25     296 ..      24     296 .. 0.96

  Alignments for each domain:
  == domain 1  score: 294.0 bits;  conditional E-value: 2.1e-91
                                       CEXEEEEEEEEE....SSSSHHHHHHHHHHHHHHHHHHHHHHH...TSTGGGEEEEEEEEESS-HHHHHHHHHHHHH CS
                     Peptidase_M22   2 vlanvvasqkelhakyGGvvPelasraHserllplieealaea...glsledldaIavtkgPGlftgLrvGvsfAkg 75 
                                       v+++v+++++   +++GG++P++as++H++    +i+++l++    g++++ lda+a+++gPGl+++Lr ++++A++
  gi|298675548|ref|YP_003727298.1|  25 VISEVTETYQ---PDTGGIHPREASQHHAKYASTVIQKLLENIkskGIDPKTLDAVAFSQGPGLGPCLRTVATAARM 98 
                                       5677777775...9**************************9987789****************************** PP

                                       HHHHCT--EEEEEHHHHHHHCCHCTSECSSCEEEEESSSTEEEEEECTTEEEEEEEESSSEHHHHHHHHHHHHT..S CS
                     Peptidase_M22  76 lalalnkPlvgVnhleahalaarleekeefPvvllvsGghtqvylvkegryeilgetlddaagealdkvarllglpy 152
                                       l+l+l++P++gVnh++ah++ ++ +++ ++Pvvl+vsG ++qv+++++g+y+++getld  +g+aldk+ar  gl++
  gi|298675548|ref|YP_003727298.1|  99 LSLTLDIPIIGVNHCIAHIEVGKWKTPAKDPVVLYVSGANSQVLAYRKGKYRVFGETLDVGIGNALDKFARSAGLNH 175
                                       ***********************998789*****************99***************************** PP

                                       SCCHHHHHHHCTC.S.......EETTEEE.CHHHHHHHHHHSTT.HHHHHHHHHHHHHHHHHHHHHHHHHHCTBSEE CS
                     Peptidase_M22 153 pggpkieklakeg.kkiefprplkgldfsfsGlktavlkeleke.vedlaasfqeavvdhlvekteralklpkakel 227
                                       pggp iek a++  k++ +p+++kg+dfsfsGl ta++ +le e +ed+++sfqe++++++ve+teral++++++e+
  gi|298675548|ref|YP_003727298.1| 176 PGGPRIEKHAENFkKYVPLPYVVKGMDFSFSGLTTAARDALEYEaMEDVCYSFQETAFAMMVEVTERALAHTGKNEV 252
                                       ***********997779************************5546******************************** PP

                                       EEESGGGGXHHHHHCHCCHHHHTTSEEEXXXHHHHSSXCHHHHH CS
                     Peptidase_M22 228 vilGGvaankrLrealeeeaeelglkliiPplkyctdnaamiaw 271
                                       +++GGv+an rLr +l  +++++g+++++P+++++ dn+amia+
  gi|298675548|ref|YP_003727298.1| 253 LLAGGVGANMRLRDMLDIMSNDRGASFYVPEKRFMGDNGAMIAY 296
                                       *****************99999********************97 PP

>> CheD  CheD chemotactic sensory transduction
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   4.6e-06     0.027       9      44 ..      42      77 ..      35      80 .. 0.86
   2 ?    3.3   0.1     0.014        85      16      51 ..     225     262 ..     214     274 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.6e-06
                                      .SS-TTSCCCBHHHHHHHHHHHHHTTT--GGG-EEE CS
                              CheD  9 keksasnpakyadtaielLinellklgakkerleak 44
                                      +++++++ akya+t i+ L+++++++g +++ l a 
  gi|298675548|ref|YP_003727298.1| 42 PREASQHHAKYASTVIQKLLENIKSKGIDPKTLDAV 77
                                      56677899***********************99886 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.014
                                       CCCBHHHHHHHHHHHHHTTT--GGG-EEEEEE-..--- CS
                              CheD  16 pakyadtaielLinellklgakkerleaklaGG..Aqm 51 
                                          + +ta  ++++  +++ a+  + e+ laGG  A+m
  gi|298675548|ref|YP_003727298.1| 225 CYSFQETAFAMMVEVTERALAHTGKNEVLLAGGvgANM 262
                                       567899**************************732555 PP

>> Carbam_trans_N  Carbamoyltransferase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.21   1.3e+03       2      30 ..       5      31 ..       4      84 .. 0.51
   2 !   14.6   0.0   3.2e-06     0.019     263     332 ..     219     292 ..     197     295 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.21
                    Carbam_trans_N  2 ilGikltlflHDgavalvddgklvaavee 30
                                      ilGi +t      ++a+vd+ +++  v e
  gi|298675548|ref|YP_003727298.1|  5 ILGIEGT--AWNLSAAVVDEDDVISEVTE 31
                                      6777777..45556666776666665543 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 3.2e-06
                    Carbam_trans_N 263 ekdedlaAsiqvflErlvvevlnivyeklkirnLclaGGvalNiklN..sallesglFedvwvq..PaanDsGs 332
                                       e  ed+  s+q+    ++vev++ + ++++ +   laGGv++N+ l   + ++++    + +v+   +++D+G+
  gi|298675548|ref|YP_003727298.1| 219 EAMEDVCYSFQETAFAMMVEVTERALAHTGKNEVLLAGGVGANMRLRdmLDIMSNDRGASFYVPekRFMGDNGA 292
                                       2235***************************************9986224456666666777752246777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2372.70
//
Query:       gi|298675549|ref|YP_003727299.1|  [L=190]
Description: Mn2+dependent serine/threonine protein kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-09   38.1   0.1      1e-05   25.6   0.1    2.1  2  APH             Phosphotransferase enzyme family
    5.4e-09   35.9   0.0    8.2e-09   35.3   0.0    1.3  1  RIO1            RIO1 family
    1.5e-05   24.5   0.3    3.7e-05   23.2   0.3    1.7  1  Pkinase         Protein kinase domain
    3.3e-05   23.3   0.0     0.0056   16.0   0.0    2.2  2  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
     0.0024   17.5   0.1       0.43   10.1   0.0    2.4  2  Choline_kinase  Choline/ethanolamine kinase
  ------ inclusion threshold ------
      0.018   14.7   0.1      0.033   13.8   0.1    1.6  1  WaaY            Lipopolysaccharide core biosynthesis protein 
      0.024   13.9   0.0      0.032   13.5   0.0    1.5  1  Pkinase_Tyr     Protein tyrosine kinase


Domain annotation for each model (and alignments):
>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00013      0.32      30     107 ..      34     100 ..      18     102 .. 0.83
   2 !   25.6   0.1     4e-09     1e-05     167     199 ..     102     131 ..     100     174 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00013
                                       TTS-HHHHHHHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE----EE-SSHHHHHHHHHHHHHHHHHHCCHH CS
                               APH  30 paraaeeirrevallrlLakagvpvPevlagdtddeeigllfalieyvpgrsllrklsaaqlpellealgeflaalh 106
                                       ++  +e++r+e++l    +++g+p+P +++    ++++      +ey++g++l +     + pel  ++ge+ + lh
  gi|298675549|ref|YP_003727299.1|  34 DKIRKERTRAEARLISETRRLGIPTPIIYD---IQNFKI----EMEYIDGEPLKN----VINPELSKRVGELTGLLH 99 
                                       44567899*********************9...788888....6***********....788999999999999888 PP

                                       C CS
                               APH 107 q 107
                                       +
  gi|298675549|ref|YP_003727299.1| 100 N 100
                                       6 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 4e-09
                                       EEE-SS-SGGGEEEC..TTEEEEE---TT-EEE CS
                               APH 167 vllHgDlhpgNllvdpddgrvtGviDfedaglg 199
                                       +++HgDl + Nl+++  dgr+ ++iDf++a + 
  gi|298675549|ref|YP_003727299.1| 102 GIIHGDLTTSNLILK--DGRI-YFIDFGLAFID 131
                                       68*************..9**9.********876 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.0   3.2e-12   8.2e-09      43     154 ..      29     130 ..      15     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 3.2e-12
                                       -GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEEETTEEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHH CS
                              RIO1  43 sktnprklvklwaekEfrnLkrleeagvpvPkpielkrhvlvmefigedgvaapklkdveeeeeaeelyeevleemr 119
                                        k    k+ k  ++ E r +++ ++ g+p P  +++++  + me+i+  g +++++ + e        + + + e+ 
  gi|298675549|ref|YP_003727299.1|  29 IKVLDDKIRKERTRAEARLISETRRLGIPTPIIYDIQNFKIEMEYID--GEPLKNVINPE--------LSKRVGELT 95 
                                       4555678889999**********************************..99988887766........556677789 PP

                                       HHHHTSTEEESS-STTSEEEETTEEEE--GTTEEE CS
                              RIO1 120 klykeaglvHaDLSeyNvlvdedkvviIDvsQave 154
                                        l+++ g++H+DL   N++++++++++ID++ a  
  gi|298675549|ref|YP_003727299.1|  96 GLLHNGGIIHGDLTTSNLILKDGRIYFIDFGLAFI 130
                                       99***************************987665 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.3   1.4e-08   3.7e-05      46     145 ..      42     128 ..      16     153 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.4e-08
                                       HHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-S CS
                           Pkinase  46 lrEikilkklkhpnivrlyevfeekdelylvleyveggeladllerkgslseeeakkiakqilegleylHskgiiHr 122
                                       ++E +++ +++   i +   ++++ +++ + +ey++g+ l+++++           ++ k++ e    lH+ giiH 
  gi|298675549|ref|YP_003727299.1|  42 RAEARLISETRRLGIPT--PIIYDIQNFKIEMEYIDGEPLKNVINP----------ELSKRVGELTGLLHNGGIIHG 106
                                       55555555555555543..356677788888888888888888873..........3344444445569******** PP

                                       S-SGGGEEEETTTEEEE-SGTTS CS
                           Pkinase 123 DlKpeNiLidekgelKitDFGla 145
                                       Dl ++N++++ +g +  +DFGla
  gi|298675549|ref|YP_003727299.1| 107 DLTTSNLILK-DGRIYFIDFGLA 128
                                       **********.***********9 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.0    0.0025       6.4      53      85 ..      36      68 ..      14      75 .. 0.73
   2 !   16.0   0.0   2.2e-06    0.0056     117     169 ..      81     128 ..      60     166 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0025
                               Kdo 53 lgrtravrEfrllkrLeeagvavpkpvaagavk 85
                                      + + r ++E rl+ + +++g+++p +   +  k
  gi|298675549|ref|YP_003727299.1| 36 IRKERTRAEARLISETRRLGIPTPIIYDIQNFK 68
                                      5677999**************998665555555 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 2.2e-06
                               Kdo 117 eelkrallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDldka 169
                                       +  + +l k+vg l   lh+ g+ H+dl   n+ l+ +      i++iD+  a
  gi|298675549|ref|YP_003727299.1|  81 NVINPELSKRVGELTGLLHNGGIIHGDLTTSNLILKDGR-----IYFIDFGLA 128
                                       556678899**************************9995.....*****9755 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.8   0.0    0.0074        19      44      81 ..      65     101 ..      33     104 .. 0.80
   2 !   10.1   0.0   0.00017      0.43     149     171 ..     105     125 ..     102     131 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0074
                                       TTEEEE.E--TCEE--TTGGGCHHHHHHHHHHHHHHTTC CS
                    Choline_kinase  44 enGrie.efiesrtlstedlrepeiskkiAkklaelHsl 81 
                                       +n  ie e+i++++l+  ++ +pe+sk++++ ++ lH+ 
  gi|298675549|ref|YP_003727299.1|  65 QNFKIEmEYIDGEPLK--NVINPELSKRVGELTGLLHNG 101
                                       5556667999999996..799************999985 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00017
                                       -S--SGGGEEE.-CTTEEEE--G CS
                    Choline_kinase 149 HnDlqegNillnkeekklvlIDF 171
                                       H Dl  +N++l  +++++++IDF
  gi|298675549|ref|YP_003727299.1| 105 HGDLTTSNLIL--KDGRIYFIDF 125
                                       99*********..********** PP

>> WaaY  Lipopolysaccharide core biosynthesis protein (WaaY)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   1.3e-05     0.033     115     178 ..      64     125 ..      19     140 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.3e-05
                              WaaY 115 vkvyimiieyiegielvdmpeiddevkakikqsieklhqlgmvsgdphrgnfivkkdevriidl 178
                                       ++ + + +eyi+g  l ++  i+ e+ +++ +    lh+ g++ gd    n+i+k++ +  id+
  gi|298675549|ref|YP_003727299.1|  64 IQNFKIEMEYIDGEPLKNV--INPELSKRVGELTGLLHNGGIIHGDLTTSNLILKDGRIYFIDF 125
                                       56677889*****999875..8999999999999****************************97 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.3e-05     0.032     112     151 ..      91     129 ..       3     158 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.3e-05
                                       HHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHE CS
                       Pkinase_Tyr 112 vAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLar 151
                                       v +    L++  ++H dl++ N +l+ +  +   DfGLa 
  gi|298675549|ref|YP_003727299.1|  91 VGELTGLLHNGGIIHGDLTTSNLILK-DGRIYFIDFGLAF 129
                                       55555679999***********9999.5566677****84 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1337.61
//
Query:       gi|298675550|ref|YP_003727300.1|  [L=181]
Description: non-canonical purine NTP pyrophosphatase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.7e-54  182.9   0.0    6.4e-54  182.7   0.0    1.0  1  Ham1p_like  Ham1 family
  ------ inclusion threshold ------
      0.059   12.0   0.0      0.077   11.6   0.0    1.1  1  MutL        MutL protein


Domain annotation for each model (and alignments):
>> Ham1p_like  Ham1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.7   0.0   7.1e-58   6.4e-54       1     187 []       4     179 ..       4     179 .. 0.90

  Alignments for each domain:
  == domain 1  score: 182.7 bits;  conditional E-value: 7.1e-58
                                       EEEC-S-HHHHHHHHHHTTTECCCE...EECCCCEE----BS.SSHHHHHHHHHHHHHH.HTS-EEEEEEEEEEGGG CS
                        Ham1p_like   1 ivfaTgNkgKlrevkeilaeellevk..slkelelpeveEtq.gtfeenalkKaraaae.aglpvladDsgLevdaL 73 
                                       ivf+TgN++K+revkeil+++++++   +       e++E q +++e +a+  a+  a+  ++pv++dDsg++++aL
  gi|298675550|ref|YP_003727300.1|   4 IVFVTGNEDKYREVKEILEKKDIKIIqkD------LEYPELQeDDLEPIAYYGAKWTADrLNMPVIVDDSGIFIEAL 74 
                                       8*****************88777665223......4666899899**********999747999************* PP

                                       TTTBGGGTTTTTHTTCHHHHHHHHHHHHCTHTTS--EEEEEEEEEEEETTTTEEEEEEEEEEEEE-SS.--SSSSTT CS
                        Ham1p_like  74 nglPGvysarfagegaedeenlaklleeleeeeedrsArfvcvlaladpeeeeellfeGeveGeiveeprgeggfGy 150
                                       ng+PG+ysa ++     ++ +++k+l+ ++ +e+ r A+f++v+++++pe+e+ ++f+G+veG+i+ ++rgeggfG+
  gi|298675550|ref|YP_003727300.1|  75 NGFPGPYSAFVE-----KHLGNQKVLKLMD-DETVRDATFKSVIGYCEPENEP-IVFTGKVEGKIAYSERGEGGFGF 144
                                       *********994.....34588*******7.55689*************6666.*********************** PP

                                       GGGEEETT-SSBTTTS.CHHHHHHSHHHHHHHHHHHH CS
                        Ham1p_like 151 DpiFvpeegektfaelskeeknaiShRgkAlekllef 187
                                       DpiF++ + +ktfae+ + ekn++ShR +Alek+ e+
  gi|298675550|ref|YP_003727300.1| 145 DPIFEY-Q-GKTFAEIGDYEKNKVSHRMRALEKFYEW 179
                                       *****9.4.79***********************987 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   8.6e-06     0.077     154     195 ..       5      46 ..       1      50 [. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.6e-06
                              MutL 154 viyAGNkaareeveeiLeeagkelvvtdNvlPkldelnvepa 195
                                       v + GN++ ++ev+eiLe+++++++  d  +P+l+e ++ep+
  gi|298675550|ref|YP_003727300.1|   5 VFVTGNEDKYREVKEILEKKDIKIIQKDLEYPELQEDDLEPI 46 
                                       7799*******************************9999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.19s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1453.38
//
Query:       gi|298675551|ref|YP_003727301.1|  [L=221]
Description: arylformamidase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-27   94.3   0.0    8.8e-27   94.0   0.0    1.1  1  Cyclase   Putative cyclase


Domain annotation for each model (and alignments):
>> Cyclase  Putative cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.0   0.0   4.9e-31   8.8e-27       1     136 []      11     165 ..      11     165 .. 0.89

  Alignments for each domain:
  == domain 1  score: 94.0 bits;  conditional E-value: 4.9e-31
                           Cyclase   1 idLshplsedtpvwp.dp...................islsehtGTHlDapgHfae..ktidelpleelvgpavvld 55 
                                       id+s+ +s++tpv+p dp                   is+++htGTH+Dap+H+ e  k++d+l l++l+g+a+v+d
  gi|298675551|ref|YP_003727301.1|  11 IDISVGISSSTPVYPgDPvpdikkvyclpddrasvssISMGSHTGTHIDAPSHILEdgKSVDSLSLDTLIGNALVVD 87 
                                       8*************656677889999****************************99999****************** PP

                           Cyclase  56 vsakaaaedyeiitaedleaalakqgveikpgdivlirTgwskrl..edkeky...rnpglseeaaewlaekgvkav 127
                                       +s+    ++  +i+++dle+ ++k +   ++ di+li+T  s+ +     ++    +   l+++a e ++e+g+k v
  gi|298675551|ref|YP_003727301.1|  88 LSDV---SE--TIKKSDLENIFNKLD-AAENLDILLIKTQNSNLWndF--STVgmeSMISLDKSAGECIVENGFKTV 156
                                       *986...33..47************9.779*********999997431..22233444789**************** PP

                           Cyclase 128 GvDtlsvDa 136
                                       G+D +svD+
  gi|298675551|ref|YP_003727301.1| 157 GIDGFSVDV 165
                                       *******95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1772.42
//
Query:       gi|298675552|ref|YP_003727302.1|  [L=212]
Description: PHP domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.2e-10   41.1   0.1    2.4e-10   40.9   0.1    1.3  1  PHP          PHP domain
    1.8e-06   27.6   0.1    3.2e-06   26.8   0.1    1.4  1  RNase_P_p30  RNase P subunit p30


Domain annotation for each model (and alignments):
>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.1   2.7e-14   2.4e-10       1      74 [.       3      94 ..       3     205 .. 0.72

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 2.7e-14
                                      EEEE--CCC--.S-H..HHHHHHHHHCT-SEEEEEEEEBTT......HHHHHHHHHHHHTTTTSEEEEEEE........ CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP  1 dlHvHteyslldgalsieelvkkakelglkaiaiTDhgnlf......gyvefykaakkkykagikpiiGleayvaddse 73
                                      dlH+Ht +s     l ++elv++a   g++aiaiTDh+++       ++ e +k++++    +ik++ G+e++ ++  +
  gi|298675552|ref|YP_003727302.1|  3 DLHTHTVFSDG--ELIPSELVRRAVVTGYEAIAITDHADYTnfeqlvDVAEKAKYLEDV--YDIKILSGVELTHVPPAK 77
                                      7999*999944..3337***********************9666444444444444333..68********88887776 PP

                                      ................. CS
                                      ................x RF
                               PHP 74 ................k 74
                                                       
  gi|298675552|ref|YP_003727302.1| 78 ieplveksrkkgadivV 94
                                      66666666444444440 PP

>> RNase_P_p30  RNase P subunit p30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.1   3.5e-10   3.2e-06      10     145 ..      12     145 ..       2     149 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 3.5e-10
                                       ........HHHHHHHHH-SEEEEEEEEEESS---HHHHH.......HHHHHHHH..HHSSEEEEEEES-H..HHHHH CS
                       RNase_P_p30  10 ddskkksrtiktlaelgytgvainftveaekekkpnasepikeelkelkkelsglkllsRvtlvvsdpskl.qrlsk 85 
                                       d++  +s++++++   gy+++ai+ + ++ + ++  +      e+ +  ++++++k+ls+v+l+   p+k+   ++k
  gi|298675552|ref|YP_003727302.1|  12 DGELIPSELVRRAVVTGYEAIAITDHADYTNFEQLVDVA----EKAKYLEDVYDIKILSGVELTHVPPAKIePLVEK 84 
                                       44555668999999**************88877777777....67788888899***************99866666 PP

                                       HHHH.--EEEEE--SHH......HHHHHHHT.T-SEEE-TTTTSSS-S--HHHHHHHHHHT-EEEEE CS
                       RNase_P_p30  86 vrqk.fdllavrPttek......alraacenldvDiisidltsrlpfglkhktiraAvergvafEin 145
                                        r+k  d+++v++ t +       +  ++e  +vDi+s++        ++   ++ A ++ + +Ei+
  gi|298675552|ref|YP_003727302.1|  85 SRKKgADIVVVHGETVTepvisgTNSTVVELGEVDILSHPG------LITQDDVQKAYDNDICLEIT 145
                                       6654389****9977533333326788888889******98......68888999999999998885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1676.34
//
Query:       gi|298675553|ref|YP_003727303.1|  [L=207]
Description: hypothetical protein Metev_1667 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-06   27.5   2.2      3e-06   27.1   2.2    1.2  1  Imp-YgjV  Bacterial inner membrane protein
  ------ inclusion threshold ------
      0.014   15.4   1.5      0.027   14.5   1.5    1.4  1  MtN3_slv  Sugar efflux transporter for intercellular exchange
      0.089   13.3   0.9       0.43   11.1   0.9    2.1  2  Pox_D5    Poxvirus D5 protein-like


Domain annotation for each model (and alignments):
>> Imp-YgjV  Bacterial inner membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   2.2   5.1e-10     3e-06      91     158 ..       3      70 ..       1      71 [. 0.96

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 5.1e-10
                          Imp-YgjV  91 isllpiaasllatialfslngikmRllflvssllWlvynilvgsigglllevlflisnlitiyRlrkk 158
                                       i+++ +a+sll  + l++ n+ik+R++ l+++  + +y  l+ ++  ++++ ++++ n++ iyRl+++
  gi|298675553|ref|YP_003727303.1|   3 IEYIGYAGSLLWLLSLTMSNSIKLRIFSLLGAGAYTLYGYLLNAYPVSIVNGIIVLLNIYHIYRLKRR 70 
                                       788999***********************************************************875 PP

>> MtN3_slv  Sugar efflux transporter for intercellular exchange
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.5   4.5e-06     0.027      36      75 ..      24      63 ..      18      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.5e-06
                          MtN3_slv 36 fllflagllsallWllYGllkkdaliiivNlvgvlleliy 75
                                      + l +++ll+a  ++lYG l++ + + ivN++ vll++  
  gi|298675553|ref|YP_003727303.1| 24 IKLRIFSLLGAGAYTLYGYLLNAYPVSIVNGIIVLLNIYH 63
                                      567899**************************99998765 PP

>> Pox_D5  Poxvirus D5 protein-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.11   6.5e+02      28      42 ..     159     173 ..     153     176 .. 0.87
   2 ?   11.1   0.9   7.2e-05      0.43      12      42 ..     165     194 ..     158     203 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.11
                            Pox_D5  28 YeaYkafcekngykp 42 
                                       Y  Y++ ++++gyk+
  gi|298675553|ref|YP_003727303.1| 159 YMDYRQSLKEKGYKE 173
                                       778**********98 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 7.2e-05
                            Pox_D5  12 elfeeekstrvpsdvlYeaYkafcekngykp 42 
                                        l+e  +   + ++v++++Yk+++++ gy++
  gi|298675553|ref|YP_003727303.1| 165 SLKE-KGYKEMVVKVTHNKYKKYLSSLGYTE 194
                                       4444.66677889****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       926  (0.0516482); expected 358.6 (0.02)
Passed bias filter:                      644  (0.0359195); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1546.08
//
Query:       gi|298675554|ref|YP_003727304.1|  [L=568]
Description: peptidase M50 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.2e-24   84.9   0.0    2.2e-23   82.8   0.0    1.9  1  Peptidase_M50  Peptidase family M50
    1.4e-23   83.0   2.7    1.2e-11   44.8   0.9    2.3  2  PDZ_2          PDZ domain
    1.5e-15   56.7   0.0    1.7e-07   31.0   0.0    2.6  3  PDZ_6          PDZ domain
    6.9e-13   48.8   4.7    1.1e-07   32.1   0.3    2.5  2  PDZ            PDZ domain
      2e-05   24.5   1.9        0.2   11.7   0.1    2.4  2  PDZ_1          PDZ-like domain
    2.1e-05   24.4   1.6      0.042   13.8   0.1    2.3  2  Tricorn_PDZ    Tricorn protease PDZ domain
     0.0018   18.6   0.2       0.16   12.3   0.0    2.5  2  GRASP55_65     GRASP55/65 PDZ-like domain
  ------ inclusion threshold ------
      0.064   12.9   3.2        1.5    8.5   0.1    3.2  3  DUF3394        Domain of unknown function (DUF3394)


Domain annotation for each model (and alignments):
>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.8   0.0     1e-26   2.2e-23       3     245 ..     125     546 ..     123     552 .. 0.76

  Alignments for each domain:
  == domain 1  score: 82.8 bits;  conditional E-value: 1e-26
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                     Peptidase_M50   3 illlgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeaka. 78 
                                       i++l++ +vvHE+ H+++   ++v+v++++i++                al+p+GG+ + ++e+      +e  ++ 
  gi|298675554|ref|YP_003727304.1| 125 IIALVVTLVVHEFSHAILSIVENVRVKSMGILL----------------ALVPIGGFAEPDEEQLFGVSRDE--NVg 183
                                       89***************************9999................************99955443333..345 PP

                                       .............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.................................. CS
                                       .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................. RF
                     Peptidase_M50  79 .............flkkspwqrllivlAGplanfilailvfvv.................................. 108
                                                     ++++  qr +i++AG + nf++a+++f++                                  
  gi|298675554|ref|YP_003727304.1| 184 ssessideksgetKKAATTNQRSRILAAGVMSNFVVAFIAFLLffgpvlggigsvsdamitdvnsespankagiden 260
                                       588999******999999*********************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Peptidase_M50 109 ............................................................................. 108
                                                                                                                    
  gi|298675554|ref|YP_003727304.1| 261 mvitqindtqtrnandvinymmnvspgstvevhavkdgttstyevdiqdkeheqvqgiyisdvvegspaensglekg 337
                                       ****************************9999999999988888888888888888888877777776666666666 PP

                                       ................................................-EEECE.....CTTTSCEE-SEEEC-XXX CS
                                       ................................................xxxxxx.....xxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 109 ................................................pkkske.....seeekrgviGvspkpvkk 132
                                                                                                    ++++g+iG+  +    
  gi|298675554|ref|YP_003727304.1| 338 mlivgidnnsvqsindfsnymentspgqeveikalkpnqtdaspeqlnL----TlatspDGTQDKGFIGIFYER--- 407
                                       6666666666666666666666666666666666665555555333330....033333555566666665555... PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.........................XXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........................xxxx RF
                     Peptidase_M50 133 egllealkegvektlkvvvltvkalgklitgklslktlggpisiaqla.........................seaa 184
                                          le+ + gve     ++  +++l+++      l++lgg i i+ l                          +e +
  gi|298675554|ref|YP_003727304.1| 408 -RNLESNSLGVEIGNFPATRYLEMLKSI---PSRLDELGGWIIIFGLPivgfggegfrgfsgtfaqffepigwAEPL 480
                                       .444444445554444444444444444...4458888888888887777888888888876666666666555555 PP

                                       XXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXX CS
                                       xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx RF
                     Peptidase_M50 185 eagls...sflqllalisvnLgilNLlPipvLDGghllfalleairrkplser..keevanlvgla 245
                                        +g+    + l ++a++++ +g++N lP  +LDGgh+++  l+ ++++    +  +e++a  v ++
  gi|298675554|ref|YP_003727304.1| 481 GIGIFwlaNALLWIAWLNFYVGLFNCLPAVPLDGGHVFRGYLQSFAQRITGSEgsAENIAGAVTMI 546
                                       55555888*************************************988765441144444444444 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.9   5.3e-15   1.2e-11      15      81 ..     240     306 ..     230     307 .. 0.95
   2 !   37.9   0.0   7.4e-13   1.7e-09      12      74 ..     314     376 ..     307     388 .. 0.89

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 5.3e-15
                                       -EEEEEE-TTSGGGGT.--TT-EEEEETTB--SSHHHHHHHHHTS-TT-EEEEEEEETTEEEEEEEE CS
                             PDZ_2  15 gvlvvsVkeggPaakaglkagDvilkvdgkkvksledlislllkkkpGdtVkltvlRdgkkktvevk 81 
                                        + +++V++++Pa+kag+  + vi+++++++  +  d+i+++++ +pG+tV++    dg++ t+ev 
  gi|298675554|ref|YP_003727304.1| 240 DAMITDVNSESPANKAGIDENMVITQINDTQTRNANDVINYMMNVSPGSTVEVHAVKDGTTSTYEVD 306
                                       5899*************************************************************96 PP

  == domain 2  score: 37.9 bits;  conditional E-value: 7.4e-13
                                       -..-EEEEEE-TTSGGGGT.--TT-EEEEETTB--SSHHHHHHHHHTS-TT-EEEEEEEETTE CS
                             PDZ_2  12 dtggvlvvsVkeggPaakaglkagDvilkvdgkkvksledlislllkkkpGdtVkltvlRdgk 74 
                                       + +g+++ +V eg+Pa+++gl++g  i+ +d++ v+s  d+ +++ +++pG++V+++ l  ++
  gi|298675554|ref|YP_003727304.1| 314 QVQGIYISDVVEGSPAENSGLEKGMLIVGIDNNSVQSINDFSNYMENTSPGQEVEIKALKPNQ 376
                                       4579****************************************************9887555 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       3.4   7.7e+03      22      39 ..      90     107 ..      89     110 .. 0.81
   2 !   22.8   0.0   2.6e-08   5.8e-05       2      50 ..     243     289 ..     242     293 .. 0.87
   3 !   31.0   0.0   7.5e-11   1.7e-07       2      52 ..     320     369 ..     319     372 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.4
                             PDZ_6  22 ilsvNGqpveglsladva 39 
                                       ++s++Gq+ e+++ ++ +
  gi|298675554|ref|YP_003727304.1|  90 LTSFGGQTPEPGKFNEPQ 107
                                       8999***99999988866 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 2.6e-08
                             PDZ_6   2 VtaVdpgsPAdrAGlrvGDiilsvNGqpveglsladvaallrgsagesv 50 
                                       +t V  +sPA +AG+  + +i+++N++ +  ++ +dv++++ +  + s+
  gi|298675554|ref|YP_003727304.1| 243 ITDVNSESPANKAGIDENMVITQINDTQT--RNANDVINYMMNVSPGST 289
                                       78999************************..*********995544444 PP

  == domain 3  score: 31.0 bits;  conditional E-value: 7.5e-11
                             PDZ_6   2 VtaVdpgsPAdrAGlrvGDiilsvNGqpveglsladvaallr.gsagesvvl 52 
                                       ++ V++gsPA++ Gl+ G +i+ +++ +v  +s++d++++++ +s+g++v++
  gi|298675554|ref|YP_003727304.1| 320 ISDVVEGSPAENSGLEKGMLIVGIDNNSV--QSINDFSNYMEnTSPGQEVEI 369
                                       899**************************..***********9999998887 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.5   1.3e-06    0.0028      27      79 ..     240     292 ..     228     295 .. 0.89
   2 !   32.1   0.3   4.9e-11   1.1e-07      23      80 ..     311     370 ..     297     372 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.3e-06
                                       SEEEEEECTTSHHHHHTSSTTEEEEEETTEETTTSHHHHHHHHHHTTTSEEEE CS
                               PDZ  27 gifvsevlpggaaeadglkvGDkIlsvNgvdvenvsheeavqaikgskgkvtL 79 
                                        + +++v+  ++a+++g+ ++ +I+++N++ ++n ++  +  ++ +++++v +
  gi|298675554|ref|YP_003727304.1| 240 DAMITDVNSESPANKAGIDENMVITQINDTQTRNANDVINYMMNVSPGSTVEV 292
                                       578*********************************99999999999997765 PP

  == domain 2  score: 32.1 bits;  conditional E-value: 4.9e-11
                                       S..SSSSEEEEEECTTSHHHHHTSSTTEEEEEETTEETTTSHHHHHHHHHHTTTSEEEEE CS
                               PDZ  23 r..gdkgifvsevlpggaaeadglkvGDkIlsvNgvdvenvsheeavqaikgskgkvtLt 80 
                                       +  + +gi++s+v++g++ae +gl++G  I+++++ +v ++++  +  ++++++++v ++
  gi|298675554|ref|YP_003727304.1| 311 EheQVQGIYISDVVEGSPAENSGLEKGMLIVGIDNNSVQSINDFSNYMENTSPGQEVEIK 370
                                       235889****************************************99999999998765 PP

>> PDZ_1  PDZ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.3   9.5e-05      0.21      41      75 ..     250     284 ..     237     285 .. 0.80
   2 !   11.7   0.1   8.8e-05       0.2      29      74 ..     314     360 ..     309     362 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.5e-05
                             PDZ_1  41 sfklsskekkgviitsinnqptpnLdefievvkki 75 
                                       s++ + +++ +++it+in+++t+n +++i+ + ++
  gi|298675554|ref|YP_003727304.1| 250 SPANKAGIDENMVITQINDTQTRNANDVINYMMNV 284
                                       55555668999******************999775 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 8.8e-05
                             PDZ_1  29 pvkgvyvse.asgsfklsskekkgviitsinnqptpnLdefievvkk 74 
                                        v+g+y+s+  +gs++ +s+ +kg++i  i+n  +++ ++f + +++
  gi|298675554|ref|YP_003727304.1| 314 QVQGIYISDvVEGSPAENSGLEKGMLIVGIDNNSVQSINDFSNYMEN 360
                                       57788888625888888999**********************99975 PP

>> Tricorn_PDZ  Tricorn protease PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.2   0.00036      0.81      25      77 ..     244     295 ..     235     307 .. 0.81
   2 !   13.8   0.1   1.9e-05     0.042      25      78 ..     321     373 ..     302     380 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00036
                                       TSSS-B-GGGGGS---.TT-EEEEETTEE-BTTB-HHHHHHTTT.TSEEEEEEE CS
                       Tricorn_PDZ  25 wdeearSPLaepGvnvreGdlilavdgepvskekgiaelLvgka.gkeveLtvk 77 
                                       +d + +SP ++ G++  e  +i+++++ ++++ +++ +++++ + g++ve++  
  gi|298675554|ref|YP_003727304.1| 244 TDVNSESPANKAGID--ENMVITQINDTQTRNANDVINYMMNVSpGSTVEVHAV 295
                                       678899*********..999***********99999998888652678887654 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.9e-05
                                       TSSS-B-GGGGGS---.TT-EEEEETTEE-BTTB-HHHHHHTTT.TSEEEEEEE- CS
                       Tricorn_PDZ  25 wdeearSPLaepGvnvreGdlilavdgepvskekgiaelLvgka.gkeveLtvkr 78 
                                       +d  + SP +++G++  +G li+ +d ++v++ +++++++++++ g+eve++  +
  gi|298675554|ref|YP_003727304.1| 321 SDVVEGSPAENSGLE--KGMLIVGIDNNSVQSINDFSNYMENTSpGQEVEIKALK 373
                                       344578*********..9************************9747999998655 PP

>> GRASP55_65  GRASP55/65 PDZ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.028        62      47      64 ..     243     260 ..     238     305 .. 0.79
   2 !   12.3   0.0   7.3e-05      0.16      35      89 ..     308     361 ..     280     389 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.028
                                       EEEEBTTSHHHHHT--TT CS
                        GRASP55_65  47 vldvlegsPaakagLvpk 64 
                                       + dv+++sPa+kag+ ++
  gi|298675554|ref|YP_003727304.1| 243 ITDVNSESPANKAGIDEN 260
                                       789***********9765 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 7.3e-05
                                       EE-TTTTTS-EEEEEEBTTSHHHHHT--TTTEEEEEEE.SSSSSTSCSHHHHTTT CS
                        GRASP55_65  35 aslekaaeevwhvldvlegsPaakagLvpksDYiiGldkgllkgeedlselveah 89 
                                       ++ e+ + + + + dv egsPa+++gL +    i+G+d++ +++ +d+s+ +e++
  gi|298675554|ref|YP_003727304.1| 308 QDKEHEQVQGIYISDVVEGSPAENSGLEK-GMLIVGIDNNSVQSINDFSNYMENT 361
                                       44444455667799************975.569****************999986 PP

>> DUF3394  Domain of unknown function (DUF3394)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1   0.00065       1.5     123     160 ..     241     278 ..     232     285 .. 0.87
   2 ?    3.7   0.1     0.019        43      98     152 ..     291     347 ..     279     362 .. 0.73
   3 ?   -3.4   0.0       2.9   6.5e+03     141     172 ..     525     556 ..     522     559 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00065
                           DUF3394 123 vlvdevefgspaekagldfdfeivevevpadrppkelv 160
                                       +++  v+++spa+kag+d ++ i++++  + r +++++
  gi|298675554|ref|YP_003727304.1| 241 AMITDVNSESPANKAGIDENMVITQINDTQTRNANDVI 278
                                       68999*********************999988777665 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.019
                           DUF3394  98 plgeeatgeerLeaaGltlleedg..kvlvdevefgspaekagldfdfeivevevpa 152
                                       ++++ ++g +   ++ ++  e+++   + ++ v  gspae++gl+ ++ iv +  ++
  gi|298675554|ref|YP_003727304.1| 291 EVHAVKDGTTSTYEVDIQDKEHEQvqGIYISDVVEGSPAENSGLEKGMLIVGIDNNS 347
                                       555555666666666665555433336789******************999987665 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 2.9
                           DUF3394 141 fdfeivevevpadrppkelvyipAllllalva 172
                                       f ++i+  e +a++ +  ++ i +l++l+ +a
  gi|298675554|ref|YP_003727304.1| 525 FAQRITGSEGSAENIAGAVTMILTLFILISFA 556
                                       67788888889999999999999998887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (568 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:01.62
# Mc/sec: 1060.77
//
Query:       gi|298675555|ref|YP_003727305.1|  [L=102]
Description: CutA1 divalent ion tolerance protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-34  117.9   0.4    1.6e-34  117.7   0.4    1.0  1  CutA1     CutA1 divalent ion tolerance protein
  ------ inclusion threshold ------
       0.12   12.6   0.0       0.14   12.4   0.0    1.3  1  DUF4873   Domain of unknown function (DUF4873)


Domain annotation for each model (and alignments):
>> CutA1  CutA1 divalent ion tolerance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.7   0.4   1.7e-38   1.6e-34       3      98 ..       5      98 ..       3      99 .. 0.98

  Alignments for each domain:
  == domain 1  score: 117.7 bits;  conditional E-value: 1.7e-38
                                      EEEEESSHHHHHHHHHHHHHTTS-SEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEGGGHHHHHHHHHHHSSSSS-EEE CS
                             CutA1  3 vlvtapseeeakklaralveeklaACvnilpkieSvYrWkgkieedkEvllliktreekveelekrvkelhpyevpeii 81
                                      v++ta s+eea+++ +alv+ekl+ACvn++p i+S+Y+W+g++eed+E+ +l+kt+++++e+++krv+elh+y+ p+i+
  gi|298675555|ref|YP_003727305.1|  5 VYITAGSMEEAREIGSALVSEKLVACVNMFP-ISSIYEWQGNMEEDEEIAMLVKTTSDRFEKIKKRVQELHSYDQPCIV 82
                                      8******************************.*********************************************** PP

                                      EEEESEEEHHHHHHHHH CS
                             CutA1 82 alpieagseaYlkWiee 98
                                      +++i+ g++ Y+kW+ +
  gi|298675555|ref|YP_003727305.1| 83 TWDIS-GETGYMKWVYD 98
                                      ****9.********975 PP

>> DUF4873  Domain of unknown function (DUF4873)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.6e-05      0.14      26      53 ..      32      59 ..      12      90 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.6e-05
                           DUF4873 26 hfePidGryrWyGrvaaeeelkealekk 53
                                      ++ Pi+  y+W+G ++++ee++  ++++
  gi|298675555|ref|YP_003727305.1| 32 NMFPISSIYEWQGNMEEDEEIAMLVKTT 59
                                      566*****************99988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1048  (0.0584528); expected 358.6 (0.02)
Passed bias filter:                      777  (0.0433376); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 746.68
//
Query:       gi|298675556|ref|YP_003727306.1|  [L=278]
Description: tartrate/fumarate subfamily hydro-lyase subunit alpha [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-95  318.3   0.0    4.7e-95  318.1   0.0    1.0  1  Fumerase  Fumarate hydratase (Fumerase)


Domain annotation for each model (and alignments):
>> Fumerase  Fumarate hydratase (Fumerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  318.1   0.0   2.6e-99   4.7e-95       3     269 ..      12     272 ..      10     273 .. 0.97

  Alignments for each domain:
  == domain 1  score: 318.1 bits;  conditional E-value: 2.6e-99
                          Fumerase   3 aveealkeastelpedvlealkkalekEesenakevleqlleNaeiAaeeklplCqDTGiavvfvkigeevevetgd 79 
                                       a+ ++lk+ +t+lp+dv++alk+a ++E+se+a+++++++l+N++iA+++++p+CqDTGi +++++ig++++  + d
  gi|298675556|ref|YP_003727306.1|  12 ATINVLKKSETSLPDDVVDALKSAENTESSEVARSQINAVLKNVDIARKHEIPMCQDTGILIFYIQIGKKLR-LDFD 87 
                                       5668899****************************************************************8.999* PP

                          Fumerase  80 leeaineGvreaykegplRksvvadplerkntgd....nlPavihielvpgdeleitvlakGgGsenksklkmlnps 152
                                       le+ai+eGvr a+++ plR+++v dp++rkn+g+    +lP  i++++++g+ l+itv++kG+Gsen+s+l+m+np+
  gi|298675556|ref|YP_003727306.1|  88 LEDAIEEGVRYATSDIPLRPNAV-DPITRKNSGNnvgtGLP-DIKYQFIEGNCLTITVAPKGAGSENMSRLQMFNPT 162
                                       ***********************.**********999999*.**********************************7 PP

                          Fumerase 153 dglegvkkfvletvkeagtnaCpPlvlgvgiGgtseeaallakkallrelgeenpdeelaeleeellekinklgiGp 229
                                       + l+++kkf  etv +ag+++CpPl+lg+giGg++++a +lak all++++e        ++e+++l+++n+lgiGp
  gi|298675556|ref|YP_003727306.1| 163 Q-LDSIKKFATETVLNAGGKPCPPLILGIGIGGSFDKAPRLAKSALLENISEM------DDFEKDILDDVNSLGIGP 232
                                       7.********************************************9999554......59**************** PP

                          Fumerase 230 qGlGGkttvldvkierlprhiAslpvavnvsCsadRrakv 269
                                       +G+GG+tt+l+vk+++ ++h+Aslpvavn++C+a+R+a+v
  gi|298675556|ref|YP_003727306.1| 233 MGIGGDTTALSVKVKKSHCHTASLPVAVNIQCWANRHASV 272
                                       *************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1568.03
//
Query:       gi|298675557|ref|YP_003727307.1|  [L=190]
Description: tartrate/fumarate subfamily hydro-lyase subunit beta [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    9.8e-46  155.7   0.0    1.2e-45  155.4   0.0    1.0  1  Fumerase_C  Fumarase C-terminus


Domain annotation for each model (and alignments):
>> Fumerase_C  Fumarase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.4   0.0   6.7e-50   1.2e-45      36     205 ..       9     178 ..       4     179 .. 0.93

  Alignments for each domain:
  == domain 1  score: 155.4 bits;  conditional E-value: 6.7e-50
                        Fumerase_C  36 eteeelskykvgtrlllsGkllvaRDaaHkrlkerlekgeelpeyvklkdrviYyaGPv..ktpedeavgsaGPTTa 110
                                       + ++++ k+++g+ + l+G++l+aRD aHkr+ e  ekg++lp  ++l+++v+Y++GP   k ++++ v +aGPTT+
  gi|298675557|ref|YP_003727307.1|   9 IDKQDIMKLNTGDIVYLTGTVLTARDEAHKRILEIAEKGKNLP--FELNGSVVYHCGPLmkKDNGGWDVVAAGPTTS 83 
                                       567899*************************************..9999*********98788899*********** PP

                        Fumerase_C 111 tRmdkyvekllkktgllimlaKgnrskkvleaikkhggvYLgaiGGaAilakkaikkvevvefeelGm.EAiyeiev 186
                                       +Rm   + +ll+k+++++ ++Kg++  +v +++ k+++vYL   GG A la ++ikkv+ v + +lGm EA++e+e+
  gi|298675557|ref|YP_003727307.1|  84 SRMSGMTPELLEKFNVRALVGKGGMQ-NVSDSM-KNRCVYLAYTGGCAALAVESIKKVSNVYWLDLGMpEAVWELEI 158
                                       ***********************995.566666.679**************************************** PP

                        Fumerase_C 187 edf.pafvvvddkGndlfke 205
                                       ++f p +v +d+kGndl++e
  gi|298675557|ref|YP_003727307.1| 159 KNFgPLIVGIDAKGNDLYSE 178
                                       ***778888*********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1165.89
//
Query:       gi|298675558|ref|YP_003727308.1|  [L=173]
Description: hypothetical protein Metev_1672 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-48  163.7   0.0    2.1e-48  163.3   0.0    1.2  1  Ribo_biogen_C  Ribosome biogenesis protein, C-terminal
    1.6e-11   43.8   0.3    2.5e-11   43.2   0.3    1.3  1  RLI            Possible Fer4-like domain in RNase L inhibitor
  ------ inclusion threshold ------
      0.024   14.2   0.0      0.034   13.7   0.0    1.3  1  RNA_Me_trans   Predicted SAM-dependent RNA methyltransferase


Domain annotation for each model (and alignments):
>> Ribo_biogen_C  Ribosome biogenesis protein, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.3   0.0   3.5e-52   2.1e-48       1     127 []      48     172 ..      48     172 .. 0.96

  Alignments for each domain:
  == domain 1  score: 163.3 bits;  conditional E-value: 3.5e-52
                                       EEE-TT-SSB--GGGHHHHHHT-EEEE---TTT--GGGTTT-E.....EB--S-B--STTTTT-BS---HHHHHHHH CS
                     Ribo_biogen_C   1 ivlspkakkvlspaDreiveksgiavvdcsWarleevkfkklkak.eerlLPyLvAaNpvnYgkplkLscvEAlaaa 76 
                                       i+l+p+a+++lspaD+    ++gi+v+dcsW+++++v  + lk + ++r+LP+LvAaNpvn+gkp++L++vEA+aaa
  gi|298675558|ref|YP_003727308.1|  48 ILLDPMAEQALSPADD---VSKGITVLDCSWEEIDKVLPQILKRNlKHRALPFLVAANPVNFGKPFRLNSVEAFAAA 121
                                       79*************4...469***************9887776679****************************** PP

                                       HHHTT-HHHHHHHHTSSTTHHHHHHHCHHHHHHH.TT--HHHHHHHHHHHH CS
                     Ribo_biogen_C  77 lyilglkeeaeellskfkwgeeFlelnkelleeYakckdseevvevqkeyl 127
                                       lyi+g+k++a+++lskfkwg +F+e+nke+leeY+++kds+e++++q++yl
  gi|298675558|ref|YP_003727308.1| 122 LYITGHKQQASDILSKFKWGLHFIEMNKEPLEEYSRAKDSTEIIQIQNQYL 172
                                       *************************************************97 PP

>> RLI  Possible Fer4-like domain in RNase L inhibitor, RLI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.3   4.1e-15   2.5e-11       2      34 ..       9      45 ..       8      46 .. 0.89

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 4.1e-15
                                      -EEEES---------TTHHHHHTTSEEE....ESS-- CS
                               RLI  2 rlAivdadqCdPKKCtgkkcarfcpvrl....vrtgk 34
                                       l+i++  qCdPKKCtgkk+arf ++++    +++++
  gi|298675558|ref|YP_003727308.1|  9 ELYIYHVSQCDPKKCTGKKMARFYLAQIfdkiNKIPR 45
                                      69************************99877777776 PP

>> RNA_Me_trans  Predicted SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.7e-06     0.034      62      93 ..      34      64 ..       3      71 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.7e-06
                      RNA_Me_trans 62 eellkelkevkkekvclLDpkaekelspedae 93
                                       +++++ +++  + ++lLDp ae++lsp+d  
  gi|298675558|ref|YP_003727308.1| 34 AQIFDKINKI-PRGCILLDPMAEQALSPADDV 64
                                      4555555433.6789**************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1095.22
//
Query:       gi|298675559|ref|YP_003727309.1|  [L=375]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-26   92.3   1.8    2.5e-26   92.3   1.8    1.8  2  OrfB_IS605      Probable transposase
      7e-24   83.5   0.4    1.4e-23   82.5   0.4    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    2.8e-19   68.3   1.0    6.2e-19   67.2   1.0    1.6  1  HTH_OrfB_IS605  Helix-turn-helix domain
     0.0069   16.5   0.3      0.016   15.4   0.3    1.5  1  zf-piccolo      Piccolo Zn-finger
  ------ inclusion threshold ------
      0.015   15.6   5.5        0.2   11.9   1.2    2.4  2  MapZ_EC1        MapZ extracellular domain 1
      0.033   14.1   0.7       0.31   10.9   0.1    2.3  2  LemA            LemA family
      0.084   12.7   6.9       0.28   11.0   1.7    2.4  2  Phage_GP20      Phage minor structural protein GP20
       0.33   11.0   1.9       0.61   10.1   0.6    2.0  2  HypA            Hydrogenase/urease nickel incorporation, meta
        2.4    8.0   5.7         21    5.0   1.0    2.9  2  DivIC           Septum formation initiator
        3.8    8.4   6.1        1.4    9.7   0.4    2.5  3  Ima1_N          Ima1 N-terminal domain


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       5.6     1e+04      42      54 ..      55      68 ..      41      73 .. 0.59
   2 !   92.3   1.8   1.4e-29   2.5e-26      10     117 ..     172     276 ..     159     278 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 5.6
                        OrfB_IS605 42 kg.rrlksdykyla 54
                                      k  r lk dy++l+
  gi|298675559|ref|YP_003727309.1| 55 KQiRALKDDYEWLK 68
                                      33255566666554 PP

  == domain 2  score: 92.3 bits;  conditional E-value: 1.4e-29
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsr 86 
                                       +++  + +++g+D+Gi+++a++++++   ++ ++r lk+  ++l+  +++l++k+k+s+ny+k + ++a++h+k+++
  gi|298675559|ref|YP_003727309.1| 172 KQTFYEVNTIGVDVGIKDFAVTSDGE---KIDNPRYLKNSIERLKVLQKRLSRKKKGSNNYRKLKHQIAKYHEKIAN 245
                                       44555689******************...************************************************ PP

                        OrfB_IS605  87 rrkhllhklathliktlkevgvetLnvgnmk 117
                                       +r +++hkl+++li ++++v++e Lnv+++ 
  gi|298675559|ref|YP_003727309.1| 246 QREDFQHKLSSRLISENQAVALECLNVKGLL 276
                                       ****************************986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.5   0.4   8.1e-27   1.4e-23       1      68 [.     290     359 ..     290     360 .. 0.98

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 8.1e-27
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpay.TSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       ++++ ++leyka++yG+++++++++  +Sk C++Cg+ +++ +l++r+++Cp+C++ +drD+nA++Ni k
  gi|298675559|ref|YP_003727309.1| 290 WSSFVQKLEYKAEWYGKNIIKIERFDpSSKICHVCGYHHQDlELKDREWECPDCKTIHDRDINASVNIKK 359
                                       99******************************************************************87 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.2   1.0   3.5e-22   6.2e-19       1      47 []       1      46 [.       1      46 [. 0.98

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 3.5e-22
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeegk 47
                                      M lkaykyr yP+++Q+e++ +++G++Rf+YN+aL+ +++ ye+ gk
  gi|298675559|ref|YP_003727309.1|  1 M-LKAYKYRMYPNQTQQELITKHIGASRFIYNWALENKIKSYEQDGK 46
                                      8.******************************************997 PP

>> zf-piccolo  Piccolo Zn-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.3   8.7e-06     0.016      28      55 ..     318     345 ..     314     348 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.7e-06
                        zf-piccolo  28 kqvCnlCGFnptphltekkeWlclnCQt 55 
                                       +++C +CG+  ++   + +eW c  C t
  gi|298675559|ref|YP_003727309.1| 318 SKICHVCGYHHQDLELKDREWECPDCKT 345
                                       79************************86 PP

>> MapZ_EC1  MapZ extracellular domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.2     0.011        20      47      84 ..      33      73 ..      20     101 .. 0.81
   2 ?   11.9   1.2   0.00011       0.2      37      78 ..     205     246 ..     166     269 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.011
                          MapZ_EC1 47 eLekkLeklk.gskeYk..klkkkldslkkqisaieavNsq 84
                                      +Le+k++ ++ + k  +  +l+k++ +lk+ ++ ++++Nsq
  gi|298675559|ref|YP_003727309.1| 33 ALENKIKSYEqDGKAISrfELNKQIRALKDDYEWLKEINSQ 73
                                      577777777754444332279******************98 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00011
                          MapZ_EC1  37 lknsefaklseLekkLeklk.gskeYkklkkkldslkkqisai 78 
                                       lkns ++ l+ L+k L   k gs++Y+klk+++++  ++i+ +
  gi|298675559|ref|YP_003727309.1| 205 LKNS-IERLKVLQKRLSRKKkGSNNYRKLKHQIAKYHEKIANQ 246
                                       4443.688999*****98777*****************99865 PP

>> LemA  LemA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0       0.2   3.6e+02      45      82 ..      67     104 ..      36     108 .. 0.80
   2 ?   10.9   0.1   0.00018      0.31      55     107 ..     200     253 ..     172     260 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.2
                              LemA  45 aeaesveekaeaenqlssalsrllavaEnYPdLkanen 82 
                                        ++ + ++ + a  +l++a+ +++     +P++k+++n
  gi|298675559|ref|YP_003727309.1|  67 LKEINSQSLQGATLNLENAFTKFFKEKSGFPKFKSKKN 104
                                       56667788899999999********9999***999987 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00018
                              LemA  55 eaenqlssalsrllavaEnY.PdLkanenfleLqeelegtEnriavaRrrYnea 107
                                       ++ + l+++++rl +++ +   + k ++n+++L++++++  ++ia++R++++++
  gi|298675559|ref|YP_003727309.1| 200 DNPRYLKNSIERLKVLQKRLsRKKKGSNNYRKLKHQIAKYHEKIANQREDFQHK 253
                                       5556677777777777776414567899**********************9876 PP

>> Phage_GP20  Phage minor structural protein GP20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.3      0.02        36     112     136 ..      42      69 ..      12      84 .. 0.64
   2 ?   11.0   1.7   0.00016      0.28      32      90 ..     210     268 ..     197     278 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.02
                        Phage_GP20 112 kedgelkg...LdeqikkLkesdkyLFe 136
                                       ++dg+ +    L++qi +Lk+++++L e
  gi|298675559|ref|YP_003727309.1|  42 EQDGKAISrfeLNKQIRALKDDYEWLKE 69 
                                       3455544333377777777777777754 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00016
                        Phage_GP20  32 eqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeyeakiadlkldnaielaLk 90 
                                       e+lk  +k L+  kk +++  +L+ qi+++ +k++++ ++ + k++ + +++    aL+
  gi|298675559|ref|YP_003727309.1| 210 ERLKVLQKRLSRKKKGSNNYRKLKHQIAKYHEKIANQREDFQHKLSSRLISENQAVALE 268
                                       6788889999999********************************99888776666666 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       4.8   8.6e+03      43      66 ..      59      84 ..      55      89 .. 0.65
   2 ?   10.1   0.6   0.00034      0.61      68      95 ..     316     346 ..     292     361 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 4.8
                                      HHHHHHHHHH..CC.TTTT-EEEEEE CS
                              HypA 43 aLefafella..egtvlegaeLeiee 66
                                      aL+  +e+l+  +++ l+ga+L++e+
  gi|298675559|ref|YP_003727309.1| 59 ALKDDYEWLKeiNSQSLQGATLNLEN 84
                                      56666777762234558888888876 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00034
                                       --EEEETTTS-EEE.CHH.H.HHS-TTTSSS CS
                              HypA  68 pvkvrCreCgkefe.lee.k.alrCpkCgsa 95 
                                       p +  C++Cg++ + le  + + +Cp+C++ 
  gi|298675559|ref|YP_003727309.1| 316 PSSKICHVCGYHHQdLELkDrEWECPDCKTI 346
                                       55678*****9988444343688*****975 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.2     0.019        34      18      42 ..      49      73 ..      32      80 .. 0.80
   2 ?    5.0   1.0     0.012        21      13      39 ..     223     249 ..     214     258 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.019
                                      HHHHHHHHHHHHHHHHHHHHHHHHH CS
                             DivIC 18 aykqlkqeiaalqaelaklkaenee 42
                                      ++++l+++i al+++++ lk+ n +
  gi|298675559|ref|YP_003727309.1| 49 SRFELNKQIRALKDDYEWLKEINSQ 73
                                      5678888888888888888887765 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.012
                                       XXXXXHHHHHHHHHHHHHHHHHHHHHH CS
                             DivIC  13 kkgllaykqlkqeiaalqaelaklkae 39 
                                       kkg ++y++lk +ia+  +++a+++++
  gi|298675559|ref|YP_003727309.1| 223 KKGSNNYRKLKHQIAKYHEKIANQRED 249
                                       68999******************9987 PP

>> Ima1_N  Ima1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2       1.2   2.1e+03      91     121 ..     214     244 ..     202     254 .. 0.71
   2 ?    0.1   0.6      0.78   1.4e+03      61      97 ..     250     286 ..     221     314 .. 0.44
   3 ?    9.7   0.4   0.00081       1.4       3      31 ..     321     349 ..     320     367 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.2
                            Ima1_N  91 klaeylpkededdpeyeekeealeeykkele 121
                                        l++ l+++++ +++y++ ++++ +y++++ 
  gi|298675559|ref|YP_003727309.1| 214 VLQKRLSRKKKGSNNYRKLKHQIAKYHEKIA 244
                                       5555566566777778888888888887765 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.78
                            Ima1_N  61 skskseeaessssssllCskClknqe.lkvsklaeylp 97 
                                        ++k  +++  s+++ +  +Cl+ +  lk+++la+ + 
  gi|298675559|ref|YP_003727309.1| 250 FQHK-LSSRLISENQAVALECLNVKGlLKNHNLAQHIT 286
                                       1111.123344445555555554443134445555544 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00081
                            Ima1_N   3 CffCnkkskvkyeeknsfeCpsCeayNgf 31 
                                       C+ C+ + +    +++++eCp+C+ +   
  gi|298675559|ref|YP_003727309.1| 321 CHVCGYHHQDLELKDREWECPDCKTIHDR 349
                                       ********999999999******987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1496  (0.0834402); expected 358.6 (0.02)
Passed bias filter:                      643  (0.0358637); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.52
# Mc/sec: 2176.37
//
Query:       gi|298675560|ref|YP_003727310.1|  [L=184]
Description: ferritin Dps family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.2e-23   82.3   0.0    3.8e-23   82.0   0.0    1.1  1  Ferritin    Ferritin-like domain
     0.0032   17.7   0.0     0.0042   17.3   0.0    1.2  1  Ferritin_2  Ferritin-like domain


Domain annotation for each model (and alignments):
>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.0   0.0   4.2e-27   3.8e-23       2     138 ..      21     162 ..      20     165 .. 0.92

  Alignments for each domain:
  == domain 1  score: 82.0 bits;  conditional E-value: 4.2e-27
                                       HHHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHH......C CS
                          Ferritin   2 kaLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraelee......i 72 
                                       ++L +  a+e+t  y+y  + +++ g + eg++e  ++  +e r+h+++l+ ri +lGg+ + + +e+++       
  gi|298675560|ref|YP_003727310.1|  21 DLLVKNAAAEFTTFYYYTLLRFNLIGLDGEGIKEIAEDARIEDRNHFEALLPRIYELGGEIPNDMKEFHDisgcppA 97 
                                       6899999***************************************************************7776652 PP

                                       -SSSSCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin  73 eapkefgsveevleaalehekkvteslrelielaeeegDpatadfledfleeqeeheweleallek 138
                                       + p++ ++v+e+l+ ++e+e+++++++  ++++++ + D+ t+d++  +l+e+++he++++++l++
  gi|298675560|ref|YP_003727310.1|  98 YLPENPNDVQEILKVLVEAERCAVRQYTHICNMTAGK-DHRTYDLALAILHEEVQHEAWFAEFLGE 162
                                       2233356****************************96.************************9986 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   4.6e-07    0.0042      19     136 .]      34     162 ..      20     162 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.6e-07
                        Ferritin_2  19 fYtaalegaslddkalldaevrevaeeiakheeaHveflkaale..Gaaa.vakptf.df.......afdpfadeks 84 
                                       fY + l +++l   +l  + ++e+ae+++ + ++H e+l   +   G++   ++ +f d+         ++ +d ++
  gi|298675560|ref|YP_003727310.1|  34 FYYYTLLRFNL--IGLDGEGIKEIAEDARIEDRNHFEALLPRIYelGGEIpNDMKEFhDIsgcppayLPENPNDVQE 108
                                       66666666654..45555667999999999999999999998888955551344444333777766678888999** PP

                        Ferritin_2  85 flalaavlEdvgvsAYlgaapllsnke..lltaaasIlsvEArHaavirtllge 136
                                       +l++    E+ +v+ Y    ++ + k+     +a+ Il  E +H a++++ lge
  gi|298675560|ref|YP_003727310.1| 109 ILKVLVEAERCAVRQYTHICNMTAGKDhrTYDLALAILHEEVQHEAWFAEFLGE 162
                                       *********************998666448899***************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1092.06
//
Query:       gi|298675561|ref|YP_003727311.1|  [L=273]
Description: zinc/iron permease [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-17   64.3  17.3    2.8e-12   46.5  10.0    2.2  2  Zip       ZIP Zinc transporter


Domain annotation for each model (and alignments):
>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.5   2.7e-09   4.8e-05       9     101 ..      21     106 ..      13     121 .. 0.77
   2 !   46.5  10.0   1.5e-16   2.8e-12     185     332 ..     122     268 ..     111     269 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 2.7e-09
                               Zip   9 iaililsllgllgpllvpkiskllsklllslllafavGvllgtaflhLlPealealeesqleeehthplagllvllG 85 
                                       + + +++l g + +++++    + ++l++ ++l fa+Gv+++ +  +Ll++++e+  + q+++  ++  a + +llG
  gi|298675561|ref|YP_003727311.1|  21 VFTWMMTLTGASAVFIIR----DVDRLIMDVMLGFAAGVMIAASYWSLLAPSIEM--SLQNGQ-LPWFPALVGFLLG 90 
                                       444555666666666666....56899***************************5..444444.8998899999*** PP

                               Zip  86 flllllveklltmive 101
                                        ++l  ++kll ++  
  gi|298675561|ref|YP_003727311.1|  91 GVFLRGIDKLLPHLQY 106
                                       *********9988754 PP

  == domain 2  score: 46.5 bits;  conditional E-value: 1.5e-16
                               Zip 185 raiilllglilHsfidGLAlG...........vssssstgislfiAvllHelpeelglgaiLlkaglsrkkavllnl 250
                                       r+ +l+l++ lH++++GLA+G             ++ s +++l+i + + +lpe+  + ++L + g+s+ k +l+  
  gi|298675561|ref|YP_003727311.1| 122 RSTLLVLAVTLHNIPEGLAIGvafgavagggyPYATLSGAMALTIGIGIQNLPEGTVVSVPLRRDGMSSFKSFLYGQ 198
                                       6789*****************99887666665578999*************************************** PP

                               Zip 251 lfaltaplGiliGilvrsisessgaeivsgillalsaGtflYvalvellphEllnekgssslkqsllqllglllGfa 327
                                        +a++ p++ ++G +            + ++ la++aG ++ v + e++p E  +        +  l+ +g ++Gf 
  gi|298675561|ref|YP_003727311.1| 199 SSAIVEPVASVVGAA-----LVILVRPLLPYALAFAAGAMIFVVVEEMIP-ESQRGG------NAPLATMGSMVGFS 263
                                       ***************.....777788899999******************.666666......7999********** PP

                               Zip 328 lmlll 332
                                       lm++l
  gi|298675561|ref|YP_003727311.1| 264 LMMVL 268
                                       **998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1669.89
//
Query:       gi|298675562|ref|YP_003727312.1|  [L=263]
Description: ABC transporter-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.9e-35  121.4   0.0    6.2e-35  120.7   0.0    1.3  1  ABC_tran     ABC transporter
    1.6e-10   41.3   3.0    1.3e-06   28.4   0.2    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    8.4e-07   29.7   1.7    1.3e-06   29.1   1.7    1.3  1  AAA_23       AAA domain
    1.2e-05   25.3   2.8      0.014   15.1   1.3    2.3  2  AAA_15       AAA ATPase domain
    0.00022   20.7   0.3    0.00032   20.2   0.3    1.3  1  SMC_N        RecF/RecN/SMC N terminal domain
     0.0006   19.8   0.1    0.00094   19.2   0.1    1.4  1  Rad17        Rad17 P-loop domain
    0.00087   19.7   0.5     0.0067   16.8   0.5    2.3  1  AAA          ATPase family associated with various cellular a
     0.0011   18.7   0.2     0.0022   17.7   0.2    1.4  1  AAA_29       P-loop containing region of AAA domain
     0.0034   17.3   1.0      0.015   15.3   0.0    2.2  3  RsgA_GTPase  RsgA GTPase
     0.0036   17.6   0.3      0.015   15.6   0.3    1.9  1  AAA_22       AAA domain
  ------ inclusion threshold ------
      0.011   14.4   0.2       0.88    8.1   0.0    2.2  2  AAA_13       AAA domain
      0.024   14.3   0.4      0.088   12.4   0.1    1.9  2  SRP54        SRP54-type protein, GTPase domain
      0.035   14.7   0.0      0.088   13.4   0.0    1.7  1  TNT          Tuberculosis necrotizing toxin
      0.035   13.8   0.0      0.055   13.2   0.0    1.5  1  AAA_30       AAA domain
      0.055   13.1   0.0      0.079   12.5   0.0    1.4  1  AAA_27       AAA domain
       0.21   11.8   0.3        1.7    8.9   0.1    2.4  3  AAA_28       AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.7   0.0   5.5e-38   6.2e-35       2     136 ..      38     180 ..      37     181 .. 0.98

  Alignments for each domain:
  == domain 1  score: 120.7 bits;  conditional E-value: 5.5e-38
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       ++++++++ege+ a++G+nGaGK+t lk+l+  l+pt+G+i+++g d+ + +++ +rk+igv++q ++l+++lt++e
  gi|298675562|ref|YP_003727312.1|  38 DDITFNVNEGEIFAFLGPNGAGKTTSLKILTTILQPTSGNIKVNGYDVLH-KKNDVRKSIGVIFQSNSLDEKLTAYE 113
                                       89************************************************.999*********************** PP

                                       H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n             e + +++k+l++++l + kd+ +    +++SgG+k+r+++ar l+  p++l+lDEpt
  gi|298675562|ref|YP_003727312.1| 114 NmeyhavlykvpkkEIKGRVNKLLENVELLDRKDDLI----KTFSGGMKRRIEIARGLIHTPQVLFLDEPT 180
                                       **********999888899*****************9....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.5   4.5e-05      0.05       2      26 ..      50      82 ..      49     113 .. 0.68
   2 !   28.4   0.2   1.2e-09   1.3e-06     209     299 ..     143     213 ..      80     215 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.5e-05
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarl........d 26
                                       ++ GpNg+GK++ L++l  + +          
  gi|298675562|ref|YP_003727312.1| 50 FAFLGPNGAGKTTSLKILTTILQPtsgnikvnG 82
                                      6899**************877664444444443 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 1.2e-09
                            AAA_21 209 iasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkel 285
                                        ++ d++++                   +S G+kr + ++  l+ ++    +l++DEp  gL+ +  + l+e +++l
  gi|298675562|ref|YP_003727312.1| 143 LDRKDDLIKT------------------FSGGMKRRIEIARGLIHTP---QVLFLDEPTIGLDAHTRAFLWEYIRNL 198
                                       3333333333..................6888888888888888888...9***********************888 PP

                            AAA_21 286 sr.ngaQviltTHSp 299
                                       ++ n+  v+ltTH+ 
  gi|298675562|ref|YP_003727312.1| 199 KDnNNLTVFLTTHNL 213
                                       888**********95 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   1.7   1.1e-09   1.3e-06      11     175 ..      38     211 ..      28     255 .. 0.62

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1.1e-09
                            AAA_23  11 rdqeidF...skgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayveltfenkdg 84 
                                       +d  i F   +  ++++ GpNGaGKTT l  ++ +L   +++ +       +  dv  +++++v++++ + f++++ 
  gi|298675562|ref|YP_003727312.1|  38 DD--ITFnvnEGEIFAFLGPNGAGKTTSLKILTTILQPTSGNIKV------NGYDVL-HKKNDVRKSIGVIFQSNSL 105
                                       44..455546668***********************986544444......445654.4556888888888877777 PP

                            AAA_23  85 ry....trsiererelskkkgkttkkaklellei....deleqfisellgskki.........ilnlilflgqer.. 142
                                       ++    ++++e+   l+k  +k++k+   +lle     d ++++i++  g  k+           +++lfl++    
  gi|298675562|ref|YP_003727312.1| 106 DEkltaYENMEYHAVLYKVPKKEIKGRVNKLLENvellDRKDDLIKTFSGGMKRrieiargliHTPQVLFLDEPTig 182
                                       66888878888888888877777777766666664557666777777555555534444444344555555444433 PP

                            AAA_23 143 feefelkdkkerleelekeleeledekkllekl 175
                                            ++++   l e+++ l+++++   +l ++
  gi|298675562|ref|YP_003727312.1| 183 L----DAHTRAFLWEYIRNLKDNNNLTVFLTTH 211
                                       1....3444445555555555555555544444 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   1.3   1.2e-05     0.014      24      83 ..      47     113 ..      29     159 .. 0.58
   2 !    9.3   0.0   0.00075      0.84     323     365 ..     170     212 ..     157     214 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.2e-05
                            AAA_15  24 e.ltvliGkNnsGKSsilealdlFlnnkekkn.........kkvikiekedleifeniseskdikIdvef 83 
                                         +  + G+N++GK++ l++l  +l+ + + n         +k+ ++ k+   i   +s+s d k++ ++
  gi|298675562|ref|YP_003727312.1|  47 GeIFAFLGPNGAGKTTSLKILTTILQPT-SGNikvngydvlHKKNDVRKSIGVI--FQSNSLDEKLTAYE 113
                                       36889*********************88.3334666777653222222222222..35566666666555 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00075
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                       ++ +l+++EP + L       l++++++l ++n+  v++tTH+
  gi|298675562|ref|YP_003727312.1| 170 TPQVLFLDEPTIGLDAHTRAFLWEYIRNLKDNNNLTVFLTTHN 212
                                       67899*************************************8 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.3   2.9e-07   0.00032      25     209 ..      48     223 ..      19     233 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.9e-07
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEE.SSSSSSCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkk.lkiekeevsis 100
                                       ++ a +GpNG+GK+  l  +  +L  +s  +++ + + d++hk    ++  + ++ ++f+ ++ +   +  e+++  
  gi|298675562|ref|YP_003727312.1|  48 EIFAFLGPNGAGKTTSLKILTTILQPTSG-NIKVNGY-DVLHK----KNDVRKSIGVIFQSNSLDeKLTAYENMEYH 118
                                       456789**************999*97777.9999876.67787....233333566666444333133444444444 PP

                                       EEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 101 rrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvk 177
                                         +++  +   +i+g+  +  e  ell +++  ++++SgG k  + +a  +      p+   +lDe    LD++ ++
  gi|298675562|ref|YP_003727312.1| 119 AVLYKVPK--KEIKGRVNKLLENVELLDRKDDLIKTFSGGMKRRIEIARGL---IHTPQV-LFLDEPTIGLDAHTRA 189
                                       44444433..4599999999999*******************998887543...234555.568************* PP

                                       HHHHHHHHHCTT..SEEEEE-SSHHHCCC-SCEE CS
                                       xxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 178 kvaellkekskn..aQfivislreemlekadklv 209
                                        + e++++ ++n    ++ ++++ +  ek    +
  gi|298675562|ref|YP_003727312.1| 190 FLWEYIRNLKDNnnLTVFLTTHNLDEAEKIADRI 223
                                       *******776552277777888777766654444 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   8.4e-07   0.00094      46     129 ..      48     131 ..      13     176 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 8.4e-07
                             Rad17  46 riLLisGPsGCgkstvvkvLskelgiklre.wlnpvslkepdnqksdfkgltekesrflsqiesfkeleLkdakylk 121
                                       +i    GP G gk+t +k+L+ +l +   +  +n+  + + +n +    g++ + +++  ++ +++++e ++  y+ 
  gi|298675562|ref|YP_003727312.1|  48 EIFAFLGPNGAGKTTSLKILTTILQPTSGNiKVNGYDVLHKKNDVRKSIGVIFQSNSLDEKLTAYENMEYHAVLYK- 123
                                       478889******************987654279**999999999999999999999999*********99999994. PP

                             Rad17 122 lqklGddl 129
                                       + k+  + 
  gi|298675562|ref|YP_003727312.1| 124 VPKKEIKG 131
                                       44343333 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.5     6e-06    0.0067       3     117 ..      52     218 ..      50     229 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6e-06
                                       EESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSS........................................ CS
                               AAA   3 lyGppGtGKTllakavakelg..vefleisgsellsk........................................ 37 
                                       + Gp G GKT+  k + + l+  +  ++++g ++l k                                        
  gi|298675562|ref|YP_003727312.1|  52 FLGPNGAGKTTSLKILTTILQptSGNIKVNGYDVLHKkndvrksigvifqsnsldekltayenmeyhavlykvpkke 128
                                       78******************754667999999999667999999999999999999999999999999999999999 PP

                                       ....................STTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHH CS
                               AAA  38 ....................yvgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLltel 93 
                                                           +++  +  ++  ++ a+    +p +lf+DE      +           + + L + +
  gi|298675562|ref|YP_003727312.1| 129 ikgrvnkllenvelldrkddLIKTFSGGMKRRIEIARGLIhTPQVLFLDEPTIGLDAH----------TRAFLWEYI 195
                                       99999999999988888888666666666666666655557899******76655555..........668888888 PP

                                       HHTTTSSSTEEEEEEESSGGGSTH CS
                               AAA  94 dgvkkkeskvivigatnrpdkldp 117
                                        ++k++ ++++v ++t++ d+ ++
  gi|298675562|ref|YP_003727312.1| 196 RNLKDN-NNLTVFLTTHNLDEAEK 218
                                       888885.66999999998887654 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.2     2e-06    0.0022      15      55 ..      40      81 ..      32      82 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2e-06
                            AAA_29 15 htieidlkgatlltGpsGsGKSTllDAiqalLvpak.kvrfN 55
                                       t+++++ +++ + Gp+G+GK+T l  ++++L p++ +++ N
  gi|298675562|ref|YP_003727312.1| 40 ITFNVNEGEIFAFLGPNGAGKTTSLKILTTILQPTSgNIKVN 81
                                      4566665559************************98777666 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.3e-05     0.015      68     127 ..      15      75 ..       3      84 .. 0.84
   2 ?    0.2   0.1      0.54     6e+02      62      98 ..     102     138 ..      75     143 .. 0.75
   3 ?   -3.3   0.0       6.5   7.3e+03      51      70 ..     206     224 ..     195     252 .. 0.52

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.3e-05
                                       HHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT----- CS
                       RsgA_GTPase  68 lkeelealgyevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelkt 127
                                         ++++a++++ l+ + k+ + +++++ ++++ ++ +++G+ G+GK+t ++ l+  l+   
  gi|298675562|ref|YP_003727312.1|  15 RLDKVNAIEVDSLTKQYKKFTVVDDITFNVNEgEIFAFLGPNGAGKTTSLKILTTILQPTS 75 
                                       56788999999999999999**********999***************9998887655555 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.54
                                       HHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCT CS
                       RsgA_GTPase  62 eeeleelkeelealgyevllvsaktkegleelkellk 98 
                                       +++l+e  +++e+++y+ +l ++ +ke   ++++ll+
  gi|298675562|ref|YP_003727312.1| 102 SNSLDEKLTAYENMEYHAVLYKVPKKEIKGRVNKLLE 138
                                       3367888889999999999998887777777776665 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 6.5
                                       EEEE-GGG--HHHHHHHHHH CS
                       RsgA_GTPase  51 ivlnKiDlleeeeeleelke 70 
                                       + l+  +l e e+ + +  +
  gi|298675562|ref|YP_003727312.1| 206 VFLTTHNLDEAEK-IADRIA 224
                                       4444444444443.333333 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.3   1.3e-05     0.015       7     128 ..      49     209 ..      44     219 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.3e-05
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee.....................................erpevvfvt 46 
                                       i +  G+ G+GKTt+l+ l+  l+  +   +                                     ++ + v+++
  gi|298675562|ref|YP_003727312.1|  49 IFAFLGPNGAGKTTSLKILTTILQPTSG--NikvngydvlhkkndvrksigvifqsnsldekltayenMEYHAVLYK 123
                                       67788*****************965444..25599999999999999999999999999988888877777777888 PP

                            AAA_22  47 lpsstsskdllrellralglelkaerlsseellealeqalrarav........ielliiDEaqh.lr...seealee 111
                                       +p+++  k   ++ll++++l       ++++l++++   +++r          +++l +DE    l+   ++ ++e+
  gi|298675562|ref|YP_003727312.1| 124 VPKKE-IKGRVNKLLENVELLD-----RKDDLIKTFSGGMKRRIEiarglihtPQVLFLDEPTIgLDahtRAFLWEY 194
                                       88887.8888888888888644.....45555555555555555555568999999999999988988655999999 PP

                            AAA_22 112 LrsllnlsrkgvqliLv 128
                                       +r+l +    +++++L 
  gi|298675562|ref|YP_003727312.1| 195 IRNLKD--NNNLTVFLT 209
                                       999999..888887665 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0    0.0099        11      22      39 ..      53      70 ..      42     149 .. 0.76
   2 ?    8.1   0.0   0.00079      0.88     524     581 ..     168     223 ..     160     248 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0099
                            AAA_13 22 YGwNGaGKTtLSrllrsl 39
                                       G NGaGKTt  ++l  +
  gi|298675562|ref|YP_003727312.1| 53 LGPNGAGKTTSLKILTTI 70
                                      69********87777665 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00079
                            AAA_13 524 igkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevkknt 581
                                       i + ++ ++D P   LD+    +   +i++    +++   +f+ THnl+   ++ +++
  gi|298675562|ref|YP_003727312.1| 168 IHTPQVLFLDEPTIGLDAHTRAFLWEYIRNLK--DNNNLTVFLTTHNLDEAEKIADRI 223
                                       567899*************************7..777788*******98777776665 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   7.9e-05     0.088       3      33 ..      49      79 ..      47      87 .. 0.80
   2 ?   -0.5   0.0      0.71     8e+02      92     183 ..     154     244 ..     108     253 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.9e-05
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EE CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvl 33
                                      +++++G++GaGKTt+l  L  +l+    ++ 
  gi|298675562|ref|YP_003727312.1| 49 IFAFLGPNGAGKTTSLKILTTILQPTSGNIK 79
                                      6789************999999987765555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.71
                                       --SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEES.TTSSSSTTHHHHHHHHHT CS
                             SRP54  92 aGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltk.lDgdakgGaalsiaaelk 167
                                       +G ++   e+ + l ++ +v+  de  + lda t     + +++ k++ ++t +  t  lD+  k    ++i ++  
  gi|298675562|ref|YP_003727312.1| 154 SGGMKRRIEIARGLIHTPQVLFLDEPTIGLDAHTRAFLWEYIRNLKDNNNLTVFLTTHnLDEAEKIADRIAIIDK-- 228
                                       555555555555666666666666666666666666666666666666666666655336666665555555443.. PP

                                       S-EEEEE-SSSTTGEE CS
                             SRP54 168 lPikfigvGekiedle 183
                                         i+ ig+ e+i+++ 
  gi|298675562|ref|YP_003727312.1| 229 GKIQTIGTFEQIKEMT 244
                                       3356666666666655 PP

>> TNT  Tuberculosis necrotizing toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   7.9e-05     0.088      30      71 ..      21      64 ..      16      86 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.9e-05
                                      T--GGGGGS-EEEEEE.----..EEEEEB--BTTB----EEEEE CS
                               TNT 30 aLppsnlnknyhvYevlkple..veaGeiapwfgqpGgGvqyel 71
                                      a+  ++l+k+y++++v+++++  v++Gei +  g +G G    l
  gi|298675562|ref|YP_003727312.1| 21 AIEVDSLTKQYKKFTVVDDITfnVNEGEIFAFLGPNGAGKTTSL 64
                                      89999*************99999**************9976655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.9e-05     0.055      19      50 ..      48      79 ..      40     179 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.9e-05
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrvi 50
                                       + +  Gp G+GKtt+lk l+ +++   g++ 
  gi|298675562|ref|YP_003727312.1| 48 EIFAFLGPNGAGKTTSLKILTTILQPTSGNIK 79
                                      477789***************99998844443 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   7.1e-05     0.079      18      69 ..      39      93 ..      26     159 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.1e-05
                            AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrAisdllf...GipertkdnflhdakkLr 69
                                       ++f+ +e ++   +GpN AGK+t+l+ ++ +l    G  +   ++ lh++++ r
  gi|298675562|ref|YP_003727312.1| 39 DITFNVNEGEIFAFLGPNGAGKTTSLKILTTILQptsGNIKVNGYDVLHKKNDVR 93
                                      678888888999999***********99998886222334445677777777766 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1    0.0015       1.7       2      20 ..      50      68 ..      49      87 .. 0.85
   2 ?   -0.6   0.0       1.2   1.4e+03     100     121 ..     105     129 ..      98     153 .. 0.72
   3 ?   -1.2   0.0       1.9   2.2e+03      70     101 ..     167     199 ..     135     222 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0015
                            AAA_28  2 ivitGgestGKTtlleaLa 20
                                      ++++G+ ++GKTt l+ L+
  gi|298675562|ref|YP_003727312.1| 50 FAFLGPNGAGKTTSLKILT 68
                                      589************9997 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.2
                            AAA_28 100 lea...aarekrydlvfllppapei 121
                                       l++   a + ++y++v++  p +ei
  gi|298675562|ref|YP_003727312.1| 105 LDEkltAYENMEYHAVLYKVPKKEI 129
                                       4543435668899999999999988 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.9
                            AAA_28  70 a.aankvlfcDrglldtlaYarayggeaeaele 101
                                         ++++vlf+D  ++   a  ra+ +e+ ++l+
  gi|298675562|ref|YP_003727312.1| 167 LiHTPQVLFLDEPTIGLDAHTRAFLWEYIRNLK 199
                                       366777777777666666666666665554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       897  (0.0500307); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.51
# Mc/sec: 1553.52
//
Query:       gi|298675563|ref|YP_003727313.1|  [L=249]
Description: ABC-2 type transporter [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-37  128.0  14.3    3.2e-37  128.0  14.3    1.7  2  ABC2_membrane    ABC-2 type transporter
    1.3e-13   50.8  23.9    1.7e-13   50.4  23.9    1.1  1  ABC2_membrane_3  ABC-2 family transporter protein
    1.6e-08   34.2  10.2    1.6e-08   34.2  10.2    2.0  2  ABC2_membrane_2  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.0  14.3   5.3e-41   3.2e-37       3     209 ..       5     214 ..       4     215 .. 0.92
   2 ?   -0.9   0.6      0.15     9e+02     101     122 ..     222     243 ..     221     246 .. 0.78

  Alignments for each domain:
  == domain 1  score: 128.0 bits;  conditional E-value: 5.3e-41
                     ABC2_membrane   3 ikallkreflqrwrdpslgllwrliqplllalvfgtvfgnlg...nsedglnr.....pgllffsvlflafsaltsv 71 
                                       i+++++r+++ +wr++  + +++++qp ++++ +g+  g +       d   +     pg+l++++lf +   + +v
  gi|298675563|ref|YP_003727313.1|   5 IRIMWMRQIKEYWRSKPRL-IASIAQPTIFLMALGFGLGPVFqqaGGGD---YvqfltPGILGMALLFGS--VFNGV 75 
                                       689*************999.99*****9999999999985332233334...244489************..99999 PP

                     ABC2_membrane  72 apvferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldls..rf.flflllllltalaas 145
                                       +++++++ g+l++ lv+p+ ++ + ++++ ++ ++ +++q++++l ++yf+ g++l+   f  l++l+++l+++++s
  gi|298675563|ref|YP_003727313.1|  76 SILWDKQFGFLKESLVAPV-PRISLLIGHSIGGATTAVFQGVVLLPVSYFI-GFRLDslLFiPLIILFMFLISFLFS 150
                                       99*****************.******************************9.*****775578889*********** PP

                     ABC2_membrane 146 slgllisalapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsnl 209
                                        lg+ ++a + + e + ++++lv++p+++lsG+++pi+++p ++  +a+lnPl+y+v++lr+++
  gi|298675563|ref|YP_003727313.1| 151 LLGISMGAKLDDPEAFPLIINLVIIPIFFLSGALFPINNLPDVVTTLAKLNPLSYGVDGLRGSM 214
                                       ****************************************99*******************987 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.15
                     ABC2_membrane 101 vlvelpvsllqalifllivyfl 122
                                       +++++ + l++++i+l+i+ +l
  gi|298675563|ref|YP_003727313.1| 222 IVTDIGILLIVTFILLVISNYL 243
                                       5678888888888888888776 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4  23.9   2.8e-17   1.7e-13     157     343 ..      51     240 ..      16     242 .. 0.86

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 2.8e-17
                   ABC2_membrane_3 157 snvasflvg.liliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll..afg 230
                                        ++++fl + ++ + l+f ++++ + si+ +k+ + ++  lv++v ++++++++ +g ++ +++q +++l +  ++g
  gi|298675563|ref|YP_003727313.1|  51 GDYVQFLTPgILGMALLFGSVFNGV-SILWDKQFGFLKESLVAPVPRISLLIGHSIGGATTAVFQGVVLLPVsyFIG 126
                                       7899999996666666666666555.8*********99999*************************99996522555 PP

                   ABC2_membrane_3 231 lgipfg..nlgl.llllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsii 304
                                         +  +   ++  ++l+++l +++++ lg  +++  +++e+  ++i +vi+++++++g+lfp+++lp+ + +++ ++
  gi|298675563|ref|YP_003727313.1| 127 --FRLDslLFIPlIILFMFLISFLFSLLGISMGAKLDDPEAFPLIINLVIIPIFFLSGALFPINNLPDVVTTLAKLN 201
                                       ..6666323333266************************************************************** PP

                   ABC2_membrane_3 305 Pffapglgllrlitgdplweillsliilalfavvyllla 343
                                       P+++  +gl   +tg + + i ++++il++ ++++l+++
  gi|298675563|ref|YP_003727313.1| 202 PLSYGVDGLRGSMTGSSDFGIVTDIGILLIVTFILLVIS 240
                                       ****************888999**************996 PP

>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.8   0.5    0.0097        58     129     187 ..      24      78 ..      21      83 .. 0.77
   2 !   34.2  10.2   2.7e-12   1.6e-08     106     286 ..      86     247 ..      80     249 .] 0.80

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.0097
                   ABC2_membrane_2 129 aiglaiavallatvllalaiilalgivlaledllllvvasvlllllvvflalglllSsv 187
                                       ++++a   ++l ++ ++l+++ +     ++ ++l+  ++ ++ll+     +++ ++S++
  gi|298675563|ref|YP_003727313.1|  24 IASIAQPTIFLMALGFGLGPVFQQAGGGDYVQFLTPGILGMALLF----GSVFNGVSIL 78 
                                       5556645566777789999999999999*************8888....7777777765 PP

  == domain 2  score: 34.2 bits;  conditional E-value: 2.7e-12
                   ABC2_membrane_2 106 lkllLskPvsRdeillgKfigglaigla.iavallatvllalaiilalgivlaledllllvvasvlllllvvflalg 181
                                       lk  L  Pv+R ++l+g  igg++ +++ ++v+l ++          + i ++l++ll++ + +++++l+ ++++l 
  gi|298675563|ref|YP_003727313.1|  86 LKESLVAPVPRISLLIGHSIGGATTAVFqGVVLLPVS----------YFIGFRLDSLLFIPLIILFMFLISFLFSL- 151
                                       78889********************666666666555..........55678888888877777777776655554. PP

                   ABC2_membrane_2 182 lllSsvar.ssreaaalalglfvvlailvpivlygvaellagpavpqeindflsllsptsayntllneilagsdlna 257
                                       l++S+ a+ +  ea  l + l+++  ++ +++l+++++l+ + +        l  l+p s+   +l+   +gs+   
  gi|298675563|ref|YP_003727313.1| 152 LGISMGAKlDDPEAFPLIINLVIIPIFFLSGALFPINNLPDVVTT-------LAKLNPLSYGVDGLRGSMTGSS--- 218
                                       6777777744789**********************9999997777.......8888888886555555555553... PP

                   ABC2_membrane_2 258 lgstatnllilllllavllvlgyvlFkrk 286
                                        +  +t ++ill+++ +llv++ +lF++ 
  gi|298675563|ref|YP_003727313.1| 219 DFGIVTDIGILLIVTFILLVISNYLFEKL 247
                                       489***********************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1769.93
//
Query:       gi|298675564|ref|YP_003727314.1|  [L=308]
Description: aspartate carbamoyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-48  163.3   0.0    6.8e-48  162.4   0.0    1.4  1  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl
    6.5e-33  114.0   0.0    9.3e-33  113.5   0.0    1.2  1  OTCace    Aspartate/ornithine carbamoyltransferase, Asp/Orn b


Domain annotation for each model (and alignments):
>> OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.4   0.0   7.6e-52   6.8e-48       2     147 ..       7     147 ..       6     148 .. 0.96

  Alignments for each domain:
  == domain 1  score: 162.4 bits;  conditional E-value: 7.6e-52
                                       -BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTSC CS
                          OTCace_N   2 hllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaediq 78 
                                       +++s++d+s++ i+++ld+a++l+   k+e+k+++l+gk+la+lF+epStRTr+Sfe+A+krl g+vlsl++    +
  gi|298675564|ref|YP_003727314.1|   7 DIISMKDFSRDMIDHILDTAEKLEPIAKNEEKSDILNGKILAVLFFEPSTRTRMSFETAIKRLNGDVLSLGAV---D 80 
                                       589********************************************************************55...6 PP

                                       TTTGGSTTSSCHHHHHHHHHHHTSEEEEEESSHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHH CS
                          OTCace_N  79 lssvskgrkEsleDtarvlsryvdaiviRhpgaeeleelakyasvpviNagdgdgeHPtQaLaDlltir 147
                                        ss++kg  E+l+Dt+rv+++y+d+iv+Rhp++ +++  a++ ++pviNagdg+g+HPtQ+++Dl+t+r
  gi|298675564|ref|YP_003727314.1|  81 ASSITKG--ENLADTIRVIEGYADGIVLRHPKEGSAKMAAEMTTIPVINAGDGAGHHPTQTFLDLYTMR 147
                                       89999**..**********************776799999999*************************8 PP

>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.5   0.0     1e-36   9.3e-33       1     156 [.     153     302 ..     153     303 .. 0.94

  Alignments for each domain:
  == domain 1  score: 113.5 bits;  conditional E-value: 1e-36
                                       CC.EEEEESS.TTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEE CS
                            OTCace   1 kglkiafvGd.kknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvy 76 
                                       +g+kia+ Gd k++++++sl ++l+ ++++++lv+Pk+l++  e+++ +    k+ g +++ t+++e+a++++Dv+y
  gi|298675564|ref|YP_003727314.1| 153 DGVKIAIAGDlKYGRTVHSLCYALSHYNAEITLVSPKDLRMPREIIRDL----KNRGIEVKQTDSMEDAIQDVDVLY 225
                                       699***********************************99999999655....5569******************** PP

                                       E--SSETTCCGGHH...HHHHHHCC.CSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHH CS
                            OTCace  77 tdvwvsmgeekere...erlkklkd.yqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlht 149
                                        ++++     ker+   ++++ +    qvt+ellk+a++d++++H+LP  r +E+++ V+   ++ +f+q  +++ +
  gi|298675564|ref|YP_003727314.1| 226 VTRIQ-----KERFpdpAEYQRVSTsLQVTNELLKNANPDLKIMHPLP--RVNEIDSGVDFTSHACYFKQSFYGVPV 295
                                       *****.....8888888777777777**********************..*************************** PP

                                       HHHHHHH CS
                            OTCace 150 ikAllvl 156
                                       ++All l
  gi|298675564|ref|YP_003727314.1| 296 RMALLSL 302
                                       ****987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2054.75
//
Query:       gi|298675565|ref|YP_003727315.1|  [L=160]
Description: aspartate carbamoyltransferase regulatory subunit [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-30  104.9   2.9    2.7e-30  104.4   2.9    1.2  1  PyrI          Aspartate carbamoyltransferase regulatory chain
    1.1e-16   60.5  11.0    1.1e-16   60.4   8.8    2.0  2  PyrI_C        Aspartate carbamoyltransferase regulatory chain
  ------ inclusion threshold ------
       0.02   14.4   0.1      0.041   13.4   0.1    1.5  1  TF_Zn_Ribbon  TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> PyrI  Aspartate carbamoyltransferase regulatory chain, allosteric domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.4   2.9   4.6e-34   2.7e-30       2      94 .]      13     103 ..      12     103 .. 0.95

  Alignments for each domain:
  == domain 1  score: 104.4 bits;  conditional E-value: 4.6e-34
                                       -----SCEEEEEEEETT-HHHHHHHCT--T...TS-EEEEEEEEETTTEEEEEEEEET----HHHHHHHCCC-TT-E CS
                              PyrI   2 kvkkienGiViDHIkagkalkvlklLkldklkseekvaiiknvkskklgkKdiikiegkelseeeldklaliapnat 78 
                                       +v++ienG+ViDHI+ag+al+vlk+++  + +se  +++++n++s++ gkKd+ikieg+e++ +e+dk+aliapnat
  gi|298675565|ref|YP_003727315.1|  13 RVQPIENGTVIDHITAGQALNVLKIIGKPG-TSEGIMSVLINAPSSH-GKKDVIKIEGREINAQEFDKIALIAPNAT 87 
                                       79***************************8.55559*********98.9**************************** PP

                                       EEEEETTEEEEEE--. CS
                              PyrI  79 iniIkdgevveKkkve 94 
                                       iniI++++v++Kk+v+
  gi|298675565|ref|YP_003727315.1|  88 INIIRNFKVASKKQVQ 103
                                       *************985 PP

>> PyrI_C  Aspartate carbamoyltransferase regulatory chain, metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.24   1.4e+03      19      33 ..      89     103 ..      83     104 .. 0.78
   2 !   60.4   8.8   1.9e-20   1.1e-16       2      46 ..     108     154 ..     107     155 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.24
                                       S-.-EEEEEETTTTE CS
                            PyrI_C  19 pveskFkvedkekvk 33 
                                       ++  +Fkv +k++v+
  gi|298675565|ref|YP_003727315.1|  89 NIIRNFKVASKKQVQ 103
                                       67789**99988876 PP

  == domain 2  score: 60.4 bits;  conditional E-value: 1.9e-20
                                       EESSS--S-TTBGGGT.TS-.-EEEE.EETTTTEEEETTT--EEEHH CS
                            PyrI_C   2 iegvlkCpNpnCItnn.epveskFkv.edkekvklkCkYCekeisee 46 
                                       iegv+kC NpnCItn+ ep++s+F+v +++ +v l+C YCe++ise+
  gi|298675565|ref|YP_003727315.1| 108 IEGVVKCVNPNCITNSnEPIKSNFTVnNENRNVFLRCDYCERIISEN 154
                                       9***************99********99999*************996 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   6.8e-06     0.041       7      36 ..     128     158 ..     126     160 .] 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.8e-06
                                       TCEECHEETSTTCE.EESSSSBEEEECCCCC CS
                      TF_Zn_Ribbon   7 gstnlveDpergel.vCtdCGlVlednside 36 
                                       +s ++v++++r+ + +C  C+ ++ +n++d+
  gi|298675565|ref|YP_003727315.1| 128 KSNFTVNNENRNVFlRCDYCERIISENIADN 158
                                       577799999999999*************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1204.70
//
Query:       gi|298675566|ref|YP_003727316.1|  [L=263]
Description: dihydrodipicolinate reductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.9e-46  155.4   0.1    8.3e-46  155.0   0.1    1.2  1  DapB_C          Dihydrodipicolinate reductase, C-terminus
    4.4e-34  117.3   0.9    6.9e-34  116.6   0.9    1.3  1  DapB_N          Dihydrodipicolinate reductase, N-terminus
  ------ inclusion threshold ------
      0.029   13.9   0.0      0.047   13.2   0.0    1.4  1  DUF166          Domain of unknown function
      0.031   13.8   0.0      0.041   13.3   0.0    1.2  1  ABC_transp_aux  ABC-type uncharacterized transport system


Domain annotation for each model (and alignments):
>> DapB_C  Dihydrodipicolinate reductase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.0   0.1   1.8e-49   8.3e-46       1     121 []     131     261 ..     131     261 .. 0.92

  Alignments for each domain:
  == domain 1  score: 155.0 bits;  conditional E-value: 1.8e-49
                                       HHHHHHHHHHHHCCCSTTT-EEEEEEEESTT--SSS-HHHHHHHHHHH.................-S-ETTCCCEEE CS
                            DapB_C   1 GvnlllklveeaakllkeaydveiiEkHhnkKaDaPSGTAlalaeaia.....egke........arkkkeigihsv 64 
                                       Gvn+++k+++e++++l++ ydve++E+Hhn+K+DaPSGTAl+ a+ i+     +  +        a + +eigih+v
  gi|298675566|ref|YP_003727316.1| 131 GVNVFFKMIKEMSRYLSD-YDVEVLEAHHNNKKDAPSGTALKAADVISetlggK--KyvygrqghAPRGDEIGIHAV 204
                                       9***************99.*****************************666550..15555556566679******* PP

                                       ETTT--CCCCEEEECTTEEEEEEEEEESCHHHHHHHHHHHHHH.HCTSSEESHHHHH CS
                            DapB_C  65 RgggvvgehevlfagegevieikhealsreiFaeGallaaewlakkkkglysmedvL 121
                                       Rgg++vgeh+vlfagege++eikh+a sr+ Fa Ga++aa+w++++k+g+y+medvL
  gi|298675566|ref|YP_003727316.1| 205 RGGDIVGEHTVLFAGEGERMEIKHQAGSRQAFAGGAIKAARWITGAKPGIYTMEDVL 261
                                       ********************************************************8 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.6   0.9   1.5e-37   6.9e-34       1     124 []       2     128 ..       2     128 .. 0.96

  Alignments for each domain:
  == domain 1  score: 116.6 bits;  conditional E-value: 1.5e-37
                                       EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEB..SSHHHHHHH..-SEEEE CS
                            DapB_N   1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavt..ddleevlek..advliD 73 
                                       ik av Ga GrmGk +++ + +++d+el+aa+d  +   +g+dagel g+g++gv+++  +++ e+l++  +dv+iD
  gi|298675566|ref|YP_003727316.1|   2 IKAAVSGAYGRMGKMLIDNIVNSDDFELSAAFDIFN---IGNDAGELSGVGTVGVPISdpENMGEILADtnTDVMID 75 
                                       6889*******************************9...9******************8889999999999****** PP

                                       -S-HHHHHHHHHHHHHTT-EEEE--SS--HHHHHHHHHHTTT..SEEEE-S-- CS
                            DapB_N  74 FTtpeavlenlklalekgvklViGTTGlseeelaeleelakk..igvviapNf 124
                                       FT+p+a+++n+ +a e+gv+lViGTTG++ee+++++e++  k   ++viapN+
  gi|298675566|ref|YP_003727316.1|  76 FTAPDATVQNVTAASENGVNLVIGTTGFTEEQRNTIEQFIMKnnNSAVIAPNY 128
                                       **************************************887768********7 PP

>> DUF166  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.1e-05     0.047       6     103 ..      11     117 ..       6     157 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.1e-05
                            DUF166   6 geyGervvenilnepdferslivavvevpe.........eldefiedpeelLpe..lkeaDiviaytlhpDlllela 71 
                                       g+ G+ +++ni n+ dfe s +++++++ +         +++  i dpe++ +     + D++i +t  pD +++ +
  gi|298675566|ref|YP_003727316.1|  11 GRMGKMLIDNIVNSDDFELSAAFDIFNIGNdagelsgvgTVGVPISDPENMGEIlaDTNTDVMIDFT-APDATVQNV 86 
                                       789999************999666666655344444455666668888887555447889*****65.6******** PP

                            DUF166  72 ekakekkvkalivpaeapkaglrkelkeklee 103
                                         a+e++v+++i  +   +   r+ +++ + +
  gi|298675566|ref|YP_003727316.1|  87 TAASENGVNLVIGTTGFTE-EQRNTIEQFIMK 117
                                       ************9998777.444444443333 PP

>> ABC_transp_aux  ABC-type uncharacterized transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   9.2e-06     0.041     197     261 ..      95     153 ..      50     156 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.2e-06
                    ABC_transp_aux 197 lviakptkdlseeelykldqflmnGgkllvfldpvaeeqdslsepsaaprtsnLedllaeyGvri 261
                                        +++ +t+ ++ee+   ++qf+m+ ++ +v +  +++        ++++  +++ + l++y v++
  gi|298675566|ref|YP_003727316.1|  95 NLVI-GTTGFTEEQRNTIEQFIMKNNNSAVIAPNYSVGV-----NVFFKMIKEMSRYLSDYDVEV 153
                                       4566.89*************************9999876.....456666778888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1692.68
//
Query:       gi|298675567|ref|YP_003727317.1|  [L=291]
Description: dihydrodipicolinate synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-93  313.0   0.4    1.4e-93  312.8   0.4    1.0  1  DHDPS     Dihydrodipicolinate synthetase family
  ------ inclusion threshold ------
       0.12   11.1   0.0       0.16   10.7   0.0    1.1  1  GDC-P     Glycine cleavage system P-protein


Domain annotation for each model (and alignments):
>> DHDPS  Dihydrodipicolinate synthetase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  312.8   0.4   1.5e-97   1.4e-93       2     288 ..       2     286 ..       1     287 [. 0.97

  Alignments for each domain:
  == domain 1  score: 312.8 bits;  conditional E-value: 1.5e-97
                                       -SEEEEE----B-TTSSB-HHHHHHHHHHHHHCT-SEEEESSCCCTGGGS-HHHHHHHHHHHHHHHTTSSEEEEE-- CS
                             DHDPS   2 fsgiitalvtpfdedgkldkealrklieflinkgvdglvvaGttGEsatlsteekeqlveiaveaakgripviagvG 78 
                                       f+g+++al+tpf+ed  ++ +  + +i +  + gv+g+v +GttGEsatlst+e+++l+ iave+a+  +pv+ag+G
  gi|298675567|ref|YP_003727317.1|   2 FEGVMPALITPFNEDDSVNIQGFKDNISYVEKGGVSGVVACGTTGESATLSTSEHKELIDIAVECAN--VPVVAGTG 76 
                                       89***************************99999*******************************95..******** PP

                                       -SSHHHHHHHHHCCCCCT-SEEEEE---SS---HHHHHHHHHHHHHCHSS-EEEEE-HHHHSHHHHHHHHHHHHTST CS
                             DHDPS  79 snstseaiklakkaeeaGadgvlavtPYYnkpsqeglyqhfkaiieatdlpvilYnvpsrtgadlspetvkrLaele 155
                                       sn+t+ea++l++ ae+aGadg+l++ PYYnkp+ +gl++hfk+++e  + p+ilYnvpsrtg+d+ +e++++L++++
  gi|298675567|ref|YP_003727317.1|  77 SNNTAEALELTRFAEDAGADGALLISPYYNKPNNAGLINHFKTVAENVNIPIILYNVPSRTGQDMPLEVIQELSKVD 153
                                       ***************************************************************************** PP

                                       TEEEEEE-SS-CTHHHHHH.CCCSTTSEEEES-GGGHHHHHHTT-SEEEESCHHCHHHHHHHHHHHHHTT-HHHHHH CS
                             DHDPS 156 nivgvKeavgdleevikik.kevgkdlviysGddelllsalslGadGvisvtsniagermrqlikalkeGdlaeaae 231
                                       niv++K+a gdl ++ +++ +++++++++ sG d l+l++ls+G++Gvisvt+ni++ +m +l++a++e d+++a++
  gi|298675567|ref|YP_003727317.1| 154 NIVAIKDACGDLAKMSHMIeNTADENFTVISGEDPLTLPILSIGGEGVISVTANIIPDKMVKLVNAARENDIKTARQ 230
                                       ************9998766156789**************************************************** PP

                                       HHHHHHHHHHHCCCCSCCHHHHHHHHCTTSSSBB.--TTS--S-HHHHHHHHHHHHH CS
                             DHDPS 232 lnekllplikilfaepnvilvktalellGlvveatlrkPltpleeeekeeleallka 288
                                       ++ ++ p+i ++f e+n+i+vk a+el+Gl  ++ lr Pl++l++++++ l ++lk 
  gi|298675567|ref|YP_003727317.1| 231 VHYEIAPVIRAMFTETNPIPVKRAAELVGLAGGH-LRLPLAQLSNDNEHILTDALKT 286
                                       *******************************999.************9999999885 PP

>> GDC-P  Glycine cleavage system P-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   1.8e-05      0.16     168     247 ..     114     199 ..      64     206 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 1.8e-05
                                       HHHHHHHHGGGT-EEEEE-GGG--S-.......S-EEEE..EEEES-TTSB----HHHHHHHHHTT-EEEEEE-TTG CS
                             GDC-P 168 levlktrakglgieivevdlteekvtd....kekevagv..lvqypnteGriedlkelvekakkkkslvvvaadlla 238
                                       ++  kt a++++i i++ ++ +++ +d    + +e++ v  +v   ++ G + ++++++e++ +++ +v+   d+l+
  gi|298675567|ref|YP_003727317.1| 114 INHFKTVAENVNIPIILYNVPSRTGQDmpleVIQELSKVdnIVAIKDACGDLAKMSHMIENTADENFTVISGEDPLT 190
                                       455799**********999887777777888444444433378899******************************* PP

                                       GGTB--HHH CS
                             GDC-P 239 LtllkpPge 247
                                       L +l   ge
  gi|298675567|ref|YP_003727317.1| 191 LPILSIGGE 199
                                       ***987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1736.60
//
Query:       gi|298675568|ref|YP_003727318.1|  [L=66]
Description: 30S ribosomal protein S17e [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-13   50.3   3.1    2.3e-13   50.1   3.1    1.0  1  Ribosomal_S17e  Ribosomal S17
  ------ inclusion threshold ------
      0.015   15.7   0.5      0.019   15.5   0.5    1.1  1  PNPase          Polyribonucleotide nucleotidyltransferase, RN
      0.072   12.5   0.1      0.076   12.4   0.1    1.0  1  DUF620          Protein of unknown function (DUF620)


Domain annotation for each model (and alignments):
>> Ribosomal_S17e  Ribosomal S17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   3.1   3.9e-17   2.3e-13       1      58 [.       1      58 [.       1      63 [. 0.97

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 3.9e-17
                                      XX----HHHHHHHHHHHHS-TTT--S-HHHHHHHHHHHS----SHHHHHHHHHHHHHH CS
                    Ribosomal_S17e  1 mgrvrtktvKkaarviiekyyskltndFhtnkkvceevaiipskklrnkiaGyvthlm 58
                                      mg++r+  +K  ++ +i++y + +++dF++nk+++ + ++i+sk +rn++aGy+t+ m
  gi|298675568|ref|YP_003727318.1|  1 MGNIRQTNIKNISERLINNYQNVFSKDFEKNKHLVTKYSTIKSKVIRNRVAGYITRRM 58
                                      99*****************************************************988 PP

>> PNPase  Polyribonucleotide nucleotidyltransferase, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.5   3.1e-06     0.019      26      72 ..       5      50 ..       3      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.1e-06
                                      HHHHHHHHHHHHHHHHH...HHSTTS-HHHHHHHHHHHHHHHHHHHH CS
                            PNPase 26 RyaaldeikekvveafaaeleeedeedekeikeifkalekkvvRsri 72
                                      R++++++i+e  +++++ ++  +d e++k + + ++++++kv+R+r+
  gi|298675568|ref|YP_003727318.1|  5 RQTNIKNISERLINNYQ-NVFSKDFEKNKHLVTKYSTIKSKVIRNRV 50
                                      999**************.5668899********************98 PP

>> DUF620  Protein of unknown function (DUF620)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.3e-05     0.076     104     154 ..      10      61 ..       5      66 .] 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
                            DUF620 104 acvgekkind.edcfvLkleadkealkarseseaevirhtvfgyfsqrtGll 154
                                       + + e+ in+ +++f   +e +k+ +++ s+ +  vir  v gy+++r  l 
  gi|298675568|ref|YP_003727318.1|  10 KNISERLINNyQNVFSKDFEKNKHLVTKYSTIKSKVIRNRVAGYITRRMSLK 61 
                                       679999999846789999*****************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1002  (0.0558871); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 488.34
//
Query:       gi|298675569|ref|YP_003727319.1|  [L=99]
Description: hypothetical protein Metev_1684 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.17   11.9   2.8       0.24   11.4   2.8    1.2  1  DUF5317   Family of unknown function (DUF5317)
       0.46    8.7   3.1       0.51    8.6   3.1    1.0  1  DUF2070   Predicted membrane protein (DUF2070)
          7    7.0   8.1        2.4    8.5   0.2    2.9  3  YiaAB     yiaA/B two helix domain


Domain annotation for each model (and alignments):
>> DUF5317  Family of unknown function (DUF5317)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   2.8     4e-05      0.24      25      69 ..      19      72 ..       1      74 [. 0.55

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4e-05
                           DUF5317 25 v........elleflk..klsallsilsylllllflllnrklkglllialGvllN 69
                                               ++++++    ++ ++ +++ ll ++ +l+n ++ glll+++G+++N
  gi|298675569|ref|YP_003727319.1| 19 LrdiriykrTRYQSYRkgAMKGIAAMFATLLGAILTLANPSI-GLLLVLIGLFIN 72
                                      212233322333333301455666666677777777777777.***********9 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   3.1   8.6e-05      0.51      41     104 ..       4      65 ..       1      76 [. 0.72

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 8.6e-05
                           DUF2070  41 illfglpalvaflltlpvlrilggr.ltykrslflalltelivviisllaillsallqalvllal 104
                                       +l+ +  ++v ++ltl+ +ri++++ +++ r+  +  ++++++ ++  + +l+    +++ ll +
  gi|298675569|ref|YP_003727319.1|   4 LLIAITAYIVVLFLTLRDIRIYKRTrYQSYRKGAMKGIAAMFATLLGAILTLAN---PSIGLLLV 65 
                                       3455556***************9999******9999999999988665555555...23333333 PP

>> YiaAB  yiaA/B two helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.4     0.075   4.5e+02       9      23 ..       4      17 ..       1      22 [. 0.77
   2 ?    1.3   0.4     0.071   4.2e+02      11      24 ..      42      54 ..      38      59 .. 0.64
   3 ?    8.5   0.2    0.0004       2.4      11      33 ..      60      82 ..      52      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.075
                             YiaAB  9 fllalvlllvGlwyl 23
                                      +l+a++++ v l+ l
  gi|298675569|ref|YP_003727319.1|  4 LLIAITAYIVVLF-L 17
                                      7899999998887.5 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.071
                             YiaAB 11 lalvlllvGlwylp 24
                                      +a++++l+G + l+
  gi|298675569|ref|YP_003727319.1| 42 AAMFATLLGAI-LT 54
                                      56666666665.44 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0004
                             YiaAB 11 lalvlllvGlwylpldlseKgfy 33
                                      ++l+l+l+Gl+ +     eK f 
  gi|298675569|ref|YP_003727319.1| 60 IGLLLVLIGLFINRKGVREKVFQ 82
                                      89*********998888888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       906  (0.0505327); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 802.42
//
Query:       gi|298675570|ref|YP_003727320.1|  [L=364]
Description: DNA-directed DNA polymerase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.7e-51  172.2   0.0    9.9e-51  171.7   0.0    1.3  1  IMS              impB/mucB/samB family
      2e-18   67.2   0.0    3.6e-18   66.4   0.0    1.4  1  IMS_C            impB/mucB/samB family C-terminal domain
    2.4e-09   37.0   0.0    6.7e-09   35.6   0.0    1.8  1  IMS_HHH          IMS family HHH motif
     0.0039   17.4   0.0      0.014   15.7   0.0    1.9  1  Cdd1             Pathogenicity locus
  ------ inclusion threshold ------
       0.11   12.4   0.0       0.23   11.3   0.0    1.6  1  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
       0.11   13.1   0.2       0.46   11.1   0.0    2.2  2  HHH_5            Helix-hairpin-helix domain


Domain annotation for each model (and alignments):
>> IMS  impB/mucB/samB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.7   0.0   3.3e-54   9.9e-51       1     150 []      12     162 ..      12     162 .. 0.98

  Alignments for each domain:
  == domain 1  score: 171.7 bits;  conditional E-value: 3.3e-54
                                       EEETTHHHHHHHHHT.T-TTS-EEEEET.......TEEEEE-HHHHTTT--TTSBHHHHHTTHTT-EEEEEE-HHHH CS
                               IMS   1 iDmdaFyasverardpeLkgkPvvvaqgsek...rgiviavsyeArayGvkrgmrikeakklcpdlivvkvdlekyr 74 
                                       iDmd+Fy sve +++peL+g Pv+v++  ++   rg+v ++syeAr+yG++++m++++a++lcp++++++v++e+y+
  gi|298675570|ref|YP_003727320.1|  12 IDMDSFYSSVEVRENPELQGFPVIVGSDPKNgtgRGVVSTCSYEARKYGISSAMPVSKAYRLCPHAVFLPVNMELYK 88 
                                       8***************************888********************************************** PP

                                       HHHHHHHHHHHHH-S..EEEEETTEEEEE-HHHHHHHH-SHHHHHHHHHHHHHHHH---EEEEEESSHHHHHHHHH CS
                               IMS  75 raskkileilkrfispkvekasiDEayldltgleelaesegaalakelrkaikeelgltvsiGiasnkllAKlase 150
                                       ++s+++++i+k+f s+k e++s+DEayl++++++ ++e+   ++a++++++i++  +lt+siGia+nk++AK+as+
  gi|298675570|ref|YP_003727320.1|  89 QVSSRVMNIIKKF-SDKFEQVSVDEAYLEIGKTVGNYEDA-VRYAQQIKDKIYNYEKLTCSIGIAPNKTIAKIASD 162
                                       *************.77***********************6.*********************************96 PP

>> IMS_C  impB/mucB/samB family C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.4   0.0   1.2e-21   3.6e-18       2     113 ..     242     356 ..     241     360 .. 0.92

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 1.2e-21
                             IMS_C   2 vearpepksissektfpe.pydesklkkelreLaeelarrLrdkglvartitlklrysdfh.asrsatLprptsdtr 76 
                                       ve++ e ksis+e+tf+e   d++ +++++  L++e++  L++k+ + +t+tlklr +df+  +rs+t+  ++s ++
  gi|298675570|ref|YP_003727320.1| 242 VEEQTEVKSISKEDTFDEdIADPITAEEIIDILSDEVHNSLVKKKYLFKTVTLKLRLDDFTtCTRSKTFVSYRSEAG 318
                                       6788999***********5556888*********************************9999*************** PP

                             IMS_C  77 eileaalkLlrrlide.pglpirligvsasnlvekaes 113
                                        i ++ ++L+++ i+   + ++rl+gv +s+l + +++
  gi|298675570|ref|YP_003727320.1| 319 VIKKESKELMNQFIKNnGNCKFRLLGVEVSKLFKIKDG 356
                                       *******************************9855444 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0   2.2e-12   6.7e-09       1      32 []     174     205 ..     174     205 .. 0.97

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 2.2e-12
                           IMS_HHH   1 pddvkefLwplpitkipGiGgklgekLeklGi 32 
                                       p++v++fL+plp++kipG+G+k+ e L++lG+
  gi|298675570|ref|YP_003727320.1| 174 PEEVENFLSPLPVSKIPGVGKKTNEALDNLGV 205
                                       799***************************97 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   4.5e-06     0.014       9      42 ..     187     220 ..     183     227 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.5e-06
                              Cdd1   9 qdiPniGkalaedlvelGirsveelkgedpeely 42 
                                        +iP++Gk++ e l +lG++++ +lk+ d + l 
  gi|298675570|ref|YP_003727320.1| 187 SKIPGVGKKTNEALDNLGVKTIGDLKNFDVQVLI 220
                                       58************************98877665 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   7.7e-05      0.23       4      30 ..     187     213 ..     186     232 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.7e-05
                   DNA_pol_lambd_f   4 tkvyGVGpktAkkwyakGirtledlra 30 
                                       +k+ GVG kt + + + G++t+ dl++
  gi|298675570|ref|YP_003727320.1| 187 SKIPGVGKKTNEALDNLGVKTIGDLKN 213
                                       589**********************99 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00015      0.46       5      37 ..     187     219 ..     153     221 .. 0.86
   2 ?   -2.4   0.0       2.5   7.6e+03      45      56 ..     264     275 ..     260     276 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
                                       HTSTT--HHHHHHHHTTT--SHHHHHHS-HHHH CS
                             HHH_5   5 lsvsGiGpktAlallsaGiesvedlaaadveeL 37 
                                        +++G+G+kt  al + G++++ dl++ dv+ L
  gi|298675570|ref|YP_003727320.1| 187 SKIPGVGKKTNEALDNLGVKTIGDLKNFDVQVL 219
                                       578999999999988889999999988888765 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.5
                                       HHHHHHHHHHHH CS
                             HHH_5  45 kktAeriilelk 56 
                                       + tAe ii+ l 
  gi|298675570|ref|YP_003727320.1| 264 PITAEEIIDILS 275
                                       679999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2680.80
//
Query:       gi|298675571|ref|YP_003727321.1|  [L=255]
Description: hypothetical protein Metev_1686 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-71  239.3  21.0    4.2e-71  239.1  21.0    1.0  1  DUF1624        Protein of unknown function (DUF1624)
    4.2e-06   26.1  39.0     0.0034   16.5  23.5    2.4  2  Acyl_transf_3  Acyltransferase family
    0.00031   19.7  10.6     0.0021   17.0   6.9    2.3  2  OpgC_C         OpgC protein


Domain annotation for each model (and alignments):
>> DUF1624  Protein of unknown function (DUF1624)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  239.1  21.0     7e-75   4.2e-71       1     223 []       8     236 ..       8     236 .. 0.98

  Alignments for each domain:
  == domain 1  score: 239.1 bits;  conditional E-value: 7e-75
                           DUF1624   1 RieeiDalRGiAlilMiifHflfdLeffgylavslatsglwvvfarliaslFlfiaGvslvlahskslrw....... 70 
                                       R++e+D++RGi +ilM++fHfl+dL++fg ++ +l+ sg + +++r++a++F++++G+sl+++ s++++        
  gi|298675571|ref|YP_003727321.1|   8 RFWELDFFRGIGIILMVVFHFLYDLNYFGGYDFNLH-SGSLLFMGRSAAIIFILLVGISLTISISRTKKYaenvwnl 83 
                                       9***********************************.9999999999*******************999899***** PP

                           DUF1624  71 .rkflkRglkilaaallitaatylllpdsfivFGiLhlialalllallflrlpkalllllallilalglllreaifd 146
                                         k++kRgl+i++++ll+t++t++++ ++ ivFGiLh+i+++++la++flr++  +l+l +ll+++lg +l++  +d
  gi|298675571|ref|YP_003727321.1|  84 yPKYIKRGLRIFGWGLLLTLITWIFIGQGVIVFGILHFIGISIILAYPFLRFKSMNLVL-GLLFILLGSYLQTFSVD 159
                                       *********************************************************99.8888889********** PP

                           DUF1624 147 lplllwlglssekfetndYvplfPWfgvvllGialgkllyekgkrrlklpslpkaklvrplallGrhsLliYlihqp 223
                                       +p++lwlg+++e+f+t dY+p+fPWfgv+l+Gi++g+lly++++r++++ +l+++  +++++l+Gr sL+iYlihqp
  gi|298675571|ref|YP_003727321.1| 160 FPWFLWLGFVPEGFYTFDYFPIFPWFGVILIGIFTGNLLYPNYTRKFSIMDLSRKYPINMFCLMGRYSLFIYLIHQP 236
                                       ****************************************************************************9 PP

>> Acyl_transf_3  Acyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5  23.5   5.6e-07    0.0034       3     141 ..      11     168 ..       9     169 .. 0.74
   2 !    6.1  19.8   0.00084         5     217     314 ..     139     248 ..     121     255 .] 0.66

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.6e-07
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxx RF
                     Acyl_transf_3   3 ylDllRgiAillVvflHaliayspdagrgspiqasqssqiaflggfgvplFFllSGffla.......amlyrrrgls 72 
                                       +lD  Rgi i+l+v++H+l+ +++++g       s+s+   f+g+ +  +F+ll G  l+       ++ ++  +l 
  gi|298675571|ref|YP_003727321.1|  11 ELDFFRGIGIILMVVFHFLYDLNYFGGYDFNL-HSGSLL--FMGRSAAIIFILLVGISLTisisrtkKYAENVWNLY 84 
                                       69******************998888877544.344444..***********************9998888888888 PP

                                       xxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxx RF
                     Acyl_transf_3  73 klikrRilrll.....iplliwllliillialvaghiqanasanvtlfdet..........kglmfllfefpatghl 134
                                         + +R lr++     + l+ w+++   +i++++ h    +  +   f+ +          ++l +  ++++ +   
  gi|298675571|ref|YP_003727321.1|  85 PKYIKRGLRIFgwgllLTLITWIFIGQGVIVFGILHFIGISIILAYPFLRFksmnlvlgllFILLGSYLQTFSVDFP 161
                                       88899999999988886666666666666666666666666666666655577777777774444444444444455 PP

                                       xxxxxxx RF
                     Acyl_transf_3 135 WfLwalf 141
                                       WfLw+ f
  gi|298675571|ref|YP_003727321.1| 162 WFLWLGF 168
                                       7777655 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.00084
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Acyl_transf_3 217 nlsrglkislllsllllalillalfgqtdg...........gglvasvliqsaslllvslgimllllllfalpsrsa 282
                                       nl +gl+++ll s+l ++                            +++ + + ++++ + +++++   +++p++++
  gi|298675571|ref|YP_003727321.1| 139 NLVLGLLFILLGSYLQTF-----------SvdfpwflwlgfVPEGFYTFDYFPIFPWFGVILIGIFTGNLLYPNYTR 204
                                       333333333333333222...........233333334443344555555555666667777777777888888888 PP

                                       xx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Acyl_transf_3 283 fk............llrylgkiSygiYliHlpllmllqkllrdw 314
                                       ++             +  +g++S+ iYliH+p+l ++ +ll   
  gi|298675571|ref|YP_003727321.1| 205 KFsimdlsrkypinMFCLMGRYSLFIYLIHQPFLIIILYLLGFL 248
                                       8899******************************9999988776 PP

>> OpgC_C  OpgC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   6.9   3.6e-07    0.0021       1     118 [.       8     131 ..       8     166 .. 0.77
   2 !    4.4   0.1    0.0024        14     295     323 ..     215     243 ..     178     253 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.6e-07
                            OpgC_C   1 RdlrlDlfRGlalvlivvdHi..pgsvls..kltlrnfGfs....daAevFVflSGlavglvYgraae.regalaaa 68 
                                       R ++lD+fRG+ ++l+vv H     +++    ++l+   +     +aA +F++l G+++ +  +r+ + +e+ +   
  gi|298675571|ref|YP_003727321.1|   8 RFWELDFFRGIGIILMVVFHFlyDLNYFGgyDFNLHSGSLLfmgrSAAIIFILLVGISLTISISRTKKyAENVWNLY 84 
                                       6799****************98844444434555555333222449**************999876542788999** PP

                            OpgC_C  69 arilrRawelYvahiallvlvlaliallallfeesdlieelnlepllekp 118
                                        + ++R ++++   ++l++++ ++i    ++f    +++ ++++ +l+ p
  gi|298675571|ref|YP_003727321.1|  85 PKYIKRGLRIFGWGLLLTLITWIFIGQGVIVF---GILHFIGISIILAYP 131
                                       ********************999998877765...455555555555555 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0024
                            OpgC_C 295 avlrplillGrhsLavFvvgvvlslllqv 323
                                        + ++++l+Gr+sL ++ ++  + +++ +
  gi|298675571|ref|YP_003727321.1| 215 YPINMFCLMGRYSLFIYLIHQPFLIIILY 243
                                       4678999***********99755555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1511.32
//
Query:       gi|298675572|ref|YP_003727322.1|  [L=139]
Description: hypothetical protein Metev_1687 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.7e-47  159.9   0.5    4.3e-47  159.7   0.5    1.0  1  DUF2072      Zn-ribbon containing protein
     0.0027   17.5   0.3     0.0035   17.1   0.3    1.0  1  Rho_GDI      RHO protein GDP dissociation inhibitor
  ------ inclusion threshold ------
       0.07   13.2   0.5       0.35   11.0   0.5    2.0  2  Spt4         Spt4/RpoE2 zinc finger
       0.07   13.3   1.1       0.19   11.9   1.1    1.7  1  Zn-ribbon_8  Zinc ribbon domain
      0.071   13.1   0.8       0.12   12.4   0.8    1.3  1  Prok-RING_1  Prokaryotic RING finger family 1


Domain annotation for each model (and alignments):
>> DUF2072  Zn-ribbon containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.7   0.5   1.2e-50   4.3e-47       1     132 [.       2     135 ..       2     136 .. 0.82

  Alignments for each domain:
  == domain 1  score: 159.7 bits;  conditional E-value: 1.2e-50
                           DUF2072   1 PHkCtkCekvfedgskeilkGCpsCGgkkFlyvkeeekkedvseeke..elvaeaeeeieevldaeeteeeklekke 75 
                                       PHkCtkCe++fedg+++il+GCp+CG++kFlyv +e++++++++++e  +++++a e+ ++    +e +e    k++
  gi|298675572|ref|YP_003727322.1|   2 PHKCTKCEQIFEDGNSVILNGCPNCGWNKFLYVGNESQADTSVANEEqsSIDNKAPESTNDEKLVREVNEVLGTKTS 78 
                                       9***********************************99998887777333333333444443333333444334447 PP

                           DUF2072  76 kekaekekeeedrvesvrilepGsYelNlekLlerdelvmalkeegkYvvdlpsvlk 132
                                       k ++++ ++++drvesvril+pGsYelNl++++er+e++ma+ke+g+Y+++lpsv++
  gi|298675572|ref|YP_003727322.1|  79 KLQKSSVMQDDDRVESVRILGPGSYELNLSSIMERKEIIMAIKENGTYALHLPSVFD 135
                                       78889999***********************************************97 PP

>> Rho_GDI  RHO protein GDP dissociation inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.3   9.6e-07    0.0035      10     107 ..      37     129 ..      33     135 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 9.6e-07
                           Rho_GDI  10 eeeeekklklgpqkslkeqleldkdDesLrryKeqLLgsakvdleavetnepevkilkltilsserpdevleldlte 86 
                                       e++++++++  +q s++++     +De L r  ++ Lg+++++l++++ ++ + +++++ il +++     el+l++
  gi|298675572|ref|YP_003727322.1|  37 ESQADTSVANEEQSSIDNKAPESTNDEKLVREVNEVLGTKTSKLQKSSVMQDDDRVESVRILGPGSY----ELNLSS 109
                                       445557889999***********************************999999**********9998....566665 PP

                           Rho_GDI  87 dleklkkkaftlkegseyklk 107
                                          + k+   ++ke+ +y l+
  gi|298675572|ref|YP_003727322.1| 110 -IMERKEIIMAIKENGTYALH 129
                                       .4444889999****999986 PP

>> Spt4  Spt4/RpoE2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.5   9.7e-05      0.35       4      39 ..       5      43 ..       3      53 .. 0.70
   2 ?   -0.7   0.0      0.44   1.6e+03      64      75 ..     118     129 ..     104     130 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.7e-05
                              Spt4  4 CllCklvkte.dqFeeegCpnC..eilelkgdkekvsec 39
                                      C++C+ + ++ ++   +gCpnC  + + + g++++ +++
  gi|298675572|ref|YP_003727322.1|  5 CTKCEQIFEDgNSVILNGCPNCgwNKFLYVGNESQADTS 43
                                      ****998765277899******66444444555555444 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.44
                              Spt4  64 ldkkvpglYAlk 75 
                                       +  k+ g+YAl+
  gi|298675572|ref|YP_003727322.1| 118 MAIKENGTYALH 129
                                       567789999986 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.1   5.4e-05      0.19       7      33 ..       4      27 ..       3      30 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.4e-05
                       Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCg 33
                                      +C++C + fe   s+    l  CP+Cg
  gi|298675572|ref|YP_003727322.1|  4 KCTKCEQIFEDGNSVI---LNGCPNCG 27
                                      7*********888887...777****9 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.8   3.3e-05      0.12       5      27 ..       3      27 ..       1      30 [. 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.3e-05
                       Prok-RING_1  5 kkCpvCgkelkeedDiVv..CpeCg 27
                                      +kC+ C++ +++++ ++   Cp+Cg
  gi|298675572|ref|YP_003727322.1|  3 HKCTKCEQIFEDGNSVILngCPNCG 27
                                      69***********9999778****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       995  (0.0554967); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 838.94
//
Query:       gi|298675573|ref|YP_003727323.1|  [L=287]
Description: methylthioadenosine phosphorylase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.2e-44  150.2   0.0      6e-44  150.0   0.0    1.0  1  PNP_UDP_1  Phosphorylase superfamily
  ------ inclusion threshold ------
      0.092   13.1   0.6       0.22   11.9   0.6    1.6  1  DUF2209    Uncharacterized protein conserved in archaea (DUF2


Domain annotation for each model (and alignments):
>> PNP_UDP_1  Phosphorylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.0   0.0   6.7e-48     6e-44       1     233 [.       6     243 ..       6     244 .. 0.93

  Alignments for each domain:
  == domain 1  score: 150.0 bits;  conditional E-value: 6.7e-48
                                       CEEEEESSH....HHHHHHHHHEEEEEEEEEE.TTEEEEEEEETTEEE.EEEE--....SSHHHHHHHHHHHHHHHC CS
                         PNP_UDP_1   1 kiaiivgsp....gevellaespleetpfgregrgfkfvtGtlkgkpv.vivstG....iGkpnaavvaeirllkef 68 
                                       +iaii+gs+      ++++++    +tpfg++  + ++++G+++ ++v ++ ++     i++++ + +a+i +lk +
  gi|298675573|ref|YP_003727323.1|   6 DIAIIGGSGiydlSWFDNVRQV-DIDTPFGKP--SDEITIGEYGDRTVcFLPRHDaghrISPTQLNSRANIFALKKL 79 
                                       69********555555555555.*********..*********44444255555599******************** PP

                                       --SEEEEEEEEEESSTTT-TT-EEEEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTTEEE CS
                         PNP_UDP_1  69 gvkaiiriGtaGglnpdlkvGDvvipddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealgikvhr 145
                                       gvk+ii+ +++G+l++++ + D+vip+++++ +  +++++++e+++ + +++d+ ++pel +++   a+ +g++vh 
  gi|298675573|ref|YP_003727323.1|  80 GVKRIISASAVGSLKNEISPLDLVIPNQIYDRTKSRTSTFFEEGIVVHAGFADP-FCPELSETITDIARSKGYNVHD 155
                                       *************************************9***9999*********.********************** PP

                                       .EEEEEESESS-CHHHHHHHHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTBETTCTCH.HCCCHHHHHH CS
                         PNP_UDP_1 146 .GvvatadgfyaeteaelrllrrlgadaveMEtaavaqlArelgipfaairvvsdlaaggadaeatheeveefaqea 221
                                        G++++ +g++++t+ae++ +++lg d+++M++ +++ lAre++i++  i++v+d ++ + ++  + ++v e+++++
  gi|298675573|ref|YP_003727323.1| 156 sGTYVCIEGPQFSTRAESSVYQSLGFDVIGMTALPEVKLAREAEICYTMIATVTD-YDVWKEQDVDIATVIENTRKN 231
                                       *******************************************************.888****************** PP

                                       HHHHHHHHHHHH CS
                         PNP_UDP_1 222 aknaaalllall 233
                                       +++++ ++  ++
  gi|298675573|ref|YP_003727323.1| 232 VNAVKDIVSDAI 243
                                       *******99877 PP

>> DUF2209  Uncharacterized protein conserved in archaea (DUF2209)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.6   2.5e-05      0.22      19      72 ..     200     253 ..     191     260 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.5e-05
                           DUF2209  19 vcaaVslevsadriekveqvkilvvaseeepkledvvklieeaveelkeegtiv 72 
                                       +c +  ++v+  ++ k ++v+i +v +++ +++++v +++++a+e++  e   v
  gi|298675573|ref|YP_003727323.1| 200 ICYTMIATVTDYDVWKEQDVDIATVIENTRKNVNAVKDIVSDAIEKIPLERDCV 253
                                       788888999999**********************************96555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.60
# Mc/sec: 1448.75
//
Query:       gi|298675574|ref|YP_003727324.1|  [L=234]
Description: phosphoribosyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.1e-19   68.7   0.0    5.5e-19   68.2   0.0    1.1  1  Pribosyltran  Phosphoribosyl transferase domain
  ------ inclusion threshold ------
        0.2   11.1   0.0        0.3   10.5   0.0    1.3  1  UPRTase       Uracil phosphoribosyltransferase


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.2   0.0   6.1e-23   5.5e-19       6     154 ..      12     158 ..      10     162 .. 0.87

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 6.1e-23
                                       TT---EEEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........... CS
                      Pribosyltran   6 lenpaildavarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes... 79 
                                       ++++ i++ +++ + ei ++ +++pd++++ argG+  +  l d L+  l+++ + k+++ +++ a+ g  +++   
  gi|298675574|ref|YP_003727324.1|  12 TNWEYIYNLCRDVSTEIKKS-EFQPDIIIAHARGGWFAGRVLCDFLG--LDDLTSLKVEHYTGTAAISGEGAQIkyp 85 
                                       566677889***********.*************************9..7777777777777777776666666777 PP

                                       EE----TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHHHHH-TTS.....EEEEEEE-S CS
                      Pribosyltran  80 rlledpagkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpateeevdknakrvfslspdnfvavvgf 154
                                         +  + +k VliVDDi+dtG ++++a e++ e++p ev++a+l +  ++++e+d++  ++++    ++v++++f
  gi|298675574|ref|YP_003727324.1|  86 LSSDAVVDKNVLIVDDIIDTGESMKYAKEHVLEQNPNEVKTATLQYLYTSQMEPDYWSEYIDEWA--WIVFPWNF 158
                                       99999***************************************************999998655..88888876 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   3.3e-05       0.3     120     153 ..      92     125 ..      65     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 3.3e-05
                           UPRTase 120 aertvlllDpviaTGgsaaaaiqlLkergvgeek 153
                                        +++vl++D +i TG+s+  a ++++e++ +e k
  gi|298675574|ref|YP_003727324.1|  92 VDKNVLIVDDIIDTGESMKYAKEHVLEQNPNEVK 125
                                       6889*******************99997765544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1740.14
//
Query:       gi|298675575|ref|YP_003727325.1|  [L=440]
Description: GTP-binding signal recognition particle SRP54 G- domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-71  239.7   0.3    5.7e-71  238.2   0.0    1.8  2  SRP54            SRP54-type protein, GTPase domain
    3.4e-28   98.2   4.2    3.4e-28   98.2   4.2    2.6  2  SRP_SPB          Signal peptide binding domain
    1.4e-20   73.3   2.4    2.6e-20   72.4   1.0    2.3  1  SRP54_N          SRP54-type protein, helical bundle domain
    2.6e-06   27.1   0.7    5.3e-05   22.9   0.7    2.3  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
    4.9e-06   26.6   0.0    1.5e-05   25.1   0.0    1.9  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    0.00022   20.6   0.0    0.00049   19.5   0.0    1.5  1  6PF2K            6-phosphofructo-2-kinase
    0.00037   19.8   0.0    0.00088   18.6   0.0    1.7  1  Zeta_toxin       Zeta toxin
    0.00066   19.5   0.0     0.0014   18.4   0.0    1.6  1  AAA_24           AAA domain
     0.0026   16.8   0.1      0.029   13.4   0.0    2.2  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0028   17.5   0.0     0.0068   16.3   0.0    1.6  1  APS_kinase       Adenylylsulphate kinase
     0.0037   16.2   0.0     0.0064   15.5   0.0    1.3  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
     0.0057   16.4   0.6      0.042   13.5   0.1    2.5  2  Thymidylate_kin  Thymidylate kinase
     0.0062   17.1   0.2      0.024   15.2   0.0    2.2  1  AAA_18           AAA domain
     0.0062   16.3   0.2      0.029   14.2   0.0    2.2  2  ATP_bind_1       Conserved hypothetical ATP binding protein
      0.007   16.3   0.0      0.028   14.4   0.0    2.0  1  TFIIA_gamma_N    Transcription initiation factor IIA, gamma s
  ------ inclusion threshold ------
       0.01   16.0   0.0      0.019   15.1   0.0    1.5  1  AAA_33           AAA domain
      0.015   15.6   0.1      0.068   13.5   0.0    2.1  1  AAA_22           AAA domain
      0.015   15.2   0.1      0.032   14.1   0.1    1.5  1  MobB             Molybdopterin guanine dinucleotide synthesis
      0.019   14.4   0.0      0.042   13.3   0.0    1.6  1  KTI12            Chromatin associated protein KTI12
      0.028   13.8   0.2        4.6    6.6   0.0    2.5  2  SRPRB            Signal recognition particle receptor beta su
      0.028   14.8   0.0      0.073   13.5   0.0    1.8  1  AAA_16           AAA ATPase domain
      0.029   13.5   0.1      0.056   12.5   0.1    1.4  1  LpxK             Tetraacyldisaccharide-1-P 4'-kinase
      0.032   13.9   0.0      0.057   13.1   0.0    1.4  1  T3SS_HrpK1       Type III secretion system translocator prote
      0.033   14.5   0.1      0.055   13.8   0.1    1.7  1  AAA_19           AAA domain
      0.035   12.7   2.4      0.034   12.8   0.5    1.7  2  Cullin           Cullin family
      0.047   13.4   0.1       0.25   11.0   0.0    2.3  2  AAA_30           AAA domain
      0.056   13.4   0.6       0.65    9.9   0.0    2.9  3  AAA_31           AAA domain
      0.094   12.4   0.1       0.46   10.2   0.0    2.0  2  PRK              Phosphoribulokinase / Uridine kinase family
        0.1   11.7   0.0        0.2   10.8   0.0    1.6  1  G-alpha          G-protein alpha subunit
       0.11   12.7   0.0       0.27   11.5   0.0    1.7  1  AAA_28           AAA domain
       0.11   12.4   0.8        1.2    9.0   0.1    2.5  2  NTPase_1         NTPase
       0.11   12.2   0.2        2.5    7.8   0.1    2.7  2  IstB_IS21        IstB-like ATP binding protein
       0.12   12.5   1.5       0.39   10.8   0.3    2.4  1  MMR_HSR1         50S ribosome-binding GTPase
       0.24   11.5   1.5         20    5.4   0.3    2.7  2  Tape_meas_lam_C  Lambda phage tail tape-measure protein (Tape
       0.37   11.2   3.8       0.46   10.9   0.4    2.9  2  AAA_17           AAA domain


Domain annotation for each model (and alignments):
>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.2   0.0   1.1e-73   5.7e-71       2     196 .]      98     290 ..      97     290 .. 0.99
   2 ?   -1.8   0.1       3.9     2e+03      99     139 ..     323     364 ..     317     376 .. 0.75

  Alignments for each domain:
  == domain 1  score: 238.2 bits;  conditional E-value: 1.1e-73
                                       EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHH CS
                             SRP54   2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavek 78 
                                       + i+++GlqG+GKTtt++KLa++++k+g k+++++aDtfR++A+ QLk l +k  +p+++++ ++d+  +++++++k
  gi|298675575|ref|YP_003727325.1|  98 QTIMMIGLQGSGKTTTTSKLARYFQKKGLKPAVICADTFRPGAYHQLKSLCDKNSIPFYGEEGNEDSLGIVERGMDK 174
                                       789************************************************************************99 PP

                                       HHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSS CS
                             SRP54  79 akeekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgdak 155
                                         +  +dv+++DTaGr+  +++l+ee+++i++++kpd++llvlda++gq+a +qa+aF+e++gi+gv++tklDg+ak
  gi|298675575|ref|YP_003727325.1| 175 LGK--YDVLIIDTAGRHSLEQDLIEEMEQINSIAKPDKKLLVLDAAIGQQASEQARAFNESIGISGVVITKLDGTAK 249
                                       988..************************************************************************ PP

                                       TTHHHHHHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHHT CS
                             SRP54 156 gGaalsiaaelklPikfigvGekiedleefdperlvsrllg 196
                                       gG+als+++e+++ i+figvGe+  dle+f+p+r++srllg
  gi|298675575|ref|YP_003727325.1| 250 GGGALSAVSETNSSIAFIGVGETSGDLEKFEPDRFISRLLG 290
                                       ***************************************95 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.9
                                       HHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHH.HHHHHHHH CS
                             SRP54  99 kelmeelkkikkvvkpdevllvldattgqeavk.qakaFkea 139
                                       k++ ++l++++k+   ++v+  + + +gq+  + q +  +e+
  gi|298675575|ref|YP_003727325.1| 323 KDMYKQLEAVNKMGPLKQVMQMMPGGMGQNISEeQFQVTSEK 364
                                       567899999999999999999999999999876455555555 PP

>> SRP_SPB  Signal peptide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       9.1   4.7e+03       5      22 ..     193     210 ..     191     234 .. 0.66
   2 !   98.2   4.2   6.6e-31   3.4e-28       2      99 .]     320     419 ..     319     419 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 9.1
                                       HHHHHHHHHHHCCCCCCH CS
                           SRP_SPB   5 rdlleqlqqikkmGplsk 22 
                                       +dl+e+++qi+++ + +k
  gi|298675575|ref|YP_003727325.1| 193 QDLIEEMEQINSIAKPDK 210
                                       578888888887765544 PP

  == domain 2  score: 98.2 bits;  conditional E-value: 6.6e-31
                                       SCTHHHHHHHHHHHCCCCCCHHHHCCC........H...CCCCCHHHHHHHHHTTSBHHHHHSGCG-..HHHHHHHH CS
                           SRP_SPB   2 ftlrdlleqlqqikkmGplskllsmiPgmsae...akaeeeaekklkrieaiidSMTkeErdspekllkesRkrRiA 75 
                                       ftl+d+++ql+ ++kmGpl+++++m+Pg + +   +++ + +++kl+r+ +i+dSMT +E+d+p+ l+ +sR++Ri+
  gi|298675575|ref|YP_003727325.1| 320 FTLKDMYKQLEAVNKMGPLKQVMQMMPGGMGQnisEEQFQVTSEKLSRYRIIMDSMTVDEMDDPK-LIGSSRIKRIS 395
                                       9**************************7554556543448889**********************.8889******* PP

                                       HHTTS-HHHHHHHHHHHHHHHHHT CS
                           SRP_SPB  76 rGsGtsvqevnellkqfeqmkkmm 99 
                                       rGsG + ++v+ellk +++m++ m
  gi|298675575|ref|YP_003727325.1| 396 RGSGSKPDDVRELLKYHKTMQNAM 419
                                       *********************987 PP

>> SRP54_N  SRP54-type protein, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.4   1.0   5.1e-23   2.6e-20       1      75 []       6      83 ..       6      83 .. 0.97

  Alignments for each domain:
  == domain 1  score: 72.4 bits;  conditional E-value: 5.1e-23
                                      HHHHHHHHHHHHCCSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTS....S-HHHHHHHHHHHHH CS
                           SRP54_N  1 LgkklnsalkklsgkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekk....lkpkqqvkkivkdeL 75
                                      Lg++l++alkkl ++++ide+ +++++k++++aLl+aDV+v++v+++ +++k++a++ ++    ++p+++v++iv++eL
  gi|298675575|ref|YP_003727325.1|  6 LGSSLQDALKKLVNSGRIDEKSVNDVVKDIQRALLQADVNVQLVMNMSKQIKERALK-EEvpsgMNPREHVIRIVYQEL 83
                                      899**************************************************9999.555*****************8 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.7     1e-07   5.3e-05       3     156 ..     100     250 ..      98     265 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1e-07
                                       EEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT.EEEETTTTECCHCTT-HHHHHHHHH CS
                              cobW   3 tvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgveivelenGciCctlredllkeleale 77 
                                       +++ G  GsGKTt  ++l    +++glk avi  +    +  ++l + ++++ + +         +ed l  +e+ +
  gi|298675575|ref|YP_003727325.1| 100 IMMIGLQGSGKTTTTSKLAryFQKKGLKPAVICADTFRPGAYHQLKSLCDKNSIPFYG----EEGNEDSLGIVERGM 172
                                       5678999***********988788************9988888888777666555432....234689999999999 PP

                                       HHHTT-SEEEEEECT.TTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHH CS
                              cobW  78 ereerldviliEttG.laePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDll 153
                                       ++ +++dv++i t G  +  + ++ + e+++s ++ d ++ v+Da ++ ++ +++++ +++ +  + + v++K D  
  gi|298675575|ref|YP_003727325.1| 173 DKLGKYDVLIIDTAGrHSLEQDLIEEMEQINSIAKPDKKLLVLDA-AIGQQASEQARAFNESIGISGV-VITKLDGT 247
                                       9999***********87888888788*******************.77799999**********9986.67899977 PP

                                       CHC CS
                              cobW 154 dee 156
                                        + 
  gi|298675575|ref|YP_003727325.1| 248 AKG 250
                                       665 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   2.8e-08   1.5e-05       9      91 ..     107     251 ..     102     332 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 2.8e-08
                                       TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................... RF
                              CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................... 54 
                                       G+GKTt++ +Lar+++++gl+ +++ aD+ ++ + +  ++  d++                                
  gi|298675575|ref|YP_003727325.1| 107 GSGKTTTTSKLARYFQKKGLKPAVICADTFRPGAYHQLKSLCDKNSipfygeegnedslgivergmdklgkydvlii 183
                                       99********************************994444444444555666666666******************* PP

                                       ....................................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-T CS
                                       ....................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ....................................dlkrllellealgkkkalllkiagvvlnrvdgeneet 91 
                                                                           + ++ +e ++a+ +     + i gvv+++ dg +   
  gi|298675575|ref|YP_003727325.1| 184 dtagrhsleqdlieemeqinsiakpdkkllvldaaiG-QQASEQARAFNE----SIGISGVVITKLDGTAKGG 251
                                       ********************99999999999855431.222333333333....3889999999999886555 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   9.6e-07   0.00049      10      53 ..      94     137 ..      88     175 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 9.6e-07
                                       ..S-EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHH CS
                             6PF2K  10 knsklvivlvGLpargKtyiskkltrylkwlgvrtkvFnvgkyr 53 
                                       + ++  i+++GL   gKt++++kl ry +  g++  v  +  +r
  gi|298675575|ref|YP_003727325.1|  94 NLEPQTIMMIGLQGSGKTTTTSKLARYFQKKGLKPAVICADTFR 137
                                       556789**********************9888875554443333 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.7e-06   0.00088      14      56 ..      95     138 ..      84     188 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.7e-06
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdele.rqgnvvrldpDdlRe 56 
                                        +P  i++ G +G+GK+++ ++l+++++ ++ +  ++ +D++R+
  gi|298675575|ref|YP_003727325.1|  95 LEPQTIMMIGLQGSGKTTTTSKLARYFQkKGLKPAVICADTFRP 138
                                       5799************************88889**********6 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.8e-06    0.0014       3      93 ..      98     207 ..      96     231 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.8e-06
                            AAA_24   3 lkiliyGpsgiGKTtlakel.........gpkplfidtek.Glksldadkfpdie........swedfldevvel.. 59 
                                       + i+++G +g+GKTt+ ++l         +p +++ dt++ G+ +      +  +        + e        +  
  gi|298675575|ref|YP_003727325.1|  98 QTIMMIGLQGSGKTTTTSKLaryfqkkglKPAVICADTFRpGAYHQLKSLCD-KNsipfygeeGNE--------Dsl 165
                                       689*****************9******8888888889999766332222222.2213344444555........355 PP

                            AAA_24  60 ......aaeladyktlviDtide..leelclaevirqnekae 93 
                                              ++l +y++l+iDt++   le+  ++e+ + n++a+
  gi|298675575|ref|YP_003727325.1| 166 givergMDKLGKYDVLIIDTAGRhsLEQDLIEEMEQINSIAK 207
                                       555555***************862256666666666666554 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   5.6e-05     0.029      31      66 ..      99     134 ..      84     142 .. 0.91
   2 ?    0.5   0.0      0.47   2.4e+02     122     145 ..     178     201 ..     167     209 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.6e-05
                                       EEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                              MeaB  31 vvGltGvPGaGkstlvealglelrrrGkrvavlavD 66 
                                        + + G+ G+Gk t++++l+  ++++G + av+  D
  gi|298675575|ref|YP_003727325.1|  99 TIMMIGLQGSGKTTTTSKLARYFQKKGLKPAVICAD 134
                                       677899***************************988 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.47
                                       -SEEEEEEESSTTHHHHHHTT-SE CS
                              MeaB 122 fDvvlietvGvGqsevdvaevvdt 145
                                       +Dv++i+t G    e d++e ++ 
  gi|298675575|ref|YP_003727325.1| 178 YDVLIIDTAGRHSLEQDLIEEMEQ 201
                                       9*********99999999886665 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.3e-05    0.0068       2      49 ..      97     144 ..      96     150 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.3e-05
                                       -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT- CS
                        APS_kinase   2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdL 49 
                                       + ++++ Gl gsGK+t + +l+++ ++kg +  ++  d+ R g +++L
  gi|298675575|ref|YP_003727325.1|  97 PQTIMMIGLQGSGKTTTTSKLARYFQKKGLKPAVICADTFRPGAYHQL 144
                                       6799**********************************9998877766 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.2e-05    0.0064      11      50 ..      93     134 ..      84     143 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.2e-05
                     TrwB_AAD_bind  11 keretqhilivGttGsGKtqalekllrairarg..draivlD 50 
                                        + e q i+++G +GsGKt++++kl r  +++g    +i +D
  gi|298675575|ref|YP_003727325.1|  93 INLEPQTIMMIGLQGSGKTTTTSKLARYFQKKGlkPAVICAD 134
                                       67899*************************999644555555 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.1   8.2e-05     0.042       3      28 ..     104     130 ..     103     134 .. 0.90
   2 ?   -0.7   0.0       1.9   9.6e+02     131     166 ..     390     425 ..     387     435 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.2e-05
                                       ESTTSSHHHHHHHHHHHHHHTTE..EE CS
                   Thymidylate_kin   3 GlDGaGKttqaellkerlkeegik.vv 28 
                                       Gl G+GKtt + +l+++++++g+k +v
  gi|298675575|ref|YP_003727325.1| 104 GLQGSGKTTTTSKLARYFQKKGLKpAV 130
                                       999*******************98654 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.9
                                       HHTSCCTTSSTT.TSHHHHHHHHHHHHHHHHHHHHTT CS
                   Thymidylate_kin 131 alkRlakrdeld.eeeeeqldflrkvrerylelaked 166
                                       ++kR+++++ ++ +++ e l++++++ +++++ ++  
  gi|298675575|ref|YP_003727325.1| 390 RIKRISRGSGSKpDDVRELLKYHKTM-QNAMKNFRGA 425
                                       67888888886625555555555555.5588877644 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   4.7e-05     0.024       1      86 [.     100     190 ..     100     231 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.7e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf...................gvnlrdvakenglllevdpealdeskrldedkld 58 
                                       I+  G +G+GKtt +  L++   f                     +l++++ +n + ++ ++         +ed l 
  gi|298675575|ref|YP_003727325.1| 100 IMMIGLQGSGKTTTTSKLARY--FqkkglkpavicadtfrpgaYHQLKSLCDKNSIPFYGEEG--------NEDSLG 166
                                       7889**************666..2234668889999966666666666666666666666666........555555 PP

                            AAA_18  59 klldaleenssaleegknlvidghlael 86 
                                        + +++++     ++ ++l+id    + 
  gi|298675575|ref|YP_003727325.1| 167 IVERGMDKL----GKYDVLIIDTAGRHS 190
                                       555555553....456666666655555 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   5.6e-05     0.029       2      33 ..     103     134 ..     102     139 .. 0.92
   2 ?   -2.1   0.0       5.2   2.7e+03      46      60 ..     404     418 ..     403     436 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.6e-05
                        ATP_bind_1   2 vGpaGsGKttfvgalseilelrgrsvavvNLD 33 
                                       +G  GsGKtt +++l+ +++++g ++av+  D
  gi|298675575|ref|YP_003727325.1| 103 IGLQGSGKTTTTSKLARYFQKKGLKPAVICAD 134
                                       899**********************9998665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.2
                        ATP_bind_1  46 direlitledvmedl 60 
                                       d+rel+++ + m+++
  gi|298675575|ref|YP_003727325.1| 404 DVRELLKYHKTMQNA 418
                                       899999999999883 PP

>> TFIIA_gamma_N  Transcription initiation factor IIA, gamma subunit, helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   5.5e-05     0.028      10      36 ..       6      32 ..       5      36 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.5e-05
                     TFIIA_gamma_N 10 lGtaLtdaLDeliqegkIspqlamkVL 36
                                      lG +L+daL  l+++g+I+++ ++ V 
  gi|298675575|ref|YP_003727325.1|  6 LGSSLQDALKKLVNSGRIDEKSVNDVV 32
                                      8******************99888876 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   3.7e-05     0.019       2      21 ..     100     119 ..     100     230 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.7e-05
                            AAA_33   2 vllvGlpGsGKstlaerllk 21 
                                       ++++Gl+GsGK+t   +l++
  gi|298675575|ref|YP_003727325.1| 100 IMMIGLQGSGKTTTTSKLAR 119
                                       79************999864 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   0.00013     0.068       7     113 ..      99     203 ..      95     218 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00013
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst...sskdllrellralglelkaerlsseelle 80 
                                        ++ +G  G+GKTt+  +l++ +++       +p v+  +   ++    +    + l+ +   +  + +  +e+ l 
  gi|298675575|ref|YP_003727325.1|  99 TIMMIGLQGSGKTTTTSKLARYFQKK----GLKPAVICADTFRPGayhQL----KSLCDKNSIPFYG-EEGNEDSLG 166
                                       57889****************99633....25788887777776622244....4444444444444.556666667 PP

                            AAA_22  81 aleqalraravielliiDEaqhlr.s...eealeeLr 113
                                        +e+ +++ ++  +liiD a + + +    e +e++ 
  gi|298675575|ref|YP_003727325.1| 167 IVERGMDKLGKYDVLIIDTAGRHSlEqdlIEEMEQIN 203
                                       7777777777777799998876522334544444444 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   6.3e-05     0.032       2      33 ..     100     131 ..      99     136 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.3e-05
                              MobB   2 lgivgksgsGKTtLleklipelkarglrvgti 33 
                                       + ++g +gsGKTt  +kl + ++++gl+ ++i
  gi|298675575|ref|YP_003727325.1| 100 IMMIGLQGSGKTTTTSKLARYFQKKGLKPAVI 131
                                       6789************************9998 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   8.2e-05     0.042       4      41 ..     100     137 ..      99     186 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.2e-05
                                       EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH CS
                             KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvviddeslg 41 
                                       +++ Gl  sGK+t +++La+++++++ +  vi  ++++
  gi|298675575|ref|YP_003727325.1| 100 IMMIGLQGSGKTTTTSKLARYFQKKGLKPAVICADTFR 137
                                       7899***********************99999888876 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0091       4.6       4      25 ..      98     119 ..      96     133 .. 0.85
   2 ?    4.4   0.0     0.043        22      50      90 ..     179     222 ..     168     237 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0091
                                       -EEEEE-STTSSHHHHHHHHHH CS
                             SRPRB   4 pavllvGlsdsGKTslftrLtt 25 
                                       ++++++Gl+ sGKT+   +L  
  gi|298675575|ref|YP_003727325.1|  98 QTIMMIGLQGSGKTTTTSKLAR 119
                                       689************9998875 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.043
                                       T-SEEEETT-GCCSHHHHHHHHHHGGE.E..EEEEEEETTS-HH CS
                             SRPRB  50 kltliDfPGheklrqklleklkakssl.k..glvfvvDStidpk 90 
                                        + +iD  G ++l q+l+e++ + +s+ k  + + v+D++i ++
  gi|298675575|ref|YP_003727325.1| 179 DVLIIDTAGRHSLEQDLIEEMEQINSIaKpdKKLLVLDAAIGQQ 222
                                       5779***************9988777413224677888888776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   0.00014     0.073      24     142 ..      97     216 ..      72     234 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00014
                            AAA_16  24 pelvllsGesGvGKsslvrellralekd..............ggif.lrgkcdqlesaipysalaqalareellrql 85 
                                       p+ ++ +G +G+GK++   +l+r+++k+              g++  l+  cd++                  +   
  gi|298675575|ref|YP_003727325.1|  97 PQTIMMIGLQGSGKTTTTSKLARYFQKKglkpavicadtfrpGAYHqLKSLCDKN-----------------SIPFY 156
                                       5789999******************999554444444444332222333333333.................22222 PP

                            AAA_16  86 ldeaesaeleawrekleeala................avpelagaeasrllellkrllallsrderplvlvlD 142
                                       ++e ++++l           +                +  + + +++++l e++ ++ + +++d++  +lvlD
  gi|298675575|ref|YP_003727325.1| 157 GEEGNEDSL-----------GivergmdklgkydvliIDTAGRHSLEQDLIEEMEQINSIAKPDKK--LLVLD 216
                                       222222111...........1222222222223333222222233335555555555555555444..45554 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00011     0.056      46      71 ..     106     131 ..      97     133 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                                       S-HSHHHHHHHHHHHTTTS..-EEEE CS
                              LpxK  46 GGtGKTPlvialvkllqarglkvgvl 71 
                                        G+GKT ++  l++++q++glk++v+
  gi|298675575|ref|YP_003727325.1| 106 QGSGKTTTTSKLARYFQKKGLKPAVI 131
                                       59***********************8 PP

>> T3SS_HrpK1  Type III secretion system translocator protein, HrpF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00011     0.057      40      91 ..      11      63 ..       5     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                        T3SS_HrpK1 40 d.ntgglkaDGtidkkklkaflknveknldsadkdlkdYlkkhPdaDadslel 91
                                      + +   l   G+id+k +++++k+++++l +ad +++  ++   +   ++l+ 
  gi|298675575|ref|YP_003727325.1| 11 QdALKKLVNSGRIDEKSVNDVVKDIQRALLQADVNVQLVMNMSKQIKERALKE 63
                                      4344556678***************************9999888888887765 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   0.00011     0.055       7      62 ..      94     148 ..      89     382 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00011
                            AAA_19   7 alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerl 62 
                                       +l+ +++++++  G+GKT+++ +  +++++ g +kp+ i + +f   A ++l+  +
  gi|298675575|ref|YP_003727325.1|  94 NLEPQTIMMIGLQGSGKTTTTSKLARYFQKKG-LKPAVICADTFRPGAYHQLKSLC 148
                                       56788999************998888877776.88888888888888888888766 PP

>> Cullin  Cullin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       1.2     6e+02       3      57 ..       9      62 ..       7      82 .. 0.76
   2 ?   12.8   0.5   6.6e-05     0.034     237     328 ..     296     422 ..     294     438 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.2
                            Cullin  3 kleeaiqeilk.knvsklsfeelYravynlvlskekkqgekLydklkelieehlke 57
                                      +l++a++++++  ++ ++s +++ ++++   l+   +   +L  +++++i+e   +
  gi|298675575|ref|YP_003727325.1|  9 SLQDALKKLVNsGRIDEKSVNDVVKDIQRALLQA--DVNVQLVMNMSKQIKERALK 62
                                      6888999999856999999999999999998854..47777777777777776554 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 6.6e-05
                            Cullin 237 elikkhleelleee..lkklledekledLkrlykllsrvdgleeLrkaleeyikeegkaivkdake........... 300
                                        li+k  e+l eee  +++++ +  +  Lk +yk l+ v+++ +L+++++ +   +g++i++++ +           
  gi|298675575|ref|YP_003727325.1| 296 SLIEKAEESLSEEEldVESMM-Q-GRFTLKDMYKQLEAVNKMGPLKQVMQMMPGGMGQNISEEQFQvtseklsryri 370
                                       689999999999999999***.4.6899*********************************9976699999999999 PP

                            Cullin 301 ........................kektedakkyveklLelkdkfdklvkea 328
                                                               +  +  + + v +lL++++ +++ +k+ 
  gi|298675575|ref|YP_003727325.1| 371 imdsmtvdemddpkligssrikriSRGSGSKPDDVRELLKYHKTMQNAMKNF 422
                                       9999999999999999999999996666777777999999999999998764 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00049      0.25      20      57 ..      99     137 ..      92     215 .. 0.66
   2 ?   -2.4   0.0       6.6   3.4e+03     126     142 ..     327     343 ..     325     350 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00049
                            AAA_30  20 vavltGpAGtGKttalkalreaweaag.grviglAptgk 57 
                                       + ++ G  G+GKtt+ ++l++ ++++g ++ +++A t +
  gi|298675575|ref|YP_003727325.1|  99 TIMMIGLQGSGKTTTTSKLARYFQKKGlKPAVICADTFR 137
                                       567899********************8677778887765 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.6
                            AAA_30 126 rQlasVeaGgvlrdlve 142
                                       +Ql++V++ g+l+++++
  gi|298675575|ref|YP_003727325.1| 327 KQLEAVNKMGPLKQVMQ 343
                                       7999**99999999875 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0    0.0013      0.65      12      39 ..     107     134 ..      98     143 .. 0.88
   2 ?   -1.1   0.0         3   1.5e+03     116     126 ..     176     186 ..     158     192 .. 0.82
   3 ?   -1.7   0.0       4.5   2.3e+03      25      46 ..     204     225 ..     200     244 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0013
                            AAA_31  12 GvGKTTtsvnlaaalaklgkkvLlvDlD 39 
                                       G GKTTt+ +la  + k+g k  ++ +D
  gi|298675575|ref|YP_003727325.1| 107 GSGKTTTTSKLARYFQKKGLKPAVICAD 134
                                       89******************98888777 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3
                            AAA_31 116 deYDyiiiDcp 126
                                        +YD+ iiD+ 
  gi|298675575|ref|YP_003727325.1| 176 GKYDVLIIDTA 186
                                       47*******85 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 4.5
                            AAA_31  25 alaklgkkvLlvDlDpQanatt 46 
                                       ++ak +kk L+ D+   + a+ 
  gi|298675575|ref|YP_003727325.1| 204 SIAKPDKKLLVLDAAIGQQASE 225
                                       679999*****99876555555 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       2.3   1.2e+03     170     192 ..      28      50 ..      22      54 .. 0.83
   2 ?   10.2   0.0    0.0009      0.46       4      38 ..     102     136 ..      99     151 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.3
                               PRK 170 kpdyvnyikpqfseadliiqrvp 192
                                        +d v+ i++ + +ad+++q v 
  gi|298675575|ref|YP_003727325.1|  28 VNDVVKDIQRALLQADVNVQLVM 50 
                                       57889999***********9875 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0009
                               PRK   4 vagsSGaGkttvarklekifgrekvkaaeiegdsf 38 
                                       + g  G+Gktt++ kl   f+++++k+a+i  d f
  gi|298675575|ref|YP_003727325.1| 102 MIGLQGSGKTTTTSKLARYFQKKGLKPAVICADTF 136
                                       55778**********************99976655 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0004       0.2      24      80 ..      98     153 ..      83     381 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0004
                                       EEEEEEESTTSSHHHHHHHHHHHCS--.--HHHHHCCHHHHHHHHHHHHHHHHHHHHH CS
                           G-alpha  24 vkllllGqseSGKsTilkqlkllykkg.fseeelatwraviqlnivrsiktileales 80 
                                        +++++G ++SGK+T+  +l ++++k+  +     +  +  +   ++++k+++++ + 
  gi|298675575|ref|YP_003727325.1|  98 QTIMMIGLQGSGKTTTTSKLARYFQKKgLKPA--VICADTFRPGAYHQLKSLCDKNSI 153
                                       579*************9999988866635555..334444444555555555555444 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00053      0.27       2      22 ..     100     120 ..      99     154 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00053
                            AAA_28   2 ivitGgestGKTtlleaLaar 22 
                                       i+++G +++GKTt++++La+ 
  gi|298675575|ref|YP_003727325.1| 100 IMMIGLQGSGKTTTTSKLARY 120
                                       889****************75 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1    0.0024       1.2       2      30 ..     100     128 ..      99     142 .. 0.84
   2 ?    1.1   0.1      0.64   3.3e+02      94     130 ..     176     214 ..     161     241 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0024
                                       EEEE--TTSSHHHHHHHHHHHH...GGGE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkv 30 
                                       +++ G +G+GKtT  +k+++  +++g+k 
  gi|298675575|ref|YP_003727325.1| 100 IMMIGLQGSGKTTTTSKLARYFQKKGLKP 128
                                       667799*******************9985 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.64
                                       HHH-EEEE---ST..TGGG-HHHHHHHHHHHTTTSEEEE CS
                          NTPase_1  94 seadviviDEiGk..mElkskkfkeaveevLksekpvla 130
                                        + dv++iD  G+  +E    +  e+++ + k++k +l+
  gi|298675575|ref|YP_003727325.1| 176 GKYDVLIIDTAGRhsLEQDLIEEMEQINSIAKPDKKLLV 214
                                       5789********733666666666778888887776664 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.55   2.8e+02      48      71 ..      98     121 ..      82     132 .. 0.84
   2 ?    7.8   0.1    0.0049       2.5      97     130 ..     166     199 ..     160     228 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.55
                         IstB_IS21  48 enivllGpsGvGKshlaialgvea 71 
                                       + i+++G  G GK+  +  l++  
  gi|298675575|ref|YP_003727325.1|  98 QTIMMIGLQGSGKTTTTSKLARYF 121
                                       7899**********9888887655 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0049
                         IstB_IS21  97 gklaralkrllkvdllilDdlgllpldqaeaell 130
                                       g ++r +++l k d+li+D  g + l+q+  e++
  gi|298675575|ref|YP_003727325.1| 166 GIVERGMDKLGKYDVLIIDTAGRHSLEQDLIEEM 199
                                       5678999********************9876665 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.3   0.00075      0.39       2      93 ..     100     223 ..      99     243 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00075
                                       EEEEESTTSSHHHHHHHHHT......STEEESSSTTSSSSE.EEEEEE....ETTEE.................... CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg......ekaivsdkpgtTrdi.negrvk....lkgke.................... 47 
                                       ++ +G   +GK+t  ++l +         + + +   T  +  ++++k    +   +                    
  gi|298675575|ref|YP_003727325.1| 100 IMMIGLQGSGKTTTTSKLARyfqkkgL--KPAVICADTFRPgAYHQLKslcdK---Nsipfygeegnedslgiverg 171
                                       788999999999999999874332220..222222333333333333332210...123344444444455555555 PP

                                       ........EEEEECGGCSSHHHHHH...HHHHHHHHHHCTSEEEEEEETT..TTCSHHH CS
                          MMR_HSR1  48 ........ielvDtpGliegaseek...glgkaflaleeadlillvvdas..eeklkpl 93 
                                               + ++Dt+G  +  s e+   ++ +++ ++ + d  llv+da+  +    + 
  gi|298675575|ref|YP_003727325.1| 172 mdklgkydVLIIDTAG-RH--SLEQdliEEMEQINSIAKPDKKLLVLDAAigQ----QA 223
                                       55555555********.54..4555113445555556667999****977442....22 PP

>> Tape_meas_lam_C  Lambda phage tail tape-measure protein (Tape_meas_lam_C)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.097        50      34      69 ..       8      42 ..       2      49 .. 0.88
   2 ?    5.4   0.3     0.039        20      35      57 ..     414     436 ..     409     439 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.097
                   Tape_meas_lam_C 34 dsmedalaefvttGklsfsdlaesviadlakiaarq 69
                                      +s++dal ++v+ G  + ++ ++ v++d+ ++++++
  gi|298675575|ref|YP_003727325.1|  8 SSLQDALKKLVNSGRIDEKS-VNDVVKDIQRALLQA 42
                                      7999*************999.688999999999886 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.039
                   Tape_meas_lam_C  35 smedalaefvttGklsfsdlaes 57 
                                        m++a+ +f  +Gk++++ + + 
  gi|298675575|ref|YP_003727325.1| 414 TMQNAMKNFRGAGKFNMKKMMKK 436
                                       699****************9886 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.4   0.00091      0.46       1     110 [.     103     217 ..     103     229 .. 0.67
   2 ?   -1.4   0.0       5.6   2.9e+03      55      93 ..     295     333 ..     282     337 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00091
                                       EE-TTSSHHHHHHHHHHHH...TEE.EEEHHHHHHHHHHTT.TSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSS CS
                            AAA_17   1 lGgPGsGKgtqceklveky...gft.hlsaGdllreeakrg.glakardemrklpleekkelqkeaaekiaeeakkk 72 
                                       +G+ GsGK+t  +kl++ +   g++  +   d +r  a ++ ++  +++ +    +e +++ + ++++ + +  k +
  gi|298675575|ref|YP_003727325.1| 103 IGLQGSGKTTTTSKLARYFqkkGLKpAVICADTFRPGAYHQlKSLCDKNSIPFYGEEGNEDSLGIVERGMDKLGKYD 179
                                       599************97662224432455567777444333233334444444566677777777777777766778 PP

                                       EEEEEE-SEEEETTEEEESSHHHHHHHH..SE.EEEEE- CS
                            AAA_17  73 gvlvdghprikeqagfldglpkevleelkpda.iillea 110
                                        +++d+  r   ++++++++++ +   +kpd+ +++l+a
  gi|298675575|ref|YP_003727325.1| 180 VLIIDTAGRHSLEQDLIEEMEQ-INSIAKPDKkLLVLDA 217
                                       8999999999999999999985.8888899661444554 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 5.6
                                       HHHHHHHHHHHHHHHHSSEEEEEE-SEEEETTEEEESSH CS
                            AAA_17  55 kelqkeaaekiaeeakkkgvlvdghprikeqagfldglp 93 
                                       + l ++a+e++ ee+ + + ++ g +++k++ ++l+ + 
  gi|298675575|ref|YP_003727325.1| 295 RSLIEKAEESLSEEELDVESMMQGRFTLKDMYKQLEAVN 333
                                       567888999999998888889999999988888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       881  (0.0491383); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); expected 358.6 (0.02)
Passed Vit filter:                       111  (0.00619109); expected 17.9 (0.001)
Passed Fwd filter:                        35  (0.00195214); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              35  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 3158.52
//
Query:       gi|298675576|ref|YP_003727326.1|  [L=189]
Description: GMP synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-34  119.3   0.0    2.1e-34  119.0   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    1.4e-11   44.5   0.5    2.1e-10   40.7   0.2    2.5  2  Peptidase_C26  Peptidase C26


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.0   0.0   2.3e-38   2.1e-34       2     187 ..       8     183 ..       7     185 .. 0.93

  Alignments for each domain:
  == domain 1  score: 119.0 bits;  conditional E-value: 2.3e-38
                                       EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-EEEET CS
                            GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspgvegkieaikearenkiPiLGIC 78 
                                       +++n+ ++ + +++ ++ l++++++v ++ s +eil  +++p+g+++sgGp    ++++ e +++    ++PiLGIC
  gi|298675576|ref|YP_003727326.1|   8 VVNNHGQFCHLIHRTVRDLDMDTKIVSNTLSVDEIL--EEEPQGLILSGGPTMDRIGNCREYVEN---IDVPILGIC 79 
                                       789999*****************************6..79*****************99988887...578****** PP

                                       HHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEE CS
                            GATase  79 LGmQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelm 155
                                       LG+Ql+a+ fg++    ++ ++     ++ + ++++l+g ++++ ++ +H +ev++    p+++  +a+s+  +e +
  gi|298675576|ref|YP_003727326.1|  80 LGHQLIAKTFGGEYGTGNHGGYASIDVEIIE-KNDILKGFGSSISTWASHADEVTR---MPDNFLKLARSQY-CETE 151
                                       ***************9999999999999999.67**********************...9***999999966.69** PP

                                       EEEEETTTEEEESSBTTSTTSTTHHHHHHHHH CS
                            GATase 156 eiiekknpfvgvQFHPEststpegpellfnfl 187
                                       ++ + ++p++gvQ+HPE+ +t++g+el+ nfl
  gi|298675576|ref|YP_003727326.1| 152 AMKHPERPIYGVQWHPEVAHTEKGEELFLNFL 183
                                       ***********************999888874 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.16   1.4e+03      58      70 ..      46      58 ..      31      61 .. 0.72
   2 !   40.7   0.2   2.4e-14   2.1e-10     105     216 .]      72     168 ..      64     168 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.16
                     Peptidase_C26 58 kldgllltGgqdv 70
                                      + +gl+l+Gg+++
  gi|298675576|ref|YP_003727326.1| 46 EPQGLILSGGPTM 58
                                      4589******976 PP

  == domain 2  score: 40.7 bits;  conditional E-value: 2.4e-14
                     Peptidase_C26 105 gvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievnslHhqaikel 181
                                       +vPilgiC+G+ql++ ++GG+  +  +             + as +v++ ++  + + +g ++i++   H   ++++
  gi|298675576|ref|YP_003727326.1|  72 DVPILGICLGHQLIAKTFGGEYGTGNHG-----------GY-ASIDVEIIEKNDILKGFG-SSISTWASHADEVTRM 135
                                       79******************97655442...........23.366777766555556666.699999********** PP

                     Peptidase_C26 182 aeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                        +++   A+++    Ea++++e+  +++gvQwHPE
  gi|298675576|ref|YP_003727326.1| 136 PDNFLKLARSQYCETEAMKHPER--PIYGVQWHPE 168
                                       **********************4..6********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1168.92
//
Query:       gi|298675577|ref|YP_003727327.1|  [L=265]
Description: putative phospho-2-dehydro-3-deoxyheptonate aldolase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-63  214.4   0.0      2e-63  214.2   0.0    1.0  1  DeoC      DeoC/LacD family aldolase


Domain annotation for each model (and alignments):
>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.2   0.0   1.1e-67     2e-63       2     235 .]      22     237 ..      21     237 .. 0.99

  Alignments for each domain:
  == domain 1  score: 214.2 bits;  conditional E-value: 1.1e-67
                                       EEEEECCSHHHHHHHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCTTSEEEEETECSSCCTTSTTE CS
                              DeoC   2 vilavDqrvankddtasaqneqledlkalvkealtpgasavlldpgviasaskeyakdiallvkldkgtyllkskqr 78 
                                       vi+++D+++  +++++        ++   +++++++ga+avl+++g++ +++++y+ d++l+v+++++t l +++++
  gi|298675577|ref|YP_003727327.1|  22 VIIPMDHGITVGPIKGL------SNISDSINKVAKGGANAVLMQKGMVTHGHRGYGLDVGLIVHMSASTSLGPDPND 92 
                                       89***************......8***************************************************** PP

                                       EEETTCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEEEEE-CTTBSSTTCHHHHHHH CS
                              DeoC  79 dvdevasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplilelylrdeaikdekvdpdlvae 155
                                       +v+  ++veea+++GAdav+++v++   gse+e+ +l++++ v+++c+ +g+pl+ ++y+r+++i++ + dp+lva+
  gi|298675577|ref|YP_003727327.1|  93 KVL-TCTVEEAVKMGADAVSIHVNI---GSETEADQLKKLGHVAKQCDRWGMPLLSMMYPRGKNIQNSN-DPELVAH 164
                                       **9.*********************...*************************************9988.******* PP

                                       HHHHHTCCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTEEEEETTS...SHHHHHHHHHHHHHHHTHCEEEES CS
                              DeoC 156 AarvsaelGaDiiKvevpkevvnateedaevfkdvikaapvpgvvlsGGv...seedfletvedAvkeagasGvlsG 229
                                        arv+aelG+D+iK++++        +d e+fkdv+k++pvp v+ +GG+   ++++fle+++ ++ eaga Gv++G
  gi|298675577|ref|YP_003727327.1| 165 VARVGAELGSDVIKTNYT--------GDPESFKDVVKGCPVP-VITAGGPkteTDREFLEMIRGSM-EAGARGVAIG 231
                                       ******************........****************.********99999**********.********** PP

                                       HHHHTT CS
                              DeoC 230 Raifqk 235
                                       R++fq+
  gi|298675577|ref|YP_003727327.1| 232 RNTFQH 237
                                       ****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2046.18
//
Query:       gi|298675578|ref|YP_003727328.1|  [L=381]
Description: 3-dehydroquinate synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   6.1e-151  502.3   4.2   6.9e-151  502.1   4.2    1.0  1  DHQS      3-dehydroquinate synthase II
  ------ inclusion threshold ------
      0.024   14.7   0.2        1.7    8.8   0.0    2.4  2  OapA      Opacity-associated protein A LysM-like domain


Domain annotation for each model (and alignments):
>> DHQS  3-dehydroquinate synthase II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  502.1   4.2  7.7e-155  6.9e-151       1     352 []       6     381 .]       6     381 .] 0.97

  Alignments for each domain:
  == domain 1  score: 502.1 bits;  conditional E-value: 7.7e-155
                              DHQS   1 kevwikadeeeweerkelvtaaleagvdavlveeedaekvkelgkikviakeed....davlvgkd........... 62 
                                       k++wikad+++we+rk+ + ++le+g+d+vlv++ed++kv++lg+i+v+a+ +     d+v+vgk            
  gi|298675578|ref|YP_003727328.1|   6 KSIWIKADKGNWENRKNKIINGLESGADCVLVNSEDVDKVRKLGNINVAAFGDStsnaDIVVVGKGgegdgtkplps 82 
                                       89************************************************995556789******9*********** PP

                              DHQS  63 .........dleklkka.kkvaalveikskeeeeeaaeaakeadyvivelkdwtvIPlEnliAalqgeetkiiaavk 129
                                                 +++lk++ kkva +v ik+k++e++a+e+++ +dyvi  + dw+vIPlEnliA+lq++e++ii++vk
  gi|298675578|ref|YP_003727328.1|  83 dfsgswditTINQLKENgKKVAGYVVIKNKDYENFAVELGEICDYVITIGIDWQVIPLENLIAKLQDKEVQIISGVK 159
                                       ******655555555559*********************************************************** PP

                              DHQS 130 saeeAklaletLEkGadgvllktedveeikelaelleeaeeekleLkeaevtkveevgmgdRvcvDtcslmkegeGm 206
                                       ++eeA++aletLE+G+dgvll+++d+++ike++ ++e+++ +k eL++a +t++e+vgmgdRvcvDtc+lm++geGm
  gi|298675578|ref|YP_003727328.1| 160 TSEEANIALETLEHGSDGVLLDSDDPNTIKETVGIAEKSQISKTELTPAVITRIEPVGMGDRVCVDTCNLMQRGEGM 236
                                       ***************************************************************************** PP

                              DHQS 207 LvGsssrglfLvhsEtlespYvasRPFRVNAGavhaYvlvpggkTkYLseLkaGdevlvvdkkGktreavvGRvKiE 283
                                       LvGs+s+glfLvhsE++espYvasRPFRVNAGavhaYv+v g+kT+YLseL++Gdev++vd++Gk+++ +vGRvKiE
  gi|298675578|ref|YP_003727328.1| 237 LVGSQSKGLFLVHSESEESPYVASRPFRVNAGAVHAYVQV-GEKTRYLSELESGDEVTIVDADGKQKTGIVGRVKIE 312
                                       ****************************************.************************************ PP

                              DHQS 284 kRPlllveaeaegkkvstilQnaetirlvtedgkaisvteLkeGdevlvyleekaRHfGikieEtiiEk 352
                                       +RPl+lveaea+g  ++tilQnaeti+lv++d++++sv++Lk+Gde+lv+le++aRHfG+k++EtiiEk
  gi|298675578|ref|YP_003727328.1| 313 RRPLMLVEAEADGAVIRTILQNAETIKLVNSDKNPVSVSDLKKGDEILVHLEKGARHFGTKVNETIIEK 381
                                       ********************************************************************8 PP

>> OapA  Opacity-associated protein A LysM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00019       1.7      23      80 ..     266     326 ..     260     331 .. 0.71
   2 ?    3.6   0.0    0.0082        74      36      55 ..     346     365 ..     329     377 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00019
                              OapA  23 plsdvnalakveGadkplSnlksGqkvrik....lnaqgkvdelqlekgaksvlftRqsDGs 80 
                                       +   v+a ++v  + + lS+l sG++v+i      +++g v  +++e+    +l   ++DG+
  gi|298675578|ref|YP_003727328.1| 266 NAGAVHAYVQVGEKTRYLSELESGDEVTIVdadgKQKTGIVGRVKIERRPL-MLVEAEADGA 326
                                       5667999*****9***************95222234566677777777655.4444555665 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0082
                              OapA  36 adkplSnlksGqkvriklna 55 
                                       +  ++S+lk+G+++ ++l++
  gi|298675578|ref|YP_003727328.1| 346 NPVSVSDLKKGDEILVHLEK 365
                                       3335789*******999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2850.57
//
Query:       gi|298675579|ref|YP_003727329.1|  [L=234]
Description: 3-dehydroquinate dehydratase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-54  185.6   0.0    1.9e-54  185.3   0.0    1.0  1  DHquinase_I    Type I 3-dehydroquinase
  ------ inclusion threshold ------
      0.074   13.0   0.0       0.14   12.2   0.0    1.4  1  Hydrophobin_2  Fungal hydrophobin
       0.13   11.3   0.0       0.17   11.0   0.0    1.1  1  Spatacsin_C    Spatacsin C-terminus


Domain annotation for each model (and alignments):
>> DHquinase_I  Type I 3-dehydroquinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.3   0.0   3.2e-58   1.9e-54      14     228 ..      31     229 ..      17     230 .. 0.91

  Alignments for each domain:
  == domain 1  score: 185.3 bits;  conditional E-value: 3.2e-58
                                       HHHHHHTT.S-SEEEEEGGG-.TT.THHHHHHHHHHHHHHTTS-EEEE---GGGT-S.SSS-HHHHHHHHHHHHHCT CS
                       DHquinase_I  14 aelesgke.kaDlvElRlDllketseaedvseeleelrstsdlpliftlrtkaeggrfkrkseeeylellrtaielg 89 
                                       a    +++ +aD++ElR Dll  +   ed  + +e++r++ +lp i+tlr+ +egg + +++e+++++ll  +i + 
  gi|298675579|ref|YP_003727329.1|  31 A----ANQlGADILELRFDLLGIQ-TPEDAWNIIEKIRNKVNLPFIATLRSGQEGGDW-QGTEKDRIKLLLDIIPS- 100
                                       3....34456***********655.4699**********99****************9.9**************97. PP

                                       -SEEEEEGG-.HHGHHHHHHHHHHHTT-EEEEEEEESS----HHHHHHHHHHHHHTT-SEEEEEE--SSHHHHHHHH CS
                       DHquinase_I  90 adyvDvElteapeeskkrlieekreggtkvIvSyhdfegtpsaeelkallekmqalgaDivKiavmaksieDvlrll 166
                                       +d vD+El +ap  +k+ +i+++ ++ + vIvS+h f++tps +e+k++l ++++ gaDi+K+avm+ks++Dvl+ll
  gi|298675579|ref|YP_003727329.1| 101 VDAVDIEL-SAP--EKNWIIKSAANTDVNVIVSSHCFTSTPSVKEMKSILDNCHNSGADIAKLAVMPKSSQDVLNLL 174
                                       ********.678..4568999999***************************************************** PP

                                       HHHHHHHHHT-SS-EEEEE-TTTTGHHHCHHHHHTB-EEEEESSS-..SSTT-EEHHHHHHH CS
                       DHquinase_I 167 sltseakeekdeaplIamamGelGkiSRilgevfGspvtfasleeakasapGqltarelrei 228
                                       ++ts     + ++p+ ++amGe Gk SRi+++ +Gs++t++s++ a   apGql +++l+e 
  gi|298675579|ref|YP_003727329.1| 175 QVTS-----DSTKPVSTIAMGEIGKHSRIISPCYGSVLTYGSVTGA--VAPGQLRVDKLKEF 229
                                       **94.....4569*****************************8888..9*********9985 PP

>> Hydrophobin_2  Fungal hydrophobin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.3e-05      0.14      12      61 ..     121     171 ..     117     173 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.3e-05
                     Hydrophobin_2  12 CatdvlgvadldCatpsktptsaaefkaiCaasgqq.akCCvlpvagqall 61 
                                        +tdv+ +++ +C t + +++++++  + C +sg + ak  v+p   q++l
  gi|298675579|ref|YP_003727329.1| 121 ANTDVNVIVSSHCFTSTPSVKEMKSILDNCHNSGADiAKLAVMPKSSQDVL 171
                                       689***************************9999998*9999999999887 PP

>> Spatacsin_C  Spatacsin C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   2.8e-05      0.17      26      63 ..     118     154 ..      72     162 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.8e-05
                       Spatacsin_C  26 kkeleieVeLlikAhdcFvlecsmeGiaevlqaakqlt 63 
                                       k+  +  V+ ++ + +cF+++ s+ +++++l+ +++  
  gi|298675579|ref|YP_003727329.1| 118 KSAANTDVNVIVSS-HCFTSTPSVKEMKSILDNCHNSG 154
                                       55566778877766.5******************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1854.35
//
Query:       gi|298675580|ref|YP_003727330.1|  [L=275]
Description: shikimate 5-dehydrogenase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-26   91.3   0.0    8.2e-26   90.1   0.0    1.7  2  Shikimate_dh_N   Shikimate dehydrogenase substrate binding do
    2.2e-13   49.7   0.1    3.6e-13   49.0   0.1    1.4  1  SDH_C            Shikimate 5'-dehydrogenase C-terminal domain
    4.6e-13   49.4   0.1    7.3e-13   48.8   0.1    1.2  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    0.00024   20.5   0.1    0.00061   19.2   0.1    1.6  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
     0.0041   16.7   0.2      0.011   15.3   0.1    1.8  2  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
     0.0064   16.0   0.2      0.013   15.0   0.2    1.6  1  adh_short        short chain dehydrogenase
  ------ inclusion threshold ------
      0.022   15.0   0.1      0.057   13.7   0.1    1.6  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.067   12.5   0.3       0.11   11.8   0.3    1.2  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain


Domain annotation for each model (and alignments):
>> Shikimate_dh_N  Shikimate dehydrogenase substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.1   0.0   3.6e-29   8.2e-26       1      83 []       7      88 ..       7      88 .. 0.99
   2 ?   -3.4   0.0       5.5   1.2e+04      69      79 ..     225     235 ..     216     236 .. 0.69

  Alignments for each domain:
  == domain 1  score: 90.1 bits;  conditional E-value: 3.6e-29
                                      EEESS-TT-SHHHHHHHHHHHCTSSEEEEEEE-SCCTHHHHHHHHHHTTESEEEE-TTSCCHHHGGSSEE-HHHHHHT- CS
                    Shikimate_dh_N  1 viGnpikhSlSPaihnaafkalglngsyeafeveedelekaveelralglaGlnvTiPfKeaviplldelseeAkaigA 79
                                      v+G+p++hSlSP +hnaaf +lg++  y+af+v++++le a+++++a g+ G+n+T+P+K++++++++  ++ A +igA
  gi|298675580|ref|YP_003727330.1|  7 VFGDPVEHSLSPDMHNAAFSELGMDSIYHAFRVDKKSLEYALNGANAMGFGGVNITVPLKQEALKFVN-TDPLASKIGA 84
                                      89*****************************************************************8.9********* PP

                                      -SEE CS
                    Shikimate_dh_N 80 vNti 83
                                      vNti
  gi|298675580|ref|YP_003727330.1| 85 VNTI 88
                                      ***8 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 5.5
                                       EE-HHHHHHT- CS
                    Shikimate_dh_N  69 elseeAkaigA 79 
                                       +l +eAk++gA
  gi|298675580|ref|YP_003727330.1| 225 RLLKEAKSAGA 235
                                       45677888887 PP

>> SDH_C  Shikimate 5'-dehydrogenase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.1   1.6e-16   3.6e-13       1      31 []     240     270 ..     240     270 .. 0.96

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 1.6e-16
                                       HHHHHHHHHHHHHHHHHS----HHHHHHHHH CS
                             SDH_C   1 GLgMLveQgaeqFelWTGrepPvevMreall 31 
                                       GL M+v+Qgae+F++WTG  pP+evM++++l
  gi|298675580|ref|YP_003727330.1| 240 GLMMFVYQGAEAFKIWTGENPPIEVMKNTVL 270
                                       788*************************996 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.1   3.3e-16   7.3e-13       9     111 ..     116     217 ..     108     225 .. 0.81

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 3.3e-16
                                       ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.E.T-EEEEGCGHHHHHHT-SEEEE-SS CS
                      Shikimate_DH   9 slkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkge.eiealkleelkellaeadvvisata 84 
                                       ++k+k++l++GaG  ++ ++ ++++ g++ +++aNRt ++a elae++k++ +++ + +++l+el+ae+d++i  t 
  gi|298675580|ref|YP_003727330.1| 116 DVKNKNILILGAGGASRAICFQFANDGAD-LIIANRTESKALELAEDVKSVgNARGIGFSNLEELIAESDILINTTT 191
                                       689*************************9.******************665378999****************9987 PP

                                       SSS-SB-HHHHHCCHHH.S..EEEEE- CS
                      Shikimate_DH  85 seepilekeeveealkkrkkplllvDi 111
                                          +  +k+ +  + +  ++ l+++Di
  gi|298675580|ref|YP_003727330.1| 192 VGMHPNTKDTIITSEH-MHSGLVVFDI 217
                                       5544444444443332.2355566666 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.3   2.9e+03      95     111 ..      59      75 ..      24      80 .. 0.56
   2 !   19.2   0.1   2.7e-07   0.00061      29     108 ..     112     201 ..      96     211 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.3
                                       EEE-S--STTTTTSBSH CS
                      2-Hacid_dh_C  95 vslhlpltpetrhlina 111
                                       v +++pl++e  +++n 
  gi|298675580|ref|YP_003727330.1|  59 VNITVPLKQEALKFVNT 75 
                                       34555666665555555 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 2.7e-07
                                       GSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH........CHHHHTCEECSHHHHHHH-SEEEE CS
                      2-Hacid_dh_C  29 llgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee........eeeelgvelvsleellaesDivsl 97 
                                         g ++++k + i+G+G   +a+   ++  g+++i+ +r+++k            ++ g+ + +leel+aesDi+++
  gi|298675580|ref|YP_003727330.1| 112 DAGVDVKNKNILILGAGGASRAICFQFANDGADLIIANRTESKALelaedvksVGNARGIGFSNLEELIAESDILIN 188
                                       56889***********************************9965445443433345668899*************98 PP

                                       -S-..-STTTTTS CS
                      2-Hacid_dh_C  98 hlp..ltpetrhl 108
                                       ++   ++p+t++ 
  gi|298675580|ref|YP_003727330.1| 189 TTTvgMHPNTKDT 201
                                       7653356666654 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.85   1.9e+03       9      30 ..      96     117 ..      95     118 .. 0.90
   2 !   15.3   0.1   5.1e-06     0.011       2      67 ..     117     189 ..     116     223 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.85
                                       EES-SHHHHHHHHHHHHTT--E CS
                              IlvN   9 viGyGsqGhaqalnlrdsgldv 30 
                                       +iGy + G    + + d+g+dv
  gi|298675580|ref|YP_003727330.1|  96 MIGYNTDGVGARRAIADAGVDV 117
                                       5999999999999999**9998 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 5.1e-06
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHH.......TT-EEEEHHHHHHT-SEEEE- CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAke.......egfevltvaeavkkadvvmil 67 
                                       +k+k+i ++G G   +a   ++ + g d+++++r++sk ++ A++       +g+   +++e+++++d++++ 
  gi|298675580|ref|YP_003727330.1| 117 VKNKNILILGAGGASRAICFQFANDGADLIIANRTESKALELAEDvksvgnaRGIGFSNLEELIAESDILINT 189
                                       689**********************************877777532111111566667788888888887765 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   5.8e-06     0.013       1      47 [.     120     165 ..     120     201 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.8e-06
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee 47 
                                       k +l+ Ga+ G  rai+ ++a++Ga++++++r+e+k+ e+a+ +k+ 
  gi|298675580|ref|YP_003727330.1| 120 KNILILGAG-GASRAICFQFANDGADLIIANRTESKALELAEDVKSV 165
                                       679999998.********************************99986 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   2.5e-05     0.057       1      77 [.     122     190 ..     122     197 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.5e-05
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-S CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnls 77 
                                       +li+GaG+ ++a+    a+ +    ++++a r+++k+ +la+++ ++  +a+ +  +n    L++l++e d+++n +
  gi|298675580|ref|YP_003727330.1| 122 ILILGAGGASRAICFQFANDGA---DLIIANRTESKALELAEDV-KSVGNARGIGFSN----LEELIAESDILINTT 190
                                       89***********999998886...6**********88888764.3334444444444....666999999999976 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.3   4.8e-05      0.11      18     127 ..     110     217 ..     103     220 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.8e-05
                                       ETTCEETCB---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTTCECEEHCHHHHHHHHHHHH-S CS
                       AlaDh_PNT_C  18 tlaGgvpgvepakvlviGgGvaGlqAiatakglgakVtvlDvrparleqles.lgakfvevlksqeellaeavkead 93 
                                       ++ +gv  v++ ++l++G+G a  +     ++ ga+  + +  ++++ +l + +++   +++    ++l+e ++e+d
  gi|298675580|ref|YP_003727330.1| 110 IADAGVD-VKNKNILILGAGGASRAICFQFANDGADLIIANRTESKALELAEdVKSV-GNARGIGFSNLEELIAESD 184
                                       6778888.99**********9988777777788999999987776666555525555.77899999*********** PP

                                       EEEE---B..TTSS---SC-HHHHHTS-TTEEEEET CS
                       AlaDh_PNT_C  94 vvigtvli..pGkkaPkLvteemvksMkpgsVivDv 127
                                       ++i t  +  + ++  +++t+e+   M++g V+ D+
  gi|298675580|ref|YP_003727330.1| 185 ILINTTTVgmHPNTKDTIITSEH---MHSGLVVFDI 217
                                       ***66555115556666999875...8888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 2079.94
//
Query:       gi|298675581|ref|YP_003727331.1|  [L=443]
Description: prephenate dehydrogenase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-62  210.9   0.0    2.4e-62  210.3   0.0    1.3  1  PDH             Prephenate dehydrogenase
    2.1e-12   47.5   0.0      5e-12   46.3   0.0    1.6  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    4.1e-09   36.9   0.0    2.1e-08   34.7   0.0    2.2  2  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    2.1e-08   33.7   0.0    3.9e-08   32.9   0.0    1.4  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    6.5e-05   23.0   4.4      0.012   15.6   1.3    3.1  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
    0.00012   22.4   0.1    0.00043   20.6   0.0    1.9  2  FDX-ACB         Ferredoxin-fold anticodon binding domain
    0.00028   20.5   0.0    0.00052   19.6   0.0    1.4  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
     0.0011   18.8   0.1        1.1    9.1   0.0    2.6  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
     0.0026   17.8   0.0      0.013   15.5   0.0    2.2  2  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
     0.0067   16.1   0.1      0.036   13.7   0.0    2.2  2  ApbA            Ketopantoate reductase PanE/ApbA
      0.008   16.3   0.0      0.021   14.9   0.0    1.7  1  DpaA_N          Dipicolinate synthase subunit A N-terminal do
  ------ inclusion threshold ------
      0.013   15.7   0.6      0.076   13.1   0.0    2.6  3  DapB_N          Dihydrodipicolinate reductase, N-terminus
       0.02   13.8   0.0       0.03   13.3   0.0    1.1  1  WzyE            WzyE protein, O-antigen assembly polymerase
       0.03   14.8   0.0      0.098   13.1   0.0    1.9  1  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai
      0.038   14.7   0.0       0.29   11.8   0.0    2.5  2  CoA_binding     CoA binding domain
      0.044   13.1   0.1       0.83    8.9   0.0    2.5  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
       0.06   13.2   0.0       0.31   10.9   0.0    2.1  3  KR              KR domain
      0.086   13.5   0.0       0.23   12.1   0.0    1.6  1  TIR_2           TIR domain
        0.1   12.1   0.1       0.32   10.5   0.1    1.9  1  NmrA            NmrA-like family
       0.12   13.3   0.1       0.44   11.4   0.0    2.0  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
       0.19   12.1   0.2       0.42   10.9   0.2    1.5  1  CKS             Cyclin-dependent kinase regulatory subunit


Domain annotation for each model (and alignments):
>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.3   0.0   2.9e-65   2.4e-62       1     257 [.      18     265 ..      18     266 .. 0.97

  Alignments for each domain:
  == domain 1  score: 210.3 bits;  conditional E-value: 2.9e-65
                                       HHHHHHHTT--SEEEEE-SSHHHHHHHHHTTSSSEEES-GGGGCCGSEEEE-S-GGGHHHHHHHHHHHS-TT-EEEE CS
                               PDH   1 laralrrkgfkvtvigydideekaeaalelglvdeatddieavkeadivvlavPvevilevlkelaphlkedalitD 77 
                                       +a++ +r+gf+vt+ g ++   + + a +lg+ ++ + d +a+++ div+++vP++ +++v+ e ap++k++ l++D
  gi|298675581|ref|YP_003727331.1|  18 FAKFFKREGFEVTLWGSSQ---RVDIADKLGVNFASDLD-NAIEKSDIVIVSVPIDITEKVISETAPKMKPGSLLMD 90 
                                       799*********9999764...55666689*******98.************************************* PP

                                       --S--CHHHHHHHHHCC..GCEEEEEES---S-SSGGG--TTTTTT-EEEEEE-TTS-HHHHHHHHHHHHHCT-EEE CS
                               PDH  78 vgsvKekvvreleellkegksfvgghPmaGteksGvdaareelfenavviLtPtektdkealekvkelleevgarvi 154
                                        +s+K+k+v+++e+  +e++++ g+hPm+G+        +  ++ +++vi+tP      +++  vk+++e+ ga+++
  gi|298675581|ref|YP_003727331.1|  91 FTSIKTKPVEAMEKYAPENVEILGTHPMFGP--------SIPSLYGQIVIMTPISGRCDNWFPVVKSVFENNGAHIE 159
                                       *******************************........888889**********9999****************** PP

                                       E--HHHHHHHHHHHTHHHHHHHHHHHHHHHCHHCCCCHHHHCGTCCHHHHH....CGGGS-HHHHHHHHHHTHHHHH CS
                               PDH 155 lmspeeHDrvvavvshlphvvaialaatlkekkndekeirklasggfrdvt....RiaksnPelwadilleNkeavl 227
                                       +++p+eHD+ v+vv++l+h+++i +  t k+   d  e+rk+ s+ +  ++    Ri+++nP+l+a i++eN e vl
  gi|298675581|ref|YP_003727331.1| 160 VIDPKEHDKFVSVVQGLTHFAYITIGSTFKRLDFDVSESRKFMSPVYDIMIdfvgRIIGQNPYLYALIQMENPE-VL 235
                                       **************************************************************************.** PP

                                       HHHHHHHHHHHHHHHHHHTT-HHHHHHHHH CS
                               PDH 228 ealdkfikelkklkelienedaeeLvellk 257
                                       +++d f+ke+++++e+++++d e++ve +k
  gi|298675581|ref|YP_003727331.1| 236 KVHDAFKKECNNISEIVRQQDVESFVENMK 265
                                       ****************************98 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.0   5.9e-15     5e-12       6     154 ..      10     159 ..       5     162 .. 0.88

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 5.9e-15
                                       --SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC--T CS
                     NAD_binding_2   6 GlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdeviegllealkk 82 
                                       G+G+MG+ +a+ ++++g++v+++  + ++v+ + + g++ a+++ +++++ d+vi+ v+  + +++vi++ ++++k+
  gi|298675581|ref|YP_003727331.1|  10 GTGEMGQWFAKFFKREGFEVTLWGSS-QRVDIADKLGVNFASDLDNAIEKSDIVIVSVPI-DITEKVISETAPKMKP 84 
                                       89*********************966.899999999***********************8.89************** PP

                                       T-EEEE-S---HHHHHHHHHHHHHTT-EEEEE.EEESHHHHHHHT-EEEEE..EE-.HHHHHHHHHHHHHHEEEEE CS
                     NAD_binding_2  83 gdilidgstsspedtrelakelkekglkflda.PVSGGeegAekGtLsimv..GGs.eeafervkpvleaigakvt 154
                                       g++l+d+++++ +  + ++k++  +++++l++ P  G       G++ im   +G+ ++ f+ vk+v+e+ ga++ 
  gi|298675581|ref|YP_003727331.1|  85 GSLLMDFTSIKTKPVEAMEKYAP-ENVEILGThPMFGPSIPSLYGQIVIMTpiSGRcDNWFPVVKSVFENNGAHIE 159
                                       ************99999988865.567788755****************963356615567999999999999775 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.0   2.4e-11   2.1e-08       2      94 ..       5      91 ..       4      93 .. 0.91
   2 ?   -1.7   0.0       5.4   4.6e+03      26      55 ..     394     422 ..     371     429 .. 0.59

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 2.4e-11
                                      EEEE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHH CS
                     F420_oxidored  2 igii.GaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevls 79
                                      i ii G+G+mg+ +a+ + ++g    e+++      +++  +a++lgv+  + d   a+e++d+v+++v+   +e+v+s
  gi|298675581|ref|YP_003727331.1|  5 ILIIgGTGEMGQWFAKFFKREG---FEVTLW---GSSQRVDIADKLGVNFAS-DLDNAIEKSDIVIVSVPIDITEKVIS 76
                                      77999*****************...999966...55566799*******999.************************** PP

                                      HCGHHHHTTSEEEEE CS
                     F420_oxidored 80 elakdalkgklvisv 94
                                      e a++ + g+l+ + 
  gi|298675581|ref|YP_003727331.1| 77 ETAPKMKPGSLLMDF 91
                                      **9999999998886 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 5.4
                                       GCEEEEEESSCCCHHHHHHHHC-EEECECH CS
                     F420_oxidored  26 heivvansrnpekaeelaeelgvkvtavdn 55 
                                       +ei+ +  +  e +e l +++ ++v + +n
  gi|298675581|ref|YP_003727331.1| 394 TEIIDI-YSGFENIENLSATYRITVLEDSN 422
                                       444433.45556667777777766666665 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   4.6e-11   3.9e-08      37     124 ..       4      89 ..       1      92 [. 0.87

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 4.6e-11
                                       SEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEEC.SHHHHHHH-SEEEE-S--STTTTTSBSHH CS
                      2-Hacid_dh_C  37 ktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelv.sleellaesDivslhlpltpetrhlinae 112
                                       + + i G+G++Gq +ak +k  g++v+ +  s++ +  +++lgv+++ +l++++++sDiv++ +p+ + t+++i+++
  gi|298675581|ref|YP_003727331.1|   4 SILIIGGTGEMGQWFAKFFKREGFEVTLWGSSQRVDI-ADKLGVNFAsDLDNAIEKSDIVIVSVPI-DITEKVISET 78 
                                       5566889*************************99666.9999**99889****************5.7889998765 PP

                                       HHHCSTTTEEEE CS
                      2-Hacid_dh_C 113 elakmkkgaili 124
                                          kmk+g++l+
  gi|298675581|ref|YP_003727331.1|  79 -APKMKPGSLLM 89 
                                       .58999999886 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   1.3   1.4e-05     0.012      56     102 ..      45      91 ..       4     124 .. 0.70
   2 ?   -1.1   0.1       1.9   1.6e+03      75      89 ..     370     384 ..     293     424 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.4e-05
                                       TEEEES-HHHHHTT--EEEE---HHHHHHHHHHHCCC--TT-EEEE- CS
                    NAD_Gly3P_dh_N  56 nlvattdlaealkgadiivlvvPsqalrevlkklkgllkkkailvsl 102
                                        + + +dl++a++++di+++ vP  ++++v+ + ++++k+   l+  
  gi|298675581|ref|YP_003727331.1|  45 GVNFASDLDNAIEKSDIVIVSVPIDITEKVISETAPKMKPGSLLMDF 91 
                                       477899*******************************9998877764 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.9
                                       E---HHHHHHHHHHH CS
                    NAD_Gly3P_dh_N  75 lvvPsqalrevlkkl 89 
                                       + +P++a+ e+++++
  gi|298675581|ref|YP_003727331.1| 370 VFIPTNAVPETIRDV 384
                                       234444444444333 PP

>> FDX-ACB  Ferredoxin-fold anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       9.4     8e+03      19      37 ..     244     263 ..     232     269 .. 0.62
   2 !   20.6   0.0     5e-07   0.00043       5      79 ..     363     435 ..     360     438 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 9.4
                                       -HHHHHHHHHHHH-T.TEEE CS
                           FDX-ACB  19 eaaelleavreaage.lles 37 
                                       e +++ e+vr+++ e ++e+
  gi|298675581|ref|YP_003727331.1| 244 ECNNISEIVRQQDVEsFVEN 263
                                       45566666666654435554 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 5e-07
                                       -EEEEEEEEEESSS-HHHHHHHHHHHH-TTEEEEEEEEEEESTTS-SSEEEEEEEEE.E--SSS---HHHHHHHHH CS
                           FDX-ACB   5 averDlalvvdekveaaelleavreaagellesvqlfDvYrgkklaegkkSlalrlt.lqskertLtdeevnaaie 79 
                                       +++rD+++ ++ +   +++ ++++++a   + + +++D+Y g + + ++ S ++r+t l++++  L ++ev+++ e
  gi|298675581|ref|YP_003727331.1| 363 HITRDISVFIPTNAVPETIRDVISNNA--NVVDTEIIDIYSGFE-NIENLSATYRITvLEDSNPNLIQDEVKKLLE 435
                                       589*********************999..899*********955.34799*****974678889999999999877 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   6.1e-07   0.00052       6      92 ..       4      89 ..       1     103 [. 0.85

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 6.1e-07
                                      -EEEE.S-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEE.EHHHHHHT-SEEEE-S-HHHHHHHHHHHTG CS
                              IlvN  6 kiavi.GyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevl.tvaeavkkadvvmiliPDelqkevyeeeie 82
                                       i +i G G  G+  a+ ++  g++v++    +s+ v+ A + g++ + ++++a++k+d+v++ +P  + ++v+ +e +
  gi|298675581|ref|YP_003727331.1|  4 SILIIgGTGEMGQWFAKFFKREGFEVTLWG--SSQRVDIADKLGVNFAsDLDNAIEKSDIVIVSVPIDITEKVI-SETA 79
                                      56666369*****************98655..5556999*****997526999*********************.8899 PP

                                      GG--TT-EEE CS
                              IlvN 83 pnlkegkala 92
                                      p++k g+ l+
  gi|298675581|ref|YP_003727331.1| 80 PKMKPGSLLM 89
                                      ****999774 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0013       1.1       6      32 ..      10      36 ..       4      43 .. 0.84
   2 !    7.1   0.1    0.0054       4.6      67     142 ..      46     122 ..      39     127 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0013
                                      --SCCHHHHHHHHHHTT-EEEEE-S-H CS
                           3HCDH_N  6 GaGtmGagiaavfasagleVvlvdise 32
                                      G+G mG+  a+ f ++g+eV+l   s+
  gi|298675581|ref|YP_003727331.1| 10 GTGEMGQWFAKFFKREGFEVTLWGSSQ 36
                                      67*******************988765 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0054
                                       EEEES-HHHHH.C-SEEEE-S-SSHHHHHHHHHHHHCCS-TTSEEEE--S..SS-HHHHCCCSSSGGGEEEEEE-SS CS
                           3HCDH_N  67 isfttdleeav.dadlviEavvEnlelKrkvfaelekiakpdailasnTS..slsiselaealkrperviglHFfnP 140
                                       ++f++dl++a+ + d+vi +v+  +++ +kv+ e +  +kp ++l   TS  + +++++ +   ++ +++g+H++  
  gi|298675581|ref|YP_003727331.1|  46 VNFASDLDNAIeKSDIVIVSVP--IDITEKVISETAPKMKPGSLLMDFTSikTKPVEAMEKYAPENVEILGTHPMFG 120
                                       7899*******9******9998..777789****************999955679999***999*********9976 PP

                                       TT CS
                           3HCDH_N 141 pp 142
                                       p 
  gi|298675581|ref|YP_003727331.1| 121 PS 122
                                       65 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.6e-05     0.013      13      83 ..       3      66 ..       1      92 [. 0.80
   2 ?   -1.7   0.0       3.4   2.9e+03      48      82 ..     256     287 ..     240     293 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.6e-05
                                      -EEEEE.S-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-S CS
                      Shikimate_DH 13 kkvlli.GaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisat 83
                                      + +l+i G+Gem++  ak + ++g++ v+  + ++    ++a++l+ +       ++l+++++++d+vi+++
  gi|298675581|ref|YP_003727331.1|  3 NSILIIgGTGEMGQWFAKFFKREGFE-VTLWGSSQ--RVDIADKLGVN-----FASDLDNAIEKSDIVIVSV 66
                                      568888358****************9.88888554..4689****555.....679*************997 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.4
                                       HHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE- CS
                      Shikimate_DH  48 rakelaeelkgeeiealkleelkellaeadvvisa 82 
                                        +++++e++k+    a ++ + +++l+++d +i +
  gi|298675581|ref|YP_003727331.1| 256 DVESFVENMKS---AASHFGDTTSALHRSDKLINS 287
                                       34555555544...488888888888888877766 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   4.2e-05     0.036       3      95 ..       8      85 ..       5      92 .. 0.81
   2 ?   -3.7   0.0       9.9   8.4e+03      83      99 ..     376     392 ..     373     411 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.2e-05
                                      EES-SHHHHHHHHHHHHHTHCEEEE-SCHHHHHHHHHCEEEEETTCEEEEEECEEECCHSCCCCS-ESEEEE-SSGGGH CS
                              ApbA  3 ilGaGaiGsllaakLakagadvtlilrsrrlealkknGlrltseggeeilrppealsaeekselepidlvivtvKayqt 81
                                      i G+G +G+ +a   ++ g +vtl++ s+r++   k G+++ s+        ++a++++        d+viv+v+   t
  gi|298675581|ref|YP_003727331.1|  8 IGGTGEMGQWFAKFFKREGFEVTLWGSSQRVDIADKLGVNFASDL-------DNAIEKS--------DIVIVSVPIDIT 71
                                      5589****************************9999999999998.......4444444........888888888888 PP

                                      HHHHHHHGGGECTC CS
                              ApbA 82 eealeeikplldpn 95
                                      e++++e +p ++p 
  gi|298675581|ref|YP_003727331.1| 72 EKVISETAPKMKPG 85
                                      88887777777776 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 9.9
                                       HHHHHHGGGECTCEEEE CS
                              ApbA  83 ealeeikplldpntvvl 99 
                                       ++ e+i++++ +n++v+
  gi|298675581|ref|YP_003727331.1| 376 AVPETIRDVISNNANVV 392
                                       45566899999998876 PP

>> DpaA_N  Dipicolinate synthase subunit A N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.5e-05     0.021      13      68 ..      17      75 ..       4      90 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.5e-05
                                      HHHHHHHHTT-EEEEES-...TSSS-BTTEEEE-GGGS-GGG-SEEE--TT-BETTTEE CS
                            DpaA_N 13 ylarkLaekgakvslygl...eleekiegvekaesleealedadviilPvpgtkdggei 68
                                      + a+ ++++g++v+l+g           gv+ a++l+ a+e++d++i+ vp+   ++ i
  gi|298675581|ref|YP_003727331.1| 17 WFAKFFKREGFEVTLWGSsqrVDIADKLGVNFASDLDNAIEKSDIVIVSVPIDITEKVI 75
                                      678999***********98543334455899*******************976555555 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   8.9e-05     0.076       2      72 ..       4      63 ..       3      85 .. 0.81
   2 ?   -1.3   0.0       2.6   2.2e+03      50      74 ..     188     212 ..     159     220 .. 0.78
   3 ?   -2.6   0.0       6.8   5.8e+03      39      52 ..     252     265 ..     223     286 .. 0.50

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.9e-05
                                      EEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS.--S-BEBSSHHHHHHH-SEEE CS
                            DapB_N  2 kvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglg.klgvavtddleevlekadvli 72
                                      +++++G +G mG+  +k  ++ e++e++   ++++      d      +  klgv++ +dl++++ek+d++i
  gi|298675581|ref|YP_003727331.1|  4 SILIIGGTGEMGQWFAKFFKR-EGFEVTLWGSSQR-----VD------IAdKLGVNFASDLDNAIEKSDIVI 63
                                      589****************99.9***999988887.....33......44499**************99554 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.6
                                       SS--S-BEBSSHHHHHHH-SEEEE- CS
                            DapB_N  50 lgklgvavtddleevlekadvliDF 74 
                                       +++l++ v+++ + +    d++iDF
  gi|298675581|ref|YP_003727331.1| 188 FKRLDFDVSESRKFMSPVYDIMIDF 212
                                       346788888888888888999**99 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 6.8
                                       TTTTBHHHHSSSS- CS
                            DapB_N  39 legkdagellglgk 52 
                                       ++++d+ ++++  k
  gi|298675581|ref|YP_003727331.1| 252 VRQQDVESFVENMK 265
                                       22233333333333 PP

>> WzyE  WzyE protein, O-antigen assembly polymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.5e-05      0.03     272     330 ..     343     403 ..     332     414 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.5e-05
                              WzyE 272 enlalllqn.ydkidfqglapivrdfyvfipswlwpdr.pslvlnsanyftwevlnnhsgl 330
                                       en+ ll +n + + +++ l  i+rd+ vfip+   p+   +++ n an    e+++ +sg+
  gi|298675581|ref|YP_003727331.1| 343 ENVRLLSENeLRQWKINNLKHITRDISVFIPTNAVPETiRDVISNNANVVDTEIIDIYSGF 403
                                       8888887653789999********************97257888**************997 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00011     0.098       2      87 ..       5      79 ..       4      94 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                                      EEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHHHHH CS
                    Semialdhyde_dh  2 vaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpagvsk 80
                                      + i+G+tG +Gq +++  ++   +e++   ss+r     +a++ +       +++ +  ++++++ div+ ++p ++++
  gi|298675581|ref|YP_003727331.1|  5 ILIIGGTGEMGQWFAKFFKR-EGFEVTLWGSSQR---VDIADKLG-------VNFASDLDNAIEKSDIVIVSVPIDITE 72
                                      67****************99.5699999999999...77777755.......55666557889**************** PP

                                      HHHHHHH CS
                    Semialdhyde_dh 81 elapkla 87
                                      ++  + a
  gi|298675581|ref|YP_003727331.1| 73 KVISETA 79
                                      9998874 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00034      0.29       4      83 ..       3      79 ..       1      89 [. 0.85
   2 ?   -1.7   0.0       5.6   4.8e+03      27      47 ..     412     432 ..     408     441 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00034
                                      EEEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHHHH CS
                       CoA_binding  4 tkviviGagglgiaglyhfkeklkygikavfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavdel 82
                                      +++++iG +g+ ++   +f+++ +++++  +  +  +++++ lg+    ++d+++ek   d+ ++ vP +  ++++ e 
  gi|298675581|ref|YP_003727331.1|  3 NSILIIGGTGEMGQWFAKFFKREGFEVTLWGSSQRVDIADK-LGVNFASDLDNAIEK--SDIVIVSVPIDITEKVISET 78
                                      689*******************9999987766666666665.6777777********..****************9997 PP

                                      H CS
                       CoA_binding 83 v 83
                                      +
  gi|298675581|ref|YP_003727331.1| 79 A 79
                                      6 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 5.6
                                       HECEEEEEEC-TTTTTCEETT CS
                       CoA_binding  27 kygikavfgvnprkvgtevlg 47 
                                        y+i+++ + np+ + +ev+ 
  gi|298675581|ref|YP_003727331.1| 412 TYRITVLEDSNPNLIQDEVKK 432
                                       5889999999***99999983 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00097      0.83      83     127 ..      50      91 ..      14     113 .. 0.87
   2 ?    1.2   0.0      0.22   1.8e+02     131     161 ..     154     184 ..     147     190 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00097
                                       HHHHHHHHH-SEEEE---BTTSS---SC-HHHHHTS-TTEEEEET CS
                       AlaDh_PNT_C  83 ellaeavkeadvvigtvlipGkkaPkLvteemvksMkpgsVivDv 127
                                       + l++a++++d+vi +v  p   + k+++e+   +Mkpgs ++D 
  gi|298675581|ref|YP_003727331.1|  50 SDLDNAIEKSDIVIVSV--PIDITEKVISET-APKMKPGSLLMDF 91 
                                       568999********775..556778888765.689********96 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.22
                                       GT-SBTT--TBBTTSEEEEETTEEEEEBSTG CS
                       AlaDh_PNT_C 131 qGGnvetsrltthgepvveekgvvhygvanl 161
                                       +G  +e + + +h++ v +++g +h ++  +
  gi|298675581|ref|YP_003727331.1| 154 NGAHIEVIDPKEHDKFVSVVQGLTHFAYITI 184
                                       7999**99*****************998766 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00036      0.31       3      65 ..       5      73 ..       3      82 .. 0.72
   2 ?   -3.4   0.0         9   7.7e+03      80     103 ..     171     194 ..     164     199 .. 0.77
   3 ?   -1.5   0.0       2.4     2e+03     111     144 ..     240     274 ..     225     281 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00036
                                      EEEETTTSHHHHHHHHHHHHHH.S-EEEEE-SS........--HHHHHHHHHHHHTT-EEEE----TT-H CS
                                KR  3 ylitGGlGgLGlelarwlaekg.arhlvllsRsa......aadedskaliaelealgaevevvaaDvsdk 65
                                       li+GG+G +G+ +a++  ++g + +l   s +          + +++l +++e++++ +  v++D+++k
  gi|298675581|ref|YP_003727331.1|  5 ILIIGGTGEMGQWFAKFFKREGfEVTLWGSSQRVdiadklG-VNFASDLDNAIEKSDIVIVSVPIDITEK 73
                                      69********************5555555555545544422.1222246677888888999999999876 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 9
                                       S---EEEE---------TTT--HH CS
                                KR  80 ppikGvihaAgvlrdklleemtae 103
                                       + ++G  h A ++  +++++++ +
  gi|298675581|ref|YP_003727331.1| 171 SVVQGLTHFAYITIGSTFKRLDFD 194
                                       668999999999988888887765 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.4
                                       TTTHHHHHHHHHTTTS--SEEE.EEEEHHHHH--T CS
                                KR 111 pKvkGawnLhelledesldffv.lfSSiagllgsa 144
                                       +  k + n+ e++++++++ fv  + S+a+ +g +
  gi|298675581|ref|YP_003727331.1| 240 AFKKECNNISEIVRQQDVESFVeNMKSAASHFGDT 274
                                       55556778899999999998884467888877766 PP

>> TIR_2  TIR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00027      0.23      14      57 ..      16      65 ..      12      78 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00027
                             TIR_2 14 eklaeaLeaagirvwl....drwdl..kpgedweeeieeaiessdvvlvv 57
                                      +++a+  +++g++v l    +r d+  k g ++   +++aie+sd+v+v 
  gi|298675581|ref|YP_003727331.1| 16 QWFAKFFKREGFEVTLwgssQRVDIadKLGVNFASDLDNAIEKSDIVIVS 65
                                      799**********9666777566777799****************99985 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00037      0.32       1      27 [.       5      31 ..       5      78 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00037
                                      EEESSTTSHHHHHHHHHHHHHT-EEEE CS
                              NmrA  1 IlviGaTGrqGksvvrallkaghkvra 27
                                      Il+iG+TG++G+ +++++ ++g++v  
  gi|298675581|ref|YP_003727331.1|  5 ILIIGGTGEMGQWFAKFFKREGFEVTL 31
                                      89*********************9975 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00052      0.44       3      72 ..       5      68 ..       4      83 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00052
                                      EEEETT.SHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-G CS
                      GFO_IDH_MocA  3 vaiiGa.Gkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpn 72
                                      ++iiG+ G +g++++ ++ ++ ++ ev+ l+ +++ r  ++a+++gv++ sdl++  +  + d+viv +p 
  gi|298675581|ref|YP_003727331.1|  5 ILIIGGtGEMGQWFA-KFFKR-EGFEVT-LWGSSQ-RV-DIADKLGVNFASDLDNAIE--KSDIVIVSVPI 68
                                      5677666*******9.55555.478888.454443.44.579****************..77888888874 PP

>> CKS  Cyclin-dependent kinase regulatory subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   0.00049      0.42      15      44 ..     324     359 ..     317     362 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00049
                               CKS  15 RhViLpkellk......kipksrlLsekewraLgIq 44 
                                       RhV+L+k+++k      ki++ rlLse+e+r+ +I+
  gi|298675581|ref|YP_003727331.1| 324 RHVVLSKPYQKnksislKIENVRLLSENELRQWKIN 359
                                       9*****9999866666678888*********98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2973.28
//
Query:       gi|298675582|ref|YP_003727332.1|  [L=225]
Description: triosephosphate isomerase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-14   52.7   0.2    1.8e-13   50.4   0.1    1.8  2  TIM             Triosephosphate isomerase
    2.3e-05   23.8   0.3    2.3e-05   23.8   0.3    1.9  3  ThiG            Thiazole biosynthesis protein ThiG
    0.00018   21.5   0.2       0.57   10.3   0.0    2.3  2  Hydrolase_like  HAD-hyrolase-like
    0.00039   19.9   5.3    0.00048   19.6   1.1    2.3  3  NMO             Nitronate monooxygenase
     0.0013   18.3   0.1      0.037   13.5   0.0    2.5  3  His_biosynth    Histidine biosynthesis protein
     0.0035   16.4   0.7     0.0062   15.6   0.2    1.7  2  FMN_dh          FMN-dependent dehydrogenase
  ------ inclusion threshold ------
      0.012   14.8   0.0      0.028   13.6   0.0    1.5  1  IGPS            Indole-3-glycerol phosphate synthase
       0.07   12.6   1.0        0.1   12.1   1.0    1.6  1  PcrB            PcrB family
      0.076   12.8   0.0       0.12   12.1   0.0    1.2  1  PRT_C           Plant phosphoribosyltransferase C-terminal


Domain annotation for each model (and alignments):
>> TIM  Triosephosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.1   9.2e-17   1.8e-13       2     126 ..       8     127 ..       7     136 .. 0.89
   2 ?    0.5   0.0      0.16   3.2e+02     159     185 ..     140     166 ..     126     188 .. 0.68

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 9.2e-17
                                       EEEEE-TBTS..-HHHHHHHHHHHHHHCHGCTSEEEEE--GGGHHHHHHHHTTSSECEEES--BSSSSBS-TT--BH CS
                               TIM   2 liagNwKmnk..tleeakellkklkaklkeekvevviappflylekvkklleesklklgaqnvsaeksGafTGevsa 76 
                                       li+ N K++   t e+a +++k++k+  ++ +v++ + p+f+ + +v+++++   + +++q ++  + G++TG++ a
  gi|298675582|ref|YP_003727332.1|   8 LIVVNLKTYLqgTGEKAVTIAKACKNVSEKYNVDIGVSPQFCDIYQVASQVD---VPVYSQHIDGIDGGSHTGQILA 81 
                                       6888999887557889999999999999999**************9999886...9********************* PP

                                       HHHHHTT-SEEEES-HHHHHHST--HHHHHHHHHHHHHTT-EEEEEE--- CS
                               TIM  77 emlkdlgvkyviiGHsErrqlfkEtdelvakKvkaalksglkpilCvGEt 126
                                       + +kd+g+  +++ HsErr  + +    +   vkaa k+gl++i+C  + 
  gi|298675582|ref|YP_003727332.1|  82 QCVKDAGAIGTLVNHSERRLTLAD----IDSSVKAAGKAGLSTIVCTNNV 127
                                       *******************99876....5667899***********8765 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.16
                                       EEEE--GGGSSSS----HHHHHHHHHH CS
                               TIM 159 viAYePvWAiGtgktatpeqaqevhaa 185
                                       +iA eP   iGtg +++  + q v   
  gi|298675582|ref|YP_003727332.1| 140 YIAIEPPELIGTGVPVSSADPQVVKGS 166
                                       799999999***987665554443333 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.1   2.3e+03      74      98 ..      20      44 ..      18      53 .. 0.78
   2 ?   -1.9   0.1      0.83   1.7e+03     183     219 ..      69     106 ..      43     135 .. 0.49
   3 !   23.8   0.3   1.1e-08   2.3e-05     154     215 ..     154     216 ..     147     223 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.1
                                      SHHHHHHHHHHHHHTTS-SEEEE-- CS
                              ThiG 74 taeeAvriarlarevletdliklEv 98
                                      t e Av+ia+  ++v e+  + + v
  gi|298675582|ref|YP_003727332.1| 20 TGEKAVTIAKACKNVSEKYNVDIGV 44
                                      5688999999999988877776666 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.83
                                       ---SHHHHHHHHHTT-.SEEEESHHHHTSSSHHHHHHH CS
                              ThiG 183 GigspsdaaqamelGa.davllntavaeakdpvamAra 219
                                       Gi   s+  q +   + da  + t v++++   ++A  
  gi|298675582|ref|YP_003727332.1|  69 GIDGGSHTGQILAQCVkDAGAIGTLVNHSERRLTLADI 106
                                       55555555555433322555556666666665555542 PP

  == domain 3  score: 23.8 bits;  conditional E-value: 1.1e-08
                                       STTS----S-HHHHHHHHHH-.SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHH CS
                              ThiG 154 piGsglGllnkealkiiieea.kvPvivDAGigspsdaaqamelGadavllntavaeakdpva 215
                                       p+ s+   + k  +  + +   +v v+  AGi + +d  +a+elG  +vll++ v +a+dp +
  gi|298675582|ref|YP_003727332.1| 154 PVSSADPQVVKGSVDAVKNVNeDVKVLCGAGISKGEDLQAALELGSAGVLLASGVVKAEDPEK 216
                                       5555555555566666666555999***********************************975 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.1   0.00066       1.3      19      69 ..      95     142 ..      86     145 .. 0.81
   2 !   10.3   0.0   0.00029      0.57      33      61 ..     189     216 ..     186     225 .] 0.81

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00066
                                       --GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHHHHHHHT--- CS
                    Hydrolase_like  19 sdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedleepehkptyva 69 
                                        ++e+ l   D  ++ +++A +aG++++  +  v++ + ++    +p+y+a
  gi|298675582|ref|YP_003727332.1|  95 NHSERRLTLADI-DSSVKAAGKAGLSTIVCTNNVNTSASAA--SLGPDYIA 142
                                       566666666777.999******************9998855..67899986 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00029
                                       THHHHHHHCT-EEEEESSSSS-TTTHHHH CS
                    Hydrolase_like  33 tDiagAnnaGwksvLVltGvtrpedleep 61 
                                        D+++A + G  +vL ++Gv ++ed e +
  gi|298675582|ref|YP_003727332.1| 189 EDLQAALELGSAGVLLASGVVKAEDPE-K 216
                                       69******************9998833.2 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.064   1.3e+02      67     120 ..      11      66 ..       4      72 .. 0.78
   2 ?   -2.1   0.0      0.96   1.9e+03      22      40 ..      75      93 ..      66      98 .. 0.70
   3 !   19.6   1.1   2.4e-07   0.00048     128     229 ..     109     212 ..     100     219 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.064
                               NMO  67 vnlflpkkdaadraekykkeleeaalelnieegvr..fyrkvevvldekvevvsfg 120
                                       vnl    + ++++a + +k ++++ +++n+  gv   f    +v +++ v+v s +
  gi|298675582|ref|YP_003727332.1|  11 VNLKTYLQGTGEKAVTIAKACKNVSEKYNVDIGVSpqFCDIYQVASQVDVPVYSQH 66 
                                       677777788889999999***************99875555566666677777665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.96
                               NMO 22 iskarLaaavsnaGgLGvl 40
                                       +++ La  v +aG++G l
  gi|298675582|ref|YP_003727332.1| 75 HTGQILAQCVKDAGAIGTL 93
                                      4666677778888888876 PP

  == domain 3  score: 19.6 bits;  conditional E-value: 2.4e-07
                               NMO 128 vvarlkeagvvliptissvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavd.....iPviAa 199
                                        v++  +ag+  i+ +  v+    ++++G+D + ++ pe  G    ++       ++v+  +dav+     + v+  
  gi|298675582|ref|YP_003727332.1| 109 SVKAAGKAGLSTIVCTNNVNTSASAASLGPDYIAIEPPELIGTGVPVS---SADPQVVKGSVDAVKnvnedVKVLCG 182
                                       67888899999***************************9888544233...3456666666666666667899**** PP

                               NMO 200 GGiidrrgvaaaLalGAsgvqigtrfLltk 229
                                        Gi ++++++aaL lG +gv +++  + ++
  gi|298675582|ref|YP_003727332.1| 183 AGISKGEDLQAALELGSAGVLLASGVVKAE 212
                                       *********************999776665 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.072   1.4e+02      46      83 ..       8      45 ..       3      58 .. 0.90
   2 ?   -1.9   0.0      0.93   1.8e+03     142     167 ..      99     124 ..      85     126 .. 0.62
   3 !   13.5   0.0   1.9e-05     0.037      62     110 ..     167     213 ..     158     224 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.072
                                      EEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEEESSSS CS
                      His_biosynth 46 lhvvDldaakegreanldlveeiaeevfipvqvGGGIr 83
                                      l+vv l+   +g++++   +++ +++v+ +  v+ G++
  gi|298675582|ref|YP_003727332.1|  8 LIVVNLKTYLQGTGEKAVTIAKACKNVSEKYNVDIGVS 45
                                      7899999999999****************999999986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.93
                                       TEEEEEEHHHHHHHHHHTT-SEEEEE CS
                      His_biosynth 142 reetgldavelakkleelgageillt 167
                                       r+ t  d+ + +k++ ++g+++i++t
  gi|298675582|ref|YP_003727332.1|  99 RRLTLADIDSSVKAAGKAGLSTIVCT 124
                                       44444555566666666666666666 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 1.9e-05
                                       HHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-TH CS
                      His_biosynth  62 ldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpe 110
                                        d+v+++ e   ++v  G GI++ ed++++le+g   v +++ +vk  +
  gi|298675582|ref|YP_003727332.1| 167 VDAVKNVNED--VKVLCGAGISKGEDLQAALELGSAGVLLASGVVKAED 213
                                       5788888888..99999*********************99999998655 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.7   3.3e+03     127     143 ..     108     124 ..     103     131 .. 0.68
   2 !   15.6   0.2   3.1e-06    0.0062     264     304 ..     169     209 ..     157     224 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.7
                                       HHHHHHHHCTESEEEEE CS
                            FMN_dh 127 ellkraeaagykalvlt 143
                                       + +k a +ag++++v t
  gi|298675582|ref|YP_003727332.1| 108 SSVKAAGKAGLSTIVCT 124
                                       55666777777777766 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 3.1e-06
                                       HHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHH CS
                            FMN_dh 264 iveavggrievlvDgGirrGsDvlkAlalGAdavllGRpfl 304
                                        v++v+++++vl+  Gi++G+D   Al lG  +vll+  ++
  gi|298675582|ref|YP_003727332.1| 169 AVKNVNEDVKVLCGAGISKGEDLQAALELGSAGVLLASGVV 209
                                       46777889***************************987665 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.4e-05     0.028     151     254 .]     110     221 ..      98     221 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.4e-05
                                       HHHHCCTT-EEEEEESSHHHHHHHHHTT-SEEEEESEETTTTEE-CHH........HHHHCHCC-TTSEEEEESSS- CS
                              IGPS 151 aeaakslglevLvEvhdeeeleralklgakiiGvNnRnLktlevdlnt........teeLaklvpkdvllvaeSGik 219
                                       ++aa + gl  +v +++ ++ + a +lg + i +   +L    v +          + + +k v++dv + +  Gi+
  gi|298675582|ref|YP_003727332.1| 110 VKAAGKAGLSTIVCTNNVNTSASAASLGPDYIAIEPPELIGTGVPVSSadpqvvkgSVDAVKNVNEDVKVLCGAGIS 186
                                       5677777777777777777777777777777777777776555543321111111145667788899********** PP

                                       SHHHHHHHCCTT-SEEEESHHHHC-TTHHHHHHHH CS
                              IGPS 220 tredveklkeegvnafLvGeslmrqedvekairel 254
                                       + ed+++  e g  ++L  + ++++ed eka+++l
  gi|298675582|ref|YP_003727332.1| 187 KGEDLQAALELGSAGVLLASGVVKAEDPEKALEHL 221
                                       ******************************99875 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.0     5e-05       0.1     168     223 ..     163     222 ..      17     225 .] 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5e-05
                                       H.HHHHHHHHHHSSSEEEEESS--SHHHHHHHHCC..SSEEEE-CHHHHHH.HCHHHHHH CS
                              PcrB 168 v.eevialkkklekarlivGGGirsaEkAkevvea..ADvivvGnvveekd.erkidail 223
                                       v   v a+k++ e+ +++ G Gi ++E+ +  +e   A v++   vv+ +d e++++ ++
  gi|298675582|ref|YP_003727332.1| 163 VkGSVDAVKNVNEDVKVLCGAGISKGEDLQAALELgsAGVLLASGVVKAEDpEKALEHLV 222
                                       356788999******************877766655599999888887555499988765 PP

>> PRT_C  Plant phosphoribosyltransferase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     6e-05      0.12      48      91 ..     153     197 ..     150     207 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6e-05
                             PRT_C  48 fP.ssrdldvvrmRYdrlRsvagrvqtvlGdvAtqgErlqallsw 91 
                                       +P ss d++vv+   d +++v++ v+++ G   ++gE lqa+l +
  gi|298675582|ref|YP_003727332.1| 153 VPvSSADPQVVKGSVDAVKNVNEDVKVLCGAGISKGEDLQAALEL 197
                                       688999***********************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1363.75
//
Query:       gi|298675583|ref|YP_003727333.1|  [L=392]
Description: formaldehyde-activating enzyme [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.2e-71  238.0   0.5    9.6e-71  236.9   0.5    1.6  1  Fae             Formaldehyde-activating enzyme (Fae)
    1.2e-24   87.1   0.9    3.5e-24   85.7   0.4    1.9  2  OMPdecase       Orotidine 5'-phosphate decarboxylase / HUMPS 
    2.7e-05   23.6   1.4    0.00015   21.3   1.3    2.3  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
    0.00046   20.0   0.6     0.0054   16.5   0.3    2.3  2  QRPTase_C       Quinolinate phosphoribosyl transferase, C-ter
     0.0038   16.8   1.1     0.0095   15.5   1.1    1.6  1  Peripla_BP_4    Periplasmic binding protein domain
  ------ inclusion threshold ------
      0.013   14.2   0.6      0.024   13.3   0.4    1.4  1  AtuA            Acyclic terpene utilisation family protein At


Domain annotation for each model (and alignments):
>> Fae  Formaldehyde-activating enzyme (Fae)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  236.9   0.5   3.2e-74   9.6e-71       1     159 []       4     162 ..       4     162 .. 0.99

  Alignments for each domain:
  == domain 1  score: 236.9 bits;  conditional E-value: 3.2e-74
                               Fae   1 vGEalvgegeevAhidliiGekdgpvgtAfanalanqskghtpllavlrpnllvkPatlmvnkvtiknekqaellfG 77 
                                       vGEal+ge++e+Ah+dl++G+kdgpvg+Afa+ +++ s+ghtp+l+v+rpnl++kP+tl+v+kvt++n+kqae++fG
  gi|298675583|ref|YP_003727333.1|   4 VGEALIGEEPELAHVDLMVGDKDGPVGQAFATGMTQLSAGHTPMLSVIRPNLPAKPSTLIVPKVTVQNMKQAEQVFG 80 
                                       8**************************************************************************** PP

                               Fae  78 paQaavakavadaveegiipkeeaddlviivsvfidpeakdkkkiyeynyeAtklAikrAlkeePsidevleekdka 154
                                       paQaavakavad+ve+g+ipk++a++lv+++svfi+p+a+d++kiy+yny AtklA+krA++++P++d++ eekdk+
  gi|298675583|ref|YP_003727333.1|  81 PAQAAVAKAVADSVEDGVIPKDKAEELVLVASVFIHPKASDYNKIYRYNYGATKLALKRAMDGFPDVDTMCEEKDKS 157
                                       ***************************************************************************** PP

                               Fae 155 khpfv 159
                                        h+++
  gi|298675583|ref|YP_003727333.1| 158 MHAIM 162
                                       **975 PP

>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.37   1.1e+03     115     156 ..      60      99 ..      31     118 .. 0.71
   2 !   85.7   0.4   1.2e-27   3.5e-24       2     224 ..     174     373 ..     173     374 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.37
                                       EEEEEESTSSGGHHHHHHH.SHHHHHHHHHHHHHHHTTESEEE CS
                         OMPdecase 115 gllilaqmsskgnlmlqek.gytqacveaarehkaedfvmGfv 156
                                         li+ +++ ++  + ++  g +qa+v +a +++ e   +G++
  gi|298675583|ref|YP_003727333.1|  60 STLIVPKVTVQNMKQAEQVfGPAQAAVAKAVADSVE---DGVI 99 
                                       567777777777666666468999999999888877...5555 PP

  == domain 2  score: 85.7 bits;  conditional E-value: 1.2e-27
                                       EEEEEE-SSSHHHHHHHHHHHGG.GSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHT..SEEEEEEEE-S-HHHHHHH CS
                         OMPdecase   2 nLclalDvatarelleladkvgp.sivvlKthydlvegwgfegtgaklaalarkhg..flifeDrKfaDIGntvekq 75 
                                        L++alD ++ +++  ++ ++ +  +++l+ +++l++++g     +++++++r+ +  + i++D+K+ D Gn ++++
  gi|298675583|ref|YP_003727333.1| 174 YLQVALDNPNLDAVKNIISQLPQsDHLILEAGTPLIKRYG-----VDVVSRLREVKpdAFIVADLKTLDTGNLEARM 245
                                       69*********************9****************.....**********999******************* PP

                                       HHSTCHHHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHH.SHHHHHHHHHHHHHHHTT CS
                         OMPdecase  76 atagsarikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqek.gytqacveaarehkaedf 151
                                       +      +++ ad++ v+a+a  +++ +++++a k+g    ++ + ++ ++ ++  ++     ++ve  r+     +
  gi|298675583|ref|YP_003727333.1| 246 V------SDATADAIVVSALAPVSTINKAINEAHKTG--IYVVMDTLNEPDPMSILKQlDELPDVVELHRAID--VE 312
                                       *......69***************************7..8888888899999888884444444444444444..11 PP

                                       ESEEECCCHTHHHHHHTTCSCEEEHHHTTEEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHHH CS
                         OMPdecase 152 vmGfvaqetlnateedaddfihltpgigleqggdgkgqqyntpekligiagadiiivGRgIlkagdpveeaer 224
                                          + +++         d ++ l p+i +   ++++g++ +t++++ + agadi+++GR+I++a+d ++  e+
  gi|298675583|ref|YP_003727333.1| 313 ETEYAWGSI--------DAIKELSPKIMV---AVAGGIRVDTIPDALK-AGADIVVAGRAITNAKDVRQVSEK 373
                                       224444444........789*******96...**************88.99***************9998886 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   1.3   4.9e-08   0.00015     160     197 ..     324     361 ..     213     362 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 4.9e-08
                                       HHHHT---EEEEESS--TTTCHHHHHHT--EEEESHHH CS
                    Ribul_P_3_epim 160 idekeldlkievDGGvkldnieqiaeagadvlVagsav 197
                                       i+e + ++ + v GG+++d+i  + +agad++Vag+a+
  gi|298675583|ref|YP_003727333.1| 324 IKELSPKIMVAVAGGIRVDTIPDALKAGADIVVAGRAI 361
                                       3334456999**************************98 PP

>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.12   3.6e+02     104     125 ..     177     198 ..     147     208 .. 0.85
   2 !   16.5   0.3   1.8e-06    0.0054      69     162 ..     265     365 ..     241     368 .. 0.67

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.12
                                       EEEES--HHHHHHHHHHHHHHS CS
                         QRPTase_C 104 imLDnfsveelkkaveelkekn 125
                                       + LDn++ + +k+++ +l + +
  gi|298675583|ref|YP_003727333.1| 177 VALDNPNLDAVKNIISQLPQSD 198
                                       78*************9885544 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.8e-06
                                       HHHHHHHHHTTTSEEEEEESSHHHHHHHHHHT...-SEEEEES-.-HHHHHHH...HHHHHHHSTTSEEEEESS--T CS
                         QRPTase_C  69 avksvreavdkevkievevesleeleevleae...adiimLDnf.sveelkka...veelkeknkrvlievSGgvtl 138
                                       + k+++ea++  + + +++ ++ +   +l+     +d++ L    +vee++ a   ++ +ke  +++++ v+Gg+  
  gi|298675583|ref|YP_003727333.1| 265 INKAINEAHKTGIYVVMDTLNEPDPMSILKQLdelPDVVELHRAiDVEETEYAwgsIDAIKELSPKIMVAVAGGIRV 341
                                       333333333333334445555444444554325569999998754666666552227777888999*********** PP

                                       TTHHHHHCTT-SEEEECHHCHTB- CS
                         QRPTase_C 139 enveeyaksgvdvisvgalthsvk 162
                                       +++ +  k g d++  g +++++k
  gi|298675583|ref|YP_003727333.1| 342 DTIPDALKAGADIVVAGRAITNAK 365
                                       ******************999987 PP

>> Peripla_BP_4  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   1.1   3.2e-06    0.0095      54     154 ..     249     382 ..     240     389 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.2e-06
                                       TT-SEEEE--SSH.HHHHHHHHHHHHTT-EEEE..............ESTT.GCTTT-CEEEEEC-HHHHHHHHH.. CS
                      Peripla_BP_4  54 kgvdgiivapvds.talapalkkakaaGIpVva..............fdsd.dapsgerlayvgfdneaaGelqa.. 112
                                       + +d+i+v++  + +++++a+++a++ GI+Vv                d + d ++  r+  v  +++a+G + a  
  gi|298675583|ref|YP_003727333.1| 249 ATADAIVVSALAPvSTINKAINEAHKTGIYVVMdtlnepdpmsilkqLDELpDVVELHRAIDVEETEYAWGSIDAik 325
                                       579*********99***************888766666666666555555555555666667777777777777777 PP

                                       ................HHHHHHCTTH.EEEEEE.TSCCCHHHHHHHHHHHHHHHHH-TT CS
                      Peripla_BP_4 113 ................eylaeklggkkgkvvil.aGspgdpnaeeriegfrkvlkeypg 154
                                                       + + ++l+++ +++v+  ++  ++++ ++  e f +vl++ p+
  gi|298675583|ref|YP_003727333.1| 326 elspkimvavaggirvDTIPDALKAG-ADIVVAgRAITNAKDVRQVSEKFLDVLNK-PE 382
                                       77777777777777777777777777.77777744444466666667777777776.54 PP

>> AtuA  Acyclic terpene utilisation family protein AtuA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.4   8.1e-06     0.024     140     161 ..     339     360 ..     262     365 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.1e-06
                              AtuA 140 lGaegIveALeagAdiVitGRv 161
                                       + ++ I +AL+agAdiV++GR 
  gi|298675583|ref|YP_003727333.1| 339 IRVDTIPDALKAGADIVVAGRA 360
                                       3467899**************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 3001.50
//
Query:       gi|298675584|ref|YP_003727334.1|  [L=203]
Description: DNA-(apurinic or apyrimidinic site) lyase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.3e-25   88.0   0.0      7e-25   87.6   0.0    1.2  1  HhH-GPD        HhH-GPD superfamily base excision DNA repair p
      8e-10   38.1   0.0    2.7e-09   36.4   0.0    1.9  2  HHH            Helix-hairpin-helix motif
    0.00061   20.4   0.0       0.47   11.1   0.0    2.5  3  HHH_5          Helix-hairpin-helix domain
      0.001   19.1   0.0      0.065   13.2   0.0    2.1  2  DUF2400        Protein of unknown function (DUF2400)
     0.0041   17.4   4.7     0.0068   16.7   4.7    1.4  1  EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
     0.0089   16.1   0.0        3.4    7.8   0.0    2.3  2  HHH_2          Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.018   14.2   0.0      0.027   13.7   0.0    1.2  1  DUF763         Protein of unknown function (DUF763)
       0.12   12.2   0.0        0.2   11.6   0.0    1.3  1  ProQ           ProQ/FINO family
       0.14   13.0   0.1       0.35   11.7   0.0    1.6  2  DUF3349        Protein of unknown function (DUF3349)
       0.16   11.8   0.0       0.45   10.3   0.0    1.8  1  GAD-like       GAD-like domain
       0.21   11.5   1.5        1.1    9.2   0.2    2.8  3  DUF1409        Protein of unknown function (DUF1409)


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.6   0.0   4.3e-28     7e-25       1     107 [.      30     164 ..      30     165 .. 0.97

  Alignments for each domain:
  == domain 1  score: 87.6 bits;  conditional E-value: 4.3e-28
                                       HHHHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH........... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........... RF
                           HhH-GPD   1 vsailsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv........... 66 
                                       + ++lsq+t+d+++n++ + lf++++  +p++l   de+++++li+ +Gfyr K ++ik+++++++           
  gi|298675584|ref|YP_003727334.1|  30 ITTVLSQRTRDSVTNSSAKTLFNKYN--SPNELVHTDEDEIESLIKNVGFYRVKTQRIKQISEMILdeydgqvpdnl 104
                                       5689********************98..************************************************* PP

                                       ....................S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHHHHHHHHHHH CS
                                       ....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           HhH-GPD  67 ....................gkpdvlivvDvhvrrilkrlrsikekktkkkvekkleelle 107
                                                           ++ +++i+vD+hv+ri +rl+++++ kt++k+ek+l+++++
  gi|298675584|ref|YP_003727334.1| 105 ndllklpgvgrktancvltyAFSKKAIAVDTHVHRISNRLGLVET-KTPEKTEKDLKKIVP 164
                                       ********************77789******************99.6*********99887 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.0   1.6e-12   2.7e-09       1      30 []      95     124 ..      95     124 .. 0.95
   2 ?   -2.8   0.0       4.4   7.2e+03       8      16 ..     154     162 ..     153     164 .. 0.75

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 1.6e-12
                                       SHHHHHTSSHHHHHTSTT-SHHHHHHHHHH CS
                               HHH   1 sleglipasreeLlalPGVGpktAeaIlsy 30 
                                       +++g +p+++ +Ll+lPGVG+ktA+++l y
  gi|298675584|ref|YP_003727334.1|  95 EYDGQVPDNLNDLLKLPGVGRKTANCVLTY 124
                                       599************************987 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.4
                                       SSHHHHHTS CS
                               HHH   8 asreeLlal 16 
                                        ++++L+++
  gi|298675584|ref|YP_003727334.1| 154 KTEKDLKKI 162
                                       588999994 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0     0.006       9.8      13      44 ..      45      76 ..      40      90 .. 0.82
   2 !   11.1   0.0   0.00029      0.47      35      48 ..     105     118 ..      80     125 .. 0.81
   3 !   10.5   0.0   0.00046      0.75      36      48 ..     106     118 ..     104     133 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.006
                                      HHHHHHHTTT--SHHHHHHS-HHHHHT.STTS- CS
                             HHH_5 13 ktAlallsaGiesvedlaaadveeLak.ipGiG 44
                                      + A++l ++ ++s+ +l++ d++e+ + i+ +G
  gi|298675584|ref|YP_003727334.1| 45 SSAKTLFNK-YNSPNELVHTDEDEIESlIKNVG 76
                                      679999***.**************988555554 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00029
                                       HHHHTSTTS-HHHH CS
                             HHH_5  35 eeLakipGiGkktA 48 
                                       ++L k+pG+G ktA
  gi|298675584|ref|YP_003727334.1| 105 NDLLKLPGVGRKTA 118
                                       56777777777777 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00046
                                       HHHTSTTS-HHHH CS
                             HHH_5  36 eLakipGiGkktA 48 
                                       +L k+pG+G ktA
  gi|298675584|ref|YP_003727334.1| 106 DLLKLPGVGRKTA 118
                                       4555555555555 PP

>> DUF2400  Protein of unknown function (DUF2400)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.026        43      13      75 ..      22      84 ..      13     110 .. 0.69
   2 !   13.2   0.0     4e-05     0.065     172     195 ..     130     153 ..     123     166 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.026
                           DUF2400 13 edieiaallaallayGnrkqiikkleellelmdkspydfvleeeeekdlkelekf.kyRffnse 75
                                      ++  +  l++++l+   r+++ ++  + l    +sp++ v + e ++  + ++++  yR+ +++
  gi|298675584|ref|YP_003727334.1| 22 NNDPFYVLITTVLSQRTRDSVTNSSAKTLFNKYNSPNELVHTDE-DEIESLIKNVgFYRVKTQR 84
                                      55566778999999999999998766665556678999998666.4444455553249987653 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 4e-05
                           DUF2400 172 iiPlDvHvarvarklgllkrkqad 195
                                        i +D+Hv+r++++lgl+++k+ +
  gi|298675584|ref|YP_003727334.1| 130 AIAVDTHVHRISNRLGLVETKTPE 153
                                       5889**************988654 PP

>> EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   4.7   4.2e-06    0.0068       1      17 []     183     199 ..     183     199 .. 0.97

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.2e-06
                     EndIII_4Fe-2S   1 CTARkPkCeaCPLaDlC 17 
                                       C + +P+C+ C+L+D C
  gi|298675584|ref|YP_003727334.1| 183 CRPVSPRCDVCVLNDTC 199
                                       99*************99 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0    0.0084        14      14      43 ..      45      75 ..      41      78 .. 0.84
   2 !    7.8   0.0    0.0021       3.4      34      55 ..     104     125 ..     102     133 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0084
                             HHH_2 14 ktAklLakrFksldaLkkasleeLle.vddi 43
                                      + Ak+L ++++s  +L +++++e+ + ++++
  gi|298675584|ref|YP_003727334.1| 45 SSAKTLFNKYNSPNELVHTDEDEIESlIKNV 75
                                      68*********************98635555 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0021
                             HHH_2  34 leeLlevddiGeeiAqsivefF 55 
                                       l++Ll+++++G ++A+ + ++ 
  gi|298675584|ref|YP_003727334.1| 104 LNDLLKLPGVGRKTANCVLTYA 125
                                       689***************9984 PP

>> DUF763  Protein of unknown function (DUF763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.6e-05     0.027     184     276 ..      32     119 ..      18     126 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.6e-05
                            DUF763 184 giagekkeeevlnlvskeseearkaildlvkekpekllkelkelkallkgekklklpakhevlekvlekayelqped 260
                                       ++ +++++++v n ++k+  ++ ++  +lv+ +++++++ +k++          k+++ +++ e +l++   + p++
  gi|298675584|ref|YP_003727334.1|  32 TVLSQRTRDSVTNSSAKTLFNKYNSPNELVHTDEDEIESLIKNVGFYRV-----KTQRIKQISEMILDEYDGQVPDN 103
                                       6777888888888888888888899999999999999999998853333.....333446889999***999***** PP

                            DUF763 261 feellllkgvGpktlr 276
                                       +++ll l+gvG+kt  
  gi|298675584|ref|YP_003727334.1| 104 LNDLLKLPGVGRKTAN 119
                                       *************976 PP

>> ProQ  ProQ/FINO family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00012       0.2       3      60 ..       2      56 ..       1      63 [. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                              ProQ  3 svkeliaelaekFPkaFskegeakPLkiGIfedllerladkeklskkklrkaLktyts 60
                                      +v+e++++l +++P++F  ++   P+ + I + l +  + ++ +++++ ++++++y s
  gi|298675584|ref|YP_003727334.1|  2 NVEEVLHRLENEYPEIFYYQN-NDPFYVLITTVLSQ--RTRDSVTNSSAKTLFNKYNS 56
                                      689***************987.9************9..88888999999999888865 PP

>> DUF3349  Protein of unknown function (DUF3349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00022      0.35       3      86 ..       3      92 ..       2      96 .. 0.79
   2 ?   -2.4   0.0       5.2   8.5e+03      79      86 ..     137     144 ..     125     165 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00022
                                      HHHHHHHHHHH-TT-B-HHHHHHHHHHHCTT--HHHHHHHHHHHHHH-....-...SSS.BSHHHCHHHHHHHCTS--- CS
                           DUF3349  3 lasileWLragYPegvPeqdyvpLlalLrrrLsdeevkevaeelvaea....a..eadeavdeedieelitkvteeeps 75
                                      ++++l+ L + YPe    q+  p  +l++  Ls++  ++v+++ +++     +  ++  ++de++ie+li++v     +
  gi|298675584|ref|YP_003727334.1|  3 VEEVLHRLENEYPEIFYYQNNDPFYVLITTVLSQRTRDSVTNSSAKTLfnkyNspNELVHTDEDEIESLIKNVGFYRVK 81
                                      578999********999999888888888888887777777666665544443356677899***********999999 PP

                                      HHHHHHHHHHH CS
                           DUF3349 76 eedvarVaarL 86
                                       + ++++++ +
  gi|298675584|ref|YP_003727334.1| 82 TQRIKQISEMI 92
                                      99999988765 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.2
                                       HHHHHHHH CS
                           DUF3349  79 varVaarL 86 
                                       v+r+++rL
  gi|298675584|ref|YP_003727334.1| 137 VHRISNRL 144
                                       44444443 PP

>> GAD-like  GAD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00027      0.45       3      41 ..      68     110 ..      66     118 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00027
                          GAD-like   3 leefleafg....kplaveevseeilerykgklPeklleywre 41 
                                       +e++++++g    k+   +++se il++y g++P++l +  + 
  gi|298675584|ref|YP_003727334.1|  68 IESLIKNVGfyrvKTQRIKQISEMILDEYDGQVPDNLNDLLKL 110
                                       6888889988887777779*****************9887665 PP

>> DUF1409  Protein of unknown function (DUF1409)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       5.3   8.6e+03      20      30 ..       3      13 ..       3      15 .. 0.81
   2 ?    9.2   0.2   0.00067       1.1       5      30 ..      67      95 ..      64     112 .. 0.84
   3 ?   -2.5   0.0       3.1   5.1e+03      23      36 ..     159     172 ..     157     173 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 5.3
                           DUF1409 20 veeiqdqlpdd 30
                                      vee+ ++l ++
  gi|298675584|ref|YP_003727334.1|  3 VEEVLHRLENE 13
                                      78999999775 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00067
                           DUF1409  5 sidsLvndvGsIRs...Rveeiqdqlpdd 30
                                       i+sL+++vG  R    R++ i + ++d+
  gi|298675584|ref|YP_003727334.1| 67 EIESLIKNVGFYRVktqRIKQISEMILDE 95
                                      79*********996445888888888876 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 3.1
                           DUF1409  23 iqdqlpddladvla 36 
                                        ++ +p++l + ++
  gi|298675584|ref|YP_003727334.1| 159 LKKIVPENLWNKIN 172
                                       56778999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       981  (0.0547158); expected 358.6 (0.02)
Passed bias filter:                      716  (0.0399353); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:01.01
# Mc/sec: 607.84
//
Query:       gi|298675585|ref|YP_003727335.1|  [L=383]
Description: geranylgeranyl reductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-16   60.0   1.3    2.8e-11   43.3   0.3    3.0  2  FAD_binding_3   FAD binding domain
    1.1e-08   34.4   0.1    0.00062   18.7   0.0    2.4  2  Trp_halogenase  Tryptophan halogenase
    1.1e-07   31.4   0.8     0.0023   17.3   0.0    2.2  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    4.7e-07   29.3   1.5      4e-06   26.3   1.5    2.0  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    5.6e-07   29.5   0.2    0.00097   18.8   0.0    2.5  2  DAO             FAD dependent oxidoreductase
    1.3e-06   27.4   0.4    6.3e-05   21.9   0.0    2.2  2  HI0933_like     HI0933-like protein
    2.2e-06   27.1   0.4    1.2e-05   24.7   0.0    2.0  2  Thi4            Thi4 family
    2.8e-06   27.0   0.1      4e-06   26.5   0.1    1.3  1  FAD_oxidored    FAD dependent oxidoreductase
    1.6e-05   24.1   0.2     0.0001   21.5   0.5    2.0  2  Lycopene_cycl   Lycopene cyclase protein
    2.1e-05   23.8   0.2    3.5e-05   23.1   0.2    1.3  1  FAD_binding_2   FAD binding domain
    2.9e-05   23.3   1.3    5.3e-05   22.5   1.3    1.5  1  GIDA            Glucose inhibited division protein A
    0.00019   21.6   0.0     0.0005   20.2   0.0    1.8  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
     0.0027   18.2   0.6       0.32   11.6   0.0    2.8  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   0.3     2e-14   2.8e-11       3     182 ..       3     164 ..       1     188 [. 0.83
   2 !   12.4   0.0     5e-05     0.068     280     339 ..     253     313 ..     248     318 .. 0.83

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 2e-14
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEEE CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmellrqlGledrilaegapnelmgealyne 79 
                                       dV++VGaGpaG ++a   ++aG +++++ek s   +++ a+g++++ +  l+   +  ++ ++       + +ly++
  gi|298675585|ref|YP_003727335.1|   3 DVIVVGAGPAGSTAAEYTAKAGLSTMIIEKDSLPRDKTCAGGISSQALKHLDYD-VPVNLVKRQ---CFGARVLYGN 75 
                                       8**********************************************9999853.333343333...2333444444 PP

                                       CCCCCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEE CS
                     FAD_binding_3  80 lsdtpkaradlelesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrak 156
                                                 le +s     ++++ +e++++L  +a++ g+++ +kt+v+sl    ++v+   +         ++ k
  gi|298675585|ref|YP_003727335.1|  76 --------QVLESRSDELIASMVSRKEFDNYLTTKAVNSGTKLLQKTRVKSLDIKSNHVEIHTTAG------VFKTK 138
                                       ........56675677778899****************************9998888887766655......47899 PP

                                       EEEE--GTT-HHHHHHTGGEEEEEEE CS
                     FAD_binding_3 157 YlvGaDGgrStvrktlgiefegeetv 182
                                        ++GaDG++S +++ +  +++  et 
  gi|298675585|ref|YP_003727335.1| 139 VVIGADGVNSVCARYVRAQLKPDETA 164
                                       *************9999887776655 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 5e-05
                                       SSEETTEEE-GGGTEEE-STTSHHHHHHHHHHHHHHHH.HHHHHTTSS-GGGGHHHHHHHH CS
                     FAD_binding_3 280 kyrkgrvflaGDAaHihpPtgGqGlNtaiqDavnLawk.LaavlkGeAkeelLdtYeeerr 339
                                       k  ++rv+l GDAa  +    G G+N a++     a     a++k + ++++L  Y+++++
  gi|298675585|ref|YP_003727335.1| 253 KTYNNRVLLTGDAAGFVDAFLGEGINYALMSGRLAAETvVDAFYKNDFSKAMLSKYQDKCK 313
                                       55678***********************998877665515688999999999999998886 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.1   1.8e-05     0.024       1      38 [.       3      37 ..       3      50 .. 0.91
   2 !   18.7   0.0   4.5e-07   0.00062     273     372 ..     214     317 ..      62     328 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.8e-05
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS-- CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlveseeigt 38
                                      ++++vG+G+aG++aA + aka+   l+  ++e++ +++
  gi|298675585|ref|YP_003727335.1|  3 DVIVVGAGPAGSTAAEYTAKAG---LSTMIIEKDSLPR 37
                                      699*******************...99999***99997 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 4.5e-07
                                       EE-TTTS-HHHHHHHHHHHCT--TTTS-.EEEE---EEES-SEETTEEE-CCCTEE--CCCS-HHHHHHH....HHH CS
                    Trp_halogenase 273 vyssahadddeAlaellaeldgkleaep.rkirfttGrrkqawvknvvalGlasgfvePlestsihliqa....alr 344
                                       + + +  d  +   e++++++++  + + + ++   G +++++++ v++ G+a+gfv++  + +i  +      a++
  gi|298675585|ref|YP_003727335.1| 214 IDAAKSSDSLKSYYEFINNFGFDYIKPSgHFLP-IGGVERKTYNNRVLLTGDAAGFVDAFLGEGINYALMsgrlAAE 289
                                       444445555566667777777776655533333.45889999***********************999888999*** PP

                                       HHHHT--BTT--HHHHHHHHHHHHHHHH CS
                    Trp_halogenase 345 rLlallpdksdepaaiaefnrevarele 372
                                       +++  + ++ +++a ++++ ++ ++e++
  gi|298675585|ref|YP_003727335.1| 290 TVVDAFYKNDFSKAMLSKYQDKCKHEFG 317
                                       ************************9987 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.6e-06    0.0023       1      31 [.       5      34 ..       5      37 .. 0.92
   2 !   12.6   0.1   4.3e-05      0.06      75     134 ..      87     146 ..      70     153 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.6e-06
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgn 31
                                      i++GaGPaG +aa    kagl + +i+Ek++
  gi|298675585|ref|YP_003727335.1|  5 IVVGAGPAGSTAAEYTAKAGL-STMIIEKDS 34
                                      89*******************.678****86 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 4.3e-05
                       Pyr_redox_3  75 eeklsrkealeYlrevaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGe 134
                                          +srke+ +Yl++ a +   +  ++++V+s++ ++++ e++t+ +++++k vi A G 
  gi|298675585|ref|YP_003727335.1|  87 ASMVSRKEFDNYLTTKAVNSGTKLLQKTRVKSLDIKSNHVEIHTTAGVFKTKVVIGADGV 146
                                       567899*************************************************99996 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   1.5   2.9e-09     4e-06       2      90 ..       3     131 ..       2     151 .. 0.71

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 2.9e-09
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEE.....TTHCHHHCSHHHHCHHHHHHHHHHHHH................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxx................ RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve.....legtclnggcllskallgvaedaeias................ 57 
                                       dv+v+G+GpAG +aa++ a+ag+ ++++e     +++tc +g  + s+al +   d  + +                
  gi|298675585|ref|YP_003727335.1|   3 DVIVVGAGPAGSTAAEYTAKAGLSTMIIEkdslpRDKTCAGG--ISSQALKHLDYDVPVNLvkrqcfgarvlygnqv 77 
                                       8***************************88887755656555..555555555555544445566666666666666 PP

                                       .....................HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEE CS
                                       .....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 .....................evvkklnqgielllgeevvkidpgkkkvklekk 90 
                                                              +k +n+g +ll ++ v ++d ++ +v++ ++
  gi|298675585|ref|YP_003727335.1|  78 lesrsdeliasmvsrkefdnyLTTKAVNSGTKLLQKTRVKSLDIKSNHVEIHTT 131
                                       666666666669988888888556677888888888778888888877777443 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0     7e-07   0.00097       1      33 [.       3      37 ..       3      85 .. 0.77
   2 !    8.7   0.0   0.00085       1.2     147     204 ..      94     148 ..      87     290 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 7e-07
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                      dv+++G+G +G+++A + a++g  + ++ek++ + 
  gi|298675585|ref|YP_003727335.1|  3 DVIVVGAGPAGSTAAEYTAKAGlsTMIIEKDSLPR 37
                                      9******************************7755 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00085
                                       HHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE.EECTEEEEEEEEEEE--GGGH CS
                               DAO 147 kltaalaraaealGveilegtevtgleeedgkvwgve.rttpgendaadavVnaaGaws 204
                                       ++ ++l  +a + G ++l++t+v++l+    k  +ve +tt+g   + + v+ a G+ s
  gi|298675585|ref|YP_003727335.1|  94 EFDNYLTTKAVNSGTKLLQKTRVKSLDI---KSNHVEiHTTAGVF-KTKVVIGADGVNS 148
                                       66788999******************55...46667667777874.4366888888776 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   4.5e-08   6.3e-05       2      40 ..       3      41 ..       2      61 .. 0.89
   2 ?    3.8   0.1     0.013        19     113     167 ..      97     149 ..      73     152 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 4.5e-08
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHH CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKil 40
                                      dviv+G+G+AG  aA+  ak+g +++++ek + +  K  
  gi|298675585|ref|YP_003727335.1|  3 DVIVVGAGPAGSTAAEYTAKAGLSTMIIEKDSLPRDKTC 41
                                      8*****************************987777755 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.013
                                       HHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS- CS
                       HI0933_like 113 dallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlSi 167
                                       + l++++ ++g kl  +t+vks++ ++++ ++++t +++ ++++ ++ A G +S+
  gi|298675585|ref|YP_003727335.1|  97 NYLTTKAVNSGTKLLQKTRVKSLDIKSNH-VEIHT-TAGVFKTKVVIGADGVNSV 149
                                       678899999**************998877.99999.9999999999999998886 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   8.5e-09   1.2e-05      18      61 ..       2      44 ..       1      55 [. 0.85
   2 ?    0.3   0.0      0.25   3.5e+02      98     136 ..      94     135 ..      68     158 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 8.5e-09
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTS CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGG 61
                                      +Dv++vGaG++G taa y ak+ +l ++i+e+   p   +  GG
  gi|298675585|ref|YP_003727335.1|  2 QDVIVVGAGPAGSTAAEYTAKA-GLSTMIIEKDSLPRDKTCAGG 44
                                      6*********************.********9765555555555 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.25
                                       HHHHHHHHHHHTSTTEEEEESEEEEEEEEET...B.TEEEEEE CS
                              Thi4  98 lftstllskvlqlanvkllnavaveDlivre...g.egvaGvv 136
                                       +f   l++k+++ ++ kll+ + v  l ++    + ++ aGv 
  gi|298675585|ref|YP_003727335.1|  94 EFDNYLTTKAVN-SGTKLLQKTRVKSLDIKSnhvEiHTTAGVF 135
                                       666778889998.999999999999988887444334455554 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.1   2.9e-09     4e-06       1      48 [.       3      56 ..       3     155 .. 0.68

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 2.9e-09
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLve......ergvlGGlltsglvatdig 48
                                      Dv+VvG+gpaG +AA   a+aG +++++e      ++ + GG ++++l   d  
  gi|298675585|ref|YP_003727335.1|  3 DVIVVGAGPAGSTAAEYTAKAGLSTMIIEkdslprDKTCAGGISSQALKHLDYD 56
                                      9****************************4444433457788888877766655 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.5   7.3e-08    0.0001       1     145 [.       3     150 ..       3     163 .. 0.73
   2 ?   -1.2   0.0       0.6   8.3e+02     243     300 ..     245     301 ..     242     354 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 7.3e-08
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnnyvWsdefedlga.....leecvehsWsgtiv.yldd 71 
                                       Dv+v+GaGpAg   A+    ak+gl+ ++ie  +sl++          ++l+        ++v+ +  g++v y ++
  gi|298675585|ref|YP_003727335.1|   3 DVIVVGAGPAGSTAAEYT--AKAGLSTMIIE-KDSLPRDKTCAGGISSQALKHldydvPVNLVKRQCFGARVlYGNQ 76 
                                       9**********9988888..**********6.466656666566666666666332332345555555555515555 PP

                     Lycopene_cycl  72 gkkillg.raYgrvsskrlkeellerlvengvkll.eakvesveeeeageslvvleggrkirarlvvdarglaslk 145
                                         +  ++ +   +vs+k++ + l  + v++g kll + +v+s   +++ ++ + + +g+  + ++v+ a g+ s +
  gi|298675585|ref|YP_003727335.1|  77 VLESRSDeLIASMVSRKEFDNYLTTKAVNSGTKLLqKTRVKSLDIKSN-HVEIHTTAGV-FKTKVVIGADGVNSVC 150
                                       555555567889****************88887761578999888888.8899999885.7899999999976655 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.6
                     Lycopene_cycl 243 iPvtlggslprleqk.vlaiGaaaglvhPaTGYsvarslaeapllasaiaaalressls 300
                                       +P+  gg  +++ ++ vl  G aag v    G  +  +l   +l a+ +++a  +++ s
  gi|298675585|ref|YP_003727335.1| 245 LPI--GGVERKTYNNrVLLTGDAAGFVDAFLGEGINYALMSGRLAAETVVDAFYKNDFS 301
                                       788..776666655549999999999998888888888888888888888887765333 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.2   2.5e-08   3.5e-05       1      32 [.       3      34 ..       3      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2.5e-08
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSS CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeq 32
                                      DviV+G+G AG +AA   a+aGl+++++ek +
  gi|298675585|ref|YP_003727335.1|  3 DVIVVGAGPAGSTAAEYTAKAGLSTMIIEKDS 34
                                      9****************************986 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   1.3   3.9e-08   5.3e-05       1      54 [.       3      55 ..       3     170 .. 0.66

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 3.9e-08
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SSSSEEE-TTHHHHHH CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldtiaelsCnpsiggiakgllvr 54
                                      dviV+G+G AG+ AA  +a++G+++++i +k +      C   i ++a  +l  
  gi|298675585|ref|YP_003727335.1|  3 DVIVVGAGPAGSTAAEYTAKAGLSTMII-EKDSLPRDKTCAGGISSQALKHLDY 55
                                      8*************************99.3333334455666666666666555 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   3.7e-07    0.0005       1      28 [.       6      33 ..       6      61 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.7e-07
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekr 28
                                      +vGaG +G++aA + akag++  ++ek 
  gi|298675585|ref|YP_003727335.1|  6 VVGAGPAGSTAAEYTAKAGLSTMIIEKD 33
                                      8*************************96 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00023      0.32       2      41 ..       4      40 ..       3      57 .. 0.84
   2 ?    3.8   0.1     0.061        84      38      74 ..      91     127 ..      73     134 .. 0.79
   3 ?   -2.0   0.0       4.1   5.6e+03       3      18 ..     139     154 ..     137     159 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHH CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDee 41
                                      v+vvG+G  g  +A++ a+ g ++ ++e  + ++   D++
  gi|298675585|ref|YP_003727335.1|  4 VIVVGAGPAGSTAAEYTAKAGLSTMIIEKDSLPR---DKT 40
                                      89**************************999998...444 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.061
                                       SSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEE CS
                         Pyr_redox  38 lDeeaskilqeklekngievllntkveeiegsedgve 74 
                                         +e+ ++l++k  + g ++l +t+v++++ +++ ve
  gi|298675585|ref|YP_003727335.1|  91 SRKEFDNYLTTKAVNSGTKLLQKTRVKSLDIKSNHVE 127
                                       557899999********************97776543 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 4.1
                                       EEECSSHHHHHHHHHH CS
                         Pyr_redox   3 vvvGgGyiglElAgal 18 
                                       vv+G++ ++  +A + 
  gi|298675585|ref|YP_003727335.1| 139 VVIGADGVNSVCARYV 154
                                       899*999999888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 2381.47
//
Query:       gi|298675586|ref|YP_003727336.1|  [L=598]
Description: signal transduction histidine kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.2e-28   97.6   1.9    3.2e-28   97.6   1.9    2.4  2  HisKA_2      Histidine kinase
      2e-21   76.2   4.7    3.5e-09   36.8   0.1    4.9  5  PAS_9        PAS domain
    6.4e-21   74.5   0.0    3.3e-08   33.5   0.0    3.9  4  PAS          PAS fold
    1.2e-20   73.8   0.0    2.1e-06   28.0   0.0    4.9  5  PAS_4        PAS fold
    3.9e-19   68.2   0.1    2.2e-05   24.4   0.0    3.6  3  PAS_8        PAS domain
    1.4e-09   38.4   0.2    9.2e-09   35.8   0.2    2.3  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    2.2e-07   31.1   0.0     0.0018   18.6   0.0    3.0  3  PAS_3        PAS fold
    1.7e-05   25.4   0.6      4e-05   24.2   0.1    1.9  2  HWE_HK       HWE histidine kinase
    0.00035   20.5   0.0    0.00091   19.2   0.0    1.7  1  HATPase_c_2  Histidine kinase-like ATPase domain
     0.0014   18.4   0.2     0.0047   16.8   0.2    1.8  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
     0.0071   16.0   0.0        6.1    6.5   0.0    3.4  3  PAS_12       UPF0242 C-terminal PAS-like domain
  ------ inclusion threshold ------
       0.16   11.7   2.3        1.1    9.1   2.2    2.5  3  SPOB_a       Sensor_kinase_SpoOB-type, alpha-helical domain


Domain annotation for each model (and alignments):
>> HisKA_2  Histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1      0.62   9.2e+02      23      43 ..     256     276 ..     246     279 .. 0.76
   2 !   97.6   1.9   2.2e-31   3.2e-28       1      76 []     407     482 ..     407     482 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.62
                           HisKA_2  23 kakdeevkealresqnRvlsi 43 
                                        ++ +e+++ l+es++R +++
  gi|298675586|ref|YP_003727336.1| 256 ITERKETEKELKESEERFRTL 276
                                       4567788999*****998876 PP

  == domain 2  score: 97.6 bits;  conditional E-value: 2.2e-31
                           HisKA_2   1 EihHRvkNnLqvisslLslqarkakdeevkealresqnRvlsialiheeLyksedletvdfseylekLvenlfksy 76 
                                       E+hHR+kNnLqvisslLslq++k++d++vk+a+ ++qnRv+s++l+h++Ly+ ++le+v+ ++y+ ++v++l ++y
  gi|298675586|ref|YP_003727336.1| 407 ELHHRIKNNLQVISSLLSLQSEKFTDDNVKDAFIDTQNRVISMSLVHNKLYQAKGLENVNTKDYIGDIVDHLNELY 482
                                       99*********************************************************************98765 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.1   1.4e-08   2.1e-05      11      85 ..      34     122 ..      20     134 .. 0.74
   2 !   12.3   0.0    0.0001      0.15       3     104 .]     140     258 ..     136     258 .. 0.59
   3 !   36.8   0.1   2.3e-12   3.5e-09       4     103 ..     284     381 ..     281     381 .. 0.87
   4 ?   -1.9   0.1       2.6   3.9e+03      46      78 ..     390     420 ..     385     440 .. 0.63
   5 ?   -1.9   0.0       2.7     4e+03      43      81 ..     511     547 ..     505     553 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.4e-08
                             PAS_9  11 g....rilyaNeaalrllGyspeevlgksitdlf.vtdpeanerlraaleqgrk.........kerevevvlirkng 73 
                                       +    ri++aN+a + ++G+++ee+ g++ + ++ +++p + +  +++ e+g+k           ++++v  i ++ 
  gi|298675586|ref|YP_003727336.1|  34 HpvdyRIIDANPAYESITGFKREEIAGQRASIVYnKENPPHLNIYARVAETGEKanfetytpqLRKHFNVSVISPEK 110
                                       45666*****************************9999999999999999999776666666655556666666665 PP

                             PAS_9  74 etfwvlltaspv 85 
                                       ++f + lt ++ 
  gi|298675586|ref|YP_003727336.1| 111 GKFITILTDITS 122
                                       666665555555 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.0001
                             PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlf.................vtdpeanerlraaleqgrk... 59 
                                         +++++d ril+ N+ a+ + G s+ee++g +  + +                  +d   ++++ + +e   +   
  gi|298675586|ref|YP_003727336.1| 140 VLMMVDSDRRILKLNKNAELFAGKSSEELVGSRGGEALgclhslddpegcgfgphCKDCIVRNTVLDTFE---Tgnn 213
                                       344588**************************97766666668777777765443222223333333333...2443 PP

                             PAS_9  60 ...kerevevvlirkngetfw.vlltaspvkdddgelvgiivilrDite 104
                                          +  e  + +i + +e+ + +ll+as +  +++  v+  v ++Dite
  gi|298675586|ref|YP_003727336.1| 214 hynI--EASLPFIVDGREKNLtFLLSASLINTENKSKVL--VSIQDITE 258
                                       6443..333333333334444134777777444444444..88999987 PP

  == domain 3  score: 36.8 bits;  conditional E-value: 2.3e-12
                             PAS_9   4 ilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwv 78 
                                       i+  + dg+i+yaNe+a + lGy ++e+l  ++td+   v+ +  +++ ++   + +   +   + + rk+g+ f+v
  gi|298675586|ref|YP_003727336.1| 284 IIAHDFDGNIIYANETASKNLGYPRDEILSLNVTDIDpyVDIDVFRDKYWNKTSSDT--SYFIGTYHKRKDGTIFPV 358
                                       55555799****************************966666666666666666666..9999************** PP

                             PAS_9  79 lltaspvkdddgelvgiivilrDit 103
                                       +++++++  +++ +++  + +rDit
  gi|298675586|ref|YP_003727336.1| 359 EVRLTRINLNEKPVIL--AYIRDIT 381
                                       *******999999999..******9 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 2.6
                             PAS_9  46 anerlraaleqgrkkerevevvlirkngetfwv 78 
                                        +e +++++e+ r   r+ e++++ kn+ ++  
  gi|298675586|ref|YP_003727336.1| 390 IKEQKEQVIETER--IRQLELHHRIKNNLQVIS 420
                                       4555666777777..888888888888855543 PP

  == domain 5  score: -1.9 bits;  conditional E-value: 2.7
                             PAS_9  43 dpeanerlraaleqgrkkerevevvlirkngetfwvllt 81 
                                       ++   + l+ a+ + +      e+ l+ +n+++ ++l+ 
  gi|298675586|ref|YP_003727336.1| 511 NEILSNSLKYAFSESE--TGKIEIKLYQNNNNKNYTLIV 547
                                       4455666777777777..888888888888888887765 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.3e-06     0.002      22      91 ..      39     118 ..      36     131 .. 0.71
   2 !   18.4   0.0   1.1e-06    0.0016       2      44 ..     129     171 ..     128     172 .. 0.95
   3 ?   -2.5   0.0       3.4     5e+03      59     113 .]     201     256 ..     193     256 .. 0.72
   4 !   33.5   0.0   2.2e-11   3.3e-08       1     113 []     271     380 ..     271     380 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.3e-06
                                       BEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEEC...........TTSSEE CS
                               PAS  22 rilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfkl...........rdgrpi 87 
                                       ri+ +N+a+e+++G++ree+ g+  +++++ e +  +  ++ +++e+ge+++ +  +  l            +g++i
  gi|298675586|ref|YP_003727336.1|  39 RIIDANPAYESITGFKREEIAGQRASIVYNKENPP-HLNIYARVAETGEKANFETYTPQLrkhfnvsvispEKGKFI 114
                                       8999*************************998554.66666666666666666666665555555555555555555 PP

                                       EEEE CS
                               PAS  88 hlev 91 
                                        +++
  gi|298675586|ref|YP_003727336.1| 115 TILT 118
                                       5555 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 1.1e-06
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTS CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgk 44 
                                       +l+++ e+ p+  ++vD d ril  N++ae + G s ee++g+
  gi|298675586|ref|YP_003727336.1| 129 ELETVYENVPVVLMMVDSDRRILKLNKNAELFAGKSSEELVGS 171
                                       68999************************************96 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 3.4
                                       HHHHHHHHHHTT-ECCCCEEEEC.TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  59 aelleqlleqgeesrageisfkl.rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       +  ++   e+g++  + e s+++ +dgr++ l    s  +   ++   +l+ ++di
  gi|298675586|ref|YP_003727336.1| 201 RNTVLDTFETGNNHYNIEASLPFiVDGREKNLTFLLSASLINTENKSKVLVSIQDI 256
                                       55566677788888888888888889998887777777777777777788877776 PP

  == domain 4  score: 33.5 bits;  conditional E-value: 2.2e-11
                                       HHHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCE CS
                               PAS   1 edlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesragei 77 
                                       e++r++ e ++d+i++ D dg+i+y+N++a + lG++r+e+l+ ++ d  +  d + +++++++  ++ ++  +g  
  gi|298675586|ref|YP_003727336.1| 271 ERFRTLTEKAADAIIAHDFDGNIIYANETASKNLGYPRDEILSLNVTDIDPYVDIDVFRDKYWNKTSSDTSYFIGTY 347
                                       68999*****************************************85444444447******************** PP

                                       EEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  78 sfklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                         ++ dg+++++evr + +   ++    +l  +rdi
  gi|298675586|ref|YP_003727336.1| 348 HKRK-DGTIFPVEVRLTRINLNEKP--VILAYIRDI 380
                                       ****.**********9988777665..666666665 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   1.4e-09   2.1e-06      14     107 ..      37     122 ..      36     125 .. 0.91
   2 !   17.4   0.0   2.7e-06    0.0041       2      42 ..     135     175 ..     134     188 .. 0.92
   3 ?    1.6   0.0      0.22   3.2e+02      94     110 .]     246     261 ..     207     261 .. 0.74
   4 !   19.5   0.0   5.9e-07   0.00089       3     110 .]     279     385 ..     277     385 .. 0.93
   5 ?    0.4   0.1       0.5   7.5e+02      49      74 ..     387     412 ..     384     425 .. 0.73

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.4e-09
                             PAS_4  14 dgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgeerhyelrllPlrd 90 
                                       d+r+++aN+a++++ g+ +ee+ G++   ++++   +++ ++++rv+e++e + f++++   + ++h++++++    
  gi|298675586|ref|YP_003727336.1|  37 DYRIIDANPAYESITGFKREEIAGQRASIVYNK-ENPPHLNIYARVAETGEKANFETYTP--QLRKHFNVSVISP-- 108
                                       89**************************88888.9**********************554..699999*999887.. PP

                             PAS_4  91 esGevigvlvisrDiTe 107
                                       e+G+   ++ i++DiT 
  gi|298675586|ref|YP_003727336.1| 109 EKGK---FITILTDITS 122
                                       6788...9999999996 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 2.7e-06
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlae 42 
                                       +++p++l ++d+d r+l +N++a+  +g + eel+G++  e
  gi|298675586|ref|YP_003727336.1| 135 ENVPVVLMMVDSDRRILKLNKNAELFAGKSSEELVGSRGGE 175
                                       899*********************************98766 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.22
                             PAS_4  94 evigvlvisrDiTerrr 110
                                       +   vlv ++DiTer++
  gi|298675586|ref|YP_003727336.1| 246 K-SKVLVSIQDITERKE 261
                                       4.689**********85 PP

  == domain 4  score: 19.5 bits;  conditional E-value: 5.9e-07
                             PAS_4   3 slpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pgee 78 
                                       +  da+++ d dg+++yaN++a + +g+p++e+l   + ++ p  d + +++ +    +++++++  +++++ +g  
  gi|298675586|ref|YP_003727336.1| 279 KAADAIIAHDFDGNIIYANETASKNLGYPRDEILSLNVTDIDPYVDIDVFRDKYWNKTSSDTSYFIGTYHKRkDGTI 355
                                       567999999********************************9999********9999******************** PP

                             PAS_4  79 rhyelrllPlrdesGevigvlvisrDiTerrr 110
                                        ++e+rl+++ + + +   +l+++rDiT r++
  gi|298675586|ref|YP_003727336.1| 356 FPVEVRLTRI-NLNEK-PVILAYIRDITIRKQ 385
                                       **********.54555.8999*******9985 PP

  == domain 5  score: 0.4 bits;  conditional E-value: 0.5
                             PAS_4  49 aarleralrrvlegeepiefleelll 74 
                                        +r+ ++ ++v+e+e+  + + +++ 
  gi|298675586|ref|YP_003727336.1| 387 EERIKEQKEQVIETERIRQLELHHRI 412
                                       58999999******877777776654 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   1.5e-08   2.2e-05       4      48 ..      12      66 ..      10      86 .. 0.76
   2 !   17.2   0.0   2.6e-06    0.0039       3      53 ..     130     181 ..     129     191 .. 0.80
   3 !   22.3   0.0   6.5e-08   9.6e-05       1      46 [.     271     317 ..     271     335 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.5e-08
                             PAS_8  4 ralfesspdgiav...vdlgd......rivdvNqaalellGys.adlkgellgql 48
                                       +++es+ dg+++   +++++      ri+d+N+a++ ++G++ +++ g+   ++
  gi|298675586|ref|YP_003727336.1| 12 NSVYESVGDGVCInevIYNDNdhpvdyRIIDANPAYESITGFKrEEIAGQRASIV 66
                                      6899********9888443334688889*************88888888776544 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 2.6e-06
                             PAS_8   3 lralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpvlr 53 
                                       l++++e++p+ +++vd ++ri+  N+ a+ + G s ++l g+  g+ l  l+
  gi|298675586|ref|YP_003727336.1| 130 LETVYENVPVVLMMVDSDRRILKLNKNAELFAGKSsEELVGSRGGEALGCLH 181
                                       789*************9999*************6666666666665555554 PP

  == domain 3  score: 22.3 bits;  conditional E-value: 6.5e-08
                             PAS_8   1 erlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellg 46 
                                       er+r+l e ++d+i+  d +g+ i+++N++a + lGy+ ++++   + 
  gi|298675586|ref|YP_003727336.1| 271 ERFRTLTEKAADAIIAHDfDGN-IIYANETASKNLGYPrDEILSLNVT 317
                                       7**************9999999.***************8888776653 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.2   6.2e-12   9.2e-09       5     107 ..     505     595 ..     502     597 .. 0.78

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 6.2e-12
                                       HHHHHHHHHHHHHHHH...HSTTTEEEEEEEEEE..TEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSH CS
                         HATPase_c   5 rLrqiisnlvdNavkf...atkageieveikase..ddlvisveDnGiGipkedlkklfekfsqddstkrggggtGl 76 
                                        L  +i+++++N++k+   ++++g+ie+++ +++  +++++ v DnG+G+p++      +  +             l
  gi|298675586|ref|YP_003727336.1| 505 PLGMLINEILSNSLKYafsESETGKIEIKLYQNNnnKNYTLIVADNGKGMPENVDV---KDAD------------TL 566
                                       57789***********5544477777777776325579*************94433...2444............59 PP

                                       HHHHHHHHHHHTTTEEEEEEETTTEEEEEEE CS
                         HATPase_c  77 GlsivkklvelmgGeiwvesepgrGttftft 107
                                       Gl + k+l++++gG+++v++e+  Gt+f+++
  gi|298675586|ref|YP_003727336.1| 567 GLQLIKNLIDQIGGDFEVNKEK--GTKFIIE 595
                                       **********9*******6666..***9986 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0011       1.7       1      54 [.      40      90 ..      40      99 .. 0.84
   2 ?   -2.0   0.0       3.1   4.7e+03       3      31 ..     152     181 ..     150     186 .. 0.75
   3 !   18.6   0.0   1.2e-06    0.0018       1      83 [.     293     372 ..     293     377 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0011
                             PAS_3  1 iiyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyeg 54
                                      ii +++++e i+G+ +ee+ g+    +++v+  + +   + +++++++ge+ ++
  gi|298675586|ref|YP_003727336.1| 40 IIDANPAYESITGFKREEIAGQ---RASIVYNKENPPHLNIYARVAETGEKANF 90
                                      5899*****************9...77888888888888888888888886555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.1
                             PAS_3   3 yvserveeilGyspeellgk.veswldlvh 31 
                                        ++++ e   G s+eel g+   + l ++h
  gi|298675586|ref|YP_003727336.1| 152 KLNKNAELFAGKSSEELVGSrGGEALGCLH 181
                                       67888899999999**99986666666666 PP

  == domain 3  score: 18.6 bits;  conditional E-value: 1.2e-06
                             PAS_3   1 iiyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvird 77 
                                       iiy++e+ ++ lGy ++e+l+   ++ d+    D++ +r+++++  +++++y +    +rkdG+++ ve r + i +
  gi|298675586|ref|YP_003727336.1| 293 IIYANETASKNLGYPRDEILSL--NVTDIDPYVDIDVFRDKYWNKTSSDTSYFIGTYHKRKDGTIFPVEVRLTRI-N 366
                                       69********************..**************************88555449*************9999.7 PP

                             PAS_3  78 engkpv 83 
                                        n kpv
  gi|298675586|ref|YP_003727336.1| 367 LNEKPV 372
                                       777776 PP

>> HWE_HK  HWE histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       6.2   9.3e+03      13      41 ..     250     276 ..     244     287 .. 0.58
   2 !   24.2   0.1   2.7e-08     4e-05       1      52 [.     407     460 ..     407     477 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 6.2
                                       HHHHHHHHSSSXS-HHHHHHHHHHHHHHH CS
                            HWE_HK  13 vqsiarqtlrsaesleefaeklsgRLqAL 41 
                                       + si  +t r+++  e+  ++ ++R ++L
  gi|298675586|ref|YP_003727336.1| 250 LVSIQDITERKET--EKELKESEERFRTL 276
                                       5566667755333..33334445555555 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 2.7e-08
                                       HHHHHHHHHHHHHHHHHHHHSSS..XS-HHHHHHHHHHHHHHHHHHHHHHHHCT CS
                            HWE_HK   1 ElnHRvKNlLavvqsiarqtlrs..aesleefaeklsgRLqALsaahdllsree 52 
                                       El+HR+KN L v++s+ +  +++   ++++++  + ++R+ ++s +h+ l +++
  gi|298675586|ref|YP_003727336.1| 407 ELHHRIKNNLQVISSLLSLQSEKftDDNVKDAFIDTQNRVISMSLVHNKLYQAK 460
                                       9***************9987664113455667777789**********998876 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   6.1e-07   0.00091      32     120 ..     506     591 ..     493     596 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 6.1e-07
                       HATPase_c_2  32 irlaveEactNavehayleapegpvevrlesdeea..ltvevaDsGpgfdpetlpdpteeepkeslkegGrGlalik 106
                                       + + ++E+++N  ++a  e ++g++e++l ++++    t+ vaD+G+g +             + ++   +Gl lik
  gi|298675586|ref|YP_003727336.1| 506 LGMLINEILSNSLKYAFSESETGKIEIKLYQNNNNknYTLIVADNGKGMPENV----------DVKDADTLGLQLIK 572
                                       66789***********************8777766679**********66643..........33445569****** PP

                       HATPase_c_2 107 glvDev....ey.dgegnv 120
                                       +l D++    e+ +++g++
  gi|298675586|ref|YP_003727336.1| 573 NLIDQIggdfEVnKEKGTK 591
                                       ****997744446666666 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.2   3.2e-06    0.0047       8      53 ..     511     563 ..     508     572 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.2e-06
                       HATPase_c_3   8 aelvdNsld...Adaen....vkievnknr.gktgeivieDdGkGmsee.elkna 53 
                                        e++ Nsl    +  e+    ++i++ +n+ +k+ ++ + D+GkGm+e+ ++k+a
  gi|298675586|ref|YP_003727336.1| 511 NEILSNSLKyafS--ESetgkIEIKLYQNNnNKNYTLIVADNGKGMPENvDVKDA 563
                                       5899999998442..3344556666655543678999**********99888764 PP

>> PAS_12  UPF0242 C-terminal PAS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.023        34      66      97 ..      37      68 ..      27      99 .. 0.85
   2 ?    0.7   0.0      0.24   3.6e+02      54      88 ..     135     169 ..     125     173 .. 0.88
   3 !    6.5   0.0    0.0041       6.1      54      89 ..     278     313 ..     260     325 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.023
                            PAS_12 66 enkllfaNaqirallGwssdkflqdfseivqe 97
                                      + +++ aN   ++++G+  +++  + ++iv +
  gi|298675586|ref|YP_003727336.1| 37 DYRIIDANPAYESITGFKREEIAGQRASIVYN 68
                                      679999*****************999999976 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.24
                            PAS_12  54 EnlgailvysqkenkllfaNaqirallGwssdkfl 88 
                                       En  ++l+    ++++l  N++ + + G ss++++
  gi|298675586|ref|YP_003727336.1| 135 ENVPVVLMMVDSDRRILKLNKNAELFAGKSSEELV 169
                                       8899999999********************99987 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0041
                            PAS_12  54 EnlgailvysqkenkllfaNaqirallGwssdkflq 89 
                                       E+++  ++   ++  +++aN+   + lG+  d++l+
  gi|298675586|ref|YP_003727336.1| 278 EKAADAIIAHDFDGNIIYANETASKNLGYPRDEILS 313
                                       66666777788999******************9986 PP

>> SPOB_a  Sensor_kinase_SpoOB-type, alpha-helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       1.5   2.2e+03      41      59 ..     385     403 ..     372     406 .. 0.79
   2 ?    9.1   2.2   0.00071       1.1      19      42 ..     408     431 ..     385     450 .. 0.78
   3 ?   -2.7   0.0       3.5   5.2e+03      43      56 ..     468     481 ..     466     486 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.5
                            SPOB_a  41 kaeeyieevvkelkeeski 59 
                                       +aee i+e  +++ e+++i
  gi|298675586|ref|YP_003727336.1| 385 QAEERIKEQKEQVIETERI 403
                                       7888888888888888876 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00071
                            SPOB_a  19 qRHDflNhLQvIsGylqLgkydka 42 
                                       ++H   N+LQvIs++l L+     
  gi|298675586|ref|YP_003727336.1| 408 LHHRIKNNLQVISSLLSLQSEKFT 431
                                       579999***********9876555 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 3.5
                            SPOB_a  43 eeyieevvkelkee 56 
                                       ++yi ++v++l+e 
  gi|298675586|ref|YP_003727336.1| 468 KDYIGDIVDHLNEL 481
                                       78999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (598 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1130  (0.0630264); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 4232.01
//
Query:       gi|298675587|ref|YP_003727337.1|  [L=104]
Description: hypothetical protein Metev_1702 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 811.81
//
Query:       gi|298675588|ref|YP_003727338.1|  [L=929]
Description: PBS lyase HEAT domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   2.5e-136  444.4  34.0    8.1e-19   67.8   1.1   12.8 12  HEAT_2         HEAT repeats
    2.5e-88  281.8   4.9    2.8e-06   27.5   0.2   23.9 24  HEAT_PBS       PBS lyase HEAT-like repeat
    5.5e-76  243.9   1.4    0.00027   21.0   0.0   20.9 21  HEAT           HEAT repeat
    2.9e-49  165.0  18.5      0.035   14.6   0.0   21.2 22  HEAT_EZ        HEAT-like repeat
    2.8e-34  116.1   8.0      0.062   13.4   0.0   19.6 22  Arm            Armadillo/beta-catenin-like repeat
    4.4e-29  101.6  25.6    0.00032   20.8   0.0   12.5 12  Cnd1           non-SMC mitotic condensation complex subunit 1
    3.1e-14   52.5  25.1     0.0034   16.0   3.8    8.6  6  Adaptin_N      Adaptin N terminal region
    1.5e-10   41.4  17.9        3.2    7.8   0.0   11.3 12  Aconitase_B_N  Aconitate B N-terminal domain
    1.3e-09   38.5   3.1         42    4.8   0.0   10.1  9  Vac14_Fab1_bd  Vacuolar 14 Fab1-binding region
    3.2e-08   33.5  12.9       0.18   11.3   0.2    6.9  7  ERAP1_C        ERAP1-like C-terminal domain
    7.7e-06   26.0   1.6         24    5.2   0.0    8.8 11  BRCC36_C       BRCC36 C-terminal helical domain
    6.4e-05   22.9   0.0         25    4.7   0.1    5.8  4  DUF3385        Domain of unknown function (DUF3385)
    0.00055   19.6   6.4        0.5    9.9   0.0    6.7  6  CLASP_N        CLASP N terminal
     0.0033   17.2   0.7          3    7.7   0.0    6.0  7  RICTOR_M       Rapamycin-insensitive companion of mTOR, middl
  ------ inclusion threshold ------
       0.05   13.5   1.0        5.3    7.0   0.0    5.0  6  IBN_N          Importin-beta N-terminal domain
       0.26   11.4   3.3        1.6    8.9   0.3    3.4  3  SGS            SGS domain
       0.27   11.7   1.9    1.1e+02    3.3   0.1    4.5  4  DUF2274        Protein of unknown function (DUF2274)
       0.42    9.8  16.1          6    6.1   0.0    6.2  7  V-ATPase_H_N   V-ATPase subunit H
       0.43   11.1  35.4        1.1    9.8   0.2    9.7 11  DUF1829        Domain of unknown function DUF1829
       0.67   10.4  12.5         17    6.0   0.3    7.2  7  GlutR_dimer    Glutamyl-tRNAGlu reductase, dimerisation domai


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.0   8.4e-14   7.5e-11       2      68 ..      80     146 ..      79     148 .. 0.95
   2 !   61.0   1.4   1.2e-19   1.1e-16       4      87 ..     144     227 ..     141     227 .. 0.96
   3 !   67.8   1.1     9e-22   8.1e-19       2      85 ..     205     289 ..     204     292 .. 0.96
   4 !   51.8   0.9   9.1e-17   8.2e-14       1      82 [.     300     380 ..     300     390 .. 0.90
   5 !   37.7   0.1   2.3e-12     2e-09       1      77 [.     392     468 ..     392     475 .. 0.87
   6 ?    6.7   0.0      0.01       9.4      54      76 ..     477     499 ..     474     509 .. 0.84
   7 !   64.9   0.1   7.3e-21   6.5e-18       2      88 .]     578     663 ..     576     663 .. 0.98
   8 !   50.7   0.4   1.9e-16   1.7e-13      12      88 .]     618     696 ..     617     696 .. 0.94
   9 !   52.4   0.1     6e-17   5.3e-14       6      88 .]     676     759 ..     673     759 .. 0.92
  10 !   48.8   0.1     8e-16   7.2e-13       8      71 ..     742     805 ..     741     806 .. 0.97
  11 !   56.1   0.0   3.9e-18   3.5e-15       2      87 ..     799     881 ..     798     882 .. 0.95
  12 !   17.7   0.0   3.9e-06    0.0035       2      72 ..     860     926 ..     859     929 .] 0.85

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 8.4e-14
                            HEAT_2   2 daLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLk 68 
                                       d L++ l n++++++r++a+++Lg+++ + a++ L+++ ede+ +v  aaa++Lg+ig+p++ ++L+
  gi|298675588|ref|YP_003727338.1|  80 DSLIKDLLNSSNEDTRIKAAKSLGEKRGQNAIDSLIKAFEDESVYVKIAAANSLGKIGNPATGDLLE 146
                                       78999999****************************************************9887775 PP

  == domain 2  score: 61.0 bits;  conditional E-value: 1.2e-19
                            HEAT_2   4 LlqalendpdpevrraairaLgrignpealpaLvell.ededpavRraaaeaLgaigdpealpaLkellddddddvv 79 
                                       Ll++l ++ +++vr+  ++aLg+i+n+ + + L ++l +d++++vR+ aa+aLg igd++a++ L ++l++d+d++v
  gi|298675588|ref|YP_003727338.1| 144 LLEVL-DSQNEDVRKYSVKALGNIRNENTADELSDVLlNDKSSDVRESAAKALGDIGDKRAAEPLIDALLNDTDEDV 219
                                       89999.9****************************777*************************************** PP

                            HEAT_2  80 ReaAaeaL 87 
                                       R +++ aL
  gi|298675588|ref|YP_003727338.1| 220 RSKSVVAL 227
                                       *9998876 PP

  == domain 3  score: 67.8 bits;  conditional E-value: 9e-22
                            HEAT_2   2 daLlqalendpdpevrraairaLgrignpealpaLvell.ededpavRraaaeaLgaigdpealpaLkelldddddd 77 
                                       ++L+ al nd d++vr + + aLg+i+n+ +++ L ++l +de+++vR+ aa+aLg igd++a++ L  +l++d+dd
  gi|298675588|ref|YP_003727338.1| 205 EPLIDALLNDTDEDVRSKSVVALGKIKNENVVKPLSNALlNDESSDVRESAAKALGDIGDKRAAEPLINALLNDTDD 281
                                       79***********************************887************************************* PP

                            HEAT_2  78 vvReaAae 85 
                                       +vR +++e
  gi|298675588|ref|YP_003727338.1| 282 DVRYQVVE 289
                                       ***99887 PP

  == domain 4  score: 51.8 bits;  conditional E-value: 9.1e-17
                            HEAT_2   1 ldaLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkelldddddd 77 
                                       +d+L+++l nd d +vr  a+++Lg+i +++a + Lv++l+d++++vR++ a+a+ +ig+p++ p+  e ld+ ++ 
  gi|298675588|ref|YP_003727338.1| 300 VDPLVKILLNDRDVDVRSSAAEVLGDIEDEKAAEPLVKALNDDSEEVRENSADAILEIGEPATSPLVNE-LDNRNKN 375
                                       689**********************************************************66666555.8888877 PP

                            HEAT_2  78 vvRea 82 
                                       vv +a
  gi|298675588|ref|YP_003727338.1| 376 VVNTA 380
                                       77655 PP

  == domain 5  score: 37.7 bits;  conditional E-value: 2.3e-12
                            HEAT_2   1 ldaLlqalendpdpevrraairaLgrignpealpaLvelleded.pavRraaaeaLgaigdpealpaLkellddddd 76 
                                       +d+L+q l+n+ +++ +++a++ Lg+i+n++ ++ L++ l++e+ ++v   +a+aL+ ig p a++ L + l++ dd
  gi|298675588|ref|YP_003727338.1| 392 VDPLIQTLSNSNSDNAKIKAADILGKIRNESNIKPLIKTLNNENsRDVKLSVADALVNIGKP-AVDPLIKTLNNNDD 467
                                       689*************************************8888579***************.66666666665555 PP

                            HEAT_2  77 d 77 
                                        
  gi|298675588|ref|YP_003727338.1| 468 K 468
                                       3 PP

  == domain 6  score: 6.7 bits;  conditional E-value: 0.01
                            HEAT_2  54 aLgaigdpealpaLkellddddd 76 
                                       aL++igd++a+++L+++l+ ++ 
  gi|298675588|ref|YP_003727338.1| 477 ALVQIGDEKAIESLTRSLNKEKT 499
                                       89***************987764 PP

  == domain 7  score: 64.9 bits;  conditional E-value: 7.3e-21
                            HEAT_2   2 daLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkellddddddv 78 
                                       ++L++al +d+  +vr+ ai+aL++ign+++++ + e++  ++p++R++aa aLg+igd +a ++L +++++d+ + 
  gi|298675588|ref|YP_003727338.1| 578 EKLVKAL-KDEKGYVRISAIMALAEIGNDKTVKPIAEVMFKDNPEIRATAAYALGEIGDIDAEKHLIRAMLHDEYEN 653
                                       589****.9******************************************************************** PP

                            HEAT_2  79 vReaAaeaLa 88 
                                       v+  Aa aL+
  gi|298675588|ref|YP_003727338.1| 654 VKSNAALALG 663
                                       ********96 PP

  == domain 8  score: 50.7 bits;  conditional E-value: 1.9e-16
                            HEAT_2  12 pdpevrraairaLgrignpealpaLvell.ededpavRraaaeaLgaigdpealpaLkellddddd.dvvReaAaea 86 
                                        +pe+r++a+ aLg+ig+ +a + L++++  de ++v  +aa aLg+igd+e++  L++ l+d ++ d vR +Aa a
  gi|298675588|ref|YP_003727338.1| 618 DNPEIRATAAYALGEIGDIDAEKHLIRAMlHDEYENVKSNAALALGKIGDDETAHYLTRVLTDGEEkDQVRSSAALA 694
                                       589************************9989999***************************998755********** PP

                            HEAT_2  87 La 88 
                                       L+
  gi|298675588|ref|YP_003727338.1| 695 LG 696
                                       96 PP

  == domain 9  score: 52.4 bits;  conditional E-value: 6e-17
                            HEAT_2   6 qalen.dpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkellddddddvvRe 81 
                                        +l++  + ++vr  a+ aLg+i++ +++  L++ +++e+ + R+  a aLg+igd++a+++L  ll+++d+++v++
  gi|298675588|ref|YP_003727338.1| 676 RVLTDgEEKDQVRSSAALALGKIKESSSVSPLLKTVNHENKEMRHYSALALGKIGDERAVKSLIILLQNEDNREVKN 752
                                       55644356668****************************************************************** PP

                            HEAT_2  82 aAaeaLa 88 
                                        A+ aL+
  gi|298675588|ref|YP_003727338.1| 753 GAIYALG 759
                                       ***9996 PP

  == domain 10  score: 48.8 bits;  conditional E-value: 8e-16
                            HEAT_2   8 lendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkell 71 
                                       l+n  + ev+  ai aLg+i+n++a++ L+e+l+d+++ +R++a+ aLg+i ++++++ L ++l
  gi|298675588|ref|YP_003727338.1| 742 LQNEDNREVKNGAIYALGEIRNEKAVEPLIECLDDANSKIRKNAVIALGKINSDKTVSPLIQRL 805
                                       88999********************************************************998 PP

  == domain 11  score: 56.1 bits;  conditional E-value: 3.9e-18
                            HEAT_2   2 daLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkellddddddv 78 
                                       ++L+q+l nd dpe+r+  ++ Lg+ig+++a+  L++ l+d++ +vR+a  +aL++ig p a++ L  +ld+ ++++
  gi|298675588|ref|YP_003727338.1| 799 SPLIQRL-NDNDPEIRKYSAIILGKIGDKKAVHPLINTLDDSNKDVRKATTNALAKIGKP-AVQPLINSLDS-RNPD 872
                                       69*****.****************************************************.99*****9975.7777 PP

                            HEAT_2  79 vReaAaeaL 87 
                                       v+e A+ aL
  gi|298675588|ref|YP_003727338.1| 873 VKEHATNAL 881
                                       8****9998 PP

  == domain 12  score: 17.7 bits;  conditional E-value: 3.9e-06
                            HEAT_2   2 daLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkelld 72 
                                       ++L++ l ++ +p+v+ +a  aL +ig+p +++ L+++l  ++  + + a   L +igd++a++ L ++++
  gi|298675588|ref|YP_003727338.1| 860 QPLINSL-DSRNPDVKEHATNALIKIGEP-CVQPLIKAL--DNDKIKKPATIVLIEIGDKKAIEPLIDAYN 926
                                       6899999.999999999999999999998.788888888..688899999999999999999999998765 PP

>> HEAT_PBS  PBS lyase HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00088      0.79       2      27 .]      95     120 ..      94     120 .. 0.94
   2 !    8.6   0.0    0.0038       3.4       1      21 [.     125     145 ..     125     150 .. 0.82
   3 !    8.2   0.0    0.0051       4.5       1      25 [.     155     179 ..     155     181 .. 0.89
   4 !   26.6   0.2   5.8e-09   5.2e-06       1      26 [.     187     212 ..     187     213 .. 0.96
   5 ?    4.5   0.0     0.078        70       1      26 [.     219     244 ..     219     245 .. 0.92
   6 !   27.5   0.2   3.1e-09   2.8e-06       1      26 [.     251     276 ..     251     277 .. 0.96
   7 ?    6.7   0.0     0.016        14       1      25 [.     283     307 ..     283     309 .. 0.93
   8 !   18.6   0.0   2.3e-06    0.0021       1      27 []     315     341 ..     315     341 .. 0.98
   9 ?   -0.3   0.0       2.8   2.5e+03       9      25 ..     384     399 ..     382     401 .. 0.83
  10 ?    2.1   0.0      0.46   4.2e+02       4      26 ..     410     432 ..     407     433 .. 0.85
  11 ?    4.7   0.0     0.068        61       2      26 ..     440     463 ..     439     464 .. 0.86
  12 ?    4.9   0.0      0.06        54       8      25 ..     477     494 ..     476     496 .. 0.89
  13 ?   -0.4   0.0         3   2.7e+03      12      27 .]     571     586 ..     534     586 .. 0.82
  14 ?    6.1   0.0     0.024        21       1      21 [.     591     611 ..     591     615 .. 0.80
  15 !   12.7   0.2   0.00018      0.16       1      25 [.     622     646 ..     622     648 .. 0.89
  16 !   12.9   0.0   0.00016      0.14       1      27 []     654     680 ..     654     680 .. 0.91
  17 !   11.0   0.0   0.00064      0.57       1      23 [.     687     709 ..     687     713 .. 0.93
  18 !   15.4   0.0   2.4e-05     0.022       2      26 ..     719     743 ..     718     744 .. 0.93
  19 !   20.4   0.0   5.8e-07   0.00052       5      27 .]     754     776 ..     750     776 .. 0.94
  20 !   11.3   0.0   0.00052      0.47       2      27 .]     782     807 ..     781     807 .. 0.94
  21 !   12.7   0.0   0.00018      0.16       2      27 .]     813     838 ..     812     838 .. 0.93
  22 !    8.4   0.0    0.0045         4       1      26 [.     843     867 ..     843     868 .. 0.93
  23 !    9.3   0.0    0.0023       2.1       3      27 .]     875     898 ..     873     898 .. 0.90
  24 ?    6.9   0.0     0.014        12       5      24 ..     905     924 ..     905     926 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00088
                                       HHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   2 RraAakaLgqlgdeeaipaLleaLqd 27 
                                       R  Aak+Lg+ + + ai+ L++a +d
  gi|298675588|ref|YP_003727338.1|  95 RIKAAKSLGEKRGQNAIDSLIKAFED 120
                                       789********************987 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0038
                                       HHHHHHHHHHHCTSGGGHHHH CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaL 21 
                                       v  aAa +Lg++g ++  ++L
  gi|298675588|ref|YP_003727338.1| 125 VKIAAANSLGKIGNPATGDLL 145
                                       678***********7777766 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0051
                                       HHHHHHHHHHHCTSGGGHHHHHHHC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaL 25 
                                       vR + +kaLg+++ e  ++ L  +L
  gi|298675588|ref|YP_003727338.1| 155 VRKYSVKALGNIRNENTADELSDVL 179
                                       899***********99999998877 PP

  == domain 4  score: 26.6 bits;  conditional E-value: 5.8e-09
                                       HHHHHHHHHHHCTSGGGHHHHHHHCT CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLq 26 
                                       vR +AakaLg +gd++a+++L+ aL 
  gi|298675588|ref|YP_003727338.1| 187 VRESAAKALGDIGDKRAAEPLIDALL 212
                                       9***********************96 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.078
                                       HHHHHHHHHHHCTSGGGHHHHHHHCT CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLq 26 
                                       vR   + aLg+++ e ++ +L +aL 
  gi|298675588|ref|YP_003727338.1| 219 VRSKSVVALGKIKNENVVKPLSNALL 244
                                       8999999**************99996 PP

  == domain 6  score: 27.5 bits;  conditional E-value: 3.1e-09
                                       HHHHHHHHHHHCTSGGGHHHHHHHCT CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLq 26 
                                       vR +AakaLg +gd++a+++L++aL 
  gi|298675588|ref|YP_003727338.1| 251 VRESAAKALGDIGDKRAAEPLINALL 276
                                       9***********************96 PP

  == domain 7  score: 6.7 bits;  conditional E-value: 0.016
                                       HHHHHHHHHHHCTSGGGHHHHHHHC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaL 25 
                                       vR+  ++   +++d+ a+++L++ L
  gi|298675588|ref|YP_003727338.1| 283 VRYQVVEVFSEIKDKNAVDPLVKIL 307
                                       8********************9988 PP

  == domain 8  score: 18.6 bits;  conditional E-value: 2.3e-06
                                       HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                       vR +Aa+ Lg + de a+++L++aL+d
  gi|298675588|ref|YP_003727338.1| 315 VRSSAAEVLGDIEDEKAAEPLVKALND 341
                                       9************************98 PP

  == domain 9  score: -0.3 bits;  conditional E-value: 2.8
                                       HHHCTSGGGHHHHHHHC CS
                          HEAT_PBS   9 LgqlgdeeaipaLleaL 25 
                                       L ++gd  ++++L++ L
  gi|298675588|ref|YP_003727338.1| 384 LVEIGD-PSVDPLIQTL 399
                                       668999.9999999977 PP

  == domain 10  score: 2.1 bits;  conditional E-value: 0.46
                                       HHHHHHHHCTSGGGHHHHHHHCT CS
                          HEAT_PBS   4 aAakaLgqlgdeeaipaLleaLq 26 
                                        Aa  Lg+++ e  i +L++ L+
  gi|298675588|ref|YP_003727338.1| 410 KAADILGKIRNESNIKPLIKTLN 432
                                       599********999999998765 PP

  == domain 11  score: 4.7 bits;  conditional E-value: 0.068
                                       HHHHHHHHHHCTSGGGHHHHHHHCT CS
                          HEAT_PBS   2 RraAakaLgqlgdeeaipaLleaLq 26 
                                         + a aL ++g   a+++L++ L+
  gi|298675588|ref|YP_003727338.1| 440 KLSVADALVNIGK-PAVDPLIKTLN 463
                                       567899*******.******99776 PP

  == domain 12  score: 4.9 bits;  conditional E-value: 0.06
                                       HHHHCTSGGGHHHHHHHC CS
                          HEAT_PBS   8 aLgqlgdeeaipaLleaL 25 
                                       aL q+gde ai+ L + L
  gi|298675588|ref|YP_003727338.1| 477 ALVQIGDEKAIESLTRSL 494
                                       99************9877 PP

  == domain 13  score: -0.4 bits;  conditional E-value: 3
                                       CTSGGGHHHHHHHCTC CS
                          HEAT_PBS  12 lgdeeaipaLleaLqd 27 
                                       ++++ a + L++aL+d
  gi|298675588|ref|YP_003727338.1| 571 INSKNAQEKLVKALKD 586
                                       4558899999999997 PP

  == domain 14  score: 6.1 bits;  conditional E-value: 0.024
                                       HHHHHHHHHHHCTSGGGHHHH CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaL 21 
                                       vR +A+ aL+++g +  + ++
  gi|298675588|ref|YP_003727338.1| 591 VRISAIMALAEIGNDKTVKPI 611
                                       8************96666555 PP

  == domain 15  score: 12.7 bits;  conditional E-value: 0.00018
                                       HHHHHHHHHHHCTSGGGHHHHHHHC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaL 25 
                                       +R+ Aa+aLg++gd +a  +L++a 
  gi|298675588|ref|YP_003727338.1| 622 IRATAAYALGEIGDIDAEKHLIRAM 646
                                       5999**********99999999986 PP

  == domain 16  score: 12.9 bits;  conditional E-value: 0.00016
                                       HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                       v  +Aa aLg++gd+e +  L ++L d
  gi|298675588|ref|YP_003727338.1| 654 VKSNAALALGKIGDDETAHYLTRVLTD 680
                                       6679*****************999976 PP

  == domain 17  score: 11.0 bits;  conditional E-value: 0.00064
                                       HHHHHHHHHHHCTSGGGHHHHHH CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLle 23 
                                       vR +Aa aLg+++   ++ +Ll+
  gi|298675588|ref|YP_003727338.1| 687 VRSSAALALGKIKESSSVSPLLK 709
                                       9****************999986 PP

  == domain 18  score: 15.4 bits;  conditional E-value: 2.4e-05
                                       HHHHHHHHHHCTSGGGHHHHHHHCT CS
                          HEAT_PBS   2 RraAakaLgqlgdeeaipaLleaLq 26 
                                       R++ a aLg++gde+a+  L+ +Lq
  gi|298675588|ref|YP_003727338.1| 719 RHYSALALGKIGDERAVKSLIILLQ 743
                                       9*****************9999988 PP

  == domain 19  score: 20.4 bits;  conditional E-value: 5.8e-07
                                       HHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   5 AakaLgqlgdeeaipaLleaLqd 27 
                                       A++aLg+++ e a+++L+e+L+d
  gi|298675588|ref|YP_003727338.1| 754 AIYALGEIRNEKAVEPLIECLDD 776
                                       9********************98 PP

  == domain 20  score: 11.3 bits;  conditional E-value: 0.00052
                                       HHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   2 RraAakaLgqlgdeeaipaLleaLqd 27 
                                       R +A+ aLg+++++  + +L++ L+d
  gi|298675588|ref|YP_003727338.1| 782 RKNAVIALGKINSDKTVSPLIQRLND 807
                                       899*******************9987 PP

  == domain 21  score: 12.7 bits;  conditional E-value: 0.00018
                                       HHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   2 RraAakaLgqlgdeeaipaLleaLqd 27 
                                       R + a  Lg++gd+ a+ +L++ L+d
  gi|298675588|ref|YP_003727338.1| 813 RKYSAIILGKIGDKKAVHPLINTLDD 838
                                       8899******************9997 PP

  == domain 22  score: 8.4 bits;  conditional E-value: 0.0045
                                       HHHHHHHHHHHCTSGGGHHHHHHHCT CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLq 26 
                                       vR a + aL+++g   a+++L++ L+
  gi|298675588|ref|YP_003727338.1| 843 VRKATTNALAKIGK-PAVQPLINSLD 867
                                       89999*********.*******9987 PP

  == domain 23  score: 9.3 bits;  conditional E-value: 0.0023
                                       HHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   3 raAakaLgqlgdeeaipaLleaLqd 27 
                                         A+ aL ++g   ++++L++aL++
  gi|298675588|ref|YP_003727338.1| 875 EHATNALIKIGE-PCVQPLIKALDN 898
                                       6699********.**********86 PP

  == domain 24  score: 6.9 bits;  conditional E-value: 0.014
                                       HHHHHHHCTSGGGHHHHHHH CS
                          HEAT_PBS   5 AakaLgqlgdeeaipaLlea 24 
                                       A+  L ++gd+ ai++L+ a
  gi|298675588|ref|YP_003727338.1| 905 ATIVLIEIGDKKAIEPLIDA 924
                                       677899************98 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.022        20       4      26 ..      82     104 ..      81     104 .. 0.89
   2 !   10.5   0.0    0.0007      0.63       3      27 ..     112     136 ..     110     138 .. 0.91
   3 !    8.9   0.0    0.0023         2       5      27 ..     144     166 ..     143     166 .. 0.92
   4 !   19.6   0.0   8.3e-07   0.00074       8      28 ..     179     199 ..     177     201 .. 0.92
   5 !   12.5   0.0   0.00016      0.14       3      27 ..     206     230 ..     206     231 .. 0.94
   6 !   21.0   0.0     3e-07   0.00027       8      28 ..     243     263 ..     235     265 .. 0.84
   7 !   10.9   0.0   0.00052      0.47       3      27 ..     270     294 ..     269     296 .. 0.86
   8 !   13.8   0.0   6.1e-05     0.055       3      27 ..     302     326 ..     300     327 .. 0.87
   9 !   15.1   0.0   2.2e-05      0.02       4      28 ..     334     358 ..     333     359 .. 0.90
  10 ?   -0.2   0.0       1.9   1.7e+03       3      27 ..     394     418 ..     394     418 .. 0.88
  11 ?    3.6   0.0      0.11     1e+02       4      28 ..     426     451 ..     424     452 .. 0.81
  12 !    8.7   0.0    0.0026       2.3       5      27 ..     580     602 ..     577     605 .. 0.92
  13 !   10.2   0.0   0.00085      0.76      12      28 ..     618     634 ..     610     636 .. 0.89
  14 !   13.1   0.0    0.0001     0.092       4      28 ..     642     666 ..     641     668 .. 0.89
  15 !    7.8   0.0    0.0052       4.6       9      27 ..     678     698 ..     672     702 .. 0.78
  16 ?    5.8   0.0     0.023        20       4      28 ..     706     730 ..     704     732 .. 0.90
  17 ?    0.1   0.0       1.5   1.3e+03       5      27 ..     738     761 ..     735     761 .. 0.75
  18 !   16.0   0.0   1.1e-05      0.01       3      27 ..     768     792 ..     766     795 .. 0.92
  19 !   13.3   0.0   8.4e-05     0.075       4      28 ..     800     824 ..     798     826 .. 0.85
  20 !   10.9   0.0   0.00051      0.46       4      28 ..     831     855 ..     829     856 .. 0.89
  21 ?    4.5   0.0     0.057        51       3      29 ..     860     886 ..     858     888 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.022
                                       HHHHHHT-SSHHHHHHHHHHHHH CS
                              HEAT   4 lllkllsDpspeVReaAakaLga 26 
                                       l+  ll++++ + R  Aak+Lg+
  gi|298675588|ref|YP_003727338.1|  82 LIKDLLNSSNEDTRIKAAKSLGE 104
                                       566799***************96 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0007
                                       HHHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   3 PlllkllsDpspeVReaAakaLgal 27 
                                       + l+k+ +D+s  V  aAa++Lg++
  gi|298675588|ref|YP_003727338.1| 112 DSLIKAFEDESVYVKIAAANSLGKI 136
                                       6799*******************98 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0023
                                       HHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   5 llkllsDpspeVReaAakaLgal 27 
                                       ll+ l +++ +VR+ ++kaLg++
  gi|298675588|ref|YP_003727338.1| 144 LLEVLDSQNEDVRKYSVKALGNI 166
                                       6788999**************97 PP

  == domain 4  score: 19.6 bits;  conditional E-value: 8.3e-07
                                       HHT-SSHHHHHHHHHHHHHHH CS
                              HEAT   8 llsDpspeVReaAakaLgala 28 
                                       ll+D+s++VRe+AakaLg++ 
  gi|298675588|ref|YP_003727338.1| 179 LLNDKSSDVRESAAKALGDIG 199
                                       79*****************96 PP

  == domain 5  score: 12.5 bits;  conditional E-value: 0.00016
                                       HHHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   3 PlllkllsDpspeVReaAakaLgal 27 
                                       Pl+  ll+D++ +VR+ ++ aLg++
  gi|298675588|ref|YP_003727338.1| 206 PLIDALLNDTDEDVRSKSVVALGKI 230
                                       7889999****************87 PP

  == domain 6  score: 21.0 bits;  conditional E-value: 3e-07
                                       HHT-SSHHHHHHHHHHHHHHH CS
                              HEAT   8 llsDpspeVReaAakaLgala 28 
                                       ll+D+s++VRe+AakaLg++ 
  gi|298675588|ref|YP_003727338.1| 243 LLNDESSDVRESAAKALGDIG 263
                                       46*****************96 PP

  == domain 7  score: 10.9 bits;  conditional E-value: 0.00052
                                       HHHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   3 PlllkllsDpspeVReaAakaLgal 27 
                                       Pl+  ll+D++ +VR+ +++ + ++
  gi|298675588|ref|YP_003727338.1| 270 PLINALLNDTDDDVRYQVVEVFSEI 294
                                       5666778*************99887 PP

  == domain 8  score: 13.8 bits;  conditional E-value: 6.1e-05
                                       HHHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   3 PlllkllsDpspeVReaAakaLgal 27 
                                       Pl+  ll+D + +VR++Aa+ Lg++
  gi|298675588|ref|YP_003727338.1| 302 PLVKILLNDRDVDVRSSAAEVLGDI 326
                                       5555678****************98 PP

  == domain 9  score: 15.1 bits;  conditional E-value: 2.2e-05
                                       HHHHHHT-SSHHHHHHHHHHHHHHH CS
                              HEAT   4 lllkllsDpspeVReaAakaLgala 28 
                                       +l+k+l+D+s eVRe++a a+ ++ 
  gi|298675588|ref|YP_003727338.1| 334 PLVKALNDDSEEVRENSADAILEIG 358
                                       5899****************99886 PP

  == domain 10  score: -0.2 bits;  conditional E-value: 1.9
                                       HHHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   3 PlllkllsDpspeVReaAakaLgal 27 
                                       Pl+++l +++s +    Aa  Lg++
  gi|298675588|ref|YP_003727338.1| 394 PLIQTLSNSNSDNAKIKAADILGKI 418
                                       8999999999999999999999986 PP

  == domain 11  score: 3.6 bits;  conditional E-value: 0.11
                                       HHHHHHT-SSHH.HHHHHHHHHHHHH CS
                              HEAT   4 lllkllsDpspe.VReaAakaLgala 28 
                                       +l+k l+ ++++ V  ++a aL+++ 
  gi|298675588|ref|YP_003727338.1| 426 PLIKTLNNENSRdVKLSVADALVNIG 451
                                       5788897777777**********996 PP

  == domain 12  score: 8.7 bits;  conditional E-value: 0.0026
                                       HHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   5 llkllsDpspeVReaAakaLgal 27 
                                       l+k+l+D+   VR +A+ aL+++
  gi|298675588|ref|YP_003727338.1| 580 LVKALKDEKGYVRISAIMALAEI 602
                                       899******************98 PP

  == domain 13  score: 10.2 bits;  conditional E-value: 0.00085
                                       SSHHHHHHHHHHHHHHH CS
                              HEAT  12 pspeVReaAakaLgala 28 
                                       ++pe+R++Aa+aLg++ 
  gi|298675588|ref|YP_003727338.1| 618 DNPEIRATAAYALGEIG 634
                                       69*************96 PP

  == domain 14  score: 13.1 bits;  conditional E-value: 0.0001
                                       HHHHHHT-SSHHHHHHHHHHHHHHH CS
                              HEAT   4 lllkllsDpspeVReaAakaLgala 28 
                                       l+  +l+D+  +V ++Aa+aLg++ 
  gi|298675588|ref|YP_003727338.1| 642 LIRAMLHDEYENVKSNAALALGKIG 666
                                       567889****************995 PP

  == domain 15  score: 7.8 bits;  conditional E-value: 0.0052
                                       HT-..SSHHHHHHHHHHHHHH CS
                              HEAT   9 lsD..pspeVReaAakaLgal 27 
                                       l+D  +  +VR++Aa+aLg++
  gi|298675588|ref|YP_003727338.1| 678 LTDgeEKDQVRSSAALALGKI 698
                                       566657788**********98 PP

  == domain 16  score: 5.8 bits;  conditional E-value: 0.023
                                       HHHHHHT-SSHHHHHHHHHHHHHHH CS
                              HEAT   4 lllkllsDpspeVReaAakaLgala 28 
                                       +llk  ++++ e R  +a+aLg++ 
  gi|298675588|ref|YP_003727338.1| 706 PLLKTVNHENKEMRHYSALALGKIG 730
                                       689999****************995 PP

  == domain 17  score: 0.1 bits;  conditional E-value: 1.5
                                       HHHHH.T-SSHHHHHHHHHHHHHH CS
                              HEAT   5 llkll.sDpspeVReaAakaLgal 27 
                                       l+ ll + ++ eV   A++aLg++
  gi|298675588|ref|YP_003727338.1| 738 LIILLqNEDNREVKNGAIYALGEI 761
                                       566774556666**********97 PP

  == domain 18  score: 16.0 bits;  conditional E-value: 1.1e-05
                                       HHHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   3 PlllkllsDpspeVReaAakaLgal 27 
                                        +l+++l D ++++R++A+ aLg++
  gi|298675588|ref|YP_003727338.1| 768 EPLIECLDDANSKIRKNAVIALGKI 792
                                       6799*******************98 PP

  == domain 19  score: 13.3 bits;  conditional E-value: 8.4e-05
                                       HHHHHHT-SSHHHHHHHHHHHHHHH CS
                              HEAT   4 lllkllsDpspeVReaAakaLgala 28 
                                       +l++ l+D++pe+R+ +a  Lg++ 
  gi|298675588|ref|YP_003727338.1| 800 PLIQRLNDNDPEIRKYSAIILGKIG 824
                                       466669****************996 PP

  == domain 20  score: 10.9 bits;  conditional E-value: 0.00051
                                       HHHHHHT-SSHHHHHHHHHHHHHHH CS
                              HEAT   4 lllkllsDpspeVReaAakaLgala 28 
                                       +l++ l D++ +VR+a+ +aL+++ 
  gi|298675588|ref|YP_003727338.1| 831 PLINTLDDSNKDVRKATTNALAKIG 855
                                       578899****************996 PP

  == domain 21  score: 4.5 bits;  conditional E-value: 0.057
                                       HHHHHHHT-SSHHHHHHHHHHHHHHHH CS
                              HEAT   3 PlllkllsDpspeVReaAakaLgalae 29 
                                        +l++ l + +p+V e A +aL ++ e
  gi|298675588|ref|YP_003727338.1| 860 QPLINSLDSRNPDVKEHATNALIKIGE 886
                                       5689999***************99876 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.55   4.9e+02      36      53 ..      86     103 ..      81     104 .. 0.91
   2 ?    5.7   0.0     0.024        21      23      55 .]     108     136 ..      99     136 .. 0.79
   3 ?    4.3   0.0     0.065        58      36      55 .]     147     166 ..     138     166 .. 0.76
   4 !   10.2   0.1   0.00095      0.85      36      54 ..     179     197 ..     175     198 .. 0.91
   5 !    9.9   0.0    0.0012       1.1      31      55 .]     206     230 ..     201     230 .. 0.83
   6 !   12.9   0.0   0.00014      0.12      29      54 ..     235     261 ..     233     262 .. 0.79
   7 ?    6.8   0.0     0.011        10      32      54 ..     270     293 ..     265     294 .. 0.76
   8 !    7.4   0.1     0.007       6.3      29      53 ..     299     324 ..     297     326 .. 0.88
   9 !   11.6   0.0   0.00034      0.31      31      52 ..     333     354 ..     329     354 .. 0.89
  10 ?    1.8   0.0      0.41   3.7e+02      30      55 .]     392     418 ..     390     418 .. 0.82
  11 ?    3.1   0.0      0.15   1.4e+02      30      54 ..     424     449 ..     421     450 .. 0.89
  12 ?   -0.7   0.0       2.5   2.2e+03      29      43 ..     454     469 ..     452     473 .. 0.74
  13 ?    1.6   0.0      0.46   4.2e+02      32      54 ..     579     601 ..     573     602 .. 0.77
  14 !    9.9   0.0    0.0012       1.1       3      55 .]     591     633 ..     589     633 .. 0.67
  15 ?    1.4   0.0      0.53   4.7e+02      33      55 .]     642     665 ..     639     665 .. 0.74
  16 ?    6.6   0.1     0.013        12       4      55 .]     655     698 ..     652     698 .. 0.66
  17 ?    5.9   0.0     0.022        19      30      55 .]     704     729 ..     700     729 .. 0.92
  18 ?    5.3   0.0     0.032        28      29      55 .]     734     761 ..     732     761 .. 0.79
  19 !   12.8   0.0   0.00014      0.13      28      55 .]     765     792 ..     764     792 .. 0.91
  20 !   11.4   0.0   0.00039      0.35      30      55 .]     798     823 ..     795     823 .. 0.93
  21 !   14.6   0.0   3.9e-05     0.035      28      55 .]     827     854 ..     826     854 .. 0.93
  22 ?    6.7   0.0     0.012        11      29      55 .]     858     884 ..     856     884 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.55
                           HEAT_EZ  36 lLnddsdeVRaaAagaLg 53 
                                       lLn+++ ++R +Aa  Lg
  gi|298675588|ref|YP_003727338.1|  86 LLNSSNEDTRIKAAKSLG 103
                                       89************9998 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.024
                           HEAT_EZ  23 qplvpeilpaLlalLnddsd.eVRaaAagaLgnl 55 
                                       q +++ +++a+      d++  V+ aAa  Lg++
  gi|298675588|ref|YP_003727338.1| 108 QNAIDSLIKAFE-----DESvYVKIAAANSLGKI 136
                                       666777777777.....7777***********97 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.065
                           HEAT_EZ  36 lLnddsdeVRaaAagaLgnl 55 
                                        L + + +VR++++ aLgn+
  gi|298675588|ref|YP_003727338.1| 147 VLDSQNEDVRKYSVKALGNI 166
                                       4444455***********98 PP

  == domain 4  score: 10.2 bits;  conditional E-value: 0.00095
                           HEAT_EZ  36 lLnddsdeVRaaAagaLgn 54 
                                       lLnd+s++VR+ Aa aLg 
  gi|298675588|ref|YP_003727338.1| 179 LLNDKSSDVRESAAKALGD 197
                                       89***************95 PP

  == domain 5  score: 9.9 bits;  conditional E-value: 0.0012
                           HEAT_EZ  31 paLlalLnddsdeVRaaAagaLgnl 55 
                                       p+  alLnd + +VR +++ aLg++
  gi|298675588|ref|YP_003727338.1| 206 PLIDALLNDTDEDVRSKSVVALGKI 230
                                       444588899999***********97 PP

  == domain 6  score: 12.9 bits;  conditional E-value: 0.00014
                           HEAT_EZ  29 ilpaLl.alLnddsdeVRaaAagaLgn 54 
                                       ++++L  alLnd+s++VR+ Aa aLg 
  gi|298675588|ref|YP_003727338.1| 235 VVKPLSnALLNDESSDVRESAAKALGD 261
                                       677777355699999**********95 PP

  == domain 7  score: 6.8 bits;  conditional E-value: 0.011
                           HEAT_EZ  32 aLl.alLnddsdeVRaaAagaLgn 54 
                                       +L+ alLnd +d+VR++++  ++ 
  gi|298675588|ref|YP_003727338.1| 270 PLInALLNDTDDDVRYQVVEVFSE 293
                                       566266699999*****9988876 PP

  == domain 8  score: 7.4 bits;  conditional E-value: 0.007
                           HEAT_EZ  29 ilpaLlalLnddsd.eVRaaAagaLg 53 
                                       ++++L++ L +d d +VR  Aa  Lg
  gi|298675588|ref|YP_003727338.1| 299 AVDPLVKILLNDRDvDVRSSAAEVLG 324
                                       7899*****999999*******9998 PP

  == domain 9  score: 11.6 bits;  conditional E-value: 0.00034
                           HEAT_EZ  31 paLlalLnddsdeVRaaAagaL 52 
                                        +L+++Lndds eVR+++a a+
  gi|298675588|ref|YP_003727338.1| 333 EPLVKALNDDSEEVRENSADAI 354
                                       689***************9986 PP

  == domain 10  score: 1.8 bits;  conditional E-value: 0.41
                           HEAT_EZ  30 lpaLlalL.nddsdeVRaaAagaLgnl 55 
                                       +++L+++L n+ sd+ + +Aa  Lg++
  gi|298675588|ref|YP_003727338.1| 392 VDPLIQTLsNSNSDNAKIKAADILGKI 418
                                       57899999566666**********987 PP

  == domain 11  score: 3.1 bits;  conditional E-value: 0.15
                           HEAT_EZ  30 lpaLlalLnddsd.eVRaaAagaLgn 54 
                                       +++L+++Ln++++ +V+  +a aL n
  gi|298675588|ref|YP_003727338.1| 424 IKPLIKTLNNENSrDVKLSVADALVN 449
                                       899******************99966 PP

  == domain 12  score: -0.7 bits;  conditional E-value: 2.5
                           HEAT_EZ  29 ilpaLlalLnddsd.e 43 
                                       ++++L+++Ln+ +d e
  gi|298675588|ref|YP_003727338.1| 454 AVDPLIKTLNNNDDkE 469
                                       6899*****8776624 PP

  == domain 13  score: 1.6 bits;  conditional E-value: 0.46
                           HEAT_EZ  32 aLlalLnddsdeVRaaAagaLgn 54 
                                        L+++L+d++  VR  A+ aL+ 
  gi|298675588|ref|YP_003727338.1| 579 KLVKALKDEKGYVRISAIMALAE 601
                                       57888887777999999999876 PP

  == domain 14  score: 9.9 bits;  conditional E-value: 0.0012
                           HEAT_EZ   3 vRraAawaLGrlaggepellqplvpeilpaLlalLnddsdeVRaaAagaLgnl 55 
                                       vR +A++aL+  + g++ +++     i   +      d++e+Ra+Aa+aLg +
  gi|298675588|ref|YP_003727338.1| 591 VRISAIMALA--EIGNDKTVK----PIAEVMF----KDNPEIRATAAYALGEI 633
                                       6666777776..444555555....4444444....4677***********86 PP

  == domain 15  score: 1.4 bits;  conditional E-value: 0.53
                           HEAT_EZ  33 LlalLnddsd.eVRaaAagaLgnl 55 
                                       L++++ +d+  +V+ +Aa aLg++
  gi|298675588|ref|YP_003727338.1| 642 LIRAMLHDEYeNVKSNAALALGKI 665
                                       565555555569999999999987 PP

  == domain 16  score: 6.6 bits;  conditional E-value: 0.013
                           HEAT_EZ   4 RraAawaLGrlaggepellqplvpeilpaLlalLnddsdeVRaaAagaLgnl 55 
                                       + +Aa+aLG     +++  + +++++l         ++d VR  Aa aLg++
  gi|298675588|ref|YP_003727338.1| 655 KSNAALALG---KIGDDETAHYLTRVLTDGE-----EKDQVRSSAALALGKI 698
                                       556677777...5555555555555555445.....7789**********97 PP

  == domain 17  score: 5.9 bits;  conditional E-value: 0.022
                           HEAT_EZ  30 lpaLlalLnddsdeVRaaAagaLgnl 55 
                                       + +Ll++ n++++e R ++a aLg++
  gi|298675588|ref|YP_003727338.1| 704 VSPLLKTVNHENKEMRHYSALALGKI 729
                                       6789********************97 PP

  == domain 18  score: 5.3 bits;  conditional E-value: 0.032
                           HEAT_EZ  29 ilpaLlalLnddsd.eVRaaAagaLgnl 55 
                                       +++ L+ lL++++  eV+  A++aLg +
  gi|298675588|ref|YP_003727338.1| 734 AVKSLIILLQNEDNrEVKNGAIYALGEI 761
                                       567777789775556***********86 PP

  == domain 19  score: 12.8 bits;  conditional E-value: 0.00014
                           HEAT_EZ  28 eilpaLlalLnddsdeVRaaAagaLgnl 55 
                                       +++ +L+ +L d ++++R++A++aLg++
  gi|298675588|ref|YP_003727338.1| 765 KAVEPLIECLDDANSKIRKNAVIALGKI 792
                                       578999999999999***********97 PP

  == domain 20  score: 11.4 bits;  conditional E-value: 0.00039
                           HEAT_EZ  30 lpaLlalLnddsdeVRaaAagaLgnl 55 
                                       + +L+++Lnd ++e+R+++a+ Lg++
  gi|298675588|ref|YP_003727338.1| 798 VSPLIQRLNDNDPEIRKYSAIILGKI 823
                                       678*********************97 PP

  == domain 21  score: 14.6 bits;  conditional E-value: 3.9e-05
                           HEAT_EZ  28 eilpaLlalLnddsdeVRaaAagaLgnl 55 
                                       +++ +L+++L d++++VR+a+  aL+++
  gi|298675588|ref|YP_003727338.1| 827 KAVHPLINTLDDSNKDVRKATTNALAKI 854
                                       57899********************987 PP

  == domain 22  score: 6.7 bits;  conditional E-value: 0.012
                           HEAT_EZ  29 ilpaLlalLnddsdeVRaaAagaLgnl 55 
                                       ++ +L++ L + +++V++ A  aL ++
  gi|298675588|ref|YP_003727338.1| 858 AVQPLINSLDSRNPDVKEHATNALIKI 884
                                       5779*******************9876 PP

>> Arm  Armadillo/beta-catenin-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       5.4   4.8e+03      19      33 ..      85      99 ..      85     103 .. 0.79
   2 ?   -1.5   0.0       3.4     3e+03      11      37 ..     108     134 ..     107     136 .. 0.87
   3 !    8.8   0.0    0.0019       1.7      17      39 ..     144     166 ..     143     167 .. 0.93
   4 ?    2.3   0.0      0.21   1.9e+02      20      37 ..     179     196 ..     175     200 .. 0.91
   5 ?    3.2   0.0      0.11        98      16      37 ..     206     228 ..     202     230 .. 0.84
   6 !    9.1   0.0    0.0016       1.4       9      37 ..     231     260 ..     229     263 .. 0.92
   7 ?   -1.4   0.0       3.2   2.8e+03      16      33 ..     270     288 ..     269     294 .. 0.70
   8 !    9.1   0.0    0.0015       1.3       7      37 ..     293     324 ..     288     326 .. 0.89
   9 !   10.6   0.0   0.00052      0.47      15      36 ..     333     354 ..     328     359 .. 0.89
  10 ?   -0.4   0.0       1.5   1.4e+03      13      33 ..     361     381 ..     354     388 .. 0.82
  11 ?    0.8   0.0      0.61   5.4e+02      14      29 ..     392     408 ..     381     419 .. 0.76
  12 ?    2.4   0.0       0.2   1.8e+02      14      39 ..     424     450 ..     418     452 .. 0.89
  13 ?    0.4   0.0      0.86   7.7e+02      13      26 ..     454     467 ..     450     470 .. 0.79
  14 ?    2.5   0.0      0.18   1.6e+02      12      39 ..     606     633 ..     600     635 .. 0.85
  15 ?    4.1   0.0     0.059        53      19      38 ..     645     664 ..     640     667 .. 0.81
  16 ?    3.1   0.0      0.12   1.1e+02      10      38 ..     700     728 ..     697     731 .. 0.87
  17 ?    2.7   0.0      0.16   1.4e+02      10      39 ..     731     761 ..     728     762 .. 0.87
  18 !   13.4   0.0     7e-05     0.062       8      37 ..     761     790 ..     759     792 .. 0.89
  19 ?    2.1   0.0      0.24   2.2e+02      14      32 ..     798     816 ..     794     817 .. 0.89
  20 ?    6.1   0.0     0.013        12      12      37 ..     827     852 ..     822     856 .. 0.89
  21 !   11.4   0.0   0.00029      0.26      13      36 ..     858     881 ..     854     881 .. 0.94
  22 ?    0.6   0.0      0.71   6.3e+02      12      25 ..     887     900 ..     884     906 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.4
                                      HHTTTSSHHHHHHHH CS
                               Arm 19 rLLssedeevqeeAa 33
                                      +LL+s +e+++  Aa
  gi|298675588|ref|YP_003727338.1| 85 DLLNSSNEDTRIKAA 99
                                      69**99999987777 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.4
                                       TTHHHHHHHHTTTSSHHHHHHHHHHHH CS
                               Arm  11 aGavppLvrLLssedeevqeeAawALs 37 
                                       ++a++ L++  ++e++ v+ +Aa  L+
  gi|298675588|ref|YP_003727338.1| 108 QNAIDSLIKAFEDESVYVKIAAANSLG 134
                                       689999***999******999998776 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0019
                                       HHHHTTTSSHHHHHHHHHHHHHH CS
                               Arm  17 LvrLLssedeevqeeAawALsNL 39 
                                       L++ L+s++e+v++ ++ AL+N+
  gi|298675588|ref|YP_003727338.1| 144 LLEVLDSQNEDVRKYSVKALGNI 166
                                       778899****************8 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.21
                                       HTTTSSHHHHHHHHHHHH CS
                               Arm  20 LLssedeevqeeAawALs 37 
                                       LL++++ +v+e Aa AL+
  gi|298675588|ref|YP_003727338.1| 179 LLNDKSSDVRESAAKALG 196
                                       899*************98 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.11
                                       HHHHHTT.TSSHHHHHHHHHHHH CS
                               Arm  16 pLvrLLs.sedeevqeeAawALs 37 
                                       pL++ L  ++de+v+  ++ AL+
  gi|298675588|ref|YP_003727338.1| 206 PLIDALLnDTDEDVRSKSVVALG 228
                                       67777777*************98 PP

  == domain 6  score: 9.1 bits;  conditional E-value: 0.0016
                                       HHTTHHHHHHHHTT.TSSHHHHHHHHHHHH CS
                               Arm   9 ieaGavppLvrLLs.sedeevqeeAawALs 37 
                                        + ++v+pL + L  +e+ +v+e Aa AL+
  gi|298675588|ref|YP_003727338.1| 231 KNENVVKPLSNALLnDESSDVRESAAKALG 260
                                       5789************************98 PP

  == domain 7  score: -1.4 bits;  conditional E-value: 3.2
                                       HHHHHTT.TSSHHHHHHHH CS
                               Arm  16 pLvrLLs.sedeevqeeAa 33 
                                       pL++ L  ++d++v+ +++
  gi|298675588|ref|YP_003727338.1| 270 PLINALLnDTDDDVRYQVV 288
                                       6666666699999988776 PP

  == domain 8  score: 9.1 bits;  conditional E-value: 0.0015
                                       HHHHTTHHHHHHHHTT.TSSHHHHHHHHHHHH CS
                               Arm   7 avieaGavppLvrLLs.sedeevqeeAawALs 37 
                                       ++ + +av+pLv+ L  + d++v+  Aa  L+
  gi|298675588|ref|YP_003727338.1| 293 EIKDKNAVDPLVKILLnDRDVDVRSSAAEVLG 324
                                       577889*********************98886 PP

  == domain 9  score: 10.6 bits;  conditional E-value: 0.00052
                                       HHHHHHTTTSSHHHHHHHHHHH CS
                               Arm  15 ppLvrLLssedeevqeeAawAL 36 
                                       +pLv+ L++++eev+e++a A+
  gi|298675588|ref|YP_003727338.1| 333 EPLVKALNDDSEEVRENSADAI 354
                                       79******************98 PP

  == domain 10  score: -0.4 bits;  conditional E-value: 1.5
                                       HHHHHHHHTTTSSHHHHHHHH CS
                               Arm  13 avppLvrLLssedeevqeeAa 33 
                                       a  pLv+ L++ + +v+  A 
  gi|298675588|ref|YP_003727338.1| 361 ATSPLVNELDNRNKNVVNTAS 381
                                       6689***********999886 PP

  == domain 11  score: 0.8 bits;  conditional E-value: 0.61
                                       HHHHHHHTT.TSSHHHH CS
                               Arm  14 vppLvrLLs.sedeevq 29 
                                       v+pL++ Ls s +++ +
  gi|298675588|ref|YP_003727338.1| 392 VDPLIQTLSnSNSDNAK 408
                                       99*******85555544 PP

  == domain 12  score: 2.4 bits;  conditional E-value: 0.2
                                       HHHHHHHTT.TSSHHHHHHHHHHHHHH CS
                               Arm  14 vppLvrLLs.sedeevqeeAawALsNL 39 
                                       ++pL++ L+   + +v+  +a AL N+
  gi|298675588|ref|YP_003727338.1| 424 IKPLIKTLNnENSRDVKLSVADALVNI 450
                                       89*******999999*9999**99998 PP

  == domain 13  score: 0.4 bits;  conditional E-value: 0.86
                                       HHHHHHHHTTTSSH CS
                               Arm  13 avppLvrLLssede 26 
                                       av+pL++ L++ d+
  gi|298675588|ref|YP_003727338.1| 454 AVDPLIKTLNNNDD 467
                                       8*********5553 PP

  == domain 14  score: 2.5 bits;  conditional E-value: 0.18
                                       THHHHHHHHTTTSSHHHHHHHHHHHHHH CS
                               Arm  12 GavppLvrLLssedeevqeeAawALsNL 39 
                                         v+p  + +  +++e++  Aa AL+ +
  gi|298675588|ref|YP_003727338.1| 606 KTVKPIAEVMFKDNPEIRATAAYALGEI 633
                                       568888999999*************987 PP

  == domain 15  score: 4.1 bits;  conditional E-value: 0.059
                                       HHTTTSSHHHHHHHHHHHHH CS
                               Arm  19 rLLssedeevqeeAawALsN 38 
                                       ++L++e e+v+ +Aa AL+ 
  gi|298675588|ref|YP_003727338.1| 645 AMLHDEYENVKSNAALALGK 664
                                       4566**************86 PP

  == domain 16  score: 3.1 bits;  conditional E-value: 0.12
                                       HTTHHHHHHHHTTTSSHHHHHHHHHHHHH CS
                               Arm  10 eaGavppLvrLLssedeevqeeAawALsN 38 
                                       e+  v pL++  ++e+ e+++ +a AL+ 
  gi|298675588|ref|YP_003727338.1| 700 ESSSVSPLLKTVNHENKEMRHYSALALGK 728
                                       566699********************986 PP

  == domain 17  score: 2.7 bits;  conditional E-value: 0.16
                                       HTTHHHHHHHHTT.TSSHHHHHHHHHHHHHH CS
                               Arm  10 eaGavppLvrLLs.sedeevqeeAawALsNL 39 
                                       +  av+ L+ LL+  ++ ev+  A  AL+ +
  gi|298675588|ref|YP_003727338.1| 731 DERAVKSLIILLQnEDNREVKNGAIYALGEI 761
                                       67799********999999999999999876 PP

  == domain 18  score: 13.4 bits;  conditional E-value: 7e-05
                                       HHHTTHHHHHHHHTTTSSHHHHHHHHHHHH CS
                               Arm   8 vieaGavppLvrLLssedeevqeeAawALs 37 
                                       +++  av+pL+++L++ + +++++A+ AL+
  gi|298675588|ref|YP_003727338.1| 761 IRNEKAVEPLIECLDDANSKIRKNAVIALG 790
                                       78899********************97776 PP

  == domain 19  score: 2.1 bits;  conditional E-value: 0.24
                                       HHHHHHHTTTSSHHHHHHH CS
                               Arm  14 vppLvrLLssedeevqeeA 32 
                                       v pL++ L++ d+e+++ +
  gi|298675588|ref|YP_003727338.1| 798 VSPLIQRLNDNDPEIRKYS 816
                                       89*************9976 PP

  == domain 20  score: 6.1 bits;  conditional E-value: 0.013
                                       THHHHHHHHTTTSSHHHHHHHHHHHH CS
                               Arm  12 GavppLvrLLssedeevqeeAawALs 37 
                                        av pL++ L++ + +v+++ + AL+
  gi|298675588|ref|YP_003727338.1| 827 KAVHPLINTLDDSNKDVRKATTNALA 852
                                       6899*******************997 PP

  == domain 21  score: 11.4 bits;  conditional E-value: 0.00029
                                       HHHHHHHHTTTSSHHHHHHHHHHH CS
                               Arm  13 avppLvrLLssedeevqeeAawAL 36 
                                       av+pL++ L+s +++v+e A+ AL
  gi|298675588|ref|YP_003727338.1| 858 AVQPLINSLDSRNPDVKEHATNAL 881
                                       8********************998 PP

  == domain 22  score: 0.6 bits;  conditional E-value: 0.71
                                       THHHHHHHHTTTSS CS
                               Arm  12 GavppLvrLLssed 25 
                                        +v+pL++ L++++
  gi|298675588|ref|YP_003727338.1| 887 PCVQPLIKALDNDK 900
                                       59********9765 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.19   1.7e+02      22      48 ..     110     136 ..      95     153 .. 0.83
   2 !   13.1   0.1     8e-05     0.071       2      86 ..     155     231 ..     154     232 .. 0.87
   3 !   16.2   0.2   9.4e-06    0.0084      26      94 ..     208     272 ..     201     276 .. 0.85
   4 !   17.3   0.7   4.2e-06    0.0038       2      89 ..     219     298 ..     218     307 .. 0.87
   5 !   12.8   2.1    0.0001     0.093      16     131 ..     297     407 ..     283     433 .. 0.72
   6 ?    0.6   0.1      0.56     5e+02      58      92 ..     514     548 ..     507     565 .. 0.76
   7 !   16.2   0.0     9e-06    0.0081      24      88 ..     578     636 ..     569     643 .. 0.86
   8 !   11.3   0.0    0.0003      0.27      20      90 ..     605     670 ..     604     680 .. 0.83
   9 ?    3.8   0.0      0.06        54       3      88 ..     655     732 ..     653     747 .. 0.68
  10 !   17.2   0.0   4.5e-06     0.004       2      51 ..     750     795 ..     749     799 .. 0.76
  11 !   20.8   0.0   3.6e-07   0.00032      20      94 ..     795     863 ..     793     867 .. 0.87
  12 !    8.6   0.1    0.0019       1.7      22      85 ..     828     884 ..     826     906 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.19
                              Cnd1  22 lvepLrkrLkDedpyVRktaaivvakL 48 
                                        ++ L k+++De+ yV+  aa  + k+
  gi|298675588|ref|YP_003727338.1| 110 AIDSLIKAFEDESVYVKIAAANSLGKI 136
                                       678899999*********999998887 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 8e-05
                              Cnd1   2 iRalairtlgcirvpnlveylvepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvana 78 
                                       +R   +++lg ir +n+ ++l++ L   L+D+++ VR+ aa ++  + ++   +       +  ll+D+++ V++ +
  gi|298675588|ref|YP_003727338.1| 155 VRKYSVKALGNIRNENTADELSDVL---LNDKSSDVRESAAKALGDIGDKRAAE-----PLIDALLNDTDEDVRSKS 223
                                       89999*****************977...9**************99876665554.....5567789*********** PP

                              Cnd1  79 laalteis 86 
                                       + al +i+
  gi|298675588|ref|YP_003727338.1| 224 VVALGKIK 231
                                       ***99886 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 9.4e-06
                              Cnd1  26 LrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaalteisek.senaiy 94 
                                       + + L+D+d+ VR   ++++ k+ ++++vk        + ll+De++ V+++a  al +i +k + ++++
  gi|298675588|ref|YP_003727338.1| 208 IDALLNDTDEDVRSKSVVALGKIKNENVVKPLS-----NALLNDESSDVRESAAKALGDIGDKrAAEPLI 272
                                       56789*****************99999999877.....7889******************9995445555 PP

  == domain 4  score: 17.3 bits;  conditional E-value: 4.2e-06
                              Cnd1   2 iRalairtlgcirvpnlveylvepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvana 78 
                                       +R+  +++lg i+ +n+v +l++ L   L+De++ VR+ aa ++  + ++   +       ++ ll+D+++ V+  +
  gi|298675588|ref|YP_003727338.1| 219 VRSKSVVALGKIKNENVVKPLSNAL---LNDESSDVRESAAKALGDIGDKRAAE-----PLINALLNDTDDDVRYQV 287
                                       89999***************99876...9**************98776665554.....6789999*********** PP

                              Cnd1  79 laalteiseks 89 
                                       + +++ei++k+
  gi|298675588|ref|YP_003727338.1| 288 VEVFSEIKDKN 298
                                       ********995 PP

  == domain 5  score: 12.8 bits;  conditional E-value: 0.0001
                              Cnd1  16 pnlveylvepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaalteisekse.. 90 
                                       +n v++lv+     L+D+d  VR  aa v+        +++++  + l k+l+D++++V++n+  a+ ei e ++  
  gi|298675588|ref|YP_003727338.1| 297 KNAVDPLVKI---LLNDRDVDVRSSAAEVLGD------IEDEKAAEPLVKALNDDSEEVRENSADAILEIGEPATsp 364
                                       5555555544...5899*********999976......677788899**************************7733 PP

                              Cnd1  91 ..naiynllpdiisklsdalnecsewgqitilefLlsyipkdk 131
                                         n++ n ++++++  sd l e+   +    +++L++  ++++
  gi|298675588|ref|YP_003727338.1| 365 lvNELDNRNKNVVNTASDLLVEIGDPSVDPLIQTLSNSNSDNA 407
                                       5555556666666666666666666666666666665555554 PP

  == domain 6  score: 0.6 bits;  conditional E-value: 0.56
                              Cnd1  58 gflselaklleDenprVvanalaalteiseksena 92 
                                       g ++ l+++ + en++ ++n  +al +i++k ++ 
  gi|298675588|ref|YP_003727338.1| 514 GEIQPLKEAYKQENKNSISNIANALDDINDKHTKS 548
                                       56778899999999999999999999999995433 PP

  == domain 7  score: 16.2 bits;  conditional E-value: 9e-06
                              Cnd1  24 epLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaalteisek 88 
                                       e+L k+LkDe+ yVR  a++++a++ + ++vk       +a+ +  +np+++a a +al ei + 
  gi|298675588|ref|YP_003727338.1| 578 EKLVKALKDEKGYVRISAIMALAEIGNDKTVK------PIAEVMFKDNPEIRATAAYALGEIGDI 636
                                       7899********************98888877......5778888889************99876 PP

  == domain 8  score: 11.3 bits;  conditional E-value: 0.0003
                              Cnd1  20 eylvepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaalteisekse 90 
                                       +++v+p+ + +  ++p +R taa+++ ++ + d  k     + ++ +l+De ++V +na +al +i + ++
  gi|298675588|ref|YP_003727338.1| 605 DKTVKPIAEVMFKDNPEIRATAAYALGEIGDIDAEK-----HLIRAMLHDEYENVKSNAALALGKIGDDET 670
                                       6789999999999**************996655544.....457889*****************9998863 PP

  == domain 9  score: 3.8 bits;  conditional E-value: 0.06
                              Cnd1   3 RalairtlgcirvpnlveylvepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanal 79 
                                       +++a  +lg i  +++  yl+  L+ +   e+ +VR  aa+++ k      +ke+  +s l+k ++ en++ +  + 
  gi|298675588|ref|YP_003727338.1| 655 KSNAALALGKIGDDETAHYLTRVLTDG--EEKDQVRSSAALALGK------IKESSSVSPLLKTVNHENKEMRHYSA 723
                                       566666666666666666555555554..4677888888888877......67777888888888888888888888 PP

                              Cnd1  80 aalteisek 88 
                                       +al +i ++
  gi|298675588|ref|YP_003727338.1| 724 LALGKIGDE 732
                                       888877766 PP

  == domain 10  score: 17.2 bits;  conditional E-value: 4.5e-06
                              Cnd1   2 iRalairtlgcirvpnlveylvepLrkrLkDedpyVRktaaivvakLiln 51 
                                       +++ ai +lg ir ++ ve    pL ++L D ++ +Rk+a+i++ k+ + 
  gi|298675588|ref|YP_003727338.1| 750 VKNGAIYALGEIRNEKAVE----PLIECLDDANSKIRKNAVIALGKINSD 795
                                       5666777777777766665....566799**************9997554 PP

  == domain 11  score: 20.8 bits;  conditional E-value: 3.6e-07
                              Cnd1  20 eylvepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaalteiseksenaiy 94 
                                       +++v+pL +rL+D+dp +Rk  ai++ k+       +k+ ++ l + l+D+n+ V++ + +al +i + + ++++
  gi|298675588|ref|YP_003727338.1| 795 DKTVSPLIQRLNDNDPEIRKYSAIILGKI------GDKKAVHPLINTLDDSNKDVRKATTNALAKIGKPAVQPLI 863
                                       7899**********************996......5566678999*******************99887655555 PP

  == domain 12  score: 8.6 bits;  conditional E-value: 0.0019
                              Cnd1  22 lvepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaaltei 85 
                                        v pL ++L D++  VRk +  ++ak+ ++        ++ l + l+  np V + a +al +i
  gi|298675588|ref|YP_003727338.1| 828 AVHPLINTLDDSNKDVRKATTNALAKIGKP-------AVQPLINSLDSRNPDVKEHATNALIKI 884
                                       578999999999999999999999997544.......345556666666666666666666666 PP

>> Adaptin_N  Adaptin N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   3.8   3.8e-06    0.0034      81     362 ..     111     355 ..     109     384 .. 0.71
   2 !    7.0   0.6    0.0021       1.9     309     348 ..     396     435 ..     361     456 .. 0.83
   3 ?   -1.3   0.2      0.67     6e+02     311     372 ..     461     542 ..     456     564 .. 0.60
   4 !   14.7   0.0   9.6e-06    0.0086      84     193 ..     580     674 ..     576     680 .. 0.85
   5 !    7.6   0.0    0.0013       1.2      85     185 ..     644     766 ..     640     774 .. 0.69
   6 !   13.5   0.4   2.2e-05     0.019      88     208 ..     774     877 ..     766     911 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.8e-06
                                       CHHHHHHCCSSSHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHT-SSHHHHHHHHHHHHHCCCCCHHCCCCCHHHHH CS
                         Adaptin_N  81 tnslqkDlkdpnqlirglALrvLssirvpelaedlapaikkllkdrspyvrkkAalailklykkdpdllrkqlveei 157
                                       ++sl k+++d + +++  A ++L++i+ p +      ++ ++l +++  vrk ++ a+  +   +         +e+
  gi|298675588|ref|YP_003727338.1| 111 IDSLIKAFEDESVYVKIAAANSLGKIGNPAT-----GDLLEVLDSQNEDVRKYSVKALGNIRNENTA-------DEL 175
                                       6788888888888888888888888888764.....5677788888888888888888777543322.......233 PP

                                       HH.CTT-SSHHHHHHHHHHHHHHHCCCCCCCHHHHHHHCCHHHHHHCS-HHHHHHHHHHHCC---SSHHHH..HHHH CS
                         Adaptin_N 158 ke.llsdkdpgvvlaAvalleeikkndrlllkllpklvrrLcnllteldpwlqvkiiklltrlarqepeerskkell 233
                                        + ll+dk+  v  +A ++l  i    +   ++++ l+  L    +++d+    k +  l +  +++  ++      
  gi|298675588|ref|YP_003727338.1| 176 SDvLLNDKSSDVRESAAKALGDI---GDK--RAAEPLIDALL---NDTDEDVRSKSVVALGKIKNENVVKP------ 238
                                       33056888888888888888888...444..56777888877...88888888888888888888777777...... PP

                                       HHHCGGCGCSSCHHHHHHHHHCCHCCCCSTHHHCCHHCHHHHHHSSCCTCHHHHHCHHHHHHHHXXTTTTTTTCCCC CS
                         Adaptin_N 234 esllnllqssnnaVlletvnlivelapknelivlavnaLvrllsskdenlryvaLrtllkivkkepkavqhldlkif 310
                                          ++ll+  +  V  ++++++ ++ +k + ++ ++naL   l + d  +ry +++ +++i  k+  av   d  ++
  gi|298675588|ref|YP_003727338.1| 239 -LSNALLNDESSDVRESAAKALGDIGDKRA-AEPLINAL---LNDTDDDVRYQVVEVFSEIKDKN--AV---DPLVK 305
                                       .34567778888888888888888888887.46666654...55666669999999999998888..44...34444 PP

                                       SXXTTSXHHHHHHHHHHHCCCXXTTTHHHHHHHHHHHTTSSXXHHHHHHHHH CS
                         Adaptin_N 311 llktdddvsirlkaldlllklvdesNvkeivkeLkkyvkevadedfksklvk 362
                                        l +d+dv++r+ a ++l ++ de+ ++ +vk L    +ev ++   ++++ 
  gi|298675588|ref|YP_003727338.1| 306 ILLNDRDVDVRSSAAEVLGDIEDEKAAEPLVKALNDDSEEVREN--SADAIL 355
                                       55558999999999999999999999999999887766555444..333333 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0021
                                       CCSXXTTSXHHHHHHHHHHHCCCXXTTTHHHHHHHHHHHT CS
                         Adaptin_N 309 ifllktdddvsirlkaldlllklvdesNvkeivkeLkkyv 348
                                       i+ l+++ + + ++ka d+l k+ +esN+k ++k+L ++ 
  gi|298675588|ref|YP_003727338.1| 396 IQTLSNSNSDNAKIKAADILGKIRNESNIKPLIKTLNNEN 435
                                       67788899999*************************9875 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.67
                                       SXXTTSXHHHHHHHHHHHCCCXXTTTHHHHHHHHHHH......TTSSXXHH...........HHHHHHHHHHHHHHH CS
                         Adaptin_N 311 llktdddvsirlkaldlllklvdesNvkeivkeLkky......vkevaded...........fksklvkaIgrlaek 370
                                        l+++dd +  ++    l++++de+ ++ + + L k+      ++++++e+           +k++  ++I+++a +
  gi|298675588|ref|YP_003727338.1| 461 TLNNNDDKELEKYLQLALVQIGDEKAIESLTRSLNKEktytanIESLQNEQldgeiqplkeaYKQENKNSISNIANA 537
                                       56666666666665555778888888888888888775555444444444455555555555666655555555555 PP

                                       S...C CS
                         Adaptin_N 371 f...a 372
                                            
  gi|298675588|ref|YP_003727338.1| 538 LddiN 542
                                       53322 PP

  == domain 4  score: 14.7 bits;  conditional E-value: 9.6e-06
                                       HHHHCCSSSHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHT-SSHHHHHHHHHHHHHCCCCCHHCCCCCHHHHHHHC CS
                         Adaptin_N  84 lqkDlkdpnqlirglALrvLssirvpelaedlapaikkllkdrspyvrkkAalailklykkdpdllrkqlveeikel 160
                                       l k+lkd   ++r +A+ +L+ i+ +++++ +a+ ++    +++p +r +Aa+a+  + ++d++   +     i   
  gi|298675588|ref|YP_003727338.1| 580 LVKALKDEKGYVRISAIMALAEIGNDKTVKPIAEVMF----KDNPEIRATAAYALGEIGDIDAEK--HL----IRAM 646
                                       789*************************999887766....59******************9999..65....8899 PP

                                       TT-SSHHHHHHHHHHHHHHHCCCCCCCHHHHHH CS
                         Adaptin_N 161 lsdkdpgvvlaAvalleeikkndrlllkllpkl 193
                                       l+d+   v+++A  +l +i   d+     +++l
  gi|298675588|ref|YP_003727338.1| 647 LHDEYENVKSNAALALGKI-GDDE----TAHYL 674
                                       99***********999999.3333....24444 PP

  == domain 5  score: 7.6 bits;  conditional E-value: 0.0013
                                       HHHCCSSSHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHT-SSHHHHHHHHHHHHHCCCCCHHCCCCCHHHHHHHCT CS
                         Adaptin_N  85 qkDlkdpnqlirglALrvLssirvpelaedlapaikkllkdrspyvrkkAalailklykkdpdllrkqlveeikell 161
                                       +  l+d  ++++++A  +L++i+++e+a +l++ +++    ++ +vr++Aala+ k+ ++++    + l++ + +  
  gi|298675588|ref|YP_003727338.1| 644 RAMLHDEYENVKSNAALALGKIGDDETAHYLTRVLTDG--EEKDQVRSSAALALGKIKESSSVS--P-LLKTVNHEN 715
                                       55588999999999999**********99999888875..66779***********98775443..4.355555544 PP

                                       T-SSH............................HHHHHHHHHHHHHHCCCCC CS
                         Adaptin_N 162 sdkdp............................gvvlaAvalleeikkndrl 185
                                       ++ ++                             v+  A+ +l ei +n+++
  gi|298675588|ref|YP_003727338.1| 716 KEMRHysalalgkigderavksliillqnednrEVKNGAIYALGEI-RNEKA 766
                                       4444445555555566666666666666666667777777777777.66655 PP

  == domain 6  score: 13.5 bits;  conditional E-value: 2.2e-05
                                       CCSSSHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHT-SSHHHHHHHHHHHHHCCCC....CHHCCCCCHHHHHHHC CS
                         Adaptin_N  88 lkdpnqlirglALrvLssirvpelaedlapaikkllkdrspyvrkkAalailklykk....dpdllrkqlveeikel 160
                                       l d n+ ir +A+ +L++i +++++  l     + l+d +p +rk +a+++ k+ +k                +++ 
  gi|298675588|ref|YP_003727338.1| 774 LDDANSKIRKNAVIALGKINSDKTVSPLI----QRLNDNDPEIRKYSAIILGKIGDKkavhP-----------LINT 835
                                       7899******************9998765....5689*****************98844440...........5555 PP

                                       TT-SSHHHHHHHHHHHHHHHCCCCCCCHHHHHHHCCHHHHHHCS-HHH CS
                         Adaptin_N 161 lsdkdpgvvlaAvalleeikkndrlllkllpklvrrLcnllteldpwl 208
                                       l+d++  v  a++++l +i    +    +++ l++ L+  + ++ +++
  gi|298675588|ref|YP_003727338.1| 836 LDDSNKDVRKATTNALAKI---GKP---AVQPLINSLDSRNPDVKEHA 877
                                       6666666666666666666...222...22222222222233333333 PP

>> Aconitase_B_N  Aconitate B N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.2     0.018        16      79     120 ..      94     135 ..      82     193 .. 0.84
   2 ?    1.0   0.1      0.44     4e+02      66     119 ..     176     228 ..     168     262 .. 0.61
   3 ?    3.4   0.0     0.079        70      80     118 ..     316     354 ..     301     358 .. 0.88
   4 ?    5.7   0.1     0.016        15      79     118 ..     407     447 ..     359     452 .. 0.82
   5 ?   -1.9   0.0       3.4     3e+03      93     113 ..     452     473 ..     443     509 .. 0.69
   6 ?   -0.5   0.1       1.3   1.2e+03      64     119 ..     579     631 ..     515     655 .. 0.73
   7 !    7.3   0.0     0.005       4.4      62     119 ..     671     727 ..     667     729 .. 0.91
   8 !    7.8   0.0    0.0036       3.2      80     120 ..     751     791 ..     737     793 .. 0.87
   9 ?    3.8   0.0     0.061        55      81     119 ..     783     821 ..     782     824 .. 0.91
  10 ?    5.1   0.0     0.024        22      76     120 ..     810     853 ..     801     855 .. 0.84
  11 ?    4.5   0.0     0.038        34      92     120 ..     855     883 ..     852     885 .. 0.90
  12 ?   -1.1   0.0         2   1.8e+03      92     118 ..     885     909 ..     883     912 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.018
                     Aconitase_B_N  79 speeAvelLgtMlGGynvksLidllkekdeelaeeaaeaLkk 120
                                       ++ +A + Lg+  G  +++sLi+++++++  ++ +aa+ L k
  gi|298675588|ref|YP_003727338.1|  94 TRIKAAKSLGEKRGQNAIDSLIKAFEDESVYVKIAAANSLGK 135
                                       567889999999999999999999997777777777777754 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.44
                     Aconitase_B_N  66 aaiakgeaesplispeeAvelLgtMlGGynvksLidllk.ekdeelaeeaaeaLk 119
                                       ++++ ++++s++  +e+A + Lg++    + ++Lid+l  ++de+++++ + aL 
  gi|298675588|ref|YP_003727338.1| 176 SDVLLNDKSSDV--RESAAKALGDIGDKRAAEPLIDALLnDTDEDVRSKSVVALG 228
                                       555555555543..56677777877777788888876541445556665555554 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.079
                     Aconitase_B_N  80 peeAvelLgtMlGGynvksLidllkekdeelaeeaaeaL 118
                                       +++A e+Lg++    + ++L+++l++++ee++e+ a+a+
  gi|298675588|ref|YP_003727338.1| 316 RSSAAEVLGDIEDEKAAEPLVKALNDDSEEVRENSADAI 354
                                       46799**************************99998875 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.016
                     Aconitase_B_N  79 speeAvelLgtMlGGynvksLidllkekd.eelaeeaaeaL 118
                                        + +A ++Lg++    n+k+Li+ l++++ ++++ ++a+aL
  gi|298675588|ref|YP_003727338.1| 407 AKIKAADILGKIRNESNIKPLIKTLNNENsRDVKLSVADAL 447
                                       4678999****************999654145666666666 PP

  == domain 5  score: -1.9 bits;  conditional E-value: 3.4
                     Aconitase_B_N  93 GynvksLidllkekd.eelaee 113
                                         +v++Li+ l+++d +el++ 
  gi|298675588|ref|YP_003727338.1| 452 KPAVDPLIKTLNNNDdKELEKY 473
                                       5677788888875440333333 PP

  == domain 6  score: -0.5 bits;  conditional E-value: 1.3
                     Aconitase_B_N  64 fLaaiakgeaesplispeeAvelLgtMlGGynvksLidllkekdeelaeeaaeaLk 119
                                        L + +k+e+        +A+  L+++     vk++ +++ +++ e++++aa aL 
  gi|298675588|ref|YP_003727338.1| 579 KLVKALKDEKGYVR---ISAIMALAEIGNDKTVKPIAEVMFKDNPEIRATAAYALG 631
                                       33333444444333...445555666656678888888888888888888888875 PP

  == domain 7  score: 7.3 bits;  conditional E-value: 0.005
                     Aconitase_B_N  62 AefLaaiakgeaesplispeeAvelLgtMlGGynvksLidllkekdeelaeeaaeaLk 119
                                       A++L++++++ +e + + ++ A+  Lg+++   +v++L++ ++++++e+++  a aL 
  gi|298675588|ref|YP_003727338.1| 671 AHYLTRVLTDGEEKDQVRSSAAL-ALGKIKESSSVSPLLKTVNHENKEMRHYSALALG 727
                                       89***************998887.58***********************999988885 PP

  == domain 8  score: 7.8 bits;  conditional E-value: 0.0036
                     Aconitase_B_N  80 peeAvelLgtMlGGynvksLidllkekdeelaeeaaeaLkk 120
                                       ++ A+  Lg++    +v++Li+ l++++++++++a+ aL k
  gi|298675588|ref|YP_003727338.1| 751 KNGAIYALGEIRNEKAVEPLIECLDDANSKIRKNAVIALGK 791
                                       567999*****************************999865 PP

  == domain 9  score: 3.8 bits;  conditional E-value: 0.061
                     Aconitase_B_N  81 eeAvelLgtMlGGynvksLidllkekdeelaeeaaeaLk 119
                                       ++Av  Lg+++    v++Li+ l+++d e+++  a +L 
  gi|298675588|ref|YP_003727338.1| 783 KNAVIALGKINSDKTVSPLIQRLNDNDPEIRKYSAIILG 821
                                       78999**************************99988775 PP

  == domain 10  score: 5.1 bits;  conditional E-value: 0.024
                     Aconitase_B_N  76 plispeeAvelLgtMlGGynvksLidllkekdeelaeeaaeaLkk 120
                                       p+i + +A+ +Lg++    +v++Li+ l++++++++++ ++aL k
  gi|298675588|ref|YP_003727338.1| 810 PEIRKYSAI-ILGKIGDKKAVHPLINTLDDSNKDVRKATTNALAK 853
                                       566666665.789998899***********************987 PP

  == domain 11  score: 4.5 bits;  conditional E-value: 0.038
                     Aconitase_B_N  92 GGynvksLidllkekdeelaeeaaeaLkk 120
                                       G  +v++Li+ l++++ +++e+a++aL k
  gi|298675588|ref|YP_003727338.1| 855 GKPAVQPLINSLDSRNPDVKEHATNALIK 883
                                       6679*********************9965 PP

  == domain 12  score: -1.1 bits;  conditional E-value: 2
                     Aconitase_B_N  92 GGynvksLidllkekdeelaeeaaeaL 118
                                       G   v++Li++l+  ++++++ a+ +L
  gi|298675588|ref|YP_003727338.1| 885 GEPCVQPLIKALD--NDKIKKPATIVL 909
                                       55679********..888888887666 PP

>> Vac14_Fab1_bd  Vacuolar 14 Fab1-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.087        78      26      86 ..     108     168 ..      94     182 .. 0.76
   2 ?    4.7   0.2      0.05        45      34      55 ..     274     295 ..     255     326 .. 0.74
   3 ?    2.2   0.0       0.3   2.7e+02      29      79 ..     332     382 ..     326     393 .. 0.82
   4 ?    1.2   0.0      0.65   5.8e+02      28      67 ..     423     463 ..     411     469 .. 0.86
   5 ?   -2.0   0.0       6.5   5.8e+03      31      49 ..     579     597 ..     563     618 .. 0.63
   6 ?    0.9   0.0      0.78     7e+02      28      54 ..     703     729 ..     689     745 .. 0.79
   7 ?    4.8   0.0     0.046        42      26      51 ..     764     789 ..     757     794 .. 0.85
   8 ?    2.2   0.0      0.31   2.8e+02      26      48 ..     795     817 ..     790     826 .. 0.86
   9 ?    4.2   0.0     0.074        66      27      65 ..     827     865 ..     820     869 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.087
                     Vac14_Fab1_bd  26 eeivkpvlkcfsDkdsrvRyyacEslyniakvakgevlkllneifdalvklvaDsdesvks 86 
                                       ++ +++++k+f+D++  v+  a+ sl  i   a g++l++l +  + + k +  +  ++++
  gi|298675588|ref|YP_003727338.1| 108 QNAIDSLIKAFEDESVYVKIAAANSLGKIGNPATGDLLEVLDSQNEDVRKYSVKALGNIRN 168
                                       6678889999999999999999999999999999988888887777777766666666664 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.05
                     Vac14_Fab1_bd  34 kcfsDkdsrvRyyacEslynia 55 
                                       + ++D+d+ vRy ++E +  i 
  gi|298675588|ref|YP_003727338.1| 274 ALLNDTDDDVRYQVVEVFSEIK 295
                                       45799********999887765 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.3
                     Vac14_Fab1_bd  29 vkpvlkcfsDkdsrvRyyacEslyniakvakgevlkllneifdalvklvaD 79 
                                        +p++k+++D++++vR  +++++  i   a + +++ l +  + +v+ ++D
  gi|298675588|ref|YP_003727338.1| 332 AEPLVKALNDDSEEVRENSADAILEIGEPATSPLVNELDNRNKNVVNTASD 382
                                       6899**************999999999888888888887766666666666 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.65
                     Vac14_Fab1_bd  28 ivkpvlkcfsDkdsr.vRyyacEslyniakvakgevlklln 67 
                                        +kp++k+++ ++sr v+  ++++l ni k a + ++k+ln
  gi|298675588|ref|YP_003727338.1| 423 NIKPLIKTLNNENSRdVKLSVADALVNIGKPAVDPLIKTLN 463
                                       58999999998887769*************99998888887 PP

  == domain 5  score: -2.0 bits;  conditional E-value: 6.5
                     Vac14_Fab1_bd  31 pvlkcfsDkdsrvRyyacE 49 
                                        ++k+++D+   vR  a+ 
  gi|298675588|ref|YP_003727338.1| 579 KLVKALKDEKGYVRISAIM 597
                                       3455555555555555555 PP

  == domain 6  score: 0.9 bits;  conditional E-value: 0.78
                     Vac14_Fab1_bd  28 ivkpvlkcfsDkdsrvRyyacEslyni 54 
                                        v+p+lk+++ +++++R+y++ +l  i
  gi|298675588|ref|YP_003727338.1| 703 SVSPLLKTVNHENKEMRHYSALALGKI 729
                                       5899***************98877555 PP

  == domain 7  score: 4.8 bits;  conditional E-value: 0.046
                     Vac14_Fab1_bd  26 eeivkpvlkcfsDkdsrvRyyacEsl 51 
                                       e+ v+p+++c++D++s++R  a+ +l
  gi|298675588|ref|YP_003727338.1| 764 EKAVEPLIECLDDANSKIRKNAVIAL 789
                                       6789***************8877655 PP

  == domain 8  score: 2.2 bits;  conditional E-value: 0.31
                     Vac14_Fab1_bd  26 eeivkpvlkcfsDkdsrvRyyac 48 
                                       ++ v+p+++ ++D+d ++R y++
  gi|298675588|ref|YP_003727338.1| 795 DKTVSPLIQRLNDNDPEIRKYSA 817
                                       67899**************9875 PP

  == domain 9  score: 4.2 bits;  conditional E-value: 0.074
                     Vac14_Fab1_bd  27 eivkpvlkcfsDkdsrvRyyacEslyniakvakgevlkl 65 
                                       + v+p++++++D+++ vR  ++ +l  i k a + +++ 
  gi|298675588|ref|YP_003727338.1| 827 KAVHPLINTLDDSNKDVRKATTNALAKIGKPAVQPLINS 865
                                       6799*********************99999887776665 PP

>> ERAP1_C  ERAP1-like C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.22     2e+02     161     213 ..      90     141 ..      56     164 .. 0.68
   2 !    6.6   0.1    0.0057       5.1     170     234 ..     160     226 ..     143     234 .. 0.74
   3 !   11.3   0.2    0.0002      0.18     107     247 ..     236     364 ..     233     413 .. 0.76
   4 ?    2.7   0.1     0.082        74      68     153 ..     419     496 ..     395     509 .. 0.63
   5 ?    3.4   0.2     0.051        45      83     228 ..     516     655 ..     505     675 .. 0.69
   6 !    6.9   0.0    0.0046       4.1     169     232 ..     722     786 ..     678     795 .. 0.74
   7 ?    0.7   0.0      0.33     3e+02     105     205 ..     796     881 ..     791     889 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.22
                                       S-HHHHHHHHHHHHHHS-HHHHHHHHHHHHC-SSHHHHHHHHHHHCC-S-HHH CS
                           ERAP1_C 161 ippdlrwavycalaanggeaewdallerykdtsapsekeaalralaatpdpel 213
                                        + d+r  +  +l  + g++ +d+l++ ++d+s    k aa+++l+ + +p+ 
  gi|298675588|ref|YP_003727338.1|  90 SNEDTRIKAAKSLGEKRGQNAIDSLIKAFEDESV-YVKIAAANSLGKIGNPAT 141
                                       4455666666666555578888888888888887.788888888888777765 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0057
                                       HHHHHHHS-HHHHHHHHHHH.HC-SSHHHHHHHHHHHCC-S-HHHHHHHHHHCTT..T..S-GGGHHH CS
                           ERAP1_C 170 ycalaanggeaewdallery.kdtsapsekeaalralaatpdpellerllnfvle..sdevrnqdlra 234
                                       + al    +e+  d+l +   +d s+ + +e a++al+ + d+ + e l++ +l+  +++vr+  + a
  gi|298675588|ref|YP_003727338.1| 160 VKALGNIRNENTADELSDVLlNDKSS-DVRESAAKALGDIGDKRAAEPLIDALLNdtDEDVRSKSVVA 226
                                       44552224666677777666357777.9999******9999999999999999944588898887766 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.0002
                                       HHHHHHHHHHT.TTS-HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHCSTT-S-HHHHHHHHHHHHHHS-HHHHH CS
                           ERAP1_C 107 leplaeklgwepgeshldaqlrslllsaacaagdpevveearklfkawlegddlippdlrwavycalaanggeaewd 183
                                       ++pl ++l  +       +++r+++  a+++ gd+   ++a  l +a l++    + d+r  v+ +    ++++ +d
  gi|298675588|ref|YP_003727338.1| 236 VKPLSNALLND-----ESSDVRESAAKALGDIGDK---RAAEPLINALLND---TDDDVRYQVVEVFSEIKDKNAVD 301
                                       66666666422.....568999999********99...7788999999986...8************9999****** PP

                                       HHHHHH.HC-SSHHHHHHHHHHHCC-S-HHHHHHHHHHCTT..T..S-GGGHHHHHH.HH.HSTTHHH CS
                           ERAP1_C 184 allery.kdtsapsekeaalralaatpdpellerllnfvle..sdevrnqdlralla.glannpegre 247
                                        l ++  +d +  + +  a++ l+ ++d+++ e l + + +  s+evr   + a+l+ g    p++++
  gi|298675588|ref|YP_003727338.1| 302 PLVKILlNDRDV-DVRSSAAEVLGDIEDEKAAEPLVKAL-NddSEEVRENSADAILEiGE---PATSP 364
                                       *****9455555.*********************88888.335999*9999999987444...44444 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.082
                                       GG--SHHHHHHHHHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHHHHHHHT.TTS-HHHHHHHHHHHHHHHTT-HHHH CS
                           ERAP1_C  68 anEtdylvwsqalsqlatlksllsadplyaalkaflrklleplaeklgwepgeshldaqlrslllsaacaagdpevv 144
                                       +nE+++ ++   l++ ++ +  ls   +++al +  +  ++pl++ l+   +   +d++l + l  a+++ gd++++
  gi|298675588|ref|YP_003727338.1| 419 RNESNIKPLIKTLNNENSRDVKLS---VADALVNIGKPAVDPLIKTLNN--N---DDKELEKYLQLALVQIGDEKAI 487
                                       455555555555555555444442...3336667777778888888863..2...4555555555666788888888 PP

                                       HHHHHHHHH CS
                           ERAP1_C 145 eearklfka 153
                                       e +++ +++
  gi|298675588|ref|YP_003727338.1| 488 ESLTRSLNK 496
                                       888777766 PP

  == domain 5  score: 3.4 bits;  conditional E-value: 0.051
                                       HHHHHHHHTTST..THHHHHHHHHHHHHHHHHHHHHT.TTS-HHHHHHHHHHHHHH.HTT-HHHHHHHHHHHHHHHC CS
                           ERAP1_C  83 latlksllsadp..lyaalkaflrklleplaeklgwepgeshldaqlrslllsaac.aagdpevveearklfkawle 156
                                       ++ lk  +++++    +++++ l+++ ++  + l+w+   +++++  r ++ saa+ + ++++++e++ k +k+  +
  gi|298675588|ref|YP_003727338.1| 516 IQPLKEAYKQENknSISNIANALDDINDKHTKSLAWS--LKYNNNPAR-SCASAAGvDINSKNAQEKLVKALKDE-K 588
                                       5566666642222344467777888888888888885..234777777.44444443888888888888887777.4 PP

                                       STT-S-HHHHHHHHHHHHHHS-HHHHHHHHHHHHC-SSHHHHHHHHHHHCC-S-HHHHHHHHHHCTT..T..S- CS
                           ERAP1_C 157 gddlippdlrwavycalaanggeaewdallerykdtsapsekeaalralaatpdpellerllnfvle..sdevr 228
                                       g       +r +++ ala  g+++ ++ + e     ++p+ + +a++al+ + d ++ + l+  +l+   ++v+
  gi|298675588|ref|YP_003727338.1| 589 G------YVRISAIMALAEIGNDKTVKPIAEVM-FKDNPEIRATAAYALGEIGDIDAEKHLIRAMLHdeYENVK 655
                                       4......79999999999999999999999885.2334589999999999999999888888887722233343 PP

  == domain 6  score: 6.9 bits;  conditional E-value: 0.0046
                                       HHHHHHHHS-HHHHHHHHHHHHC-SSHHHHHHHHHHHCC-S-HHHHHHHHHHCTT..T..S-GGGH CS
                           ERAP1_C 169 vycalaanggeaewdallerykdtsapsekeaalralaatpdpellerllnfvle..sdevrnqdl 232
                                          al + g+e  +++l+ + +++++ + k+ a++al+ +++++++e l++ + +  ++++r+  +
  gi|298675588|ref|YP_003727338.1| 722 SALALGKIGDERAVKSLIILLQNEDNREVKNGAIYALGEIRNEKAVEPLIECL-DdaNSKIRKNAV 786
                                       333333557999******99988888788******************988777.335667765554 PP

  == domain 7  score: 0.7 bits;  conditional E-value: 0.33
                                       HHHHHHHHHHHHT.TTS-HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHCSTT-S-HHHHHHHHHHHHHHS-HHH CS
                           ERAP1_C 105 klleplaeklgwepgeshldaqlrslllsaacaagdpevveearklfkawlegddlippdlrwavycalaanggeae 181
                                       k ++pl+++l+ +     +d + r+    ++++ gd+++v  + + +++        ++d+r+a  +ala+  g+  
  gi|298675588|ref|YP_003727338.1| 796 KTVSPLIQRLN-D-----NDPEIRKYSAIILGKIGDKKAVHPLINTLDDS-------NKDVRKATTNALAKI-GKPA 858
                                       55677777775.2.....67777766666788888887777777666666.......368888888888877.4555 PP

                                       HHHHHHHHHC-SSHHHHHHHHHHH CS
                           ERAP1_C 182 wdallerykdtsapsekeaalral 205
                                       ++ l++   d+ +p+ ke+a +al
  gi|298675588|ref|YP_003727338.1| 859 VQPLINSL-DSRNPDVKEHATNAL 881
                                       77777665.666677777777776 PP

>> BRCC36_C  BRCC36 C-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.92   8.3e+02      29      65 ..     112     153 ..      75     164 .. 0.73
   2 ?   -2.9   0.0         9     8e+03      50      65 ..     329     344 ..     328     351 .. 0.80
   3 ?    5.2   0.0     0.027        24      45      74 ..     354     383 ..     350     388 .. 0.87
   4 ?    1.8   0.0       0.3   2.7e+02      47      68 ..     386     407 ..     384     417 .. 0.77
   5 ?   -2.8   0.0       8.3   7.4e+03      53      64 ..     424     435 ..     415     438 .. 0.79
   6 ?   -1.0   0.0       2.3   2.1e+03      44      71 ..     446     473 ..     443     480 .. 0.74
   7 ?    0.1   0.0         1   8.9e+02      44      66 ..     694     717 ..     685     725 .. 0.78
   8 ?    0.0   0.0       1.1   9.5e+02      30      62 ..     776     807 ..     743     813 .. 0.71
   9 ?   -2.0   0.0       4.7   4.2e+03      53      66 ..     829     842 ..     825     853 .. 0.80
  10 ?    1.8   0.0      0.31   2.7e+02      42      67 ..     848     873 ..     835     879 .. 0.88
  11 ?    2.1   0.0      0.25   2.2e+02      42      62 ..     878     898 ..     874     906 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.92
                          BRCC36_C  29 ndllskihnsavytk.....slcalseviavPllqtLesrlk 65 
                                       ++l++ +  ++vy k     sl+++ +  ++ ll++L s+++
  gi|298675588|ref|YP_003727338.1| 112 DSLIKAFEDESVYVKiaaanSLGKIGNPATGDLLEVLDSQNE 153
                                       367777778899986544446777777777778888888876 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 9
                          BRCC36_C  50 eviavPllqtLesrlk 65 
                                       e+ a Pl+++L++  +
  gi|298675588|ref|YP_003727338.1| 329 EKAAEPLVKALNDDSE 344
                                       67889*****998766 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.027
                          BRCC36_C  45 lcalseviavPllqtLesrlkenknrlaaL 74 
                                       + ++ e  ++Pl++ L +r+k+  n++ +L
  gi|298675588|ref|YP_003727338.1| 354 ILEIGEPATSPLVNELDNRNKNVVNTASDL 383
                                       556788999****************99988 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.3
                          BRCC36_C  47 alseviavPllqtLesrlkenk 68 
                                       ++ + ++ Pl+qtL + +  n 
  gi|298675588|ref|YP_003727338.1| 386 EIGDPSVDPLIQTLSNSNSDNA 407
                                       66677899*******9998874 PP

  == domain 5  score: -2.8 bits;  conditional E-value: 8.3
                          BRCC36_C  53 avPllqtLesrl 64 
                                        +Pl++tL++ +
  gi|298675588|ref|YP_003727338.1| 424 IKPLIKTLNNEN 435
                                       689999999876 PP

  == domain 6  score: -1.0 bits;  conditional E-value: 2.3
                          BRCC36_C  44 slcalseviavPllqtLesrlkenknrl 71 
                                       +l+++    + Pl++tL++   +   ++
  gi|298675588|ref|YP_003727338.1| 446 ALVNIGKPAVDPLIKTLNNNDDKELEKY 473
                                       67777788889*****998876665555 PP

  == domain 7  score: 0.1 bits;  conditional E-value: 1
                          BRCC36_C  44 slcalsevi.avPllqtLesrlke 66 
                                       +l+++ e + ++Pll+t++  +ke
  gi|298675588|ref|YP_003727338.1| 694 ALGKIKESSsVSPLLKTVNHENKE 717
                                       678888865157*****9998886 PP

  == domain 8  score: 0.0 bits;  conditional E-value: 1.1
                          BRCC36_C  30 dllskihnsavytkslcal.seviavPllqtLes 62 
                                       d  ski  +av  ++l+++ s+++++Pl+q L++
  gi|298675588|ref|YP_003727338.1| 776 DANSKIRKNAV--IALGKInSDKTVSPLIQRLND 807
                                       55566666665..567777345677788888765 PP

  == domain 9  score: -2.0 bits;  conditional E-value: 4.7
                          BRCC36_C  53 avPllqtLesrlke 66 
                                       + Pl++tL + +k 
  gi|298675588|ref|YP_003727338.1| 829 VHPLINTLDDSNKD 842
                                       68******998876 PP

  == domain 10  score: 1.8 bits;  conditional E-value: 0.31
                          BRCC36_C  42 tkslcalseviavPllqtLesrlken 67 
                                       t +l+++    + Pl++ L sr+   
  gi|298675588|ref|YP_003727338.1| 848 TNALAKIGKPAVQPLINSLDSRNPDV 873
                                       7899*****************98665 PP

  == domain 11  score: 2.1 bits;  conditional E-value: 0.25
                          BRCC36_C  42 tkslcalseviavPllqtLes 62 
                                       t +l ++ e ++ Pl+++L +
  gi|298675588|ref|YP_003727338.1| 878 TNALIKIGEPCVQPLIKALDN 898
                                       67999*************986 PP

>> DUF3385  Domain of unknown function (DUF3385)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.15   1.3e+02      15      39 ..     175     199 ..     170     207 .. 0.92
   2 ?    4.5   0.0     0.033        29      11      39 ..     235     263 ..     230     378 .. 0.89
   3 ?    4.7   0.1     0.028        25      15      92 ..     427     508 ..     424     617 .. 0.65
   4 ?    2.5   0.1      0.14   1.2e+02      24      47 ..     619     661 ..     611     726 .. 0.63

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.15
                           DUF3385  15 LlnilkteqsqsirrevikllGilG 39 
                                       L ++l +++s ++r++++k lG +G
  gi|298675588|ref|YP_003727338.1| 175 LSDVLLNDKSSDVRESAAKALGDIG 199
                                       7889999***************999 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.033
                           DUF3385  11 LLelLlnilkteqsqsirrevikllGilG 39 
                                       +++ L n l +++s ++r++++k lG +G
  gi|298675588|ref|YP_003727338.1| 235 VVKPLSNALLNDESSDVRESAAKALGDIG 263
                                       667799999*****************999 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.028
                           DUF3385  15 LlnilkteqsqsirrevikllGilG..ALDPykh.................................kqveeraedk 56 
                                       L++ l++e+s +++++v+  l  +G  A+DP                                              
  gi|298675588|ref|YP_003727338.1| 427 LIKTLNNENSRDVKLSVADALVNIGkpAVDPLIKtlnnnddkelekylqlalvqigdekaiesltrsL--------- 494
                                       8999***************************9993333333333333333333333332222222220......... PP

                           DUF3385  57 krreeaaretdlsllmvglspsneeyyptvvinaLl 92 
                                                             n+e   t  i++L 
  gi|298675588|ref|YP_003727338.1| 495 ----------------------NKEKTYTANIESLQ 508
                                       ......................23333333333333 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.14
                           DUF3385  24 sqsirrevikllGilGALDPykh...................k 47 
                                       + +ir  ++  lG +G +D  kh                    
  gi|298675588|ref|YP_003727338.1| 619 NPEIRATAAYALGEIGDIDAEKHliramlhdeyenvksnaalA 661
                                       7899*******************44433333333333333330 PP

>> CLASP_N  CLASP N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1       0.2   1.7e+02     175     195 ..     202     222 ..     148     260 .. 0.70
   2 ?    0.4   0.1      0.46   4.1e+02     175     200 ..     266     291 ..     240     320 .. 0.74
   3 ?    0.6   0.0      0.39   3.5e+02     179     202 ..     333     356 ..     327     397 .. 0.80
   4 ?    0.3   0.0      0.49   4.4e+02      94     126 ..     575     607 ..     552     653 .. 0.74
   5 !    9.9   0.0   0.00056       0.5     118     196 ..     704     785 ..     679     793 .. 0.66
   6 ?    0.4   0.0      0.44   3.9e+02     160     197 ..     826     848 ..     788     884 .. 0.60

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.2
                           CLASP_N 175 dliekslkkgleDanptVRet 195
                                       +++e+++ ++l+D +  VR++
  gi|298675588|ref|YP_003727338.1| 202 RAAEPLIDALLNDTDEDVRSK 222
                                       567777888888888888875 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.46
                           CLASP_N 175 dliekslkkgleDanptVRetaRstf 200
                                       +++e+++ ++l+D +  VR +  ++f
  gi|298675588|ref|YP_003727338.1| 266 RAAEPLINALLNDTDDDVRYQVVEVF 291
                                       56777888888888888886665555 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.39
                           CLASP_N 179 kslkkgleDanptVRetaRstfwe 202
                                       + l+k+l+D + +VRe++ +++ e
  gi|298675588|ref|YP_003727338.1| 333 EPLVKALNDDSEEVRENSADAILE 356
                                       66999***********98776655 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.49
                           CLASP_N  94 illptLlkllgdtKkiisqnanqalaallsnas 126
                                       +  + L+k l d K  ++ +a +ala + ++ +
  gi|298675588|ref|YP_003727338.1| 575 NAQEKLVKALKDEKGYVRISAIMALAEIGNDKT 607
                                       455668888888888888888888887766555 PP

  == domain 5  score: 9.9 bits;  conditional E-value: 0.00056
                           CLASP_N 118 laallsnasfsprilqvlsvalqdKnvqpReysaiwLkilltrfe..........shkskleaslll.......dli 177
                                       ++ ll+ ++ +++ ++++s+++ +K    R              +          ++++++++ +++       + +
  gi|298675588|ref|YP_003727338.1| 704 VSPLLKTVNHENKEMRHYSALALGKIGDER--------------AvksliillqnEDNREVKNGAIYalgeirnEKA 766
                                       444455555444445555555555555555..............444444444334577777777777777888999 PP

                           CLASP_N 178 ekslkkgleDanptVReta 196
                                       ++ l+++l Dan+++R++a
  gi|298675588|ref|YP_003727338.1| 767 VEPLIECLDDANSKIRKNA 785
                                       999*************987 PP

  == domain 6  score: 0.4 bits;  conditional E-value: 0.44
                           CLASP_N 160 rfeshkskleasllldliekslkkgleDanptVRetaR 197
                                       + +               +  l+  l D+n  VR+++ 
  gi|298675588|ref|YP_003727338.1| 826 KKA---------------VHPLINTLDDSNKDVRKATT 848
                                       333...............33455555566665555543 PP

>> RICTOR_M  Rapamycin-insensitive companion of mTOR, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0033         3      68     102 ..      68     104 ..      47     106 .. 0.82
   2 ?   -0.5   0.0       1.1     1e+03      83     102 ..     146     165 ..     143     167 .. 0.88
   3 ?   -1.9   0.0       3.1   2.8e+03      77     101 ..     236     260 ..     207     262 .. 0.68
   4 ?   -0.5   0.0       1.1     1e+03      45      81 ..     287     323 ..     283     355 .. 0.65
   5 ?   -1.9   0.0       3.1   2.8e+03      75     101 ..     574     600 ..     569     602 .. 0.83
   6 ?   -3.5   0.0       9.7   8.7e+03      82     102 ..     771     791 ..     768     792 .. 0.82
   7 ?   -1.4   0.0       2.3   2.1e+03      81     102 ..     832     853 ..     825     854 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0033
                          RICTOR_M  68 sl..dysvdghiRiilskaLtnssekiRlyatkhLrk 102
                                       s+  +y+ d+ +  +++  L +s+e++R++a+k L++
  gi|298675588|ref|YP_003727338.1|  68 SVftNYKNDKSTDSLIKDLLNSSNEDTRIKAAKSLGE 104
                                       44469****************************9987 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.1
                          RICTOR_M  83 kaLtnssekiRlyatkhLrk 102
                                       ++L +++e++R y++k L++
  gi|298675588|ref|YP_003727338.1| 146 EVLDSQNEDVRKYSVKALGN 165
                                       68999***********9986 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3.1
                          RICTOR_M  77 iRiilskaLtnssekiRlyatkhLr 101
                                       ++ + +  L ++s+++R  a+k L+
  gi|298675588|ref|YP_003727338.1| 236 VKPLSNALLNDESSDVRESAAKALG 260
                                       4445555666888999999999887 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 1.1
                          RICTOR_M  45 iftllyklvelksrddllklilssldysvdghiRiil 81 
                                       + +++ ++ ++++ d l+k +l+  d +v + + ++l
  gi|298675588|ref|YP_003727338.1| 287 VVEVFSEIKDKNAVDPLVKILLNDRDVDVRSSAAEVL 323
                                       5566666666666666777777777766666555554 PP

  == domain 5  score: -1.9 bits;  conditional E-value: 3.1
                          RICTOR_M  75 ghiRiilskaLtnssekiRlyatkhLr 101
                                       +++++ l kaL++++  +R+ a+  L 
  gi|298675588|ref|YP_003727338.1| 574 KNAQEKLVKALKDEKGYVRISAIMALA 600
                                       56777899************9998776 PP

  == domain 6  score: -3.5 bits;  conditional E-value: 9.7
                          RICTOR_M  82 skaLtnssekiRlyatkhLrk 102
                                        ++L ++++kiR  a+  L+k
  gi|298675588|ref|YP_003727338.1| 771 IECLDDANSKIRKNAVIALGK 791
                                       57899999****999887765 PP

  == domain 7  score: -1.4 bits;  conditional E-value: 2.3
                          RICTOR_M  81 lskaLtnssekiRlyatkhLrk 102
                                       l + L +s++++R + t+ L k
  gi|298675588|ref|YP_003727338.1| 832 LINTLDDSNKDVRKATTNALAK 853
                                       5578999**********99976 PP

>> IBN_N  Importin-beta N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       2.8   2.5e+03      15      36 ..     172     192 ..     167     196 .. 0.82
   2 ?   -2.1   0.0       4.1   3.6e+03      18      36 ..     303     320 ..     294     323 .. 0.83
   3 ?   -2.6   0.0       6.1   5.4e+03      18      39 ..     395     415 ..     394     445 .. 0.78
   4 ?    7.0   0.0     0.006       5.3      15      39 ..     671     695 ..     667     760 .. 0.92
   5 ?   -1.7   0.0       3.1   2.7e+03      16      38 ..     736     757 ..     730     789 .. 0.76
   6 ?   -2.9   0.0       7.6   6.9e+03      25      39 ..     807     820 ..     801     822 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.8
                                       HHHHHHHHHCTTSHHHHHHHHH CS
                             IBN_N  15 lsallqilanseselevRqlAa 36 
                                       +  l+ +l n++s+  vR +Aa
  gi|298675588|ref|YP_003727338.1| 172 ADELSDVLLNDKSS-DVRESAA 192
                                       667999********.9998887 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.1
                                       HHHHHHCTTSHHHHHHHHH CS
                             IBN_N  18 llqilanseselevRqlAa 36 
                                       l+ il n+ ++  vR +Aa
  gi|298675588|ref|YP_003727338.1| 303 LVKILLNDRDV-DVRSSAA 320
                                       8999*******.***9998 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 6.1
                                       HHHHHHCTTSHHHHHHHHHHHH CS
                             IBN_N  18 llqilanseselevRqlAalyL 39 
                                       l+q l+ns+s+ +++  Aa +L
  gi|298675588|ref|YP_003727338.1| 395 LIQTLSNSNSD-NAKIKAADIL 415
                                       67888999999.8887777555 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.006
                                       HHHHHHHHHCTTSHHHHHHHHHHHH CS
                             IBN_N  15 lsallqilanseselevRqlAalyL 39 
                                       + +l ++l+++e + +vR +Aal L
  gi|298675588|ref|YP_003727338.1| 671 AHYLTRVLTDGEEKDQVRSSAALAL 695
                                       679*******99999*******998 PP

  == domain 5  score: -1.7 bits;  conditional E-value: 3.1
                                       HHHHHHHHCTTSHHHHHHHHHHH CS
                             IBN_N  16 sallqilanseselevRqlAaly 38 
                                        +l+ +l+n+++  ev+  A+  
  gi|298675588|ref|YP_003727338.1| 736 KSLIILLQNEDNR-EVKNGAIYA 757
                                       5667777777777.777766544 PP

  == domain 6  score: -2.9 bits;  conditional E-value: 7.6
                                       TTSHHHHHHHHHHHH CS
                             IBN_N  25 seselevRqlAalyL 39 
                                       + +++e+R  +a++L
  gi|298675588|ref|YP_003727338.1| 807 D-NDPEIRKYSAIIL 820
                                       4.4459**9999998 PP

>> SGS  SGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.3    0.0018       1.6       6      55 ..      50     107 ..      42     111 .. 0.77
   2 ?   -2.1   0.0       4.9   4.4e+03      18      43 ..     195     220 ..     170     224 .. 0.70
   3 ?    0.5   0.0      0.73   6.5e+02      17      52 ..     258     293 ..     241     298 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0018
                               SGS   6 lekelekeekeekke............eegeaalnklFkklYadadedtrrammKSyveSnG 55 
                                       +++e+++e+k    +            +++++++++l k+l + ++edtr    KS  e  G
  gi|298675588|ref|YP_003727338.1|  50 VNTETTDEDK----QgfqinipsvftnYKNDKSTDSLIKDLLNSSNEDTRIKAAKSLGEKRG 107
                                       3333332222....2355688888888999**************************988777 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.9
                               SGS  18 kkeeegeaalnklFkklYadadedtr 43 
                                         + ++++a++ l   l +d+ded+r
  gi|298675588|ref|YP_003727338.1| 195 LGDIGDKRAAEPLIDALLNDTDEDVR 220
                                       23366777888899999999999998 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.73
                               SGS  17 ekkeeegeaalnklFkklYadadedtrrammKSyve 52 
                                          + ++++a++ l + l +d+d+d+r  ++  + e
  gi|298675588|ref|YP_003727338.1| 258 ALGDIGDKRAAEPLINALLNDTDDDVRYQVVEVFSE 293
                                       33336778889999*************988887776 PP

>> DUF2274  Protein of unknown function (DUF2274)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1      0.12   1.1e+02       4      55 ..     597     648 ..     595     649 .. 0.93
   2 ?    3.3   0.0      0.13   1.2e+02       3      21 ..     723     741 ..     721     774 .. 0.79
   3 ?   -0.5   0.0       1.9   1.7e+03       6      34 ..     758     786 ..     753     814 .. 0.78
   4 ?   -1.2   0.0       3.2   2.8e+03       5      50 ..     788     833 ..     784     837 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.12
                           DUF2274   4 LkLgplpddkpvkltvelpaalhrdLaaYaellaretgeaadpakLiapMLe 55 
                                       + L+++ +dk vk   e+  + + +++a a++   e g+    ++Li +ML 
  gi|298675588|ref|YP_003727338.1| 597 MALAEIGNDKTVKPIAEVMFKDNPEIRATAAYALGEIGDIDAEKHLIRAMLH 648
                                       57999**************************9999***99999*******96 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.13
                           DUF2274   3 kLkLgplpddkpvkltvel 21 
                                        L Lg++ d+++vk  + l
  gi|298675588|ref|YP_003727338.1| 723 ALALGKIGDERAVKSLIIL 741
                                       699***********87765 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.9
                           DUF2274   6 LgplpddkpvkltvelpaalhrdLaaYae 34 
                                       Lg++ ++k+v   +e+  + ++++++ a 
  gi|298675588|ref|YP_003727338.1| 758 LGEIRNEKAVEPLIECLDDANSKIRKNAV 786
                                       89999999999999998888888776655 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 3.2
                           DUF2274   5 kLgplpddkpvkltvelpaalhrdLaaYaellaretgeaadpakLi 50 
                                        Lg+++ dk v   ++   +   ++++Y ++   + g+++ +  Li
  gi|298675588|ref|YP_003727338.1| 788 ALGKINSDKTVSPLIQRLNDNDPEIRKYSAIILGKIGDKKAVHPLI 833
                                       5788888888877777777777777777777777666666666665 PP

>> V-ATPase_H_N  V-ATPase subunit H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.73   6.5e+02      78     130 ..      81     135 ..      45     138 .. 0.79
   2 ?    1.1   0.1      0.21   1.9e+02      48     131 ..     147     230 ..     140     238 .. 0.70
   3 ?    3.3   0.2     0.045        40      80     130 ..     272     325 ..     265     388 .. 0.77
   4 ?   -1.1   1.4         1   9.3e+02      63     115 ..     427     479 ..     395     558 .. 0.46
   5 ?   -1.0   0.4      0.95   8.5e+02      18     104 ..     471     562 ..     463     583 .. 0.69
   6 ?    6.1   0.0    0.0066         6      48     131 ..     646     729 ..     630     739 .. 0.84
   7 ?    3.0   0.0     0.056        50      58     131 ..     752     823 ..     731     883 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.73
                      V-ATPase_H_N  78 vlidDllsedk..srvelflslakkeeqdpwkpflkllnrqddfivllalrllak 130
                                        li+Dll++ +  +r ++ +sl +k+ q+ +++++k+ + +  +++  a++ l k
  gi|298675588|ref|YP_003727338.1|  81 SLIKDLLNSSNedTRIKAAKSLGEKRGQNAIDSLIKAFEDESVYVKIAAANSLGK 135
                                       5899999876656899999999999999999999998888887777777776665 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.21
                      V-ATPase_H_N  48 lldedgpqyvklllnLlsklskedtlqy.iLvlidDllsedk.srvelflslakkeeqdpwkpflk.llnrqddfiv 121
                                       +ld++++++ k  ++ l ++++e+t    + vl++D  s+ + s ++++ ++    +++ ++p+++ lln +d+ + 
  gi|298675588|ref|YP_003727338.1| 147 VLDSQNEDVRKYSVKALGNIRNENTADElSDVLLNDKSSDVReSAAKALGDI---GDKRAAEPLIDaLLNDTDEDVR 220
                                       6778888888888888888877777754145677774444331444444443...3455899999989999999999 PP

                      V-ATPase_H_N 122 llalrllakl 131
                                        +++  l k+
  gi|298675588|ref|YP_003727338.1| 221 SKSVVALGKI 230
                                       9999888776 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.045
                      V-ATPase_H_N  80 idDllsedk..srvelflslakkeeqdpwkpflk.llnrqddfivllalrllak 130
                                       i+ ll++++   r ++++ +++ ++++ ++p++k lln +d  +   a+ +l  
  gi|298675588|ref|YP_003727338.1| 272 INALLNDTDddVRYQVVEVFSEIKDKNAVDPLVKiLLNDRDVDVRSSAAEVLGD 325
                                       555555444336788888888888888888888877887788888888877764 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 1
                      V-ATPase_H_N  63 LlsklskedtlqyiLvlidDllsedksrvelflslakkeeqdpwkpflkllnr 115
                                       L+++l++e+ + + L + d l++  k  v+ + ++ ++++++ ++ +l+l   
  gi|298675588|ref|YP_003727338.1| 427 LIKTLNNENSRDVKLSVADALVNIGKPAVDPLIKTLNNNDDKELEKYLQLALV 479
                                       44444444444444444444444444333333333333333333344432222 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 0.95
                      V-ATPase_H_N  18 egyvrsqliseedlkliksldkakkeqraklldedgpqyvklll.....nLlskl..skedtlqyiLvlidDllsed 87 
                                       e y +  l++  d k+i+sl+    +++  + +++ ++ ++  l      L +    ++++ + +i + +dD+ ++ 
  gi|298675588|ref|YP_003727338.1| 471 EKYLQLALVQIGDEKAIESLTRSLNKEK--TYTANIESLQNEQLdgeiqPLKEAYkqENKNSISNIANALDDINDKH 545
                                       6677788888888888888888665554..33444444444444444425555558888999999999999999988 PP

                      V-ATPase_H_N  88 ksrvelflslakkeeqd 104
                                       ++  +  l+++++  ++
  gi|298675588|ref|YP_003727338.1| 546 TKSLAWSLKYNNNPARS 562
                                       88888888887776666 PP

  == domain 6  score: 6.1 bits;  conditional E-value: 0.0066
                      V-ATPase_H_N  48 lldedgpqyvklllnLlsklskedtlqyiLvlidDllsedksrvelflslakkeeqdpwkpflkllnrqddfivlla 124
                                       +l  + +++++ +   l k+  ++t +y+ +++ D  ++d+ r+++ l l k +e++ ++p+lk+ n++++ + + +
  gi|298675588|ref|YP_003727338.1| 646 MLHDEYENVKSNAALALGKIGDDETAHYLTRVLTDGEEKDQVRSSAALALGKIKESSSVSPLLKTVNHENKEMRHYS 722
                                       5555555555555555788899***************************************************9999 PP

                      V-ATPase_H_N 125 lrllakl 131
                                       +  l k+
  gi|298675588|ref|YP_003727338.1| 723 ALALGKI 729
                                       9998876 PP

  == domain 7  score: 3.0 bits;  conditional E-value: 0.056
                      V-ATPase_H_N  58 klllnLlsklskedtlqyiLvlidDllsedksrvelflslakkeeqdpwkpflkllnrqddfivllalrllakl 131
                                       + ++  l ++++e+ ++ +   +dD  s+   r++++  l k + ++ ++p+++ ln +d  i + ++ +l k+
  gi|298675588|ref|YP_003727338.1| 752 NGAIYALGEIRNEKAVEPLIECLDDANSKI--RKNAVIALGKINSDKTVSPLIQRLNDNDPEIRKYSAIILGKI 823
                                       455555667788888888888888876664..556666666666777899999999999999999999988876 PP

>> DUF1829  Domain of unknown function DUF1829
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.062        55      23      74 ..     144     195 ..     138     197 .. 0.83
   2 ?    7.3   0.2    0.0073       6.5      33      74 ..     186     227 ..     179     240 .. 0.81
   3 ?    5.9   0.1      0.02        18      17      74 ..     201     259 ..     197     260 .. 0.74
   4 ?    9.8   0.2    0.0012       1.1      31      76 ..     248     293 ..     229     295 .. 0.83
   5 ?    3.0   0.1      0.16   1.4e+02      45      74 ..     294     323 ..     290     327 .. 0.82
   6 ?    0.4   0.9         1   9.3e+02      24      75 ..     396     448 ..     391     456 .. 0.62
   7 ?   -2.1   0.3       6.3   5.6e+03      31      80 ..     527     547 ..     521     558 .. 0.59
   8 ?   -0.0   0.1       1.4   1.3e+03      16      61 ..     573     618 ..     569     662 .. 0.73
   9 ?    6.7   0.0     0.012        10      22      75 ..     706     759 ..     697     770 .. 0.89
  10 ?   -1.3   0.0       3.5   3.1e+03      18      67 ..     765     813 ..     757     830 .. 0.72
  11 ?   -1.1   0.1         3   2.7e+03      55      75 ..     832     852 ..     792     855 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.062
                           DUF1829  23 likvinnpnknavkkalfaweDvkeareensklyvilnDkekkisseiedal 74 
                                       l++v+ + n++  k ++ a+  ++++++++    v+lnDk +++++++ +al
  gi|298675588|ref|YP_003727338.1| 144 LLEVLDSQNEDVRKYSVKALGNIRNENTADELSDVLLNDKSSDVRESAAKAL 195
                                       5667777777777777888888888888899999*************99987 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0073
                           DUF1829  33 navkkalfaweDvkeareensklyvilnDkekkisseiedal 74 
                                       +  ++a+ a+ D+ ++r++++ + ++lnD++++++s+   al
  gi|298675588|ref|YP_003727338.1| 186 DVRESAAKALGDIGDKRAAEPLIDALLNDTDEDVRSKSVVAL 227
                                       55567788899************************9876665 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.02
                           DUF1829  17 kkqperlikvi.nnpnknavkkalfaweDvkeareensklyvilnDkekkisseiedal 74 
                                       k++ e li+++ n  +++  +k+++a+  +k+++  ++   ++lnD+ +++++++ +al
  gi|298675588|ref|YP_003727338.1| 201 KRAAEPLIDALlNDTDEDVRSKSVVALGKIKNENVVKPLSNALLNDESSDVRESAAKAL 259
                                       66677777764155666666778888888888888888899999999999998888876 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.0012
                           DUF1829  31 nknavkkalfaweDvkeareensklyvilnDkekkisseiedalee 76 
                                       + +  ++a+ a+ D+ ++r++++ + ++lnD++++++ ++ + ++e
  gi|298675588|ref|YP_003727338.1| 248 SSDVRESAAKALGDIGDKRAAEPLINALLNDTDDDVRYQVVEVFSE 293
                                       4455567788899************************999988875 PP

  == domain 5  score: 3.0 bits;  conditional E-value: 0.16
                           DUF1829  45 vkeareensklyvilnDkekkisseiedal 74 
                                       +k++++ ++ + ++lnD++ +++s++ + l
  gi|298675588|ref|YP_003727338.1| 294 IKDKNAVDPLVKILLNDRDVDVRSSAAEVL 323
                                       667777788999************998876 PP

  == domain 6  score: 0.4 bits;  conditional E-value: 1
                           DUF1829  24 ikvinnpnknavkkalfaweDvk.earee...nsklyvilnDkekkisseiedale 75 
                                       i   +++++++  +a ++  D+  + r+e   ++ + ++ n++ ++++ ++ dal 
  gi|298675588|ref|YP_003727338.1| 396 I---QTLSNSNSDNAKIKAADILgKIRNEsniKPLIKTLNNENSRDVKLSVADALV 448
                                       4...4455566666666666665233444433555555668888888888888875 PP

  == domain 7  score: -2.1 bits;  conditional E-value: 6.3
                           DUF1829  31 nknavkkalfaweDvkeareensklyvilnDkekkisseiedaleeydik 80 
                                       nkn++++++ a++D++++                               k
  gi|298675588|ref|YP_003727338.1| 527 NKNSISNIANALDDINDKH-----------------------------TK 547
                                       5555556665555555543.............................33 PP

  == domain 8  score: -0.0 bits;  conditional E-value: 1.4
                           DUF1829  16 skkqperlikvinnpnknavkkalfaweDvkeareensklyvilnD 61 
                                       sk+++e+l+k+++  +     +a++a+  + + ++ ++ + v++ D
  gi|298675588|ref|YP_003727338.1| 573 SKNAQEKLVKALKDEKGYVRISAIMALAEIGNDKTVKPIAEVMFKD 618
                                       7888899999888777766667777666666666665555555555 PP

  == domain 9  score: 6.7 bits;  conditional E-value: 0.012
                           DUF1829  22 rlikvinnpnknavkkalfaweDvkeareensklyvilnDkekkisseiedale 75 
                                        l+k++n+ nk++ + +++a+  + ++r+ +s ++++ n+ ++++++ ++ al 
  gi|298675588|ref|YP_003727338.1| 706 PLLKTVNHENKEMRHYSALALGKIGDERAVKSLIILLQNEDNREVKNGAIYALG 759
                                       589**************************999999999*********9998875 PP

  == domain 10  score: -1.3 bits;  conditional E-value: 3.5
                           DUF1829  18 kqperlikvinnpnknavkkalfaweDvkeareensklyvilnDkekkis 67 
                                       k+ e li+ +   n +  k+a++a+  +++ ++  s l+  lnD++ +i+
  gi|298675588|ref|YP_003727338.1| 765 KAVEPLIECLDDANSKIRKNAVIALGKINSDKT-VSPLIQRLNDNDPEIR 813
                                       556677777777777777777777776666655.5556666677777776 PP

  == domain 11  score: -1.1 bits;  conditional E-value: 3
                           DUF1829  55 lyvilnDkekkisseiedale 75 
                                       l+  l+D++k+++++ ++al 
  gi|298675588|ref|YP_003727338.1| 832 LINTLDDSNKDVRKATTNALA 852
                                       444568999999998888875 PP

>> GlutR_dimer  Glutamyl-tRNAGlu reductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.7   1.5e+03      19      49 ..     201     231 ..     187     261 .. 0.71
   2 ?   -1.3   0.0       3.3     3e+03      19      49 ..     265     295 ..     253     309 .. 0.71
   3 ?    3.7   0.0     0.094        84      19      44 ..     329     354 ..     320     363 .. 0.86
   4 ?   -1.5   0.0       3.9   3.5e+03      21      57 ..     391     426 ..     376     439 .. 0.72
   5 ?    6.0   0.3     0.019        17      21      67 ..     454     496 ..     442     541 .. 0.69
   6 ?   -1.7   0.0       4.5     4e+03      18      41 ..     763     786 ..     757     807 .. 0.73
   7 ?   -0.5   0.0       1.9   1.7e+03      24      47 ..     831     853 ..     825     884 .. 0.51

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHS-S. CS
                       GlutR_dimer  19 slevvptIkalrekaeeireeeleralkkla 49 
                                       +++++p+I al + ++e +++    al k++
  gi|298675588|ref|YP_003727338.1| 201 KRAAEPLIDALLNDTDEDVRSKSVVALGKIK 231
                                       6788888888888888888777777777775 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.3
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHS-S. CS
                       GlutR_dimer  19 slevvptIkalrekaeeireeeleralkkla 49 
                                       +++++p+I+al + +++ ++ ++ +++++++
  gi|298675588|ref|YP_003727338.1| 265 KRAAEPLINALLNDTDDDVRYQVVEVFSEIK 295
                                       6788888988888888777777766666665 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.094
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       GlutR_dimer  19 slevvptIkalrekaeeireeelera 44 
                                       +++++p++kal++  ee+re+  + +
  gi|298675588|ref|YP_003727338.1| 329 EKAAEPLVKALNDDSEEVRENSADAI 354
                                       67899**************9987665 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 3.9
                                       HHHHHHHHHHHHHHHHHHHHHHHHHS-S..------- CS
                       GlutR_dimer  21 evvptIkalrekaeeireeeleralkklaldgedree 57 
                                       +v+p+I+ l ++ ++ ++   + +l k++ ++ + + 
  gi|298675588|ref|YP_003727338.1| 391 SVDPLIQTLSNSNSDNAKIKAADILGKIR-NESNIKP 426
                                       57888888888777777777777777776.6655554 PP

  == domain 5  score: 6.0 bits;  conditional E-value: 0.019
                                       HHHHHHHHHHHHHHHHHHHHHHHHHS-S..--------TTHHHHHHH CS
                       GlutR_dimer  21 evvptIkalrekaeeireeeleralkklaldgedreelekltrslvn 67 
                                       +v+p+Ik l+++ ++  e+ l+ al    ++  d++++e+ltrsl +
  gi|298675588|ref|YP_003727338.1| 454 AVDPLIKTLNNNDDKELEKYLQLAL----VQIGDEKAIESLTRSLNK 496
                                       4667777766665555555555555....555577889999998865 PP

  == domain 6  score: -1.7 bits;  conditional E-value: 4.5
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                       GlutR_dimer  18 kslevvptIkalrekaeeireeel 41 
                                       ++++v+p+I  l +  ++ir++ +
  gi|298675588|ref|YP_003727338.1| 763 NEKAVEPLIECLDDANSKIRKNAV 786
                                       567888999998888888888766 PP

  == domain 7  score: -0.5 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHHHHHHHHHHHHS- CS
                       GlutR_dimer  24 ptIkalrekaeeireeeleralkk 47 
                                       p+I+ l ++ +++r+++ + + +k
  gi|298675588|ref|YP_003727338.1| 831 PLINTLDDSNKDVRKATTNAL-AK 853
                                       555555555555554443322.22 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (929 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       956  (0.0533214); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.89u 0.27s 00:00:01.16 Elapsed: 00:00:00.48
# Mc/sec: 5848.14
//
Query:       gi|298675589|ref|YP_003727339.1|  [L=104]
Description: hypothetical protein Metev_1704 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 744.01
//
Query:       gi|298675590|ref|YP_003727340.1|  [L=357]
Description: cobalamin synthesis protein P47K [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-38  132.0   2.0    2.7e-38  131.3   2.0    1.3  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
      4e-05   22.7   0.9       0.01   14.8   0.2    2.3  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0038   15.3   3.3       0.31    9.0   0.0    2.1  2  Herpes_ori_bp    Origin of replication binding protein
     0.0066   16.3   1.0        2.4    7.9   0.1    2.3  2  ATP_bind_1       Conserved hypothetical ATP binding protein
     0.0074   15.9   0.1       0.02   14.5   0.1    1.7  1  SRP54            SRP54-type protein, GTPase domain
  ------ inclusion threshold ------
      0.032   14.1   1.8       0.45   10.4   0.0    2.8  3  TK               Thymidine kinase
      0.046   13.6   1.3       0.36   10.7   0.3    2.4  2  MobB             Molybdopterin guanine dinucleotide synthesis
      0.066   13.3   0.2      0.066   13.3   0.2    2.2  2  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
      0.099   11.7   0.5       0.21   10.6   0.5    1.6  1  T2SSE            Type II/IV secretion system protein
       0.18   11.7   0.1       0.18   11.7   0.1    2.7  3  AAA_31           AAA domain
       0.18   12.3   0.3       0.18   12.3   0.3    2.9  3  AAA_18           AAA domain
       0.29   10.8   2.1       0.67    9.6   0.2    2.2  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.79    9.8   3.6        1.3    9.0   0.1    2.6  2  AAA_14           AAA domain


Domain annotation for each model (and alignments):
>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.3   2.0   1.9e-41   2.7e-38       2     176 ..       3     178 ..       2     179 .. 0.93

  Alignments for each domain:
  == domain 1  score: 131.3 bits;  conditional E-value: 1.9e-41
                                       EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT.EEEETTTTECCHCTT-HHHHHHHH CS
                              cobW   2 vtvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgveivelenGciCctlredllkeleal 76 
                                       +++++GflGsGKTt l +l      +g+k+a+ivNe+ge++iD++ ++++g  + e++nGciCctl+ ++  +le+l
  gi|298675590|ref|YP_003727340.1|   3 IIIVGGFLGSGKTTSLLNLGkhLIDNGQKVAIIVNEIGEIGIDGDTITNSGIVTKEITNGCICCTLKINMEYTLENL 79 
                                       689***********999988665678*************************************************** PP

                                       HHHHTT-SEEEEEECTTTTHHHHHTT.SHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHH CS
                              cobW  77 eereerldviliEttGlaePapvaft.eeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDl 152
                                        ++  ++d ++iE tGla P+++    e+   ++l    +v++vD+++++ae ++i++ +  q++ ad+l +nK D 
  gi|298675590|ref|YP_003727340.1|  80 NDEL-NPDTVIIEPTGLAFPNQIKQDlENMDIKNLSFAPIVTLVDGSRFKAEVDQIPKFILTQIEEADILGINKNDI 155
                                       ****.9*****************444444455689999*************************************** PP

                                       HCHC..HHHHHHHHHHHHTTS-EE CS
                              cobW 153 ldeeallekleerlrqlnpeakvl 176
                                       +d+e+ +e+ ++ l++ npeak+l
  gi|298675590|ref|YP_003727340.1| 156 ADAEN-IENTRKFLKDKNPEAKIL 178
                                       ***95.6**************997 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.2   7.4e-06      0.01      32      63 ..       4      35 ..       1      45 [. 0.91
   2 !    6.4   0.0    0.0028       3.9     165     193 ..     141     169 ..     108     224 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.4e-06
                                      EEEEE-TTSSHHHHHHHHHHHHHCTT--EEEE CS
                              MeaB 32 vGltGvPGaGkstlvealglelrrrGkrvavl 63
                                      + + G+ G+Gk t + +lg +l+++G++va++
  gi|298675590|ref|YP_003727340.1|  4 IIVGGFLGSGKTTSLLNLGKHLIDNGQKVAII 35
                                      55789**************************8 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0028
                                       CHHH-SEEEEE---HHHHHHHHHHHHHHH CS
                              MeaB 165 ileiaDiivvnkaDkkeaekaarelraal 193
                                        +e aDi+ +nk+D ++ae+ +++ ++  
  gi|298675590|ref|YP_003727340.1| 141 QIEEADILGINKNDIADAENIENTRKFLK 169
                                       5799**********999998877655443 PP

>> Herpes_ori_bp  Origin of replication binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0   0.00022      0.31      51      84 ..       3      36 ..       1      38 [. 0.90
   2 !    6.5   1.2    0.0013       1.9     427     553 ..     200     330 ..     183     350 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00022
                     Herpes_ori_bp 51 vlvvRApmGsGkttALiewLkevldsedlsvlvv 84
                                      + +v   +GsGktt L++  k+++d+ ++ +++v
  gi|298675590|ref|YP_003727340.1|  3 IIIVGGFLGSGKTTSLLNLGKHLIDNGQKVAIIV 36
                                      67888889******************99999998 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0013
                     Herpes_ori_bp 427 sasalfsrFkykHylErctltslsDslnlLhtLLaenkikvrldGkdlplsa...edFcsFlsilredalaaerklr 500
                                       s+++    F yk  ++ + +   s  +++    L++ + +  ++   ++++    ++  +F+ +++++  + ++ ++
  gi|298675590|ref|YP_003727340.1| 200 SNKHSLDGFEYKNSIDMSQVSMFSGEFTVFSKQLTSESSERIVNEIVNDIRYrvlNTSPDFIGHIKTSMEFSNKRIK 276
                                       55555667888888888888888888888888777765443333333333332235566899999999999999999 PP

                     Herpes_ori_bp 501 elraknnstaeeleaqllekdavgkfvekyLr..eavdaeeiiallkdlaeplkr 553
                                       +  +  n+   ++e+++le+++++  + k+L    ++ ++e+++++k+  ++  +
  gi|298675590|ref|YP_003727340.1| 277 SSVTSSNE-DPQVEKSILENENIALPRLKFLAavTGISEDELTDIVKNTISQNLE 330
                                       76645444.4578999**************9722578889******987664444 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.1    0.0018       2.4       2      30 ..       7      35 ..       5      37 .. 0.87
   2 !    7.1   0.1    0.0031       4.3     126     214 ..     118     202 ..      60     220 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0018
                        ATP_bind_1  2 vGpaGsGKttfvgalseilelrgrsvavv 30
                                       G  GsGKtt   +l ++l ++g++va++
  gi|298675590|ref|YP_003727340.1|  7 GGFLGSGKTTSLLNLGKHLIDNGQKVAII 35
                                      5778*******************999875 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0031
                        ATP_bind_1 126 vvyLvDsqrltdptkfisgllsalsamlrlelPhvvvlnkfDllkek.lekeleffedvealslllekeeekykkla 201
                                       +v LvD  r +  ++ i +      ++ ++e   +  +nk D+++ +  e   +f++d +   ++l+   +   +++
  gi|298675590|ref|YP_003727340.1| 118 IVTLVDGSRFKAEVDQIPK-----FILTQIEEADILGINKNDIADAEnIENTRKFLKDKNPEAKILNFSAKHKDENF 189
                                       6889999999999999999.....8999***************9988889999999999999999999999999999 PP

                        ATP_bind_1 202 eaiaelleefalv 214
                                       +++ +ll+e +  
  gi|298675590|ref|YP_003727340.1| 190 QNLINLLDENSNK 202
                                       9999999998765 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   1.4e-05      0.02       3      35 ..       3      35 ..       1      39 [. 0.91

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.4e-05
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEE CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllv 35
                                      +i++ G+ G+GKTt+l  L ++l ++g+kv+++
  gi|298675590|ref|YP_003727340.1|  3 IIIVGGFLGSGKTTSLLNLGKHLIDNGQKVAII 35
                                      788889************************998 PP

>> TK  Thymidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00033      0.45       3      59 ..       3      59 ..       1     120 [. 0.67
   2 ?   -1.7   0.0       1.6   2.2e+03      78     128 ..     145     196 ..     118     205 .. 0.67
   3 ?    2.0   0.2      0.12   1.7e+02       3      68 ..     214     280 ..     212     299 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00033
                                TK  3 ielilgpmfaGKsteLlrrvkryqlaekkvvvikaakdnRysegkvvthdgisleak 59
                                      i ++ g + +GK+t+Ll+  k++  + +kv +i +++ +    g+ +t +gi ++  
  gi|298675590|ref|YP_003727340.1|  3 IIIVGGFLGSGKTTSLLNLGKHLIDNGQKVAIIVNEIGEIGIDGDTITNSGIVTKEI 59
                                      777888899************************999988877777777777776655 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.6
                                TK  78 vdvvlvDEaqFfe.qdivelseklanegkivivagLdtdFerklFenilkll 128
                                        d++++      + ++i++  + l +++    +    ++++ + F+n  +ll
  gi|298675590|ref|YP_003727340.1| 145 ADILGINKNDIADaENIENTRKFLKDKNPEAKILNFSAKHKDENFQNLINLL 196
                                       5666666666666666666666666666666666677777777777777776 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.12
                                TK   3 ielilgpmfaGKsteLlrrvkryqlaekkvvvikaakdnRyseg....kvvthdgisleakksktsslee 68 
                                       i +   +mf+G  t     +k+++  + + +v   ++d Ry +     + + h+++s+e  +++++s+ +
  gi|298675590|ref|YP_003727340.1| 214 IDMSQVSMFSGEFTV---FSKQLTSESSERIVNEIVNDIRYRVLntspDFIGHIKTSMEFSNKRIKSSVT 280
                                       666677899997775...4677888888889999999999987644567888999999988555555443 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   0.00026      0.36       2      40 ..       4      42 ..       3      50 .. 0.83
   2 ?    0.8   0.0       0.3   4.1e+02      32      57 ..     324     349 ..     314     354 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00026
                              MobB  2 lgivgksgsGKTtLleklipelkarglrvgtiKhahhgf 40
                                      + + g+ gsGKTt l +l ++l ++g +v++i  +  ++
  gi|298675590|ref|YP_003727340.1|  4 IIVGGFLGSGKTTSLLNLGKHLIDNGQKVAIIVNEIGEI 42
                                      5566899***********************997766555 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.3
                              MobB  32 tiKhahhgfdvdkpgkDsyrhrkAGA 57 
                                       ti ++ ++ +++ ++kDs+ h +  A
  gi|298675590|ref|YP_003727340.1| 324 TISQNLENKNMNVEEKDSHCHSQNDA 349
                                       6777788899*********9998665 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   4.8e-05     0.066       1      33 [.       3      35 ..       3      38 .. 0.92
   2 ?   -0.3   0.3      0.78   1.1e+03      51      51 ..     211     211 ..     110     323 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.8e-05
                                      EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  1 iaiastkGGvGKTtlaanLaralarrglrVllv 33
                                      i+i+++  G+GKTt ++nL++ l ++g +V+ +
  gi|298675590|ref|YP_003727340.1|  3 IIIVGGFLGSGKTTSLLNLGKHLIDNGQKVAII 35
                                      67888888**********************976 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.78
                                       H CS
                                       x RF
                              CbiA  51 d 51 
                                       +
  gi|298675590|ref|YP_003727340.1| 211 K 211
                                       1 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.5   0.00015      0.21     131     175 ..       3      48 ..       1      89 [. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00015
                             T2SSE 131 lilvsGgTgsGKttll.yallkeinksderivtvEDpvEiqlegan 175
                                       +i+v G  gsGKtt+l +   + i++ ++  ++v    Ei ++g+ 
  gi|298675590|ref|YP_003727340.1|   3 IIIVGGFLGSGKTTSLlNLGKHLIDNGQKVAIIVNEIGEIGIDGDT 48 
                                       7999999*******98577777888877777778888888877665 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00013      0.18      12      36 ..      11      35 ..       1     110 [. 0.83
   2 ?    1.5   0.3      0.18   2.5e+02      54     137 ..     184     268 ..     148     277 .. 0.65
   3 ?   -1.3   0.1       1.3   1.7e+03      48      75 ..     310     342 ..     276     357 .] 0.46

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                            AAA_31 12 GvGKTTtsvnlaaalaklgkkvLlv 36
                                      G GKTT+ +nl++ l  +g+kv ++
  gi|298675590|ref|YP_003727340.1| 11 GSGKTTSLLNLGKHLIDNGQKVAII 35
                                      89********************876 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.18
                            AAA_31  54 eiektlyevli..eeknikeaiiktkvenldlipssidLaeaeielvelekkeeilkellekvkdeYDyiiiDcpPs 128
                                       ++++++ ++++  +e++ k+ +      ++++  s++++ + e  +++++ + e  +++++++ ++  y ++ ++P+
  gi|298675590|ref|YP_003727340.1| 184 HKDENFQNLINllDENSNKHSLD-GFEYKNSIDMSQVSMFSGEFTVFSKQLTSESSERIVNEIVNDIRYRVLNTSPD 259
                                       33444444442212333333332.22334467778888888888888888888888888888888888888888887 PP

                            AAA_31 129 LglltenaL 137
                                            ++++
  gi|298675590|ref|YP_003727340.1| 260 FIGHIKTSM 268
                                       655555555 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.3
                            AAA_31  48 lgiekne....iektlyevl.ieeknikeaiik 75 
                                       +gi+++e    +++t+ + l ++++n++e   +
  gi|298675590|ref|YP_003727340.1| 310 TGISEDEltdiVKNTISQNLeNKNMNVEEKDSH 342
                                       444444422222233333332234444443333 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3   0.00013      0.18       1      25 [.       4      33 ..       4      91 .. 0.79
   2 ?    0.7   0.7       0.5     7e+02      32      70 ..     168     207 ..     138     296 .. 0.64
   3 ?   -1.4   0.0       2.3   3.2e+03      11      25 ..     322     337 ..     311     354 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                            AAA_18  1 IlltGtpGvGKttlakeLskrl.gf....g 25
                                      I++ G  G+GKtt   +L k+l  +     
  gi|298675590|ref|YP_003727340.1|  4 IIVGGFLGSGKTTSLLNLGKHLiDNgqkvA 33
                                      99*******************966644430 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.5
                            AAA_18  32 akenglllevdpealdeskrldedkldklldaleenss.....a 70 
                                       +k+++++    ++    s + ++++ ++l+++l+ens+      
  gi|298675590|ref|YP_003727340.1| 168 LKDKNPEAKILNF----SAKHKDENFQNLINLLDENSNkhsldG 207
                                       3444444444444....444444444667777777665433440 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.3
                            AAA_18  11 KttlakeLskrl.gfg 25 
                                       K t++++L++++ ++ 
  gi|298675590|ref|YP_003727340.1| 322 KNTISQNLENKNmNVE 337
                                       6688888877753432 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2   0.00049      0.67       1      36 [.       4      37 ..       4      63 .. 0.84
   2 ?    0.4   0.1      0.33   4.6e+02     121     168 ..     237     287 ..     209     340 .. 0.50

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00049
                   Viral_helicase1  1 ivvhGvpGcGKStlirkllrtsliltvnrptaellt 36
                                      i+v G+ G+GK+t++ +l ++   +  +++ a++++
  gi|298675590|ref|YP_003727340.1|  4 IIVGGFLGSGKTTSLLNLGKH--LIDNGQKVAIIVN 37
                                      6899************99988..6666666666655 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.33
                   Viral_helicase1 121 rvgrrttyllpsdvaeilsakvgteveversgel..kvetepkgqe.kvlv 168
                                        ++r    + ++ ++ +l+ +  +  +++ s+e+  k++ +++ ++ ++ +
  gi|298675590|ref|YP_003727340.1| 237 SSERIVNEIVNDIRYRVLNTSPDFIGHIKTSMEFsnKRIKSSVTSSnEDPQ 287
                                       333333445555555555555444444444444433111111111122222 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   0.00097       1.3       3      32 ..       2      30 ..       1      61 [. 0.81
   2 ?    0.8   0.6      0.33   4.6e+02      48      75 ..     172     201 ..     133     291 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00097
                            AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkes 32
                                      +i+++ G   +GKTt l +l k+l+ ++ +
  gi|298675590|ref|YP_003727340.1|  2 RIIIVGGFLGSGKTTSLLNLGKHLI-DNGQ 30
                                      6999*****************9998.3333 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.33
                            AAA_14  48 dpe.kllelilek.lkeekktylflDEiqe 75 
                                       +pe k+l++  ++  ++ ++ + +lDE ++
  gi|298675590|ref|YP_003727340.1| 172 NPEaKILNFSAKHkDENFQNLINLLDENSN 201
                                       222233333333222223444445555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       987  (0.0550505); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2526.28
//
Query:       gi|298675591|ref|YP_003727341.1|  [L=550]
Description: 4Fe-4S ferredoxin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-69  234.5   2.9    4.7e-69  232.3   2.9    1.9  1  RACo_C_ter   C-terminal domain of RACo the ASKHA domain
      3e-13   49.8   0.4    7.8e-13   48.4   0.2    1.9  2  Raco_middle  RACo middle region
    6.5e-07   28.9   7.4      0.003   17.3   0.8    2.7  2  Fer4         4Fe-4S binding domain
    6.3e-06   26.2   4.5      0.019   15.1   0.5    2.5  2  Fer4_10      4Fe-4S dicluster domain
      7e-06   26.1  10.4    1.5e-05   25.1  10.4    1.6  1  Fer4_9       4Fe-4S dicluster domain
    7.2e-06   26.9   9.1    0.00051   20.9   1.3    2.6  2  Fer4_16      4Fe-4S double cluster binding domain
      3e-05   24.1   8.6    6.6e-05   23.0   8.6    1.6  1  Fer4_21      4Fe-4S dicluster domain
    3.7e-05   24.2  11.4    0.00043   20.8  12.3    2.2  3  Fer4_7       4Fe-4S dicluster domain
     0.0001   22.2  11.7    0.00053   20.0   2.2    2.5  2  Fer4_6       4Fe-4S binding domain
    0.00031   21.1   5.2      0.072   13.5   0.2    2.5  2  Fer4_8       4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.013   15.5   2.2      0.013   15.5   2.2    2.5  2  Fer4_2       4Fe-4S binding domain
      0.033   14.7  11.8      0.056   14.0   2.7    2.6  2  Fer4_4       4Fe-4S binding domain
       0.09   13.8  14.7       0.51   11.4   4.3    2.7  2  Fer4_3       4Fe-4S binding domain
        1.1    9.8  12.7        1.7    9.3   3.0    2.5  2  Fer4_17      4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> RACo_C_ter  C-terminal domain of RACo the ASKHA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  232.3   2.9   3.6e-72   4.7e-69       1     259 [.     168     426 ..     168     427 .. 0.95

  Alignments for each domain:
  == domain 1  score: 232.3 bits;  conditional E-value: 3.6e-72
                                       S-EEEEEESSSEEEEEE-SS-EEEEEEE--SCCCTTTSTTBE-SSTTEEEEEEEEGGGSSEEEEECTSS-....... CS
                        RACo_C_ter   1 elslliDiGTNaEivlgnkdellaasaaaGPAlEGaeikcGmrAapgAIedveidpetlevelkvigdek....... 70 
                                       e s+++D+GTNaE++l+++d+++++saaaGPA+EG++i+cGm+A pgAI dv  +pe   ++l+v++d+        
  gi|298675591|ref|YP_003727341.1| 168 EPSMVTDYGTNAEMALKVGDRIITGSAAAGPAIEGQGINCGMLAGPGAITDV--NPEGNYWRLTVLDDSMlerkgdl 242
                                       679*************************************************..777778******98767889999 PP

                                       ...............-SEEEHHHHHHHHHHHHHTTSB-TTS-B-GGG-TTTEEEETTCEEEEEE-GGGSSSS-EEEE CS
                        RACo_C_ter  71 ...............akGicGsGiidliaelleagiidkkgklnkelkserireeeetleyvlakaeetetkdivit 132
                                                      a Gi+G+G+i+l++ +le+g+i++ +kl                +++l         +i it
  gi|298675591|ref|YP_003727341.1| 243 vnpvagevieqsetrAIGITGTGMISLLSVALETGLIKTMPKL-------------PDGRLILGG-------GIEIT 299
                                       999999999999999****************************.............344555543.......8**** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHTT--GGG--EEEEESSGGGCEEHHHHHHHTSS-SS-GGGEEEECSHHHHHHHH CS
                        RACo_C_ter 133 ekDieelikakaAiyagiktLleevglevediekvylAGafGsyidaekAitiGllPdlelekvvqvGNtslagAre 209
                                       e+D++e++ka +Ai+a + t+l e+gl+++d+e++y++Ga+G+y+da+kA+++G++P  +++++vq+GNts+++A+e
  gi|298675591|ref|YP_003727341.1| 300 EDDVREAGKAVGAIRASHLTMLMEAGLDFKDLENMYMTGASGTYVDADKARKLGICPG-SAKNIVQFGNTSISLAKE 375
                                       **********************************************************.****************** PP

                                       HHCBHHHHHHHHHHHHHE..EE--TTSSSHHHHHHHHHSSSS-SSGGG-ST- CS
                        RACo_C_ter 210 allseealeeleeiarki..tyielateeeFqeeyvaalflphtdlelfpsv 259
                                       ++l+e++l+e+ e a+ki  +++++a++e F+  y+++ +++++++ +++++
  gi|298675591|ref|YP_003727341.1| 376 LILNESKLDEVVEFAHKIetDHLMMAKSEMFKLIYSCEFSYWTQGM-PLEMY 426
                                       ******************999************************9.77765 PP

>> Raco_middle  RACo middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4   0.2   6.1e-16   7.8e-13       1     161 [.       2     164 ..       2     166 .. 0.85
   2 ?   -3.5   0.0       5.8   7.4e+03     125     150 ..     322     347 ..     311     349 .. 0.77

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 6.1e-16
                       Raco_middle   1 yGlavDiGtTtvvaaLvdletgkelaeasalNpQikyGeDvlsRiayakeeeegleklqkavveeinelieelleea 77 
                                       yG+a+D+Gt+ + a+L+dl+t++++++  ++ +    G +v+  + +a +        +++++e i++ +ee++++ 
  gi|298675591|ref|YP_003727341.1|   2 YGIAMDLGTSGIRAQLIDLDTEETIKTVLTMRHPLP-GGNVIDQLDFAIQ------LGEDVATEIIQDTVEEIIDNF 71 
                                       9**************************999977665.889*********9......224566777889999999999 PP

                       Raco_middle  78 giekeeiyevvvagNttMlhlllgldpkslakap........yvpvvseavelkakelglki.npeakvyvlpnvss 145
                                       +i+  ei+++ v+gN + l l+ +++ + la a            v ++a++++a+e+  ++  p++++++ p++ +
  gi|298675591|ref|YP_003727341.1|  72 NIDLLEIKKLSVCGNPIQLSLFQDTEIRDLAYAGesmqkelgVENVKRDAKVVPANEVFKNLdLPNCTIIIPPSIQH 148
                                       ***************************99987641111112245677899999****988874599*********** PP

                       Raco_middle 146 yvGgDivagilasglh 161
                                        vG+D++a ++ +++ 
  gi|298675591|ref|YP_003727341.1| 149 EVGADALAMMIETDFM 164
                                       ***********99875 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.8
                       Raco_middle 125 kelglkinpeakvyvlpnvssyvGgD 150
                                        e gl+ ++  ++y+  + ++yv +D
  gi|298675591|ref|YP_003727341.1| 322 MEAGLDFKDLENMYMTGASGTYVDAD 347
                                       57788888888899999999999888 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.9   1.7e-05     0.022       7      23 ..     479     495 ..     478     496 .. 0.92
   2 !   17.3   0.8   2.4e-06     0.003       9      24 .]     516     531 ..     516     531 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.7e-05
                                       TSSS-THHHHHSTTTEE CS
                              Fer4   7 kCigCGaCvevCPvgAI 23 
                                        C +C  C++ CP  A+
  gi|298675591|ref|YP_003727341.1| 479 NCSFCYMCEDKCPEKAL 495
                                       5*************997 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 2.4e-06
                                       SS-THHHHHSTTTEEE CS
                              Fer4   9 igCGaCvevCPvgAIt 24 
                                       + C++Cv+vCP  AI+
  gi|298675591|ref|YP_003727341.1| 516 VSCKRCVDVCPKKAIQ 531
                                       57************95 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.3   0.00013      0.16      30      56 .]     465     491 ..     458     499 .. 0.85
   2 !   15.1   0.5   1.5e-05     0.019       3      23 ..     507     529 ..     505     546 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                           Fer4_10  30 geaseeeavrkkvekCtgcgaCveaCP 56 
                                         ++ + +++  +++C +c +C ++CP
  gi|298675591|ref|YP_003727341.1| 465 VLRDLGIVIERPIKNCSFCYMCEDKCP 491
                                       556677788888999999999999999 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.5e-05
                           Fer4_10   3 vidddtC..irCgkCvkaCPadl 23 
                                       v+d+++C  + C++Cv++CP ++
  gi|298675591|ref|YP_003727341.1| 507 VHDSQRClgVSCKRCVDVCPKKA 529
                                       67999**6669*********955 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1  10.4   1.1e-08   1.5e-05       1      51 []     479     530 ..     479     530 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.1e-08
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaC..igCgaCveaCpkgai 51 
                                       +C  C  C+++Cp ++ +  + ++ + + ++s+ +C  ++C++Cv++Cpk+ai
  gi|298675591|ref|YP_003727341.1| 479 NCSFCYMCEDKCPEKALQIVSYKEDVYQVHDSQ-RClgVSCKRCVDVCPKKAI 530
                                       5*****************999999999988887.9*7777**********997 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   2.2    0.0024       3.1       1      20 [.     479     498 ..     479     515 .. 0.71
   2 !   20.9   1.3     4e-07   0.00051       3      30 ..     516     543 ..     512     549 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0024
                           Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                       +C  C  C + CP++a++  
  gi|298675591|ref|YP_003727341.1| 479 NCSFCYMCEDKCPEKALQIV 498
                                       5999************8743 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 4e-07
                           Fer4_16   3 gtCgkCaevCPtnaikekkekeiearec 30 
                                       ++C++C++vCP +ai+ k+ k+++a+e+
  gi|298675591|ref|YP_003727341.1| 516 VSCKRCVDVCPKKAIQFKNVKVLNAHES 543
                                       58****************9999888775 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   8.6   5.2e-08   6.6e-05       7      58 ..     479     531 ..     475     532 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 5.2e-08
                           Fer4_21   7 kCigCgkCliaCedtshqaieidaktvlkvvedeCvG..CnlCssvCPvedcie 58 
                                       +C  C  C   C++++ q ++++++ +  + +++C G  C+ C++vCP +++i+
  gi|298675591|ref|YP_003727341.1| 479 NCSFCYMCEDKCPEKALQIVSYKEDVYQVHDSQRCLGvsCKRCVDVCP-KKAIQ 531
                                       799999999*************9999999999***7666*********.68886 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   3.0   0.00053      0.67      35      52 .]     477     494 ..     450     494 .. 0.84
   2 !   20.8  12.3   3.3e-07   0.00043       2      52 .]     480     529 ..     479     529 .. 0.81
   3 !   15.5   2.5   1.5e-05      0.02       3      23 ..     516     536 ..     512     544 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00053
                            Fer4_7  35 pekClgCgaCvavCPtga 52 
                                         +C++C++C++ CP +a
  gi|298675591|ref|YP_003727341.1| 477 IKNCSFCYMCEDKCPEKA 494
                                       579************876 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 3.3e-07
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekv.eidpekClg..CgaCvavCPtga 52 
                                       C  C  C++ Cp ka+++  ++   + + + ++d+++Clg  C++Cv+vCP++a
  gi|298675591|ref|YP_003727341.1| 480 CSFCYMCEDKCPEKALQIVSYK---E-DVYqVHDSQRCLGvsCKRCVDVCPKKA 529
                                       999***************9883...3.344155799**7555*********986 PP

  == domain 3  score: 15.5 bits;  conditional E-value: 1.5e-05
                            Fer4_7   3 igCgaCvaaCpvkaieldeee 23 
                                       + C++Cv++Cp kai++++++
  gi|298675591|ref|YP_003727341.1| 516 VSCKRCVDVCPKKAIQFKNVK 536
                                       47**************98764 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   2.2     0.005       6.4       9      24 .]     480     495 ..     478     495 .. 0.85
   2 !   20.0   2.2   4.1e-07   0.00053       3      24 .]     507     530 ..     507     530 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.005
                            Fer4_6   9 CigCgdCvrvCPegai 24 
                                       C  C+ C++ CPe+a+
  gi|298675591|ref|YP_003727341.1| 480 CSFCYMCEDKCPEKAL 495
                                       555**********996 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 4.1e-07
                            Fer4_6   3 eidpdkCig..CgdCvrvCPegai 24 
                                       ++d ++C+g  C +Cv+vCP +ai
  gi|298675591|ref|YP_003727341.1| 507 VHDSQRCLGvsCKRCVDVCPKKAI 530
                                       589*****666*********9998 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.2   5.6e-05     0.072      44      64 ..     458     493 ..     411     494 .. 0.74
   2 !    9.0   1.1    0.0015       1.9      49      64 ..     511     528 ..     496     529 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.6e-05
                            Fer4_8  44 e...............eealwsCttcgaCtevCpvg 64 
                                                       e+ +++C+ c +C+++Cp++
  gi|298675591|ref|YP_003727341.1| 458 LgkesvqvlrdlgiviERPIKNCSFCYMCEDKCPEK 493
                                       13334455556777779999**************97 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0015
                            Fer4_8  49 wsC..ttcgaCtevCpvg 64 
                                       ++C  ++c++C++vCp++
  gi|298675591|ref|YP_003727341.1| 511 QRClgVSCKRCVDVCPKK 528
                                       5665578*********97 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   1.7      0.46   5.8e+02      10      21 ..     480     491 ..     473     492 .. 0.74
   2 ?   15.5   2.2     1e-05     0.013       4      21 ..     507     526 ..     505     527 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.46
                            Fer4_2  10 CigCgaCvsaCP 21 
                                       C  C  C + CP
  gi|298675591|ref|YP_003727341.1| 480 CSFCYMCEDKCP 491
                                       444778889998 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1e-05
                            Fer4_2   4 vvdtdrCig..CgaCvsaCP 21 
                                       v d++rC+g  C+ Cv++CP
  gi|298675591|ref|YP_003727341.1| 507 VHDSQRCLGvsCKRCVDVCP 526
                                       6799****999********9 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   1.8      0.03        39       2      16 ..     478     492 ..     477     500 .. 0.87
   2 ?   14.0   2.7   4.4e-05     0.056       1      16 [.     510     527 ..     510     533 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.03
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       ++C  C  C++ CP 
  gi|298675591|ref|YP_003727341.1| 478 KNCSFCYMCEDKCPE 492
                                       57888*********5 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 4.4e-05
                            Fer4_4   1 qerC..igCgsCvaaCPq 16 
                                       ++rC  + C++Cv++CP 
  gi|298675591|ref|YP_003727341.1| 510 SQRClgVSCKRCVDVCPK 527
                                       589*666**********5 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   2.7    0.0078        10       1      15 []     480     494 ..     480     494 .. 0.95
   2 ?   11.4   4.3    0.0004      0.51       1      15 []     513     529 ..     513     529 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0078
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C  C+ C++ CP++A
  gi|298675591|ref|YP_003727341.1| 480 CSFCYMCEDKCPEKA 494
                                       999*********998 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0004
                            Fer4_3   1 Ctg..CgaCvevCPvgA 15 
                                       C+g  C +Cv+vCP++A
  gi|298675591|ref|YP_003727341.1| 513 CLGvsCKRCVDVCPKKA 529
                                       66555*9********98 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   3.0    0.0013       1.7      41      58 ..     475     492 ..     439     495 .. 0.79
   2 ?    5.5   2.2     0.019        25      41      58 ..     508     527 ..     493     530 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0013
                           Fer4_17  41 ekaslCieCgeCerkCPq 58 
                                       + +++C+ C +Ce kCP+
  gi|298675591|ref|YP_003727341.1| 475 RPIKNCSFCYMCEDKCPE 492
                                       56899***********98 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.019
                           Fer4_17  41 ekaslC..ieCgeCerkCPq 58 
                                       +  ++C  ++C++C+ +CP+
  gi|298675591|ref|YP_003727341.1| 508 HDSQRClgVSCKRCVDVCPK 527
                                       55667733479999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (550 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 3856.23
//
Query:       gi|298675592|ref|YP_003727342.1|  [L=541]
Description: chaperonin Cpn60/TCP-1 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   1.6e-110  370.1   2.9   1.8e-110  369.9   2.9    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  369.9   2.9    1e-114  1.8e-110       3     488 ..      59     539 ..      57     541 .] 0.94

  Alignments for each domain:
  == domain 1  score: 369.9 bits;  conditional E-value: 1e-114
                                       HHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHHHH CS
                        Cpn60_TCP1   3 divkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleeaek 79 
                                       d++++++GP+G +K++ n+ +++ +TnDG+til+e +i hP++ +l ++a s+d+ +GDGT t+v+La++L+++a  
  gi|298675592|ref|YP_003727342.1|  59 DLLSSSFGPRGFNKIILNPVNDIYLTNDGKTILEETDILHPVVTSLKDLAGSMDKTCGDGTKTAVLLAATLVNRAIP 135
                                       799************************************************************************** PP

                                       HHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTS.SXXSTHHHHHHHHHHHHHCHCC CS
                        Cpn60_TCP1  80 liaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslssk.ltskeaeelsklvvdAvkliee 155
                                       li++g+hpt ii+gy+kal+k  e+L+  +++++s+    e+ ++++  ++ssk +  ++ae+l+k+++d++k ++ 
  gi|298675592|ref|YP_003727342.1| 136 LINRGIHPTIIIDGYQKALNKSYEILQFETKSVKSQ----EDTYSAVFAAASSKgIETHQAERLAKIMIDSIKRLNA 208
                                       **************************7666677777....888999999999998889999***********66655 PP

                                       CS..EECSCCC.EECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HH..CCHHHCCCCSC CS
                        Cpn60_TCP1 156 ne..keldlgr.ikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiekt..etkttvvlsda 227
                                        +  ++ldl+  ++++k++g s +    ++G++ld++++  +mp  +e ++vl+l++ L+ +++  + ++++++++ 
  gi|298675592|ref|YP_003727342.1| 209 MSenTDLDLNDnVRIIKKTGASGIV--SLNGVILDEKPARFEMPDYIESPNVLILNHDLKVDSEylNPQHNINMDSF 283
                                       5546788887679999999998754..68*********************************9966779******** PP

                                       CHHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGG CS
                        Cpn60_TCP1 228 eeleklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledl 304
                                           ++e+  +++l++  +ki ++g+++v+c++++d++++ +l kn+il  +++k +d+e+l++at a + s  +dl
  gi|298675592|ref|YP_003727342.1| 284 GTAYQFEECRKTILKNYADKILETGADLVFCEGEVDPYIEFLLTKNNILMFKKMKVNDIEKLSRATDAGISSIKDDL 360
                                       **********************************************************************9999*** PP

                                       GCGC-EEEEEEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHH CS
                        Cpn60_TCP1 305 tpeelGtakkveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatel 381
                                       t+ ++G+a+k+e++k + e++++++  +s+ i ti++  + ++ l+++e+a +dAln ++ +++++ vv+GGG +e 
  gi|298675592|ref|YP_003727342.1| 361 TK-SIGYADKIEVKKENGEHLVYVTV-NSKMITTIIIWEPVKYNLEKVEEAADDALNNAAFILKNGLVVAGGGGIEF 435
                                       99.5*********************6.99************************************************ PP

                                       HHHHHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCT CS
                        Cpn60_TCP1 382 elakklkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveag 458
                                        l+++lk ya++++g+eqla++ +akALe+ip++La N G++pi+ +a++ +  nkg     idv sg++++  +  
  gi|298675592|ref|YP_003727342.1| 436 GLSQMLKLYASTIDGKEQLAVMEYAKALEQIPRILAFNMGMNPIDSIADMNSYYNKGI-DSRIDV-SGQVVNN-NPP 509
                                       ****************************************************999999.*****9.7776555.456 PP

                                       XEEEHHHHHHHHHHHHHHHHHHHCEEEEEX CS
                        Cpn60_TCP1 459 vvDplkvkrqalksAteaastiLrideiik 488
                                        +D++++k+ a+ sAte+a+ iLridei+ 
  gi|298675592|ref|YP_003727342.1| 510 LYDSVTIKKLAIISATETATNILRIDEIVP 539
                                       ****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (541 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3914.82
//
Query:       gi|298675593|ref|YP_003727343.1|  [L=663]
Description: hydantoinase/oxoprolinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-31  109.2   0.5    2.2e-31  109.2   0.5    2.3  2  Hydantoinase_A  Hydantoinase/oxoprolinase
    1.7e-29  102.8   7.2      1e-26   93.7   1.3    3.4  2  Hydant_A_N      Hydantoinase/oxoprolinase N-terminal region
    0.00013   20.7   4.4      0.068   11.8   0.7    2.2  2  MutL            MutL protein
  ------ inclusion threshold ------
      0.059   12.6   0.0       0.14   11.4   0.0    1.6  1  StbA            StbA protein
       0.18   11.3   1.9        1.8    8.0   0.3    2.4  2  BcrAD_BadFG     BadF/BadG/BcrA/BcrD ATPase family


Domain annotation for each model (and alignments):
>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.6     0.079   2.8e+02      82     102 ..       5      27 ..       2      52 .. 0.73
   2 !  109.2   0.5     6e-35   2.2e-31       1     137 [.     179     313 ..     179     368 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.079
                    Hydantoinase_A  82 ItfDmGGTstDvsl..ikdgeve 102
                                       +++D+GGT tD +   i++g+v+
  gi|298675593|ref|YP_003727343.1|   5 LGVDTGGTYTDTIImdISTGTVM 27 
                                       689********765115555554 PP

  == domain 2  score: 109.2 bits;  conditional E-value: 6e-35
                    Hydantoinase_A   1 rtetavvnAylspilreylesvekslekrgakarlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaatsklag 77 
                                       r +ta++nA l p  +++++s+ + +++++++a+lm+m++dG+l++++ea kkpveti SGPaa++vga++   l++
  gi|298675593|ref|YP_003727343.1| 179 RSVTALLNAQLIPETNQFIKSIHSVMDEKNITATLMMMKCDGSLIKIEEALKKPVETIFSGPAASLVGASH---LTN 252
                                       789********************************************************************...888 PP

                    Hydantoinase_A  78 ekkvItfDmGGTstDvslikdgevevsletei.agvkvrlpaldirtvgagGgsilvvdeg 137
                                        + + t+D+GGTstDvs+++dg +e+s    + +g k+ ++a++++t ++gG+s ++ +++
  gi|298675593|ref|YP_003727343.1| 253 LDTCATIDVGGTSTDVSFMSDGIPEISETGAVvGGWKTMVKAINMDTSAMGGDSHVWIQKK 313
                                       8899**********************98877669**********************76653 PP

>> Hydant_A_N  Hydantoinase/oxoprolinase N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.7   1.3   2.8e-30     1e-26       2     177 ..       5     159 ..       4     160 .. 0.88
   2 !    7.6   0.5   0.00079       2.8       3      18 ..     258     273 ..     257     304 .. 0.81

  Alignments for each domain:
  == domain 1  score: 93.7 bits;  conditional E-value: 2.8e-30
                        Hydant_A_N   2 igIDvGGTfTDavaldeke.eevavlKllstpdavaegirealeevleesiprtskidvvrmGTTvatNallerkge 77 
                                       +g+D+GGT+TD++++d  + +++ + K l+t  + ++gi++al+ + ++     +++++v ++TT+atN +lerkg+
  gi|298675593|ref|YP_003727343.1|   5 LGVDTGGTYTDTIIMDISTgTVMDTNKSLTTYPELITGIKNALNGLNSKYL---EDVKFVSVSTTLATNSILERKGR 78 
                                       69**************87768899**********************88865...69********************* PP

                        Hydant_A_N  78 rvaLittkgfrdlleigrqnrpdlfelrikkplvlyeevvevderveadgevlkpl.deeevrealkalkaagvesi 153
                                       +++Li +         g++ +++l           ++ v+ v+++++a+g++++pl d + ++e + a k++ v+s+
  gi|298675593|ref|YP_003727343.1|  79 QAGLILI---------GYSIHKKL----------STDVVISVSGGHDANGDEIEPLnDLDTLKEFILANKSK-VSSF 135
                                       ****975.........55545555..........56779*****************5667777777777766.**** PP

                        Hydant_A_N 154 avvllhSylnpehElrvaeiarei 177
                                       a+++++ ++npehElrv+++++++
  gi|298675593|ref|YP_003727343.1| 136 AISSYFGVRNPEHELRVKKLVQNL 159
                                       ********************9975 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00079
                        Hydant_A_N   3 gIDvGGTfTDavalde 18 
                                        IDvGGT TD+ ++++
  gi|298675593|ref|YP_003727343.1| 258 TIDVGGTSTDVSFMSD 273
                                       59*********99985 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.7   1.9e-05     0.068       3      61 ..       6      64 ..       5      73 .. 0.80
   2 !   10.2   0.2   5.8e-05      0.21     222     274 ..     234     281 ..     220     292 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.9e-05
                              MutL  3 viDiGSttTkvtlvdlekvderllgqaeapTtveeedvleGleealeeleeklgkt....evd 61
                                       +D G t+T  +++d ++  ++++ + +++Tt    ++ +G+++al+ l++k  +     +v+
  gi|298675593|ref|YP_003727343.1|  6 GVDTGGTYTDTIIMDIST--GTVMDTNKSLTTYP--ELITGIKNALNGLNSKYLEDvkfvSVS 64
                                      58**************77..*************6..8************99854323333333 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 5.8e-05
                              MutL 222 aeimpTPaAvlkavellaeeeekglgdllvvDvGGaTTdvhsvaegspekekv 274
                                       ++i   PaA l +++ l +     l+ + ++DvGG++Tdv  +++g pe++++
  gi|298675593|ref|YP_003727343.1| 234 ETIFSGPAASLVGASHLTN-----LDTCATIDVGGTSTDVSFMSDGIPEISET 281
                                       4677889999999999988.....66899**************9999998876 PP

>> StbA  StbA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.9e-05      0.14     150     267 ..     240     354 ..     231     365 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.9e-05
                              StbA 150 Pagfealke.ldeleslLiiDlGGttLDvakvrgklegiskvkgdskiGvslitdavkealetaktrtssfl.adel 224
                                       Pa+  + ++ l +l+    iD+GGt  Dv+ +   + +is++ +    G   +++a++  ++t+ + + s++ +++ 
  gi|298675593|ref|YP_003727343.1| 240 PAASLVGAShLTNLDTCATIDVGGTSTDVSFMSDGIPEISETGA-VVGGWKTMVKAIN--MDTSAMGGDSHVwIQK- 312
                                       66666665559****************************99754.4456777777775..5555554444330332. PP

                              StbA 225 iknrkdeeyLkrrindedkresvlevinekvkkLkerviravs 267
                                        k+    + +    +++ ++ ++++ ++ ++kk+++r+++ v 
  gi|298675593|ref|YP_003727343.1| 313 -KAYTGPKRVVPLCQAASEYPQITDKLETNKKKISKRIMDDVI 354
                                       .233344444556788889999999999999999999988775 PP

>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.3   0.00051       1.8       1      29 [.       5      34 ..       5     161 .. 0.84
   2 ?    2.4   0.1     0.025        91       3      29 ..     259     292 ..     258     383 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00051
                                      EEEEE-SSEEEEEEEE.TTTEEEEEEEE-- CS
                       BcrAD_BadFG  1 vGiDgGsTttkavlmd.ekgevlgrgitns 29
                                      +G+D G+T t +++md   g v+ + ++ +
  gi|298675593|ref|YP_003727343.1|  5 LGVDTGGTYTDTIIMDiSTGTVMDTNKSLT 34
                                      7***************54555887777666 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.025
                                       EEE-SSEEEEEEEE.......TTTEEEEEEEE-- CS
                       BcrAD_BadFG   3 iDgGsTttkavlmd.......ekgevlgrgitns 29 
                                       iD+G+T+t +  m        e g v+g ++t  
  gi|298675593|ref|YP_003727343.1| 259 IDVGGTSTDVSFMSdgipeisETGAVVGGWKTMV 292
                                       9*********999978888878888888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (663 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.40
# Mc/sec: 4992.74
//
Query:       gi|298675594|ref|YP_003727344.1|  [L=640]
Description: methyltransferase cognate corrinoid protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.6e-58  196.7   0.0    1.7e-57  195.1   0.0    1.8  2  URO-D          Uroporphyrinogen decarboxylase (URO-D)
      1e-23   83.6   0.0    5.3e-23   81.4   0.3    2.1  2  B12-binding    B12 binding domain
    7.3e-15   55.2   0.0    7.3e-15   55.2   0.0    2.9  4  B12-binding_2  B12 binding domain
     0.0086   15.8   0.1      0.023   14.4   0.1    1.7  1  Peripla_BP_6   Periplasmic binding protein


Domain annotation for each model (and alignments):
>> URO-D  Uroporphyrinogen decarboxylase (URO-D)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       0.2   9.1e+02     258     277 ..     124     147 ..      72     220 .. 0.59
   2 !  195.1   0.0   3.8e-61   1.7e-57       1     345 [.     279     629 ..     279     630 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.2
                                       S--SEEE--TTS-HHHHHH....S CS
                             URO-D 258 lgadvlsldwtvdlkeaar....e 277
                                       +g++++ l + v+l e ++    +
  gi|298675594|ref|YP_003727344.1| 124 SGFNAIDLGNDVQLDEFVEkakeN 147
                                       556666666666662222222220 PP

  == domain 2  score: 195.1 bits;  conditional E-value: 3.8e-61
                                       ----HHHHHHTT---SS--B--TT-SSTTSHHHHHHHTSSSHHHHHH-HHHHHHHHHHHHHHH--S-EE-S--TTGG CS
                             URO-D   1 tknerllralrgekvdrvPvwlmRqaGrylpeyraeragvsflelcknpelaaevtlqpvrrfglDaailfsdilve 77 
                                       t+ er+ + l ++kvdr+Pv++       ++   +++  +++++++ +pe++a+ +++  +++++D+++ ++d+++ 
  gi|298675594|ref|YP_003727344.1| 279 TSIERVTSSLADKKVDRLPVYP------LACGVTRKFVPTTYKQYAIDPEMFAQSAYAGAKYLDYDMFVGLIDLSIT 349
                                       567999****************......************************************************* PP

                                       GGGGT-EEEEETTTEEEEE--S-....GGGS----GGG.G..HHHHHHHHHHHHH.--.SS-EEEEEE-HHHHHHHH CS
                             URO-D  78 aealGlevefeegegPvvekpvrtaedveklevpddveegrlpyvleaikllkkelgg.evpligfvgaPftlasyl 153
                                       a  lG+e++++e+++P+ + +   +ed+e++evp+++e +r  ++++a+kl+k++l +   p++gf+ +P+ ++++l
  gi|298675594|ref|YP_003727344.1| 350 AGDLGCEITYPEEDTPSSKGH---LEDYEEIEVPEVKEGTRAYELVQATKLAKEKLHEiGKPVVGFHEGPLLTLTQL 423
                                       ********************8...569999****997558**************9955489**************** PP

                                       HCTT-SS-HHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHH.HTT-SEEEEEE..TTGGGS-HHHHHHHTHHHH.HH CS
                             URO-D 154 veGgskgfekllkllykdpeevhklldkltdvvieylkaqi.eagAdaiqifD..swagllspedfeefvlpyl.kr 226
                                       +     g++++++++ ++pe+v++++dk++d+v  + ++++ e  +da++i +  s+++++s++d+++f  +++  +
  gi|298675594|ref|YP_003727344.1| 424 M-----GADRVMMDMKTNPEVVRDAVDKCADYVNLVTEKFFeEDACDALCIDNlwSNNKIMSEDDYWKFDGKFIvDK 495
                                       *.....***********************************888899*************************9989* PP

                                       HHHHHHH.H--S-EEEEESSHH.HHHHHHTTS--SEEE--TTS-HHHHHH........SS....EEE--B-G.GGGG CS
                             URO-D 227 ivdevkaegpkvpvilfikgagaeiledlaelgadvlsldwtvdlkeaar........evgdkvalqGnldPialLl 295
                                       +v  +k++ +  p++++ ++++ ++ +++ + g d +s+    + +e+ +        + g++++++G++dPi+++ 
  gi|298675594|ref|YP_003727344.1| 496 HVPLFKKYDQ--PYMIHSCADSVHYDTQISKFGTDLFSYAYYPNEREQGSknysdlipKYGHECCMMGEVDPIQFMD 570
                                       ********98..**********9999999**********6665544444456667776888**************** PP

                                       S-HHHHHH...HHHHHHT.......T---SSSEEB-BSS---TTS-HHHHHHHHHHHHT CS
                             URO-D 296 gspeeiek...evkeile......kgaggkkgyilnlGhgippetppenvkalveavke 345
                                       +s e+i+k    ++++l       +++g +++y++++G++ipp+ ++  vk ++++vke
  gi|298675594|ref|YP_003727344.1| 571 NSSETIDKiksDTDNVLTgalntlNENGLQSKYVVSTGCEIPPGGSLTGVKEMIDLVKE 629
                                       999999888885555555555566579999***************************97 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.4   0.3   1.2e-26   5.3e-23       3     108 ..     100     202 ..      98     213 .. 0.93
   2 ?   -2.8   0.0       1.3     6e+03      64      81 ..     616     633 ..     612     634 .. 0.84

  Alignments for each domain:
  == domain 1  score: 81.4 bits;  conditional E-value: 1.2e-26
                       B12-binding   3 vllatvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvel..lkr 77 
                                       v+++tv+gd+h++G+++++ +l ++gf+ ++lg +v+ +++v++++++k+d++ +Sal+t+++ +++ +++   +++
  gi|298675594|ref|YP_003727344.1| 100 VIIGTVQGDVHDIGKNLVKTMLTASGFNAIDLGNDVQLDEFVEKAKENKADAISMSALMTTTMGGMETVIDKlkEEG 176
                                       7999********************************************************************98889 PP

                       B12-binding  78 irprvkvvvGGahpsldpeetleaklgiddv 108
                                        r+ v+v+vGGa++s d++    + +g +d+
  gi|298675594|ref|YP_003727344.1| 177 LRDSVIVMVGGAPVSEDYAN---E-IG-ADA 202
                                       999**************999...7.88.554 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.3
                       B12-binding  64 qleavkelvellkrirpr 81 
                                       +l++vke+++l+k+++p+
  gi|298675594|ref|YP_003727344.1| 616 SLTGVKEMIDLVKEKGPG 633
                                       68899******9998885 PP

>> B12-binding_2  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   0.0   1.6e-18   7.3e-15       2      74 ..      11      85 ..      10      86 .. 0.94
   2 ?   -2.3   0.1       1.4   6.2e+03      12      49 ..     132     171 ..     126     176 .. 0.65
   3 ?   -3.7   0.0       3.9   1.7e+04      63      74 ..     210     221 ..     204     222 .. 0.62
   4 ?   -1.4   0.1      0.76   3.4e+03       5      38 ..     233     267 ..     229     269 .. 0.76

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 1.6e-18
                     B12-binding_2  2 aerlhwaivhgdkegieelidealaqg..saavdvlndvllpamkeVGdlfgagelflpqvllsaevmkkavahL 74
                                      ++ l++a+++gd+++++el+ +++++g   ++ +++ d+l+++m ++ d++++ge+f+p++l ++++m+++++ L
  gi|298675594|ref|YP_003727344.1| 11 LNGLTNAVIQGDQDSAKELATKVIENGgvVDPYEAIVDGLAKGMSIMSDKYENGEVFVPHLLVASNAMYAGMKEL 85
                                      5789********************8886666****************************************9877 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.4
                     B12-binding_2  12 gdkegieelidealaqgsa...avdvlndvllpamkeVGdl 49 
                                       g++ +++e +++a +++ a    + +l +  + +m+ V d+
  gi|298675594|ref|YP_003727344.1| 132 GNDVQLDEFVEKAKENK-AdaiSMSALMTTTMGGMETVIDK 171
                                       55566667777777433.33676777777788888877665 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 3.9
                     B12-binding_2  63 saevmkkavahL 74 
                                       +a+++k av+ L
  gi|298675594|ref|YP_003727344.1| 210 AADWLKDAVKEL 221
                                       566777777666 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 0.76
                     B12-binding_2   5 lhwaivhgdkegieelidealaqgsa.avdvlndv 38 
                                       +  + v+  +e +++ + e ++ g + a +++++v
  gi|298675594|ref|YP_003727344.1| 233 ISTSKVKYREELAKKTVSEEVDIGREtAKEIIDEV 267
                                       55566778888888888888887766799999886 PP

>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   5.1e-06     0.023      97     239 ..      57     202 ..      19     239 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.1e-06
                                       EESS-HHCCTTSTTEEESS--HHHHHHHHHHHHHHHTT.SCEEEEEEESSHHHHHHHHHH.HHHHHCCTEEEEEEEE CS
                      Peripla_BP_6  97 igpagltgekcspyvfslgpsysaqasalveylakelg.gkkvalvyadyafgregiaal.kaaakaaGgevvgeep 171
                                       ++    +ge   p+  ++++  +a ++ l  y+++++  +  ++++++     +++ ++l k +++a+G++ +   +
  gi|298675594|ref|YP_003727344.1|  57 MSDKYENGEVFVPHLLVASNAMYAGMKELTPYIKTDEAsKQAIVIIGTVQGDVHDIGKNLvKTMLTASGFNAI---D 130
                                       444455667777889999999999********9998662556777777766666665554499********65...3 PP

                                       E-TTHHHHHHHHHHHHTTT-SE....EEEESSHHHHHHHHHHHHHTT-SSSCEEEECCC.-CHHHHHHHHHHH CS
                      Peripla_BP_6 172 vplgttdfsaqvlqikaagada....vllagtgadlaallkaaaeaGldakrillvsws.gseedlkalggea 239
                                       +  ++ +++++v ++k+ +ada     l+++t + + +++  ++e Gl+   i +v+ + +se  +  +g++a
  gi|298675594|ref|YP_003727344.1| 131 LG-NDVQLDEFVEKAKENKADAismsALMTTTMGGMETVIDKLKEEGLRDSVIVMVGGApVSEDYANEIGADA 202
                                       44.55999*************977777788888889999999*******98777776668*********9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (640 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       812  (0.0452898); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.27s 00:00:00.93 Elapsed: 00:00:00.91
# Mc/sec: 2122.40
//
Query:       gi|298675595|ref|YP_003727345.1|  [L=258]
Description: ArsR family transcriptional regulator [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-23   81.7   0.4    6.7e-23   80.6   0.4    1.6  1  DUF1724   Domain of unknown function (DUF1724)
    5.4e-07   29.4   0.0      1e-06   28.5   0.0    1.5  1  HTH_5     Bacterial regulatory protein, arsR family
     0.0067   16.4   0.6      0.016   15.2   0.4    1.8  2  HTH_45    Winged helix-turn-helix
  ------ inclusion threshold ------
      0.067   13.0   0.1        2.6    8.0   0.1    2.3  1  DUF1495   Winged helix DNA-binding domain (DUF1495)


Domain annotation for each model (and alignments):
>> DUF1724  Domain of unknown function (DUF1724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.6   0.4   1.5e-26   6.7e-23       3      62 .]     198     258 .]     197     258 .] 0.96

  Alignments for each domain:
  == domain 1  score: 80.6 bits;  conditional E-value: 1.5e-26
                           DUF1724   3 lyvyd.eeikplsltvtDkflslslfdkdgkydhkdlisfdesAlkWGeeLFeyYlkrSep 62 
                                       ly++d + ikp++l++tD+++++slf+++g +dhk+lisfd+ Al+W++eLFeyY++++e+
  gi|298675595|ref|YP_003727345.1| 198 LYICDdNIIKPATLVITDDMMLVSLFNEEGVFDHKKLISFDSCALQWAKELFEYYKNKAEK 258
                                       8****77789************************************************985 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   2.2e-10     1e-06       2      46 ..      13      57 ..      12      58 .. 0.96

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 2.2e-10
                                      HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                       +R  IL++L +g++ + ++ +el  + s++  + k+L+++GLV+
  gi|298675595|ref|YP_003727345.1| 13 DKRKNILMYLLDGPKNIDDIKDELATNTSAIMTQMKILMDQGLVT 57
                                      689*****************************************6 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.4   3.5e-06     0.016      34      73 ..      41      80 ..      16      84 .. 0.77
   2 ?   -2.9   0.0       1.5   6.9e+03      46      59 ..     130     144 ..     124     144 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.5e-06
                            HTH_45 34 kllnkYLdmLvekglikkskekYvlTekGlelleklkele 73
                                      + +   +++L+++gl++++ + Y+lT  G  +++k+k l 
  gi|298675595|ref|YP_003727345.1| 41 SAIMTQMKILMDQGLVTHNADVYELTTIGNVIVKKMKPLL 80
                                      555566899**************************99765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.5
                            HTH_45  46 kglikk.skekYvlT 59 
                                       ++l++  ++++Yv+T
  gi|298675595|ref|YP_003727345.1| 130 NELVESlKSTQYVMT 144
                                       688877688899988 PP

>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1   0.00057       2.6       8      88 ..      12      74 ..       6      76 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00057
                           DUF1495  8 SkvRkkvllyLysiypeksnlqeisrrvrskpsnvkGaleGmgkrynsessLielGLveeeeeseglklYklteeGiei 86
                                      S  Rk++l+yL++     +n+ +i  + +++ s +          +++ + L+ +GLv+     ++  +Y+lt+ G  i
  gi|298675595|ref|YP_003727345.1| 12 SDKRKNILMYLLDGP---KNIDDIKDELATNTSAI----------MTQMKILMDQGLVT-----HNADVYELTTIGNVI 72
                                      677888888888433...46666666666665544..........34445677777774.....677777777777777 PP

                           DUF1495 87 ve 88
                                      v+
  gi|298675595|ref|YP_003727345.1| 73 VK 74
                                      76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1644.92
//
Query:       gi|298675596|ref|YP_003727346.1|  [L=864]
Description: PAS/PAC sensor signal transduction histidine kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.5e-29  100.5   0.0    1.6e-28   99.5   0.0    1.5  1  MEDS         MEDS: MEthanogen/methylotroph, DcmR Sensory doma
    2.9e-24   85.9   0.0      1e-23   84.1   0.0    1.9  2  GAF_2        GAF domain
    1.3e-22   80.4   0.1    2.4e-22   79.6   0.1    1.5  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    2.2e-21   76.0   0.0    2.1e-15   56.8   0.1    3.4  3  PAS_3        PAS fold
      1e-17   64.1   0.0    8.6e-11   41.8   0.0    3.4  3  PAS          PAS fold
      8e-15   55.0   0.1    6.8e-08   32.7   0.0    3.0  2  PAS_9        PAS domain
    1.3e-10   41.5   0.0    6.2e-07   29.6   0.0    2.7  2  PAS_4        PAS fold
    2.1e-06   27.6   0.1    8.4e-06   25.7   0.0    2.1  2  PAS_8        PAS domain
    0.00081   19.5   0.0     0.0034   17.5   0.0    2.1  2  PAS_7        PAS fold
     0.0096   15.7   0.4      0.027   14.3   0.0    1.9  2  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
  ------ inclusion threshold ------
      0.069   12.4   0.0       0.23   10.6   0.0    1.8  2  RsmJ         Ribosomal RNA large subunit methyltransferase D,
      0.094   13.3   0.1       0.48   11.1   0.2    2.1  2  DUF3067      Domain of unknown function (DUF3067)
       0.16   12.2   1.4        1.1    9.5   0.3    2.4  2  CTNNBL       Catenin-beta-like, Arm-motif containing nuclear
       0.48   10.5   4.3       0.78    9.8   0.4    3.0  3  HisKA        His Kinase A (phospho-acceptor) domain


Domain annotation for each model (and alignments):
>> MEDS  MEDS: MEthanogen/methylotroph, DcmR Sensory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.5   0.0   1.3e-31   1.6e-28       2     160 ..       4     159 ..       3     160 .. 0.97

  Alignments for each domain:
  == domain 1  score: 99.5 bits;  conditional E-value: 1.3e-31
                              MEDS   2 Hvclfyedeeellealvpfikaglargekvlyvas...astldelrealrkagldvdaalesgqleildaeetylrg 75 
                                       H  lfy++ +el+e+l +f+k+g+++++ +++v+s     t++++++ l++ g dvd + es+++ei+++++     
  gi|298675596|ref|YP_003727346.1|   4 HGNLFYNSLDELMELLPSFFKSGVENNQYCIWVISdydFVTVERAKNTLKNTGFDVDFYIESDKFEIIHENQ----L 76 
                                       889********************************8888899***************************997....6 PP

                              MEDS  76 ggfdpermlealrralakaladgyaglrvigemtwalrspaereelleyEallneliadepvtalClYdrrrfsaev 152
                                       g +d + +l++++++  +a+++g++gl++i + t ++++   ++ +l+yE+ll+e+i++++++ lC Yd++++s++ 
  gi|298675596|ref|YP_003727346.1|  77 GFSDFTGVLNFWKQKYLNAIDNGFNGLWMIENLTPVFEN--YPSYYLNYESLLDEIIKNRNMVSLCSYDLTKCSQSN 151
                                       99999******************************9*99..79********************************** PP

                              MEDS 153 ladvlrtH 160
                                         d++++H
  gi|298675596|ref|YP_003727346.1| 152 TLDLISSH 159
                                       *******9 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.4     3e+03      67     109 ..     262     300 ..     203     317 .. 0.72
   2 !   84.1   0.0   8.1e-27     1e-23       2     138 .]     470     613 ..     469     613 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.4
                                       S-EEES-GGG-S-HHHHHHHHHTT--EEEEEE-T.TS---EEEE CS
                             GAF_2  67 rpvilndleedpdkkglpaghaglrsflavPlis.egrvvGvln 109
                                       +pv  n           p g+  +++++ +Pl+   g+  G+l+
  gi|298675596|ref|YP_003727346.1| 262 EPVTYNA-----LAFLTPDGKMSYHNGVLIPLFNeAGNYQGILG 300
                                       4444333.....44455667777888899999885688777777 PP

  == domain 2  score: 84.1 bits;  conditional E-value: 8.1e-27
                                       HHHHHHHHHHHHHHHHS.S..EEEEEEE-TTS-.EEEEEEEES-TTSTT-S-B--.....-TTHHHHHHHHTS-EEE CS
                             GAF_2   2 adleelldlvldelvel.gaalgyillvdddgg.lrlaawgeaeeefgaaldrpl.....geglvgealrtgrpvil 71 
                                       a+l+e+ d++ +e+v+l ++ lgy+++++ d++ l +++w+e  ++ +    +p+       gl+gea+r+++p+i 
  gi|298675596|ref|YP_003727346.1| 470 ASLQEITDFAREEAVRLtNSKLGYLAFLNYDESiLIMHSWSEGAMKECKVENKPFvypvkTTGLWGEAVRQRKPIIT 546
                                       699*************967********99777746677*********9999996677788888************** PP

                                       S-.GGG-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHHH CS
                             GAF_2  72 nd.leedpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiaie 138
                                       n+ +e +  kkg+p gh+ l +++ vP+++++++v v ++ +nk++++de+d+++L++l++ +++ i+
  gi|298675596|ref|YP_003727346.1| 547 NNyTEPSSLKKGYPGGHVELTRHMNVPIFDGEHIVLVAGV-GNKEQEYDESDVRQLTLLMQGMWRLIQ 613
                                       **8888************************999999***8.8**********************9986 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.6   0.1   1.9e-25   2.4e-22       1     111 [.     747     858 ..     747     859 .. 0.93

  Alignments for each domain:
  == domain 1  score: 79.6 bits;  conditional E-value: 1.9e-25
                                       EHHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTSSSH CS
                         HATPase_c   1 gdekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsq.ddstkrggggtGl 76 
                                       gd+ +L+ ++  l+dN++k+++ +g+i ++  +se++l i+v DnG Gipk+ ++ lf+ fs  +d+ ++g + +G 
  gi|298675596|ref|YP_003727346.1| 747 GDKNKLTDMFTYLIDNSLKYTPRGGNINISAFKSENNLYIKVNDNGEGIPKDLVPTLFKGFSHsEDTLTHGLEKSGS 823
                                       68999***************88*****99999888****************************6666666679**** PP

                                       HHHHHHHHHHHTTTEEEEEEETTTEEEEEEEEESS CS
                         HATPase_c  77 GlsivkklvelmgGeiwvesepgrGttftftlple 111
                                       +l+++kk+v+ +gG+i+v+s++++Gtt+t+ lpl+
  gi|298675596|ref|YP_003727346.1| 824 SLYVCKKIVNAHGGQISVDSKEEIGTTVTIVLPLK 858
                                       ********************************985 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.51   6.5e+02      58      74 ..     163     179 ..     156     187 .. 0.82
   2 !   14.0   0.0   3.7e-05     0.048       2      89 .]     213     302 ..     212     302 .. 0.82
   3 !   56.8   0.1   1.6e-18   2.1e-15       3      89 .]     351     438 ..     349     438 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.51
                             PAS_3  58 irrkdGeyrwveararv 74 
                                       +++kdGe+  +e++ + 
  gi|298675596|ref|YP_003727346.1| 163 LLKKDGEWKFLEEKSKT 179
                                       6799*******998765 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3.7e-05
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeD...rervrealqealkkgepy.egeyRirrkdGeyrwveararv 74 
                                       ++ ++++e i+G+ +ee+lg+  s++d++  +     +r++e + +  k++ep+      ++++dG++ +      +
  gi|298675596|ref|YP_003727346.1| 213 VFFNNTMESIFGVPREEILGT--SFMDYIAEQRpvgDSRLEELYLHTKKSREPVtYNALAFLTPDGKMSYHNGVLIP 287
                                       799******************..99999988876645555555555557777773556999******9999999999 PP

                             PAS_3  75 irdengkpvrvigva 89 
                                       +++e g+ + ++g++
  gi|298675596|ref|YP_003727346.1| 288 LFNEAGNYQGILGTV 302
                                       999999999999985 PP

  == domain 3  score: 56.8 bits;  conditional E-value: 1.6e-18
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealq..ealkkgepyegeyRirrkdGeyrwveararvird 77 
                                       yvse++  ++Gy ++e+l+ + +++d+vhp+D +++++++   e  +k++ ++ +yRi++k Ge+rwv ++  +ir+
  gi|298675596|ref|YP_003727346.1| 351 YVSENI-TYFGYKSDEFLSGKLTYADIVHPDDVDKLKSDFSvyEKQNKNSYFTSDYRILTKTGETRWVTEKSLIIRN 426
                                       666666.789******************************944555555566************************* PP

                             PAS_3  78 engkpvrvigva 89 
                                       ++g + +++g++
  gi|298675596|ref|YP_003727346.1| 427 QKGAVKYLQGII 438
                                       *********985 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.4   1.8e+03      27      60 ..     133     166 ..     132     183 .. 0.81
   2 !   41.8   0.0   6.7e-14   8.6e-11       2     110 ..     191     302 ..     190     305 .. 0.83
   3 !   17.9   0.0   1.8e-06    0.0023       4     113 .]     328     441 ..     326     441 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.4
                                       CHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHH CS
                               PAS  27 NaaaeellGlsreevlgkslldliheeddaelae 60 
                                       N+++ +l+ ++   ++ ++ ldli+  d+  l++
  gi|298675596|ref|YP_003727346.1| 133 NRNMVSLCSYDLTKCSQSNTLDLISSHDRTLLKK 166
                                       999*********************9988874444 PP

  == domain 2  score: 41.8 bits;  conditional E-value: 6.7e-14
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       +++ il+s+  +++vvD + +++++N ++e+++G +ree+lg s++d+i e+ +  + +l e +l+++++++ +  +
  gi|298675596|ref|YP_003727346.1| 191 FYEKILDSIWLGVWVVDSSDNVVFFNNTMESIFGVPREEILGTSFMDYIAEQRPVGDSRLEELYLHTKKSREPVTYN 267
                                       7999***********************************************99986666666666666666665555 PP

                                       EEC...TTSSEEEEEEEEEEEEETTEEEEEEEEEE CS
                               PAS  79 fkl...rdgrpihlevraspvrdaggeilgflgvl 110
                                             +dg+  +      p++++ g+  g+lg++
  gi|298675596|ref|YP_003727346.1| 268 ALAfltPDGKMSYHNGVLIPLFNEAGNYQGILGTV 302
                                       55577899999999999999999999888888886 PP

  == domain 3  score: 17.9 bits;  conditional E-value: 1.8e-06
                                       HHHHHHSSSEEEEEE.TTSBEEEECHHHHHHHSSTH.HHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHT.T-ECCCC CS
                               PAS   4 raileslpdpifvvD.edgrilyvNaaaeellGlsr.eevlgkslldliheedda.elaelleqlleqg.eesrage 76 
                                       + i e++p+  f++   + + ++  ++  + +G++  e ++gk  + +i+++dd  +l++ ++ +++q+ ++  + +
  gi|298675596|ref|YP_003727346.1| 328 EKIYETSPVIAFLWKaINDWPVEYVSENITYFGYKSdEFLSGKLTYADIVHPDDVdKLKSDFSVYEKQNkNSYFTSD 404
                                       6678888888888887777777777777899*****999****************9999999999887616678999 PP

                                       EEEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  77 isfklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                        ++ ++ g+++++      +r+ +g ++++ g++ di
  gi|298675596|ref|YP_003727346.1| 405 YRILTKTGETRWVTEKSLIIRNQKGAVKYLQGIIIDI 441
                                       99999*****************************998 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0   5.3e-11   6.8e-08       3     101 ..     202     304 ..     201     307 .. 0.91
   2 !   18.8   0.1   1.1e-06    0.0015      22     104 .]     357     443 ..     342     443 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 5.3e-11
                             PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlf.vtdpeanerlraaleqgrk...kerevevvlirknget 75 
                                       g+++++++ +++++N++++ ++G  +ee+lg+s+ d + ++ p +++rl++++   +k   ++    + + +++g+ 
  gi|298675596|ref|YP_003727346.1| 202 GVWVVDSSDNVVFFNNTMESIFGVPREEILGTSFMDYIaEQRPVGDSRLEELYLHTKKsrePVTYNALAFLTPDGKM 278
                                       7888778888*****************************9999999999888888888798999999********99 PP

                             PAS_9  76 fwvlltaspvkdddgelvgiivilrD 101
                                        + +  ++p++++ g+++gi+++++ 
  gi|298675596|ref|YP_003727346.1| 279 SYHNGVLIPLFNEAGNYQGILGTVEE 304
                                       9999***************9999976 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 1.1e-06
                             PAS_9  22 rllGyspeevlgks..itdlfvtdpeanerlraaleqgrk....kerevevvlirkngetfwvlltaspvkdddgel 92 
                                       + +Gy+++e+l  +  + d++  +p++ ++l+  +   +k    + ++ ++ + +k+get wv  +   +++++g +
  gi|298675596|ref|YP_003727346.1| 357 TYFGYKSDEFLSGKltYADIV--HPDDVDKLKSDFSVYEKqnknSYFTSDYRILTKTGETRWVTEKSLIIRNQKGAV 431
                                       468********9997788999..777777777666666666666999*****************999999******* PP

                             PAS_9  93 vgiivilrDite 104
                                       + + +i++Dite
  gi|298675596|ref|YP_003727346.1| 432 KYLQGIIIDITE 443
                                       ***********8 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   4.9e-10   6.2e-07       1     110 []     196     310 ..     196     310 .. 0.86
   2 !    9.1   0.0    0.0012       1.5      17     109 ..     349     445 ..     332     446 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 4.9e-10
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee...daarleralrrvlegeepie..fleel 72 
                                       lds+  ++ v+d+  +v++ N++++++fg+p+ee+lG ++ ++  e+      rle+ + +  +++ep++   l +l
  gi|298675596|ref|YP_003727346.1| 196 LDSIWLGVWVVDSSDNVVFFNNTMESIFGVPREEILGTSFMDYIAEQrpvGDSRLEELYLHTKKSREPVTynALAFL 272
                                       56777789999********************************9999898777777777777766666532277777 PP

                             PAS_4  73 llpgeerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                       +++g+  +++  l+Pl++e G  +g+l+++ + T ++r
  gi|298675596|ref|YP_003727346.1| 273 TPDGKMSYHNGVLIPLFNEAGNYQGILGTVEEATSTKR 310
                                       77******************************998875 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0012
                             PAS_4  17 vlyaNaaaaelfgappeellGktla.ellpeedaarleralrrvlegeepiefleelll...pgeerhyelrllPlr 89 
                                       v+y+++++ + +  ++e l Gk  + +++ ++d + l ++     ++++  +f+  ++     ge+r++    l +r
  gi|298675596|ref|YP_003727346.1| 349 VEYVSENITYFGYKSDEFLSGKLTYaDIVHPDDVDKLKSDFSVYEKQNKNSYFTSDYRIltkTGETRWVTEKSLIIR 425
                                       778888888866677777777766668888888888888888888888888888888878899************** PP

                             PAS_4  90 desGevigvlvisrDiTerr 109
                                       + +G v  + +i++DiTer+
  gi|298675596|ref|YP_003727346.1| 426 NQKGAVKYLQGIIIDITERK 445
                                       *******************8 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   6.5e-09   8.4e-06       2      47 ..     191     237 ..     190     257 .. 0.81
   2 ?   -3.6   0.0       9.6   1.2e+04      34      54 ..     359     379 ..     357     385 .. 0.67

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 6.5e-09
                             PAS_8   2 rlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellgq 47 
                                       +++ +++s+  g++vvd  ++ +v+ N++++ ++G++ ++++g  + +
  gi|298675596|ref|YP_003727346.1| 191 FYEKILDSIWLGVWVVDsSDN-VVFFNNTMESIFGVPrEEILGTSFMD 237
                                       7999*************7777.***************99998877753 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 9.6
                             PAS_8  34 lGys.adlkgellgqllpvlrp 54 
                                       +Gy+ ++++  +l ++ + ++p
  gi|298675596|ref|YP_003727346.1| 359 FGYKsDEFLSGKL-TYADIVHP 379
                                       9999777777766.66555555 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.6e-06    0.0034       1      58 [.     196     252 ..     196     311 .. 0.79
   2 ?   -1.7   0.0       2.5   3.2e+03     106     115 .]     440     449 ..     429     449 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.6e-06
                             PAS_7   1 lenmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagd 58 
                                       l+++  G+ v+D+++++v++N+ + +++++p+e +  g+++ + ++ ++  g+ + ++
  gi|298675596|ref|YP_003727346.1| 196 LDSIWLGVWVVDSSDNVVFFNNTMESIFGVPREEI-LGTSFMDYIAEQRPVGDSRLEE 252
                                       678889***************************99.9999988888777666665444 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.5
                             PAS_7 106 DiTerrraee 115
                                       DiTer++ae+
  gi|298675596|ref|YP_003727346.1| 440 DITERKKAEK 449
                                       9******995 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1         4   5.1e+03      82     115 ..     147     180 ..     144     191 .. 0.74
   2 !   14.3   0.0   2.1e-05     0.027      10      62 ..     759     813 ..     753     849 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4
                       HATPase_c_3  82 lslgkkltvitkkegesstltldvdkidkenekv 115
                                       +s++++l++i++++ +  +   ++++++++++ +
  gi|298675596|ref|YP_003727346.1| 147 CSQSNTLDLISSHDRTLLKKDGEWKFLEEKSKTD 180
                                       7888999999999988888888888888766544 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 2.1e-05
                       HATPase_c_3  10 lvdNsld..AdaenvkievnknrgktgeivieDdGkGmseeelknalr.latsske 62 
                                       l+dNsl    +  n++i++ k + ++  i++ D+G+G++++ +   ++ + +s+ +
  gi|298675596|ref|YP_003727346.1| 759 LIDNSLKytPRGGNINISAFKSE-NNLYIKVNDNGEGIPKDLVPTLFKgFSHSEDT 813
                                       89999765588899***999987.79**************9887777535555544 PP

>> RsmJ  Ribosomal RNA large subunit methyltransferase D, RlmJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0         2   2.5e+03     131     153 ..     286     307 ..     269     331 .. 0.82
   2 ?   10.6   0.0   0.00018      0.23      28      59 ..     603     634 ..     582     650 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2
                                       E----SSCCHHHHHHHHHHHHHH CS
                              RsmJ 131 iDPPyeakdeydrvvaalrealk 153
                                       i P ++++ +y+ ++ +++ea +
  gi|298675596|ref|YP_003727346.1| 286 I-PLFNEAGNYQGILGTVEEATS 307
                                       4.889999*********999864 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00018
                                       GGGGTGGGTTT-TT--GGGHHHHHHHHHTTTT CS
                              RsmJ  28 eaeeGiaRliaqadlpaeleryldvvrklnkg 59 
                                          +G+ Rli++++  + l++yld + ++n++
  gi|298675596|ref|YP_003727346.1| 603 LLMQGMWRLIQRKQFEEALKKYLDEIANINSE 634
                                       5679************************9986 PP

>> DUF3067  Domain of unknown function (DUF3067)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00037      0.48      23      65 ..     600     642 ..     590     652 .. 0.82
   2 ?   -2.5   0.0       6.2   7.9e+03      76      93 ..     843     860 ..     808     862 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00037
                                       TTEEEEEEEEEETTSTT-SS-HHHHHHHHHHHHHHHHHHS-HH CS
                           DUF3067  23 keklylqvmwkyleqasfplteqeYlehldavaellnelgavd 65 
                                       + +l++q mw+ +++++f+   ++Yl ++ ++ + l++l++++
  gi|298675596|ref|YP_003727346.1| 600 QLTLLMQGMWRLIQRKQFEEALKKYLDEIANINSELKSLEKMK 642
                                       456899*******************999999988888877654 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 6.2
                                       ---BTTB-EEEEE--HHH CS
                           DUF3067  76 kkPrlgkavsipLdleer 93 
                                       +k ++g++v+i L l++r
  gi|298675596|ref|YP_003727346.1| 843 SKEEIGTTVTIVLPLKGR 860
                                       477889999999999877 PP

>> CTNNBL  Catenin-beta-like, Arm-motif containing nuclear
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.51   6.5e+02      45      80 ..     113     148 ..     107     162 .. 0.78
   2 ?    9.5   0.3   0.00082       1.1      15      88 ..     589     667 ..     580     678 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.51
                            CTNNBL  45 yeddpekfmeSEadLdeeikelsvlaeapelYpelv 80 
                                       +e+ p+ +++ E  Lde ik+ ++++ ++   ++  
  gi|298675596|ref|YP_003727346.1| 113 FENYPSYYLNYESLLDEIIKNRNMVSLCSYDLTKCS 148
                                       8999*****************999988765554444 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00082
                            CTNNBL  15 eeekldeaalkklllklekkvkknqelRikyeddpekfmeSEadLdeeikels.....vlaeapel..Ypelvelga 84 
                                       +e+++de+ +++l+l ++   +    +R ++e+  +k+++  a++++e+k+l+     +l  +p+   Y+el++ ++
  gi|298675596|ref|YP_003727346.1| 589 KEQEYDESDVRQLTLLMQGMWRL--IQRKQFEEALKKYLDEIANINSELKSLEkmkneILNGKPTStdYKELLDRET 663
                                       47899*******99999988875..56999********************998777778888998889999999888 PP

                            CTNNBL  85 vesL 88 
                                       +e++
  gi|298675596|ref|YP_003727346.1| 664 LETI 667
                                       8775 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1         1   1.3e+03      21      46 ..     606     630 ..     604     647 .. 0.63
   2 ?    9.8   0.4   0.00061      0.78      34      67 .]     668     701 ..     655     701 .. 0.75
   3 ?   -0.4   0.0      0.98   1.2e+03      13      46 ..     712     747 ..     711     763 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1
                                       HHHHHHHHC..T-HSSCHHHHHHHHH CS
                             HisKA  21 lgnaeaLkregklteelkeyleties 46 
                                       +g+  +++r+ +  e lk+yl+ i +
  gi|298675596|ref|YP_003727346.1| 606 QGMWRLIQRK-QFEEALKKYLDEIAN 630
                                       6777788885.667888888876643 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00061
                                       HSSCHH.HHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                             HisKA  34 teelke.yletiesearrldhlvedlLdlsrieag 67 
                                       +e+  + +++ti+++++++++l+  lL +s +e+g
  gi|298675596|ref|YP_003727346.1| 668 NEQR-DiAINTIIRSSEQINSLIGSLLYMSMEESG 701
                                       2444.359**********************99987 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.98
                                       HHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHH CS
                             HisKA  13 LrtPLsailgnaeaLkre..gklteelkeyleties 46 
                                       ++ P+++ ++n+ +  +e  ++l+ +  e+l  i  
  gi|298675596|ref|YP_003727346.1| 712 IKEPINSAYLNLALSIDEkdIDLNIDIPENLPEIYG 747
                                       688*********997554466666666666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (864 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       833  (0.046461); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 5412.57
//
Query:       gi|298675597|ref|YP_003727347.1|  [L=414]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-22   78.8   0.3    1.5e-21   76.9   0.0    2.1  3  OrfB_IS605      Probable transposase
    2.2e-09   37.1   0.3    7.7e-09   35.4   0.0    2.1  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.026   14.3   0.5      0.067   13.0   0.5    1.7  1  DUF919          Nucleopolyhedrovirus protein of unknown funct
      0.074   13.4   0.0       0.18   12.2   0.0    1.6  1  RuvX            Holliday junction resolvase


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.5   6.5e+03      71      87 ..      16      32 ..       7      40 .. 0.66
   2 ?   -1.5   0.1      0.61   2.8e+03      37      57 ..      39      59 ..      18      72 .. 0.60
   3 !   76.9   0.0   3.2e-25   1.5e-21      10     119 ..     185     292 ..     176     293 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.5
                        OrfB_IS605 71 kkasrklarlhrkrsrr 87
                                       ++ ++l++l+++++++
  gi|298675597|ref|YP_003727347.1| 16 YETLKRLTKLSKNLYNF 32
                                      45666777777777766 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.61
                        OrfB_IS605 37 twflykgrrlksdykylakei 57
                                      + f+++g+ l +d  y + + 
  gi|298675597|ref|YP_003727347.1| 39 QYFFNNGKYLNKDTAYHTVKE 59
                                      235556666666666555554 PP

  == domain 3  score: 76.9 bits;  conditional E-value: 3.2e-25
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsr 86 
                                        ++ + n++++iDlG+ n+at+vt+ gt+f+ +gr +ks +++++ke+ +lqs ++k+        k+ r ++kr  
  gi|298675597|ref|YP_003727347.1| 185 IAELDYNSHLSIDLGVDNFATCVTTGGTAFILDGRVIKSYNRWWNKEKSRLQSVYDKQD--VDNGIKMDRFFNKRFW 259
                                       56677899**************************************************9..9*************** PP

                        OrfB_IS605  87 rrkhllhklathliktlkevgvetLnvgnmkdi 119
                                       ++++l+++ ++h++k++ e+ ++++++g++k+i
  gi|298675597|ref|YP_003727347.1| 260 KINDLMNQCVNHVVKHCLENRIGNVVIGKLKEI 292
                                       ******************************987 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.5   6.9e+03       9      21 ..     167     179 ..     167     181 .. 0.87
   2 !   35.4   0.0   1.7e-12   7.7e-09       1      69 []     311     385 ..     311     385 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.5
                    OrfB_Zn_ribbon   9 eykakeyGikvee 21 
                                       +yk +++ i++++
  gi|298675597|ref|YP_003727347.1| 167 KYKGRWFEIEFVY 179
                                       69*******9987 PP

  == domain 2  score: 35.4 bits;  conditional E-value: 1.7e-12
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke......alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f+++k++++ k++ +G k++ev++ayTSk  +   +  ++      ++ +r    ++ g  +++D+n+a+Nil++
  gi|298675597|ref|YP_003727347.1| 311 FARFKQKMASKCEYHGLKYQEVDEAYTSKVDALALEPIRRhkkylgKRPKRGIFQSSTGRLINADINGALNILRK 385
                                       899**************************9776666555555588999999999999***************986 PP

>> DUF919  Nucleopolyhedrovirus protein of unknown function (DUF919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.5   1.5e-05     0.067      15      58 ..       4      45 ..       2      47 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.5e-05
                            DUF919 15 qaKrkltiksqHfErlkkitKnpkElqdlekklnklRqeFLnfg 58
                                       +K  l+ + q +E lk++tK +k l +    l ++Rq+F+n g
  gi|298675597|ref|YP_003727347.1|  4 TQKNHLRADKQTYETLKRLTKLSKNLYNF--ILYNIRQYFFNNG 45
                                      58999******************777665..699*******987 PP

>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     4e-05      0.18      37     106 ..     266     345 ..     255     361 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4e-05
                                       HHHHHHHHHHHHHTT--EEEEE--........----SSS---SSTTHHHHHHHHHT....T-EEEEE--S----XXX CS
                              RuvX  37 ekdleelkelvkeeeveeiVvGlP........lnldgsegesakkvrkfaeeLakrl..kklpvelvDErlttveae 103
                                       ++ ++++ + + e+++ ++V+G          +  +++++ ++  +++f +++a+++  ++l+   vDE +t++  +
  gi|298675597|ref|YP_003727347.1| 266 NQCVNHVVKHCLENRIGNVVIGKLkeikqeqnIGKENTQNFQTIPFARFKQKMASKCeyHGLKYQEVDEAYTSKVDA 342
                                       67899999**************9967776655566677777788889999999999877899***********8755 PP

                                       XXX CS
                              RuvX 104 ril 106
                                        +l
  gi|298675597|ref|YP_003727347.1| 343 LAL 345
                                       554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1034  (0.0576719); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 3009.36
//
Query:       gi|298675598|ref|YP_003727348.1|  [L=170]
Description: dUTP pyrophosphatase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-10   40.1   0.0    3.9e-10   39.5   0.0    1.2  1  dUTPase   dUTPase
     0.0052   15.6   0.0     0.0095   14.8   0.0    1.5  1  DCD       2'-deoxycytidine 5'-triphosphate deaminase (DCD)


Domain annotation for each model (and alignments):
>> dUTPase  dUTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.0   4.3e-14   3.9e-10      30     106 ..      79     155 ..      69     168 .. 0.83

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 4.3e-14
                                       EEEEEEEEEEEE--TTEEEEEEE-HHHHHHHEEEEEEEEETTBTS..EEEEEEEE-SSS-EEE-TT-EEEEEEEEEB CS
                           dUTPase  30 etvlvptdisiklpdglaalilpRSglaakglivvpgvidsdyrG..evkvvlfnltkkdvkikkgdRiAqLifari 104
                                       + + v ++  + +p+++aa+  pRS+l + g+  ++ v+d+ yrG  e ++v+ n+++  +++kk++Ri q++f  +
  gi|298675598|ref|YP_003727348.1|  79 GIYKVIFNEIVNMPKNIAAIAKPRSSLIRCGVSLETAVWDAGYRGrsESMLVVHNFSG--FRLKKNARIMQMLFYTL 153
                                       555677889999*********************************5555666666666..**************866 PP

                                       EC CS
                           dUTPase 105 lt 106
                                       + 
  gi|298675598|ref|YP_003727348.1| 154 DS 155
                                       55 PP

>> DCD  2'-deoxycytidine 5'-triphosphate deaminase (DCD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.1e-06    0.0095       4     113 ..       3     110 ..       1     150 [. 0.78

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.1e-06
                               DCD   4 ilpdqeiealieeg.aikaeepleeeqiqPaslDLrLgkk.ayrvrasFlpgkgekvaekleelklheldLtegavl 78 
                                       +l+++e+++++++   ++ + + +++qiqP+ +++ L +  + +   s    + ++ ++ + e ++ e+d +    l
  gi|298675598|ref|YP_003727348.1|   3 LLSENELKKMMSQTpPLMENLQDQNTQIQPNGIEMTLKEIrTIKGTGSV---DFDNKQRVIPEGETLEFDSEGWINL 76 
                                       68889999988776256677777889**********9874133333333...3344455677777777885555555 PP

                               DCD  79 ekgcvYivplleslaLpadlsaaanpksstGRlDv 113
                                         + +Y v ++e +++p++++a+a p+ss  R  v
  gi|298675598|ref|YP_003727348.1|  77 -PNGIYKVIFNEIVNMPKNIAAIAKPRSSLIRCGV 110
                                       .5669************************988665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1260.71
//
Query:       gi|298675599|ref|YP_003727349.1|  [L=267]
Description: putative phospho-2-dehydro-3-deoxyheptonate aldolase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      1e-59  202.1   0.0    1.2e-59  201.8   0.0    1.1  1  DeoC       DeoC/LacD family aldolase
      0.004   16.8   0.3     0.0067   16.0   0.1    1.4  2  OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS famil


Domain annotation for each model (and alignments):
>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.8   0.0   1.3e-63   1.2e-59       2     234 ..      22     236 ..      21     237 .. 0.99

  Alignments for each domain:
  == domain 1  score: 201.8 bits;  conditional E-value: 1.3e-63
                                       EEEEECCSHHHHHHHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCTTSEEEEETECSSCCTTSTTE CS
                              DeoC   2 vilavDqrvankddtasaqneqledlkalvkealtpgasavlldpgviasaskeyakdiallvkldkgtyllkskqr 78 
                                       +i+++D++v  +++++       +d+ ++v+ ++++ga+avl + g+  +++++y++di+l+++l+++t l +++ +
  gi|298675599|ref|YP_003727349.1|  22 IIIPMDHGVGAGPIKGL------IDMPTTVNSVAEGGANAVLGHMGLPKHGHRGYGRDIGLIIHLSASTSLGPDPDH 92 
                                       699**************......9***************************************************** PP

                                       EEETTCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEEEEE-CTTBSSTTCHHHHHHH CS
                              DeoC  79 dvdevasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplilelylrdeaikdekvdpdlvae 155
                                       +v+ v+++eea++ GAd v+v++++   g+++e+++l++++ ++++c+e+g+pl++++y+r+e+i+ e+ d++ v++
  gi|298675599|ref|YP_003727349.1|  93 KVL-VTTIEEAIKVGADTVSVHINI---GADDEAEMLQDLGYIGKKCDEWGIPLLAMMYPRGEKISSEH-DAEYVKH 164
                                       ***.*********************...*****************************************.******* PP

                                       HHHHHTCCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTEEEEETTS...SHHHHHHHHHHHHHHHTHCEEEES CS
                              DeoC 156 AarvsaelGaDiiKvevpkevvnateedaevfkdvikaapvpgvvlsGGv...seedfletvedAvkeagasGvlsG 229
                                        arv+aelGaDi+K++++        +d+++f++v+k++pvp v+++GG+   +e+++l++v d++ +ag+ Gv++G
  gi|298675599|ref|YP_003727349.1| 165 VARVGAELGADIVKTNYT--------GDIDSFSEVVKGCPVP-VIIAGGPhmeDERQILQMVYDSI-QAGGKGVALG 231
                                       ******************........****************.*********99************.********** PP

                                       HHHHT CS
                              DeoC 230 Raifq 234
                                       R++fq
  gi|298675599|ref|YP_003727349.1| 232 RNVFQ 236
                                       ****9 PP

>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0      0.58   5.2e+03      66      82 ..      39      54 ..      38      60 .. 0.74
   2 !   16.0   0.1   7.4e-07    0.0067      80     222 ..     100     244 ..      93     247 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.58
                                      -S-HHHHHHHHHSTCHH CS
                         OMPdecase 66 aDIGntvekqatagsar 82
                                       D + tv+  a++g+ +
  gi|298675599|ref|YP_003727349.1| 39 IDMPTTVNSVAEGGA-N 54
                                      699999999998554.4 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 7.4e-07
                                       CHHHHTTESEEEEEGTGH....HHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHHSHHHHHHHHHHHHHHHTTE CS
                         OMPdecase  80 sarikewadivtvhavaG....kasvkalaeaaekwgnrgllilaqmsskgnlmlqekgytqacveaarehkaedfv 152
                                         +ik +ad v vh+  G     ++++ l    +k+++ g+ +la+m   g+    e   + + v+++++  ae   
  gi|298675599|ref|YP_003727349.1| 100 EEAIKVGADTVSVHINIGaddeAEMLQDLGYIGKKCDEWGIPLLAMMYPRGEKISSE--HDAEYVKHVARVGAE--- 171
                                       5679999********999333334566665566677799******************..999999999999977... PP

                                       SEEECCCHTHHHHHHTTCSCEEEHHHTT...EEEEECTTCCG...GGHHHHHHHTTCSEEEESHHHHTSSSHHHHH CS
                         OMPdecase 153 mGfvaqetlnateedaddfihltpgigl...eqggdgkgqqy...ntpekligiagadiiivGRgIlkagdpveea 222
                                        G+   +t      d d f  +++g+ +    +gg + + ++   +++ + i+ ag + +  GR +++a+dp + +
  gi|298675599|ref|YP_003727349.1| 172 LGADIVKTNY--TGDIDSFSEVVKGCPVpviIAGGPHMEDERqilQMVYDSIQ-AGGKGVALGRNVFQANDPTAMV 244
                                       6776666644..34569***********9995555544444401055666666.8999**************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2011.63
//
Query:       gi|298675600|ref|YP_003727350.1|  [L=582]
Description: glycyl-tRNA synthetase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-22   79.2   0.0    4.8e-22   77.9   0.0    1.7  1  HGTP_anticodon  Anticodon binding domain
    1.3e-12   48.0   0.0    6.5e-12   45.8   0.0    2.0  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
      0.006   15.7   0.1        1.7    7.7   0.0    2.8  3  tRNA-synt_2     tRNA synthetases class II (D, K and N)
     0.0084   16.2   0.1      0.017   15.1   0.1    1.5  1  CpXC            CpXC protein
  ------ inclusion threshold ------
       0.48   11.4   2.3        8.9    7.4   0.1    2.8  2  zf-C2H2_4       C2H2-type zinc finger
        1.7    9.0   5.9       0.19   12.0   0.9    2.0  2  Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase


Domain annotation for each model (and alignments):
>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.9   0.0   1.6e-25   4.8e-22       1      91 [.     475     563 ..     475     566 .. 0.95

  Alignments for each domain:
  == domain 1  score: 77.9 bits;  conditional E-value: 1.6e-25
                                       SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTC CS
                    HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtr 77 
                                       qv+v+pl +k++ l + a+++ +++r++g+ v +d ++++ig+++r+ d++g+p+ v++++++le++tvt+rdrdt+
  gi|298675600|ref|YP_003727350.1| 475 QVAVLPLMSKSD-LIKPARDISARFRKKGLMVSYD-DSGTIGRRYRRNDEIGTPYSVTIDYQTLEDNTVTIRDRDTM 549
                                       8********777.*****************99998.79*************************************** PP

                                       EEEEEETTHHHHHH CS
                    HGTP_anticodon  78 eqervsldelvekl 91 
                                       +q+r+s d++++ +
  gi|298675600|ref|YP_003727350.1| 550 KQIRLSKDNIEDTV 563
                                       *********99987 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.0   2.2e-15   6.5e-12      11     178 ..     158     446 ..     153     447 .. 0.73

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 2.2e-15
                                       EEE-SSSHHHHHHHHHHHEEEB..GGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEES.GGGHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                      tRNA-synt_2b  11 yiLkPtneetfvelirdevlrs..krLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfha.easlddslrdli 84 
                                        +L+P+  +++   +    +r   ++LP+ ++qi+  yR+E s  +G++R+reF+q ++++f   e++   ++ ++ 
  gi|298675600|ref|YP_003727350.1| 158 AYLRPETAQGMFINFLRL-ARYyrEKLPFGVTQIGKSYRNEISPRQGVIRLREFTQAEAEIFIPpEDKTHPEFDKYA 233
                                       689999988865555433.4442244****************9566******************8899999999999 PP

                                       HHHHHHHHHT..T.SCEEEEEEGTTSC..........................................BTTSEEEE CS
                                       xxxxxxxxxx..xxxxxxxxxxxxxxx..........................................xxxxxxxx RF
                      tRNA-synt_2b  85 kaisriferl..glefraiielmsaks..........................................adykdkke 117
                                        ++ +++ +   g  +r i+++   k+                                          a       
  gi|298675600|ref|YP_003727350.1| 234 DTVLNMYIEDdnGGVVRPIRLDDAVKEgyiaheylayhialtkdfllriginpdklrfrqhkkdemahyA------- 303
                                       9999999654447677889988544445677778888888888888888777777754444444444440....... PP

                                       EEEEETT...................................................................... CS
                                       xxxxxxx...................................................................... RF
                      tRNA-synt_2b 118 feavses...................................................................... 124
                                                                                                                    
  gi|298675600|ref|YP_003727350.1| 304 ------Adcwdaeiesdrfgwietvgiadrtnydlkahtdtsgtelsiyreyeepetvnqftvkpdmsklgpsykgk 374
                                       ......35566666666666666666677777777777777777788888888888888888888888888888888 PP

                                       ...............TSEEEEEEEEEEEETHHHHHTTE...EEECTTSSEEEEEEEEEEEEHHHHHHHHHHH CS
                                       ...............xxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b 125 ...............ltkgieigtiqklgtrlserlga...tvldennreksvimicaaigveRllsaileq 178
                                                      l+k    + +++ +   ++ +     ++++  ++  ++++i  + g+ R++ ++le+
  gi|298675600|ref|YP_003727350.1| 375 aktiaeklkqlppeeLEKDNIQVNVEGEEYTVPSDMVEfteETVKVSGETVFPHVIEPSYGIDRIIYCVLEH 446
                                       8888888889999996665444555555555555544336688899999******************99997 PP

>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.0    0.0035        10      26      50 ..      42      67 ..      38      75 .. 0.73
   2 !    7.7   0.0   0.00055       1.7      81     122 ..     178     217 ..     145     359 .. 0.84
   3 ?   -2.3   0.0      0.62   1.9e+03      77     103 ..     494     519 ..     491     523 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0035
                                      HHHHHHHHH.HHHHTT-EE----SEE CS
                                      xxxxxxxxx.xxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 26 stvtkavrk.yleengfieietPiLs 50
                                       ++ ++ r+ y  ++gf+eietP++ 
  gi|298675600|ref|YP_003727350.1| 42 RRIEQIWRDmYVVQEGFMEIETPTIG 67
                                      566677776245677********986 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00055
                                       HHHHHHHHCTHSEEEEEEEEE--S--BTT..B-S-CEEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx RF
                       tRNA-synt_2  81 lylellivagidrvfqiaraFRaEdsrtd..rhlaEFtqieaem 122
                                        y+e l  +    v qi++++R+E s  +    l EFtq eae+
  gi|298675600|ref|YP_003727350.1| 178 YYREKLPFG----VTQIGKSYRNEISPRQgvIRLREFTQAEAEI 217
                                       566666666....889********98655225799********8 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.62
                                       S-SHHHHHHHHHCTHSEEEEEEEEE-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  77 qspqlylellivagidrvfqiaraFRa 103
                                       +s  + ++ l+v+ +d+  +i+r +R 
  gi|298675600|ref|YP_003727350.1| 494 ISARFRKKGLMVS-YDDSGTIGRRYRR 519
                                       577788999****.***********97 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   5.7e-06     0.017       2      53 ..      87     142 ..      86     166 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.7e-06
                              CpXC   2 tCpaCgkefeae..iwtsidadedpelkeklldgsl..featCpkCgatakleapl 53 
                                       +C +Cg+ f+a+  +++ +d+++ + + +++l++s+  +e+ Cp Cg ++   +++
  gi|298675600|ref|YP_003727350.1|  87 ECEECGEAFRADhlVEDELDIESAEAMSNNILEDSIkdNEIPCPVCGGKFGSVYSF 142
                                       6********99944589******************9555799*****998777765 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.3       0.1     3e+02       2      12 ..      87      96 ..      86     101 .. 0.79
   2 ?    7.4   0.1     0.003       8.9       2      16 ..     128     142 ..     127     144 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.1
                         zf-C2H2_4  2 kCpiCgksFss 12
                                      +C+ Cg+ F +
  gi|298675600|ref|YP_003727350.1| 87 ECEECGEAF-R 96
                                      7******99.4 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.003
                         zf-C2H2_4   2 kCpiCgksFsskkaL 16 
                                       +Cp+Cg+ F s +++
  gi|298675600|ref|YP_003727350.1| 128 PCPVCGGKFGSVYSF 142
                                       7********999886 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.3       3.3   9.9e+03       5      10 ..      87      92 ..      67      94 .. 0.70
   2 ?   12.0   0.9   6.3e-05      0.19       3      12 ..     126     135 ..     124     137 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.3
                                      --TTTT CS
                    Prim_Zn_Ribbon  5 pCPvCG 10
                                      +C  CG
  gi|298675600|ref|YP_003727350.1| 87 ECEECG 92
                                      444444 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 6.3e-05
                                       EE--TTTT-T CS
                    Prim_Zn_Ribbon   3 hspCPvCGGr 12 
                                       ++pCPvCGG+
  gi|298675600|ref|YP_003727350.1| 126 EIPCPVCGGK 135
                                       79*******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (582 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.22s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 4253.39
//
Query:       gi|298675601|ref|YP_003727351.1|  [L=759]
Description: ERCC4 domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-26   93.6   0.3    5.6e-26   91.6   0.3    2.2  1  ERCC4           ERCC4 domain
    5.1e-25   88.0   0.1    1.7e-21   76.7   0.0    2.8  2  Helicase_C      Helicase conserved C-terminal domain
    6.5e-17   61.8   0.0    2.5e-16   60.0   0.0    2.0  1  DEAD            DEAD/DEAH box helicase
    1.9e-15   57.3   0.6      8e-15   55.2   0.0    2.4  3  ResIII          Type III restriction enzyme, res subunit
    1.7e-10   40.8   0.0    5.8e-10   39.1   0.0    1.9  1  HHH_2           Helix-hairpin-helix motif
    2.6e-08   34.3   0.0    8.2e-08   32.7   0.0    1.8  1  HHH_5           Helix-hairpin-helix domain
    4.2e-06   26.3   0.3    4.8e-05   23.0   0.0    2.8  3  HHH             Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.011   16.4   2.5      0.039   14.5   0.0    3.2  3  5_3_exonuc      5'-3' exonuclease, C-terminal SAM fold
      0.028   14.8   0.0       0.14   12.5   0.0    2.3  1  HHH_8           Helix-hairpin-helix domain
       0.13   12.7   0.0       0.34   11.4   0.0    1.7  1  COX6A           Cytochrome c oxidase subunit VIa
       0.39   11.4   3.7       0.66   10.7   0.5    2.8  3  Organ_specific  Organ specific protein


Domain annotation for each model (and alignments):
>> ERCC4  ERCC4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.6   0.3   3.5e-29   5.6e-26       1     154 [.     552     670 ..     552     672 .. 0.97

  Alignments for each domain:
  == domain 1  score: 91.6 bits;  conditional E-value: 3.5e-29
                                       EEGGGCTSHHHH..HHTTTSEEEEE--SSSSE.EE...CTT...............EEEEEEEHHHHHHHHCCSHHH CS
                             ERCC4   1 iDsrelksgieeylleelgvevvietlpigdyilwrrkvkaeynleldieepceekvlverksaddlvasikdgrle 77 
                                       +D+re ks + +  le+l+v  +i+tl+i dy ++   +++               +++erks +d+v+s++d++l+
  gi|298675601|ref|YP_003727351.1| 552 VDQRETKSTVVRS-LEKLDVDFTIKTLEIADY-IV---SDR---------------IAIERKSSVDFVNSLIDKTLF 608
                                       8************.9*****************.99...9**...............********************* PP

                                       HHHHHHHH.H-SEEEEEEES-GGGTT................THHH.HHHHHHHHHHHHS-EEEEESSHHHHHHHHH CS
                             ERCC4  78 eqvsrlkrngykkpillvegldqykrknknsrnkqykakvrqinrktiesaLvqlqldfgvsilttesanetaewla 154
                                       eqvs l+r  ykkp+l++eg   ++ +               in++++++ L++l+ldfgvsi +t+++++ta ++ 
  gi|298675601|ref|YP_003727351.1| 609 EQVSNLSR-MYKKPCLILEGDGMFSARQ--------------INPNAVYGTLISLELDFGVSIYYTRDEKDTASVIR 670
                                       ********.***********99999986..............*******************************9886 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0018       2.9      10      99 ..      49     147 ..      43     151 .. 0.79
   2 !   76.7   0.0     1e-24   1.7e-21       6     110 ..     358     470 ..     350     471 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0018
                                       H....HHTTTTSEEEEEESSHHHHHH.HHHHHHHT....TSTEEEESTTSTHHHHHHHHHHHH.TTSSSEEEESGGG CS
                        Helicase_C  10 l....kleeeggkilifvntidrlek.vklllekk....gikvavlhgelpqnereeileqfn.kgesdvLiatdva 76 
                                       l     le+ gg++l+ ++t+  +e+ +++l ++     + ++ +++g+++ ++r e  e+     ++  +i  d +
  gi|298675601|ref|YP_003727351.1|  49 LviasRLEKFGGRALVLSPTKPLVEQhAHFL-KSTlaipENNIQAFTGNTSPEKRAELWENSSvIVSTPQVIENDLL 124
                                       233456899*************999955555.3335788889999***************9984344559999999* PP

                                       TSSSTSTTESEEEESSSSSSHHH CS
                        Helicase_C  77 erGidipkvnlVinfdlprnvts 99 
                                       ++ id+++v+++ + ++ r v +
  gi|298675601|ref|YP_003727351.1| 125 AKRIDLNDVSHITFDEAHRAVGN 147
                                       **********9987777666655 PP

  == domain 2  score: 76.7 bits;  conditional E-value: 1e-24
                                       HHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHT........TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEES CS
                        Helicase_C   6 llellkleeeggkilifvntidrlek.vklllekk........gikvavlhgelpqnereeileqfnkgesdvLiat 73 
                                       + + l +e+ ++++++f+n++d++e+ ++ll e          g ++ + +  l+q+++ ei+++f+ ge++v+++t
  gi|298675601|ref|YP_003727351.1| 358 VSKQL-EENPDSRAIVFTNYRDTAEMlANLLSEMDgvypirfvGQSSKYNDKGLTQKQQVEIIDKFKTGEYNVIVST 433
                                       44555.89999***********9988777775555666666677888888888************************ PP

                                       GGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSST CS
                        Helicase_C  74 dvaerGidipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                       +vae+G+dip+ +lV ++++  +  + iqr+GRt+R 
  gi|298675601|ref|YP_003727351.1| 434 SVAEEGLDIPSTDLVLFYEPVPSEIRSIQRKGRTARK 470
                                       ************************************6 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.0   0.0   1.5e-19   2.5e-16      16     139 ..      32     151 ..      17     179 .. 0.82

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 1.5e-19
                                       EEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  16 dvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqls 92 
                                       + lv  +TG GKT+++l+ + +++    +k g +al+++Pt+ L+eq+++ lk+ +   + ++++++g+++ + +++
  gi|298675601|ref|YP_003727351.1|  32 SSLVVLPTGLGKTTVALLVIASRL----EKFGGRALVLSPTKPLVEQHAHFLKSTLAIPENNIQAFTGNTSPE-KRA 103
                                       568999***************999....68888************************7666777677766665.555 PP

                                       HHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHT.TTH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                              DEAD  93 kldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldq.gfs 139
                                       +l ++  ++v+tp+ + + l  ++++l++v+ + +DEa+r   + ++ 
  gi|298675601|ref|YP_003727351.1| 104 ELWENSSVIVSTPQVIENDLLAKRIDLNDVSHITFDEAHRAVGNySYT 151
                                       55599************97778999***************99883443 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   0.0   4.9e-18     8e-15      24     169 ..      30     173 ..      10     175 .. 0.81
   2 ?   -2.2   0.1       2.1   3.5e+03      72     118 ..     339     383 ..     330     422 .. 0.57
   3 ?   -3.5   0.1       5.6   9.2e+03      85      87 ..     513     515 ..     468     542 .. 0.50

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 4.9e-18
                                       TSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.......GEEEESSS-B--. CS
                            ResIII  24 dkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayke...igkkvsgdkkkak 97 
                                       ++  l++++TG GKT va+ +i++ l+k++  ++l+l p+k l+eq  + +k++l  + ++    ++++s +k   +
  gi|298675601|ref|YP_003727351.1|  30 NTSSLVVLPTGLGKTTVALLVIASRLEKFGG-RALVLSPTKPLVEQHAHFLKSTLAIPENNiqaFTGNTSPEK---R 102
                                       56789*************8888888877774.***************98888888877765333333344444...4 PP

                                       ......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHHHHT-....--SEEEEEESS- CS
                            ResIII  98 ekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswreilekf....keavllglTATp 169
                                       ++  +n++++v+t q + +d+       ++ + +    i +DEaHr+ ++ s++ i+ek+    k+ + lg+TA p
  gi|298675601|ref|YP_003727351.1| 103 AELWENSSVIVSTPQVIENDL-----LAKRIDLNDVSHITFDEAHRAVGNYSYTYIAEKYyengKNPLCLGITASP 173
                                       44889****************.....89999999999************99****97766455577********88 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.1
                                       HHGGGGTGG......GEEEESSS-B--.......-SEEEEEHHHHHHTH CS
                            ResIII  72 eefkkflseayke..igkkvsgdkkkakekdstnkkilvttiqsldads 118
                                       +++k+++se+ k   + ++vs++ +++     +++ i++t++    + +
  gi|298675601|ref|YP_003727351.1| 339 HRLKECSSEHPKLemTREIVSKQLEEN----PDSRAIVFTNYRDTAEML 383
                                       555555555433344334444443333....688888888887766555 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 5.6
                                       GEE CS
                            ResIII  85 igk 87 
                                       +++
  gi|298675601|ref|YP_003727351.1| 513 NNE 515
                                       222 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.0   3.5e-13   5.8e-10       8      53 ..     706     751 ..     702     756 .. 0.95

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 3.5e-13
                             HHH_2   8 IrhVGektAklLakrFksldaLkkasleeLlevddiGeeiAqsive 53 
                                       I ++G ++A+ L k F+s+++++ka++eeL+e + iG+++A++i+e
  gi|298675601|ref|YP_003727351.1| 706 ISDIGPRAARSLLKYFGSVENIMKANYEELQEAELIGPKTASKIRE 751
                                       889*****************************************97 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0     5e-11   8.2e-08       6      53 ..     705     751 ..     701     754 .. 0.95

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 5e-11
                                       TSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHH CS
                             HHH_5   6 svsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriil 53 
                                        +s iGp+ A++ll+  ++sve +++a+ eeL+++  iG+ktA +i +
  gi|298675601|ref|YP_003727351.1| 705 AISDIGPRAARSLLKY-FGSVENIMKANYEELQEAELIGPKTASKIRE 751
                                       69**************.****************************976 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.8   2.9e+03       5      16 ..     250     261 ..     247     262 .. 0.85
   2 ?   -1.1   0.0       1.3   2.1e+03      15      30 .]     705     720 ..     704     720 .. 0.88
   3 !   23.0   0.0     3e-08   4.8e-05       1      30 []     723     752 ..     723     752 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.8
                                       HHTSSHHHHHTS CS
                               HHH   5 lipasreeLlal 16 
                                        + a+ ++Ll+l
  gi|298675601|ref|YP_003727351.1| 250 KKKATKKDLLSL 261
                                       578******998 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.3
                                       TSTT-SHHHHHHHHHH CS
                               HHH  15 alPGVGpktAeaIlsy 30 
                                       a++ +Gp  A++ l y
  gi|298675601|ref|YP_003727351.1| 705 AISDIGPRAARSLLKY 720
                                       7899***999999987 PP

  == domain 3  score: 23.0 bits;  conditional E-value: 3e-08
                                       SHHHHHTSSHHHHHTSTT-SHHHHHHHHHH CS
                               HHH   1 sleglipasreeLlalPGVGpktAeaIlsy 30 
                                       s+e+++ a++eeL++ + +GpktA +I+++
  gi|298675601|ref|YP_003727351.1| 723 SVENIMKANYEELQEAELIGPKTASKIREI 752
                                       689************************986 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       6.9   1.1e+04      36      50 ..     220     236 ..     216     272 .. 0.48
   2 ?   -0.7   0.1       1.4   2.3e+03      40      79 ..     304     347 ..     278     368 .. 0.54
   3 ?   14.5   0.0   2.4e-05     0.039      22      53 ..     705     737 ..     702     755 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 6.9
                        5_3_exonuc  36 keygsleeilenl..de 50 
                                        e+++l+++le++  d+
  gi|298675601|ref|YP_003727351.1| 220 DEIKKLKQLLEKIldDR 236
                                       56667777777664312 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.4
                        5_3_exonuc  40 sleeilenldelke.......kklkekLeenkeearlskkLatiktd 79 
                                        l + +++ld   +       +k+ ++L+e+  + ++s++L +   +
  gi|298675601|ref|YP_003727351.1| 304 ALTKYYDRLD---ReaglksgSKASKRLAEDPYMQQISHRLKECSSE 347
                                       2333333333...1112222356667777776666677666665554 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 2.4e-05
                        5_3_exonuc  22 GvpgiGektAakLlkeygsleeilenld.elke 53 
                                        ++ iG+++A +Llk +gs+e+i+++   el+e
  gi|298675601|ref|YP_003727351.1| 705 AISDIGPRAARSLLKYFGSVENIMKANYeELQE 737
                                       6899********************954324444 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   8.7e-05      0.14      30      67 ..     712     753 ..     711     754 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.7e-05
                                       HHHCCCCC-SS-HHHH.TT...HCTTSTT--HHHHHHHHHHH CS
                             HHH_8  30 rAaraiealpeeitsl.ee...eltklpgiGkkiaakieeil 67 
                                       rAar++ ++   ++++ ++   el++   iG+k+a ki+ei+
  gi|298675601|ref|YP_003727351.1| 712 RAARSLLKYFGSVENImKAnyeELQEAELIGPKTASKIREIV 753
                                       89999999999999998556778*****************97 PP

>> COX6A  Cytochrome c oxidase subunit VIa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00021      0.34      35      96 ..     100     161 ..      87     166 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00021
                             COX6A  35 eettdlwrklslyvaipalilaainaynlekeHaeHvehlkeleerteYeYqnirtknffwG 96 
                                       e+ ++lw + s++v  p +i   + a+++  + + H++  +      +Y+Y  i +k +  G
  gi|298675601|ref|YP_003727351.1| 100 EKRAELWENSSVIVSTPQVIENDLLAKRIDLNDVSHITFDEAHRAVGNYSYTYIAEKYYENG 161
                                       56789************************************99999***********99766 PP

>> Organ_specific  Organ specific protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.91   1.5e+03      86     107 ..     401     422 ..     332     427 .. 0.71
   2 ?   10.7   0.5   0.00041      0.66       2      62 ..     485     540 ..     484     564 .. 0.87
   3 ?   -3.4   0.0       9.3   1.5e+04      67      89 ..     707     729 ..     676     737 .. 0.64

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.91
                    Organ_specific  86 nvsvYeddevaskeeksfvkDf 107
                                       + s+Y+d++++ k++ ++++ f
  gi|298675601|ref|YP_003727351.1| 401 QSSKYNDKGLTQKQQVEIIDKF 422
                                       5578888888888888777766 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00041
                    Organ_specific   2 dpGeYWkavmkdqpmPkaikgllsktkeqvlsskkancettlvteaknkfvkdFepkpsvt 62 
                                       d   YW  v k+++m  ++k l     ++++s++++n   + ++e ++k   dFe + +v 
  gi|298675601|ref|YP_003727351.1| 485 DEAYYWSSVSKERKMQDNMKYL-----QDIMSQNNENTSGSGKSENNQKKLFDFESETNVD 540
                                       6678***************999.....7899999999999999999998999999988775 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 9.3
                    Organ_specific  67 ediklkeeksfvkdfeprpnvsv 89 
                                       +di +   +s++k f ++ n+ +
  gi|298675601|ref|YP_003727351.1| 707 SDIGPRAARSLLKYFGSVENIMK 729
                                       35666666677777777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (759 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       995  (0.0554967); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.39
# Mc/sec: 5815.40
//
Query:       gi|298675602|ref|YP_003727352.1|  [L=142]
Description: Sjogrens syndrome scleroderma autoantigen 1 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.2e-14   51.3   2.7    1.4e-13   50.8   2.7    1.3  1  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
     0.0044   17.0   1.9     0.0079   16.2   1.9    1.4  1  DZR             Double zinc ribbon
      0.005   16.8   1.0       0.24   11.4   0.0    2.6  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
  ------ inclusion threshold ------
      0.045   13.8   0.9      0.078   13.0   0.9    1.4  1  Zn_Tnp_IS91     Transposase zinc-binding domain
       0.07   13.1   2.1       0.16   12.0   2.1    1.5  1  zinc-ribbons_6  zinc-ribbons


Domain annotation for each model (and alignments):
>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   2.7   3.9e-17   1.4e-13       2      40 .]      10      46 ..       9      46 .. 0.95

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 3.9e-17
                     Auto_anti-p27  2 kmgelLlkGwtMLaetCpvCgvPLmrdrkggkvyCvaCd 40
                                      k++++L  G+tML+++C+ Cg+PL+r  ++g+++C++C+
  gi|298675602|ref|YP_003727352.1| 10 KISKMLECGATMLSQHCQSCGSPLFR--YQGEIICPVCQ 46
                                      89************************..679*******6 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.9   2.2e-06    0.0079      12      37 ..      23      48 ..      15      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.2e-06
                               DZR 12 arfCseCgtklkavaaedrCpsCgek 37
                                      ++ C+ Cg++l +++ e+ Cp C+  
  gi|298675602|ref|YP_003727352.1| 23 SQHCQSCGSPLFRYQGEIICPVCQDR 48
                                      689********************975 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   6.7e-05      0.24       1      17 [.      25      41 ..      25      41 .. 0.91
   2 ?    3.1   0.6     0.028     1e+02       2       6 ..      42      46 ..      42      48 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.7e-05
                    DNA_ligase_ZBD  1 hCPvCGsavvReegeai 17
                                      hC +CGs++ R +ge i
  gi|298675602|ref|YP_003727352.1| 25 HCQSCGSPLFRYQGEII 41
                                      8889**********976 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.028
                    DNA_ligase_ZBD  2 CPvCG 6 
                                      CPvC 
  gi|298675602|ref|YP_003727352.1| 42 CPVCQ 46
                                      ****6 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.9   2.2e-05     0.078      17      67 ..       4      49 ..       1      59 [. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.2e-05
                       Zn_Tnp_IS91 17 rpsqrkavekilrCrtaalGfaryeCeeCghekivyfsCksrhCpsCqkka 67
                                      ++++ ++++k+l+C+         +C++Cg+  + y+  ++  Cp Cq ++
  gi|298675602|ref|YP_003727352.1|  4 EDQELDKISKMLECGATM---LSQHCQSCGSPLFRYQ--GEIICPVCQDRE 49
                                      5678899********966...6678****98655554..5677****9886 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.1   4.5e-05      0.16      17      40 ..      24      50 ..      12      61 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.5e-05
                                      EE-TTT--...EEEEEEE-SSS-S--- CS
                    zinc-ribbons_6 17 yhCeaCqe...dlkkealCpeCeqele 40
                                       hC++C +   +++ e +Cp C+++ e
  gi|298675602|ref|YP_003727352.1| 24 QHCQSCGSplfRYQGEIICPVCQDREE 50
                                      578888888888888888888887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1068  (0.0595683); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1121.93
//
Query:       gi|298675603|ref|YP_003727353.1|  [L=91]
Description: hypothetical protein Metev_1719 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.2e-37  125.3   2.1    8.1e-37  125.1   2.1    1.0  1  UPF0147   Uncharacterised protein family (UPF0147)
     0.0028   17.9   0.2      0.032   14.5   0.2    2.1  2  UPF0253   Uncharacterised protein family (UPF0253)


Domain annotation for each model (and alignments):
>> UPF0147  Uncharacterised protein family (UPF0147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.1   2.1   9.1e-41   8.1e-37       2      81 .]       8      87 ..       7      87 .. 0.98

  Alignments for each domain:
  == domain 1  score: 125.1 bits;  conditional E-value: 9.1e-41
                                      HHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHH CS
                           UPF0147  2 eekikevielLeeiiedtsvPrniRraakeakekLkdekeslavraataisiLdeisnDpnmPlhaRtliwevvskLEt 80
                                      +e+i++++++Le+i++d+svPrniRr+a+e+++kL++ +e+l +ra+++isiL+++snDpn+Plh+Rtliw+vvs+LEt
  gi|298675603|ref|YP_003727353.1|  8 DEVINQCVQILEQIANDNSVPRNIRRSASEVVDKLQNGDEQLFLRASSSISILEDVSNDPNIPLHTRTLIWNVVSQLET 86
                                      589***************************************************************************9 PP

                                      H CS
                           UPF0147 81 i 81
                                      i
  gi|298675603|ref|YP_003727353.1| 87 I 87
                                      8 PP

>> UPF0253  Uncharacterised protein family (UPF0253)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.2   3.6e-06     0.032      23      51 ..       7      35 ..       2      42 .. 0.90
   2 ?    1.3   0.0     0.048   4.3e+02      30      48 ..      56      74 ..      50      76 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.6e-06
                           UPF0253 23 ipdAiscalktLdevaanealpeevrekA 51
                                      +++ i+  ++ L+++a+++++p+++r +A
  gi|298675603|ref|YP_003727353.1|  7 VDEVINQCVQILEQIANDNSVPRNIRRSA 35
                                      78889999******************988 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.048
                           UPF0253 30 alktLdevaanealpeevr 48
                                       +  L++v ++ ++p ++r
  gi|298675603|ref|YP_003727353.1| 56 SISILEDVSNDPNIPLHTR 74
                                      6889*********998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 757.90
//
Query:       gi|298675604|ref|YP_003727354.1|  [L=210]
Description: translin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.7e-08   32.4   0.0    4.2e-07   30.2   0.0    1.9  1  Translin  Translin family
  ------ inclusion threshold ------
        0.1   12.7   0.2       0.59   10.2   0.0    2.0  2  BLOC1S3   Biogenesis of lysosome-related organelles complex 1


Domain annotation for each model (and alignments):
>> Translin  Translin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   4.7e-11   4.2e-07       9     193 ..      26     185 ..      18     187 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 4.7e-11
                                       HHHHHHHHHHHHHHHHHTTGSSTTTHHHHHHH.HHHHHHHHHHHTTSS..........GHHHHGGGTH.HHHHHHHH CS
                          Translin   9 asrditaaskkiifllhrvrsekteaqdkkakikkeakeklkeiakllasvaeelqgsnayrYqrqisgglqeliea 85 
                                       +srd+ +  + ++  +h+      ++ dk+ k+ ++a+e l++i++ l  +       +   Y   + ++ qe++e+
  gi|298675604|ref|YP_003727354.1|  26 LSRDVVRICRSVMYNIHN------KKFDKAHKMLNDAHESLEQINTEL-GIY------PDIYYGGFVGHAQQEYVEC 89 
                                       555555555555444444......234455555677777777777777.444......55569************** PP

                                       HHHHHHHHHSS---HHHHHHHTT.---SSSSSS---HHHHHHHHHHHHHHHHHHHHHHHCTT--S.HHHHHHHHHHH CS
                          Translin  86 lsfahYletqtLitleevqkilealkeneedafhltpedYllGlfdLtgELmRfainsvalgdkeekplqilkflre 162
                                       +  +h l ++      +++ki +       d++++    Yl G++d  gEL R     + ++dk ek  + l+ +++
  gi|298675604|ref|YP_003727354.1|  90 VVVYHLLYNEG-----DINKIPS------PDDLNVGYAAYLNGMADAGGELRRHILD-LIRQDKPEKGETYLDIMES 154
                                       *****998854.....4444433......57899*****************988665.55566667*********** PP

                                       HHHHHHTS----HH...HHHHHTTHHHHHHH CS
                          Translin 163 lragfellnlkndsakdlrkKldvlkqsvkK 193
                                       +++++ +++ +  ++++lr+K d l++ v++
  gi|298675604|ref|YP_003727354.1| 155 MFSNLMMFDYPDAITHNLRQKTDRLRSIVER 185
                                       ***********76699**********99986 PP

>> BLOC1S3  Biogenesis of lysosome-related organelles complex 1 subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   6.6e-05      0.59      97     144 ..      18      66 ..      16      72 .. 0.89
   2 ?    0.4   0.0     0.072   6.4e+02      74     102 ..     176     203 ..     143     210 .] 0.63

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 6.6e-05
                           BLOC1S3  97 KLrEsNarLrkdvkeavsqv.ysaaskelesvtsqLnksqsaiqnashs 144
                                       K rE+  +L  dv+  ++ v y+  +k++ ++ ++Ln +   +++++++
  gi|298675604|ref|YP_003727354.1|  18 KAREKGLTLSRDVVRICRSVmYNIHNKKFDKAHKMLNDAHESLEQINTE 66 
                                       679999***********9854999*****************99999876 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.072
                           BLOC1S3  74 veevespaskqsqsgkydtLLhqKLrEsN 102
                                       +++  s ++   ++   + L +qKL+E  
  gi|298675604|ref|YP_003727354.1| 176 TDRLRSIVE-RTRGDLTNALRQQKLEETM 203
                                       334434443.2334456777788888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1168  (0.0651459); expected 358.6 (0.02)
Passed bias filter:                      753  (0.041999); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 1602.03
//
Query:       gi|298675605|ref|YP_003727355.1|  [L=539]
Description: O-phosphoseryl-tRNA(Cys) synthetase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-53  181.9   0.0    5.3e-49  166.9   0.0    2.1  2  tRNA-synt_2d     tRNA synthetases class II core domain (F)
    5.8e-13   48.7   0.2    1.5e-12   47.4   0.2    1.8  1  SepRS_C          O-phosphoseryl-tRNA synthetase C-terminal do
    3.7e-11   42.9   0.0    1.4e-07   31.2   0.0    2.2  2  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
  ------ inclusion threshold ------
       0.14   12.2   0.0       0.37   10.8   0.0    1.7  1  Lambda_Bor       Bor protein


Domain annotation for each model (and alignments):
>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   1.2e-05     0.054       5      48 ..      35      78 ..      31      89 .. 0.87
   2 !  166.9   0.0   1.2e-52   5.3e-49      17     241 ..     121     355 ..     103     359 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.2e-05
                                      SSCTSCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHH CS
                      tRNA-synt_2d  5 tlpgkrieagklhpltkvleeikeiflelgfeevegpevesefy 48
                                      ++p+ +++ gk hp+ +++++++e +l++gf e+ +p + +e  
  gi|298675605|ref|YP_003727355.1| 35 QYPHISLKYGKPHPVYDTINKLREAYLRMGFDEMMNPLIVDEQE 78
                                      667778899****************************9977654 PP

  == domain 2  score: 166.9 bits;  conditional E-value: 1.2e-52
                                       SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-ECESEEE-SSTHHHHHH CS
                      tRNA-synt_2d  17 hpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpekaveekllLRthttavqir 93 
                                       ++ ++ +e i++i++++++  +eg+++   + + + L v++ h +  ++ +F+  k+  +++++++LR+h+t+ +++
  gi|298675605|ref|YP_003727355.1| 121 DIGDEGIETIRKILHSYKKGDIEGDDL--VIEISEQLGVSDTHVVEMIDKVFPEFKELVPQSTRKTLRSHMTSGWFI 195
                                       55677899***************8887..799********************************************* PP

                                       HH....TTS-SSEEEEEEEEEEBSST.-SSSB-SEEEEEEEEEEETT--HHHHHHHHHHHHHHHCTST.EEEEEEEC CS
                      tRNA-synt_2d  94 tl....ekkkppikiisigrvfRrda.vDathlaeFhqveglvvdenvsladlkgvleellkklfgae.vkvrfrps 164
                                       +l    e++ pp+ ++si+r+fRr++ +Da +l+++++++++++ e+vs++  k+v+e ll+++ g+e +k++ +++
  gi|298675605|ref|YP_003727355.1| 196 SLssllEREYPPFHFFSIDRCFRREQqEDAARLMTYYSASCVIMAEDVSVDYGKAVAEGLLSQF-GFEkFKFKPDEK 271
                                       **99999999***************999************************************.999799999999 PP

                                       EETTEEEEEEEEEEE.........CCSSSSEEEEEEEEEE-HHHHHHTT-.TTSEEEEEEEEHHHHHHHHHT-SSGH CS
                      tRNA-synt_2d 165 yfpftePsaevdvyl.........vekkkkwlEllgaGmvrpevleavgideevsgfafGlGveRlamlkygieDiR 232
                                        ++++ P+++++v++         ++ +++w+E++++G+++p +l++++i   ++++++G+GveRlam+ +  eD+R
  gi|298675605|ref|YP_003727355.1| 272 RSKYYVPDTQIEVFAyhpklvgsnTSYSDGWIEIATFGIYSPVALAQYDI--PYPVMNLGMGVERLAMILNLAEDVR 346
                                       **********9999999******999************************..************************* PP

                                       HHHTT.HHH CS
                      tRNA-synt_2d 233 elvendlrf 241
                                       ++ +++l  
  gi|298675605|ref|YP_003727355.1| 347 AMTYPQLTK 355
                                       ***998765 PP

>> SepRS_C  O-phosphoseryl-tRNA synthetase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4   0.2   3.2e-16   1.5e-12       1      31 []     436     467 ..     436     467 .. 1.00

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 3.2e-16
                                       EEEEEETTEEEEEES-TTTCCHHHH.SEEEEE CS
                           SepRS_C   1 NEvyVYdGnIlGvPdtekwkearen.GvsTGI 31 
                                       NEv+ Y ++IlG+P+++kw++a+en +++TGI
  gi|298675605|ref|YP_003727355.1| 436 NEVVAYYNDILGIPNNKKWQKAFENdSARTGI 467
                                       *******************************9 PP

>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00014      0.62       3      49 ..      34      80 ..      32      91 .. 0.90
   2 !   31.2   0.0   3.2e-11   1.4e-07      70     208 ..     181     326 ..     178     330 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00014
                   tRNA_synthFbeta  3 stlPkapttegelnkeqklrrklrdllagaGlnEvitysfvsekeld 49
                                      ++ P+ +++ g++++  ++ +klr++   +G+ E+++   v+e+e+ 
  gi|298675605|ref|YP_003727355.1| 34 EQYPHISLKYGKPHPVYDTINKLREAYLRMGFDEMMNPLIVDEQEIH 80
                                      6889*********************************9999988765 PP

  == domain 2  score: 31.2 bits;  conditional E-value: 3.2e-11
                   tRNA_synthFbeta  70 dqsvlRtsLlpglLevlarNlargnedvrlFEigkvflkdseeelpeeerhlaivltgkreeeswsekaravdfydl 146
                                        +++lR+ +++g    l++ l+r+ + + +F i ++f+ +++e+ ++  ++ ++              a++v++   
  gi|298675605|ref|YP_003727355.1| 181 TRKTLRSHMTSGWFISLSSLLEREYPPFHFFSIDRCFRREQQEDAARLMTYYSAS---------CVIMAEDVSVDYG 248
                                       5789************************************444443333333332.........233346699999* PP

                   tRNA_synthFbeta 147 kgivealleslgiekvefep..aehpalhpgrsAei....kvdgk.............evGvlGelhpevleafdlk 204
                                       k+++e ll+++g+ek++f+p  +  +++ p  + e+        k             e+  +G  +p  l+++d++
  gi|298675605|ref|YP_003727355.1| 249 KAVAEGLLSQFGFEKFKFKPdeKRSKYYVPDTQIEVfayhP---KlvgsntsysdgwiEIATFGIYSPVALAQYDIP 322
                                       ********************766699**********55550...24555566666669******************* PP

                   tRNA_synthFbeta 205 qrvy 208
                                       ++v+
  gi|298675605|ref|YP_003727355.1| 323 YPVM 326
                                       *986 PP

>> Lambda_Bor  Bor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   8.3e-05      0.37      48      69 ..     293     314 ..     287     319 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 8.3e-05
                        Lambda_Bor  48 etqqtfvngLlgvvTlGIYtPr 69 
                                        + ++  +g +++ T+GIY+P 
  gi|298675605|ref|YP_003727355.1| 293 GSNTSYSDGWIEIATFGIYSPV 314
                                       5678999**************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (539 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3931.84
//
Query:       gi|298675606|ref|YP_003727356.1|  [L=252]
Description: deoxyribonuclease V [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-63  213.1   0.0    3.8e-63  212.8   0.0    1.0  1  Endonuclease_5  Endonuclease V
  ------ inclusion threshold ------
        0.2   11.1   0.0       0.88    9.0   0.0    1.9  2  DUF99           Protein of unknown function DUF99


Domain annotation for each model (and alignments):
>> Endonuclease_5  Endonuclease V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.8   0.0   4.2e-67   3.8e-63       2     196 ..      26     217 ..      25     218 .. 0.95

  Alignments for each domain:
  == domain 1  score: 212.8 bits;  conditional E-value: 4.2e-67
                                       HHHCC-------SGG-SEEEEEEEEEEECTCEEEEEEEEEEETTTTEEEEEEEEEEE--S-SSTT-CHHHCHHHHHH CS
                    Endonuclease_5   2 elakkveledklkeklklvaGvDvsfvkeekkeavaalvvldlpslevvekavavvklsfpYipgfLaFRElpvllk 78 
                                       ++a++++ ed+++   ++++G D++fv++     ++ +vvl++++++v+ek++ ++k++fpYi++fL+FRE +++ +
  gi|298675606|ref|YP_003727356.1|  26 KIASSISYEDDFEPL-EIIGGSDCAFVDDLI---ICGIVVLNYNTMDVIEKTHIIQKVTFPYISTFLSFREGDAIAS 98 
                                       578899999999986.**********65444...9****************************************** PP

                                       HHCC-SS--SEEEEEC-SSSSTTS--HHHHHHHHHTS-EEEEESS-SSSBE-.---SSTTEEEEEEETTEEEEEEEE CS
                    Endonuclease_5  79 aleklkqkpdvllvDGnGiaHprrlGlAshlGvlldlptiGvaKsllvgkve.epekekgsvvplvsegevigaalr 154
                                       al kl++ pd+l++DG Gi Hpr++G+Ash+G +ld+ptiGvaK++l+g+++  + ++ g ++plv ++++ig+ ++
  gi|298675606|ref|YP_003727356.1|  99 ALFKLDNIPDLLMFDGCGINHPRKVGIASHVGAVLDIPTIGVAKKILCGNTQsGTPESVGVSKPLVYKSKTIGYLYK 175
                                       *************************************************888688899999*****99********* PP

                                       SSTTS--EEEEEECSS-HHHHHHHHHHCS-T-SS-HHHHHHH CS
                    Endonuclease_5 155 tkknvkpiyvSvGhrisletalelvlallkkyrlPepirqAd 196
                                       +kk ++pi++++Ghr+sle++l++v+ ++k+++lPep+r+A+
  gi|298675606|ref|YP_003727356.1| 176 SKKGTNPIIIAPGHRVSLESSLAIVKDCIKNHKLPEPTRLAH 217
                                       *****************************************9 PP

>> DUF99  Protein of unknown function DUF99
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0     0.097   8.7e+02      72     112 ..      57     100 ..      40     107 .. 0.57
   2 ?    9.0   0.0   9.8e-05      0.88     149     176 ..     190     217 ..     164     222 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.097
                                       SSSEETTTEE--H...HHHHHHH---EEEEESS---HHHHHHCC CS
                             DUF99  72 dGitiagFNvvDl...erlheetglPviavtreepdlgklekaL 112
                                        Gi++  +N +D+    ++ +++  P i+ +    + +++ +aL
  gi|298675606|ref|YP_003727356.1|  57 CGIVVLNYNTMDViekTHIIQKVTFPYISTFLSFREGDAIASAL 100
                                       45555555544432225567777777776555555545565555 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 9.8e-05
                                       SS-HHHHHHHHHHC-SSSSS-HHHHHHH CS
                             DUF99 149 GieleeaaklvrkltlegriPEPlRvAh 176
                                        ++le   ++v+ ++++ ++PEP R+Ah
  gi|298675606|ref|YP_003727356.1| 190 RVSLESSLAIVKDCIKNHKLPEPTRLAH 217
                                       567788889******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1976.17
//
Query:       gi|298675607|ref|YP_003727357.1|  [L=219]
Description: hypothetical protein Metev_1723 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-31  110.0   0.0    1.6e-31  109.8   0.0    1.0  1  DUF169    Uncharacterised ArCR, COG2043


Domain annotation for each model (and alignments):
>> DUF169  Uncharacterised ArCR, COG2043
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.8   0.0   9.1e-36   1.6e-31       9     205 ..      21     209 ..      15     210 .. 0.89

  Alignments for each domain:
  == domain 1  score: 109.8 bits;  conditional E-value: 9.1e-36
                            DUF169   9 ktePVavkfsdekpe..lpekkekieekkrlCqmvalarakgktvvftaetlgCpgGaaalGfkelp.eklksgegy 82 
                                       + ePV+v+f+d+k    + e+++       +C mv++ar +g+t+ ++  +  Cp G ++lG+++++  ++    g 
  gi|298675607|ref|YP_003727357.1|  21 DGEPVCVTFIDSKTGnqISENTQF-----LFCEMVQKAR-YGETFNVE--KDRCPVGNYVLGINDKKpFEYYLKSGR 89 
                                       569**********97555555443.....9*********.*****994..4458*********84444555566888 PP

                            DUF169  83 lkspeaakkfveslprleagevkyvvvapLekaefePdvvvffanpeqlmrLvqlalydrgggrlnvsfpgngaaCa 159
                                       +k+ +aa ++   lpr+ ++ + y+ ++pL++ +++ dv ++f +p+ +mr++q++ y++g+ ++n+++ g +++C 
  gi|298675607|ref|YP_003727357.1|  90 YKDRDAAYNASVLLPRI-KKIYNYIRIEPLSRNKKQFDVLILFLKPASAMRIIQAFSYQEGK-QVNINTLGAASVCG 164
                                       99*************99.5677**************************************99.9************* PP

                            DUF169 160 divaypykegepniglgdpgarkfaklkddelafgiPyelleemve 205
                                       d++a p+  g   +++g+ g+rk+++ +++e+ +gi +e++e++++
  gi|298675607|ref|YP_003727357.1| 165 DCTAVPISDG-IGVSFGCKGSRKHSNYRNTEVPLGIGFEMIERIEK 209
                                       ***9998766.89******************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1559.66
//
Query:       gi|298675608|ref|YP_003727358.1|  [L=129]
Description: hypothetical protein Metev_1724 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.5e-47  158.0   0.8    8.5e-47  157.9   0.8    1.0  1  DUF473    Protein of unknown function (DUF473)


Domain annotation for each model (and alignments):
>> DUF473  Protein of unknown function (DUF473)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.9   0.8   4.7e-51   8.5e-47       1     118 []       1     118 [.       1     118 [. 0.99

  Alignments for each domain:
  == domain 1  score: 157.9 bits;  conditional E-value: 4.7e-51
                            DUF473   1 MkvvaLtGiseevieeLkknklrtielrsahNvitllklevgdlvFlTsvsleDltkGteGiiaevlsveistkrvv 77 
                                       M++vaLtGi+e+v++eLk+++lrt+e+rs+hN++t+lkl+vgd+vFlT++s++Dlt+Gt+G++a++++++ist+r++
  gi|298675608|ref|YP_003727358.1|   1 MEYVALTGIAENVMRELKNDTLRTVEIRSPHNFFTALKLNVGDFVFLTHTSIQDLTSGTTGVVARIMKHQISTHRTF 77 
                                       9**************************************************************************** PP

                            DUF473  78 essesfieErEttvarvqlkllglgrvrevkeeellkptkv 118
                                       +s+e+f+eErEtt+ar+ql++++++rvr+v+++++++ t+v
  gi|298675608|ref|YP_003727358.1|  78 SSTETFYEERETTTARIQLDPRASARVRKVHSNDIGEITRV 118
                                       ************************************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 931.27
//
Query:       gi|298675609|ref|YP_003727359.1|  [L=253]
Description: hypothetical protein Metev_1725 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.8e-50  171.9   0.1    2.1e-50  171.7   0.1    1.0  1  PAC2        PAC2 family
  ------ inclusion threshold ------
       0.14   12.2   0.0       0.27   11.2   0.0    1.4  1  Laminin_II  Laminin Domain II


Domain annotation for each model (and alignments):
>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.7   0.1   2.3e-54   2.1e-50       1     212 [.      28     232 ..      28     233 .. 0.95

  Alignments for each domain:
  == domain 1  score: 171.7 bits;  conditional E-value: 2.3e-54
                                       EEEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETTEEE-SEEEEEETTT.SEEEEEEE... CS
                              PAC2   1 LilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveegrelepprlyakdsgsrdllvlqg... 74 
                                       Li+GfpgiG+Vg +a + +i++ ++++ g+i+s+y +p     p+v++ +g   +p+r+y +  ++ +ll++++   
  gi|298675609|ref|YP_003727359.1|  28 LIEGFPGIGLVGNIASQQIIDKINMTYKGSIESKY-FP-----PIVVLYQGLVTMPVRVYES--KEYNLLLVVSdvp 96 
                                       8**********************************.**.....********99*******66..4699******9*9 PP

                                       E-HSCHHHHHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHHCT....-CEEEEHHH CS
                              PAC2  75 repilqyeefakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleelees....eyggivgit 147
                                       + p++ y+ ++kal+ w ++++vkevv ++g+ ++e+      +++ v+gaat+ e+l+++ ++    ++g+i+gi+
  gi|298675609|ref|YP_003727359.1|  97 INPSVSYD-ISKALVGWSKSINVKEVVSIAGITTMEES-----EETHVFGAATNSEMLDKIRDHievfNMGTISGIS 167
                                       99999999.************************99874.....6669**************7666789********* PP

                                       HHHHHHHHHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT---HCHHHHHHHHHHHHHHHHH CS
                              PAC2 148 glLlsaakergipavgllaevphylpdPkaaaalleflskllglevdtedLeedaeeleeqleel 212
                                       g+ +s++ +r++pav+ll++++ + pdP+aaaa+le+l+ l+gl+++te+L e+ae++e+++++l
  gi|298675609|ref|YP_003727359.1| 168 GSVMSECLMRDLPAVSLLGSTQTQNPDPRAAAAVLEVLNSLYGLSINTEELFEQAEKIESEMQRL 232
                                       **************************************************************987 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0     3e-05      0.27      10      52 ..     199     241 ..     195     244 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II  10 etakevleqlaplsqnlentkeklseinrsveetnekvkdank 52 
                                         + evl+ l +ls n+e++ e++++i++++++  e+vk++ +
  gi|298675609|ref|YP_003727359.1| 199 AAVLEVLNSLYGLSINTEELFEQAEKIESEMQRLAEDVKSSEQ 241
                                       5677999********************************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       965  (0.0538234); expected 358.6 (0.02)
Passed bias filter:                      829  (0.0462379); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1690.43
//
Query:       gi|298675610|ref|YP_003727360.1|  [L=51]
Description: hypothetical protein Metev_1726 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.095   12.3   0.1      0.095   12.3   0.1    1.2  1  UL45      UL45 protein, carbohydrate-binding C-type lectin-li


Domain annotation for each model (and alignments):
>> UL45  UL45 protein, carbohydrate-binding C-type lectin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   5.3e-06     0.095      52      73 ..       3      24 ..       1      48 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.3e-06
                              UL45 52 ilggialGvlltvfvivatlvf 73
                                      il  +++G++++ +v+++t +f
  gi|298675610|ref|YP_003727360.1|  3 ILIAFTIGIIIFLVVVAFTAAF 24
                                      7999**************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       985  (0.0549389); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 402.20
//
Query:       gi|298675611|ref|YP_003727361.1|  [L=277]
Description: methylenetetrahydromethanopterin dehydrogenase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.4e-126  421.4   0.2   1.6e-126  421.2   0.2    1.0  1  MTD       methylene-5,6,7,8-tetrahydromethanopterin dehydroge


Domain annotation for each model (and alignments):
>> MTD  methylene-5,6,7,8-tetrahydromethanopterin dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  421.2   0.2    9e-131  1.6e-126       1     273 [.       2     276 ..       2     277 .] 0.98

  Alignments for each domain:
  == domain 1  score: 421.2 bits;  conditional E-value: 9e-131
                                       EEEEEEEES--HHHHHTTGGGSTTS--SSEEEEEEEEET--SHHHHHHHHHHHHHH--SEEEEE-S-TTSHHHHHHH CS
                               MTD   1 vkigiiklGnigtslvidlllDeradRedievrvvgsgaklkkeeveevveklkefdpdlvivisPnaaapgptkar 77 
                                       vk+g+iklGn+g+s+v+dll De+a+Re+i++rv+g+g+k++ke+++++ +  +efdpd+vi+isPna++pgpt+ar
  gi|298675611|ref|YP_003727361.1|   2 VKVGFIKLGNLGMSQVVDLLEDEIAAREGITTRVYGTGPKMSKEDAADTEAFKEEFDPDFVIIISPNASTPGPTEAR 78 
                                       79*********************************************8777778*********************** PP

                                       HHHHHSSS-EEEEEEGGGGGGH.HHHHHTT-EEEEETTS------TTT--HHHHHHHHHHHHHHHHHTTHHHHHHHH CS
                               MTD  78 ellsekdvpaivisDapgkkek.deleeeglGYiivkaDpliGarrefLDptemalfnadvlkvLaatGavRlvqee 153
                                       +l+  kd+p+++isD+p+kk++ +++e+eg+GYii+++DpliGa+ efLDp ema+fn+dv+kvL+++GavRlvqee
  gi|298675611|ref|YP_003727361.1|  79 QLW--KDKPCLIISDGPTKKDDrQAIEDEGFGYIILPVDPLIGAKTEFLDPEEMASFNSDVMKVLSTCGAVRLVQEE 153
                                       ***..99*************998****************************************************** PP

                                       HHHHHHHHTTT-...GGGS-EEEESGGGGGGSS--SSHHHHHHHHHHHHHHHHHHHHHHHHHHT---HHHHHHHHHH CS
                               MTD 154 ldkviekvkagk...eielPkividaekaveaaefsnPYakakalaayeiaekvadidvkaCfmekelekyilivas 227
                                       ldk++++v++gk   eie+P+i++++++++e+++fsnPYakakalaa+++aekv++i++ aCfm k+le++++++a+
  gi|298675611|ref|YP_003727361.1| 154 LDKLTSQVDEGKsgdEIEMPHIYAKPQTCIERSGFSNPYAKAKALAALHMAEKVSQINLPACFMLKDLEEVAFTAAT 230
                                       **********998889************************************************************* PP

                                       HHHHHHHHHHHHHHHHHHHHHTT---B--B-TTSSB--BSSTTS-- CS
                               MTD 228 ahellraaakLadeaReieksndtvlRkphakdGkvlsktkllekP 273
                                       +he++raaa+La eaReiek+ndtvlRkph+k+Gkvlsktkl+ekP
  gi|298675611|ref|YP_003727361.1| 231 GHEMIRAAAELAVEAREIEKTNDTVLRKPHSKKGKVLSKTKLYEKP 276
                                       *********************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2023.42
//
Query:       gi|298675612|ref|YP_003727362.1|  [L=274]
Description: phosphoserine phosphatase SerB [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-17   64.2   0.0    2.8e-17   63.7   0.0    1.2  1  HAD              haloacid dehalogenase-like hydrolase
    7.1e-17   62.4   0.1    9.7e-17   61.9   0.1    1.2  1  Hydrolase        haloacid dehalogenase-like hydrolase
    4.4e-12   46.3   0.1    1.5e-10   41.3   0.0    2.4  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
    4.4e-11   42.6   0.1    3.2e-06   26.7   0.0    2.2  2  Put_Phosphatase  Putative Phosphatase
    1.2e-07   32.0   1.0      3e-06   27.5   1.0    2.6  1  HAD_2            Haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.011   15.8   0.0      0.033   14.3   0.0    1.7  2  Hydrolase_like   HAD-hyrolase-like
      0.069   12.6   0.0       0.13   11.7   0.0    1.4  1  DUF705           Protein of unknown function (DUF705)
       0.16   11.5   0.0         10    5.6   0.0    2.2  2  S6PP             Sucrose-6F-phosphate phosphohydrolase


Domain annotation for each model (and alignments):
>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.7   0.0   1.3e-20   2.8e-17       1     187 [.      66     233 ..      66     234 .. 0.84

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 1.3e-20
                               HAD   1 alfDfDgTLldgdslelllrfllrrgaprlwralreklllalfrellrldraglaelleallaglseelaaelerfv 77 
                                       ++fD+D TL+d + ++ l++   +     +++++ e +++a+    ++ d+++       ll+g + e a+e+ + +
  gi|298675612|ref|YP_003727362.1|  66 IVFDMDSTLIDAECIDKLAE---A---AGAGEEVSEITEQAM---EGDIDYKESLVKRVQLLEGTEIETAQEVIHSL 133
                                       79**********54444444...2...223777777777777...44444556666667799999988888888888 PP

                               HAD  78 aevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevdd.rltgelglegkpvrgeg 153
                                            p ++ pga+el+  +++ G++++++S+g+   +  +  +l++++v+++el  d+ ++tge  ++g+++ ++ 
  gi|298675612|ref|YP_003727362.1| 134 -----P-IM-PGAKELVYYVKSLGYKTAMISSGFTLATDYIGSLLDIEHVVSNELVIDNgYITGE--VRGPLTEQDS 201
                                       .....4.36.*******************************************************..********** PP

                               HAD 154 kvaalrewlaaegegidleevvayGDspsDlpll 187
                                       k  + ++   a+ +g ++e+++a+GD+ +D++ +
  gi|298675612|ref|YP_003727362.1| 202 KKYVFEQ--IAQMNGVHPENCIAVGDGANDICVF 233
                                       *******..88888899999***********976 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.9   0.1   4.3e-20   9.7e-17       2     210 .]      64     237 ..      63     237 .. 0.81

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 4.3e-20
                                       SEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   2 ktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpewlt 78 
                                       k++vfD+d TL++ e     +i+++                     a+a + +++++++++     ++++g  ++ +
  gi|298675612|ref|YP_003727362.1|  64 KLIVFDMDSTLIDAE-----CIDKL---------------------AEAAGAGEEVSEITE-----QAMEGDIDYKE 109
                                       89*************.....*****.....................***************.....*********** PP

                                       HHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  79 aldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanql 155
                                       +l                 r + l+  ++    ++ ++l+++p+a+e+v++ k+ g++++++++++    + + + l
  gi|298675612|ref|YP_003727362.1| 110 SL---------------VKRVQLLEGTEIETAQEVIHSLPIMPGAKELVYYVKSLGYKTAMISSGFTLATDYIGSLL 171
                                       **...............44555554445555666666777************************************* PP

                                       T.GGGESEEEEHHCES....STTT......SHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       x.xxxxxxxxxxxxxx....xxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 156 G.ddyfdaviasdiet....vakp......spegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                       + ++ +++++ +d+      v +p      ++  ++++++  ++ pe++++VGDg+nD+  +++Ag
  gi|298675612|ref|YP_003727362.1| 172 DiEHVVSNELVIDNGYitgeVRGPlteqdsKKYVFEQIAQMNGVHPENCIAVGDGANDICVFKKAG 237
                                       *74444555554444463455555885554555555555555799**************9999997 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.04        90       1      12 [.      66      77 ..      66     106 .. 0.85
   2 !   41.3   0.0   6.5e-14   1.5e-10     186     251 ..     200     264 ..     196     268 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.04
                                      EEEEIIIIIS-T CS
                       Hydrolase_3  1 ialDlDGTLlns 12
                                      i++D+D TL++ 
  gi|298675612|ref|YP_003727362.1| 66 IVFDMDSTLIDA 77
                                      89*******985 PP

  == domain 2  score: 41.3 bits;  conditional E-value: 6.5e-14
                                       -SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGGTHH CS
                       Hydrolase_3 186 vsKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnnedGV 251
                                        sK    +++a++ ++++e++ia+GDg NDi  +++ag+++A  n+++ ++++Ad v++ ++  ++
  gi|298675612|ref|YP_003727362.1| 200 DSKKYVFEQIAQMNGVHPENCIAVGDGANDICVFKKAGYSIAF-NSKPILQEYADVVITRKDLRAI 264
                                       6899999***********************************8.899**********998876665 PP

>> Put_Phosphatase  Putative Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   1.4e-09   3.2e-06       2     106 ..      65     167 ..      64     191 .. 0.82
   2 !   14.0   0.0   1.1e-05     0.024     151     187 ..     202     235 ..     195     261 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 1.4e-09
                   Put_Phosphatase   2 lvvfDFDktiidedsdnwvvdelpatelfeelretlrkglwnelmdrvlkelhe.qgvseadikkvlrsiplspglv 77 
                                       l+vfD D t+id +  + + ++++a e+ +e+ e+  +g   ++ + ++k+++  +g +++  ++v++s+p+ pg  
  gi|298675612|ref|YP_003727362.1|  65 LIVFDMDSTLIDAECIDKLAEAAGAGEEVSEITEQAMEGD-IDYKESLVKRVQLlEGTEIETAQEVIHSLPIMPGAK 140
                                       89******************************99988653.4566666666553267899999************** PP

                   Put_Phosphatase  78 elikslakkkleldliiiSDaNsffieei 106
                                       el+  +  k+l++   +iS   ++  + i
  gi|298675612|ref|YP_003727362.1| 141 ELVYYV--KSLGYKTAMISSGFTLATDYI 167
                                       *****9..689999999998776666555 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.1e-05
                   Put_Phosphatase 151 KgkvleelvaeqaregveyerliYvGDganDlCpvlk 187
                                       K+ v+e++ +    +gv+ e  i vGDganD+C  +k
  gi|298675612|ref|YP_003727362.1| 202 KKYVFEQIAQM---NGVHPENCIAVGDGANDICVFKK 235
                                       77777777777...79*****************8776 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   1.0   1.3e-09     3e-06       1     175 [.      66     240 ..      66     242 .. 0.68

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.3e-09
                             HAD_2   1 iiFDlDgTlldteeliiqafnelleeyglselseeelrkliglslrellrklgeseeeeekieel.lrkyneekkkk 76 
                                       i+FD+D Tl+d e +i + ++ + + +++se++e+ ++  i  +   l+++++        +e   +++ +e  +  
  gi|298675612|ref|YP_003727362.1|  66 IVFDMDSTLIDAE-CIDKLAEAAGAGEEVSEITEQAMEGDIDYKE-SLVKRVQL-------LEGTeIETAQEVIHS- 132
                                       89*********64.4555555555555555555555555444444.33333333.......333303444555555. PP

                             HAD_2  77 evkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdv......ivtsedvekk......KPdpevi 141
                                        + +++g+kel+ ++k+ gyk + ++s+ + a++   + l+ie++ +        +++ +v ++      K    v+
  gi|298675612|ref|YP_003727362.1| 133 -LPIMPGAKELVYYVKSLGYKTAMISSGFTLATDYIGSLLDIEHVVSNelvidnGYITGEVRGPlteqdsK--KYVF 206
                                       .*****************************************99875411111133444444433332224..6778 PP

                             HAD_2 142 ekaleklklkkeeviyvGDsptDieaakkagikv 175
                                       e++ +  ++++e++i vGD  +Di   kkag  +
  gi|298675612|ref|YP_003727362.1| 207 EQIAQMNGVHPENCIAVGDGANDICVFKKAGYSI 240
                                       8888888**********************99765 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.2     5e+03      41      58 ..     149     166 ..     147     179 .. 0.71
   2 ?   14.3   0.0   1.5e-05     0.033       7      44 ..     203     239 ..     201     242 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.2
                                       CT-EEEEESSSSS-TTTH CS
                    Hydrolase_like  41 aGwksvLVltGvtrpedl 58 
                                        G+k++++ +G t ++d 
  gi|298675612|ref|YP_003727362.1| 149 LGYKTAMISSGFTLATDY 166
                                       689999999998877765 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.5e-05
                                       SHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-E CS
                    Hydrolase_like   7 pemydfalevlgsdpeevlmiGDrlatDiagAnnaGwk 44 
                                       + +++++++ +g++pe+++++GD  a Di   ++aG++
  gi|298675612|ref|YP_003727362.1| 203 KYVFEQIAQMNGVHPENCIAVGDG-ANDICVFKKAGYS 239
                                       6799********************.****888888865 PP

>> DUF705  Protein of unknown function (DUF705)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.6e-05      0.13     120     149 ..      49      78 ..      28      87 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.6e-05
                            DUF705 120 vssiikelslylkikhvvvfDlDstLitde 149
                                       v+s+  + ++  + k ++vfD+DstLi  e
  gi|298675612|ref|YP_003727362.1|  49 VNSTDSNFNNDKGRKKLIVFDMDSTLIDAE 78 
                                       5555566778888899***********765 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.015        34       2      27 ..      63      86 ..      62     111 .. 0.84
   2 ?    5.6   0.0    0.0045        10     165     205 ..     201     241 ..     192     261 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.015
                                      SEEEEE-TBTTTB.S-HHHHHHHHHH CS
                              S6PP  2 klllvsdLDntlvdgdnealarlnel 27
                                      k+l+v d+D+tl+  d+e +++l e 
  gi|298675612|ref|YP_003727362.1| 63 KKLIVFDMDSTLI--DAECIDKLAEA 86
                                      689**********..77777777665 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0045
                                       SHHHHHHHHHHHHT--GGGEEEEE-SGGGHHHHTSSSEEEE CS
                              S6PP 165 skgeAlryLakkleleleqilvcGdsgnDeellignvlgVv 205
                                       sk +  + +a+  ++++e+ + +Gd  nD+ ++++  +++ 
  gi|298675612|ref|YP_003727362.1| 201 SKKYVFEQIAQMNGVHPENCIAVGDGANDICVFKKAGYSIA 241
                                       6666667777778889*****************99988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2153.19
//
Query:       gi|298675613|ref|YP_003727363.1|  [L=288]
Description: phosphoserine phosphatase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0041   17.4  21.9     0.0041   17.4  21.9    3.9  3  OmpH            Outer membrane protein (OmpH-like)
  ------ inclusion threshold ------
       0.28   10.6  37.0       0.51    9.7  28.6    3.4  2  HBM             Helical bimodular sensor domain
       0.31   11.4  27.4        1.9    8.9   4.9    4.3  3  DUF2935         Domain of unknown function (DUF2935)
       0.33   11.4  29.6       0.49   10.8   5.3    4.8  4  DUF1771         Domain of unknown function (DUF1771)
        6.4    7.1  61.4      0.052   13.8  20.6    4.0  4  Seryl_tRNA_N    Seryl-tRNA synthetase N-terminal domain
        7.4    5.4  60.6        5.6    5.7  27.1    2.2  2  Spc7            Spc7 kinetochore protein
        8.6    6.4  40.4        3.3    7.7   6.3    4.0  5  Laminin_II      Laminin Domain II


Domain annotation for each model (and alignments):
>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4  21.9   1.6e-06    0.0041      11      95 ..       2      87 ..       1      96 [. 0.89
   2 ?    1.0  28.3      0.19   4.9e+02      17     108 ..     100     193 ..      98     208 .. 0.64
   3 ?    1.1   9.2      0.17   4.5e+02      12      65 ..     205     253 ..     199     282 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.6e-06
                                      HHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS..-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH 11 leespegkaaqeqlekkfkklqaeleakekelqklqeelqkkakkl.ekeekeqelqkkeqelqqkqqqkaqelqkkqq 88
                                      l+e +e+k+  ++l++++k+ ++el++++ el ++++el+kk+k+l ++++++++l++++++l q+ + k+ el+++ +
  gi|298675613|ref|YP_003727363.1|  2 LKELNERKNELKKLAEQYKEKRNELNTQASELASKRNELNKKTKDLiNEAQEYKKLRDENNKLVQENKDKRDELNSEAN 80
                                      78999**************************************999889999999999999999978888899999999 PP

                                      HHHHHHH CS
                              OmpH 89 ellkpil 95
                                      +l+ +i 
  gi|298675613|ref|YP_003727363.1| 81 KLYSKIE 87
                                      9888653 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.19
                                       HHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHHTTTS.-HHHHHH..HHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  17 gkaaqeqlekkfkklqael..eakekelqklqeelqkkakklekeekeqe..lqkkeqelqqkqqqkaqelqkkqqe 89 
                                        k++++++++ + + q+e+   +kekel +++++l+k+ +++ k++ e+   +qk+ +e q+ ++ +a ++ ++ +e
  gi|298675613|ref|YP_003727363.1| 100 LKEIEKEIQRLEFTQQTEVltPQKEKELVNKIQDLKKQYENK-KQQLENNteIQKLSEEAQK-YRDEASQYHNALAE 174
                                       677888888877444444411567888888888888777775.5555555568888888888.66666666666656 PP

                                       HHHHHHHHHHHHHHHHHHH CS
                              OmpH  90 llkpildkinkaikevake 108
                                         ++ ++  nk ++ + k+
  gi|298675613|ref|YP_003727363.1| 175 YAQKAQEYHNKMVETFKKA 193
                                       5555555555555555444 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.17
                                       HHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHH.H CS
                              OmpH  12 eespegkaaqeqlekkfkklqaeleakekelqklqeelqkkakklekeekeqe.l 65 
                                       +++ e+++a ++  kkf + q+++++ eke+++ ++    +      +++e+e  
  gi|298675613|ref|YP_003727363.1| 205 KQFVEYQDAADEQHKKFIAVQKDIRDIEKEIRNVKKSETSS------KKAEEEtT 253
                                       678899999999999999******99999999666544322......22222211 PP

>> HBM  Helical bimodular sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7  28.6    0.0002      0.51      49     228 ..      15     185 ..       1     194 [. 0.78
   2 ?    8.5  18.5   0.00048       1.2      30     141 ..     108     226 ..     106     253 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0002
                                       HHHHHHHHHHHHHHH.....--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               HBM  49 kldelkaqlqklkak.....fkspenvrlLqeqlalvqeyrksfnelraayesrnaaRqeldsaaeraleaidelea 120
                                         +++k++ ++l+++     +k  e  ++ ++ ++ +qey+k  +e ++ ++++++ R el+s+a+++   i+++++
  gi|298675613|ref|YP_003727363.1|  15 LAEQYKEKRNELNTQaselaSKRNELNKKTKDLINEAQEYKKLRDENNKLVQENKDKRDELNSEANKLYSKIEQIRS 91 
                                       444444444444444111112333444666777888999*9999999*************************99987 PP

                                       HHHCS-S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHHHHHHHHH-GG.GHHHHHHH CS
                               HBM 121 evlqtpeadserlaqlqaiaelkrqvqlaryqvrgYtfsenedseqaavtaldaalaeldqlrqalasdpraalqql 197
                                       +                +++e+++++q+  +  +  t   ++++e+ +v+ ++  +++ ++ +q+l++  + ++q+l
  gi|298675613|ref|YP_003727363.1|  92 KNNID----------GPSLKEIEKEIQRLEFTQQ--TEVLTPQKEKELVNKIQDLKKQYENKKQQLEN--NTEIQKL 154
                                       65442..........4478999999999999887..667789999*********************98..899**** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               HBM 198 esalskYRaaleqfkaavaaieqarkemteq 228
                                       +++ +kYR+  +q+ +a+a+ +q  +e  ++
  gi|298675613|ref|YP_003727363.1| 155 SEEAQKYRDEASQYHNALAEYAQKAQEYHNK 185
                                       ********************99998886655 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00048
                                       HHHHHHHTT...T-HHHHHHHHHHHHHHHHHHHHHHH--SHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHHHH CS
                               HBM  30 aRlqyelsn...gdataaavqkkldelkaqlqklkakfkspenvrlLqeqlal....vqeyrksfnelraayesrna 99 
                                       +Rl++ ++    ++++++++ +k+++lk+q ++ k+++++  ++++L e +++    +++y ++++e ++  ++  +
  gi|298675613|ref|YP_003727363.1| 108 QRLEFTQQTevlTPQKEKELVNKIQDLKKQYENKKQQLENNTEIQKLSEEAQKyrdeASQYHNALAEYAQKAQEYHN 184
                                       67777666523357778889999999999999999999999999999887764211155666666666555555555 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHCS-S-HHHHHHHHHHHHH CS
                               HBM 100 aRqeldsaaeraleaideleaevlqtpeadserlaqlqaiae 141
                                          e  ++a+++ e  de  ++ ++  +a +e+ +++ a+++
  gi|298675613|ref|YP_003727363.1| 185 KMVETFKKADQVREEADETHKQFVEYQDAADEQHKKFIAVQK 226
                                       555555555555555555555555555555666666655554 PP

>> DUF2935  Domain of unknown function (DUF2935)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   7.7    0.0074        19      25      79 ..       5      55 ..       1     111 [. 0.83
   2 ?    8.9   4.9   0.00072       1.9      19      93 ..     114     183 ..     108     186 .. 0.80
   3 ?    7.5   5.0    0.0019       4.8      25      93 ..     154     218 ..     149     254 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0074
                           DUF2935 25 ldpkekdlikeakefkkeFekllaeavelseglvrasseleeavakLneealklt 79
                                      l+++ ++l k a+++k++ ++l ++a el+    + ++el+++ ++L++ea ++ 
  gi|298675613|ref|YP_003727363.1|  5 LNERKNELKKLAEQYKEKRNELNTQASELA----SKRNELNKKTKDLINEAQEYK 55
                                      778889999999999999999999999986....556888888888888877663 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00072
                           DUF2935  19 lfiealldpkekdlikeakefkkeFekllaeavelseglvrasseleeavakLneealkltreliqFkkellekv 93 
                                          e l ++kek+l+++ +++kk++e+  ++ ++      +  ++l e+ +k  +ea ++ ++l +++++ +e +
  gi|298675613|ref|YP_003727363.1| 114 QQTEVLTPQKEKELVNKIQDLKKQYENKKQQLENN-----TEIQKLSEEAQKYRDEASQYHNALAEYAQKAQEYH 183
                                       556788999*****************999988663.....33478888888888888888888888888887766 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0019
                           DUF2935  25 ldpkekdlikeakefkkeFekllaeavelseglvrasseleeavakLneealkltreliqFkkellekv 93 
                                       l+++ +++ +ea ++++++ ++ ++a+e+ + +     e++++  ++ eea +  ++++++++   e++
  gi|298675613|ref|YP_003727363.1| 154 LSEEAQKYRDEASQYHNALAEYAQKAQEYHNKM----VETFKKADQVREEADETHKQFVEYQDAADEQH 218
                                       67788999*******************999888....56666666666666666666666666555544 PP

>> DUF1771  Domain of unknown function (DUF1771)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   5.3   0.00019      0.49       3      53 ..      11      63 ..      10      64 .. 0.94
   2 ?    0.3   0.0      0.38   9.6e+02       9      28 ..      66      85 ..      63      90 .. 0.77
   3 ?    3.8   3.3     0.029        74      35      54 ..     152     171 ..     125     177 .. 0.84
   4 ?    6.9   9.9    0.0032       8.1       2      56 ..     159     215 ..     159     220 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00019
                           DUF1771  3 rlRaeAdeharkrnelfekAaeAyrrGd..gaaAkelseqGkehgekmeeanr 53
                                      +l + A ++ +krnel  +A+e  ++ +   ++ k+l ++++e+++  +e n+
  gi|298675613|ref|YP_003727363.1| 11 ELKKLAEQYKEKRNELNTQASELASKRNelNKKTKDLINEAQEYKKLRDENNK 63
                                      58899*****************999999999***************9999886 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.38
                           DUF1771  9 deharkrnelfekAaeAyrr 28
                                      +e  +kr+el ++A + y++
  gi|298675613|ref|YP_003727363.1| 66 QENKDKRDELNSEANKLYSK 85
                                      56668888998888888875 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.029
                           DUF1771  35 kelseqGkehgekmeeanre 54 
                                       ++lse++++++ ++ +++  
  gi|298675613|ref|YP_003727363.1| 152 QKLSEEAQKYRDEASQYHNA 171
                                       58999999999999999864 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.0032
                           DUF1771   2 erlRaeAdeharkrnelfekAaeAyrrGd..gaaAkelseqGkehgekmeeanreAa 56 
                                       +++R+eA +++++ +e+ +kA+e  ++     ++A +  e++ e  ++  e+   A 
  gi|298675613|ref|YP_003727363.1| 159 QKYRDEASQYHNALAEYAQKAQEYHNKMVetFKKADQVREEADETHKQFVEYQDAAD 215
                                       68*********************9998777778888888888888888888887775 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8  20.6     2e-05     0.052      19     104 ..       6      89 ..       1      90 [. 0.85
   2 ?   -1.3   8.4         1   2.6e+03      54      91 ..     102     146 ..      87     150 .. 0.59
   3 ?   -0.5  13.7      0.57   1.5e+03      37      95 ..     123     177 ..     100     187 .. 0.44
   4 ?    4.4  10.9     0.017        43      12      99 ..     188     273 ..     185     279 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2e-05
                                       CCCTCCCHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  19 kkRgedkadvdellel.dekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkele 94 
                                       +   e k+++++l e   ekr el++++ el ++rNel+k+ + ++++ ++ ++l++e ++l +e k++ +el+   
  gi|298675613|ref|YP_003727363.1|   6 N---ERKNELKKLAEQyKEKRNELNTQASELASKRNELNKKTKDLINEAQEYKKLRDENNKLVQENKDKRDELNSEA 79 
                                       3...4456677776651567889***************************************************999 PP

                                       HHHHHHHCTS CS
                      Seryl_tRNA_N  95 aeleklllai 104
                                       ++l +++ +i
  gi|298675613|ref|YP_003727363.1|  80 NKLYSKIEQI 89 
                                       9999887766 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1
                                       HHHHHCCCCCCTT.......S-TCCCCCCCHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  54 elskeIgkakkkk.......edaeeliaevkelkeelkaleaelk 91 
                                       e+ keI+++   +       ++ +el++++++lk++ ++++++l+
  gi|298675613|ref|YP_003727363.1| 102 EIEKEIQRLEFTQqtevltpQKEKELVNKIQDLKKQYENKKQQLE 146
                                       555666655554433444444455566666666666665555554 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.57
                                       HHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  37 krrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkelea 95 
                                       k +el +++++l+++  +  ++ ++      ++++l +e+++  +e +++ ++l+e  +
  gi|298675613|ref|YP_003727363.1| 123 KEKELVNKIQDLKKQYENKKQQLENNT----EIQKLSEEAQKYRDEASQYHNALAEYAQ 177
                                       333344444444443333333333333....3334444444444444444444443333 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.017
                                       HHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHH CS
                      Seryl_tRNA_N  12 eavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkalea 88 
                                       e++k++ + R+e++++ ++++e +++  e  +++ ++q+    + keI + kk+  ++++ +ae ++   + +++  
  gi|298675613|ref|YP_003727363.1| 188 ETFKKADQVREEADETHKQFVEYQDAADEQHKKFIAVQKDIRDIEKEIRNVKKS--ETSSKKAEEETTDRDAETIFS 262
                                       788999999*******************************************97..588888888888888888888 PP

                                       HHHHHHHHHHH CS
                      Seryl_tRNA_N  89 elkeleaelek 99 
                                       + k  e++l++
  gi|298675613|ref|YP_003727363.1| 263 QFKSGEKKLTT 273
                                       88887777765 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7  27.1    0.0022       5.6     156     268 ..       3     118 ..       2     132 .. 0.76
   2 ?    4.8  26.4    0.0042        11     137     270 ..     131     262 ..     128     282 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0022
                              Spc7 156 elLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelre..ela.elkaeieekkkelaelqeql 229
                                       ++L+++++el++l ++++e+++el+ ++ +l ++++el++ +k+ ++e++e  +l+ e+++ ++e k++ +el+++ 
  gi|298675613|ref|YP_003727363.1|   3 KELNERKNELKKLAEQYKEKRNELNTQASELASKRNELNKKTKDLINEAQEykKLRdENNKLVQENKDKRDELNSEA 79 
                                       57999999999999999999999999999999999999999999999988633454145555778888899999999 PP

                              Spc7 230 eeleekieelkeqkseleeeiaeaervleeckgwsesev 268
                                       ++l +kie+++++ +     ++e e+ +++ +  +++ev
  gi|298675613|ref|YP_003727363.1|  80 NKLYSKIEQIRSKNNIDGPSLKEIEKEIQRLEFTQQTEV 118
                                       999999999988876666666666666666666666666 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0042
                              Spc7 137 legLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelka 213
                                       +++Lk+++e++ ++le+ +++++k  ee++++ +e ++++++l e ++k qe ++++ + + ++  ++ree +e ++
  gi|298675613|ref|YP_003727363.1| 131 IQDLKKQYENKKQQLEN-NTEIQKLSEEAQKYRDEASQYHNALAEYAQKAQEYHNKMVE-TFKKADQVREEADETHK 205
                                       789***********987.5679******************************8887655.34556899999999999 PP

                              Spc7 214 eieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsr 270
                                       +  e ++  +e  ++  +++++i +++++++++++   ++++  ee+ + +++ + +
  gi|298675613|ref|YP_003727363.1| 206 QFVEYQDAADEQHKKFIAVQKDIRDIEKEIRNVKKSETSSKKAEEETTDRDAETIFS 262
                                       999999999999999999999999999999999999999999888888877777654 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3  15.2    0.0036       9.2       2      94 ..      13     109 ..       1     111 [. 0.84
   2 ?    0.6   6.1      0.21   5.4e+02      59     106 ..     122     165 ..      99     169 .. 0.51
   3 ?   -0.4   9.7      0.42   1.1e+03       2      71 ..     125     196 ..     115     206 .. 0.73
   4 ?    7.7   6.3    0.0013       3.3      12      85 ..     172     245 ..     158     252 .. 0.84
   5 ?    6.6   4.0    0.0029       7.4       5      80 ..     193     269 ..     191     277 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0036
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHH CS
                        Laminin_II   2 kelaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkel 78 
                                       k+la++ +e+ +e   q  +l+ + +++++k + + ++++e +++ ++ nk +++ +++  +L+ +a++L +k++++
  gi|298675613|ref|YP_003727363.1|  13 KKLAEQYKEKRNELNTQASELASKRNELNKKTKDLINEAQEYKKLRDENNKLVQENKDKRDELNSEANKLYSKIEQI 89 
                                       67788888888899999999999999999999999999999999999999***********************9999 PP

                                       HHHHHH.......HHHHHHH CS
                        Laminin_II  79 kqleeasss....lsdnise 94 
                                       + +++  +     + ++i++
  gi|298675613|ref|YP_003727363.1|  90 RSKNNIDGPslkeIEKEIQR 109
                                       98877644344556666665 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.21
                                       XXXXXX--TTTTTGGGHHHHHHHHHH...HHHHHHHHHHHHHHHHHHH CS
                        Laminin_II  59 rsvkkLeklapqLldklkelkqleeassslsdniseikelIaqARkaA 106
                                       ++ k+L +++++L ++ ++ kq+ e+      +i+++ e  ++ R+ A
  gi|298675613|ref|YP_003727363.1| 122 QKEKELVNKIQDLKKQYENKKQQLEN----NTEIQKLSEEAQKYRDEA 165
                                       44444444444444444444444444....334555555555556655 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.42
                                       XXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTT CS
                        Laminin_II   2 kelaaeanetakevleqlaplsqn..lentkeklseinrsveetnekvkdankairdArrsvkkLeklapqL 71 
                                       kel++++++  k+ ++++++l++n  +++++e++++ ++++ + ++ + ++ +  ++  +++++  k+a+q+
  gi|298675613|ref|YP_003727363.1| 125 KELVNKIQDLKKQYENKKQQLENNteIQKLSEEAQKYRDEASQYHNALAEYAQKAQEYHNKMVETFKKADQV 196
                                       667777777777777777777765224577888888888888888888877777777777777777777765 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0013
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH. CS
                        Laminin_II  12 akevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeas 85 
                                       ++e  ++ ++ ++++ +t +k+ +++++++et+++  +++ a ++  ++   ++k + ++++ ++++k+ e  s
  gi|298675613|ref|YP_003727363.1| 172 LAEYAQKAQEYHNKMVETFKKADQVREEADETHKQFVEYQDAADEQHKKFIAVQKDIRDIEKEIRNVKKSETSS 245
                                       55666777888999999999999999999999999999999999999999999999999999999999988764 PP

  == domain 5  score: 6.6 bits;  conditional E-value: 0.0029
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XX--TTTTTGGGHHHHHH CS
                        Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvk.kLeklapqLldklkelkq 80 
                                       a+++ e a e+ +q  + +   ++  +k   ++++++ +++++++ +k   + +++   + ++ a+ +++++k+ ++
  gi|298675613|ref|YP_003727363.1| 193 ADQVREEADETHKQFVEYQDAADEQHKKFIAVQKDIRDIEKEIRNVKKSETSSKKAEEeTTDRDAETIFSQFKSGEK 269
                                       56666777777777777777777777777777777777777777766666655554431445677777777776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      4750  (0.264934); expected 358.6 (0.02)
Passed bias filter:                      663  (0.0369792); expected 358.6 (0.02)
Passed Vit filter:                       282  (0.0157287); expected 17.9 (0.001)
Passed Fwd filter:                       124  (0.00691617); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 1.63u 0.30s 00:00:01.93 Elapsed: 00:00:00.62
# Mc/sec: 1392.66
//
Query:       gi|298675614|ref|YP_003727364.1|  [L=382]
Description: radical SAM domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-20   74.3   0.0    2.8e-20   73.3   0.0    1.5  2  Radical_SAM     Radical SAM superfamily
    9.3e-07   29.3   0.2    1.9e-06   28.3   0.2    1.6  1  SPASM           Iron-sulfur cluster-binding domain
    7.8e-05   22.8   0.0    0.00016   21.8   0.0    1.6  1  Fer4_14         4Fe-4S single cluster domain
    0.00037   20.8   0.0     0.0008   19.7   0.0    1.5  1  Fer4_12         4Fe-4S single cluster domain
  ------ inclusion threshold ------
        0.1   11.2   0.0       0.15   10.7   0.0    1.1  1  Acetate_kinase  Acetokinase family


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.3   0.0   7.9e-24   2.8e-20       1     166 [.      94     249 ..      94     250 .. 0.93
   2 ?   -3.8   0.0       4.1   1.5e+04     126     144 ..     281     299 ..     272     305 .. 0.69

  Alignments for each domain:
  == domain 1  score: 73.3 bits;  conditional E-value: 7.9e-24
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpg 77 
                                       +++t+ C+++C++Ca p     +   +sl ++ +++++++   ++g  +vi+ ggepl+y+ + e l  ++      
  gi|298675614|ref|YP_003727364.1|  94 ISITEQCPNNCVHCALPD----TNNKKSLEPDTVKDIIDQC-LDMGSTFVIFDGGEPLVYDGL-ENLVSYVDS--TR 162
                                       68999************5....8******************.8****************8866.666666665..48 PP

                                       EEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  78 iritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglp 153
                                           + t+g+ +++ k+e l+++g+d ++++l++a +   +++m+ r + f+e + a+++  +ag+   v+++v+l 
  gi|298675614|ref|YP_003727364.1| 163 AISGLFTSGVGLNRQKAEDLKKAGLDMLTVSLDSAKEY-NHDMMRgREGVFKEAMSAIKNSLDAGLL--VNMYVVLT 236
                                       8899999999999*************************.*************************999..9******* PP

                                       TTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxx RF
                       Radical_SAM 154 Gendeeleellel 166
                                         n +el +++el
  gi|298675614|ref|YP_003727364.1| 237 KRNIDELYDFYEL 249
                                       ********99987 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 4.1
                                       HHHHHHHHHHHHHHTTSET CS
                                       xxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 126 tfeevlealeklreagikr 144
                                       ++e++ + ++++++  ++r
  gi|298675614|ref|YP_003727364.1| 281 DYERFDRFVKYANSIKGPR 299
                                       5677777777777776665 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.2   5.4e-10   1.9e-06       1      44 [.     312     349 ..     312     374 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 5.4e-10
                             SPASM   1 CfapsrslfInsdGdVvpC.cvdkktyveelklGnireesleeIw 44 
                                       Cfa+++ l  +++GdV+pC c++       l+ Gni +++++e+w
  gi|298675614|ref|YP_003727364.1| 312 CFAGKKWLHFTPEGDVYPCaCMP-------LSYGNIYKNTIKELW 349
                                       9******************5555.......*************** PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   4.5e-08   0.00016       5      74 ..      97     161 ..      94     197 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 4.5e-08
                           Fer4_14   5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrl 74 
                                       + +C+ +C+ C   +t ++++ +p+t +++ ++       ++   ++ + GGePL y   ++l+  v+  
  gi|298675614|ref|YP_003727364.1|  97 TEQCPNNCVHCALPDTNNKKSLEPDTVKDIIDQC-----LDMGSTFVIFDGGEPLVYDGLENLVSYVDST 161
                                       678*********8888888777777766664444.....45556899**********8888888777654 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   2.2e-07    0.0008      13     102 ..      98     180 ..      89     209 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.2e-07
                           Fer4_12  13 sgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiw 89 
                                       + C+ +C  C    + + +++k  + ++ + ii+++ +   + +++ GGEPl+   ++ l +lv +v ++    + +
  gi|298675614|ref|YP_003727364.1|  98 EQCPNNCVHCA---LPDTNNKKSLEPDTVKDIIDQCLDMGSTFVIFDGGEPLV---YDGLENLVSYVDSTRA-ISGL 167
                                       56777777766...6666667777788899999***9****************...6777777777776665.4556 PP

                           Fer4_12  90 lytgytleelskk 102
                                        ++g+ l+  +++
  gi|298675614|ref|YP_003727364.1| 168 FTSGVGLNRQKAE 180
                                       6666666666555 PP

>> Acetate_kinase  Acetokinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   4.2e-05      0.15     326     375 ..     167     219 ..     155     223 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.2e-05
                    Acetate_kinase 326 vFTgGigenaalvrelvlkalevlglevdkekn..k.nrsGedelisteqskv 375
                                        FT+G+g n ++  +l+ ++l +l +++d++k   +   +G++++  ++ s++
  gi|298675614|ref|YP_003727364.1| 167 LFTSGVGLNRQKAEDLKKAGLDMLTVSLDSAKEynHdMMRGREGVFKEAMSAI 219
                                       5****************************876532467889999988888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2819.99
//
Query:       gi|298675615|ref|YP_003727365.1|  [L=385]
Description: fumarate reductase/succinate dehydrogenase flavoprotein domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.4e-11   42.3   0.5    1.4e-10   40.9   0.5    1.7  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    6.6e-11   41.5   0.2    8.1e-07   28.1   0.1    2.2  2  HI0933_like     HI0933-like protein
    1.3e-08   34.4   0.7    0.00034   19.9   0.0    2.4  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    5.1e-08   32.5   0.0    0.00031   20.1   0.0    2.4  3  FAD_binding_3   FAD binding domain
    8.7e-07   28.8   0.0      0.036   13.6   0.0    2.3  2  DAO             FAD dependent oxidoreductase
    1.7e-06   27.4   0.0     0.0016   17.5   0.0    2.0  2  Lycopene_cycl   Lycopene cyclase protein
    8.2e-06   25.4   0.1    1.4e-05   24.6   0.1    1.4  1  FAD_oxidored    FAD dependent oxidoreductase
      3e-05   23.4   0.2    0.00032   20.0   0.0    2.3  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
    3.1e-05   23.2   0.1    0.00011   21.4   0.0    1.8  2  FAD_binding_2   FAD binding domain
    7.2e-05   22.9   0.1     0.0019   18.4   0.0    2.7  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    0.00029   20.0   0.1    0.00065   18.9   0.1    1.5  1  GIDA            Glucose inhibited division protein A
     0.0016   17.7   0.1     0.0033   16.7   0.0    1.7  2  Thi4            Thi4 family
     0.0043   17.6   0.0       0.18   12.3   0.0    2.9  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.085   13.3   0.0        4.9    7.6   0.0    2.4  2  NAD_binding_7   Putative NAD(P)-binding
        0.1   12.6   0.1       0.24   11.4   0.1    1.6  1  SAM_LFY         Floricaula / Leafy protein SAM domain
       0.26   10.1   0.6        5.2    5.8   0.1    2.1  2  Trp_halogenase  Tryptophan halogenase


Domain annotation for each model (and alignments):
>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.5   1.3e-13   1.4e-10       1     134 [.       6     146 ..       6     158 .. 0.77

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 1.3e-13
                       Pyr_redox_3   1 iIiGaGPaGlaaaielkkagledylilEkg.nignsiyrypkemtfispsftsekleipdlnaiseets........ 68 
                                       ++iGa PaGl aa ++   g  d+  l+k+ +ig+s +  p++ tf+ +   +++ e+++  +i +  +        
  gi|298675615|ref|YP_003727365.1|   6 LVIGASPAGLMAARNASSGGA-DVKLLDKKpEIGTSTH--PAN-TFFKSMIDKTGEEVDQSYVIKK-LNgahiisps 77 
                                       69******************9.8*******9***9975..544.4555444444444444333332.2223344433 PP

                       Pyr_redox_3  69 .pafslkee..klsrkealeYlrevaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGe 134
                                          +s+k+    + r ++  Y++e +++  ++i+++ e  +v k+++ f+v+ts++t++Ak v++A G 
  gi|298675615|ref|YP_003727365.1|  78 gNYVSVKSAgfFIDRSKFDTYYAEQVRNTGVDIRTDVEAYNVIKSGDFFVVSTSQGTFRAKVVVVADGI 146
                                       32333444344899****************************************************995 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.1   7.3e-10   8.1e-07       2      36 ..       4      38 ..       3      41 .. 0.96
   2 !   11.3   0.0   9.3e-05       0.1     116     167 ..     100     149 ..      94     161 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 7.3e-10
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                      dv+viG+ +AGlmaA +a++ g++V ll+k++++g
  gi|298675615|ref|YP_003727365.1|  4 DVLVIGASPAGLMAARNASSGGADVKLLDKKPEIG 38
                                      89******************************998 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 9.3e-05
                                       HHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS- CS
                       HI0933_like 116 lkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlSi 167
                                        ++++++gv++r++ e  +v k+ d  f v+t s+++++a+ +v+A G +S+
  gi|298675615|ref|YP_003727365.1| 100 AEQVRNTGVDIRTDVEAYNVIKSGDF-FVVST-SQGTFRAKVVVVADGIKSY 149
                                       578999**************775555.999*9.9**************9997 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0     3e-07   0.00034       2      50 ..       4      51 ..       3      92 .. 0.65
   2 !   12.7   0.1   4.9e-05     0.055     184     239 ..      94     148 ..      88     157 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3e-07
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgva 50
                                      dv+viG+ pAGl aa++++  ga+v l++ ++   +    +++++ +++
  gi|298675615|ref|YP_003727365.1|  4 DVLVIGASPAGLMAARNASSGGADVKLLD-KKPEIGTSTHPANTFFKSM 51
                                      89**************************6.3333333333333333333 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 4.9e-05
                                       HHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 184 elsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrp 239
                                       ++  +++e++++ Gv++++  ++ ++++ g+   vv +++ ++ a+ vvva G++ 
  gi|298675615|ref|YP_003727365.1|  94 KFDTYYAEQVRNTGVDIRTDVEAYNVIKSGD-FFVVSTSQGTFRAKVVVVADGIKS 148
                                       678899**********************998.7799999999***********875 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   2.7e-07   0.00031       2      34 ..       3      35 ..       2      46 .. 0.92
   2 !    9.9   0.0   0.00035      0.39     112     185 ..     100     166 ..      89     201 .. 0.71
   3 ?   -3.4   0.0       3.8   4.3e+03      12      44 ..     286     319 ..     285     332 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.7e-07
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrs 34
                                      +dVl++Ga+paGlm+a+  s+ G +v l++k  
  gi|298675615|ref|YP_003727365.1|  3 ADVLVIGASPAGLMAARNASSGGADVKLLDKKP 35
                                      69****************************975 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00035
                                       HHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--GTT-HHHHHHTGG.EEEEEEEEEE CS
                     FAD_binding_3 112 vehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaDGgrStvrktlgie.fegeetvyea 185
                                       +e+ +++g+++r + e  ++ + ++         +t  + t+rak +v aDG +S +++ lg++ ++ ++++  a
  gi|298675615|ref|YP_003727365.1| 100 AEQVRNTGVDIRTDVEAYNVIKSGDF-----FVVSTS-QGTFRAKVVVVADGIKSYIARLLGLNpVKYPDDI--A 166
                                       56666666666666666655555554.....222233.3499********************9977776666..3 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 3.8
                                       HHHHHHHHHHHTTHHEEEEESSSSSCCSS.S--E CS
                     FAD_binding_3  12 aGlmlallLseaGvrvvlvekrsttvvlp.radg 44 
                                       aG ++a  Ls+  v+  ++ ++++  ++  ra++
  gi|298675615|ref|YP_003727365.1| 286 AGDVAAEALSKNDVSKSVLSQYRKIWNKEfRAEY 319
                                       6778899999999999998888887665557765 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   5.4e-05      0.06       1      38 [.       4      42 ..       4      62 .. 0.85
   2 !   13.6   0.0   3.2e-05     0.036     139     208 ..      85     152 ..      57     163 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.4e-05
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGG CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSg 38
                                      dv++iG+  +Gl +A+ ++  g  V ll+k++++g  +++
  gi|298675615|ref|YP_003727365.1|  4 DVLVIGASPAGLMAARNASSGGadVKLLDKKPEIG-TSTH 42
                                      8*****************8877*********9999.4443 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 3.2e-05
                                       TEEEE.EHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHHHHH CS
                               DAO 139 dtgqv.dpakltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsdllg 208
                                       ++g + d  k+  ++a+++++ Gv+i++  e+ ++  ++g+   v   t+ g+ + a+ vV+a G+ s +++
  gi|298675615|ref|YP_003727365.1|  85 SAGFFiDRSKFDTYYAEQVRNTGVDIRTDVEAYNVI-KSGDFFVV--STSqGTFR-AKVVVVADGIKSYIAR 152
                                       4555559999*******************9999974.45665666..77769754.488******9986443 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.4e-06    0.0016       1     143 [.       4     148 ..       4     198 .. 0.78
   2 !    8.1   0.0    0.0011       1.2     225     346 ..     232     348 ..     212     355 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.4e-06
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnny.vWsdefedlga.....leecvehsWsgtivyldd 71 
                                       Dv+viGa pAgl  A +   +  g  v l++  p++  +  +    ++++ +++      ++ v ++ +g+ +  + 
  gi|298675615|ref|YP_003727365.1|   4 DVLVIGASPAGLMAARNA--SSGGADVKLLDKKPEI-GTSTHpANTFFKSMIDKtgeevDQSYVIKKLNGAHIISPS 77 
                                       9**********9777777..9999**********99.6666757777777778733343344444455666666666 PP

                     Lycopene_cycl  72 gkkillgraYgrvsskrlkeellerlvengv.klleakvesveeeeageslvvleggrkirarlvvdarglas 143
                                       g+ + +  a   + ++++    +e++ + gv ++++  + +v ++ +    vv     + ra++vv+a g+ s
  gi|298675615|ref|YP_003727365.1|  78 GNYVSVKSAGFFIDRSKFDTYYAEQVRNTGVdIRTDVEAYNVIKSGD--FFVVSTSQGTFRAKVVVVADGIKS 148
                                       77777767777788889999999999966662456666777766665..888888888************655 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0011
                     Lycopene_cycl 225 lralglkvkevveeEqgviPvtlggslprleqk.vlaiGaaaglvhPaTGYsvarslaeapllasaiaaalressls 300
                                        + +gl+ +++  + +g  P+  +  + ++ +   + +G+aag      GY + + + + ++ a+a+++   + +  
  gi|298675615|ref|YP_003727365.1| 232 KKSKGLNDLKILDTKTGGDPI--ACIPDEIVSDgIMVVGGAAGQ--SGIGYGMRAGQIAGDVAAEALSKNDVS-KSV 303
                                       466999***************..99999999887999*****95..589************999999988774.455 PP

                     Lycopene_cycl 301 arawatlwprerkrqreffrllglalllkldiegrrrfldaFfrlp 346
                                        ++ ++ w +e + +  +   + l++l+k++ +++  +++ F + +
  gi|298675615|ref|YP_003727365.1| 304 LSQYRKIWNKEFRAEYYLG-RIALETLRKMNDDEIDDMMKSFEGKD 348
                                       5556666666655443333.45567899999999999999997655 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.1   1.3e-08   1.4e-05       1     139 [.       4     140 ..       4     146 .. 0.62

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.3e-08
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaeeqvvtgiareflerlrqrgga...r 74 
                                       Dv+V+G+ paG++AA  A   Ga v L+++++ +G ++t    +t+ + ++ +   +     ++++l  +g++   +
  gi|298675615|ref|YP_003727365.1|   4 DVLVIGASPAGLMAARNASSGGADVKLLDKKPEIG-TSTH-PANTFFKSMIDKTGEEVDQSYVIKKL--NGAHiisP 76 
                                       9*********************************8.4443.44566665544422222222233333..22222221 PP

                      FAD_oxidored  75 lkkrskwn.......tfepevakavleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvf 139
                                        ++    +       + + + + + + e +++ gv++ ++ ++ +v+k+g +   v +     + t+rAkv+
  gi|298675615|ref|YP_003727365.1|  77 SGNY---VsvksagfFIDRSKFDTYYAEQVRNTGVDIRTDVEAYNVIKSG-DFFVVST----SQGTFRAKVV 140
                                       1111...0122344478888888888888888888888888888888887.3333333....2566666666 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   2.9e-07   0.00032      28      68 ..       2      42 ..       1      74 [. 0.81
   2 ?    0.7   0.0      0.23   2.6e+02      11      38 ..     119     146 ..     113     153 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.9e-07
                                      --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHH CS
                       AlaDh_PNT_C 28 pakvlviGgGvaGlqAiatakglgakVtvlDvrparleqle 68
                                      +a vlviG+  aGl A+++a++ ga+V++lD++p+     +
  gi|298675615|ref|YP_003727365.1|  2 NADVLVIGASPAGLMAARNASSGGADVKLLDKKPEIGTSTH 42
                                      599*****************************998766555 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.23
                                       CGCTSEEETTCEETCB---EEEEESTSH CS
                       AlaDh_PNT_C  11 kffggkgtlaGgvpgvepakvlviGgGv 38 
                                         + g   ++++ +g+ +akv+v+  G+
  gi|298675615|ref|YP_003727365.1| 119 VIKSGDFFVVSTSQGTFRAKVVVVADGI 146
                                       566788889999999999****998887 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   9.7e-08   0.00011       1      42 [.       4      45 ..       4      64 .. 0.90
   2 ?   -1.6   0.1      0.95   1.1e+03     148     200 ..     100     145 ..      97     151 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 9.7e-08
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG-- CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsq 42
                                      Dv+ViG+  AGL+AA +a+  G++v +++k++e g +t+ + 
  gi|298675615|ref|YP_003727365.1|  4 DVLVIGASPAGLMAARNASSGGADVKLLDKKPEIGTSTHPAN 45
                                      9**********************************9998775 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.95
                                       HHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE--- CS
                     FAD_binding_2 148 vesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatg 200
                                       +e++r+ gvd+++  ea ++i      +G+ +    s ++ ++rak vv+a g
  gi|298675615|ref|YP_003727365.1| 100 AEQVRNTGVDIRTDVEAYNVIK-----SGDFFV--VSTSQGTFRAKVVVVADG 145
                                       6889999999999999999998.....666666..334444556887777765 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.7e-06    0.0019       1      37 [.       7      43 ..       7      85 .. 0.80
   2 ?    1.4   0.0      0.35   3.9e+02       5      23 ..     284     302 ..     283     309 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.7e-06
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-E CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraas 37
                                      ++Ga  +Gl aA+ ++  g+dv ll+k + +G   + 
  gi|298675615|ref|YP_003727365.1|  7 VIGASPAGLMAARNASSGGADVKLLDKKPEIGTSTHP 43
                                      8******************************977665 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.35
                                       SHHHHHHHHHHHCCTEEEE CS
                     NAD_binding_8   5 GlsGlvaAylLakagfdvl 23 
                                        ++G vaA +L+k++++  
  gi|298675615|ref|YP_003727365.1| 284 QIAGDVAAEALSKNDVSKS 302
                                       69999********977544 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   5.8e-07   0.00065       1     149 [.       4     145 ..       4     155 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5.8e-07
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SSSSEEE-TTHHHHHHHHHHHT-SHHHHHHHHEEEEEEE CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGakvlLithkldtiaelsCnpsiggiakgllvrEidalggliikaadkagiqfril 77 
                                       dv ViG+  AG+ AA +a+  Ga+v+L+ +k +   +    +++      +  +E+d+  + +ik  + a+i   i 
  gi|298675615|ref|YP_003727365.1|   4 DVLVIGASPAGLMAARNASSGGADVKLLDKKPEIGTSTHPANTFFKSMIDKTGEEVDQ--SYVIKKLNGAHI---IS 75 
                                       79**************************555443333334444444455556677877..888888888888...55 PP

                                       STTS-CCC-EEEEEE-HHHHHHHHHHHHHTSTTEEEEES.-EEEEEECTTEEEEEEETTS-EEEECEEEE--T CS
                              GIDA  78 NrskGpavralraqvdrelyskevteklenepnleiiee.eveeliveekkvkgvvtedgetikakavviatG 149
                                        +    +v++    +dr+++ +++ e+++n   ++i+++ e+ ++ ++++   +v t+ + t++ak+vv+a G
  gi|298675615|ref|YP_003727365.1|  76 PSGNYVSVKSAGFFIDRSKFDTYYAEQVRN-TGVDIRTDvEAYNV-IKSGDFFVVSTS-QGTFRAKVVVVADG 145
                                       56666789999999***************9.89999887234444.545666666555.557999*****988 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0     3e-06    0.0033      16      99 ..       1      89 [.       1     123 [. 0.77
   2 ?   -2.9   0.0       2.8   3.2e+03      17     219 ..     260     268 ..     216     281 .. 0.57

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3e-06
                                      TEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBSEEEEETTTHHHHHHTT--.......-EEE CS
                              Thi4 16 aesDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfsaivvrkpakelLdelgik.......yede 87
                                      +++Dv+++Ga ++GL aa+  +   +  v +l+++  +G  +      f+ ++  k ++e+ +   ik        +++
  gi|298675615|ref|YP_003727365.1|  1 MNADVLVIGASPAGLMAARNASSG-GADVKLLDKKPEIGTSTHPANTFFKSMID-KTGEEVDQSYVIKklngahiISPS 77
                                      579*****************9988.99999**********99999999999874.455555444444311111112456 PP

                                      SSEEEESEHHHH CS
                              Thi4 88 gdyvvvkdaalf 99
                                      g+yv vk a  f
  gi|298675615|ref|YP_003727365.1| 78 GNYVSVKSAGFF 89
                                      677777666555 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.8
                                       EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBSEEEEETTTHHHHHHTT---EEESSEEEE CS
                              Thi4  17 esDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfsaivvrkpakelLdelgikyedegdyvvv 93 
                                       +sD                                                                          
  gi|298675615|ref|YP_003727365.1| 260 VSD-------------------------------------------------------------------------- 262
                                       222.......................................................................... PP

                                       SEHHHHHHHHHHHHHTSTTEEEEESEEEEEEEEETBTEEEEEEEEEHHHHTCTTTSS.-B-EEEEEEEEEE--GSSS CS
                              Thi4  94 kdaalftstllskvlqlanvkllnavaveDlivregegvaGvvinwtlvelahdtqscvDPlvirakvvvdatGhdg 170
                                                                                                                    
  gi|298675615|ref|YP_003727365.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       TTTTHHHHHHHHCTTTS-----ECB-HHHHHHHHHHHECEEETTEEE-T CS
                              Thi4 171 eivavvvkkikleakiekvkgeksldaekaedaivkktrevvpnlyvaG 219
                                                                                  +++v G
  gi|298675615|ref|YP_003727365.1| 263 -------------------------------------------GIMVVG 268
                                       ...........................................222222 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00016      0.18       2      52 ..       5      54 ..       4      72 .. 0.77
   2 ?    1.7   0.0      0.35     4e+02      43      71 ..      96     124 ..      92     132 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHH CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklek 52
                                      v+v+G++  gl++A +++  g++V++++ ++++     + a + ++  + k
  gi|298675615|ref|YP_003727365.1|  5 VLVIGASPAGLMAARNASSGGADVKLLDKKPEIG-TSTHPANTFFKSMIDK 54
                                      89******************************99.5555555555555555 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.35
                                       HHHHHHHHHHTTEEEECSEEEEEEEEETT CS
                         Pyr_redox  43 skilqeklekngievllntkveeiegsed 71 
                                        ++ +e++++ g++++++ ++ ++ +s+d
  gi|298675615|ref|YP_003727365.1|  96 DTYYAEQVRNTGVDIRTDVEAYNVIKSGD 124
                                       577899***********999999888877 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0044       4.9       8      41 ..       3      45 ..       1      86 [. 0.67
   2 ?    3.1   0.0      0.11   1.3e+02      30      62 ..     136     168 ..     131     174 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0044
                     NAD_binding_7  8 kkvlvvGgGevAarkvrklleagakvtvvapev.........k 41
                                        vlv+G+ + ++  +r+  + ga+v++++++          +
  gi|298675615|ref|YP_003727365.1|  3 ADVLVIGASPAGLMAARNASSGGADVKLLDKKPeigtsthpaN 45
                                      689**************************99954443332221 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.11
                     NAD_binding_7  30 gakvtvvapevkeeleelvklaeeelekdlega 62 
                                        akv+vva  +k+ + +l+ l++ ++++d+++a
  gi|298675615|ref|YP_003727365.1| 136 RAKVVVVADGIKSYIARLLGLNPVKYPDDIAWA 168
                                       69********9999999999******9999876 PP

>> SAM_LFY  Floricaula / Leafy protein SAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00021      0.24      30      48 ..     326     344 ..     320     348 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00021
                           SAM_LFY  30 vstlvnmkeeelddmmksl 48 
                                        +tl +m+++e+ddmmks+
  gi|298675615|ref|YP_003727365.1| 326 LETLRKMNDDEIDDMMKSF 344
                                       689**************97 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1     0.034        38       1      38 [.       4      39 ..       4      53 .. 0.79
   2 ?    5.8   0.1    0.0046       5.2     119     212 ..      59     149 ..      39     160 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.034
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-.SSS-- CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlves.eeigt 38
                                      +++++G+ +aG +aA   +  +   ++v+l+++ +eigt
  gi|298675615|ref|YP_003727365.1|  4 DVLVIGASPAGLMAARNASSGG---ADVKLLDKkPEIGT 39
                                      699************8877666...89999975156655 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0046
                                       HHHHH-SCHHHHHTTB-SB-TTS-B-S--EEEE-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS CS
                    Trp_halogenase 119 ledysleavaakakkfsprekdglsalsyAyhldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrledg 195
                                       + d+s+  + ++ +++++++ +++s+ s ++ +d+++++ +  +   + Gv+++ + v+  ++ ++g+   + +++g
  gi|298675615|ref|YP_003727365.1|  59 V-DQSYVIKKLNGAHIISPSGNYVSVKSAGFFIDRSKFDTYYAEQVRNTGVDIRTD-VEAYNVIKSGDFFVVSTSQG 133
                                       3.445555666666777777777999999**********************98765.66777777777777788777 PP

                                       -EEE-SEEEE-SGGG-I CS
                    Trp_halogenase 196 reveadlfiDcsGfrgl 212
                                       + + a  ++ + G ++ 
  gi|298675615|ref|YP_003727365.1| 134 T-FRAKVVVVADGIKSY 149
                                       6.788888878777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2688.58
//
Query:       gi|298675616|ref|YP_003727366.1|  [L=313]
Description: prenyltransferase UbiA [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-39  134.7  13.7    4.5e-39  134.3  13.7    1.1  1  UbiA      UbiA prenyltransferase family


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.3  13.7   2.5e-43   4.5e-39       4     243 ..      32     278 ..      29     296 .. 0.86

  Alignments for each domain:
  == domain 1  score: 134.3 bits;  conditional E-value: 2.5e-43
                              UbiA   4 palvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilg 80 
                                       +al++  la g+ p+   ++++++g+++a+++++++Nd  D++ D++  + p+RPl+s ++s+k+al+++++l++++
  gi|298675616|ref|YP_003727366.1|  32 SALLASYLAMGSLPPVIPFIIAVIGGYAAITSSYVYNDCCDVDVDKI--NLPDRPLASSQLSVKKALMYSLFLVVVA 106
                                       6788899999999999*******************************..**************************** PP

                              UbiA  81 llllalllnpltallgllalllyvvYtglrlKrrtllgtvvggiafglppllgwaavtgsl..........sllall 147
                                        + + l+lnp ++++++la++   +Y+  + K  t++  v +gia+gl+p++ w a+              +++ ++
  gi|298675616|ref|YP_003727366.1| 107 SVAA-LYLNPESFVVLILAVATISIYS-KFAKSETFFSFVPVGIAYGLVPIGIWLAFDPAGilmgadevilPIPGIF 181
                                       **99.**********************.5***************************666666699999********* PP

                              UbiA 148 lalavflltwaialandlrdregDrkagiktlpvvlGrkaaril.lalllavlllallllllalllllylllallla 223
                                       l++++ +  w++ l    rd++gDr+ +++t+pvv+G  a++ +  a++++++l++ l+++l + l++ ++++++++
  gi|298675616|ref|YP_003727366.1| 182 LGIMMCVTDWGFTLSGVARDVDGDREKNKPTFPVVFGVTATAKFvTACWVIGVLAS-LIIGLTARLGPVFFIGSVIG 257
                                       ****99999**********************************9767677777776.44555555555555555555 PP

                              UbiA 224 alallra.arlvrrrdakkaa 243
                                       +l+++++ + ++++ +++++ 
  gi|298675616|ref|YP_003727366.1| 258 GLWIIMQsFDFIKKSTPERGG 278
                                       555555404555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2425.32
//
Query:       gi|298675617|ref|YP_003727367.1|  [L=486]
Description: archaeosine tRNA-ribosyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-91  305.6   0.0      6e-91  305.2   0.0    1.1  1  TGT       Queuine tRNA-ribosyltransferase
     0.0073   16.2   0.3      0.019   14.8   0.1    1.8  2  DUF5591   Domain of unknown function (DUF5591)
  ------ inclusion threshold ------
       0.11   12.8   0.0        8.1    6.8   0.0    2.4  2  ArsD      Arsenical resistance operon trans-acting repressor 


Domain annotation for each model (and alignments):
>> TGT  Queuine tRNA-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  305.2   0.0     1e-94     6e-91       2     349 ..      13     335 ..      11     336 .. 0.96

  Alignments for each domain:
  == domain 1  score: 305.2 bits;  conditional E-value: 1e-94
                                       TEEEEEEEETTEEEEESEEEEBETTSSBTTB-HHHHH.HTTES-EEEEHHHHHHTTTHHHHHHTTHHHHHHT--S-E CS
                               TGT   2 gaRlGklelphgtietPafmpvgtqgtvkgltpdelkeelgaqiilsntyhlelrpgeelvakagglhkflgwdkpi 78 
                                       ++R+Gkl ++hgtietP++mpv  +++++ +  de+k ++gaqi+++n+y+++ +++ +  a  +glh+++g+d+pi
  gi|298675617|ref|YP_003727367.1|  13 SGRIGKLVTRHGTIETPTIMPV-INPNIPLIDIDEMK-DIGAQILITNSYIIYRSEKLHDKALNEGLHELIGFDGPI 87 
                                       48********************.999**********5.***************988888889999************ PP

                                       EEE-SHHHHHHHEEEESSEEEEE-TTTS-EEEE-HHHHHHHHHHHT-SEEE-------SS--HHHHHHHHHHHHHHH CS
                               TGT  79 ltdsggfqvfslkkiteegvsfqsridGskvlltpeesieiqeklgsDiimalddvvpspaskkrveksverTlrwl 155
                                       +tdsg+fq   l           s + G+ v++t+ee+i++q+k+gsDi+++ld ++p++ s+++++ ++++T+++l
  gi|298675617|ref|YP_003727367.1|  88 MTDSGSFQ---L-----------SVY-GD-VEITNEEIIDFQKKIGSDIAVPLDIPTPPDVSYEKASSEINTTVERL 148
                                       ********...3...........336.**.*********************************************** PP

                                       HHHHHHH..SE.EEEEE--TT-HHHHHHHHHHHHHH--SEEEE-S.SSSSS..HHHHHHHHHHHHGGGS-TTS-EEE CS
                               TGT 156 drcleah..qa.lfgivqGglyedlreesaeelakrdfdgyaigG.lsvge..ekeellevveavtellpedkpryl 226
                                       +++ e++  ++ l g+vqG++y dlre++a+el+++dfd+y+ig+ ++++e  ++++l++v+ ++++ l  + p++l
  gi|298675617|ref|YP_003727367.1| 149 KKAREKFtdDMlLAGPVQGSTYSDLREKCAQELTELDFDVYPIGAvVPLMEdyRYSKLVDVIVSSKKGLKPSSPVHL 225
                                       *****99**777*********************************888***8889********************** PP

                                       TTB-SHHHHHHHHHTT--EEEESHHHHHHHTTEEEETTEEEETTSGGGTT--SBSSSS--SHHHHH-BHHHHHHHHH CS
                               TGT 227 mGvgtPedlleavalGvDmfdcvyptrtarngraltsegelnlknakyaedfspldegCsCytCknytraylhhllk 303
                                       +G+g+P+ ++  valG+D+fd+++++++a+n+r++t +g+++l+n +y     p    CsC++C nyt ++l++  +
  gi|298675617|ref|YP_003727367.1| 226 FGAGHPMGFALEVALGCDLFDSAAYALYAKNKRYITVYGTYHLENLHYL----P----CSCPVCANYTAQELKSAEN 294
                                       **********************************************999....9....*****************99 PP

                                       TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHT CS
                               TGT 304 tkemlgaiLltiHNlhyylelfkriReaIkegtfeefveefarkye 349
                                       + e     Ll+ HNl++++e+++ i+++Ikeg++ e+ve+++r+++
  gi|298675617|ref|YP_003727367.1| 295 NVE-----LLAKHNLYVTFEEMNLIKQSIKEGDLLELVEQRCRSHP 335
                                       999.....***********************************997 PP

>> DUF5591  Domain of unknown function (DUF5591)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       1.5   8.9e+03      80     103 ..     279     302 ..     277     322 .. 0.69
   2 !   14.8   0.1   3.2e-06     0.019       9      95 ..     351     447 ..     344     482 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.5
                                       -------HHHHHHHHHHHHHHHHH CS
                           DUF5591  80 avtgewseeeiefvaellakylek 103
                                       +v  +++++e++ +++ ++   ++
  gi|298675617|ref|YP_003727367.1| 279 PVCANYTAQELKSAENNVELLAKH 302
                                       677778888888777777644443 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3.2e-06
                                       HHH---S..SSEEEEEE--SSSS..GGGSHHHHHHHH....HS---........SEEEEE-SS-.EEEGGGTT---- CS
                           DUF5591   9 lerYeppeekkvlvLlPcsakkP..yseskshrkfae....aikkrka.....kvheviltsPlGvvPreleevYPa 74 
                                       le+Y+p +++++    P+s+k+P   + sk+ ++f       i+++ +       + ++   PlG  P el e+YP+
  gi|298675617|ref|YP_003727367.1| 351 LEKYNPVTKSTIFYCGPESSKRPevLHFSKRIERFTVngsaIIRSNSTkqddeFDNILMFKPPLGTFPVELLETYPF 427
                                       467*****999************666899999999876665444444233452445567799**************9 PP

                                       ------------HHHHHHHHH CS
                           DUF5591  75 aqYdiavtgewseeeiefvae 95 
                                       +  ++  ++++++ e++++++
  gi|298675617|ref|YP_003727367.1| 428 NI-ETISSPDYESIEVALLNT 447
                                       64.555555677666666554 PP

>> ArsD  Arsenical resistance operon trans-acting repressor ArsD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.017        99      12      50 ..     275     315 ..     272     320 .. 0.82
   2 ?    6.8   0.0    0.0013       8.1      17      56 ..     364     405 ..     351     423 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.017
                              ArsD  12 cCstgvCgpsvdqelvriaadvdalkkkgvev..eRynlaq 50 
                                        Cs  vC +   qel + +++v+ l k+++ v  e +nl +
  gi|298675617|ref|YP_003727367.1| 275 PCSCPVCANYTAQELKSAENNVELLAKHNLYVtfEEMNLIK 315
                                       69************************998766224566665 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0013
                              ArsD  17 vCgpsvd..qelvriaadvdalkkkgveveRynlaqepqaFv 56 
                                        Cgp+    +e++++++ ++  + +g  + R n +++  +F 
  gi|298675617|ref|YP_003727367.1| 364 YCGPESSkrPEVLHFSKRIERFTVNGSAIIRSNSTKQDDEFD 405
                                       68887642279**************************99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (486 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.73
# Mc/sec: 1997.86
//
Query:       gi|298675618|ref|YP_003727368.1|  [L=109]
Description: translation initiation factor eIF-1A [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-17   62.9   0.3    2.9e-17   62.2   0.3    1.4  1  eIF-1a    Translation initiation factor 1A / IF-1


Domain annotation for each model (and alignments):
>> eIF-1a  Translation initiation factor 1A / IF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2   0.3   1.6e-21   2.9e-17       1      64 []      28      90 ..      28      90 .. 0.96

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 1.6e-21
                                      EEEEEEEEEEETTTEEEEEE.SSSSBEEEEE-HHHHCT----TT-EEEEEE-TT-TTEEEEES- CS
                            eIF-1a  1 gevigkViealgnnlfrVelpdngkevlaeipgkfRnkiwikrGdyVlVelspydltkGrIvyr 64
                                      ge+ ++V   lg n+ r + +d g+ ++++ipg +++kiwi++Gd+V+  +++++++k++++++
  gi|298675618|ref|YP_003727368.1| 28 GEILAIVDSRLGANRLRLRSMD-GVVRMGRIPGSMKKKIWIREGDIVIAVPWDFQDSKADVIWK 90
                                      57899***************96.***************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 839.63
//
Query:       gi|298675619|ref|YP_003727369.1|  [L=259]
Description: Non-specific serine/threonine protein kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-61  206.8   0.2    3.2e-61  206.2   0.2    1.2  1  RIO1             RIO1 family
    5.7e-05   22.6   0.4     0.0002   20.8   0.3    1.7  2  Pkinase          Protein kinase domain
    0.00053   19.4   0.0     0.0057   16.0   0.0    2.1  1  Kdo              Lipopolysaccharide kinase (Kdo/WaaP) family
    0.00057   18.8   0.1    0.00086   18.2   0.1    1.2  1  Pkinase_fungal   Fungal protein kinase
     0.0062   16.5   0.0      0.061   13.2   0.0    2.1  2  APH              Phosphotransferase enzyme family
  ------ inclusion threshold ------
       0.03   13.6   0.0      0.045   13.0   0.0    1.3  1  Pkinase_Tyr      Protein tyrosine kinase
      0.036   13.6   0.1        0.1   12.2   0.1    1.7  2  Choline_kinase   Choline/ethanolamine kinase
       0.05   12.8   0.0       0.11   11.7   0.0    1.5  1  Fructosamin_kin  Fructosamine kinase


Domain annotation for each model (and alignments):
>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.2   0.2   1.4e-64   3.2e-61       2     181 ..      68     247 ..      67     253 .. 0.95

  Alignments for each domain:
  == domain 1  score: 206.2 bits;  conditional E-value: 1.4e-64
                                       EEEEEETTTEEEEEEEE-S---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEE CS
                              RIO1   2 VyhavsedgkevaiKiyktstteFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpiel 78 
                                       ++ a s ++k +a+Kiy+++t++F+ +++y+ g++rfk+   ++++r+++ +w++kE+rnL r+++ag++vP+pi+ 
  gi|298675619|ref|YP_003727369.1|  68 IFFAES-SDKPIALKIYRITTSTFRAMEEYILGDPRFKNI--RHEKRDIIMAWTRKEYRNLIRAQNAGIRVPSPITT 141
                                       677755.6778***************************88..89********************************* PP

                                       ETTEEEEE--EETTEEGGBHHHCG.-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETT..EEEE--GTTE CS
                              RIO1  79 krhvlvmefigedgvaapklkdve.eeeeaeelyeevleemrklykeaglvHaDLSeyNvlvded..kvviIDvsQa 152
                                       ++++lvm+f+ge++v +p lk+v+ ++e+a+++ye++ ++mrklyk+ +lvH+DLSeyN+++d +  ++++ID++Q+
  gi|298675619|ref|YP_003727369.1| 142 EKNILVMDFLGENEVSYPLLKEVKlDTEQAHQIYETIKSYMRKLYKHGNLVHGDLSEYNIMIDPNniEPIFIDMGQS 218
                                       ************************7799***********************************998999******** PP

                                       EETTSTTHHHHHHHHHHHHHHHHHTTC-- CS
                              RIO1 153 veldhpnalefLerDveniikfFrrkgve 181
                                       v+ldhp+a+ fL+rD++ni +fF+r +++
  gi|298675619|ref|YP_003727369.1| 219 VTLDHPRAEYFLNRDIKNITRFFKRFKIS 247
                                       *************************9987 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.23   5.2e+02     166     243 ..      39     116 ..      19     132 .. 0.68
   2 !   20.8   0.3   8.8e-08    0.0002      70     150 ..     141     223 ..     103     239 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.23
                                       HHHHTTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCTSHH...HHHTTS-HHHHHHHH CS
                           Pkinase 166 PEvlkeneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilgetkeklpeaseiseeakdllk 242
                                       P +++  + s+k  +++lG  + +    +  f+++++k  + k+++ ++++++ ++e+ +  p+ ++i +e +d++ 
  gi|298675619|ref|YP_003727369.1|  39 PTLISLYNLSNKDILYALGGAISTGKEANIFFAESSDKPIALKIYRITTSTFRAMEEYILGDPRFKNIRHEKRDIIM 115
                                       55555555555555677777777776666777777777766777777778888888888888888888777777775 PP

                                       H CS
                           Pkinase 243 k 243
                                        
  gi|298675619|ref|YP_003727369.1| 116 A 116
                                       5 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 8.8e-08
                                       SSEEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTT.EE-SS-SGGGEEEE.TTTEEEE-SGTT CS
                           Pkinase  70 kdelylvleyveggeladllerkgslseeeakkiakqilegleylHskg.iiHrDlKpeNiLid.ekgelKitDFGl 144
                                       +++ +lv++++ ++e+   l ++++l+ e+a +i ++i + ++ l+++g ++H Dl   Ni+id ++ e   +D G 
  gi|298675619|ref|YP_003727369.1| 141 TEKNILVMDFLGENEVSYPLLKEVKLDTEQAHQIYETIKSYMRKLYKHGnLVHGDLSEYNIMIDpNNIEPIFIDMGQ 217
                                       455678******99999999899***********************8877**************7777788899998 PP

                                       SEESSS CS
                           Pkinase 145 akeles 150
                                       +  l++
  gi|298675619|ref|YP_003727369.1| 218 SVTLDH 223
                                       877765 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.5e-06    0.0057      60     205 ..     120     258 ..     104     259 .] 0.79

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.5e-06
                               Kdo  60 rEfrllkrLeeagvavpkpvaagavkvgleyrAlllterlegaqdLedllakwaelaeelkrallkavgrliaklhr 136
                                       +E+r+l r ++ag++vp p+  +          +l++  l g +++   l k  +l+ e  +++++ +   ++kl +
  gi|298675619|ref|YP_003727369.1| 120 KEYRNLIRAQNAGIRVPSPITTEK--------NILVMDFL-GENEVSYPLLKEVKLDTEQAHQIYETIKSYMRKLYK 187
                                       677777777777777777776653........34555544.344444444444568999999*************98 PP

                               Kdo 137 ag.vnHadlyaknillqqeeeeeaeiwliDldkarlrlr..adrwrekdLarLkrsfl..kielteadweallr 205
                                        g + H+dl   ni+++ ++   +e ++iD+ ++ +     a+   ++d++++ r f+  ki+ +  d  a++r
  gi|298675619|ref|YP_003727369.1| 188 HGnLVHGDLSEYNIMIDPNN---IEPIFIDMGQSVTLDHprAEYFLNRDIKNITRFFKrfKISDSPEDLSAFVR 258
                                       75389*************97...***********987763466778*********9998889999999998875 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   3.8e-07   0.00086     313     363 ..     175     222 ..     154     239 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.8e-07
                    Pkinase_fungal 313 rDaIkgh.rsLflkagiLHrDiSenNilitdskkegerkglLiDLDlakels 363
                                       ++ Ik + r+L+++++++H D Se+Ni+i      ++ + + iD+   ++l+
  gi|298675619|ref|YP_003727369.1| 175 YETIKSYmRKLYKHGNLVHGDLSEYNIMID----PNNIEPIFIDMGQSVTLD 222
                                       5677776589*******************8....334455566665555555 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.14   3.1e+02      37      59 ..     118     140 ..      60     177 .. 0.66
   2 !   13.2   0.0   2.7e-05     0.061     152     194 ..     174     216 ..     153     227 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHHTT-B--B-CT CS
                               APH  37 irrevallrlLakagvpvPevla 59 
                                       +r+e++ l   ++ag++vP ++ 
  gi|298675619|ref|YP_003727369.1| 118 TRKEYRNLIRAQNAGIRVPSPIT 140
                                       34666677677777778888887 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2.7e-05
                                       HHHHHHHH--S.SS-EEEE-SS-SGGGEEEC..TTEEEEE---T CS
                               APH 152 vlaalaallpg.elptvllHgDlhpgNllvdpddgrvtGviDfe 194
                                       ++++++  +++   +  l+HgDl+  N+++dp++ +   +iD +
  gi|298675619|ref|YP_003727369.1| 174 IYETIKSYMRKlYKHGNLVHGDLSEYNIMIDPNNIEP-IFIDMG 216
                                       666666666665566679*************665443.378765 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     2e-05     0.045      72     141 ..     140     208 ..     104     229 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2e-05
                                       SSSSEEEEEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHT.TEEEST-SGGGEEEEETTE CS
                       Pkinase_Tyr  72 keepllivteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLesk.klvHrdlaarNvLlsenkv 141
                                        +e+ ++v++++ +++++  L k+   kl++++  ++   + + m+ L ++ +lvH dl+  N++++ n++
  gi|298675619|ref|YP_003727369.1| 140 TTEKNILVMDFLGENEVSYPLLKE--VKLDTEQAHQIYETIKSYMRKLYKHgNLVHGDLSEYNIMIDPNNI 208
                                       3567899**********9999997..9*******************9977637*************98775 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.1   2.5e+03      91     120 ..      87     115 ..      74     134 .. 0.59
   2 ?   12.2   0.1   4.6e-05       0.1     122     170 ..     166     214 ..     152     218 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.1
                                       -HHHHHHHHHHHCCS.TT..ECHHGGCCHC CS
                    Choline_kinase  91 pslwktmqkwllnkeaqtkakkekkkkqlk 120
                                       +s+++ m+++ + ++ + k  +++k++ + 
  gi|298675619|ref|YP_003727369.1|  87 TSTFRAMEEY-ILGDPRFKNIRHEKRDIIM 115
                                       5667777777.4444444444444444444 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 4.6e-05
                                       CTHHHHHHHHHTHHHHHHCHGG-EEEE-S--SGGGEEE.-CTTEEEE-- CS
                    Choline_kinase 122 inledlekelekleklleelespvvfcHnDlqegNillnkeekklvlID 170
                                       +++e+ ++  e++++++ +l+++ ++ H Dl e Ni+ + ++ + ++ID
  gi|298675619|ref|YP_003727369.1| 166 LDTEQAHQIYETIKSYMRKLYKHGNLVHGDLSEYNIMIDPNNIEPIFID 214
                                       56788889999999999999************************9**99 PP

>> Fructosamin_kin  Fructosamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.8e-05      0.11     159     212 ..     160     214 ..     148     219 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.8e-05
                   Fructosamin_kin 159 lakekglefakieelvervaellskhqpkpsllHGdLWsgNaaltkd.gepvifd 212
                                       l+ke +l++++++++ e++++ ++k   +  l+HGdL + N++++ +  ep+++d
  gi|298675619|ref|YP_003727369.1| 160 LLKEVKLDTEQAHQIYETIKSYMRKLYKHGNLVHGDLSEYNIMIDPNnIEPIFID 214
                                       5778888999********************************9998844577766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1020  (0.0568911); expected 358.6 (0.02)
Passed bias filter:                      726  (0.0404931); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1597.76
//
Query:       gi|298675620|ref|YP_003727370.1|  [L=185]
Description: KH domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-10   40.2  11.2    4.8e-06   26.3   1.3    2.4  2  KH_1      KH domain
     0.0031   17.3   9.6      0.081   12.8   0.4    3.4  4  KH_2      KH domain
  ------ inclusion threshold ------
      0.048   13.8   0.0      0.098   12.8   0.0    1.5  1  KH_8      Krr1 KH1 domain
       0.54   10.4   4.8        6.7    6.9   0.1    3.1  3  KH_5      NusA-like KH domain
       0.62   10.0   7.1        5.1    7.0   1.4    3.2  3  KH_4      KH domain


Domain annotation for each model (and alignments):
>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   1.3   1.3e-09   4.8e-06       3      51 ..       3      45 ..       1      78 [. 0.75
   2 !   18.7   2.9   3.1e-07    0.0011      10      64 ..     101     147 ..      97     149 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.3e-09
                                      EEEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEE CS
                              KH_1  3 rilvPsslvgriIGkgGsnIkeIreetgakIkvpksedegsderevtis 51
                                       i+vP++ +g+iIG+ Gs+   I++++  k  ++ s+++      v+i+
  gi|298675620|ref|YP_003727370.1|  3 HIKVPQDRIGAIIGPEGSVKETIEQKSASKLEID-SDSG-----SVEIT 45
                                      699**********************99999**87.4433.....33333 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 3.1e-07
                                       HHHHHHTGGGHHHHHHHHHH.T-EEEEESSTT...T.-EEEEEESHHHHHHHHHHH CS
                              KH_1  10 lvgriIGkgGsnIkeIreet.gakIkvpksedegsderevtisGspeavekAkeli 64 
                                         griIGk+G++ +eI e   +++I v  +       ++v ++G+pe++++ + +i
  gi|298675620|ref|YP_003727370.1| 101 IKGRIIGKNGKT-REIAESLiNVHISVY-G-------KTVSVIGKPEQIQAIRTAI 147
                                       569********8.9****8899999987.4.......59**********9877666 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.4   2.3e-05     0.081      29      60 ..       4      35 ..       2      45 .. 0.84
   2 ?   -1.0   0.0      0.44   1.6e+03      19      43 ..      43      66 ..      33      66 .. 0.72
   3 !    7.7   1.6   0.00085       3.1      36      67 ..     102     132 ..      86     139 .. 0.84
   4 ?   -0.2   0.0      0.25     9e+02      39      70 ..     133     163 ..     128     169 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.3e-05
                                      EEEEESCHHHHHTGGGHHHHHHHHHHHHHHHH CS
                              KH_2 29 iviresqpgivIGkgGsnikkigkelrkdiek 60
                                      i +   + g +IG +Gs  ++i+++   ++e+
  gi|298675620|ref|YP_003727370.1|  4 IKVPQDRIGAIIGPEGSVKETIEQKSASKLEI 35
                                      56667799*****************9999974 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.44
                                      EEECCS.CEEEEEEEESCHHHHHTGG CS
                              KH_2 19 eIerta.nrviiviresqpgivIGkg 43
                                      eI  t+ n+ +  +r+s+  ++IG+g
  gi|298675620|ref|YP_003727370.1| 43 EI--TPgNDPVSGMRASETIRAIGRG 66
                                      55..4445555667899999999997 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.00085
                                       HHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEE CS
                              KH_2  36 pgivIGkgGsnikkigkelrkdieklegkkVk 67 
                                       +g++IGk+G++ +  ++ ++  i  + gk V+
  gi|298675620|ref|YP_003727370.1| 102 KGRIIGKNGKTREIAESLINVHIS-VYGKTVS 132
                                       8*********99999988888884.7777776 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.25
                                       HHTGGGHHHHHHHHHHHHHHHHHHTTCEEEEE CS
                              KH_2  39 vIGkgGsnikkigkelrkdieklegkkVklni 70 
                                       vIGk  + i++i++++   ++   ++ V+ ++
  gi|298675620|ref|YP_003727370.1| 133 VIGKP-EQIQAIRTAIDMLVGGANHGTVYSYL 163
                                       56653.78999999999988877777777555 PP

>> KH_8  Krr1 KH1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.7e-05     0.098      21      81 .]      20      78 ..       4      78 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.7e-05
                              KH_8 21 kikklleekk.lklevdlkerslkvsTtekTrDPyiilkardlikLisrgvpleeakkvleD 81
                                      ++k+++e+k   kle+d + +s+++       DP   ++a + i+ i+rg + e+a ++l+D
  gi|298675620|ref|YP_003727370.1| 20 SVKETIEQKSaSKLEIDSDSGSVEITP---GNDPVSGMRASETIRAIGRGFNPEKAIQLLDD 78
                                      677777666515789999999988865...46****************************99 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1    0.0019       6.7      17      36 ..       9      28 ..       2      35 .. 0.88
   2 ?    2.3   1.1     0.051   1.8e+02      19      50 ..     102     139 ..      91     147 .. 0.71
   3 ?    2.2   0.0     0.054   1.9e+02      13      47 ..     137     173 ..     128     178 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0019
                              KH_5 17 dpvGaivgkkGsrikavsse 36
                                      d +Gai+g +Gs  ++++++
  gi|298675620|ref|YP_003727370.1|  9 DRIGAIIGPEGSVKETIEQK 28
                                      78**********99999886 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.051
                              KH_5  19 vGaivgkkGsrikavsseLk......gekidvvewseD 50 
                                        G i+gk+G+  +  +s ++      g+ + v+ + e 
  gi|298675620|ref|YP_003727370.1| 102 KGRIIGKNGKTREIAESLINvhisvyGKTVSVIGKPEQ 139
                                       5999****987555555555777777777777766665 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.054
                              KH_5  13 npnvdpvGaivgk..kGsrikavsseLkgekidvvew 47 
                                        +++ ++++++ +  +G++  +v s L++++ d++++
  gi|298675620|ref|YP_003727370.1| 137 PEQIQAIRTAIDMlvGGANHGTVYSYLEKKRQDLIQE 173
                                       4579999999986558999999999999999999987 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1    0.0084        30      31      49 ..       2      20 ..       1      27 [. 0.89
   2 ?    7.0   1.4    0.0014       5.1      40      50 ..     102     112 ..      97     134 .. 0.75
   3 ?   -0.0   0.1      0.23   8.3e+02      43      60 ..     133     149 ..     113     160 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0084
                              KH_4 31 ielnvegedlGrvIGkrGr 49
                                      ++++v ++ +G +IG +G 
  gi|298675620|ref|YP_003727370.1|  2 VHIKVPQDRIGAIIGPEGS 20
                                      68999**********9996 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0014
                              KH_4  40 lGrvIGkrGrt 50 
                                       +Gr+IGk+G+t
  gi|298675620|ref|YP_003727370.1| 102 KGRIIGKNGKT 112
                                       6*********9 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.23
                              KH_4  43 vIGkrGrtldAlqylvsa 60 
                                       vIGk  + ++A+++ +  
  gi|298675620|ref|YP_003727370.1| 133 VIGKP-EQIQAIRTAIDM 149
                                       66665.567888886655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1111.46
//
Query:       gi|298675621|ref|YP_003727371.1|  [L=230]
Description: hypothetical protein Metev_1737 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.9e-33  114.3  13.6    8.2e-33  113.8  13.6    1.2  1  DUF1614    Protein of unknown function (DUF1614)


Domain annotation for each model (and alignments):
>> DUF1614  Protein of unknown function (DUF1614)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.8  13.6   4.6e-37   8.2e-33       2     169 ..      51     225 ..      50     226 .. 0.92

  Alignments for each domain:
  == domain 1  score: 113.8 bits;  conditional E-value: 4.6e-37
                           DUF1614   2 lgslinipvaelkske.el.ve.vkvlgisykvpvleeeekk......tvvavNvGGaviPlllslylllrlavsll 69 
                                       ++ +++ip++++++k+ +   + +++l+  ++vpvl+e e++      t +++N+GG+viP+ +++yll+++    +
  gi|298675621|ref|YP_003727371.1|  51 AANNLEIPIKTVRTKKiKNiSNnAQILEQLFSVPVLKELETRkelvfnTKLTLNLGGFVIPASMIIYLLFTQF--NV 125
                                       56789*********776553336**************9999899**************************999..89 PP

                           DUF1614  70 aallavlivaavvyllarpvpgvGivvpllipplvaalaalllaeeeaaavaYisgvlGtLiGadllnl.kkieklg 145
                                       aa+ ++l++ ++++lla++v+gvGivvp +i+ + + +a l+la+e+ a v+++s++ G+LiG+ +  +  + ek g
  gi|298675621|ref|YP_003727371.1| 126 AAIEIFLVMLVATVLLAEMVNGVGIVVPDYIGLISVPMA-LILAPENVAYVIFVSSISGILIGTVISFFtIDREKNG 201
                                       ********************************9988887.**************************99965667778 PP

                           DUF1614 146 apvvsIGGaGtFdGifltgilavl 169
                                       + +++ GG+G F+++++ +++a l
  gi|298675621|ref|YP_003727371.1| 202 SAYINFGGVGSFKAVYIITLIAGL 225
                                       88********************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       873  (0.0486921); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1425.01
//
Query:       gi|298675622|ref|YP_003727372.1|  [L=295]
Description: putative circadian clock protein KaiC [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-38  132.2   0.1    1.4e-37  129.3   0.1    2.0  1  ATPase           KaiC
    1.7e-09   37.5   0.0    3.4e-09   36.6   0.0    1.5  1  AAA_25           AAA domain
    1.1e-08   34.9   0.0    1.4e-08   34.5   0.0    1.2  1  RecA             recA bacterial DNA recombination protein
    1.4e-07   31.1   0.0    2.3e-07   30.4   0.0    1.4  1  DnaB_C           DnaB-like helicase C terminal domain
    3.3e-07   29.3   0.0     0.0066   15.1   0.0    2.1  2  GvpD             GvpD gas vesicle protein
    1.8e-05   25.3   0.1    0.00016   22.2   0.0    2.5  3  AAA_18           AAA domain
    3.1e-05   23.4   0.0    4.8e-05   22.8   0.0    1.3  1  Rad51            Rad51
    0.00013   22.0   0.0    0.00038   20.5   0.0    1.9  1  AAA_14           AAA domain
    0.00015   21.6   0.0    0.00027   20.7   0.0    1.5  1  IstB_IS21        IstB-like ATP binding protein
     0.0005   19.2   0.0    0.00074   18.7   0.0    1.3  1  T2SSE            Type II/IV secretion system protein
    0.00065   19.5   0.0     0.0015   18.3   0.0    1.6  1  AAA_24           AAA domain
    0.00091   19.6   0.0     0.0015   18.9   0.0    1.4  1  AAA_19           AAA domain
     0.0011   19.4   0.0     0.0017   18.8   0.0    1.3  1  AAA_16           AAA ATPase domain
     0.0012   19.3   0.0     0.0032   17.9   0.0    1.6  1  AAA              ATPase family associated with various cellul
     0.0016   18.4   0.3      0.004   17.1   0.2    1.8  1  NTPase_1         NTPase
     0.0027   18.0   0.0     0.0092   16.3   0.0    2.0  1  AAA_22           AAA domain
     0.0028   17.5   0.0       0.01   15.6   0.0    1.9  2  AAA_11           AAA domain
     0.0047   16.5   0.0      0.012   15.2   0.0    1.6  1  AAA_7            P-loop containing dynein motor region
     0.0083   15.4   0.0      0.011   15.0   0.0    1.3  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.009   16.4   0.0      0.056   13.8   0.0    2.2  1  RNA_helicase     RNA helicase
     0.0092   15.9   0.1      0.018   14.9   0.0    1.5  2  ATPase_2         ATPase domain predominantly from Archaea
  ------ inclusion threshold ------
      0.027   14.9   0.1       0.12   12.8   0.1    2.2  1  AAA_17           AAA domain
      0.029   14.1   0.0       0.08   12.6   0.0    1.7  2  Sigma54_activat  Sigma-54 interaction domain
      0.033   14.3   0.0      0.077   13.2   0.0    1.8  1  AAA_33           AAA domain
      0.034   14.1   0.0      0.062   13.2   0.0    1.6  1  NACHT            NACHT domain
      0.035   13.7   0.1      0.097   12.2   0.0    2.1  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.042   13.5   0.0       0.15   11.8   0.0    1.9  2  Thymidylate_kin  Thymidylate kinase
      0.057   13.4   0.0       0.11   12.5   0.0    1.6  1  AAA_5            AAA domain (dynein-related subfamily)
      0.071   13.4   0.0       0.12   12.6   0.0    1.5  1  AAA_28           AAA domain
      0.073   12.8   0.0       0.13   11.9   0.0    1.4  1  AAA_30           AAA domain
      0.076   11.8   0.1       0.19   10.5   0.0    1.6  2  PPV_E1_C         Papillomavirus helicase


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.3   0.1   2.4e-40   1.4e-37       2     225 ..      63     271 ..      62     276 .. 0.91

  Alignments for each domain:
  == domain 1  score: 129.3 bits;  conditional E-value: 2.4e-40
                            ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekle 78 
                                        tgI+ lD+ l+gGip+g +v +tG pGtGKt+f+ q l++ +++ +e++vf ++ee+ae+l +++ + Gwd+ +  
  gi|298675622|ref|YP_003727372.1|  63 GTGIPSLDDSLEGGIPKGFSVIVTGPPGTGKTTFCVQILMERIRN-NEKCVFFSFEEDAEHLVQQFMRYGWDIGEAI 138
                                       59*******************************************.******************************* PP

                            ATPase  79 eegklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitglayeekeavaRe..ilrqlvrvlkk 153
                                       ++g l i  +s  ++               ee+++++++++   vv Ds++++   ++++++R+  + r++ r lk 
  gi|298675622|ref|YP_003727372.1| 139 DKGYLEIFGMSIITS---------------EEMTQIVDSYRPDVVVFDSLNVF---SNPEEFRTagTWRNVHRSLKR 197
                                       *****9999998875...............589********************...555555542279********* PP

                            ATPase 154 lgvTailvsekssseeaaggygveefivdgvivLdlkeiee...elvRtleivkmRgtkhskkehpfeIteegik 225
                                       +++T+++v+ek+++  ++++++   f+ dg+i Ld    ++   +   ++ + kmR+tk+++   pf+ te gi 
  gi|298675622|ref|YP_003727372.1| 198 KKITSLMVTEKKHGL-ETKQFDDYDFLGDGIIFLDTVPTNDinpTPMSVMVVQKMRSTKIDTSPQPFTFTETGIH 271
                                       **********98874.45555556789********9888878999***************************996 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   5.9e-12   3.4e-09      12     164 ..      59     186 ..      48     206 .. 0.81

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 5.9e-12
                            AAA_25  12 vadlaapppprrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrr 88 
                                       + +  + +p++++ ++g +p+g  ++++G+pgtGKtt+++++  +  +             k+++ s+E+++++l +
  gi|298675622|ref|YP_003727372.1|  59 IKRMGTGIPSLDDSLEGGIPKGFSVIVTGPPGTGKTTFCVQILMERIRNN----------EKCVFFSFEEDAEHLVQ 125
                                       5566678999999**********************************866..........39**********99998 PP

                            AAA_25  89 RlravgealrddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralggdensnsd 164
                                        + + g ++    ++++ ++        + +++g++++t++  ++ + +++ +++++vv+D+l+ + + +e + + 
  gi|298675622|ref|YP_003727372.1| 126 QFMRYGWDI----GEAIDKG--------YLEIFGMSIITSE--EMTQIVDS-YRPDVVVFDSLNVFSNPEEFRTAG 186
                                       888888777....4444443........2345778898886..79999999.78**********999998876655 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.0   2.5e-11   1.4e-08      26     145 ..      54     178 ..      33     204 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 2.5e-11
                                       -.-----EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEE....ESS----H..H CS
                              RecA  26 keklkvetissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafi....daehaldp..k 96 
                                       + +++++ + +G  +ld +l  GG+pkG  + + Gp  +Gktt++++++ e  +++  ++f     daeh ++   +
  gi|298675622|ref|YP_003727372.1|  54 NIDVNIKRMGTGIPSLDDSLE-GGIPKGFSVIVTGPPGTGKTTFCVQILMERIRNNEKCVFFsfeeDAEHLVQQfmR 129
                                       44688999************8.*************************************99766779***9985337 PP

                                       HHHHTT--GGG-EEE--SSHHHHHHHHHHHHTTT--SEEEEE-TTT--- CS
                              RecA  97 yakklGvdidellvsqpdtGeqaleiadalvrsgaidlivvdsvaalvp 145
                                       y   +G  id+ ++        + e + ++v+s   d++v ds+  +  
  gi|298675622|ref|YP_003727372.1| 130 YGWDIGEAIDKGYLEIFGMSIITSEEMTQIVDSYRPDVVVFDSLNVFSN 178
                                       999***********9999999999999****************987655 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0     4e-10   2.3e-07       4      74 ..      64     134 ..      62     204 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 4e-10
                                       SSTHHHH.HHCTSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHHHHHTX CS
                                       xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C   4 tgfkdLD.kltsGlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRllsseaei 74 
                                       tg  +LD +l +G+ kg  +i+ + p++Gkt+++++i  +    ++ ++++fs+e +ae+lvq+++    +i
  gi|298675622|ref|YP_003727372.1|  64 TGIPSLDdSLEGGIPKGFSVIVTGPPGTGKTTFCVQILMERIR-NNEKCVFFSFEEDAEHLVQQFMRYGWDI 134
                                       6778888356678999999******************987664.5778***************998766555 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.1e-05    0.0066      10      55 ..      80     126 ..      77     151 .. 0.83
   2 !   12.2   0.0   8.9e-05     0.052     117     208 ..     168     268 ..     148     283 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.1e-05
                              GvpD  10 GktllikGaPGtGktlftlrgl.dvlrresdvlyvstrvddetvsea 55 
                                       G ++++ G PGtGkt+f ++ l + +r++++ ++ s   d e + + 
  gi|298675622|ref|YP_003727372.1|  80 GFSVIVTGPPGTGKTTFCVQILmERIRNNEKCVFFSFEEDAEHLVQQ 126
                                       7799****************874679999999999988887766655 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 8.9e-05
                              GvpD 117 lvyeylaerydsPediktv...kndlvvlaresgvrlvlv.....letaansrleyivdGvvtl.nvkeddrgrlrr 184
                                       +v++ l + + +Pe+++t    +n    l r++   l++      let++ +  +++ dG++ l  v  +d   +  
  gi|298675622|ref|YP_003727372.1| 168 VVFDSLNV-FSNPEEFRTAgtwRNVHRSLKRKKITSLMVTekkhgLETKQFDDYDFLGDGIIFLdTVPTNDINPTPM 243
                                       45566654.566777654321156666666777666665433333699****************8787777776655 PP

                              GvpD 185 d.lrleklrGvrignrlqPftladG 208
                                       + + ++k+r  +i+   qPft+++ 
  gi|298675622|ref|YP_003727372.1| 244 SvMVVQKMRSTKIDTSPQPFTFTET 268
                                       51679***************99765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       6.6   3.8e+03      63      83 ..      11      38 ..       2      57 .. 0.53
   2 !   22.2   0.0   2.8e-07   0.00016       1      89 [.      83     180 ..      83     206 .. 0.58
   3 ?   -0.7   0.0       3.4   1.9e+03      99     116 ..     276     293 ..     263     295 .] 0.82

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 6.6
                            AAA_18 63 aleenss.......aleegknlvidghl 83
                                      +l en+s       ++  +knlv++  l
  gi|298675622|ref|YP_003727372.1| 11 TLSENASrvleryeKELGAKNLVLEKAL 38
                                      3333333344444444444555555544 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 2.8e-07
                            AAA_18   1 IlltGtpGvGKttlakeL.skrl.gf........gvnlrdvakenglllevdpealdeskrldedkldklldaleen 67 
                                       +++tG+pG+GKtt++  +  +r  ++         +   +++++  +++++d  +  ++  l++  +  + ++ + +
  gi|298675622|ref|YP_003727372.1|  83 VIVTGPPGTGKTTFCVQIlMERIrNNekcvffsfEEDAEHLVQQ-FMRYGWDIGEAIDKGYLEIFGMSIITSEEMTQ 158
                                       79*************88765555344555667754444444444.44444444423333333333332222222222 PP

                            AAA_18  68 ssaleegknlvidghlaelese 89 
                                       + ++  ++++v+d++ +   +e
  gi|298675622|ref|YP_003727372.1| 159 IVDSYRPDVVVFDSLNVFSNPE 180
                                       2245556666666666655555 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 3.4
                            AAA_18  99 LtaspeelleRlekRgye 116
                                       + as ++l++Rl+k +++
  gi|298675622|ref|YP_003727372.1| 276 MNASSKILRDRLQKNNNQ 293
                                       678999999999998754 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   8.3e-08   4.8e-05       7     105 ..      50     140 ..      44     178 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 8.3e-08
                                       HHHHHHHHSS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS-- CS
                             Rad51   7 vellekrsellqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtf 83 
                                        ++++   ++ ++ tG  +lD+ L+GGi+ g    + G  ++Gkt +c +      + +e    ++k+v+ + e   
  gi|298675622|ref|YP_003727372.1|  50 HDVNNIDVNIKRMGTGIPSLDDSLEGGIPKGFSVIVTGPPGTGKTTFCVQ------ILMERIRNNEKCVFFSFEE-- 118
                                       5666667788899**********************************965......5556667889999999887.. PP

                                       -GGGGHHHHHHTT--HHHHGGG CS
                             Rad51  84 rperlveiaerykldkeevlen 105
                                        +e+lv+   ry+ d  e++++
  gi|298675622|ref|YP_003727372.1| 119 DAEHLVQQFMRYGWDIGEAIDK 140
                                       4678888888888888888876 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   6.6e-07   0.00038       5      49 ..      83     127 ..      79     192 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 6.6e-07
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladp 49 
                                       +++tG+  +GKTt++ q++ e++ ++e++++++++++ +   +++
  gi|298675622|ref|YP_003727372.1|  83 VIVTGPPGTGKTTFCVQILMERIRNNEKCVFFSFEEDAEHLVQQF 127
                                       89*********************9***********9888655544 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   4.6e-07   0.00027      44      90 ..      77     123 ..      36     131 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 4.6e-07
                         IstB_IS21  44 iekkenivllGpsGvGKshlaialgveavraglsvlfvrvedLveel 90 
                                       i k  +++++Gp+G+GK+ + + + +e +r++ + +f++ e+  e+l
  gi|298675622|ref|YP_003727372.1|  77 IPKGFSVIVTGPPGTGKTTFCVQILMERIRNNEKCVFFSFEEDAEHL 123
                                       5666789****************************999987655554 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.3e-06   0.00074     115     161 ..      51     113 ..       8     130 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.3e-06
                             T2SSE 115 k...............ekiaevlrkavrerglilvsGgTgsGKttll.yallkeinksderiv 161
                                       +               + +++ l+  + +  +++v+G+ g+GKtt+   +l++ i ++++++ 
  gi|298675622|ref|YP_003727372.1|  51 DvnnidvnikrmgtgiPSLDDSLEGGIPKGFSVIVTGPPGTGKTTFCvQILMERIRNNEKCVF 113
                                       2444444444444455788888999999999**************984666677877766653 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   2.5e-06    0.0015       4      37 ..      82     122 ..      79     180 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.5e-06
                            AAA_24   4 kiliyGpsgiGKTtlakel.......gpkplfidtekGlks 37 
                                       +++++Gp+g+GKTt++ ++        +k +f+ +e+ + +
  gi|298675622|ref|YP_003727372.1|  82 SVIVTGPPGTGKTTFCVQIlmerirnNEKCVFFSFEEDAEH 122
                                       789**********************999*****99984433 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   2.6e-06    0.0015      13      56 ..      83     122 ..      77     175 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.6e-06
                            AAA_19  13 llvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAak 56 
                                       ++vt++pGtGKT+  ++i+ + ++++    e+++  +f + A +
  gi|298675622|ref|YP_003727372.1|  83 VIVTGPPGTGKTTFCVQILMERIRNN----EKCVFFSFEEDAEH 122
                                       79****************99999999....77888888777655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0     3e-06    0.0017      26      69 ..      82     130 ..      69     172 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3e-06
                            AAA_16  26 lvllsGesGvGKsslv.rellralekdg.giflrgkcdql...esaipy 69 
                                       +v+++G++G+GK++   + l+++++ ++ ++f++ + d     ++ ++y
  gi|298675622|ref|YP_003727372.1|  82 SVIVTGPPGTGKTTFCvQILMERIRNNEkCVFFSFEEDAEhlvQQFMRY 130
                                       79************98688889999996688855555544235555555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   5.5e-06    0.0032       1      22 [.      83     104 ..      83     180 .. 0.60

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 5.5e-06
                                       EEEESSTTSSHHHHHHHHHHHH CS
                               AAA   1 vllyGppGtGKTllakavakel 22 
                                       v+++GppGtGKT+++ ++  e 
  gi|298675622|ref|YP_003727372.1|  83 VIVTGPPGTGKTTFCVQILMER 104
                                       6899**********99988773 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.2     7e-06     0.004       2      21 ..      83     102 ..      82     134 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 7e-06
                                       EEEE--TTSSHHHHHHHHHH CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvle 21 
                                       v++TGppG+GKtT++ ++l 
  gi|298675622|ref|YP_003727372.1|  83 VIVTGPPGTGKTTFCVQILM 102
                                       89************988864 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.6e-05    0.0092       8      29 ..      83     104 ..      79     207 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.6e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleql 29 
                                       ++vtG++GtGKTt + ++l++ 
  gi|298675622|ref|YP_003727372.1|  83 VIVTGPPGTGKTTFCVQILMER 104
                                       79*************9999886 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       2.7   1.5e+03     199     216 ..       8      25 ..       3      62 .. 0.83
   2 !   15.6   0.0   1.8e-05      0.01      20      42 ..      83     105 ..      68     129 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.7
                            AAA_11 199 vltTlsgagsklleklak 216
                                       v tTls  +s++le+++k
  gi|298675622|ref|YP_003727372.1|   8 VHTTLSENASRVLERYEK 25 
                                       778888888888888765 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.8e-05
                            AAA_11  20 tliqGPPGtgKTktivellsqll 42 
                                       +++ GPPGtgKT++ v++l++ +
  gi|298675622|ref|YP_003727372.1|  83 VIVTGPPGTGKTTFCVQILMERI 105
                                       6899************9998764 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0     2e-05     0.012      32      71 ..      79     118 ..      72     130 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2e-05
                             AAA_7  32 nkkpvllvGptGtGKtviikd.llkkldkekylsltinfsa 71 
                                       ++ +v+++Gp GtGKt+ + + l++++  ++ ++++++f  
  gi|298675622|ref|YP_003727372.1|  79 KGFSVIVTGPPGTGKTTFCVQiLMERIR-NNEKCVFFSFEE 118
                                       67899*************9996777777.555666666544 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.8e-05     0.011       4      47 ..      83     124 ..      81     214 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.8e-05
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvl 47 
                                       v+VtG +GtGKt   +++l e    +++++ v++s  ++  + +
  gi|298675622|ref|YP_003727372.1|  83 VIVTGPPGTGKTTFCVQILMER--IRNNEKCVFFSFEEDAEHLV 124
                                       79******************99..56666666655555444444 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   9.6e-05     0.056       1      41 [.      83     120 ..      83     214 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.6e-05
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnped 41 
                                       ++++Gp+g+GK+t++ +    l++++ +++k  ++s + + 
  gi|298675622|ref|YP_003727372.1|  83 VIVTGPPGTGKTTFCVQ---ILMERIRNNEKCVFFSFEEDA 120
                                       6799***********99...444445444444444444443 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       7.8   4.5e+03      85     116 ..      33      62 ..       7      67 .. 0.50
   2 !   14.9   0.0   3.2e-05     0.018      23      96 ..      83     161 ..      72     200 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 7.8
                          ATPase_2  85 avpkaeleeilkeksklvfkaielllekikkk 116
                                       +++ka l   l++ + +++  ++++  +ik+ 
  gi|298675622|ref|YP_003727372.1|  33 VLEKALL--NLDNSRFKAKHDVNNIDVNIKRM 62 
                                       3333333..33455555566666666666655 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 3.2e-05
                          ATPase_2  23 yfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie......eeeekkklekalgiavpkaelee 93 
                                       + ++Gp g GKt++  +i+ ++   +++ +++ +++e++++ +++f++      e  +k +le   ++ + + e+ +
  gi|298675622|ref|YP_003727372.1|  83 VIVTGPPGTGKTTFCVQILMERIRNNEKCVFF-SFEEDAEHLVQQFMRygwdigEAIDKGYLEIFGMSIITSEEMTQ 158
                                       679****************9997767666664.79999999999998888877766666666666666666666666 PP

                          ATPase_2  94 ilk 96 
                                       i++
  gi|298675622|ref|YP_003727372.1| 159 IVD 161
                                       655 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   0.00021      0.12       1     112 [.      86     207 ..      86     216 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00021
                                       EE-TTSSHHHHHHHHHHHH.....TEEEEEH...HHHHHHHHHTTTSHSSHHHHCTSHHHH..HHHHHHHHHHHHHH CS
                            AAA_17   1 lGgPGsGKgtqceklveky.....gfthlsa...Gdllreeakrgglakardemrklplee..kkelqkeaaekiae 67 
                                       +G+PG GK+t c ++  +      +  ++s+    + l +   r g  +  ++++k++le+     ++ e + +i +
  gi|298675622|ref|YP_003727372.1|  86 TGPPGTGKTTFCVQILMERirnneKCVFFSFeedAEHLVQQFMRYGW-DIGEAIDKGYLEIfgMSIITSEEMTQIVD 161
                                       7***********99863322444466666665557777777777776.57777888777776677788888888888 PP

                                       HHHSSEEEEEE-SEEEETTEE.EESSHHHHHHHH..SEEEEEE--H CS
                            AAA_17  68 eakkkgvlvdghprikeqagf.ldglpkevleelkpdaiilleadp 112
                                         + + v++d   ++ ++++f  +g  ++v ++lk ++i+ l + +
  gi|298675622|ref|YP_003727372.1| 162 SYRPDVVVFDSLNVFSNPEEFrTAGTWRNVHRSLKRKKITSLMVTE 207
                                       8788888888888888888884467777888888888777776665 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00014      0.08      21      67 ..      79     125 ..      66     135 .. 0.86
   2 ?   -2.5   0.0         6   3.5e+03      94     106 ..     225     237 ..     223     258 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                                       SSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHH CS
                   Sigma54_activat  21 tdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelle 67 
                                       +  sv++tG  GtGK+++  +i  ++ r++++ v +   + +e+l++
  gi|298675622|ref|YP_003727372.1|  79 KGFSVIVTGPPGTGKTTFCVQILMERIRNNEKCVFFSFEEDAEHLVQ 125
                                       5689********************99999999999988888888776 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 6
                                       TSEEEEETGGGS- CS
                   Sigma54_activat  94 gGtlfLDeigelp 106
                                       +G++fLD + + +
  gi|298675622|ref|YP_003727372.1| 225 DGIIFLDTVPTND 237
                                       6999999986554 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00013     0.077       2      25 ..      83     102 ..      83     198 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00013
                            AAA_33   2 vllvGlpGsGKstlaerllkklga 25 
                                       v++ G+pG+GK+t+  ++l    +
  gi|298675622|ref|YP_003727372.1|  83 VIVTGPPGTGKTTFCVQIL----M 102
                                       7899**********98876....3 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00011     0.062       3      31 ..      83     111 ..      82     213 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                                       EEEEC-TTTCHHHHHHHHHHHHCTS-SCC CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaegklpq 31 
                                       vi++G++G GKTt+  ++ ++  +++ ++
  gi|298675622|ref|YP_003727372.1|  83 VIVTGPPGTGKTTFCVQILMERIRNNEKC 111
                                       89************999988766665333 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       4.2   2.4e+03      64      89 ..      10      35 ..       8      41 .. 0.79
   2 ?   12.2   0.0   0.00017     0.097       3      22 ..      83     104 ..      81     254 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 4.2
                                      H.CTT-HHHHHHHHHHHHTT-SEEEEE CS
                              cobW 64 t.lredllkelealeereerldviliE 89
                                      t l+e+++++le++e++      +++E
  gi|298675622|ref|YP_003727372.1| 10 TtLSENASRVLERYEKEL-GAKNLVLE 35
                                      448899999999999998.57777777 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00017
                                       EEEEESTTCCHHHHHHHHH..C CS
                              cobW   3 tvltGflGsGKTtLlnhll..e 22 
                                       +++tG++G+GKTt+  ++l  +
  gi|298675622|ref|YP_003727372.1|  83 VIVTGPPGTGKTTFCVQILmeR 104
                                       79************99999542 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00025      0.15       3      35 ..      87     120 ..      85     130 .. 0.83
   2 ?   -1.5   0.0         3   1.7e+03     116     128 ..     160     175 ..     141     204 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00025
                                       ESTTSSHHHHH.HHHHHHHHHTTE.EEEESSSTT CS
                   Thymidylate_kin   3 GlDGaGKttqa.ellkerlkeegikvvltrepgg 35 
                                       G  G+GKtt++ ++l+er++++ + v++++e++ 
  gi|298675622|ref|YP_003727372.1|  87 GPPGTGKTTFCvQILMERIRNNEKCVFFSFEEDA 120
                                       777******9858899999999977******986 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3
                                       S...E-SEEEEEESSH CS
                   Thymidylate_kin 116 l...kPdltflldvdp 128
                                           +Pd++++ ++ +
  gi|298675622|ref|YP_003727372.1| 160 VdsyRPDVVVFDSLNV 175
                                       2345899999988765 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00019      0.11       2      31 ..      83     113 ..      82     174 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00019
                                       EEEE--SSSSHHHH.HHHGGGGBS--EEEEE CS
                             AAA_5   2 vlLvGppGtgKsel.aerlaaalnreveyvq 31 
                                       v++ GppGtgK+++ ++ l ++++++   v 
  gi|298675622|ref|YP_003727372.1|  83 VIVTGPPGTGKTTFcVQILMERIRNNEKCVF 113
                                       89*********98636777788854444444 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00021      0.12       2      19 ..      83     100 ..      82     172 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00021
                            AAA_28   2 ivitGgestGKTtlleaL 19 
                                       +++tG+++tGKTt + ++
  gi|298675622|ref|YP_003727372.1|  83 VIVTGPPGTGKTTFCVQI 100
                                       89***********87443 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00023      0.13      21      38 ..      83     100 ..      78     126 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00023
                            AAA_30  21 avltGpAGtGKttalkal 38 
                                       +++tGp+GtGKtt   ++
  gi|298675622|ref|YP_003727372.1|  83 VIVTGPPGTGKTTFCVQI 100
                                       699*********976554 PP

>> PPV_E1_C  Papillomavirus helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00033      0.19     258     282 ..      76     100 ..      66     114 .. 0.87
   2 ?   -2.4   0.0       2.7   1.6e+03     223     246 ..     180     203 ..     161     211 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00033
                          PPV_E1_C 258 gvPkknclvllGppntGkslfamsl 282
                                       g+Pk  +++++Gpp tGk++f++ +
  gi|298675622|ref|YP_003727372.1|  76 GIPKGFSVIVTGPPGTGKTTFCVQI 100
                                       79********************875 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.7
                          PPV_E1_C 223 kevedegdWkeivkflryqgveli 246
                                       +e    g+W+++ + l+ +++  +
  gi|298675622|ref|YP_003727372.1| 180 EEFRTAGTWRNVHRSLKRKKITSL 203
                                       566778999999999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 1819.12
//
Query:       gi|298675623|ref|YP_003727373.1|  [L=455]
Description: dihydroorotase, multifunctional complex type [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-22   79.4   0.0    4.6e-22   78.8   0.0    1.2  1  Amidohydro_1  Amidohydrolase family
    1.4e-10   41.2   0.0    0.00059   19.4   0.0    2.4  2  Amidohydro_3  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8   0.0   5.1e-26   4.6e-22       3     320 ..      53     397 ..      51     426 .. 0.74

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 5.1e-26
                                       EE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTH.....HHHHHHH.HHHTS CS
                      Amidohydro_1   3 lPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattst.....giealle.aaeel 73 
                                       lP++IDaHvH++             +p++t +e   +g   a  +G+ttv+d+++t+++     +++  l+ a+++ 
  gi|298675623|ref|YP_003727373.1|  53 LPAGIDAHVHFR-------------EPGQTRKEDWYTGSCSAAAGGITTVIDHPNTAPPtidekSFNKKLNlASKKS 116
                                       8**********9.............*******************************999999997777777355558 PP

                                       SSEEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHHHHHTTEEEE CS
                      Amidohydro_1  74 plglrilggkvsldrgsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrdlpvai 150
                                       +++++i gg   ++  ++++   ++e  ++ +        +++++      +   +s+e   +al+e k+ ++  +i
  gi|298675623|ref|YP_003727373.1| 117 IVDFGINGG---VT-NNFDNLSRLWELGATAF--------GEIFM--AESTGELNISEESFNQALSEIKELGAVACI 179
                                       999999988...22.55555666666666665........33333..344566899********************* PP

                                       EETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEE.........EHCTCEEEHHHHHHHHHHHHHHCEE.. CS
                      Amidohydro_1 151 Haletkgevedaeaafgetiehgthlevaeslglldeikli.........lahgvhltpteaellkerlkeagva.. 216
                                       Ha +++      e   +++   ++h + +  ++  + ++ +           h +h++ +ea  ++++  ++  a  
  gi|298675623|ref|YP_003727373.1| 180 HAEDEDIRL-KNESLLKNDMSPQSHSRARPNICESTAVQKAvdmissfdtQSHFCHISTSEALGIIRN--QKYMAyk 253
                                       **5544444.6677777566666777777765555554444455566666999999998866666666..4444434 PP

                                       .....HHHHHHHH..............................SEHHHHHHHHHHHHTSCEEEEEECT......... CS
                      Amidohydro_1 217 .....hcpfsnsi..............................lrsgrealrkaldeGvkvglgtDga......... 249
                                            +      i                               r+ ++al +a++eG+  ++++D+a         
  gi|298675623|ref|YP_003727373.1| 254 gnrksS------ItcesaphhlflsdkswddlgsfgkmnpplrTRKSVQALVNAINEGTVDMVASDHAphrefekdm 324
                                       444540......24444455577777789*******************************************99887 PP

                                       .....TSSCCGGHHHHHHHHHHHHHHCCTT.TTHCHCHHHHHHHHHTHHHHHHTT-TT.TSSSS-TTSB--EEEECC CS
                      Amidohydro_1 250 .....asgnslnlleelrlalklqrgllye.deegglslkealrmaTingAkalgldd.kvGsievGkdADlvvvdl 319
                                             sg       ++  +l    +l    +++  ++l +++++++ n+Ak +gld+ ++G +++G+dADl++v++
  gi|298675623|ref|YP_003727373.1| 325 dikntPSGV-----PGVETLL----PLMLAgVKKNLFPLGKVIDVTSKNPAKRFGLDSnYKGLFKEGFDADLILVNP 392
                                       544443333.....3333333....22222367888********************85279**************77 PP

                                       ....C CS
                      Amidohydro_1 320 ....d 320
                                           +
  gi|298675623|ref|YP_003727373.1| 393 qdmrK 397
                                       53332 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   6.6e-08   0.00059       1      55 [.      43      96 ..      43     113 .. 0.83
   2 !   19.4   0.0   6.6e-08   0.00059     406     452 ..     350     397 ..     329     430 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 6.6e-08
                      Amidohydro_3  1 eviDakGrlvlPGFvDsHtHlagggvnlrllrlpdarvtslegvltavrdqagtt 55
                                      ++iDa+++l lP+++D+H H  + g   r  ++   ++++++g +t+v d+ +t+
  gi|298675623|ref|YP_003727373.1| 43 REIDADNALTLPAGIDAHVHFREPG-QTRKEDWYTGSCSAAAGGITTVIDHPNTA 96
                                      58******************99999.55677777778888888888888877764 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 6.6e-08
                      Amidohydro_3 406 eelsleealalyTrgpAkalgled.rkGtLevGadADlvvldadpldv 452
                                       + ++l ++++ ++++pAk++gl+   kG  ++G+dADl++ + + ++ 
  gi|298675623|ref|YP_003727373.1| 350 NLFPLGKVIDVTSKNPAKRFGLDSnYKGLFKEGFDADLILVNPQDMRK 397
                                       57899*******************545**************9555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2710.78
//
Query:       gi|298675624|ref|YP_003727374.1|  [L=383]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-27   96.6   2.8    2.6e-27   95.4   2.8    1.5  1  OrfB_IS605      Probable transposase
    1.7e-23   82.3   0.2    3.6e-23   81.3   0.2    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    1.8e-19   68.9   1.4    4.1e-19   67.8   1.4    1.6  1  HTH_OrfB_IS605  Helix-turn-helix domain
  ------ inclusion threshold ------
      0.013   15.6   0.3       0.03   14.5   0.3    1.6  1  zf-piccolo      Piccolo Zn-finger
      0.029   14.2   0.9       0.34   10.8   0.2    2.3  2  LemA            LemA family
       0.26   11.1   7.0       0.63    9.8   3.5    2.3  2  Phage_GP20      Phage minor structural protein GP20


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.4   2.8   8.8e-31   2.6e-27      10     117 ..     180     284 ..     167     286 .. 0.91

  Alignments for each domain:
  == domain 1  score: 95.4 bits;  conditional E-value: 8.8e-31
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsr 86 
                                       +++  + +++g+D+Gi+++a++++++   ++ ++r lk++ ++l+  +++l++k+k+s+ny+k + ++a++h+k+++
  gi|298675624|ref|YP_003727374.1| 180 KQTFYEVNTVGVDVGIKDFAVTSDGE---KIDNPRYLKNTIERLKVLQKRLSRKKKGSNNYRKLKHQIAKYHEKIAN 253
                                       45555789******************...************************************************ PP

                        OrfB_IS605  87 rrkhllhklathliktlkevgvetLnvgnmk 117
                                       +r +++hkl+++li ++++v +etLnv+++ 
  gi|298675624|ref|YP_003727374.1| 254 QREDFQHKLSNKLISENQAVTLETLNVKGLL 284
                                       ****************************986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.3   0.2   1.2e-26   3.6e-23       1      68 [.     298     367 ..     298     368 .. 0.98

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 1.2e-26
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpay.TSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       ++++ ++leyka++yG++++++ ++  +Sk C++Cg+ +++ +l++r+++Cp+C++ +drD+nA++Ni k
  gi|298675624|ref|YP_003727374.1| 298 WGSFVQKLEYKAEWYGKNIIKIGRFDpSSKICHVCGYYHQDlELKDREWECPDCKTIHDRDINASVNIKK 367
                                       99******************************************************************87 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.8   1.4   1.4e-22   4.1e-19       1      47 []       9      54 ..       9      54 .. 0.98

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 1.4e-22
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeegk 47
                                      M lkaykyr yP++ Q+e++a+++G++Rf+YN+aL+ + + ye+ gk
  gi|298675624|ref|YP_003727374.1|  9 M-LKAYKYRMYPNQIQQELIAKHIGACRFIYNWALENKLKSYEQDGK 54
                                      8.******************************************997 PP

>> zf-piccolo  Piccolo Zn-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.3     1e-05      0.03      28      55 ..     326     353 ..     322     356 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1e-05
                        zf-piccolo  28 kqvCnlCGFnptphltekkeWlclnCQt 55 
                                       +++C +CG+  ++   + +eW c  C t
  gi|298675624|ref|YP_003727374.1| 326 SKICHVCGYYHQDLELKDREWECPDCKT 353
                                       79***********999**********86 PP

>> LemA  LemA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.087   2.6e+02      36      82 ..      66     112 ..      52     116 .. 0.80
   2 ?   10.8   0.2   0.00011      0.34      57     108 ..     210     262 ..     181     273 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.087
                              LemA  36 evteaRakaaeaesveekaeaenqlssalsrllavaEnYPdLkanen 82 
                                       +v +  ++  ++ + ++ + a  +l++a+ +++     +P++k+++n
  gi|298675624|ref|YP_003727374.1|  66 RVLKQDHEWLKEINSQSLQGATLNLENAFTKFFREKSGFPKFKSKKN 112
                                       5555556667788889999999**********************987 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00011
                              LemA  57 enqlssalsrllavaEnY.PdLkanenfleLqeelegtEnriavaRrrYneav 108
                                        + l+++++rl +++ +   + k ++n+++L++++++  ++ia++R++++++ 
  gi|298675624|ref|YP_003727374.1| 210 PRYLKNTIERLKVLQKRLsRKKKGSNNYRKLKHQIAKYHEKIANQREDFQHKL 262
                                       55667777777777666414557899***********************8765 PP

>> Phage_GP20  Phage minor structural protein GP20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1     0.051   1.5e+02     113     136 ..      51      77 ..      24      89 .. 0.71
   2 ?    9.8   3.5   0.00021      0.63      30      94 ..     216     280 ..     203     289 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.051
                        Phage_GP20 113 edgelkg...LdeqikkLkesdkyLFe 136
                                       +dg+ +    L++qi  Lk+++++L e
  gi|298675624|ref|YP_003727374.1|  51 QDGKAISrfeLNKQIRVLKQDHEWLKE 77 
                                       455555444488888888888888765 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00021
                        Phage_GP20  30 lkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeyeakiadlkldnaielaLkeaka 94 
                                         e+lk  +k L+  kk +++  +L+ qi+++ +k++++ ++ + k+++  +++    +L++ ++
  gi|298675624|ref|YP_003727374.1| 216 TIERLKVLQKRLSRKKKGSNNYRKLKHQIAKYHEKIANQREDFQHKLSNKLISENQAVTLETLNV 280
                                       557788899999999********************************998777666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1601  (0.0892967); expected 358.6 (0.02)
Passed bias filter:                      664  (0.037035); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 2437.86
//
Query:       gi|298675625|ref|YP_003727375.1|  [L=216]
Description: phosphate uptake regulator PhoU [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.8e-39  131.9  10.3    1.7e-20   73.3   0.3    2.1  2  PhoU      PhoU domain


Domain annotation for each model (and alignments):
>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.4   4.6   2.4e-21   4.2e-17       2      88 ..      18     104 ..      17     105 .. 0.97
   2 !   73.3   0.3   9.5e-25   1.7e-20       2      89 .]     120     204 ..     119     204 .. 0.94

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 2.4e-21
                                       HHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHH CS
                              PhoU   2 rrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERi 78 
                                         m++++++ + d+ +al++ d ela+e ie+d+ id+  ++ie+s+  +la + pla dlr +++++++a+dlERi
  gi|298675625|ref|YP_003727375.1|  18 LNMGDTSQKVIIDSTKALRDLDLELADETIEMDNNIDDSAEDIEKSATHLLALQHPLAGDLRLIIASIKVATDLERI 94 
                                       68********************************************99999************************** PP

                                       HHHHHHHHHH CS
                              PhoU  79 gDhavniaer 88 
                                       +D   niae+
  gi|298675625|ref|YP_003727375.1|  95 SDLGINIAEI 104
                                       ********98 PP

  == domain 2  score: 73.3 bits;  conditional E-value: 9.5e-25
                                       HHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHH CS
                              PhoU   2 rrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERi 78 
                                        +maei+e+ml+++l+a+e+ d+ela+e  +rdde+d+l++    +l++++ ++  l   +  +++ll + r+lERi
  gi|298675625|ref|YP_003727375.1| 120 PKMAEITEDMLQKSLQAFENLDVELAKEAAARDDEVDKLFYGTWMELINMMVEDPTL---ITNATHLLFVLRYLERI 193
                                       68*****************************************99999999877776...678999*********** PP

                                       HHHHHHHHHHH CS
                              PhoU  79 gDhavniaerv 89 
                                       gDh+ ni+e+v
  gi|298675625|ref|YP_003727375.1| 194 GDHVSNICESV 204
                                       ********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1340.97
//
Query:       gi|298675626|ref|YP_003727376.1|  [L=913]
Description: DNA polymerase Pol2 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.3e-114  383.4   0.0   2.1e-114  382.8   0.0    1.2  1  DNA_pol_B       DNA polymerase family B
    8.4e-60  202.7   0.9    1.4e-59  202.0   0.9    1.3  1  DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
    7.6e-05   22.5   0.1    0.00073   19.3   0.0    2.1  2  DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the ex
     0.0013   18.8   0.1     0.0046   17.0   0.1    2.1  1  RNase_H_2       RNase_H superfamily


Domain annotation for each model (and alignments):
>> DNA_pol_B  DNA polymerase family B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  382.8   0.0  4.6e-118  2.1e-114       5     456 ..     400     850 ..     397     852 .. 0.90

  Alignments for each domain:
  == domain 1  score: 382.8 bits;  conditional E-value: 4.6e-118
                                       HHHHS-HHHHHHHHHHHHHHHTTBE-B-----.--SS....-S----BE----EEESS-EEEEEETTHHHHHHHHTT CS
                         DNA_pol_B   5 rvledgqqirveslLlrlakeegfilpdrtekkgkeee...gYqGatVlePkkglydkpvlvlDFaSLYPsiiqahN 78 
                                        v+ +gq+  ve lL+r++ ++g+++p +++++ +++e   + +G+ VlePkkgl d +v++lD++SLYP i++ahN
  gi|298675626|ref|YP_003727376.1| 400 DVVDGGQSSMVENLLFREFGKQGRVIPPKPDNRPDDNEqgeEIKGGEVLEPKKGLLD-NVVILDYKSLYPTIMMAHN 475
                                       57899*********************9866655444444436*************87.5889*************** PP

                                       -STTTCE-HCCHCC.T--BTT...TEEE-TCC-EEE-TTS---HHHHHHHHHHHHHHHHHHHHHCS--HHHHHHHHH CS
                         DNA_pol_B  79 lcyttlvaseeeak.eleaedeyleveveprlvefvkksvregllpklLkdllakRkaikkelkeekdefekalldk 154
                                       lcytt+v +++ +  ++            p++ efv+++v +g++p++L++ll++R ++kk++k+ +d  + +++d+
  gi|298675626|ref|YP_003727376.1| 476 LCYTTVVVNDHPNGeTI----------NPPSGGEFVNPDVLKGIVPSILETLLNQRSEVKKKMKSISDGDTYRMYDA 542
                                       *******9988865233..........3477899******************************************* PP

                                       HHHHHHHHHHHHHHHHTSTTSTT--HHHHHHHHHHHHHHHHHHHHHHHHT.....SSG.GGT-SS............ CS
                         DNA_pol_B 155 qQlalKvtaNsvYGftGvansrlpclalAasvTtiGRemLektkelvekk..aellsk.llalpeea.....eee.. 221
                                        QlalK++ Ns+YG+ G+a  rl++l lA+ vT++GRe++++t++l++++  + +l++ ++ lp+e+     +e+  
  gi|298675626|ref|YP_003727376.1| 543 TQLALKILLNSFYGYSGYARARLYSLTLANAVTSYGRENIQNTRDLINNNirKVVLKDnQAYLPDEIspedeSEDvi 619
                                       *************************************************9743334443444455655654323489 PP

                                       T-EEEEEBSSEEEEE-.....S-SSHHHHHHHHHHHHHHHHT.TSTTT--EEEEEEEEEEEEEETTEEEEEEEEESS CS
                         DNA_pol_B 222 klkviYGDTDSvfiel.....kvkdveellkigkelaeevseklfkkplklefekvykkllLisKKkYaglkvekts 293
                                       +l+v+YGDTDSvfi++     +  ++e++  +g+ +ae+vs+  +++p++lefe + k+ l+++KK+Ya  ++e+++
  gi|298675626|ref|YP_003727376.1| 620 NLSVVYGDTDSVFIHCspeynNDISLEDAECVGTRIAEKVSQ-SLPDPMELEFESIAKRGLFLAKKRYALWVFEQEN 695
                                       ****************8888666899999*************.99************************99999665 PP

                                       TTS..EEEEESSGGGSTTS-HHHHHHHHHHHHHHSSS....S-HHHHHHHHHHHHHHHH.HHHHTT-S-GGGG-EEE CS
                         DNA_pol_B 294 kan..klliKGvdlvRrdncklvkevikkvlelllkdeteersleeglealksilkdvl.eeleenkvplekfvlsk 367
                                       ++   ++ +KG+++vRrd+c+l++++ ++vlel+lk+     ++++++e++ks++++v+  ++++ k  ++++++++
  gi|298675626|ref|YP_003727376.1| 696 DEWedSIKVKGMETVRRDWCELTSKTLNRVLELVLKE----GDVDKAVEYVKSVVNRVRnIDVQKDKDVIDDLTMTR 768
                                       544546*******************************....******************89**************** PP

                                       EESS.CCCSSGCCSHHHHHHHHHHHHCSS---TTCEEEEEEBETSS.....SS-GGGTEEEHHHHHHCCSEB-HHHH CS
                         DNA_pol_B 368 elskepenyksknlphlevakrlkkrneeapevgdrisYvivekkkevkkknllaseraedpeyvleknlpidieyY 444
                                        +sk++++yksk+ phl+v+++ kkr +  p +g+r+++viv+        n+l  +raedpeyv+e+nl++d++yY
  gi|298675626|ref|YP_003727376.1| 769 LYSKKKDSYKSKQ-PHLTVIEKTKKRTGISPPIGERVPFVIVAG-------NDLFVNRAEDPEYVRENNLTLDVDYY 837
                                       ************9.******************************.......569*********************** PP

                                       HH.TTHHHHHHHH CS
                         DNA_pol_B 445 ls.qllkevarll 456
                                       ++ q+l++v+r+l
  gi|298675626|ref|YP_003727376.1| 838 IKkQILPPVERIL 850
                                       ***********97 PP

>> DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.0   0.9     3e-63   1.4e-59       3     337 .]      26     332 ..      24     332 .. 0.87

  Alignments for each domain:
  == domain 1  score: 202.0 bits;  conditional E-value: 3e-63
                                       CTTSEEEEEEEE---EEEEEESSCGGHHHHHHHHHHHCCTTCCCEEEEEEEECCCCEECCTSSCCHHCEEEEEESST CS
                    DNA_pol_B_exo1   3 eegksvcvnvfgfkpyfYceapdgkeleevkeelkelyeelskkvtkivkvelvlkkslygyekkpvpylkvsvsnp 79 
                                       e+g svc+ v gf+pyfY+ + d++ l+ +++ +k +++         ++ve+v k + +gy++ ++p+lk+++ +p
  gi|298675626|ref|YP_003727376.1|  26 EDGSSVCCFVPGFEPYFYANVADDSYLQTLPQFIKNKFDTV-------KDVEPVQKFEPIGYQESKKPMLKITTFYP 95 
                                       799*******************9999988888888777655.......5688************************* PP

                                       CHHHHHHHHHHHCCCCCCCCSSS--HHHHHHHHCTS-TTCEEEEETEEEEGCC--C-.SEEEEEETTTSCEETTTCC CS
                    DNA_pol_B_exo1  80 nelkkirkelspleeivdvyeydvdylerflidnkivgfgwysvkkylvraegkisncdveidcdvddliakpkese 156
                                       +++++ir+ ++ le i+dvye+d+ +  rf+id++++g++  s +    +a++  s +d +++c  d++i++++ +e
  gi|298675626|ref|YP_003727376.1|  96 KNVPEIRDDVQGLEGIEDVYETDILFKNRFMIDKGLHGMALVSAE----PASTSESINDRDVKC--DNIITSYNVEE 166
                                       *****************************************9999....555555555555555..55666666555 PP

                                       ....S-EEE..EEEEEEETEETTSEETTTT..--EEEEEEEE.CCTC.SS.SEEEEEEECCCTSS----EE--SSTC CS
                    DNA_pol_B_exo1 157 ....pplrv..lsFDIeckskkgkfpdaensedpiiqIscvl.dglgekepearklftlrecaseeeedfeltpkpe 226
                                           p++ +  l+FDIec   +g +p++e    pii+Is+ +  +++    +++++++ ++                
  gi|298675626|ref|YP_003727376.1| 167 inkiPNIGLkyLAFDIECLPPEGGMPEPES--SPIIMISLSFePEYK---GNNTLVLVCKNLK------------D- 225
                                       55566655455*******************..**********54444...6777888888888............3. PP

                                       STTEEEEEESSHHHHHHHHHHHHHHH--SEEEESSTTTTHHHHHHHHHHHCCTCCHCG.SCCS.CTCEECCCCESEE CS
                    DNA_pol_B_exo1 227 ypgvkvlefdsEkelLqaflefikqydPdvitgYNidnFDlpYilnRakelykvklsklgrln.kggrskvseigfs 302
                                         ++++ +fd+E ++L++f++++++ydPdv++gYN ++FD+pYi++Ra++l++   s + r+  +g ++  ++ g +
  gi|298675626|ref|YP_003727376.1| 226 -VESDIEIFDEEEDMLTRFFDIFQEYDPDVVVGYNMNDFDIPYIKDRADYLNNKGASIVPRVGrDGRLMTYRRLGTR 301
                                       .4779999********************************************9887777777757788888888888 PP

                                       EEEECEEEETTSEEEEHHHHHHHHSSSSG-SHHHH CS
                    DNA_pol_B_exo1 303 kqarekvkisgrihlDlyrvvkrklklpsYkLnav 337
                                           + v++ gri++D++++++++++l+ Y+L +v
  gi|298675626|ref|YP_003727376.1| 302 ----TMVSMTGRIVMDTLPLIRQQFSLKRYTLRNV 332
                                       ....****************************987 PP

>> DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the exonuclease domain of PolB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.6e-07   0.00073      35      72 ..     234     272 ..     209     287 .. 0.86
   2 ?    0.3   0.0      0.11   4.8e+02      79     111 ..     349     380 ..     338     393 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.6e-07
                    DNA_pol_B_exo2  35 ssekelikkffegvekkkpql.VsfngrgfDlpvleyra 72 
                                       ++e++++++ff++++++ p + V++n + fD+p ++ ra
  gi|298675626|ref|YP_003727376.1| 234 DEEEDMLTRFFDIFQEYDPDVvVGYNMNDFDIPYIKDRA 272
                                       5799**************986279***********9998 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.11
                    DNA_pol_B_exo2  79 apkyfdegdedrekkwnnylsrystrhlDLmdl 111
                                       + +y+++g  +++kk+ +y  r s+  l L+  
  gi|298675626|ref|YP_003727376.1| 349 MVEYWNDGG-EKTKKFIDYARRDSELALELVTK 380
                                       567999998.79999999*99999988888655 PP

>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1     1e-06    0.0046      41     146 ..     233     377 ..     178     385 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1e-06
                         RNase_H_2  41 peeekailelflellekk..kalvtfngksFDvpflkrlf...kkyklde........................... 85 
                                        +ee+ +l  f ++++++  + +v +n + FD+p++k+++   +    ++                           
  gi|298675626|ref|YP_003727376.1| 233 FDEEEDMLTRFFDIFQEYdpDVVVGYNMNDFDIPYIKDRAdylN----NKgasivprvgrdgrlmtyrrlgtrtmvs 305
                                       345556665566888888546699****************4441....23355577788888888887776666655 PP

                         RNase_H_2  86 .eefrhiDLlkelrkkkl.esysLksvekelgierreedlsGsqavklyqe..........ylrtgdeellek 146
                                          +  +D l  +r++   ++y L +v kel  + +  d++ +q+v+++++          y r+ +e +le 
  gi|298675626|ref|YP_003727376.1| 306 mTGRIVMDTLPLIRQQFSlKRYTLRNVSKELLGREK-LDVEPHQMVEYWNDggektkkfidYARRDSELALEL 377
                                       555566677777777665799999999999888777.699999999999853333344343766666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (913 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.74u 0.31s 00:00:01.05 Elapsed: 00:00:00.47
# Mc/sec: 5804.47
//
Query:       gi|298675627|ref|YP_003727377.1|  [L=876]
Description: signal transduction histidine kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-80  269.2  33.0    3.8e-80  268.7  33.0    1.2  1  MASE3          Membrane-associated sensor domain
      7e-46  154.8   6.1      6e-19   68.2   0.0    3.9  4  PAS_9          PAS domain
    5.6e-39  132.6   0.2    7.6e-14   51.7   0.0    3.7  3  PAS            PAS fold
    9.5e-31  105.7   2.5    9.5e-31  105.7   2.5    2.7  3  HisKA_2        Histidine kinase
    2.7e-29  101.6   0.0    4.4e-09   36.6   0.0    3.7  3  PAS_4          PAS fold
    8.5e-24   83.1   0.0      5e-08   32.8   0.0    3.8  3  PAS_8          PAS domain
    5.5e-18   65.0   0.0    1.8e-05   25.0   0.1    3.5  3  PAS_3          PAS fold
    3.9e-09   37.0   0.8    2.8e-08   34.3   0.3    2.6  2  HATPase_c      Histidine kinase-, DNA gyrase B-, and HSP90-li
    4.7e-09   36.8   0.0    5.5e-05   23.7   0.0    3.5  3  PAS_10         PAS domain
    3.1e-06   27.2   0.0    5.8e-06   26.3   0.0    1.4  1  HATPase_c_2    Histidine kinase-like ATPase domain
      6e-06   26.9   0.2    1.9e-05   25.3   0.2    1.9  1  HWE_HK         HWE histidine kinase
    2.1e-05   24.7   2.2      0.031   14.5   0.0    5.0  4  PAS_7          PAS fold
  ------ inclusion threshold ------
      0.011   16.3   0.7      0.093   13.3   0.3    2.5  2  Vac14_Fab1_bd  Vacuolar 14 Fab1-binding region
      0.062   13.1   0.2        0.2   11.5   0.2    1.8  1  HATPase_c_3    Histidine kinase-, DNA gyrase B-, and HSP90-li


Domain annotation for each model (and alignments):
>> MASE3  Membrane-associated sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  268.7  33.0     3e-83   3.8e-80       1     226 []      35     271 ..      35     271 .. 0.99

  Alignments for each domain:
  == domain 1  score: 268.7 bits;  conditional E-value: 3e-83
                             MASE3   1 islenyllfHtllElfsivvallifliawntrkftknnyllflGiaflfvglldllHtlsykgmpiftessanlatq 77 
                                       isl+nyllfH+l+Elfsi++al++f++++++++f++nnyl+f+Gia++fv+ +d+lHtlsy+ m++f++ ++nlatq
  gi|298675627|ref|YP_003727377.1|  35 ISLSNYLLFHVLVELFSILIALMVFILVLKSKHFLENNYLIFIGIAYFFVAGFDILHTLSYENMGVFSSLGSNLATQ 111
                                       6899************************************************************************* PP

                             MASE3  78 lwiaaRllealslllavlllkrkv...........lrayavflvyalvtlllllsifypkifPalfiegsGlTpfki 143
                                        w+ aR++e++sllla++++ +k+           +  + vfl++a+v+++lll+if++++fP+++i+g+GlT fki
  gi|298675627|ref|YP_003727377.1| 112 VWVTARYIESISLLLAPVFFVSKFkqsikldlsrkTDYRVVFLLFAVVSFILLLTIFHWGVFPDCYIKGVGLTAFKI 188
                                       *********************99999********988999************************************* PP

                             MASE3 144 isEyliilllllalllllrrrkkfekkvlrlllaalvllilsellftlyvsvydilnllGHlfkilsfyliykaivv 220
                                       isEy+i+++ll +l+ll+r+r  f+ +v +ll+++++l+i++e++ftlyv+vy+iln+lGH+fk++sfy+i+ ai+ 
  gi|298675627|ref|YP_003727377.1| 189 ISEYIISIILLGSLVLLYRYRAYFSVYVQNLLSLSIFLTIIAEFTFTLYVDVYGILNILGHYFKLFSFYFIFLAIID 265
                                       ***************************************************************************** PP

                             MASE3 221 tgveeP 226
                                       tg+ +P
  gi|298675627|ref|YP_003727377.1| 266 TGFYRP 271
                                       ***998 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.2   0.0   4.7e-22     6e-19       2     104 .]     298     402 ..     297     402 .. 0.97
   2 !   34.3   0.2   1.7e-11   2.1e-08       4     104 .]     445     549 ..     442     549 .. 0.93
   3 !   52.9   0.4   2.8e-17   3.6e-14       2     104 .]     573     672 ..     572     672 .. 0.91
   4 ?   -1.7   0.0       2.6   3.4e+03      60      80 ..     852     872 ..     818     875 .. 0.73

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 4.7e-22
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk....kerevevvlirknge 74 
                                       ++++  +++ +il++N++a+ l+Gys++evlg ++++++  +++ +++l++ l++ +     + + +e+ ++rk+ge
  gi|298675627|ref|YP_003727377.1| 298 EAVITLDSNEKILSWNKGAEHLFGYSKDEVLGEPLSQFI--PSYKHCNLSNHLNNSSFnganNSQKFEIKMVRKSGE 372
                                       56777789999****************************..************************************ PP

                             PAS_9  75 tfwvlltaspvkdddgelvgiivilrDite 104
                                       +f++l+++s  kd++g++ g+i+ + Dite
  gi|298675627|ref|YP_003727377.1| 373 KFYALMSCSVSKDGEGNISGAICYVLDITE 402
                                       *****************************8 PP

  == domain 2  score: 34.3 bits;  conditional E-value: 1.7e-11
                             PAS_9   4 ili.dnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.....kerevevvlirknge 74 
                                       i+i  npd+ i  +N+a +++lGys++e+ gk +++++  +++ + +++++++ +         + +e+ ++++n e
  gi|298675627|ref|YP_003727377.1| 445 IIIaLNPDFSIKLVNRAGREILGYSKNELKGKTLFEFI--PKRYALEVDKVIKGLMFqrnvsLIEYFETAIVNRNLE 519
                                       566799***888**************************..99999999999998888899999999*********** PP

                             PAS_9  75 tfwvlltaspvkdddgelvgiivilrDite 104
                                       +  +  + + vk+dd e++ i++  +Dite
  gi|298675627|ref|YP_003727377.1| 520 KRIIAWNGRIVKNDDYEITCILISGNDITE 549
                                       *******************999*******8 PP

  == domain 3  score: 52.9 bits;  conditional E-value: 2.8e-17
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfw 77 
                                       d+i+i++++g+i+ aN+ a+++ Gy+  e++g +i d+    ++ ++++ +++++  + k +++e+++ +k+g+ fw
  gi|298675627|ref|YP_003727377.1| 573 DAIFIIDTEGNIIEANKVAANMHGYTVSELIGSNIMDIE--TEDVAQKFPNLVQRVLDqKWFDEEITHKKKDGTVFW 647
                                       7899999********************************..8888888888888888889***************** PP

                             PAS_9  78 vlltaspvkdddgelvgiivilrDite 104
                                       v+++a  +  +++ +++  +i rDite
  gi|298675627|ref|YP_003727377.1| 648 VEVSAEYFELENQYYIL--AIERDITE 672
                                       ********777666666..*******8 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 2.6
                             PAS_9  60 kerevevvlirkngetfwvll 80 
                                        + ++++++ + ng++f +++
  gi|298675627|ref|YP_003727377.1| 852 DQINGTMEFENCNGTKFTIKF 872
                                       478899999999999998765 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   0.0     6e-17   7.6e-14       5     113 .]     291     400 ..     288     400 .. 0.91
   2 !   26.4   0.0   4.2e-09   5.4e-06      10     113 .]     442     547 ..     433     547 .. 0.88
   3 !   50.4   0.1   1.5e-16   1.9e-13       2     101 ..     563     660 ..     562     670 .. 0.84

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 6e-17
                                       HHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEEE CS
                               PAS   5 aileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda.elaelleqlleqgeesrageisfk 80 
                                       +il++l+++++ +D + +il +N+ ae l+G+s +evlg++l+ +i+  ++    + l     + +++s+ +ei+  
  gi|298675627|ref|YP_003727377.1| 291 QILDQLHEAVITLDSNEKILSWNKGAEHLFGYSKDEVLGEPLSQFIPSYKHCnLSNHLNNSSFNGANNSQKFEIKMV 367
                                       79*********************************************998884444444556888899999999999 PP

                                       CTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  81 lrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       ++ g+++++++ +s   d++g+i g+++ + di
  gi|298675627|ref|YP_003727377.1| 368 RKSGEKFYALMSCSVSKDGEGNISGAICYVLDI 400
                                       99**************************99987 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 4.2e-09
                                       SSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEEC..TTS CS
                               PAS  10 lpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfkl..rdg 84 
                                       + + i++++ d  i +vN+a +e+lG+s +e+ gk+l+++i+  +  e+ + ++ l+ q++ s ++        r+ 
  gi|298675627|ref|YP_003727377.1| 442 AGSIIIALNPDFSIKLVNRAGREILGYSKNELKGKTLFEFIPKRYALEVDKVIKGLMFQRNVSLIEYFETAIvnRNL 518
                                       77899************************************988777**************9999988777788888 PP

                                       SEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  85 rpihlevraspvrdaggeilgflgvlrdi 113
                                       +++ +  + + v + + ei+++l  ++di
  gi|298675627|ref|YP_003727377.1| 519 EKRIIAWNGRIVKNDDYEITCILISGNDI 547
                                       88888888888888888888888888887 PP

  == domain 3  score: 50.4 bits;  conditional E-value: 1.5e-16
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda.elaelleqlleqgeesragei 77 
                                       ++r ++e++ d+if++D  g+i+++N+ a+ + G++ +e++g++++d   e+  a +++ l++++l   +++ ++ei
  gi|298675627|ref|YP_003727377.1| 563 RYRLLFENAGDAIFIIDTEGNIIEANKVAANMHGYTVSELIGSNIMDIETED-VAqKFPNLVQRVLD--QKWFDEEI 636
                                       89********************************************666555.44488888877776..589999** PP

                                       EEECTTSSEEEEEEEEEEEEETTE CS
                               PAS  78 sfklrdgrpihlevraspvrdagg 101
                                       + k++dg+++++ev a  +  + +
  gi|298675627|ref|YP_003727377.1| 637 THKKKDGTVFWVEVSAEYFELENQ 660
                                       **************9987766655 PP

>> HisKA_2  Histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       3.4   4.4e+03      16      40 ..     397     421 ..     393     423 .. 0.84
   2 ?   -2.9   0.0       5.8   7.4e+03      13      41 ..     599     627 ..     597     644 .. 0.76
   3 !  105.7   2.5   7.5e-34   9.5e-31       1      76 []     683     758 ..     683     758 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.4
                           HisKA_2  16 lLslqarkakdeevkealresqnRv 40 
                                       +L++  rk  +++ +++ +e+++Rv
  gi|298675627|ref|YP_003727377.1| 397 VLDITERKQYEQQLQKMHDELEKRV 421
                                       6888899999999999999999999 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.8
                           HisKA_2  13 isslLslqarkakdeevkealresqnRvl 41 
                                       +s l+  +  ++++e+v + + ++ +Rvl
  gi|298675627|ref|YP_003727377.1| 599 VSELIGSNIMDIETEDVAQKFPNLVQRVL 627
                                       66677777788888888888888888886 PP

  == domain 3  score: 105.7 bits;  conditional E-value: 7.5e-34
                           HisKA_2   1 EihHRvkNnLqvisslLslqarkakdeevkealresqnRvlsialiheeLyksedletvdfseylekLvenlfksy 76 
                                       EihHRvkNnLqvisslL+lq+++++d++v +a++esqnRv+sial he+Ly+s+d+ ++df++y+++L++ l+++y
  gi|298675627|ref|YP_003727377.1| 683 EIHHRVKNNLQVISSLLNLQSTNFEDKSVIKAFEESQNRVRSIALAHEKLYNSSDMVSIDFGNYIQTLTDYLLQAY 758
                                       9***********************************************************************9986 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   4.7e-11     6e-08       1     110 []     293     405 ..     293     405 .. 0.92
   2 !   27.9   0.0   1.7e-09   2.2e-06       6     109 ..     444     551 ..     439     552 .. 0.81
   3 !   36.6   0.0   3.4e-12   4.4e-09       1     110 []     568     675 ..     568     675 .. 0.87

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 4.7e-11
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegee..piefleelll. 74 
                                       ld+l +a++ ld++ ++l +N+ a++lfg++ +e+lG++l ++ p     +l+++l+     ++  +++f++ +++ 
  gi|298675627|ref|YP_003727377.1| 293 LDQLHEAVITLDSNEKILSWNKGAEHLFGYSKDEVLGEPLSQFIPSYKHCNLSNHLNNSSFNGAnnSQKFEIKMVRk 369
                                       7999*******************************************999999999886655442278999999999 PP

                             PAS_4  75 pgeerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                       +ge  + +++++  +d +G + g+++++ DiTer++
  gi|298675627|ref|YP_003727377.1| 370 SGEKFYALMSCSVSKDGEGNISGAICYVLDITERKQ 405
                                       999999****************************85 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 1.7e-09
                             PAS_4   6 dalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.....pge 77 
                                        ++++l+pd+ +  +N+a++e++g++  el Gktl+e+ p++ a +++  ++ ++ ++  ++  e+  +     + e
  gi|298675627|ref|YP_003727377.1| 444 SIIIALNPDFSIKLVNRAGREILGYSKNELKGKTLFEFIPKRYALEVDKVIKGLMFQR-NVSLIEYFETaivnrNLE 519
                                       578999**********************************955555555555555443.333333333367878*** PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerr 109
                                        r++ ++ + +++++ e+  +l+ + DiTer+
  gi|298675627|ref|YP_003727377.1| 520 KRIIAWNGRIVKNDDYEITCILISGNDITERK 551
                                       ******************************98 PP

  == domain 3  score: 36.6 bits;  conditional E-value: 3.4e-12
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll..p 75 
                                       +++  da++++d++g+++ aN+ aa + g++  el+G+   ++ +e++a+ + + ++rvl+++  ++++e+++   +
  gi|298675627|ref|YP_003727377.1| 568 FENAGDAIFIIDTEGNIIEANKVAANMHGYTVSELIGSNIMDIETEDVAQKFPNLVQRVLDQK--WFDEEITHKkkD 642
                                       7899**********************************************************7..666666666668 PP

                             PAS_4  76 geerhyelrl..lPlrdesGevigvlvisrDiTerrr 110
                                       g   ++e+++  + l++   +   +l+i rDiTer+r
  gi|298675627|ref|YP_003727377.1| 643 GTVFWVEVSAeyFELEN---Q-YYILAIERDITERKR 675
                                       88889898885555544...3.6899999******97 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.0   1.1e-10   1.4e-07       2      51 ..     288     338 ..     287     343 .. 0.89
   2 !   14.2   0.0   2.6e-05     0.034      14      55 ..     446     488 ..     434     500 .. 0.78
   3 !   32.8   0.0   3.9e-11     5e-08       2      45 ..     563     607 ..     562     632 .. 0.82

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 1.1e-10
                             PAS_8   2 rlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpv 51 
                                       ++ +++++++++++ +d +++i+ +N+ a++l+Gys ++++ge+l q++p 
  gi|298675627|ref|YP_003727377.1| 288 KHAQILDQLHEAVITLDSNEKILSWNKGAEHLFGYSkDEVLGEPLSQFIPS 338
                                       6789*************4456************************988875 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 2.6e-05
                             PAS_8  14 iavvd.lgdrivdvNqaalellGys.adlkgellgqllpvlrpl 55 
                                       i+ ++ +   i  vN+a  e+lGys ++lkg++l +++p  + l
  gi|298675627|ref|YP_003727377.1| 446 IIALNpDFS-IKLVNRAGREILGYSkNELKGKTLFEFIPKRYAL 488
                                       344564455.99*******************9998777766655 PP

  == domain 3  score: 32.8 bits;  conditional E-value: 3.9e-11
                             PAS_8   2 rlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgell 45 
                                       r+r lfe++ d+i+++d +g+ i+++N+ a+ + Gy+  +l+g+ +
  gi|298675627|ref|YP_003727377.1| 563 RYRLLFENAGDAIFIIDtEGN-IIEANKVAANMHGYTvSELIGSNI 607
                                       9****************6766.***************777777655 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   6.9e-07   0.00088       2      88 ..     310     396 ..     309     397 .. 0.89
   2 !   16.5   0.0     6e-06    0.0077       4      85 ..     458     540 ..     455     542 .. 0.87
   3 !   25.0   0.1   1.4e-08   1.8e-05       2      76 ..     585     656 ..     584     665 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 6.9e-07
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge..pyegeyRirrkdGeyrwveararvir 76 
                                       +++++  e+++Gys++e+lg    + +++      ++ ++l+++  +g+  + ++e++++rk+Ge ++   +++v +
  gi|298675627|ref|YP_003727377.1| 310 LSWNKGAEHLFGYSKDEVLGE--PLSQFIPSYKHCNLSNHLNNSSFNGAnnSQKFEIKMVRKSGEKFYALMSCSVSK 384
                                       79*******************..999999999999999999999977765444899********************* PP

                             PAS_3  77 dengkpvrvigv 88 
                                       d +g++   i++
  gi|298675627|ref|YP_003727377.1| 385 DGEGNISGAICY 396
                                       ****99988875 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 6e-06
                             PAS_3   4 vserveeilGyspeellgkveswldlvhpeDrervrealqealkkge..py.egeyRirrkdGeyrwveararvird 77 
                                       v+++ +eilGys++el+gk  ++ +++      +v + ++ ++ ++    +  +e  i++++ e r + + +r++++
  gi|298675627|ref|YP_003727377.1| 458 VNRAGREILGYSKNELKGK--TLFEFIPKRYALEVDKVIKGLMFQRNvsLIeYFETAIVNRNLEKRIIAWNGRIVKN 532
                                       789999*************..*********************955554244678899******************99 PP

                             PAS_3  78 engkpvrv 85 
                                       ++ +++++
  gi|298675627|ref|YP_003727377.1| 533 DDYEITCI 540
                                       88777765 PP

  == domain 3  score: 25.0 bits;  conditional E-value: 1.4e-08
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvir 76 
                                       i +++   ++ Gy+ +el+g+  +++d+   +  +++ + +q++l+++  +++e+  ++kdG+++wve +a+++ 
  gi|298675627|ref|YP_003727377.1| 585 IEANKVAANMHGYTVSELIGS--NIMDIETEDVAQKFPNLVQRVLDQKW-FDEEITHKKKDGTVFWVEVSAEYFE 656
                                       77888999*************..*****99999************7777.9********************9984 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       4.4   5.6e+03      88     109 ..     632     651 ..     617     653 .. 0.62
   2 !   34.3   0.3   2.2e-11   2.8e-08       5     108 ..     783     872 ..     779     875 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.4
                                       TTTEEEEEEETTTEEEEEEEEE CS
                         HATPase_c  88 mgGeiwvesepgrGttftftlp 109
                                       ++ ei+ ++  + Gt f++++ 
  gi|298675627|ref|YP_003727377.1| 632 FDEEITHKK--KDGTVFWVEVS 651
                                       444555544..55999999875 PP

  == domain 2  score: 34.3 bits;  conditional E-value: 2.2e-11
                                       HHHHHHHHHHHHHHHHHS...TTTEEEEEEEEEETEEEEEEEESSSSSTT.HHHTGTCSTTCHHCSTCHTSTSSSHH CS
                         HATPase_c   5 rLrqiisnlvdNavkfat...kageieveikaseddlvisveDnGiGipk.edlkklfekfsqddstkrggggtGlG 77 
                                        L  i+++lv+N++k+a    ++g+i v+ + ++  +++ v DnG Gip+  d++                    lG
  gi|298675627|ref|YP_003727377.1| 783 PLGIIVNELVTNSLKHAFsdkSSGQINVSFTEDDSVYTLIVDDNGDGIPEyVDIN----E------------TDSLG 843
                                       67779***********445336667777777555799999*********944444....2............4559* PP

                                       HHHHHHHHHHTTTEEEEEEETTTEEEEEEEE CS
                         HATPase_c  78 lsivkklvelmgGeiwvesepgrGttftftl 108
                                       l +v++lv++++G++++e+    Gt+ft+++
  gi|298675627|ref|YP_003727377.1| 844 LQLVNSLVDQINGTMEFENCN--GTKFTIKF 872
                                       *****************9999..*****987 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   4.3e-08   5.5e-05       4     106 .]     292     401 ..     290     401 .. 0.74
   2 ?   -0.7   0.0       1.7   2.2e+03      12      68 ..     446     503 ..     435     548 .. 0.66
   3 !    8.4   0.0    0.0024       3.1       8      87 ..     571     652 ..     565     662 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 4.3e-08
                            PAS_10   4 lLnstpieltflDdnlqirrFtpaakklfklipadv.Grpladihpkkavknv.....eeviealrtgekdevevvv 74 
                                       +L+++  +++ lD+n +i+ +++ a++lf + +++v G+pl+++ p+ +  n+     ++ ++   +++k e ++v+
  gi|298675627|ref|YP_003727377.1| 292 ILDQLHEAVITLDSNEKILSWNKGAEHLFGYSKDEVlGEPLSQFIPSYKHCNLsnhlnNSSFNGANNSQKFEIKMVR 368
                                       5777788999********************9987644*******888444444111113444555566666666666 PP

                            PAS_10  75 pkngkwv.lvrylpyrdedgeiaGvvetfvDit 106
                                       ++ +k++ l+  +  +d +g+i G++ +++Dit
  gi|298675627|ref|YP_003727377.1| 369 KSGEKFYaLMSCSVSKDGEGNISGAICYVLDIT 401
                                       677777526777788899**************7 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.7
                            PAS_10  12 ltflDdnlqirrFtpaakklfklipadv.Grpladihpkkavknveeviealrtgekd 68 
                                       ++ l+ +  i+  ++a ++++ + ++++ G +l ++ pk++  +v +vi+ l  ++++
  gi|298675627|ref|YP_003727377.1| 446 IIALNPDFSIKLVNRAGREILGYSKNELkGKTLFEFIPKRYALEVDKVIKGLMFQRNV 503
                                       5666666777777777777777766665599999999999999999999988877763 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0024
                            PAS_10   8 tpieltflDdnlqirrFtp.aakklfklipadvGrpladihpkkavknveeviealrtgek.devevvvpkngkwvl 82 
                                       +  ++  +D++ +i+  ++ aa+++   +++ +G ++ di +++  +++ ++++++ +++  de+ ++ +k+g+++ 
  gi|298675627|ref|YP_003727377.1| 571 AGDAIFIIDTEGNIIEANKvAANMHGYTVSELIGSNIMDIETEDVAQKFPNLVQRVLDQKWfDEEITHKKKDGTVFW 647
                                       555666778888888888867789999999*********************99999988873555555569999999 PP

                            PAS_10  83 vrylp 87 
                                       v++++
  gi|298675627|ref|YP_003727377.1| 648 VEVSA 652
                                       98877 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   4.5e-09   5.8e-06      25     123 ..     777     870 ..     769     872 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 4.5e-09
                       HATPase_c_2  25 seelldeirlaveEactNavehayleapegpvevrlesdeealtvevaDsGpg.fdpetlpdpteeepkeslkegGr 100
                                       + +++  + + v+E++tN  +ha  ++++g+++v+++ d+   t+ v D+G g  ++ +            +++  +
  gi|298675627|ref|YP_003727377.1| 777 NMDVAIPLGIIVNELVTNSLKHAFSDKSSGQINVSFTEDDSVYTLIVDDNGDGiPEYVD-----------INETDSL 842
                                       5677778899*******************************************777764...........4556779 PP

                       HATPase_c_2 101 GlalikglvDev....ey.dgegnvvtm 123
                                       Gl l+++lvD++    e+ + +g++ t+
  gi|298675627|ref|YP_003727377.1| 843 GLQLVNSLVDQIngtmEFeNCNGTKFTI 870
                                       **********995544445555666655 PP

>> HWE_HK  HWE histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.2   1.5e-08   1.9e-05       1      53 [.     683     737 ..     683     768 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.5e-08
                                       HHHHHHHHHHHHHHHHHHHHSSS..XS-HHHHHHHHHHHHHHHHHHHHHHHHCTT CS
                            HWE_HK   1 ElnHRvKNlLavvqsiarqtlrs..aesleefaeklsgRLqALsaahdllsreew 53 
                                       E++HRvKN L v++s+ +  + +   +s+ ++ e+ ++R+++++ ah+ l +++ 
  gi|298675627|ref|YP_003727377.1| 683 EIHHRVKNNLQVISSLLNLQSTNfeDKSVIKAFEESQNRVRSIALAHEKLYNSSD 737
                                       89**************987655511455567788999**********99877653 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   2.4e-05     0.031       1      47 [.     293     338 ..     293     408 .. 0.81
   2 ?   -1.3   0.1       1.9   2.4e+03     112     115 .]     405     408 ..     397     448 .. 0.48
   3 ?    2.0   0.1      0.18   2.3e+02      13     114 ..     451     554 ..     439     555 .. 0.48
   4 ?    3.5   0.1     0.059        76       2      44 ..     569     610 ..     568     678 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.4e-05
                             PAS_7   1 lenmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellry 47 
                                       l++++++++ +D++++++ wN+   +l++++++ v  g pl++++  
  gi|298675627|ref|YP_003727377.1| 293 LDQLHEAVITLDSNEKILSWNKGAEHLFGYSKDEV-LGEPLSQFIPS 338
                                       78999****************************99.99999998865 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.9
                             PAS_7 112 raee 115
                                       + e+
  gi|298675627|ref|YP_003727377.1| 405 QYEQ 408
                                       3222 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.18
                             PAS_7  13 adlrLvawNrrylelldlpeelvqvgvpleellrynaergefg.agdveae.verrlaaaragkphsfererpdgrv 87 
                                        d  + ++Nr  +e+l+++++ +  g++l e++    +r +++ ++ ++   ++r ++ ++ ++   ++r+  + r+
  gi|298675627|ref|YP_003727377.1| 451 PDFSIKLVNRAGREILGYSKNEL-KGKTLFEFIP---KRYALEvDKVIKGLmFQRNVSLIEYFETAIVNRNL-EKRI 522
                                       55566667777777777777666.3433333332...22222211122222133444444444444444433.4455 PP

                             PAS_7  88 ievrgnpl.....pdgGfVttytDiTerrrae 114
                                       i  +g+ +     +  +++++ +DiTer+++e
  gi|298675627|ref|YP_003727377.1| 523 IAWNGRIVknddyEITCILISGNDITERKNTE 554
                                       55555544222224456677777777777766 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.059
                             PAS_7   2 enmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleel 44 
                                       en  ++i ++D +++++  N+   ++++++ + + +g ++ ++
  gi|298675627|ref|YP_003727377.1| 569 ENAGDAIFIIDTEGNIIEANKVAANMHGYTVSEL-IGSNIMDI 610
                                       7778899999999999999999999999887666.55555554 PP

>> Vac14_Fab1_bd  Vacuolar 14 Fab1-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.5   1.9e+03      68      94 ..     270     296 ..     258     298 .. 0.88
   2 ?   13.3   0.3   7.2e-05     0.093      30      85 ..     709     766 ..     695     776 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.5
                     Vac14_Fab1_bd  68 eifdalvklvaDsdesvksgaelldrl 94 
                                       + +d+l++ +   +e+ k+ a++ld+l
  gi|298675627|ref|YP_003727377.1| 270 RPYDILFRELKRREEDFKKHAQILDQL 296
                                       5689999999999************87 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 7.2e-05
                     Vac14_Fab1_bd  30 kpvlkcfsDkdsrvRyy..acEslyniakvakgevlkllneifdalvklvaDsdesvk 85 
                                       k+v+k+f+++++rvR    a E lyn + ++  ++ ++++++ d+l + + D ++++ 
  gi|298675627|ref|YP_003727377.1| 709 KSVIKAFEESQNRVRSIalAHEKLYNSSDMVSIDFGNYIQTLTDYLLQAYLDDNNNIE 766
                                       589************862267********************************99986 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   0.00015       0.2       7      49 ..     788     835 ..     784     849 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00015
                       HATPase_c_3   7 laelvdNsld...Adaen..vkievnknrgktgeivieDdGkGmsee.e 49 
                                       + elv Nsl    +d  +  +++++ +++ ++ ++ + D+G+G++e  +
  gi|298675627|ref|YP_003727377.1| 788 VNELVTNSLKhafSDKSSgqINVSFTEDD-SVYTLIVDDNGDGIPEYvD 835
                                       779******97554444355777777775.79************98645 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (876 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1537  (0.085727); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.85u 0.32s 00:00:01.17 Elapsed: 00:00:00.50
# Mc/sec: 5228.65
//
Query:       gi|298675628|ref|YP_003727378.1|  [L=155]
Description: hypothetical protein Metev_1744 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.16   11.7   1.0       0.42   10.4   0.1    2.0  2  Imm27     Immunity protein 27


Domain annotation for each model (and alignments):
>> Imm27  Immunity protein 27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1     0.055   9.9e+02      33      50 ..      35      52 ..      15      66 .. 0.75
   2 ?   10.4   0.1   2.4e-05      0.42      17      52 ..     110     145 ..      98     150 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.055
                             Imm27 33 wetlYkdpndgrlWeLaY 50
                                       ++ Y+  ++g +    Y
  gi|298675628|ref|YP_003727378.1| 35 TKKIYQHRKNGSYFHYRY 52
                                      567899999998877666 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 2.4e-05
                             Imm27  17 sliknkLkelksdedgwetlYkdpndgrlWeLaYpe 52 
                                        l +  +k ++++ d+    Y d +   +WeL Yp 
  gi|298675628|ref|YP_003727378.1| 110 ILVASCIKDIDANIDNYLDSYSDTEGKTMWELLYPV 145
                                       467888999**************99999******95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 933.80
//
Query:       gi|298675629|ref|YP_003727379.1|  [L=100]
Description: hypothetical protein Metev_1745 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00075   19.4   0.1     0.0011   18.9   0.1    1.3  1  HTH_11          HTH domain
     0.0039   16.7   0.2     0.0061   16.1   0.2    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.018   14.7   0.0      0.029   14.0   0.0    1.3  1  GntR            Bacterial regulatory proteins, gntR family
      0.026   14.9   0.1      0.032   14.6   0.1    1.2  1  Rrf2            Transcriptional regulator
      0.056   14.0   0.0      0.069   13.8   0.0    1.1  1  DnaG_DnaB_bind  DNA primase DnaG DnaB-binding
      0.096   12.6   0.0        0.1   12.5   0.0    1.1  1  DUF1824         Domain of unknown function (DUF1824)
       0.13   12.1   0.0       0.18   11.5   0.0    1.2  1  HTH_DeoR        DeoR-like helix-turn-helix domain
       0.18   12.5   1.2        1.4    9.6   1.2    2.0  1  Pre-PUA         Pre-PUA-like domain


Domain annotation for each model (and alignments):
>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   4.9e-07    0.0011       3      33 ..      17      45 ..      15      56 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4.9e-07
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvr 33
                                      ++i ++L ++ + i++ eLA ++nvS++ vr
  gi|298675629|ref|YP_003727379.1| 17 KAIKQCL-KNSD-ITIGELANRFNVSKTLVR 45
                                      4566777.4443.*************98887 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.2   2.7e-06    0.0061      14      42 ..      24      52 ..       8      55 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.7e-06
                            HTH_24 14 knprisqreLAerlglSpstvnrrlkrLe 42
                                      kn++i++ eLA r ++S++ v++  ++L 
  gi|298675629|ref|YP_003727379.1| 24 KNSDITIGELANRFNVSKTLVREIKQELR 52
                                      6*******************998766665 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.3e-05     0.029       9      51 ..      15      54 ..      11      55 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.3e-05
                                      HHHHHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHT CS
                              GntR  9 LredIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeae 51
                                      Lr  I++     ++ + +  eLa +f+Vs+t vRe  ++L +e
  gi|298675629|ref|YP_003727379.1| 15 LRKAIKQ--CLKNSDI-TIGELANRFNVSKTLVREIKQELRRE 54
                                      5555555..5556777.899***************88888776 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   1.4e-05     0.032      22      53 ..      24      55 ..      13      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.4e-05
                                      TCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTT CS
                              Rrf2 22 eeepvsseeiaerqnispsylekilakLrkag 53
                                      +++ +++ e+a+r+n+s++ ++ i ++Lr+++
  gi|298675629|ref|YP_003727379.1| 24 KNSDITIGELANRFNVSKTLVREIKQELRREN 55
                                      45669************************985 PP

>> DnaG_DnaB_bind  DNA primase DnaG DnaB-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.1e-05     0.069      27      72 ..       7      54 ..       2      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.1e-05
                    DnaG_DnaB_bind 27 fedpglallreliealaaepelntaaLlerlrgtp..eeallaeLave 72
                                       + +++++lr++i+++ ++ +++ ++L  r+  ++   +++ +eL  e
  gi|298675629|ref|YP_003727379.1|  7 YNSKDYKALRKAIKQCLKNSDITIGELANRFNVSKtlVREIKQELRRE 54
                                      47889**************************97665677777777665 PP

>> DUF1824  Domain of unknown function (DUF1824)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.5e-05       0.1      14      74 ..       6      65 ..       1      87 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.5e-05
                           DUF1824 14 alseeekeklrqallllaseadyqtlGicAdsaeeaiaaLrsylkalgyeeelkleeveee 74
                                      + ++++ + lr+a++++++++d +t+G +A+  +   + +r+++++l  e++++ + + + 
  gi|298675629|ref|YP_003727379.1|  6 KYNSKDYKALRKAIKQCLKNSD-ITIGELANRFNVSKTLVREIKQELRRENDTNYQRILPD 65
                                      56788999*************9.589**********************9999998887654 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   8.2e-05      0.18       5      32 ..      19      45 ..      16      51 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.2e-05
                          HTH_DeoR  5 ilellkqqgklsveelvellgvSeaTiR 32
                                      i + lk++  +++ el+++++vS++ +R
  gi|298675629|ref|YP_003727379.1| 19 IKQCLKNS-DITIGELANRFNVSKTLVR 45
                                      55555554.69*************9888 PP

>> Pre-PUA  Pre-PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.2   0.00064       1.4       9      79 ..       3      81 ..       1      91 [. 0.74

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00064
                           Pre-PUA  9 sntqlksSdrrkLraklleqfpslseeqleellpk....keevkvvklq.....gehvelyvvdgeplffqdregellP 78
                                      +n++ +s+d ++Lr+ ++++ ++  + ++ el +     k+ v  +k +     +++ + ++ d+  +f+ ++++++ P
  gi|298675629|ref|YP_003727379.1|  3 NNNKYNSKDYKALRKAIKQCLKNS-DITIGELANRfnvsKTLVREIKQElrrenDTNYQRILPDKSDWFYCYKSETYTP 80
                                      688899999999999999999877.544444433332237777777777888766677778888888888888888888 PP

                           Pre-PUA 79 t 79
                                      t
  gi|298675629|ref|YP_003727379.1| 81 T 81
                                      8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1681  (0.0937587); expected 358.6 (0.02)
Passed bias filter:                      842  (0.046963); expected 358.6 (0.02)
Passed Vit filter:                       119  (0.00663729); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.53u 0.34s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 593.99
//
Query:       gi|298675630|ref|YP_003727380.1|  [L=134]
Description: hypothetical protein Metev_1746 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-62  207.4   2.3    5.3e-62  207.3   2.3    1.0  1  DUF1699   Protein of unknown function (DUF1699)


Domain annotation for each model (and alignments):
>> DUF1699  Protein of unknown function (DUF1699)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.3   2.3     3e-66   5.3e-62       1     130 []       1     130 [.       1     130 [. 0.99

  Alignments for each domain:
  == domain 1  score: 207.3 bits;  conditional E-value: 3e-66
                           DUF1699   1 mkirvvsskeeietlnenekivHlafrpsntdilslvkkcpklkaiqvpeSykktlsksakmfleiqgiellegdvw 77 
                                       mkirvvs+k+ei++lne+++i+H+afrpsn+d++s+v++cp+lkai++++Syk+tls+sakmfl++qgiellegdvw
  gi|298675630|ref|YP_003727380.1|   1 MKIRVVSTKDEIKDLNEKDEIIHMAFRPSNKDVFSIVSSCPNLKAIHLSKSYKQTLSESAKMFLDMQGIELLEGDVW 77 
                                       9**************************************************************************** PP

                           DUF1699  78 ghrkdineyyevseevierikelkseglseeeiaeklsketklspdlikfllk 130
                                       ghrkdiney+evse+v+++i++lk++g+se+ei ek++ et+lspd++kfl++
  gi|298675630|ref|YP_003727380.1|  78 GHRKDINEYSEVSENVYNKIEDLKHKGFSENEILEKMEYETNLSPDFVKFLIE 130
                                       ***************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 849.04
//
Query:       gi|298675631|ref|YP_003727381.1|  [L=126]
Description: molybdopterin dinucleotide-binding region [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-12   47.4   0.0    1.9e-12   47.2   0.0    1.1  1  Molydop_binding  Molydopterin dinucleotide binding domain
  ------ inclusion threshold ------
      0.011   15.9   0.0      0.015   15.5   0.0    1.2  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal


Domain annotation for each model (and alignments):
>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.2   0.0   2.2e-16   1.9e-12       3     109 ..       7     102 ..       5     105 .. 0.80

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 2.2e-16
                                       EEEE-BTTBSTTTTTCGCCHHHHCSSS-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEEESS CS
                   Molydop_binding   3 LitgrsldqlhsqtrtrpvlrlakpepevveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfmpfg 79 
                                       Li+ r+ +q    + + ++ +++  e++++e+n +d ++lGi++Gd ++v++++G+v+v ak++++ ++    +p+g
  gi|298675631|ref|YP_003727381.1|   7 LISARTAWQGS--FLEHKMNNAYFNECAYCELNSNDFSKLGINEGDYIKVKTDYGEVVVYAKINDDNPEKLGHIPMG 81 
                                       55555555555..445555555555667************************************************* PP

                                       HCC.....S-GHCTS--SCSTTT--CSTT- CS
                   Molydop_binding  80 wweagekggnaNaltddatdplsgtpefks 109
                                        w+        Na+ +++t+  +g+p fk+
  gi|298675631|ref|YP_003727381.1|  82 PWS--------NAVLNPETH-GCGMPGFKG 102
                                       ***........999855554.567777776 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   1.7e-06     0.015      19      62 ..      36      80 ..      20      83 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.7e-06
                                      E-HHHHHHHTS-TTSEEEEEC.CCCEEEEEEEBSTTSTTTTEEEE CS
                           CDC48_N 19 idpedmeelglepgdvveieg.krkTvaivwpaepedegkgiIrm 62
                                      ++++d+++lg+++gd+++++    + v+++  +++  e+ g+I m
  gi|298675631|ref|YP_003727381.1| 36 LNSNDFSKLGINEGDYIKVKTdYGEVVVYAKINDDNPEKLGHIPM 80
                                      899******************666688888777777778999977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 866.60
//
Query:       gi|298675632|ref|YP_003727382.1|  [L=434]
Description: formylmethanofuran dehydrogenase subunit B [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-14   54.4   0.0      3e-14   52.8   0.0    1.7  1  Molybdopterin   Molybdopterin oxidoreductase
  ------ inclusion threshold ------
      0.086   12.6   0.3         13    5.6   0.0    2.8  2  SpoVIF          Stage VI sporulation protein F
      0.089   12.8   0.6       0.23   11.5   0.6    1.7  1  Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   0.0   5.1e-18     3e-14       1     430 [.      51     425 ..      51     427 .. 0.77

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 5.1e-18
                                       B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BE CS
                     Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfy 77 
                                       R++ Pm+R   + +G++v+vs deA e  a+ l++     +      + s+++  ++s  ++++ ++l    + s++
  gi|298675632|ref|YP_003727382.1|  51 RIESPMIR---K-DGELVEVSYDEAIEKAAETLVN----SNR-----TLSYGWA-STSCEAIREGIQLAEE-TRSVI 112
                                       999*****...6.9*********************....555.....5666666.4445555555555555.46699 PP

                                       ECCGGGTTHHHH...CHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHH...HHHHHHHHHTTC....... CS
                     Molybdopterin  78 dwyadlppasaq...qtigsdsrsnyessnpledlensdliilwGsNvreerpil...narirkaalkkk....... 141
                                       d+ a+++++  +   q  g   + + ++         +d+i+ wG N+ + +p     +   +++            
  gi|298675632|ref|YP_003727382.1| 113 DSTANVCHGPSAlaiQEKGLPAATVGQMK------NRADVIVFWGCNPVHAHPRHmgrY-SSYAKG---Fftpkgrk 179
                                       *******9999866555555544444444......67****************994431.223333...13346777 PP

                                       .-EEEEECSSB-HCGGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCSHHHHH CS
                     Molybdopterin 142 .akvivigpryaellkfadewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleeetgkkk 217
                                         k++ ++ r ++++k  d+ + + +g d+ l+ a++ +i ++  v  ++                           
  gi|298675632|ref|YP_003727382.1| 180 nRKIVTVDVRNTDTAKLSDKLVQVEQGKDLLLLTAIRSAINENEDVIPDS-------------------------VA 231
                                       8************99*****************999996666555553322.........................33 PP

                                       HCCHHHHHHHHHHHHHHTSSEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHTC CS
                     Molybdopterin 218 evvariarelarnaaktagksmiivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekvga 294
                                       +v ++ + e+a+ + +++  s i++G+g +++++   +  av +L++ +++  +  + + +++G +++ag      +
  gi|298675632|ref|YP_003727382.1| 232 GVSKDDILEVADTLKNANY-SCIFFGMGTTQSRSKYKNGDAVSSLVADINQHSK--CVMLSMRGHYNVAG---FGQT 302
                                       4555677788888877777.9999********8888888888888886665544..77888887454555...7777 PP

                                       CTTCCCCCCCTTHHHHHCCCTTTCSTSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHHCSSEEEE CS
                     Molybdopterin 295 lpvllsvkslkeekikfaaeqpgnlgnfprnlfversnllkssgkkvlyllgnnpevdhadenevekalekldlvvv 371
                                         ++  +++    + ++a+ +pg+ g    n      +ll +++ ++  ++  +p  + ++++ +   +     ++ 
  gi|298675632|ref|YP_003727382.1| 303 ALWEVGFPMAIDFSHGYAYYNPGETGA---N------DLLYREEADAALIAAADPGSHFPQKSVR---QLANIPLIQ 367
                                       7799**********************9...3......3445677778888887777777777777...236678899 PP

                                       EESCSSHHHHTSSEEEEBE-C.CGSEEEEE-TTSEEEEEEESSS-STT-BEHHHHHHHHH CS
                     Molybdopterin 372 ldgrltstalyaDiiLPaatw.yEkedlytndegrfqhlkqavsppgeaksdwkIlkaLa 430
                                       +d + + t ++aD++ P+a   +E e++   ++    ++k++v++ +++  d +I+++L 
  gi|298675632|ref|YP_003727382.1| 368 IDPFENPTTHIADVVIPSAVVgIEAEGTAYRMDNIPLRMKKLVDTEFNS--DEQIVRDLI 425
                                       999****************8757*********************99985..667777665 PP

>> SpoVIF  Stage VI sporulation protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0    0.0022        13       9      26 ..     232     249 ..     226     251 .. 0.91
   2 ?    4.0   0.1     0.007        42      24      43 ..     411     431 ..     395     434 .] 0.75

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0022
                            SpoVIF   9 nvkkedilkLansvqkad 26 
                                       +v+k+dil++a+++++a+
  gi|298675632|ref|YP_003727382.1| 232 GVSKDDILEVADTLKNAN 249
                                       79**************99 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.007
                            SpoVIF  24 kadl.kdektlRqlikqvskl 43 
                                       ++++ +de+ +R+li++v +l
  gi|298675632|ref|YP_003727382.1| 411 DTEFnSDEQIVRDLIQKVREL 431
                                       5555258999*******9765 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.6   3.9e-05      0.23       5      30 ..       7      33 ..       3      44 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.9e-05
                                      EEE-SSBTT--E.EEEEEETTEEEEEE CS
                    Molybdop_Fe4S4  5 ktaCpyCgvgCg.levhvkdgkivkve 30
                                      + +C++Cg+ C  ++v+v+++ki+ +e
  gi|298675632|ref|YP_003727382.1|  7 DAICSFCGTLCDdITVTVENNKITNAE 33
                                      689********55**********8665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2653.27
//
Query:       gi|298675633|ref|YP_003727383.1|  [L=575]
Description: formylmethanofuran dehydrogenase subunit A [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-82  279.1   0.1    1.2e-82  278.9   0.1    1.0  1  Amidohydro_3  Amidohydrolase family
    3.3e-05   23.4   0.0     0.0011   18.3   0.0    2.2  2  Amidohydro_1  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  278.9   0.1   1.3e-86   1.2e-82       1     473 []      43     509 ..      43     509 .. 0.96

  Alignments for each domain:
  == domain 1  score: 278.9 bits;  conditional E-value: 1.3e-86
                      Amidohydro_3   1 eviDakGrlvlPGFvDsHtHlagggvnl.rllrlpdarvtslegvltavrdqagttpkgrwivgeGwdeaqfaeerf 76 
                                       ++iDa+Grl ++G  D HtH  +g++n+ r++++ d+r++ + g+  + +      p  ++++  G+ ++++++ ++
  gi|298675633|ref|YP_003727383.1|  43 KEIDADGRLTMAGAFDGHTH-WAGKINVgRMMSPHDMRRNPIPGLSGKEA------PTETTRAQAGYATPNTYAIGY 112
                                       58******************.55568*******************99933......444558*************** PP

                      Amidohydro_3  77 pyalaeldevledapvllaaldtHaavrnsaaldlagiteatpdpaggeilrdangegatgllregafhlvldlapl 153
                                       +ya+ +++++ e+a +ll+a++ H+++ ++++ d+             ++  +++++ +++++r++           
  gi|298675633|ref|YP_003727383.1| 113 RYAKLGYTTATEAALPLLNARHVHEEFESIPIQDK------------LGLSLFGDNWMVMEYIRDN----------- 166
                                       ***********************************............9999***************........... PP

                      Amidohydro_3 154 areaeaaavaaalaalasyGitsv.......eagggnvsslddleplfeltaeeklplrviikelldaaerlglpls 223
                                       ++e++aa+va+al+  ++yGi++v       +++g+nv++l+d +p f++t+++      i  +l + +erl lp+s
  gi|298675633|ref|YP_003727383.1| 167 EPEKLAAYVAWALKSSRGYGIKIVnpgggesWSWGKNVTGLYDNVPNFDVTPAD------ILLGLGKTNERLNLPHS 237
                                       ******************************************************......999************** PP

                      Amidohydro_3 224 ..........pgseeltigavklfad...gvlgsrtalltepyf.....tgwpdfedea..laelvaaadergldva 280
                                                 pg++e+t++++kl +d      +++ a++t+++f     +gw+df ++a  +a++++   + ++d++
  gi|298675633|ref|YP_003727383.1| 238 vhihcnnlgkPGNYETTLETMKLMEDnikPKRDRQAAHFTHVQFhsyagDGWRDFKSGApmVADYLNTTENLTFDLG 314
                                       **************************6443349******************************************** PP

                      Amidohydro_3 281 ihaigdaavd..dvldafeaa...aekngnqdrrrlehaegv...tesqiervaalqvaagvqpvfnfedelldsrl 349
                                       ++++g a ++  d++ ++++    +ek++n+d+ +le ++gv   +++++  v a+q+a+g++              
  gi|298675633|ref|YP_003727383.1| 315 QVIFGPAMTMtaDGPLEYANSrmlHEKWSNKDV-ELEGTSGVvpiDYKKKVFVNAVQWAIGLE-------------- 376
                                       ********************************9.*****************************.............. PP

                      Amidohydro_3 350 gperargstpvkellnagvkvalgsD.apvgpfdpwprigaavmrktrrgg.............evlrpdeelslee 412
                                                 +++l ++++k ++++D +++g+f ++p+ ++ +m+ + r++             +++++d+elsl+e
  gi|298675633|ref|YP_003727383.1| 377 ----------LGLLVDDPWKAMFTTDnPNGGSFVNYPEAYTYLMSSKKRDEimsqftdttfdriKLPDIDRELSLYE 443
                                       ..........******************************************************************* PP

                      Amidohydro_3 413 alalyTrgpAkalgledrkGtLevGadADlvvldadpldvdppelaear.......vrltvvdGrvvy 473
                                       ++ +++  p k+++++++ G+L+vGadAD++++d +p++vd++   +++        ++t++dG+vv+
  gi|298675633|ref|YP_003727383.1| 444 LAIMTRGVPSKIYSMPQK-GNLGVGADADIAIYDLKPDEVDTTV-ENDKvveafrgTKYTIKDGNVVV 509
                                       *****************8.***************8888888664.4444488**************97 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.8   0.0    0.0068        61       3      28 ..      53      91 ..      51     129 .. 0.75
   2 !   18.3   0.0   1.3e-07    0.0011     243     344 .]     388     508 ..     377     508 .. 0.66

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.0068
                                      EE-EEEEEEECETTECSSS..GHHHHH...........S CS
                      Amidohydro_1  3 lPGlIDaHvHleqsllrga..tledwl...........v 28
                                      ++G  D H+H  +  ++g+    +d++           +
  gi|298675633|ref|YP_003727383.1| 53 MAGAFDGHTHWAGKINVGRmmSPHDMRrnpipglsgkeA 91
                                      799*************99988777777666555555541 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 1.3e-07
                                       EEEEECTTSSCCGGHHHH.............HHHHHHHHHHCCTT.TTHCHCHHHHHHHHHTHH.HHHHTT-TTTSS CS
                      Amidohydro_1 243 glgtDgaasgnslnllee.............lrlalklqrgllye.deegglslkealrmaTin.gAkalglddkvG 304
                                       +++tD+ + g+ +n  e              + + + +++   +  d +  lsl+e l+++T + + k+++++ ++G
  gi|298675633|ref|YP_003727383.1| 388 MFTTDNPNGGSFVNYPEAytylmsskkrdeiMSQFTDTTFDRIKLpDIDRELSLYE-LAIMTRGvPSKIYSMP-QKG 462
                                       56666555555554433344444444444445555555554455555667789999.5555554399*****7.*** PP

                                       SS-TTSB--EEEECCCT........CGGGTTTCTSEEEEEEEETTEEE CS
                      Amidohydro_1 305 sievGkdADlvvvdldi........laafvglkkdgnvkkvivkGklv 344
                                        + vG dAD+++ dl++        + ++v+  +   +k +i++G++v
  gi|298675633|ref|YP_003727383.1| 463 NLGVGADADIAIYDLKPdevdttveNDKVVEAFR--GTKYTIKDGNVV 508
                                       ***************6666777887666666665..688999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (575 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 3664.31
//
Query:       gi|298675634|ref|YP_003727384.1|  [L=252]
Description: formylmethanofuran dehydrogenase subunit C [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-10   39.5  20.5    3.8e-08   33.2  20.5    3.0  1  GXGXG         GXGXG motif
  ------ inclusion threshold ------
        2.1    8.7   6.5         25    5.3   0.1    4.1  5  Toast_rack_N  N-terminal domain of toast_rack, DUF2154
        7.6    6.4   5.9        4.1    7.3   0.3    3.3  3  NAGLU_N       Alpha-N-acetylglucosaminidase (NAGLU) N-termina


Domain annotation for each model (and alignments):
>> GXGXG  GXGXG motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2  20.5   6.3e-12   3.8e-08      11     148 ..      66     215 ..      60     243 .. 0.84

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 6.3e-12
                                       THHHHHHHHH.HHTTT---.-EEEEEEEEEE-TTTTTT--TTEEEEEEEEE-STTTTT-ESSEEEEE--T....... CS
                             GXGXG  11 gtilsneiak.rygeeglpedtikiklkGsaGqslgaflakGltleleGdandyvGkglsgGkivikpsk....... 79 
                                       + i+s+  ++ + + +g++  t +++++G+     g+ + +G +++++Gda++ +G  ++gG+iv+++++       
  gi|298675634|ref|YP_003727384.1|  66 KIIMSGDFSRmKRIGQGMN--TGEMEINGNVDMHCGCHM-SGGKITVNGDADNWLGREMTGGEIVVNGNAgyyvgsg 139
                                       5555665554245667777..6678899***********.9****************************97776665 PP

                                       ....T-SS-GGGSB-S-SSTTT...T--SEEEEESSB--SSTTTT-SS-EEEESEB-SSTTTT-EEEEEEE-S-B- CS
                             GXGXG  80 ....eskfkaeeniivGnvvly...gatgGklfirgkageRfavrnsgatavvegvgdhgceYmtGGvvvvLgktg 148
                                              +   + +i G+v  y    + gG++ ++g+ag   a+ n+g t+++eg+  +++  m  G+vvv g+ +
  gi|298675634|ref|YP_003727384.1| 140 yrgeGCGMGGGKITINGDVRDYlgeHMCGGEILVNGNAGLLPAISNNGGTIIIEGNSTMAAVEMKKGTVVVKGQLA 215
                                       55444556677899*****988544589*******************************************99875 PP

>> Toast_rack_N  N-terminal domain of toast_rack, DUF2154
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.73   4.4e+03      31      50 ..      14      33 ..      10      50 .. 0.72
   2 ?   -0.7   0.0      0.29   1.8e+03      12      23 ..      83      94 ..      72     102 .. 0.82
   3 ?    5.3   0.1    0.0042        25      11      30 ..     101     120 ..      91     131 .. 0.85
   4 ?   -1.2   0.1      0.44   2.6e+03      12      27 ..     147     162 ..     145     177 .. 0.81
   5 ?    3.8   0.1     0.012        70       9      47 ..     200     238 ..     193     246 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.73
                      Toast_rack_N 31 veynakewepevkyevkgkr 50
                                      + ++a++++p+v  +  +++
  gi|298675634|ref|YP_003727384.1| 14 IPVEAENIKPDVFASKSKEE 33
                                      66788888888876665554 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.29
                      Toast_rack_N 12 lgaGeltvsgga 23
                                      +++Ge++++g+ 
  gi|298675634|ref|YP_003727384.1| 83 MNTGEMEINGNV 94
                                      889999999985 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.0042
                      Toast_rack_N  11 elgaGeltvsggaeellegk 30 
                                       ++  G++tv+g+a+++l  +
  gi|298675634|ref|YP_003727384.1| 101 HMSGGKITVNGDADNWLGRE 120
                                       6889************9655 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 0.44
                      Toast_rack_N  12 lgaGeltvsggaeell 27 
                                       +g G++t++g+ +++l
  gi|298675634|ref|YP_003727384.1| 147 MGGGKITINGDVRDYL 162
                                       8889999999877754 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.012
                      Toast_rack_N   9 nlelgaGeltvsggaeellegkveynakewepevkyevk 47 
                                       ++e++ G + v+g+  el+    e   +e+e e  ++ +
  gi|298675634|ref|YP_003727384.1| 200 AVEMKKGTVVVKGQLAELMPSYREEGTEEYEGETYRKFT 238
                                       689****************99988888888888777665 PP

>> NAGLU_N  Alpha-N-acetylglucosaminidase (NAGLU) N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.3      0.13   7.9e+02      37      50 ..     122     135 ..      88     141 .. 0.69
   2 ?   -1.7   0.0      0.42   2.5e+03      61      61 ..     165     165 ..     147     182 .. 0.52
   3 ?    7.3   0.3   0.00068       4.1      34      51 ..     183     200 ..     180     206 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.13
                                       SSS-EEEEESSHHH CS
                           NAGLU_N  37 kggkilIrGnsgva 50 
                                       +gg+i+++Gn g  
  gi|298675634|ref|YP_003727384.1| 122 TGGEIVVNGNAGYY 135
                                       45677777777655 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.42
                                       H CS
                           NAGLU_N  61 y 61 
                                       +
  gi|298675634|ref|YP_003727384.1| 165 H 165
                                       2 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.00068
                                       EE-SSS-EEEEESSHHHH CS
                           NAGLU_N  34 isskggkilIrGnsgval 51 
                                       is++gg+i+I+Gns +a+
  gi|298675634|ref|YP_003727384.1| 183 ISNNGGTIIIEGNSTMAA 200
                                       8999**********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1574.22
//
Query:       gi|298675635|ref|YP_003727385.1|  [L=190]
Description: hypothetical protein Metev_1751 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1481.36
//
Query:       gi|298675636|ref|YP_003727386.1|  [L=920]
Description: S-layer protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   3.9e-162  537.4  40.7    5.7e-82  274.6  14.2    2.3  2  S-layer          S-layer protein
    2.3e-22   78.6  20.2    1.3e-11   44.2   2.1    4.6  5  PKD              PKD domain
    1.2e-09   37.8   2.7    2.5e-09   36.8   2.7    1.6  1  PGF-CTERM        PGF-CTERM motif
    1.5e-09   37.4  11.5     0.0003   20.5   1.5    4.1  3  PKD_3            PKD-like domain
     0.0054   17.1   0.3        3.1    8.3   0.1    2.6  2  Saccharop_dh_N   LOR/SDH bifunctional enzyme conserved region
     0.0089   16.2   2.3         45    4.3   0.0    5.9  6  PTAC             Phosphate propanoyltransferase
     0.0099   16.2   8.3         25    5.2   0.1    4.8  4  GbpA_2           N-acetylglucosamine binding protein domain 2
  ------ inclusion threshold ------
      0.041   14.0   0.7         14    5.9   0.1    3.1  2  Lipocalin_3      Lipocalin-like
       0.34   10.5   3.5         16    5.0   0.1    2.8  2  MecA             Negative regulator of genetic competence (Me
        1.1    9.1   7.2         18    5.1   0.0    4.2  5  DUF4923          Lipocalin-like domain (DUF4923)
        1.1    9.4   8.2         19    5.5   0.0    4.3  4  ZoocinA_TRD      Target recognition domain of lytic exoenzyme
        6.3    7.3   7.0         66    4.0   1.7    3.4  2  Cadherin         Cadherin domain


Domain annotation for each model (and alignments):
>> S-layer  S-layer protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  268.3  18.6   3.3e-83   4.9e-80       8     258 .]     158     407 ..     152     407 .. 0.95
   2 !  274.6  14.2   3.8e-85   5.7e-82       9     258 .]     442     696 ..     433     696 .. 0.94

  Alignments for each domain:
  == domain 1  score: 268.3 bits;  conditional E-value: 3.3e-83
                           S-layer   8 eeltwtasnFsgfyydiddglssEsltlele.sksdrtiee..gelvYsttp...vekefef....eewgsYevigf 74 
                                        +l+ +++nF++f+yd+ d++ssE+++++++ s+sd+++e+  + l Y++t+   +e+ef+f    ++ ++Y++igf
  gi|298675636|ref|YP_003727386.1| 158 VTLEANSDNFAAFWYDLADDESSENIIVNVSeSTSDKKLEDdtEALLYKSTIvsgIESEFDFnnneSNPWTYQKIGF 234
                                       467799***********************9954477777765689******9888899***9777766777****** PP

                           S-layer  75 laekYfagydnsaetsddvsllsdekLskvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeev 151
                                       lae+Y+++++++a           +kLsk+++d+d+++t+++g+sleL++gY+++++qiDv+gdkvwleLtkdge+v
  gi|298675636|ref|YP_003727386.1| 235 LAEEYVPIVEDEA-----------DKLSKLVMDDDTSHTIRTGESLELADGYAITPQQIDVEGDKVWLELTKDGEFV 300
                                       *********9999...........***************************************************** PP

                           S-layer 152 dskvissskadstyvyekdlgdeddvviiavhvdevfrgtedslvviegifqisddvleieegdefgkmevksvsen 228
                                       d+kvi++++ ++t++y++d+++edd+v+++v++devf+g++dsl+vieg++qi dd +e+e++d++g+me+++v+ n
  gi|298675636|ref|YP_003727386.1| 301 DDKVITVTEGTNTWTYDQDVMGEDDIVTLKVNIDEVFQGQVDSLAVIEGVWQIADDGIELESEDSYGNMEIDTVDGN 377
                                       *******999******************************************************************* PP

                           S-layer 229 eiemenddsitLsrdktieimddlkfkvaD 258
                                       +i m  ++sitL++d+t ++m+d++f++aD
  gi|298675636|ref|YP_003727386.1| 378 TIDMILSSSITLNKDDTYNVMEDIHFTTAD 407
                                       *****************************8 PP

  == domain 2  score: 274.6 bits;  conditional E-value: 3.8e-85
                           S-layer   9 eltwtas.....nFsgfyydiddglssEsltlele..sksdrtiee..gelvYsttp...vekefef....eewgsY 69 
                                       ++twt++     +F+gf+yd+ d+ +sE+l++++   s++dr++++  ++++Y++t+   +e+ef+f    ++ ++Y
  gi|298675636|ref|YP_003727386.1| 442 TITWTPKgetgySFAGFWYDLADNRDSEKLMVDVGhlSDTDRQLSDdpSDVRYKSTIvsgIESEFDFnnneSNPWTY 518
                                       667888777777********************99877669999987679*******9888899***9777766777* PP

                           S-layer  70 evigflaekYfagydnsaetsddvsllsdekLskvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtk 146
                                       ++igflae+Y+++++++a           +kLsk+++d+d+++t+++g+sleL++gY+++++qiDv+gdkvwleLtk
  gi|298675636|ref|YP_003727386.1| 519 QKIGFLAEEYVPIVEDEA-----------DKLSKLVMDDDTSHTIRTGESLELADGYAITPQQIDVEGDKVWLELTK 584
                                       **************9999...........************************************************ PP

                           S-layer 147 dgeevdskvissskadstyvyekdlgdeddvviiavhvdevfrgtedslvviegifqisddvleieegdefgkmevk 223
                                       dge+vd+kvi++++ ++t++y++d+++edd+v+++v++devf+g++dsl+vieg++qi dd +e+e++d++g+me++
  gi|298675636|ref|YP_003727386.1| 585 DGEFVDDKVITVTEGTNTWTYDQDVMGEDDIVTLKVNIDEVFQGQVDSLAVIEGVWQIADDGIELESEDSYGNMEID 661
                                       ************999************************************************************** PP

                           S-layer 224 svseneiemenddsitLsrdktieimddlkfkvaD 258
                                       +v+ n+i m  ++sitLs+d+++++m+d++fkvaD
  gi|298675636|ref|YP_003727386.1| 662 TVDGNTIDMILSSSITLSDDSEQHLMEDIYFKVAD 696
                                       **********************************9 PP

>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       2.6   3.9e+03      16      36 ..     337     357 ..     332     374 .. 0.83
   2 ?    2.6   0.0     0.084   1.3e+02      51      67 ..     420     436 ..     404     439 .. 0.88
   3 ?   -2.4   0.0       3.1   4.6e+03      16      36 ..     626     646 ..     622     655 .. 0.81
   4 !   44.2   2.1   8.4e-15   1.3e-11       2      70 ..     725     788 ..     723     789 .. 0.80
   5 !   38.9   4.4   3.8e-13   5.6e-10       3      70 ..     813     875 ..     811     876 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.6
                                       EEEES.-SS-SEEEEE--SS- CS
                               PKD  16 ftaavpdganvtysWdfgdgs 36 
                                       f+++v++ a +   W+  d++
  gi|298675636|ref|YP_003727386.1| 337 FQGQVDSLAVIEGVWQIADDG 357
                                       999999**********99953 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.084
                                       -SSEEEEEEEEEE-SS- CS
                               PKD  51 lspGeYeVtvtasnavg 67 
                                       ++pG+YeV+ t+ n+ +
  gi|298675636|ref|YP_003727386.1| 420 TEPGTYEVRGTVANESE 436
                                       78***********9865 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 3.1
                                       EEEES.-SS-SEEEEE--SS- CS
                               PKD  16 ftaavpdganvtysWdfgdgs 36 
                                       f+++v++ a +   W+  d++
  gi|298675636|ref|YP_003727386.1| 626 FQGQVDSLAVIEGVWQIADDG 646
                                       9999************99953 PP

  == domain 4  score: 44.2 bits;  conditional E-value: 8.4e-15
                                       E---S--BSSEEEEEEEES.-SS-SEEEEE--SS--EEEEETTEEEEEE-SSEEEEEEEEEE-SS-EEE CS
                               PKD   2 sasptvlvpgatvaftaavpdganvtysWdfgdgsvvqvlseptvthtYlspGeYeVtvtasnavgsat 70 
                                       sasp +  +  +v+ft  +   +   y+Wdfg+   + +++  ++t tY+++GeY+Vt+t+sn++g  t
  gi|298675636|ref|YP_003727386.1| 725 SASPMSGNAPLEVTFTDES--ENADEYEWDFGN---GETSTDANPTTTYEEAGEYTVTLTVSNDAGEDT 788
                                       5664444455555555555..66678*******...*****************************9877 PP

  == domain 5  score: 38.9 bits;  conditional E-value: 3.8e-13
                                       ---S--BSSEEEEEEEES.-SS-SEEEEE--SS--EEEEETTEEEEEE-SSEEEEEEEEEE-SS-EEE CS
                               PKD   3 asptvlvpgatvaftaavpdganvtysWdfgdgsvvqvlseptvthtYlspGeYeVtvtasnavgsat 70 
                                       a+ t+  +  tv+ft  +   +  +y+Wdfg+   + +++e ++t tY+++ eY+Vt+t+sn++g  t
  gi|298675636|ref|YP_003727386.1| 813 ANTTSGTAPLTVEFTDNS--ENAENYEWDFGN---GETSTEANPTVTYEEADEYTVTLTVSNDAGEDT 875
                                       666667777899999999..56667*******...*****************************9877 PP

>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   2.7   1.7e-12   2.5e-09       2      22 ..     897     917 ..     896     918 .. 0.96

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 1.7e-12
                         PGF-CTERM   2 PGFGavlAlaGLLaaalLaRR 22 
                                       PGF+av+A+aGLLa+a+L+RR
  gi|298675636|ref|YP_003727386.1| 897 PGFEAVFAIAGLLAIAFLVRR 917
                                       ********************* PP

>> PKD_3  PKD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.92   1.4e+03      50      68 .]     415     433 ..     413     433 .. 0.83
   2 !   20.0   1.3   2.8e-07   0.00042      29      68 .]     742     782 ..     732     782 .. 0.86
   3 !   20.5   1.5     2e-07    0.0003      28      68 .]     828     869 ..     821     869 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.92
                             PKD_3  50 ytfteeelgsyevtleven 68 
                                       +t + +e g+yev+ +v n
  gi|298675636|ref|YP_003727386.1| 415 LTRSITEPGTYEVRGTVAN 433
                                       788999*******977765 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 2.8e-07
                             PKD_3  29 naenaa.faWtieGkivsteptytfteeelgsyevtleven 68 
                                        +ena+ ++W     + st+++ t t ee+g+y+vtl+v+n
  gi|298675636|ref|YP_003727386.1| 742 ESENADeYEWDFGNGETSTDANPTTTYEEAGEYTVTLTVSN 782
                                       4566666******99************************98 PP

  == domain 3  score: 20.5 bits;  conditional E-value: 2e-07
                             PKD_3  28 enaenaa.faWtieGkivsteptytfteeelgsyevtleven 68 
                                       +n+ena+ ++W     + ste++ t t ee+++y+vtl+v+n
  gi|298675636|ref|YP_003727386.1| 828 DNSENAEnYEWDFGNGETSTEANPTVTYEEADEYTVTLTVSN 869
                                       48899989******99************************98 PP

>> Saccharop_dh_N  LOR/SDH bifunctional enzyme conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.1    0.0021       3.1      41      89 ..     361     411 ..     333     418 .. 0.79
   2 !    6.3   0.0    0.0085        13      41      89 ..     650     700 ..     622     706 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0021
                                       TTSXEEEEEEEEESSHHHHHHHHHHHHHHHHHSC..CCCEEEECESSCTTB CS
                    Saccharop_dh_N  41 kkdtSyaelevsaedeevLeeileeltelgaelv..eeedvklekaekdgv 89 
                                       +++ Sy ++e+ + d ++++ il++ ++l++  +   +ed+++++a++d+ 
  gi|298675636|ref|YP_003727386.1| 361 ESEDSYGNMEIDTVDGNTIDMILSSSITLNKDDTynVMEDIHFTTADADEL 411
                                       5678************************98877765779999999999875 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0085
                                       TTSXEEEEEEEEESSHHHHHHHHHHHHHHHHHSC..CCCEEEECESSCTTB CS
                    Saccharop_dh_N  41 kkdtSyaelevsaedeevLeeileeltelgaelv..eeedvklekaekdgv 89 
                                       +++ Sy ++e+ + d ++++ il++ ++l + +    +ed+ ++ a++d+v
  gi|298675636|ref|YP_003727386.1| 650 ESEDSYGNMEIDTVDGNTIDMILSSSITLSDDSEqhLMEDIYFKVADSDDV 700
                                       5678**********************9997766643568898888888877 PP

>> PTAC  Phosphate propanoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.3     2e+03      35      70 ..      97     130 ..      85     138 .. 0.76
   2 ?    0.6   0.0      0.44   6.6e+02      30      47 ..     292     309 ..     284     334 .. 0.82
   3 ?    1.0   0.0      0.32   4.7e+02      62      80 ..     361     379 ..     355     381 .. 0.87
   4 ?    4.3   0.0      0.03        45      10      43 ..     401     431 ..     399     439 .. 0.85
   5 ?    0.6   0.0      0.44   6.6e+02      30      47 ..     581     598 ..     573     623 .. 0.82
   6 ?    1.0   0.0      0.32   4.7e+02      62      80 ..     650     668 ..     644     670 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.3
                              PTAC  35 gqfadketVtvkvpeekglilenVrvlgperkatqv 70 
                                        +f ++   ++ ++  + + ++nV + g  ++  qv
  gi|298675636|ref|YP_003727386.1|  97 RDFKNNVLANINTS--TTAEINNVTITGLYNEDAQV 130
                                       56778888888886..55559*****9998888887 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.44
                              PTAC  30 dLsqpgqfadketVtvkv 47 
                                       +L+++g+f+d++++tv  
  gi|298675636|ref|YP_003727386.1| 292 ELTKDGEFVDDKVITVTE 309
                                       69999*********9975 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.32
                              PTAC  62 gperkatqveidtddanal 80 
                                        +e+++ ++eidt d+n++
  gi|298675636|ref|YP_003727386.1| 361 ESEDSYGNMEIDTVDGNTI 379
                                       5788999*********987 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.03
                              PTAC  10 iHltqedaekl.fgyeltkkkdLsqpgqfadketV 43 
                                       iH+t++da++l f+     +++++ pg +  + tV
  gi|298675636|ref|YP_003727386.1| 401 IHFTTADADELrFH----LTRSITEPGTYEVRGTV 431
                                       9*************....77888888888766555 PP

  == domain 5  score: 0.6 bits;  conditional E-value: 0.44
                              PTAC  30 dLsqpgqfadketVtvkv 47 
                                       +L+++g+f+d++++tv  
  gi|298675636|ref|YP_003727386.1| 581 ELTKDGEFVDDKVITVTE 598
                                       69999*********9975 PP

  == domain 6  score: 1.0 bits;  conditional E-value: 0.32
                              PTAC  62 gperkatqveidtddanal 80 
                                        +e+++ ++eidt d+n++
  gi|298675636|ref|YP_003727386.1| 650 ESEDSYGNMEIDTVDGNTI 668
                                       5788999*********987 PP

>> GbpA_2  N-acetylglucosamine binding protein domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.017        25       6      52 ..     276     316 ..     272     318 .. 0.82
   2 ?    5.2   0.1     0.017        25       6      52 ..     565     605 ..     561     607 .. 0.82
   3 ?    3.7   0.0     0.049        73      18      40 ..     775     797 ..     759     805 .. 0.81
   4 ?    3.3   0.1     0.069     1e+02      17      41 ..     861     885 ..     846     891 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.017
                                       EE---S---TT-EEEEEEEETTEE-GGG--EEE--SCGGGSHHHHHH CS
                            GbpA_2   6 avtptqdlkaGdtvtlrvfdangeeleletlliiasaaegkaanWay 52 
                                       a+tp+q   +Gd+v+l++  ++ge ++ + ++++     +++++W+y
  gi|298675636|ref|YP_003727386.1| 276 AITPQQIDVEGDKVWLELT-KDGEFVDDKVITVT-----EGTNTWTY 316
                                       6788888899********7.89999888888888.....77888877 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.017
                                       EE---S---TT-EEEEEEEETTEE-GGG--EEE--SCGGGSHHHHHH CS
                            GbpA_2   6 avtptqdlkaGdtvtlrvfdangeeleletlliiasaaegkaanWay 52 
                                       a+tp+q   +Gd+v+l++  ++ge ++ + ++++     +++++W+y
  gi|298675636|ref|YP_003727386.1| 565 AITPQQIDVEGDKVWLELT-KDGEFVDDKVITVT-----EGTNTWTY 605
                                       6788888899********7.89999888888888.....77888877 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.049
                                       EEEEEEEETTEE-GGG--EEE-- CS
                            GbpA_2  18 tvtlrvfdangeeleletlliia 40 
                                       tvtl+v ++ ge+++ et+++ +
  gi|298675636|ref|YP_003727386.1| 775 TVTLTVSNDAGEDTAEETITVNP 797
                                       8************9999999874 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.069
                                       -EEEEEEEETTEE-GGG--EEE--S CS
                            GbpA_2  17 dtvtlrvfdangeeleletlliias 41 
                                        tvtl+v ++ ge+++  t+++ a 
  gi|298675636|ref|YP_003727386.1| 861 YTVTLTVSNDAGEDTAETTITVDAA 885
                                       58************66666666533 PP

>> Lipocalin_3  Lipocalin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1    0.0091        14      44      87 ..     351     395 ..     341     399 .. 0.89
   2 ?    4.7   0.1     0.022        32      44      86 ..     640     682 ..     630     691 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0091
                                       EEEETTEEEEEEEEEETTEEEEEEEEEEEEEE-SSEEEEEET.TE CS
                       Lipocalin_3  44 WklegdkLiLegksigngqtieftdTleiekltkdsltlkkg.ey 87 
                                       W++ +d + Le++    + +i+ +d  +i+++ + s+tl+k+ +y
  gi|298675636|ref|YP_003727386.1| 351 WQIADDGIELESEDSYGNMEIDTVDGNTIDMILSSSITLNKDdTY 395
                                       ************99988999*******************988444 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.022
                                       EEEETTEEEEEEEEEETTEEEEEEEEEEEEEE-SSEEEEEETT CS
                       Lipocalin_3  44 WklegdkLiLegksigngqtieftdTleiekltkdsltlkkge 86 
                                       W++ +d + Le++    + +i+ +d  +i+++ + s+tl++++
  gi|298675636|ref|YP_003727386.1| 640 WQIADDGIELESEDSYGNMEIDTVDGNTIDMILSSSITLSDDS 682
                                       ************99988899******************97663 PP

>> MecA  Negative regulator of genetic competence (MecA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.011        16      15      88 ..     321     394 ..     320     484 .. 0.84
   2 ?    5.0   0.5     0.011        17      15      81 ..     610     683 ..     609     782 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.011
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXX.XXXXXXXXXXXX...... CS
                              MecA  15 ltkeDLeerglklselaygsekakelFremmeeaseelgFeaediplmieaiplssdsleliitkvedpeeldt 88 
                                       + ++D+   +++++e+++g+  +   ++ + + a++ ++ e ed    +e+  ++ +++++i + +   ++ dt
  gi|298675636|ref|YP_003727386.1| 321 MGEDDIVTLKVNIDEVFQGQVDSLAVIEGVWQIADDGIELESEDSYGNMEIDTVDGNTIDMILSSSITLNKDDT 394
                                       6789999********************************************************97733222232 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.011
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXX.XXXXXXXXXX.......X CS
                              MecA  15 ltkeDLeerglklselaygsekakelFremmeeaseelgFeaediplmieaiplssdsleliitkv.......e 81 
                                       + ++D+   +++++e+++g+  +   ++ + + a++ ++ e ed    +e+  ++ +++++i + +       e
  gi|298675636|ref|YP_003727386.1| 610 MGEDDIVTLKVNIDEVFQGQVDSLAVIEGVWQIADDGIELESEDSYGNMEIDTVDGNTIDMILSSSitlsddsE 683
                                       6789999********************************************************97755543321 PP

>> DUF4923  Lipocalin-like domain (DUF4923)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.3   1.9e+03      72     102 ..      43      73 ..      25      87 .. 0.84
   2 ?   -3.9   0.0       6.9     1e+04      87     105 ..     111     129 ..     100     139 .. 0.68
   3 ?   -2.0   0.0       1.9   2.8e+03      43      83 ..     180     221 ..     179     231 .. 0.79
   4 ?    5.0   0.0     0.013        20      13      46 ..     332     365 ..     318     370 .. 0.78
   5 ?    5.1   0.0     0.012        18      13      46 ..     621     654 ..     607     663 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.3
                           DUF4923  72 ikegkvsitfnkdstftiklkkktlkGtYsl 102
                                       +++++v++t+ +d+t t +++  +  G++ +
  gi|298675636|ref|YP_003727386.1|  43 MQADEVNVTIGHDGTTTETFTLGKDAGSWGI 73 
                                       67889999*******9999998888887766 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 6.9
                           DUF4923  87 ftiklkkktlkGtYsldak 105
                                        t+++++ t++G Y+ da+
  gi|298675636|ref|YP_003727386.1| 111 TTAEINNVTITGLYNEDAQ 129
                                       4667777777777776554 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.9
                           DUF4923  43 sdnllakagGaaaataveekLkeyykkvgikeg.kvsitfnk 83 
                                       s+n++ +++ ++  +++e++ +  + k  i +g + ++ fn+
  gi|298675636|ref|YP_003727386.1| 180 SENIIVNVSESTSDKKLEDDTEALLYKSTIVSGiESEFDFNN 221
                                       899999999999999999999999999999865344455554 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.013
                           DUF4923  13 vvekvtgkkkvtqedlaGtWkysgpavefesdnl 46 
                                        +++v +++    + ++G W++++ ++e+es++ 
  gi|298675636|ref|YP_003727386.1| 332 NIDEVFQGQVDSLAVIEGVWQIADDGIELESEDS 365
                                       4566666655556789****************96 PP

  == domain 5  score: 5.1 bits;  conditional E-value: 0.012
                           DUF4923  13 vvekvtgkkkvtqedlaGtWkysgpavefesdnl 46 
                                        +++v +++    + ++G W++++ ++e+es++ 
  gi|298675636|ref|YP_003727386.1| 621 NIDEVFQGQVDSLAVIEGVWQIADDGIELESEDS 654
                                       4566666655556789****************96 PP

>> ZoocinA_TRD  Target recognition domain of lytic exoenzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1       1.2   1.7e+03      55     102 ..     247     297 ..     212     331 .. 0.59
   2 ?    5.4   0.1     0.013        19       5      23 ..     340     358 ..     336     397 .. 0.76
   3 ?   -0.9   0.1       1.2   1.7e+03      55     102 ..     536     586 ..     501     620 .. 0.59
   4 ?    5.5   0.0     0.012        19       5      23 ..     629     647 ..     625     686 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.2
                       ZoocinA_TRD  55 lkvGdyfvfnPksvlsveep..iygvaGltfakvkfa.egesiWlsveskk 102
                                         + + +v++ ++ +++ ++  +    G+ ++  ++  eg+++Wl+ ++ +
  gi|298675636|ref|YP_003727386.1| 247 ADKLSKLVMDDDTSHTIRTGesLELADGYAITPQQIDvEGDKVWLELTKDG 297
                                       444445555555444443321134455666666665326677777765554 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.013
                       ZoocinA_TRD   5 rvddlkvvnGvWqvkndvl 23 
                                       +vd l v++GvWq+  d +
  gi|298675636|ref|YP_003727386.1| 340 QVDSLAVIEGVWQIADDGI 358
                                       89************98865 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.2
                       ZoocinA_TRD  55 lkvGdyfvfnPksvlsveep..iygvaGltfakvkfa.egesiWlsveskk 102
                                         + + +v++ ++ +++ ++  +    G+ ++  ++  eg+++Wl+ ++ +
  gi|298675636|ref|YP_003727386.1| 536 ADKLSKLVMDDDTSHTIRTGesLELADGYAITPQQIDvEGDKVWLELTKDG 586
                                       444445555555444443321134455666666665326677777765554 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.012
                       ZoocinA_TRD   5 rvddlkvvnGvWqvkndvl 23 
                                       +vd l v++GvWq+  d +
  gi|298675636|ref|YP_003727386.1| 629 QVDSLAVIEGVWQIADDGI 647
                                       89************98865 PP

>> Cadherin  Cadherin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.3     0.066        98      61      89 ..     768     796 ..     763     796 .. 0.90
   2 ?    4.0   1.7     0.044        66      58      88 ..     850     882 ..     807     884 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.066
                                       TTTSSEEEEEEEEEECTGCCEEEEEEEEE CS
                          Cadherin  61 rEsqgeYeLtveatDesgspplsstttvt 89 
                                       +E+ geY++t+ +++ +g+   ++t tv+
  gi|298675636|ref|YP_003727386.1| 768 YEEAGEYTVTLTVSNDAGEDTAEETITVN 796
                                       8999************9899999888885 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.044
                                       T..C-TTTSSEEEEEEEEEECTGCCEEEEEEEE CS
                          Cadherin  58 p..LdrEsqgeYeLtveatDesgspplsstttv 88 
                                       +  + +E+ +eY++t+ +++ +g+   ++t tv
  gi|298675636|ref|YP_003727386.1| 850 NptVTYEEADEYTVTLTVSNDAGEDTAETTITV 882
                                       335889***************766666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (920 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.83u 0.32s 00:00:01.14 Elapsed: 00:00:00.55
# Mc/sec: 5072.24
//
Query:       gi|298675637|ref|YP_003727387.1|  [L=259]
Description: putative circadian clock protein KaiC [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-72  241.5   0.5    7.9e-72  241.3   0.5    1.0  1  ATPase    KaiC
    0.00058   18.6   0.1    0.00075   18.2   0.1    1.1  1  GvpD      GvpD gas vesicle protein
     0.0026   17.4   0.0     0.0038   16.8   0.0    1.3  1  AAA_25    AAA domain
  ------ inclusion threshold ------
      0.023   14.0   0.0      0.039   13.3   0.0    1.5  1  DnaB_C    DnaB-like helicase C terminal domain
      0.059   13.4   0.1      0.077   13.0   0.1    1.3  1  ResIII    Type III restriction enzyme, res subunit
      0.059   13.2   0.0      0.095   12.5   0.0    1.4  1  MEDS      MEDS: MEthanogen/methylotroph, DcmR Sensory domain


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.3   0.5   2.6e-75   7.9e-72       1     229 [.      19     252 ..      19     254 .. 0.98

  Alignments for each domain:
  == domain 1  score: 241.3 bits;  conditional E-value: 2.6e-75
                            ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekl 77 
                                       vktgI+g+De++ gG+ ++r++li+G++G+GKt f+ qF+++g+ kyge+g+++++ee++e++r+n++++Gwdl+kl
  gi|298675637|ref|YP_003727387.1|  19 VKTGIPGFDELCGGGLIRDRTYLISGTSGAGKTNFGIQFIYNGITKYGENGIIIATEERPEQIRKNVSKFGWDLKKL 95 
                                       79*************************************************************************** PP

                            ATPase  78 eeegklaiidasesaeesaee.....kdkedleelieelaeaikeikakrvviDsitgl.ayeekeavaReilrqlv 148
                                       e+egklaiida +++++ +++      + +d++++++++ +  ++i+akr ++Ds t++    +++a++R +l +l 
  gi|298675637|ref|YP_003727387.1|  96 EDEGKLAIIDACSTKIGVPSQekyvdVRPFDIRSMLDQIITTQEQINAKRAIVDSTTSIsFFLQEPAKIRIELLKLS 172
                                       *****************999999999999******************************999*************** PP

                            ATPase 149 rvlkklgvTailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegik 225
                                       ++l+ lg+T+++++e+  +e++ +++gve+f+ dg+i L +++ e+ +  ++ei kmRgt+hskk+hp++It++g +
  gi|298675637|ref|YP_003727387.1| 173 TTLEILGLTSMMTCEI-IDETNPSRFGVENFVTDGTIMLYYDRHENVRLHSMEIYKMRGTDHSKKIHPYDITPDGFV 248
                                       ***************7.56699******************************************************* PP

                            ATPase 226 vlee 229
                                       ++++
  gi|298675637|ref|YP_003727387.1| 249 IHPH 252
                                       *987 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   2.5e-07   0.00075      11     206 ..      38     243 ..      35     257 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.5e-07
                              GvpD  11 ktllikGaPGtGktlftlrgl.dvlrr.esdvlyvstrvddetvseay.........fsgeaeldktalldllkdpl 76 
                                       +t li G  G+Gkt f ++++ + + +  ++ + ++t    e +             +++e+   k a++d     +
  gi|298675637|ref|YP_003727387.1|  38 RTYLISGTSGAGKTNFGIQFIyNGITKyGENGIIIATEERPEQIRKNVskfgwdlkkLEDEG---KLAIIDACSTKI 111
                                       689****************9844566514567888998888888877656555544444444...6799******** PP

                              GvpD  77 eldl.dvdvPiekldlesllefvdeiaaiatkliialdswelvyeylaerydsPediktvkndlvvlaresgvrlvl 152
                                       +++  ++ v +  +d+ s+l+ +   ++  +     +ds   +  +l e  ++  +++ +   l +l   s +   +
  gi|298675637|ref|YP_003727387.1| 112 GVPSqEKYVDVRPFDIRSMLDQIITTQEQINAKRAIVDSTTSISFFLQEPAKIRIELLKLSTTLEILGLTSMMTCEI 188
                                       **962578999999******98766655544445558**8999999999999999999999******9999999999 PP

                              GvpD 153 vletaans.rle.yivdGvvtlnvkeddrgrlrrdlrleklrGvrignrlqPftla 206
                                       + et+     +e ++ dG + l     +  r   ++ + k+rG    ++++P+ ++
  gi|298675637|ref|YP_003727387.1| 189 IDETNPSRfGVEnFVTDGTIMLYYDRHENVR-LHSMEIYKMRGTDHSKKIHPYDIT 243
                                       9998754323452778******877775555.5799****************9876 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.3e-06    0.0038      12     150 ..      16     150 ..       5     162 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.3e-06
                            AAA_25  12 vadlaapppprrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrr 88 
                                        +++++ +p  + l++g l+++ + l+ G +g+GKt + ++  +   t     g       + +++++E++ +++r+
  gi|298675637|ref|YP_003727387.1|  16 ENRVKTGIPGFDELCGGGLIRDRTYLISGTSGAGKTNFGIQFIYNGITKY---G------ENGIIIATEERPEQIRK 83 
                                       4568889999999***9999*************************99866...4......3789************* PP

                            AAA_25  89 Rlravgeal...rddarllvldlagveslpLfakdrggtl....ltadvdaleaaieevegvrlvviDp 150
                                        +++ g +l   +d ++l+++d+ + +++ + ++++   +    + + +d+++ + e+++ ++  ++D+
  gi|298675637|ref|YP_003727387.1|  84 NVSKFGWDLkklEDEGKLAIIDACS-TKIGVPSQEKYVDVrpfdIRSMLDQIITTQEQIN-AKRAIVDS 150
                                       ****996665558888888888533.3444444443333312234555555555555543.55555555 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.3e-05     0.039       2      64 ..      19      82 ..      18     165 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.3e-05
                                      BXSSTHHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHH CS
                                      xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  2 lstgfkdLDklts.GlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlv 64
                                      ++tg   +D+l + Gl +   ++i + ++ Gkt + ++++ n  +k+  + +++  e   eq+ 
  gi|298675637|ref|YP_003727387.1| 19 VKTGIPGFDELCGgGLIRDRTYLISGTSGAGKTNFGIQFIYNGITKYGENGIIIATEERPEQIR 82
                                      6889999999885279999**********************98888887777777777777764 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   2.6e-05     0.077      23      79 ..      36      90 ..      11     191 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.6e-05
                                      TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTG CS
                            ResIII 23 rdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkfls 79
                                      rd+ +li  + G+GKT   +++i++  +k++e + +++  +++  eq +++++kf  
  gi|298675637|ref|YP_003727387.1| 36 RDRTYLISGTSGAGKTNFGIQFIYNGITKYGE-NGIII-ATEERPEQIRKNVSKFGW 90
                                      7899*************************996.44444.455557787777766654 PP

>> MEDS  MEDS: MEthanogen/methylotroph, DcmR Sensory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.2e-05     0.095      19      71 ..      56     109 ..      51     164 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.2e-05
                              MEDS  19 pfikagl.argekvlyvasastldelrealrkagldvdaalesgqleildaeet 71 
                                       +fi +g+ + ge  +++a++++ +++r+ ++k g d+ +++++g+l i+da  t
  gi|298675637|ref|YP_003727387.1|  56 QFIYNGItKYGENGIIIATEERPEQIRKNVSKFGWDLKKLEDEGKLAIIDACST 109
                                       68888885569999************************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1691.37
//
Query:       gi|298675638|ref|YP_003727388.1|  [L=406]
Description: exodeoxyribonuclease VII large subunit [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-88  296.7   1.2      4e-76  256.5   0.5    2.1  2  Exonuc_VII_L     Exonuclease VII, large subunit
    1.4e-32  111.7   0.2      4e-32  110.3   0.2    1.8  1  tRNA_anti_2      OB-fold nucleic acid binding domain
    1.6e-06   28.0   0.2    9.4e-06   25.5   0.0    2.4  3  tRNA_anti-codon  OB-fold nucleic acid binding domain
     0.0015   18.7   0.2     0.0035   17.6   0.2    1.6  1  RecJ_OB          RecJ OB domain
     0.0064   16.9   0.3        5.1    7.5   0.0    2.6  2  RbsD_FucU        RbsD / FucU transport protein family
  ------ inclusion threshold ------
      0.033   14.1   0.0       0.13   12.2   0.0    2.0  1  DUF1508          Domain of unknown function (DUF1508)
       0.07   13.5   2.4       0.23   11.8   2.4    2.0  1  V-SNARE          Vesicle transport v-SNARE protein N-terminus
       0.28   12.0   3.0       0.71   10.7   3.0    1.7  1  Csm2_III-A       Csm2 Type III-A


Domain annotation for each model (and alignments):
>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  256.5   0.5   1.8e-79     4e-76       2     215 ..     122     335 ..     121     338 .. 0.97
   2 !   45.5   0.0   3.2e-15   7.1e-12     240     303 ..     324     389 ..     316     390 .. 0.90

  Alignments for each domain:
  == domain 1  score: 256.5 bits;  conditional E-value: 1.8e-79
                      Exonuc_VII_L   2 fdeerkkplpklpkrigvvtsptgaairDilrtlkrrgplveillfpalvQGeeaaaeiikalekanalkeaDvlii 78 
                                       f++ +kk++p++p+rigv ts++gaai+Di++++krr+p v il+ p+ vQGe++a++i++ +ek+n+ +  Dv+i+
  gi|298675638|ref|YP_003727388.1| 122 FKDTNKKSIPEFPHRIGVATSTKGAAIHDIMNVVKRRFP-VDILISPTIVQGEQSASSIVDSIEKLNQCSV-DVIIL 196
                                       8999***********************************.***************************8776.***** PP

                      Exonuc_VII_L  79 aRGGGSleDLwaFndeelaraiaaskiPvisavGHEtDttiaDfvAdlrapTPtaaAelvvpdkaeleeqleelerr 155
                                       +RGGGSleDLw+Fn+e +arai++s+ PvisavGHEtD+tiaDf Ad+rapTP+aaAelvvpd  ++ +++++l++r
  gi|298675638|ref|YP_003727388.1| 197 GRGGGSLEDLWSFNEEIVARAIYSSQKPVISAVGHETDYTIADFTADMRAPTPSAAAELVVPDYMDIIRRINNLSSR 273
                                       ***************************************************************************** PP

                      Exonuc_VII_L 156 lekaikrlleekkqrleklasrl..kspeellerkrqrldeleerleralkkqlkkkrerle 215
                                       +e+ai+++++ek+++l  +++r+  ++  + +++++q++del +r+e ++k+ lk+k++ l+
  gi|298675638|ref|YP_003727388.1| 274 MENAITNKITEKSTQLYYVQKRMhpERLYDNIRQNQQQVDELLSRMEYSIKNVLKSKKSSLQ 335
                                       **********************964488889************************9999886 PP

  == domain 2  score: 45.5 bits;  conditional E-value: 3.2e-15
                      Exonuc_VII_L 240 e.lleekkerleeleeklealsplkvLkrGyaivrk.edgkvvtsakdlkkgdeleirladgevka 303
                                       +  l++kk++l+  +++l+a+splk+L+rGy+i+++ ++g+v++s++++++gd+l+i ++dg +k+
  gi|298675638|ref|YP_003727388.1| 324 KnVLKSKKSSLQIHANHLQAVSPLKTLERGYSITTDsKNGSVIKSIDNVSNGDSLDIIVKDGIIKC 389
                                       346999********************************************************9876 PP

>> tRNA_anti_2  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.3   0.2   1.8e-35     4e-32       1      94 [.       3      97 ..       3      98 .. 0.96

  Alignments for each domain:
  == domain 1  score: 110.3 bits;  conditional E-value: 1.8e-35
                       tRNA_anti_2  1 lsVseltraikelleaelk.kavwvrGeisnlkrkasghvYftLkDekakisavifrsraaklkftledGmkVlvkgrl 78
                                      ++Vsel+++ik+ll++el+ +++wvrGeisn+k+++sgh+YftLkD + +is+v frs+++++kf++ed m+Vl+ g++
  gi|298675638|ref|YP_003727388.1|  3 YTVSELNTHIKQLLKNELSiNQIWVRGEISNFKKHTSGHYYFTLKDRNNQISCVSFRSTNRNIKFEPEDSMQVLIFGSI 81
                                      79************88888799**********8888******************************************* PP

                       tRNA_anti_2 79 svYeprGsyqlivedi 94
                                      +vY+ rG+yql+v di
  gi|298675638|ref|YP_003727388.1| 82 DVYKVRGQYQLNVFDI 97
                                      *************998 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   4.2e-09   9.4e-06       2      74 ..      26      98 ..      25     100 .. 0.88
   2 ?   -1.8   0.0       1.4   3.1e+03      52      74 ..     321     342 ..     287     344 .. 0.75
   3 ?   -2.1   0.0       1.7   3.9e+03      28      37 ..     385     394 ..     365     405 .. 0.56

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 4.2e-09
                                      EEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEEC..TTSSEEEEEEEEE CS
                   tRNA_anti-codon  2 tvaGrvtsisdrsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrr..pggelelkveeie 74
                                      +v+G++++ + ++++++ +++l+D+  +i +v fr+  ++++ + +  + v ++G +  +  +g +++l+v +i+
  gi|298675638|ref|YP_003727388.1| 26 WVRGEISNFK-KHTSGHYYFTLKDRNNQISCVSFRSTNRNIKFEPEDSMQVLIFGSIDVYkvRG-QYQLNVFDIR 98
                                      89*******8.************************8888888888888888889******6555.5****99987 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.4
                                       EEEEEEEEECTTSSEEEEEEEEE CS
                   tRNA_anti-codon  52 vrvtGrvkrrpggelelkveeie 74 
                                       + ++  +k+ +   l+++++ ++
  gi|298675638|ref|YP_003727388.1| 321 YSIKNVLKSKKSS-LQIHANHLQ 342
                                       5666677777777.999998876 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.7
                                       EEEEEEEETH CS
                   tRNA_anti-codon  28 griqvvlfre 37 
                                       g+i++++ ++
  gi|298675638|ref|YP_003727388.1| 385 GIIKCSVKNT 394
                                       4444444442 PP

>> RecJ_OB  RecJ OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.2   1.5e-06    0.0035      48     106 ..      37      94 ..      15      96 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.5e-06
                           RecJ_OB  48 keknhlklkledesgksleaiaFnlaekleelekgdkvdiaytleinefngretlqlri 106
                                       +++ h  ++l+d++ ++++++ F+ +++  ++e++d ++++   +i+ ++ r ++ql++
  gi|298675638|ref|YP_003727388.1|  37 HTSGHYYFTLKDRN-NQISCVSFRSTNRNIKFEPEDSMQVLIFGSIDVYKVRGQYQLNV 94 
                                       3468********98.******************************************98 PP

>> RbsD_FucU  RbsD / FucU transport protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0    0.0023       5.1      33      86 ..     130     185 ..     123     194 .. 0.78
   2 !    6.9   0.0    0.0036       8.1      14      82 ..     225     303 ..     216     344 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0023
                                       HHCCSCEEE.-CBTTBS-HHHHHHHHHCTS-EEEEEEETCHHHHT...HHHHHHHHH CS
                         RbsD_FucU  33 ipsgveridlalragvpsfldvleavlselpvekvivaeevkeen...pevleelke 86 
                                       ip+  +ri +a +  +  + d++++v + +pv+ ++++  +++++   +++++++++
  gi|298675638|ref|YP_003727388.1| 130 IPEFPHRIGVATSTKGAAIHDIMNVVKRRFPVD-ILISPTIVQGEqsaSSIVDSIEK 185
                                       67778999*************************.77777775555344556666555 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0036
                                       HHHH--TT-EEEEE-TTS-HHCCSCEEE.-CBTTBS-HHHHHHHHHCTS-EEEEEEETCHHHHT............H CS
                         RbsD_FucU  14 vlaelGHgDeiviaDaglPipsgveridlalragvpsfldvleavlselpvekvivaeevkeen............p 78 
                                       v++++GH    +iaD    + + +     a ++ vp+ +d+++ + ++    ++ +++++ e++            +
  gi|298675638|ref|YP_003727388.1| 225 VISAVGHETDYTIADFTADMRAPTPS--AAAELVVPDYMDIIRRINNLSSRMENAITNKITEKStqlyyvqkrmhpE 299
                                       7999**********977666665433..5677777788888877777655434667777755552232222222333 PP

                                       HHHH CS
                         RbsD_FucU  79 evle 82 
                                       ++++
  gi|298675638|ref|YP_003727388.1| 300 RLYD 303
                                       3333 PP

>> DUF1508  Domain of unknown function (DUF1508)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   5.7e-05      0.13       3      17 ..      39      53 ..      38      55 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.7e-05
                                      TTEEEEEEE-TTS-E CS
                           DUF1508  3 nGefrFrLkaaNgev 17
                                      +G+++F+Lk++N+++
  gi|298675638|ref|YP_003727388.1| 39 SGHYYFTLKDRNNQI 53
                                      79************8 PP

>> V-SNARE  Vesicle transport v-SNARE protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   2.4    0.0001      0.23      27      60 ..     302     335 ..     264     343 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
                           V-SNARE  27 lreiekkldeaeelldqMelEvrnlpsserasyk 60 
                                         +i + +++++ell++Me+ ++n+ +s ++s++
  gi|298675638|ref|YP_003727388.1| 302 YDNIRQNQQQVDELLSRMEYSIKNVLKSKKSSLQ 335
                                       567999*******************889999987 PP

>> Csm2_III-A  Csm2 Type III-A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   3.0   0.00032      0.71      28      93 ..     264     331 ..     261     344 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00032
                                       THHHHHHHHHHHHHHHHTHHHHHHHTHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHH--SH.H CS
                        Csm2_III-A  28 iRkfydevkrieekikkkkeeeseeilrklkllkpklaYaagre..eavkelsevlkkaidkvkkske 93 
                                       iR++ +   r+e+ i++k +e+s ++++  k ++p+ +Y+  r+  ++v el + ++  i+ v ksk+
  gi|298675638|ref|YP_003727388.1| 264 IRRINNLSSRMENAITNKITEKSTQLYYVQKRMHPERLYDNIRQnqQQVDELLSRMEYSIKNVLKSKK 331
                                       89999999**********9999999******************5559****************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1424  (0.0794244); expected 358.6 (0.02)
Passed bias filter:                      678  (0.0378158); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2659.48
//
Query:       gi|298675639|ref|YP_003727389.1|  [L=80]
Description: exodeoxyribonuclease VII small subunit [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.8e-21   74.3   5.6    7.9e-21   73.9   5.6    1.2  1  Exonuc_VII_S  Exonuclease VII small subunit
  ------ inclusion threshold ------
      0.063   13.6   4.4        1.7    9.1   4.0    2.0  1  TBCA          Tubulin binding cofactor A
      0.064   13.0   0.5      0.064   13.0   0.5    1.9  2  DivIC         Septum formation initiator
      0.071   13.3   1.7      0.093   12.9   1.7    1.2  1  EF1_GNE       EF-1 guanine nucleotide exchange domain
      0.097   13.4   5.9       0.14   12.9   5.9    1.3  1  RecG_N        RecG N-terminal helical domain
       0.16   12.3   3.3        1.2    9.5   0.3    2.1  2  DUF2524       Protein of unknown function (DUF2524)
       0.27   11.3   4.5       0.57   10.3   1.4    1.9  2  COG2          COG (conserved oligomeric Golgi) complex compon
       0.96    9.0   7.2        3.7    7.1   0.3    2.3  2  YvrJ          YvrJ protein family
       0.97    9.6   7.7        1.2    9.3   0.8    2.1  2  bZIP_1        bZIP transcription factor
        1.8    8.5   7.2       0.23   11.3   2.5    1.8  2  Shugoshin_N   Shugoshin N-terminal coiled-coil region


Domain annotation for each model (and alignments):
>> Exonuc_VII_S  Exonuclease VII small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.9   5.6   4.4e-24   7.9e-21       1      52 []      11      62 ..      11      62 .. 0.98

  Alignments for each domain:
  == domain 1  score: 73.9 bits;  conditional E-value: 4.4e-24
                      Exonuc_VII_S  1 FEealaeLeeIvekLEsgelsLeeslklyeeGvkLlkeCekkLdeaeqkvek 52
                                      FE++l+eLe+Iv++LE+g+l+L+esl+ +e G+kL+++C++k++ ae+k+e+
  gi|298675639|ref|YP_003727389.1| 11 FEDSLEELEQIVKQLENGDLTLDESLETFEYGIKLVQKCNSKINMAEKKIEE 62
                                      9*************************************************85 PP

>> TBCA  Tubulin binding cofactor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   4.0   0.00093       1.7      31      84 ..      20      73 ..      13      77 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00093
                              TBCA 31 klkadgded.eydlkkqeevleetkamipdlkkrlekavekLeelleeeeeleet 84
                                      ++ ++  e+ + +l +  e  e   +++++++++++ a +k eel+ee++el+++
  gi|298675639|ref|YP_003727389.1| 20 QIVKQL-ENgDLTLDESLETFEYGIKLVQKCNSKINMAEKKIEELIEENSELKTK 73
                                      333333.44477888888888888899**********************888543 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.2      0.18   3.2e+02      41      54 ..      16      29 ..       9      36 .. 0.65
   2 ?   13.0   0.5   3.6e-05     0.064      11      45 ..      38      72 ..      35      75 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.18
                                      HHHHHHHCC-XXXX CS
                             DivIC 41 eeLeaevkdLksde 54
                                      eeLe+ vk+L++++
  gi|298675639|ref|YP_003727389.1| 16 EELEQIVKQLENGD 29
                                      56666666666655 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 3.6e-05
                                      XXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             DivIC 11 fgkkgllaykqlkqeiaalqaelaklkaeneeLea 45
                                      ++++g+  +++ +++i+  ++++++l +en eL+ 
  gi|298675639|ref|YP_003727389.1| 38 TFEYGIKLVQKCNSKINMAEKKIEELIEENSELKT 72
                                      678999999************************97 PP

>> EF1_GNE  EF-1 guanine nucleotide exchange domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.7   5.2e-05     0.093      12      73 ..      12      72 ..       1      78 [. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.2e-05
                                      ---HHHHHHHHHH.HS-TSEE--.--EEE-SSS-EEEE.EEEEESSS-GGGGHHHHHHTTS-S CS
                           EF1_GNE 12 etdleelekkvksikleglvwgeasklepiafGlkkLq.iscvieddkvstdeleekieeieg 73
                                      e  leele+ vk+++  +l++ e   le + +G+k +q ++  i+  + +++el+e+ +e++ 
  gi|298675639|ref|YP_003727389.1| 12 EDSLEELEQIVKQLENGDLTLDE--SLETFEYGIKLVQkCNSKINMAEKKIEELIEENSELKT 72
                                      4559*********88888****8..9********99973455677777788888888776665 PP

>> RecG_N  RecG N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   5.9   7.5e-05      0.14       3      58 ..      12      66 ..      10      78 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.5e-05
                                      HHHHHHHHHHHTS---TTT........HHHHHHH---GGGG-HHHH.HHHHHHHHH CS
                            RecG_N  3 EeFLeelekllkkvlsgkleteelieeikkkleliddplleneevlkeklskfldY 58
                                      E+ Leele+++k+ ++g l  +e +e ++  ++l+++   + +  + +k++++++ 
  gi|298675639|ref|YP_003727389.1| 12 EDSLEELEQIVKQLENGDLTLDESLETFEYGIKLVQKCNSKINMAE-KKIEELIEE 66
                                      999******************************9999888887777.99**99985 PP

>> DUF2524  Protein of unknown function (DUF2524)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.3   0.00068       1.2      32      55 ..       4      27 ..       1      35 [. 0.91
   2 ?    3.7   0.2     0.043        77      10      27 ..      45      62 ..      36      78 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00068
                           DUF2524 32 ehyndeeYteAqlkLEeavneLek 55
                                      e ++d+ + + +++LE++v++Le+
  gi|298675639|ref|YP_003727389.1|  4 EDNDDTRFEDSLEELEQIVKQLEN 27
                                      8899*****************985 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.043
                           DUF2524 10 llqkceqaieeaeeqfee 27
                                      l+qkc++ i+ ae++ ee
  gi|298675639|ref|YP_003727389.1| 45 LVQKCNSKINMAEKKIEE 62
                                      678888888888887766 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.073   1.3e+02      28      44 ..      11      27 ..       3      39 .. 0.58
   2 ?   10.3   1.4   0.00032      0.57      83     113 ..      44      74 ..      30      79 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.073
                              COG2 28 LeslrrdLeaylkllek 44
                                      +e+  ++Le+++k+le+
  gi|298675639|ref|YP_003727389.1| 11 FEDSLEELEQIVKQLEN 27
                                      44455555555555543 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00032
                              COG2  83 kkvesvreklsereeeveskleeakeleekr 113
                                       k v++ ++k++++e+++e+ +ee +el+ k+
  gi|298675639|ref|YP_003727389.1|  44 KLVQKCNSKINMAEKKIEELIEENSELKTKQ 74 
                                       668999*********************9887 PP

>> YvrJ  YvrJ protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.3    0.0021       3.7      17      34 ..       9      26 ..       9      27 .. 0.92
   2 ?    4.9   1.8      0.01        18      20      35 ..      57      72 ..      56      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0021
                              YvrJ 17 vRiEkkLdeLtksIeeLs 34
                                      +R+E  L+eL + +++L 
  gi|298675639|ref|YP_003727389.1|  9 TRFEDSLEELEQIVKQLE 26
                                      7*************9996 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.01
                              YvrJ 20 EkkLdeLtksIeeLse 35
                                      Ekk++eL++   eL++
  gi|298675639|ref|YP_003727389.1| 57 EKKIEELIEENSELKT 72
                                      9*******99888876 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.8   0.00068       1.2      26      53 ..      13      40 ..       9      54 .. 0.83
   2 ?    3.8   2.4     0.036        64      46      61 ..      57      72 ..      44      75 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00068
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1 26 aeieeLerrvkaLekeNksLkseleelk 53
                                       + eeLe+ vk+Le+   +L + le+ +
  gi|298675639|ref|YP_003727389.1| 13 DSLEELEQIVKQLENGDLTLDESLETFE 40
                                      5789*******************99987 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.036
                                      HHHHHHHHHHHHHHHH CS
                            bZIP_1 46 kseleelkkevekLks 61
                                       +++eel +e+++Lk+
  gi|298675639|ref|YP_003727389.1| 57 EKKIEELIEENSELKT 72
                                      4555555555555555 PP

>> Shugoshin_N  Shugoshin N-terminal coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2      0.82   1.5e+03      25      35 ..      17      27 ..      15      32 .. 0.66
   2 ?   11.3   2.5   0.00013      0.23      21      43 ..      51      73 ..      44      74 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.82
                       Shugoshin_N 25 elekevseLls 35
                                      ele  v +L +
  gi|298675639|ref|YP_003727389.1| 17 ELEQIVKQLEN 27
                                      67777777744 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00013
                       Shugoshin_N 21 lkirelekevseLlsENlnLRel 43
                                       ki+  ek+++eL+ EN +L+++
  gi|298675639|ref|YP_003727389.1| 51 SKINMAEKKIEELIEENSELKTK 73
                                      699999**************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2273  (0.126778); expected 358.6 (0.02)
Passed bias filter:                      968  (0.0539907); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 637.88
//
Query:       gi|298675640|ref|YP_003727390.1|  [L=458]
Description: putative circadian clock protein KaiC [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-79  265.3   5.5    7.1e-51  172.8   0.7    2.7  2  ATPase           KaiC
    3.5e-10   39.6   0.0    1.1e-05   24.9   0.0    3.0  3  DnaB_C           DnaB-like helicase C terminal domain
    3.6e-08   33.2   0.0      0.012   15.2   0.1    3.1  2  AAA_25           AAA domain
      1e-06   29.3   0.2    0.00018   22.0   0.0    2.8  2  AAA_18           AAA domain
    1.9e-06   27.7   0.0     0.0063   16.2   0.0    2.5  2  Sigma54_activat  Sigma-54 interaction domain
    5.9e-06   25.9   0.1     0.0075   15.8   0.0    2.3  2  RecA             recA bacterial DNA recombination protein
      1e-05   26.0   0.0      0.011   16.1   0.0    2.3  2  AAA_16           AAA ATPase domain
    2.6e-05   23.0   0.6      0.049   12.3   0.0    3.1  4  GvpD             GvpD gas vesicle protein
    3.2e-05   24.3   0.1      0.031   14.6   0.0    2.6  2  AAA_19           AAA domain
    5.1e-05   23.3   0.1       0.03   14.4   0.0    2.9  2  AAA_14           AAA domain
      8e-05   22.6   0.1       0.22   11.5   0.0    2.4  2  NACHT            NACHT domain
    0.00012   22.4   0.0       0.61   10.4   0.0    2.4  2  AAA_22           AAA domain
    0.00014   21.2   0.0       0.39    9.9   0.0    2.2  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    0.00014   21.6   3.4        0.1   12.3   0.1    2.9  3  AAA_24           AAA domain
    0.00024   21.1   0.0       0.42   10.6   0.0    2.6  2  ResIII           Type III restriction enzyme, res subunit
    0.00042   20.1   0.0       0.41   10.4   0.0    2.3  2  DEAD             DEAD/DEAH box helicase
    0.00045   19.8   0.3       0.29   10.6   0.2    2.4  2  AAA_7            P-loop containing dynein motor region
    0.00072   19.3   0.1       0.43   10.3   0.1    2.6  2  IstB_IS21        IstB-like ATP binding protein
     0.0009   18.4   0.2       0.73    8.8   0.1    2.3  2  T2SSE            Type II/IV secretion system protein
     0.0011   18.2   0.2       0.33   10.2   0.0    2.6  2  Rad51            Rad51
     0.0013   18.0   0.0        1.8    7.7   0.0    2.4  2  DAP3             Mitochondrial ribosomal death-associated pro
     0.0016   18.4   0.5        1.4    8.9   0.0    2.8  2  AAA_5            AAA domain (dynein-related subfamily)
     0.0017   18.1   0.0       0.23   11.1   0.0    2.3  2  AAA_30           AAA domain
      0.003   16.7   0.5       0.67    9.0   0.0    3.1  3  PAXNEB           PAXNEB protein
     0.0031   17.9   0.1       0.66   10.4   0.0    2.9  2  RNA_helicase     RNA helicase
     0.0033   17.8   0.4        2.8    8.4   0.2    2.7  2  AAA              ATPase family associated with various cellul
     0.0034   16.3   0.0       0.05   12.5   0.0    2.2  2  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
     0.0056   15.9   0.2       0.02   14.1   0.1    2.0  2  ArsA_ATPase      Anion-transporting ATPase
     0.0098   16.0   0.0      0.024   14.7   0.0    1.8  2  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
  ------ inclusion threshold ------
      0.017   15.0   0.0      0.035   14.0   0.0    1.5  1  MEDS             MEDS: MEthanogen/methylotroph, DcmR Sensory 
      0.022   14.5   3.0       0.46   10.2   0.0    3.2  3  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.031   14.2   0.0      0.074   13.0   0.0    1.6  1  ATPase_2         ATPase domain predominantly from Archaea
      0.035   13.9   0.0       0.94    9.2   0.0    2.3  2  AAA_11           AAA domain
      0.038   13.2   0.1       0.43    9.7   0.0    2.2  2  NB-ARC           NB-ARC domain
      0.038   13.6   0.0        0.1   12.2   0.0    1.7  1  SRP54            SRP54-type protein, GTPase domain
       0.04   13.4   0.5        6.6    6.1   0.0    2.3  2  PhoH             PhoH-like protein
      0.051   13.6   1.4         13    5.8   0.2    2.8  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.06   13.5   0.0         11    6.2   0.0    2.3  2  AAA_33           AAA domain
      0.067   12.1   0.0       0.92    8.4   0.0    2.2  2  AAA_10           AAA-like domain
      0.068   13.4   0.1        2.9    8.1   0.0    2.6  2  Roc              Ras of Complex, Roc, domain of DAPkinase
       0.11   12.3   0.1        1.1    9.0   0.0    2.2  2  CLP1_P           mRNA cleavage and polyadenylation factor CLP
       0.11   12.0   0.0       0.62    9.5   0.0    2.0  2  KdpD             Osmosensitive K+ channel His kinase sensor d
       0.13   11.9   0.0        2.3    7.8   0.0    2.3  2  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
       0.14   12.0   0.1       0.35   10.7   0.0    1.8  1  AAA_26           AAA domain
       0.35   10.8   4.8        1.4    8.8   0.4    3.2  4  NTPase_1         NTPase


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.9   0.4   2.4e-29   9.4e-27       3     229 ..       9     224 ..       7     226 .. 0.84
   2 !  172.8   0.7   1.8e-53   7.1e-51       1     229 [.     238     457 ..     238     458 .] 0.97

  Alignments for each domain:
  == domain 1  score: 93.9 bits;  conditional E-value: 2.4e-29
                            ATPase   3 tgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepa.edlrenakslGwdlekle 78 
                                        gI+glDeil gG+   ++vl++G++G GKt+++l+ l +  ++ ge++++v +  ++  +++  +++    le + 
  gi|298675640|ref|YP_003727390.1|   9 CGIPGLDEIL-GGFVTPSTVLVAGTAGVGKTTMSLHILSNATKN-GEKTLYVPITTESsDKFQDYVST----LEFYD 79 
                                       79*******9.*************************99999777.******98765551444444444....44566 PP

                            ATPase  79 eegklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitglayeekeavaReilrqlvrvlkklg 155
                                       ++  + i ++ ++++       ++d+ + + ++ +++++ +  r+viD+it+l     e++ R+ + +l +++++++
  gi|298675640|ref|YP_003727390.1|  80 DS--IEIHEINRQNA-------EKDPLSTLIDIGNVVSSANPDRIVIDPITPLGFGFVEQEKRRFFYTLDSMIQEWN 147
                                       66..66666666654.......6888888899*********************66677788999************* PP

                            ATPase 156 vTailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRg......tkhskkehpfeIteegikv 226
                                          il+ e    e+++ +  +++ ++dg+i L ++e+  ++ ++l+i+kmRg      ++ s++++ +++++eg k+
  gi|298675640|ref|YP_003727390.1| 148 ALVILTGEL--FEDEIHTTVISH-LADGIIYLFREEVGFRTDKYLKIIKMRGidpqikSNYSSQKIHYDVSSEGFKI 221
                                       ********6..667999999***.***************************83333334678889999999999999 PP

                            ATPase 227 lee 229
                                       +++
  gi|298675640|ref|YP_003727390.1| 222 YPR 224
                                       986 PP

  == domain 2  score: 172.8 bits;  conditional E-value: 1.8e-53
                            ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekl 77 
                                       +++gI+g+D +l +Gip+++++li GepGtGKtif+lq++++g+ + gep+++vt ee +++++ +a+++Gw+l+ +
  gi|298675640|ref|YP_003727390.1| 238 IESGIKGFDPLLGDGIPKASSILIEGEPGTGKTIFSLQYIMNGLIN-GEPCIIVTYEEIPQQIILEASKFGWNLQSY 313
                                       579****************************************999.****************************** PP

                            ATPase  78 eeegklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitgl.ayeekeavaReilrqlvrvlkk 153
                                        +eg l +i +   + +         + +  + +++ ++e++akr+v D i ++ ++++++ ++R  ++ +++ lk 
  gi|298675640|ref|YP_003727390.1| 314 IDEGVLKFIYTNPVDVH---------PAKHESFIKSNVEEMGAKRIVFDGIVNMeMTIQDPIKLRGHFQAVINYLKS 381
                                       *********99999765.........6667778999***************************************** PP

                            ATPase 154 lgvTailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegikvlee 229
                                       ++vT+++++e+  ++e++++   + fi+d v+v+++++ +e+++  l i+k R+t+h+++  +++It++gi++l++
  gi|298675640|ref|YP_003727390.1| 382 KNVTSLFTTEILPGKEEITTSHDASFIMDIVVVMEYTKSSEQIKNNLHIMKSRRTSHDPQLKEYQITDSGIEILND 457
                                       *************************************************************************975 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   2.9e-08   1.1e-05       2     110 ..       7     121 ..       7     152 .. 0.70
   2 !   10.6   0.0   0.00062      0.25       2      63 ..     238     299 ..     238     311 .. 0.80
   3 ?   -0.8   0.1         2   7.8e+02     203     237 ..     403     436 ..     396     441 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 2.9e-08
                                       BXSSTHHHHHHCTSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSE..EEEEESSSXH..HHHHHHHHHHHHTX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx..xxxxxxxxxxxxxx RF
                            DnaB_C   2 lstgfkdLDkltsGlqkgdliiiAarpsmGktalalniaenaavkeklp..vavfslemsa..eqlvqRllsseaei 74 
                                       ls+g   LD++++G+     +++A+ +++Gkt++ l+i +na+++ +++  v +   e s+  ++ v+ l   + +i
  gi|298675640|ref|YP_003727390.1|   7 LSCGIPGLDEILGGFVTPSTVLVAGTAGVGKTTMSLHILSNATKNGEKTlyVPI-TTESSDkfQDYVSTLEFYDDSI 82 
                                       5789999**********************************9987665532333.3333321134455555677788 PP

                                       XHHHHHHTTSXHHHHHHHHHHHHHHHHSE...EEEEEXS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxx RF
                            DnaB_C  75 dskklrtgklkeedweklteaieelseak...lfiddtp 110
                                       + +++++ + +++ +++l +  + +s+a+   ++id  +
  gi|298675640|ref|YP_003727390.1|  83 EIHEINRQNAEKDPLSTLIDIGNVVSSANpdrIVIDPIT 121
                                       888888888777777766665444444322226666555 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00062
                                       BXSSTHHHHHHC.TSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHH CS
                                       xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C   2 lstgfkdLDklt.sGlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeql 63 
                                       +++g k +D l+  G+ k+  i+i + p++Gkt + l+ + n  ++ + p++++  e   +q+
  gi|298675640|ref|YP_003727390.1| 238 IESGIKGFDPLLgDGIPKASSILIEGEPGTGKTIFSLQYIMNGLINGE-PCIIVTYEEIPQQI 299
                                       5678888887662699999*********************99988555.66666666555554 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 2
                                       CCXSEEEEEEECCHHHHHHCHHCEEEEEEEEETTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C 203 qdADvvlflyrdeyykedseekgkaeiiiaKhRnG 237
                                        dA +++ +     y+++se + k+++ i+K R  
  gi|298675640|ref|YP_003727390.1| 403 HDASFIMDIVVVMEYTKSSE-QIKNNLHIMKSRRT 436
                                       68999998887777776554.55789999999975 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1     3e-05     0.012      13      63 ..       5      55 ..       2     155 .. 0.77
   2 !   12.8   0.0   0.00017     0.066      18      60 ..     241     284 ..     225     297 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3e-05
                            AAA_25 13 adlaapppprrwlvkgllpagelallaGapgtGKttlaldlalava.tGkpw 63
                                       +l   +p ++ +++g++   +++l+aG  g+GKtt+ l++    +  G++ 
  gi|298675640|ref|YP_003727390.1|  5 QKLSCGIPGLDEILGGFV-TPSTVLVAGTAGVGKTTMSLHILSNATkNGEKT 55
                                      5566778999999***96.799******************998888666544 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00017
                            AAA_25  18 pppprrwlvkgllpagelallaGapgtGKttlaldlalava.tG 60 
                                        ++  + l+++ +p+ + +l+ G pgtGKt + l+     +  G
  gi|298675640|ref|YP_003727390.1| 241 GIKGFDPLLGDGIPKASSILIEGEPGTGKTIFSLQYIMNGLiNG 284
                                       5555677889899********************99876655555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   4.6e-07   0.00018       1      81 [.      27     119 ..      27     153 .. 0.81
   2 ?    4.6   0.2      0.11        45       1      14 [.     259     272 ..     259     360 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 4.6e-07
                            AAA_18   1 IlltGtpGvGKttlakeL.skrlgf.............gvnlrdvakenglllevdpealdeskrldedkldkllda 63 
                                       +l++Gt+GvGKtt++ ++ s+ +++             +++ +d+++  + +++  +   +e +r + +k d l+++
  gi|298675640|ref|YP_003727390.1|  27 VLVAGTAGVGKTTMSLHIlSNATKNgektlyvpittesSDKFQDYVSTLEFYDDSIEI--HEINRQNAEK-DPLSTL 100
                                       79*************98844444667788899*9999999*******99999999999..8888888877.556555 PP

                            AAA_18  64 leenss.aleegknlvidg 81 
                                       ++  +  ++++++ +vid 
  gi|298675640|ref|YP_003727390.1| 101 IDIGNVvSSANPDRIVIDP 119
                                       5554447788888888885 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.11
                            AAA_18   1 IlltGtpGvGKttl 14 
                                       Il+ G pG+GKt +
  gi|298675640|ref|YP_003727390.1| 259 ILIEGEPGTGKTIF 272
                                       89*********966 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0037       1.5      21      52 ..      23      54 ..      15      67 .. 0.81
   2 !   16.2   0.0   1.6e-05    0.0063      21      76 ..     255     311 ..     247     316 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0037
                                      SSS-EEEECSTTSSHHHHHHHHHHHSTTTTS- CS
                   Sigma54_activat 21 tdlsvlitGesGtGKellaraiheaskrkekp 52
                                      t+++vl+ G  G+GK++++ +i ++ +++ ++
  gi|298675640|ref|YP_003727390.1| 23 TPSTVLVAGTAGVGKTTMSLHILSNATKNGEK 54
                                      6789**************99988877666554 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.6e-05
                                       SSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TT.CHHHHHHEBSSS CS
                   Sigma54_activat  21 tdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipee.lleseLFGhekG 76 
                                       + +s+li+Ge GtGK++++ ++  +   + +p + v   +ip++ +le++ FG +  
  gi|298675640|ref|YP_003727390.1| 255 KASSILIEGEPGTGKTIFSLQYIMNGLINGEPCIIVTYEEIPQQiILEASKFGWNLQ 311
                                       6689****************9999999**************9995679999997655 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.9e-05    0.0075      31      89 ..       4      60 ..       1     124 [. 0.72
   2 !    8.0   0.0    0.0045       1.8      29      88 ..     233     291 ..     224     311 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.9e-05
                                      --EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEES CS
                              RecA 31 vetissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafida 89
                                       + +s+G  +ld  lG  G+     + + G+   Gktt++lh++++a k+g  + ++  
  gi|298675640|ref|YP_003727390.1|  4 FQKLSCGIPGLDEILG--GFVTPSTVLVAGTAGVGKTTMSLHILSNATKNGEKTLYVPI 60
                                      6778999999999987..8888889999***********************99888653 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0045
                                       ----EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEE CS
                              RecA  29 lkvetissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafid 88 
                                        +   i sG  ++d  lG  G+pk   i i G   +Gkt ++l+ i +   +g  +  + 
  gi|298675640|ref|YP_003727390.1| 233 FEDTKIESGIKGFDPLLG-DGIPKASSILIEGEPGTGKTIFSLQYIMNGLINGEPCIIVT 291
                                       45567899999*******.89*************************99888888777665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.8e-05     0.011      24      63 ..      24      71 ..      15     147 .. 0.72
   2 ?    7.5   0.0     0.012       4.8      24      38 ..     254     270 ..     246     278 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.8e-05
                            AAA_16 24 pelvllsGesGvGKsslvrellralekd...ggif.....lrgkcdql 63
                                      p+ vl+ G +GvGK+++  ++l  ++k+     ++      + k++++
  gi|298675640|ref|YP_003727390.1| 24 PSTVLVAGTAGVGKTTMSLHILSNATKNgekTLYVpitteSSDKFQDY 71
                                      689********************9999976423333212233333333 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.012
                            AAA_16  24 p..elvllsGesGvGKs 38 
                                       p  +++l+ Ge+G+GK+
  gi|298675640|ref|YP_003727390.1| 254 PkaSSILIEGEPGTGKT 270
                                       34489***********9 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.1    0.0042       1.7      11      75 ..      25      96 ..      21     109 .. 0.67
   2 ?   -1.1   0.0       1.3   5.4e+02     162     195 ..     166     198 ..     154     205 .. 0.81
   3 !   12.3   0.0   0.00012     0.049      11      31 ..     257     277 ..     253     343 .. 0.87
   4 ?   -3.0   0.0       5.3   2.1e+03     165     315 ..     408     434 ..     376     449 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0042
                              GvpD 11 ktllikGaPGtGktlftlrgldvlrre.sdvlyvstrvddetvseay......fsgeaeldktalldllkdp 75
                                       t+l+ G  G Gkt++ l+ l    ++ ++ lyv   ++ +  ++ y      +++  e+ + +  +  kdp
  gi|298675640|ref|YP_003727390.1| 25 STVLVAGTAGVGKTTMSLHILSNATKNgEKTLYVPITTESSDKFQDYvstlefYDDSIEIHEINRQNAEKDP 96
                                      589******************877665156899976666655555553333323334455555555555555 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.3
                              GvpD 162 leyivdGvvtlnvkeddrgrlrrdlrleklrGvr 195
                                       + +++dG++ l  +e+   r+ + l++ k+rG+ 
  gi|298675640|ref|YP_003727390.1| 166 ISHLADGIIYLF-REEVGFRTDKYLKIIKMRGID 198
                                       567899999995.555577999**********95 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00012
                              GvpD  11 ktllikGaPGtGktlftlrgl 31 
                                        ++li+G+PGtGkt+f l+++
  gi|298675640|ref|YP_003727390.1| 257 SSILIEGEPGTGKTIFSLQYI 277
                                       689**************9975 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 5.3
                              GvpD 165 ivdGvvtlnvkeddrgrlrrdlrleklrGvrignrlqPftladGkfksitrvelvtidtvtdeakyePlandkakfs 241
                                       i                                                                            
  gi|298675640|ref|YP_003727390.1| 408 I---------------------------------------------------------------------------- 408
                                       3............................................................................ PP

                              GvpD 242 vglrdldkllseGtdrGsvvildlgkdlsrdawsvlvlaairdflsqemgvavvppkegspgllkndlnivlsk 315
                                                                                       m + vv     s   +kn+l i++s+
  gi|298675640|ref|YP_003727390.1| 409 ------------------------------------------------MDIVVVMEYTKSSEQIKNNLHIMKSR 434
                                       ................................................34444444444444455555554444 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   7.8e-05     0.031       9      64 ..      23      74 ..      16     166 .. 0.80
   2 ?    7.0   0.0     0.017       6.8      10      35 ..     256     282 ..     253     302 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7.8e-05
                            AAA_19  9 kekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaa 64
                                      + +++lv + +G GKT++  hi++ + ++g    e+ l v  t  + ++ ++ +++
  gi|298675640|ref|YP_003727390.1| 23 TPSTVLVAGTAGVGKTTMSLHILSNATKNG----EKTLYVPITTESSDKFQDYVST 74
                                      56789*********************9999....7789999998888888886644 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.017
                            AAA_19  10 ekvllvtaGpGtGKTrv.lkhivallv 35 
                                       ++ +l+ + pGtGKT   l+ i++ l+
  gi|298675640|ref|YP_003727390.1| 256 ASSILIEGEPGTGKTIFsLQYIMNGLI 282
                                       5678999********752555555444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   7.5e-05      0.03       4      59 ..      26      81 ..      23     155 .. 0.83
   2 ?    6.3   0.0     0.024       9.4       5      48 ..     259     302 ..     255     390 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.5e-05
                            AAA_14  4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelilek 59
                                       +++ G   vGKTt+  +++++   + e++ly+ + +e+ +k++d+ + le++ ++
  gi|298675640|ref|YP_003727390.1| 26 TVLVAGTAGVGKTTMSLHILSNATKNGEKTLYVPITTESSDKFQDYVSTLEFYDDS 81
                                      57899***************9999999************99998875444544443 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.024
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkklad 48 
                                       ++i+G   +GKT +  q+i + l++ e ++ ++ ++ +++ + +
  gi|298675640|ref|YP_003727390.1| 259 ILIEGEPGTGKTIFSLQYIMNGLINGEPCIIVTYEEIPQQIILE 302
                                       78999999***********99999*********99988854443 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00054      0.22       2      29 ..      26      53 ..      25      67 .. 0.84
   2 !    8.9   0.0    0.0034       1.4       3      24 ..     259     281 ..     257     287 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00054
                                      CEEEEC-TTTCHHHHHHHHHHHHCTS-S CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawaegkl 29
                                      +v++ G aG+GKTt+  ++ + + ++  
  gi|298675640|ref|YP_003727390.1| 26 TVLVAGTAGVGKTTMSLHILSNATKNGE 53
                                      89*************9999998877664 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0034
                                       EEEEC-TTTCHHHH.HHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtL.lqklalaw 24 
                                       ++++Ge+G GKT++ lq ++  +
  gi|298675640|ref|YP_003727390.1| 259 ILIEGEPGTGKTIFsLQYIMNGL 281
                                       89***********9667776655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0028       1.1       7      56 ..      26      71 ..      22     120 .. 0.74
   2 !   10.4   0.0    0.0015      0.61       5      26 ..     256     277 ..     254     305 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0028
                            AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdl 56
                                       ++v G +G+GKTt    +l+++++      e+  +v +t  ss + +d 
  gi|298675640|ref|YP_003727390.1| 26 TVLVAGTAGVGKTTMSLHILSNATKN----GEKTLYVPITTESSDKFQDY 71
                                      57899***********9999998543....13444444444444455444 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0015
                            AAA_22   5 agilvvtGesGtGKTtllrrll 26 
                                       a+++++ Ge+GtGKT    ++ 
  gi|298675640|ref|YP_003727390.1| 256 ASSILIEGEPGTGKTIFSLQYI 277
                                       789************8766665 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0015      0.61       3      36 ..      26      57 ..      24      91 .. 0.80
   2 !    9.9   0.0   0.00098      0.39       4      21 ..     259     276 ..     256     302 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0015
                           DUF2075  3 vvlVtGvaGtGKtvvllnllaeleddeeertavy 36
                                       vlV G aG GKt + l++l ++  +++++++ y
  gi|298675640|ref|YP_003727390.1| 26 TVLVAGTAGVGKTTMSLHILSNA--TKNGEKTLY 57
                                      699******************99..444444444 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00098
                           DUF2075   4 vlVtGvaGtGKtvvllnl 21 
                                       +l++G++GtGKt+  l+ 
  gi|298675640|ref|YP_003727390.1| 259 ILIEGEPGTGKTIFSLQY 276
                                       89**********998876 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.1   0.00026       0.1       4      68 ..      26      99 ..      23     163 .. 0.74
   2 !    9.4   0.2     0.002      0.79       3      23 ..     257     283 ..     255     380 .. 0.81
   3 ?   -2.5   0.0       8.8   3.5e+03     163     183 ..     408     431 ..     376     439 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00026
                            AAA_24  4 kiliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdieswedfldevvel......aaeladykt 68
                                       +l+ G +g+GKTt+ +++       g+k+l++ +   +     dkf+d  s  +f+d+  e+      +ae+++++t
  gi|298675640|ref|YP_003727390.1| 26 TVLVAGTAGVGKTTMSLHIlsnatknGEKTLYVPITTES----SDKFQDYVSTLEFYDDSIEIheinrqNAEKDPLST 99
                                      689****************99999999999998554422....23333333444444444444444455444444444 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.002
                            AAA_24   3 lkiliyGpsgiGKTtlakel......g 23 
                                        +ili G++g+GKT + +++       
  gi|298675640|ref|YP_003727390.1| 257 SSILIEGEPGTGKTIFSLQYimngliN 283
                                       6899*************9986655553 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 8.8
                            AAA_24 163 evDlvlranlkred...kvgervl 183
                                       ++D+v+ +++++++   k++ +++
  gi|298675640|ref|YP_003727390.1| 408 IMDIVVVMEYTKSSeqiKNNLHIM 431
                                       578888888886666554444444 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0     0.001      0.42      26      61 ..      26      59 ..      14     120 .. 0.78
   2 !    8.0   0.0    0.0064       2.5      22      69 ..     254     298 ..     191     359 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.001
                                      EEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEE CS
                            ResIII 26 rglikmaTGtGKTlvaaklierllkkgkeekflflv 61
                                       +l++ + G+GKT +++++  + +k+g+  k+l + 
  gi|298675640|ref|YP_003727390.1| 26 TVLVAGTAGVGKTTMSLHILSNATKNGE--KTLYVP 59
                                      67889999*****************977..777764 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0064
                                       .TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHH CS
                            ResIII  22 krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleq 69 
                                        +   +li+ + GtGKT+ +++ i + l +g+     ++v  +++ +q
  gi|298675640|ref|YP_003727390.1| 254 PKASSILIEGEPGTGKTIFSLQYIMNGLINGE---PCIIVTYEEIPQQ 298
                                       6677899*************988776555433...3444455555555 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0     0.001      0.41      15      94 ..      25     100 ..      13     121 .. 0.71
   2 !    7.3   0.0    0.0093       3.7      14      73 ..     256     309 ..     247     346 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.001
                                       CEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST.SEEEEEETTSSHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                              DEAD  15 gdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyid.lrvlliiggvaardq 90 
                                         vlva+  G GKT++ ++ +l++     +k+g k+l+v  t+e   +  + ++++  y d ++++ i  ++a++d 
  gi|298675640|ref|YP_003727390.1|  25 STVLVAGTAGVGKTTM-SLHILSNA----TKNGEKTLYVPITTESSDKFQDYVSTLEFYDDsIEIHEINRQNAEKDP 96 
                                       789***********99.77777666....689999999988888777777777777666444666666777788888 PP

                                       HHHH CS
                                       xxxx RF
                              DEAD  91 lskl 94 
                                       ls+l
  gi|298675640|ref|YP_003727390.1|  97 LSTL 100
                                       8877 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0093
                                       TCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  14 ggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkky 73 
                                         ++l+++e G+GKT   l  +++ +++          i++  +e+ +q++ +++kf+ +
  gi|298675640|ref|YP_003727390.1| 256 ASSILIEGEPGTGKTIFSLQYIMNGLIN------GEPCIIVTYEEIPQQIILEASKFGWN 309
                                       46899**********9887777766643......45557778999999999999998874 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.2   0.00074      0.29      35      80 ..      26      70 ..      22      76 .. 0.78
   2 ?    6.7   0.0     0.012       4.7      32      56 ..     255     280 ..     245     292 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00074
                             AAA_7 35 pvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqd 80
                                       vl+ G++G+GKt++  ++l++  k+  ++l + ++   s+ ++qd
  gi|298675640|ref|YP_003727390.1| 26 TVLVAGTAGVGKTTMSLHILSNATKNGEKTLYVPITTE-SSDKFQD 70
                                      69****************99999988777777777654.4455555 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.012
                             AAA_7  32 nkkpvllvGptGtGKtviikd.llkk 56 
                                       +  ++l+ G+ GtGKt+   + +++ 
  gi|298675640|ref|YP_003727390.1| 255 KASSILIEGEPGTGKTIFSLQyIMNG 280
                                       66789***********9988856665 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.1    0.0011      0.43      49      83 ..      26      60 ..      19      67 .. 0.91
   2 ?    6.1   0.0     0.021       8.5      44      83 ..     253     292 ..     229     313 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0011
                         IstB_IS21 49 nivllGpsGvGKshlaialgveavraglsvlfvrv 83
                                       +++ G +GvGK+ ++  +  +a ++g ++l+v +
  gi|298675640|ref|YP_003727390.1| 26 TVLVAGTAGVGKTTMSLHILSNATKNGEKTLYVPI 60
                                      68999***************************976 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.021
                         IstB_IS21  44 iekkenivllGpsGvGKshlaialgveavraglsvlfvrv 83 
                                       i k+ +i++ G +G+GK+ ++    +++  +g   + v+ 
  gi|298675640|ref|YP_003727390.1| 253 IPKASSILIEGEPGTGKTIFSLQYIMNGLINGEPCIIVTY 292
                                       678899************9988776666666655555555 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.1    0.0018      0.73     130     163 ..      25      58 ..      12      93 .. 0.82
   2 !    7.4   0.0    0.0051         2     117     164 ..     244     293 ..     191     304 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0018
                             T2SSE 130 glilvsGgTgsGKttllyallkeinksderivtv 163
                                        ++lv+G+ g GKtt+   +l+   k+ e+ + v
  gi|298675640|ref|YP_003727390.1|  25 STVLVAGTAGVGKTTMSLHILSNATKNGEKTLYV 58 
                                       579************9999988888876666555 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0051
                             T2SSE 117 kiaevlrkavrerglilvsGgTgsGKttll..yallkeinksderivtvE 164
                                        ++ +l   + +  +il+ G  g+GKt++   y++   in +   ivt E
  gi|298675640|ref|YP_003727390.1| 244 GFDPLLGDGIPKASSILIEGEPGTGKTIFSlqYIMNGLINGEPCIIVTYE 293
                                       556667777788899************98666888888887755666665 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.028        11      16      57 ..       4      44 ..       1      91 [. 0.77
   2 !   10.2   0.0   0.00084      0.33      18      57 ..     237     276 ..     229     324 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.028
                                      S-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHH CS
                             Rad51 16 llqlttGskklDelLgGGietgsiteifGefrsGktqlchtl 57
                                        +l+ G   lDe+L GG+ t s   + G  + Gkt ++  +
  gi|298675640|ref|YP_003727390.1|  4 FQKLSCGIPGLDEIL-GGFVTPSTVLVAGTAGVGKTTMSLHI 44
                                      5678999999****9.6788899999**********876543 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00084
                                       EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHH CS
                             Rad51  18 qlttGskklDelLgGGietgsiteifGefrsGktqlchtl 57 
                                       ++  G k +D lLg Gi+  s   i Ge ++Gkt ++ + 
  gi|298675640|ref|YP_003727390.1| 237 KIESGIKGFDPLLGDGIPKASSILIEGEPGTGKTIFSLQY 276
                                       6889******************************998775 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0044       1.8      26      60 ..      27      61 ..      23      79 .. 0.84
   2 !    7.7   0.0    0.0045       1.8      22      51 ..     255     284 ..     250     306 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0044
                                      EEEE-SSSSSTTTTHHHHHHHGGGS--EEEEES-G CS
                              DAP3 26 lvltGekgsGKSvlLlqalayAlekgwvvlhvpea 60
                                      +++ G  g+GK+++ l++l  A+++g   l vp +
  gi|298675640|ref|YP_003727390.1| 27 VLVAGTAGVGKTTMSLHILSNATKNGEKTLYVPIT 61
                                      6789*********************9888888765 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0045
                                       ---EEEEE-SSSSSTTTTHHHHHHHGGGS- CS
                              DAP3  22 kvkrlvltGekgsGKSvlLlqalayAlekg 51 
                                       k+  ++++Ge+g+GK++  lq +  +l +g
  gi|298675640|ref|YP_003727390.1| 255 KASSILIEGEPGTGKTIFSLQYIMNGLING 284
                                       667889***************999988773 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0036       1.4       2      35 ..      27      63 ..      26      74 .. 0.83
   2 ?    7.0   0.0     0.013       5.4       2      19 ..     259     276 ..     258     364 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0036
                                      EEEE--SSSSHHHHHHHGGGGB...S--EEEEE--TT CS
                             AAA_5  2 vlLvGppGtgKselaerlaaal...nreveyvqltrd 35
                                      vl+ G  G+gK++++ ++++     + +++yv +t  
  gi|298675640|ref|YP_003727390.1| 27 VLVAGTAGVGKTTMSLHILSNAtknGEKTLYVPITTE 63
                                      8999***********9987655598888999988865 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.013
                                       EEEE--SSSSHHHHHHHG CS
                             AAA_5   2 vlLvGppGtgKselaerl 19 
                                       +l+ G+pGtgK+ ++ ++
  gi|298675640|ref|YP_003727390.1| 259 ILIEGEPGTGKTIFSLQY 276
                                       7899********887664 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00058      0.23      20      66 ..      26      72 ..      19     124 .. 0.71
   2 ?    4.5   0.0     0.063        25      21      33 ..     259     271 ..     254     284 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00058
                            AAA_30 20 vavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeel 66
                                      ++++ G AG GKtt+  ++   ++++g++ + +  t + +++ ++ +
  gi|298675640|ref|YP_003727390.1| 26 TVLVAGTAGVGKTTMSLHILSNATKNGEKTLYVPITTESSDKFQDYV 72
                                      57899**********99999999999999998888888888777644 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.063
                            AAA_30  21 avltGpAGtGKtt 33 
                                        +++G +GtGKt 
  gi|298675640|ref|YP_003727390.1| 259 ILIEGEPGTGKTI 271
                                       579*********6 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.2      0.17        68      19      42 ..       7      29 ..       5      34 .. 0.80
   2 ?    1.2   0.0      0.41   1.6e+02     236     281 ..     134     176 ..     115     180 .. 0.87
   3 !    9.0   0.0    0.0017      0.67      20      82 ..     239     300 ..     235     303 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.17
                            PAXNEB 19 tStGtpsLDklLgGGLplGsilli 42
                                       S G+p LD++L GG+   s +l+
  gi|298675640|ref|YP_003727390.1|  7 LSCGIPGLDEIL-GGFVTPSTVLV 29
                                      599*********.66776666666 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.41
                            PAXNEB 236 kFLhsLrallrssnlvalitlplsliarssslvrkieqlvDtvieL 281
                                       +F+++L +++++ n+ ++ t   +l+ +++ +++ i +l+D++i L
  gi|298675640|ref|YP_003727390.1| 134 RFFYTLDSMIQEWNALVILT--GELF-EDEIHTTVISHLADGIIYL 176
                                       79999999999888766655..7999.99**************987 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0017
                            PAXNEB  20 StGtpsLDklLgGGLplGsillieEdgttdfakvLlkyFlAeGvvqkhevlvlsldddpeewl 82 
                                        +G++ +D lLg G+p  s++lie +   + +++    ++ +G++++   ++++++++p++++
  gi|298675640|ref|YP_003727390.1| 239 ESGIKGFDPLLGDGIPKASSILIEGEPG-TGKTIFSLQYIMNGLINGEPCIIVTYEEIPQQII 300
                                       59*********99***********6643.3466777789999************999999975 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0    0.0017      0.66       1      62 [.      27      85 ..      27     110 .. 0.63
   2 ?    4.3   0.0      0.13        50       1      17 [.     259     275 ..     259     295 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0017
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklklkkkdsvys..rnpeddfwdgYtgqevvvidDfgqvk 62
                                      +++ G +g+GK+t++ ++ ++ +k+     ++++y+   + ++d ++ Y   +   +dD  +++
  gi|298675640|ref|YP_003727390.1| 27 VLVAGTAGVGKTTMSLHILSNATKNG----EKTLYVpiTTESSDKFQDYV-STLEFYDDSIEIH 85
                                      5789*************777777444....45555544566667777776.4455566654444 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.13
                      RNA_helicase   1 iwlyGpsgeGKStlake 17 
                                       i++ G++g+GK+ ++ +
  gi|298675640|ref|YP_003727390.1| 259 ILIEGEPGTGKTIFSLQ 275
                                       6899********99744 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.2    0.0069       2.8       1      24 [.      27      50 ..      27     117 .. 0.74
   2 ?    6.8   0.0     0.021       8.3       1      14 [.     259     272 ..     259     304 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0069
                                      EEEESSTTSSHHHHHHHHHHHHTH CS
                               AAA  1 vllyGppGtGKTllakavakelgv 24
                                      vl+ G+ G+GKT++   + +++  
  gi|298675640|ref|YP_003727390.1| 27 VLVAGTAGVGKTTMSLHILSNATK 50
                                      799***********9999888742 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.021
                                       EEEESSTTSSHHHH CS
                               AAA   1 vllyGppGtGKTll 14 
                                       +l+ G pGtGKT++
  gi|298675640|ref|YP_003727390.1| 259 ILIEGEPGTGKTIF 272
                                       6899********86 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   0.00013      0.05      18      60 ..      27      69 ..      22      77 .. 0.85
   2 ?    1.3   0.0      0.33   1.3e+02      16      38 ..     257     280 ..     254     293 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                     TrwB_AAD_bind 18 ilivGttGsGKtqalekllrairargdraivlDltGafvsrfy 60
                                      +l++Gt+G GKt++  ++l ++ + g++ + +  t +  ++f 
  gi|298675640|ref|YP_003727390.1| 27 VLVAGTAGVGKTTMSLHILSNATKNGEKTLYVPITTESSDKFQ 69
                                      7899***********************9987777777776665 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.33
                     TrwB_AAD_bind  16 qhilivGttGsGKtqalek.llra 38 
                                       + ili G  G+GKt    + ++++
  gi|298675640|ref|YP_003727390.1| 257 SSILIEGEPGTGKTIFSLQyIMNG 280
                                       5799**********8644404444 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.1     5e-05      0.02       4      66 ..      27      86 ..      25     112 .. 0.68
   2 ?   -2.0   0.0         4   1.6e+03      43      43 ..     408     408 ..     355     441 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5e-05
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEE..E-STTTHHHHHHTS.--BSS-EEETSSEEEEE CS
                       ArsA_ATPase  4 ilvgGKGGVGKttvsaatavklsekgkkvlli..stDPAhslsDsfdq.klgkeptkvkeNLsavE 66
                                      +lv+G  GVGKtt+s  +  + +++g+k+l +  +t       D  ++ ++  + + +       E
  gi|298675640|ref|YP_003727390.1| 27 VLVAGTAGVGKTTMSLHILSNATKNGEKTLYVpiTTESSDKFQDYVSTlEFYDDSIEI------HE 86
                                      89***************************98621455444444444333333333333......33 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4
                                       H CS
                       ArsA_ATPase  43 l 43 
                                       +
  gi|298675640|ref|YP_003727390.1| 408 I 408
                                       1 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0     6e-05     0.024       3      33 ..      28      58 ..      26     221 .. 0.90
   2 ?   -2.0   0.0       8.5   3.4e+03       7      17 ..     264     274 ..     258     279 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6e-05
                                      EEESSTTSSHHHHHHHHHHHHHHTT--EEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  3 iastkGGvGKTtlaanLaralarrglrVllv 33
                                      +++++ GvGKTt++++++    ++g ++l v
  gi|298675640|ref|YP_003727390.1| 28 LVAGTAGVGKTTMSLHILSNATKNGEKTLYV 58
                                      678999*******************999976 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 8.5
                                       STTSSHHHHHH CS
                                       xxxxxxxxxxx RF
                              CbiA   7 kGGvGKTtlaa 17 
                                         G+GKT +++
  gi|298675640|ref|YP_003727390.1| 264 EPGTGKTIFSL 274
                                       569****9986 PP

>> MEDS  MEDS: MEthanogen/methylotroph, DcmR Sensory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   8.7e-05     0.035      19      95 ..     275     346 ..     272     383 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.7e-05
                              MEDS  19 pfikaglargekvlyvasastldelrealrkagldvdaalesgqleildaeetylrgggfdpermlealrralakal 95 
                                       ++i +gl +ge++++v+ ++  +++  + +k g +++++ ++g l+++     y++    +p++  +++++ +++  
  gi|298675640|ref|YP_003727390.1| 275 QYIMNGLINGEPCIIVTYEEIPQQIILEASKFGWNLQSYIDEGVLKFI-----YTNPVDVHPAKHESFIKSNVEEMG 346
                                       89*****************************************77665.....455666666666666666666654 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0012      0.46      35      97 ..      26      91 ..      22      98 .. 0.73
   2 ?    2.1   0.0      0.35   1.4e+02      35      50 ..     258     273 ..     254     283 .. 0.82
   3 ?    0.1   0.1       1.5     6e+02      59     120 ..     356     416 ..     347     432 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0012
                            RuvB_N 35 hvllyGpPGlGkttla.kiiakelgvklkitsgPvlekagd.laalltnlee.kdvlfideihrls 97
                                       vl++G  G+Gktt++ +i+++  +   k+   P+  +++d +   +++le  +d + i ei r +
  gi|298675640|ref|YP_003727390.1| 26 TVLVAGTAGVGKTTMSlHILSNATKNGEKTLYVPITTESSDkFQDYVSTLEFyDDSIEIHEINRQN 91
                                      599************956888888888888888987766652566777777514556666666654 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.35
                            RuvB_N  35 hvllyGpPGlGkttla 50 
                                        +l+ G PG Gkt ++
  gi|298675640|ref|YP_003727390.1| 258 SILIEGEPGTGKTIFS 273
                                       589**********765 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.5
                            RuvB_N  59 vklkitsgPvlekagdlaalltnleekdv..lfideihrlsraveevlysamedfrldivigkG 120
                                       v++++t    ++  g + a+++ l++k+v  lf  ei    +  ee+  s    f +div+   
  gi|298675640|ref|YP_003727390.1| 356 VNMEMTIQDPIKLRGHFQAVINYLKSKNVtsLFTTEI---LPGKEEITTSHDASFIMDIVVVME 416
                                       6778888888899999999999999999866777776...356678887777788888877554 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00019     0.074      21      75 ..      25      80 ..      14     118 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00019
                          ATPase_2 21 eiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie..eeeek 75
                                      + +++ G  g+GKt++  +i++n  + +++   y ++ +es++k+++++   e +++
  gi|298675640|ref|YP_003727390.1| 25 STVLVAGTAGVGKTTMSLHILSNATKNGEK-TLYVPITTESSDKFQDYVStlEFYDD 80
                                      567899******************887765.55568899999999988766633332 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.31   1.2e+02      18      44 ..      25      51 ..      15      89 .. 0.77
   2 ?    9.2   0.0    0.0024      0.94      20      41 ..     259     281 ..     250     341 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.31
                            AAA_11 18 eitliqGPPGtgKTktivellsqllsr 44
                                      + +l+ G  G gKT++ +++ls+++++
  gi|298675640|ref|YP_003727390.1| 25 STVLVAGTAGVGKTTMSLHILSNATKN 51
                                      45899****************999433 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0024
                            AAA_11  20 tliqGPPGtgKT.ktivellsql 41 
                                        li+G PGtgKT + + ++++ l
  gi|298675640|ref|YP_003727390.1| 259 ILIEGEPGTGKTiFSLQYIMNGL 281
                                       69**********55555555555 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0    0.0011      0.43      22      46 ..      26      49 ..      19      95 .. 0.83
   2 ?    0.7   0.0      0.62   2.5e+02      22      39 ..     258     275 ..     247     285 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0011
                                      EEEEEESTTSSHHHHHHHHCCSHCC CS
                            NB-ARC 22 vvalvGmgGvGKttlakqilnksde 46
                                       v + G +GvGKtt++ +il++ ++
  gi|298675640|ref|YP_003727390.1| 26 TVLVAGTAGVGKTTMSLHILSN-AT 49
                                      57899**************998.33 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.62
                                       EEEEEESTTSSHHHHHHH CS
                            NB-ARC  22 vvalvGmgGvGKttlakq 39 
                                        + + G +G GKt+ + q
  gi|298675640|ref|YP_003727390.1| 258 SILIEGEPGTGKTIFSLQ 275
                                       67899********98654 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00025       0.1       2      90 ..      25     118 ..      24     122 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00025
                                       EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEE.....EESTSSTTHHHHHHHHHHHTTEEEEE.SSTTSCHHHHH CS
                             SRP54   2 nvillvGlqGaGKTttlaKLaallkkegkkvllv.....aaDtfRaaAveQLktlaeklgvpvik.kkeeadpaava 72 
                                       + +l++G+ G+GKTt    +    +k+g+k+l v     + D f    v  L+ + ++++++ i+ ++ e+dp +++
  gi|298675640|ref|YP_003727390.1|  25 STVLVAGTAGVGKTTMSLHILSNATKNGEKTLYVpitteSSDKFQD-YVSTLEFYDDSIEIHEINrQNAEKDPLSTL 100
                                       6799***********9999999999998888766333335677754.567788888888888777677777899888 PP

                                       HHHHHHHHHTTSSEEEEE CS
                             SRP54  73 keavekakeekidvvlvD 90 
                                        +  +   + + d +++D
  gi|298675640|ref|YP_003727390.1| 101 IDIGNVVSSANPDRIVID 118
                                       888888888888888888 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2     0.038        15      21      47 ..      26      52 ..      16      61 .. 0.83
   2 ?    6.1   0.0     0.016       6.6      19      47 ..     256     284 ..     249     295 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.038
                                      EEEEE--TTSSTTHHHHHHHHHHHHTT CS
                              PhoH 21 ivfaiGpaGtGKtylavalavealkkk 47
                                       v ++G aG GKt +++ +  +a+k++
  gi|298675640|ref|YP_003727390.1| 26 TVLVAGTAGVGKTTMSLHILSNATKNG 52
                                      68899**********998877777665 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.016
                                       -SEEEEE--TTSSTTHHHHHHHHHHHHTT CS
                              PhoH  19 ndivfaiGpaGtGKtylavalavealkkk 47 
                                        + + + G+ GtGKt +++++ ++ l ++
  gi|298675640|ref|YP_003727390.1| 256 ASSILIEGEPGTGKTIFSLQYIMNGLING 284
                                       5567899***********99887777665 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.2     0.033        13      20      42 ..      25      47 ..      11      56 .. 0.80
   2 ?    5.7   0.0     0.036        14      20      38 ..     257     275 ..     236     289 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.033
                                      EEEEEEESTTSSHHHHHHHHHHH CS
                              TsaE 20 dvilLeGdLGaGKTtlvrglaka 42
                                      +++l  G  G+GKTt++ +++++
  gi|298675640|ref|YP_003727390.1| 25 STVLVAGTAGVGKTTMSLHILSN 47
                                      56999***********9988876 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.036
                                       EEEEEEESTTSSHHHHHHH CS
                              TsaE  20 dvilLeGdLGaGKTtlvrg 38 
                                       + il+eG+ G+GKT ++ +
  gi|298675640|ref|YP_003727390.1| 257 SSILIEGEPGTGKTIFSLQ 275
                                       4699***********9744 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.027        11       2      24 ..      27      49 ..      27     107 .. 0.82
   2 ?    4.9   0.0     0.067        27       2      20 ..     259     277 ..     259     298 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.027
                            AAA_33  2 vllvGlpGsGKstlaerllkklg 24
                                      vl+ G +G+GK+t + ++l + +
  gi|298675640|ref|YP_003727390.1| 27 VLVAGTAGVGKTTMSLHILSNAT 49
                                      7899**********998876554 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.067
                            AAA_33   2 vllvGlpGsGKstlaerll 20 
                                       +l+ G pG+GK+ ++ +++
  gi|298675640|ref|YP_003727390.1| 259 ILIEGEPGTGKTIFSLQYI 277
                                       5789*********998775 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0023      0.92      22      94 ..      25      98 ..      15     107 .. 0.75
   2 ?    1.0   0.0       0.4   1.6e+02      21      50 ..     256     285 ..     251     297 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0023
                            AAA_10 22 sasliiGdlGnGKSvlakllvlyisllggkaliiDpkke.rekfketlpe...iakkinvvtLdseeenegvLdPlv 94
                                      s +l+ G  G GK  ++  +  +++  g+k l++  + e   kf+  +     + ++i++ +++   +++ + dPl+
  gi|298675640|ref|YP_003727390.1| 25 STVLVAGTAGVGKTTMSLHILSNATKNGEKTLYVPITTEsSDKFQDYVSTlefYDDSIEIHEIN---RQNAEKDPLS 98
                                      45799*********************************96677877775522144455554444...5556667765 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.4
                            AAA_10  21 asasliiGdlGnGKSvlakllvlyisllgg 50 
                                       as  li G++G GK +++   +++ ++ g+
  gi|298675640|ref|YP_003727390.1| 256 ASSILIEGEPGTGKTIFSLQYIMNGLINGE 285
                                       67789*********9988766666666555 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0074       2.9       2      38 ..      27      62 ..      26      81 .. 0.73
   2 ?    2.4   0.0      0.43   1.7e+02       2      22 ..     259     279 ..     258     296 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0074
                                      EEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEE CS
                               Roc  2 vvlvGdsgvGKtsllkrfvedkfsekekstigvdflt 38
                                      v++ G +gvGKt++  +++++  ++ e +t+ v ++t
  gi|298675640|ref|YP_003727390.1| 27 VLVAGTAGVGKTTMSLHILSNATKNGE-KTLYVPITT 62
                                      6789*************9988776554.555555544 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.43
                                       EEEESSTTSSHHHHHHCHCT- CS
                               Roc   2 vvlvGdsgvGKtsllkrfved 22 
                                       +++ G+ g+GKt +  +++ +
  gi|298675640|ref|YP_003727390.1| 259 ILIEGEPGTGKTIFSLQYIMN 279
                                       5677**********9999876 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0029       1.1       1      30 [.      31      60 ..      31     116 .. 0.80
   2 ?    1.0   0.0       0.8   3.2e+02     128     152 ..     406     431 ..     394     450 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0029
                            CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDl 30
                                      G   +GK+T++  +l +a+++g+k++yv +
  gi|298675640|ref|YP_003727390.1| 31 GTAGVGKTTMSLHILSNATKNGEKTLYVPI 60
                                      7789***********************965 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.8
                            CLP1_P 128 alepdvvvvldqeellnelkrdlp.l 152
                                        + +d+vvv++  ++ +++k++l+  
  gi|298675640|ref|YP_003727390.1| 406 SFIMDIVVVMEYTKSSEQIKNNLHiM 431
                                       566799*************9999833 PP

>> KdpD  Osmosensitive K+ channel His kinase sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0    0.0015      0.62       7      59 ..      27      87 ..      24     133 .. 0.72
   2 ?   -0.7   0.0         2   7.9e+02       9      42 ..     261     294 ..     257     304 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0015
                              KdpD  7 iflGaapGvGktyamLeeaqelkeegvdvviglvethgrketealleglevi........p 59
                                      + +  ++GvGkt   L+   +++++g + +   + t++ ++ ++ +++le           
  gi|298675640|ref|YP_003727390.1| 27 VLVAGTAGVGKTTMSLHILSNATKNGEKTLYVPITTESSDKFQDYVSTLEFYddsieiheI 87
                                      6677799******************************************988333322221 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2
                              KdpD   9 lGaapGvGktyamLeeaqelkeegvdvviglvet 42 
                                       +   pG Gkt+  L+  ++   +g  ++i + e+
  gi|298675640|ref|YP_003727390.1| 261 IEGEPGTGKTIFSLQYIMNGLINGEPCIIVTYEE 294
                                       55679*******9999999999999888877665 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0057       2.3      11      52 ..      21      63 ..      10      93 .. 0.75
   2 ?    2.0   0.0      0.35   1.4e+02      13      47 ..     255     290 ..     241     422 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0057
                                      EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSS.EEEEEEESEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                       ATP-synt_ab 11 ivqGqrtlipgafgvGktvisqslskqsnsdd.aiiyvgiGer 52
                                      +v   ++l+ g +gvGkt++s +++ +++++   + yv i   
  gi|298675640|ref|YP_003727390.1| 21 FVTPSTVLVAGTAGVGKTTMSLHILSNATKNGeKTLYVPITTE 63
                                      56667999*************5555555454338888877544 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.35
                                       TT-EEEEEESTTSSHHHHH.HHHHHHSSTSSEEEEE CS
                                       xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  13 qGqrtlipgafgvGktvis.qslskqsnsddaiiyv 47 
                                       +   +li g+ g+Gkt  s q +++   + + +i+v
  gi|298675640|ref|YP_003727390.1| 255 KASSILIEGEPGTGKTIFSlQYIMNGLINGEPCIIV 290
                                       55678999*********9988888876444555555 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00088      0.35       2      57 ..      26      80 ..      25     167 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00088
                            AAA_26  2 tifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiqtgiee.dedselikellgl 57
                                      t++v+gt +gvGKT+ sl +++  +++g k+ y+ Pi t++++  +d   + e+++ 
  gi|298675640|ref|YP_003727390.1| 26 TVLVAGT-AGVGKTTMSLHILSNATKNGEKTLYV-PITTESSDkFQDYVSTLEFYDD 80
                                      6777777.7***************9999999998.9999887523333333333333 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.4    0.0034       1.4       2      27 ..      27      52 ..      26      64 .. 0.88
   2 ?   -2.2   0.0       8.7   3.5e+03      95     128 ..     111     150 ..     102     175 .. 0.67
   3 ?    2.1   0.0       0.4   1.6e+02       2      15 ..     259     272 ..     258     283 .. 0.84
   4 ?   -2.2   0.0       8.6   3.4e+03      98     113 ..     349     364 ..     327     404 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0034
                                      EEEE--TTSSHHHHHHHHHHHH...G CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssg 27
                                      v++ G  GvGKtT+   +l++  ++g
  gi|298675640|ref|YP_003727390.1| 27 VLVAGTAGVGKTTMSLHILSNATKNG 52
                                      899************99999887776 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 8.7
                                       HH-EEEE---.....STTGGG-HHHHHHHHHHHT.TTSEE CS
                          NTPase_1  95 eadviviDEi.....GkmElkskkfkeaveevLk.sekpv 128
                                       ++d iviD i     G  E + ++f  +++ +++  +  v
  gi|298675640|ref|YP_003727390.1| 111 NPDRIVIDPItplgfGFVEQEKRRFFYTLDSMIQeWNALV 150
                                       6777888887444445667777777777777777444444 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.4
                                       EEEE--TTSSHHHH CS
                          NTPase_1   2 vfiTGppGvGKtTl 15 
                                       ++i G+pG+GKt +
  gi|298675640|ref|YP_003727390.1| 259 ILIEGEPGTGKTIF 272
                                       8899*******976 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 8.6
                                       EEEE---STTGGG-HH CS
                          NTPase_1  98 viviDEiGkmElkskk 113
                                        iv D i +mE++++ 
  gi|298675640|ref|YP_003727390.1| 349 RIVFDGIVNMEMTIQD 364
                                       5677777777777664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                        45  (0.0025099); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              45  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 3154.90
//
Query:       gi|298675641|ref|YP_003727391.1|  [L=79]
Description: hypothetical protein Metev_1758 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.068   13.1   0.1      0.092   12.7   0.1    1.2  1  DUF5345          Family of unknown function (DUF5345)


Domain annotation for each model (and alignments):
>> DUF5345  Family of unknown function (DUF5345)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   5.1e-06     0.092      35      58 ..      45      68 ..      39      76 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.1e-06
                           DUF5345 35 krlrrElllFlliAllilslllla 58
                                         +r +l+F+l+Al++++++ ++
  gi|298675641|ref|YP_003727391.1| 45 DVVYRNVLIFTLVALVFVTVTYSI 68
                                      556899*************98766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1295  (0.0722293); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 636.78
//
Query:       gi|298675642|ref|YP_003727392.1|  [L=447]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-18   65.3   0.9    7.1e-18   64.3   0.9    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    6.6e-11   42.5   1.0    1.4e-10   41.4   1.0    1.5  1  OrfB_IS605      Probable transposase
    3.5e-10   39.2   0.0    8.4e-10   38.0   0.0    1.7  1  HTH_OrfB_IS605  Helix-turn-helix domain
  ------ inclusion threshold ------
        1.3    9.0   5.7        2.4    8.1   5.7    1.4  1  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.3   0.9   1.6e-21   7.1e-18       2      69 .]     346     413 ..     345     413 .. 0.97

  Alignments for each domain:
  == domain 1  score: 64.3 bits;  conditional E-value: 1.6e-21
                    OrfB_Zn_ribbon   2 rklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       +++ ++l+yk  + G+ ++e++++yTS++C +Cg+++k +l +r+++Cp C  ++drD n+ai i++r
  gi|298675642|ref|YP_003727392.1| 346 GRFAQFLAYKSLRVGKRIIEIDESYTSQDCCNCGYRQKMPLYERNYNCPYCRQSMDRDKNSAIVIMER 413
                                       5899*************************************************************986 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   1.0   3.2e-14   1.4e-10      13     117 ..     216     322 ..     205     324 .. 0.90

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 3.2e-14
                        OrfB_IS605  13 pkgnkaagiDlGinnLatvvtedgtw.flykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsrrr 88 
                                       + + k +++D+G+n+  t+v++dg+  ++++ r+ k ++ + ++ + +l+ ++  sk++ + +r l r+ +k s+++
  gi|298675642|ref|YP_003727392.1| 216 KHNDKYLAMDIGVNK-HTMVDSDGNLrEMINKRPDKYREPKIQQIQSRLDHCKRYSKKWYRLKRNLNRMKQKSSNQL 291
                                       567899*******99.689999999879************************************************* PP

                        OrfB_IS605  89 khllhklathliktlkev..gvetLnvgnmk 117
                                       k+++hk +++++++ ++    +++L  ++m+
  gi|298675642|ref|YP_003727392.1| 292 KDFQHKKTRNIVDNTDASviIIGDLSAKQMA 322
                                       **************99985567888888876 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.0   1.9e-13   8.4e-10       6      45 ..       5      44 ..       1      46 [. 0.90

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 1.9e-13
                    HTH_OrfB_IS605  6 ykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeee 45
                                        +r+ PT +Qee+l+   + +R+ YN+aLaerk+ay ++
  gi|298675642|ref|YP_003727392.1|  5 LPVRIIPTSQQEELLWILSEKCRLLYNFALAERKDAYSNG 44
                                      568**********************************876 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   5.7   0.00054       2.4      26      48 ..     375     401 ..     373     402 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00054
                                       -HHHHHHHHH....TT-B-TTT--B-- CS
                        zf-C3HC4_3  26 CeeCaekllk....rkkkCpiCrrpie 48 
                                       C +C  + +     r+ +Cp+Cr++++
  gi|298675642|ref|YP_003727392.1| 375 CCNCGYRQKMplyeRNYNCPYCRQSMD 401
                                       999*****989**9**********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1218  (0.0679346); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.23s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3162.34
//
Query:       gi|298675643|ref|YP_003727393.1|  [L=105]
Description: RNAse P [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-18   66.6   0.6    2.3e-18   66.2   0.6    1.2  1  Rpr2            RNAse P Rpr2/Rpp21/SNM1 subunit domain
  ------ inclusion threshold ------
      0.034   14.0   3.3       0.54   10.2   0.1    2.2  2  ADD_ATRX        Cysteine Rich ADD domain
      0.086   12.9   0.0      0.086   12.9   0.0    1.2  1  Haem_degrading  Haem-degrading
       0.09   12.7   3.1        7.6    6.5   0.0    2.3  2  HNH_5           HNH endonuclease
        0.2   11.4   1.1        3.3    7.5   0.0    2.2  2  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII


Domain annotation for each model (and alignments):
>> Rpr2  RNAse P Rpr2/Rpp21/SNM1 subunit domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.2   0.6   6.5e-22   2.3e-18       1      90 []      19      96 ..      19      96 .. 0.94

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 6.5e-22
                                      HHHHHHHHHH.HHHHH-HHHHHHHHHHHHHHHHHCT---SSTCCCTB-TTT--B--CTTTEEEEEE-SSS-E....... CS
                              Rpr2  1 rlnfLyqaahlqlaeaspalsrylakqlrevskkaqlrlppsvkrtvCkkCgsvlipgvtcsvrvenkskkkkkkkkka 79
                                      r++ L++ a+ + ++++ + s+++a+ +r++ +k+++rlpp++kr++Ck+C+s+l+pg t++vr++n++          
  gi|298675643|ref|YP_003727393.1| 19 RIQLLFSFAENEARQSNLEWSNRYAYLARKIGMKYRIRLPPELKRRICKQCNSYLLPGKTSRVRLKNNN---------- 87
                                      89999999*99999***************************************************8733.......... PP

                                      ..EEEEETTTT CS
                              Rpr2 80 dvlvvtClaCg 90
                                        ++vtCl+Cg
  gi|298675643|ref|YP_003727393.1| 88 --VTVTCLNCG 96
                                      ..569*****7 PP

>> ADD_ATRX  Cysteine Rich ADD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00015      0.54      26      54 ..      52      80 ..      48      82 .. 0.83
   2 ?    5.0   0.5     0.006        21       6      20 ..      84      98 ..      79     105 .] 0.77

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00015
                          ADD_ATRX 26 kdslykHPvLkVLiCksCfkyyssddisk 54
                                      k  ++  P Lk  iCk+C +y   ++ s+
  gi|298675643|ref|YP_003727393.1| 52 KYRIRLPPELKRRICKQCNSYLLPGKTSR 80
                                      566777799999*********98887776 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.006
                          ADD_ATRX  6 keleeivsCtaCgqq 20
                                      k+ + +v+C  Cg+q
  gi|298675643|ref|YP_003727393.1| 84 KNNNVTVTCLNCGNQ 98
                                      445568*******99 PP

>> Haem_degrading  Haem-degrading
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.4e-05     0.086      16      65 ..       3      52 ..       1      88 [. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.4e-05
                    Haem_degrading 16 karekgkpvviaivdaggqllffarmdgaspdnedwaerKantaarfgks 65
                                      +ar+k+k ++ +i+ +  qllf  + + a   n +w++r a+ a+++g++
  gi|298675643|ref|YP_003727393.1|  3 RARKKKKVLIKDIAYQRIQLLFSFAENEARQSNLEWSNRYAYLARKIGMK 52
                                      5777788888899**999***************************99975 PP

>> HNH_5  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0021       7.6      35      43 ..      65      73 ..      58      78 .. 0.85
   2 ?    6.2   0.9    0.0027       9.6      28      44 ..      84     100 ..      82     104 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0021
                             HNH_5 35 lCkkCNqkk 43
                                      +Ck+CN+++
  gi|298675643|ref|YP_003727393.1| 65 ICKQCNSYL 73
                                      7*****986 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0027
                             HNH_5  28 tisnlvtlCkkCNqkkg 44 
                                       + +n++++C  C ++k 
  gi|298675643|ref|YP_003727393.1|  84 KNNNVTVTCLNCGNQKR 100
                                       6799**********996 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0   0.00092       3.3       3      13 ..      62      72 ..      60      74 .. 0.83
   2 ?    2.5   0.4     0.032   1.1e+02      24      30 ..      92      98 ..      89     101 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00092
                           zf-RRN7  3 kgppCgvCgcr 13
                                      k+ +C +C+++
  gi|298675643|ref|YP_003727393.1| 62 KRRICKQCNSY 72
                                      7889*****97 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.032
                           zf-RRN7 24 CrrChtq 30
                                      C +C++q
  gi|298675643|ref|YP_003727393.1| 92 CLNCGNQ 98
                                      6667766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 824.70
//
Query:       gi|298675644|ref|YP_003727394.1|  [L=234]
Description: hypothetical protein Metev_1761 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-35  123.0   0.4    1.9e-35  122.2   0.1    1.5  2  Lactamase_B_3  Beta-lactamase superfamily domain
    1.7e-14   53.8   0.1    3.9e-14   52.6   0.1    1.6  2  Lactamase_B_2  Beta-lactamase superfamily domain
    0.00023   21.3   1.4       0.42   10.6   0.3    2.4  2  Lactamase_B    Metallo-beta-lactamase superfamily


Domain annotation for each model (and alignments):
>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.2   0.1   3.1e-39   1.9e-35       1     163 []      21     200 ..      21     200 .. 0.88
   2 ?   -2.2   0.0      0.57   3.4e+03      31      42 ..     219     230 ..     208     232 .. 0.49

  Alignments for each domain:
  == domain 1  score: 122.2 bits;  conditional E-value: 3.1e-39
                     Lactamase_B_3   1 eltwlghnsflletagarilvDPfkanlgyeppaeeaDlvlisqaledHahletlkql.................ae 60 
                                       +++wlgh+ f+++ a+ ++++DP+   +   + +++aD++li++++ dH+++e ++++                 + 
  gi|298675644|ref|YP_003727394.1|  21 TIKWLGHAGFMIKEAEINVYIDPYVLPTSIINFEDQADVLLITHEHFDHCNPESIRKVrksyattlipesvtldfKG 97 
                                       59**********************8666777777************************8866666665555555544 PP

                     Lactamase_B_3  61 nvkvlee....geslevggleiravatshdavggsergenngflleqdgltiyhlGhlahelsseelkelgrvDvvl 133
                                       +++ +++     ++l +++++i+  ++++ +++ +++g ++g+l+e +gl+iyh G+++     +e +    +Dvvl
  gi|298675644|ref|YP_003727394.1|  98 DARRVRDgdmlRDHLSIKDVNIEVLPAYNIDKQYHPKGMGVGYLIELGGLRIYHTGDTDF---IPEMNDV-SADVVL 170
                                       44444444555567*********************************************9...7888777.9***** PP

                     Lactamase_B_3 134 tPvggpltlgqeealelakrLkpklvlPmh 163
                                       +P+gg++t++  ea++++  ++pk+ +Pmh
  gi|298675644|ref|YP_003727394.1| 171 VPIGGTYTMDESEAADAVASMSPKIAIPMH 200
                                       *****************************9 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.57
                     Lactamase_B_3  31 eppaeeaDlvli 42 
                                       +++++++D+v++
  gi|298675644|ref|YP_003727394.1| 219 NENNPDVDVVIL 230
                                       334445555544 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.1   6.5e-18   3.9e-14      30     201 .]      56     201 ..      41     201 .. 0.80
   2 ?   -3.1   0.0      0.75   4.5e+03     141     162 ..     209     230 ..     209     232 .. 0.73

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 6.5e-18
                                       SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-.TTSEEEECSTTEEE CS
                     Lactamase_B_2  30 pidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheld.wgesfelgdgglei 105
                                       + d++l+th+H+DH+ +  ++r+ r+     ya+  + + ++  f+ +a+      +v++ d + + ++++d  ++i
  gi|298675644|ref|YP_003727394.1|  56 QADVLLITHEHFDHC-NPESIRKVRK----SYATTLIPESVTLDFKGDAR------RVRDGDmLRDHLSIKD--VNI 119
                                       78*************.789****765....35555555555555433222......2333333788899995..569 PP

                                       EEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHHHHT---ST CS
                     Lactamase_B_2 106 tatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipeeigerlggadllllditayeddemirhmgHltpe 182
                                       ++ pa    ++     +g  +G++ie gg r+y++gDt +ipe+    +  ad++l++i+         + ++++ +
  gi|298675644|ref|YP_003727394.1| 120 EVLPAYNIDKQ--YHPKGMGVGYLIELGGLRIYHTGDTDFIPEMN--DVS-ADVVLVPIG---------GTYTMDES 182
                                       99999998888..6788899**********************884..455.*********.........8899999* PP

                                       SHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 183 eaveaaadlgakrlvliHi 201
                                       ea++a+a +++k+++++H+
  gi|298675644|ref|YP_003727394.1| 183 EAADAVASMSPKIAIPMHY 201
                                       ******************7 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.75
                                       SS-S---HHHHHHHCT-SEEEE CS
                     Lactamase_B_2 141 gDtgyipeeigerlggadllll 162
                                       gDt+ +++ + e   ++d+++l
  gi|298675644|ref|YP_003727394.1| 209 GDTEKFKQLVNENNPDVDVVIL 230
                                       6788888777777777888776 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.3     7e-05      0.42      45      58 ..      57      70 ..      47      71 .. 0.89
   2 !    9.2   0.0   0.00019       1.1     134     181 ..     138     190 ..     130     200 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 7e-05
                                      EEEEE-SBSSHHHH CS
                       Lactamase_B 45 vdavilTHlHlDHi 58
                                       d +++TH H+DH+
  gi|298675644|ref|YP_003727394.1| 57 ADVLLITHEHFDHC 70
                                      5899*********7 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00019
                                       CEEEEEETTCCEEEECTTTSSHHCCCCCC......TTCEEE-SHCHHHHHHHH CS
                       Lactamase_B 134 ghgvveygggkvlftGDallagetgridl.....tlrgaevrdpsdaekylds 181
                                       +++ +e+gg ++  tGD+ +++e  +++      +++g +++d s+a+++ +s
  gi|298675644|ref|YP_003727394.1| 138 VGYLIELGGLRIYHTGDTDFIPEMNDVSAdvvlvPIGGTYTMDESEAADAVAS 190
                                       67899***************999999999888888888888888888887754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1356.68
//
Query:       gi|298675645|ref|YP_003727395.1|  [L=278]
Description: transcriptional regulator TrmB [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-23   80.7   0.4    5.2e-23   80.7   0.4    2.3  2  TrmB      Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.018   15.0   0.0      0.043   13.8   0.0    1.6  1  PadR      Transcriptional regulator PadR-like family
      0.026   14.6   0.3      0.079   13.1   0.1    2.0  2  DUF2250   Uncharacterized protein conserved in archaea (DUF22
       0.16   12.3   0.0        0.3   11.5   0.0    1.3  1  Rrf2      Transcriptional regulator
       0.21   11.4   0.0       0.37   10.6   0.0    1.4  1  HTH_IclR  IclR helix-turn-helix domain


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.7   0.4   1.5e-26   5.2e-23       1      68 []       7      74 ..       7      74 .. 0.98
   2 ?   -0.8   0.2      0.39   1.4e+03      19      48 ..      79     108 ..      75     111 .. 0.79

  Alignments for each domain:
  == domain 1  score: 80.7 bits;  conditional E-value: 1.5e-26
                                      HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--HH CS
                              TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdpe 68
                                      L+++GL++yEa +Yl+Ll++g ++a+++++++++p  kvYevL+sL++ GlV+++++rpk+Yr+v+p+
  gi|298675645|ref|YP_003727395.1|  7 LKDMGLNKYEALAYLTLLEEGISEANTVSKKSDIPMGKVYEVLESLKNHGLVDIQESRPKKYRPVEPK 74
                                      789**************************************************************995 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.39
                                       HHCCCHHCHHCCCTTSSCHCHHHHHHHHHH CS
                              TrmB  19 klgpatadeiaeelgvprskvYevLrsLed 48 
                                       ++ +++ ++  +el++ + ++ ++ ++L++
  gi|298675645|ref|YP_003727395.1|  79 NYYSKREKDTEKELNRLKETISKAEEKLSQ 108
                                       556677889999999999999999888876 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.2e-05     0.043      27      54 ..      38      65 ..      24      71 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.2e-05
                                      CCTTHHHHHHHHHHHHHTTSEEEEEE-S CS
                              PadR 27 lelseGslYpaLkrLekeglvesewees 54
                                       ++ +G++Y +L++L+++glv+ ++++ 
  gi|298675645|ref|YP_003727395.1| 38 SDIPMGKVYEVLESLKNHGLVDIQESRP 65
                                      46789*****************998764 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   2.2e-05     0.079      24      65 ..      30      71 ..       8      82 .. 0.79
   2 ?   -3.1   0.0       2.5   9.1e+03      47      65 ..     244     262 ..     233     266 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.2e-05
                           DUF2250 24 YaksiakeleipleevrellkkLeelGLlervegktikrtea 65
                                       a +++k+ +ip+ +v e+l++L++ GL++ +e++  k++  
  gi|298675645|ref|YP_003727395.1| 30 EANTVSKKSDIPMGKVYEVLESLKNHGLVDIQESRPKKYRPV 71
                                      48899************************9999887776655 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.5
                           DUF2250  47 eelGLlervegktikrtea 65 
                                       ++lGL++ ++ +  ++ + 
  gi|298675645|ref|YP_003727395.1| 244 KTLGLIKIYDTNFSQKLKT 262
                                       4567777666554444444 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   8.4e-05       0.3      12      58 ..      16      61 ..      14      64 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.4e-05
                                      HHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              Rrf2 12 hallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksv 58
                                       al+yL++ ee+   ++++++++ +i+   +  +l+ L+++glv  +
  gi|298675645|ref|YP_003727395.1| 16 EALAYLTLLEEGI-SEANTVSKKSDIPMGKVYEVLESLKNHGLVDIQ 61
                                      5899****99986.9*****************************866 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0001      0.37      22      48 ..      32      58 ..      17      61 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0001
                                      HHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_IclR 22 selArrtglpkStvhRlLqtLvelGyv 48
                                        +++++++p  +v+  L +L ++G+v
  gi|298675645|ref|YP_003727395.1| 32 NTVSKKSDIPMGKVYEVLESLKNHGLV 58
                                      568999********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1157  (0.0645323); expected 358.6 (0.02)
Passed bias filter:                      689  (0.0384294); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 1765.73
//
Query:       gi|298675646|ref|YP_003727396.1|  [L=745]
Description: hydrophobe/amphiphile efflux-3 (HAE3) family transporter [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-60  203.3   4.8    6.2e-30  104.3   0.1    2.1  2  MMPL             MMPL family
    9.7e-17   60.0  13.1    5.5e-11   40.9   4.4    2.2  2  ACR_tran         AcrB/AcrD/AcrF family
    6.5e-15   55.3   7.5    4.6e-08   33.1   3.9    2.4  2  Sterol-sensing   Sterol-sensing domain of SREBP cleavage-acti
      1e-11   44.6   7.6      1e-11   44.6   7.6    3.0  3  SecD_SecF        Protein export membrane protein
    1.3e-09   36.7  13.3    4.8e-05   21.7   2.4    2.3  2  Patched          Patched family
     0.0016   18.5  14.8        1.4    8.9   1.9    4.6  5  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
  ------ inclusion threshold ------
        2.1    7.9   7.6       0.22   11.1   0.6    2.9  4  Fzo_mitofusin    fzo-like conserved region
        7.1    6.2   9.2        2.5    7.7   0.1    3.5  4  Saf_2TM          SAVED-fused 2TM effector domain


Domain annotation for each model (and alignments):
>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.3   0.1   2.8e-33   6.2e-30      27     292 ..      30     311 ..      10     328 .. 0.83
   2 !  100.1   1.4   5.2e-32   1.2e-28      96     314 ..     514     729 ..     492     738 .. 0.91

  Alignments for each domain:
  == domain 1  score: 104.3 bits;  conditional E-value: 2.8e-33
                              MMPL  27 dkiivvvlaegdealgsaaaeaavdelvdelkkdtkhvgevsdf..........................lsdpdva 77 
                                       ++i+v+v++ + ++ +  ++++ ++++vd l   +++v+ +s++                          ls+  ++
  gi|298675646|ref|YP_003727396.1|  30 QSIVVLVEGDDVKTPEVMKSMNRLEKQVDPL---SGVVQVTSAAsiveemnyqkigkreipdtkeeinslLSN--TN 101
                                       4444444444444444444444444444444...444444444455677666666666665555554433333..66 PP

                              MMPL  78 aafvSkDgkaaralvtlegdpgsteadesvaairaaveearpleglkvevtGpaatladlrdasdrdlklievvtlv 154
                                       ++ + +D++ a + v++egd +++e  + +++ ++ v+ +  + g  v vtG +a    ++++ ++++  + ++++v
  gi|298675646|ref|YP_003727396.1| 102 TGKTLPDDTHALVFVEVEGDISNDELRDILHETEKSVSMTGFPPGYSVTVTGEPAFSLAMEELMNESMPPLMAIAAV 178
                                       66666899999****************************************************************** PP

                              MMPL 155 vilviLlivyrSlvaallplltvvvsllaalglvlilalllglelstfvlgl.lvvlliavGtDYallLvsRyreel 230
                                       + ++ L +v+r +   llpl+ v ++++ ++g       +  le+ ++++++ ++ +li+ G+DYa+ + sR+ eel
  gi|298675646|ref|YP_003727396.1| 179 LMIIALYLVFRHVRWRLLPLIIVFLGIIYTFGA------MGYLEIPMSMVSMsAFPILIGLGIDYAIQFHSRIEEEL 249
                                       ********************************9......55667777777776899********************* PP

                              MMPL 231 aagedreeaviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivl 292
                                       ++ +d++eavi++v+ tg++v++a ++  + +++L ++++p+++ ++  + +Gv++ +l +l
  gi|298675646|ref|YP_003727396.1| 250 ERLHDEKEAVIETVKHTGPAVLIALIITSLGFVSLYTSTVPMVQDFAKLLLIGVIMCFLSSL 311
                                       ********************************************************999876 PP

  == domain 2  score: 100.1 bits;  conditional E-value: 5.2e-32
                              MMPL  96 gdpgsteadesvaairaaveear....pleglkvevtGpaatladlrdasdrdlklievvtlvvilviLlivyrSlv 168
                                       gd+ s+++ e ++++ ++v++      p+++++v +tG +++++ +  a ++ +  +++++l +i++ Ll +yr  +
  gi|298675646|ref|YP_003727396.1| 514 GDAMSNLGLEGIDELVKVVRKDIswtqPPADADVTITGNSVVFTTVITALTSGRIAMTLLGLSLIFAGLLFIYRDWL 590
                                       689999999999999999999888999************************************************** PP

                              MMPL 169 aallplltvvvsllaalglvlilalllglelstfvlgllvvlliavGtDYallLvsRyreelaagedreeavirava 245
                                        a+ p++t  + ++ a g+     + +g++ + ++++l  +l++++G+ Ya+l++ Ry ee  +ge+  ea+ +  +
  gi|298675646|ref|YP_003727396.1| 591 KAITPVITMFMVVGWAGGV----MYYSGIKYTPMTATL-GALILGIGSEYAVLMMERYFEEKSKGENPIEAMRESSR 662
                                       ***************9999....667888887777766.57889********************************* PP

                              MMPL 246 stgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTllPAllvll.Graalakprrkr 314
                                       ++gk+++ +G+t ++ + +L+++ +++ +++G++  + v +++l+++ + PA++ ll G +   +++++ 
  gi|298675646|ref|YP_003727396.1| 663 KIGKAIVTSGFTTVFGFSALLASPFSMNRNFGLVTVIDVGLALLATFIVFPAVIILLdGHR---EKKKQK 729
                                       ****************************************************998873555...333332 PP

>> ACR_tran  AcrB/AcrD/AcrF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   4.4   2.4e-14   5.5e-11     338     550 ..     174     397 ..     109     441 .. 0.78
   2 !   24.1   1.4   2.9e-09   6.5e-06     338     499 ..     572     728 ..     524     743 .. 0.78

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 2.4e-14
                                       HHHHHHHHHHHHHHHSSHHHHHHHHHHHHHHHHHHHHHHHHTT--BCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          ACR_tran 338 leaivLvvlvvflFLqnlratlipaiavPlsllgtfavlkalgfslNlltLfgLvlAiGlvvDdAiVvvEnierkle 414
                                        +a+vL ++ ++l  + +r  l p+i+v l ++ tf ++  l++ + + ++ +  + iGl +D Ai     ie++le
  gi|298675646|ref|YP_003727396.1| 174 AIAAVLMIIALYLVFRHVRWRLLPLIIVFLGIIYTFGAMGYLEIPMSMVSMSAFPILIGLGIDYAIQFHSRIEEELE 250
                                       4899************************************************************************* PP

                                       HHTS-HHHHHHHHHHHHHHHHHHHHHHHHHHCTGGGGSBHHHHHHHHH.HHHHHHHHHHHHHHHHHCCHHHHHHHHS CS
                          ACR_tran 415 eegekpleaalksmkeiqgalvaialvllavflPilflgGveGklfrq.faltivlaillsvlvaltltPalcallL 490
                                           +++ea+++++k  + a++   ++ +  f+ + + +    + f++ + + ++++ l s++v + ++  l +++ 
  gi|298675646|ref|YP_003727396.1| 251 R-LHDEKEAVIETVKHTGPAVLIALIITSLGFVSLYTSTVPMVQDFAKlLLIGVIMCFLSSLFVGVSVIYGLDSIFK 326
                                       9.778899999999998888777777777778777766655444444415689**********************99 PP

                                       ---STT-CT..........SHHHHHHHHHHHHHHHH.HHHHHHHHHSHHHHHHHHHHHHHHHHHHHHCS-B CS
                          ACR_tran 491 kerkeekek..........kffrefnrlfealeraY.akllekvlrhravvllvalvllvlsvllfvripk 550
                                       k++k  ++           +  ++ ++  + + ++Y  k+ ++ ++h+  +ll+a +l+v  +++   +p 
  gi|298675646|ref|YP_003727396.1| 327 KNNKLINAInskikydsnsNSGKNTEEQKNDIIERYiDKVTSFTIKHPVTILLIAGLLCVSGLYVDQDVPL 397
                                       99887666567776776653333344444445555626777889999999999999999999888887773 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 2.9e-09
                                       HHHHHHHHHHHHHHHSSHHHHHHHHHHHHHHHHHHHHHHHHTT--BCHH..HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          ACR_tran 338 leaivLvvlvvflFLqnlratlipaiavPlsllgtfavlkalgfslNll..tLfgLvlAiGlvvDdAiVvvEnierk 412
                                       l+++ L++  ++   +++  ++ p+i++ +++  +  v++  g+    +  tL++L l+iG     A+ ++E  +++
  gi|298675646|ref|YP_003727396.1| 572 LLGLSLIFAGLLFIYRDWLKAITPVITMFMVVGWAGGVMYYSGIKYTPMtaTLGALILGIGS--EYAVLMMERYFEE 646
                                       45667777777777799*****999999999988888998888766655227******9997..89**********9 PP

                                       HHHHTS-HHHHHHHHHHHHHHHHHHHHHHHHHHCTGGGGSBHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHH CS
                          ACR_tran 413 leeegekpleaalksmkeiqgalvaialvllavflPilflgGveGklfrqfaltivlaillsvlvaltltPalcall 489
                                        ++ ge+p ea+++s+++i+ a+v + ++ +  f    +l  +   + r+f+l  v+ ++l++l   ++ Pa+  +l
  gi|298675646|ref|YP_003727396.1| 647 KSK-GENPIEAMRESSRKIGKAIVTSGFTTVFGFS---ALLASPFSMNRNFGLVTVIDVGLALLATFIVFPAVI-IL 718
                                       998.*********************9998877664...55568889*************************987.67 PP

                                       S---STT-CT CS
                          ACR_tran 490 Lkerkeekek 499
                                       L  ++e+k++
  gi|298675646|ref|YP_003727396.1| 719 LDGHREKKKQ 728
                                       7777666654 PP

>> Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   3.9     2e-11   4.6e-08      13     131 ..     198     316 ..     190     326 .. 0.89
   2 !   23.1   0.1   2.3e-08   5.1e-05       9     146 ..     592     730 ..     586     737 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 2e-11
                                       HHHHHCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCHHCCHHCHHHHHHHHTT.TCHHHHHHHHHHHHCCCCHHC CS
                    Sterol-sensing  13 viivllsvasslgllaylgltltliilevlPflvlavgvdnifvlvkavqrtsrs.ldeseriaealgevgpsillt 88 
                                       +iiv l ++ ++g + yl+++++++++  +P  ++  g+d    +   +++  ++ +de+e + e+++++gp++l+ 
  gi|298675646|ref|YP_003727396.1| 198 LIIVFLGIIYTFGAMGYLEIPMSMVSMSAFPI-LIGLGIDYAIQFHSRIEEELERlHDEKEAVIETVKHTGPAVLIA 273
                                       799****************************5.5799***9999998887655550556****************** PP

                                       CCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHTHHHH CS
                    Sterol-sensing  89 sltellalllgaltdvpavqeFclfaavavlvdFllqitfFva 131
                                       ++  +l ++  + ++vp vq F+    ++v++ Fl  +++ v+
  gi|298675646|ref|YP_003727396.1| 274 LIITSLGFVSLYTSTVPMVQDFAKLLLIGVIMCFLSSLFVGVS 316
                                       *********7789*********************988776555 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 2.3e-08
                                       HHHHHHHHHCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCHHCCHHCHHHHHHHH.TTTCHHHHHHHHHHHHCCC CS
                    Sterol-sensing   9 glagviivllsvasslgllaylgltltliilevlPflvlavgvdnifvlvkavqrts.rsldeseriaealgevgps 84 
                                       +++ vi++ + v  + g+++y g+++t++++  l  l+l +g +   ++++ + + + + ++  e + e  +++g +
  gi|298675646|ref|YP_003727396.1| 592 AITPVITMFMVVGWAGGVMYYSGIKYTPMTA-TLGALILGIGSEYAVLMMERYFEEKsKGENPIEAMRESSRKIGKA 667
                                       68889*************************9.999*********887777766555505555699999********* PP

                                       CHHCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHH.HHHHHHHCTXXT CS
                    Sterol-sensing  85 illtsltellalllgaltdvpavqeFclfaavavlvdFllqitfFvavLs.ldirreeserld 146
                                       i+ + +t ++ +   +++ ++  ++F l +++ v +  l   ++F av+  ld  re++++ +
  gi|298675646|ref|YP_003727396.1| 668 IVTSGFTTVFGFSALLASPFSMNRNFGLVTVIDVGLALLATFIVFPAVIIlLDGHREKKKQKK 730
                                       *******9999997778999999************************8752688888555444 PP

>> SecD_SecF  Protein export membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   7.6   4.6e-15     1e-11      34     184 ..     172     319 ..     158     323 .. 0.86
   2 ?   -0.3   0.0      0.26   5.7e+02     121     154 ..     356     389 ..     344     399 .. 0.53
   3 ?    2.7   5.0     0.032        73      20     181 ..     554     714 ..     540     722 .. 0.73

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 4.6e-15
                                       HHHHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHTTSSSHHHHHHHHHHHH CS
                         SecD_SecF  34 vlallialvliliyvalrFewrvalaaiialvhDviitvgvlsllgievdlatvaalLtiiGYSvndtvvvfdrvre 110
                                       ++a+++ l++i++y+++r   r+ l  +i ++  +i t g++  l+i++++ +++a   +iG  ++  +    r++e
  gi|298675646|ref|YP_003727396.1| 172 LMAIAAVLMIIALYLVFRH-VRWRLLPLIIVFLGIIYTFGAMGYLEIPMSMVSMSAFPILIGLGIDYAIQFHSRIEE 247
                                       4566666666666666664.5788899999999******************************************** PP

                                       HHHH--SS-HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHTTTTHHHHHHHHHHTSTTTTTHHHHHHHHHH CS
                         SecD_SecF 111 nlrkkkratlkeiinlslnqtLtrtiltslttllvvvallllggdslkdfalallvGlivgtyssifiasplll 184
                                       +l++ +  + ke++ + +++t    +++ ++t l  v+l+  +  +++dfa  ll+G+i+  +ss+f+   +++
  gi|298675646|ref|YP_003727396.1| 248 ELERLH--DEKEAVIETVKHTGPAVLIALIITSLGFVSLYTSTVPMVQDFAKLLLIGVIMCFLSSLFVGVSVIY 319
                                       *99855..5578888999***9999******************************************9887765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.26
                                       HHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHT CS
                         SecD_SecF 121 keiinlslnqtLtrtiltslttllvvvallllgg 154
                                       ++ii++ + +  + ti   +t+ll++  l++ g 
  gi|298675646|ref|YP_003727396.1| 356 NDIIERYIDKVTSFTIKHPVTILLIAGLLCVSGL 389
                                       5555555555555555555555555544444443 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.032
                                       EE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-.HHHHHHHHHHHHHHHHHHHHHHHHTT----H..HHHHHHHHH CS
                         SecD_SecF  20 tvgpsvskelaekavlallialvliliyvalrFe.wrvalaaiialvhDviitvgvlsllgievdl..atvaalLti 93 
                                       +v  +v   l+   +   l+ l li+  + ++++ w  a+  +i+++  v  + gv+   gi+ ++  at++al  i
  gi|298675646|ref|YP_003727396.1| 554 VVFTTVITALTSGRIAMTLLGLSLIFAGLLFIYRdWLKAITPVITMFMVVGWAGGVMYYSGIKYTPmtATLGAL--I 628
                                       55556666666655555566666666666666653888***********************9999722456666..6 PP

                                       TTSSSHHHHHHHHHHHHHHHH--SS-HHHHHHHHHHHHHHHHHHTTHH.HHHHHHHHHHHHTTTTHHHHHHHHHHTS CS
                         SecD_SecF  94 iGYSvndtvvvfdrvrenlrkkkratlkeiinlslnqtLtrtiltslt.tllvvvallllggdslkdfalallvGli 169
                                       +G   +  v++++r  e+  k+k ++  e++ +s  + + ++i+ts   t++   all  + ++ ++f l+ ++ + 
  gi|298675646|ref|YP_003727396.1| 629 LGIGSEYAVLMMERYFEE--KSKGENPIEAMRESSRK-IGKAIVTSGFtTVFGFSALLASPFSMNRNFGLVTVIDVG 702
                                       77777899*******999..77788888999998665.6778888765166667777777789999**999999988 PP

                                       TTTTTHHHHHHH CS
                         SecD_SecF 170 vgtyssifiasp 181
                                       +  + +  +  +
  gi|298675646|ref|YP_003727396.1| 703 LALLATFIVFPA 714
                                       887777655444 PP

>> Patched  Patched family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   3.4   5.7e-08   0.00013     261     451 ..     198     380 ..     172     394 .. 0.76
   2 !   21.7   2.4   2.1e-08   4.8e-05     255     398 ..     590     734 ..     557     745 .] 0.86

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 5.7e-08
                           Patched 261 vlspvlAivsslGlllwlGfrfnsivtvtPF.LvLaiGvDdmflmvaaw.krteaklsvkkrigealseagvaitiT 335
                                       ++  +l i+  +G++ +l ++   +  ++ F + +++G+D +     ++ +++e+ ++ k+ ++e++ ++g+a++i 
  gi|298675646|ref|YP_003727396.1| 198 LIIVFLGIIYTFGAMGYLEIPMSMV-SMSAFpILIGLGIDYAIQFHSRIeEELERLHDEKEAVIETVKHTGPAVLIA 273
                                       5666788888889988888886554.4444425579***9886655555246788899******************* PP

                           Patched 336 slTdvlsFgiGaittlpaiqlFciytavailfdfiYqitffaavlaiaakaeaegrhsllliiekeespsklqeies 412
                                        +   l F    ++t+p +q F++   + ++++f+  + f +  + +  +   +++++l+  i+     sk++  ++
  gi|298675646|ref|YP_003727396.1| 274 LIITSLGFVSLYTSTVPMVQDFAKLLLIGVIMCFLSSL-FVGVSVIYGLDSIFKKNNKLINAIN-----SKIKYDSN 344
                                       ********999999********************9765.6677777788888899999998887.....44555556 PP

                           Patched 413 essekdddkskeaeelkskffreiyapfllnksvrlvvl 451
                                        +s k   + +e+++ + +++++++++f +++ v ++ +
  gi|298675646|ref|YP_003727396.1| 345 SNSGK---NTEEQKNDIIERYIDKVTSFTIKHPVTILLI 380
                                       66555...3444444466778888888877766666554 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 2.1e-08
                           Patched 255 ilailgvlspvlAivsslGlllwlGfrfnsivtvtPFLvLaiGvDdmflmvaawkr.teaklsvkkrigealseagv 330
                                       + ai+ v++ ++ +  + G++++ G+++  ++     L+L+iG   + lm++++ +  ++ ++  + + e     g 
  gi|298675646|ref|YP_003727396.1| 590 LKAITPVITMFMVVGWAGGVMYYSGIKYTPMTATLGALILGIGSEYAVLMMERYFEeKSKGENPIEAMRESSRKIGK 666
                                       569999******************************************999987550555566889*********** PP

                           Patched 331 aitiTslTdvlsFgiGaittlpaiqlFciytavailfdfiYqitffaavlaiaakaeaegrhslllii 398
                                       ai+   +T v+ F +   ++      F ++t + + ++ + ++++f av+ +   +  +++++ + i 
  gi|298675646|ref|YP_003727396.1| 667 AIVTSGFTTVFGFSALLASPFSMNRNFGLVTVIDVGLALLATFIVFPAVIILLDGHREKKKQKKQNIS 734
                                       ***********************************************999988766666655555542 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   5.0      0.72   1.6e+03      48      88 ..     174     214 ..     171     223 .. 0.53
   2 ?    3.2   0.0     0.038        84      15      80 ..     245     309 ..     236     340 .. 0.57
   3 ?   -2.8   0.0       2.8   6.3e+03      74      88 ..     375     389 ..     366     402 .. 0.72
   4 !    8.9   1.9   0.00064       1.4      44     102 ..     568     624 ..     526     628 .. 0.67
   5 !    8.6   0.0   0.00082       1.8      26      85 ..     657     719 ..     655     742 .. 0.64

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.72
                   Phage_holin_3_6  48 llalllllvalalalaa.lwlaalivaavllvlagvlalvgl 88 
                                       ++a++l+++al l++     +  l + +v+l +   ++++g+
  gi|298675646|ref|YP_003727396.1| 174 AIAAVLMIIALYLVF-RhVRWRLLPLIIVFLGIIYTFGAMGY 214
                                       223333333333333.12333334466778888777777776 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.038
                   Phage_holin_3_6  15 vrteleLakaElkeeakragsgagllgaagvlallalllllvalalalaalwlaalivaavllvla 80 
                                       ++ ele +  E ++  + +   + ++++a++++ l++++l    + +++   +  l++++++  l 
  gi|298675646|ref|YP_003727396.1| 245 IEEELERLHDEKEAVIETVKHTGPAVLIALIITSLGFVSLYTSTVPMVQ-DFAKLLLIGVIMCFLS 309
                                       5566666666666666666666666777777777777777777763332.3333333333333332 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.8
                   Phage_holin_3_6  74 avllvlagvlalvgl 88 
                                       +  l++ag+l + gl
  gi|298675646|ref|YP_003727396.1| 375 VTILLIAGLLCVSGL 389
                                       566777777777765 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.00064
                   Phage_holin_3_6  44 gvlallalllllvalalalaa..lwlaali.vaavllvlagvlalvglkklkkakplperti 102
                                        +++ll+l l++++l++   +   wl a+  v  +++v++++ +++ ++ +k   +++++t+
  gi|298675646|ref|YP_003727396.1| 568 IAMTLLGLSLIFAGLLF---IyrDWLKAITpVITMFMVVGWAGGVMYYSGIKY--TPMTATL 624
                                       22222232222222222...2569******9************9999998887..3466665 PP

  == domain 5  score: 8.6 bits;  conditional E-value: 0.00082
                   Phage_holin_3_6  26 lkeeakragsgagllgaagvlallalllllval..alala.a..lwlaalivaavllvlagvlal 85 
                                       ++e+ +++g++++  g + v+++ all+  + +   ++l  +    la l +++v    a++ +l
  gi|298675646|ref|YP_003727396.1| 657 MRESSRKIGKAIVTSGFTTVFGFSALLASPFSMnrNFGLVtVidVGLALLATFIV--FPAVIILL 719
                                       6788899999999999999999999999998886646774445433333333322..23333333 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.4   5.4e+03     118     143 ..      83     108 ..      73     113 .. 0.81
   2 ?   11.1   0.6   9.6e-05      0.22      12      55 ..     167     210 ..     158     216 .. 0.82
   3 ?   -1.8   0.0      0.87     2e+03       4      32 ..     356     384 ..     353     387 .. 0.83
   4 ?   -2.2   0.2       1.2   2.6e+03      16      55 ..     548     587 ..     543     590 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.4
                     Fzo_mitofusin 118 eeeikelekeiekleevqkkakllrn 143
                                       ++ei + ++ei++l + +++ k+l +
  gi|298675646|ref|YP_003727396.1|  83 KREIPDTKEEINSLLSNTNTGKTLPD 108
                                       56899999999999999999999866 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 9.6e-05
                     Fzo_mitofusin  12 lglasltsrtslgvlvvggvvlravgWrvialslalygllYlyE 55 
                                        ++  l++ +++ +++   +v r v Wr++ l ++  g++Y + 
  gi|298675646|ref|YP_003727396.1| 167 ESMPPLMAIAAVLMIIALYLVFRHVRWRLLPLIIVFLGIIYTFG 210
                                       44666777889999999************************986 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.87
                     Fzo_mitofusin   4 eelmvslalglasltsrtslgvlvvggvv 32 
                                       ++++ + + +++s+t ++ +++l+++g++
  gi|298675646|ref|YP_003727396.1| 356 NDIIERYIDKVTSFTIKHPVTILLIAGLL 384
                                       467777788999***************97 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 1.2
                     Fzo_mitofusin  16 sltsrtslgvlvvggvvlravgWrvialslalygllYlyE 55 
                                        +t ++ + ++v++++ +  ++  ++ lsl   gll++y 
  gi|298675646|ref|YP_003727396.1| 548 TITGNSVVFTTVITALTSGRIAMTLLGLSLIFAGLLFIYR 587
                                       567788888999999999999999999999999***9995 PP

>> Saf_2TM  SAVED-fused 2TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       1.2   2.8e+03      70      88 ..     171     189 ..     156     192 .. 0.76
   2 ?    2.9   0.1     0.033        74      30      83 ..     226     279 ..     216     288 .. 0.82
   3 ?   -3.1   0.3       2.4   5.3e+03      70      88 ..     569     587 ..     551     592 .. 0.62
   4 ?    7.7   0.1    0.0011       2.5      27     102 ..     663     733 ..     658     734 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.2
                           Saf_2TM  70 iilvigvllivvGavllil 88 
                                        +++i+ +l+++ ++l ++
  gi|298675646|ref|YP_003727396.1| 171 PLMAIAAVLMIIALYLVFR 189
                                       5678999999999988876 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.033
                           Saf_2TM  30 valllailgtdwalkialklaggslevsfssse.ipeivlaiilvigvllivvGa 83 
                                       ++ +l +lg d a+++  +++ ++le   +++e ++e v  +  ++ ++li++++
  gi|298675646|ref|YP_003727396.1| 226 AFPILIGLGIDYAIQFHSRIE-EELERLHDEKEaVIETVKHTGPAVLIALIITSL 279
                                       444556699999999999998.899999999999*****************9985 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2.4
                           Saf_2TM  70 iilvigvllivvGavllil 88 
                                        ++++g  li +G++ +++
  gi|298675646|ref|YP_003727396.1| 569 AMTLLGLSLIFAGLLFIYR 587
                                       3455666666666555555 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0011
                           Saf_2TM  27 tigvalllailgtdwalkialklaggslevsfssseipeivlaiilvigvllivvGavllilryvneakrqskkkv 102
                                       +ig+a++++++ t + ++ +l ++  s++ +f+       v  + l++  ++iv+ av+++l+  +e+k+q+k ++
  gi|298675646|ref|YP_003727396.1| 663 KIGKAIVTSGFTTVFGFSALLASP-FSMNRNFGLVT----VIDVGLALLATFIVFPAVIILLDGHREKKKQKKQNI 733
                                       578888888877776666666666.44444444444....3345788889999***********888887777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (745 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1284  (0.0716158); expected 358.6 (0.02)
Passed bias filter:                      634  (0.0353617); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.86u 0.38s 00:00:01.24 Elapsed: 00:00:00.50
# Mc/sec: 4476.44
//
Query:       gi|298675647|ref|YP_003727397.1|  [L=369]
Description: hypothetical protein Metev_1764 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.1e-07   30.2   4.3     0.0016   18.7   0.6    2.7  3  CARDB        CARDB
      2e-06   27.9   0.0      0.012   15.8   0.0    3.4  3  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi
  ------ inclusion threshold ------
      0.013   15.6   1.1        1.5    8.9   0.1    3.5  3  DUF1573      Protein of unknown function (DUF1573)
      0.023   15.0   0.1        0.2   12.0   0.1    2.5  2  DUF11        Domain of unknown function DUF11
      0.031   14.5   0.0       0.46   10.7   0.0    2.7  3  ASH          Abnormal spindle-like microcephaly-assoc'd, ASPM
       0.29   11.7   4.1         14    6.3   0.5    2.8  3  DUF5114      Domain of unknown function (DUF5114)


Domain annotation for each model (and alignments):
>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.2   6.1e-05      0.18       1      90 [.      58     146 ..      58     150 .. 0.88
   2 ?    1.5   0.1      0.12   3.5e+02      37      73 ..     131     170 ..     124     192 .. 0.61
   3 !   18.7   0.6   5.2e-07    0.0016       2      81 ..     227     309 ..     226     326 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.1e-05
                                       S--EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CE CS
                             CARDB   1 tpDLtvtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtteatege 77 
                                       +pDL   + l+  e + ge+ +i+++++N+G  +  ++ +++ +d+++ ++   ++ + ++++tv + ++t++t+ +
  gi|298675647|ref|YP_003727397.1|  58 KPDLYA-SVLGDPEFERGETAQIEINLANKGILYGFKSVTNVDADDKTEAELAQKEFEYEKQRTVALGIKTNLTSTT 133
                                       589998.888999999********************************99888899999999999999999988888 PP

                                       EEEEEEESTT-SS CS
                             CARDB  78 vtltvvvDpdnev 90 
                                        ++ v  ++++++
  gi|298675647|ref|YP_003727397.1| 134 QYIDVDSESSGQI 146
                                       8788877776666 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.12
                                       EEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S....- CS
                             CARDB  37 atkvalyldgelvgtvtvpsLaagesttvsftwtte....a 73 
                                       +t+  + +d e+ + +++ +La+g+  +  + +t++    +
  gi|298675647|ref|YP_003727397.1| 131 STTQYIDVDSES-SGQIIDKLAPGDILKKPLRFTIDisdnT 170
                                       444444444444.77889******98887777777643322 PP

  == domain 3  score: 18.7 bits;  conditional E-value: 5.2e-07
                                       --EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE...EEEEESEE-CTEEEEEEEEEE-S..- CS
                             CARDB   2 pDLtvtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv...gtvtvpsLaagesttvsftwtte..a 73 
                                       +D+ +  t   +++++g++  i+vt kN+G++++ +  +++++ + l    ++v++  L+++es+t +f++ ++  a
  gi|298675647|ref|YP_003727397.1| 227 ADFQI--TNINGNLSPGSSGDIEVTYKNTGEKTANDAIARIVAMRPLSmqdSEVNLGDLNPDESKTANFKISASsdA 301
                                       57777..77788999*****************************999997777778**************9998665 PP

                                       S-CEEEEE CS
                             CARDB  74 tegevtlt 81 
                                        ++++ l+
  gi|298675647|ref|YP_003727397.1| 302 VKKSYVLN 309
                                       56666565 PP

>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       3.3   9.7e+03       2      17 ..      72      87 ..      71      88 .. 0.83
   2 !    7.9   0.0    0.0012       3.6      38      78 ..     141     183 ..     139     184 .. 0.82
   3 !   15.8   0.0   4.1e-06     0.012       2      78 ..     239     314 ..     238     315 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.3
                       NPCBM_assoc  2 epGetvtltltvtndg 17
                                      e+Get ++++ ++n+g
  gi|298675647|ref|YP_003727397.1| 72 ERGETAQIEINLANKG 87
                                      7899999999999887 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0012
                       NPCBM_assoc  38 evspasaaslapGetve..atvkVtppagaaaGdyevtakarl 78 
                                       e+s++ +++lapG+ ++    +++ +++++ aG+y +++ +++
  gi|298675647|ref|YP_003727397.1| 141 ESSGQIIDKLAPGDILKkpLRFTIDISDNTPAGEYILKLPLTY 183
                                       5677778899999987733689**************9998775 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 4.1e-06
                       NPCBM_assoc   2 epGetvtltltvtndgtaaatnvslslsl..PeGWtvvevspasaaslapGetveatvkVtppagaaaGdyevtaka 76 
                                       +pG++  +++t +n+g+++a +   ++ +  P   +    s  ++ +l p+e+ +a++k++++++a+   y +  ++
  gi|298675647|ref|YP_003727397.1| 239 SPGSSGDIEVTYKNTGEKTANDAIARIVAmrPLSMQ---DSEVNLGDLNPDESKTANFKISASSDAVKKSYVLNSEI 312
                                       689999999999999988887766665552366544...8999999**************************99999 PP

                       NPCBM_assoc  77 rl 78 
                                       r+
  gi|298675647|ref|YP_003727397.1| 313 RY 314
                                       86 PP

>> DUF1573  Protein of unknown function (DUF1573)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.35   1.1e+03      55      85 ..      72     102 ..      68     111 .. 0.70
   2 ?    8.9   0.1    0.0005       1.5      51      73 ..     235     257 ..     195     267 .. 0.69
   3 ?    2.6   0.0     0.047   1.4e+02       2      29 ..     272     299 ..     271     304 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.35
                           DUF1573  55 apGesgkikvtfnakgrpgefnktvtvyant 85 
                                       + Ge+++i+++  +kg    f+    v a+ 
  gi|298675647|ref|YP_003727397.1|  72 ERGETAQIEINLANKGILYGFKSVTNVDADD 102
                                       6799999999999888655565555565555 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0005
                           DUF1573  51 kepiapGesgkikvtfnakgrpg 73 
                                       +  + pG sg+i+vt++++g++ 
  gi|298675647|ref|YP_003727397.1| 235 NGNLSPGSSGDIEVTYKNTGEKT 257
                                       35689*************99543 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.047
                           DUF1573   2 kfeettidfgkieegekvtatFeftNtg 29 
                                       +++ +++++g+++ +e++ta+F++   +
  gi|298675647|ref|YP_003727397.1| 272 SMQDSEVNLGDLNPDESKTANFKISASS 299
                                       678899*****************97665 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.1   3.3e+03      38      75 ..      41      82 ..      33      86 .. 0.59
   2 ?   12.0   0.1   6.7e-05       0.2       5      85 ..     213     304 ..     210     310 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.1
                             DUF11 38 tlPaglayvsvsas.qgtasaltsv...gsLeagesatlsft 75
                                       lP++  y  +     g  +   sv   ++ e ge+a++++ 
  gi|298675647|ref|YP_003727397.1| 41 FLPPNHHYSVNYYEsFGKPDLYASVlgdPEFERGETAQIEIN 82
                                      566666654443332333344444467788899999998876 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 6.7e-05
                             DUF11   5 vdks....................evrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsv 61 
                                       vd++                    ++ pG   +  +t +Ntg ++an++  +     +++  s + s      +++ 
  gi|298675647|ref|YP_003727397.1| 213 VDNTidipitikesadfqitningNLSPGSSGDIEVTYKNTGEKTANDAIARI---VAMRPLSMQDS------EVNL 280
                                       55555555555555555566666688899999999***********6655554...56666666666......4445 PP

                             DUF11  62 gsLeagesatlsftvrvtrtaasg 85 
                                       g+L++ es+t +f+++++  a ++
  gi|298675647|ref|YP_003727397.1| 281 GDLNPDESKTANFKISASSDAVKK 304
                                       9***************99988766 PP

>> ASH  Abnormal spindle-like microcephaly-assoc'd, ASPM-SPD-2-Hydin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.3   6.8e+03      51      91 ..     127     169 ..     116     171 .. 0.63
   2 ?   10.7   0.0   0.00015      0.46      41      84 ..     217     260 ..     202     268 .. 0.83
   3 ?    0.2   0.0       0.3   8.9e+02       4      37 ..     267     301 ..     264     348 .. 0.63

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.3
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXX CS
                               ASH  51 kgfsveetelevqpgesvtltvtwtPteega..vrevLqflvn 91 
                                       ++++ +++ ++v+ ++s ++  +++P +  +   r+++ + +n
  gi|298675647|ref|YP_003727397.1| 127 TNLTSTTQYIDVDSESSGQIIDKLAPGDILKkpLRFTIDISDN 169
                                       4555555557777777777777777766533225666666655 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00015
                                       EEEEEEE--XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                               ASH  41 vkvskvpaaekgfsveetelevqpgesvtltvtwtPteegavre 84 
                                       +++  +++++  f++++ + +++pg+s  ++vt+++t e + ++
  gi|298675647|ref|YP_003727397.1| 217 IDIPITIKESADFQITNINGNLSPGSSGDIEVTYKNTGEKTAND 260
                                       55666788999**************************9877655 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.3
                                       EE-TTB--.EEEEE-----EEEEEEE-EEESS-SS CS
                               ASH   4 llapfsrk.pfvsFgdvkvGssaerlLtveNpsee 37 
                                       +++p s +   v++gd +  +s++++ +++  s++
  gi|298675647|ref|YP_003727397.1| 267 AMRPLSMQdSEVNLGDLNPDESKTANFKISASSDA 301
                                       56777777788888888888888888887777763 PP

>> DUF5114  Domain of unknown function (DUF5114)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.2    0.0069        21      18      57 ..      74     113 ..      69     147 .. 0.78
   2 ?   -2.7   0.0       3.1   9.3e+03      72      89 ..     165     181 ..     163     183 .. 0.78
   3 ?    6.3   0.5    0.0046        14      15      84 ..     189     257 ..     181     260 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0069
                           DUF5114  18 ttatnvtiqisGtGklYnnetvsgdnatDdakaietpvaF 57 
                                        + +++ i++  +G lY  ++v++ +a D+++a   +  F
  gi|298675647|ref|YP_003727397.1|  74 GETAQIEINLANKGILYGFKSVTNVDADDKTEAELAQKEF 113
                                       5678899****************98888988887555555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.1
                           DUF5114  72 ditvsvpaaGectlvldl 89 
                                       di+ + p aGe++l l l
  gi|298675647|ref|YP_003727397.1| 165 DISDNTP-AGEYILKLPL 181
                                       6777777.9999999876 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0046
                           DUF5114  15 ftattatnvtiqisGtGklYnnetvsgdnatDdakaietpvaFggnaeqltf.getAgditvsvpaaGect 84 
                                       +  t + +v++ i+   ++  ++t   dn +D   +i+ +  F  +  +  +   + gdi v+  ++Ge t
  gi|298675647|ref|YP_003727397.1| 189 VRMTRGEQVNLGIRDLDHTTHYKT--VDNTIDIPITIKESADFQITNINGNLsPGSSGDIEVTYKNTGEKT 257
                                       666777777777777777777777..5899999999888888888877777745679************88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       766  (0.0427241); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 2405.13
//
Query:       gi|298675648|ref|YP_003727398.1|  [L=387]
Description: hypothetical protein Metev_1765 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-05   24.2   0.8       0.54   10.6   0.1    3.2  3  NPCBM_assoc     NPCBM-associated, NEW3 domain of alpha-galact
  ------ inclusion threshold ------
      0.029   14.2   0.2       0.19   11.6   0.0    2.2  2  DUF824          Salmonella repeat of unknown function (DUF824
      0.038   14.6   0.7       0.57   10.8   0.0    3.0  4  YtkA            YtkA-like
      0.094   12.7   0.0        3.6    7.6   0.0    2.4  2  Lip_prot_lig_C  Bacterial lipoate protein ligase C-terminus


Domain annotation for each model (and alignments):
>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.27   1.2e+03       2      17 ..      89     104 ..      88     107 .. 0.89
   2 !   10.6   0.1   0.00012      0.54      38      74 ..     155     193 ..     153     197 .. 0.90
   3 !   10.0   0.0   0.00017      0.77       3      78 ..     254     328 ..     252     329 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.27
                       NPCBM_assoc   2 epGetvtltltvtndg 17 
                                       ++G+tvtl++ ++n+g
  gi|298675648|ref|YP_003727398.1|  89 SKGDTVTLKINLVNKG 104
                                       68**********9998 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00012
                       NPCBM_assoc  38 evspasaaslapGetvea..tvkVtppagaaaGdyevta 74 
                                       +++p++a sl+ Ge++ a  ++++ + ++a++G+y++ +
  gi|298675648|ref|YP_003727398.1| 155 KSTPQEAGSLPSGEETNAppKFTIEIAENAKPGTYPLAL 193
                                       6899***********998779***************976 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00017
                       NPCBM_assoc   3 pGetvtltltvtndgtaaatnvslslslPeGWtvvevspasaaslapGetveatvkVtppagaaaGdyevtakarl 78 
                                        Ge+  l++t +n g++++++  +++++ +  + ++ + a + s+apGet e  + + + + a    y +  ++++
  gi|298675648|ref|YP_003727398.1| 254 TGEKGLLRVTYKNVGNQPVKDATVRITASDPFS-TTDDQAYLGSIAPGETSEGVFSINVDQAATSKLYGINSEIKY 328
                                       699999******************999999999.999999999************999999998888888877765 PP

>> DUF824  Salmonella repeat of unknown function (DUF824)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.26   1.1e+03      11      20 ..      90      99 ..      88     103 .. 0.86
   2 ?   11.6   0.0   4.2e-05      0.19      12      39 ..     255     282 ..     249     284 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.26
                            DUF824 11 kGEsipltit 20
                                      kG++++l+i 
  gi|298675648|ref|YP_003727398.1| 90 KGDTVTLKIN 99
                                      8*******96 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 4.2e-05
                            DUF824  12 GEsipltitvkDasGnPvpnapftltRg 39 
                                       GE   l +t k+  ++Pv++a++++t +
  gi|298675648|ref|YP_003727398.1| 255 GEKGLLRVTYKNVGNQPVKDATVRITAS 282
                                       6666799******************966 PP

>> YtkA  YtkA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.35   1.6e+03       4      30 ..      75     103 ..      72     105 .. 0.79
   2 ?   -1.6   0.0      0.97   4.3e+03      53      70 ..     173     190 ..     166     194 .. 0.71
   3 ?   10.8   0.0   0.00013      0.57       6      47 ..     240     284 ..     237     314 .. 0.75
   4 ?   -2.7   0.0       2.2   9.8e+03      23      43 ..     325     346 ..     320     355 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.35
                              YtkA   4 sddlevelvspeepkagen.tivvt.vtq 30 
                                       s dl++++v+++e+++g++ t++++ v++
  gi|298675648|ref|YP_003727398.1|  75 SPDLTANIVGNNEFSKGDTvTLKINlVNK 103
                                       678999**********9996678764655 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.97
                              YtkA  53 eemttkvelkesedGvYe 70 
                                       ++++t   +++ ++G Y 
  gi|298675648|ref|YP_003727398.1| 173 PPKFTIEIAENAKPGTYP 190
                                       556667778889999996 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00013
                              YtkA   6 dlevelvspe.epkagent.ivvt.vtqggkpVedadvkvefwmp 47 
                                       ++e+e++  + ++ +ge+  + vt ++ g++pV+da+v++++++p
  gi|298675648|ref|YP_003727398.1| 240 EAEFEITNISaNLRTGEKGlLRVTyKNVGNQPVKDATVRITASDP 284
                                       455666644425699999537888799***************999 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 2.2
                              YtkA  23 tivvtvtqggkpVedad.vkve 43 
                                       +i++++ +g++ V+d   ++v 
  gi|298675648|ref|YP_003727398.1| 325 EIKYEDVDGNERVSDTQkIQVR 346
                                       5777777889999988547765 PP

>> Lip_prot_lig_C  Bacterial lipoate protein ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1     0.037   1.6e+02      11      56 ..      87     130 ..      79     137 .. 0.73
   2 ?    7.6   0.0   0.00081       3.6       2      47 ..     174     219 ..     173     227 .. 0.96

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.037
                                       EETTE.EEEEEEEE.ETTEEEEEEEEESBSSSSHCHHHHHHHTTSBSS CS
                    Lip_prot_lig_C  11 rfdwG.tvevrldv.ekgiIkdikiyGDffgpkdieeleekLigvkye 56 
                                        f+ G tv++++++ +kg+I+ +k + D    +d+++le++L+ +++ 
  gi|298675648|ref|YP_003727398.1|  87 EFSKGdTVTLKINLvNKGVITGFKSEKD----DDLSKLEKALQKTEMG 130
                                       5665535778887668888888886655....8999999999988765 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00081
                                       -EESEEEEEEETTEEEEEEEEEETTEEEEEEEEESBSSSSHCHHHH CS
                    Lip_prot_lig_C   2 pefnvkkkkrfdwGtvevrldvekgiIkdikiyGDffgpkdieele 47 
                                       p+f+++ ++  + Gt  + l+   g  k+++++GD   +++i++le
  gi|298675648|ref|YP_003727398.1| 174 PKFTIEIAENAKPGTYPLALNTLYGYQKNVQVSGDNVTNGQITNLE 219
                                       89*****************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2280.56
//
Query:       gi|298675649|ref|YP_003727399.1|  [L=177]
Description: putative ModE family transcriptional regulator [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-13   51.0   0.1    2.1e-13   50.3   0.1    1.4  1  TOBE            TOBE domain
    3.1e-09   36.7   0.0    5.2e-09   35.9   0.0    1.4  1  HTH_1           Bacterial regulatory helix-turn-helix protein
     0.0056   16.4   0.1      0.012   15.4   0.1    1.5  1  HTH_23          Homeodomain-like domain
  ------ inclusion threshold ------
      0.025   14.1   0.3      0.035   13.6   0.3    1.2  1  14-3-3          14-3-3 protein
      0.075   13.0   0.4        0.2   11.6   0.1    2.0  2  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an


Domain annotation for each model (and alignments):
>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3   0.1     6e-17   2.1e-13       2      64 .]     113     174 ..     112     174 .. 0.98

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 6e-17
                              TOBE   2 sarNqlpgtVvvveplgseveVrvdlgggatLtArvtrrsaeeLgLapGeeVfalikaakvhl 64 
                                       sarNq+ g+Vv ve +++ + + + +++ + + + +tr+++e+L+++ G+eV+a +k+++v++
  gi|298675649|ref|YP_003727399.1| 113 SARNQISGKVVSVENGDVISKLSISIEPST-IKSLITREAVEKLDIKEGDEVYAIVKSTEVMI 174
                                       9*****************************.******************************86 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.0   1.4e-12   5.2e-09       5      59 ..      23      81 ..      20      82 .. 0.88

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 1.4e-12
                                      HHHHHHHHHSSHHHHHHHHTS-HHHHHHHHHHHHHHHTS-SEEESSSE....EEE-HHH CS
                             HTH_1  5 rlfvavaeegsftrAAeeLglsqpavsrqikrLEeelgvpLfeRtgrg....lrLTeaG 59
                                      +l+ a+ +e+s+++A+++L +s+ ++++++k+ Ee+ + + +e  ++g    + LTe +
  gi|298675649|ref|YP_003727399.1| 23 QLLRAIDKEKSLNKACKKLDISYRHAWKMLKKIEERADNKVVESVKGGknqgTFLTEFA 81
                                      799****************************************7555444559999976 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   3.4e-06     0.012       7      44 ..      21      57 ..      21      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.4e-06
                            HTH_23  7 RlrillllaeGlsvreIAreLgvsrrTvyrwlkryree 44
                                      +++ l++ ++ +s  +++++L++s+r+ ++ lk+  ee
  gi|298675649|ref|YP_003727399.1| 21 KAQLLRAIDKEKSLNKACKKLDISYRHAWKMLKKI-EE 57
                                      7999*****************************97.44 PP

>> 14-3-3  14-3-3 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3   9.7e-06     0.035      31      98 ..      29      99 ..      17     113 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.7e-06
                                      CHHHHHHHHHHHHHHHHHHHCHHHHHHHCCCCTCC...HHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                            14-3-3 31 eernlLsvayKnvvgarRaswrvlssieqkeeske...ekkve...likeyrekiekeLkeiceevlelldktl 98
                                      ++++ L+ a K++  + R +w++l++ie++ ++k        +      ++ ++++keL +  ++ ++++++t+
  gi|298675649|ref|YP_003727399.1| 29 DKEKSLNKACKKLDISYRHAWKMLKKIEERADNKVvesV---KggkNQGTFLTEFAKELLQEYDNQMNIIHETV 99
                                      567889*********************999888874332...33335556666777777777777777776665 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       2.8     1e+04      30      40 ..     124     133 ..     122     135 .. 0.49
   2 ?   11.6   0.1   5.7e-05       0.2      15      38 ..     151     174 ..     149     177 .] 0.79

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.8
                                       EECTTCCCCCC CS
                    MazE_antitoxin  30 evdgdkiilrp 40 
                                       +v++ ++++++
  gi|298675649|ref|YP_003727399.1| 124 SVEN-GDVISK 133
                                       4444.455555 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 5.7e-05
                                       CHHHCCEECTCEEEEEECTTCCCC CS
                    MazE_antitoxin  15 vrfelgireGdevelevdgdkiil 38 
                                        +++l+i+eGdev  +v++   ++
  gi|298675649|ref|YP_003727399.1| 151 AVEKLDIKEGDEVYAIVKSTEVMI 174
                                       5799**********9999765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       947  (0.0528195); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1175.37
//
Query:       gi|298675650|ref|YP_003727400.1|  [L=348]
Description: ABC transporter-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.9e-32  112.6   0.0    3.2e-32  111.9   0.0    1.4  1  ABC_tran    ABC transporter
    4.6e-15   55.7   2.3    2.5e-14   53.3   0.0    2.8  3  TOBE        TOBE domain
    3.8e-09   36.6   0.0    9.1e-09   35.4   0.0    1.7  1  TOBE_2      TOBE domain
      1e-08   35.3   1.5    0.00024   21.0   0.1    2.1  2  AAA_21      AAA domain, putative AbiEii toxin, Type IV TA sys
     0.0022   17.8   0.0       0.26   11.0   0.0    2.2  2  AAA_30      AAA domain
     0.0024   17.3   0.1      0.031   13.7   0.0    2.1  2  SMC_N       RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.019   14.7   0.1      0.042   13.6   0.1    1.5  1  AAA_29      P-loop containing region of AAA domain
      0.056   12.7   0.0       0.22   10.8   0.0    1.8  2  Zeta_toxin  Zeta toxin
      0.085   13.3   0.1       0.47   10.9   0.1    2.1  1  AAA         ATPase family associated with various cellular ac
      0.099   12.9   0.0        1.4    9.2   0.0    2.2  1  SbcCD_C     Putative exonuclease SbcCD, C subunit
        0.1   13.1   0.3       0.18   12.3   0.3    1.4  1  AAA_23      AAA domain
       0.11   12.3   0.0       0.21   11.4   0.0    1.4  1  DEAD        DEAD/DEAH box helicase
       0.15   12.5   0.0       0.29   11.5   0.0    1.4  1  AAA_16      AAA ATPase domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.9   0.0   2.3e-35   3.2e-32       2     136 ..      17     154 ..      16     155 .. 0.97

  Alignments for each domain:
  == domain 1  score: 111.9 bits;  conditional E-value: 2.3e-35
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       kn++l++++ge  +++G++GaGK+ +l+l+ag ++p++G i ++g+++++  l+  +++ig++ q+ +lfp+++v++
  gi|298675650|ref|YP_003727400.1|  17 KNLDLTIQNGEYFVLLGPTGAGKTLVLELIAGFHQPEKGYISFNGNNIDS--LPPEKRNIGFVYQNYSLFPHMNVEQ 91 
                                       89***********************************************9..************************* PP

                                       H.........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n          ++ +i ++++ l+++++ +++      +LSgG++qrvalaral+ +p++lllDEp 
  gi|298675650|ref|YP_003727400.1|  92 NigfgarmrgIKNPKIRDMAEYLNISHILHRNP----ITLSGGEQQRVALARALIINPDILLLDEPL 154
                                       *****9999999999************888887....*****************************7 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.5       1.2   1.7e+03       9      25 ..     178     194 ..     177     195 .. 0.84
   2 ?    0.1   0.0      0.76     1e+03       3      15 ..     229     241 ..     228     256 .. 0.81
   3 !   53.3   0.0   1.8e-17   2.5e-14       1      64 []     284     347 ..     284     347 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.2
                              TOBE   9 gtVvvveplgseveVrv 25 
                                       +tVv+v++ + e++V +
  gi|298675650|ref|YP_003727400.1| 178 VTVVHVTHDQTEARVLA 194
                                       6999****999999865 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.76
                              TOBE   3 arNqlpgtVvvve 15 
                                        +N+++g V+++ 
  gi|298675650|ref|YP_003727400.1| 229 VENVFKGIVTRSN 241
                                       589******9875 PP

  == domain 3  score: 53.3 bits;  conditional E-value: 1.8e-17
                              TOBE   1 ssarNqlpgtVvvveplgseveVrvdlgggatLtArvtrrsaeeLgLapGeeVfalikaakvhl 64 
                                       ssarN++ +tVv+ e  g+  +V +  g    + + +tr+sa+eL+L+pG++V++++kaa++h+
  gi|298675650|ref|YP_003727400.1| 284 SSARNTFYATVVEMELMGVLLRVKLNMGKDFNINSLITRQSATELDLKPGDRVVVSFKAAAIHI 347
                                       79****************7777777777777*******************************96 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.0   6.6e-12   9.1e-09       2      75 ..     269     347 ..     268     348 .] 0.79

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 6.6e-12
                            TOBE_2   2 aiRPEklrla....aagganglsGtVedveylGsstryvvelaggqlvvv...rqpnadrdsalapGdtVelswdpd 71 
                                       ++RPE+++++    + +++n++ +tV++ e +G  +r+ +  +    +     rq+++  + +l+pGd+V +s++++
  gi|298675650|ref|YP_003727400.1| 269 CLRPENVTISktefESSARNTFYATVVEMELMGVLLRVKLNMGKDFNINSlitRQSAT--ELDLKPGDRVVVSFKAA 343
                                       89********9999777779*************9999777777643333222133333..47999************ PP

                            TOBE_2  72 davv 75 
                                       ++++
  gi|298675650|ref|YP_003727400.1| 344 AIHI 347
                                       **97 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.1   3.1e-05     0.042       2      47 ..      29      69 ..      28     100 .. 0.74
   2 !   21.0   0.1   1.7e-07   0.00024     198     298 ..     123     186 ..      87     189 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.1e-05
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkips 47
                                       vl Gp g+GK+ +L+++ ++++        ++++ +g++i++ p 
  gi|298675650|ref|YP_003727400.1| 29 FVLLGPTGAGKTLVLELIAGFHQ-----PEKGYISFNGNNIDSLPP 69
                                      59****************99965.....555555555555554444 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 1.7e-07
                            AAA_21 198 elsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkl 274
                                       ++ +l                                   S G ++  al+ al+  +   ++ll+DEp + L+P+ 
  gi|298675650|ref|YP_003727400.1| 123 NPITL-----------------------------------SGGEQQRVALARALIINP---DILLLDEPLSALDPRT 161
                                       44444...................................888888889999999999...9*************** PP

                            AAA_21 275 lrrllellkelsr.ngaQviltTHS 298
                                       ++   ++lk+ ++ +g+ v+ +TH+
  gi|298675650|ref|YP_003727400.1| 162 QEDTRKILKKVHEdTGVTVVHVTHD 186
                                       ********777777**********8 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00019      0.26      16      45 ..      25      53 ..      18      67 .. 0.82
   2 ?    4.3   0.0     0.021        28      37      68 ..     168     199 ..     165     211 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00019
                            AAA_30 16 sgdrvavltGpAGtGKttalkalreaweaa 45
                                      +g  + vl Gp G+GKt +l+ ++  ++ +
  gi|298675650|ref|YP_003727400.1| 25 NG-EYFVLLGPTGAGKTLVLELIAGFHQPE 53
                                      34.5899****************9998877 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.021
                            AAA_30  37 alreaweaaggrviglAptgkaAkvLaeelgi 68 
                                        l++++e+ g +v+ +++ ++ A+vLa+ +g+
  gi|298675650|ref|YP_003727400.1| 168 ILKKVHEDTGVTVVHVTHDQTEARVLADRIGV 199
                                       57899***********************9997 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1      0.13   1.7e+02      26      44 ..      28      46 ..      12      67 .. 0.82
   2 !   13.7   0.0   2.2e-05     0.031     125     213 ..     118     201 ..      78     207 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.13
                                      EEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKsnlldAi 44
                                        +++Gp G+GK+ +l+ i
  gi|298675650|ref|YP_003727400.1| 28 YFVLLGPTGAGKTLVLELI 46
                                      45789********998866 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2.2e-05
                                       HHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 125 ellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreem 201
                                       ++l++  i   +LSgGe++ vala  + i   +p  + llDe  +aLD +  +   ++lk+ ++++ + v+ +++++
  gi|298675650|ref|YP_003727400.1| 118 HILHRNPI---TLSGGEQQRVALARALII---NP-DILLLDEPLSALDPRTQEDTRKILKKVHEDTGVTVVHVTHDQ 187
                                       33333333...6*******9999877655...44.4789***********************999999888777776 PP

                                       CCC-..SCEEEEEE CS
                                       xxxx..xxxxxxxx RF
                             SMC_N 202 leka..dklvgvtk 213
                                       +e       +gv++
  gi|298675650|ref|YP_003727400.1| 188 TEARvlADRIGVMM 201
                                       66543366666666 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1     3e-05     0.042       8      55 ..      10      60 ..       6      62 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3e-05
                            AAA_29  8 NWgtfdghtieidlkg..atlltGpsGsGKSTllDAiqalLvpak.kvrfN 55
                                      +Wg f+ + ++++ ++   ++l Gp+G+GK+ +l  i+    p+k  ++fN
  gi|298675650|ref|YP_003727400.1| 10 DWGDFSIKNLDLTIQNgeYFVLLGPTGAGKTLVLELIAGFHQPEKgYISFN 60
                                      7****998888877666899**********988766666666666555555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00016      0.22      20      60 ..      30      70 ..      22      81 .. 0.88
   2 ?   -1.2   0.0      0.76     1e+03     151     179 ..     165     194 ..     155     207 .. 0.49

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00016
                        Zeta_toxin 20 llgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPe 60
                                      +l G +GAGK+ ++el++  ++++++++ +++ ++ +l Pe
  gi|298675650|ref|YP_003727400.1| 30 VLLGPTGAGKTLVLELIAGFHQPEKGYISFNGNNIDSLPPE 70
                                      56799**************************9988777776 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.76
                        Zeta_toxin 151 gRlvpkeehdea.feglresvealeeekql 179
                                        R++ k++h+++ ++ +  + ++ e + ++
  gi|298675650|ref|YP_003727400.1| 165 TRKILKKVHEDTgVTVVHVTHDQTEARVLA 194
                                       445544444433133333333444444444 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00034      0.47       2      35 ..      30      65 ..      29     193 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00034
                                      EEESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCS CS
                               AAA  2 llyGppGtGKTllakavakelg..vefleisgsell 35
                                      +l Gp G GKTl+ + +a   +    +++++g ++ 
  gi|298675650|ref|YP_003727400.1| 30 VLLGPTGAGKTLVLELIAGFHQpeKGYISFNGNNID 65
                                      689**************9875422334555554444 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0     0.001       1.4      32      89 ..     126     170 ..     108     171 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.001
                           SbcCD_C  32 tlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                       tlSGGe+q    +ala     ++        ++++++LDE  s lD+++++   ++l+
  gi|298675650|ref|YP_003727400.1| 126 TLSGGEQQR---VALA----RALII------NPDILLLDEPLSALDPRTQEDTRKILK 170
                                       666666632...2233....33333......5899*************9998887776 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3   0.00013      0.18      15      39 ..      19      46 ..       2      64 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                            AAA_23 15 idF...skgltlItGpNGaGKTTildAi 39
                                      +d+   +   +++ Gp+GaGKT +l+ i
  gi|298675650|ref|YP_003727400.1| 19 LDLtiqNGEYFVLLGPTGAGKTLVLELI 46
                                      34455666789*************9988 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00015      0.21      11     107 ..      23     213 ..      16     226 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                                       HHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS........................................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................................ RF
                              DEAD  11 ilgggdvlvaaeTGsGKTlaflipvlqivyetkgktg........................................ 47 
                                       i +g+ +++ ++TG+GKTl+  + +   + +   ++g                                        
  gi|298675650|ref|YP_003727400.1|  23 IQNGEYFVLLGPTGAGKTLVLELIAG--FHQ--PEKGyisfngnnidslppekrnigfvyqnyslfphmnveqnigf 95 
                                       4577888999*********9655554..533..22224556777778888888889999999999999999999999 PP

                                       .................................................-EEEEE.ESSHHHHHHHHHHHHHHTTTS CS
                                       .................................................xxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  48 .................................................pkaliv.ePtreLaeqtlnnlkkfkkyi 74 
                                                                                        p +l++ eP+ +L   t ++++k++k++
  gi|298675650|ref|YP_003727400.1|  96 garmrgiknpkirdmaeylnishilhrnpitlsggeqqrvalaraliinPDILLLdEPLSALDPRTQEDTRKILKKV 172
                                       99999999999999999999999999999999999999999977777764443333677777777777777777753 PP

                                       T....SEEE.EEETTSSHHHHHHHH...HTTCSEEEEEHHH CS
                                       x....xxxx.xxxxxxxxxxxxxxx...xxxxxxxxxxxxx RF
                              DEAD  75 d....lrvl.liiggvaardqlskl...dngvdivvgtpgr 107
                                       +    ++v+ ++  +++ar   +++     g  + vgtpg 
  gi|298675650|ref|YP_003727400.1| 173 HedtgVTVVhVTHDQTEARVLADRIgvmMDGGLMQVGTPGE 213
                                       33443333312222333333333332223445566666665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00021      0.29      23      62 ..      25      65 ..      17      93 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00021
                            AAA_16 23 rpelvllsGesGvGKsslvrellralekdggif.lrgkcdq 62
                                       +e+ +l G+ G GK+ +++ ++   + ++g+  ++g++ +
  gi|298675650|ref|YP_003727400.1| 25 NGEYFVLLGPTGAGKTLVLELIAGFHQPEKGYIsFNGNNID 65
                                      448899**************999766666566556555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2460.07
//
Query:       gi|298675651|ref|YP_003727401.1|  [L=275]
Description: binding-protein-dependent transporter inner membrane component [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.8e-17   62.0  10.9    5.8e-17   62.0  10.9    2.1  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -5.4   9.3         1   1.8e+04      31      44 ..      16      63 ..       6      83 .. 0.46
   2 !   62.0  10.9   3.3e-21   5.8e-17       1     173 [.      82     262 ..      78     271 .. 0.84

  Alignments for each domain:
  == domain 1  score: -5.4 bits;  conditional E-value: 1
                      BPD_transp_1 31 Psfvlail.....lvlvf.............................v 44
                                      P++v+++l     l++vf                             +
  gi|298675651|ref|YP_003727401.1| 16 PMLVIFFLslsilLFFVFitlsnmilqqivtdfsglieavrdssvleA 63
                                      444433332211122222444455556556666655555555544444 PP

  == domain 2  score: 62.0 bits;  conditional E-value: 3.3e-21
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf..........vilsilghlilpviillllsaapy 67 
                                       g+++++l+a ++ + +++++  + +++  +P+ v +i l+ +f            +  + +++ + ++++l+ +apy
  gi|298675651|ref|YP_003727401.1|  82 GVPTAYLLA-RKDFAGKRIIESILDIPVVVPHTVAGIALLTIFgangligdplESIVRFRDAMAGTVVAMLFVSAPY 157
                                       788899999.*****************************************98444478899999************ PP

                      BPD_transp_1  68 vrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtlllea 144
                                        +   r++++s++  l++aar lGa+ w+ f  v++P+a + ++tg i+ +++++ ++ ++ +l+ +p +g +l+  
  gi|298675651|ref|YP_003727401.1| 158 LTNSAREGFQSVDPRLENAARSLGAPLWKAFLFVTFPLASRHLLTGSIMCWARAISEFGAVIMLAYYPMVGPTLIYE 234
                                       *****************************************************************777666555544 PP

                      BPD_transp_1 145 ilgydyseisnggvlalviavlllnlvad 173
                                          ++  + s  ++++l+i+v l ++v+ 
  gi|298675651|ref|YP_003727401.1| 235 RFTSMGLSES-RPIAVLLILVTLTIFVIL 262
                                       4444444344.344444444444444332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 1832.11
//
Query:       gi|298675652|ref|YP_003727402.1|  [L=357]
Description: extracellular solute-binding protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      1e-30  107.2   0.0    1.3e-30  106.9   0.0    1.1  1  SBP_bac_11  Bacterial extracellular solute-binding protein
    3.1e-07   30.7   0.0      5e-07   30.0   0.0    1.3  1  SBP_bac_1   Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
       0.02   15.1   0.4       0.05   13.9   0.4    1.6  1  DUF4064     Protein of unknown function (DUF4064)
      0.086   12.2   0.0       0.32   10.4   0.0    1.9  2  SBP_bac_6   Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.9   0.0   2.9e-34   1.3e-30       1     228 [.      50     334 ..      50     335 .. 0.88

  Alignments for each domain:
  == domain 1  score: 106.9 bits;  conditional E-value: 2.9e-34
                                       .EEEE-SSTHHHHHHHHHHH.HHHH---EEEEESSHHHHHHHHHH.H..-SEEEESSH.HHHHHHHHGGGGGGG-EE CS
                        SBP_bac_11   1 ltvaaagslaaalrelaaaF.eahtgvkvevsaggsgklarqiad.garpDvwipassawlellaaaglvqaesavp 75 
                                       l+v+ agsl+ +++el + + ++h++v+v+ +aggs + +r+i++ g+++Dv+  a+   + ++  +++++   +++
  gi|298675652|ref|YP_003727402.1|  50 LNVFHAGSLTIPFKELEQMYeKRHPNVDVRREAGGSVATVRKITEvGKQADVVGVADYSLIPNMMMNEYTD--CYSA 124
                                       79******************5559*******************66166***********************..**** PP

                                       EEEEEEEEEESTT-....TT---SHHH.HHHSS--EEEE--T-TTTTHH.HHHHGGG--....HHHHHHHHHTEEEE CS
                        SBP_bac_11  76 lassplviavpkgn....pkkikgwad.LlkpglklavadPttspsGlaalalleaaga....qellkalekkvvkl 143
                                       +a++++via+ +++      + ++w d L++ ++++++++P+ +p G++ +++ + a+     +++++ l  + + +
  gi|298675652|ref|YP_003727402.1| 125 FAKNQMVIAYTEDSkysdEINNDNWYDiLRRSDVTFGFSNPNDDPCGYRSQMTTQLAEIyyndSQIYDDLMASNTAM 201
                                       **************765434666777726668****************99999999866666655666655554445 PP

                                       ESSH............................HHHHHHHHTTT-SEEEEEHHHHH..HSTTSSEEEE--TTT--... CS
                        SBP_bac_11 144 gess............................rqlltaveageadagivyeseakaaengdkleavylpeglnl.d. 190
                                        ++s                            + l +a+e ge+d++ +y+s a     ++++e+v+lp ++ l + 
  gi|298675652|ref|YP_003727402.1| 202 DTTSsngtytvnvpnseninpnsdkimmrsmeTELSSALEMGEIDYFYIYRSVAV----QHGFEFVELPSEIDLsSv 274
                                       44446888888888889999999999998888888888*****************....9************9966* PP

                                       ........................EEEEEEEE-TT--HHHHHHHHHTTSHHHHHHHHHTT CS
                        SBP_bac_11 191 ......................pldypaavlkkaakreaAraFlafLrspeaqailrkyG 228
                                                             p++y+++++++ +++e A  F+++L+s+++q++l+ +G
  gi|298675652|ref|YP_003727402.1| 275 khedmyskvkvergngdiskgkPIVYGVTIPDTVNQKEHAVGFIKLLHSEDGQQVLENNG 334
                                       *********************************************************998 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   1.1e-10     5e-07      17     315 .]      64     328 ..      55     328 .. 0.81

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 1.1e-10
                                       H....HHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEE.CGGHHHHHHHTTSBECCHHHHHHTTECTTCC CS
                         SBP_bac_1  17 a....fekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviav.dndwiarlakaglllpldpyvkaylapgvkd 88 
                                       +    +ek+hp+++V+ e +  gs+a+ +++ ++ G+ +aDv+ v d++ i+ +  + +    ++++k++++  + +
  gi|298675652|ref|YP_003727402.1|  64 EleqmYEKRHPNVDVRREAG--GSVAT-VRKITEVGK-QADVVGVaDYSLIPNMMMNEYTDCYSAFAKNQMVIAYTE 136
                                       334469*************9..66666.666667777.66*****55555554444445555555555555544444 PP

                                       TEEEEHHHHTHHHHCEEEESEEEEEEEEEEEETTTHHCTTGGGSHBHH.HHHHHHHHHHHHCTCT...HCCHCCEEH CS
                         SBP_bac_1  89 aadklsssvlpkildskvlyvPlyaargliYNkdlfekagldppwtWd.elveaakklkekgkkp...iggarggsa 161
                                       + ++ ++ +                                    +W   l + ++ ++ +++++   ++++ + ++
  gi|298675652|ref|YP_003727402.1| 137 DSKYSDEIN----------------------------------NDNWYdILRRSDVTFGFSNPNDdpcGYRSQMTTQ 179
                                       333333333..................................336665999************************* PP

                                       HHHHHHHHHHHHHHHTGGGEECCCTHHCSHHHHS...HHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTTSC CS
                         SBP_bac_1 162 sgtayyfalalakslggkvfdkdgggldnpegvt...aatylvklyavanltkelkgkgaenkdgaaalalfeaGea 235
                                       + + yy++++++ +l            ++ ++ +   ++++++  + + +    +++k +  + ++++ +++e Ge+
  gi|298675652|ref|YP_003727402.1| 180 LAEIYYNDSQIYDDLM-----------ASNTAMDttsSNGTYTVNVPNSENINPNSDKIMMRSMETELSSALEMGEI 245
                                       ********99999999...........333333336777777777777777889999******************** PP

                                       SEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEE...EEEEEEEEBTTCSTHHHHHHHHHHHT CS
                         SBP_bac_1 236 amaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgi...lgayglaipkgsknpeaAkkFldfll 309
                                       + ++++ + a +++ +  + + ++d +++k e+ +  +  ++g+++ +   +++yg++ip +  ++e A  F+++l 
  gi|298675652|ref|YP_003727402.1| 246 DYFYIYRSVAVQHGFEFVELPSEIDLSSVKHEDMYSKVKVERGNGDISkgkPIVYGVTIPDTVNQKEHAVGFIKLLH 322
                                       **********************************************99***************************** PP

                                       SHHHHH CS
                         SBP_bac_1 310 speaqa 315
                                       s+++q+
  gi|298675652|ref|YP_003727402.1| 323 SEDGQQ 328
                                       **9995 PP

>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.4   1.1e-05      0.05       6      55 ..       5      54 ..       2      61 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.1e-05
                           DUF4064  6 iiLglIGgilgillglllllflfllssgefsqelteeqalsgedasavle 55
                                       iL +IG+i  il +++++++++ ++++ +++++++e++++g+++ +v +
  gi|298675652|ref|YP_003727402.1|  5 NILKIIGIIAMILVIFAGIGCMSDTGESTTQDNQGTESQQQGDVVLNVFH 54
                                      69*******************99999988888888877776666655555 PP

>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.37   1.7e+03     115     161 ..     175     225 ..     168     231 .. 0.58
   2 ?   10.4   0.0   7.2e-05      0.32     184     230 ..     304     351 ..     297     356 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.37
                         SBP_bac_6 115 gvkkllrnlkanlhpaq.....mvkaagslesgepavsvvpyffadilpekk 161
                                       ++++ l+++  n  +++     +++a+++ +s+ ++++v +  + +i p+++
  gi|298675652|ref|YP_003727402.1| 175 QMTTQLAEIYYNDSQIYddlmaSNTAMDTTSSN-GTYTVNVPNSENINPNSD 225
                                       555566666666666665555555555555555.356666666666666665 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 7.2e-05
                         SBP_bac_6 184 vkkg.kkkelakafidfllspevqailakagg..vfPvvtnpavlnelpe 230
                                       ++    +ke a  fi  l+s+++q++l+++g+   +P+    +  n++pe
  gi|298675652|ref|YP_003727402.1| 304 IPDTvNQKEHAVGFIKLLHSEDGQQVLENNGQppIVPA--STNTINKVPE 351
                                       444466999**********************9444443..4444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2177.70
//
Query:       gi|298675653|ref|YP_003727403.1|  [L=336]
Description: phosphate uptake regulator PhoU [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-28   99.4   9.8    5.7e-19   68.4   1.3    2.4  2  PhoU            PhoU domain
    7.4e-09   35.3   0.0    1.4e-08   34.4   0.0    1.5  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
  ------ inclusion threshold ------
      0.055   13.8   0.8          1    9.7   0.8    2.6  1  DUF2935         Domain of unknown function (DUF2935)
      0.061   13.7   0.7        3.5    8.1   0.0    2.7  3  HAMP            HAMP domain
      0.087   13.1   0.6       0.24   11.7   0.4    1.9  2  DUF5405         Domain of unknown function (DUF5405)
      0.089   12.8   2.8       0.12   12.4   0.6    2.1  2  TcpS            Toxin-coregulated pilus protein S
       0.27   11.9   2.9        1.2    9.8   0.8    2.5  2  DUF643          Protein of unknown function (DUF643)


Domain annotation for each model (and alignments):
>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.4   1.3   2.2e-22   5.7e-19       1      88 [.     137     227 ..     137     228 .. 0.87
   2 !   35.6   1.8   3.7e-12   9.6e-09       4      88 ..     246     322 ..     243     323 .. 0.85

  Alignments for each domain:
  == domain 1  score: 68.4 bits;  conditional E-value: 2.2e-22
                                       HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SH....HHHHHHHHHHHHH CS
                              PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplae....dlrellsllriar 73 
                                       ++rm+ i+++m +da++al++kd +la +vi rdde+drl+ +i+++ ++a+ ++ +l       ++e  ++++ a+
  gi|298675653|ref|YP_003727403.1| 137 VKRMFLISNSMHKDAIRALKTKDSDLAMDVIHRDDEVDRLFLLISKQ-FRAVLRGAQLPDtaetSIDEYHDFRMTAS 212
                                       589*****************************************999.77776633333333577888889****** PP

                                       HHHHHHHHHHHHHHH CS
                              PhoU  74 dlERigDhavniaer 88 
                                        lERi+Dha++ia+ 
  gi|298675653|ref|YP_003727403.1| 213 PLERIADHARKIAKV 227
                                       *************96 PP

  == domain 2  score: 35.6 bits;  conditional E-value: 3.7e-12
                                       HHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHH CS
                              PhoU   4 maeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigD 80 
                                        ++++++++++++ al++ ++ela++vi++ d++ +   +i + ll++ ++        +++++l  +a ++ RigD
  gi|298675653|ref|YP_003727403.1| 246 ASDTSRKIVENSINALYDSNVELANQVIDQGDQMREQVTKINETLLKLDSH--------EAIVALGTVADSIDRIGD 314
                                       57899***********************99999999999999995544443........345666779********* PP

                                       HHHHHHHH CS
                              PhoU  81 havniaer 88 
                                       + +niae+
  gi|298675653|ref|YP_003727403.1| 315 YGANIAEI 322
                                       ******97 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.0   5.5e-12   1.4e-08       1      43 [.       8      51 ..       8      54 .. 0.94

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 5.5e-12
                                      EEETTEEEEEE-CCCHHHCCEECTCEEEEEECTT.CCCCCCCHH CS
                    MazE_antitoxin  1 fkvGnsgavriPkevrfelgireGdevelevdgd.kiilrplks 43
                                      +++G+++++++Pk ++++  i+ G+ v l +++d  +++ p+++
  gi|298675653|ref|YP_003727403.1|  8 QTGGSTYIISLPKKWAEKVRIKSGSQVFLQQHPDgTLVIDPVSE 51
                                      699*******************************9999999876 PP

>> DUF2935  Domain of unknown function (DUF2935)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.8    0.0004         1      25      78 ..     235     293 ..     112     298 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0004
                           DUF2935  25 ldpkekdlikeakef.....kkeFekllaeavelseglvrasseleeavakLneealkl 78 
                                        ++   dli+ a +      +++ ++l+ ++vel++ ++ +  ++ e+v k+ne  lkl
  gi|298675653|ref|YP_003727403.1| 235 ITQDSMDLIENASDTsrkivENSINALYDSNVELANQVIDQGDQMREQVTKINETLLKL 293
                                       44444566666666577777899999999999999999999999999****99999887 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1     0.052   1.3e+02      15      40 ..     150     176 ..     149     177 .. 0.87
   2 ?    8.1   0.0    0.0014       3.5       5      22 ..     209     226 ..     208     237 .. 0.87
   3 ?   -3.4   0.0       5.3   1.4e+04      12      21 ..     304     313 ..     301     320 .. 0.56

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.052
                                       HHHHHHTTTBTSSTCCT.TSSSHHHHH CS
                              HAMP  15 raarriaaGdldtrlpv.sgrDEiGeL 40 
                                       +a+r++   d d   +v +++DE+++L
  gi|298675653|ref|YP_003727403.1| 150 DAIRALKTKDSDLAMDViHRDDEVDRL 176
                                       6788888889999999********998 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0014
                                       TTHHHHHHHHHHHHHHTT CS
                              HAMP   5 rilrPLrrLaraarriaa 22 
                                        +  PL+r+a++ar+ia+
  gi|298675653|ref|YP_003727403.1| 209 MTASPLERIADHARKIAK 226
                                       5678************95 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 5.3
                                       HHHHHHHHHT CS
                              HAMP  12 rLaraarria 21 
                                        +a++++ri+
  gi|298675653|ref|YP_003727403.1| 304 TVADSIDRIG 313
                                       4455555554 PP

>> DUF5405  Domain of unknown function (DUF5405)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       5.7   1.5e+04      44      65 ..      98     119 ..      97     120 .. 0.75
   2 ?   11.7   0.4   9.3e-05      0.24       7      70 ..     233     290 ..     218     303 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 5.7
                           DUF5405  44 vlvadlVselvkrevfrkqvks 65 
                                       ++++d+  +l++ e+ + + ks
  gi|298675653|ref|YP_003727403.1|  98 NVIRDVCYKLIGPEIIEETSKS 119
                                       6889999888888887766665 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 9.3e-05
                           DUF5405   7 vvitetryqfaLievkldkedgareelsviavYdsevvlvadlVselvkrevfrkqvksitell 70 
                                       + it+++    Lie   d   + +e+ s+ a Yds+v l ++++ +  + ++ r qv++i+e l
  gi|298675653|ref|YP_003727403.1| 233 FSITQDS--MDLIENASDTSRKIVEN-SINALYDSNVELANQVIDQ--GDQM-REQVTKINETL 290
                                       4556666..56777777777777777.9**************9986..3444.67788877654 PP

>> TcpS  Toxin-coregulated pilus protein S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.6   4.7e-05      0.12      43     122 ..      84     161 ..      76     167 .. 0.74
   2 ?   -0.3   0.1      0.37   9.6e+02      45      74 ..     267     292 ..     214     315 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.7e-05
                              TcpS  43 qLeLkkk.i.leveieikeaedkl.qPkvskaipvlskpkavvkvellkeiesfdekLvkLlyLvgngeekkavlay 116
                                       ++eLk k i  e +  i++   kl  P++++       +k+v+  +ll+  e+  +k vk ++L++n+ +k a+ a+
  gi|298675653|ref|YP_003727403.1|  84 IIELKSKrIlAEQKNVIRDVCYKLiGPEIIEE-----TSKSVIIQDLLNPNEVSIKKSVKRMFLISNSMHKDAIRAL 155
                                       56665432313444445555444314666655.....5799*********99999999******************* PP

                              TcpS 117 kdkten 122
                                       k k  +
  gi|298675653|ref|YP_003727403.1| 156 KTKDSD 161
                                       *99765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.37
                              TcpS  45 eLkkkileveieikeaedklqPkvskaipv 74 
                                       eL  ++ +   +++e+      k+++++ +
  gi|298675653|ref|YP_003727403.1| 267 ELANQVIDQGDQMREQV----TKINETLLK 292
                                       22222222222222222....233333333 PP

>> DUF643  Protein of unknown function (DUF643)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.8   0.00046       1.2      26      81 ..      90     145 ..      83     161 .. 0.75
   2 ?    1.2   0.1      0.22   5.6e+02      10      46 ..     249     289 ..     235     312 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00046
                            DUF643  26 eqltleqkkqlysavkki.q.eykiktGksveeiindiiepekefikdvlkdknlikk 81 
                                       +++  eqk+ +     k+   e    t ksv  ii+d+++p+   ik  +k+ +li  
  gi|298675653|ref|YP_003727403.1|  90 KRILAEQKNVIRDVCYKLiGpEIIEETSKSV--IIQDLLNPNEVSIKKSVKRMFLISN 145
                                       5566677777665444331325566899999..********************99975 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.22
                            DUF643  10 nlskdtkkeinklyete....qltleqkkqlysavkkiqey 46 
                                       +  k +  +in ly+ +    +  ++q  q+ + v+ki+e 
  gi|298675653|ref|YP_003727403.1| 249 TSRKIVENSINALYDSNvelaNQVIDQGDQMREQVTKINET 289
                                       44444455566666543111122345555666666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1071  (0.0597356); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2318.44
//
Query:       gi|298675654|ref|YP_003727404.1|  [L=212]
Description: small GTP-binding protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-15   56.4   0.0    3.9e-15   55.9   0.0    1.2  1  MMR_HSR1      50S ribosome-binding GTPase
    1.6e-13   50.6   1.2    2.4e-05   24.0   0.1    2.9  2  GTP_EFTU      Elongation factor Tu GTP binding domain
    1.1e-07   31.4   0.0     0.0043   16.5   0.0    2.4  2  Arf           ADP-ribosylation factor family
    1.9e-06   27.9   0.1      0.016   15.2   0.0    2.1  2  RsgA_GTPase   RsgA GTPase
    5.9e-05   23.3   0.0      0.018   15.3   0.0    2.3  2  Roc           Ras of Complex, Roc, domain of DAPkinase
    0.00022   20.8   0.4      0.003   17.1   0.4    2.4  1  FeoB_N        Ferrous iron transport protein B
    0.00052   19.4   0.0    0.00078   18.8   0.0    1.3  1  Septin        Septin
    0.00054   19.7   0.1     0.0021   17.8   0.1    2.1  1  AAA_24        AAA domain
     0.0011   19.0   0.0     0.0018   18.2   0.0    1.4  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
     0.0039   16.6   0.0       0.16   11.4   0.0    2.3  2  SRPRB         Signal recognition particle receptor beta subun
     0.0053   17.2   0.0      0.016   15.6   0.0    1.9  1  AAA           ATPase family associated with various cellular 
     0.0087   16.0   0.1      0.017   15.0   0.1    1.7  1  ATPase_2      ATPase domain predominantly from Archaea
  ------ inclusion threshold ------
      0.011   15.0   0.0      0.018   14.2   0.0    1.3  1  NB-ARC        NB-ARC domain
      0.011   15.3   0.1        0.8    9.3   0.0    2.1  2  AAA_25        AAA domain
      0.013   16.0   0.0      0.021   15.3   0.0    1.5  1  ABC_tran      ABC transporter
      0.014   15.5   0.0        2.5    8.1   0.0    2.3  2  Dynamin_N     Dynamin family
      0.014   15.9   0.0       0.05   14.1   0.0    1.9  1  AAA_18        AAA domain
      0.018   15.4   0.0      0.028   14.8   0.0    1.4  1  AAA_16        AAA ATPase domain
      0.037   14.4   0.0      0.078   13.4   0.0    1.6  1  RNA_helicase  RNA helicase
      0.072   13.0   0.0       0.19   11.6   0.0    1.8  2  NTPase_1      NTPase
      0.078   12.4   0.1       0.46    9.9   0.0    2.1  2  TniB          Bacterial TniB protein
      0.095   11.8   0.1      0.089   11.9   0.1    1.4  1  Parvo_NS1     Parvovirus non-structural protein NS1
       0.11   11.5   0.0        1.2    8.1   0.0    2.3  2  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
       0.12   11.2   0.0       0.19   10.5   0.0    1.2  1  PPV_E1_C      Papillomavirus helicase
       0.15   12.3   0.0       0.68   10.2   0.0    2.2  2  AAA_22        AAA domain
       0.16   12.1   0.0       0.21   11.7   0.0    1.2  1  MnmE_helical  MnmE helical domain


Domain annotation for each model (and alignments):
>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.9   0.0   5.6e-18   3.9e-15       1     114 []      26     169 ..      26     169 .. 0.71

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 5.6e-18
                                       EEEEEESTTSSHHHHHHHHHT.....STEEESSSTTSSSSEEEEE...EEETT..EEEEEEECGGC........... CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltg.....ekaivsdkpgtTrdinegr...vklkg..keielvDtpGl........... 56 
                                       +++i+G pN+GK+tL n++++     +   vs++   Tr  ++++   +k++g    + ++DtpGl           
  gi|298675654|ref|YP_003727404.1|  26 RIGIYGPPNAGKTTLANRILRdwtgdAMGPVSHIEHETRSARRREgvtIKTNGhsIGLDVIDTPGLatkidfhnfmd 102
                                       69*****************9844433245888888888887666421133444224489******977777776655 PP

                                       S..S......HHHHHH.HHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  57 i..e......gaseek.glgkaflaleeadlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                       +  e      +a+e   g+ +a++ l++ d i+lv+da+++ +++++ ++   +e +k pl++v nk
  gi|298675654|ref|YP_003727404.1| 103 YemEedeakrRAKEATeGVIEAVKWLDDLDGIILVMDATQDPFTQVNVTVVGNMEARKLPLLIVSNK 169
                                       2332333333222222467777777888**********999********999999999999999998 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.1   3.4e-08   2.4e-05       3      80 ..      24      91 ..      22     106 .. 0.86
   2 !   23.3   0.1   5.4e-08   3.7e-05      91     187 ..     128     206 ..     118     211 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 3.4e-08
                                      EEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHH.HHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSS CS
                          GTP_EFTU  3 irnigiighvDhGKtTLtdrLlyktgaiskkgeka.eeervlDtlkeErergiTiksaaisleketkkylinliDtPGH 80
                                         igi g  ++GKtTL  r+l +   +++    + e      t+++ r+ g+Tik++  s+        + +iDtPG 
  gi|298675654|ref|YP_003727404.1| 24 NARIGIYGPPNAGKTTLANRILRDWTGDAMGPVSHiE----HETRSARRREGVTIKTNGHSIG-------LDVIDTPGL 91
                                      5789********************9998886665533....789*************999999.......99*****94 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 5.4e-08
                                       HHT-SEEEEEEETTTBSTHHHH.HHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT CS
                          GTP_EFTU  91 lrvlDgavlvvdaveGvepqte.evlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrkeeklekygekgek 166
                                       l  lDg +lv+da++++ +q + +v+  + ++++p+ ++ NK+D+++a+ + i ++  q+                 
  gi|298675654|ref|YP_003727404.1| 128 LDDLDGIILVMDATQDPFTQVNvTVVGNMEARKLPLLIVSNKVDMPEASPNTIMNAFPQH----------------- 187
                                       6789************8888753999********************99998887766533................. PP

                                       TEEEEEEBTTTTBTHHHHHHH CS
                          GTP_EFTU 167 evpvvfgSalkgegvktllea 187
                                         p+v +Sal+g +++tl + 
  gi|298675654|ref|YP_003727404.1| 188 --PMVSISALEGNNIDTLYQE 206
                                       ..4555666666666655555 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   6.3e-06    0.0043       2      51 ..      12      62 ..      11      76 .. 0.81
   2 !   12.9   0.0   8.3e-05     0.057      79     134 ..     128     179 ..     124     204 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.3e-06
                                      HHHHHGGTT.TTEEEEEEEESTTSSHHHHHHHHHHSSCEE.CSSSSSEEEE CS
                               Arf  2 lsilaklklkkkelrilllGLDnaGKtTilkklkleelvt.tvPTigfnve 51
                                       + ++kl++kkk++ri + G  naGKtT+ +++  + + + + P  + + e
  gi|298675654|ref|YP_003727404.1| 12 RDFFKKLFKKKKNARIGIYGPPNAGKTTLANRILRDWTGDaMGPVSHIEHE 62
                                      57899*************************998877654425566666555 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 8.3e-05
                                       CTTESEEEEEEETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HH CS
                               Arf  79 fektdavifvvDsadreRleeakeeLkalleeeelkevallvlaNKqDlpealsee 134
                                       +++ d++i v+D+++   +++ +    +++ + e ++ +ll+++NK D+pea  ++
  gi|298675654|ref|YP_003727404.1| 128 LDDLDGIILVMDATQD-PFTQVN---VTVVGNMEARKLPLLIVSNKVDMPEASPNT 179
                                       5678899999998764.344443...3567788999***************97654 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.3e-05     0.016      89     162 ..      14      92 ..       3      97 .. 0.71
   2 !   10.8   0.0   0.00049      0.34      16      99 ..     131     209 ..     112     211 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.3e-05
                                       THHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT.-----S--------------SEEEEEETT.....TEEEESS- CS
                       RsgA_GTPase  89 gleelkellkdktsvlvGqSGvGKStLinallpe.lelktgevseklgrGkhTTtavellelae.....gglliDtP 159
                                        +++l ++ k+  + + G+  +GK+tL n++l + +  ++g vs+  ++ +   +++e + +++     g  +iDtP
  gi|298675654|ref|YP_003727404.1|  14 FFKKLFKKKKNARIGIYGPPNAGKTTLANRILRDwTGDAMGPVSHIEHETRS-ARRREGVTIKTnghsiGLDVIDTP 89 
                                       56777788888888899*************9986246677778776665554.4555555555523444557***** PP

                                       SSS CS
                       RsgA_GTPase 160 Gfr 162
                                       G+ 
  gi|298675654|ref|YP_003727404.1|  90 GLA 92 
                                       *86 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00049
                                       --EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHH CS
                       RsgA_GTPase  16 vdqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkeglee 92 
                                       +d +++v+ ++++ +++  ++ ++  +e+++++++iv nK+D+ e +   +++++++ +   +++ +sa +++++++
  gi|298675654|ref|YP_003727404.1| 131 LDGIILVMDATQDPFTQVNVT-VVGNMEARKLPLLIVSNKVDMPEASP--NTIMNAFPQH--PMVSISALEGNNIDT 202
                                       688999999998888887776.7889*****************99988..8999999887..899999999999999 PP

                                       HHHHCTT CS
                       RsgA_GTPase  93 lkellkd 99 
                                       l +++++
  gi|298675654|ref|YP_003727404.1| 203 LYQEIAK 209
                                       9988875 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.6e-05     0.018       2      66 ..      27      91 ..      26     109 .. 0.89
   2 ?    5.9   0.0     0.021        14      79     120 .]     130     172 ..     122     172 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.6e-05
                                      EEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SG CS
                               Roc  2 vvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGq 66
                                      + + G  ++GKt+l++r+++d   +   +   ++  t+++ + +gv+ +++ +++ l++ Dt G 
  gi|298675654|ref|YP_003727404.1| 27 IGIYGPPNAGKTTLANRILRDWTGDAMGPVSHIEHETRSARRREGVTIKTNGHSIGLDVIDTPGL 91
                                      56789********************************9999999***99999**********985 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.021
                                       TSCEEEEEEEGHHHHCHHHHHHHHHHHCS.SS-EEEEEE-TTT CS
                               Roc  79 eaalailvydsrssenlkeWlkelkkvag.kspvilvgnkiDl 120
                                       + + +ilv+d++++   +  ++ + ++   k p+++v nk+D+
  gi|298675654|ref|YP_003727404.1| 130 DLDGIILVMDATQDPFTQVNVTVVGNMEArKLPLLIVSNKVDM 172
                                       567899****99998888888999887551669********96 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.4   4.3e-06     0.003       3     156 .]      27     207 ..      25     207 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.3e-06
                                       EEEEESTTSSHHHHHHHHHTTS..EEEEESTTSSSE.....EEEE.EEEETTEEE..EEEE----...........S CS
                            FeoB_N   3 valvGnpnvGkttlfnaltgak..qkvgNwpGvtve.....kkeg.klklkgkev..eivDlPGi...........Y 58 
                                       + + G pn+Gkttl n++        +g  + +  e     ++eg ++k++g+++  +++D PG            Y
  gi|298675654|ref|YP_003727404.1|  27 IGIYGPPNAGKTTLANRILRDWtgDAMGPVSHIEHEtrsarRREGvTIKTNGHSIglDVIDTPGLatkidfhnfmdY 103
                                       7789************9965331133333333322200011333314555666543389*****9888888666666 PP

                                       SS.......SSSSHHHHHHHHHHHCTSSSEEEEEEEGGG...HHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE CS
                            FeoB_N  59 sl.......sayseeekvardflleeepdvvvnvvdatn...lernLyLtlqllelgvpvvlalnmideaekkgiei 125
                                       ++        a    e v + +   ++ d ++ v+dat+    + n++++ ++   ++p++++ n++d  e++  +i
  gi|298675654|ref|YP_003727404.1| 104 EMeedeakrRAKEATEGVIEAVKWLDDLDGIILVMDATQdpfTQVNVTVVGNMEARKLPLLIVSNKVDMPEASPNTI 180
                                       6655544332333334455555557899*********985545677777778888889***********99998887 PP

                                       -HHHHHHHHTS-EEEEBTTTTBTHHHHHHHH CS
                            FeoB_N 126 dlkkLsekLgvpvvktsakkkegieellkai 156
                                           +++  + p+v++sa ++++i++l ++i
  gi|298675654|ref|YP_003727404.1| 181 ----MNAFPQHPMVSISALEGNNIDTLYQEI 207
                                       ....56667789999*****99999998876 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.1e-06   0.00078       9      80 ..      29      99 ..      23     119 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.1e-06
                                      EEEBTTSSCCCCCCTTSSSS------------------S-EEEEEEEEETTCEEEEEEEE---BSSSSSHHC CS
                            Septin  9 vvGesglGkttlintlfetdlieeekleeasekkkktveikkkkvvieedgvklnltviDtpgfGdavdnsk 80
                                      + G    Gkttl n ++++   ++    ++  ++++    +++ v+i+ +g  + l viDtpg   ++d ++
  gi|298675654|ref|YP_003727404.1| 29 IYGPPNAGKTTLANRILRDWTGDAMGPVSHI-EHETRSARRREGVTIKTNGHSIGLDVIDTPGLATKIDFHN 99
                                      5688899*********998888875433333.3334445568899********************9999766 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   3.1e-06    0.0021       2      22 ..      24      44 ..      23     172 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.1e-06
                            AAA_24  2 klkiliyGpsgiGKTtlakel 22
                                      +++i iyGp+ +GKTtla+++
  gi|298675654|ref|YP_003727404.1| 24 NARIGIYGPPNAGKTTLANRI 44
                                      799***************998 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   2.7e-06    0.0018      50     102 ..     153     209 ..     132     212 .] 0.69

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.7e-06
                      MMR_HSR1_Xtn  50 egnr..vYipclyvlNKiDlisleeldelar..epnsvviSaekelnldeLkekiwe 102
                                        gn     +p l+v NK+D+ + +    ++   ++ +v iSa ++ n+d+L ++i +
  gi|298675654|ref|YP_003727404.1| 153 VGNMeaRKLPLLIVSNKVDMPEASPNTIMNAfpQHPMVSISALEGNNIDTLYQEIAK 209
                                       44442355799*********6666655555522567899**************9976 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00023      0.16       4      58 ..      25      90 ..      21     112 .. 0.67
   2 ?    3.1   0.0     0.081        56      67     130 ..     122     178 ..     115     186 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00023
                                      -EEEEE-STTSSHHHHHHHHHHS...........S---B---S.S-EEETTG...GGTT-SEEEETT CS
                             SRPRB  4 pavllvGlsdsGKTslftrLttd...........svkktvtSq.essaalkvksekgskltliDfPG 58
                                       ++ + G+ ++GKT+l +r++ d             ++t  +   + ++ k ++ +   l++iD PG
  gi|298675654|ref|YP_003727404.1| 25 ARIGIYGPPNAGKTTLANRILRDwtgdamgpvshIEHETRSARrREGVTIK-TNGHSIGLDVIDTPG 90
                                      567799****************96665555444222222222223333333.466677788888888 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.081
                                       HHHHHHHGGEEEEEEEEETTS-HHHHHHHHHHHHHHHHHHHHHTT---EEEEEE-TTSTT---H CS
                             SRPRB  67 leklkaksslkglvfvvDStidpkevkevAEllyeilliteklkdavdiliACnKqelflaksp 130
                                       +e +k  + l g++ v+D+t dp    +v     +++ ++  +  ++++li  nK ++  a ++
  gi|298675654|ref|YP_003727404.1| 122 IEAVKWLDDLDGIILVMDATQDPFTQVNV-----TVVGNM--EARKLPLLIVSNKVDMPEASPN 178
                                       66777778888999999999887544332.....333333..3567788888888887777655 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.3e-05     0.016       3      74 ..      29     138 ..      27     180 .. 0.48

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.3e-05
                                       EESSTTSSHHHHHHHHHHHH.....T.HE.........................EEEEETTTCSSS........... CS
                               AAA   3 lyGppGtGKTllakavakel.....g.ve.........................fleisgsellsk........... 37 
                                       +yGpp  GKT+la+ + +++     g v+                         +          +           
  gi|298675654|ref|YP_003727404.1|  29 IYGPPNAGKTTLANRILRDWtgdamGpVShiehetrsarrregvtiktnghsigL----------Dvidtpglatki 95 
                                       7****************99733322122223333334444444422222333330..........134444444445 PP

                                       .......STTHHHHHHHHHHHHHHHTSTS.EEEEEETGGGHHHHH CS
                               AAA  38 .......yvgesekkirelfkeakekakp.silfiDEidalaksr 74 
                                              y +  e++ +   kea e      + ++D++d ++   
  gi|298675654|ref|YP_003727404.1|  96 dfhnfmdY-EMEEDEAKRRAKEATEGV-IeAVKWLDDLDGIILVM 138
                                       55543322.222223333333444443.33666777777776666 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   2.5e-05     0.017      13      43 ..      17      47 ..      13     153 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.5e-05
                          ATPase_2 13 eilerepneiyfiYGpegsGKtaLlkeiien 43
                                      ++ ++++n  + iYGp + GKt+L ++i+  
  gi|298675654|ref|YP_003727404.1| 17 KLFKKKKNARIGIYGPPNAGKTTLANRILRD 47
                                      677788888899**************99876 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.6e-05     0.018       8      43 ..      14      47 ..       8      51 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.6e-05
                                      HHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC  8 viekLlekdelqslvvalvGmgGvGKttlakqilnk 43
                                        +kL++k++     ++++G +  GKttla+ il++
  gi|298675654|ref|YP_003727404.1| 14 FFKKLFKKKKNA--RIGIYGPPNAGKTTLANRILRD 47
                                      578999866666..7******************998 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0012       0.8      35      59 ..      26      50 ..      18      91 .. 0.81
   2 ?    4.2   0.1     0.041        28      77     127 ..     101     147 ..      99     179 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0012
                            AAA_25 35 lallaGapgtGKttlaldlalavat 59
                                       + ++G+p +GKttla  +  +++ 
  gi|298675654|ref|YP_003727404.1| 26 RIGIYGPPNAGKTTLANRILRDWTG 50
                                      56689***********999999984 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.041
                            AAA_25  77 vsaEdsedelrrRlravgeal.rddarllvldlagveslpLfakdrggtllt 127
                                        + E+ ede +rR++++ e + ++ ++l+ ld+     + L+++ ++++ ++
  gi|298675654|ref|YP_003727404.1| 101 MDYEMEEDEAKRRAKEATEGViEAVKWLDDLDG-----IILVMDATQDPFTQ 147
                                       6789*************9999755666666553.....67777666666533 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   3.1e-05     0.021       7      58 ..      20      67 ..      17     151 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.1e-05
                                      EEETTSEEEEEESTTSSHHHHHHHHTTSS--.SEEEEEETTCEGGGB-HHHCC CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  7 klkegekvaivGenGaGKStLlkllagllkp.teGeilldgkdlkeqeleslr 58
                                      k k++ +++i G+  aGK+tL++ +++  +  ++G +     +++++++ s+r
  gi|298675654|ref|YP_003727404.1| 20 KKKKNARIGIYGPPNAGKTTLANRILRDWTGdAMGPV----SHIEHETR-SAR 67
                                      567899*****************99998765466776....34444222.222 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.025        17       1      20 [.      27      46 ..      27      58 .. 0.89
   2 ?    8.1   0.0    0.0036       2.5     100     167 ..      80     169 ..      51     170 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.025
                                      EEEEEBTTTTHHHHHHHHHT CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLlg 20
                                      i + G  ++GK++++n +l+
  gi|298675654|ref|YP_003727404.1| 27 IGIYGPPNAGKTTLANRILR 46
                                      6788999***********96 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0036
                                       S-SEEEEE---B-SSSGTTS......................HHHHHHHSTTEEEEEEEETTS-CCC-CHHHHHHHH CS
                         Dynamin_N 100 vkgltlvDlPGldsvnkrdq......................elvkeyikkadiilavtsanhdlsnsealflarev 154
                                         gl ++D+PGl    + +                         + + +++ d i++v++a +d  ++ +  +  ++
  gi|298675654|ref|YP_003727404.1|  80 SIGLDVIDTPGLATKIDFHNfmdyemeedeakrrakeategvIEAVKWLDDLDGIILVMDATQDPFTQVNVTVVGNM 156
                                       557889******99999998999999999999999999986644445678999999999999987777777777777 PP

                                       STTBTTEEEEEE- CS
                         Dynamin_N 155 dpkgkrtivvltk 167
                                       + ++   ++v +k
  gi|298675654|ref|YP_003727404.1| 157 EARKLPLLIVSNK 169
                                       7777777777666 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   7.3e-05      0.05       1      19 [.      27      51 ..      27     153 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.3e-05
                            AAA_18  1 IlltGtpGvGKttlakeL......s 19
                                      I++ G+p +GKttla+++       
  gi|298675654|ref|YP_003727404.1| 27 IGIYGPPNAGKTTLANRIlrdwtgD 51
                                      89*************9985444440 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   4.1e-05     0.028      28      93 ..      28     112 ..      11     188 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.1e-05
                            AAA_16  28 llsGesGvGKsslvrellralekd..................ggiflrgkcdqlesa.ipysa.laqalareellrq 84 
                                        ++G++  GK++l++++lr +++d                  +g++++++ ++ + + i   + la+ ++++ ++  
  gi|298675654|ref|YP_003727404.1|  28 GIYGPPNAGKTTLANRILRDWTGDamgpvshiehetrsarrrEGVTIKTNGHSIGLDvI-DTPgLATKIDFHNFMDY 103
                                       59*********************988777777777766666546666666665533322.23347777777666666 PP

                            AAA_16  85 lldeaesae 93 
                                       + +e+e++ 
  gi|298675654|ref|YP_003727404.1| 104 EMEEDEAKR 112
                                       666644433 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00011     0.078       3      25 ..      29      51 ..      27      73 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
                      RNA_helicase  3 lyGpsgeGKStlakeLakallkk 25
                                      +yGp++ GK+tla+++ ++++++
  gi|298675654|ref|YP_003727404.1| 29 IYGPPNAGKTTLANRILRDWTGD 51
                                      8***************9998855 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00028      0.19       2      51 ..      27      76 ..      26     139 .. 0.87
   2 ?   -1.1   0.0       2.3   1.6e+03     133     167 ..     173     207 ..     145     208 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00028
                                      EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-------EEEEEE CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevreggrrigFkivd 51
                                      + i Gpp  GKtTl +++l+    + +     + +e r+  rr g +i +
  gi|298675654|ref|YP_003727404.1| 27 IGIYGPPNAGKTTLANRILRDWTGDAMGPVSHIEHETRSARRREGVTIKT 76
                                      7899***************9998877776677778888888888877765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.3
                                       -SS--SHHHHHHHT-TT-EEEE--TTTTTTHHHHH CS
                          NTPase_1 133 hrrkdlalveeirerkdvkvfevteenrdalleei 167
                                       ++++++ +++ + ++  v++  +  +n d+l++ei
  gi|298675654|ref|YP_003727404.1| 173 PEASPNTIMNAFPQHPMVSISALEGNNIDTLYQEI 207
                                       34447788888888888888889999999988888 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00066      0.46      24      58 ..      16      47 ..       8      65 .. 0.80
   2 ?   -0.3   0.0      0.85   5.9e+02      66      93 ..     183     210 ..     149     212 .] 0.80

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00066
                              TniB 24 eeLleypkrkrmpnlllvGdsnnGKtmivekFarl 58
                                      ++L+++ k+ r   + ++G++n GKt+++++  r+
  gi|298675654|ref|YP_003727404.1| 16 KKLFKKKKNAR---IGIYGPPNAGKTTLANRILRD 47
                                      55666666666...89*************998776 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.85
                              TniB  66 daekvpvlvvqappkpdekrlyaaiLea 93 
                                          + p++ ++a +  + + ly++i ++
  gi|298675654|ref|YP_003727404.1| 183 AFPQHPMVSISALEGNNIDTLYQEIAKT 210
                                       4457899999999999999999999665 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00013     0.089     113     135 ..      22      45 ..      14     193 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                         Parvo_NS1 113 krnt.vwfyGpantGktnlaeaIa 135
                                       k+n+ +++yGp+n Gkt la+ I 
  gi|298675654|ref|YP_003727404.1|  22 KKNArIGIYGPPNAGKTTLANRIL 45 
                                       444449***************886 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0017       1.2      19      50 ..      15      45 ..       7      52 .. 0.79
   2 ?    0.8   0.0      0.29     2e+02     204     226 ..     186     208 ..     134     211 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0017
                                      HHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHH CS
                              MeaB 19 lerllakaGraqvvGltGvPGaGkstlvealg 50
                                      +++l++k     ++G+ G P aGk tl +++ 
  gi|298675654|ref|YP_003727404.1| 15 FKKLFKKKK-NARIGIYGPPNAGKTTLANRIL 45
                                      566666654.569**************99875 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.29
                                       --EEEEEBCCCTBSHHHHHHHHH CS
                              MeaB 204 rpkvlktsavegeGidelvdaie 226
                                       + +++ +sa+eg+ id+l ++i 
  gi|298675654|ref|YP_003727404.1| 186 QHPMVSISALEGNNIDTLYQEIA 208
                                       45788899999999999998886 PP

>> PPV_E1_C  Papillomavirus helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00028      0.19     248     290 ..       7      52 ..       3      62 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00028
                          PPV_E1_C 248 fltalkefLkgv..Pkknc.lvllGppntGkslfamslikfLkGkv 290
                                       f +++++f+k+    kkn+ + ++Gppn+Gk+++a+ +++  +G  
  gi|298675654|ref|YP_003727404.1|   7 FKNNFRDFFKKLfkKKKNArIGIYGPPNAGKTTLANRILRDWTGDA 52 
                                       6677888887751134555378*************99988777765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00099      0.68      10      27 ..      29      46 ..      20     126 .. 0.89
   2 ?   -0.8   0.0       2.4   1.7e+03      38      65 ..     185     212 .]     168     212 .] 0.78

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00099
                            AAA_22 10 vtGesGtGKTtllrrlle 27
                                      ++G++ +GKTtl++r+l+
  gi|298675654|ref|YP_003727404.1| 29 IYGPPNAGKTTLANRILR 46
                                      89************9986 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.4
                            AAA_22  38 erpevvfvtlpsstsskdllrellralg 65 
                                       ++ + v++ + ++++ ++l++e+++ +g
  gi|298675654|ref|YP_003727404.1| 185 PQHPMVSISALEGNNIDTLYQEIAKTFG 212
                                       566778888999999999***9998775 PP

>> MnmE_helical  MnmE helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0    0.0003      0.21      82     130 ..      59     209 ..      49     212 .] 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0003
                                       xxxxxxxxxxxxxxx.............................................................. RF
                      MnmE_helical  82 latakrgellreGik.............................................................. 96 
                                       +++  r+ + reG++                                                              
  gi|298675654|ref|YP_003727404.1|  59 IEHETRSARRREGVTiktnghsigldvidtpglatkidfhnfmdyemeedeakrrakeategvieavkwlddldgii 135
                                       56666677777777777777778888888888888888888888878777777777777777778888888888888 PP

                                       ...................................xxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      MnmE_helical  97 ...................................Dllkeke.....ekeeeevlkiSaktgegieeLeeaike 130
                                                                          D+ +++      +  ++++++iSa++g++i++L ++i++
  gi|298675654|ref|YP_003727404.1| 136 lvmdatqdpftqvnvtvvgnmearklpllivsnkvDMPEASPntimnAFPQHPMVSISALEGNNIDTLYQEIAK 209
                                       8888888888888888888889999998888888876666667888778888899*****************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       800  (0.0446204); expected 358.6 (0.02)
Passed bias filter:                      691  (0.0385409); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.50
# Mc/sec: 1263.63
//
Query:       gi|298675655|ref|YP_003727405.1|  [L=115]
Description: hypothetical protein Metev_1772 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-44  149.6   0.3    2.6e-44  149.4   0.3    1.0  1  DUF2073   Uncharacterized protein conserved in archaea (DUF20


Domain annotation for each model (and alignments):
>> DUF2073  Uncharacterized protein conserved in archaea (DUF2073)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.4   0.3   1.4e-48   2.6e-44       1     105 []       9     112 ..       9     112 .. 0.98

  Alignments for each domain:
  == domain 1  score: 149.4 bits;  conditional E-value: 1.4e-48
                           DUF2073   1 lekmtsmekirlildkvkegkivvlEkgLtpeeeakliettmeeikpdeFsGieietypkkekdkgllekllgkkes 77 
                                       l+ m+++ek+r+i+d+vk++k++vlEkgLtp+eea+lie+tm++i+pd+FsGie+e+yp+++  +++++kl++k  +
  gi|298675655|ref|YP_003727405.1|   9 LSGMNPVEKVRFIIDEVKKDKVLVLEKGLTPDEEANLIEMTMTKIQPDGFSGIEMESYPAQSG-NSIINKLFNKGGH 84 
                                       6789*********************************************************99.************* PP

                           DUF2073  78 eerltvigPanqlktlkkdkdlisalvs 105
                                       ++rlt+igPanqlktlkkd+dli++l+s
  gi|298675655|ref|YP_003727405.1|  85 RTRLTIIGPANQLKTLKKDRDLITTLLS 112
                                       ************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 826.18
//
Query:       gi|298675656|ref|YP_003727406.1|  [L=169]
Description: hypothetical protein Metev_1773 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0062   16.6   0.6      0.009   16.1   0.6    1.3  1  HA70_C    Haemagglutinin 70 C-terminal domain


Domain annotation for each model (and alignments):
>> HA70_C  Haemagglutinin 70 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.6     5e-07     0.009      37      92 ..     101     158 ..      66     163 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5e-07
                                       E---TT-E.EEE.EEE-SS---SS-EEEEEEE.ESSSEEEEEEEEEEEETTEEEEEEEE CS
                            HA70_C  37 lspdvnky.isy.eftvpgnfnnkdtsnirly.tsdnqglgtlfrvtetidgydlidik 92 
                                         p  n+  + y   ++  ++nnkd  ni ly t dn g+ +l+   +ti+ +++ +i+
  gi|298675656|ref|YP_003727406.1| 101 NVPFSNDKaLHYlTSSIKTQLNNKDV-NINLYwTGDNAGIIQLYEKLKTIQDWKIKQIN 158
                                       44544443133312358899*****7.78887699******************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 1180.85
//
Query:       gi|298675657|ref|YP_003727407.1|  [L=202]
Description: 6-phospho 3-hexuloisomerase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.5e-18   65.1   0.0    9.9e-18   64.3   0.0    1.4  1  SIS            SIS domain
  ------ inclusion threshold ------
      0.014   15.4   3.2      0.024   14.7   0.4    2.2  2  SIS_2          SIS domain
      0.041   13.2   0.2      0.058   12.7   0.2    1.3  1  THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase,
       0.12   11.8   0.0       0.18   11.2   0.0    1.3  1  Epimerase      NAD dependent epimerase/dehydratase family


Domain annotation for each model (and alignments):
>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.3   0.0   2.2e-21   9.9e-18       4     110 ..      44     144 ..      41     150 .. 0.95

  Alignments for each domain:
  == domain 1  score: 64.3 bits;  conditional E-value: 2.2e-21
                                       TSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTT CS
                               SIS   4 kakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakerg 80 
                                        a++i+++GaG+s+ ++k +a+ l+++g+ v++v ++++      + ++e+d+vi+is sget++++++ + ak  g
  gi|298675657|ref|YP_003727407.1|  44 GADNIFLMGAGRSGLVGKAFAMRLMHLGYSVYVVGESTT------PAVKENDVVIAISGSGETRSVADLGKIAKDIG 114
                                       6899******************************99999......99****************************** PP

                                       SEEEEEESSTTSHHHHHSSEEEEEEEECHC CS
                               SIS  81 akiiaITdskgsplareadlalyinaepet 110
                                        +++++T++++s+l + +d +++++   +t
  gi|298675657|ref|YP_003727407.1| 115 STLVTVTSNEDSTLGNLSDTVVEVPGRTKT 144
                                       *********************999987766 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.11     5e+02      32      58 ..      42      68 ..      36      76 .. 0.80
   2 ?   14.7   0.4   5.3e-06     0.024     101     138 .]      85     122 ..      73     122 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.11
                                      HHTT--EEEEESGGGHHHHHHTSSSTT CS
                             SIS_2 32 lenggkvlvfGsGhSaalaeelaarag 58
                                      +     ++++G+G S +  + +a r+ 
  gi|298675657|ref|YP_003727407.1| 42 IMGADNIFLMGAGRSGLVGKAFAMRLM 68
                                      55566799********99999999876 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 5.3e-06
                                       --TT-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEEE- CS
                             SIS_2 101 lkpgDvLlviSnsGnnavvveaaeaakergmkviAlts 138
                                       +k++Dv + iS sG+  +v ++ + ak++g +++ +ts
  gi|298675657|ref|YP_003727407.1|  85 VKENDVVIAISGSGETRSVADLGKIAKDIGSTLVTVTS 122
                                       799*********************************98 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   1.3e-05     0.058      43      91 ..      54      99 ..      37     142 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.3e-05
                                      ---TTTHHHHHHHHHCTT-EEEEE-TTSCCHHHHHCCSSEEEE-SS-TT CS
                     THF_DHG_CYH_C 43 GrsnivgkplallLleknatVtvchsktkdlaeitreadivvvavGkpe 91
                                      Grs +vgk+ a+ L++ +  V v+ ++t   +  ++e d+v++  G+ e
  gi|298675657|ref|YP_003727407.1| 54 GRSGLVGKAFAMRLMHLGYSVYVVGEST---TPAVKENDVVIAISGSGE 99
                                      9***********************9999...678999****99888766 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   4.1e-05      0.18       4      40 ..      53      89 ..      50     132 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.1e-05
                                      ETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHC CS
                         Epimerase  4 tGatGfiGsalvkallekgyevigldrlssasntarl 40
                                      +G +G++G+a++ +l+  gy v ++   ++   ++++
  gi|298675657|ref|YP_003727407.1| 53 AGRSGLVGKAFAMRLMHLGYSVYVVGESTTPAVKEND 89
                                      699**********************999766555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1297.25
//
Query:       gi|298675658|ref|YP_003727408.1|  [L=375]
Description: class I/II aminotransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-65  221.9   0.0    1.6e-65  221.7   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    6.7e-12   45.0   0.0    1.3e-11   44.1   0.0    1.4  1  Aminotran_5      Aminotransferase class-V
      1e-09   38.2   0.0    1.6e-09   37.6   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    3.8e-06   25.7   0.1    5.9e-06   25.1   0.1    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
     0.0043   16.4   0.0      0.007   15.7   0.0    1.6  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.037   14.0   0.0       0.27   11.2   0.0    2.4  3  DUF1246          Protein of unknown function (DUF1246)
      0.063   12.4   1.2       0.33   10.0   0.4    2.1  2  Zfx_Zfy_act      Zfx / Zfy transcription activation region


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.7   0.0   6.1e-69   1.6e-65       3     361 ..      34     369 ..      32     371 .. 0.96

  Alignments for each domain:
  == domain 1  score: 221.7 bits;  conditional E-value: 6.1e-69
                                       EEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHH CS
                     Aminotran_1_2   3 vinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGaga 79 
                                        inLg +++++d    t++++++a+++  + ++++++y+   g pel++al   ++++++ ++  + +++v+sGa++
  gi|298675658|ref|YP_003727408.1|  34 SINLGLGQPDFD----TPDHIKQAAID--AINEGFTSYTVGAGIPELRNALSLKFKKENNFDVSSD-EIIVTSGASE 103
                                       69**********....***********..***************************9*********.********** PP

                                       HHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEES CS
                     Aminotran_1_2  80 liealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilves 156
                                       ++e++ + l +npgde+l+p+p + sy+   +++gg+ v++pl   +d ++  +++++ ++       ktk ++++s
  gi|298675658|ref|YP_003727408.1| 104 ALEIALASL-VNPGDEVLIPNPGFVSYSALTEIMGGKSVSIPLG--KDLNVQPDDVLDNITP------KTKALVLNS 171
                                       *********.9*******************************99..***************9......********* PP

                                       S-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT.EEEEEESSSTTSSGGG-EEE CS
                     Aminotran_1_2 157 phNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepn.llivgslsKafGlaGeRvGy 232
                                       p+NPtG+v +++ +++ +++a+ + + +++De+Y++fv++ +     ++  +++++ +++v+ +sK ++++G+R+Gy
  gi|298675658|ref|YP_003727408.1| 172 PSNPTGAVQSRDNIKAFAEIAEDHDITIISDEVYEHFVYEGE-----HVSPAQYTDnVITVNAVSKTYSMTGWRLGY 243
                                       ****************************************65.....4444555445******************** PP

                                       EEEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSE CS
                     Aminotran_1_2 233 ilgnaavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmf 307
                                       ++++ ++++q+ k+++ +    ss+ q+a++aa+  + +    +++m +++++rr+ l d+L++lg+k+ ++ ++++
  gi|298675658|ref|YP_003727408.1| 244 VAAKGEYIEQMLKAHQYVQAcaSSISQKAALAAVTGPME---PVHKMHDEFKERRDLLLDGLESLGIKCEKPSGAFY 317
                                       ***************9887777**************997...8********************************** PP

                                       EEEEETHHCHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHH CS
                     Aminotran_1_2 308 lltdlsaetakelskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelve 361
                                        + +++ +   +  +kL+ + gv+v+pg  f+   +g++R+++ ++++++++++++
  gi|298675658|ref|YP_003727408.1| 318 AFPEIPDS--LKTTEKLVSN-GVIVVPGIAFGEngEGHIRLSY-ATSSSQIQKALD 369
                                       ******99..9*********.**********************.999999999876 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.0   5.2e-15   1.3e-11      58     176 ..      90     203 ..      75     208 .. 0.87

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 5.2e-15
                                       -STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHH CS
                       Aminotran_5  58 aeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelek 134
                                       ++s +eii+tsG++ea+++++ sl   ++pgde+++ + +  +   +  e++   g k + ipl ++ ++++d++ +
  gi|298675658|ref|YP_003727408.1|  90 VSS-DEIIVTSGASEALEIALASL---VNPGDEVLIPNPGFVSYS-ALTEIM---GGKSVSIPLGKDLNVQPDDVLD 158
                                       565.9*******************...9*************9999.666665...7777799*************** PP

                                       H--TTEEEEEEESBETTTTEB-...-HHHHHHHHHHTT-EEEEE- CS
                       Aminotran_5 135 llnektklvaithvsnvtGtiq...pveeigklakkkgalvlvDa 176
                                       ++++ktk++ ++  sn tG +q    +++++++a ++++ ++ D 
  gi|298675658|ref|YP_003727408.1| 159 NITPKTKALVLNSPSNPTGAVQsrdNIKAFAEIAEDHDITIISDE 203
                                       ********************9822256677778888888888876 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.0   6.1e-13   1.6e-09      37     144 ..      91     202 ..      67     207 .. 0.88

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 6.1e-13
                                       T-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEE CS
                   DegT_DnrJ_EryC1  37 gvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitertk 113
                                        ++  i +s +++Al++aL  l v+pgdeV++p  +Fv+  +    +g k v +    +++n++p+++   it++tk
  gi|298675658|ref|YP_003727408.1|  91 SSDEIIVTSGASEALEIALASL-VNPGDEVLIPNPGFVSYSALTEIMGGKSVSIPLG-KDLNVQPDDVLDNITPKTK 165
                                       56677899999********776.9******************************887.99***************** PP

                                       EEE...EB-GGGB--...-HHHHHHHHHHCT-EEEEE CS
                   DegT_DnrJ_EryC1 114 aIl...pVhlyGqva...dmdalkaiaakhglkvieD 144
                                       a +   p +  G+v    +++a  +ia++h++ +i+D
  gi|298675658|ref|YP_003727408.1| 166 ALVlnsPSNPTGAVQsrdNIKAFAEIAEDHDITIISD 202
                                       *995555778888875668999999**********99 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.1   2.3e-09   5.9e-06      71     176 ..      95     205 ..      86     235 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 2.3e-09
                                       EEESSHHH.HHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHH.TTCEEEEESTTSHHHHHHHCCTTEEEEEEES CS
                   Cys_Met_Meta_PP  71 lavssGma.AiaaailallkaGdeivvsddlYggtqrllkkvlkk.lgievkfvdtsdleelekaikentklvylEt 145
                                       ++v+sG + A++ a+ +l++ Gde+++ +  + + ++l + +  k ++i        +++++   i+++tk++ l +
  gi|298675658|ref|YP_003727408.1|  95 IIVTSGASeALEIALASLVNPGDEVLIPNPGFVSYSALTEIMGGKsVSIPLGKDLNVQPDDVLDNITPKTKALVLNS 171
                                       5677777659999*******************9877777777665355555555557899***************** PP

                                       S-TTTT---...-HHHHHHHHHHTT-EEEEEGTT CS
                   Cys_Met_Meta_PP 146 ptnpllkvv...DiekiaklakkagvlvvvDntf 176
                                       p+np+  v     i++ a++a +++++++ D ++
  gi|298675658|ref|YP_003727408.1| 172 PSNPTGAVQsrdNIKAFAEIAEDHDITIISDEVY 205
                                       ****9888544369999***********999865 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.7e-06     0.007      58     167 ..     103     202 ..      53     371 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.7e-06
                                       HHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEE CS
                   Beta_elim_lyase  58 aAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlknkeaGkmdlekleaaikevgaheekiklislt 134
                                        A +i+l+ l+++g+ev++ +p+ +      a+ e+ g k + ++  ++ +++++++ + i++      k+k+++l 
  gi|298675658|ref|YP_003727408.1| 103 EALEIALASLVNPGDEVLIPNPGFV---SYSALTEIMGGKSVSIPLGKDLNVQPDDVLDNITP------KTKALVLN 170
                                       5667899999999999998888754...45567777777788888888889999999999999......46666666 PP

                                       SSBTTTTTB---HHHHHHHHHHHHHCT-EEEEE CS
                   Beta_elim_lyase 135 vTnntagGqvvsleelrevaaiakkygiplhlD 167
                                          n   G v s +++++ a+ia++++i+++ D
  gi|298675658|ref|YP_003727408.1| 171 SPSNP-TGAVQSRDNIKAFAEIAEDHDITIISD 202
                                       66663.6**********************9998 PP

>> DUF1246  Protein of unknown function (DUF1246)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00011      0.27      37      85 ..      87     136 ..      52     146 .. 0.81
   2 ?   -3.1   0.1       2.8   7.2e+03      33      51 ..     203     231 ..     201     236 .. 0.69
   3 ?   -1.1   0.0      0.67   1.7e+03      57      75 ..     327     345 ..     316     348 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                                       TTTT-.SEEEE.S.S..TTSS--HHHHHHTTCEE--BTTHHHHC-HHHHH CS
                           DUF1246  37 kfkvi.devivldkfkdilkeevqeklreenailvPhgsfveYvgiekie 85 
                                       +f v  de+iv +  ++ l+  +++ ++  + +l+P+  fv+Y ++ +i 
  gi|298675658|ref|YP_003727408.1|  87 NFDVSsDEIIVTSGASEALEIALASLVNPGDEVLIPNPGFVSYSALTEIM 136
                                       454444*************************************9998875 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.8
                                       HHHHTT..........TT-SEEEE.S.S. CS
                           DUF1246  33 klYekf..........kvidevivldkfk 51 
                                       ++Ye+f          +  d+vi+++ ++
  gi|298675658|ref|YP_003727408.1| 203 EVYEHFvyegehvspaQYTDNVITVNAVS 231
                                       67888877777777766778888777665 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.67
                                       --HHHHHHTTCEE--BTTH CS
                           DUF1246  57 evqeklreenailvPhgsf 75 
                                       +++ekl+++ +i+vP  +f
  gi|298675658|ref|YP_003727408.1| 327 KTTEKLVSNGVIVVPGIAF 345
                                       56799**********8766 PP

>> Zfx_Zfy_act  Zfx / Zfy transcription activation region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0       0.1   2.6e+02      91     111 ..      85     105 ..      48     114 .. 0.87
   2 ?   10.0   0.4   0.00013      0.33     235     311 ..     192     270 ..     178     275 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.1
                       Zfx_Zfy_act  91 alsedlvseevlVadaaseav 111
                                        ++ d+ s+e++V++ asea+
  gi|298675658|ref|YP_003727408.1|  85 ENNFDVSSDEIIVTSGASEAL 105
                                       56678999***********96 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00013
                       Zfx_Zfy_act 235 dedlnvaeiadevymevivgeeeaavl..keqqledsevnktfvpvawaaaygnnldrienkngtasalLqideslg 309
                                        ed +++ i+devy  ++   e+ + +   ++ ++ ++v+kt+    w + y     +  ++   a +++q + s  
  gi|298675658|ref|YP_003727408.1| 192 AEDHDITIISDEVYEHFVYEGEHVSPAqyTDNVITVNAVSKTYSMTGWRLGYVAAKGEYIEQMLKAHQYVQACASSI 268
                                       58899*********999998887766522566788999**************9988876677888999999887765 PP

                       Zfx_Zfy_act 310 ln 311
                                        +
  gi|298675658|ref|YP_003727408.1| 269 SQ 270
                                       55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2305.55
//
Query:       gi|298675659|ref|YP_003727409.1|  [L=328]
Description: nucleolar GTP-binding-1 domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.3e-51  172.7   0.5      8e-51  172.2   0.5    1.3  1  NOG1_N     NOG1 N-terminal helical domain
    3.1e-22   78.1   0.1    7.1e-22   77.0   0.1    1.6  1  NOG1       Nucleolar GTP-binding protein 1 (NOG1)
    2.5e-17   63.0   0.0    5.7e-17   61.8   0.0    1.6  1  MMR_HSR1   50S ribosome-binding GTPase
    4.9e-08   32.6   0.0    1.2e-07   31.3   0.0    1.6  1  FeoB_N     Ferrous iron transport protein B
  ------ inclusion threshold ------
      0.012   15.7   0.1       0.47   10.5   0.0    2.5  2  Dynamin_N  Dynamin family
      0.015   14.7   0.0       0.03   13.7   0.0    1.5  1  AIG1       AIG1 family
      0.099   11.5   0.0       0.15   10.9   0.0    1.3  1  ISN1       IMP-specific 5'-nucleotidase


Domain annotation for each model (and alignments):
>> NOG1_N  NOG1 N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.2   0.5   3.1e-54     8e-51       1     160 []       3     157 ..       3     157 .. 0.97

  Alignments for each domain:
  == domain 1  score: 172.2 bits;  conditional E-value: 3.1e-54
                            NOG1_N   1 FekiptvptseelidkalrrakraakttkkkkneikrlrnlearkvrtasntlsdkLeeivkkfPnldelhpFyrel 77 
                                       Feki +vpts+el+dka+rra+ra + ++ k+   k  r+++++++ t +n+lsd+L++iv++fP++del  Fy++l
  gi|298675659|ref|YP_003727409.1|   3 FEKIHSVPTSDELLDKAFRRASRARRGKVIKNM--KSNREAYESMILTSANILSDNLANIVRRFPDFDELSDFYYDL 77 
                                       9*****************************964..56688************************************* PP

                            NOG1_N  78 ldvlvdkdelkksLaqvkwarklirkigkeyvnklkkaddkkeakelrreafgrvasvlkkvdkaldfLedvrkkLr 154
                                       +dv+v++d+lkksL++v+wa+++i + g+e+++k++ +++++    +++e +gr++s++k++dk+l+fL+++r++Lr
  gi|298675659|ref|YP_003727409.1|  78 ADVIVGVDKLKKSLGSVNWASEKIHDMGREQIGKIRSSNNPQ---SIQKEVYGRMSSIMKSIDKDLKFLNEARNTLR 151
                                       ************************************999987...99****************************** PP

                            NOG1_N 155 kLpaiD 160
                                       kLp++D
  gi|298675659|ref|YP_003727409.1| 152 KLPDVD 157
                                       *****9 PP

>> NOG1  Nucleolar GTP-binding protein 1 (NOG1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.0   0.1   2.8e-25   7.1e-22       1      58 []     227     283 ..     227     283 .. 0.99

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 2.8e-25
                              NOG1   1 eIEkqAiaALkhladavlFllDpseecgysleeQlsLleeikelfankpvivvlnKiD 58 
                                       +IE+qAi+ALkhl ++ l+l+D+se+cgy++++Q +L+eeik++f+  p++ v nK+D
  gi|298675659|ref|YP_003727409.1| 227 DIELQAITALKHLGSVLLYLVDASETCGYTVDDQKRLYEEIKQQFD-LPMFAVSNKSD 283
                                       6*********************************************.9*********9 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.8   0.0   2.2e-20   5.7e-17       2     114 .]     163     281 ..     162     281 .. 0.78

  Alignments for each domain:
  == domain 1  score: 61.8 bits;  conditional E-value: 2.2e-20
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS..HHHHHHHHHHHHHHHHCT CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGlie..gaseekglgkaflaleea 76 
                                       ++++G+pN+GKS+++   t+++ +v+ +p+tT+ i  g+++ ++ +++++DtpGl++  +++++  + +a+ al+  
  gi|298675659|ref|YP_003727409.1| 163 IVVAGYPNTGKSSFVALATKARPEVAIYPFTTKGISIGHFTRDNIRYQVIDTPGLLDrpMSDRNDIELQAITALKHL 239
                                       89***************************************999**********99654333333566666666665 PP

                                       .SEEEEEEETTTT...CSHHHHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  77 .dlillvvdasee...klkpldeeleelleeakkplilvlnk 114
                                        +++l++vdase+   +++++++  ee++++ + p++ v nk
  gi|298675659|ref|YP_003727409.1| 240 gSVLLYLVDASETcgyTVDDQKRLYEEIKQQFDLPMFAVSNK 281
                                       59*******993343355666555666666677888888776 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.0   4.8e-11   1.2e-07       2      89 ..     162     250 ..     161     253 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 4.8e-11
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHH..C CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardfll..e 76 
                                       t++++G pn+Gk++++   t+a+ +v+ +p +t   + g+++ ++ +++++D PG  +  ++s  + +  + ++  +
  gi|298675659|ref|YP_003727409.1| 162 TIVVAGYPNTGKSSFVALATKARPEVAIYPFTTKGISIGHFTRDNIRYQVIDTPGLLD-RPMSDRNDIELQAITalK 237
                                       699***************************************9************976.456666666666554224 PP

                                       TSSSEEEEEEEGG CS
                            FeoB_N  77 eepdvvvnvvdat 89 
                                       +   v++ +vda+
  gi|298675659|ref|YP_003727409.1| 238 HLGSVLLYLVDAS 250
                                       4456666666665 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.045   1.1e+02       1      15 [.     163     177 ..     163     195 .. 0.92
   2 ?   10.5   0.0   0.00018      0.47     101     167 ..     207     281 ..     180     282 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.045
                                       EEEEEBTTTTHHHHH CS
                         Dynamin_N   1 iavvGsqSsGKSSvl 15 
                                       i+v G  + GKSS++
  gi|298675659|ref|YP_003727409.1| 163 IVVAGYPNTGKSSFV 177
                                       899**********97 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00018
                                       -SEEEEE---B-SSSGTTS.....HHHHHHHSTTEEEEEEEETTS-CCC-..CHHHHHHHHSTTBTT.EEEEEE- CS
                         Dynamin_N 101 kgltlvDlPGldsvnkrdq.....elvkeyikkadiilavtsanhdlsns..ealflarevdpkgkr.tivvltk 167
                                        ++ ++D+PGl +++  d      + ++ + +  +++l++++a+  +  +  ++++l +e++++ +  ++ v +k
  gi|298675659|ref|YP_003727409.1| 207 IRYQVIDTPGLLDRPMSDRndielQAITALKHLGSVLLYLVDASETCGYTvdDQKRLYEEIKQQFDLpMFAVSNK 281
                                       45689********9999998887555555558899********99764433499999999999988867777766 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.2e-05      0.03       3     112 ..     163     272 ..     161     279 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.2e-05
                                       EEEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEEEEEE--SCCCTTCC.HHCHHHHHHHHHH CS
                              AIG1   3 ivlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkkinViDTPglfdlsvs.adkiskeivrcll 78 
                                       iv+ G   +GkS+ +   l +ka    +     tk  +  + t+d+ + +ViDTPgl+d   s  ++i+   +    
  gi|298675659|ref|YP_003727409.1| 163 IVVAGYPNTGKSSFVA--LATKARPEVAIYPFTTKGISIGHFTRDNIRYQVIDTPGLLDRPMSdRNDIE--LQAITA 235
                                       6666666666666552..4444433333344455666666779999*************8765133333..333345 PP

                                       HCTT-ESEEEEE.EETT.B-SHHHHH.HHHHHHHHHC CS
                              AIG1  79 lseegihalllv.lslg.rfteedek.alktlkelFG 112
                                       l++ g   l lv  s +  +t +d+k + +++k+ F+
  gi|298675659|ref|YP_003727409.1| 236 LKHLGSVLLYLVdASETcGYTVDDQKrLYEEIKQQFD 272
                                       6666665555664333347888877624577888876 PP

>> ISN1  IMP-specific 5'-nucleotidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   5.9e-05      0.15     305     368 ..      34      97 ..      16     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.9e-05
                              ISN1 305 evklareqLeevvlvvqkklelseaareikfcafnGGsDvfvDiGdkslGvevlqkyfgkeeka 368
                                       ++k +re  e ++l+  ++l+ + a+   +f  f+  sD + D+ d  +Gv  l+k +g+ + a
  gi|298675659|ref|YP_003727409.1|  34 NMKSNREAYESMILTSANILSDNLANIVRRFPDFDELSDFYYDLADVIVGVDKLKKSLGSVNWA 97 
                                       67899***************9999988899************************9999886654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       861  (0.0480228); expected 358.6 (0.02)
Passed bias filter:                      731  (0.0407719); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 2072.93
//
Query:       gi|298675660|ref|YP_003727410.1|  [L=291]
Description: putative signal transduction protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-36  124.1   0.6    3.3e-36  122.8   0.3    1.8  2  HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor
    1.4e-22   79.9   2.1    6.2e-12   45.8   0.3    2.6  2  CBS           CBS domain
    2.7e-08   34.0   0.1    1.8e-07   31.4   0.1    2.2  2  Rrf2          Transcriptional regulator
    1.1e-05   25.3   0.1    2.3e-05   24.3   0.1    1.6  1  HTH_11        HTH domain
  ------ inclusion threshold ------
      0.033   14.1   0.0      0.089   12.7   0.0    1.8  1  TrmB          Sugar-specific transcriptional regulator TrmB
       0.15   12.0   0.0        0.4   10.6   0.0    1.7  1  MarR_2        MarR family
       0.22   11.2   0.1        1.7    8.4   0.0    2.5  3  Sigma70_r4_2  Sigma-70, region 4


Domain annotation for each model (and alignments):
>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.8   0.3   1.3e-39   3.3e-36       1      77 [.       2      78 ..       2      80 .. 0.97
   2 ?   -2.7   0.0       1.9   4.9e+03      12      28 ..      83      98 ..      82     110 .. 0.65

  Alignments for each domain:
  == domain 1  score: 122.8 bits;  conditional E-value: 1.3e-39
                      HrcA_DNA-bdg  1 eLtsvqkeilqaLielyrkkkravKgeeiAevlkrneGtvRNqlqsLkalgLvegvpGPkGGYkPtlkayealkiqt 77
                                      eLt++qk+i+ aLi+l+r+k++a+Kge+iAev++rn+GtvRNq+qsLk+lgLvegvpGPkGGYk t kayeal+i +
  gi|298675660|ref|YP_003727410.1|  2 ELTPIQKDIIIALINLQRQKNHAIKGEDIAEVIQRNPGTVRNQMQSLKVLGLVEGVPGPKGGYKATGKAYEALNIPS 78
                                      69************************************************************************976 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.9
                      HrcA_DNA-bdg 12 aLielyrkkkravKgee 28
                                      a++++yr++k  v g  
  gi|298675660|ref|YP_003727410.1| 83 AIVKIYRNNK-LVEGST 98
                                      6778887654.455544 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.1   1.9e-11   4.8e-08       1      51 [.     173     222 ..     173     228 .. 0.89
   2 !   45.8   0.3   2.4e-15   6.2e-12       1      56 [.     235     289 ..     235     290 .. 0.95

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.9e-11
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDl 51 
                                       V+ + t+d v+v+ ++tl ea+++++++++++ PV d++  +vG+vt +D+
  gi|298675660|ref|YP_003727410.1| 173 VKNYVTKDSVMVNVNATLQEAARIFVKNNIHGSPVEDKSS-IVGVVTFTDI 222
                                       677889*******************9*********87666.*********9 PP

  == domain 2  score: 45.8 bits;  conditional E-value: 2.4e-15
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       V+dimt++++tv+ dt+l ea++++ ++++++l VV  +g + G v+++D+l  l+
  gi|298675660|ref|YP_003727410.1| 235 VRDIMTKELITVDGDTPLNEAVKIFNKHNIGGL-VVTINGVPEGFVSKTDVLHELA 289
                                       89***********************9999****.8889**************9885 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.1   7.2e-11   1.8e-07      11      67 ..      11      66 ..       1      73 [. 0.89
   2 ?   -0.4   0.0      0.57   1.5e+03      26      64 ..     239     277 ..     230     280 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 7.2e-11
                                      HHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEEE CS
                              Rrf2 11 lhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyrL 67
                                      + al+ L++++++  ++ e+iae  + +p  ++  ++ L+  glv+ v G++GGy+ 
  gi|298675660|ref|YP_003727410.1| 11 IIALINLQRQKNHA-IKGEDIAEVIQRNPGTVRNQMQSLKVLGLVEGVPGPKGGYKA 66
                                      67999999999987.****************************************85 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.57
                                       B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TC CS
                              Rrf2  26 vsseeiaerqnispsylekilakLrkaglvksvrGkgGG 64 
                                       ++ e i    +++ + + ki++k +  glv ++ G+  G
  gi|298675660|ref|YP_003727410.1| 239 MTKELITVDGDTPLNEAVKIFNKHNIGGLVVTINGVPEG 277
                                       555566667788899999999999999999999998666 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.1   8.9e-09   2.3e-05       6      55 .]      14      65 ..       7      65 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 8.9e-09
                            HTH_11  6 lelLleargp.isgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepgr..GYr 55
                                      l+ L +++++ i ge++Ae + +   tvr+ +++L+ lg  +e++pg+  GY+
  gi|298675660|ref|YP_003727410.1| 14 LINLQRQKNHaIKGEDIAEVIQRNPGTVRNQMQSLKVLG-LVEGVPGPkgGYK 65
                                      34488899999****************************.*********9996 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.5e-05     0.089      21      64 ..      23      66 ..       3      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.5e-05
                                      CCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE CS
                              TrmB 21 gpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYra 64
                                         + ++iae + +   +v + ++sL+  GlVe ++g +  Y+a
  gi|298675660|ref|YP_003727410.1| 23 HAIKGEDIAEVIQRNPGTVRNQMQSLKVLGLVEGVPGPKGGYKA 66
                                      566789******************************99777776 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00016       0.4       4      58 ..       4      61 ..       2      63 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00016
                                      -HHHHHHHHHHHCTTTS...EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSS CS
                            MarR_2  4 tpaqarvLaaLgrrpgr...dltvgelarrlglsksavsrilkrLvaaGLverrpgpe 58
                                      tp q +++ aL +  ++    +   ++a+  +  +++v +  + L   GLve +pgp 
  gi|298675660|ref|YP_003727410.1|  4 TPIQKDIIIALINLQRQknhAIKGEDIAEVIQRNPGTVRNQMQSLKVLGLVEGVPGPK 61
                                      5555555555555554455588999*****************************9985 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0         1   2.6e+03      10      20 ..       2      12 ..       1      13 [. 0.88
   2 ?    8.4   0.0   0.00066       1.7      30      48 ..      28      46 ..      25      47 .. 0.92
   3 ?   -2.7   0.0         2   5.1e+03      24      33 ..      94     103 ..      93     103 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1
                                      TS-HHHHHHHH CS
                      Sigma70_r4_2 10 eLperqreifl 20
                                      eL+++q+ i++
  gi|298675660|ref|YP_003727410.1|  2 ELTPIQKDIII 12
                                      79******986 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00066
                                      HHHHHHHT--HHHHHHHHH CS
                      Sigma70_r4_2 30 kEIAellgisegtVksrls 48
                                      ++IAe++  ++gtV+++++
  gi|298675660|ref|YP_003727410.1| 28 EDIAEVIQRNPGTVRNQMQ 46
                                      79**************986 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 2
                                       TS---HHHHH CS
                      Sigma70_r4_2  24 leglsykEIA 33 
                                       +eg++ +EI+
  gi|298675660|ref|YP_003727410.1|  94 VEGSTAAEIS 103
                                       79******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1870.50
//
Query:       gi|298675661|ref|YP_003727411.1|  [L=101]
Description: phosphoribosyl-ATP diphosphatase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-16   59.6   0.2    3.5e-16   59.4   0.2    1.0  1  PRA-PH    Phosphoribosyl-ATP pyrophosphohydrolase
     0.0013   18.9   1.1     0.0013   18.9   1.1    1.6  2  MazG      MazG nucleotide pyrophosphohydrolase domain
  ------ inclusion threshold ------
       0.12   12.8   0.4       0.21   12.0   0.2    1.5  2  MKRN1_C   E3 ubiquitin-protein ligase makorin-1, C-terminal


Domain annotation for each model (and alignments):
>> PRA-PH  Phosphoribosyl-ATP pyrophosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.4   0.2   5.9e-20   3.5e-16       2      82 ..      12      99 ..      11     100 .. 0.96

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 5.9e-20
                                      HHHHHHCT----SS----.-HHHHHH......HHHHHHHHHHHHHHHT-SCHHHHHHHHHHHHHHHHHHHHHHCT--CH CS
                            PRA-PH  2 kefhrligerkpetPeas.taelasl......raaligEEavElleaasegdlaeladelaDllYvtygllvllGidld 73
                                      +e +++i++rk +  e+s   +l+++      ++++igEE+vE++ a+++++++++++e  Dl+++++++l++++i+l 
  gi|298675661|ref|YP_003727411.1| 12 NEIYDVIQDRKHNPVEKSyVCSLLNHnkgidkILEKIGEESVETVLAVKNKNREDIVYESSDLIFHLLVMLAANDIQLS 90
                                      78999********999999************************************************************ PP

                                      HHHHHHHHH CS
                            PRA-PH 74 avfeevhra 82
                                      ++ +e++++
  gi|298675661|ref|YP_003727411.1| 91 EIADELEKR 99
                                      ******998 PP

>> MazG  MazG nucleotide pyrophosphohydrolase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.78   4.7e+03      16      25 ..      13      22 ..       9      28 .. 0.58
   2 !   18.9   1.1   2.1e-07    0.0013       4      62 ..      42      96 ..      39     100 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.78
                                      HHHHHHHTT- CS
                              MazG 16 EvaeaIkked 25
                                      E+ ++I+  +
  gi|298675661|ref|YP_003727411.1| 13 EIYDVIQDRK 22
                                      5566665544 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 2.1e-07
                                      HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHH CS
                              MazG  4 etllaylleEvgEvaeaIkkedrdeleeELGDvLlqvlflaniaeeeggidledvaeti 62
                                      + +l+ + eE  E + a+k+++r+++  E  D+++++l +        +i+l+++a+++
  gi|298675661|ref|YP_003727411.1| 42 DKILEKIGEESVETVLAVKNKNREDIVYESSDLIFHLLVMLAA----NDIQLSEIADEL 96
                                      5688999******************************999996....999999999764 PP

>> MKRN1_C  E3 ubiquitin-protein ligase makorin-1, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.95   5.7e+03      18      28 ..      12      22 ..       3      29 .. 0.69
   2 ?   12.0   0.2   3.4e-05      0.21      28      65 ..      54      91 ..      33      98 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.95
                           MKRN1_C 18 thlweileere 28
                                      +++++++++r+
  gi|298675661|ref|YP_003727411.1| 12 NEIYDVIQDRK 22
                                      56777777765 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 3.4e-05
                           MKRN1_C 28 esespfdnddeelvtfeLselLlmllaagaddEltdse 65
                                      e   +++n++ e +++e s+l++ ll+ +a +++ +se
  gi|298675661|ref|YP_003727411.1| 54 ETVLAVKNKNREDIVYESSDLIFHLLVMLAANDIQLSE 91
                                      4556789******************9999999999888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.37s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 583.32
//
Query:       gi|298675662|ref|YP_003727412.1|  [L=427]
Description: homoaconitate hydratase family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.6e-98  328.2   0.5    8.4e-96  321.7   0.5    2.0  1  Aconitase  Aconitase family (aconitate hydratase)
     0.0059   15.4   0.0     0.0096   14.7   0.0    1.2  1  DUF521     Protein of unknown function (DUF521)


Domain annotation for each model (and alignments):
>> Aconitase  Aconitase family (aconitate hydratase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  321.7   0.5  9.4e-100   8.4e-96      12     461 .]      25     419 ..      12     419 .. 0.88

  Alignments for each domain:
  == domain 1  score: 321.7 bits;  conditional E-value: 9.4e-100
                         Aconitase  12 egiayv...pdrvllqdvtgvqalvdlaaareavrrlggtlatidhlvpvdlvidhsvgaeealeknledefernke 85 
                                        g ++v    dr +++d+tg+ a++++ +  e++    +++++ d++  v    dh+v          +d+++  + 
  gi|298675662|ref|YP_003727412.1|  25 AG-DFVfadIDRAMTHDITGPLAVKGFYEIMENK----ENPKVWDPNKIVI-IFDHQV---------PADSLNA-AS 85 
                                       33.3334478*****************7666555....5778888887776.788888.........2222222.23 PP

                         Aconitase  86 ryefLksaakafgirvvppgqGIvHqvnlEyglalpgktvvgtDSHTtmigglGvlaiGvGgieaeavllgqplelk 162
                                       +  +L+++ak+  i  +++ +GI+Hqv++E+g + pg +vvg+DSHT+ +g++G++ +GvG+++++av++  +l++k
  gi|298675662|ref|YP_003727412.1|  86 NHIMLREFAKEQAILNYDVYEGICHQVMPEKGHIKPGDLVVGSDSHTCAYGAIGAFSTGVGSTDMAAVFASGKLWFK 162
                                       44679999******9************************************************************** PP

                         Aconitase 163 ipkvvgvkltGklkegvtakDlvlavigklrkkgvvgkvvEffGegvesLsledraTiaNMaaEvGAttglfpvdek 239
                                       +p++++++++G+l++ v +kD++l+vig ++++ ++ k  Ef G++v+++s+ +r+T++NMa+E+G ++g+++ d+ 
  gi|298675662|ref|YP_003727412.1| 163 VPETIRFEIDGELPDNVYSKDVILHVIGDVGADCAMYKTAEFGGSAVRNMSVSERMTMSNMAIEMGGKAGIIESDKV 239
                                       ***************************************************************************** PP

                         Aconitase 240 tleYLkatgreeaavlveaydkaqalfelaadedaeydkvleldlstlepsvagpkrPqdavplselvkkefkeele 316
                                       t +Y+k  +r  ++     y+  ++ +  ++d++a+y+++ + d+s+lep+va p++++++ p+ ++v         
  gi|298675662|ref|YP_003727412.1| 240 TEDYIK--ER--VP----GYK-LDSEW--KSDDGANYSEIRKYDVSNLEPQVACPHNVDNVKPV-TEV--------- 295
                                       ******..66..44....333.34446..7999***************************9999.323......... PP

                         Aconitase 317 keaaekaleyklkegtklkdgkvdiaaigSCTNssnedvraaagllakavekglkvkpgvktsvaPGSevvkaylea 393
                                                         + +++d+++igSCTN+++ed+++aa++++     g+kv+++v++++ P+S+    +l +
  gi|298675662|ref|YP_003727412.1| 296 ------------------EGTELDQVFIGSCTNGRYEDLEIAAKIMD-----GKKVADNVRLLIIPASRTEYMKLLK 349
                                       ..................344588***********************.....************************* PP

                         Aconitase 394 eGlleiLekaGfevvgagCstCig.nsdrleegeaivsssNRNFegRqg.pntrayLaSPelvvaaAlaG 461
                                       +G+ e++++aG+ v ++ C++C+g   + l +ge+++ +sNRNF+gR+g p++  yL SP+ ++a+Al+G
  gi|298675662|ref|YP_003727412.1| 350 AGYIEQFMEAGAIVESPCCGPCMGgSFGLLGDGEVGLATSNRNFKGREGsPESFVYLSSPATAAASALTG 419
                                       ************************8889999*****************8577777*************98 PP

>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.1e-06    0.0096     287     357 ..     296     368 ..     282     377 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.1e-06
                            DUF521 287 keekvdlvalG.cPhlsleElrelaellkgkkkkvkvelwvt.tsrevkeeaerlglveklekaGvkvlsdtC 357
                                       + +++d v++G c    +e+l+  a++++gkk++++v+l+++ +sr+ + ++ ++g++e+  +aG+ v s +C
  gi|298675662|ref|YP_003727412.1| 296 EGTELDQVFIGsCTNGRYEDLEIAAKIMDGKKVADNVRLLIIpASRTEYMKLLKAGYIEQFMEAGAIVESPCC 368
                                       567788899985677789999999*************9876538899999***************96655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 2522.25
//
Query:       gi|298675663|ref|YP_003727413.1|  [L=499]
Description: TrkA-N domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-26   92.6   0.7    5.3e-26   91.2   0.3    2.0  1  TrkA_N           TrkA-N domain
    3.4e-16   59.3   1.1    7.3e-15   55.1   0.9    2.4  2  DHH              DHH family
    1.1e-12   48.5   1.7    2.6e-12   47.3   0.1    2.4  3  DHHA1            DHHA1 domain
    0.00013   22.2   0.0    0.00031   21.0   0.0    1.7  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    0.00044   19.8   0.0      0.001   18.6   0.0    1.7  2  Epimerase        NAD dependent epimerase/dehydratase family
    0.00055   20.5   0.0     0.0017   18.9   0.0    2.0  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
     0.0012   18.5   0.0     0.0025   17.5   0.0    1.5  1  ApbA             Ketopantoate reductase PanE/ApbA
     0.0068   16.0   0.0      0.015   14.9   0.0    1.5  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
     0.0078   16.7   0.0      0.061   13.8   0.0    2.3  3  XdhC_C           XdhC Rossmann domain
  ------ inclusion threshold ------
      0.011   16.3   0.0          1    9.9   0.0    3.2  3  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
      0.014   14.7   0.0      0.027   13.8   0.0    1.5  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
      0.016   15.6   0.0      0.047   14.1   0.0    1.7  1  NAD_binding_7    Putative NAD(P)-binding
      0.018   15.1   0.0       0.14   12.1   0.0    2.1  2  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
      0.022   14.1   0.0      0.059   12.7   0.0    1.7  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
      0.032   14.3   0.0      0.096   12.8   0.0    1.8  1  TyeA             TyeA
       0.06   12.8   0.0       0.11   11.9   0.0    1.5  1  adh_short        short chain dehydrogenase
      0.062   13.5   0.0       0.12   12.6   0.0    1.5  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
      0.068   12.7   0.0       0.14   11.7   0.0    1.6  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase


Domain annotation for each model (and alignments):
>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.2   0.3   5.3e-29   5.3e-26       1     116 []      30     146 ..      30     146 .. 0.95

  Alignments for each domain:
  == domain 1  score: 91.2 bits;  conditional E-value: 5.3e-29
                                       EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddean 76 
                                       ++++G G +G ++a+eL+e ++ d v+idkd++++e+lree++e+++gd +++e+L ++++ +  av+++ +d+e+n
  gi|298675663|ref|YP_003727413.1|  30 YLVLGSGSIGFAVAKELRElDK-DLVIIDKDPAKIETLREEEYEAIQGDISNPETLNQINVRNLTAVLVLSSDNESN 105
                                       68*****************777.8***************************************************** PP

                                       HHHHHHH.HHHTSSSEEEEEESSGGGHHHHHHHTTSEEEEH CS
                            TrkA_N  77 ilavlla.kelnpkkkiiaraqdpehaellkklgadvvisp 116
                                         a++++ k   p+ +++ara+d  +++ +++ gad+vi p
  gi|298675663|ref|YP_003727413.1| 106 KSAIENIkKLVSPDVYCVARASDVINKKEMESKGADYVIIP 146
                                       *******4555667*************************87 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.25   2.5e+02      26      60 ..      33      65 ..      22     106 .. 0.76
   2 !   55.1   0.9   7.3e-18   7.3e-15       4     101 .]     184     325 ..     181     325 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.25
                                      CS--TCGGCGCCHHCCCSEEEEEEE-S---SS--- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH 26 vDhneksqavegeakeeaedviiiDHHrlgeefet 60
                                      +  ++   av++e++e ++d++iiD    +  +et
  gi|298675663|ref|YP_003727413.1| 33 LGSGSIGFAVAKELRELDKDLVIIDKDPAK--IET 65
                                      55666677889999***********87764..444 PP

  == domain 2  score: 55.1 bits;  conditional E-value: 7.3e-18
                                       EE-ECSSSHHHHHHHHHHHHC...............................................ECS--TCGG CS
                                       xxxxxxxxxxxxxxxxxxxxx...............................................xxxxxxxxx RF
                               DHH   4 ivghknpDtDsigSaialanl...............................................lvDhneksq 33 
                                       +v h npD D+i+Sa+al+++                                               lvD+  +  
  gi|298675663|ref|YP_003727413.1| 184 VVVHDNPDPDAIASAMALKEIaktygiestifyhgeighqenkafvnlldidlnrmeetdisdfqniaLVDCAVPGS 260
                                       667*****************666666666667777777777777777777777777777777777777****99999 PP

                                       CGCCHHCCCSEEEEEEE-S---SS---SS--EEEE-SSS-HHHHHHHHHHHTT----HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH  34 avegeakeeaedviiiDHHrlgeefetlapilflnepvgstaeivaelleekkeeiskeiaellllgi 101
                                             ++++   i++DHH ++ ++e  a+++ +++++g+ta+i++++l+e +++i++++a++ll gi
  gi|298675663|ref|YP_003727413.1| 261 NNML--DRDTHVGIVLDHHPVE-DAEIDADYIDIRPNIGATATILTKYLQELNIDITSNLATALLYGI 325
                                       9876..9999999********8.999999*************************************98 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       4.3   4.3e+03      19      65 ..      67     114 ..      46     133 .. 0.55
   2 ?   -2.0   0.0       4.3   4.3e+03      26      59 ..     166     198 ..     154     214 .. 0.64
   3 !   47.3   0.1   2.6e-15   2.6e-12      26     124 ..     368     470 ..     351     484 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 4.3
                                       HHHHHHHHHHHHHHTCEEEC..TCEEEEEECHCCHHHHHHHHHHHHHHT CS
                             DHHA1  19 kealaklkaeellekaeevk..gvkvlvaevgeewdagalgiaadklks 65 
                                       +e++ ++ ++++ + ++ ++  +v  l+a +    d+   ++a++++k+
  gi|298675663|ref|YP_003727413.1|  67 REEEYEAIQGDISNPET-LNqiNVRNLTAVLVLSSDNESNKSAIENIKK 114
                                       44444444444444422.2234333333333344444444444444444 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.3
                                       HHHHHHHTCEEECTCEEEEEECHCCHHHHHHHHH CS
                             DHHA1  26 kaeellekaeevkgvkvlvaevgeewdagalgia 59 
                                          +l   ++++ ++k+ v+   ++ d++a+++a
  gi|298675663|ref|YP_003727413.1| 166 RGTKLTRWLKDIADKKLGVVVH-DNPDPDAIASA 198
                                       4444444455554555555555.88888888776 PP

  == domain 3  score: 47.3 bits;  conditional E-value: 2.6e-15
                                       HHHHHHHTCEEEC.TCEEEEEECHCCHHHHHHHHHHHHHHTHGBT.TCEEEEEEEECTEEEEEEEESSH.SS-HHHH CS
                             DHHA1  26 kaeellekaeevk.gvkvlvaevgeewdagalgiaadklksklkk.pvivfvakeegdkvkvsarskkd.gvdagel 99 
                                       + e + e +++ +   ++l+++vg+  d+++l +aad+l++   +  +  +v++  +dk+++s+rs+ d ++++g++
  gi|298675663|ref|YP_003727413.1| 368 TLEVFGEAIKNRQvFGSYLLSNVGTVRDRDTLPQAADYLLN--LEgISTSIVFGVSKDKIYLSGRSN-DiKINLGDV 441
                                       4444444444444678999999*9*****************..444444444444444*********.55******* PP

                                       HHHHHHHTTCCEEEETCEEEEEEE......H CS
                             DHHA1 100 akeaaaklgggGGGHdlAaGagip......a 124
                                       +k+  a    + GGH+ Aa+a++p      a
  gi|298675663|ref|YP_003727413.1| 442 MKR--AFGEQSAGGHATAAAAQVPlgvfsaA 470
                                       ***..33335559**********95555542 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   3.1e-07   0.00031       2      82 ..      31     104 ..      30     116 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.1e-07
                                       EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHH.HTTSSEEEE-S CS
                   Sacchrp_dh_NADP   2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaal.lkegdlvvnls 77 
                                       l++G+Gs+G ava++l + ++   +++++d++ +k e l    ++++ eai+ d++n+e  L ++ ++  ++v+ ls
  gi|298675663|ref|YP_003727413.1|  31 LVLGSGSIGFAVAKELRELDK---DLVIIDKDPAKIETL----REEEYEAIQGDISNPET-LNQInVRNLTAVLVLS 99 
                                       89**************98765...6**********6666....8899************9.9998788888888888 PP

                                       SGGGH CS
                   Sacchrp_dh_NADP  78 ppiss 82 
                                        + +s
  gi|298675663|ref|YP_003727413.1| 100 SDNES 104
                                       77754 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0     1e-06     0.001       3      83 ..      32     107 ..      30     171 .. 0.85
   2 ?   -3.3   0.0       4.9   4.9e+03     100     122 ..     304     326 ..     280     351 .. 0.60

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1e-06
                                       EETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHH CS
                         Epimerase   3 VtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggvaa 79 
                                       V+G +G iG a++k+l e + +++ +d+++ + +t r+e+ e +++d+ +++ l+++  + + +av+ l   ++ ++
  gi|298675663|ref|YP_003727413.1|  32 VLG-SGSIGFAVAKELRELDKDLVIIDKDPAKIETLREEEYEAIQGDISNPETLNQINVR-NLTAVLVL---SSDNE 103
                                       555.5**************************************************98765.78888888...33333 PP

                                       HHHS CS
                         Epimerase  80 ssed 83 
                                       s+++
  gi|298675663|ref|YP_003727413.1| 104 SNKS 107
                                       3333 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.9
                                       HHHHHHTCTEEEEEEEGGGGTSC CS
                         Epimerase 100 eaarkagvkrllflsSsevYGkd 122
                                       +++++ +++   +l ++ +YG  
  gi|298675663|ref|YP_003727413.1| 304 KYLQELNIDITSNLATALLYGIR 326
                                       34444455555555555555544 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.7e-06    0.0017       4      79 ..      32     110 ..      29     130 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.7e-06
                                       EETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.......-EEECECHHHHHHH-SEEEE-S-HHH CS
                     F420_oxidored   4 iiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.......vkvtavdneeaaeeadvvvlavkped 73 
                                       ++G+G++g+a+a+ l + +   +++v++ +++p k+e l+ee +        + ++ ++  + + + v+vl+   e 
  gi|298675663|ref|YP_003727413.1|  32 VLGSGSIGFAVAKELRELD---KDLVII-DKDPAKIETLREEEYeaiqgdiSNPETLNQINVRNLTAVLVLSSDNES 104
                                       79*****************...****89.**********96654366666544555444444445556666655555 PP

                                       HHHHHH CS
                     F420_oxidored  74 veevls 79 
                                        +++++
  gi|298675663|ref|YP_003727413.1| 105 NKSAIE 110
                                       555555 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.5e-06    0.0025       2      95 ..      31     119 ..      30     126 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.5e-06
                                       EEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETTCEEEEEECEEECCHSCCCCS-ESEEEE-SS CS
                              ApbA   2 ailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseggeeilrppealsaeekselepidlvivtvK 77 
                                       ++lG+G+iG  +a +L +   d ++i++++ ++e+l+++ ++  + +    +++pe+l++          +++++  
  gi|298675663|ref|YP_003727413.1|  31 LVLGSGSIGFAVAKELRELDKDLVIIDKDPaKIETLREEEYEAIQGD----ISNPETLNQI--NVRNLTAVLVLSSD 101
                                       79***************************************999988....6666666666..33444566667777 PP

                                       GGGHHHHHHHHGGGECTC CS
                              ApbA  78 ayqteealeeikplldpn 95 
                                       + ++++a+e+ik+l+ p+
  gi|298675663|ref|YP_003727413.1| 102 NESNKSAIENIKKLVSPD 119
                                       788888888888888876 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.5e-05     0.015       5      48 ..      32      75 ..      29     104 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.5e-05
                                      EE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS-- CS
                    UDPG_MGDP_dh_N  5 viGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiye 48
                                      v+G+G +G   a  l e+ ++++++D+d +k+++l++++ + ++
  gi|298675663|ref|YP_003727413.1| 32 VLGSGSIGFAVAKELRELDKDLVIIDKDPAKIETLREEEYEAIQ 75
                                      89**********************************99877655 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   6.1e-05     0.061       2      65 ..      31     113 ..      30     140 .. 0.79
   2 ?   -0.7   0.0       1.9   1.9e+03      45      78 ..     181     223 ..     132     249 .. 0.62
   3 ?   -1.5   0.0       3.5   3.5e+03      10      45 ..     198     269 ..     193     289 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.1e-05
                                       EEE--STTHHHHHHHHHHHTEEEEEEES-GGGG......-GGG-TT-SE.....................-EEEE-- CS
                            XdhC_C   2 vifGaghvaqalarlaaalgfrvtvvdpreefa......tkerfpeade.....................tavvvlt 51 
                                       +++G g ++ a+a+ +++l+ +++++d++++        +                              tav+vl+
  gi|298675663|ref|YP_003727413.1|  31 LVLGSGSIGFAVAKELRELDKDLVIIDKDPAKIetlreeE--------YeaiqgdisnpetlnqinvrnlTAVLVLS 99 
                                       699***************************5332443330........234556777777788888899******** PP

                                       S-HHHHHHHHHHHS CS
                            XdhC_C  52 hdhklDaealeaal 65 
                                        d +  + a+e++ 
  gi|298675663|ref|YP_003727413.1| 100 SDNESNKSAIENIK 113
                                       *****999999886 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.9
                                       -EEEE--S-HHHHHHHHHHHSSS-.........-SEEEESS-H CS
                            XdhC_C  45 tavvvlthdhklDaealeaalrkk.........aayigllGSr 78 
                                       +  vv++ +++ Da a + al++          ++y g +G +
  gi|298675663|ref|YP_003727413.1| 181 KLGVVVHDNPDPDAIASAMALKEIaktygiestIFYHGEIGHQ 223
                                       5666777777777777666664222223332222355555555 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 3.5
                                       HHHHHHHHHHHTEEEEEEES-G.GGG-GGG-TT-SE...................................- CS
                            XdhC_C  10 aqalarlaaalgfrvtvvdpre.efatkerfpeade...................................t 45 
                                       a al ++a++ g++ t++ + e  +++++ f +  +                                   +
  gi|298675663|ref|YP_003727413.1| 198 AMALKEIAKTYGIESTIFYHGEiGHQENKAFVNLLDidlnrmeetdisdfqnialvdcavpgsnnmldrdtH 269
                                       566777777777777777666654443333332211233333333334444444444444455555555533 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0     0.001         1       3      31 ..      31      59 ..      29      77 .. 0.90
   2 ?   -1.3   0.0       3.3   3.3e+03      39      66 ..     167     195 ..     157     204 .. 0.73
   3 ?    2.1   0.0      0.29   2.9e+02      41      60 ..     297     316 ..     286     322 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.001
                                      EEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                         Pyr_redox  3 vvvGgGyiglElAgalaelgkkVtvvers 31
                                      +v+G+G ig  +A++l+el k+  +++  
  gi|298675663|ref|YP_003727413.1| 31 LVLGSGSIGFAVAKELRELDKDLVIIDKD 59
                                      79********************9999865 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.3
                                       SHHHHHHHHHHHHHT.TEEEECSEEEEEE CS
                         Pyr_redox  39 Deeaskilqeklekn.gievllntkveei 66 
                                       + ++ ++l++   k+ g+ v+ n  + +i
  gi|298675663|ref|YP_003727413.1| 167 GTKLTRWLKDIADKKlGVVVHDNPDPDAI 195
                                       56678889999966669999999777766 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.29
                                       HHHHHHHHHHHHTTEEEECS CS
                         Pyr_redox  41 easkilqeklekngievlln 60 
                                       ++++il+++l++++i++  n
  gi|298675663|ref|YP_003727413.1| 297 ATATILTKYLQELNIDITSN 316
                                       5699***********99766 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.7e-05     0.027      29      87 ..      28      86 ..       2     144 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.7e-05
                                      -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHH CS
                       AlaDh_PNT_C 29 akvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellae 87
                                       + lv+G G  G + ++  ++l+ + +++D++pa++e l++ + + ++   s+ e+l++
  gi|298675663|ref|YP_003727413.1| 28 PTYLVLGSGSIGFAVAKELRELDKDLVIIDKDPAKIETLREEEYEAIQGDISNPETLNQ 86
                                      4689***********************************99777767775555555443 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.7e-05     0.047       9      84 ..      29     114 ..      27     128 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.7e-05
                     NAD_binding_7   9 kvlvvGgGevAarkvrklleagakvtvvapevkeele....elvklaeeelekd...........legadlviaatd 70 
                                       + lv G G+++   ++ l e ++++++++++  +++e    e ++++    ++d           + +   v++  +
  gi|298675663|ref|YP_003727413.1|  29 TYLVLGSGSIGFAVAKELRELDKDLVIIDKDP-AKIEtlreEEYEAI----QGDisnpetlnqinVRNLTAVLVLSS 100
                                       579****************************4.33342222333333....33433334555555667889999999 PP

                     NAD_binding_7  71 drelneriaeaaka 84 
                                       d+e n+   e++k+
  gi|298675663|ref|YP_003727413.1| 101 DNESNKSAIENIKK 114
                                       99999998888774 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00014      0.14       4      42 ..      32      70 ..      30     100 .. 0.73
   2 ?   -0.7   0.0       1.2   1.2e+03      35      71 ..     127     162 ..     114     165 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                                      EE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHS CS
                    NAD_Gly3P_dh_N  4 vlGaGswGtalAkvlaenghevrlwvreeelieeineeh 42
                                      vlG+Gs G a+Ak l e  ++ +++ ++++ ie+++ee+
  gi|298675663|ref|YP_003727413.1| 32 VLGSGSIGFAVAKELRELDKDLVIIDKDPAKIETLREEE 70
                                      9***************************96666665543 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.2
                                       HHHHHHHSSBTTTBTT----TTEEEES-HHHHHTT-- CS
                    NAD_Gly3P_dh_N  35 ieeineehenvkyLpgiklpenlvattdlaealkgad 71 
                                        ++in+++ ++k  + + +p+ +vat+ la++l++a+
  gi|298675663|ref|YP_003727413.1| 127 SDVINKKEMESKGADYVIIPSRVVATS-LARTLERAE 162
                                       688999999999999999999999875.667776665 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.9e-05     0.059      28      80 ..      19      71 ..       3     116 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.9e-05
                                      CGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTC CS
                      2-Hacid_dh_C 28 allgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgv 80
                                       l+ k+  + t  ++G G+IG avak l++++ +++++d+ + k e+ +e+++
  gi|298675663|ref|YP_003727413.1| 19 YLPAKSKIKPTYLVLGSGSIGFAVAKELRELDKDLVIIDKDPAKIETLREEEY 71
                                      5555555667899****************************998884444443 PP

>> TyeA  TyeA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   9.6e-05     0.096      47      74 ..     459     486 ..     454     490 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.6e-05
                                       GGGS-GGGSS-HHHHHHHHHHHHHHHHH CS
                              TyeA  47 lrelPlkvFadeeqRqklLaaaqeAlDq 74 
                                        +++Pl+vF+  ++Rq+lL  ++eA+ +
  gi|298675663|ref|YP_003727413.1| 459 AAQVPLGVFSAAKDRQTLLRLVNEAVVK 486
                                       6789*********************855 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00011      0.11       7      66 ..      34      86 ..      29     122 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                      STTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHH CS
                         adh_short  7 GassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevea 66
                                      G s+ IG a+akel + + ++v++d+ ++k+e++ +e      ++ aiq+D+++ e +++
  gi|298675663|ref|YP_003727413.1| 34 G-SGSIGFAVAKELRELDKDLVIIDKDPAKIETLREE------EYEAIQGDISNPETLNQ 86
                                      4.568************************99666665......47899999999888776 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00012      0.12       4      90 ..      32     126 ..      29     144 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                                       EE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT.......EEE-SSHHHHHHHC.....SEEEE-SSSHHH CS
                     NAD_binding_2   4 fiGlGvMGsnmalnllkagykvavynrtkekveelvaeg.......akaaesieelvasl.....dvvitmvkagka 68 
                                       ++G G +G   a++l + + ++++++ +++k+e+l +e+       +    s  e ++++      +v+++ ++++ 
  gi|298675663|ref|YP_003727413.1|  32 VLGSGSIGFAVAKELRELDKDLVIIDKDPAKIETLREEEyeaiqgdI----SNPETLNQInvrnlTAVLVLSSDNES 104
                                       789***********************************988855553....33333333344433999999999999 PP

                                       HHHHHHSHCCC--TT-EEEE-S CS
                     NAD_binding_2  69 vdeviegllealkkgdilidgs 90 
                                        ++ ie++++ ++++ +++  +
  gi|298675663|ref|YP_003727413.1| 105 NKSAIENIKKLVSPDVYCVARA 126
                                       9999*99999999988877654 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00014      0.14       5      59 ..      37      87 ..      33     136 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
                                      SHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEEEE--TTSHHHHHHH CS
                      adh_short_C2  5 gIGraiAkalaeeGaevvltdlneeakkrveelaeelgaevlecDVtdeeqveal 59
                                      +IG+a+Ak+l e   ++v+ d + ++   +e+l ee + e+++ D++++e+++++
  gi|298675663|ref|YP_003727413.1| 37 SIGFAVAKELRELDKDLVIIDKDPAK---IETLREE-EYEAIQGDISNPETLNQI 87
                                      9************************9...8888886.6679********998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (499 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.71u 0.30s 00:00:01.01 Elapsed: 00:00:00.51
# Mc/sec: 2917.30
//
Query:       gi|298675664|ref|YP_003727414.1|  [L=494]
Description: carbohydrate kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.8e-55  187.4   0.1    4.4e-55  186.8   0.1    1.3  1  Carb_kinase  Carbohydrate kinase
    2.1e-40  138.4   0.7    1.3e-39  135.8   0.0    2.2  2  YjeF_N       YjeF-related protein N-terminus
    6.8e-06   25.6   0.3    6.4e-05   22.4   0.1    2.4  3  HK           Hydroxyethylthiazole kinase family
  ------ inclusion threshold ------
       0.23    8.9   0.0       0.31    8.5   0.0    1.1  1  Herpes_MCP   Herpes virus major capsid protein


Domain annotation for each model (and alignments):
>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.8   0.1   9.7e-59   4.4e-55       2     243 ..     244     487 ..     243     488 .. 0.95

  Alignments for each domain:
  == domain 1  score: 186.8 bits;  conditional E-value: 9.7e-59
                                       EEEE-BTTCHHHHHHHHHHHHCTT-SEEEEEESSTTTCCCCTTTTTCEECCTT....HTTTS....--SSS-SEEEE CS
                       Carb_kinase   2 lvigGsedytGAallaalaalrlgaglvsvateseaiavlksylpevivhpll....edeqa.kileklerldavvi 73 
                                       l+igG   y+GA+ l+ laalr ga+lv++at ++ +  + s +p++iv+ l+     +e+  ki ++ +  d+v+i
  gi|298675664|ref|YP_003727414.1| 244 LIIGG-GAYSGAPGLTSLAALRTGADLVTIATPKNVADIIASFSPNLIVDSLSsevlCSEDIpKIKDLVKSHDVVII 319
                                       78888.99************************9999999**************9999778888************** PP

                                       -TT-SSSHCHHHHCHHHCCCCS-EEEEGGGGGSGGGG...TTTTSSEEEE--HHHHHHHCTTTCH.HCCSHHHHHHH CS
                       Carb_kinase  74 GpGLgrdekikklleevlekdeplviDAdgLnllaqknelserkaeviLTPhkkEfkrLlkaivk.keddrlelare 149
                                       G+G grd++ k ++e++    + +v+DAdgL+ l++++ +se  +evi+TPh++Ef++L +       d+r+  + +
  gi|298675664|ref|YP_003727414.1| 320 GMGIGRDDRSKSAIEKIIPCCQKVVVDADGLYGLNYNS-ISESGCEVIITPHAGEFSYLQNKNTPkDRDSRACDVMD 395
                                       ************************************85.9*******************98766437888888899* PP

                                       HHHHHTTEEEEESTTSEEEECTTEEEEE----GGG-STTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHHHC CS
                       Carb_kinase 150 laqklnavvllkgekdvivspegevlinstgssalakGGsGDvLaGligalLaqneasyeaaiaaawlhgaasdeaa 226
                                       ++++ + + +lkg++d+i + ++ +l n+tg++++++GG+GDvLaG+ gal+a+n  + +aa ++a+++gaa+d+a+
  gi|298675664|ref|YP_003727414.1| 396 FSKNNHLITILKGKEDIISD-GERILYNQTGNPGMTVGGTGDVLAGITGALFAVNS-AIDAASCGAFINGAAGDLAF 470
                                       ****************9877.99********************************9.99****************** PP

                                       CCT-TS-HCHHHHHHHC CS
                       Carb_kinase 227 ekkgvgmlatelskiip 243
                                       e+kg+g+lat++++ i+
  gi|298675664|ref|YP_003727414.1| 471 EEKGYGLLATDIIDRIT 487
                                       *************9886 PP

>> YjeF_N  YjeF-related protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.8   0.0   2.9e-43   1.3e-39       3     171 .]      25     192 ..      23     192 .. 0.91
   2 ?    0.7   0.1     0.095   4.3e+02       9      58 ..     221     272 ..     218     342 .. 0.80

  Alignments for each domain:
  == domain 1  score: 135.8 bits;  conditional E-value: 2.9e-43
                            YjeF_N   3 eLmenagravaevlrallgnspaekkvlvlvGsgnnGgdglaaArhLaqe.gakVtv.llleeeekldedaeralel 77 
                                       +Lmenag+++a+ +++ +    ++ +++v++G+gnnGgd+++aArhLaq  ++kV++ ll ++++  ++da +++++
  gi|298675664|ref|YP_003727414.1|  25 QLMENAGAGIAKEVKNFI----ESGTIVVIAGRGNNGGDAFVAARHLAQYsNYKVKIiLLGRSSQIKTDDAIKNYQI 97 
                                       8*****************....999**********************8862688***55666667999********* PP

                            YjeF_N  78 lkkaggkvveekpeedleekls..apvdlviDAllGiglrgelreelaeliewlnsseapvlavDiPSGldadtGav 152
                                       lk++ ++ + e +++    +l    ++d++iDA+lG+g++ ++re+  ++i+ +n+s+a++++vD+PSG+d+d G+ 
  gi|298675664|ref|YP_003727414.1|  98 LKHCDITDILEVSDSTQILNLDwiDSADVIIDAILGTGVKSKIREPESTAIDMINNSKAKTISVDVPSGFDPDGGDF 174
                                       ******998777776655444499***************************************************** PP

                            YjeF_N 153 sgtavkadvtvtfgapkrg 171
                                       + + v +dvt+tf+ +k+g
  gi|298675664|ref|YP_003727414.1| 175 E-KSVFSDVTLTFHRMKPG 192
                                       *.6788***********97 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.095
                            YjeF_N   9 gravaevlrallg..nspaekkvlvlvGsgnnGgdglaaArhLaqegak.Vtv 58 
                                       gr+  e+l+++++   + ++ ++l++ G+  +G+ gl   + L ++ga+ Vt+
  gi|298675664|ref|YP_003727414.1| 221 GRGNLEMLKKRSEssHKGNSGRILIIGGGAYSGAPGLTSLAAL-RTGADlVTI 272
                                       6666777777777544555667888888889999999999888.777775555 PP

>> HK  Hydroxyethylthiazole kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.28   1.3e+03      88     125 ..     213     250 ..     198     280 .. 0.74
   2 ?   -0.6   0.0      0.15   6.8e+02      17      66 ..     280     330 ..     260     350 .. 0.77
   3 !   22.4   0.1   1.4e-08   6.4e-05     148     244 ..     397     490 ..     374     491 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.28
                                       TBTTBHHHHHHHHHHHHHS--SEEEEEHHHHHHHHTSS CS
                                HK  88 gvgAtelRrelalellkevklavikGNasEilslagle 125
                                        + A ++  + +le+lk+   +  kGN + il + g +
  gi|298675664|ref|YP_003727414.1| 213 CSDAEKIVGRGNLEMLKKRSESSHKGNSGRILIIGGGA 250
                                       55566666677889999999999999999999887765 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.15
                                       TTTHHHHHHHHHHHT-EEEE.--STTTHHHHHHTSSEEEEE-TT--HHHHH CS
                                HK  17 kVaqnfsANvllAlgaSPim.seaeeEvselakianaLllNiGtleekaie 66 
                                       ++ + fs N ++   +S ++ se+   +++l+k  + +++ +G+ ++ + +
  gi|298675664|ref|YP_003727414.1| 280 DIIASFSPNLIVDSLSSEVLcSEDIPKIKDLVKSHDVVIIGMGIGRDDRSK 330
                                       466789999988777776552788999999999999999999987775544 PP

  == domain 3  score: 22.4 bits;  conditional E-value: 1.4e-08
                                       HHHHTSEEEEESSSEEEEESSEEEEEE-S-GGGGGSTTHHHHHHHHHHHHHTTBSSHHHHHHHHHHHHHHHH.HHHH CS
                                HK 148 AqklrvvvvvtGevDvvsdgkkvyklknGtellgkitasGCllgsvvaaflavkkdkllaaveavllykvAgkeaaa 224
                                        ++ +++ ++ G+ D++sdg++++  + G++ ++ + ++G +l+ + +a  av+++   +a++  ++ + A+   a 
  gi|298675664|ref|YP_003727414.1| 397 SKNNHLITILKGKEDIISDGERILYNQTGNPGMT-VGGTGDVLAGITGALFAVNSA--IDAASCGAFINGAAGDLAF 470
                                       56778999*************************7.9****************9765..5555666666777779999 PP

                                       HHHTTHHHHHHHHHHHHH-- CS
                                HK 225 rsegsgsFqvelldalsqlt 244
                                       +++g g   + ++d+++ ++
  gi|298675664|ref|YP_003727414.1| 471 EEKGYGLLATDIIDRITDVI 490
                                       999***********998775 PP

>> Herpes_MCP  Herpes virus major capsid protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0   6.9e-05      0.31    1178    1210 ..     361     393 ..     355     406 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 6.9e-05
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Herpes_MCP 1178 avCEviltPVtadvnYFkspnnPRGRascvvsv 1210
                                        + CEvi+tP + + +Y ++ n P+ R s +  v
  gi|298675664|ref|YP_003727414.1|  361 SGCEVIITPHAGEFSYLQNKNTPKDRDSRACDV 393 
                                        67************************9644443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (494 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.36s 00:00:01.01 Elapsed: 00:00:00.53
# Mc/sec: 2803.37
//
Query:       gi|298675665|ref|YP_003727415.1|  [L=60]
Description: hypothetical protein Metev_1783 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 353.41
//
Query:       gi|298675666|ref|YP_003727416.1|  [L=158]
Description: molybdenum cofactor biosynthesis protein C [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-49  165.7   4.5    6.5e-49  165.5   4.5    1.0  1  MoaC      MoaC family


Domain annotation for each model (and alignments):
>> MoaC  MoaC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.5   4.5   3.6e-53   6.5e-49       1     135 [.      15     154 ..      15     155 .. 0.98

  Alignments for each domain:
  == domain 1  score: 165.5 bits;  conditional E-value: 3.6e-53
                                       E---TTS--EEEEEEEEEEEEE-HHHHHHHHTTSSTTB-HHHHHHHHHHHHHHHHHHHSTT-----EEEEEEEEEEE CS
                              MoaC   1 mvdvsekeetkrtAvAegrvklseetlelikekklkkGdvlavariagimaaKktseliplcHplpltkvevelele 77 
                                       mvd s+k++++r+AvA+g++ l+e+t++ i++++++kG+vla+ar+a+imaaKkts++ip+cHp+p+t ++++++++
  gi|298675666|ref|YP_003727416.1|  15 MVDTSKKDSVSRQAVASGKIILTEDTINNIQSSSIEKGNVLATARVAAIMAAKKTSDTIPMCHPIPITGIDTNFDIN 91 
                                       9*************************************************************************987 PP

                                       TTTTEEEEEEEEEEEESS--HHHHHHHHHHHHHHHHHHHTTTHTT.......-EEEEEEEEEEES CS
                              MoaC  78 eeeesveieatvktegktGvemEALtavsvaaltvyDmvKavdke.......mvieevrlveKsg 135
                                         ++ ++ +++vk  gktGvemEAL +vs+a+lt++DmvK+++k+       ++i+++++veK++
  gi|298675666|ref|YP_003727416.1|  92 --NNYITASVKVKSVGKTGVEMEALNGVSTALLTIWDMVKSAEKDetgnyphTKIQDIEVVEKTK 154
                                       ..79****************************************99*****************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 984.33
//
Query:       gi|298675667|ref|YP_003727417.1|  [L=285]
Description: ribose-phosphate pyrophosphokinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.8e-26   91.0   0.1    1.2e-22   80.1   0.0    2.2  2  Pribosyltran_N  N-terminal domain of ribose phosphate pyropho
      1e-19   70.6   0.2    1.8e-19   69.8   0.2    1.4  1  Pribosyltran    Phosphoribosyl transferase domain
    1.9e-07   31.3   1.1    3.7e-07   30.4   1.1    1.4  1  Pribosyl_synth  Phosphoribosyl synthetase-associated domain
    5.3e-06   26.0   0.1    9.7e-06   25.2   0.1    1.4  1  UPRTase         Uracil phosphoribosyltransferase
     0.0082   15.7   0.1      0.018   14.6   0.1    1.5  1  PRTase_2        Phosphoribosyl transferase


Domain annotation for each model (and alignments):
>> Pribosyltran_N  N-terminal domain of ribose phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.1   0.0   3.3e-26   1.2e-22       1     114 [.       1     112 [.       1     113 [. 0.95
   2 !    9.0   0.0   0.00036       1.3       8      57 ..     163     213 ..     156     245 .. 0.84

  Alignments for each domain:
  == domain 1  score: 80.1 bits;  conditional E-value: 3.3e-26
                    Pribosyltran_N   1 lkifagssskeLaekiakrlgvelgkakvsrfadgEikveiee.svrgkdvfiiqslskpvndnlmelllmidalrr 76 
                                       +ki+ g +s+ La+++a++l+ + + ++  +f+dgE +++i + ++ ++ v iiq + ++   +l+ ll +ida++ 
  gi|298675667|ref|YP_003727417.1|   1 MKIIGGPASQLLASRVARELNDKPILCEFDKFPDGEQYIRILDeDIENERVAIIQCTYSD--SDLISLLQLIDACE- 74 
                                       89**************************************96549**********99987..89***********7. PP

                    Pribosyltran_N  77 asakritaViPylgysrqdrk.ksrepisaklvaklLea 114
                                         ak+i+++iPylgysrqd+k k+ e+isa+ + + L+a
  gi|298675667|ref|YP_003727417.1|  75 -DAKQINVIIPYLGYSRQDKKfKNGEAISARAITRTLTA 112
                                       .99******************9***********999975 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00036
                    Pribosyltran_N   8 sskeLaekiakrlgvelgkakvsrfadgEikveiee.svrgkdvfiiqsls 57 
                                        +  Lae+ ++++g+e    + +r + +E++++ ++ ++ g+dv++i ++ 
  gi|298675667|ref|YP_003727417.1| 163 GAIYLAENASSKTGIEYDYLEKERISGDEVSIKTKNmDITGRDVVLIDDMI 213
                                       56689*****************************9989*********9987 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.8   0.2   5.1e-23   1.8e-19      14     152 ..     138     272 ..     127     278 .. 0.87

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 5.1e-23
                                       EEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEE CS
                      Pribosyltran  14 avarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkV 90 
                                       ++  l+ +++e+ + k++++v++++g++ +a   +++ +++++y++k++ ++d  +  +        +  d+ g+ V
  gi|298675667|ref|YP_003727417.1| 138 EASYLLGNHIESLDLKNPLIVAPDSGAIYLAENASSKTGIEYDYLEKERISGDEVSIKT--------KNMDITGRDV 206
                                       5678999******************************************9999988887........6679****** PP

                                       EEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEE...E-HHHHHHHHHH-TTS......EEEEEEE CS
                      Pribosyltran  91 liVDDildtGgTllaalelLkekgpeevriavlv...dkpateeevdknakrvfsls.pdnfvavv 152
                                       +++DD+++tGgT+ + +++Lk++g+  v +a+++   +k+a  +   ++++ ++s+  ++  + +v
  gi|298675667|ref|YP_003727417.1| 207 VLIDDMIATGGTMAESIKILKSQGANDVYLACVHpvlAKNAVLRLFNAGVRDIISTDtIEKAESAV 272
                                       ********************************9988888877777777777777777666666555 PP

>> Pribosyl_synth  Phosphoribosyl synthetase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   1.1     1e-10   3.7e-07      80     147 ..     200     267 ..     189     281 .. 0.94

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 1e-10
                                       --TTSEEEEEEEEE-S-HHHHHHHHHHHHTT--EEEEEEEEE---TTHHHHHHHSS--EEEEESSS-- CS
                    Pribosyl_synth  80 dvgGriaiivddliddvesfvaaaevlkerGaykiyvlathGllssdaprlleesaidevvvtntiph 147
                                       d++Gr  +++dd+i    ++ ++ ++lk +Ga  +y  + h +l+++a  +l ++ + +++ t+ti +
  gi|298675667|ref|YP_003727417.1| 200 DITGRDVVLIDDMIATGGTMAESIKILKSQGANDVYLACVHPVLAKNAVLRLFNAGVRDIISTDTIEK 267
                                       99***************************************************************976 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.1   2.7e-09   9.7e-06     118     172 ..     200     254 ..     177     270 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.7e-09
                           UPRTase 118 kiaertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrlaee 172
                                       +i+ r v+l+D +iaTGg++a+ i++Lk++g++     ++  + ++++v rl ++
  gi|298675667|ref|YP_003727417.1| 200 DITGRDVVLIDDMIATGGTMAESIKILKSQGANDVYLACVHPVLAKNAVLRLFNA 254
                                       567889***********************99998888888888898888887765 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   4.9e-06     0.018     120     154 ..     202     236 ..     189     246 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.9e-06
                          PRTase_2 120 aakelvLvDDEistGktalnliralqeklprkryv 154
                                       + + +vL+DD i+tG t+++ i+ l+++  ++ y 
  gi|298675667|ref|YP_003727417.1| 202 TGRDVVLIDDMIATGGTMAESIKILKSQGANDVYL 236
                                       5588*********************9998877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1893.06
//
Query:       gi|298675668|ref|YP_003727418.1|  [L=172]
Description: hypothetical protein Metev_1786 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1521  (0.0848346); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1138.78
//
Query:       gi|298675669|ref|YP_003727419.1|  [L=207]
Description: HhH-GPD family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.6e-17   62.8   0.0    5.4e-17   62.2   0.0    1.2  1  HhH-GPD      HhH-GPD superfamily base excision DNA repair pro
    2.9e-05   23.7   0.0    5.9e-05   22.7   0.0    1.5  1  HHH          Helix-hairpin-helix motif
     0.0046   17.5   0.0      0.018   15.6   0.0    1.9  2  HHH_5        Helix-hairpin-helix domain
  ------ inclusion threshold ------
        0.3   11.3   2.1          8    6.7   0.3    2.5  2  CRAL_TRIO_N  CRAL/TRIO, N-terminal domain


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2   0.0   1.2e-20   5.4e-17       1      98 [.      27     156 ..      27     165 .. 0.91

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 1.2e-20
                                       HHHHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH........... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........... RF
                           HhH-GPD   1 vsailsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv........... 66 
                                       v+ail+qqt++ +++++i +l++++  ++ ++la+ad ek++eli+++Gfyr+Ka ++k++A  +            
  gi|298675669|ref|YP_003727419.1|  27 VGAILTQQTKWINVEKAISNLKNNY-LLDKKALAYADIEKIEELIYCCGFYRQKATRLKNVANYFFengldsvfnqd 102
                                       799**********************.7************************************************** PP

                                       ...........................S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHH CS
                                       ...........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           HhH-GPD  67 ...........................gkpdvlivvDvhvrrilkrlrsikekktkkkv 98 
                                                                   kp+  +v D +++ri++ l++  +    k++
  gi|298675669|ref|YP_003727419.1| 103 inklrstllslkgigeetadsiilysaEKPK--FVIDAYTKRIMGCLGIDGNY---KQL 156
                                       *************************876655..999********998876553...444 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   1.3e-08   5.9e-05       3      30 .]     100     127 ..      99     127 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.3e-08
                                       HHHHTSSHHHHHTSTT-SHHHHHHHHHH CS
                               HHH   3 eglipasreeLlalPGVGpktAeaIlsy 30 
                                       + +i+  r  Ll+l+G+G++tA++I+ y
  gi|298675669|ref|YP_003727419.1| 100 NQDINKLRSTLLSLKGIGEETADSIILY 127
                                       567888899****************987 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       0.7   3.2e+03      27      39 ..      56      68 ..      41      72 .. 0.71
   2 !   15.6   0.0     4e-06     0.018      34      53 ..     107     126 ..      79     129 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.7
                                      HHHHHS-HHHHHT CS
                             HHH_5 27 edlaaadveeLak 39
                                       +la ad+e++ +
  gi|298675669|ref|YP_003727419.1| 56 KALAYADIEKIEE 68
                                      5778888887765 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 4e-06
                                       HHHHHTSTTS-HHHHHHHHH CS
                             HHH_5  34 veeLakipGiGkktAeriil 53 
                                       + +L +++GiG++tA++iil
  gi|298675669|ref|YP_003727419.1| 107 RSTLLSLKGIGEETADSIIL 126
                                       45699*************97 PP

>> CRAL_TRIO_N  CRAL/TRIO, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.015        69      41      54 .]      35      49 ..      35      49 .. 0.91
   2 ?    6.7   0.3    0.0018         8       2      35 ..     153     196 ..     152     197 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.015
                       CRAL_TRIO_N 41 rkw.dvekAikrLed 54
                                      +kw +vekAi  L++
  gi|298675669|ref|YP_003727419.1| 35 TKWiNVEKAISNLKN 49
                                      7999********997 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0018
                       CRAL_TRIO_N   2 ydellahlqeseyk...........lteeekfW.ltredhddaclL 35 
                                       y++l++h+++  +            ++e+ k + ++++   d+clL
  gi|298675669|ref|YP_003727419.1| 153 YKQLQSHFESKLPVdvnlyqeyhalIVEYAKNYcVKKQ--CDNCLL 196
                                       9*******999988999988888888888888877777..888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       930  (0.0518713); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1584.82
//
Query:       gi|298675670|ref|YP_003727420.1|  [L=261]
Description: hypothetical protein Metev_1788 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-49  166.3   5.1    3.1e-49  166.3   5.1    1.6  2  TPD              Protein of unknown function TPD sequence-mot
    0.00028   21.2   0.7    0.00039   20.8   0.7    1.2  1  RNA_pol_3_Rpc31  DNA-directed RNA polymerase III subunit Rpc3
  ------ inclusion threshold ------
      0.016   15.6   0.4      0.048   14.1   0.4    1.8  1  HTH_40           Helix-turn-helix domain
       0.57   10.0   5.9       0.81    9.6   0.3    3.2  3  IF2_N            Translation initiation factor IF-2, N-termin


Domain annotation for each model (and alignments):
>> TPD  Protein of unknown function TPD sequence-motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1      0.65   2.9e+03      38      46 ..      69      77 ..      37     105 .. 0.43
   2 !  166.3   5.1   6.9e-53   3.1e-49       2     134 ..     107     238 ..     106     240 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.65
                               TPD 38 lekllkekg 46
                                      ++++ ke++
  gi|298675670|ref|YP_003727420.1| 69 IQDIAKENK 77
                                      222222222 PP

  == domain 2  score: 166.3 bits;  conditional E-value: 6.9e-53
                               TPD   2 dkrlakevkeaieedsvyspladairssvGeeyEellekllkekgiafkteedlrekgldktPDvkLevpvavegkv 78 
                                       d+rl+ke ke+ie+d +ysp+a++ +s++G+++E+++ek+l +++i+++te dlre g++ktPD++L++++++eg+ 
  gi|298675670|ref|YP_003727420.1| 107 DERLKKETKEVIESDFHYSPKAHKLQSIRGQMGEDIIEKWLIQNNIDYYTEYDLREYGHTKTPDFVLNDTLIIEGTD 183
                                       99*************************************************************************** PP

                               TPD  79 vnWiesKalfgdeeehkkylkkQlssYvnrfGpGlviYwfGyvdelesekgvlikd 134
                                       ++WiesKa+fgde+eh++y+kkQ+++Y+++fG+G+++Yw+Gy+d+++ + +++ikd
  gi|298675670|ref|YP_003727420.1| 184 IQWIESKAIFGDEKEHSHYFKKQFKQYEEKFGQGMIVYWYGYLDNIDLN-NHIIKD 238
                                       ************************************************9.888887 PP

>> RNA_pol_3_Rpc31  DNA-directed RNA polymerase III subunit Rpc31
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.7   8.7e-08   0.00039      97     159 ..      43     106 ..      19     155 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 8.7e-08
                   RNA_pol_3_Rpc31  97 atfdpft.gierYsdkylkkertlpklderpyvkefFPkELwptlkdgkdekkeikgkskkkk.......e 159
                                       +++ +++  +++Ys++ lkk+++++++++    ++ +P++L++t+       k + g skk+        +
  gi|298675670|ref|YP_003727420.1|  43 SKVKKTQpKVQKYSHRHLKKWEKGQSIQDIA-KENKLPESLMATILL-----K-EMGYSKKQVfnnpdilS 106
                                       333455557*******************995.779**********41.....1.22333333323222221 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.4   1.1e-05     0.048       6      80 ..      60     142 ..      56     144 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.1e-05
                            HTH_40   6 lelleeglsieeIAkerglkesTIegHLaelieeg..eeidlerlvse.eeekeIeeaiek.....vgseklkpike 74 
                                       l+ +e+g+si++IAke +l es  ++ L++ +     + ++  +++s+ + +ke +e+ie       + +kl+ i+ 
  gi|298675670|ref|YP_003727420.1|  60 LKKWEKGQSIQDIAKENKLPESLMATILLKEMGYSkkQVFNNPDILSDeRLKKETKEVIESdfhysPKAHKLQSIRG 136
                                       5679******************9999999955553333333344443324444444444444443444667999998 PP

                            HTH_40  75 alpeev 80 
                                       +++e++
  gi|298675670|ref|YP_003727420.1| 137 QMGEDI 142
                                       888875 PP

>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1     0.081   3.7e+02      18      47 ..      20      45 ..      17      48 .. 0.62
   2 ?    9.6   0.3   0.00018      0.81       5      33 ..      68      96 ..      64      98 .. 0.91
   3 ?    0.1   0.1      0.16   7.4e+02      11      22 ..     108     119 ..     108     122 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.081
                             IF2_N 18 kevikkLfkelGievkshsssLDeetaeli 47
                                      +e+ +k+++    +v  +ss+L++ t+ ++
  gi|298675670|ref|YP_003727420.1| 20 EELAEKFME----PVGVISSILSQKTVSKV 45
                                      555566655....33344888888887776 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00018
                             IF2_N  5 rVyeLAkeLgvkskevikkLfkelGievk 33
                                      +++++Ake +++     + L ke+G+++k
  gi|298675670|ref|YP_003727420.1| 68 SIQDIAKENKLPESLMATILLKEMGYSKK 96
                                      89*************************55 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.16
                             IF2_N  11 keLgvkskevik 22 
                                       ++L+++ kevi+
  gi|298675670|ref|YP_003727420.1| 108 ERLKKETKEVIE 119
                                       5799*******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1298  (0.0723967); expected 358.6 (0.02)
Passed bias filter:                      601  (0.0335211); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2020.52
//
Query:       gi|298675671|ref|YP_003727421.1|  [L=101]
Description: hypothetical protein Metev_1789 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.083   13.1   0.0       0.13   12.5   0.0    1.5  1  DUF3130   Protein of unknown function (DUF3130


Domain annotation for each model (and alignments):
>> DUF3130  Protein of unknown function (DUF3130
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   7.4e-06      0.13      10      45 ..      55      86 ..      42      99 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.4e-06
                           DUF3130 10 tlekfatklkskksseylklkggnlsYskansindl 45
                                       + +f t lk k     +k k  n+sY++++s+n+l
  gi|298675671|ref|YP_003727421.1| 55 VAGNFGTVLKKK----EVKSKPVNFSYASGKSLNHL 86
                                      556677777777....799****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 584.05
//
Query:       gi|298675672|ref|YP_003727422.1|  [L=75]
Description: hypothetical protein Metev_1790 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   12.0   0.0       0.14   11.9   0.0    1.0  1  DIM1      Mitosis protein DIM1


Domain annotation for each model (and alignments):
>> DIM1  Mitosis protein DIM1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.8e-06      0.14      44     112 ..       3      71 ..       1      74 [. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.8e-06
                                       HHHHHTTTTEEEEEEETTT--TTSCCCTT-SSSEEEEEETTEEEEEE-SSS--SSB-S----HHHHHHH CS
                              DIM1  44 kiaeklknfaviylvdidevpdfnkmyeledpvtilffyrnkhmkvDfgtgdnnKlnfvledkqelidi 112
                                       +i+++++  +  +l+di e+ ++ +  e e ++ +++  ++  +  D  tg+n+ +nf  e+ +++  i
  gi|298675672|ref|YP_003727422.1|   3 RISNEIQGNSLSALIDIFELYKYREPVEEEVNTMLMLMGNQGSLYKDRETGNNELINFQSENFDSMSRI 71 
                                       6788888888889******************99*****9999****************99998887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 476.16
//
Query:       gi|298675673|ref|YP_003727423.1|  [L=530]
Description: lysyl-tRNA synthetase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     1e-128  429.3   0.0   4.9e-127  423.8   0.0    2.1  2  tRNA-synt_1f    tRNA synthetases class I (K)
      3e-08   32.8   0.1    0.00035   19.4   0.0    2.4  2  tRNA-synt_1g    tRNA synthetases class I (M)
    2.9e-06   26.8   0.0      0.047   13.0   0.0    2.5  2  tRNA-synt_1e    tRNA synthetases class I (C) catalytic domain
  ------ inclusion threshold ------
       0.13   12.6   0.0       0.37   11.1   0.0    1.7  1  Transpos_assoc  Transposase-associated domain


Domain annotation for each model (and alignments):
>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  423.8   0.0  1.1e-130  4.9e-127       1     338 [.       5     333 ..       5     350 .. 0.96
   2 !    3.6   0.0    0.0057        26     287     323 ..     395     431 ..     389     474 .. 0.85

  Alignments for each domain:
  == domain 1  score: 423.8 bits;  conditional E-value: 1.1e-130
                      tRNA-synt_1f   1 kaWadklaeklieerkkkkaekdevvvesGispSGliHiGnlrevltadlvaralrkrgeevrlilisDdmDglRkv 77 
                                       k+Wad+ a+k +e+        ++++v++Gi+pSG+iHiGn+rev+tad+v+ral ++ ++++li+i+D++D+lRkv
  gi|298675673|ref|YP_003727423.1|   5 KHWADVAADKAMEHG-------QKHLVATGITPSGHIHIGNMREVVTADAVYRALLDKDQNAELIYIADTYDPLRKV 74 
                                       69*********9444.......468**************************************************** PP

                      tRNA-synt_1f  78 penlpekllekylgkpltsiPdpkgkhesyaehfnaelvesLdelgievefisatelYksglydeaikealenreki 154
                                       +++lp++ +++++gkpl++iP+p g++e+ya+hf  +++esL+++gi+ ++++  elYksg+y++aik+al nr+ki
  gi|298675673|ref|YP_003727423.1|  75 YPFLPDS-YSEHIGKPLSEIPCPCGNCENYAQHFLTPFLESLSKMGIHPKVYKGDELYKSGAYTDAIKTALLNRDKI 150
                                       *******.********************************************************************* PP

                      tRNA-synt_1f 155 keilekyrgeereetyspylpvcekcgrvdttevvevdaeeeeieYkceecGeeeevdiregngKLqWkvdwamrWa 231
                                       ++i+e+ +g++   ++sp++p+c+ cgr++tt+vv++d e+e++ ++c ++G++++v++++g gKL+W+vdw++rW+
  gi|298675673|ref|YP_003727423.1| 151 SRIIEEETGKDPDPEWSPFNPICNVCGRINTTKVVDYDIENETVDFVC-SNGHSGTVSMTGG-GKLSWRVDWPARWQ 225
                                       ************************************************.**********997.************** PP

                      tRNA-synt_1f 232 algVdfEpaGkDhaaaGgSvdvsskia.eilggeaPekvvYelillkggekmssSkGnvltledwlevaepevlrfl 307
                                       +lgV++Ep+GkDha+ GgS+d++++ia ei+g+e+P++vvYe+i+l ++++mssS+G+v+t++d+l+v++pevlr+l
  gi|298675673|ref|YP_003727423.1| 226 ILGVTVEPFGKDHASRGGSYDTGERIAkEIYGYEPPYPVVYEWIMLGKQGAMSSSSGVVVTISDMLKVVPPEVLRYL 302
                                       ***************************************************************************** PP

                      tRNA-synt_1f 308 ilrrkPkkakkldldleilrlvdeYdklerk 338
                                       i+++kP+k++++++++ +l lvde+++l+ +
  gi|298675673|ref|YP_003727423.1| 303 IIKTKPEKHISFEPGMPLLTLVDEFERLKSS 333
                                       ***************************8764 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0057
                      tRNA-synt_1f 287 GnvltledwlevaepevlrflilrrkPkkakkldldl 323
                                       G v  +e+wle++ p+ ++f + ++ P+ka +l+ ++
  gi|298675673|ref|YP_003727423.1| 395 GLVSNVENWLEMYAPDFVKFSVKEKLPEKAANLSDEQ 431
                                       778899************************9998664 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.1   3.1e-05      0.14      10      41 ..      30      61 ..      22      69 .. 0.71
   2 !   19.4   0.0   7.8e-08   0.00035     315     361 ..     264     310 ..     246     316 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.1e-05
                                      -SS---HHHHHHHHHHHHHHHHHHHTT-EEEE CS
                      tRNA-synt_1g 10 angklHlGhllevisaDifaRykrlrgeevlf 41
                                      ++g++H+G+++ev+ aD+++R    ++++   
  gi|298675673|ref|YP_003727423.1| 30 PSGHIHIGNMREVVTADAVYRALLDKDQNAEL 61
                                      6899*****************87555444333 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 7.8e-08
                                       EEEE--EEE.--------------HHHHHHHH-HHHHHHHHHHHS-TT CS
                      tRNA-synt_1g 315 vvaheyltv.egkKlSkSrgvvvkakealerldadllRYylaaeapek 361
                                       v + e++++ +++ +S+S gvvv+++++l+ +++++lRY +++++pek
  gi|298675673|ref|YP_003727423.1| 264 V-VYEWIMLgKQGAMSSSSGVVVTISDMLKVVPPEVLRYLIIKTKPEK 310
                                       4.445555427789****************************999986 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0     4e-05      0.18       8      51 ..      19      64 ..      13     125 .. 0.83
   2 !   13.0   0.0     1e-05     0.047     246     291 ..     268     314 ..     261     318 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4e-05
                                      TEEEEEEEEEBTTS--BHHHHHHHHHHHHHHHHHHH..TT-EEEEE CS
                      tRNA-synt_1e  8 kkvtlYvCGptvydashlGhaRslvafDilrrilqa..lgYdvqfv 51
                                      ++ +l   G+t   ++h+G+ R++v+ D + r l +  ++ ++ ++
  gi|298675673|ref|YP_003727423.1| 19 GQKHLVATGITPSGHIHIGNMREVVTADAVYRALLDkdQNAELIYI 64
                                      55667788********************999988762344455555 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 1e-05
                                       -EEETTB.E--TTTT---BHHHHHTTS-HHHHHHHHHSS-TTS-EEE CS
                      tRNA-synt_1e 246 hlkiege.kmsksLknfitikdvlkkfdprqlRllllsahyrsqldf 291
                                       ++++ ++  ms s + ++ti d+lk + p++lR+l+++++ ++++ f
  gi|298675673|ref|YP_003727423.1| 268 WIMLGKQgAMSSSSGVVVTISDMLKVVPPEVLRYLIIKTKPEKHISF 314
                                       677766637****************************9998888877 PP

>> Transpos_assoc  Transposase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   8.2e-05      0.37      30      48 ..      88     106 ..      67     123 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.2e-05
                    Transpos_assoc  30 skeeeilCpckkCknkksl 48 
                                       +  +ei Cpc +C+n+ ++
  gi|298675673|ref|YP_003727423.1|  88 KPLSEIPCPCGNCENYAQH 106
                                       44579**********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (530 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       777  (0.0433376); expected 358.6 (0.02)
Passed bias filter:                      731  (0.0407719); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.70u 0.30s 00:00:01.00 Elapsed: 00:00:00.49
# Mc/sec: 3268.63
//
Query:       gi|298675674|ref|YP_003727424.1|  [L=220]
Description: type 11 methyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-21   74.6   0.0    1.3e-20   73.8   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    2.7e-19   69.6   0.0    7.3e-19   68.3   0.0    1.7  2  Methyltransf_25  Methyltransferase domain
    1.6e-15   57.4   0.0    1.9e-15   57.1   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    2.9e-15   56.4   0.0    1.8e-14   53.8   0.0    1.9  2  Methyltransf_31  Methyltransferase domain
    2.5e-11   44.2   0.0    4.6e-11   43.3   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
      3e-09   36.6   0.0    4.1e-09   36.1   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
      2e-07   30.6   0.0    3.1e-07   30.0   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    1.2e-06   27.7   0.0    1.4e-06   27.5   0.0    1.2  1  Methyltransf_9   Protein of unknown function (DUF1698)
    3.3e-06   26.7   0.0    4.4e-06   26.2   0.0    1.3  1  TehB             Tellurite resistance protein TehB
    9.8e-05   21.9   0.0    0.00016   21.2   0.0    1.3  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00019   21.0   0.0    0.00027   20.5   0.0    1.3  1  MTS              Methyltransferase small domain
    0.00022   20.9   0.0    0.00041   20.0   0.0    1.6  1  MetW             Methionine biosynthesis protein MetW
      0.002   17.8   0.0     0.0029   17.3   0.0    1.3  1  TPMT             Thiopurine S-methyltransferase (TPMT)
  ------ inclusion threshold ------
       0.02   14.4   0.1       0.64    9.5   0.0    2.7  2  CheR             CheR methyltransferase, SAM binding domain
      0.029   14.3   0.1      0.086   12.8   0.0    1.7  2  Methyltransf_18  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.8   0.0   1.1e-23   1.3e-20       1      96 []      46     142 ..      46     142 .. 0.94

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 1.1e-23
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-...EEEETTEECCCTSS-TT-EEEEEEES-CCC- CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl...kvefvvadaeklpfednsfDlvvssevlhhv 74 
                                       Ld+GcG+Gr++ +l k + +v+gvD+s+ +lk +k + ++++    +    v+++++lpf dn fD+vvs  vl+h+
  gi|298675674|ref|YP_003727424.1|  46 LDAGCGNGRHLLPLSKVY-HVTGVDISPSALKNSKLHLEKNNCfayQ---SVSTVTHLPFSDNIFDCVVSLGVLQHF 118
                                       8**************666.*******************999985444...89999********************** PP

                                       ..CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  75 ..edpekalkeiaRvLkpgGllvi 96 
                                         +++e ++ e+ RvL  gG+lv+
  gi|298675674|ref|YP_003727424.1| 119 yeHERELTIYEFSRVLASGGILVL 142
                                       999******************985 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.3   0.0   6.1e-22   7.3e-19       1      97 []      45     138 ..      45     138 .. 0.96
   2 ?   -2.1   0.0       5.7   6.8e+03      75      88 ..     173     186 ..     170     203 .. 0.60

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 6.1e-22
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                       +Ld+GcG+Gr++l l+k    ++vtgvDis+++l++ + ++e++++ +   +  +++lpf d+ fD+vvs g+l+h+
  gi|298675674|ref|YP_003727424.1|  45 ILDAGCGNGRHLLPLSKV---YHVTGVDISPSALKNSKLHLEKNNCFAYQSVSTVTHLPFSDNIFDCVVSLGVLQHF 118
                                       8***************87...7*******************99998888899999***************988**** PP

                                       SHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  78 sdedlekalkeiarvLkpgG 97 
                                        ++++e ++ e++rvL  gG
  gi|298675674|ref|YP_003727424.1| 119 YEHERELTIYEFSRVLASGG 138
                                       9******************9 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.7
                                       GGSSHHHHHHHHHH CS
                   Methyltransf_25  75 hhlsdedlekalke 88 
                                       h+++d++++ +l++
  gi|298675674|ref|YP_003727424.1| 173 HYFTDKEIKSLLEK 186
                                       55555555555554 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.1   0.0   1.6e-18   1.9e-15      11     163 ..      30     192 ..      14     194 .. 0.83

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 1.6e-18
                   Methyltransf_23  11 dklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae........kakkaqkdqfdeqeaaep 79 
                                       + +e ++ +  +g ++Ld GcG G+ l  l++  ++vtgvD+sp a +  +         a++++++ +     +++
  gi|298675674|ref|YP_003727424.1|  30 RSIEMVSSRISPGHKILDAGCGNGRHLLPLSKV-YHVTGVDISPSALKNSKlhleknncFAYQSVSTVT---HLPFS 102
                                       55666777778889**********888888665.9*********9887766888877664555555544...7777* PP

                   Methyltransf_23  80 qgkfdlIvlrevlehvpdppellr..qiatllkpgGylllseplasl....kedrllldwlylvpagrhisffsars 150
                                       ++ fd++v+  vl h+  +++ l+   + + l+ gG l+l+++++++    k d+  +++++l++ g   ++f+ ++
  gi|298675674|ref|YP_003727424.1| 103 DNIFDCVVSLGVLQHFYEHERELTiyEFSRVLASGGILVLEVFGVDDmrygKGDNVGEENTFLRNGGIIYHYFTDKE 179
                                       ******************999887336899***************999998899999*******775555******* PP

                   Methyltransf_23 151 lkelleeaGlevv 163
                                       +k lle++ +++ 
  gi|298675674|ref|YP_003727424.1| 180 IKSLLEKYKFQIT 192
                                       ********99986 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.8   0.0   1.5e-17   1.8e-14       3     120 ..      41     156 ..      39     187 .. 0.78
   2 ?    0.9   0.0      0.29   3.5e+02      52      75 ..     183     203 ..     176     208 .. 0.79

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 1.5e-17
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlil 79 
                                        g ++lD+GCG+G+ ++ l  +++   +v+G+Dis+ a++ ++ +++k++   +  +++ +++l+  ++d+ fD ++
  gi|298675674|ref|YP_003727424.1|  41 PGHKILDAGCGNGRHLLPLS-KVY---HVTGVDISPSALKNSKLHLEKNNC-FAYQSVSTVTHLP--FSDNIFDCVV 110
                                       6789****************.775...7*****************999888.4555677788888..********** PP

                   Methyltransf_31  80 snevlnaladpdkile..eiervlkpggilliedprllaelp....a 120
                                       s +vl+++++ +  l   e +rvl +ggil++e +   ++++    +
  gi|298675674|ref|YP_003727424.1| 111 SLGVLQHFYEHERELTiyEFSRVLASGGILVLEVFG-VDDMRygkgD 156
                                       *****9999887766666*************98877.4444444444 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.29
                   Methyltransf_31  52 gldnveFeqgdieeleklledekf 75 
                                        l+ ++F++ di+++++    ++f
  gi|298675674|ref|YP_003727424.1| 183 LLEKYKFQITDITNIKTE---KRF 203
                                       57899*********8853...555 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   0.0   3.9e-14   4.6e-11       1      99 []      46     140 ..      46     140 .. 0.77

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 3.9e-14
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg..ssfDlvvasnv 75 
                                       L+ GcG+G+ l +l +     ++tgvDispsa+++ k +l k++  ++ +   ++++l        + fD vv+++v
  gi|298675674|ref|YP_003727424.1|  46 LDAGCGNGRHLLPLSKV---YHVTGVDISPSALKNSKLHLEKNNC-FAYQSVSTVTHLP----FsdNIFDCVVSLGV 114
                                       89******999999888...*************555555555443.2223333333333....23369********* PP

                   Methyltransf_12  76 lhhl..kdirevldnirklLkpgGrl 99 
                                       l+h+   +++ ++ ++ ++L+ gG+l
  gi|298675674|ref|YP_003727424.1| 115 LQHFyeHERELTIYEFSRVLASGGIL 140
                                       *****989999*************86 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.0   3.4e-12   4.1e-09      59     174 ..      38     152 ..      30     203 .. 0.79

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 3.4e-12
                                       T--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---.--SEEEEE CS
                              CMAS  59 elkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde.kvdrvvsv 134
                                       ++ pG+++Ld GcG G  +    + y  +v g+ +S    k +k ++++ +    ++v+   +  +++  +d vvs+
  gi|298675674|ref|YP_003727424.1|  38 RISPGHKILDAGCGNGRHLLPLSKVY--HVTGVDISPSALKNSKLHLEKNNCFAYQSVSTVTHLPFSDnIFDCVVSL 112
                                       789*****************999997..678***********************************99689****** PP

                                       S-GGGTSGGGHHHHHHHHHHHS-TT-EEEEEEEEE--HHH CS
                              CMAS 135 gafehvgkenydtffkklkkllkedGllllhtitslhkke 174
                                       g+++h+ +++ +  + +++++l ++G+l+l+     + + 
  gi|298675674|ref|YP_003727424.1| 113 GVLQHFYEHERELTIYEFSRVLASGGILVLEVFGVDDMRY 152
                                       ******998889999999***********99877666554 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   2.6e-10   3.1e-07      43     153 ..      37     143 ..      20     152 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 2.6e-10
                                       --S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEE CS
                   Ubie_methyltran  43 vavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDv 119
                                       +   +g+k+lD  +G g   + ls+     ++v+++Di+++ Lk ++ +l+++     + + +   +Lpf+d+ fD+
  gi|298675674|ref|YP_003727424.1|  37 SRISPGHKILDAGCGNGRHLLPLSKV----YHVTGVDISPSALKNSKLHLEKNNCFAYQSV-STVTHLPFSDNIFDC 108
                                       3345799***********99999875....67999***************99999888776.56789*********9 PP

                                       EEEES-.GGG-S-HHHHH..HHHHHHEEEEEEEEEEE CS
                   Ubie_methyltran 120 vtvsfG.lrnvtDklkaL..keayrvlkpGGrlvvle 153
                                       v vs G l+ + ++++ L   e  rvl  GG+lv le
  gi|298675674|ref|YP_003727424.1| 109 V-VSLGvLQHFYEHERELtiYEFSRVLASGGILV-LE 143
                                       8.8898356777766655116999*******875.44 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   1.2e-09   1.4e-06      98     223 ..      26     148 ..       7     200 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.2e-09
                                       EEHHHHHHHHGGGS.--TT-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---G CS
                    Methyltransf_9  98 WrsdwkWdrvlphlsdlkgrtildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllgedqrahllplgi 174
                                       W   +  + v+  +s+  g++ild GcgnG hl  +      + v i Ps l   +++    l  ++  a++   ++
  gi|298675674|ref|YP_003727424.1|  26 WGGSRSIEMVSSRISP--GHKILDAGCGNGRHLLPLSKVYHVTGVDISPSALKNSKLH----LEKNNCFAYQSVSTV 96 
                                       6666666677777776..789*************998877777777888887766654....555666677777789 PP

                                       GGS-T.---EEEEEEES-GGG-S-HHH..HHHHHHCTEEEEEEEEEEEE-BS CS
                    Methyltransf_9 175 eqlpe.leafdtvfsmGvlyhrrsPld..hllqlkdqlvkgGelvletlvie 223
                                        +lp   + fd v s+Gvl h        ++ ++   l +gG lvle   ++
  gi|298675674|ref|YP_003727424.1|  97 THLPFsDNIFDCVVSLGVLQHFYEHERelTIYEFSRVLASGGILVLEVFGVD 148
                                       ****96778**********996554441156789999**********99987 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   3.7e-09   4.4e-06       6     128 ..      19     138 ..      14     186 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 3.7e-09
                                       CCHHHHHHT-----HHHHHHCCCS-S-.EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEE CS
                              TehB   6 edyfskkynltathsevveavkivkpg.kvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknis 81 
                                       ++yf+ k+  ++    v      ++pg k+ld gcg+gr  l ls   y+vt +d   +++++ +   ek+n  +  
  gi|298675674|ref|YP_003727424.1|  19 QEYFHVKWGGSRSIEMVS---SRISPGhKILDAGCGNGRHLLPLSK-VYHVTGVDISPSALKNSKLHLEKNNCFA-Y 90 
                                       678888877665543333...346776599************9996.6***********************9994.5 PP

                                       EEE--GGG----S-.EEEEEEESSGG.GS-GGGHHHHHHHHHHTEEEEE CS
                              TehB  82 talydineaklder.ydfilstvvlm.fleaeripsiienmqectkvgg 128
                                        ++  + ++ ++++ +d ++s  vl  f e+er    i ++ +    gg
  gi|298675674|ref|YP_003727424.1|  91 QSVSTVTHLPFSDNiFDCVVSLGVLQhFYEHER-ELTIYEFSRVLASGG 138
                                       5677888888876549*****988861555554.444555555555555 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.3e-07   0.00016     151     232 ..      31     111 ..      28     143 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.3e-07
                              PrmA 151 clealeklvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseell.keek 226
                                       ++e++ + + +g+++lD G+G G   +  +k+   +v++vDi + A+k +k  +e+N++ a  +v +  +l+ +++ 
  gi|298675674|ref|YP_003727424.1|  31 SIEMVSSRISPGHKILDAGCGNGRHLLPLSKV--YHVTGVDISPSALKNSKLHLEKNNCFAYQSVSTVTHLPfSDNI 105
                                       78999999***************776666664..689**********************997778766666644688 PP

                              PrmA 227 adviva 232
                                       +d +v+
  gi|298675674|ref|YP_003727424.1| 106 FDCVVS 111
                                       999986 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   2.3e-07   0.00027      31     103 ..      41     111 ..      28     140 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.3e-07
                                       TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS-EEEEEE CS
                               MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeveekkfdlivs 103
                                         +k+lD GcG+G     l+  s+  +vt vd++  Al+ +k  le+n++   + v +     ++++ fd++vs
  gi|298675674|ref|YP_003727424.1|  41 PGHKILDAGCGNGRH---LLPLSKVYHVTGVDISPSALKNSKLHLEKNNCFaYQSVSTVTHLPFSDNIFDCVVS 111
                                       5789********975...5555556779********************98744444444444566788888875 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   3.4e-07   0.00041       5     118 ..      33     151 ..      30     220 .] 0.72

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3.4e-07
                              MetW   5 eliaelikpgsrvldlGcGdGellellkeekqvdgrGlelde.egvaecvakGlsviqgdldkdle.nfedksfdyv 79 
                                       e++   i pg ++ld GcG+G  l  l +  +v+g  +  ++ ++ +  ++k      + + +  +  f+d+ fd v
  gi|298675674|ref|YP_003727424.1|  33 EMVSSRISPGHKILDAGCGNGRHLLPLSKVYHVTGVDISPSAlKNSKLHLEKNNCFAYQSVSTVTHlPFSDNIFDCV 109
                                       688999****************999998888888777766652233334566666666666554431599999**99 PP

                              MetW  80 vlsqtlqatrnpke..vldellri.grraivsfPnfGhWrvr 118
                                       v    lq   + ++   + e  r+ +   i+ +  fG   +r
  gi|298675674|ref|YP_003727424.1| 110 VSLGVLQHFYEHERelTIYEFSRVlASGGILVLEVFGVDDMR 151
                                       999999987554431145566665344556666666666666 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.4e-06    0.0029      31      91 ..      36      91 ..      12     123 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.4e-06
                                      HT.T-S--EEEEEET-TT-HHHHHH-BTTEEEEEE-S-HHHHHHHHHHHTTSGGGGGEEEE CS
                              TPMT 31 dalkakaglrvlvPlCGkaldlvwlAeqgrevvGvelselAvekffeeanlepkvkelsgv 91
                                      ++ +  +g ++l  +CG++  l  l++  ++v Gv++s++A+++  ++ +l +k ++++ +
  gi|298675674|ref|YP_003727424.1| 36 SS-RISPGHKILDAGCGNGRHLLPLSK-VYHVTGVDISPSALKN--SKLHL-EKNNCFAYQ 91
                                      33.678999****************85.689***********99..33343.444444444 PP

>> CheR  CheR methyltransferase, SAM binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.11   1.3e+02      65      80 ..      63      78 ..      15      86 .. 0.69
   2 ?    9.5   0.0   0.00053      0.64     121     173 ..      87     142 ..      76     145 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.11
                                      EEEEEEESSCHHHHHH CS
                              CheR 65 vkilAtDidlkvlekA 80
                                      ++++++Di+ ++l++ 
  gi|298675674|ref|YP_003727424.1| 63 YHVTGVDISPSALKNS 78
                                      4566667776666665 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00053
                                       EEEE--TTT..-SGGG--.EEEEEE-SSGGGC-CHHHHHHHHHHHCCEEEEEEEEE CS
                              CheR 121 kFeklnlle..kksvlgk.lDvifcrnvliYfdeetqekvlerfaeklkpgglLll 173
                                       +F+++ + +  + +++++ +D +++  vl  f e+++e  + +f++ l+ gg+L+l
  gi|298675674|ref|YP_003727424.1|  87 CFAYQSVSTvtHLPFSDNiFDCVVSLGVLQHFYEHERELTIYEFSRVLASGGILVL 142
                                       56666555543344444349**********************************97 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   7.2e-05     0.086       5      66 ..      32      90 ..      29     114 .. 0.80
   2 ?   -1.8   0.1       2.2   2.6e+03     122     146 ..     178     202 ..     175     204 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.2e-05
                   Methyltransf_18  5 LkaiaslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledk 66
                                      ++++ s +++g++++D G+  g    +l+  +k+ +v+ +Di++++l+++k ++ek+++   
  gi|298675674|ref|YP_003727424.1| 32 IEMVSSRISPGHKILDAGCGNGR---HLLPLSKVYHVTGVDISPSALKNSKLHLEKNNCFAY 90
                                      688999***************97...556666899*********************998544 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.2
                   Methyltransf_18 122 eelRkylvengfkiedEelvkeegk 146
                                       +e+++ l + +f+i+d + +k e++
  gi|298675674|ref|YP_003727424.1| 178 KEIKSLLEKYKFQITDITNIKTEKR 202
                                       5788889999999998887777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1455.02
//
Query:       gi|298675675|ref|YP_003727425.1|  [L=85]
Description: hypothetical protein Metev_1793 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.8e-11   41.7  25.1    1.1e-10   41.5  25.1    1.0  1  BofA      SigmaK-factor processing regulatory protein BofA
  ------ inclusion threshold ------
        7.2    5.2   7.6        7.9    5.0   7.6    1.2  1  Tweety    Tweety
          8    6.8  11.0       0.59   10.4   4.5    1.9  2  DUF2530   Protein of unknown function (DUF2530)


Domain annotation for each model (and alignments):
>> BofA  SigmaK-factor processing regulatory protein BofA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5  25.1   1.9e-14   1.1e-10       2      74 ..      11      80 ..      10      81 .. 0.97

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 1.9e-14
                              BofA  2 gilllllvikllkkplkillkllinavlGlvlLflvNllgavfglhipiNlitaliagflGipGvilLillkl 74
                                      +i+++++++ +l+  lk + kl+in+v+Glv+L+ +N   +vfgl i++++i  li++++Gi+G++l+ill++
  gi|298675675|ref|YP_003727425.1| 11 VIVIAIIAAVVLYILLKSVKKLIINTVMGLVVLIGAN---IVFGLGIAYSWIVFLICAIGGIFGALLIILLNY 80
                                      589999*******************************...9******************************98 PP

>> Tweety  Tweety
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   7.6    0.0013       7.9     194     241 ..      12      58 ..       7      80 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0013
                            Tweety 194 lldlviClvlllglarkskcllivvsvlgllalvlsWaslglelasav 241
                                       ++  +i +v+l  l ++ k  li+ +v+gl++l+ +  + gl +a + 
  gi|298675675|ref|YP_003727425.1|  12 IVIAIIAAVVLYILLKSVKK-LIINTVMGLVVLIGANIVFGLGIAYSW 58 
                                       45567777888778877776.666799****************99885 PP

>> DUF2530  Protein of unknown function (DUF2530)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   4.5   9.9e-05      0.59      13      58 ..       5      48 ..       3      55 .. 0.74
   2 ?   -0.3   2.4      0.21   1.3e+03      38      54 ..      57      73 ..      42      79 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 9.9e-05
                           DUF2530 13 prpvivvgtllWlvalvvllvvgdaleswlpvclaGlvvGllGlai 58
                                      p+p + v++++ ++a+v+ +++ +++++++  +++Glvv l+G  i
  gi|298675675|ref|YP_003727425.1|  5 PTPELSVIVIAIIAAVVL-YILLKSVKKLIINTVMGLVV-LIGANI 48
                                      567777777776555555.55569*************99.666665 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.21
                           DUF2530 38 leswlpvclaGlvvGll 54
                                         ++ +c++G + G+l
  gi|298675675|ref|YP_003727425.1| 57 SWIVFLICAIGGIFGAL 73
                                      33457788888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1324  (0.0738468); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 528.17
//
Query:       gi|298675676|ref|YP_003727426.1|  [L=147]
Description: hypothetical protein Metev_1794 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-07   30.6   0.0    3.2e-07   30.4   0.0    1.1  1  Nuc_deoxyrib_tr  Nucleoside 2-deoxyribosyltransferase
  ------ inclusion threshold ------
      0.044   12.9   0.2      0.049   12.7   0.2    1.2  1  Prenylcys_lyase  Prenylcysteine lyase


Domain annotation for each model (and alignments):
>> Nuc_deoxyrib_tr  Nucleoside 2-deoxyribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   3.6e-11   3.2e-07       1     106 [.       3     104 ..       3     129 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 3.6e-11
                                       EEEESGGGCSCCCHHHHHHHHHHHHTTTTEEE-CCTT-TT.....--SSHHHHHHHHHHHHHC-SEEEEE--SSSSS CS
                   Nuc_deoxyrib_tr   1 iYLAgplvFrpdakalaarlkallaengldglaPldneaelel.paeetaraiyeadialirqaDavianldpfrgp 76 
                                       +++ g++   +d    ++++ +ll ++g++++     + +le+ ++e  +++i+++d+ li+ +D++ia ++     
  gi|298675676|ref|YP_003727426.1|   3 VFFSGSIRGGRDMLPVYNHICNLLYNHGFRVMSWHVVDSNLEDtESEMSEQEIFKRDAGLIDMSDLLIAEVSV---- 75 
                                       678899989999999**************87765545555566689999************************.... PP

                                       S--HHHHHHHHHHHHCT-EEEEE-S-GCGH CS
                   Nuc_deoxyrib_tr  77 eaDsGtafEvGyavalgkpvlayttdarel 106
                                        +  G+ +E+  a++ + pv+++ +   ++
  gi|298675676|ref|YP_003727426.1|  76 -PSIGVGYEICHAISKNVPVICLHKSGSNV 104
                                       .89********************9887774 PP

>> Prenylcys_lyase  Prenylcysteine lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   5.5e-06     0.049      80     154 ..      64     142 ..      21     147 .] 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.5e-06
                   Prenylcys_lyase  80 gisekfinelvqavlrvnYgqsvkinalvgavslAgaqsglwavegGn...kqvcsgllkkskanv.inatVtsiel 152
                                       ++s+ +i e+  +++ v Y     i+  v +++l  + s++ +   Gn   k+++++ l++ + n  i++++tsi+ 
  gi|298675676|ref|YP_003727426.1|  64 DMSDLLIAEVSVPSIGVGYEICHAISKNVPVICLHKSGSNVSSMVLGNtydKLIVAQYLNTDELNKiIQNSITSITS 140
                                       6899*******************************************977679******99996555********98 PP

                   Prenylcys_lyase 153 ks 154
                                       ++
  gi|298675676|ref|YP_003727426.1| 141 EE 142
                                       54 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1012.21
//
Query:       gi|298675677|ref|YP_003727427.1|  [L=817]
Description: peptidase U32 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.9e-122  406.8   0.0    1.2e-84  283.1   0.0    2.2  2  Peptidase_U32  Peptidase family U32
    9.4e-26   90.6   0.3    2.7e-25   89.1   0.3    1.8  1  DUF3656        Collagenase
  ------ inclusion threshold ------
      0.034   14.1   0.0        2.4    8.1   0.0    2.8  2  Phage_Coat_B   Phage Coat protein B


Domain annotation for each model (and alignments):
>> Peptidase_U32  Peptidase family U32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  283.1   0.0     2e-88   1.2e-84       2     231 ..      77     300 ..      76     302 .. 0.97
   2 !  121.7   0.0   4.4e-39   2.6e-35       1     198 [.     604     792 ..     604     813 .. 0.93

  Alignments for each domain:
  == domain 1  score: 283.1 bits;  conditional E-value: 2e-88
                     Peptidase_U32   2 eklrkyleklaelgvdavivqDpgvlelareeapelelhlStqanitnseavrflkelGasrvvlaRElsleeikai 78 
                                       e++ ++l  l+++g+davi+qD+g+++lar+ +pel++h+Stq++++n e+vrfl+++G+ rv+laRElslee++ i
  gi|298675677|ref|YP_003727427.1|  77 EDAVNLLYYLHDIGADAVILQDLGLITLARKLVPELPVHASTQMTVHNLESVRFLEDMGVGRVILARELSLEELEYI 153
                                       77889999********************************************************************* PP

                     Peptidase_U32  79 kekvpdvelEvfvhGalcvaysGrcllssylsgrsanrgecaqpcrldyrlieekekgeeepieedekgtyllspkd 155
                                       ++++  v +E+fvhGalc++ysG+cl+ss+++grs+nrg caqpcr++y+l+++++k e         g+yllspkd
  gi|298675677|ref|YP_003727427.1| 154 TKNT-AVGIETFVHGALCISYSGQCLFSSMIGGRSGNRGFCAQPCRKKYNLYKDGKKVETS-------GKYLLSPKD 222
                                       ****.**************************************************998887.......669****** PP

                     Peptidase_U32 156 lclieelpelleaGvdslKIeGRmkspeyvatvvrvYreaidallagr..eevkeelkeeleklanrgltsgfllgr 230
                                       l++ + lpel++  vd++KIeGRmk+peyva vv++Yr++id++++++  +  + +  ++l +l+nr++t+++ll++
  gi|298675677|ref|YP_003727427.1| 223 LNTAKILPELINTEVDAFKIEGRMKRPEYVAGVVSIYRKLIDRYVENPsdYYISDNELKQLGQLFNRDFTTAYLLNK 299
                                       ************************************************9988899999****************988 PP

                     Peptidase_U32 231 k 231
                                       +
  gi|298675677|ref|YP_003727427.1| 300 P 300
                                       6 PP

  == domain 2  score: 121.7 bits;  conditional E-value: 4.4e-39
                     Peptidase_U32   1 leklrkyleklaelgvdavivqDpgvlelareeapelelhlStqanitnseavrflkelGasrvvlaRElsleeika 77 
                                       +++++k l+++++++ d+v+v+ +gvl++a+ +  +l++ +++  ni n  +++f+ + Ga++vvl+ El++++ik 
  gi|298675677|ref|YP_003727427.1| 604 MDDIKKSLARAKSNNFDGVMVSNLGVLKVAKSM--NLPVIVNASLNIFNKISFDFMLKCGAEKVVLSPELTIDQIKS 678
                                       6899*****************************..****************************************** PP

                     Peptidase_U32  78 ikekvpdvelEvfvhGalcvaysGrcllssylsgrsanrgecaqpcrl.dyrlieekekgeeepieedek.gtylls 152
                                       +  k    + E+ vhG l v++s  c++   ++     + +c  pcr+ +y++++ek      p e de+  t++ +
  gi|298675677|ref|YP_003727427.1| 679 VSSKG---QAECIVHGPLEVMVSEYCFVGDIFGS----KKSCGYPCRNsEYEIVDEKGYS--FPLEMDENcRTHIYN 746
                                       ***99...8**********************888....89************99998754..44455555146**** PP

                     Peptidase_U32 153 pkdlclieelpelleaGvdslKIeGRmkspeyvatvvrvYreaida 198
                                       ++ lc++++++++l+  v+s++I   +++p yv++ +++Y++a++ 
  gi|298675677|ref|YP_003727427.1| 747 SRNLCMLDNIDDILKSDVASIRINAGTYEPFYVEKLTKTYKKAVNG 792
                                       *******************************************975 PP

>> DUF3656  Collagenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.1   0.3   4.5e-29   2.7e-25       1     106 [.     388     506 ..     388     507 .. 0.96

  Alignments for each domain:
  == domain 1  score: 89.1 bits;  conditional E-value: 4.5e-29
                           DUF3656   1 vyrtsdkklteelekslek.seerkipvdlelaakegeplkltvtde...........leeAkkrplteenirkqLs 65 
                                       vy+t+dk+l+e+lek++++  + rkipv++ ++a +g++l+l+++d            +e A ++p+++++i+kq+ 
  gi|298675677|ref|YP_003727427.1| 388 VYKTFDKHLNESLEKTFTSsVPARKIPVSIIVKAFSGSNLELQISDGtnnvsvvsdyvVENALSKPTSKKQIEKQIA 464
                                       8******************999**********************9779***************************** PP

                           DUF3656  66 klGgtpFeleeieidld.glfiPvseLnelRRealekLeear 106
                                       k+G+t F  +ei+i++d ++fiP+s+Ln ++ +a+ +Le++r
  gi|298675677|ref|YP_003727427.1| 465 KMGNTVFDPSEITIHTDnKIFIPISQLNSIKNKAITRLEKKR 506
                                       **************999455********************98 PP

>> Phage_Coat_B  Phage Coat protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.023   1.4e+02      38      65 ..     420     447 ..     401     451 .. 0.75
   2 ?    8.1   0.0    0.0004       2.4      15      52 ..     519     556 ..     509     561 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.023
                      Phage_Coat_B  38 svidtsavesaitdgksdmkaiggyivg 65 
                                            s +e  i+dg ++++ +  y+v 
  gi|298675677|ref|YP_003727427.1| 420 KAFSGSNLELQISDGTNNVSVVSDYVVE 447
                                       34567999*****************995 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0004
                      Phage_Coat_B  15 asfrnlciagsvtaasslpvfaasvidtsavesaitdg 52 
                                        s+r    + s+t+ ss p  a +v+ t  +esa++ g
  gi|298675677|ref|YP_003727427.1| 519 ESYRMYLNSDSITSRSSSPQIAVNVVSTKQLESAVSGG 556
                                       5788888899************************9977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (817 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       865  (0.0482459); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.76u 0.27s 00:00:01.03 Elapsed: 00:00:00.45
# Mc/sec: 5428.84
//
Query:       gi|298675678|ref|YP_003727428.1|  [L=83]
Description: hypothetical protein Metev_1796 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        2.5    7.7   4.6        3.3    7.4   0.1    2.0  2  DUF2981   Protein of unknown function (DUF2981)


Domain annotation for each model (and alignments):
>> DUF2981  Protein of unknown function (DUF2981)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1   0.00018       3.3     265     305 ..       4      43 ..       2      59 .. 0.84
   2 ?    2.1   1.3    0.0076   1.4e+02       7      25 ..      62      80 ..      57      82 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00018
                           DUF2981 265 kdLtpegksevvaiykiqkRpvklaaaglltvlllfnlYsy 305
                                        d t +++s  +++    k+ v +a a  ++vl+lf++Y+ 
  gi|298675678|ref|YP_003727428.1|   4 SDTTDNSQSRTIVMEDYFKKGV-FALAIGFMVLALFQIYFL 43 
                                       578999**************99.677777788999****85 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.0076
                           DUF2981  7 iafqqlLlGvslYlvlhYL 25
                                        f  +++G+slY++  YL
  gi|298675678|ref|YP_003727428.1| 62 ALFNLVVFGISLYIIRLYL 80
                                      55677899*******9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 564.78
//
Query:       gi|298675679|ref|YP_003727429.1|  [L=317]
Description: hypothetical protein Metev_1797 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2073.70
//
Query:       gi|298675680|ref|YP_003727430.1|  [L=273]
Description: imidazoleglycerol phosphate synthase cyclase subunit [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-87  292.0   0.4    3.3e-87  291.8   0.4    1.0  1  His_biosynth  Histidine biosynthesis protein
    9.7e-07   28.3   0.2     0.0065   15.8   0.0    2.2  2  ThiG          Thiazole biosynthesis protein ThiG
    5.6e-06   26.0   0.7      0.018   14.5   0.1    2.2  2  NMO           Nitronate monooxygenase
      5e-05   22.8   0.2     0.0014   18.1   0.1    2.1  2  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
    0.00019   20.7   0.1    0.00066   18.9   0.0    1.8  2  Dus           Dihydrouridine synthase (Dus)
    0.00058   19.2   0.1      0.056   12.6   0.1    2.1  2  DHO_dh        Dihydroorotate dehydrogenase
    0.00064   18.8   0.7       0.13   11.2   0.1    2.1  2  IMPDH         IMP dehydrogenase / GMP reductase domain
     0.0037   16.6   0.3       0.24   10.7   0.1    2.2  2  TMP-TENI      Thiamine monophosphate synthase
  ------ inclusion threshold ------
       0.02   14.3   0.0      0.037   13.4   0.0    1.3  1  SBP_bac_3     Bacterial extracellular solute-binding proteins


Domain annotation for each model (and alignments):
>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  291.8   0.4   1.6e-90   3.3e-87       1     229 []       5     256 ..       5     256 .. 0.95

  Alignments for each domain:
  == domain 1  score: 291.8 bits;  conditional E-value: 1.6e-90
                                       EEEEEEEE....ETTEEEEECTTCSTCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-S CS
                      His_biosynth   1 riipalDl....kdGkvVrlvkGdrfqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevf 73 
                                       riip+lD+    + G vV   kG++f +lr+agdpve+ak y+e+gade++++D++a++egr +++d++e++a+evf
  gi|298675680|ref|YP_003727430.1|   5 RIIPCLDVtldsEGGTVV---KGVEFFNLRHAGDPVEFAKLYNEQGADEIVFLDITASHEGRATMIDVIERTADEVF 78 
                                       8*******9994555666...******************************************************** PP

                                       SEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEE..C............... CS
                      His_biosynth  74 ipvqvGGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarr..g............... 133
                                       ip++vGGG+ s+edv+++l+agadkv+i+t+avknp+like ++ fgsq+iv aiD++r  +               
  gi|298675680|ref|YP_003727430.1|  79 IPLTVGGGVGSVEDVRQILRAGADKVSINTSAVKNPNLIKETSDIFGSQCIVTAIDCKRntNvadnsdktiltledg 155
                                       ***********************************************************661555667778888889 PP

                                       ....EEEEETTTTEEEEEEHHHHHHHHHHTT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHH CS
                      His_biosynth 134 ....ykvaikgwreetgldavelakkleelgageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledl 206
                                           y+v+i+g+r+ tg+dav++akk+ elg gei+lt++drdGt +G+d+++t++++e+v++p+iasGG+g+++++
  gi|298675680|ref|YP_003727430.1| 156 tpawYEVVIYGGRKPTGVDAVQWAKKVVELGSGEIMLTSMDRDGTYDGFDVPVTRAVSESVEVPIIASGGAGNPQHM 232
                                       9**************************************************************************** PP

                                       HHHHHTTC.SEEEESHHHHTTSS- CS
                      His_biosynth 207 kelksegv.davivgsalyegelt 229
                                       +e +++g+ da++++s++++ge+t
  gi|298675680|ref|YP_003727430.1| 233 YEGFTSGKaDAALAASIFHFGEYT 256
                                       *********************986 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   3.2e-06    0.0065     160     211 ..      62     114 ..      23     148 .. 0.78
   2 !   10.7   0.0   0.00012      0.24     134     203 ..     176     246 ..     169     253 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.2e-06
                                       --S-H.HHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSS CS
                              ThiG 160 Gllnk.ealkiiieeakvPvivDAGigspsdaaqamelGadavllntavaeak 211
                                       G +++  +++   +e+ +P+ v  G+gs +d+ q +  Gad v +nt+  +  
  gi|298675680|ref|YP_003727430.1|  62 GRATMiDVIERTADEVFIPLTVGGGVGSVEDVRQILRAGADKVSINTSAVKNP 114
                                       44443145677778889*****************************9765554 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00012
                                       HHHHHHHHHTT-SEBEEBSS.STTS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT.-SEEEE CS
                              ThiG 134 lvlarrleevGcaavmPlaa.piGsglGllnkealkiiieeakvPvivDAGigspsdaaqamelG.adavll 203
                                       +  a+++ e+G   +m  +    G+  G   +   + + e+++vP+i   G g+p++  + +  G ada l 
  gi|298675680|ref|YP_003727430.1| 176 VQWAKKVVELGSGEIMLTSMdRDGTYDGFDVPV-TRAVSESVEVPIIASGGAGNPQHMYEGFTSGkADAALA 246
                                       457999999999999976651568888987775.58999*******************99999984456554 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   8.9e-06     0.018     170     223 ..      60     108 ..      35     113 .. 0.78
   2 !   10.0   0.1    0.0002       0.4     183     224 ..     207     248 ..     170     268 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8.9e-06
                               NMO 170 hqGtpevgdkglfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigt 223
                                       h+G ++      + ++++ +d v iP+   GG+   ++v  +L++GA  v i t
  gi|298675680|ref|YP_003727430.1|  60 HEG-RA----TMIDVIERTADEVFIPLTVGGGVGSVEDVRQILRAGADKVSINT 108
                                       555.22....36788888899999**************************9988 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0002
                               NMO 183 aLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtr 224
                                        +   v + v++P+iA GG  + + +   ++ G + +++++ 
  gi|298675680|ref|YP_003727430.1| 207 PVTRAVSESVEVPIIASGGAGNPQHMYEGFTSGKADAALAAS 248
                                       46778999***********99988888888888776666665 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   6.9e-07    0.0014     126     170 ..      65     109 ..      64     111 .. 0.92
   2 ?    2.4   0.0     0.045        89     130     156 ..     208     234 ..     203     246 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 6.9e-07
                                       GGHHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE--H CS
                      G3P_antiterm 126 lvpkvikeikkelkipiiaGGLietkedveealkaGaiavstsnk 170
                                       ++ +vi+++ +e+ ip+  GG + + edv+++l+aGa+ vs  ++
  gi|298675680|ref|YP_003727430.1|  65 TMIDVIERTADEVFIPLTVGGGVGSVEDVRQILRAGADKVSINTS 109
                                       6899************************************98665 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.045
                                       HHCTSTTS...EEEEESS--SHHHHHH CS
                      G3P_antiterm 130 vikeikkelkipiiaGGLietkedvee 156
                                       v++++++++++piia+G   + +++ e
  gi|298675680|ref|YP_003727430.1| 208 VTRAVSESVEVPIIASGGAGNPQHMYE 234
                                       678999**********97766666665 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   3.3e-07   0.00066     166     227 ..      62     122 ..      32     151 .. 0.76
   2 ?   -0.8   0.0      0.33   6.6e+02     176     198 ..     210     232 ..     173     247 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.3e-07
                                       T-CG--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHH.HH CS
                               Dus 166 yegtadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfae.st 227
                                        +    ++ I+   ++v ip+ + G++ ++ed+++il+  Gad v i   a +nP+l++e s 
  gi|298675680|ref|YP_003727430.1|  62 GR-ATMIDVIERTADEVFIPLTVGGGVGSVEDVRQILRA-GADKVSINTSAVKNPNLIKEtSD 122
                                       33.345778889999999********************9.******************97443 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.33
                                       HHHHHH-SS-EEEESS--SHHHH CS
                               Dus 176 kevkqavsipviaNGdIkdaeda 198
                                       ++v ++v++p+ia G+  +++ +
  gi|298675680|ref|YP_003727430.1| 210 RAVSESVEVPIIASGGAGNPQHM 232
                                       67889999999999987777766 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   2.8e-05     0.056     232     279 ..      68     113 ..      62     123 .. 0.77
   2 !    4.4   0.0     0.009        18     235     291 ..     210     264 ..     205     267 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.8e-05
                                       HHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHH CS
                            DHO_dh 232 kvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfe 279
                                        vi + ++++   ip+   GG+ s eD+   ++aGA  v + t  v++
  gi|298675680|ref|YP_003727430.1|  68 DVIERTADEVF--IPLTVGGGVGSVEDVRQILRAGADKVSINTSAVKN 113
                                       44444444444..899999************************99665 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.009
                                       HHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHHH CS
                            DHO_dh 235 relykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikkel 291
                                       r++++ ++  +piI++GG    +  +e ++ G +  ++ + +   g + ++ +k+ l
  gi|298675680|ref|YP_003727430.1| 210 RAVSESVE--VPIIASGGAGNPQHMYEGFTSGKADAALAASIFHFGEYTVPGVKEYL 264
                                       56666666..**********9999999999997777777666666666666666665 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.1   6.7e-05      0.13     109     172 ..      40     106 ..      30     109 .. 0.71
   2 !    6.2   0.1    0.0022       4.4     196     238 ..     206     249 ..     171     267 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.7e-05
                                       HHHHHHTT-S.EEEEE-STSS..SHHHHHHHHHHHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEEEE CS
                                       xxxxxxxxxx.xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 109 vkalveagvd.vlvvdsahgh..sekvleavkeikkkveeveviaGnvataegakaLieagadavkv 172
                                       +k   e+g+d ++++d++  h   +++++++++  ++v     ++G v + e ++++++agad v +
  gi|298675680|ref|YP_003727430.1|  40 AKLYNEQGADeIVFLDITASHegRATMIDVIERTADEVFIPLTVGGGVGSVEDVRQILRAGADKVSI 106
                                       556667888734557765555114567777777776664334689******************9976 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0022
                                       HHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT.-SEEEESCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                             IMPDH 196 vaevaeaakkagvpviaDGGikysgdivkAlaaG.adavmlGsl 238
                                       v  + ++ ++ +vp+ia GG  + +++   ++ G ada +  s+
  gi|298675680|ref|YP_003727430.1| 206 VPVTRAVSESVEVPIIASGGAGNPQHMYEGFTSGkADAALAASI 249
                                       444556778889***************99999985666665555 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1   0.00012      0.24     112     177 ..      43     106 ..      33     110 .. 0.81
   2 ?    4.2   0.0     0.012        23     122     164 ..     187     232 ..     171     249 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00012
                          TMP-TENI 112 aealgadYigvGpifpTdtKkdaeplgleglkelaealeiPvvaiGGit.lenvaevleagadgvav 177
                                        +++gad i++  i  T++++++ +  ++ ++++a+++ iP+ + GG+   e+v ++l+agad v++
  gi|298675680|ref|YP_003727430.1|  43 YNEQGADEIVFLDI--TASHEGR-ATMIDVIERTADEVFIPLTVGGGVGsVEDVRQILRAGADKVSI 106
                                       56777777777777..7777776.566999******************7269************986 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.012
                          TMP-TENI 122 vGpifpTdtKkda..eplgleglkelaealeiPvvaiGGi.tlenv 164
                                        G i+ T+   d   +  ++   ++++e++e+P++a GG  +++++
  gi|298675680|ref|YP_003727430.1| 187 SGEIMLTSMDRDGtyDGFDVPVTRAVSESVEVPIIASGGAgNPQHM 232
                                       56666666655553444556678999*************7345555 PP

>> SBP_bac_3  Bacterial extracellular solute-binding proteins, family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.9e-05     0.037      14      65 ..     194     247 ..     192     250 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.9e-05
                                       EE-TTS-EESHHHHHHHHHHHHCT-EEEEEE.-.SGGGHHHHHHTTSSSEEESS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x.xxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3  14 ykdengeltGfdvdlakaiakrlgvkvefvp.v.swdelipalksgkvDiaiaa 65 
                                        +d +g++ Gfdv + +a+ ++  v +       + +++ ++ +sgk+D+a aa
  gi|298675680|ref|YP_003727430.1| 194 SMDRDGTYDGFDVPVTRAVSESVEVPIIASGgAgNPQHMYEGFTSGKADAALAA 247
                                       5789*******************99955554656****************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 1535.03
//
Query:       gi|298675681|ref|YP_003727431.1|  [L=235]
Description: hypothetical protein Metev_1799 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-57  192.9  13.1      4e-57  192.9  13.1    1.8  2  DUF1614   Protein of unknown function (DUF1614)


Domain annotation for each model (and alignments):
>> DUF1614  Protein of unknown function (DUF1614)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.4     0.058     1e+03      62      92 ..      16      41 ..       5      49 .. 0.52
   2 !  192.9  13.1   2.2e-61     4e-57       1     170 []      56     234 ..      56     234 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.058
                           DUF1614 62 lrlavsllaallavlivaavvyllarpvpgv 92
                                      +     ll ++l+v++ ++   l+++    +
  gi|298675681|ref|YP_003727431.1| 16 F-----LLLIILSVIVGILFFSLVSTAFTKI 41
                                      2.....3334444444444444444444444 PP

  == domain 2  score: 192.9 bits;  conditional E-value: 2.2e-61
                           DUF1614   1 llgslinipvaelkskeelve...vkvlgisykvpvleeeekktvvavNvGGaviPlllslylllrlavsllaalla 74 
                                       l+gs +nipv++lks++++ve   v+++g+ yk+p+ ++ +k+t++avN+GGaviP l+slylll ++ +++ ++++
  gi|298675681|ref|YP_003727431.1|  56 LFGSHVNIPVTKLKSSKPVVEresVRFMGMVYKLPFKKAVQKQTTLAVNLGGAVIPGLVSLYLLLIFPEAFFYSIAG 132
                                       79*************886644479********************************************99******* PP

                           DUF1614  75 vlivaavvyllarpvpgvGivvpllipplvaalaa.lllaeeea.....aavaYisgvlGtLiGadllnlkkieklg 145
                                       +l+v++v+y +++pv+gvGiv+p+l++p++aal+a l+++  +      +++aY++g+lGtLiGad++nl+ki+++g
  gi|298675681|ref|YP_003727431.1| 133 ILLVSVVTYSISKPVKGVGIVTPVLVSPIAAALSAiLIVSVFSVppdliFVIAYTGGTLGTLIGADIFNLDKIRDIG 209
                                       ***********************************666666555999999*************************** PP

                           DUF1614 146 apvvsIGGaGtFdGifltgilavll 170
                                       apv+sIGGaGtFdGifl+g++avll
  gi|298675681|ref|YP_003727431.1| 210 APVASIGGAGTFDGIFLAGVIAVLL 234
                                       ***********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1063  (0.0592894); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 1367.34
//
Query:       gi|298675682|ref|YP_003727432.1|  [L=146]
Description: hypothetical protein Metev_1800 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-40  138.3   0.1    1.2e-40  138.2   0.1    1.0  1  DNase-RNase  Bifunctional nuclease


Domain annotation for each model (and alignments):
>> DNase-RNase  Bifunctional nuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.2   0.1   6.6e-45   1.2e-40       5     128 ..      12     134 ..       5     135 .. 0.91

  Alignments for each domain:
  == domain 1  score: 138.2 bits;  conditional E-value: 6.6e-45
                                       EEEETTTTEEEEEEEETTSSEEEEEE--HHHHHHHHHHHCT---SS--HHHHHHHHHHHTTEEEEEEEEEEEETTEE CS
                       DNase-RNase   5 ialdassqspvvlLreeegrrvlpIwigaaeaqaialalegeeppRPlthDLlasllealgakvervvItdledgtf 81 
                                       +++ +  ++p vlL++++gr ++pI+ig+ ea +i++ l++e++pRP+thDL++s+l++l+++v ++ I+d  ++t+
  gi|298675682|ref|YP_003727432.1|  12 VRVREGFGAPTVLLEDSTGR-IMPIYIGHPEALSINMVLNQETMPRPMTHDLMISILDRLETDVVNIFIDDKIENTY 87 
                                       344444479**********9.******************************************************** PP

                                       EEEEEEEET---EEEEE-HHHHHHHHHHHT--EEEEHHHHHHH-EE- CS
                       DNase-RNase  82 yAelvlrkeeeeleidaRpSDaiaLAlrtgapIyveeevleeasiev 128
                                       yA+lv++++  +++idaRpSD+iaLAlr +apIyv+e+++e+ +i+ 
  gi|298675682|ref|YP_003727432.1|  88 YARLVINRDGLSMDIDARPSDCIALALRSEAPIYVKEDIFESVAIDK 134
                                       *******97444*****************************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 975.52
//
Query:       gi|298675683|ref|YP_003727433.1|  [L=426]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-18   65.9   0.3    2.3e-18   65.9   0.3    1.9  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    1.9e-13   50.7   1.7    3.6e-13   49.8   1.7    1.5  1  OrfB_IS605      Probable transposase
    3.5e-08   32.8   0.1    6.8e-08   31.9   0.1    1.5  1  HTH_OrfB_IS605  Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.2       1.3   7.5e+03      43      58 ..     226     241 ..     221     241 .. 0.74
   2 !   65.9   0.3   3.8e-22   2.3e-18       2      67 ..     315     379 ..     314     381 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.3
                    OrfB_Zn_ribbon  43 sgrtfkCpnCgfeadr 58 
                                       ++ + ++++C+ + +r
  gi|298675683|ref|YP_003727433.1| 226 NQAKSRRDHCKKYSHR 241
                                       6677788889888887 PP

  == domain 2  score: 65.9 bits;  conditional E-value: 3.8e-22
                    OrfB_Zn_ribbon   2 rklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNil 67 
                                       ++++e+l yk + +G+++++++++yTSk C +Cg++++ +l +r++ C+ Cg e+drD n+aiNi+
  gi|298675683|ref|YP_003727433.1| 315 SRFIEFLTYKSEFAGKQLTKIDESYTSKICYVCGKVHDMPLYKRNLSCD-CGNEIDRDKNSAINIM 379
                                       589**********************************************.***************8 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.8   1.7   6.1e-17   3.6e-13       2     118 ..     173     292 ..     172     294 .. 0.94

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 6.1e-17
                        OrfB_IS605   2 ipvevevelpkpkgnkaagiDlGinnLatvvtedgtw.flykgrrlksdykylakeiaelqsklkksknykkasrkl 77 
                                       +++e  ++++ ++++k  +iDlGi + +t v++dg+  +++++r+ k   k+ ++++ + + ++k s+++ +    +
  gi|298675683|ref|YP_003727433.1| 173 VVYETFPQTNYKDNEKNQAIDLGITKTITAVNTDGKIlEITNPRFDKYWDKKINQAKSRRDHCKKYSHRWFRINDAI 249
                                       68898899999999**********************99*************************************** PP

                        OrfB_IS605  78 arlhrkrsrrrkhllhklathliktlkev..gvetLnvgnmkd 118
                                       + + +k ++++k+ +hkl+++ +++   +   v++L+v++m++
  gi|298675683|ref|YP_003727433.1| 250 RVMTKKKNNQIKDWQHKLSRKMVDNTRLNtiIVGDLDVKDMTN 292
                                       ***********************976555449*********96 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.1   1.1e-11   6.8e-08       1      47 []       1      46 [.       1      46 [. 0.97

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 1.1e-11
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeegk 47
                                      M l++ ky ++PT eQ   l++    + + YN  L+erkea+++e+k
  gi|298675683|ref|YP_003727433.1|  1 M-LLTKKYKIKPTSEQLDVLWKLSKRCTLLYNLSLSERKEAWKHERK 46
                                      7.8999*************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1234  (0.068827); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2926.54
//
Query:       gi|298675684|ref|YP_003727434.1|  [L=142]
Description: transposase IS200-family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-35  121.1   0.3      3e-35  120.9   0.3    1.0  1  Y1_Tnp    Transposase IS200 like


Domain annotation for each model (and alignments):
>> Y1_Tnp  Transposase IS200 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.9   0.3   1.7e-39     3e-35       1     121 []      12     132 ..      12     132 .. 0.97

  Alignments for each domain:
  == domain 1  score: 120.9 bits;  conditional E-value: 1.7e-39
                            Y1_Tnp   1 vsnlkyhivlvtkyRrkvltge.veerlkeiikeiaekkevkilelelmpDHvHllvelppklsiskivkalkgass 76 
                                       v++l+yh+v ++kyRr+ l++  v + lk  i ei+++++v++l++e+++DH+H++++ +p+l+i+k+++++k+ +s
  gi|298675684|ref|YP_003727434.1|  12 VYSLNYHFVQCVKYRRNALKNPdVVDLLKRKIYEISQTFDVDVLNIECDEDHFHMIFKSNPSLDIPKYINSVKSITS 88 
                                       689*******************9****************************************************** PP

                            Y1_Tnp  77 rlinkefpelkkkklkkeslWqrgYfvstvgeasletvkrYIenq 121
                                       r i++++pe+k ++l k ++W+r+Yf++t+g+++l+++krYI+nq
  gi|298675684|ref|YP_003727434.1|  89 REIRRNYPEVK-EMLGKDAFWSRSYFLATTGQVTLDVLKRYIDNQ 132
                                       *********88.6688899************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 872.77
//
Query:       gi|298675685|ref|YP_003727435.1|  [L=216]
Description: protein-L-isoaspartate O-methyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.6e-71  238.4   0.0    7.9e-71  238.1   0.0    1.0  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    3.8e-12   46.2   0.0    5.5e-12   45.7   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    2.4e-07   30.7   0.0      3e-07   30.4   0.0    1.1  1  GCD14            tRNA methyltransferase complex GCD14 subunit
      4e-07   29.6   0.0    5.2e-07   29.2   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    5.1e-07   30.3   0.0    8.8e-07   29.6   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    2.2e-06   27.5   0.0    3.5e-06   26.8   0.0    1.4  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    2.6e-06   26.7   0.0    3.5e-06   26.3   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
    2.7e-05   23.4   0.1    3.9e-05   22.9   0.1    1.2  1  Fibrillarin      Fibrillarin
     0.0015   19.1   0.0     0.0046   17.6   0.0    1.8  1  Methyltransf_11  Methyltransferase domain
     0.0018   17.5   0.0     0.0025   17.0   0.0    1.2  1  Methyltransf_3   O-methyltransferase
     0.0044   17.0   0.0      0.006   16.6   0.0    1.1  1  Methyltransf_32  Methyltransferase domain
     0.0047   16.5   0.0     0.0076   15.8   0.0    1.3  1  MTS              Methyltransferase small domain
     0.0068   16.2   0.0     0.0098   15.7   0.0    1.2  1  Met_10           Met-10+ like-protein
  ------ inclusion threshold ------
      0.014   16.4   0.0      0.026   15.5   0.0    1.4  1  Methyltransf_24  Methyltransferase domain
      0.016   14.5   0.0      0.022   14.1   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
      0.084   12.7   0.0       0.21   11.4   0.0    1.7  1  Methyltransf_23  Methyltransferase domain
       0.22   11.0   0.0       0.33   10.4   0.0    1.3  1  Methyltransf_4   Putative methyltransferase


Domain annotation for each model (and alignments):
>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.1   0.0   7.5e-74   7.9e-71       5     208 ..       9     209 ..       5     211 .. 0.98

  Alignments for each domain:
  == domain 1  score: 238.1 bits;  conditional E-value: 7.5e-74
                                       HHHHHHHHTTS---HHHHHHHHHS-GGGGSSCGGGGGTTSSS-EEEETTEEE--HHHHHHHHHHTT--TT-EEEEES CS
                              PCMT   5 alieelkkkgviksdkvaealeevdReefvpesfkekaYedaplsigynatiSaphmvalalellelkkgarvLevG 81 
                                       +li++lk +g   s+++++a+  v+R+ fvp++ +  aY+dap+ ig+n+tiSaphmva++++ll+l++g+ vLevG
  gi|298675685|ref|YP_003727435.1|   9 RLINSLKYQG--LSQEILDAMYRVPRHLFVPSESQIDAYVDAPIMIGQNQTISAPHMVAMMCDLLDLSEGQVVLEVG 83 
                                       699*******..99******************9999***************************************** PP

                                       -TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-SEEEEEESSBBSS--HH CS
                              PCMT  82 sGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeekaPYdaihvgaaapeiPea 158
                                       +GsGy++av+++lvge+g+v sie i+elv+ +++nlk+ +++nv+v++gDG +Gy+e+aPYd+i+v+a+ap++P++
  gi|298675685|ref|YP_003727435.1|  84 AGSGYHAAVISELVGESGHVYSIECIEELVNFSRNNLKNAGYSNVTVIHGDGSEGYPEYAPYDRILVTAGAPDVPDS 160
                                       ***************************************************************************** PP

                                       HHHTEEEEEEEEEEESBSSSEEEEEEEEETTTEEEEEEEEEE---B-BCC CS
                              PCMT 159 lidQLkeGGrlvvPvgeeeeQvlklvdkkadgkvvikkleevrfvpltdk 208
                                       l++ Lk+ G+lv+Pvg  + Q+l +++k+ dg+++ +++  v+fvpl +k
  gi|298675685|ref|YP_003727435.1| 161 LLNHLKPEGILVIPVG-FYFQDLYQIKKELDGSISKNEKGGVMFVPLIGK 209
                                       ****************.9*****************************876 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.0   5.2e-15   5.5e-12       3     109 ..      75     173 ..      73     201 .. 0.83

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 5.2e-15
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDli 78 
                                       +g +vl++G+G+G+ + ++ e++g+ ++v++i+  ee ++++r+n+++ g++nv++ +gd  e  ++    +++D i
  gi|298675685|ref|YP_003727435.1|  75 EGQVVLEVGAGSGYHAAVISELVGESGHVYSIECIEELVNFSRNNLKNAGYSNVTVIHGDGSEgYPEY---APYDRI 148
                                       6789***********************************************************99963...689998 PP

                   Methyltransf_31  79 lsnevlnaladpdkileeiervlkpggilli 109
                                       l        a  +++  ++ + lkp+gil+i
  gi|298675685|ref|YP_003727435.1| 149 LVT------AGAPDVPDSLLNHLKPEGILVI 173
                                       874......3333344444446777777765 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   2.8e-10     3e-07      29     100 ..      64     134 ..      54     169 .. 0.88

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 2.8e-10
                             GCD14  29 isliimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrD 100
                                       ++++   L+l +G vv+e G+Gsg  +  i+  v+  Gh++++e  e+ ++++r+++++ + s +vtv h D
  gi|298675685|ref|YP_003727435.1|  64 VAMMCDLLDLSEGQVVLEVGAGSGYHAAVISELVGESGHVYSIECIEELVNFSRNNLKNAGYS-NVTVIHGD 134
                                       6888999***************************************************99976.67777777 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   4.9e-10   5.2e-07      43     133 ..      71     161 ..      52     188 .. 0.90

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 4.9e-10
                                       --S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEE CS
                   Ubie_methyltran  43 vavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDv 119
                                           +g+ vl+v +G+g  a+ +s+ vge+g+v  ++  e++++ +++ lk+ g++n+  +++++ e   e   +D 
  gi|298675685|ref|YP_003727435.1|  71 LDLSEGQVVLEVGAGSGYHAAVISELVGESGHVYSIECIEELVNFSRNNLKNAGYSNVTVIHGDGSEGYPEYAPYDR 147
                                       4556899***********************************************************999899999*9 PP

                                       EEEES-GGG-S-HH CS
                   Ubie_methyltran 120 vtvsfGlrnvtDkl 133
                                       + v+ G  +v+D l
  gi|298675685|ref|YP_003727435.1| 148 ILVTAGAPDVPDSL 161
                                       99999999999964 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   8.3e-10   8.8e-07       1      72 [.      79     152 ..      79     169 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 8.3e-10
                                       EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEES CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssg 72 
                                       vL++G+G+G +++ +++ +g +++v+ +++ ee+++  r++++++g+ nv++++gd ++   e + +D ++++ 
  gi|298675685|ref|YP_003727435.1|  79 VLEVGAGSGYHAAVISELVGeSGHVYSIECIEELVNFSRNNLKNAGYsNVTVIHGDGSEGYPEYAPYDRILVTA 152
                                       9******************779**********************999**********997778899**999853 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   3.4e-09   3.5e-06       3      87 ..      70     152 ..      68     172 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 3.4e-09
                                       HH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC.. CS
                   Methyltr_RsmB-F   3 lLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggel 79 
                                       lL++ e++ +l++ a+ G   + i+el+ ++g+v+ ++  +e ++   +nlk  g  n++v+++D+++     +   
  gi|298675685|ref|YP_003727435.1|  70 LLDLSEGQVVLEVGAGSGYHAAVISELVGESGHVYSIECIEELVNFSRNNLKNAGYSNVTVIHGDGSEGYPEYA--P 144
                                       6999**************************************************************99744444..5 PP

                                       EEEEEEEE CS
                   Methyltr_RsmB-F  80 fDriLlDa 87 
                                       +DriL+ a
  gi|298675685|ref|YP_003727435.1| 145 YDRILVTA 152
                                       9****976 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   3.3e-09   3.5e-06      17      85 ..      62     135 ..      50     155 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 3.3e-09
                                       HHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-...SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S-C CS
                            RrnaAD  17 kvineIldklnleekltvleigpGkGilTeeLakra...kqvvvlElderLakllqkkls..kdeklkvvhqDf 85 
                                        +++   d l+l+e + vle+g+G G   + + + +    +v ++E  e+L+++ +++l+   +++++v+h D+
  gi|298675685|ref|YP_003727435.1|  62 HMVAMMCDLLDLSEGQVVLEVGAGSGYHAAVISELVgesGHVYSIECIEELVNFSRNNLKnaGYSNVTVIHGDG 135
                                       5556677889********************9999999878999*****************999*********97 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.1   3.7e-08   3.9e-05      64     107 ..      69     112 ..      60     138 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 3.7e-08
                                       S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHH CS
                       Fibrillarin  64 kelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprv 107
                                       + l +++g+ vL +Ga+sG  ++ +s++vge+g vy++e  +  
  gi|298675685|ref|YP_003727435.1|  69 DLLDLSEGQVVLEVGAGSGYHAAVISELVGESGHVYSIECIEEL 112
                                       4567899********************************87754 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   4.4e-06    0.0046       1      67 [.      80     150 ..      80     173 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.4e-06
                                       EEET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-T.T-EEEEEE CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg...arvvgvDlskemlklakekaseegl.kvefvvadaeklpfed.nsfDlvvs 67 
                                       L+vG+G+G++a+ + + +   ++v+ ++  +e+++ ++++ +++g  +v+++++d ++  +++ + +D +++
  gi|298675685|ref|YP_003727435.1|  80 LEVGAGSGYHAAVISELVgesGHVYSIECIEELVNFSRNNLKNAGYsNVTVIHGDGSE-GYPEyAPYDRILV 150
                                       89*************7777999*********************************998.5555355666555 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   2.4e-06    0.0025      41     108 ..      69     135 ..      49     143 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.4e-06
                                       HHHHHHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-H CS
                    Methyltransf_3  41 lLvklvnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekieliegda 108
                                        L++l++ + vle+G   Gy +  ++  + e G++ +i+  +e ++ +++ ++ ag+ + + +i+gd+
  gi|298675685|ref|YP_003727435.1|  69 DLLDLSEGQVVLEVGAGSGYHAAVISELVGESGHVYSIECIEELVNFSRNNLKNAGYSN-VTVIHGDG 135
                                       489999**************************************************975.78888887 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   5.7e-06     0.006      12      75 ..      63     124 ..      55     143 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.7e-06
                   Methyltransf_32  12 lvakllkelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklg 75 
                                       +va +++   + s+ + v++vGaG gY + v++   +  + +v++i++ eelv+ +++  ++ g
  gi|298675685|ref|YP_003727435.1|  63 MVAMMCDL-LDLSEGQVVLEVGAGSGYHAAVISE-LVGESGHVYSIECIEELVNFSRNNLKNAG 124
                                       45555555.45577899****************9.55689*************99888777766 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   7.2e-06    0.0076      23     102 ..      67     149 ..      63     151 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.2e-06
                                       HHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTT.S CS
                               MTS  23 LletlpkelsgkvlDlGcGaGvlgaalakespeae.vtlvdvdarAlesakenleankle.vevvasdvleevee.k 96 
                                       + + l+ ++ + vl +G+G G+ +a++ +   e   v  ++   + ++++++nl++ + + v+v++ d+ e  +e +
  gi|298675685|ref|YP_003727435.1|  67 MCDLLDLSEGQVVLEVGAGSGYHAAVISELVGESGhVYSIECIEELVNFSRNNLKNAGYSnVTVIHGDGSEGYPEyA 143
                                       566677777888****************99988766999*******************999********99987425 PP

                                       -EEEEE CS
                               MTS  97 kfdliv 102
                                        +d i+
  gi|298675685|ref|YP_003727435.1| 144 PYDRIL 149
                                       567665 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   9.3e-06    0.0098      98     165 ..      73     140 ..      62     164 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.3e-06
                                       --TT-EEEETT-TTTCCHHHCCHH.TTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG--- CS
                            Met_10  98 veegevVvdvfAGiGpfaipiaky.skakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevir 165
                                        +eg+vV++v AG G++a +i+ + ++   v++i+   e v++ ++n+k     + v++i +Dg e  +
  gi|298675685|ref|YP_003727435.1|  73 LSEGQVVLEVGAGSGYHAAVISELvGESGHVYSIECIEELVNFSRNNLKN-AGYSNVTVIHGDGSEGYP 140
                                       579**************999987538999**************9999985.555556699999988666 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   2.5e-05     0.026       1     102 [.      80     172 ..      80     173 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.5e-05
                   Methyltransf_24   1 vEiGvysGvstlwllralrrngagrlvavdhdpg.aeeaaalareaglddrvrlikadseealaslaagsiDllfiD 76 
                                       +E+G+ sG+ ++++ +++ + g  ++++++  ++  +  ++++++ag+++ v++i++d +e +++ a  ++D +++ 
  gi|298675685|ref|YP_003727435.1|  80 LEVGAGSGYHAAVISELVGESG--HVYSIECIEElVNFSRNNLKNAGYSN-VTVIHGDGSEGYPEYA--PYDRILVT 151
                                       79*****************999..59999997744455777777788876.9************999..89988887 PP

                   Methyltransf_24  77 gghaaeavledl.eallprlapggvvl 102
                                       +g      ++d+ + ll++l+p g+++
  gi|298675685|ref|YP_003727435.1| 152 AG------APDVpDSLLNHLKPEGILV 172
                                       66......3333134567777777766 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.1e-05     0.022      51     131 ..      64     148 ..      53     157 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.1e-05
                                       HHHHHTTTT--TT-EEEEES-TTSHHHH...HHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG- CS
                              CMAS  51 ldlileklelkpGmtlLdiGcGWGslvr...raverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedl 124
                                       + ++++ l+l +G+ +L++G+G G+ +    + v +   +v ++   +e  + +++++++++ ++ + ++  + e  
  gi|298675685|ref|YP_003727435.1|  64 VAMMCDLLDLSEGQVVLEVGAGSGYHAAvisELVGE-SGHVYSIECIEELVNFSRNNLKNAGYSNVTVIHGDGSEGY 139
                                       5789******************99865500044555.6789999999999999999999999988888877777777 PP

                                       --..--SEE CS
                              CMAS 125 de..kvdrv 131
                                       +e  ++dr+
  gi|298675685|ref|YP_003727435.1| 140 PEyaPYDRI 148
                                       777777777 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0002      0.21      20     116 ..      73     172 ..      62     201 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                   Methyltransf_23  20 lraggrvLdiGcGtGillevlren.gf..svtgvDlspeaveiae.........kakkaqkdqfdeqeaaepqg... 81 
                                       l +g+ vL++G+G+G+ + v++e  g   +v+ ++  +e+v+  +         +                      
  gi|298675685|ref|YP_003727435.1|  73 LSEGQVVLEVGAGSGYHAAVISELvGEsgHVYSIECIEELVNFSRnnlknagysN------------------Vtvi 131
                                       456889**********999996642552333333333333332223222222211..................0222 PP

                   Methyltransf_23  82 ............kfdlIvlrevlehvpdppellrqiatllkpgGyll 116
                                                    +d I  + +   vpd      ++ ++lkp+G l+
  gi|298675685|ref|YP_003727435.1| 132 hgdgsegypeyaPYDRILVTAGAPDVPD------SLLNHLKPEGILV 172
                                       2222223444446666666666666665......4555555666555 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00032      0.33       3      64 ..      77     139 ..      75     148 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00032
                                       EEEEEET-TTSHHHHHHHHHSTTS.EEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHH CS
                    Methyltransf_4   3 pvvleiGcGkGeflvalAkknPdk.nflGiEirvkvvakvlkkiealelkNlrilrgdalkvl 64 
                                        vvle+G G+G +   +++   +   +  iE  +++v+   ++ ++ +++N+ +++gd  +  
  gi|298675685|ref|YP_003727435.1|  77 QVVLEVGAGSGYHAAVISELVGESgHVYSIECIEELVNFSRNNLKNAGYSNVTVIHGDGSEGY 139
                                       689***************99887626779*****************************87655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1357.34
//
Query:       gi|298675686|ref|YP_003727436.1|  [L=213]
Description: hypothetical protein Metev_1804 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.059   13.5   0.5        0.2   11.8   0.0    2.1  3  Tox-REase-2    Restriction endonuclease fold toxin 2
        1.1    9.2   3.7        6.1    6.8   3.7    2.3  1  zinc_ribbon_4  zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Tox-REase-2  Restriction endonuclease fold toxin 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.45     4e+03      34      71 ..      45      80 ..      42      97 .. 0.54
   2 ?   -0.6   0.1      0.16   1.4e+03      42      58 ..     104     120 ..      68     160 .. 0.57
   3 ?   11.8   0.0   2.2e-05       0.2      24      61 ..     168     206 ..     138     213 .] 0.78

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.45
                       Tox-REase-2 34 edgtvvdaKyVkdpdkssyrstsrlrstlelkvevdGe 71
                                      e+++ v  K V   + +++  t+ + +     vevd e
  gi|298675686|ref|YP_003727436.1| 45 EKDKSVYIKTVISKGGKTFTHTNLMYKGEL--VEVDDE 80
                                      555555566666666566655555554222..333333 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.16
                       Tox-REase-2  42 KyVkdpdkssyrstsrl 58 
                                       K V+ ++ +   s + +
  gi|298675686|ref|YP_003727436.1| 104 KRVDSAEVDYIDSVWGR 120
                                       44444444444443333 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 2.2e-05
                       Tox-REase-2  24 kvlmvDGlriedgtvvdaKyVkdpd.kssyrstsrlrst 61 
                                         +   G+ri++g vv+aKy+k    ++++r  +r r++
  gi|298675686|ref|YP_003727436.1| 168 IKIRNNGFRIKEGDVVEAKYIKRLFaQEIFREKHRGRTA 206
                                       467889***************986547889888887775 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   3.7   0.00068       6.1       3      33 ..       7      38 ..       6      40 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.00068
                     zinc_ribbon_4  3 itCpsCkakyeiddeklp.akgvkvrCskCgh 33
                                      ++CpsC+    +  e l+ ++ v v+C+ C +
  gi|298675686|ref|YP_003727436.1|  7 VECPSCSPDIPVLHEVLKsGQNVLVKCKECEE 38
                                      89**********99999988999*******76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1650.73
//
Query:       gi|298675687|ref|YP_003727437.1|  [L=289]
Description: agmatinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.9e-74  249.6   0.0    4.4e-74  249.5   0.0    1.0  1  Arginase    Arginase family
     0.0014   18.2   0.0     0.0021   17.6   0.0    1.2  1  LDcluster4  SLOG cluster4 family


Domain annotation for each model (and alignments):
>> Arginase  Arginase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.5   0.0     5e-78   4.4e-74       2     277 ..      18     280 ..      17     283 .. 0.95

  Alignments for each domain:
  == domain 1  score: 249.5 bits;  conditional E-value: 5e-78
                                       EEEEEEEE--TTTSSSGGGGGHHHHHHHHHHTSBTHCHEETTTTE.SCCSEEEEEEEEE--SSCHHHHHHHHHHHHH CS
                          Arginase   2 dvallGvPfdaagsgrpGarfGPraireasarleealeynlelgv.leelkivdlgdvavtpvdneevleqieeava 77 
                                       + +++GvPfd++ s+r G+r +P+++r+as+++e+   yn + ++ + +l+i+d+g++++ + + +++l++++++++
  gi|298675687|ref|YP_003727437.1|  18 RYVIFGVPFDGTSSYRVGSRWAPDSVRTASSNFES---YNSYFDIdFVDLNIYDAGNLETFA-SVDDTLRELYNETD 90 
                                       679*******************************8...6666666688**********9986.9999********** PP

                                       HHHHTTCEEEEEESSGGGHHHHHHHHHHHHSTTEEEEEESSS----SSCTTTBSSSTTSHHHHHHHHTSECGCEEEE CS
                          Arginase  78 eilkagklpivlGGDHsialgilralaekygkplgvihfDAHaDlrtpetegsgnshGtpfrraaeegllkpkklvq 154
                                       ++l+++k+p+++GG+Hs+++++++a++e++g+++gv+ +DAH+Dlr++  +g ++sh+++ r++  +++   +++v 
  gi|298675687|ref|YP_003727437.1|  91 SLLRNNKVPLMVGGEHSLTYPCVKACKENVGDDFGVVVLDAHFDLRDEF-DGVKHSHASVSRHIT-DDIS--SNYVL 163
                                       ***********************************************88.9*************9.5555..69*** PP

                                       EEE-STCSHHHHHHHHTTSEEEEHHHHHHHHHHHHHHHHHHHHTCTTSEEEEEEEGGGBBTTTSTSSSS-BSS-B-H CS
                          Arginase 155 iGirsvdneeyelakelgirvitmreidelglkavveeilervgaeedpvylSfDiDvlDpavaPGtGtpepgGltl 231
                                       +G+rs ++ee+e+a++ +i+++t ++i+++g++ v++e+ e+++   d +ylS+D+D++D + aP+tGtpep Gl++
  gi|298675687|ref|YP_003727437.1| 164 LGVRSGTREEWEFARDNNIKFYTPEDIRKQGINTVISEVVEYLN--SDSIYLSLDMDAFDSTHAPATGTPEPFGLDP 238
                                       *******************************************6..68***************************** PP

                                       HHHHHHHHHHHCHSEEEEEEEE-B-GGGSSTTTHHHHHHHHHHHHH CS
                          Arginase 232 rellallrelaeklnlvgaDvvEvnPaldteaeqtarlaarlvrel 277
                                        ++++++++la     +g+D++E+ P +dt + qta+l+a+l+re+
  gi|298675687|ref|YP_003727437.1| 239 FDVRHIIHALAP--ISIGFDLMEIVPGYDT-G-QTAILGAKLMREF 280
                                       **********77..67**************.6.9**********96 PP

>> LDcluster4  SLOG cluster4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   2.4e-07    0.0021      18     123 ..      82     184 ..      69     212 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.4e-07
                        LDcluster4  18 alelaeelGrliAkegavlltGgrtGvmeaaskGakeagGltvGilpassekehsnkyvdiiiyTGlglagRnlilv 94 
                                        +el  e+  l+ ++++ l+ Gg++++ + + k++ke+ G   G++  + + +  ++ +d +  +   ++ R ++  
  gi|298675687|ref|YP_003727437.1|  82 LRELYNETDSLLRNNKVPLMVGGEHSLTYPCVKACKENVGDDFGVVVLDAHFDLRDE-FDGVKHSHASVS-RHITDD 156
                                       4567778888899999********************************999999999.9*********99.999999 PP

                        LDcluster4  95 lssdvviaiggrsGTlsEialaleegkpv 123
                                        ss+ v ++g rsGT +E  +a +++ + 
  gi|298675687|ref|YP_003727437.1| 157 ISSNYV-LLGVRSGTREEWEFARDNNIKF 184
                                       999987.589************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1773.04
//
Query:       gi|298675688|ref|YP_003727438.1|  [L=128]
Description: translation initiation factor eIF-5A [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-08   34.5   0.3    3.2e-08   33.5   0.3    1.4  1  eIF-5a    Eukaryotic elongation factor 5A hypusine, DNA-bindi
    0.00016   21.6   0.1    0.00028   20.8   0.1    1.4  1  EFP_N     Elongation factor P (EF-P) KOW-like domain


Domain annotation for each model (and alignments):
>> eIF-5a  Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.3   3.6e-12   3.2e-08       1      65 [.      68     124 ..      68     126 .. 0.93

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 3.6e-12
                                       --EEEEEEEEEE-SS.EEEEEE.TT--EEE.EEGG..GB-HHHHTT--TT-E..EEEEEETTEEEE CS
                            eIF-5a   1 nVkrkeyqLidIqdDgflsLmd.ddgetkeDlklpegelgkqikekfeegkdvlVtVlsamGeeki 65 
                                       +V+rk +q+++ +   + +Lmd dd++t+e l++p     ++ k+k +eg++  +t+++amG++ki
  gi|298675688|ref|YP_003727438.1|  68 VVERKSAQVLSFD-GSVAQLMDmDDYSTFE-LPVP-----EEYKDKVNEGEE--ITYITAMGNQKI 124
                                       69**********5.449*************.8888.....999*********..*********998 PP

>> EFP_N  Elongation factor P (EF-P) KOW-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   3.1e-08   0.00028       2      33 ..       7      38 ..       6      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.1e-08
                                      GGG--TT-EEEETTEEEEEEEEEEEEETTS-- CS
                             EFP_N  2 aselkkGlvieidgklyvVlefehvkpGkGqa 33
                                      ++elk G  + id ++++++++  +kpGk ++
  gi|298675688|ref|YP_003727438.1|  7 VKELKEGRYVVIDEEPCIIKSISKSKPGKHGS 38
                                      78**************************9764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 854.88
//
Query:       gi|298675689|ref|YP_003727439.1|  [L=571]
Description: aldehyde ferredoxin oxidoreductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-93  313.3   0.0    3.1e-93  312.8   0.0    1.2  1  AFOR_C    Aldehyde ferredoxin oxidoreductase, domains 2 & 3
    5.9e-68  228.6   0.1      9e-68  228.1   0.1    1.3  1  AFOR_N    Aldehyde ferredoxin oxidoreductase, N-terminal doma


Domain annotation for each model (and alignments):
>> AFOR_C  Aldehyde ferredoxin oxidoreductase, domains 2 & 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  312.8   0.0   3.5e-97   3.1e-93       7     382 .]     220     566 ..     214     566 .. 0.94

  Alignments for each domain:
  == domain 1  score: 312.8 bits;  conditional E-value: 3.5e-97
                                       HHHHHHSH.HHHHHHHH-GGGHHHHHHHTT---BTTTTBS--TTGGGGSHHHHHHHTEEEE.E.-TT-SS--EEEEE CS
                            AFOR_C   7 qkeiksspqvtaelrkyGTaelvnianetgalptknfqegtfekaekisgealeekylvkneg.CfsCpiaCgrevk 82 
                                        + + ++p+v+++l+ yGT++ + ++n +++lp++nf++++f + + +s+e+++++y +++ + C +CpiaC+ ++k
  gi|298675689|ref|YP_003727439.1| 220 GQLLDANPVVSKGLKVYGTSAFMALMNYMNVLPAYNFRYTSFGGIDLLSAEYIKNNYDTEKLSgCSGCPIACKFQTK 296
                                       5678899*999************************************************99999************9 PP

                                       ......ETEE---HHHHHHHTGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHHHHHHHHHTTSS-HHHHTS----T CS
                            AFOR_C  83 veegkkvkvegpeyetlaalGsnlgiddleailklnelcdelGlDtisaGntiafamelyekGllkkedtdglelef 159
                                        ++        p+y t++a+G+++g++d+++i+k+ +lc ++G+D++s+G+tia + el +k +             
  gi|298675689|ref|YP_003727439.1| 297 DNR------LIPDYDTIWAFGPAVGNNDFDTIIKACNLCRDYGIDSVSCGSTIASYLELASKNIG------------ 355
                                       433......469**************************************************776............ PP

                                       T-THHHHHHHHHHHTT-TTHHHHTT-HHHHHHCTT-GGG--EETTEE--SS-GGG-HHHHHHHHH-TTSS-SGGG-T CS
                            AFOR_C 160 gdaeallellekiAkregigdllAeGvkrlaeklgaeelamhvkGlelpaydprgakgmalaYatsnrGacHlrayl 236
                                          e+ll+++e+i+++++    l +G+  +++++g +++ m+vk  elp ydprg++g+al+Yatsn G+c+ ++y+
  gi|298675689|ref|YP_003727439.1| 356 --SENLLQMIEDIGEGKS---KLCNGSSSFMNAIG-KDVGMSVKSFELPGYDPRGIQGQALGYATSNHGGCYRDSYM 426
                                       ..4699********7666...599***********.***************************************** PP

                                       HHHH.....S---TT--HHHHHHHHHHHHHHHHHHHHT--GGGG-HHH......HHHHHHHHHT----HHHHHHHHH CS
                            AFOR_C 237 iale.....ekvdpletegkaelvkwfqdltalvdslglCkftseaeerldlelyakllsavtGidvteeellkaGe 308
                                       ia+e     + +d+++ +gka ++ +fq+l a+++sl lC+++      ld++ +a++ls+vtG+ +t+e+ll+ Ge
  gi|298675689|ref|YP_003727439.1| 427 IAPEvlgkpKLLDRQTFSGKAGILQYFQNLIAAINSLSLCNYSV---FALDETVLASMLSSVTGVYYTPEDLLRSGE 500
                                       *******9988999999***************************...67899************************* PP

                                       HHHHHHHHHHHHHT--HHHS---HHHHHS---SSTTTT---..-HHHHHHHHHHHHT--TTS---HHHHHHCT- CS
                            AFOR_C 309 RiynleRlfnlreGltrkddtlperlleeplkegpakgkvledeleemldeyYelrGWdetGvPtketlkrLgL 382
                                       R +nleRlfn+r G+t +ddtlp r++++   +g +k     +e+ee++ +yY +rGW+++GvP   +l++Lg+
  gi|298675689|ref|YP_003727439.1| 501 RTWNLERLFNNRSGFTVSDDTLPGRFFDD---NGIDK-----NEFEEAVFDYYHFRGWNKKGVPESNKLDELGI 566
                                       ***************************64...44445.....369****************************7 PP

>> AFOR_N  Aldehyde ferredoxin oxidoreductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  228.1   0.1     1e-71     9e-68       1     197 [.       6     200 ..       6     201 .. 0.97

  Alignments for each domain:
  == domain 1  score: 228.1 bits;  conditional E-value: 1e-71
                                       SEEEEEETTTTEEEEEE--HHHHHHH-SCHHHHHHHHHHHS-TTS-TTSTTS-EEEEE-TTTTSSSTTB-EEEEEEE CS
                            AFOR_N   1 gkilrvdLstgkieveelpeelaekylGgrglaakllldevppgvdplspenplvfatGpltgtpapgsgrlvvvak 77 
                                       gk ++vdLs+ ++++ +++e+ +++y+Ggrgl++++l+d   p+v+plsp+npl+++t+pl+gt  p  g +++++k
  gi|298675689|ref|YP_003727439.1|   6 GKTITVDLSSSTVTETTTDEKNLRTYIGGRGLGVRILCDLCSPRVNPLSPDNPLIVTTSPLAGTETPLNGMCSITSK 82 
                                       68899************************************************************************ PP

                                       -TTTSSEEEEEEETCHHHHHHHCT-SEEEEES--SS-EEEEEETTEEEEEE-TTTTTS-HHHHHHHHHHHHTSEEEE CS
                            AFOR_N  78 sPltgtlgesnaGgrfgaelkraGydaivieGkaekpvylvieddkveiedaedlwgldtyettealkeelgdkvav 154
                                       sPlt+t+ +++ Gg+fg+elk aG+da+vi+Gka++pvyl ied++ve+++a++lw+++t ett+ l++  g kva+
  gi|298675689|ref|YP_003727439.1|  83 SPLTNTIFSAETGGFFGKELKLAGIDALVIKGKAKSPVYLQIEDNHVELKSATHLWNKNTVETTDILHH--GGKVAC 157
                                       *******************************************************************87..78**** PP

                                       E-HHHHTT-TTB-E.EETTE.EE-SSSHHHHHHHTTEEEEEEE- CS
                            AFOR_N 155 iGpaGenlvrfAsisvddgr.aagrgGlGavmgsKnlkaivvrg 197
                                       iG+ Gen++ +A+i v+d+  +  rgGlGa+ gsKnlkaivv+g
  gi|298675689|ref|YP_003727439.1| 158 IGKSGENQILLANI-VNDYMySSERGGLGAISGSKNLKAIVVKG 200
                                       **************.77555378*******************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (571 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 4316.02
//
Query:       gi|298675690|ref|YP_003727440.1|  [L=401]
Description: sodium/hydrogen exchanger [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.2e-47  160.8  48.1    4.9e-47  160.5  48.1    1.0  1  Na_H_Exchanger  Sodium/hydrogen exchanger family


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.5  48.1   2.8e-51   4.9e-47       4     380 ..       9     394 ..       6     395 .. 0.85

  Alignments for each domain:
  == domain 1  score: 160.5 bits;  conditional E-value: 2.8e-51
                                       HHHHHHHHHH..H.HHHTTSXHHHHHHHHHHHHTTTTTS........HHHCHCCHHHHCHHCCHHHHCTCGCCTGCC CS
                    Na_H_Exchanger   4 lillallvgl..l.arrlklpeivgliiaGlllGpsglg..lieps.eedlevlselglilllFlaGleldlrelrk 74 
                                       ++++++++ +    ++ +++p+++ + ++G l+  +     li+++   ++++l+elg+i+llF +Gle +  +l +
  gi|298675690|ref|YP_003727440.1|   9 VGAIVVFAMIlrSgMKEIGIPSMISFFVLGFLVRFMDNQwnLISEQgFQIFNFLAELGVIVLLFRVGLESKVTKLIR 85 
                                       4444444444465599******************99988444776689***************************** PP

                                       THHHHHHHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHH CS
                    Na_H_Exchanger  75 nlksilllallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvln 151
                                        l ++ ++ ++gv+++ +l G+l++++ +lg++l+++l+++++++at+++v+++i +e++++ ++ g +ll ++ l+
  gi|298675690|ref|YP_003727440.1|  86 WLPTASKIWIGGVFFSGLL-GFLASYY-LLGWELVQSLFVSVAMTATSVGVTVSIWQEANLLYTHHGEILLDVAELD 160
                                       *******************.*****85.8999********************************************* PP

                                       HHHCCCCCHHHHHHTX..XXXXTSSSTS........XHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTHHHHHHHH CS
                    Na_H_Exchanger 152 Davavvllavllalak..eeaggetsll........lllliflvvavgglllglvigwllrlitrftdddrelevll 218
                                       D+++v+l a+l a+a+  ++ + +++l          +l+ ++++a+ +++ + +  +++++++r   +  +  +l+
  gi|298675690|ref|YP_003727440.1| 161 DISGVILMALLFAVAPvlKSGNIVAALPmlpeilglFILKLIAFIAFCIFFSRYLEAHITEFLERI--QVGKGTLLV 235
                                       ***************975444444444467765555555555555555555555555555555555..888889999 PP

                                       HHHHHHHHHHHHHTSXXXHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHSXHHHHHXXHHHHHH CS
                    Na_H_Exchanger 219 vlllallaallaellgvsgilgaflaGlvlseyefsnklseklesfreglfnplfFvlvGlsldlkvlnnhlsvlil 295
                                       +l +  ++a++ae+lg+s ++gaf+aGl++s+ + s k   ++e++  +lf p+fFv +Gl+++++v++   s++++
  gi|298675690|ref|YP_003727440.1| 236 ILGIGMVVAATAEMLGFSVAIGAFFAGLIFSRDPDSVKFDGSFEPLY-DLFMPFFFVGIGLKINPEVIT--GSLVPV 309
                                       99999999***************************************.9*******************6..888888 PP

                                       HHHHHHHHHTHHHHHHHHHTTTXSSXHHHHHHCCCCSS.BHHHHHHHHHHHHHH..XHHHHTTSSTTTCSTSXHHHH CS
                    Na_H_Exchanger 296 vllilvaillgrilavflllrllglslrealiigfgglqrgavalalaalgpal..gllarelyallivvvlftvlv 370
                                       v+lilva+ +g++++   +++++  +++ ali+g+++++r ++al++ + g +l   + + + +a +++v  +t l 
  gi|298675690|ref|YP_003727440.1| 310 VILILVAF-AGKLIGHGSIAYFV-TGSSGALILGTSMIPRAEIALIIMQKGLSLgdWAVTPQIFANMVIVSAVTSLT 384
                                       88888888.8**********988.9*****************************87677888866666666666666 PP

                                       HHHHHHHHHH CS
                    Na_H_Exchanger 371 qGlslkpllk 380
                                        +l+l+p+l+
  gi|298675690|ref|YP_003727440.1| 385 IPLILRPVLN 394
                                       9999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       898  (0.0500865); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2494.61
//
Query:       gi|298675691|ref|YP_003727441.1|  [L=76]
Description: putative ferredoxin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-20   71.4   7.2    7.7e-20   71.2   7.2    1.1  1  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    6.1e-09   36.5   5.1    8.6e-09   36.0   5.1    1.2  1  Fer4_15   4Fe-4S single cluster domain
    0.00035   20.3   8.7     0.0043   16.8   1.2    2.7  3  Fer4      4Fe-4S binding domain
    0.00049   20.1   2.7     0.0013   18.8   2.7    1.6  1  Fer4_10   4Fe-4S dicluster domain
     0.0011   19.0   4.8      0.066   13.3   1.1    2.1  2  Fer4_21   4Fe-4S dicluster domain
     0.0018   18.3   1.4     0.0018   18.3   1.4    2.3  2  Fer4_2    4Fe-4S binding domain
     0.0064   16.6   2.4      0.034   14.3   3.0    1.8  2  Fer4_9    4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.013   16.1   4.2       0.06   14.0   4.3    2.0  1  Fer4_7    4Fe-4S dicluster domain
      0.054   14.4   3.9        7.5    7.6   0.6    2.3  3  Fer4_16   4Fe-4S double cluster binding domain
      0.064   13.4   2.6       0.18   12.0   2.6    1.7  1  Fer4_18   4Fe-4S dicluster domain
        5.4    8.2   9.3         21    6.3   2.6    2.4  2  Fer4_3    4Fe-4S binding domain
        7.4    6.8   9.4        2.5    8.3   1.2    2.5  2  Fer4_6    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.2   7.2   5.2e-23   7.7e-20       1      57 [.      18      73 ..      18      74 .. 0.98

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 5.2e-23
                           Fer4_13  1 VDrdtCiacgaCvelaPdvFeeddeggasvvaeqptseeekadaeeAadaCPvesIg 57
                                      VD + C+acg+Cv++ P++F+++d++++ +v++qp++++e++ +eeA++aCPve+Ig
  gi|298675691|ref|YP_003727441.1| 18 VD-EDCTACGLCVDTDPEHFAMNDDESYTYVYKQPETDDEIDACEEALEACPVEAIG 73
                                      89.9****************************************************8 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   5.1   5.8e-12   8.6e-09       6      64 ..      20      72 ..      17      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 5.8e-12
                           Fer4_15  6 daCigcglCvaeapevfeldedglasvllddgeiaegevpddeeeaaqeAaraCPvdAI 64
                                      + C+ cglCv+ +pe f +++d   + + +      ++ +dde++a +eA +aCPv+AI
  gi|298675691|ref|YP_003727441.1| 20 EDCTACGLCVDTDPEHFAMNDDESYTYVYK------QPETDDEIDACEEALEACPVEAI 72
                                      56******************8877666654......6779******************9 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   1.2   2.9e-06    0.0043       2      16 ..      16      30 ..      15      31 .. 0.83
   2 ?   -1.9   0.1       2.4   3.6e+03      13      17 ..      59      63 ..      58      63 .. 0.63
   3 !    8.1   0.1    0.0017       2.5      16      23 ..      65      72 ..      64      73 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.9e-06
                                      EEETTTSSS-THHHH CS
                              Fer4  2 videekCigCGaCve 16
                                      ++  e+C++CG+Cv+
  gi|298675691|ref|YP_003727441.1| 16 YYVDEDCTACGLCVD 30
                                      566788*******97 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.4
                                      HHHHH CS
                              Fer4 13 aCvev 17
                                      aC+e+
  gi|298675691|ref|YP_003727441.1| 59 ACEEA 63
                                      67765 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0017
                                      HHSTTTEE CS
                              Fer4 16 evCPvgAI 23
                                      e+CPv+AI
  gi|298675691|ref|YP_003727441.1| 65 EACPVEAI 72
                                      89*****9 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   2.7   8.5e-07    0.0013       4      56 .]      17      68 ..      15      70 .. 0.59

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 8.5e-07
                           Fer4_10  4 idddtCirCgkCvkaCPadl.tsvgakgeaseeeavrk..kvekCtgcgaCveaCP 56
                                      + d+ C+ Cg Cv+  P ++   ++ + ++   ++ ++   +++   c++  eaCP
  gi|298675691|ref|YP_003727441.1| 17 YVDEDCTACGLCVDTDPEHFaM-NDDESYTYVYKQPETddEIDA---CEEALEACP 68
                                      56899*************9962.333333333333333023444...455555555 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   1.1   4.4e-05     0.066      36      52 ..      17      33 ..       3      39 .. 0.82
   2 !    8.1   0.1     0.002       2.9      35      57 ..      51      72 ..      31      73 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.4e-05
                           Fer4_21 36 vvedeCvGCnlCssvCP 52
                                      +v+++C++C lC++  P
  gi|298675691|ref|YP_003727441.1| 17 YVDEDCTACGLCVDTDP 33
                                      589*********98766 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.002
                           Fer4_21 35 kvvedeCvGCnlCssvCPvedci 57
                                      + ++de  +C+  ++ CPv ++i
  gi|298675691|ref|YP_003727441.1| 51 PETDDEIDACEEALEACPV-EAI 72
                                      44688999**********9.665 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   1.4   1.2e-06    0.0018       2      21 ..      15      33 ..      14      34 .. 0.86
   2 ?    0.5   0.7      0.55   8.2e+02      17      21 ..      64      68 ..      56      69 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.2e-06
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                      p++vd+d C++Cg Cv+  P
  gi|298675691|ref|YP_003727441.1| 15 PYYVDED-CTACGLCVDTDP 33
                                      7899999.********9866 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.55
                            Fer4_2 17 vsaCP 21
                                      + aCP
  gi|298675691|ref|YP_003727441.1| 64 LEACP 68
                                      36798 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.4   0.00021      0.32      33      45 ..      15      31 ..       2      37 .. 0.64
   2 !   14.3   3.0   2.3e-05     0.034       1      51 []      21      72 ..      21      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00021
                            Fer4_9 33 e....eaCigCgaCvea 45
                                           e+C+ Cg Cv+ 
  gi|298675691|ref|YP_003727441.1| 15 PyyvdEDCTACGLCVDT 31
                                      0333368*******975 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 2.3e-05
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase.eaCigCgaCveaCpkgai 51
                                      +Ct Cg Cv+  p + +++d+  ++  +++ +  ++   C++ +eaCp +ai
  gi|298675691|ref|YP_003727441.1| 21 DCTACGLCVDTDPEHFAMNDDESYTYVYKQPETdDEIDACEEALEACPVEAI 72
                                      5****************999999999998887764556799*******9887 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   4.3     4e-05      0.06       2      52 .]      22      71 ..       2      71 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4e-05
                            Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      C+ Cg Cv++ p +  + d+e++    +++e d ++   C++  ++CP++a
  gi|298675691|ref|YP_003727441.1| 22 CTACGLCVDTDPEHFAMNDDESYTYVYKQPETD-DEIDACEEALEACPVEA 71
                                      999999999999998888887655544444443.34456777778999876 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.6     0.005       7.5      42      62 ..       9      30 ..       2      35 .. 0.61
   2 ?    5.9   2.3     0.016        25       2      23 ..      22      44 ..      21      60 .. 0.68
   3 ?    7.2   0.1    0.0067        10       5      20 ..      60      75 ..      58      76 .] 0.85

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.005
                           Fer4_16 42 aedeekck.kqeaitgCdiCqd 62
                                      +e+ e  +   e++t C+ C+d
  gi|298675691|ref|YP_003727441.1|  9 PENVEGPYyVDEDCTACGLCVD 30
                                      4444444435677888888876 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.016
                           Fer4_16  2 CgtCgkCaevCPtn.aikekkek 23
                                      C+ Cg C+++ P++ a++ ++++
  gi|298675691|ref|YP_003727441.1| 22 CTACGLCVDTDPEHfAMNDDESY 44
                                      999****9998875255555444 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0067
                           Fer4_16  5 CgkCaevCPtnaikek 20
                                      C++ +e+CP++ai ++
  gi|298675691|ref|YP_003727441.1| 60 CEEALEACPVEAIGND 75
                                      88889********875 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.6   0.00012      0.18      58     102 ..      19      67 ..       2      74 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                           Fer4_18  58 agdcidcescvkvcPtgidirkGlqleci....scllcidacdkvmekl 102
                                       + dc++c+ cv+  P +  + +   +  +    +    idac++ +e+ 
  gi|298675691|ref|YP_003727441.1|  19 DEDCTACGLCVDTDPEHFAMNDDESYTYVykqpETDDEIDACEEALEAC 67 
                                       679***************9999877766622225667899999888765 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   2.6     0.014        21       1       9 [.      22      30 ..      22      31 .. 0.92
   2 ?    5.8   0.5     0.021        32       4      15 .]      60      71 ..      58      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.014
                            Fer4_3  1 CtgCgaCve 9 
                                      Ct Cg+Cv+
  gi|298675691|ref|YP_003727441.1| 22 CTACGLCVD 30
                                      9******96 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.021
                            Fer4_3  4 CgaCvevCPvgA 15
                                      C+  +e+CPv A
  gi|298675691|ref|YP_003727441.1| 60 CEEALEACPVEA 71
                                      88889****976 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   1.2    0.0016       2.5       6      17 ..      19      30 ..      15      31 .. 0.81
   2 ?    2.8   1.6     0.093   1.4e+02      15      24 .]      60      72 ..      57      72 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0016
                            Fer4_6  6 pdkCigCgdCvr 17
                                      ++ C+ Cg Cv+
  gi|298675691|ref|YP_003727441.1| 19 DEDCTACGLCVD 30
                                      577*******96 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.093
                            Fer4_6 15 Cvrv...CPegai 24
                                      C+ +   CP  ai
  gi|298675691|ref|YP_003727441.1| 60 CEEAleaCPVEAI 72
                                      6444444**9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 441.51
//
Query:       gi|298675692|ref|YP_003727442.1|  [L=126]
Description: methylated-DNA--protein-cysteine methyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-26   92.3   0.0    1.8e-26   92.1   0.0    1.1  1  DNA_binding_1  6-O-methylguanine DNA methyltransferase, DNA b
  ------ inclusion threshold ------
      0.078   12.7   0.0       0.11   12.2   0.0    1.2  1  hSac2          Inositol phosphatase
      0.083   12.4   0.1       0.14   11.7   0.1    1.3  1  Sigma70_r4     Sigma-70, region 4
       0.91    9.4   4.2        1.7    8.5   4.2    1.4  1  CAMSAP_CC1     Spectrin-binding region of Ca2+-Calmodulin


Domain annotation for each model (and alignments):
>> DNA_binding_1  6-O-methylguanine DNA methyltransferase, DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.1   0.0     4e-30   1.8e-26       1      80 [.      36     119 ..      36     120 .. 0.94

  Alignments for each domain:
  == domain 1  score: 92.1 bits;  conditional E-value: 4e-30
                                       HHHHHHHHHHTTS-TT-BEEHHHHHHHTT.TSCHHHHHHHHHTSSBTTTSGGGGEEBTTSBCCTTTT.....CHHHH CS
                     DNA_binding_1   1 afqqrVwellrqIpyGkvttYgeiAkllgkpkaaraVgqalaanplailvPcHRVvgadgklggyag.....glerk 72 
                                       +f+q V++ +r+IpyG+++tY+e+Ak+++kp+a++aVg++l +np++i++PcHRVv+++g lgg+ g     +le+k
  gi|298675692|ref|YP_003727442.1|  36 EFEQMVLNETREIPYGETITYSELAKRIKKPRASQAVGKVLSKNPYPIVIPCHRVVSKSG-LGGFGGgfnpqKLEEK 111
                                       69**********************************************************.****555666699*** PP

                                       HHHHHHTT CS
                     DNA_binding_1  73 ralLeaEg 80 
                                       ++l+e E+
  gi|298675692|ref|YP_003727442.1| 112 KKLIELEK 119
                                       ****9996 PP

>> hSac2  Inositol phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.6e-05      0.11      64      97 ..      26      59 ..      20      73 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.6e-05
                             hSac2 64 kydfnlekvssfervpLedikkIelGtyitstls 97
                                      +yd +l  +++fe++ L++ ++I +G+ it +  
  gi|298675692|ref|YP_003727442.1| 26 EYDLDLSHLTEFEQMVLNETREIPYGETITYSEL 59
                                      7**************************6654433 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   3.2e-05      0.14       2      34 ..      31      67 ..      31      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.2e-05
                                      HHHS-HHHHHHHHHHH....TTT--HHHHHHHHTS-H CS
                        Sigma70_r4  2 LasLpererevlelrf....geglTleEIgerlgiSr 34
                                      L++L+e e++vl   +    ge  T++E+++r   +r
  gi|298675692|ref|YP_003727442.1| 31 LSHLTEFEQMVLNETReipyGETITYSELAKRIKKPR 67
                                      789*****************************98887 PP

>> CAMSAP_CC1  Spectrin-binding region of Ca2+-Calmodulin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   4.2   0.00038       1.7      22      35 ..     107     120 ..     106     122 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00038
                        CAMSAP_CC1  22 kLEEKRRaIEaqKr 35 
                                       kLEEK++ IE +K 
  gi|298675692|ref|YP_003727442.1| 107 KLEEKKKLIELEKN 120
                                       9**********995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 804.85
//
Query:       gi|298675693|ref|YP_003727443.1|  [L=240]
Description: peptidase M10A and M12B matrixin and adamalysin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-16   61.1   0.0    1.6e-16   60.6   0.0    1.2  1  Peptidase_M10  Matrixin
     0.0021   17.7   0.1     0.0049   16.5   0.0    1.6  2  Astacin        Astacin (Peptidase family M12A)
     0.0035   16.4   0.2     0.0046   15.9   0.2    1.2  1  Peptidase_M66  Peptidase M66
     0.0077   16.7   0.1     0.0097   16.4   0.1    1.3  1  Reprolysin_3   Metallo-peptidase family M12B Reprolysin-like
  ------ inclusion threshold ------
      0.023   13.3   0.0       0.03   12.9   0.0    1.1  1  Metallopep     Putative peptidase family
      0.031   13.9   0.0      0.036   13.7   0.0    1.2  1  Peptidase_M57  Dual-action HEIGH metallo-peptidase
        0.1   12.5   0.0       0.17   11.8   0.0    1.3  1  Peptidase_M54  Peptidase family M54
       0.13   12.4   0.0       0.17   12.0   0.0    1.2  1  Reprolysin_5   Metallo-peptidase family M12


Domain annotation for each model (and alignments):
>> Peptidase_M10  Matrixin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.6   0.0   7.1e-20   1.6e-16       2     143 ..      36     184 ..      35     189 .. 0.85

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 7.1e-20
                                       TSSSEEEEEESSSX.TTSXHHHHHHHHHHHHHHHHTTS..SSEEEEE.....SSSCESEEEEEESSSSSSSSSXBSS CS
                                       xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M10   2 wekknltyrilnet.pdleeeevrkairrAfkvwsevt..plkFtev.....kkgeadikieFgrgehgdgypfdgk 70 
                                       w+++ +t  i +e+ p+  + +  k+i++A + w+e    +l+F        +++ adi++++ ++ ++ ++  dg 
  gi|298675693|ref|YP_003727443.1|  36 WDHSPITVYINDENvPEHYSPTYYKQIEKAVEYWDEGGngHLNFDPDfkfveSSEGADINVKWVENLEEVEKAPDGV 112
                                       9999999999999878899999**************98663555433333357778********************* PP

                                       SSESEEEBSSSSTTTTEEEEETTS-EESSTS-.SSSEEHHHHHHHHHHHHTTBESXSSTTSTTSSSCTXTTTX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M10  71 ggvlahafapgeglggdihfdddeqWtlgeekveqgvslflVaaHEiGHalGLeHssdkdalmyplykeekkv 143
                                        g+    ++ g+ +++di ++  +   ++  ++   ++++ +a HE+GHalGL Hs+d++++myp y++++++
  gi|298675693|ref|YP_003727443.1| 113 AGYCRPYVIDGKYVRADIVLEVGNYQGYSW-QQYGDANMYAIAKHEFGHALGLGHSDDRNDIMYPEYEMRDNI 184
                                       ***9999999**********9887655554.447899******************************976654 PP

>> Astacin  Astacin (Peptidase family M12A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.5   3.3e+03      14      31 ..      52      69 ..      35      72 .. 0.50
   2 !   16.5   0.0   2.2e-06    0.0049      78     101 ..     149     172 ..     130     184 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.5
                                      TTS-HHHHHHHHHHHHHH CS
                           Astacin 14 esleekeraaikkaleey 31
                                      e+++ +  ++i+ka+e +
  gi|298675693|ref|YP_003727443.1| 52 EHYSPTYYKQIEKAVEYW 69
                                      234445556666666666 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 2.2e-06
                                       -SHHHHHHHHHHHHTB--GGGSTT CS
                           Astacin  78 eklgiivHElmHalGffHeqsRtd 101
                                       + ++i+ HE++HalG+ H   R+d
  gi|298675693|ref|YP_003727443.1| 149 NMYAIAKHEFGHALGLGHSDDRND 172
                                       5689******************99 PP

>> Peptidase_M66  Peptidase M66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.2   2.1e-06    0.0046     187     210 ..     145     168 ..     122     183 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.1e-06
                     Peptidase_M66 187 tgdatltgefiHEqGHalGLpHyl 210
                                        gda++  +  HE GHalGL+H+ 
  gi|298675693|ref|YP_003727443.1| 145 YGDANMYAIAKHEFGHALGLGHSD 168
                                       68999999**************33 PP

>> Reprolysin_3  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   4.3e-06    0.0097      76     124 .]     110     167 ..      46     167 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.3e-06
                      Reprolysin_3  76 sgvgGlAyv..........gsvcnsskkagvnsgssvlgk.vgadtvaHEiGHnfganHt 124
                                       +gv+G+               v ++++ +g+++++  +g+  ++  + HE GH +g+ H+
  gi|298675693|ref|YP_003727443.1| 110 DGVAGYCRPyvidgkyvraDIVLEVGNYQGYSWQQ--YGDaNMYAIAKHEFGHALGLGHS 167
                                       55555543344444444444455555557778877..56647789999***********5 PP

>> Metallopep  Putative peptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.4e-05      0.03     319     341 ..     155     179 ..     116     191 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.4e-05
                        Metallopep 319 lHEiGHllglpHqed..Gvmlrdyd 341
                                        HE GH+lgl+H  d   +m  +y 
  gi|298675693|ref|YP_003727443.1| 155 KHEFGHALGLGHSDDrnDIMYPEYE 179
                                       5***********9987799998886 PP

>> Peptidase_M57  Dual-action HEIGH metallo-peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.6e-05     0.036     122     151 ..     139     168 ..      63     174 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.6e-05
                     Peptidase_M57 122 gtglesysvdvnehvithelGhtvGlRhsD 151
                                       g+++++y+ + +  +  he+Gh++Gl hsD
  gi|298675693|ref|YP_003727443.1| 139 GYSWQQYGDANMYAIAKHEFGHALGLGHSD 168
                                       68999999999999999************9 PP

>> Peptidase_M54  Peptidase family M54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   7.6e-05      0.17     150     176 ..     155     182 ..     149     185 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.6e-05
                                       HHHHHHHTT----S-.TSTTS--SSHHH CS
                     Peptidase_M54 150 lhelGhlyGLshCke.dCvmnfsndlkd 176
                                        he Gh +GL+h ++ + +m +  +++d
  gi|298675693|ref|YP_003727443.1| 155 KHEFGHALGLGHSDDrNDIMYPEYEMRD 182
                                       6**************999**99988877 PP

>> Reprolysin_5  Metallo-peptidase family M12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.5e-05      0.17     134     161 ..     142     169 ..      88     181 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.5e-05
                      Reprolysin_5 134 svvvstatevqvvaHElGHnfGavHDcd 161
                                        + +++a+ + +  HE+GH++G  H  d
  gi|298675693|ref|YP_003727443.1| 142 WQQYGDANMYAIAKHEFGHALGLGHSDD 169
                                       44566788889999***********544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1432.01
//
Query:       gi|298675694|ref|YP_003727444.1|  [L=267]
Description: haloacid dehalogenase domain-containing protein hydrolase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.2e-18   65.5   0.1    3.4e-17   63.4   0.1    1.9  1  Hydrolase       haloacid dehalogenase-like hydrolase
    5.6e-05   23.0   6.7      0.053   13.2   0.9    2.8  3  Hydrolase_3     haloacid dehalogenase-like hydrolase
    0.00071   19.6   0.5      0.032   14.3   0.2    2.4  2  Hydrolase_like  HAD-hyrolase-like
  ------ inclusion threshold ------
      0.044   13.9   1.8       0.13   12.3   0.6    2.3  2  HAD_2           Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4   0.1   7.6e-21   3.4e-17       2     210 .]       5     230 ..       4     230 .. 0.65

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 7.6e-21
                                       SEEEEESBTTTBCHH.....HHHHHHHHHH.................CHHHHHHHHHHHHCHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxx.....xxxxxxxxxx.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   2 ktvvfDkdGTLttge.....psvedvivsa.................alalaaaletgsehpigkalvaaakarsga 56 
                                       k+vvfD  GTL++       p   ++++ +                   +l+ + et se+ +   + +   ++ ++
  gi|298675694|ref|YP_003727444.1|   5 KAVVFDSAGTLLQMYrvgkkPGSGQIFDNIestsvvakypnralvviNTELQTIAETNSETRLIDFIHENNVDMDIS 81 
                                       89999999999977766778777777777733333333333333333333333333333333333333333333333 PP

                                       H..HHHHHETTTEHHHHTHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHH............................ CS
                                       x..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................ RF
                         Hydrolase  57 l..tgfatfigrgayaigkpewltaldippdlgaaigsaqsqgrtvall............................ 103
                                       +  ++f +                                    +++++                            
  gi|298675694|ref|YP_003727444.1|  82 CssSNFKK------------------------------------EQIFDiikkndvivgdihdvicavrkgcppdlf 122
                                       33233333....................................111112333333333555555555555555555 PP

                                       ...........TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTTGGGESEEEEHHCE CS
                                       ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 104 ...........qaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlGddyfdaviasdie 169
                                                   + +l v+       ++p +  ++++L+ ++i+v++++gd+ ++ +++a+ ++         + ie
  gi|298675694|ref|YP_003727444.1| 123 ylaagviidagINTVLCVLSTGGW--LYPNTSITIRKLQNMNIDVYIASGDSTKNLKKLAHSIN---------VPIE 188
                                       666666664332244445555555..***********************************999.........7899 PP

                                       S.STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 170 t.vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                       + ++ ++  +k+++i  L+ k + vamVGDg+nD+ al+aA+
  gi|298675694|ref|YP_003727444.1| 189 GvFGIANAHDKERIIHDLKNKYNTVAMVGDGMNDIFALKAAD 230
                                       999999***********************************8 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.31   1.4e+03     120     145 ..      70      95 ..      34     110 .. 0.52
   2 !   12.4   0.0   2.1e-05     0.096      18      55 ..     149     186 ..     139     197 .. 0.86
   3 !   13.2   0.9   1.2e-05     0.053     193     226 ..     200     233 ..     192     256 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.31
                                       HHHCHCTCEEEESHHHHHCHCSESEE CS
                       Hydrolase_3 120 eeektkkkkeeidseeeledeeiaki 145
                                        +++++ +++++ s+++ ++e+i+ i
  gi|298675694|ref|YP_003727444.1|  70 FIHENNVDMDISCSSSNFKKEQIFDI 95 
                                       22333333333333333333333333 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 2.1e-05
                                       HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCC CS
                       Hydrolase_3  18 ektkeaikklkekgikvviATGRslravlpvleelgld 55 
                                       ++t  +i+kl++ +i v iA+G s+++++++++++++ 
  gi|298675694|ref|YP_003727444.1| 149 PNTSITIRKLQNMNIDVYIASGDSTKNLKKLAHSINVP 186
                                       678899***************************99965 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 1.2e-05
                                       HHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEE CS
                       Hydrolase_3 193 kklakelnisleeviafGDgeNDieMLeaaglgv 226
                                       +++++ l+ + + v+ +GDg+NDi  L+aa++g+
  gi|298675694|ref|YP_003727444.1| 200 ERIIHDLKNKYNTVAMVGDGMNDIFALKAADMGI 233
                                       5677888888999*******************98 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.023     1e+02      21      43 ..      97     117 ..      64     121 .. 0.70
   2 !   14.3   0.2   7.1e-06     0.032      12      71 ..     201     256 ..     194     262 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.023
                                       GGGEEEEES-TTTHHHHHHHCT- CS
                    Hydrolase_like  21 peevlmiGDrlatDiagAnnaGw 43 
                                       +++ +++GD   +D+++A + G+
  gi|298675694|ref|YP_003727444.1|  97 KKNDVIVGDI--HDVICAVRKGC 117
                                       566799****..******99886 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 7.1e-06
                                       HHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHHHHHHHT---SE CS
                    Hydrolase_like  12 falevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedleepehkptyvadd 71 
                                       ++ ++l+ + + v m+GD    Di + ++a +  + V +G +rpe+l+     ++ ++ d
  gi|298675694|ref|YP_003727444.1| 201 RIIHDLKNKYNTVAMVGDG-MNDIFALKAADMGILTVQQGDSRPEKLRNS---ANTIITD 256
                                       677888899999*******.************************999844...3444444 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.32   1.4e+03     150     172 ..      95     116 ..      53     118 .. 0.78
   2 ?   12.3   0.6   2.9e-05      0.13      81     176 ..     148     234 ..     145     236 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.32
                             HAD_2 150 lkkeeviyvGDsptDieaakkag 172
                                       + k++ ++vGD ++D+++a + g
  gi|298675694|ref|YP_003727444.1|  95 IIKKNDVIVGD-IHDVICAVRKG 116
                                       44555567887.67888887766 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 2.9e-05
                             HAD_2  81 ydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklklkkeeviy 157
                                       y++   ++ +L+++++ + i++  s++++++    +++   ++ + +  +++ k       e+++  lk k + v +
  gi|298675694|ref|YP_003727444.1| 148 YPNTSITIRKLQNMNIDVYIASGDSTKNLKKLAHSINV--PIEGVFGIANAHDK-------ERIIHDLKNKYNTVAM 215
                                       77888889999999999999999999999998888885..88999999988888.......8999999********* PP

                             HAD_2 158 vGDsptDieaakkagikvi 176
                                       vGD  +Di a k+a + ++
  gi|298675694|ref|YP_003727444.1| 216 VGDGMNDIFALKAADMGIL 234
                                       *************999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.55
# Mc/sec: 1459.95
//
Query:       gi|298675695|ref|YP_003727445.1|  [L=532]
Description: methyl coenzyme M reductase system subunit A2 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.9e-54  181.9   0.1    8.3e-27   94.4   0.0    2.3  2  ABC_tran        ABC transporter
    1.3e-05   24.7   1.0       0.17   11.3   0.0    3.0  2  SMC_N           RecF/RecN/SMC N terminal domain
    0.00023   20.9   0.2       0.26   10.9   0.0    2.4  2  ATP-synt_ab     ATP synthase alpha/beta family, nucleotide-bi
    0.00035   20.5   2.9       0.22   11.4   0.0    3.0  2  RsgA_GTPase     RsgA GTPase
     0.0012   18.6   0.1       0.64    9.7   0.0    2.4  2  PRK             Phosphoribulokinase / Uridine kinase family
     0.0022   18.6   0.3        1.4    9.5   0.1    2.9  3  AAA_18          AAA domain
     0.0026   17.6   0.0          4    7.2   0.0    3.2  3  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
      0.003   17.3   2.8       0.22   11.2   0.0    2.8  2  AAA_30          AAA domain
     0.0046   16.8   0.2          4    7.3   0.0    2.5  2  MobB            Molybdopterin guanine dinucleotide synthesis 
     0.0063   16.2   0.1        2.3    8.1   0.0    2.4  2  AAA_29          P-loop containing region of AAA domain
     0.0065   15.8   3.3        1.1    8.6   0.1    3.4  3  ATPase          KaiC
     0.0083   15.0   0.1      0.016   14.0   0.1    1.4  1  DLIC            Dynein light intermediate chain (DLIC)
       0.01   16.1   0.0         12    6.2   0.0    3.3  2  SbcCD_C         Putative exonuclease SbcCD, C subunit
  ------ inclusion threshold ------
      0.012   14.9   0.1       0.32   10.2   0.0    2.4  2  Zeta_toxin      Zeta toxin
      0.012   14.8   1.4       0.51    9.5   0.0    2.7  2  NB-ARC          NB-ARC domain
      0.017   15.7   0.8        5.6    7.4   0.1    2.5  2  AAA_23          AAA domain
      0.029   14.5   4.9        2.6    8.1   0.1    3.3  4  DUF87           Helicase HerA, central domain
      0.041   14.1   3.2        2.7    8.3   0.1    3.0  2  AAA_22          AAA domain
      0.055   13.6   0.2        2.3    8.3   0.0    2.7  2  AAA_33          AAA domain
      0.058   13.8   0.2        1.9    8.8   0.0    2.5  2  AAA_16          AAA ATPase domain
       0.08   13.0   2.4         11    6.2   0.0    3.7  4  MMR_HSR1        50S ribosome-binding GTPase
       0.13   10.9   0.3         31    3.0   0.0    3.1  3  AAA_13          AAA domain
       0.39   10.4   1.6         35    4.1   0.0    3.1  4  IstB_IS21       IstB-like ATP binding protein
       0.55   10.0   2.6          9    6.2   0.1    2.4  2  zinc_ribbon_2   zinc-ribbon domain
          5    7.1   5.4        2.7    7.9   0.3    2.5  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.4   0.0   6.8e-27   4.9e-24       1     136 [.      20     202 ..      20     203 .. 0.81
   2 !   94.4   0.0   1.2e-29   8.3e-27       2     136 ..     307     461 ..     306     462 .. 0.86

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 6.8e-27
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--..SEEEE................................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxx................................. RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp..teGei................................. 42 
                                       lknv+l+++ege+v+i+G++GaGK+ L+ +l g ++   ++Ge+                                 
  gi|298675695|ref|YP_003727445.1|  20 LKNVNLNINEGEVVGILGRSGAGKTVLMHVLRGVEEYknASGEViyhlarcskcgyieppskvgeecrecgeelqsy 96 
                                       79*****************************9965554499***888888888888888888888887777777766 PP

                                       ..EETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH..........HHHTCHHHHHHHSTTGGTTCBGESTTS CS
                                       ..xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  43 ..lldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren..........esdeeiekalsklglkelkdtvvkssp 106
                                          l + ++++++++   k+i+++ q    l  + +v +n          + ++ ++ka++ l+ +e+ ++ + + +
  gi|298675695|ref|YP_003727445.1|  97 evDLLKLPSNDKNRRNIVKRIAIMLQRtFALYGDDRVIDNvisslkeigyKGKDALSKAMELLDEVEMSHRMM-HVA 172
                                       5544466666688888888888888884444444447777999999999766666888888888888777777.556 PP

                                       GGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 107 ssLSgGqkqrvalarallkkpkllllDEpt 136
                                       + LSgG+kqrv+lar l+++p +l++DEpt
  gi|298675695|ref|YP_003727445.1| 173 RDLSGGEKQRVVLARQLVRNPMMLIADEPT 202
                                       9****************************9 PP

  == domain 2  score: 94.4 bits;  conditional E-value: 1.2e-29
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET.TCEGGG......B-HHHCCHCEEEE-SS--S- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx......xxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilld.gkdlke......qeleslrkeigvlpqepqlf 71 
                                       ++vs++++ege+ +i G +GaGK+t  ++l+g+++pt+G+i+++ g+d+ +      +++ ++ + +g+l+qe  l 
  gi|298675695|ref|YP_003727445.1| 307 NDVSFDVYEGEIFGIAGVSGAGKTTTSQILIGNVQPTKGSIEVRvGDDWVDmtvpgaENRGHATQYMGILHQEYGLY 383
                                       89***************************************9999999999999999******************** PP

                                       TTSBHHHH.........HHHTCHHHHHHHSTTGGTTCBGESTTS....GGS-HHHHHHHHHHHHHHHTSSEEEEEST CS
                                       xxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  72 peltvren.........esdeeiekalsklglkelkdtvvkssp....ssLSgGqkqrvalarallkkpkllllDEp 135
                                        + tv +n          ++  ++ka+s+l  ++++++ +ks      ++LS+G++ rvala++l+k+p+++++DEp
  gi|298675695|ref|YP_003727445.1| 384 TNRTVIDNltesigidlPYELAVKKAISTLTTTGFTEDEAKSLLhnmaEELSEGERHRVALAQVLMKEPNIVIMDEP 460
                                       ********9999999994444455555555555544444433333336***************************** PP

                                       T CS
                                       x RF
                          ABC_tran 136 t 136
                                       t
  gi|298675695|ref|YP_003727445.1| 461 T 461
                                       9 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.3   0.00047      0.34     135     206 ..     149     243 ..      14     255 .. 0.68
   2 !   11.3   0.0   0.00024      0.17     135     205 ..     401     500 ..     260     513 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00047
                                       T........................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHH. CS
                                       x........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                             SMC_N 135 e........................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkek. 186
                                       +                         LSgGek+     +++A q v+   + + De    LD k  ++v +++  + 
  gi|298675695|ref|YP_003727445.1| 149 KdalskamelldevemshrmmhvarDLSGGEKQ----RVVLARQLVRNPMMLIADEPTGTLDPKTARIVHDVISDAv 221
                                       25555555555555555556666668******8....56778889999999999*******************9651 PP

                                       .CTTSEEEEE-SSHHHCCC-.S CS
                                       .xxxxxxxxxxxxxxxxxxx.x RF
                             SMC_N 187 .sknaQfivislreemleka.d 206
                                        s n+ + ++s+  ++++++ d
  gi|298675695|ref|YP_003727445.1| 222 nSYNMTMTITSHWPDVIKQMaD 243
                                       1556888999999999988744 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00024
                                       T...............................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHH CS
                                       x...............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 135 e...............................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkva 180
                                                                       +LS Ge+  vala ++    +k   ++++De    +D    k v 
  gi|298675695|ref|YP_003727445.1| 401 PyelavkkaistltttgftedeaksllhnmaeELSEGERHRVALAQVL----MKEPNIVIMDEPTGTMDPVTKKDVT 473
                                       155555555555555555555666666666669**********99884....5666799*****************9 PP

                                       HHHHHHCTT..SEEEEE-SSHHHCCC- CS
                                       xxxxxxxxx..xxxxxxxxxxxxxxxx RF
                             SMC_N 181 ellkekskn..aQfivislreemleka 205
                                       + + +++++    fi++s++ ++l ++
  gi|298675695|ref|YP_003727445.1| 474 KSILKTRDKmgDTFIIVSHDMDFLVDV 500
                                       9988777773458******99887655 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00036      0.26      10      49 ..      26     144 ..      16     294 .. 0.77
   2 !    8.3   0.0    0.0023       1.6       6      51 ..     308     353 ..     304     490 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00036
                                       -EBTT-EEEEEESTTSSHHHHH...HHHHHHSSTSSEEEEEE................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxx................................... RF
                       ATP-synt_ab  10 pivqGqrtlipgafgvGktvis...qslskqsnsddaiiyvg................................... 48 
                                        i +G+ ++i+g +g Gktv++   + + +++n++  +iy +                                   
  gi|298675695|ref|YP_003727445.1|  26 NINEGEVVGILGRSGAGKTVLMhvlRGVEEYKNASGEVIYHLarcskcgyieppskvgeecrecgeelqsyevdllk 102
                                       678999****************4444445665555588888888999999999888777766655555555555555 PP

                                       .........................................E CS
                                       .........................................x RF
                       ATP-synt_ab  49 .........................................i 49 
                                                                                i
  gi|298675695|ref|YP_003727445.1| 103 lpsndknrrnivkriaimlqrtfalygddrvidnvisslkeI 144
                                       555555555555555555555555555555555555555554 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0023
                                       HHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEESE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab   6 DalfpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvgiGe 51 
                                       D+ f + +G+  +i g +g Gkt+ sq l+ + + ++ +i v +G 
  gi|298675695|ref|YP_003727445.1| 308 DVSFDVYEGEIFGIAGVSGAGKTTTSQILIGNVQPTKGSIEVRVGD 353
                                       7889999**********************99987766555555433 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00031      0.22      85     124 ..      15      55 ..       4      70 .. 0.73
   2 !    7.5   0.9    0.0049       3.5      90     130 ..     306     347 ..     206     354 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00031
                                       TTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-- CS
                       RsgA_GTPase  85 ktkegleelkellkd.ktsvlvGqSGvGKStLinallpele 124
                                       + ++ l++++ ++++ +++ ++G SG+GK+ L+ +l++ +e
  gi|298675695|ref|YP_003727445.1|  15 DGTSVLKNVNLNINEgEVVGILGRSGAGKTVLMHVLRGVEE 55 
                                       55556677777777769999****************99543 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0049
                                       HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                       RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinallpelelktgev 130
                                       +++++  + + ++  ++G SG+GK+t    l+++ +   g++
  gi|298675695|ref|YP_003727445.1| 306 VNDVSFDVYEgEIFGIAGVSGAGKTTTSQILIGNVQPTKGSI 347
                                       555554444439999***********9999999977666665 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0    0.0073       5.3       1      22 [.      32      53 ..      32      76 .. 0.79
   2 !    9.7   0.0    0.0009      0.64       1      21 [.     318     338 ..     318     401 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0073
                               PRK  1 vIgvagsSGaGkttvarkleki 22
                                      v+g+ g SGaGkt +++ l+ +
  gi|298675695|ref|YP_003727445.1| 32 VVGILGRSGAGKTVLMHVLRGV 53
                                      79************99988765 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0009
                               PRK   1 vIgvagsSGaGkttvarklek 21 
                                       + g+ag SGaGktt+++ l  
  gi|298675695|ref|YP_003727445.1| 318 IFGIAGVSGAGKTTTSQILIG 338
                                       679***********9987654 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.022        15       1      65 [.      33     102 ..      33     141 .. 0.71
   2 ?   -2.4   0.0       9.3   6.7e+03      25      44 ..     183     202 ..     148     250 .. 0.58
   3 !    9.5   0.1     0.002       1.4       3      18 ..     321     336 ..     320     372 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.022
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf....gvnlrdvakenglllevdpe.aldeskrldedkldklldale 65 
                                       +++ G +G+GKt l + L+  +++    g+++ ++a+ + + + + p    +e+++  e+ + + +d+l+
  gi|298675695|ref|YP_003727445.1|  33 VGILGRSGAGKTVLMHVLRGVEEYknasGEVIYHLARCSKCGYIEPPSkVGEECRECGEELQSYEVDLLK 102
                                       6899**************5544555677888888887766655444445555666666666666666555 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 9.3
                            AAA_18  25 gvnlrdvakenglllevdpe 44 
                                       +v  r+++++ ++l+ ++p 
  gi|298675695|ref|YP_003727445.1| 183 VVLARQLVRNPMMLIADEPT 202
                                       56666666666666666665 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.002
                            AAA_18   3 ltGtpGvGKttlakeL 18 
                                       ++G++G+GKtt ++ L
  gi|298675695|ref|YP_003727445.1| 321 IAGVSGAGKTTTSQIL 336
                                       99***********998 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.016        11       2      79 ..      33     101 ..      32     153 .. 0.80
   2 !    7.2   0.0    0.0056         4       2      54 ..     319     365 ..     318     370 .. 0.88
   3 ?    0.5   0.0      0.59   4.2e+02     235     298 ..     432     493 ..     429     499 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.016
                            AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrl 78 
                                        ++ G+ g+GK+ L+  l+++         + +++ +g  i   ++ +  +++e+p++ + e+ +  +   +y+++l
  gi|298675695|ref|YP_003727445.1|  33 VGILGRSGAGKTVLMHVLRGV---------EEYKNASGEVIYHLARCSKCGYIEPPSKVGEECRECGEELQSYEVDL 100
                                       6899**************999.........66777778888888888888888888888777777777777777666 PP

                            AAA_21  79 e 79 
                                        
  gi|298675695|ref|YP_003727445.1| 101 L 101
                                       5 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0056
                            AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydp 54 
                                        ++ G  g+GK++  ++l      +++v++++ +   ++g ++++   ++ + 
  gi|298675695|ref|YP_003727445.1| 319 FGIAGVSGAGKTTTSQIL------IGNVQPTKGSIEVRVGDDWVDMTVPGAEN 365
                                       6899**************......****************9999988777665 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.59
                            AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHP....kllrrllellkelsrngaQviltTHS 298
                                        elS+G ++  al+  l   +    +++ DEp   ++P     +++++l+  ++  +    +i+++H+
  gi|298675695|ref|YP_003727445.1| 432 EELSEGERHRVALAQVLMKEP---NIVIMDEPTGTMDPvtkkDVTKSILKTRDKMGD---TFIIVSHD 493
                                       578999999999999999888...89******9999996666666666654444433...67888887 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00031      0.22      18      50 ..      30      64 ..      22      73 .. 0.69
   2 ?    3.8   2.0      0.06        43      20      47 ..     318     358 ..     313     484 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00031
                            AAA_30 18 drvavltGpAGtGKttalkalrea..weaaggrvi 50
                                        v+ + G+ G+GKt ++ +lr +  +++a g+vi
  gi|298675695|ref|YP_003727445.1| 30 GEVVGILGRSGAGKTVLMHVLRGVeeYKNASGEVI 64
                                      459999************99965511444434444 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.06
                            AAA_30  20 vavltGpAGtGKttalkalreaweaa.g............g 47 
                                       +  + G+ G+GKtt+ + l   ++   g            +
  gi|298675695|ref|YP_003727445.1| 318 IFGIAGVSGAGKTTTSQILIGNVQPTkGsievrvgddwvdM 358
                                       56689*********988875555444245555555555555 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0056         4       1      19 [.      32      50 ..      32      68 .. 0.83
   2 !    7.0   0.0    0.0071       5.1       1      24 [.     318     341 ..     318     360 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0056
                              MobB  1 vlgivgksgsGKTtLlekl 19
                                      v+gi g+sg+GKT L++ l
  gi|298675695|ref|YP_003727445.1| 32 VVGILGRSGAGKTVLMHVL 50
                                      689************9866 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0071
                              MobB   1 vlgivgksgsGKTtLleklipelk 24 
                                       ++gi+g sg+GKTt  + li  ++
  gi|298675695|ref|YP_003727445.1| 318 IFGIAGVSGAGKTTTSQILIGNVQ 341
                                       689***********9999997765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0031       2.3      16      39 ..      24      47 ..      18      57 .. 0.82
   2 ?    5.6   0.0     0.019        13      16      37 ..     310     331 ..     303     334 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0031
                            AAA_29 16 tieidlkgatlltGpsGsGKSTll 39
                                       ++i++ +++ + G+sG+GK+ l+
  gi|298675695|ref|YP_003727445.1| 24 NLNINEGEVVGILGRSGAGKTVLM 47
                                      56777555999**********997 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.019
                            AAA_29  16 tieidlkgatlltGpsGsGKST 37 
                                       ++++ + +++ ++G sG+GK+T
  gi|298675695|ref|YP_003727445.1| 310 SFDVYEGEIFGIAGVSGAGKTT 331
                                       55555444889**********9 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.1    0.0015       1.1      16     136 ..      27     144 ..      21     213 .. 0.67
   2 ?   -1.0   0.0       1.3   9.4e+02     106     151 ..     229     273 ..     213     278 .. 0.76
   3 ?    5.6   0.2     0.012       8.8      17      37 ..     314     334 ..     310     345 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0015
                            ATPase  16 ipegrvvlitGepGtGKtifalqFlikgaekyge...pgvfvtveepaedlrenakslGwdlekleeegklaiidas 89 
                                       i eg+vv i G +G+GKt++    +++g+e+y +   ++++     ++   +e  +++G + ++  ee + + +d+ 
  gi|298675695|ref|YP_003727445.1|  27 INEGEVVGILGRSGAGKTVLM--HVLRGVEEYKNasgEVIYHLARCSKCGYIEPPSKVGEECRECGEELQSYEVDLL 101
                                       6799**************985..577888777551114556555555566666666666666666666666666666 PP

                            ATPase  90 esaeesaeekdkedleelieelaeaikeikakrvviDsitglayeek 136
                                       +  ++   +++++ ++ ++  l++  + ++  rv iD++ +   +e 
  gi|298675695|ref|YP_003727445.1| 102 KLPSN--DKNRRNIVKRIAIMLQRTFALYGDDRV-IDNVISS-LKEI 144
                                       66554..335677777777777777777777775.4554443.3444 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.3
                            ATPase 106 elieelaeaikeikakrvviDsitglayeekeavaReilrqlvrvl 151
                                        ++++  ++ik++  k++++D+ + + +e +++++ +++ +l+  +
  gi|298675695|ref|YP_003727445.1| 229 TITSHWPDVIKQMADKAIILDKGEIV-NEGNPSEMADEFTNLACSI 273
                                       56667788999999999999998888.8888888888888887666 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.012
                            ATPase  17 pegrvvlitGepGtGKtifal 37 
                                       +eg++  i+G++G+GKt+ ++
  gi|298675695|ref|YP_003727445.1| 314 YEGEIFGIAGVSGAGKTTTSQ 334
                                       6889999**********9986 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   2.3e-05     0.016      25      56 ..      30      61 ..      18      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.3e-05
                              DLIC 25 gksvlvlGedgsGkttliaklqGveeekkGrG 56
                                      g  v +lG +g+Gkt l+  l+Gvee+k  +G
  gi|298675695|ref|YP_003727445.1| 30 GEVVGILGRSGAGKTVLMHVLRGVEEYKNASG 61
                                      566889**********************9998 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0      0.03        21      18      42 ..     160     184 ..     149     218 .. 0.78
   2 ?    6.2   0.0     0.017        12      18      82 ..     419     470 ..     411     477 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.03
                           SbcCD_C  18 dedgkekelsrssgtlSGGekqfla 42 
                                       de + + ++ + ++ lSGGekq ++
  gi|298675695|ref|YP_003727445.1| 160 DEVEMSHRMMHVARDLSGGEKQRVV 184
                                       566667778899999******8765 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.017
                           SbcCD_C  18 dedgkekelsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesia 82 
                                       +ed++++ l++++++lS Ge+          ala+++ ++      + +v++DE  +++D+ + +
  gi|298675695|ref|YP_003727445.1| 419 TEDEAKSLLHNMAEELSEGER-------HRVALAQVLMKE------PNIVIMDEPTGTMDPVTKK 470
                                       566677678888888888888.......456777888884......899***********87665 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.16   1.1e+02      22      38 ..      36      52 ..      21      63 .. 0.81
   2 ?   10.2   0.0   0.00045      0.32      21      61 ..     321     363 ..     317     395 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.16
                        Zeta_toxin 22 gGqpGAGKselaellkd 38
                                       G +GAGK+ l++ l+ 
  gi|298675695|ref|YP_003727445.1| 36 LGRSGAGKTVLMHVLRG 52
                                      5899******9998875 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00045
                        Zeta_toxin  21 lgGqpGAGKselaellkdelerqgnv..vrldpDdlRelhPey 61 
                                       ++G +GAGK+++++ l  +++++++   vr+  D +    P +
  gi|298675695|ref|YP_003727445.1| 321 IAGVSGAGKTTTSQILIGNVQPTKGSieVRVGDDWVDMTVPGA 363
                                       79*******************6666512555555555555555 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00071      0.51      18      38 ..      30      48 ..      19     148 .. 0.85
   2 ?    3.0   0.9     0.068        48      22      49 ..     318     345 ..     308     459 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00071
                                      SCSEEEEEEESTTSSHHHHHH CS
                            NB-ARC 18 lqslvvalvGmgGvGKttlak 38
                                       +  vv++ G+ G GKt+l++
  gi|298675695|ref|YP_003727445.1| 30 GE--VVGILGRSGAGKTVLMH 48
                                      44..9**************96 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.068
                                       EEEEEESTTSSHHHHHHHHCCSHCCCCC CS
                            NB-ARC  22 vvalvGmgGvGKttlakqilnksdeveg 49 
                                       + ++ G  G GKtt ++  + + + ++g
  gi|298675695|ref|YP_003727445.1| 318 IFGIAGVSGAGKTTTSQILIGNVQPTKG 345
                                       7899**********88766666555555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0079       5.6      16      39 ..      13      50 ..       4      61 .. 0.71
   2 ?    6.1   0.1     0.019        14      13      34 ..     309     331 ..     303     336 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0079
                            AAA_23 16 dF..............skgltlItGpNGaGKTTildAi 39
                                      dF              +  ++ I G  GaGKT ++  +
  gi|298675695|ref|YP_003727445.1| 13 DFdgtsvlknvnlninEGEVVGILGRSGAGKTVLMHVL 50
                                      554444444444444555699***********998665 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.019
                            AAA_23  13 qeidF.skgltlItGpNGaGKTT 34 
                                       +++d  +  ++ I G  GaGKTT
  gi|298675695|ref|YP_003727445.1| 309 VSFDVyEGEIFGIAGVSGAGKTT 331
                                       4455566789************9 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1    0.0036       2.6      26      43 ..      33      50 ..      14      61 .. 0.86
   2 ?   -1.0   0.0       2.2   1.6e+03     162     210 ..     131     177 ..      88     191 .. 0.59
   3 ?    6.5   0.1     0.011       7.9      26      45 ..     319     338 ..     307     347 .. 0.88
   4 ?   -2.8   0.0       7.9   5.7e+03     161     161 ..     440     440 ..     387     492 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0036
                             DUF87 26 lAilgsTGsGKSntvavL 43
                                      ++ilg++G+GK+ ++ vL
  gi|298675695|ref|YP_003727445.1| 33 VGILGRSGAGKTVLMHVL 50
                                      89*************998 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.2
                             DUF87 162 nqaiarlldkledllrkggsfsnsstdliallleklekegkitii.dlsg 210
                                       ++ i +++++l+++ +kg++     ++ ++ll e++ +++ +++  dlsg
  gi|298675695|ref|YP_003727445.1| 131 DRVIDNVISSLKEIGYKGKDA---LSKAMELLDEVEMSHRMMHVArDLSG 177
                                       334444444444444444444...44555555555555555555555555 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.011
                             DUF87  26 lAilgsTGsGKSntvavLle 45 
                                       ++i g +G+GK++t  +L+ 
  gi|298675695|ref|YP_003727445.1| 319 FGIAGVSGAGKTTTSQILIG 338
                                       89*************99985 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 7.9
                             DUF87 161 k 161
                                        
  gi|298675695|ref|YP_003727445.1| 440 H 440
                                       1 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1    0.0038       2.7      10      51 ..      35      82 ..      28     200 .. 0.80
   2 ?    5.1   0.6     0.036        26      10      30 ..     321     341 ..     314     459 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0038
                            AAA_22 10 vtGesGtGKTtllrrlleqldeeakaee.......erpevvfvtlpsst 51
                                      + G sG+GKT+l+  l+   +e+++a         +++++ ++++ps+ 
  gi|298675695|ref|YP_003727445.1| 35 ILGRSGAGKTVLMHVLRGV-EEYKNASGeviyhlaRCSKCGYIEPPSKV 82
                                      78**********9877665.45666655788877666666677777765 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.036
                            AAA_22  10 vtGesGtGKTtllrrlleqld 30 
                                       + G sG+GKTt+ + l  + +
  gi|298675695|ref|YP_003727445.1| 321 IAGVSGAGKTTTSQILIGNVQ 341
                                       789********9998877664 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1      0.28     2e+02       2      18 ..      33      49 ..      32      64 .. 0.82
   2 ?    8.3   0.0    0.0033       2.3       5      57 ..     322     381 ..     319     400 .. 0.66

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.28
                            AAA_33  2 vllvGlpGsGKstlaer 18
                                      v + G +G+GK+ l + 
  gi|298675695|ref|YP_003727445.1| 33 VGILGRSGAGKTVLMHV 49
                                      557799******99875 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0033
                            AAA_33   5 vGlpGsGKstlaerllkklg......avllssdtlrrrlfg.tdqqsktdytrvldrlyq 57 
                                        G++G+GK+t ++ l+ + +       v++  d +  ++ g + + + t+y  +l++ y+
  gi|298675695|ref|YP_003727445.1| 322 AGVSGAGKTTTSQILIGNVQptkgsiEVRVGDDWVDMTVPGaENRGHATQYMGILHQEYG 381
                                       6***********999554444447755666666555566555555566666666666554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0026       1.9      21      63 ..      27      73 ..      17     128 .. 0.80
   2 ?    2.2   0.1      0.28     2e+02      25      40 ..     317     332 ..     310     351 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0026
                            AAA_16 21 sgrpelvllsGesGvGKsslvrellr..alekd.....ggiflrgkcdql 63
                                       +++e+v + G sG GK+ l+  l+   +         ++i+  ++c ++
  gi|298675695|ref|YP_003727445.1| 27 INEGEVVGILGRSGAGKTVLMHVLRGveE---YknasgEVIYHLARCSKC 73
                                      55668999************977763222...123353377777777776 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.28
                            AAA_16  25 elvllsGesGvGKssl 40 
                                       e+  + G sG GK++ 
  gi|298675695|ref|YP_003727445.1| 317 EIFGIAGVSGAGKTTT 332
                                       566689********96 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.015        11       2      21 ..      33      52 ..      32      66 .. 0.84
   2 ?    0.0   0.0       1.2   8.7e+02      16      43 ..     186     214 ..     184     303 .. 0.80
   3 ?    3.7   0.1     0.085        61       3      23 ..     320     340 ..     318     355 .. 0.83
   4 ?   -1.9   0.0       4.8   3.5e+03      46      55 ..     452     461 ..     407     515 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.015
                                      EEEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                                      v+i+Gr+ +GK+ L+  l g
  gi|298675695|ref|YP_003727445.1| 33 VGILGRSGAGKTVLMHVLRG 52
                                      89************998865 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.2
                                       HHHHHTS.TEEESSSTTSSSSEEEEEEEE CS
                          MMR_HSR1  16 inaltge.kaivsdkpgtTrdinegrvkl 43 
                                        ++l+++    ++d+p  T+d++++r+ +
  gi|298675695|ref|YP_003727445.1| 186 ARQLVRNpMMLIADEPTGTLDPKTARIVH 214
                                       56777775678899999999999998863 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.085
                                       EEEESTTSSHHHHHHHHHTST CS
                          MMR_HSR1   3 aivGrpNvGKStLinaltgek 23 
                                       +i+G + +GK+t  + l+g++
  gi|298675695|ref|YP_003727445.1| 320 GIAGVSGAGKTTTSQILIGNV 340
                                       89***********99999974 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 4.8
                                       EEEEEEECGG CS
                          MMR_HSR1  46 keielvDtpG 55 
                                       ++i+++D p 
  gi|298675695|ref|YP_003727445.1| 452 PNIVIMDEPT 461
                                       3344444442 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.043        31      21      43 ..      35      57 ..      26      74 .. 0.84
   2 ?    2.8   0.0     0.051        37      23      37 ..     323     337 ..     317     359 .. 0.83
   3 ?    0.6   0.0      0.24   1.7e+02     495     511 ..     429     445 ..     423     505 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.043
                            AAA_13 21 iYGwNGaGKTtLSrllrslelge 43
                                      i G+ GaGKT L  +lr +e+ +
  gi|298675695|ref|YP_003727445.1| 35 ILGRSGAGKTVLMHVLRGVEEYK 57
                                      6799**************97643 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.051
                            AAA_13  23 GwNGaGKTtLSrllr 37 
                                       G  GaGKTt S++l 
  gi|298675695|ref|YP_003727445.1| 323 GVSGAGKTTTSQILI 337
                                       778*********985 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.24
                            AAA_13 495 qaaetLSeGEktaIafl 511
                                       + ae+LSeGE+  +a+ 
  gi|298675695|ref|YP_003727445.1| 429 NMAEELSEGERHRVALA 445
                                       56899******999975 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.059        42      44      66 ..      27      49 ..      14      66 .. 0.85
   2 ?    4.1   0.0     0.049        35     102     159 ..     185     239 ..     162     250 .. 0.71
   3 ?   -1.8   0.0         3   2.2e+03      46      61 ..     315     330 ..     297     336 .. 0.79
   4 ?   -2.8   0.0       6.4   4.6e+03      87     116 ..     427     459 ..     409     476 .. 0.61

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.059
                         IstB_IS21 44 iekkenivllGpsGvGKshlaia 66
                                      i++ e + +lG sG+GK+ l   
  gi|298675695|ref|YP_003727445.1| 27 INEGEVVGILGRSGAGKTVLMHV 49
                                      67788999**********98765 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.049
                         IstB_IS21 102 alkrllkvdllilDdlgllpldqaeaellfeviekryerrsiiitsnlpfaewdevlg 159
                                        +++l++  ++++ d  + +ld + a+ + +vi+++++   + +t      +w +v++
  gi|298675695|ref|YP_003727445.1| 185 LARQLVRNPMMLIADEPTGTLDPKTARIVHDVISDAVNSYNMTMTITS---HWPDVIK 239
                                       45778888777777778899*****************99888877654...4555554 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 3
                         IstB_IS21  46 kkenivllGpsGvGKs 61 
                                       + e + + G sG+GK+
  gi|298675695|ref|YP_003727445.1| 315 EGEIFGIAGVSGAGKT 330
                                       55667799*******9 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 6.4
                         IstB_IS21  87 veelkrarrdgklar.alkr..llkvdllilDd 116
                                       +++++ + ++g+ +r al++  + +++++i+D+
  gi|298675695|ref|YP_003727445.1| 427 LHNMAEELSEGERHRvALAQvlMKEPNIVIMDE 459
                                       444444444443333122220033457888887 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.3     0.093        67       2       6 ..      70      74 ..      68      76 .. 0.62
   2 ?    6.2   0.1     0.013         9       2      12 ..      86      96 ..      85      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.093
                     zinc_ribbon_2  2 CpnCG 6 
                                      C++CG
  gi|298675695|ref|YP_003727445.1| 70 CSKCG 74
                                      66665 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.013
                     zinc_ribbon_2  2 CpnCGaelqdn 12
                                      C +CG+elq  
  gi|298675695|ref|YP_003727445.1| 86 CRECGEELQSY 96
                                      99*****9976 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.3    0.0037       2.7      23      34 ..      69      80 ..      56      82 .. 0.82
   2 ?    0.6   0.8      0.74   5.3e+02      23      28 ..      85      90 ..      79      93 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0037
                                      EESSSS-EEESS CS
                    RNA_POL_M_15KD 23 eCrqCgYeepad 34
                                       C++CgY+ep +
  gi|298675695|ref|YP_003727445.1| 69 RCSKCGYIEPPS 80
                                      4********965 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.74
                                      EESSSS CS
                    RNA_POL_M_15KD 23 eCrqCg 28
                                      eCr Cg
  gi|298675695|ref|YP_003727445.1| 85 ECRECG 90
                                      799997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (532 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1008  (0.0562218); expected 358.6 (0.02)
Passed bias filter:                      847  (0.0472419); expected 358.6 (0.02)
Passed Vit filter:                       123  (0.00686039); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.80u 0.37s 00:00:01.17 Elapsed: 00:00:00.54
# Mc/sec: 2984.34
//
Query:       gi|298675696|ref|YP_003727446.1|  [L=527]
Description: methanogenesis marker protein 3 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-06   27.2   0.3       0.37   11.1   0.0    5.0  5  Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans iso
  ------ inclusion threshold ------
      0.055   13.1   0.0        0.1   12.3   0.0    1.4  1  DUF3830        Protein of unknown function (DUF3830)
      0.064   13.3   0.0       0.14   12.2   0.0    1.6  1  Fer2_4         2Fe-2S iron-sulfur cluster binding domain
      0.085   10.8   0.0       0.13   10.2   0.0    1.1  1  IKI3           IKI3 family


Domain annotation for each model (and alignments):
>> Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0     0.093   4.2e+02       3      20 ..      68      84 ..      66      91 .. 0.87
   2 ?    1.0   0.0     0.099   4.5e+02     123     144 ..     166     187 ..     145     196 .. 0.79
   3 ?    2.5   0.0     0.035   1.6e+02      12      38 ..     221     246 ..     212     254 .. 0.88
   4 ?    3.8   0.0     0.014        63      87     139 ..     274     320 ..     246     335 .. 0.73
   5 !   11.1   0.0   8.2e-05      0.37      12      36 ..     395     430 ..     389     484 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.093
                     Pro_isomerase  3 dietsskGrivieLfadk 20
                                      +i+ts kG+++ieL++++
  gi|298675696|ref|YP_003727446.1| 68 KITTS-KGEFQIELYGNE 84
                                      78996.*********987 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.099
                     Pro_isomerase 123 vFGkVveGmdvvekiekvetde 144
                                        F +V++G ++v ++e+ +t +
  gi|298675696|ref|YP_003727446.1| 166 SFAHVISGRKIVSNLEQSDTIK 187
                                       599*************987655 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.035
                     Pro_isomerase  12 ivieLfadkaPktvenFlklvkegfYd 38 
                                       +++e+++d  P+ +e F +lvk+g+++
  gi|298675696|ref|YP_003727446.1| 221 FEVEINPDA-PEGAESFFALVKDGTFK 246
                                       788999987.*************9876 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.014
                     Pro_isomerase  87 krGalamartgkepnsagsqFfItlkeaphldgkytvFGkVveGmdvvekiek 139
                                       + Ga++   +g     ++   +I+ k+ p     + v G+V++G+++++ i+k
  gi|298675696|ref|YP_003727446.1| 274 QTGAVSIRTAG----YNTGRTYISRKDRPSSIA-HSVIGYVTKGIELIK-IAK 320
                                       66888887775....566666999999998877.9***********995.655 PP

  == domain 5  score: 11.1 bits;  conditional E-value: 8.2e-05
                     Pro_isomerase  12 ivieLfadkaPktvenFlklvkeg...........f 36 
                                       i+ieLf+d+aPktv+ F++ ++ +           +
  gi|298675696|ref|YP_003727446.1| 395 IKIELFDDSAPKTVDFFRHAARLQfknvghlsvyfT 430
                                       99****************999755444444444444 PP

>> DUF3830  Protein of unknown function (DUF3830)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.3e-05       0.1      10      80 ..     395     472 ..     390     497 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.3e-05
                                       EEEEE-TTTSHHHHHHHHHH--EEEE.-EE..-SSSSSEEEEEEE--S...SS---S-SEES.S--TTEEEEEEEEH CS
                           DUF3830  10 ataeLledkAPetcaavwealplssd.viH..akyagneiyvllpefa...atelpaENaTv.tPipGdvvlfsfek 79 
                                       +++eL++d+AP+t++++++a  l+++ v H  + ++ +++y+   e++    +e+ +EN+     + Gdv   ++++
  gi|298675696|ref|YP_003727446.1| 395 IKIELFDDSAPKTVDFFRHAARLQFKnVGHlsVYFTYENTYLFKAELEaekYKEIMPENTPEnKVNAGDVGITNQAA 471
                                       679******************77764255644678888898765444433378888888643134566666665555 PP

                                       H CS
                           DUF3830  80 t 80 
                                       +
  gi|298675696|ref|YP_003727446.1| 472 K 472
                                       5 PP

>> Fer2_4  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.1e-05      0.14       2      31 ..      14      43 ..      13      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.1e-05
                            Fer2_4  2 rpvtltfDGkevtvpeGdtvasAllangvd 31
                                      +++++++DG+++t pe +t+ +Al + +v+
  gi|298675696|ref|YP_003727446.1| 14 NEIEVEVDGQKITLPEESTLEDALKKSDVT 43
                                      6899*********************99975 PP

>> IKI3  IKI3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   2.9e-05      0.13     104     165 ..     294     354 ..     282     363 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 2.9e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              IKI3 104 vdsdaeekeveivGsiesGieaaawspdeellalvtgeekvvlmtrdfepisetsldaddlk 165
                                       +++ +++ + +++G + +Gie ++    e++l ++t  ++++l+ + f+  +e +l++ d+k
  gi|298675696|ref|YP_003727446.1| 294 RKDRPSSIAHSVIGYVTKGIELIKIAKQEDVLSVATIPNQIMLLGKGFKE-AESRLENLDIK 354
                                       5567899999**************************************87.56666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (527 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 3145.63
//
Query:       gi|298675697|ref|YP_003727447.1|  [L=152]
Description: methanogenesis marker protein 6 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-42  143.7   0.0    2.1e-42  143.0   0.0    1.3  1  DUF2102   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2102  Uncharacterized protein conserved in archaea (DUF2102)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.0   0.0   1.2e-46   2.1e-42       2     103 .]      19     120 ..      18     120 .. 0.98

  Alignments for each domain:
  == domain 1  score: 143.0 bits;  conditional E-value: 1.2e-46
                           DUF2102   2 vvieseaevtpselvrkvyeleedvtiketCfGllvegeeeevekvveevrkldpnkifvkeRgfppgderrCRakr 78 
                                       vvi+s+  v+ps+ ++k+ye+e++vt+ketCfGl+v+g++e+v+++ve+v ++d+n+ifvk+RgfppgderrCRa r
  gi|298675697|ref|YP_003727447.1|  19 VVIDSDW-VLPSDAAMKIYESETEVTVKETCFGLMVHGPSEAVNRAVEDVVSMDRNHIFVKQRGFPPGDERRCRAVR 94 
                                       8899998.********************************************************************* PP

                           DUF2102  79 .ggaRpGfhqlekEvelleliskaLe 103
                                        gg+RpG+++l++Ev++l++i+kaL+
  gi|298675697|ref|YP_003727447.1|  95 gGGPRPGYYFLREEVNMLPTIGKALD 120
                                       99**********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 956.28
//
Query:       gi|298675698|ref|YP_003727448.1|  [L=157]
Description: methanogenesis marker protein 5 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-66  222.0   0.0      3e-66  221.8   0.0    1.0  1  DUF2112   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2112  Uncharacterized protein conserved in archaea (DUF2112)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.8   0.0   1.7e-70     3e-66       1     143 []       2     144 ..       2     144 .. 0.99

  Alignments for each domain:
  == domain 1  score: 221.8 bits;  conditional E-value: 1.7e-70
                           DUF2112   1 mkvaviPdnsliladlverfgheplslakeikekvktaeldspplniteedpkkGlkyaavevPsGvrGRlsligpl 77 
                                       +kv+++P+nslil+dlverfghepl+++ +++ek++t+++dspp+ni++edpk GlkyaavevPsGvrGRl++ gpl
  gi|298675698|ref|YP_003727448.1|   2 AKVFIYPTNSLILYDLVERFGHEPLAMMGRVHEKITTPGIDSPPININPEDPKYGLKYAAVEVPSGVRGRLAMAGPL 78 
                                       59*************************************************************************** PP

                           DUF2112  78 ieeaeaaiiveeadilfgcvGCartnelvkalirkkdiPileleyPkseeeaielvkkineFLksl 143
                                       ie+aeaaiiv+++ i+fgc+GCartne+vk++ r+kdiPileleyP++eee++++v+ki++FLksl
  gi|298675698|ref|YP_003727448.1|  79 IEKAEAAIIVNDSAISFGCMGCARTNEMVKYMARQKDIPILELEYPSTEEEGKDFVYKIADFLKSL 144
                                       ***************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1038.71
//
Query:       gi|298675699|ref|YP_003727449.1|  [L=418]
Description: methanogenesis marker protein 15 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-61  208.3   4.3      2e-61  207.8   4.3    1.2  1  BcrAD_BadFG    BadF/BadG/BcrA/BcrD ATPase family
    0.00021   21.7   0.3      0.004   17.5   0.3    2.4  1  FtsA           Cell division protein FtsA
     0.0019   17.1   0.1     0.0044   15.9   0.1    1.7  1  MreB_Mbl       MreB/Mbl protein
  ------ inclusion threshold ------
      0.026   14.2   0.2      0.069   12.9   0.2    1.7  1  Hydant_A_N     Hydantoinase/oxoprolinase N-terminal region
      0.028   14.1   0.0        1.8    8.2   0.0    2.4  2  Peptidase_M22  Glycoprotease family
      0.062   11.9   0.2        1.2    7.6   0.0    2.6  3  Actin          Actin
      0.068   13.1   0.0       0.14   12.0   0.0    1.5  1  DUF4934        Domain of unknown function (DUF4934)


Domain annotation for each model (and alignments):
>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.8   4.3   7.9e-65     2e-61       2     267 .]     158     411 ..     157     411 .. 0.97

  Alignments for each domain:
  == domain 1  score: 207.8 bits;  conditional E-value: 7.9e-65
                                       EEEE-SSEEEEEEEETTTEEEEEEEE--TTS-HHH.........HHHHHHHHHHT--GGGECEE..EEESTTCCCTC CS
                       BcrAD_BadFG   2 GiDgGsTttkavlmdekgevlgrgitnsanlesvrfeaaekvleealtealerageeeadieetylvgtgyGratlp 78 
                                       GiD+GsTttkav+m++++ +   ++ + + +es++         ea+++al++ag +++di+++  ++tgyGr  ++
  gi|298675699|ref|YP_003727449.1| 158 GIDSGSTTTKAVVMRDNQVIGHGWVPTIKVIESAE---------EAYKKALDEAGVNREDIQSI--GTTGYGRFLVG 223
                                       9****************888888899999999776.........9*****************99..*********** PP

                                       TTBSEEE-..HHHHHHHHHHHH-TT--...EEEEEETTEEEEEEEETTEEEEEEEESS--TTSHHHHHHHHHHHT-- CS
                       BcrAD_BadFG  79 ekfekeiirseilvhgdGavalypgtr...tvldigGqdskgiqidkgkvenfqmndrcaageGrylgiiadelnmg 152
                                       +k++++  ++ei+v+++Gav+l+++++   tv+digG+d+k+i++++g++  f+m++ ca+ +Gr+l+++a++l++ 
  gi|298675699|ref|YP_003727449.1| 224 KKYDAQLSQEEITVNSKGAVYLADKQKgsaTVIDIGGMDNKAITVEDGIPGMFSMGGVCAGASGRFLEMTAKRLGVD 300
                                       ***************************************************************************** PP

                                       TTTHHHHHTT--.S-------SHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHTT---SS.EEEESGGGG CS
                       BcrAD_BadFG 153 lreldglaekat.kkarinstcavfaeaelrdalsggekaedIlaglhraialrvialisrsggvtdevtltGGvak 228
                                       + el++la k+  +++ +ns+c vf  + l++ l++g++ ed+ a ++ ++++++ +++ ++ ++++ v+l+GG + 
  gi|298675699|ref|YP_003727449.1| 301 ITELGSLAVKGIeNNIEMNSYCIVFGIQSLVNSLAKGASPEDVAAAACYSVIEQIFEQQLQEVDIREPVILVGGSSL 377
                                       ***********95559************************************************************* PP

                                       -HHHHHHH.....HHHH-S-EE--GGGGGHHHHHHHHHH CS
                       BcrAD_BadFG 229 neaavkelrklvkenygevkininpdsiytgalGAalfA 267
                                        e++ ++l     e++++v++ ++pds+y ga+GA+++A
  gi|298675699|ref|YP_003727449.1| 378 IEGIPRTL-----EKFLKVEVIVPPDSQYIGAVGASMLA 411
                                       ********.....************************98 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.3   1.6e-06     0.004       1      87 [.     157     390 ..     157     413 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.6e-06
                                       EEEEE-SSSEEEEEEETTEEEEEEEES-...-HHHHHHHHHHHHT--HHHHHHHHH...HH--S--........... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxx........... RF
                              FtsA   1 alvDiGagktdvavaedgalvhlrvigv...ggngitkdiakalrtaveeAeriki...kyGsala........... 60 
                                       a++D G+++t+++v++d+     +vig    +   + +++++a+++a++eA        ++G               
  gi|298675699|ref|YP_003727449.1| 157 AGIDSGSTTTKAVVMRDN-----QVIGHgwvPTIKVIESAEEAYKKALDEAGVNREdiqSIG---Ttgygrflvgkk 225
                                       79***************6.....555555557788889999999999999965553111222...133345555777 PP

                                       .EEEEEHHHHH.................................................................. CS
                                       .xxxxxxxxxx.................................................................. RF
                              FtsA  61 .ekeigrkels.................................................................. 70 
                                        + +++++e++                                                                  
  gi|298675699|ref|YP_003727449.1| 226 yDAQLSQEEITvnskgavyladkqkgsatvidiggmdnkaitvedgipgmfsmggvcagasgrflemtakrlgvdit 302
                                       76666666666888888888899999999999999999999999999999999999999999999999999999999 PP

                                       .......................................................................GGGGST CS
                                       .......................................................................xxxxxx RF
                              FtsA  71 .......................................................................ggsalp 76 
                                                                                                              g+s ++
  gi|298675699|ref|YP_003727449.1| 303 elgslavkgienniemnsycivfgiqslvnslakgaspedvaaaacysvieqifeqqlqevdirepvilvgGSSLIE 379
                                       99999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                       THHHHHHHHHT CS
                                       xxxxxxxxxxx RF
                              FtsA  77 nleelaerals 87 
                                       ++ + +e+ l+
  gi|298675699|ref|YP_003727449.1| 380 GIPRTLEKFLK 390
                                       99999998873 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.7e-06    0.0044     271     319 ..     364     411 ..     296     417 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.7e-06
                                       HHHHH-EEEESGGGGSBTHHHHHHHHHSS-EEE-SSTTTHHHHHHHHTT CS
                          MreB_Mbl 271 divdrgivltGGgallkgldkllseetglpvkvaedpltcvakGtgkvl 319
                                       d +++ ++l+GG++l++g+ ++l++ ++++v+v  d+    a G+ +++
  gi|298675699|ref|YP_003727449.1| 364 D-IREPVILVGGSSLIEGIPRTLEKFLKVEVIVPPDSQYIGAVGASMLA 411
                                       3.46678999**************************9999999988765 PP

>> Hydant_A_N  Hydantoinase/oxoprolinase N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   2.7e-05     0.069       3      67 ..     158     217 ..     156     235 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.7e-05
                        Hydant_A_N   3 gIDvGGTfTDavaldekeeevavlKllstpdavaegirealeevleesiprtskidvvrmGTTva 67 
                                       gID G+T T av+++++ +++    +++   +v+e   ea +++l+e++ ++++i++  +GTT  
  gi|298675699|ref|YP_003727449.1| 158 GIDSGSTTTKAVVMRDN-QVIGHGWVPTI--KVIESAEEAYKKALDEAGVNREDIQS--IGTTGY 217
                                       9**************87.88888889988..89999999999999999998888886..477765 PP

>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.021        53      31      57 ..     189     215 ..     169     217 .. 0.82
   2 ?    8.2   0.0   0.00071       1.8     141     267 ..     290     407 ..     230     410 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.021
                                       HHHHHHHHHHHHHHTSTGGGEEEEEEE CS
                     Peptidase_M22  31 erllplieealaeaglsledldaIavt 57 
                                       e   ++ ++al+eag++ ed++ I  t
  gi|298675699|ref|YP_003727449.1| 189 ESAEEAYKKALDEAGVNREDIQSIGTT 215
                                       5667889***************99876 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00071
                                       HHHHHHHHT..SSCCHHHHHHHCTC..S.......EETTEEE.CHHHHHHHHHHST.THHHHHHHHHHHHHHHHHHH CS
                     Peptidase_M22 141 ldkvarllglpypggpkieklakeg..kkiefprplkgldfsfsGlktavlkelek.evedlaasfqeavvdhlvek 214
                                       l  +a+ lg+++    ++ +la +g  ++ie     ++  ++  G+++ v ++++  + ed+aa+   +v+++   +
  gi|298675699|ref|YP_003727449.1| 290 LEMTAKRLGVDIT---ELGSLAVKGieNNIE-----MNSYCIVFGIQSLVNSLAKGaSPEDVAAAACYSVIEQ---I 355
                                       5556666655553...455666677644466.....333367779988888888444599***9999987777...5 PP

                                       HHHHHHHCTBSEEEEESGGGGXHHHHHCHCCHHHHTTSEEEXXXHH.HHSSXCH CS
                     Peptidase_M22 215 teralklpkakelvilGGvaankrLrealeeeaeelglkliiPplk.yctdnaa 267
                                        e+ l++ +++e vil  v++ ++++   +++++ l++++i+Pp + y+   +a
  gi|298675699|ref|YP_003727449.1| 356 FEQQLQEVDIREPVIL--VGGSSLIEGIPRTLEKFLKVEVIVPPDSqYIGAVGA 407
                                       5666788999999888..77777777666654445899***9997779888776 PP

>> Actin  Actin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.19   4.9e+02     147     168 ..     159     180 ..     135     184 .. 0.83
   2 ?    0.4   0.0     0.076   1.9e+02     140     163 ..     249     272 ..     235     296 .. 0.86
   3 ?    7.6   0.0   0.00048       1.2     326     380 ..     367     412 ..     345     414 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.19
                             Actin 147 vDsGasvtsvvpVldGyvLkka 168
                                       +DsG+++t +v   d++v+ ++
  gi|298675699|ref|YP_003727449.1| 159 IDSGSTTTKAVVMRDNQVIGHG 180
                                       8**********99999999886 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.076
                             Actin 140 gkstglvvDsGasvtsvvpVldGy 163
                                        k ++ v+D+G     +++V dG+
  gi|298675699|ref|YP_003727449.1| 249 QKGSATVIDIGGMDNKAITVEDGI 272
                                       567899****************97 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.00048
                             Actin 326 anivvtGGnsllpglteRlekelaqlaskgvkvkiiapeeerkysaWiGGSiLAs 380
                                       + ++++GG+sl++g+   lek l        kv +i p+ + +y   +G+S+LAs
  gi|298675699|ref|YP_003727449.1| 367 EPVILVGGSSLIEGIPRTLEKFL--------KVEVIVPP-DSQYIGAVGASMLAS 412
                                       679***********998887755........45788888.777777788888886 PP

>> DUF4934  Domain of unknown function (DUF4934)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   5.7e-05      0.14      21      53 ..     220     252 ..     207     270 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.7e-05
                           DUF4934  21 vLvGnspkikllkdkivvsskkqCllfdketGk 53 
                                        LvG++++++l++++i v sk   +l dk++G 
  gi|298675699|ref|YP_003727449.1| 220 FLVGKKYDAQLSQEEITVNSKGAVYLADKQKGS 252
                                       69*****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 2643.30
//
Query:       gi|298675700|ref|YP_003727450.1|  [L=199]
Description: methanogenesis marker protein 17 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-70  236.5   1.8    1.5e-70  236.3   1.8    1.0  1  DUF2113   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2113  Uncharacterized protein conserved in archaea (DUF2113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  236.3   1.8   8.5e-75   1.5e-70       1     184 [.       7     194 ..       7     195 .. 0.98

  Alignments for each domain:
  == domain 1  score: 236.3 bits;  conditional E-value: 8.5e-75
                           DUF2113   1 fevectdeegaeaYeeiirdilqDlnllrsierlkvyidpeeplFiiavllrktsspiklgdvaeveedk.eegkvk 76 
                                       f+ve+++++++e+Y++i++d+++D++l++si+r+kv+i+p+e+lF++a +lr  +sp+k++d+a+v++ +  +++v+
  gi|298675700|ref|YP_003727450.1|   7 FVVEAPQQSESEQYRQILKDVISDMVLAQSIGRIKVVIRPDESLFQMALVLRGGLSPVKTSDFADVNVGEfGKNEVV 83 
                                       78******************************************************************999****** PP

                           DUF2113  77 ikiedEtylpelLkkLwekygrenveqpdRfeiiiesdedl...eeleelvVaDpkeelkkkvidaliriaPEGfrv 150
                                       iki++E+yl++lLk+Lw+kygr nv+qp+R ++ +++++ +   +++e ++V+Dp+++lkk+v+d+++r+aPEGfrv
  gi|298675700|ref|YP_003727450.1|  84 IKINNEKYLSQLLKILWDKYGRLNVRQPERKTVAVKTENPMdkiSDIEYIIVDDPRNTLKKRVVDMAVRVAPEGFRV 160
                                       *************************************988798999******************************* PP

                           DUF2113 151 rkealednsfvfvAseetlkeewieeakelkeel 184
                                       r+++l++++f+fvAse+++k+ewieea+++ +el
  gi|298675700|ref|YP_003727450.1| 161 RYHSLKGDNFIFVASEDAMKQEWIEEAHQMLDEL 194
                                       *******************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       796  (0.0443973); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1342.85
//
Query:       gi|298675701|ref|YP_003727451.1|  [L=311]
Description: methanogenesis marker protein 7 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.3e-127  424.5   0.1   1.5e-127  424.3   0.1    1.0  1  MCR_C     Methyl-coenzyme M reductase operon protein C


Domain annotation for each model (and alignments):
>> MCR_C  Methyl-coenzyme M reductase operon protein C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  424.3   0.1  8.6e-132  1.5e-127       1     271 []       5     274 ..       5     274 .. 0.99

  Alignments for each domain:
  == domain 1  score: 424.3 bits;  conditional E-value: 8.6e-132
                             MCR_C   1 lepltyeGGvykhdellelieDlGGyilqknvialevvltllvPkedvelieelakellgklteaPlagteiavvsp 77 
                                       lep++yeGG+ykh ++lel+eDlGGy++qk+ + +ev+l++l+Pkedv+l+++lak+llg+lt+aPl+gteiavvsp
  gi|298675701|ref|YP_003727451.1|   5 LEPYIYEGGMYKHGLILELLEDLGGYLVQKTPAGSEVTLVMLIPKEDVHLVQDLAKKLLGTLTKAPLTGTEIAVVSP 81 
                                       689************************************************************************** PP

                             MCR_C  78 tLarhhlPhsaCDvaeylrraGaktnmiGlarGvgkriaqikeeekrlinehDlavfvlGnfkdCikkkkeklfedi 154
                                       tLa+hhlPhsaCDvaeylrr G++tnmiGlarG+g+r++  +++e++linehD+avf++G f+dCi +kk+klf++i
  gi|298675701|ref|YP_003727451.1|  82 TLASHHLPHSACDVAEYLRRGGSNTNMIGLARGMGRRVSLSEDYERKLINEHDVAVFSFGVFSDCIINKKPKLFKGI 158
                                       ***************************************************************************** PP

                             MCR_C 155 evPvvvtggPeelkleevpgaeayvgglGriahrlrkeeeiealdelveeveevldkkreelakDpllvsparvkke 231
                                       +vP+v tggP el++e+vpga++yvgg+Griahr+rke e+++ld l+e+v+e++++kre+lakDpl+v parv++e
  gi|298675701|ref|YP_003727451.1| 159 KVPIVATGGP-ELNTEDVPGADMYVGGIGRIAHRMRKEGELNSLDVLNEKVGEMIENKREKLAKDPLSVIPARVMQE 234
                                       **********.****************************************************************** PP

                             MCR_C 232 ieeqveeieevlsPapitlqldglrvklpydeyaekieev 271
                                       ie+q+++i++vlsPapitlqldglr+klpy++y+++ie++
  gi|298675701|ref|YP_003727451.1| 235 IERQISDIQNVLSPAPITLQLDGLRIKLPYEDYHKNIENL 274
                                       *************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1908.16
//
Query:       gi|298675702|ref|YP_003727452.1|  [L=162]
Description: alkylhydroperoxidase-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.8e-13   48.3   0.0    1.2e-12   47.7   0.0    1.3  1  CMD       Carboxymuconolactone decarboxylase family


Domain annotation for each model (and alignments):
>> CMD  Carboxymuconolactone decarboxylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   0.0   6.8e-17   1.2e-12      20      70 ..      62     112 ..      50     126 .. 0.84

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 6.8e-17
                                       TS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHH CS
                               CMD  20 gLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaqaaay 70 
                                       + dp + eLi+++vs a++ce+C+++H+r A++ G+++eei ++++++   
  gi|298675702|ref|YP_003727452.1|  62 RMDPETVELISIGVSSALRCEHCLKMHIRVAKRLGLSKEEIFDAIMIGGTL 112
                                       489******************************************987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      626  (0.0349155); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1161.54
//
Query:       gi|298675703|ref|YP_003727453.1|  [L=299]
Description: hypothetical protein Metev_1821 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   4.2e-101  338.1  24.7     5e-101  337.9  24.7    1.0  1  SPP             Signal-peptide peptidase, presenilin aspartyl
    4.7e-09   36.2  11.0    9.7e-09   35.1  11.0    1.5  1  Peptidase_A22B  Signal peptide peptidase
     0.0081   15.0  19.5     0.0094   14.8  15.1    2.1  2  Presenilin      Presenilin


Domain annotation for each model (and alignments):
>> SPP  Signal-peptide peptidase, presenilin aspartyl protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  337.9  24.7  8.3e-105    5e-101       2     282 ..      19     295 ..      18     296 .. 0.98

  Alignments for each domain:
  == domain 1  score: 337.9 bits;  conditional E-value: 8.3e-105
                               SPP   2 alfvvvqvlalllavplesaelqatedPtqvlnsvvyivlllvftlfvlivikkdkkliiskviyvivvavifyvfl 78 
                                       +++++vq+lal la+p+e ++++a+e+P+ ++ns +yi +++vftl +l++ik+d+++ii++ i+ +v+++++y ++
  gi|298675703|ref|YP_003727453.1|  19 GILLLVQILALTLAMPMEVNNMRAFENPESASNSFYYIGIIIVFTLILLLAIKRDQQWIIQLFILFAVASTLYYGLF 95 
                                       799************************************************************************** PP

                               SPP  79 vllsivlvvaglvnlaslvvaialvvllyaypeWyvidlaGvilavGvsalfGislgvlpavvllialavydaisvy 155
                                       +  s++ +   l   +sl+ ai+++++ly++peWy+id++G+i++  +s++fGisl+++pa++ll++lavydaisvy
  gi|298675703|ref|YP_003727453.1|  96 AFTSMFNIAPTLGMSVSLISAIGMTGILYKFPEWYIIDIVGIIIGAAASSIFGISLAIMPAIILLVILAVYDAISVY 172
                                       ******99999999*************************************************************** PP

                               SPP 156 ktkhmialaegvvdlklPillvvPetlaysfveeafeeaeeaearnvlfiGlGdavlPsilvvsaavfleshilagl 232
                                       ktkhm++laegv+dlklPil+v+P++l ysf+ee+f++ ++   r+++f+GlGdav+P+ilvvsa+vf e   +  +
  gi|298675703|ref|YP_003727453.1| 173 KTKHMVSLAEGVMDLKLPILFVIPKRLDYSFREESFNNDDK--ERDAFFMGLGDAVMPTILVVSANVFIEHSGI--I 245
                                       *************************************9998..4689***********************9777..9 PP

                               SPP 233 elavllalaGtlvGllvlsilvlrgrpaaGlPllnsGaiaGfligvlaag 282
                                       ++++l+ ++Gt++G+  ls+++++g+p+aGlP+lnsG i G+++gv+ +g
  gi|298675703|ref|YP_003727453.1| 246 SYPALGGVIGTVIGFFALSVFIMKGKPQAGLPFLNSGVILGYFVGVILSG 295
                                       **********************************************9987 PP

>> Peptidase_A22B  Signal peptide peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1  11.0   1.6e-12   9.7e-09      47     202 ..      64     234 ..       8     243 .. 0.63

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 1.6e-12
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXX------S--XXXXXXXXXXXXXXX CS
                    Peptidase_A22B  47 livllgvvalasllsplvtrlflkkvelakvklefla...ielkaaeivalllsiviavlwllkrhwilndilglal 120
                                       li ll+++  ++ + +l   lf   ++l++  + f+    i  +  + v+l+ +i ++ + + +++w + di+g+ +
  gi|298675703|ref|YP_003727453.1|  64 LILLLAIKRDQQWIIQLFI-LFAVASTLYYGLFAFTSmfnIAPTLGMSVSLISAIGMTGILYKFPEWYIIDIVGIII 139
                                       2222333332222222222.2233333333333333233355556666677777777777888889********987 PP

                                       ..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXX.........XXXXXXXXX CS
                    Peptidase_A22B 121 ..ailviellrlpslkvgalLLvglflYDifwVFgtdvmvevAk...eldiPillklPq.........lsneieeas 183
                                         a  +i  + l+ ++ + +LLv l +YD   V+ t+ mv++A+   +l++Pil+++P+         ++n+ ++++
  gi|298675703|ref|YP_003727453.1| 140 gaAASSIFGISLA-IMPAIILLVILAVYDAISVYKTKHMVSLAEgvmDLKLPILFVIPKrldysfreeSFNNDDKER 215
                                       2144556666665.5667899999********************99999*********9999877655556666777 PP

                                       XXXXXXXXXXXXXXXXXXX CS
                    Peptidase_A22B 184 kfsiLGlGDivlPGllial 202
                                       +   +GlGD v+P +l+  
  gi|298675703|ref|YP_003727453.1| 216 DAFFMGLGDAVMPTILVVS 234
                                       78899***********976 PP

>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8  15.1   1.6e-06    0.0094      59     189 ..      47     171 ..      26     177 .. 0.85
   2 !    2.4   0.1     0.009        54     312     368 ..     208     265 ..     197     291 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.6e-06
                        Presenilin  59 nsllnalililvivvvtfllvlLykyrcykvikgwlilsslllLflvsglllaevlkaynipldyitlllllwnfgv 135
                                       +s  n++  i++i+v t++l+l  k + + +i+        ++Lf v+ +l++ ++   +++  + tl + +  +++
  gi|298675703|ref|YP_003727453.1|  47 ESASNSFYYIGIIIVFTLILLLAIKRDQQWIIQL-------FILFAVASTLYYGLFAFTSMFNIAPTLGMSVSLISA 116
                                       6789******************999997766665.......5666667777777777777777789999999999** PP

                        Presenilin 136 vGviaifwkgpll.lqqaYlilisalmAlvfikylpewTtwvlLvvisiyDlvAV 189
                                       +G+  i +k p + +  +  i+i+a  + +f   l    +++lLv++++yD + V
  gi|298675703|ref|YP_003727453.1| 117 IGMTGILYKFPEWyIIDIVGIIIGAAASSIFGISLAIMPAIILLVILAVYDAISV 171
                                       ***********75377888899999999999999*******************99 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.009
                        Presenilin 312 eeeseseergvkLGLGDFiFYSvLvgkAalsgdlntvv.acfvailiGLclTLllLai 368
                                        ++ ++e+++  +GLGD +   +Lv  A    + + ++   +++ +iG ++  + L++
  gi|298675703|ref|YP_003727453.1| 208 FNNDDKERDAFFMGLGDAVMPTILVVSANVFIEHSGIIsYPALGGVIGTVIGFFALSV 265
                                       334445667999*************999885444433313455556666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1041  (0.0580624); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 1837.00
//
Query:       gi|298675704|ref|YP_003727454.1|  [L=107]
Description: hypothetical protein Metev_1822 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0015   18.6   1.9     0.0019   18.2   1.9    1.1  1  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
     0.0029   17.8   0.1     0.0055   16.9   0.1    1.5  1  DUF948           Bacterial protein of unknown function (DUF94
  ------ inclusion threshold ------
      0.021   14.4   0.0      0.022   14.3   0.0    1.0  1  LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
      0.026   14.4   0.2      0.028   14.3   0.2    1.1  1  DUF3611          Protein of unknown function (DUF3611)
      0.047   13.4   0.1      0.058   13.1   0.1    1.2  1  Tetraspanin      Tetraspanin family
       0.12   12.7   0.0       0.12   12.7   0.0    1.1  1  DUF1772          Domain of unknown function (DUF1772)
       0.62   10.1   2.9         18    5.4   0.4    2.3  2  TMEMspv1-c74-12  Plectrovirus spv1-c74 ORF 12 transmembrane p


Domain annotation for each model (and alignments):
>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   1.9   7.5e-07    0.0019      31      92 ..      43     103 ..      36     104 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 7.5e-07
                      Baculo_PEP_C  31 qilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlns 92 
                                        + + la l+ +i t+L +l++ ++    +l+ +++++ +nL++ +  +q++++n+++ ln 
  gi|298675704|ref|YP_003727454.1|  43 MV-GSLAVLILSIITRLRNLEQMMETKERSLRINIQSVEDNLDKRIGDVQNSVNNAMDELNR 103
                                       44.89999999************************************************996 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   2.2e-06    0.0055       2      66 ..      39     104 ..      38     107 .] 0.69

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.2e-06
                            DUF948   2 AglIaAiAFvvLviflivvllklkktldeaaat....ieelekqvdpilkevedllakvnelledvnek 66 
                                       A++++ ++++vL++ +i  l++l+++++  +++    i+++e+++d+ + +v++ ++++ +   ++n+k
  gi|298675704|ref|YP_003727454.1|  39 AAIVMVGSLAVLILSIITRLRNLEQMMETKERSlrinIQSVEDNLDKRIGDVQNSVNNAMD---ELNRK 104
                                       8899999****************99998766651111556666666666666665555544...66555 PP

>> LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   8.7e-06     0.022     120     169 ..       5      58 ..       3      84 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.7e-06
                   LPG_synthase_TM 120 dllalvllgllallllggllaegaa....vllllalallllavlalllllllrr 169
                                       d+++ v++++ a++l +++l+ +++     l+++a++++++ + +l+l ++ r 
  gi|298675704|ref|YP_003727454.1|   5 DIVFSVIMVISAFILTYQWLGRFGEssknPLIIFAAIVMVGSLAVLILSIITRL 58 
                                       566666677777777777776666677779999999999998888876555444 PP

>> DUF3611  Protein of unknown function (DUF3611)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   1.1e-05     0.028      24      89 ..      10      73 ..       6      92 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.1e-05
                           DUF3611 24 vLgvvsalillfallgrslaeetnaglgfglflavlglvvllfsifwafrytrlarrLraenpelr 89
                                      v+ v+sa il ++ lgr  ++++n+ + f  ++ v++l+vl++si+   r  +l + +++++++lr
  gi|298675704|ref|YP_003727454.1| 10 VIMVISAFILTYQWLGRFGESSKNPLIIFAAIVMVGSLAVLILSIITRLR--NLEQMMETKERSLR 73
                                      6789*************765599**********************98665..45555555555555 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   2.3e-05     0.058      47     137 ..       5      99 ..       1     105 [. 0.59

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.3e-05
                                       ......XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--HHH.........HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                       Tetraspanin  47 ailaillivvGvllfllgflGcigalkenkcllltfsllllvlfllelaagilgfvfsdk.argkvseiinnaievk 122
                                       +i+  +++v++++++    lG +g   +n   l +f+ +++v  l+ l++ i++   + +   ++ +++++ +i ++
  gi|298675704|ref|YP_003727454.1|   5 DIVFSVIMVISAFILTYQWLGRFGESSKNP--LIIFAAIVMVGSLAVLILSIITRLRNLEqMMETKERSLRINI-QS 78 
                                       567778999999999999999999777776..556666666666666666664444333312333344466666.55 PP

                                       HHHHHHHHHH.T.....HHHH CS
                                       xxxxxxxxxx.x.....xxxx RF
                       Tetraspanin 123 yrddldlkkc.q.....nlld 137
                                       ++d+ld +         n++d
  gi|298675704|ref|YP_003727454.1|  79 VEDNLDKRIGdVqnsvnNAMD 99 
                                       666666543321444444444 PP

>> DUF1772  Domain of unknown function (DUF1772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.8e-05      0.12      37      96 ..       6      65 ..       1     103 [. 0.62

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.8e-05
                           DUF1772 37 avfpplallsalafayla.araasrgarllylaaaal.lllsivpyTllvmvPtNnkLaalk 96
                                       vf +++++sa  ++y +  r   +++  l+ + aa+  + s++++ l ++  +   L+++ 
  gi|298675704|ref|YP_003727454.1|  6 IVFSVIMVISAFILTYQWlGRFGESSKNPLI-IFAAIvMVGSLAVLILSIITRLR-NLEQMM 65
                                      5788999999999999995444444444454.55555266666666666666643.233442 PP

>> TMEMspv1-c74-12  Plectrovirus spv1-c74 ORF 12 transmembrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.4    0.0068        18       7      19 ..       6      18 ..       4      26 .. 0.84
   2 ?    4.8   0.1     0.011        28       7      34 ..      36      63 ..      35      74 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0068
                   TMEMspv1-c74-12  7 tiFSvvivLgiFl 19
                                      ++FSv++v++ F+
  gi|298675704|ref|YP_003727454.1|  6 IVFSVIMVISAFI 18
                                      79******99886 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.011
                   TMEMspv1-c74-12  7 tiFSvvivLgiFlyiGLsiyqKikqirg 34
                                      +iF+ ++++g  + + Lsi  + + ++ 
  gi|298675704|ref|YP_003727454.1| 36 IIFAAIVMVGSLAVLILSIITRLRNLEQ 63
                                      89*****************999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1493  (0.0832729); expected 358.6 (0.02)
Passed bias filter:                      798  (0.0445089); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 652.44
//
Query:       gi|298675705|ref|YP_003727455.1|  [L=112]
Description: hypothetical protein Metev_1823 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 776.93
//
Query:       gi|298675706|ref|YP_003727456.1|  [L=338]
Description: flap structure-specific endonuclease [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-27   95.5   0.0    4.2e-27   94.3   0.0    1.7  1  XPG_I         XPG I-region
    6.2e-23   81.2   0.0    1.3e-22   80.2   0.0    1.5  1  XPG_N         XPG N-terminal domain
     0.0017   18.3   0.0     0.0036   17.2   0.0    1.6  1  5_3_exonuc_N  5'-3' exonuclease, N-terminal resolvase-like do
     0.0034   18.0   0.0     0.0078   16.8   0.0    1.7  1  5_3_exonuc    5'-3' exonuclease, C-terminal SAM fold
  ------ inclusion threshold ------
       0.01   15.8   0.0        4.2    7.4   0.0    2.7  2  RelB          RelB antitoxin
      0.018   15.6   0.0      0.043   14.4   0.0    1.6  1  HHH_5         Helix-hairpin-helix domain
      0.046   14.2   1.1      0.092   13.2   0.1    2.0  2  eIF3_N        eIF3 subunit 6 N terminal domain


Domain annotation for each model (and alignments):
>> XPG_I  XPG I-region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.3   0.0   1.6e-30   4.2e-27       2      94 .]     141     236 ..     140     236 .. 0.94

  Alignments for each domain:
  == domain 1  score: 94.3 bits;  conditional E-value: 1.6e-30
                                       HHT--EEE-SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT-SEEEESTT..ECECTT....EEECEEEEEEHHHHHH CS
                             XPG_I   2 lmgipyvvApgEAEAqcayLqkkglvdaviseDsDlllFGapkvlrnls.kkkskkk..kekekkkvevidlekvlk 75 
                                       +mgipy+++p+E+EAq+a++++kg++d+v s+D+D+llFGap+v+rnl+ ++k+k    +++ + k+e id+e+ lk
  gi|298675706|ref|YP_003727456.1| 141 SMGIPYLQSPSEGEAQAAHMVQKGDADYVGSQDYDALLFGAPHVIRNLTiTGKRKLPgkNTYIDLKPETIDMEENLK 217
                                       79**********************************************9755555548799999************* PP

                                       HHT--HHHHHHHHHHHCET CS
                             XPG_I  76 elgltreqlidlaillgcD 94 
                                        +g+tr++lid+a+++g+D
  gi|298675706|ref|YP_003727456.1| 218 SMGITRSKLIDIALCVGTD 236
                                       *****************99 PP

>> XPG_N  XPG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.2   0.0     5e-26   1.3e-22      17     100 ..      12     100 ..       4     101 .. 0.95

  Alignments for each domain:
  == domain 1  score: 80.2 bits;  conditional E-value: 5e-26
                                       EEEEGGGGTTEEEEEEHHHHHHHHHHHSE.ETTEE-BS.....-HHHHHHHHHHHHHHHTTEEEEEEE--S--GGGH CS
                             XPG_N  17 rsvsiealegkklaiDaslwlyrfliavreqlgnalen.....tshlmglfsrllrlldfgikPifVFdgkapdlkk 88 
                                       ++v+i +l++k++aiDa+  ly+fl  +r+++g+ l+      tshl g+++r+  l++  ikP+fVFdgk+pd+k 
  gi|298675706|ref|YP_003727456.1|  12 KEVEISNLSNKTVAIDAYNTLYQFLSIIRQRDGTPLQDskgrtTSHLSGILYRITNLVEEDIKPVFVFDGKPPDFKT 88 
                                       789**********************************9999************************************ PP

                                       HHHHHHHHHHHH CS
                             XPG_N  89 eelekrserrqe 100
                                       ++lekr++ r++
  gi|298675706|ref|YP_003727456.1|  89 DTLEKRKQSREN 100
                                       ********9986 PP

>> 5_3_exonuc_N  5'-3' exonuclease, N-terminal resolvase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.4e-06    0.0036       4      81 ..      25     107 ..      22     178 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.4e-06
                      5_3_exonuc_N   4 LiDgsslifRayyal.......lttsdgeptnavygflnmllklleeekpthlavvfDakkktfRhelypeYKanRe 73 
                                        iD+ + +++    +       l+ s+g+ t+ + g+l  +++l+ee    + ++vfD k++ f+++ +++ K+ Re
  gi|298675706|ref|YP_003727456.1|  25 AIDAYNTLYQFLSIIrqrdgtpLQDSKGRTTSHLSGILYRITNLVEEDI--KPVFVFDGKPPDFKTDTLEKRKQSRE 99 
                                       56777777664444477777788899*******************9754..469****999***************7 PP

                      5_3_exonuc_N  74 etpeelke 81 
                                       +++++ +e
  gi|298675706|ref|YP_003727456.1| 100 NANQKWNE 107
                                       76665543 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0     3e-06    0.0078      18      52 ..     236     271 ..     221     292 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3e-06
                        5_3_exonuc  18 DnipGvpgiGektAakLlkeygsleeilenld.elk 52 
                                       D  +G ++iG+k A kL+k+++s+++i++++  +++
  gi|298675706|ref|YP_003727456.1| 236 DYNKGLEKIGPKRALKLVKTHDSIKSIIDETGqNIE 271
                                       6668************************97642333 PP

>> RelB  RelB antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0017       4.2       5      26 ..     124     145 ..     122     149 .. 0.93
   2 ?    5.4   0.0    0.0069        18      19      35 ..     215     231 ..     204     233 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0017
                                       EEEEEHHHHHHHHHHHHCCT-- CS
                              RelB   5 slRidedlKaeatdvlekmGlt 26 
                                       s+Rid+++   a+  le mG++
  gi|298675706|ref|YP_003727456.1| 124 SARIDDQILDDAKYLLESMGIP 145
                                       69******************98 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0069
                                       HHHCCT--HHHHHHHHH CS
                              RelB  19 vlekmGltiSqairlfL 35 
                                        l+ mG+t S++i++ L
  gi|298675706|ref|YP_003727456.1| 215 NLKSMGITRSKLIDIAL 231
                                       589**********9977 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.7e-05     0.043       6      35 ..     240     268 ..     237     279 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.7e-05
                                       TSTT--HHHHHHHHTTT--SHHHHHHS-HH CS
                             HHH_5   6 svsGiGpktAlallsaGiesvedlaaadve 35 
                                       ++++iGpk+Al+l+++  +s+  +++++ +
  gi|298675706|ref|YP_003727456.1| 240 GLEKIGPKRALKLVKT-HDSIKSIIDETGQ 268
                                       5899************.8899999987433 PP

>> eIF3_N  eIF3 subunit 6 N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.2       1.7   4.4e+03      62      86 ..     100     125 ..      85     140 .. 0.47
   2 ?   13.2   0.1   3.6e-05     0.092      72     125 ..     260     318 ..     235     322 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.7
                            eIF3_N  62 evpe.elekkreevleeleeleeeae 86 
                                       ++ +   e+k++ + ee  ++ + ++
  gi|298675706|ref|YP_003727456.1| 100 NANQkWNEAKEKGLTEEAYKYAQGSA 125
                                       22221223333444444445555444 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 3.6e-05
                            eIF3_N  72 eevleeleeleeeaekvlelledeevvsn.....lrsdkkqnlefLkeehgitpemida 125
                                       +++++e  +  e+++kv +++ ++ev++       r +k ++++fL eeh++++e +++
  gi|298675706|ref|YP_003727456.1| 260 KSIIDETGQNIENVDKVKDFFMNPEVTDDyhlkwNRPNKDKIIQFLCEEHDFSEERVAK 318
                                       5667777777799***************966554444******************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1035  (0.0577277); expected 358.6 (0.02)
Passed bias filter:                      661  (0.0368676); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2314.48
//
Query:       gi|298675707|ref|YP_003727457.1|  [L=524]
Description: phosphoglycerate mutase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.4e-86  286.7   1.0    1.3e-85  286.2   1.0    1.2  1  iPGM_N           BPG-independent PGAM N-terminus (iPGM_N)
    7.4e-81  271.2   0.2    8.6e-81  271.0   0.2    1.0  1  Metalloenzyme    Metalloenzyme superfamily
    0.00044   19.7   0.0      0.015   14.7   0.0    2.6  2  Sulfatase        Sulfatase
  ------ inclusion threshold ------
      0.017   14.1   0.1       0.28   10.1   0.1    2.1  2  Alk_phosphatase  Alkaline phosphatase


Domain annotation for each model (and alignments):
>> iPGM_N  BPG-independent PGAM N-terminus (iPGM_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  286.2   1.0   2.9e-89   1.3e-85       1     215 []      91     307 ..      91     307 .. 0.97

  Alignments for each domain:
  == domain 1  score: 286.2 bits;  conditional E-value: 2.9e-89
                                       HHHHHHCTGGGG-HHHHHHHHHHHHCTSEEEEEEE-SS--SS--CHHHHHHHHHHHHTT-SEEEEEEEE-SSSSTTT CS
                            iPGM_N   1 inkaiedgslfenealkeaiekakkngkalHllGLlSdGgVHShidhllallelakeegvkkvvvhaflDGRDtapk 77 
                                       ink+ie+ ++++n++l++aie++k+n++++Hl+GL+S GgVHSh+dh++al+++++++gv+++++haflDGRD++p 
  gi|298675707|ref|YP_003727457.1|  91 INKSIETSEIYKNKVLTDAIENVKQNNSKIHLMGLFSYGGVHSHMDHVHALVKMCADKGVDEIYIHAFLDGRDVSPY 167
                                       89*************************************************************************** PP

                                       -HHHHHHHHHHHHHHCT--EEEEEEEHHHHT--SS-HHHHHHHHHHHCCSSSEEECTTHHHHHHHHHHTT--GGG-- CS
                            iPGM_N  78 saleyleeleeklkelgvgkiasvsGRyyaMDRdkrwervekaydalvkgegeskaesaveaieesyakgetDefve 154
                                        +l+ +++ e  l+e g++kia+vsGRyyaMDRdkrw+r++ ayd+l+ g+g   a++av+a++esy++getDefv+
  gi|298675707|ref|YP_003727457.1| 168 AGLDDIQKNEPVLQEKGNAKIATVSGRYYAMDRDKRWDRTKLAYDVLTLGNGLY-AKDAVTAVRESYDRGETDEFVK 243
                                       **************************************************9977.789******************* PP

                                       -EEE....TCCGGS--TT-EEEE----CCCCHHHHHHHHSTTHHCC...--TT-EEEESS-S-T CS
                            iPGM_N 155 ptviae.egkkegtikdgDaviffNFRaDRareltraltdkefkefe..kakklklvtmteYde 215
                                       ptvi++ +g++++ti+d+D+viffNFR+DRar+lt  ++ ++f++fe  k+ ++++v+mteYd+
  gi|298675707|ref|YP_003727457.1| 244 PTVITDeNGNPTATIDDNDSVIFFNFRPDRARQLTYSFVLDDFDGFErqKHPDVYFVCMTEYDK 307
                                       *****999*******************************999****866667889*******96 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  271.0   0.2   1.9e-84   8.6e-81       2     248 .]      14     509 ..      13     509 .. 0.98

  Alignments for each domain:
  == domain 1  score: 271.0 bits;  conditional E-value: 1.9e-84
                                       EEEEEEETTBB----GGGTTHHHS--HHHHHHHHH.......SEEEEEESSSTT----HHHHHHHH........... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........... RF
                     Metalloenzyme   2 kvvlvvlDGlGeapadelnaihvAktPtldkLkkeaPerwlikahgtavglpeddmgnsevgHlel........... 67 
                                       +v+l++lDG+G+ p +e na+  A+tP+ld+L +++P + +++a+g+avglpe++mgnsevgHl++           
  gi|298675707|ref|YP_003727457.1|  14 PVLLMILDGWGYLPRKEGNAVFAANTPNLDNLLNKYPST-ILQASGEAVGLPEGQMGNSEVGHLNIgagrvvyqdft 89 
                                       799************************************.8************************************ PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Metalloenzyme  68 ............................................................................. 67 
                                                                                                                    
  gi|298675707|ref|YP_003727457.1|  90 kinksietseiyknkvltdaienvkqnnskihlmglfsyggvhshmdhvhalvkmcadkgvdeiyihafldgrdvsp 166
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Metalloenzyme  68 ............................................................................. 67 
                                                                                                                    
  gi|298675707|ref|YP_003727457.1| 167 yaglddiqknepvlqekgnakiatvsgryyamdrdkrwdrtklaydvltlgnglyakdavtavresydrgetdefvk 243
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Metalloenzyme  68 ............................................................................. 67 
                                                                                                                    
  gi|298675707|ref|YP_003727457.1| 244 ptvitdengnptatiddndsviffnfrpdrarqltysfvlddfdgferqkhpdvyfvcmteydktldvpiayppeti 320
                                       ***************************************************************************** PP

                                       ...............HHHHTT-----EEEEEEEE-S---SSHHHHHT--EEEE--SHHSTT--HHHHHHHHHHHH.C CS
                                       ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme  68 ...............lrisetvkfahvtffwnggrsgyfnpleereeipsdtvitfdlqpemkavevaekaldails 129
                                                      lr++et+k+ahvtff ngg +++f++ e+r+ ips++v+t+dl+pem+a+ev++ +++ i+s
  gi|298675707|ref|YP_003727457.1| 321 entlgkvlsennltqLRTAETEKYAHVTFFLNGGIETQFEG-EHRCLIPSPKVATYDLKPEMSAYEVTDDLVQRINS 396
                                       ***************9*************************.*********************************** PP

                                       C.-SEEEEEE-HHHHHHHTT-HHHHHHHHHHHHHHHHHHHTTS-TTTEEEEEE-SSB--TTTSS..........--- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                     Metalloenzyme 130 gkfdlvvvniknaDmvGHtgdleatiaaieaaDeavkeildaieqvdgilvvtADHgnaedmvkrdk..qplTsHtl 204
                                       g++d+++vn++n+DmvGHtgd+ at+ a+e +D +v++++++++ ++g  ++t+DHgnae+m++ d+  +++T+Ht 
  gi|298675707|ref|YP_003727457.1| 397 GDYDVLIVNYANMDMVGHTGDFDATVTAVEVVDDCVGRVIETLKRSGGRAFITGDHGNAEQMQEYDDgsKIHTAHTS 473
                                       ****************************************************************99889******** PP

                                       --EEEEEESTT----S--SSHHHHTT-TTEEEEGGGHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 205 epVPilivgkglapdkvkegakfrekggLanvaatllnllglea 248
                                       +pV +++++++ +         + + g L+++a+t+l+llg+++
  gi|298675707|ref|YP_003727457.1| 474 NPVQCIYIDDNSDC--------ELSGGCLCDIAPTILELLGIKK 509
                                       **********8543........34589*************9985 PP

>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.027   1.2e+02     132     184 ..      84     133 ..      36     164 .. 0.71
   2 !   14.7   0.0   3.3e-06     0.015     211     308 ..     418     506 ..     375     507 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.027
                                       CCCCCCCCCECTCCCTTTTCSHHHHHHHHHHHHHHCCCTSSEEE.EEEE-TTSS CS
                         Sulfatase 132 kdpekseyngevlrvppeggysddrlldealefllarndkpffl.ylatlapHa 184
                                        ++++ + n ++   ++++ y  ++l+d ++++ +++n+k +++  +++ ++H+
  gi|298675707|ref|YP_003727457.1|  84 VYQDFTKINKSI---ETSEIYKNKVLTDAIENV-KQNNSKIHLMgLFSYGGVHS 133
                                       344444444333...456666666666666666.99995555551668888887 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 3.3e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSSCCCGHHTTSSSCTTCSSSHHHHBEEEEEEETTTSHC CS
                         Sulfatase 211 leaylnsveyvDdligrvlaaLeenglldntlvvftSDhgasleesngplrggkganayeggtrvPllvwwpgekap 287
                                        +a   +ve vDd++grv+++L+++g +     ++t+Dhg   e+++ +  g+k    +  +t  P    + + ++ 
  gi|298675707|ref|YP_003727457.1| 418 FDATVTAVEVVDDCVGRVIETLKRSGGRA----FITGDHGN-AEQMQEYDDGSKI---HTAHTSNPVQCIYIDDNSD 486
                                       56778899**************9998886....899****9.5566666666666...6666777776666666666 PP

                                       EEECSEEEGGGHHHHHHHHTT CS
                         Sulfatase 288 rvseelvshiDlfptildlag 308
                                         +     + D++ptil+l+g
  gi|298675707|ref|YP_003727457.1| 487 -CELSGGCLCDIAPTILELLG 506
                                       .33333336677777777777 PP

>> Alk_phosphatase  Alkaline phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.018        80     198     227 ..     109     137 ..      80     192 .. 0.79
   2 ?   10.1   0.1   6.3e-05      0.28     255     318 ..     402     464 ..     331     490 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.018
                                       HHHHHHHCTST.SSCEEEESSSSSCS-CCCS CS
                   Alk_phosphatase 198 rkeLlkakeen.vkplLGLFadgdlkveldr 227
                                       + e  ++k++n + +l+GLF  g+++ ++d 
  gi|298675707|ref|YP_003727457.1| 109 AIE--NVKQNNsKIHLMGLFSYGGVHSHMDH 137
                                       333..344444468*******9999998876 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 6.3e-05
                                       EEEEETCHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHCHHCTTEEEEEEESSEESEEEESTTST CS
                   Alk_phosphatase 255 LlVEGsrIDhaaHendavgalsEvvefdeAvkaalefakkeketlvvvTaDHshvfsfggyttr 318
                                       L+V  +++D  +H +d    ++ v  +d+ v +++e  k+ +      T DH  + +++ y+ +
  gi|298675707|ref|YP_003727457.1| 402 LIVNYANMDMVGHTGDFDATVTAVEVVDDCVGRVIETLKR-SGGRAFITGDHGNAEQMQEYDDG 464
                                       89999**********************************5.5556677***********99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (524 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.27s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 3306.64
//
Query:       gi|298675708|ref|YP_003727458.1|  [L=365]
Description: peptidase M50 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-27   96.3   1.9    5.4e-14   52.4   0.2    2.4  2  CBS             CBS domain
    2.3e-15   56.5   9.5    1.6e-08   34.1   0.1    3.4  3  Peptidase_M50   Peptidase family M50
    0.00017   21.3   5.3    0.00047   19.9   5.1    1.9  1  Peptidase_M50B  Peptidase M50B-like
  ------ inclusion threshold ------
      0.084   12.7   3.6        2.5    7.9   0.1    2.2  2  FA_desaturase   Fatty acid desaturase


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   0.1   8.2e-15   3.7e-11       1      56 [.     242     296 ..     242     297 .. 0.87
   2 !   52.4   0.2   1.2e-17   5.4e-14       1      55 [.     304     357 ..     304     358 .. 0.96

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 8.2e-15
                                       HHHHSBSSCEEEETTSBHHHHHHH.HHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   1 Vgdimtrdvvtvppdttleealel.mrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       V+dimt+dv tv+p++++ e+l+  + ek++ ++PV+++++ l G+v+ +D+ ++++
  gi|298675708|ref|YP_003727458.1| 242 VKDIMTTDVETVNPSMSIQELLDFmF-EKKHMGYPVMEGNN-LKGVVSFTDVRKVMP 296
                                       89**********************55.55544*****6666.**********99875 PP

  == domain 2  score: 52.4 bits;  conditional E-value: 1.2e-17
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       V+dimt+d+++ + dt+ +ea++l+ +++v+rl+V+ ++g+l Giv+++Dl+r l
  gi|298675708|ref|YP_003727458.1| 304 VSDIMTKDIISTTSDTNASEAFKLISRNNVGRLLVI-DNGELKGIVSRTDLIRTL 357
                                       89***********************9999*******.6**************976 PP

>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   2.8     6e-09   2.7e-05       2     104 ..      56     123 ..      55     137 .. 0.79
   2 !   34.1   0.1   3.7e-12   1.6e-08     185     248 ..     140     200 ..     128     202 .. 0.83
   3 ?   -0.0   0.1     0.095   4.3e+02      92     136 ..     204     243 ..     186     319 .. 0.54

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 6e-09
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50   2 filllgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeaka 78 
                                       +++ll+ +vv+HElGH ++Ak++gvk+ +                    i+l  +GG+ +m++              
  gi|298675708|ref|YP_003727458.1|  56 TAILLFTSVVLHELGHSYFAKKFGVKISN--------------------ITLHLFGGVSSMEEIP------------ 100
                                       6799***********************88....................6666677777777766............ PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50  79 flkkspwqrllivlAGplanfilail 104
                                          ++p ++  +++AGpl+ fi++  
  gi|298675708|ref|YP_003727458.1| 101 ---RDPGEEGKMAFAGPLVSFIIGGT 123
                                       ...45667777777777777777665 PP

  == domain 2  score: 34.1 bits;  conditional E-value: 3.7e-12
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 185 eaglssflqllalisvnLgilNLlPipvLDGghllfalleairrkplserkeevanlvglalll 248
                                       e+    +++++  i++ Lgi+NL+P +++DGg++l++ +    r+ +  r+++ a  vg ++ +
  gi|298675708|ref|YP_003727458.1| 140 ESYPYRIFFIIGTINIVLGIFNLIPAFPMDGGRILRSWFA---RRMSYIRATQRAASVGKFFAV 200
                                       5555688999**************************9865...677999999999999888876 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.095
                                       XXXXXXXXXXXXXXXXX...-EEECECTTTSCEE-SEEEC-XXXXXXX CS
                                       xxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50  92 lAGplanfilailvfvv...pkkskeseeekrgviGvspkpvkkegll 136
                                       l G l+n +l +++f++         s+e +  ++ v+ +    +++ 
  gi|298675708|ref|YP_003727458.1| 204 LIGLLINPWLILIAFFIyigA-----SQEAQSTTVSVTLEK---YTVK 243
                                       446777877777777773331.....222222223332222...2222 PP

>> Peptidase_M50B  Peptidase M50B-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   5.1     1e-07   0.00047      22      89 ..      61     129 ..      47     230 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1e-07
                    Peptidase_M50B  22 llvvffHElGHalaalLtGgrvkgielhsdesGvtvtrg..pgglgqiltllaGYlgpallGlllillsa 89 
                                         +v++HElGH  +a+ +G ++++i+lh   +Gv+ ++   +   +   +++aG+l + ++G++l+ll +
  gi|298675708|ref|YP_003727458.1|  61 FTSVVLHELGHSYFAKKFGVKISNITLHLF-GGVSSMEEipRDPGEEGKMAFAGPLVSFIIGGTLLLLNF 129
                                       56899***********************85.7899888885333345679***************99975 PP

>> FA_desaturase  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1   0.00056       2.5       6      56 ..      50      93 ..      46      97 .. 0.61
   2 ?    5.6   0.6    0.0028        13     108     175 ..     160     222 ..     116     266 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00056
                     FA_desaturase  6 lllalllglfllgitgslaHeaaHgalfkkrklnrwlndllgallglplgi 56
                                      ++l+++ +++  ++t ++ He++H ++f k+   ++ n  l     l+ g+
  gi|298675708|ref|YP_003727458.1| 50 YILGFTTAIL--LFTSVVLHELGH-SYFAKKFGVKISNITL----HLFGGV 93
                                      4444444554..44469*******.6776777777766665....444444 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0028
                     FA_desaturase 108 wllalvlglwlrrlarrrapsksrrrkwrllawlllllawlglwlalllllglalllwlvplllllfl 175
                                       ++l++++++     +  r  +  ++r+  ++ +   ++++  +++++ +l gl+ + wl+ +++++ +
  gi|298675708|ref|YP_003727458.1| 160 FNLIPAFPM-----DGGRILRSWFARRMSYIRATQRAASVGKFFAVFMGLIGLLINPWLILIAFFIYI 222
                                       333333222.....222222222233355555555555556677777777777666777776666544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2461.41
//
Query:       gi|298675709|ref|YP_003727459.1|  [L=462]
Description: TraB family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-33  115.1   0.0    9.7e-33  114.2   0.0    1.4  1  TraB      TraB family


Domain annotation for each model (and alignments):
>> TraB  TraB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.2   0.0   5.4e-37   9.7e-33       7     253 ..      58     283 ..      55     286 .. 0.88

  Alignments for each domain:
  == domain 1  score: 114.2 bits;  conditional E-value: 5.4e-37
                              TraB   7 kggttsyLfGTiHvskksvyplspeveealeksdtvvvEldlsdd....tdeatqkelaklkllpdgktlsdllsee 79 
                                       +++t++ ++GT+Hvs+ks++++ + +++  ek+d v+vEl+ s++     ++++ +e++ ++l+  ++++  +l++ 
  gi|298675709|ref|YP_003727459.1|  58 SEPTQIKIIGTAHVSQKSIDEVVDSIKQ--EKPDIVAVELCRSRYeglkGEDKSNEEVSIKQLIG-EGKIYFFLMQW 131
                                       4677899*********************..9**************99976777777777777777.9********** PP

                              TraB  80 lyarlqkalakrglplaaldkmkPwllalllslaelakkkagldpelvDrylaktakragkpvgglEtveeqlslls 156
                                       l+a +qk++ k ++++      kP  +++++s+++  +++ g d++lvDr++++t++r + ++g++E+++   sl+ 
  gi|298675709|ref|YP_003727459.1| 132 LLAYMQKKIGK-EMGV------KP--GSEMISAIDA-AEEIGADIALVDRDIQITLRRFWNKMGFFEKIKMIGSLVG 198
                                       ***********.9***......**..*********7.6888999**************************9999995 PP

                              TraB 157 slpdeeqlealeetldeleeakdlleelveaykegdlealeleaeaeeefpelkevlldeRnrrwaekieall.kep 232
                                       ++     +++ + ++d++   +d ++ lve              e+++++p+  evl+deR+++ a ++ +   + +
  gi|298675709|ref|YP_003727459.1| 199 GIVGIGGKQMQNVDMDNIT-NQDVVTMLVE--------------ELRKIAPTAAEVLIDERDAYIAGSLVNVAaNAG 260
                                       5777777777777788888.4566777777..............**************************8774333 PP

                              TraB 233 ..gsvfvaVGagHlaGedgvlal 253
                                         +++ ++VGagH  G++++l +
  gi|298675709|ref|YP_003727459.1| 261 sgKKIIAVVGAGHKSGIQKYLSQ 283
                                       5799**************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1052  (0.0586759); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 2934.19
//
Query:       gi|298675710|ref|YP_003727460.1|  [L=298]
Description: formylmethanofuran/tetrahydromethanopterin N-formyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-65  219.6   1.5    2.7e-65  218.9   1.5    1.3  1  FTR_C     FTR, proximal lobe
    2.5e-63  212.3   0.2    5.5e-63  211.2   0.0    1.6  2  FTR       Formylmethanofuran-tetrahydromethanopterin formyltr


Domain annotation for each model (and alignments):
>> FTR_C  FTR, proximal lobe
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.9   1.5     3e-69   2.7e-65       1     149 []     147     296 ..     147     296 .. 0.99

  Alignments for each domain:
  == domain 1  score: 218.9 bits;  conditional E-value: 3e-69
                                       EEEEEES-EEEEEEEEEEEEEEEESSHHHHHHHHHHHHHHHHTSTTEE--SGGGEESS-EEES-.S-TT-SEEE-GG CS
                             FTR_C   1 geflieeklgvvkgvaGgnllilaedqeaaleaaeaaveaikkvegvitpFpGgivrsgSKvgs.kykflkastNea 76 
                                       g+fliee++g+v+gvaGgn++i++++q++al+aa++aveai+kveg+itpFpGgiv+sgSK+g+ ky+flka++Ne+
  gi|298675710|ref|YP_003727460.1| 147 GDFLIEESIGAVEGVAGGNFFIFGDSQMSALNAAQSAVEAINKVEGTITPFPGGIVASGSKPGAnKYTFLKATANEK 223
                                       8***************************************************************9************ PP

                                       G-TTSTT....----TT--EEEEEEEEESSHHHHHHHHHHHHHHHTTSTTEEEEE---STTSS-SEEEEGGGG CS
                             FTR_C  77 fcptlkekveeselpedveavlEiVidgldeeavaeamkagieaavkvegvlkisAgNygGkLGkykfkLkel 149
                                       +cp++k+kve s++p+dv+av+EiVi+gld++ v+ea+++g++aav+ +g++kisAgNygG+LG+++f+Lke+
  gi|298675710|ref|YP_003727460.1| 224 YCPSIKDKVEGSMIPKDVNAVYEIVINGLDTDVVSEAIETGVKAAVTLPGIKKISAGNYGGNLGPHQFYLKEI 296
                                       **********************************************************************996 PP

>> FTR  Formylmethanofuran-tetrahydromethanopterin formyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.2   0.0   6.1e-67   5.5e-63       1     142 []       1     144 [.       1     144 [. 0.98
   2 ?   -2.0   0.0      0.36   3.2e+03      86     104 ..     226     244 ..     175     268 .. 0.55

  Alignments for each domain:
  == domain 1  score: 211.2 bits;  conditional E-value: 6.1e-67
                                       -EETTEEE-S-EEEEEEEEEEEEEEE-SSHHHHHHHHHHHHSS-S-TTTSS-EEEESEEB-GGGSTTSS-EEEEEEE CS
                               FTR   1 leingveiedtfaEaFeikvtrviiTaatkkwakeaateatgfatsvigceaEagiervlspeetpDgRpGvailif 77 
                                       +e+ngve+e+tfaEaF+ikv+r++iTaatk wak aa+eatgf+tsvi+c+aEagier+ + +etpDgRpG++i+i+
  gi|298675710|ref|YP_003727460.1|   1 MEVNGVEVEETFAEAFPIKVSRILITAATKYWAKVAAQEATGFGTSVIMCPAEAGIERFANWNETPDGRPGYYIQIC 77 
                                       89*************************************************************************** PP

                                       ESSHHHHHHHHHHHHHHHTTTSTT-EEEE--..GG-SEEHHHHHHGGGTT--EEEEETTEEEEEEEE CS
                               FTR  78 aaskkklekqlleRigqcvLtapttavfngl..aeekiklgkklrffgDgyeiekelggrkvwriPv 142
                                       ++s k+le+q+l+R+gqcvLtapttavfngl  a++++++g kl+ffgDg+e+e+++ +rk+++iP+
  gi|298675710|ref|YP_003727460.1|  78 NFSYKDLEDQVLKRLGQCVLTAPTTAVFNGLleAKKQFDTGYKLKFFGDGMESETQILDRKMYSIPI 144
                                       *******************************54459******************************8 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.36
                                       HHHHHHHHHHTTTSTT-EE CS
                               FTR  86 kqlleRigqcvLtapttav 104
                                        ++++++  +++ +   av
  gi|298675710|ref|YP_003727460.1| 226 PSIKDKVEGSMIPKDVNAV 244
                                       3333444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1975.15
//
Query:       gi|298675711|ref|YP_003727461.1|  [L=660]
Description: copper-translocating P-type ATPase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.7e-51  172.4   0.4    6.7e-51  172.4   0.4    2.0  2  E1-E2_ATPase  E1-E2 ATPase
    4.8e-45  154.4   0.0      7e-45  153.9   0.0    1.3  1  Hydrolase     haloacid dehalogenase-like hydrolase
    1.3e-05   25.7   0.0    3.4e-05   24.3   0.0    1.7  1  HAD           haloacid dehalogenase-like hydrolase
      3e-05   23.9   0.8     0.0039   17.0   0.7    2.7  3  Hydrolase_3   haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.012   15.7   0.0      0.026   14.6   0.0    1.5  1  HAD_2         Haloacid dehalogenase-like hydrolase
      0.045   13.0   1.7       0.16   11.3   0.9    2.0  2  WBS28         Williams-Beuren syndrome chromosomal region 28 


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.4       2.7   8.2e+03     127     156 ..      30      67 ..      21      70 .. 0.52
   2 !  172.4   0.4   2.3e-54   6.7e-51       2     180 ..     152     332 ..     151     333 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 2.7
                                       HHHHHHHHHS-STTTSSTT........HHHHHHHHHHH CS
                      E1-E2_ATPase 127 lliallvflialllgksla........eallralallv 156
                                       +++++ +fl+ +l++++l         ++ll++l+++v
  gi|298675711|ref|YP_003727461.1|  30 TILTIPIFLLSPLIQQFLGisigftgdQYLLFVLSTVV 67 
                                       33344444444443333333333556677777777776 PP

  == domain 2  score: 172.4 bits;  conditional E-value: 2.3e-54
                                       SS--EEEEE.-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEE CS
                      E1-E2_ATPase   2 llpptakvi.rdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvv 77 
                                       l+p++a+++  dg +e++   e++ GDivl+k+g+++paDg iveg++++des+LTGEs+pv+k+ gd+v++G+++ 
  gi|298675711|ref|YP_003727461.1| 152 LMPSEAHRVkSDGDLEDVSLTEIQEGDIVLVKPGEKIPADGDIVEGESSLDESMLTGESRPVSKSVGDEVIGGSING 228
                                       78889988889****************************************************************** PP

                                       E-EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT.HHHHHHHH CS
                      E1-E2_ATPase  78 sgeakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgksla.eallrala 153
                                       + ++k++V +tged++l+++++lv+ea+ +k+++q+ +++ + +l++++l  ++++f+++ ++ ++   ++l r+++
  gi|298675711|ref|YP_003727461.1| 229 EASLKVEVKKTGEDSFLSQLINLVQEAQGSKSRTQNLANRAALWLTIIALSGGAITFALWTIVMNTDLaFSLERSVT 305
                                       **********************************************************9988666555599999*** PP

                                       HHHHHS-TTHHHHHHHHHHHHHHHHHH CS
                      E1-E2_ATPase 154 llvaaiPcaLplavplalalgarrlak 180
                                       ++v+++P aL+la+pl++a++ +  ak
  gi|298675711|ref|YP_003727461.1| 306 VMVITCPHALGLAIPLVVAISSTLGAK 332
                                       *******************99988887 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.9   0.0   2.3e-48     7e-45       1     210 []     349     562 ..     349     562 .. 0.92

  Alignments for each domain:
  == domain 1  score: 153.9 bits;  conditional E-value: 2.3e-48
                                       SSEEEEESBTTTBCHHHHHHHHHHHH.CHHHHHHHHHH......HHCHHHHHHHHHHHHHHHHHHHHHHETTTE... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsa.alalaaaletg......sehpigkalvaaakarsgaltgfatfigrg... 67 
                                       i+ ++fDk+GTLt+ge  v+d+i+   +l+++++l ++      sehpi+k +v   +++ + +++f+ ++g+g   
  gi|298675711|ref|YP_003727461.1| 349 INSILFDKTGTLTKGEFGVTDTIPFTnDLDENQILKYAaslesnSEHPIAKGIVSSSNEH-FYVENFQSIPGKGaeg 424
                                       7889***********************55555555555555566*********9999998.999************* PP

                                       .....HHHHTHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHH..TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEE CS
                                       .....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  68 .....ayaigkpewltaldippdlgaaigsaqsqgrtvall..qaralavftiadplkvkpeaaeavasLkaagiev 137
                                             + + +p +l+++ i+   ++ i+++ +qg+tv+++  ++++ + +++ad   ++pe +eav +Lk++g++ 
  gi|298675711|ref|YP_003727461.1| 425 tvesrNVKVVSPGYLDENGISIPENKHIDKLRTQGKTVVYVllDDELTGAIALADI--IRPESKEAVSKLKSMGVRC 499
                                       ******************8999999999999999999999999*************..******************* PP

                                       EEEESSEHHHHHHHHHHTTGGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 138 vlltgdnpetaeraanqlGddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                        +ltgdn++ a+ +an++G           +e +++++p++k ++++e+q ++  vam GDgvnDa+ala+A+
  gi|298675711|ref|YP_003727461.1| 500 MMLTGDNEQVARWVANEVG----------LDEYFSEVLPQDKSKKVKEIQSRGYIVAMTGDGVNDAPALAQAD 562
                                       *******************..........7888*****************77666*****************8 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   1.1e-08   3.4e-05      82     187 ..     477     558 ..     460     559 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.1e-08
                               HAD  82 rpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkvaal 158
                                       +  +++p+ +e++++ ++ G+r+ +++g ++++++ +++e+g    l++      +++    l+++ ++   kv+++
  gi|298675711|ref|YP_003727461.1| 477 LADIIRPESKEAVSKLKSMGVRCMMLTGDNEQVARWVANEVG----LDE------YFSEV--LPQDKSK---KVKEI 538
                                       334678************************************....***......88888..5444444...47888 PP

                               HAD 159 rewlaaegegidleevvay.GDspsDlpll 187
                                       ++    +g+      +va  GD+++D p+l
  gi|298675711|ref|YP_003727461.1| 539 QS----RGY------IVAMtGDGVNDAPAL 558
                                       88....443......88888********98 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.94   2.8e+03      75     114 ..     373     416 ..     357     456 .. 0.68
   2 ?    3.7   0.0     0.015        44      16      58 ..     481     523 ..     478     526 .. 0.92
   3 !   17.0   0.7   1.3e-06    0.0039     206     251 ..     545     591 ..     530     593 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.94
                                       EE--B-HHHHHHHHHHHHHTT.....CEEEEEESSEEEESTT.TH CS
                       Hydrolase_3  75 ykstiskedvkeiikllkenn.....veillytedkvyvlnkeks 114
                                       ++++++++++ +  + l++n        i+ ++++++yv+n  +s
  gi|298675711|ref|YP_003727461.1| 373 FTNDLDENQILKYAASLESNSehpiaKGIVSSSNEHFYVENF-QS 416
                                       677777777777777777777666766777777888888887.33 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.015
                                       --HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEE CS
                       Hydrolase_3  16 isektkeaikklkekgikvviATGRslravlpvleelgldlpv 58 
                                       i +++kea+ klk+ g+  +  TG + + ++ v++e+gld ++
  gi|298675711|ref|YP_003727461.1| 481 IRPESKEAVSKLKSMGVRCMMLTGDNEQVARWVANEVGLDEYF 523
                                       6789**********************************99875 PP

  == domain 3  score: 17.0 bits;  conditional E-value: 1.3e-06
                                       EEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGG.THH CS
                       Hydrolase_3 206 viafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnne.dGV 251
                                       v+  GDg ND + L +a++g+A+g +++ + + Ad +  + n  d+V
  gi|298675711|ref|YP_003727461.1| 545 VAMTGDGVNDAPALAQADVGIAIGAGTDVAVETADIILVKSNPmDAV 591
                                       6778********************************88777766888 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   8.8e-06     0.026      82     135 ..     483     536 ..     480     558 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.8e-06
                             HAD_2  82 dgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkK 135
                                       ++ ke++ +Lk++g+++   T  ++++++   +++g+++yF+ ++ +++ +k K
  gi|298675711|ref|YP_003727461.1| 483 PESKEAVSKLKSMGVRCMMLTGDNEQVARWVANEVGLDEYFSEVLPQDKSKKVK 536
                                       6789********************************************999988 PP

>> WBS28  Williams-Beuren syndrome chromosomal region 28 protein homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.9   5.2e-05      0.16      47     116 ..     248     322 ..     243     336 .. 0.72
   2 ?   -0.4   0.0      0.19   5.7e+02     115     134 ..     588     607 ..     573     612 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.2e-05
                             WBS28  47 vsGLaqeaqGstskqahppaevaacplgralrag...laLlevPv..wLvlrgprLvlaavlgcaralglalklg 116
                                       +  L qeaqGs s+  ++++ +a      al  g   +aL+++ +   L++   r v++ v++c +algla+ l 
  gi|298675711|ref|YP_003727461.1| 248 LINLVQEAQGSKSRTQNLANRAALWLTIIALSGGaitFALWTIVMntDLAFSLERSVTVMVITCPHALGLAIPLV 322
                                       56799******99988887666544444455443323567776552269999*******************8743 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.19
                             WBS28 115 lgaweqlGLsvatwtdllls 134
                                       ++a   lGLs at+++++  
  gi|298675711|ref|YP_003727461.1| 588 MDAVSILGLSRATYKKMIQN 607
                                       789999*********99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (660 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.46
# Mc/sec: 4314.23
//
Query:       gi|298675712|ref|YP_003727462.1|  [L=212]
Description: endonuclease III [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-25   90.2   0.1    1.4e-25   89.9   0.1    1.1  1  HhH-GPD        HhH-GPD superfamily base excision DNA repair p
    3.3e-06   26.7   0.0    7.4e-05   22.4   0.0    2.4  2  HHH            Helix-hairpin-helix motif
    4.8e-06   27.1   0.0      0.032   14.8   0.0    2.5  2  HHH_5          Helix-hairpin-helix domain
    0.00061   19.7   0.3     0.0011   19.0   0.3    1.3  1  DUF4294        Domain of unknown function (DUF4294)
    0.00062   20.0   3.2      0.001   19.4   3.2    1.4  1  EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
  ------ inclusion threshold ------
      0.065   13.2   0.2       0.28   11.1   0.0    1.9  2  DUF2400        Protein of unknown function (DUF2400)
       0.12   13.1   0.1       0.42   11.4   0.1    2.1  1  DUF3349        Protein of unknown function (DUF3349)
       0.18   11.9   0.0        6.7    6.9   0.0    2.5  2  HHH_2          Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.9   0.1     6e-29   1.4e-25       1     106 [.      37     171 ..      37     173 .. 0.96

  Alignments for each domain:
  == domain 1  score: 89.9 bits;  conditional E-value: 6e-29
                                       HHHHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH........... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........... RF
                           HhH-GPD   1 vsailsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv........... 66 
                                       +++ils+q +d  +nr++e+lf++   p ++dla+ad ++L++ i+++Gfy++Kak+ik++A+++            
  gi|298675712|ref|YP_003727462.1|  37 IATILSAQATDTQVNRVTEHLFKK--YPYVDDLANADIKELEKDIYSTGFYKNKAKNIKKCAQMIKsqfnskvpdnm 111
                                       789*********************..59************************************************* PP

                                       ......................S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHHHHHHHHHH CS
                                       ......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           HhH-GPD  67 ......................gkpdvlivvDvhvrrilkrlrsikekktkkkvekkleell 106
                                                             g   ++i+vD+hv+r+ +rl+++++ kt++k+e++l++l 
  gi|298675712|ref|YP_003727462.1| 112 ndmmelsgvgrktanivlsrgfGVH-EGIAVDTHVKRLSQRLGLTQN-KTPEKIEQDLMKLA 171
                                       ********************99654.59*****************99.6*********9875 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1      0.14   3.2e+02       3      15 ..      65      77 ..      64      77 .. 0.86
   2 !   22.4   0.0   3.3e-08   7.4e-05       2      29 ..     103     130 ..     102     131 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.14
                                      HHHHTSSHHHHHT CS
                               HHH  3 eglipasreeLla 15
                                      + l +a+++eL++
  gi|298675712|ref|YP_003727462.1| 65 DDLANADIKELEK 77
                                      6789*******86 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 3.3e-08
                                       HHHHHTSSHHHHHTSTT-SHHHHHHHHH CS
                               HHH   2 leglipasreeLlalPGVGpktAeaIls 29 
                                       +++ +p+++ + ++l+GVG+ktA+ +ls
  gi|298675712|ref|YP_003727462.1| 103 FNSKVPDNMNDMMELSGVGRKTANIVLS 130
                                       78899*******************9997 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00046         1      23      55 ..      61      96 ..      52      98 .. 0.82
   2 !   14.8   0.0   1.4e-05     0.032       3      40 ..     113     151 ..     111     169 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00046
                                      --SHHHHHHS-HHHHHT.S..TTS-HHHHHHHHHHH CS
                             HHH_5 23 iesvedlaaadveeLak.i..pGiGkktAeriilel 55
                                      +  v+dla+ad++eL k i  +G+ k +A++i+  +
  gi|298675712|ref|YP_003727462.1| 61 YPYVDDLANADIKELEKdIysTGFYKNKAKNIKKCA 96
                                      4569************97788999999999998665 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.4e-05
                                       HHHTSTT--HHHHHHHHTTT--SHHHHH.HS-HHHHHTS CS
                             HHH_5   3 eLlsvsGiGpktAlallsaGiesvedla.aadveeLaki 40 
                                       +++++sG+G+ktA  +ls G++  e +a +  v++L++ 
  gi|298675712|ref|YP_003727462.1| 113 DMMELSGVGRKTANIVLSRGFGVHEGIAvDTHVKRLSQR 151
                                       7899******************99999734568888875 PP

>> DUF4294  Domain of unknown function (DUF4294)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.3   4.7e-07    0.0011      22      83 ..      44     106 ..      32     112 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4.7e-07
                           DUF4294  22 kkerkrylrlrrkvkkvyPyak.laaerlieleeeletlkdkkerkkyikevekelkkefeke 83 
                                       +    + +r+ +++ k yPy+  la++ ++ele+++ ++   k++ k ik++ + +k++f+ +
  gi|298675712|ref|YP_003727462.1|  44 QATDTQVNRVTEHLFKKYPYVDdLANADIKELEKDIYSTGFYKNKAKNIKKCAQMIKSQFNSK 106
                                       56677889999*********9548999*********************************987 PP

>> EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   3.2   4.5e-07     0.001       1      17 []     191     207 ..     191     207 .. 0.98

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 4.5e-07
                     EndIII_4Fe-2S   1 CTARkPkCeaCPLaDlC 17 
                                       C A++P Ce C+++ lC
  gi|298675712|ref|YP_003727462.1| 191 CHAKNPECENCVVNTLC 207
                                       ***************99 PP

>> DUF2400  Protein of unknown function (DUF2400)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.38   8.5e+02      99     120 ..      80     104 ..      27     125 .. 0.55
   2 ?   11.1   0.0   0.00013      0.28     173     194 ..     139     160 ..     138     173 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.38
                           DUF2400  99 lk...aeeeeeeleealeafreafl 120
                                       ++   ++++++++++  + ++++f 
  gi|298675712|ref|YP_003727462.1|  80 YStgfYKNKAKNIKKCAQMIKSQFN 104
                                       2233333444444444444444444 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00013
                           DUF2400 173 iPlDvHvarvarklgllkrkqa 194
                                       i +D+Hv+r++++lgl+++k+ 
  gi|298675712|ref|YP_003727462.1| 139 IAVDTHVKRLSQRLGLTQNKTP 160
                                       679**************99875 PP

>> DUF3349  Protein of unknown function (DUF3349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00019      0.42       4      84 ..      10      97 ..       7     106 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                                      HHHHHHHHHH-TT-B-H...HHHHHHH..HHHCTT--HHHHHHHHHHHHHH--.SSS.BSHHHCHHHHHHHCT...S-- CS
                           DUF3349  4 asileWLragYPegvPe...qdyvpLl..alLrrrLsdeevkevaeelvaeaaeadeavdeedieelitkvte...eep 74
                                      ++i + L++ YP+  P+   ++ + Ll   +L+ + +d +v++v+e+l ++     + + ++di+el +++ +    + 
  gi|298675712|ref|YP_003727462.1| 10 ENIWSLLQKEYPNPEPAlrfNNPFQLLiaTILSAQATDTQVNRVTEHLFKKY-PYVDDLANADIKELEKDIYStgfYKN 87
                                      6777889999999888633345566653358999999999****99999999.44455555555555444433111455 PP

                                      -HHHHHHHHH CS
                           DUF3349 75 seedvarVaa 84
                                      +++++++ a+
  gi|298675712|ref|YP_003727462.1| 88 KAKNIKKCAQ 97
                                      5666666555 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0     0.003       6.7      16      38 ..      54      76 ..      51      79 .. 0.89
   2 ?    2.1   0.0     0.094   2.1e+02      35      51 ..     112     128 ..     109     131 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.003
                             HHH_2 16 AklLakrFksldaLkkasleeLl 38
                                       + L k++  +d L++a+++eL 
  gi|298675712|ref|YP_003727462.1| 54 TEHLFKKYPYVDDLANADIKELE 76
                                      57899****************96 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.094
                             HHH_2  35 eeLlevddiGeeiAqsi 51 
                                       +++ e+ ++G ++A+ +
  gi|298675712|ref|YP_003727462.1| 112 NDMMELSGVGRKTANIV 128
                                       68889999999999866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1255  (0.0699983); expected 358.6 (0.02)
Passed bias filter:                      767  (0.0427799); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1250.75
//
Query:       gi|298675713|ref|YP_003727463.1|  [L=292]
Description: thiamine pyrophosphate domain-containing TPP-binding protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-26   92.3   0.1    3.4e-26   91.9   0.1    1.2  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.9   0.1   1.9e-30   3.4e-26       2     152 ..      39     201 ..      38     202 .. 0.91

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 1.9e-30
                                       SSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHH......STTSEEEEEEEHHHHHHT.GGGHHHHHHT CS
                      TPP_enzyme_C   2 iGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGakla......kpdrevvaivGDGgflmi.lqelatavrr 71 
                                       +Gcl++++  +    + +s+  + +++ + ++ ++A+G++ a      + d + v+i+GDGg+ +i +  ++ a +r
  gi|298675713|ref|YP_003727463.1|  39 TGCLEVMTTPY----PDTSWNVPWIHSLFENAGAVASGIESAwkamnkDDDTKFVVIAGDGGTVDIgMRSISGAFER 111
                                       69999955555....566677799****************955556534479************************* PP

                                       T-SEEEEEEE-SBCCCHHHH...HHHHTCCTTTTSBB......BS----HHHHHHHTTSE.EEEESSH.HHHHHHHH CS
                      TPP_enzyme_C  72 nlpitvvvlnNegygmtggq...qepfggkrksgpagk.....dlkpvdfaklaealGak.garvekadveeleeal 139
                                       +++it+++++Ne+y++tg q    +p+ ++++++pagk     + +++++ ++++a+G + +a+ + a++++l ++ 
  gi|298675713|ref|YP_003727463.1| 112 GHDITYICMDNEAYMNTGVQrsgATPYDASTTTSPAGKesfgnERPKKNMPEIMAAHGSPyVATASLAYPKDLMKKA 188
                                       *****************************************98899**************999999*********** PP

                                       HHHHCSSSEEEEE CS
                      TPP_enzyme_C 140 kealekkgpalie 152
                                       k+a + +gp++i+
  gi|298675713|ref|YP_003727463.1| 189 KKAADIEGPTYIH 201
                                       ************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1817.50
//
Query:       gi|298675714|ref|YP_003727464.1|  [L=404]
Description: pyruvate flavodoxin/ferredoxin oxidoreductase domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-67  228.3   0.0    1.3e-67  227.9   0.0    1.1  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    1.9e-30  105.2   0.1    3.9e-30  104.2   0.1    1.6  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
      1e-07   31.9   0.1    2.3e-07   30.7   0.1    1.5  1  Transketolase_C  Transketolase, C-terminal domain
  ------ inclusion threshold ------
      0.089   12.5   1.9       0.18   11.6   1.9    1.4  1  Lantibiotic_a    Lantibiotic alpha


Domain annotation for each model (and alignments):
>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.9   0.0   2.9e-71   1.3e-67       2     228 ..      24     246 ..      23     249 .. 0.96

  Alignments for each domain:
  == domain 1  score: 227.9 bits;  conditional E-value: 2.9e-71
                                       HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCC CS
                             POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmien 78 
                                       a + ++++vi+aYPITP++ i+e l++++a+ge+++ +++++esE++a s+ +G++a+Gar+   T +qGl+Lm+e 
  gi|298675714|ref|YP_003727464.1|  24 ATKVCKPNVISAYPITPQTHIVEDLSQFIADGEIENCDYINVESEFSALSTLVGSSATGARTYSSTTSQGLALMHEV 100
                                       5677899***************************99***************************************** PP

                                       HHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHH..CTSEEEEEE CS
                             POR_N  79 lglaageelPvvivvvaRalpstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAek..vrvPvivlf 153
                                       l+ a+g++lP+v++vv+Ral+++ ++i++dq+D +  rd+g+i+l++e+vqea d++++A+++ e+  v++Pv+v++
  gi|298675714|ref|YP_003727464.1| 101 LFNASGMRLPIVVTVVNRALSAP-INIWNDQQDSVSERDSGWIQLYAEDVQEAGDMIAQAYKVGEDpdVMLPVMVCM 176
                                       ***********************.***************************************************** PP

                                       EHHHH.HEEEEEEC-SGG.GS-----SBXXXXXXXXSXXXBXXTXXTSSXXEEESBXBXTTSXBXXXXHHHHHHH CS
                             POR_N 154 Dgfllshevekvelpdeedelklikekleeyerkeyaldpekpiargtaanpdtglehrekgneaedaaekvvee 228
                                       Dgfllsh +e+v l++e+    li++ l++ ++ ey+ldp+ p ++g+ a+p+ + e+r+++++a++aa   +e+
  gi|298675714|ref|YP_003727464.1| 177 DGFLLSHVYEPVVLLEED----LIDDYLPPFDP-EYKLDPKDPKTFGAFAPPASYTEFRYAQEQAMSAALDKIEK 246
                                       ******************....99999999988.55******************************987666665 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.2   0.1   8.7e-34   3.9e-30       1      98 [.     271     371 ..     271     385 .. 0.97

  Alignments for each domain:
  == domain 1  score: 104.2 bits;  conditional E-value: 8.7e-34
                                       -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G.-HHHHHHHH CS
                           PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgse.Gqlveevka 76 
                                       Ae++i+a Gs++gt+++++d+lRe+g+kvGll++r+lrPFP++++ke++k+++ vv+ld+nis g++ G+l +e ka
  gi|298675714|ref|YP_003727464.1| 271 AEIIIMAKGSIIGTIRDVIDSLRENGVKVGLLKVRALRPFPKDAIKEVVKDTSVVVTLDKNISPGVNeGALCTETKA 347
                                       9**************************************************************************** PP

                                       HTGGG..TSEEEEEE--GGG---- CS
                           PFOR_II  77 alkks..kvkvvnfvaglgGrdit 98 
                                       ++++s  +v+v+ ++ glgGrdi 
  gi|298675714|ref|YP_003727464.1| 348 CMYNSdiNVPVIGYMIGLGGRDIP 371
                                       *****99***************85 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.1   5.1e-11   2.3e-07       7      75 ..     268     336 ..     265     365 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 5.1e-11
                                       ETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTS CS
                   Transketolase_C   7 regkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgG 75 
                                        +  ++++ a Gs   +  ++++ L+++g+++ ++ +r ++p+ k+ i+e+vk t  +v+++ +   g 
  gi|298675714|ref|YP_003727464.1| 268 TDDAEIIIMAKGSIIGTIRDVIDSLRENGVKVGLLKVRALRPFPKDAIKEVVKDTSVVVTLDKNISPGV 336
                                       56789***************************************************9999987665443 PP

>> Lantibiotic_a  Lantibiotic alpha
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.9   3.9e-05      0.18      13      26 ..     337     350 ..     335     352 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.9e-05
                     Lantibiotic_a  13 NkGylCTvTkECMp 26 
                                       N G+lCT Tk CM 
  gi|298675714|ref|YP_003727464.1| 337 NEGALCTETKACMY 350
                                       99***********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2628.63
//
Query:       gi|298675715|ref|YP_003727465.1|  [L=86]
Description: pyruvate ferredoxin/flavodoxin oxidoreductase subunit delta [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.6e-15   53.9  13.0    5.9e-08   32.2   3.9    2.4  2  Fer4      4Fe-4S binding domain
    2.4e-11   43.6   6.2    3.2e-11   43.2   6.2    1.2  1  Fer4_21   4Fe-4S dicluster domain
    3.5e-10   39.9  18.9    3.1e-08   33.6   8.4    1.6  2  Fer4_9    4Fe-4S dicluster domain
    4.6e-10   39.1  11.1    1.8e-05   24.6   2.5    2.2  2  Fer4_6    4Fe-4S binding domain
    1.3e-08   35.2  10.5    1.7e-08   34.9   9.7    1.6  1  Fer4_7    4Fe-4S dicluster domain
    1.5e-08   35.4   7.6    0.00083   20.3   1.9    2.3  2  Fer4_16   4Fe-4S double cluster binding domain
    6.9e-08   32.1   8.5    0.00042   20.2   1.8    2.3  2  Fer4_2    4Fe-4S binding domain
    2.1e-06   27.8  22.1    0.00046   20.3  12.5    2.1  2  Fer4_10   4Fe-4S dicluster domain
    4.2e-05   23.7  16.2     0.0071   16.8   1.6    2.5  3  Fer4_4    4Fe-4S binding domain
    7.5e-05   23.2   9.0      0.028   14.9   1.3    2.2  2  Fer4_17   4Fe-4S dicluster domain
    0.00087   19.7  12.8      0.068   13.6   3.6    2.2  2  Fer4_8    4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.013   16.2  10.8       0.19   12.5   3.6    2.7  2  Fer4_15   4Fe-4S single cluster domain
      0.018   15.6  12.6       0.14   12.7   1.5    2.5  3  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
       0.15   13.0  12.2       0.23   12.3   1.9    2.2  2  Fer4_22   4Fe-4S dicluster domain
       0.31   12.1  16.7        1.2   10.3   2.3    2.4  2  Fer4_3    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   1.7   2.2e-09   2.7e-06       3      23 ..      29      49 ..      27      50 .. 0.90
   2 !   32.2   3.9   4.9e-11   5.9e-08       2      24 .]      58      80 ..      57      80 .. 0.94

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 2.2e-09
                                      EETTTSSS-THHHHHSTTTEE CS
                              Fer4  3 ideekCigCGaCvevCPvgAI 23
                                      + ++kCi+C++C+  CP +AI
  gi|298675715|ref|YP_003727465.1| 29 FLYDKCIKCKLCELLCPDEAI 49
                                      668*****************9 PP

  == domain 2  score: 32.2 bits;  conditional E-value: 4.9e-11
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                      ++d++ C gCG C++ CPv AI+
  gi|298675715|ref|YP_003727465.1| 58 EYDYDYCKGCGVCANECPVSAIE 80
                                      68*******************96 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   6.2   2.6e-14   3.2e-11       6      59 .]      32      81 ..      28      81 .. 0.96

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 2.6e-14
                           Fer4_21  6 dkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59
                                      dkCi+C++C + C+d   +ai+  ++  +++  d C GC +C++ CPv  +iem
  gi|298675715|ref|YP_003727465.1| 32 DKCIKCKLCELLCPD---EAINPREDGFFEYDYDYCKGCGVCANECPV-SAIEM 81
                                      89************9...9****************************9.99998 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   2.7   2.6e-06    0.0031      12      51 .]       9      49 ..       7      49 .. 0.73
   2 !   33.6   8.4   2.6e-11   3.1e-08       1      51 []      33      79 ..      33      79 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.6e-06
                            Fer4_9 12 Cpagvvvedaaerkarlraase.eaCigCgaCveaCpkgai 51
                                      C+ g++++ + ++ ++++     ++Ci+C+ C+  Cp +ai
  gi|298675715|ref|YP_003727465.1|  9 CEPGTTKKNKTGGWRNYKPIFLyDKCIKCKLCELLCPDEAI 49
                                      6666666666666666655544899************9887 PP

  == domain 2  score: 33.6 bits;  conditional E-value: 2.6e-11
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      kC++C+ C+  Cp +++++++ + +     +    C gCg C++ Cp  ai
  gi|298675715|ref|YP_003727465.1| 33 KCIKCKLCELLCPDEAINPREDGFFEYDYDY----CKGCGVCANECPVSAI 79
                                      7********************9999887664....************9887 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   1.5   5.1e-07   0.00061       3      24 .]      28      49 ..      26      49 .. 0.88
   2 !   24.6   2.5   1.5e-08   1.8e-05       2      24 .]      57      79 ..      56      79 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.1e-07
                            Fer4_6  3 eidpdkCigCgdCvrvCPegai 24
                                       + +dkCi C  C+  CP  ai
  gi|298675715|ref|YP_003727465.1| 28 IFLYDKCIKCKLCELLCPDEAI 49
                                      5668**************9998 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 1.5e-08
                            Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                       e+d+d C gCg C++ CP  ai
  gi|298675715|ref|YP_003727465.1| 57 FEYDYDYCKGCGVCANECPVSAI 79
                                      689*****************998 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   9.7   1.4e-11   1.7e-08       1      52 []      33      78 ..      33      78 .. 0.92

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 1.4e-11
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      +Ci+C+ C+  Cp +ai+ +e+    g    e+d+++C gCg+C+++CP+ a
  gi|298675715|ref|YP_003727465.1| 33 KCIKCKLCELLCPDEAINPRED----G--FFEYDYDYCKGCGVCANECPVSA 78
                                      7*****************9886....5..678999**************986 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.4   2.1e-06    0.0025       1      22 [.      33      54 ..      33      62 .. 0.85
   2 !   20.3   1.9   6.9e-07   0.00083       2      20 ..      64      82 ..      63      86 .] 0.89

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.1e-06
                           Fer4_16  1 rCgtCgkCaevCPtnaikekke 22
                                      +C++C+ C   CP +ai+ +++
  gi|298675715|ref|YP_003727465.1| 33 KCIKCKLCELLCPDEAINPRED 54
                                      6****************98855 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 6.9e-07
                           Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                      C++Cg Ca+ CP++ai++ 
  gi|298675715|ref|YP_003727465.1| 64 CKGCGVCANECPVSAIEMV 82
                                      ****************976 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.7   7.9e-06    0.0094       2      21 ..      26      45 ..      25      46 .. 0.90
   2 !   20.2   1.8   3.5e-07   0.00042       3      21 ..      57      75 ..      55      76 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7.9e-06
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                      ++ +  d+Ci C+ C   CP
  gi|298675715|ref|YP_003727465.1| 26 KPIFLYDKCIKCKLCELLCP 45
                                      578889***********9*9 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 3.5e-07
                            Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                      +++d d C gCg C + CP
  gi|298675715|ref|YP_003727465.1| 57 FEYDYDYCKGCGVCANECP 75
                                      689**************** PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3  12.5   3.8e-07   0.00046       4      56 .]      29      75 ..      26      75 .. 0.78
   2 !   18.7   2.0   1.2e-06    0.0014       3      23 ..      58      78 ..      56      86 .] 0.82

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.8e-07
                           Fer4_10  4 idddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      +  d+Ci+C+ C   CP      +a++   e++  + +++ C gcg C+ +CP
  gi|298675715|ref|YP_003727465.1| 29 FLYDKCIKCKLCELLCPD-----EAINP-REDGFFEYDYDYCKGCGVCANECP 75
                                      5579**************.....33333.344455668**************9 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 1.2e-06
                           Fer4_10  3 vidddtCirCgkCvkaCPadl 23
                                      ++d d C +Cg C + CP+++
  gi|298675715|ref|YP_003727465.1| 58 EYDYDYCKGCGVCANECPVSA 78
                                      5799**************954 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       9.4   1.1e+04       8      11 ..       7      10 ..       7      11 .. 0.67
   2 !   16.8   1.6   5.9e-06    0.0071       1      16 [.      31      46 ..      31      53 .. 0.93
   3 !   14.9   4.0   2.4e-05     0.028       1      16 [.      61      76 ..      61      77 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 9.4
                            Fer4_4  8 gsCv 11
                                      g+C+
  gi|298675715|ref|YP_003727465.1|  7 GVCE 10
                                      5786 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 5.9e-06
                            Fer4_4  1 qerCigCgsCvaaCPq 16
                                      +++Ci C+ C+  CP+
  gi|298675715|ref|YP_003727465.1| 31 YDKCIKCKLCELLCPD 46
                                      59*************7 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 2.4e-05
                            Fer4_4  1 qerCigCgsCvaaCPq 16
                                      ++ C gCg+C + CP+
  gi|298675715|ref|YP_003727465.1| 61 YDYCKGCGVCANECPV 76
                                      589************6 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   1.3   2.4e-05     0.028      42      59 ..      30      47 ..       8      49 .. 0.81
   2 !   13.0   1.3   9.6e-05      0.11       2      14 ..      64      76 ..      58      85 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.4e-05
                           Fer4_17 42 kaslCieCgeCerkCPqg 59
                                        ++Ci+C++Ce  CP +
  gi|298675715|ref|YP_003727465.1| 30 LYDKCIKCKLCELLCPDE 47
                                      5689************75 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 9.6e-05
                           Fer4_17  2 CiqCgyClpeCps 14
                                      C +Cg C++eCp 
  gi|298675715|ref|YP_003727465.1| 64 CKGCGVCANECPV 76
                                      7777777777775 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   1.9   0.00042      0.51       3      16 ..      32      45 ..      30      61 .. 0.78
   2 !   13.6   3.6   5.7e-05     0.068       3      18 ..      62      77 ..      60      82 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00042
                            Fer4_8  3 ekCieCgaCqsaCp 16
                                      +kCi+C +C+  Cp
  gi|298675715|ref|YP_003727465.1| 32 DKCIKCKLCELLCP 45
                                      57888888888887 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 5.7e-05
                            Fer4_8  3 ekCieCgaCqsaCpvl 18
                                      ++C +Cg C ++Cpv 
  gi|298675715|ref|YP_003727465.1| 62 DYCKGCGVCANECPVS 77
                                      5677788888888764 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.8    0.0082       9.8       6      20 ..      32      46 ..      31      56 .. 0.76
   2 ?   12.5   3.6   0.00016      0.19       2      19 ..      58      75 ..      57      79 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0082
                           Fer4_15  6 daCigcglCvaeape 20
                                      d+Ci c lC  ++p+
  gi|298675715|ref|YP_003727465.1| 32 DKCIKCKLCELLCPD 46
                                      89***********64 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00016
                           Fer4_15  2 vvDrdaCigcglCvaeap 19
                                      ++D d C gcg+C+ e+p
  gi|298675715|ref|YP_003727465.1| 58 EYDYDYCKGCGVCANECP 75
                                      589**************8 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.5   0.00011      0.14       4      18 ..      32      46 ..      31      47 .. 0.95
   2 ?    7.9   3.4    0.0037       4.4       2      17 ..      60      75 ..      59      77 .. 0.90
   3 ?    4.8   0.1     0.034        41      48      57 ..      71      80 ..      71      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                           Fer4_13  4 dtCiacgaCvelaPd 18
                                      d+Ci c++C  l+Pd
  gi|298675715|ref|YP_003727465.1| 32 DKCIKCKLCELLCPD 46
                                      79************8 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0037
                           Fer4_13  2 DrdtCiacgaCvelaP 17
                                      D d C +cg+C++ +P
  gi|298675715|ref|YP_003727465.1| 60 DYDYCKGCGVCANECP 75
                                      5688***********9 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.034
                           Fer4_13 48 adaCPvesIg 57
                                      a++CPv++I+
  gi|298675715|ref|YP_003727465.1| 71 ANECPVSAIE 80
                                      579******7 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   2.7     0.012        15       1      13 [.      33      45 ..      33      55 .. 0.92
   2 ?   12.3   1.9   0.00019      0.23      76      95 ..      58      77 ..      48      78 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.012
                           Fer4_22  1 rClsCgaCtlvCp 13
                                      +C++C  C l+Cp
  gi|298675715|ref|YP_003727465.1| 33 KCIKCKLCELLCP 45
                                      7***********9 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00019
                           Fer4_22 76 kfgesgCvGCgRCieacpvk 95
                                      +++   C GCg C + cpv+
  gi|298675715|ref|YP_003727465.1| 58 EYDYDYCKGCGVCANECPVS 77
                                      568899***********985 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   2.3   0.00099       1.2       1      12 [.      34      45 ..      34      48 .. 0.94
   2 ?    7.3   6.8    0.0085        10       1      15 []      64      78 ..      64      78 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00099
                            Fer4_3  1 CtgCgaCvevCP 12
                                      C+ C +C+  CP
  gi|298675715|ref|YP_003727465.1| 34 CIKCKLCELLCP 45
                                      ***********9 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0085
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C gCg C + CPv A
  gi|298675715|ref|YP_003727465.1| 64 CKGCGVCANECPVSA 78
                                      9***********977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      180  (0.0100396); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 580.56
//
Query:       gi|298675716|ref|YP_003727466.1|  [L=182]
Description: pyruvate/ketoisovalerate oxidoreductase subunit gamma [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-42  145.0   0.1    2.7e-42  144.8   0.1    1.0  1  POR       Pyruvate ferredoxin/flavodoxin oxidoreductase


Domain annotation for each model (and alignments):
>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.8   0.1   1.5e-46   2.7e-42       1     177 []      10     175 ..      10     175 .. 0.97

  Alignments for each domain:
  == domain 1  score: 144.8 bits;  conditional E-value: 1.5e-46
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHH..HHGGG CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetls..ehldg 75 
                                       GGqG+vta+++la aa++ G+  qa++++g e+rG+++ +  ri+d+pi+ + +++e+d++++ d+++++  ++++g
  gi|298675716|ref|YP_003727466.1|  10 GGQGSVTAAELLAIAAFSDGKFSQAFPSFGVERRGAPVQAFTRIGDKPIRLRSQIYEPDYVIVQDPTLIDivDVAHG 86 
                                       9**************************************************************************** PP

                                       EEEEEEEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHT.S-HHHHH CS
                               POR  76 lkpggiiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggneraaNtvmlGalaallg.lpleale 151
                                       ++++gi+i+ns +++p++++ +            +++ +vdatkia +i g ++++Nt++lGa+a++++ + +e+++
  gi|298675716|ref|YP_003727466.1|  87 MDENGIVIINS-DFNPEDFNIDTD----------AKIMTVDATKIALDIIG-RPIVNTILLGAFAGATDeINPESIK 151
                                       ***********.79***9999886..........4799*************.************************* PP

                                       HHHHCCS-CH.HHHHHHHHHHHHHHH CS
                               POR 152 eaikkrfpkkkeviekNlkafragye 177
                                       ea+k+rfp+k  + +kN +a++++y+
  gi|298675716|ref|YP_003727466.1| 152 EAVKERFPGK--IGDKNAEAVQKAYD 175
                                       ********95..************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1124.62
//
Query:       gi|298675717|ref|YP_003727467.1|  [L=477]
Description: microtubule-severing ATPase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-43  148.3   0.0    3.2e-43  147.3   0.0    1.6  1  AAA              ATPase family associated with various cellul
    7.4e-07   29.0   0.0    1.9e-06   27.7   0.0    1.6  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    5.1e-06   26.2   0.0    1.1e-05   25.1   0.0    1.6  1  AAA_lid_3        AAA+ lid domain
    6.9e-06   26.4   0.2     0.0031   17.8   0.0    3.1  3  AAA_22           AAA domain
    9.9e-06   26.0   0.0     0.0011   19.3   0.0    2.3  2  AAA_16           AAA ATPase domain
      1e-05   25.7   0.0    2.5e-05   24.5   0.0    1.6  1  AAA_2            AAA domain (Cdc48 subfamily)
    2.6e-05   23.6   0.0      5e-05   22.7   0.0    1.4  1  TIP49            TIP49 P-loop domain
    3.9e-05   23.7   0.0    0.00027   21.0   0.0    2.3  2  AAA_14           AAA domain
    4.8e-05   23.7   0.0      0.013   15.9   0.0    2.7  2  RNA_helicase     RNA helicase
    0.00012   22.7   0.0    0.00038   21.0   0.0    2.0  1  AAA_18           AAA domain
    0.00027   20.4   0.2     0.0013   18.1   0.1    2.0  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00044   20.4   0.0    0.00074   19.7   0.0    1.4  1  AAA_33           AAA domain
     0.0013   18.8   0.1     0.0069   16.4   0.1    2.2  1  AAA_5            AAA domain (dynein-related subfamily)
     0.0018   18.0   0.0     0.0046   16.7   0.0    1.7  1  IstB_IS21        IstB-like ATP binding protein
     0.0055   17.0   0.0       0.01   16.1   0.0    1.4  1  AAA_28           AAA domain
  ------ inclusion threshold ------
      0.012   14.8   0.0      0.024   13.9   0.0    1.4  1  Zeta_toxin       Zeta toxin
      0.015   14.8   0.0      0.043   13.3   0.0    1.7  1  AAA_7            P-loop containing dynein motor region
      0.016   15.1   0.0       0.52   10.2   0.0    2.2  2  NACHT            NACHT domain
      0.027   13.6   0.0      0.048   12.8   0.0    1.4  1  DUF815           Protein of unknown function (DUF815)
       0.03   14.7   0.0      0.073   13.5   0.0    1.8  1  AAA_17           AAA domain
      0.031   14.0   0.0       0.14   11.8   0.0    2.0  1  Sigma54_activat  Sigma-54 interaction domain
       0.04   13.3   0.1        1.5    8.1   0.0    2.4  2  ATPase           KaiC
      0.044   13.2   0.0       0.16   11.4   0.0    1.8  2  PhoH             PhoH-like protein
      0.046   13.8   0.0        0.2   11.8   0.0    2.0  2  Cytidylate_kin2  Cytidylate kinase-like family
      0.052   13.4   0.0      0.084   12.7   0.0    1.4  1  CPT              Chloramphenicol phosphotransferase-like prot
      0.054   13.2   0.0       0.13   12.0   0.0    1.6  1  AAA_24           AAA domain
       0.09   13.3   0.0       0.21   12.1   0.0    1.6  1  ABC_tran         ABC transporter
       0.09   12.6   0.0       0.19   11.6   0.0    1.6  1  AAA_3            ATPase family associated with various cellul
        0.1   12.6   0.0       0.21   11.6   0.0    1.6  1  ResIII           Type III restriction enzyme, res subunit
       0.13   11.5   0.1       0.65    9.2   0.1    2.1  1  DUF2075          Uncharacterized conserved protein (DUF2075)
       0.17   11.5   0.3       0.69    9.5   0.2    1.9  2  AAA_25           AAA domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.3   0.0   5.5e-46   3.2e-43       1     131 [.     241     369 ..     241     370 .. 0.96

  Alignments for each domain:
  == domain 1  score: 147.3 bits;  conditional E-value: 5.5e-46
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       +ll+GppGtGKTllakava+el+++f+ + gs+++sk+ ge+e++i+e+f+  ++   ++ilfiDEid+++++r ++
  gi|298675717|ref|YP_003727467.1| 241 ILLFGPPGTGKTLLAKAVATELETPFIHVHGSDIVSKWYGEAEQNIKEMFEISRSRP-HTILFIDEIDSITPAR-EG 315
                                       69************************************************9877765.6***************.99 PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       ++e ++r+v++Ll e+dg k++++ vi++gatnrp+++d+a++r gRfd+k++++
  gi|298675717|ref|YP_003727467.1| 316 SHEATQRIVSTLLDEMDGIKSSDD-VILMGATNRPESIDSAFMRpGRFDKKVHVP 369
                                       9********************855.***************************997 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   3.3e-09   1.9e-06      30     100 ..     235     313 ..     202     320 .. 0.72

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 3.3e-09
                            RuvB_N  30 eealdhvllyGpPGlGkttlakiiakelgvklkitsgP.vlek.....agdlaal..ltnleekdvlfideihrlsr 98 
                                        e+   +ll+GpPG Gkt lak +a+el++ + +  g  +++k     ++++  +  +++ +++ +lfidei  +++
  gi|298675717|ref|YP_003727467.1| 235 AEHPHGILLFGPPGTGKTLLAKAVATELETPFIHVHGSdIVSKwygeaEQNIKEMfeISRSRPHTILFIDEIDSITP 311
                                       4555669**********************997666555144442222145566552234567899*******99887 PP

                            RuvB_N  99 av 100
                                       a 
  gi|298675717|ref|YP_003727467.1| 312 AR 313
                                       65 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0     2e-08   1.1e-05       1      24 [.     392     415 ..     392     430 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 2e-08
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcr 24 
                                       ++dl+++A+++eG+SGAD + +++
  gi|298675717|ref|YP_003727467.1| 392 NIDLEKIASKSEGFSGADVKGVVD 415
                                       79*****************99985 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0         2   1.2e+03      44      67 ..      66      89 ..      45     117 .. 0.84
   2 !   17.8   0.0   5.4e-06    0.0031       8      30 ..     241     263 ..     235     282 .. 0.84
   3 ?    4.4   0.0     0.075        43      84     117 ..     291     329 ..     278     350 .. 0.62

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2
                            AAA_22 44 fvtlpsstsskdllrellralgle 67
                                      +++l ++t+s+++++ +l++++++
  gi|298675717|ref|YP_003727467.1| 66 RMDLGEDTESEKIWQSFLENYQEK 89
                                      78999999************9976 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 5.4e-06
                            AAA_22   8 lvvtGesGtGKTtllrrlleqld 30 
                                       ++++G++GtGKT+l++ ++ +l+
  gi|298675717|ref|YP_003727467.1| 241 ILLFGPPGTGKTLLAKAVATELE 263
                                       89*****************9994 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.075
                            AAA_22  84 qalraravielliiDEaqhlr.....seealeeL.rslln 117
                                       + +r+r    +l iDE++ ++     s+ea + + ++ll+
  gi|298675717|ref|YP_003727467.1| 291 EISRSRPH-TILFIDEIDSITparegSHEATQRIvSTLLD 329
                                       45556666.8**********87755436666665333344 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0     2e-06    0.0011      20      51 ..     234     265 ..     229     291 .. 0.79
   2 ?    4.5   0.0     0.071        41     123     161 ..     286     330 ..     281     337 .. 0.67

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2e-06
                            AAA_16  20 rsgrpelvllsGesGvGKsslvrellralekd 51 
                                        +  p+ +ll G++G+GK+ l+++++++le+ 
  gi|298675717|ref|YP_003727467.1| 234 QAEHPHGILLFGPPGTGKTLLAKAVATELETP 265
                                       5566899*********************9998 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.071
                            AAA_16 123 lkrllallsrderplvlvlDdlqwade.......aslqllaaLlrl 161
                                       +k++++ ++++ + ++l++D+++ + +       a++ + ++Ll++
  gi|298675717|ref|YP_003727467.1| 286 IKEMFEISRSRPH-TILFIDEIDSITParegsheATQRIVSTLLDE 330
                                       5566656666455.*********55553444444777777777766 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   4.3e-08   2.5e-05       6     105 ..     241     330 ..     237     341 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 4.3e-08
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTSEEEEETGGG--- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegGivllDEidKihp 82 
                                       ill gp g+Gkt+laka+a  l+     ++i +  s++    +     ++ i +   + +   + i+++DEid i+p
  gi|298675717|ref|YP_003727467.1| 241 ILLFGPPGTGKTLLAKAVATELET----PFIHVHGSDIVS--KWYGEAEQNIKEMFEISRSRPHTILFIDEIDSITP 311
                                       7899******************95....*********999..55566666667777788888999************ PP

                                       ----------HHHHHHHHHHHH- CS
                             AAA_2  83 kessgadvSregVqrdLLqileg 105
                                            ++ S+e  qr+   +l++
  gi|298675717|ref|YP_003727467.1| 312 ----AREGSHEATQRIVSTLLDE 330
                                       ....8999999999998888886 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   8.7e-08     5e-05      51      95 ..     239     281 ..     232     296 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 8.7e-08
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkk 95 
                                       +++Ll Gp+gtGkt la a++ el   +pf+++ gs++ s     
  gi|298675717|ref|YP_003727467.1| 239 HGILLFGPPGTGKTLLAKAVATELE--TPFIHVHGSDIVSKWYGE 281
                                       589*********************7..9**********9976555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2       2.6   1.5e+03      44      83 ..     179     217 ..     142     222 .. 0.50
   2 !   21.0   0.0   4.7e-07   0.00027       5     124 ..     241     369 ..     238     376 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.6
                            AAA_14  44 kkladpekllelileklke........ekktylflDEiqevpewekal 83 
                                       +++a+++           e        +++  + +D i  ++e++k l
  gi|298675717|ref|YP_003727467.1| 179 DRIAEEKGS---------EsekfetisPEQLNVKFDDIGGCEEAKKEL 217
                                       222222111.........112233333366778899999998888776 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 4.7e-07
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev..... 76 
                                       +++ G+  +GKT l+k ++ el      ++ +   d   k + + e+++++++e  +++ +t+lf+DEi  +     
  gi|298675717|ref|YP_003727467.1| 241 ILLFGPPGTGKTLLAKAVATELE---TPFIHVHGSDIVSKWYGEAEQNIKEMFEISRSRPHTILFIDEIDSItpare 314
                                       67899*************98888...9999999999999888887777888888744458999*********99998 PP

                            AAA_14  77 ...pewekalkslvd..eg..knldvivtGSnskllskeiatslagrvaeielyp 124
                                          +  ++++  l+d  +g  +  dvi+ G  +   s + a    gr ++    p
  gi|298675717|ref|YP_003727467.1| 315 gshEATQRIVSTLLDemDGikSSDDVILMGATNRPESIDSAFMRPGRFDKKVHVP 369
                                       8886667777777774311333458888888887777777777777776655555 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.055        32      31      83 ..     178     229 ..     166     237 .. 0.77
   2 !   15.9   0.0   2.2e-05     0.013       1      32 [.     241     272 ..     241     326 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.055
                      RNA_helicase  31 kdsvys.rnpeddfwdgYt.gqevvvidDfgqvkdeenpsdlaelirlvsstpyp 83 
                                       +d++   +++e++ ++  + +q  v +dD+g +++    + + +++     +py 
  gi|298675717|ref|YP_003727467.1| 178 NDRIAEeKGSESEKFETISpEQLNVKFDDIGGCEEA---KKELDMVAYGIKYPYV 229
                                       466666688999999999999************988...6666777666666665 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 2.2e-05
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl....klkkkd 32 
                                       i+l+Gp+g+GK++lak +a++l++ +    +    +
  gi|298675717|ref|YP_003727467.1| 241 ILLFGPPGTGKTLLAKAVATELETPFihvhG----S 272
                                       689******************9977733331....2 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   6.5e-07   0.00038       1     107 [.     241     376 ..     241     399 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 6.5e-07
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf...gvnlrdvakenglllevdpe........................aldesk 50 
                                       Ill G+pG+GKt lak+++ +l+    +v+ +d++++ + + e++ +                        a + s+
  gi|298675717|ref|YP_003727467.1| 241 ILLFGPPGTGKTLLAKAVATELETpfiHVHGSDIVSKWYGEAEQNIKemfeisrsrphtilfideidsitpAREGSH 317
                                       99****************99997788*89999998887777777776777777777777777777777777777788 PP

                            AAA_18  51 rldedkldklldaleenssaleegknlvidghlaeleseaakdikk......vvLtaspeell 107
                                       ++ +  +  lld+++++ s     +++++ g  + +es +  ++        v++ ++++e l
  gi|298675717|ref|YP_003727467.1| 318 EATQRIVSTLLDEMDGIKS----SDDVILMGATNRPESIDSAFMRPgrfdkkVHVPLPDKEAL 376
                                       8888887777777777765....6666666666666665555555456666666666666555 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   2.3e-06    0.0013      22      44 ..     238     260 ..     232     267 .. 0.88
   2 ?   -1.1   0.0       1.8     1e+03      97     117 ..     287     308 ..     258     312 .. 0.62

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.3e-06
                      Mg_chelatase  22 gHnlllvGppGsGKtmlakrlps 44 
                                        H +ll+GppG+GKt+lak++++
  gi|298675717|ref|YP_003727467.1| 238 PHGILLFGPPGTGKTLLAKAVAT 260
                                       599****************9876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.8
                      Mg_chelatase  97 pkpGeislah.nGvLfLDElpe 117
                                        +  eis+++ + +Lf+DE+  
  gi|298675717|ref|YP_003727467.1| 287 KEMFEISRSRpHTILFIDEIDS 308
                                       4455888876478999999875 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.3e-06   0.00074       2      50 ..     241     291 ..     241     371 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.3e-06
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqsktdytr 50 
                                       +ll G+pG+GK+ la+ ++ +l   ++++   ++ ++ +g+ +q++++  +
  gi|298675717|ref|YP_003727467.1| 241 ILLFGPPGTGKTLLAKAVATELEtpFIHVHGSDIVSKWYGEAEQNIKEMFE 291
                                       6899******************999*****999999999988888775444 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   1.2e-05    0.0069       2      33 ..     241     272 ..     240     356 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.2e-05
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE-- CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqlt 33 
                                       +lL GppGtgK+ la+ +a  l++++  v ++
  gi|298675717|ref|YP_003727467.1| 241 ILLFGPPGTGKTLLAKAVATELETPFIHVHGS 272
                                       89*****************9999888777665 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0     8e-06    0.0046      48      71 ..     239     262 ..     231     334 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8e-06
                         IstB_IS21  48 enivllGpsGvGKshlaialgvea 71 
                                       ++i+l+Gp+G+GK+ la a+++e 
  gi|298675717|ref|YP_003727467.1| 239 HGILLFGPPGTGKTLLAKAVATEL 262
                                       689***************998764 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.7e-05      0.01       2      48 ..     241     288 ..     240     304 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.7e-05
                            AAA_28   2 ivitGgestGKTtlleaLaar.gypvvpEaareileeklakgedalpw 48 
                                       i ++G+++tGKT l++a a + ++p ++  + +i+++ + + e+++++
  gi|298675717|ref|YP_003727467.1| 241 ILLFGPPGTGKTLLAKAVATElETPFIHVHGSDIVSKWYGEAEQNIKE 288
                                       789****************877*****999999999888777776654 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.1e-05     0.024      12      52 ..     234     272 ..     229     283 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.1e-05
                        Zeta_toxin  12 sqerPklillgGqpGAGKselaellkdelerqgnvvrldpD 52 
                                       + e+P  ill G pG GK+ la+++++el  +  ++++ + 
  gi|298675717|ref|YP_003727467.1| 234 QAEHPHGILLFGPPGTGKTLLAKAVATEL--ETPFIHVHGS 272
                                       4599*************************..7888888765 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   7.4e-05     0.043      30      58 ..     235     263 ..     223     277 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.4e-05
                             AAA_7  30 lknkkpvllvGptGtGKtviikdllkkld 58 
                                        ++ + +ll Gp GtGKt+++k + ++l+
  gi|298675717|ref|YP_003727467.1| 235 AEHPHGILLFGPPGTGKTLLAKAVATELE 263
                                       567788****************9999887 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0009      0.52       3      26 ..     241     264 ..     239     269 .. 0.90
   2 ?    2.6   0.0       0.2   1.1e+02      57     104 ..     274     319 ..     268     337 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0009
                                       EEEEC-TTTCHHHHHHHHHHHHCT CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawae 26 
                                       ++l G++G GKT L++ +a+++ +
  gi|298675717|ref|YP_003727467.1| 241 ILLFGPPGTGKTLLAKAVATELET 264
                                       6889***************99875 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.2
                                       HHCCCCTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH..... CS
                             NACHT  57 llfsqlpepaapvsevwavllelperlLlilDglDelvtdlgqkekqp 104
                                       ++ + + e +++++e++++  ++p+ +L+i D +D +    +    ++
  gi|298675717|ref|YP_003727467.1| 274 IVSKWYGEAEQNIKEMFEISRSRPHTILFI-DEIDSITPAREG-SHEA 319
                                       555667788899999888888888888886.777777664443.2233 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   8.2e-05     0.048      15      84 ..     191     269 ..     179     367 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.2e-05
                            DUF815  15 alepve.evdevklddLvgidkqkealvente.....qfleglpann...vLLwGarGtGKSslvkallneyaeegL 82 
                                       ++e+++ e  +vk+dd+ g ++ k++l   +         e ++a++   +LL+G  GtGK  l ka+ +e+++  +
  gi|298675717|ref|YP_003727467.1| 191 KFETISpEQLNVKFDDIGGCEEAKKELDMVAYgikypYVFEEYQAEHphgILLFGPPGTGKTLLAKAVATELETPFI 267
                                       45555314457888888888888888765443111112345555544444*********************998764 PP

                            DUF815  83 rl 84 
                                       ++
  gi|298675717|ref|YP_003727467.1| 268 HV 269
                                       43 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   0.00013     0.073       1      46 [.     244     289 ..     244     344 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00013
                                       EE-TTSSHHHHHHHHHHHH..TEEEEEHHHHHHHHHHTTTSHSSHHHH CS
                            AAA_17   1 lGgPGsGKgtqceklveky..gfthlsaGdllreeakrgglakardem 46 
                                       +G+PG GK+ +++ ++ ++   f h+  +d++ +   +   +++ +em
  gi|298675717|ref|YP_003727467.1| 244 FGPPGTGKTLLAKAVATELetPFIHVHGSDIVSKWYGEA--EQNIKEM 289
                                       6***************99966799999999998765333..3344444 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00025      0.14      19      61 ..     235     274 ..     228     316 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00025
                                       CTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS CS
                   Sigma54_activat  19 aktdlsvlitGesGtGKellaraiheaskrkekpfvavncaai 61 
                                       a+++  +l+ G  GtGK+lla+a+ ++ +   +pf++v  ++i
  gi|298675717|ref|YP_003727467.1| 235 AEHPHGILLFGPPGTGKTLLAKAVATELE---TPFIHVHGSDI 274
                                       5667889***************9976554...77887776655 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0026       1.5      21      37 ..     240     256 ..     234     262 .. 0.87
   2 ?    2.5   0.0      0.14        79     108     154 ..     286     334 ..     268     348 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0026
                            ATPase  21 vvlitGepGtGKtifal 37 
                                        +l+ G pGtGKt++a+
  gi|298675717|ref|YP_003727467.1| 240 GILLFGPPGTGKTLLAK 256
                                       5899***********97 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.14
                            ATPase 108 ieelaeaikeikakrvviDsitgl..ayeekeavaReilrqlvrvlkkl 154
                                       i+e+ e+ ++   + + iD i+++  a+e +++ + +i+ +l+ ++ ++
  gi|298675717|ref|YP_003727467.1| 286 IKEMFEISRSRPHTILFIDEIDSItpAREGSHEATQRIVSTLLDEMDGI 334
                                       5556666666666777777666665458888999999999999999765 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00027      0.16      23      42 ..     242     261 ..     234     266 .. 0.88
   2 ?   -2.2   0.0       3.9   2.3e+03      73     114 ..     317     358 ..     304     366 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00027
                                       EEE--TTSSTTHHHHHHHHH CS
                              PhoH  23 faiGpaGtGKtylavalave 42 
                                         +Gp GtGKt+la a+a e
  gi|298675717|ref|YP_003727467.1| 242 LLFGPPGTGKTLLAKAVATE 261
                                       679*************9976 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.9
                                       -----TTTHHHHHHHTTTS-TTCHHHHHHTTSEEEEEGGGGT CS
                              PhoH  73 eekvdpylrplydaLkdllgaekvekllekgkievaplaymR 114
                                       +e  + ++++l d+++ + +++ v  +  +++ e ++ a+mR
  gi|298675717|ref|YP_003727467.1| 317 HEATQRIVSTLLDEMDGIKSSDDVILMGATNRPESIDSAFMR 358
                                       667778889999999999999999999999999999999999 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       4.3   2.5e+03      28      52 ..     173     197 ..     170     222 .. 0.77
   2 ?   11.8   0.0   0.00034       0.2       8      92 ..     247     331 ..     241     346 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 4.3
                   Cytidylate_kin2  28 ydreiieevakelglseeeveevde 52 
                                       y +e  +++a+e+g + e++e+++ 
  gi|298675717|ref|YP_003727467.1| 173 YYNESNDRIAEEKGSESEKFETISP 197
                                       5566778999999999999988765 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00034
                   Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeeveevde..rsrlssflskllaarvagdtl..dekldde 80 
                                        G+g++ +++a+A++L+ pf+  +  + v+k  g  e+ ++e+ e  rsr       ++++   +  +  +e + ++
  gi|298675717|ref|YP_003727467.1| 247 PGTGKTLLAKAVATELETPFIHVHGSDIVSKWYGEAEQNIKEMFEisRSR--PHTILFIDEI--DSITpaREGSHEA 319
                                       69*********************999999999999999998888854222..2222222222..1111234444444 PP

                   Cytidylate_kin2  81 lfeaqervirel 92 
                                        +++ ++++ e+
  gi|298675717|ref|YP_003727467.1| 320 TQRIVSTLLDEM 331
                                       444444444443 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00015     0.084       4      56 ..     241     294 ..     239     349 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00015
                                       EEEEE-TTSSHHHHHHHHHHHSSS-EEEE.EHHHHHHHS-GGGGTSTTSEEEET CS
                               CPT   4 ilLnGgsssGKsslaralqevldepwlhl.gvDafvealppkrqdeadglefet 56 
                                       ilL G + +GK+ la+a+ + l++p++h+ g+D   +    + q+ ++ +e + 
  gi|298675717|ref|YP_003727467.1| 241 ILLFGPPGTGKTLLAKAVATELETPFIHVhGSDIVSKWYGEAEQNIKEMFEISR 294
                                       89**************************93455554445555555555555554 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00023      0.13       5      28 ..     241     266 ..     238     325 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00023
                            AAA_24   5 iliyGpsgiGKTtlakel..gpkplf 28 
                                       il++Gp+g+GKT lak    + ++ f
  gi|298675717|ref|YP_003727467.1| 241 ILLFGPPGTGKTLLAKAVatELETPF 266
                                       89*************99855333333 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00037      0.21      14      75 ..     241     300 ..     233     350 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00037
                                       EEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  14 vaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpelt 75 
                                       + ++G+ G+GK+ L+k++a +l+     i++ g d+ ++   +++++i+ +++ ++  p++ 
  gi|298675717|ref|YP_003727467.1| 241 ILLFGPPGTGKTLLAKAVATELE--TPFIHVHGSDIVSKWYGEAEQNIKEMFEISRSRPHTI 300
                                       6799***************9986..5788889999999888888888888888777777765 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00032      0.19       2      31 ..     241     270 ..     239     349 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00032
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriq 31 
                                       +ll g PG++ktll+ka+a+ l++ f  + 
  gi|298675717|ref|YP_003727467.1| 241 ILLFGPPGTGKTLLAKAVATELETPFIHVH 270
                                       7899*******************9998774 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00037      0.21      19      85 ..     233     299 ..     198     356 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00037
                                       ....TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG..........G CS
                            ResIII  19 lkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayke......i 85 
                                       +++++ + +l+  + GtGKTl+a +++ +l +       ++ v++ +++++++ e ++ ++e ++       +
  gi|298675717|ref|YP_003727467.1| 233 YQAEHPHGILLFGPPGTGKTLLAKAVATELETP------FIHVHGSDIVSKWYGEAEQNIKEMFEIsrsrphT 299
                                       4447777888999**********9999999984......56699*********99988888877545444441 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1    0.0011      0.65       5      32 ..     242     263 ..     238     330 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0011
                           DUF2075   5 lVtGvaGtGKtvvllnllaeleddeeer 32 
                                       l  G +GtGKt+++ ++++el      +
  gi|298675717|ref|YP_003727467.1| 242 LLFGPPGTGKTLLAKAVATEL------E 263
                                       56699**************99......2 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.2    0.0012      0.69      36      56 ..     241     261 ..     238     289 .. 0.82
   2 ?   -0.6   0.0       1.5   8.6e+02     130     172 ..     286     327 ..     265     332 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0012
                            AAA_25  36 allaGapgtGKttlaldlala 56 
                                       +ll+G+pgtGKt la  +a +
  gi|298675717|ref|YP_003727467.1| 241 ILLFGPPGTGKTLLAKAVATE 261
                                       69************9887765 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.5
                            AAA_25 130 vdaleaaieevegvrlvviDplsralggdensnsdvgalveal 172
                                       ++++ +  ++      + iD +++++++ e s+++++++v+ l
  gi|298675717|ref|YP_003727467.1| 286 IKEMFEISRS-RPHTILFIDEIDSITPAREGSHEATQRIVSTL 327
                                       5555555555.3478899**********999999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.47
# Mc/sec: 3067.29
//
Query:       gi|298675718|ref|YP_003727468.1|  [L=327]
Description: hypothetical protein Metev_1837 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.4e-17   61.7   0.8    2.2e-16   60.5   0.8    1.6  1  AAA_17       AAA domain
    1.7e-16   60.6   0.1    5.1e-16   59.0   0.1    1.8  1  RNA_binding  RNA binding
    6.9e-10   39.6   0.4      3e-09   37.5   0.2    2.0  2  AAA_18       AAA domain
      2e-05   24.8   0.0      4e-05   23.8   0.0    1.5  1  AAA_33       AAA domain
     0.0042   16.8   0.3        0.7    9.5   0.0    2.9  3  CoaE         Dephospho-CoA kinase
  ------ inclusion threshold ------
      0.015   15.4   0.3      0.033   14.3   0.3    1.9  1  ADK          Adenylate kinase


Domain annotation for each model (and alignments):
>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.5   0.8   7.3e-20   2.2e-16       1     135 [.       7     136 ..       7     137 .. 0.83

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 7.3e-20
                                       EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHC..TSHHHHHHHHHHHHHHHHHHHH..HSSE CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemr..klpleekkelqkeaaekiaeea..kkkg 73 
                                       +G+P sGK++++  +vek+g++++++Gd++ree++r++l++++ ++    ++l+ ++ ++  a++++ +    +++ 
  gi|298675718|ref|YP_003727468.1|   7 VGMPASGKSEAS-SVVEKLGIKVVNMGDVIREEVERRSLEPTDANIGgvANQLRNEEGFDVVAKRSVPKIMklSEDL 82 
                                       7*********99.********************************99777789999999999999886643347778 PP

                                       EEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHTTST-TS-SHHHH CS
                            AAA_17  74 vlvdghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdrtrgrdddneesi 135
                                       + +dg   i e    +++++ke+ e++   +++ ++ + +  ++r++k r+r++d  +++++
  gi|298675718|ref|YP_003727468.1|  83 IAIDGIRGIAE----VERFKKEFGEKF---TLVSIDSPLDMRFKRVQK-RKRSDDMADINEL 136
                                       9*******976....556899999999...899999999866666666.5666666666665 PP

>> RNA_binding  RNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.0   0.1   1.7e-19   5.1e-16       1     118 [.     182     295 ..     182     296 .. 0.91

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 1.7e-19
                                       EEEEEEEE-TTC-HHHHHHHHHTTSTTSE---EEEEEE-CCC-EEEEEEEEESSHHHHHHHHHHHHHHCCCCH.... CS
                       RNA_binding   1 kievrafvhaTEdeekVlealsnllpeeeveieeeeaeGhygnpitileaelekkkakkvlkkllellreeei.... 73 
                                       ++ev+a+v++TE+e  V++al+n++ ++  e+e+ ++   ++        +l++  + ++lk+l+e++r+e+i    
  gi|298675718|ref|YP_003727468.1| 182 EVEVSAVVNPTENETYVANALKNIFGDI--ELETLDTAQQHK-------KRLSGTGDVETLKNLHEMFRKEKIldtg 249
                                       59************************66..577777777776.......6888888899****************99 PP

                                       .HHHHHCCHCCB-TTSEEEEEEEHHHHHTT---BESSSS...EEEEEEE CS
                       RNA_binding  74 .keLlkeleervdekgklylrldKQaaylgklslvegdd...vIkvkik 118
                                        ++L+ +l+    ++ ++++ ++KQ a +g+++++++++   +I+v+i 
  gi|298675718|ref|YP_003727468.1| 250 rMQLEGGLSI---DGLSTHFIINKQVASVGRMNFPADEEplgSIHVTIT 295
                                       9999999999...7**********************999*******996 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.2     1e-12     3e-09       1     121 [.       4     132 ..       4     145 .. 0.87
   2 ?   -0.4   0.0      0.54   1.6e+03      54      92 ..     226     272 ..     192     301 .. 0.57

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 1e-12
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpe.aldeskrldedkldklldaleenssal 71 
                                       I+  G+p++GK++ +  ++k+ g+     g+++r+ +  + l+ ++ +   + +++r +e+++ ++ + + ++ +  
  gi|298675718|ref|YP_003727468.1|   4 IAFVGMPASGKSEASSVVEKL-GIkvvnmGDVIREEVERRSLEPTDANIgGVANQLRNEEGFDVVAKRSVPKIMK-- 77 
                                       7899**************888.556588899999999998888888888*9999999999999999999999976.. PP

                            AAA_18  72 eegknlvidghlaeleseaakdikk.....vvLtaspeelleRlekRgyeeakik 121
                                        +++ + idg+++  e e++k+  +     v ++ + +++++R++kR+++++   
  gi|298675718|ref|YP_003727468.1|  78 LSEDLIAIDGIRGIAEVERFKKEFGekftlVSIDSPLDMRFKRVQKRKRSDDMAD 132
                                       788999***************9999**********************98876554 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.54
                            AAA_18  54 edkldklldaleenss........aleegknlvidghlaeleseaak 92 
                                          + + l++l+e  +        +++ ++ l idg+  +++  +++
  gi|298675718|ref|YP_003727468.1| 226 GTGDVETLKNLHEMFRkekildtgRMQLEGGLSIDGLSTHFIINKQV 272
                                       33333444444444334444555545555555666666666655555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   1.3e-08     4e-05       2     125 ..       4     130 ..       3     142 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.3e-08
                            AAA_33   2 vllvGlpGsGKstlaerllkklg......avllssdtlrrrlfgtdqq..sktdytrvldrlyqilnelarkalsag 70 
                                       + +vG+p+sGKs  +  +++klg      + ++++ ++rr l++td +     ++ r ++ +    ++ + k ++  
  gi|298675718|ref|YP_003727468.1|   4 IAFVGMPASGKSEASS-VVEKLGikvvnmGDVIREEVERRSLEPTDANigGVANQLRNEEGFDVVAKRSVPKIMKLS 79 
                                       789*********9877.677***9999999999999999999999888543346666667788899999******** PP

                            AAA_33  71 rnvildatnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaangddr 125
                                        ++i+  + +  +e +rf k +     ++++v ++++ +   +R++kR+++ dd 
  gi|298675718|ref|YP_003727468.1|  80 EDLIAIDGIRGIAEVERFKKEFG---EKFTLVSIDSPLDMRFKRVQKRKRS-DDM 130
                                       ******************99995...599*********************6.443 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00024       0.7       2      39 ..       3      40 ..       2      48 .. 0.85
   2 ?    3.8   0.0     0.014        41     125     178 ..     107     166 ..      97     167 .. 0.68
   3 ?   -0.9   0.0      0.38   1.1e+03      18      63 ..     204     251 ..     199     254 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00024
                                      EEEEEESTTSSHHHHHHHHHHTT-EEEEHHHHHHHTTC CS
                              CoaE  2 ivgltGgiasGKstvanlfadlgvpivDaDlvArqvve 39
                                      i++  G  asGKs ++++ ++lg+++v    v r+ ve
  gi|298675718|ref|YP_003727468.1|  3 IIAFVGMPASGKSEASSVVEKLGIKVVNMGDVIREEVE 40
                                      68888999*******************98777777666 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.014
                                       EEEEE--HHHHHHHHHHCC....TSTHHHHHHHHHHS--..HHHHHHH-SEEEE-.SSHH CS
                              CoaE 125 vlvvdvelelqveRlvard....gvseeevkaiiaaQls..eeerlaladvvldNdssla 178
                                        +++d +l+ + +R+ +r+      + +e+k++ +  ls   ++ +++ad+v++N ++l+
  gi|298675718|ref|YP_003727468.1| 107 LVSIDSPLDMRFKRVQKRKrsddMADINELKERDERELSwgMDKAMEIADIVIENTGTLD 166
                                       467888999999999988632211233455666666665325678999*******98875 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.38
                                       HHHHHTT-EEEEHHHH.HHHTT.CCTHHHHHHHHHHHGGGCB.TTSSE CS
                              CoaE  18 nlfadlgvpivDaDlv.Arqvv.epgsealkkiveeFgeeildedGeL 63 
                                       n+f d+ ++ +D+ +   +++  + + e+lk++ e F +e + + G++
  gi|298675718|ref|YP_003727468.1| 204 NIFGDIELETLDTAQQhKKRLSgTGDVETLKNLHEMFRKEKILDTGRM 251
                                       666777777777544303444413456889999999998888888876 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.3   1.1e-05     0.033       2      39 ..       7      43 ..       6     243 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.1e-05
                                      EESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHCT- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK  2 lGaPgaGKGtqaeklvkkyglahlstGdllRaevksgt 39
                                      +G P++GK   a+++v+k+g++ +  Gd++R+ev++ +
  gi|298675718|ref|YP_003727468.1|  7 VGMPASGKS-EASSVVEKLGIKVVNMGDVIREEVERRS 43
                                      8*******6.7899********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2002.37
//
Query:       gi|298675719|ref|YP_003727469.1|  [L=257]
Description: xylose isomerase domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-33  115.2   0.0    3.2e-33  115.0   0.0    1.1  1  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.0   0.0   1.8e-37   3.2e-33       3     210 .]      23     221 ..      21     221 .. 0.95

  Alignments for each domain:
  == domain 1  score: 115.0 bits;  conditional E-value: 1.8e-37
                                       HHHHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHHH CS
                      AP_endonuc_2   3 aaaeaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederearreesvdalkraiela 79 
                                       +++++G++g E+   + ++ ++   + l+ +r++ + ++l i+ + +f++ + +  + + +r  e ++++k  +e+a
  gi|298675719|ref|YP_003727469.1|  23 ELEDYGYTGWEIVQEGSQKLDN---DSLKNVRELYETTNLDITTHLPFSDLNLSSLNPGIHR--EVLNQMKYNLEIA 94 
                                       6789****************97...7************************999999855555..77*********** PP

                                       HHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTC..HHHHHHHHHHTTT CS
                      AP_endonuc_2  80 aaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgd..eelarlldavdsp 154
                                       +++ a++ v+hpG  + ++ + +e aw++ +esl+ ++dya+++++++a+E++++ ++ +g   +e+ ++++ v+++
  gi|298675719|ref|YP_003727469.1|  95 SEF-ADIAVIHPGYKSPHGAQVPEKAWNKTIESLEIICDYADDYNMQIAVENMPNIPHIFGKepREMIDIIKSVNRD 170
                                       ***.*********98889999999**********************************9999*************** PP

                                       TEEEEEEHHHHHHHTTTHHHHHHHHHGGEEEEEE.EESSTTTTSSTTEESTTSSSS CS
                      AP_endonuc_2 155 nvgvclDtgHlliaeedvddalraladrikhvHikDakgdlgagrdrhvpigeGei 210
                                       n+g+++D+gH++   + vdd+l++ ++ i h+Hi+D+ g    ++d+h+p+g G+i
  gi|298675719|ref|YP_003727469.1| 171 NLGITFDIGHANTL-NMVDDFLNECKNWITHIHIHDNTG----KKDEHLPVGSGDI 221
                                       ************99.9***********************....***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1664.99
//
Query:       gi|298675720|ref|YP_003727470.1|  [L=603]
Description: hypothetical protein Metev_1839 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-13   51.1   0.0    1.2e-12   48.4   0.0    2.1  1  DUF87          Helicase HerA, central domain
    1.1e-12   47.4   0.0    2.2e-08   33.2   0.0    2.1  2  DUF853         Bacterial protein of unknown function (DUF853)
    4.7e-06   25.8   0.0      0.063   12.2   0.0    2.2  2  AAA_10         AAA-like domain
    6.4e-05   23.4   0.0      0.034   14.5   0.0    2.3  2  AAA_16         AAA ATPase domain
    6.6e-05   22.0   0.0    0.00021   20.3   0.0    1.7  2  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
    0.00012   22.5   0.5       0.98    9.9   0.0    2.7  2  AAA            ATPase family associated with various cellular
    0.00018   21.8   0.0      0.007   16.7   0.0    2.4  2  AAA_22         AAA domain
    0.00032   20.7   0.1      0.089   12.8   0.1    2.5  1  ResIII         Type III restriction enzyme, res subunit
    0.00075   19.3   0.0       0.72    9.6   0.0    2.3  2  DEAD           DEAD/DEAH box helicase
    0.00087   18.7   0.0       0.14   11.5   0.0    2.4  2  FtsK_SpoIIIE   FtsK/SpoIIIE family
     0.0012   19.3   0.1     0.0023   18.3   0.1    1.5  1  RNA_helicase   RNA helicase
      0.005   16.4   0.0      0.011   15.3   0.0    1.4  1  AAA_7          P-loop containing dynein motor region
  ------ inclusion threshold ------
      0.025   14.5   0.0        7.1    6.6   0.0    2.6  2  PriA_3primeBD  3′ DNA-binding domain (3′BD)
      0.098   11.7   0.0       0.19   10.8   0.0    1.4  1  T2SSE          Type II/IV secretion system protein
        0.1   12.8   0.0       0.26   11.5   0.0    1.7  1  AAA_33         AAA domain


Domain annotation for each model (and alignments):
>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4   0.0     1e-15   1.2e-12      19     212 ..     226     453 ..     202     555 .. 0.86

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 1e-15
                             DUF87  19 nklvtrHlAilgsTGsGKSntvavLleelle.............kkgatililDpHGEYgkalekllsekvkvitps 82 
                                       + lv rH+++ gsTG+GK++ ++ +l++ l+              k+  ++i Dp+ EY++ +    +e+ ++ t++
  gi|298675720|ref|YP_003727470.1| 226 DPLVFRHMLVCGSTGTGKTFMTKNILRQFLSdgnryvlrsdenrWKNPCVVIMDPQDEYSQVY----EENPEINTQD 298
                                       5699************************************976666669**************....5555555555 PP

                             DUF87  83 psa................................kdkelkinpwsldpeelldlleeddkpaaavqrsvleealdq 127
                                       +++                                ++ e++i++ +++ +  l  + +    +++ q+ +l+ +l+ 
  gi|298675720|ref|YP_003727470.1| 299 EYSfnsenvefgswsntktfvakvdgysyngksraQQVEFTIPFELVKNNSWLIAAAG----LTELQYLALDILLED 371
                                       44455555555555677788888888888888899***************99999999....788899999999999 PP

                             DUF87 128 akakeekeklssdepveklleelkkeke.elrklknqaiarlldkledllrkggsfsnsstdliallleklekegki 203
                                       +   ++ ++ +++ ++ ++++e  +++  ++ k+ +++  ++ +++++  +++ ++  +++++i+++l++  k+g++
  gi|298675720|ref|YP_003727470.1| 372 YF--KKSGEHTYRGFLDYIEDEATRSAYvDSGKIHESSYDGIVRRVKNRAFEKVFD--QDARPITDILDEVFKPGQV 444
                                       98..999*****************77667788888888888888888877777777..8999999999********* PP

                             DUF87 204 tiidlsgvd 212
                                       ++++   ++
  gi|298675720|ref|YP_003727470.1| 445 SVFPTEYIN 453
                                       999766655 PP

>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   5.1e-05     0.061      20      49 ..     229     258 ..     219     267 .. 0.77
   2 !   33.2   0.0   1.8e-11   2.2e-08     153     318 ..     382     550 ..     379     560 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.1e-05
                            DUF853  20 anrhGliaGatGtGktvtLqvlaeslseaG 49 
                                       + rh l++G+tGtGkt   + +  ++ ++G
  gi|298675720|ref|YP_003727470.1| 229 VFRHMLVCGSTGTGKTFMTKNILRQFLSDG 258
                                       67**************87777666665544 PP

  == domain 2  score: 33.2 bits;  conditional E-value: 1.8e-11
                            DUF853 153 rallkevadnake.lskqygnvskasvgaiqreLltLeqqGaekffGePaLdledllrtdadGrGvislLaadkllq 228
                                       r  l++++d+a +    + g++ ++s + i r++   +++  ek+f + a  ++d+l       G +s++ ++  ++
  gi|298675720|ref|YP_003727470.1| 382 RGFLDYIEDEATRsAYVDSGKIHESSYDGIVRRV---KNRAFEKVFDQDARPITDILDEV-FKPGQVSVFPTE-YIN 453
                                       6678999998875156799*************85...788999**************988.66899***9875.799 PP

                            DUF853 229 sPklyatfLlWllseLfe.eLPevGd..ldkPklvfffdeahLLfndap....kallekveqvvrLirskGvGvyfv 298
                                       sP +    +l l++ + + +L   G+  + k  +v+ +deah  + +a+    + ++ k     r  r  G G++++
  gi|298675720|ref|YP_003727470.1| 454 SPLIRDLIVLTLMTTIVDnKLSTSGNesVRKTPIVLGLDEAHRYLAKASgehsRRIISKFADAARQGRKEGLGLFLI 530
                                       *************999853799999822468889********999877522227899999***************** PP

                            DUF853 299 tqnPldlPdtvLaqLGnrvq 318
                                       tq+P+d+ dtv+ q+ +r+ 
  gi|298675720|ref|YP_003727470.1| 531 TQDPQDIDDTVFKQINTRII 550
                                       *****************995 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0    0.0001      0.12      23      73 ..     232     296 ..     227     309 .. 0.88
   2 !   12.2   0.0   5.2e-05     0.063     236     308 ..     481     558 ..     455     582 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0001
                            AAA_10  23 asliiGdlGnGKSvlakllvlyisllg..............gkaliiDpkkerekfketlpeiak 73 
                                       ++l+ G++G GK +++k +  + +  g                ++i+Dp+ e  + +e+ pei  
  gi|298675720|ref|YP_003727470.1| 232 HMLVCGSTGTGKTFMTKNILRQFLSDGnryvlrsdenrwknPCVVIMDPQDEYSQVYEENPEINT 296
                                       789****************99998888999999***99998889999*****9999999999654 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 5.2e-05
                            AAA_10 236 sdkkefkvvifDEawiftssaeGk...kllke...lvRiGRsynaavylvtqsadDvlkeelknniglklaFretdk 306
                                       s +k+  v  +DEa  +   a G+   +++++     R+GR+    ++l+tq+++D+++   k +i ++++ + t+ 
  gi|298675720|ref|YP_003727470.1| 481 SVRKTPIVLGLDEAHRYLAKASGEhsrRIISKfadAARQGRKEGLGLFLITQDPQDIDDTVFK-QINTRIILNLTND 556
                                       4455556777899998888888852225666512258********************987655.5677777665544 PP

                            AAA_10 307 ee 308
                                       ++
  gi|298675720|ref|YP_003727470.1| 557 NA 558
                                       44 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   2.9e-05     0.034      20      61 ..     223     268 ..     217     291 .. 0.87
   2 !    6.5   0.0    0.0084        10      47     164 ..     391     519 ..     382     540 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.9e-05
                            AAA_16  20 rsgrp...elvllsGesGvGKsslvrellralekdg.giflrgkcd 61 
                                       ++g+p   + +l+ G  G+GK+ + + +lr++  dg  ++lr +  
  gi|298675720|ref|YP_003727470.1| 223 SMGDPlvfRHMLVCGSTGTGKTFMTKNILRQFLSDGnRYVLRSDEN 268
                                       678888889*************************987888887655 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0084
                            AAA_16  47 alekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleeala...........avpela 112
                                       +++++ +++ +gk +++    +y+ +++   +++ ++++ d+    ++++  + l+e+++           + ++l 
  gi|298675720|ref|YP_003727470.1| 391 EATRS-AYVDSGKIHES----SYDGIVRRV-KNRAFEKVFDQ----DARPITDILDEVFKpgqvsvfpteyINSPLI 457
                                       44555.88888888888....899999999.55999999999....7888888888888877776666666444444 PP

                            AAA_16 113 gaeasrllellkrll.allsrder......plvlvlDdlq.....wadeaslqllaaLlrlles 164
                                       ++    +l l++ ++ ++ls+ +       p+vl lD+++        e+s+ +++ +++++ +
  gi|298675720|ref|YP_003727470.1| 458 RD--LIVLTLMTTIVdNKLSTSGNesvrktPIVLGLDEAHrylakASGEHSRRIISKFADAARQ 519
                                       44..777777777777777775557788889999999999666655556899999988888776 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.8e-07   0.00021      16      89 ..     231     299 ..     223     306 .. 0.77
   2 ?   -1.9   0.0      0.97   1.2e+03     258     304 ..     510     557 ..     508     567 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.8e-07
                     TrwB_AAD_bind  16 qhilivGttGsGKtqalekllrairargdraivlDltGafvsrfydegkdillnPlDaRsaaWsvfaeikeksd 89 
                                       +h+l+ G+tG+GKt +++++lr+  + g+r +    +    +r+ ++   ++++P D+ s+  +   ei+++ +
  gi|298675720|ref|YP_003727470.1| 231 RHMLVCGSTGTGKTFMTKNILRQFLSDGNRYVLRSDE----NRWKNPC-VVIMDPQDEYSQVYEENPEINTQDE 299
                                       8***************************999876444....3444444.7777777777777776666666655 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.97
                     TrwB_AAD_bind 258 leelksllaegRkfGgavvlglqsiaqlre.vYGedaaqsilslvntk 304
                                       ++++++++ +gRk G  + l  q+ + + + v+ + +++ il+l+n +
  gi|298675720|ref|YP_003727470.1| 510 ISKFADAARQGRKEGLGLFLITQDPQDIDDtVFKQINTRIILNLTNDN 557
                                       567888888888888888888888887765245555666666655554 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.1   0.00086         1       1      22 [.     233     254 ..     233     268 .. 0.85
   2 !    9.9   0.0   0.00082      0.98      57     128 ..     482     549 ..     467     553 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00086
                                       EEEESSTTSSHHHHHHHHHHHH CS
                               AAA   1 vllyGppGtGKTllakavakel 22 
                                       +l++G  GtGKT + k + +++
  gi|298675720|ref|YP_003727470.1| 233 MLVCGSTGTGKTFMTKNILRQF 254
                                       79***************99885 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00082
                                       S..TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEE CS
                               AAA  57 a..kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrki 128
                                          +p +l +DE+++   +    + e+++r+++++  +  + +k+   + + ++t++p+++d+ +  + ++ +i
  gi|298675720|ref|YP_003727470.1| 482 VrkTPIVLGLDEAHRYLAKA---SGEHSRRIISKFADAARQGRKE--GLGLFLITQDPQDIDDTVF-KQINTRI 549
                                       14468***********9999...8999************999994..699************9988.6666655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   5.8e-06     0.007       7      46 ..     232     279 ..     231     289 .. 0.71
   2 ?    2.3   0.0      0.16   1.9e+02      88     128 ..     484     530 ..     465     539 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.8e-06
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee............erpevvfvt 46 
                                       +++v+G +GtGKT+  +++l+q+  +                 ++p vv ++
  gi|298675720|ref|YP_003727470.1| 232 HMLVCGSTGTGKTFMTKNILRQFLSD----GnryvlrsdenrwKNPCVVIMD 279
                                       799*******************9643....1234455666665555555555 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.16
                            AAA_22  88 aravielliiDEaqh.lr..seealeeL.rsllnl....srkgvqliLv 128
                                       ++  + +l +DEa++ l   s e+ + + +++++     ++ g+ l+L+
  gi|298675720|ref|YP_003727470.1| 484 KT--PIVLGLDEAHRyLAkaSGEHSRRIiSKFADAarqgRKEGLGLFLI 530
                                       33..46999******9977656666555344455466666666666666 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1   7.4e-05     0.089      25      77 ..     231     294 ..     228     520 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.4e-05
                                       SEEEEEESTTSTHHHHHHHHHHHH-S................-EEEEESSHHHHHHHHHHGGGG CS
                            ResIII  25 krglikmaTGtGKTlvaaklierllkkgkee...........kflflvprkslleqtleefkkf 77 
                                       +++l+   TGtGKT++  ++ +++l+ g++             ++++ + ++ ++q +ee  ++
  gi|298675720|ref|YP_003727470.1| 231 RHMLVCGSTGTGKTFMTKNILRQFLSDGNRYvlrsdenrwknPCVVIMDPQDEYSQVYEENPEI 294
                                       57788889****************9988766888888888888888888888888888655333 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0    0.0006      0.72      15      58 ..     231     283 ..     223     302 .. 0.77
   2 !    7.3   0.0    0.0031       3.7     125     157 ..     489     521 ..     459     539 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0006
                                       CEEEEEESTTSSHHHHHHHHHHHHHHHS.........TTSTS-EEEEEESSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxx RF
                              DEAD  15 gdvlvaaeTGsGKTlaflipvlqivyet.........kgktgpkalivePtre 58 
                                       +++lv++ TG+GKT +    + q +++          ++ ++p ++i+ P  e
  gi|298675720|ref|YP_003727470.1| 231 RHMLVCGSTGTGKTFMTKNILRQFLSDGnryvlrsdeNRWKNPCVVIMDPQDE 283
                                       689***********996655555554448888888777777788888888766 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0031
                                       EEEETHHHHHHTTTHHHHHHHHHHSHHHCTTST CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 125 lVlDEadrlldqgfsdfinrilnqlpqitcdgk 157
                                       l lDEa+r+l +  +++ +ri+++++++  +g+
  gi|298675720|ref|YP_003727470.1| 489 LGLDEAHRYLAKASGEHSRRIISKFADAARQGR 521
                                       459*********************988877776 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00012      0.14      14      59 ..     210     250 ..     204     256 .. 0.71
   2 ?    4.6   0.0     0.015        17     183     242 ..     476     535 ..     457     536 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                                       ---TTEEEEEEET.TS-EEEEEGGGS-.SEEEE--TTSSHHHHHHHH CS
                      FtsK_SpoIIIE  14 essqlpvalgkei.sgnplvldlkkmashllvaGatgsGKStalntL 59 
                                       e++ +p  l+ +  +g+plv+       h+lv+G+tg+GK+ + +++
  gi|298675720|ref|YP_003727470.1| 210 EPPNVPYYLRNDYsMGDPLVF------RHMLVCGSTGTGKTFMTKNI 250
                                       555566666666666666665......4************9876665 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.015
                                       ----B-----EEEEEEC-HHHHHHHHHHH....HHHHHHHHHHHCGGGTEEEEEEES--- CS
                      FtsK_SpoIIIE 183 tagrelekrpslvvivderieLrlaapkdssvlvedaivRlarkgraaglHlllatqrls 242
                                       t+g e+ ++ ++v ++de       a+++ s+++++ ++  ar+gr++gl l l+tq ++
  gi|298675720|ref|YP_003727470.1| 476 TSGNESVRKTPIVLGLDEAHRYLAKASGEHSRRIISKFADAARQGRKEGLGLFLITQDPQ 535
                                       66666778888999999998888899999999999999999999*************987 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   1.9e-06    0.0023       2      62 ..     234     304 ..     233     335 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.9e-06
                      RNA_helicase   2 wlyGpsgeGKStlakeLakallkkl........klkkkdsvys.rnpeddfwdgYt.gqevvvidDfgqvk 62 
                                       +++G++g+GK+ ++k++ +++l++         ++ +k+ +++   p+d++ + Y+ ++e++  d+ + ++
  gi|298675720|ref|YP_003727470.1| 234 LVCGSTGTGKTFMTKNILRQFLSDGnryvlrsdENRWKNPCVViMDPQDEYSQVYEeNPEINTQDEYSFNS 304
                                       69********************7778889999977777777777999*****9999666666666655444 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   8.9e-06     0.011      34      58 ..     231     255 ..     229     263 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8.9e-06
                             AAA_7  34 kpvllvGptGtGKtviikdllkkld 58 
                                       +++l++G+tGtGKt ++k++l+++ 
  gi|298675720|ref|YP_003727470.1| 231 RHMLVCGSTGTGKTFMTKNILRQFL 255
                                       689****************999875 PP

>> PriA_3primeBD  3′ DNA-binding domain (3′BD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0059       7.1      21      61 ..      83     123 ..      66     143 .. 0.76
   2 ?    4.9   0.0     0.021        25      34      70 ..     405     441 ..     398     454 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0059
                     PriA_3primeBD  21 evkiGsrVlVpfgkrklvGiVvalkeeseveeeklkpieev 61 
                                       +v+ G+ VlVp g + l + +++l   +e+e ++  +i++ 
  gi|298675720|ref|YP_003727470.1|  83 DVRLGTYVLVPYGDEDLFARIWKLRYIQEFEVDDATEIHSR 123
                                       5667*********************9999999999999864 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.021
                     PriA_3primeBD  34 krklvGiVvalkee..seveeeklkpieevldeepllte 70 
                                       ++++ GiV ++k++  ++v +++ +pi+++lde  ++++
  gi|298675720|ref|YP_003727470.1| 405 ESSYDGIVRRVKNRafEKVFDQDARPITDILDE--VFKP 441
                                       56789*******99888889************5..4554 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00016      0.19     131     161 ..     232     262 ..     227     273 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00016
                             T2SSE 131 lilvsGgTgsGKttllyallkeinksderiv 161
                                        +lv G Tg+GKt ++  +l ++ ++ +r v
  gi|298675720|ref|YP_003727470.1| 232 HMLVCGSTGTGKTFMTKNILRQFLSDGNRYV 262
                                       589*************888877766655554 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00021      0.26       3      33 ..     234     283 ..     233     320 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00021
                            AAA_33   3 llvGlpGsGKstlaerllkklg....avllssdt...............l 33 
                                       l++G  G+GK++  +++l++       ++l+sd+               +
  gi|298675720|ref|YP_003727470.1| 234 LVCGSTGTGKTFMTKNILRQFLsdgnRYVLRSDEnrwknpcvvimdpqdE 283
                                       79***************988666777777888875555555544444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (603 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.44
# Mc/sec: 4161.59
//
Query:       gi|298675721|ref|YP_003727471.1|  [L=417]
Description: NurA domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-08   34.9   0.0    1.7e-08   34.5   0.0    1.3  1  NurA           NurA domain
  ------ inclusion threshold ------
       0.48   10.8   4.4        1.4    9.3   0.2    2.9  3  Borrelia_orfD  Borrelia orf-D family


Domain annotation for each model (and alignments):
>> NurA  NurA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.0   1.9e-12   1.7e-08      59     242 .]     167     387 ..      73     387 .. 0.80

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 1.9e-12
                                       HHHHHHHHHHHHHHHCGGCCSCEEEEECSHHCCCH.........HHHHHHHHHHHHHHHHHHHHHTT-...TTCEEE CS
                              NurA  59 rllmetlElklgallleekgedllllDGsligslv.........efdelheeleyeeylyslsrllea...glnlvg 123
                                        l+++  E+  +  l   +++++l++DG+ +++ +         + + +++ +    + ++++ + e+    ++l g
  gi|298675721|ref|YP_003727471.1| 167 ALYLAESEHI-NWMLDGLDDNGVLIMDGPVYPKRLmywlvveseDIQIQYDPHTKTILQNYIDIMDEHikkQKPLMG 242
                                       5555555555.3334456899*********************98555555555555444444444455888****** PP

                                       EESS-SCTCCHCCC......S.--HHHHCCHHCCHCH............................---STTS-HHHH CS
                              NurA 124 vaKsfrskellnllletllig.esisDiallgallrk............................pgytspllkilr 171
                                        +K+ +  + ++ ++++  +g ++  D+++++ ll +                             + tspl +   
  gi|298675721|ref|YP_003727471.1| 243 FVKNPEDIQVMQAMKQNGMRGiPWTMDAQFFKNLL-SlknddadenkyitytnwfiqpnkfyermLNTTSPLVEDT- 317
                                       **************555555515677999999999.8777777777777777777777666664444444444333. PP

                                       TT-HCCHHHHHH-EEEEEEESSTTTTEEEEEHHHHHH.CCHHHHHHHHHH..TTB-SSSBCCHHHHHHHHCC CS
                              NurA 172 ekpllrealidkeiyfaYvrlegggsilrleipaevs.takdedvlsllasqrlsisGYprpLalAhelaki 242
                                            ++  +d+  +f+ v +   ++i+++e p+ ++  +++ d++ +  +  +si+G+p++L +A++ aki
  gi|298675721|ref|YP_003727471.1| 318 --LEHKYPADDYSLTFFMVYVPWMDVIFKIESPYGLTkNENIRDMVKRKVLYDISINGIPKALSKADSIAKI 387
                                       ..89999999999***********************999*******987778******************98 PP

>> Borrelia_orfD  Borrelia orf-D family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1      0.92   8.2e+03      58      87 ..      19      44 ..      16      56 .. 0.46
   2 ?    9.3   0.2   0.00015       1.4      54      91 ..     206     241 ..     195     246 .. 0.85
   3 ?    1.3   0.1     0.048   4.3e+02      12      41 ..     274     303 ..     265     312 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.92
                     Borrelia_orfD 58 dlvtld.eegskeanilknritiylryikkt 87
                                      d+++ d +e  +++      i  yl+ +k  
  gi|298675721|ref|YP_003727471.1| 19 DVSLEDkDESEITT-----DIFSYLQELKYK 44
                                      55554413333444.....444444444444 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00015
                     Borrelia_orfD  54 feyfdlvtldeegskeanilknritiylryikktkPiv 91 
                                        e  d+ +  + ++k+   l+n i+i  ++ikk kP++
  gi|298675721|ref|YP_003727471.1| 206 VESEDIQIQYDPHTKTI--LQNYIDIMDEHIKKQKPLM 241
                                       56778888899999987..*****************86 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.048
                     Borrelia_orfD  12 edlkslakdeaelsrystalvvfllkvksk 41 
                                       ++l sl  d+a+  +y t+ + f+   k +
  gi|298675721|ref|YP_003727471.1| 274 KNLLSLKNDDADENKYITYTNWFIQPNKFY 303
                                       5677899999*********99998877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3094.22
//
Query:       gi|298675722|ref|YP_003727472.1|  [L=636]
Description: Na+/solute symporter [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.2e-37  128.0  35.7    4.2e-37  128.0  35.7    2.0  3  SSF           Sodium:solute symporter family
  ------ inclusion threshold ------
        0.1   11.5  36.1      0.018   14.1  16.3    3.2  3  Nramp         Natural resistance-associated macrophage protei
       0.12   11.1   0.0       0.18   10.5   0.0    1.1  1  Alginate_exp  Alginate export
       0.39   10.5   0.0       0.39   10.5   0.0    4.8  7  DUF2976       Protein of unknown function (DUF2976)


Domain annotation for each model (and alignments):
>> SSF  Sodium:solute symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.5      0.41   1.9e+03     295     307 ..       8      20 ..       4      22 .. 0.85
   2 !  128.0  35.7   9.3e-41   4.2e-37       1     406 []      35     436 ..      35     436 .. 0.82
   3 ?   -2.0   0.1      0.28   1.2e+03     137     183 ..     450     496 ..     438     512 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.41
                               SSF 295 GlllavmlAaims 307
                                        ++lav lAa++s
  gi|298675722|ref|YP_003727472.1|   8 LIMLAVYLAALVS 20 
                                       599*******998 PP

  == domain 2  score: 128.0 bits;  conditional E-value: 9.3e-41
                               SSF   1 yflagrsltgfvlglslaasnisaasfvGlaGavaasGlavvllelgalllvlllllllaerlrnagalTlpdylsk 77 
                                       ++lagr+++++ +g s+aas + a+ ++ + G+  + G++ ++  +   +l+ll++ +l+ r  ++ a+T p++l++
  gi|298675722|ref|YP_003727472.1|  35 FWLAGRNIGSIGVGFSAAASWLTAGALLSVIGLYLLNGMGSIWGFVVPNILALLIIAILVSRIKHLPAITQPELLEQ 111
                                       89***************************************9999999999999999******************** PP

                               SSF  78 RfkgkrilvylsalslllvitlklsvdlvggaklielalGlnyetavlllaaltalYtviGGllAvvytdtiqavlm 154
                                       R+ +   +  ++ ++++++i +++ +d+ g a  +e  +Gl+   a  ++a+++ +Y+ +GGl Avv+td++q + +
  gi|298675722|ref|YP_003727472.1| 112 RYSSAI-RAPVATIITIVMILFAV-ADIKGFALVLEVFFGLSPIYAAAIVAIAVSIYVTLGGLSAVVWTDVLQFTFL 186
                                       **9876.999*9999999998876.7****************999999*************************8866 PP

                               SSF 155 lvgalilliivllevG.gleslveklkeaapkv.vdlltpdslkllrdpl.talslwlglvlGvaglphilvRflaa 228
                                          +l++  ++++ vG + + ++e   +++++    ++++   + +   + +al++ ++++ G +  +   +R+ aa
  gi|298675722|ref|YP_003727472.1| 187 ---SLFVISMAIVTVGaASSGAFEASSAMTVSDvFGNVNSSWWNPFSVGIpFALIFLIAIIPGWITEQDPWQRVWAA 260
                                       ...6677778888888555555555544444222333443333333332214455558888888888********** PP

                               SSF 229 kdakailkgvlkltivlilvligmisiilfaikla.gavpkavgtevgvsniaypeLvvkllpnllaGlllavml.A 303
                                       kd k+++ g+  +  ++ +v++   +i l+ ++l  g+  +   + +  ++ a+ + ++  +  ++ Gl +a+ l A
  gi|298675722|ref|YP_003727472.1| 261 KDRKSARFGMTLGAFLITVVFAACAVIALGLNSLYpGIAEAGFPAGMARAETALLQFINSSFSTFVVGL-SAIGLaA 336
                                       *************9999999999888888877765144446667778899******************8.5665516 PP

                               SSF 304 aimstltslllsassaftkDlYkkirrkasakekelvgvsriivlvvislaillavqeeqkgvlklvelafaglasa 380
                                       a ms  ++   s++s +++D+Y+++++   a+ k++  + ri vl +++ a ++   +    +l+ +++a+ ++ + 
  gi|298675722|ref|YP_003727472.1| 337 AAMSCTDTFATSGASCVSRDIYQRFIKPD-ATMKQMRVINRISVLFIVASATII--SFYITSILDAIHIATYIASAS 410
                                       79**********************99988.555555555555555444333333..33333489************* PP

                               SSF 381 vlavillalfwkrvneqGAlagliiG 406
                                        +  ++ +++wkr++++GA+agli+G
  gi|298675722|ref|YP_003727472.1| 411 YFFPLMGGIYWKRATKEGAIAGLIVG 436
                                       *************************9 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.28
                               SSF 137 iGGllAvvytdtiqavlmlvgalilliivllevGgleslveklkeaa 183
                                         G +A  y +ti  +l   g ++ ++++ +++ g++ +++k  +++
  gi|298675722|ref|YP_003727472.1| 450 NTGSMAQPYLQTIHPILRSHGVIVGMLLSAVAFFGVSFATQKSSNIN 496
                                       45677888999999999999988888888888878888888877775 PP

>> Nramp  Natural resistance-associated macrophage protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1  16.3   3.9e-06     0.018      23     140 ..      84     198 ..      71     214 .. 0.78
   2 ?   -1.6   0.1      0.22     1e+03     331     344 ..     230     243 ..     218     246 .. 0.90
   3 ?    6.1   7.0     0.001       4.5     200     325 ..     264     399 ..     247     417 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.9e-06
                             Nramp  23 tllaillqelsarLGlvTgkglaelirerlpkkvsillwilaelaiiatdlaeviGaAialnllfgipllvgvlita 99 
                                       +l+++++  l+ r+      + +el+++r++ ++++ ++ ++ +++i++ +a++ G A++l+++fg++ ++++ i+a
  gi|298675722|ref|YP_003727472.1|  84 ILALLIIAILVSRIKHLPAITQPELLEQRYSSAIRAPVATIITIVMILFAVADIKGFALVLEVFFGLSPIYAAAIVA 160
                                       3444556667778877777888999*******************************************999999999 PP

                             Nramp 100 vlvllllflekggyrklEaliialvlvialsFiaelflvkp 140
                                       + v + ++   gg + +  +  +l ++++  F++++++v +
  gi|298675722|ref|YP_003727472.1| 161 IAVSIYVT--LGGLSAVV-WTDVLQFTFLSLFVISMAIVTV 198
                                       99999999..55555443.3344444444568888887765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.22
                             Nramp 331 slllPfalipllll 344
                                       s+++Pfali+l+ +
  gi|298675722|ref|YP_003727472.1| 230 SVGIPFALIFLIAI 243
                                       799********976 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.001
                             Nramp 200 kyeriDtiial..ivaflinlailivaAavlysggkdv...esledaaeaLepllGskaa...svlFaigLlaaGls 268
                                       k +r+ +++++  i + + ++a++++  + ly+g ++    + ++ a  aL + ++s+++     l aigL aa++s
  gi|298675722|ref|YP_003727472.1| 264 KSARFGMTLGAflITVVFAACAVIALGLNSLYPGIAEAgfpAGMARAETALLQFINSSFStfvVGLSAIGLAAAAMS 340
                                       44444444444116677889999999999999888877677777777777777666544422267789********* PP

                             Nramp 269 Stitgtlagqyvm.egflglrislwlrrlitralafvpalivilligaele...lvkllvl 325
                                        t t +++g+  +  ++++  i++++     r++  + +l++++ +   +    ++++l +
  gi|298675722|ref|YP_003727472.1| 341 CTDTFATSGASCVsRDIYQRFIKPDATMKQMRVINRISVLFIVASAT--IIsfyITSILDA 399
                                       ****9999987551566666677655553333333333333333333..222243334444 PP

>> Alginate_exp  Alginate export
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0     4e-05      0.18     161     249 ..     481     573 ..     478     584 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4e-05
                                       EEEEEEEEEETTEEEEEEEEEEEETT-S--....B--TTS-SEEEEEEEEEEEEEESTT-SSEEEEEEEEEEEEEEE CS
                      Alginate_exp 161 lFygvsvewrkvepgelsaYysrlkedlkk....avdeldatgderlttlglraagkakntrldydlelmyqtGrvg 233
                                        F+gvs+  +k+  ++l++++ +  ++l+     ++de+d  +++ l+ +  ++ g+ +  +l+ +++++  +G+ +
  gi|298675722|ref|YP_003727472.1| 481 AFFGVSFATQKSSNINLAPFFKESAKELSTyyskEIDESDPGYNKFLNRIEEKVVGERGHLHLNIETSATINWGKFV 557
                                       79********************999999999999******************************************* PP

                                       EEETTEEEEEEEEEEE CS
                      Alginate_exp 234 ttvarawnavaaelGy 249
                                       ++ ++   a+ + +Gy
  gi|298675722|ref|YP_003727472.1| 558 NQLKSSYPAWVTSTGY 573
                                       ***************7 PP

>> DUF2976  Protein of unknown function (DUF2976)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.1       2.9   1.3e+04      74      83 ..       8      17 ..       6      30 .. 0.58
   2 ?   -2.1   0.5      0.76   3.4e+03      71      83 ..      59      71 ..      44      99 .. 0.59
   3 ?   -4.2   4.1       3.5   1.6e+04      38      49 ..     156     167 ..     100     203 .. 0.59
   4 ?   -0.6   0.4      0.26   1.2e+03      28      52 ..     183     207 ..     175     213 .. 0.82
   5 ?   -3.0   0.6       1.4   6.5e+03      27      42 ..     273     288 ..     268     293 .. 0.62
   6 ?   -1.6   0.1      0.55   2.4e+03      29      43 ..     429     443 ..     422     450 .. 0.76
   7 ?   10.5   0.0   8.7e-05      0.39      11      46 ..     453     488 ..     449     494 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 2.9
                           DUF2976 74 llvvviwLlt 83
                                      l++++++L++
  gi|298675722|ref|YP_003727472.1|  8 LIMLAVYLAA 17
                                      4444444432 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.76
                           DUF2976 71 GvvllvvviwLlt 83
                                      G++l v+ ++Ll+
  gi|298675722|ref|YP_003727472.1| 59 GALLSVIGLYLLN 71
                                      3333333333333 PP

  == domain 3  score: -4.2 bits;  conditional E-value: 3.5
                           DUF2976  38 vaflaVakaalk 49 
                                       +a++a+a +++ 
  gi|298675722|ref|YP_003727472.1| 156 AAIVAIAVSIYV 167
                                       333333333333 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 0.26
                           DUF2976  28 villgLvlaavaflaVakaalkkfn 52 
                                       ++ l L + ++a+++V  a  + f+
  gi|298675722|ref|YP_003727472.1| 183 FTFLSLFVISMAIVTVGAASSGAFE 207
                                       5678899999999999998887775 PP

  == domain 5  score: -3.0 bits;  conditional E-value: 1.4
                           DUF2976  27 gvillgLvlaavafla 42 
                                       g+ l+ +v+aa+a++a
  gi|298675722|ref|YP_003727472.1| 273 GAFLITVVFAACAVIA 288
                                       4455666666666554 PP

  == domain 6  score: -1.6 bits;  conditional E-value: 0.55
                           DUF2976  29 illgLvlaavaflaV 43 
                                       +++gL+++a+a ++ 
  gi|298675722|ref|YP_003727472.1| 429 AIAGLIVGAIAQITL 443
                                       578999999987654 PP

  == domain 7  score: 10.5 bits;  conditional E-value: 8.7e-05
                           DUF2976  11 ekggdllelikgylkdgvillgLvlaavaflaVaka 46 
                                       + ++ +l++i+  l    +++g++l+avaf+ V  a
  gi|298675722|ref|YP_003727472.1| 453 SMAQPYLQTIHPILRSHGVIVGMLLSAVAFFGVSFA 488
                                       556789**************************9766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (636 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1131  (0.0630822); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.87u 0.33s 00:00:01.20 Elapsed: 00:00:00.52
# Mc/sec: 3662.09
//
Query:       gi|298675723|ref|YP_003727473.1|  [L=302]
Description: hypothetical protein Metev_1842 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.06   13.7   0.1       0.14   12.5   0.1    1.6  1  DUF4969   Domain of unknown function (DUF4969)


Domain annotation for each model (and alignments):
>> DUF4969  Domain of unknown function (DUF4969)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1     8e-06      0.14       2      58 ..       3      56 ..       2      64 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8e-06
                           DUF4969  2 kkRgllLvsvLvlFillavaCsds..edneesveiilkeielsvddpiklvdengeatv 58
                                      +k  llLvsvL+   l+a  C d     ne+  e+ +++ el     + l +  ++++v
  gi|298675723|ref|YP_003727473.1|  3 YKTALLLVSVLI-PTLFASGCIDQivPMNETNDEPDTSKYELE----VFLDKTENDTFV 56
                                      8999******97.6899****9953368***********9999....344434444555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1700.73
//
Query:       gi|298675724|ref|YP_003727474.1|  [L=369]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-25   87.7   3.0    1.7e-24   85.5   1.1    2.7  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
    7.4e-11   42.3   1.7      2e-10   40.9   1.7    1.7  1  OrfB_IS605       Probable transposase
  ------ inclusion threshold ------
      0.033   14.2   1.2       0.89    9.7   0.1    2.3  2  UPF0547          Uncharacterised protein family UPF0547
      0.052   13.6   0.1        0.1   12.6   0.1    1.4  1  HypA             Hydrogenase/urease nickel incorporation, met
       0.41   10.8   6.0        7.8    6.7   0.2    3.4  3  DUF2387          Probable metal-binding protein (DUF2387)
       0.92    9.3   4.0        7.2    6.5   0.6    2.4  2  zinc_ribbon_2    zinc-ribbon domain
        1.1   10.1   6.9        2.6    8.9   6.9    1.6  1  Tnp_zf-ribbon_2  DDE_Tnp_1-like zinc-ribbon
        1.1    9.2   4.5        2.5    8.1   4.5    1.6  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
        2.1    8.1   5.9          8    6.2   5.9    2.0  1  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.22   4.4e+02      15      28 ..     195     208 ..     166     238 .. 0.71
   2 !   85.5   1.1   8.6e-28   1.7e-24       1      69 []     285     354 ..     285     354 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.22
                    OrfB_Zn_ribbon  15 yGikveevnpayTS 28 
                                       +G k  e+ ++yTS
  gi|298675724|ref|YP_003727474.1| 195 KGTKADEIRERYTS 208
                                       35555555555555 PP

  == domain 2  score: 85.5 bits;  conditional E-value: 8.6e-28
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f++l+ ++ yk k +Gi+v+ +np yTS++CseCg+++k+ ++++ +fkC++Cg++ ++D+nA+ Ni++r
  gi|298675724|ref|YP_003727474.1| 285 FSELTDFILYKSKLEGIPVVIINPMYTSQQCSECGYIDKNnRQKQSNFKCKKCGHKDNADYNASKNIAHR 354
                                       899*************************************99*************************997 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   1.7     1e-13     2e-10       4     106 ..     162     254 ..     159     264 .. 0.87

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 1e-13
                        OrfB_IS605   4 vevevelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarl 80 
                                       +ev++  +++ +  + g+DlG+ n+at+++++    +ykg ++++  ++++  + +lqsk   s     a++ l++l
  gi|298675724|ref|YP_003727474.1| 162 MEVGE-NEVEYNDDVMGVDLGVVNIATTSDNE----VYKGTKADEIRERYTSLKSRLQSKGTWS-----AKKHLKKL 228
                                       56665.6677778899****************....************************6666.....79999*** PP

                        OrfB_IS605  81 hrkrsrrrkhllhklathliktlkev 106
                                       ++k +r+ ++l h +a++l+k+ k++
  gi|298675724|ref|YP_003727474.1| 229 SKKERRFKRDLNHRVAKQLVKRAKDT 254
                                       ********************998765 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00045      0.89      15      25 ..     313     323 ..     311     324 .. 0.87
   2 ?    3.3   0.2     0.044        87      16      25 ..     333     342 ..     332     343 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00045
                           UPF0547  15 qfCphCGyvFq 25 
                                       q C++CGy+++
  gi|298675724|ref|YP_003727474.1| 313 QQCSECGYIDK 323
                                       89******986 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.044
                           UPF0547  16 fCphCGyvFq 25 
                                       +C  CG+ ++
  gi|298675724|ref|YP_003727474.1| 333 KCKKCGHKDN 342
                                       6999999876 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   5.1e-05       0.1      63      96 ..     299     341 ..     269     351 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.1e-05
                                       E......EEEE--EEEETTTS-EEECHH..H.HHS-TTTSSS- CS
                              HypA  63 e......ieevpvkvrCreCgkefelee..k.alrCpkCgsad 96 
                                       e      i+ +  + +C+eCg+  + ++  + +++C+kCg++d
  gi|298675724|ref|YP_003727474.1| 299 EgipvviINPMYTSQQCSECGYIDKNNRqkQsNFKCKKCGHKD 341
                                       4444434677778899*****9888555333788******975 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.038        76      38      73 ..     224     259 ..     221     261 .. 0.87
   2 ?    6.7   0.2    0.0039       7.8      31      48 ..     313     330 ..     307     333 .. 0.85
   3 ?    5.2   2.0     0.012        23      33      49 ..     315     331 ..     314     358 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.038
                           DUF2387  38 ftdelsekgqsvakelktrvnkdeekeasakvqtvq 73 
                                       ++ +ls+k++ ++++l+ rv+k+  k+a+++ +++ 
  gi|298675724|ref|YP_003727474.1| 224 HLKKLSKKERRFKRDLNHRVAKQLVKRAKDTSRAIA 259
                                       7889999****************9999988887775 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0039
                           DUF2387  31 rECvsCgftdelsekgqs 48 
                                         C +Cg++d+ + ++qs
  gi|298675724|ref|YP_003727474.1| 313 QQCSECGYIDKNNRQKQS 330
                                       57***********99776 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.012
                           DUF2387  33 CvsCgftdelsekgqsv 49 
                                       C +Cg++d+ + ++qs 
  gi|298675724|ref|YP_003727474.1| 315 CSECGYIDKNNRQKQSN 331
                                       77777777777775554 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.028        57      14      21 ..     313     320 ..     311     321 .. 0.75
   2 ?    6.5   0.6    0.0036       7.2       1       8 [.     333     340 ..     323     345 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.028
                     zinc_ribbon_2  14 kFCpyCGt 21 
                                       + C++CG+
  gi|298675724|ref|YP_003727474.1| 313 QQCSECGY 320
                                       67999986 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0036
                     zinc_ribbon_2   1 fCpnCGae 8  
                                       +C++CG++
  gi|298675724|ref|YP_003727474.1| 333 KCKKCGHK 340
                                       56666655 PP

>> Tnp_zf-ribbon_2  DDE_Tnp_1-like zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   6.9    0.0013       2.6       3      23 ..     315     338 ..     313     343 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0013
                   Tnp_zf-ribbon_2   3 CkvClk...kkikkeTriiCqeCd 23 
                                       C  C +   ++++k++++ C++C+
  gi|298675724|ref|YP_003727474.1| 315 CSECGYidkNNRQKQSNFKCKKCG 338
                                       999*****8899999********6 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   4.5    0.0013       2.5      19      45 ..     313     339 ..     309     340 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0013
                     Zn_Tnp_IS1595  19 fvCPhCgsr.kayriktrglfqCkeCrk 45 
                                       + C  Cg+  k  r k+   f+Ck+C++
  gi|298675724|ref|YP_003727474.1| 313 QQCSECGYIdKNNRQKQ-SNFKCKKCGH 339
                                       57*******77777777.********98 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   5.9     0.004         8       3      26 ..     315     340 ..     313     340 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.004
                                       -SSS-..-B----SSS----SSS--- CS
                    DNA_RNApol_7kD   3 CgeCg..aevslkkgdpiRCkeCGhR 26 
                                       C eCg  +++  +k+   +Ck+CGh+
  gi|298675724|ref|YP_003727474.1| 315 CSECGyiDKNNRQKQSNFKCKKCGHK 340
                                       99998666888899999********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1160  (0.0646996); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2374.95
//
Query:       gi|298675725|ref|YP_003727475.1|  [L=247]
Description: beta-lactamase-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-26   92.1   0.3    4.1e-26   91.7   0.3    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
    5.1e-20   72.3   0.4    6.7e-20   71.9   0.4    1.2  1  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
      0.089   12.7   1.1       0.29   11.0   1.1    1.8  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.7   0.3   6.9e-30   4.1e-26       3     201 .]      49     222 ..      48     222 .. 0.89

  Alignments for each domain:
  == domain 1  score: 91.7 bits;  conditional E-value: 6.9e-30
                                       EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHC CS
                     Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylal 79 
                                       iLiD++pd+  q    l      ++++ +d+V++th+HyDH+ag++ + + ++ k+++y+ +++l+++ + f++  l
  gi|298675725|ref|YP_003727475.1|  49 ILIDTSPDMKWQ----L----IANDVSGVDGVIWTHGHYDHFAGFPEFYRVQK-KVDVYGVPETLDYIMDYFHF--L 114
                                       9*******6555....4....356999***********************765.6****999********9755..4 PP

                                       HTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S.---HHHHHHHC CS
                     Lactamase_B_2  80 eeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtg.yipeeigerlg 155
                                       ++     +h++++ e+fel   gl++ +++++h   +       +++G+++ +g+k+v+ +gDt+  +p++  ++++
  gi|298675725|ref|YP_003727475.1| 115 KPR----RHDVQLYEPFELI--GLTFVLFEVNHLPIK-------KAVGVMVCEGEKKVVITGDTNkDVPQKSMDLIH 178
                                       454....88**********5..89************9.......9*******************9678899999*** PP

                                       T-SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 156 gadllllditayeddemirhmgHltpeeaveaaadlgakrlvliHi 201
                                       ++dll++d+ +  +        H++  +a+++ ++++ak++v++H+
  gi|298675725|ref|YP_003727475.1| 179 KPDLLVVDAIVPPSI--TSIKKHMNAIQALDFSEKIKAKKVVFVHM 222
                                       ********7755543..4468************************8 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.9   0.4   1.1e-23   6.7e-20       6     195 ..      37     219 ..      33     224 .. 0.85

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 1.1e-23
                                       SEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCC CS
                       Lactamase_B   6 vnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapal 82 
                                        +s+l+e d g iLiDt  +  ++++         +   vd vi TH+H+DH++g +++ +  + + ++   e+  +
  gi|298675725|ref|YP_003727475.1|  37 RFSILVESDAGKILIDTSPDMKWQLI-------ANDVSGVDGVIWTHGHYDHFAGFPEFYRVQKKVDVYGVPETLDY 106
                                       689**********************7.......58****************************************** PP

                                       HCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCC CS
                       Lactamase_B  83 fmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgr 159
                                       +m++  +            ++++++   e+ +++++  ++++v + p   ++++ v+ g++kv++tGD+    ++ +
  gi|298675725|ref|YP_003727475.1| 107 IMDYFHFLK----------PRRHDVQLYEPFELIGLTFVLFEVNHLPIKKAVGVMVCEGEKKVVITGDTNKDVPQKS 173
                                       *****8765..........56799***************************************************** PP

                                       CCC...........TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEE CS
                       Lactamase_B 160 idl..........tlrgaevrdpsdaekyldsllklaglkaevlvp 195
                                       +dl           + ++       +++++++l+  ++ ka+++v+
  gi|298675725|ref|YP_003727475.1| 174 MDLihkpdllvvdAIVPPSITSIKKHMNAIQALDFSEKIKAKKVVF 219
                                       9998877777777444444444555555555555555555555554 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.1   4.9e-05      0.29       9     149 ..      39     207 ..      37     221 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.9e-05
                     Lactamase_B_3   9 sflletagarilvDPfkanlgyeppa...eeaDlvlisqaledHah.letlkqlaenvkvleeges........... 70 
                                       s+l+e++  +il+D   + ++++  a     +D v+ ++++ dH++  ++  +++++v+v   +e+           
  gi|298675725|ref|YP_003727475.1|  39 SILVESDAGKILIDTS-PDMKWQLIAndvSGVDGVIWTHGHYDHFAgFPEFYRVQKKVDVYGVPETldyimdyfhfl 114
                                       7899999999****55.466666666566899************973345566655555555543322222222222 PP

                     Lactamase_B_3  71 ......lev.ggleiravatshdavggsergenngflleqdgltiyhlGhlahelsseelkelgrvDvvltPvgg.. 138
                                             +++ + +e+ + +    +v+  + ++ +g ++ +++ +++  G++  +  +++ + + ++D++++  +   
  gi|298675725|ref|YP_003727475.1| 115 kprrhdVQLyEPFELIGLTFVLFEVNHLPIKKAVGVMVCEGEKKVVITGDTNKDVPQKSMDLIHKPDLLVVDAIVpp 191
                                       22222233323444444444445555567777888888888889999999999988999999999998888766664 PP

                     Lactamase_B_3 139 .....pltlgqeeale 149
                                            ++ +++ +al+
  gi|298675725|ref|YP_003727475.1| 192 sitsiKKHMNAIQALD 207
                                       4444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1629.59
//
Query:       gi|298675726|ref|YP_003727476.1|  [L=422]
Description: AAA ATPase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-37  128.6   0.1    1.8e-36  125.5   0.0    2.4  2  AAA              ATPase family associated with various cellul
    2.8e-09   36.6   0.2    9.3e-09   35.0   0.2    1.9  1  AAA_lid_3        AAA+ lid domain
    5.6e-08   32.9   0.3    1.2e-06   28.6   0.1    2.9  2  AAA_5            AAA domain (dynein-related subfamily)
    1.2e-05   25.8   0.1     0.0036   17.7   0.1    2.6  2  AAA_16           AAA ATPase domain
    3.8e-05   23.0   0.1      8e-05   21.9   0.1    1.6  1  DUF815           Protein of unknown function (DUF815)
    0.00029   21.1   0.7      0.052   13.8   0.0    2.9  2  AAA_22           AAA domain
     0.0004   20.9   0.1     0.0021   18.6   0.0    2.3  2  AAA_18           AAA domain
      0.003   17.7   0.1       0.01   16.0   0.0    1.8  1  AAA_33           AAA domain
     0.0037   17.1   0.5     0.0067   16.3   0.0    1.7  1  Bac_DnaA         Bacterial dnaA  protein
     0.0043   16.8   0.0       0.01   15.6   0.0    1.7  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.006   16.8   0.0      0.021   15.1   0.0    1.9  1  AAA_28           AAA domain
     0.0078   15.5   0.0      0.023   13.9   0.0    1.9  2  TIP49            TIP49 P-loop domain
     0.0094   16.1   1.8      0.078   13.1   0.0    3.0  3  AAA_2            AAA domain (Cdc48 subfamily)
  ------ inclusion threshold ------
      0.013   15.3   0.0      0.029   14.1   0.0    1.6  1  IstB_IS21        IstB-like ATP binding protein
      0.016   15.6   1.3        1.1    9.7   0.0    2.8  3  AAA_17           AAA domain
      0.021   14.4   0.6        1.4    8.5   0.1    2.7  2  AAA_25           AAA domain
      0.023   14.8   0.0      0.083   13.0   0.0    2.0  1  SKI              Shikimate kinase
       0.04   13.3   0.2      0.094   12.1   0.2    1.8  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.041   13.6   0.0        0.1   12.3   0.0    1.6  1  Sigma54_activat  Sigma-54 interaction domain
      0.042   14.2   0.6       0.19   12.1   0.3    2.3  1  AAA_19           AAA domain
      0.063   13.1   0.1       0.24   11.3   0.0    2.2  1  AAA_3            ATPase family associated with various cellul
      0.065   13.2   0.1       0.17   11.9   0.0    1.8  2  ResIII           Type III restriction enzyme, res subunit
      0.091   12.3   0.0       0.23   11.0   0.0    1.7  1  AAA_7            P-loop containing dynein motor region
      0.092   12.7   0.1         10    6.0   0.0    2.5  2  NACHT            NACHT domain
      0.095   12.8   0.0       0.22   11.7   0.0    1.6  1  Sigma54_activ_2  Sigma-54 interaction domain
        0.1   12.5   0.0       0.18   11.6   0.0    1.5  1  CPT              Chloramphenicol phosphotransferase-like prot


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       1.4   9.5e+02      75     100 ..     132     157 ..     125     196 .. 0.76
   2 !  125.5   0.0   2.6e-39   1.8e-36       1     132 []     212     341 ..     212     341 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.4
                                       TTCCCHHHHHHHHHHHHHHHHTTTSS CS
                               AAA  75 sgseseeeervvnqLlteldgvkkke 100
                                       +++ +e++++ v+ L+te+++++  e
  gi|298675726|ref|YP_003727476.1| 132 KSAPKEVDREWVDSLITEIEQEEGGE 157
                                       45678899999999999999998753 PP

  == domain 2  score: 125.5 bits;  conditional E-value: 2.6e-39
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       +ll+G pGtGKT++a+av + l+ +f+e+ +s ++++y+ge++k+i  +f+ ak+ + p++lfiDE+d +ak+r+++
  gi|298675726|ref|YP_003727476.1| 212 LLLIGAPGTGKTSVARAVSHRLSLPFVEVRLSMVTDQYLGETAKNIDRVFTLAKRLN-PCVLFIDEFDFVAKKRTSD 287
                                       69******************************************************9.******************* PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEEETTS CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrkieiel 132
                                       es   +r+vn+Ll+++d+v+  ++ v++i+atn+p++ld a   +Rfd++++++l
  gi|298675726|ref|YP_003727476.1| 288 ESAALKRAVNTLLKAIDEVSLTNDGVLLIAATNHPNMLDTAAW-RRFDEVMNFPL 341
                                       *******************************************.7******9985 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.2   1.3e-11   9.3e-09       1      45 []     361     405 ..     361     405 .. 0.97

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 1.3e-11
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedfee 45 
                                       d+d +e+A+ TeGy G Dl  ++re +l Al +++k++t++d+++
  gi|298675726|ref|YP_003727476.1| 361 DLDTEEIAQITEGYAGSDLRMVIREGVLSALMEDRKALTQDDLKK 405
                                       7899**************************************986 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.66   4.5e+02      77     135 ..     138     196 ..     136     198 .. 0.84
   2 !   28.6   0.1   1.7e-09   1.2e-06       2     138 .]     212     333 ..     211     333 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.66
                                       --HHHHHHHHHHHHSSEEE..-SSSEEE---.......-EEEEEESS--.-TT-TTHHHH CS
                             AAA_5  77 aesevlnsLlslleerrllleeggelvkakndd.llerfrviatanpldrslnelspalr 135
                                       +++e+++sL++ +e+++   e++ +l + ++++ ++++f  i ++ +++ +++++ +a++
  gi|298675726|ref|YP_003727476.1| 138 VDREWVDSLITEIEQEEGG-EDMLKLAHIEAPEdIMQTFEDIVLTDEQEDEVEKIVKAIQ 196
                                       5689999999999999999.8999999999999999999999999999988888887776 PP

  == domain 2  score: 28.6 bits;  conditional E-value: 1.7e-09
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGGG- CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEvera 77 
                                       +lL+G+pGtgK+++a+ ++++l  ++++v l+    +++ +g++       +  d +++ a r ++++l++DE++ +
  gi|298675726|ref|YP_003727476.1| 212 LLLIGAPGTGKTSVARAVSHRLSLPFVEVRLSM--VTDQYLGETA------KNIDRVFTLAKRlNPCVLFIDEFDFV 280
                                       89***************************9986..4444455444......7889999988889***********99 PP

                                       -HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHTT- CS
                             AAA_5  78 esevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrsRf 138
                                        ++ ++     l +    l +   +v+  nd+    + +ia++n ++     l+ a ++Rf
  gi|298675726|ref|YP_003727476.1| 281 AKKRTSDESAALKRAVNTLLKAIDEVSLTNDG----VLLIAATNHPN----MLDTAAWRRF 333
                                       98888888899999999999999999999998....99999999998....7788888887 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   5.2e-06    0.0036      15      50 ..     200     235 ..     185     254 .. 0.80
   2 ?    5.4   0.0     0.032        22     125     156 ..     259     294 ..     250     316 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5.2e-06
                            AAA_16  15 alervrsgrpelvllsGesGvGKsslvrellralek 50 
                                        l+++ + + + +ll+G++G+GK+s++r++ ++l+ 
  gi|298675726|ref|YP_003727476.1| 200 HLKTIGMYDIGKLLLIGAPGTGKTSVARAVSHRLSL 235
                                       5566666666789*****************998875 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.032
                            AAA_16 125 rllallsrderplvlvlDdlq.....wadeaslqlla 156
                                       r + l++r   p vl++D+++     +  ++s++l +
  gi|298675726|ref|YP_003727476.1| 259 RVFTLAKR-LNPCVLFIDEFDfvakkRTSDESAALKR 294
                                       55667777.778*********9776633334443333 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.1   1.2e-07     8e-05      55     155 ..     211     325 ..     157     338 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.2e-07
                            DUF815  55 nvLLwGarGtGKSslvkallneyaeeg..Lrlievekedlkelpklvellr...erperfilfvDDLsFeeeeeey. 125
                                       ++LL+Ga GtGK s+ +a+ ++++     +rl  v+ + l e  k ++ +    +r + ++lf+D   F ++ ++  
  gi|298675726|ref|YP_003727476.1| 211 KLLLIGAPGTGKTSVARAVSHRLSLPFveVRLSMVTDQYLGETAKNIDRVFtlaKRLNPCVLFIDEFDFVAKKRTSd 287
                                       68********************99987779999999999998888777665111555669********976654332 PP

                            DUF815 126 ......ksLksvLeG..sleakpenvliyaTsNrRhLl 155
                                             +++ ++L     ++ + + vl+ a +N+ ++l
  gi|298675726|ref|YP_003727476.1| 288 esaalkRAVNTLLKAidEVSLTNDGVLLIAATNHPNML 325
                                       33233333333333222344556677777777777766 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   7.5e-05     0.052       8      43 ..     212     238 ..     208     258 .. 0.83
   2 ?    4.7   0.0      0.05        35      87     114 ..     265     302 ..     243     325 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.5e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv 43 
                                       l+++G +GtGKT ++r + ++l         + ++v
  gi|298675726|ref|YP_003727476.1| 212 LLLIGAPGTGKTSVARAVSHRL---------SLPFV 238
                                       799***************9998.........45555 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.05
                            AAA_22  87 raravielliiDEaqhlr....s......eealeeL.rs 114
                                       ++   + +l iDE++++     s      ++a+++L + 
  gi|298675726|ref|YP_003727476.1| 265 KRLN-PCVLFIDEFDFVAkkrtSdesaalKRAVNTLlKA 302
                                       3333.69*********98765425556666666666333 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       4.2   2.9e+03      47      75 ..     129     156 ..     110     193 .. 0.58
   2 !   18.6   0.0   3.1e-06    0.0021       2      44 ..     213     276 ..     212     348 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 4.2
                            AAA_18  47 deskrldedkldklldaleenssaleegk 75 
                                        +sk + ++++ +++d l   ++ +eeg+
  gi|298675726|ref|YP_003727476.1| 129 TRSKSAPKEVDREWVDSLITEIE-QEEGG 156
                                       55666666666666666666555.23333 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 3.1e-06
                            AAA_18   2 lltGtpGvGKttlakeLskrlgf.....................gvnlrdvakenglllevdpe 44 
                                       ll G+pG+GKt++a+++s rl +                      +++  +ak  +++  + +e
  gi|298675726|ref|YP_003727476.1| 213 LLIGAPGTGKTSVARAVSHRLSLpfvevrlsmvtdqylgetaknIDRVFTLAKRLNPCVLFIDE 276
                                       689*****************97788666666666555555555444444444444444444444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.5e-05      0.01       3      92 ..     213     337 ..     212     341 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.5e-05
                            AAA_33   3 llvGlpGsGKstlaerllkklg..avllssdt..................lrrrlfgtdqqskt............. 46 
                                       ll+G+pG+GK+ +a+ +  +l   +v ++                     l                          
  gi|298675726|ref|YP_003727476.1| 213 LLIGAPGTGKTSVARAVSHRLSlpFVEVRLSMvtdqylgetaknidrvftL------------Akrlnpcvlfidef 277
                                       79***************9999888666666662244455555544444442............03333444444444 PP

                            AAA_33  47 .........dytrvldrlyqilnelarkalsagrnvil.dat....nlsrrerarflkla 92 
                                                d + +l+r+ ++l + ++++   + +v+l  at    +l+ ++++rf+++ 
  gi|298675726|ref|YP_003727476.1| 278 dfvakkrtsDESAALKRAVNTLLKAIDEVSLTNDGVLLiAATnhpnMLDTAAWRRFDEVM 337
                                       444444333666677777777777777776666555543555666666678888887765 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   9.8e-06    0.0067      37     196 ..     212     372 ..     199     394 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.8e-06
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHTT-SEEEEE-GGGGTT-H CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklrkvDvLliDDiqflagke 113
                                       l++ g  G Gkt + +a+++++   + e r++ + ++++l e +k +    + ++ ++l +  vL iD+  f+a+k 
  gi|298675726|ref|YP_003727476.1| 212 LLLIGAPGTGKTSVARAVSHRLSLPFVEVRLSMV-TDQYLGETAKNIDR--VFTLAKRL-NPCVLFIDEFDFVAKKR 284
                                       78999*************************9976.58899999998865..44555555.4569************9 PP

                                       HHHHH..HHHHHHHHHTTT-EEEEEES.....S-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHHHHHHTT CS
                          Bac_DnaA 114 ktqee..lfhtfnalleegkqvvlssD.....rsPkeleeledrlrsrfeaGlvvdieppdletrlailkkkieaek 183
                                       +++e   l   +n+ll++   v l+ D      + ++ + l+     rf+  +  +   pd+e+r  il +  +  +
  gi|298675726|ref|YP_003727476.1| 285 TSDESaaLKRAVNTLLKAIDEVSLTNDgvlliAATNHPNMLDTAAWRRFDEVM--NFPLPDMEMRKMILDRVTSDID 359
                                       88875337789999999888888887722222233444556666777888755..5566999999999999888888 PP

                                       ----TTHHHHHHH CS
                          Bac_DnaA 184 levpeevlefiae 196
                                        ++ +e +  i+e
  gi|298675726|ref|YP_003727476.1| 360 GDLDTEEIAQITE 372
                                       8876665555554 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.4e-05      0.01       8      97 ..     177     281 ..     172     337 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.4e-05
                            RuvB_N   8 eyigqekvkeklkifieaakkree.......aldhvllyGpPGlGkttlakiiakelg.....vklkitsgPvl.ek 71 
                                       + +  ++ +++++ +++a + re+        +  +ll+G+PG Gkt++a+ +++ l      v+l + +   l e 
  gi|298675726|ref|YP_003727476.1| 177 DIVLTDEQEDEVEKIVKAIQYREHlktigmyDIGKLLLIGAPGTGKTSVARAVSHRLSlpfveVRLSMVTDQYLgET 253
                                       555555566666666666666654222221135589******************99852221145555555555244 PP

                            RuvB_N  72 agdlaalltnle..ekdvlfideihrls 97 
                                       a+++  ++t  +  +  vlfide   ++
  gi|298675726|ref|YP_003727476.1| 254 AKNIDRVFTLAKrlNPCVLFIDEFDFVA 281
                                       4555444443331144699999987655 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0     3e-05     0.021       3      28 ..     213     239 ..     211     268 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3e-05
                            AAA_28   3 vitGgestGKTtlleaLaar.gypvvp 28 
                                        ++G+++tGKT++++a + r   p v+
  gi|298675726|ref|YP_003727476.1| 213 LLIGAPGTGKTSVARAVSHRlSLPFVE 239
                                       79***************9986666664 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   3.4e-05     0.023      53      88 ..     212     245 ..     175     261 .. 0.87
   2 ?   -2.6   0.0       3.4   2.4e+03     278     289 ..     268     279 ..     262     316 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.4e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  53 vLlaGpsgtGktalaiaiskelgedvpfvalsgsev 88 
                                       +Ll G +gtGkt++a a+s+ l+  +pfv +  s v
  gi|298675726|ref|YP_003727476.1| 212 LLLIGAPGTGKTSVARAVSHRLS--LPFVEVRLSMV 245
                                       7899******************9..99999877665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.4
                                       XXXXXXXXXXXX CS
                             TIP49 278 vpGvlfiDevhm 289
                                        p vlfiDe  +
  gi|298675726|ref|YP_003727476.1| 268 NPCVLFIDEFDF 279
                                       588999999765 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.3      0.97   6.7e+02      67      82 ..     153     193 ..     117     200 .. 0.64
   2 !   13.1   0.0   0.00011     0.078       3     110 ..     209     310 ..     207     329 .. 0.75
   3 ?   -2.2   0.0       5.6   3.8e+03      97      99 ..     389     391 ..     341     417 .. 0.57

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.97
                                       HTTS.....................EEEEE....TGGG--- CS
                             AAA_2  67 eegG.....................ivllD....EidKihp 82 
                                       eegG                     ivl D    E++Ki +
  gi|298675726|ref|YP_003727476.1| 153 EEGGedmlklahieapedimqtfedIVLTDeqedEVEKIVK 193
                                       44445555555555555555555557776522225777766 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00011
                                       ---EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTSEEEEETGGG CS
                             AAA_2   3 iisilllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegGivllDEidK 79 
                                       i+++ll+g  g+Gkt +a+a++  l++    +++ +  s ++   +     ++ i       ++ +  ++++DE d 
  gi|298675726|ref|YP_003727476.1| 209 IGKLLLIGAPGTGKTSVARAVSHRLSL----PFVEVRLSMVTD--QYLGETAKNIDRVFTLAKRLNPCVLFIDEFDF 279
                                       678999*******************96....555444444444..44444455555555566666788********* PP

                                       -------------HHHHHHHHHHHH--EE-- CS
                             AAA_2  80 ihpkessgadvSregVqrdLLqileggtltd 110
                                       +++k++s +    +  ++ LL+ +++  lt+
  gi|298675726|ref|YP_003727476.1| 280 VAKKRTSDESAALKRAVNTLLKAIDEVSLTN 310
                                       ***987888888889999*******999884 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 5.6
                                       HHH CS
                             AAA_2  97 rdL 99 
                                        +L
  gi|298675726|ref|YP_003727476.1| 389 SAL 391
                                       222 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.1e-05     0.029      31     122 ..     188     282 ..     158     303 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.1e-05
                         IstB_IS21  31 dkrkvkeLatlsfiek.....kenivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkrarrdgklara 102
                                        +++vk+++  +++++        ++l+G +G+GK+ +a a++++     ++v+   v+d     ++a++ +++ + 
  gi|298675726|ref|YP_003727476.1| 188 VEKIVKAIQYREHLKTigmydIGKLLLIGAPGTGKTSVARAVSHRLSLPFVEVRLSMVTDQYL-GETAKNIDRVFTL 263
                                       45555555555555431111134689*****************99998888888887777543.3677777787776 PP

                         IstB_IS21 103 lkrllkvdllilDdlgllpl 122
                                       +krl ++ +l +D++ ++  
  gi|298675726|ref|YP_003727476.1| 264 AKRL-NPCVLFIDEFDFVAK 282
                                       6665.566788888876654 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.4      0.12        80      45      99 ..     130     182 ..     115     194 .. 0.76
   2 ?    9.7   0.0    0.0016       1.1       1      25 [.     215     239 ..     215     269 .. 0.76
   3 ?   -2.6   0.0       9.6   6.6e+03     103     125 ..     334     356 ..     276     368 .. 0.55

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.12
                                       HHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE-SEEEETTEEEESSHHHHHHH CS
                            AAA_17  45 emrklpleekkelqkeaaekiaeeakkkgvlvdghprikeqagfldglpkevlee 99 
                                       + + +p+e+++e+ + ++ +i++e++ +++l   h   ++++++++++++ vl++
  gi|298675726|ref|YP_003727476.1| 130 RSKSAPKEVDREWVDSLITEIEQEEGGEDMLKLAHI--EAPEDIMQTFEDIVLTD 182
                                       4457899****************9988888875665..78999999999877765 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0016
                                       EE-TTSSHHHHHHHHHHHHTEEEEE CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthls 25 
                                       +G PG GK+ +++ + +++ +++++
  gi|298675726|ref|YP_003727476.1| 215 IGAPGTGKTSVARAVSHRLSLPFVE 239
                                       69*******************9998 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 9.6
                                       SEEEEEE--HHHHHHHHHHHTTS CS
                            AAA_17 103 daiilleadpeeilerrlkdrtr 125
                                       d +  +  ++ e+++  l + t+
  gi|298675726|ref|YP_003727476.1| 334 DEVMNFPLPDMEMRKMILDRVTS 356
                                       44444444444555555554444 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1     0.002       1.4      34      56 ..     210     232 ..     181     248 .. 0.76
   2 ?    3.9   0.0      0.05        35     123     177 ..     251     304 ..     230     324 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.002
                            AAA_25  34 elallaGapgtGKttlaldlala 56 
                                       +  ll+GapgtGKt +a  +++ 
  gi|298675726|ref|YP_003727476.1| 210 GKLLLIGAPGTGKTSVARAVSHR 232
                                       55799**********99777765 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.05
                            AAA_25 123 gtlltadvdaleaaieevegvrlvviDplsralggdensnsdv.galvealeriar 177
                                       g++ +  +d++   +++  ++ ++ iD ++++      ++s++ +++v+ l +  +
  gi|298675726|ref|YP_003727476.1| 251 GET-AKNIDRVFTLAKR-LNPCVLFIDEFDFVAKKRTSDESAAlKRAVNTLLKAID 304
                                       444.4678889988888.56***********9999666666655776666654444 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00012     0.083       1      23 [.     218     240 ..     218     265 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00012
                                       TTSSHHHHHHHHHHHHTSEEEEH CS
                               SKI   1 mGaGKstvGkllAkklglefiDl 23 
                                       +G+GK++v+++++++l+l+f+++
  gi|298675726|ref|YP_003727476.1| 218 PGTGKTSVARAVSHRLSLPFVEV 240
                                       69******************985 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   0.00014     0.094      24      45 ..     211     232 ..     191     323 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                      Mg_chelatase  24 nlllvGppGsGKtmlakrlpsl 45 
                                       +lll+G+pG+GKt +a++++  
  gi|298675726|ref|YP_003727476.1| 211 KLLLIGAPGTGKTSVARAVSHR 232
                                       79**************998764 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00015       0.1      11      63 ..     197     247 ..     187     253 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                                       HHHHHHHHCTSS.S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-T CS
                   Sigma54_activat  11 lleqikkvaktd.lsvlitGesGtGKellaraiheaskrkekpfvavncaaipe 63 
                                        +e++k++  +d  ++l+ G  GtGK+ +ara+   s+r + pfv+v  + +++
  gi|298675726|ref|YP_003727476.1| 197 YREHLKTIGMYDiGKLLLIGAPGTGKTSVARAV---SHRLSLPFVEVRLSMVTD 247
                                       56677777777755899**************98...455667888887766655 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   0.00028      0.19      12      34 ..     211     233 ..     201     314 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00028
                            AAA_19  12 vllvtaGpGtGKTrvlkhivall 34 
                                        ll+++ pGtGKT v +++ + l
  gi|298675726|ref|YP_003727476.1| 211 KLLLIGAPGTGKTSVARAVSHRL 233
                                       589**********9987655444 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00035      0.24       2      33 ..     212     243 ..     211     351 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00035
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriqft 33 
                                       +ll g+PG++kt +++a+++ l+l f  +++ 
  gi|298675726|ref|YP_003727476.1| 212 LLLIGAPGTGKTSVARAVSHRLSLPFVEVRLS 243
                                       6999*******************999877653 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       8.2   5.7e+03      64     111 ..      27      56 ..      13      80 .. 0.54
   2 ?   11.9   0.0   0.00024      0.17       3      52 ..     179     237 ..     177     307 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 8.2
                                       HHHHHHHHHHGGGGTGG....GEEEESSS-B--.......-SEEEEEH CS
                            ResIII  64 kslleqtleefkkflseaykeigkkvsgdkkkakekdstnkkilvtti 111
                                       ++l +q ++++ +  ++++ +                   +++ v+ i
  gi|298675726|ref|YP_003727476.1|  27 NDLPKQIRKNYWDREKKTVPK------------------PINVSVSDI 56 
                                       455555555554443333322..................233333333 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00024
                                       EE-HHHHHHHHHHT......TTS..........EEEEEESTTSTHHHHHHHHHHHH-S.. CS
                            ResIII   3 elreyQeeaienlleklkskrdk..........rglikmaTGtGKTlvaaklierllkkg 52 
                                        l + Qe+ +e+++++++  r++          ++l+  a GtGKT va ++  rl+  +
  gi|298675726|ref|YP_003727476.1| 179 VLTDEQEDEVEKIVKAIQY-REHlktigmydigKLLLIGAPGTGKTSVARAVSHRLSLPF 237
                                       57899999999**999984.4444555555556****************99988887655 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00033      0.23      35      71 ..     211     246 ..     191     292 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00033
                             AAA_7  35 pvllvGptGtGKtviikdllkkldkekylsltinfsa 71 
                                       ++ll+G  GtGKt++++ + ++l+   ++ + +++  
  gi|298675726|ref|YP_003727476.1| 211 KLLLIGAPGTGKTSVARAVSHRLS-LPFVEVRLSMVT 246
                                       689***************999998.333333333333 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.015        10       3      24 ..     212     233 ..     211     239 .. 0.87
   2 ?    3.9   0.0     0.065        45      64     131 ..     252     321 ..     241     342 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.015
                                       EEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklalaw 24 
                                       ++l G++G GKT  ++ + + +
  gi|298675726|ref|YP_003727476.1| 212 LLLIGAPGTGKTSVARAVSHRL 233
                                       5899**********99987765 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.065
                                       S--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH.............HHHHHCTTTTT--EEEEEEECCC CS
                             NACHT  64 epaapvsevwavllelperlLlilDglDelvtdlgq....kekqpvrtlLselirkkllpeasllltvrpra 131
                                       e a+++++v+  l+++ +  +l +D +D ++++       + k++v+tlL + i + +l++  +ll++ ++ 
  gi|298675726|ref|YP_003727476.1| 252 ETAKNIDRVF-TLAKRLNPCVLFIDEFDFVAKKRTSdesaALKRAVNTLL-KAIDEVSLTNDGVLLIAATNH 321
                                       5566777744.4667777777889****9998777766655566666666.677778888887777776665 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00031      0.22      12      59 ..     199     244 ..     191     301 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00031
                                       HHHHHHH.T-SS-EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH CS
                   Sigma54_activ_2  12 erLeqaa.qsklpvfltGekGsgkelvArlLhknsgpwleifvverlak 59 
                                       e+L+ +  +    ++l+G++G+gk++vAr+ ++  +    +fv+ rl+ 
  gi|298675726|ref|YP_003727476.1| 199 EHLKTIGmYDIGKLLLIGAPGTGKTSVARAVSHRLS---LPFVEVRLSM 244
                                       56666653455579****************987544...3555555554 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00026      0.18       5      41 ..     213     249 ..     210     334 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00026
                                       EEEE-TTSSHHHHHHHHHHHSSS-EEEEEHHHHHHHS CS
                               CPT   5 lLnGgsssGKsslaralqevldepwlhlgvDafveal 41 
                                       lL G++ +GK+s+ara+ + l  p++++ +   +++ 
  gi|298675726|ref|YP_003727476.1| 213 LLIGAPGTGKTSVARAVSHRLSLPFVEVRLSMVTDQY 249
                                       899**********************876654443332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1092  (0.0609069); expected 358.6 (0.02)
Passed bias filter:                      748  (0.0417201); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.70u 0.33s 00:00:01.03 Elapsed: 00:00:00.48
# Mc/sec: 2637.28
//
Query:       gi|298675727|ref|YP_003727477.1|  [L=168]
Description: hypothetical protein Metev_1846 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00021   21.5   2.1    0.00032   20.9   2.1    1.4  1  DUF1922         Domain of unknown function (DUF1922)
  ------ inclusion threshold ------
      0.017   15.2   0.3      0.017   15.2   0.3    1.8  2  Zn-ribbon_8     Zinc ribbon domain
      0.028   14.3   1.1      0.058   13.3   1.1    1.5  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.032   14.0   2.3      0.097   12.4   2.4    1.8  2  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
       0.15   11.8   2.5       0.28   10.9   2.5    1.4  1  Ribosomal_S27e  Ribosomal protein S27
       0.27   11.0   2.9       0.72    9.6   2.9    1.7  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
       0.67    9.8   3.6         19    5.2   0.1    2.8  3  zf-HYPF         HypF finger


Domain annotation for each model (and alignments):
>> DUF1922  Domain of unknown function (DUF1922)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   2.1   1.2e-07   0.00032      13      64 ..      19      71 ..       4      74 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.2e-07
                                      EEETT-SEEEET.TTEEEE--SSS-BS--SSHHHHHHHHHHHSS---S-TTSS CS
                           DUF1922 13 YakegaktrkCv.CGktikvkerrilkkaedaeeAselVrklqeekyGltafk 64
                                        ++++kt kC  CG t++v + r + + ++ ++A  +  k+q +++G+ +++
  gi|298675727|ref|YP_003727477.1| 19 IENDNKKTTKCQnCGSTLNVDKLRFFYQCDNLDDAVSARTKVQSQIQGQEQIQ 71
                                      4578899999*55***********************************98876 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.3   6.7e-06     0.017       7      36 ..       8      36 ..       1      41 [. 0.68
   2 ?   -4.4   0.1         7   1.8e+04       6      10 ..      45      49 ..      45      49 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.7e-06
                       Zn-ribbon_8  7 rCeeCghefevlqsisdaplta.CPeCgsev 36
                                       C++C +   ++   +d+++t+ C +Cgs++
  gi|298675727|ref|YP_003727477.1|  8 VCTKCRQHAQIIE--NDNKKTTkCQNCGSTL 36
                                      3*****6666555..36667777******43 PP

  == domain 2  score: -4.4 bits;  conditional E-value: 7
                       Zn-ribbon_8  6 YrCee 10
                                      Y+C++
  gi|298675727|ref|YP_003727477.1| 45 YQCDN 49
                                      88975 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.1   2.3e-05     0.058      30      59 ..      11      39 ..       4      43 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.3e-05
                    OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfeadrD 59
                                      +C ++ ++ ++ ++++t kC+nCg +++ D
  gi|298675727|ref|YP_003727477.1| 11 KCRQHAQIIEN-DNKKTTKCQNCGSTLNVD 39
                                      56666666666.*************99977 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   2.4   3.8e-05     0.097      22      53 ..       6      35 ..       2      36 .. 0.81
   2 ?   -2.9   0.0       2.3     6e+03       2      14 ..     142     154 ..     142     163 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.8e-05
                    zinc_ribbon_10 22 alICskChshnGlapkeeleevkyrCpkCgal 53
                                       ++C+kC+ h     ++++++++ +C +Cg++
  gi|298675727|ref|YP_003727477.1|  6 VIVCTKCRQHAQII-ENDNKKTT-KCQNCGST 35
                                      489***********.66666665.9****985 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.3
                    zinc_ribbon_10   2 fDrvldvLvGdde 14 
                                       f++++d +  ++e
  gi|298675727|ref|YP_003727477.1| 142 FEKIIDSMFKTGE 154
                                       6899998887776 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.5   0.00011      0.28       8      36 ..       7      36 ..       3      38 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                                      EE-TTTS.-EEEEESS-SS-EEESSSTCEE CS
                    Ribosomal_S27e  8 vkCpdCe.netvvFshaatvvkCisCgkvL 36
                                      + C +C  + +++ +  ++  kC+ Cg++L
  gi|298675727|ref|YP_003727477.1|  7 IVCTKCRqHAQIIENDNKKTTKCQNCGSTL 36
                                      67****62679999999***********98 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.9   0.00028      0.72       3      25 ..       9      34 ..       8      36 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00028
                                      -SSS--B----SSS...----SSS-- CS
                    DNA_RNApol_7kD  3 CgeCgaevslkkgd...piRCkeCGh 25
                                      C +C +  +++++d     +C++CG+
  gi|298675727|ref|YP_003727477.1|  9 CTKCRQHAQIIENDnkkTTKCQNCGS 34
                                      *********98877333699*****6 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1    0.0073        19      17      27 ..       2      12 ..       1      19 [. 0.88
   2 ?    5.0   0.1    0.0081        21      21      31 ..      26      36 ..      24      38 .. 0.82
   3 ?   -2.6   0.0       1.9     5e+03      16      20 ..      42      46 ..      39      49 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0073
                                      TT-TT---TTT CS
                           zf-HYPF 17 fhaqfisCtnC 27
                                      f++  i Ct+C
  gi|298675727|ref|YP_003727477.1|  2 FRYAVIVCTKC 12
                                      89********* PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0081
                                      T---TTTS--E CS
                           zf-HYPF 21 fisCtnCGPrl 31
                                      ++ C nCG +l
  gi|298675727|ref|YP_003727477.1| 26 TTKCQNCGSTL 36
                                      578*****887 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.9
                                      TTT-T CS
                           zf-HYPF 16 Rfhaq 20
                                      Rf++q
  gi|298675727|ref|YP_003727477.1| 42 RFFYQ 46
                                      89998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1546  (0.086229); expected 358.6 (0.02)
Passed bias filter:                      708  (0.0394891); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1107.18
//
Query:       gi|298675728|ref|YP_003727478.1|  [L=140]
Description: ribosomal-protein-alanine acetyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-16   61.2   0.1    1.2e-16   61.0   0.1    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    4.6e-12   46.2   0.6    6.3e-12   45.8   0.6    1.1  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
      2e-11   43.9   0.1    2.4e-11   43.6   0.1    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    0.00097   19.3   0.7    0.00097   19.3   0.7    1.5  2  Acetyltransf_4   Acetyltransferase (GNAT) domain
     0.0012   18.9   0.0      0.014   15.5   0.0    2.1  1  Acetyltransf_9   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0   0.1   3.4e-20   1.2e-16       3     117 .]      12     117 ..      10     117 .. 0.95

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 3.4e-20
                                       HHHHHHHHHTHHHHHHHHHHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHH CS
                    Acetyltransf_1   3 dlvellvesffppnedaseeefeesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGs 79 
                                       ++ e++++sf +p++d  ++   +     ++g++v+e+++ ++G++ + ++ +    +a+i  +aV+p+y+++ +Gs
  gi|298675728|ref|YP_003727478.1|  12 AVLEIEELSFQIPWPDYLFRT--IL---GNPGFVVYEKNNIIVGYVVIDIVKN----YAHIANIAVHPKYHRMKIGS 79 
                                       6889999**99********99..77...889***************9999988....9******************* PP

                                       HHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  80 aLlealeerareegikkivlaveedndaairlYeklGF 117
                                        L++ +  + +++g++++ l+v+e n  a+r+Y + GF
  gi|298675728|ref|YP_003727478.1|  80 YLINWCKLFGKKRGADALILEVREKNINAQRFYHENGF 117
                                       *********************************88998 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.6   1.8e-15   6.3e-12       5      74 ..      39     117 ..      35     119 .. 0.74

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 1.8e-15
                                       EEEEEETTEEEEEEEEEEES..TCTEEEEE-GGGTTSSHHHHHHHH.....TTSEEE..EE.EEEETHH.HHHHHHH CS
                    Acetyltransf_7   5 vfVaeddgkivGfialslld..aeitrlaVdpeyrgkGiGraLlea.....aekgii..le.qlelnae.kaikfYe 70 
                                       + V+e+++ ivG++++ +++  a+i ++aV+p+y++  iG+ L++      +++g    l+ +++ + + +a++fY 
  gi|298675728|ref|YP_003727478.1|  39 FVVYEKNNIIVGYVVIDIVKnyAHIANIAVHPKYHRMKIGSYLINWcklfgKKRG-AdaLIlEVREK-NiNAQRFYH 113
                                       66788889999****999999999999******************6444432244.13322222333.2489***** PP

                                       HTTE CS
                    Acetyltransf_7  71 klGF 74 
                                        +GF
  gi|298675728|ref|YP_003727478.1| 114 ENGF 117
                                       **** PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.1   6.8e-15   2.4e-11      33     106 ..      39     117 ..      28     137 .. 0.92

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 6.8e-15
                   Acetyltransf_10  33 llvaeeggkivGvi..el.rdgshisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYekl 104
                                       ++v+e+++ ivG++   + ++  hi+ ++V+p+y++ +ig+ L++ ++   +k+g     l+v++++ +a++fY+  
  gi|298675728|ref|YP_003727478.1|  39 FVVYEKNNIIVGYVviDIvKNYAHIANIAVHPKYHRMKIGSYLINWCKLFGKKRGADAlILEVREKNiNAQRFYHEN 115
                                       78999999999*98777778888***************************999999999****************** PP

                   Acetyltransf_10 105 GF 106
                                       GF
  gi|298675728|ref|YP_003727478.1| 116 GF 117
                                       *9 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.71   2.6e+03       1      16 [.       2      17 ..       2      23 .. 0.85
   2 !   19.3   0.7   2.7e-07   0.00097      52     144 ..      39     127 ..      29     133 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.71
                    Acetyltransf_4  1 iraateeDakeilaiy 16
                                      ir a+++D+ + l+i 
  gi|298675728|ref|YP_003727478.1|  2 IRKAKKSDISAVLEIE 17
                                      8999999*99999886 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 2.7e-07
                    Acetyltransf_4  52 flvae.sdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiq 127
                                       f v+e +  ivGy  +  +k   + + a + v     +   + +g+ li+ ++ + k+ +   l  e+  +n+n++ 
  gi|298675728|ref|YP_003727478.1|  39 FVVYEkNNIIVGYVVIDIVKN--YAHIANIAVHP---KYHRMKIGSYLINWCKLFGKKRGADALILEVREKNINAQR 110
                                       789998899999999998887..88887777766...47899**********9999********************* PP

                    Acetyltransf_4 128 fhkalGFelvgifkkci 144
                                       f+ + GF + gi+ +++
  gi|298675728|ref|YP_003727478.1| 111 FYHENGFYIKGIVPEYY 127
                                       ***********998876 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   3.9e-06     0.014       2      96 ..       2      83 ..       1     119 [. 0.85

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.9e-06
                                      EEEE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEEEE CS
                    Acetyltransf_9  2 irelteedldevlellkyaFqdeespleeireyfrklleesrvlgaedngelvgqlallplelnvpGktlkaagvtgVa 80
                                      ir+++++d+ +vle+ + +Fq   ++     + fr +l++  +++ e+n+ +vg + +        +   ++a ++ +a
  gi|298675728|ref|YP_003727478.1|  2 IRKAKKSDISAVLEIEELSFQIPWPD-----YLFRTILGNPGFVVYEKNNIIVGYVVI--------DIVKNYAHIANIA 67
                                      8************************9.....68*********************8755........6667889999999 PP

                                      E-CCGTTS-HHHHHHH CS
                    Acetyltransf_9 81 vapehrgrgvlskLla 96
                                      v+p++ + ++ s L++
  gi|298675728|ref|YP_003727478.1| 68 VHPKYHRMKIGSYLIN 83
                                      9999999988777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1028.56
//
Query:       gi|298675729|ref|YP_003727479.1|  [L=221]
Description: Di-trans-poly-cis-decaprenylcistransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.3e-29  101.1   0.0    7.8e-27   94.3   0.0    2.0  2  Prenyltransf  Putative undecaprenyl diphosphate synthase


Domain annotation for each model (and alignments):
>> Prenyltransf  Putative undecaprenyl diphosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.0   0.00078        14      22      47 ..      39      64 ..      32      86 .. 0.90
   2 !   94.3   0.0   4.3e-31   7.8e-27      94     224 .]      91     220 ..      76     220 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.00078
                                      HHHHHHHHHHHHHHHHTT-SEEEEEE CS
                      Prenyltransf 22 kaGaealkeilelclelgvkvvtvYa 47
                                      k G+++l +++ +  +lg++++++Y+
  gi|298675729|ref|YP_003727479.1| 39 KDGLSKLFSVILWYRKLGINIISIYV 64
                                      67999********************6 PP

  == domain 2  score: 94.3 bits;  conditional E-value: 4.3e-31
                                       GS-HHHHHHHHHHHHHHT...TTTSEEEEEEEEE-HHHHHHHHHHHHHHTT..SSSG.GGHSHHHHHCTSTT..TSS CS
                      Prenyltransf  94 llpedvlealekaeeatkk..nnkklvlniavnYgsrdeiveavrelvkekseekkk.eeideetlekhlytakalp 167
                                       +lp+dv  ++ +     kk  + +++++ + + +g+++ei++avr++++++s++k + e+ide+++e++l +  +  
  gi|298675729|ref|YP_003727479.1|  91 RLPKDVGFEIYDNNGYLKKehKGSSMHVYLFLGFGGKSEITNAVRSVLSDVSSQKIDpEDIDENEIESRLLV--K-H 164
                                       5666665555554444443114456***********************99988877768899*********9..4.6 PP

                                       S-SEEEEESS--S-TTSSTTTTTT-EEEEESSSGGG--HHHHHHHHHHHHHCHHHTT CS
                      Prenyltransf 168 dpDlliRtsGeeRlSnFllwqlayselyfldvlWPdfskedllealleyqkrerrfg 224
                                       +pD++iR +G++ lS+Fl+wq++yselyf+dv W +++k d+++a++++qkr+r+fg
  gi|298675729|ref|YP_003727479.1| 165 EPDMIIRAGGKN-LSDFLIWQSVYSELYFTDVNWDKVRKIDMIRAIRDFQKRQRKFG 220
                                       7*******9976.******************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1544.83
//
Query:       gi|298675730|ref|YP_003727480.1|  [L=393]
Description: GTPase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.8e-33  113.8   0.3    1.3e-32  112.7   0.2    1.7  2  MMR_HSR1_C    GTPase of unknown function C-terminal
    2.3e-18   66.3   0.0    1.5e-17   63.7   0.0    2.2  2  MMR_HSR1      50S ribosome-binding GTPase
    5.2e-14   52.0   0.0    1.1e-13   51.0   0.0    1.5  1  TGS           TGS domain
    4.5e-10   39.3   1.2    6.7e-07   29.0   0.0    2.7  3  FeoB_N        Ferrous iron transport protein B
      0.005   16.8   0.3      0.012   15.6   0.3    1.6  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
  ------ inclusion threshold ------
      0.022   14.5   0.4       0.39   10.5   0.1    2.2  2  ATP_bind_1    Conserved hypothetical ATP binding protein
      0.077   12.8   0.3        1.2    8.9   0.1    2.4  2  NOG1          Nucleolar GTP-binding protein 1 (NOG1)


Domain annotation for each model (and alignments):
>> MMR_HSR1_C  GTPase of unknown function C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       5.1   1.3e+04      66      91 ..     153     178 ..     145     186 .. 0.70
   2 !  112.7   0.2   5.2e-36   1.3e-32       1     112 []     220     323 ..     220     323 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 5.1
                        MMR_HSR1_C  66 ldekqkkaLekirdlvlkrygsTGVq 91 
                                       l++k k++  k+++ + ++ g+ GV+
  gi|298675730|ref|YP_003727480.1| 153 LSRKIKAENLKLEEALANQLGGAGVS 178
                                       56666666667777777788888876 PP

  == domain 2  score: 112.7 bits;  conditional E-value: 5.2e-36
                        MMR_HSR1_C   1 alNKaDlpaadenieklkekypkdkkvvpvsAaaElaLrkaakqglikYepgdedfeikedklkeldekqkkaLeki 77 
                                       a+NK+D+ a++eniekl + +    +vv +sAaaE+aL++a+k+++ikY pg++df+i  +   +++++qkk +e++
  gi|298675730|ref|YP_003727480.1| 220 AANKIDV-ASEENIEKLLNLDI---MVVSTSAAAEFALKSASKNNAIKYLPGSDDFTIISE---NMTKEQKKGIEDL 289
                                       89*****.************88...7********************************776...59*********** PP

                        MMR_HSR1_C  78 rdlvlkrygsTGVqealnaavfelldlivVYPVed 112
                                       rd +lk+ g+TGVqe++n+avf+lld+++VYPVed
  gi|298675730|ref|YP_003727480.1| 290 RD-FLKSRGGTGVQECINRAVFDLLDMVIVYPVED 323
                                       **.9*****************************97 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.7   0.0   5.7e-21   1.5e-17       2      87 ..       5     118 ..       4     152 .. 0.79
   2 ?   -0.3   0.1      0.44   1.1e+03      31      53 ..     186     209 ..     166     278 .. 0.62

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 5.7e-21
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE.....................EEEEECGGCS CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke.....................ielvDtpGli 57 
                                       ++++G+pN+GKSt++++ t + + ++++p+tT+  n+g   ++  e                     +e++D++Gl+
  gi|298675730|ref|YP_003727480.1|   5 IGLAGKPNSGKSTFFKSATMADVDIANYPFTTISANHGVTYVRT-EcpcmklnqrcgncvegirfvpVEVIDVAGLV 80 
                                       89************************************776432.2345555556666777777777********99 PP

                                       SHHHHHHHHHHHHHHHHC.TSEEEEEEETT.......T CS
                          MMR_HSR1  58 egaseekglgkaflalee.adlillvvdas.......e 87 
                                        +a +++glg+afl+  + a++i++v+das       +
  gi|298675730|ref|YP_003727480.1|  81 PDAWKGRGLGNAFLDELRqAKAIIHVIDASgstdiegN 118
                                       9999999*******977669********9865554440 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.44
                                       TSSSSEEEEEEEETT.EEEEEEEC CS
                          MMR_HSR1  31 gtTrdinegrvklkg.keielvDt 53 
                                        +T +  + +vk+ + + ++l+D 
  gi|298675730|ref|YP_003727480.1| 186 LVTSELSRNHVKWTDdNLVTLCDN 209
                                       455555555555444344455553 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.0   4.3e-17   1.1e-13      10      59 ..     334     389 ..     327     390 .. 0.87

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 4.3e-17
                                       EEE....EETTB-HHHHHHHHSTTHHHHEEEEEECS..EEEETTSBB-SSEEEEEE CS
                               TGS  10 vpd....lprgatveDfAykIhrslakkfiyAlVnG..qrvgldhvLedgdvveIv 59 
                                       +      ++rg+t+ D+Ay++h++++++f+yA      +r g +h+L++gdvv+Iv
  gi|298675730|ref|YP_003727480.1| 334 ILPdaylMKRGSTPHDLAYQVHSDIGDHFLYAVDGRtrMRMGEKHELDNGDVVKIV 389
                                       43336669************************887799*****************9 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   2.6e-10   6.7e-07       1      43 [.       3      45 ..       3      53 .. 0.91
   2 ?   -3.4   0.0       2.4   6.2e+03      78      89 ..      99     110 ..      95     111 .. 0.83
   3 !    8.4   0.1   0.00055       1.4      96     148 ..     205     252 ..     187     261 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 2.6e-10
                                      EEEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEE CS
                            FeoB_N  1 itvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklk 43
                                      it+ l+G+pn+Gk+t+f + t a+ +++N+p +t+  ++g + 
  gi|298675730|ref|YP_003727480.1|  3 ITIGLAGKPNSGKSTFFKSATMADVDIANYPFTTISANHGVTY 45
                                      5899********************************9999775 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.4
                                       SSSEEEEEEEGG CS
                            FeoB_N  78 epdvvvnvvdat 89 
                                       +++++++v+da+
  gi|298675730|ref|YP_003727480.1|  99 QAKAIIHVIDAS 110
                                       6789999*9996 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.00055
                                       HHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBT CS
                            FeoB_N  96 yLtlqllelgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkeg 148
                                       +L  ++  +++pv++a n+id+a++++ie    kL  +L++ vv+tsa+ +  
  gi|298675730|ref|YP_003727480.1| 205 TLCDNIRSISKPVIVAANKIDVASEENIE----KLL-NLDIMVVSTSAAAEFA 252
                                       4666788999**************99874....443.5888999998887655 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.3   4.6e-06     0.012      40      91 ..     198     251 ..     175     260 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.6e-06
                      MMR_HSR1_Xtn  40 vtvDdlidvieg.nrvYipclyvlNKiDlisleeldelarep.nsvviSaekel 91 
                                        t D+l+    +     +p++++ NKiD +s+e++++l + +  +v +Sa+ e+
  gi|298675730|ref|YP_003727480.1| 198 WTDDNLVTLCDNiRSISKPVIVAANKIDVASEENIEKLLNLDiMVVSTSAAAEF 251
                                       5678888777773446789*******************9974244446666555 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.066   1.7e+02       2      16 ..       8      22 ..       7      30 .. 0.87
   2 ?   10.5   0.1   0.00015      0.39     129     233 ..     186     291 ..     180     299 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.066
                        ATP_bind_1  2 vGpaGsGKttfvgal 16
                                      +G + sGK+tf ++ 
  gi|298675730|ref|YP_003727480.1|  8 AGKPNSGKSTFFKSA 22
                                      79999******9875 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00015
                        ATP_bind_1 129 LvDsqrltdptkfisgllsal.samlrlelPhvvvlnkfDllkeklekeleffedvealslllekee...ekykkla 201
                                       Lv s+ +++ +k+ +  l++l   + +++ P +v+ nk+D+++   e+++e + +++ +   +        k ++ +
  gi|298675730|ref|YP_003727480.1| 186 LVTSELSRNHVKWTDDNLVTLcDNIRSISKPVIVAANKIDVAS---EENIEKLLNLDIMVVSTSAAAefaLKSASKN 259
                                       677777788888887766665055556899***********88...6777777777666555554445666667777 PP

                        ATP_bind_1 202 eaiaelleefalvlrflplssekeesiedlls 233
                                       +ai+ l    + ++    +  e++++iedl +
  gi|298675730|ref|YP_003727480.1| 260 NAIKYLPGSDDFTIISENMTKEQKKGIEDLRD 291
                                       88877777777776677777777788877765 PP

>> NOG1  Nucleolar GTP-binding protein 1 (NOG1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.13   3.3e+02      14      27 ..     100     113 ..      94     116 .. 0.85
   2 ?    8.9   0.1   0.00048       1.2      36      58 .]     205     225 ..     201     225 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.13
                              NOG1  14 adavlFllDpseec 27 
                                       a+a++ ++D+s++ 
  gi|298675730|ref|YP_003727480.1| 100 AKAIIHVIDASGST 113
                                       579********975 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00048
                              NOG1  36 sLleeikelfankpvivvlnKiD 58 
                                        L+++i++  + kpviv++nKiD
  gi|298675730|ref|YP_003727480.1| 205 TLCDNIRSI-S-KPVIVAANKID 225
                                       799999988.4.8*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.71u 0.33s 00:00:01.04 Elapsed: 00:00:00.56
# Mc/sec: 2131.52
//
Query:       gi|298675731|ref|YP_003727481.1|  [L=139]
Description: hypothetical protein Metev_1850 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 866.14
//
Query:       gi|298675732|ref|YP_003727482.1|  [L=1017]
Description: FAD linked oxidase domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-38  130.1   0.2    2.3e-37  127.8   0.1    2.0  2  FAD_binding_4  FAD binding domain
    2.6e-31  107.7   1.8    8.8e-16   57.9   0.3    2.7  2  CCG            Cysteine-rich domain
    4.3e-09   36.8   6.9    1.6e-08   35.0   6.9    2.1  1  Fer4_17        4Fe-4S dicluster domain
    3.1e-06   27.5   6.2      8e-06   26.2   6.2    1.7  1  Fer4_8         4Fe-4S dicluster domain
    0.00074   19.6   2.3    0.00074   19.6   2.3    2.3  2  Fer4_9         4Fe-4S dicluster domain
     0.0014   19.2   5.4     0.0014   19.2   5.4    1.9  2  Fer4_7         4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.42   10.7  10.4       0.91    9.7   8.4    2.6  2  Fer4_10        4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.8   0.1   9.1e-41   2.3e-37       1     138 [.      54     192 ..      54     193 .. 0.98
   2 ?   -0.5   0.0      0.37   9.5e+02       7      28 ..     230     251 ..     227     254 .. 0.88

  Alignments for each domain:
  == domain 1  score: 127.8 bits;  conditional E-value: 9.1e-41
                                       EEEEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTC.SCCEEEEEETTS--EEEEETTTTEEEEETTSBHHH CS
                     FAD_binding_4   1 paavvrpeseeevaaalrlaneaglpvlvrGgGssllgqav.atggvvldlsrlnrileideeegtatveaGvtlgd 76 
                                       p+avv++e+e+e ++++++an++++pv++r+g ss  g+++ ++gg+v d++ +n+i +id e+  atv+aG+++++
  gi|298675732|ref|YP_003727482.1|  54 PSAVVKVENEDEAVKLIKFANKYNIPVVPRAGASSGYGGVIpTKGGIVADITTMNQIQDIDHENLKATVGAGIRWER 130
                                       79***************************************99********99************************ PP

                                       HHHHHHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSEEEEE CS
                     FAD_binding_4  77 lvealaakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGevvrl 138
                                       l++ l+ +gl ++  p+s  ++tvGG++a+n++G gs  yG ++++ ++++vvl++Gev ++
  gi|298675732|ref|YP_003727482.1| 131 LEKKLNNQGLSVQALPTSAPSSTVGGWLAQNGIGFGSFEYGWSQNTMESARVVLPTGEVKEF 192
                                       ***********************************************************987 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.37
                                       ESSHHHHHHHHHHHHHCTSCEE CS
                     FAD_binding_4   7 peseeevaaalrlaneaglpvl 28 
                                        +++e +++a++ a+e+++p++
  gi|298675732|ref|YP_003727482.1| 230 FKDAESLKKAIHSADEQNIPLW 251
                                       68999***************97 PP

>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.1   2.8e-16   7.2e-13       1      83 [.     638     720 ..     638     722 .. 0.97
   2 !   57.9   0.3   3.4e-19   8.8e-16       1      85 []     766     853 ..     766     853 .. 0.98

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 2.8e-16
                               CCG   1 vayfdgChllraaypevrkalkkllealgveleel.ekesCCGagggrsgkeelaealakrnvetaeetgadaivta 76 
                                       + yf gC  +    ++    +++ l  + +++ +l +kesCCG +   +gk +++e+++k+n+++++++g++ ++t 
  gi|298675732|ref|YP_003727482.1| 638 YGYFAGC-TASFVEKDIAVGTARMLDDADIDFTVLgDKESCCGIPMLMAGKWDVFEKIMKMNISNMKSKGVETVITS 713
                                       67*****.89999**************************************************************** PP

                               CCG  77 cpgCllq 83 
                                       cp C ++
  gi|298675732|ref|YP_003727482.1| 714 CPACWMM 720
                                       ****887 PP

  == domain 2  score: 57.9 bits;  conditional E-value: 3.4e-19
                               CCG   1 vayfdgChllraa..ypevrkalkkllealgveleel.ekesCCGagggrsgkeelaealakrnvetaeetgadaiv 74 
                                       v+++d+Ch++ra   y+ +r++lk ++++++ ele + +k+ CCG+  +     ++a ++a+ ++++a++++ad+++
  gi|298675732|ref|YP_003727482.1| 766 VTWHDSCHIGRAGgvYEPPRQLLKSVPGVEFKELENNrDKAHCCGSVMTLVADPHVAHNVANIRLDEAKDVNADVVA 842
                                       89**************************************************999********************** PP

                               CCG  75 tacpgCllqlk 85 
                                       t cp Cl+q++
  gi|298675732|ref|YP_003727482.1| 843 TLCPCCLVQFR 853
                                       ********985 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   6.9   6.2e-12   1.6e-08       2      60 ..     509     574 ..     508     575 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 6.2e-12
                           Fer4_17   2 CiqCgyClpeCpsyeaydnepkkllraakl.....glleeaeke..ekaslCieCgeCerkCPqgl 60 
                                       C+qCgyC+ eC +y+ +++e ++++ ++ +     +  +e  +   +++ +C++C++C+++C  ++
  gi|298675732|ref|YP_003727482.1| 509 CSQCGYCVSECDQYYGRGWESQSPRGKWFFikeylAGRDELDQGqtNTFLSCTTCEMCDTRCELNM 574
                                       ***************************9777776633444433334799*************8765 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   6.2   3.1e-09     8e-06       3      63 ..     507     572 ..     505     574 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 3.1e-09
                            Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaae.....dvqeeqvlee..eealwsCttcgaCtevCpv 63 
                                       ++C +Cg+C s+C  +  ++ +++++rg+          ++e    +   +++ sCttc++C+++C  
  gi|298675732|ref|YP_003727482.1| 507 YSCSQCGYCVSECDQYYGRGWESQSPRGKWFFikeylAGRDELD--QgqTNTFLSCTTCEMCDTRCEL 572
                                       68******************999999999887666542222222..255899**************75 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   2.3   2.9e-07   0.00074       2      48 ..     509     572 ..     508     575 .. 0.70
   2 ?   -2.8   0.0         3   7.7e+03      10      22 ..     712     724 ..     708     730 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.9e-07
                            Fer4_9   2 CtgCgaCveaC..............pagvvvedaaerkarlraase.........eaCigCgaCveaCpk 48 
                                       C +Cg+Cv+ C               ++ ++++  ++ +      e          +C++C+ C  +C+ 
  gi|298675732|ref|YP_003727482.1| 509 CSQCGYCVSECdqyygrgwesqsprGKWFFIKEYLAGRD------EldqgqtntfLSCTTCEMCDTRCEL 572
                                       ***********9998888866665533444444444444......144444578878***********75 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3
                            Fer4_9  10 eaCpagvvvedaa 22 
                                       ++Cpa+ ++ +++
  gi|298675732|ref|YP_003727482.1| 712 TSCPACWMMWHDV 724
                                       4688887777666 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   5.4   5.5e-07    0.0014       1      49 [.     508     571 ..     508     574 .. 0.72
   2 ?   -4.1   0.1         7   1.8e+04      11      20 ..     713     722 ..     711     727 .. 0.63

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 5.5e-07
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgt.....ekv...........eidpekClgCgaCvavCP 49 
                                       +C +Cg+Cv+ C ++  + +e+++++g+     e +           +    +C++C++C ++C 
  gi|298675732|ref|YP_003727482.1| 508 SCSQCGYCVSECDQYYGRGWESQSPRGKwffikE-YlagrdeldqgqTNTFLSCTTCEMCDTRCE 571
                                       5************999999999999975555531.244444444333334568***********5 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 7
                            Fer4_7  11 aCpvkaield 20 
                                        Cp+ +++++
  gi|298675732|ref|YP_003727482.1| 713 SCPACWMMWH 722
                                       4666666665 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   8.4   0.00035      0.91       7      55 ..     507     570 ..     501     571 .. 0.82
   2 ?   -1.7   0.0       1.3   3.2e+03      42      48 ..     711     717 ..     694     736 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00035
                           Fer4_10   7 dtCirCgkCvkaCPadl.................tsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                        +C +Cg Cv+ C  d                   +    g ++ ++ +     +Ct+c++C   C
  gi|298675732|ref|YP_003727482.1| 507 YSCSQCGYCVSEC--DQyygrgwesqsprgkwffIKEYLAGRDELDQGQTNTFLSCTTCEMCDTRC 570
                                       58***********..6667**************855555666666666666899********9999 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.3
                           Fer4_10  42 vekCtgc 48 
                                       + +C++c
  gi|298675732|ref|YP_003727482.1| 711 ITSCPAC 717
                                       4445444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1017 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      606  (0.0338); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.79u 0.30s 00:00:01.09 Elapsed: 00:00:00.46
# Mc/sec: 6598.54
//
Query:       gi|298675733|ref|YP_003727483.1|  [L=555]
Description: thermosome [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   4.8e-182  606.0  21.7   5.5e-182  605.8  21.7    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  605.8  21.7  3.1e-186  5.5e-182       1     489 [.      43     532 ..      43     534 .. 0.99

  Alignments for each domain:
  == domain 1  score: 605.8 bits;  conditional E-value: 3.1e-186
                                       HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHH CS
                        Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleea 77 
                                       +a++v++tlGP GmdKmlv+++g+vv+TnDGatilke++iehPaak++ve+a++qd+evGDGTt+++++ageLl++a
  gi|298675733|ref|YP_003727483.1|  43 VANAVRSTLGPIGMDKMLVDSMGDVVITNDGATILKEMDIEHPAAKMIVEVAKTQDDEVGDGTTSATVIAGELLKKA 119
                                       689************************************************************************** PP

                                       HHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHCHC CS
                        Cpn60_TCP1  78 ekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvklie 154
                                       e+l+++gvhpt i +gy+ a++ka e+++ei  +++++ +d+e+L+k+a+t++++k  ++ ++ l++l vdAvk++ 
  gi|298675733|ref|YP_003727483.1| 120 EELLDDGVHPTIIASGYRNAADKAAEYINEI--AVDVSPDDTETLKKIASTAITGKGGEEYKDTLAQLSVDAVKAVS 194
                                       *******************************..7777788*********************************7777 PP

                                       CCS...EECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCC CS
                        Cpn60_TCP1 155 ene...keldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdae 228
                                       e++   +++d ++ik++k  ggs++dsel++G+v+dk+ l+++mpkk+enakvlll+ ++e++kte+++++++++++
  gi|298675733|ref|YP_003727483.1| 195 EKTesgTSVDTDEIKIEKHAGGSMRDSELINGVVIDKERLHTNMPKKVENAKVLLLSAPIEFQKTEMDAEIKITSPD 271
                                       7777*99********************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGG CS
                        Cpn60_TCP1 229 eleklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledlt 305
                                       ++++++++eek+++++++kii+sg++vv+cqkgidd+a+h+l+k+gi+alrrvk++d++rlakatGa++v+++++++
  gi|298675733|ref|YP_003727483.1| 272 QMQQFLDQEEKMIKDMVDKIINSGADVVFCQKGIDDMAQHYLQKEGIFALRRVKQSDMDRLAKATGANIVQDVDEIS 348
                                       ***************************************************************************** PP

                                       CGC-EEEEEEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHH CS
                        Cpn60_TCP1 306 peelGtakkveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatele 382
                                       +++lG+a++vee++++ +k+t++++++s+k+++++l g t++v+d +e a++dAl+vv  a+ed+kvv+GGGa+e+e
  gi|298675733|ref|YP_003727483.1| 349 ESDLGSAGNVEEKDVSGTKMTYVTDCESQKSVSVILHGGTEHVVDSLEIALNDALRVVGVAVEDGKVVVGGGASEVE 425
                                       ***************************************************************************** PP

                                       HHHHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTX CS
                        Cpn60_TCP1 383 lakklkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveagv 459
                                       la kl +ya s++g+eqla+++fa+AL +ip+tLaeNaGld+i+ l +lr++h+kg+k +g+dv++gei++++e+ v
  gi|298675733|ref|YP_003727483.1| 426 LAMKLYNYAASLEGREQLAAHKFAEALDIIPQTLAENAGLDAIDKLVELRSQHEKGNKYAGLDVRNGEIVNMWEDDV 502
                                       ***************************************************************************** PP

                                       EEEHHHHHHHHHHHHHHHHHHHCEEEEEXX CS
                        Cpn60_TCP1 460 vDplkvkrqalksAteaastiLrideiika 489
                                       ++pl++k+qa+++Ateaa +iLrid+++ +
  gi|298675733|ref|YP_003727483.1| 503 IEPLRIKTQAINAATEAAVMILRIDDVVAT 532
                                       ***************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (555 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.54
# Mc/sec: 3079.80
//
Query:       gi|298675734|ref|YP_003727484.1|  [L=226]
Description: TrkA-C domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.7e-14   51.5   0.1    1.1e-13   50.8   0.1    1.4  1  TrkA_C           TrkA-C domain
    7.3e-05   22.7   0.0    0.00013   21.9   0.0    1.4  1  Castor_Poll_mid  Castor and Pollux, part of voltage-gated ion
  ------ inclusion threshold ------
       0.21   11.6   2.6        1.2    9.1   0.3    2.1  2  Halogen_Hydrol   5-bromo-4-chloroindolyl phosphate hydrolysis
       0.69    8.6   2.8       0.88    8.3   2.8    1.2  1  DUF2207          Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.1   2.4e-17   1.1e-13       1      64 [.     158     222 ..     158     226 .] 0.94

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 2.4e-17
                                       CEEEEEE--GGGTTSBHHHHTHHHHS-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHH CS
                            TrkA_C   1 lvevtvpagsplvGktlkelnlrargvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlae 64 
                                       l++v v+++s l G++l +l+l +++ lv++i R+ +++ +p +d v++e+D+l+v+g+ ++l+ 
  gi|298675734|ref|YP_003727484.1| 158 LIRVIVKEDSILSGTSLNDLKLSEKNLLVIGIERNgEWISVPKSDEVIKENDRLVVYGPLNALKS 222
                                       6799****************************9999**********************9998875 PP

>> Castor_Poll_mid  Castor and Pollux, part of voltage-gated ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0     3e-08   0.00013      32      91 ..     161     218 ..     144     225 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 3e-08
                   Castor_Poll_mid  32 fylkelpelegkkyedvllafqeavviGikvassgkiylnPeddevlqegdkllviaedd 91 
                                       + +ke + l+g++ +d++l+ ++  viGi   ++g+ +  P++dev++e+d+l+v ++ +
  gi|298675734|ref|YP_003727484.1| 161 VIVKEDSILSGTSLNDLKLSEKNLLVIGI--ERNGEWISVPKSDEVIKENDRLVVYGPLN 218
                                       56788899*********************..899*********************98876 PP

>> Halogen_Hydrol  5-bromo-4-chloroindolyl phosphate hydrolysis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.024   1.1e+02      15      66 ..       7      60 ..       3      65 .. 0.58
   2 ?    9.1   0.3   0.00026       1.2       7      45 ..      81     119 ..      71     184 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.024
                    Halogen_Hydrol 15 alvsffllgfsfflallia.ilggilvyvasrknkkkkhlkk....sglsrkelkyi 66
                                      + ++ +l  f++fl+   + + +++l++ +  +++++ +        g+++ke ++i
  gi|298675734|ref|YP_003727484.1|  7 FPFTTLLVIFTSFLI---VrASSIALMMTGLDQKRSRFQALSaftgTGFTTKEAELI 60
                                      334444433444444...546666666666665566655555788888888888776 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00026
                    Halogen_Hydrol   7 siliavivalvsffllgfsfflalliailggilvyvasr 45 
                                       +++++v++  +++++ gf++ + ++i++lg+++vy    
  gi|298675734|ref|YP_003727484.1|  81 IVTVIVTMTSTVVVSEGFQIPINIVILFLGLVVVYKIAT 119
                                       3334444445677788999999999*********98765 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   2.8    0.0002      0.88     367     451 ..      55     141 ..       5     143 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0002
                           DUF2207 367 kergyfdkkg..kkklkklsalglgliilglilillallllvlllvfllilllillliaiivlllfsrllgrrteeG 441
                                       ke +++ +++  ++++ +l +lg ++i+ +++ ++ ++++  ++ ++++i++l+l+l+++  ++  +++l+r+    
  gi|298675734|ref|YP_003727484.1|  55 KEAELIVNNPrrRRIIIWLMILGNAGIVTVIVTMTSTVVVSEGFQIPINIVILFLGLVVVYKIATHTGFLQRWDVFI 131
                                       66667777773345556666666666666666666666666666999999999999999999999999999997666 PP

                           DUF2207 442 aellakwkgF 451
                                          l k+ +F
  gi|298675734|ref|YP_003727484.1| 132 ENRLLKTTNF 141
                                       6666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1383.34
//
Query:       gi|298675735|ref|YP_003727485.1|  [L=160]
Description: hypothetical protein Metev_1854 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-06   26.6   0.1      1e-05   25.6   0.1    1.5  1  bPH_1            Bacterial PH domain
    0.00022   21.6   0.4     0.0017   18.7   0.0    2.3  3  bPH_3            Bacterial PH domain
     0.0061   16.5   0.8       0.43   10.6   0.0    2.3  2  Gram_pos_anchor  LPXTG cell wall anchor motif
     0.0078   15.8   4.1        0.3   10.7   0.1    2.3  2  DUF3098          Protein of unknown function (DUF3098)
  ------ inclusion threshold ------
        1.1    9.0   3.7        3.9    7.2   0.2    2.1  2  Neurensin        Neurensin


Domain annotation for each model (and alignments):
>> bPH_1  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.1   2.8e-09     1e-05      22      76 ..       5      60 ..       2      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 2.8e-09
                                      HGCGCGCT--EEEEEE-T.SEEEEEESSEEEEEE---SSS--EEEEEEETTTEEEE CS
                             bPH_1 22 lgellidgEkilfafkli.rDevvFTnkrlilvdkqgvtgkKkeyksipyssIsev 76
                                      ++++l dgE+ l   k+  r  + FTnkr+i +  +g++ kK + k i+y +Is++
  gi|298675735|ref|YP_003727485.1|  5 FEKYLADGEDLLYKVKSRnRADIGFTNKRIISLKPTGLVNKKENCKDISYTHISSI 60
                                      57899*****99999885267788*****************************986 PP

>> bPH_3  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   4.8e-07    0.0017      22      58 ..      24      62 ..       8      79 .. 0.79
   2 ?   -1.6   0.0         1   3.6e+03       7      25 ..      83     103 ..      82     124 .. 0.74
   3 ?    0.0   0.1      0.31   1.1e+03      67      95 .]     127     157 ..     113     157 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 4.8e-07
                             bPH_3 22 pglivvTnkRiifldpkmfgg..kdfeeipYksIksvdl 58
                                         i +TnkRii l+p ++ +  ++ ++i+Y+ I+s+ +
  gi|298675735|ref|YP_003727485.1| 24 RADIGFTNKRIISLKPTGLVNkkENCKDISYTHISSIVT 62
                                      45689***********6655524555*********9975 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1
                             bPH_3   7 ilyltkgqinak..ldkpgli 25 
                                       +lylt+g++n     +k+g+i
  gi|298675735|ref|YP_003727485.1|  83 VLYLTSGYYNPMdiFSKSGSI 103
                                       789999988866664444444 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.31
                             bPH_3  67 itletsgktitidni..dksevrkiveaire 95 
                                       +t+ t ++++++     + +++++i e+ire
  gi|298675735|ref|YP_003727485.1| 127 VTFVTCSEKYKVSLKgsSIEQAQTINEIIRE 157
                                       6677766777776554477888888888885 PP

>> Gram_pos_anchor  LPXTG cell wall anchor motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00012      0.43      12      36 ..      62      86 ..      62      88 .. 0.92
   2 ?    4.4   0.1      0.01        37      19      34 ..     103     118 ..      98     124 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00012
                                      XXXXXXXXXXXXXXXXXXXXXXXXX CS
                   Gram_pos_anchor 12 TGengnifltaaGllallggllLlv 36
                                      TG ++ +++++aG  +ll+g++L++
  gi|298675735|ref|YP_003727485.1| 62 TGYKNHYWMLLAGPVILLAGFVLYL 86
                                      788999*****************97 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.01
                                       XXXXXXXXXXXXXXXX CS
                   Gram_pos_anchor  19 fltaaGllallggllL 34 
                                       + +aaG++++++g+l+
  gi|298675735|ref|YP_003727485.1| 103 IVMAAGVFVFVAGFLI 118
                                       5578888888888887 PP

>> DUF3098  Protein of unknown function (DUF3098)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1   8.4e-05       0.3       4      41 ..      65      98 ..      63     100 .. 0.83
   2 !    8.1   0.8   0.00055         2       1      23 [.      96     118 ..      96     119 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8.4e-05
                           DUF3098  4 kknyillliglaviilGfiLmsGggsddpnvFnediFs 41
                                      k++y +ll+g +++++Gf+L   +g  +p     diFs
  gi|298675735|ref|YP_003727485.1| 65 KNHYWMLLAGPVILLAGFVLYLTSGYYNPM----DIFS 98
                                      78999***************9887766554....7877 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00055
                           DUF3098   1 afgkknyillliglaviilGfiL 23 
                                       +f+k+  i++++g+ v ++Gf++
  gi|298675735|ref|YP_003727485.1|  96 IFSKSGSIVMAAGVFVFVAGFLI 118
                                       699******************85 PP

>> Neurensin  Neurensin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.3     0.016        58      44      64 ..      70      91 ..      31      97 .. 0.66
   2 ?    7.2   0.2    0.0011       3.9      44      67 ..      97     120 ..      91     144 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.016
                         Neurensin 44 slvvgtlvlllGvt.allvGyl 64
                                      +l  g ++ll+G +  l+ Gy 
  gi|298675735|ref|YP_003727485.1| 70 MLLAGPVILLAGFVlYLTSGYY 91
                                      5667777777775414666665 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0011
                         Neurensin  44 slvvgtlvlllGvtallvGylvpr 67 
                                       +  +g +v+++Gv + + G+l+ +
  gi|298675735|ref|YP_003727485.1|  97 FSKSGSIVMAAGVFVFVAGFLIRE 120
                                       445677777777777777777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       832  (0.0464053); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1102.20
//
Query:       gi|298675736|ref|YP_003727486.1|  [L=182]
Description: BioY protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.6e-40  136.5  20.3    9.4e-40  135.8  20.3    1.3  1  BioY             BioY family
    0.00069   19.7  24.6      0.011   15.8  24.6    2.8  1  ECF-ribofla_trS  ECF-type riboflavin transporter, S component
  ------ inclusion threshold ------
       0.54   10.4   5.4          1    9.5   0.2    2.6  2  Pox_A9           A9 protein conserved region


Domain annotation for each model (and alignments):
>> BioY  BioY family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.8  20.3   1.6e-43   9.4e-40       1     132 [.      39     179 ..      39     181 .. 0.92

  Alignments for each domain:
  == domain 1  score: 135.8 bits;  conditional E-value: 1.6e-43
                              BioY   1 lgpvpitlqtlavllaglllgprrgalavllYlllGalglPvfagg.gGlavllgptgGYllGFlvaalvvgll... 73 
                                       +gpvpit+q+l+v+lag +lg+++g l++++Y+llG++glPvfagg +G++vl+gptgGY++GF++a++v+g+l   
  gi|298675736|ref|YP_003727486.1|  39 IGPVPITFQVLFVFLAGSILGKKWGPLSMIVYILLGVAGLPVFAGGaSGIGVLFGPTGGYIIGFVLATFVIGMLtek 115
                                       58*******************************************66***************************886 PP

                              BioY  74 .kk..laelllallagllviyalGvlwlalv..lslaaalaagvlpfipgdlvkavlaallaka 132
                                        k+  l+   + +++gl++iy+lG+++l++   l+  +a+++gv+pf+ gdl+++++aa ++++
  gi|298675736|ref|YP_003727486.1| 116 vKSagLVLNSFYMIIGLIIIYTLGATQLMIEaqLEPIEAIMSGVAPFVTGDLISILIAAYITTK 179
                                       531467777899999***************435778889*********************9876 PP

>> ECF-ribofla_trS  ECF-type riboflavin transporter, S component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8  24.6   1.8e-06     0.011       3     167 ..      15     177 ..      13     181 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.8e-06
                                       .TTHHHHHHHHHHHHHHHHHH---B-S.SS-B--TTHHHHHHHHHHSS--STHHHHHHHHHHHHHHHSS.-G.GGHH CS
                   ECF-ribofla_trS   3 stkkvvatailaAlvvvltlfisIplpantegsinlgdavlalaallfGpvvGflvGaiGsalaDllsg.Yg.iwap 77 
                                       ++kk+v+ +++aA++++  + ++Ip+++ +   i+++  +++la+ ++G++ G l+  +  +l  +  + ++     
  gi|298675736|ref|YP_003727486.1|  15 EIKKMVFASLFAAMTAIGAY-MKIPIGP-V--PITFQVLFVFLAGSILGKKWGPLSMIVYILLGVAGLPvFAgGASG 87 
                                       69*************99888.9****94.4..6********************998766666655544445533334 PP

                                       HHHHHHHHHHHHHHHH--S-S-SSH...HHHHHHHHHHHHHHHHHHHHHHHH..........S-HHHHHHH.HHHHH CS
                   ECF-ribofla_trS  78 ftliikgliGlivGliakklkknkengvfkilalvlfaivmvigyviaegllpildiiiysepaekvalqs.ipani 153
                                       + +++  + G+i+G++  +       +++k ++lvl +++m+ig +i+++l  + +++i ++ +   a+ s +   +
  gi|298675736|ref|YP_003727486.1|  88 IGVLFGPTGGYIIGFVLATFVIGMLTEKVKSAGLVLNSFYMIIGLIIIYTLG-ATQLMIEAQLEPIEAIMSgVAPFV 163
                                       5578888889****999999888888999999*******************9.666666555544333333033333 PP

                                       HHHHHHHHHHHHHH CS
                   ECF-ribofla_trS 154 iqavvgaiialpLl 167
                                       +  +++++ia  ++
  gi|298675736|ref|YP_003727486.1| 164 TGDLISILIAAYIT 177
                                       33344444444444 PP

>> Pox_A9  A9 protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.2   0.00017         1      31      47 ..      65      81 ..      63      85 .. 0.86
   2 ?    2.1   1.0     0.038   2.2e+02      35      46 ..     126     137 ..     120     143 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00017
                            Pox_A9 31 isMvmyLvlGvaLlyis 47
                                      +sM++y++lGva l ++
  gi|298675736|ref|YP_003727486.1| 65 LSMIVYILLGVAGLPVF 81
                                      79*********987765 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.038
                            Pox_A9  35 myLvlGvaLlyi 46 
                                        y+++G++++y 
  gi|298675736|ref|YP_003727486.1| 126 FYMIIGLIIIYT 137
                                       599999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.33s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1119.09
//
Query:       gi|298675737|ref|YP_003727487.1|  [L=276]
Description: ABC transporter-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-32  111.1   0.1    8.7e-32  110.5   0.1    1.3  1  ABC_tran         ABC transporter
    6.3e-13   48.7   1.0    1.1e-12   47.8   1.0    1.4  1  SMC_N            RecF/RecN/SMC N terminal domain
    2.9e-11   43.7   0.0    5.2e-07   29.8   0.0    2.3  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    2.3e-05   24.3   0.0    3.4e-05   23.7   0.0    1.4  1  AAA_15           AAA ATPase domain
    3.7e-05   23.4   0.0    7.4e-05   22.4   0.0    1.5  1  AAA_29           P-loop containing region of AAA domain
    6.4e-05   23.4   0.0     0.0001   22.8   0.0    1.3  1  AAA_16           AAA ATPase domain
    0.00036   21.1   0.1     0.0006   20.4   0.1    1.6  1  AAA_23           AAA domain
    0.00061   19.7   0.3       0.54   10.1   0.0    2.2  2  NTPase_1         NTPase
      0.001   19.4   0.1     0.0058   16.9   0.1    2.1  1  AAA_22           AAA domain
     0.0018   18.3   0.2       0.78    9.8   0.0    2.5  2  AAA_14           AAA domain
     0.0019   17.7   0.4       0.16   11.4   0.1    2.2  2  TniB             Bacterial TniB protein
     0.0022   18.0   0.0      0.026   14.5   0.0    2.2  2  AAA_5            AAA domain (dynein-related subfamily)
     0.0026   18.1   0.6      0.012   16.0   0.0    2.1  2  RNA_helicase     RNA helicase
     0.0035   16.7   0.4        1.9    7.7   0.0    2.2  2  ATPase           KaiC
     0.0058   17.0   0.2        4.1    7.8   0.0    2.2  2  AAA              ATPase family associated with various cellul
     0.0069   16.3   0.7       0.03   14.2   0.7    2.0  1  Rad17            Rad17 P-loop domain
     0.0076   16.2   0.2      0.016   15.1   0.1    1.6  2  RsgA_GTPase      RsgA GTPase
  ------ inclusion threshold ------
       0.01   15.0   0.1      0.087   12.0   0.1    2.1  2  NB-ARC           NB-ARC domain
       0.01   15.7   0.0      0.019   14.9   0.0    1.4  1  NACHT            NACHT domain
      0.017   14.6   0.1      0.023   14.2   0.1    1.2  1  KdpD             Osmosensitive K+ channel His kinase sensor d
      0.029   13.9   0.0       0.24   11.0   0.0    2.0  2  AAA_25           AAA domain
      0.045   13.1   0.0      0.074   12.4   0.0    1.4  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.046   13.5   0.2       0.29   10.9   0.0    2.1  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
      0.052   13.3   0.0       0.25   11.1   0.0    1.9  1  AAA_30           AAA domain
      0.073   12.7   0.0       0.13   11.9   0.0    1.4  1  Acid_phosphat_B  HAD superfamily, subfamily IIIB (Acid phosph
      0.078   12.0   0.0       0.12   11.3   0.0    1.4  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.088   12.3   0.1       0.15   11.5   0.1    1.4  1  AAA_7            P-loop containing dynein motor region
       0.11   12.4   0.0       0.19   11.6   0.0    1.5  1  DUF4823          Domain of unknown function (DUF4823)
       0.15   11.4   0.0       0.28   10.4   0.0    1.4  1  Zeta_toxin       Zeta toxin
       0.16   12.0   1.2       0.43   10.6   0.6    2.0  1  DUF910           Bacterial protein of unknown function (DUF91


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.5   0.1   1.5e-34   8.7e-32       1     137 []      20     167 ..      20     167 .. 0.95

  Alignments for each domain:
  == domain 1  score: 110.5 bits;  conditional E-value: 1.5e-34
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS.--S-TTSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx.xxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqe.pqlfpelt 75 
                                       l+ ++l++k+ge v ivGenG+GKStL++ l   l p +G+++++g d+k+  ++ s r+++g+++q+ ++ f ++t
  gi|298675737|ref|YP_003727487.1|  20 LNSINLQVKKGEFVSIVGENGCGKSTLVQHLNAILIPSKGTVQIEGLDTKKqSNIWSIRQKVGMVFQNpQSQFIGTT 96 
                                       689*******************************************999997899*************767788999 PP

                                       HHHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  76 vren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       v+e              e + ++++al+++g+ ++k+ +      sLSgGqkq va+a +l+ kp+ ++lDE t+
  gi|298675737|ref|YP_003727487.1|  97 VQEDvafgpenlalsnhEIRTRLDDALEQVGMLDFKEYNP----MSLSGGQKQCVAIAGVLAMKPEYIVLDEITS 167
                                       *************999999999************888887....9***************************985 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   1.0   1.9e-15   1.1e-12      24     211 ..      30     210 ..      20     215 .. 0.81

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 1.9e-15
                                       SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsis 100
                                        +f +ivG+NG+GKs l++ +  +L  ++       +++ l +k++++  + + +v ++f+n+++++  ++ +  + 
  gi|298675737|ref|YP_003727487.1|  30 GEFVSIVGENGCGKSTLVQHLNAILIPSKG----TVQIEGLDTKKQSNIWSIRQKVGMVFQNPQSQFIGTTVQEDVA 102
                                       4699*****************999986555....6678888888888899999*************55544444455 PP

                                       EEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 101 rrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvk 177
                                          ++   s+++i  +     e   +l  ++ ++ +LSgG+k+ va+a ++A++   p+   +lDei + LD+k  k
  gi|298675737|ref|YP_003727487.1| 103 FGPENLALSNHEIRTRLDDALEQVGMLDFKEYNPMSLSGGQKQCVAIAGVLAMK---PE-YIVLDEITSMLDDKSQK 175
                                       55555555677777777777777788888999999**************99975...54.4689************* PP

                                       HHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEEEE CS
                                       xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 178 kvaellkekskn.aQfivislreemlekadklvgv 211
                                        + +++k  +kn   +i +++r + + ++d+++ +
  gi|298675737|ref|YP_003727487.1| 176 TIFDIMKYLQKNgITIIYVTHRIKDVVNSDRIIVL 210
                                       *******99998788999****9999999988765 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.1   0.00028      0.17       3      22 ..      34      53 ..      32      88 .. 0.78
   2 !   29.8   0.0   8.8e-10   5.2e-07     223     297 ..     125     196 ..      99     198 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00028
                            AAA_21  3 vliGpNgsGKSnLLdaldll 22
                                       ++G Ng+GKS+L + l  +
  gi|298675737|ref|YP_003727487.1| 34 SIVGENGCGKSTLVQHLNAI 53
                                      69***********9988444 PP

  == domain 2  score: 29.8 bits;  conditional E-value: 8.8e-10
                            AAA_21 223 flengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       ++ + d +e ++ +lS G+k++ a++  l+  +     +++DE+ + L+ k ++++++++k+l++ng+ +i +TH
  gi|298675737|ref|YP_003727487.1| 125 QVGMLDFKEYNPMSLSGGQKQCVAIAGVLAMKP---EYIVLDEITSMLDDKSQKTIFDIMKYLQKNGITIIYVTH 196
                                       55555667788999****************999...66************************************* PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   5.7e-08   3.4e-05      19      84 ..      23     149 ..      19     265 .. 0.66

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 5.7e-08
                            AAA_15  19 idlsee...ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdikIdvef......... 83 
                                       i+l+ +   +  ++G+N++GKS++++ l+ +l  +    k ++ ie  d++++ ++  s++ k+ + f         
  gi|298675737|ref|YP_003727487.1|  23 INLQVKkgeFVSIVGENGCGKSTLVQHLNAILIPS----KGTVQIEGLDTKKQ-SNIWSIRQKVGMVFqnpqsqfig 94 
                                       444444447999*********************99....89999999999998.55567777888888777777777 PP

                            AAA_15  84 ......................................................a 84 
                                                                                             +
  gi|298675737|ref|YP_003727487.1|  95 ttvqedvafgpenlalsnheirtrlddaleqvgmldfkeynpmslsggqkqcvaI 149
                                       7777777777777777777777777777777666666666666666665555551 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.2e-07   7.4e-05      18      50 ..      26      58 ..      19      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.2e-07
                            AAA_29 18 eidlkg.atlltGpsGsGKSTllDAiqalLvpak 50
                                      +++  g ++ ++G++G GKSTl+  ++a+L+p+k
  gi|298675737|ref|YP_003727487.1| 26 QVKK-GeFVSIVGENGCGKSTLVQHLNAILIPSK 58
                                      4553.45999**********************98 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   1.7e-07    0.0001      20     155 ..      28     177 ..      20     192 .. 0.59

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.7e-07
                            AAA_16  20 rsgrpelvllsGesGvGKsslvrellralekdggif.lrgkcdqlesa.............ipysalaqalareell 82 
                                       ++g  e v ++Ge G+GKs+lv++l   l  ++g + ++g  ++ +s+              p s+++ +  + e +
  gi|298675737|ref|YP_003727487.1|  28 KKG--EFVSIVGENGCGKSTLVQHLNAILIPSKGTVqIEGLDTKKQSNiwsirqkvgmvfqNPQSQFIGTTVQ-EDV 101
                                       444..789******************99999988887666555556665555544444444444554433323.333 PP

                            AAA_16  83 rqlldeaesaeleawrekleeala.....avpelagaea.....srllellkrll.allsrderplvlvlDdlq.wa 147
                                       +   ++++  +  + r++l++al+     +      +e      s    ++ +++ +l+ +   p ++vlD++   +
  gi|298675737|ref|YP_003727487.1| 102 AFGPENLA-LSNHEIRTRLDDALEqvgmlD-----FKEYnpmslSGGQKQCVAIAgVLAMK---PEYIVLDEITsML 169
                                       33333333.355667777777777444443.....33333333355666666666444554...5577777777556 PP

                            AAA_16 148 deaslqll 155
                                       d+ s++ +
  gi|298675737|ref|YP_003727487.1| 170 DDKSQKTI 177
                                       66666665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1     1e-06    0.0006      20      45 ..      31      56 ..      20     186 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1e-06
                            AAA_23 20 gltlItGpNGaGKTTildAiklaLyg 45
                                       ++ I+G+NG+GK+T+++ +  +L  
  gi|298675737|ref|YP_003727487.1| 31 EFVSIVGENGCGKSTLVQHLNAILIP 56
                                      4678****************999975 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00091      0.54       2      37 ..      33      70 ..      32      90 .. 0.81
   2 !    7.8   0.0    0.0046       2.8      94     138 ..     155     201 ..     129     218 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00091
                                      EEEE--TTSSHHHHHHHHHHHH.....GGGEEEEEEEE CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkss..gvkvgGfytee 37
                                      v i G+ G GK+Tlv+ +   l  s   v+++G+ t++
  gi|298675737|ref|YP_003727487.1| 33 VSIVGENGCGKSTLVQHLNAILIPSkgTVQIEGLDTKK 70
                                      5689*************998874332257777877765 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0046
                                       HHH-EEEE---STT.GGG-HHHHHHHHHHHT.TTSEEEEE--SS--S CS
                          NTPase_1  94 seadviviDEiGkm.ElkskkfkeaveevLk.sekpvlavihrrkdl 138
                                        +++ iv+DEi +m   ks+k +  + + L+ ++  ++ v hr kd 
  gi|298675737|ref|YP_003727487.1| 155 MKPEYIVLDEITSMlDDKSQKTIFDIMKYLQkNGITIIYVTHRIKDV 201
                                       57889******9986899************97888888899987643 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   9.8e-06    0.0058       4     103 ..      29     169 ..      25     199 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 9.8e-06
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevv...fvtlpsstsskdllrellralglelka....... 70 
                                       +  ++ ++Ge G+GK+tl++ l   l        +++++v     + +++++  ++++++   ++++++        
  gi|298675737|ref|YP_003727487.1|  29 KGEFVSIVGENGCGKSTLVQHLNAILI-------PSKGTVqieGLDTKKQSNIWSIRQKVGMVFQNPQSQfigttvq 98 
                                       567899****************99983.......2444443345555555566677777777777777667777777 PP

                            AAA_22  71 .........erlsseellealeqalrarav............................ielliiDEaqh.l 103
                                                  ls++e++++l +al++ ++                            +e +++DE+   l
  gi|298675737|ref|YP_003727487.1|  99 edvafgpenLALSNHEIRTRLDDALEQVGMldfkeynpmslsggqkqcvaiagvlamkPEYIVLDEITSmL 169
                                       77777777755666666666666666555555555555555555555555555566667777777777755 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0013      0.78       3      40 ..      31      67 ..      29      93 .. 0.74
   2 ?    6.5   0.0     0.013         8      63      92 ..     155     189 ..     107     217 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0013
                            AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldd 40
                                      + + i+G   +GK+tl+++l   l ++++ ++ i+  d
  gi|298675737|ref|YP_003727487.1| 31 EFVSIVGENGCGKSTLVQHLNAIL-IPSKGTVQIEGLD 67
                                      67899************9986444.4777777776443 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.013
                            AAA_14  63 ekktylflDEiqev......pewekalkslvdegkn 92 
                                        k +y++lDEi  +      +++++++k+l ++g  
  gi|298675737|ref|YP_003727487.1| 155 MKPEYIVLDEITSMlddksqKTIFDIMKYLQKNG-I 189
                                       4679********9999888888888888888877.3 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.036        21      38      55 ..      33      50 ..      22      62 .. 0.85
   2 !   11.4   0.1   0.00027      0.16     114     172 ..     151     205 ..     132     209 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.036
                              TniB 38 lllvGdsnnGKtmivekF 55
                                      + +vG+  +GK+++v++ 
  gi|298675737|ref|YP_003727487.1| 33 VSIVGENGCGKSTLVQHL 50
                                      789************985 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00027
                              TniB 114 llrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlvGteealralrtD 172
                                          ++k++ +++DEi ++l    ++q++++ ++k+L+    i+i++v t+++ +++++D
  gi|298675737|ref|YP_003727487.1| 151 GVLAMKPEYIVLDEITSML--DDKSQKTIFDIMKYLQK-NGITIIYV-THRIKDVVNSD 205
                                       55679999***********..8999***********75.57899888.77777777777 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   4.3e-05     0.026       4      29 ..      35      60 ..      33      79 .. 0.80
   2 ?    1.0   0.0      0.66     4e+02      65      79 ..     156     170 ..     132     212 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.3e-05
                                      EE--SSSSHHHHHHHGGGGBS--EEE CS
                             AAA_5  4 LvGppGtgKselaerlaaalnrevey 29
                                      +vG+ G+gKs+l+++l a l  +  +
  gi|298675737|ref|YP_003727487.1| 35 IVGENGCGKSTLVQHLNAILIPSKGT 60
                                      79****************99333333 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.66
                                       G-SEEEEESGGG--H CS
                             AAA_5  65 egeilvlDEveraes 79 
                                       ++e +vlDE++ + +
  gi|298675737|ref|YP_003727487.1| 156 KPEYIVLDEITSMLD 170
                                       788999***997653 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.9e-05     0.012       2      36 ..      34      76 ..      33      99 .. 0.65
   2 ?   -0.3   0.1       2.3   1.4e+03      50     103 ..     157     209 ..     153     212 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.9e-05
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkkl........klkkkdsvys 36
                                       ++G++g+GKStl+++L + l  +         ++kk+++++s
  gi|298675737|ref|YP_003727487.1| 34 SIVGENGCGKSTLVQHLNAILIPSKgtvqieglDTKKQSNIWS 76
                                      589*************766666333334444444444444444 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.3
                      RNA_helicase  50 qevvvidDfgqvkdeenpsdlaelirlvsstpyplnmasleekgtlftSkvviv 103
                                       +e++v d++ ++ d+++++ ++++++  + + +++       k  +++S  +iv
  gi|298675737|ref|YP_003727487.1| 157 PEYIVLDEITSMLDDKSQKTIFDIMKYLQKNGITIIYVTHRIK-DVVNSDRIIV 209
                                       6788999999999887666888888877777666555555544.3556666665 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0032       1.9      17      38 ..      28      49 ..      22      54 .. 0.90
   2 !    7.0   0.1    0.0055       3.3     117     164 ..     154     197 ..     132     214 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0032
                            ATPase 17 pegrvvlitGepGtGKtifalq 38
                                       +g+ v i+Ge G+GK++++++
  gi|298675737|ref|YP_003727487.1| 28 KKGEFVSIVGENGCGKSTLVQH 49
                                      57899*************9986 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0055
                            ATPase 117 eikakrvviDsitglayeekeavaReilrqlvrvlkklgvTailvsek 164
                                       ++k + +v+D it++     +++  ++++ +++ l+k+g+T i v+ +
  gi|298675737|ref|YP_003727487.1| 154 AMKPEYIVLDEITSM-L---DDKSQKTIFDIMKYLQKNGITIIYVTHR 197
                                       578899*********.3...4445578999999********9999875 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0069       4.1       3      35 ..      35      69 ..      33     101 .. 0.70
   2 !    7.5   0.1     0.009       5.4      53     115 ..     150     201 ..     110     208 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0069
                                      EESSTTSSHHHHHHHHHHHH..THEEEEEETTTCS CS
                               AAA  3 lyGppGtGKTllakavakel..gvefleisgsell 35
                                      ++G  G+GK++l++ +   l  +   ++i+g +  
  gi|298675737|ref|YP_003727487.1| 35 IVGENGCGKSTLVQHLNAILipSKGTVQIEGLDTK 69
                                      79***********9987776443445555555555 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.009
                                       HHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGS CS
                               AAA  53 akeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkl 115
                                       a   a kp  +++DEi ++  ++           +++++  ++ ++k  + +++i +t+r++++
  gi|298675737|ref|YP_003727487.1| 150 AGVLAmKPEYIVLDEITSMLDDK----------SQKTIFDIMKYLQK--NGITIIYVTHRIKDV 201
                                       4444567899*********9999..........79999999999999..469******997655 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.7   5.1e-05      0.03      37      87 ..      22      73 ..      16     206 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.1e-05
                             Rad17 37 advLesrkkriLLisGPsGCgkstvvkvLskelgikl.rewlnpvslkepdn 87
                                      +  L+ +k + + i G  GCgkst v+ L  +l ++     + ++  k+ +n
  gi|298675737|ref|YP_003727487.1| 22 SINLQVKKGEFVSIVGENGCGKSTLVQHLNAILIPSKgTVQIEGLDTKKQSN 73
                                      5567777777999*****************9998764134555655555555 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   2.6e-05     0.016      89     122 ..      19      53 ..       2      88 .. 0.74
   2 ?   -2.7   0.0         8   4.8e+03      68      82 ..     180     194 ..     161     216 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.6e-05
                                       THHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  89 gleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                        l++++ ++k+ +++ +vG+ G GKStL+ +l+  
  gi|298675737|ref|YP_003727487.1|  19 VLNSINLQVKKgEFVSIVGENGCGKSTLVQHLNAI 53 
                                       55667667776699****************99865 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 8
                                       HHHHHHHTTSEEEE- CS
                       RsgA_GTPase  68 lkeelealgyevllv 82 
                                       +++ l++ g+++++v
  gi|298675737|ref|YP_003727487.1| 180 IMKYLQKNGITIIYV 194
                                       334444444444443 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00015     0.087      21      41 ..      31      51 ..      19      61 .. 0.86
   2 ?    0.5   0.0      0.46   2.7e+02     108     176 ..     168     233 ..     133     250 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
                                      EEEEEEESTTSSHHHHHHHHC CS
                            NB-ARC 21 lvvalvGmgGvGKttlakqil 41
                                       +v++vG  G+GK+tl+++ +
  gi|298675737|ref|YP_003727487.1| 31 EFVSIVGENGCGKSTLVQHLN 51
                                      499*************99865 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.46
                                       EEEEE-SHHHH.....HHHHCHTTSEEE.EEESBCCCCCCS-S-EEEEEESS--HHHHHHHHHHCCTS-G CS
                            NB-ARC 108 vlDDVweeedwdkigvvlparenrlrvl.lTTRdeevanavsatsekievelLekdeawellenkvfekk 176
                                       +lDD  ++  +  i+  l  ++n++ ++ +T R ++v n+        + ++L +d+  ++l++   +++
  gi|298675737|ref|YP_003727487.1| 168 MLDDKSQKTIF-DIMKYL--QKNGITIIyVTHRIKDVVNSDRI-IVLSKGSILYNDKPQTVLKEPSLPES 233
                                       45666666555.333333..35665544388899999776554.56666666666666666666555555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   3.2e-05     0.019       3      21 ..      33      51 ..      31      59 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.2e-05
                                      EEEEC-TTTCHHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqkla 21
                                      v + Ge+G+GK+tL+q+l 
  gi|298675737|ref|YP_003727487.1| 33 VSIVGENGCGKSTLVQHLN 51
                                      7799************985 PP

>> KdpD  Osmosensitive K+ channel His kinase sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   3.8e-05     0.023      51     127 ..     125     201 ..     107     254 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.8e-05
                              KdpD  51 llegleviprkeveykgkeleeldldailarkpevvlvDelahtnapgsrhekryqdveelLeagidVi.ttvnvqh 126
                                       ++  l+  + + ++ +g + + + +  +la+kpe +++De+     ++ ++++ ++ ++ l ++gi +i  t  +++
  gi|298675737|ref|YP_003727487.1| 125 QVGMLDFKEYNPMSLSGGQKQCVAIAGVLAMKPEYIVLDEITSML-DDKSQKTIFDIMKYLQKNGITIIyVTHRIKD 200
                                       333444445666778899999999*****************8765.67777888999999999***97515666666 PP

                              KdpD 127 l 127
                                       +
  gi|298675737|ref|YP_003727487.1| 201 V 201
                                       5 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0004      0.24      31      54 ..      28      51 ..      12      61 .. 0.87
   2 ?    0.5   0.0      0.63   3.7e+02      85     157 ..     114     171 ..     110     196 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0004
                            AAA_25 31 pagelallaGapgtGKttlaldla 54
                                       +ge++ ++G  g+GK+tl+ +l 
  gi|298675737|ref|YP_003727487.1| 28 KKGEFVSIVGENGCGKSTLVQHLN 51
                                      689****************99885 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.63
                            AAA_25  85 elrrRlravgealrddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralgg 157
                                       e+r Rl  ++e++   + l++  +     + L    +gg++   +  a++  + ++ +++ +v+D ++++l+ 
  gi|298675737|ref|YP_003727487.1| 114 EIRTRLDDALEQV---GMLDFKEYNP---MSL----SGGQK---QCVAIA-GVLAM-KPEYIVLDEITSMLDD 171
                                       5666666666665...4444444311...111....22222...222233.33443.4889999999988765 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00012     0.074      25      65 ..      33      76 ..      16      99 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                      Mg_chelatase 25 lllvGppGsGKtmlakrlpsllpplseeeale...vakiasvag 65
                                      + +vG  G+GK+ l + l+++l p + + ++e   ++k + + +
  gi|298675737|ref|YP_003727487.1| 33 VSIVGENGCGKSTLVQHLNAILIPSKGTVQIEgldTKKQSNIWS 76
                                      5689******************9987664444111444444444 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00048      0.29       5      35 ..      34      64 ..      31      70 .. 0.83
   2 ?   -0.1   0.0       1.2   7.1e+02      99     125 ..     168     194 ..     133     207 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00048
                         PduV-EutP  5 lliGkvgsGKttLtqalkgeelkYkktqaie 35
                                       ++G+ g+GK tL q+l+   +  k t +ie
  gi|298675737|ref|YP_003727487.1| 34 SIVGENGCGKSTLVQHLNAILIPSKGTVQIE 64
                                      589**************99888777776665 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.2
                         PduV-EutP  99 idlaedeenieaveelLksaGaekife 125
                                       +   ++++ i    ++L++ G++ i+ 
  gi|298675737|ref|YP_003727487.1| 168 MLDDKSQKTIFDIMKYLQKNGITIIYV 194
                                       322334444555555555555555554 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00041      0.25      18      97 ..      30     165 ..      22     197 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00041
                            AAA_30  18 drvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkv...Laeelgi.....eastiakllkrlk..... 81 
                                         ++ ++G  G GK+t++++l++++  ++g+v +     k   +   +++++g+     +++ i   +++       
  gi|298675737|ref|YP_003727487.1|  30 GEFVSIVGENGCGKSTLVQHLNAILIPSKGTVQIEGLDTKKQSNiwsIRQKVGMvfqnpQSQFIGTTVQEDVafgpe 106
                                       348899***************99988886555443333322222112333333322222222222222222133333 PP

                            AAA_30  82 ............................................grarlepgtllivDEa 97 
                                                                                   g +   + + ++ DE+
  gi|298675737|ref|YP_003727487.1| 107 nlalsnheirtrlddaleqvgmldfkeynpmslsggqkqcvaiaG-VLAMKPEYIVLDEI 165
                                       333333334455555556666666666666666666666666532.22233366666664 PP

>> Acid_phosphat_B  HAD superfamily, subfamily IIIB (Acid phosphatase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00021      0.13     115     144 ..     171     200 ..     162     227 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00021
                                       GCCECCHHHHHHHHHHTTEEEEEEEEEECC CS
                   Acid_phosphat_B 115 akaipgalelikkvverGvkiffvsgRsee 144
                                       +k+ +  ++ +k+++++G++i++v+ R ++
  gi|298675737|ref|YP_003727487.1| 171 DKSQKTIFDIMKYLQKNGITIIYVTHRIKD 200
                                       4556667899*****************876 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0002      0.12      17      62 ..      18      63 ..       6      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0002
                                      HHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEE CS
                              MeaB 17 ellerllakaGraqvvGltGvPGaGkstlvealglelrrrGkrvav 62
                                       +l+ +  +  + + v + G  G Gkstlv++l + l+     v +
  gi|298675737|ref|YP_003727487.1| 18 PVLNSINLQVKKGEFVSIVGENGCGKSTLVQHLNAILIPSKGTVQI 63
                                      678888889999999******************9999876555555 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00026      0.15      26      57 ..      23      54 ..      13      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00026
                             AAA_7 26 lelllknkkpvllvGptGtGKtviikdllkkl 57
                                      ++l +k++  v +vG+ G+GK++++++l   l
  gi|298675737|ref|YP_003727487.1| 23 INLQVKKGEFVSIVGENGCGKSTLVQHLNAIL 54
                                      5678999999****************987655 PP

>> DUF4823  Domain of unknown function (DUF4823)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00032      0.19      39     133 ..     131     228 ..      88     230 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00032
                           DUF4823  39 fveyfpsvrrakdpldleealkearavgadYllyprilsw.edr.atewsdke...draevqlmlietetknlvdsa 110
                                       f ey p+   + + +    a++   a++ +Y+++ +i s+ +d+  ++  d+    ++  + ++ +  + k +v+s 
  gi|298675737|ref|YP_003727487.1| 131 FKEYNPMSLSGGQKQCV--AIAGVLAMKPEYIVLDEITSMlDDKsQKTIFDIMkylQKNGITIIYVTHRIKDVVNSD 205
                                       55666655554443332..46777788889999999988636667555555556889******************** PP

                           DUF4823 111 rirgksglltfgddkPqdllaeP 133
                                       ri   s+   +++dkPq  l+eP
  gi|298675737|ref|YP_003727487.1| 206 RIIVLSKGSILYNDKPQTVLKEP 228
                                       **9999999*************9 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00047      0.28      14      54 ..      28      68 ..      19      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00047
                        Zeta_toxin 14 erPklillgGqpGAGKselaellkdelerqgnvvrldpDdl 54
                                      ++   + ++G  G+GKs+l + l++ l + ++ v++++ d 
  gi|298675737|ref|YP_003727487.1| 28 KKGEFVSIVGENGCGKSTLVQHLNAILIPSKGTVQIEGLDT 68
                                      555678899*************************9987555 PP

>> DUF910  Bacterial protein of unknown function (DUF910)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.6   0.00071      0.43       2      26 ..     175     200 ..     174     202 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00071
                                       -SHHHHHHHHHTTS-.----S-HHHH CS
                            DUF910   2 ktlyDVqqlLKkfGi.iiYvgdrlad 26 
                                       kt++D+ ++L+k Gi iiYv+ r+ d
  gi|298675737|ref|YP_003727487.1| 175 KTIFDIMKYLQKNGItIIYVTHRIKD 200
                                       8*************7589*****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                       115  (0.00641419); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.38
# Mc/sec: 2154.43
//
Query:       gi|298675738|ref|YP_003727488.1|  [L=271]
Description: ABC transporter-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.8e-31  108.1   0.0      6e-30  104.6   0.0    2.0  2  ABC_tran    ABC transporter
      1e-05   25.5   0.2       0.17   11.7   0.7    2.2  2  AAA_21      AAA domain, putative AbiEii toxin, Type IV TA sys
    7.1e-05   22.5   0.0    0.00014   21.5   0.0    1.4  1  AAA_29      P-loop containing region of AAA domain
    0.00055   20.0   0.0     0.0074   16.3   0.0    2.4  2  AAA_14      AAA domain
     0.0032   16.9   0.3       0.82    9.1   0.0    2.2  2  SMC_N       RecF/RecN/SMC N terminal domain
     0.0042   16.8   0.0     0.0067   16.1   0.0    1.4  1  CoaE        Dephospho-CoA kinase
     0.0042   16.1   0.0     0.0065   15.5   0.0    1.3  1  MeaB        Methylmalonyl Co-A mutase-associated GTPase MeaB
  ------ inclusion threshold ------
      0.012   15.8   0.0       0.06   13.6   0.0    2.3  2  AAA_22      AAA domain
      0.035   14.7   0.0       0.11   13.0   0.0    1.9  2  AAA_18      AAA domain
      0.072   12.0   0.1       0.15   11.0   0.1    1.4  2  Spore_IV_A  Stage IV sporulation protein A (spore_IV_A)
      0.079   12.9   0.0       0.13   12.2   0.0    1.4  1  ATPase_2    ATPase domain predominantly from Archaea
      0.083   13.3   0.0       0.12   12.7   0.0    1.3  1  AAA_16      AAA ATPase domain
       0.12   12.3   0.1       0.37   10.7   0.1    1.8  2  NTPase_1    NTPase
       0.13   12.8   2.5       0.24   11.9   2.2    1.5  1  AAA_23      AAA domain
       0.13   12.1   0.0       0.24   11.2   0.0    1.6  1  dNK         Deoxynucleoside kinase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.6   0.0     5e-33     6e-30       1     137 []      23     167 ..      23     167 .. 0.92
   2 ?    1.6   0.0      0.31   3.7e+02      29      67 ..     203     242 ..     200     270 .. 0.66

  Alignments for each domain:
  == domain 1  score: 104.6 bits;  conditional E-value: 5e-33
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S-TTSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe..pqlfpelt 75 
                                       l+n++l++ ++e v+i+G+ G+GKStL+kl+ gl  p++G + +dg+d ++   +++rk++g l+q+  +q+f+++ 
  gi|298675738|ref|YP_003727488.1|  23 LENINLTIDKNEFVGITGKIGSGKSTLIKLFNGLFVPDNGYVYVDGADASD---KKTRKKVGLLFQNphDQIFSKT- 95 
                                       78************************************************9...*************766777777. PP

                                       HHHH..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  76 vren..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       v+e+            de  e+++++l l++l++++ + sp +LSgG+ +rvala +l+ kp+ l+lDEpt+
  gi|298675738|ref|YP_003727488.1|  96 VYEEiafapsnfgiRGDELTERVHESLHLVGLDTKITDISPFKLSGGEMRRVALAGVLAMKPEYLILDEPTS 167
                                       88888***99999866666888888888888888999999******************************96 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.31
                                       HHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                          ABC_tran  29 kllagllkpteGeilldgkdlke.qeleslrkeigvlpqe 67 
                                        l+ + +  ++G+i++ g+++++ ++++s   ei  l q 
  gi|298675738|ref|YP_003727488.1| 203 PLVNKIVLMDNGKITFAGTPSEYlENISSPVPEITQLMQG 242
                                       56666777899**********9965666555555555554 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.7   0.00014      0.17       1      38 [.      35      80 ..      35     118 .. 0.61
   2 !   11.5   0.0   0.00016       0.2     230     298 ..     132     197 ..     110     202 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarl........drdvegltdelsg 38
                                      + +++G+ gsGKS+L++++ +l+           +d+ + ++ +  
  gi|298675738|ref|YP_003727488.1| 35 FVGITGKIGSGKSTLIKLFNGLFVPdngyvyvdGADASDKKTRKKV 80
                                      56899999**************755644444443333333333333 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00016
                            AAA_21 230 qelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                        ++++++lS G  r  al+  l+  +     l++DEp +g++ k  ++l+  lk+ + +g+ v++++H+
  gi|298675738|ref|YP_003727488.1| 132 TDISPFKLSGGEMRRVALAGVLAMKP---EYLILDEPTSGMDIKGKKELYSNLKKIHGTGTCVVIVSHQ 197
                                       5789999****99999*******999...66***********999999998888888888888999997 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   1.2e-07   0.00014      17      50 ..      28      61 ..      22      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.2e-07
                            AAA_29 17 ieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      ++id ++++ +tG++GsGKSTl+  ++ l+vp++
  gi|298675738|ref|YP_003727488.1| 28 LTIDKNEFVGITGKIGSGKSTLIKLFNGLFVPDN 61
                                      6788778999*************99999999987 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   6.2e-06    0.0074       2      49 ..      33      79 ..      32     102 .. 0.79
   2 ?    1.0   0.0      0.35   4.1e+02      65      77 ..     157     175 ..     129     238 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.2e-06
                            AAA_14  2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladp 49
                                      ++ + itG   +GK+tl+ +l++ l+v+++ ++y++  d +dkk +++
  gi|298675738|ref|YP_003727488.1| 33 NEFVGITGKIGSGKSTLI-KLFNGLFVPDNGYVYVDGADASDKKTRKK 79
                                      67899************8.56678889***************998855 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.35
                            AAA_14  65 ktylflDEiqev......p 77 
                                        +yl+lDE          +
  gi|298675738|ref|YP_003727488.1| 157 PEYLILDEPTSGmdikgkK 175
                                       5677777755443333332 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.2    0.0059       7.1      24      41 ..      33      50 ..      20      57 .. 0.83
   2 !    9.1   0.0   0.00069      0.82     135     198 ..     130     197 ..      65     213 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0059
                                      SSEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                             SMC_N 24 ksftaivGpNGSGKsnll 41
                                      ++f  i+G+ GSGKs l+
  gi|298675738|ref|YP_003727488.1| 33 NEFVGITGKIGSGKSTLI 50
                                      56999**********997 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00069
                                       T.......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SS CS
                                       x.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                             SMC_N 135 e.......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislr 198
                                       +        LSgGe   vala ++A++   p+   +lDe  + +D k  k++ + lk+ + + + ++++s++
  gi|298675738|ref|YP_003727488.1| 130 KitdispfKLSGGEMRRVALAGVLAMK---PEY-LILDEPTSGMDIKGKKELYSNLKKIHGTgTCVVIVSHQ 197
                                       444444449************999974...554.479********999999999998755443777777776 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   5.6e-06    0.0067       2      24 ..      35      57 ..      34      94 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.6e-06
                                      EEEEEESTTSSHHHHHHHHHHTT CS
                              CoaE  2 ivgltGgiasGKstvanlfadlg 24
                                      +vg+tG i+sGKst+ +lf+ l 
  gi|298675738|ref|YP_003727488.1| 35 FVGITGKIGSGKSTLIKLFNGLF 57
                                      59***************998653 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   5.5e-06    0.0065      15      54 ..      19      58 ..       6      77 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.5e-06
                                      HHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHH CS
                              MeaB 15 akellerllakaGraqvvGltGvPGaGkstlvealglelr 54
                                       +++le++  +  + + vG+tG  G+Gkstl++ +   ++
  gi|298675738|ref|YP_003727488.1| 19 ETRVLENINLTIDKNEFVGITGKIGSGKSTLIKLFNGLFV 58
                                      45789999999999******************98876555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     5e-05      0.06       7      70 ..      35      90 ..      30     229 .. 0.72
   2 ?   -2.9   0.0       6.4   7.6e+03      81     100 ..     238     260 ..     230     264 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5e-05
                            AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka 70
                                      ++ +tG  G+GK+tl++ +   ++       ++ ++v+v+ +  +  k+ ++++   ++++++ 
  gi|298675738|ref|YP_003727488.1| 35 FVGITGKIGSGKSTLIKLFNGLFV-------PDNGYVYVDGADAS-DKKTRKKVGLLFQNPHDQ 90
                                      6679****************9996.......36777777766666.555567777777766666 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.4
                            AAA_22  81 aleqalrarav...ielliiDEa 100
                                       +l q l++++      +l +D+a
  gi|298675738|ref|YP_003727488.1| 238 QLMQGLKSKGFnvrNDVLTVDDA 260
                                       55666666666777789999987 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   9.3e-05      0.11       1      18 [.      36      53 ..      36      90 .. 0.81
   2 ?   -2.2   0.0       4.7   5.6e+03      52      69 ..     169     186 ..     157     211 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.3e-05
                            AAA_18  1 IlltGtpGvGKttlakeL 18
                                      +++tG++G+GK+tl k  
  gi|298675738|ref|YP_003727488.1| 36 VGITGKIGSGKSTLIKLF 53
                                      78************9976 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.7
                            AAA_18  52 ldedkldklldaleenss 69 
                                       +d++  ++l ++l+++  
  gi|298675738|ref|YP_003727488.1| 169 MDIKGKKELYSNLKKIHG 186
                                       555555666666666544 PP

>> Spore_IV_A  Stage IV sporulation protein A (spore_IV_A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00012      0.15       4      42 ..      20      58 ..      18      68 .. 0.88
   2 ?   -3.5   0.0       3.1   3.7e+03     325     344 ..     166     185 ..     156     195 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00012
                        Spore_IV_A  4 ldiykdiaertngdiyigvvGpvRtGKStfikrfmellv 42
                                      ++++++i+   + + ++g+ G + +GKSt+ik f  l+v
  gi|298675738|ref|YP_003727488.1| 20 TRVLENINLTIDKNEFVGITGKIGSGKSTLIKLFNGLFV 58
                                      568889999999999*****************9987776 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.1
                        Spore_IV_A 325 lvgleiedeaellkllkela 344
                                       ++g++i++++el + lk+++
  gi|298675738|ref|YP_003727488.1| 166 TSGMDIKGKKELYSNLKKIH 185
                                       56888999999988888775 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00011      0.13      15      55 ..      30      67 ..      19     130 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                          ATPase_2 15 lerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyi 55
                                      +  ++ne++ i+G +gsGK++L+k +       d   +y++
  gi|298675738|ref|YP_003727488.1| 30 I--DKNEFVGITGKIGSGKSTLIKLFNGLFVP-DNGYVYVD 67
                                      4..4599999*************987655533.33445554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0    0.0001      0.12      25      58 ..      34      68 ..      17     138 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0001
                            AAA_16 25 elvllsGesGvGKsslvrellralekdggif.lrg 58
                                      e v ++G  G+GKs+l++ +   +  d+g++ + g
  gi|298675738|ref|YP_003727488.1| 34 EFVGITGKIGSGKSTLIKLFNGLFVPDNGYVyVDG 68
                                      67889**************9999998887774333 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00031      0.37       2      18 ..      36      52 ..      35      80 .. 0.85
   2 ?   -1.7   0.0         2   2.4e+03     113     146 ..     176     210 ..     133     217 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00031
                                      EEEE--TTSSHHHHHHH CS
                          NTPase_1  2 vfiTGppGvGKtTlvkk 18
                                      v iTG+ G+GK+Tl+k 
  gi|298675738|ref|YP_003727488.1| 36 VGITGKIGSGKSTLIKL 52
                                      67************986 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2
                                       HHHHHHHHHHTTTSEEEEE--SS-.-SHHHHHHHT CS
                          NTPase_1 113 kfkeaveevLksekpvlavihrrk.dlalveeire 146
                                       ++ + ++++  +++ v++v h+ +  l+lv++i  
  gi|298675738|ref|YP_003727488.1| 176 ELYSNLKKIHGTGTCVVIVSHQIDdLLPLVNKIVL 210
                                       45566666666777888888877756677777765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.2    0.0002      0.24      14      37 ..      25      51 ..       2      58 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                            AAA_23 14 eidF...skgltlItGpNGaGKTTild 37
                                      +i++   ++ ++ ItG+ G+GK+T++ 
  gi|298675738|ref|YP_003727488.1| 25 NINLtidKNEFVGITGKIGSGKSTLIK 51
                                      4566777778999************97 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0002      0.24       3      19 ..      38      54 ..      36     104 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0002
                                      EEESTTSSHHHHHHHHH CS
                               dNK  3 veGnIgaGKstlvklLs 19
                                      + G+Ig+GKstl+kl++
  gi|298675738|ref|YP_003727488.1| 38 ITGKIGSGKSTLIKLFN 54
                                      89************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 1930.83
//
Query:       gi|298675739|ref|YP_003727489.1|  [L=106]
Description: ArsR family transcriptional regulator [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-13   48.5   1.9    1.1e-12   47.6   1.9    1.5  1  HTH_5     Bacterial regulatory protein, arsR family
    0.00073   19.5   0.1     0.0012   18.9   0.1    1.3  1  HTH_20    Helix-turn-helix domain
  ------ inclusion threshold ------
        0.1   12.6   0.1       0.24   11.4   0.1    1.6  1  HTH_1     Bacterial regulatory helix-turn-helix protein, lysR


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   1.9   1.9e-16   1.1e-12       2      41 ..      40      79 ..      39      82 .. 0.93

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 1.9e-16
                                      HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHH CS
                             HTH_5  2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLre 41
                                      + RlkIL +L+++++ vce + +lg+sqs++Sh L++L  
  gi|298675739|ref|YP_003727489.1| 40 KSRLKILLILSKKSMRVCEMVYALGMSQSAISHSLRVLNY 79
                                      78***********************************975 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   1.9e-07    0.0012       2      48 ..      32      77 ..      31      86 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.9e-07
                                      HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHH CS
                            HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvL 48
                                      +++ AL +++R++il  L +++ + + e   +l++s++ +s+ LrvL
  gi|298675739|ref|YP_003727489.1| 32 RVFQALQSKSRLKILLIL-SKKSMRVCEMVYALGMSQSAISHSLRVL 77
                                      689***************.9999999999999**************9 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1     4e-05      0.24      22      38 ..      62      78 ..      61      80 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4e-05
                                      HHTS-HHHHHHHHHHHH CS
                             HTH_1 22 eLglsqpavsrqikrLE 38
                                      +Lg+sq+a+s++++ L+
  gi|298675739|ref|YP_003727489.1| 62 ALGMSQSAISHSLRVLN 78
                                      69***********9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 675.27
//
Query:       gi|298675740|ref|YP_003727490.1|  [L=357]
Description: permease [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-49  166.7  10.4    8.3e-49  166.3  10.4    1.1  1  ArsP_1    Predicted permease


Domain annotation for each model (and alignments):
>> ArsP_1  Predicted permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.3  10.4   4.6e-53   8.3e-49      14     292 ..      22     309 ..      12     311 .. 0.90

  Alignments for each domain:
  == domain 1  score: 166.3 bits;  conditional E-value: 4.6e-53
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ArsP_1  14 leallaLvlgflisgaiqvfvkeekiielLg.prnrlisllvaallGfllpvCscsavPlarrllkkGaplgaavaF 89 
                                        ea + + lgf  +++i +fv+ eki+ +Lg ++ +++s+l a+l+G+ lp+Csc+++P+a++l k+Ga  ga+++F
  gi|298675740|ref|YP_003727490.1|  22 EEAAPYMFLGFGAAALIHIFVPDEKIMDYLGsSAGKFKSVLNASLAGIPLPLCSCGVIPTAISLKKRGATRGATLSF 98 
                                       57889999********************************************************************* PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xx RF
                            ArsP_1  90 lvaaPainiiaiiltlillgwqllvarivlalivaiviglvleylfkeeelekaarevaeaglek..........lt 156
                                       l++ P + +  i++t++l+   ++v+r v+++i+a+ +g+   +  k+e    ++   +     +            
  gi|298675740|ref|YP_003727490.1|  99 LISTPETGVDSIAITYALIDPIMTVFRPVVTFITALSAGITNNIFIKDEIPNFSNPSNESS---NcacescdldkVN 172
                                       ************************************9999988888777655444333332...1234668887755 PP

                                       xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ArsP_1 157 lkpklealka..faknevkewlelgkyLiiGvaiagviqaflpesvllsllggnsvsssllamligvvlyvcslgev 231
                                         +k+++++   f +  v+ ++ + k Li+G+++agvi   +p+++++s+lg +++ s l++ +ig++ly+c+ +  
  gi|298675740|ref|YP_003727490.1| 173 TEQKMSKRFIegFRYSFVELLGDISKWLILGIIFAGVISYAVPDNWIQSYLG-GGINSMLIMLIIGIPLYICASAST 248
                                       5555555555568888888889999*************************66.679********************* PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ArsP_1 232 pfiaalfesglalGsalAfLlagpllslpellillkvlkkklvavllglvvvsvvlaglvi 292
                                       p+++al+++g + G+a  fLlagp+ +  +l +++ +l+k  ++++l+++++ ++ +gl++
  gi|298675740|ref|YP_003727490.1| 249 PLASALIAKGTSPGTAFVFLLAGPATNTATLTMVTRYLGKFTAIIYLMIIAICSLGFGLIL 309
                                       **********************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2415.41
//
Query:       gi|298675741|ref|YP_003727491.1|  [L=154]
Description: phage shock protein C [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-23   82.5   0.4    1.3e-23   82.5   0.4    2.4  1  PspC            PspC domain
    0.00016   21.4   0.0    0.00023   20.9   0.0    1.2  1  DUF2370         Protein of unknown function (DUF2370)
    0.00096   18.2   0.6     0.0015   17.5   0.6    1.3  1  MFS_1           Major Facilitator Superfamily
  ------ inclusion threshold ------
      0.031   14.4   0.0      0.038   14.1   0.0    1.1  1  MCU             Mitochondrial calcium uniporter
      0.032   14.7   0.0      0.032   14.7   0.0    2.4  2  DUF3899         Domain of unknown function (DUF3899)
       0.06   13.5   0.0      0.097   12.8   0.0    1.5  1  DUF2371         Uncharacterised conserved protein (DUF2371)
       0.08   13.1   0.0       0.15   12.3   0.0    1.4  1  UPF0239         Uncharacterised protein family (UPF0239)
       0.15   13.0   0.0       0.15   13.0   0.0    2.2  2  DUF4834         Domain of unknown function (DUF4834)
       0.21   11.4   0.0       0.28   11.0   0.0    1.1  1  Tir_receptor_N  Translocated intimin receptor (Tir) N-terminu
        0.3    9.8   5.2      0.094   11.5   0.4    1.9  2  DUF2207         Predicted membrane protein (DUF2207)
        0.4   10.7   0.0        0.4   10.7   0.0    2.7  3  DUF2116         Uncharacterized protein containing a Zn-ribbo
        2.6    8.4   6.7       0.35   11.2   0.3    2.4  3  Orf78           Orf78 (ac78)


Domain annotation for each model (and alignments):
>> PspC  PspC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.5   0.4   8.7e-27   1.3e-23       2      52 ..      11      66 ..      10      67 .. 0.98

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 8.7e-27
                              PspC  2 rLyRspdnkvlgGVcaGlAeyfgvdptlvRlifvlll.....glllYiilwiilPe 52
                                      +L++s+++++l+GVc+G+Aeyf+vdp+lvR++fv+l+     g+llYiil+i++Pe
  gi|298675741|ref|YP_003727491.1| 11 KLTKSKSDRMLAGVCGGIAEYFDVDPVLVRVAFVVLAlvnglGILLYIILAIVMPE 66
                                      89*****************************************************8 PP

>> DUF2370  Protein of unknown function (DUF2370)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.5e-07   0.00023     146     211 ..      63     129 ..      57     132 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.5e-07
                           DUF2370 146 epsdpnshdldkekvaekgekeeaaalsdlelaeeek.nkesssewlayvlmilGlfiliksvvdyl 211
                                        +++p+++d ++e+++++++ +++++ +d+ +++++k n+++++ wl ++l+ilG+f++i  +  ++
  gi|298675741|ref|YP_003727491.1|  63 VMPEPENNDKTPEQNTTSENGTDEYSENDTYTKTQHKsNRTDRTLWLGVILIILGIFLIIDRFNVFW 129
                                       56789999999999988888899999999988887773558999****************9877766 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.6     1e-06    0.0015     143     222 ..      27     121 ..      20     151 .. 0.59

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1e-06
                             MFS_1 143 llasslg.....Wravfyilaivsllafvlfllllpeepperkrkspkeee...........kgtgpaplvpawkal 203
                                        +a+++       r++f++la+v  l+++l ++l  + p ++ ++++ e+            +       ++  k+ 
  gi|298675741|ref|YP_003727491.1|  27 GIAEYFDvdpvlVRVAFVVLALVNGLGILLYIILAIVMPEPENNDKTPEQNttsengtdeysE-NDTYTKTQ-HKSN 101
                                       3444444555559**************996666665555555555555554577777777742.33333333.5777 PP

                             MFS_1 204 lkdpvlw.illialllfffg 222
                                       ++d+ lw  +++++l++f++
  gi|298675741|ref|YP_003727491.1| 102 RTDRTLWlGVILIILGIFLI 121
                                       88887775333333333222 PP

>> MCU  Mitochondrial calcium uniporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.5e-05     0.038      60     121 ..      77     138 ..      31     140 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.5e-05
                                       HHHHHHHHHH-SHHHHHHHHTCCCGGGCHHHHGGGHHHHHHHHTHHHHHH.HTTTS-S----H CS
                               MCU  60 eekleelreelepleekkeeidekAerrtrrllwagLallavqlgilarL.TwweysWDvmEP 121
                                       ++  e+ ++e+++  +  ++ ++k++r  r+l+ + ++++   + i+ r+  +w + WDv+ P
  gi|298675741|ref|YP_003727491.1|  77 NTTSENGTDEYSENDT-YTKTQHKSNRTDRTLWLGVILIILGIFLIIDRFnVFWWLGWDVLWP 138
                                       3333444445544444.67778888887777777777777778888889857********866 PP

>> DUF3899  Domain of unknown function (DUF3899)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   1.1       1.3   1.9e+03      73      81 ..      55      63 ..      39      65 .. 0.61
   2 ?   14.7   0.0   2.2e-05     0.032      49      83 ..      85     121 ..      68     122 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.3
                           DUF3899 73 lllivlsiv 81
                                      ll+i+l+iv
  gi|298675741|ref|YP_003727491.1| 55 LLYIILAIV 63
                                      455555555 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.2e-05
                           DUF3899  49 syyeykek..kkesskkstrplliiGlllivlsivll 83 
                                       + y +++   k+++++++t  +l+ G++li+l+i+l+
  gi|298675741|ref|YP_003727491.1|  85 DEYSENDTytKTQHKSNRTDRTLWLGVILIILGIFLI 121
                                       34444444668888*********************97 PP

>> DUF2371  Uncharacterised conserved protein (DUF2371)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.5e-05     0.097      43     120 ..      47     122 ..       4     129 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.5e-05
                           DUF2371  43 vlllGllvllvGiamavlgywpkkaklaseekssssstaessseklgllarfleqylysdklkvlGPlimGiGiflf 119
                                        l+ Gl +ll  i +a++  +p++++++ e++++s ++ + + ++  + ++  ++   +d+   lG +++ +Gifl+
  gi|298675741|ref|YP_003727491.1|  47 ALVNGLGILL-YIILAIVMPEPENNDKTPEQNTTS-ENGTDEYSENDTYTKTQHKSNRTDRTLWLGVILIILGIFLI 121
                                       2333333333.356777777887765555444433.333333444456888888899999999*************9 PP

                           DUF2371 120 i 120
                                       i
  gi|298675741|ref|YP_003727491.1| 122 I 122
                                       8 PP

>> UPF0239  Uncharacterised protein family (UPF0239)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0    0.0001      0.15      35      81 ..      58     101 ..      48     106 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                           UPF0239  35 CilAiillpsskseesveeeaesseeksseqvkkpkaaaaqrlkkik 81 
                                        ilAi+ +p+ ++++++ e+  +se+  +++ +++  + +++++k+ 
  gi|298675741|ref|YP_003727491.1|  58 IILAIV-MPEPENNDKTPEQNTTSENG-TDEYSEND-TYTKTQHKSN 101
                                       478888.********988888888884.44443333.3444445544 PP

>> DUF4834  Domain of unknown function (DUF4834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0    0.0001      0.15       8      75 ..      41     104 ..      37     108 .. 0.55
   2 ?   -1.8   1.5       4.2   6.3e+03      10      19 ..     112     121 ..     105     131 .. 0.48

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.0001
                           DUF4834   8 lifiiailviglsilsvilrtvfglgsrkkssksaqkqfgnstnsnqqksqsrsetkeegeiieeers 75 
                                       + f+++ lv gl il  i+ ++       +  ++ +  ++n t++n + ++s++ t+++++ ++++++
  gi|298675741|ref|YP_003727491.1|  41 VAFVVLALVNGLGILLYIILAIVM--PEPE--NNDKTPEQNTTSENGTDEYSENDTYTKTQHKSNRTD 104
                                       67899999*******999999933..2222..233333334444444444444444444444444443 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.2
                           DUF4834  10 fiiailvigl 19 
                                       ++i++ ++ +
  gi|298675741|ref|YP_003727491.1| 112 ILIILGIFLI 121
                                       2222222222 PP

>> Tir_receptor_N  Translocated intimin receptor (Tir) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00019      0.28     186     241 ..      65     118 ..      57     122 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00019
                    Tir_receptor_N 186 pkdtgeskakdresesgavnsaetkvvsetstststsslrsdpklwlslgtiaagl 241
                                       p+ ++  + k  e++++++n ++  +  +t t t   s r+d  lwl +  i  g+
  gi|298675741|ref|YP_003727491.1|  65 PEPEN--NDKTPEQNTTSENGTDEYSENDTYTKTQHKSNRTDRTLWLGVILIILGI 118
                                       44443..4455677788888899889999******************998877765 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.3     0.082   1.2e+02     382     401 ..      42      61 ..       2      80 .. 0.55
   2 ?   11.5   0.4   6.3e-05     0.094     367     433 ..      88     151 ..      68     154 .] 0.50

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.082
                           DUF2207 382 klsalglgliilglililla 401
                                        + +l+l+ ++ +l+ i+la
  gi|298675741|ref|YP_003727491.1|  42 AFVVLALVNGLGILLYIILA 61 
                                       22222222222222222222 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 6.3e-05
                           DUF2207 367 kergyfdkkgkkklkklsalglgliilglilillallllvlllvfllilllillliaiivlllfsrl 433
                                       +e+  ++k++ k   + ++l+lg+ il++++i+l++  ++  ++++l + ++++ i+i++ +++ ++
  gi|298675741|ref|YP_003727491.1|  88 SENDTYTKTQHKSNRTDRTLWLGV-ILIILGIFLIIDRFN--VFWWLGWDVLWPGILILIGFWIITR 151
                                       344556666444444444444444.444445555666666..4444444444444444444444444 PP

>> DUF2116  Uncharacterized protein containing a Zn-ribbon (DUF2116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   3.2       8.7   1.3e+04      41      41 ..      55      55 ..      37      65 .. 0.56
   2 ?   10.7   0.0   0.00026       0.4      27      56 ..      92     122 ..      75     125 .. 0.84
   3 ?   -1.7   0.3         2     3e+03      44      57 ..     139     151 ..     135     153 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 8.7
                           DUF2116 41 i 41
                                      +
  gi|298675741|ref|YP_003727491.1| 55 L 55
                                      2 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00026
                           DUF2116  27 eyekkrkkvars.qqilfgililllavvlvl 56 
                                        y+k + k  r+ + + +g+++++l ++l++
  gi|298675741|ref|YP_003727491.1|  92 TYTKTQHKSNRTdRTLWLGVILIILGIFLII 122
                                       689999887665389999*********9987 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2
                           DUF2116  44 gililllavvlvlk 57 
                                       gilil +  +++++
  gi|298675741|ref|YP_003727491.1| 139 GILIL-IGFWIITR 151
                                       67777.88888876 PP

>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   1.5       1.3     2e+03      71      86 ..      47      62 ..      34      69 .. 0.57
   2 ?   11.2   0.3   0.00023      0.35      27      79 ..      68     121 ..      56     131 .. 0.60
   3 ?   -1.3   0.1       1.8   2.7e+03      79      92 ..     140     153 ..     139     154 .] 0.85

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.3
                             Orf78 71 lavvcvlvllyviyYf 86
                                        v  + +lly+i+ +
  gi|298675741|ref|YP_003727491.1| 47 ALVNGLGILLYIILAI 62
                                      2222344667777654 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00023
                             Orf78  27 dnddndkaenkkekksaaeknditekesnaaekaqalnillisllavvc.vlvl 79 
                                       +n+d++ ++n+++++ + e+++ ++ ++++++++ +   l+++++ ++  ++++
  gi|298675741|ref|YP_003727491.1|  68 ENNDKTPEQNTTSENGTDEYSENDTYTKTQHKSNRTDRTLWLGVILIILgIFLI 121
                                       444444444555555555555666666666777888899999988776514444 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.8
                             Orf78  79 llyviyYfvilrer 92 
                                       +l++i +++i+r r
  gi|298675741|ref|YP_003727491.1| 140 ILILIGFWIITRVR 153
                                       7889999***9977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1246  (0.0694963); expected 358.6 (0.02)
Passed bias filter:                      718  (0.0400469); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.59
# Mc/sec: 780.28
//
Query:       gi|298675742|ref|YP_003727492.1|  [L=153]
Description: hypothetical protein Metev_1862 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-31  106.9   0.0    6.9e-31  106.6   0.0    1.1  1  DUF123    Domain of unknown function DUF123


Domain annotation for each model (and alignments):
>> DUF123  Domain of unknown function DUF123
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.6   0.0   3.9e-35   6.9e-31       1      94 []      30     125 ..      30     125 .. 0.94

  Alignments for each domain:
  == domain 1  score: 106.6 bits;  conditional E-value: 3.9e-35
                            DUF123   1 ielkkgvylYvGsalgsgglasRvkrHaslskkkekklhWhiDyLleseeaelaevvva.seerlEcalaeal.e.a 74 
                                       i++k+g+++YvGsalg+ggl +RvkrH+slsk+++k+ +WhiD L+ s+ ++l ++++a +++++Ec +a++l + +
  gi|298675742|ref|YP_003727492.1|  30 ISFKEGYHVYVGSALGPGGL-KRVKRHISLSKNRDKNPRWHIDNLHISQCFKLFATICAiTDKKYECLVAQKLiQnN 105
                                       589*****************.************************************955*************7645 PP

                            DUF123  75 eapvagfGasDckcesHLlk 94 
                                       ++++++fG+sDc+c+sHL++
  gi|298675742|ref|YP_003727492.1| 106 WNYIPDFGCSDCSCQSHLFY 125
                                       56****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 1050.63
//
Query:       gi|298675743|ref|YP_003727493.1|  [L=116]
Description: small multidrug resistance protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-28   98.9   7.8    2.6e-28   98.5   7.8    1.1  1  Multi_Drug_Res  Small Multidrug Resistance protein
    6.3e-05   23.2  11.2    9.3e-05   22.6  11.2    1.3  1  EamA            EamA-like transporter family
  ------ inclusion threshold ------
       0.18   11.4   0.3       0.18   11.4   0.3    2.6  3  DUF4044         Protein of unknown function (DUF4044)


Domain annotation for each model (and alignments):
>> Multi_Drug_Res  Small Multidrug Resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.5   7.8   4.3e-32   2.6e-28       1      93 []      12     104 ..      12     104 .. 0.99

  Alignments for each domain:
  == domain 1  score: 98.5 bits;  conditional E-value: 4.3e-32
                                       XX-HHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHH CS
                    Multi_Drug_Res   1 mnwvllvlAillevvgailLklsegftkltpsllvivgygisfllLskalkslpvsvAYavwsGiGtvlivlvgill 77 
                                       m+w++l++A+ +e+ +a++Lk++egf+kl p++++++++++sf++Ls+a+k+lp+++ Yavw+G  +++++++g+ l
  gi|298675743|ref|YP_003727493.1|  12 MEWIYLFIAATFEIGWAVSLKYTEGFSKLYPTIVMVIFMVLSFYFLSQAVKNLPIGTGYAVWTGTAVIGTAILGVFL 88 
                                       89*************************************************************************** PP

                                       H--------HHHHHHH CS
                    Multi_Drug_Res  78 fgeslslkkliglali 93 
                                       f+e+ ++ +++ ++li
  gi|298675743|ref|YP_003727493.1|  89 FNEPYNIGRVLCIMLI 104
                                       **************98 PP

>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6  11.2   1.6e-08   9.3e-05      43     135 ..      15     111 ..       9     113 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.6e-08
                              EamA  43 illliiallkegkl..aklslkd.wllllllgllgtvlafllffyalkktsasnasli.tslePvftlilsvlllge 115
                                       i l+i a ++ g+    k++     l+  ++ ++ +vl f+++ +a+k+++ ++   + t ++++ t+il+v+l++e
  gi|298675743|ref|YP_003727493.1|  15 IYLFIAATFEIGWAvsLKYTEGFsKLYPTIVMVIFMVLSFYFLSQAVKNLPIGTGYAVwTGTAVIGTAILGVFLFNE 91 
                                       556666666666665434444443566699***********************998777****************** PP

                              EamA 116 kltlkqllgivlillGvlli 135
                                       + ++  +l i+li  G++ +
  gi|298675743|ref|YP_003727493.1|  92 PYNIGRVLCIMLIATGIVGL 111
                                       *****************975 PP

>> DUF4044  Protein of unknown function (DUF4044)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   2.9e-05      0.18      12      21 ..      43      52 ..      36      53 .. 0.78
   2 ?   -3.1   0.8      0.99   5.9e+03      22      30 ..      77      85 ..      76      86 .. 0.67
   3 ?    1.6   0.3     0.034     2e+02      18      23 ..     101     106 ..      98     110 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.9e-05
                           DUF4044 12 TkvvvwlMli 21
                                      T+v+v++M++
  gi|298675743|ref|YP_003727493.1| 43 TIVMVIFMVL 52
                                      99******96 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.99
                           DUF4044 22 aTVGSvllg 30
                                      a +G  +lg
  gi|298675743|ref|YP_003727493.1| 77 AVIGTAILG 85
                                      567777777 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.034
                           DUF4044  18 lMliaT 23 
                                       +MliaT
  gi|298675743|ref|YP_003727493.1| 101 IMLIAT 106
                                       8****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       839  (0.0467957); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 729.58
//
Query:       gi|298675744|ref|YP_003727494.1|  [L=133]
Description: hypothetical protein Metev_1864 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-40  138.3   0.0    1.3e-40  138.2   0.0    1.0  1  UPF0047   Uncharacterised protein family UPF0047


Domain annotation for each model (and alignments):
>> UPF0047  Uncharacterised protein family UPF0047
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.2   0.0   7.1e-45   1.3e-40       1     114 [.      17     129 ..      17     130 .. 0.97

  Alignments for each domain:
  == domain 1  score: 138.2 bits;  conditional E-value: 7.1e-45
                                       E-HHHHHHHHHHHT.SEEEEEEEESSSSEEEEEEESSSHHHHHHHHHHHHHHSTTT..T-GGGTTS..THHHHHHHH CS
                           UPF0047   1 diteeveeavkesgvkeGlvlvfsrhttasltinEnadpdvqeDleealeklvpee..eYrhnaegpdnadaHlkss 75 
                                       dit+ev++a+ke + ++G++++++rhtt ++tinEnadp+vq+D+ e+l+klvp +   ++h  eg  nad+H+kss
  gi|298675744|ref|YP_003727494.1|  17 DITSEVKNALKELNADNGIATIYCRHTTGGITINENADPSVQHDIIEFLNKLVPANqsYFKHM-EG--NADSHVKSS 90 
                                       8******************************************************99778888.99..********* PP

                                       HH-SEEEEEEETTEE---TTEEEEEEESS-SSEEEEEEE CS
                           UPF0047  76 llgssltipvedgklalGtwqsiylveldgpreRkvvvq 114
                                       ++g+s+++++e+gk +lG+wq+i++ e+dgpr+Rkv+v+
  gi|298675744|ref|YP_003727494.1|  91 IIGTSEQVIIEEGKPVLGRWQGIFFTEFDGPRNRKVHVK 129
                                       ************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 875.29
//
Query:       gi|298675745|ref|YP_003727495.1|  [L=319]
Description: hypothetical protein Metev_1865 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00012   21.5   0.0     0.0002   20.9   0.0    1.4  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
  ------ inclusion threshold ------
      0.033   13.9   0.1       0.11   12.1   0.0    1.9  2  DUF1367       Protein of unknown function (DUF1367)


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   2.2e-08    0.0002      69     210 .]      80     236 ..      30     236 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.2e-08
                                       HHHHHHHHHHHHHHTBSEEEEEBCC.GBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTCHHH CS
                      AP_endonuc_2  69 vdalkraielaaaLGapllvlhpGt.agagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgdeel 144
                                       ++++++aie+     +   ++h  +  + +     +++++ ++++l+ + +y++  +  l++E  +  +++ +  +l
  gi|298675745|ref|YP_003727495.1|  80 RKYVESAIEFLTGTSGTGYIVH--DeTDPYLTTLSDSRLNSYINALKLIEPYLKNLNNNLYIEFSNTLEINYY-LKL 153
                                       5566666666655555555555..235567777788999******************************9777.788 PP

                                       HHHHHHHTTTTEEEEEEHHHHHHH................TTTHHHHHHHHHGGEEEEEE.EESS.TTTTSSTTEES CS
                      AP_endonuc_2 145 arlldavdspnvgvclDtgHllia................eedvddalraladrikhvHikDakg.dlgagrdrhvp 204
                                        r ++ ++ +++g c+D+gH ++                 +  + d+ ++  + + hvH +D ++     g+ +h  
  gi|298675745|ref|YP_003727495.1| 154 IRQISHTNMEHIGSCIDIGHVYYFyrvkqgytknesieklKQFIVDVKNTGVPVYYHVHDCDPYNpHPWYGVADHKC 230
                                       88888888888******************888888865555555555666666688888888888666669999999 PP

                                       TTSSSS CS
                      AP_endonuc_2 205 igeGei 210
                                       ig+Gei
  gi|298675745|ref|YP_003727495.1| 231 IGDGEI 236
                                       999987 PP

>> DUF1367  Protein of unknown function (DUF1367)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.3e-05      0.11      68     126 ..      75     133 ..      70     165 .. 0.87
   2 ?   -1.9   0.1      0.25   2.3e+03      67     108 ..     267     308 ..     264     316 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.3e-05
                           DUF1367  68 isqkErklvrglakflaavagsesvlkeaadeylakvakkRaeklisidksldafrewv 126
                                       i++++rk v+  ++fl+ ++g   ++++ +d yl ++++ R + +i++ k ++ +++ +
  gi|298675745|ref|YP_003727495.1|  75 IPERNRKYVESAIEFLTGTSGTGYIVHDETDPYLTTLSDSRLNSYINALKLIEPYLKNL 133
                                       88999************************************************998765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.25
                           DUF1367  67 visqkErklvrglakflaavagsesvlkeaadeylakvakkR 108
                                       +++++E + + ++ak+ +  a ++    +++ + l+ + k R
  gi|298675745|ref|YP_003727495.1| 267 ILTESETQKLIAYAKKHNLDAEKQIRDGKIIKQTLDDIVKSR 308
                                       566677777777777766666666555667777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       817  (0.0455686); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1958.05
//
Query:       gi|298675746|ref|YP_003727496.1|  [L=134]
Description: response regulator receiver protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-26   93.1   0.4    1.3e-26   92.9   0.4    1.0  1  Response_reg  Response regulator receiver domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.9   0.4   7.4e-31   1.3e-26       1     111 [.      15     129 ..      15     130 .. 0.96

  Alignments for each domain:
  == domain 1  score: 92.9 bits;  conditional E-value: 7.4e-31
                                       EEEESSSHHHHHHHHHHHH...HTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCT..TTS CS
                      Response_reg   1 vlivdDdplvrellrqlle...eegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireed..pel 72 
                                       +l+++D++l+r+l+++++e   ++ y ++  +e+g eal++++  k dlillDi++p +dGlell++ +e++  +++
  gi|298675746|ref|YP_003727496.1|  15 ILVIEDNKLNRQLMNDFIElidSDSY-NIINVENGLEALKKVDYYKLDLILLDIQLPLIDGLELLSKFKEKPnvKNT 90 
                                       89*****************9966777.999******************************************9999* PP

                                       EEEEEESSTSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                      Response_reg  73 pviiltahseeedavealkagaddflsKpfdpeeLlkal 111
                                       p+i++ta++ e d+++ l+ag d++l Kp+d ++  +++
  gi|298675746|ref|YP_003727496.1|  91 PIIAVTAYAMEGDREKFLNAGCDEYLPKPLDVDDFEDKI 129
                                       *********************************998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 903.83
//
Query:       gi|298675747|ref|YP_003727497.1|  [L=209]
Description: hypothetical protein Metev_1868 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.016   14.8   0.2      0.031   13.8   0.2    1.5  1  Baculo_11_kDa  Baculovirus 11 kDa family
      0.032   14.1   2.8      0.075   12.9   2.8    1.6  1  ODV-E18        Occlusion-derived virus envelope protein ODV-E


Domain annotation for each model (and alignments):
>> Baculo_11_kDa  Baculovirus 11 kDa family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   3.5e-06     0.031      29      74 ..       3      48 ..       1      54 [. 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.5e-06
                     Baculo_11_kDa 29 NrsflrdFvLvicglvvfvvivlfilLlvvilknaeaeeaekekre 74
                                      N+sf+++  ++i  lvv+vvi  f+lL +  ++++ +++++ ++++
  gi|298675747|ref|YP_003727497.1|  3 NKSFITSKNMLIFLLVVVVVISAFLLLDFKAATSQTNSNTQSNSYS 48
                                      99****************************9999999998877765 PP

>> ODV-E18  Occlusion-derived virus envelope protein ODV-E18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   2.8   8.4e-06     0.075      25      65 ..      11      56 ..       5      71 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.4e-06
                           ODV-E18 25 sllltilvvlviii.llvllvqs..sstGsd..ssssnannartGf 65
                                      ++l+ +lvv+v+i  +l+l +++  s t s+  s s ++nn+ + f
  gi|298675747|ref|YP_003727497.1| 11 NMLIFLLVVVVVISaFLLLDFKAatSQTNSNtqSNSYSTNNTGINF 56
                                      8999999988888514444455411334443114445677776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1408  (0.078532); expected 358.6 (0.02)
Passed bias filter:                      739  (0.0412181); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1471.86
//
Query:       gi|298675748|ref|YP_003727498.1|  [L=112]
Description: hypothetical protein Metev_1869 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0019   18.2   0.2     0.0039   17.2   0.0    1.6  2  HTH_3           Helix-turn-helix
      0.009   15.8   0.0      0.026   14.3   0.0    1.7  2  HTH_23          Homeodomain-like domain
     0.0099   15.7   0.0      0.022   14.6   0.0    1.6  1  P22_Cro         DNA-binding transcriptional regulator Cro
  ------ inclusion threshold ------
      0.011   15.9   0.0      0.027   14.7   0.0    1.6  1  DUF2811         Protein of unknown function (DUF2811)
      0.015   14.0   0.1      0.016   13.8   0.1    1.0  1  Cpn60_TCP1      TCP-1/cpn60 chaperonin family
      0.022   14.8   0.1       0.03   14.4   0.1    1.3  1  Cro             Cro
      0.039   13.8   0.0      0.075   12.9   0.0    1.6  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.054   13.5   0.0       0.14   12.1   0.0    1.7  2  HTH_37          Helix-turn-helix domain
      0.054   14.0   0.0      0.091   13.3   0.0    1.4  1  DUF4473         Domain of unknown function (DUF4473)
      0.057   13.6   0.0      0.096   12.8   0.0    1.4  1  HTH_28          Helix-turn-helix domain
      0.094   12.8   0.1        0.3   11.2   0.0    1.8  2  HTH_7           Helix-turn-helix domain of resolvase
       0.11   13.0   0.0       0.15   12.5   0.0    1.3  1  HTH_40          Helix-turn-helix domain
       0.11   12.0   0.0       0.27   10.8   0.0    1.6  1  HTH_24          Winged helix-turn-helix DNA-binding


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.8e-06    0.0039       4      34 ..      23      53 ..      20      58 .. 0.88
   2 ?   -3.2   0.0       6.9   9.6e+03      12      19 ..      67      74 ..      64      77 .. 0.57

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.8e-06
                                      HHHHTTHHHHHHHHHHTSSHHHHHHHHTTSS CS
                             HTH_3  4 lRkqlglsqeeLAeklGvsrstisriEnGer 34
                                       + ++g sq+++Ae+ ++ +s++s+++  +r
  gi|298675748|ref|YP_003727498.1| 23 ELVKNGVSQRKVAELFDMAPSAVSQYITKKR 53
                                      56799*********************98765 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6.9
                                      HHHHHHHH CS
                             HTH_3 12 qeeLAekl 19
                                      + +LA ++
  gi|298675748|ref|YP_003727498.1| 67 ISQLASEI 74
                                      44566554 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   1.9e-05     0.026       8      39 ..      19      50 ..      13      58 .. 0.76
   2 ?   -1.8   0.0       2.2   3.1e+03      19      27 ..      85      93 ..      79      94 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.9e-05
                            HTH_23  8 lrillllaeGlsvreIAreLgvsrrTvyrwlk 39
                                      +++  l+++G s+r++A+++++ ++ v++++ 
  gi|298675748|ref|YP_003727498.1| 19 ALASELVKNGVSQRKVAELFDMAPSAVSQYIT 50
                                      334444555*******************9964 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.2
                            HTH_23 19 svreIAreL 27
                                       + eI+++L
  gi|298675748|ref|YP_003727498.1| 85 KICEICKKL 93
                                      567899887 PP

>> P22_Cro  DNA-binding transcriptional regulator Cro
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.6e-05     0.022      11      42 ..      30      58 ..      21      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.6e-05
                                      SHHHHHHHHTS-HHHHHHHHTC--HHHHHHHH CS
                           P22_Cro 11 gvekvAkalgvtksAVsqWgeeiPelrayqie 42
                                      +++kvA++ + ++sAVsq    i ++r y+ie
  gi|298675748|ref|YP_003727498.1| 30 SQRKVAELFDMAPSAVSQY---ITKKRGYRIE 58
                                      689****************...999****999 PP

>> DUF2811  Protein of unknown function (DUF2811)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0     2e-05     0.027      24      51 ..      10      37 ..       6      39 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2e-05
                           DUF2811 24 WDqdrllqaALslFLlqngssdravarv 51
                                      WD    + aAL+  L++ng+s+r+va++
  gi|298675748|ref|YP_003727498.1| 10 WDVLPAIRAALASELVKNGVSQRKVAEL 37
                                      999999*******************987 PP

>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   1.2e-05     0.016      77     150 ..      21      90 ..      18     110 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.2e-05
                                       HHHHHHCTXXHHHHHHHHHHHHHHHHHHH.HHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHH CS
                        Cpn60_TCP1  77 aekliaagvhpttiiegyekalekaleaL.keiaveisseekdreeLlkvartslsskltskeaeelsklvvdAv 150
                                       a++l+++gv  +++ e +++a +++ +++ k+   +i+ +e+ ++++ ++a+ + ++ +++ + ++++++    +
  gi|298675748|ref|YP_003727498.1|  21 ASELVKNGVSQRKVAELFDMAPSAVSQYItKKRGYRIEFDEDIKNSISQLASEIQKGTVDDVS-DKICEI----C 90 
                                       7899*************************5444445555566677777777777777743333.555555....4 PP

>> Cro  Cro
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   2.2e-05      0.03      13      46 ..      29      62 ..      17      76 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.2e-05
                                      HHHHHHHHHHTS-HHHHHHHHHCT-EEEEEEETT CS
                               Cro 13 vGQaktAkdlgvkqsaIsKAlkakRnIylivded 46
                                      v Q k+A+ + +++sa+s  + +kR   +  ded
  gi|298675748|ref|YP_003727498.1| 29 VSQRKVAELFDMAPSAVSQYITKKRGYRIEFDED 62
                                      45***********************766666655 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.5e-05     0.075      10      38 ..      30      58 ..      21      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.5e-05
                    YdaS_antitoxin 10 gqkaLAealgvsqqaVsqWlkgkkqvpae 38
                                      +q+++Ae+ +++++aVsq +  k++  +e
  gi|298675748|ref|YP_003727498.1| 30 SQRKVAELFDMAPSAVSQYITKKRGYRIE 58
                                      8*******************988875554 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0    0.0001      0.14      22      50 ..      19      47 ..      14      60 .. 0.86
   2 ?   -1.9   0.0       2.4   3.3e+03      15      25 ..      66      76 ..      57      81 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0001
                                      HHHHHHHHCT--HHHHHHHHT--HHHHHH CS
                            HTH_37 22 aiaeliekrelsqseaaqllgiaqPkvsr 50
                                      a+a  + k++ sq+++a+l+ +a + vs+
  gi|298675748|ref|YP_003727498.1| 19 ALASELVKNGVSQRKVAELFDMAPSAVSQ 47
                                      57888899*******************97 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.4
                                      HHHHHHHHHHH CS
                            HTH_37 15 aKaqlalaiae 25
                                        +qla++i++
  gi|298675748|ref|YP_003727498.1| 66 SISQLASEIQK 76
                                      55677777775 PP

>> DUF4473  Domain of unknown function (DUF4473)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.6e-05     0.091       8      39 ..      21      52 ..      17      76 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.6e-05
                           DUF4473  8 kaeLvaaGlsekaadglvkiaekfksefakak 39
                                       +eLv++G+s+  +++l+++a  + s++ ++k
  gi|298675748|ref|YP_003727498.1| 21 ASELVKNGVSQRKVAELFDMAPSAVSQYITKK 52
                                      57*********************999998874 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.9e-05     0.096       7      33 ..      23      49 ..      17      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.9e-05
                            HTH_28  7 kllaaGhsvreaArelgisrrtvyrWi 33
                                      +l+++G+s+r +A+++ + ++ v++ i
  gi|298675748|ref|YP_003727498.1| 23 ELVKNGVSQRKVAELFDMAPSAVSQYI 49
                                      57889******************9876 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00022       0.3      12      43 ..      19      50 ..      14      52 .. 0.87
   2 ?   -1.9   0.0       2.6   3.6e+03      23      30 ..      66      73 ..      64      75 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                                      GGGGSSTTTT--STTTSSSS---SSSS--SS- CS
                             HTH_7 12 nrvvkLleeGisiskIAkevnisRsTvYRyla 43
                                      + + +L+++G s +k+A+ ++ ++s v +y +
  gi|298675748|ref|YP_003727498.1| 19 ALASELVKNGVSQRKVAELFDMAPSAVSQYIT 50
                                      6799********************99987766 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.6
                                      -STTTSSS CS
                             HTH_7 23 siskIAke 30
                                      sis++A e
  gi|298675748|ref|YP_003727498.1| 66 SISQLASE 73
                                      89999977 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00011      0.15       6      72 ..      22      82 ..      17      97 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                            HTH_40  6 lelleeglsieeIAkerglkesTIegHLaelieegeeidlerlvseeeekeIeeaiekvgseklkpi 72
                                       el+++g s  ++A+   +++s + +++++  + g++i++    +e++++ I +   ++++    ++
  gi|298675748|ref|YP_003727498.1| 22 SELVKNGVSQRKVAELFDMAPSAVSQYITK--KRGYRIEF----DEDIKNSISQLASEIQKGTVDDV 82
                                      5899**************************..99998888....56777777777666655444444 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0002      0.27      17      39 ..      28      50 ..      21      52 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0002
                            HTH_24 17 risqreLAerlglSpstvnrrlk 39
                                      + sqr +Ae  ++ ps+v++++ 
  gi|298675748|ref|YP_003727498.1| 28 GVSQRKVAELFDMAPSAVSQYIT 50
                                      79*******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       961  (0.0536003); expected 358.6 (0.02)
Passed bias filter:                      745  (0.0415528); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 804.18
//
Query:       gi|298675749|ref|YP_003727499.1|  [L=392]
Description: cysteine desulfurase NifS [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-93  312.0   0.1    5.9e-93  311.8   0.1    1.0  1  Aminotran_5      Aminotransferase class-V
    1.1e-05   24.9   0.8    1.7e-05   24.4   0.3    1.5  2  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    3.8e-05   23.1   0.2    6.2e-05   22.4   0.2    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
    4.6e-05   22.8   0.0     0.0002   20.7   0.0    1.8  1  Aminotran_1_2    Aminotransferase class I and II
  ------ inclusion threshold ------
       0.05   12.1   0.1      0.095   11.2   0.1    1.4  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
       0.12   11.1   0.0       0.19   10.4   0.0    1.3  1  Pyridoxal_deC    Pyridoxal-dependent decarboxylase conserved 


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  311.8   0.1     2e-96   5.9e-93       1     371 []      11     372 ..      11     372 .. 0.98

  Alignments for each domain:
  == domain 1  score: 311.8 bits;  conditional E-value: 2e-96
                                       EEEBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHH CS
                       Aminotran_5   1 iyldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlv 77 
                                       +y+d aAtt + +eV++a+  y+t+y +n+ +s ++ +ke  +a+e+arekva+ ina++ +++ ftsG+te+ n +
  gi|298675749|ref|YP_003727499.1|  11 VYMDHAATTSTDPEVVNAMVPYFTEYFGNP-SSPYTIAKESEEAIEKAREKVANAINAKT-DRVFFTSGGTESDNWA 85 
                                       79****************************.999*************************7.**************** PP

                                       HHHCCCC.-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTT CS
                       Aminotran_5  78 alslars.lkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtG 153
                                       ++++a +  ++g++i++t++ehha l p++ l+ ++g++v+++p+d+ g++ +d+++++++++t l++++ ++n++G
  gi|298675749|ref|YP_003727499.1|  86 IKGVAFAnKNKGNHIITTAIEHHAVLHPCEWLE-KQGFDVTYLPVDKYGRVSVDDVRDAITDQTILITVMFANNEIG 161
                                       ****9999************************9.66***************************************** PP

                                       EB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTSSTT-EEEEEEHHHHHTS..SS.STTS CS
                       Aminotran_5 154 tiqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghKllgPtGiGvlyvrkellekleplllggem 230
                                       ti+p+eeig++a+++g+++++Da+qa+g+  +dv+++++D+l++sghK++gP+G+G+ly++k   +k+  ++ gg  
  gi|298675749|ref|YP_003727499.1| 162 TIEPIEEIGEVARENGVYFHTDAVQAIGQLLVDVEDMNIDLLSLSGHKFYGPKGTGALYIKK--GVKIDNFMHGGA- 235
                                       **************************************************************..99**********. PP

                                       EEEEETTEEEEHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CT CS
                       Aminotran_5 231 veevsleettfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaer 307
                                             +e++        +aGT+nv+gi+glg+a+e++   ++e+ +k+ ++l+++l ++l ++p++ l g +++er
  gi|298675749|ref|YP_003727499.1| 236 ------QEKQ-------RRAGTENVPGIVGLGEAIEHV-TSDIENHAKRMQSLRDRLINGLLEIPKTHLCG-HPTER 297
                                       ......8877.......89*******************.99******************************.799** PP

                                       CBSEEEEEETTCSHHHHHHHHHHTTEEEEEE-TTT....HHHHHHTT.S.......-EEEEE--TTS-HHHHHHH CS
                       Aminotran_5 308 rasivsfnfkgvhaedvatlLdeegIavrsGhhca....qplmkrlale.......gtvRaSlyiynteeevdrl 371
                                        ++ v+++f++++ e +  +Ld++ Ia ++G++c+    +p++++++         g++R+Sl+  ntee+vd++
  gi|298675749|ref|YP_003727499.1| 298 LPNNVNIVFEYIEGESILLMLDSYSIAASTGSACTsaslEPSHVLVGCGlpheiahGSLRLSLGKENTEEDVDYV 372
                                       ***********************************9999999999999999*********************975 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.3   5.5e-09   1.7e-05      44     151 ..      75     190 ..      47     205 .. 0.81
   2 ?   -3.5   0.0       1.6   4.9e+03     335     359 ..     351     375 ..     349     376 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 5.5e-09
                                       ESSHHHHHHHHHHH...TTTTTT-EEEEESSS-THHHHHHHHT...T-EEEEE-B-TTTSSB-GGGCGGG--TTE.. CS
                   DegT_DnrJ_EryC1  44 vssGtaAlhlaLra...lgvgpgdeVIvpsltFvatanavlel...gakpvfvDvdpdtynidpaaieaaitert.. 112
                                       +s Gt++   a++     + ++g+ +I++++   a  ++  +l   g ++ ++ vd +   +++++++ ait +t  
  gi|298675749|ref|YP_003727499.1|  75 TSGGTESDNWAIKGvafANKNKGNHIITTAIEHHAVLHPCEWLekqGFDVTYLPVD-KYGRVSVDDVRDAITDQTil 150
                                       5666666666666533344569**************99987653338889999999.899***************66 PP

                                       .EEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT- CS
                   DegT_DnrJ_EryC1 113 .kaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlGa 151
                                           ++ +  G +  ++++ ++a++ g+++  Da +A+G 
  gi|298675749|ref|YP_003727499.1| 151 iTVMFANNEIGTIEPIEEIGEVARENGVYFHTDAVQAIGQ 190
                                       3344445679****************************95 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.6
                                       HHHHEEEEEGGTTGSHHHHHHHHHH CS
                   DegT_DnrJ_EryC1 335 laervlsLplypelteedvdrVvea 359
                                       +a+  l L+l +e teedvd+V + 
  gi|298675749|ref|YP_003727499.1| 351 IAHGSLRLSLGKENTEEDVDYVLSV 375
                                       67888999999999*******9875 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.2   2.1e-08   6.2e-05      35     168 ..      55     184 ..      46     277 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2.1e-08
                                       HHHHHHHHHHTT-S..EEEEES-HHHHHHHHHHHH-....-TTEEEEEETT.-HHHHSSTTHHHHCC--EEEEE-EB CS
                   Beta_elim_lyase  35 nrLedavaelfgke..aalfvpqGtaAnsillkill....qrgeevivtep.ahihfdetgaiaelagvklrdlknk 104
                                       ++  ++va+++ ++   ++f+  Gt +++ ++k ++    ++g+ +i t    h   + +  + e +g  ++ l+ +
  gi|298675749|ref|YP_003727499.1|  55 EKAREKVANAINAKtdRVFFTSGGTESDNWAIKGVAfankNKGNHIITTAIeHHAVLHPCEWL-EKQGFDVTYLPVD 130
                                       555666666665542145677779*****9995444223244445555444356666666555.6689999999999 PP

                                       TTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEE CS
                   Beta_elim_lyase 105 eaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDg 168
                                       + G ++++++++ai++      ++ li++  +nn     + ++e ++e+ ++a+++g+ +h D+
  gi|298675749|ref|YP_003727499.1| 131 KYGRVSVDDVRDAITD------QTILITVMFANNE----IGTIEPIEEIGEVARENGVYFHTDA 184
                                       99*************9......467*********5....77899999999*************8 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   6.6e-08    0.0002      41     296 ..      42     294 ..      37     376 .. 0.63

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 6.6e-08
                                       -BTTHHHHHHHHHHHHHC.TCTTCHTTGGEGEEEESHHHHHHHHHH...HHHHHTTT-EEEEEESS-THHHHHHHH. CS
                     Aminotran_1_2  41 gpidglpeleealakflg.rseklklkreaavvvgsGagalieali...fllklnpgdeilvpdptyasyknilrl. 112
                                       +p+++++e eea+ k      ++++ k++ +v ++sG ++ ++ +i   +++++n+g  i+  +  +  + + +++ 
  gi|298675749|ref|YP_003727499.1|  42 SPYTIAKESEEAIEKAREkVANAINAKTD-RVFFTSGGTESDNWAIkgvAFANKNKGNHIITTAIEHHAVLHPCEWl 117
                                       57788888888888888866677888888.*********987776533344458*****************999984 PP

                                       ..TTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEE CS
                     Aminotran_1_2 113 ..sggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvD 187
                                          g+ v + p++  +  ++ ++++ +a+++      +t +i v  ++N  Gt+ + ee+ ++   a++++++   D
  gi|298675749|ref|YP_003727499.1| 118 ekQGFDVTYLPVD--KYGRVSVDDVRDAITD------QTILITVMFANNEIGTIEPIEEIGEV---ARENGVYFHTD 183
                                       4457778888866..999*************......788***********************...99988888888 PP

                                       ETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEH.......HHHHHHHHHHHHHTSSHHHH CS
                     Aminotran_1_2 188 eaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgna.......avvsqlrklsrpflsssllq 257
                                        + a++ +        +++ve+   +l+  s  K +G  G   G++++++           +++k  r+++   ++ 
  gi|298675749|ref|YP_003727499.1| 184 AVQAIGQL--------LVDVEDMNIDLLSLSGHKFYGPKG--TGALYIKKgvkidnfMHGGAQEKQRRAGTENVPGI 250
                                       66554444........455555444577777777777777..77777766665553222222223333322233333 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS........T CS
                     Aminotran_1_2 258 aavaaalsdallkqseleemrqrlqkrrkelrdeLael........g 296
                                         + +a++++    s++e+ ++r+q++r++l ++L e+         
  gi|298675749|ref|YP_003727499.1| 251 VGLGEAIEHVT---SDIENHAKRMQSLRDRLINGLLEIpkthlcghP 294
                                       33344444444...366666777777777777766666666666552 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   3.2e-05     0.095      79     201 ..      85     212 ..      46     238 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.2e-05
                                       HHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHH.TTCEEEEEST...TSHHHHHHHCCTTEEEEEEESS-TTTT CS
                   Cys_Met_Meta_PP  79 AiaaailallkaGdeivvsddlYggtqrllkkvlkk.lgievkfvdt...sdleelekaikentklvylEtptnpll 151
                                       Ai+ + +a  ++G++i+++   +    + ++ + k+ + +++  vd+    ++++++ ai+++t l+ +    n   
  gi|298675749|ref|YP_003727499.1|  85 AIKGVAFANKNKGNHIITTAIEHHAVLHPCEWLEKQgFDVTYLPVDKygrVSVDDVRDAITDQTILITVMFANNEIG 161
                                       444444445567999999887777777777665555455555555554447899*********************** PP

                                       ----HHHHHHHHHHTT-EEEEEGTTTHT.TTS-GGGGT-SEEEEETTTTTT CS
                   Cys_Met_Meta_PP 152 kvvDiekiaklakkagvlvvvDntfasp.llqrplklgaDivvhSaTKylg 201
                                        +  ie+i ++a+++gv    D++ a + ll+   ++++D+   S+ K+ g
  gi|298675749|ref|YP_003727499.1| 162 TIEPIEEIGEVARENGVYFHTDAVQAIGqLLVDVEDMNIDLLSLSGHKFYG 212
                                       ************************999977888888999999999999865 PP

>> Pyridoxal_deC  Pyridoxal-dependent decarboxylase conserved domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   6.4e-05      0.19     166     241 ..     121     190 ..     103     223 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 6.4e-05
                                       T-EEEEE--BTTTBB-HHHHHHHHHHHHCTT.EEEEEEEEBS-TTT-BB--HHHHHHHHHHCT-EEEEE-TTGGGG CS
                     Pyridoxal_deC 166 gvklrvipldengklrgaalekaieedkekGlipffvvatlGttvlgaFddlkelgdicekydlwlHvDAAyaGsa 241
                                       g+ + ++p+d+ g++ +++ + ai ++         +++ +     g  + ++e+g++ ++ ++  H DA  a + 
  gi|298675749|ref|YP_003727499.1| 121 GFDVTYLPVDKYGRVSVDDVRDAITDQTIL------ITVMFANNEIGTIEPIEEIGEVARENGVYFHTDAVQAIGQ 190
                                       566889999999999999999999876554......44455555666689********************887444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      657  (0.0366445); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.73u 0.35s 00:00:01.08 Elapsed: 00:00:00.58
# Mc/sec: 2020.74
//
Query:       gi|298675750|ref|YP_003727500.1|  [L=137]
Description: FeS cluster assembly scaffold protein NifU [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-50  170.9   0.2    1.5e-50  170.6   0.2    1.0  1  NifU_N         NifU-like N terminal domain
  ------ inclusion threshold ------
      0.086   13.0   0.1       0.14   12.3   0.1    1.3  1  CO_deh_flav_C  CO dehydrogenase flavoprotein C-terminal domai


Domain annotation for each model (and alignments):
>> NifU_N  NifU-like N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.6   0.2   1.7e-54   1.5e-50       1     126 [.       3     123 ..       3     125 .. 0.98

  Alignments for each domain:
  == domain 1  score: 170.6 bits;  conditional E-value: 1.7e-54
                                       CSCHHHHHHHHSSSSBSS-TTSSS--EEEEEEETTTTEEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHHHHH CS
                            NifU_N   1 aysdkvldhyknPrnvGvleeedakvgvgevgapacGDavrLqikvdeetdriedakFktfGCgsaiAssslltelv 77 
                                       +ys+kv+dh+ nPrnvG +e+ d   gvgevg+p cGD +r+++k+++  ++i+dakF tfGCg+aiAsss++tel+
  gi|298675750|ref|YP_003727500.1|   3 MYSKKVMDHFMNPRNVGEMENPD---GVGEVGNPKCGDIMRMYLKIED--NIIQDAKFMTFGCGAAIASSSMATELI 74 
                                       69*********************...8*********************..5************************** PP

                                       TTSBHHHHCCCCHHHHHHHHTCSCSSSCHCSCHHHHHHHHHHHHHHHHC CS
                            NifU_N  78 kgktleealkitnkeiaeelgglpkeklhcsvlaedalkaavkkYkakk 126
                                       kgktleea  ++nk +a++l+glp+ k+hcsvlae+a+++a+++Y++k+
  gi|298675750|ref|YP_003727500.1|  75 KGKTLEEAWDVSNKAVADALEGLPSIKMHCSVLAEEAIHKAINDYRQKQ 123
                                       ***********************************************98 PP

>> CO_deh_flav_C  CO dehydrogenase flavoprotein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.6e-05      0.14      21      74 ..      42      96 ..      39     106 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.6e-05
                                      EEEEETTCEECEEEEEEESSSSS-EE-HHHHHHHTTSBSSH..HHHHHHHHHHHTT CS
                     CO_deh_flav_C 21 rveleedgkiedariafggvaptpvraekaeaaLiGkplse..elleeaakaleee 74
                                       +++e++ +i+da+++  g+++   + + a ++++Gk l+e  ++ ++a++ + e 
  gi|298675750|ref|YP_003727500.1| 42 YLKIEDN-IIQDAKFMTFGCGAAIASSSMATELIKGKTLEEawDVSNKAVADALEG 96
                                      5677655.*******************************99666777776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 792.92
//
Query:       gi|298675751|ref|YP_003727501.1|  [L=267]
Description: PP-loop domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.8e-08   32.2   0.0    1.4e-07   30.9   0.0    1.6  2  NAD_synthase   NAD synthase
     0.0023   17.7   0.0      0.014   15.2   0.0    2.1  2  ATP_bind_3     PP-loop family
     0.0058   16.2   0.0       0.02   14.5   0.0    1.9  1  ThiI           Thiamine biosynthesis protein (ThiI)
     0.0087   15.6   0.0      0.057   12.9   0.0    2.2  2  QueC           Queuosine biosynthesis protein QueC
  ------ inclusion threshold ------
      0.014   14.2   0.0       0.23   10.2   0.0    2.2  2  tRNA_Me_trans  tRNA methyl transferase
      0.038   13.7   0.0       0.05   13.3   0.0    1.2  1  Asn_synthase   Asparagine synthase
       0.18   11.8   0.0       0.22   11.6   0.0    1.3  1  PAPS_reduct    Phosphoadenosine phosphosulfate reductase fami


Domain annotation for each model (and alignments):
>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   5.6e-11   1.4e-07       6      83 ..       7      81 ..       3     106 .. 0.87
   2 ?   -2.6   0.0      0.94   2.4e+03      70      84 ..     244     258 ..     236     264 .. 0.74

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 5.6e-11
                                      HHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---HH CS
                      NAD_synthase  6 vdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidikp 83
                                      vd lke ++k+g   +v+  SGGvDSsl + la++ lg +++l +ll s   +++++e+a+++ ++++++++ ++ k 
  gi|298675751|ref|YP_003727501.1|  7 VDTLKEVIAKKG--PMVIAFSGGVDSSLLSLLAKETLG-NQHLCILLDSPLVPQHSIEQAKKISNEFDLNFEILPFKA 81
                                      566777777766..4899*******************5.68899*************************999888775 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.94
                                       HHHTSEEEE---HHH CS
                      NAD_synthase  70 enlgievktidikpi 84 
                                       ++lgi + t+di+ +
  gi|298675751|ref|YP_003727501.1| 244 KDLGITYITVDIEGY 258
                                       677888888888765 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   5.3e-06     0.014       2      40 ..      20      55 ..      19     129 .. 0.75
   2 ?    0.4   0.0      0.19   4.8e+02     136     164 ..     138     168 ..     100     175 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.3e-06
                                      EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSS CS
                        ATP_bind_3  2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglr 40
                                      +++A+SgG+DS +L ll+++   +   +  +i +d  l 
  gi|298675751|ref|YP_003727501.1| 20 MVIAFSGGVDSSLLSLLAKETLGN---QHLCILLDSPLV 55
                                      68**********999998887554...445555555555 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.19
                                       TTCCEE-CCC..T--HHHHHHHHHHTT---B CS
                        ATP_bind_3 136 asirlvRPlL..kvskeeleeylkekkikwv 164
                                       +++++  P++  ++sk ++++++ke++ ++ 
  gi|298675751|ref|YP_003727501.1| 138 EEENIAHPFVdaEISKPDIRKIAKERGYDFW 168
                                       4578888988556889999999999888775 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   7.7e-06      0.02       4     122 ..      18     128 ..      15     202 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.7e-06
                              ThiI   4 gkvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkeil 80 
                                       g  +   SgG+DS   + l+ +   + +l+ l ++p  +++ ie+ +k+    +e++    +++ +++fk + k+ +
  gi|298675751|ref|YP_003727501.1|  18 GPMVIAFSGGVDSSLLSLLAKETLGNQHLCILLDSPLVPQHSIEQAKKIS---NEFD----LNFEILPFKALNKSGI 87 
                                       5667789*********9999888777788888889999999988877775...5777....68999*****999866 PP

                              ThiI  81 ekvkekltivllkrkmlriAekvaeeegakalvtGesLgqVa 122
                                          ++k ++  +k+   ++ + +a ++g +++ +G +L+   
  gi|298675751|ref|YP_003727501.1|  88 VD-NPKDRCYHCKKASSQLLKCYALNKGFNCIADGTNLSDLG 128
                                       55.4577999****************************9765 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   2.2e-05     0.057       3      66 ..      21      84 ..      19     109 .. 0.81
   2 ?   -0.3   0.0      0.24   6.3e+02     148     183 ..     136     175 ..     122     182 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.2e-05
                                      EEE--SSHHHHHHHHHHHHH-.SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGGG CS
                              QueC  3 vvllSGGlDSttvlalakkeg.kevealtfdYgqrhkkeleaakkiakelgveehkildldllke 66
                                      v+ +SGG+DS+ + +lak++  ++  ++ +d     ++ +e akki++e+++ + +il  + l++
  gi|298675751|ref|YP_003727501.1| 21 VIAFSGGVDSSLLSLLAKETLgNQHLCILLDSPLVPQHSIEQAKKISNEFDL-NFEILPFKALNK 84
                                      899**************9986255556777777779999999*********9.888888876554 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.24
                                       HTS--EEE-TTTT..--HHHHHHHHHHTTHHHHH..-B-S CS
                              QueC 148 edkkieieaPlid..lsKaeivklgkelgvplee..tlsC 183
                                        +++ +i  P++d  +sK +i k++ke g+++ +  + sC
  gi|298675751|ref|YP_003727501.1| 136 AGEEENIAHPFVDaeISKPDIRKIAKERGYDFWNlpSSSC 175
                                       45566788899753379**********9976543225666 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0     9e-05      0.23       4      79 ..      21      88 ..      19      97 .. 0.67
   2 ?    1.4   0.0     0.043   1.1e+02     169     194 ..     149     174 ..     138     197 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 9e-05
                     tRNA_Me_trans  4 vvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfekeykekvf 79
                                      v+a+SgGVDSs+  +l ke   +   ++l  +            ++ +++a+++++++++++e++ f+   k+ ++
  gi|298675751|ref|YP_003727501.1| 21 VIAFSGGVDSSLLSLLAKETLGNQHLCILLDSPL--------VPQHSIEQAKKISNEFDLNFEILPFKALNKSGIV 88
                                      799*********9988888765554444432222........2344577777777777777777777766666555 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.043
                     tRNA_Me_trans 169 geltKeevrkiAkeaglavaekkdSq 194
                                       +e+ K+++rkiAke+g +  + + S 
  gi|298675751|ref|YP_003727501.1| 149 AEISKPDIRKIAKERGYDFWNLPSSS 174
                                       5788***********99877766664 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.9e-05      0.05      16      42 ..      16      42 ..       7      75 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.9e-05
                      Asn_synthase 16 advpvGalLSGGlDSSliaalaarqsk 42
                                         p+ + +SGG+DSSl++ la++ + 
  gi|298675751|ref|YP_003727501.1| 16 KKGPMVIAFSGGVDSSLLSLLAKETLG 42
                                      56789999**************99765 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   8.5e-05      0.22       2      93 ..      20     113 ..      19     202 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.5e-05
                                       EEEE--SSCTCHHHHHHHHHHCTTHE.EEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-TH CS
                       PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpvp.vvfvdtghefpetiefvdeleeryglrlkvyepeeevaekinaekhgssl 77 
                                       +v+++sgG ds+ l  La +++ + +  + +d     +  ie  ++++++++l++++   +   + +i+ + +    
  gi|298675751|ref|YP_003727501.1|  20 MVIAFSGGVDSSLLSLLAKETLGNQHlCILLDSPLVPQHSIEQAKKISNEFDLNFEILPFKALNKSGIVDNPKDRCY 96 
                                       689*********************7559***********************99977765555555555544432222 PP

                                       HHC..HHHHHHTHHHHHH CS
                       PAPS_reduct  78 yee..aaeriaKveplkk 93 
                                       +    a +++ K ++l+k
  gi|298675751|ref|YP_003727501.1|  97 H-CkkASSQLLKCYALNK 113
                                       2.2356667777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 1772.16
//
Query:       gi|298675752|ref|YP_003727502.1|  [L=48]
Description: hypothetical protein Metev_1873 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       186  (0.0103743); expected 358.6 (0.02)
Passed bias filter:                      153  (0.00853366); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 346.07
//
Query:       gi|298675753|ref|YP_003727503.1|  [L=362]
Description: thiamine biosynthesis/tRNA modification protein ThiI [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-63  212.9   0.0    4.7e-63  212.4   0.0    1.2  1  ThiI           Thiamine biosynthesis protein (ThiI)
    6.8e-18   65.2   0.0    1.2e-17   64.4   0.0    1.4  1  THUMP          THUMP domain
    0.00013   21.5   0.0     0.0036   16.8   0.0    2.2  1  QueC           Queuosine biosynthesis protein QueC
    0.00026   19.9   0.0    0.00058   18.8   0.0    1.5  2  tRNA_Me_trans  tRNA methyl transferase


Domain annotation for each model (and alignments):
>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.4   0.0     1e-66   4.7e-63       1     192 [.     165     357 ..     165     361 .. 0.97

  Alignments for each domain:
  == domain 1  score: 212.4 bits;  conditional E-value: 1e-66
                              ThiI   1 gtqgkvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlk 77 
                                       g++g  +aL+SgGiDSpVaay+++kRGc +  ++++ +p+ +e+ +e+  k+++ l +yq ++e++++  d+  + k
  gi|298675753|ref|YP_003727503.1| 165 GVEGSLVALMSGGIDSPVAAYMMMKRGCSIIPIYVDIDPYLGEKGKERAFKVVDALKQYQPGIELEVIGDDYLYTAK 241
                                       7899************************************************************************* PP

                              ThiI  78 eilekv.kekltivllkrkmlriAekvaeeegakalvtGesLgqVaSqtleNlrvisavvnllilrPLigldKeeii 153
                                       +il++   +k+t++++kr ++riAe +a++++a  +vtG+sLgqVaSqtl+Nl v+++++nl++ rPLig+dKee+i
  gi|298675753|ref|YP_003727503.1| 242 KILKHYnSDKYTCLICKRRLYRIAEDLANKYKALGIVTGDSLGQVASQTLDNLYVLDEATNLPVYRPLIGFDKEEVI 318
                                       *99998589******************************************************************** PP

                              ThiI 154 klAkeigtyeisiekedkCsvlakhPttkakleevekae 192
                                       ++A++igty +s++ +  C++++++P tkakl+ v+  e
  gi|298675753|ref|YP_003727503.1| 319 DIARRIGTYSLSTISTGGCGAVPEKPATKAKLDIVKSFE 357
                                       *********************************999876 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.4   0.0   2.6e-21   1.2e-17      42     143 ..      56     154 ..      25     155 .. 0.90

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 2.6e-21
                                       HHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHHHHHHCT-EEEEEEEESSSTSSSHHHHHHHHHHHHHHCCTT. CS
                             THUMP  42 ealekargiqrvipvcevceadledileaakeivkkkfeeeketFaVrvkrrgkhfeftsreinrevGkaivektg. 117
                                       e+l+ ++gi + +p    ++  l+++ ++  e+ + k ++  +tFa r+kr+g h +f+s++ +re+G +i++ +  
  gi|298675753|ref|YP_003727503.1|  56 EKLKNVFGIRSYSPC---IYCPLDELSKCLLEYCENKNFGDVQTFALRIKRVGAH-DFSSQDKARELGNLIRKHYPh 128
                                       567788899999998...7778*********************************.********************* PP

                                       -EE-SSS-SEEEEEEEETTEEEEEEE CS
                             THUMP 118 lkVdlenPdivvrveiikdkayisid 143
                                       lkVdl+nP++ +++ei+++ +y++ +
  gi|298675753|ref|YP_003727503.1| 129 LKVDLDNPEKEIFIEIRDSDCYLFSE 154
                                       **********************9965 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0     8e-07    0.0036       3     181 ..     171     332 ..     169     341 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8e-07
                                       EEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-T.TSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCGGG------ CS
                              QueC   3 vvllSGGlDSttvlalakkegkevealtfdYgqr.hkkeleaakkiakelgveehkildldllkelggsaLtdeeie 78 
                                       v l+SGG+DS +++++++k+g  ++ + +d +    +k  e a k++++l+   +    ++ l+ +g+  L ++++ 
  gi|298675753|ref|YP_003727503.1| 171 VALMSGGIDSPVAAYMMMKRGCSIIPIYVDIDPYlGEKGKERAFKVVDALKQ-YQP--GIE-LEVIGDDYLYTAKKI 243
                                       889***************************9988788888888888888876.444..444.558899999999876 PP

                                       -----...--------TTHHHHHHHHHHHHHHHHT-SEEEE---S-STT--GGGSHHHHHHHHHHHHHHHTS--EEE CS
                              QueC  79 vpkeeleeeelpntfVpaRNliflslaasyaealgaeaiiiGvneedfsgYPDcrdefvkalnkalnlgedkkieie 155
                                       +++  +++++     +  R   ++ +a  +a++++a  i++G +  +            ++l++++ l e++++ + 
  gi|298675753|ref|YP_003727503.1| 244 LKH--YNSDKYTCL-ICKRR--LYRIAEDLANKYKALGIVTGDSLGQ---------VASQTLDNLYVLDEATNLPVY 306
                                       666..555555544.45553..6899999999999999998866655.........344677777788888889999 PP

                                       -TTTT--HHHHHHHHHHTTHHHHH-B CS
                              QueC 156 aPlidlsKaeivklgkelgvpleetl 181
                                        Pli ++K+e++ ++ ++g     t+
  gi|298675753|ref|YP_003727503.1| 307 RPLIGFDKEEVIDIARRIGTYSLSTI 332
                                       99999999999999999996555544 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.3e-07   0.00058       4      42 ..     171     209 ..     169     232 .. 0.85
   2 ?   -3.9   0.0         1   4.6e+03     165     184 ..     306     325 ..     294     327 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.3e-07
                     tRNA_Me_trans   4 vvalSgGVDSsvaaallkeqgyevigvflklweeedeeg 42 
                                       v+++SgG+DS vaa+++ ++g ++i +++ +    +e+g
  gi|298675753|ref|YP_003727503.1| 171 VALMSGGIDSPVAAYMMMKRGCSIIPIYVDIDPYLGEKG 209
                                       789*************************99887766666 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 1
                     tRNA_Me_trans 165 lfPlgeltKeevrkiAkeag 184
                                       + Pl  + Keev +iA+++g
  gi|298675753|ref|YP_003727503.1| 306 YRPLIGFDKEEVIDIARRIG 325
                                       56999999***999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2322.19
//
Query:       gi|298675754|ref|YP_003727504.1|  [L=68]
Description: heavy metal transport/detoxification protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-20   72.3   0.3    3.7e-20   72.1   0.3    1.0  1  HMA       Heavy-metal-associated domain


Domain annotation for each model (and alignments):
>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.1   0.3   2.1e-24   3.7e-20       1      62 []       5      66 ..       5      66 .. 0.98

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 2.1e-24
                               HMA  1 tvrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagyk 62
                                      t++++gm CagC   ve +L +++g+ sv+++l+++++tV++d+e+t++ ki+ a+++agyk
  gi|298675754|ref|YP_003727504.1|  5 TIKIEGMKCAGCQENVENALNSVNGILSVNINLEEGSATVNYDPEKTDIDKIKSAVSNAGYK 66
                                      789**********************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.31s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 437.80
//
Query:       gi|298675755|ref|YP_003727505.1|  [L=325]
Description: Serine O-acetyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.2e-09   36.2  11.7    0.00011   21.8   0.7    3.7  3  Hexapep    Bacterial transferase hexapeptide (six repeats)
     0.0019   18.5   0.0     0.0044   17.4   0.0    1.6  1  SATase_N   Serine acetyltransferase, N-terminal
  ------ inclusion threshold ------
        1.3    8.8  17.3      0.076   12.8   1.5    3.9  4  Hexapep_2  Hexapeptide repeat of succinyl-transferase


Domain annotation for each model (and alignments):
>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.29   1.7e+03      21      27 ..      17      23 ..      16      23 .. 0.74
   2 !   21.8   0.7   1.8e-08   0.00011       2      35 ..     213     248 ..     212     249 .. 0.95
   3 !   18.9   1.8   1.5e-07   0.00091       1      35 [.     267     302 ..     267     303 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.29
                                      EE-TTEE CS
                           Hexapep 21 kIGdnvk 27
                                      +IGd+vk
  gi|298675755|ref|YP_003727505.1| 17 IIGDDVK 23
                                      5888876 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 1.8e-08
                                       EEEETTEEE-T..TEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   2 tvIGsnvlIgp..faviggnVkIGdnvkIgagvvig 35 
                                       + IG++ +I++  ++vig+ ++IGd v+I  gv++g
  gi|298675755|ref|YP_003727505.1| 213 AEIGEHFFIDHgtGVVIGETCQIGDSVRIYQGVTLG 248
                                       78********************************98 PP

  == domain 3  score: 18.9 bits;  conditional E-value: 1.5e-07
                                       TEEEETTEEE-T.TEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   1 stvIGsnvlIgp.faviggnVkIGdnvkIgagvvig 35 
                                       +++I ++v+I +  +++gg+++IG++++Ig +v ++
  gi|298675755|ref|YP_003727505.1| 267 HPTIKDDVIIYAgATILGGDTVIGERSVIGGNVWLT 302
                                       5799********6667799*************9887 PP

>> SATase_N  Serine acetyltransferase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   7.4e-07    0.0044      60     103 ..     133     176 ..      95     177 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 7.4e-07
                                       HHHHHH-THHHHHHHHHHHHHHHH-TT---THHHHHH-HHHHHH CS
                          SATase_N  60 eealeadpeiveaaraDlkAvlerDpAcksylepllyfKGFhAl 103
                                        ++l++ pe++e +++D+ A +e DpA+k y e++  + G  A+
  gi|298675755|ref|YP_003727505.1| 133 LDFLKKIPELREVLASDILAAYEGDPAAKCYDEIIFSYPGVLAV 176
                                       57788899***************************999999886 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.2      0.97   5.8e+03       3       8 ..      17      22 ..      17      22 .. 0.59
   2 ?   -1.1   0.1      0.27   1.6e+03      14      26 ..     203     215 ..     201     217 .. 0.63
   3 ?    5.7   0.8     0.002        12       2      21 ..     227     248 ..     224     249 .. 0.78
   4 ?   12.8   1.5   1.3e-05     0.076       6      34 .]     272     303 ..     269     303 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.97
                                      EE-TT- CS
                         Hexapep_2  3 iIGdnC 8 
                                      iIGd++
  gi|298675755|ref|YP_003727505.1| 17 IIGDDV 22
                                      577764 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.27
                                       -EESEEE-TT-EE CS
                         Hexapep_2  14 agiGvslGdncvv 26 
                                       +++G+++  ++ +
  gi|298675755|ref|YP_003727505.1| 203 SIVGIDIHPGAEI 215
                                       6778877655555 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.002
                                       EEE-TT-EE-TT-EE..SEEE- CS
                         Hexapep_2   2 viIGdnCliGanagi..GvslG 21 
                                       v IG+ C iG +  i  Gv+lG
  gi|298675755|ref|YP_003727505.1| 227 VVIGETCQIGDSVRIyqGVTLG 248
                                       7788888888887788888887 PP

  == domain 4  score: 12.8 bits;  conditional E-value: 1.3e-05
                                       TT-EE-TT-EE..S.EEE-TT-EE-TT-EE-S CS
                         Hexapep_2   6 dnCliGanagi..G.vslGdncvvgaGvvita 34 
                                       d+++i a a+i  G + +G+++v+g +v +t+
  gi|298675755|ref|YP_003727505.1| 272 DDVIIYAGATIlgGdTVIGERSVIGGNVWLTK 303
                                       899999****99637*************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      587  (0.0327403); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2182.06
//
Query:       gi|298675756|ref|YP_003727506.1|  [L=311]
Description: cysteine synthase A [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-72  243.2   0.0    4.3e-72  243.0   0.0    1.0  1  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  243.0   0.0   2.4e-76   4.3e-72       1     294 []       8     295 ..       8     295 .. 0.95

  Alignments for each domain:
  == domain 1  score: 243.0 bits;  conditional E-value: 2.4e-76
                                       GGGCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTT...TTTSEEEEEBSSHHHHHHHHHH CS
                              PALP   1 ltlgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkeg...tgaktvveassGNhgralAaaa 74 
                                       +t  ig+TPl++l++++ + ++ + +KlEs+np+ S+KdR a+++++++++    t+ +++ve +sGN+g++lA+++
  gi|298675756|ref|YP_003727506.1|   8 ITETIGNTPLIQLNNITNNSQATIIAKLESFNPLSSVKDRIAYNMIESAEKDgclTSDTVIVEPTSGNTGIGLAFVC 84 
                                       5789********************************************77777************************ PP

                                       HHHT-EEEEEEETTS-HHHHHHHHHTT-EEEEECCH..HHHHHHHHHHHHHHSTTCEE--TTTSHHHHHH.HHTHHH CS
                              PALP  75 allGlkvtivvpadaspekvallrllGaevvevggd..ydeavaaaaelaaegegaylvsqfdnptvieg.ygtigl 148
                                       a  G+k+++ +p+++s e+++ l+l+Gae+ +++g+   + av++a++la+e ++a++ +qf np++ e   +t++ 
  gi|298675756|ref|YP_003727506.1|  85 ASKGYKLILTMPDTMSVERRKILKLFGAEIDLTPGSkgMNGAVEKANQLANEYDKAFIPQQFMNPANPEIhRKTTAE 161
                                       *********************************77767**************9999999****************** PP

                                       HHHHHTTTTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCS.C CS
                              PALP 149 EileqlggkpdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavg.s 224
                                       Ei+ ++ g++d +v++vG+Gg+i+G+a  +ker+p+ + i+vepe s+ l ++          ++++ ++gl++g +
  gi|298675756|ref|YP_003727506.1| 162 EIWNDTEGDVDILVAGVGTGGTITGVANVIKERKPEFKAIAVEPEDSPVLSGGS---------PGPHKIQGLGAGfV 229
                                       ******************************************************.........88**********77 PP

                                       GTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEEEEEEE-B CS
                              PALP 225 pselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaal.klreagelkegdrvvviltg 294
                                       p  l+++l+    dei+++s++e +e++r+la+regi+++ ss+aal+a+ k +++ e +++ ++vv+l++
  gi|298675756|ref|YP_003727506.1| 230 PDILDISLV----DEIIQISNDESFETARELAKREGILAGISSGAALCAAlKIAKKPENRDK-TIVVVLPD 295
                                       777777665....77888********************************788888888888.99999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2040.08
//
Query:       gi|298675757|ref|YP_003727507.1|  [L=136]
Description: UspA domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-32  111.4   0.0    5.3e-32  111.3   0.0    1.0  1  Usp       Universal stress protein family
  ------ inclusion threshold ------
       0.04   14.7   0.1      0.074   13.8   0.1    1.5  1  GARS_N    Phosphoribosylglycinamide synthetase, N domain


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.3   0.0   5.9e-36   5.3e-32       1     141 []       4     136 .]       4     136 .] 0.98

  Alignments for each domain:
  == domain 1  score: 111.3 bits;  conditional E-value: 5.9e-36
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaea 77 
                                       +y ++l+a+Dgs++s++A+ +++e+ak +ga++++++v+ + ++  ++  d++ ++    +  +           + 
  gi|298675757|ref|YP_003727507.1|   4 HYNKMLIATDGSDNSENAIYRGIEFAKITGAKVYAIYVLNTGTYFDEPVFDKQKARRYTTDHVEDIG--------NN 72 
                                       699*************************************************************997........77 PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                        g++ve vv  g+pa ei+++ae++++dliV+Gs g+sg+ r+llGSvs++vl+ha+  Vl+V+
  gi|298675757|ref|YP_003727507.1|  73 NGINVESVVIIGNPAKEIIDFAEKNEIDLIVMGSLGKSGVVRFLLGSVSDNVLKHASSEVLIVP 136
                                       9**************************************************************7 PP

>> GARS_N  Phosphoribosylglycinamide synthetase, N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   8.3e-06     0.074      33      59 ..      42     106 ..       8     116 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.3e-06
                                       --CGG......................................TTHHHHHHHHHHCTESEEEE-S CS
                            GARS_N  33 gNagt......................................edlealvefakeekidlvvvGp 59 
                                        N gt                                      + ++++++fa++++idl+v+G 
  gi|298675757|ref|YP_003727507.1|  42 LNTGTyfdepvfdkqkarryttdhvedignnnginvesvviigNPAKEIIDFAEKNEIDLIVMGS 106
                                       555555555555555555555544444444444355555555433457**************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 883.45
//
Query:       gi|298675758|ref|YP_003727508.1|  [L=177]
Description: hypothetical protein Metev_1881 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.071   13.0   0.1       0.28   11.1   0.0    2.0  2  Dioxygenase_N  Catechol dioxygenase N terminus


Domain annotation for each model (and alignments):
>> Dioxygenase_N  Catechol dioxygenase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   1.5e-05      0.28       9      36 ..      86     113 ..      82     120 .. 0.92
   2 ?   -2.0   0.0      0.19   3.4e+03      16      25 ..     153     162 ..     140     168 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 1.5e-05
                                       HHHHHHHHHHHHHTT--HHHHHHHHHHH CS
                     Dioxygenase_N   9 erlvrhlhdfirevdlteeEwwaavdfL 36 
                                       ++++++l d+i+e  +t++E++  +d++
  gi|298675758|ref|YP_003727508.1|  86 RDIIENLKDTINEKPITHHEFKLVIDYI 113
                                       6799***********************8 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.19
                                       HHHHHHTT-- CS
                     Dioxygenase_N  16 hdfirevdlt 25 
                                       +++++e+ l+
  gi|298675758|ref|YP_003727508.1| 153 MKVADELGLS 162
                                       3344444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       832  (0.0464053); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1064.13
//
Query:       gi|298675759|ref|YP_003727509.1|  [L=535]
Description: choline/carnitine/betaine transporter [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   4.2e-186  619.1  41.1   4.8e-186  618.9  41.1    1.0  1  BCCT      BCCT, betaine/carnitine/choline family transporter


Domain annotation for each model (and alignments):
>> BCCT  BCCT, betaine/carnitine/choline family transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  618.9  41.1  2.7e-190  4.8e-186       2     485 .]      20     504 ..      19     504 .. 0.98

  Alignments for each domain:
  == domain 1  score: 618.9 bits;  conditional E-value: 2.7e-190
                              BCCT   2 flvslliivlfvllalvfpealeevlsslnswilekfgwlylllvllflvfllvlafskygkikLGkddekpefstl 78 
                                       flvs+++ v+fv++++vf+e +++ ++ +++wi++++gw ++l   +fl+++++l++s++g+ikLG+dde+p +s++
  gi|298675759|ref|YP_003727509.1|  20 FLVSIALAVGFVIIGIVFQEPFSDRMDLTFNWIVDTLGWTFILGSSTFLFLIVYLMLSPMGDIKLGGDDEEPAYSYM 96 
                                       89*************************************************************************** PP

                              BCCT  79 sWfamlfaaglgigllfwgvaEplahylspppgaeagteeaaqeAlaytffhwGlhaWaiyalvalalayfayrkgl 155
                                        Wf+mlf++g+gigllfwgv+Ep+ hy+  pp +e+gt+ea  +A++y+ffhwG+h+Waiya+va  layf+yrkgl
  gi|298675759|ref|YP_003727509.1|  97 AWFSMLFSCGMGIGLLFWGVSEPILHYMV-PPLGEGGTNEAIYTAIRYSFFHWGFHPWAIYAVVAGSLAYFSYRKGL 172
                                       *****************************.55668****************************************** PP

                              BCCT 156 pltissalypllger.ingllgkvvDvlavlatvfGvatslGlgvlqinaglselfgieesltvqlaiivvitalat 231
                                       p+ +ss+l p+lg++ i+g++g +++++ vlat+fG++t+lGlgv+qi +gl++lfgi++++++ l ii+v+t+la+
  gi|298675759|ref|YP_003727509.1| 173 PMLLSSCLEPILGRKgIDGPWGIIINTIGVLATLFGISTTLGLGVIQIGGGLESLFGIPSNSILWLSIITVVTILAV 249
                                       *************855************************************************************* PP

                              BCCT 232 vsavsGldkGikrlSnlnlvlalllllfvllvGptlfilntfvqslgdylqnlvalslatdaae..eaeewlasWTv 306
                                       +s+v+G+d+Gik+lS++n++ a+lll+f+l+vGptlfil++f++s+g+ylqn++ +s+ +d+a+  ++ +w  +WT+
  gi|298675759|ref|YP_003727509.1| 250 MSTVTGIDRGIKWLSEINITAAALLLIFILIVGPTLFILDLFTHSIGEYLQNFLFMSFSIDPAGvsPE-GWHGDWTI 325
                                       **************************************************************774244.6******* PP

                              BCCT 307 FyWawwiawapfvGlFiAriSrGRtiRefilgvllvptlvtflwftvlGgtaielelegeaelaeaaeasveaalfa 383
                                       FyWawwiaw+pfvG FiAr+SrGRtiR f++gv+lvptlv+++wf+v+Gg+a+++++ g+a + ++++++ +  +f+
  gi|298675759|ref|YP_003727509.1| 326 FYWAWWIAWSPFVGSFIARVSRGRTIRSFVIGVMLVPTLVSMIWFSVFGGAALYIQHFGAAGIGDVVAQDEALGFFT 402
                                       ***************************************************************************** PP

                              BCCT 384 lleqlplgsilsvlavvliiiffvTsaDSatlvlatltsggdenpprkqrvfWgvllgavaavlllagglealqsas 460
                                        l+++p++ il+++a++ +++ff+Ts+DS+t+v+++lts+g+ npp  +r++Wgv++ga+aa+lllaggl+alq+as
  gi|298675759|ref|YP_003727509.1| 403 ALSHFPISGILIAVAMISVAVFFITSSDSGTYVIGMLTSKGNPNPPLPLRIIWGVMEGAFAAILLLAGGLAALQTAS 479
                                       ***************************************************************************** PP

                              BCCT 461 iiaalPftlvlllmvvsllkalree 485
                                       +i+++Pf++++ lm++ l+ +lr+e
  gi|298675759|ref|YP_003727509.1| 480 LIGGFPFMIIMALMLYCLVISLRKE 504
                                       ******************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (535 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       980  (0.05466); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.69u 0.34s 00:00:01.03 Elapsed: 00:00:00.51
# Mc/sec: 3165.65
//
Query:       gi|298675760|ref|YP_003727510.1|  [L=364]
Description: small GTP-binding protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-31  108.9   0.4    3.6e-31  107.3   0.4    1.9  1  MMR_HSR1_Xtn   C-terminal region of MMR_HSR1 domain
      6e-21   74.7   0.0    1.1e-20   73.8   0.0    1.5  1  MMR_HSR1       50S ribosome-binding GTPase
    2.6e-19   69.0   0.0    5.4e-19   68.0   0.0    1.6  1  TGS            TGS domain
    6.6e-13   48.5   0.1    1.4e-12   47.4   0.1    1.5  1  FeoB_N         Ferrous iron transport protein B
     0.0015   18.6   1.1        0.1   12.7   0.1    2.6  3  Dynamin_N      Dynamin family
     0.0036   17.2   0.1      0.037   13.9   0.0    2.3  2  RsgA_GTPase    RsgA GTPase
  ------ inclusion threshold ------
      0.011   15.1   0.1      0.028   13.8   0.0    1.7  2  AIG1           AIG1 family
      0.023   14.8   0.3       0.14   12.4   0.0    2.3  3  YchF-GTPase_C  Protein of unknown function (DUF933)
      0.031   13.7   0.1      0.078   12.4   0.1    1.8  1  Arf            ADP-ribosylation factor family
      0.048   13.1   0.0      0.086   12.3   0.0    1.4  1  SRPRB          Signal recognition particle receptor beta subu
      0.073   12.7   0.4        2.4    7.7   0.0    2.5  2  cobW           CobW/HypB/UreG, nucleotide-binding domain
        0.1   11.6   0.1       0.22   10.5   0.1    1.5  1  MeaB           Methylmalonyl Co-A mutase-associated GTPase Me
       0.18   12.1   0.1       0.66   10.3   0.1    1.9  2  AAA_16         AAA ATPase domain


Domain annotation for each model (and alignments):
>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.3   0.4   2.6e-34   3.6e-31       1     105 [.     182     287 ..     182     288 .. 0.97

  Alignments for each domain:
  == domain 1  score: 107.3 bits;  conditional E-value: 2.6e-34
                      MMR_HSR1_Xtn   1 kgGikitstvkltkldeetvkkilkeykihnaevliredvtvDdlidviegnrvYipclyvlNKiDlisleeldela 77 
                                       +gG+ + stv+l+ l+ +t+k++l eykihna+vlire++tvD+lid++ +nrvYip l ++NK+Dl+++ +++ + 
  gi|298675760|ref|YP_003727510.1| 182 RGGVIVDSTVDLDYLSVDTIKTVLGEYKIHNAHVLIRENITVDQLIDAVLENRVYIPGLPIINKVDLADEGTIEYCV 258
                                       69*************************************************************************99 PP

                      MMR_HSR1_Xtn  78 re.pnsvviSaekelnldeLkekiweeLn 105
                                       ++ p++++iSa++e+n++ +ke i+++++
  gi|298675760|ref|YP_003727510.1| 259 QTfPEAIMISADQEMNIEGVKEGIFSSID 287
                                       9769*********************9876 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.8   0.0   8.2e-24   1.1e-20       2      99 ..      64     163 ..      63     183 .. 0.88

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 8.2e-24
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC.TS CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee.ad 77 
                                       v +vG p vGKStL+n+ltg++++v+d+ +tT++++ g +++kg +i+++D+pGl++ga +++g gk++ ++++ ++
  gi|298675760|ref|YP_003727510.1|  64 VSLVGFPSVGKSTLLNKLTGAQSEVADYEFTTLEVIPGVLEYKGAKIQMLDVPGLVKGAASGRGRGKEVISVIRnSN 140
                                       89*********************************************************************88879* PP

                                       EEEEEEETTTT.CSHHHHHHHHH CS
                          MMR_HSR1  78 lillvvdasee.klkpldeelee 99 
                                       l+++++d+ +  +++ l++el +
  gi|298675760|ref|YP_003727510.1| 141 LVVFILDVFQIyQYDVLKQELYD 163
                                       *******8833345555555544 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.0   0.0   3.9e-22   5.4e-19       1      59 [.     289     361 ..     289     362 .. 0.98

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 3.9e-22
                                       EEEEE.TTSSEEE......EETTB-HHHHHHHHSTTHHHHEEEEEECS.......EEEETTSBB-SSEEEEEE CS
                               TGS   1 irvyt.PdGkvpd......lprgatveDfAykIhrslakkfiyAlVnG.......qrvgldhvLedgdvveIv 59 
                                       irvy+ P+G+  d      +++g+tveD++ ++hr+++kkf+yA+++G       qr g+dhvL d d+++++
  gi|298675760|ref|YP_003727510.1| 289 IRVYMkPQGESADleepmiIRKGSTVEDVCESLHRDFKKKFRYARIWGssakhpgQRAGIDHVLHDKDILSLI 361
                                       89********************************************************************987 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4   0.1     1e-15   1.4e-12       2     105 ..      63     165 ..      62     179 .. 0.79

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 1e-15
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHH.CT CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardfll.ee 77 
                                       tv lvG p vGk+tl+n+ltga+++v+ +  +t e   g l++kg +++++D+PG  +  a  +     ++++   +
  gi|298675760|ref|YP_003727510.1|  63 TVSLVGFPSVGKSTLLNKLTGAQSEVADYEFTTLEVIPGVLEYKGAKIQMLDVPGLVKGAASGRGR--GKEVISvIR 137
                                       799****************************************************86644433332..222222135 PP

                                       SSSEEEEEEEGGGHHHHHHHHHHHHHTT CS
                            FeoB_N  78 epdvvvnvvdatnlernLyLtlqllelg 105
                                       + ++vv ++d  ++ +  +L  +l + g
  gi|298675760|ref|YP_003727510.1| 138 NSNLVVFILDVFQIYQYDVLKQELYDAG 165
                                       5677777888777777777777776666 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       6.9   9.6e+03      66      76 ..       8      18 ..       4      49 .. 0.50
   2 !   12.7   0.1   7.3e-05       0.1       1      32 [.      64      95 ..      64     106 .. 0.83
   3 ?    4.2   0.0     0.029        40     101     137 ..     108     147 ..      99     164 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 6.9
                                      HHHHHHHHHHH CS
                         Dynamin_N 66 sevreeieket 76
                                      ++v+eei++  
  gi|298675760|ref|YP_003727510.1|  8 NKVQEEIKNTP 18
                                      44444444332 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 7.3e-05
                                      EEEEEBTTTTHHHHHHHHHTS--S---SSS-- CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnptT 32
                                      + +vG  S GKS++ln+L+g++  + + + tT
  gi|298675760|ref|YP_003727510.1| 64 VSLVGFPSVGKSTLLNKLTGAQSEVADYEFTT 95
                                      5789999*************997666666665 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.029
                                       -SEEEEE---B-SSSGTTS...HHHHHHHSTTEEEEEEEE CS
                         Dynamin_N 101 kgltlvDlPGldsvnkrdq...elvkeyikkadiilavts 137
                                        ++ ++D+PGl + ++      + v + i+++++++++++
  gi|298675760|ref|YP_003727510.1| 108 AKIQMLDVPGLVKGAASGRgrgKEVISVIRNSNLVVFILD 147
                                       68999********999888899999999988888888876 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   2.7e-05     0.037      98     123 ..      60      85 ..       8      95 .. 0.83
   2 ?    0.5   0.0      0.36     5e+02      51      95 ..     241     280 ..     219     289 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.7e-05
                                       TTSEEEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpel 123
                                        d t+ lvG   vGKStL+n+l++ +
  gi|298675760|ref|YP_003727510.1|  60 GDATVSLVGFPSVGKSTLLNKLTGAQ 85 
                                       568999****************9973 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.36
                                       EEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHH CS
                       RsgA_GTPase  51 ivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelke 95 
                                        ++nK+Dl++e + +e   +++     e +++sa+++ ++e +ke
  gi|298675760|ref|YP_003727510.1| 241 PIINKVDLADEGT-IEYCVQTF----PEAIMISADQEMNIEGVKE 280
                                       579******9998.55444444....3446666666666666655 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       1.8   2.5e+03     180     205 ..       6      31 ..       3      37 .. 0.79
   2 ?   13.8   0.0     2e-05     0.028       2     101 ..      63     159 ..      62     164 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.8
                                       HHHHHHHHTTTT--B-HHHHHHHHCC CS
                              AIG1 180 lveaivkenggkpytnelyekikeea 205
                                        ++++++e ++ py + ++++i + +
  gi|298675760|ref|YP_003727510.1|   6 EINKVQEEIKNTPYNKATSHHIGRLK 31 
                                       68899999999999999999887665 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 2e-05
                                       EEEEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEEEEEE--SCCCTTCCHHCHHHHHHHHHH CS
                              AIG1   2 tivlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkkinViDTPglfdlsvsadkiskeivrcll 78 
                                       t+ lvG   +GkS+  N + g +        +  t ++   + + +g ki+  D Pgl+   +s     ke++  + 
  gi|298675760|ref|YP_003727510.1|  63 TVSLVGFPSVGKSTLLNKLTGAQSEVAD--YEFTTLEVIPGVLEYKGAKIQMLDVPGLVKGAASGRGRGKEVISVI- 136
                                       67799**************999754443..3556677778888******************************744. PP

                                       HCTT-ESEEEEEEETTB-SHHHH CS
                              AIG1  79 lseegihalllvlslgrfteede 101
                                        +++ + ++l v+++++++   +
  gi|298675760|ref|YP_003727510.1| 137 RNSNLVVFILDVFQIYQYDVLKQ 159
                                       44444666677899998876555 PP

>> YchF-GTPase_C  Protein of unknown function (DUF933)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       4.6   6.4e+03      50      71 ..      35      54 ..      29      61 .. 0.64
   2 ?   12.4   0.0    0.0001      0.14      17      43 ..     308     334 ..     305     341 .. 0.91
   3 ?   -1.8   0.0       2.6   3.6e+03      65      79 ..     344     358 ..     337     361 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.6
                     YchF-GTPase_C 50 velgseaaakeagklrlegkdy 71
                                       +l+ ea+ ke+gk +  g  y
  gi|298675760|ref|YP_003727510.1| 35 ARLRDEAERKESGKSKGAG--Y 54
                                      5556677777777765444..4 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.0001
                     YchF-GTPase_C  17 ikkgttapqaAgviHsDfekgFiraev 43 
                                       i+kg+t+++ +   H Df+k+F  a++
  gi|298675760|ref|YP_003727510.1| 308 IRKGSTVEDVCESLHRDFKKKFRYARI 334
                                       89********************99987 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 2.6
                     YchF-GTPase_C  65 rlegkdyvvqdgDii 79 
                                       ++ g d+v++d Di+
  gi|298675760|ref|YP_003727510.1| 344 QRAGIDHVLHDKDIL 358
                                       5679999******97 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   5.7e-05     0.078      16     104 ..      63     161 ..      54     223 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.7e-05
                                       EEEEEESTTSSHHHHHHHHHHSSCEE...CSSSSSEEEEEEEETTEEEEEEEE-S....SGGGGGGGGG...GCTTE CS
                               Arf  16 rilllGLDnaGKtTilkklkleelvt...tvPTigfnveeleiknlkftvwDvGG....qeklRplWkn...Yfekt 82 
                                        + l+G  + GK+T+l+kl+  + +       T+      le+k+ k+++ Dv G      + R   k+     ++ 
  gi|298675760|ref|YP_003727510.1|  63 TVSLVGFPSVGKSTLLNKLTGAQSEVadyEFTTLEVIPGVLEYKGAKIQMLDVPGlvkgAASGRGRGKEvisVIRNS 139
                                       5678999************8655443234677888888899***********9761111445555555411145667 PP

                                       SEEEEEEETT-CTTHHHHHHHH CS
                               Arf  83 davifvvDsadreRleeakeeL 104
                                       + v+f++D+ +    +  k+eL
  gi|298675760|ref|YP_003727510.1| 140 NLVVFILDVFQIYQYDVLKQEL 161
                                       7788888887777777777777 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.2e-05     0.086       5      61 ..      63     120 ..      59     150 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.2e-05
                                       EEEEE-STTSSHHHHHHHHHHSS---B---S.S-EEETTG...GGTT-SEEEETT-GC CS
                             SRPRB   5 avllvGlsdsGKTslftrLttdsvkktvtSq.essaalkvksekgskltliDfPGhek 61 
                                       +v lvG    GK +l+++Lt  + + +       ++   v + kg k++++D+PG +k
  gi|298675760|ref|YP_003727510.1|  63 TVSLVGFPSVGKSTLLNKLTGAQSEVADYEFtTLEVIPGVLEYKGAKIQMLDVPGLVK 120
                                       7889****************88544444333244444444566************877 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0017       2.4       3      22 ..      64      84 ..      62      97 .. 0.81
   2 ?    2.8   0.1     0.057        78     130     156 ..     226     252 ..     129     264 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0017
                                      EEEEESTTCCHHHHHHHHH.C CS
                              cobW  3 tvltGflGsGKTtLlnhll.e 22
                                      + l+Gf+  GK+tLln+l+ +
  gi|298675760|ref|YP_003727510.1| 64 VSLVGFPSVGKSTLLNKLTgA 84
                                      6799*************9952 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.057
                                       CHHHHHHHHHHTSSEEEEE-HHHHCHC CS
                              cobW 130 kieekaedqlaaadllvlnKtDlldee 156
                                        i   +e+ +    l ++nK+Dl+de 
  gi|298675760|ref|YP_003727510.1| 226 LIDAVLENRVYIPGLPIINKVDLADEG 252
                                       55666677777777889******9986 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00016      0.22      25      50 ..      58      82 ..      42     101 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00016
                                      G-S-SEEEEEEE-TTSSHHHHHHHHH CS
                              MeaB 25 kaGraqvvGltGvPGaGkstlvealg 50
                                      ++G a+ v l G+P +Gkstl+++l+
  gi|298675760|ref|YP_003727510.1| 58 RSGDAT-VSLVGFPSVGKSTLLNKLT 82
                                      667665.789**************97 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00048      0.66      21      45 ..      59      82 ..      52     101 .. 0.83
   2 ?   -2.5   0.0       4.2   5.8e+03     130     152 ..     136     157 ..     122     165 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00048
                            AAA_16 21 sgrpelvllsGesGvGKsslvrell 45
                                      sg+   v l+G + vGKs+l+++l 
  gi|298675760|ref|YP_003727510.1| 59 SGD-ATVSLVGFPSVGKSTLLNKLT 82
                                      344.6899*************9986 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.2
                            AAA_16 130 lsrderplvlvlDdlqwadeasl 152
                                       +++ +  +v++lD +q  + + l
  gi|298675760|ref|YP_003727510.1| 136 IRN-SNLVVFILDVFQIYQYDVL 157
                                       555.3448999999996666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2401.65
//
Query:       gi|298675761|ref|YP_003727511.1|  [L=637]
Description: molybdenum cofactor synthesis domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.1e-45  152.5   0.0      1e-44  152.0   0.0    1.2  1  PBP_like       PBP superfamily domain
    1.8e-41  141.6   0.0    2.7e-41  141.0   0.0    1.3  1  MoeA_N         MoeA N-terminal region (domain I and II)
    5.4e-26   91.0   0.0    9.4e-26   90.2   0.0    1.4  1  MoCF_biosynth  Probable molybdopterin binding domain
    1.1e-12   47.9   0.0    2.6e-12   46.7   0.0    1.7  1  MoeA_C         MoeA C-terminal region (domain IV)


Domain annotation for each model (and alignments):
>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.0   0.0   2.3e-48     1e-44       7     192 ..     426     612 ..     421     613 .. 0.93

  Alignments for each domain:
  == domain 1  score: 152.0 bits;  conditional E-value: 2.3e-48
                                       H-TTCEEEEEES-HHHHHHHHHTTS-SEEEESS---CCCHHCCCCCEEEEEEEEEEEE-CC-HCHCCCCHCCHHHS- CS
                          PBP_like   7 knpgvrvavanvGsggGlkalrageadiagshlldketeeynapalrkaldgievvlvnlarreqglvvakgnpkki 83 
                                       + +g++++v n Gs+gG++++  g  diag++++d+ +++yn++ ++k+    +vvlv++++reqgl+v+++   +i
  gi|298675761|ref|YP_003727511.1| 426 ELSGLKFRVLNNGSSGGFSSVSTGFSDIAGINMPDD-SGNYNISMIEKMKLS-DVVLVKGYKREQGLIVRQNS--DI 498
                                       4699*******************************7.99********99998.79*****************5..5* PP

                                       -BGGGC-S-B-EEEEE-TTSHHHHHHHHHHC-CEECT.........E-SSTTSEEESSHHHHHCCHCCETTCCECCC CS
                          PBP_like  84 tnwkdladaplrlvnRetGSGtrdlfdellkkegisk.........ssikgyaqearshlavaaaVaagradvgvgi 151
                                       +++ d+ d   rl+nR++G+Gtr l+d  lk+  ++k         +s+ gy++ a++hlav+ aV+ g advg+g+
  gi|298675761|ref|YP_003727511.1| 499 SGIDDILD--KRLINRNRGTGTRSLLDLNLKQF-ADKmgmsfnnlkESLAGYNSGAKTHLAVCNAVKEGFADVGFGL 572
                                       ******66..6*******************774.5668889999********************************* PP

                                       GG-HCCCCCCECTTCE-EEEEEEEECTCCCSHHHHHHHHHH CS
                          PBP_like 152 eavaeelkgldfvplaeerydlvvrkealddpevqaflefl 192
                                       +++ae+  gl+f+ + ee++d++v+kea+d  e++ +++ +
  gi|298675761|ref|YP_003727511.1| 573 RTMAEN-SGLKFISICEEEFDFLVQKEAMDLTEIKTLISCI 612
                                       ****98.6****************************99865 PP

>> MoeA_N  MoeA N-terminal region (domain I and II)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.0   0.0     6e-45   2.7e-41       1     157 []      10     174 ..      10     174 .. 0.90

  Alignments for each domain:
  == domain 1  score: 141.0 bits;  conditional E-value: 6e-45
                                       B-HHHHHHHHHHH-HH.-EEE.EEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--............ CS
                            MoeA_N   1 lsveealaiilaalel.eeee.vplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeep....... 68 
                                       ++v+ea + +l+++++ ++++ +pl +ealg +lae vv+++dvP fd+S+mDGYAvra+++ +a e++p       
  gi|298675761|ref|YP_003727511.1|  10 IPVDEAHR-LLKQIPInHSTKsLPL-EEALGYTLAEHVVSSIDVPSFDKSIMDGYAVRADDTYQAGETNPltlcftg 84 
                                       57999999.5566655556666***.99************************************************* PP

                                       .......-S---TT-.EEEE-TTSB--TT--EEEEGGGE..E....EETTE.S--STTTTEE-TTSSB-TTSEEE-T CS
                            MoeA_N  69 .saageeperllpgg.avrimTGaplPegadaVvpvEdte.eeeaketvev.kavkpgenvrraGedikaGevllra 141
                                        + ag   +  l++g a+ i+TGap+P gadaVv+vEdt+ +   +++v v ++v+ gen+  +G+di +Ge +l +
  gi|298675761|ref|YP_003727511.1|  85 sIDAGFVGDFYLNKGeAMSIATGAPIPYGADAVVKVEDTKrA---NSKVSVyRPVHTGENIMSRGSDIMRGEQVLCR 158
                                       *888988888888888***********************632...33344479************************ PP

                                       TBB--CCCHHHHHHCT CS
                            MoeA_N 142 gtrltpaeigllasvG 157
                                       +tr++++eig+l ++G
  gi|298675761|ref|YP_003727511.1| 159 NTRIGSREIGVLSAIG 174
                                       *************998 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.2   0.0   2.1e-29   9.4e-26       1     143 [.     186     322 ..     186     323 .. 0.95

  Alignments for each domain:
  == domain 1  score: 90.2 bits;  conditional E-value: 2.1e-29
                                       EEEEE-HHHH.......TTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSST CS
                     MoCF_biosynth   1 avitvGdell.......sgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptp 70 
                                       ++i++G+el+       +g i+Dtn++ l++ +ke g++   y++v D+e+++ +a+ +a++e ++++t+G t++++
  gi|298675761|ref|YP_003727511.1| 186 GIISTGNELTtpgnpldKGMIYDTNSYALSASVKECGATPVMYGIVEDEEKAMFNAINRAVQECNLVLTSGSTSAGA 262
                                       69*******************************************************9999**************** PP

                                       T--HHHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHHHHGGHH CS
                     MoCF_biosynth  71 dDvtpealaklfekelegfeeafrrvslkpgkpvgvapgailsravgktiigLPGspkavkealeeillpale 143
                                        D++++++++ +         +f++++ kpgkpv+ +++   ++    + igLPG+p ++ +++ e++ p ++
  gi|298675761|ref|YP_003727511.1| 263 GDIMYKVIEEKGR-------TLFHGINIKPGKPVVAGMI---NG---VPTIGLPGNPTSALTIFNEFIAPLIH 322
                                       ************9.......7************998888...43...379******************99886 PP

>> MoeA_C  MoeA C-terminal region (domain IV)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.0   5.9e-16   2.6e-12       2      72 .]     339     403 ..     338     403 .. 0.92

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 5.9e-16
                                       EEESS-EE--SSS-EEEEEEEES-S-EEEEEE-S---TT-GGGCTT--EEEEE-TT--EE-TT-EEEEEE- CS
                            MoeA_C   2 arlaedlksdpgrreflRvilteedgeyvaeptgkqgSglLsslaeAnglivipegtegleaGeeVevill 72 
                                       a+l++ ++s + r+++l+v +     + +++p   +gSg++++la+A+g+i+i ++te++e+G++V+v l+
  gi|298675761|ref|YP_003727511.1| 339 AVLGTGINSQG-RQQLLPVGMV----RGKVYPA-DKGSGAITTLADADGFIEISAETEYIESGTSVNVTLF 403
                                       67777777777.**********....789***9.**********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (637 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.73u 0.33s 00:00:01.06 Elapsed: 00:00:00.54
# Mc/sec: 3536.33
//
Query:       gi|298675762|ref|YP_003727512.1|  [L=298]
Description: branched-chain amino acid aminotransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-55  188.5   0.0    1.7e-55  188.3   0.0    1.0  1  Aminotran_4  Amino-transferase class IV
  ------ inclusion threshold ------
      0.065   13.1   0.0       0.11   12.4   0.0    1.3  1  Ig_J_chain   Immunoglobulin J chain


Domain annotation for each model (and alignments):
>> Aminotran_4  Amino-transferase class IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.3   0.0   1.9e-59   1.7e-55       1     223 []      32     258 ..      32     258 .. 0.93

  Alignments for each domain:
  == domain 1  score: 188.3 bits;  conditional E-value: 1.9e-59
                       Aminotran_4   1 glfEtmrvyngeiffldeHleRLrksaellglelpfdeeelrkileelleannsengrlrllvsrgggglg.aatse 76 
                                       g+fE++r+yng++f ldeH++RL  sa+++ l++p++++e+++++ ++l++nn   +++r++vsrg g+lg ++ ++
  gi|298675762|ref|YP_003727512.1|  32 GVFEGIRAYNGRVFKLDEHIDRLYDSAKAIVLDIPLTKNEMKEAILQTLRKNNLMDAYIRPIVSRGIGDLGlDPRKC 108
                                       8**************************9999*****************************************66666 PP

                       Aminotran_4  77 psvavyvsalppgpeseke....lplvtssdvrrdapsplpgaKtlnyldnvlarreakergadevllvdedgnvtE 149
                                        +  v++++ ++++ + +     l++vt + +r  +    p++K++nyl+n+la+ ea+++g de++++d +g+v+E
  gi|298675762|ref|YP_003727512.1| 109 TKPNVFIITQQWDALYGDLyevgLTAVTVTTRRNAPDALSPNIKSMNYLNNILAKVEANNKGGDEAIFLDNNGYVSE 185
                                       666666666666666655555**8888888799999999************************************** PP

                       Aminotran_4 150 gstsNvfivkggelitPplssgiLpGitrrallelakalgleveereitlkdleeadeafltntlrgvlpvrsi 223
                                       gs  N+f v +g+++tPp  +  L+Gitr++ +e++k+ g ev e+   l dl  ade+f+t+t+++  p+++i
  gi|298675762|ref|YP_003727512.1| 186 GSGDNIFAVNNGKVYTPPTIN-NLKGITRAVSIEILKDMGYEVNEQHMGLFDLYTADEIFVTGTAAEAAPITQI 258
                                       *****************9988.7************************************************997 PP

>> Ig_J_chain  Immunoglobulin J chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.2e-05      0.11      41     128 ..     135     221 ..     108     226 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.2e-05
                        Ig_J_chain  41 vplkarenisdptsplrtkfvyklselckkcdpveveledqvvtasqsnicdeesetcytydrnkcytskvpltyeG 117
                                       v +++r n  d +sp  + + y l ++  k ++ +   ++ ++  +++ + + + ++ ++ +  k yt     + +G
  gi|298675762|ref|YP_003727512.1| 135 VTVTTRRNAPDALSPNIKSMNY-LNNILAKVEANNKGGDEAIFLDNNGYVSEGSGDNIFAVNNGKVYTPPTINNLKG 210
                                       7899***********9999988.8999************************************************** PP

                        Ig_J_chain 118 etklveaaltp 128
                                        t+ v+  +  
  gi|298675762|ref|YP_003727512.1| 211 ITRAVSIEILK 221
                                       ***99876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1683.84
//
Query:       gi|298675763|ref|YP_003727513.1|  [L=667]
Description: aldehyde ferredoxin oxidoreductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.4e-29  100.7   0.0    1.5e-28  100.0   0.0    1.3  1  AFOR_N    Aldehyde ferredoxin oxidoreductase, N-terminal doma
    1.2e-12   47.5   0.0      3e-12   46.3   0.0    1.6  1  AFOR_C    Aldehyde ferredoxin oxidoreductase, domains 2 & 3
  ------ inclusion threshold ------
       0.16   12.0   0.1       0.33   11.0   0.1    1.5  1  Pico_P2A  Picornavirus core protein 2A


Domain annotation for each model (and alignments):
>> AFOR_N  Aldehyde ferredoxin oxidoreductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.0   0.0   2.6e-32   1.5e-28      24     197 ..      31     234 ..      15     235 .. 0.87

  Alignments for each domain:
  == domain 1  score: 100.0 bits;  conditional E-value: 2.6e-32
                                       HHH-SCHHHHHHHHHHHS-TTS-TTSTTS-EEEEE-TTTTSSSTTB-EEEEEEE-TTTSSEEEEEEETCHHHHHHHC CS
                            AFOR_N  24 ekylGgrglaakllldevppgvdplspenplvfatGpltgtpapgsgrlvvvaksPltgtlgesnaGgrfgaelkra 100
                                       ++ +G++  ++k ++d+   ++  +s++n+l+f+ G l+g+++pg++rl++ ++sPl++++  s  Gg +++ +kr+
  gi|298675763|ref|YP_003727513.1|  31 KDIVGPVDWGLKNHFDYRSYEYSEYSKNNVLCFGLGKLAGSKLPGTQRLIFSFRSPLWKGFFVSALGG-AAHVFKRV 106
                                       5679************999*************************************************.******** PP

                                       T-SEEEEES--SS-EEEEEETT.....EEEEEE-..TTTTT..........S-HHHHHHHHHH....HHTS....EE CS
                            AFOR_N 101 GydaivieGkaekpvylviedd.....kveieda..edlwg..........ldtyettealke....elgd....kv 152
                                       G+d + ieG++ekp+++v++       +ve++++  ++              ++y++ e+l +    +       ++
  gi|298675763|ref|YP_003727513.1| 107 GVDYVTIEGRSEKPSIIVLKGRkegyvDVEFHEIteNK--LlnvykgyngkEGVYALSEYLISnfssK--YnndyRC 179
                                       *******************7665668889***995533..344788888866********88856553..0457899 PP

                                       EEE-HHHHTT-TTB-E.EE.........TTEEE-SSSHHHHHH.HTTEEEEEEE- CS
                            AFOR_N 153 aviGpaGenlvrfAsisvd.........dgraagrgGlGavmg.sKnlkaivvrg 197
                                       +v+Gp    +  +A++s +         +++ agrgG G+v+   +++  iv+ g
  gi|298675763|ref|YP_003727513.1| 180 MVVGPGSLYSNMGATFSATlknnemvvgSEEWAGRGGSGSVLYqGHGVAGIVFGG 234
                                       9***********999988898888888655578**********99*******998 PP

>> AFOR_C  Aldehyde ferredoxin oxidoreductase, domains 2 & 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.0     5e-16     3e-12      37     301 ..     296     583 ..     263     609 .. 0.67

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 5e-16
                                       ---BTTTTBS--TTGGGGSH.....HHHHH.....HTEEEE.E.-TT.-SS--EEEEE......ETEE---HHHHHH CS
                            AFOR_C  37 alptknfqegtfekaekisg.....ealee.....kylvkneg.Cfs.CpiaCgrevkveegkkvkvegpeyetlaa 101
                                        +p  n++  ++++ e+i+      +++++     +++ +n   C   Cp+ C+++ k   g     +  +ye + a
  gi|298675763|ref|YP_003727513.1| 296 FIPLMNWKMIYMPRDERINIhekllDKYWKpfnkeSMEPRNWTtCGEpCPVVCKKHRK---G-----QHVDYEPYEA 364
                                       567778888776666665555455533333444434666776689888********99...3.....3469****** PP

                                       HTGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHHHHHHHHHTTSS-HHHH..........TS---...-TT-THHH CS
                            AFOR_C 102 lGsnlgiddleailklnelcdelGlDtisaGntiafamelyekGllkkedt..........dglel...efgdaeal 165
                                        G+  g ++++++    + +d+ G+D i++Gn+ a++ el ++ ll+++++          ++++    +  +a+ +
  gi|298675763|ref|YP_003727513.1| 365 DGPLAGSYEIHKTDVSVKKIDTIGIDAIEFGNLSAWILELISERLLSSKELglsanprfdmKNFDYekdSEINANLV 441
                                       ***********************************************************994444411134488999 PP

                                       HHHHHHHHTT-T.THHHHTT-HHHHHHCTT...-GGG--EETT....EE--SS-GGG-HHHHH........HHHH-T CS
                            AFOR_C 166 lellekiAkreg.igdllAeGvkrlaeklg...aeelamhvkG....lelpaydprgakgmal........aYatsn 226
                                        el + +A+++  + ++l +G+++ a k++   +e++  h  G     +++ y p g  g           ++ + +
  gi|298675763|ref|YP_003727513.1| 442 AELADNVAYGKTeVCKVLRQGIRKSASKFDemfKERIKNHSSGynsyKDFAVYVPFGEDGCIAptmywavgNFVPVP 518
                                       ******************************77766666666662221122222222111111111111111333333 PP

                                       TSS-SGGG-THHHHS---TT--HHHHHHHHHHHHHHHHHHHHT--GGGG-HHH......HHHHHHHHHT----HH CS
                            AFOR_C 227 rGacHlraylialeekvdpletegkaelvkwfqdltalvdslglCkftseaeerldlelyakllsavtGidvtee 301
                                         +++l  y +        +++e  ae +     +  + +  g+C+f +      ++e ++ ll+ + +id+++ 
  gi|298675763|ref|YP_003727513.1| 519 IQGKYLTYYQFG------FFDPETLAEECFKKAVYELYSENTGMCRFHR----NWATEVIPLLLKKAWDIDIDKS 583
                                       333333322222......2233445555555555555666677777777....3445666667776666666665 PP

>> Pico_P2A  Picornavirus core protein 2A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   5.5e-05      0.33      46     113 ..     169     237 ..     144     253 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.5e-05
                          Pico_P2A  46 ycksrrkyypvsvekptlieieeseyyparlqshvll..gvGfaePGdCGGilrCehGviGivtaGGegl 113
                                       ++++++  y  +v +p++ + +   ++ a l+++ ++  ++  a  G  G +l   hGv Giv  GGe  
  gi|298675763|ref|YP_003727513.1| 169 FSSKYNNDYRCMVVGPGSLYSNMGATFSATLKNNEMVvgSEEWAGRGGSGSVLYQGHGVAGIVF-GGEME 237
                                       77889999************999999999998765441145678999***************96.55543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (667 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.72u 0.33s 00:00:01.05 Elapsed: 00:00:00.50
# Mc/sec: 4009.71
//
Query:       gi|298675764|ref|YP_003727514.1|  [L=78]
Description: hypothetical protein Metev_1887 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 619.73
//
Query:       gi|298675765|ref|YP_003727515.1|  [L=306]
Description: glycine betaine ABC transporter substrate-binding protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.3e-60  202.9   0.2    7.2e-60  202.7   0.2    1.0  1  OpuAC          Substrate binding domain of ABC-type glycine b
  ------ inclusion threshold ------
      0.071   12.9   0.0       0.15   11.9   0.0    1.4  1  LEAP-2         Liver-expressed antimicrobial peptide 2 precur
      0.093   13.0   0.0       0.17   12.1   0.0    1.4  1  Chi-conotoxin  chi-Conotoxin or t superfamily


Domain annotation for each model (and alignments):
>> OpuAC  Substrate binding domain of ABC-type glycine betaine transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.7   0.2   1.2e-63   7.2e-60       1     256 [.      46     294 ..      46     295 .. 0.97

  Alignments for each domain:
  == domain 1  score: 202.7 bits;  conditional E-value: 1.2e-63
                                       CEEEEEEESSHHHHHHHHHHHHHHHHTTEEEEEEEEESHHHHHHHHHTTSSSEEEEEEHHHHHHHHHHHHHHHHEEE CS
                             OpuAC   1 ktivigsknwteqevlaeilkqllekkGykveltnlgstavlfaalasGdiDvypeewtgtayeaykkaveekkgle 77 
                                       kti++gs++w+++++++++ k++le+ Gy+vel+ ++  + ++++l+++d+D+y+++w++ ++  y+ +++e+  ++
  gi|298675765|ref|YP_003727515.1|  46 KTIKLGSTTWDDGRATSNMFKHILESEGYNVELVYGDL-GGVYQGLSDKDLDFYVSAWLPGTQGNYWNRYSEDLIIV 121
                                       79************************************.667*****************************666666 PP

                                       EEEEESEEECEEEEEEHHHHHHHTTTBHHHHCTHHGGTEEEEEHHCCHSTTSHHCCHHHHHHHHHHT-TTCEEEGSC CS
                             OpuAC  78 vlgplgagnteglavpkyvaekygiksisDLkkpaedlelgakgeflgrpdgwgcekvtegllkaYgldkvelvegs 154
                                         + l  g++ gl+vp+yv     +++i  Lk + +    +++g+++g+++g+g++k te+++ +Y+l +++l ++s
  gi|298675765|ref|YP_003727515.1| 122 --NNLSSGARTGLVVPSYV----PVDTINGLKENRD----KFDGQIQGIEPGAGIMKQTENAISEYNL-DYKLQSSS 187
                                       ..9****************....********99999....9***************************.799999** PP

                                       EEEEHHHHHHHHHTTCSSEEEEETTSTHHHHT......TEEE-B-TTSTS-SSEEEEEEEEHHHHHHSCTHHHHHHH CS
                             OpuAC 155 eaamdaelyaaykrgepvvvyawtPdwaikky......dlvvLedpkglfppaynvvpvvrkefaekaPevaafLek 225
                                       + am +el  a+k++e++vv++w P+w ++++      dl++Ledpk++++  ++++ ++r++f+e++P+++++ + 
  gi|298675765|ref|YP_003727515.1| 188 TVAMSTELGDAIKDEEWIVVTLWNPHWSFSRMkqeygvDLKYLEDPKSVYGESDDITMIAREGFKEDYPKIYKLASD 264
                                       ***************************************************************************** PP

                                       HC--HHHHHHHHHHHHTTTT-HHHHHHHHHH CS
                             OpuAC 226 lsldtetlnelnaqvdvegkdpeevAkawla 256
                                        s+ ++++++++ ++++ g++p+++A++w++
  gi|298675765|ref|YP_003727515.1| 265 SSMGISEIESMMLDIEN-GMSPADAAQKWID 294
                                       ****************7.***********97 PP

>> LEAP-2  Liver-expressed antimicrobial peptide 2 precursor (LEAP-2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.5e-05      0.15       7      33 ..       8      34 ..       2      43 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.5e-05
                            LEAP-2  7 lavllvcllllsqvdssplpqqssakr 33
                                      l+v+++clll+  + ss   qq+s++ 
  gi|298675765|ref|YP_003727515.1|  8 LSVFIICLLLIFSLASSGCMQQNSEQT 34
                                      78*****************99999875 PP

>> Chi-conotoxin  chi-Conotoxin or t superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.9e-05      0.17       4      29 ..       8      33 ..       6      50 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.9e-05
                     Chi-conotoxin  4 lpVFvILLLLiaSaPsvdaqpktkdd 29
                                      l+VF+I LLLi S +s    +++ ++
  gi|298675765|ref|YP_003727515.1|  8 LSVFIICLLLIFSLASSGCMQQNSEQ 33
                                      89***********9998776666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.36s 00:00:00.96 Elapsed: 00:00:00.56
# Mc/sec: 1636.04
//
Query:       gi|298675766|ref|YP_003727516.1|  [L=144]
Description: hypothetical protein Metev_1889 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-37  128.4   0.5    1.7e-37  128.3   0.5    1.0  1  DUF61     Protein of unknown function DUF61
  ------ inclusion threshold ------
       0.17   11.9   0.0       0.28   11.2   0.0    1.4  1  Exc       Excisionase-like protein


Domain annotation for each model (and alignments):
>> DUF61  Protein of unknown function DUF61
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.3   0.5   1.9e-41   1.7e-37       2     126 ..      16     142 ..      15     143 .. 0.99

  Alignments for each domain:
  == domain 1  score: 128.3 bits;  conditional E-value: 1.9e-41
                                       S---SHHHHHGGGSBSS-EEHHHHHHT--EEEB.TTS-EEE--HHHHHHHHTTS-GGGGGT-EESEEEEE-SSSSE. CS
                             DUF61   2 rilakeiksinkhlPaerktLkelLeeekptivtkdgsehrfdkeeleklkeilpeelwdklkLPIllemdpelges 78 
                                       r+++ ei++in+++++ rktL +lLee++p+++tkdg+e++f+ke ++kl+++lpe+++++lkLPIl+++d ++++s
  gi|298675766|ref|YP_003727516.1|  16 RWMNLEIGKINNSIVTARKTLYQLLEEDNPSSKTKDGREYLFKKEIINKLENRLPEHIQTRLKLPILFFFDLQIDDS 92 
                                       9**************************************************************************** PP

                                       .EEEES-HH..HHHHHHHHT--...-SSEEEHH.HHHHHHHH-ST...TE CS
                             DUF61  79 vylvrgkae..vkvvskilgkereeedelviykpevrelrrklptatqli 126
                                       +y+++++a   ++++ +i  k++++++++++ k+ ++++++k+p+a+q++
  gi|298675766|ref|YP_003727516.1|  93 CYINDKTAFeaLQILGEIGYKREFRNNRHWMGKAIAYSIKKKYPSAVQIV 142
                                       ********999*************************************97 PP

>> Exc  Excisionase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.2e-05      0.28      36      58 ..      49      71 ..      28      76 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.2e-05
                                      EEETTEEEEETT-EE--SSX... CS
                               Exc 36 vkdGreylveedavkvelerlpr 58
                                       kdGreyl++++ + +  +rlp 
  gi|298675766|ref|YP_003727516.1| 49 TKDGREYLFKKEIINKLENRLPE 71
                                      69*************99999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 947.41
//
Query:       gi|298675767|ref|YP_003727517.1|  [L=122]
Description: hypothetical protein Metev_1890 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.32    9.7   1.7       0.37    9.5   1.7    1.1  1  DUF2207   Predicted membrane protein (DUF2207)
       0.44   10.4   6.0       0.44   10.4   0.4    2.5  2  DUF2975   Protein of unknown function (DUF2975)
        8.3    6.5   7.1        1.6    8.8   2.7    2.0  2  TssO      Type VI secretion system, TssO


Domain annotation for each model (and alignments):
>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   1.7   6.2e-05      0.37     368     432 ..       9     114 ..       1     119 [. 0.72

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 6.2e-05
                           DUF2207 368 ergyfdkkgkkklkklsalglgliilglilillallllvll.................................... 408
                                       e++yf+kk    ++ l++  +++++++++++ll+l++ v++                                    
  gi|298675767|ref|YP_003727517.1|   9 ESEYFEKK----TNQLNLSPFMVMVFIYFCLLLGLVSSVSVflieyfnlnyplswevklyplfltvmfyvlrkefqg 81 
                                       34555555....5555666666666666666666665555567899******************************* PP

                           DUF2207 409 .........lvfllilllillliaiivlllfsr 432
                                                + ++l+l+ +  +i++iv+l+  +
  gi|298675767|ref|YP_003727517.1|  82 ikdendideSKIILLLGALGSVIMVIVALVRVW 114
                                       ******999666666666666666666666555 PP

>> DUF2975  Protein of unknown function (DUF2975)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.8     0.028   1.6e+02      92     112 ..      23      43 ..       6      49 .. 0.61
   2 ?   10.4   0.4   7.4e-05      0.44      10      43 ..      85     118 ..      49     121 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.028
                           DUF2975  92 vvllllgvafaslvigllvlv 112
                                        + +++++++++l++gl++ v
  gi|298675767|ref|YP_003727517.1|  23 SPFMVMVFIYFCLLLGLVSSV 43 
                                       344455555666666665544 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 7.4e-05
                           DUF2975  10 ypeaaglrvpvlllgvlallafvvalvqlwkLlr 43 
                                        ++++ +++++ll ++  +++++valv +w+L +
  gi|298675767|ref|YP_003727517.1|  85 ENDIDESKIILLLGALGSVIMVIVALVRVWALGN 118
                                       5788889999********************9965 PP

>> TssO  Type VI secretion system, TssO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   2.7   0.00028       1.6       8      38 ..      28      58 ..      26      65 .. 0.91
   2 ?   -1.8   0.0      0.52   3.1e+03       5      28 ..      85     108 ..      82     111 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00028
                              TssO  8 sgflyflllFlvtvlllflivffffkssplq 38
                                      + f+yf+ll+ +++ ++++++ +f+ ++pl+
  gi|298675767|ref|YP_003727517.1| 28 MVFIYFCLLLGLVSSVSVFLIEYFNLNYPLS 58
                                      67************************99986 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.52
                              TssO   5 ErrsgflyflllFlvtvlllfliv 28 
                                       E  +   + +ll+ ++  ++++iv
  gi|298675767|ref|YP_003727517.1|  85 ENDIDESKIILLLGALGSVIMVIV 108
                                       555566677777777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       985  (0.0549389); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 676.77
//
Query:       gi|298675768|ref|YP_003727518.1|  [L=42]
Description: hypothetical protein Metev_1891 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       143  (0.0079759); expected 358.6 (0.02)
Passed bias filter:                      129  (0.00719505); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.52
# Mc/sec: 244.19
//
Query:       gi|298675769|ref|YP_003727519.1|  [L=178]
Description: ArsR family transcriptional regulator [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      2e-12   46.7   0.1      5e-12   45.5   0.1    1.7  1  HTH_5       Bacterial regulatory protein, arsR family
    2.4e-08   33.9   0.0    3.6e-08   33.3   0.0    1.3  1  HTH_20      Helix-turn-helix domain
    4.3e-05   23.0   0.3    0.00011   21.7   0.3    1.7  1  HTH_24      Winged helix-turn-helix DNA-binding
    0.00015   21.6   0.0     0.0004   20.3   0.0    1.7  1  MarR        MarR family
     0.0013   19.3   0.2     0.0056   17.2   0.2    2.0  1  DUF4430     Domain of unknown function (DUF4430)
     0.0049   16.7   0.0      0.026   14.4   0.0    2.1  2  TrmB        Sugar-specific transcriptional regulator TrmB
     0.0078   16.1   0.0      0.012   15.5   0.0    1.3  1  MarR_2      MarR family
  ------ inclusion threshold ------
      0.015   15.6   0.2      0.043   14.2   0.1    1.7  1  Rrf2        Transcriptional regulator
      0.065   13.4   0.1       0.49   10.6   0.0    2.3  3  HTH_34      Winged helix DNA-binding domain
      0.066   13.2   0.5       0.31   11.0   0.1    2.1  2  HTH_45      Winged helix-turn-helix
      0.087   12.7   0.1       0.12   12.2   0.1    1.1  1  HCV_NS5a_C  HCV NS5a protein C-terminal region
      0.089   12.9   0.0       0.17   12.1   0.0    1.5  1  HTH_28      Helix-turn-helix domain
      0.097   12.6   0.0       0.17   11.9   0.0    1.3  1  HTH_1       Bacterial regulatory helix-turn-helix protein, ly
       0.11   12.3   0.0       0.88    9.4   0.0    2.1  2  HTH_IclR    IclR helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.1   3.9e-15     5e-12       3      46 ..      18      61 ..      16      62 .. 0.97

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 3.9e-15
                                      HHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  3 tRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      tRl ILklLa++e+ ++ +a+elg+s + +  H ++L++a LVe
  gi|298675769|ref|YP_003727519.1| 18 TRLNILKLLADNEMHITGIANELGISVPVTAKHIRILENAELVE 61
                                      9******************************************7 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   2.8e-11   3.6e-08       2      60 ..       9      66 ..       8      67 .. 0.96

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 2.8e-11
                                      HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                      +i++AL+  +R+ il++L  + ++  + +a +l++s     +H+r+Le a+Lve+++ g
  gi|298675769|ref|YP_003727519.1|  9 KIFKALGCNTRLNILKLL-ADNEMHITGIANELGISVPVTAKHIRILENAELVERQKFG 66
                                      69****************.************************************9876 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.3   8.4e-08   0.00011       4      48 .]      18      61 ..      17      61 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 8.4e-08
                            HTH_24  4 tdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      t+++IL+lL +   + ++ +A +lg+S++ + ++++ Le+++l++
  gi|298675769|ref|YP_003727519.1| 18 TRLNILKLLAD-NEMHITGIANELGISVPVTAKHIRILENAELVE 61
                                      78899999988.89****************************996 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   3.1e-07    0.0004       8      51 ..      22      64 ..      17      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.1e-07
                                      HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR  8 iLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                      iL +l+++ ++ ++ +a+ lg+s + + + ++ Le ++l+eR+k
  gi|298675769|ref|YP_003727519.1| 22 ILKLLADN-EMHITGIANELGISVPVTAKHIRILENAELVERQK 64
                                      56556554.58899****************************97 PP

>> DUF4430  Domain of unknown function (DUF4430)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.2   4.4e-06    0.0056       1      71 [.      96     157 ..      96     158 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.4e-06
                           DUF4430   1 GttvfdvleaaakkkedkteaqsgehyitsIngleqdtakksyWmyevNGepsdvGagsyklkdgdkivfr 71 
                                       Gt+++d+l+++ +++ +k   +++   + s +g      +  + +yevNG++sd+ + +++ +d+  ++++
  gi|298675769|ref|YP_003727519.1|  96 GTNLLDILKKVSSVEVKKIGDREA---VVSTDG------DEGFFVYEVNGKMSDKTVHECTFEDDAIVEWK 157
                                       788888888888888888866663...666666......478999*****************999999996 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0     2e-05     0.026      15      58 ..      23      67 ..      22      84 .. 0.86
   2 ?    0.8   0.0      0.35   4.5e+02      30      58 ..      69      97 ..      68     111 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2e-05
                                      HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.ST CS
                              TrmB 15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek.gr 58
                                      l+Ll+  ++ ++ ia+elg++ +   + +r Le++ lVer+k g+
  gi|298675769|ref|YP_003727519.1| 23 LKLLADNEMHITGIANELGISVPVTAKHIRILENAELVERQKfGN 67
                                      5899*************************************9666 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.35
                                      CCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 30 eelgvprskvYevLrsLedkGlVerekgr 58
                                      ++l+v   ++Y +L +      +e+e+g+
  gi|298675769|ref|YP_003727519.1| 69 HILKVNTENIYTILDKFAPTKDIEVERGT 97
                                      678999999***99998887777777766 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   9.3e-06     0.012       8      55 ..      20      64 ..      14      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 9.3e-06
                                      HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                      + +L  L++++   + ++ +a +lg+s + + ++++ L+ a Lver++
  gi|298675769|ref|YP_003727519.1| 20 LNILKLLADNE---MHITGIANELGISVPVTAKHIRILENAELVERQK 64
                                      56777888888...899*****************************85 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   3.3e-05     0.043      16      58 ..      22      63 ..      16      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.3e-05
                                      HHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              Rrf2 16 yLakeeeeepvsseeiaerqnispsylekilakLrkaglvksv 58
                                      +L++ +++e + ++ ia++ +is ++ +k ++ L++a+lv+ +
  gi|298675769|ref|YP_003727519.1| 22 ILKLLADNE-MHITGIANELGISVPVTAKHIRILENAELVERQ 63
                                      567777777.9*****************************976 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00038      0.49       2      48 ..      19      64 ..      18      72 .. 0.90
   2 ?   -1.0   0.0       1.6   2.1e+03      23      48 ..      70      95 ..      68      99 .. 0.83
   3 ?   -1.1   0.0       1.7   2.2e+03       5      29 ..      99     125 ..      96     126 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00038
                            HTH_34  2 RlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdk 48
                                      Rl++l +La++ e+  + + ++l+++    ++h+++Le+a+ +e++k
  gi|298675769|ref|YP_003727519.1| 19 RLNILKLLADN-EMHITGIANELGISVPVTAKHIRILENAELVERQK 64
                                      99999988865.6899***************************9998 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.6
                            HTH_34 23 aleatdgnLsvhlkkLekagYievdk 48
                                       l++++ n+++ l+k+   + iev+ 
  gi|298675769|ref|YP_003727519.1| 70 ILKVNTENIYTILDKFAPTKDIEVER 95
                                      57899999999999999999998876 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.7
                            HTH_34   5 vlsyLasvdeadfvel..kealeatdg 29 
                                       +l +L +v++++ +++  +ea+  tdg
  gi|298675769|ref|YP_003727519.1|  99 LLDILKKVSSVEVKKIgdREAVVSTDG 125
                                       677888888888888866667777776 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00024      0.31      10      53 ..      21      64 ..      17      91 .. 0.85
   2 ?   -0.2   0.0      0.78     1e+03      61      75 ..      95     109 ..      93     113 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00024
                            HTH_45 10 dILeaisegeakkTkimykanLsykllnkYLdmLvekglikksk 53
                                      +IL+ + ++e + T i  +  +s  ++ k + +L + +l++ +k
  gi|298675769|ref|YP_003727519.1| 21 NILKLLADNEMHITGIANELGISVPVTAKHIRILENAELVERQK 64
                                      79**************************************5543 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.78
                            HTH_45  61 kGlelleklkeleel 75 
                                       +G +ll+ lk++ ++
  gi|298675769|ref|YP_003727519.1|  95 RGTNLLDILKKVSSV 109
                                       666666666666544 PP

>> HCV_NS5a_C  HCV NS5a protein C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   9.4e-05      0.12      48      99 ..      54     105 ..      42     111 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.4e-05
                        HCV_NS5a_C  48 lieanllwrqemgg.nitrvesenkvvildsfdplvaeederevsvpaeilrk 99 
                                       l +a+l+ rq++g   i +v++en   ild f p    e er   +  +il+k
  gi|298675769|ref|YP_003727519.1|  54 LENAELVERQKFGNsHILKVNTENIYTILDKFAPTKDIEVERGTNL-LDILKK 105
                                       44689999****963699****************999999997665.355555 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00013      0.17       2      26 ..      19      44 ..      18      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                            HTH_28  2 RleiikllaaGh.svreaArelgisr 26
                                      Rl i+klla+ +  ++ +A+elgis 
  gi|298675769|ref|YP_003727519.1| 19 RLNILKLLADNEmHITGIANELGISV 44
                                      9********8766***********96 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00013      0.17       3      40 ..      19      57 ..      18      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                                      HHHHHHHHHHHS.SHHHHHHHHTS-HHHHHHHHHHHHHH CS
                             HTH_1  3 qlrlfvavaeeg.sftrAAeeLglsqpavsrqikrLEee 40
                                      +l +++ +a+++ ++t+ A eLg+s p   ++i+ LE++
  gi|298675769|ref|YP_003727519.1| 19 RLNILKLLADNEmHITGIANELGISVPVTAKHIRILENA 57
                                      6788999999999************************84 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00069      0.88       7      51 ..      21      63 ..      20      64 .. 0.87
   2 ?    0.3   0.0      0.49   6.3e+02       2      13 ..      93     104 ..      92     106 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00069
                                      HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                       iL++la  + e+ ++ +A+++g++ + +  +++ L++  +ve++
  gi|298675769|ref|YP_003727519.1| 21 NILKLLA--DNEMHITGIANELGISVPVTAKHIRILENAELVERQ 63
                                      5677776..56788****************************986 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.49
                                       HHHHHHHHCT-C CS
                          HTH_IclR   2 ldRalaiLdala 13 
                                       ++R+  +Ld+l 
  gi|298675769|ref|YP_003727519.1|  93 VERGTNLLDILK 104
                                       89*******996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1115.47
//
Query:       gi|298675770|ref|YP_003727520.1|  [L=400]
Description: hypothetical protein Metev_1893 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.2e-08   32.4   0.1    1.1e-07   31.6   0.1    1.4  1  PGF-CTERM        PGF-CTERM motif
      5e-06   26.7   0.9       0.34   11.2   0.0    4.1  4  WXG100           Proteins of 100 residues with WXG
    2.8e-05   24.3  25.5      0.002   18.3   5.9    3.3  3  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
    0.00094   19.4   2.3        1.3    9.3   0.1    2.8  2  TcdB_N           TcdB toxin N-terminal helical domain
     0.0019   17.6   7.5      0.079   12.2   0.3    3.1  3  HemX             HemX, putative uroporphyrinogen-III C-methyl
     0.0047   16.9  25.4       0.18   11.8   0.9    3.4  4  Laminin_II       Laminin Domain II
  ------ inclusion threshold ------
      0.011   16.1   5.4        7.7    7.0   0.7    4.1  4  LPP              Lipoprotein leucine-zipper
      0.015   14.9   0.1        2.1    8.0   0.0    2.8  2  CENP-B_N         CENP-B N-terminal DNA-binding domain
      0.016   15.3   5.9        4.5    7.4   0.1    4.6  3  HisKA            His Kinase A (phospho-acceptor) domain
      0.019   15.3  21.8        2.9    8.3   2.2    4.5  4  Syntaxin_2       Syntaxin-like protein
       0.03   13.6  13.6       0.25   10.6   2.4    2.5  2  CorA             CorA-like Mg2+ transporter protein
      0.033   13.8  16.4       0.12   11.9   2.5    3.0  2  TPD52            Tumour protein D52 family
      0.035   14.7   2.5        6.3    7.4   0.2    2.4  2  DUF3502          Domain of unknown function (DUF3502)
      0.062   13.0   8.1        1.9    8.2   0.3    3.0  2  DUF4874          Domain of unknown function (DUF4874)
      0.068   13.2   0.6         12    5.9   0.1    2.6  2  ER               Enhancer of rudimentary
      0.083   13.2   2.2        8.1    6.7   0.2    2.4  2  Apocytochr_F_N   Apocytochrome F, N-terminal
      0.093   12.7   4.3        7.2    6.6   0.2    3.1  2  DUF1107          Protein of unknown function (DUF1107)
      0.098   13.1  15.4         13    6.3   0.1    4.4  4  DUF4208          Domain of unknown function (DUF4208)
      0.098   13.0  26.2        1.2    9.6   1.1    4.4  4  CC2-LZ           Leucine zipper of domain CC2 of NEMO, NF-kap
       0.13   13.0  14.4        6.8    7.4   1.5    4.3  4  PMC2NT           PMC2NT (NUC016) domain
       0.45   10.8   4.0        9.8    6.5   0.3    2.9  2  DUF4226          Domain of unknown function (DUF4226)
        0.5   10.7   3.6        9.1    6.6   0.5    2.5  2  IL5              Interleukin 5
       0.53    9.8  11.8        2.7    7.5   2.7    2.6  2  4HB_MCP_1        Four helix bundle sensory module for signal 
       0.59   10.0  25.0        1.9    8.3   6.0    5.0  4  CdvA             CdvA-like coiled-coil domain
       0.67    9.8  32.4        1.6    8.6   0.5    4.0  4  SKA1             Spindle and kinetochore-associated protein 1
       0.69   10.5  22.0        2.4    8.8   4.6    4.0  4  ING              Inhibitor of growth proteins N-terminal hist
       0.69   10.2  20.4        3.1    8.1   0.8    4.9  3  DUF948           Bacterial protein of unknown function (DUF94
        0.7    9.9  26.4       0.84    9.7   1.0    4.3  4  DUF1664          Protein of unknown function (DUF1664)
       0.97    9.8   9.2         28    5.1   0.1    4.1  4  KxDL             Uncharacterized conserved protein
          1    7.4  34.4       0.15   10.2   2.5    3.7  3  EzrA             Septation ring formation regulator, EzrA
        1.1    8.2  15.7        1.1    8.3   2.6    2.2  2  RNA_pol_Rpb2_6   RNA polymerase Rpb2, domain 6
        1.2    8.6  25.6        1.2    8.6   8.4    2.3  2  Leu_zip          Leucine zipper
        1.3    8.7  14.1        2.1    8.1   3.8    2.7  2  DUF745           Protein of unknown function (DUF745)
        1.4    9.2  20.9         11    6.3   0.2    5.1  5  Syntaxin-18_N    SNARE-complex protein Syntaxin-18 N-terminus
        1.6    8.9  13.5        4.4    7.4   2.2    3.2  4  GIT1_C           G protein-coupled receptor kinase-interactin
        1.6    9.2  23.7       0.43   11.0   2.2    3.9  4  TBCC_N           Tubulin-specific chaperone C N-terminal doma
          2    8.2  14.9        4.6    7.0   3.8    2.4  2  HeLo             Prion-inhibition and propagation
        2.2    7.6  29.0        1.1    8.6   7.9    2.9  3  Cluap1           Clusterin-associated protein-1
        2.6    8.4  31.8        3.3    8.1   4.1    3.5  3  Fez1             Fez1
        2.9    7.6  20.2        6.9    6.4   4.9    3.1  3  Borrelia_lipo_1  Borrelia burgdorferi virulent strain associa
        2.9    7.9  28.5       0.65   10.1   5.6    3.1  3  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
        3.2    7.8   9.6        7.9    6.6   0.9    3.2  2  ENTH             ENTH domain
        3.2    8.1  17.9        8.3    6.8   3.5    4.2  5  BLOC1_2          Biogenesis of lysosome-related organelles co
        3.2    8.5  18.4         18    6.1   0.6    4.6  5  Occludin_ELL     Occludin homology domain
        4.6    4.9  26.9        3.1    5.5   8.6    2.0  2  PI3K_1B_p101     Phosphoinositide 3-kinase gamma adapter prot
        5.8    7.6  10.3         11    6.7   0.1    4.0  4  DUF883           Bacterial protein of unknown function (DUF88
        8.9    6.5  27.0        7.9    6.6   1.0    4.6  5  DUF148           Domain of unknown function DUF148
        9.1    5.5  10.5        4.1    6.7   4.2    2.4  2  DUF4407          Domain of unknown function (DUF4407)
        9.4    5.6  11.7        9.8    5.6   1.8    2.4  2  FAP206           Domain of unknown function


Domain annotation for each model (and alignments):
>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.1   2.9e-10   1.1e-07       1      23 []     378     400 .]     378     400 .] 0.97

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 2.9e-10
                         PGF-CTERM   1 tPGFGavlAlaGLLaaalLaRRr 23 
                                       +PGFG++lA+ G+ a+++L++R+
  gi|298675770|ref|YP_003727520.1| 378 SPGFGSLLAISGMFAVVYLVKRK 400
                                       6*********************8 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0    0.0017      0.64       8      78 ..      72     143 ..      70     146 .. 0.92
   2 ?   -1.4   0.0       7.8   2.9e+03       3      26 ..     158     181 ..     156     186 .. 0.80
   3 !   11.2   0.0   0.00093      0.34       7      78 ..     231     303 ..     230     306 .. 0.93
   4 ?   -1.6   0.0       8.9   3.3e+03       4      26 ..     319     341 ..     316     344 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0017
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHC.GCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100   8 elrqaaarfqkqaeeledelqrlkaevdal.qsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaa 78 
                                       +lr++a ++ k++ e+e + +++ ++v+ l +     + +d+ + e+ e+++++++l+++L++ s+a++++ 
  gi|298675770|ref|YP_003727520.1|  72 DLRTKAETVHKSSHEMEHIAKEIINHVETLeSIEHPDENKDKVKTEISEINEHIDELANLLNSKSDAVHEVE 143
                                       799***************************555999***************************999998765 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 7.8
                                       CSHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100   3 kvdpeelrqaaarfqkqaeelede 26 
                                         ++ el +  ++++++a+e+e+ 
  gi|298675770|ref|YP_003727520.1| 158 HHEFHELGDIGSHLKEHASEIESD 181
                                       567788888899999999999886 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00093
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC.GCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100   7 eelrqaaarfqkqaeeledelqrlkaevdal.qsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaa 78 
                                       ++lr++a ++ k++ e+e + +++ ++v+ l +     + +d+ + e+ e+++++++l+++L++ s+a++++ 
  gi|298675770|ref|YP_003727520.1| 231 DDLREKAETVHKSSHEMEHIAKEIISHVETLeGIEHPDENKDKVKTEISEINEHIDELANLLNSKSDAVHEVE 303
                                       689****************************777999***************************999998765 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 8.9
                                       SHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100   4 vdpeelrqaaarfqkqaeelede 26 
                                        ++ el +  ++++++a+e+e+ 
  gi|298675770|ref|YP_003727520.1| 319 HEFHELGDIGSHLKEHASEIESD 341
                                       56788888889999999999876 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   5.9   5.5e-06     0.002      23      99 ..      68     144 ..      55     159 .. 0.93
   2 ?   -1.7   0.1       8.9   3.2e+03      36      75 ..     169     208 ..     155     213 .. 0.64
   3 !   16.6   4.9   1.8e-05    0.0067      26      99 ..     231     304 ..     226     319 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 5.5e-06
                       TMF_TATA_bd  23 rlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetlLellGeksEeveELra 99 
                                       +l ++l++  e++ + ++e + +++ei++ +++ e+ ++ +++ +++++e++e++e+ ++l  ll  ks+ v E ++
  gi|298675770|ref|YP_003727520.1|  68 SLNADLRTKAETVHKSSHEMEHIAKEIINHVETLESIEHPDENKDKVKTEISEINEHIDELANLLNSKSDAVHEVEE 144
                                       677889999999**************************************************************886 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 8.9
                       TMF_TATA_bd  36 erleaerdeareeivklmkeneelkelkkeleelekelee 75 
                                       + l++  +e++++++   +e +  +e+ + l+e+e++ +e
  gi|298675770|ref|YP_003727520.1| 169 SHLKEHASEIESDVIGTGEEYDHEHEEGSALAEVEEHANE 208
                                       5566666666666666666666666666666666666554 PP

  == domain 3  score: 16.6 bits;  conditional E-value: 1.8e-05
                       TMF_TATA_bd  26 gElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetlLellGeksEeveELra 99 
                                        +l++  e++ + ++e + +++ei++ +++ e  ++ +++ +++++e++e++e+ ++l  ll  ks+ v E ++
  gi|298675770|ref|YP_003727520.1| 231 DDLREKAETVHKSSHEMEHIAKEIISHVETLEGIEHPDENKDKVKTEISEINEHIDELANLLNSKSDAVHEVEE 304
                                       566777788999999********************************************************876 PP

>> TcdB_N  TcdB toxin N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.2    0.0042       1.5      14      42 ..     104     131 ..      98     139 .. 0.85
   2 !    9.3   0.1    0.0036       1.3      13      42 ..     263     291 ..     259     302 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0042
                                       HHTTTTS-HHHHHHHHHHHHHHHHHHHHH CS
                            TcdB_N  14 lnklseeqskkkyellkklkkeidnYnnl 42 
                                       +  + +e++ k++++++++++ id+  nl
  gi|298675770|ref|YP_003727520.1| 104 I-EHPDENKDKVKTEISEINEHIDELANL 131
                                       5.6779******************97766 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0036
                                       HHHTTTTS-HHHHHHHHHHHHHHHHHHHHH CS
                            TcdB_N  13 klnklseeqskkkyellkklkkeidnYnnl 42 
                                        +  + +e++ k++++++++++ id+  nl
  gi|298675770|ref|YP_003727520.1| 263 GI-EHPDENKDKVKTEISEINEHIDELANL 291
                                       56.7789******************97766 PP

>> HemX  HemX, putative uroporphyrinogen-III C-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.24        89      10      89 ..      12      94 ..       7      96 .. 0.57
   2 !   12.2   0.3   0.00022     0.079     149     224 ..      85     161 ..      77     166 .. 0.77
   3 !    7.7   0.3    0.0051       1.9     149     220 ..     245     317 ..     235     326 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.24
                              HemX 10 lallvalavgag...lyylgqqqvqeltaevaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleql 85
                                      +  l++ a+ +       +++  v++   ev+++++++  + ++ ++ +a+ ++++ l ++l+++ae+++++++e+e+ 
  gi|298675770|ref|YP_003727520.1| 12 VSTLIVFALSVPvsaHEGHSHDNVSQSLVEVEDHANEIIIVAETIHTESAKIADDKSLNADLRTKAETVHKSSHEMEHI 90
                                      4445555555441112334444444444555666666666666666656666777778888888888888888888777 PP

                              HemX 86 qkql 89
                                      +k++
  gi|298675770|ref|YP_003727520.1| 91 AKEI 94
                                      7665 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00022
                              HemX 149 psllavRralaedlkaLravnqvDrd..giilrLeqLanqvdeL.pladneldeapsdadnaelsdslsdWkqnlek 222
                                        ++ ++ + + + +++L++++++D +   +   ++++++++deL +l+++++d+  ++++n    +s +++ +n++ 
  gi|298675770|ref|YP_003727520.1|  85 HEMEHIAKEIINHVETLESIEHPDENkdKVKTEISEINEHIDELaNLLNSKSDAVHEVEEN--TPQSHKEYAENIHH 159
                                       567888899***************862269999***********44555555554455555..58899999999987 PP

                              HemX 223 sa 224
                                       + 
  gi|298675770|ref|YP_003727520.1| 160 EF 161
                                       65 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0051
                              HemX 149 psllavRralaedlkaLravnqvDrd..giilrLeqLanqvdeL.pladneldeapsdadnaelsdslsdWkqnl 220
                                        ++ ++ + + + +++L+ ++++D +   +   ++++++++deL +l+++++d+  ++++n+   +s +++ + +
  gi|298675770|ref|YP_003727520.1| 245 HEMEHIAKEIISHVETLEGIEHPDENkdKVKTEISEINEHIDELaNLLNSKSDAVHEVEENT--PQSHKEYAKDI 317
                                       5677888999999***********762268999***********556666666655566655..55566666555 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7  10.2    0.0022       0.8       7     100 ..      34     126 ..      30     154 .. 0.75
   2 !   10.7   1.0    0.0011      0.39      14      94 ..      99     177 ..      98     183 .. 0.80
   3 !   11.3   6.6   0.00072      0.26      12     100 ..     199     286 ..     192     314 .. 0.74
   4 !   11.8   0.9   0.00049      0.18      13      93 ..     258     336 ..     251     342 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0022
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHH CS
                        Laminin_II   7 eanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqlee 83 
                                       +++++++ev++  +++    e +  +  +i+++ +  n++++ + +++   ++++ ++ k++ + ++ l+++++  e
  gi|298675770|ref|YP_003727520.1|  34 NVSQSLVEVEDHANEIIIVAETIHTESAKIADD-KSLNADLRTKAETVHKSSHEMEHIAKEIINHVETLESIEHPDE 109
                                       567889999999999999999999999999999.6666666666665555555555555555555555555555555 PP

                                       H...HHHHHHHHHHHHH CS
                        Laminin_II  84 assslsdniseikelIa 100
                                       ++  ++ +isei e I 
  gi|298675770|ref|YP_003727520.1| 110 NKDKVKTEISEINEHID 126
                                       5555*********9986 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0011
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-.-TTTTTGGGHHHHHHHHHH...HH CS
                        Laminin_II  14 evleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLe.klapqLldklkelkqleeasssls 89 
                                       e+le ++  ++n +++k ++sein++++e  +++++++ a+ +++++  +   + a+++   ++el    ++   l+
  gi|298675770|ref|YP_003727520.1|  99 ETLESIEHPDENKDKVKTEISEINEHIDELANLLNSKSDAVHEVEENTPQSHkEYAENIHHEFHELGDIGSH---LK 172
                                       67788888899999******************************9998765415688888888888777666...55 PP

                                       HHHHH CS
                        Laminin_II  90 dnise 94 
                                       +  se
  gi|298675770|ref|YP_003727520.1| 173 EHASE 177
                                       55555 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00072
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH.... CS
                        Laminin_II  12 akevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeasss. 87 
                                       ++ev+e  +++      +  k  +++++ +  n+   d+ +  + + +s+ ++e+ a ++++ +++l+  e + ++ 
  gi|298675770|ref|YP_003727520.1| 199 LAEVEEHANEIISVAGTIHTKSAKVADD-KSLND---DLREKAETVHKSSHEMEHIAKEIISHVETLEGIEHPDENk 271
                                       5677777777777777777777777777.55555...5555556666777777777777777777777666665555 PP

                                       ..HHHHHHHHHHHHH CS
                        Laminin_II  88 ..lsdniseikelIa 100
                                         ++ +isei e I 
  gi|298675770|ref|YP_003727520.1| 272 dkVKTEISEINEHID 286
                                       66********99986 PP

  == domain 4  score: 11.8 bits;  conditional E-value: 0.00049
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-.-TTTTTGGGHHHHHHHHHH...H CS
                        Laminin_II  13 kevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLe.klapqLldklkelkqleeasssl 88 
                                       +e+le ++  ++n +++k ++sein++++e  +++++++ a+ +++++  +   + a ++   ++el    ++   l
  gi|298675770|ref|YP_003727520.1| 258 VETLEGIEHPDENKDKVKTEISEINEHIDELANLLNSKSDAVHEVEENTPQSHkEYAKDIHHEFHELGDIGSH---L 331
                                       467788999999*********************************9998665414577888887777766666...5 PP

                                       HHHHH CS
                        Laminin_II  89 sdnis 93 
                                       ++  s
  gi|298675770|ref|YP_003727520.1| 332 KEHAS 336
                                       55555 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.7     0.021       7.7       3      35 ..     112     144 ..     110     146 .. 0.91
   2 ?   -1.1   0.0         7   2.6e+03      10      29 ..     169     188 ..     161     196 .. 0.73
   3 ?    7.0   0.7     0.021       7.7       3      35 ..     272     304 ..     270     306 .. 0.91
   4 ?   -1.4   0.0       8.6   3.1e+03      10      26 ..     329     345 ..     322     355 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.021
                               LPP   3 deLssqVsqLkskvdqlssdvnsakaaaqaake 35 
                                       d++ +++s+ ++ +d+l++ +ns ++a+ ++ e
  gi|298675770|ref|YP_003727520.1| 112 DKVKTEISEINEHIDELANLLNSKSDAVHEVEE 144
                                       678899**********************99887 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 7
                               LPP  10 sqLkskvdqlssdvnsakaa 29 
                                       s+Lk+  ++++sdv  + ++
  gi|298675770|ref|YP_003727520.1| 169 SHLKEHASEIESDVIGTGEE 188
                                       57888888888888666555 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.021
                               LPP   3 deLssqVsqLkskvdqlssdvnsakaaaqaake 35 
                                       d++ +++s+ ++ +d+l++ +ns ++a+ ++ e
  gi|298675770|ref|YP_003727520.1| 272 DKVKTEISEINEHIDELANLLNSKSDAVHEVEE 304
                                       678899**********************99887 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 8.6
                               LPP  10 sqLkskvdqlssdvnsa 26 
                                       s+Lk+  ++++sdv  +
  gi|298675770|ref|YP_003727520.1| 329 SHLKEHASEIESDVIGT 345
                                       56788888888887655 PP

>> CENP-B_N  CENP-B N-terminal DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.13        48       9      33 ..     132     158 ..     131     162 .. 0.88
   2 ?    8.0   0.0    0.0058       2.1       9      33 ..     292     318 ..     291     327 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.13
                                       HHHHHHHHHHHHCTT..-HHHHHHHHT CS
                          CENP-B_N   9 lreKievIqrleege..Skaelarrfn 33 
                                       l+ K++++ ++ee+   S +e a  ++
  gi|298675770|ref|YP_003727520.1| 132 LNSKSDAVHEVEENTpqSHKEYAENIH 158
                                       688***********9999999887665 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0058
                                       HHHHHHHHHHHHCTT..-HHHHHHHHT CS
                          CENP-B_N   9 lreKievIqrleege..Skaelarrfn 33 
                                       l+ K++++ ++ee+   S +e a++++
  gi|298675770|ref|YP_003727520.1| 292 LNSKSDAVHEVEENTpqSHKEYAKDIH 318
                                       688***********99*********98 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.7      0.15        55      31      58 ..      67      94 ..      48     177 .. 0.75
   2 ?    7.4   0.1     0.012       4.5      30      58 ..     222     254 ..     207     263 .. 0.79
   3 ?    1.6   0.0       0.8   2.9e+02      24      54 ..     299     327 ..     254     337 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.15
                                      .T-HSSCHHHHHHHHHHHHHHHHHHHHH CS
                             HisKA 31 gklteelkeyletiesearrldhlvedl 58
                                      ++l+ +l+   et++++++ ++h+ +++
  gi|298675770|ref|YP_003727520.1| 67 KSLNADLRTKAETVHKSSHEMEHIAKEI 94
                                      4667777777788888888777776655 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.012
                                       ......T-HSSCHHHHHHHHHHHHHHHHHHHHH CS
                             HisKA  30 e....gklteelkeyletiesearrldhlvedl 58 
                                       +    ++l+++l+e  et++++++ ++h+ +++
  gi|298675770|ref|YP_003727520.1| 222 KvaddKSLNDDLREKAETVHKSSHEMEHIAKEI 254
                                       355556899********************9887 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.8
                                       HHHHHC..T-HSSCHHHHHHHHHHHHHHHHH CS
                             HisKA  24 aeaLkregklteelkeyletiesearrldhl 54 
                                       ++  ++  +++++ key ++i+ e + l ++
  gi|298675770|ref|YP_003727520.1| 299 VHEVEE--NTPQSHKEYAKDIHHEFHELGDI 327
                                       444444..56788889999999888777666 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   2.2    0.0081       2.9      28      79 ..      70     118 ..      35     121 .. 0.77
   2 ?    7.5   1.1     0.014       5.2      39      81 ..     111     163 ..     108     179 .. 0.66
   3 ?    7.7   1.8     0.013       4.6      27      71 ..     226     275 ..     197     279 .. 0.70
   4 ?    7.0   1.0      0.02       7.4      38      67 ..     270     305 ..     265     343 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0081
                        Syntaxin_2  28 teelr...eklhelieeinelikktnellkklsqldnsssdsqqklqkekLkkdf 79 
                                       + +lr   e +h++ +e+  ++k++ ++++ l+++++ +++      k+k k+++
  gi|298675770|ref|YP_003727520.1|  70 NADLRtkaETVHKSSHEMEHIAKEIINHVETLESIEHPDEN------KDKVKTEI 118
                                       55566444677**************************9985......55555554 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.014
                        Syntaxin_2  39 ieeinelikktnellkklsqldnsssds..........qqklqkekLkkdfke 81 
                                        +++++ i+++ne++ +l++l ns+sd           ++k  +e + ++f e
  gi|298675770|ref|YP_003727520.1| 111 KDKVKTEISEINEHIDELANLLNSKSDAvheveentpqSHKEYAENIHHEFHE 163
                                       56667777777777777777777777665555555555555555555555554 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.013
                        Syntaxin_2  27 d...teelrekl...helieeinelikktnellkklsqldnsssdsqqklq 71 
                                       d   +++lrek+   h++ +e+  ++k++ ++++ l+ +++ +++ + k++
  gi|298675770|ref|YP_003727520.1| 226 DkslNDDLREKAetvHKSSHEMEHIAKEIISHVETLEGIEHPDEN-KDKVK 275
                                       133577888665555************************999876.44443 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.02
                        Syntaxin_2  38 lieeinelikktnellkklsqldnsssds......q 67 
                                       + +++++ i+++ne++ +l++l ns+sd       +
  gi|298675770|ref|YP_003727520.1| 270 NKDKVKTEISEINEHIDELANLLNSKSDAvheveeN 305
                                       566777777777777777777777777764444330 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   3.6    0.0033       1.2     120     218 ..      84     178 ..      34     190 .. 0.76
   2 ?   10.6   2.4   0.00068      0.25     123     218 ..     243     338 ..     199     345 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0033
                              CorA 120 vdrlfellekleeeldeledel.....edstkkeilrelaqlrrrlvklrralapnrevlkrllakaddkllddedk 191
                                        ++++++ +++  +++     l      d++k++   e++++ +++ +l   l+ + ++++++ +     + ++ +k
  gi|298675770|ref|YP_003727520.1|  84 SHEMEHIAKEIINHVET----LesiehPDENKDKVKTEISEINEHIDELANLLNSKSDAVHEVEE-----NTPQSHK 151
                                       34455555555555555....44445789999999999**********************55555.....6777777 PP

                              CorA 192 eylrdlldelerllemlealrerlesl 218
                                       ey ++++ e++ l +  ++l+e ++ +
  gi|298675770|ref|YP_003727520.1| 152 EYAENIHHEFHELGDIGSHLKEHASEI 178
                                       888999999988777666666666555 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00068
                              CorA 123 lfellekleeeldeledel.....edstkkeilrelaqlrrrlvklrralapnrevlkrllakaddkllddedkeyl 194
                                         +++e++ +e+    ++l      d++k++   e++++ +++ +l   l+ + ++++++ +     + ++ +key 
  gi|298675770|ref|YP_003727520.1| 243 SSHEMEHIAKEIISHVETLegiehPDENKDKVKTEISEINEHIDELANLLNSKSDAVHEVEE-----NTPQSHKEYA 314
                                       4444555555555555555555578999999999***********************55555.....7777888999 PP

                              CorA 195 rdlldelerllemlealrerlesl 218
                                       +d++ e++ l +  ++l+e ++ +
  gi|298675770|ref|YP_003727520.1| 315 KDIHHEFHELGDIGSHLKEHASEI 338
                                       9***99999877777777766665 PP

>> TPD52  Tumour protein D52 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.5   0.00034      0.12       7      84 ..      88     165 ..      82     186 .. 0.78
   2 ?    9.7   2.9    0.0017      0.61       8      64 ..     249     306 ..     242     343 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00034
                             TPD52   7 tetsedaaesvsasep.tlteeereeLkseLakleeeivtLrqvLaakekhlaelkrklGltalneLrqnlskswhd 82 
                                       +   ++  ++v++ e+ +  +e+++++k+e+ +++e+i  L ++L +k   ++e+      +  +e  +n+   +h+
  gi|298675770|ref|YP_003727520.1|  88 EHIAKEIINHVETLESiEHPDENKDKVKTEISEINEHIDELANLLNSKSDAVHEVEENTPQSH-KEYAENIHHEFHE 163
                                       555566667777777667899*********************************988766555.7777777777777 PP

                             TPD52  83 vq 84 
                                       + 
  gi|298675770|ref|YP_003727520.1| 164 LG 165
                                       65 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0017
                             TPD52   8 etsedaaesvsasep.tlteeereeLkseLakleeeivtLrqvLaakekhlaelkrkl 64 
                                          ++  ++v++ e  +  +e+++++k+e+ +++e+i  L ++L +k   ++e+    
  gi|298675770|ref|YP_003727520.1| 249 HIAKEIISHVETLEGiEHPDENKDKVKTEISEINEHIDELANLLNSKSDAVHEVEENT 306
                                       55556666676666557789*******************************9997765 PP

>> DUF3502  Domain of unknown function (DUF3502)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.2     0.017       6.3      65     108 ..     106     152 ..      42     158 .. 0.76
   2 ?    7.1   0.1     0.022       7.9      68     107 ..     269     311 ..     186     316 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.017
                           DUF3502  65 gFtfDsspvkteiaalsnvveeykkaletG..lv.Dpeetlpkfnek 108
                                           ++++vktei+++++ ++e ++ l++   +v ++ee+ p+  ++
  gi|298675770|ref|YP_003727520.1| 106 HPDENKDKVKTEISEINEHIDELANLLNSKsdAVhEVEENTPQSHKE 152
                                       556799*******************9997644556777777776655 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.022
                           DUF3502  68 fDsspvkteiaalsnvveeykkaletG..lv.Dpeetlpkfne 107
                                        ++++vktei+++++ ++e ++ l++   +v ++ee+ p+  +
  gi|298675770|ref|YP_003727520.1| 269 ENKDKVKTEISEINEHIDELANLLNSKsdAVhEVEENTPQSHK 311
                                       6899******************999763455677777776655 PP

>> DUF4874  Domain of unknown function (DUF4874)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.3    0.0051       1.9      79     112 ..     109     142 ..     103     145 .. 0.86
   2 ?    8.1   0.3    0.0052       1.9      79     112 ..     269     302 ..     264     305 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0051
                           DUF4874  79 kateeedasleqilrHieqlkpileenkdvIavv 112
                                       +++++  ++++ i +Hi++l+++l++++d++  v
  gi|298675770|ref|YP_003727520.1| 109 ENKDKVKTEISEINEHIDELANLLNSKSDAVHEV 142
                                       567788899********************98765 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0052
                           DUF4874  79 kateeedasleqilrHieqlkpileenkdvIavv 112
                                       +++++  ++++ i +Hi++l+++l++++d++  v
  gi|298675770|ref|YP_003727520.1| 269 ENKDKVKTEISEINEHIDELANLLNSKSDAVHEV 302
                                       567778899********************98765 PP

>> ER  Enhancer of rudimentary
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.034        12      37      66 ..     102     131 ..      73     162 .. 0.78
   2 ?    5.1   0.1      0.06        22      39      66 ..     264     291 ..     235     321 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.034
                                ER  37 eaLkeanpskksitYdisdLfefidsladl 66 
                                       e++++   +k++++ +is++ e+id+la+l
  gi|298675770|ref|YP_003727520.1| 102 ESIEHPDENKDKVKTEISEINEHIDELANL 131
                                       35677778899****************987 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.06
                                ER  39 LkeanpskksitYdisdLfefidsladl 66 
                                       +++   +k++++ +is++ e+id+la+l
  gi|298675770|ref|YP_003727520.1| 264 IEHPDENKDKVKTEISEINEHIDELANL 291
                                       4556678899***************987 PP

>> Apocytochr_F_N  Apocytochrome F, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.2     0.022       8.1      64     120 ..      44     100 ..      29     117 .. 0.80
   2 ?    5.9   0.2      0.04        15      77     119 ..     217     259 ..     189     277 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.022
                    Apocytochr_F_N  64 GskgalnvGavlllPeGfklapedriseelkekveklyfqkyseekenilivgplpg 120
                                        +  ++ + a  +  e  k+a+++ ++++l+ k e ++ ++++ e+    i++ +++
  gi|298675770|ref|YP_003727520.1|  44 DHANEIIIVAETIHTESAKIADDKSLNADLRTKAETVHKSSHEMEHIAKEIINHVET 100
                                       45556667788888999***********************99999988888888765 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.04
                    Apocytochr_F_N  77 lPeGfklapedriseelkekveklyfqkyseekenilivgplp 119
                                         +  k+a+++ ++++l+ek e ++ ++++ e+    i++ ++
  gi|298675770|ref|YP_003727520.1| 217 HTKSAKVADDKSLNDDLREKAETVHKSSHEMEHIAKEIISHVE 259
                                       456789*******************999998876666665554 PP

>> DUF1107  Protein of unknown function (DUF1107)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.2      0.02       7.2      42      63 .]     107     128 ..     103     128 .. 0.88
   2 ?    6.6   0.1      0.02       7.2      42      63 .]     267     288 ..     263     288 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.02
                           DUF1107  42 pkkadkkhlkvvseiNeeikrl 63 
                                       p++++ k++  +seiNe+i +l
  gi|298675770|ref|YP_003727520.1| 107 PDENKDKVKTEISEINEHIDEL 128
                                       789999*************986 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.02
                           DUF1107  42 pkkadkkhlkvvseiNeeikrl 63 
                                       p++++ k++  +seiNe+i +l
  gi|298675770|ref|YP_003727520.1| 267 PDENKDKVKTEISEINEHIDEL 288
                                       7899999************986 PP

>> DUF4208  Domain of unknown function (DUF4208)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.9     0.076        28       7      60 ..      83     131 ..      75     140 .. 0.77
   2 ?    6.3   0.1     0.036        13      21      62 ..     138     179 ..     130     189 .. 0.83
   3 ?    4.6   0.9      0.12        46       7      61 ..     243     292 ..     236     303 .. 0.76
   4 ?    5.7   0.1     0.055        20      15      62 ..     292     339 ..     286     351 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.076
                           DUF4208   7 deeeckellrpvkksLkrLkkltkekllskkerakilkkeLlkiGdfIdellke 60 
                                       ++ e++++ + + ++ ++L++       + +e+  ++k+e+ +i ++Idel++ 
  gi|298675770|ref|YP_003727520.1|  83 SSHEMEHIAKEIINHVETLESI-----EHPDENKDKVKTEISEINEHIDELANL 131
                                       4445777777788888888755.....67899999**************98765 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.036
                           DUF4208  21 sLkrLkkltkekllskkerakilkkeLlkiGdfIdellkekk 62 
                                       + +++++ t+++ ++ +e++++  +eL  iG++++e++ e +
  gi|298675770|ref|YP_003727520.1| 138 AVHEVEENTPQSHKEYAENIHHEFHELGDIGSHLKEHASEIE 179
                                       5678888999988999999999999*********99988865 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.12
                           DUF4208   7 deeeckellrpvkksLkrLkkltkekllskkerakilkkeLlkiGdfIdellkek 61 
                                       ++ e++++ + + ++ ++L+        + +e+  ++k+e+ +i ++Idel++  
  gi|298675770|ref|YP_003727520.1| 243 SSHEMEHIAKEIISHVETLEGI-----EHPDENKDKVKTEISEINEHIDELANLL 292
                                       4455778888888888888866.....56799999**************988765 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.055
                           DUF4208  15 lrpvkksLkrLkkltkekllskkerakilkkeLlkiGdfIdellkekk 62 
                                       l+   ++ +++++ t+++ ++ ++ +++  +eL  iG++++e++ e +
  gi|298675770|ref|YP_003727520.1| 292 LNSKSDAVHEVEENTPQSHKEYAKDIHHEFHELGDIGSHLKEHASEIE 339
                                       555566777888888887788888888888889999999999888765 PP

>> CC2-LZ  Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.1    0.0032       1.2       8      55 ..      58     105 ..      53     107 .. 0.88
   2 ?    5.7   2.2     0.053        19       9      54 ..     110     157 ..     105     161 .. 0.82
   3 ?    7.6   0.8     0.014         5      10      55 ..     220     265 ..     214     267 .. 0.87
   4 ?    5.6   1.7     0.054        20       9      51 ..     270     313 ..     264     322 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0032
                            CC2-LZ   8 aekvkkeeieeLkaqlqaaeealaakqeeidelkeeikkkeeeletis 55 
                                       +e  k ++ ++L+a l ++ e ++++++e++++++ei ++ e le i+
  gi|298675770|ref|YP_003727520.1|  58 TESAKIADDKSLNADLRTKAETVHKSSHEMEHIAKEIINHVETLESIE 105
                                       45556677789**********************************997 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.053
                            CC2-LZ   9 ekvk.keeieeLkaqlqaaeealaakqeeidelkeeikkkeeele.ti 54 
                                       +k k k ei+e+++++++  + l++k++ ++e++e+  + ++e   +i
  gi|298675770|ref|YP_003727520.1| 110 NKDKvKTEISEINEHIDELANLLNSKSDAVHEVEENTPQSHKEYAeNI 157
                                       3444599****************************9998887654355 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.014
                            CC2-LZ  10 kvkkeeieeLkaqlqaaeealaakqeeidelkeeikkkeeeletis 55 
                                         k ++ ++L+  l ++ e ++++++e++++++ei ++ e le i+
  gi|298675770|ref|YP_003727520.1| 220 SAKVADDKSLNDDLREKAETVHKSSHEMEHIAKEIISHVETLEGIE 265
                                       455667789*******************************999886 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.054
                            CC2-LZ   9 ekvk.keeieeLkaqlqaaeealaakqeeidelkeeikkkeeel 51 
                                       +k k k ei+e+++++++  + l++k++ ++e++e+  + ++e 
  gi|298675770|ref|YP_003727520.1| 270 NKDKvKTEISEINEHIDELANLLNSKSDAVHEVEENTPQSHKEY 313
                                       4445599****************************999988764 PP

>> PMC2NT  PMC2NT (NUC016) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   1.7     0.022       7.9      10      79 ..      63     128 ..      55     133 .. 0.84
   2 ?    5.3   0.1     0.089        33      29      83 ..     121     175 ..     119     178 .. 0.73
   3 ?    7.4   1.5     0.019       6.8      13      79 ..     225     288 ..     212     294 .. 0.85
   4 ?    5.1   0.1     0.098        36      29      83 ..     281     335 ..     279     338 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.022
                            PMC2NT  10 LpaeDldfyrsldpefaksldeqserllslinsllklaaskseisassklededdveekfksvvdvvDsl 79 
                                       ++ +D + +  l +  a+ + ++s+++ ++++++++++++ ++i+++  +e++d+v++  +++ + +D+l
  gi|298675770|ref|YP_003727520.1|  63 IA-DDKSLNADL-RTKAETVHKSSHEMEHIAKEIINHVETLESIEHP--DENKDKVKTEISEINEHIDEL 128
                                       44.777777778.8888999999*********************886..889999999999999999887 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.089
                            PMC2NT  29 ldeqserllslinsllklaaskseisassklededdveekfksvvdvvDsllEka 83 
                                       ++e+ ++l +l+ns  +++++ +e+  +s++e ++++ + f++++d+  +l E+a
  gi|298675770|ref|YP_003727520.1| 121 INEHIDELANLLNSKSDAVHEVEENTPQSHKEYAENIHHEFHELGDIGSHLKEHA 175
                                       566666677777776666666666655578899999**********988888876 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.019
                            PMC2NT  13 eDldfyrsldpefaksldeqserllslinsllklaaskseisassklededdveekfksvvdvvDsl 79 
                                       +D + +  l +e a+ + ++s+++ ++++++++++++ + i+++  +e++d+v++  +++ + +D+l
  gi|298675770|ref|YP_003727520.1| 225 DDKSLNDDL-REKAETVHKSSHEMEHIAKEIISHVETLEGIEHP--DENKDKVKTEISEINEHIDEL 288
                                       777777778.8889999999*********************886..889999999999999999987 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.098
                            PMC2NT  29 ldeqserllslinsllklaaskseisassklededdveekfksvvdvvDsllEka 83 
                                       ++e+ ++l +l+ns  +++++ +e+  +s++e + d+ + f++++d+  +l E+a
  gi|298675770|ref|YP_003727520.1| 281 INEHIDELANLLNSKSDAVHEVEENTPQSHKEYAKDIHHEFHELGDIGSHLKEHA 335
                                       566666666666666666666666555578899999999*******988888876 PP

>> DUF4226  Domain of unknown function (DUF4226)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.4      0.12        44      21      63 ..      60     102 ..      51     108 .. 0.85
   2 ?    6.5   0.3     0.027       9.8      19      63 ..     218     262 ..     194     267 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.12
                           DUF4226  21 sataelDrqlaevlrsahakaaegrrrLdalqaeidqavatqa 63 
                                       sa    D++l + lr  +++  ++ + ++++++ei + v+t +
  gi|298675770|ref|YP_003727520.1|  60 SAKIADDKSLNADLRTKAETVHKSSHEMEHIAKEIINHVETLE 102
                                       555577999****************************999876 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.027
                           DUF4226  19 rlsataelDrqlaevlrsahakaaegrrrLdalqaeidqavatqa 63 
                                        +sa    D++l + lr+ +++  ++ + ++++++ei   v+t +
  gi|298675770|ref|YP_003727520.1| 218 TKSAKVADDKSLNDDLREKAETVHKSSHEMEHIAKEIISHVETLE 262
                                       456677889*****************************9998875 PP

>> IL5  Interleukin 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.5     0.025       9.1      37      79 ..      83     127 ..      41     141 .. 0.78
   2 ?    4.6   0.1       0.1        38      41      79 ..     249     287 ..     224     301 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.025
                                       S-GGG..GHHHHHHHHHHHHTTS--SSTHHHHHHHHHHHHHHHHH CS
                               IL5  37 knhql..cieeifqGidtlknqtvqgeaveklfqnlslikkyidl 79 
                                         h++    +ei + ++tl++    +e  +k+  ++s i ++id 
  gi|298675770|ref|YP_003727520.1|  83 SSHEMehIAKEIINHVETLESIEHPDENKDKVKTEISEINEHIDE 127
                                       3444322679*********************************96 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.1
                                       GGHHHHHHHHHHHHTTS--SSTHHHHHHHHHHHHHHHHH CS
                               IL5  41 lcieeifqGidtlknqtvqgeaveklfqnlslikkyidl 79 
                                          +ei   ++tl+     +e  +k+  ++s i ++id 
  gi|298675770|ref|YP_003727520.1| 249 HIAKEIISHVETLEGIEHPDENKDKVKTEISEINEHIDE 287
                                       35799********************************96 PP

>> 4HB_MCP_1  Four helix bundle sensory module for signal transduction
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   2.7    0.0073       2.7     102     175 ..      68     141 ..      41     146 .. 0.89
   2 ?    7.1   1.7    0.0099       3.6     100     175 ..     226     301 ..     197     306 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0073
                         4HB_MCP_1 102 ilteeEkelleefkeqlnaYrevrkkvlelakegkkdeAyqlyetegrparekliealeelvdlnlkvAeeayk 175
                                       +l+++ ++++e+++++  +   + k++++ +++ +  e  +  ++++++  ++++e ++el++l +++++ +++
  gi|298675770|ref|YP_003727520.1|  68 SLNADLRTKAETVHKSSHEMEHIAKEIINHVETLESIEHPDENKDKVKTEISEINEHIDELANLLNSKSDAVHE 141
                                       566777899999****************************************************9999988876 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0099
                         4HB_MCP_1 100 ktilteeEkelleefkeqlnaYrevrkkvlelakegkkdeAyqlyetegrparekliealeelvdlnlkvAeeayk 175
                                       + +l+++ +e++e+++++  +   + k+++  +++ +  e  +  ++++++  ++++e ++el++l +++++ +++
  gi|298675770|ref|YP_003727520.1| 226 DKSLNDDLREKAETVHKSSHEMEHIAKEIISHVETLEGIEHPDENKDKVKTEISEINEHIDELANLLNSKSDAVHE 301
                                       5678888899********************************************************9999988776 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   6.0    0.0052       1.9      67     118 ..      86     138 ..      31     144 .. 0.83
   2 ?    7.9   6.1    0.0072       2.6      82     118 ..     102     138 ..      83     193 .. 0.87
   3 ?    6.1   6.6     0.025       9.1      83     118 ..     263     298 ..     185     304 .. 0.86
   4 ?   -0.6   0.0       3.1   1.1e+03      24      54 ..     310     340 ..     301     347 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0052
                              CdvA  67 kisyasGEidEe.aYksaieairellesaleekeeikklleklskleleeeev 118
                                       ++++++ Ei    +  ++ie+ +e++++++ e++ei++++++l++l ++++++
  gi|298675770|ref|YP_003727520.1|  86 EMEHIAKEIINHvETLESIEHPDENKDKVKTEISEINEHIDELANLLNSKSDA 138
                                       5566666643331334689999***********************99987765 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0072
                              CdvA  82 saieairellesaleekeeikklleklskleleeeev 118
                                       ++ie+ +e++++++ e++ei++++++l++l ++++++
  gi|298675770|ref|YP_003727520.1| 102 ESIEHPDENKDKVKTEISEINEHIDELANLLNSKSDA 138
                                       57899999*******************9999887665 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.025
                              CdvA  83 aieairellesaleekeeikklleklskleleeeev 118
                                        ie+ +e++++++ e++ei++++++l++l ++++++
  gi|298675770|ref|YP_003727520.1| 263 GIEHPDENKDKVKTEISEINEHIDELANLLNSKSDA 298
                                       5788899********************999987765 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 3.1
                              CdvA  24 kekleealkklkekakelkeklkkrlkeled 54 
                                       ++++ + +     +  ++ + lk++ +e+e+
  gi|298675770|ref|YP_003727520.1| 310 HKEYAKDIHHEFHELGDIGSHLKEHASEIES 340
                                       5555555555556666666666666666665 PP

>> SKA1  Spindle and kinetochore-associated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   4.3      0.11        40      27      99 ..      44     116 ..      24     119 .. 0.83
   2 ?    8.6   0.5    0.0043       1.6     150     192 ..     119     163 ..     116     192 .. 0.78
   3 ?    4.4   2.6     0.078        29      28      97 ..     205     274 ..     185     277 .. 0.83
   4 ?    8.5   6.6    0.0045       1.6      16     118 ..     269     370 ..     259     381 .. 0.61

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.11
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              SKA1  27 kieaevsaleellnklkkelqeeeeaikklkkeieaslkqqeklqhlkenlpshlpkktaassaeeskssspe 99 
                                       +  +e+  + e+++   + +++ ++++ +l+ + e   k++++++h+++++ +h++  ++ ++ +e+k++ ++
  gi|298675770|ref|YP_003727520.1|  44 DHANEIIIVAETIHTESAKIADDKSLNADLRTKAETVHKSSHEMEHIAKEIINHVETLESIEHPDENKDKVKT 116
                                       445788899999999999*************999999999999***********9999999999888887665 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0043
                                       HHHHHHHHHHHHHHHHHHHHTT--TTT--HHHHHHHHHHHHH..T CS
                              SKA1 150 ekiNaaidelnkaveakykilaqpkkklsesdrelalefkee..e 192
                                        +iN+ idel++++++k++ +++ +++  +s +e a ++ +e  e
  gi|298675770|ref|YP_003727520.1| 119 SEINEHIDELANLLNSKSDAVHEVEENTPQSHKEYAENIHHEfhE 163
                                       579999***********9999999977777777766666655333 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.078
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              SKA1  28 ieaevsaleellnklkkelqeeeeaikklkkeieaslkqqeklqhlkenlpshlpkktaassaeesksss 97 
                                         +e+ ++  +++   + +++ ++++++l+++ e   k++++++h+++++ sh++  +  ++ +e+k++ 
  gi|298675770|ref|YP_003727520.1| 205 HANEIISVAGTIHTKSAKVADDKSLNDDLREKAETVHKSSHEMEHIAKEIISHVETLEGIEHPDENKDKV 274
                                       45788888999999999*************999999999999***********99988888887777765 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.0045
                                       ........XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......XXXXXXXXXXXXXXXXXXXXXX CS
                              SKA1  16 qdpallkedlskieaevsaleellnklkkelqeeeeaikklkkeieaslkqqek.lqhlkenlpshlpkktaassae 91 
                                       ++++  k+ +s+i++++ +l +lln+  ++++e ee  ++  ke  + ++++ + l  + ++l +h  +  ++   +
  gi|298675770|ref|YP_003727520.1| 269 ENKDKVKTEISEINEHIDELANLLNSKSDAVHEVEENTPQSHKEYAKDIHHEFHeLGDIGSHLKEHASEI-ESDVIG 344
                                       5566668888888888888888888888888888888888888888888777777777777777774433.333344 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              SKA1  92 eskssspeeeeeteskkekeeeaekak 118
                                       + ++ + e+ee ++s++ + + +++++
  gi|298675770|ref|YP_003727520.1| 345 TGEEHDHEHEEGSSSES-ESSSKSSES 370
                                       44444444444333322.222222222 PP

>> ING  Inhibitor of growth proteins N-terminal histone-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   4.9     0.032        12      11      80 ..      68     139 ..      61     156 .. 0.86
   2 ?    0.4   0.0       2.7   9.7e+02      15      41 ..     156     182 ..     144     213 .. 0.62
   3 ?    8.8   4.6    0.0067       2.4      11      81 ..     228     300 ..     223     318 .. 0.87
   4 ?    1.4   0.1       1.4     5e+02      14      42 ..     315     343 ..     304     373 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.032
                                       GHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..TS..S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               ING  11 nLPlelqrnltelreiDakvqellkeidskiekfl..kngslqknekeeelsriqeelkeaqelldeKiqla 80 
                                       +L ++l+ + + +++   +++++ kei +++e++   ++ +++k++ + e+s+i+e+++e+ +ll+ K   +
  gi|298675770|ref|YP_003727520.1|  68 SLNADLRTKAETVHKSSHEMEHIAKEIINHVETLEsiEHPDENKDKVKTEISEINEHIDELANLLNSKSDAV 139
                                       6888999999999999999999999999999998888888899999999999**************997655 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 2.7
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               ING  15 elqrnltelreiDakvqellkeidski 41 
                                        +++ + el +i  +++e+  ei+s +
  gi|298675770|ref|YP_003727520.1| 156 NIHHEFHELGDIGSHLKEHASEIESDV 182
                                       566777777777777777777776544 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0067
                                       GHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..TS..S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               ING  11 nLPlelqrnltelreiDakvqellkeidskiekfl..kngslqknekeeelsriqeelkeaqelldeKiqlaq 81 
                                       +L ++l+++ + +++   +++++ kei s++e++   ++ +++k++ + e+s+i+e+++e+ +ll+ K   + 
  gi|298675770|ref|YP_003727520.1| 228 SLNDDLREKAETVHKSSHEMEHIAKEIISHVETLEgiEHPDENKDKVKTEISEINEHIDELANLLNSKSDAVH 300
                                       78999999999999999999*******9999999988888899999999999***************986655 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               ING  14 lelqrnltelreiDakvqellkeidskie 42 
                                       +++++ + el +i  +++e+  ei+s + 
  gi|298675770|ref|YP_003727520.1| 315 KDIHHEFHELGDIGSHLKEHASEIESDVI 343
                                       57788888888888888888888876543 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.8    0.0084       3.1      12      83 ..      10      93 ..       8      98 .. 0.81
   2 ?    5.4   1.1     0.061        22      36      75 ..      99     144 ..      85     173 .. 0.76
   3 ?    2.6   5.3      0.43   1.6e+02      38      87 ..     240     288 ..     161     340 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0084
                            DUF948 12 vLviflivvllkl......kktldeaaatieelekqvdpilkevedllakvne......lledvneklekvdplteava 78
                                      +Lv  liv+ l++      ++  d++++++ e+e+++++i+  +e++ +++ +      l +d++ k e+v +  ++++
  gi|298675770|ref|YP_003727520.1| 10 ILVSTLIVFALSVpvsaheGHSHDNVSQSLVEVEDHANEIIIVAETIHTESAKiaddksLNADLRTKAETVHKSSHEME 88
                                      78888888888888888999**********************9999999999955555566666668888888777777 PP

                            DUF948 79 dlges 83
                                      ++++ 
  gi|298675770|ref|YP_003727520.1| 89 HIAKE 93
                                      77765 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.061
                            DUF948  36 eele......kqvdpilkevedllakvnelledvneklekvdplte 75 
                                       e+le      ++ d++ +e+ ++ +++ el++ +n+k+++v ++ e
  gi|298675770|ref|YP_003727520.1|  99 ETLEsiehpdENKDKVKTEISEINEHIDELANLLNSKSDAVHEVEE 144
                                       3333444555888889999999999999999999999999887755 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.43
                            DUF948  38 lekqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                       + k  +++ + +++++++v++ le++++  e+ d++ +++ ++ e++ el
  gi|298675770|ref|YP_003727520.1| 240 VHKSSHEMEHIAKEIISHVET-LEGIEHPDENKDKVKTEISEINEHIDEL 288
                                       333333444444444555555.5555555555555555555555555554 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   2.6       0.3   1.1e+02      65     114 ..      53     102 ..      29     107 .. 0.62
   2 ?    9.7   1.0    0.0023      0.84      59     114 ..     109     165 ..     104     181 .. 0.83
   3 ?    3.6   0.9      0.18        66      70     114 ..     218     262 ..     197     267 .. 0.61
   4 ?    9.0   1.0    0.0036       1.3      59     113 ..     269     324 ..     264     341 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.3
                           DUF1664  65 ssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                       ++ i++  +k+ + k + ++++ + ++v++  +e+++  +++ + ve+le
  gi|298675770|ref|YP_003727520.1|  53 AETIHTESAKIADDKSLNADLRTKAETVHKSSHEMEHIAKEIINHVETLE 102
                                       44555556666666777777777777777777777777777777777776 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0023
                           DUF1664  59 atkrhLssridrvdkkldeqkeiskeikeevtevredlseiged.vesvkeavegle 114
                                       + k++ + +i ++++++de +++ ++ ++ v+ev+e++ + +++  e++++ +++l+
  gi|298675770|ref|YP_003727520.1| 109 ENKDKVKTEISEINEHIDELANLLNSKSDAVHEVEENTPQSHKEyAENIHHEFHELG 165
                                       67999999999***************9*******99998877762467888777765 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.18
                           DUF1664  70 rvdkkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                       +  +k+ + k +  +++e+ ++v++  +e+++  +++ + ve+le
  gi|298675770|ref|YP_003727520.1| 218 TKSAKVADDKSLNDDLREKAETVHKSSHEMEHIAKEIISHVETLE 262
                                       334455555555555666666666666666666666666666655 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.0036
                           DUF1664  59 atkrhLssridrvdkkldeqkeiskeikeevtevredlseigedv.esvkeavegl 113
                                       + k++ + +i ++++++de +++ ++ ++ v+ev+e++ + +++  + +++ +++l
  gi|298675770|ref|YP_003727520.1| 269 ENKDKVKTEISEINEHIDELANLLNSKSDAVHEVEENTPQSHKEYaKDIHHEFHEL 324
                                       67999999999**************999******9999888776525677777666 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1      0.85   3.1e+02      45      83 ..      68     107 ..      64     110 .. 0.67
   2 ?    4.2   0.2      0.14        53      17      72 ..     124     179 ..     111     180 .. 0.79
   3 ?    1.7   0.1      0.85   3.1e+02      45      72 ..     228     255 ..     223     269 .. 0.74
   4 ?    5.1   0.1     0.076        28      19      71 ..     286     338 ..     272     340 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.85
                              KxDL  45 klrarfkqgtkllkevkkdLesifkki.rslkaklakkyP 83 
                                       +l+a+++ +++++++  +++e+i k i ++ ++  + ++P
  gi|298675770|ref|YP_003727520.1|  68 SLNADLRTKAETVHKSSHEMEHIAKEIiNHVETLESIEHP 107
                                       5677888888888888888888888752444444445555 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.14
                              KxDL  17 lQaqtsgrlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkir 72 
                                          ++ + ln+k+  ++e+ + + + ++++ +++   ++ l ++ + L+   + i+
  gi|298675770|ref|YP_003727520.1| 124 HIDELANLLNSKSDAVHEVEENTPQSHKEYAENIHHEFHELGDIGSHLKEHASEIE 179
                                       55567788999999999999999999999999999999999999888887776665 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.85
                              KxDL  45 klrarfkqgtkllkevkkdLesifkkir 72 
                                       +l+++++++++++++  +++e+i k i 
  gi|298675770|ref|YP_003727520.1| 228 SLNDDLREKAETVHKSSHEMEHIAKEII 255
                                       5778888999999999999999988864 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.076
                              KxDL  19 aqtsgrlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkki 71 
                                        ++ + ln+k+  ++e+ + + + ++++ +++   ++ l ++ + L+   + i
  gi|298675770|ref|YP_003727520.1| 286 DELANLLNSKSDAVHEVEENTPQSHKEYAKDIHHEFHELGDIGSHLKEHASEI 338
                                       55667788888888888888888888888888888888888877777666665 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   4.1       1.3   4.6e+02     344     409 ..      40     105 ..      31     116 .. 0.72
   2 ?    2.2  18.7      0.11        40     252     408 ..      85     264 ..      80     269 .. 0.69
   3 ?   10.2   2.5    0.0004      0.15     273     327 ..     271     326 ..     267     334 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.3
                                       TTHHHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              EzrA 344 eklrelekelkelekdyeeleekleekkvaYSelqeeleeleekleeieekqeeileslkslrkdE 409
                                        ++++  +e+  + + +++   k++++k    +l+ + e++ ++  e+e   +ei +++++l++ E
  gi|298675770|ref|YP_003727520.1|  40 VEVEDHANEIIIVAETIHTESAKIADDKSLNADLRTKAETVHKSSHEMEHIAKEIINHVETLESIE 105
                                       455566666677777777777777788888888888888888888888888888888777777766 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.11
                                       SHHHHHHHHHHHHHHHHTT-.....-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTSSSS.SHHH....... CS
                              EzrA 252 keieelekkieeilerlkel.....eledveeelktieeeidsLyddlekEveAkkeveknlkel.kekl....... 315
                                        e+e++ k+i + +e l+++     + ++v+ e+++i+e+id+L ++l+   +A +eve+n+++  ke+        
  gi|298675770|ref|YP_003727520.1|  85 HEMEHIAKEIINHVETLESIehpdeNKDKVKTEISEINEHIDELANLLNSKSDAVHEVEENTPQShKEYAenihhef 161
                                       577788888888888888773333346899************************99999998764133441111111 PP

                                       .......HT--HHHHTTGGG-TTTS-GGGSSTTTSTTHHHHHHHHHHHHHHHHHHH...HHHS-SS---STTGGGTH CS
                              EzrA 316 .......ehlekqnkelkeeldrlkqsYeLseeeleklrelekelkelekdyeele...ekleekkvaYSelqeele 382
                                              +hl++  +e+++++    ++Y+ ++ee + l e+e++ +e+ +   +++    k++++k    +l+e+ e
  gi|298675770|ref|YP_003727520.1| 162 helgdigSHLKEHASEIESDVIGTGEEYDHEHEEGSALAEVEEHANEIISVAGTIHtksAKVADDKSLNDDLREKAE 238
                                       11111114555555555555556668899999998888888887777766665554111567788888889999999 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              EzrA 383 eleekleeieekqeeileslkslrkd 408
                                       ++ ++  e+e   +ei  ++++l+  
  gi|298675770|ref|YP_003727520.1| 239 TVHKSSHEMEHIAKEIISHVETLEGI 264
                                       99999999998888888888888765 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.0004
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTSSSS.SHHHHT--HHHHTTGG CS
                              EzrA 273 ledveeelktieeeidsLyddlekEveAkkeveknlkel.keklehlekqnkelke 327
                                        ++v+ e+++i+e+id+L ++l+   +A +eve+n+++  ke+ + +  +++el +
  gi|298675770|ref|YP_003727520.1| 271 KDKVKTEISEINEHIDELANLLNSKSDAVHEVEENTPQShKEYAKDIHHEFHELGD 326
                                       58999******************************987516677778888877765 PP

>> RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   2.6    0.0029       1.1     160     227 ..      46     114 ..      25     125 .. 0.78
   2 ?    6.4   4.2     0.011       4.1     122     231 ..     169     275 ..     143     285 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0029
                                       TT-EEE---...B-----...-----------..-B---EE--TT-EEEEEEEEE.......EE-TT-- CS
                    RNA_pol_Rpb2_6 160 egdilvgkvt.kgeteltpeekllraifgekarevkdtslrvksgeegvVdkvkvfsrekgdelkagvn 227
                                       +++i++   t ++e+   +++k l+a   +ka++v+++s ++++  + ++++v+++++ ++ ++++++ 
  gi|298675770|ref|YP_003727520.1|  46 ANEIIIVAETiHTESAKIADDKSLNADLRTKAETVHKSSHEMEHIAKEIINHVETLESIEHPDENKDKV 114
                                       4555555556699999***************************************87755544444433 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.011
                                       --SSSS---.-S--..--SS-GGGS-TTSB--SS-EEETT-EEE---...B-----...-----------..-B--- CS
                    RNA_pol_Rpb2_6 122 rdtklgeeeitrdipnvseealkkLdedGivrvgaevkegdilvgkvt.kgeteltpeekllraifgekarevkdts 197
                                       ++ k++++ei  d+     e++++  e+G    + e ++++i+    t ++++   +++k l+    eka++v+++s
  gi|298675770|ref|YP_003727520.1| 169 SHLKEHASEIESDVIGT-GEEYDHEHEEGSALAEVEEHANEIISVAGTiHTKSAKVADDKSLNDDLREKAETVHKSS 244
                                       55556666666666555.4455555677777777777777777666666888999999******************* PP

                                       EE--TT-EEEEEEEEE.......EE-TT--EEEE CS
                    RNA_pol_Rpb2_6 198 lrvksgeegvVdkvkvfsrekgdelkagvnklvk 231
                                        ++++  + ++ +v++++     e++++ +  vk
  gi|298675770|ref|YP_003727520.1| 245 HEMEHIAKEIISHVETLEG---IEHPDENKDKVK 275
                                       ***************9654...444444444444 PP

>> Leu_zip  Leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   8.3    0.0098       3.6     137     250 ..      65     185 ..      52     191 .. 0.60
   2 ?    8.6   8.4    0.0033       1.2     112     250 ..     200     345 ..     181     349 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0098
                           Leu_zip 137 rLkeenekLkerlkelEkqatsaleeksklekalkelqkelgekkdekenskeiskleeklaelkldlek....... 206
                                         k  n  L+++ +++ k  +++ +  +++ ++++ l++  +  +++ + ++eis+++e++ el + l++       
  gi|298675770|ref|YP_003727520.1|  65 DDKSLNADLRTKAETVHKSSHEMEHIAKEIINHVETLESIEHPDENKDKVKTEISEINEHIDELANLLNSksdavhe 141
                                       44556677777776666665555444444444444444444433434444444444444444433322221112221 PP

                           Leu_zip 207 tleektasaksleedlastkhelLkvqeqLelaekeLekkfqqt 250
                                         e++ +s+k+ +e++ +  hel  + ++L+   +e+e  +  t
  gi|298675770|ref|YP_003727520.1| 142 VEENTPQSHKEYAENIHHEFHELGDIGSHLKEHASEIESDVIGT 185
                                       4555677889999********************99999877666 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0033
                           Leu_zip 112 eelkkkkLePlnegGgaeLLkkeierLkeenekLkerlkelEkqatsaleeksklekalkelqkelgekkdekensk 188
                                       +e++++  e +  +G+++    +++  k  n+ L+e+ +++ k  +++ +  +++ ++++ l+   +  +++ + ++
  gi|298675770|ref|YP_003727520.1| 200 AEVEEHANEIISVAGTIHTKSAKVADDKSLNDDLREKAETVHKSSHEMEHIAKEIISHVETLEGIEHPDENKDKVKT 276
                                       55555555666666777777778888888899999999888887777666666666666666555554444444555 PP

                           Leu_zip 189 eiskleeklaelkldlek.......tleektasaksleedlastkhelLkvqeqLelaekeLekkfqqt 250
                                       eis+++e++ el + l++         e++ +s+k+ ++d+ +  hel  + ++L+   +e+e  +  t
  gi|298675770|ref|YP_003727520.1| 277 EISEINEHIDELANLLNSksdavheVEENTPQSHKEYAKDIHHEFHELGDIGSHLKEHASEIESDVIGT 345
                                       5555555555444333331122221445556788999*********************99999877655 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   3.8    0.0056       2.1      53     136 ..      69     155 ..      43     159 .. 0.74
   2 ?    6.0   1.9     0.024       8.9      84     164 ..     236     315 ..     220     319 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0056
                            DUF745  53 AeAaLaGKqqlveqleqelre.aeavvqeek..kslqsseanakaaakaakqaqqqlealkallkaakenlenaeqv 126
                                        +A L  K   v++  +e+++ a++++++++  +s+++  +n + +++  ++++++++ l +ll++ +++++++e+ 
  gi|298675770|ref|YP_003727520.1|  69 LNADLRTKAETVHKSSHEMEHiAKEIINHVEtlESIEHPDENKDKVKTEISEINEHIDELANLLNSKSDAVHEVEEN 145
                                       56778888888888888887734555554432267888888888888888888888888888888888888888888 PP

                            DUF745 127 aagaqqelae 136
                                         ++ +e ae
  gi|298675770|ref|YP_003727520.1| 146 TPQSHKEYAE 155
                                       8888887776 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.024
                            DUF745  84 slqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkkRveeLkkqlkeark 160
                                       + ++ +++ +  +++ak++ +++e+l+  +++  en +++++  ++ ++ ++e ++ll++    v+e++++  + +k
  gi|298675770|ref|YP_003727520.1| 236 KAETVHKSSHEMEHIAKEIISHVETLEG-IEHPDENKDKVKTEISEINEHIDELANLLNSKSDAVHEVEENTPQSHK 311
                                       3444455556667888999999999964.688899999999999999999999999999999999999999999988 PP

                            DUF745 161 dlek 164
                                       +++k
  gi|298675770|ref|YP_003727520.1| 312 EYAK 315
                                       8875 PP

>> Syntaxin-18_N  SNARE-complex protein Syntaxin-18 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.7     0.057        21      17      60 ..      60     103 ..      49     104 .. 0.74
   2 ?    6.3   0.2     0.031        11      34      65 ..     104     135 ..     102     153 .. 0.84
   3 ?    4.4   0.5      0.12        43      12      59 ..     217     262 ..     207     264 .. 0.66
   4 ?    5.8   0.1     0.043        16      36      65 ..     266     295 ..     263     317 .. 0.83
   5 ?   -0.9   0.1       5.3   1.9e+03      25      37 ..     357     367 ..     326     377 .. 0.47

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.057
                     Syntaxin-18_N  17 sssskseekeakkrkkkrlkkskekdeFikeAkeilkhItkLrk 60 
                                       s++++  ++ +++ ++k ++ +k+ +e    Akei++h+ +L++
  gi|298675770|ref|YP_003727520.1|  60 SAKIADDKSLNADLRTKAETVHKSSHEMEHIAKEIINHVETLES 103
                                       4555556666666777777788888899999***********86 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.031
                     Syntaxin-18_N  34 rlkkskekdeFikeAkeilkhItkLrkfLlei 65 
                                       +++  ++kd+  +e  ei++hI++L ++L++ 
  gi|298675770|ref|YP_003727520.1| 104 IEHPDENKDKVKTEISEINEHIDELANLLNSK 135
                                       5677788999999999*************985 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.12
                     Syntaxin-18_N  12 ktvkasssskseekeakkrkkkrlkkskekdeFikeAkeilkhItkLr 59 
                                       +t+  s++ +  ++ + + ++k ++ +k+ +e    Akei++h+ +L+
  gi|298675770|ref|YP_003727520.1| 217 HTK--SAKVADDKSLNDDLREKAETVHKSSHEMEHIAKEIISHVETLE 262
                                       444..2333333344444556666666677788888**********97 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.043
                     Syntaxin-18_N  36 kkskekdeFikeAkeilkhItkLrkfLlei 65 
                                       +  ++kd+  +e  ei++hI++L ++L++ 
  gi|298675770|ref|YP_003727520.1| 266 HPDENKDKVKTEISEINEHIDELANLLNSK 295
                                       55677888889999*************985 PP

  == domain 5  score: -0.9 bits;  conditional E-value: 5.3
                     Syntaxin-18_N  25 keakkrkkkrlkk 37 
                                       +  ++++++++k+
  gi|298675770|ref|YP_003727520.1| 357 S--SSESESSSKS 367
                                       1..1111111111 PP

>> GIT1_C  G protein-coupled receptor kinase-interacting protein 1 C term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1      0.28     1e+02      66     115 ..      47      95 ..      25      97 .. 0.72
   2 ?    7.4   2.2     0.012       4.4      29     101 ..      82     158 ..      73     167 .. 0.75
   3 ?    1.3   0.8      0.98   3.6e+02      44      75 ..     138     157 ..     108     223 .. 0.47
   4 ?    7.2   1.3     0.014       5.2      29     100 ..     242     317 ..     231     327 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.28
                            GIT1_C  66 kqLtssaerLqeeCeelqeaeseskedikketqqviqcAydiAkaaKqLv 115
                                       +++   ae +++e ++ +  +++ + d++ + + v ++++++   aK+++
  gi|298675770|ref|YP_003727520.1|  47 NEIIIVAETIHTESAKIAD-DKSLNADLRTKAETVHKSSHEMEHIAKEII 95 
                                       3444455666677777766.888999999999********9999999998 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.012
                            GIT1_C  29 ekkesfvpcaerIqsaVqdlvalfpenlseetlrtaLkqLtss....aerLqeeCeelqeaeseskedikketqqvi 101
                                       ++++++ ++a+ I + V+ l ++ +++ ++++++t++++++++    a++L+++  +++e e++ ++++k+  +++ 
  gi|298675770|ref|YP_003727520.1|  82 KSSHEMEHIAKEIINHVETLESIEHPDENKDKVKTEISEINEHidelANLLNSKSDAVHEVEENTPQSHKEYAENIH 158
                                       67789999***************************998888772222555566666666677777777777766665 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.98
                            GIT1_C  44 aVqdlvalfpenlseetlrtaLkqLtssaerL 75 
                                       aV+++ +  p            ++ ++ ae +
  gi|298675770|ref|YP_003727520.1| 138 AVHEVEENTP------------QSHKEYAENI 157
                                       2222222222............2222222222 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.014
                            GIT1_C  29 ekkesfvpcaerIqsaVqdlvalfpenlseetlrtaLkqLtss....aerLqeeCeelqeaeseskedikketqqv 100
                                       ++++++ ++a+ I s V+ l  + +++ ++++++t++++++++    a++L+++  +++e e++ ++++k+  +++
  gi|298675770|ref|YP_003727520.1| 242 KSSHEMEHIAKEIISHVETLEGIEHPDENKDKVKTEISEINEHidelANLLNSKSDAVHEVEENTPQSHKEYAKDI 317
                                       67789999***************************99888877222244455555555555555555555555554 PP

>> TBCC_N  Tubulin-specific chaperone C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   3.2    0.0028         1      13      83 ..      63     136 ..      54     141 .. 0.78
   2 ?    1.0   0.1       1.5   5.6e+02      10      73 ..     143     207 ..     137     213 .. 0.71
   3 ?   11.0   2.2    0.0012      0.43      12      83 ..     222     296 ..     215     301 .. 0.79
   4 ?   -1.1   0.7       6.6   2.4e+03      24      53 ..     317     346 ..     294     373 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0028
                            TBCC_N  13 qlekrkeereseaveeekvdsFlkaFteekaaieellesve....esadksklkqkldeitaeiqeLqkllaess 83 
                                        ++ ++ +  +  ++ e+v + + + ++ +++i + +e++e    ++++k+k+k ++ ei++ i+eL +ll+  s
  gi|298675770|ref|YP_003727520.1|  63 IADDKSLN-ADLRTKAETVHKSSHEMEHIAKEIINHVETLEsiehPDENKDKVKTEISEINEHIDELANLLNSKS 136
                                       44444433.33666788888888889999999988888888888999************************9765 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 1.5
                            TBCC_N  10 rqeqlekrkeereseaveeekvdsFlkaFteekaaieellesve.esadksklkqkldeitaeiq 73 
                                        ++  ++ ke +e+ + e+ +   + ++++e + +ie+ + +   e   + ++ + l+e+++  +
  gi|298675770|ref|YP_003727520.1| 143 EENTPQSHKEYAENIHHEFHELGDIGSHLKEHASEIESDVIGTGeEYDHEHEEGSALAEVEEHAN 207
                                       56667777888888888888888999999999999999987777433444445566666666555 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.0012
                            TBCC_N  12 eqlekrkeereseaveeekvdsFlkaFteekaaieellesve....esadksklkqkldeitaeiqeLqkllaess 83 
                                       + ++ ++  +++  ++ e+v + + + ++ +++i + +e++e    ++++k+k+k ++ ei++ i+eL +ll+  s
  gi|298675770|ref|YP_003727520.1| 222 KVADDKS-LNDDLREKAETVHKSSHEMEHIAKEIISHVETLEgiehPDENKDKVKTEISEINEHIDELANLLNSKS 296
                                       4444433.4445667788888888889999999988888888888999************************9765 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 6.6
                            TBCC_N  24 eaveeekvdsFlkaFteekaaieellesve 53 
                                        + e+ +   + ++++e + +ie+ + +  
  gi|298675770|ref|YP_003727520.1| 317 IHHEFHELGDIGSHLKEHASEIESDVIGTG 346
                                       444455555556666666666666554444 PP

>> HeLo  Prion-inhibition and propagation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   3.8     0.012       4.6     109     202 ..      66     164 ..      24     167 .. 0.67
   2 ?    6.5   3.3     0.018       6.5     111     200 ..     228     322 ..     174     327 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.012
                                       ...G-B--GGGS-HHHHHHH.HHHHHHHHHS----S-----EEE-SHHHHHHHHHHHHHHHHHHHHTTT-H..HHHH CS
                              HeLo 109 slalssereksfraefellkrlmrkaakkrqkrtslpkrlrWaivdkkkfeelvkdlkelvdsLeeLlpasqqqrvq 185
                                       +++l  + +++ +  +++ ++ m+ +ak+  + ++  + +      k+k ++ ++++ e++d+L +Ll ++ ++ v+
  gi|298675770|ref|YP_003727520.1|  66 DKSLNADLRTKAETVHKSSHE-MEHIAKEIINHVETLESIEHPDENKDKVKTEISEINEHIDELANLLNSK-SDAVH 140
                                       334444444444555555553.666667777788888888888899999*******************988.67777 PP

                                       HHHHHH.......CTT--.SHHHH CS
                              HeLo 186 rlvree.......ieqlskdveeL 202
                                       +  +++        e+++++  eL
  gi|298675770|ref|YP_003727520.1| 141 EVEENTpqshkeyAENIHHEFHEL 164
                                       776666555555567777777666 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.018
                                       .G-B--GGGS-HHHHHHH.HHHHHHHHHS----S-----EEE-SHHHHHHHHHHHHHHHHHHHHTTT-H..HHHHHH CS
                              HeLo 111 alssereksfraefellkrlmrkaakkrqkrtslpkrlrWaivdkkkfeelvkdlkelvdsLeeLlpasqqqrvqrl 187
                                       +l ++ +++ +  +++ +  m+ +ak+  + ++  + +      k+k ++ ++++ e++d+L +Ll ++ ++ v++ 
  gi|298675770|ref|YP_003727520.1| 228 SLNDDLREKAETVHKSSH-EMEHIAKEIISHVETLEGIEHPDENKDKVKTEISEINEHIDELANLLNSK-SDAVHEV 302
                                       334444444444444444.3666666666777888888888889**********************988.7777776 PP

                                       HHHH.......CTT--.SHH CS
                              HeLo 188 vree.......ieqlskdve 200
                                        +++        ++++++  
  gi|298675770|ref|YP_003727520.1| 303 EENTpqshkeyAKDIHHEFH 322
                                       66664444444455555555 PP

>> Cluap1  Clusterin-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   7.9     0.003       1.1      99     236 ..      26     160 ..       8     167 .. 0.82
   2 ?    7.7   8.6    0.0057       2.1     106     232 ..     190     315 ..     158     324 .. 0.80
   3 ?    0.2   4.7       1.1   3.9e+02     129     211 ..     278     372 ..     269     375 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.003
                            Cluap1  99 eeekeeeekststeldlssklsdlkaarqlaseitekgasLydlLekevelreartkalsrqleleeiekalkeaik 175
                                       ++e +++++ +++ ++++++++++  +   a++i +++a++ d  + + +lr + +++ +++ e+e+i k++ ++++
  gi|298675770|ref|YP_003727520.1|  26 AHEGHSHDNVSQSLVEVEDHANEIIIV---AETIHTESAKIADDKSLNADLRTKAETVHKSSHEMEHIAKEIINHVE 99 
                                       455666666777777777777777665...9*********************************************9 PP

                            Cluap1 176 kvkeelektkkalenlesdeanLeakiekkkqeleraqkrLqslqsvrPafmdey.ekleee 236
                                       ++ e++e+  ++ ++++++ +++++ i+   + l+ +++  +++++  P   +ey e++ +e
  gi|298675770|ref|YP_003727520.1| 100 TL-ESIEHPDENKDKVKTEISEINEHIDELANLLNSKSDAVHEVEENTPQSHKEYaENIHHE 160
                                       96.6799999999**************99999999999999999999998888884445555 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0057
                            Cluap1 106 ekststeldlssklsdlkaarqlaseitekgasLydlLekevelreartkalsrqleleeiekalkeaikkvkeele 182
                                       +++++   +l++  +  ++  ++a +i +k+a++ d  + + +lre+ +++ +++ e+e+i k++ ++++++ e +e
  gi|298675770|ref|YP_003727520.1| 190 DHEHEEGSALAEVEEHANEIISVAGTIHTKSAKVADDKSLNDDLREKAETVHKSSHEMEHIAKEIISHVETL-EGIE 265
                                       33334455555556666777889*********************************************9986.6899 PP

                            Cluap1 183 ktkkalenlesdeanLeakiekkkqeleraqkrLqslqsvrPafmdeyek 232
                                       +  ++ ++++++ +++++ i+   + l+ +++  +++++  P   +ey k
  gi|298675770|ref|YP_003727520.1| 266 HPDENKDKVKTEISEINEHIDELANLLNSKSDAVHEVEENTPQSHKEYAK 315
                                       99999999999999999999999999999998888888888888888865 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.1
                            Cluap1 129 aseitekgasLydlLekeve............lreartkalsrqleleeiekalkeaikkvkeelektkkalenles 193
                                        sei e+  +L +lL+ +++            ++e  +++ ++  el +i ++lke+ +++++++  t ++ ++ ++
  gi|298675770|ref|YP_003727520.1| 278 ISEINEHIDELANLLNSKSDavheveentpqsHKEYAKDIHHEFHELGDIGSHLKEHASEIESDVIGTGEEHDHEHE 354
                                       3445555555555555555544444444444566666666678889*********************9999999999 PP

                            Cluap1 194 deanLeakiekkkqeler 211
                                       + ++ e+    k++e+e+
  gi|298675770|ref|YP_003727520.1| 355 EGSSSESESSSKSSESEQ 372
                                       999999999999999987 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   9.7     0.071        26      24     146 ..      40     173 ..      34     195 .. 0.56
   2 ?    8.1   4.1    0.0089       3.3      24     104 ..     200     286 ..     197     290 .. 0.68
   3 ?    6.0   5.8      0.04        15      31     124 ..     276     370 ..     267     380 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.071
                              Fez1  24 aevtqklseivalkaqlrelrakleekeeeikele...esleektlelevcenelqrk...kseaellrekveklee 94 
                                        ev   ++ei+ +  +++  +ak+ +  + + +l+   e++++ ++e+e++ +e+ ++    ++ e  +e+ +k+++
  gi|298675770|ref|YP_003727520.1|  40 VEVEDHANEIIIVAETIHTESAKIADDKSLNADLRtkaETVHKSSHEMEHIAKEIINHvetLESIEHPDENKDKVKT 116
                                       58889999999999999999999987776666665111455667777888888877765552333333455556666 PP

                              Fez1  95 elkelreelselsl...eeeeaalesdeakaqrqe..aeeleelkreverlraeLke 146
                                       e++e+ e++ el++   ++++a++e +e+  q ++  ae+++++ +e+  + ++Lke
  gi|298675770|ref|YP_003727520.1| 117 EISEINEHIDELANllnSKSDAVHEVEENTPQSHKeyAENIHHEFHELGDIGSHLKE 173
                                       666666555444330003333333333322222222244444444444444445554 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0089
                              Fez1  24 aevtqklseivalkaqlrelrakleekeeeikeleesl...eektlelevcenelqrk...kseaellrekveklee 94 
                                       aev + ++ei+++ ++++  +ak+ +  + +++l+e++   ++ ++e+e++ +e+  +    +  e  +e+ +k+++
  gi|298675770|ref|YP_003727520.1| 200 AEVEEHANEIISVAGTIHTKSAKVADDKSLNDDLREKAetvHKSSHEMEHIAKEIISHvetLEGIEHPDENKDKVKT 276
                                       7999********************99888888777765111556667777777776654332333444556666666 PP

                              Fez1  95 elkelreels 104
                                       e++e+ e++ 
  gi|298675770|ref|YP_003727520.1| 277 EISEINEHID 286
                                       6666666554 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.04
                              Fez1  31 seivalkaqlrelrakleekeeeikeleesleektlel.evcenelqrkkseaellrekvekleeelkelreelsel 106
                                        ei ++  ++ el + l++k ++++e+ee++ + ++e  + +++e+++  +  + l+e+++++e+++ ++ ee  + 
  gi|298675770|ref|YP_003727520.1| 276 TEISEINEHIDELANLLNSKSDAVHEVEENTPQSHKEYaKDIHHEFHELGDIGSHLKEHASEIESDVIGTGEEHDHE 352
                                       46777778888888889999999999998888877775256888999999999999999999999999999987776 PP

                              Fez1 107 sleeeeaalesdeakaqr 124
                                       ++e +++++es+++  + 
  gi|298675770|ref|YP_003727520.1| 353 HEEGSSSESESSSKSSES 370
                                       655555544444433222 PP

>> Borrelia_lipo_1  Borrelia burgdorferi virulent strain associated lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       3.6   1.3e+03     175     206 ..      65      96 ..      50     100 .. 0.79
   2 ?    6.4   4.9     0.019       6.9     163     202 ..     105     144 ..      75     148 .. 0.83
   3 ?    6.1   6.4     0.023       8.3     129     202 ..     229     304 ..     197     308 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3.6
                   Borrelia_lipo_1 175 dnskLksyvnklykqikkkekeakklkkeIls 206
                                       d++ L   + +  + ++k ++e+++++keI++
  gi|298675770|ref|YP_003727520.1|  65 DDKSLNADLRTKAETVHKSSHEMEHIAKEIIN 96 
                                       77778888888888888888888888888875 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.019
                   Borrelia_lipo_1 163 lDYqnntnsIktdnskLksyvnklykqikkkekeakklkk 202
                                       +  ++n++++kt++s+  +++++l + +++k++ ++++++
  gi|298675770|ref|YP_003727520.1| 105 EHPDENKDKVKTEISEINEHIDELANLLNSKSDAVHEVEE 144
                                       55579**************************999998876 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.023
                   Borrelia_lipo_1 129 LdkleiedLkklknslekllslreifskmikkl..LlDYqnntnsIktdnskLksyvnklykqikkkekeakklkk 202
                                       L+    e+ + + +s  ++  + + +++ ++ l  ++  ++n++++kt++s+  +++++l + +++k++ ++++++
  gi|298675770|ref|YP_003727520.1| 229 LNDDLREKAETVHKSSHEMEHIAKEIISHVETLegIEHPDENKDKVKTEISEINEHIDELANLLNSKSDAVHEVEE 304
                                       44444466666777777777777777777776666778899**************************999998876 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   8.6    0.0058       2.1       8     110 ..      54     155 ..      35     163 .. 0.82
   2 ?   10.1   5.6    0.0018      0.65       8     108 ..     214     313 ..     207     323 .. 0.80
   3 ?    2.5   5.7      0.39   1.4e+02       4      52 ..     272     320 ..     269     377 .. 0.51

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0058
                        TPR_MLP1_2   8 eeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesak 84 
                                       e+i++ ++++++ ++  + l+++ e+ +++  e++   ++e+++h e++++++   e  +++k+ei+e+++  +++ 
  gi|298675770|ref|YP_003727520.1|  54 ETIHTESAKIADDKSLNADLRTKAETVHKSSHEMEH-IAKEIINHVETLESIEHPDENKDKVKTEISEINEHIDELA 129
                                       555566666777777777888888888888888887.999*************999999999999999999999999 PP

                        TPR_MLP1_2  85 aeleeseesweeqkeelekelselek 110
                                       + l+ +  + +e +e+  +  +e  +
  gi|298675770|ref|YP_003727520.1| 130 NLLNSKSDAVHEVEENTPQSHKEYAE 155
                                       99999999998888877666666554 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0018
                        TPR_MLP1_2   8 eeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesak 84 
                                        +i++++++ ++ ++    l+e+ e+ +++  e++   ++e++ h e+++ ++   e  +++k+ei+e+++  +++ 
  gi|298675770|ref|YP_003727520.1| 214 GTIHTKSAKVADDKSLNDDLREKAETVHKSSHEMEH-IAKEIISHVETLEGIEHPDENKDKVKTEISEINEHIDELA 289
                                       566777777777788888888888888888888888.999************9999999999999999999999999 PP

                        TPR_MLP1_2  85 aeleeseesweeqkeelekelsel 108
                                       + l+ +  + +e +e+  +  +e 
  gi|298675770|ref|YP_003727520.1| 290 NLLNSKSDAVHEVEENTPQSHKEY 313
                                       999999888888887766655554 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.39
                        TPR_MLP1_2   4 ksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkh 52 
                                       +++++ei++++e ++e+++ l++  + + + +e + + ++ Y++ + + 
  gi|298675770|ref|YP_003727520.1| 272 DKVKTEISEINEHIDELANLLNSKSDAVHEVEENTPQSHKEYAKDIHHE 320
                                       4445555555555555555555555555555555555555555555544 PP

>> ENTH  ENTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.9     0.021       7.9      72     123 ..      82     136 ..      75     138 .. 0.73
   2 ?    5.3   0.9     0.052        19      72     123 ..     242     296 ..     239     298 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.021
                                       HS-HHHHHHHHHTHHHHHGGGG---B-TTS-B-HHH....HHHHHHHHHHHHT-HH CS
                              ENTH  72 nGseqvidwlkenisiiktlsefkyideegkdegln....iRkkakkiislledee 123
                                       ++s ++ + +ke i+ ++tl+++++ de +kd++++    i + ++++++ll+ ++
  gi|298675770|ref|YP_003727520.1|  82 KSSHEMEHIAKEIINHVETLESIEHPDE-NKDKVKTeiseINEHIDELANLLNSKS 136
                                       5666666777999999999999999777.333333334559999999999998765 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.052
                                       HS-HHHHHHHHHTHHHHHGGGG---B-TTS-B-HHH....HHHHHHHHHHHHT-HH CS
                              ENTH  72 nGseqvidwlkenisiiktlsefkyideegkdegln....iRkkakkiislledee 123
                                       ++s ++ + +ke is ++tl+ +++ de +kd++++    i + ++++++ll+ ++
  gi|298675770|ref|YP_003727520.1| 242 KSSHEMEHIAKEIISHVETLEGIEHPDE-NKDKVKTeiseINEHIDELANLLNSKS 296
                                       5666666777999999999999999777.333333334559999999999998765 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   3.5     0.023       8.3      19      80 ..      70     131 ..      63     146 .. 0.86
   2 ?    2.8   0.4      0.41   1.5e+02      34      93 ..     123     180 ..     115     182 .. 0.65
   3 ?    4.3   0.5      0.13        48      48      92 ..     218     262 ..     178     266 .. 0.62
   4 ?    5.9   1.9     0.042        16      28      80 ..     239     291 ..     224     294 .. 0.73
   5 ?    3.2   0.4      0.29   1.1e+02      34      93 ..     283     340 ..     273     342 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.023
                           BLOC1_2  19 vedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeea 80 
                                       ++d+++  +  +++s++ + +++++ +  ++le ++  +e+ ++ +++i +i+++++eL ++
  gi|298675770|ref|YP_003727520.1|  70 NADLRTKAETVHKSSHEMEHIAKEIINHVETLESIEHPDENKDKVKTEISEINEHIDELANL 131
                                       5677777778888999999999999999999999999999******************9876 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.41
                           BLOC1_2  34 ekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEa 93 
                                       e++++l++ ++s ++ +++++e  ++ q++++  ++i+ +  eL ++ s+L e  +e+E+
  gi|298675770|ref|YP_003727520.1| 123 EHIDELANLLNSKSDAVHEVEE--NTPQSHKEYAENIHHEFHELGDIGSHLKEHASEIES 180
                                       4555555555555555555555..567777777778888888888888888887777776 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.13
                           BLOC1_2  48 kkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLE 92 
                                       +k+ k+   +   + + ++ + ++k+  e+e++++e+ + +  LE
  gi|298675770|ref|YP_003727520.1| 218 TKSAKVADDKSLNDDLREKAETVHKSSHEMEHIAKEIISHVETLE 262
                                       555555554444455555555555555555555555544444444 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.042
                           BLOC1_2  28 lNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeea 80 
                                         +++s++ + +++++ s  ++le ++  +e+ ++ +++i +i+++++eL ++
  gi|298675770|ref|YP_003727520.1| 239 TVHKSSHEMEHIAKEIISHVETLEGIEHPDENKDKVKTEISEINEHIDELANL 291
                                       44566666777777777777777777788889999999999999999999875 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.29
                           BLOC1_2  34 ekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEa 93 
                                       e++++l++ ++s ++ +++++e  ++ q++++  ++i+ +  eL ++ s+L e  +e+E+
  gi|298675770|ref|YP_003727520.1| 283 EHIDELANLLNSKSDAVHEVEE--NTPQSHKEYAKDIHHEFHELGDIGSHLKEHASEIES 340
                                       4555555555555555555555..577777888888888888888888888888888877 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.6      0.05        18      39      80 ..      71     112 ..      54     117 .. 0.78
   2 ?    4.1   0.6      0.22        79      25      69 ..     119     164 ..     113     177 .. 0.61
   3 ?    2.7   0.4      0.56     2e+02      10      88 ..     150     236 ..     145     240 .. 0.59
   4 ?    4.4   1.1      0.16        60      39      73 ..     231     265 ..     187     279 .. 0.81
   5 ?    3.8   0.8      0.25        92      26      69 ..     280     324 ..     269     340 .. 0.56

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.05
                      Occludin_ELL  39 seLerelkelkegskeykkieeeilqeykklkkdpeyqekkk 80 
                                       ++L+++ ++ +++s+e+++i++ei+++ + l++ ++  e+k 
  gi|298675770|ref|YP_003727520.1|  71 ADLRTKAETVHKSSHEMEHIAKEIINHVETLESIEHPDENKD 112
                                       679999999******************999987555555554 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.22
                      Occludin_ELL  25 kelhaeleevskkfseLerelkelkegsk.eykkieeeilqeykkl 69 
                                       +e++++++e+++ ++  ++ ++e +e++   +k+ +e+i +e+++l
  gi|298675770|ref|YP_003727520.1| 119 SEINEHIDELANLLNSKSDAVHEVEENTPqSHKEYAENIHHEFHEL 164
                                       3444555555555555556666666666557777777777777766 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.56
                      Occludin_ELL  10 rerYkaeFnkeYkeY....kelhaeleevskkfseLerelkelkegsk...eykkieeeilqeykklkk.dpeyqek 78 
                                       +++Y ++ ++e++e     ++l+++ +e+++++    +e ++ +e+ +   e+++ ++ei++    ++  +++  ++
  gi|298675770|ref|YP_003727520.1| 150 HKEYAENIHHEFHELgdigSHLKEHASEIESDVIGTGEEYDHEHEEGSalaEVEEHANEIISVAGTIHTkSAKVADD 226
                                       45555555555555511114455555666666666777777776666657777777777777766666556666677 PP

                      Occludin_ELL  79 kkrceyLkek 88 
                                       k   ++L+ek
  gi|298675770|ref|YP_003727520.1| 227 KSLNDDLREK 236
                                       7666677666 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.16
                      Occludin_ELL  39 seLerelkelkegskeykkieeeilqeykklkkdp 73 
                                        +L+++ ++ +++s+e+++i++ei+++ + l+  +
  gi|298675770|ref|YP_003727520.1| 231 DDLREKAETVHKSSHEMEHIAKEIISHVETLEGIE 265
                                       57889999999999**********99988886544 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.25
                      Occludin_ELL  26 elhaeleevskkfseLerelkelkegsk.eykkieeeilqeykkl 69 
                                       e++++++e+++ ++  ++ ++e +e++   +k+ +++i +e+++l
  gi|298675770|ref|YP_003727520.1| 280 EINEHIDELANLLNSKSDAVHEVEENTPqSHKEYAKDIHHEFHEL 324
                                       334444444444444445555555555456666666666666665 PP

>> PI3K_1B_p101  Phosphoinositide 3-kinase gamma adapter protein p101 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8  11.0     0.014         5     215     354 ..      80     222 ..      31     239 .. 0.72
   2 ?    5.5   8.6    0.0084       3.1     216     341 ..     241     368 ..     229     384 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.014
                      PI3K_1B_p101 215 qsktveeleeilsevtealetaaaasdpekaRekllqkleelreklelpassgkksegklqtlelpvakcytysWek 291
                                        +k+ +e+e+i +e+ +++et  ++++p++ ++k++++++e++e+++  a+  ++++ +++ +e  ++++++   e+
  gi|298675770|ref|YP_003727520.1|  80 VHKSSHEMEHIAKEIINHVETLESIEHPDENKDKVKTEISEINEHIDELANLLNSKSDAVHEVEENTPQSHKEYAEN 156
                                       357889********************************************999999999*****9999999877665 PP

                      PI3K_1B_p101 292 ..dnfDvLneilekeselaspeeledeeeedeedvdeeedleeee.eeeeedslarsstlstvsss 354
                                          +f  L +i ++ +e+as  e+ +  + +e d ++ee     e ee+ +++++ + t+ t s +
  gi|298675770|ref|YP_003727520.1| 157 ihHEFHELGDIGSHLKEHASEIESDVIGTGEEYDHEHEEGSALAEvEEHANEIISVAGTIHTKSAK 222
                                       337888899987776666665555554444554444444333333022223344455555555554 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0084
                      PI3K_1B_p101 216 sktveeleeilsevtealetaaaasdpekaRekllqkleelreklelpassgkksegklqtlelpvakcyt.ysWe. 290
                                       +k+ +e+e+i +e+  ++et   +++p++ ++k++++++e++e+++  a+  ++++ +++ +e  ++++++ y  + 
  gi|298675770|ref|YP_003727520.1| 241 HKSSHEMEHIAKEIISHVETLEGIEHPDENKDKVKTEISEINEHIDELANLLNSKSDAVHEVEENTPQSHKeYAKDi 317
                                       58899********************************************999999999*****99999997233332 PP

                      PI3K_1B_p101 291 kdnfDvLneilekeselaspeeledeeeedeedvdeeedleeeeeeeeeds 341
                                       + +f  L +i ++ +e+as  e+ +  + +e+d ++ee  ++e+e+++++s
  gi|298675770|ref|YP_003727520.1| 318 HHEFHELGDIGSHLKEHASEIESDVIGTGEEHDHEHEEGSSSESESSSKSS 368
                                       457777777766665555555554444445554444444444444433333 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1       4.2   1.5e+03      45      66 ..      71      92 ..      33     105 .. 0.58
   2 ?    6.7   0.1      0.03        11       2      80 ..     123     213 ..     118     217 .. 0.78
   3 ?    1.0   0.3       1.9   6.8e+02      36      60 ..     229     253 ..     198     261 .. 0.48
   4 ?    3.8   0.1      0.25        90       5      52 ..     279     326 ..     272     345 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 4.2
                            DUF883 45 erlrdaeeavaerakeaaeaad 66
                                      + lr  +e+v ++++e+ + a+
  gi|298675770|ref|YP_003727520.1| 71 ADLRTKAETVHKSSHEMEHIAK 92
                                      2333333333333333333333 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.03
                            DUF883   2 eleaeleslladleellkeaadeageeaeelRerleerlerarerlrdaeeavaerakeaaeaaddy.......... 68 
                                       e+ +el++ll++  + ++e ++++ ++ +e  e+++ +++++ +  ++++e++ e  ++++ + ++y          
  gi|298675770|ref|YP_003727520.1| 123 EHIDELANLLNSKSDAVHEVEENTPQSHKEYAENIHHEFHELGDIGSHLKEHASEIESDVIGTGEEYdheheegsal 199
                                       67788888888888889999999999999999999999999999999999999999999999999996666666666 PP

                            DUF883  69 ..VrenPwqavGiA 80 
                                         V+e+  + +++A
  gi|298675770|ref|YP_003727520.1| 200 aeVEEHANEIISVA 213
                                       66666666666665 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 1.9
                            DUF883  36 leerlerarerlrdaeeavaerake 60 
                                       l++ l++  e++++ ++++++ ake
  gi|298675770|ref|YP_003727520.1| 229 LNDDLREKAETVHKSSHEMEHIAKE 253
                                       2333333333333333333333333 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.25
                            DUF883   5 aeleslladleellkeaadeageeaeelRerleerlerarerlrdaee 52 
                                       +e+++ +++l++ll++++d   e  e+  +  +e++++  ++++++ +
  gi|298675770|ref|YP_003727520.1| 279 SEINEHIDELANLLNSKSDAVHEVEENTPQSHKEYAKDIHHEFHELGD 326
                                       577777888888888888777776666767777777777776666554 PP

>> DUF148  Domain of unknown function DUF148
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   2.9      0.32   1.2e+02      42      83 ..      33      74 ..      29     104 .. 0.77
   2 ?    4.3   3.1      0.11        41      41      88 ..     111     158 ..      80     166 .. 0.74
   3 ?    6.2   1.2      0.03        11      15      63 ..     116     165 ..     110     191 .. 0.67
   4 ?    6.6   1.0     0.022       7.9      45      89 ..     196     242 ..     184     262 .. 0.66
   5 ?    4.8   1.0     0.082        30      42      87 ..     272     317 ..     265     325 .. 0.68

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.32
                            DUF148 42 akvkaqkeevkknvtavisnLssvqekleaIldnkslTrkeq 83
                                       +v++   ev+++++++i   ++++++  +I d+ksl  + +
  gi|298675770|ref|YP_003727520.1| 33 DNVSQSLVEVEDHANEIIIVAETIHTESAKIADDKSLNADLR 74
                                      578888999999999999999999999999999999876544 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.11
                            DUF148  41 eakvkaqkeevkknvtavisnLssvqekleaIldnkslTrkeqkeaie 88 
                                       + kvk++ +e+++++++  + L s ++ + ++ +n+ ++ ke  e i+
  gi|298675770|ref|YP_003727520.1| 111 KDKVKTEISEINEHIDELANLLNSKSDAVHEVEENTPQSHKEYAENIH 158
                                       566777777777777777777777777777777777777777777765 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.03
                            DUF148  15 ltiaeieeqleawaeky.gvtdeykefeakvkaqkeevkknvtavisnLs 63 
                                         i+ei+e ++++a+   + +d+++e e++  + ++e+ +n+     +L 
  gi|298675770|ref|YP_003727520.1| 116 TEISEINEHIDELANLLnSKSDAVHEVEENTPQSHKEYAENIHHEFHELG 165
                                       45666777777777665455666677777766666666666665555555 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.022
                            DUF148  45 kaqkeevkknvtavisnLssvqekleaIldnkslTrk..eqkeaiee 89 
                                         + +ev+++++++is   ++++k  ++ d+ksl  +  e+ e +++
  gi|298675770|ref|YP_003727520.1| 196 GSALAEVEEHANEIISVAGTIHTKSAKVADDKSLNDDlrEKAETVHK 242
                                       55678888888888888888888888888888886431144444433 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.082
                            DUF148  42 akvkaqkeevkknvtavisnLssvqekleaIldnkslTrkeqkeai 87 
                                        kvk++ +e+++++++  + L s ++ + ++ +n+ ++ ke  + i
  gi|298675770|ref|YP_003727520.1| 272 DKVKTEISEINEHIDELANLLNSKSDAVHEVEENTPQSHKEYAKDI 317
                                       4566667777777777777777777777777777777776666555 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   4.2     0.011       4.1     121     254 ..     108     244 ..      45     267 .. 0.52
   2 ?    2.5   0.3      0.21        78     126     168 ..     273     318 ..     251     383 .. 0.50

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.011
                           DUF4407 121 kelkeqlaaa...ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk..............gtgttgvaG 180
                                       +e+k++++++    ++ ++el + +++ + ++ + e+   +  +e++++++ ++              ++ ++ v G
  gi|298675770|ref|YP_003727520.1| 108 DENKDKVKTEiseINEHIDELANLLNSKSDAVHEVEENTPQSHKEYAENIHHEFhelgdigshlkehaSEIESDVIG 184
                                       22222222223334444444444444555555555555555555555444444455555555555544333344445 PP

                           DUF4407 181 kgpaakekkaqldaaqaelaelkakld.....atarlaalraelaeleaerakeraasqaaaaaddGllarlealdr 252
                                        g+++++                   +     a a+++++ +e+ +++  ++++ a+ +++++ +d+l ++ e  ++
  gi|298675770|ref|YP_003727520.1| 185 TGEEYDH-------------------EheegsALAEVEEHANEIISVAGTIHTKSAKVADDKSLNDDLREKAETVHK 242
                                       5555554...................044444555555555555555555555555555555555555444444444 PP

                           DUF4407 253 lt 254
                                        +
  gi|298675770|ref|YP_003727520.1| 243 SS 244
                                       33 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.21
                           DUF4407 126 qlaaa...ltaelaeleaqiaalqaeidaaearldalraeaqkeld 168
                                       +++++    ++ ++el + +++ + ++ + e+   +  +e++k ++
  gi|298675770|ref|YP_003727520.1| 273 KVKTEiseINEHIDELANLLNSKSDAVHEVEENTPQSHKEYAKDIH 318
                                       2221122233333333333333333333333333333333333333 PP

>> FAP206  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   2.6     0.045        16       4      88 ..      71     152 ..      66     163 .. 0.75
   2 ?    5.6   1.8     0.027       9.8       3      88 ..     230     312 ..     227     320 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.045
                            FAP206   4 eaipatreaiekeleeaqelasrytalleklveeseaevaeeqlerlkqalinvrqyeaylrilledveksaeevee 80 
                                         +++ +e+++k+ +e++++a++    +e+l   ++ e+++e+ +++k ++  ++ +   l  ll++ + + +evee
  gi|298675770|ref|YP_003727520.1|  71 ADLRTKAETVHKSSHEMEHIAKEIINHVETL---ESIEHPDENKDKVKTEISEINEHIDELANLLNSKSDAVHEVEE 144
                                       4455555666666666666655555555555...8889999999999999999999999999999999999999999 PP

                            FAP206  81 llkrfeae 88 
                                       ++ +  +e
  gi|298675770|ref|YP_003727520.1| 145 NTPQSHKE 152
                                       99876655 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.027
                            FAP206   3 eeaipatreaiekeleeaqelasrytalleklveeseaevaeeqlerlkqalinvrqyeaylrilledveksaeeve 79 
                                       ++ +++ +e+++k+ +e++++a++  + +e+l   +  e+++e+ +++k ++  ++ +   l  ll++ + + +eve
  gi|298675770|ref|YP_003727520.1| 230 NDDLREKAETVHKSSHEMEHIAKEIISHVETL---EGIEHPDENKDKVKTEISEINEHIDELANLLNSKSDAVHEVE 303
                                       45555556666666666666666555555555...99999*****************************9******9 PP

                            FAP206  80 ellkrfeae 88 
                                       e++ +  +e
  gi|298675770|ref|YP_003727520.1| 304 ENTPQSHKE 312
                                       999886665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2124  (0.118467); expected 358.6 (0.02)
Passed bias filter:                      617  (0.0344135); expected 358.6 (0.02)
Passed Vit filter:                       119  (0.00663729); expected 17.9 (0.001)
Passed Fwd filter:                        87  (0.00485247); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              49  [number of targets reported over threshold]
# CPU time: 1.38u 0.41s 00:00:01.78 Elapsed: 00:00:00.62
# Mc/sec: 1947.46
//
Query:       gi|298675771|ref|YP_003727521.1|  [L=220]
Description: cobalamin (vitamin B12) biosynthesis protein CbiM [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-46  158.2  20.0    2.7e-46  158.0  20.0    1.0  1  CbiM      Cobalt uptake substrate-specific transmembrane regi
  ------ inclusion threshold ------
        1.1    9.2   9.9        1.1    9.2   7.3    2.1  2  DctQ      Tripartite ATP-independent periplasmic transporters
        5.9    7.2   8.5        1.1    9.6   0.5    2.7  2  DUF2530   Protein of unknown function (DUF2530)


Domain annotation for each model (and alignments):
>> CbiM  Cobalt uptake substrate-specific transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.0  20.0   4.5e-50   2.7e-46       1     207 []       2     199 ..       2     199 .. 0.94

  Alignments for each domain:
  == domain 1  score: 158.0 bits;  conditional E-value: 4.5e-50
                              CbiM   1 HipdgiLspavllaayavalallalalrrlrkeld.earvpllallaafifaaqminipipggtslHllgavlaaiL 76 
                                       Hi+dg+Ls+ v+ +++ ++++l  l l+++++e+d  +++p++++++a++f+a++i++pi g+ts+H++ ++l++++
  gi|298675771|ref|YP_003727521.1|   2 HISDGVLSATVVTGGWTITIVLAFLTLWWMNQETDiTEEIPKFSVMTAAFFVASLIHLPI-GPTSVHMIFNGLVGVV 77 
                                       *********************************997777*********************.**************** PP

                              CbiM  77 lGpwaaflavavvlllqallfgdGGitaLGaNilnmavigvllaylvyrllsrlasskkrvalaaflaallsvvlaa 153
                                       lG  +a l+++v+l+lqa+lf++GG+t++G+N++n++++++l +y++ +     +    ++++ +++++ +++++++
  gi|298675771|ref|YP_003727521.1|  78 LG-PLAYLSLVVGLILQAFLFQHGGVTTIGVNAMNIGIPALLSYYAFKK----GYDFGISEKIMGAFSGGAAIFMTV 149
                                       **.5689***********************************9995555....454567788999999********* PP

                              CbiM 154 llvalelalsgleaslsltaalaamllvhlpvgilEgviTaaivkalkkvrpel 207
                                       +l++++l+ +g+e    +  ++++ +++h+p++++E++iT+ +v++l kv+pel
  gi|298675771|ref|YP_003727521.1| 150 ILLSITLLTTGQE----FIGVAQVSAAAHAPLMVVEAIITGSVVTYLSKVKPEL 199
                                       **********997....***********************************96 PP

>> DctQ  Tripartite ATP-independent periplasmic transporters, DctQ component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   7.3   0.00018       1.1      14      86 ..      30     110 ..      13     158 .. 0.77
   2 ?    0.3   0.5       0.1     6e+02      28      53 ..     144     169 ..     121     193 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00018
                              DctQ  14 llnsslpwteelarylfvwlvflgaalalrrgshirvdllverlpprvrrlleliadllallfaavliwagw..... 85 
                                        +n+ +  tee+ ++++++++f+ a+l++   +  +v ++++ l   v   l ++++++ l++ a+l+  g      
  gi|298675771|ref|YP_003727521.1|  30 WMNQETDITEEIPKFSVMTAAFFVASLIHLPIGPTSVHMIFNGLVGVVLGPLAYLSLVVGLILQAFLFQHGGvttig 106
                                       35888889***********************************************************9999855444 PP

                              DctQ  86 ...l 86 
                                          +
  gi|298675771|ref|YP_003727521.1| 107 vnaM 110
                                       3330 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.1
                              DctQ  28 ylfvwlvflgaalalrrgshirvdll 53 
                                       ++f+++++l++ l +  ++ i v  +
  gi|298675771|ref|YP_003727521.1| 144 AIFMTVILLSITLLTTGQEFIGVAQV 169
                                       34555555555555555555555444 PP

>> DUF2530  Protein of unknown function (DUF2530)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   1.7     0.072   4.3e+02      17      40 ..      10      33 ..       3      40 .. 0.78
   2 ?    9.6   0.5   0.00018       1.1      12      56 ..      39      83 ..      35      94 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.072
                           DUF2530 17 ivvgtllWlvalvvllvvgdales 40
                                      + v+t  W + +v+++++  ++++
  gi|298675771|ref|YP_003727521.1| 10 ATVVTGGWTITIVLAFLTLWWMNQ 33
                                      5678889***99999998776665 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00018
                           DUF2530 12 dprpvivvgtllWlvalvvllvvgdaleswlpvclaGlvvGllGl 56
                                      +  p   v t++++va ++ l +g++  +++   l+G+v+G l++
  gi|298675771|ref|YP_003727521.1| 39 EEIPKFSVMTAAFFVASLIHLPIGPTSVHMIFNGLVGVVLGPLAY 83
                                      55677899***************999999************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1330.69
//
Query:       gi|298675772|ref|YP_003727522.1|  [L=167]
Description: hypothetical protein Metev_1895 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0069   16.6   0.1      0.011   15.9   0.1    1.3  1  SdrD_B           SdrD B-like domain
  ------ inclusion threshold ------
      0.014   15.5   0.0      0.018   15.1   0.0    1.3  1  bMG3             Bacterial alpha-2-macroglobulin MG3 domain
      0.061   13.3   0.3       0.11   12.5   0.3    1.5  1  CarbopepD_reg_2  CarboxypepD_reg-like domain
      0.089   13.1   0.0       0.15   12.3   0.0    1.4  1  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
       0.11   13.2   0.1       0.25   12.1   0.1    1.5  1  TTR-52           Transthyretin-like family
       0.22   11.4   2.2       0.29   11.1   1.8    1.3  1  EMP24_GP25L      emp24/gp25L/p24 family/GOLD
       0.69    9.2   2.1          1    8.6   2.1    1.2  1  CorA             CorA-like Mg2+ transporter protein


Domain annotation for each model (and alignments):
>> SdrD_B  SdrD B-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   4.4e-06     0.011      27      81 ..      57     118 ..      46     138 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.4e-06
                            SdrD_B  27 vtVtLkdakgevv..atttTdasGkYkFtnltpGe.YkVefta.pagy...tvtakkaGsdd 81 
                                       v+V L+++++e+   +   Td++G Y+F+  +  e YkV  +   +++   ++ +++++s +
  gi|298675772|ref|YP_003727522.1|  57 VNVYLITENDEEPyiEDKSTDEKGMYSFEPKQGHEvYKVVASDfGHQVekkVILESQSSSSS 118
                                       556666666655434899**********98776668**987543322211111111122222 PP

>> bMG3  Bacterial alpha-2-macroglobulin MG3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0     7e-06     0.018      25      76 ..      49      99 ..      28     129 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7e-06
                              bMG3 25 gkPvagaeVrll....dkkgevlaegtTDaqGvarfaallargkegaapylvsArk 76
                                      g+P++++eV+++    ++++  +    TD++G+++f+++     +g + y v+A +
  gi|298675772|ref|YP_003727522.1| 49 GDPMKDVEVNVYliteNDEEPYIEDKSTDEKGMYSFEPK-----QGHEVYKVVASD 99
                                      89******999833322344469**************99.....678888888873 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3   4.3e-05      0.11      28      71 ..      74     117 ..      53     129 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.3e-05
                   CarbopepD_reg_2  28 tvTdenGnFelknlpagk..ytLvvsyvGyktqekkvtvskektld 71 
                                        +Tde+G ++++ +++g   y++v+s  G +  ekkv ++++++ +
  gi|298675772|ref|YP_003727522.1|  74 KSTDEKGMYSFE-PKQGHevYKVVASDFGHQV-EKKVILESQSSSS 117
                                       57*********8.44442249********999.5677777666554 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.9e-05      0.15      10      61 ..      48     104 ..      39     119 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.9e-05
                   CarboxypepD_reg  10 sgapiagatVtvtn....adtgtvastttdadGafrlrglpp.gtysvtvsapGyat 61 
                                        g p++ ++V v+     +++       td++G ++++  +    y+v++s  G + 
  gi|298675772|ref|YP_003727522.1|  48 GGDPMKDVEVNVYLitenDEEPYIEDKSTDEKGMYSFEPKQGhEVYKVVASDFGHQV 104
                                       588998888887542111344568999**********96666888888888777664 PP

>> TTR-52  Transthyretin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   9.6e-05      0.25       7      46 ..      48      87 ..      46     102 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.6e-05
                                      TT-GGSS-EEEEEEHHHHTS--EEEEEE--TTSEEEEEEE CS
                            TTR-52  7 ggkpaknvkVkLwekdtldpddlldetkTdedGnFelsgs 46
                                      gg+p+k+v+V+++     d++  +++++Tde+G+++ + +
  gi|298675772|ref|YP_003727522.1| 48 GGDPMKDVEVNVYLITENDEEPYIEDKSTDEKGMYSFEPK 87
                                      689****999999865568999*************99843 PP

>> EMP24_GP25L  emp24/gp25L/p24 family/GOLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.8   0.00011      0.29      18     103 ..      32     120 ..      15     134 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00011
                       EMP24_GP25L  18 lkkgtlltgsyqvtdgg..aaldvdlsvk.dpdgngerlvkkkdresegdfsftakesgeykvCfdnsfstksskkv 91 
                                       + ++++ +++++++ gg  + +dv+++v+  +++++e ++++k ++++g +sf+ k+  e++  + + f +  +kkv
  gi|298675772|ref|YP_003727522.1|  32 VIEKSTDKIKVKAYYGGgdPMKDVEVNVYlITENDEEPYIEDKSTDEKGMYSFEPKQGHEVYKVVASDFGHQVEKKV 108
                                       43333344444444333554455555544313677899****999999*******9998888888888999999999 PP

                       EMP24_GP25L  92 sfdievgseasd 103
                                        ++ + +s+++ 
  gi|298675772|ref|YP_003727522.1| 109 ILESQSSSSSNG 120
                                       999998655444 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   2.1   0.00039         1     229     248 ..       4      23 ..       1      24 [. 0.92

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00039
                              CorA 229 rlNrvmkvLTvltaiflPlT 248
                                       + Nr++ v+++lt++f+P+T
  gi|298675772|ref|YP_003727522.1|   4 NFNRILLVISILTMVFVPAT 23 
                                       77****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       898  (0.0500865); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1002.68
//
Query:       gi|298675773|ref|YP_003727523.1|  [L=252]
Description: cobalt ABC transporter inner membrane subunit CbiQ [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-38  131.8   9.9    4.1e-38  131.2   9.9    1.2  1  CbiQ             Cobalt transport protein
  ------ inclusion threshold ------
        3.3    8.4   6.9         10    6.9   0.4    3.3  3  NADH-u_ox-rdase  NADH-ubiquinone oxidoreductase complex I, 21


Domain annotation for each model (and alignments):
>> CbiQ  Cobalt transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.2   9.9   4.6e-42   4.1e-38       3     214 ..      14     220 ..      13     226 .. 0.90

  Alignments for each domain:
  == domain 1  score: 131.2 bits;  conditional E-value: 4.6e-42
                                       CCCCS-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHTTS---.HHHHHHHCCCHCHHHHHHHHHHE..... CS
                              CbiQ   3 svlhrldprvkliwlfllllalvlapnlvtlliiiallllllllvilp.rvlaqalilpllflllgllillfqlitt 78 
                                       sv+h  dpr k i++  l++ + ++ +l ++++ + + + l+ ++ lp  + ++ l +p +f+++ ++i+ f   t+
  gi|298675773|ref|YP_003727523.1|  14 SVIHNFDPRAKIITFTVLIFSFAFIESLTVAMFAVLFSVSLIFISKLPiEFVYARLKYPIIFIFAIFVIMCF---TV 87 
                                       89******************99999999888554444444444444447999999999**************...79 PP

                                       ..EECTTEEE...E-TTHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHCCCSS--HHHHHHHHHHHHHHHHHHH CS
                              CbiQ  79 egefvfagggqisitseGllrglllalRiltllslllllalTTppeeltsslerlgvPlelalillLayRfiflLle 155
                                       eg+++++    +s+t eGl  gll++lR +++l++++l+++T  + +++++l  l+ P  ++ ++   yR+if+L++
  gi|298675773|ref|YP_003727523.1|  88 EGNIIIDSYF-VSVTLEGLKIGLLIFLRATAALIIAFLMLATNRFDTVIKALYMLKLPNAVVQMIVFSYRYIFVLVD 163
                                       **********.****************************************************************** PP

                                       HHHHHHHHHHHTTTTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS-SS... CS
                              CbiQ 156 evqrikqAqklRlgdsklgirrslrslgkliaalflralkraervalAmeaRGYtgsee 214
                                       e+q++k+++++ ++++k+++   l+++g li++l++++++r+erv  +m ++GY+g + 
  gi|298675773|ref|YP_003727523.1| 164 EFQNMKKSMSAKGFEIKANRYG-LSTIGNLIGMLLVKSYERGERVHKSMISKGYEG-KP 220
                                       ****************666666.*********************************.33 PP

>> NADH-u_ox-rdase  NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.4    0.0011        10       3      39 ..       2      37 ..       1      84 [. 0.81
   2 ?   -0.9   0.1       0.3   2.7e+03      56      56 ..     143     143 ..     110     206 .. 0.60
   3 ?    4.1   0.1    0.0087        78      17      38 ..     225     247 ..     219     251 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0011
                   NADH-u_ox-rdase  3 aYpvIdsdPsfsrvlrnfrpsDYvkaaaita.afplal 39
                                      +Yp Id+  +++ v+ nf p   +k++++t+ +f +a+
  gi|298675773|ref|YP_003727523.1|  2 NYPRIDAYSEIESVIHNFDPR--AKIITFTVlIFSFAF 37
                                      6******************98..666766665555554 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.3
                   NADH-u_ox-rdase  56 l 56 
                                       l
  gi|298675773|ref|YP_003727523.1| 143 L 143
                                       0 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.0087
                   NADH-u_ox-rdase  17 lrnfrpsDYvkaaaita.afpla 38 
                                         n+ +sDYv+ +++ + af + 
  gi|298675773|ref|YP_003727523.1| 225 NYNLMFSDYVLTIFMMIfAFGVH 247
                                       56889*********977666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1072  (0.0597914); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1611.96
//
Query:       gi|298675774|ref|YP_003727524.1|  [L=307]
Description: ABC transporter-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.1e-28   97.5   0.0    2.3e-27   96.2   0.0    1.6  2  ABC_tran      ABC transporter
    1.1e-14   55.0   0.6    2.6e-10   40.6   0.0    2.3  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
      4e-09   36.2   0.3    1.6e-07   31.0   0.3    2.2  1  SMC_N         RecF/RecN/SMC N terminal domain
    3.5e-05   23.7   2.7       0.13   12.0   0.2    2.4  2  AAA_15        AAA ATPase domain
    7.6e-05   23.3   0.1    0.00016   22.3   0.1    1.7  1  AAA_23        AAA domain
    0.00027   19.8   0.4      0.056   12.1   0.0    2.2  2  AAA_13        AAA domain
     0.0021   17.7   0.0       0.03   13.9   0.0    2.5  3  AAA_25        AAA domain
      0.004   17.4   0.0      0.014   15.7   0.0    1.9  1  AAA_22        AAA domain
     0.0046   16.0   0.1     0.0073   15.4   0.1    1.3  1  T2SSE         Type II/IV secretion system protein
     0.0065   16.2   0.1      0.018   14.8   0.0    1.8  2  AAA_24        AAA domain
     0.0066   16.4   0.1      0.015   15.2   0.1    1.8  1  ATPase_2      ATPase domain predominantly from Archaea
  ------ inclusion threshold ------
       0.01   15.2   0.2       0.18   11.2   0.0    2.2  2  TniB          Bacterial TniB protein
      0.014   15.0   0.3       0.06   12.9   0.0    1.9  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
      0.014   15.0   0.0      0.022   14.4   0.0    1.3  1  ATP-synt_ab   ATP synthase alpha/beta family, nucleotide-bind
      0.016   15.1   0.0      0.036   14.0   0.0    1.5  1  RsgA_GTPase   RsgA GTPase
      0.018   14.8   0.0      0.043   13.6   0.0    1.6  1  AAA_29        P-loop containing region of AAA domain
       0.03   14.3   0.0      0.048   13.6   0.0    1.3  1  NACHT         NACHT domain
      0.039   14.4   1.5       0.39   11.1   1.5    2.2  1  AAA           ATPase family associated with various cellular 
      0.067   13.2   0.0       0.32   11.0   0.0    2.2  2  AAA_14        AAA domain
      0.069   13.7   0.3       0.42   11.2   0.2    2.2  2  AAA_18        AAA domain
       0.07   12.6   0.3       0.21   11.1   0.1    1.8  2  AAA_7         P-loop containing dynein motor region
      0.072   13.3   0.1       0.17   12.2   0.0    1.6  1  AAA_28        AAA domain
      0.074   13.0   0.0       0.13   12.2   0.0    1.5  1  BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette 
      0.098   12.7   1.0        0.3   11.2   0.2    2.1  2  YqzH          YqzH-like protein
       0.11   12.4   0.1       0.33   10.9   0.1    1.8  1  NTPase_1      NTPase
       0.12   11.9   0.4       0.52    9.9   0.1    2.0  2  SRP54         SRP54-type protein, GTPase domain
       0.13   12.7   0.0       0.33   11.3   0.0    1.7  2  AAA_16        AAA ATPase domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.2   0.0   3.4e-30   2.3e-27       1     137 []      22     169 ..      22     169 .. 0.95
   2 ?   -1.7   0.0       5.6   3.7e+03      46      67 ..     198     217 ..     176     297 .. 0.49

  Alignments for each domain:
  == domain 1  score: 96.2 bits;  conditional E-value: 3.4e-30
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp.teGeilldgkdlkeqeleslrkeigvlpqe..pqlfpel 74 
                                       l+nv++++ egek+ i+G+nGaGK+tLl  l g lk  +++++ + ++ +++ +++   + +g+l+++  +qlf  +
  gi|298675774|ref|YP_003727524.1|  22 LDNVNMEVFEGEKITIMGPNGAGKTTLLLHLNGTLKTsNSDNVYIFEQAISSMNIKDRIQYVGILFEDpdDQLFMPT 98 
                                       79*******************************9998688999999**********************877888877 PP

                                       BHHHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  75 tvren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                        v++              e d++++k ++++gl++++++v     ++LS Gqk++vala+++  +pk+l+lDEpta
  gi|298675774|ref|YP_003727524.1|  99 -VYDDvafgpynmgldkkEVDKRVKKSMTRVGLQGFENEVP----QHLSTGQKKKVALAAVISMEPKILVLDEPTA 169
                                       .88888**********9999999*****************9....*****************************97 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 5.6
                                       TCEGGGB-HHHCCHCEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  46 gkdlkeqeleslrkeigvlpqe 67 
                                        +d+++  ++ l  ++ vl ++
  gi|298675774|ref|YP_003727524.1| 198 THDVNT--ISYLTDRVYVLNEK 217
                                       444444..33333333333333 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.3    0.0002      0.14       4      22 ..      37      55 ..      35     101 .. 0.67
   2 !   40.6   0.0   3.9e-13   2.6e-10     231     302 ..     135     204 ..     111     205 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                            AAA_21  4 liGpNgsGKSnLLdaldll 22
                                      + GpNg+GK++LL  l + 
  gi|298675774|ref|YP_003727524.1| 37 IMGPNGAGKTTLLLHLNGT 55
                                      77***********877554 PP

  == domain 2  score: 40.6 bits;  conditional E-value: 3.9e-13
                            AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSplll 302
                                       +  + +lS G+k+  al++ +   +   ++l++DEp ++L+Pk  ++++ ++kel++ +g+  i++TH+   +
  gi|298675774|ref|YP_003727524.1| 135 NEVPQHLSTGQKKKVALAAVISMEP---KILVLDEPTANLDPKSKSEIISFIKELNEkEGITTIIATHDVNTI 204
                                       5567899****************99...9***********************888888**********97655 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.3   2.4e-10   1.6e-07      21     205 ..      29     207 ..      16     219 .. 0.68

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 2.4e-10
                                       ETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  21 pfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeev 97 
                                        f+ +   i+GpNG+GK+ ll  +  +L ++++       +++ i++   + +    +v i+f+++d++l + +   
  gi|298675774|ref|YP_003727524.1|  29 VFEGEKITIMGPNGAGKTTLLLHLNGTLKTSNS--DNVYIFEQAISS--MNIKDRIQYVGILFEDPDDQLFMPTVYD 101
                                       566677889*********999777655554333..233444555554..5555566789999999999966666555 PP

                                       EEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  98 sisrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDek 174
                                        +    ++ g  + +++++  ++     l   ++  ++ LS G+k+ vala +++   ++p+ + +lDe  a+LD k
  gi|298675774|ref|YP_003727524.1| 102 DVAFGPYNMGLDKKEVDKRVKKSMTRVGLQGFENEVPQHLSTGQKKKVALAAVIS---MEPK-ILVLDEPTANLDPK 174
                                       555555555555555554433333333333333334569**********997755...5665.779*********** PP

                                       HHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC- CS
                                       xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx RF
                             SMC_N 175 nvkkvaellkekskn..aQfivislreemleka 205
                                         +++ +++ke +++     i+ +++ ++++  
  gi|298675774|ref|YP_003727524.1| 175 SKSEIISFIKELNEKegITTIIATHDVNTISYL 207
                                       **********88776457889999988887765 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.3   0.00026      0.18      25      69 ..      34      75 ..      20     120 .. 0.73
   2 !   12.0   0.2   0.00019      0.13     321     365 ..     156     200 ..     139     204 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00026
                            AAA_15 25 ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleife 69
                                        ++ G+N++GK+++l  l+  l+++ + n   ++i ++ ++ ++
  gi|298675774|ref|YP_003727524.1| 34 KITIMGPNGAGKTTLLLHLNGTLKTSNSDN---VYIFEQAISSMN 75
                                      7899***************99999996666...222222222222 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00019
                            AAA_15 321 eeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                       + +++il+++EP a+L p+ ++++i  +kel +++   +ii TH 
  gi|298675774|ref|YP_003727524.1| 156 SMEPKILVLDEPTANLDPKSKSEIISFIKELNEKEGITTIIATHD 200
                                       55789******************************99*******6 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.1   2.4e-07   0.00016      23     167 ..      36     191 ..      23     302 .. 0.61

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.4e-07
                            AAA_23  23 lItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayveltfenkdgry............. 86 
                                        I GpNGaGKTT+l  +   L        ++++  ++++ ++  + ++  +yv + fe+ d++              
  gi|298675774|ref|YP_003727524.1|  36 TIMGPNGAGKTTLLLHLNGTLKTS-----NSDNVYIFEQAISSMNIKDRIQYVGILFEDPDDQLfmptvyddvafgp 107
                                       699***********9999999774.....3445578888888888889999*******9999877777777665554 PP

                            AAA_23  87 ......................trsiererelskkkgkttkkaklelleideleqfisellgskkiilnlilflgqe 141
                                                                                         +  e++++++l+            gq+
  gi|298675774|ref|YP_003727524.1| 108 ynmgldkkevdkrvkksmtrvgL---------------------------QGFENEVPQHLS-----------TGQK 146
                                       44444433332222222222220...........................222222222222...........1111 PP

                            AAA_23 142 r...................feefelkdkkerleelekeleeled 167
                                       +                      +++ + k+++ +++kel+e+e 
  gi|298675774|ref|YP_003727524.1| 147 KkvalaavismepkilvldePTANLDPKSKSEIISFIKELNEKEG 191
                                       111111111111111222211112223333344444444444444 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.1    0.0063       4.2      21      36 ..      37      52 ..      31      80 .. 0.82
   2 !   12.1   0.0   8.5e-05     0.056     497     580 ..     138     210 ..     106     222 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0063
                            AAA_13 21 iYGwNGaGKTtLSrll 36
                                      i G NGaGKTtL   l
  gi|298675774|ref|YP_003727524.1| 37 IMGPNGAGKTTLLLHL 52
                                      78*********96555 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 8.5e-05
                            AAA_13 497 aetLSeGEktaIaflYFlkslkeddseigkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnlef 573
                                        ++LS+G k  +a+    + ++     + + ki v+D P   LD +s   ++s+ik+   +k+ +   +i TH ++ 
  gi|298675774|ref|YP_003727524.1| 138 PQHLSTGQKKKVALA---AVIS-----M-EPKILVLDEPTANLDPKSKSEIISFIKELN-EKEGIT-TIIATHDVNT 203
                                       466666666666653...3333.....4.899*************************97.666666.5799***998 PP

                            AAA_13 574 fkevkkn 580
                                         +++++
  gi|298675774|ref|YP_003727524.1| 204 ISYLTDR 210
                                       8888765 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   4.5e-05      0.03      30      53 ..      29      52 ..       1      69 [. 0.77
   2 ?   -0.6   0.0       1.3   8.3e+02     133     185 ..     151     196 ..     113     201 .. 0.66
   3 ?   -0.3   0.0         1   6.9e+02     117     142 ..     255     281 ..     235     286 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.5e-05
                            AAA_25 30 lpagelallaGapgtGKttlaldl 53
                                      + +ge + ++G+ g+GKttl+l+l
  gi|298675774|ref|YP_003727524.1| 29 VFEGEKITIMGPNGAGKTTLLLHL 52
                                      358*******************98 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.3
                            AAA_25 133 leaaieevegvrlvviDplsralggdensnsdvgalvealeriarrtgaavll 185
                                       l+a+i   e ++ +v+D    + + d++s+s++ ++++ l++   + g+++++
  gi|298675774|ref|YP_003727524.1| 151 LAAVISM-E-PKILVLDEP--TANLDPKSKSEIISFIKELNE---KEGITTII 196
                                       4444444.4.888888854..445577777777777777666...44555554 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1
                            AAA_25 117 fakdrggtl.ltadvdaleaaieeveg 142
                                        ++ ++++l ++++ ++l++a++e  +
  gi|298675774|ref|YP_003727524.1| 255 GYDSKNHPLsINEAAENLINAMQENGD 281
                                       46677777779***********99544 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.1e-05     0.014       8     123 ..      35     192 ..      30     204 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.1e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka.............. 70 
                                       ++++G+ G+GKTtll  l  +l+      + +  ++f ++ ss++ kd  + +   ++++ +               
  gi|298675774|ref|YP_003727524.1|  35 ITIMGPNGAGKTTLLLHLNGTLKTS----NSDNVYIFEQAISSMNIKDRIQYVGILFEDPDDQlfmptvyddvafgp 107
                                       789******************9543....234444477777888999998888888888887788888888888888 PP

                            AAA_22  71 ..........................erlsseell.ealeqalrarav...ielliiDEaqh.lr..s.eealeeLr 113
                                                                 e+   ++l   +  + + a+     +++l++DE    l+  s  e++++++
  gi|298675774|ref|YP_003727524.1| 108 ynmgldkkevdkrvkksmtrvglqgfENEVPQHLStGQKKKVALAAVIsmePKILVLDEPTAnLDpkSkSEIISFIK 184
                                       88777777777777777755555555333333433333333333333366777888887666576652466666666 PP

                            AAA_22 114 sllnlsrkgv 123
                                       +l +  + g+
  gi|298675774|ref|YP_003727524.1| 185 ELNE--KEGI 192
                                       6666..5555 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.1e-05    0.0073     102     166 ..       5      70 ..       1      83 [. 0.87

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.1e-05
                             T2SSE 102 eltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinks.derivtvEDp 166
                                       ++++++l ++  +++k+ + ++  v e   i + G+ g GKttll  l  ++++s ++++ + E +
  gi|298675774|ref|YP_003727524.1|   5 AVSIKNLDYTYPNSKKVLDNVNMEVFEGEKITIMGPNGAGKTTLLLHLNGTLKTSnSDNVYIFEQA 70 
                                       67899999999999*******************************999999998866788777765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   2.7e-05     0.018       3      25 ..      33      54 ..      31      79 .. 0.87
   2 ?   -2.3   0.0       4.5     3e+03     117     169 ..     185     213 ..     174     227 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.7e-05
                            AAA_24  3 lkiliyGpsgiGKTtlakelgpk 25
                                       ki i+Gp+g+GKTtl+++l + 
  gi|298675774|ref|YP_003727524.1| 33 EKITIMGPNGAGKTTLLLHL-NG 54
                                      69***************999.44 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.5
                            AAA_24 117 klqelrknvifiahektrkdedpegeakytrlepklgkktanelkeevDlvlr 169
                                        l+e                          ++++ +   + n + +  D v  
  gi|298675774|ref|YP_003727524.1| 185 ELNEK------------------------EGITTIIATHDVNTISYLTDRVYV 213
                                       33333........................345555555555555555555555 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   2.2e-05     0.015      23      65 ..      35      76 ..      25     214 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.2e-05
                          ATPase_2 23 yfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskl 65
                                      + i Gp g GKt+Ll ++   l+ ++ + +y+++   +s  ++
  gi|298675774|ref|YP_003727524.1| 35 ITIMGPNGAGKTTLLLHLNGTLKTSNSDNVYIFEQAISSM-NI 76
                                      6799******************999999999987543333.33 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0       0.2   1.3e+02      37      54 ..      34      51 ..      14      70 .. 0.82
   2 ?   11.2   0.0   0.00027      0.18      92     159 ..     131     196 ..     119     207 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.2
                              TniB 37 nlllvGdsnnGKtmivek 54
                                      ++ ++G+   GKt+++ +
  gi|298675774|ref|YP_003727524.1| 34 KITIMGPNGAGKTTLLLH 51
                                      688***********9865 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00027
                              TniB  92 ealgaplkararvskleqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivl 159
                                       + ++ ++ ++ ++ ++++ +l+   ++++++L++DE    l    +++ e++ ++k L+++  i+ ++
  gi|298675774|ref|YP_003727524.1| 131 QGFENEVPQHLSTGQKKKVALAAVISMEPKILVLDEPTANL--DPKSKSEIISFIKELNEKEGITTII 196
                                       556666777778889999999999************99888..88999************99998775 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   9.1e-05      0.06       3      29 ..      35      64 ..      33      81 .. 0.72
   2 ?   -0.5   0.0       1.2   8.1e+02      85     124 ..     161     204 ..     129     227 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.1e-05
                                      EEEEESTTCCHHHHHHHHH...CT--SS-E CS
                              cobW  3 tvltGflGsGKTtLlnhll...enraglkl 29
                                      + + G+ G+GKTtLl hl    + +++ ++
  gi|298675774|ref|YP_003727524.1| 35 ITIMGPNGAGKTTLLLHLNgtlKTSNSDNV 64
                                      5799***********998765555555555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.2
                                       EEEE.EECTTTTHHHH..HTT.SHHHHHCCCECEEEEEEETTTH CS
                              cobW  85 vili.EttGlaePapv..aft.eeelksdltldavvavvDaknl 124
                                       ++++ E t +++P+    +++  +el+++  +++++a  D++ +
  gi|298675774|ref|YP_003727524.1| 161 ILVLdEPTANLDPKSKseIISfIKELNEKEGITTIIATHDVNTI 204
                                       34333677788888776533358888899999999998888766 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.3e-05     0.022       4      48 ..      21      69 ..      18     198 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.3e-05
                                      HHHHH.S-EBTT-EEEEEESTTSSHHHHH...HHHHHHSSTSSEEEEEE CS
                                      xxxxx.xxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  4 vlDal.fpivqGqrtlipgafgvGktvis...qslskqsnsddaiiyvg 48
                                      vlD + + + +G+++ i+g +g Gkt+++   +  +k snsd++ i+  
  gi|298675774|ref|YP_003727524.1| 21 VLDNVnMEVFEGEKITIMGPNGAGKTTLLlhlNGTLKTSNSDNVYIFEQ 69
                                      66655256889*****************977777789999997777654 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.4e-05     0.036      88     125 ..      20      58 ..       4      66 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.4e-05
                                       TTHHHHH.HHCTTSEEEEECSTTSSHHHHHHHHCTT--- CS
                       RsgA_GTPase  88 egleelk.ellkdktsvlvGqSGvGKStLinallpelel 125
                                       + l++++ e+++++ ++++G+ G+GK+tL+ +l+++l++
  gi|298675774|ref|YP_003727524.1|  20 KVLDNVNmEVFEGEKITIMGPNGAGKTTLLLHLNGTLKT 58 
                                       55555551456669999****************998654 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   6.5e-05     0.043      16      39 ..      26      49 ..      20      53 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.5e-05
                            AAA_29 16 tieidlkgatlltGpsGsGKSTll 39
                                       +e+ + + + ++Gp+G+GK+Tll
  gi|298675774|ref|YP_003727524.1| 26 NMEVFEGEKITIMGPNGAGKTTLL 49
                                      55555444899***********98 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   7.2e-05     0.048       3      32 ..      35      64 ..      33      90 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.2e-05
                                      EEEEC-TTTCHHHHHHHHHHHHCTS-SCCC CS
                             NACHT  3 vilqGeaGsGKTtLlqklalawaegklpqg 32
                                      + + G++G GKTtLl +l  ++++++ +++
  gi|298675774|ref|YP_003727524.1| 35 ITIMGPNGAGKTTLLLHLNGTLKTSNSDNV 64
                                      6799******************99997774 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.5   0.00059      0.39       3     116 ..      37     205 ..      35     219 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00059
                                       EESSTTSSHHHHHHHHHHHHT......HEEEEEETTTCSSS.................................... CS
                               AAA   3 lyGppGtGKTllakavakelg......vefleisgsellsk.................................... 37 
                                       ++Gp G GKT+l   +  +l+      v+++e   s++  k                                    
  gi|298675774|ref|YP_003727524.1|  37 IMGPNGAGKTTLLLHLNGTLKtsnsdnVYIFEQAISSMNIKdriqyvgilfedpddqlfmptvyddvafgpynmgld 113
                                       78*****************9533344466777777777644477788888888888888888888888888888888 PP

                                       ...................STTHHHHHHHHHHHHHHHTS.........TSEEEEEETGGGHHHHHTTCCCHHHHHHH CS
                               AAA  38 ...................yvgesekkirelfkeakeka.........kpsilfiDEidalaksrsgseseeeervv 86 
                                                          +  e +++++   k    k+         +p+il++DE  a    +            
  gi|298675774|ref|YP_003727524.1| 114 kkevdkrvkksmtrvglqgFENEVPQHLSTGQK----KKvalaavismEPKILVLDEPTANLDPK----------SK 176
                                       888888888888888655533333333333333....2233446666779999999988776655..........47 PP

                                       HHHHHHHHHTTTSSSTEEEEEEESSGGGST CS
                               AAA  87 nqLlteldgvkkkeskvivigatnrpdkld 116
                                       ++++++++++++ke+ ++ i+at+++++++
  gi|298675774|ref|YP_003727524.1| 177 SEIISFIKELNEKEG-ITTIIATHDVNTIS 205
                                       888888888888655.99999999988876 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00049      0.32       5      36 ..      35      66 ..      31      98 .. 0.74
   2 ?   -1.6   0.0       3.9   2.6e+03      64      87 ..     158     187 ..     131     199 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00049
                            AAA_14  5 lvitGaRrvGKTtllkqlikellvkkesilyi 36
                                      ++i+G+  +GKTtll +l  +l +++++ +yi
  gi|298675774|ref|YP_003727524.1| 35 ITIMGPNGAGKTTLLLHLNGTLKTSNSDNVYI 66
                                      78***************987777555555555 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.9
                            AAA_14  64 kktylflDEiqev......pewekalkslv 87 
                                       + ++l+lDE          +e+ +++k+l 
  gi|298675774|ref|YP_003727524.1| 158 EPKILVLDEPTANldpkskSEIISFIKELN 187
                                       567777887554444444444444555544 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00063      0.42       1      23 [.      35      57 ..      35      89 .. 0.72
   2 ?   -1.4   0.0       4.9   3.3e+03      16      88 ..     184     205 ..     138     244 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00063
                            AAA_18  1 IlltGtpGvGKttlakeLskrlg 23
                                      I ++G+ G+GKttl  +L+  l+
  gi|298675774|ref|YP_003727524.1| 35 ITIMGPNGAGKTTLLLHLNGTLK 57
                                      89*************99965553 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.9
                            AAA_18  16 keLskrlgfgvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknlvidghlaeles 88 
                                       keL++++g+                                                   + +i  h ++ +s
  gi|298675774|ref|YP_003727524.1| 184 KELNEKEGI---------------------------------------------------TTIIATHDVNTIS 205
                                       333333333...................................................2233333333333 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00032      0.21      32      82 ..      31      80 ..      20      83 .. 0.84
   2 ?   -2.1   0.0       3.5   2.3e+03      12      36 ..     194     218 ..     172     223 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00032
                             AAA_7 32 nkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdii 82
                                      ++ ++ ++Gp G GKt+++ +l  +l+ ++ + ++  f +  s+++++d i
  gi|298675774|ref|YP_003727524.1| 31 EGEKITIMGPNGAGKTTLLLHLNGTLK-TSNSDNVYIFEQAISSMNIKDRI 80
                                      6778999**************999999.66667777799999999998877 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.5
                             AAA_7  12 ilVptvdtvrysyllelllknkkpv 36 
                                       +++ t d   +syl++ +   + ++
  gi|298675774|ref|YP_003727524.1| 194 TIIATHDVNTISYLTDRVYVLNEKI 218
                                       5677777777777777766655555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00025      0.17       1      21 [.      34      54 ..      34      74 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00025
                            AAA_28  1 kivitGgestGKTtlleaLaa 21
                                      ki i+G+ ++GKTtll +L+ 
  gi|298675774|ref|YP_003727524.1| 34 KITIMGPNGAGKTTLLLHLNG 54
                                      699*************99984 PP

>> BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0    0.0002      0.13       1      16 [.     217     232 ..     217     232 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0002
                      BCA_ABC_TP_C   1 rvIAeGtPaEvrndPr 16 
                                       ++ A+GtP ++ ++P+
  gi|298675774|ref|YP_003727524.1| 217 KIVASGTPHDIFSNPE 232
                                       689************6 PP

>> YqzH  YqzH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       3.5   2.3e+03       2      17 ..     113     128 ..     112     134 .. 0.81
   2 ?   11.2   0.2   0.00045       0.3       9      58 ..     246     299 ..     245     304 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3.5
                              YqzH   2 dekfieKmirkclrqY 17 
                                       d+k ++K ++k++ + 
  gi|298675774|ref|YP_003727524.1| 113 DKKEVDKRVKKSMTRV 128
                                       7888999999998765 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00045
                              YqzH   9 mirkclrqYgrdtelmplseeeq.keLveriqek...kkeqedeDlyeiveDiv 58 
                                       +i + l+ +g+d +  pls +e  ++L++++qe+    + q d D ye ++  v
  gi|298675774|ref|YP_003727524.1| 246 KIFRMLECFGYDSKNHPLSINEAaENLINAMQENgdvMNLQMDKDAYENIKQLV 299
                                       57789**************9885388******9744468899******998776 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00049      0.33       1      27 [.      34      60 ..      34      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00049
                                      EEEEE--TTSSHHHHHHHHHHHH...G CS
                          NTPase_1  1 kvfiTGppGvGKtTlvkkvlellkssg 27
                                      k+ i Gp G GKtTl+  +  +lk s+
  gi|298675774|ref|YP_003727524.1| 34 KITIMGPNGAGKTTLLLHLNGTLKTSN 60
                                      58899***************9999887 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00078      0.52       4      30 ..      35      61 ..      33      68 .. 0.82
   2 ?   -0.8   0.0       1.5     1e+03     121     148 ..     171     198 ..     145     201 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00078
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS CS
                             SRP54  4 illvGlqGaGKTttlaKLaallkkegk 30
                                      i ++G++GaGKTt l  L   lk+++ 
  gi|298675774|ref|YP_003727524.1| 35 ITIMGPNGAGKTTLLLHLNGTLKTSNS 61
                                      7799***********999999888754 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.5
                                       EETTBHTHHHHHHHHHHHHSSCSEEEEE CS
                             SRP54 121 ldattgqeavkqakaFkeavgitgvilt 148
                                       ld  +++e ++ +k+ +e+ git++i t
  gi|298675774|ref|YP_003727524.1| 171 LDPKSKSEIISFIKELNEKEGITTIIAT 198
                                       4556677888889999999999999987 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00049      0.33      22      52 ..      32      62 ..      19     107 .. 0.72
   2 ?   -2.0   0.0       6.1   4.1e+03      56      71 ..     195     208 ..     176     279 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00049
                            AAA_16 22 grpelvllsGesGvGKsslvrellralekd..g 52
                                      g  e + + G+ G GK++l+ +l   l+++  +
  gi|298675774|ref|YP_003727524.1| 32 G--EKITIMGPNGAGKTTLLLHLNGTLKTSnsD 62
                                      4..45789************9998877777442 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 6.1
                            AAA_16  56 lrgkcdqlesaipysa 71 
                                       + ++ d +   i+y++
  gi|298675774|ref|YP_003727524.1| 195 IIATHDVN--TISYLT 208
                                       44444444..333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       862  (0.0480785); expected 358.6 (0.02)
Passed bias filter:                      662  (0.0369234); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.49
# Mc/sec: 1888.94
//
Query:       gi|298675775|ref|YP_003727525.1|  [L=361]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.1e-25   87.2   2.3    3.6e-24   84.5   1.0    2.7  3  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    1.6e-09   38.1   1.3    1.6e-09   38.1   1.3    1.7  2  OrfB_IS605      Probable transposase
  ------ inclusion threshold ------
      0.019   15.0   0.1      0.032   14.2   0.1    1.4  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.045   13.4   6.1       0.15   11.8   6.1    1.9  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
       0.14   11.7   0.2        0.3   10.6   0.2    1.5  1  TF_Zn_Ribbon    TFIIB zinc-binding
       0.68    9.9   4.1        9.9    6.2   1.2    2.4  2  zinc_ribbon_4   zinc-ribbon domain
        1.6    8.8   5.3        3.5    7.7   5.3    1.6  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
        2.9    7.7   5.6        8.9    6.1   0.4    2.4  2  Rubredoxin_2    Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.53   1.2e+03       7      30 ..     160     183 ..     158     198 .. 0.80
   2 ?   -0.3   0.0      0.46     1e+03      15      29 ..     187     201 ..     181     206 .. 0.85
   3 !   84.5   1.0   1.6e-27   3.6e-24       1      69 []     277     346 ..     277     346 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.53
                    OrfB_Zn_ribbon   7 qleykakeyGikveevnpayTSkt 30 
                                        +ey     G+ + +vn a TS +
  gi|298675775|ref|YP_003727525.1| 160 EVEYNDDVMGVDLGVVNIATTSNN 183
                                       678888889999999999999975 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.46
                    OrfB_Zn_ribbon  15 yGikveevnpayTSk 29 
                                       +G k  e+ ++yTS 
  gi|298675775|ref|YP_003727525.1| 187 KGTKADEIRERYTSL 201
                                       589999*******96 PP

  == domain 3  score: 84.5 bits;  conditional E-value: 1.6e-27
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f++l+ ++ yk k +G++v+ +np yTS++CseCg++nk  ++++ +f+C+ Cg++ ++D+nA+ Ni++r
  gi|298675775|ref|YP_003727525.1| 277 FSELTDFILYKSKLEGVPVIIINPMYTSQQCSECGHINKSnRQKQANFRCKTCGHRENADYNASKNIAHR 346
                                       899*************************************9**************************997 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   1.3   6.9e-13   1.6e-09       4     106 ..     154     246 ..     151     256 .. 0.87
   2 ?   -3.7   0.1         6   1.3e+04      41      66 ..     314     339 ..     308     346 .. 0.61

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 6.9e-13
                        OrfB_IS605   4 vevevelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarl 80 
                                       +ev++  +++ +  + g+DlG+ n+at+++++    +ykg ++++  ++++  + +lqs    s     a++ l++l
  gi|298675775|ref|YP_003727525.1| 154 MEVGE-NEVEYNDDVMGVDLGVVNIATTSNNE----VYKGTKADEIRERYTSLKSRLQSAGTWS-----AKEHLKKL 220
                                       56665.6677778899****************....***********************95555.....7999**** PP

                        OrfB_IS605  81 hrkrsrrrkhllhklathliktlkev 106
                                       ++k +r+ ++l h +a++l+k+ k++
  gi|298675775|ref|YP_003727525.1| 221 SKKERRFKRDLNHRVAKQLVKRAKDT 246
                                       ********************998765 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 6
                        OrfB_IS605  41 ykgrrlksdykylakeiaelqsklkk 66 
                                       +k++r k+++++ + +  +    ++ 
  gi|298675775|ref|YP_003727525.1| 314 NKSNRQKQANFRCKTCGHRENADYNA 339
                                       56666666666666655555555555 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.4e-05     0.032      63      96 ..     291     333 ..     235     343 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.4e-05
                                       E......EEEE--EEEETTTS-EEECHH..H.HHS-TTTSSS- CS
                              HypA  63 e......ieevpvkvrCreCgkefelee..k.alrCpkCgsad 96 
                                       e      i+ +  + +C+eCg+  ++++  + ++rC++Cg+++
  gi|298675775|ref|YP_003727525.1| 291 EgvpviiINPMYTSQQCSECGHINKSNRqkQaNFRCKTCGHRE 333
                                       3444434777788999*****9988665333788******874 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   6.1   6.5e-05      0.15       3      26 ..     307     332 ..     306     333 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.5e-05
                                       -SSS--B--..--SSS----SSS--- CS
                    DNA_RNApol_7kD   3 CgeCgaevs..lkkgdpiRCkeCGhR 26 
                                       C eCg+ ++   +k++  RCk+CGhR
  gi|298675775|ref|YP_003727525.1| 307 CSECGHINKsnRQKQANFRCKTCGHR 332
                                       99**9977755788899********9 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   0.00013       0.3       2      27 ..     306     331 ..     305     344 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00013
                                       EETTTTCEECHEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon   2 kCPnCgstnlveDpergelvCtdCGl 27 
                                       +C +Cg+ n  +  ++++++C+ CG 
  gi|298675775|ref|YP_003727525.1| 306 QCSECGHINKSNRQKQANFRCKTCGH 331
                                       8******776899************7 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.021        47      27      34 ..     306     313 ..     298     313 .. 0.85
   2 ?    6.2   1.2    0.0044       9.9      20      33 ..     318     331 ..     314     332 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.021
                     zinc_ribbon_4  27 rCskCghv 34 
                                       +Cs Cgh+
  gi|298675775|ref|YP_003727525.1| 306 QCSECGHI 313
                                       8******6 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0044
                     zinc_ribbon_4  20 pakgvkvrCskCgh 33 
                                       ++k ++ rC+ Cgh
  gi|298675775|ref|YP_003727525.1| 318 RQKQANFRCKTCGH 331
                                       5788999******9 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   5.3    0.0015       3.5      19      45 ..     305     331 ..     301     332 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0015
                     Zn_Tnp_IS1595  19 fvCPhCgsr.kayriktrglfqCkeCrk 45 
                                       + C  Cg+  k+ r k+   f+Ck C++
  gi|298675775|ref|YP_003727525.1| 305 QQCSECGHInKSNRQKQ-ANFRCKTCGH 331
                                       57*****9999999998.********98 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.7     0.025        56       2       8 ..     306     312 ..     306     316 .. 0.82
   2 ?    6.1   0.4     0.004       8.9       1      10 [.     324     333 ..     324     335 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.025
                      Rubredoxin_2   2 vCsqCGf 8  
                                       +Cs+CG+
  gi|298675775|ref|YP_003727525.1| 306 QCSECGH 312
                                       6999998 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.004
                      Rubredoxin_2   1 YvCsqCGfes 10 
                                       ++C+ CG++ 
  gi|298675775|ref|YP_003727525.1| 324 FRCKTCGHRE 333
                                       8******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1042  (0.0581181); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2467.96
//
Query:       gi|298675776|ref|YP_003727526.1|  [L=289]
Description: hypothetical protein Metev_1899 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       998  (0.055664); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 1964.27
//
Query:       gi|298675777|ref|YP_003727527.1|  [L=119]
Description: hypothetical protein Metev_1900 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-08   33.3   0.3    5.6e-08   32.8   0.3    1.2  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
    1.7e-06   27.8   0.1    2.9e-06   27.1   0.1    1.3  1  MarR            MarR family
    0.00041   20.2   0.0    0.00059   19.7   0.0    1.3  1  MarR_2          MarR family
    0.00075   19.0   0.1     0.0011   18.5   0.1    1.2  1  HTH_24          Winged helix-turn-helix DNA-binding
     0.0076   16.1   0.0      0.011   15.6   0.0    1.3  1  TrmB            Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.013   16.0   0.0      0.017   15.6   0.0    1.3  1  HTH_27          Winged helix DNA-binding domain
        0.1   12.0   1.0       0.57    9.5   0.0    1.9  2  RNA_pol_Rpc34   RNA polymerase Rpc34 subunit


Domain annotation for each model (and alignments):
>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.3   2.2e-11   5.6e-08      16      67 ..      15      62 ..       6      64 .. 0.94

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 2.2e-11
                    B-block_TFIIIC 16 ysGitqsdLakeskqdprslfyrlksLekkgLIvkqsiidsatkksistsll 67
                                       +Gi q++L+ke+++d+r+   ++ +L kkgLI + s+    t k+ +t+ll
  gi|298675777|ref|YP_003727527.1| 15 PEGIYQNQLWKEMNIDSRKCSRIVSKLLKKGLIIRESA----TSKGSRTYLL 62
                                      58************************************....99*9999998 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.1   1.1e-09   2.9e-06       7      51 ..       6      51 ..       2      54 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1.1e-09
                                      HHHHHHHHSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR  7 viLrilyeqgp.lsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                      ++L  ++e+++ +++ +L+k +++++   +r++ +L kkGli R+ 
  gi|298675777|ref|YP_003727527.1|  6 LALKVIKEHPEgIYQNQLWKEMNIDSRKCSRIVSKLLKKGLIIRES 51
                                      578999***999*******************************986 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   2.3e-07   0.00059      10      56 ..       7      52 ..       3      59 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.3e-07
                                      HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                      +L ++  +p++ + +++l ++++++    sri+ +L ++GL+ r+++
  gi|298675777|ref|YP_003727527.1|  7 ALKVIKEHPEG-IYQNQLWKEMNIDSRKCSRIVSKLLKKGLIIRESA 52
                                      67789999987.99****************************99854 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   4.4e-07    0.0011       9      47 ..       8      47 ..       6      48 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4.4e-07
                            HTH_24  9 LelLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      L++++++p  i q++L ++ ++ +  ++r + +L ++GlI
  gi|298675777|ref|YP_003727527.1|  8 LKVIKEHPEgIYQNQLWKEMNIDSRKCSRIVSKLLKKGLI 47
                                      789999999999***************************9 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   4.4e-06     0.011      27      58 ..      22      53 ..      15      69 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.4e-06
                                      HHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 27 eiaeelgvprskvYevLrsLedkGlVerekgr 58
                                      ++ +e +++  k+ +++++L++kGl+ re  +
  gi|298675777|ref|YP_003727527.1| 22 QLWKEMNIDSRKCSRIVSKLLKKGLIIRESAT 53
                                      567899**********************9876 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.0   6.8e-06     0.017      10      62 ..       9      60 ..       2      67 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.8e-06
                            HTH_27 10 hlirhrrrrkkl.adlcgrlnvedshisyslkkLtekGLv.ertgdeadrrekrv 62
                                       +i+ ++ + +   +l + +n+++   s +++kL +kGL+    +++++++++++
  gi|298675777|ref|YP_003727527.1|  9 KVIK-EHPEGIYqNQLWKEMNIDSRKCSRIVSKLLKKGLIiR--ESATSKGSRTY 60
                                      5555.44444545788999*********************42..34455666554 PP

>> RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00022      0.57      20      81 ..      11      71 ..       3      81 .. 0.77
   2 ?    1.5   0.2     0.061   1.6e+02     322     335 ..      90     103 ..      73     104 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00022
                                      HCSSSSSHCCHHHHHHHSTTSHHHHHHHHHHHHHHCTSEECCC..STTSCECEE--CCCHHHH CS
                     RNA_pol_Rpc34 20 rkaseqklfsqqdLqddipslslklllsavqeLldkkllvllk.nsndeLvyravsreeAkkk 81
                                      +k+ ++++++q++L ++  +++ ++  ++v +Ll+k+l+      s+++  y  +s ee k +
  gi|298675777|ref|YP_003727527.1| 11 IKE-HPEGIYQNQLWKE-MNIDSRKCSRIVSKLLKKGLIIRESaTSKGSRTYLLKSAEEPKPS 71
                                      444.7999999999999.7899999999*******9998766655666668888888887765 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.061
                                       SSSSSSTTSSSSXX CS
                     RNA_pol_Rpc34 322 avspkncvYlkeWl 335
                                       a +p+ c+Yl+eW 
  gi|298675777|ref|YP_003727527.1|  90 ACEPEYCEYLTEWI 103
                                       6789*********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 788.23
//
Query:       gi|298675778|ref|YP_003727528.1|  [L=74]
Description: Sm ribonucleoprotein-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-18   64.6   0.3    5.1e-18   64.5   0.3    1.0  1  LSM       LSM domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.5   0.3   2.9e-22   5.1e-18       2      66 ..       6      70 ..       5      71 .. 0.96

  Alignments for each domain:
  == domain 1  score: 64.5 bits;  conditional E-value: 2.9e-22
                                      HHHHTTTSEEEEEETTS.EEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEE CS
                               LSM  2 flkklinkkvtvelkng.relrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivlis 66
                                      +++kl+++kv+ve+k++ ++l+G+L+++D+++Nl+L + +e+ +++ + r+lg v++RGnnivl+ 
  gi|298675778|ref|YP_003727528.1|  6 KVHKLLGSKVQVEMKGDlHQLEGVLESVDDYLNLHLVESVEIANGE-RLRSLGSVVLRGNNIVLLA 70
                                      6799*************9***************************9.****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 509.96
//
Query:       gi|298675779|ref|YP_003727529.1|  [L=120]
Description: hypothetical protein Metev_1902 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.8e-16   57.7   0.0    1.3e-15   57.4   0.0    1.1  1  DUF3467   Protein of unknown function (DUF3467)
  ------ inclusion threshold ------
       0.16   12.0   0.0       0.29   11.1   0.0    1.3  1  Sdh5      Flavinator of succinate dehydrogenase


Domain annotation for each model (and alignments):
>> DUF3467  Protein of unknown function (DUF3467)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.0   1.4e-19   1.3e-15       5      90 ..       4      97 ..       1      98 [. 0.84

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 1.4e-19
                           DUF3467  5 ekaagkkiralrie.vdesvaggsYsngaivmtspsEfiidF....lqlvpgrpearvksr.....vvlspaaakqlva 73
                                      ++++gk  +++ +e  + +++++ Y++ga   +sp++f+i F     + + +++ +rv++r     v+lsp aa +l +
  gi|298675779|ref|YP_003727529.1|  4 DNNEGK--KKVTVEfKKAEDFKQAYAIGAVGGHSPYDFRIGFyndsQKGFGQQSDSRVIERtleteVILSPMAAYELSK 80
                                      333444..46999955569***********************777555775555679999999999************* PP

                           DUF3467 74 aLqknldlyetrfGeik 90
                                      +L++++++ye+ fG+i 
  gi|298675779|ref|YP_003727529.1| 81 WLNQHIQEYENLFGPIS 97
                                      **************996 PP

>> Sdh5  Flavinator of succinate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   3.3e-05      0.29      13      43 ..      63      93 ..      62      94 .. 0.96

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.3e-05
                                      SHHHHHTTTTHHHHHTTT--HHHHHHHHHHH CS
                              Sdh5 13 mlElDllLgrFaekhlatlseeeldaferLL 43
                                      +lE++++L++ a+ +l+++ ++ ++++e+L 
  gi|298675779|ref|YP_003727529.1| 63 TLETEVILSPMAAYELSKWLNQHIQEYENLF 93
                                      69**************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       880  (0.0490825); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 781.86
//
Query:       gi|298675780|ref|YP_003727530.1|  [L=827]
Description: DEAD/DEAH box helicase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.9e-23   81.1   0.0      2e-22   79.8   0.0    1.7  1  DEAD        DEAD/DEAH box helicase
    1.5e-13   51.0   0.0    5.6e-13   49.2   0.0    2.1  1  Helicase_C  Helicase conserved C-terminal domain
    8.6e-12   45.4   0.1      2e-11   44.2   0.1    1.7  1  ResIII      Type III restriction enzyme, res subunit
    0.00087   18.1   0.0     0.0012   17.6   0.0    1.2  1  SNF2_N      SNF2 family N-terminal domain
  ------ inclusion threshold ------
      0.036   13.0   0.0      0.063   12.2   0.0    1.4  1  AAA_34      P-loop containing NTP hydrolase pore-1


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.8   0.0   5.6e-26     2e-22       2     170 ..     220     385 ..     219     389 .. 0.83

  Alignments for each domain:
  == domain 1  score: 79.8 bits;  conditional E-value: 5.6e-26
                                       HHHHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSE CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   2 diQaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlr 77 
                                       ++Q+ +++  l +g++ lv  +T++GKTl+  ++ +++v++    ++ k+l+++P+ +La+q +++++k  ++++++
  gi|298675780|ref|YP_003727530.1| 220 PVQSLSVQKGLlDGNNQLVMSATATGKTLIGELAGINNVLN----KRGKMLFLVPLVALANQKYDQFTKNYSHLGIK 292
                                       678888877666999************************64....5669***********************99988 PP

                                       EEEEETTSSHHHHHHHH.HTT..CSEEEEEHHHHHHHHHCTSSH.CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSH CS
                                       xxxxxxxxxxxxxxxxx.xxx..xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  78 vlliiggvaardqlskl.dng..vdivvgtpgrlddllstgkln.lsqvrflVlDEadrlldqgfsdfinrilnqlp 150
                                       ++  +g+++ +  +++  + +   di+vgt + ld +l+tg  + l ++ ++V+DE+++l d +++  i+ ++++l+
  gi|298675780|ref|YP_003727530.1| 293 TSIRVGSSRIKTSKTASmRTTldSDIIVGTYEGLDYVLRTGDADkLGNIGTVVIDEVHMLEDAERGHRIDGLISRLK 369
                                       88777755553333333133356***************9998777*******************************5 PP

                                       HHCTTSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                              DEAD 151 qitcdgklqrqvivlSATlp 170
                                        +    + + q+i lSAT+ 
  gi|298675780|ref|YP_003727530.1| 370 YTV---P-EAQFIYLSATVA 385
                                       433...3.345*******86 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.0   1.6e-16   5.6e-13      11     109 ..     436     535 ..     419     537 .. 0.80

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 1.6e-16
                                       HHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESE CS
                        Helicase_C  11 kleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnl 87 
                                       +++  +g+++if+n++++++    +     +++a++h+ l+  er++i ++f++ge   +++t +++ G+d+p ++ 
  gi|298675780|ref|YP_003727530.1| 436 SSKGYRGQSIIFTNSRKNCH---RISDALPMSSAAYHAGLTGYERKKIENKFQNGELPAVVTTAALAAGVDFP-ASQ 508
                                       678899*************5...443445899****************************************9.555 PP

                                       EEESSSS....SS.HHHHHHHHTTSSS CS
                        Helicase_C  88 Vinfdlp....rn.vtsyiqriGRtgR 109
                                       Vi+ +l     +  ++++ q+ GR+gR
  gi|298675780|ref|YP_003727530.1| 509 VIFESLAmgidWItMQEFLQMLGRAGR 535
                                       665555535544347************ PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.1   5.4e-15     2e-11      25     169 ..     234     384 ..     144     386 .. 0.80

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 5.4e-15
                                       SEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG........GEEEESSS-B-- CS
                            ResIII  25 krglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkflseayke....igkkvsgdkkka 96 
                                       ++ l+  aT tGKTl+  ++ i ++l+k++  k+lflvp  +l +q +++f+k +s    +    +     g ++++
  gi|298675780|ref|YP_003727530.1| 234 NNQLVMSATATGKTLIGeLAGINNVLNKRG--KMLFLVPLVALANQKYDQFTKNYSHLGIKtsirV-----GSSRIK 303
                                       4667888*********************99..*******************999987653333332.....222222 PP

                                       ............-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHH......HHT-.--SE CS
                            ResIII  97 .....kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswrei......lekf.keav 161
                                            +++ + +++i+v t++ ld  +    ++ +  + +++  ++iDE+H l +++   +i      l++  +ea 
  gi|298675780|ref|YP_003727530.1| 304 tsktaSMRTTLDSDIIVGTYEGLDYVL----RTGDADKLGNIGTVVIDEVHMLEDAERGHRIdglisrLKYTvPEAQ 376
                                       455557999******************....778888889999************9766666555555444337799 PP

                                       EEEEESS- CS
                            ResIII 162 llglTATp 169
                                        ++l+AT 
  gi|298675780|ref|YP_003727530.1| 377 FIYLSATV 384
                                       9*****97 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   3.5e-07    0.0012      98     192 ..     234     355 ..      42     372 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.5e-07
                                       -..............................EEEE--H.HHHHHHHHHHHHH-TTS-EEE--SSHHHH--------- CS
                                       x..............................xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N  98 p..............................tLivvPa.slldqWeneierhvsssalrvlvyggqkkmkkkntkva 143
                                                                      +L +vP  +l++q ++++ +  s   ++  +  g+++ k + ++ +
  gi|298675780|ref|YP_003727530.1| 234 NnqlvmsatatgktligelaginnvlnkrgkMLFLVPLvALANQKYDQFTKNYSHLGIKTSIRVGSSRIKTS-KTAS 309
                                       0555555555555555555555555555555999****9*****************9999999998877766.6667 PP

                                       --------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 144 pklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlkns 192
                                        ++  d d+++ tY+ l  +  +    ++l ++    vv+DE h+l+  
  gi|298675780|ref|YP_003727530.1| 310 MRTTLDSDIIVGTYEGLDYVL-RTGDADKLGNI--GTVVIDEVHMLEDA 355
                                       88889*************877.56667777765..68*********987 PP

>> AAA_34  P-loop containing NTP hydrolase pore-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.7e-05     0.063     174     222 ..     342     385 ..     243     405 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.7e-05
                            AAA_34 174 GvivfDEchkaknlakseekkatktgkavlelqkklpkArvvYvsaTga 222
                                       G +v DE h +++++        +    + +l+ ++p+A+++Y+saT a
  gi|298675780|ref|YP_003727530.1| 342 GTVVIDEVHMLEDAER-----GHRIDGLISRLKYTVPEAQFIYLSATVA 385
                                       89*********99985.....4678889*******************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (827 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       827  (0.0461264); expected 358.6 (0.02)
Passed bias filter:                      614  (0.0342462); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.74u 0.28s 00:00:01.02 Elapsed: 00:00:00.45
# Mc/sec: 5531.70
//
Query:       gi|298675781|ref|YP_003727531.1|  [L=250]
Description: hypothetical protein Metev_1904 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.7e-13   48.3   0.3    9.2e-13   48.1   0.3    1.1  1  ATPase    KaiC
     0.0014   17.8   0.0     0.0023   17.1   0.0    1.3  1  PAXNEB    PAXNEB protein


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.3     1e-16   9.2e-13       2     229 ..      20     246 ..      19     248 .. 0.84

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 1e-16
                            ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepa.....edlrenakslGwd 73 
                                       +tgI  lD+il gG+p g+ + i+ +p +    +++ Fl++      ++  + t++ ++       + + + +  ++
  gi|298675781|ref|YP_003727531.1|  20 QTGIFALDRILGGGLPAGSLTYISADPKS----MSEVFLYQFTLA--RKSYYFTTNRKPlyvhqDIINQGFDASNVN 90 
                                       69*************************87....666666666444..678899999999788734445668899999 PP

                            ATPase  74 lekleeegklaiidasesaeesaee.kdkedleelieelaeaikeika..krvviDsitgl.ayeekeavaReilrq 146
                                       + ++ +e  l+     ++++++  +  d++ +e    +l+++i++ k    +++iD+ t + + + + +++++i++q
  gi|298675781|ref|YP_003727531.1|  91 FIDIYSEYYLTSSGEISDNIGN--QyADTKIIEFTEYNLKNIINDAKNddVNIIIDNFTFFmNLNVNISLLKRIIHQ 165
                                       9999999666666666666653..2488888999999********99966789********888889999******* PP

                            ATPase 147 lvrvlkklgvTailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteeg 223
                                       l++  k+++  + l   k s++ +  ++++ + ++d ++ ++l+   +++   l++ k+Rg + +++++ f+I e+g
  gi|298675781|ref|YP_003727531.1| 166 LYESTKEIQSLTYLYGLKGSHS-EDIENDLFN-ASDVIFDIHLEHSVDKVNNKLSVPKIRGMTPKTEIIKFNIAEGG 240
                                       ********99999988866665.555677888.8*********9********************************* PP

                            ATPase 224 ikvlee 229
                                       i++  +
  gi|298675781|ref|YP_003727531.1| 241 IQIDTS 246
                                       **9765 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.6e-07    0.0023      17      48 ..      17      48 ..       9      61 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.6e-07
                            PAXNEB 17 lltStGtpsLDklLgGGLplGsillieEdgtt 48
                                       +  tG+  LD++LgGGLp Gs+  i +d ++
  gi|298675781|ref|YP_003727531.1| 17 SIKQTGIFALDRILGGGLPAGSLTYISADPKS 48
                                      56679*********************998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1788.07
//
Query:       gi|298675782|ref|YP_003727532.1|  [L=271]
Description: purine or other phosphorylase family 1 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.2e-33  114.3   0.0    5.8e-33  114.1   0.0    1.0  1  PNP_UDP_1  Phosphorylase superfamily


Domain annotation for each model (and alignments):
>> PNP_UDP_1  Phosphorylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.1   0.0   3.2e-37   5.8e-33      24     233 ..      40     251 ..      21     252 .. 0.90

  Alignments for each domain:
  == domain 1  score: 114.1 bits;  conditional E-value: 3.2e-37
                                       EEEEE.TTEEEEEEEE.TTEEEEEEE--.....SSHHHHHHHHHHHHHHHC--SEEEEEEEEEESSTTT-TT-EEEE CS
                         PNP_UDP_1  24 pfgregrgfkfvtGtl.kgkpvvivstG.....iGkpnaavvaeirllkefgvkaiiriGtaGglnpdlkvGDvvip 94 
                                       p+ +++   ++++G++  +   vi ++      + ++ ++++a+i ++ e+++++ii+++++G+++ ++ +G +++ 
  gi|298675782|ref|YP_003727532.1|  40 PVNTSFGKVDVYIGKIfDRNIAVIPRHSgeqnhVPPHRINYRANIQAVYELKAERIISVNSVGSMKDHI-PGSFILF 115
                                       4444455569******7777779999989************************************8777.******* PP

                                       EEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTTEEEEEEEEESESS-CHHHHHHHHHHTC-C CS
                         PNP_UDP_1  95 ddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealgikvhrGvvatadgfyaeteaelrllrrlgad 171
                                       dd+++f+  + +++++++   ++d++ + ++p++ ++l e++ ++g ++  Gv+a+++g+++et+ae+++l+ +  d
  gi|298675782|ref|YP_003727532.1| 116 DDFLDFTKHRISTFFDNK-TMHVDMSQP-YCPQIKKRLSESLVCRGLNYFGGVYACTEGPRFETKAEINMLSHFA-D 189
                                       *******99999999999.*********.*********************************************9.* PP

                                       EEESSHHHHHHHHHHTT--EEEEEEEEETTTBETTCTCH.HCCCHHHHHHHHHHHHHHHHHH CS
                         PNP_UDP_1 172 aveMEtaavaqlArelgipfaairvvsdlaaggadaeatheeveefaqeaaknaaalllall 233
                                        v+M+++++ +lA+el+i++a+i +v+++a g  ++  t++ev+++ + +++ +  ++   +
  gi|298675782|ref|YP_003727532.1| 190 FVGMTGVPEIILAKELDICYASIGLVTNYACGLSSERLTVDEVMDVVNDSRNLLYDVISDTI 251
                                       ************************************************99999888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1574.56
//
Query:       gi|298675783|ref|YP_003727533.1|  [L=376]
Description: hypothetical protein Metev_1906 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   6.8e-126  420.2   4.7   7.7e-126  420.1   4.7    1.0  1  DUF373    Domain of unknown function (DUF373)


Domain annotation for each model (and alignments):
>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  420.1   4.7  4.3e-130  7.7e-126       1     335 []       2     350 ..       2     350 .. 0.99

  Alignments for each domain:
  == domain 1  score: 420.1 bits;  conditional E-value: 4.3e-130
                            DUF373   1 ktLvlcvDrDdDlgrkagvktPvvGreavleaavklaladPeDSDvNalfgaikvydeLkaegedvevavvtGdekv 77 
                                       +tLv+c+DrD+Dlg+ka+++tPv+Gr+++++aavkla+adPeDSD+N++fg+i+v d+L ++g d+e+++++Gd++v
  gi|298675783|ref|YP_003727533.1|   2 QTLVICIDRDNDLGEKAHINTPVIGRKDNIDAAVKLATADPEDSDTNTIFGGIQVLDDLLNRGIDAEIVLLAGDRNV 78 
                                       59*************************************************************************** PP

                            DUF373  78 gveadrkiaeqldevlskleadsaivVsDGaeDesvlpiiqsrvkvdsvkrVvVkqsrniEstyyllkkalkdpelr 154
                                       +v ad++i++qlde+l++++a++ai++sDGaeDe+++pi+qsr+k+dsvkrV V+qs n+Estyyllk+a++dp+++
  gi|298675783|ref|YP_003727533.1|  79 NVVADQHISRQLDEILKTYNAKNAIFISDGAEDETLMPIVQSRIKIDSVKRVTVMQSANLESTYYLLKHAFNDPKIS 155
                                       ***************************************************************************** PP

                            DUF373 155 ktiLvplGlllliyalllllglpelalaiillllGlylllrGfgldelleelleklkesleegritfvtyvvallll 231
                                       +t++vplGl+ liya++ll+++pe a++ il+++Gly+l+rGf+ld++++ +l+++k++++ gr+tfvty++a+l++
  gi|298675783|ref|YP_003727533.1| 156 QTFFVPLGLAALIYAIFLLMNYPEGAVIGILAAVGLYMLYRGFNLDDQFAVFLNNVKNAFHGGRLTFVTYLTAFLIA 232
                                       ***************************************************************************** PP

                            DUF373 232 ligiisgyislesvss..asvssglltlilafiygavewlalailtaslgkiideylkreekdiarllllpflvlai 306
                                       +i++i+g+ +++++++  + +++g+ltl+++fi+++++w+++a+l+ + gk++d     + k+i+ +++++f+++++
  gi|298675783|ref|YP_003727533.1| 233 IIATIQGTLEIWTYYTqgGIWYYGILTLATVFINESIWWYTAAFLAGYSGKLVDLKA--RGKSIYPCMSTVFFAVSM 307
                                       ****************9999**********************************988..567*************** PP

                            DUF373 307 glvlygasaylls..............lsilalslvvgivval 335
                                       gl+++g+s+ylls              l+++++s+++++++al
  gi|298675783|ref|YP_003727533.1| 308 GLLFWGSSTYLLSinallsspeipdfgLQYFVYSIIGAFIIAL 350
                                       ***********99***************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       803  (0.0447878); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2431.04
//
Query:       gi|298675784|ref|YP_003727534.1|  [L=214]
Description: hypothetical protein Metev_1907 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-31  109.7   0.2    1.5e-31  109.4   0.2    1.1  1  MAF_flag10  Protein of unknown function DUF115
  ------ inclusion threshold ------
      0.078   12.8   0.2       0.38   10.6   0.2    1.9  1  DUF2100     Uncharacterized protein conserved in archaea (DUF


Domain annotation for each model (and alignments):
>> MAF_flag10  Protein of unknown function DUF115
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.4   0.2   1.7e-35   1.5e-31      13     169 ..      45     191 ..      35     193 .. 0.85

  Alignments for each domain:
  == domain 1  score: 109.4 bits;  conditional E-value: 1.7e-35
                        MAF_flag10  13 pslkellnkfkgnkpaiivgaGPSLeknlellkelrdkaviiaadtalkaLlkegIkPDivvs.lDpqeasyevfke 88 
                                       ++l+ l++++++ k+++++g+ PSL ++l++     +++ iiaad+a++aL+++gI+PDi+v+ lD+   + e   +
  gi|298675784|ref|YP_003727534.1|  45 SDLSILRKTINE-KNILVCGNAPSLVDDLKNFD-F-QDYAIIAADGAVEALMDAGIVPDIIVTdLDG---NVEKEID 115
                                       346666676677.************99888885.3.7999***************************...7787889 PP

                        MAF_flag10  89 aekkgdiplvfasgvnpellkkykgpkiflvtgstqalelleeekneilfgGgsvantaldlAvklgfkeIiliGqD 165
                                       a++kg+ ++v+a+g+n+++l+ky ++ ++++ + tq ++l+    n+ +fgG++++++++ lA ++ +++I l+G+D
  gi|298675784|ref|YP_003727534.1| 116 ANYKGSLMVVHAHGDNIDKLRKYVPRFKNVIGT-TQSHPLY----NVYNFGGFTDGDRCVYLAKRFSASKIELAGFD 187
                                       99999***********************87765.4434444....558***************************** PP

                        MAF_flag10 166 layt 169
                                       +  +
  gi|298675784|ref|YP_003727534.1| 188 FTDK 191
                                       *876 PP

>> DUF2100  Uncharacterized protein conserved in archaea (DUF2100)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   4.2e-05      0.38      89     147 ..      12      73 ..       6     138 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 4.2e-05
                                       HHHHHHHTTT---X..X..XXXXSSSEEEESXHHHHHHHHHHXSSSXEEEXSSX..SSSHHHH CS
                           DUF2100  89 klekvLeefgveee..edieeldkdalyivsnkkvlKaLkeinvdlniisteGv..LeieDmk 147
                                       + +k+L++fg+  +  e+   + +d l   sn++ l +L++  ++ ++i++ G     ++D+k
  gi|298675784|ref|YP_003727534.1|  12 IYQKILSDFGFSRKedERSAFILSDLLSSLSNTSDLSILRKT-INEKNILVCGNapSLVDDLK 73 
                                       4589*******9995556667889************999998.77777777775333455554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.94
# Mc/sec: 685.18
//
Query:       gi|298675785|ref|YP_003727535.1|  [L=1065]
Description: isoleucyl-tRNA synthetase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   3.3e-197  656.4   7.8   5.7e-197  655.7   7.8    1.4  1  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    5.6e-36  123.8   1.3    1.3e-35  122.6   1.3    1.7  1  Anticodon_1    Anticodon-binding domain of tRNA
    1.4e-24   86.6   8.7    7.9e-12   44.6   1.0    4.1  3  tRNA-synt_1g   tRNA synthetases class I (M)
    6.7e-05   22.4   0.2     0.0033   16.8   0.0    2.8  3  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
     0.0011   18.0   0.0     0.0055   15.7   0.0    2.1  2  tRNA-synt_1f   tRNA synthetases class I (K)
     0.0014   18.2   0.0     0.0038   16.8   0.0    1.7  1  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  655.7   7.8  1.9e-200  5.7e-197       2     599 ..      18     633 ..      17     636 .. 0.96

  Alignments for each domain:
  == domain 1  score: 655.7 bits;  conditional E-value: 1.9e-200
                       tRNA-synt_1   2 lyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaiea 78 
                                       +  +Wee++++k+ +e+++ + +f +vdgPPy tG++H+G a++k++kd + ry +m+ ++ + + GwD++Gl+ie 
  gi|298675785|ref|YP_003727535.1|  18 IHRFWEENNAYKRVRESREGASKFFFVDGPPYTTGHIHLGTAWNKVIKDSILRYFSMNNYDIHERAGWDMHGLPIEV 94 
                                       5689************************************************************************* PP

                       tRNA-synt_1  79 kvekklgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgl 155
                                       kve  lg + kk+ + +g+ +f++k+++++ e+++++++q+k lGv++D++++y+Tl +e+ ea ++++++ +dk+l
  gi|298675785|ref|YP_003727535.1|  95 KVEGILGFQSKKDIETYGVGNFINKCKNFAIEQKDNMTEQFKSLGVWLDWENPYMTLRDEYIEAAWWTLKQAYDKDL 171
                                       ***************************************************************************** PP

                       tRNA-synt_1 156 iyrgkklvnwstklktalselEveykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyv..... 227
                                       + +g+++vnw+++++ta+++ Ev+y + +d++i+++f l+++e++++vi+TTtP+T+++++avav+p ++y+     
  gi|298675785|ref|YP_003727535.1| 172 LEEGQRVVNWCPRCETAIADSEVDYFEITDPSIYIKFRLKEEENTYVVIWTTTPWTIPSNMAVAVHPSFEYSkvkat 248
                                       ***********************************************************************999*99 PP

                       tRNA-synt_1 228 ...itkeklilaeallkslvkke..sekkiledergkeLegkevelpl.......vnrkipiiaddyvdkeaGtGvV 292
                                           ++e lila++l++ ++k+   +++++le++ gk+Leg+ +++pl       ++ +  i + dyv++e+ tG+V
  gi|298675785|ref|YP_003727535.1| 249 npeGNDEVLILASDLVEDVLKQGryTDYEVLEKMSGKDLEGLSYHHPLadavskqAEFEHNIYTADYVTAEK-TGCV 324
                                       998899**************99887788********************9*9999999999*********998.**** PP

                       tRNA-synt_1 293 kiaPahdedDyevgkkynlevinildedgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcersk 369
                                       +iaP+h+ +D+evg +++++v +++ +dg++ +ea++++g ++ da+++++++lk++g+ll +e+i+h +++c+r k
  gi|298675785|ref|YP_003727535.1| 325 HIAPGHGMEDFEVGVENGIPVFCPVGADGKYLDEAGKYSGEHIRDANQTIINDLKHRGVLLAEESINHRYGHCWRCK 401
                                       ***************************************************************************** PP

                       tRNA-synt_1 370 kpiiyrateqWfvrvkeladaalkavekvqfvpks.kekryaswleniqdWciSRqrwWGhriplfvsketeevvvr 445
                                       +p iy at qWf +++++++++l++++kv ++p++ +++r+++w+e ++dWciSRqr+WG +ip++  +  + + v+
  gi|298675785|ref|YP_003727535.1| 402 TPNIYLATVQWFLKISDIKQNMLSEIQKVDWYPEWaGTSRFKDWVEGARDWCISRQRYWGIPIPVWKCSGCGSIDVV 478
                                       ***********************************99*************************************999 PP

                       tRNA-synt_1 446 eelkelvagreeeeaekkalekeakdkl...kkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadm 519
                                         ++el ++   +++++ +l++  +d+l    +  g+++++edv+DvWF+S+    +tlgyp++ ++++++ +pad+
  gi|298675785|ref|YP_003727535.1| 479 GTKQELINK--SNADKHIELHRPYVDDLtmeCDCGGSMSRVEDVFDVWFDSAVASWATLGYPQS-EKDFHRWWPADF 552
                                       999999984..45556667789999999664445689***************************.9*********** PP

                       tRNA-synt_1 520 lleGlDiirgWvarlillslaltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltli.lsdv 595
                                       ++eG D++rgW+++ +  s+  ++++P+k+v++hg+++d+ G+KmSKs gNv+dpl+v++kygad lR +++ +s  
  gi|298675785|ref|YP_003727535.1| 553 ITEGHDQTRGWFYSQLGASMVAFEQSPYKSVMMHGFTLDKYGKKMSKSQGNVVDPLEVVDKYGADTLRAYVLsTSAP 629
                                       **********************************************************************9945555 PP

                       tRNA-synt_1 596 grdi 599
                                         d+
  gi|298675785|ref|YP_003727535.1| 630 WDDL 633
                                       5555 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.6   1.3   4.3e-39   1.3e-35       1     149 [.     684     835 ..     684     839 .. 0.90

  Alignments for each domain:
  == domain 1  score: 122.6 bits;  conditional E-value: 4.3e-39
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkra.aqevllevletllrl 76 
                                       d+wils++++++k+v+ a+ +y+++ka++a+ ef+++dl++wy++l++pr + es+++++  a++vl++v+ tl++l
  gi|298675785|ref|YP_003727535.1| 684 DKWILSRMQSVIKDVDYAMSDYQLHKAIRAINEFVLEDLSRWYIQLIRPRTWVESEDPDKLaAYRVLYDVFVTLSKL 760
                                       9******************************************************999977799************* PP

                       Anticodon_1  77 laPfmPfitEelwqr...eeeelgkkesimlaewpe.kaeelekeleeeevellkeivkairklrselkikpsselk 149
                                       +aPf+P+i+Ee++q+   +      + ++++++wp  ++e+ +kel e++++++++iv+   ++r++ k k +++++
  gi|298675785|ref|YP_003727535.1| 761 IAPFTPHIAEEMYQNlvrNV-DQYAPITVHMNDWPLpEEEKVDKEL-ESHMQIARSIVESSANARQKVKRKLRWPVS 835
                                       ***************98522.3367799*******74444448888.9*******************9999998865 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.1   2.8e-09   8.3e-06       8     133 ..      48     192 ..      43     198 .. 0.60
   2 !   18.8   0.1   1.8e-07   0.00054     168     238 ..     396     465 ..     369     472 .. 0.85
   3 !   44.6   1.0   2.6e-15   7.9e-12     242     373 ..     518     642 ..     505     653 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 2.8e-09
                                       B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHH.......HTTS-..........HHHHH CS
                      tRNA-synt_1g   8 pYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAe.......kegvt..........peelv 67 
                                       pY++g++HlG + + ++ D + Ry  +++++++  +g D+hG pie+k e       k++++           ++++
  gi|298675785|ref|YP_003727535.1|  48 PYTTGHIHLGTAWNKVIKDSILRYFSMNNYDIHERAGWDMHGLPIEVKVEgilgfqsKKDIEtygvgnfinkCKNFA 124
                                       8*********************************************9976322221122222111001111122222 PP

                                       HHHHHHHHHHHHHTT---S..EEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GG CS
                      tRNA-synt_1g  68 ekvheeikelfkklnisfd..kygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdr 133
                                        + +++++e+fk+l++  d  + + t  +e  e++   +k+ ++k+l++e++  + +cp++e+ ++d+
  gi|298675785|ref|YP_003727535.1| 125 IEQKDNMTEQFKSLGVWLDweNPYMTLRDEYIEAAWWTLKQAYDKDLLEEGQRVVNWCPRCETAIADS 192
                                       33334444555555543331144445555555555555555555566666666666666666555555 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 1.8e-07
                                       .........EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET CS
                      tRNA-synt_1g 168 ksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP 238
                                       ++  +++ +++  t ++f+k+s++++++ + i++ +   e   ++  k+w++   +d++isr+  wGip+P
  gi|298675785|ref|YP_003727535.1| 396 HCWRCKTPNIYLATVQWFLKISDIKQNMLSEIQKVDWYPEWAGTSRFKDWVEG-ARDWCISRQRYWGIPIP 465
                                       7899999999999****************99966665566666788999*976.9***************9 PP

  == domain 3  score: 44.6 bits;  conditional E-value: 2.6e-15
                                       CEEE-HHHHHHHHHHHTTTTT-...TTSGGGG.G--S......EEEE..EGGGHH..HHHTHHHHHHHHTT----S- CS
                      tRNA-synt_1g 242 kkvlYVWldAligYisatkelakkkgeeekwkeyWakdkevelvhfi..gkdiik..FHtifwPaillgaelklpkk 314
                                       + v+ VW+d  +   +++++      +e++++++W +        fi  g d ++  F +  + a + + e +  k+
  gi|298675785|ref|YP_003727535.1| 518 EDVFDVWFDSAVASWATLGYPQ----SEKDFHRWWPA-------DFIteGHDQTRgwFYSQ-LGASMVAFEQSPYKS 582
                                       56899*******9999999986....689******44.......45522566664424444.456666777788899 PP

                                       EEEE--.EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHHHH CS
                      tRNA-synt_1g 315 vvahey.ltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedfve 373
                                       v+ h++ l   gkK+SkS+g+vv++ e+++++ ad+lR y+++++   +Dl+f+we + +
  gi|298675785|ref|YP_003727535.1| 583 VMMHGFtLDKYGKKMSKSQGNVVDPLEVVDKYGADTLRAYVLSTSAPWDDLKFNWEGVNQ 642
                                       *****955688********************************************98765 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.029        87      21      48 ..      52      79 ..      38      81 .. 0.90
   2 !   16.8   0.0   1.1e-06    0.0033     228     284 ..     570     627 ..     555     645 .. 0.79
   3 ?   -2.8   0.1         1   3.1e+03     220     267 ..     766     814 ..     764     825 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.029
                                      S--BHHHHHHHHHHHHHHHHHHHTT-EE CS
                      tRNA-synt_1e 21 dashlGhaRslvafDilrrilqalgYdv 48
                                       ++hlG a + v+ D + r++ + +Yd+
  gi|298675785|ref|YP_003727535.1| 52 GHIHLGTAWNKVIKDSILRYFSMNNYDI 79
                                      579***********************98 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1.1e-06
                                       HHHHHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS- CS
                      tRNA-synt_1e 228 qseaafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRllllsah 284
                                        s+ af+ +++    +h   l   g+kmsks +n++   +v+ k+ + +lR ++ls+ 
  gi|298675785|ref|YP_003727535.1| 570 ASMVAFEqSPYKSVMMHGFTLDKYGKKMSKSQGNVVDPLEVVDKYGADTLRAYVLSTS 627
                                       566677746677788898899999***************************9988754 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1
                                       THHHHHHHHHHHHSSS--EEEEEE.E--EEETTBE--TTTT---BHHHH CS
                      tRNA-synt_1e 220 Phhenelaqseaafdkqlvkyflh.nghlkiegekmsksLknfitikdv 267
                                       Ph   e+ q+  +   q++ + +h n++   e+ek+ k L+  ++i   
  gi|298675785|ref|YP_003727535.1| 766 PHIAEEMYQNLVRNVDQYAPITVHmNDWPLPEEEKVDKELESHMQIARS 814
                                       8999999999999989999999994456677999999999998888654 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.26   7.9e+02       3      54 ..      22      71 ..      20      82 .. 0.59
   2 !   15.7   0.0   1.8e-06    0.0055     268     331 ..     583     646 ..     546     656 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.26
                      tRNA-synt_1f  3 WadklaeklieerkkkkaekdevvvesGispSGliHiGnlrevltadlvara 54
                                      W ++ a k ++e+++    ++   v+    + G+iH+G++ + +  d + r 
  gi|298675785|ref|YP_003727535.1| 22 WEENNAYKRVRESREG--ASKFFFVDGPPYTTGHIHLGTAWNKVIKDSILRY 71
                                      5555555555444333..2233334444457899999998877766666655 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.8e-06
                      tRNA-synt_1f 268 kvvYelillkggekmssSkGnvltledwlevaepevlr.flilrrkPkkakkldldleilrlvde 331
                                        ++  + l+k g+kms+S+Gnv+ + ++++ +  ++lr +++  + P   +k++ + ++ +++ +
  gi|298675785|ref|YP_003727535.1| 583 VMMHGFTLDKYGKKMSKSQGNVVDPLEVVDKYGADTLRaYVLSTSAPWDDLKFNWE-GVNQVYSN 646
                                       3566777888899**************99888888887255566789999999999.88888876 PP

>> tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.3e-06    0.0038      11     142 ..     205     351 ..     202     387 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.3e-06
                     tRNA-synt_1_2  11 eiefkvees.eeklevfttrpdtlfGvtfvalapehplvekl...aekkkel....aafieevkkksesereletke 79 
                                        i+f+++e+ ++ + ++tt p t+ +   va+ p+ +  +      e ++e+    ++++e+v k+ + +     ++
  gi|298675785|ref|YP_003727535.1| 205 YIKFRLKEEeNTYVVIWTTTPWTIPSNMAVAVHPSFEYSKVKatnPEGNDEVlilaSDLVEDVLKQGRYTDYEVLEK 281
                                       6999999996678999**********999999998877665444655566653444678889999988888777777 PP

                     tRNA-synt_1_2  80 keGv.ftglkaihPitgek.......ipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikqvikp 142
                                        +G   +gl   hP+ +          +i++a+yv +e  tg+v   P+h  +Dfe   + ++p+   +  
  gi|298675785|ref|YP_003727535.1| 282 MSGKdLEGLSYHHPLADAVskqaefeHNIYTADYVTAE-KTGCVHIAPGHGMEDFEVGVENGIPVFCPVGA 351
                                       889877999*****98554456777789*******976.79****************99999998765554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1065 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       942  (0.0525406); expected 358.6 (0.02)
Passed bias filter:                      730  (0.0407162); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.98u 0.33s 00:00:01.31 Elapsed: 00:00:00.56
# Mc/sec: 5733.07
//
Query:       gi|298675786|ref|YP_003727536.1|  [L=160]
Description: PUA domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-20   72.5   0.5    3.1e-20   71.9   0.5    1.3  1  PUA       PUA domain
    5.5e-06   27.0   0.3    1.9e-05   25.2   0.3    1.9  1  Pre-PUA   Pre-PUA-like domain
    3.5e-05   24.0   0.4    7.9e-05   22.9   0.3    1.7  1  DUF1947   Domain of unknown function (DUF1947)
      0.003   17.8   0.2     0.0073   16.5   0.1    1.7  2  UPF0113   UPF0113 PUA domain


Domain annotation for each model (and alignments):
>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.9   0.5     7e-24   3.1e-20       3      73 ..      80     150 ..      78     151 .. 0.90

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 7e-24
                                       EEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETT.SCEEEEEEESS-HHHHHHHCTSEEEEEEEE CS
                               PUA   3 vvvddgAvkallsgasLlapGvvevegdfeegdvVaivded.gelvavGlanysseelakikggksveierv 73 
                                       v vd gAvk++++ga+++ pG+v+ + ++++gd V i+ e+ g+++avG+a++++ee++  + gk+v+ +++
  gi|298675786|ref|YP_003727536.1|  80 VYVDSGAVKFVSKGADVMSPGIVKSDPNIKKGDLVIIKEENhGKPLAVGRAMMDGEEMTG-ESGKAVQSIHY 150
                                       89***************************************9****************65.56666666655 PP

>> Pre-PUA  Pre-PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.3   4.3e-09   1.9e-05       6      81 ..       2      68 ..       1      73 [. 0.87

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 4.3e-09
                           Pre-PUA  6 kvksntqlksSdrrkLraklleqfpslseeqleellpkkeevkvvklqgehvelyvvdgeplffqdregellPtly 81
                                      k+ks+ ql++S + kL ++l+++f       +++l     ++++vk+   + ++++vd++pl+f    +e++Pt++
  gi|298675786|ref|YP_003727536.1|  2 KIKSRVQLRKSTKNKLLNELVSTFGDE----IKKLSDS--KFECVKTD--KYSIIMVDNNPLLFFI-GDEIFPTVR 68
                                      79*********************9655....6666654..56699998..9*************99.89******8 PP

>> DUF1947  Domain of unknown function (DUF1947)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.3   1.8e-08   7.9e-05      11      61 ..      16      68 ..       5      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.8e-08
                                      HHHHHHHHTTT---TT--...-EEEE-SS-EEEEETTEEEEEE.SSSEEE-HH CS
                           DUF1947 11 keileklkekyisislesdk.iEieeekkeklYlingvpilfe.eekliPtLk 61
                                      k + e +  ++ +i+  sd+  E  +++k +++++++ p+lf+ +++++Pt++
  gi|298675786|ref|YP_003727536.1| 16 KLLNELVSTFGDEIKKLSDSkFECVKTDKYSIIMVDNNPLLFFiGDEIFPTVR 68
                                      344455677888999999999******************************96 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.94   4.2e+03      16      40 ..      27      52 ..      24      60 .. 0.47
   2 !   16.5   0.1   1.6e-06    0.0073       3      60 ..      81     141 ..      79     153 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.94
                           UPF0113 16 rdvlkesilkit.esvkenqvvvVln 40
                                       ++ k s  k++  ++++   ++V+n
  gi|298675786|ref|YP_003727536.1| 27 DEIKKLSDSKFEcVKTDKYSIIMVDN 52
                                      44445555555522333333344433 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.6e-06
                           UPF0113   3 vvkekaeklFLYGrdvlkesilkitesvkenqvvvVlnen.geplGiGkirkdt.k.aspg 60 
                                       +v+  a k +  G dv+  +i+k ++++k+++ v++  en g+pl++G++  d+ +   ++
  gi|298675786|ref|YP_003727536.1|  81 YVDSGAVKFVSKGADVMSPGIVKSDPNIKKGDLVIIKEENhGKPLAVGRAMMDGeEmTGES 141
                                       55544444444699**********************6665489*******99886434444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 957.70
//
Query:       gi|298675787|ref|YP_003727537.1|  [L=126]
Description: hypothetical protein Metev_1910 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.7e-12   45.5   0.3    1.1e-11   44.9   0.3    1.3  1  SepF      Cell division protein SepF


Domain annotation for each model (and alignments):
>> SepF  Cell division protein SepF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   0.3     6e-16   1.1e-11       1      72 []      43     116 ..      43     116 .. 0.95

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 6e-16
                                       EEEEE-SSGGGHHHHHHHHHTT-EEEEE-CCCTC..HHHHHHHHHHHHHHHHCT-EEEEECTTEEEEE-TT-EE CS
                              SepF   1 vvvveprsfedaqeiadalkegkiVilnledldk..eeakrivdflsgvvyaldGdiqkvgkkvflitPknvdi 72 
                                       + v e++++++  ++++++++g+i++l++++++     + r+++ l++vv +++Gdi+ ++++ +l+tP++v+i
  gi|298675787|ref|YP_003727537.1|  43 IRVGELTNLDELSQLKKEIYDGNILMLDISNIKAdkLLLDRALKDLKEVVTDVQGDIAGLKEDQVLVTPAGVKI 116
                                       5677999***********************999876889*********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 707.62
//
Query:       gi|298675788|ref|YP_003727538.1|  [L=207]
Description: ZPR1-like zinc finger protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-36  125.8   0.0    1.7e-36  125.5   0.0    1.1  1  zf-ZPR1   ZPR1 zinc-finger domain
  ------ inclusion threshold ------
      0.011   16.0   0.5        2.8    8.2   0.0    2.3  2  CTU2      Cytoplasmic tRNA 2-thiolation protein 2
      0.018   14.3   0.0      0.023   14.0   0.0    1.1  1  TraH      Conjugative relaxosome accessory transposon protein


Domain annotation for each model (and alignments):
>> zf-ZPR1  ZPR1 zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.5   0.0   2.8e-40   1.7e-36       1     158 [.      15     168 ..      15     169 .. 0.92

  Alignments for each domain:
  == domain 1  score: 125.5 bits;  conditional E-value: 2.8e-40
                           zf-ZPR1   1 slCpsCgkengetrlllt.kiPyfkeviimsfeCehCgyknnevksageieekGkritlkveseedlnrqvlkSeta 76 
                                       s+Cp C+ ++  t+ ++t +iPyf e++ ++ +C+ Cg+k  ++++++++++  +++++++e+++dl  ++++S+++
  gi|298675788|ref|YP_003727538.1|  15 SSCPLCH-DK-LTMHWQTdHIPYFDEILYITARCS-CGFKFADTMITTQKDP--VHYEITIENNNDLYARIVRSTSG 86 
                                       58****7.54.66666666***************9.****************..*********************** PP

                           zf-ZPR1  77 tveipeleleippg.tlegrlttvEGlLeqikeelekeegdqaeredeekekieeflekleeliegeepftlildDp 152
                                       t+++pe+++ ++pg ++e+++t++EGlL+++k+ ++++++ ++e+e e+++++ e+ + l+++ieg++++t+ +dDp
  gi|298675788|ref|YP_003727538.1|  87 TIRVPEFGIAVEPGpASESYVTNIEGLLNRVKSVVQTAAKWSKEEE-EKYNQCLEIESALDDTIEGHRKLTIEIDDP 162
                                       ***********************************75555555554.59**************************** PP

                           zf-ZPR1 153 agnSfi 158
                                       +gnS+i
  gi|298675788|ref|YP_003727538.1| 163 LGNSAI 168
                                       ****98 PP

>> CTU2  Cytoplasmic tRNA 2-thiolation protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1    0.0022        13      35      61 ..       4      27 ..       1      35 [. 0.74
   2 ?    8.2   0.0   0.00047       2.8       7      65 ..     104     154 ..     102     191 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0022
                              CTU2 35 ksseeaeletsekCalCglplddkake 61
                                      ++++e+ ++t+++C+lC+ +l     +
  gi|298675788|ref|YP_003727538.1|  4 ENHSENGFSTESSCPLCHDKL---TMH 27
                                      455677899*********988...334 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00047
                              CTU2   7 ekFilklekdfpstvstvvrTgeKLvknksseeaeletsekCalCglplddkakewkrt 65 
                                       e++++++e +  + v+ vv+T++K +k++++      + ++C+  +++ldd   e  r+
  gi|298675788|ref|YP_003727538.1| 104 ESYVTNIE-GLLNRVKSVVQTAAKWSKEEEE------KYNQCLEIESALDD-TIEGHRK 154
                                       78999999.56677899***********986......78888888887733.3333333 PP

>> TraH  Conjugative relaxosome accessory transposon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.9e-06     0.023     208     316 ..      72     185 ..      56     191 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.9e-06
                              TraH 208 sgdkelaellmslvGtvii.....kenaadgkgkkd...vrvlpslaknsalledLldGgskkvyrCdseedtqkCl 276
                                       + ++ +a +++s +Gt+ +        ++          v+ +++l++    ++  ++   +  ++ ++ee+ ++Cl
  gi|298675788|ref|YP_003727538.1|  72 NNNDLYARIVRSTSGTIRVpefgiA-VEPGPA---SesyVTNIEGLLNR---VKSVVQT--AAKWSKEEEEKYNQCL 139
                                       55677999***********544321.111111...12235666666543...6666666..4449999999****** PP

                              TraH 277 ept....stidttkglksrvrell..esivekiandtaltaeekaf 316
                                       e++     ti  +++l+ ++ + l    i+++ an+++l++ee + 
  gi|298675788|ref|YP_003727538.1| 140 EIEsaldDTIEGHRKLTIEIDDPLgnSAIISDRANSRKLSDEEVEN 185
                                       ***9999999999999999999999878889999******998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1046  (0.0583412); expected 358.6 (0.02)
Passed bias filter:                      750  (0.0418317); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1347.61
//
Query:       gi|298675789|ref|YP_003727539.1|  [L=479]
Description: prolyl-tRNA synthetase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-25   90.4   0.0    2.2e-25   89.7   0.0    1.4  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    7.8e-21   74.0   0.1    1.6e-20   73.0   0.1    1.6  1  HGTP_anticodon  Anticodon binding domain
    1.4e-14   54.0   0.0    2.8e-14   53.0   0.0    1.5  1  ProRS-C_1       Prolyl-tRNA synthetase, C-terminal
     0.0067   16.5   0.7      0.028   14.6   0.5    2.3  1  ProRS-C_2       Prolyl-tRNA synthetase, C-terminal
  ------ inclusion threshold ------
      0.085   13.1   0.9       0.21   11.9   0.9    1.6  1  Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase


Domain annotation for each model (and alignments):
>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.7   0.0   6.1e-29   2.2e-25       8     178 ..     104     274 ..      93     275 .. 0.91

  Alignments for each domain:
  == domain 1  score: 89.7 bits;  conditional E-value: 6.1e-29
                                       SEEEEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEE.EEEEEEES.GGGHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx.xxxxxxxxx RF
                      tRNA-synt_2b   8 dreyiLkPtneetfvelirdevlrs.krLPlklyqiqtkyRdEksdsrGLlRvreFhq.kdgyvfha.easlddslr 81 
                                       + +++L+Pt+e++++ +++ + +rs  +LP+k+yqi   +R+E++ +r+L+R+re++  k+++ +h   +++  ++ 
  gi|298675789|ref|YP_003727539.1| 104 EVNLALRPTSETAIYPIYKLW-VRShADLPIKYYQIVNTFRYETKHTRPLIRLREITSfKEAHTVHEtWEDAAAQVD 179
                                       5689**************988.9**778*****************9**********8659******97699****** PP

                                       HHHHHHHHHHHHTT.SCEEEEEE.GTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTSSEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  82 dlikaisriferlglefraiiel.msaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvldennrek 157
                                       + i  +++++erl l++   ++  +++  + ++++  ++a+++  ++++++gt++ lg+++++++++++ d n+++ 
  gi|298675789|ref|YP_003727539.1| 180 EAIDRYHEFYERLCLPVLTSKRPeWDK-FPGADYTIAVDALMP-DGRTLQVGTAHHLGNNFAKTFDIEYEDPNGEQV 254
                                       ****************77555556664.5999***********.9******************************** PP

                                       EEEEEEEEEEHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b 158 svimicaaigveRllsaileq 178
                                         +  c++i+ eR ++a++++
  gi|298675789|ref|YP_003727539.1| 255 YAYQSCYGIS-ERCIAAMISV 274
                                       **********.******9875 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.0   0.1   4.5e-24   1.6e-20       1      92 [.     291     385 ..     291     387 .. 0.95

  Alignments for each domain:
  == domain 1  score: 73.0 bits;  conditional E-value: 4.5e-24
                                       SEEEEESSSS...HHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEET CS
                    HGTP_anticodon   1 qvvviplnek...aeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdr 74 
                                       qv++ip+  k   +e +++ +k ++  L+ ag+++++d s++++g k+ +++++g+p+++++G+k+l++++v   +r
  gi|298675789|ref|YP_003727539.1| 291 QVIIIPIIFKnkdKESILDACKNVKGSLESAGVKTKIDTSDRRPGAKYYRWEMKGVPLRIEIGPKDLKNESVMMVRR 367
                                       8999999887788999************************************************************* PP

                                       TTCEEEEEETTHHHHHHH CS
                    HGTP_anticodon  75 dtreqervsldelveklk 92 
                                       dt+++e++++de+ + + 
  gi|298675789|ref|YP_003727539.1| 368 DTGDKEQIAMDEINDTVA 385
                                       ************999886 PP

>> ProRS-C_1  Prolyl-tRNA synthetase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.0   7.9e-18   2.8e-14       2      69 .]     414     479 .]     413     479 .] 0.93

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 7.9e-18
                                       HHHHHHHHTT-EEEEEESSGHHHHHHHHHHHS-EEEEEESSB-SSCCCSB-TTT-SB-SEEEEEE-B- CS
                         ProRS-C_1   2 eefkealekkgfvlapWcgeeecEekIkeetgakslcipfdqepseegtkCivcgkpakkwvlfgrsY 69 
                                       +e+ +++ k g++++pWcg+eec ++++e++ga +l+ip++q ++ +++ C vcg +a++ +++ r+Y
  gi|298675789|ref|YP_003727539.1| 414 DEIENKIVK-GILKIPWCGQEECNDELEENIGAGILGIPVNQ-ENSSSSPCPVCGGEANTKIYVSRTY 479
                                       677777765.8******************************9.688999*****************99 PP

>> ProRS-C_2  Prolyl-tRNA synthetase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.5   7.7e-06     0.028      13      51 ..     413     450 ..     394     456 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7.7e-06
                                       HHHHHHHCTTT-SEEEEE-.-GGG-SHHHHHHHSS-EEEE CS
                         ProRS-C_2  13 lenikeklsekkGvvLvPf.neeiYneefeeeidasvLGe 51 
                                       l++i +k+   kG++ +P+   e  n+e+ee+i+a +LG 
  gi|298675789|ref|YP_003727539.1| 413 LDEIENKIV--KGILKIPWcGQEECNDELEENIGAGILGI 450
                                       466777764..8******9535668*************95 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.9   5.9e-05      0.21       4      12 ..     460     468 ..     458     471 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.9e-05
                                       E--TTTT-T CS
                    Prim_Zn_Ribbon   4 spCPvCGGr 12 
                                       spCPvCGG+
  gi|298675789|ref|YP_003727539.1| 460 SPCPVCGGE 468
                                       8*******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       755  (0.0421105); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.46
# Mc/sec: 3107.89
//
Query:       gi|298675790|ref|YP_003727540.1|  [L=357]
Description: nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.053   12.7   0.2      0.084   12.1   0.2    1.3  1  DBI_PRT         Phosphoribosyltransferase
       0.31   11.0   1.2       0.96    9.4   0.1    2.0  2  Staphostatin_A  Staphostatin A


Domain annotation for each model (and alignments):
>> DBI_PRT  Phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   9.3e-06     0.084     136     254 ..     129     249 ..     116     288 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.3e-06
                                       HHHHHHHHHHHHHCTTECEEEEEEE-TTCHHHHHHHHHHHHT--HHHH---TTT--HHHHHHHHHHHHHHHHCH... CS
                           DBI_PRT 136 aleaGieladeladagadllalGemGigNttaaaallaallglepeevvGrGtglddeglarKiavieqalarh... 209
                                        +e + ++ ++ +++ +d l++Ge   g tt+a a+l al        v   +  + + ++ K++v+++ ++     
  gi|298675790|ref|YP_003727540.1| 129 IFERAYKIGKK-IQTKTDFLMIGESIAGGTTTAMAVLNALGYD---GNVSSSS--SLNPVELKTEVVKEGMDASgvt 199
                                       55555666555.67789******************99998543...3343444..55678899********999887 PP

                                       ..-.TT.HHHHHHHHS-HHHHHHHHHHHHHHHTT..--EEE-SHHHHHHH CS
                           DBI_PRT 210 ..a.ekdplevLakvGGleiaalaGailgAaarr..ipvvlDGfistaAa 254
                                         + +++p+++++++G   + ++aG++ g  + +    vvl G   +aA+
  gi|298675790|ref|YP_003727540.1| 200 fgSlRDNPIHAIKTLGDPMMPTVAGVVTGFKESNnaSRVVLAGGTQMAAI 249
                                       6533459************9999999987655431134555554444444 PP

>> Staphostatin_A  Staphostatin A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1       0.1   9.1e+02      35      63 ..       2      30 ..       1      34 [. 0.84
   2 ?    9.4   0.1   0.00011      0.96      66      97 ..     258     289 ..     251     294 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.1
                    Staphostatin_A 35 edsplkiilskeidsdyvcklineeskkl 63
                                      e+s   i +sk +++ ++c l n++  ++
  gi|298675790|ref|YP_003727540.1|  2 ETSDSSINVSKPNNPLFLCVLSNTKTSHI 30
                                      678888999999*********99987665 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00011
                    Staphostatin_A  66 snkdnssivieiilindkkllltiiskealGt 97 
                                       +n dn siv   +++ndk   ++ +++e lG 
  gi|298675790|ref|YP_003727540.1| 258 YNTDNISIVTTQYVVNDKTANFEKLTTEMLGV 289
                                       9*****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 2335.49
//
Query:       gi|298675791|ref|YP_003727541.1|  [L=40]
Description: hypothetical protein Metev_1914 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00013   21.9   2.4    0.00015   21.7   2.4    1.1  1  DZR             Double zinc ribbon
     0.0012   18.8   2.7     0.0013   18.7   2.7    1.1  1  zinc-ribbons_6  zinc-ribbons
  ------ inclusion threshold ------
      0.034   14.4   6.5       0.54   10.5   0.3    2.1  2  DUF2757         Protein of unknown function (DUF2757)
       0.08   13.1   4.9        1.1    9.5   3.4    2.2  1  zf-RING_7       C4-type zinc ribbon domain
      0.085   13.0   4.4        5.4    7.2   0.0    2.1  2  zf-B_box        B-box zinc finger
       0.15   12.0   4.2        2.2    8.3   0.7    2.1  2  ADK_lid         Adenylate kinase, active site lid
       0.17   11.7   4.6       0.48   10.2   0.7    2.2  2  Rubredoxin_2    Rubredoxin metal binding domain
        0.2   11.8   5.0        3.5    7.8   0.9    2.1  2  Zn-ribbon_8     Zinc ribbon domain
       0.33   10.7   7.6        2.2    8.0   0.7    2.2  2  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII
       0.44   10.8   2.7        3.6    7.8   0.3    2.0  2  Rdx             Rdx family


Domain annotation for each model (and alignments):
>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   2.4   8.2e-08   0.00015       9      40 ..       2      37 ..       1      39 [. 0.85

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 8.2e-08
                               DZR  9 ppdarfCseCgtklkavaa....edrCpsCgekvdp 40
                                      ++++  C+ C+t+l+++       ++C +Cg+++++
  gi|298675791|ref|YP_003727541.1|  2 QKEQCICDSCNTQLRKQVLgmniLYFCRNCGRMTSA 37
                                      567889********965559************9886 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   2.7     7e-07    0.0013      27      62 ..       3      38 ..       1      40 [] 0.90

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 7e-07
                                      EEEEE-SSS-S---EEEETTEEEE--TTTT----TT CS
                    zinc-ribbons_6 27 kkealCpeCeqelevlkaCgavdyfCnkcneLiSkk 62
                                      k++ +C+ C+ +l +      + yfC++c  + S +
  gi|298675791|ref|YP_003727541.1|  3 KEQCICDSCNTQLRKQVLGMNILYFCRNCGRMTSAE 38
                                      57889***************************9976 PP

>> DUF2757  Protein of unknown function (DUF2757)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   1.5    0.0037       6.7      52      64 ..       5      17 ..       3      19 .. 0.87
   2 ?   10.5   0.3    0.0003      0.54       1      12 [.      22      33 ..      22      37 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0037
                                      EE--HHHHHHHHH CS
                           DUF2757 52 kviCedCqealer 64
                                      + iC++C+++l++
  gi|298675791|ref|YP_003727541.1|  5 QCICDSCNTQLRK 17
                                      57********987 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0003
                                      ---EEEETTT-- CS
                           DUF2757  1 MaihYrCrhCgk 12
                                      M+i Y Cr Cg+
  gi|298675791|ref|YP_003727541.1| 22 MNILYFCRNCGR 33
                                      9*********97 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   3.4   0.00063       1.1      13      32 ..      15      34 ..       7      34 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00063
                                      HHHHHCCSTB-EE-TTT--E CS
                         zf-RING_7 13 vlselragdevvtCpeCGRI 32
                                      + +++ + + + +C +CGR+
  gi|298675791|ref|YP_003727541.1| 15 LRKQVLGMNILYFCRNCGRM 34
                                      344444556689*******8 PP

>> zf-B_box  B-box zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   1.8    0.0043       7.7      22      31 ..       4      13 ..       2      17 .. 0.83
   2 ?    7.2   0.0     0.003       5.4      14      23 ..      24      33 ..      21      35 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0043
                          zf-B_box 22 qqplCeeCst 31
                                      +q++C++C+t
  gi|298675791|ref|YP_003727541.1|  4 EQCICDSCNT 13
                                      79******65 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.003
                          zf-B_box 14 atlfCedCqq 23
                                      + +fC++C+ 
  gi|298675791|ref|YP_003727541.1| 24 ILYFCRNCGR 33
                                      669*****86 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.7    0.0012       2.2      19      31 ..       3      15 ..       2      18 .. 0.85
   2 ?    5.4   0.1      0.01        18       3       9 ..      27      33 ..      26      36 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0012
                                      SSTTB-TTT--.- CS
                           ADK_lid 19 kveglCDkCGepL 31
                                      k+  +CD C+ +L
  gi|298675791|ref|YP_003727541.1|  3 KEQCICDSCNTQL 15
                                      67789*****998 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.01
                                      E-TTT-- CS
                           ADK_lid  3 vCpkCGr 9 
                                       C++CGr
  gi|298675791|ref|YP_003727541.1| 27 FCRNCGR 33
                                      69****9 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.2     0.036        64       3       8 ..       8      13 ..       7      18 .. 0.67
   2 ?   10.2   0.7   0.00027      0.48       1      11 [.      26      36 ..      26      39 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.036
                      Rubredoxin_2  3 CsqCGf 8 
                                      C++C+ 
  gi|298675791|ref|YP_003727541.1|  8 CDSCNT 13
                                      777765 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00027
                      Rubredoxin_2  1 YvCsqCGfesa 11
                                      Y C++CG  ++
  gi|298675791|ref|YP_003727541.1| 26 YFCRNCGRMTS 36
                                      99*****9876 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.9    0.0019       3.5      26      40 .]       4      19 ..       1      19 [. 0.79
   2 ?    6.4   0.2    0.0055       9.9       6      13 ..      26      33 ..      25      38 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0019
                       Zn-ribbon_8 26 lta.CPeCgsevrrvi 40
                                      +++ C +C+ ++r+++
  gi|298675791|ref|YP_003727541.1|  4 EQCiCDSCNTQLRKQV 19
                                      5666*********986 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0055
                       Zn-ribbon_8  6 YrCeeCgh 13
                                      Y C++Cg+
  gi|298675791|ref|YP_003727541.1| 26 YFCRNCGR 33
                                      89****95 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   1.1    0.0033       5.9      23      30 ..       7      14 ..       5      15 .. 0.90
   2 ?    8.0   0.7    0.0013       2.2      21      28 ..      25      32 ..      25      34 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0033
                           zf-RRN7 23 yCrrChtq 30
                                      +C++C tq
  gi|298675791|ref|YP_003727541.1|  7 ICDSCNTQ 14
                                      8******9 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0013
                           zf-RRN7 21 fyyCrrCh 28
                                      +y+Cr+C+
  gi|298675791|ref|YP_003727541.1| 25 LYFCRNCG 32
                                      6******9 PP

>> Rdx  Rdx family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.2     0.026        47       7      20 ..       8      21 ..       6      26 .. 0.80
   2 ?    7.8   0.3     0.002       3.6       5      18 ..      26      39 ..      22      40 .] 0.86

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.026
                                      ETTTTTHHHHHHHH CS
                               Rdx  7 CtqCkwmlraaela 20
                                      C++C+ +lr + l 
  gi|298675791|ref|YP_003727541.1|  8 CDSCNTQLRKQVLG 21
                                      ********987665 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.002
                                      EEETTTTTHHHHHH CS
                               Rdx  5 eYCtqCkwmlraae 18
                                       +C +C+ m  a++
  gi|298675791|ref|YP_003727541.1| 26 YFCRNCGRMTSAEY 39
                                      68*********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.49
# Mc/sec: 247.06
//
Query:       gi|298675792|ref|YP_003727542.1|  [L=69]
Description: hypothetical protein Metev_1915 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0087   16.2   1.2      0.011   15.9   1.2    1.1  1  zf-RRPl_C4   Putative ribonucleoprotein zinc-finger pf C4 typ
  ------ inclusion threshold ------
      0.015   15.1   2.5      0.022   14.6   2.5    1.2  1  PADR1        PADR1 (NUC008) domain
      0.016   14.7   0.1      0.095   12.2   0.1    1.9  2  Mu-like_Com  Mu-like prophage protein Com
        1.6    8.9   9.2         22    5.3   9.2    2.0  1  zf-Dof       Dof domain, zinc finger


Domain annotation for each model (and alignments):
>> zf-RRPl_C4  Putative ribonucleoprotein zinc-finger pf C4 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   1.2   2.4e-06     0.011       2      31 ..      29      57 ..      28      68 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.4e-06
                        zf-RRPl_C4  2 kkCkyClskklknlnetvyCeaCeiyfkvk 31
                                       kC+ C+sk l ++++  yC  C+ + k k
  gi|298675792|ref|YP_003727542.1| 29 DKCPRCKSKTLYESENFQYCGICRYWTK-K 57
                                      59*********************96554.3 PP

>> PADR1  PADR1 (NUC008) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   2.5   4.8e-06     0.022      13      42 ..      28      56 ..      23      58 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.8e-06
                             PADR1 13 lekCpeCkegqlvfdssgYkCtGnmsewtk 42
                                      l+kCp Ck ++  ++s++++  G    wtk
  gi|298675792|ref|YP_003727542.1| 28 LDKCPRCK-SKTLYESENFQYCGICRYWTK 56
                                      79******.99999*******9*9999997 PP

>> Mu-like_Com  Mu-like prophage protein Com
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   2.1e-05     0.095      12      30 ..      15      34 ..      13      40 .. 0.86
   2 ?    0.4   0.0       0.1   4.6e+02       7      19 ..      48      60 ..      44      67 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.1e-05
                       Mu-like_Com 12 RLLaKaeAlDelti..KCPRC 30
                                      +LL+ +e  D ++i  KCPRC
  gi|298675792|ref|YP_003727542.1| 15 KLLSEGEFAD-MQIldKCPRC 34
                                      6999999999.99988***** PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.1
                       Mu-like_Com  7 CGeCaRLLaKaeA 19
                                      CG C     K+ A
  gi|298675792|ref|YP_003727542.1| 48 CGICRYWTKKGTA 60
                                      9999887777776 PP

>> zf-Dof  Dof domain, zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   9.2     0.005        22       4      45 ..      29      61 ..      26      65 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.005
                            zf-Dof  4 lkCprCestntkFcYyNNyslsqPRyfCkaCrryWtkgGklR 45
                                       kCprC+s+      y  ++ +    +C  C ryWtk G+ R
  gi|298675792|ref|YP_003727542.1| 29 DKCPRCKSKT----LYESENFQ----YCGIC-RYWTKKGTAR 61
                                      58*****985....57777775....79999.59*****988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 481.86
//
Query:       gi|298675793|ref|YP_003727543.1|  [L=268]
Description: hypothetical protein Metev_1916 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.012   15.2   7.9      0.012   15.2   7.9    1.8  2  ABC2_membrane_5  ABC-2 family transporter protein
       0.41   10.4   8.0        0.6    9.9   8.0    1.2  1  DUF2157          Predicted membrane protein (DUF2157)
        0.6   10.0   5.0        5.2    6.9   0.1    2.7  3  DUF4307          Domain of unknown function (DUF4307)
        3.2    8.2   7.3        1.1    9.7   4.3    1.9  2  DUF2583          Protein of unknown function (DUF2583)


Domain annotation for each model (and alignments):
>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   7.9   2.7e-06     0.012     119     198 ..      27     104 ..      14     111 .. 0.80
   2 ?   -1.2   0.3      0.28   1.3e+03      78      92 ..     117     131 ..     112     150 .. 0.48

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.7e-06
                   ABC2_membrane_5 119 siliglvialiflaivlPlyfkfgvekgrivliiiifgiifllvaifslsklelslidlsnyilliillviilllii 195
                                        +++g+v+ ++ +a+++  ++ +g e g+i+l +i++g     + ++   +l++++++  +yi + + ++ +l+l i
  gi|298675793|ref|YP_003727543.1|  27 IFAAGIVLLIVGVAFIIMSQIHYGSEPGKIILSVIFMGGG--ASLVLTGTNLMMKQTKYGYYITAAGTILALLALAI 101
                                       356677777777999**************99999999964..45556778999999999999988888877777777 PP

                   ABC2_membrane_5 196 vSy 198
                                       +S 
  gi|298675793|ref|YP_003727543.1| 102 FSS 104
                                       664 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.28
                   ABC2_membrane_5  78 iVksKYlfvlilili 92 
                                       +V + Y+++++  l 
  gi|298675793|ref|YP_003727543.1| 117 YVLAMYIVGILALLG 131
                                       344444444433322 PP

>> DUF2157  Predicted membrane protein (DUF2157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   8.0   0.00013       0.6      35     142 ..      24     131 ..       8     136 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00013
                           DUF2157  35 leallvlGalllglGlilfvAanWqglsrlvkfllllvllllslllgavlwrdrrvpprlgeallllaalllgaaia 111
                                       + ++++ G++ll +G+ +++ +     s+  k++l ++ + + + l++   +   ++ + g ++  ++++l + a+a
  gi|298675793|ref|YP_003727543.1|  24 GSVIFAAGIVLLIVGVAFIIMSQIHYGSEPGKIILSVIFMGGGASLVLTGTNLMMKQTKYGYYITAAGTILALLALA 100
                                       78999*****************************999999988877766666668999******************* PP

                           DUF2157 112 lvgqifqlsgdaysllllwalllllmayllr 142
                                       +++ i+  + + +++  + a+ ++ +  ll 
  gi|298675793|ref|YP_003727543.1| 101 IFSSIYPQGWYYPTVSYVLAMYIVGILALLG 131
                                       **********999999888888887777665 PP

>> DUF4307  Domain of unknown function (DUF4307)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.3    0.0049        22       4      30 ..      26      52 ..      23      82 .. 0.85
   2 ?   -3.2   0.1       1.6   7.1e+03       8      19 ..      90     101 ..      84     109 .. 0.50
   3 ?    6.9   0.1    0.0012       5.2       5      52 ..     123     170 ..     120     179 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0049
                           DUF4307  4 llvillvvlvvvalalvawigysqgsa 30
                                      +++++++vl++v++a++++  +++gs+
  gi|298675793|ref|YP_003727543.1| 26 VIFAAGIVLLIVGVAFIIMSQIHYGSE 52
                                      677888899999999999888888655 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.6
                           DUF4307   8 llvvlvvvalal 19 
                                       ++++l+++ala+
  gi|298675793|ref|YP_003727543.1|  90 AGTILALLALAI 101
                                       344444444433 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0012
                           DUF4307   5 lvillvvlvvvalalvawigysqgsadvsaevvgfevvddstvevtfe 52 
                                       +v +l++l+  ++ +v wi+ s++++  ++++ +++v +d++++ ++e
  gi|298675793|ref|YP_003727543.1| 123 IVGILALLGNGFANVVLWIISSKSETATRSSQENYTVHNDESIQRDIE 170
                                       56778888999999***************************9997765 PP

>> DUF2583  Protein of unknown function (DUF2583)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   4.3   0.00025       1.1       6      63 ..      20      76 ..      14      90 .. 0.74
   2 ?   -1.8   0.1      0.95   4.3e+03      48      53 ..     119     124 ..      77     143 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00025
                           DUF2583  6 alllGnvlmglGlllmvaslaysvlnqlpelelpellaeaallgifi..GallWlaGarv 63
                                      + + G v+ + G++l+++++a+ +++q+   + p  +    l  if+  Ga l l+G+++
  gi|298675793|ref|YP_003727543.1| 20 VYYAGSVIFAAGIVLLIVGVAFIIMSQIHYGSEPGKI---ILSVIFMggGASLVLTGTNL 76
                                      45789**********************9877776644...34444442257777777665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.95
                           DUF2583  48 lgifiG 53 
                                       l+++i 
  gi|298675793|ref|YP_003727543.1| 119 LAMYIV 124
                                       333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2201  (0.122762); expected 358.6 (0.02)
Passed bias filter:                      878  (0.0489709); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 1685.02
//
Query:       gi|298675794|ref|YP_003727544.1|  [L=349]
Description: hypothetical protein Metev_1917 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-07   29.3   0.1    0.00041   19.3   0.0    2.4  3  MreB_Mbl  MreB/Mbl protein
    2.1e-05   24.9   0.1    8.8e-05   22.9   0.0    2.0  2  FtsA      Cell division protein FtsA


Domain annotation for each model (and alignments):
>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0      0.49   4.4e+03       5      22 ..       4      22 ..       4      26 .. 0.65
   2 !   19.3   0.0   4.6e-08   0.00041      34     185 ..      53     206 ..      38     214 .. 0.79
   3 !    7.6   0.0   0.00016       1.5     252     320 ..     245     321 ..     228     327 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 0.49
                                      EEEE-SSEEEEE.ETTTEE CS
                          MreB_Mbl  5 giDLGtantlvy.vkgkgi 22
                                      g+D+Gt n++    +g+ +
  gi|298675794|ref|YP_003727544.1|  4 GLDIGTMNIICAeNEGEDV 22
                                      6899**9998741344444 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 4.6e-08
                                       TTT--EEEESHHHHTTTTS-GTTEEEE-SEETTEESSHHH.HHHHHHHHHHHHHTSS-SS--EEEEEE-SS--HHH. CS
                          MreB_Mbl  34 kktkkvlavGeeAkkmlgktpgnikavrPlkdGviadlev.aeellkyfikkvkkkkslskprvvicvPsgiteve. 108
                                       +k+ k+  +Ge+A ++        ++ rP++ G+i+  e  a  ++k ++++v  +  ++++ + i+ P +  +++ 
  gi|298675794|ref|YP_003727544.1|  53 EKDDKISVLGEDAFNFAT--IFGKETRRPMRFGIISPKEKdAIPMIKLIVDRVLGDPGYQNEALCISSPADPIDLDm 127
                                       455677778888877643..3344678********987652779*************************98766661 PP

                                       ....HHHHHHHHHHTT-SEEEEEEHHHHHHHHTT--TTSSS-EEEEEE-SS-EEEEEEETTEEEEEEEES-SHHHHH CS
                          MreB_Mbl 109 ....rrAvkeaakkaGarevllieeplaAAiGaglpveepsgnmvvdiGggttevavislggivtsksvrvaGdeld 181
                                           ++ ++ea +k  + + ++i+e l A + ++l  ++ +g + + iG+g t+v++  ++  v s s+  +Gd +d
  gi|298675794|ref|YP_003727544.1| 128 ntlyHKKMTEALTKKMSYDTKVIDEGL-AVVYSELADSNFTG-LGISIGAGLTNVTLAYMATPVLSFSIGRGGDWID 202
                                       111155567777778888999***997.56888887666665.889******************************* PP

                                       HHHH CS
                          MreB_Mbl 182 eaii 185
                                       e++ 
  gi|298675794|ref|YP_003727544.1| 203 EQVS 206
                                       *986 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.00016
                                       HHHHHHHHHHHTS-HHHHHHHHHH-EEEESGGGGSBTHHHHHHHHHS.....S...-EEE-SSTTTHHHHHHHHTTC CS
                          MreB_Mbl 252 aiveavkevLektppeLaadivdrgivltGGgallkgldkllseetg.....l...pvkvaedpltcvakGtgkvle 320
                                       a+++ v + L+k  +e++   v+  + ++GG++   g+ k+++++++     +   ++++a dpl +va+G+ +++ 
  gi|298675794|ref|YP_003727544.1| 245 ALMTYVIQNLNKKLAEITPPNVKFPVAVAGGSSNPPGFIKMFEKKLKeanlqIdisNINIATDPLYSVARGCLIAAR 321
                                       566667777777778888888888999*****9887777777665422221142234689***********988765 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.21   1.9e+03       3      22 ..       5      24 ..       4     120 .. 0.70
   2 !   22.9   0.0   9.8e-09   8.8e-05       2     103 .]     170     315 ..     169     315 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.21
                                      EEE-SSSEEEEEEETTEEEE CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                              FtsA  3 vDiGagktdvavaedgalvh 22
                                      +DiG+  + +a  e++ +v+
  gi|298675794|ref|YP_003727544.1|  5 LDIGTMNIICAENEGEDVVF 24
                                      78887777766555555544 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 9.8e-09
                                       EEEE-SSSEEEEEEETTEEEEEEEES--HHHHHHHHHHHHT--HHHHHHHHH...HH--S--............... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxx............... RF
                              FtsA   2 lvDiGagktdvavaedgalvhlrvigvggngitkdiakalrtaveeAeriki...kyGsala............... 60 
                                       ++ iGag t+v++a +  +v + +ig gg+ i++ +++a + + + A   k    k Gs ++               
  gi|298675794|ref|YP_003727544.1| 170 GISIGAGLTNVTLAYMATPVLSFSIGRGGDWIDEQVSNATGLPKDHACVTKEkgfKLGSEVEiggpegaltiyydal 246
                                       789*************99999999999************************42223444444777777666666666 PP

                                       ....EEEEEHHHHH......................GGGGSTTHHHHHHHHHT-.........HH.HT-GGGHHHHH CS
                                       ....xxxxxxxxxx......................xxxxxxxxxxxxxxxxxxx.......xxx.xxxxxxxxxxx RF
                              FtsA  61 ....ekeigrkels......................ggsalpnleelaeralspk.......lee.vsdpeyasalg 103
                                                    +                      g+s+ p++++++e+ l+         + + + dp y++a g
  gi|298675794|ref|YP_003727544.1| 247 mtyvI--------QnlnkklaeitppnvkfpvavagGSSNPPGFIKMFEKKLKEAnlqidisNINiATDPLYSVARG 315
                                       65553........04444455677999999999999***************84334555566666688999988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2319.15
//
Query:       gi|298675795|ref|YP_003727545.1|  [L=202]
Description: AMMECR1 domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-50  171.3   0.0    1.4e-50  171.1   0.0    1.0  1  AMMECR1   AMMECR1


Domain annotation for each model (and alignments):
>> AMMECR1  AMMECR1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.1   0.0     8e-55   1.4e-50       2     166 .]      12     183 ..      11     183 .. 0.94

  Alignments for each domain:
  == domain 1  score: 171.1 bits;  conditional E-value: 8e-55
                                       HHHHHHHHHHTTSS-S-H...H---HHHHSEEEEEEEEEEE..CCECCCECEEEEEEHHHHHHHHHHHHHHT-TTS- CS
                           AMMECR1   2 klareaieealkeekkle...eeakeelkekaglFVtlkekkgeLRGCiGtleperpLaeevaenAlaaAfeDpRFs 75 
                                        lar+aie++l+++++++    + ++ +kek+g+FVtlk k+g+LRGCiG+  p+ +L +++++ +++aA++DpRF+
  gi|298675795|ref|YP_003727545.1|  12 TLARRAIETYLETGEMIDpseLDLSSIFKEKRGVFVTLK-KDGDLRGCIGHPYPDSQLDSAIIDSSISAATRDPRFP 87 
                                       79***************987777788************9.77*********************************** PP

                                       ---HHHHTTEEEEEEEE---EE--......GGG--TTT-EEEEEETTEEEEE-THHHHHTT--HHHHHHHHHHHHTS CS
                           AMMECR1  76 pvtaeElpeleveVsvLtepepiv......ledlevgkhGliiekgsrsatlLPqvaveqgwdkeeflasllrKagl 146
                                       pv+  E++ +++eV+vL++pe ++      +e +evgkhGli +kg  +++lLPqva+eqg d  efl++++ Kagl
  gi|298675795|ref|YP_003727545.1|  88 PVELPEMNAITLEVTVLSQPELVDvspeelPEYVEVGKHGLIAKKGYSQGLLLPQVATEQGFDSSEFLSHTCLKAGL 164
                                       ***********************4454455677******************************************** PP

                                       -TTCCCSTTSEEEEE-EEEE CS
                           AMMECR1 147 rpdewkdseikltryevekf 166
                                       +pdew ++  +++ +e+++f
  gi|298675795|ref|YP_003727545.1| 165 SPDEW-KKGAQIYCFEGQIF 183
                                       *****.67********9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 1248.89
//
Query:       gi|298675796|ref|YP_003727546.1|  [L=403]
Description: phosphoglycerate kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   8.8e-108  360.6   0.7     1e-107  360.4   0.7    1.0  1  PGK       Phosphoglycerate kinase


Domain annotation for each model (and alignments):
>> PGK  Phosphoglycerate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  360.4   0.7  5.6e-112    1e-107       1     377 [.       9     390 ..       9     391 .. 0.92

  Alignments for each domain:
  == domain 1  score: 360.4 bits;  conditional E-value: 5.6e-112
                                       GGGS--TT-EEEEEE-----EECTTEES--HHHHHHHHHHHHHHHTT-EEEEEE--S--TTS-GGG-SHHHHHHHHH CS
                               PGK   1 vkdldlkgkrvlvRvDfNvplkkegkitddtriraalpTikyllekgakvvllsHlgrpkgekeklslkpvaerLse 77 
                                       ++d+d ++k+vlvRvD+N+p++ eg+i dd rir+++ T+k+l  k+akvvll+H++rp g+++ ++++p+a+++s+
  gi|298675796|ref|YP_003727546.1|   9 IDDFDTEDKTVLVRVDLNSPMDPEGNILDDMRIRSHVATVKEL--KNAKVVLLAHQSRP-GKNDFTTMSPHASKMSK 82 
                                       689****************************************..99************.89*************** PP

                                       HHTT-EEEESSTTSHHHHHHHHT-TTT-EEEES-GGGSTTTTTT-H.......HHHHHHHHT-SEEEE--GGGTTS- CS
                               PGK  78 llgkeVkfvedvvgeeveeaiaelkegevllLeNvrfykeEeknde.......elakklasladvyVnDAFgtahra 147
                                       +lg+++k+++d++g+ ++++i+++++g+v lLeNvrfy+eE+ +++       +l++kla l+d+y nDAF+++hr+
  gi|298675796|ref|YP_003727546.1|  83 YLGQDIKYIDDIFGTYARQKISSMEKGDVALLENVRFYSEESLERPvsehektHLVRKLAPLFDIYLNDAFSVSHRS 159
                                       *****************************************7443333333447*********************** PP

                                       -TTTTHHHHCSEEEE-HHHHHHHHHHHHHHHS--SSEEEEEEES-HHHCHHHHHHHTTT-..SEEEEETCHHHHHHH CS
                               PGK 148 haStvgiakvlsaaaGllmekElealskvlenperplvailGGakvsdkikvienLlekv..dkliigGgmantFlk 222
                                       h S++g+++vl++ aG++mekE++ l+   +   rp +++lGGakv+d +kvie++l++   d+++++G++ n++l+
  gi|298675796|ref|YP_003727546.1| 160 HLSIMGFTNVLPSGAGRIMEKEVTSLDLGKSGGGRPSIFVLGGAKVDDSMKVIEHVLSNNdvDRVLVTGLVGNVMLA 236
                                       ***********88********************************************87544*************** PP

                                       HTT-B-TTSS-...-G....GGHHHHHHHHHHHHHHT-EEE--SEEEEESSSSTTS.EEEECCG.--TT-EEEEE-H CS
                               PGK 223 aqgleigkslv...ee....dklelakellekakkkgvkillpvDvvvakeeaekeakvvevea.ipedemalDigp 291
                                       a+g++ig++ +   e+    d+++ ak ll+k++   +ki +p D++++++   k+ +v  v++    ++ + Dig 
  gi|298675796|ref|YP_003727546.1| 237 ASGVDIGEENMrfiEKqgytDQIDRAKTLLDKFN---DKIGVPQDLALNDNG--KRIEV-GVNElATTNHPVNDIGL 307
                                       *******999866544566678***********8...89**********942..22233.44441467779****** PP

                                       HHHHHHHHHHCC-SEEEEES-SS-TTSGCCCHHHHHHHHHHHHHCHTSEEEEESHHHHHHHHHTT-GGGSSEEESSS CS
                               PGK 292 ktielfaeaikeaktvvwnGpmGvfeiekfakGTkaiakalaeatkgalsivGGgdsaaaveklgladkvshvStGG 368
                                       +ti  ++++i++aktvv+nGp+Gv e+e+fa GT++i+ka+a+a    +sivGGg+  a v ++g++d++ h+St+G
  gi|298675796|ref|YP_003727546.1| 308 ETIVSYSKEIENAKTVVLNGPAGVSENEEFALGTREIIKAAAKA---SYSIVGGGHISAEVLNMGVEDSFYHLSTAG 381
                                       *******************************************6...49**************************** PP

                                       HHHHHHHCT CS
                               PGK 369 gAsLelLeg 377
                                       gA++++L g
  gi|298675796|ref|YP_003727546.1| 382 GACIDYLAG 390
                                       *******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.55
# Mc/sec: 2209.78
//
Query:       gi|298675797|ref|YP_003727547.1|  [L=355]
Description: DRTGG domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-33  115.1   0.2    2.8e-33  113.8   0.2    1.7  1  DRTGG         DRTGG domain
    4.9e-33  114.6   0.0    1.5e-32  113.0   0.0    1.8  2  AAA_26        AAA domain
    9.3e-06   25.7   0.0     0.0011   19.0   0.0    2.7  2  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
     0.0011   18.9   0.0      0.012   15.7   0.0    2.4  2  Hpr_kinase_N  HPr Serine kinase N terminus


Domain annotation for each model (and alignments):
>> DRTGG  DRTGG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.8   0.2   6.3e-37   2.8e-33       1     104 [.     215     320 ..     215     321 .. 0.98

  Alignments for each domain:
  == domain 1  score: 113.8 bits;  conditional E-value: 6.3e-37
                                       HHHHHTT-EEEE--..SS--E-EEEE-SS-HHHHHHHHHT..SEEEEEETT-HHHHHHHTT-TEEEEEEETT----H CS
                             DRTGG   1 eiaealgaevlnggeeelrrvekvvvgamsvenmlerlke..gdlvivpGDRediqlaaleagiaalilTgglepse 75 
                                       +i+++l+aevl+g ++ ++ ve+++vgam+v+++++++++  +++vi++GDR+diqlaa+ea++++l+lTg+l+pse
  gi|298675797|ref|YP_003727547.1| 215 DIVDDLNAEVLTGADNLNTLVERYLVGAMEVNSAIKYFRRvpNCAVITGGDRSDIQLAAIEAKAKCLVLTGNLRPSE 291
                                       79************988888*******************999*********************************** PP

                                       HHHHHHHHHT--EEE-SS-HHHHHHHHHT CS
                             DRTGG  76 evlklaeeaglpvlsveldtfttakrinq 104
                                       +vl  aeea++pv+ v+ dt++t+kr+++
  gi|298675797|ref|YP_003727547.1| 292 AVLGSAEEANIPVILVRGDTMSTIKRMES 320
                                       **************************986 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.0   0.0   3.4e-36   1.5e-32       2     196 ..       3     210 ..       2     212 .. 0.89
   2 ?   -2.0   0.0      0.59   2.7e+03     125     152 ..     298     325 ..     296     350 .. 0.64

  Alignments for each domain:
  == domain 1  score: 113.0 bits;  conditional E-value: 3.4e-36
                            AAA_26   2 tifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiqtgie......ededselikellgldqtyelpeplalsap 72 
                                       +i++++ ++++GK+ ++ gL r+lk++g+++gy+KPi++ +       +ded+e  ++llgld++ ++++p++ ++ 
  gi|298675797|ref|YP_003727547.1|   3 SILISSSEEYSGKSGICNGLGRILKDRGYSIGYMKPIGNLLIdkdgflTDEDAEESRTLLGLDDSLSDITPILQTE- 78 
                                       69************************************9888666666777*********************7664. PP

                            AAA_26  73 lspelaarqegedidlekiv....kelekdadivvVEGagglgvpiteellnadiaknlgapvilVarggl.gtinq 144
                                         + + ++++g++ + +ki     + ++ + div++EG+gg+g++  ++l++ +ia  lg++++lV+r+++  ++++
  gi|298675797|ref|YP_003727547.1|  79 --NLIHDALMGVEKHFDKILtdaySNISRNRDIVFIEGSGGIGSGAMYNLSDPEIASILGSKILLVTRYDSiYAVDR 153
                                       ..578888888888888888888788999******************************************88**** PP

                            AAA_26 145 llltiealrqknvrvlGvilNkvrnp......envetlekksgipvlGvvPylpdlea 196
                                       +l  ++++ +    ++G+ilN+v++       e v  + + +gi+v+Gv+P++ +l++
  gi|298675797|ref|YP_003727547.1| 154 ILCDLKLVPD-SDMIAGIILNEVPESnlekvsELVIPYLERKGIKVFGVIPQDITLRS 210
                                       ******9988.689********987755444336666677778***********9987 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.59
                            AAA_26 125 knlgapvilVargglgtinqllltieal 152
                                       ++ ++pvilV   + +ti+++   i  +
  gi|298675797|ref|YP_003727547.1| 298 EEANIPVILVRGDTMSTIKRMESLIGRA 325
                                       6678899998777777777664444444 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   2.5e-07    0.0011      10     120 ..      13     210 ..       4     216 .. 0.81
   2 ?    3.7   0.0     0.014        61      54      88 ..     279     348 ..     224     353 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.5e-07
                                       SSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH................................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................ RF
                              CbiA  10 vGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep................................ 54 
                                       +GK+ ++ +L+r+l++rg+ +   +  p +n+l   +g   d++                                 
  gi|298675797|ref|YP_003727547.1|  13 SGKSGICNGLGRILKDRGYSIGYMK--PIGNLLIDKDGFLTDEDAeesrtllglddslsditpilqtenlihdalmg 87 
                                       7999999999999999999999998..66566543444444444456799999999999999999999999999999 PP

                                       ...........................................................CCHCCCHHHHHHCHCHHH CS
                                       ...........................................................xxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ...........................................................dlkrllellealgkkkal 72 
                                                                                                  ++  + ++l +l+ + ++
  gi|298675797|ref|YP_003727547.1|  88 vekhfdkiltdaysnisrnrdivfiegsggigsgamynlsdpeiasilgskillvtrydSIYAVDRILCDLKLV-PD 163
                                       99999999999999999999999999999999999999999999999999999999998555555666666655.44 PP

                                       H..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  73 llkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavae 120
                                         +iag++ln v ++n  ++ +e +  +++r g++v+gvip+d  +  
  gi|298675797|ref|YP_003727547.1| 164 SDMIAGIILNEVPESN-LEKVSELVIPYLERKGIKVFGVIPQDITLRS 210
                                       49**********9996.666888888888899***********98865 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.014
                                       H..................................CCHCCCHHHHHHCHCHHHH...EEEEEEEEESS.. CS
                                       x..................................xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                              CbiA  54 p..................................dlkrllellealgkkkall.lkiagvvlnrvdgen 88 
                                       +                                  ++kr++ l+ + ++k++l+  k++ ++ n vd +n
  gi|298675797|ref|YP_003727547.1| 279 KclvltgnlrpseavlgsaeeanipvilvrgdtmsTIKRMESLIGRARIKQELKiKKMMELINNNVDVDN 348
                                       0455555555555556666666667788888888899*******99999999999999999999999886 PP

>> Hpr_kinase_N  HPr Serine kinase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.13     6e+02       1      24 [.     211     234 ..     211     263 .. 0.86
   2 !   15.7   0.0   2.6e-06     0.012      77     123 ..     274     320 ..     261     322 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.13
                                       EEHHHHHHHTTEEEEEGGTT-E.. CS
                      Hpr_kinase_N   1 vtvkelieklklelllgeegldrr 24 
                                       v +++++++l+ e+l+g+++l++ 
  gi|298675797|ref|YP_003727547.1| 211 VPISDIVDDLNAEVLTGADNLNTL 234
                                       67999***********99998654 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 2.6e-06
                                       HTT--S-EEEETTT---HHHHHHHHHH---EEEESS-HHHHHTTHHH CS
                      Hpr_kinase_N  77 fskkipciiltrgleppeellelaeeygvpllrtklstsefiaelir 123
                                       ++ k  c++lt +l+p e +l  aee+++p++  +  t ++i+++ +
  gi|298675797|ref|YP_003727547.1| 274 IEAKAKCLVLTGNLRPSEAVLGSAEEANIPVILVRGDTMSTIKRMES 320
                                       567889*********************************99998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 2071.83
//
Query:       gi|298675798|ref|YP_003727548.1|  [L=697]
Description: acetyl coenzyme A synthetase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-81  273.4   0.2    2.7e-81  272.2   0.1    1.6  1  ATP-grasp_5    ATP-grasp domain
    1.9e-55  186.5   2.5    7.1e-55  184.6   0.1    2.8  4  Succ_CoA_lig   Succinyl-CoA ligase like flavodoxin domain
      1e-25   90.5   0.1    8.5e-25   87.5   0.0    2.5  2  CoA_binding_2  CoA binding domain
    2.1e-13   50.7   1.0    4.8e-13   49.6   0.2    2.1  2  CoA_binding    CoA binding domain
  ------ inclusion threshold ------
      0.043   13.4   0.4       0.18   11.3   0.4    2.1  1  ATP-grasp_2    ATP-grasp domain
      0.066   12.7   0.1       0.13   11.7   0.1    1.4  1  CPSase_L_D2    Carbamoyl-phosphate synthase L chain, ATP bind
       0.16   12.8   0.0        2.1    9.2   0.0    2.4  2  GFO_IDH_MocA   Oxidoreductase family, NAD-binding Rossmann fo


Domain annotation for each model (and alignments):
>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  272.2   0.1   1.1e-84   2.7e-81       7     222 .]     477     693 ..     472     693 .. 0.96

  Alignments for each domain:
  == domain 1  score: 272.2 bits;  conditional E-value: 1.1e-84
                       ATP-grasp_5   7 rtlLteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraaaee 83 
                                       ++l    e+ ++l+ay+ip+v+t+++++ +ea++a+++igypvv+Kivspdi+hKtdvgGvrlnl++a++v++a+++
  gi|298675798|ref|YP_003727548.1| 477 KRLTLGLESLDILRAYEIPTVKTKIVKNLKEAIKACKQIGYPVVMKIVSPDISHKTDVGGVRLNLNNADDVERAYHT 553
                                       44455889********************************************************************* PP

                       ATP-grasp_5  84 ilervkekspeariegvlVqemakrggrElivgvteDpvFGpvilfGlGGtavevlkdvavalpplnstlarelier 160
                                       ++++v ++ p+a i+gv+Vqem+  gg E+i+g+++D +FGp+++fG+GG++ve+lkdv+++++p+n+ +a+++i++
  gi|298675798|ref|YP_003727548.1| 554 MMADVYRYMPDADITGVQVQEMVS-GGKEVIIGMNQDVQFGPLLMFGMGGIYVELLKDVSFNVAPINRDEAKHMISS 629
                                       ************************.**************************************************** PP

                       ATP-grasp_5 161 tkaskllkgvrgekkadlaaleellvrlsqLvvdlpeIreldinPllvee..egvvalDarirl 222
                                       +k++++l g+rgek+ d+++++++l+++sqLv d+p+I eldinPl+v +  +g+va+D r++l
  gi|298675798|ref|YP_003727548.1| 630 IKTYPILAGIRGEKPYDINSVADTLIKISQLVNDFPQILELDINPLVVLPdnQGCVAMDLRLTL 693
                                       ************************************************764477*******986 PP

>> Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.21   5.4e+02      81     106 ..      89     114 ..      75     120 .. 0.78
   2 !  184.6   0.1   2.8e-58   7.1e-55       1     138 []     150     287 ..     150     287 .. 0.99
   3 ?   -3.5   0.0       3.2   8.1e+03       3      30 ..     297     324 ..     296     325 .. 0.86
   4 ?   -3.5   0.0       3.3   8.3e+03      21      43 ..     565     587 ..     560     591 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.21
                      Succ_CoA_lig  81 kkpvvvlksGrseagaraaashtgal 106
                                        k v+v+ +G +eag + a+ + +++
  gi|298675798|ref|YP_003727548.1|  89 VKSVIVISAGFKEAGVEGAKLERESV 114
                                       399**********9999888776665 PP

  == domain 2  score: 184.6 bits;  conditional E-value: 2.8e-58
                      Succ_CoA_lig   1 pGkialisqSGalalalldwaasrglgfskvvslGneadvdvadlleylaedpetkvillylEsirdgrkflsaarr 77 
                                       +G+i+l+sqSGa++++ ldwa ++++gfsk++slGn+ad++++d+l+ l +d++t vi++ylE++++g +f+++arr
  gi|298675798|ref|YP_003727548.1| 150 KGNIGLMSQSGAICTSTLDWADKNRVGFSKFISLGNKADLSENDFLQELCNDDSTAVIAAYLEGVKNGPEFIDIARR 226
                                       69*************************************************************************** PP

                      Succ_CoA_lig  78 aarkkpvvvlksGrseagaraaashtgalagsdavvdaafrqaGvlrvdsleelfdaaell 138
                                       ++  kpvv++ksGr++ag+ra++shtg lagsd++++aafrq+G++r+dsl+e++d+++++
  gi|298675798|ref|YP_003727548.1| 227 VTSIKPVVMVKSGRTSAGSRAVSSHTGTLAGSDEAYNAAFRQSGIIRADSLQEMLDYIRAF 287
                                       ********************************************************99875 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 3.2
                      Succ_CoA_lig   3 kialisqSGalalalldwaasrglgfsk 30 
                                       ++a+++  G++++  +d++ ++gl +++
  gi|298675798|ref|YP_003727548.1| 297 NMAILTNAGGFGILTADACYNEGLSLAS 324
                                       67999999****9999999999988876 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 3.3
                      Succ_CoA_lig  21 aasrglgfskvvslGneadvdva 43 
                                       a   g++++++vs G+e+ ++++
  gi|298675798|ref|YP_003727548.1| 565 ADITGVQVQEMVSGGKEVIIGMN 587
                                       55578999999999999988775 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.5   0.0   3.3e-28   8.5e-25       2     113 ..      10     132 ..       9     135 .. 0.97
   2 ?   -1.0   0.0      0.91   2.3e+03      21      57 ..     606     646 ..     601     682 .. 0.68

  Alignments for each domain:
  == domain 1  score: 87.5 bits;  conditional E-value: 3.3e-28
                                       -EEEET--S-TTSHHHHHHHHHHH..HT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHHHH CS
                     CoA_binding_2   2 tiaVvGasdnpgkfgykvlrylle..hglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivkeal 76 
                                       ++aV+Gas ++gk g+ vl++l++   g ++vp+np++eei g k+y+++ + p ++dl+++++p+  +pe++++++
  gi|298675798|ref|YP_003727548.1|  10 SVAVIGASRTEGKVGNSVLKNLVNdfDG-DIVPINPNSEEIMGLKSYPDILDVPDNIDLAVIVIPARFVPETIDKCG 85 
                                       69**********************9999.**********************758*********************** PP

                                       HH--SEEEE-TT..........---HHHHHHHHHTT-EEE.ES-HHH CS
                     CoA_binding_2  77 algakavwlqpg..........sedeeaaelaeeagirvvgdrCilv 113
                                       ++g+k+v++ ++            ++e +e a+++gir++g++C+++
  gi|298675798|ref|YP_003727548.1|  86 RAGVKSVIVISAgfkeagvegaKLERESVETARKYGIRMLGPNCLGL 132
                                       ***********99********************************97 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.91
                                       HHHHHHT--EEEESSS-..SEETTEES----T......T-- CS
                     CoA_binding_2  21 ryllehglpvvpVnpke..eeilgekvyaslae.d.pepvd 57 
                                       + l++ +++v p+n  e  + i   k y+ la    ++p d
  gi|298675798|ref|YP_003727548.1| 606 ELLKDVSFNVAPINRDEakHMISSIKTYPILAGiRgEKPYD 646
                                       567788999****9999777778888888888533444444 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.2   1.9e-16   4.8e-13       3      96 .]       8      98 ..       6      98 .. 0.93
   2 ?   -3.0   0.0       4.8   1.2e+04      74      92 ..     388     406 ..     358     409 .. 0.70

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 1.9e-16
                                      TEEEEEETTTSHHHHHHHHHHHHHHECEE.EEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHH CS
                       CoA_binding  3 dtkviviGagglgiaglyhfkeklkygik.avfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavd 80
                                       ++v+viGa++++++++ ++ ++l   +   ++++np+  ++e+ gl+ y+++ +++++  +d avi++Pa+++ e++d
  gi|298675798|ref|YP_003727548.1|  8 AGSVAVIGASRTEGKVGNSVLKNLVNDFDgDIVPINPN--SEEIMGLKSYPDILDVPDN--IDLAVIVIPARFVPETID 82
                                      679**************66666666688889*******..*******************..****************** PP

                                      HHHHTT-SEEEEESST CS
                       CoA_binding 81 elveagikgiviiteg 96
                                      ++ +ag+k +++i++g
  gi|298675798|ref|YP_003727548.1| 83 KCGRAGVKSVIVISAG 98
                                      *************976 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.8
                                       HHHHHHHHHHHTT-SEEEE CS
                       CoA_binding  74 saqeavdelveagikgivi 92 
                                       +++ +v + v+++ k+i++
  gi|298675798|ref|YP_003727548.1| 388 KVAGIVADKVQTSTKPILC 406
                                       3455566666677777766 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.4     7e-05      0.18       7     134 ..     485     607 ..     482     677 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7e-05
                                       HHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE.--SSSTCCCTTCEEE.ESSHHHHHHHHHCCTTSEEE CS
                       ATP-grasp_2   7 akeilakygvkvpegevaesaeeaeeaakklgekelvvKa.QvlaGGRGKagGvkl.vkskeeakeaakellgkelv 81 
                                       + +il+ y++++ +++++++ +ea +a k++g  + v+K     +  +   gGv+l  ++++++++a ++++    +
  gi|298675798|ref|YP_003727548.1| 485 SLDILRAYEIPTVKTKIVKNLKEAIKACKQIGYPV-VMKIvSPDISHKTDVGGVRLnLNNADDVERAYHTMMADVYR 560
                                       678******************************99.666413455666667***98346778888888888877665 PP

                                       -TTS-TT-EEE--EEEEE---ECEEEEEEEEEETTTTEEEEEEESSTTS-HHH CS
                       ATP-grasp_2  82 tkqtgkeGkkvekvlveealdikkElYlsivlDraskkvvviaSseGGvdiEe 134
                                        +        +  v v+e++   kE+ +++  D +  ++++++  +GG+ +E 
  gi|298675798|ref|YP_003727548.1| 561 -Y---MPDADITGVQVQEMVSGGKEVIIGMNQDVQF-GPLLMF-GMGGIYVEL 607
                                       .2...2334566666777777777777766555443.344443.356666665 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1     5e-05      0.13       9      44 ..     489     522 ..     484     526 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5e-05
                                       HHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEE CS
                       CPSase_L_D2   9 lkkinvpvvpssaapvetleealaiakeigyPviik 44 
                                       l++ ++p+v+ +++  ++l+ea+++ k+igyPv++k
  gi|298675798|ref|YP_003727548.1| 489 LRAYEIPTVKTKIV--KNLKEAIKACKQIGYPVVMK 522
                                       66778899998888..*****************998 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00082       2.1       3      90 ..      11      93 ..      10      94 .. 0.75
   2 ?    0.4   0.0      0.43   1.1e+03      54      74 ..     362     382 ..     330     398 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00082
                                      EEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHHHHH CS
                      GFO_IDH_MocA  3 vaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngtheelaka 81
                                      va+iGa +   k ++++ ++    +  + + p ++++e++   +g+++y d+ ++++  +id++++++p++   e + +
  gi|298675798|ref|YP_003727548.1| 11 VAVIGASRTEGKVGNSVLKN-LVNDFDGDIVPINPNSEEI---MGLKSYPDILDVPD--NIDLAVIVIPARFVPETIDK 83
                                      67777766644444444444.3335666566666777766...8999**********..******************** PP

                                      HHHTT-.EEE CS
                      GFO_IDH_MocA 82 aleagk.hvl 90
                                      + +ag+ +v+
  gi|298675798|ref|YP_003727548.1| 84 CGRAGVkSVI 93
                                      9999997777 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.43
                                       HHHHHTCTTESEEEE-S-GGG CS
                      GFO_IDH_MocA  54 leelladpeidavivatpngt 74 
                                       ++ ll+dp++d +iv t ++ 
  gi|298675798|ref|YP_003727548.1| 362 IDVLLEDPHVDGIIVLTSPQA 382
                                       6779999*********99965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (697 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.74u 0.30s 00:00:01.04 Elapsed: 00:00:00.50
# Mc/sec: 4152.69
//
Query:       gi|298675799|ref|YP_003727549.1|  [L=186]
Description: NADPH-dependent FMN reductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.5e-39  133.0   0.0    9.5e-39  132.6   0.0    1.1  1  FMN_red       NADPH-dependent FMN reductase
    1.1e-11   44.8   0.0    1.4e-11   44.5   0.0    1.2  1  Flavodoxin_2  Flavodoxin-like fold
  ------ inclusion threshold ------
       0.26   10.9   3.9       0.12   11.9   1.6    1.6  2  RecR          RecR protein


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.6   0.0   1.6e-42   9.5e-39       1     145 [.       1     149 [.       1     155 [. 0.93

  Alignments for each domain:
  == domain 1  score: 132.6 bits;  conditional E-value: 1.6e-42
                                       -EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS..--.....---HCHGHTCGGSHHHHHHHHHHHH- CS
                           FMN_red   1 mkilvisGSlrkgsntrklaewaaealkeagaevelidladl.ilpc...alcdkdlesegqtsddvaellekiaaa 73 
                                       mkil+isGS+++++n++kl++ ++e++k++g+e++++ +++l i+pc    +c+ ++  +++ +dd+ ++++++++a
  gi|298675799|ref|YP_003727549.1|   1 MKILGISGSPNENGNNEKLINLCLETAKKRGFETDHVFISSLnIKPCkacGVCKNGE--PCPIDDDMDQVYQQLKDA 75 
                                       9**********************************************9755555555..479*************** PP

                                       SCEEEEEEECTTCE-HHHHHHHHCHT-..SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHH.HTT-EEEEC CS
                           FMN_red  74 daliivtPeYngsysgllKnalDrlsr.trgkkelrgKpvalvavgggrrgglraeeqlrqvla.elgaivvpr 145
                                       d++i+++P+Y+gs+++++K+++Dr +  +r++ +l++Kp++++a+gg+r+gg++ + q  + ++ ++g+i+ ++
  gi|298675799|ref|YP_003727549.1|  76 DGIIVSSPVYFGSVTAQIKALFDRSVLlRRQGFQLENKPGGALAIGGSRNGGQEKTLQTIHDWMhIHGMIIAGD 149
                                       *************************99*********************************99996788877665 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.0   2.3e-15   1.4e-11       1     110 [.       1     108 [.       1     144 [. 0.78

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 2.3e-15
                                       -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCCT-----CCCCHCC.HHHHTT.CHHHHHHH.HHH CS
                      Flavodoxin_2   1 mkiLiinahprpeksfssalaqafvealekagphevtvrdLyadflpvlttrdlaak.layeek.padveseq.iek 74 
                                       mkiL i ++p++ + ++ +l +  +e+++k g  e + + +  + +  +++    ++   + e  p+d +++q  ++
  gi|298675799|ref|YP_003727549.1|   1 MKILGISGSPNE-NGNNEKLINLCLETAKKRG-FETDHVFISSLNIKPCKA----CGvCKNGEPcPIDDDMDQvYQQ 71 
                                       9**********9.6999***************.788888888774444443....22222333336*********** PP

                                       HHCSSEEEEEEE-BTTB--HHHHHHHHH.HS-TTTSC CS
                      Flavodoxin_2  75 llaadaivlqfPlwwfgvPailKgwiDr.vltagfaf 110
                                       l++ad i++++P+++ +v a+ K+ +Dr vl + + f
  gi|298675799|ref|YP_003727549.1|  72 LKDADGIIVSSPVYFGSVTAQIKALFDRsVLLRRQGF 108
                                       ***************************9344444455 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.6   2.1e-05      0.12      15      33 ..      43      61 ..      41      64 .. 0.96
   2 ?   -3.0   0.0      0.97   5.8e+03      26      33 ..     174     181 ..     172     181 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.1e-05
                                      H-EE-TTT--EESSSS-CC CS
                              RecR 15 kvrhCsrCgnlteedlCaI 33
                                      ++++C+ Cg     ++C+I
  gi|298675799|ref|YP_003727549.1| 43 NIKPCKACGVCKNGEPCPI 61
                                      8*****************9 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.97
                                       ESSSS-CC CS
                              RecR  26 teedlCaI 33 
                                       t e lC+I
  gi|298675799|ref|YP_003727549.1| 174 TVEKLCDI 181
                                       56778988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1272.90
//
Query:       gi|298675800|ref|YP_003727550.1|  [L=579]
Description: Cl- channel voltage-gated family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-88  297.4  31.8    1.5e-88  297.4  31.8    2.0  2  Voltage_CLC  Voltage gated chloride channel
      2e-22   79.4   1.4    9.1e-12   45.2   0.2    2.8  2  CBS          CBS domain


Domain annotation for each model (and alignments):
>> Voltage_CLC  Voltage gated chloride channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   1.3     2e-05      0.18     160     222 ..      22      86 ..       4      88 .. 0.81
   2 !  297.4  31.8   1.7e-92   1.5e-88       2     353 ..      73     413 ..      72     414 .. 0.96

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2e-05
                                       -GGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHH.CHHHHHHH.HHHHHHHHHHHHCCCSCC CS
                       Voltage_CLC 160 sllelilfvllGilgGllgalfvrlllkverlfrkle.klkikkrl.epalvgllvgllglllpa 222
                                       s++   l+ ++Gil Gl+ +++  l   ++ +f     +++ + ++  pa +gllvgl+++++++
  gi|298675800|ref|YP_003727550.1|  22 SVFTNTLATVVGILTGLAIVIYEHLIKDFTDFFFGTVsQYPSYFVIlVPATGGLLVGLISYMFVN 86 
                                       5556667899********************97777666999996666**************9865 PP

  == domain 2  score: 297.4 bits;  conditional E-value: 1.7e-92
                                       HHHHHHHCCCCC-GGGSC-SHHHHHHHCTTSS---HHHHHHHHHHHHHHHHCTT-S-BTHHHHHHHHHHHHHHHHHH CS
                       Voltage_CLC   2 ggllagllvklvapeaagsGipevkaalngvkgplslrvllvkflasvltvgsGlslGreGplvqiGAavgsglsrl 78 
                                       ggll+gl+ + +  +++ s + e+++  + ++g+++ + +++ +l+s+++++sG+s+G+e+p v +G+ +gs+++++
  gi|298675800|ref|YP_003727550.1|  73 GGLLVGLISYMF-VNSRRSDVEEIIESSALHDGKIRHKYAFLEVLSSLISISSGGSVGKESPGVLAGSGIGSYVAHI 148
                                       789999999999.9999************************************************************ PP

                                       TT.--SHHHHHHHHHHHHHHHHHHHT-HHHHHHHHCTTTSTSS--TTHHHHHHHHHHHHHHHHHHCTTS-S....-. CS
                       Voltage_CLC  79 lklsrndrdrrlvaaGaAAGiAAaFnaPlgGvlfalEevsrefslrallpvfvasvvaalvlrlllgeepa....fg 151
                                       lk++r++  ++lv +Ga++GiAAaFnaPl+Gv+f++E++ +e+++++++p++va+v+++lv+++++g  p+    f+
  gi|298675800|ref|YP_003727550.1| 149 LKTNREH-SKILVGCGASGGIAAAFNAPLAGVVFVVEVIFGELKSNTFIPIVVAAVFSNLVSNMIFGVMPIevsyFK 224
                                       **76666.999**********************************************************99766555 PP

                                       T---...--GGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHHHHCCCSCC.CSSSS CS
                       Voltage_CLC 152 eveslfalsllelilfvllGilgGllgalfvrlllkverlfrkleklkikkrlepalvgllvgllglllpasvlggg 228
                                        ++     +++el+l+++lG+l+G+++++ +r+++ +   f+kl   + +++ +pa++gl vgl+gl++p+ ++g g
  gi|298675800|ref|YP_003727550.1| 225 -LV----SPVNELFLYLILGVLAGVVSIIIIRSMYLFYDGFHKL---PFHPISKPAIGGLGVGLIGLFYPQ-IFGVG 292
                                       .55....599********************************99...888788******************.***** PP

                                       CCHHHHHCTT-S-HHHHHH...HHHHHHHHHHHHHCTT-CSBSHHHHHHHHHHHHHHHHHHHHHH-CTSSC...HHH CS
                       Voltage_CLC 229 yeliasllegstlllsllllllllllkllataltlgsgvpgGifaPsLviGAalGrlvglvlalllpgaassdpgaf 305
                                       y+ i ++l+++   +++ l+l+ll+lk++a +ltlgsg +gG ++P L++GA+lG ++g++++ ++p+ ++ + ga+
  gi|298675800|ref|YP_003727550.1| 293 YNVIMNVLANE---FTMQLMLILLFLKIFAFSLTLGSGGSGGSIVPALFVGAMLGGVYGNIVNGIFPDMTA-EAGAY 365
                                       ********998...9****************************************************7666.57*** PP

                                       HHHCCTHHHHHCCS-HHHHHHHHHHCC--GCCHHHHHHHHHHHHHHHC CS
                       Voltage_CLC 306 alvGmaaflagvtrapltaiviviEltgdlelllplmlavliAkavad 353
                                       a+vGm++++ag+++aplt ++i++Elt+d++l+lplm+a++i++a+a+
  gi|298675800|ref|YP_003727550.1| 366 AMVGMGSVFAGTLHAPLTGMLILFELTRDYQLILPLMFACVISNAIAN 413
                                       *********************************************986 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.1   1.2e-11   1.1e-07       1      56 [.     446     501 ..     446     502 .. 0.94
   2 !   45.2   0.2     1e-15   9.1e-12       1      53 [.     509     563 ..     509     566 .. 0.93

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 1.2e-11
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       V+d m +dv +v ++ t++ ++ +m +++++++PV+d + kl Givtl Dl ++++
  gi|298675800|ref|YP_003727550.1| 446 VEDAMVKDVQSVLENNTVGTLIHMMQSSKHGGFPVLDLNRKLRGIVTLQDLREKVK 501
                                       7899*********************8788********999***********99875 PP

  == domain 2  score: 45.2 bits;  conditional E-value: 1e-15
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE..ETTTBEEEEEEHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVV..dedgklvGivtlrDllr 53 
                                       +++im ++v +++pd+tl  +l+++++ +++rlPVV  d++ +l+G++t++D+++
  gi|298675800|ref|YP_003727550.1| 509 ISEIMYKNVAVAYPDETLDTVLNRLAKLDIGRLPVVsrDDETELLGLITRSDIIN 563
                                       589**********************7777********999999**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (579 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.24s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 4046.68
//
Query:       gi|298675801|ref|YP_003727551.1|  [L=384]
Description: quinoprotein glucose dehydrogenase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-89  300.8   0.1    1.6e-89  300.5   0.1    1.1  1  GSDH       Glucose / Sorbosone dehydrogenase
  ------ inclusion threshold ------
       0.11   12.4   0.8        0.8    9.5   0.9    2.2  2  SmpA_OmlA  SmpA / OmlA family


Domain annotation for each model (and alignments):
>> GSDH  Glucose / Sorbosone dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  300.5   0.1   1.8e-93   1.6e-89       3     329 ..      63     359 ..      61     371 .. 0.94

  Alignments for each domain:
  == domain 1  score: 300.5 bits;  conditional E-value: 1.8e-93
                                       -EEEEEE-TTS-EEEEETTTEEEEEE..TTEE.EEEEE-.----STT-SEEEEEE-TTTTTS-EEEEEEEE-...TT CS
                              GSDH   3 hPwslaflpdgrlLvtersGrlrlvk.adgklkepiagvpevvakgqgGlldvalhpdfaenrlvYltyaeaeeekg 78 
                                       +Pws++flpdg++++ter+Gr+++++ ++g+l++p+ +++ev+++g+gGll+++lhpdf++n++vY++y+ +  +++
  gi|298675801|ref|YP_003727551.1|  63 IPWSINFLPDGSIIFTERPGRIQMIDvEQGQLQKPLLTIDEVAHSGEGGLLGITLHPDFSDNHWVYVYYTYE--DGE 137
                                       7*************************999999**************************************55..777 PP

                                       SSEEEEEEEEE-SS..-EEEEEEEEEEE---TT-------EEE-TTS-EEEE---TT-GGGGG-TT-SSSEEEEE-T CS
                              GSDH  79 gagtavararlsedeaaledlevifrqepkvesgahfGsrlafgpdgtLfvtvGdrskreeaqdlsselGkilrlnk 155
                                       ++ ++v+r++ ++   +l + ++i +++p   s  h+G+r+ fgpdg+L++t+Gd ++ e aq+ +s +Gkilrl++
  gi|298675801|ref|YP_003727551.1| 138 NTANKVVRFEKNKR--NLVNKTTIIDDIPG--SFIHNGGRIKFGPDGYLYITTGDSANGELAQNKNSLAGKILRLED 210
                                       77889999999666..**************..889****************************************** PP

                                       TSSB-TT-TTTT-TTS-TTEEEE--SCE---EE-TTT--EEEEEE--SSSEEEEEE-TT-B--TTT-S......S-. CS
                              GSDH 156 dGsvpadnpfvgkagakpeiwsyGhRnpqGlaldpdtgeLwesEhGprggDelnlieaGknYGWplvsygeeYsgkk 232
                                       dGsvp++npf      ++ i+s+GhRnpqGla+d++ ++Lw++EhG++  Delnli++G+nYGWp+++      g+ 
  gi|298675801|ref|YP_003727551.1| 211 DGSVPKNNPF-----PDSPIYSLGHRNPQGLAWDKQ-DRLWSTEHGSSATDELNLIKPGNNYGWPVIQ------GD- 274
                                       **********.....5899***************99.******************************9......44. PP

                                       ....-S-TTS---SE.EETT---EEEEEEE........TTEEEEEETTTTEEEEEEEEEEEEEEEEEEEEESS-.-E CS
                              GSDH 233 igesetreglekpvl.vwtpsiapsglafytgdafpewkgdllvggLksqsllrleldegekvveeerlleelgeri 308
                                           et  gle+pv+ + ++++apsg+a+ +g+ +        ++gL+sqsl+  e+ +++++  +++l +++g r+
  gi|298675801|ref|YP_003727551.1| 275 ----ETSTGLENPVIhSGSQTWAPSGAAYLNGSVY--------FAGLRSQSLYEAEIGDNKSIDLKRHLKRKFG-RL 338
                                       ....77899****98578899******99877665........9*************87888888888889999.** PP

                                       EEEEE-TTS-EEEEE-TTTTT CS
                              GSDH 309 RdVeqgpdGalyvltdeedgk 329
                                       R V +gpd  ly+ t+++dg+
  gi|298675801|ref|YP_003727551.1| 339 RGVVVGPDDFLYIFTSNRDGR 359
                                       *******************97 PP

>> SmpA_OmlA  SmpA / OmlA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.9   8.9e-05       0.8      34      66 ..     121     151 ..     116     155 .. 0.83
   2 ?   -1.0   0.0      0.17   1.6e+03      35      51 ..     344     360 ..     342     373 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 8.9e-05
                                       SSSSEEEEEEEETTE.....EEEEEEEE-TTSB CS
                         SmpA_OmlA  34 fdpnrwdYvynfkrggkaveqqvlavyFdddgl 66 
                                       f +n+w Yvy++ + g++  + + +v+F+++++
  gi|298675801|ref|YP_003727551.1| 121 FSDNHWVYVYYTYEDGEN--TANKVVRFEKNKR 151
                                       899***********8755..7777899999876 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.17
                                       SSSEEEEEEEETTE... CS
                         SmpA_OmlA  35 dpnrwdYvynfkrggka 51 
                                       +p+ + Y+++  r g  
  gi|298675801|ref|YP_003727551.1| 344 GPDDFLYIFTSNRDGRG 360
                                       789999***99987555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2448.84
//
Query:       gi|298675802|ref|YP_003727552.1|  [L=94]
Description: hypothetical protein Metev_1926 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 678.18
//
Query:       gi|298675803|ref|YP_003727553.1|  [L=195]
Description: resolvase domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.7e-19   69.7   0.1    3.2e-19   69.5   0.1    1.1  1  Resolvase  Resolvase, N terminal domain
     0.0067   16.6   0.0      0.013   15.7   0.0    1.5  1  HTH_17     Helix-turn-helix domain
  ------ inclusion threshold ------
      0.074   13.1   0.0       0.18   11.9   0.0    1.7  1  HTH_7      Helix-turn-helix domain of resolvase
      0.077   11.8   0.0       0.11   11.3   0.0    1.2  1  Trp_syntA  Tryptophan synthase alpha chain


Domain annotation for each model (and alignments):
>> Resolvase  Resolvase, N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.5   0.1   7.1e-23   3.2e-19       2     134 ..      56     186 ..      55     195 .] 0.83

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 7.1e-23
                                       EEEEEES-----THHHHHHHHHHHH-S--..SE...EEEE.S-TT-TT.-HHHHHHHHHHTT-EE.EEEESSCCCC- CS
                         Resolvase   2 igYaRvSteeqddslerQkealrayakenglkivkefeDkgvSGakle.RpglkrllaalregkgdvlvvekldRLa 77 
                                       ++YaRvSt++q+++le+Q+++l+ +a + g+++  +++D   SG + e R+++ ++l+++++ k++ +++   dRL+
  gi|298675803|ref|YP_003727553.1|  56 VIYARVSTSKQKKDLENQVQMLETWAFNSGYQVNHIYSDV-SSGISFEkRKDFFKMLDEITNYKVENVIISYKDRLS 131
                                       89*******************************9******.*****555**************************** PP

                                       S...S-HHHHHHHHHTT-EEEESS..SS----H.HHHHHHHHHHHHHHHHHHHHCT-T CS
                         Resolvase  78 Rsvrdlltlleelrekgvslvsldegidtstpm.grlllqilaalaeferelirertk 134
                                       R  ++l+  ++ +++ g +++++++ i  ++    +++ +i + l  +  +l ++  +
  gi|298675803|ref|YP_003727553.1| 132 RVGFELF--YHLFSKYGTNIIVVSD-IGNKKLDdEEVFSEITSLLHCYSMKLYSKTRA 186
                                       *999998..789************8.43333332666777776666555555555554 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.8e-06     0.013       5      50 ..       4      50 ..       1      51 [. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.8e-06
                            HTH_17  5 eEaAelLgvsrstvyrlirrgelpaak.iGrrwriprsdleewlekr 50
                                       ++ + L++ r t+yr++ +g ++ +   ++++ ++ +++ ++l+k+
  gi|298675803|ref|YP_003727553.1|  4 GDVLKTLRITRPTLYRYVENGYIKRTLlPNGQYEYDDESVYAFLNKD 50
                                      577788*****************888345666999999999999985 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.9e-05      0.18      22      42 ..       1      21 [.       1      24 [. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.9e-05
                                      --STTTSSSS---SSSS--SS CS
                             HTH_7 22 isiskIAkevnisRsTvYRyl 42
                                      +++ ++ k + i+R T+YRy 
  gi|298675803|ref|YP_003727553.1|  1 MKAGDVLKTLRITRPTLYRYV 21
                                      5678999*************7 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.4e-05      0.11      72     128 ..     105     159 ..      95     173 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.4e-05
                                       HHHHHHHHHHHHHCSSS-EEEEE-CHHHCCC-HHHHCHHHHHCTEEEEEETTSBCCC CS
                         Trp_syntA  72 ekvlelveevrkkevevPivlltylnlvlsygeerflaelkeagvdglivpDlPlee 128
                                       ++++++++e++  + +v  v+++y + + ++g e f++ + + g + ++v D+  ++
  gi|298675803|ref|YP_003727553.1| 105 KDFFKMLDEIT--NYKVENVIISYKDRLSRVGFELFYHLFSKYGTNIIVVSDIGNKK 159
                                       67999*****9..667777999******************************97654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1043  (0.0581739); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1182.64
//
Query:       gi|298675804|ref|YP_003727554.1|  [L=401]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.2e-24   84.8   0.1    1.1e-23   83.8   0.1    1.5  1  OrfB_IS605      Probable transposase
    2.4e-12   46.6   0.0    5.7e-12   45.4   0.0    1.7  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    9.8e-05   21.8   0.7    0.00016   21.0   0.7    1.4  1  Glyco_hydro_97  Glycoside hydrolase 97
  ------ inclusion threshold ------
      0.027   14.5   0.6      0.056   13.5   0.1    1.8  2  Dynamin_N       Dynamin family
       0.11   12.9   1.8       0.47   10.9   0.3    2.7  3  ACP_PD          Acyl carrier protein phosphodiesterase
       0.12   12.7   2.2       0.13   12.6   0.3    2.0  2  Muted           Organelle biogenesis, Muted-like protein


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.8   0.1   3.6e-27   1.1e-23       3     117 ..     172     285 ..     170     288 .. 0.92

  Alignments for each domain:
  == domain 1  score: 83.8 bits;  conditional E-value: 3.6e-27
                        OrfB_IS605   3 pvevevelpkpkgnkaagiDlGinnLatvvtedgtw.flykgrrlksdykylakeiaelqsklkksknykkasrkla 78 
                                       +++++ e+   ++n+ a+iDlGinn++t+v++ g+  +++kg  +ks ++y++k++ +  s+++k +     +++l 
  gi|298675804|ref|YP_003727554.1| 172 VYKQKIEHINLNENNIASIDLGINNIITMVNNIGEKpIVIKGGGVKSINQYYNKKKSQWKSFYDKRG--FDETKRLE 246
                                       5555555667789**********************99*****************************9..78888999 PP

                        OrfB_IS605  79 rlhrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       ++++kr++++++++hk+++++i+++ e++++tL+vg+  
  gi|298675804|ref|YP_003727554.1| 247 KIYQKRNNKINDFFHKVSKKIINYCIENNIGTLIVGYNE 285
                                       ************************************986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.0   1.9e-15   5.7e-12       1      69 []     306     380 ..     306     380 .. 0.92

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 1.9e-15
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke......alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f klk+q+eyka+++Gikv+  +++yTSk +    + +++      ++ +r + +++ g+ +++Dvn+a+Ni+k+
  gi|298675804|ref|YP_003727554.1| 306 FFKLKKQIEYKAEDAGIKVVFQEESYTSKCSFLDDEPVERrtsylgKRIKRGLFRSSNGTIINADVNGAYNIMKK 380
                                       789*************************98888888888899999*99999999999****************96 PP

>> Glyco_hydro_97  Glycoside hydrolase 97
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.7   5.5e-08   0.00016      28     108 ..     255     334 ..     216     359 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 5.5e-08
                    Glyco_hydro_97  28 fkhgantetvkryiDfAaengleyvlvegwdegWee..kkkkekefdftkpypdfdleelvaYakekgvgvelwlhs 102
                                       + + +  +  k+ i+++ en++ +++v g++egW++  +   +k+++ + ++p f+l++ ++Y +e   g++++ ++
  gi|298675804|ref|YP_003727554.1| 255 KINDFFHKVSKKIINYCIENNIGTLIV-GYNEGWKQdsN-IGKKNNQNFVQIPFFKLKKQIEYKAEDA-GIKVVFQE 328
                                       44555567789****************.*******9843.445556666789***********65554.67777776 PP

                    Glyco_hydro_97 103 etsgnv 108
                                       e ++++
  gi|298675804|ref|YP_003727554.1| 329 ESYTSK 334
                                       665444 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.3     4e+03      41      41 ..      71      71 ..      13     113 .. 0.61
   2 ?   13.5   0.1   1.9e-05     0.056      35      97 ..     208     274 ..     192     281 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.3
                                      C CS
                         Dynamin_N 41 g 41
                                      +
  gi|298675804|ref|YP_003727554.1| 71 Q 71
                                      2 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.9e-05
                                       -EEEEECCT---C..CS...SSEEEE..T-EB--CHHHHHHHHHHHHHHHTSSSS--SS-EEEEEEE CS
                         Dynamin_N  35 plelqlgeeeeas..eravkeelkek..ekkledfsevreeieketekiagankgiskkvillkils 97 
                                       p++++ g  ++++   ++ k ++k++  ++ +++ +++++ ++k+++ki++   ++skk+i+++i +
  gi|298675804|ref|YP_003727554.1| 208 PIVIKGGGVKSINqyYNKKKSQWKSFydKRGFDETKRLEKIYQKRNNKINDFFHKVSKKIINYCIEN 274
                                       5556555444444334567888999999***********************************9875 PP

>> ACP_PD  Acyl carrier protein phosphodiesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.3   0.00016      0.47      34      92 ..      26      87 ..      13      95 .. 0.72
   2 ?   -2.2   0.0       1.9   5.8e+03      81     101 ..     215     235 ..     196     239 .. 0.83
   3 ?   -1.9   0.1       1.5   4.6e+03      85      99 ..     245     259 ..     218     269 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00016
                            ACP_PD 34 alPerlqrllprmieedwLesY..aelegieralqrma.rrlkrasklaeaieeleenyael 92
                                      +++++l + ++++i+++wL+ Y   + e +++ l++ + + +  ++  +++++ +++n + +
  gi|298675804|ref|YP_003727554.1| 26 HISKNLYNQANYIIRQNWLNGYgyTKYEKVNEELKGTEnYSILPSQTAQQTLKMVDKNWKSF 87
                                      6678889999*********9762267899999999999444444444666666666665554 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.9
                            ACP_PD  81 aieeleenyaeleadFleffp 101
                                        ++ +++ y++ ++++++f+ 
  gi|298675804|ref|YP_003727554.1| 215 GVKSINQYYNKKKSQWKSFYD 235
                                       677889999999999999996 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.5
                            ACP_PD  85 leenyaeleadFlef 99 
                                       le+ y++ +++ ++f
  gi|298675804|ref|YP_003727554.1| 245 LEKIYQKRNNKINDF 259
                                       222233333333333 PP

>> Muted  Organelle biogenesis, Muted-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       1.1   3.2e+03      96     114 ..      70      88 ..      11      96 .. 0.61
   2 ?   12.6   0.3   4.4e-05      0.13      56     146 .]     176     267 ..     167     267 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.1
                             Muted  96 seqlqekeeerkaeweefl 114
                                       s++ q++ +   ++w++f 
  gi|298675804|ref|YP_003727554.1|  70 SQTAQQTLKMVDKNWKSFF 88 
                                       2333333344444444444 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 4.4e-05
                             Muted  56 lpkclesmkenLselnkkleaalekverllqkeleeekrkseqlqekeeerkaeweeflkel.qekkeevDeefeek 131
                                         + ++  ++n+ ++   +++   +v+++ +k    +    + +++  +++k++w++f ++   ++++++++ +++ 
  gi|298675804|ref|YP_003727554.1| 176 KIEHINLNENNIASIDLGINNIITMVNNIGEKPIVIKGGGVKSINQYYNKKKSQWKSFYDKRgFDETKRLEKIYQKR 252
                                       444556678999999999**************999999999*****************9765268999********* PP

                             Muted 132 veelkekYselekkL 146
                                        +++++ ++++ kk+
  gi|298675804|ref|YP_003727554.1| 253 NNKINDFFHKVSKKI 267
                                       *********999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1263  (0.0704445); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 2556.81
//
Query:       gi|298675805|ref|YP_003727555.1|  [L=433]
Description: MiaB-like tRNA modifying enzyme [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.6e-23   81.7   0.1    8.4e-22   78.3   0.0    2.2  2  Radical_SAM  Radical SAM superfamily
    1.5e-21   76.3   0.2    3.1e-21   75.3   0.2    1.6  1  UPF0004      Uncharacterized protein family UPF0004
    9.4e-05   22.3   0.0    0.00018   21.4   0.0    1.6  1  TRAM         TRAM domain
  ------ inclusion threshold ------
       0.11   12.6   0.0       0.22   11.6   0.0    1.5  1  B12-binding  B12 binding domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.11   4.9e+02      27      66 ..      48      85 ..      10     126 .. 0.53
   2 !   78.3   0.0   1.9e-25   8.4e-22       3     167 .]     148     320 ..     146     320 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.11
                                      HHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 27 rslsveeileevkelkaekgvkevilgggepllypdfvel 66
                                      ++ + ++il+++ el  +kg  ev+++g  p ++ d + +
  gi|298675805|ref|YP_003727555.1| 48 KYTTEQKILHKIGELG-RKG-LEVVVSGCMPEVQHDDILD 85
                                      3444444555555552.442.2222222224433333332 PP

  == domain 2  score: 78.3 bits;  conditional E-value: 1.9e-25
                                       EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS..........TTHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly..........pdfveller 69 
                                       +++gCn+rC +C +++    +g+ +s ++++i+e v+++ ++ g++e+++++++   y          p   +ll+r
  gi|298675805|ref|YP_003727555.1| 148 ISQGCNNRCAYCVVRT---ARGKLKSFDIDSIVEDVRKA-VSEGCREIWITSQDNAQYgidrqngvllP---QLLDR 217
                                       789************9...8*******************.9**********999999899977775443...34444 PP

                                       HHHTCCCTEEEEEEE.CSSCHG...HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxx.xxxxxx...xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  70 laklavpgiritvet.ngtlpd...eeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreag 141
                                        a ++  +++i+v   n++ ++   ++ l+   +      ++l++++a+++ vl +mnr++t +ev e + k+r++ 
  gi|298675805|ref|YP_003727555.1| 218 VASIE-GNFKIRVGMmNPFSVYpilDDLLKVYENNKiYKFLHLPIQSASEK-VLGYMNRNYTMSEVDEIITKFRSR- 291
                                       44443.333333332033333234477777777777***************.************************. PP

                                       SET...EEEEEEEBTTTSHHHHHHHHHHH CS
                                       xxx...xxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 142 ikr...vvdrivglpGendeeleellell 167
                                       +++   v+d+ivg+pGe+++++ + ++++
  gi|298675805|ref|YP_003727555.1| 292 FNDltlVTDIIVGFPGETEDDFYKSIDWV 320
                                       ************************99986 PP

>> UPF0004  Uncharacterized protein family UPF0004
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3   0.2   6.9e-25   3.1e-21       1      94 [.       2      91 ..       2      94 .. 0.93

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 6.9e-25
                                      XEEEE--S-CCCCHHHHHHHHHTTTSSS----SSS--SEEEEEE--SSSSHHHHTHHHHHHHHTTST.--EEEEEEHHH CS
                           UPF0004  1 kvaietlGCqmNevdseelaslLkkegyelvedeeeAdvvlvnTCavrekaekkviqalrelkalkkpekkvvvlGCma 79
                                      kv++ t+GC   ++ se++++++k++g+elv++ ++Advv++nTC+v+ ++e+k++++++el ++     +vvv GCm+
  gi|298675805|ref|YP_003727555.1|  2 KVHVATYGCPSSQAASEIMMDAIKRQGHELVDE-KSADVVVFNTCTVKYTTEQKILHKIGELGRKG---LEVVVSGCMP 76
                                      799***************************988.69**************************9977...9********* PP

                                      HS-HHHHHHH-TTS- CS
                           UPF0004 80 qrekeellkeepevd 94
                                      + +++++l++++ ++
  gi|298675805|ref|YP_003727555.1| 77 EVQHDDILDNNQDAH 91
                                      *********998643 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   4.1e-08   0.00018      20      61 ..     390     431 ..     372     432 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 4.1e-08
                                       SEEEEEET.TEEEEETT-..-T..TEEEEEEEEEE-SSEEEEEE CS
                              TRAM  20 gegiGrtdngkvvfvpgd..lpgIGdfVeVkItkvkrqyLrGel 61 
                                          ++rt+ +k+v++p     p  G++ +V+It+++++y  G+l
  gi|298675805|ref|YP_003727555.1| 390 KGVMARTESYKPVVIPESnlPP--GQWCDVEITDTTSGYFLGKL 431
                                       5579**************9999..***************98886 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.9e-05      0.22      46     110 ..      31      93 ..       5     100 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.9e-05
                       B12-binding  46 airaekpdvvglSalltsqleavkelvel.lkrirprvkvvvGGahpsldpeetleaklgiddvvv 110
                                        + +  +dvv++ +  t +++  +++++   +  r+++ vvv G  p++ ++++l + ++ d  ++
  gi|298675805|ref|YP_003727555.1|  31 LVDEKSADVVVFNT-CTVKYTTEQKILHKiGELGRKGLEVVVSGCMPEVQHDDILDN-NQ-DAHIL 93 
                                       566789******99.9*******999999744456799*****************97.55.55555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.54
# Mc/sec: 2412.95
//
Query:       gi|298675806|ref|YP_003727556.1|  [L=363]
Description: fructose-1,6-bisphosphatase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   4.4e-115  383.8   5.9   5.1e-115  383.6   5.9    1.0  1  FBPase_glpX     Bacterial fructose-1,6-bisphosphatase, glpX-e
  ------ inclusion threshold ------
      0.038   13.4   0.2       0.59    9.5   0.1    2.2  2  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family


Domain annotation for each model (and alignments):
>> FBPase_glpX  Bacterial fructose-1,6-bisphosphatase, glpX-encoded
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  383.6   5.9  5.7e-119  5.1e-115       2     307 ..      20     350 ..      19     351 .. 0.97

  Alignments for each domain:
  == domain 1  score: 383.6 bits;  conditional E-value: 5.7e-119
                       FBPase_glpX   2 nlalelvrvteaAAlaaarlvGrgdkeaadqaAveamrkalneleikgevviGegekdeapmLyiGekvGsgeg.pe 77 
                                       nl   l++vte+AA+aaa+ vG g+k+ ad+++ve+mr++ln+l++kg + iGege+deapmLyiGe++G+g+g  e
  gi|298675806|ref|YP_003727556.1|  20 NLLPRLINVTESAAIAAAHEVGLGNKNYADHVSVESMRRMLNSLDMKGLIKIGEGERDEAPMLYIGEEIGTGKGdLE 96 
                                       677889********************************************************************99* PP

                       FBPase_glpX  78 vdiavdpleGttlvAkglpnaisviAvaekgsllkapdvYmeKlvvgpea.k.......gvidldapveenlkavak 146
                                       vdiavdpleGt+lvA+g+p+aisv+A++e+g l++ pdvYmeK+vvg+++ k       ++idldapv++nl++vak
  gi|298675806|ref|YP_003727556.1|  97 VDIAVDPLEGTNLVADGMPGAISVMAMSERGGLFHGPDVYMEKIVVGSDVvKyerehpdEKIDLDAPVADNLNIVAK 173
                                       ************************************************99559999999****************** PP

                       FBPase_glpX 147 algkevedltvvvLdrpRheelieeireagarvklisdGDvaaaiaaaleesgvdvllGiGgapEGvlaAaalkclg 223
                                       al++++++++vv+Ldr+R+ ++i++ir+agarv+l++dGD+ + +a+a+++sgv+v++G+Gg+ E+vl+Aaa+k+lg
  gi|298675806|ref|YP_003727556.1| 174 ALNRNIDEIVVVILDRERNYKIINDIRQAGARVNLVTDGDLIPGVATAIRGSGVHVVMGSGGSGEAVLTAAAIKILG 250
                                       ***************************************************************************** PP

                       FBPase_glpX 224 Gemqarlvpr..............keeereraekmgi..edldkvltledLvkgddvifaatgvTdgelLkgvrfkg 284
                                       G++ +rl++               k e++ r++kmgi  +++d+vl+++ +v g+dvifaatg+T+g++Lk v+++g
  gi|298675806|ref|YP_003727556.1| 251 GKILTRLLLPtvakgksgeeiekeKLEKMPRLNKMGIteDNMDTVLDTDMIVPGRDVIFAATGITSGHFLKQVNLFG 327
                                       *******97669*********998889999*******77789*********************************99 PP

                       FBPase_glpX 285 gg.arteslvmrsksgtvrfiesi 307
                                       +g ar++s+ m s sg+vrf +s+
  gi|298675806|ref|YP_003727556.1| 328 TGdARVHSISMGS-SGVVRFTDSM 350
                                       999********99.6*****9986 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   6.6e-05      0.59      38     112 ..     136     210 ..     130     222 .. 0.93
   2 ?    1.5   0.0     0.018   1.6e+02     130     170 ..     256     297 ..     244     308 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 6.6e-05
                                       SSS-B-B-HHHHHHHGGGE-S-EEEEEESSSHHHCHHHHHHCT-SEEEEE-ST-TTHHHHHHHHHHTTSEEEEEE CS
                    Ribul_P_3_epim  38 fvpNltigplvvealrkltelpldvHLmveevdrivpefaeagasiisvHaEalehlkrtiqeikeaGakaglvl 112
                                       +++ +++g  vv+  r++ + ++d+   v++  +iv + ++ + + i+v + + e   ++i++i++aGa++ lv 
  gi|298675806|ref|YP_003727556.1| 136 YMEKIVVGSDVVKYEREHPDEKIDLDAPVADNLNIVAKALNRNIDEIVVVILDRERNYKIINDIRQAGARVNLVT 210
                                       8999**************************99999999999999999999999999**************99985 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.018
                                       EEEEESS-TT-SS----CCHHHHHHHHHHH.HHHHT---EEE CS
                    Ribul_P_3_epim 130 lvllmsvePgfgGQkFipevlekikkvrkl.idekeldlkie 170
                                        +ll +v  g++G +  +e lek+ ++ k+ i+e ++d+ + 
  gi|298675806|ref|YP_003727556.1| 256 RLLLPTVAKGKSGEEIEKEKLEKMPRLNKMgITEDNMDTVLD 297
                                       568889999999999999999999999888344445666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2500.48
//
Query:       gi|298675807|ref|YP_003727557.1|  [L=169]
Description: hypothetical protein Metev_1931 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-09   37.1   0.1    4.3e-09   36.7   0.1    1.0  1  CGI-121   Kinase binding protein CGI-121


Domain annotation for each model (and alignments):
>> CGI-121  Kinase binding protein CGI-121
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.1   2.4e-13   4.3e-09       9     161 ..      17     164 ..      10     164 .. 0.83

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 2.4e-13
                                       HHHHTH..C..CHCTT-EEE-GGG---HHHHHHHHHHHHHHHHHS---SSSHHHHHHHHHSSSS-HHHHHHHHB--T CS
                           CGI-121   9 elrkql..lskraeldfafldaslilskehllsAvlrallaaargklktktlhsEilfsLspnnnIgealkrfgisd 83 
                                         +k+l  ++  +++ +  l+a+++  k hl  +v +al a ++g  + k    Ei+ + s++++I++a++  gi +
  gi|298675807|ref|YP_003727557.1|  17 GFIKKLddIASVNNVTVQALNADKLAGKRHLEFSVKKALRAIENGYNRAKDTGIEIMRYASGKRQIEDAFN-IGIHN 92 
                                       5555665655556788999***************************************************9.***** PP

                                       T-S-EEEEEEESSS--HHHHHHHHHHHS-SEEE.--SHHHHHH--HHHHHHHTT--..TT---SSHHHHHHHHHHHH CS
                           CGI-121  84 kttsllvvkvssseadeeevlkslkevvegelv.pleeeleeltdwkkikkiYklneleeekeeevkeledlvvsav 159
                                        t+++  v ++++ ++ + v+++l+ ++  ++v   +e     +  + i   + ++ + e ++  ++++ +lv+++v
  gi|298675807|ref|YP_003727557.1|  93 GTNNIAFVILGNP-ENISYVSEKLNGLITENPVlAYDE-----SKRDFILSEFEIT-QPEVDAVGEHKIPELVLERV 162
                                       ***********99.788999*********999966666.....5678888999999.33333344444888888888 PP

                                       HT CS
                           CGI-121 160 al 161
                                       al
  gi|298675807|ref|YP_003727557.1| 163 AL 164
                                       86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 1036.64
//
Query:       gi|298675808|ref|YP_003727558.1|  [L=406]
Description: threonine synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-79  267.1   0.4    2.3e-79  266.9   0.4    1.0  1  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  266.9   0.4   1.3e-83   2.3e-79       2     294 .]      69     372 ..      68     372 .. 0.97

  Alignments for each domain:
  == domain 1  score: 266.9 bits;  conditional E-value: 1.3e-83
                                       GGCSSS--EEEECCTCCCCCCE.EEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHH CS
                              PALP   2 tlgigpTPlvrlprlskelgvp.lflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaall 77 
                                       + ++g+TPl r++rl++++g++ l++K E+lnptgSfKdRg++  ++++ e  g ktv++as+GN+ ++l +++a++
  gi|298675808|ref|YP_003727558.1|  69 SIEEGGTPLYRCDRLADKIGIKgLYVKHEGLNPTGSFKDRGMTVGVSKAIEL-GMKTVACASTGNTSASLGIYGARA 144
                                       6689************************************************.************************ PP

                                       T-EEEEEEETTS-H.HHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHH CS
                              PALP  78 Glkvtivvpadasp.ekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileq 153
                                       G+++++++p+++ + +kva+  ++Ga+v  v g++dea+ ++++l+ + e++yl+++  np++ eg++tig+Ei++q
  gi|298675808|ref|YP_003727558.1| 145 GIPAVVLLPEGKVAlGKVAQALMHGAKVLSVRGNFDEALVLVRQLCDD-EKFYLLNSV-NPYRLEGQKTIGFEIIDQ 219
                                       *************88*********************************.*********.9***************** PP

                                       TT.TTEEEEEEE-SSSHHHHHHHHHHHH......HSTT..-EEEEEEECTTCGGTTCCS..S.SS..B...SSS.CC CS
                              PALP 154 lg.gkpdavvvpvGgGgliaGiaaglke......rrpd..vrvigvepegsdalarslragrrvtvpvs..dtiadg 219
                                       lg ++p+ vv+pvG++g+i++i++g+ke         d  +r+ g+++eg++++ +++r+gr + +p++  dtia++
  gi|298675808|ref|YP_003727558.1| 220 LGfNVPERVVLPVGNAGNITAIYKGFKEfmnigiT--DkvPRMTGIQSEGAAPIVDAYRNGRDDITPEKnpDTIATA 294
                                       ****************************9987433..367***********************99999999****** PP

                                       STCS..CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEEEEEEE- CS
                              PALP 220 lavg..spselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaal.klreagelkegdrvvvilt 293
                                       +++g  +++ +a++++ ++++ + tv+d+e+++a+r la+ egi vep+sa ++a+l kl+++g ++++++vv++ t
  gi|298675808|ref|YP_003727558.1| 295 IRIGnpVNAKKALKAIYESNGMADTVTDDEIVQAQRDLAQLEGIGVEPASASSVAGLkKLVNDGIIGKDETVVCVTT 371
                                       ****99999******************************************************************99 PP

                                       B CS
                              PALP 294 g 294
                                       g
  gi|298675808|ref|YP_003727558.1| 372 G 372
                                       8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 2491.51
//
Query:       gi|298675809|ref|YP_003727559.1|  [L=964]
Description: leucyl-tRNA synthetase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-62  210.1   8.7    1.4e-44  152.3   2.4    2.7  3  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    1.5e-26   93.0   1.9      5e-12   45.3   0.0    3.5  2  tRNA-synt_1g   tRNA synthetases class I (M)
    5.6e-23   81.6   1.9    5.9e-23   81.5   0.3    1.9  2  Anticodon_1    Anticodon-binding domain of tRNA
    5.6e-10   39.0   0.1    9.6e-07   28.4   0.0    2.8  2  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
    2.7e-09   36.8   0.1    7.1e-09   35.4   0.1    1.6  1  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
     0.0031   16.5   0.0      0.013   14.5   0.0    2.0  2  tRNA-synt_1d   tRNA synthetases class I (R)
  ------ inclusion threshold ------
      0.019   13.9   0.0      0.019   13.9   0.0    2.2  4  tRNA-synt_1f   tRNA synthetases class I (K)


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.3   2.4   5.6e-48   1.4e-44       1     305 [.      13     329 ..      13     335 .. 0.84
   2 !   60.9   0.2   2.7e-20     7e-17     319     601 ..     396     672 ..     377     673 .. 0.85
   3 ?   -3.7   0.0      0.97   2.5e+03      35      56 ..     862     883 ..     860     886 .. 0.89

  Alignments for each domain:
  == domain 1  score: 152.3 bits;  conditional E-value: 5.6e-48
                       tRNA-synt_1   1 klyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaie 77 
                                       k++++W+ee++f++     +++++f ++++ Py +G+lH Gh  + t+ d v r krmkG++vly +G+   G +  
  gi|298675809|ref|YP_003727559.1|  13 KWQKRWDEEKIFEAD---PDNREKFLITVPYPYLNGNLHAGHTRTFTIGDAVARHKRMKGYNVLYPMGFHVTGTPLV 86 
                                       5899*********99...8889***************************************************9974 PP

                       tRNA-synt_1  78 akvekklgakekkerkklgr.....e...efrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkev 146
                                         + + + ++e k+ + +++         e  +   +++++++ e +k++k +G s+D+ r+  T ++ +++ +++ 
  gi|298675809|ref|YP_003727559.1|  87 G-LSELIKKQESKTMEVYSKyhgipRnilENLDTPDKIVDYFTVEAEKSMKSIGYSIDWRRKFTTTEEAYKQFIEWQ 162
                                       3.34444445555555444411112211133445578999************************************* PP

                       tRNA-synt_1 147 fvrladkgliyrgkklvnwstklktalselEveykdkkdal..ihvafpladkeevklviaTTtPeTllgdtavavn 221
                                       f  l++kg i +g+++v+w+++   ++ + ++ + ++ + +  + ++f+   ++ v++  aT +PeT++g t + vn
  gi|298675809|ref|YP_003727559.1| 163 FNLLYKKGYIVKGSHPVKWCPSDDNPVEDHDILHGEEANIVdyTLIKFKY--DD-VTIPCATLRPETVFGVTNLWVN 236
                                       ********************************777776554113344443..33.5899****************** PP

                       tRNA-synt_1 222 peldyv.........itkeklilaeallkslvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGt 289
                                       pe++yv          + e++i+ +    +l   +++ +  ed+ +++L+g +ve+p+++ ++  +   +v+ e G+
  gi|298675809|ref|YP_003727559.1| 237 PEIEYVkvkvkkdgeDKSEYWIVSKRTYTKLQYTDKNVEYIEDVPASSLIGIKVENPVTGDDVISLPASFVTDEYGS 313
                                       *********99998445556666666666666666888*************************************** PP

                       tRNA-synt_1 290 GvVkiaPahdedDyev 305
                                       G+V   Pah + Dy +
  gi|298675809|ref|YP_003727559.1| 314 GIVMSVPAHAPYDYLA 329
                                       **************75 PP

  == domain 2  score: 60.9 bits;  conditional E-value: 2.7e-20
                       tRNA-synt_1 319 edgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyra.teqWfvrvke..ladaal 392
                                       ++g+l+e++++++ ++v + +++++++l e+   + +   e s p+  r ++p ++++   qWf + ++   ++++ 
  gi|298675809|ref|YP_003727559.1| 396 HNGVLKENTGKYANIEVSKIKDILTQDLIEQ--TIGEIFYEFSEPVVCRCGTPCVVKMvRGQWFLNYSDpeWKKNVY 470
                                       589***************************9..6677789999***999999976655167****99976799**** PP

                       tRNA-synt_1 393 kavekvqfvpkskekryaswleniqdWciSRqrwWGhriplfvsketeevvvre..elkelvagreeeeaekkalek 467
                                       + ++++ ++p  +++++++ +  i+d +  R++  G+r+p+ ++   e +  ++     ++v++ ++e+ + +++  
  gi|298675809|ref|YP_003727559.1| 471 RCIDQMDIIPPEYRNEFKNKVDWIKDKACARKKGLGTRLPFDRQWLIESLADSTiyMAYYIVRKFVQENFTPEQMVP 547
                                       ****************************************9555555544443321455667777777777777777 PP

                       tRNA-synt_1 468 eakdklkkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlillslaltgs 544
                                       e+ d +  +kg+le + +      +Sg     +l+   + + e++  +p d+ ++G D +   +   ++  +a++++
  gi|298675809|ref|YP_003727559.1| 548 EMFDFVLLGKGNLEDVAE------KSGID-KDILE---QMRYEFEYWYPVDLRSSGKDLVPNHLLFFLFHHVAIFDE 614
                                       888877788888875555......78875.55676...5588********************************999 PP

                       tRNA-synt_1 545 ePf.kevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltli.lsdvgrdinl 601
                                         + + + v+g+v   eG KmSKs+g  +  +d +++ygad+ R +++ ++++++d ++
  gi|298675809|ref|YP_003727559.1| 615 DKWpQAIAVNGFVS-LEGEKMSKSKGPLLTLNDAVDNYGADISRVYILsNAEQTQDADW 672
                                       97725678999986.68*****************************9989999999877 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 0.97
                       tRNA-synt_1  35 tGslHiGhalaktlkdiviryk 56 
                                        G+l iG+ ++  +kd vi+++
  gi|298675809|ref|YP_003727559.1| 862 EGNLNIGNLMKDLMKDPVIKSY 883
                                       699****************975 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.4   2.7e-13     7e-10       1     127 [.      34     186 ..      34     198 .. 0.58
   2 !   45.3   0.0   1.9e-15     5e-12     288     371 ..     592     677 ..     571     692 .. 0.89

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 2.7e-13
                                       EEEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHH...HHTTS-HHHHHHHHHHHH CS
                      tRNA-synt_1g   1 vlvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkA...ekegvtpeelvekvheei 74 
                                       +l+t++ pY ng+lH Gh ++  ++D++aR+kr++g++vl+  g    Gtp        +k++ +  e+ +k+h + 
  gi|298675809|ref|YP_003727559.1|  34 FLITVPYPYLNGNLHAGHTRTFTIGDAVARHKRMKGYNVLYPMGFHVTGTPLVGLSeliKKQESKTMEVYSKYHGIP 110
                                       59**************************************9888888888864332111455555555666666555 PP

                                       HHHHHHTT-...--SEEE....................ETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTT CS
                      tRNA-synt_1g  75 kelfkklni...sfdkyg....................rttseehkelvqeifkklkekgliyekeieqlycpkde 127
                                       ++++++l+      d+++                    +tt+e+ k++ +  f+ l++kg+i +++  + +cp+d+
  gi|298675809|ref|YP_003727559.1| 111 RNILENLDTpdkIVDYFTveaeksmksigysidwrrkfTTTEEAYKQFIEWQFNLLYKKGYIVKGSHPVKWCPSDD 186
                                       5555555431112233330000000000000000001134455555555555555666666666666555555555 PP

  == domain 2  score: 45.3 bits;  conditional E-value: 1.9e-15
                                       EEGGGHHHHHTHHHHHHHH..TT----S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS CS
                      tRNA-synt_1g 288 igkdiikFHtifwPaillg..aelklpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekk 362
                                        gkd ++ H +f+     +   e k p+++++++++ +eg+K+SkS+g + + ++a++++ ad+ R y++++a++++
  gi|298675809|ref|YP_003727559.1| 592 SGKDLVPNHLLFFLFHHVAifDEDKWPQAIAVNGFVSLEGEKMSKSKGPLLTLNDAVDNYGADISRVYILSNAEQTQ 668
                                       49***********999999988999**************************************************** PP

                                       -EEE-HHHH CS
                      tRNA-synt_1g 363 Dldfswedf 371
                                       D+d++ + +
  gi|298675809|ref|YP_003727559.1| 669 DADWRSSGI 677
                                       ***987765 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       2.7   6.8e+03      11      32 ..     150     171 ..     145     173 .. 0.77
   2 !   81.5   0.3   2.3e-26   5.9e-23       1     149 [.     711     839 ..     711     852 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.7
                       Anticodon_1  11 lvkevteayeeyrfnkaasaly 32 
                                       + +e+ + + e++fn  +++ y
  gi|298675809|ref|YP_003727559.1| 150 TTEEAYKQFIEWQFNLLYKKGY 171
                                       6788888888899988777665 PP

  == domain 2  score: 81.5 bits;  conditional E-value: 2.3e-26
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrll 77 
                                       drwils+l++++ ++++a++  + ++a+++ + f++nd+ +wy +   +              ++l+++l+t++rl+
  gi|298675809|ref|YP_003727559.1| 711 DRWILSRLQHYIMDTNDALDAIKTRNALQNSFFFLSNDI-KWYQRRGGE--------------KLLYDILDTWVRLM 772
                                       9**************************************.***777443..............67************ PP

                       Anticodon_1  78 aPfmPfitEelwqreeeelgkk..esimlaewpe.kaeel..ekeleeeevellkeivkairklrselkikpsselk 149
                                       +Pf+P+i+Ee+w    e++g+k  e+++la++pe ++e    ++el     el   i +++ ++ +++k+ + +++k
  gi|298675809|ref|YP_003727559.1| 773 SPFAPHICEEIW----ESMGNKepEFVSLAPYPEhDPELIdnTAEL---GEEL---ISNTLSDIEEIIKVTKINPKK 839
                                       ************....88876667**********888777543333...5555...444444444444444444444 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0     0.001       2.6      21      50 ..      45      74 ..      30      81 .. 0.90
   2 !   28.4   0.0   3.7e-10   9.6e-07     207     295 ..     586     676 ..     576     682 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.001
                                      S--BHHHHHHHHHHHHHHHHHHHTT-EEEE CS
                      tRNA-synt_1e 21 dashlGhaRslvafDilrrilqalgYdvqf 50
                                       + h Gh+R++ + D ++r  +++gY+v +
  gi|298675809|ref|YP_003727559.1| 45 GNLHAGHTRTFTIGDAVARHKRMKGYNVLY 74
                                      578*************************88 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 3.7e-10
                                       SEEEEEEEGGGTTTHHHHHHHHHHHHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHS CS
                      tRNA-synt_1e 207 eidihsGGiDLafPhhenelaqseaafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRlllls 282
                                        +d+ s G+DL+  h    l  + a fd  ++ +    ng++++egekmsks + ++t++d++ ++ + + R+++ls
  gi|298675809|ref|YP_003727559.1| 586 PVDLRSSGKDLVPNHLLFFLFHHVAIFDeDKWPQAIAVNGFVSLEGEKMSKSKGPLLTLNDAVDNYGADISRVYILS 662
                                       58999******999999999********999*****************************************99887 PP

                                       S-.TTS-EEE-HHH CS
                      tRNA-synt_1e 283 ah.yrsqldfkeel 295
                                       +    +  d++ + 
  gi|298675809|ref|YP_003727559.1| 663 NAeQTQDADWRSSG 676
                                       64044445665555 PP

>> tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.1   2.8e-12   7.1e-09      13     126 ..     209     327 ..     205     335 .. 0.72

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 2.8e-12
                     tRNA-synt_1_2  13 efkveeseeklevfttrpdtlfGvtfvalapehplvekl.aekkkelaaf.ieevkkksesereletke.....keG 82 
                                       +fk ++   ++   t rp+t+fGvt + + pe + v+   +++ ++ +++ i + ++ ++ + + ++ e        
  gi|298675809|ref|YP_003727559.1| 209 KFKYDD--VTIPCATLRPETVFGVTNLWVNPEIEYVKVKvKKDGEDKSEYwIVSKRTYTKLQYTDKNVEyiedvPAS 283
                                       455554..4688899*******************9997645544555554144333333333333333321122344 PP

                     tRNA-synt_1_2  83 vftglkaihPitgekipiwvanyvlmeygtgavmavPahdqrDf 126
                                          g+k+ +P+tg+++    a +v  eyg+g vm+vPah   D+
  gi|298675809|ref|YP_003727559.1| 284 SLIGIKVENPVTGDDVISLPASFVTDEYGSGIVMSVPAHAPYDY 327
                                       578************************************98887 PP

>> tRNA-synt_1d  tRNA synthetases class I (R)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0     5e-06     0.013      17      61 ..      29      73 ..      18     101 .. 0.88
   2 ?   -2.3   0.0      0.62   1.6e+03     126     177 ..     380     435 ..     369     441 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5e-06
                                      SST-EEEEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEE CS
                      tRNA-synt_1d 17 rekkkvvvdfssPniakemhvGhLrstiiGdavsrlleflGydvi 61
                                       +++k ++    P +  ++h+Gh r+  iGdav+r   + Gy+v+
  gi|298675809|ref|YP_003727559.1| 29 DNREKFLITVPYPYLNGNLHAGHTRTFTIGDAVARHKRMKGYNVL 73
                                      56677778888899999**************************97 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.62
                                       HCT-HHHHHH..HHHHHHHHHHHHHHHHHHCT---EC..--CCCCCCCHHHHHHHH CS
                      tRNA-synt_1d 126 qsgdedirkl..wkllvditrtelqklydrldvtlie..rGeslykeslneivkel 177
                                       +s+ ed +k+  +k  ++ + +e+   y++++v+ i+    + l ++++ ei  e+
  gi|298675809|ref|YP_003727559.1| 380 DSRAEDATKAvyRKEFHNGVLKENTGKYANIEVSKIKdiLTQDLIEQTIGEIFYEF 435
                                       55556644431145589999999999999999999886656666666666666665 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.1         2   5.2e+03      35      59 ..      45      69 ..      43      72 .. 0.86
   2 ?   -3.5   0.1       1.5   3.8e+03     136     202 ..     396     462 ..     388     475 .. 0.60
   3 ?   13.9   0.0   7.4e-06     0.019     263     347 ..     615     701 ..     583     716 .. 0.62
   4 ?   -3.3   0.0       1.3   3.3e+03      35      90 ..     863     924 ..     844     925 .. 0.65

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 2
                      tRNA-synt_1f 35 GliHiGnlrevltadlvaralrkrg 59
                                      G +H G  r    +d+var  r +g
  gi|298675809|ref|YP_003727559.1| 45 GNLHAGHTRTFTIGDAVARHKRMKG 69
                                      999**************99877766 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.5
                      tRNA-synt_1f 136 ksglydeaikeale.nrekikeilekyrgee.reet.yspylpvcekcgrvdttevvevdaeeeeieYkc 202
                                       ++g+++e++ +  + + +kik+il + + e+ + e  y   +pv  +cg      vv++   ++ ++Y++
  gi|298675809|ref|YP_003727559.1| 396 HNGVLKENTGKYANiEVSKIKDILTQDLIEQtIGEIfYEFSEPVVCRCGT---PCVVKMVRGQWFLNYSD 462
                                       55555555544443146788888887766664333325555677778887...33344444667777765 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 7.4e-06
                      tRNA-synt_1f 263 geaPekvvYelillkggekmssSkGnvltledwlevaepevlrflilrrkPkkakkldldl.eil...rlvdeYdkl 335
                                        + P+ +  + +   +gekms+SkG  ltl+d+++ +  ++ r +il+ + ++  + d +  +i    + ++ ++++
  gi|298675809|ref|YP_003727559.1| 615 DKWPQAIAVNGFVSLEGEKMSKSKGPLLTLNDAVDNYGADISRVYILS-NAEQTQDADWRSsGIEatrKQIERFHNF 690
                                       455766666655555666**********************99999988.5555555544321444111456666666 PP

                      tRNA-synt_1f 336 erkyfaeqeeee 347
                                        r++  ++  ++
  gi|298675809|ref|YP_003727559.1| 691 AREIL-NSGVSQ 701
                                       66665.333333 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 1.3
                      tRNA-synt_1f  35 GliHiGnlrevltadlvaralrkrgee.vrlil...isDdmDglRkvpe.nlpek.llekyl 90 
                                       G + iGnl   l  d v +++ k  ++ v+ i+   +s d  ++ k+++ +l+e+ +l+++l
  gi|298675809|ref|YP_003727559.1| 863 GNLNIGNLMKDLMKDPVIKSYGKEVQKfVQKIApniTSMDRKKFDKIYNsDLDEEsVLKENL 924
                                       77788888877777777777777766665554321134444456677766777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (964 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.85u 0.34s 00:00:01.19 Elapsed: 00:00:00.58
# Mc/sec: 5047.31
//
Query:       gi|298675810|ref|YP_003727560.1|  [L=594]
Description: multi-sensor signal transduction histidine kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      6e-50  170.2   5.0      6e-50  170.2   5.0    1.8  2  Cache_3-Cache_2  Cache 3/Cache 2 fusion domain
    5.4e-24   84.7   2.1    1.7e-23   83.1   1.6    2.2  2  sCache_3_3       Single cache domain 3
    9.9e-22   77.6   0.1    3.4e-21   75.8   0.1    1.9  1  HATPase_c        Histidine kinase-, DNA gyrase B-, and HSP90-
    3.5e-16   59.3   0.0      7e-16   58.3   0.0    1.6  1  HAMP             HAMP domain
    2.1e-14   53.9  10.5    2.1e-14   53.9  10.5    1.9  3  dCache_1         Cache domain
    1.8e-12   47.1   2.2    1.8e-12   47.1   2.2    3.3  3  dCache_2         Cache domain
    4.5e-11   42.8   0.6    4.5e-11   42.8   0.6    2.3  2  sCache_2         Single Cache domain 2
    7.6e-07   29.1   0.1    2.1e-06   27.7   0.1    1.8  1  HisKA            His Kinase A (phospho-acceptor) domain
    7.8e-06   26.1   0.0    0.00036   20.7   0.0    2.5  2  sCache_3_2       Single cache domain 3
     0.0037   17.0   0.9      0.068   12.9   0.1    3.0  2  SPOB_a           Sensor_kinase_SpoOB-type, alpha-helical doma
  ------ inclusion threshold ------
      0.014   15.4   0.0      0.032   14.2   0.0    1.6  1  HATPase_c_2      Histidine kinase-like ATPase domain


Domain annotation for each model (and alignments):
>> Cache_3-Cache_2  Cache 3/Cache 2 fusion domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.2   5.0   3.7e-53     6e-50       3     291 ..      34     300 ..      32     301 .. 0.93
   2 ?   -1.6   0.2      0.79   1.3e+03      51      79 ..     389     436 ..     340     450 .. 0.59

  Alignments for each domain:
  == domain 1  score: 170.2 bits;  conditional E-value: 3.7e-53
                   Cache_3-Cache_2   3 sakeevnklieeelekevedlaetletqdellrekverdlnvfakllsnewrvdnqetvkvgevslPklklggewln 79 
                                       ++++ ++++ +e+l+ +v++ ++ +++  +++rekv ++ln+ +++l++           + ++   k+  +g ++n
  gi|298675810|ref|YP_003727560.1|  34 QTQNYIDSELKEKLQDQVKLEKDYINATFSTAREKVSNNLNTSSDELYS---------RGIPDIVDNKMVINGYVVN 101
                                       688999999***************************************9.........344444444556666666* PP

                   Cache_3-Cache_2  80 knfelvdefteltgatatvFqrmnddllRVsTsvkkedGkraigtylpasspvyka.vlagetYvGrakvfgkwYvT 155
                                       +n+++v ++t+ tg+ +++F ++n++ + +s s++++d      t   as++vy + v++++tY+ r k+ g+wY+ 
  gi|298675810|ref|YP_003727560.1| 102 NNSDIVADITNQTGGRVAIFKVKNNRAVEISESIEQNDNINYTETENFASDKVYREvVIKNNTYIDRSKIQGQWYLN 178
                                       **************************************9877778777888***872689***************** PP

                   Cache_3-Cache_2 156 aYePikdadgkViGilyVgvdqsealkslrkelkklkvGktGylyvldgkgdkkgkliihptlkgknvldlkdadge 232
                                       aY+Pikd++ k iGil  g++++ +++++++++k++++G+tGy+yv++++    gk+iihp l+g+nvl++      
  gi|298675810|ref|YP_003727560.1| 179 AYRPIKDSSDKTIGILCAGIPEKPFINKIKSQMKNIVIGETGYFYVINSD----GKVIIHPNLEGENVLNY------ 245
                                       **************************************************....*****************...... PP

                   Cache_3-Cache_2 233 svvkkllkkksgsleyelkkdekgreklavftyfepwdWvivasvyedefqeevnrvrn 291
                                       +++k++++kk+g ++y +k    gr+kl+ +ty+e+ dWvi++++  +ef + ++++r+
  gi|298675810|ref|YP_003727560.1| 246 DFAKEMIAKKEGNIKYIWK----GRDKLVGYTYYEQRDWVIASGAFVEEFYAPLHSIRD 300
                                       9******************....******************************999986 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.79
                   Cache_3-Cache_2  51 n..................ewrvdnqetvkvgevslPklklggewl.n 79 
                                       n                  e ++++ et+k ++ +l  + ++  +l +
  gi|298675810|ref|YP_003727560.1| 389 NpvtvikgysdvllkmeddEKKIKTLETIKRNTNKLINMIENASKLtK 436
                                       444444444444444444477888888888888888888888777741 PP

>> sCache_3_3  Single cache domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.1   1.6     1e-26   1.7e-23       2     106 ..      99     209 ..      98     210 .. 0.92
   2 ?   -2.9   0.0       5.8   9.4e+03      85     104 ..     313     332 ..     309     334 .. 0.82

  Alignments for each domain:
  == domain 1  score: 83.1 bits;  conditional E-value: 1e-26
                        sCache_3_3   2 ringntelvDqikeltggevTiFl....ddvriaTtvkkedgeravGt..klseevaeavlkkGetysgraeilgkk 72 
                                        +n+n+++v +i+++tgg+v+iF+      v i+ ++ ++d+   ++t   +s++v+++v+ k++ty++r +i+g++
  gi|298675810|ref|YP_003727560.1|  99 VVNNNSDIVADITNQTGGRVAIFKvknnRAVEISESIEQNDNINYTETenFASDKVYREVVIKNNTYIDRSKIQGQW 175
                                       689********************7788888*******999998777773367999********************** PP

                        sCache_3_3  73 yltaYePlkdadgkviGmlfvGlpeeevqalike 106
                                       yl aY+P+kd+++k+iG+l++G+pe+++ ++ik+
  gi|298675810|ref|YP_003727560.1| 176 YLNAYRPIKDSSDKTIGILCAGIPEKPFINKIKS 209
                                       *****************************99986 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.8
                        sCache_3_3  85 gkviGmlfvGlpeeevqali 104
                                       g+v G++f  + +++v++++
  gi|298675810|ref|YP_003727560.1| 313 GSVFGIWFSRTITKPVDEML 332
                                       8999***9999988888886 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.8   0.1   2.1e-24   3.4e-21       5     109 ..     487     590 ..     484     593 .. 0.92

  Alignments for each domain:
  == domain 1  score: 75.8 bits;  conditional E-value: 2.1e-24
                                       HHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHH CS
                         HATPase_c   5 rLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsiv 81 
                                       +++ ++snl++Na+k+++++++i +ei+   +  +++v+D G Gi  ++ +++fe+f +  ++k g +g+GlGl+iv
  gi|298675810|ref|YP_003727560.1| 487 FIEDVFSNLLSNAIKYSPEKSKIIIEIHDAGKFWEVTVTDFGEGIADKNKQLIFERFKR--AEKGGVKGSGLGLAIV 561
                                       67889***********99**********533899*************************..777788********** PP

                                       HHHHHHTTTEEEEEEET.TTEEEEEEEEE CS
                         HATPase_c  82 kklvelmgGeiwvesep.grGttftftlp 109
                                       k+++el+gGe+ v+++p g+G+ f++t+ 
  gi|298675810|ref|YP_003727560.1| 562 KRIIELHGGELGVRDNPqGKGSVFWVTVE 590
                                       *************99999********987 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   0.0   4.3e-19     7e-16       1      53 []     319     371 ..     319     371 .. 0.98

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 4.3e-19
                                       HHHHTTHHHHHHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHHHH CS
                              HAMP   1 llarrilrPLrrLaraarriaaGdldtrlpvsgrDEiGeLarafNaMldrLre 53 
                                       +++r+i++P+ ++ +aa+++++Gd+d+++ ++++DEiG+L +a+N M+ +Lr+
  gi|298675810|ref|YP_003727560.1| 319 WFSRTITKPVDEMLEAANKVSEGDFDVDIKDTSKDEIGQLSKALNSMIANLRD 371
                                       799************************************************96 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9  10.5   1.3e-17   2.1e-14       6     248 ..      42     284 ..      34     285 .. 0.71
   2 ?   -3.3   0.0       3.9   6.4e+03      29      50 ..     355     374 ..     346     402 .. 0.51
   3 ?   -3.2   0.1       3.6   5.8e+03      15      37 ..     414     436 ..     403     464 .. 0.54

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 1.3e-17
                          dCache_1   6 qaeeqllglaeqlanniedvlds.lenlaetlasnpslqdlleepnraneasreslqallksilksnpdisgvylvd 81 
                                       + +e l++++++ ++ i++++ + +e+ ++ l+++++            e++ + + ++++     n  + + y+v+
  gi|298675810|ref|YP_003727560.1|  42 ELKEKLQDQVKLEKDYINATFSTaREKVSNNLNTSSD------------ELYSRGIPDIVD-----NKMVINGYVVN 101
                                       5678889999999999999996625566666655543............334444444444.....44455567777 PP

                          dCache_1  82 adGqviassdpssppnleg..............................tddpadrdwykealaggggkpvisdpyv 128
                                       ++ +++a        n+ g                              t+++a+   y+e++ ++   +     y+
  gi|298675810|ref|YP_003727560.1| 102 NNSDIVAD--IT---NQTGgrvaifkvknnraveisesieqndninyteTENFASDKVYREVVIKN--NT-----YI 166
                                       77777652..22...222223456666766667776666666666667788888888999998888..56.....54 PP

                          dCache_1 129 dqt..ggkpvitiavpiyddsgkfiGvlaadldldn....lqdllsniklgetgyvfivdsdGniiahpd.kdllgk 198
                                       d +   g++++   +pi d s k iG+l+a +++      + + ++ni +getgy+++++sdG++i hp+ +   g+
  gi|298675810|ref|YP_003727560.1| 167 DRSkiQGQWYLNAYRPIKDSSDKTIGILCAGIPEKPfinkIKSQMKNIVIGETGYFYVINSDGKVIIHPNlE---GE 240
                                       444558***************************977333356666688*********************963...34 PP

                          dCache_1 199 nlrdelkaqealekalakiesgvssvklngeeylvayapiptglgWylvv 248
                                       n+ + +     + k++  +++g  +++++g+++lv y+  + + +W +++
  gi|298675810|ref|YP_003727560.1| 241 NVLNYD-----FAKEMIAKKEGNIKYIWKGRDKLVGYTYYE-QRDWVIAS 284
                                       444554.....45555567889999***********98888.69**9986 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.9
                          dCache_1  29 lenlaetlasnpslqdlleepn 50 
                                       + +l++ l+s+  +++l +++n
  gi|298675810|ref|YP_003727560.1| 355 IGQLSKALNSM--IANLRDSNN 374
                                       33344444333..333333222 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 3.6
                          dCache_1  15 aeqlanniedvldslenlaetla 37 
                                       +e+++ n +  ++ +en +++  
  gi|298675810|ref|YP_003727560.1| 414 LETIKRNTNKLINMIENASKLTK 436
                                       44444444444444444443333 PP

>> dCache_2  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   2.5     0.027        44      18      59 ..      41      82 ..      31     170 .. 0.74
   2 !   47.1   2.2   1.1e-15   1.8e-12     190     296 .]     200     292 ..     171     294 .. 0.80
   3 ?    1.9   2.3     0.064     1e+02      20      76 ..     413     469 ..     401     475 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.027
                          dCache_2 18 kerkellksevdsaielieyeknsleeslkesLksrveeays 59
                                       e ke+l+++v+  +++i+ + ++++e++ ++L++  +e ys
  gi|298675810|ref|YP_003727560.1| 41 SELKEKLQDQVKLEKDYINATFSTAREKVSNNLNTSSDELYS 82
                                      467999*****************************9999993 PP

  == domain 2  score: 47.1 bits;  conditional E-value: 1.1e-15
                          dCache_2 190 k....qellktlksirygnngyifiydtdgniilhplkkelngknllevkdkkgkl..lqelleaakkkgegfveYk 260
                                       +    ++++ + k+i +g++gy+++++ dg++i+hp   +l+g+n+l     +  +   +e+++  kk+g+  ++Y+
  gi|298675810|ref|YP_003727560.1| 200 EkpfiNKIKSQMKNIVIGETGYFYVINSDGKVIIHP---NLEGENVL-----N--YdfAKEMIA--KKEGN--IKYI 262
                                       05555889999*************************...99999999.....3..243778877..55555..**** PP

                          dCache_2 261 wpkpsgdkerkKisyvryfppwdWiigtgvyldeie 296
                                       w      k r+K++ + y+++ dW+i++g++++e++
  gi|298675810|ref|YP_003727560.1| 263 W------KGRDKLVGYTYYEQRDWVIASGAFVEEFY 292
                                       9......78999*********************986 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.064
                          dCache_2  20 rkellksevdsaielieyeknsleeslkesLksrveeaysiaeeiyekyknelseee 76 
                                         e++k++++++i+ ie   + ++ ++ e+L+ +  ++ si+ee  ++y+ +l+e++
  gi|298675810|ref|YP_003727560.1| 413 TLETIKRNTNKLINMIENASKLTKLNTVEELDFKQLDIKSIFEEVINNYQPTLDEKQ 469
                                       467888999999999998888899999999999999999999999999988888876 PP

>> sCache_2  Single Cache domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   0.6   2.8e-14   4.5e-11      39     153 ..     205     299 ..     197     301 .. 0.91
   2 ?   -0.8   0.2      0.75   1.2e+03       7      34 ..     415     442 ..     407     460 .. 0.77

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 2.8e-14
                          sCache_2  39 eevkelvnglkfgdGkgYffvldedgtllvhPfnpqleGknasnlkDanGkyiirelvkeakkkgggfvtylwkkpg 115
                                        ++k+ ++++  g+  gYf+v+++dg++++hP    leG+n+ n+       +++e++++ +    g ++y wk ++
  gi|298675810|ref|YP_003727560.1| 205 NKIKSQMKNIVIGE-TGYFYVINSDGKVIIHPN---LEGENVLNYD------FAKEMIAKKE----GNIKYIWKGRD 267
                                       578999999*****.*****************8...********98......9999998766....999****9877 PP

                          sCache_2 116 egeveeklayvkyfepWdwvigtgvylddinkavekil 153
                                       +      l+   y+e+ dwvi +g++++++++++ +i 
  gi|298675810|ref|YP_003727560.1| 268 K------LVGYTYYEQRDWVIASGAFVEEFYAPLHSIR 299
                                       6......*************************999875 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.75
                          sCache_2   7 aelknqvetaislieavykqvesgkite 34 
                                       + +k +++++i++ie   k  + +   e
  gi|298675810|ref|YP_003727560.1| 415 ETIKRNTNKLINMIENASKLTKLNTVEE 442
                                       5688899999999999888877776655 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.1   1.3e-09   2.1e-06       4      64 ..     378     437 ..     375     439 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.3e-09
                                       HHHHHHHHHHHHHHHHHHHHHHHH.HC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCH CS
                             HisKA   4 rflagvaHELrtPLsailgnaeaL.kregklteelkeyletiesearrldhlvedlLdlsri 64 
                                        f+  + H+L +P+++i+g++++L k   + +e+  + leti+++++ l +++e+   l+++
  gi|298675810|ref|YP_003727560.1| 378 LFTDILRHDLLNPVTVIKGYSDVLlKM--EDDEKKIKTLETIKRNTNKLINMIENASKLTKL 437
                                       5778899****************8555..56788888*****************98777665 PP

>> sCache_3_2  Single cache domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   2.2e-07   0.00036      79     137 ..     151     209 ..     102     212 .. 0.91
   2 ?    2.7   0.0     0.077   1.3e+02      55      72 ..     221     238 ..     209     255 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.2e-07
                        sCache_3_2  79 sgpataaalkagrayvgtvtgtlgpslrvklPvfdadgrviGivsvGvkqdeisaelre 137
                                       s+  + +++ ++++y++   + +  +l ++ P++d++++ iGi+ +G+ ++++  ++++
  gi|298675810|ref|YP_003727560.1| 151 SDKVYREVVIKNNTYIDRSKIQGQWYLNAYRPIKDSSDKTIGILCAGIPEKPFINKIKS 209
                                       556677899****************************************9999888877 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.077
                        sCache_3_2  55 yvvitDeegrvlahpdpa 72 
                                       y ++++++g+v+ hp+ +
  gi|298675810|ref|YP_003727560.1| 221 YFYVINSDGKVIIHPNLE 238
                                       99*************966 PP

>> SPOB_a  Sensor_kinase_SpoOB-type, alpha-helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.21   3.5e+02      33      49 ..      26      42 ..      24      52 .. 0.84
   2 !   12.9   0.1   4.2e-05     0.068      18      46 ..     382     411 ..     368     437 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.21
                            SPOB_a 33 ylqLgkydkaeeyieev 49
                                      +l L+ yd+ ++yi++ 
  gi|298675810|ref|YP_003727560.1| 26 LLGLYAYDQTQNYIDSE 42
                                      78899*********975 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 4.2e-05
                            SPOB_a  18 sqRHDflNhLQvIsGylq.Lgkydkaeeyi 46 
                                        +RHD lN   vI+Gy + L k+++ e+ i
  gi|298675810|ref|YP_003727560.1| 382 ILRHDLLNPVTVIKGYSDvLLKMEDDEKKI 411
                                       47**************76433444444433 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     2e-05     0.032      40     109 ..     496     565 ..     480     577 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2e-05
                       HATPase_c_2  40 ctNavehayleapegpvevrlesdeealtvevaDsGpg.fdpetl..pdpteeepkeslkegGrGlalikglv 109
                                       ++Na+++  +   + ++ +++ ++++  +v+v+D G+g  d  ++   ++ + + k+  k +G+Gla++k++ 
  gi|298675810|ref|YP_003727560.1| 496 LSNAIKYSPE---KSKIIIEIHDAGKFWEVTVTDFGEGiADKNKQliFERFKRAEKGGVKGSGLGLAIVKRII 565
                                       6777777775...578999999****************887775411444555558999**********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (594 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1305  (0.0727871); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.49
# Mc/sec: 3655.09
//
Query:       gi|298675811|ref|YP_003727561.1|  [L=258]
Description: nitrilase/cyanide hydratase and apolipoprotein n-acyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.5e-51  173.7   0.0      5e-51  173.5   0.0    1.0  1  CN_hydrolase  Carbon-nitrogen hydrolase


Domain annotation for each model (and alignments):
>> CN_hydrolase  Carbon-nitrogen hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.5   0.0   2.8e-55     5e-51       2     260 ..       6     243 ..       5     244 .. 0.95

  Alignments for each domain:
  == domain 1  score: 173.5 bits;  conditional E-value: 2.8e-55
                                       EEEEEBB-STTHHHHHHHHHHHHHHHHHHTTESEEEEETTTTTBSSSHHHHHHHHBHSSSHHHHHHHHHHHHHTEEE CS
                      CN_hydrolase   2 vAvvQlpqkaadleanlqklleliaeAarkgadLivlPElfitgykeeahfleaAeaglgetlallaalarkngiav 78 
                                       vA++Q+ +  +++++n++k+++++++Aa  ga++ivlPE+f tg+ + +++  +Ae+++ +tl++la +++++++++
  gi|298675811|ref|YP_003727561.1|   6 VACIQMDISHCNKQYNIDKAVSMSEKAAMDGAQIIVLPEVFSTGF-CYENMKSSAETYPYPTLEKLAVVSKTYDCTI 81 
                                       9*******99***********************************.******************************* PP

                                       EEEEEEEECCTTEEEEEEEEEEEETTSEEEEEEE-SS--EECTTSCECCGHHTSCS-SSS-EEEETTEEEEEEEGGG CS
                      CN_hydrolase  79 vigliereltngklqayntavlldldgklvgkyrKlhLfpgeprpptaverelfepgdgipvfdtpvgkiGaaiCye 155
                                       ++ +ie+  ++ ++  yn ++++ ++g+++g yrK+h f         +e+++f++gd+i++++++   +G+ iCye
  gi|298675811|ref|YP_003727561.1|  82 IGSIIEK--KEHSY--YNLGFCI-ESGEFAGFYRKTHPF--------GREKSYFSKGDSIAPVKLQNLTVGLVICYE 145
                                       *******..99999..*******.778889*******65........9***********9999************** PP

                                       GGSHHHHHHHHHTT-SEEEEBH.GCCCTCHHHHHHHHHHHHHHHHHHTSEEEEEEBEEEHCETTEEEE--EEEE-TT CS
                      CN_hydrolase 156 igfpellralalkgaeilvnlserapvpksmgppqwellgraralengcfviaanqvggyeqlilwpvghSaiidpd 232
                                        +fpe++r+l l g +++v+++        +   +w +l +ar++en+++ ia+n++g   +l   + g+S+iid +
  gi|298675811|ref|YP_003727561.1| 146 LRFPEIARKLTLSGSDVIVTIA----EFPDPRINHWYTLVKARSIENQIPHIACNRTGS--DLCSTYSGGSMIIDAW 216
                                       ********************33....3445677899***********************..**************** PP

                                       S-EEEECCSSSTEEEEEEEEHHHHHHHH CS
                      CN_hydrolase 233 Grilaglgeeeegvliaeidladvratr 260
                                       G++ a++g  e g++   idl+++ ++r
  gi|298675811|ref|YP_003727561.1| 217 GNVKADAGNSE-GIIFYNIDLDETSKIR 243
                                       ********998.9*********998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1765.89
//
Query:       gi|298675812|ref|YP_003727562.1|  [L=202]
Description: hypothetical protein Metev_1936 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0069   16.4   0.2       0.26   11.4   0.1    2.5  3  HTH_56    Cch helix turn helix domain


Domain annotation for each model (and alignments):
>> HTH_56  Cch helix turn helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0     0.084   1.5e+03      55      78 ..      10      32 ..       6      37 .. 0.81
   2 ?    2.1   0.0     0.011   1.9e+02      68     109 ..      41      82 ..      21      84 .. 0.74
   3 !   11.4   0.1   1.4e-05      0.26      52     110 ..     107     167 ..     103     168 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.084
                            HTH_56 55 dkileeagFedtkvvlkelkekGl 78
                                       +il+  +  + + + +elk++G+
  gi|298675812|ref|YP_003727562.1| 10 SEILDGRQL-SISGITRELKNEGY 32
                                      577888888.89999999999998 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.011
                            HTH_56  68 vvlkelkekGllesekdrntkkrtvkkksegkkvrvyvlkld 109
                                         l++lk+++ l+  +   +k +++ ++s++ ++ vy l  d
  gi|298675812|ref|YP_003727562.1|  41 GYLRALKDMDKLVEIEVPPSKIYRLMDDSDETSEDVYSLLCD 82 
                                       458999999999988888888888899999999999998765 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 1.4e-05
                            HTH_56  52 nvfdkileeagFedtkvvlkelkekGllesek.drntkkrtvkkksegkk....vrvyvlklde 110
                                        vf++ l+  gF ++k++ +++++   ++ e+ d n kk+++  ++ +++    +r y +k d+
  gi|298675812|ref|YP_003727562.1| 107 PVFRQELKLIGF-SEKQIQNQMDDFANIVQEStDTNLKKYRS--DITRINipsgDRAYEIKSDD 167
                                       59**********.***********877776653666666666..55555555899999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       996  (0.0555525); expected 358.6 (0.02)
Passed bias filter:                      651  (0.0363099); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1191.52
//
Query:       gi|298675813|ref|YP_003727563.1|  [L=163]
Description: arginine decarboxylase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-60  202.9   0.0      3e-60  202.7   0.0    1.0  1  PvlArgDC  Pyruvoyl-dependent arginine decarboxylase (PvlArgDC


Domain annotation for each model (and alignments):
>> PvlArgDC  Pyruvoyl-dependent arginine decarboxylase (PvlArgDC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.7   0.0   1.7e-64     3e-60       1     162 []       4     162 ..       4     162 .. 0.98

  Alignments for each domain:
  == domain 1  score: 202.7 bits;  conditional E-value: 1.7e-64
                          PvlArgDC   1 vPkkvfltkGvgeskeelasFdlALldAgIenfNLvkvSSilPpeaeivsveeglkelppGsivevvmarassnepg 77 
                                       vPkk+f+t+G+g+++e+l+sF++AL++AgIe+fNLv+vSSilPp+++ivs+eegl+el pG+iv++v++r+ss+ p+
  gi|298675813|ref|YP_003727563.1|   4 VPKKMFFTSGIGRHSEHLESFEAALRNAGIEKFNLVTVSSILPPNCKIVSKEEGLSELYPGEIVFCVLSRISSDGPE 80 
                                       7**************************************************************************** PP

                          PvlArgDC  78 rliaaavgvaipkdekkgGyiaEysgfgeseeeaeeeaeelaaemlattrglleekiietkeievaaveakvekygt 154
                                       + i+a++g+a+p+d+++ Gyi+Ey+g g++++ a+++ae+la+em++++++      ++t++i ++a+ +++ k++t
  gi|298675813|ref|YP_003727563.1|  81 DQITASIGCAVPSDQNTIGYISEYHGAGQTKTSAGNYAEKLAREMYQSWTEK---DPLKTTHIAITAEADDKLKWTT 154
                                       ***********************************************98888...999******************* PP

                          PvlArgDC 155 vlaaavfv 162
                                       ++aaa+f+
  gi|298675813|ref|YP_003727563.1| 155 AVAAAIFI 162
                                       ******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1138.27
//
Query:       gi|298675814|ref|YP_003727564.1|  [L=169]
Description: ArsR family transcriptional regulator [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.9e-69  231.3   0.3    4.4e-69  231.1   0.3    1.0  1  ArsR           ArsR transcriptional regulator
     0.0019   18.1   0.6     0.0042   17.0   0.2    1.6  2  Sec8_exocyst   Sec8 exocyst complex component specific domain
  ------ inclusion threshold ------
      0.057   13.9   1.1       0.31   11.5   0.4    1.9  2  TBCC_N         Tubulin-specific chaperone C N-terminal domain
      0.083   12.5   0.0        3.2    7.4   0.0    2.2  2  SMC_ScpB       Segregation and condensation complex subunit S
      0.091   12.9   0.7       0.27   11.3   0.3    2.0  2  ApoLp-III      Apolipophorin-III precursor (apoLp-III)
       0.21   11.1   3.1       0.33   10.5   1.6    1.8  2  PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subun


Domain annotation for each model (and alignments):
>> ArsR  ArsR transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.1   0.3   1.5e-72   4.4e-69       1     157 [.       8     164 ..       8     166 .. 0.99

  Alignments for each domain:
  == domain 1  score: 231.1 bits;  conditional E-value: 1.5e-72
                              ArsR   1 indpveLvpllqvfdsetkkkvyeelskeWlteeeleeklgeeveealklLkkikliEsqWrmpepgekpekeYhts 77 
                                       indp+eLvpll++f+s+++k+vy++ls+ W++e++lee++g++v++++++Lkk++liEsqW+mpepg+kpekeYh++
  gi|298675814|ref|YP_003727564.1|   8 INDPSELVPLLKTFGSQKHKQVYDALSNMWMSEKQLEEYIGDDVTSSINILKKGGLIESQWQMPEPGKKPEKEYHSA 84 
                                       8**************************************************************************** PP

                              ArsR  78 YskvqanfqcsledlsdiievafmsdeeleelvekiekeveegntsisdlsrklglsplfiralakrsekldvkGqr 154
                                       Yskvq nfqcsl+dlsdii++a++++ee++++ e++e++v++gn+s+++l+r+l++spl++r+la+rs+kl+v+Gqr
  gi|298675814|ref|YP_003727564.1|  85 YSKVQSNFQCSLDDLSDIITLALQPYEEIKDTLEELEEMVKQGNNSLNNLARSLNKSPLYLRSLARRSDKLSVMGQR 161
                                       ***************************************************************************** PP

                              ArsR 155 lel 157
                                       l++
  gi|298675814|ref|YP_003727564.1| 162 LRV 164
                                       987 PP

>> Sec8_exocyst  Sec8 exocyst complex component specific domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.84   2.5e+03     116     129 ..      23      36 ..       5      47 .. 0.66
   2 !   17.0   0.2   1.4e-06    0.0042      42     126 ..      78     162 ..      74     168 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.84
                      Sec8_exocyst 116 sakykevieiLdai 129
                                       s+k+k+v + L+++
  gi|298675814|ref|YP_003727564.1|  23 SQKHKQVYDALSNM 36 
                                       66777776666665 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1.4e-06
                      Sec8_exocyst  42 lkefkqlkkqieeaLqevvnehhqaFnssiasYskilssiqesqekvselKesleeakkklstkkkeLkelnarsak 118
                                        ke++  +++++++ q   ++ ++  + + + Y++i ++++e +e v++  +sl++  ++l++    L+ l+ rs k
  gi|298675814|ref|YP_003727564.1|  78 EKEYHSAYSKVQSNFQCSLDDLSDIITLALQPYEEIKDTLEELEEMVKQGNNSLNNLARSLNKSPLYLRSLARRSDK 154
                                       589*************************************************************************9 PP

                      Sec8_exocyst 119 ykevieiL 126
                                       ++ + + L
  gi|298675814|ref|YP_003727564.1| 155 LSVMGQRL 162
                                       99886655 PP

>> TBCC_N  Tubulin-specific chaperone C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.15   4.6e+02      36      77 ..      19      60 ..       9      72 .. 0.70
   2 ?   11.5   0.4    0.0001      0.31      17      95 ..      75     154 ..      64     165 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.15
                            TBCC_N 36 kaFt.eekaaieellesveesadksklkqkldeitaeiqeLqk 77
                                      k+F  ++ +++ ++l+++   ++k+ ++   d++t++i+ L+k
  gi|298675814|ref|YP_003727564.1| 19 KTFGsQKHKQVYDALSNMW-MSEKQLEEYIGDDVTSSINILKK 60
                                      5664145578888888888.45555555555889999988887 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.0001
                            TBCC_N  17 rkeereseaveeekvdsFlkaFteekaaieellesve.esadksklkqkldeitaeiqeLqkllaessmfLpsYdlr 92 
                                       +k e+e +++ ++  + F+ ++++ ++ i  +l+  e  +   ++l++ +++ ++++++L ++l++s ++L s   r
  gi|298675814|ref|YP_003727564.1|  75 KKPEKEYHSAYSKVQSNFQCSLDDLSDIITLALQPYEeIKDTLEELEEMVKQGNNSLNNLARSLNKSPLYLRSLARR 151
                                       5667777777777778899999999999999999999766777889999999999****************998887 PP

                            TBCC_N  93 saq 95 
                                       s +
  gi|298675814|ref|YP_003727564.1| 152 SDK 154
                                       765 PP

>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0011       3.2      99     135 ..      39      75 ..      32      82 .. 0.92
   2 ?    3.2   0.0     0.021        61      14      48 ..      94     131 ..      88     150 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0011
                          SMC_ScpB  99 traeieeiRGvnsdsvvrtLlerglieekgrkeepgr 135
                                       + +++ee  G +++s ++ L + glie++ + +epg+
  gi|298675814|ref|YP_003727564.1|  39 SEKQLEEYIGDDVTSSINILKKGGLIESQWQMPEPGK 75 
                                       5689999***************************997 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.021
                          SMC_ScpB  14 lsleeLakilels...keeveealeeLkeeyeeedrgl 48 
                                        sl++L++i+ l     ee+++ leeL+e  ++ ++ l
  gi|298675814|ref|YP_003727564.1|  94 CSLDDLSDIITLAlqpYEEIKDTLEELEEMVKQGNNSL 131
                                       57788888887545578999999999999987766554 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       0.4   1.2e+03      35      35 ..      55      55 ..      17     101 .. 0.56
   2 ?   11.3   0.3   9.2e-05      0.27      44      78 ..     108     141 ..      85     155 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.4
                         ApoLp-III 35 v 35
                                      +
  gi|298675814|ref|YP_003727564.1| 55 I 55
                                      0 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 9.2e-05
                         ApoLp-III  44 slqeelkkksdeleealkevkkkieetadklseen 78 
                                       +  ee+k++ +elee++k+ ++ +++ a +l++ +
  gi|298675814|ref|YP_003727564.1| 108 QPYEEIKDTLEELEEMVKQGNNSLNNLARSLNK-S 141
                                       4569****************************9.4 PP

>> PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.24     7e+02      91     117 ..      27      53 ..      23      60 .. 0.72
   2 ?   10.5   1.6   0.00011      0.33      86     145 ..      99     158 ..      63     168 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.24
                     PI3K_P85_iSH2  91 eqlksrlkelhsskekLeedlkqqkee 117
                                       +q+ + l+++  s ++Lee++   +++
  gi|298675814|ref|YP_003727564.1|  27 KQVYDALSNMWMSEKQLEEYIGDDVTS 53 
                                       566667888888889999988776655 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00011
                     PI3K_P85_iSH2  86 lqenleqlksrlkelhsskekLeedlkqqkeeereleReinalkpellqLqkrkdkylew 145
                                       l++ + ++ +  +e++++ e+Lee +kq  ++  +l R++n++   l +L++r dk+  +
  gi|298675814|ref|YP_003727564.1|  99 LSDIITLALQPYEEIKDTLEELEEMVKQGNNSLNNLARSLNKSPLYLRSLARRSDKLSVM 158
                                       5566666778889****************************************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1102  (0.0614647); expected 358.6 (0.02)
Passed bias filter:                      721  (0.0402142); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1038.90
//
Query:       gi|298675815|ref|YP_003727565.1|  [L=262]
Description: helix-turn-helix type 11 domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-10   39.5   0.0    9.2e-10   37.9   0.0    1.9  1  HTH_24          Winged helix-turn-helix DNA-binding
    6.7e-08   32.3   0.0    1.8e-07   30.9   0.0    1.7  1  MarR_2          MarR family
    9.8e-08   31.8   0.0    4.1e-07   29.8   0.0    2.0  2  MarR            MarR family
    6.2e-06   26.1   0.3    4.3e-05   23.4   0.0    2.4  2  HTH_Crp_2       Crp-like helix-turn-helix domain
    2.8e-05   23.9   0.0    6.4e-05   22.8   0.0    1.6  1  HTH_11          HTH domain
    0.00015   21.8   0.1     0.0028   17.7   0.0    2.5  2  HTH_3           Helix-turn-helix
    0.00052   20.3   0.0     0.0015   18.8   0.0    1.8  1  Rrf2            Transcriptional regulator
     0.0027   17.9   0.0      0.024   14.9   0.0    2.3  2  Mnd1            Mnd1 HTH domain
      0.003   17.5   0.0     0.0072   16.3   0.0    1.7  1  HTH_45          Winged helix-turn-helix
     0.0032   17.2   0.0     0.0064   16.3   0.0    1.5  1  HTH_IclR        IclR helix-turn-helix domain
     0.0037   17.4   0.0      0.011   15.9   0.0    1.8  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0061   16.3   0.0      0.013   15.3   0.0    1.6  1  HTH_23          Homeodomain-like domain
     0.0089   16.5   0.0      0.018   15.5   0.0    1.5  1  HTH_27          Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.011   16.4   0.0       0.11   13.2   0.0    2.3  2  RPA_C           Replication protein A C terminal
      0.015   15.2   0.0      0.038   13.9   0.0    1.7  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.033   14.3   0.0      0.086   13.0   0.0    1.7  1  HTH_28          Helix-turn-helix domain
      0.041   13.7   0.0       0.09   12.7   0.0    1.6  1  HTH_5           Bacterial regulatory protein, arsR family
       0.05   13.5   0.0        0.2   11.6   0.0    2.0  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.055   13.4   0.0       0.12   12.4   0.0    1.6  1  HTH_36          Helix-turn-helix domain
        0.1   12.4   0.0       0.42   10.5   0.0    2.1  2  HTH_AsnC-type   AsnC-type helix-turn-helix domain
       0.12   12.4   0.0       0.28   11.3   0.0    1.6  1  HTH_13          HTH DNA binding domain
       0.13   12.1   0.0       0.36   10.7   0.0    1.7  1  P22_Cro         DNA-binding transcriptional regulator Cro


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.0   1.1e-12   9.2e-10       4      47 ..      12      56 ..       9      57 .. 0.93

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 1.1e-12
                            HTH_24  4 tdrkILelLqk.nprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      t++ IL ++ + +p+  q+e+A+++g++p++v++++k+L+e+G+I
  gi|298675815|ref|YP_003727565.1| 12 TKFLILIEVAAhQPNVRQKEIARKIGVTPQAVSEYMKELVEDGFI 56
                                      788999888887999*****************************9 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   2.2e-10   1.8e-07       6      52 ..      12      57 ..      10      65 .. 0.92

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 2.2e-10
                                      HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2  6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                      + + +L +++++ ++ ++++e+ar+ g++++avs   k+Lv+ G++ 
  gi|298675815|ref|YP_003727565.1| 12 TKFLILIEVAAHQPN-VRQKEIARKIGVTPQAVSEYMKELVEDGFIY 57
                                      67899********97.9****************************96 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0     5e-10   4.1e-07       4      50 ..      12      59 ..      11      63 .. 0.88
   2 ?   -1.5   0.0         3   2.4e+03      34      45 ..     240     251 ..     239     252 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 5e-10
                                      HHHHHHHHHHHSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  4 tqfviLrilyeqgp.lsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      t f+iL  ++ ++p  +++e+a+k+gv++ +v++  ++L+++G+i+++
  gi|298675815|ref|YP_003727565.1| 12 TKFLILIEVAAHQPnVRQKEIARKIGVTPQAVSEYMKELVEDGFIYSE 59
                                      678888888766666******************************975 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3
                                       HHHHHHHHHHTT CS
                              MarR  34 vtrvldrLekkG 45 
                                       +t++l rLe ++
  gi|298675815|ref|YP_003727565.1| 240 ITTILSRLESEN 251
                                       799999**9876 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   5.2e-08   4.3e-05      20      57 ..      25      62 ..      10      69 .. 0.80
   2 ?   -1.1   0.1       2.3   1.9e+03      35      49 ..     237     251 ..     229     253 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 5.2e-08
                                      EEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEEE CS
                         HTH_Crp_2 20 lpltqeelAsmlGltretvsrilseLkreglis.rgrri 57
                                       ++ q+e+A+ +G+t++ vs  ++eL ++g i   gr +
  gi|298675815|ref|YP_003727565.1| 25 PNVRQKEIARKIGVTPQAVSEYMKELVEDGFIYsEGR-V 62
                                      5799****************************96565.3 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.3
                                       HHHHHHHHHHHHHTT CS
                         HTH_Crp_2  35 retvsrilseLkreg 49 
                                        e ++ ils+L+ e+
  gi|298675815|ref|YP_003727565.1| 237 DEEITTILSRLESEN 251
                                       588999*****9986 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   7.9e-08   6.4e-05       4      52 ..      15      62 ..      12      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 7.9e-08
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepgr 52
                                       il+ + ++++++  +e+A++++v+ ++v  ++k+L e g  I+se ++
  gi|298675815|ref|YP_003727565.1| 15 LILIEVAAHQPNVRQKEIARKIGVTPQAVSEYMKELVEDG-FIYSEGRV 62
                                      688889778888****************************.89988775 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   3.4e-06    0.0028      10      31 ..      27      48 ..      24      52 .. 0.90
   2 ?    1.0   0.0      0.54   4.4e+02      28      46 ..     169     188 ..     169     195 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.4e-06
                                      HHHHHHHHHHTSSHHHHHHHHT CS
                             HTH_3 10 lsqeeLAeklGvsrstisriEn 31
                                        q+e+A+k+Gv+++++s +++
  gi|298675815|ref|YP_003727565.1| 27 VRQKEIARKIGVTPQAVSEYMK 48
                                      579*****************87 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.54
                                       HHHTT.SSCSBHHHHHHHHH CS
                             HTH_3  28 riEnG.ernPsletlkklak 46 
                                       + E+G   + +le+l+ l+k
  gi|298675815|ref|YP_003727565.1| 169 KVERGgSKRVDLERLQTLSK 188
                                       67999977799**9999987 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.9e-06    0.0015      12      58 ..      15      59 ..       6      61 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.9e-06
                                      HHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              Rrf2 12 hallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksv 58
                                       +l++ a+++    v+ +eia++ ++ p+ ++  +++L + g++ s+
  gi|298675815|ref|YP_003727565.1| 15 LILIEVAAHQP--NVRQKEIARKIGVTPQAVSEYMKELVEDGFIYSE 59
                                      46677777777..59*****************************985 PP

>> Mnd1  Mnd1 HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0     3e-05     0.024      19      48 ..      30      59 ..      28      60 .. 0.88
   2 ?   -0.4   0.0       1.7   1.4e+03      36      52 ..     193     209 ..     187     210 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3e-05
                              Mnd1 19 klapkekgivsqsVkdvlqsLvdDglveve 48
                                      k+++++ g+++q V +++++Lv+Dg + +e
  gi|298675815|ref|YP_003727565.1| 30 KEIARKIGVTPQAVSEYMKELVEDGFIYSE 59
                                      6666679******************99776 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.7
                              Mnd1  36 lqsLvdDglveveKiGs 52 
                                       + +   ++l+  +KiG+
  gi|298675815|ref|YP_003727565.1| 193 IAAIGTESLIALKKIGQ 209
                                       55666799********7 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   8.8e-06    0.0072      29      70 ..      36      79 ..      15      86 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.8e-06
                            HTH_45 29 anLsykllnkYLdmLvekgli.kkskekYvlTekGlel.leklk 70
                                         + + +++Y++ Lve g+i ++   +Y++T+ G e  le+  
  gi|298675815|ref|YP_003727565.1| 36 IGVTPQAVSEYMKELVEDGFIySEGRVQYRITKYGVEWvLENAA 79
                                      555667889************8889**********985155555 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   7.8e-06    0.0064      11      50 ..      19      58 ..      14      60 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.8e-06
                                      T-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 11 alaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                       +a++++ ++ +e+Ar++g+++ +v+ +++ Lve G++  
  gi|298675815|ref|YP_003727565.1| 19 EVAAHQPNVRQKEIARKIGVTPQAVSEYMKELVEDGFIYS 58
                                      568889999****************************976 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.3e-05     0.011      23      53 ..      27      57 ..      20      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.3e-05
                                      B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress 23 vktkdlaerLnvspssVsemlkkLekdGyve 53
                                      v++k++a+ ++v p  Vse +k+L +dG++ 
  gi|298675815|ref|YP_003727565.1| 27 VRQKEIARKIGVTPQAVSEYMKELVEDGFIY 57
                                      899*************************975 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.6e-05     0.013       6      46 ..      12      55 ..       7      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-05
                            HTH_23  6 eRlrillllae...GlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                       +++il  +a      +++eIAr+ gv+++ v+ + k  +e+G+
  gi|298675815|ref|YP_003727565.1| 12 TKFLILIEVAAhqpNVRQKEIARKIGVTPQAVSEYMKELVEDGF 55
                                      6778888888667999*********************9999985 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.2e-05     0.018       8      66 ..      16      68 ..      13      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.2e-05
                            HTH_27  8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTd 66
                                      +L  ++  +  +++++++++  v+ +++s+ +k+L+e G++       + +++++r+T 
  gi|298675815|ref|YP_003727565.1| 16 ILIEVAAHQPNVRQKEIARKIGVTPQAVSEYMKELVEDGFI------YSEGRVQYRITK 68
                                      55556667778899***************************......77799*****97 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00013      0.11      68      99 ..      27      58 ..      14      59 .. 0.90
   2 ?   -0.1   0.0       1.8   1.5e+03      55      88 ..     122     155 ..     108     158 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00013
                                      EEHHHHHHHSTSXHHHHHHHHHHHHHTTSEEE CS
                             RPA_C 68 vhvdeiaqklrlsvndvkqavdeLsneGiiYs 99
                                      v  +eia+k+++  + v + ++eL+++G iYs
  gi|298675815|ref|YP_003727565.1| 27 VRQKEIARKIGVTPQAVSEYMKELVEDGFIYS 58
                                      66789**************************8 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.8
                                       HHHHHH.SXSTTTEEHHHHHHHSTSXHHHHHHHH CS
                             RPA_C  55 lnlikqspeseeGvhvdeiaqklrlsvndvkqav 88 
                                       l + ++++ +  G+ +de +++  + v d++  +
  gi|298675815|ref|YP_003727565.1| 122 LYVSNNKVTNSTGITIDEAKKGEDVGVTDLRGLI 155
                                       5555778999999999999998888888887766 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.7e-05     0.038      22      56 ..      26      60 ..      14      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.7e-05
                                      CCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB 22 patadeiaeelgvprskvYevLrsLedkGlVerek 56
                                      + + +eia+++gv  + v e++++L++ G+++ e 
  gi|298675815|ref|YP_003727565.1| 26 NVRQKEIARKIGVTPQAVSEYMKELVEDGFIYSEG 60
                                      66789**************************9884 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00011     0.086       2      38 ..      13      52 ..      12      56 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                            HTH_28  2 RleiikllaaGh...svreaArelgisrrtvyrWikryee 38
                                      ++ i+ ++aa+    +++e+Ar+ g++++ v+  +k + e
  gi|298675815|ref|YP_003727565.1| 13 KFLILIEVAAHQpnvRQKEIARKIGVTPQAVSEYMKELVE 52
                                      5668889998644349999***********9877776655 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00011      0.09      20      47 .]      31      58 ..      27      58 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                                      HHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5 20 elaeelglsqstvShHLkkLreaGLVek 47
                                      e+a+++g+++ +vS++ k L e G++++
  gi|298675815|ref|YP_003727565.1| 31 EIARKIGVTPQAVSEYMKELVEDGFIYS 58
                                      9************************975 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00024       0.2      11      29 ..      29      47 ..      24      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00024
                    YdaS_antitoxin 11 qkaLAealgvsqqaVsqWl 29
                                      qk+ A+++gv++qaVs  +
  gi|298675815|ref|YP_003727565.1| 29 QKEIARKIGVTPQAVSEYM 47
                                      899************9875 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00015      0.12       8      55 .]      14      56 ..      10      56 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00015
                            HTH_36  8 klllgslasfanknggcfpsqetlakrlglsknTvsraikeLeqlGyi 55
                                      +l+l++ a++       +  q+ +a++ g+  + vs + keL++ G+i
  gi|298675815|ref|YP_003727565.1| 14 FLILIEVAAHQ-----PNVRQKEIARKIGVTPQAVSEYMKELVEDGFI 56
                                      67777788887.....6667************************9987 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00052      0.42      20      39 ..      29      48 ..      17      51 .. 0.84
   2 ?   -2.6   0.0       6.4   5.3e+03      30      39 ..      58      67 ..      58      68 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00052
                     HTH_AsnC-type 20 yaeLAervGlSestvlrRvr 39
                                       +e+A+++G+++++v + ++
  gi|298675815|ref|YP_003727565.1| 29 QKEIARKIGVTPQAVSEYMK 48
                                      58*************87555 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.4
                     HTH_AsnC-type 30 SestvlrRvr 39
                                      Se +v+ R+ 
  gi|298675815|ref|YP_003727565.1| 58 SEGRVQYRIT 67
                                      8999****96 PP

>> HTH_13  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00034      0.28       4      37 ..      17      50 ..      16      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00034
                            HTH_13  4 LvelvlsrPlVsagmvakeLkvtpraalklvkel 37
                                      L+e    +P V  + +a+++ vtp+a+ + +kel
  gi|298675815|ref|YP_003727565.1| 17 LIEVAAHQPNVRQKEIARKIGVTPQAVSEYMKEL 50
                                      7888889999**********************98 PP

>> P22_Cro  DNA-binding transcriptional regulator Cro
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00044      0.36      12      31 ..      29      48 ..      28      53 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00044
                                      HHHHHHHHTS-HHHHHHHHT CS
                           P22_Cro 12 vekvAkalgvtksAVsqWge 31
                                      ++ +A+ +gvt++AVs+  +
  gi|298675815|ref|YP_003727565.1| 29 QKEIARKIGVTPQAVSEYMK 48
                                      5789************9854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       832  (0.0464053); expected 358.6 (0.02)
Passed bias filter:                      644  (0.0359195); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 1649.26
//
Query:       gi|298675816|ref|YP_003727566.1|  [L=178]
Description: phosphodiesterase family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.1e-28   98.3   0.0    6.3e-28   98.0   0.0    1.1  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    3.9e-05   24.2   1.0     0.0037   17.8   0.1    2.2  2  Metallophos    Calcineurin-like phosphoesterase


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.0   0.0   7.1e-32   6.3e-28       1     157 [.       1     141 [.       1     149 [. 0.92

  Alignments for each domain:
  == domain 1  score: 98.0 bits;  conditional E-value: 7.1e-32
                     Metallophos_2   1 MklaiiSDlH.snldaleavlealkevgvdaiihaGDleeeepevleellelapvlaVrGNnDeevveedvlreaae 76 
                                       Mk+ +iSD+H ++ ++++++  ++++   d iihaGD+  ++  + +e+++  +++aV+GN D             e
  gi|298675816|ref|YP_003727566.1|   1 MKIFAISDTHmKQAQIPQNLTGIIDDY--DIIIHAGDF--TSKGCYDEFESTGKLKAVYGNAD-----------DPE 62 
                                       **********88888888888899989..********9..8888*******************...........999 PP

                     Metallophos_2  77 lgtdlpeeaelelagekvlliHgdplgvkdalaellkeaeegsdvvvcGHtHvpevekeggvlvvnPGsvgeprdgd 153
                                       l++ lpe+ ++e++g++v++iH+  l+v+d la+++ + e+++dv+v+GH H+p veke +v++v PGs++ pr + 
  gi|298675816|ref|YP_003727566.1|  63 LKEILPERTKFEIDGVRVGIIHQGALSVTDTLAYRYLALEMEVDVLVFGHLHRPIVEKE-DVMLVCPGSPTKPRMSP 138
                                       ************************99************99*****************99.8************9998 PP

                     Metallophos_2 154 pety 157
                                       p   
  gi|298675816|ref|YP_003727566.1| 139 PT-G 141
                                       84.3 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   4.2e-07    0.0037       1      55 [.       1      47 [.       1      77 [. 0.73
   2 !    5.2   0.1     0.003        27     185     204 .]      97     116 ..      80     116 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.2e-07
                                      EEEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHH CS
                       Metallophos  1 lrilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekelle 55
                                      ++i  i+D+H        +++ + l  +++  + d++++aGD++  g +++ ++ 
  gi|298675816|ref|YP_003727566.1|  1 MKIFAISDTH-----MKQAQIPQNLTGIID--DYDIIIHAGDFTSKGCYDE-FES 47
                                      79********.....777777777766633..69*************5555.333 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.003
                                       HHHHHHTTESEEEEESSSSE CS
                       Metallophos 185 edllkkygvdlvisGHtHvy 204
                                       + l  + +vd+ ++GH H++
  gi|298675816|ref|YP_003727566.1|  97 RYLALEMEVDVLVFGHLHRP 116
                                       34477889**********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       229  (0.0127726); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1322.00
//
Query:       gi|298675817|ref|YP_003727567.1|  [L=78]
Description: hypothetical protein Metev_1941 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 551.88
//
Query:       gi|298675818|ref|YP_003727568.1|  [L=188]
Description: hypothetical protein Metev_1942 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       894  (0.0498633); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1402.82
//
Query:       gi|298675819|ref|YP_003727569.1|  [L=311]
Description: nucleic acid-binding OB-fold tRNA/helicase-type protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.064   13.1   0.0       0.12   12.2   0.0    1.6  1  PAZ       PAZ domain


Domain annotation for each model (and alignments):
>> PAZ  PAZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   6.8e-06      0.12      49      93 ..      30      77 ..      23     162 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.8e-06
                                      ESS--TTSEECCTTCT..CECCHHHHCCT---S.....T-TT--EEEEEE CS
                               PAZ 49 ttdlapsstFpdkdkeneitfaeYfkkkYniei.....kdqdqplldvdk 93
                                      +++l+++ + p+++   ++++ +Yf k+Yni        + + pl++v+ 
  gi|298675819|ref|YP_003727569.1| 30 LEKLTSKFKVPMNE--ARRSVTNYFLKEYNISRgefygSQTETPLVNVKD 77
                                      45555566666664..56*************8777787666788888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       858  (0.0478554); expected 358.6 (0.02)
Passed bias filter:                      635  (0.0354175); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 1973.89
//
Query:       gi|298675820|ref|YP_003727570.1|  [L=611]
Description: sodium/hydrogen exchanger [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-46  157.5  47.8    5.3e-46  157.1  47.8    1.1  1  Na_H_Exchanger   Sodium/hydrogen exchanger family
    3.1e-28   98.4   0.4    6.8e-28   97.3   0.4    1.6  1  TrkA_N           TrkA-N domain
    6.9e-11   41.8   0.6    1.5e-10   40.7   0.6    1.5  1  TrkA_C           TrkA-C domain
    2.8e-08   34.1   0.5    6.3e-08   33.0   0.5    1.6  1  NAD_binding_7    Putative NAD(P)-binding
    3.6e-07   29.8   0.0    4.8e-07   29.3   0.0    1.1  1  FAD_binding_3    FAD binding domain
    9.3e-06   25.9   0.2    2.4e-05   24.6   0.2    1.8  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    1.3e-05   24.9   0.1    2.4e-05   24.0   0.1    1.4  1  ApbA             Ketopantoate reductase PanE/ApbA
    2.5e-05   24.5   0.1    4.7e-05   23.6   0.1    1.5  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    2.9e-05   24.6   0.1    9.9e-05   22.8   0.1    2.0  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    7.6e-05   22.4   0.3    0.00013   21.6   0.3    1.4  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
    0.00019   21.4   0.4    0.00034   20.6   0.4    1.4  1  NAD_binding_10   NAD(P)H-binding
    0.00037   20.6   0.5     0.0027   17.8   0.2    2.3  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
     0.0025   17.3   0.2      0.004   16.7   0.2    1.2  1  Epimerase        NAD dependent epimerase/dehydratase family
     0.0028   18.3   1.8        1.7    9.4   0.4    2.6  2  PglD_N           PglD N-terminal domain
     0.0034   16.8   0.0      0.008   15.6   0.0    1.5  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
     0.0049   16.2   0.1     0.0089   15.3   0.1    1.3  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
     0.0056   16.2   0.1      0.013   14.9   0.1    1.6  1  adh_short        short chain dehydrogenase
     0.0073   15.9   0.3      0.012   15.1   0.3    1.3  1  NmrA             NmrA-like family
  ------ inclusion threshold ------
      0.012   16.2   0.1      0.036   14.6   0.0    1.9  1  XdhC_C           XdhC Rossmann domain
      0.017   14.4   0.1      0.029   13.6   0.1    1.3  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
       0.02   15.4   0.4       0.02   15.4   0.4    2.7  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
      0.039   13.9   0.0      0.098   12.6   0.0    1.7  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
       0.06   12.0   0.1      0.089   11.5   0.1    1.2  1  HI0933_like      HI0933-like protein
      0.064   13.1   0.2       0.12   12.3   0.2    1.4  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
      0.099   11.7   0.0       0.15   11.1   0.0    1.2  1  Lycopene_cycl    Lycopene cyclase protein
       0.12   12.0   0.1       0.18   11.4   0.1    1.2  1  DAO              FAD dependent oxidoreductase


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.1  47.8   7.7e-49   5.3e-46       2     380 ..      11     389 ..       9     390 .. 0.88

  Alignments for each domain:
  == domain 1  score: 157.1 bits;  conditional E-value: 7.7e-49
                                       HHHHHHHHHHHHHHHHTTSXHHHHHHHHHHHHTTTTTS.......HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTH CS
                    Na_H_Exchanger   2 vllillallvgllarrlklpeivgliiaGlllGpsglglieps..eedlevlselglilllFlaGleldlrelrknl 76 
                                       v++++lall+  l + +k+p+i++l++ G+++Gp +l++++p+   + l+vl  l + +++F+ Gl+ldl++lr   
  gi|298675820|ref|YP_003727570.1|  11 VIVLILALLAQQLGKIFKVPPILFLLAEGIIIGPEVLNIFDPNilGDGLTVLVSLSVAIIVFDGGLNLDLKYLRTIH 87 
                                       5666668888889**************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHH CS
                    Na_H_Exchanger  77 ksilllallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDa 153
                                       ks+l+l+++g+lit++l+++l++l  +lgi l  a l+ga++ at p v+++++ ++ +v+ +   +l+ e+v+nDa
  gi|298675820|ref|YP_003727570.1|  88 KSTLKLSTIGLLITFILTTILTHL--LLGIQLEMAALYGALMGATGPTVITPLV-KNVKVNHKTSKVLELEGVFNDA 161
                                       *****************9999997..79**************************.********************** PP

                                       HCCCCCHHHHHHTXXXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.CTHHHHHHHHHHHHHHHHHHH CS
                    Na_H_Exchanger 154 vavvllavllalakeeaggetslllllliflvvavgglllglvigwllrlitrft.dddrelevllvlllallaall 229
                                       ++v+l av+ +++   +  + s + ++  +++ +++g  +g++ g+ l++++      ++++  ll+l l+++++ +
  gi|298675820|ref|YP_003727570.1| 162 ASVILAAVIFEFI---V-FQLSGIEAIAGIFYRFIAGASMGVLSGFALSKFLSKGpFISPQTARLLTLTLVIGTYVI 234
                                       ************9...5.555666666677788899999999999999999998899******************** PP

                                       HHTS.XXXHHHHHHHHHHHHHHHHHHTTHHHH..HHHHHHHHHHHHHHHHHHHHSXHHHHHXXHHHHHHHHHHHHHH CS
                    Na_H_Exchanger 230 aell.gvsgilgaflaGlvlseyefsnklsek..lesfreglfnplfFvlvGlsldlkvlnnhlsvlilvllilvai 303
                                       +e++   sg+l++ l G+++++++++ k+  k   + +    ++ l+F+l+ + l +  +      ++ ++++l+++
  gi|298675820|ref|YP_003727570.1| 235 SEMIgSESGVLAVALFGIIMGTSNVRYKMVLKefKSDLV-VMMLSLIFILLAALLKFDNII--QIGFTGIIIVLLLM 308
                                       ****7779*************999999966664444455.99**************66553..55556666666666 PP

                                       HTHHHHHHHHHTTTXSSXHHHHHHCCCCSS.BHHHHH....HHHHHHHHHXHHHHTT.SSTTTCSTSXHHHHHHHHH CS
                    Na_H_Exchanger 304 llgrilavflllrllglslrealiigfgglqrgaval....alaalgpalgllarel.yallivvvlftvlvqGlsl 375
                                       +l+r+l+vf  +  ++l+++++l+i++ g  +g v +    ++a+++ al++   ++ + l++++v++tv+  G+  
  gi|298675820|ref|YP_003727570.1| 309 FLIRPLSVFSTTIGSQLGRNDKLFISLIGP-KGVVPAsiatYFAIRLDALNIEGGQTlVGLVFLTVIITVFMTGTLS 384
                                       69************************9999.887765111155666677799999999*************999999 PP

                                       HHHHH CS
                    Na_H_Exchanger 376 kpllk 380
                                       kpl +
  gi|298675820|ref|YP_003727570.1| 385 KPLAN 389
                                       99876 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.3   0.4   9.9e-31   6.8e-28       1     107 [.     398     506 ..     398     513 .. 0.93

  Alignments for each domain:
  == domain 1  score: 97.3 bits;  conditional E-value: 9.9e-31
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeani 77 
                                       i+i+G G+vG+ la++L+++g++vvv+d+++e+++el + g+++v+gd+ d ++L++agie+a++v+a+t++d +n+
  gi|298675820|ref|YP_003727570.1| 398 ILIVGGGNVGQLLAKRLEKRGENVVVVDSSKEKCHELMNSGIRAVHGDVEDMNILKDAGIENAKYVVATTDKDNTNL 474
                                       79*****************7778****************************************************** PP

                                       HHHHHHHHHTSS..SEEEEEESSGGGHHHHHH CS
                            TrkA_N  78 lavllakelnpk..kkiiaraqdpehaellkk 107
                                       l++++ak+ ++    +++ar++d e+ +++ +
  gi|298675820|ref|YP_003727570.1| 475 LVCQVAKSKFGFnkDQVVARVNDVENLHAFWD 506
                                       ******9988765588*********9998755 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.6   2.2e-13   1.5e-10       3      65 ..     545     605 ..     543     609 .. 0.91

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 2.2e-13
                                       EEEEE--GGGTTSBHHHHTHHHHS-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHH CS
                            TrkA_C   3 evtvpagsplvGktlkelnlrargvlvvairRggeliipsgdtvLeeGDvllvvgspsdlael 65 
                                       e++v+ +  +vGk +k+l l++   l + +rR++e ii+ gd+vLe +D+++v+g+ ++ + +
  gi|298675820|ref|YP_003727570.1| 545 EIAVT-NPNVVGKAVKDLALPR-ESLMLMVRRDDESIIAHGDLVLEYNDIVTVIGEGDSAKVV 605
                                       78887.888*************.********************************99987655 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.5   9.2e-11   6.3e-08       9      84 ..     397     482 ..     393     504 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 9.2e-11
                     NAD_binding_7   9 kvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeeelekd...........legadlviaatddrel 74 
                                       ++l+vGgG+v++  +++l + g +v+vv+   ke+++el++   + +++d           +e+a+ v+a+td+++ 
  gi|298675820|ref|YP_003727570.1| 397 EILIVGGGNVGQLLAKRLEKRGENVVVVDSS-KEKCHELMNSGIRAVHGDvedmnilkdagIENAKYVVATTDKDNT 472
                                       69**************************999.78899998877777776655557777777888************* PP

                     NAD_binding_7  75 neriaeaaka 84 
                                       n  +++ ak+
  gi|298675820|ref|YP_003727570.1| 473 NLLVCQVAKS 482
                                       ******9996 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0     7e-10   4.8e-07       3      80 ..     397     487 ..     395     526 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 7e-10
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSS.....S--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEE CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlp.....radglnqrtmellrqlGledrilaegapnelmge 74 
                                       ++lIVG+G +G +la+ L ++G +vv+v+  +++  +      ra   + + m++l+++G+e+  +  +++ + ++ 
  gi|298675820|ref|YP_003727570.1| 397 EILIVGGGNVGQLLAKRLEKRGENVVVVDSSKEKCHELmnsgiRAVHGDVEDMNILKDAGIENAKYVVATTDKDNTN 473
                                       79***************************99999877666689*******************998888888888888 PP

                                       EEEEE........C CS
                     FAD_binding_3  75 alyne........l 80 
                                       +l ++         
  gi|298675820|ref|YP_003727570.1| 474 LLVCQvakskfgfN 487
                                       88887444444440 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.2   3.5e-08   2.4e-05       1      60 [.     398     450 ..     398     491 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 3.5e-08
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHH CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenye 60 
                                       +li+G+G+vGq +a+ l+++++   +++v+d skek+++l +  +g+r+     d+e+  
  gi|298675820|ref|YP_003727570.1| 398 ILIVGGGNVGQLLAKRLEKRGE---NVVVVDSSKEKCHELMN--SGIRAVH--GDVEDMN 450
                                       89******************98...5*************985..4444444..4444443 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.1   3.4e-08   2.4e-05       1      62 [.     398     464 ..     398     480 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 3.4e-08
                                       EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETT.CEEEEEECEEECCH...S CS
                              ApbA   1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseg.geeilrppealsae...e 62 
                                       i+i+G G +G+lla +L k g++v++++ s+ ++ +l + G+r    + ++ ++++++ ++++    
  gi|298675820|ref|YP_003727570.1| 398 ILIVGGGNVGQLLAKRLEKRGENVVVVDSSKeKCHELMNSGIRAVHGDvEDMNILKDAGIENAkyvV 464
                                       89*****************************************999997777666666666654552 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.1   6.8e-08   4.7e-05       2      47 ..     398     443 ..     397     481 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 6.8e-08
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-S CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaae 47 
                                       i ++G G+ G+ +a++l+k+g +v+v++ +kek+ el+++g++a++
  gi|298675820|ref|YP_003727570.1| 398 ILIVGGGNVGQLLAKRLEKRGENVVVVDSSKEKCHELMNSGIRAVH 443
                                       5689*************************************87765 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.1   1.4e-07   9.9e-05       2      58 ..     398     449 ..     397     466 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.4e-07
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHH CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneea 58 
                                       i i+G+Gn+g+ la++l ++g   +++vv+ ++++ek  el ++ g+++ ++d e++
  gi|298675820|ref|YP_003727570.1| 398 ILIVGGGNVGQLLAKRLEKRG---ENVVVV-DSSKEKCHELMNS-GIRAVHGDVEDM 449
                                       6799*****************...****88.9999999999777.677777777765 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.3     2e-07   0.00013       1      54 [.     396     449 ..     396     476 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2e-07
                                       SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHH CS
                    UDPG_MGDP_dh_N   1 mkisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLeel 54 
                                       m+i ++G G vG   a  l ++g +v++vD ++ek ++l ++ i  ++ + e++
  gi|298675820|ref|YP_003727570.1| 396 MEILIVGGGNVGQLLAKRLEKRGENVVVVDSSKEKCHELMNSGIRAVHGDVEDM 449
                                       789***********************************9999988888777654 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.4   4.9e-07   0.00034       3      73 ..     403     472 ..     402     500 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 4.9e-07
                                       TSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHH.HTT-SEEEES---TCC CS
                    NAD_binding_10   3 tGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaea.lkgadaVvsalggggk 73 
                                        G+vG+ll+k+l +rg  +v+++  ++ek +el  ++g+++v+gdv+d + l++a +++a  Vv+++ ++++
  gi|298675820|ref|YP_003727570.1| 403 GGNVGQLLAKRLEKRG-ENVVVVDSSKEKCHELM-NSGIRAVHGDVEDMNILKDAgIENAKYVVATTDKDNT 472
                                       59*************6.899999999*******7.8****************99967999999999865554 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.2   3.9e-06    0.0027      14      86 ..     397     470 ..     387     491 .. 0.79
   2 ?    0.0   0.0       1.2     8e+02      15      31 ..     593     609 ..     586     611 .] 0.87

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.9e-06
                                       EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHH.T.ET-EEEEGCGHHHH.HHT-SEEEE-SSSS CS
                      Shikimate_DH  14 kvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeel.kgeeiealkleelkel.laeadvvisatase 86 
                                       ++l++G G++++l+ak L ++g + vvv+  + e+ +el ++  ++++  + +++ lk++ +++a  v++ t   
  gi|298675820|ref|YP_003727570.1| 397 EILIVGGGNVGQLLAKRLEKRGEN-VVVVDSSKEKCHELMNSGiRAVHGDVEDMNILKDAgIENAKYVVATTDKD 470
                                       79****************977655.**************987547777777777777754477777777776655 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.2
                                       EEEES-SHHHHHHHHHH CS
                      Shikimate_DH  15 vlliGaGemaelvakhL 31 
                                       v++iG G  a+ va +L
  gi|298675820|ref|YP_003727570.1| 593 VTVIGEGDSAKVVADML 609
                                       89***********9988 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   5.8e-06     0.004       1      68 [.     398     463 ..     398     470 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.8e-06
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEE CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdav 68 
                                       il++G+ G +G+ l+k+l+++g +v+++d+ +++ ++  +  ++ v++d+ d + l+++  e ++ +v
  gi|298675820|ref|YP_003727570.1| 398 ILIVGG-GNVGQLLAKRLEKRGENVVVVDSSKEKCHELMNSGIRAVHGDVEDMNILKDAGIE-NAKYV 463
                                       899999.************************999999999999********99988877654.45555 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.4    0.0024       1.7       1      55 [.     397     453 ..     397     471 .. 0.71
   2 !    7.7   0.0    0.0081       5.6       3      20 ..     594     611 .]     592     611 .] 0.91

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0024
                            PglD_N   1 kivIiGaGGhgkvvadiieangeyeiigflDdnkk..teve..gypvlgkaiellksls 55 
                                       +i+I+G G  g+  a+ +e++g  e ++++D++k+  +e++  g++ + +++e+ + l+
  gi|298675820|ref|YP_003727570.1| 397 EILIVGGGNVGQLLAKRLEKRG--ENVVVVDSSKEkcHELMnsGIRAVHGDVEDMNILK 453
                                       599*******************..78999999876232222237777777777766663 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0081
                            PglD_N   3 vIiGaGGhgkvvadiiea 20 
                                        +iG G  +kvvad++e+
  gi|298675820|ref|YP_003727570.1| 594 TVIGEGDSAKVVADMLEK 611
                                       69*************986 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.2e-05     0.008      37      82 ..     396     441 ..     385     452 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-05
                                       SEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEE CS
                      2-Hacid_dh_C  37 ktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvel 82 
                                       +++ i+G G++Gq +akrl++ g +v+++d sk+k +e  + g++ 
  gi|298675820|ref|YP_003727570.1| 396 MEILIVGGGNVGQLLAKRLEKRGENVVVVDSSKEKCHELMNSGIRA 441
                                       5789****************************99888777777765 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   1.3e-05    0.0089      25      98 ..     392     466 ..     378     477 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.3e-05
                                       CB---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHH.HHH-SEEEE- CS
                       AlaDh_PNT_C  25 gvepakvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaea.vkeadvvigt 98 
                                       gv p ++l++GgG +G+  ++   + g +V+v+D ++++ ++l + g + v+   ++++ l++a +++a  v+ t
  gi|298675820|ref|YP_003727570.1| 392 GVIPMEILIVGGGNVGQLLAKRLEKRGENVVVVDSSKEKCHELMNSGIRAVHGDVEDMNILKDAgIENAKYVVAT 466
                                       68899****************************************999999988888877776446777777666 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   1.9e-05     0.013       3      66 ..     398     454 ..     397     530 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.9e-05
                                       EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHH CS
                         adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevea 66 
                                       +l++G++  +G+ +ak+l k+G +vvvvd+s+ek++e++++       + a+++Dv+d++ +++
  gi|298675820|ref|YP_003727570.1| 398 ILIVGGG-NVGQLLAKRLEKRGENVVVVDSSKEKCHELMNS------GIRAVHGDVEDMNILKD 454
                                       6888887.69***********************99766655......37888899988877665 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.3   1.8e-05     0.012       1      74 [.     398     469 ..     398     480 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.8e-05
                                       EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHH.HTT-SEEEE---G CS
                              NmrA   1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvea.lkgvdvvfsvtgf 74 
                                       Il++G+ G+ G+ +++ l k+g +v  +v d+++e+ ++l ++G   v+gd++d ++l+ a +++++ v ++t  
  gi|298675820|ref|YP_003727570.1| 398 ILIVGG-GNVGQLLAKRLEKRGENV--VVVDSSKEKCHELMNSGIRAVHGDVEDMNILKDAgIENAKYVVATTDK 469
                                       667765.9**************998..566****************************99879999999999874 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   5.2e-05     0.036       2      64 ..     399     480 ..     398     520 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.2e-05
                                       EEE--STTHHHHHHHHHHHTEEEEEEES-GGGG.............-GGG-TT-SE..............-EEEE-- CS
                            XdhC_C   2 vifGaghvaqalarlaaalgfrvtvvdpreefa.............tkerfpeade..............tavvvlt 51 
                                       +i+G+g+v+q la+ +++ g +v+vvd+ +e               +                       ++vv+ t
  gi|298675820|ref|YP_003727570.1| 399 LIVGGGNVGQLLAKRLEKRGENVVVVDSSKEKChelmnsgiravhgD--------VedmnilkdagienaKYVVATT 467
                                       89****************************74434444443333332........0333334445556655555555 PP

                                       S-HHHHHHHHHHH CS
                            XdhC_C  52 hdhklDaealeaa 64 
                                        + ++   +++ a
  gi|298675820|ref|YP_003727570.1| 468 DKDNTNLLVCQVA 480
                                       5555555555444 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   4.2e-05     0.029     140     188 ..     393     442 ..     377     493 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.2e-05
                                       S-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSS.TTS-HHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                       Pyr_redox_2 140 llpkrivvvGgGyiGvElAaalaklgkevtlveardrll.raldkelsaa 188
                                         p  i++vGgG++G  lA  l k g++v++v+  ++ + + +++ ++a 
  gi|298675820|ref|YP_003727570.1| 393 VIPMEILIVGGGNVGQLLAKRLEKRGENVVVVDSSKEKChELMNSGIRAV 442
                                       4557899***********************99998887766666666654 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.4     3e-05      0.02       2      43 ..     398     440 ..     397     458 .. 0.85
   2 ?   -0.8   0.0       3.4   2.3e+03       2      19 ..     593     610 ..     593     611 .] 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3e-05
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TTSSHHHH CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkll.rllDeeas 43 
                                       +++vGgG++g  lA+ l + g +V vv+ s++ +  l++  ++
  gi|298675820|ref|YP_003727570.1| 398 ILIVGGGNVGQLLAKRLEKRGENVVVVDSSKEKChELMNSGIR 440
                                       89**************************999887666666655 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 3.4
                                       EEEECSSHHHHHHHHHHH CS
                         Pyr_redox   2 vvvvGgGyiglElAgala 19 
                                       v+v+G G+++  +A +l 
  gi|298675820|ref|YP_003727570.1| 593 VTVIGEGDSAKVVADMLE 610
                                       689******999998875 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00014     0.098       2      40 ..     398     436 ..     397     480 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                                       EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHH CS
                    NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaenghevrlwvreeelieeine 40 
                                       i ++G+G+ G  lAk l+++g++v++   ++e ++e+ +
  gi|298675820|ref|YP_003727570.1| 398 ILIVGGGNVGQLLAKRLEKRGENVVVVDSSKEKCHELMN 436
                                       789*************************99988877654 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00013     0.089       2      43 ..     397     438 ..     396     442 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHCG CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKilisG 43 
                                       +++++GgG  G + A +++krg++V+++++ k+  + ++ sG
  gi|298675820|ref|YP_003727570.1| 397 EILIVGGGNVGQLLAKRLEKRGENVVVVDSSKEKCHELMNSG 438
                                       689****************************99888888887 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   0.00017      0.12       2      65 ..     398     461 ..     397     480 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00017
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHH CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaala 65 
                                       + ++G G +G+ +a+ + ++g +Vv+vd s+e+ ++ +++  + ++  ve+ ++ ++   + ++
  gi|298675820|ref|YP_003727570.1| 398 ILIVGGGNVGQLLAKRLEKRGENVVVVDSSKEKCHELMNSGIRAVHGDVEDMNILKDAGIENAK 461
                                       679***************************9999998877666666666665555444444444 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00022      0.15       2      35 ..     398     429 ..     397     435 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00022
                     Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieasps 35 
                                       ++++G+G  g +lA+rl  +k g +vv++++s++
  gi|298675820|ref|YP_003727570.1| 398 ILIVGGGNVGQLLAKRL--EKRGENVVVVDSSKE 429
                                       79***************..***********9976 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00026      0.18       2      30 ..     398     428 ..     397     444 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00026
                                       EEEECTSHHHHHHHHHHHHTT..EEEEESSS CS
                               DAO   2 vviiGGGiiGlstAyeLarrg..Vtllekgd 30 
                                       ++i+GGG +G   A  L +rg  V+++++++
  gi|298675820|ref|YP_003727570.1| 398 ILIVGGGNVGQLLAKRLEKRGenVVVVDSSK 428
                                       99******************99******975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (611 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1039  (0.0579508); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.74u 0.32s 00:00:01.06 Elapsed: 00:00:00.49
# Mc/sec: 3745.96
//
Query:       gi|298675821|ref|YP_003727571.1|  [L=467]
Description: dimethylamine methyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     2e-262  870.7   5.7   2.2e-262  870.5   5.7    1.0  1  Dimeth_Pyl       Dimethylamine methyltransferase (Dimeth_PyL)
  ------ inclusion threshold ------
      0.044   14.0   0.0      0.093   13.0   0.0    1.5  1  Antimicrobial_7  Scorpion antimicrobial peptide


Domain annotation for each model (and alignments):
>> Dimeth_Pyl  Dimethylamine methyltransferase (Dimeth_PyL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  870.5   5.7  2.5e-266  2.2e-262       2     463 .]       4     465 ..       3     465 .. 1.00

  Alignments for each domain:
  == domain 1  score: 870.5 bits;  conditional E-value: 2.5e-266
                        Dimeth_Pyl   2 eyklrlGdgkrvyltkekiledieaGiadaadlaevpalsedeiekladilvskeklvsveaGkevvltydiGtlkl 78 
                                       +y++r+Gd+++ y++k++i+edieaG++daa+l+++pals+d++ek+adil+s++k+vsv+aG+ev++t+diGtl++
  gi|298675821|ref|YP_003727571.1|   4 GYRIRMGDSTTEYHSKDRIMEDIEAGTNDAAELGGIPALSDDDKEKIADILMSPQKMVSVDAGNEVPVTHDIGTLRI 80 
                                       79*************************************************************************** PP

                        Dimeth_Pyl  79 egdqgnsglgieisrlegvliheralgadtlelahidysikpvkpvvaeeaqameviqqnlvvpllyGampnlglyy 155
                                       +gdqgnsg+gi++srl+gv++hera+g+dt+el+hidys+kpvkpvv++e+q+mev+qqn++vpl+yGampn+glyy
  gi|298675821|ref|YP_003727571.1|  81 DGDQGNSGTGIPASRLTGVMTHERAFGTDTMELGHIDYSFKPVKPVVSQECQTMEVCQQNMTVPLMYGAMPNMGLYY 157
                                       ***************************************************************************** PP

                        Dimeth_Pyl 156 apdGpfenpadllrefkieeakesiekaadhlardivyvvskllkagadGvnfdttasaGdadfvatlkavealrkk 232
                                       +pdGpf+np+dl+refk++eake+ie aad+l++d+v++v+kl+k++adGvnfdt+++aGd+df+a+++a+ealrk+
  gi|298675821|ref|YP_003727571.1| 158 QPDGPFKNPSDLMREFKLQEAKEEIEGAADELTNDMVWTVDKLYKSAADGVNFDTIGAAGDGDFYASVQAIEALRKR 234
                                       ***************************************************************************** PP

                        Dimeth_Pyl 233 fpniyielGmagelvlGihGeleydGktlaGlyphqqvklvekaGanvfGpvvntntskslawnlaravtlvkeavk 309
                                       fpn+yie+Gma+e+vlG+hGe+eydG+tlaGl+ph+q +lv+kaGan++Gpv+n +t++s++wnlaravt++k+av+
  gi|298675821|ref|YP_003727571.1| 235 FPNMYIEAGMASESVLGMHGEFEYDGTTLAGLWPHEQGPLVAKAGANLYGPVCNASTGHSTSWNLARAVTFIKSAVE 311
                                       ***************************************************************************** PP

                        Dimeth_Pyl 310 asdipvhvnlGmGvGGiplletppidavsraskalveiakvdGikvGvGdpvGmaiahvlasGmgGirtaGdlvarm 386
                                        ++ip+hvn+GmGvGGip++etpp+dav+r+ska+ve+a+vdGi+vGvGdpvGm+iahv+asGm+G+r++Gdlvarm
  gi|298675821|ref|YP_003727571.1| 312 STPIPCHVNMGMGVGGIPMFETPPVDAVTRCSKAMVEVAGVDGIOVGVGDPVGMPIAHVSASGMTGMRAGGDLVARM 388
                                       ***************************************************************************** PP

                        Dimeth_Pyl 387 elsknmkideakeyvakklgveeldladevvmrdlreelgiGvvtsvaGaakGiaaklnieklldikinscekfrnk 463
                                       +lsknm+i+eak+yv+kklgve++dl+de+vmrdlreelgiGv+tsv+Ga+kGi+ak+nie+lldikinscekfrn+
  gi|298675821|ref|YP_003727571.1| 389 QLSKNMRINEAKDYVSKKLGVEPMDLSDEYVMRDLREELGIGVLTSVEGAPKGISAKMNIEELLDIKINSCEKFRNQ 465
                                       ***************************************************************************96 PP

>> Antimicrobial_7  Scorpion antimicrobial peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     1e-05     0.093      24      43 .]     392     411 ..     387     411 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1e-05
                   Antimicrobial_7  24 KnkalNAAKNfVAeKiGatP 43 
                                       Kn  +N AK +V  K+G+ P
  gi|298675821|ref|YP_003727571.1| 392 KNMRINEAKDYVSKKLGVEP 411
                                       8999**************88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3416.67
//
Query:       gi|298675822|ref|YP_003727572.1|  [L=217]
Description: methyltransferase cognate corrinoid protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.7e-27   94.8   0.9      6e-27   94.1   0.9    1.3  1  B12-binding    B12 binding domain
    7.4e-20   71.2   1.0    1.1e-19   70.6   0.3    1.7  2  B12-binding_2  B12 binding domain


Domain annotation for each model (and alignments):
>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.1   0.9   6.7e-31     6e-27       2     116 ..      94     202 ..      93     206 .. 0.93

  Alignments for each domain:
  == domain 1  score: 94.1 bits;  conditional E-value: 6.7e-31
                       B12-binding   2 kvllatvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvel..lk 76 
                                        v+ +tv+gd+h++G+ ++  +l+++gfeV+++g +v+++d++++i+++++dvvg+Sal+t++l++ k+++el  ++
  gi|298675822|ref|YP_003727572.1|  94 VVINGTVEGDVHDIGKSIVSTMLQASGFEVYDIGRDVPAQDFIDKIKEHNADVVGISALMTTTLQGQKDIIELlkEA 170
                                       58899********************************************************************9999 PP

                       B12-binding  77 rirprvkvvvGGahpsldpeetleaklgiddvvvgegeda 116
                                       ++r+++ v+vGGa+++ ++++   + +g+d+    ++e+a
  gi|298675822|ref|YP_003727572.1| 171 GMRDDTVVMVGGAPATQAWAD---K-IGADI----YAENA 202
                                       99************9999999...7.99554....66665 PP

>> B12-binding_2  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.6   0.3   1.2e-23   1.1e-19       2      75 .]       8      80 ..       7      80 .. 0.94
   2 ?   -3.0   0.0       1.1     1e+04      31      31 ..     163     163 ..     144     178 .. 0.56

  Alignments for each domain:
  == domain 1  score: 70.6 bits;  conditional E-value: 1.2e-23
                     B12-binding_2  2 aerlhwaivhgdkegieelidealaqgsa..avdvlndvllpamkeVGdlfgagelflpqvllsaevmkkavahLe 75
                                      ++++ +ai+  +k+ + e++++a+    +  a d+++++l+++m+eVG +f++g+lflp+v+++ae+m  av+ Le
  gi|298675822|ref|YP_003727572.1|  8 LKEISDAIISCKKDNVLEAVNKAR---GDleASDIIENGLAAGMNEVGMKFERGKLFLPHVMMAAEAMTDAVKTLE 80
                                      57899*******************...2346*****************************************9996 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.1
                     B12-binding_2  31 a 31 
                                        
  gi|298675822|ref|YP_003727572.1| 163 I 163
                                       2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1449.18
//
Query:       gi|298675823|ref|YP_003727573.1|  [L=46]
Description: hypothetical protein Metev_1947 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.052   13.2   0.4      0.052   13.2   0.4    1.5  2  DUF3149   Protein of unknown function (DUF3149)


Domain annotation for each model (and alignments):
>> DUF3149  Protein of unknown function (DUF3149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1      0.26   4.6e+03       1       7 [.       5      11 ..       5      12 .. 0.75
   2 ?   13.2   0.4   2.9e-06     0.052      14      33 ..      25      44 ..      25      46 .] 0.92

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.26
                           DUF3149  1 wkdLFss 7 
                                      w+ L+s+
  gi|298675823|ref|YP_003727573.1|  5 WEILISN 11
                                      7888887 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2.9e-06
                           DUF3149 14 liVIvftigmgaffiryFir 33
                                      ++VI+++ g++++ +r F +
  gi|298675823|ref|YP_003727573.1| 25 MLVILIMAGIALWQARVFAK 44
                                      89**************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 297.96
//
Query:       gi|298675824|ref|YP_003727574.1|  [L=110]
Description: hypothetical protein Metev_1948 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.021   14.5   0.1      0.036   13.8   0.1    1.4  1  DUF2963         Protein of unknown function (DUF2963)
      0.058   12.4   0.0      0.067   12.2   0.0    1.1  1  Glyco_hydro_56  Hyaluronidase


Domain annotation for each model (and alignments):
>> DUF2963  Protein of unknown function (DUF2963)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1     4e-06     0.036       5      25 ..      23      44 ..      20      51 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4e-06
                           DUF2963  5 GktIkki.deYnpqtgkkiKrt 25
                                      + +++++ +eY++++ k +K t
  gi|298675824|ref|YP_003727574.1| 23 NDLVNQVaKEYDSENNKFMKET 44
                                      7899***77***********98 PP

>> Glyco_hydro_56  Hyaluronidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.5e-06     0.067     124     166 ..       6      47 ..       1      57 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.5e-06
                                       HHHHHHHHHHHHSSS--HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Glyco_hydro_56 124 YrekSielvrqkhpelseeeveklAkleFekaarkfmeetlkl 166
                                       ++ +  el  +++p+++++ v+++Ak e+++  +kfm+etl+ 
  gi|298675824|ref|YP_003727574.1|   6 FKFRLLELCTDEEPHWNNDLVNQVAK-EYDSENNKFMKETLNF 47 
                                       56666789999*************97.7*************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 818.07
//
Query:       gi|298675825|ref|YP_003727575.1|  [L=350]
Description: hypothetical protein Metev_1949 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-11   43.3  51.2    7.9e-06   26.1  23.4    3.1  2  EamA      EamA-like transporter family


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9  19.8   1.7e-08   0.00031       2     134 ..      18     176 ..      17     179 .. 0.81
   2 !   26.1  23.4   4.4e-10   7.9e-06       2     137 .]     195     339 ..     194     339 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.7e-08
                              EamA   2 lgillallaalfwaiyfvlskillrkv.................spltltfvrfliagillliiallkegkl.akls 60 
                                       +g+++al  a++w+++++   ++ +                   + + ++++ + + ++ ++i ++++ g+l + + 
  gi|298675825|ref|YP_003727575.1|  18 SGYMWALFCAILWGLWYIPGEVVWTVEpfvgmydeisvgipgdaPMVIVAALVTAFNALTVIIALMVWNGTLlRLPE 94 
                                       7999**************99998444455888888899999885555555555555566666666666666663333 PP

                              EamA  61 lkd........wllllllgllgtvlafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlil 129
                                       l           +++l+ ++ g+ +a +  f+a+  ++ ++a+++ +l Pv+ ++ + l++gek+t++  +gi++i+
  gi|298675825|ref|YP_003727575.1|  95 LGRtlrefkpcSKWFLIGSVCGGPIAIFGSFMAMAFIGGAFAAVAGLLYPVVGAVTANLWYGEKITKRAAVGILVII 171
                                       333666678888999999*********************************************************** PP

                              EamA 130 lGvll 134
                                        G + 
  gi|298675825|ref|YP_003727575.1| 172 GGGVT 176
                                       99665 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 4.4e-10
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfl....iagillliiallkegkl....aklslkdwlll.ll 69 
                                       lg+l    aal w++ + ++ ++l+  ++ + ++ rf+    +  i+ ++ +++ + ++    a   +++++ll l+
  gi|298675825|ref|YP_003727575.1| 195 LGYLGGAMAALGWGLEGAIAGVGLEVSESDAGLTARFVfellLWWIIIIPALAIAGFPMlkytALVLQSPIALLvLI 271
                                       6899999****************99998775555555511114444445555555555555555566666666669* PP

                              EamA  70 lgllgtvlafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllill 137
                                       ++ + + ++++ +++++  +++++   + +l  ++++i+ +l+lg ++ ++ ++g +l+++G++++++
  gi|298675825|ref|YP_003727575.1| 272 FAGITFGFCYVSWYKSFPLIGVGRGQAVANLYGLMSVIFLFLFLGSTPAWTVFVGGILCIAGAFIMFT 339
                                       ****************************************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.56
# Mc/sec: 1869.91
//
Query:       gi|298675826|ref|YP_003727576.1|  [L=217]
Description: methyltransferase cognate corrinoid protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-22   78.3   0.7      1e-21   77.2   0.7    1.5  1  B12-binding    B12 binding domain
    4.2e-19   68.8   1.6      1e-18   67.5   0.4    2.2  2  B12-binding_2  B12 binding domain
  ------ inclusion threshold ------
       0.02   13.6   0.1      0.027   13.2   0.1    1.3  1  SpoVAD         Stage V sporulation protein AD (SpoVAD)
      0.032   14.4   0.1        0.5   10.6   0.0    2.2  2  CRS1_YhbY      CRS1 / YhbY (CRM) domain


Domain annotation for each model (and alignments):
>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.2   0.7   2.2e-25     1e-21       3     120 ..      98     209 ..      96     210 .. 0.95

  Alignments for each domain:
  == domain 1  score: 77.2 bits;  conditional E-value: 2.2e-25
                       B12-binding   3 vllatvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvel..lkr 77 
                                       v+++t++gd+h++G++++a +l+ agfe ++lg +v  e  v+++++ ++d+v+ Sal+t ++++   l e+  +++
  gi|298675826|ref|YP_003727576.1|  98 VVIGTIAGDIHTIGKDIVATMLKIAGFELYDLGRDVAIESYVNKAKEVDADIVASSALMTPTMTEQLTLEEQlkEAG 174
                                       799*********************************************************************9999* PP

                       B12-binding  78 irprvkvvvGGahpsldpeetleaklgiddvvvgegedaleal 120
                                       ir++vk+++GGa++s  +++   + +g +d    ++e+a++a+
  gi|298675826|ref|YP_003727576.1| 175 IRDKVKTMIGGAPVSQKWAD---E-IG-AD---IYAENAADAV 209
                                       *************9999999...7.**.55...5999988775 PP

>> B12-binding_2  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.5   0.4   2.3e-22     1e-18       6      73 ..      12      79 ..       8      81 .. 0.96
   2 ?   -0.6   0.0      0.43   1.9e+03      12      32 ..     170     188 ..     168     215 .. 0.76

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 2.3e-22
                     B12-binding_2  6 hwaivhgdkegieelidealaqgsaavdvlndvllpamkeVGdlfgagelflpqvllsaevmkkavah 73
                                      ++ai ++d+++++e+++e ++++ ++v++++d++ +am eVGd f++g lflp+v+ ++e+m +av+ 
  gi|298675826|ref|YP_003727576.1| 12 KNAIKEFDEDAAKEVAQEGIDSNVDLVKLIEDGFTAAMTEVGDQFEEGSLFLPHVIAASEAMSAAVEL 79
                                      689***************************************************************86 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.43
                     B12-binding_2  12 gdkegieelidealaqgsaav 32 
                                       ++++gi++ +++++  g a+v
  gi|298675826|ref|YP_003727576.1| 170 LKEAGIRDKVKTMI--GGAPV 188
                                       78888888888888..55543 PP

>> SpoVAD  Stage V sporulation protein AD (SpoVAD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   6.1e-06     0.027     203     280 ..      74     154 ..      65     195 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.1e-06
                                       HHHHHHHHHHHHHTT--GG.G-S.EE...EESS-HHHHHHHHHHHHHHTT---GGGEEEHHHHSS-TT.S--TT-EE CS
                            SpoVAD 203 paavdtieahlkdterkpe.dyD.li...vtGDlgkvGkeileellkekgldiseeykDCGlliydeekqdvlaGgs 274
                                        aav+ i+  l++    +e ++  ++   ++GD+ ++Gk+i+  +lk  g+++ +  +D  ++ y +++++v a   
  gi|298675826|ref|YP_003727576.1|  74 SAAVELITPVLEEQRGGAEeKHGgVVigtIAGDIHTIGKDIVATMLKIAGFELYDLGRDVAIESYVNKAKEVDADI- 149
                                       4677777777776543332033213323368*************************************99998853. PP

                                       SHHHHH CS
                            SpoVAD 275 Gcgcsa 280
                                         ++sa
  gi|298675826|ref|YP_003727576.1| 150 -VASSA 154
                                       .34444 PP

>> CRS1_YhbY  CRS1 / YhbY (CRM) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.082   3.7e+02      44      77 ..      37     104 ..      22     110 .. 0.78
   2 ?   10.6   0.0   0.00011       0.5       7      38 ..     168     199 ..     164     206 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.082
                         CRS1_YhbY  44 lvkvkcegppalnmkrmaeiLee...................................ktgglviqrsg 77 
                                       lvk+  +g +a  m ++ ++ ee                                   k gg+vi ++ 
  gi|298675826|ref|YP_003727576.1|  37 LVKLIEDGFTAA-MTEVGDQFEEgslflphviaaseamsaavelitpvleeqrggaeeKHGGVVIGTIA 104
                                       677777777777.88888888887777777777777777777777788888888888899999998875 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00011
                         CRS1_YhbY   7 rrLrhlairlkpkvkiGkaGvtkevvdeihek 38 
                                       ++L++ +ir k k++iG+a v++++ dei   
  gi|298675826|ref|YP_003727576.1| 168 EQLKEAGIRDKVKTMIGGAPVSQKWADEIGAD 199
                                       5899************************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1311.86
//
Query:       gi|298675827|ref|YP_003727577.1|  [L=495]
Description: trimethylamine [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-93  312.2   0.0    4.9e-93  311.8   0.0    1.0  1  MTTB      Trimethylamine methyltransferase (MTTB)


Domain annotation for each model (and alignments):
>> MTTB  Trimethylamine methyltransferase (MTTB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  311.8   0.0   2.7e-97   4.9e-93      30     500 ..      16     491 ..       9     493 .. 0.93

  Alignments for each domain:
  == domain 1  score: 311.8 bits;  conditional E-value: 2.7e-97
                              MTTB  30 pyellseeeleaieeaalriLeeiGiefldpealellkaaGakv..egervrfdrglvreliakapreftlharnPe 104
                                       ++el+se el +i++a ++++++ Gi++ dpea++l+k++G++v  +++ v++++ lv+ +++ ap++f l +r  e
  gi|298675827|ref|YP_003727577.1|  16 NLELFSEGELGEIHRATMELFQDPGIRVEDPEARQLFKENGCDVdeNTHVVKIPEYLVNRALQLAPSSFYLYGRTKE 92 
                                       6799****************************************655667*************************** PP

                              MTTB 105 rdveiggknvvfapvagaPf.vrDlerg....rregtledfrnlvkLaqmldvlhhsggtvvepvDvpvnkr.hldv 175
                                       ++ +   k  v  +  g    +  +e +      ++  +d+++ +k+++ +d++  ++  +v ++D  ++   +++ 
  gi|298675827|ref|YP_003727577.1|  93 NTFKQSHKGQVHWTCFGTGIkMCRYEGHgkfkTEDSVEQDVADCAKVCDWADNIDYFS-LPVSARDWAIKGAqDVHE 168
                                       ***988776666555554430333333222323467789******************9.7788*****99766**** PP

                              MTTB 176 lyakltlsdkvfmgsvtekeraedsiemlrivfGaeeeefranpvvttiinvnsPlkfdetmlealeayaragqavi 252
                                       +y+ l  ++k+f  +     ++e  +++++++ G +eee r++p+  ++   +sPl + +++++++++ ar g+++ 
  gi|298675827|ref|YP_003727577.1| 169 TYTPLVNTAKHFQHIDPVGDSMEYYFDICKAFYGGDEEEARNKPIFSALLCPTSPLELGDNACQVIMKGARYGIPLN 245
                                       ***************************************************************************** PP

                              MTTB 253 vtpfilaGAmaPvtvagavaqalAEaLagialtqlvrpgapviyGtftssvdlksGApafGtpeaalatlvagqlAr 329
                                       v++  +aG  +Pv +ag+++  +AE+L+gi+l+q+ +pga+v yG+ t++ dlk G    G+pe  l++ ++g+l+ 
  gi|298675827|ref|YP_003727577.1| 246 VLSMAMAGGSSPVDLAGTLVTHNAEVLSGIVLAQITQPGARVWYGSSTTTFDLKRGTAPVGSPELGLISGAVGKLGH 322
                                       ***************************************************************************** PP

                              MTTB 330 rlglPlrssggltasklpDaQaayesanslwaavlaganlvlhaAGwleggLvasyekfilDadvlgmiarllegie 406
                                       ++glP  ++g+ ++sk+pDaQa++e++++ +  +l+gan  +   G+le g+++s+e+++ D+d++ m ++++egie
  gi|298675827|ref|YP_003727577.1| 323 YYGLPSYVAGSOADSKVPDAQAGHEKTMTTLLPALSGANTLYG-SGMLELGMTFSLEQLLFDNDMISMTKKVMEGIE 398
                                       ***************************************9986.6******************************** PP

                              MTTB 407 vseealaldairevgpgghflgtahTlaryetafyepelsdnknfeeWeeeGakdaeerAnekvkkiLaeyeepkld 483
                                       v++e l +d ir+vg g++fl+ + T ++      +p+  d++ f++We++G+kd+ ++A+ekv++iL++ye  ++d
  gi|298675827|ref|YP_003727577.1| 399 VTDESLNIDNIRKVGIGNNFLALKDTRQKIDLP-SDPMFIDRRMFGDWEKDGSKDIIDVAHEKVEDILKNYEVEPID 474
                                       ***************************999866.69***************************************** PP

                              MTTB 484 eaideeLrdfiarrkae 500
                                       ++i++ ++++++r  +e
  gi|298675827|ref|YP_003727577.1| 475 SDIQKDMKAVMDRADKE 491
                                       **********9998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3523.43
//
Query:       gi|298675828|ref|YP_003727578.1|  [L=82]
Description: hypothetical protein Metev_1952 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.30s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 552.88
//
Query:       gi|298675829|ref|YP_003727579.1|  [L=541]
Description: 4Fe-4S ferredoxin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-71  240.1   0.9    6.6e-71  238.4   0.9    1.8  1  RACo_C_ter   C-terminal domain of RACo the ASKHA domain
      3e-11   43.3   0.0    7.7e-11   41.9   0.0    1.8  1  Raco_middle  RACo middle region
    5.7e-07   29.6   6.4    1.2e-06   28.6   6.4    1.6  1  Fer4_9       4Fe-4S dicluster domain
    1.5e-06   27.8  19.4    9.5e-05   22.1   3.7    2.8  3  Fer4         4Fe-4S binding domain
    1.7e-06   28.0   9.2    4.2e-06   26.8   9.2    1.6  1  Fer4_21      4Fe-4S dicluster domain
    4.5e-06   27.1   8.0    1.3e-05   25.7   8.1    1.7  1  Fer4_7       4Fe-4S dicluster domain
    5.2e-05   23.6   1.9      0.028   14.9   0.0    2.5  2  Fer4_8       4Fe-4S dicluster domain
    0.00013   22.8  10.5      0.044   14.7   1.6    2.5  2  Fer4_16      4Fe-4S double cluster binding domain
    0.00034   20.5  13.7    0.00094   19.2   2.4    2.5  2  Fer4_6       4Fe-4S binding domain
    0.00038   20.9   2.9      0.042   14.4   0.2    2.5  2  Fer4_17      4Fe-4S dicluster domain
    0.00054   20.0  11.6      0.024   14.8  12.7    2.4  2  Fer4_10      4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.11   13.5  14.2       0.89   10.6   2.5    2.6  2  Fer4_3       4Fe-4S binding domain
       0.28   11.8  11.9        0.4   11.3   3.1    2.5  2  Fer4_4       4Fe-4S binding domain
       0.44   10.8  11.6       0.74   10.0   3.2    2.6  2  Fer4_2       4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> RACo_C_ter  C-terminal domain of RACo the ASKHA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.4   0.9   5.2e-74   6.6e-71       1     259 [.     169     427 ..     169     428 .. 0.95

  Alignments for each domain:
  == domain 1  score: 238.4 bits;  conditional E-value: 5.2e-74
                                       S-EEEEEESSSEEEEEE-SS-EEEEEEE--SCCCTTTSTTBE-SSTTEEEEEEEEGGGSSEEEEECTSS-....... CS
                        RACo_C_ter   1 elslliDiGTNaEivlgnkdellaasaaaGPAlEGaeikcGmrAapgAIedveidpetlevelkvigdek....... 70 
                                       e s+++D+GTNaE++l+++d+++++saaaGPA+EG++i cGm+A+pgAI dv  +pe   ++l+v++d+        
  gi|298675829|ref|YP_003727579.1| 169 EPSIVTDYGTNAEMALKVGDKIVTGSAAAGPAIEGQGIGCGMLASPGAITDV--NPEGDYWRLTVLDDNMsekkgdl 243
                                       6799************************************************..777888******87666788999 PP

                                       ...............-SEEEHHHHHHHHHHHHHTTSB-TTS-B-GGG-TTTEEEETTCEEEEEE-GGGSSSS-EEEE CS
                        RACo_C_ter  71 ...............akGicGsGiidliaelleagiidkkgklnkelkserireeeetleyvlakaeetetkdivit 132
                                                        Gi+G+G+i++++ +l++g+i+k ++l              + +++l +       d+v+t
  gi|298675829|ref|YP_003727579.1| 244 iepatgkvvedsgvkTIGITGTGMISVLSVALDTGLIEKLPQL-------------PNGKIILGD-------DLVLT 300
                                       9999*********99***************************9.............566777755.......8**** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHTT--GGG--EEEEESSGGGCEEHHHHHHHTSS-SS-GGGEEEECSHHHHHHHH CS
                        RACo_C_ter 133 ekDieelikakaAiyagiktLleevglevediekvylAGafGsyidaekAitiGllPdlelekvvqvGNtslagAre 209
                                       ++Diee++ka++Ai+a++ tL+ e gl++ed+e++y++Ga+G+y+d ekA+++G +P+   +++vq+GNts+++Ar+
  gi|298675829|ref|YP_003727579.1| 301 NRDIEEAGKAIGAIRAAHLTLIVESGLKYEDLENIYMSGASGTYVDSEKARRLGTCPN-FGKRIVQFGNTSISLARD 376
                                       **********************************************************.999*************** PP

                                       HHCBHHHHHHHHHHHHHE..EE--TTSSSHHHHHHHHHSSSS-SSGGG-ST- CS
                        RACo_C_ter 210 allseealeeleeiarki..tyielateeeFqeeyvaalflphtdlelfpsv 259
                                       +++++++l+e++e a++i  +++++at+e+F++ y+ +l+++++++ +++++
  gi|298675829|ref|YP_003727579.1| 377 LVFDDNKLDEITEFAHTItaDHLMMATSETFKNFYIFELSYWTQGM-PIETY 427
                                       ******************999*************************.88887 PP

>> Raco_middle  RACo middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.0     6e-14   7.7e-11       1     160 [.       2     164 ..       2     167 .. 0.82

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 6e-14
                       Raco_middle   1 yGlavDiGtTtvvaaLvdletgkelaeasalNpQikyGeDvlsRiayakeeeegleklqkavveeinelieelleea 77 
                                       yG+a+D+Gt+   a+L+dle+++++++  ++ +    G +v+  + +a e   g +  +  +     ++++++++  
  gi|298675829|ref|YP_003727579.1|   2 YGIALDLGTSGYRAQLIDLEREETIKTVITMGHPLP-GGNVIDHLDFAIE--LGEDIANGII----LNAVKRIISAF 71 
                                       9*****************************998776.779*********9..3333334444....45666777777 PP

                       Raco_middle  78 giekeeiyevvvagNttMlhlllgldpkslakap........yvpvvseavelkakelglki..npeakvyvlpnvs 144
                                       +++ +e+++++++gN + l l+ +++ + la a            v +++ +++a+++  +i   p+++v+v p++ 
  gi|298675829|ref|YP_003727579.1|  72 NVNLSEVKKLAICGNPIQLSLFQNMEIRDLAYAGrnkqarlgVEDVKRDSRVVPANDIFGDIldMPNCNVVVPPAIK 148
                                       9999**************************98761111111134566788999*****888755799********** PP

                       Raco_middle 145 syvGgDivagilasgl 160
                                       + +G+D++a +l +++
  gi|298675829|ref|YP_003727579.1| 149 HEIGADALAMMLKTEF 164
                                       ************9986 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   6.4   9.4e-10   1.2e-06       2      51 .]     481     531 ..     469     531 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 9.4e-10
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaC..igCgaCveaCpkgai 51 
                                       C+ C++C+e Cp ++++  +  +    +  ++++C  ++C++Cv +Cp +ai
  gi|298675829|ref|YP_003727579.1| 481 CIFCHKCEEECPEDAITILDTDEGLIANY-NAQRClgTSCRRCVGICPVNAI 531
                                       ****************7666666555443.3348*7778*********9987 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.5       7.4   9.5e+03       9      12 ..     206     209 ..     206     210 .. 0.85
   2 !   22.1   3.7   7.4e-08   9.5e-05       5      24 .]     478     497 ..     475     497 .. 0.92
   3 !   16.8   1.6   3.3e-06    0.0043      10      24 .]     518     532 ..     517     532 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 7.4
                                       SS-T CS
                              Fer4   9 igCG 12 
                                       igCG
  gi|298675829|ref|YP_003727579.1| 206 IGCG 209
                                       8**9 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 7.4e-08
                                       TTTSSS-THHHHHSTTTEEE CS
                              Fer4   5 eekCigCGaCvevCPvgAIt 24 
                                       ++ Ci+C +C+e CP +AIt
  gi|298675829|ref|YP_003727579.1| 478 TDGCIFCHKCEEECPEDAIT 497
                                       688****************7 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 3.3e-06
                                       S-THHHHHSTTTEEE CS
                              Fer4  10 gCGaCvevCPvgAIt 24 
                                        C +Cv +CPv+AI+
  gi|298675829|ref|YP_003727579.1| 518 SCRRCVGICPVNAIK 532
                                       7*************6 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   9.2   3.3e-09   4.2e-06       6      58 ..     479     532 ..     476     533 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 3.3e-09
                           Fer4_21   6 dkCigCgkCliaCedtshqaieidaktvlkvvedeCvG..CnlCssvCPvedcie 58 
                                       d Ci C kC   C++ +++ +++d+  ++++ +++C G  C  C+ +CPv ++i+
  gi|298675829|ref|YP_003727579.1| 479 DGCIFCHKCEEECPEDAITILDTDEGLIANYNAQRCLGtsCRRCVGICPV-NAIK 532
                                       78*****************99***************7777*********9.8886 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   8.1   9.8e-09   1.3e-05       2      52 .]     481     530 ..     480     530 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 9.8e-09
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClg..CgaCvavCPtga 52 
                                       Ci C++C++ Cp +ai++ +    ++   +++++++Clg  C++Cv  CP++a
  gi|298675829|ref|YP_003727579.1| 481 CIFCHKCEEECPEDAITILDT---DEGLIANYNAQRCLGtsCRRCVGICPVNA 530
                                       ******************887...455889*******7444**********97 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.2e-05     0.028      44      64 ..     459     494 ..     427     495 .. 0.74
   2 !    7.6   0.4    0.0041       5.3      45      64 ..     508     529 ..     497     530 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.2e-05
                            Fer4_8  44 e...............eealwsCttcgaCtevCpvg 64 
                                                       ee+ + C  c++C+e+Cp++
  gi|298675829|ref|YP_003727579.1| 459 VgkegietignvgiilEEITDGCIFCHKCEEECPED 494
                                       0333445566777777999***************85 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0041
                            Fer4_8  45 eealwsC..ttcgaCtevCpvg 64 
                                       ++++++C  t+c++C+  Cpv+
  gi|298675829|ref|YP_003727579.1| 508 NYNAQRClgTSCRRCVGICPVN 529
                                       56677887799*********97 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   3.1   0.00035      0.45       2      18 ..     481     497 ..     480     515 .. 0.84
   2 !   14.7   1.6   3.5e-05     0.044       3      20 ..     517     534 ..     513     541 .] 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00035
                           Fer4_16   2 CgtCgkCaevCPtnaik 18 
                                       C+ C+kC e CP++ai+
  gi|298675829|ref|YP_003727579.1| 481 CIFCHKCEEECPEDAIT 497
                                       999************98 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 3.5e-05
                           Fer4_16   3 gtCgkCaevCPtnaikek 20 
                                       ++C++C+ +CP+naik +
  gi|298675829|ref|YP_003727579.1| 517 TSCRRCVGICPVNAIKYE 534
                                       68*************987 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   3.8    0.0075       9.6       9      24 .]     481     496 ..     479     496 .. 0.91
   2 !   19.2   2.4   7.4e-07   0.00094       2      24 .]     507     531 ..     506     531 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0075
                            Fer4_6   9 CigCgdCvrvCPegai 24 
                                       Ci C +C+  CPe+ai
  gi|298675829|ref|YP_003727579.1| 481 CIFCHKCEEECPEDAI 496
                                       77799*********98 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 7.4e-07
                            Fer4_6   2 veidpdkCig..CgdCvrvCPegai 24 
                                       + +++++C+g  C++Cv +CP +ai
  gi|298675829|ref|YP_003727579.1| 507 ANYNAQRCLGtsCRRCVGICPVNAI 531
                                       67899****666***********98 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.2   3.3e-05     0.042      40      59 ..     475     494 ..     441     496 .. 0.81
   2 ?    6.4   0.3      0.01        13      36      58 ..     504     528 ..     497     531 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.3e-05
                           Fer4_17  40 eekaslCieCgeCerkCPqg 59 
                                       ee  + Ci C++Ce++CP++
  gi|298675829|ref|YP_003727579.1| 475 EEITDGCIFCHKCEEECPED 494
                                       466789************97 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.01
                           Fer4_17  36 eaekeekaslC..ieCgeCerkCPq 58 
                                       + +++ +a++C  ++C++C+  CP 
  gi|298675829|ref|YP_003727579.1| 504 GLIANYNAQRClgTSCRRCVGICPV 528
                                       5567788999944579999999996 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8  12.7   1.9e-05     0.024       6      56 .]     478     527 ..     473     527 .. 0.91
   2 !   12.9   1.8   7.3e-05     0.094       3      25 ..     508     532 ..     506     541 .] 0.71

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.9e-05
                           Fer4_10   6 ddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtg..cgaCveaCP 56 
                                       +d Ci C kC + CP       ++  ++e+   + + ++C g  c  Cv +CP
  gi|298675829|ref|YP_003727579.1| 478 TDGCIFCHKCEEECPE---DAITILDTDEGLIANYNAQRCLGtsCRRCVGICP 527
                                       689*************...8888899999999999*****9988********9 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 7.3e-05
                           Fer4_10   3 vidddtC..irCgkCvkaCPadlts 25 
                                        +++++C  + C++Cv  CP+++ +
  gi|298675829|ref|YP_003727579.1| 508 NYNAQRClgTSCRRCVGICPVNAIK 532
                                       678999*7779**********4422 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   2.5   0.00069      0.89       1      15 []     481     495 ..     481     495 .. 0.97
   2 ?    8.0   4.1    0.0049       6.2       1      15 []     514     530 ..     514     530 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00069
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+ C  C+e CP++A
  gi|298675829|ref|YP_003727579.1| 481 CIFCHKCEEECPEDA 495
                                       ************998 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0049
                            Fer4_3   1 Ctg..CgaCvevCPvgA 15 
                                       C+g  C++Cv  CPv+A
  gi|298675829|ref|YP_003727579.1| 514 CLGtsCRRCVGICPVNA 530
                                       6655599********98 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   1.5     0.033        42       2      16 ..     479     493 ..     478     501 .. 0.89
   2 ?   11.3   3.1   0.00031       0.4       2      17 .]     512     529 ..     511     529 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.033
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       + Ci C +C+  CP 
  gi|298675829|ref|YP_003727579.1| 479 DGCIFCHKCEEECPE 493
                                       56999*********5 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00031
                            Fer4_4   2 erC..igCgsCvaaCPqg 17 
                                       +rC  + C++Cv +CP++
  gi|298675829|ref|YP_003727579.1| 512 QRClgTSCRRCVGICPVN 529
                                       799666**********75 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   1.3     0.021        27       7      22 .]     478     493 ..     474     493 .. 0.87
   2 ?   10.0   3.2   0.00058      0.74       5      21 ..     509     527 ..     508     528 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.021
                            Fer4_2   7 tdrCigCgaCvsaCPa 22 
                                       td Ci C +C   CP+
  gi|298675829|ref|YP_003727579.1| 478 TDGCIFCHKCEEECPE 493
                                       677999*********5 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00058
                            Fer4_2   5 vdtdrCig..CgaCvsaCP 21 
                                       ++++rC+g  C+ Cv  CP
  gi|298675829|ref|YP_003727579.1| 509 YNAQRCLGtsCRRCVGICP 527
                                       7999**9999********* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (541 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.54
# Mc/sec: 3039.31
//
Query:       gi|298675830|ref|YP_003727580.1|  [L=191]
Description: hypothetical protein Metev_1954 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.2   0.3        0.3   10.9   0.3    1.7  1  HCV_NS4a  Hepatitis C virus non-structural protein NS4a


Domain annotation for each model (and alignments):
>> HCV_NS4a  Hepatitis C virus non-structural protein NS4a
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.3   1.7e-05       0.3      20      55 ..     108     152 ..     106     153 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 1.7e-05
                          HCV_NS4a  20 tGSvvvvtrwsvnGkg..........ppvvvvpdeevlyqgeemee 55 
                                       tG + v++++++ +k           p vvv+p++e  +  ee++e
  gi|298675830|ref|YP_003727580.1| 108 TGDALVIGNIVIYDKSsissltgtskPLVVVMPPKE-CPTVEEVPE 152
                                       6666777777777777777777999999*******9.888999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1195.07
//
Query:       gi|298675831|ref|YP_003727581.1|  [L=106]
Description: hypothetical protein Metev_1955 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 723.30
//
Query:       gi|298675832|ref|YP_003727582.1|  [L=288]
Description: nucleic acid-binding OB-fold tRNA/helicase-type protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0036   17.6   1.5      0.014   15.7   0.2    2.4  3  Mnd1      Mnd1 HTH domain
  ------ inclusion threshold ------
      0.034   14.4   0.0      0.073   13.3   0.0    1.5  1  PaaX      PaaX-like protein


Domain annotation for each model (and alignments):
>> Mnd1  Mnd1 HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.17   1.5e+03      46      57 ..      58      69 ..      54      70 .. 0.86
   2 ?   -3.2   0.0       1.3   1.1e+04      31      38 ..     205     212 ..     203     213 .. 0.81
   3 !   15.7   0.2   1.5e-06     0.014      18      55 ..     250     286 ..     246     287 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.17
                              Mnd1 46 eveKiGssnvyW 57
                                      ev+ iG+ n  W
  gi|298675832|ref|YP_003727582.1| 58 EVDNIGTDNNIW 69
                                      789******999 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.3
                              Mnd1  31 sVkdvlqs 38 
                                       s+kd+l+s
  gi|298675832|ref|YP_003727582.1| 205 SIKDCLES 212
                                       89**9987 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 1.5e-06
                              Mnd1  18 eklapkekgivsqsVkdvlqsLvdDglveveKiGssnv 55 
                                         la+  kg+++q+V+d + s++++g+  + KiG ++v
  gi|298675832|ref|YP_003727582.1| 250 IDLAQE-KGVSEQTVEDAVSSMLSNGKCYEPKIGIIKV 286
                                       555666.***************************9875 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   8.2e-06     0.073      17      55 ..     240     278 ..     237     286 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.2e-06
                              PaaX  17 rggaiwlgsLirllaelGiseslvRaalsRlakaGwlvr 55 
                                       +g  +  g+Li l +e G+se++v  a+s +  +G   +
  gi|298675832|ref|YP_003727582.1| 240 EGKGVDYGELIDLAQEKGVSEQTVEDAVSSMLSNGKCYE 278
                                       5667899************************99998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1904.53
//
Query:       gi|298675833|ref|YP_003727583.1|  [L=435]
Description: nucleic acid-binding OB-fold tRNA/helicase-type protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-07   30.4   4.5       0.56   10.2   0.0    4.5  4  tRNA_anti-codon  OB-fold nucleic acid binding domain
    0.00016   21.4   0.9     0.0017   18.1   0.1    2.5  2  CDC24_OB3        Cell division control protein 24, OB domain 
  ------ inclusion threshold ------
      0.052   13.4   0.1        9.8    6.0   0.0    2.5  2  POT1             Telomeric single stranded DNA binding POT1/C
       0.11   12.7   0.4       0.43   10.8   0.1    2.2  2  NUMOD4           NUMOD4 motif


Domain annotation for each model (and alignments):
>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.1   0.00022         1       3      70 ..      71     138 ..      69     144 .. 0.93
   2 !    8.5   0.0   0.00044         2      14      72 ..     195     248 ..     180     255 .. 0.86
   3 ?    0.0   0.1      0.19   8.5e+02       1      19 [.     289     305 ..     289     306 .. 0.90
   4 !   10.2   0.0   0.00012      0.56      19      73 ..     334     411 ..     321     413 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00022
                                       EEEEEEEEE......EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTSSEEEEE CS
                   tRNA_anti-codon   3 vaGrvtsis......drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpggelelkv 70 
                                       + Gr+++i+      ++++  +++ ++ D tg    +l+         +l +Gd ++++  + ++++++ ++l++
  gi|298675833|ref|YP_003727583.1|  71 ITGRIIDIQnktvnvKGEKVPISSGIIADSTGACYFTLWE------DMSLNIGDALKIKnAYTRKWQNR-VQLNI 138
                                       899**********99999999*******************......999********************.99986 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00044
                                       EETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTSSEEEEEEE CS
                   tRNA_anti-codon  14 sggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpggelelkvee 72 
                                        +  ++  +l D+tg++  + +       +e +++G+v++ +   v++++g  ++++++e
  gi|298675833|ref|YP_003727583.1| 195 RKTTILEGVLADETGKLPFTSWT-----PLEGVDIGKVIQFEgAFVQTFKGV-PSININE 248
                                       5556777889*************.....9*************9999999999.9999987 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.19
                                       EEEEEEEEEEEEEEETTEE CS
                   tRNA_anti-codon   1 VtvaGrvtsisdrsggkvi 19 
                                       V+++G ++s   rsg+++i
  gi|298675833|ref|YP_003727583.1| 289 VSIEGNIISL--RSGSGII 305
                                       89********..9999987 PP

  == domain 4  score: 10.2 bits;  conditional E-value: 0.00012
                                       EEEEEEETTEEEEEEEET.....................HHHHHHHTTS-...TTSEEEEEEEEEECTTSSEEEEEE CS
                   tRNA_anti-codon  19 ifidlrDgtgriqvvlfr.....................eeatklaenlk...eGdvvrvtGrvkrrpggelelkve 71 
                                       i ++l+Dgtg i+v+l+r                      ++++++e+ +   +G++++v G  + ++ g ++l+++
  gi|298675833|ref|YP_003727583.1| 334 IKAILDDGTGAITVILNRelseivygssmyeaediiqntLSQDAVYEDMRrrlIGKYLGVCGNSSNTDFG-PTLVAK 409
                                       5689**************9999999999988888888885555555555555588888888888888888.887777 PP

                                       EE CS
                   tRNA_anti-codon  72 ei 73 
                                       ++
  gi|298675833|ref|YP_003727583.1| 410 SV 411
                                       65 PP

>> CDC24_OB3  Cell division control protein 24, OB domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   3.8e-07    0.0017       1      73 [.      61     128 ..      61     152 .. 0.80
   2 ?    1.3   0.1     0.054   2.4e+02     160     186 ..     307     343 ..     168     357 .. 0.55

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.8e-07
                         CDC24_OB3   1 DLrekmlnvtLlGrvvaifreknsek.kkmdryslrieDttGaidatlweeagklhfkrlrvGhlvllsgLats 73 
                                       +L+++  ++ + Gr+++i +++ ++k +k+ ++s  i+D+tGa+  tlwe +      +l++G+ + +++ +t 
  gi|298675833|ref|YP_003727583.1|  61 NLKANSKGLEITGRIIDIQNKTVNVKgEKVPISSGIIADSTGACYFTLWEDM------SLNIGDALKIKNAYTR 128
                                       57788888999*******888888999**********************994......3666666666665555 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.054
                         CDC24_OB3 160 eCefCqcsv..........aevvrefeleitLdddts 186
                                        C  C++ +           e  + + ++  Ldd+t+
  gi|298675833|ref|YP_003727583.1| 307 RCPTCNRVIfknkcrahgtVEGYHDMRIKAILDDGTG 343
                                       3444443333444444434444455556666666654 PP

>> POT1  Telomeric single stranded DNA binding POT1/CDC13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0    0.0052        23      68     100 ..     114     144 ..     104     184 .. 0.82
   2 ?    6.0   0.0    0.0022       9.8      66     126 ..     219     276 ..     214     279 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0052
                                       CGGCCCCEEECCCCEEEESTTSCECCSEEEEEE CS
                              POT1  68 ivkkvgdiirlhraklqsyngepqglanigfss 100
                                          ++gd++++++a  ++++++ q ++++++ +
  gi|298675833|ref|YP_003727583.1| 114 L--NIGDALKIKNAYTRKWQNRVQLNIGNRSEI 144
                                       4..79***********************99884 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0022
                                       CCCGGCCCCEEECCCCEEEESTTSCECCSEEEEEEECCCTTSCEEEEECCCCCSTSTTCCC CS
                              POT1  66 LpivkkvgdiirlhraklqsyngepqglanigfssswalFngnlnailletppilsskffe 126
                                       L  v ++g++i+++ a +q+++g p  ++n  +s    + ++ +n + +++  ++ sk++ 
  gi|298675833|ref|YP_003727583.1| 219 LEGV-DIGKVIQFEGAFVQTFKGVPSININESTS--LEIVDSTENLPFTYETASNTSKPVP 276
                                       6667.99******************999999999..6788888887777777777776665 PP

>> NUMOD4  NUMOD4 motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.94   4.2e+03      18      29 ..      72      83 ..      60      97 .. 0.78
   2 ?   10.8   0.1   9.6e-05      0.43       7      42 ..     278     328 ..     273     335 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.94
                            NUMOD4 18 yGRvrslkrkvt 29
                                      +GR+  +++k+ 
  gi|298675833|ref|YP_003727583.1| 72 TGRIIDIQNKTV 83
                                      588888887765 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 9.6e-05
                            NUMOD4   7 p...gyegkYevSnyGRvrslkrkvt........kgriLkp....gsksnG 42 
                                       +     +g++evS  G++ sl+  +         +  i k+      + +G
  gi|298675833|ref|YP_003727583.1| 278 KnilNKDGIFEVSIEGNIISLRSGSGiitrcptcNRVIFKNkcraHGTVEG 328
                                       24446689**************88777777777766666655554555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3018.16
//
Query:       gi|298675834|ref|YP_003727584.1|  [L=68]
Description: transcription factor CBF/NF-Y/histone domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.7e-18   65.0   0.0    6.6e-18   64.7   0.0    1.0  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
      2e-09   37.9   0.0    2.5e-09   37.6   0.0    1.1  1  Histone        Core histone H2A/H2B/H3/H4
    2.9e-08   33.6   0.0    3.5e-08   33.4   0.0    1.0  1  Bromo_TP       Bromodomain associated
    8.2e-08   32.3   0.0    8.6e-08   32.3   0.0    1.1  1  CENP-T_C       Centromere kinetochore component CENP-T histon
    4.9e-06   26.6   0.0    5.7e-06   26.4   0.0    1.0  1  TFIID-31kDa    Transcription initiation factor IID, 31kD subu
    1.3e-05   25.5   0.0    1.4e-05   25.4   0.0    1.1  1  CENP-S         CENP-S protein
    0.00045   20.3   0.1    0.00052   20.1   0.1    1.0  1  TAF            TATA box binding protein associated factor (TA
     0.0046   17.4   0.0      0.005   17.3   0.0    1.1  1  TFIID_20kDa    Transcription initiation factor TFIID subunit 
  ------ inclusion threshold ------
      0.015   15.4   0.1      0.016   15.3   0.1    1.0  1  DUF1931        Domain of unknown function (DUF1931)
      0.023   14.9   0.0      0.023   14.9   0.0    1.1  1  Bromo_TP_like  Histone-fold protein
      0.027   14.5   0.0       0.03   14.4   0.0    1.1  1  TFIID-18kDa    Transcription initiation factor IID, 18kD subu


Domain annotation for each model (and alignments):
>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.7   0.0   4.1e-21   6.6e-18       3      64 ..       4      64 ..       2      64 .. 0.98

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 4.1e-21
                                      XXHHHHHHHHHCCTTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHHHH CS
                     CBFD_NFYB_HMF  3 LPiarvkkImksdpdarkiakdAkeliaecveefieelaseAaeickkekrKtikaehiklA 64
                                      LP+a+v+++++s+ +a++++++A   ++e++ee+ +++++eA++++++++rKt+k+e+i+lA
  gi|298675834|ref|YP_003727584.1|  4 LPLAPVERVIRSA-GAERVSESAGNALTEILEEYGQDISKEAVKLAEHAGRKTVKEEDIRLA 64
                                      9************.*********************************************998 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.0   1.5e-12   2.5e-09      65     127 ..       7      64 ..       3      67 .. 0.91

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 1.5e-12
                                       HHHHHHHHHHH.TTSSSXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHHHHHH CS
                           Histone  65 lpfaRvvreivksekedlrisaeavlalqealEallvelfeeAnllakhaKRvTitpkDiqlA 127
                                       +p++Rv+r          r+s +a +al+e+lE +  ++ +eA +la+ha R+T+  +Di+lA
  gi|298675834|ref|YP_003727584.1|   7 APVERVIRSAGA-----ERVSESAGNALTEILEEYGQDISKEAVKLAEHAGRKTVKEEDIRLA 64 
                                       688887776665.....9********************************************9 PP

>> Bromo_TP  Bromodomain associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0   2.1e-11   3.5e-08      15      67 ..      12      64 ..       6      67 .. 0.94

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 2.1e-11
                                      HHHHHT-SEE-HHHHHHHHHHHHHHHHHHHHHHHHHHTTSS-SS--HHHHHHH CS
                          Bromo_TP 15 ileeaGfdsaeesaLEtLteiaqkYirelgeqaksfaehagRseptlkDvvlt 67
                                      + ++aG +++ esa ++Ltei+++Y + ++++a + aehagR +++ +D++l+
  gi|298675834|ref|YP_003727584.1| 12 VIRSAGAERVSESAGNALTEILEEYGQDISKEAVKLAEHAGRKTVKEEDIRLA 64
                                      6789**********************************************986 PP

>> CENP-T_C  Centromere kinetochore component CENP-T histone fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0   5.3e-11   8.6e-08      14      71 ..      10      62 ..       1      66 [. 0.84

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 5.3e-11
                          CENP-T_C 14 kklakrfakasgskaklekealkalekasdkffeqvgeDLeayakHagRKtidesDvi 71
                                       ++ ++     +  ++++++a +al+++++++ + ++++    a+HagRKt++e+D+ 
  gi|298675834|ref|YP_003727584.1| 10 ERVIRS-----AGAERVSESAGNALTEILEEYGQDISKEAVKLAEHAGRKTVKEEDIR 62
                                      444433.....46789****************************************86 PP

>> TFIID-31kDa  Transcription initiation factor IID, 31kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   3.5e-09   5.7e-06      11      66 ..       9      64 ..       5      67 .. 0.95

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 3.5e-09
                       TFIID-31kDa 11 ihliLaslgvteyeerVvlqLldfayrytssvLedAkvlaehakkkevslddvrlA 66
                                      ++ +++s g + ++e   + L ++   y +++ ++A  laeha++k+v+ +d+rlA
  gi|298675834|ref|YP_003727584.1|  9 VERVIRSAGAERVSESAGNALTEILEEYGQDISKEAVKLAEHAGRKTVKEEDIRLA 64
                                      677899*************************************************9 PP

>> CENP-S  CENP-S protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   8.6e-09   1.4e-05      24      68 ..      19      63 ..       7      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 8.6e-09
                            CENP-S 24 veatkqfiaaltelvykqlenlakDLeaFakHAkRstittdDvlL 68
                                       ++++++ +alte+  +  ++++k     a+HA+R+t++ +D+ L
  gi|298675834|ref|YP_003727584.1| 19 ERVSESAGNALTEILEEYGQDISKEAVKLAEHAGRKTVKEEDIRL 63
                                      56889999**********************************988 PP

>> TAF  TATA box binding protein associated factor (TAF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   3.2e-07   0.00052       1      63 [.       1      63 [.       1      66 [. 0.95

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3.2e-07
                                      S----HHHHHHHHHHTT---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHH CS
                               TAF  1 tsilpkesvkviAeslGitnLsdeaaalLaedveyrlkeivqeaakfmrhskRqkLtvaDvds 63
                                      ++ilp   v+ +  s G + +s+ a ++L+e +e+  + i +ea+k  +h+ R++   +D+  
  gi|298675834|ref|YP_003727584.1|  1 MTILPLAPVERVIRSAGAERVSESAGNALTEILEEYGQDISKEAVKLAEHAGRKTVKEEDIRL 63
                                      68899999999*************************************************975 PP

>> TFIID_20kDa  Transcription initiation factor TFIID subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   3.1e-06     0.005      16      61 ..      19      64 ..       9      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.1e-06
                                      ----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHH CS
                       TFIID_20kDa 16 tkldedvedlLleiaddFvesvtkfacklakhRksdklevrDiqlh 61
                                      +++ e   + L ei +++ ++++k a+kla h   +++   Di+l 
  gi|298675834|ref|YP_003727584.1| 19 ERVSESAGNALTEILEEYGQDISKEAVKLAEHAGRKTVKEEDIRLA 64
                                      56677778899********************************985 PP

>> DUF1931  Domain of unknown function (DUF1931)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.1   9.6e-06     0.016       2      59 ..      10      67 ..       9      68 .] 0.93

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9.6e-06
                                      HHHHHHHHS----HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS---HHH CS
                           DUF1931  2 erlfreaagLdvdkedlkrisdfVekklydLllvaeenAkangrdviepaDLPiTkgl 59
                                      er++r+a    v ++  + +++++e+  +d+   a + A+  gr++++++D+ ++k +
  gi|298675834|ref|YP_003727584.1| 10 ERVIRSAGAERVSESAGNALTEILEEYGQDISKEAVKLAEHAGRKTVKEEDIRLAKEM 67
                                      788899999999999999***********************************99986 PP

>> Bromo_TP_like  Histone-fold protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.4e-05     0.023       3      51 ..       4      56 ..       2      68 .] 0.67

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.4e-05
                     Bromo_TP_like  3 lklvivE.illQvGferiseqslniltdllkyyiekillkikk...evdkdll 51
                                      l l+ vE ++   G er+se + n lt++l+ y + i+++  k   + +  ++
  gi|298675834|ref|YP_003727584.1|  4 LPLAPVErVIRSAGAERVSESAGNALTEILEEYGQDISKEAVKlaeHAGRKTV 56
                                      5555555377788******************9976666544442224444444 PP

>> TFIID-18kDa  Transcription initiation factor IID, 18kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.8e-05      0.03      26      61 ..      27      62 ..      12      65 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.8e-05
                                      HHHHHHHHHHHHHHHHHHHC-XXXX...XXXXXXXX CS
                       TFIID-18kDa 26 qlledlvrgyliellqqaakvaklrgsrkitlEDll 61
                                      + l +++++y  ++ ++a+k+a++ g++ ++ ED+ 
  gi|298675834|ref|YP_003727584.1| 27 NALTEILEEYGQDISKEAVKLAEHAGRKTVKEEDIR 62
                                      67999*****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 445.28
//
Query:       gi|298675835|ref|YP_003727585.1|  [L=88]
Description: 4Fe-4S ferredoxin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-14   52.1  27.7    7.7e-09   36.0   8.9    1.7  3  Fer4_7    4Fe-4S dicluster domain
      1e-13   50.5  12.4    8.5e-07   28.5   2.8    2.3  2  Fer4      4Fe-4S binding domain
    5.2e-12   45.7   5.2    1.4e-05   25.1   0.8    2.1  2  Fer4_10   4Fe-4S dicluster domain
      2e-11   43.8   7.6    1.7e-06   28.0   0.8    2.1  2  Fer4_21   4Fe-4S dicluster domain
    7.4e-11   41.6  10.3    1.6e-05   24.8   1.4    2.4  2  Fer4_6    4Fe-4S binding domain
    3.2e-10   40.0  17.6    1.2e-07   31.8   9.3    1.9  2  Fer4_9    4Fe-4S dicluster domain
    3.8e-10   39.2  10.3    4.7e-05   23.2   1.2    2.3  2  Fer4_2    4Fe-4S binding domain
    1.2e-09   38.5   5.8    1.9e-09   37.8   5.8    1.3  1  Fer4_8    4Fe-4S dicluster domain
    1.1e-08   35.9   7.4    9.1e-05   23.3   0.3    2.2  2  Fer4_16   4Fe-4S double cluster binding domain
    4.7e-06   27.1   7.3      2e-05   25.0   7.2    1.8  1  Fer4_17   4Fe-4S dicluster domain
      1e-05   25.7   7.6     0.0088   16.5   0.5    2.2  2  Fer4_4    4Fe-4S binding domain
    9.7e-05   22.5   9.5       0.01   16.1   0.9    2.1  2  Fer4_18   4Fe-4S dicluster domain
    0.00013   22.4  14.4      0.069   13.7   3.0    2.8  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    0.00048   20.9  11.6      0.024   15.5   1.6    2.1  2  Fer4_22   4Fe-4S dicluster domain
      0.003   18.2   8.7       0.17   12.6   2.1    2.4  2  Fer4_15   4Fe-4S single cluster domain
     0.0049   17.7  16.5     0.0056   17.5   3.7    2.3  2  Fer4_3    4Fe-4S binding domain
  ------ inclusion threshold ------
       0.14   11.4   0.0       0.14   11.4   0.0    1.0  1  DUF4938   Domain of unknown function (DUF4938)
        4.2    7.6   8.1          5    7.3   1.8    2.5  2  ETF_QO    Electron transfer flavoprotein-ubiquinone oxidoredu


Domain annotation for each model (and alignments):
>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   1.4   4.1e-07   0.00041      26      52 .]       6      32 ..       2      32 .. 0.76
   2 !   36.0   8.9   7.7e-12   7.7e-09       1      52 []      17      77 ..      17      77 .. 0.75
   3 !   17.6   2.5   4.5e-06    0.0045       1      23 [.      62      84 ..      62      87 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 4.1e-07
                            Fer4_7 26 kgtekveidpekClgCgaCvavCPtga 52
                                      k ++ +e++++ C+gCg C +vCP +a
  gi|298675835|ref|YP_003727585.1|  6 KNNKVLEMEESHCIGCGICFSVCPINA 32
                                      455677888889999999999999776 PP

  == domain 2  score: 36.0 bits;  conditional E-value: 7.7e-12
                            Fer4_7  1 rCigCgaCvaaCp.vkaieldeeenek........gtekveidpekClgCgaCvavCPtga 52
                                      +CigCg C ++Cp +  +e ++e +++         + k+ i++e+C+ Cg C + CP g+
  gi|298675835|ref|YP_003727585.1| 17 HCIGCGICFSVCPiNAKLEKKDEFDPDdenlairvVNGKALINEETCIVCGTCTKHCPIGV 77
                                      6************5444555555555544455544338889*****************986 PP

  == domain 3  score: 17.6 bits;  conditional E-value: 4.5e-06
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeee 23
                                      +Ci Cg C++ Cp +++++++ e
  gi|298675835|ref|YP_003727585.1| 62 TCIVCGTCTKHCPIGVLSVKKLE 84
                                      5****************998865 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   2.8   8.5e-10   8.5e-07       5      22 ..      15      32 ..      12      33 .. 0.92
   2 !   27.3   2.2   2.2e-09   2.1e-06       3      23 ..      58      78 ..      56      79 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 8.5e-10
                                      TTTSSS-THHHHHSTTTE CS
                              Fer4  5 eekCigCGaCvevCPvgA 22
                                      e+ CigCG+C +vCP +A
  gi|298675835|ref|YP_003727585.1| 15 ESHCIGCGICFSVCPINA 32
                                      789*************99 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 2.2e-09
                                      EETTTSSS-THHHHHSTTTEE CS
                              Fer4  3 ideekCigCGaCvevCPvgAI 23
                                      i+ee Ci CG+C + CP g++
  gi|298675835|ref|YP_003727585.1| 58 INEETCIVCGTCTKHCPIGVL 78
                                      9****************9987 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.3   5.4e-08   5.4e-05       5      36 ..      14      45 ..      10      53 .. 0.74
   2 !   25.1   0.8   1.4e-08   1.4e-05       2      23 ..      56      77 ..      55      88 .] 0.80

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 5.4e-08
                           Fer4_10  5 dddtCirCgkCvkaCPadltsvgakgeaseee 36
                                      +++ Ci+Cg C ++CP +++  ++ +++ ++e
  gi|298675835|ref|YP_003727585.1| 14 EESHCIGCGICFSVCPINAKLEKKDEFDPDDE 45
                                      6789*************776666665555555 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 1.4e-08
                           Fer4_10  2 vvidddtCirCgkCvkaCPadl 23
                                      + i+++tCi Cg+C+k CP  +
  gi|298675835|ref|YP_003727585.1| 56 ALINEETCIVCGTCTKHCPIGV 77
                                      689****************944 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.8   1.8e-09   1.7e-06      29      54 ..       6      31 ..       2      36 .. 0.84
   2 !   20.0   1.0   5.6e-07   0.00056       1      19 [.      56      74 ..      48      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.8e-09
                           Fer4_21 29 daktvlkvvedeCvGCnlCssvCPve 54
                                      ++++vl++ e++C+GC +C svCP++
  gi|298675835|ref|YP_003727585.1|  6 KNNKVLEMEESHCIGCGICFSVCPIN 31
                                      467788999***************96 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 5.6e-07
                           Fer4_21  1 AridedkCigCgkCliaCe 19
                                      A i+e++Ci Cg C++ C+
  gi|298675835|ref|YP_003727585.1| 56 ALINEETCIVCGTCTKHCP 74
                                      6789999999999999997 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   2.0   1.6e-07   0.00016       6      23 ..      15      32 ..      10      32 .. 0.83
   2 !   24.8   1.4   1.6e-08   1.6e-05       2      24 .]      56      78 ..      55      78 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.6e-07
                            Fer4_6  6 pdkCigCgdCvrvCPega 23
                                      ++ CigCg C++vCP +a
  gi|298675835|ref|YP_003727585.1| 15 ESHCIGCGICFSVCPINA 32
                                      666************776 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 1.6e-08
                            Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                      + i+++ Ci Cg C+++CP g++
  gi|298675835|ref|YP_003727585.1| 56 ALINEETCIVCGTCTKHCPIGVL 78
                                      679****************8875 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   1.2   1.2e-06    0.0012      29      49 ..      11      31 ..       1      33 [. 0.65
   2 !   31.8   9.3   1.2e-10   1.2e-07       2      49 ..      18      76 ..      17      78 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.2e-06
                            Fer4_9 29 raaseeaCigCgaCveaCpkg 49
                                       + +e+ CigCg C+ +Cp +
  gi|298675835|ref|YP_003727585.1| 11 LEMEESHCIGCGICFSVCPIN 31
                                      2223368***********965 PP

  == domain 2  score: 31.8 bits;  conditional E-value: 1.2e-10
                            Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraase...........eaCigCgaCveaCpkg 49
                                      C+gCg C ++Cp ++  e++ e     ++              e Ci Cg+C+++Cp g
  gi|298675835|ref|YP_003727585.1| 18 CIGCGICFSVCPINAKLEKKDEFDPDDENLAIrvvngkalineETCIVCGTCTKHCPIG 76
                                      ***********9888876666666555443337789999****99************76 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   1.2   4.7e-08   4.7e-05       5      21 ..      13      29 ..       9      29 .. 0.88
   2 !   20.6   2.4   3.2e-07   0.00032       3      21 ..      56      74 ..      54      74 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 4.7e-08
                            Fer4_2  5 vdtdrCigCgaCvsaCP 21
                                       ++ +CigCg+C s+CP
  gi|298675835|ref|YP_003727585.1| 13 MEESHCIGCGICFSVCP 29
                                      6789************9 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 3.2e-07
                            Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                      + +++++Ci Cg+C++ CP
  gi|298675835|ref|YP_003727585.1| 56 ALINEETCIVCGTCTKHCP 74
                                      689***************9 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   5.8   1.9e-12   1.9e-09       3      65 .]      16      77 ..      14      77 .. 0.82

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 1.9e-12
                            Fer4_8  3 ekCieCgaCqsaCpvlrrtk.khlldargeaae.dvqeeqvleeeealwsCttcgaCtevCpvgi 65
                                      ++Ci+Cg C+s Cp+  +   k+ +d+ +e+ + +     + ++  + ++C  cg Ct+ Cp+g+
  gi|298675835|ref|YP_003727585.1| 16 SHCIGCGICFSVCPINAKLEkKDEFDPDDENLAiR--VVNG-KALINEETCIVCGTCTKHCPIGV 77
                                      69************999988899999999988852..3322.33456789************986 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.3   9.1e-08   9.1e-05       1      29 [.      17      44 ..       3      61 .. 0.73
   2 !   16.0   2.1   1.8e-05     0.017       1      22 [.      62      83 ..      62      88 .] 0.82

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 9.1e-08
                           Fer4_16  1 rCgtCgkCaevCPtnaikekkekeieare 29
                                      +C++Cg C +vCP na  ek + e+++++
  gi|298675835|ref|YP_003727585.1| 17 HCIGCGICFSVCPINAKLEK-KDEFDPDD 44
                                      68888888888888886665.46666555 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.8e-05
                           Fer4_16  1 rCgtCgkCaevCPtnaikekke 22
                                      +C+ Cg C++ CP ++++ kk 
  gi|298675835|ref|YP_003727585.1| 62 TCIVCGTCTKHCPIGVLSVKKL 83
                                      5***************998844 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   7.2     2e-08     2e-05       2      59 ..      18      76 ..      17      78 .. 0.67

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 2e-08
                           Fer4_17  2 CiqCgyClpeCpsyea....ydnepk..kllraaklglleeaekeekaslCieCgeCerkCPqg 59
                                      Ci+Cg C  +Cp +++     +++p+  +l+ ++ +g     ++  + ++Ci Cg C++ CP g
  gi|298675835|ref|YP_003727585.1| 18 CIGCGICFSVCPINAKlekkDEFDPDdeNLAIRVVNG-----KALINEETCIVCGTCTKHCPIG 76
                                      ************9998443322233321444443332.....22346689************76 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.5   8.8e-06    0.0088       4      15 ..      18      29 ..       8      44 .. 0.88
   2 !   13.0   1.5   0.00012      0.11       2      15 ..      61      74 ..      60      84 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8.8e-06
                            Fer4_4  4 CigCgsCvaaCP 15
                                      CigCg C ++CP
  gi|298675835|ref|YP_003727585.1| 18 CIGCGICFSVCP 29
                                      ***********9 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00012
                            Fer4_4  2 erCigCgsCvaaCP 15
                                      e+Ci Cg C+  CP
  gi|298675835|ref|YP_003727585.1| 61 ETCIVCGTCTKHCP 74
                                      79***********9 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.9     1e-05      0.01      48      76 ..       5      33 ..       1      41 [. 0.79
   2 !   11.6   2.2   0.00023      0.23      49      75 ..      51      77 ..      35      85 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1e-05
                           Fer4_18 48 kekeerkekgagdcidcescvkvcPtgid 76
                                      k++++  e ++++ci c+ c +vcP++  
  gi|298675835|ref|YP_003727585.1|  5 KKNNKVLEMEESHCIGCGICFSVCPINAK 33
                                      455566678899*************9865 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00023
                           Fer4_18 49 ekeerkekgagdcidcescvkvcPtgi 75
                                       ++ ++  ++  ci c++c k cP+g+
  gi|298675835|ref|YP_003727585.1| 51 VVNGKALINEETCIVCGTCTKHCPIGV 77
                                      555556667889*************98 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   3.0   6.9e-05     0.069       3      17 ..      15      29 ..      13      56 .. 0.68
   2 !   13.2   3.7   9.6e-05     0.096       1      17 [.      58      74 ..      58      75 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.9e-05
                           Fer4_13  3 rdtCiacgaCvelaP 17
                                      ++ Ci+cg+C +++P
  gi|298675835|ref|YP_003727585.1| 15 ESHCIGCGICFSVCP 29
                                      689************ PP

  == domain 2  score: 13.2 bits;  conditional E-value: 9.6e-05
                           Fer4_13  1 VDrdtCiacgaCvelaP 17
                                      ++++tCi cg+C + +P
  gi|298675835|ref|YP_003727585.1| 58 INEETCIVCGTCTKHCP 74
                                      799*************9 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   1.6   2.4e-05     0.024      72      94 ..       8      30 ..       1      32 [. 0.78
   2 !   11.2   2.7   0.00051      0.51      75      94 ..      56      75 ..      32      77 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.4e-05
                           Fer4_22 72 efkekfgesgCvGCgRCieacpv 94
                                      + + +++es+C+GCg C ++cp 
  gi|298675835|ref|YP_003727585.1|  8 NKVLEMEESHCIGCGICFSVCPI 30
                                      445567999************96 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00051
                           Fer4_22 75 ekfgesgCvGCgRCieacpv 94
                                      + ++e++C+ Cg C+++cp 
  gi|298675835|ref|YP_003727585.1| 56 ALINEETCIVCGTCTKHCPI 75
                                      55678888888888888886 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   2.1   0.00018      0.17       3      27 ..      13      37 ..      11      56 .. 0.69
   2 !    9.5   0.6    0.0016       1.6       3      19 ..      58      74 ..      57      82 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00018
                           Fer4_15  3 vDrdaCigcglCvaeapevfelded 27
                                       +++ Cigcg C  ++p   +l+++
  gi|298675835|ref|YP_003727585.1| 13 MEESHCIGCGICFSVCPINAKLEKK 37
                                      57899***********655544442 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0016
                           Fer4_15  3 vDrdaCigcglCvaeap 19
                                      +++++Ci cg C + +p
  gi|298675835|ref|YP_003727585.1| 58 INEETCIVCGTCTKHCP 74
                                      7899*********9998 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   3.7   5.7e-06    0.0056       1      15 []      18      32 ..      18      32 .. 0.97
   2 ?    6.1   5.0     0.026        26       1      14 [.      63      76 ..      63      77 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.7e-06
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+gCg C+ vCP +A
  gi|298675835|ref|YP_003727585.1| 18 CIGCGICFSVCPINA 32
                                      ************998 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.026
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      C+ Cg+C + CP g
  gi|298675835|ref|YP_003727585.1| 63 CIVCGTCTKHCPIG 76
                                      777*********87 PP

>> DUF4938  Domain of unknown function (DUF4938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00014      0.14      77     111 ..      18      51 ..       9      83 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
                           DUF4938  77 aigaelcryvvdginaelghdeswdpdepllalrd 111
                                       +ig+ +c + v  ina+l + + +dpd+  la+r 
  gi|298675835|ref|YP_003727585.1|  18 CIGCGIC-FSVCPINAKLEKKDEFDPDDENLAIRV 51 
                                       6899999.56779*******************996 PP

>> ETF_QO  Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   1.1      0.07        70      62      81 ..       5      24 ..       1      36 [. 0.82
   2 ?    7.3   1.8     0.005         5      67      86 ..      55      74 ..      26      87 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.07
                                      TTSSEEEEE-CCC--S--HH CS
                            ETF_QO 62 eakekklqinaqnCvhCktC 81
                                      ++++k l+++ + C+ C  C
  gi|298675835|ref|YP_003727585.1|  5 KKNNKVLEMEESHCIGCGIC 24
                                      5678999**********999 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.005
                                      EEEE-CCC--S--HHHHH-T CS
                            ETF_QO 67 klqinaqnCvhCktCdikdp 86
                                      k  in + C+ C tC  + p
  gi|298675835|ref|YP_003727585.1| 55 KALINEETCIVCGTCTKHCP 74
                                      44567777777777765444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 531.40
//
Query:       gi|298675836|ref|YP_003727586.1|  [L=168]
Description: putative small multi-drug export [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-40  138.1   2.7    2.8e-40  137.7   2.7    1.2  1  Sm_multidrug_ex  Putative small multi-drug export protein


Domain annotation for each model (and alignments):
>> Sm_multidrug_ex  Putative small multi-drug export protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.7   2.7   1.5e-44   2.8e-40       1     121 []      30     152 ..      30     152 .. 0.98

  Alignments for each domain:
  == domain 1  score: 137.7 bits;  conditional E-value: 1.5e-44
                   Sm_multidrug_ex   1 Elrgaiplgill.gldpllallvsvlgnllpvplillflrkllellkkkkllkklfekleekaek.ksekiekygfl 75 
                                       Elrg+ip+++++ +++p+la+l++vlgn+lpv+ illfl ++++ l++++l++++f++l e+++k +sek+ekyg+l
  gi|298675836|ref|YP_003727586.1|  30 ELRGSIPVALVIyEMNPVLAYLMAVLGNMLPVIPILLFLGPVSNSLRRFRLWDNFFTWLFERTHKrHSEKFEKYGTL 106
                                       9********9655****************************************************899999****** PP

                   Sm_multidrug_ex  76 GLllFvaiPLpgTGawtGsliasllglkkkkallaillGvliaglI 121
                                       +L++Fv iPLp+TGawtG+++++++g+k+++allail Gvli+g+I
  gi|298675836|ref|YP_003727586.1| 107 ALVMFVSIPLPVTGAWTGCVASFVFGIKFRHALLAILSGVLISGII 152
                                       ********************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1080.45
//
Query:       gi|298675837|ref|YP_003727587.1|  [L=318]
Description: replication factor C [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-26   91.5   0.1    7.5e-26   90.4   0.1    1.6  1  Rep_fac_C        Replication factor C C-terminal domain
    1.9e-19   70.4   0.0    3.1e-18   66.5   0.0    2.2  2  AAA              ATPase family associated with various cellul
    1.5e-16   60.6   0.0    9.7e-11   41.7   0.0    2.5  2  DNA_pol3_delta2  DNA polymerase III, delta subunit
    2.5e-08   33.8   0.0    2.9e-07   30.4   0.0    2.4  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    1.2e-06   28.6   0.0    1.9e-06   27.9   0.0    1.5  1  Rad17            Rad17 P-loop domain
    1.5e-06   28.7   0.1    0.00024   21.5   0.0    2.8  3  AAA_16           AAA ATPase domain
      4e-06   26.9   0.0    8.1e-06   25.9   0.0    1.5  1  AAA_14           AAA domain
      1e-05   25.4   0.0      2e-05   24.4   0.0    1.4  1  AAA_3            ATPase family associated with various cellul
    1.9e-05   24.5   0.0    0.00051   19.9   0.0    2.2  2  DNA_pol3_delta   DNA polymerase III, delta subunit
    3.7e-05   23.2   0.0     0.0055   16.1   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
      4e-05   23.0   0.0    0.00012   21.4   0.0    1.7  2  TIP49            TIP49 P-loop domain
    0.00011   22.5   0.2    0.00022   21.5   0.2    1.6  1  AAA_assoc_2      AAA C-terminal domain
    0.00022   21.3   0.0    0.00081   19.4   0.0    1.9  1  ResIII           Type III restriction enzyme, res subunit
    0.00076   20.0   0.0      0.015   15.8   0.0    2.5  2  AAA_18           AAA domain
      0.002   17.9   0.0          1    9.0   0.0    2.4  2  Sigma54_activat  Sigma-54 interaction domain
     0.0021   18.3   0.0        1.6    9.0   0.0    2.7  3  AAA_22           AAA domain
     0.0037   17.0   0.0       0.01   15.6   0.0    1.8  1  IstB_IS21        IstB-like ATP binding protein
     0.0063   16.5   0.0      0.054   13.5   0.0    2.3  1  AAA_5            AAA domain (dynein-related subfamily)
     0.0066   16.6   0.0      0.041   14.0   0.0    2.3  3  AAA_2            AAA domain (Cdc48 subfamily)
     0.0083   15.9   0.0      0.012   15.5   0.0    1.2  1  AAA_11           AAA domain
  ------ inclusion threshold ------
      0.045   13.2   0.0        3.5    7.0   0.0    2.3  2  PhoH             PhoH-like protein
      0.054   13.0   0.0       0.13   11.7   0.0    1.7  2  AAA_7            P-loop containing dynein motor region
      0.077   12.7   0.0       0.64    9.7   0.0    2.0  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.084   13.3   0.0       0.19   12.1   0.0    1.6  1  RNA_helicase     RNA helicase


Domain annotation for each model (and alignments):
>> Rep_fac_C  Replication factor C C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.4   0.1     1e-28   7.5e-26       2      87 ..     226     310 ..     225     311 .. 0.97

  Alignments for each domain:
  == domain 1  score: 90.4 bits;  conditional E-value: 1e-28
                                       -HHHHHHHHHHHHHT-HHHHHHHHHHHHHHC---HHHHHHHHHHHGCCS..S-HHHHHHHHHHHHHHHHHHHCTH-H CS
                         Rep_fac_C   2 hpteieeileaclngdfeeaykklrellvekGysaediltqlhrvvkeqeelpeaqkleilellgeiekrlveGase 78 
                                       hp+eiee+++++l g+f++a++++++l+ e+G+s+ed++ q++r +++  ++pe++ +e+++++gei++rl+eGa+e
  gi|298675837|ref|YP_003727587.1| 226 HPEEIEELVQKALDGNFKAARETMEKLMSEQGLSGEDVVGQIYRAIFNL-DIPEKLMVELVDKIGEIDFRLTEGANE 301
                                       9***********************************************6.7************************** PP

                                       HHHHHHHHH CS
                         Rep_fac_C  79 hlqlsalla 87 
                                       ++ql+alla
  gi|298675837|ref|YP_003727587.1| 302 RIQLEALLA 310
                                       *******99 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.5   0.0   4.2e-21   3.1e-18       1     128 [.      40     156 ..      40     160 .. 0.88
   2 ?    1.6   0.0      0.48   3.6e+02      80     126 ..     194     240 ..     178     246 .. 0.71

  Alignments for each domain:
  == domain 1  score: 66.5 bits;  conditional E-value: 4.2e-21
                                       EEEESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHH CS
                               AAA   1 vllyGppGtGKTllakavakel.....gvefleisgsellskyvgesekkirelfkeakeka.kpsilfiDEidala 71 
                                       +l++GppG+GKT++a a+akel     +++f e+++s+ +   +     ki+++ k+      + +i+f+DE+dal+
  gi|298675837|ref|YP_003727587.1|  40 LLFSGPPGVGKTAAAVAIAKELfgdawHQNFTELNASDER--GIDVVRTKIKDFSKTSPIGGaDFKIIFLDEADALT 114
                                       69*******************8666567************..88888888888887754444555************ PP

                                       HHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEE CS
                               AAA  72 ksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrki 128
                                       ++            +++L + ++++++   ++ +i+ +n+ +k+ +++  +R+ +  
  gi|298675837|ref|YP_003727587.1| 115 PDA-----------QSALRRTMERYTN---NCRFILSCNYSSKIIEPIQ-SRCAVYR 156
                                       ***...........*************...6******************.9*98765 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.48
                                       HHHHHHHHHHH..HHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSE CS
                               AAA  80 eeeervvnqLl..teldgvkkkeskvivigatnrpdkldpallrgRfdr 126
                                       ++ ++++n+L   + +d+v +k +++  i+at +p+++++ +  + +d 
  gi|298675837|ref|YP_003727587.1| 194 GDMRKAINALQasALIDDVIDK-DTIYKITATAHPEEIEELVQ-KALDG 240
                                       5556666666521457777775.55999999999999999887.56655 PP

>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   6.2e-06    0.0047       1      47 [.      20      65 ..      20      75 .. 0.91
   2 !   41.7   0.0   1.3e-13   9.7e-11      83     162 ..      79     160 ..      64     161 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.2e-06
                   DNA_pol3_delta2  1 gqeealkilskalksgrlahayLfeGdegigkkelalnlakallcee 47
                                      gq ea+k l++ +++++l h +Lf+G+ g+gk ++a ++ak+l+ + 
  gi|298675837|ref|YP_003727587.1| 20 GQGEAIKRLKSYISTNNLPH-LLFSGPPGVGKTAAAVAIAKELFGDA 65
                                      68899**************9.8********************99765 PP

  == domain 2  score: 41.7 bits;  conditional E-value: 1.3e-13
                   DNA_pol3_delta2  83 ikldqirelieelsrkpre..skkkiiiiedaekmtksAaNalLktlEEPsenaifiLitsdtnklLktirSRcqel 157
                                         +d +r  i+++s+++ +  +  kii +++a+ +t+ A+ al +t+E   +n  fiL  + ++k++++i+SRc ++
  gi|298675837|ref|YP_003727587.1|  79 RGIDVVRTKIKDFSKTSPIggADFKIIFLDEADALTPDAQSALRRTMERYTNNCRFILSCNYSSKIIEPIQSRCAVY 155
                                       47999**88888887776646689***************************************************** PP

                   DNA_pol3_delta2 158 kfspl 162
                                       +f++l
  gi|298675837|ref|YP_003727587.1| 156 RFRSL 160
                                       **987 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   3.9e-10   2.9e-07       2      61 ..      11      65 ..      10     135 .. 0.71

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 3.9e-10
                            RuvB_N  2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvkl 61
                                      rP +l++ +gq +  ++lk +i++     ++l h+l++GpPG+Gkt+ a  iakel  + 
  gi|298675837|ref|YP_003727587.1| 11 RPFKLDDIVGQGEAIKRLKSYIST-----NNLPHLLFSGPPGVGKTAAAVAIAKELFGDA 65
                                      99******************9986.....6799**********************96544 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   2.6e-09   1.9e-06       6      77 ..       3      70 ..       1     124 [. 0.84

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 2.6e-09
                             Rad17  6 nelWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskel.giklrewl 77
                                       e W+eky+P k++++    + i+ +k ++ ++ L++     LL sGP+G gk+ +   ++kel g   +++ 
  gi|298675837|ref|YP_003727587.1|  3 EEIWIEKYRPFKLDDIVGQGEAIKRLKSYISTNNLPH-----LLFSGPPGVGKTAAAVAIAKELfGDAWHQNF 70
                                      689********************************97.....5*******************98244444444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   3.3e-07   0.00024       3      53 ..      19      66 ..      17      97 .. 0.81
   2 ?    4.1   0.0     0.073        54     137     163 ..     103     129 ..      72     136 .. 0.77
   3 ?   -0.6   0.0         2   1.5e+03      75     105 ..     225     253 ..     163     310 .. 0.60

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3.3e-07
                            AAA_16  3 vGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdgg 53
                                      vG +e +++L+s++++      + +l+sG++GvGK++ + +++++l +d +
  gi|298675837|ref|YP_003727587.1| 19 VGQGEAIKRLKSYISTN---NLPHLLFSGPPGVGKTAAAVAIAKELFGDAW 66
                                      899999******99844...5689******************999998833 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.073
                            AAA_16 137 lvlvlDdlqwadeaslqllaaLlrlle 163
                                        +++lD+++ + ++ +++l+ ++++ +
  gi|298675837|ref|YP_003727587.1| 103 KIIFLDEADALTPDAQSALRRTMERYT 129
                                       58*****************99998755 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 2
                            AAA_16  75 alareellrqlldeaesaeleawrekleeal 105
                                       a    e +++l ++a + ++ a+re+ e+ +
  gi|298675837|ref|YP_003727587.1| 225 AH-P-EEIEELVQKALDGNFKAARETMEKLM 253
                                       22.2.33333444444444444444444433 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   1.1e-08   8.1e-06       5     126 ..      40     161 ..      36     165 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.1e-08
                            AAA_14   5 lvitGaRrvGKTtllkqlikell..vkkesilyinldderdkkladpekllelilek.lkeekktylflDEiqev.p 77 
                                       l+ +G+  vGKT  +  ++kel+  + ++++ ++n  der  +   + k+ ++ + + + + + +++flDE+  + p
  gi|298675837|ref|YP_003727587.1|  40 LLFSGPPGVGKTAAAVAIAKELFgdAWHQNFTELNASDERGIDVVRT-KIKDFSKTSpIGGADFKIIFLDEADALtP 115
                                       5678999****************998889999999999998776544.355555554555578899******97659 PP

                            AAA_14  78 ewekalkslvdeg.knldvivtGSnskllskeiatslagrvaeielypls 126
                                       ++++al++ ++++ +n+++i++       s++i +  + r a+++   ls
  gi|298675837|ref|YP_003727587.1| 116 DAQSALRRTMERYtNNCRFILSCNY----SSKIIEPIQSRCAVYRFRSLS 161
                                       ***********99889999986543....344555555555555555555 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   2.7e-08     2e-05       1      88 [.      39     127 ..      39     133 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 2.7e-08
                             AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkk..Gpvfanllladeinrap 75 
                                       h+l+ g PG++kt ++ a+ak l  +     ft +l  sd  G++v+++k k+f+ ++  G    ++++ de +  +
  gi|298675837|ref|YP_003727587.1|  39 HLLFSGPPGVGKTAAAVAIAKELFGDAWHQNFT-ELNASDERGIDVVRTKIKDFSKTSpiGGADFKIIFLDEADALT 114
                                       99*********************9999998887.79*****************98654335566789999******* PP

                             AAA_3  76 pktqsalleamee 88 
                                       p +qsal  +me 
  gi|298675837|ref|YP_003727587.1| 115 PDAQSALRRTMER 127
                                       ********99985 PP

>> DNA_pol3_delta  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   6.8e-07   0.00051      18     170 ..      61     204 ..      56     208 .. 0.91
   2 ?    2.2   0.0      0.18   1.3e+02     147     173 ..     226     253 ..     211     264 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 6.8e-07
                                       HHHHHHTTTEEEEEEEE-STTS-HHH.HTTTSTTTTSS.SSEEEEEEE--.....TT-S-TTHHHHHHHHTTT--SS CS
                    DNA_pol3_delta  18 ilkqalkqgfedlnyikfdlnedwiddvleecetlpff.sdkrivvlknpklltkesklnekllkeLeeylsnlped 93 
                                       ++  a +q+f++ln ++  + ++  +++ +  +t p + +d +i++l+ +      + l+ + + +L ++++++  +
  gi|298675837|ref|YP_003727587.1|  61 LFGDAWHQNFTELNASDERGIDVVRTKIKDFSKTSPIGgADFKIIFLDEA------DALTPDAQSALRRTMERYTNN 131
                                       66677899999999999999999999999999999997257799999999......568999999************ PP

                                       EEEEEEES.S--HHHHHHHHHTTTEEEEEE----TTTHHHHHHHHHHHTT-EE-HHHHHHHHHHHTT-HHHHHHHHH CS
                    DNA_pol3_delta  94 tlLiliapkklderkklvklLkkkatvveaktlkeeelkkwiqkraqelglkiekealelLlelvennlsaikqele 170
                                       + +il ++       k++  ++++  v ++  l+ e + k + ++a+++gl+i+++ +e + + + ++++ + ++l+
  gi|298675837|ref|YP_003727587.1| 132 CRFILSCN----YSSKIIEPIQSRCAVYRFRSLSYEAVEKRVRYIAEQEGLQISEDGVEAIKYVSQGDMRKAINALQ 204
                                       ********....55789********************************************************9997 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.18
                                       -HHHHHHHHH.HHTT-HHHHHHHHHHHH CS
                    DNA_pol3_delta 147 ekealelLle.lvennlsaikqelekLa 173
                                        +e++e+L++ ++ +n++a+   +ekL+
  gi|298675837|ref|YP_003727587.1| 226 HPEEIEELVQkALDGNFKAARETMEKLM 253
                                       3555666654145677777777777764 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   7.4e-06    0.0055       2      56 ..      15      72 ..      14      89 .. 0.80
   2 ?    4.9   0.0     0.021        15     105     132 ..     100     127 ..      90     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7.4e-06
                      Mg_chelatase  2 lkdvkGqeeakrale..iaaaGgHnlllvGppGsGKtmlakrlp.sllpplseeeale 56
                                      l d++Gq ea + l+  i+     +ll+ GppG GKt  a +++ +l+ +  +++  e
  gi|298675837|ref|YP_003727587.1| 15 LDDIVGQGEAIKRLKsyISTNNLPHLLFSGPPGVGKTAAAVAIAkELFGDAWHQNFTE 72
                                      789****99999987557888889*************999887514666666665555 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.021
                      Mg_chelatase 105 ahnGvLfLDElpefkrkvlevLRePled 132
                                       a   ++fLDE+  ++ ++  +LR+ +e+
  gi|298675837|ref|YP_003727587.1| 100 ADFKIIFLDEADALTPDAQSALRRTMER 127
                                       555699*******************997 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.6e-07   0.00012      39      96 ..      28      86 ..      12      96 .. 0.75
   2 ?   -2.4   0.0       2.8   2.1e+03     281     305 ..     104     128 ..     100     145 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.6e-07
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 39 ivelikekklaGravLlaGpsgtGktalaiaiskelg...edvpfvalsgsevyslevkkt 96
                                      + + i +++l    +L++Gp+g Gkta a+ai+kel     +  f+ l++s+    +v +t
  gi|298675837|ref|YP_003727587.1| 28 LKSYISTNNLP--HLLFSGPPGVGKTAAAVAIAKELFgdaWHQNFTELNASDERGIDVVRT 86
                                      55667777776..79********************96222346899999998766666655 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.8
                                       XXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 281 vlfiDevhmlDiecfsylnralese 305
                                       ++f+De+  l  ++ s l r++e  
  gi|298675837|ref|YP_003727587.1| 104 IIFLDEADALTPDAQSALRRTMERY 128
                                       689*******999999999999975 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.2     3e-07   0.00022       3      56 ..     176     235 ..     174     259 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3e-07
                                       X.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.......XXXXXXXXXXXXXXXX CS
                       AAA_assoc_2   3 kklkleddalealaeladGDaRkaLnlLElaaeaaeak......egkieitledleealq 56 
                                       + l++++d +ea+  +++GD+Rka+n+L++ a   +        + +++   e++ee++q
  gi|298675837|ref|YP_003727587.1| 176 EGLQISEDGVEAIKYVSQGDMRKAINALQASALIDDVIdkdtiyKITATAHPEEIEELVQ 235
                                       6789*************************8877665433444443333344455555555 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.1e-06   0.00081       8      57 ..      21      70 ..      18     143 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.1e-06
                                      HHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-E CS
                            ResIII  8 QeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekf 57
                                      Q eai++l++ ++ ++  ++l+  + G+GKT  a++++++l+  ++ ++f
  gi|298675837|ref|YP_003727587.1| 21 QGEAIKRLKSYISTNNLPHLLFSGPPGVGKTAAAVAIAKELFGDAWHQNF 70
                                      99***********99999************************99999877 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0     2e-05     0.015       3      36 ..      42      74 ..      40     128 .. 0.78
   2 ?    2.1   0.1      0.35   2.6e+02      26      69 ..     167     208 ..     142     312 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2e-05
                            AAA_18  3 ltGtpGvGKttlakeLskrlgfgvnlrdvakeng 36
                                       +G+pGvGKt  a +++k+l fg+   ++++e +
  gi|298675837|ref|YP_003727587.1| 42 FSGPPGVGKTAAAVAIAKEL-FGDAWHQNFTELN 74
                                      68*****************8.5444444444443 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.35
                            AAA_18  26 vnlrdvakenglllevdpealdeskrldedkldklldaleenss 69 
                                        ++r +a ++gl +++d    +  k + ++ + k+++al++++ 
  gi|298675837|ref|YP_003727587.1| 167 KRVRYIAEQEGLQISEDGV--EAIKYVSQGDMRKAINALQASAL 208
                                       5677788888888888888..88888888888888888888764 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0014         1      11      59 ..      24      76 ..      18      83 .. 0.78
   2 !    6.4   0.0     0.009       6.7      92     119 ..     100     127 ..      91     132 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0014
                                      HHHHHHHHCTSS..S-EEEECSTTSSHHHHHHHHHH..HSTTTTS-EEEEETT CS
                   Sigma54_activat 11 lleqikkvaktd..lsvlitGesGtGKellaraihe..askrkekpfvavnca 59
                                      +++++k++++t+   ++l  G  G+GK+  a ai +    +  +++f ++n +
  gi|298675837|ref|YP_003727587.1| 24 AIKRLKSYISTNnlPHLLFSGPPGVGKTAAAVAIAKelFGDAWHQNFTELNAS 76
                                      4566666666665568999***************9855567788889888876 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.009
                                       TTTSEEEEETGGGS-HHHHHHHHHHHHH CS
                   Sigma54_activat  92 adgGtlfLDeigelplelQekLlrvlqe 119
                                       ad  ++fLDe   l++++Q+ L r +++
  gi|298675837|ref|YP_003727587.1| 100 ADFKIIFLDEADALTPDAQSALRRTMER 127
                                       67779*****************999986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0022       1.6       7      29 ..      39      61 ..      35      96 .. 0.80
   2 ?    6.6   0.0     0.012       8.8      92     128 ..     102     137 ..      66     142 .. 0.75
   3 ?   -1.6   0.0       4.2   3.1e+03      38      72 ..     214     257 ..     196     288 .. 0.52

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0022
                            AAA_22  7 ilvvtGesGtGKTtllrrlleql 29
                                      +l+  G++G+GKT  +  ++++l
  gi|298675837|ref|YP_003727587.1| 39 HLLFSGPPGVGKTAAAVAIAKEL 61
                                      68899*********998888876 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.012
                            AAA_22  92 ielliiDEaqhlrseealeeLrsllnlsrkgvqliLv 128
                                        +++ +DEa+ l +++a + Lr+ ++  + ++++iL 
  gi|298675837|ref|YP_003727587.1| 102 FKIIFLDEADAL-TPDAQSALRRTMERYTNNCRFILS 137
                                       5799********.999999998888866777777775 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 4.2
                            AAA_22  38 erpevvfvtlpsst.sskdl.lrellralglelka.......er 72 
                                        +++++++t+++   + ++l  ++l  +++  +++       ++
  gi|298675837|ref|YP_003727587.1| 214 DKDTIYKITATAHPeEIEELvQKALDGNFKAARETmeklmseQG 257
                                       44445555555555444444222233333333333444444444 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.3e-05      0.01      45      84 ..      35      74 ..      20     140 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.3e-05
                         IstB_IS21 45 ekkenivllGpsGvGKshlaialgveavraglsvlfvrve 84
                                      ++   +++ Gp+GvGK+  a+a+++e   + ++  f+ ++
  gi|298675837|ref|YP_003727587.1| 35 NNLPHLLFSGPPGVGKTAAAVAIAKELFGDAWHQNFTELN 74
                                      344468999*****************99999988888765 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   7.2e-05     0.054       1      90 [.      39     126 ..      39     133 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.2e-05
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                       ++l  GppG+gK+  a  +a+ l    +  + +++ te +   +r i+  +t+ +d + +  +     +i++lDE +
  gi|298675837|ref|YP_003727587.1|  39 HLLFSGPPGVGKTAAAVAIAKEL----FGDAWHQNFTELNASDERGIDVVRTKIKDFSKTSPIGgaDFKIIFLDEAD 111
                                       68999********9988888776....33334444444444444444444455555444444443488999999999 PP

                                       G--HHHHHHHHHHHH CS
                             AAA_5  76 raesevlnsLlslle 90 
                                        + ++++++L + +e
  gi|298675837|ref|YP_003727587.1| 112 ALTPDAQSALRRTME 126
                                       999999999987776 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   5.4e-05     0.041       5      83 ..      39     116 ..      35     128 .. 0.78
   2 ?   -0.7   0.0       1.7   1.3e+03      42      42 ..     189     189 ..     123     245 .. 0.61
   3 ?   -0.9   0.0         2   1.5e+03      48      48 ..     229     229 ..     175     270 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.4e-05
                                       -EEEE--TTSSHHHHHHHHHHHTT-.....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTSEEEEETGGG- CS
                             AAA_2   5 silllgptgvGktelakalaellfv.kkekkliradaselleeeevehlvsrligappgyvgaeegGivllDEidKi 80 
                                        +l+ gp gvGkt +a a+a+ lf    +++++ ++as+    + v++ ++ +  ++p  +g ++  i++lDE d  
  gi|298675837|ref|YP_003727587.1|  39 HLLFSGPPGVGKTAAAVAIAKELFGdAWHQNFTELNASDERGIDVVRTKIKDFSKTSP--IGGADFKIIFLDEADAL 113
                                       579********************95334678888888888887777777777766666..5667777*******998 PP

                                       --- CS
                             AAA_2  81 hpk 83 
                                       +p 
  gi|298675837|ref|YP_003727587.1| 114 TPD 116
                                       884 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.7
                                       G CS
                             AAA_2  42 e 42 
                                       +
  gi|298675837|ref|YP_003727587.1| 189 K 189
                                       1 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2
                                       - CS
                             AAA_2  48 e 48 
                                       e
  gi|298675837|ref|YP_003727587.1| 229 E 229
                                       1 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.6e-05     0.012      11     167 ..      29     249 ..      20     269 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.6e-05
                            AAA_11  11 ksalsese..itliqGPPGtgKTktivellsqll........................................... 42 
                                       ks +s+++    l++GPPG gKT + v++ ++l                                            
  gi|298675837|ref|YP_003727587.1|  29 KSYISTNNlpHLLFSGPPGVGKTAAAVAIAKELFgdawhqnftelnasdergidvvrtkikdfsktspiggadfkii 105
                                       4455555555689********************99999988888888888888888777777776666666666666 PP

                            AAA_11  43 .........sr......rkseeeksakpriLvCapSNaAvDellerllr.glldsegekykpkivRvgnee...... 97 
                                                +       r+ e+  ++ + iL C  S + +  + +r +  ++ + ++e  + k vR  +e+      
  gi|298675837|ref|YP_003727587.1| 106 fldeadaltPDaqsalrRTMERYTNNCRFILSCNYSSKIIEPIQSRCAVyRFRSLSYEAVE-KRVRYIAEQeglqis 181
                                       5555544440044455434667777777788888888888888888766444444444444.444544444476333 PP

                            AAA_11  98 eriseavksvsleek..vekrlekeekaqlakeiskeleklakelrafeeeeekeklkkskekskskleqer 167
                                       e   + v++++  ++  ++k +++ +  +l +++ ++   ++ ++ a  ee+ +e ++k+ + + + ++++ 
  gi|298675837|ref|YP_003727587.1| 182 E---DGVEAIKYVSQgdMRKAINALQASALIDDVIDKDTIYKITATAHPEEI-EELVQKALDGNFKAARETM 249
                                       2...334443333330033333333344444444443333333333333333.3444444444444444444 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0046       3.5      21      45 ..      39      63 ..      18      87 .. 0.76
   2 ?    3.9   0.0     0.043        32     121     156 ..     103     141 ..     100     175 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0046
                                      EEEEE--TTSSTTHHHHHHHHHHHH CS
                              PhoH 21 ivfaiGpaGtGKtylavalavealk 45
                                       +   Gp G GKt  ava+a e++ 
  gi|298675837|ref|YP_003727587.1| 39 HLLFSGPPGVGKTAAAVAIAKELFG 63
                                      45678**************988765 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.043
                                       EEEEE-SGGG--HH...HHHHHHTTB-TT-EEEEEE--- CS
                              PhoH 121 afvilDEAQnttke...qmkmfltRlGenskvvvtGdvt 156
                                       ++++lDEA  +t+     ++  + R  +n+++++  + +
  gi|298675837|ref|YP_003727587.1| 103 KIIFLDEADALTPDaqsALRRTMERYTNNCRFILSCNYS 141
                                       589********98621156778999*******9987655 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00018      0.13      34      72 ..      38      76 ..      25     117 .. 0.85
   2 ?   -3.7   0.0       9.5   7.1e+03     121     147 ..     204     231 ..     200     237 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00018
                             AAA_7 34 kpvllvGptGtGKtviikdllkkldkekylsltinfsaq 72
                                       ++l+ Gp G+GKt+ +  + k+l  + +  ++ +++a+
  gi|298675837|ref|YP_003727587.1| 38 PHLLFSGPPGVGKTAAAVAIAKELFGDAWHQNFTELNAS 76
                                      5799*******************9999999999998875 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 9.5
                             AAA_7 121 ppiellRqlldyggwYdrkkl.efkeik 147
                                       ++ +l+  ++d+  +Y+ + + + +ei+
  gi|298675837|ref|YP_003727587.1| 204 QASALIDDVIDKDTIYKITATaHPEEIE 231
                                       5667777788888888775432555555 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00086      0.64       3      75 ..      42     114 ..      40     122 .. 0.79
   2 ?    0.8   0.0      0.46   3.4e+02     119     159 ..     146     191 ..     129     224 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00086
                   Viral_helicase1   3 vhGvpGcGKStlirkllrtsliltvnrptaelltegkpklpnlsvrtvdsflmalvks.tkgkililDEylllh 75 
                                        +G pG GK+ + + ++++ l   + ++++  l+++ ++  +     +++f ++   +  ++ki++lDE+ +l+
  gi|298675837|ref|YP_003727587.1|  42 FSGPPGVGKTAAAVAIAKE-LFGDAWHQNFTELNASDERGIDVVRTKIKDFSKTSPIGgADFKIIFLDEADALT 114
                                       6799***************.66677777788888887666666666677777777777778********97665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.46
                   Viral_helicase1 119 shrvgrrttyllpsdvaeilsak...vgteveversgel..kvete 159
                                       +   +r+ +y+++s+ +e+ +++     ++  ++ s+ +   +++ 
  gi|298675837|ref|YP_003727587.1| 146 EPIQSRCAVYRFRSLSYEAVEKRvryIAEQEGLQISEDGveAIKYV 191
                                       6677899999999999999999976644444444444443233344 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00025      0.19       2      38 ..      41      74 ..      40      83 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00025
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsvysrn 38
                                      +++Gp+g+GK+ +a  +ak+l    ++ +++++   n
  gi|298675837|ref|YP_003727587.1| 41 LFSGPPGVGKTAAAVAIAKELF---GDAWHQNFTELN 74
                                      799*****************99...455666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       860  (0.047967); expected 358.6 (0.02)
Passed bias filter:                      726  (0.0404931); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.46
# Mc/sec: 2072.97
//
Query:       gi|298675838|ref|YP_003727588.1|  [L=110]
Description: hypothetical protein Metev_1962 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00016   21.8   4.3     0.0002   21.4   4.3    1.1  1  DUF4870          Domain of unknown function (DUF4870)
  ------ inclusion threshold ------
       0.16   12.2   3.8       0.24   11.6   3.8    1.3  1  CobS             Cobalamin-5-phosphate synthase
          3    7.9  10.1        4.2    7.4   0.6    3.0  2  TM_helix         Conserved TM helix


Domain annotation for each model (and alignments):
>> DUF4870  Domain of unknown function (DUF4870)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   4.3   3.3e-08    0.0002      22     105 ..      21      99 ..       4     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 3.3e-08
                           DUF4870  22 niilPlviwllkkdksefvdeqgkealNFqislliysiilivlsllvligflllllllllllnlvlviiaaikaneg 98 
                                       ++ l  v++ll +++++fv+ ++ +++   + l++++++   + +l ++g+  ll+ +++ ++l+l++i ai+a++g
  gi|298675838|ref|YP_003727588.1|  21 GFWLTGVLFLLIENNNKFVRFHALQSFLTFLPLSLLVFL---IGWLPFVGW--LLADFVGFMALFLMLILAIQAYRG 92 
                                       5666678899999999*******9998665666555544...4455899*9..************************ PP

                           DUF4870  99 eeyrypl 105
                                        ++r p 
  gi|298675838|ref|YP_003727588.1|  93 LKFRLPY 99 
                                       ****997 PP

>> CobS  Cobalamin-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   3.8   4.1e-05      0.24       3      41 ..      46      85 ..      44     104 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.1e-05
                              CobS  3 sflTrlPvpelaralaffPlvGlllGlll.llalllllll 41
                                      sflT lP+  l   + ++P+vG+ll+ ++ ++al+l+l+l
  gi|298675838|ref|YP_003727588.1| 46 SFLTFLPLSLLVFLIGWLPFVGWLLADFVgFMALFLMLIL 85
                                      7*******75577*************99865555555543 PP

>> TM_helix  Conserved TM helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   3.2     0.012        72       7      29 ..      44      63 ..      33      63 .. 0.81
   2 ?    7.4   0.6   0.00071       4.2      25      36 ..      65      76 ..      65      87 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.012
                                      XHHHHTTHSHHHHHHHHHHHHHH CS
                          TM_helix  7 lnellsflPnLvgAilILlvGwi 29
                                      l+++l+flP   + +l++l+Gw+
  gi|298675838|ref|YP_003727588.1| 44 LQSFLTFLP---LSLLVFLIGWL 63
                                      667777777...799*******7 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00071
                                      HHHHHHHHHHHH CS
                          TM_helix 25 lvGwiiAkfvsr 36
                                      +vGw++A fv  
  gi|298675838|ref|YP_003727588.1| 65 FVGWLLADFVGF 76
                                      8********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 651.31
//
Query:       gi|298675839|ref|YP_003727589.1|  [L=290]
Description: RnfABCDGE type electron transport complex subunit B [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-20   72.2  46.1    7.3e-08   31.9   4.4    5.8  6  Fer4      4Fe-4S binding domain
    2.8e-17   62.6  49.3    4.2e-08   33.2  12.6    4.0  4  Fer4_9    4Fe-4S dicluster domain
    4.7e-15   55.9  36.3    3.5e-08   33.9  11.5    4.7  4  Fer4_7    4Fe-4S dicluster domain
    4.9e-15   54.9   4.2    4.9e-15   54.9   4.2    4.1  5  FeS       Putative Fe-S cluster
    3.6e-14   52.1  42.8    6.7e-05   22.8   0.9    5.6  5  Fer4_6    4Fe-4S binding domain
    1.7e-10   41.7  37.3    0.00044   21.1  14.2    5.0  4  Fer4_16   4Fe-4S double cluster binding domain
    3.2e-10   39.5  45.9    8.2e-05   22.5   2.1    6.0  5  Fer4_2    4Fe-4S binding domain
    1.3e-09   38.0  41.0    1.2e-05   25.3  17.0    4.1  4  Fer4_21   4Fe-4S dicluster domain
    6.1e-09   35.9  52.4    0.00018   21.5  16.7    5.1  6  Fer4_10   4Fe-4S dicluster domain
    1.6e-06   28.5  29.8    0.00093   19.7  14.7    4.4  3  Fer4_17   4Fe-4S dicluster domain
     0.0007   20.4  49.9      0.029   15.3   2.3    6.5  6  Fer4_3    4Fe-4S binding domain
     0.0021   18.8  32.2     0.0061   17.3   1.7    5.8  5  Fer4_15   4Fe-4S single cluster domain
     0.0024   18.4  39.1     0.0036   17.8   1.9    5.7  6  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
     0.0051   17.2  44.5      0.038   14.5   2.5    4.6  6  Fer4_8    4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.052   14.1  53.4      0.053   14.0   1.0    6.2  6  Fer4_4    4Fe-4S binding domain
       0.11   13.3   1.1       0.11   13.3   1.1    4.9  5  Fer4_22   4Fe-4S dicluster domain
       0.32   11.3   0.0       0.32   11.3   0.0    1.7  2  DUF3646   DNA polymerase III gamma and tau subunits C termina
        9.5    6.5  34.1        1.3    9.2   2.8    4.0  3  Fer4_18   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   1.4       1.1   1.1e+03      11      14 ..      52      55 ..      51      58 .. 0.77
   2 ?   -1.9   0.0       3.6   3.6e+03      18      21 ..      77      80 ..      74      82 .. 0.81
   3 !   16.3   1.4   6.1e-06     0.006      12      24 .]     147     159 ..     143     159 .. 0.92
   4 !   27.7   1.5   1.6e-09   1.6e-06       2      23 ..     167     188 ..     166     189 .. 0.92
   5 !   21.3   4.7   1.6e-07   0.00016       8      24 .]     218     234 ..     215     234 .. 0.95
   6 !   31.9   4.4   7.3e-11   7.3e-08       2      24 .]     241     263 ..     240     263 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.1
                                      -THH CS
                              Fer4 11 CGaC 14
                                      CGaC
  gi|298675839|ref|YP_003727589.1| 52 CGAC 55
                                      9999 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.6
                                      STTT CS
                              Fer4 18 CPvg 21
                                      CPvg
  gi|298675839|ref|YP_003727589.1| 77 CPVG 80
                                      **98 PP

  == domain 3  score: 16.3 bits;  conditional E-value: 6.1e-06
                                       THHHHHSTTTEEE CS
                              Fer4  12 GaCvevCPvgAIt 24 
                                       G+Cv +CP+gAIt
  gi|298675839|ref|YP_003727589.1| 147 GTCVRACPFGAIT 159
                                       99**********7 PP

  == domain 4  score: 27.7 bits;  conditional E-value: 1.6e-09
                                       EEETTTSSS-THHHHHSTTTEE CS
                              Fer4   2 videekCigCGaCvevCPvgAI 23 
                                        i++++C+ CG+C+e CP++ +
  gi|298675839|ref|YP_003727589.1| 167 HINKNLCTSCGLCIESCPNDIL 188
                                       79*****************976 PP

  == domain 5  score: 21.3 bits;  conditional E-value: 1.6e-07
                                       SSS-THHHHHSTTTEEE CS
                              Fer4   8 CigCGaCvevCPvgAIt 24 
                                       CigC++C++ CP +AI+
  gi|298675839|ref|YP_003727589.1| 218 CIGCKICEKNCPEDAIK 234
                                       ****************6 PP

  == domain 6  score: 31.9 bits;  conditional E-value: 7.3e-11
                                       EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                       +id+ekC++CG+Cve CP g I+
  gi|298675839|ref|YP_003727589.1| 241 EIDQEKCTACGICVEKCPQGTIE 263
                                       79******************996 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1  12.2       1.1   1.1e+03      33      51 .]     124     158 ..      50     158 .. 0.66
   2 !   28.1   6.4   1.7e-09   1.7e-06       2      50 ..     143     187 ..     138     188 .. 0.83
   3 !   27.9  14.3   1.9e-09   1.9e-06       2      51 .]     173     233 ..     172     233 .. 0.96
   4 !   33.2  12.6   4.3e-11   4.2e-08       2      51 .]     218     262 ..     217     262 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.1
                            Fer4_9  33 e............eaC.igCga...CveaCpkgai 51 
                                       +            + C +gC+    Cv aCp gai
  gi|298675839|ref|YP_003727589.1| 124 QdcnavmmlsegeKGCsYGCMGrgtCVRACPFGAI 158
                                       03333444555554566667666669999999887 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 1.7e-09
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                       C+g g+Cv+aCp+g+++  + +    +++     C++Cg C+e Cp+++
  gi|298675839|ref|YP_003727589.1| 143 CMGRGTCVRACPFGAITIGEDRLPHINKN----LCTSCGLCIESCPNDI 187
                                       555589**********8888888877765....6************994 PP

  == domain 3  score: 27.9 bits;  conditional E-value: 1.9e-09
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase...........eaCigCgaCveaCpkgai 51 
                                       Ct+Cg C+e+Cp+++ v  +  +k+ +r++s            + CigC+ C++ Cp++ai
  gi|298675839|ref|YP_003727589.1| 173 CTSCGLCIESCPNDILVFGKESEKVHVRCRSHdkpkavkavctTGCIGCKICEKNCPEDAI 233
                                       *****************99999999999999999*********99*************997 PP

  == domain 4  score: 33.2 bits;  conditional E-value: 4.3e-11
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       C+gC+ C++ Cp ++++  ++  ++ ++     +C+ Cg Cve+Cp+g i
  gi|298675839|ref|YP_003727589.1| 218 CIGCKICEKNCPEDAIKVNNFLAEIDQE-----KCTACGICVEKCPQGTI 262
                                       *********************9999974.....6*************865 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   4.9       9.6   9.6e+03       4      14 ..      51      62 ..      50     129 .. 0.56
   2 !   29.0   5.4   1.2e-09   1.2e-06       2      51 ..     143     186 ..     138     187 .. 0.90
   3 !   33.9  11.5   3.5e-11   3.5e-08       2      51 ..     218     260 ..     217     261 .. 0.94
   4 !   19.4   3.6   1.2e-06    0.0012       1      27 [.     246     272 ..     246     285 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 9.6
                            Fer4_7  4 gCgaCvaa.Cpv 14
                                      +CgaC  a C++
  gi|298675839|ref|YP_003727589.1| 51 NCGACGYAgCSA 62
                                      577776443542 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 1.2e-09
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51 
                                       C+g g Cv+aCp +ai++ e+      + ++i+ + C++Cg C++ CP +
  gi|298675839|ref|YP_003727589.1| 143 CMGRGTCVRACPFGAITIGED------RLPHINKNLCTSCGLCIESCPND 186
                                       88889*************997......3578999**************87 PP

  == domain 3  score: 33.9 bits;  conditional E-value: 3.5e-11
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51 
                                       CigC+ C+++Cp +ai+++++        +eid+ekC+ Cg Cv+ CP g
  gi|298675839|ref|YP_003727589.1| 218 CIGCKICEKNCPEDAIKVNNF-------LAEIDQEKCTACGICVEKCPQG 260
                                       ******************998.......479*****************87 PP

  == domain 4  score: 19.4 bits;  conditional E-value: 1.2e-06
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekg 27 
                                       +C+ Cg Cv+ Cp+++ie++e  ++ +
  gi|298675839|ref|YP_003727589.1| 246 KCTACGICVEKCPQGTIEMKETGEKTK 272
                                       7******************99755543 PP

>> FeS  Putative Fe-S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   4.2     5e-18   4.9e-15       1      33 []      47      79 ..      47      79 .. 0.98
   2 ?   -2.7   0.7       4.9   4.9e+03       8      15 ..     138     144 ..     131     145 .. 0.60
   3 ?   -2.4   1.8       3.9   3.9e+03       6      10 ..     173     177 ..     165     183 .. 0.67
   4 ?   -3.3   0.5       7.8   7.8e+03       6      10 ..     221     225 ..     219     237 .. 0.64
   5 ?   -3.5   3.2       8.8   8.8e+03       6      10 ..     247     251 ..     242     257 .. 0.81

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 5e-18
                               FeS  1 LPgtNCgaCGypgCmafAealvegeaqledCpp 33
                                      LPg+NCgaCGy+gC+afAea+v+ +a+++ Cp+
  gi|298675839|ref|YP_003727589.1| 47 LPGANCGACGYAGCSAFAEAVVSEDAPIDGCPV 79
                                      9******************************96 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.9
                               FeS   8 aCGypgCm 15 
                                       +C y gCm
  gi|298675839|ref|YP_003727589.1| 138 GCSY-GCM 144
                                       3444.555 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 3.9
                               FeS   6 CgaCG 10 
                                       C  CG
  gi|298675839|ref|YP_003727589.1| 173 CTSCG 177
                                       55555 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 7.8
                               FeS   6 CgaCG 10 
                                       C+ C 
  gi|298675839|ref|YP_003727589.1| 221 CKICE 225
                                       66663 PP

  == domain 5  score: -3.5 bits;  conditional E-value: 8.8
                               FeS   6 CgaCG 10 
                                       C aCG
  gi|298675839|ref|YP_003727589.1| 247 CTACG 251
                                       77887 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   1.5      0.67   6.6e+02      11      21 ..      51      62 ..      50      67 .. 0.80
   2 !   12.0   3.1   0.00018      0.18      11      24 .]     142     158 ..     138     158 .. 0.79
   3 !   22.8   0.9   6.7e-08   6.7e-05       2      22 ..     166     186 ..     165     188 .. 0.90
   4 !   16.5   5.7   6.4e-06    0.0063       9      24 .]     218     233 ..     218     233 .. 0.98
   5 !   22.1   2.0   1.1e-07   0.00011       2      22 ..     240     260 ..     239     262 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.67
                            Fer4_6 11 gCgdC.vrvCPe 21
                                       Cg+C ++ C +
  gi|298675839|ref|YP_003727589.1| 51 NCGACgYAGCSA 62
                                      59***9998975 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00018
                            Fer4_6  11 gC.gd..CvrvCPegai 24 
                                       gC g+  Cvr+CP+gai
  gi|298675839|ref|YP_003727589.1| 142 GCmGRgtCVRACPFGAI 158
                                       6745577*********8 PP

  == domain 3  score: 22.8 bits;  conditional E-value: 6.7e-08
                            Fer4_6   2 veidpdkCigCgdCvrvCPeg 22 
                                       ++i++++C++Cg C+  CP +
  gi|298675839|ref|YP_003727589.1| 166 PHINKNLCTSCGLCIESCPND 186
                                       79*****************65 PP

  == domain 4  score: 16.5 bits;  conditional E-value: 6.4e-06
                            Fer4_6   9 CigCgdCvrvCPegai 24 
                                       CigC  C+++CPe+ai
  gi|298675839|ref|YP_003727589.1| 218 CIGCKICEKNCPEDAI 233
                                       **************98 PP

  == domain 5  score: 22.1 bits;  conditional E-value: 1.1e-07
                            Fer4_6   2 veidpdkCigCgdCvrvCPeg 22 
                                       +eid++kC+ Cg Cv  CP g
  gi|298675839|ref|YP_003727589.1| 240 AEIDQEKCTACGICVEKCPQG 260
                                       79*****************65 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.1    0.0012       1.2       2      20 ..     143     161 ..     142     171 .. 0.80
   2 !   21.1  14.2   4.4e-07   0.00044       2      65 ..     173     229 ..     172     229 .. 0.84
   3 !   15.8   2.6     2e-05      0.02       2      20 ..     218     236 ..     217     245 .. 0.86
   4 !   19.8   4.2   1.2e-06    0.0012       1      37 [.     246     277 ..     246     289 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0012
                           Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                       C + g C+ +CP +ai+  
  gi|298675839|ref|YP_003727589.1| 143 CMGRGTCVRACPFGAITIG 161
                                       788899*********9865 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 4.4e-07
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCP 65 
                                       C++Cg C+e+CP + +   ke e    +c s     +++ +  ++ c+  + ++gC+iC++ CP
  gi|298675839|ref|YP_003727589.1| 173 CTSCGLCIESCPNDILVFGKESEKVHVRCRS-----HDKPKAVKAVCT--TGCIGCKICEKNCP 229
                                       *****************99666666666655.....577777788888..88***********9 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 2e-05
                           Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                       C++C+ C + CP++aik +
  gi|298675839|ref|YP_003727589.1| 218 CIGCKICEKNCPEDAIKVN 236
                                       ****************987 PP

  == domain 4  score: 19.8 bits;  conditional E-value: 1.2e-06
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiearecisyntae 37 
                                       +C+ Cg C+e CP++ i++k  ++ e+ ++  +   +
  gi|298675839|ref|YP_003727589.1| 246 KCTACGICVEKCPQGTIEMK--ETGEKTKTSTK---Q 277
                                       5*******************..33333332222...2 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   2.8      0.93   9.3e+02      12      20 ..      51      60 ..      50      62 .. 0.71
   2 !    7.7   2.7    0.0041       4.1      10      21 ..     139     154 ..     135     155 .. 0.80
   3 !   21.4   1.5   1.8e-07   0.00018       3      22 .]     166     185 ..     164     185 .. 0.92
   4 !   10.1   6.4    0.0007       0.7      10      22 .]     218     230 ..     207     230 .. 0.90
   5 !   22.5   2.1   8.3e-08   8.2e-05       4      22 .]     241     259 ..     239     259 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.93
                            Fer4_2 12 gCgaCvsa.C 20
                                      +CgaC  a C
  gi|298675839|ref|YP_003727589.1| 51 NCGACGYAgC 60
                                      7999966667 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0041
                            Fer4_2  10 Ci.gC...gaCvsaCP 21 
                                       C  gC   g+Cv aCP
  gi|298675839|ref|YP_003727589.1| 139 CSyGCmgrGTCVRACP 154
                                       655887667******* PP

  == domain 3  score: 21.4 bits;  conditional E-value: 1.8e-07
                            Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                       ++++ + C++Cg C+ +CP+
  gi|298675839|ref|YP_003727589.1| 166 PHINKNLCTSCGLCIESCPN 185
                                       89*****************5 PP

  == domain 4  score: 10.1 bits;  conditional E-value: 0.0007
                            Fer4_2  10 CigCgaCvsaCPa 22 
                                       CigC++C ++CP+
  gi|298675839|ref|YP_003727589.1| 218 CIGCKICEKNCPE 230
                                       ************5 PP

  == domain 5  score: 22.5 bits;  conditional E-value: 8.3e-08
                            Fer4_2   4 vvdtdrCigCgaCvsaCPa 22 
                                       ++d ++C++Cg+Cv  CP+
  gi|298675839|ref|YP_003727589.1| 241 EIDQEKCTACGICVEKCPQ 259
                                       79****************6 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.6       2.5   2.5e+03      10      22 ..      51      63 ..      49      79 .. 0.62
   2 !   22.5   7.4   9.4e-08   9.4e-05       8      53 ..     143     185 ..     138     189 .. 0.92
   3 !   13.9   7.5   4.4e-05     0.044      29      58 ..     206     234 ..     194     235 .. 0.82
   4 !   25.3  17.0   1.2e-08   1.2e-05       6      59 .]     216     264 ..     212     264 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.5
                           Fer4_21 10 gCgkClia.Cedts 22
                                      +Cg C  a C+ + 
  gi|298675839|ref|YP_003727589.1| 51 NCGACGYAgCS-AF 63
                                      68888554255.33 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 9.4e-08
                           Fer4_21   8 CigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPv 53 
                                       C+g g C+ aC+     ai+i +++  ++ ++ C+ C lC++ CP 
  gi|298675839|ref|YP_003727589.1| 143 CMGRGTCVRACP---FGAITIGEDRLPHINKNLCTSCGLCIESCPN 185
                                       9999********...89********99999***************3 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 4.4e-05
                           Fer4_21  29 daktvlkvvedeCvGCnlCssvCPvedcie 58 
                                       ++k+v +v +  C+GC++C + CP ed+i+
  gi|298675839|ref|YP_003727589.1| 206 KPKAVKAVCTTGCIGCKICEKNCP-EDAIK 234
                                       4567778889**************.89997 PP

  == domain 4  score: 25.3 bits;  conditional E-value: 1.2e-08
                           Fer4_21   6 dkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59 
                                         CigC+ C + C++   +ai+++ +  +++ +++C++C +C++ CP ++ iem
  gi|298675839|ref|YP_003727589.1| 216 TGCIGCKICEKNCPE---DAIKVN-NFLAEIDQEKCTACGICVEKCP-QGTIEM 264
                                       57************6...***985.778899****************.799998 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   3.6       3.3   3.3e+03      18      52 ..      76     115 ..      47     117 .. 0.47
   2 ?    2.6   7.6      0.15   1.5e+02      33      56 .]     131     154 ..     101     154 .. 0.67
   3 !    7.9   2.1    0.0032       3.2       9      21 ..     143     155 ..     130     164 .. 0.68
   4 !   20.2  16.4   4.7e-07   0.00047       3      56 .]     167     229 ..     165     229 .. 0.95
   5 !   21.5  16.7   1.8e-07   0.00018       8      56 .]     217     258 ..     212     258 .. 0.91
   6 !   20.6   3.4   3.6e-07   0.00036       2      35 ..     240     273 ..     239     285 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.3
                           Fer4_10  18 aCPadl.....tsvgakgeaseeeavrkkvekCtgcgaCv 52 
                                        CP+       +  g  g++  +++++  v +C g  +Cv
  gi|298675839|ref|YP_003727589.1|  76 GCPVGGfelaqQIGGILGKEVTQGEKQYPVVRCKGGVNCV 115
                                       3444336555544455555555555555566666666665 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.15
                           Fer4_10  33 seeeavrkkvekCtgcgaCveaCP 56 
                                       + +e +++ ++ C+g g Cv+aCP
  gi|298675839|ref|YP_003727589.1| 131 MLSEGEKGCSYGCMGRGTCVRACP 154
                                       45555566778999999******9 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0032
                           Fer4_10   9 CirCgkCvkaCPa 21 
                                       C++ g+Cv+aCP+
  gi|298675839|ref|YP_003727589.1| 143 CMGRGTCVRACPF 155
                                       5555566666665 PP

  == domain 4  score: 20.2 bits;  conditional E-value: 4.7e-07
                           Fer4_10   3 vidddtCirCgkCvkaCPadl.........tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +i+++ C+ Cg C ++CP d+          +v+ +  +++++++ +    C+gc  C + CP
  gi|298675839|ref|YP_003727589.1| 167 HINKNLCTSCGLCIESCPNDIlvfgkesekVHVRCRSHDKPKAVKAVCTTGCIGCKICEKNCP 229
                                       7999************************99999999999999999999**************9 PP

  == domain 5  score: 21.5 bits;  conditional E-value: 1.8e-07
                           Fer4_10   8 tCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                        Ci+C+ C k CP         +++ ++   +++ ekCt+cg Cve+CP
  gi|298675839|ref|YP_003727589.1| 217 GCIGCKICEKNCPE-------DAIKVNNFLAEIDQEKCTACGICVEKCP 258
                                       6*************.......77888888888899*************9 PP

  == domain 6  score: 20.6 bits;  conditional E-value: 3.6e-07
                           Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeasee 35 
                                       ++id+++C+ Cg Cv+ CP+   +++ +ge+++ 
  gi|298675839|ref|YP_003727589.1| 240 AEIDQEKCTACGICVEKCPQGTIEMKETGEKTKT 273
                                       579*****************66444444444444 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   1.1   1.5e-05     0.015      42      60 ..     169     187 ..     156     188 .. 0.83
   2 !   19.7  14.7   9.4e-07   0.00093       2      59 ..     173     231 ..     172     233 .. 0.90
   3 !   17.1   0.5   6.2e-06    0.0062      44      59 ..     245     260 ..     234     286 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.5e-05
                           Fer4_17  42 kaslCieCgeCerkCPqgl 60 
                                       + +lC++Cg+C ++CP+++
  gi|298675839|ref|YP_003727589.1| 169 NKNLCTSCGLCIESCPNDI 187
                                       5689************986 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 9.4e-07
                           Fer4_17   2 CiqCgyClpeCpsyea.ydnepkkllraaklglleeaekeekaslCieCgeCerkCPqg 59 
                                       C++Cg C+++Cp  +   ++e +k+  + +++++ +a k      Ci+C+ Ce+ CP++
  gi|298675839|ref|YP_003727589.1| 173 CTSCGLCIESCPNDILvFGKESEKVHVRCRSHDKPKAVKAVCTTGCIGCKICEKNCPED 231
                                       ************97765899999999999999888887888899*************97 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 6.2e-06
                           Fer4_17  44 slCieCgeCerkCPqg 59 
                                       ++C+ Cg C++kCPqg
  gi|298675839|ref|YP_003727589.1| 245 EKCTACGICVEKCPQG 260
                                       5788888888888875 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.7         2     2e+03       3       7 ..      51      55 ..      51      58 .. 0.78
   2 ?   -0.9   0.1       4.5   4.5e+03      11      14 ..      77      80 ..      75      81 .. 0.81
   3 !   11.6   4.2   0.00045      0.45       3      15 .]     142     157 ..     138     157 .. 0.78
   4 !   15.3   2.3   2.9e-05     0.029       1      14 [.     173     186 ..     173     187 .. 0.93
   5 !   10.2   2.9    0.0012       1.2       1      15 []     218     232 ..     218     232 .. 0.96
   6 !    8.0   5.2    0.0063       6.3       1      14 [.     247     260 ..     247     261 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 2
                            Fer4_3  3 gCgaC 7 
                                      +CgaC
  gi|298675839|ref|YP_003727589.1| 51 NCGAC 55
                                      6**** PP

  == domain 2  score: -0.9 bits;  conditional E-value: 4.5
                            Fer4_3 11 CPvg 14
                                      CPvg
  gi|298675839|ref|YP_003727589.1| 77 CPVG 80
                                      **98 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00045
                            Fer4_3   3 gCg...aCvevCPvgA 15 
                                       gC+   +Cv++CP gA
  gi|298675839|ref|YP_003727589.1| 142 GCMgrgTCVRACPFGA 157
                                       7845669*******98 PP

  == domain 4  score: 15.3 bits;  conditional E-value: 2.9e-05
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       Ct Cg+C e+CP++
  gi|298675839|ref|YP_003727589.1| 173 CTSCGLCIESCPND 186
                                       ************87 PP

  == domain 5  score: 10.2 bits;  conditional E-value: 0.0012
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+gC  C++ CP++A
  gi|298675839|ref|YP_003727589.1| 218 CIGCKICEKNCPEDA 232
                                       ****99******998 PP

  == domain 6  score: 8.0 bits;  conditional E-value: 0.0063
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       Ct Cg Cve CP g
  gi|298675839|ref|YP_003727589.1| 247 CTACGICVEKCPQG 260
                                       9***********87 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.2       1.5   1.5e+03       7      33 ..     107     131 ..     106     138 .. 0.70
   2 ?    4.8   0.4     0.049        49      56      66 .]     150     160 ..     142     160 .. 0.73
   3 !   11.9   0.5   0.00029      0.29       3      20 ..     168     185 ..     167     210 .. 0.82
   4 ?    0.7   4.6      0.89   8.9e+02       7      20 ..     217     230 ..     213     234 .. 0.85
   5 !   17.3   1.7   6.1e-06    0.0061       2      44 ..     241     281 ..     241     289 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.5
                           Fer4_15   7 aCigcglCvaeapevfeldedglasvl 33 
                                       +C g  +Cv +  +++ ++ d  a++ 
  gi|298675839|ref|YP_003727589.1| 107 RCKGGVNCVNRF-DYVGIQ-DCNAVMM 131
                                       7********995.577776.5555555 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.049
                           Fer4_15  56 araCPvdAIrv 66 
                                       +raCP +AI++
  gi|298675839|ref|YP_003727589.1| 150 VRACPFGAITI 160
                                       57888888876 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00029
                           Fer4_15   3 vDrdaCigcglCvaeape 20 
                                       +++++C++cglC++ +p+
  gi|298675839|ref|YP_003727589.1| 168 INKNLCTSCGLCIESCPN 185
                                       7899************86 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.89
                           Fer4_15   7 aCigcglCvaeape 20 
                                        Cigc  C +++pe
  gi|298675839|ref|YP_003727589.1| 217 GCIGCKICEKNCPE 230
                                       69999999999986 PP

  == domain 5  score: 17.3 bits;  conditional E-value: 6.1e-06
                           Fer4_15   2 vvDrdaCigcglCvaea.pevfeldedglasvllddgeiaegev 44 
                                       ++D+++C+ cg Cv+ + +  +e++e g ++ +   ++ ++++ 
  gi|298675839|ref|YP_003727589.1| 241 EIDQEKCTACGICVEKCpQGTIEMKETGEKTKT---STKQSADT 281
                                       59***************4457888888877333...33334433 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.9       2.6   2.6e+03       8      22 ..      51      65 ..      50      72 .. 0.79
   2 ?   -2.1   0.1       5.9   5.9e+03      48      53 ..      74      79 ..      70      80 .. 0.83
   3 ?    4.2   0.3     0.063        63       5      17 ..     142     154 ..     140     155 .. 0.93
   4 !   12.7   2.1   0.00015      0.15       1      24 [.     168     194 ..     168     215 .. 0.74
   5 ?    6.2   4.1     0.016        16       5      18 ..     217     230 ..     213     231 .. 0.92
   6 !   17.8   1.9   3.6e-06    0.0036       1      27 [.     242     269 ..     242     289 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.6
                           Fer4_13  8 acgaCvelaPdvFee 22
                                      +cgaC+ +    F+e
  gi|298675839|ref|YP_003727589.1| 51 NCGACGYAGCSAFAE 65
                                      699998887777765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.9
                           Fer4_13 48 adaCPv 53
                                      +d+CPv
  gi|298675839|ref|YP_003727589.1| 74 IDGCPV 79
                                      799**9 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.063
                           Fer4_13   5 tCiacgaCvelaP 17 
                                        C++ g+Cv ++P
  gi|298675839|ref|YP_003727589.1| 142 GCMGRGTCVRACP 154
                                       6***********9 PP

  == domain 4  score: 12.7 bits;  conditional E-value: 0.00015
                           Fer4_13   1 VDrdtCiacgaCvelaPd...vFeedd 24 
                                       ++++ C++cg+C e +P+   vF  + 
  gi|298675839|ref|YP_003727589.1| 168 INKNLCTSCGLCIESCPNdilVFGKES 194
                                       79999************7544555555 PP

  == domain 5  score: 6.2 bits;  conditional E-value: 0.016
                           Fer4_13   5 tCiacgaCvelaPd 18 
                                        Ci+c++C + +P+
  gi|298675839|ref|YP_003727589.1| 217 GCIGCKICEKNCPE 230
                                       7************7 PP

  == domain 6  score: 17.8 bits;  conditional E-value: 3.6e-06
                           Fer4_13   1 VDrdtCiacgaCvelaPd.vFeeddegg 27 
                                       +D+++C+acg+Cve +P+ + e+++ g+
  gi|298675839|ref|YP_003727589.1| 242 IDQEKCTACGICVEKCPQgTIEMKETGE 269
                                       8****************73455555544 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7  10.3         2     2e+03      44      64 ..     124     156 ..      50     157 .. 0.50
   2 !   12.5   2.1   0.00016      0.16      49      65 .]     171     187 ..     162     187 .. 0.84
   3 !   12.2  16.4   0.00019      0.19       5      64 ..     173     231 ..     169     235 .. 0.73
   4 !    7.7   5.1    0.0049       4.9       5      16 ..     218     229 ..     214     244 .. 0.77
   5 !   12.6   2.8   0.00015      0.15      49      64 ..     245     260 ..     229     261 .. 0.79
   6 !   14.5   2.5   3.8e-05     0.038       3      22 ..     245     268 ..     243     289 .. 0.57

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2
                            Fer4_8  44 e............eealwsCttcgaCtevCpvg 64 
                                       +            +   + C++ g C+++Cp g
  gi|298675839|ref|YP_003727589.1| 124 QdcnavmmlsegeKGCSYGCMGRGTCVRACPFG 156
                                       0344444444555778899***********975 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00016
                            Fer4_8  49 wsCttcgaCtevCpvgi 65 
                                       + Ct+cg C e Cp++i
  gi|298675839|ref|YP_003727589.1| 171 NLCTSCGLCIESCPNDI 187
                                       68999999999999876 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 0.00019
                            Fer4_8   5 CieCgaCqsaCp.....vlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                       C+ Cg+C ++Cp     + +++ k +   r   +  +  + v         C +c+ C+++Cp++
  gi|298675839|ref|YP_003727589.1| 173 CTSCGLCIESCPndilvFGKESEKVHVRCRSHDKP-KAVKAV-----CTTGCIGCKICEKNCPED 231
                                       ***********999964444444555555555555.333333.....589*************85 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0049
                            Fer4_8   5 CieCgaCqsaCp 16 
                                       Ci+C  C+++Cp
  gi|298675839|ref|YP_003727589.1| 218 CIGCKICEKNCP 229
                                       888888888888 PP

  == domain 5  score: 12.6 bits;  conditional E-value: 0.00015
                            Fer4_8  49 wsCttcgaCtevCpvg 64 
                                       ++Ct+cg C+e+Cp+g
  gi|298675839|ref|YP_003727589.1| 245 EKCTACGICVEKCPQG 260
                                       5788888888888875 PP

  == domain 6  score: 14.5 bits;  conditional E-value: 3.8e-05
                            Fer4_8   3 ekCieCgaCqsaCp....vlrrtk 22 
                                       ekC+ Cg C ++Cp     +++t+
  gi|298675839|ref|YP_003727589.1| 245 EKCTACGICVEKCPqgtiEMKETG 268
                                       688888888888885544344444 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   1.3       3.5   3.5e+03       6      10 ..      51      55 ..      50      62 .. 0.75
   2 ?   -1.9   0.0       6.8   6.8e+03      12      16 ..      75      79 ..      74      80 .. 0.69
   3 ?    8.5   3.1    0.0033       3.3       4      17 .]     143     156 ..     136     156 .. 0.78
   4 ?   14.0   1.0   5.3e-05     0.053       2      15 ..     171     184 ..     170     193 .. 0.90
   5 ?    9.6   4.5    0.0015       1.4       4      16 ..     218     230 ..     207     235 .. 0.92
   6 ?   11.7   5.3   0.00031      0.31       1      17 []     244     260 ..     244     260 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 3.5
                            Fer4_4  6 gCgsC 10
                                      +Cg+C
  gi|298675839|ref|YP_003727589.1| 51 NCGAC 55
                                      69999 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 6.8
                            Fer4_4 12 aaCPq 16
                                      + CP+
  gi|298675839|ref|YP_003727589.1| 75 DGCPV 79
                                      67987 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0033
                            Fer4_4   4 CigCgsCvaaCPqg 17 
                                       C g g Cv+aCP+g
  gi|298675839|ref|YP_003727589.1| 143 CMGRGTCVRACPFG 156
                                       666669******86 PP

  == domain 4  score: 14.0 bits;  conditional E-value: 5.3e-05
                            Fer4_4   2 erCigCgsCvaaCP 15 
                                       + C+ Cg C+ +CP
  gi|298675839|ref|YP_003727589.1| 171 NLCTSCGLCIESCP 184
                                       78************ PP

  == domain 5  score: 9.6 bits;  conditional E-value: 0.0015
                            Fer4_4   4 CigCgsCvaaCPq 16 
                                       CigC+ C+  CP 
  gi|298675839|ref|YP_003727589.1| 218 CIGCKICEKNCPE 230
                                       ************5 PP

  == domain 6  score: 11.7 bits;  conditional E-value: 0.00031
                            Fer4_4   1 qerCigCgsCvaaCPqg 17 
                                       qe+C+ Cg Cv  CPqg
  gi|298675839|ref|YP_003727589.1| 244 QEKCTACGICVEKCPQG 260
                                       79*************96 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.4       8.5   8.5e+03       4      11 ..      51      58 ..      49      71 .. 0.66
   2 ?    2.3   3.4       0.3     3e+02      79      94 ..     140     155 ..     123     157 .. 0.84
   3 ?   10.9   0.5   0.00065      0.65      76      96 .]     167     187 ..     161     187 .. 0.86
   4 ?    7.2   6.0    0.0093       9.2      60      94 ..     197     230 ..     190     233 .. 0.71
   5 ?   13.3   1.1   0.00011      0.11      69      95 ..     234     260 ..     231     261 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 8.5
                           Fer4_22  4 sCgaCtlv 11
                                      +CgaC ++
  gi|298675839|ref|YP_003727589.1| 51 NCGACGYA 58
                                      57777664 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.3
                           Fer4_22  79 esgCvGCgRCieacpv 94 
                                       ++gC+G g C++acp 
  gi|298675839|ref|YP_003727589.1| 140 SYGCMGRGTCVRACPF 155
                                       679***********95 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00065
                           Fer4_22  76 kfgesgCvGCgRCieacpvki 96 
                                       +++++ C+ Cg Cie+cp++i
  gi|298675839|ref|YP_003727589.1| 167 HINKNLCTSCGLCIESCPNDI 187
                                       568999************986 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.0093
                           Fer4_22  60 erlrqrllhklsefkekfgesgCvGCgRCieacpv 94 
                                        ++r r  +k  + ++ + ++gC+GC  C+++cp+
  gi|298675839|ref|YP_003727589.1| 197 VHVRCRSHDKP-KAVKAVCTTGCIGCKICEKNCPE 230
                                       44555555554.455677899************97 PP

  == domain 5  score: 13.3 bits;  conditional E-value: 0.00011
                           Fer4_22  69 klsefkekfgesgCvGCgRCieacpvk 95 
                                       k+++f +++++++C+ Cg C+e+cp++
  gi|298675839|ref|YP_003727589.1| 234 KVNNFLAEIDQEKCTACGICVEKCPQG 260
                                       8899999*****************985 PP

>> DUF3646  DNA polymerase III gamma and tau subunits C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00033      0.32      92     110 ..      33      51 ..      26      54 .. 0.86
   2 ?   -3.0   0.8       8.8   8.8e+03      71      93 ..     265     287 ..     260     289 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00033
                           DUF3646  92 earahPlVkavlaaFPgAk 110
                                       +++ +PlV++vl+a+PgA+
  gi|298675839|ref|YP_003727589.1|  33 HVETDPLVEEVLEALPGAN 51 
                                       7899**************7 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 8.8
                           DUF3646  71 keegepTlaeqeeaaeearraea 93 
                                       ke+ge+T   ++++a   + aea
  gi|298675839|ref|YP_003727589.1| 265 KETGEKTKTSTKQSADTSETAEA 287
                                       45677777777776666666555 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   8.7     0.019        19      58     100 ..     140     188 ..     120     200 .. 0.69
   2 ?    4.7  15.6     0.033        33      45      96 ..     202     258 ..     189     265 .. 0.73
   3 ?    9.2   2.8    0.0013       1.3      56      74 ..     242     260 ..     231     283 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.019
                           Fer4_18  58 agdcidcescvkvcPtg.idirkG.l....qleciscllcidacdkvme 100
                                       +  c+  ++cv+ cP g i i +  l    +  c sc+lci++c + + 
  gi|298675839|ref|YP_003727589.1| 140 SYGCMGRGTCVRACPFGaITIGEDrLphinKNLCTSCGLCIESCPNDIL 188
                                       456889999999999874677543222122456999*****99976444 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.033
                           Fer4_18  45 kalkekeerkekgagdcidcescvkvcPtg.idirkGl....qleciscllcidacd 96 
                                       +++ + +  k+  ++ ci c+ c k cP + i + + l    q +c +c+ c++ c 
  gi|298675839|ref|YP_003727589.1| 202 RSHDKPKAVKAVCTTGCIGCKICEKNCPEDaIKVNNFLaeidQEKCTACGICVEKCP 258
                                       3444555566778899************75378877655555899*********996 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0013
                           Fer4_18  56 kgagdcidcescvkvcPtg 74 
                                        ++ +c++c+ cv+ cP g
  gi|298675839|ref|YP_003727589.1| 242 IDQEKCTACGICVEKCPQG 260
                                       56789************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 1705.12
//
Query:       gi|298675840|ref|YP_003727590.1|  [L=197]
Description: RnfABCDGE type electron transport complex subunit A [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-55  186.4  19.6    4.7e-55  186.2  19.6    1.0  1  Rnf-Nqr   Rnf-Nqr subunit, membrane protein
  ------ inclusion threshold ------
       0.18   11.0  10.0       0.46    9.6  10.0    1.8  1  7tm_7     7tm Chemosensory receptor
       0.44   10.4   9.4       0.59   10.0   9.4    1.4  1  DUF5079   Domain of unknown function (DUF5079)


Domain annotation for each model (and alignments):
>> Rnf-Nqr  Rnf-Nqr subunit, membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.2  19.6   7.8e-59   4.7e-55       2     168 ..       7     187 ..       6     193 .. 0.98

  Alignments for each domain:
  == domain 1  score: 186.2 bits;  conditional E-value: 7.8e-59
                                       -HHHHHHHHHTS-TTTTT--HHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHH------.....---HHHHHHHH CS
                           Rnf-Nqr   2 lkillsgilkeNpvlvqflGiCpflavskklknalgmglavtfvlvlsnlvisllrklipk.....klriivfilvi 73 
                                       l++l++g++++N++l+qflG+Cpf++v+k++k++ gm+lav+fv+++++++++++++++++     +lrii+fi+vi
  gi|298675840|ref|YP_003727590.1|   7 LSVLMQGVFVQNLILIQFLGLCPFIGVTKDTKSSAGMSLAVIFVVTMASVATYFIYTFLLDpmglqFLRIISFIVVI 83 
                                       6899************************************************************************* PP

                                       HHHHHHHHHHT------THHHHHHHHHHHHS-HHHHHHHHT-----.---THHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           Rnf-Nqr  74 AalvtlvelvlkaflpslykaLgiflpLivvNCiilgraeafaskn.svleslldglgsglGftlalvllaairell 149
                                       A+lv+lve+vl++++p++y++Lgi+lpLi++NC++lg +++++ +  ++++s+++gl++g+Gft++l+++a++re+ 
  gi|298675840|ref|YP_003727590.1|  84 ASLVQLVEFVLRKMSPAVYRSLGIYLPLITTNCAVLGSVLLNIRAGyDFAQSVTFGLAAGIGFTIVLLIMAGLRERS 160
                                       *******************************************7779****************************** PP

                                       T........S-SSS.-----SHHHHHH CS
                           Rnf-Nqr 150 g........kGtliglilagllagaFl 168
                                       +        kG++ ++ +a+ll++aF+
  gi|298675840|ref|YP_003727590.1| 161 SlvhvhssvKGVPHAFFFATLLSMAFV 187
                                       **************************8 PP

>> 7tm_7  7tm Chemosensory receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6  10.0   7.7e-05      0.46       6      75 ..      20      90 ..      18     193 .. 0.96

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 7.7e-05
                             7tm_7  6 rysqllGlvpfefdrrrrrlrw.rrlllllllllllvllvllvlflivlkreeyffrrsallevvynlqlv 75
                                       ++q+lGl+pf  +++ ++ +  ++l++++++++  v+++ ++ fl   +  ++    s++++++ ++qlv
  gi|298675840|ref|YP_003727590.1| 20 ILIQFLGLCPFIGVTKDTKSSAgMSLAVIFVVTMASVATYFIYTFLLDPMGLQFLRIISFIVVIASLVQLV 90
                                      578**************************************************999999999999999886 PP

>> DUF5079  Domain of unknown function (DUF5079)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   9.4   9.9e-05      0.59      13     101 ..      41     124 ..      30     193 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 9.9e-05
                           DUF5079  13 qalsllslfvvlfdaltfffakdyeklpnylkvttiielviliisllqwirfidfekekaekykkiekrflvilnvl 89 
                                         +sl+ +fvv + ++  +f   +   p+ l+ + ii  +++i sl+q + f+ + k +   y+       + l ++
  gi|298675840|ref|YP_003727590.1|  41 AGMSLAVIFVVTMASVATYFIYTFLLDPMGLQFLRIISFIVVIASLVQLVEFV-LRKMSPAVYRS----LGIYLPLI 112
                                       46899******9888888887788888*********************88887.56667667766....33344555 PP

                           DUF5079  90 vtitlvlltvsl 101
                                       +t  +vl  v l
  gi|298675840|ref|YP_003727590.1| 113 TTNCAVLGSVLL 124
                                       555555544433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       971  (0.0541581); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1227.94
//
Query:       gi|298675841|ref|YP_003727591.1|  [L=203]
Description: RnfABCDGE type electron transport complex subunit E [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-59  201.4  15.0    1.2e-59  201.2  15.0    1.0  1  Rnf-Nqr   Rnf-Nqr subunit, membrane protein
  ------ inclusion threshold ------
      0.095   12.0   0.0       0.15   11.3   0.0    1.3  1  ECH_1     Enoyl-CoA hydratase/isomerase


Domain annotation for each model (and alignments):
>> Rnf-Nqr  Rnf-Nqr subunit, membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.2  15.0   1.3e-63   1.2e-59       3     174 .]       5     188 ..       3     188 .. 0.98

  Alignments for each domain:
  == domain 1  score: 201.2 bits;  conditional E-value: 1.3e-63
                                       HHHHHHHHHTS-TTTTT--HHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHHHHHHHHH CS
                           Rnf-Nqr   3 killsgilkeNpvlvqflGiCpflavskklknalgmglavtfvlvlsnlvisllrklipkklriivfilviAalvtl 79 
                                       + +l+gi ++Np++  +lG+Cp+lav+++l+na+gm++a+ fvl++sn++is +rk ip+ +ri++fi+ iA++vt+
  gi|298675841|ref|YP_003727591.1|   5 DEFLRGITRDNPIFGLVLGLCPTLAVTTTLENAIGMSAATAFVLICSNVLISTFRKQIPAVVRIPIFIMTIATFVTI 81 
                                       6799************************************************************************* PP

                                       HHHHT------THHHHHHHHHHHHS-HHHHHHHHT--------THHHHHHHHHHHHHHHHHHHHHHHHHHTS-SSS. CS
                           Rnf-Nqr  80 velvlkaflpslykaLgiflpLivvNCiilgraeafasknsvleslldglgsglGftlalvllaairellgkGtlig 156
                                       + +v++a++ps+++aLg+fl LivvNC+i+graea+as+n+ l s++d+lg ++Gf++al ++++irellg+G +++
  gi|298675841|ref|YP_003727591.1|  82 ISMVMEAYFPSMFAALGVFLSLIVVNCVIMGRAEAYASRNNTLYSFIDALGISAGFLVALGVMGSIRELLGTGEIVT 158
                                       ***************************************************************************99 PP

                                       ............-----SHHHHHHHHHHHH CS
                           Rnf-Nqr 157 ............lilagllagaFlglggli 174
                                                   l +++ ++gaFl++g+l+
  gi|298675841|ref|YP_003727591.1| 159 fgyqlisvpidpLDYMIFPPGAFLTIGVLM 188
                                       99************************9985 PP

>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   1.7e-05      0.15     117     158 ..      14      52 ..      10      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.7e-05
                                       TTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT-E CS
                             ECH_1 117 dnasfglnelklGlipgaggtqilarkvGkskAeeilllgkk 158
                                       dn+ fgl    lGl+p   +t +l++++G+s+A   +l++ +
  gi|298675841|ref|YP_003727591.1|  14 DNPIFGL---VLGLCPTLAVTTTLENAIGMSAATAFVLICSN 52 
                                       6666665...59**************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1027  (0.0572815); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1336.09
//
Query:       gi|298675842|ref|YP_003727592.1|  [L=185]
Description: RnfABCDGE type electron transport complex subunit G [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-15   56.1   0.2    7.9e-15   55.2   0.2    1.5  1  FMN_bind  FMN-binding domain
  ------ inclusion threshold ------
      0.035   13.9   0.0      0.044   13.5   0.0    1.1  1  UPF0259   Uncharacterised protein family (UPF0259)


Domain annotation for each model (and alignments):
>> FMN_bind  FMN-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   0.2   8.8e-19   7.9e-15       1      66 [.      94     175 ..      94     178 .. 0.79

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 8.8e-19
                                       SSSSEEEEEEEEETTTS.BEEEEEEEESSS-TTTGGG.............CTTHHHH........SSEEETCTTBHH CS
                          FMN_bind   1 Gyggtikvlvtvkdgdg.tItgievlehsETpglgsk.............avkkdgg........dqevDaiSGATi 55 
                                       Gy ++ik++ +v d++  +I+g+evl ++ETpg gsk                            +++vDaiSGAT+
  gi|298675842|ref|YP_003727592.1|  94 GYDDDIKMAAAV-DTNFeKIYGMEVLRQAETPGKGSKitnaefknqfsnlP-----LdglalsqnSGNVDAISGATV 164
                                       9***********.66666****************99888866654444330.....044555555678********* PP

                                       HHHHHHHHHHH CS
                          FMN_bind  56 ssravkdavna 66 
                                       ss av++++n+
  gi|298675842|ref|YP_003727592.1| 165 SSSAVVTGLNN 175
                                       *******9998 PP

>> UPF0259  Uncharacterised protein family (UPF0259)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     5e-06     0.044      17      97 ..       6      86 ..       1      92 [. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5e-06
                           UPF0259 17 rnkiaailllsllsafitvlidsiilPnaeellilsilendkvinsgsssllelvqklsieqkkiLlklsiaktlssLi 95
                                      ++ i++i  l+l+sa+ + +++ ++ P++e+l i  + ++++ ++  + +  e+    s e+++++l++ + ++   Li
  gi|298675842|ref|YP_003727592.1|  6 KEIIVIIAKLVLISAVASAVLGATYVPTQEQLRIAEQRQTQETLSQLMPEAEEFEPVYSGENEEEVLYYQAYDSGGNLI 84
                                      3445566689*************************99999988888777888888888888888888888877777777 PP

                           UPF0259 96 gn 97
                                      g 
  gi|298675842|ref|YP_003727592.1| 85 GY 86
                                      75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1214.33
//
Query:       gi|298675843|ref|YP_003727593.1|  [L=311]
Description: NQR2 and RnfD family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-65  222.0  21.7    1.3e-65  221.7  21.7    1.1  1  NQR2_RnfD_RnfE  NQR2, RnfD, RnfE family
  ------ inclusion threshold ------
       0.28   11.0  13.7       0.31   10.8   0.4    2.8  2  PAP2            PAP2 superfamily
        4.8    7.4   7.8         15    5.8   2.0    2.5  2  DUF872          Eukaryotic protein of unknown function (DUF87


Domain annotation for each model (and alignments):
>> NQR2_RnfD_RnfE  NQR2, RnfD, RnfE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.7  21.7   2.2e-69   1.3e-65       2     292 .]       5     280 ..       4     280 .. 0.96

  Alignments for each domain:
  == domain 1  score: 221.7 bits;  conditional E-value: 2.2e-69
                    NQR2_RnfD_RnfE   2 vsssphvrdkestkrimldvliallpallfgvynfglqalllilvavvvavlaEvlfaklrkkevkvtdlsavvtgl 78 
                                       vs  ph +++ s+++  +  ++al+p +++++y+fgl +l  i+  +++a ++Ev++ ++  ++++v+d+ ++  g+
  gi|298675843|ref|YP_003727593.1|   5 VSPPPHKKTSFSVQNFIWYKIFALIPLVIVSIYFFGLPVLSHIIAGIFAAAAIEVVILRFLDQKITVNDGDVIFIGM 81 
                                       7889************************************************************************* PP

                    NQR2_RnfD_RnfE  79 LlalilPptlplwvvvigsvfaivvvKelfGGlGqNifNPAlvgrafllisfpaqmtwvaDavsgatpLaalksasl 155
                                       + al++P+ +p+w++++gs+fa+ ++K++fGG+G+  fNP l++++fl +++++ mt     + +   L+      l
  gi|298675843|ref|YP_003727593.1|  82 ITALVIPAGAPWWLPMLGSAFAVGFGKHIFGGIGSYSFNPVLAAWVFLSLAYSSYMT----PI-SVPQLG-----VL 148
                                       ********************************************************6....22.333455.....36 PP

                    NQR2_RnfD_RnfE 156 ldlflgniagsigetsalalllgglyLlvrkiiswripvsvlatvavlsllfnllaapplfhllsGglllgafFmat 232
                                        dl+l++ ag    +s l++l+ g+yL++rk+i+wr+p+s+++tv++l++l++      l   ++G+l+lg +F++t
  gi|298675843|ref|YP_003727593.1| 149 SDLILETGAGYPIGVSPLLILIPGIYLVMRKYIEWRVPLSFFVTVFALAYLAG-----HLSYAFTGALVLGGLFLIT 220
                                       78999999999999**************************************9.....58999************** PP

                    NQR2_RnfD_RnfE 233 dpvtspitkkGklifglliGlltvliRvfgaypeGvafaiLlmNllvplidkltrprnfg 292
                                       d +tspitk+G++i+g+++G+l+++  +f+ y  G+++  Ll+N++  +i++ t p++fg
  gi|298675843|ref|YP_003727593.1| 221 DTATSPITKNGRIIYGFIAGVLVFIYGFFSDYVAGTFYGLLLANAFSAFIENNTYPKPFG 280
                                       *********************************************************997 PP

>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.4   5.3e-05      0.31      90     134 ..      24      68 ..       8      70 .. 0.84
   2 ?    3.3   7.2     0.011        65      58     133 ..     200     272 ..     186     275 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.3e-05
                              PAP2  90 illllavlvalsRlylgvHflsDvlaGlliGialaalayrlvqkk 134
                                        +++l+ lv++s +++g   ls+++aG++ ++a+ +++ r+ ++k
  gi|298675843|ref|YP_003727593.1|  24 KIFALIPLVIVSIYFFGLPVLSHIIAGIFAAAAIEVVILRFLDQK 68 
                                       3566779*******************************9998765 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.011
                              PAP2  58 SgHsafafalalllalllrrkrkkiglvllalillllavlvalsRlylgvHflsDvlaGlliGialaalayrlvqk 133
                                        gH + af++al+l  l+      +   ++++  +++ +   ++ l++ + f+sD +aG+++G++la ++ ++ ++
  gi|298675843|ref|YP_003727593.1| 200 AGHLSYAFTGALVLGGLFLITDTAT-SPITKNGRIIYGFI--AGVLVFIYGFFSDYVAGTFYGLLLANAFSAFIEN 272
                                       5777777777777765554444442.56778888886655..556778888***************9988777666 PP

>> DUF872  Eukaryotic protein of unknown function (DUF872)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.4    0.0064        38      83     102 ..     165     184 ..     155     195 .. 0.87
   2 ?    5.8   2.0    0.0026        15      55      94 ..     213     251 ..     200     259 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0064
                            DUF872  83 GlllfiPGvYhvvyiylavr 102
                                        ll++iPG+Y v+  y+ +r
  gi|298675843|ref|YP_003727593.1| 165 PLLILIPGIYLVMRKYIEWR 184
                                       5899********99998887 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0026
                            DUF872  55 lGlvLlllgvvilvepseGvssavf.lvlGlllfiPGvYhv 94 
                                       lG + l++ ++  ++p + +   ++ +++G+l+fi G++  
  gi|298675843|ref|YP_003727593.1| 213 LGGLFLITDTA--TSPITKNGRIIYgFIAGVLVFIYGFFSD 251
                                       33333333333..4444555568999************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       810  (0.0451782); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 2487.33
//
Query:       gi|298675844|ref|YP_003727594.1|  [L=453]
Description: RnfABCDGE type electron transport complex subunit C [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-23   82.1   0.8    2.2e-23   82.1   0.8    2.1  2  RnfC_N        RnfC Barrel sandwich hybrid domain
    1.5e-16   60.6   0.0    2.4e-16   59.9   0.0    1.3  1  Complex1_51K  Respiratory-chain NADH dehydrogenase 51 Kd subu
    4.1e-08   33.7   8.6    1.1e-07   32.4   8.6    1.8  1  Fer4_7        4Fe-4S dicluster domain
    7.3e-08   32.3  10.1     0.0022   18.4   1.3    2.7  2  Fer4_4        4Fe-4S binding domain
      1e-07   31.7  12.5    0.00026   20.9   1.7    2.6  2  Fer4_6        4Fe-4S binding domain
    1.4e-07   31.5  12.4    1.2e-06   28.5  13.3    2.1  2  Fer4_10       4Fe-4S dicluster domain
      1e-06   28.8  11.9    3.8e-06   27.0  12.2    1.8  1  Fer4_9        4Fe-4S dicluster domain
    1.9e-05   24.2  15.5      0.011   15.5   4.0    2.6  2  Fer4          4Fe-4S binding domain
    3.9e-05   23.2   0.0    5.6e-05   22.7   0.0    1.2  1  NQRA          Na(+)-translocating NADH-quinone reductase subu
    9.6e-05   22.3  14.3      0.013   15.5   3.6    2.6  2  Fer4_2        4Fe-4S binding domain
    0.00012   22.5  24.4     0.0024   18.3   3.3    2.4  3  Fer4_8        4Fe-4S dicluster domain
    0.00017   22.4  13.5      0.066   14.2   3.9    2.7  2  Fer4_16       4Fe-4S double cluster binding domain
    0.00049   19.9   0.0    0.00098   19.0   0.0    1.6  1  SLBB          SLBB domain
     0.0012   18.9  14.6      0.045   13.9  14.8    2.7  3  Fer4_21       4Fe-4S dicluster domain
     0.0017   18.9  15.7      0.027   15.0  14.6    2.4  3  Fer4_17       4Fe-4S dicluster domain
     0.0038   18.1  15.9       0.46   11.5   4.8    2.8  2  Fer4_3        4Fe-4S binding domain
     0.0078   16.4  10.9       0.19   11.9   1.3    2.5  2  Fer4_18       4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.022   15.6   8.4        2.1    9.2   3.8    2.5  2  Fer4_22       4Fe-4S dicluster domain
       0.28   11.8  14.8        2.6    8.7   2.8    2.9  2  Fer4_13       4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> RnfC_N  RnfC Barrel sandwich hybrid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.1   0.8   2.4e-26   2.2e-23      21      99 ..       3      82 ..       1      85 [. 0.93
   2 ?   -1.8   0.0       3.2     3e+03      56      98 ..     305     349 ..     268     352 .. 0.60

  Alignments for each domain:
  == domain 1  score: 82.1 bits;  conditional E-value: 2.4e-26
                            RnfC_N 21 ieklp.lpkelvlplsqhiGapakplvkvgdkVlkGqkiaeaegfvsapvhasvsGtVkaiekrlvahgsgveavvien 98
                                      ie+l+ lp+++v+pl+qh G+ ++plv+vgd+V +Gqki+ea+++  +pvh+sv G+V+ai++  ++ gs++++++i++
  gi|298675844|ref|YP_003727594.1|  3 IETLNiLPEKMVIPLKQHTGEICEPLVDVGDTVITGQKIGEAKSYSDVPVHSSVCGEVTAIQDSHHPDGSKIKSIIIKP 81
                                      66665479*********************************************************************97 PP

                            RnfC_N 99 D 99
                                      +
  gi|298675844|ref|YP_003727594.1| 82 N 82
                                      5 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.2
                            RnfC_N  56 qkiaeaegfvsapvhasvsGtVkaiekrlvahg..sgveavvien 98 
                                       ++i + +g+    v     Gt + i++++   +  ++++ ++i++
  gi|298675844|ref|YP_003727594.1| 305 DVIEHLGGYRENSVKLIANGTMTGIAQYTDEVPviKTTTGITIQT 349
                                       455555555566666666777777777764443103455666665 PP

>> Complex1_51K  Respiratory-chain NADH dehydrogenase 51 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9   0.0   2.6e-19   2.4e-16       1     151 [.     105     268 ..     105     269 .. 0.93

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 2.6e-19
                      Complex1_51K   1 vkeagivGrGGagfPthvKlkakakkkkkylivNaaEcEPgltkDrllmreepheileGlkiaaealgaekgvigvr 77 
                                       +k+ag+v + G   P+h  l+++++ +++++i+Na+ +E +++ + + + + p+++le lk++ +a ga+kg i++ 
  gi|298675844|ref|YP_003727594.1| 105 IKDAGVVDYTGE--PIHSILQPENN-EIHTVIINATCSE-WMYGHFKSVSNSPEQLLEMLKLLIQASGASKGAIVLS 177
                                       79**********..**********8.89***********.99999999***************************** PP

                      Complex1_51K  78 dekpeaiealekalaeakaagl.................ldievvklagkYpaGeekaLiesltgrevprgkppadv 137
                                       ++++e+i+a+e+   + +  ++                  d  vv+ ++ Y    ++  ++ +tg ++++ k+p d+
  gi|298675844|ref|YP_003727594.1| 178 NDDEESIDAFERTTVDGNPVHVgplvgkrtidyyledmnSDRVVVSQDRIYGKNTQNLFTYFVTGCKLSPDKHPNDA 254
                                       ***********99555544445677888888889999999999********************************** PP

                      Complex1_51K 138 gvvvnNveTlaavy 151
                                       g++++ v++++a+y
  gi|298675844|ref|YP_003727594.1| 255 GIAICSVKSAKALY 268
                                       ***********998 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   8.6   1.1e-10   1.1e-07       2      50 ..     361     412 ..     360     430 .. 0.85

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 1.1e-10
                            Fer4_7   2 CigCgaCvaaCpvkaield..eeenekgtekv.eidpekClgCgaCvavCPt 50 
                                       Ci+C +Cv+ Cp++ +  +    +++ +++++ e++ ++C+ Cg+C+a CP+
  gi|298675844|ref|YP_003727594.1| 361 CIHCTKCVDICPMELVPSRlaILADQGRFDECrEMHVMNCIECGRCAAICPS 412
                                       **************9987622334444556664689***************8 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   2.0   3.9e-06    0.0037       4      16 ..     361     373 ..     356     376 .. 0.92
   2 !   18.4   1.3   2.3e-06    0.0022       3      16 ..     399     412 ..     398     419 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.9e-06
                            Fer4_4   4 CigCgsCvaaCPq 16 
                                       Ci+C +Cv++CP+
  gi|298675844|ref|YP_003727594.1| 361 CIHCTKCVDICPM 373
                                       ************7 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 2.3e-06
                            Fer4_4   3 rCigCgsCvaaCPq 16 
                                       +Ci+Cg+C a+CP+
  gi|298675844|ref|YP_003727594.1| 399 NCIECGRCAAICPS 412
                                       7************7 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   1.7   2.7e-07   0.00026       2      21 ..     354     373 ..     353     380 .. 0.89
   2 !   15.4   3.5   1.6e-05     0.015       8      21 ..     399     412 ..     399     416 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.7e-07
                            Fer4_6   2 veidpdkCigCgdCvrvCPe 21 
                                       ++++  +Ci+C +Cv++CP+
  gi|298675844|ref|YP_003727594.1| 354 PVYNTYPCIHCTKCVDICPM 373
                                       6788889************7 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.6e-05
                            Fer4_6   8 kCigCgdCvrvCPe 21 
                                       +Ci Cg+C+++CP 
  gi|298675844|ref|YP_003727594.1| 399 NCIECGRCAAICPS 412
                                       6************6 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5  13.3   1.3e-09   1.2e-06       3      56 .]     355     411 ..     353     411 .. 0.87
   2 !   16.0   2.7     1e-05    0.0097       8      24 ..     399     422 ..     394     447 .. 0.66

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.3e-09
                           Fer4_10   3 vidddtCirCgkCvkaCPadl...tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       v+++  Ci+C+kCv+ CP+ l   +     ++   +e  +  v +C++cg C+++CP
  gi|298675844|ref|YP_003727594.1| 355 VYNTYPCIHCTKCVDICPMELvpsRLAILADQGRFDECREMHVMNCIECGRCAAICP 411
                                       678889*************99887666777777888888999**************9 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1e-05
                           Fer4_10   8 tCirCgkCvkaCPadl.......t 24 
                                        Ci+Cg+C + CP++         
  gi|298675844|ref|YP_003727594.1| 399 NCIECGRCAAICPSKRhllqlnqY 422
                                       599999999999995544433330 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0  12.2     4e-09   3.8e-06       2      49 ..     361     413 ..     360     414 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 4e-09
                            Fer4_9   2 CtgCgaCveaC.....pagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                       C+ C++Cv+ C     p+ +++  +++r++++r+    +Ci+Cg+C+++Cp++
  gi|298675844|ref|YP_003727594.1| 361 CIHCTKCVDICpmelvPSRLAILADQGRFDECREMHVMNCIECGRCAAICPSK 413
                                       ***********444444455555566666666665559*************86 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   3.8   3.6e-05     0.034       2      20 ..     355     373 ..     354     375 .. 0.85
   2 !   15.5   4.0   1.2e-05     0.011       7      20 ..     399     412 ..     396     413 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.6e-05
                                       EEETTTSSS-THHHHHSTT CS
                              Fer4   2 videekCigCGaCvevCPv 20 
                                       v+++  Ci+C +Cv++CP 
  gi|298675844|ref|YP_003727594.1| 355 VYNTYPCIHCTKCVDICPM 373
                                       567777************6 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.2e-05
                                       TSSS-THHHHHSTT CS
                              Fer4   7 kCigCGaCvevCPv 20 
                                        Ci CG+C+ +CP 
  gi|298675844|ref|YP_003727594.1| 399 NCIECGRCAAICPS 412
                                       6************5 PP

>> NQRA  Na(+)-translocating NADH-quinone reductase subunit A (NQRA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   5.9e-08   5.6e-05      44     128 ..      28     111 ..       9     197 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 5.9e-08
                              NQRA  44 kvkegdkVkkGqvlfedKknpgvlftspasGevveinrGek...Rvlqsvvievdgdeeeefekfskkelaslsree 117
                                       +v +gd+V +Gq + e K+ ++v + s + Gev++i+  +     +++s++i+ +  ++ee  ++s   l++ ++++
  gi|298675844|ref|YP_003727594.1|  28 LVDVGDTVITGQKIGEAKSYSDVPVHSSVCGEVTAIQDSHHpdgSKIKSIIIKPN--DSEESVNYS--PLENPTQSQ 100
                                       799*********************************9876533368*******99..444444444..467777777 PP

                              NQRA 118 vkeqLlksGlw 128
                                       + +++ ++G+ 
  gi|298675844|ref|YP_003727594.1| 101 LISRIKDAGVV 111
                                       77777777765 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   3.6   1.4e-05     0.013       3      21 ..     354     372 ..     352     373 .. 0.92
   2 !   11.8   3.0   0.00022      0.21       9      21 ..     399     411 ..     394     412 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.4e-05
                            Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                       +v++t  Ci+C +Cv+ CP
  gi|298675844|ref|YP_003727594.1| 354 PVYNTYPCIHCTKCVDICP 372
                                       899**************** PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00022
                            Fer4_2   9 rCigCgaCvsaCP 21 
                                       +Ci+Cg C   CP
  gi|298675844|ref|YP_003727594.1| 399 NCIECGRCAAICP 411
                                       6*******999** PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   3.1    0.0033       3.1      49      63 ..     359     373 ..     334     375 .. 0.71
   2 !   18.0  13.2     3e-06    0.0029       4      64 ..     360     413 ..     357     413 .. 0.88
   3 !   18.3   3.3   2.6e-06    0.0024       2      34 ..     397     429 ..     396     450 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0033
                            Fer4_8  49 wsCttcgaCtevCpv 63 
                                       + C +c +C++ Cp+
  gi|298675844|ref|YP_003727594.1| 359 YPCIHCTKCVDICPM 373
                                       455555555555554 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 3e-06
                            Fer4_8   4 kCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                        Ci+C  C + Cp+     +    a +++ + + +e++      + +C +cg+C+  Cp +
  gi|298675844|ref|YP_003727594.1| 360 PCIHCTKCVDICPMELVPSRLAILADQGRFD-ECREMH------VMNCIECGRCAAICPSK 413
                                       6************999999888888888888.677777......79*************75 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 2.6e-06
                            Fer4_8   2 lekCieCgaCqsaCpvlrrtkkhlldargeaae 34 
                                       +++CieCg+C + Cp+ r+  + +++a++    
  gi|298675844|ref|YP_003727594.1| 397 VMNCIECGRCAAICPSKRHLLQLNQYAKEAIRR 429
                                       579************988887777766665444 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   2.1   0.00018      0.17       2      16 ..     361     375 ..     360     395 .. 0.84
   2 !   14.2   3.9     7e-05     0.066       1      30 [.     399     430 ..     399     449 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00018
                           Fer4_16   2 CgtCgkCaevCPtna 16 
                                       C+ C+kC+++CP + 
  gi|298675844|ref|YP_003727594.1| 361 CIHCTKCVDICPMEL 375
                                       ************876 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 7e-05
                           Fer4_16   1 rCgtCgkCaevCPtnaikek..kekeiearec 30 
                                       +C++Cg+Ca +CP++    +  ++++ ++r++
  gi|298675844|ref|YP_003727594.1| 399 NCIECGRCAAICPSKRHLLQlnQYAKEAIRRS 430
                                       6************9874444113333333333 PP

>> SLBB  SLBB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0     1e-06   0.00098      14      58 .]     295     330 ..     281     330 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1e-06
                                       EEEETT-BHHHHHHTTT-SBSS.........-EEEE-SSSSS--E CS
                              SLBB  14 yevpigttlsdlieqaGGltddadlksvnLarlavipgGpmmgil 58 
                                         v+ gt ++d+ie+ GG+ ++           ++i +G+m+gi+
  gi|298675844|ref|YP_003727594.1| 295 ELVKVGTLFKDVIEHLGGYRENSV---------KLIANGTMTGIA 330
                                       5699********************.........8899******95 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   3.0   0.00014      0.13      25      53 ..     344     373 ..     339     378 .. 0.76
   2 !   13.9  14.8   4.7e-05     0.045       7      53 ..     360     412 ..     355     418 .. 0.73
   3 !   11.7   3.1   0.00023      0.22       5      23 ..     397     415 ..     393     447 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                           Fer4_21  25 aieidaktvlkvv.edeCvGCnlCssvCPv 53 
                                        i+i+++  l+v  +  C+ C+ C+++CP+
  gi|298675844|ref|YP_003727594.1| 344 GITIQTEDELPVYnTYPCIHCTKCVDICPM 373
                                       577777778888536789999999999997 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 4.7e-05
                           Fer4_21   7 kCigCgkCliaCedt...shqaieidaktvl...kvvedeCvGCnlCssvCPv 53 
                                        Ci+C+kC+  C+ +   s  ai  d+ +     ++   +C+ C  C+++CP 
  gi|298675844|ref|YP_003727594.1| 360 PCIHCTKCVDICPMElvpSRLAILADQGRFDecrEMHVMNCIECGRCAAICPS 412
                                       6***********9642226678866655543111455679************5 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00023
                           Fer4_21   5 edkCigCgkCliaCedtsh 23 
                                         +Ci+Cg+C+  C+ + h
  gi|298675844|ref|YP_003727594.1| 397 VMNCIECGRCAAICPSKRH 415
                                       568***********96544 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   1.5   9.7e-05     0.092      41      60 ..     356     375 ..     330     376 .. 0.78
   2 !   15.0  14.6   2.8e-05     0.027       2      58 ..     361     412 ..     360     415 .. 0.79
   3 !   10.7   5.4   0.00063      0.59       1      45 [.     399     445 ..     399     451 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.7e-05
                           Fer4_17  41 ekaslCieCgeCerkCPqgl 60 
                                        +   Ci+C +C+  CP++l
  gi|298675844|ref|YP_003727594.1| 356 YNTYPCIHCTKCVDICPMEL 375
                                       46778************997 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.8e-05
                           Fer4_17   2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPq 58 
                                       Ci+C  C++ Cp+    + + + l+ +   g+++e  +e+ + +CieCg+C++ CP+
  gi|298675844|ref|YP_003727594.1| 361 CIHCTKCVDICPMELVPS-RLAILADQ---GRFDEC-REMHVMNCIECGRCAAICPS 412
                                       ************987733.34555555...888885.5567788************8 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00063
                           Fer4_17   1 rCiqCgyClpeCpsyea...ydnepkkllraaklglleeaekeekasl 45 
                                       +Ci+Cg C++ Cps +     +++ k+ +r+ ++++ +  e+++++ l
  gi|298675844|ref|YP_003727594.1| 399 NCIECGRCAAICPSKRHllqLNQYAKEAIRR-SYEDYQPKEESSNVTL 445
                                       6999999999999977654333344444444.3444444444444433 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   4.8   0.00049      0.46       1      12 [.     361     372 ..     361     374 .. 0.96
   2 !   11.3   3.3   0.00058      0.55       1      14 [.     400     413 ..     400     413 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00049
                            Fer4_3   1 CtgCgaCvevCP 12 
                                       C++C  Cv+ CP
  gi|298675844|ref|YP_003727594.1| 361 CIHCTKCVDICP 372
                                       ************ PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00058
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       C+ Cg+C   CP++
  gi|298675844|ref|YP_003727594.1| 400 CIECGRCAAICPSK 413
                                       ************85 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   1.3    0.0002      0.19      46      74 ..     346     374 ..     322     382 .. 0.81
   2 !    9.1   2.5    0.0015       1.4      51      74 ..     390     413 ..     376     423 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                           Fer4_18  46 alkekeerkekgagdcidcescvkvcPtg 74 
                                       ++++++e    ++  ci+c +cv++cP++
  gi|298675844|ref|YP_003727594.1| 346 TIQTEDELPVYNTYPCIHCTKCVDICPME 374
                                       556666666777888***********987 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0015
                           Fer4_18  51 eerkekgagdcidcescvkvcPtg 74 
                                       +e +e  + +ci+c+ c ++cP +
  gi|298675844|ref|YP_003727594.1| 390 DECREMHVMNCIECGRCAAICPSK 413
                                       6677888999************75 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1    0.0051       4.8      76      95 ..     355     374 ..     333     375 .. 0.76
   2 ?    9.2   3.8    0.0022       2.1      77      94 ..     395     412 ..     386     414 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0051
                           Fer4_22  76 kfgesgCvGCgRCieacpvk 95 
                                        ++++ C+ C +C++ cp++
  gi|298675844|ref|YP_003727594.1| 355 VYNTYPCIHCTKCVDICPME 374
                                       56777888888888888865 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0022
                           Fer4_22  77 fgesgCvGCgRCieacpv 94 
                                       ++ + C+ CgRC + cp+
  gi|298675844|ref|YP_003727594.1| 395 MHVMNCIECGRCAAICPS 412
                                       567789999999999986 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   2.8    0.0028       2.6       6      17 ..     361     372 ..     357     375 .. 0.92
   2 ?    7.5   4.3    0.0062       5.9       5      18 ..     399     412 ..     398     413 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0028
                           Fer4_13   6 CiacgaCvelaP 17 
                                       Ci c++Cv+++P
  gi|298675844|ref|YP_003727594.1| 361 CIHCTKCVDICP 372
                                       ************ PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0062
                           Fer4_13   5 tCiacgaCvelaPd 18 
                                       +Ci+cg C++++P 
  gi|298675844|ref|YP_003727594.1| 399 NCIECGRCAAICPS 412
                                       6************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3033.04
//
Query:       gi|298675845|ref|YP_003727595.1|  [L=519]
Description: hypothetical protein Metev_1969 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.5e-06   25.9  33.2     0.0011   18.9   0.8    5.1  3  Cytochrome_C7   Cytochrome c7 and related cytochrome c
     0.0022   18.4   0.5     0.0022   18.4   0.5    5.1  4  Cytochrom_c3_2  Cytochrome c3
  ------ inclusion threshold ------
      0.064   12.8   0.0       0.13   11.9   0.0    1.5  1  EF-hand_5       EF hand
       0.19   11.4  27.7       0.36   10.5   7.3    5.3  5  Cytochrom_NNT   NapC/NirT cytochrome c family, N-terminal reg


Domain annotation for each model (and alignments):
>> Cytochrome_C7  Cytochrome c7 and related cytochrome c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.6   0.00035       1.6      14      60 ..      46     126 ..      33     154 .. 0.65
   2 ?    2.4  18.7     0.034   1.5e+02       8      72 ..     219     281 ..     177     286 .. 0.70
   3 !   18.9   0.8   2.5e-07    0.0011      13      59 ..     440     475 ..     426     491 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00035
                     Cytochrome_C7  14 ykCtdCHskl.f.eska.kkk..maemekgkskkaeveslt...............................CgaCH 54 
                                         C  CH ++     ++ +++  + +++++k +  + +  +                               C+ CH
  gi|298675845|ref|YP_003727595.1|  46 SVCGGCHYNAdLnPLANdAEQsyHVQTDMDKWNPLDNF--HiseqgkdawvkefgpqhpgggplkeygvdldCMVCH 120
                                       56888998884332222112223333333333333333..1345677788888888888888888888888899999 PP

                     Cytochrome_C7  55 dgknaf 60 
                                       d++ + 
  gi|298675845|ref|YP_003727595.1| 121 DQTGEY 126
                                       988765 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.034
                     Cytochrome_C7   8 hlkatgykCtdCHsklfeska.kkkmaemekgkskkaevesltCga..CHdgknaf....svakkaeCakCH 72 
                                       h+   + +C +CH+++ e++  +++m + ++        e  +C++  CH+g  +     ++ +  +C++CH
  gi|298675845|ref|YP_003727595.1| 219 HA---EESCMECHETI-EHQIgSSTMPAAQEV-----GAEVQSCQSsgCHEGISHGgtvdAHLEFLDCKSCH 281
                                       43...46899999999.222222223332211.....22224466555998877755566888999*****9 PP

  == domain 3  score: 18.9 bits;  conditional E-value: 2.5e-07
                     Cytochrome_C7  13 gykCtdCHsklfeskakkkmaemekgkskkaeves.ltCgaCHdgkna 59 
                                         +C+dCH+               ++ ++++++++ ++C++CHd+k a
  gi|298675845|ref|YP_003727595.1| 440 PLECDDCHGVS------------RTNALQNIHFNQsRDCTTCHDKKPA 475
                                       45677777776............1233445566666778888877765 PP

>> Cytochrom_c3_2  Cytochrome c3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   2.0     0.018        79      28      46 ..     110     133 ..      34     161 .. 0.62
   2 ?   -0.2  18.2      0.32   1.4e+03       8      79 ..     191     281 ..     186     282 .. 0.62
   3 ?    3.9   3.4     0.017        75       9      35 ..     255     283 ..     248     293 .. 0.74
   4 !   18.4   0.5   4.9e-07    0.0022       7      40 ..     441     477 ..     437     496 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.018
                                       H.....HHHHH--HHHCHTTSST. CS
                    Cytochrom_c3_2  28 k.....ClsCHgkleelakktkea 46 
                                             C+ CH+++ e++  ++ +
  gi|298675845|ref|YP_003727595.1| 110 YgvdldCMVCHDQTGEYNFDERAE 133
                                       044444888888888777665543 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.32
                                       TGGG.TSSSST-SSTTHHHHHH...........HHHHH--HHHCHTTSST.TSSBTTSSCTSSS-GGGTS-TTT..S CS
                    Cytochrom_c3_2   8 kCad.CHtkekpkkdkaveeek...........ClsCHgkleelakktkeakeanphkshekeleCteCHkeHk..k 70 
                                       +C++ CH+++ +k+  +  +e+           C++CH++ e+   +++    a++  +  ++ + + CH++ +   
  gi|298675845|ref|YP_003727595.1| 191 SCEEyCHSDQVVKTGVNWADEDysecdvhaeesCMECHETIEHQIGSSTM-PAAQEVGAEVQSCQSSGCHEGIShgG 266
                                       565338887776655555555566777777777*******9987776664.33333334446666778998644333 PP

                                       BT......-GGGGT- CS
                    Cytochrom_c3_2  71 se......kvCaeCH 79 
                                       ++        C++CH
  gi|298675845|ref|YP_003727595.1| 267 TVdahlefLDCKSCH 281
                                       334445567899999 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.017
                                       GGGTSS..SST-SSTTHHHHHHHHHHH-- CS
                    Cytochrom_c3_2   9 CadCHt..kekpkkdkaveeekClsCHgk 35 
                                        + CH+  ++  + d++ e  +C+sCH +
  gi|298675845|ref|YP_003727595.1| 255 SSGCHEgiSHGGTVDAHLEFLDCKSCHVT 283
                                       34599876666677889999999999976 PP

  == domain 4  score: 18.4 bits;  conditional E-value: 4.9e-07
                                       .TGGGTSSSST-SSTTHHHHHH...HHHHH--HHHCH CS
                    Cytochrom_c3_2   7 vkCadCHtkekpkkdkaveeek...ClsCHgkleela 40 
                                       ++C+dCH+ +++++ ++++ ++   C++CH+k+ +++
  gi|298675845|ref|YP_003727595.1| 441 LECDDCHGVSRTNALQNIHFNQsrdCTTCHDKKPAMD 477
                                       79******77766666555444444******998776 PP

>> EF-hand_5  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.8e-05      0.13       6      24 ..     385     403 ..     385     404 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.8e-05
                                       HHH-SS-SSCE-HHHHHHH CS
                         EF-hand_5   6 qaiDlNgDGkIskeELktl 24 
                                       +++D NgDG ++  E + +
  gi|298675845|ref|YP_003727595.1| 385 RQADSNGDGNVTQKEMRSF 403
                                       79*************9987 PP

>> Cytochrom_NNT  NapC/NirT cytochrome c family, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.052   2.3e+02      27      59 ..      36      71 ..       2      87 .. 0.63
   2 ?    0.7   0.1     0.081   3.6e+02     125     142 ..     113     131 ..     108     147 .. 0.68
   3 ?   10.5   7.3     8e-05      0.36     107     169 ..     203     264 ..     187     269 .. 0.72
   4 ?   -0.1   0.1      0.15   6.6e+02      68      74 ..     277     283 ..     272     291 .. 0.67
   5 ?    4.4   5.3     0.006        27     114     140 ..     452     479 ..     443     489 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.052
                     Cytochrom_NNT 27 ntaleatsteeFCvsCHemedn...veeykesiHys 59
                                      +++++   +e+ C  CH   d    +++ ++s H++
  gi|298675845|ref|YP_003727595.1| 36 HYMIDGRWSESVCGGCHYNADLnplANDAEQSYHVQ 71
                                      445555567778888887554323467777777776 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.081
                     Cytochrom_NNT 125 sreCrnCHsee.amdlekq 142
                                       + +C+ CH+++ + +++++
  gi|298675845|ref|YP_003727595.1| 113 DLDCMVCHDQTgEYNFDER 131
                                       4568888877655555544 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 8e-05
                     Cytochrom_NNT 107 akrlelaerewarmkandsreCrnCHseeamdlekqkkkaakahkkaaeeektCid..CHkgiaH 169
                                       +   ++a++ +++   + ++ C++CH++++ ++ + +  aa++     +e ++C +  CH+gi H
  gi|298675845|ref|YP_003727595.1| 203 KTGVNWADEDYSECDVHAEESCMECHETIEHQIGSSTMPAAQEV---GAEVQSCQSsgCHEGISH 264
                                       555678999999999999999******99888866666655544...44445554333*****99 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.15
                     Cytochrom_NNT  68 CsdCHvP 74 
                                       C++CHv 
  gi|298675845|ref|YP_003727595.1| 277 CKSCHVT 283
                                       5555554 PP

  == domain 5  score: 4.4 bits;  conditional E-value: 0.006
                     Cytochrom_NNT 114 erewarmkandsreCrnCHsee.amdle 140
                                       +++ ++++ n+sr+C +CH+++ amd +
  gi|298675845|ref|YP_003727595.1| 452 TNALQNIHFNQSRDCTTCHDKKpAMDWA 479
                                       67789999************99888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (519 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       746  (0.0416086); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 3164.10
//
Query:       gi|298675846|ref|YP_003727596.1|  [L=135]
Description: hypothetical protein Metev_1970 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 799.88
//
Query:       gi|298675847|ref|YP_003727597.1|  [L=341]
Description: ApbE family lipoprotein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.4e-78  262.4   0.1    5.1e-78  262.2   0.1    1.0  1  ApbE        ApbE family
  ------ inclusion threshold ------
       0.22   11.6   4.3       0.55   10.2   1.0    2.5  2  Cadherin_3  Cadherin-like


Domain annotation for each model (and alignments):
>> ApbE  ApbE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  262.2   0.1   5.7e-82   5.1e-78       1     257 [.      47     322 ..      47     323 .. 0.89

  Alignments for each domain:
  == domain 1  score: 262.2 bits;  conditional E-value: 5.7e-82
                                       TTEEEEEEEE..........HHHHHHHHHHHHHHHC-SS-TTSHHHHHHCTSS-EEE-HHHHHHHHHHHHHHHHTTT CS
                              ApbE   1 mgttvsitlyg.........leaaieaelerlekllsryrpdSelsrlNrakkevkvspelaellkaaleiseltdg 68 
                                       m+ttv+i++ +         + ++ ++e++ ++k++s+y+++S+ls+lN+++   ++sp++++++k+ +++++ ++g
  gi|298675847|ref|YP_003727597.1|  47 MDTTVTIHIKDnnkthakkvI-DETFSEINSVDKMMSSYKNNSQLSKLNNNGFVKNASPDFLHVIKKTKHYYNVSNG 122
                                       9*******9734455644433.555599999******************995556999******************* PP

                                       SS-TTTHHHHHHHC..TTSG.G.----HHHHHHHHTT.-GGGEEE.....EESTT..-----TTTHHHHHHHHHHHH CS
                              ApbE  69 afdptvgplvklwg..fgee.karvpsaeeidaalalvgykkiel.....lakkgpgmkLDlggiaKGyavdrvael 137
                                       afd+tv+p+++lw+  f ++  ++ ps++ei++ l+lv+ ++i++       kk+  m + lgg+aKG+avd++++ 
  gi|298675847|ref|YP_003727597.1| 123 AFDVTVKPILDLWEkkFAPGgPQKPPSEKEINKTLKLVNNSNITIensniSIKKD--MGIVLGGVAKGFAVDEAIKS 197
                                       *************844555534477******************999999644445..******************** PP

                                       HHH.TT-EEEEEETTEEEEEC..-ECT-EEEEEE-TTS..SEEEEEEESSSEEEEEETTSSEEE.TEEEES-B-TTT CS
                              ApbE 138 lka.giksalvnlGGdiralG..pdgkpwrvgiedPra..ellavlslsddavaTSGdyeryfe.gkryhHiidprt 208
                                       lk+ gi++++vn+GGd r +G  +d+k w+vg+++P++  ++++v+++++ avaTSG+yery++ +  ++Hi dprt
  gi|298675847|ref|YP_003727597.1| 198 LKNsGIENGFVNAGGDGRYIGykNDNKSWKVGLRNPNKtgDAITVMNINNMAVATSGNYERYYNkSASVSHISDPRT 274
                                       **********************88889*********94578999*****77************7688********** PP

                                       SSB---SECEEEEEESC.HHHHHHHHHHHHHHHHHHHHHHCCGGGTCTEE CS
                              ApbE 209 gyPaesglasvtViads.alADalaTalfvlgeekalellekkeegveal 257
                                       gyP  ++++s tVia++ ++ADa++Ta+fvlge+k+le++e+  ++ve+l
  gi|298675847|ref|YP_003727597.1| 275 GYPS-RKIISSTVIAETaMDADAYSTAIFVLGEDKGLEMIEQ-LDNVECL 322
                                       ****.8********9755***********************6.5679987 PP

>> Cadherin_3  Cadherin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.0   6.2e-05      0.55       6      50 ..      17      61 ..      14      72 .. 0.81
   2 ?    1.6   0.1     0.029   2.6e+02      23      45 ..     153     175 ..     145     178 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 6.2e-05
                        Cadherin_3  6 tleitikpvndeaPvlttntglrvlegsskvit.tenLsaeDeDtp 50
                                      +++i+i + nd++Pv+ +n +l+ +++s+++++ t +++++D++++
  gi|298675847|ref|YP_003727597.1| 17 IVSISIST-NDNQPVVENNDTLQSFQESRSLMDtTVTIHIKDNNKT 61
                                      56777765.999**************99999973567888888765 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.029
                        Cadherin_3  23 tntglrvlegsskvittenLsae 45 
                                       +n++l+++++s+ +i+++n+s++
  gi|298675847|ref|YP_003727597.1| 153 INKTLKLVNNSNITIENSNISIK 175
                                       6899**************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       979  (0.0546043); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2557.45
//
Query:       gi|298675848|ref|YP_003727598.1|  [L=181]
Description: 2'-5' RNA ligase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.6e-27   93.5   0.0    8.3e-17   61.2   0.0    2.0  2  LigT_PEase       LigT like Phosphoesterase
      2e-11   44.0   0.0    2.3e-11   43.8   0.0    1.1  1  2_5_RNA_ligase2  2'-5' RNA ligase superfamily
    6.4e-07   29.5   0.1    8.2e-07   29.1   0.1    1.2  1  AKAP7_NLS        AKAP7 2'5' RNA ligase-like domain
     0.0022   17.5   0.1     0.0037   16.8   0.1    1.4  1  HVSL             Uncharacterised conserved protein
  ------ inclusion threshold ------
      0.046   13.3   0.0      0.074   12.6   0.0    1.4  1  AAA_25           AAA domain


Domain annotation for each model (and alignments):
>> LigT_PEase  LigT like Phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2   0.0   2.3e-20   8.3e-17       2      87 .]       9      88 ..       8      88 .. 0.96
   2 !   30.7   0.0   7.6e-11   2.7e-07      12      87 .]      96     172 ..      90     172 .. 0.92

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 2.3e-20
                                      E-CHHHHHHHHHHHHHHHHHHCCTTEEETSGGGSEEEEEEEEEESHHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEEC CS
                        LigT_PEase  2 gppeeiaeelarlaaeleralaklglkpvrpfnpHiTLaflgevdeekvpellealaeiasgaepfelkvdgvglfpsr 80
                                      + pee  e++a+++++++    ++++k+v p+ +HiTL+flg+v++++++e+ ++l++i     pf+ +++ +g+fp +
  gi|298675848|ref|YP_003727598.1|  9 DFPEEYHEKIAEIQSRFR----DFKVKMVNPELVHITLKFLGDVEDDQIQEIAKSLDNI--DCGPFHATIENIGVFPKP 81
                                      679999************....99***********************************..788*************** PP

                                      CSCCEEE CS
                        LigT_PEase 81 lrprviy 87
                                      ++p v++
  gi|298675848|ref|YP_003727598.1| 82 KYPKVVW 88
                                      *****99 PP

  == domain 2  score: 30.7 bits;  conditional E-value: 7.6e-11
                                       HHHHHHHHHHHCCTTEEET.SGGGSEEEEEEEEEES...HHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEECC.SC CS
                        LigT_PEase  12 arlaaeleralaklglkpv.rpfnpHiTLaflgevd...eekvpellealaeiasgaepfelkvdgvglfpsrl.rp 83 
                                         l++++ + l+++++k + ++f  H T+a+++  +   ++ + + le+l++i+ g+    + vd v l +s+l ++
  gi|298675848|ref|YP_003727598.1|  96 KTLHDNVNSVLKDFNFKEDnKKFSAHATIARVKHLSkndKDLFLKTLEELEGIEIGT----MWVDTVKLKKSTLtPQ 168
                                       67889999999**********************99988888888999******8886....**************** PP

                                       CEEE CS
                        LigT_PEase  84 rviy 87 
                                       +++y
  gi|298675848|ref|YP_003727598.1| 169 GPVY 172
                                       **99 PP

>> 2_5_RNA_ligase2  2'-5' RNA ligase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.0   6.5e-15   2.3e-11       2     136 ..      11     148 ..      10     164 .. 0.82

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 6.5e-15
                   2_5_RNA_ligase2   2 ppslaapiealr...rslydkayprwppHitLlypfvededl.adlaellsrlaketepfevrldgfgvFeh.kks. 72 
                                       p++  ++i++++   r +  k ++   +HitL+++++ ++d  +++a+ l ++  ++ pf ++++++gvF+  k   
  gi|298675848|ref|YP_003727598.1|  11 PEEYHEKIAEIQsrfRDFKVKMVNPELVHITLKFLGDVEDDQiQEIAKSLDNI--DCGPFHATIENIGVFPKpKYPk 85 
                                       667777888888666666677788888*********99998778888888888..799**************98889 PP

                   2_5_RNA_ligase2  73 vvylsvsdsealqalraallealpeagdkedsgeftPHlTiaqsadstsa.aelleklaqalppl 136
                                       vv+l +  + +++ l++ + + l+    ked ++f  H+Tia+ ++     ++l+ k  ++l+ +
  gi|298675848|ref|YP_003727598.1|  86 VVWLGA--EGDFKTLHDNVNSVLKDFNFKEDNKKFSAHATIARVKHLSKNdKDLFLKTLEELEGI 148
                                       ******..9*********************************98876665666666554555544 PP

>> AKAP7_NLS  AKAP7 2'5' RNA ligase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.1   2.3e-10   8.2e-07      24     206 ..      20     179 ..       6     180 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 2.3e-10
                                       HHHHH-GGGGGGB.--TT--EEEEEEE---SHHHHHHHHHHHHHHHHHHHHHHTTS--EEEEEEEEEE.....TTTE CS
                         AKAP7_NLS  24 svlsklpgldeslfikpeklHlTllvlkLknkeeiaaakevLkevkeeikdaldnkplslrlkGletfnddpakarV 100
                                       ++ s +++ + ++ ++pe  H+Tl  l   ++++i++ ++ L ++       +   p++ +++ +++f  +p+  +V
  gi|298675848|ref|YP_003727598.1|  20 EIQSRFRDFKVKM-VNPELVHITLKFLGDVEDDQIQEIAKSLDNID------C--GPFHATIENIGVF-PKPKYPKV 86 
                                       4555777788889.999**********9999999999999999984......4..9************.79999*** PP

                                       EEEEE--SHHHHHHHHHHHHHHHHHHTTT--B--SS-.---EEEEEEGGG-THHHHTT--S--GG.GGGGGTT-EEE CS
                         AKAP7_NLS 101 lYakveeesneekLqeladriikafeeaglvlekdkkkvklHaTlmnsrkrkkkqakskesfdareilkqfkdfefg 177
                                       ++++ e     + +++l+d ++  +++ +++  +d+kk+  HaT++ +++ +k+ +       + + l++ +  e g
  gi|298675848|ref|YP_003727598.1|  87 VWLGAE-----GDFKTLHDNVNSVLKDFNFK--EDNKKFSAHATIARVKHLSKNDKDL-----FLKTLEELEGIEIG 151
                                       *****8.....56677777777777665654..445559***********99877632.....23468888888888 PP

                                       EEE--EEEEEESSS---TTS--EEEEEEE CS
                         AKAP7_NLS 178 eekineihLsqlesddesdgyYkviasvk 206
                                       +  + +++L + + + +    Y+++ +vk
  gi|298675848|ref|YP_003727598.1| 152 TMWVDTVKLKKSTLTPQ-GPVYETLHEVK 179
                                       88888888888888877.77888887776 PP

>> HVSL  Uncharacterised conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1     1e-06    0.0037      82     229 ..      31     161 ..       4     165 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1e-06
                              HVSL  82 dlgaplplHiSLSrplvlrthqkdsfldslkkelkssakrrFevsfsglkwvsndektRsFlvlrvkspendeLkkl 158
                                       ++  p+  Hi+L     ++ +q++++ +sl +        +F+ +++++ +++ ++  ++   + +    +  +k+l
  gi|298675848|ref|YP_003727598.1|  31 KMVNPELVHITLKFLGDVEDDQIQEIAKSLDNI----DCGPFHATIENIGVFPKPKYPKVV--W-LG--AEGDFKTL 98 
                                       556666677776666666666666665555432....335788888888888877777752..2.22..23579*** PP

                              HVSL 159 leavnkvleefglpplykdeaFHiSiawslgepseeekeellselekaledaekeeelkqleikveevkvk 229
                                        ++vn+vl++f+ ++  k+ + H  ia   +  s++ k+ +l++le       ++e ++  ++ v++vk+k
  gi|298675848|ref|YP_003727598.1|  99 HDNVNSVLKDFNFKEDNKKFSAHATIARVKHL-SKNDKDLFLKTLE-------ELEGIEIGTMWVDTVKLK 161
                                       ***************************88774.3444443433332.......244555555555666655 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.1e-05     0.074      69     105 ..      81     117 ..      68     159 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.1e-05
                            AAA_25  69 peqgkVlyvsaEdsedelrrRlravgealrddarllv 105
                                       p+  kV+++ aE++ ++l+  +  v+++++++++   
  gi|298675848|ref|YP_003727598.1|  81 PKYPKVVWLGAEGDFKTLHDNVNSVLKDFNFKEDNKK 117
                                       6788*************************55444322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1143.78
//
Query:       gi|298675849|ref|YP_003727599.1|  [L=293]
Description: hypothetical protein Metev_1973 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-21   75.9   1.7    5.4e-21   74.4   0.3    2.2  2  DisA_N    DisA bacterial checkpoint controller nucleotide-bin
  ------ inclusion threshold ------
       0.89    9.4   4.9       0.49   10.3   0.1    2.9  4  YmgB      Biofilm development protein YmgB/AriR


Domain annotation for each model (and alignments):
>> DisA_N  DisA bacterial checkpoint controller nucleotide-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1      0.07   6.2e+02      89     106 ..      10      27 ..       8      32 .. 0.88
   2 !   74.4   0.3     6e-25   5.4e-21       3     118 ..     150     275 ..     148     276 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.07
                                       HHHHHHHHSSSEEEEE-T CS
                            DisA_N  89 aAlgiseetdalvivVSe 106
                                       +Al ++e+ +a +i+VS 
  gi|298675849|ref|YP_003727599.1|  10 TALDLAEKLEAEAIIVSG 27 
                                       899*************95 PP

  == domain 2  score: 74.4 bits;  conditional E-value: 6e-25
                                       HHHHHHHHT--EEEEEESSSC............CCTTCCTSEEEEEE--HHHHHHHTSTTSTTCSSEEEE.ETTEEE CS
                            DisA_N   3 aveelskkkiGaliviereee............lkeiietgvkldaevskellkeifekksplhDGAvii.rdgriv 66 
                                       a++++++++iG+ ++i++ +e                 +   ++ ++ ++e +ke+     +++DG +++ +dg i 
  gi|298675849|ref|YP_003727599.1| 150 AATGREGSQIGTAFIIGDVDEvmsrshqmilnpYAGHSKPNRDILNKQNWESIKEF-----SQLDGVFVVsEDGVIE 221
                                       78899****************88887777643323444677788899999999999.....*********88***** PP

                                       EEEEEE--.TT-TTS.ST-SHHHHHHHHHHHHSSSEEEEE-TTTS-EEEEETTE CS
                            DisA_N  67 aagviLpl.senkel.kelGtRHraAlgiseetdalvivVSeetgkislakdgk 118
                                       aag +L++ +++  + k+lG RH +A++i+++t a++i+VSe+ g ++++kdgk
  gi|298675849|ref|YP_003727599.1| 222 AAGKYLDVdAKDLVInKGLGGRHVSAAAITRDTVAIAITVSESGGIVRVYKDGK 275
                                       ********666666677***********************************97 PP

>> YmgB  Biofilm development protein YmgB/AriR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2      0.15   1.4e+03      27      44 ..      12      29 ..       2      30 .. 0.71
   2 ?   -3.8   0.0       1.4   1.2e+04      23      31 ..      48      56 ..      48      58 .. 0.81
   3 ?   10.3   0.1   5.4e-05      0.49       3      35 ..      66      98 ..      64     102 .. 0.92
   4 ?   -2.4   0.0      0.48   4.3e+03      29      50 ..     123     144 ..     122     146 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.15
                                      HHHHHHHHT---HHHHHH CS
                              YmgB 27 lkLiekLEsesdvvqldv 44
                                      l L ekLE e+ +v+ d+
  gi|298675849|ref|YP_003727599.1| 12 LDLAEKLEAEAIIVSGDI 29
                                      467889999988887776 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 1.4
                                      HHHHHHHHH CS
                              YmgB 23 KaIIlkLie 31
                                      K II +L++
  gi|298675849|ref|YP_003727599.1| 48 KSIIDYLVS 56
                                      889999985 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 5.4e-05
                                      HHHHHHHHHHHHHTT---SHHHHHHHHHHHHHT CS
                              YmgB  3 tevLgaiireilasggkvtnKaIIlkLiekLEs 35
                                      +e+ ++i++e++ + ++v n a I +L+ +LE 
  gi|298675849|ref|YP_003727599.1| 66 KEIADKITQEVAGNTKNVENVAAIEHLLGELER 98
                                      578899*************************95 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 0.48
                                       HHHHHHT---HHHHHHHHHHHH CS
                              YmgB  29 LiekLEsesdvvqldvyRqaLE 50 
                                       Li+ + + ++ v+ +v+R +L 
  gi|298675849|ref|YP_003727599.1| 123 LIKAMRECEERVSPEVMRAVLT 144
                                       5666666667788899999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1714.52
//
Query:       gi|298675850|ref|YP_003727600.1|  [L=218]
Description: NADPH-dependent FMN reductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-14   52.1   0.0    8.7e-14   51.5   0.0    1.3  1  FMN_red   NADPH-dependent FMN reductase


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   0.0   4.8e-18   8.7e-14       1     118 [.       1     118 [.       1     138 [. 0.92

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 4.8e-18
                                       -EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS..--..---HCHGHT.CGGSHHHHHHHHHHHH-SC CS
                           FMN_red   1 mkilvisGSlrkgsntrklaewaaealkeagaevelidladl.ilpcalcdkdlese.gqtsddvaellekiaaada 75 
                                       mk+l++sGS+ +++nt+ +++ a++a+   g+++e++ l+++ i pc +c+k  +++ ++ +d+ + l +k ++ada
  gi|298675850|ref|YP_003727600.1|   1 MKVLGVSGSPIDDGNTDSALKTALAAT---GMDTEFVKLKNYnIEPCRACLKCVNTNvCVINDAGNILAQKAKNADA 74 
                                       9**************************...*****************66666665557******************* PP

                                       EEEEEEECTTCE-HHHHHHHHCHT-..SSCHCCTT-EEEEEEE- CS
                           FMN_red  76 liivtPeYngsysgllKnalDrlsr.trgkkelrgKpvalvavg 118
                                       li++  +   +  +  K++++rl + ++++  ++gKp+++v + 
  gi|298675850|ref|YP_003727600.1|  75 LIVAGYTPYSTLDSRSKAFIERLYPlRHKYGFMQGKPGGAVITC 118
                                       ****9999***************779************999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1456.09
//
Query:       gi|298675851|ref|YP_003727601.1|  [L=348]
Description: translation factor pelota [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-26   90.5   1.2    1.3e-25   89.8   1.2    1.3  1  eRF1_1    eRF1 domain 1
      4e-25   88.5   0.5    9.4e-25   87.3   0.5    1.7  1  eRF1_3    eRF1 domain 3
    1.5e-08   35.0   0.0    6.7e-07   29.7   0.0    2.5  1  eRF1_2    eRF1 domain 2


Domain annotation for each model (and alignments):
>> eRF1_1  eRF1 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.8   1.2   2.2e-29   1.3e-25       1     128 [.       1     124 [.       1     125 [. 0.93

  Alignments for each domain:
  == domain 1  score: 89.8 bits;  conditional E-value: 2.2e-29
                                       HEEEEECTBTTSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......-...-CEEEEEEEEEEEEEEE CS
                            eRF1_1   1 mkllkrdlekdgsgsvtLipeddedlwhlynliapgdsvrastvrkvqresstgsre...servklkLtikvekvdf 74 
                                       m+++kr+l+++ +g ++L pe+ +dlwhl  +i++gd + a t+rk  ++  t +      e+++++L i+v +++f
  gi|298675851|ref|YP_003727601.1|   1 MRVTKRNLKGR-EGEISLTPETLDDLWHLKYIIEKGDLIFALTKRKADSD--TDKLRpekAEKKTTRLGIRVDSLEF 74 
                                       9*******976.9*********************************9774..444334459**************** PP

                                       CTTSSEEEEEEEEEEGGGG--TTSEEEEEE-TTSEEEEEECEESHHHHHHHHHH CS
                            eRF1_1  75 dkdagvlrisGkvieenehvklgafhtldlelkrpftiikeewdsfalerLkea 128
                                       +k +++lri+G + ++ +   +g +htl++e   +++iik  w++ +ler++ea
  gi|298675851|ref|YP_003727601.1|  75 HKFSNRLRINGLIEQGMD---QGYYHTLNIEDSTDVSIIK-TWKKDQLERIDEA 124
                                       *****************9...9******************.9*********998 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.3   0.5   1.6e-28   9.4e-25       1     113 []     250     348 .]     250     348 .] 0.94

  Alignments for each domain:
  == domain 1  score: 87.3 bits;  conditional E-value: 1.6e-28
                                       HHHHHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS-HHH-HHHHHHHHHHHHHH CS
                            eRF1_3   1 liqekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekvketgeelelvelieelven 77 
                                       +++e++l++e+l+e+a+d gka YG eev++a+ +gAvetLL+++e+ r++   +ek        e ++ i+ l+++
  gi|298675851|ref|YP_003727601.1| 250 IARESSLMDELLKEMATD-GKAEYGLEEVENAIYFGAVETLLITDEMLRQE---REK--------EDID-IDTLLQS 313
                                       689***************.******************************97...444........4455.9****** PP

                                       HHHTT-EEEEE-TTSHHHHHHHHHTTTEEEEESS-- CS
                            eRF1_3  78 veesgakveiisseseeGeqlvkafgGiaaiLRykv 113
                                       v++ +++v+++s+e+e G++l +++gGiaa+LR+kv
  gi|298675851|ref|YP_003727601.1| 314 VDQAQGTVVVFSTEFEPGKKL-DSLGGIAALLRFKV 348
                                       *********************.************97 PP

>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   1.1e-10   6.7e-07       3     128 ..     134     241 ..     132     246 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 1.1e-10
                                       EEEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTTESE CS
                            eRF1_2   3 glivldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafllvdkdklkg 79 
                                        ++ ++eg A igl++++ +e  ++i++s  k +  G              +e f++++ ++++ a         ++
  gi|298675851|ref|YP_003727601.1| 134 VIVAIEEGDADIGLVRHYGIEQYSHITQSSGKGE--GT------------LREVFFENILNQLKYA-----APGSEA 191
                                       5677788888888888888888888877642222..22............2355777777666666.....67889* PP

                                       EEEEESSTHHHHHHHHHHHHHHHHTCCEEEEE-S-TSCHHHHHHHHC.CH CS
                            eRF1_2  80 iilagpgfvkeefldkdlldaelkkkviklvdvsyggesglnevlek.aa 128
                                       i++agpgf+ke+f++    ++ ++++ +++ d+s+ g sg +evl+  a 
  gi|298675851|ref|YP_003727601.1| 192 IVVAGPGFTKEDFMEFFKNKEPEMASSAVVEDTSSIGMSGYQEVLRRgAV 241
                                       ***************99999999**********************98644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2391.04
//
Query:       gi|298675852|ref|YP_003727602.1|  [L=670]
Description: fibronectin-binding A domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-98  330.4   7.2    2.2e-98  330.0   7.2    1.1  1  FbpA       Fibronectin-binding protein A N-terminus (FbpA)
      2e-25   89.6   0.0    4.5e-25   88.4   0.0    1.7  1  NFACT-R_1  NFACT protein RNA binding domain


Domain annotation for each model (and alignments):
>> FbpA  Fibronectin-binding protein A N-terminus (FbpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  330.0   7.2  2.5e-102   2.2e-98       2     421 ..       9     451 ..       8     458 .. 0.95

  Alignments for each domain:
  == domain 1  score: 330.0 bits;  conditional E-value: 2.5e-102
                                       HHHHHHHHHHHHHH...HTTXEEEEEEEEETTEEEEEEE.ETTEEEEEEEEXXTTTXEEEEXXXXXXXXSSXXHHHH CS
                              FbpA   2 glvlaavvaELqke...llggridkiyqpekdelvltlr.anrgrhkLllsahpsyarihltekpkenpkeppnFcm 74 
                                       ++++ a+++EL++    +++++i+kiyqp++de++++++  + gr +L+++a   ++rihl+++ + npk+p  F+m
  gi|298675852|ref|YP_003727602.1|   9 SADISALISELSDGsnsIVDAKINKIYQPTPDEVRINIYiPRVGRDNLVIEA---GKRIHLSKHLRSNPKMPGPFPM 82 
                                       57899******988888**********************9999**99*****...********************** PP

                                       HHHHHHTTXEEEEEEEXTTSSEEEEEEEEEXTTSXEEEEEEEEEXXGGGXEEEEEETTTEEEEESSXBXXXSSXSXX CS
                              FbpA  75 lLRkyLkgarivsieqlgfdRivelsiekrdElgdeeeytLivEimgrhSNiiLvdeenkIidaikhvspkqsrvRe 151
                                       lLRk+++g+ri+ i+q +fdRive++i+k      ++   Li+E + + +N+iL+++e+kIi ++k  +++    R+
  gi|298675852|ref|YP_003727602.1|  83 LLRKHIMGGRITFIRQYDFDRIVEIGISKG-----DVDTILIAEFFSQ-GNVILLNNERKIILPMKPRTFR---GRK 150
                                       ******************************.....99999********.**********************...9** PP

                                       BSTTXBXXXSXXXSXBXTTSXXH.HHHHHHHHHS.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH............ CS
                              FbpA 152 ilpgekYelPpsqdklnPleaeeleefkellskkekdlvkaLvkafqGlspllaeelleragldketsakelseedl 228
                                       i+ ge Ye+P+s  +++Pleae+ +++++++s +e+d+v++++++f +l++llaee+++rag+dk++++++++ ++ 
  gi|298675852|ref|YP_003727602.1| 151 IQGGEMYEYPES--QISPLEAEK-DDLEQAFSSSEDDVVRTIATSF-NLGGLLAEEVCARAGVDKNKPVDDVTLDEK 223
                                       ************..*****9999.99999999999***********.****************************** PP

                                       ...HHHHHHHHTXXX....XXEE.......XSSSEESSX..XTTXX.SSXXXXSXHHHHHHHHTTTXXX--SHH.HH CS
                              FbpA 229 erlyealqelleeleeekfepqlvlkee..kpeefsvvp..lkslselekesfdslsealdeyYakkaerdrve.qk 300
                                       ++l ++l+++++++ +++++p+++++++  + e+++v+p  l++++e+ek++fds+++alde+++k+  + + + q+
  gi|298675852|ref|YP_003727602.1| 224 SKLTDTLKDVFTPIVTGELNPCIIKQKTnnQSEYVDVLPfeLEQYKEYEKQYFDSFNKALDEFFGKEVVEAERKiQE 300
                                       ***********************999888889999***99988999******************9987766666599 PP

                                       HHHHHHH..HHHHHHHHHHHHHHHHHHHHCCGGH.....HHHHCCHH-----------------------..--... CS
                              FbpA 301 rsdlekr..veneleklekklkklekelekaeka.....enyrligelltaylyaikkgmsevelenyyde.ge... 366
                                       +++ ek+  ++++l++++  ++k+eke++k ++       +y  ++e++t++ +a+k g+s++++++ ++e +    
  gi|298675852|ref|YP_003727602.1| 301 SAKKEKVdiYQRRLQQQQGAIEKFEKEANKYNSIaeaiySHYPFVEEVITVLTNARKSGYSWDDIKSKLKEaNDips 377
                                       999999899*********************999889999*******************************9666*** PP

                                       ...................---------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              FbpA 367 ...................evtIpLdprkspsenAqkyfkkykKlkraveaveeqieetkeeleylesveaale 421
                                                          +++ +Ld+r s+++nAq y++k+k++ +++e++  +ieetk+ +e  ++ +++  
  gi|298675852|ref|YP_003727602.1| 378 akliqsidpksgtivmdldGTKATLDIRYSVPQNAQTYYEKAKRVMKKREGALRAIEETKRIIENRDKPQQQTR 451
                                       *************************************************************9998887777655 PP

>> NFACT-R_1  NFACT protein RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.4   0.0   5.1e-29   4.5e-25       2     109 .]     465     574 ..     464     574 .. 0.96

  Alignments for each domain:
  == domain 1  score: 88.4 bits;  conditional E-value: 5.1e-29
                         NFACT-R_1   2 vfwFkssdgylvimGkDkqeneelikkyleesdvwfhvdkessahvylrlsegeleeipeelleeaaqlakanSia. 77 
                                       ++wF+ssdg+lv++G+D+ +nee++kky+e++d+ +h  + +++ ++++ s+    ++pe+++ eaaq+++++S+  
  gi|298675852|ref|YP_003727602.1| 465 FRWFISSDGFLVVGGRDADTNEEIFKKYMEKQDIILHTQVPGAPLAIVK-SKRY--NVPEQTMYEAAQFVVSYSSIw 538
                                       99***********************************************.4444..7******************99 PP

                         NFACT-R_1  78 gnklssvdvvyvpasnlsktap....ldtGsvgfkg 109
                                       ++ +   d+++v+++++skt++    l++Gs++++g
  gi|298675852|ref|YP_003727602.1| 539 KSGQFGGDCYWVYPNQVSKTPEsgefLKKGSFIIRG 574
                                       ****9****************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (670 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1565  (0.0872888); expected 358.6 (0.02)
Passed bias filter:                      718  (0.0400469); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.76u 0.33s 00:00:01.09 Elapsed: 00:00:00.50
# Mc/sec: 4037.99
//
Query:       gi|298675853|ref|YP_003727603.1|  [L=391]
Description: DNA primase small subunit [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.9e-20   71.5   0.0    2.8e-19   69.8   0.0    1.8  1  DNA_primase_S  DNA primase small subunit
  ------ inclusion threshold ------
      0.016   15.8   0.1        1.8    9.2   0.0    2.5  2  HHH_5          Helix-hairpin-helix domain


Domain annotation for each model (and alignments):
>> DNA_primase_S  DNA primase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.8   0.0   3.1e-23   2.8e-19       1     172 [.      97     322 ..      97     325 .. 0.77

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 3.1e-23
                                       EEEEEETTT-.TT--HHHHHHHHHHHHHHHHHHHH-----GG..GEEEEE--SEEEEEEE--TTEEES-HHHHHHHH CS
                     DNA_primase_S   1 FDiDmddyddcseatvcekcwkfvsvavkvldellredfgfk..dilwvfsgrrGfHcwvsdkdarpltdeeraaiv 75 
                                       FD+D+d+++    +++ e++ ++ ++a k+ d +l++dfgf   di +vfsg+rG+H ++s   +r+l+++er++iv
  gi|298675853|ref|YP_003727603.1|  97 FDLDADHLPH-VPDSYPEMLENVKQEALKLYD-FLSDDFGFGedDINIVFSGGRGYHFHISHPSVRSLGSAERREIV 171
                                       9********8.667888999999999999997.778*****999********************************* PP

                                       HH........................................................................... CS
                     DNA_primase_S  76 nylnly........................................rplhpflsrsmlkivkpvveeiileeqdpf. 111
                                       +y++                                          r+  +++s+   +++kp+++         f 
  gi|298675853|ref|YP_003727603.1| 172 DYISGRgldisqiigksyvsgdsgrrdasmfvfpsendggwgakinRYIISYISNI-VNSNKPIKK------LTGFs 241
                                       *7655579999988888888888888888777777777766665554444444443.334444422......22335 PP

                                       .....HCHHHHCT--------..................................-----------------....- CS
                     DNA_primase_S 112 .....eikkllrllpdkslre...kkkw.............eakedivlvllyprldeqvtkgikhllkapfcihgk 167
                                            + +kl + + d+++     k                e++ ++ ++ l    de+vt+++k+l++ p+++hg+
  gi|298675853|ref|YP_003727603.1| 242 gvgktTAEKLVNIFNDEKQLAllkK--GkidmvsntsknlfEYLGKQAVDNLIANVDEPVTADVKRLIRVPGSLHGG 316
                                       6677666666666666666666551..0446666666666899********************************** PP

                                       --.--- CS
                     DNA_primase_S 168 tg.nvc 172
                                       +g +v 
  gi|298675853|ref|YP_003727603.1| 317 SGlKVT 322
                                       *97774 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0002       1.8      34      52 ..     234     252 ..     215     269 .. 0.75
   2 ?    3.9   0.0     0.009        81      19      42 ..     288     311 ..     277     312 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0002
                                       HHHHHTSTTS-HHHHHHHH CS
                             HHH_5  34 veeLakipGiGkktAerii 52 
                                       +++L+   G+Gk tAe+++
  gi|298675853|ref|YP_003727603.1| 234 IKKLTGFSGVGKTTAEKLV 252
                                       5666666666666666665 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.009
                                       HTTT--SHHHHHHS-HHHHHTSTT CS
                             HHH_5  19 lsaGiesvedlaaadveeLakipG 42 
                                       +++ i  v++ + adv++L ++pG
  gi|298675853|ref|YP_003727603.1| 288 VDNLIANVDEPVTADVKRLIRVPG 311
                                       45556667777889*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2585.90
//
Query:       gi|298675854|ref|YP_003727604.1|  [L=248]
Description: hypothetical protein Metev_1978 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
        1.6    7.9   3.1          2    7.5   3.1    1.2  1  Zip             ZIP Zinc transporter
          2    7.1   5.0        2.3    6.9   5.0    1.2  1  Presenilin      Presenilin
        2.9    8.5  10.0         18    6.0  10.0    2.3  1  EST1            Telomerase activating protein Est1


Domain annotation for each model (and alignments):
>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   3.1   0.00034         2     110     169 ..     131     193 ..      71     220 .. 0.56

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00034
                               Zip 110 tpkkasssssesaakksvsndkveeseek...edhvaeadtdadskeelrngkqeksesekeq 169
                                       + +k+s+++++ ++++s +++++ee e++   +   ++ dt+++ k+e  ++++++s+++k+ 
  gi|298675854|ref|YP_003727604.1| 131 IRDKSSNQTENTDTESSEPEHPIEEVEDSqetTATPSNSDTEKSRKSEIDKNESKTSSNSKND 193
                                       333444444455555555555555555441003333333344443333333333333333333 PP

>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   5.0   0.00039       2.3     250     309 ..     135     192 ..      72     224 .. 0.54

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00039
                        Presenilin 250 esskeeeseeesseksaqsseseeeseeesseaessaeesseekeseessesseeeeeee 309
                                       +s+++e++++esse ++  +e e+++e+++++++s++e+s++  ++  ++es++++++++
  gi|298675854|ref|YP_003727604.1| 135 SSNQTENTDTESSEPEHPIEEVEDSQETTATPSNSDTEKSRK--SEIDKNESKTSSNSKN 192
                                       111122222222222222222222222222222222222211..1112222222222222 PP

>> EST1  Telomerase activating protein Est1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  10.0     0.003        18      31     105 ..      83     186 ..      21     204 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.003
                                       ---H.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-B-........HTT........................... CS
                              EST1  31 kkkkpvekrklklklvkflksaigfYqsliqrllsefel........elssvlkvilk................... 80 
                                        ++++ +k   k+ l k+l ++ ++Y s++  + ++++         e         +                   
  gi|298675854|ref|YP_003727604.1|  83 ARSHAFSKNPSKNDLDKLLPEERKVYDSILSAIHTSHKEliepiinpE---------Irdkssnqtentdtessepe 150
                                       55677788888999**********************994343333331.........24446656666777777777 PP

                                       ..............-.....-----.----TTB--T CS
                              EST1  81 ..........sktklpekessekse.teseeekssl 105
                                                 + t +p + ++eks+ +e+++++s++
  gi|298675854|ref|YP_003727604.1| 151 hpieevedsqETTATPSNSDTEKSRkSEIDKNESKT 186
                                       777777777633333333333333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2043  (0.113949); expected 358.6 (0.02)
Passed bias filter:                      622  (0.0346924); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1599.01
//
Query:       gi|298675855|ref|YP_003727605.1|  [L=92]
Description: 50S ribosomal protein L44E [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-25   87.7  11.0    7.9e-25   87.1  11.0    1.3  1  Ribosomal_L44  Ribosomal protein L44
  ------ inclusion threshold ------
      0.046   13.7   5.7       0.88    9.6   1.3    2.1  2  RNHCP          RNHCP domain
      0.071   13.1   1.8        3.1    7.8   0.1    2.3  2  Zn_Tnp_IS1595  Transposase zinc-ribbon domain
        2.6    8.2   6.3         20    5.4   6.4    2.0  1  zf-Mss51       Zinc-finger of mitochondrial splicing suppress


Domain annotation for each model (and alignments):
>> Ribosomal_L44  Ribosomal protein L44
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.1  11.0   1.8e-28   7.9e-25       2      75 ..      17      90 ..      16      91 .. 0.98

  Alignments for each domain:
  == domain 1  score: 87.1 bits;  conditional E-value: 1.8e-28
                                      EEEEEEEE-------SSSHHHHHHHH.H-SSS..GGGGS----.--SSBB--EEEEETTT--EEE----BBS--EE CS
                     Ribosomal_L44  2 HtehkveqykkgkdselaqgkRrydrkqsgyg..GqtkpvfkkkaKttKKivlrleCteCkkkrlkalkRakkfel 75
                                      Htehk+e++kkgk+s++++++R+++r +sg+g  G++++v+++ +K+tKK+ l++ Ct+C+k+++++++R+k+fe+
  gi|298675855|ref|YP_003727605.1| 17 HTEHKIEKAKKGKESSMTHITRQKKR-RSGIGndGKFSKVPGG-DKPTKKVRLKYSCTKCGKSHQRPGFRTKRFEF 90
                                      **************************.9***************.*******************************8 PP

>> RNHCP  RNHCP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.3    0.0002      0.88      20      56 ..       5      39 ..       1      47 [. 0.68
   2 ?    7.1   0.4    0.0012       5.4      58      77 ..      60      79 ..      34      86 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0002
                             RNHCP 20 sakrnHCpsCLlskHvdeepgdraseCkglmepiave 56
                                      ++ r HCp C   +H++++ +  ++  +++m+ i+ +
  gi|298675855|ref|YP_003727605.1|  5 KKMRTHCPFCK--MHTEHKIEKAKKGKESSMTHITRQ 39
                                      4689******5..566666666666666677666555 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0012
                             RNHCP 58 kkkkewvivhrCekCgelkk 77
                                      k +k++ + + C+kCg+ ++
  gi|298675855|ref|YP_003727605.1| 60 KPTKKVRLKYSCTKCGKSHQ 79
                                      667899999*******9876 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1   0.00069       3.1      19      34 ..       9      24 ..       1      43 [. 0.78
   2 ?    5.3   0.2    0.0043        19      20      27 ..      70      77 ..      51      91 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00069
                     Zn_Tnp_IS1595 19 fvCPhCgsrkayrikt 34
                                       +CP+C+  + ++i++
  gi|298675855|ref|YP_003727605.1|  9 THCPFCKMHTEHKIEK 24
                                      56*****887777776 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0043
                     Zn_Tnp_IS1595 20 vCPhCgsr 27
                                       C +Cg++
  gi|298675855|ref|YP_003727605.1| 70 SCTKCGKS 77
                                      36666666 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   6.4    0.0045        20       2      24 ..      11      76 ..      10      80 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0045
                          zf-Mss51  2 CPvpkhkqt...........................................apkhvdfeCpdCGi 24
                                      CP++k + +                                           ++ + ++ C +CG 
  gi|298675855|ref|YP_003727605.1| 11 CPFCKMHTEhkiekakkgkessmthitrqkkrrsgigndgkfskvpggdkptKKVRLKYSCTKCGK 76
                                      999976666889999999999999999999999999999999999999999899999********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1026  (0.0572257); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 651.48
//
Query:       gi|298675856|ref|YP_003727606.1|  [L=61]
Description: 30S ribosomal protein S27E [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-25   87.4   0.7    4.1e-25   87.2   0.7    1.0  1  Ribosomal_S27e  Ribosomal protein S27
     0.0031   17.1   0.1     0.0051   16.4   0.0    1.4  1  zf-C2H2_12      Zinc-finger C2H2-type
     0.0044   16.5   1.4     0.0056   16.2   1.4    1.2  1  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0047   16.9   0.2     0.0049   16.9   0.2    1.1  1  Zn_Tnp_IS91     Transposase zinc-binding domain
  ------ inclusion threshold ------
      0.013   15.5   0.4      0.014   15.4   0.4    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.051   14.1   1.4       0.07   13.7   1.4    1.3  1  Stc1            Stc1 domain
      0.066   13.2   0.9       0.81    9.8   0.1    2.1  2  zf-BED          BED zinc finger
      0.072   13.0   1.0        4.4    7.3   0.1    2.1  2  zf-trcl         Probable zinc-ribbon domain
       0.08   13.0   2.8       0.34   10.9   2.6    2.0  3  zinc_ribbon_6   Zinc-ribbon
       0.32   10.6   0.1       0.32   10.6   0.1    2.1  2  Sgf11           Sgf11 (transcriptional regulation protein)


Domain annotation for each model (and alignments):
>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.2   0.7   2.3e-28   4.1e-25       1      54 [.       7      60 ..       7      61 .] 0.98

  Alignments for each domain:
  == domain 1  score: 87.2 bits;  conditional E-value: 2.3e-28
                                      -S--EEEEE-TTTS-EEEEESS-SS-EEESSSTCEEEEECSSSEEESSCEEEEE CS
                    Ribosomal_S27e  1 prskFldvkCpdCenetvvFshaatvvkCisCgkvLvePtGGkaklkaqilerl 54
                                      p+s+Fl+vkC dCene+++F++a++ ++C  Cg++L+ePtGGk+ +k +i+e+l
  gi|298675856|ref|YP_003727606.1|  7 PKSRFLRVKCNDCENEQIIFGSASREITCTMCGRTLAEPTGGKSTIKTHIIEVL 60
                                      89*************************************************997 PP

>> zf-C2H2_12  Zinc-finger C2H2-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   2.9e-06    0.0051      17      46 ..      27      58 ..      23      59 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.9e-06
                        zf-C2H2_12 17 dpqrrglvCmvCgeslaslk..lstikrHIrq 46
                                      +++ r + C +Cg++la+     stik HI +
  gi|298675856|ref|YP_003727606.1| 27 GSASREITCTMCGRTLAEPTggKSTIKTHIIE 58
                                      6678999*********97652379******76 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.4   3.1e-06    0.0056       2      29 ..      15      42 ..      14      49 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.1e-06
                                      EETTTTCEECHEETSTTCEEESSSSBEE CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVl 29
                                      kC +C ++++++  ++ e++Ct CG  l
  gi|298675856|ref|YP_003727606.1| 15 KCNDCENEQIIFGSASREITCTMCGRTL 42
                                      9************************766 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.2   2.7e-06    0.0049      37      68 ..      11      43 ..       3      58 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.7e-06
                       Zn_Tnp_IS91 37 faryeCeeCghekivyfsCksrh.CpsCqkkat 68
                                      f r++C++C++e+i++ s  +   C+ C++  +
  gi|298675856|ref|YP_003727606.1| 11 FLRVKCNDCENEQIIFGSASREItCTMCGRTLA 43
                                      7799***********999999988****98755 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.4   7.8e-06     0.014      69     104 ..      12      50 ..       7      59 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.8e-06
                                       -EEEETTTS-EEECHH..H.HHS-TTTSSS-EEEEESSS CS
                              HypA  69 vkvrCreCgkefelee..k.alrCpkCgsadveivsGee 104
                                       ++v+C++C++e  +    + +++C  Cg++  e ++G+ 
  gi|298675856|ref|YP_003727606.1|  12 LRVKCNDCENEQIIFGsaSrEITCTMCGRTLAEPTGGKS 50 
                                       689******9977443333589*******9999999885 PP

>> Stc1  Stc1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.4   3.9e-05      0.07      39      63 ..      13      43 ..       2      55 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.9e-05
                                      ----TTTS-----E......EE-SSS--EEE CS
                              Stc1 39 kikCkectakqate......leCsaCqktkp 63
                                      ++kC++c ++q         ++C++C++t++
  gi|298675856|ref|YP_003727606.1| 13 RVKCNDCENEQIIFgsasreITCTMCGRTLA 43
                                      799****9998654455555*******9986 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.086   1.5e+02      16      24 ..      13      21 ..       8      23 .. 0.87
   2 ?    9.8   0.1   0.00045      0.81      16      39 ..      32      56 ..      26      59 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.086
                                      --EETTTTE CS
                            zf-BED 16 kavCryCgk 24
                                      +++C+ C++
  gi|298675856|ref|YP_003727606.1| 13 RVKCNDCEN 21
                                      79*****98 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00045
                                      --EETTTTEE----.SSTHHHHHHH CS
                            zf-BED 16 kavCryCgkilsrg.ggttnLkrHL 39
                                       ++C  Cg++l+   gg +  k+H+
  gi|298675856|ref|YP_003727606.1| 32 EITCTMCGRTLAEPtGGKSTIKTHI 56
                                      689*********9999999999997 PP

>> zf-trcl  Probable zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1    0.0025       4.4       5      15 ..      14      24 ..      12      28 .. 0.85
   2 ?    4.9   0.1     0.014        24       3      13 ..      31      41 ..      29      43 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0025
                           zf-trcl  5 ltCkdCgaefv 15
                                      ++C+dC++e++
  gi|298675856|ref|YP_003727606.1| 14 VKCNDCENEQI 24
                                      68*****9987 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.014
                           zf-trcl  3 ktltCkdCgae 13
                                      +++tC+ Cg++
  gi|298675856|ref|YP_003727606.1| 31 REITCTMCGRT 41
                                      689******85 PP

>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.6   0.00019      0.34      24      40 ..       8      24 ..       2      40 .. 0.71
   2 ?    0.8   0.1      0.28     5e+02      28      38 ..      31      41 ..      25      46 .. 0.75
   3 ?   -3.0   0.0       4.3   7.6e+03      38      46 ..      49      57 ..      47      58 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00019
                     zinc_ribbon_6 24 knkkvkilCnDCekkse 40
                                      k++  ++ CnDCe+++ 
  gi|298675856|ref|YP_003727606.1|  8 KSRFLRVKCNDCENEQI 24
                                      567889******99875 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.28
                     zinc_ribbon_6 28 vkilCnDCekk 38
                                       +i+C  C+++
  gi|298675856|ref|YP_003727606.1| 31 REITCTMCGRT 41
                                      57888888765 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 4.3
                     zinc_ribbon_6 38 ksevkfhvl 46
                                      ks++k h++
  gi|298675856|ref|YP_003727606.1| 49 KSTIKTHII 57
                                      788888875 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.8       0.4   7.1e+02       5      11 ..      14      20 ..      13      22 .. 0.81
   2 ?   10.6   0.1   0.00018      0.32       2      15 ..      30      43 ..      29      44 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.4
                                      EE-TTTS CS
                             Sgf11  5 vtCpnCg 11
                                      v+C+ C+
  gi|298675856|ref|YP_003727606.1| 14 VKCNDCE 20
                                      7899996 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00018
                                      C-EEE-TTTSSEEE CS
                             Sgf11  2 seyvtCpnCgRqia 15
                                      s+ +tC +CgR+ a
  gi|298675856|ref|YP_003727606.1| 30 SREITCTMCGRTLA 43
                                      7889*******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 391.70
//
Query:       gi|298675857|ref|YP_003727607.1|  [L=271]
Description: translation initiation factor 2 subunit alpha [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      5e-27   94.3   0.2    9.2e-27   93.5   0.2    1.4  1  EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha
    1.2e-13   51.2   0.3    5.1e-13   49.2   0.3    1.9  2  S1           S1 RNA binding domain
  ------ inclusion threshold ------
      0.041   13.9   0.0       0.12   12.4   0.0    1.7  1  PI_PP_C      Phosphoinositide phosphatase C-terminal domain
      0.087   13.1   1.3          2    8.8   0.1    3.1  3  Dodecin      Dodecin
       0.35   10.7   1.5       0.95    9.3   0.6    2.0  2  3HCDH_N      3-hydroxyacyl-CoA dehydrogenase, NAD binding dom


Domain annotation for each model (and alignments):
>> EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.5   0.2   2.6e-30   9.2e-27       9     116 .]     129     235 ..     122     235 .. 0.95

  Alignments for each domain:
  == domain 1  score: 93.5 bits;  conditional E-value: 2.6e-30
                                       HTTTTS-HHHHH.HHHHSTTHHHHHTTS-TTTHHHHHHCTHHHHHHT-EEEEEEEEEEE-STTHHHHHHHHHHHHST CS
                       EIF_2_alpha   9 lyekyghaydaF.klaitdeevldkleipeeveeaLveiikkklkpqkvkiradieltcftkdGveaIkeaLkagee 84 
                                       + +++g+ y aF ++a+ +e+++++++i++++ee++++i++ ++k++ v+i ++++lt+ ++dG+e+Ik+aL+   +
  gi|298675857|ref|YP_003727607.1| 129 FTDEFGSPYAAFeEAAMYGEDAFENIKIDKSLEEKITKIAQDNIKIPYVEIAGYVDLTSNAPDGIENIKQALN--DA 203
                                       6799*********************************************************************..66 PP

                                       .S..TTSSSEEEEEEEESSSSEEEEEEEES.. CS
                       EIF_2_alpha  85 asneeeveeeeevkikliapPeYvltvetldk 116
                                       +s++e+++++++++i++ ++P+Y+++v+++d+
  gi|298675857|ref|YP_003727607.1| 204 DSTKENYSSNVKIDISYTGAPRYRIKVNAPDY 235
                                       678899***********************997 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.3   1.4e-16   5.1e-13       2      75 .]      10      84 ..      10      84 .. 0.97
   2 ?   -1.0   0.0      0.64   2.3e+03      43      67 ..     147     171 ..     127     174 .. 0.82

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 1.4e-16
                                      STTTCEEEEEEEEEETTEEEEEET..TTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEEEC CS
                                S1  2 pekgevveGeVtsvtkgGafVelg..ngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriilsik 75
                                      p++g+ v  +V++vt++Ga+V l+  ++ egf+++se+++   v+   + +++G+++  kvlkvd +rr i+ls+k
  gi|298675857|ref|YP_003727607.1| 10 PNVGDFVVCTVKNVTDFGAYVTLDeyGDKEGFIHISEIKAG-WVKYVRDYVREGQKIVCKVLKVDPNRRHIDLSLK 84
                                      689999999****************99*************9.9999****************************86 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.64
                                       ESCHHHCEETTEEEEEEEEEEETTT CS
                                S1  43 vedpdevlkvGdevkvkvlkvdkdr 67 
                                       +ed  e +k+++ ++ k++k+  d+
  gi|298675857|ref|YP_003727607.1| 147 GEDAFENIKIDKSLEEKITKIAQDN 171
                                       5666688999999999999987765 PP

>> PI_PP_C  Phosphoinositide phosphatase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.3e-05      0.12      38      63 ..     186     211 ..     179     219 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.3e-05
                                       TS-S-HHHHHHHHHCSS---TTHHHH CS
                           PI_PP_C  38 sssaPtGieqikellqdkksgkdnvl 63 
                                       +s+aP+Gie+ik+ l+d +s k+n  
  gi|298675857|ref|YP_003727607.1| 186 TSNAPDGIENIKQALNDADSTKENYS 211
                                       5899**************99998865 PP

>> Dodecin  Dodecin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       3.8   1.4e+04      28      36 ..     120     128 ..     119     132 .. 0.82
   2 ?    1.8   0.0     0.081   2.9e+02       5      32 ..     183     209 ..     179     220 .. 0.84
   3 ?    8.8   0.1   0.00055         2      13      33 ..     236     256 ..     227     259 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3.8
                                       HH-SSEEEE CS
                           Dodecin  28 ktlrnirwv 36 
                                       ktl n++++
  gi|298675857|ref|YP_003727607.1| 120 KTLSNLKSI 128
                                       899999986 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.081
                                       EEEEEEESS-HHHHHHHHHHHHHHH-SS CS
                           Dodecin   5 ielvGsSpkSwedAiqnAiaeAsktlrn 32 
                                       ++l+ + p+++e+ i++A++ A  t +n
  gi|298675857|ref|YP_003727607.1| 183 VDLTSNAPDGIEN-IKQALNDADSTKEN 209
                                       7788899999987.9*******999877 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00055
                                       S-HHHHHHHHHHHHHHH-SSE CS
                           Dodecin  13 kSwedAiqnAiaeAsktlrni 33 
                                       k  e+A +nA ++A++t+rn+
  gi|298675857|ref|YP_003727607.1| 236 KTAENALKNAAETATNTIRNL 256
                                       56799***************8 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.6   0.00026      0.95      23     107 ..      79     171 ..      72     174 .. 0.70
   2 ?   -0.8   0.0      0.35   1.2e+03      29      55 ..     236     262 ..     223     269 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00026
                                       -EEEEE-S-HHHHHHHHHHHHH.....HHHCCTTTTSS-HHHHCCCHHCEE...EES-HHHHHC-SEEEE-S-SSHH CS
                           3HCDH_N  23 leVvlvdiseealekalekiek.....sleklvekgklkeeeveaalaris...fttdleeavdadlviEavvEnle 91 
                                       ++  l d++e++ ++  ++ ++     ++ ++v+++  ++e++ + l+ i    f + ++++ +a ++ E ++En++
  gi|298675857|ref|YP_003727607.1|  79 IDLSLKDVNEHQKREKIQQWKNeqkasKWLQFVAEETGTDEKTLSNLKSIFtdeFGSPYAAFEEAAMYGEDAFENIK 155
                                       566777887777777777766633333444555555555666666666664233556788888************** PP

                                       HHHHHHHHHHCCS-TT CS
                           3HCDH_N  92 lKrkvfaelekiakpd 107
                                       + +++ +++ kia+++
  gi|298675857|ref|YP_003727607.1| 156 IDKSLEEKITKIAQDN 171
                                       ************9876 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.35
                                       -S-HHHHHHHHHHHHHHHHCCTTTTSS CS
                           3HCDH_N  29 diseealekalekieksleklvekgkl 55 
                                        ++e+al++a+e++++++++l  kg++
  gi|298675857|ref|YP_003727607.1| 236 KTAENALKNAAETATNTIRNLGGKGEF 262
                                       347788888888888888887777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1059  (0.0590663); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1596.93
//
Query:       gi|298675858|ref|YP_003727608.1|  [L=55]
Description: RNA-binding protein Nop10p [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-25   88.1   3.8    3.1e-25   88.0   3.8    1.0  1  Nop10p    Nucleolar RNA-binding protein, Nop10p family
    0.00052   20.0   1.3    0.00063   19.8   1.3    1.1  1  DUF1272   Protein of unknown function (DUF1272)
      0.001   18.6   0.8     0.0013   18.2   0.8    1.2  1  RecR      RecR protein
     0.0043   15.0   0.4     0.0043   15.0   0.4    1.0  1  PolC_DP2  DNA polymerase II large subunit DP2
  ------ inclusion threshold ------
       0.11   11.3   0.6      0.087   11.6   0.6    1.0  1  NRDD      Anaerobic ribonucleoside-triphosphate reductase
       0.17   11.9   1.8       0.22   11.6   1.8    1.1  1  HypA      Hydrogenase/urease nickel incorporation, metallocha
       0.28   11.1   3.3       0.54   10.2   3.3    1.5  1  DUF35_N   Rubredoxin-like zinc ribbon domain (DUF35_N)


Domain annotation for each model (and alignments):
>> Nop10p  Nucleolar RNA-binding protein, Nop10p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.0   3.8   1.2e-28   3.1e-25       1      50 [.       1      50 [.       1      51 [. 0.98

  Alignments for each domain:
  == domain 1  score: 88.0 bits;  conditional E-value: 1.2e-28
                                      .----EE-TTT--EESSSB-TTT-SB-B-SS--S--TT-TTCHHHHHCHH CS
                            Nop10p  1 mksylrkcgkcrvYTLkkvcpecggptksahPaRFSPdDkyskyRralKk 50
                                      m +++rkc++c++YTL+++cp+cgg+t++++PaRFSP+D+y+kyRr+ K+
  gi|298675858|ref|YP_003727608.1|  1 MGYKIRKCKQCSRYTLEESCPYCGGKTVNPQPARFSPADRYGKYRRQSKQ 50
                                      89*********************************************996 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   1.3   2.4e-07   0.00063      32      53 ..       8      29 ..       2      34 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.4e-07
                           DUF1272 32 CaeCaeevlenvCPncgGelvk 53
                                      C++C   +le+ CP cgG+ v+
  gi|298675858|ref|YP_003727608.1|  8 CKQCSRYTLEESCPYCGGKTVN 29
                                      ******************9764 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.8   5.2e-07    0.0013      15      34 ..       4      23 ..       2      27 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 5.2e-07
                                      H-EE-TTT--EESSSS-CCC CS
                              RecR 15 kvrhCsrCgnlteedlCaIC 34
                                      k+r C++C  +t e+ C+ C
  gi|298675858|ref|YP_003727608.1|  4 KIRKCKQCSRYTLEESCPYC 23
                                      79****************** PP

>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.4   1.7e-06    0.0043     618     642 ..       5      29 ..       1      54 [. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.7e-06
                          PolC_DP2 618 rrkCkkCgketlearCeeCgektee 642
                                        rkCk+C + tle  C+ Cg kt +
  gi|298675858|ref|YP_003727608.1|   5 IRKCKQCSRYTLEESCPYCGGKTVN 29 
                                       69*******************9976 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.6   3.4e-05     0.087     506     528 ..       4      26 ..       1      49 [. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.4e-05
                                       -EEEETT.--EESSSB-TTT--B CS
                              NRDD 506 kidvCnecgykgeiekCpkCgse 528
                                       ki  C++c +  + e+Cp+Cg +
  gi|298675858|ref|YP_003727608.1|   4 KIRKCKQCSRYTLEESCPYCGGK 26 
                                       6889******999999*****65 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.8   8.5e-05      0.22      72      98 ..       7      29 ..       4      34 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.5e-05
                                      EETTTS-EEECHHHHHS-TTTSSS-EE CS
                              HypA 72 rCreCgkefeleekalrCpkCgsadve 98
                                      +C++C+ +++le   ++Cp Cg++ v+
  gi|298675858|ref|YP_003727608.1|  7 KCKQCS-RYTLE---ESCPYCGGKTVN 29
                                      7****9.66666...37*****99886 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   3.3   0.00021      0.54      11      35 ..       5      27 ..       4      29 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00021
                           DUF35_N 11 gqrCpdCGtvqfPPravCphCgsdd 35
                                      +++C+ C ++    + +Cp+Cg+++
  gi|298675858|ref|YP_003727608.1|  5 IRKCKQCSRYTL--EESCPYCGGKT 27
                                      579999999986..9******9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 368.58
//
Query:       gi|298675859|ref|YP_003727609.1|  [L=256]
Description: hypothetical protein Metev_1983 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-51  175.8   0.0    1.3e-51  175.6   0.0    1.0  1  PAC2         PAC2 family
  ------ inclusion threshold ------
      0.071   13.5   0.8       0.65   10.4   0.0    2.3  2  Gp_dh_N      Glyceraldehyde 3-phosphate dehydrogenase, NAD bi
        1.1    9.7   3.7        1.3    9.4   2.5    1.8  2  Glu-tRNAGln  Glu-tRNAGln amidotransferase C subunit


Domain annotation for each model (and alignments):
>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.6   0.0   2.2e-55   1.3e-51       2     212 ..      21     233 ..      20     234 .. 0.92

  Alignments for each domain:
  == domain 1  score: 175.6 bits;  conditional E-value: 2.2e-55
                                       EEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETT..EEE-SEEEEEETTT.SEEEEEEE.. CS
                              PAC2   2 ilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveeg..relepprlyakdsgsrdllvlqg.. 74 
                                       ++G+pg+G+Vg+l+v++Lie+le ekv ei+s+y +p     p+vlv+++   +l ++++ya + +++d+l+l g  
  gi|298675859|ref|YP_003727609.1|  21 FVGLPGVGHVGKLVVEHLIENLEGEKVIEIYSPY-FP-----PQVLVNNDntIKLVNNEIYACNINGQDILILAGdh 91 
                                       78********************************.**.....********9999*******99888*********77 PP

                                       ..E-HSCHHHHHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHH.......CT.-CE CS
                              PAC2  75 ..repilqyeefakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleele.......es.eyg 141
                                          + +++ye + +  ld+aee+gv+++++Lgg+++ge +       e+v+ga+++ +l+eele       e+ ++ 
  gi|298675859|ref|YP_003727609.1|  92 qsSTNEGHYE-LGSLYLDLAEEFGVSRIYTLGGFPTGEFN-----HNEGVIGAVNNINLVEELEgygvefrENePGN 162
                                       6666666666.************************99774.....3458**************86666654227*** PP

                                       EEEHHHHHHHHHHHHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT---HCHHHHHHHHHHHHHHHHH CS
                              PAC2 142 givgitglLlsaakergipavgllaevphylpdPkaaaalleflskllglevdtedLeedaeeleeqleel 212
                                       givg++gl+l++++ r+i+a++l++ +++y++dPk+a+++l++++++l++e+d e+Le++a+e+e+ +e++
  gi|298675859|ref|YP_003727609.1| 163 GIVGASGLILGLCDFRNIDAACLMGLTSGYIVDPKSAQSILRVIDRILDIEIDEEELEKRAKEMEKVVEKI 233
                                       *******************************************************************9986 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00011      0.65       3      49 ..      22      67 ..      20      99 .. 0.71
   2 ?    1.3   0.2     0.073   4.4e+02      55      92 ..     218     256 .]     197     256 .] 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00011
                                      EEEESTSHHHHHHHHHHHHHT.TCEEEEEE-.TS-HHHHHHHHHEETTT CS
                           Gp_dh_N  3 vainGfGRIGrlvlralleek.elevvaind.ltdletlayllkyDsvh 49
                                      v++ G G +G+lv+ +l+e+    +v++i +    ++    l++ D + 
  gi|298675859|ref|YP_003727609.1| 22 VGLPGVGHVGKLVVEHLIENLeGEKVIEIYSpYFPPQ---VLVNNDNTI 67
                                      8999**************7654899999987444443...344555555 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.073
                                       -EEEETTEEEETTEEEEEE--SS.GGGS-CHHHTSSEEE CS
                           Gp_dh_N  55 eveaeeealvvngkkikvlaekd.peelpwkelgvdlVv 92 
                                       e+e + ++++   +kik+++e++   +lp k+ ++++++
  gi|298675859|ref|YP_003727609.1| 218 ELEKRAKEMEKVVEKIKTMKEQQeTGNLPQKDEDINYII 256
                                       445555666666679999998875889999999999986 PP

>> Glu-tRNAGln  Glu-tRNAGln amidotransferase C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.7     1e+04      21      27 ..     140     146 ..     133     160 .. 0.49
   2 ?    9.4   2.5   0.00022       1.3       1      29 [.     214     242 ..     214     251 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.7
                                       TTCGCS- CS
                       Glu-tRNAGln  21 eqLqevd 27 
                                       ++++ v+
  gi|298675859|ref|YP_003727609.1| 140 NNINLVE 146
                                       4444333 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00022
                                       --HHHHHHHHHHHHHHHHHHTTCGCS--T CS
                       Glu-tRNAGln   1 lseeEleklakelnsildyveqLqevdtt 29 
                                       ++eeElek ake++++++ +++++e   t
  gi|298675859|ref|YP_003727609.1| 214 IDEEELEKRAKEMEKVVEKIKTMKEQQET 242
                                       68**********************97755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1850  (0.103185); expected 358.6 (0.02)
Passed bias filter:                     1197  (0.0667633); expected 358.6 (0.02)
Passed Vit filter:                       116  (0.00646996); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 1666.82
//
Query:       gi|298675860|ref|YP_003727610.1|  [L=413]
Description: PHP domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0069   16.7   0.1     0.0081   16.5   0.1    1.5  1  PHP       PHP domain
     0.0085   15.8   0.0      0.021   14.6   0.0    1.7  1  PHP_C     PHP-associated


Domain annotation for each model (and alignments):
>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   9.1e-07    0.0081       1      52 [.       6      57 ..       6     362 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 9.1e-07
                                      EEEE--CCC.--.S-H..HHHHHHHHHCT-SEEEEEEEEBTTHHHHHHHHHHH CS
                                      xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP  1 dlHvHteys.lldgalsieelvkkakelglkaiaiTDhgnlfgyvefykaakk 52
                                      dlH+H++ys ++++ +++  ++++a ++g+  ++  D  +  + ++++k+a  
  gi|298675860|ref|YP_003727610.1|  6 DLHLHSKYSmATSQKMNLPTMAEEAGKKGINLVGTGDCTH-PKWLQEIKKASS 57
                                      89********8889****************9998766554.566666666644 PP

>> PHP_C  PHP-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.4e-06     0.021       7      53 ..     176     224 ..     172     226 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.4e-06
                             PHP_C   7 ArrfAeklglpgtgGSDAHrle..eVGrayTefeepiatpdelleaire 53 
                                       A+r+ e + l ++ +SDAH+++  ++ r +T fe p  +++ + +ai +
  gi|298675860|ref|YP_003727610.1| 176 ADRIKELHRLTFLTNSDAHSPWsnKLAREFTRFEVPDINFEGIEKAILR 224
                                       8999999*************98446999999999999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2573.86
//
Query:       gi|298675861|ref|YP_003727611.1|  [L=292]
Description: RNA methylase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-55  187.6   0.0    2.5e-55  187.3   0.0    1.1  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    2.3e-08   34.4   0.0      8e-08   32.7   0.0    1.9  2  Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransfer
    1.5e-07   31.7   0.0      5e-07   30.0   0.0    1.8  2  FtsJ             FtsJ-like methyltransferase
    6.9e-07   29.2   0.1      2e-06   27.7   0.0    1.8  2  Methyltransf_31  Methyltransferase domain
    0.00013   21.4   0.0     0.0058   16.0   0.0    2.2  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    0.00062   19.6   0.0     0.0015   18.4   0.0    1.6  2  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
  ------ inclusion threshold ------
       0.03   14.1   0.0      0.058   13.1   0.0    1.4  1  Met_10           Met-10+ like-protein
      0.032   14.9   0.0       0.31   11.7   0.0    2.2  1  Methyltransf_11  Methyltransferase domain
      0.056   13.7   0.0       0.09   13.0   0.0    1.3  1  DUF2431          Domain of unknown function (DUF2431)
       0.11   12.0   0.0       0.26   10.7   0.0    1.6  2  Methyltransf_4   Putative methyltransferase


Domain annotation for each model (and alignments):
>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.3   0.0   1.4e-58   2.5e-55       2     200 .]      88     289 ..      87     289 .. 0.90

  Alignments for each domain:
  == domain 1  score: 187.3 bits;  conditional E-value: 1.4e-58
                                       HHH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC. CS
                   Methyltr_RsmB-F   2 llLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgge 78 
                                       l+L+p + +++lD+caaPG+KT+ ++ lm+n+g+++A+d++k+R++++ +n++rLg+ n++vle D+r+i++ +   
  gi|298675861|ref|YP_003727611.1|  88 LALNPIPYDRVLDMCAAPGSKTSQMSVLMENTGEILANDISKNRIRSLLSNVSRLGCVNVQVLERDGRNIPEKSK-- 162
                                       689*******************************************************************87665.. PP

                                       .EEEEEEEE--CCGGGTTT-TCHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES--STTTTHHHHHHHHH CS
                   Methyltr_RsmB-F  79 lfDriLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLk 155
                                        fDr+L+DaPCs+ g  r+++d+    + ++i+++++lq  ll+ a+ l k+gG++vYsTC+ ++eEne v+ ++L+
  gi|298675861|ref|YP_003727611.1| 163 -FDRVLVDAPCSAEGNARKNNDLLNGADTETITRISELQTSLLKKAFRLCKTGGTVVYSTCTFAPEENEIVVSKFLN 238
                                       .**********************99999************************************************9 PP

                                       H....-TTEEE.ESSBSTTSTTSSECEEC.TSEEE-TTTTSS-SEEEEEEE CS
                   Methyltr_RsmB-F 156 k....redvel.vetelsepkglklgeea.gtlrllPhtenkdgffiaklk 200
                                       +    ++d +l  ++ lse +  klg+e  + +r++Ph+ +  g+f+ak+k
  gi|298675861|ref|YP_003727611.1| 239 HgkleKPDLNLpHSLGLSEWNDKKLGKELeNCIRVYPHQLDSGGIFVAKFK 289
                                       622224455552345566666677776656789****************96 PP

>> Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransferase RsmF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0   4.4e-11     8e-08       8      87 ..       3      81 ..       1      83 [. 0.89
   2 ?   -2.5   0.0       4.1   7.4e+03       8      40 ..     111     143 ..     107     158 .. 0.71

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 4.4e-11
                                      HHHHHHGGGHHHHHHHHH-----EEE--TTS..TTHHHHHHH..-SS--B-TT-TTEEES---...TTSHHHHTTS-EE CS
                   Methyltr_RsmF_N  8 kmkellgeeaeaflaaleeprkkglRvNtlKisveeleklse..efelepvpwceeGfyleeeerpgkhplheaGlyYi 84
                                      +++++++ e+++f + +++p+++ +R+Nt+K++v e+++l +  +f++e+ +w +e  +l+ + +pgk+ lh  G y++
  gi|298675861|ref|YP_003727611.1|  3 RYRNIIP-EFKRFKKVIHSPQPYDIRINTIKANVPEIKSLLTqtGFSFEQRDWNNE--FLKVDFEPGKSILHWIGKYHV 78
                                      5666654.89****************************9877789********987..7888889************** PP

                                      --T CS
                   Methyltr_RsmF_N 85 QEp 87
                                      QE 
  gi|298675861|ref|YP_003727611.1| 79 QES 81
                                      **6 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.1
                                       HHHHHHGGGHHHHHHHHH-----EEE--TTS.. CS
                   Methyltr_RsmF_N   8 kmkellgeeaeaflaaleeprkkglRvNtlKis 40 
                                       +m+ l+++  e + + ++++r ++l  N  ++ 
  gi|298675861|ref|YP_003727611.1| 111 QMSVLMENTGEILANDISKNRIRSLLSNVSRLG 143
                                       677777777777777888888888877776655 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   2.8e-10     5e-07      23     144 ..      96     231 ..      40     253 .. 0.73
   2 ?   -1.0   0.0      0.92   1.7e+03     119     135 ..     272     288 ..     266     291 .. 0.81

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 2.8e-10
                                       -EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS...HHHTTEEEE.CS-CCCSSHHHHHCHCHHHSSEEEEEE-- CS
                              FtsJ  23 ktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm...aplpgvtti.qgditdpetiekikealserkvdlvvsDg 95 
                                       ++v+D +aaPG+ +  ++  ++++g ++a D+ ++   ++l++v+ + + +++  e   +     +++k+d v+ D 
  gi|298675861|ref|YP_003727611.1|  96 DRVLDMCAAPGSKTSQMSVLMENTGEILANDISKNrirSLLSNVSRLgCVNVQVLERDGRNI--PEKSKFDRVLVDA 170
                                       67***********999999998899*******999666444777777766665554444222..23579*******9 PP

                                       S-SS-CH.HHHHHHHH..........CCCCHHHHCCHCCCCECCCEEEECCCHCCCHH.HH CS
                              FtsJ  96 apdvsgv.hdldeylq..........sqLllaalelalkllkpggtfvlkifrgeete.al 144
                                         + +g+ ++   +l+          s+L  + l+ a++l+k+ggt+v  +++++  e ++
  gi|298675861|ref|YP_003727611.1| 171 PCSAEGNaRKNNDLLNgadtetitriSELQTSLLKKAFRLCKTGGTVVYSTCTFAPEEnEI 231
                                       876777643344444467777777777999******************9999965554233 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.92
                                       CCHCCCCECCCEEEECC CS
                              FtsJ 119 elalkllkpggtfvlki 135
                                       ++  ++l+ gg+fv+k+
  gi|298675861|ref|YP_003727611.1| 272 RVYPHQLDSGGIFVAKF 288
                                       5667899********97 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.3   2.3e+03      54      67 ..      45      59 ..      37      67 .. 0.72
   2 !   27.7   0.0   1.1e-09     2e-06       6     123 ..      97     233 ..      95     284 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.3
                   Methyltransf_31 54 dnveFeqgdiee.le 67
                                      + ++Feq d+++ + 
  gi|298675861|ref|YP_003727611.1| 45 TGFSFEQRDWNNeFL 59
                                      46789**99998554 PP

  == domain 2  score: 27.7 bits;  conditional E-value: 1.1e-09
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsn. 81 
                                       rvlD  ++ G +t ++  ++   +e+   Dis++ i++  +n ++lg  nv++ + d  +++++   +kfD +l + 
  gi|298675861|ref|YP_003727611.1|  97 RVLDMCAAPGSKTSQMSVLMENTGEILANDISKNRIRSLLSNVSRLGCVNVQVLERDGRNIPEK---SKFDRVLVDa 170
                                       79***************888889***************************************54...9********6 PP

                   Methyltransf_31  82 ....................evlnaladpd.kileeiervlkpggilliedprllaelpakve 123
                                                           e++  +++++ + l++++r+ k+gg ++ +++  + e  ++v 
  gi|298675861|ref|YP_003727611.1| 171 pcsaegnarknndllngadtETITRISELQtSLLKKAFRLCKTGGTVVYSTCTFAPEENEIVV 233
                                       66666666666666666555555555544415667****************994444444444 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   3.3e-06    0.0058      49     120 ..      96     166 ..      72     170 .. 0.91
   2 ?    3.3   0.0     0.024        43     133     150 ..     201     218 ..     175     238 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.3e-06
                                       TEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEE CS
                   Ubie_methyltran  49 akvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvv 120
                                        +vlD+++  g  + ++s  ++++g++   Di++n ++     + + g +n++ l  ++ ++p++   fD v
  gi|298675861|ref|YP_003727611.1|  96 DRVLDMCAAPGSKTSQMSVLMENTGEILANDISKNRIRSLLSNVSRLGCVNVQVLERDGRNIPEK-SKFDRV 166
                                       589***********************************************************976.456665 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.024
                                       HHHHHHHHHHEEEEEEEE CS
                   Ubie_methyltran 133 lkaLkeayrvlkpGGrlv 150
                                       +  Lk+a+r  k GG++v
  gi|298675861|ref|YP_003727611.1| 201 TSLLKKAFRLCKTGGTVV 218
                                       34589**********987 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   8.1e-07    0.0015      74     150 ..      95     170 ..      73     177 .. 0.93
   2 ?   -3.3   0.0       3.5   6.3e+03     161     170 ..     276     285 ..     273     288 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 8.1e-07
                                       T-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-SEEEEEESS CS
                              PCMT  74 garvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeekaPYdaihvga 150
                                        +rvL++ +  G +t  ++ l++++g +++ + +k+ +++   n+ +l+  nv+v + DGr+  +ek+ +d+++v a
  gi|298675861|ref|YP_003727611.1|  95 YDRVLDMCAAPGSKTSQMSVLMENTGEILANDISKNRIRSLLSNVSRLGCVNVQVLERDGRN-IPEKSKFDRVLVDA 170
                                       689*********************************************************97.89********9987 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.5
                                       HTEEEEEEEE CS
                              PCMT 161 dQLkeGGrlv 170
                                       +QL++GG++v
  gi|298675861|ref|YP_003727611.1| 276 HQLDSGGIFV 285
                                       69*****988 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.2e-05     0.058     102     181 ..      96     175 ..      89     187 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.2e-05
                                       -EEEETT-TTTCCHHHCCHH.TTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---TT-EEEEEE--T CS
                            Met_10 102 evVvdvfAGiGpfaipiaky.skakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevireqladrvvmnlp 177
                                       ++V+d+ A  G  +  ++++  +  ++la+d+  + ++ l +n+ +    + v++++ Dgr++ +++++drv+ ++p
  gi|298675861|ref|YP_003727611.1|  96 DRVLDMCAAPGSKTSQMSVLmENTGEILANDISKNRIRSLLSNVSRLGCVN-VQVLERDGRNIPEKSKFDRVLVDAP 171
                                       68999999999877666665146789*****************97655443.557********************99 PP

                                       TTGG CS
                            Met_10 178 ksai 181
                                        sa+
  gi|298675861|ref|YP_003727611.1| 172 CSAE 175
                                       8875 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00018      0.31       7      93 ..     109     216 ..      99     219 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00018
                                       TSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC-.C...... CS
                   Methyltransf_11   7 tGrlaealakrgarvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhhv.e...... 75 
                                       t +++  ++ + +++++ D+sk+ ++   +++s+ g  +v++++ d +++p  +++fD v++        +      
  gi|298675861|ref|YP_003727611.1| 109 TSQMSVLME-NTGEILANDISKNRIRSLLSNVSRLGCvNVQVLERDGRNIPE-KSKFDRVLVDAPCSAEgNarknnd 183
                                       444444444.446***************9999999999***********995.559**9998763322221223333 PP

                                       ...............CHHHHHHHHHHHEEEEEE CS
                   Methyltransf_11  76 ...............dpekalkeiaRvLkpgGl 93 
                                                       + ++lk++ R++k gG+
  gi|298675861|ref|YP_003727611.1| 184 llngadtetitriseLQTSLLKKAFRLCKTGGT 216
                                       444444444444444556666666666666666 PP

>> DUF2431  Domain of unknown function (DUF2431)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     5e-05      0.09      53     134 ..     139     234 ..     107     275 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5e-05
                           DUF2431  53 vkvlfgVDatkleksklqeklkkekfdriifnFPhvggkstdvnr.........qvranqeLlvsffksakellsek 120
                                       v+ l  V+++ le+   ++  +k+kfdr+++  P+   + + +n+          +    eL +s++k+a +l + +
  gi|298675861|ref|YP_003727611.1| 139 VSRLGCVNVQVLER-DGRNIPEKSKFDRVLVDAPCSAEGNARKNNdllngadteTITRISELQTSLLKKAFRLCKTG 214
                                       44444566666663.3356677888***********888777776688888888888888***************** PP

                           DUF2431 121 pgeilvtlfegep.......y 134
                                        g+++ + ++  p        
  gi|298675861|ref|YP_003727611.1| 215 -GTVVYSTCTFAPeeneivvS 234
                                       .99999999888743333330 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00015      0.26       5      60 ..      98     154 ..      96     171 .. 0.86
   2 ?   -3.2   0.0       2.7   4.8e+03      96     118 ..     200     222 ..     197     246 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00015
                                       EEEET-TTSHHHHHHHH.HSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-C CS
                    Methyltransf_4   5 vleiGcGkGeflvalAk.knPdknflGiEirvkvvakvlkkiealelkNlrilrgda 60 
                                       vl+++ + G+ +++++  ++ + ++l+ +i++++++ +l+++ +l++ N+++l+ d 
  gi|298675861|ref|YP_003727611.1|  98 VLDMCAAPGSKTSQMSVlMENTGEILANDISKNRIRSLLSNVSRLGCVNVQVLERDG 154
                                       7899***********962678889******************************998 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.7
                                       SHHHHHHHHHHEEEEEEEEEEES CS
                    Methyltransf_4  96 qpellkelarvLkkgGvlelaTD 118
                                       q  llk++ r  k gG ++  T 
  gi|298675861|ref|YP_003727611.1| 200 QTSLLKKAFRLCKTGGTVVYSTC 222
                                       66778888888888888877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2066.44
//
Query:       gi|298675862|ref|YP_003727612.1|  [L=153]
Description: hypothetical protein Metev_1987 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00015   21.6   0.9    0.00031   20.7   0.4    1.9  2  Methyltranf_PUA  RNA-binding PUA-like domain of methyltransfe


Domain annotation for each model (and alignments):
>> Methyltranf_PUA  RNA-binding PUA-like domain of methyltransferase RsmF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.25   4.4e+03       4      14 ..      30      40 ..      29      50 .. 0.76
   2 !   20.7   0.4   1.7e-08   0.00031      17      47 ..     108     138 ..      86     141 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.25
                   Methyltranf_PUA  4 YlkGetielep 14
                                      Yl G++i l++
  gi|298675862|ref|YP_003727612.1| 30 YLLGNSIWLTS 40
                                      88899988876 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 1.7e-08
                   Methyltranf_PUA  17 kkGwvlVcydgyplGwgKlvggrlKNkyPkg 47 
                                       ++G+v + y+gy++G+g  +   +KN+ Pk 
  gi|298675862|ref|YP_003727612.1| 108 DNGYVALRYKGYIIGCGMKNSSGVKNQIPKK 138
                                       23***************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1163.05
//
Query:       gi|298675863|ref|YP_003727613.1|  [L=334]
Description: hypothetical protein Metev_1988 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00073   18.8   1.1    0.00096   18.4   1.1    1.1  1  LGT           Prolipoprotein diacylglyceryl transferase
  ------ inclusion threshold ------
      0.026   14.2   0.0        4.4    7.0   0.0    2.3  2  mRNA_triPase  mRNA capping enzyme, beta chain
      0.032   13.3   2.8      0.046   12.8   2.8    1.1  1  COX15-CtaA    Cytochrome oxidase assembly protein
      0.038   14.3   0.7        0.1   12.9   0.7    1.7  1  MapZ_C2       MapZ extracellular C-terminal domain 2
      0.058   13.0   2.1       0.13   11.9   2.1    1.6  1  Wzy_C         O-Antigen ligase
      0.058   12.7   0.3      0.081   12.2   0.3    1.2  1  Peptidase_U4  Sporulation factor SpoIIGA
       0.21   11.9   2.7       0.43   10.9   2.7    1.5  1  DUF4022       Protein of unknown function (DUF4022)
        1.1    9.0   5.1        1.8    8.4   5.1    1.2  1  DUF4118       Domain of unknown function (DUF4118)


Domain annotation for each model (and alignments):
>> LGT  Prolipoprotein diacylglyceryl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   1.1   4.3e-07   0.00096      12      72 ..       3      68 ..       1      91 [. 0.83

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 4.3e-07
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxx RF
                               LGT 12 rwYgllialgfllavllakrrakkeglkeekdkvddlliyavilgiiGaRlgyvl.....fYylsn 72
                                        +gl+ +++ ++ v+l+ + +kk++l++ k+++++ll+++v+++ + +   yvl      Yy ++
  gi|298675863|ref|YP_003727613.1|  3 GIFGLMTLVAGIVFVVLMVWLWKKSNLSTLKKSILSLLLIVVLIAGVFGSFAYVLissdhAYYSAD 68
                                      579**********************99996668999999999999998888888878888554444 PP

>> mRNA_triPase  mRNA capping enzyme, beta chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0    0.0068        15      84     140 ..     113     171 ..      75     177 .. 0.78
   2 ?    7.0   0.0     0.002       4.4      74     122 ..     190     237 ..     182     303 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0068
                                       H..HTTCCCTTTEEEEEEEEEEEEEE-S-SSS--EEEEEE..ETTT--EEEEEEEEEEE CS
                      mRNA_triPase  84 rrneeenskrekvslkeskevDkfYelkkkeekskirvsk..dsenqevlkkieKeria 140
                                       + +++  + + +v+++ ++++D+f+el+ ++++s ++v+    s++     + +Ke++ 
  gi|298675863|ref|YP_003727613.1| 113 ELEQQFGKDYWVVAINGYYTQDTFFELRFPRDESGTKVTFfnGSRTDPYFSSFKKENLP 171
                                       3356777889999***************7777777777765477799999999999975 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.002
                                       HHHHHHHHHHH..HTTCCCTTTEEEEEEEEEEEEEE-S-SSS--EEEEE CS
                      mRNA_triPase  74 elnnfLnelsrrneeenskrekvslkeskevDkfYelkkkeekskirvs 122
                                       + + +Ln+l+ +  + n++   ++++++  +D++Y+   ++++s+i +s
  gi|298675863|ref|YP_003727613.1| 190 QSQDYLNQLKDKIRNVNKTSVGITIQKTPDIDSIYKSY-QNKSSNITLS 237
                                       45678888888889999******************998.7777777766 PP

>> COX15-CtaA  Cytochrome oxidase assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   2.8   2.1e-05     0.046      88     130 ..      11      53 ..       7      63 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.1e-05
                        COX15-CtaA  88 llGllilvpllyflakkrisrelkkllllllllvglQGllGww 130
                                       ++G++++v++++ ++k ++s+  k  l lll++v++ G++G +
  gi|298675863|ref|YP_003727613.1|  11 VAGIVFVVLMVWLWKKSNLSTLKKSILSLLLIVVLIAGVFGSF 53 
                                       78***************************************87 PP

>> MapZ_C2  MapZ extracellular C-terminal domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.7   4.5e-05       0.1      25      59 ..      77     110 ..      56     133 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.5e-05
                           MapZ_C2  25 kekviatsierGyiveggyilervriengegyYnl 59 
                                       + kvi++++e Gy v+g y ++  +ien +g Y  
  gi|298675863|ref|YP_003727613.1|  77 YGKVINNARESGYTVNGPYFVN-SEIENANGLYSP 110
                                       469****************986.69******9964 PP

>> Wzy_C  O-Antigen ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.1   5.9e-05      0.13      20     136 ..       8     240 ..       3     242 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.9e-05
                             Wzy_C  20 igllvalivlliifykrri......pfllllgilvgvilliilfv................................ 58 
                                       ++l++++++++++++ ++       ++ +l+++l++v+++ ++ +                                
  gi|298675863|ref|YP_003727613.1|   8 MTLVAGIVFVVLMVWLWKKsnlstlKKSILSLLLIVVLIAGVFGSfayvlissdhayysadglnldevdygkvinna 84 
                                       45555555555555555555599987777777777777777666678888888888888888888888888888888 PP

                             Wzy_C  59 ...................lstnletlknitkafgkldkk..................................... 79 
                                                                      +  + l+++                                     
  gi|298675863|ref|YP_003727613.1|  85 resgytvngpyfvnseienA-------NGLYSPLSELEQQfgkdywvvaingyytqdtffelrfprdesgtkvtffn 154
                                       88888877777744444441.......33333333333335555555566666666677777777777777777777 PP

                             Wzy_C  80 ..............................kgkdksgssRlyiwkralplikdspilGtGvfdfpqgdligkyyayd 126
                                                                     + ++++++  l+  k+ ++ ++++   G+  + +p+ d+i+k y+++
  gi|298675863|ref|YP_003727613.1| 155 gsrtdpyfssfkkenlpddewiidrfmllfDIDNNQSQDYLNQLKDKIRNVNKTS-VGITIQKTPDIDSIYKSYQNK 230
                                       7777777777777777888888888888877788888888888888888888887.666688888888888888888 PP

                             Wzy_C 127 tpnivvdkaH 136
                                       ++ni+   +H
  gi|298675863|ref|YP_003727613.1| 231 SSNITLSPTH 240
                                       8888777766 PP

>> Peptidase_U4  Sporulation factor SpoIIGA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3   3.6e-05     0.081      59     113 ..       7      60 ..       2     114 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.6e-05
                      Peptidase_U4  59 llsillkilvsllmvliafgpkslkeflkalllfylvsfllgGilfalsylllks 113
                                       l+++++ i++ +lmv++  ++ +l+ + k +l ++l+ +l++G+   + y+l++s
  gi|298675863|ref|YP_003727613.1|   7 LMTLVAGIVFVVLMVWL-WKKSNLSTLKKSILSLLLIVVLIAGVFGSFAYVLISS 60 
                                       5678888999*****99.8************************999999977654 PP

>> DUF4022  Protein of unknown function (DUF4022)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.7   0.00019      0.43      30      72 ..      16      58 ..       4      62 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00019
                           DUF4022 30 sieicsygwkksngikysclllslllgtasilgllaapayffi 72
                                       + +  + wkksn       +lslll    i g++ + ay +i
  gi|298675863|ref|YP_003727613.1| 16 FVVLMVWLWKKSNLSTLKKSILSLLLIVVLIAGVFGSFAYVLI 58
                                      44566788*****99999999*******************998 PP

>> DUF4118  Domain of unknown function (DUF4118)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   5.1   0.00081       1.8       5      51 ..      12      60 ..       5      65 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00081
                           DUF4118  5 vlllalatllallldkl.ls.l.anivllfllavllvallgglgpgllaa 51
                                      +++++ ++l+ +l++k  ls l ++i+ l+l++vl++ ++g++++ l+++
  gi|298675863|ref|YP_003727613.1| 12 AGIVF-VVLMVWLWKKSnLStLkKSILSLLLIVVLIAGVFGSFAYVLISS 60
                                      22233.33333444443455345888889999999999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1549  (0.0863963); expected 358.6 (0.02)
Passed bias filter:                     1070  (0.0596798); expected 358.6 (0.02)
Passed Vit filter:                       187  (0.01043); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.47
# Mc/sec: 2152.40
//
Query:       gi|298675864|ref|YP_003727614.1|  [L=399]
Description: hypothetical protein Metev_1989 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.6e-26   91.3   0.3    9.6e-26   91.3   0.3    2.4  3  MacB_PCD  MacB-like periplasmic core domain
    3.8e-13   49.7  15.2    4.3e-13   49.5   2.5    3.2  3  FtsX      FtsX-like permease family
  ------ inclusion threshold ------
      0.096   12.9   0.0       0.23   11.7   0.0    1.6  1  DUF2543   Protein of unknown function (DUF2543)
       0.17   11.3   3.3       0.55    9.6   0.0    2.7  3  Jiraiya   Jiraiya
          3    7.9   6.1        4.9    7.3   0.4    2.6  2  DUF3042   Protein of unknown function (DUF3042)


Domain annotation for each model (and alignments):
>> MacB_PCD  MacB-like periplasmic core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.3   0.3   2.7e-29   9.6e-26       1     193 [.      17     232 ..      17     234 .. 0.79
   2 ?   -4.8   6.1         5   1.8e+04       5      57 ..     275     320 ..     271     370 .. 0.52
   3 ?   -2.4   0.2       1.4   5.1e+03       8      21 ..     365     378 ..     362     381 .. 0.58

  Alignments for each domain:
  == domain 1  score: 91.3 bits;  conditional E-value: 2.7e-29
                          MacB_PCD   1 slltvLGiaiGvaaviaivslgeglqasvlsqisdlgnlvtvtpgkgsgeslsdpdvealrrevp.veavapvv... 73 
                                       s+lt LGi+iGvaavia vslg+++++ ++++i ++g++++v  + ++ + + d+++++l+ + p +++v+pv+   
  gi|298675864|ref|YP_003727614.1|  17 SMLTTLGIVIGVAAVIANVSLGASFSQFFEDEIGAAGDNFIVIFS-NDVNLFYDNQFDLLK-STPgIVGVSPVIqkp 91 
                                       78********************************99987766555.788889999997775.5699******99999 PP

                          MacB_PCD  74 .tvrgggsgeeevtvvgvdpdyfkvfglklaeGrffteadlrggpnvvvigeelaerlf........pvGdtirl.. 139
                                        tv +g+s e+++ + g+++dy ++ +++l++G f++++    +++v+v+g+e+a++ f         +     +  
  gi|298675864|ref|YP_003727614.1|  92 aTVEYGSS-ERSIEIFGTTEDYKRIGNINLESGNFLSDN----DKYVAVLGYEIANDKFdrdisnrnSID----Itf 159
                                       87788876.55599***999********9999**99774....689***********9999775544344....355 PP

                          MacB_PCD 140 .........kpftVvGvled.pp...gsgsalg..ddavylplttlqrrs........itvrlkdgadleaaaaele 193
                                                ++f+V G+ ed  p   g+g      + ++++p++t+q  +        +++++++ +++ +++++++
  gi|298675864|ref|YP_003727614.1| 160 rrndgtertETFRVKGITEDrDPsfvGGG---PnpEERIFIPMSTMQD-MlnredyggFALTASSLENIREISDDVD 232
                                       66999999999******988644454322...245889****998842.2244556778888888777777777766 PP

  == domain 2  score: -4.8 bits;  conditional E-value: 5
                          MacB_PCD   5 vLGiaiG.vaaviaivslgeglqasvlsqisdlgnlvtvtpgkgsgeslsdpdv 57 
                                        L i ++ +  v++ +++++ ++ +v+++ ++ g l+  ++g       ++ dv
  gi|298675864|ref|YP_003727614.1| 275 ALLISVAlISLVVGSIGIMNIMLVTVTERTREIG-LM-KSVG------YTYYDV 320
                                       3333333355566666788888888888777666.23.2232......355555 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.4
                          MacB_PCD   8 iaiGvaaviaivsl 21 
                                       i+iG+++ ++++++
  gi|298675864|ref|YP_003727614.1| 365 IIIGFGVAVLVGVI 378
                                       55555555555544 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.3    0.0025       8.9      14      65 ..      12      63 ..       6      81 .. 0.80
   2 ?    1.2   0.6      0.15   5.2e+02      65      85 ..     272     292 ..     252     302 .. 0.53
   3 !   49.5   2.5   1.2e-16   4.3e-13       2      96 .]     305     392 ..     304     392 .. 0.97

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0025
                              FtsX 14 kkqvlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisid 65
                                      + +++ +l+t +++i++ a ++ + lg+ ++q++ d +++  +++ + +s d
  gi|298675864|ref|YP_003727614.1| 12 SSKLRSMLTTLGIVIGVAAVIANVSLGASFSQFFEDEIGAAGDNFIVIFSND 63
                                      5678888888888888888888899999999999999999877655555544 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.15
                              FtsX  65 dlitvliiivlllllallagl 85 
                                        l+++li ++l+ l++  +g+
  gi|298675864|ref|YP_003727614.1| 272 ALSALLISVALISLVVGSIGI 292
                                       333333333333333333333 PP

  == domain 3  score: 49.5 bits;  conditional E-value: 1.2e-16
                              FtsX   2 reigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivllll 78 
                                       reig+++++G++  +vl l+++e+++i+l++ +iG+ +g+l a+  +++l        l+  ++++ ++i++++++l
  gi|298675864|ref|YP_003727614.1| 305 REIGLMKSVGYTYYDVLILFIVESVVIGLFGGIIGTTVGILGAYGANTFL-------DLPNVFPVELIIIGFGVAVL 374
                                       9*******************************************988886.......899***************** PP

                              FtsX  79 lallagllsiskilkkep 96 
                                       + ++ag++++sk++k++p
  gi|298675864|ref|YP_003727614.1| 375 VGVIAGVYPASKAAKMDP 392
                                       ****************98 PP

>> DUF2543  Protein of unknown function (DUF2543)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.4e-05      0.23      36      70 ..     214     248 ..     202     254 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.4e-05
                           DUF2543  36 fqllitrltnneeiseeaqkemareagideqride 70 
                                       f l  + l n  eis++  k++ar  g++e+++d+
  gi|298675864|ref|YP_003727614.1| 214 FALTASSLENIREISDDVDKRLARSLGVPERQLDN 248
                                       7788889**************************96 PP

>> Jiraiya  Jiraiya
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.3     0.063   2.3e+02     134     157 ..      14      37 ..       2      46 .. 0.79
   2 ?    9.6   0.0   0.00015      0.55      38      76 ..     255     293 ..     235     312 .. 0.77
   3 ?   -2.3   0.0       0.7   2.5e+03     138     162 ..     365     388 ..     361     392 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.063
                           Jiraiya 134 ivtsiilgvGivllllalvhnvyv 157
                                        + s++  +Giv+ ++a++ nv +
  gi|298675864|ref|YP_003727614.1|  14 KLRSMLTTLGIVIGVAAVIANVSL 37 
                                       556788899999999999999865 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00015
                           Jiraiya  38 stvvseeeaavvlevavaLsaLaltlnlscllvcalqll 76 
                                       +++ ++e   +v ++++aLsaL +++ l +l+v ++ ++
  gi|298675864|ref|YP_003727614.1| 255 TIFNQAEILDQVGQISAALSALLISVALISLVVGSIGIM 293
                                       45556677899**********************988654 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.7
                           Jiraiya 138 iilgvGivllllalvhnvyvwqrek 162
                                       ii+g G+ +l+ +++  vy +++++
  gi|298675864|ref|YP_003727614.1| 365 IIIGFGVAVLV-GVIAGVYPASKAA 388
                                       78999988764.5666777776665 PP

>> DUF3042  Protein of unknown function (DUF3042)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.9     0.041   1.5e+02       6      19 ..      22      35 ..      21      42 .. 0.83
   2 ?    7.3   0.4    0.0014       4.9      10      35 ..     369     394 ..     367     397 .. 0.95

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.041
                           DUF3042  6 kGflvGvlatiaav 19
                                       G+++Gv+a ia v
  gi|298675864|ref|YP_003727614.1| 22 LGIVIGVAAVIANV 35
                                      79*********976 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0014
                           DUF3042  10 vGvlatiaavagavfvfKkkviePiE 35 
                                       +Gv++ ++++ag+  + K    +P+E
  gi|298675864|ref|YP_003727614.1| 369 FGVAVLVGVIAGVYPASKAAKMDPVE 394
                                       7***********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       793  (0.04423); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.62
# Mc/sec: 1931.87
//
Query:       gi|298675865|ref|YP_003727615.1|  [L=404]
Description: hypothetical protein Metev_1990 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-26   94.4   3.7    1.1e-26   94.4   3.7    1.8  2  MacB_PCD  MacB-like periplasmic core domain
    1.8e-11   44.3   4.0    1.8e-11   44.3   4.0    3.1  3  FtsX      FtsX-like permease family
  ------ inclusion threshold ------
       0.12   12.6   0.1       0.24   11.7   0.1    1.4  1  DUF525    ApaG domain
          7    6.6  14.2         13    5.8  11.7    2.5  2  Rhomboid  Rhomboid family


Domain annotation for each model (and alignments):
>> MacB_PCD  MacB-like periplasmic core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.4   3.7   2.5e-30   1.1e-26       1     193 [.      22     237 ..      22     239 .. 0.79
   2 ?   -5.4   4.1         4   1.8e+04      13      37 ..     289     313 ..     277     377 .. 0.61

  Alignments for each domain:
  == domain 1  score: 94.4 bits;  conditional E-value: 2.5e-30
                          MacB_PCD   1 slltvLGiaiGvaaviaivslgeglqasvlsqisdlgnlvtvtpgkgsgeslsdpdvealrrevp.veavapvv... 73 
                                       s+lt LGi+iGvaavia vslg+++ +++++++ ++gn++++  g ++ + + ++++e+++r  p v++v+pvv   
  gi|298675865|ref|YP_003727615.1|  22 SALTTLGIIIGVAAVIANVSLGASFGQYFDDEVGAAGNNFILIEG-QDVNIFHENELETIKR-TPgVVGVSPVVqqs 96 
                                       89********************************99997765555.5566677888887765.589******98766 PP

                          MacB_PCD  74 ..tvrgggsgeeevtvvgvdpdyfkvfglklaeGrffteadlrggpnvvvigeelaerlf........pvGdtirl. 139
                                         +++ +g  +++v+v+gv++dy +v ++++a+G f+++     +++++vige++ ++ f         +  t+r  
  gi|298675865|ref|YP_003727615.1|  97 gqVQYMSG--TRQVNVQGVTEDYEEVANFNMAAGNFLSDK----DKYSAVIGEDVSTDKFdkdisnrnSIDITLRRn 167
                                       53223333..5669****999********99****99774....5889********999999887766454444447 PP

                          MacB_PCD 140 ......kpftVvGvledppgsgsalg.....ddavylplttlqrrs.........itvrlkdgadleaaaaele 193
                                             ++f+V G++++p g++ +l+     d ++++p++t++  +         ++v++++ +++ ++++e++
  gi|298675865|ref|YP_003727615.1| 168 dgtevtQTFKVKGIIKSP-GTT-FLQsgiepDERIFIPISTMN--EmlgreyyggFFVQATNLESVGEVSEEID 237
                                       777778*********765.444.23335778*******99992..2235556677****************996 PP

  == domain 2  score: -5.4 bits;  conditional E-value: 4
                          MacB_PCD  13 aaviaivslgeglqasvlsqisdlg 37 
                                         +++ +++++ ++ +v+++ ++ g
  gi|298675865|ref|YP_003727615.1| 289 SLIVGSIGIMNIMLVTVTERTREIG 313
                                       3334444566666666665555444 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   0.1    0.0084        38       9      54 ..      11      57 ..       7      98 .. 0.76
   2 ?   -0.7   1.0      0.46   2.1e+03      38      48 ..     282     292 ..     269     306 .. 0.46
   3 !   44.3   4.0     4e-15   1.8e-11       2      96 .]     310     397 ..     309     397 .. 0.97

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0084
                              FtsX  9 alGmkkkqvlllllteillitlvalviG.lglgllaaqllsdvllss 54
                                      a+G  + + l+  lt + +i+ va+vi+ + lg+ + q++ d +++ 
  gi|298675865|ref|YP_003727615.1| 11 AIGSISSSKLRSALTTLGIIIGVAAVIAnVSLGASFGQYFDDEVGAA 57
                                      66766666667777777777777777776888888888888777766 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.46
                              FtsX  38 glgllaaqlls 48 
                                       +++++++ l+ 
  gi|298675865|ref|YP_003727615.1| 282 LVSVALISLIV 292
                                       22222222222 PP

  == domain 3  score: 44.3 bits;  conditional E-value: 4e-15
                              FtsX   2 reigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivllll 78 
                                       reig+++++G++  +vl l+++e++++++++ ++G ++g+  a +++++l       +l+  ++++ +++++ +++l
  gi|298675865|ref|YP_003727615.1| 310 REIGLMKSIGFTYYDVLMLFIVESIIVGILGGILGAVFGVSGALAVNNLL-------NLPNVFPVELIIAGFSVAVL 379
                                       9*****************************************99999996.......89****************** PP

                              FtsX  79 lallagllsiskilkkep 96 
                                       + l+ag++++sk++k++p
  gi|298675865|ref|YP_003727615.1| 380 VGLIAGVYPASKAAKMDP 397
                                       ****************98 PP

>> DUF525  ApaG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   5.4e-05      0.24      36      77 ..      71     112 ..      58     117 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.4e-05
                                       EEETTS-EEEEEEESBTTB--EE-TTEEEEEEEEEEESSSEE CS
                            DUF525  36 itdadgkveevegeGvvGeqPlLepgesFeYtSgvsletpsG 77 
                                       i ++++ ++  + +GvvG  P++++  + +Y Sg++  + +G
  gi|298675865|ref|YP_003727615.1|  71 IFHENELETIKRTPGVVGVSPVVQQSGQVQYMSGTRQVNVQG 112
                                       5665555555589*********************99877666 PP

>> Rhomboid  Rhomboid family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.25   1.1e+03      11      42 ..      24      55 ..      15      64 .. 0.71
   2 ?    5.8  11.7    0.0028        13      40     123 ..     294     390 ..     270     400 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.25
                                      HHGGG--SSHHHHHHHHHHHHHHHHHHHHHHH CS
                          Rhomboid 11 ltsmflHagwlHllfNmlallvfGsplerrlG 42
                                      lt + + +g++ +++N+    +fG+ + +++G
  gi|298675865|ref|YP_003727615.1| 24 LTTLGIIIGVAAVIANVSLGASFGQYFDDEVG 55
                                      55555556777788888888888888777776 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0028
                                       HHHHHHHHHHHHH.....HHHHHHHHHHHHH-S...........-EESSHHHHHHHHHHHHHHHHCCCCGS----HC CS
                          Rhomboid  40 rlGslrflllyll.....sglagsllsllfsaeses........plvGaSGaifgllgallvlvprnrkllrkliia 103
                                        +G ++++l++++      gl+ s+++ +++  +          +l G  Ga+fg+ gal+v+ + n  +++ + ++
  gi|298675865|ref|YP_003727615.1| 294 SIGIMNIMLVTVTertreIGLMKSIGFTYYDVLMLFivesiivgILGGILGAVFGVSGALAVNNLLNLPNVFPVELI 370
                                       3344444444444888888888888888888886448888899999******************************9 PP

                                       ...CCCCCCCCCCHHHCTSS CS
                          Rhomboid 104 llllllfillnlvlgllpra 123
                                       +  + + +l+ l+ g++p  
  gi|298675865|ref|YP_003727615.1| 371 IAGFSVAVLVGLIAGVYPAS 390
                                       99999999999999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2729.93
//
Query:       gi|298675866|ref|YP_003727616.1|  [L=411]
Description: hypothetical protein Metev_1991 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0053   16.7   1.0     0.0079   16.1   0.1    1.7  2  Gram_pos_anchor  LPXTG cell wall anchor motif
     0.0056   16.9   0.5         11    6.3   0.0    3.8  4  CARDB            CARDB
  ------ inclusion threshold ------
       0.04   14.2   0.0         11    6.4   0.0    2.6  2  DUF11            Domain of unknown function DUF11
      0.054   13.9   0.3      0.095   13.1   0.3    1.4  1  FeoB_associated  FeoB-associated Cys-rich membrane protein


Domain annotation for each model (and alignments):
>> Gram_pos_anchor  LPXTG cell wall anchor motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       1.2   5.4e+03      13      22 ..     166     175 ..     166     175 .. 0.87
   2 !   16.1   0.1   1.8e-06    0.0079      14      43 .]     379     410 ..     379     410 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.2
                                       XXXXXXXXXX CS
                   Gram_pos_anchor  13 Gengniflta 22 
                                       G++g+i++t+
  gi|298675866|ref|YP_003727616.1| 166 GDTGTISFTL 175
                                       8999999996 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.8e-06
                                       XXXXXXXXXXXXXXXXXXXXX..XXXXXXXX. CS
                   Gram_pos_anchor  14 engnifltaaGllallggllL..lvkrRKkek 43 
                                       e+++++  ++G+l++++g++    ++rRK+++
  gi|298675866|ref|YP_003727616.1| 379 EQSSNIAAIGGVLVIVAGAVAfmIYRRRKNKN 410
                                       799********77777777777*999999875 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.0    0.0025        11       5      42 ..      38      74 ..      33     114 .. 0.89
   2 ?   -1.1   0.0      0.53   2.4e+03      34      52 ..      99     118 ..      89     134 .. 0.74
   3 !    5.1   0.0     0.006        27       9      78 ..     157     244 ..     150     275 .. 0.80
   4 ?    0.5   0.1      0.16   7.2e+02      18      92 ..     284     362 ..     270     367 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0025
                                      EE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEE CS
                             CARDB  5 tvtntlnpseafvgeentitvtvkNqGtaasgatkval 42
                                       + +++nps+a  ge + + ++v N G+++ +++++++
  gi|298675866|ref|YP_003727616.1| 38 SI-SKYNPSPAQIGEYVDVWIKVDNVGSGKVEDVSIEI 74
                                      45.8899**********************999998876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.53
                                       -EEEEEEEEEETTEEE.EEE CS
                             CARDB  34 asgatkvalyldgelv.gtv 52 
                                       +s ++k +ly+d++ + +t+
  gi|298675866|ref|YP_003727616.1|  99 SSVEHKYRLYVDENAKpSTS 118
                                       46667778888877765444 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.006
                                       EEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEE................SEE-CTEEEEEEEEE CS
                             CARDB   9 tlnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtv................psLaagesttvsftw 69 
                                       +++p+ + +g++ ti++t+kN+ ++   ++  +++ +    + +t+                  L +g+s ++s+++
  gi|298675866|ref|YP_003727616.1| 157 HAEPEVMMPGDTGTISFTLKNTASQRTVKIGDEIFENNVRIQRATLhgcdridvesesyqggGLLGPGDSMDISYNI 233
                                       67788999999***********9999999999999999999888887777777788888887778888888888877 PP

                                       E-S..-S-CEE CS
                             CARDB  70 tte..ategev 78 
                                        ++  a+ g+ 
  gi|298675866|ref|YP_003727616.1| 234 NVDenAEVGTC 244
                                       77754444555 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.16
                                       TSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE..EEEEESEE-CTEEEEEEEEEE-S..-S-CEEEEEEEESTT-SS CS
                             CARDB  18 geentitvtvkNqGtaasgatkvalyldgelv..gtvtvpsLaagesttvsftwtte..ategevtltvvvDpdnev 90 
                                       + e t+++ v+N       +++v+l ++g +   +   +  ++++e  t+++   ++    +g+ +l +++   n  
  gi|298675866|ref|YP_003727616.1| 284 NGEGTLEFDVANVRPNPLSSVNVELQAEGVEFspSPYFIGTMSPDELFTIEVDTSVIsdNLTGTRELMITANYRNGM 360
                                       55668888888888888999999999999988666677788888887777666666555667777788887777777 PP

                                       -- CS
                             CARDB  91 aE 92 
                                       +E
  gi|298675866|ref|YP_003727616.1| 361 NE 362
                                       76 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0    0.0063        28       6      35 ..      43      72 ..      39     114 .. 0.91
   2 ?    6.4   0.0    0.0025        11       8      83 ..     161     240 ..     157     248 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0063
                             DUF11  6 dksevrpGdtvtytltvtNtgpasangvvv 35
                                      ++s+++ G+ v++ + v N g  + ++v +
  gi|298675866|ref|YP_003727616.1| 43 NPSPAQIGEYVDVWIKVDNVGSGKVEDVSI 72
                                      6789******************99999876 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0025
                             DUF11   8 sevrpGdtvtytltvtNtgpasangvvvtDtlP.aglayvsvsasqgtasaltsv......gsLeagesatlsftvr 77 
                                       + + pGdt t   t++Nt  +    v++ D     ++++++++   g  + ++ +      g L +g s  +s+ ++
  gi|298675866|ref|YP_003727616.1| 161 EVMMPGDTGTISFTLKNTASQRT--VKIGDEIFeNNVRIQRATLH-GCDRIDVESesyqggGLLGPGDSMDISYNIN 234
                                       56789************988777..99999775377888888888.6666666666677888889999999999888 PP

                             DUF11  78 vtrtaa 83 
                                       v   a+
  gi|298675866|ref|YP_003727616.1| 235 VDENAE 240
                                       877766 PP

>> FeoB_associated  FeoB-associated Cys-rich membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.3   2.1e-05     0.095       5      24 ..     390     409 ..     387     411 .] 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.1e-05
                   FeoB_associated   5 Vgliiaaavafvirrlikkk 24 
                                       V++i+a+avaf+i+r +k+k
  gi|298675866|ref|YP_003727616.1| 390 VLVIVAGAVAFMIYRRRKNK 409
                                       89999*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      692  (0.0385967); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 2515.03
//
Query:       gi|298675867|ref|YP_003727617.1|  [L=238]
Description: ABC transporter-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-33  116.6   0.0    1.5e-33  116.2   0.0    1.2  1  ABC_tran         ABC transporter
    1.7e-07   30.9   0.2    9.7e-07   28.4   0.2    1.8  1  SMC_N            RecF/RecN/SMC N terminal domain
    1.9e-07   31.2   0.0     0.0095   15.8   0.0    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    0.00017   21.2   0.1    0.00032   20.4   0.1    1.4  1  AAA_29           P-loop containing region of AAA domain
    0.00042   20.3   0.0    0.00081   19.3   0.0    1.5  1  RsgA_GTPase      RsgA GTPase
     0.0043   17.6   0.1      0.007   16.9   0.1    1.3  1  AAA_23           AAA domain
     0.0045   17.3   0.3      0.039   14.2   0.0    2.2  2  AAA_22           AAA domain
     0.0054   17.1   0.0     0.0059   17.0   0.0    1.4  1  AAA_16           AAA ATPase domain
     0.0058   15.8   0.0     0.0075   15.5   0.0    1.1  1  G-alpha          G-protein alpha subunit
  ------ inclusion threshold ------
       0.03   13.5   0.2       0.15   11.2   0.1    1.9  2  NB-ARC           NB-ARC domain
      0.034   14.2   0.1      0.087   12.9   0.0    1.7  2  MMR_HSR1         50S ribosome-binding GTPase
      0.034   14.0   0.0       0.15   11.9   0.0    1.9  2  ATPase_2         ATPase domain predominantly from Archaea
      0.037   13.7   0.0       0.24   11.1   0.0    2.0  2  AAA_24           AAA domain
       0.04   13.6   0.0       0.28   10.8   0.0    1.9  2  AAA_15           AAA ATPase domain
      0.042   12.6   0.0       0.63    8.8   0.0    2.0  2  T4SS-DNA_transf  Type IV secretory system Conjugative DNA tra
      0.058   12.4   0.0        0.1   11.7   0.0    1.3  1  T2SSE            Type II/IV secretion system protein
      0.092   12.9   0.1          1    9.5   0.0    2.0  2  AAA_33           AAA domain
      0.094   13.3   0.2       0.17   12.4   0.2    1.9  1  AAA_18           AAA domain
      0.098   12.4   0.0       0.75    9.5   0.0    2.0  2  IstB_IS21        IstB-like ATP binding protein
      0.099   11.4   0.0       0.24   10.1   0.0    1.5  2  RNA12            RNA12 protein
       0.11   12.2   0.0       0.35   10.6   0.0    1.7  2  AAA_30           AAA domain
       0.15   11.8   0.4       0.33   10.6   0.1    1.7  2  Cytidylate_kin   Cytidylate kinase
       0.15   11.6   0.0       0.37   10.3   0.0    1.6  1  AAA_25           AAA domain
       0.15   11.9   0.2        6.1    6.7   0.0    2.4  2  NTPase_1         NTPase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.2   0.0   2.1e-36   1.5e-33       1     136 [.      39     187 ..      39     188 .. 0.92

  Alignments for each domain:
  == domain 1  score: 116.2 bits;  conditional E-value: 2.1e-36
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpe 73 
                                       lkn++l++k+ge vai+G++G+GKStL++++  l +pt G++ ++g+d+++    +  ++    ig+++q  +l p+
  gi|298675867|ref|YP_003727617.1|  39 LKNINLDVKQGEFVAIMGPSGSGKSTLMNIIGCLDRPTCGTLFVEGRDISKmsddELARVRGMVIGFVFQSYNLVPR 115
                                       79************************************************999844444555679************ PP

                                       SBHHHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       lt+ en             + d+++ ++l+ ++l+e    +++++p++LSgGq qrva+ara++++p+l+l+DEpt
  gi|298675867|ref|YP_003727617.1| 116 LTALENvklptyanskgnmDFDKRARDLLKMVRLEE----RMHYKPNKLSGGQSQRVAVARAMINDPSLILADEPT 187
                                       ***********9999888888888888888888887....778999*****************************9 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.2   1.3e-09   9.7e-07      23     210 ..      48     230 ..      33     234 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1.3e-09
                                       TSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  23 sksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsi 99 
                                       + +f ai+Gp GSGKs l++ i  +L   +  +l  e  +d+ + s+++ +  ++ v  ++ ++ + ++  +   ++
  gi|298675867|ref|YP_003727617.1|  48 QGEFVAIMGPSGSGKSTLMNII-GCLDRPTCGTLFVEG-RDISKMSDDELARVRGMVIGFVFQSYNLVPRLTALENV 122
                                       34699***************99.899988877776654.44444455555555555555445555555777777788 PP

                                       EEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 100 srrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknv 176
                                       +   + + + ++ ++++     ++ +l e+++ +++ LSgG+ + va+a      +++  +l l De   +LD k  
  gi|298675867|ref|YP_003727617.1| 123 KLPTYANSKGNMDFDKRARDLLKMVRLEERMHYKPNKLSGGQSQRVAVA----RAMINDPSLILADEPTGNLDSKTS 195
                                       88888888889*******************************9988875....5689999***************** PP

                                       HHHHHHHHHHCTTSEEEE.E-SSHHHCCC-SCEEE CS
                                       xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                             SMC_N 177 kkvaellkeksknaQfiv.islreemlekadklvg 210
                                        ++ +++   +++   iv i+++ ++ e a ++v 
  gi|298675867|ref|YP_003727617.1| 196 DEIMKIFTDLNNKGRTIVmITHEPDVSEYAGRIVH 230
                                       ********999996666538999999998888776 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.1   6.8e-05     0.051       1      22 [.      51      72 ..      51     111 .. 0.85
   2 !   15.8   0.0   1.3e-05    0.0095     240     300 ..     163     220 ..     156     223 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.8e-05
                            AAA_21  1 lnvliGpNgsGKSnLLdaldll 22
                                      + ++ Gp gsGKS+L+ ++ +l
  gi|298675867|ref|YP_003727617.1| 51 FVAIMGPSGSGKSTLMNIIGCL 72
                                      57899**************998 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.3e-05
                            AAA_21 240 GtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpl 300
                                       G+ +  a++ a++ ++   sl+l DEp  +L+ k   ++++++ +l+++g  +++ TH p 
  gi|298675867|ref|YP_003727617.1| 163 GQSQRVAVARAMINDP---SLILADEPTGNLDSKTSDEIMKIFTDLNNKGRTIVMITHEPD 220
                                       5555545555555555...9**************************************996 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   4.2e-07   0.00032      17      39 ..      44      66 ..      37      72 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 4.2e-07
                            AAA_29 17 ieidlkgatlltGpsGsGKSTll 39
                                      +++++ +++ ++GpsGsGKSTl+
  gi|298675867|ref|YP_003727617.1| 44 LDVKQGEFVAIMGPSGSGKSTLM 66
                                      455544499*************8 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.1e-06   0.00081      87     119 ..      36      69 ..       5      79 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.1e-06
                                       HTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHH CS
                       RsgA_GTPase  87 kegleelkellkd.ktsvlvGqSGvGKStLinal 119
                                        + l++++  +k+ ++++++G+SG GKStL+n +
  gi|298675867|ref|YP_003727617.1|  36 LQILKNINLDVKQgEFVAIMGPSGSGKSTLMNII 69 
                                       556677777777779*****************86 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   9.4e-06     0.007      11      39 ..      40      69 ..      20      71 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 9.4e-06
                            AAA_23 11 rdqeidFsk.gltlItGpNGaGKTTildAi 39
                                      ++ ++d ++  +++I Gp G+GK+T+++ i
  gi|298675867|ref|YP_003727617.1| 40 KNINLDVKQgEFVAIMGPSGSGKSTLMNII 69
                                      44555555526889*************987 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   5.2e-05     0.039       4      23 ..      48      67 ..      44      73 .. 0.89
   2 ?    0.5   0.0      0.88   6.6e+02      59     117 ..     142     207 ..     111     224 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.2e-05
                            AAA_22  4 tagilvvtGesGtGKTtllr 23
                                      +  +++++G+sG+GK+tl++
  gi|298675867|ref|YP_003727617.1| 48 QGEFVAIMGPSGSGKSTLMN 67
                                      67899*************96 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.88
                            AAA_22  59 ellralglelkaerlsseell.ealeqalrarav...ielliiDEaqh.lr...seealeeLrslln 117
                                       +ll+ + le      +   l   + ++ + ara+   ++l++ DE    l+   s+e+++ + +l n
  gi|298675867|ref|YP_003727617.1| 142 DLLKMVRLEERM-HYKPNKLSgGQSQRVAVARAMindPSLILADEPTGnLDsktSDEIMKIFTDLNN 207
                                       555555555554.333333333566666666666677888888886655764333444444444444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   7.9e-06    0.0059      11      43 ..      38      68 ..      32     215 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 7.9e-06
                            AAA_16 11 qLlsalervrsgrpelvllsGesGvGKsslvre 43
                                       L+++  +v++g  e v + G+sG+GKs+l++ 
  gi|298675867|ref|YP_003727617.1| 38 ILKNINLDVKQG--EFVAIMGPSGSGKSTLMNI 68
                                      454444467777..79**************964 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0     1e-05    0.0075      26     154 ..      52     230 ..      33     236 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1e-05
                                       EEEEESTTSSHHHHHHHHHHHCS--.............--HHHHHCCHHHHHHHHHHHHHHH..HHHHHHTT..... CS
                           G-alpha  26 llllGqseSGKsTilkqlkllykkg.............fseeelatwraviqlnivrsikti..lealesleselse 87 
                                       + ++G s+SGKsT+++ + +l +++             +s++ela  r +++  + +s +++  l ale+ + +   
  gi|298675867|ref|YP_003727617.1|  52 VAIMGPSGSGKSTLMNIIGCLDRPTcgtlfvegrdiskMSDDELARVRGMVIGFVFQSYNLVprLTALENVKLPT-- 126
                                       6789**********************************9999***************999883345555532222.. PP

                                       .........HHHC-SS-SCCCS-HCHHHH..............................................HH CS
                           G-alpha  88 sf.......elqelkerldplkkveasliaklssateee....................................qe 121
                                        +       + +++ ++l ++  +e++++    ++++ +                                      
  gi|298675867|ref|YP_003727617.1| 127 -YanskgnmDFDKRARDLLKMVRLEERMH---YKPNKLSggqsqrvavaramindpsliladeptgnldsktsdeIM 199
                                       .1333444455555555555555555443...333333334444466666666665555555555544444322211 PP

                                       CCHHC....-HCHHHHHHHHCCSHHHHHHHCCGCCTT CS
                           G-alpha 122 iefnp....raevgedikaLwndpgiqelyerrnkik 154
                                           +     ++ g+ i+++ ++p ++e+  r   ++
  gi|298675867|ref|YP_003727617.1| 200 ----KiftdLNNKGRTIVMITHEPDVSEYAGRI--VH 230
                                       ....12222344455888888888888877766..44 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1    0.0002      0.15      20      38 ..      49      67 ..      34      71 .. 0.81
   2 ?   -0.0   0.0      0.54     4e+02     113     148 ..     190     226 ..     141     232 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0002
                                      SEEEEEEESTTSSHHHHHH CS
                            NB-ARC 20 slvvalvGmgGvGKttlak 38
                                        +va++G  G+GK+tl++
  gi|298675867|ref|YP_003727617.1| 49 GEFVAIMGPSGSGKSTLMN 67
                                      359**************97 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.54
                                       -SHHHH.....HHHHCHTTSE.EEEEESBCCCCCCS- CS
                            NB-ARC 113 weeedwdkigvvlparenrlr.vllTTRdeevanavs 148
                                        ++++ d+i+  + + +n+ r +++ T + +v+++++
  gi|298675867|ref|YP_003727617.1| 190 LDSKTSDEIMKIFTDLNNKGRtIVMITHEPDVSEYAG 226
                                       4556677777777777776652556677777777665 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00012     0.087       2      19 ..      52      69 ..      51      91 .. 0.92
   2 ?   -2.6   0.0       7.8   5.8e+03      46      55 ..     178     187 ..     163     226 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                                      EEEEESTTSSHHHHHHHH CS
                          MMR_HSR1  2 vaivGrpNvGKStLinal 19
                                      vai+G + +GKStL+n +
  gi|298675867|ref|YP_003727617.1| 52 VAIMGPSGSGKSTLMNII 69
                                      89**************75 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 7.8
                                       EEEEEEECGG CS
                          MMR_HSR1  46 keielvDtpG 55 
                                       ++++l+D p 
  gi|298675867|ref|YP_003727617.1| 178 PSLILADEPT 187
                                       4455555443 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00021      0.15       7      38 ..      35      67 ..      33      83 .. 0.84
   2 ?   -0.4   0.0       1.2     9e+02     101     123 ..     193     215 ..     118     219 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00021
                          ATPase_2  7 elkeleei.lerepneiyfiYGpegsGKtaLlk 38
                                      el+ l++i l+ ++ e++ i Gp gsGK++L++
  gi|298675867|ref|YP_003727617.1| 35 ELQILKNInLDVKQGEFVAIMGPSGSGKSTLMN 67
                                      66666666467788999**************98 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.2
                          ATPase_2 101 lvfkaielllekikkkgkkiiii 123
                                       +    i +++ ++++kg+ i++i
  gi|298675867|ref|YP_003727617.1| 193 KTSDEIMKIFTDLNNKGRTIVMI 215
                                       44557888899999999988887 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00032      0.24       5      22 ..      52      69 ..      49     105 .. 0.86
   2 ?    0.0   0.0      0.78   5.8e+02     108     131 ..     195     218 ..     189     222 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00032
                            AAA_24  5 iliyGpsgiGKTtlakel 22
                                      ++i+Gpsg+GK+tl++ +
  gi|298675867|ref|YP_003727617.1| 52 VAIMGPSGSGKSTLMNII 69
                                      78************9876 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.78
                            AAA_24 108 aeefrrllkklqelrknvifiahe 131
                                        +e++++ ++l++ + ++++i he
  gi|298675867|ref|YP_003727617.1| 195 SDEIMKIFTDLNNKGRTIVMITHE 218
                                       6899999999999999****9997 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00038      0.28      14      71 ..      39      93 ..      37     151 .. 0.81
   2 ?    0.3   0.0      0.61   4.5e+02     322     367 ..     176     220 ..     165     221 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00038
                            AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeni 71
                                      lk++ +d++   +  + G+ +sGKS++++++  +   +    + ++++e  d++++ ++
  gi|298675867|ref|YP_003727617.1| 39 LKNINLDVKQGeFVAIMGPSGSGKSTLMNIIGCLDRPT----CGTLFVEGRDISKMSDD 93
                                      577667776668*******************9888877....78888888888777655 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.61
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSph 367
                                       +++ ++l +EP  +L  +   +++k + +l n+++  +++ TH p 
  gi|298675867|ref|YP_003727617.1| 176 NDPSLILADEPTGNLDSKTSDEIMKIFTDLNNKGR-TIVMITHEPD 220
                                       67889999999999999999999999999999999.8888899885 PP

>> T4SS-DNA_transf  Type IV secretory system Conjugative DNA transfer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00085      0.63      11      59 ..      10      64 ..       2      74 .. 0.63
   2 ?    1.8   0.0      0.11        83     145     221 ..     134     210 ..     116     230 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00085
                   T4SS-DNA_transf 11 agllkrektikgevltkdkkalyagg..........llntdGdfehvlvvAptrsgKgv 59
                                        +  r+k i++  l   +k++++g+          l +++G  e+v +++p++sgK++
  gi|298675867|ref|YP_003727617.1| 10 LESDVRDKSIIT--LNNICKSYWVGDmelqilkninLDVKQG--EFVAIMGPSGSGKST 64
                                      444455555555..4444556777776665533233444555..66***********97 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.11
                   T4SS-DNA_transf 145 dffsntarqLlval....iaevllkketetegqtlkvvramlsepnledenkeeaklleelkgkeedrvgdnlrvlv 217
                                         f + ar+Ll+ +     ++++ +k    ++q + v ram  +p      ++ ++ + +l+ k +d++++ + +l 
  gi|298675867|ref|YP_003727617.1| 134 MDFDKRARDLLKMVrleeRMHYKPNKLSGGQSQRVAVARAMINDP----SLILADEPTGNLDSKTSDEIMKIFTDLN 206
                                       45999*******998665555555666666677777788888888....8999999999999999999999999999 PP

                   T4SS-DNA_transf 218 ektd 221
                                       +k++
  gi|298675867|ref|YP_003727617.1| 207 NKGR 210
                                       8887 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00013       0.1     111     149 ..      31      69 ..       8      75 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                             T2SSE 111 eealkekiaevlrkavrerglilvsGgTgsGKttllyal 149
                                        ++++ +i + ++  v++   + + G+ gsGK+tl++++
  gi|298675867|ref|YP_003727617.1|  31 VGDMELQILKNINLDVKQGEFVAIMGPSGSGKSTLMNII 69 
                                       566778889999999999999***************975 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0    0.0014         1       2      16 ..      52      66 ..      51      83 .. 0.90
   2 ?    1.7   0.0      0.36   2.7e+02      63     108 ..     171     221 ..      90     230 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0014
                            AAA_33  2 vllvGlpGsGKstla 16
                                      v + G++GsGKstl 
  gi|298675867|ref|YP_003727617.1| 52 VAIMGPSGSGKSTLM 66
                                      5678*********96 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.36
                            AAA_33  63 arkalsagrnvildat..nlsrrerarflklarrlgvp...vrivvvetde 108
                                       ar +      +++d +  nl+ ++ ++++k++ +l+ +   + +++ e+d 
  gi|298675867|ref|YP_003727617.1| 171 ARAMINDPSLILADEPtgNLDSKTSDEIMKIFTDLNNKgrtIVMITHEPDV 221
                                       444444444455566566999999999999999888663224444444444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   0.00023      0.17       1      18 [.      52      69 ..      52     231 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00023
                            AAA_18  1 IlltGtpGvGKttlakeL 18
                                      ++++G++G+GK+tl + +
  gi|298675867|ref|YP_003727617.1| 52 VAIMGPSGSGKSTLMNII 69
                                      689***********9887 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0     0.001      0.75      44      68 ..      46      70 ..      33      81 .. 0.86
   2 ?    0.5   0.0       0.6   4.5e+02     108     154 ..     176     224 ..     141     231 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.001
                         IstB_IS21 44 iekkenivllGpsGvGKshlaialg 68
                                      +++ e ++++GpsG GKs l   +g
  gi|298675867|ref|YP_003727617.1| 46 VKQGEFVAIMGPSGSGKSTLMNIIG 70
                                      678899************9977666 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.6
                         IstB_IS21 108 kvdllilDdlgllpldqaeaellfeviekrye..rrsiiitsnlpfaew 154
                                       +   lil d  + +ld++ + +++++  +  +  r+ ++it +  ++e+
  gi|298675867|ref|YP_003727617.1| 176 NDPSLILADEPTGNLDSKTSDEIMKIFTDLNNkgRTIVMITHEPDVSEY 224
                                       3344666666788899999999999998876511556677877777776 PP

>> RNA12  RNA12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00033      0.24      13      56 ..      45      90 ..      36      97 .. 0.68
   2 ?   -1.2   0.0      0.84   6.3e+02     342     395 ..      87     141 ..      85     147 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00033
                             RNA12 13 eEnvntFivvkGPrGSGkkeLvldrvlkdrkk..vlvidCdelvka 56
                                      + ++  F+ + GP GSGk+ L+      dr +  +l+++ +++ k 
  gi|298675867|ref|YP_003727617.1| 45 DVKQGEFVAIMGPSGSGKSTLMNIIGCLDRPTcgTLFVEGRDISKM 90
                                      556778*************998322233333355666666666665 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.84
                             RNA12 342 ikklskkgsieynellleelfkgsaes.alkaLekaelisvstedgrpskikagk 395
                                       i+k+s+++  + + ++   +f++ +    l+aLe+  l +  +++g ++  k ++
  gi|298675867|ref|YP_003727617.1|  87 ISKMSDDELARVRGMVIGFVFQSYNLVpRLTALENVKLPTYANSKGNMDFDKRAR 141
                                       6789999999999999999999955445999****99999999999877655555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00046      0.35      18      38 ..      49      69 ..      42      82 .. 0.86
   2 ?   -1.3   0.0         2   1.5e+03      81     114 ..     167     204 ..     136     215 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00046
                            AAA_30 18 drvavltGpAGtGKttalkal 38
                                        ++++ Gp G+GK+t+++ +
  gi|298675867|ref|YP_003727617.1| 49 GEFVAIMGPSGSGKSTLMNII 69
                                      35899*************976 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2
                            AAA_30  81 k...grarlepgtllivDE.agmvdtkqlaallkaaek 114
                                       +   +ra +++ +l++ DE +g +d+k+ ++++k+ ++
  gi|298675867|ref|YP_003727617.1| 167 RvavARAMINDPSLILADEpTGNLDSKTSDEIMKIFTD 204
                                       04444455666688888886677788888887777666 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00044      0.33       1      18 [.      52      69 ..      52      73 .. 0.90
   2 ?   -2.5   0.0       4.7   3.5e+03     115     123 ..      80      88 ..      76      90 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00044
                                      EEEE-STTSSHHHHHHHH CS
                    Cytidylate_kin  1 iaiDGPagsGKssvaral 18
                                      +ai GP+gsGKs++  ++
  gi|298675867|ref|YP_003727617.1| 52 VAIMGPSGSGKSTLMNII 69
                                      799**********98876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.7
                                       EEEEESSII CS
                    Cytidylate_kin 115 vvveGRDig 123
                                       + veGRDi+
  gi|298675867|ref|YP_003727617.1|  80 LFVEGRDIS 88 
                                       679****96 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00049      0.37      31      49 ..      47      65 ..      38      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00049
                            AAA_25 31 pagelallaGapgtGKttl 49
                                        ge+++++G++g+GK+tl
  gi|298675867|ref|YP_003727617.1| 47 KQGEFVAIMGPSGSGKSTL 65
                                      689***************9 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0082       6.1       2      19 ..      52      69 ..      51      89 .. 0.84
   2 ?    2.9   0.0      0.12        89      86     149 ..     168     233 ..     135     236 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0082
                                      EEEE--TTSSHHHHHHHH CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkv 19
                                      v+i Gp+G+GK+Tl++ +
  gi|298675867|ref|YP_003727617.1| 52 VAIMGPSGSGKSTLMNII 69
                                      6899**********8754 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHH-EEEE--.-STTGGG-HHHHHHHHHHHT.TTSEEEEE--SS--SHHHHHHHT-TT CS
                          NTPase_1  86 lealrkalseadviviDE.iGkmElkskkfkeaveevLk.sekpvlavihrrkdlalveeirerkd 149
                                       +++ r +++++ +i+ DE  G++  k+   + ++ + L+ +++ ++++ h+++ ++   +i + kd
  gi|298675867|ref|YP_003727617.1| 168 VAVARAMINDPSLILADEpTGNLDSKTSDEIMKIFTDLNnKGRTIVMITHEPDVSEYAGRIVHLKD 233
                                       445566669999*****988***9998877777777777699999999999998888888877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 1612.40
//
Query:       gi|298675868|ref|YP_003727618.1|  [L=170]
Description: hypothetical protein Metev_1993 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0014   18.5   0.0     0.0021   17.9   0.0    1.3  1  MarR_2    MarR family
     0.0017   18.5   0.0     0.0032   17.6   0.0    1.4  1  HTH_34    Winged helix DNA-binding domain
     0.0044   16.9   0.0     0.0091   15.9   0.0    1.6  1  MarR      MarR family
  ------ inclusion threshold ------
      0.012   15.1   0.0      0.025   14.1   0.0    1.5  1  HTH_24    Winged helix-turn-helix DNA-binding
      0.014   15.3   0.0       0.04   13.9   0.0    1.8  1  HTH_11    HTH domain
      0.021   15.2   1.6       0.03   14.7   0.4    2.0  2  YbbR      YbbR-like protein
      0.025   14.7   0.3       0.14   12.3   0.0    1.9  2  FUR       Ferric uptake regulator family
      0.026   15.0   1.1      0.029   14.9   1.1    1.1  1  AAA_23    AAA domain
      0.034   13.7   0.1      0.067   12.7   0.1    1.5  1  HTH_CodY  CodY helix-turn-helix domain
      0.041   13.8   0.3        6.3    6.8   0.0    2.8  3  CtsR      CtsR N-terminal HTH domain
      0.062   13.4   0.0       0.12   12.5   0.0    1.4  1  DprA_WH   DprA winged helix domain


Domain annotation for each model (and alignments):
>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.3e-06    0.0021      17      58 ..      35      75 ..      20      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.3e-06
                                      TTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSS CS
                            MarR_2 17 rpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpe 58
                                      +p+ +++++ela+++g+s +++s+ ++ L+  G+v+r++ p+
  gi|298675868|ref|YP_003727618.1| 35 EPD-EIAMSELADETGYSLASISNKIRFLEISGYVVRSKKPG 75
                                      554.49*******************************98765 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0     2e-06    0.0032      12      53 ..      36      77 ..      26      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2e-06
                            HTH_34 12 vdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgk 53
                                       de+ ++el ++++ + + +s +++ Le  gY++++k+   k
  gi|298675868|ref|YP_003727618.1| 36 PDEIAMSELADETGYSLASISNKIRFLEISGYVVRSKKPGTK 77
                                      69999******************************9986555 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   5.6e-06    0.0091      18      57 ..      39      78 ..      31      80 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.6e-06
                                      EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTT CS
                              MarR 18 lsvseLakklgvskstvtrvldrLekkGlieRskspeDrR 57
                                      + +seLa+  g s +++++ ++ Le  G++ Rsk+p+ ++
  gi|298675868|ref|YP_003727618.1| 39 IAMSELADETGYSLASISNKIRFLEISGYVVRSKKPGTKK 78
                                      6789********************************8666 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.5e-05     0.025      18      47 ..      39      68 ..      35      69 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.5e-05
                            HTH_24 18 isqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      i ++eLA+++g S++ ++  ++ Le +G++
  gi|298675868|ref|YP_003727618.1| 39 IAMSELADETGYSLASISNKIRFLEISGYV 68
                                      889**********************99998 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.5e-05      0.04       8      50 ..      31      73 ..      25      75 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.5e-05
                            HTH_11  8 lLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIesep 50
                                      +L+ + + i  +eLA+e++ S + + + I+ Le +g+ + s++
  gi|298675868|ref|YP_003727618.1| 31 RLFIEPDEIAMSELADETGYSLASISNKIRFLEISGYVVRSKK 73
                                      566666669999************************9999885 PP

>> YbbR  YbbR-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.4   1.8e-05      0.03      14      46 ..      65     101 ..      64     133 .. 0.77
   2 ?   -2.1   0.0       3.1     5e+03      35      54 ..     149     166 ..     148     168 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.8e-05
                                       TT-EEEE--.-EEEEEEEE-HHHH....HHHTTS--- CS
                              YbbR  14 egyvvvsgtpepvtVtvtGpesvl....dkieevkae 46 
                                       +gyvv s +p +++V +++ +++l    ++i++v+++
  gi|298675868|ref|YP_003727618.1|  65 SGYVVRSKKPGTKKVYLYARKEILdvviEQISNVRTN 101
                                       69**********************8888777777664 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.1
                                       HHHHHHTTS----EEE-TT- CS
                              YbbR  35 svldkieevkaevyvDlsgl 54 
                                       + ++kiee+k +    ls++
  gi|298675868|ref|YP_003727618.1| 149 DMVKKIEEIKSSS--HLSDV 166
                                       6789999999877..77776 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   8.9e-05      0.14      23     103 ..      33     109 ..      25     121 .. 0.79
   2 ?    0.4   0.1      0.41   6.6e+02      14      41 ..     130     158 ..     121     162 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.9e-05
                                       SBEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEESSSSSEEEEEETTT--EEEE--HHHHH CS
                               FUR  23 hlsaeevykelkeedpeislaTVYrtLklleeaglvkelefedgesryelakkehhdhlicekCgkviefkddeiek 99 
                                       +++ +e+ ++   ++   sla++ + +++le +g v + +  +++++y  a ke  d +i+ +   + +++ +ei+k
  gi|298675868|ref|YP_003727618.1|  33 FIEPDEIAMSELADETGYSLASISNKIRFLEISGYVVRSKKPGTKKVYLYARKEILDVVIE-Q---ISNVRTNEIKK 105
                                       67889999999999999*************************9999999996555554444.3...55555666665 PP

                                       HHHH CS
                               FUR 100 iqee 103
                                        + e
  gi|298675868|ref|YP_003727618.1| 106 AKFE 109
                                       5544 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.41
                                       HHHHHHHSS.SBEHHHHHHHHHHTTTT-- CS
                               FUR  14 levleksee.hlsaeevykelkeedpeis 41 
                                       +++l+ + +  l+++++ ++++++ +ei 
  gi|298675868|ref|YP_003727618.1| 130 ITILRGYYNdLLKIDDILEDMVKKIEEIK 158
                                       45666655558889999999999998884 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   1.1   1.8e-05     0.029      75     183 ..      57     158 ..      15     166 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-05
                            AAA_23  75 veltfenkdgrytrsiererelskkkgkttkkaklelleideleqfisellgskkiilnlilflgqerfeefelkdk 151
                                        +++f  ++g   + ++ +++ +kk   + +k++l+ + ++ ++ +++e+ + k++i ++i ++ +e+     ++++
  gi|298675868|ref|YP_003727618.1|  57 NKIRFLEISG---YVVRSKKPGTKKVYLYARKEILDVVIEQISNVRTNEIKKAKFEIPSMIEYYNSENL----NESQ 126
                                       6777888888...77888888888888888999999999999999999999999999999999999998....7888 PP

                            AAA_23 152 kerleelekeleeledekkllekleqekekek 183
                                       k+++  l+  +++l ++++ le+  ++ e+ k
  gi|298675868|ref|YP_003727618.1| 127 KQKITILRGYYNDLLKIDDILEDMVKKIEEIK 158
                                       89999999999999999998888855555444 PP

>> HTH_CodY  CodY helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   4.1e-05     0.067       6      47 ..      40      82 ..      37      98 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.1e-05
                          HTH_CodY  6 taskiaDriGitrsvivnaLrkLesaG.iiesrsLGmkGtYlk 47
                                        s++aD+ G   + i n +r Le +G ++ s+  G k  Yl 
  gi|298675868|ref|YP_003727618.1| 40 AMSELADETGYSLASISNKIRFLEISGyVVRSKKPGTKKVYLY 82
                                      5699********************8886899********9984 PP

>> CtsR  CtsR N-terminal HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0038       6.3      45      62 ..      58      75 ..      34      83 .. 0.80
   2 ?    4.1   0.1     0.026        43       3      27 ..     111     135 ..     109     143 .. 0.86
   3 ?   -2.6   0.0       3.3   5.3e+03       2      13 ..     143     154 ..     142     161 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0038
                              CtsR 45 ktRFtaekGylvesrrGg 62
                                      k RF   +Gy+v s++ g
  gi|298675868|ref|YP_003727618.1| 58 KIRFLEISGYVVRSKKPG 75
                                      459************977 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.026
                              CtsR   3 sdlieeyikelleeseeeeveikRn 27 
                                         +ie y  e l+es++++++i R 
  gi|298675868|ref|YP_003727618.1| 111 PSMIEYYNSENLNESQKQKITILRG 135
                                       578******************9985 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 3.3
                              CtsR   2 lsdlieeyikel 13 
                                       + d++e+++k++
  gi|298675868|ref|YP_003727618.1| 143 IDDILEDMVKKI 154
                                       456666666654 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   7.2e-05      0.12      10      57 ..      21      70 ..      15      72 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.2e-05
                           DprA_WH 10 lddlerrvLaaL..gpePvhvDqLvrrtglpaaevsaaLleLELaGlver 57
                                       d+l ++++a+L  +p+ +++ +L+ +tg + a++s     LE++G+v r
  gi|298675868|ref|YP_003727618.1| 21 MDELTATLFARLfiEPDEIAMSELADETGYSLASISNKIRFLEISGYVVR 70
                                      68899999999999999*******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       849  (0.0473534); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1147.82
//
Query:       gi|298675869|ref|YP_003727619.1|  [L=411]
Description: SufBD protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.3e-57  192.6   0.1    1.1e-56  192.0   0.1    1.3  1  UPF0051   Uncharacterized protein family (UPF0051)


Domain annotation for each model (and alignments):
>> UPF0051  Uncharacterized protein family (UPF0051)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.0   0.1   6.1e-61   1.1e-56       2     218 .]     160     383 ..     159     383 .. 0.96

  Alignments for each domain:
  == domain 1  score: 192.0 bits;  conditional E-value: 6.1e-61
                           UPF0051   2 qfertlivveegaevtiieeyagc............gvveifvgenAklkyvkvqnwsedavnlstkraeegrdakl 66 
                                       q+++++i+vee+ae++ii   +gc            g++e++v+++ kl++++++nw+ed+ + +++++++++  ++
  gi|298675869|ref|YP_003727619.1| 160 QTVHNIIIVEENAELEII---TGCttkeevmsglhlGISEMYVKKGGKLTFTMIHNWAEDIGVRPRTKIKVEEGGTF 233
                                       899***************...888888999999999*********************************999999** PP

                           UPF0051  67 elttvslggkltrk.epsvelkgegaeaelnglylakgkqhldtrtkvdhngpntssrilskgvlkdearavfrgki 142
                                         +++ l+   +++ +p++ l+g+ga a++n++++++ +++ld+++kv+ n p+t+++++s+++ + ++++v rg++
  gi|298675869|ref|YP_003727619.1| 234 INNYIALKPVKSIQsYPTAFLDGKGAVARFNTIAVGHPGSELDLGSKVEFNSPETKAELISRTITT-GGNVVARGEM 309
                                       *******998654449**************************************************.599******* PP

                           UPF0051 143 kvrkgaqktdahqenrnLllsdkaradtiPeleidaddvkasHgAtvGkideeqlfYLmsRGlseeeArrlivrgf 218
                                        v  +a ++++h e+r L+lsd+++  +iP+le++ ++v+++H+A+vGki+ +q+ YLmsRGlse+eA  +ivrgf
  gi|298675869|ref|YP_003727619.1| 310 -VG-NADNAKGHLECRGLVLSDDGSQRAIPILEANLQNVELTHEAAVGKIARDQVEYLMSRGLSEDEAVGMIVRGF 383
                                       .55.5**********************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2582.47
//
Query:       gi|298675870|ref|YP_003727620.1|  [L=252]
Description: ABC transporter-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-20   74.0   0.0    2.5e-20   73.4   0.0    1.3  1  ABC_tran     ABC transporter
    5.1e-08   33.1   0.3      6e-06   26.3   0.2    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    3.2e-06   26.8   0.3     0.0012   18.3   0.1    2.2  2  SMC_N        RecF/RecN/SMC N terminal domain
    2.8e-05   24.7   0.2    5.9e-05   23.7   0.2    1.7  1  AAA_23       AAA domain
     0.0012   18.6   0.0     0.0035   17.1   0.0    1.6  2  AAA_15       AAA ATPase domain
     0.0014   18.4   0.1     0.0044   16.7   0.0    1.8  2  AAA_29       P-loop containing region of AAA domain
     0.0035   16.1   0.2      0.006   15.3   0.2    1.3  1  AAA_13       AAA domain
  ------ inclusion threshold ------
       0.02   14.8   0.1       0.41   10.5   0.0    2.6  3  RsgA_GTPase  RsgA GTPase
      0.026   15.1   0.1        3.1    8.3   0.1    2.3  1  AAA_18       AAA domain
       0.03   14.7   0.3       0.32   11.4   0.3    2.2  1  AAA          ATPase family associated with various cellular a
      0.036   14.0   0.1      0.067   13.1   0.0    1.6  2  ATPase_2     ATPase domain predominantly from Archaea
       0.21   12.0   0.0        0.5   10.7   0.0    1.8  2  AAA_16       AAA ATPase domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.4   0.0   1.7e-23   2.5e-20       1     136 [.      21     161 ..      21     162 .. 0.91

  Alignments for each domain:
  == domain 1  score: 73.4 bits;  conditional E-value: 1.7e-23
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTS..S--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagl..lkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpel 74 
                                       l+nv+l++  g + +++G+nG+GKS Ll++++g   +k  eG+il++g+d+++    e+++k +g++ q p    ++
  gi|298675870|ref|YP_003727620.1|  21 LNNVNLTVDFGYTNVLFGPNGSGKSALLRAIMGFgdYKVVEGRILFNGEDITNlSVDERAEKGLGIMLQRPPNMTGV 97 
                                       79*****************************986226669*************99999************7777777 PP

                                       BHHHH.....HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  75 tvren.....esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       ++ +      +++ +i+k+++ l++k + d+ +      +SgG+ +r +l ++++++p ++l+DEp 
  gi|298675870|ref|YP_003727620.1|  98 KLSSLikaiaKENMDIDKVAEDLDMKRFMDREI---NVGFSGGEIKRSELLQLIAQNPCMYLIDEPE 161
                                       666659999999999*****************9...689**************************95 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.2     4e-09     6e-06       2      25 ..      34      57 ..      33     138 .. 0.74
   2 ?    5.2   0.0     0.011        16     259     274 ..     153     168 ..     134     203 .. 0.67

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 4e-09
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarl 25
                                      nvl GpNgsGKS LL+a+ ++ ++
  gi|298675870|ref|YP_003727620.1| 34 NVLFGPNGSGKSALLRAIMGFGDY 57
                                      9*****************555332 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.011
                            AAA_21 259 sllliDEpEngLHPkl 274
                                         +liDEpE+g +   
  gi|298675870|ref|YP_003727620.1| 153 CMYLIDEPESGVDLVS 168
                                       578********98744 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   8.3e-07    0.0012      26      50 ..      33      54 ..      19      84 .. 0.84
   2 !    6.8   0.0    0.0026       3.9     137     186 ..     134     179 ..      85     191 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 8.3e-07
                                      EEEEEESTTSSHHHHHHHHHHHCTT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKsnlldAilFvLGe 50
                                       +++ GpNGSGKs ll Ai   +G+
  gi|298675870|ref|YP_003727620.1| 33 TNVLFGPNGSGKSALLRAI---MGF 54
                                      6899***************...444 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0026
                                       S-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 137 LSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkek 186
                                       +SgGe + + l  l+    ++  ++yl+De ++  D   ++kv + ++e 
  gi|298675870|ref|YP_003727620.1| 134 FSGGEIKRSELLQLI----AQNPCMYLIDEPESGVDLVSINKVGTKIQEM 179
                                       577776655544443....3667********************9999875 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.2   3.9e-08   5.9e-05      12      39 ..      25      51 ..      18     151 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 3.9e-08
                            AAA_23 12 dqeidFskgltlItGpNGaGKTTildAi 39
                                      + ++dF+   ++++GpNG+GK+++l+Ai
  gi|298675870|ref|YP_003727620.1| 25 NLTVDFG-YTNVLFGPNGSGKSALLRAI 51
                                      4578888.89*****************9 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.3e-06    0.0035      17      50 ..      26      58 ..      21     152 .. 0.68
   2 ?   -1.6   0.0       1.2   1.7e+03     321     333 ..     149     161 ..     138     184 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.3e-06
                            AAA_15 17 veidlseeltvliGkNnsGKSsilealdlFlnnk 50
                                       ++d+   ++vl G+N+sGKS +l+a+  F + k
  gi|298675870|ref|YP_003727620.1| 26 LTVDFGY-TNVLFGPNGSGKSALLRAIMGFGDYK 58
                                      5678888.9******************8887744 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.2
                            AAA_15 321 eeknvilliEEPE 333
                                        +++  +li+EPE
  gi|298675870|ref|YP_003727620.1| 149 AQNPCMYLIDEPE 161
                                       5678889999999 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0     3e-06    0.0044      19      43 ..      28      52 ..      20      54 .. 0.78
   2 ?   -2.1   0.0       2.3   3.4e+03      33      39 ..     193     199 ..     186     201 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3e-06
                            AAA_29 19 idlkg.atlltGpsGsGKSTllDAiq 43
                                      +d  g + +l Gp+GsGKS+ll Ai+
  gi|298675870|ref|YP_003727620.1| 28 VDF-GyTNVLFGPNGSGKSALLRAIM 52
                                      443.337799************9986 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.3
                            AAA_29  33 sGKSTll 39 
                                        GKS+l+
  gi|298675870|ref|YP_003727620.1| 193 KGKSALI 199
                                       69**997 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2     4e-06     0.006      11      39 ..      26      54 ..      18      76 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4e-06
                            AAA_13 11 eledfkriNliYGwNGaGKTtLSrllrsl 39
                                       + df+  N+++G NG+GK+ L r++  +
  gi|298675870|ref|YP_003727620.1| 26 LTVDFGYTNVLFGPNGSGKSALLRAIMGF 54
                                      4668******************9999776 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00027      0.41     100     126 ..      32      58 ..       5      72 .. 0.83
   2 ?   -0.2   0.0      0.55   8.2e+02     108     135 ..      95     121 ..      94     129 .. 0.82
   3 ?   -0.2   0.0      0.54   8.1e+02      90     117 ..     173     200 ..     157     211 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00027
                                       SEEEEECSTTSSHHHHHHHHCTT---- CS
                       RsgA_GTPase 100 ktsvlvGqSGvGKStLinallpelelk 126
                                        t vl G+ G GKS+L+ a+++  + k
  gi|298675870|ref|YP_003727620.1|  32 YTNVLFGPNGSGKSALLRAIMGFGDYK 58 
                                       689****************99855555 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.55
                                       TTSSHHHHHHHHCTT-----S------- CS
                       RsgA_GTPase 108 SGvGKStLinallpelelktgevseklg 135
                                       +Gv  S+Li+a++ e ++ + +v e+l+
  gi|298675870|ref|YP_003727620.1|  95 TGVKLSSLIKAIAKE-NMDIDKVAEDLD 121
                                       688889*****9998.888888888765 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.54
                                       HHHHHHHCTTSEEEEECSTTSSHHHHHH CS
                       RsgA_GTPase  90 leelkellkdktsvlvGqSGvGKStLin 117
                                        ++++e+l+ ++ ++   S  GKS+Li 
  gi|298675870|ref|YP_003727620.1| 173 GTKIQEMLNANLECIGERSVKGKSALII 200
                                       4678899999999998889999999985 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1    0.0021       3.1      12      12 ..     100     100 ..      35     250 .. 0.47

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0021
                            AAA_18  12 t 12 
                                       +
  gi|298675870|ref|YP_003727620.1| 100 S 100
                                       1 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   0.00021      0.32       2      25 ..      35      58 ..      34     217 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00021
                                      EEESSTTSSHHHHHHHHHHHHTHE CS
                               AAA  2 llyGppGtGKTllakavakelgve 25
                                      +l+Gp G GK++l +a++   + +
  gi|298675870|ref|YP_003727620.1| 35 VLFGPNGSGKSALLRAIMGFGDYK 58
                                      599**************9875444 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.5e-05     0.067      23      41 ..      34      52 ..      21     125 .. 0.86
   2 ?   -3.1   0.0         4   5.9e+03      32      36 ..     194     198 ..     154     217 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.5e-05
                          ATPase_2 23 yfiYGpegsGKtaLlkeii 41
                                       +++Gp gsGK+aLl+ i+
  gi|298675870|ref|YP_003727620.1| 34 NVLFGPNGSGKSALLRAIM 52
                                      689*************986 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4
                          ATPase_2  32 GKtaL 36 
                                       GK+aL
  gi|298675870|ref|YP_003727620.1| 194 GKSAL 198
                                       33333 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00034       0.5      28      45 ..      35      52 ..      18     121 .. 0.90
   2 ?   -1.4   0.0       1.8   2.7e+03      31      42 ..     188     204 ..     134     223 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00034
                            AAA_16 28 llsGesGvGKsslvrell 45
                                      +l G+ G+GKs+l+r+++
  gi|298675870|ref|YP_003727620.1| 35 VLFGPNGSGKSALLRAIM 52
                                      488************986 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.8
                            AAA_16  31 GesGv.GKsslv....r 42 
                                       Ge+ v GKs+l+     
  gi|298675870|ref|YP_003727620.1| 188 GERSVkGKSALIithtG 204
                                       34333366666644444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 1481.19
//
Query:       gi|298675871|ref|YP_003727621.1|  [L=76]
Description: hypothetical protein Metev_1996 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-14   53.1  13.6    8.9e-14   51.9  11.1    2.0  2  DUF2769   Protein of unknown function (DUF2769)


Domain annotation for each model (and alignments):
>> DUF2769  Protein of unknown function (DUF2769)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.024   4.3e+02       6      11 ..      14      19 ..      12      22 .. 0.74
   2 !   51.9  11.1     5e-18   8.9e-14       1      57 [.      23      73 ..      23      74 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.024
                           DUF2769  6 Cpsyta 11
                                      Cpsy++
  gi|298675871|ref|YP_003727621.1| 14 CPSYHH 19
                                      ****94 PP

  == domain 2  score: 51.9 bits;  conditional E-value: 5e-18
                           DUF2769  1 CiCkkCpsytaeckkkelellFCargksekcieeekgClCpeCevykeykLkeeyyC 57
                                      C+C+ Cpsy+     +  e++FCarg++ k   +e gClC+eCe+yk+++L+++y+C
  gi|298675871|ref|YP_003727621.1| 23 CKCTVCPSYP-----QTGEMMFCARGTN-KPSGKELGCLCSECELYKKFRLEGGYFC 73
                                      **********.....33468********.8888888********************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 479.50
//
Query:       gi|298675872|ref|YP_003727622.1|  [L=642]
Description: hydantoinase/oxoprolinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-32  113.2   0.8    4.8e-28   98.1   0.1    3.4  2  Hydant_A_N       Hydantoinase/oxoprolinase N-terminal region
      4e-29  101.8   1.2      2e-28   99.5   0.3    2.4  3  Hydantoinase_A   Hydantoinase/oxoprolinase
    1.9e-07   30.1   0.5     0.0015   17.2   0.1    2.2  2  MutL             MutL protein
     0.0022   17.5   0.0      0.056   12.9   0.0    2.3  2  BcrAD_BadFG      BadF/BadG/BcrA/BcrD ATPase family
  ------ inclusion threshold ------
      0.072   13.5   1.1        5.5    7.5   0.1    2.5  2  FtsA             Cell division protein FtsA
       0.41   11.6   1.8         14    6.7   0.2    2.6  2  Ribosomal_L18_c  Ribosomal L18 C-terminal region


Domain annotation for each model (and alignments):
>> Hydant_A_N  Hydantoinase/oxoprolinase N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.1   0.1   1.6e-31   4.8e-28       2     175 ..       5     157 ..       4     160 .. 0.92
   2 !    9.0   0.1   0.00035       1.1       3      30 ..     258     299 ..     257     314 .. 0.75

  Alignments for each domain:
  == domain 1  score: 98.1 bits;  conditional E-value: 1.6e-31
                        Hydant_A_N   2 igIDvGGTfTDavaldeke.eevavlKllstpdavaegirealeevleesiprtskidvvrmGTTvatNallerkge 77 
                                       +gID+GGT+TDav+l++ + + + + K+l+t  +++ gi++a++ + e+     + +++v ++TT+ tN +le++g 
  gi|298675872|ref|YP_003727622.1|   5 LGIDAGGTYTDAVILRNSDeKIIGANKALTTYPDPMAGIKNAIDGLDESY---LKSVKTVSVSTTLSTNSILEGTGF 78 
                                       79*************98876778899*******************97664...469********************* PP

                        Hydant_A_N  78 rvaLittkgfrdlleigrqnrpdlfelrikkplvlyeevvevderveadgevlkpldeeevrealkalkaagvesia 154
                                       +v+Li + +f                     ++++++  ++v+++++++g +  pld e+++  + ++k++ v+++a
  gi|298675872|ref|YP_003727622.1|  79 PVGLILIGDFDFK------------------QELPTKHYIQVSGGHNHKGGEKAPLDIESIEDFVYKVKDK-VSAFA 136
                                       ********99744..................445667789*****************************99.***** PP

                        Hydant_A_N 155 vvllhSylnpehElrvaeiar 175
                                       +++ +S +np+hE+ v+e ++
  gi|298675872|ref|YP_003727622.1| 137 ISSFFSNRNPDHEEDVREWIN 157
                                       *****************9886 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00035
                        Hydant_A_N   3 gIDvGGTfTDavaldeke..............eevavlKlls 30 
                                        IDvGGT TD+ ++ +                ++v+++K+ +
  gi|298675872|ref|YP_003727622.1| 258 VIDVGGTSTDISVIYNSVpemsekgavvggweTKVKAIKMET 299
                                       69*********9988443677777777776666666666666 PP

>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.19   5.8e+02      82      99 ..       5      22 ..       2      37 .. 0.83
   2 !   99.5   0.3   6.8e-32     2e-28       1     138 [.     179     314 ..     179     326 .. 0.95
   3 ?   -1.7   0.0      0.46   1.4e+03     164     182 ..     419     437 ..     414     547 .. 0.54

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.19
                    Hydantoinase_A 82 ItfDmGGTstDvslikdg 99
                                      +++D GGT tD+  +++ 
  gi|298675872|ref|YP_003727622.1|  5 LGIDAGGTYTDAVILRNS 22
                                      578********9998865 PP

  == domain 2  score: 99.5 bits;  conditional E-value: 6.8e-32
                    Hydantoinase_A   1 rtetavvnAylspilreylesvekslekrgakarlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaatsklag 77 
                                       r++ta  nA l p+  +++  ve++++ rg+ a+++++++dG++v +++a +kp+e i SGPaa++vg a    l++
  gi|298675872|ref|YP_003727622.1| 179 RAVTAFFNAQLIPVTDKFMHTVESEIKSRGMDANIFMLKCDGSVVGIKKALEKPIESIFSGPAASLVGGAF---LTE 252
                                       889******************************************************************99...899 PP

                    Hydantoinase_A  78 ekkvItfDmGGTstDvslikdgevevsletei.agvkvrlpaldirtvgagGgsilvvdegg 138
                                       ++++ ++D+GGTstD+s+i +  +e+s +  + +g  ++++a++++t ++gG+s ++v+e++
  gi|298675872|ref|YP_003727622.1| 253 NDSCAVIDVGGTSTDISVIYNSVPEMSEKGAVvGGWETKVKAIKMETSAMGGDSHIWVKENE 314
                                       999***********************99987769**********************998854 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.46
                    Hydantoinase_A 164 tvTDanlvLGrlqpedfls 182
                                       t TDa  vLG  ++++   
  gi|298675872|ref|YP_003727622.1| 419 TPTDALHVLGNYTERNVEA 437
                                       6777777777766655443 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1     5e-07    0.0015       2      60 ..       5      63 ..       4      75 .. 0.80
   2 !   11.0   0.0   3.7e-05      0.11     212     272 ..     224     279 ..     207     292 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5e-07
                              MutL  2 lviDiGSttTkvtlvdlekvderllgqaeapTtveeedvleGleealeeleeklgkt....ev 60
                                      l iD G t+T ++++++++  e+++g  +a+Tt    d + G+++a++ l e+  k+    +v
  gi|298675872|ref|YP_003727622.1|  5 LGIDAGGTYTDAVILRNSD--EKIIGANKALTTYP--DPMAGIKNAIDGLDESYLKSvktvSV 63
                                      569**************66..*************5..99***********9996543433333 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 3.7e-05
                              MutL 212 glskleelvsaeimpTPaAvlkavellaeeeekglgdllvvDvGGaTTdvhsvaegspeke 272
                                       g++k+ e   + i   PaA l +  +l e  ++    + v+DvGG++Td+  + +  pe++
  gi|298675872|ref|YP_003727622.1| 224 GIKKALEKPIESIFSGPAASLVGGAFLTE--ND---SCAVIDVGGTSTDISVIYNSVPEMS 279
                                       6666666677889999************9..33...689***********99877777665 PP

>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   1.9e-05     0.056       1      30 [.       5      35 ..       5     231 .. 0.78
   2 ?    2.5   0.0     0.029        85       3      33 ..     259     296 ..     258     414 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.9e-05
                                      EEEEE-SSEEEEEEEETTTE.EEEEEEE--T CS
                       BcrAD_BadFG  1 vGiDgGsTttkavlmdekge.vlgrgitnsa 30
                                      +GiD G+T t av+++++ e ++g  ++ ++
  gi|298675872|ref|YP_003727622.1|  5 LGIDAGGTYTDAVILRNSDEkIIGANKALTT 35
                                      8**************9998889999888773 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.029
                                       EEE-SSEEEEEEEE.......TTTEEEEEEEE--TTS- CS
                       BcrAD_BadFG   3 iDgGsTttkavlmd.......ekgevlgrgitnsanle 33 
                                       iD+G+T+t   ++        ekg v+g + t+ + ++
  gi|298675872|ref|YP_003727622.1| 259 IDVGGTSTDISVIYnsvpemsEKGAVVGGWETKVKAIK 296
                                       9*******986655588888789999999888875444 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.018        53       2      36 ..       6      46 ..       5      70 .. 0.68
   2 ?    7.5   0.1    0.0018       5.5       1      18 [.     257     274 ..     257     302 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.018
                                      EEEE-SSSEEEEEEETTE..EEE....EEEES--HHHHHHH CS
                                      xxxxxxxxxxxxxxxxxx..xxx....xxxxxxxxxxxxxx RF
                              FtsA  2 lvDiGagktdvavaedga..lvh....lrvigvggngitkd 36
                                      ++D G++ td+++++++   ++     l++ + +  gi++ 
  gi|298675872|ref|YP_003727622.1|  6 GIDAGGTYTDAVILRNSDekIIGankaLTTYPDPMAGIKNA 46
                                      79*************96433222333344444466666665 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0018
                                       EEEEE-SSSEEEEEEETT CS
                                       xxxxxxxxxxxxxxxxxx RF
                              FtsA   1 alvDiGagktdvavaedg 18 
                                       a++D+G+++td++v+ ++
  gi|298675872|ref|YP_003727622.1| 257 AVIDVGGTSTDISVIYNS 274
                                       79************9985 PP

>> Ribosomal_L18_c  Ribosomal L18 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.046   1.4e+02      34      85 ..     359     405 ..     347     414 .. 0.73
   2 ?    6.7   0.2    0.0047        14      14      63 ..     442     488 ..     432     501 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.046
                   Ribosomal_L18_c  34 kyikkgieaddleelykkahaaIredpvkkekkekkevkkeskkykkkkltl 85 
                                        +ik+g ++ +++e  +++++aI+++p+       +e+k++ +ky ++kl +
  gi|298675872|ref|YP_003727622.1| 359 FFIKSGYQPLEIDEGEREIFDAIKDEPTS-----ISEIKNRINKYPSRKLLK 405
                                       5899999********************96.....345555555566666655 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0047
                   Ribosomal_L18_c  14 aeYmeeLkeedeekykkqFskyikkgieaddleelykkahaaIredpvkk 63 
                                       a+Y+++L + d+   k qF k++k++++ ++  +l +  ++ I ++  +k
  gi|298675872|ref|YP_003727622.1| 442 ADYLASLTKMDD---KYQFCKFVKQEFTKNMASNLVSFFFEGISKNEIRK 488
                                       899999999998...779**************************999874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (642 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.47
# Mc/sec: 4095.55
//
Query:       gi|298675873|ref|YP_003727623.1|  [L=55]
Description: hypothetical protein Metev_1998 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00044   20.3   1.6    0.00057   19.9   1.6    1.1  1  Zn-ribbon_8  Zinc ribbon domain
  ------ inclusion threshold ------
      0.017   15.1   3.0      0.024   14.6   3.0    1.2  1  zf-C2HC5     Putative zinc finger motif, C2HC5-type
      0.026   15.2   1.6       0.52   11.0   0.4    2.0  2  Zn_ribbon_2  Putative zinc ribbon domain
       0.16   12.0   3.0        0.3   11.1   3.0    1.5  1  ADK_lid      Adenylate kinase, active site lid
       0.37   11.1   4.7        7.2    7.0   1.2    2.1  2  C1_2         C1 domain
       0.67    9.6   8.7       0.45   10.1   3.1    2.1  2  zf_C2H2_13   Zinc finger domain
        1.6    8.8   8.4        7.3    6.7   2.1    2.2  2  ADD_DNMT3    Cysteine rich ADD domain in DNMT3
        1.6    8.4   6.0        1.8    8.2   0.1    2.1  2  zf_UBZ       Ubiquitin-Binding Zinc Finger


Domain annotation for each model (and alignments):
>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   1.6   2.6e-07   0.00057       5      39 ..       4      40 ..       4      41 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.6e-07
                       Zn-ribbon_8  5 eYrCeeCghefevlqsis.daplta.CPeCgsevrrv 39
                                      eY C +Cg+  +   +i   ++ ++ C  Cg++v++ 
  gi|298675873|ref|YP_003727623.1|  4 EYICLACGSIIDSESKIEnYSKSIEiCECCGKPVTKK 40
                                      8***********99999987778888******99986 PP

>> zf-C2HC5  Putative zinc finger motif, C2HC5-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   3.0     1e-05     0.024      19      48 ..       6      41 ..       4      47 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1e-05
                          zf-C2HC5 19 nClnCGkiiCakegls......kpCsfCgspllsse 48
                                      +Cl+CG ii +  +++      + C  Cg+p+ ++ 
  gi|298675873|ref|YP_003727623.1|  6 ICLACGSIIDSESKIEnysksiEICECCGKPVTKKV 41
                                      7********999999888899999*******98765 PP

>> Zn_ribbon_2  Putative zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0      0.04        89       1      15 [.       6      20 ..       6      28 .. 0.77
   2 ?   11.0   0.4   0.00023      0.52       1      21 [.      29      47 ..      29      52 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.04
                       Zn_ribbon_2  1 iCqsCGmplkkeedl 15
                                      iC +CG  +++e+++
  gi|298675873|ref|YP_003727623.1|  6 ICLACGSIIDSESKI 20
                                      699****99988876 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00023
                       Zn_ribbon_2  1 iCqsCGmplkkeedlgteadg 21
                                      iC++CG p +k+  ++t++  
  gi|298675873|ref|YP_003727623.1| 29 ICECCGKPVTKK--VATNKTS 47
                                      7********754..4566654 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   3.0   0.00014       0.3       3      32 ..       6      38 ..       5      40 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
                                      E-TTT--EEETT..T.B--SSTTB-TTT--.-B CS
                           ADK_lid  3 vCpkCGrsYhvv..f.npPkveglCDkCGepLv 32
                                      +C +CG +   +    n  k   +C +CG p +
  gi|298675873|ref|YP_003727623.1|  6 ICLACGSIIDSEskIeNYSKSIEICECCGKPVT 38
                                      8******99755542588***********9975 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1    0.0078        17      31      44 ..       3      16 ..       1      18 [. 0.74
   2 ?    7.0   1.2    0.0032       7.2      13      29 ..      22      38 ..      19      41 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0078
                              C1_2 31 ffYsCseCdfslhv 44
                                      ++Y+C  C  ++++
  gi|298675873|ref|YP_003727623.1|  3 DEYICLACGSIIDS 16
                                      56999889888776 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0032
                              C1_2 13 edssesfnCsaCgrkid 29
                                      + s++   C++Cg++++
  gi|298675873|ref|YP_003727623.1| 22 NYSKSIEICECCGKPVT 38
                                      56788899******964 PP

>> zf_C2H2_13  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.4     0.029        66      19      31 ..       6      18 ..       4      26 .. 0.81
   2 ?   10.1   3.1    0.0002      0.45      19      28 ..      29      38 ..      20      43 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.029
                        zf_C2H2_13 19 vCnkCGkPislea 31
                                      +C +CG  i +e+
  gi|298675873|ref|YP_003727623.1|  6 ICLACGSIIDSES 18
                                      8*****8887776 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0002
                        zf_C2H2_13 19 vCnkCGkPis 28
                                      +C+ CGkP+ 
  gi|298675873|ref|YP_003727623.1| 29 ICECCGKPVT 38
                                      9*******97 PP

>> ADD_DNMT3  Cysteine rich ADD domain in DNMT3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.5    0.0037       8.4      17      25 ..       4      12 ..       2      18 .. 0.87
   2 ?    6.7   2.1    0.0032       7.3       8      26 ..      19      36 ..      13      44 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0037
                         ADD_DNMT3 17 EdiClsCGs 25
                                      E iCl+CGs
  gi|298675873|ref|YP_003727623.1|  4 EYICLACGS 12
                                      779*****8 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0032
                         ADD_DNMT3  8 evkenkrniEdiClsCGsl 26
                                      ++++ +++iE iC +CG+ 
  gi|298675873|ref|YP_003727623.1| 19 KIENYSKSIE-ICECCGKP 36
                                      5666777776.9*****85 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1   0.00081       1.8       1      18 [.       3      20 ..       3      21 .. 0.85
   2 ?    2.4   1.9     0.054   1.2e+02       4      12 ..      29      37 ..      27      40 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00081
                            zf_UBZ  1 dtylCerCgkeipeselq 18
                                      d y+C  Cg+ i ++++ 
  gi|298675873|ref|YP_003727623.1|  3 DEYICLACGSIIDSESKI 20
                                      67**********998765 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.054
                            zf_UBZ  4 lCerCgkei 12
                                      +Ce Cgk++
  gi|298675873|ref|YP_003727623.1| 29 ICECCGKPV 37
                                      6******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 360.61
//
Query:       gi|298675874|ref|YP_003727624.1|  [L=55]
Description: hypothetical protein Metev_1999 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 376.26
//
Query:       gi|298675875|ref|YP_003727625.1|  [L=185]
Description: adenylate kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-23   84.1   0.7    1.7e-23   83.6   0.7    1.3  1  AAA_18          AAA domain
    1.2e-06   28.5   1.1      0.013   15.4   0.1    2.2  2  dNK             Deoxynucleoside kinase
      3e-06   27.5   0.0     0.0038   17.4   0.0    2.3  2  AAA_33          AAA domain
    8.8e-05   22.8   0.0    0.00013   22.2   0.0    1.6  1  AAA_28          AAA domain
    9.1e-05   22.9   0.1     0.0012   19.3   0.1    2.2  1  AAA_17          AAA domain
    0.00018   21.2   0.1     0.0098   15.6   0.0    2.4  2  CoaE            Dephospho-CoA kinase
     0.0071   16.8   0.4      0.022   15.2   0.4    2.0  1  AAA             ATPase family associated with various cellula
     0.0089   15.9   0.0      0.012   15.5   0.0    1.3  1  APS_kinase      Adenylylsulphate kinase
  ------ inclusion threshold ------
      0.011   15.0   0.0      0.018   14.4   0.0    1.7  1  Zeta_toxin      Zeta toxin
      0.016   15.3   0.1      0.034   14.3   0.1    1.5  1  NikR_C          NikR C terminal nickel binding domain
      0.018   15.3   0.1      0.032   14.5   0.1    1.6  1  AAA_22          AAA domain
      0.019   14.0   0.2      0.067   12.2   0.1    1.8  2  MeaB            Methylmalonyl Co-A mutase-associated GTPase M
      0.025   14.3   0.2      0.062   13.0   0.2    1.8  1  Cytidylate_kin  Cytidylate kinase
      0.028   13.9   0.4      0.075   12.5   0.1    1.8  2  KTI12           Chromatin associated protein KTI12
      0.038   14.2   2.7        4.4    7.6   0.1    2.6  2  Seryl_tRNA_N    Seryl-tRNA synthetase N-terminal domain
      0.058   13.8   0.1       0.11   12.9   0.1    1.7  1  RNA_helicase    RNA helicase
      0.059   13.1   0.0       0.45   10.2   0.0    2.1  2  PRK             Phosphoribulokinase / Uridine kinase family
      0.064   12.6   4.2       0.88    8.9   0.1    2.6  2  ATPase          KaiC
      0.067   13.3   0.9       0.12   12.5   0.7    1.7  1  MMR_HSR1        50S ribosome-binding GTPase
      0.071   13.2   0.2        6.6    6.8   0.0    2.7  2  ADK             Adenylate kinase
       0.15   11.9   0.0       0.72    9.7   0.0    1.9  2  Ploopntkinase3  P-loop Nucleotide Kinase3
       0.27   11.7   2.8       0.39   11.2   2.3    1.5  1  ABC_tran        ABC transporter


Domain annotation for each model (and alignments):
>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.6   0.7   2.1e-26   1.7e-23       1     129 [.       3     122 ..       3     123 .. 0.93

  Alignments for each domain:
  == domain 1  score: 83.6 bits;  conditional E-value: 2.1e-26
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegkn 76 
                                       I+ltGtpG+GK++l++ L+  lg+  ++l++++k+++l+ ++d+e  ++s ++d+dk  + ++++ e ++   + ++
  gi|298675875|ref|YP_003727625.1|   3 IGLTGTPGTGKSSLSNFLETNLGYnIIHLNEMIKNENLYKYEDEE--RDSVVADMDKISERVSEITEENN---DKSV 74 
                                       89****************9999999********************..**********9999888888765...6777 PP

                            AAA_18  77 lvidghlaeleseaakdikkvvLtaspeelleRlekRgyeeakikeneeaeil 129
                                        ++++hl++++ ++      +vL+aspeel +Rl  Rgy++ ki+en +ae l
  gi|298675875|ref|YP_003727625.1|  75 TILESHLSHYIADNI-----IVLRASPEELEKRLTSRGYSNEKIQENVDAEEL 122
                                       7**********9966.....9*****************************976 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.6e-05     0.013       3      83 ..       5      80 ..       3      84 .. 0.82
   2 !   13.3   0.1   7.1e-05     0.058     121     169 ..      82     135 ..      75     169 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.6e-05
                                      EEESTTSSHHHHHHHHHCCSTCEEEE..-HHHHCCSSSSHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHCHHSSS-EEE CS
                               dNK  3 veGnIgaGKstlvklLskklgvkvfe..EpvdkwtnvqknlLekfYkdpsrwsfalqtyvllsrlkqqlealatkqvvv 79
                                      + G+ g GKs+l ++L+ +lg+++++  E++ k+     + L k Y+d +r s+  ++  + +r+ +++e  + k+v +
  gi|298675875|ref|YP_003727625.1|  5 LTGTPGTGKSSLSNFLETNLGYNIIHlnEMI-KN-----ENLYK-YEDEERDSVVADMDKISERVSEITEENNDKSVTI 76
                                      67999****************8876521444.33.....45654.9**********************99999999999 PP

                                      EES- CS
                               dNK 80 leRs 83
                                      le +
  gi|298675875|ref|YP_003727625.1| 77 LESH 80
                                      9965 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 7.1e-05
                                       CH..-SEEEEEE--HHHHHHHHHHCTTCCCT...TS-HHHHHHHHHHHHHHHTS CS
                               dNK 121 ak..pdlliYLkasletclerikkRgreeek...kieldYlekLhekyeewlkk 169
                                       ++   d +i L+as+e++++r+  Rg ++ek   +++ + l  +  +  ew + 
  gi|298675875|ref|YP_003727625.1|  82 SHyiADNIIVLRASPEELEKRLTSRGYSNEKiqeNVDAEELDVILFESVEWCSR 135
                                       3344799***********************988888887777766666666655 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   4.7e-06    0.0038       3      61 ..       4      72 ..       2      88 .. 0.59
   2 !    8.8   0.0    0.0021       1.7      98     134 ..      86     123 ..      75     128 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.7e-06
                            AAA_33  3 llvGlpGsGKstlaerllkklgavllssdtlrr..rlfg.tdqqskt.......dytrvldrlyqilne 61
                                       l G pG+GKs l+  l  +lg+ ++  +++++  +l++ +d+++++        + rv++ + +   +
  gi|298675875|ref|YP_003727625.1|  4 GLTGTPGTGKSSLSNFLETNLGYNIIHLNEMIKneNLYKyEDEERDSvvadmdkISERVSEITEENNDK 72
                                      578*******************77777777666446766433333333333322223333334444444 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0021
                            AAA_33  98 pvrivvvetdeetlkeRlakRaang.ddrsevpeeald 134
                                       ++ i+v+++++e+l++Rl  R  ++ + + +v+ e ld
  gi|298675875|ref|YP_003727625.1|  86 ADNIIVLRASPEELEKRLTSRGYSNeKIQENVDAEELD 123
                                       5789*****************99873345567777666 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   1.6e-07   0.00013       2      65 ..       3      68 ..       2     145 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.6e-07
                            AAA_28  2 ivitGgestGKTtlleaLaar.gypvv..pEaareileeklakgedalpwv.edllafaervleeqle 65
                                      i +tG+++tGK++l++ L+ + gy+++   E+       k++++e+++  v +d+ ++ erv e   e
  gi|298675875|ref|YP_003727625.1|  3 IGLTGTPGTGKSSLSNFLETNlGYNIIhlNEMIKNENLYKYEDEERDS--VvADMDKISERVSEITEE 68
                                      569****************88899987668888876666666666644..447999999988776544 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   1.5e-06    0.0012       1     122 [.       6     106 ..       6     122 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.5e-06
                                       EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEE CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeeakkkgvlvd 77 
                                       +G PG GK+ +++ l  ++g+ ++     l e++k+++l k +de r+    + +++ +++ e  +e+++k+  +++
  gi|298675875|ref|YP_003727625.1|   6 TGTPGTGKSSLSNFLETNLGYNIIH----LNEMIKNENLYKYEDEERDSVVADMDKISERVSEITEENNDKSVTILE 78 
                                       69********************999....778888888888888888888888888888988755555677778998 PP

                                       E-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHH CS
                            AAA_17  78 ghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkd 122
                                        h +      +              d ii+l a+pee+ +r+ ++
  gi|298675875|ref|YP_003727625.1|  79 SHLSH-----Y------------IADNIIVLRASPEELEKRLTSR 106
                                       88852.....1............1356777777777776666655 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.2e-05    0.0098       1      31 [.       1      32 [.       1      41 [. 0.89
   2 ?    3.1   0.0      0.08        66     114     155 ..      77     118 ..      54     123 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-05
                                      EEEEEEESTTSSHHHHHHHHHH.TT-EEEEHH CS
                              CoaE  1 livgltGgiasGKstvanlfad.lgvpivDaD 31
                                      +++gltG  ++GKs ++n ++  lg++i+   
  gi|298675875|ref|YP_003727625.1|  1 MLIGLTGTPGTGKSSLSNFLETnLGYNIIHLN 32
                                      68******************998*****9765 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.08
                                       TTTTGGGGS.SEEEEEE--HHHHHHHHHHCCTSTHHHHHHHHH CS
                              CoaE 114 vEkqlekli.ervlvvdvelelqveRlvardgvseeevkaiia 155
                                       +E++l++ i ++++v+ +++e ++e+ ++ +g s+e++++ + 
  gi|298675875|ref|YP_003727625.1|  77 LESHLSHYIaDNIIVLRASPE-ELEKRLTSRGYSNEKIQENVD 118
                                       577777766156666666665.567777777899999988766 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.4   2.7e-05     0.022       3      57 ..       5      69 ..       3     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.7e-05
                                      EESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS..........STTHHHHHHHHHHHHHHHTS CS
                               AAA  3 lyGppGtGKTllakavakelgvefleisgsellsk..........yvgesekkirelfkeakeka 57
                                      l+G+pGtGK++l + + ++lg +++ ++ +   ++           v + ++ki+e ++e+ e++
  gi|298675875|ref|YP_003727625.1|  5 LTGTPGTGKSSLSNFLETNLGYNIIHLNEMIKNENlykyedeerdSVVADMDKISERVSEITEEN 69
                                      89*******************99888775544433555666666655555555555555555544 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.5e-05     0.012       5      88 ..       3      87 ..       1     112 [. 0.87

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.5e-05
                                      EEEESSTTSSHHHHHHHHHHHHHHTT--E.EEEEHHHHTTTTTTT--SSHHHHHHHHHHHHHHHHHHHHTT-EEEEE-- CS
                        APS_kinase  5 vwltGlsgsGKstianalekkLvekgisv.ylLdGdnvRhgLnkdLgfseedRkenirrvaevaklladaglivlvafi 82
                                      + ltG  g+GKs+++n le++L  + i+  +++  +n+ +   ++     +d ++   rv+e++++ +d+++ +l + +
  gi|298675875|ref|YP_003727625.1|  3 IGLTGTPGTGKSSLSNFLETNLGYNIIHLnEMIKNENLYKYEDEERDSVVADMDKISERVSEITEENNDKSVTILESHL 81
                                      679*******************999966526788999999888888888999999999*****************9999 PP

                                      --SHHH CS
                        APS_kinase 83 sPyree 88
                                      s y ++
  gi|298675875|ref|YP_003727625.1| 82 SHYIAD 87
                                      999776 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.1e-05     0.018      19      63 ..       3      45 ..       1     173 [. 0.76

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.1e-05
                        Zeta_toxin 19 illgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPeyee 63
                                      i l G pG GKs+l++ l+++l  + n+++l++    e   +ye+
  gi|298675875|ref|YP_003727625.1|  3 IGLTGTPGTGKSSLSNFLETNL--GYNIIHLNEMIKNENLYKYED 45
                                      6689******************..9******97544444445554 PP

>> NikR_C  NikR C terminal nickel binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   4.1e-05     0.034      13      58 ..      56     101 ..      50     107 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.1e-05
                                       TTHHHHHHHHHHHHSSEEEEEEEEEESSSEEEEEEEEEE-HHHHHH CS
                            NikR_C  13 relserltdiqheyhdliisslhvhldhdncLevivlkGeaeeike 58 
                                        ++ser+++i  e++d  ++ l  hl+h     +ivl+ + ee+++
  gi|298675875|ref|YP_003727625.1|  56 DKISERVSEITEENNDKSVTILESHLSHYIADNIIVLRASPEELEK 101
                                       689***********************************99999975 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   3.9e-05     0.032      10      71 ..       5      87 ..       1     162 [. 0.66

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.9e-05
                            AAA_22 10 vtGesGtGKTtllrrlleqldeeakaee...erpevvfvtlpsstsskdllrellralglelka............... 70
                                      +tG +GtGK+ l + l  +l   + + +   ++  +++++  +  s    + ++ + + + +++               
  gi|298675875|ref|YP_003727625.1|  5 LTGTPGTGKSSLSNFLETNLGYNIIHLNemiKNENLYKYEDEERDSVVADMDKISERVSEITEEnndksvtileshlsh 83
                                      89***************99965555555999777777887777776666666666666665555222233333333333 PP

                            AAA_22 71 ...e 71
                                          
  gi|298675875|ref|YP_003727625.1| 84 yiaD 87
                                      3330 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   8.3e-05     0.067      32      53 ..       3      24 ..       1      29 [. 0.87
   2 ?   -0.6   0.0      0.64   5.2e+02     198     226 ..     115     154 ..      78     174 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.3e-05
                                      EEEEE-TTSSHHHHHHHHHHHH CS
                              MeaB 32 vGltGvPGaGkstlvealglel 53
                                      +GltG+PG+Gks l + l ++l
  gi|298675875|ref|YP_003727625.1|  3 IGLTGTPGTGKSSLSNFLETNL 24
                                      9************998887766 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.64
                                       T............TBTTB--EEEEEBCCCTBSHHHHHHHHH CS
                              MeaB 198 e............kekeWrpkvlktsavegeGidelvdaie 226
                                       e            ++ eW ++v ++  ++++ ++++v+++ 
  gi|298675875|ref|YP_003727625.1| 115 EnvdaeeldvilfESVEWCSRVFEV-DTTNRPLNNIVSNVD 154
                                       2233333333333445555555543.334455555555555 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   7.6e-05     0.062       1      91 [.       3      96 ..       3     171 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.6e-05
                                      EEEE-STTSSHHHHHHHHHHHHT-EEEEHHHHHHHHHHHHHHT...T--TT-HHHHHHHHHT--EEEEEEEEEETTEE- CS
                    Cytidylate_kin  1 iaiDGPagsGKssvaralaeklglkyldtgalYRalalaalrr...kvdlldeaalvelakevelsfeaekvllngedv 76
                                      i + G  g+GKss++  l ++lg++++   ++ +   l   +    +  ++d +++ e ++e++ + + ++v + ++++
  gi|298675875|ref|YP_003727625.1|  3 IGLTGTPGTGKSSLSNFLETNLGYNIIHLNEMIKNENLYKYEDeerDSVVADMDKISERVSEITEENNDKSVTILESHL 81
                                      5677999************************999766555443222666789999999999999999999999999999 PP

                                      TTGGGSHHHHHHHHH CS
                    Cytidylate_kin 77 eeelrsdevekavSa 91
                                      ++ +  + +  ++S 
  gi|298675875|ref|YP_003727625.1| 82 SHYIADNIIVLRASP 96
                                      998888877777773 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   9.1e-05     0.075       3      68 ..       2      62 ..       1      87 [. 0.64
   2 ?   -0.5   0.0      0.85   6.9e+02     146     171 ..     132     162 ..      80     176 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.1e-05
                                      EEEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH.TTSSS--GGGHHHHHHHHHHHHHHHH CS
                             KTI12  3 LvvltGlPssGKstrakeLakaleeekrsvvviddeslgiekdsykdsakekalRsslrsavkrdL 68
                                      L+ ltG P +GKs++++ L++ l       +++ +e ++ +++ yk + +e++   + + ++++++
  gi|298675875|ref|YP_003727625.1|  2 LIGLTGTPGTGKSSLSNFLETNLGY----NIIHLNEMIK-NENLYKYEDEERDSVVADMDKISERV 62
                                      899************9999988865....2333333333.44445555555544444444444443 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.85
                                       GGS-SEEEE......TTS---HHHHHHHHHH CS
                             KTI12 146 WDsPlftvls.....aeeklpldeilkalie 171
                                       W s +f+v++      +   ++dei+ al++
  gi|298675875|ref|YP_003727625.1| 132 WCSRVFEVDTtnrplNNIVSNVDEIITALLN 162
                                       5555555554222222222233444444444 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.4     0.013        11      63      94 ..      42      73 ..      30      82 .. 0.77
   2 ?    7.6   0.1    0.0054       4.4       5      55 ..      90     149 ..      88     173 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.013
                                      CCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N 63 kkkkedaeeliaevkelkeelkaleaelkele 94
                                      k ++e++++++a++++++e+++++++e ++ +
  gi|298675875|ref|YP_003727625.1| 42 KYEDEERDSVVADMDKISERVSEITEENNDKS 73
                                      4445999999**********999999877665 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0054
                                       HHHHH-HHHHHHHHCCCT.........CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N   5 klirenpeavkeklkkRg.........edkadvdelleldekrrelqveleelqaerNel 55 
                                         +r  pe+++++l +Rg         +d++++d +l    ++ +  +e++  ++  N++
  gi|298675875|ref|YP_003727625.1|  90 IVLRASPEELEKRLTSRGysnekiqenVDAEELDVILFESVEWCSRVFEVDTTNRPLNNI 149
                                       579999***********9544444444444445555555555666666666666555555 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00013      0.11       3      48 ..       5      44 ..       3     114 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00013
                      RNA_helicase  3 lyGpsgeGKStlakeLakallkkl....klkkkdsvysrnpeddfwdgYt 48
                                      l+G +g+GKS+l++ L ++l  ++    +++k+          + +++Y+
  gi|298675875|ref|YP_003727625.1|  5 LTGTPGTGKSSLSNFLETNLGYNIihlnEMIKN----------ENLYKYE 44
                                      79**************99999777444433333..........3333333 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00055      0.45       1      53 [.       2      55 ..       2      86 .. 0.68
   2 ?    0.6   0.0      0.49     4e+02     152     168 ..     103     119 ..      96     131 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00055
                               PRK  1 vIgvagsSGaGkttvarklekifgrekvkaaei.egdsflrldraekdleleer 53
                                      +Ig++g  G Gk+++++ le  +g + ++  e+ +   + +++  e d  +++ 
  gi|298675875|ref|YP_003727625.1|  2 LIGLTGTPGTGKSSLSNFLETNLGYNIIHLNEMiKNENLYKYEDEERDSVVADM 55
                                      69*********************9777774433245555555555555444444 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.49
                               PRK 152 iaeRGrsleavldsilr 168
                                        ++RG+s e + +++ +
  gi|298675875|ref|YP_003727625.1| 103 LTSRGYSNEKIQENVDA 119
                                       689********998876 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.5     0.019        15      22      36 ..       3      17 ..       1      29 [. 0.84
   2 ?    8.9   0.1    0.0011      0.88     158     191 ..      63      96 ..      46     117 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.019
                            ATPase 22 vlitGepGtGKtifa 36
                                      + +tG+pGtGK+ ++
  gi|298675875|ref|YP_003727625.1|  3 IGLTGTPGTGKSSLS 17
                                      568*********887 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0011
                            ATPase 158 ailvsekssseeaaggygveefivdgvivLdlke 191
                                       + +++e ++++ ++ +  ++++i+d++ivL+   
  gi|298675875|ref|YP_003727625.1|  63 SEITEENNDKSVTILESHLSHYIADNIIVLRASP 96 
                                       557888888999999***************9654 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.7   0.00015      0.12       2      56 ..       3      58 ..       2     129 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                                      EEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETTEEEEEEECGGC CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvklkgkeielvDtpGl 56
                                      +++ G p +GKS+L n l  +    + + +   ++ n ++++ ++++ +++D+  +
  gi|298675875|ref|YP_003727625.1|  3 IGLTGTPGTGKSSLSNFLETNlGYNIIHLNEMIKNENLYKYEDEERDSVVADMDKI 58
                                      799*************9955535566667777777777777755577777777774 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0081       6.6       1      35 [.       5      39 ..       5      66 .. 0.82
   2 ?    3.8   0.1      0.07        57     101     123 ..      84     121 ..      56     173 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0081
                                      EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK  1 llGaPgaGKGtqaeklvkkyglahlstGdllRaev 35
                                      l G+Pg+GK   ++ l +++g++ +   +++++e 
  gi|298675875|ref|YP_003727625.1|  5 LTGTPGTGKSSLSNFLETNLGYNIIHLNEMIKNEN 39
                                      67*****************9999888888888775 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.07
                                       SEESEEEEEE--HHHHHHHHHT...............G CS
                                       xxxxxxxxxxxxxxxxxxxxxx...............x RF
                               ADK 101 vkldlvleldvpeevlveRltg...............D 123
                                       +  d ++ l+++ e l +Rlt                +
  gi|298675875|ref|YP_003727625.1|  84 YIADNIIVLRASPEELEKRLTSrgysnekiqenvdaeE 121
                                       44677888888888888888877765555555554440 PP

>> Ploopntkinase3  P-loop Nucleotide Kinase3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00088      0.72       5      51 ..       2      47 ..       1      67 [. 0.74
   2 ?   -0.2   0.0      0.98     8e+02     162     181 ..      85     104 ..      58     106 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00088
                    Ploopntkinase3  5 liylvGqPGaGkstlmaeltkgfdrskveqeeetvphdvlvdrttGe 51
                                      li l G+PG+Gks l   l + +  + ++ + e++ +++l ++ + e
  gi|298675875|ref|YP_003727625.1|  2 LIGLTGTPGTGKSSLSNFLETNLGYNIIHLN-EMIKNENLYKYEDEE 47
                                      78899***********999988877777744.588888888776544 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.98
                    Ploopntkinase3 162 ekgkvkvlaGhPdelrsile 181
                                          +++vl+  P+el++ l 
  gi|298675875|ref|YP_003727625.1|  85 IADNIIVLRASPEELEKRLT 104
                                       33468999999999999875 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   2.3   0.00048      0.39      14      80 ..       3      94 ..       1     128 [. 0.53

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00048
                                      EEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...............B-HHHCCHCEEEE-SS--S-TTSBHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 14 vaivGenGaGKStLlkllagllkpteGeilldgkdlke...............qeleslrkeigvlpqepqlfpeltvr 77
                                      ++++G  G+GKS+L + l  +l      i+l+ + +k+                ++ + +++++ +++e++  + +t+ 
  gi|298675875|ref|YP_003727625.1|  3 IGLTGTPGTGKSSLSNFLETNLGY--NIIHLN-EMIKNenlykyedeerdsvvADMDKISERVSEITEENND-KSVTIL 77
                                      79****************999876..333333.222222232234433333444444555555555554222.222233 PP

                                      HH..............H CS
                                      xx..............x RF
                          ABC_tran 78 en..............e 80
                                      e+              +
  gi|298675875|ref|YP_003727625.1| 78 EShlshyiadniivlrA 94
                                      33566655555554441 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1265  (0.0705561); expected 358.6 (0.02)
Passed bias filter:                      674  (0.0375927); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.58u 0.35s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 1167.34
//
Query:       gi|298675876|ref|YP_003727626.1|  [L=196]
Description: glutamine amidotransferase of anthranilate synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-43  147.8   0.0    3.3e-43  147.7   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    1.5e-17   64.1   0.2    2.6e-17   63.3   0.2    1.5  1  Peptidase_C26  Peptidase C26
  ------ inclusion threshold ------
       0.15   11.8   0.0       0.22   11.3   0.0    1.2  1  DJ-1_PfpI      DJ-1/PfpI family


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.7   0.0   5.5e-47   3.3e-43       2     187 ..       5     187 ..       4     190 .. 0.96

  Alignments for each domain:
  == domain 1  score: 147.7 bits;  conditional E-value: 5.5e-47
                                       EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT....TTTHHHHHHHHCTSTS-E CS
                            GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg....vegkieaikearenkiPi 74 
                                       +i+n ds+++nlv+++   + ++ v+ ++ + ee +    npd i++s+Gpg+p+    ++ + ++i+e+   +iP+
  gi|298675876|ref|YP_003727626.1|   5 FINNKDSFVWNLVDYFSMYEPDIVVMSNKITLEEVK--SINPDVIVISPGPGTPEnkndIGSCTDIIREFCA-EIPV 78 
                                       6899**************************999994..79******************************99.**** PP

                                       EEETHHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETT CS
                            GATase  75 LGICLGmQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtaksedd 151
                                       LGICLG+Q++  +fg++v + +  + hg+ +++ +d++ +++g ++++++ ++H++ +++   ++++le +a+++d+
  gi|298675876|ref|YP_003727626.1|  79 LGICLGNQAINTAFGGTVSHSTGGPVHGKGHQVLHDNSPIFEGISSPMTAGRYHSLGIEK---LSSELEAIATTKDG 152
                                       ************************************************************...***********887 PP

                                       EEEEEEEEETTTEEEESSBTTSTTSTTHHHHHHHHH CS
                            GATase 152 eelmeiiekknpfvgvQFHPEststpegpellfnfl 187
                                         +m++++k+ p++g+QFHPEs++tp g +l+ nfl
  gi|298675876|ref|YP_003727626.1| 153 -IIMAVRHKNHPVYGLQFHPESVLTPDGLKLIGNFL 187
                                       .8*****************************99986 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.3   0.2   4.4e-21   2.6e-17      99     216 .]      69     172 ..      27     172 .. 0.86

  Alignments for each domain:
  == domain 1  score: 63.3 bits;  conditional E-value: 4.4e-21
                     Peptidase_C26  99 raalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievnslHh 175
                                        ++  +++P+lgiC+G q +n a+GGt+  +         h       + h+v  +++ +++ + +   +    +H+
  gi|298675876|ref|YP_003727626.1|  69 IREFCAEIPVLGICLGNQAINTAFGGTVSHSTGG----PVH------GKGHQVLHDNSPIFEGISS--PMTAGRYHS 133
                                       4556679********************9887773....333......5689998888888888877..888999*** PP

                     Peptidase_C26 176 qaikelaeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                        +i++l++el+ +A+++Dg+i a+++++++  v+g+Q+HPE
  gi|298675876|ref|YP_003727626.1| 134 LGIEKLSSELEAIATTKDGIIMAVRHKNHP--VYGLQFHPE 172
                                       ****************************66..********9 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   3.6e-05      0.22      51     109 ..      33      90 ..      24     111 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.6e-05
                                       SEEGGGCTCCG-SEEEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHH CS
                         DJ-1_PfpI  51 daslddvkaaeyDalvlpGGragperlrenekvvelvkefaekgklvaaICagpqlLaa 109
                                         +l++vk+ + D++v+  G   pe+  +    +++++ef   + +v  IC g q    
  gi|298675876|ref|YP_003727626.1|  33 KITLEEVKSINPDVIVISPGPGTPENKNDIGSCTDIIREFCA-EIPVLGICLGNQAINT 90 
                                       57899************999999****************985.699*******987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1259.66
//
Query:       gi|298675877|ref|YP_003727627.1|  [L=522]
Description: anthranilate synthase component I [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-95  318.3   0.0    3.2e-92  308.7   0.0    3.0  3  Chorismate_bind  chorismate binding enzyme
    5.2e-25   88.3   1.6    6.2e-23   81.6   0.1    3.3  2  Anth_synt_I_N    Anthranilate synthase component I, N termina


Domain annotation for each model (and alignments):
>> Chorismate_bind  chorismate binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.9   0.0    0.0037        33      31      89 ..      27      88 ..      21      91 .. 0.78
   2 ?    1.6   0.0     0.019   1.7e+02     160     180 ..     115     135 ..     112     137 .. 0.93
   3 !  308.7   0.0   3.6e-96   3.2e-92       2     258 .]     259     512 ..     258     512 .. 0.98

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0037
                                      EECESS-B-HHHHHHHHHCTBSSSEEEEEEETT....EEEEEEESSEEEEEETTSEEEEECEE CS
                   Chorismate_bind 31 kaeleaavdplalyralrarnpapysflleled....sellgaSPElllkveggrrietepia 89
                                       a++e++ +pl+ly  l++   ++    +e e+    ++++g+ P+ ll+++++ +++ e  +
  gi|298675877|ref|YP_003727627.1| 27 MAKVETECTPLQLYTLLQKSRCSYLLESVEKEKkharFSFVGFDPDALLTISDR-NLKLEFFK 88
                                      566778899999**99999888887777755445666999***********954.88777655 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.019
                                       EEEESTT--HHHHHHHCSS-C CS
                   Chorismate_bind 160 egelkedvslldllkalfPtg 180
                                       +g++ke+ ++ld+l+a+fPt+
  gi|298675877|ref|YP_003727627.1| 115 QGRIKEGYDVLDALRAVFPTA 135
                                       799****************96 PP

  == domain 3  score: 308.7 bits;  conditional E-value: 3.6e-96
                                       HCHHHHHHHHHHHHHHTTS-SEEEEEEEEEECESS-B-HHHHHHHHHCTBSSSEEEEEEETTEEEEEEESSEEEEEE CS
                   Chorismate_bind   2 redYaeavekvkeeiragdlykvvlsrrlkaeleaavdplalyralrarnpapysflleledsellgaSPElllkve 78 
                                       r+d+++ave++k++i +gd+++vvlsrr+ +++e   +pl+ly++lr+ np+py++++++ d +++gaSPE+l++v+
  gi|298675877|ref|YP_003727627.1| 259 RNDFEKAVENAKQHILDGDIFQVVLSRRYAVNIE--QTPLDLYKKLRNINPSPYMYIFNFRDLSIVGASPETLMTVH 333
                                       799*****************************55..689************************************** PP

                                       TTSEEEEECEEEEEEHSSSHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCBSCCEEEEECCEEEEEETTEEEE CS
                   Chorismate_bind  79 ggrrietepiaGTrargktpeedealeeelledeKeraEhlmivdlirndLgkvakpgsvkvpelfkverysevlhl 155
                                       ++ ++ t+piaGT +rgk++++d++++ ++l+deKeraEh+m+vdl rnd++ v+++gsvk ++++kv +ys+v+h+
  gi|298675877|ref|YP_003727627.1| 334 NK-EVITNPIAGTCSRGKDENKDKEYASSMLNDEKERAEHVMLVDLGRNDVRMVSRSGSVKLENFMKVVKYSHVQHI 409
                                       66.************************************************************************** PP

                                       EEEEEEEESTT--HHHHHHHCSS-CCCSEESHHHHHHHHHHHSSS--TTTTSEEEEEETTS-EEEEEE-SEEEEETT CS
                   Chorismate_bind 156 vstiegelkedvslldllkalfPtgavtGaPkkrameiidelEearRgvYaGavgyldadgeaelavvIRtavvkdk 232
                                        st++g+l+++++ +d+ +a+fP+g+++GaPk rameiid++E+++Rg+Y+G vgy + +++a++a+vIRt++++++
  gi|298675877|ref|YP_003727627.1| 410 ESTVKGTLRDECDQFDATRAIFPAGTLSGAPKIRAMEIIDKMEKSPRGIYGGGVGYYSWNSDADFAIVIRTVLINKS 486
                                       ****************************************************************************9 PP

                                       EEEEEEEEEEETT--HHHHHHHHHHH CS
                   Chorismate_bind 233 elrlgaGaGIvadSdpeaEyeEtlaK 258
                                       +++++aGaG+v dS+pe Ey+Et+ K
  gi|298675877|ref|YP_003727627.1| 487 TAYVQAGAGVVSDSSPEYEYKETERK 512
                                       9**********************998 PP

>> Anth_synt_I_N  Anthranilate synthase component I, N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.6   0.1   6.9e-27   6.2e-23       3     142 .]      34     202 ..      32     202 .. 0.89
   2 !    3.8   0.2    0.0068        61      84     101 ..     441     469 ..     292     485 .. 0.73

  Alignments for each domain:
  == domain 1  score: 81.6 bits;  conditional E-value: 6.9e-27
                     Anth_synt_I_N   3 ltplsvylklaeeehkflLeSaeneggegrySfigldpflelkskngeveveg........................ 55 
                                        tpl++y  l++++ ++lLeS+e+e++ +r+Sf+g+dp + l++ ++ +++e                         
  gi|298675877|ref|YP_003727627.1|  34 CTPLQLYTLLQKSRCSYLLESVEKEKKHARFSFVGFDPDALLTISDRNLKLEFfknsdfvdylgskighvctdesgn 110
                                       69*********************99999**********999998888888888889******************999 PP

                     Anth_synt_I_N  56 ...pegeeleeeepldalrellerfrsaedseptelp...fvgGlvGylgYDlvreieklpksakddlnlpdarlil 126
                                           +g+ +e +++ldalr+++ +++ ++  +++++    f gG++Gy gYD+v     l++ +k ++++pd++++l
  gi|298675877|ref|YP_003727627.1| 111 nnfCQGRIKEGYDVLDALRAVFPTADGVNLLNQKKFDrqtFLGGAIGYNGYDIVYDC-WLDMDKKYETDTPDLQYAL 186
                                       9987888889999*************77665555555666*************8888.55666799999******** PP

                     Anth_synt_I_N 127 ydtlivfDhkerrlyl 142
                                       + +++vfDh+++ +y+
  gi|298675877|ref|YP_003727627.1| 187 TTKTFVFDHLTGDVYI 202
                                       ***********99986 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.0068
                     Anth_synt_I_N  84 e..........ptelp.fvgGlvGylgYD 101
                                       +          +++++ ++gG vGy++ +
  gi|298675877|ref|YP_003727627.1| 441 KirameiidkmEKSPRgIYGGGVGYYSWN 469
                                       14444444444455556899999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (522 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 3369.48
//
Query:       gi|298675878|ref|YP_003727628.1|  [L=227]
Description: phosphoribosylanthranilate isomerase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-32  113.1   1.1    2.6e-32  112.2   1.1    1.4  1  PRAI          N-(5'phosphoribosyl)anthranilate (PRA) isomeras
     0.0004   19.8   0.1    0.00092   18.6   0.0    1.6  2  TMP-TENI      Thiamine monophosphate synthase
    0.00083   18.9   0.1     0.0016   18.0   0.0    1.6  2  His_biosynth  Histidine biosynthesis protein
     0.0072   15.4   0.0       0.33    9.9   0.0    2.0  2  FMN_dh        FMN-dependent dehydrogenase


Domain annotation for each model (and alignments):
>> PRAI  N-(5'phosphoribosyl)anthranilate (PRA) isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.2   1.1   5.7e-36   2.6e-32       1     193 [.       7     222 ..       7     223 .. 0.80

  Alignments for each domain:
  == domain 1  score: 112.2 bits;  conditional E-value: 5.7e-36
                                       TCE----SHHHHHHHHHHTSSEEEEE--..TTBTTB--HHHHHHHCCCS--E..EEEEESSS-HHHHHHHHHHCTEC CS
                              PRAI   1 akicgltrasdvkaavkagadelglifa..esskrevseeqaqellekvpak..lVGVfvNqpieevlriaqelgld 73 
                                       +kicg+++ +d+k+a+  gad++g+i +  + ++r+++ ++a+el+++vp+    V V +  +  + ++ +++++ d
  gi|298675878|ref|YP_003727628.1|   7 IKICGMKSTDDIKKASICGADAVGFIVDvpVDTPRKINIQKAAELIHSVPLFmdSVLVIMPDSGVQAVSMVETVRPD 83 
                                       59***********************98622468*****************653577777777777778999****** PP

                                       EEEE-CGG...-HHHHHHHHHHS-TTSEEEEEEE-S............SS--S-SSTT-SEEEEE....SSS-SSSX CS
                              PRAI  74 vvQLHGde..deqeyeellktelpvikalkvaesvd............evkearradhvdllllD....sgaGGtGe 132
                                       +vQ+HG+   d+ ey +    ++p++k  +v+   +            +++ ++++   d++llD    ++ GG+G+
  gi|298675878|ref|YP_003727628.1|  84 IVQIHGNInaDDLEYMKNR-LDIPIVKTCSVPVGNSesssgvicefenTINNLKNQGLLDAILLDsktdTKSGGSGT 159
                                       ******9854555555444.489***9999875332333342221212233333333336666669999899***** PP

                                       XXXGGGGTTSXX...TTEEEESSXXTTTHHHHHT.TXXSEEEEXGGGEEETEEXHHHHHHHHH CS
                              PRAI 133 lldwsliskllks..lkviLAGGLtpeNvaeaiklegvlgvDvssGVEtnGvkDlekirkfvq 193
                                         +w+  +++ ++  ++viLAGGL+p+Nv+ea+++  +++vDv+sGVEtn  kD +ki++f++
  gi|298675878|ref|YP_003727628.1| 160 VHNWEISKTIMNNvdIPVILAGGLNPDNVKEAVQTVFPYAVDVASGVETNNTKDIDKIHRFIH 222
                                       *****9999998899**********************************************97 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0         1   4.5e+03      50      73 ..      21      44 ..      15      47 .. 0.70
   2 !   18.6   0.0   2.1e-07   0.00092     127     170 ..     149     194 ..     123     203 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1
                          TMP-TENI 50 aalcrkygvpliindrvdlalavg 73
                                      a +c +  v +i++  vd   +++
  gi|298675878|ref|YP_003727628.1| 21 ASICGADAVGFIVDVPVDTPRKIN 44
                                      467777788888887777766666 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 2.1e-07
                          TMP-TENI 127 pTdtKkda..eplgleglkelaealeiPvvaiGGitlenvaevlea 170
                                       +TdtK++   ++ ++e  k++ +++ iPv+  GG++++nv+e++++
  gi|298675878|ref|YP_003727628.1| 149 KTDTKSGGsgTVHNWEISKTIMNNVDIPVILAGGLNPDNVKEAVQT 194
                                       5888888777999****************************99876 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.2   5.5e+03      81      98 ..      11      28 ..      10      31 .. 0.50
   2 !   18.0   0.0   3.6e-07    0.0016     148     221 ..     127     204 ..     103     212 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.2
                                      SSSSHHHHHHHHHCT-SE CS
                      His_biosynth 81 GIrsledveelleagadk 98
                                      G +s +d++++   gad 
  gi|298675878|ref|YP_003727628.1| 11 GMKSTDDIKKASICGADA 28
                                      445555555555555544 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 3.6e-07
                                       EHHHHHHHHHHTT-SEEEEEETTTT....TTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTC.SEEEE CS
                      His_biosynth 148 davelakkleelgageilltdidrd....GtlsGpdleltkelaeavkipviasGGvgsledlkelksegv.daviv 219
                                       ++++++++l+++g+ + +l d ++d    G+ + ++ e+ k++ ++v+ipvi +GG  +++ +ke++++ + +av v
  gi|298675878|ref|YP_003727628.1| 127 EFENTINNLKNQGLLDAILLDSKTDtksgGSGTVHNWEISKTIMNNVDIPVILAGGL-NPDNVKEAVQTVFpYAVDV 202
                                       567788888888877777755555522227777799********************9.99*****999888777777 PP

                                       SH CS
                      His_biosynth 220 gs 221
                                       +s
  gi|298675878|ref|YP_003727628.1| 203 AS 204
                                       65 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   7.3e-05      0.33     126     220 ..      15     108 ..      11     114 .. 0.73
   2 !    3.6   0.0    0.0063        28     201     235 ..     159     193 ..     117     198 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 7.3e-05
                                       HHHHHHHHHCTESEEEEESSTSS---BHHHHHCT--BSTT-T.G.TTGGG..STSGSCCTTH..THHHHHHCCCHB- CS
                            FMN_dh 126 eellkraeaagykalvltvDtpvlgkRerdlrngfslppklklrnllqel..akpewaaealkkasaaaefvgkqld 200
                                        + +k+a  +g++a+ + vD+pv+  R+ ++++  +l  ++    +++++    p+   +a+ ++ ++ +    q++
  gi|298675878|ref|YP_003727628.1|  15 TDDIKKASICGADAVGFIVDVPVDTPRKINIQKAAELIHSVP--LFMDSVlvIMPDSGVQAV-SMVETVRPDIVQIH 88 
                                       566999**********************99999777777755..444443003344444443.23333355556778 PP

                                       TC--HHHHHHHHHHHSSEEE CS
                            FMN_dh 201 psltwddikwlreqtklplv 220
                                        +++ dd++ +++++++p+v
  gi|298675878|ref|YP_003727628.1|  89 GNINADDLEYMKNRLDIPIV 108
                                       999*************9986 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0063
                                       TC--HHHHHHHHHHHSSEEEEEEE-SHHHHHHHHH CS
                            FMN_dh 201 psltwddikwlreqtklplvvKGvltaedakrave 235
                                       +  +w+  k++ +++++p+++ G l+++++k+av+
  gi|298675878|ref|YP_003727628.1| 159 TVHNWEISKTIMNNVDIPVILAGGLNPDNVKEAVQ 193
                                       4459*99**************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.34s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1379.54
//
Query:       gi|298675879|ref|YP_003727629.1|  [L=354]
Description: anthranilate phosphoribosyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-97  326.4   1.1    1.6e-97  326.0   1.1    1.1  1  Glycos_transf_3  Glycosyl transferase family, a/b domain
    5.9e-17   61.3   1.7    2.5e-16   59.3   0.8    2.3  2  Glycos_trans_3N  Glycosyl transferase family, helical bundle 


Domain annotation for each model (and alignments):
>> Glycos_transf_3  Glycosyl transferase family, a/b domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  326.0   1.1  1.8e-101   1.6e-97       3     253 .]      73     322 ..      71     322 .. 0.99

  Alignments for each domain:
  == domain 1  score: 326.0 bits;  conditional E-value: 1.8e-101
                                       TBEEEEESS-SSSTHHHHHHHHHHHHHHTT-BEEEEE-STCTTCS-HHHHHCTST--ST--HHHHHHHHHHHSEEEE CS
                   Glycos_transf_3   3 dlvDivgTGGdgantfNiStaaaivvAaaGvkvakhgnrsvssksGsaDvLealgvnleltpeeveklleevgvgfl 79 
                                        lvD++gTGGd++nt+NiSta++i+++a Gv+vakhgn sv+s sGsaDvL +lg+  ++tp+ev +++e+vg+gf+
  gi|298675879|ref|YP_003727629.1|  73 TLVDTCGTGGDRHNTINISTASSIIASASGVTVAKHGNHSVTSLSGSADVLSELGIMTDQTPDEVCNCIENVGFGFM 149
                                       68*************************************************************************** PP

                                       EHHSSSSHHHHHHHHHHHHTT.-SSHHHCHHHHHT..SEEEEHHHHHHHHTCHSEEEEEEEESTTSSCCSTSHHHHH CS
                   Glycos_transf_3  80 fapeyhkamkhvapvrrelgirTvfnlLGPLinparvkkqllgvyskelaeklaevlkelgveralvvhgdGldevs 156
                                       +ap +h++mk+vap+r+ lg++T+fn+LGPL+npa ++ q++gvy+k+l++++a +lk+lg ++alvvhg+G+de+s
  gi|298675879|ref|YP_003727629.1| 150 LAPVFHPSMKKVAPIRKSLGMQTIFNILGPLTNPAGANSQIIGVYDKKLCKPMALTLKKLGIKHALVVHGEGMDEIS 226
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHTTEEEEEEEEEGSSTSSSEEESHHHHSSHHHHHHHHTTHHTSCHHHHHHHHHHHHHHHHHHHTTSS CS
                   Glycos_transf_3 157 llakttvaelkdgeiteytlepedfglkraelealeggepkenaeilkavlegkksaakrdlvllnagaalvlagka 233
                                        +a+t+vaelkdg i++ytl+pedfg+kra  +++ gg+p ena+ +  +l+g+k+   rd+v+ln++aal++ g a
  gi|298675879|ref|YP_003727629.1| 227 NIAETYVAELKDGMIHTYTLTPEDFGFKRAGPHEIVGGTPGENAQDILYILNGEKGPK-RDIVVLNTAAALYVGGVA 302
                                       ********************************************************96.****************** PP

                                       SSHHHHHHHHHHHHHTSHHH CS
                   Glycos_transf_3 234 dslkegvakaeevidsGkAl 253
                                        s++egv  +ee+idsGkAl
  gi|298675879|ref|YP_003727629.1| 303 GSINEGVSIVEETIDSGKAL 322
                                       ******************95 PP

>> Glycos_trans_3N  Glycosyl transferase family, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.3   0.8   2.8e-20   2.5e-16       2      62 ..       3      62 ..       2      63 .. 0.95
   2 ?   -0.0   0.0     0.091   8.2e+02      41      60 ..     214     233 ..     213     250 .. 0.85

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 2.8e-20
                                      HHHHHHHTT.---HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHHHHHHHHHH CS
                   Glycos_trans_3N  2 diikklrdgeeLtaeeirfaihgilkgevtdaqiaAfLmAlrlkGetaeEiaalaeAmres 62
                                      ++i+kl +g++Lt ee ++a+ +i++ e t+aqi+A+L+Al++kGet +E+a++a+ m ++
  gi|298675879|ref|YP_003727629.1|  3 SYIQKLTEGKNLTIEESENAVIDIFN-ESTEAQIGALLTALKIKGETIDELAGFARGMKKA 62
                                      69***********************9.899****************************765 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.091
                                       HHHHH---HHHHHHHHHHHH CS
                   Glycos_trans_3N  41 AlrlkGetaeEiaalaeAmr 60 
                                       Al + Ge  +Ei + ae  +
  gi|298675879|ref|YP_003727629.1| 214 ALVVHGEGMDEISNIAETYV 233
                                       67888999999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2599.73
//
Query:       gi|298675880|ref|YP_003727630.1|  [L=74]
Description: putative ferredoxin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-18   65.3   3.2    6.4e-18   65.1   3.2    1.1  1  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
      1e-06   29.3   1.0    1.6e-06   28.7   1.0    1.3  1  Fer4_15   4Fe-4S single cluster domain
    0.00066   19.9   3.0       0.01   16.0   0.2    2.0  2  Fer4_18   4Fe-4S dicluster domain
     0.0011   19.1   5.4      0.039   14.1   1.1    2.0  2  Fer4_21   4Fe-4S dicluster domain
     0.0032   17.2   5.6       0.16   11.9   1.1    2.5  2  Fer4      4Fe-4S binding domain
  ------ inclusion threshold ------
      0.029   15.0   4.7        0.1   13.2   4.7    1.8  1  Fer4_7    4Fe-4S dicluster domain
      0.039   14.1   3.1       0.33   11.1   0.4    1.9  2  Fer4_9    4Fe-4S dicluster domain
      0.046   13.8   3.2       0.12   12.5   3.4    1.6  1  Fer4_10   4Fe-4S dicluster domain
       0.07   13.2   1.9      0.086   12.9   1.9    1.3  1  Fer4_19   Divergent 4Fe-4S mono-cluster


Domain annotation for each model (and alignments):
>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.1   3.2   3.2e-21   6.4e-18       1      57 [.      18      71 ..      18      72 .. 0.96

  Alignments for each domain:
  == domain 1  score: 65.1 bits;  conditional E-value: 3.2e-21
                           Fer4_13  1 VDrdtCiacgaCvelaPdvFeeddeggasvvaeqptseeekadaeeAadaCPvesIg 57
                                      VD  +Ciac++Cv++aP+ F++++  g+++v++qp++eee++ +e+A+  CPve+Ig
  gi|298675880|ref|YP_003727630.1| 18 VD-VKCIACHLCVQIAPNNFKMKN--GYAYVYKQPENEEERNSCEDAVMICPVEAIG 71
                                      78.99******************8..69****************************8 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   1.0   8.1e-10   1.6e-06       7      64 ..      21      70 ..      18      71 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 8.1e-10
                           Fer4_15  7 aCigcglCvaeapevfeldedglasvllddgeiaegevpddeeeaaqeAaraCPvdAI 64
                                      +Ci c lCv+ ap+ f+++ +g+a+v        +++ +++e+   ++A+  CPv+AI
  gi|298675880|ref|YP_003727630.1| 21 KCIACHLCVQIAPNNFKMK-NGYAYVY-------KQPENEEERNSCEDAVMICPVEAI 70
                                      7*****************9.****999.......46778999***************9 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2   5.2e-06      0.01      59      81 ..      20      42 ..       3      47 .. 0.86
   2 ?    5.1   0.3     0.013        26      54      74 ..      48      68 ..      45      74 .] 0.81

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.2e-06
                           Fer4_18 59 gdcidcescvkvcPtgidirkGl 81
                                       +ci+c+ cv++ P +  +++G 
  gi|298675880|ref|YP_003727630.1| 20 VKCIACHLCVQIAPNNFKMKNGY 42
                                      68*****************9997 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.013
                           Fer4_18 54 kekgagdcidcescvkvcPtg 74
                                      + +++ +  +ce  v +cP++
  gi|298675880|ref|YP_003727630.1| 48 QPENEEERNSCEDAVMICPVE 68
                                      5667778889*********86 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   1.1     2e-05     0.039      36      52 ..      17      33 ..       2      38 .. 0.79
   2 !   12.4   5.9   6.6e-05      0.13       7      57 ..      21      70 ..      21      71 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2e-05
                           Fer4_21 36 vvedeCvGCnlCssvCP 52
                                      +v+ +C++C+lC+++ P
  gi|298675880|ref|YP_003727630.1| 17 YVDVKCIACHLCVQIAP 33
                                      56789*********999 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 6.6e-05
                           Fer4_21  7 kCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57
                                      kCi C +C++  +++      ++   + +  e+e   C+  + +CPv ++i
  gi|298675880|ref|YP_003727630.1| 21 KCIACHLCVQIAPNNFKMKNGYAYVYKQPENEEERNSCEDAVMICPV-EAI 70
                                      7*********999644333334444455677999************9.665 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   1.1   7.9e-05      0.16       7      16 ..      21      30 ..      16      31 .. 0.88
   2 !    7.5   0.2    0.0019       3.8      15      23 ..      62      70 ..      62      71 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.9e-05
                                      TSSS-THHHH CS
                              Fer4  7 kCigCGaCve 16
                                      kCi+C +Cv+
  gi|298675880|ref|YP_003727630.1| 21 KCIACHLCVQ 30
                                      9*******97 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0019
                                      HHHSTTTEE CS
                              Fer4 15 vevCPvgAI 23
                                      v++CPv+AI
  gi|298675880|ref|YP_003727630.1| 62 VMICPVEAI 70
                                      789*****9 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   4.7   5.3e-05       0.1       1      52 []      21      69 ..      21      69 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.3e-05
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      +Ci C+ Cv+  p++  + + +++  ++  +e ++e+  +C+  v  CP++a
  gi|298675880|ref|YP_003727630.1| 21 KCIACHLCVQIAPNNFKMKNGYAYVYKQ--PE-NEEERNSCEDAVMICPVEA 69
                                      7************988887766443332..22.3334467888888999876 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.4   0.00017      0.33      34      48 ..      20      34 ..       3      37 .. 0.69
   2 ?   10.9   4.2   0.00019      0.38       1      51 []      21      70 ..      21      70 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00017
                            Fer4_9 34 eaCigCgaCveaCpk 48
                                       +Ci C+ Cv++ p+
  gi|298675880|ref|YP_003727630.1| 20 VKCIACHLCVQIAPN 34
                                      579999999998666 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00019
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      kC+ C+ Cv+  p++  ++   ++  ++ +  ee+  +C++ v +Cp +ai
  gi|298675880|ref|YP_003727630.1| 21 KCIACHLCVQIAPNNFKMKNGYAYVYKQPEN-EEERNSCEDAVMICPVEAI 70
                                      7*********999998887777777665544.4466789999999999877 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   3.4   6.3e-05      0.12       5      47 ..      18      60 ..      15      66 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.3e-05
                           Fer4_10  5 dddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtg 47
                                       d +Ci C  Cv+  P ++++++++++  ++ ++++   +C++
  gi|298675880|ref|YP_003727630.1| 18 VDVKCIACHLCVQIAPNNFKMKNGYAYVYKQPENEEERNSCED 60
                                      5679*************88665555555555555555556554 PP

>> Fer4_19  Divergent 4Fe-4S mono-cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.9   4.3e-05     0.086      14      55 ..      21      66 ..       1      71 [. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.3e-05
                           Fer4_19 14 lCihsgnCvkglpevFdpkrk.pwi..kpdeast.eeiievverCP 55
                                       Ci    Cv+ +p+ F++k+   ++  +p++++  ++ + +v+ CP
  gi|298675880|ref|YP_003727630.1| 21 KCIACHLCVQIAPNNFKMKNGyAYVykQPENEEErNSCEDAVMICP 66
                                      6*****************9986777887776655277899****** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 510.44
//
Query:       gi|298675881|ref|YP_003727631.1|  [L=326]
Description: thiamine-monophosphate kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-21   77.1   0.7    2.7e-21   76.0   0.7    1.6  1  AIRS      AIR synthase related protein, N-terminal domain
    3.5e-10   40.2   0.0    6.5e-10   39.3   0.0    1.4  1  AIRS_C    AIR synthase related protein, C-terminal domain


Domain annotation for each model (and alignments):
>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.0   0.7     3e-25   2.7e-21       1      94 []      38     149 ..      38     149 .. 0.94

  Alignments for each domain:
  == domain 1  score: 76.0 bits;  conditional E-value: 3e-25
                                       SSSEE.........EEEEEEEE.EECCTCCCC........HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......H CS
                              AIRS   1 dDaav.........vvttdshnrpvlvepvhf........iGakavavnlsDlaamGArPlalllslalp......w 54 
                                       dD+av         vvttd     +l  +++f        iG+ ++avn sD+aamGA P++ll ++ lp       
  gi|298675881|ref|YP_003727631.1|  38 DDCAVidlnneefmVVTTD-----MLHMKTDFplqmsawqIGWMSAAVNFSDIAAMGACPMGLLAAFGLPenmelgF 109
                                       8***55666666669****.....999999999999***************************************** PP

                                       HHHHHHHHHHHHHHTT-EEEEEEEEEESSEEEEEEEEEEE CS
                              AIRS  55 leevvrglaeaaeelgvplvgGdtsfsneptisvtavGlv 94 
                                       +e+v +g++++a+ +++++vgGd+ +++e+ti+ ta+G v
  gi|298675881|ref|YP_003727631.1| 110 IEDVSQGMNDCAKYCNTSVVGGDIDKHDELTITGTALGRV 149
                                       **************************************86 PP

>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.0   7.3e-14   6.5e-10       1     151 [.     161     305 ..     161     309 .. 0.83

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 7.3e-14
                                       STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHH CS
                            AIRS_C   1 kpGdvliltgslGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgala 77 
                                       k Gd++ +tg  G  ga++++++  +e +++      l  ++    +  ++++la++ g v+++ D ++ GL+ +l 
  gi|298675881|ref|YP_003727631.1| 161 KTGDLVCVTGHTGSAGAALYAIKNNIEVDDEF-----LKALFEPVPRTHEAQKLAQS-GAVTSMIDTSD-GLAMSLY 230
                                       57*************************99976.....9999999999*********8.***********.8****** PP

                                       HHHHTTTEEEEEECGTHHHHHHHH.......HHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEE CS
                            AIRS_C  78 emapasgvgaeidldkvpifdele.......splemllsensGrllvavppeeadavlaileeeglpeaavIGevta 147
                                        +a  s+vg++i++dk+p+ +e+          + +l+s     ll+++++e +  +++ +      ++++IGev++
  gi|298675881|ref|YP_003727631.1| 231 DLALSSQVGFRIYEDKLPVSNEIYsiadkkkAIYFALYSSGDFELLFTISSELKSNAVNSC------DFSIIGEVID 301
                                       **********************999999644334444445555566666666664444444......599******9 PP

                                       SSSE CS
                            AIRS_C 148 keel 151
                                       +e++
  gi|298675881|ref|YP_003727631.1| 302 SEKG 305
                                       9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2377.04
//
Query:       gi|298675882|ref|YP_003727632.1|  [L=1080]
Description: S-layer protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   9.8e-194  640.9  41.5      3e-98  328.0  16.1    3.2  3  S-layer          S-layer protein
    2.7e-09   36.8   8.3     0.0005   19.9   0.1    4.0  3  PEGA             PEGA domain
    1.4e-08   34.9   8.1    0.00079   19.7   0.7    4.2  2  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
      3e-07   30.7   3.6     0.0022   18.3   0.2    3.2  2  fn3              Fibronectin type III domain
    5.9e-07   29.4  13.0    0.00016   21.6   0.2    4.6  4  CarbopepD_reg_2  CarboxypepD_reg-like domain
    1.4e-06   28.8  12.6      0.014   15.9   2.0    4.2  3  Pur_ac_phosph_N  Purple acid Phosphatase, N-terminal domain
      6e-05   23.4   1.1          4    7.9   0.2    4.0  4  DUF2369          Uncharacterised conserved protein (DUF2369)
     0.0017   18.4   2.4      0.025   14.6   0.1    3.1  2  PapC_N           PapC N-terminal domain
  ------ inclusion threshold ------
      0.011   16.3   8.0         34    5.1   0.0    5.1  4  Ig_3             Immunoglobulin domain
      0.017   15.5   5.3       0.68   10.3   0.1    4.2  4  DUF4198          Domain of unknown function (DUF4198)
      0.073   12.9   3.8        2.5    8.0   0.0    3.4  4  DUF4307          Domain of unknown function (DUF4307)
       0.16   12.4   6.7         18    5.8   0.2    4.6  3  CBM60            Ca-dependent carbohydrate-binding module xyl
       0.17   11.0   6.5       0.21   10.7   0.3    3.0  3  Hemocyanin_M     Hemocyanin, copper containing domain
       0.22   12.1  10.8        3.3    8.4   0.1    5.7  6  YtkA             YtkA-like
       0.96    9.6  14.6         51    4.1   0.1    6.2  6  PrcB_C           PrcB C-terminal


Domain annotation for each model (and alignments):
>> S-layer  S-layer protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  320.9  13.4   3.6e-99   4.3e-96       5     258 .]     228     477 ..     224     477 .. 0.98
   2 !  328.0  16.1  2.5e-101     3e-98       8     258 .]     506     760 ..     499     760 .. 0.95
   3 ?   -1.0   0.1      0.63   7.5e+02      23      69 ..     783     836 ..     773     871 .. 0.75

  Alignments for each domain:
  == domain 1  score: 320.9 bits;  conditional E-value: 3.6e-99
                           S-layer   5 eeseeltwtasnFsgfyydiddglssEsltlelesksdrtieegelvYsttpvekefefeewgsYevigflaekYfa 81 
                                        +s+ ++wta+++sgfyyd+d+g+ssE+++++   + +++i+egel+Y+t+p+e++fe++ +gsYevigf+ae+Yfa
  gi|298675882|ref|YP_003727632.1| 228 GMSDYYEWTAESYSGFYYDLDSGISSETMSIS---DINSNIGEGELEYTTSPIETDFEHSGFGSYEVIGFMAERYFA 301
                                       5678899************************8...3799************************************** PP

                           S-layer  82 gy..dnsaetsddvsllsdekLskvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevdskvi 156
                                       gy  +n++++++d+s++ d++Lskvl+d+de+k+++sgs l+LeegY+l+i ++D++gd+v+++Ltk+gee++++v+
  gi|298675882|ref|YP_003727632.1| 302 GYigENTSFVNEDISMMGDGQLSKVLMDSDERKSVFSGSALTLEEGYRLNIVEVDLQGDSVLVRLTKNGEEIETTVV 378
                                       **9988889******************************************************************** PP

                           S-layer 157 ssskadstyvyekdlgdeddvviiavhvdevfrgtedslvviegifqisddvleieegdefgkmevksvseneieme 233
                                       s+   d+ yvy+kdlg++ddv+iiav++ +vfrgte+++v++egifqi d+++ei+egd++gkme++sv  nei+m+
  gi|298675882|ref|YP_003727632.1| 379 SA---DDYYVYKKDLGSTDDVPIIAVNFANVFRGTETNAVFVEGIFQITDEYTEISEGDDYGKMEIESVGLNEIQMD 452
                                       **...************************************************************************ PP

                           S-layer 234 nddsitLsrdktieimddlkfkvaD 258
                                       n+dsi+L++++ti+im++lk+ vaD
  gi|298675882|ref|YP_003727632.1| 453 NEDSISLEEGDTIDIMGNLKIVVAD 477
                                       ************************8 PP

  == domain 2  score: 328.0 bits;  conditional E-value: 2.5e-101
                           S-layer   8 eelt...wtasnFsgfyydiddglssEsltlelesksdrtieegelvYsttpvekefefeewgsYevigflaekYfa 81 
                                       + +t   wt+ nF+gfyydid+gl++Es++++  ++s+++i+e++l+Y + +v++efe+++wg+Y+v+gf+aekYfa
  gi|298675882|ref|YP_003727632.1| 506 NGMTvdkWTPLNFEGFYYDIDEGLQTESFEVT--DRSNSNIQENGLEYISDAVKVEFEYDDWGKYKVVGFMAEKYFA 580
                                       4444557************************9..669**************************************** PP

                           S-layer  82 gy....dnsa....etsddvsllsdekLskvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgee 150
                                       gy    d  +    +t+dd+s lsd++Lskvlid++e+k++++gssl LeegY+l+i+++Dv+gd+v++eL+k ge 
  gi|298675882|ref|YP_003727632.1| 581 GYhesnD--EnnteFTNDDISPLSDGQLSKVLIDSEEQKSIYTGSSLILEEGYTLNINEVDVNGDNVFIELRKGGEL 655
                                       **87641..1456799************************************************************* PP

                           S-layer 151 vdskvissskadstyvyekdlgdeddvviiavhvdevfrgtedslvviegifqisddvleieegdefgkmevksvse 227
                                       +++++iss    ++yvyekdlg++ddv+iiavh++e+frg+e+++v+++gifqisd+++eie+gd++gkme++++++
  gi|298675882|ref|YP_003727632.1| 656 MEQDIISS---GEEYVYEKDLGSTDDVPIIAVHFSEIFRGQETNAVFVDGIFQISDEYTEIENGDSYGKMEIDNIDS 729
                                       ********...****************************************************************** PP

                           S-layer 228 neiemenddsitLsrdktieimddlkfkvaD 258
                                       n+i+m+nd+si+L +++ti+im+d+kfkvaD
  gi|298675882|ref|YP_003727632.1| 730 NRIKMTNDNSINLGEGDTINIMGDIKFKVAD 760
                                       ******************************9 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.63
                           S-layer  23 di.ddglssEsltlelesksdrtieegelvYsttp.......vekefefeewgsY 69 
                                       di d+ ++ E +t++++s ++  ie+ e+ Y+ ++        + e++ e++g+Y
  gi|298675882|ref|YP_003727632.1| 783 DIpDTAIKGEPFTISVTS-RGAAIENAEISYNGENvgetstdGTLEYTPEDTGTY 836
                                       777899999999999987.889999999999876633322223334444666666 PP

>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   1.2   1.6e-06    0.0019      10      57 ..     805     857 ..     794     868 .. 0.74
   2 !   19.9   0.1   4.2e-07    0.0005      11      54 ..     893     941 ..     889     946 .. 0.90
   3 ?   -0.3   0.1      0.85     1e+03      28      64 ..     973    1010 ..     958    1016 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.6e-06
                              PEGA  10 peGatVyidGkylGkTP....vtls.leaGnyslrvekeGYedlektvtvtag 57 
                                        e+a+++ +G+++G+T     ++++  ++G+y+++ ek GY  ++ +v+v+  
  gi|298675882|ref|YP_003727632.1| 805 IENAEISYNGENVGETStdgtLEYTpEDTGTYTITAEKQGYVSVSGQVDVEIP 857
                                       479***********776112234555568********************9843 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 4.2e-07
                              PEGA  11 eGatVyidGkylGkTP....vtls.leaGnyslrvekeGYedlektvtv 54 
                                       e+a V +d + +GkT+    ++++  e+G ++++v+k GY+++e+ ++v
  gi|298675882|ref|YP_003727632.1| 893 ENADVFFDQSRIGKTNengkLSYTtTETGFHKITVSKQGYKEAEENIEV 941
                                       6899**********996666778889*********************98 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.85
                              PEGA   28 tls.leaGnyslrvekeGYedlektvtvtagetvklnl 64  
                                        t +   +G+y ++++  G    +k+++++ g++++++ 
  gi|298675882|ref|YP_003727632.1|  973 TNTgEVSGDYNVELVVNGSVVDSKQINLDVGDNTTVQF 1010
                                        55544479999999999999999999999777777764 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   1.3   1.5e-05     0.018       9      73 ..     800     858 ..     795     867 .. 0.83
   2 !   19.7   0.7   6.6e-07   0.00079       2      69 ..     879     941 ..     878    1013 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.5e-05
                   CarboxypepD_reg   9 asgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagq 73 
                                       + ga+i++a+++     ++ v +t td + +++ +   +gty++t++++Gy +++  +v+++  +
  gi|298675882|ref|YP_003727632.1| 800 SRGAAIENAEISYN---GENVGETSTDGTLEYTPE--DTGTYTITAEKQGYVSVSG-QVDVEIPE 858
                                       5799********99...677888999988888855..88****************7.69888665 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 6.6e-07
                   CarboxypepD_reg   2 isGrVtda.sgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtl 69 
                                       i+ +Vt a  ++pi++a V +      +++  +t+++G+ + +  ++g +++tvs++Gy++a+  ++++
  gi|298675882|ref|YP_003727632.1| 879 INITVTRAiGNEPIENADVFFD-----QSRIGKTNENGKLSYTTTETGFHKITVSKQGYKEAEE-NIEV 941
                                       7889****7889**********.....89999***********9999****************6.5655 PP

>> fn3  Fibronectin type III domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.2   1.9e-06    0.0022       6      78 ..      35     103 ..      32     107 .. 0.84
   2 !   11.5   0.3   0.00024      0.29       7      79 ..     133     201 ..     128     205 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.9e-06
                                       EEEEEESSSEEEEEEE-CSSSSSTEEEEEEEEEETTSTSTEEEEEECSTSSEEEEESSSTTEEEEEEEEEEET CS
                               fn3   6 lsvsevtstsltvsWeppkdgggpitgYeveyrekgseeewneftvprtttsvtltgLkpgteYevrVqavng 78 
                                       +sv +vt +s+t+++e     +++   Y ++y e g+   +++  v+  +++ tl+gL ++t+Y ++++a n 
  gi|298675882|ref|YP_003727632.1|  35 ISVDSVTLDSATITFEVN---QSDANTY-IKYGENGTSLNSQSDPVSDAPYEITLSGLSASTKYDFEIYAENS 103
                                       678888999999999999...5555555.9998888887788888999999*******************997 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00024
                                       EEEEESSSEEEEEEE-CSSSSSTEEEEEEEEEETTSTSTEEEEEECSTSSEEEEESSSTTEEEEEEEEEEETS CS
                               fn3   7 svsevtstsltvsWeppkdgggpitgYeveyrekgseeewneftvprtttsvtltgLkpgteYevrVqavngg 79 
                                       sv + t+ ++++++e     +++   Y ++y +  s  ++++     ++++  l+ L  gt+Y ++++a n++
  gi|298675882|ref|YP_003727632.1| 133 SVNNLTGKKVRITFEVN---QSDANTY-IKYGTNKSSLDSQSDADNDDPYEIILSELSGGTKYYFKIYAENKV 201
                                       66777777888888877...4444443.67755545542444444444558*******************987 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       3.8   4.6e+03      10      39 ..     392     424 ..     388     431 .. 0.76
   2 !   13.0   0.9   6.5e-05     0.078       6      74 ..     797     866 ..     795     879 .. 0.75
   3 !   21.6   0.2   1.3e-07   0.00016       4      65 ..     882     942 ..     882     964 .. 0.88
   4 ?   -1.0   0.1       1.5   1.8e+03      44      80 ..     980    1016 ..     976    1023 .. 0.62

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.8
                   CarbopepD_reg_2  10 tkeplpgatVyvkgtkkgtvTde...nGnFelk 39 
                                       + + +p + V + +  +gt T++   +G F+++
  gi|298675882|ref|YP_003727632.1| 392 STDDVPIIAVNFANVFRGTETNAvfvEGIFQIT 424
                                       556788888999999999999975557888886 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 6.5e-05
                   CarbopepD_reg_2   6 vdketkeplpgatVyvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvs..kektldvni 74 
                                       + ++ + +++ a ++++g ++g  T  +G+ e +  + g+yt++++  Gy +++ +v+v+  +e + +++i
  gi|298675882|ref|YP_003727632.1| 797 SVTSRGAAIENAEISYNGENVGE-TSTDGTLEYTPEDTGTYTITAEKQGYVSVSGQVDVEipEEAKEKMSI 866
                                       55667889***********9985.45677777777789**************9999998732333444444 PP

  == domain 3  score: 21.6 bits;  conditional E-value: 1.3e-07
                   CarbopepD_reg_2   4 tVvdketkeplpgatVyvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvs 65 
                                       tV+ + ++ep++ a V++ +++ g  T+enG+ + ++ + g ++++vs  Gyk++e++++v 
  gi|298675882|ref|YP_003727632.1| 882 TVTRAIGNEPIENADVFFDQSRIG-KTNENGKLSYTTTETGFHKITVSKQGYKEAEENIEVL 942
                                       68888899**********999888.79********************************984 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 1.5
                   CarbopepD_reg_2   44 gkytLvvsyvGyktqekkvtvskektldvnillkeea 80  
                                        g+y +   + G   ++k+++++ + +++v+++ +ee+
  gi|298675882|ref|YP_003727632.1|  980 GDYNVELVVNGSVVDSKQINLDVGDNTTVQFNHSEEQ 1016
                                        5555555555666666666666555666677777765 PP

>> Pur_ac_phosph_N  Purple acid Phosphatase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   1.9   1.8e-05     0.022       6      94 .]      35     119 ..      30     119 .. 0.85
   2 !   15.9   2.0   1.2e-05     0.014       5      94 .]     131     216 ..     127     216 .. 0.84
   3 ?    0.3   0.0      0.86     1e+03       3      42 ..     997    1033 ..     995    1046 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.8e-05
                   Pur_ac_phosph_N   6 lsltedtstsmtvsWitpektkksvvrygtssdalestaeatsstyettnyksgyshkatltgLepgttYyYrvgdd 82 
                                       +s+ + t +s t+++  ++++++++++yg++ ++l+s+ +           +s   +++tl+gL ++t+Y + + ++
  gi|298675882|ref|YP_003727632.1|  35 ISVDSVTLDSATITFEVNQSDANTYIKYGENGTSLNSQSD----------PVSDAPYEITLSGLSASTKYDFEIYAE 101
                                       5666667889999999999999999999999999887654..........45778899****************999 PP

                   Pur_ac_phosph_N  83 eg......gwSevysfkT 94 
                                       ++      ++Se+ +f+T
  gi|298675882|ref|YP_003727632.1| 102 NStdpaknTTSEINHFTT 119
                                       88899999*********9 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.2e-05
                   Pur_ac_phosph_N   5 hlsltedtstsmtvsWitpektkksvvrygtssdalestaeatsstyettnyksgyshkatltgLepgttYyYrvgd 81 
                                       ++s+++ t + +++++  ++++++++++ygt++++l+s+ +a++             +++ l++L  gt+Yy+++ +
  gi|298675882|ref|YP_003727632.1| 131 SISVNNLTGKKVRITFEVNQSDANTYIKYGTNKSSLDSQSDADN----------DDPYEIILSELSGGTKYYFKIYA 197
                                       57788888999*************************99988665..........345679***************** PP

                   Pur_ac_phosph_N  82 deg......gwSevysfkT 94 
                                       +++       +Se   f+T
  gi|298675882|ref|YP_003727632.1| 198 ENKvfsnynSTSEKNDFTT 216
                                       *996777777777777776 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.86
                   Pur_ac_phosph_N    3 qvhlsltedtstsmtvsWitpektkksvvrygtssdales 42  
                                        q++l +++  +t++ ++    ++ ++++v++g+ +++ + 
  gi|298675882|ref|YP_003727632.1|  997 QINLDVGD--NTTVQFNHSEEQA-GNYSVEIGELTGSFKV 1033
                                        88888888..8888888777777.999***9998877544 PP

>> DUF2369  Uncharacterised conserved protein (DUF2369)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.2    0.0034         4       8      71 ..      82     143 ..      77     163 .. 0.64
   2 !    7.5   0.0    0.0043       5.2       9      31 ..     180     202 ..     175     226 .. 0.75
   3 ?   -1.7   0.0       3.2   3.8e+03      51      75 ..     314     338 ..     301     347 .. 0.83
   4 ?    3.1   0.0       0.1   1.2e+02      47      75 ..     593     621 ..     577     629 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0034
                           DUF2369   8 kvtlseLkpdtqYyfdVFvvdqkrn....tssaytgttaqtreekkskpteLkdgkltqvklkgkkgk 71 
                                       ++tls+L+ +t+Y f++++ +++      ts +   tt  t     +   ++++ +++  +l gkk +
  gi|298675882|ref|YP_003727632.1|  82 EITLSGLSASTKYDFEIYAENSTDPakntTSEINHFTT--T----TPTSPSINNSSISVNNLTGKKVR 143
                                       589****************9986554434555554444..2....23444555555555555555555 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0043
                           DUF2369   9 vtlseLkpdtqYyfdVFvvdqkr 31 
                                       ++lseL+ +t+Yyf +++ ++  
  gi|298675882|ref|YP_003727632.1| 180 IILSELSGGTKYYFKIYAENKVF 202
                                       689***************99864 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 3.2
                           DUF2369  51 kpteLkdgkltqvklkgkkgkslfs 75 
                                        +  + dg+l++v +++ + ks+fs
  gi|298675882|ref|YP_003727632.1| 314 DISMMGDGQLSKVLMDSDERKSVFS 338
                                       567789***********99999887 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.1
                           DUF2369  47 ekkskpteLkdgkltqvklkgkkgkslfs 75 
                                         ++ +  L+dg+l++v ++++++ks+++
  gi|298675882|ref|YP_003727632.1| 593 FTNDDISPLSDGQLSKVLIDSEEQKSIYT 621
                                       45678899****************99876 PP

>> PapC_N  PapC N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.2      0.18   2.1e+02      12      57 ..     109     154 ..     102     169 .. 0.84
   2 !   14.6   0.1   2.1e-05     0.025      11      82 ..     962    1032 ..     949    1051 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.18
                                       THHHHHHHHHTT-SS-SEEEEEEEEETTEEEEEEEEEEEECCTCCC CS
                            PapC_N  12 asnvdlsrFskgnavlpGeYrvdvyvNgkeigrqevefkaekkkkk 57 
                                       +++ ++++F++  ++ p  ++ ++ vN+   ++ +++f+ ++ + +
  gi|298675882|ref|YP_003727632.1| 109 NTTSEINHFTTTTPTSPSINNSSISVNNLTGKKVRITFEVNQSDAN 154
                                       5667799**********************99999****99755444 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 2.1e-05
                                        TTHHHHHHHHHTT-SS-SEEEEEEEEETTEEEEEEEEEEEECCTCCCEEEE-BHHHHHHTTB-GGGSCCGHH CS
                            PapC_N   11 sasnvdlsrFskgnavlpGeYrvdvyvNgkeigrqevefkaekkkkklepcltrelleqlgvkleklpelak 82  
                                         ++nv++s  +++     G+Y+v+++vNg+ +++++++++   ++++++   ++e+  ++ v++ +l+ + k
  gi|298675882|ref|YP_003727632.1|  962 PDENVKISANATNTGEVSGDYNVELVVNGSVVDSKQINLDVG-DNTTVQFNHSEEQAGNYSVEIGELTGSFK 1032
                                        567788888888888899********************9776.99999999999999999999877776554 PP

>> Ig_3  Immunoglobulin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.2     0.055        65       2      79 .]      28     102 ..      27     102 .. 0.75
   2 ?    5.1   0.0     0.028        34       2      48 ..     125     172 ..     124     224 .. 0.71
   3 ?    4.3   0.0     0.052        63      15      78 ..     790     841 ..     771     841 .. 0.62
   4 ?    3.3   0.2      0.11   1.3e+02       7      75 ..     956    1022 ..     952    1024 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.055
                                       EEEECCCSCEEEETTS-EEEEEEEEEES--.EEEEEETTS...TTCSEEESSEECCCTEEEESS--GGG-EEEEEEE CS
                              Ig_3   2 PvItvppsstvvtegesvtLtCeaegnppp.titWykngeklssnstsssissegssssLtisnvtksdsGtYtCvA 77 
                                       P+I+ ++ s+     +s+t+t e+  ++++  i++  ng+ l+s+s++    +++   ++t+s +++s +  ++  A
  gi|298675882|ref|YP_003727632.1|  28 PSINNSSISVDSVTLDSATITFEVNQSDANtYIKYGENGTSLNSQSDP----VSDAPYEITLSGLSASTKYDFEIYA 100
                                       99**999999988889999*****999999666777777755554444....5667777888887777777777777 PP

                                       EE CS
                              Ig_3  78 sN 79 
                                       +N
  gi|298675882|ref|YP_003727632.1| 101 EN 102
                                       76 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.028
                                       EEEECCCSCEEEETTS-EEEEEEEEEES--EEEEEETTS....TTCSE CS
                              Ig_3   2 PvItvppsstvvtegesvtLtCeaegnppptitWykngek.lssnsts 48 
                                       P+I+ ++ s+    g++v++t e+  ++++t+  y  ++  l+s+s+ 
  gi|298675882|ref|YP_003727632.1| 125 PSINNSSISVNNLTGKKVRITFEVNQSDANTYIKYGTNKSsLDSQSDA 172
                                       9***********************999999665555555323332222 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.052
                                       TTS-EEEEEEEEEES--EEEEEETTS...TTCSEEESSEECCCTEEEESS--GGG-EEEEEEEE CS
                              Ig_3  15 egesvtLtCeaegnppptitWykngeklssnstsssissegssssLtisnvtksdsGtYtCvAs 78 
                                       +ge++t++ +  g    + +  +nge   +       ++ ++ ++L+ +   ++d+GtYt +A+
  gi|298675882|ref|YP_003727632.1| 790 KGEPFTISVTSRGAAIENAEISYNGE---N------VGETSTDGTLEYT---PEDTGTYTITAE 841
                                       55555555555555555555555555...2......1223445555555...5*******9985 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.11
                                        CCSCEEEETTS-EEEEEEE..EEES--..EEEEEETTS...TTCSEEESSEECCCTEEEESS--GGG-EEEEE CS
                              Ig_3    7 ppsstvvtegesvtLtCea..egnppp..titWykngeklssnstsssissegssssLtisnvtksdsGtYtC 75  
                                        +ps+  v + e+v+++ +a  +g  +   +++   ng++++s++    + ++g+++++++++ +++++G+Y+ 
  gi|298675882|ref|YP_003727632.1|  956 NPST--VSPDENVKISANAtnTGEVSGdyNVELVVNGSVVDSKQI---NLDVGDNTTVQFNH-SEEQAGNYSV 1022
                                        4444..579999999999964333333677888888886444222...46777778888887.9999****86 PP

>> DUF4198  Domain of unknown function (DUF4198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1         2   2.4e+03      31      94 ..     520     586 ..     491     621 .. 0.65
   2 ?   10.3   0.1   0.00057      0.68     144     203 ..     785     844 ..     780     853 .. 0.68
   3 ?    4.1   0.0     0.042        51     145     203 ..     871     931 ..     845     932 .. 0.80
   4 ?   -0.7   0.0       1.3   1.5e+03      15      87 ..     960    1031 ..     945    1038 .. 0.56

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2
                           DUF4198  31 pfead.heplkleklkvlapdg.e.ktdlgkylstfdvallkpekegtyklaaakkpgdwkeygdpk 94 
                                        f+ d  e l+ e+++v++  + + +++  +y s+   ++++ ++ g yk++ ++   ++  y + +
  gi|298675882|ref|YP_003727632.1| 520 GFYYDiDEGLQTESFEVTDRSNsNiQENGLEYISDAVKVEFEYDDWGKYKVVGFMAEKYFAGYHESN 586
                                       4666667888889999999998533333335555555555566778999998877766666555555 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00057
                           DUF4198 144 pydlkageelevqvlldGkPlagaeveveyggtryrdapdeikvktdadGvvtftlpkaG 203
                                       p +  +ge++++ v+ +G   ++ae++   ++ ++    ++ +++  + G  t+t +k+G
  gi|298675882|ref|YP_003727632.1| 785 PDTAIKGEPFTISVTSRGAAIENAEISYNGENVGETSTDGTLEYTPEDTGTYTITAEKQG 844
                                       677789*********************655555444444444444444444444444444 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.042
                           DUF4198 145 ydlkageelevqvl..ldGkPlagaeveveyggtryrdapdeikvktdadGvvtftlpkaG 203
                                        d+++g+++ ++v+  +  +P ++a+v +     ++ ++ ++  ++t + G  ++t++k+G
  gi|298675882|ref|YP_003727632.1| 871 EDIFEGDVINITVTraIGNEPIENADVFFDQSRIGKTNENGKLSYTTTETGFHKITVSKQG 931
                                       5777788888888766667888888888888777888888888888888888888888887 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 1.3
                           DUF4198   15 vsggewvtvdlafgh.dpfead.heplkleklkvlapdge.ktdlgkylstfdvallkpekegtyklaaakkpgd 86  
                                        vs++e+v++ +  ++  +  +d +++l + +  v++ + + + d+g + +t+++++ ++e++g y ++     g+
  gi|298675882|ref|YP_003727632.1|  960 VSPDENVKISANATNtGEVSGDyNVELVV-NGSVVDSK-QiNLDVG-DNTTVQFNH-SEEQAGNYSVEIGELTGS 1030
                                        44554555555555522333332222222.22333333.3366666.778888888.456679999988555555 PP

                           DUF4198   87 w 87  
                                        +
  gi|298675882|ref|YP_003727632.1| 1031 F 1031
                                        5 PP

>> DUF4307  Domain of unknown function (DUF4307)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0021       2.5      11      58 ..       9      56 ..       4      59 .. 0.77
   2 ?    4.1   0.1     0.033        40      28      58 ..     123     153 ..     114     156 .. 0.85
   3 ?   -2.2   0.1         3   3.6e+03      60      92 ..     833     866 ..     798     870 .. 0.62
   4 ?   -2.9   0.0       4.9   5.9e+03      69      94 ..     914     939 ..     913     941 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0021
                           DUF4307 11 vlvvvalalvawigysqgsadvsaevvgfevvddstvevtfeVtrddg 58
                                      ++++++ ++ + i+ +q++++++ + ++++ v+ +++++tfeV+++d 
  gi|298675882|ref|YP_003727632.1|  9 LIGLLFFGMFTGIAEAQTEPSINNSSISVDSVTLDSATITFEVNQSDA 56
                                      444445555555555568999***********************9986 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.033
                           DUF4307  28 gsadvsaevvgfevvddstvevtfeVtrddg 58 
                                       +s++++ + ++++  + ++v++tfeV+++d 
  gi|298675882|ref|YP_003727632.1| 123 TSPSINNSSISVNNLTGKKVRITFEVNQSDA 153
                                       7899999********************9986 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3
                           DUF4307  60 pavCiVrAldedgaev.Grrevlvpagdertvrv 92 
                                       +++ +++A  + +  v G+ +v++p++ ++++ +
  gi|298675882|ref|YP_003727632.1| 833 TGTYTITAEKQGYVSVsGQVDVEIPEEAKEKMSI 866
                                       4455566666655444378888887776665555 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 4.9
                           DUF4307  69 dedgaevGrrevlvpagdertvrvtv 94 
                                       ++  +e+G  +++v +++ ++ + + 
  gi|298675882|ref|YP_003727632.1| 914 SYTTTETGFHKITVSKQGYKEAEENI 939
                                       788999********998777766555 PP

>> CBM60  Ca-dependent carbohydrate-binding module xylan-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.2     0.015        18      13      59 ..     359     405 ..     351     414 .. 0.88
   2 ?    1.8   0.1      0.27   3.2e+02       1      41 [.     795     837 ..     795     856 .. 0.66
   3 ?    4.6   0.2     0.037        44       9      54 ..     977    1023 ..     965    1026 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.015
                             CBM60  13 deppefrllvdGqkvgeadvasteaktytftadltagahklqirylN 59 
                                       ++ + +rl  +G++++++ v+++++  y+ ++  t++   + + ++N
  gi|298675882|ref|YP_003727632.1| 359 GDSVLVRLTKNGEEIETTVVSADDYYVYKKDLGSTDDVPIIAVNFAN 405
                                       336889*******************************999*****99 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.27
                             CBM60   1 tivVrAagdqagdeppefrllvdGqkvg......eadvasteaktyt 41 
                                       ti+V  +g++  +     ++ ++G++vg      + + + ++  tyt
  gi|298675882|ref|YP_003727632.1| 795 TISVTSRGAAIEN----AEISYNGENVGetstdgTLEYTPEDTGTYT 837
                                       6788888888865....78999******5444443333333444444 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.037
                             CBM60    9 dqagdeppefrllvdGqkvg..eadvasteaktytftadltag.ahklq 54  
                                        +  gd   +++l+v+G++v   +++++ ++++t++f++  ++  + +++
  gi|298675882|ref|YP_003727632.1|  977 EVSGD--YNVELVVNGSVVDskQINLDVGDNTTVQFNHSEEQAgNYSVE 1023
                                        22344..67899*******988888999999999999987755466665 PP

>> Hemocyanin_M  Hemocyanin, copper containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1     0.079        94     161     208 ..     425     472 ..     419     487 .. 0.81
   2 ?   -1.0   0.2      0.66   7.8e+02     179     243 ..     528     591 ..     517     595 .. 0.78
   3 ?   10.7   0.3   0.00018      0.21     161     228 ..     708     775 ..     702     782 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.079
                                       GGHHHHHHHHHHHHHHHHHHHHSEE.EETTCEEETTSCHHHHHHHHHH CS
                      Hemocyanin_M 161 gnyeklekvedlekrirdaidsgyvltadgkkidLrkpegieilgnil 208
                                       ++y ++++ +d+ k   + +  + +++++ + i+L++ + i+i+gn+ 
  gi|298675882|ref|YP_003727632.1| 425 DEYTEISEGDDYGKMEIESVGLNEIQMDNEDSISLEEGDTIDIMGNLK 472
                                       566777777777777778899999**********************85 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.66
                                       HHHHSEE.EETTCEEETTSCHHHHHHHHHHHT-GGSB--TTS--HHHHHHHHHCT----SBTTB- CS
                      Hemocyanin_M 179 aidsgyvltadgkkidLrkpegieilgnilegnvdsidkkfygslevlarkllgdaeepddkykv 243
                                        +++  +  +d ++ +++ ++g+e++ + ++   +  d   y+ + ++a k+++  +e +d++++
  gi|298675882|ref|YP_003727632.1| 528 GLQTESFEVTDRSNSNIQ-ENGLEYISDAVKVEFEYDDWGKYKVVGFMAEKYFAGYHESNDENNT 591
                                       555566666666666665.6899999999999999999999*************99999988774 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00018
                                       GGHHHHHHHHHHHHHHHHHHHHSEE.EETTCEEETTSCHHHHHHHHHHHT-GGSB--TTS--HHHHHH CS
                      Hemocyanin_M 161 gnyeklekvedlekrirdaidsgyvltadgkkidLrkpegieilgnilegnvdsidkkfygslevlar 228
                                       ++y ++e+ +++ k   d ids+ +++++++ i+L + + i+i+g+i    +ds   ++y ++ev+ +
  gi|298675882|ref|YP_003727632.1| 708 DEYTEIENGDSYGKMEIDNIDSNRIKMTNDNSINLGEGDTINIMGDIKFKVADSDTLRYYPFVEVTTK 775
                                       5667777777788888899******************************************9998776 PP

>> YtkA  YtkA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       4.6   5.5e+03       4      42 ..      91     134 ..      89     151 .. 0.60
   2 ?   -1.4   0.0         3   3.6e+03      22      42 ..     360     380 ..     346     382 .. 0.76
   3 ?    1.6   0.0      0.35   4.2e+02      63      79 ..     490     507 ..     444     510 .. 0.85
   4 ?    3.9   0.0     0.067        81      23      73 ..     793     840 ..     778     842 .. 0.84
   5 ?    8.4   0.1    0.0027       3.3       7      72 ..     864     926 ..     858     928 .. 0.77
   6 ?   -1.9   0.1       4.6   5.4e+03      40      40 ..     998     998 ..     963    1024 .. 0.53

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4.6
                              YtkA   4 sddlevelvspeep...kagenti.vvt.vtqggkpVedadvkv 42 
                                       s+++++e+  +++    k+   +i ++t  t +   +++ +++v
  gi|298675882|ref|YP_003727632.1|  91 STKYDFEIYAENSTdpaKNTTSEInHFTtTTPTSPSINNSSISV 134
                                       56677777655544221333334445544556666666665554 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3
                              YtkA  22 ntivvtvtqggkpVedadvkv 42 
                                       +++ v+ t++g+++e  +v++
  gi|298675882|ref|YP_003727632.1| 360 DSVLVRLTKNGEEIETTVVSA 380
                                       5677889999**999998875 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.35
                              YtkA  63 esedGvYeae.vnfsmeG 79 
                                        +e+G Ye++ + f+++G
  gi|298675882|ref|YP_003727632.1| 490 RTEPGTYEVRgTVFEKNG 507
                                       479*******99999998 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.067
                              YtkA  23 tivvtvtqggkpVedadvkvefwmpameGmeemttkvelkesedGvYeaev 73 
                                        +++ vt  g+++e+a+++ +++     G   ++  +e +++  G Y +++
  gi|298675882|ref|YP_003727632.1| 793 PFTISVTSRGAAIENAEISYNGENV---GETSTDGTLEYTPEDTGTYTITA 840
                                       467789999**************99...8888899999999999***9875 PP

  == domain 5  score: 8.4 bits;  conditional E-value: 0.0027
                              YtkA   7 levelvspeepkagentivvtvtqggkpVedadvkvefwmpameGmeemttkvelkesedGvYeae 72 
                                         +++ s++ ++     i+vt+  g++p+e+adv+++ ++    G+  ++ k++ + +e G  +++
  gi|298675882|ref|YP_003727632.1| 864 MSISVDSEDIFEGDVINITVTRAIGNEPIENADVFFDQSRI---GKTNENGKLSYTTTETGFHKIT 926
                                       56666666655555557899999*************99998...8888899999888888877665 PP

  == domain 6  score: -1.9 bits;  conditional E-value: 4.6
                              YtkA  40 v 40 
                                       +
  gi|298675882|ref|YP_003727632.1| 998 I 998
                                       1 PP

>> PrcB_C  PrcB C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.046        56      16      34 ..      34      52 ..      31      60 .. 0.90
   2 ?    0.2   0.2      0.72   8.6e+02      15      53 ..      81     127 ..      81     130 .. 0.67
   3 ?    2.0   0.0       0.2   2.3e+02      16      34 ..     131     149 ..     128     155 .. 0.90
   4 ?    4.1   0.1     0.042        51      13      43 ..     346     372 ..     344     380 .. 0.79
   5 ?    2.1   0.0      0.19   2.2e+02      13      34 ..     629     650 ..     627     662 .. 0.84
   6 ?    1.0   0.0      0.39   4.7e+02      11      31 ..    1016    1042 ..    1009    1052 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.046
                            PrcB_C 16 sievdkvyetenaiyvktt 34
                                      si+vd+v+++  +i+++++
  gi|298675882|ref|YP_003727632.1| 34 SISVDSVTLDSATITFEVN 52
                                      8***************997 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.72
                            PrcB_C  15 Ysievdkvy...etenaiyvkttllgP......epgeevtqaltyPyv 53 
                                       Y i++ +++   + + +iy++ + ++P      e + ++t ++t+P +
  gi|298675882|ref|YP_003727632.1|  81 YEITLSGLSastKYDFEIYAENS-TDPaknttsEINHFTTTTPTSPSI 127
                                       55666666654444557777775.577666665778889999999987 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.2
                            PrcB_C  16 sievdkvyetenaiyvktt 34 
                                       si+v++++ ++ +i+++++
  gi|298675882|ref|YP_003727632.1| 131 SISVNNLTGKKVRITFEVN 149
                                       8***************997 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.042
                            PrcB_C  13 gGYsievdkvyetenaiyvkttllgPepgee 43 
                                       +GY++++ +v + ++++ v++t    + gee
  gi|298675882|ref|YP_003727632.1| 346 EGYRLNIVEVDLQGDSVLVRLT----KNGEE 372
                                       7*******************99....33443 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.19
                            PrcB_C  13 gGYsievdkvyetenaiyvktt 34 
                                       +GY +++++v  +++++ ++++
  gi|298675882|ref|YP_003727632.1| 629 EGYTLNINEVDVNGDNVFIELR 650
                                       7****************99987 PP

  == domain 6  score: 1.0 bits;  conditional E-value: 0.39
                            PrcB_C   11 ptgGYsievdkvy......etenaiyv 31  
                                        + g+Ys+e+ +++      e+ n i +
  gi|298675882|ref|YP_003727632.1| 1016 QAGNYSVEIGELTgsfkveESSNIILY 1042
                                        5699********988888555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1080 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       945  (0.0527079); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.83u 0.31s 00:00:01.13 Elapsed: 00:00:00.49
# Mc/sec: 6634.96
//
Query:       gi|298675883|ref|YP_003727633.1|  [L=178]
Description: transcriptional regulator, XRE family [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-08   34.9   0.0      3e-08   33.6   0.0    1.7  1  HTH_3     Helix-turn-helix
    0.00028   20.9   0.1     0.0054   16.7   0.0    2.3  2  HTH_19    Helix-turn-helix domain
    0.00042   19.9   1.1    0.00069   19.2   1.1    1.3  1  PrpR_N    Propionate catabolism activator
     0.0078   16.5   0.0      0.013   15.8   0.0    1.3  1  HTH_31    Helix-turn-helix domain
  ------ inclusion threshold ------
      0.079   12.8   0.0        0.2   11.5   0.0    1.7  1  MerR      MerR family regulatory protein
       0.13   12.7   0.0       0.25   11.8   0.0    1.5  1  HTH_26    Cro/C1-type HTH DNA-binding domain


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.0     1e-11     3e-08       7      46 ..      29      68 ..      22      71 .. 0.93

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 1e-11
                                      HTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHH CS
                             HTH_3  7 qlglsqeeLAeklGvsrstisriEnGernPsletlkklak 46
                                      +lgl+++e++ek++v++st+++i +G r+P+l+tl  + k
  gi|298675883|ref|YP_003727633.1| 29 ELGLTIAEFSEKADVPVSTLYKILSGNREPNLKTLRQIVK 68
                                      99**********************************9987 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.8e-06    0.0054       9      50 ..      28      68 ..      24      77 .. 0.93
   2 ?    1.8   0.0     0.083   2.5e+02       9      31 ..      92     113 ..      88     114 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.8e-06
                            HTH_19  9 eelgltqeelaerlgisrskisaiEngkkdvpsaelllkiae 50
                                       elglt++e +e++++  s +++i +g++ +p+ ++l++i++
  gi|298675883|ref|YP_003727633.1| 28 DELGLTIAEFSEKADVPVSTLYKILSGNR-EPNLKTLRQIVK 68
                                      79***************************.*********987 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.083
                            HTH_19   9 eelgltqeelaerlgisrskisa 31 
                                        + + t++++++++++ ++ +sa
  gi|298675883|ref|YP_003727633.1|  92 DNINETKRKVQGKNIT-IREYSA 113
                                       57899*********99.888886 PP

>> PrpR_N  Propionate catabolism activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   1.1   2.3e-07   0.00069      72     159 ..      80     170 ..      61     173 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.3e-07
                            PrpR_N  72 ekialvgfeniikglktlsell...dldieiytinseeeaeaavkelkaegvevvvGdgvvadlAekaGlksvllts 145
                                       e i++++ + +++++++ ++ +   +++i+ y+ +s e+a  +  ++ +eg +++v+  +v++++ek+    v   +
  gi|298675883|ref|YP_003727633.1|  80 EFIGVIAARPVLDNINETKRKVqgkNITIREYSATSIEDAIIVAVQAEREGAKALVCAPIVSSTVEKIIRVPVTTIM 156
                                       36999***999999999887765446667777888999999999999********************6666666666 PP

                            PrpR_N 146 gkesvrqAieeAle 159
                                        ++s+ +Aie A++
  gi|298675883|ref|YP_003727633.1| 157 PRKSIVEAIEIAVQ 170
                                       6*********9986 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   4.4e-06     0.013      12      51 ..      29      67 ..      19      77 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.4e-06
                            HTH_31 12 raGLsqeevAerlgvsestlsrlEqGrrgrpspavleala 51
                                      + GL+ +e  e + v +stl ++ +G r +p + +l++++
  gi|298675883|ref|YP_003727633.1| 29 ELGLTIAEFSEKADVPVSTLYKILSGNR-EPNLKTLRQIV 67
                                      67**************************.8**99999986 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   6.6e-05       0.2       1      16 [.      33      48 ..      33      50 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.6e-05
                                      EHHHHHHHHTTTHHHH CS
                              MerR  1 tIgevAeltGvsprtL 16
                                      tI e++e+++v+++tL
  gi|298675883|ref|YP_003727633.1| 33 TIAEFSEKADVPVSTL 48
                                      8**************9 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   8.3e-05      0.25      10      47 ..      31      67 ..      21      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.3e-05
                            HTH_26 10 gitkseLargtgisaatlsrlvkgkpervsldtLdkiC 47
                                      g+t++e+++++++  +tl+++++g  + ++l+tL  i 
  gi|298675883|ref|YP_003727633.1| 31 GLTIAEFSEKADVPVSTLYKILSGN-REPNLKTLRQIV 67
                                      6799********************8.899**9999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1125.30
//
Query:       gi|298675884|ref|YP_003727634.1|  [L=332]
Description: aliphatic sulfonates family ABC transporter periplasmic ligand-binding protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-40  139.7   0.0    1.8e-40  139.3   0.0    1.1  1  NMT1_2          NMT1-like family
    1.5e-13   51.2   0.0    2.1e-13   50.7   0.0    1.2  1  NMT1            NMT1/THI5 like
    4.9e-06   26.3   0.0    7.1e-06   25.8   0.0    1.2  1  Phosphonate-bd  ABC transporter, phosphonate, periplasmic sub
     0.0046   16.4   0.0      0.066   12.6   0.0    2.1  2  NMT1_3          NMT1-like family
  ------ inclusion threshold ------
      0.014   15.0   0.0      0.021   14.4   0.0    1.2  1  VitK2_biosynth  Menaquinone biosynthesis
      0.053   12.9   0.0      0.089   12.1   0.0    1.3  1  LysR_substrate  LysR substrate binding domain
       0.12   12.7   0.0       0.18   12.1   0.0    1.3  1  PSII_Pbs27      Photosystem II Pbs27


Domain annotation for each model (and alignments):
>> NMT1_2  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.3   0.0     7e-44   1.8e-40       6     248 ..      32     265 ..      27     269 .. 0.93

  Alignments for each domain:
  == domain 1  score: 139.3 bits;  conditional E-value: 7e-44
                            NMT1_2   6 eqlklGfialtdaaplvvakekglfake....Glt.velekqaswaelrdkllagelDaahv.ltpapllidlGigg 76 
                                       +ql++G+++ t+    + a+ekg+ ++     G++ ++  ++  ++  ++++lag++D+a+v  +p+++++d+G+  
  gi|298675884|ref|YP_003727634.1|  32 NQLTFGYQPSTHQIAYMTAAEKGWWEDNlephGIEtINENEFPTGSPEMQAMLAGDIDVAYVgAAPFVSAVDKGL-- 106
                                       79************************999999***99**************************************.. PP

                            NMT1_2  77 akadmkvlaslnlnGqaitlsnklkdkkvsdakalkdlvakkkaskplkiavtfpgsthdlllrywLaaaGldpead 153
                                          + k++a ++ +G +++l+ ++++    + ++ +dl       ++lkia+  pg  +d++lr wL+ +Gldp++d
  gi|298675884|ref|YP_003727634.1| 107 ---NAKIVAGVQIQGSSLVLRPEFAE----NYEEPQDL-------EGLKIATFPPGTIQDTILRNWLKDNGLDPDKD 169
                                       ...9****************985444....33444444.......89****************************** PP

                            NMT1_2 154 vklvvvpppqmvanlkagtidgfcvgePwnaqavaegiGvtaltsqelwkdhPekvlgvredfveknpntaralvka 230
                                       v++v + p +++++ +a ++dg + + P +a  + e+ G  +++s+e w++h ++vl+v+ ++++++p+++r +vk+
  gi|298675884|ref|YP_003727634.1| 170 VDIVGMGPGDAISAISAERVDGVFLPHPAPAIIESENNGQSVVDSGEMWNNHACCVLVVSDELINNYPEVTREIVKT 246
                                       ***************************************************************************** PP

                            NMT1_2 231 lleAtkwlda.kkenraea 248
                                       ++eAt++ ++  ++++++ 
  gi|298675884|ref|YP_003727634.1| 247 HVEATEYNKNhMDDAAQIY 265
                                       *******998555555554 PP

>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   0.0   8.3e-17   2.1e-13       3     214 ..      43     259 ..      41     261 .. 0.81

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 8.3e-17
                                       GGHHHHHHHHTTHHHH....TTEEE.EEE--SSTTHHHHHHHCTS-SEEEE-HHHHHHHHHTT--EEEEEEEE-S-- CS
                              NMT1   3 nhaglyvAkekGYFke....eGldV.eivepadpsdatelvasgkadfgvsyqesllaarakglpvvsvaallqepl 74 
                                         + +++A+ekG++++    +G++  + +e    s  ++++ +g+ d++      ++ a +kgl  + va +  +  
  gi|298675884|ref|YP_003727634.1|  43 HQIAYMTAAEKGWWEDnlepHGIETiNENEFPTGSPEMQAMLAGDIDVAYVGAAPFVSAVDKGLNAKIVAGVQIQGS 119
                                       5688999*******9944445999543333344477789999************************99998865555 PP

                                       EEEEEECCC-.-SSGGGGTTSEEEE-S.-TTHHHHHHHHHHHTT--GG.G-EEEE-.TT-HHHHHHCTSSSEEECEE CS
                              NMT1  75 sglivlkdsg.ikspkDLkGkrigyvg.spfekallkallakdggdps.dvtlvnvggtslakalltgkvDaaiggy 148
                                       s ++  + ++  ++p+DL+G +i++++ + +++++l+  l+ +g+dp+ dv +v +g  ++++a+ + +vD ++   
  gi|298675884|ref|YP_003727634.1| 120 SLVLRPEFAEnYEEPQDLEGLKIATFPpGTIQDTILRNWLKDNGLDPDkDVDIVGMGPGDAISAISAERVDGVFLPH 196
                                       55555554445*************9887999**************99638***********************9777 PP

                                       TTTHHHHHHHTT--EEEE-GGGTT-----SEEEEEEHHHHHH-HHHHHHHHHHHHHHHHHHHHSHH CS
                              NMT1 149 enwegvelesegkelrifaladlgvpdyyslvlitnekllkenpelvkkFlrAlkkGyeyalahPe 214
                                        +   +e e+ g+  +++   ++   +    vl+++++l+++ pe  +++++   +++ey  +h +
  gi|298675884|ref|YP_003727634.1| 197 PAPAIIESENNGQ--SVVDSGEMWN-NHACCVLVVSDELINNYPEVTREIVKTHVEATEYNKNHMD 259
                                       7766666555554..4444444443.777789***************************9988865 PP

>> Phosphonate-bd  ABC transporter, phosphonate, periplasmic substrate-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   2.8e-09   7.1e-06      43     165 ..      80     196 ..      75     249 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2.8e-09
                                       HHHHHTTS-SEEE--HHHHHHHHHHS.-EEEEEEEEETT--SEEEEEEEEETT..SS--SHHHHGG-EEEE--TT-T CS
                    Phosphonate-bd  43 vealragqvDiaflgplayvqardqa.gveplatrvrsdGsasyrsviivrad..sdiqsledLkgktiafvspsSt 116
                                       ++a+ ag +D+a++g+ ++v a+d+  +++ +a  +         s ++ r++  +++++ +dL+g +ia   p   
  gi|298675884|ref|YP_003727634.1|  80 MQAMLAGDIDVAYVGAAPFVSAVDKGlNAKIVAGVQI------QGSSLVLRPEfaENYEEPQDLEGLKIATFPPGTI 150
                                       69*********************99546655555554......56777777774246*****************988 PP

                                       TTTHHHHHHTCCCCT--HHHHSSEEEE--HHHHHHHHHTTSSSEEEEEH CS
                    Phosphonate-bd 117 sGylvpaalLvkeagldpeddfsevfsgshdaavlavlsgdadaaavsa 165
                                           + + +L k++gldp++d + v +g    a+ a+ + ++d  +++ 
  gi|298675884|ref|YP_003727634.1| 151 Q-DTILRNWL-KDNGLDPDKDVDIVGMG-PGDAISAISAERVDGVFLPH 196
                                       8.7788999*.9***********99776.56677888888888777554 PP

>> NMT1_3  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.071   1.8e+02     150     188 ..      77     115 ..      52     122 .. 0.78
   2 !   12.6   0.0   2.6e-05     0.066     104     180 ..     132     206 ..     119     259 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.071
                            NMT1_3 150 gesadalkdgqldgaalvaGvPvsavtqlaasediklip 188
                                       ++ ++a+  g +d+a + a++ vsav +  + + +  ++
  gi|298675884|ref|YP_003727634.1|  77 SPEMQAMLAGDIDVAYVGAAPFVSAVDKGLNAKIVAGVQ 115
                                       67899****************9**998766665555555 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 2.6e-05
                            NMT1_3 104 gsiadlkgkrvsvGpegsGtegsarailealgls.ekdlklleelgygesadalkdgqldgaalvaGvPvsavtqla 179
                                       ++ +dl+g +++  p+g+ +++  r+ l+  gl+ +kd+++   +g+g++++a+   ++dg++l+  +P+ a+ +  
  gi|298675884|ref|YP_003727634.1| 132 EEPQDLEGLKIATFPPGTIQDTILRNWLKDNGLDpDKDVDI-VGMGPGDAISAISAERVDGVFLP--HPAPAIIESE 205
                                       55689*****************************8899997.899********************..8888887765 PP

                            NMT1_3 180 a 180
                                       +
  gi|298675884|ref|YP_003727634.1| 206 N 206
                                       5 PP

>> VitK2_biosynth  Menaquinone biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   8.2e-06     0.021      42     236 ..      81     278 ..      78     286 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.2e-06
                                       HHHHTTS-SEEEEEHHHHTTCTTTEEEESEESCEEEESSSSEEEEE...SS-CCC-SSS..T.EEEESTTTSHHHHH CS
                    VitK2_biosynth  42 rallegelDvakiSsaayariaddyalLpdlsisalGrvygvllvs...kvpleelegel.gkrvalpgestTsvlL 114
                                       +a+l+g++Dva + +a ++   d+    +   ++ +    + l++     +++ee  ++l g ++a+    t   ++
  gi|298675884|ref|YP_003727634.1|  81 QAMLAGDIDVAYVGAAPFVSAVDKGLNAK--IVAGVQIQGSSLVLRpefAENYEE-PQDLeGLKIATFPPGTIQDTI 154
                                       57899999999999999999888888887..555555555555555566444555.345679999999999999999 PP

                                       HHHHHCSTS----....EEEEE-GGGHHHHHHTTS.SEEEEECCH.HHTGGGGTTEEEEEHHHHHHHHHSS-EEEEE CS
                    VitK2_biosynth 115 lrlllaeryglkp....rlvevpfdeieaavlege.dagLlIges.altyaeeglkkvlDLgelWeeltglPlvlgl 185
                                       lr +l++  gl+p    ++v +   +  +a+ +++ d++ l + + a+ ++e+  + v+D ge+W++++   l    
  gi|298675884|ref|YP_003727634.1| 155 LRNWLKDN-GLDPdkdvDIVGMGPGDAISAISAERvDGVFLPHPApAIIESENNGQSVVDSGEMWNNHACCVL---- 226
                                       99999999.787753224555655677777888888*******97467999999**************97755.... PP

                                       EEEECCCHH...HHHHHHHHHHHHHHHHHHHSHHHHHHHHHCCSTTS.HHHHHH CS
                    VitK2_biosynth 186 wvvrrdlaa...eaakeleealreSveyalahldevaeyaaeraqemddevlek 236
                                        vv+ +l +   e ++e+++   e+ ey  +h+d++a+  a++++ +  + ++k
  gi|298675884|ref|YP_003727634.1| 227 -VVSDELINnypEVTREIVKTHVEATEYNKNHMDDAAQIYANYTGWD-VSQVKK 278
                                       .5666655556699**************************9999988.444444 PP

>> LysR_substrate  LysR substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.5e-05     0.089      50     132 ..      82     168 ..      75     175 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.5e-05
                                       HHHTTSSSEEEEESSS....CCTTEEEEEEEEEEE...EEEEETTSGGGG..SSSECGGGGCTSEEEEESTTSTHHH CS
                    LysR_substrate  50 llaegelDlairagpp....edsglearpLaeepl...vlvaspdhpLar..gepvsledLadeplilleegsglrd 117
                                       ++++g++D+a ++  p     d gl a  +a  ++    lv++p+  +a+  +   +++dL++++  ++++g+    
  gi|298675884|ref|YP_003727634.1|  82 AMLAGDIDVAYVGAAPfvsaVDKGLNAKIVAGVQIqgsSLVLRPE--FAEnyE---EPQDLEGLKIATFPPGTIQDT 153
                                       4566779999999999999999999999999888733359999**..556344...567****************** PP

                                       HHHHHHHCTTEECEE CS
                    LysR_substrate 118 lledalreaglkprv 132
                                        l+++l+++gl+p+ 
  gi|298675884|ref|YP_003727634.1| 154 ILRNWLKDNGLDPDK 168
                                       ***********9975 PP

>> PSII_Pbs27  Photosystem II Pbs27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.2e-05      0.18      39      90 ..     217     291 ..     160     305 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.2e-05
                        PSII_Pbs27  39 a..............lpkaYlkdarevvktlresleldk...kddakrera.....akaakesireyvskY.rsa 90 
                                                      l ++Y + +re+vkt +e++e +k   +d a+++       ++++k+s +e+ +++  + 
  gi|298675884|ref|YP_003727634.1| 217 MwnnhaccvlvvsdeLINNYPEVTREIVKTHVEATEYNKnhmDDAAQIYANytgwdVSQVKKSLNEWDGQWiADP 291
                                       26666666666666699*********************988655555554322333899**********995443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 1987.09
//
Query:       gi|298675885|ref|YP_003727635.1|  [L=260]
Description: binding-protein-dependent transporter inner membrane component [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-21   77.3   8.3    1.2e-21   77.3   8.3    1.8  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.6     0.069   1.2e+03      92     121 ..      21      51 ..      14      78 .. 0.53
   2 !   77.3   8.3   6.7e-26   1.2e-21       1     183 [.      79     251 ..      79     253 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.069
                      BPD_transp_1  92 asrwqifrkvvlP.nalppiitglilafggl 121
                                       ++ wqi+  ++++  +l p +  ++ +f++ 
  gi|298675885|ref|YP_003727635.1|  21 VTLWQIVAEYIIRrELLLPSFFDVVTSFIST 51 
                                       5555555555443144444444444444443 PP

  == domain 2  score: 77.3 bits;  conditional E-value: 6.7e-26
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalr 77 
                                       gi++Gi+++    k+++++++p+i++l+ +P+++++++ +       +lg + +++ ++++++a+++++++++ +++
  gi|298675885|ref|YP_003727635.1|  79 GIPVGIVMG--WFKTVNRISDPIIEILRPIPPLAWIPFAL------VWLGLTHTAAGFVIFVGAVFPIIINTYTGFK 147
                                       89*******..99***************************......99***************************** PP

                      BPD_transp_1  78 slpkdlveaaralGasr.wqifrkvvlPnalppiitglilafggllggavlleflg.swpGlgtllleailgydyse 152
                                       s+pk  veaa++lG+ + + ++r++++P++lp+i +g+++ +g  +   v++ef+g s++Glg+ l+  +   +++ 
  gi|298675885|ref|YP_003727635.1| 148 SVPKINVEAAKVLGCVKqRSLIRHIAFPSSLPSITAGIRIGMGVGWMCLVAAEFFGvSKNGLGYKLWWHYGLHQMD- 223
                                       **************86515678999******************************945566888888777777777. PP

                      BPD_transp_1 153 isnggvlalviavlllnlvad.ilqrlldprv 183
                                            vl++ +++ +l l++d ++ +++d+r+
  gi|298675885|ref|YP_003727635.1| 224 ----FVLMYMFMLGILGLIIDkVFRKYIDKRL 251
                                       ....6667777776666666547888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1791.83
//
Query:       gi|298675886|ref|YP_003727636.1|  [L=253]
Description: ABC transporter-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.8e-34  116.8   0.0    1.6e-33  116.1   0.0    1.3  1  ABC_tran      ABC transporter
    3.2e-09   37.0   0.0    0.00012   22.0   0.0    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    2.6e-06   27.9   0.3    2.7e-05   24.6   0.3    2.1  1  AAA           ATPase family associated with various cellular 
    8.1e-06   26.2   0.1    4.5e-05   23.7   0.1    2.0  1  AAA_22        AAA domain
    1.6e-05   24.8   0.1    0.00011   22.1   0.1    2.0  2  AAA_15        AAA ATPase domain
    7.7e-05   22.7   0.0    0.00017   21.6   0.0    1.5  1  Rad17         Rad17 P-loop domain
    8.5e-05   23.1   0.1    0.00017   22.1   0.1    1.5  1  AAA_23        AAA domain
    0.00021   21.2   0.0    0.00034   20.5   0.0    1.3  1  RsgA_GTPase   RsgA GTPase
    0.00066   19.2   0.1       0.17   11.3   0.0    2.4  2  SMC_N         RecF/RecN/SMC N terminal domain
      0.001   19.3   0.0     0.0026   18.0   0.0    1.9  1  AAA_28        AAA domain
     0.0014   18.6   0.1     0.0052   16.7   0.0    1.8  2  ATPase_2      ATPase domain predominantly from Archaea
     0.0022   18.0   0.1      0.012   15.6   0.0    2.2  3  NACHT         NACHT domain
     0.0029   18.0   0.0     0.0081   16.6   0.0    1.7  2  AAA_16        AAA ATPase domain
     0.0077   16.0   0.0      0.015   15.0   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
     0.0082   16.7   0.0      0.016   15.8   0.0    1.6  1  AAA_18        AAA domain
  ------ inclusion threshold ------
      0.011   14.9   0.1      0.048   12.8   0.0    1.9  2  NB-ARC        NB-ARC domain
      0.013   15.5   0.0      0.031   14.3   0.0    1.6  1  AAA_5         AAA domain (dynein-related subfamily)
      0.016   14.6   0.1      0.032   13.7   0.0    1.5  1  PhoH          PhoH-like protein
      0.019   15.1   0.0      0.048   13.8   0.0    1.7  1  AAA_33        AAA domain
       0.03   14.1   0.0      0.075   12.8   0.0    1.6  2  IstB_IS21     IstB-like ATP binding protein
      0.032   14.3   0.0       0.14   12.2   0.0    2.0  2  AAA_14        AAA domain
      0.041   13.6   0.0       0.17   11.6   0.0    1.9  2  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
      0.041   13.8   0.7          3    7.7   0.1    2.6  3  NTPase_1      NTPase
      0.051   13.3   0.0       0.12   12.1   0.0    1.5  1  AAA_30        AAA domain
      0.078   12.7   0.0       0.14   11.9   0.0    1.4  1  AAA_24        AAA domain
      0.087   12.7   0.1       0.58   10.1   0.0    2.3  2  MobB          Molybdopterin guanine dinucleotide synthesis pr
      0.092   11.8   0.0       0.15   11.1   0.0    1.3  1  T2SSE         Type II/IV secretion system protein
      0.094   11.5   0.0       0.13   11.0   0.0    1.2  1  AAA_35        AAA-like domain
        0.1   13.0   0.0       0.31   11.4   0.0    1.9  1  RNA_helicase  RNA helicase
       0.12   12.4   0.0       0.39   10.7   0.0    1.7  2  ResIII        Type III restriction enzyme, res subunit
       0.13   11.7   0.0       0.56    9.6   0.0    1.9  3  Mg_chelatase  Magnesium chelatase, subunit ChlI
       0.16   10.7   0.0       0.19   10.5   0.0    1.2  1  Adeno_IVa2    Adenovirus IVa2 protein
       0.19   12.1   0.1       0.63   10.4   0.0    1.8  2  AAA_19        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.1   0.0   2.9e-36   1.6e-33       1     136 [.      24     163 ..      24     164 .. 0.95

  Alignments for each domain:
  == domain 1  score: 116.1 bits;  conditional E-value: 2.9e-36
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       lk+++l++k  e v i+G++G+GK+tLl+++agl++p +Ge++ldg+++ e      + + g+++qe +lfp  tv 
  gi|298675886|ref|YP_003727636.1|  24 LKDLNLEIKDKEFVCIIGPSGCGKTTLLRIIAGLENPSNGEVTLDGEKIIE-----PDPKRGMVFQEYSLFPWRTVI 95 
                                       799******************************************999988.....88999**************99 PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +n             +s+e +e++l+ +gl+++k++      ++LSgG++qrva+aral+++p++ll+DEp+
  gi|298675886|ref|YP_003727636.1|  96 RNitfgpemqgmdknKSQEIAEEYLKLVGLEQFKNSYP----YELSGGMRQRVAIARALANDPEVLLMDEPF 163
                                       999********99866666699**********999998....*****************************6 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   2.3e-07   0.00012       1      48 [.      36      71 ..      36      98 .. 0.72
   2 !   13.1   0.0   0.00011      0.06     233     298 ..     132     195 ..      90     198 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.3e-07
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipsl 48
                                      + ++iGp g+GK++LL+++ +l            e++++g+ + +  +
  gi|298675886|ref|YP_003727636.1| 36 FVCIIGPSGCGKTTLLRIIAGL------------ENPSNGEVTLDGEK 71
                                      679****************999............44444444444444 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00011
                            AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll..ellkelsrngaQviltTHS 298
                                        ++elS G+++  a++ al+ ++    +ll DEp  +L+   +r +l  ell++ +++ + + ++THS
  gi|298675886|ref|YP_003727636.1| 132 YPYELSGGMRQRVAIARALANDP---EVLLMDEPFGSLDA-QTRNVLqsELLDIWEKKQITIAFVTHS 195
                                       6899********99999999999...9*************.5556666888888888889*******9 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.3   5.1e-08   2.7e-05       1     100 [.      37     197 ..      37     222 .. 0.65

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 5.1e-08
                                       EEEESSTTSSHHHHHHHHHHHHTHE.................................................... CS
                               AAA   1 vllyGppGtGKTllakavakelgve.................................................... 25 
                                       v+++Gp G+GKT+l + +a   + +                                                    
  gi|298675886|ref|YP_003727636.1|  37 VCIIGPSGCGKTTLLRIIAGLENPSngevtldgekiiepdpkrgmvfqeyslfpwrtvirnitfgpemqgmdknksq 113
                                       689****************9954222323333444444445555555555555555555555555555555555555 PP

                                       .....EEEEETTTCS.SSSTTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHH CS
                               AAA  26 .....fleisgsell.skyvgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldg 95 
                                            +l++ g e + ++y  e +  +r+ ++ a++ a +p +l++DE      ++       ++ ++++Ll  +++
  gi|298675886|ref|YP_003727636.1| 114 eiaeeYLKLVGLEQFkNSYPYELSGGMRQRVAIARALAnDPEVLLMDEPFGSLDAQ------TRNVLQSELLDIWEK 184
                                       55555555555555545599999999999999999999899*******65555555......688899999999999 PP

                                       TTTS........S CS
                               AAA  96 vkkk........e 100
                                        +          +
  gi|298675886|ref|YP_003727636.1| 185 KQITiafvthsvD 197
                                       8885444444440 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.1   8.2e-08   4.5e-05       4     128 ..      33     192 ..      29     199 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 8.2e-08
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee.................................erpevv.... 43 
                                       ++ +++++G+sG+GKTtllr ++   +  ++  +                                 +    +    
  gi|298675886|ref|YP_003727636.1|  33 DKEFVCIIGPSGCGKTTLLRIIAGLEN--PS--NgevtldgekiiepdpkrgmvfqeyslfpwrtviR-N--Itfgp 102
                                       7899****************9998753..22..234678999**********9999999987665522.2..24468 PP

                            AAA_22  44 fvtlpsstsskdllrellralglelka..erlsseellealeqalrarav....ielliiDEaqh.lr...seeale 110
                                       +++   +++s+++++e l+ +gle+ +  ++ +++  +++    +r   +    +e+l+ DE    l+   ++ + +
  gi|298675886|ref|YP_003727636.1| 103 EMQGMDKNKSQEIAEEYLKLVGLEQFKnsYPYELSGGMRQRVAIAR---AlandPEVLLMDEPFGsLDaqtRNVLQS 176
                                       99999999**************999995544444444433333444...3344899999999444476543355556 PP

                            AAA_22 111 eLrsllnlsrkgvqliLv 128
                                       eL ++++  +k++++ +v
  gi|298675886|ref|YP_003727636.1| 177 ELLDIWE--KKQITIAFV 192
                                       6666666..777776665 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1     2e-07   0.00011      13      68 ..      23      75 ..      19     121 .. 0.87
   2 ?    0.4   0.0      0.75   4.1e+02     322     365 ..     152     195 ..     134     197 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2e-07
                            AAA_15 13 slkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleif 68
                                      +lkd  ++++++ + ++iG+ ++GK+++l+++  + n +    + +++++ e++ + 
  gi|298675886|ref|YP_003727636.1| 23 ALKDLNLEIKDKeFVCIIGPSGCGKTTLLRIIAGLENPS----NGEVTLDGEKIIEP 75
                                      6899999999999*******************9999988....67777777776655 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.75
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                       +++ +ll++EP  +L  q  +vl   l+++ ++++  + + THS
  gi|298675886|ref|YP_003727636.1| 152 NDPEVLLMDEPFGSLDAQTRNVLQSELLDIWEKKQITIAFVTHS 195
                                       678999***************************97777889999 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   3.1e-07   0.00017      33      69 ..      22      58 ..      18      90 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 3.1e-07
                             Rad17 33 ewlkadvLesrkkriLLisGPsGCgkstvvkvLskel 69
                                      ++lk   Le + k+ + i GPsGCgk+t +++++   
  gi|298675886|ref|YP_003727636.1| 22 QALKDLNLEIKDKEFVCIIGPSGCGKTTLLRIIAGLE 58
                                      7889999*************************98655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   3.2e-07   0.00017       2      39 ..       4      54 ..       3      57 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 3.2e-07
                            AAA_23  2 Lkienfrsf............rdqeidF.skgltlItGpNGaGKTTildAi 39
                                      +++en+ ++            +d +++  +k +++I+Gp G+GKTT+l+ i
  gi|298675886|ref|YP_003727636.1|  4 VSVENVSQYfinregyktqalKDLNLEIkDKEFVCIIGPSGCGKTTLLRII 54
                                      6677777777777666554445555666999*****************987 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   6.3e-07   0.00034      86     130 ..      20      65 ..       3      71 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 6.3e-07
                                       THTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                       RsgA_GTPase  86 tkegleelkellkd.ktsvlvGqSGvGKStLinallpelelktgev 130
                                       ++++l++l+ ++kd ++++++G+SG GK+tL+  +++ ++ + gev
  gi|298675886|ref|YP_003727636.1|  20 KTQALKDLNLEIKDkEFVCIIGPSGCGKTTLLRIIAGLENPSNGEV 65 
                                       56889999999*99899****************9998766666665 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00031      0.17       9      42 ..      18      52 ..      12      57 .. 0.75
   2 ?    5.7   0.0     0.016       8.5     135     213 ..     131     211 ..      78     218 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00031
                                      SETTEECEEEEEET.TSSEEEEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  9 nFksyagktvilpf.sksftaivGpNGSGKsnlld 42
                                      ++k+ a k   l++ +k+f +i+Gp G+GK+ ll 
  gi|298675886|ref|YP_003727636.1| 18 GYKTQALKDLNLEIkDKEFVCIIGPSGCGKTTLLR 52
                                      566666666666662578*************9986 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.016
                                       T...CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SS...HHHCCC- CS
                                       x...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxx RF
                             SMC_N 135 e...lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislr...eemleka 205
                                       +   +LSgG ++ va+a  +A    +p+ + l+De    LD++ ++ + + l    ++ Q+ +  ++   +e +  a
  gi|298675886|ref|YP_003727636.1| 131 SypyELSGGMRQRVAIARALA---NDPE-VLLMDEPFGSLDAQTRNVLQSELLDIWEKKQITIAFVThsvDEAVFLA 203
                                       244489***999999998876...4555.5689************99998887777777765433330013444455 PP

                                       SCEEEEEE CS
                                       xxxxxxxx RF
                             SMC_N 206 dklvgvtk 213
                                       dk+v +t+
  gi|298675886|ref|YP_003727636.1| 204 DKIVMLTS 211
                                       77766665 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   4.9e-06    0.0026       2      21 ..      37      61 ..      36     163 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.9e-06
                            AAA_28  2 ivitGgestGKTtlleaLa.....a 21
                                      ++i+G++++GKTtll+ +a     +
  gi|298675886|ref|YP_003727636.1| 37 VCIIGPSGCGKTTLLRIIAglenpS 61
                                      89**************999654431 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   9.6e-06    0.0052       7      41 ..      23      55 ..      13      67 .. 0.73
   2 ?   -1.1   0.0       2.6   1.4e+03     121     170 ..     156     201 ..     141     214 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 9.6e-06
                          ATPase_2  7 elkeleeilerepneiyfiYGpegsGKtaLlkeii 41
                                      +lk+l+  le + +e++ i Gp g+GKt+Ll+ i+
  gi|298675886|ref|YP_003727636.1| 23 ALKDLN--LEIKDKEFVCIIGPSGCGKTTLLRIIA 55
                                      555554..45556899***************9776 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.6
                          ATPase_2 121 iiiiDelqklidlglngaellvkeLlnliesltkekhlcvviclsSeglf 170
                                       ++++De +   d + +  + l +eLl+++e+  k+  +++v  +  e +f
  gi|298675886|ref|YP_003727636.1| 156 VLLMDEPFGSLDAQTR--NVLQSELLDIWEK--KQITIAFVTHSVDEAVF 201
                                       7788888887755555..8888999999988..44445554444445555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.1e-05     0.012       2      21 ..      36      55 ..      35      61 .. 0.90
   2 ?   -2.2   0.0       6.2   3.4e+03     146     164 ..     103     121 ..     102     122 .. 0.88
   3 ?   -1.6   0.0       4.2   2.3e+03      86     134 ..     202     218 ..     164     229 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.1e-05
                                      CEEEEC-TTTCHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqkla 21
                                       v++ G++G+GKTtLl+ +a
  gi|298675886|ref|YP_003727636.1| 36 FVCIIGPSGCGKTTLLRIIA 55
                                      589*************9886 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.2
                                       EEE--TCCHHHHHHHHCTT CS
                             NACHT 146 evegfsesrrkqlvrkyfs 164
                                       e++g+ +++ ++++++y++
  gi|298675886|ref|YP_003727636.1| 103 EMQGMDKNKSQEIAEEYLK 121
                                       6899**********99975 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 4.2
                                       EEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCCHHH CS
                             NACHT  86 ilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpralrd 134
                                       + D +                                ++lt+rp++ +d
  gi|298675886|ref|YP_003727636.1| 202 LADKI--------------------------------VMLTSRPGKIKD 218
                                       33333................................445555555444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.5e-05    0.0081      22      45 ..      32      55 ..      19      74 .. 0.81
   2 ?   -1.4   0.0       4.8   2.6e+03     144     154 ..     163     173 ..     113     247 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.5e-05
                            AAA_16 22 grpelvllsGesGvGKsslvrell 45
                                       + e v ++G+sG+GK++l+r ++
  gi|298675886|ref|YP_003727636.1| 32 KDKEFVCIIGPSGCGKTTLLRIIA 55
                                      455899**************9665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.8
                            AAA_16 144 lqwadeaslql 154
                                       +  +d++++++
  gi|298675886|ref|YP_003727636.1| 163 FGSLDAQTRNV 173
                                       33333333333 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.7e-05     0.015      16      39 ..      28      51 ..      19      62 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.7e-05
                            AAA_29 16 tieidlkgatlltGpsGsGKSTll 39
                                       +ei+ k+++ ++GpsG GK+Tll
  gi|298675886|ref|YP_003727636.1| 28 NLEIKDKEFVCIIGPSGCGKTTLL 51
                                      567887789**************8 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.9e-05     0.016       1      37 [.      37      81 ..      37     133 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.9e-05
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgf.........gvnlrdvakengl 37
                                      +++ G++G+GKttl + ++ ++ +         g+++++  +++g+
  gi|298675886|ref|YP_003727636.1| 37 VCIIGPSGCGKTTLLRIIAGLE-NpsngevtldGEKIIEPDPKRGM 81
                                      79***************98774.33566666665555555555555 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   8.8e-05     0.048      14      40 ..      30      54 ..      16      59 .. 0.75
   2 ?   -0.7   0.0       1.2   6.7e+02     111     143 ..     180     216 ..     168     226 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.8e-05
                                      CTTTSCSEEEEEEESTTSSHHHHHHHH CS
                            NB-ARC 14 ekdelqslvvalvGmgGvGKttlakqi 40
                                      e ++ +  +v + G  G+GKttl++ i
  gi|298675886|ref|YP_003727636.1| 30 EIKDKE--FVCIIGPSGCGKTTLLRII 54
                                      455556..***************9865 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.2
                                       EE-SHHHH.....HHHHCHTTS.....EEEEEESBCCC CS
                            NB-ARC 111 DVweeedwdkigvvlparenrl.....rvllTTRdeev 143
                                       D+we+++   i  v  + ++ +      v+lT+R  ++
  gi|298675886|ref|YP_003727636.1| 180 DIWEKKQI-TIAFVTHSVDEAVfladkIVMLTSRPGKI 216
                                       88998776.55555555444321222267778776665 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   5.8e-05     0.031       2      22 ..      37      57 ..      36      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.8e-05
                                      EEEE--SSSSHHHHHHHGGGG CS
                             AAA_5  2 vlLvGppGtgKselaerlaaa 22
                                      v+++Gp+G+gK++l + +a +
  gi|298675886|ref|YP_003727636.1| 37 VCIIGPSGCGKTTLLRIIAGL 57
                                      89*************999876 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.9e-05     0.032      13      48 ..      28      64 ..      18      73 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.9e-05
                                      HHHHHH-SEEEEE--TTSSTT.HHHHHHHHHHHHTTS CS
                              PhoH 13 lealkkndivfaiGpaGtGKt.ylavalavealkkkk 48
                                         +k++++v++iGp+G+GKt +l + +++e  ++++
  gi|298675886|ref|YP_003727636.1| 28 NLEIKDKEFVCIIGPSGCGKTtLLRIIAGLENPSNGE 64
                                      4567899*************82456667776666655 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   8.8e-05     0.048       2     109 ..      37     199 ..      36     204 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.8e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklg....avllssdt.......................................... 32 
                                       v ++G++G+GK+tl++ ++  +      v+l+  +                                          
  gi|298675886|ref|YP_003727636.1|  37 VCIIGPSGCGKTTLLRIIAGLENpsngEVTLDGEKiiepdpkrgmvfqeyslfpwrtvirnitfgpemqgmdknksq 113
                                       6789***********98754333445555566666666667777777777777777776666666655555555555 PP

                            AAA_33  33 ....lrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvildatnls..rrer....arflklarrlgvpv 99 
                                           ++ +l+g +q + +++ +++  ++q++ ++ar  +     ++ d ++ s  +++r    +++l ++++    +
  gi|298675886|ref|YP_003727636.1| 114 eiaeEYLKLVGLEQFKNSYPYELSGGMRQRV-AIARALANDPEVLLMDEPFGSldAQTRnvlqSELLDIWEKKQITI 189
                                       5444444444444444445566666666665.555555555555555777544223444555567777777777777 PP

                            AAA_33 100 rivvvetdee 109
                                       + v+ ++de+
  gi|298675886|ref|YP_003727636.1| 190 AFVTHSVDEA 199
                                       7776666666 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00014     0.075      36      63 ..      22      50 ..       8      60 .. 0.79
   2 ?   -2.6   0.0         7   3.8e+03     109     145 ..     154     189 ..     142     197 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00014
                         IstB_IS21 36 keLatlsf.iekkenivllGpsGvGKshl 63
                                      ++L  l+  i++ke ++++GpsG GK+ l
  gi|298675886|ref|YP_003727636.1| 22 QALKDLNLeIKDKEFVCIIGPSGCGKTTL 50
                                      455554443899***************87 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 7
                         IstB_IS21 109 vdllilDdlgllpldqaeaellfeviekryerrsiii 145
                                       +++l++D+  +  ld + +++l   + + +e++ i i
  gi|298675886|ref|YP_003727636.1| 154 PEVLLMDE-PFGSLDAQTRNVLQSELLDIWEKKQITI 189
                                       56777777.3556777777777666666666666655 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00025      0.14       3      24 ..      35      56 ..      33      88 .. 0.76
   2 ?   -1.5   0.0       4.5   2.4e+03      30      59 ..     216     245 ..     202     251 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00025
                            AAA_14  3 kilvitGaRrvGKTtllkqlik 24
                                      + ++i G+  +GKTtll+ ++ 
  gi|298675886|ref|YP_003727636.1| 35 EFVCIIGPSGCGKTTLLRIIAG 56
                                      6799************987764 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.5
                            AAA_14  30 kesilyinldderdkkladpekllelilek 59 
                                        ++i+ +nl ++r++++ d++++ + +l+ 
  gi|298675886|ref|YP_003727636.1| 216 IKDIIDVNLPRPRNRTSPDTNQFRDRVLKI 245
                                       478999999999998877776666666654 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00031      0.17       4      24 ..      37      57 ..      34      61 .. 0.87
   2 ?   -1.7   0.0       4.1   2.2e+03     103     122 ..     108     127 ..      92     132 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00031
                         PduV-EutP  4 illiGkvgsGKttLtqalkge 24
                                      + +iG++g+GKttL + + g 
  gi|298675886|ref|YP_003727636.1| 37 VCIIGPSGCGKTTLLRIIAGL 57
                                      779***********9998875 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.1
                         PduV-EutP 103 edeenieaveelLksaGaek 122
                                       +++++ e++ee+Lk +G e+
  gi|298675886|ref|YP_003727636.1| 108 DKNKSQEIAEEYLKLVGLEQ 127
                                       56677789999999999887 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.8   9.7e+02      69     101 ..       7      40 ..       3      40 .. 0.84
   2 ?    7.7   0.1    0.0055         3       2      21 ..      37      56 ..      36      69 .. 0.80
   3 ?    3.8   0.0     0.087        47      87     137 ..     145     197 ..     108     231 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.8
                                       SEETTEEE-HHHHHHHHHHHHHHHHHHH-.EEEE CS
                          NTPase_1  69 prvgkyvvdvesfeelalealrkalsead.vivi 101
                                        +v++y ++ e  ++ al+ l+ ++++++ v++i
  gi|298675886|ref|YP_003727636.1|   7 ENVSQYFINREGYKTQALKDLNLEIKDKEfVCII 40 
                                       68999****9999999999999998888877776 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0055
                                      EEEE--TTSSHHHHHHHHHH CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvle 21
                                      v+i Gp+G GKtTl++ ++ 
  gi|298675886|ref|YP_003727636.1| 37 VCIIGPSGCGKTTLLRIIAG 56
                                      6789**********987765 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.087
                                       HHHHHHH.HHH-EEEE--.-STTGGG-HH.HHHHHHHHHTTTSEEEEE--SS-- CS
                          NTPase_1  87 ealrkal.seadviviDE.iGkmElkskk.fkeaveevLksekpvlavihrrkd 137
                                       + + +al ++++v+++DE  G++  ++++ +++++ ++ +++++ +a + ++ d
  gi|298675886|ref|YP_003727636.1| 145 A-IARALaNDPEVLLMDEpFGSLDAQTRNvLQSELLDIWEKKQITIAFVTHSVD 197
                                       3.3344448999******88****998762577899999988888887766653 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00022      0.12      18      45 ..      34      61 ..      22      68 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00022
                            AAA_30 18 drvavltGpAGtGKttalkalreaweaa 45
                                      + ++++ Gp G GKtt+l+ ++ + + +
  gi|298675886|ref|YP_003727636.1| 34 KEFVCIIGPSGCGKTTLLRIIAGLENPS 61
                                      45899**************998776655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00026      0.14       5      22 ..      37      54 ..      33      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00026
                            AAA_24  5 iliyGpsgiGKTtlakel 22
                                      ++i+Gpsg GKTtl++ +
  gi|298675886|ref|YP_003727636.1| 37 VCIIGPSGCGKTTLLRII 54
                                      89***********99865 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0011      0.58       2      17 ..      37      52 ..      36      62 .. 0.83
   2 ?   -1.1   0.0         3   1.6e+03      15      39 ..     174     198 ..     170     204 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0011
                              MobB  2 lgivgksgsGKTtLle 17
                                      ++i+g sg+GKTtLl 
  gi|298675886|ref|YP_003727636.1| 37 VCIIGPSGCGKTTLLR 52
                                      79************95 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3
                              MobB  15 LleklipelkarglrvgtiKhahhg 39 
                                       L ++l+ + +++ ++++ + h++++
  gi|298675886|ref|YP_003727636.1| 174 LQSELLDIWEKKQITIAFVTHSVDE 198
                                       5678999999999******999876 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00028      0.15     113     152 ..      18      57 ..       3      68 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00028
                             T2SSE 113 alkekiaevlrkavrerglilvsGgTgsGKttllyallke 152
                                         k +  + l+  ++ +  + + G+ g GKttll ++   
  gi|298675886|ref|YP_003727636.1|  18 GYKTQALKDLNLEIKDKEFVCIIGPSGCGKTTLLRIIAGL 57 
                                       44566677799999********************887655 PP

>> AAA_35  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00025      0.13       5      66 ..       5      68 ..       1      75 [. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00025
                            AAA_35  5 sveldspfYierppieekcyeeie...kpGalirikapkkmGKtSLlarilakakqqgyktvsld 66
                                      sve  s+++i+r+ +++++++ ++   k+ + + i +p+  GKt Ll ri+a  ++ ++  v+ld
  gi|298675886|ref|YP_003727636.1|  5 SVENVSQYFINREGYKTQALKDLNleiKDKEFVCIIGPSGCGKTTLL-RIIAGLENPSNGEVTLD 68
                                      68889**************999874446677**************98.67777777777777776 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00058      0.31       1      18 [.      37      54 ..      37      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00058
                      RNA_helicase  1 iwlyGpsgeGKStlakeL 18
                                      +++ Gpsg+GK+tl + +
  gi|298675886|ref|YP_003727636.1| 37 VCIIGPSGCGKTTLLRII 54
                                      689***********9884 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00072      0.39       7      41 ..      19      51 ..      14      67 .. 0.81
   2 ?   -1.4   0.0       3.7     2e+03     126     141 ..     147     162 ..      95     191 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00072
                                      HHHHHHHHHT......TTSEEEEEESTTSTHHHHH CS
                            ResIII  7 yQeeaienlleklkskrdkrglikmaTGtGKTlva 41
                                      y ++a+++l  ++  k+++ ++i  + G+GKT ++
  gi|298675886|ref|YP_003727636.1| 19 YKTQALKDLNLEI--KDKEFVCIIGPSGCGKTTLL 51
                                      7789999999888..5999*************764 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.7
                                       .HHHTTT-SEEEEETG CS
                            ResIII 126 eellrdrfdviiiDEa 141
                                        ++l +  +v+++DE 
  gi|298675886|ref|YP_003727636.1| 147 ARALANDPEVLLMDEP 162
                                       3444555558888886 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0     0.001      0.56      20      56 ..      32      68 ..      18      82 .. 0.77
   2 ?   -1.9   0.0       3.2   1.7e+03     176     197 ..     127     148 ..     110     158 .. 0.80
   3 ?   -1.2   0.0         2   1.1e+03     109     114 ..     156     161 ..     129     223 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.001
                      Mg_chelatase 20 aGgHnlllvGppGsGKtmlakrlpsllpplseeeale 56
                                        +  + ++Gp+G+GKt l + +++l  p + e +l+
  gi|298675886|ref|YP_003727636.1| 32 KDKEFVCIIGPSGCGKTTLLRIIAGLENPSNGEVTLD 68
                                      55566889*************9999987777666665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.2
                      Mg_chelatase 176 keierYlsklsgplldRidlqv 197
                                       + +++Y   lsg +  R+ +  
  gi|298675886|ref|YP_003727636.1| 127 QFKNSYPYELSGGMRQRVAIAR 148
                                       5567899999999999998865 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 2
                      Mg_chelatase 109 vLfLDE 114
                                       vL++DE
  gi|298675886|ref|YP_003727636.1| 156 VLLMDE 161
                                       444444 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00035      0.19      79     168 ..      25     121 ..       4     188 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00035
                        Adeno_IVa2  79 sslnygl..qPviGviyGPtGsGksqllrnli.....ssklisPiPetvifitPekdmipPe.elkaWelqlvegny 147
                                         ln++   + ++  i GP G+Gk+ llr +      s+  +    e +i   P+++m+  e  l  W+  + +  +
  gi|298675886|ref|YP_003727636.1|  25 KDLNLEIkdKEFV-CIIGPSGCGKTTLLRIIAglenpSNGEVTLDGEKIIEPDPKRGMVFQEySLFPWRTVIRNITF 100
                                       4555543113444.467************764222224444555556666666667776543134456666666666 PP

                        Adeno_IVa2 148 ekredGtiiPktstlrpefve 168
                                        ++  G    k+  +  e+++
  gi|298675886|ref|YP_003727636.1| 101 GPEMQGMDKNKSQEIAEEYLK 121
                                       666666666666666666665 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0012      0.63      10      31 ..      34      55 ..      27      67 .. 0.84
   2 ?   -1.4   0.0       4.9   2.6e+03     117     128 ..     174     185 ..     134     215 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0012
                            AAA_19 10 ekvllvtaGpGtGKTrvlkhiv 31
                                      ++ ++++++ G+GKT++l+ i 
  gi|298675886|ref|YP_003727636.1| 34 KEFVCIIGPSGCGKTTLLRIIA 55
                                      67899***********998764 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.9
                            AAA_19 117 lqyrLlkallge 128
                                       lq +Ll+ + ++
  gi|298675886|ref|YP_003727636.1| 174 LQSELLDIWEKK 185
                                       333333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); expected 17.9 (0.001)
Passed Fwd filter:                        33  (0.00184059); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              33  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 1673.53
//
Query:       gi|298675887|ref|YP_003727637.1|  [L=154]
Description: hypothetical protein Metev_2012 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.9e-08   34.5   5.4      6e-07   29.7   0.9    1.8  2  Bactofilin  Polymer-forming cytoskeletal
    8.5e-05   22.1   2.3     0.0064   16.2   0.0    3.2  3  Hexapep     Bacterial transferase hexapeptide (six repeats)


Domain annotation for each model (and alignments):
>> Bactofilin  Polymer-forming cytoskeletal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.9   6.7e-11     6e-07      15      93 ..      35     123 ..      27     127 .. 0.77
   2 !   13.5   0.3   7.5e-06     0.067      24      76 ..      87     140 ..      86     152 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 6.7e-11
                        Bactofilin  15 vegdlridGkveGdi........eakgklvvgeggkvegnikaeevvva..GtvkGnveaeekvelkktakveGdik 81 
                                       +e+d+ i+G++   i        + +g+l++g+g++++gn++ae+v +    +++Gn+e++++v++ + a+v+  i 
  gi|298675887|ref|YP_003727637.1|  35 FEDDVNINGNLITGIgvnfwkdlDVNGSLKLGKGSVIRGNVRAEDVLIGpySKIDGNLEIKNTVKILDGAVVKSVIC 111
                                       344444444443333334444449999*********************6434599********************** PP

                        Bactofilin  82 aksleieegavf 93 
                                       ++++++ +g+++
  gi|298675887|ref|YP_003727637.1| 112 SGEMSVRPGCRL 123
                                       ******999875 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 7.5e-06
                        Bactofilin  24 kveGdieakgklvvgeggkvegnikaeevvva.GtvkGnveaeekvelkktakv 76 
                                       k++G++e k+++++ +g++v+  i ++e++v+ G   G v+ae+++el ++  v
  gi|298675887|ref|YP_003727637.1|  87 KIDGNLEIKNTVKILDGAVVKSVICSGEMSVRpGCRLGFVKAEKTLELIGNVDV 140
                                       678999999999999999999999999999888888899999988888766555 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.5   0.2    0.0035        32      19      32 ..      62      75 ..      44      76 .. 0.65
   2 !   16.2   0.0   7.1e-07    0.0064       6      35 ..      78     107 ..      77     108 .. 0.95
   3 ?   -3.4   0.0       1.1   9.8e+03      17      23 ..     118     124 ..     117     124 .. 0.39

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0035
                                      TEEE-TTEEEETTE CS
                           Hexapep 19 nVkIGdnvkIgagv 32
                                        k+G++++I  +v
  gi|298675887|ref|YP_003727637.1| 62 SLKLGKGSVIRGNV 75
                                      55666666666665 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 7.1e-07
                                       TTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   6 snvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       ++vlIgp+++i gn +I + vkI  g+v++
  gi|298675887|ref|YP_003727637.1|  78 EDVLIGPYSKIDGNLEIKNTVKILDGAVVK 107
                                       79**************************96 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 1.1
                                       ETTEEE- CS
                           Hexapep  17 ggnVkIG 23 
                                       ++++ +G
  gi|298675887|ref|YP_003727637.1| 118 RPGCRLG 124
                                       3444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1149.77
//
Query:       gi|298675888|ref|YP_003727638.1|  [L=99]
Description: ribonucleoprotein complex SRP, Srp19 component [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-25   88.4   0.2    5.5e-25   88.1   0.2    1.1  1  SRP19     SRP19 protein


Domain annotation for each model (and alignments):
>> SRP19  SRP19 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.1   0.2   3.1e-29   5.5e-25       1      93 [.      10      93 ..      10      94 .. 0.95

  Alignments for each domain:
  == domain 1  score: 88.1 bits;  conditional E-value: 3.1e-29
                                      EEECCCCBTTS-CCCT--S-CCCSBSS--HHHHHHHHHHCTSCEEEEEEECTTSSTT.CCEEEEEC-..........SS CS
                             SRP19  1 viYPvYldskktrkeGRrvpkelavenPtaqeiaealkalglevvvepeksyPrdwa.npGrVrvklkedgkevnekik 78
                                      vi+PvYld+++tr++GR ++k+++v++P ++ei +a+++lgl+ +ve++k+yPr+w+  +GrV+v++          + 
  gi|298675888|ref|YP_003727638.1| 10 VIWPVYLDRTRTRSDGRIISKKKSVREPELKEIEKAASKLGLNPEVEEDKAYPRSWWeVSGRVMVDK----------TA 78
                                      7******************************************************77256******7..........89 PP

                                      -CHHHHHHHHHHHHH CS
                             SRP19 79 nkkellkkiaellke 93
                                       k+ llk+ia+ +ke
  gi|298675888|ref|YP_003727638.1| 79 PKSYLLKQIAKIIKE 93
                                      9************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 622.17
//
Query:       gi|298675889|ref|YP_003727639.1|  [L=85]
Description: hypothetical protein Metev_2014 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       181  (0.0100954); expected 358.6 (0.02)
Passed bias filter:                      171  (0.00953762); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 572.93
//
Query:       gi|298675890|ref|YP_003727640.1|  [L=268]
Description: xylose isomerase domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.5e-25   88.1   0.0    7.2e-25   87.7   0.0    1.1  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
     0.0072   15.6   0.1      0.013   14.8   0.1    1.3  1  UvdE          UV-endonuclease UvdE
  ------ inclusion threshold ------
      0.017   14.7   0.0      0.037   13.6   0.0    1.5  2  HMGL-like     HMGL-like
      0.096   12.3   0.0       0.16   11.5   0.0    1.4  1  PI-PLC-X      Phosphatidylinositol-specific phospholipase C, 


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.7   0.0   1.6e-28   7.2e-25       7     199 ..      17     220 ..      15     231 .. 0.84

  Alignments for each domain:
  == domain 1  score: 87.7 bits;  conditional E-value: 1.6e-28
                                       CT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHC......HTTCS..HHHHHHHHHHH CS
                      AP_endonuc_2   7 aGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypded......erear..reesvdalkra 75 
                                       + +d++El+++    +   s+ + +e++k  del    ++l+ +  ++  d+d      + ++    ++++  +++ 
  gi|298675890|ref|YP_003727640.1|  17 HEVDSIELYIPKMGLYN-GSKLQDDEFKKVYDELSTS-SALTSMHAPYFADVDtypddlLVDTTimDDKQFGLMEES 91 
                                       56899999999999996.5788888888888888888.44444444444444446666655555788888******* PP

                                       HHHHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTC...HHHHHHHH CS
                      AP_endonuc_2  76 ielaaaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgd...eelarlld 149
                                       i la++L+++++v+hpG       +++   ++++ ++l+ la  a ++gv+l+lE+  g+++++++   +el++ ++
  gi|298675890|ref|YP_003727640.1|  92 INLANKLDTRVVVIHPG----KIHQDRYKSFAKMLDNLKSLASTASDYGVMLGLENKEGTDTNNLCcdaDELLQAVE 164
                                       *****************....8889999************************************************* PP

                                       HHTTTTEEEEEEHHHHHHH....TTTHHHHHHHHHGGEEEEEE.EESS..TTTTSS CS
                      AP_endonuc_2 150 avdspnvgvclDtgHllia....eedvddalraladrikhvHikDakg..dlgagr 199
                                       +v+s+n+gv++D+gH+++        ++ + +++ d++ h+H++D++g  ++   +
  gi|298675890|ref|YP_003727640.1| 165 EVNSDNLGVTFDIGHANLTcggdNQKLRYFANRISDYVVHMHLHDNYGvwTEDYDG 220
                                       *******************999889999999999999**********955444444 PP

>> UvdE  UV-endonuclease UvdE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   2.8e-06     0.013     100     216 ..      53     183 ..      32     206 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.8e-06
                              UvdE 100 glRltfHPeqftll.nSdrkevtesairdlayHdklldalklaeqq.davliiHvGGkfgdkeaalerfkenikrlp 174
                                          +++H   f  + + + + +++ +i d +    + + ++la++    v++iH G  ++d+ ++ +++  n+k+l+
  gi|298675890|ref|YP_003727640.1|  53 SALTSMHAPYFADVdTYPDDLLVDTTIMDDKQFGLMEESINLANKLdTRVVVIHPGKIHQDRYKSFAKMLDNLKSLA 129
                                       55566666666655234666677777777777777888999**999667999************************8 PP

                              UvdE 175 dsvke...rlvLENDdksyt......vadlLpvceel...niPlVlDyHHhnvl 216
                                           +   +l LEN + + t       ++lL+  ee    n+ + +D+ H n +
  gi|298675890|ref|YP_003727640.1| 130 STASDygvMLGLENKEGTDTnnlccdADELLQAVEEVnsdNLGVTFDIGHANLT 183
                                       776533339*****9887663333335789999887622257888999888876 PP

>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.65   2.9e+03      37      48 ..      19      30 ..      15      60 .. 0.72
   2 ?   13.6   0.0   8.2e-06     0.037     107     204 ..     109     213 ..      74     216 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.65
                                      -SEE--TSGGGT CS
                         HMGL-like 37 vdeiEvgfpaas 48
                                      vd+iE+ +p ++
  gi|298675890|ref|YP_003727640.1| 19 VDSIELYIPKMG 30
                                      778888777776 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 8.2e-06
                                       HHSSTHHHHHHHHHHHHHHHHHTT-E..TTT-BTTTBS--HHHHH....HHHHHHHHHT-SEEEEEETTS---H..H CS
                         HMGL-like 107 klkkdreevakkaeeavkaarslgkd..velsledasrtdlefla....evveaaeeaGatriniaDtvGvltP..n 175
                                       k++ dr ++++k+ + +k   s + d  v l+le    td ++l+    e+++a+ee++ + + +   +G ++    
  gi|298675890|ref|YP_003727640.1| 109 KIHQDRYKSFAKMLDNLKSLASTASDygVMLGLENKEGTDTNNLCcdadELLQAVEEVNSDNLGVTFDIGHANLtcG 185
                                       566666666666666666666666667899************99866667888889999999999999998765115 PP

                                       HHHHHHHHHHHHS-.GGGEEEEEB-TTS- CS
                         HMGL-like 176 eaaelisalkervkdkvilsvHcHndlGl 204
                                          + ++++++r++    +++H H+++G+
  gi|298675890|ref|YP_003727640.1| 186 GDNQKLRYFANRIS-DYVVHMHLHDNYGV 213
                                       66779*********.999*********96 PP

>> PI-PLC-X  Phosphatidylinositol-specific phospholipase C, X domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.6e-05      0.16      27     101 ..       6     150 ..       2     159 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.6e-05
                                       --SS-HHHHHHTT--EEEEEE-........TT............................................. CS
                          PI-PLC-X  27 ssveayrnaLlrGcRcvEidvw.....dgedee............................................ 54 
                                       ss +  + +L++ +  +E+ +      +                                                 
  gi|298675890|ref|YP_003727640.1|   6 SSLAGSIYQLKHEVDSIELYIPkmglyN----Gsklqddefkkvydelstssaltsmhapyfadvdtypddllvdtt 78 
                                       5555666666666666666655333332....122335556666666666666666666666666666666666666 PP

                                       .......................SEEEE.TTEEE..EEEHHHHHHHHHHHHHHSTT--EEEEEEETTT-THH CS
                          PI-PLC-X  55 .......................pvvlh.gytlt.kkikfrdvleaikdyafktselPvivsLevhcsaeqq 101
                                                              +vv+h g+    +  +f ++l+  k  a ++s++ v++ Le++  ++++
  gi|298675890|ref|YP_003727640.1|  79 imddkqfglmeesinlankldtrVVVIHpGKIHQdRYKSFAKMLDNLKSLASTASDYGVMLGLENKEGTDTN 150
                                       666666667777777777777777777735444445678*************************99877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1663.09
//
Query:       gi|298675891|ref|YP_003727641.1|  [L=304]
Description: tetrahydromethanopterin S-methyltransferase subunit E [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   4.2e-139  462.4  12.1   4.8e-139  462.2  12.1    1.0  1  MtrE      Tetrahydromethanopterin S-methyltransferase, subuni
  ------ inclusion threshold ------
      0.018   14.4   0.1      0.025   13.9   0.1    1.2  1  HlyE      Haemolysin E (HlyE)


Domain annotation for each model (and alignments):
>> MtrE  Tetrahydromethanopterin S-methyltransferase, subunit E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  462.2  12.1  5.3e-143  4.8e-139       1     271 []       7     280 ..       7     280 .. 0.99

  Alignments for each domain:
  == domain 1  score: 462.2 bits;  conditional E-value: 5.3e-143
                              MtrE   1 lGvlalmgalatiagaaedlesdvgsqsnpnsqvqLapqmgylhrifnkaisGePvaygllaavagavalvllsalk 77 
                                       +Gvlalmga+atiaga+edlesdvgsqsnpnsqvqLapqm+++hri+nkaisGeP++++l++a++g++a+v++sa++
  gi|298675891|ref|YP_003727641.1|   7 MGVLALMGAAATIAGATEDLESDVGSQSNPNSQVQLAPQMMHPHRIYNKAISGEPPSNALMCAIGGTIASVMMSAYG 83 
                                       8**************************************************************************** PP

                              MtrE  78 lnvvlaivlgalvaalvhgvyavtaylGriasqakfkqpvyldvlkshlgaivahafiavfaivvlsylmtlvlkhp 154
                                       l+vv+ai++ga++aa+vhg+ya+++++Gr++sq++fkqp+yld+++sh+++i+++af+++f i+v+sylm +vl+hp
  gi|298675891|ref|YP_003727641.1|  84 LSVVFAITFGAAIAAVVHGTYAASSFMGRVSSQKRFKQPLYLDIVRSHTPVIIGYAFLTTFFILVISYLMSSVLNHP 160
                                       ***************************************************************************** PP

                              MtrE 155 fplpllaliwGitvGaiGsstGdvhyGaereyqkkefGaGvpvaasGdivrkaeaGlrnsidnalfcakfggpltGl 231
                                       fplplla+iwGitvGaiGsstGdvhyGaereyq++efG+G+++a+sGdivr++e+Glrn+idna+fc+kfggp+tG+
  gi|298675891|ref|YP_003727641.1| 161 FPLPLLAFIWGITVGAIGSSTGDVHYGAEREYQNVEFGSGINAANSGDIVRYGESGLRNGIDNAWFCSKFGGPVTGI 237
                                       ***************************************************************************** PP

                              MtrE 232 afglivflelWrtivfekv...tagwlavivgliivllliiln 271
                                       afg++vfl+ W+t+vf++    t+gwl+vi+gl+iv++lii n
  gi|298675891|ref|YP_003727641.1| 238 AFGMTVFLSGWVTTVFNPGesiTMGWLSVIAGLLIVAILIIGN 280
                                       ****************9766669*****************977 PP

>> HlyE  Haemolysin E (HlyE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   2.8e-06     0.025     185     221 ..      70     106 ..      29     124 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.8e-06
                                       ........SS-HHHHHHHHHHH.....HHHHHHTHHH CS
                              HlyE 185 iftaitafvaGPiGlilalaiafppaiaavvkGklia 221
                                       i  +i++++   +Gl++ +ai+f  aiaavv+G   a
  gi|298675891|ref|YP_003727641.1|  70 IGGTIASVMMSAYGLSVVFAITFGAAIAAVVHGTYAA 106
                                       455788888999*********************8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       859  (0.0479112); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2030.74
//
Query:       gi|298675892|ref|YP_003727642.1|  [L=239]
Description: tetrahydromethanopterin S-methyltransferase subunit D [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-98  329.3  25.8    1.3e-98  329.1  25.8    1.1  1  MtrD      Tetrahydromethanopterin S-methyltransferase, subuni


Domain annotation for each model (and alignments):
>> MtrD  Tetrahydromethanopterin S-methyltransferase, subunit D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  329.1  25.8  7.2e-103   1.3e-98       2     218 .]      12     225 ..      11     225 .. 0.98

  Alignments for each domain:
  == domain 1  score: 329.1 bits;  conditional E-value: 7.2e-103
                              MtrD   2 illliliviggvligvgvhfvPvGGapaamaqatGvgtGtaqlaaGagltGlltaaalaektdslllillsGavgam 78 
                                       +l+++li+igg+l++++vhfvPvGGapaamaqa+G+gtGt+qlaaGagltGl+ta+++++ t+s++++l+sGavgam
  gi|298675892|ref|YP_003727642.1|  12 LLYVLLITIGGTLVSFSVHFVPVGGAPAAMAQAPGIGTGTVQLAAGAGLTGLITAGTVLGLTNSIAIVLASGAVGAM 88 
                                       7899************************************************************************* PP

                              MtrD  79 lmlaitmlvgnliyvygvGvvaasakvekdpitgdkqekyvsqGteGhgiPtvsfvsGviGgllgGiGGalvyyall 155
                                       lm++ tm++g+++yv+gvGv++a +k ++dpit+dkq+ y sqGteGhg+Pt+s++sG+iGg lgG+GG+lvyy+l+
  gi|298675892|ref|YP_003727642.1|  89 LMIGSTMIIGQMVYVFGVGVPPAGGKSKYDPITKDKQDIYSSQGTEGHGLPTASYISGIIGGGLGGLGGSLVYYSLV 165
                                       ***************************************************************************** PP

                              MtrD 156 ellkaalklaaaaavalaailavglflvnavlasynigGtieGfhdpkfkrlpkavvaslvas 218
                                       ++++   ++ +++ ++la+i+avg+f++nav++synigGt+eGfhdpkfkr+ +av++s++a+
  gi|298675892|ref|YP_003727642.1| 166 NVTN---NIGMTDLAGLAGIFAVGIFFINAVIPSYNIGGTTEGFHDPKFKRWYRAVISSIIAT 225
                                       8876...6788899**********************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1403.19
//
Query:       gi|298675893|ref|YP_003727643.1|  [L=270]
Description: tetrahydromethanopterin S-methyltransferase subunit C [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   5.3e-109  363.4  29.8   6.1e-109  363.2  29.8    1.0  1  MtrC      Tetrahydromethanopterin S-methyltransferase, subuni


Domain annotation for each model (and alignments):
>> MtrC  Tetrahydromethanopterin S-methyltransferase, subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  363.2  29.8  3.4e-113  6.1e-109       1     268 []       1     267 [.       1     267 [. 0.99

  Alignments for each domain:
  == domain 1  score: 363.2 bits;  conditional E-value: 3.4e-113
                              MtrC   1 msaggggkeaeeaipekkllalgivggligiylasvl....epalgsllaalgaicaivwGadavrrvasYglGTGV 73 
                                       msagg+g+ a+  i+++k++++gi+g+l+giy+a++l    +pa +s++a+lgaic+ivwGa+avrrv++YglGTGV
  gi|298675893|ref|YP_003727643.1|   1 MSAGGSGGPATGGIDHNKIIIFGIIGALVGIYAAYFLvdtiGPA-FSFIAGLGAICSIVWGASAVRRVSNYGLGTGV 76 
                                       9************************************8886666.9******************************* PP

                              MtrC  74 PSigmlalgmGivaalaglavgsalkllagpiialvvaliiglvvgvlakkvikmkipileksttelaaagalsiig 150
                                       PSigmla+g+G+va+l+g+avgs    +agp+i++++a++iglv+g+la+++i+m+ipi+e+s+te+a+ag+l+i++
  gi|298675893|ref|YP_003727643.1|  77 PSIGMLAIGTGMVASLFGMAVGS----IAGPVISFATACVIGLVIGILANRIIGMGIPIMEQSMTEIAGAGSLTIVA 149
                                       ***********************....9************************************************* PP

                              MtrC 151 lsvaiagsfeikailskviatGliallfilaglailhPfNaclGPdEkqdRTLklalekgalaliivgivsletesa 227
                                       ls++++g+f+i+++l +vi tG+ia++fi+++l+ilhPfNa+lGPdE+qdRTL++a+ekga+a+ii+giv+++t++a
  gi|298675893|ref|YP_003727643.1| 150 LSTTMSGTFMIETVLPNVIGTGYIAMIFIIGALSILHPFNANLGPDEHQDRTLSTAFEKGAIAVIIAGIVATTTAGA 226
                                       ***************************************************************************** PP

                              MtrC 228 aalvviivgliiWlisfkkfvklvkrdaakvkgtgllPkee 268
                                       a++ +i+vg++iW+++f+kf++++krda+kv+gtgllP+ee
  gi|298675893|ref|YP_003727643.1| 227 ASIPTILVGAFIWYTAFSKFYEYIKRDAHKVVGTGLLPTEE 267
                                       **************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 1600.52
//
Query:       gi|298675894|ref|YP_003727644.1|  [L=108]
Description: tetrahydromethanopterin S-methyltransferase subunit B [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-40  136.5   0.2    3.6e-40  136.3   0.2    1.0  1  MtrB      Tetrahydromethanopterin S-methyltransferase subunit
  ------ inclusion threshold ------
      0.013   14.9   0.9      0.025   14.0   0.5    1.7  2  MtrF      Tetrahydromethanopterin S-methyltransferase, F subu


Domain annotation for each model (and alignments):
>> MtrB  Tetrahydromethanopterin S-methyltransferase subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.3   0.2     4e-44   3.6e-40       2      94 .]       4      96 ..       3      96 .. 0.98

  Alignments for each domain:
  == domain 1  score: 136.3 bits;  conditional E-value: 4e-44
                              MtrB  2 vkvlpelnlvldpetgvvaearedvvllsldpvleeidkLekiaddlvnsLdpetallesypgRektlviaGlltnlfy 80
                                      v+v+pe+nlv+dp++g+va++red++ +s+dp+le++d+L+k+add+vnsL+p+++ll+s pgRe+t+++aG+ +n+fy
  gi|298675894|ref|YP_003727644.1|  4 VHVAPEVNLVMDPMSGLVATEREDIISYSMDPILEQLDELDKVADDMVNSLSPNMPLLNSNPGRERTSYYAGIASNAFY 82
                                      9****************************************************************************** PP

                              MtrB 81 Gfivglviaallal 94
                                      G+ivgl++a+++++
  gi|298675894|ref|YP_003727644.1| 83 GIIVGLIFATIIII 96
                                      **********9975 PP

>> MtrF  Tetrahydromethanopterin S-methyltransferase, F subunit (MtrF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.36   3.2e+03       5      11 ..      53      59 ..      39      63 .. 0.65
   2 ?   14.0   0.5   2.8e-06     0.025      34      57 ..      73      96 ..      66     101 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.36
                              MtrF  5 vnkpnmk 11
                                      + +pnm 
  gi|298675894|ref|YP_003727644.1| 53 SLSPNMP 59
                                      4566665 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 2.8e-06
                              MtrF 34 dSGvsatgivGfaiGfvlAllLvv 57
                                      ++G+ + +++G+++G+++A ++++
  gi|298675894|ref|YP_003727644.1| 73 YAGIASNAFYGIIVGLIFATIIII 96
                                      69*****************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 670.50
//
Query:       gi|298675895|ref|YP_003727645.1|  [L=241]
Description: tetrahydromethanopterin S-methyltransferase subunit A [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-87  289.9   1.2    8.1e-87  289.3   1.2    1.2  1  MtrA      Tetrahydromethanopterin S-methyltransferase, subuni
     0.0029   17.0   0.3     0.0075   15.6   0.3    1.8  1  MtrF      Tetrahydromethanopterin S-methyltransferase, F subu


Domain annotation for each model (and alignments):
>> MtrA  Tetrahydromethanopterin S-methyltransferase, subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  289.3   1.2     9e-91   8.1e-87       1     173 []       4     176 ..       4     176 .. 0.99

  Alignments for each domain:
  == domain 1  score: 289.3 bits;  conditional E-value: 9e-91
                                       -----TTSS-S--S-EE--TT-SEEEE-TT-SS-HHHHHHCT-SEEE----TTHHHHHHHHHHHT-TT--EEEEEE- CS
                              MtrA   1 kkepaegWPvvkGdyevGdaespvavvtlgshleeeavleaGaaiaGplktenlGiekvvanvisnpnirflivtGa 77 
                                       kkepaegWP++kG+yevGd++++vav+t+gshle +++l+aGa+i Gp+ktenlG+ekvv+++isnpnir+livtGa
  gi|298675895|ref|YP_003727645.1|   4 KKEPAEGWPILKGEYEVGDPNNCVAVITCGSHLEGQPMLDAGASIVGPCKTENLGLEKVVSHIISNPNIRYLIVTGA 80 
                                       89*************************************************************************** PP

                                       --TTT-HHHHHHHHHHH-B-TTSBBTT--SSS-B-SSS-HHHHHHHHHH-.EEEEEET---HHHHHHHHHHHHHT-- CS
                              MtrA  78 evkGhitGqalkalhenGvdkekkivgakGaiPfienlteeaverfqeqv.elvdlidtedvgaikakikelvakdp 153
                                       evkGhitG+a+++lh+nGv k+++ivga+GaiP++enltee+ver+q+q+ e+vdl++ted+++i++kikel++kdp
  gi|298675895|ref|YP_003727645.1|  81 EVKGHITGEAMMMLHKNGV-KDNRIVGATGAIPYVENLTEESVERLQQQLeECVDLLGTEDLNTITSKIKELAEKDP 156
                                       *******************.******************************88************************* PP

                                       ---SS-------XXXXXXXX CS
                              MtrA 154 gafeeeplvievkeeeeeee 173
                                       gaf++ep++i+++eeeeeee
  gi|298675895|ref|YP_003727645.1| 157 GAFDAEPMIIQLEEEEEEEE 176
                                       ***************99985 PP

>> MtrF  Tetrahydromethanopterin S-methyltransferase, F subunit (MtrF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.3   8.3e-07    0.0075      31      57 ..     208     234 ..     184     238 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 8.3e-07
                              MtrF  31 qkLdSGvsatgivGfaiGfvlAllLvv 57 
                                       +kL SGv a +i G+++G+vl l+ ++
  gi|298675895|ref|YP_003727645.1| 208 NKLHSGVLAGKIEGIMVGLVLSLFVLG 234
                                       7********************997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       996  (0.0555525); expected 358.6 (0.02)
Passed bias filter:                      753  (0.041999); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1629.54
//
Query:       gi|298675896|ref|YP_003727646.1|  [L=76]
Description: tetrahydromethanopterin S-methyltransferase F subunit [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-28   96.4   1.2      5e-28   96.3   1.2    1.0  1  MtrF      Tetrahydromethanopterin S-methyltransferase, F subu


Domain annotation for each model (and alignments):
>> MtrF  Tetrahydromethanopterin S-methyltransferase, F subunit (MtrF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.3   1.2   2.8e-32     5e-28       1      62 []      10      72 ..      10      72 .. 0.98

  Alignments for each domain:
  == domain 1  score: 96.3 bits;  conditional E-value: 2.8e-32
                              MtrF  1 gvptvnkpnmkaiksvvedirYraqLiaReqkLdSGvsatgivGfaiGfvlAllLvv.lPvll 62
                                      gvp v++p m++i+svve+irYr qLiaR+qkLdSGvsatg++GfaiGf+++++L + +P+l+
  gi|298675896|ref|YP_003727646.1| 10 GVPKVINPLMGPIESVVEKIRYRGQLIARNQKLDSGVSATGTIGFAIGFIITMILTLvIPFLV 72
                                      89*******************************************************9**985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 514.55
//
Query:       gi|298675897|ref|YP_003727647.1|  [L=76]
Description: tetrahydromethanopterin S-methyltransferase subunit G [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-35  118.9   1.3    6.7e-35  118.7   1.3    1.0  1  MtrG      Tetrahydromethanopterin S-methyltransferase, subuni


Domain annotation for each model (and alignments):
>> MtrG  Tetrahydromethanopterin S-methyltransferase, subunit G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.7   1.3   3.8e-39   6.7e-35       1      64 []       9      72 ..       9      72 .. 0.98

  Alignments for each domain:
  == domain 1  score: 118.7 bits;  conditional E-value: 3.8e-39
                              MtrG  1 kiPsvvvdpddfnevkkrLdeieekvefvnsEiaqriGkkvGRdiGilYGlviGliillvyill 64
                                      +iPsv+vdpd++nev krLd+i+ekvef+nsEiaqriGkk+GRdiGilYG+v+G++i+l+yi++
  gi|298675897|ref|YP_003727647.1|  9 SIPSVIVDPDEYNEVVKRLDRIDEKVEFANSEIAQRIGKKIGRDIGILYGAVTGILIFLIYISV 72
                                      59***********************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       914  (0.0509789); expected 358.6 (0.02)
Passed bias filter:                      713  (0.039768); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 529.99
//
Query:       gi|298675898|ref|YP_003727648.1|  [L=312]
Description: tetrahydromethanopterin S-methyltransferase subunit MtrH [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   6.7e-137  455.5   2.1   7.7e-137  455.3   2.1    1.0  1  MtrH      Tetrahydromethanopterin S-methyltransferase MtrH su


Domain annotation for each model (and alignments):
>> MtrH  Tetrahydromethanopterin S-methyltransferase MtrH subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  455.3   2.1  4.3e-141  7.7e-137       1     298 [.       6     301 ..       6     302 .. 0.99

  Alignments for each domain:
  == domain 1  score: 455.3 bits;  conditional E-value: 4.3e-141
                              MtrH   1 keqkvleiaGvkiGGqpGeyPtvlvgtifyakhkivedekkGifdkeaaealikkqeelsdktGnPalvqvvGetee 77 
                                       k+q+v++++ v +GGqpGeyPtvlvgt+fy +hkiv+de+kG fdkeaae+l+k+qee+ d+tGnP+++q+vGet+e
  gi|298675898|ref|YP_003727648.1|   6 KKQEVFKVGDVHFGGQPGEYPTVLVGTMFYNRHKIVTDEDKGEFDKEAAEELWKTQEEMGDITGNPYVNQIVGETKE 82 
                                       79*************************************************************************** PP

                              MtrH  78 aivkyidfvadvtd.aPllidstsaevklaaakyatevGladrviynsinasiedaeiealkesdveaaivlafnpm 153
                                       ai++yid++++v+d +P+lids+ + v++ aa+y+te+G+adr+i+nsinasi+++eiea+++sd+ea+ivlafn++
  gi|298675898|ref|YP_003727648.1|  83 AIRNYIDWFVEVDDsTPFLIDSSDGSVRAEAARYVTEIGVADRAIHNSINASIHEDEIEAVSQSDMEASIVLAFNAT 159
                                       **************99************************************************************* PP

                              MtrH 154 dptvegklkileegegtaekgllelaeeaGiekplidvavtplgsgagaavkaslavkaklGlPvGsgihnvpsaWd 230
                                       dp+v+gk++ileeg+g++ekglle+a e+Gi+kpl+dva+tplg+gaga+++++ +vk++lGlP G+g+hn+ saWd
  gi|298675898|ref|YP_003727648.1| 160 DPSVKGKMDILEEGGGGIEKGLLEIARESGITKPLVDVAATPLGAGAGASMRSVTTVKGHLGLPAGGGYHNMSSAWD 236
                                       ***************************************************************************** PP

                              MtrH 231 wlrefkkkekekaaeyevadvganlvqvilgsdfvlyGPienakkvfPavamvdilikeaakelgvel 298
                                       w+++fkk++ke+   y++advg+nlv+++lgs+f lyGPienak+vfPa amvdi++ e akelg+el
  gi|298675898|ref|YP_003727648.1| 237 WMKQFKKEHKEA---YMPADVGTNLVAQTLGSNFQLYGPIENAKTVFPATAMVDIILGENAKELGIEL 301
                                       *******99987...55*************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2287.83
//
Query:       gi|298675899|ref|YP_003727649.1|  [L=188]
Description: hypothetical protein Metev_2024 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1202.65
//
Query:       gi|298675900|ref|YP_003727650.1|  [L=97]
Description: hypothetical protein Metev_2025 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-32  110.3   0.0    5.1e-32  110.1   0.0    1.0  1  DUF1894   Domain of unknown function (DUF1894)


Domain annotation for each model (and alignments):
>> DUF1894  Domain of unknown function (DUF1894)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.1   0.0   2.8e-36   5.1e-32       1      88 []       1      88 [.       1      88 [. 0.99

  Alignments for each domain:
  == domain 1  score: 110.1 bits;  conditional E-value: 2.8e-36
                                      B---HHH--S-SS-EEESSHHHHHHHHTTSEEEEES--EEESSS---SS----EEEE--S-EEEE---SS-EEEEE-SS CS
                           DUF1894  1 maCleklkyeillkeasfkeceeyikkkakevyevepgykilgvrliGvppipvgideekilfpytkPCyGtfvlkvke 79
                                      m+C+++l+yei+l++++++e+e+yik++++e+++v++gyk+lgv l G ++ipvg++++++lf+y+kPC G+fvl++++
  gi|298675900|ref|YP_003727650.1|  1 MTCISDLPYEIVLSGVTPSESEKYIKQNSDEIFYVPGGYKLLGVVLRGGHEIPVGVKDSDLLFQYVKPCSGLFVLRIRN 79
                                      89***************************************************************************** PP

                                      -GGGHHHHH CS
                           DUF1894 80 seeeieklr 88
                                      +++e+++lr
  gi|298675900|ref|YP_003727650.1| 80 EPDELKRLR 88
                                      *******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 653.71
//
Query:       gi|298675901|ref|YP_003727651.1|  [L=330]
Description: phosphoribosylformylglycinamidine cyclo-ligase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.6e-19   68.2   0.0    1.6e-18   67.3   0.0    1.4  1  AIRS_C    AIR synthase related protein, C-terminal domain
    6.4e-16   58.8   0.4    1.1e-15   58.0   0.4    1.3  1  AIRS      AIR synthase related protein, N-terminal domain
      0.005   16.6   0.1       0.01   15.6   0.1    1.4  1  RRM_1     RNA recognition motif. (a.k.a. RRM, RBD, or RNP dom


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.3   0.0   2.7e-22   1.6e-18       1     148 [.     166     318 ..     166     324 .. 0.88

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 2.7e-22
                                       STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTT.......TSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TT CS
                            AIRS_C   1 kpGdvliltgslGlggagtslkrkileeegldds.......avqlgdvlleptliyvkralaalkglvkaahDvTgG 70 
                                       ++Gd++++++s G++++g+ l+rk++e +g  +s       +  +g++ll+pt+iy+  +   +k +v++++++Tg 
  gi|298675901|ref|YP_003727651.1| 166 QQGDAIVGIPSNGIHSNGYTLARKVVENSGYSYSdqfpyntSTTIGEELLKPTRIYLEVLDVVKKLEVHGLAHITGS 242
                                       68****************************9999******7777**************9999999************ PP

                                       HHHHHHHHHHHTTTEEEEEECG..THHHHHHHH.....HHHHHHHCSTTTEEEEEEEHGGH.HHHHHHHHHTTCCCE CS
                            AIRS_C  71 GLlgalaemapasgvgaeidld..kvpifdele.....splemllsensGrllvavppeea.davlaileeeglpea 139
                                       GLl  l+++ +   +g+ ++ +     if+ l+     ++lem++++n+G ++v++ pee+ d++ ++++       
  gi|298675901|ref|YP_003727651.1| 243 GLLK-LNRITE---LGFDFYDPfeVSDIFKFLQekgniEDLEMYKTFNMGMGFVIILPEEQaDEAADMVDG------ 309
                                       **95.889866...5677766676666676666777********************999998998888884...... PP

                                       EEEEEEEES CS
                            AIRS_C 140 avIGevtak 148
                                       +v+G+++++
  gi|298675901|ref|YP_003727651.1| 310 KVVGRIVES 318
                                       588988886 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   0.4   1.8e-19   1.1e-15       4      94 .]      51     154 ..      39     154 .. 0.91

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 1.8e-19
                                       EEEEEEEEEE.EECCTCCCC....HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.....HHHHHHHHHHHHHHHTT- CS
                              AIRS   4 avvvttdshnrpvlvepvhf....iGakavavnlsDlaamGArPlalllslalp.....wleevvrglaeaaeelgv 71 
                                       a+++ttd+++++vl+++       +G  ++a+n++Dl+a GA+Pl ++++la++      +e+v +gla++ae +++
  gi|298675901|ref|YP_003727651.1|  51 ALALTTDGVGTKVLIANEMQkwntVGIDCIAMNVNDLLAIGAEPLSFVDYLAVEsyskeFAEQVGEGLAKGAEIANI 127
                                       5799***********553334677**********************************999**************** PP

                                       EEEEEEEEEESS....EEEEEEEEEEE CS
                              AIRS  72 plvgGdtsfsne....ptisvtavGlv 94 
                                       ++vgG+t+  ++    + ++ t++G+v
  gi|298675901|ref|YP_003727651.1| 128 SIVGGETATLPDiikgFDLAGTCLGMV 154
                                       ********9988899999999999986 PP

>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.7e-06      0.01      13      65 ..     264     313 ..     262     315 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.7e-06
                                       HHHHHHHHTTSCEEEEEEEEETTTSEEEEEEEEESSHHHHHHHHHHHTTEEET CS
                             RRM_1  13 eeLkelFskfGpiksiklvrdetgkskgfafVeFeskedAekAlealngkklg 65 
                                       +++ +++++ G i++++++++    ++g++fV    +e+A++A + ++gk +g
  gi|298675901|ref|YP_003727651.1| 264 SDIFKFLQEKGNIEDLEMYKT---FNMGMGFVIILPEEQADEAADMVDGKVVG 313
                                       58999***************8...*************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2163.92
//
Query:       gi|298675902|ref|YP_003727652.1|  [L=469]
Description: aspartate kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      6e-49  166.8   1.1    7.1e-49  166.6   0.1    1.6  2  AA_kinase  Amino acid kinase family
    1.4e-21   76.0   5.2    5.3e-11   42.1   1.9    2.7  2  ACT_7      ACT domain
      1e-18   66.8   3.5    2.6e-10   39.9   0.5    2.8  2  ACT        ACT domain
  ------ inclusion threshold ------
      0.048   13.6   0.2       0.34   10.9   0.1    2.3  2  ACT_6      ACT domain
       0.13   12.1   0.1        1.8    8.4   0.0    2.4  2  DUF3237    Protein of unknown function (DUF3237)
       0.34   10.7   5.1        0.4   10.5   3.4    2.0  1  DUF5612    Domain of unknown function (DUF5612)


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.6   0.1   2.4e-52   7.1e-49       1     241 []       1     289 [.       1     289 [. 0.87
   2 ?   -2.0   0.1      0.74   2.2e+03      21      46 ..     308     333 ..     295     411 .. 0.48

  Alignments for each domain:
  == domain 1  score: 166.6 bits;  conditional E-value: 2.4e-52
                                       TEEEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--.HHHHHHHHHHTCCCCCHHHC............. CS
                         AA_kinase   1 krvVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGg.gsftdgllalksglssgelaa............ 64 
                                       +r+V+K+GG+s++d+++  +r +a+ ++++ +sg+++v V+++ gs+tdgll+ + ++s++++ +            
  gi|298675902|ref|YP_003727652.1|   1 MRIVMKFGGTSIADGNN--IRYVAQLLKDYYNSGYEVVAVTSAlGSVTDGLLSNAIEVSKKGKVSqikefisdlthk 75 
                                       79***************..***********************************55555555554555554444443 PP

                                       .....E..HHHHHHHHH...........................................HHHHHHHHHHHHHHHHT CS
                         AA_kinase  65 ..glrstleeagevatr...........................................dalaslgerlvaallaa 96 
                                                                                                   d++ s gerl a +++ 
  gi|298675902|ref|YP_003727652.1|  76 hyS-------------AvheaiddeeiidetiqtidcrvdelekaligicylgeltprsiDYISSYGERLAAPIVSG 139
                                       330.............03344555666666777788889999999******************************** PP

                                       THGEEEE-GGGTCEECCCE......HHHTTTCEEECCHHHHHHHT..T-EEEEESEEEEETTTE...EEEE-HHHHH CS
                         AA_kinase  97 glpavglsaaaldateagr....degsdgnvesvdaeaieellea..gvvpvltgfigldeege...lgrgssDtia 164
                                       +++++g++++ ++  + g+    ++gs++++e+  ++  e+l  +  + +pv+tgfi+ + +g    lgrg+sD +a
  gi|298675902|ref|YP_003727652.1| 140 AIRSIGIKSKMYTGGDVGIvtdnEYGSAKPLEQSYQRVGETLRTDlsECIPVVTGFIAENKDGVittLGRGGSDFSA 216
                                       *************999999***888888888887766666666334359********9999999************* PP

                                       HHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHHCSSS.TTTHHHHCHHHHHHHHHCTT-EEEEEE CS
                         AA_kinase 165 allAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaeesaselatgGmkvkhpaalaaarrggipvvItn 241
                                       +++++ ++Ad+++++++V+G+++ dpk+vp ar  + is+ ea+e    l+++G++v+hp+a+++a r+gipv+++n
  gi|298675902|ref|YP_003727652.1| 217 SIIGASIDADEIWLWKEVHGIMTTDPKIVPEARSMSWISYAEAME----LSYFGARVLHPRAIEPAIRNGIPVRVKN 289
                                       *********************************************....**************************98 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.74
                                       HHHHHHHHHHHHHTTEEEEEE--H..HH CS
                         AA_kinase  21 rrlaeqiaalkesgnklvvVhGgg..sf 46 
                                       +++++ +  +  ++  lv ++G+g  ++
  gi|298675902|ref|YP_003727652.1| 308 EDVVKAVTLI--KKVSLVNISGAGmvGT 333
                                       5555555555..3344555555542222 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   1.9   1.8e-14   5.3e-11       6      64 ..     320     380 ..     316     381 .. 0.94
   2 !   34.5   0.1   4.4e-12   1.3e-08       3      65 .]     394     458 ..     392     458 .. 0.96

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 1.8e-14
                                       EEEEEE-S-.---SS--HHHHHHHHHHTTT---EEEE...-SS-EEEEEEGGGHHHHHHHHH CS
                             ACT_7   6 wiklsvvgsglpfdvtGivaklaspLaeagIsifqiS...tyrtdyiLVpeedlekAveaLh 64 
                                       ++ ++++g+g+ + ++G +a++++ La+a+++i +iS   ++  ++i+V+e++le+Av+a +
  gi|298675902|ref|YP_003727652.1| 320 VSLVNISGAGMVG-TIGTAARVFNSLADANVNIIMISqasSESNMSIVVDEDHLEAAVNAIN 380
                                       56799******88.*********************************************987 PP

  == domain 2  score: 34.5 bits;  conditional E-value: 4.4e-12
                                       EEEEEEEEE-S-.---SS--HHHHHHHHHHTTT---EEEE...-SS-EEEEEEGGGHHHHHHHHHH CS
                             ACT_7   3 edgwiklsvvgsglpfdvtGivaklaspLaeagIsifqiS...tyrtdyiLVpeedlekAveaLhe 65 
                                       ++++ ++ vvg+g+++ ++G+  +++s L + +I++ +iS   +++ ++++V ee++  Av++Lh+
  gi|298675902|ref|YP_003727652.1| 394 DNNICVVAVVGAGMAG-IPGVSGRVFSSLGKDNINVVAISqgsSQHNISFVVSEEEAFDAVRVLHK 458
                                       578899********99.************************************************6 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.5   8.6e-14   2.6e-10       7      65 ..     330     382 ..     325     384 .. 0.93
   2 !   26.8   0.1   1.1e-09   3.2e-06       2      66 ..     402     460 ..     401     461 .. 0.91

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 8.6e-14
                                       EESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTT CS
                               ACT   7 vpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkl 65 
                                       + +  G++arvf+ lad+++Ni++i+q+ss      ++++ ivvde++le++++a+++ 
  gi|298675902|ref|YP_003727652.1| 330 MVGTIGTAARVFNSLADANVNIIMISQASS------ESNMSIVVDEDHLEAAVNAINSE 382
                                       56677*************************......99******************986 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 1.1e-09
                                       EEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTTC CS
                               ACT   2 vlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkle 66 
                                       v+  g+++ PG+ +rvf+ l++ +iN++ i+q+ss       +++ +vv+ee++ ++++ l+k +
  gi|298675902|ref|YP_003727652.1| 402 VVGAGMAGIPGVSGRVFSSLGKDNINVVAISQGSS------QHNISFVVSEEEAFDAVRVLHKEF 460
                                       56678999***************************......999999999999999999999865 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00011      0.34      14      46 ..     335     367 ..     321     386 .. 0.82
   2 ?   -1.0   0.0      0.59   1.8e+03      13      43 ..     411     441 ..     406     464 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                             ACT_6  14 GltasLtsvlaefgvnilDieqavihgrlsLgl 46 
                                       G  a+++  la+ +vni+ i qa  ++++s+++
  gi|298675902|ref|YP_003727652.1| 335 GTAARVFNSLADANVNIIMISQASSESNMSIVV 367
                                       6789************************99875 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.59
                             ACT_6  13 pGltasLtsvlaefgvnilDieqavihgrls 43 
                                       pG++ +++s l + ++n++ i q     + s
  gi|298675902|ref|YP_003727652.1| 411 PGVSGRVFSSLGKDNINVVAISQGSSQHNIS 441
                                       8999999999999999999999976655555 PP

>> DUF3237  Protein of unknown function (DUF3237)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0006       1.8      23      58 ..     127     165 ..      96     226 .. 0.76
   2 ?    1.1   0.0      0.11   3.2e+02      27      58 ..     398     433 ..     375     452 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0006
                                       T.EEEEEEEEEEEEEESTT--EEE-ST-EEEEEE-T...T CS
                           DUF3237  23 p.gkrnivpitgGtikgprldgevlpgGaDwiridp...g 58 
                                       + g+r  +pi++G i++ +++ ++  +G+D   + +   g
  gi|298675902|ref|YP_003727652.1| 127 SyGERLAAPIVSGAIRSIGIKSKMY-TGGDVGIVTDneyG 165
                                       3589*******************99.88898655552433 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.11
                                       EEEEEEEEEEES.TT--EEE-S.T-EEEEEE-T..T CS
                           DUF3237  27 nivpitgGtikg.prldgevlp.gGaDwiridp..g 58 
                                        +v ++g  + g p+++g+v +  G D i++ +  +
  gi|298675902|ref|YP_003727652.1| 398 CVVAVVGAGMAGiPGVSGRVFSsLGKDNINVVAisQ 433
                                       56778888899999******9999****99887653 PP

>> DUF5612  Domain of unknown function (DUF5612)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   3.4   0.00013       0.4      49     127 ..     300     381 ..     295     396 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00013
                                       --SHHH.HHHHHHHGGGSTTEEEEEEESSB--THHHHHHHHHHH..T.T-EEEEES-BSSHHHHSSEEESSHHHHHH CS
                           DUF5612  49 lvGeee.laeaveavsrlprvkvlvlaGslmGGkiteavkklke..ekdiivislnmaGsvtevadlvvtdpvqaGv 122
                                       +v e++   + v+av+ +++v+++ ++G+ m G+i +a +  ++  + ++ +i ++ a s ++++ +v  d ++a v
  gi|298675902|ref|YP_003727652.1| 300 VVSEQKpTEDVVKAVTLIKKVSLVNISGAGMVGTIGTAARVFNSlaDANVNIIMISQASSESNMSIVVDEDHLEAAV 376
                                       455554166789***********************8876655431156899999999999999999999999*9999 PP

                                       HHHHH CS
                           DUF5612 123 lavma 127
                                        a+ +
  gi|298675902|ref|YP_003727652.1| 377 NAINS 381
                                       88755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.66u 0.25s 00:00:00.91 Elapsed: 00:00:00.46
# Mc/sec: 3073.62
//
Query:       gi|298675903|ref|YP_003727653.1|  [L=422]
Description: hypothetical protein Metev_2028 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-11   41.6  12.7    1.1e-05   24.7   0.8    2.7  3  S-layer   S-layer protein
  ------ inclusion threshold ------
       0.11   12.4   2.2        4.2    7.4   0.1    3.5  3  DUF1344   Protein of unknown function (DUF1344)
       0.79    9.7   4.0        1.2    9.1   0.4    2.8  3  CE2_N     Carbohydrate esterase 2 N-terminal


Domain annotation for each model (and alignments):
>> S-layer  S-layer protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   1.6   2.6e-09   1.5e-05     111     198 ..      34     121 ..      17     137 .. 0.78
   2 !   24.7   0.8   1.8e-09   1.1e-05     109     201 ..     142     228 ..     132     241 .. 0.87
   3 ?   -2.0   0.1      0.25   1.5e+03     151     194 ..     284     331 ..     261     359 .. 0.55

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2.6e-09
                           S-layer 111 ektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevdskvissskadstyvyekdlgde.ddvviiavhvde 186
                                       + +l  g++++Le+gY+ ++++i+    + w+eL+ +ge+vd++   s k+++ + y k++ ++ d+  +++++++ 
  gi|298675903|ref|YP_003727653.1|  34 KDSLDIGDTYSLEQGYSFKVRDINDGTGNSWIELYFNGEKVDTDDQFS-KENDPFEYRKTVTENgDEKQYLIIRITP 109
                                       678999*******************99**************9874333.5699999999886542556677777766 PP

                           S-layer 187 vfrgtedslvvi 198
                                       +   ++++ v +
  gi|298675903|ref|YP_003727653.1| 110 IELIKTSNDVSV 121
                                       655444444555 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 1.8e-09
                           S-layer 109 deektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevdskvissskadstyvyekdlgdeddvviiavhvd 185
                                       d++++++  + leL+++Y+l++   +   ++++l+L+kdg+ v ++  ++    + ++y+++   +d  +i+  +++
  gi|298675903|ref|YP_003727653.1| 142 DDTESVNNINPLELKNNYTLHVG--NFGQESAVLTLKKDGSTVKETETNV---GDYFTYTRKTS-KDSTTIFLAKLS 212
                                       56888999999************..7778899************998888...99999998865.599********* PP

                           S-layer 186 evfrgtedslvviegi 201
                                       e f +++ + v++e +
  gi|298675903|ref|YP_003727653.1| 213 ELFTSKDYNTVFLEKM 228
                                       ************9976 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.25
                           S-layer 151 vdskvissska..dstyvye..kdlgdeddvviiavhvdevfrgteds 194
                                       +d+k i+ +++  + tyv    +  g++ + +i av+ + v + ++++
  gi|298675903|ref|YP_003727653.1| 284 LDDKQIDFRNDvdSGTYVTLtgNLTGGVHNTTITAVSEEGVNKKQTTE 331
                                       344444443334444444331122234444444444444444444444 PP

>> DUF1344  Protein of unknown function (DUF1344)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.17     1e+03      19      34 ..      36      51 ..      36      60 .. 0.67
   2 ?    1.9   0.0     0.035   2.1e+02      25      51 ..     101     127 ..      95     130 .. 0.81
   3 ?    7.4   0.1   0.00071       4.2      31      53 ..     254     276 ..     250     280 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.17
                           DUF1344 19 tLdDGktYklpeefdi 34
                                      +Ld G tY+l ++  +
  gi|298675903|ref|YP_003727653.1| 36 SLDIGDTYSLEQGYSF 51
                                      5888999999886443 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.035
                           DUF1344  25 tYklpeefdidgLkvGvkVvVfYtvvd 51 
                                       +Y +   + i+ +k+ ++V V Y+++ 
  gi|298675903|ref|YP_003727653.1| 101 QYLIIRITPIELIKTSNDVSVKYKIEQ 127
                                       555566677999***********9986 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.00071
                           DUF1344  31 efdidgLkvGvkVvVfYtvvdgk 53 
                                       + d dgL+ G k +V Yt ++g+
  gi|298675903|ref|YP_003727653.1| 254 DLDGDGLTKGDKAIVSYTLKNGN 276
                                       77889****************95 PP

>> CE2_N  Carbohydrate esterase 2 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.22   1.3e+03      38      58 ..      57      77 ..      47      97 .. 0.71
   2 ?   -0.6   0.0      0.22   1.3e+03      51      87 ..     178     213 ..     124     220 .. 0.61
   3 ?    9.1   0.4    0.0002       1.2      34     102 ..     271     336 ..     261     341 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.22
                                      ..SSS-EEEEEEETTS--EEE CS
                             CE2_N 38 kedkgknrlaviiDgkrvkdl 58
                                      ++ +g+++++++ +g++v + 
  gi|298675903|ref|YP_003727653.1| 57 NDGTGNSWIELYFNGEKVDTD 77
                                      358899999999999986554 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.22
                                       TTS--EEEEE-SS-EEEEEEEEEEEEEEEEEEEE-S- CS
                             CE2_N  51 DgkrvkdlkldgeektytlaeglepgehtvrlvkrtE 87 
                                       Dg++vk+ +++  +  +t  ++ ++   t+ l k++E
  gi|298675903|ref|YP_003727653.1| 178 DGSTVKETETNVGDY-FTYTRKTSKDSTTIFLAKLSE 213
                                       444444444333333.455555555555666666665 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0002
                                       EEEE..SSS-EEEEEEETTS--EEEEE.-SS-EEEEEEEEEEEEEEEEEEEE-S-GGG--EEEEEEEEE. CS
                             CE2_N  34 rlkdkedkgknrlaviiDgkrvkdlkl.dgeektytlaeglepgehtvrlvkrtEaeagkteflgfvlde 102
                                       +lk+    + ++++v +D+k+ +d++   ++++ +tl  +l+ g h+ +++  +E  + k +  +fv+++
  gi|298675903|ref|YP_003727653.1| 271 TLKN---GNFSEVMVELDDKQ-IDFRNdVDSGTYVTLTGNLTGGVHNTTITAVSEEGVNKKQTTEFVVKS 336
                                       4444...5667899999***9.777774566666788899****************99999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1239  (0.0691059); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.26s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 2676.76
//
Query:       gi|298675904|ref|YP_003727654.1|  [L=401]
Description: homoserine kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-59  199.0   0.0    6.9e-59  198.5   0.0    1.2  1  PhosphMutase     2,3-bisphosphoglycerate-independent phosphog
    1.4e-38  132.7   0.8    1.6e-38  132.5   0.8    1.0  1  Metalloenzyme    Metalloenzyme superfamily
    5.2e-05   23.0   0.0    0.00037   20.2   0.0    2.0  2  Phosphodiest     Type I phosphodiesterase / nucleotide pyroph
  ------ inclusion threshold ------
      0.031   13.2   0.3        1.3    7.9   0.1    2.2  2  Alk_phosphatase  Alkaline phosphatase


Domain annotation for each model (and alignments):
>> PhosphMutase  2,3-bisphosphoglycerate-independent phosphoglycerate mutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.5   0.0   1.5e-62   6.9e-59       1     170 []      37     200 ..      37     200 .. 0.97

  Alignments for each domain:
  == domain 1  score: 198.5 bits;  conditional E-value: 1.5e-62
                                       HHTSEEEEEE-----------TCHHHHTT--HHCH---HHHHHHHHTT----TT-EEEEEEEEEEC..TTCEEETTG CS
                      PhosphMutase   1 AkkGetGlldtvpegiapgSdvAnlsilGydpkkyytGRGplEAlgiGlelkpgdvafRcnlvtvdeedgiiidrra 77 
                                       Ak+G+tGl+++vpeg++pgSd+An+si+Gyd kkyytGR+plEA+++G++l+++dvafRcnl+t+  +++ii+d++a
  gi|298675904|ref|YP_003727654.1|  37 AKHGITGLAKNVPEGMHPGSDIANMSIIGYDTKKYYTGRAPLEAASMGITLEKDDVAFRCNLITI--NNDIIKDYSA 111
                                       89***************************************************************..59******** PP

                                       GG-.-TTHHHHHHHT-EEE.TTEEEEEEE-STTEEEEEE..--S-B--S--..SSTTS------BS.SGGGHHHHHH CS
                      PhosphMutase  78 gristeeakeLikalneeleegvevkfypgveyrhllvl..lsdkitdtdpphdkegkeikellplkseeaketael 152
                                       g+i te+ak L+k++n++l  +++++fypg++y+hl+v   +  +  +++pphd+ gk  ++++p +    ++++  
  gi|298675904|ref|YP_003727654.1| 112 GHIATEDAKILVKEINQQLG-NANIQFYPGMSYKHLMVAknNIGADANCTPPHDIMGKDKNTHMP-S----GKDSGT 182
                                       *******************3.68*****************9666679******************.6....9***** PP

                                       HHHHHHHHHHHHHHSHHH CS
                      PhosphMutase 153 lnelieksqeiLedhpvN 170
                                       l +li++s+ +L+dh vN
  gi|298675904|ref|YP_003727654.1| 183 LSDLIDRSYMVLKDHWVN 200
                                       ***************999 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.5   0.8   3.5e-42   1.6e-38       1     246 [.       1     397 [.       1     399 [. 0.95

  Alignments for each domain:
  == domain 1  score: 132.5 bits;  conditional E-value: 3.5e-42
                                       -EEEEEEETTBB----GGGTT...HHHS--HHHHHHHHH.......SEEEEEESSSTT----HHHHHHHH....... CS
                                       xxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
                     Metalloenzyme   1 kkvvlvvlDGlGeapadelna...ihvAktPtldkLkkeaPerwlikahgtavglpeddmgnsevgHlel....... 67 
                                       +k+++++ DG+G+ p +el+    ++ AktP++d ++k+       +++g+a+ +pe++ ++s+++++++       
  gi|298675904|ref|YP_003727654.1|   1 MKYIVLIGDGMGDYPIKELDNqtiLQNAKTPNMDYIAKH-------GITGLAKNVPEGMHPGSDIANMSIigydtkk 70 
                                       5789***************99999***************.......99***************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Metalloenzyme  68 ............................................................................. 67 
                                                                                                                    
  gi|298675904|ref|YP_003727654.1|  71 yytgrapleaasmgitlekddvafrcnlitinndiikdysaghiatedakilvkeinqqlgnaniqfypgmsykhlm 147
                                       ***************************************************************************** PP

                                       ......................................................HHHHTT-----EEEEEEEE-S-- CS
                                       ......................................................xxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme  68 ......................................................lrisetvkfahvtffwnggrsgy 90 
                                                                                              ri+ ++ +a+ +++w++g  ++
  gi|298675904|ref|YP_003727654.1| 148 vaknnigadanctpphdimgkdknthmpsgkdsgtlsdlidrsymvlkdhwvntDRINSGKSPANSIWLWGQGYAPE 224
                                       ******************************************************99********************* PP

                                       -SSHHHHHT--EEEE--SHH....................STT--HHHHHHHHHHHH.CC.-SEEEEEE-HHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme  91 fnpleereeipsdtvitfdl....................qpemkavevaekaldailsgkfdlvvvniknaDmvGH 147
                                       ++++++ +++++ ++ ++dl                    + ++++  +ae a++ +  +++d+ +v+++ +D++GH
  gi|298675904|ref|YP_003727654.1| 225 IPHFKKLYGLSGSIISAVDLikgigtyagldvidvpgatgYLDTNYSGKAEYAIESL--QNHDIAIVHVEAPDEAGH 299
                                       *********************************************************..559*************** PP

                                       TT-HHHHHHHHHHHHH.HHHHHHTTS-TT....TEEEEEE-SSB--TTTSS........-----EEEEEESTT---. CS
                                       xxxxxxxxxxxxxxxx.xxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                     Metalloenzyme 148 tgdleatiaaieaaDe.avkeildaieqv....dgilvvtADHgnaedmvkrdkqplTsHtlepVPilivgkglap. 218
                                        g + a+ +aie++D+  v++il+ ++++    d +++vt+DH+++ ++++        Ht +pVP++i+++ +++ 
  gi|298675904|ref|YP_003727654.1| 300 MGSIDAKTQAIEDFDRmVVGKILEFVQNDklneDYTILVTPDHPTPISLNT--------HTSDPVPFAIYSTIIKHp 368
                                       ****************7789******9753333789***************........*************99861 PP

                                       -S--S.SHHHHTT-TTEEEEGGGHHHHHH CS
                                       xxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 219 dkvke.gakfrekggLanvaatllnllgl 246
                                       d+v++ ++k++ +g L +v++  + +l+l
  gi|298675904|ref|YP_003727654.1| 369 DEVESfNEKSMINGCLETVNGNNIINLML 397
                                       456667777777*******9988877766 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0     0.086   3.9e+02       3      34 ..       5      43 ..       3      49 .. 0.65
   2 !   20.2   0.0   8.2e-08   0.00037     169     232 ..     279     342 ..     215     356 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.086
                                      EEEETT-B.........TTHHHHHGSTSHHHHHHHHHSEEE CS
                      Phosphodiest  3 vislDGlr.........adlldrlaellpnlaaLakegvsa 34
                                      v++ DG+           ++l++   ++pn++++ak+g+++
  gi|298675904|ref|YP_003727654.1|  5 VLIGDGMGdypikeldnQTILQN--AKTPNMDYIAKHGITG 43
                                      55566666666544332333333..59**********9976 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 8.2e-08
                                       CT.SSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHHHH.HHHHHHHHHHTTGTTTEEEEEEES- CS
                      Phosphodiest 169 el.ekpdlllvyleetDtvgHkfGpdspevedalrrvDka.igdLlealderglsaetniilvSDH 232
                                       e+ ++ d  +v++e++D +gH+    + + ++a+++ D++ +g++le ++ ++l+++++i+++ DH
  gi|298675904|ref|YP_003727654.1| 279 ESlQNHDIAIVHVEAPDEAGHMG-SID-AKTQAIEDFDRMvVGKILEFVQNDKLNEDYTILVTPDH 342
                                       235999***************55.333.34799*****9637***********************9 PP

>> Alk_phosphatase  Alkaline phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0    0.0076        34       5      17 ..       4      16 ..       2      44 .. 0.82
   2 ?    7.9   0.1   0.00029       1.3     263     323 ..     295     359 ..     274     391 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.0076
                                      EEEEETT-SHHHH CS
                   Alk_phosphatase  5 illigDGmgvstv 17
                                      i+ligDGmg+  +
  gi|298675904|ref|YP_003727654.1|  4 IVLIGDGMGDYPI 16
                                      99*******9766 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00029
                                       HHHHHTTTHHHHHHHHHHHHHH.HHHHHHHCHH...CTTEEEEEEESSEESEEEESTTSTT..TT CS
                   Alk_phosphatase 263 DhaaHendavgalsEvvefdeA.vkaalefakk...eketlvvvTaDHshvfsfggyttrgesvl 323
                                       D+a+H +++  + + + +fd+  v + lef ++   +++  ++vT DH + +s++ +t  +   +
  gi|298675904|ref|YP_003727654.1| 295 DEAGHMGSIDAKTQAIEDFDRMvVGKILEFVQNdklNEDYTILVTPDHPTPISLNTHTSDPVPFA 359
                                       999*****************9626899***9984445688899************9999855433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2878.52
//
Query:       gi|298675905|ref|YP_003727655.1|  [L=134]
Description: heat shock protein Hsp20 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-23   81.9   0.8    3.4e-23   81.7   0.8    1.0  1  HSP20            Hsp20/alpha crystallin family
    6.4e-14   51.3   0.0    8.9e-14   50.8   0.0    1.2  1  ArsA_HSP20       HSP20-like domain found in ArsA
     0.0025   17.9   0.6       0.13   12.3   0.1    2.3  2  FKBP26_C         FKBP26_C-terminal
     0.0065   16.6   0.3     0.0097   16.0   0.3    1.2  1  GvpH             GvpH
  ------ inclusion threshold ------
      0.012   16.6   0.2      0.017   16.1   0.2    1.2  1  CS               CS domain
      0.082   13.4   0.1        0.1   13.1   0.1    1.2  1  DUF2718          Protein of unknown function (DUF2718)
        0.1   12.6   0.0       0.14   12.2   0.0    1.2  1  TPP1             Shelterin complex subunit, TPP1/ACD
       0.13   12.7   0.2        2.2    8.8   0.3    2.1  2  GlcV_C_terminal  Glucose ABC transporter C-terminal domain


Domain annotation for each model (and alignments):
>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.7   0.8   1.5e-26   3.4e-23       1      93 [.      38     130 ..      38     134 .] 0.95

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 1.5e-26
                                       E--SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--..---TT----SS---EEEEEE--STTB-TTT-EEEEE CS
                             HSP20   1 dikeeeeefevkldvpglkkeelkvkvednrvlvkgeheeeeedekglikerssrkFsrkftLPenvdadkvkaslk 77 
                                       dik++++++ +++d+pg++ke+++++v dn+v ++++  +e  +e ++++er+++ Fsr++ LPe v ++  +a+l+
  gi|298675905|ref|YP_003727655.1|  38 DIKDDDNNIIINADLPGVNKEDIDITVSDNTVQINAKCSKESTEEVYYRQERTYEGFSRTIVLPEAVTEEGASAKLE 114
                                       799************************************999*********************************** PP

                                       TTEEEEEEEBSS--.. CS
                             HSP20  78 dGvLtvtvpkkepekk 93 
                                       +GvL+vt+pk e+e+k
  gi|298675905|ref|YP_003727655.1| 115 NGVLKVTLPKLEKEHK 130
                                       ************9954 PP

>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.0     4e-17   8.9e-14       1      63 []      43     122 ..      43     122 .. 0.97

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 4e-17
                        ArsA_HSP20   1 ddeyvlkldLPfvdkeeidlsrsgdeLtIkig..................nfrRqitLPsvlarkevtsAkfedgvL 59 
                                       d+++++++dLP+v+ke+id++ s+++  I+++                   f+R+i+LP+ + ++ + sAk+e+gvL
  gi|298675905|ref|YP_003727655.1|  43 DNNIIINADLPGVNKEDIDITVSDNTVQINAKcskesteevyyrqertyeGFSRTIVLPEAVTEEGA-SAKLENGVL 118
                                       68999************************************************************77.********* PP

                        ArsA_HSP20  60 eIrF 63 
                                       ++++
  gi|298675905|ref|YP_003727655.1| 119 KVTL 122
                                       **96 PP

>> FKBP26_C  FKBP26_C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.1   5.9e-05      0.13       8      33 ..      47      72 ..      41      85 .. 0.92
   2 ?    3.8   0.0     0.028        63      18      37 ..     106     125 ..      96     130 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.9e-05
                                      HHHHH-TT--..--EEEEETTEEEEE CS
                          FKBP26_C  8 lIkryiPnidlekfkieiedktvtIe 33
                                      +I+  +P +++e+++i+++d+tv+I+
  gi|298675905|ref|YP_003727655.1| 47 IINADLPGVNKEDIDITVSDNTVQIN 72
                                      788999*******************7 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.028
                                       ..--EEEEETTEEEEE--TT CS
                          FKBP26_C  18 lekfkieiedktvtIelpee 37 
                                        e +  ++e+++++++lp+ 
  gi|298675905|ref|YP_003727655.1| 106 EEGASAKLENGVLKVTLPKL 125
                                       4567889***********85 PP

>> GvpH  GvpH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.3   4.3e-06    0.0097      98     128 ..      41      71 ..      36      88 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.3e-06
                              GvpH  98 ddsdelvvvadlpGvtdedvdvaletdeqal 128
                                       dd +++++ adlpGv  ed+d+++  ++  +
  gi|298675905|ref|YP_003727655.1|  41 DDDNNIIINADLPGVNKEDIDITVSDNTVQI 71 
                                       67889999****************9555544 PP

>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.1   0.2   7.6e-06     0.017       8      76 .]      42     124 ..      37     124 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7.6e-06
                                       ETTEEEEEEE-TTCTTTTTCEEEEEETTEEEEEE....TSCEEEEECE...................BSS-BETTTE CS
                                CS   8 tldeVvvtiyvkkvnikkkdvkvefkerslkvki....gkeklliege...................LfgpIdpees 61 
                                       ++++++++  +++v  +k+d++++ + +++ ++     ++                           L + +  e +
  gi|298675905|ref|YP_003727655.1|  42 DDNNIIINADLPGV--NKEDIDITVSDNTVQINAkcskES-------TeevyyrqertyegfsrtivLPEAVTEEGA 109
                                       57899********9..*************77776224322.......123566667********************* PP

                                       EEEEETTEEEEEEEB CS
                                CS  62 swtieskkveitLkK 76 
                                       s ++e+  +++tL K
  gi|298675905|ref|YP_003727655.1| 110 SAKLENGVLKVTLPK 124
                                       *************88 PP

>> DUF2718  Protein of unknown function (DUF2718)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   4.6e-05       0.1      45      89 ..      37      80 ..      27     102 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.6e-05
                           DUF2718 45 pdpkkdddavivpddlppepkekikekdngagvvekaikteenel 89
                                      +d k dd+ +i+ +dlp + ke i+    ++++v+   k  +++ 
  gi|298675905|ref|YP_003727655.1| 37 VDIKDDDNNIIINADLPGVNKEDID-ITVSDNTVQINAKCSKEST 80
                                      456777778889*********9987.4444455555555444433 PP

>> TPP1  Shelterin complex subunit, TPP1/ACD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     6e-05      0.14      39      72 ..      54      89 ..      29     103 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6e-05
                                      .EETTEEEEEEE-SS-EEEEEE-HHHHHHHH..HHH CS
                              TPP1 39 dtsnsaitavlsDsthkIlaiftreavenfe..ree 72
                                       +++++i  ++sD+t++I a  ++e++e+    +e 
  gi|298675905|ref|YP_003727655.1| 54 GVNKEDIDITVSDNTVQINAKCSKESTEEVYyrQER 89
                                      5788999******************99986531333 PP

>> GlcV_C_terminal  Glucose ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.3     0.001       2.2      29      59 ..      41      71 ..      32      72 .. 0.88
   2 ?    1.5   0.0      0.18   4.1e+02      18      36 ..     115     133 ..     112     134 .] 0.89

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.001
                                      TS---EEEEESS---TT-EEEEEEEGGG-EE CS
                   GlcV_C_terminal 29 dseeeivvnseepikaGeevllyvrknkiKi 59
                                      d++++i++n++ p    e++ + v +n + i
  gi|298675905|ref|YP_003727655.1| 41 DDDNNIIINADLPGVNKEDIDITVSDNTVQI 71
                                      6788**********************99987 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.18
                                       TTEEEEEEEETTS---EEE CS
                   GlcV_C_terminal  18 aGiFkitvspidseeeivv 36 
                                        G+ k+t+  ++ e++i+v
  gi|298675905|ref|YP_003727655.1| 115 NGVLKVTLPKLEKEHKITV 133
                                       6999**********99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 873.11
//
Query:       gi|298675906|ref|YP_003727656.1|  [L=165]
Description: heat shock protein Hsp20 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-23   83.3   2.7    1.3e-23   83.1   2.7    1.1  1  HSP20       Hsp20/alpha crystallin family
    1.4e-12   47.0   0.0    2.4e-12   46.2   0.0    1.4  1  ArsA_HSP20  HSP20-like domain found in ArsA
    2.2e-05   25.4   0.1    3.2e-05   24.8   0.1    1.2  1  CS          CS domain
     0.0025   17.9   0.5       0.74   10.0   0.4    2.2  2  FKBP26_C    FKBP26_C-terminal
     0.0069   16.5   0.8      0.011   15.9   0.8    1.3  1  GvpH        GvpH


Domain annotation for each model (and alignments):
>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.1   2.7   3.6e-27   1.3e-23       1     101 [.      65     164 ..      65     165 .] 0.93

  Alignments for each domain:
  == domain 1  score: 83.1 bits;  conditional E-value: 3.6e-27
                                       E--SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--....---TT----SS---EEEEEE--STTB-TTT-EEE CS
                             HSP20   1 dikeeeeefevkldvpglkkeelkvkvednrvlvkgehe..eeeedekglikerssrkFsrkftLPenvdadkvkas 75 
                                       d+kee+++  v++d+pg++ke+++++v+d++v ++++h+  +e e+e +++ker+++ Fsr++ LP  v ++  +a+
  gi|298675906|ref|YP_003727656.1|  65 DVKEEDNNVVVTADMPGVNKEDVDINVRDDMVEINAQHKeeSESEEEGFYRKERTYKAFSRAVPLPASVTEEGASAK 141
                                       689************************************87777888899*************************** PP

                                       EETTEEEEEEEBSS--..-------- CS
                             HSP20  76 lkdGvLtvtvpkkepekkkkerkiqi 101
                                       l+dGvL++t+pk + +   +e+ki +
  gi|298675906|ref|YP_003727656.1| 142 LEDGVLKITLPKASGK---EEKKITV 164
                                       ************9998...6677776 PP

>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.0   6.8e-16   2.4e-12       1      63 []      70     151 ..      70     151 .. 0.97

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 6.8e-16
                        ArsA_HSP20   1 ddeyvlkldLPfvdkeeidlsrsgdeLtIkig....................nfrRqitLPsvlarkevtsAkfedg 57 
                                       d+++v+++d+P+v+ke++d+  ++d   I+++                     f+R ++LP ++ ++ + sAk+edg
  gi|298675906|ref|YP_003727656.1|  70 DNNVVVTADMPGVNKEDVDINVRDDMVEINAQhkeeseseeegfyrkertykAFSRAVPLPASVTEEGA-SAKLEDG 145
                                       6899***************************************************************77.******* PP

                        ArsA_HSP20  58 vLeIrF 63 
                                       vL+I++
  gi|298675906|ref|YP_003727656.1| 146 VLKITL 151
                                       ****96 PP

>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.1     9e-09   3.2e-05       7      76 .]      68     153 ..      63     153 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 9e-09
                                       EETTEEEEEEE-TTCTTTTTCEEEEEETTEEEEEE.TSCEEEEECE..................BSS-BETTTEEEE CS
                                CS   7 QtldeVvvtiyvkkvnikkkdvkvefkerslkvki.gkeklliege..................LfgpIdpeesswt 64 
                                       +++++Vvvt  +++v  +k+dv+++   + ++++  +k ++  ++e                  L +++  e +s +
  gi|298675906|ref|YP_003727656.1|  68 EEDNNVVVTADMPGV--NKEDVDINVRDDMVEINAqHK-EESESEEegfyrkertykafsravpLPASVTEEGASAK 141
                                       7899**********9..*************99999555.444444469***************************** PP

                                       EETTEEEEEEEB CS
                                CS  65 ieskkveitLkK 76 
                                       +e+  ++itL K
  gi|298675906|ref|YP_003727656.1| 142 LEDGVLKITLPK 153
                                       **********98 PP

>> FKBP26_C  FKBP26_C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.4   0.00021      0.74       6      33 ..      72      99 ..      67     104 .. 0.86
   2 !    5.9   0.0    0.0039        14      19      37 ..     136     154 ..     129     156 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00021
                                      HHHHHHH-TT--..--EEEEETTEEEEE CS
                          FKBP26_C  6 kelIkryiPnidlekfkieiedktvtIe 33
                                        ++   +P +++e+++i+++d  v+I+
  gi|298675906|ref|YP_003727656.1| 72 NVVVTADMPGVNKEDVDINVRDDMVEIN 99
                                      5678889********************8 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0039
                                       .--EEEEETTEEEEE--TT CS
                          FKBP26_C  19 ekfkieiedktvtIelpee 37 
                                       e +  ++ed++++I+lp+ 
  gi|298675906|ref|YP_003727656.1| 136 EGASAKLEDGVLKITLPKA 154
                                       556789***********85 PP

>> GvpH  GvpH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.8     3e-06     0.011      99     124 ..      69      94 ..      58     106 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3e-06
                              GvpH  99 dsdelvvvadlpGvtdedvdvaletd 124
                                       + +++vv ad+pGv  edvd+ +  d
  gi|298675906|ref|YP_003727656.1|  69 EDNNVVVTADMPGVNKEDVDINVRDD 94 
                                       55678999**************9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       835  (0.0465726); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1055.91
//
Query:       gi|298675907|ref|YP_003727657.1|  [L=153]
Description: heat shock protein Hsp20 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-23   83.0   2.5    1.7e-23   82.7   2.5    1.1  1  HSP20       Hsp20/alpha crystallin family
    1.5e-12   46.8   0.0    2.3e-12   46.3   0.0    1.3  1  ArsA_HSP20  HSP20-like domain found in ArsA
     0.0019   19.2   0.2     0.0027   18.7   0.2    1.2  1  CS          CS domain
  ------ inclusion threshold ------
      0.044   13.9   0.9        9.1    6.5   0.0    2.2  2  FKBP26_C    FKBP26_C-terminal
       0.14   12.2   2.9       0.36   10.9   2.4    1.7  2  GvpH        GvpH


Domain annotation for each model (and alignments):
>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.7   2.5   4.7e-27   1.7e-23       1     101 [.      53     152 ..      53     153 .] 0.95

  Alignments for each domain:
  == domain 1  score: 82.7 bits;  conditional E-value: 4.7e-27
                                       E--SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--....---TT----SS---EEEEEE--STTB-TTT-EEE CS
                             HSP20   1 dikeeeeefevkldvpglkkeelkvkvednrvlvkgehe..eeeedekglikerssrkFsrkftLPenvdadkvkas 75 
                                       d+kee+++  v++d+pg++k+ ++++v+d+ + +++++   +e+e++ +++ker++++F r++ LP  vd+++ +a+
  gi|298675907|ref|YP_003727657.1|  53 DVKEEDNNVVVTADMPGIDKDGVDITVRDDILEISAKRSeeSETEEKGYYRKERTYSEFYRTVPLPVTVDEESASAK 129
                                       689**********************************9977778888899*************************** PP

                                       EETTEEEEEEEBSS--..-------- CS
                             HSP20  76 lkdGvLtvtvpkkepekkkkerkiqi 101
                                       l+dGvL+vt+pk+e+e   kerki +
  gi|298675907|ref|YP_003727657.1| 130 LEDGVLKVTLPKSEKE---KERKITV 152
                                       *************999...7899987 PP

>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.0   6.3e-16   2.3e-12       1      63 []      58     139 ..      58     139 .. 0.97

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 6.3e-16
                        ArsA_HSP20   1 ddeyvlkldLPfvdkeeidlsrsgdeLtIkig....................nfrRqitLPsvlarkevtsAkfedg 57 
                                       d+++v+++d+P++dk+ +d++ ++d L I+++                     f R+++LP +++++ + sAk+edg
  gi|298675907|ref|YP_003727657.1|  58 DNNVVVTADMPGIDKDGVDITVRDDILEISAKrseeseteekgyyrkertysEFYRTVPLPVTVDEESA-SAKLEDG 133
                                       6899***************************************************************77.******* PP

                        ArsA_HSP20  58 vLeIrF 63 
                                       vL++++
  gi|298675907|ref|YP_003727657.1| 134 VLKVTL 139
                                       ****96 PP

>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.2   7.6e-07    0.0027       7      76 .]      56     141 ..      51     141 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 7.6e-07
                                       EETTEEEEEEE-TTCTTTTTCEEEEEETTEEEEEE.TS.CEEEEECE..................BSS-BETTTEEE CS
                                CS   7 QtldeVvvtiyvkkvnikkkdvkvefkerslkvki.gk.eklliege..................LfgpIdpeessw 63 
                                       +++++Vvvt  ++++  +k+ v+++   + l+++  ++ e+++ e e                  L   +d e++s 
  gi|298675907|ref|YP_003727657.1|  56 EEDNNVVVTADMPGI--DKDGVDITVRDDILEISAkRSeESET-E-EkgyyrkertysefyrtvpLPVTVDEESASA 128
                                       7899**********9..66666666667779999944423332.3.258**************************** PP

                                       EEETTEEEEEEEB CS
                                CS  64 tieskkveitLkK 76 
                                       ++e+  +++tL K
  gi|298675907|ref|YP_003727657.1| 129 KLEDGVLKVTLPK 141
                                       ***********88 PP

>> FKBP26_C  FKBP26_C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1    0.0038        14       6      32 ..      60      86 ..      55      90 .. 0.86
   2 ?    6.5   0.0    0.0025       9.1      16      37 ..     121     142 ..     115     144 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0038
                                      HHHHHHH-TT--..--EEEEETTEEEE CS
                          FKBP26_C  6 kelIkryiPnidlekfkieiedktvtI 32
                                        ++   +P id++ ++i+++d +++I
  gi|298675907|ref|YP_003727657.1| 60 NVVVTADMPGIDKDGVDITVRDDILEI 86
                                      5678889***************99998 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0025
                                       --..--EEEEETTEEEEE--TT CS
                          FKBP26_C  16 idlekfkieiedktvtIelpee 37 
                                       +d e +  ++ed++++++lp++
  gi|298675907|ref|YP_003727657.1| 121 VDEESASAKLEDGVLKVTLPKS 142
                                       6889999*************96 PP

>> GvpH  GvpH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.4    0.0001      0.36      99     124 ..      57      82 ..      49      91 .. 0.82
   2 ?    5.3   0.1    0.0053        19     151     171 ..      76      96 ..      74      99 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0001
                              GvpH  99 dsdelvvvadlpGvtdedvdvaletd 124
                                       + +++vv ad+pG+  + vd+++  d
  gi|298675907|ref|YP_003727657.1|  57 EDNNVVVTADMPGIDKDGVDITVRDD 82 
                                       55678999*******999****9854 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0053
                              GvpH 151 dltlrnqvlelrlarsedsdg 171
                                       d+t+r+ +le+   rse+s+ 
  gi|298675907|ref|YP_003727657.1|  76 DITVRDDILEISAKRSEESET 96 
                                       89***************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1011.77
//
Query:       gi|298675908|ref|YP_003727658.1|  [L=255]
Description: F420-dependent oxidoreductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-62  210.9   0.2    2.3e-62  210.5   0.2    1.1  1  F420_ligase    F420-0:Gamma-glutamyl ligase
  ------ inclusion threshold ------
       0.21   10.3   0.0       0.25   10.0   0.0    1.1  1  Nucleoporin_C  Non-repetitive/WGA-negative nucleoporin C-term


Domain annotation for each model (and alignments):
>> F420_ligase  F420-0:Gamma-glutamyl ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.5   0.2   2.6e-66   2.3e-62       4     244 .]      11     220 ..      10     220 .. 0.98

  Alignments for each domain:
  == domain 1  score: 210.5 bits;  conditional E-value: 2.6e-66
                                       -----TT--HHHHHHCCS-.....--TT-EEEEEHHHHHHHTT-EEEGGGS---HHHHHHHHHH.TS-H........ CS
                       F420_ligase   4 tplikegddlaeivvesvkkagleledgDivvvtekvvakaegnyvsledikpsekAeeiaeklkvidpilSrnrfs 80 
                                       +plik+gddlaei+ ++++     l dgDi v+++++vak+eg++++ledi+pse+A +ia+k    +p        
  gi|298675908|ref|YP_003727658.1|  11 IPLIKKGDDLAEIISNNIE-----LDDGDIAVIASTIVAKSEGQVFKLEDINPSENAVRIANKN-RFNP-------- 73 
                                       79****************9.....****************************************.****........ PP

                                       ..........HHHHHHHHTEEEEEE-..S-EEEE.......TTS-EEEGGG-B-TTS-TTEEE---S-HHHHHHHHH CS
                       F420_ligase  81 liLkalakatrkvevvlsepsdevgn..qlidekytdevlvklGllgsnagidesnveegllkllPedpdksaeeik 155
                                                 ++v++vl+ +++++ +   +++e+         G ++ nagid+sn+e+g+++ lPe+pd+sae i 
  gi|298675908|ref|YP_003727658.1|  74 ----------AFVQAVLNRSRECLVEspIMLVET-------YNGNVCINAGIDDSNIEKGFILDLPENPDESAELIG 133
                                       ..........*************99998788888.......89********************************** PP

                                       HHHHHHHS---EEEE..EEEEEETTEECEEEEEEEEESB-SEEE-TT-B-TTS-B-S--EEEHHHHHHHHHHHHC-S CS
                       F420_ligase 156 kklkertgkdveVliygkDpegriweladpvvaigtsglealrdlrgkkdldgkelgttpravtdelgsladLvsGs 232
                                       ++lke tgk+++V+i  +D++gr+++ ++++va+g++ l+a++++rg++dl+g++l++t++av+de++  a+L++G+
  gi|298675908|ref|YP_003727658.1| 134 SRLKELTGKQLGVII--TDTNGRAFKTGQTGVAVGVYQLPAIKNWRGETDLYGHALEITEEAVADEIAGTANLLMGE 208
                                       ***************..************************************************************ PP

                                       SSS---EEEEES CS
                       F420_ligase 233 adegtPvvlvrg 244
                                       +d g Pv++vrg
  gi|298675908|ref|YP_003727658.1| 209 GDGGNPVIIVRG 220
                                       ***********8 PP

>> Nucleoporin_C  Non-repetitive/WGA-negative nucleoporin C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   2.8e-05      0.25     254     302 ..      38      86 ..      20     130 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 2.8e-05
                                       XXXXXXX.........XXXHHHHHHHHHHHHTSXHHHHHHHHHHHHH.. CS
                     Nucleoporin_C 254 lekaydearkeqilkLlsigkleeaielaekledfralvellleiankl 302
                                       ++++   + + q++kL +i+ +e+a+++a k ++ +a v+ +l+  +++
  gi|298675908|ref|YP_003727658.1|  38 IASTIVAKSEGQVFKLEDINPSENAVRIANKNRFNPAFVQAVLNRSREC 86 
                                       55555666889********************************988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1790.68
//
Query:       gi|298675909|ref|YP_003727659.1|  [L=155]
Description: CMP/dCMP deaminase zinc-binding protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-29   99.9   3.1    7.8e-29   99.5   3.1    1.2  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
    2.4e-22   79.2   0.9    3.1e-22   78.8   0.9    1.1  1  MafB19-deam      MafB19-like deaminase
     0.0039   17.1   2.0     0.0057   16.6   2.0    1.5  1  APOBEC_N         APOBEC-like N-terminal domain
     0.0049   16.9   1.2      0.011   15.8   0.5    1.7  2  Bd3614-deam      Bd3614-like deaminase
     0.0091   16.1   0.7       0.02   15.0   0.7    1.6  1  SNAD4            Secreted Novel AID/APOBEC-like Deaminase 4
  ------ inclusion threshold ------
      0.016   15.3   0.9      0.038   14.1   0.9    1.7  1  APOBEC2          APOBEC2
      0.017   15.3   0.4      0.022   14.9   0.4    1.3  1  APOBEC3          APOBEC3
      0.022   14.8   0.2      0.037   14.0   0.2    1.4  1  OTT_1508_deam    OTT_1508-like deaminase
      0.034   14.3   0.1      0.052   13.7   0.1    1.3  1  XOO_2897-deam    Xanthomonas XOO_2897-like deaminase
      0.071   13.2   1.5       0.12   12.4   1.5    1.4  1  NAD1             Novel AID APOBEC clade 1
      0.081   12.8   1.0        0.2   11.5   1.0    1.7  1  Inv-AAD          Invertebrate-AID/APOBEC-deaminase
        0.6   10.0   6.9       0.33   10.9   3.6    2.1  2  zf-C3HC4         Zinc finger, C3HC4 type (RING finger)


Domain annotation for each model (and alignments):
>> dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.5   3.1   5.2e-32   7.8e-29       3     100 ..      10     128 ..       8     129 .. 0.96

  Alignments for each domain:
  == domain 1  score: 99.5 bits;  conditional E-value: 5.2e-32
                                       HHHHHHHHHHHHHHHHHTTTSCSEEEEEEETTEEEEEEESBHHCCTG.......................TTB-HHH CS
                   dCMP_cyt_deam_1   3 kdekllelalkaakeaqkcsnfkVGavivkngeiistgyngepaggs.......................ktiHAEv 56 
                                        de++le+a  +ak+a +c + kVGaviv++++iistgyng p + +                       + +HAE+
  gi|298675909|ref|YP_003727659.1|  10 IDEYFLEIASVVAKRA-TCLRNKVGAVIVRDKRIISTGYNGAPSNLEhcldigcirqqyniesgtqhekcRAVHAEQ 85 
                                       689*************.**************************9999****************************** PP

                                       HHHHHHHHHTSSCETTEEEEEEE--BHHHHHHHHHHT-SEEEEE CS
                   dCMP_cyt_deam_1  57 nAilkaaknggsklegatlyvtlePCsmCakaiiqsgikkvvvg 100
                                       nAi++aa   g++ ++at+y+t++PC  Cak+ii+++ikkv++ 
  gi|298675909|ref|YP_003727659.1|  86 NAIIQAALH-GVSTDNATIYCTHQPCILCAKMIINANIKKVIYF 128
                                       *******98.778888**************************96 PP

>> MafB19-deam  MafB19-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8   0.9   2.1e-25   3.1e-22       4     107 ..      11     140 ..       9     154 .. 0.87

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 2.1e-25
                       MafB19-deam   4 ekafrkalaevekatkikedkigavivkdkkviargsn.......................ekelnakataHaEiaa 57 
                                       +++f ++++ v k++ +   k+gaviv dk++i +g+n                        ++ ++    HaE +a
  gi|298675909|ref|YP_003727659.1|  11 DEYFLEIASVVAKRATCLRNKVGAVIVRDKRIISTGYNgapsnlehcldigcirqqyniesGTQHEKCRAVHAEQNA 87 
                                       6799999**************************************************99875566677888****** PP

                       MafB19-deam  58 lqqAakklkskrlddatlyvtlepCdmCagaivqaglkklvygagnpks.....l 107
                                       + qAa  + s+  d+at+y t++pC  Ca++i++a++kk++y +++p+      l
  gi|298675909|ref|YP_003727659.1|  88 IIQAALHGVST--DNATIYCTHQPCILCAKMIINANIKKVIYFSDYPDDealkfL 140
                                       ****6666666..*********************************998775553 PP

>> APOBEC_N  APOBEC-like N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   2.0   3.8e-06    0.0057      20      95 ..      57     120 ..      21     150 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.8e-06
                                       EEEEEEEESSSEEEEEEEEEEE-..SSTBCHHHHHHHHHHHHT--.TTEEEEEEEEESS-S-HH....HHHHHHHH CS
                          APOBEC_N  20 cyeVkrssgkrklskkGvLrnqsgaaaskHaEelflediedqelrepkkkyeitlYvswsPChessdeCaeklaaf 95 
                                       c+ + + +++  + ++G  + +++     HaE+    +i +++l    +  + t+Y++ +PC      Ca+++ ++
  gi|298675909|ref|YP_003727659.1|  57 CLDIGCIRQQYNI-ESGT-QHEKCR--AVHAEQN---AIIQAALH-GVSTDNATIYCTHQPCIL----CAKMIINA 120
                                       4444444333333.5666.444544..79***98...44444555.6788899***********....****9876 PP

>> Bd3614-deam  Bd3614-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.4   2.1e+03      33      45 ..      79      91 ..      72     100 .. 0.72
   2 !   15.8   0.5   7.2e-06     0.011      76      99 ..      99     122 ..      91     137 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.4
                       Bd3614-deam 33 kvLHAEvnLlapl 45
                                      + +HAE n ++++
  gi|298675909|ref|YP_003727659.1| 79 RAVHAEQNAIIQA 91
                                      5689999977655 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 7.2e-06
                       Bd3614-deam  76 egarllvtlqcCkmCAalvvaaad 99 
                                       ++a+++ t+q+C +CA ++++a  
  gi|298675909|ref|YP_003727659.1|  99 DNATIYCTHQPCILCAKMIINANI 122
                                       579****************99865 PP

>> SNAD4  Secreted Novel AID/APOBEC-like Deaminase 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.7   1.3e-05      0.02      17      62 ..      75     119 ..      62     153 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-05
                             SNAD4  17 lknkke.haEllflekikseldpsqeyrvtwylswsPCaeCaekiae 62 
                                        ++++  haE + + +    l+   + + t+y +  PC  Ca+ i++
  gi|298675909|ref|YP_003727659.1|  75 HEKCRAvHAEQNAIIQA--ALHGVSTDNATIYCTHQPCILCAKMIIN 119
                                       2223337****999888..8999999999**************9987 PP

>> APOBEC2  APOBEC2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.9   2.5e-05     0.038      35      91 ..      66     119 ..      50     154 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.5e-05
                           APOBEC2  35 eleldrGvlenkekkcHaEllflskvkkkkleekkeykvtwyvswsPCaeCaeevae 91 
                                       + ++++G+ ++k + +HaE   + +     l+  ++ + t+y+++ PC  Ca+ + +
  gi|298675909|ref|YP_003727659.1|  66 QYNIESGTQHEKCRAVHAEQNAIIQAA---LHGVSTDNATIYCTHQPCILCAKMIIN 119
                                       344555555566556699987665544...455566689*************99875 PP

>> APOBEC3  APOBEC3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.4   1.5e-05     0.022      28      72 ..      78     119 ..      56     142 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.5e-05
                           APOBEC3  28 kekkHAEerfidkirslnldslkqykitcylswsPcpkCaeelve 72 
                                        +  HAE+ +i + +    +   + + t+y +  Pc  Ca+ +++
  gi|298675909|ref|YP_003727659.1|  78 CRAVHAEQNAIIQAAL---HGVSTDNATIYCTHQPCILCAKMIIN 119
                                       4567****99977665...55555569**************9997 PP

>> OTT_1508_deam  OTT_1508-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   2.5e-05     0.037       1      40 [.      81     118 ..      81     133 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.5e-05
                     OTT_1508_deam   1 vHAEvqlleyleeekdkekqepryIgcSKpaCylCelylr 40 
                                       vHAE + + + + ++ ++ +   +I c  ++C+lC  ++ 
  gi|298675909|ref|YP_003727659.1|  81 VHAEQNAIIQAALHGVSTDN--ATIYCTHQPCILCAKMII 118
                                       8***9999999998877554..9*************9985 PP

>> XOO_2897-deam  Xanthomonas XOO_2897-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   3.5e-05     0.052      23      73 ..      75     121 ..      64     139 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.5e-05
                     XOO_2897-deam  23 sskggvmHsEekllqqleeagvepakvlelytErepClpgneCakllkesl 73 
                                       + k +  H+E++ + q++ +gv+ ++   +y   +pC     Cak++ +  
  gi|298675909|ref|YP_003727659.1|  75 HEKCRAVHAEQNAIIQAALHGVSTDNA-TIYCTHQPC---ILCAKMIINAN 121
                                       5667778************9*998886.59*******...9***9985543 PP

>> NAD1  Novel AID APOBEC clade 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.5   8.1e-05      0.12      40      91 ..      71     119 ..      55     150 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.1e-05
                              NAD1  40 kGvleneskc...HaEllflnkikslklldpsqkykvtwylswSPCseCasklae 91 
                                        G  +++  c   HaE+  + +     l +  ++ + t+y+++ PC  Ca+ +++
  gi|298675909|ref|YP_003727659.1|  71 SGTQHEK--CravHAEQNAIIQAA---L-HGVSTDNATIYCTHQPCILCAKMIIN 119
                                       4544443..333499998865553...3.55577788**************9987 PP

>> Inv-AAD  Invertebrate-AID/APOBEC-deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.0   0.00014       0.2       4      64 ..      36     111 ..      33     128 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                           Inv-AAD   4 lvdadkneilatGytlel..................eGnthaeqccliklaekhevaeeklaevlpkntvlYttmep 62 
                                       +v   +++i++tGy                      e  t  e+c     ae++++ +  l+ v ++n+ +Y t  p
  gi|298675909|ref|YP_003727659.1|  36 IVR--DKRIISTGYNGAPsnlehcldigcirqqyniESGTQHEKCRA-VHAEQNAIIQAALHGVSTDNATIYCTHQP 109
                                       543..456888888644344455778888888888744455577665.569999999******************** PP

                           Inv-AAD  63 Cs 64 
                                       C 
  gi|298675909|ref|YP_003727659.1| 110 CI 111
                                       *6 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.4      0.69     1e+03      24      38 ..      61      78 ..      55      80 .. 0.66
   2 ?   10.9   3.6   0.00022      0.33      10      33 ..      99     120 ..      74     125 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.69
                                      HHHHHHHHC...TSSB-- CS
                          zf-C3HC4 24 kCirkilks...rkkvkC 38
                                       Cir+ ++     +++kC
  gi|298675909|ref|YP_003727659.1| 61 GCIRQQYNIesgTQHEKC 78
                                      588888776555555666 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00022
                                       S-E.E-TTS--B-CHHHHHHHHCT CS
                          zf-C3HC4  10 epnelleCkHsfCskCirkilksr 33 
                                       ++  ++ C+H+ C  C + i++  
  gi|298675909|ref|YP_003727659.1|  99 DN-ATIYCTHQPCILCAKMIIN-A 120
                                       22.69*************9999.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 898.24
//
Query:       gi|298675910|ref|YP_003727660.1|  [L=300]
Description: SecD/SecF/SecDF export membrane protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      7e-34  116.9  13.7    1.2e-33  116.1  13.7    1.3  1  SecD_SecF  Protein export membrane protein
      0.007   14.5  13.3     0.0097   14.0  13.3    1.1  1  Patched    Patched family
  ------ inclusion threshold ------
      0.019   14.4   0.0      0.041   13.4   0.0    1.6  1  Sec_GG     SecD/SecF GG Motif


Domain annotation for each model (and alignments):
>> SecD_SecF  Protein export membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.1  13.7   1.9e-37   1.2e-33       7     185 ..     106     288 ..     100     292 .. 0.87

  Alignments for each domain:
  == domain 1  score: 116.1 bits;  conditional E-value: 1.9e-37
                                       --SSS-EEEEEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-HHHHHHHHHH.HHHHHHHHHHHHHHTT--- CS
                         SecD_SecF   7 kevdkdaekisvetvgpsvskelaekavlallialvliliyvalrFewrvalaaiia.lvhDviitvgvlsllgiev 82 
                                        e+ ++++++++  +gp +++ l+++a++alli++++++ +v+l+F+  v++ ++ia +v+D++i+v+++ l+gie+
  gi|298675910|ref|YP_003727660.1| 106 DEISSKYSNVEIRQIGPVYGESLQRQALMALLISFIGMAAVVYLIFRTLVPSFVVIAsAVSDITIAVALMNLTGIEL 182
                                       5667789999*******************************************99999******************* PP

                                       -HHHHHHHHHHTTSSSHHHHHHHHHHHHHHHH--SS-HHHHHHHHHHHHHHHHHHTTHH.....HHHHHHHHHHHHT CS
                         SecD_SecF  83 dlatvaalLtiiGYSvndtvvvfdrvrenlrkkkratlkeiinlslnqtLtrtiltslt.....tllvvvallllgg 154
                                       +  tvaalL+iiGYSv++++++ +r+ ++ + + ++++++++ +++ +t t t+ ++++     t  ++++ ++   
  gi|298675910|ref|YP_003727660.1| 183 SFGTVAALLMIIGYSVDSDILLNNRLLKR-KGNLDEKITRAMHTGVIMTTT-TLSAVVMlylisTYTYLIIPWISQV 257
                                       ***************************99.667888888888888755544.4444443333367777777788888 PP

                                       TTTHHHHHHHHHHTSTTTTTHHHHHHHHHHH CS
                         SecD_SecF 155 dslkdfalallvGlivgtyssifiaspllll 185
                                       ++l+d++++l++Gl+++ ++++ +++++l +
  gi|298675910|ref|YP_003727660.1| 258 SILSDISVVLIFGLAADLLNTWVFNTGVLRW 288
                                       ***************************9987 PP

>> Patched  Patched family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0  13.3   1.6e-06    0.0097     655     781 ..     128     249 ..     124     271 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.6e-06
                           Patched 655 ilpstiqnivlallcmfvvallfipelitvlvitlsivsidigviGflslWgvdLDpismitiimsiGfsvdlsaHi 731
                                       ++ +++  ++++++ m++v  l+   l+ ++v++ s vs     + ++ l g++L   ++++++m iG+svd     
  gi|298675910|ref|YP_003727660.1| 128 LQRQALMALLISFIGMAAVVYLIFRTLVPSFVVIASAVSDITIAVALMNLTGIELSFGTVAALLMIIGYSVDSDILL 204
                                       5667788899*********999999999888888888884444557***************************9999 PP

                           Patched 732 ayafvrsekddakeRvvealealgwPvvqgalSTilgvlvLlfvdsymvq 781
                                         +  + ++ + +e++++a+ + g  +    + T+ +v++L+++ +y  +
  gi|298675910|ref|YP_003727660.1| 205 NNRLLKRKG-NLDEKITRAMHT-GVIMT---TTTLSAVVMLYLISTYTYL 249
                                       999999999.9*********87.55554...4566677888888888655 PP

>> Sec_GG  SecD/SecF GG Motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   6.9e-06     0.041       4      25 ..      43      64 ..      40      67 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.9e-06
                                      HHC--EE-TTTS-EEEEEEEE- CS
                            Sec_GG  4 ftkGlNLGlDFtGGthielqfd 25
                                       + +++LG +F GG++i + ++
  gi|298675910|ref|YP_003727660.1| 43 SGSPVRLGMEFEGGSMIAMTTE 64
                                      6789*************88876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       994  (0.0554409); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1965.49
//
Query:       gi|298675911|ref|YP_003727661.1|  [L=569]
Description: SecD/SecF/SecDF export membrane protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.1e-15   55.1   5.3    1.4e-14   54.0   5.3    1.5  1  SecD_SecF  Protein export membrane protein
     0.0045   16.0  10.2     0.0095   14.9  10.2    1.5  1  MMPL       MMPL family
  ------ inclusion threshold ------
      0.028   13.9   0.1        0.1   12.1   0.1    1.9  1  Sec_GG     SecD/SecF GG Motif
       0.11   12.7   2.2       0.22   11.7   2.2    1.4  1  Big_3_5    Bacterial Ig-like domain (group 3)


Domain annotation for each model (and alignments):
>> SecD_SecF  Protein export membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   5.3     3e-18   1.4e-14      12     177 ..     385     543 ..     377     555 .. 0.90

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 3e-18
                                       -EEEEEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-HHHHHHHHHH.HHHHHHHHHHHHHHTT----HHHH CS
                         SecD_SecF  12 daekisvetvgpsvskelaekavlallialvliliyvalrFewrvalaaiia.lvhDviitvgvlsllgievdlatv 87 
                                       ++e++    +++s+++++++ avla l+al++++ +++ +++ +  l  ++   ++ +++++g+ +++g ++dl ++
  gi|298675911|ref|YP_003727661.1| 385 NVEIVGSGHIDASLGEQFKTLAVLAGLFALIGVAGVIYNKYREKRILIPMVGiSFSEAVMILGFSAAIGWQLDLPSI 461
                                       56777778899******************************987666655553899********************* PP

                                       HHHHHHTTSSSHHHHHHHHHHHHHHHH--SS-HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHTTTTHHHHHHH CS
                         SecD_SecF  88 aalLtiiGYSvndtvvvfdrvrenlrkkkratlkeiinlslnqtLtrtiltslttllvvvallllggdslkdfalal 164
                                       a+++  iG  ++  v+++d v  +     + + ++i    +++ +   i + +tt++++  l++lg ++l++fal+ 
  gi|298675911|ref|YP_003727661.1| 462 AGIIAAIGTGIDHLVIITDEVLYE----GKLPPTKIYLSRITKAFGIIIGAAATTIIAMSPLMVLGFGALRGFALTT 534
                                       *********************988....4579999999*************************************** PP

                                       HHHTSTTTTTHHH CS
                         SecD_SecF 165 lvGlivgtyssif 177
                                       +vG+++g+    f
  gi|298675911|ref|YP_003727661.1| 535 IVGVLIGV----F 543
                                       *******7....4 PP

>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9  10.2   2.1e-06    0.0095     123     293 ..     384     547 ..     360     553 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.1e-06
                              MMPL 123 lkvevtGpaatladlrdasdrdlklievvtlvvilviLlivyrSlvaallplltvvvsllaalglvlilalllglel 199
                                       ++ve++G++ + a    ++++  +l+++++l  ++ +  ++y       +++ +v++s+  a+    il + ++++ 
  gi|298675911|ref|YP_003727661.1| 384 VNVEIVGSGHIDAS---LGEQFKTLAVLAGLFALIGVAGVIYNKYREKRILIPMVGISFSEAVM---ILGFSAAIGW 454
                                       66777777777666...66666677778888888888888888888999999999999877755...5889999999 PP

                              MMPL 200 stfvlgllvvl.liavGtDYallLvsRyreelaagedreeaviravastgkvvtaaGltvaiamlgLvvarlpvlaq 275
                                       +   ++++ ++ +i++G+D  ++++     e +  +++   +   ++++ + +++a++t +iam  L+v+ +++l++
  gi|298675911|ref|YP_003727661.1| 455 QLDLPSIAGIIaAIGTGIDHLVIITDEVLYEGKLPPTK--IYLSRITKAFGIIIGAAATTIIAMSPLMVLGFGALRG 529
                                       99999998776369******999998777777777777..7888999****************************** PP

                              MMPL 276 vGvaialGvlvdvlivlT 293
                                       ++++  +Gvl+ v+i++ 
  gi|298675911|ref|YP_003727661.1| 530 FALTTIVGVLIGVFIARP 547
                                       ***************985 PP

>> Sec_GG  SecD/SecF GG Motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   2.2e-05       0.1       8      25 ..      44      61 ..      44      63 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.2e-05
                                      -EE-TTTS-EEEEEEEE- CS
                            Sec_GG  8 lNLGlDFtGGthielqfd 25
                                      lN+GlD+ GG+ ++lq +
  gi|298675911|ref|YP_003727661.1| 44 LNYGLDLEGGSWLQLQLQ 61
                                      8**********8888875 PP

>> Big_3_5  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   2.2   4.9e-05      0.22      15      53 ..      88     129 ..      78     141 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.9e-05
                                       E--CCCC...TTS--EEEEEETTEE-SS-EE--TTSEEEEEE CS
                           Big_3_5  15 tVtaasg...gtptGtVtftdggttlgtavllsanGtAtltv 53 
                                       t+t ++     ++tGtVtf++++t   +++ l + G+A+++ 
  gi|298675911|ref|YP_003727661.1|  88 TITNVNIppdDSTTGTVTFVTNSTLTQSQINLLNIGQASINR 129
                                       334332122278**************9999888789999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (569 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 3885.17
//
Query:       gi|298675912|ref|YP_003727662.1|  [L=345]
Description: replication factor C [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.6e-16   58.3   0.0    1.7e-15   57.2   0.0    1.6  1  DNA_pol3_delta2  DNA polymerase III, delta subunit
    8.5e-14   51.7   0.3    8.5e-14   51.7   0.3    2.0  1  Rep_fac_C        Replication factor C C-terminal domain
      1e-09   38.9   0.0    3.1e-09   37.3   0.0    1.8  2  AAA              ATPase family associated with various cellul
    1.8e-07   31.1   0.4    5.1e-07   29.6   0.1    1.9  2  DNA_pol3_delta   DNA polymerase III, delta subunit
    5.7e-07   29.6   0.1    1.1e-06   28.7   0.1    1.5  1  Rad17            Rad17 P-loop domain
    1.5e-05   25.0   1.6    6.6e-05   23.0   0.2    2.5  2  AAA_14           AAA domain
    8.6e-05   23.0   0.0    0.00055   20.4   0.0    2.2  2  AAA_16           AAA ATPase domain
    0.00072   19.5   1.3     0.0013   18.7   0.3    1.9  2  ATPase_2         ATPase domain predominantly from Archaea
     0.0011   19.2   0.0      0.025   14.9   0.0    2.3  2  AAA_22           AAA domain
     0.0024   17.9   0.1      0.014   15.4   0.1    2.1  1  ResIII           Type III restriction enzyme, res subunit
     0.0034   16.6   0.1        0.2   10.8   0.0    3.0  4  TIP49            TIP49 P-loop domain
      0.008   16.5   0.0      0.022   15.1   0.0    1.8  1  AAA_assoc_2      AAA C-terminal domain
  ------ inclusion threshold ------
      0.016   15.0   0.0        1.2    8.9   0.0    2.5  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.045   13.5   0.0        1.1    9.0   0.0    2.3  2  CLP1_P           mRNA cleavage and polyadenylation factor CLP
       0.08   12.8   0.5       0.16   11.8   0.5    1.5  1  RE_MjaI          MjaI restriction endonuclease
      0.088   12.9   0.0       0.26   11.4   0.0    1.8  1  Sigma54_activ_2  Sigma-54 interaction domain
        0.1   12.1   0.3        1.1    8.7   0.0    2.4  3  AAA_7            P-loop containing dynein motor region
       0.13   12.6   0.1        0.5   10.8   0.0    2.0  2  RNA_helicase     RNA helicase


Domain annotation for each model (and alignments):
>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   0.0   1.7e-18   1.7e-15       4     159 ..      22     183 ..      19     187 .. 0.85

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 1.7e-18
                   DNA_pol3_delta2   4 ealkilskalksgrlahayLfeGdegigkkelalnlakallceeknetk.pcgecksckkieqgkhpDvivi....e 75 
                                         ++ l+k+lks++l h ++f+G+ ++gk ++a++la++l  ++ +++  + + ++   + + + + D  ++    +
  gi|298675912|ref|YP_003727662.1|  22 FSINTLKKILKSNNLPH-LIFQGPVNSGKSSTAFALANELYGKHYENNFtYFNASDFFDQGKRYLVRDRRFAriigT 97 
                                       56899***********9.79*********************999877655778888888888899999888877764 PP

                   DNA_pol3_delta2  76 teekersikldqir.e.lieelsrkpreskkkiiiiedaekmtksAaNalLktlEEPsenaifiLitsdtnklLkti 150
                                       ++ k+  +++ +i  + ++e +s +p+ s +kii i+da+ +++s++ al +++E   +   fiL t++++kl++++
  gi|298675912|ref|YP_003727662.1|  98 QDPKKIRMSVLSIFkQiINEYASMRPIDSDYKIIFIDDAQSLDSSSQQALRRIMEKYTSTCRFILSTTQPSKLIQPL 174
                                       455544666666643515566788999************************************************** PP

                   DNA_pol3_delta2 151 rSRcqelkf 159
                                       +SR   l f
  gi|298675912|ref|YP_003727662.1| 175 KSRGLRLFF 183
                                       ***988776 PP

>> Rep_fac_C  Replication factor C C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   0.3   8.5e-17   8.5e-14       1      86 [.     257     341 ..     257     343 .. 0.93

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 8.5e-17
                                       --HHHHHHHHHHHHHT-HHHHHHHHHHHHHHC---HHHHHHHHHHHGCCS...S-HHHHHHHHHHHHHHHHHHHCTH CS
                         Rep_fac_C   1 phpteieeileaclngdfeeaykklrellvekGysaediltqlhrvvkeq.eelpeaqkleilellgeiekrlveGa 76 
                                       p ++ i+++++a+ n+d+++a+k++++ll+e G+s+ +il+ l++v +e+ +  ++   ++++++++ei++ +++ a
  gi|298675912|ref|YP_003727662.1| 257 PEKENIDQLFSAAVNKDIDTARKIIDNLLIESGFSGYEILESLYDVAVESgD--NDLKVADMVKKIAEIDFHMLDAA 331
                                       66789********9***********************************854..466688899************** PP

                                       -HHHHHHHHH CS
                         Rep_fac_C  77 sehlqlsall 86 
                                       + ++ql+ l+
  gi|298675912|ref|YP_003727662.1| 332 NARIQLEYLI 341
                                       *******998 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0   3.2e-12   3.1e-09       2     123 ..      40     177 ..      39     185 .. 0.80
   2 ?   -2.3   0.0       5.8   5.7e+03      66      90 ..     261     285 ..     247     288 .. 0.75

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 3.2e-12
                                       EEESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSS..............STTHHHHHHHHHHHHHHHTS.. CS
                               AAA   2 llyGppGtGKTllakavakel.....gvefleisgsellsk..............yvgesekkirelfkeakeka.. 57 
                                       ++ Gp   GK+++a a+a+el     + +f  +++s+++++              +  + +kkir+ + ++ ++   
  gi|298675912|ref|YP_003727662.1|  40 IFQGPVNSGKSSTAFALANELygkhyENNFTYFNASDFFDQgkrylvrdrrfariIGTQDPKKIRMSVLSIFKQIin 116
                                       789*****************955444488**********8899***********84445555555544333332233 PP

                                       ..........TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTT CS
                               AAA  58 ..........kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgR 123
                                                 + +i+fiD++ +l +s+           +++L + ++++++   ++ +i+ t++p+kl ++l  +R
  gi|298675912|ref|YP_003727662.1| 117 eyasmrpidsDYKIIFIDDAQSLDSSS-----------QQALRRIMEKYTS---TCRFILSTTQPSKLIQPLK-SR 177
                                       334666888555***********9999...........*************...69****************9.66 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.8
                                       TGGGHHHHHTTCCCHHHHHHHHHHH CS
                               AAA  66 EidalaksrsgseseeeervvnqLl 90 
                                       +id+l+++  +++ + ++++++ Ll
  gi|298675912|ref|YP_003727662.1| 261 NIDQLFSAAVNKDIDTARKIIDNLL 285
                                       5777777776667777777777776 PP

>> DNA_pol3_delta  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.1   5.1e-10   5.1e-07      43     165 ..     112     225 ..     108     235 .. 0.91
   2 ?   -1.8   0.0       2.3   2.3e+03     128     151 ..     259     281 ..     237     291 .. 0.59

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 5.1e-10
                                       H.HTTTSTTT.TSSSSEEEEEEE--.....TT-S-TTHHHHHHHHTTT--SSEEEEEEES.S--HHHHHHHHHTTTE CS
                    DNA_pol3_delta  43 ddvleecetl.pffsdkrivvlknpklltkesklnekllkeLeeylsnlpedtlLiliapkklderkklvklLkkka 118
                                       +++++e+ ++ p  sd +i++++++     +s l+ + +++L ++++++  ++ +il ++    +  kl++ Lk++ 
  gi|298675912|ref|YP_003727662.1| 112 KQIINEYASMrPIDSDYKIIFIDDA-----QS-LDSSSQQALRRIMEKYTSTCRFILSTT----QPSKLIQPLKSRG 178
                                       568888888768899**********.....55.99999*******************999....4458********* PP

                                       EEEEE----TTTHHHHHHHHHHHTT-EE-HHHHHHHHHHHTT-HHHH CS
                    DNA_pol3_delta 119 tvveaktlkeeelkkwiqkraqelglkiekealelLlelvennlsai 165
                                         + ++ ++e+elk++iq +a+++ ++++++ le L + + +n+s++
  gi|298675912|ref|YP_003727662.1| 179 LRLFFTYVTEKELKNYIQPIAENEDIQFTEDGLEALWYVSRGNISRA 225
                                       *******************************************9976 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.3
                                       TTTHHHHHHHHHHHTT-EE-HHHH CS
                    DNA_pol3_delta 128 eeelkkwiqkraqelglkiekeal 151
                                       +e++ + +++ ++ + ++  ++ +
  gi|298675912|ref|YP_003727662.1| 259 KENIDQLFSAAVN-KDIDTARKII 281
                                       3333333333333.3444444444 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.1   1.1e-09   1.1e-06       7     162 ..       3     157 ..       1     167 [. 0.80

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.1e-09
                             Rad17   7 elWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklrewlnpvslk 83 
                                       + W  kykP+k++++a     i+ +k+ lk++ L++      +  GP   gks +   L+ el  k  e+ n + ++
  gi|298675912|ref|YP_003727662.1|   3 DIWTVKYKPKKLDDIAGNEFSINTLKKILKSNNLPHL-----IFQGPVNSGKSSTAFALANELYGKHYEN-NFTYFN 73 
                                       67********************************975.....99******************98877776.667777 PP

                             Rad17  84 epdnqksdfkgltekesrf.............lsqiesfkeleLkdakylklqklGddlrtdkklilvedlPnkfyr 147
                                        +d+  +  + l+  + rf             +s +  fk +     +y  ++     + +d k+i+++d  +    
  gi|298675912|ref|YP_003727662.1|  74 ASDFFDQGKRYLV-RDRRFariigtqdpkkirMSVLSIFKQI---INEYASMR----PIDSDYKIIFIDDAQSLDSS 142
                                       8888444433333.3334555588888887777777777777...56676666....7789**********999999 PP

                             Rad17 148 dsdalrevirkylrs 162
                                       + +alr ++ ky  +
  gi|298675912|ref|YP_003727662.1| 143 SQQALRRIMEKYTST 157
                                       99*******999765 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.2   6.6e-08   6.6e-05       5     105 ..      39     170 ..      35     180 .. 0.74
   2 ?   -0.6   0.1       1.3   1.3e+03      30      62 ..     228     258 ..     219     279 .. 0.69

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 6.6e-08
                            AAA_14   5 lvitGaRrvGKTtllkqlikell..vkkesilyinldderd....................kkladpe....kllel 55 
                                       l+ +G+  +GK+  ++ l++el+    ++++ y+n  d  d                          +    ++l++
  gi|298675912|ref|YP_003727662.1|  39 LIFQGPVNSGKSSTAFALANELYgkHYENNFTYFNASDFFDqgkrylvrdrrfariigtqdP-----KkirmSVLSI 110
                                       67899*******************9999*******999777677777777766666444330.....2444434444 PP

                            AAA_14  56 ileklke........ekktylflDEiqevpe.wekalkslvdeg.knldvivtGSnskll 105
                                       +++ ++e        ++ +++f+D +q +++  ++al+++++++ + +++i++  + + l
  gi|298675912|ref|YP_003727662.1| 111 FKQIINEyasmrpidSDYKIIFIDDAQSLDSsSQQALRRIMEKYtSTCRFILSTTQPSKL 170
                                       44443335566778778899********97637899******997889999987776665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.3
                            AAA_14  30 kesilyinldderdkkladpekllelileklke 62 
                                         +i y+  +de++  ++ + +++e++l+++ e
  gi|298675912|ref|YP_003727662.1| 228 TTQIAYLHSKDEDTN-ISLQ-DIYEAVLNEIPE 258
                                       578888888887774.3433.477777776533 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   5.5e-07   0.00055      21     161 ..      33     153 ..      21     163 .. 0.59
   2 ?   -1.6   0.0         3     3e+03      80      91 ..     229     240 ..     175     303 .. 0.55

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 5.5e-07
                            AAA_16  21 sgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde....ae..s 91 
                                       s+  + +++ G+  +GKss + +l+++l ++          ++          +++ +++++ q ++      +   
  gi|298675912|ref|YP_003727662.1|  33 SNNLPHLIFQGPVNSGKSSTAFALANELYGK--------HYEN--------NFTYFNASDFFDQGKRYlvrdRRfaR 93 
                                       4444899999***********8888755555........4444........22223332333333222000011001 PP

                            AAA_16  92 aeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqwadeaslqllaaLlrl 161
                                           ++++k++ ++           s + + +++ ++  + d++  ++++Dd+q +d++s+q+l+ +++ 
  gi|298675912|ref|YP_003727662.1|  94 IIGTQDPKKIRMSVL----------SIFKQIINEYASMRPIDSDYKIIFIDDAQSLDSSSQQALRRIMEK 153
                                       112244444555555..........667777777775555556679******************998876 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3
                            AAA_16  80 ellrqlldeaes 91 
                                       + ++ l++++e+
  gi|298675912|ref|YP_003727662.1| 229 TQIAYLHSKDED 240
                                       333333333222 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.3   1.3e-06    0.0013       7     134 ..      23     141 ..      20     224 .. 0.64
   2 ?   -0.2   0.1       0.8   7.9e+02      97     109 ..     236     248 ..     164     289 .. 0.44

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.3e-06
                          ATPase_2   7 elkeleeilerepneiyfiY.GpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal 82 
                                        ++ l++il++ +n + +i+ Gp +sGK++    ++++l  k+++  + +   +++ ++ +++      ++++++ +
  gi|298675912|ref|YP_003727662.1|  23 SINTLKKILKS-NNLPHLIFqGPVNSGKSSTAFALANELYGKHYENNFTYFNASDFFDQGKRY---LVRDRRFARII 95 
                                       699******99.677777777******************999998877666666666666666...46777888888 PP

                          ATPase_2  83 giavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlg 134
                                       g++ pk+    +l+  ++ ++++    ++ i  +    ii+iD++q l    
  gi|298675912|ref|YP_003727662.1|  96 GTQDPKKIRMSVLSIFKQIINEYA--SMRPIDSDY--KIIFIDDAQSLD--S 141
                                       777777655455332222222222..234444444..499*****9998..2 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.8
                          ATPase_2  97 eksklvfkaiell 109
                                       +k ++ + +++++
  gi|298675912|ref|YP_003727662.1| 236 SKDEDTNISLQDI 248
                                       2222222222222 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.5e-05     0.025       7     124 ..      38     159 ..      33     170 .. 0.68
   2 ?    1.9   0.0      0.25   2.5e+02      51      99 ..     241     283 ..     213     306 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.5e-05
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst...sskdl.lrellralglelkaerlsseell 79 
                                       +l+  G++ +GK+ ++  l+++l  +   ++ +  + +++++      ++  +  r+++r++g +  +  + +  +l
  gi|298675912|ref|YP_003727662.1|  38 HLIFQGPVNSGKSSTAFALANEL--YG--KHYENNFTYFNASDFFdqgKRYLVrDRRFARIIGTQDPK--KIRMSVL 108
                                       577889****************9..33..334444555555555555255555678999999998888..4444444 PP

                            AAA_22  80 ealeqalrarav.......ielliiDEaqhlr..seealeeLrsllnlsrkgvq 124
                                       + + q ++++a         +++ iD+aq l+  s++al+ +   ++  ++ ++
  gi|298675912|ref|YP_003727662.1| 109 SIFKQIINEYASmrpidsdYKIIFIDDAQSLDssSQQALRRI---MEKYTSTCR 159
                                       6666666666666667***************76446666655...443334444 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.25
                            AAA_22  51 t..sskdllrellralglelkaerlsseell.ealeqalraravielliiDE 99 
                                       t  s++d+++++l+++ +       + ++l+ +a+++ ++++++    iiD+
  gi|298675912|ref|YP_003727662.1| 241 TniSLQDIYEAVLNEIPE-----KENIDQLFsAAVNKDIDTARK----IIDN 283
                                       246888999999999985.....346789998999999999988....6665 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.4e-05     0.014      12     121 ..      24     146 ..      17     209 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.4e-05
                                       HHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHH......HHGGGGTGG.. CS
                            ResIII  12 ienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtl......eefkkflseay 82 
                                       i+ l++ lks++  +++++ +  +GK+ +a++l+ +l+ k++e++f  +  +    +q +      ++f++++ +++
  gi|298675912|ref|YP_003727662.1|  24 INTLKKILKSNNLPHLIFQGPVNSGKSSTAFALANELYGKHYENNFTYFNASD-FFDQGKrylvrdRRFARIIGTQD 99 
                                       66666777878999****************************99998876555.44444436688888888887776 PP

                                       ...........GEEEESSS-B--.......-SEEEEEHHHHHHTH... CS
                            ResIII  83 ke.........igkkvsgdkkkakekdstnkkilvttiqsldadseee 121
                                        +          ++++++   ++  +ds+ k i++   qsld++s+++
  gi|298675912|ref|YP_003727662.1| 100 PKkirmsvlsiFKQIINEYASMR-PIDSDYKIIFIDDAQSLDSSSQQA 146
                                       55665655555445555555555.566666666777788888888554 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0    0.0002       0.2      41      90 ..      29      79 ..      23      97 .. 0.84
   2 ?    1.8   0.0      0.11   1.1e+02     280     308 ..     129     157 ..      91     172 .. 0.76
   3 ?   -1.6   0.0       1.2   1.2e+03     211     266 ..     219     274 ..     212     289 .. 0.68
   4 ?   -1.9   0.0       1.5   1.5e+03     219     237 ..     318     336 ..     290     342 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0002
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXX CS
                             TIP49 41 elikekklaGravLlaGpsgtGktalaiaiskelg...edvpfvalsgsevys 90
                                      +++k+++l    ++++Gp  +Gk++ a a+++el     +  f+ +++s+++ 
  gi|298675912|ref|YP_003727662.1| 29 KILKSNNLP--HLIFQGPVNSGKSSTAFALANELYgkhYENNFTYFNASDFFD 79
                                      667777777..7899*******************64334678********996 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.11
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 280 GvlfiDevhmlDiecfsylnraleselaP 308
                                        ++fiD+++ lD  +   l r +e+  + 
  gi|298675912|ref|YP_003727662.1| 129 KIIFIDDAQSLDSSSQQALRRIMEKYTST 157
                                       689********************987664 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.2
                                       S---S----XXXXXXXXXXXX.XXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXX CS
                             TIP49 211 kGevekkkevvqevtLhdlDv.anarpqdllslllqllkskkteiteklreeinkkv 266
                                       +G++++  +++q   Lh  D  +n   qd+   +  +  ++k +i++     +nk +
  gi|298675912|ref|YP_003727662.1| 219 RGNISRALTTTQIAYLHSKDEdTNISLQDIYEAV-LNEIPEKENIDQLFSAAVNKDI 274
                                       5777777777777777777764566667776666.3455666677777666666655 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 1.5
                                       -XXXXXXXXXXXXXXXXXX CS
                             TIP49 219 evvqevtLhdlDvanarpq 237
                                       + + e+  h lD+anar q
  gi|298675912|ref|YP_003727662.1| 318 KKIAEIDFHMLDAANARIQ 336
                                       4466778899999999875 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.2e-05     0.022       2      56 ..     201     253 ..     200     266 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.2e-05
                                       XX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXX CS
                       AAA_assoc_2   2 ekklkleddalealaeladGDaRkaLnlLElaaeaaeakegkieitledleealq 56 
                                       ++++++++d leal  ++ G + +aL++ ++a   +++  ++++i+l+d+ ea+ 
  gi|298675912|ref|YP_003727662.1| 201 NEDIQFTEDGLEALWYVSRGNISRALTTTQIAYLHSKD--EDTNISLQDIYEAVL 253
                                       67899****************************99985..999999999998875 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0012       1.2       3      58 ..      11      61 ..       9      68 .. 0.80
   2 ?    3.4   0.0     0.059        59      83     112 ..     126     155 ..      88     172 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0012
                            RuvB_N  3 PksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelg 58
                                      Pk+l++  g e   ++lk +++     +++l h++++Gp   Gk++ a  +a+el 
  gi|298675912|ref|YP_003727662.1| 11 PKKLDDIAGNEFSINTLKKILK-----SNNLPHLIFQGPVNSGKSSTAFALANELY 61
                                      7777777777777777766654.....57899**********************96 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.059
                            RuvB_N  83 eekdvlfideihrlsraveevlysamedfr 112
                                       ++ +++fid+   l+++ ++ l   me ++
  gi|298675912|ref|YP_003727662.1| 126 SDYKIIFIDDAQSLDSSSQQALRRIMEKYT 155
                                       4568***********************986 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0011       1.1       1      24 [.      43      66 ..      43      74 .. 0.87
   2 ?    2.1   0.0      0.15   1.5e+02      61     128 ..      88     153 ..      78     190 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0011
                            CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrk 24
                                      Gp++sGKS+ a  L+N++  k+++
  gi|298675912|ref|YP_003727662.1| 43 GPVNSGKSSTAFALANELYGKHYE 66
                                      9****************9977764 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.15
                            CLP1_P  61 daplvyffGdtspsdnpslylalvkelareveekleenkkakasgliIntpGwvkglgaellleliea 128
                                       d+ +   +G++ p++    +l+++k++++e+ + +++  ++  +++ I+     ++   + l +++e 
  gi|298675912|ref|YP_003727662.1|  88 DRRFARIIGTQDPKKIRMSVLSIFKQIINEYAS-MRP-IDSDYKIIFIDDAQSLDSSSQQALRRIMEK 153
                                       56677889*****99999*************94.433.234455555555555555666666666555 PP

>> RE_MjaI  MjaI restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.5   0.00016      0.16      60     125 ..     262     327 ..     231     338 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00016
                           RE_MjaI  60 ieelkeeieevdeedvrkwvedLvinktfeGlkvqeailkklakelnvkyrlatdeeeskgiDgyi 125
                                       i++l ++  + d ++ rk + +L+i+  f+G+ + e +++   +  + ++++a+   + + iD+ +
  gi|298675912|ref|YP_003727662.1| 262 IDQLFSAAVNKDIDTARKIIDNLLIESGFSGYEILESLYDVAVESGDNDLKVADMVKKIAEIDFHM 327
                                       44533333334667899***********************************************87 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00026      0.26      69     109 ..     127     166 ..      91     179 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00026
                                       TTSEEEEEE-TT--HHHHHHHHHHHHHHTTTT-EEEEEEEE CS
                   Sigma54_activ_2  69 kggtLylkdiadlskaeqkeLlellakaeksslrlVstssk 109
                                       +  ++++ d ++l+++ q+ L  +++k   s +r++ ++ +
  gi|298675912|ref|YP_003727662.1| 127 DYKIIFIDDAQSLDSSSQQALRRIMEKY-TSTCRFILSTTQ 166
                                       55789******************99999.9******99976 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0011       1.1      28      72 ..      30      75 ..      20      98 .. 0.83
   2 ?   -1.6   0.1       1.6   1.6e+03      96     110 ..     123     137 ..     116     160 .. 0.79
   3 ?    0.1   0.0      0.51     5e+02     144     177 ..     153     186 ..     137     189 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0011
                             AAA_7 28 lllknkk.pvllvGptGtGKtviikdllkkldkekylsltinfsaq 72
                                       l +n+  ++++ Gp+ +GK++++  l ++l  ++y  ++  f+a+
  gi|298675912|ref|YP_003727662.1| 30 ILKSNNLpHLIFQGPVNSGKSSTAFALANELYGKHYENNFTYFNAS 75
                                      4444444267799***************************999986 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.6
                             AAA_7  96 PpggkklvvFvDDln 110
                                       P  +   ++F+DD  
  gi|298675912|ref|YP_003727662.1| 123 PIDSDYKIIFIDDAQ 137
                                       556666789999965 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.51
                             AAA_7 144 keikdvqlvaamgppgggrneitpRllrhfnvla 177
                                       k+   + ++ + ++p++  +++++R lr f+++ 
  gi|298675912|ref|YP_003727662.1| 153 KYTSTCRFILSTTQPSKLIQPLKSRGLRLFFTYV 186
                                       5566788999999999999*********999986 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0005       0.5       2      45 ..      40      79 ..      39      87 .. 0.73
   2 ?   -2.2   0.0       5.4   5.4e+03      51      76 ..     129     154 ..     125     168 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0005
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwd 45
                                      +++Gp + GKS++a  La++l +k     ++++ +  +++df+d
  gi|298675912|ref|YP_003727662.1| 40 IFQGPVNSGKSSTAFALANELYGKH---YENNFTY-FNASDFFD 79
                                      789*******************665...3334433.25566666 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.4
                      RNA_helicase  51 evvvidDfgqvkdeenpsdlaelirl 76 
                                       +++ idD  +  +++++     + + 
  gi|298675912|ref|YP_003727662.1| 129 KIIFIDDAQSLDSSSQQALRRIMEKY 154
                                       67778887766655333333333334 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 2100.67
//
Query:       gi|298675913|ref|YP_003727663.1|  [L=547]
Description: ELP3 family histone acetyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.1e-28   96.3   0.1    1.7e-27   95.2   0.1    1.6  1  Radical_SAM_C    Radical_SAM C-terminal domain
    8.3e-20   71.8   0.0    6.8e-19   68.9   0.0    2.3  2  Radical_SAM      Radical SAM superfamily
    3.4e-07   30.5   0.2    7.1e-07   29.5   0.2    1.5  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    9.9e-05   22.3   0.2    0.00023   21.1   0.2    1.6  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
     0.0071   16.7   0.9      0.018   15.4   0.9    1.7  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
       0.16   11.7   2.5       0.34   10.7   1.4    2.0  2  zinc_ribbon_5    zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Radical_SAM_C  Radical_SAM C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.2   0.1   5.7e-31   1.7e-27       1      81 [.     314     394 ..     314     395 .. 0.98

  Alignments for each domain:
  == domain 1  score: 95.2 bits;  conditional E-value: 5.7e-31
                     Radical_SAM_C   1 pdgvKlypllvikgTeLaelyksgeykplsleeyvdlvadilellppdirvhRltgdipkelliagpwhknlrelie 77 
                                       pd +K+yp+lv++gTeL++++++gey+ l+ +e+v+l+ d++++lp+++r++R+++dip++++ ag+ ++n+r+l++
  gi|298675913|ref|YP_003727663.1| 314 PDYLKIYPTLVTEGTELYKMWERGEYTALDDDEAVELISDVKAMLPKWVRLQRIQRDIPSQQIFAGVRKSNIRQLAR 390
                                       89*************************************************************************** PP

                     Radical_SAM_C  78 krlk 81 
                                       +rl+
  gi|298675913|ref|YP_003727663.1| 391 ERLQ 394
                                       9996 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.38   1.1e+03     121     149 ..      53      79 ..      43      88 .. 0.77
   2 !   68.9   0.0   2.3e-22   6.8e-19       7     158 ..      91     297 ..      85     303 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.38
                                       HTCTSHHHHHHHHHHHHHHTTSETEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 121 mnrghtfeevlealeklreagikrvvdri 149
                                       +   +t ee+++a+e+lr++ ++ +++++
  gi|298675913|ref|YP_003727663.1|  53 I-TVGTEEEQKQAMEILRRKPVR-TISGV 79 
                                       5.568899**********99888.55555 PP

  == domain 2  score: 68.9 bits;  conditional E-value: 2.3e-22
                                       ESS-.-TTTSCCTT...................HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS.TT CS
                                       xxxx.xxxxxxxxx...................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                       Radical_SAM   7 Cnlr.CsfCarpet...................vrregrgrslsveeileevkelkaekgvkevilgggeplly.pd 62 
                                       C+++ C+ C+ + +                    r+e++++ l + ++ ++ +++ ++ ++ e+i++gg+ + +  d
  gi|298675913|ref|YP_003727663.1|  91 CPHGvCVPCPGGPDsefnspqsymglepatrraIRNEYDPYKLVTSRLSQLKEIG-HDVDKAELIVMGGTFTSRsID 166
                                       78888*******99******************66666666666666666666666.899988888888888888789 PP

                                       HHHHHHHHHHTC....................................CCTEEEEEEECSSCHGHHHHHHHHHTT-S CS
                                       xxxxxxxxxxxx....................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  63 fvellerlakla....................................vpgiritvetngtlpdeeklerllelgvd 103
                                       ++e++ + + +a                                     ++i it+et + + +  +++r+lelg +
  gi|298675913|ref|YP_003727663.1| 167 YQEWYTKKCIEAmndfydtswrnnahtigktqpyipleevqkanenapIRNIGITFETRPDWTNTQHIDRILELGAT 243
                                       9999999999999999999999999999999999999999999995555555555555555555************* PP

                                       EEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 104 rvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGende 158
                                        v++g++++ d+ vl ++nrght+ ++ ea ++lr++g+k+ +++++ lpG   e
  gi|298675913|ref|YP_003727663.1| 244 KVEIGVQSVYDF-VLSRINRGHTVNDTAEANRMLRDSGLKVGFHMMPNLPGMGYE 297
                                       ************.**************************************9887 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.2   2.4e-10   7.1e-07      33     117 .]     435     535 ..     407     535 .. 0.75

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 2.4e-10
                                       C.EEEEEEET...TEEEEEEEEEEEET....TSTTEEEEEEEEE..........SGGG.TTSSHHHHHHHHHHHHHH CS
                    Acetyltransf_1  33 e.gllvaeed...geliGfisllkipd....ekggvayieslaV..........spey.rgkGlGsaLlealeerar 90 
                                       + ++++a ed   + liGf++l+        e  + a++++l+V            +y +++G+Gs+Lle++e++  
  gi|298675913|ref|YP_003727663.1| 435 GvEHFLAFEDvkqDILIGFLRLRFPARphrnELHDAAVVRELHVygsmapfgssENKYwQHRGYGSELLEQAEKISY 511
                                       245666777754445******99999955654455566666666*********955555****************** PP

                                       HTTESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  91 eegikkivlaveedndaairlYeklGF 117
                                       + g kk+ +    +  +a+++Y+k+G+
  gi|298675913|ref|YP_003727663.1| 512 NSGHKKLAI---ISGIGAREYYRKFGY 535
                                       ******977...69********88**8 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.2   7.8e-08   0.00023      61     109 ..     491     538 ..     490     544 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 7.8e-08
                   Acetyltransf_10  61 peyrgqGigkaLleaveeeaekdgikleltvnaspyavpfYeklGFkav 109
                                       + ++++G+g++Lle++e+   + g+k +l + +   a+++Y+k+G++  
  gi|298675913|ref|YP_003727663.1| 491 KYWQHRGYGSELLEQAEKISYNSGHK-KLAIISGIGAREYYRKFGYHLD 538
                                       569****************9788888.*******************976 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.9   6.2e-06     0.018      36      75 ..     493     536 ..     488     537 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.2e-06
                                       GTTSSHHHHHHHHTT.....SEEEEEEEEETHH.....HHHHHHHHTTEE CS
                    Acetyltransf_7  36 yrgkGiGraLleaae.....kgiileqlelnae.....kaikfYeklGFe 75 
                                       ++ +G+G++Lle ae     +g    + +l         a+++Y+k+G++
  gi|298675913|ref|YP_003727663.1| 493 WQHRGYGSELLEQAEkisynSG----HKKL--AiisgiGAREYYRKFGYH 536
                                       89*********95222344433....3334..1233458999******95 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.95   2.8e+03      13      22 ..     132     144 ..     131     148 .. 0.54
   2 ?   10.7   1.4   0.00011      0.34      14      34 ..     388     408 ..     386     409 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.95
                     zinc_ribbon_5  13 klvds...klKks 22 
                                       klv+s   +lK+ 
  gi|298675913|ref|YP_003727663.1| 132 KLVTSrlsQLKEI 144
                                       7888611155555 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00011
                     zinc_ribbon_5  14 lvdsklKksgkkVrCakCaev 34 
                                       l+ ++l + g+k rC +C+ev
  gi|298675913|ref|YP_003727663.1| 388 LARERLQEKGGKCRCIRCREV 408
                                       788899**************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (547 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 3572.75
//
Query:       gi|298675914|ref|YP_003727664.1|  [L=121]
Description: hypothetical protein Metev_2039 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.3e-06   25.4   0.1    1.7e-05   24.6   0.1    1.3  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0049   16.7   0.0     0.0092   15.8   0.0    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.014   13.5   0.8      0.014   13.5   0.8    1.2  1  Sporozoite_P67  Sporozoite P67 surface antigen
      0.024   14.5   1.9      0.024   14.5   1.9    1.6  2  HeLo            Prion-inhibition and propagation
        0.2   11.7   3.6        0.4   10.8   0.4    2.0  2  ssDNA_DBD       Non-canonical single-stranded DNA-binding dom


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.1   4.9e-09   1.7e-05      16      62 ..      67     113 ..      66     117 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 4.9e-09
                                       HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEE CS
                              TrmB  16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklY 62 
                                       +Llkl++ata+eiae+++ +r+   ++L++L++ G+ ++ ++ +++Y
  gi|298675914|ref|YP_003727664.1|  67 TLLKLEQATANEIAEITEKERAVESNYLNQLVKLGYAYKFRKGKQIY 113
                                       8**************************************99998888 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.6e-06    0.0092      11      47 .]      69     105 ..      65     105 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.6e-06
                                       HTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  11 LaegelcvcelaeelglsqstvShHLkkLreaGLVek 47 
                                       L  +++++ e+ae++++ ++  S +L++L ++G+ +k
  gi|298675914|ref|YP_003727664.1|  69 LKLEQATANEIAEITEKERAVESNYLNQLVKLGYAYK 105
                                       444889***************************9875 PP

>> Sporozoite_P67  Sporozoite P67 surface antigen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.8     4e-06     0.014     370     421 ..      58     110 ..      12     115 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4e-06
                    Sporozoite_P67 370 feevkslvetlinlklaiandlveiteklkkknknyvakl.kllkgeqfdtkk 421
                                        e +++   tl++l  a an++ eitek +  + ny  +l kl  + +f + k
  gi|298675914|ref|YP_003727664.1|  58 PEHLRTTATTLLKLEQATANEIAEITEKERAVESNYLNQLvKLGYAYKFRKGK 110
                                       588899999***************************99974666677777655 PP

>> HeLo  Prion-inhibition and propagation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.9   6.6e-06     0.024     152     202 ..       4      54 ..       3      57 .. 0.88
   2 ?   -1.5   0.1      0.51   1.8e+03      78      92 ..      75      89 ..      59     101 .. 0.50

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.6e-06
                                       E-SHHHHHHHHHHHHHHHHHHHHTTT-H..HHHHHHHHHHCTT--.SHHHH CS
                              HeLo 152 ivdkkkfeelvkdlkelvdsLeeLlpasqqqrvqrlvreeieqlskdveeL 202
                                       +++k+ f++  ++l e++d+L++Ll++++++ +++  +e i++ s dv  L
  gi|298675914|ref|YP_003727664.1|   4 MSEKDTFDQIFDKLNEINDKLDRLLQDTNNSNINEKDKESIISNSMDVMTL 54 
                                       789*************************99999999999987777777666 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.51
                                      HHHHHHHHHHHHHHH CS
                              HeLo 78 ileqiealleefekl 92
                                      + ++i ++ e+ +++
  gi|298675914|ref|YP_003727664.1| 75 TANEIAEITEKERAV 89
                                      233333444444444 PP

>> ssDNA_DBD  Non-canonical single-stranded DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.4   0.00011       0.4      49      98 ..       8      57 ..       3      62 .. 0.92
   2 ?    2.4   0.2     0.046   1.6e+02      62      98 ..      64     100 ..      58     103 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
                                      HHHGGGCHHHHH-------HHCCCHHHHHHHCCTTS--SSTHHHHHHHHH CS
                         ssDNA_DBD 49 eqfqleYqelleerkqeyallqekkeelleelqkeskieepvyllslisL 98
                                      + f+  + +l e +++ ++llq +++  ++e+ kes i +++ ++ lisL
  gi|298675914|ref|YP_003727664.1|  8 DTFDQIFDKLNEINDKLDRLLQDTNNSNINEKDKESIISNSMDVMTLISL 57
                                      57999999*99999999********************************9 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.046
                                       ------HHCCCHHHHHHHCCTTS--SSTHHHHHHHHH CS
                         ssDNA_DBD  62 rkqeyallqekkeelleelqkeskieepvyllslisL 98 
                                        + +   l++++ + + e+++  +  e++yl +l+ L
  gi|298675914|ref|YP_003727664.1|  64 TATTLLKLEQATANEIAEITEKERAVESNYLNQLVKL 100
                                       5556667788888888888888888899999999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1688  (0.0941491); expected 358.6 (0.02)
Passed bias filter:                      629  (0.0350828); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 750.09
//
Query:       gi|298675915|ref|YP_003727665.1|  [L=248]
Description: chromosome partitioning ATPase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.5e-18   64.9   0.2    1.6e-17   64.0   0.1    1.4  2  AAA_31       AAA domain
    1.3e-15   57.6   0.2    2.7e-13   49.9   0.2    2.9  1  ParA         NUBPL iron-transfer P-loop NTPase
    6.9e-11   42.3   0.0    1.2e-10   41.5   0.0    1.3  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    6.8e-07   28.8   0.0    1.1e-05   24.8   0.0    2.1  1  MipZ         ATPase MipZ
    0.00018   21.1   0.0    0.00046   19.7   0.0    1.7  1  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
     0.0015   17.9   0.0      0.032   13.5   0.0    2.1  2  VirC1        VirC1 protein
  ------ inclusion threshold ------
      0.012   14.8   0.0       0.11   11.7   0.0    2.2  2  ArsA_ATPase  Anion-transporting ATPase
      0.036   13.8   0.0      0.093   12.5   0.0    1.6  1  CLP1_P       mRNA cleavage and polyadenylation factor CLP1 P-
      0.047   13.1   0.3       0.41   10.1   0.0    2.0  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
       0.06   13.0   0.1          6    6.5   0.0    2.2  2  SRP54        SRP54-type protein, GTPase domain
       0.13   11.3   0.0       0.22   10.6   0.0    1.3  1  LpxK         Tetraacyldisaccharide-1-P 4'-kinase
       0.29   10.7   0.3       0.84    9.2   0.1    1.7  2  AAA_25       AAA domain


Domain annotation for each model (and alignments):
>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.0   0.1     1e-20   1.6e-17       4     169 ..       5     178 ..       3     189 .. 0.76
   2 ?   -3.2   0.0       4.5   6.8e+03      83     115 ..     208     241 ..     193     243 .. 0.60

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 1e-20
                            AAA_31   4 IaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQana.ttglgiekneiektlyevlieeknikeaii..ktk 77 
                                       +a+   KGG GKT  ++nla a a++g+ v l D+D  a + t+ ++i   +    +++vl ++++ik+a++  +++
  gi|298675915|ref|YP_003727665.1|   5 LAVHSSKGGTGKTSIAINLAGAYASEGYNVCLLDFDFKAPSfTNFFKI---KPRYWINDVLHDRCSIKDAVNdiSND 78 
                                       68999*******************************998651555555...55568****99********9932344 PP

                            AAA_31  78 venl.dlipssidLaeaeielvelekk..........eeilkellekvkdeYDyiiiDcpPsLglltenaLvasdsv 143
                                       +e+  +l ++   L + +ie ++  ++          ++ ++ + e +++  D++i+D++P +++  +na+++sd++
  gi|298675915|ref|YP_003727665.1|  79 FETSgHLYVG---LTDPDIESIREISSkdrdwqskalRYLIRAKKELIDSGIDIVILDTSPGIDYESINAVATSDYI 152
                                       4444455444...45555544433333244465433333345555667778************************** PP

                            AAA_31 144 iipvqaeayaleGleqllktieevkk 169
                                        ++v+ ++  ++  eq+++ i ++ +
  gi|298675915|ref|YP_003727665.1| 153 AVVVKQNYTCIKSTEQVIDGIYNILH 178
                                       ******************99987755 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.5
                            AAA_31  83 lipssidL.aeaeielvelekkeeilkellekvk 115
                                        ip  +d+ a+ +++l+ +++  +++++++ k++
  gi|298675915|ref|YP_003727665.1| 208 SIPCMCDItAKTDNDLIVFSEPDHVFSRAMYKIS 241
                                       4555555424566677777777777777776665 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   0.2   1.8e-16   2.7e-13       5     244 ..       4     243 ..       1     245 [. 0.71

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 1.8e-16
                              ParA   5 viavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgvee..................ekpeqsek 63 
                                       ++av S+KGG GK+++a+nlA a a++g++v+llD D   ps  ++++++                   +++   ++
  gi|298675915|ref|YP_003727665.1|   4 TLAVHSSKGGTGKTSIAINLAGAYASEGYNVCLLDFDFKAPSFTNFFKIKPrywindvlhdrcsikdavNDI---SN 77 
                                       689**********************************************99899988888777665433211...22 PP

                              ParA  64 kliPvea.....kgikvmSigfllesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqklp 135
                                        +    +      g++   i+ + e +++   w++  +  +i+   + ++ + +D++i+D+ PG   e++  + + +
  gi|298675915|ref|YP_003727665.1|  78 DFE---TsghlyVGLTDPDIESIREISSKDRDWQSKALRYLIRAKKELID-SGIDIVILDTSPGIDYESINAVATSD 150
                                       222...12122355555566666666667778999999888887655555.559**********9999998887764 PP

                              ParA 136 lagaviVttpqevaladvkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipld 212
                                          + +V   +   ++ +++ i+ + ++  k  +++eNm +          +++      k +++ ++p++ +ip  
  gi|298675915|ref|YP_003727665.1| 151 --YIAVVVKQNYTCIKSTEQVIDGIYNILHKNCAIIENMCH--------DGYLY-----PKNSKNQNTPVIESIPCM 212
                                       ..333444555667788899999999999999999999953........12333.....233455566666666666 PP

                              ParA 213 peireasdegkplvlkepeseaakaleeiaek 244
                                        +i+ ++d+   +v +ep++  ++a+ +i ++
  gi|298675915|ref|YP_003727665.1| 213 CDITAKTDNDL-IVFSEPDHVFSRAMYKISQN 243
                                       66666666665.56666666666666666666 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.0   8.2e-14   1.2e-10       1      71 [.       5      80 ..       5     124 .. 0.80

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 8.2e-14
                                      EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.....CCHCCCHHHHHHCHCHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxx RF
                              CbiA  1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.....dlkrllellealgkkka 71
                                      +a+ s kGG+GKT++a+nLa a a +g++V l+D+D  a++ + +++ +++        d+ +++  ++++++ ++
  gi|298675915|ref|YP_003727665.1|  5 LAVHSSKGGTGKTSIAINLAGAYASEGYNVCLLDFDFKAPSFTNFFKIKPRYWIndvlhDRCSIKDAVNDISNDFE 80
                                      58999************************************99777777665556677766666666666665544 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   7.6e-09   1.1e-05       5      50 ..       7      52 ..       3     163 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 7.6e-09
                                      E--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHHH CS
                              MipZ  5 lgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlarylen 50
                                      +   kGG+Gk+ +a+ +a a +++G +v  +d+d +  +++ +++ 
  gi|298675915|ref|YP_003727665.1|  7 VHSSKGGTGKTSIAINLAGAYASEGYNVCLLDFDFKAPSFTNFFKI 52
                                      5678**************************************9975 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   3.1e-07   0.00046       4     152 ..       5     163 ..       1     207 [. 0.71

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.1e-07
                          CBP_BcsQ   4 lalqGvRGGvGttsllaaLawalhelgesvlviDlspdnlLrl.hFnvdieqregwar.aeldgapwrqaaleyapg 78 
                                       la++  +GG+G+ts++  La a  + g++v ++D+  +    + +F+++    + w++  + d+  +++a+ ++ ++
  gi|298675915|ref|YP_003727665.1|   5 LAVHSSKGGTGKTSIAINLAGAYASEGYNVCLLDFDFKAPSFTnFFKIK---PRYWINdVLHDRCSIKDAVNDISND 78 
                                       7888999***************************987654444044444...5566651566788999999999999 PP

                          CBP_BcsQ  79 ldllP..fGelnveekenlqqlaekaeallaa.lkelk........eqyrwillDlpagasaltrellaladlvllv 144
                                       ++     +  l++ + e+++++ +k+  ++++ l+ l         +  + ++lD   g +    +++a++d    v
  gi|298675915|ref|YP_003727665.1|  79 FETSGhlYVGLTDPDIESIREISSKDRDWQSKaLRYLIrakkelidSGIDIVILDTSPGIDYESINAVATSDYIAVV 155
                                       88753225667778888888888888888754133332333334457889999999999999999999999999999 PP

                          CBP_BcsQ 145 vepdanch 152
                                       v+ +  c 
  gi|298675915|ref|YP_003727665.1| 156 VKQNYTCI 163
                                       99888884 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   2.1e-05     0.032       5      43 ..       6      44 ..       3      86 .. 0.82
   2 ?    2.3   0.0     0.057        85      69     111 ..     112     154 ..     105     186 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.1e-05
                             VirC1  5 tfcslkGGaGkttalmglcsalasdgkrvalfeadenrP 43
                                      ++ s kGG+Gkt+  + l +a as+g  v+l++ d   P
  gi|298675915|ref|YP_003727665.1|  6 AVHSSKGGTGKTSIAINLAGAYASEGYNVCLLDFDFKAP 44
                                      56799**************************99997766 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.057
                             VirC1  69 lplleaayeeaegeGfdyaladtrgGsselnntiiassdllli 111
                                       l  l  a +e   +G d+++ dt  G        +a+sd++ +
  gi|298675915|ref|YP_003727665.1| 112 LRYLIRAKKELIDSGIDIVILDTSPGIDYESINAVATSDYIAV 154
                                       6667788889999*************98777777899998865 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   7.1e-05      0.11       7      49 ..       9      52 ..       4     103 .. 0.88
   2 ?    1.0   0.0      0.13   1.9e+02     119     135 ..     121     137 ..     108     216 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.1e-05
                                      EESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S.TTTHHHHHHTS CS
                       ArsA_ATPase  7 gGKGGVGKttvsaatavklsekgkkvllistD.PAhslsDsfdq 49
                                      + KGG GKt+++  +a   + +g++v l+  D  A+s    f+ 
  gi|298675915|ref|YP_003727665.1|  9 SSKGGTGKTSIAINLAGAYASEGYNVCLLDFDfKAPSFTNFFKI 52
                                      77***************************999558888888876 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.13
                                       HHHCSSSSEEEEESBSC CS
                       ArsA_ATPase 119 yvkeeeydvvvlDtaPT 135
                                       ++ ++  d+v+lDt+P 
  gi|298675915|ref|YP_003727665.1| 121 ELIDSGIDIVILDTSPG 137
                                       44466779999999995 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.2e-05     0.093       4      38 ..      13      47 ..      11      50 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.2e-05
                            CLP1_P  4 dsGKSTlarlLlNyalrkgrkpvyvDlDvGqseis 38
                                       +GK+++a +L+   +++g++++++D D   ++++
  gi|298675915|ref|YP_003727665.1| 13 GTGKTSIAINLAGAYASEGYNVCLLDFDFKAPSFT 47
                                      59**************************9988886 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00027      0.41       7      65 ..      10      68 ..       4      84 .. 0.84
   2 ?    1.0   0.4      0.15   2.3e+02     143     244 ..     151     244 ..     143     248 .] 0.61

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00027
                         Fer4_NifH  7 GkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggkaqetvldtlrekgav 65
                                       kGG Gk+  + nl+ a a+ g  v ++  D ka s    ++ k    + d+l+++ + 
  gi|298675915|ref|YP_003727665.1| 10 SKGGTGKTSIAINLAGAYASEGYNVCLLDFDFKAPSFTNFFKIKPRYWINDVLHDRCSI 68
                                      59**********************************99999988888888877776554 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.15
                         Fer4_NifH 143 evyivtsgelmalyaanniakgiekyaksggvrlgGliinsrkvddereliekfaeelgtkvlevvPrdeivrkael 219
                                       ++ +v++ + +++ +  ++  gi +  +++      +i n   + ++  l  k  ++ +t+v+e +P   +++ +  
  gi|298675915|ref|YP_003727665.1| 151 YIAVVVKQNYTCIKSTEQVIDGIYNILHKN----CAIIEN---MCHDGYLYPKNSKNQNTPVIESIPCMCDITAKTD 220
                                       555555555555555666666655555443....345555...3345556677788899999999999999998887 PP

                         Fer4_NifH 220 rkktvieyapeseqakeyrelarki 244
                                       +  +v++  p++  +    +++++i
  gi|298675915|ref|YP_003727665.1| 221 NDLIVFSE-PDHVFSRAMYKISQNI 244
                                       77777654.3333344444555555 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.004         6      11      38 ..      13      40 ..       8      47 .. 0.92
   2 ?    4.4   0.0     0.016        25      64      92 ..     107     135 ..      95     167 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.004
                                      TSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54 11 GaGKTttlaKLaallkkegkkvllvaaD 38
                                      G+GKT+ +  La  + +eg++v+l   D
  gi|298675915|ref|YP_003727665.1| 13 GTGKTSIAINLAGAYASEGYNVCLLDFD 40
                                      9**********************98777 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.016
                                       TTSCHHHHHHHHHHHHHHTTSSEEEEEE- CS
                             SRP54  64 eeadpaavakeavekakeekidvvlvDTa 92 
                                        ++++  ++ +a ++  +++id+v++DT+
  gi|298675915|ref|YP_003727665.1| 107 WQSKALRYLIRAKKELIDSGIDIVILDTS 135
                                       4667888899999999************8 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00015      0.22      45      70 ..      11      36 ..       9      41 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00015
                                      SS-HSHHHHHHHHHHHTTTS..-EEE CS
                              LpxK 45 vGGtGKTPlvialvkllqarglkvgv 70
                                       GGtGKT+++i l+ +++++g++v  
  gi|298675915|ref|YP_003727665.1| 11 KGGTGKTSIAINLAGAYASEGYNVCL 36
                                      5*********************9976 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1   0.00056      0.84      38      59 ..       8      30 ..       4      41 .. 0.83
   2 ?   -1.4   0.0      0.95   1.4e+03     130     150 ..     116     134 ..      68     136 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00056
                            AAA_25 38 laGapgtGKttlaldlalava.t 59
                                          +gtGKt +a++la a+a +
  gi|298675915|ref|YP_003727665.1|  8 HSSKGGTGKTSIAINLAGAYAsE 30
                                      56789**************9944 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.95
                            AAA_25 130 vdaleaaieevegvrlvviDp 150
                                       ++a  + i++  g++ v++D+
  gi|298675915|ref|YP_003727665.1| 116 IRAKKELIDS--GIDIVILDT 134
                                       3333333333..599999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.36
# Mc/sec: 2051.59
//
Query:       gi|298675916|ref|YP_003727666.1|  [L=281]
Description: hypothetical protein Metev_2041 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0063   16.5  18.1      0.017   15.1  18.1    1.7  1  Trep_Strep  Hypothetical bacterial integral membrane protein 
  ------ inclusion threshold ------
        1.1    8.9   3.7        2.6    7.7   3.6    1.9  1  CPP1-like   Protein CHAPERONE-LIKE PROTEIN OF POR1-like


Domain annotation for each model (and alignments):
>> Trep_Strep  Hypothetical bacterial integral membrane protein (Trep_Strep)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1  18.1   1.9e-06     0.017      15     171 ..      71     227 ..      64     236 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.9e-06
                        Trep_Strep  15 fvvvfvvgm.lglispvlmlllpaivallagivymllvakvpkfgailimglllgllllltGhgwlvlllaiiggli 90 
                                       f +++ v   ++ is  l+ ++++++++l+++v  l++++ +k+   + ++l++  +++ tG  ++ l+++ i+ l 
  gi|298675916|ref|YP_003727666.1|  71 FGIMTHVVTdTSHISANLFHFATPVFVMLSSVVSGLVITRKEKPALYIFSSLIVLWYFFDTGREVFYLPWFHILVLF 147
                                       555666666688889999999999***************************************************** PP

                        Trep_Strep  91 aeliaksggykskkknilsyavfslwllgsilplll..mkdaylaslaergmsaeyidtlvalitpwmlvvllilti 165
                                       a +i+++  y + k + +s  +f+l ++gs++ +l+  m+ +++a    + +     ++ v++++ +  ++++ +++
  gi|298675916|ref|YP_003727666.1| 148 AFIIFYKR-Y-QHKLMHVSVYTFLLLFMGSLMAILTdhMAGNITAL-LMMDLPVRLFESSVTVYPIERAILAFGAAF 221
                                       *9999665.6.55679999999**********99995333334433.345666677777777776666666666666 PP

                        Trep_Strep 166 vgallG 171
                                       ++ +l 
  gi|298675916|ref|YP_003727666.1| 222 MMFILV 227
                                       655555 PP

>> CPP1-like  Protein CHAPERONE-LIKE PROTEIN OF POR1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   3.6   0.00029       2.6     102     170 ..     118     190 ..      85     230 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00029
                         CPP1-like 102 vflvlavltlvapaes...vpalllalglgasiyflnrKekklgravlltlvgLvvGlllGsllasllqvd.v 170
                                       +f  l+vl +++ +      ++   +l l+a i+f +r + kl+   ++t+++L++G l++ l   +  +  +
  gi|298675916|ref|YP_003727666.1| 118 IFSSLIVLWYFFDTGRevfYLPWFHILVLFAFIIFYKRYQHKLMHVSVYTFLLLFMGSLMAILTDHMAGNItA 190
                                       55556666555555555776777778889999****************************9988887755543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1144  (0.0638072); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 1919.36
//
Query:       gi|298675917|ref|YP_003727667.1|  [L=144]
Description: hypothetical protein Metev_2042 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-62  209.2   2.9    1.5e-62  209.0   2.9    1.0  1  DUF1699   Protein of unknown function (DUF1699)
  ------ inclusion threshold ------
      0.035   14.6   0.6      0.067   13.7   0.6    1.6  2  IZUMO     Izumo sperm-egg fusion, Ig domain-associated


Domain annotation for each model (and alignments):
>> DUF1699  Protein of unknown function (DUF1699)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.0   2.9   1.7e-66   1.5e-62       1     130 []       1     130 [.       1     130 [. 0.99

  Alignments for each domain:
  == domain 1  score: 209.0 bits;  conditional E-value: 1.7e-66
                           DUF1699   1 mkirvvsskeeietlnenekivHlafrpsntdilslvkkcpklkaiqvpeSykktlsksakmfleiqgiellegdvw 77 
                                       mkirvvsskeeie+++e+e+ivH+afrpsntdi+slv++cp+lka+++p+Syk+t+s+sakmfle+qgi+llegdvw
  gi|298675917|ref|YP_003727667.1|   1 MKIRVVSSKEEIENVDESEEIVHMAFRPSNTDIFSLVMRCPNLKALHIPSSYKRTISSSAKMFLEMQGISLLEGDVW 77 
                                       9**************************************************************************** PP

                           DUF1699  78 ghrkdineyyevseevierikelkseglseeeiaeklsketklspdlikfllk 130
                                       ghrkdiney+evs++v++rik+l++++ls+eei++k+ ket+ls+d+i+fl+k
  gi|298675917|ref|YP_003727667.1|  78 GHRKDINEYSEVSRNVYNRIKDLRENNLSDEEIVDKMVKETRLSTDFIQFLMK 130
                                       ***************************************************96 PP

>> IZUMO  Izumo sperm-egg fusion, Ig domain-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.28   2.5e+03      37      64 ..      19      46 ..       7      62 .. 0.77
   2 ?   13.7   0.6   7.5e-06     0.067      57     110 ..      82     135 ..      35     143 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.28
                                      HHHHTTT---SGGGGGGSEEEHHHHHHH CS
                             IZUMO 37 alledlsekelaenkflgvvdeetlekv 64
                                      +++ ++ +++++ + f  v+  ++l+ +
  gi|298675917|ref|YP_003727667.1| 19 EEIVHMAFRPSNTDIFSLVMRCPNLKAL 46
                                      5677888999999888888888887766 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 7.5e-06
                                       EHHHHHHHHHHHHHHHHHHHHS---HHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                             IZUMO  57 deetlekvasslkkelkrltdsdlkgelllkeLlwllqkqkkklkealkefqke 110
                                       d ++ ++v+ ++++ +k l++++l +e +++++++  +  ++ ++ ++k+ + +
  gi|298675917|ref|YP_003727667.1|  82 DINEYSEVSRNVYNRIKDLRENNLSDEEIVDKMVKETRLSTDFIQFLMKQQESQ 135
                                       66778899***************************9999999999888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       938  (0.0523175); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1009.20
//
Query:       gi|298675918|ref|YP_003727668.1|  [L=139]
Description: hypothetical protein Metev_2043 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-32  112.6   0.0    1.3e-32  112.4   0.0    1.0  1  UPF0047   Uncharacterised protein family UPF0047


Domain annotation for each model (and alignments):
>> UPF0047  Uncharacterised protein family UPF0047
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.4   0.0   7.1e-37   1.3e-32       1     115 []      20     136 ..      20     136 .. 0.96

  Alignments for each domain:
  == domain 1  score: 112.4 bits;  conditional E-value: 7.1e-37
                                       E-HHHHHHHHHHHT.SEEEEEEEESSSSEEEEEEESSSHHHHHHHHHHHHHHSTTT.T-GGG...TTS..THHHHHH CS
                           UPF0047   1 diteeveeavkesgvkeGlvlvfsrhttasltinEnadpdvqeDleealeklvpee.eYrhn...aegpdnadaHlk 73 
                                       +it++v++a+++sg+k+G+v+vf++ +ta++t  E+ +p++ +Dl+++lek++p++ eY+h+   ++g  n+ +H++
  gi|298675918|ref|YP_003727668.1|  20 NITSDVSSAIDNSGIKNGFVTVFVPGSTAAVTSMEY-EPGLISDLTSVLEKIAPSDvEYQHDkkwHDG--NGFSHVR 93 
                                       69*********************************9.*************************766667..******* PP

                                       HHHH-SEEEEEEETTEE---TTEEEEEEESS.-SSEEEEEEEE CS
                           UPF0047  74 ssllgssltipvedgklalGtwqsiylveld.gpreRkvvvqv 115
                                       +sllg+s+t+p+ + +la G wq+++l++ld +pr R++++q+
  gi|298675918|ref|YP_003727668.1|  94 ASLLGQSETFPIINSELANGPWQQVVLINLDnRPRYRELILQI 136
                                       *******************************667*****9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 986.49
//
Query:       gi|298675919|ref|YP_003727669.1|  [L=60]
Description: hypothetical protein Metev_2044 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.5   1.4       0.19   11.7   0.2    1.7  2  MNSV_P7B  Melon necrotic spot virus P7B protein


Domain annotation for each model (and alignments):
>> MNSV_P7B  Melon necrotic spot virus P7B protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   1.1e-05      0.19      15      37 ..      13      35 ..      10      39 .. 0.90
   2 ?    0.0   0.3     0.048   8.5e+02      22      31 ..      37      46 ..      34      50 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.1e-05
                          MNSV_P7B 15 GallilfisfvlfyitslspqGn 37
                                      G+++il is+vl   t l+p G 
  gi|298675919|ref|YP_003727669.1| 13 GSVVILIISLVLVEETGLTPEGY 35
                                      899*****************995 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.048
                          MNSV_P7B 22 isfvlfyits 31
                                      +sf++f++ s
  gi|298675919|ref|YP_003727669.1| 37 VSFLVFVLLS 46
                                      5666665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       815  (0.0454571); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 469.52
//
Query:       gi|298675920|ref|YP_003727670.1|  [L=163]
Description: hypothetical protein Metev_2045 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.048   13.6   0.0       0.11   12.4   0.0    1.6  1  Hjc       Archaeal holliday junction resolvase (hjc)


Domain annotation for each model (and alignments):
>> Hjc  Archaeal holliday junction resolvase (hjc)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.4e-06      0.11      36      81 ..      45     103 ..      33     116 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.4e-06
                                       EETTEEEEEEEEEESSS....EEEE.........EHHHHHHHHHHHHHHTCEEEEEEEE CS
                               Hjc  36 irgdvvlviEvKsskke....riyl.........kkeqvekllefarkaggelllavkl 81 
                                       +  d +l iE+Ks + +     +y          + +q++++ +f +k+g   +lav l
  gi|298675920|ref|YP_003727670.1|  45 LDPDYYLGIECKSISVDkganALYFtqhfttdknDMHQINRISDFLNKSGRTGFLAVEL 103
                                       5678899*****9664435446777*******9999**************999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 969.21
//
Query:       gi|298675921|ref|YP_003727671.1|  [L=471]
Description: phosphoesterase RecJ domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-16   60.0   0.2    7.7e-16   58.8   0.2    1.7  1  DHHA1     DHHA1 domain
  ------ inclusion threshold ------
      0.034   14.4   0.2      0.065   13.5   0.2    1.5  1  DHH       DHH family


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   0.2   8.6e-20   7.7e-16      25     138 .]     348     460 ..     323     460 .. 0.78

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 8.6e-20
                                       HHHHHHHHTCEEECTCEEEEEECHCCHHHHHHHHHHHHHHTHG..BT.TCEEEEEEEECTEEEEEEEESSH....SS CS
                             DHHA1  25 lkaeellekaeevkgvkvlvaevgeewdagalgiaadklkskl..kk.pvivfvakeegdkvkvsarskkd....gv 94 
                                       +k+    + ++++++ +++ + +  +++ +++gi+a++  +     + p+i f+ +++g  vkvsar ++d    g+
  gi|298675921|ref|YP_003727671.1| 348 VKE----NGVTKLNNLQYFDSGS--NIKETIVGIIAGMSTTVVgdRSyPIIGFADTDDG--VKVSARGTQDllrqGL 416
                                       333....3334444666666555..8888899999999888556655699999999997..**************** PP

                                       -HHHHHHHHHHHTTCCEEEETCEEEEEEEHCHHHHHHHHHHHHH CS
                             DHHA1  95 dagelakeaaaklgggGGGHdlAaGagipaekleealealeeai 138
                                       +++e++++ ++++gg GGGHd A+Ga+ip e   e++ +l+e+i
  gi|298675921|ref|YP_003727671.1| 417 NLSEAISKTCEEVGGVGGGHDIASGATIPHEVKGEFIYKLDEII 460
                                       *****************************999********9986 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   7.2e-06     0.065       6      60 ..      29     113 ..      26     157 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.2e-06
                                       -ECSSSHHHHHHHHHHHH.................................CECS--TCGGCGCCHHCCCSEEEEEE CS
                                       xxxxxxxxxxxxxxxxxx.................................xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH   6 ghknpDtDsigSaialan.................................llvDhneksqavegeakeeaedviii 49 
                                        + + D+D+++Sa  + +                                 +  D ++   +++   k+ + + +i 
  gi|298675921|ref|YP_003727671.1|  29 VVSHIDADGLTSAGIICKalqrrginystrflkqldesaiediasenhelvIFTDLGSGMIEEI---KSAGINAVIS 102
                                       47899*******6665555777777777777777777777776666666666777777766665...5********* PP

                                       E-S---SS--- CS
                                       xxxxxxxxxxx RF
                               DHH  50 DHHrlgeefet 60 
                                       DHH+++ + + 
  gi|298675921|ref|YP_003727671.1| 103 DHHQPKGDTKI 113
                                       ****9864333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 3139.43
//
Query:       gi|298675922|ref|YP_003727672.1|  [L=180]
Description: hypothetical protein Metev_2047 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-10   39.7   0.0    1.4e-09   38.0   0.0    1.7  1  Zn_protease      Putative ATP-dependant zinc protease
    3.6e-05   23.4   0.1    0.00023   20.8   0.1    1.9  1  Pep_deformylase  Polypeptide deformylase


Domain annotation for each model (and alignments):
>> Zn_protease  Putative ATP-dependant zinc protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.0   1.5e-13   1.4e-09      25     136 ..      36     136 ..      31     138 .. 0.92

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 1.5e-13
                       Zn_protease  25 altsSLsagdiesferdgekwVrfkev..rldekkaegvvlEakvlrivkirqsagdaekRpViklqlllgpeieki 99 
                                       +l++SL+ g+++s+ ++  +   +k+   ++de++  g++lE                      +++l+l+pei+++
  gi|298675922|ref|YP_003727672.1|  36 PLMLSLKSGGSWSYSTEALSVMSIKNPstQYDENEDTGYTLE----------------------DIYLFLNPEIINK 90 
                                       7899*************877766665566*************......................9************ PP

                       Zn_protease 100 evtL.........tdRsavkypvllgvralikakaaVDpsrkyirk 136
                                       ++++          +R +v++p++++v++ + + a+V p +k i +
  gi|298675922|ref|YP_003727672.1|  91 QGSVyrlekcskrGERVLVERPYRITVKGERIILAQVHPEKKKIEV 136
                                       ***********999****************************9976 PP

>> Pep_deformylase  Polypeptide deformylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   2.5e-08   0.00023      63     144 ..      60     161 ..      51     167 .. 0.63

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.5e-08
                                       CSS-ETT....S.......EEEEEEEEEEECSCEEECCEE--TTSTT--CEEEEESCEEEEEE-TTS-EEEEEEEH. CS
                   Pep_deformylase  63 pseeeeeeenke.......ltvliNPkitskseetitdeEgClSvpgieakVeRskrikvkyldltgkeveleaeg. 131
                                       ++ +++ +en++        ++++NP+i  ++++ +   E+C S  g ++ VeR+ ri+vk+  +   +v  e +  
  gi|298675922|ref|YP_003727672.1|  60 KNPSTQYDENEDtgytledIYLFLNPEI-INKQGSVYRLEKC-SKRGERVLVERPYRITVKGERIILAQVHPEKKKi 134
                                       444444444444457777899*******.778888999****.78999*************9764332222222221 PP

                                       ..............HHHHHHHHHHHHC CS
                   Pep_deformylase 132 ..............llArvlqHEiDhl 144
                                                       A  + HEi hl
  gi|298675922|ref|YP_003727672.1| 135 evsepeyksiiftgSPAYSAAHEIEHL 161
                                       222244333333335666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1244.87
//
Query:       gi|298675923|ref|YP_003727673.1|  [L=259]
Description: formate dehydrogenase family accessory protein FdhD [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.3e-51  173.9   0.0    5.7e-51  173.5   0.0    1.2  1  FdhD-NarQ  FdhD/NarQ family


Domain annotation for each model (and alignments):
>> FdhD-NarQ  FdhD/NarQ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.5   0.0   3.2e-55   5.7e-51       2     236 ..      29     248 ..      28     249 .. 0.88

  Alignments for each domain:
  == domain 1  score: 173.5 bits;  conditional E-value: 3.2e-55
                                       --EEEEEEETTEEEEEEEE-SSSHHHHHHHHHHHCTS--SGGGEEEEEEETTTEEEE-S.........--------- CS
                         FdhD-NarQ   2 eEepltivvngrelatlmatpadleelalGfllsegliesaediesievdedeasvavatrakaedkeerrtakrvv 78 
                                       +Ee++++++ng+++a+++++p d +ela+G++++eg+  + +di++i  ++++ ++++     ++d+ +  +    +
  gi|298675923|ref|YP_003727673.1|  29 REENVELYINGSKIASILTSPVDIKELAVGYVICEGIA-DFADITRIYESKNRIDLEIV----DVDS-KSLSY--EL 97 
                                       79**********************************65.599*****999997666655....3323.22222..34 PP

                                       ------.---...--H-----------EEGGGHHHHHHHHHTS-SHHHHHS--EEEEEEE.TTEEEEEEEESSHHHH CS
                         FdhD-NarQ  79 tsgCglcgkesleelletlelpesdlklsaeallrlmdalrekqelfketggvHaaalfdadgellavreDvGRHnA 155
                                       +s+  + g ++     +  ++ +sd+ +++e +++  + l+  + +++ t+g+H aal++++gel++ + D+GRHnA
  gi|298675923|ref|YP_003727673.1|  98 RSSGYM-GISAK----DYPTKIQSDVIFEPESIFSSQKFLE--SGIYRLTKGTHLAALINQNGELVTQAVDIGRHNA 167
                                       444434.55533....333444679**********999998..59******************************** PP

                                       HHHHHHHHHT.TSS-SSSEEEESS-B-HHHHHHHHHHT-SEEEESS-B-HHHHHHHHHHT-EEEEEEETTEEEEEE- CS
                         FdhD-NarQ 156 lDkviGaallegldlsdkilvvsgRlssemvqKaaragipvlvsvsaptslavelAeeagltlvgfvrgkrfnvYtg 232
                                       +DkviG+  l+gld+s+ +l+ +gR s  mv K+ r g+++lv++sap + ++e+A+++gl+lvgf+ ++r+ ++++
  gi|298675923|ref|YP_003727673.1| 168 IDKVIGYSRLAGLDVSSLYLLSTGRQSNGMVLKCSRSGVSLLVTKSAPLDSGIETAKKTGLCLVGFASESRMYIFAN 244
                                       ***************************************************************************** PP

                                       GGGE CS
                         FdhD-NarQ 233 aeRi 236
                                       +eRi
  gi|298675923|ref|YP_003727673.1| 245 PERI 248
                                       ***9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1643.31
//
Query:       gi|298675924|ref|YP_003727674.1|  [L=369]
Description: orc1/cdc6 family replication initiation protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-12   46.5   0.0    5.4e-09   36.7   0.0    3.0  2  AAA_16           AAA ATPase domain
    1.4e-06   28.4   0.0    2.4e-06   27.6   0.0    1.4  1  NACHT            NACHT domain
    3.4e-06   27.4   0.0    9.6e-06   25.9   0.0    1.7  1  AAA_22           AAA domain
    1.4e-05   25.5   0.0    3.4e-05   24.3   0.0    1.7  1  AAA              ATPase family associated with various cellul
    1.6e-05   24.8   0.0    3.1e-05   23.9   0.0    1.5  1  AAA_11           AAA domain
    2.7e-05   23.7   0.2     0.0028   17.2   0.0    3.0  4  AAA_7            P-loop containing dynein motor region
    4.1e-05   23.6   0.0    8.3e-05   22.6   0.0    1.5  1  ATPase_2         ATPase domain predominantly from Archaea
     0.0009   19.2   0.0     0.0032   17.4   0.0    2.0  1  Cdc6_C           CDC6, C terminal winged helix domain
     0.0021   17.8   0.0     0.0037   17.0   0.0    1.4  1  Sigma54_activat  Sigma-54 interaction domain
     0.0022   18.0   0.0     0.0056   16.6   0.0    1.7  1  NTPase_1         NTPase
      0.003   16.8   0.0     0.0044   16.2   0.0    1.3  1  NB-ARC           NB-ARC domain
      0.004   16.3   0.0     0.0059   15.7   0.0    1.3  1  T2SSE            Type II/IV secretion system protein
     0.0085   16.4   0.0      0.015   15.7   0.0    1.5  1  AAA_19           AAA domain
     0.0095   15.2   0.0      0.013   14.7   0.0    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
  ------ inclusion threshold ------
      0.019   14.2   0.0       0.14   11.3   0.0    2.1  2  DUF815           Protein of unknown function (DUF815)
      0.031   14.0   0.0      0.054   13.2   0.0    1.3  1  AAA_30           AAA domain
      0.035   14.1   0.0        0.1   12.6   0.0    1.7  2  ResIII           Type III restriction enzyme, res subunit
      0.037   13.4   0.1       0.11   11.8   0.0    1.8  2  ATPase           KaiC
      0.038   13.9   0.0      0.078   12.9   0.0    1.7  1  Rad17            Rad17 P-loop domain
      0.042   13.6   0.2       0.14   11.9   0.2    1.8  1  AAA_24           AAA domain
      0.046   14.1   0.0       0.13   12.6   0.0    1.8  1  RNA_helicase     RNA helicase
      0.048   12.5   0.0       0.59    8.9   0.0    2.1  2  AAA_35           AAA-like domain
      0.053   12.3   0.0          1    8.0   0.0    2.1  2  AAA_32           AAA domain
       0.09   12.5   0.1       0.34   10.7   0.0    1.9  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.095   12.0   0.0       0.25   10.6   0.0    1.6  2  Zeta_toxin       Zeta toxin
        0.1   13.2   0.0       0.36   11.4   0.0    2.0  1  AAA_18           AAA domain
       0.11   12.5   0.3       0.49   10.4   0.1    2.2  2  AAA_14           AAA domain
       0.12   12.1   2.5        3.1    7.5   0.1    2.9  3  IstB_IS21        IstB-like ATP binding protein
       0.12   12.5   0.0       0.58   10.3   0.0    2.1  2  AAA_33           AAA domain
       0.18   11.8   0.0       0.45   10.5   0.0    1.7  1  AAA_5            AAA domain (dynein-related subfamily)


Domain annotation for each model (and alignments):
>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.0     9e-12   5.4e-09       2     163 ..      28     164 ..      27     174 .. 0.71
   2 ?    0.9   0.0      0.89   5.3e+02     120     167 ..     248     297 ..     201     302 .. 0.73

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 9e-12
                            AAA_16   2 lvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekd..ggiflrgkcdqlesaipysalaqa 75 
                                       + +R+++l++++  l++v  g    ++l+sG++G+GK++ v ++++++++   ++ifl+ +c+        s+   +
  gi|298675924|ref|YP_003727674.1|  28 FAYRDNQLQAIKYSLKPVINGMNpINCLISGPPGTGKTTAVMKIYNEIQEYvdDVIFLKVNCQID------STRFAV 98 
                                       889****************99998899******************99888776699999999999......332233 PP

                            AAA_16  76 lareellrqlldeaesaeleawrekleealaavpelagaeasrllellkrll.allsrderplvlvlDdlqwade.. 149
                                       +   ++++q+        ++                   +  +++ l+ + + +l ++d+r lvl+lDd+  +    
  gi|298675924|ref|YP_003727674.1|  99 I-S-RIYKQVTGV----TPPT------------------SGVSFRSLFDKTMdSLVENDSR-LVLTLDDINYLFYen 150
                                       3.1.344444444....1111..................1247777788888555666555.888888888666633 PP

                            AAA_16 150 aslqllaaLlrlle 163
                                       +  +++++Llr+ e
  gi|298675924|ref|YP_003727674.1| 151 HADEVMYSLLRAHE 164
                                       44455777776665 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.89
                            AAA_16 120 lellkrllallsrderplvlvlDdlqwadeaslql.laaLlrlles..kpl 167
                                        +llkr+   ++++++   ++ Dd++ a e+s  l ++   r+l+s  k+l
  gi|298675924|ref|YP_003727674.1| 248 IDLLKRAGLNAEKRAS-RFVTRDDVDNAYESSKLLhICRSIRSLNSneKNL 297
                                       4556666666666666.9999999999999999888887777776654355 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0     4e-09   2.4e-06       3     123 ..      54     171 ..      53     222 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 4e-09
                                       EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-C........ CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfsqlpepaapvse........ 71 
                                       +++ G++G GKTt + k+  +++e        + v+fl++ +  +s+++  ++  + +q      p s         
  gi|298675924|ref|YP_003727674.1|  54 CLISGPPGTGKTTAVMKIYNEIQEYV------DDVIFLKVNCQIDSTRF-AVISRIYKQVTGVTPPTSGvsfrslfd 123
                                       689*******************9987......33677777777777777.777777777777777777777789*** PP

                                       .CHHHHCCSCCCEEEEEE-STT-SS-TCH.........HHHHHCT.TTTT--EE CS
                             NACHT  72 .vwavllelperlLlilDglDelvtdlgqkekqpvrtlLselirk.kllpeasl 123
                                         +  l+e+  rl+l+lD++++l  ++++      ++++ +l+r+ ++ p++++
  gi|298675924|ref|YP_003727674.1| 124 kTMDSLVENDSRLVLTLDDINYLFYENHA------DEVMYSLLRAhEHYPGVKI 171
                                       9***********************98888......9999999986246666665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   1.6e-08   9.6e-06       8     113 ..      54     161 ..      52     178 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.6e-08
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv..fvtlpsstsskdllrellralglelka.erlsseellea 81 
                                       +++ G++GtGKTt + ++ ++ +e+       ++v+  +v+++ ++++  + +++ ++++  +   ++ s + l+++
  gi|298675924|ref|YP_003727674.1|  54 CLISGPPGTGKTTAVMKIYNEIQEY------VDDVIflKVNCQIDSTRFAVISRIYKQVTGVTPPtSGVSFRSLFDK 124
                                       5899*****************9876......5555555********************9977777788899999966 PP

                            AAA_22  82 leqalraravielliiDEaqhlr...s..eealeeLr 113
                                         + l + + + +l +D++ +l+   +  e +++ Lr
  gi|298675924|ref|YP_003727674.1| 125 TMDSLVENDSRLVLTLDDINYLFyenHadEVMYSLLR 161
                                       66666666667**********9986525344444443 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   5.7e-08   3.4e-05       2      96 ..      55     166 ..      54     188 .. 0.65

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 5.7e-08
                                       EEESSTTSSHHHHHHHHHHHHT.....HEEEEEETTTCSSS...............STTHHHHHHHHHHHHHHHTS. CS
                               AAA   2 llyGppGtGKTllakavakelg.....vefleisgsellsk...............yvgesekkirelfkeakeka. 57 
                                       l++GppGtGKT+++  + +e++     v fl++++                     +   s  ++r lf++   +  
  gi|298675924|ref|YP_003727674.1|  55 LISGPPGTGKTTAVMKIYNEIQeyvddVIFLKVNCQIDS-TrfavisriykqvtgvTPPTSGVSFRSLFDKTMDSLv 130
                                       899*****************8533323334444443222.2345555666666666444455555555555433334 PP

                                       ...TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHT CS
                               AAA  58 ...kpsilfiDEidalaksrsgseseeeervvnqLlteldgv 96 
                                          +  +l +D+i  l+ ++      ++++v+  Ll++ + +
  gi|298675924|ref|YP_003727674.1| 131 endSRLVLTLDDINYLFYEN------HADEVMYSLLRAHEHY 166
                                       44356999999999999988......7777777777766655 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   5.2e-08   3.1e-05       3      43 ..      31      77 ..      29     113 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 5.2e-08
                            AAA_11  3 ndsqreaiksalsese......itliqGPPGtgKTktivellsqlls 43
                                       d q++aik  l+          +li+GPPGtgKT++++++++++ +
  gi|298675924|ref|YP_003727674.1| 31 RDNQLQAIKYSLKPVIngmnpiNCLISGPPGTGKTTAVMKIYNEIQE 77
                                      577888886666655555567789*******************9953 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   4.7e-06    0.0028      34      89 ..      52     105 ..      35     126 .. 0.75
   2 ?    3.1   0.0     0.099        59      99     132 ..     133     166 ..     128     169 .. 0.88
   3 ?   -2.6   0.0       5.4   3.3e+03      77     109 ..     208     241 ..     192     242 .. 0.65
   4 ?   -2.6   0.0       5.6   3.3e+03     124     137 ..     296     309 ..     293     316 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.7e-06
                             AAA_7  34 kpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklekr 89 
                                        ++l+ Gp GtGKt+ ++++ +++++    +++++++ q +++++   + s++ k+
  gi|298675924|ref|YP_003727674.1|  52 INCLISGPPGTGKTTAVMKIYNEIQEYVDDVIFLKVNCQIDSTRFA--VISRIYKQ 105
                                       5789********************9766677777777777776654..44555555 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.099
                             AAA_7  99 gkklvvFvDDlnmpakekygaqppiellRqlldy 132
                                         +lv+ +DD+n    e+  +     llR +  y
  gi|298675924|ref|YP_003727674.1| 133 DSRLVLTLDDINYLFYENHADEVMYSLLRAHEHY 166
                                       57899************************98665 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 5.4
                             AAA_7  77 qlqdiiesklekrrk.gvygPpggkklvvFvDDl 109
                                       +lq ii+++++     +v  +    ++v +vDDl
  gi|298675924|ref|YP_003727674.1| 208 ELQGIIDDRIKNAFYpDVIPAEVRDHIVQYVDDL 241
                                       5666666666555442344445677888899997 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 5.6
                             AAA_7 124 ellRqlldyggwYd 137
                                       +llR ++d++ +Y 
  gi|298675924|ref|YP_003727674.1| 296 NLLRLIVDNNNIYA 309
                                       699******99996 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   1.4e-07   8.3e-05      17     171 ..      47     184 ..      28     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.4e-07
                          ATPase_2  17 repnei.yfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekalgiavpkaele 92 
                                       ++ n+i  +i Gp g GKt+ +++i+++ +++ ++vi++    +++++++          +++ k++  ++p +++ 
  gi|298675924|ref|YP_003727674.1|  47 NGMNPInCLISGPPGTGKTTAVMKIYNEIQEYVDDVIFLKVNCQIDSTRFAVI-------SRIYKQVTGVTPPTSG- 115
                                       45555525899************************************999999.......5667777677777777. PP

                          ATPase_2  93 eilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnliesltkekhlcvviclsSegl 169
                                                  + +++ ++++ ++  ++++ +D++ +l   + n+a +++++Ll++ e+ +   ++ v+ + s  g 
  gi|298675924|ref|YP_003727674.1| 116 -------VSFRSLFDKTMDSLVENDSRLVLTLDDINYLF--YENHADEVMYSLLRAHEHYPGV-KIGVIAVVSDTGA 182
                                       .......5667889999999*******************..9999*************96654.5667777777777 PP

                          ATPase_2 170 fi 171
                                       f 
  gi|298675924|ref|YP_003727674.1| 183 FY 184
                                       65 PP

>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   5.3e-06    0.0032      39      83 ..     324     367 ..     303     368 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.3e-06
                                       HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSSCHHHHH CS
                            Cdc6_C  39 qrevsdllseLemlgileleksskGrregrtrkisLnvdpddvle 83 
                                        + +++l+++L + + +++e s++G+r gr+r+i+L+++p+d+l+
  gi|298675924|ref|YP_003727674.1| 324 YTYFYKLINRLYAARHIDVEFSGQGKR-GRSRLIKLKTSPSDILK 367
                                       57799********************96.**************985 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   6.1e-06    0.0037       6      59 ..      33      90 ..      28     109 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.1e-06
                                      HHHHHHHHHHHHHCTSS..S-EEEECSTTSSHHHHHHHHHHHSTT..TTS-EEEEETT CS
                   Sigma54_activat  6 ealkelleqikkvaktd..lsvlitGesGtGKellaraiheaskr..kekpfvavnca 59
                                      ++l+++  ++k v++    +++li G  GtGK++   +i+++ ++  ++  f++vnc 
  gi|298675924|ref|YP_003727674.1| 33 NQLQAIKYSLKPVINGMnpINCLISGPPGTGKTTAVMKIYNEIQEyvDDVIFLKVNCQ 90
                                      556666666666665433499********************766633678999****7 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   9.4e-06    0.0056       2      25 ..      54      77 ..      53      99 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9.4e-06
                                      EEEE--TTSSHHHHHHHHHHHH.. CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellks 25
                                       +i+GppG+GKtT v k+++++++
  gi|298675924|ref|YP_003727674.1| 54 CLISGPPGTGKTTAVMKIYNEIQE 77
                                      579*****************9975 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   7.4e-06    0.0044      22     112 ..      53     143 ..      31     158 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.4e-06
                                       EEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEEEEESXXHHHH..HHHXXHHHHHCCCTTSSSS-STTS...HH CS
                            NB-ARC  22 vvalvGmgGvGKttlakqilnksdevegrFdsvawvvvsktdksee..iletilkeLslseddleekeeves...lk 93 
                                          ++G +G GKtt + +i+n+   +++  d v+++ v  + +s +  ++ +i k++          +++ s   l 
  gi|298675924|ref|YP_003727674.1|  53 NCLISGPPGTGKTTAVMKIYNE---IQEYVDDVIFLKVNCQIDSTRfaVISRIYKQVTGV----TPPTSGVSfrsLF 122
                                       56799****************9...888899*******9999888622555566666544....4444444444477 PP

                                       HHHHHHCCCT..TEEEEEEEE CS
                            NB-ARC  94 rklvrlLltk..rfllvlDDV 112
                                       +k +  L +   r +l lDD+
  gi|298675924|ref|YP_003727674.1| 123 DKTMDSLVENdsRLVLTLDDI 143
                                       777777766658999999998 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0     1e-05    0.0059     110     160 ..      30      82 ..      14     100 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1e-05
                             T2SSE 110 aeealkekiaevlrkavr..erglilvsGgTgsGKttllyallkeinksderi 160
                                       ++ ++ ++i+  l+  ++  +  + l+sG+ g+GKtt +  + +ei+++ + +
  gi|298675924|ref|YP_003727674.1|  30 YRDNQLQAIKYSLKPVINgmNPINCLISGPPGTGKTTAVMKIYNEIQEYVDDV 82 
                                       4555555555555555542256789*********************9984444 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.5e-05     0.015       9      37 ..      50      78 ..      43     165 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.5e-05
                            AAA_19  9 kekvllvtaGpGtGKTrvlkhivallvel 37
                                      +  ++l+ ++pGtGKT+ +++i ++++e 
  gi|298675924|ref|YP_003727674.1| 50 NPINCLISGPPGTGKTTAVMKIYNEIQEY 78
                                      556799**************999988775 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   2.3e-05     0.013       4      40 ..      54      88 ..      51     110 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.3e-05
                           DUF2075  4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvN 40
                                      +l++G +GtGKt   +++ +e+  +e    +++l vN
  gi|298675924|ref|YP_003727674.1| 54 CLISGPPGTGKTTAVMKIYNEI--QEYVDDVIFLKVN 88
                                      9*********************..6666666666666 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00023      0.14      33     102 ..      31     106 ..       7     111 .. 0.79
   2 ?   -0.1   0.1       0.7   4.2e+02      96     124 ..     123     151 ..     119     162 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00023
                            DUF815  33 idkqkealventeqfleglpannvLLwGarGtGKSslvkallneyaeeg.....Lrl.ievekedlkelpklvell 102
                                        d+q +a++   +  ++g++  n L+ G  GtGK + v  + ne++e       L++  +++ ++ + ++++++++
  gi|298675924|ref|YP_003727674.1|  31 RDNQLQAIKYSLKPVINGMNPINCLISGPPGTGKTTAVMKIYNEIQEYVddvifLKVnCQIDSTRFAVISRIYKQV 106
                                       578889999999999**************************99998876555655554566666666666666665 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.7
                            DUF815  96 pklvellrerperfilfvDDLsFeeeeee 124
                                       +k ++ l e++ r++l +DD+ +   e++
  gi|298675924|ref|YP_003727674.1| 123 DKTMDSLVENDSRLVLTLDDINYLFYENH 151
                                       678899999***********987555554 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     9e-05     0.054      21      45 ..      54      78 ..      30      89 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9e-05
                            AAA_30 21 avltGpAGtGKttalkalreaweaa 45
                                      +++ Gp+GtGKtta+ ++ + +++ 
  gi|298675924|ref|YP_003727674.1| 54 CLISGPPGTGKTTAVMKIYNEIQEY 78
                                      5799*********988886655555 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00018       0.1       3      60 ..      29      85 ..      27     126 .. 0.82
   2 ?   -1.6   0.0         4   2.4e+03      56      82 ..     296     324 ..     279     350 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00018
                                      EE-HHHHHHHHHHT.......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEE CS
                            ResIII  3 elreyQeeaienlleklks.krdkrglikmaTGtGKTlvaaklierllkkgkeekflfl 60
                                        r+ Q +ai+  l+ + +  +  + li  + GtGKT   +k+  ++++    + ++fl
  gi|298675924|ref|YP_003727674.1| 29 AYRDNQLQAIKYSLKPVINgMNPINCLISGPPGTGKTTAVMKIYNEIQEYV--DDVIFL 85
                                      678999999999987776334445889*****************9999854..477776 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4
                                       -EE.EEESSHHHHHHHH.HHGGGGTGG.. CS
                            ResIII  56 kfl.flvprkslleqtl.eefkkflseay 82 
                                       + l ++v++++++   l + f + ++  y
  gi|298675924|ref|YP_003727674.1| 296 NLLrLIVDNNNIYAGNLyKSFHEATEHGY 324
                                       33337888888887655566666555544 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00018      0.11      22      56 ..      54      87 ..      45     106 .. 0.89
   2 ?   -3.3   0.0       7.8   4.7e+03     106     131 ..     229     254 ..     224     276 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                            ATPase 22 vlitGepGtGKtifalqFlikgaekygepgvfvtv 56
                                       li+G pGtGKt+ +++ +++ +++y + ++f  v
  gi|298675924|ref|YP_003727674.1| 54 CLISGPPGTGKTTAVMK-IYNEIQEYVDDVIFLKV 87
                                      69***********9998.99999999999999765 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 7.8
                            ATPase 106 elieelaeaikeikakrvviDsitgl 131
                                       e+ +++ +++++++  r+ iD ++  
  gi|298675924|ref|YP_003727674.1| 229 EVRDHIVQYVDDLGDLRIGIDLLKRA 254
                                       56677888999999999999988766 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00013     0.078      28      88 ..      35      90 ..      16     173 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00013
                             Rad17 28 ieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdnq 88
                                      ++++k  lk  +   ++    LisGP+G gk+t+v  +      +++e+++ v + + + q
  gi|298675924|ref|YP_003727674.1| 35 LQAIKYSLKPVINGMNPI-NCLISGPPGTGKTTAVMKIYN----EIQEYVDDVIFLKVNCQ 90
                                      555555555544433333.368***********9975544....34555555555555555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   0.00023      0.14       2      22 ..      51      71 ..      50     133 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00023
                            AAA_24  2 klkiliyGpsgiGKTtlakel 22
                                      ++++li Gp+g+GKTt + ++
  gi|298675924|ref|YP_003727674.1| 51 PINCLISGPPGTGKTTAVMKI 71
                                      5789************99888 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00022      0.13       2      26 ..      55      79 ..      54     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00022
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkkl 26
                                      +++Gp+g+GK+t++ ++ +++++ +
  gi|298675924|ref|YP_003727674.1| 55 LISGPPGTGKTTAVMKIYNEIQEYV 79
                                      799*************999998654 PP

>> AAA_35  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.22   1.3e+02      36      77 ..      56      98 ..      52     111 .. 0.65
   2 ?    8.9   0.0   0.00099      0.59     122     156 ..     129     163 ..     112     188 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.22
                            AAA_35 36 ikapkkmGKtSLlarilakakqqgyktvsldlq.ladkeilsd 77
                                      i +p  +GKt  +++i ++ ++    ++ l+++ ++d++ ++ 
  gi|298675924|ref|YP_003727674.1| 56 ISGPPGTGKTTAVMKIYNEIQEYVDDVIFLKVNcQIDSTRFAV 98
                                      5677777777777777777777766666666653344444555 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00099
                            AAA_35 122 LkeidkplvLaldevdrlfeypeiakdflslLRsw 156
                                       L e d+ lvL+ld+++ lf +++  + + slLR+ 
  gi|298675924|ref|YP_003727674.1| 129 LVENDSRLVLTLDDINYLFYENHADEVMYSLLRAH 163
                                       4566899************9999988899999974 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0017         1      31      56 ..      52      77 ..      20      87 .. 0.74
   2 ?    2.0   0.0      0.12        69     481     511 ..     248     278 ..     244     280 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0017
                            AAA_32 31 YNifvlGesgtGrttlvkrlleeiak 56
                                       N  ++G++gtG+tt+v+++ +ei++
  gi|298675924|ref|YP_003727674.1| 52 INCLISGPPGTGKTTAVMKIYNEIQE 77
                                      4789****************999864 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.12
                            AAA_32 481 adllrEAdywakkegaevveaehVekAleek 511
                                       +dll+ A   a+k++++ v++++V++A+e+ 
  gi|298675924|ref|YP_003727674.1| 248 IDLLKRAGLNAEKRASRFVTRDDVDNAYESS 278
                                       699************************9875 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00056      0.34      36      59 ..      54      77 ..      32      92 .. 0.89
   2 ?   -1.6   0.1       3.3   1.9e+03      83     108 ..     133     160 ..     113     166 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00056
                            RuvB_N 36 vllyGpPGlGkttlakiiakelgv 59
                                      +l++GpPG Gktt  + i +e++ 
  gi|298675924|ref|YP_003727674.1| 54 CLISGPPGTGKTTAVMKIYNEIQE 77
                                      699***********9999999875 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.3
                            RuvB_N  83 eekdvlfideihrl..sraveevlysam 108
                                       +++ vl +d+i  l  +++++ev+ys +
  gi|298675924|ref|YP_003727674.1| 133 DSRLVLTLDDINYLfyENHADEVMYSLL 160
                                       4556899999998744678999999865 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00042      0.25      12      43 ..      47      78 ..      37      88 .. 0.83
   2 ?   -3.6   0.0       9.3   5.5e+03     151     165 ..     263     277 ..     252     304 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00042
                        Zeta_toxin 12 sqerPklillgGqpGAGKselaellkdelerq 43
                                      ++ +P+  l++G pG GK+++  ++ +e++++
  gi|298675924|ref|YP_003727674.1| 47 NGMNPINCLISGPPGTGKTTAVMKIYNEIQEY 78
                                      5678999*******************999855 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 9.3
                        Zeta_toxin 151 gRlvpkeehdeafeg 165
                                        R+v  +  d+a+e 
  gi|298675924|ref|YP_003727674.1| 263 SRFVTRDDVDNAYES 277
                                       488888888888765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00061      0.36       2      24 ..      55      78 ..      54     138 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00061
                            AAA_18  2 lltGtpGvGKttlakeLskrl.gf 24
                                      l++G+pG+GKtt    + ++  ++
  gi|298675924|ref|YP_003727674.1| 55 LISGPPGTGKTTAVMKIYNEIqEY 78
                                      699*********988876665444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00082      0.49       5      43 ..      54      94 ..      50     171 .. 0.68
   2 ?   -2.0   0.0       5.9   3.5e+03      64      64 ..     310     310 ..     263     347 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00082
                            AAA_14  5 lvitGaRrvGKTtllkqlikell..vkkesilyinldderd 43
                                      ++i+G+  +GKTt + ++++e    v++  +l +n++ +++
  gi|298675924|ref|YP_003727674.1| 54 CLISGPPGTGKTTAVMKIYNEIQeyVDDVIFLKVNCQIDST 94
                                      589***************98877877777778888776555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.9
                            AAA_14  64 k 64 
                                       +
  gi|298675924|ref|YP_003727674.1| 310 G 310
                                       2 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1    0.0053       3.1      49      67 ..      53      71 ..      14      97 .. 0.79
   2 ?   -1.0   0.0       2.1   1.2e+03     114     142 ..      79     107 ..      77     130 .. 0.76
   3 ?    3.3   0.1       0.1        62     110     136 ..     136     162 ..     119     171 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0053
                         IstB_IS21 49 nivllGpsGvGKshlaial 67
                                      n+++ Gp+G+GK+   + +
  gi|298675924|ref|YP_003727674.1| 53 NCLISGPPGTGKTTAVMKI 71
                                      99**********9766555 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.1
                         IstB_IS21 114 lDdlgllpldqaeaellfeviekryerrs 142
                                       +Dd+ +l+++ +  ++ f vi++ y++ +
  gi|298675924|ref|YP_003727674.1|  79 VDDVIFLKVNCQIDSTRFAVISRIYKQVT 107
                                       79999999999999********9998654 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.1
                         IstB_IS21 110 dllilDdlgllpldqaeaellfeviek 136
                                        +l lDd+ +l  ++++ e+++ ++ +
  gi|298675924|ref|YP_003727674.1| 136 LVLTLDDINYLFYENHADEVMYSLLRA 162
                                       4899*******************9975 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       5.3   3.1e+03      74      98 ..       7      31 ..       3      35 .. 0.84
   2 ?   10.3   0.0   0.00096      0.58       4      22 ..      56      74 ..      54     108 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 5.3
                            AAA_33 74 ildatnlsrrerarflklarrlgvp 98
                                      ++d t+++++e  +++++ +++ ++
  gi|298675924|ref|YP_003727674.1|  7 LWDETLFKNAEVLEIDHIPEHFAYR 31
                                      68*********99999998887765 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00096
                            AAA_33  4 lvGlpGsGKstlaerllkk 22
                                      + G+pG+GK+t + +++++
  gi|298675924|ref|YP_003727674.1| 56 ISGPPGTGKTTAVMKIYNE 74
                                      67**********9998765 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00076      0.45       2      23 ..      54      75 ..      53     109 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00076
                                      EEEE--SSSSHHHHHHHGGGGB CS
                             AAA_5  2 vlLvGppGtgKselaerlaaal 23
                                       l+ GppGtgK++ ++++   +
  gi|298675924|ref|YP_003727674.1| 54 CLISGPPGTGKTTAVMKIYNEI 75
                                      5889***********9986655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 2397.68
//
Query:       gi|298675925|ref|YP_003727675.1|  [L=547]
Description: thermosome [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   2.4e-186  620.2  19.0   2.8e-186  619.9  19.0    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  619.9  19.0  1.6e-190  2.8e-186       1     488 [.      42     529 ..      42     531 .. 0.99

  Alignments for each domain:
  == domain 1  score: 619.9 bits;  conditional E-value: 1.6e-190
                                       HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHH CS
                        Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleea 77 
                                       +a++v+ttlGPkGmdKmlv+++g+vv+TnDGatil+e++iehPaak++ve+a++qd+evGDGTtt+++LageLl++a
  gi|298675925|ref|YP_003727675.1|  42 VANAVRTTLGPKGMDKMLVDSMGDVVITNDGATILREMDIEHPAAKMIVEVAKTQDDEVGDGTTTAAVLAGELLKKA 118
                                       689************************************************************************** PP

                                       HHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHH.HCH CS
                        Cpn60_TCP1  78 ekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAv.kli 153
                                       e++i++++hpt i +gy++a+eka e+L++ia +i     dr++Llk+a+t++++k  ++++ el+++vvdA  +++
  gi|298675925|ref|YP_003727675.1| 119 EEMIEQEIHPTIIASGYRMAAEKASEILNSIASDIT--ISDRDQLLKIAETAMTGKGAEASKMELAEIVVDAAtNVV 193
                                       *******************************55555..569********************************9999 PP

                                       CCCS.EECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCH CS
                        Cpn60_TCP1 154 eene.keldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdaee 229
                                       ee + k +d+++ikv+k+ gg+++dsel++G+++dk+ ++++mpkk+e ak++l++  +e ++ et+t++ ++++++
  gi|298675925|ref|YP_003727675.1| 194 EEGDgKYVDMDNIKVEKKVGGRIDDSELIQGMLIDKERVHSNMPKKVEGAKIALINEAIELKEAETETEISITSPDQ 270
                                       8888************************************************************************* PP

                                       HHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGGC CS
                        Cpn60_TCP1 230 leklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledltp 306
                                       l++++++eek+++++++k+i+sg+nvv+cqkgidd+a+hflak+gi a+rrvkk+d+e+la atG++++++le++++
  gi|298675925|ref|YP_003727675.1| 271 LQSFLDQEEKMIRDMVQKVIDSGANVVFCQKGIDDMAQHFLAKAGIYAVRRVKKSDMEKLALATGGRLITNLEEISE 347
                                       ***************************************************************************** PP

                                       GC-EEEEEEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHH CS
                        Cpn60_TCP1 307 eelGtakkveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelel 383
                                       ++lG+a+ vee+k+g +++t+i++++++k+++illrg t++v+d +era++dAl+vv  aiedek+v+GGG+ e+el
  gi|298675925|ref|YP_003727675.1| 348 NDLGKAEFVEEKKVGGDEMTFITGCDNPKAVSILLRGGTEHVVDNVERALHDALRVVGVAIEDEKLVAGGGSPEVEL 424
                                       ***************************************************************************** PP

                                       HHHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTXE CS
                        Cpn60_TCP1 384 akklkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveagvv 460
                                       a kl++y++s+sg+eql+++afa+A+ev+p+tLaeNaGldpi++l +lra h+kge+++g+dv sg++i+++++ v+
  gi|298675925|ref|YP_003727675.1| 425 AFKLHDYSTSLSGREQLSVKAFAEAIEVVPRTLAENAGLDPIDTLMDLRAHHEKGEVNAGLDVYSGNVINMWDKSVF 501
                                       ***************************************************************************** PP

                                       EEHHHHHHHHHHHHHHHHHHHCEEEEEX CS
                        Cpn60_TCP1 461 DplkvkrqalksAteaastiLrideiik 488
                                       +pl+vk+qa+++A+eaa +iLrid++i 
  gi|298675925|ref|YP_003727675.1| 502 EPLRVKTQAINAAAEAAVMILRIDDVIA 529
                                       ***************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (547 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.50
# Mc/sec: 3316.11
//
Query:       gi|298675926|ref|YP_003727676.1|  [L=57]
Description: hypothetical protein Metev_2051 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.2e-27   93.3   5.6    9.9e-27   93.2   5.6    1.0  1  DUF5350   Family of unknown function (DUF5350)


Domain annotation for each model (and alignments):
>> DUF5350  Family of unknown function (DUF5350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.2   5.6   5.5e-31   9.9e-27       1      57 []       1      57 []       1      57 [] 0.98

  Alignments for each domain:
  == domain 1  score: 93.2 bits;  conditional E-value: 5.5e-31
                           DUF5350  1 MGKTGsveWvkvKgrkgqirlVpkkegekkkpGPnQrfkssgkkrrikrrsakaivg 57
                                      MGKTGs++WvkvKgr+g++++Vp+++++k+++GP+Qrf s+g+krr+k+rs+kaiv+
  gi|298675926|ref|YP_003727676.1|  1 MGKTGSINWVKVKGRNGNTIKVPESRANKTHTGPAQRFASNGTKRRFKKRSSKAIVK 57
                                      ******************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 384.67
//
Query:       gi|298675927|ref|YP_003727677.1|  [L=388]
Description: major facilitator superfamily protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.9e-54  183.6  42.6    4.9e-54  183.6  42.6    1.6  1  MFS_1       Major Facilitator Superfamily
    1.7e-08   33.3  23.3    2.3e-08   32.9  23.3    1.1  1  MFS_3       Transmembrane secretion effector
    5.4e-08   31.8  41.4    2.4e-06   26.4  10.5    3.0  3  MFS_2       MFS/sugar transport protein
  ------ inclusion threshold ------
       0.32    9.8  27.8         49    2.6  25.4    2.2  1  MFS_1_like  MFS_1 like family
       0.41   10.5   2.7        0.4   10.5   0.3    2.1  2  KdpC        K+-transporting ATPase, c chain


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.6  42.6   1.4e-57   4.9e-54       1     353 []      12     346 ..      12     346 .. 0.94

  Alignments for each domain:
  == domain 1  score: 183.6 bits;  conditional E-value: 1.4e-57
                             MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgll 77 
                                       ++l+af+ +++ ++ gp+lp  + e l+ s  ++g++l++y++ +a+++++lG+++d++Gr++vl+ +ll+ ++++l
  gi|298675927|ref|YP_003727677.1|  12 ICLVAFFGMAGGALMGPVLP-SMVEPLNTSREAVGWVLGVYTFSTALFMVLLGVVTDKIGRKKVLIPCLLINGVAGL 87 
                                       57999***************.9*****************************************************88 PP

                             MFS_1  78 lllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravf 154
                                       ++ fa++l++llv+r++qG+g ++++p+++++i +++ + er  a+g +s+++++G++ +pl+gg la  lgW ++f
  gi|298675927|ref|YP_003727677.1|  88 AGYFAPNLPILLVFRFIQGIGIAGMMPVVMTMIGEIYDGLERVHAMGRMSMTTAVGSVSAPLIGGTLA-VLGWNYPF 163
                                       888999999***********************************************************.9******* PP

                             MFS_1 155 yilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllp 231
                                       ++ ++   laf+   + l+ +++ ++++++++     ++  + + +k ++        ++ ++ +ff ++++++++p
  gi|298675927|ref|YP_003727677.1| 164 LFYGLTIPLAFI---AMLVLPETMNANPEQRTG----FKNMFMS-LKDIRVAY----TVFLSFAVFFLLYTIVIYVP 228
                                       **********99...889999999999999999....8899999.89999888....9999999999********** PP

                             MFS_1 232 lylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlv 308
                                       ++l++ +g++    agl+l++ ++ ++i+a  a rl+ ++++  +++l+++++ll+ + + + +v+ s + + ++l+
  gi|298675927|ref|YP_003727677.1| 229 FILKDNFGFT-SQGAGLALGVQGASMVIFASQAKRLASKYPK--YTILGIGFTLLGIAVVGMSGVY-SIPQVFMLLL 301
                                       **********.688899999999999999**********999..9999999999999999999999.4444555778 PP

                             MFS_1 309 liGfglgfvfpsllalasdlappeeagtasglfntagslggalgp 353
                                       ++G+g+g+v+p+l++l++++ap++++g++++lfnt+ ++g   +p
  gi|298675927|ref|YP_003727677.1| 302 VFGVGFGMVQPLLNTLVTQVAPNDAMGSVVSLFNTMKYIGQTAAP 346
                                       89**************************************99887 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9  23.3   6.3e-12   2.3e-08      36     393 ..      33     379 ..       7     387 .. 0.85

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 6.3e-12
                             MFS_3  36 lmtdisasplmvAlvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltll 112
                                       ++  +++s  +v  v    t  + l+ +l G+++D++ r+kvl+    ll+ + +    la +   +  +ll++ ++
  gi|298675927|ref|YP_003727677.1|  33 MVEPLNTSREAVGWVLGVYTFSTALFMVLLGVVTDKIGRKKVLIPC--LLINGVAG---LAGYFAPNLPILLVFRFI 104
                                       6778999999********************************9875..44444333...3444445556899***** PP

                             MFS_3 113 igiGaalndPaWqAsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafavnalsylalivallrw 189
                                        giG a ++P    ++ge+ +  +   A+   s+   +     P +gG  +a++G  + f +  l+     +a+l  
  gi|298675927|ref|YP_003727677.1| 105 QGIGIAGMMPVVMTMIGEIYDGLERVHAMGRMSMTTAVGSVSAPLIGGT-LAVLGWNYPFLFYGLTIPLAFIAMLVL 180
                                       *********************999999************999******7.699999999999999998888888888 PP

                             MFS_3 190 krevrksslprEkllealraglRftaasreikavlvRaalFglsasavlaLLPlvardqldgdalvyGillgalGvG 266
                                         ++++++  r  + + +  +l+  ++     +v++  a+F+l   +++  +P++ +d+ +  +   G+ lg  G+ 
  gi|298675927|ref|YP_003727677.1| 181 PETMNANPEQRTGFKNMF-MSLKDIRV---AYTVFLSFAVFFLL-YTIVIYVPFILKDNFGFTSQGAGLALGVQGAS 252
                                       888888877666655444.34444443...34455555666665.4566689************************* PP

                             MFS_3 267 AilgalllsrLRerlsserlvllaavalAlvllslalasslwvavlvlllgGaaWitalstlnvavqlavPrWvvgR 343
                                        ++ a + +rL ++  + +++ + +  l + ++ ++ + s+ ++++ ll+ G ++ ++   ln+ v  + P+   g 
  gi|298675927|ref|YP_003727677.1| 253 MVIFASQAKRLASKYPKYTILGIGFTLLGIAVVGMSGVYSIPQVFMLLLVFGVGFGMVQPLLNTLVTQVAPNDAMGS 329
                                       ***************************************************************************** PP

                             MFS_3 344 alavYltvlaGglaaGsllWGavaealsvtlaLlaaaaalllaaaillll 393
                                       +++++ t+ + g +a  ++ G++  + ++ +  + ++++ + +a+ ++ +
  gi|298675927|ref|YP_003727677.1| 330 VVSLFNTMKYIGQTAAPAVLGVILLNSNLVVVFISSGLLGFCVAISTYIM 379
                                       ************************99999999888887766666665554 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4  10.5   6.8e-10   2.4e-06     227     347 ..       9     128 ..       3     159 .. 0.81
   2 !   12.5  19.1   1.1e-05     0.039     149     347 ..     137     326 ..     127     353 .. 0.73
   3 ?    0.5   2.1     0.047   1.7e+02     299     335 ..     344     379 ..     334     385 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 6.8e-10
                             MFS_2 227 lillllfllaalalgvlnglllYyltyvlg.ngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivl 302
                                       l +++l+ ++ +a+g l g +l  +   l+ +++a+ ++l+v t s++l+++l  +++ ++g+k++ + ++l+  v 
  gi|298675927|ref|YP_003727677.1|   9 LFIICLVAFFGMAGGALMGPVLPSMVEPLNtSREAVGWVLGVYTFSTALFMVLLGVVTDKIGRKKVLIPCLLINGVA 85 
                                       3344444444444455566666677777888999******************************************* PP

                             MFS_2 303 lvlvlllqpsnlllflvllviagfgvgvaallpwsmladvvDyge 347
                                       ++  +++   nl ++lv+ +i g+g+++++ +++ m+++++D  e
  gi|298675927|ref|YP_003727677.1|  86 GLAGYFA--PNLPILLVFRFIQGIGIAGMMPVVMTMIGEIYDGLE 128
                                       *******..89999***************************9876 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 1.1e-05
                             MFS_2 149 laailafllvlilgglkserkgylifaliialLmllgviivvlgtkervemrkkekteqkeklslleqlkevfrnra 225
                                        ++  ++ + + l g++++  g + + +++  L++ +++i++l+  e  ++        ++++ + +++ ++ + r 
  gi|298675927|ref|YP_003727677.1| 137 SMTTAVGSVSAPLIGGTLAVLG-WNYPFLFYGLTIPLAFIAMLVLPETMNA------NPEQRTGFKNMFMSLKDIRV 206
                                       4444444444444432222234.4455666677777788888999999555......77888888889988888888 PP

                             MFS_2 226 flillllfllaalalgvlnglllYyltyvlg.ngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltiv 301
                                       + +++l+f +++l l+     + + l++  g + + a + l+v  +s+++++  +++la+++ k+++  +g++l+ +
  gi|298675927|ref|YP_003727677.1| 207 AYTVFLSFAVFFL-LYTIVIYVPFILKDNFGfTSQGAGLALGVQGASMVIFASQAKRLASKYPKYTILGIGFTLLGI 282
                                       8999999888888.566667888889999997777788888888999999999999999999988877666666666 PP

                             MFS_2 302 llvlvlllqpsnlllflvllviagfgvgvaallpwsmladvvDyge 347
                                         v++  +  +++  +++ll+++g+g+g+ + l+  +++ v+  ++
  gi|298675927|ref|YP_003727677.1| 283 AVVGMSGV--YSIPQVFMLLLVFGVGFGMVQPLLNTLVTQVAPNDA 326
                                       66666666..***************************999986555 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.047
                             MFS_2 299 tivllvlvlllqpsnlllflvllviagfgvgvaallp 335
                                       +++  ++v+ll  snl+++++   + gf+v+++++++
  gi|298675927|ref|YP_003727677.1| 344 AAPAVLGVILL-NSNLVVVFISSGLLGFCVAISTYIM 379
                                       45677888888.9******************999987 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6  25.4     0.014        49      34     359 ..      42     339 ..      17     364 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.014
                        MFS_1_like  34 seigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlflsllfippskerqeesklevsvaqdvdaekt 110
                                       + +g ++ +  + + l   ++gv+ D++g+ kkv+i +ll++ v+ l+ +f p                       +
  gi|298675927|ref|YP_003727677.1|  42 EAVGWVLGVYTFSTALFMVLLGVVTDKIGR-KKVLIPCLLINGVAGLAGYFAP-----------------------N 94 
                                       566777777777777777777777777764.5566666666666666666555.......................4 PP

                        MFS_1_like 111 fwilfllvvlasfflaailvlldaatlkel......gedrkdyGrqrlfGsvGyaifafitGilidhysvnllpysa 181
                                       + il++++++  +     ++ + +++++++       e+ +  Gr  +  +vG  ++a+++G  +  +  n+     
  gi|298675927|ref|YP_003727677.1|  95 LPILLVFRFIQGI----GIAGMMPVVMTMIgeiydgLERVHAMGRMSMTTAVG-SVSAPLIGGTLAVLGWNY----- 161
                                       4455555544444....444455555666611134333444456666666666.456666666666666654..... PP

                        MFS_1_like 182 llyvlaallvisllvvlilnetekesklkvtkslqvllnilknpeviifllvalilgmswgiienFlflYL.kelga 257
                                        ++++ + + ++++ +l+l+et  ++  + t + ++++  lk+ +v++ ++  + + ++   i  ++   L ++ g+
  gi|298675927|ref|YP_003727677.1| 162 PFLFYGLTIPLAFIAMLVLPETMNANPEQRTGF-KNMFMSLKDIRVAYTVFLSFAVFFLLYTIVIYVPFILkDNFGF 237
                                       455555556677777777777777777777765.5588889999998777776666666667777777778799*** PP

                        MFS_1_like 258 sntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaa 334
                                       ++  +G ++ ++ ++ +++   a++l  k+   ++l i++++  +  ++++ + +   v+++ +  g+ fg++   +
  gi|298675927|ref|YP_003727677.1| 238 TSQGAGLALGVQGASMVIFASQAKRLASKYPKYTILGIGFTLLGIAVVGMSGVYSIPQVFMLLLVFGVGFGMVQPLL 314
                                       ***************************************************************************** PP

                        MFS_1_like 335 veyvskiapksleatgqgllsglyf 359
                                        + v ++ap+ + + + +l++++ +
  gi|298675927|ref|YP_003727677.1| 315 NTLVTQVAPNDAMGSVVSLFNTMKY 339
                                       *******************999865 PP

>> KdpC  K+-transporting ATPase, c chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.51   1.8e+03      16      39 ..     110     136 ..      93     159 .. 0.61
   2 ?   10.5   0.3   0.00011       0.4       5      42 ..     297     333 ..     293     347 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.51
                                       HTHHHHHHHHHHHH...H-HHHHTT-E CS
                              KdpC  16 gliYplavtgiaql...lfpeqAnGsl 39 
                                       + + p+++t+i+++   l + +A G +
  gi|298675927|ref|YP_003727677.1| 110 AGMMPVVMTMIGEIydgLERVHAMGRM 136
                                       347799999999884444555666665 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHHHTHHHHHHHHHHHHH-HHHHTT-EEE. CS
                              KdpC   5 lrlllvltvllgliYplavtgiaqllfpeqAnGsliea 42 
                                       ++lllv+ v +g++ pl+ t+++q++ p+ A Gs+++ 
  gi|298675927|ref|YP_003727677.1| 297 FMLLLVFGVGFGMVQPLLNTLVTQVA-PNDAMGSVVSL 333
                                       67899999****************96.********983 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.25s 00:00:00.88 Elapsed: 00:00:00.42
# Mc/sec: 2762.40
//
Query:       gi|298675928|ref|YP_003727678.1|  [L=367]
Description: peptidase M50 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.8e-15   54.8  10.2      1e-07   31.5   0.5    2.5  2  Peptidase_M50  Peptidase family M50


Domain annotation for each model (and alignments):
>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   3.6   1.1e-10     2e-06       2     109 ..     130     216 ..     129     232 .. 0.85
   2 !   31.5   0.5   5.7e-12     1e-07     185     228 ..     242     286 ..     216     293 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.1e-10
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50   2 filllgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallp....LGGyVkmageepeeelsee 74 
                                       f ++++ ++  HE+GH+++Ak++g++                  +++Y+i++      +G+++k +g+ p+++    
  gi|298675928|ref|YP_003727678.1| 130 FTVAIMAVLGSHEMGHYFAAKWHGMRT-----------------SLPYFIPFPTiigtMGAIIKHRGMIPDRK---- 185
                                       899***********************9.................67888888777888************999.... PP

                                       ....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.......- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......x RF
                     Peptidase_M50  75 eakaflkkspwqrllivlAGplanfilailvfvv.......p 109
                                                  + + + ++Gpl++++++i+v vv        
  gi|298675928|ref|YP_003727678.1| 186 -----------SLFDVGVSGPLIGLVVSIIVTVVglslnpvS 216
                                       ...........99*******************9966665331 PP

  == domain 2  score: 31.5 bits;  conditional E-value: 5.7e-12
                                       XXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 185 eagls.sflqllalisvnLgilNLlPipvLDGghllfalleairr 228
                                       + g s ++++++ ++++ +++lNLlP  +LDGgh+l+a++   +r
  gi|298675928|ref|YP_003727678.1| 242 TVGNSiHPVAFAGWVGMFITLLNLLPAGQLDGGHILKAMFGNNSR 286
                                       44443499******************************9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2786.66
//
Query:       gi|298675929|ref|YP_003727679.1|  [L=141]
Description: hypothetical protein Metev_2054 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-35  119.4   0.3    7.1e-35  118.7   0.3    1.4  1  DUF126    Aconitase X swivel domain


Domain annotation for each model (and alignments):
>> DUF126  Aconitase X swivel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.7   0.3     4e-39   7.1e-35       1      80 []      27     106 ..      27     106 .. 0.99

  Alignments for each domain:
  == domain 1  score: 118.7 bits;  conditional E-value: 4e-39
                                       --TTS-B-TTT-BB-S.-SSSTT-B-TTSEEEES--S--SS-TTHHHHHHHHT-S-SEEEESS--HHHHHHHHHHT- CS
                            DUF126   1 lSflggvdpetGkvidkghplegqsiagkiLvlpsgkGStvgsyvllelakngtaPaAlilreadpilalGaivadi 77 
                                       +Sflg+vdpe+G+v+++gh+l+++si++k+Lv+p+gkGStvgsyvl++l kn++aPaA+i+ e +pi+a+Gai+++i
  gi|298675929|ref|YP_003727679.1|  27 ISFLGNVDPESGIVVEPGHELYNKSIKDKVLVFPQGKGSTVGSYVLYQLSKNDVAPAAMINIESEPIVAVGAIISGI 103
                                       8**************************************************************************** PP

                                       -EE CS
                            DUF126  78 Plv 80 
                                       Plv
  gi|298675929|ref|YP_003727679.1| 104 PLV 106
                                       *97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 901.14
//
Query:       gi|298675930|ref|YP_003727680.1|  [L=398]
Description: hypothetical protein Metev_2055 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.5e-158  527.8   0.0   1.7e-158  527.6   0.0    1.0  1  DUF521          Protein of unknown function (DUF521)
  ------ inclusion threshold ------
      0.043   13.8   2.5       0.54   10.3   0.1    2.6  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
      0.065   12.0   0.2      0.095   11.4   0.2    1.2  1  tRNA-synt_1g    tRNA synthetases class I (M)


Domain annotation for each model (and alignments):
>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  527.6   0.0  2.8e-162  1.7e-158       1     401 []       1     387 [.       1     387 [. 0.97

  Alignments for each domain:
  == domain 1  score: 527.6 bits;  conditional E-value: 2.8e-162
                            DUF521   1 mkLtkeeeamlnGeeGealqkameilvalGeilgAerLvpvtsahvsgvsyktigdaglefleelaekgakvrvptt 77 
                                       m+Ltkeee++lnGe+Ge+lqka+eilvalG+i++A+ L+p++sa+++gvsyktigdagle++++l+   ++v+vp++
  gi|298675930|ref|YP_003727680.1|   1 MHLTKEEEQILNGEHGETLQKAIEILVALGDIYDADGLIPIKSAQIAGVSYKTIGDAGLEWISDLE---GEVKVPAI 74 
                                       9*****************************************************************...******** PP

                            DUF521  78 lnpigvdlerweelgvdeefaekqeriieayeklGveltftCtpyll.gnapkkGehlawsESsavvyaNSvlGarT 153
                                       lnp+g+dle+w+e+g++++fa+kq++ii+ay+klGv++++tCtpy+l g  ++ G+hlawsESsav+yaNSv+GarT
  gi|298675930|ref|YP_003727680.1|  75 LNPAGMDLENWNEMGISKDFARKQQEIIDAYRKLGVNTKCTCTPYYLeGFDTEYGDHLAWSESSAVSYANSVIGART 151
                                       **********************************************8799*************************** PP

                            DUF521 154 nreggpsalaaAitGrtpeyGlhldenRkptvlveveaesedeadygalGylvGkkvgeriPvlkglekpsedelKa 230
                                       nreggpsal aA++G+t++yG+hldenR p+v + v++e  + +dygalGy  G+ vg+r+P+++ +++ps+delKa
  gi|298675930|ref|YP_003727680.1| 152 NREGGPSALSAALIGKTANYGYHLDENRIPDVSITVDCE-LTGSDYGALGYQTGMMVGNRVPLFHLKNTPSSDELKA 227
                                       ***************************************.9************************************ PP

                            DUF521 231 lgAalaasgavalfhiegvTPeaetleealgekekaekititkedleevleelskakeekvdlvalGcPhlsleElr 307
                                       lgA++aa+gaval+h++gvTPe    +++++ +++ e+iti++++++ev+++  ++ +++ +++a+GcPh+s +El+
  gi|298675930|ref|YP_003727680.1| 228 LGASMAATGAVALYHVDGVTPE----TQNIRFEQPSENITIEADQIQEVYNTN-SDIQNSDEIIAFGCPHCSGDELE 299
                                       **********************....4444446789***************76.88888899*************** PP

                            DUF521 308 elaellkgkkkkvkvelwvttsrevkeeaerlglveklekaGvkvlsdtCmvvsplikkkevkkvatnSgKaahYlp 384
                                        +a+ll  ++k+v++++w++ts+ev++++ ++  v+++ek+G+ v++dtCm+vsp+++  ++k +++nSgKa++Y+p
  gi|298675930|ref|YP_003727680.1| 300 YIAQLL--DNKQVDRDVWICTSKEVADKNPQI--VDRIEKSGAMVVCDTCMIVSPASE--NYKMMMVNSGKALNYVP 370
                                       ******..78888******************9..**********************99..4**************** PP

                            DUF521 385 gltgvkvalgsleecve 401
                                       g+++   ++gs+++c++
  gi|298675930|ref|YP_003727680.1| 371 GMCKIPSKFGSIKDCIR 387
                                       ***************96 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1     9e-05      0.54       5      22 ..     290     317 ..     288     319 .. 0.92
   2 ?    2.8   0.2     0.019   1.1e+02      17      25 ..     337     345 ..     335     346 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 9e-05
                    PhnA_Zn_Ribbon   5 CplCaSey.tY.........edgallvC 22 
                                       Cp+C+ ++ +Y         +d+++++C
  gi|298675930|ref|YP_003727680.1| 290 CPHCSGDElEYiaqlldnkqVDRDVWIC 317
                                       *****976489***************** PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.019
                    PhnA_Zn_Ribbon  17 gallvCpeC 25 
                                       ga+ vC++C
  gi|298675930|ref|YP_003727680.1| 337 GAMVVCDTC 345
                                       7899***** PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   1.6e-05     0.095     104     176 ..     255     321 ..     247     336 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.6e-05
                                       HHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-EE........-TTS-EE-TTSSB-E................ CS
                      tRNA-synt_1g 104 fkklkekgliyekeieqlycpkderflpdryvegtCPkckseeargdqceecgkkleptelinpksaisgskp 176
                                       f++  e+ +i+  +i+ +y ++ +   +d+ +   CP+c      gd+ e  ++ l+ ++ ++    i+ sk+
  gi|298675930|ref|YP_003727680.1| 255 FEQPSENITIEADQIQEVYNTNSDIQNSDEIIAFGCPHCS-----GDELEYIAQLLDNKQ-VDRDVWICTSKE 321
                                       667788999******************************9.....888888888888555.455556666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 2421.50
//
Query:       gi|298675931|ref|YP_003727681.1|  [L=421]
Description: UbiD family decarboxylase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   6.3e-111  371.1   0.1   7.1e-111  370.9   0.1    1.0  1  UbiD      3-octaprenyl-4-hydroxybenzoate carboxy-lyase


Domain annotation for each model (and alignments):
>> UbiD  3-octaprenyl-4-hydroxybenzoate carboxy-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  370.9   0.1  3.9e-115  7.1e-111       1     405 [.       7     382 ..       7     383 .. 0.94

  Alignments for each domain:
  == domain 1  score: 370.9 bits;  conditional E-value: 3.9e-115
                                       HHHCCCTTSEEEEESEB-TBTHHHHHHHHHHHHT--EEEEEEBTTB.TT-EEEE-TTS-HCHHHHHHTS-GHHHHHH CS
                              UbiD   1 lealekagelvrikeevdpelEiaeiarrvleeggpallFenvkgkgskfpvltnlfgtrervalalglssleeile 77 
                                       +++l+++g+l +i+ +v+ ++E+++iar++       +lF++++g     ++++nl+g+r+ +a ++++s  ++i++
  gi|298675931|ref|YP_003727681.1|   7 IDRLKNDGKLEEITYPVSRNFEAPKIARNIG----SPVLFHDIDG----NKAIMNLLGSRDELASLFNIS-KDNIIH 74 
                                       789**************************85....69******54....489****************75.5***** PP

                                       HHHHHHHS..----EE--GCG-GGGSEEECCCCC--HHHS---BSSTTSSS-EEECEEEEEE-TTTT-EEEEEEEEE CS
                              UbiD  78 klaellepkppippkvvesekapcqeevvlegddvdLskLPvltlwpgDgGpyitlglvitrdpetgkrnlgiyRmq 154
                                       kl++++ +    + + v+  + p+++ v   +d+vdL+k P++t++++DgGpyit+g+v+++   ++++n++i+R++
  gi|298675931|ref|YP_003727681.1|  75 KLSTVKPN---GETRIVD--ESPTKQIV---DDEVDLTKYPIMTHFEKDGGPYITSGIVVSEY--GDTTNASIHRLM 141
                                       **999776...7899995..47999555...79****************************97..6679******** PP

                                       EEETTEEEE--TTTHCHHHHHHHHHHCCT--EEEEEEES--HHHHHHCTS--TTT-TCHHHHHHHHTS--EEEE-SS CS
                              UbiD 155 vldknklglhwqihkggaehlrkakkkggeplpvavaiGvdPaltlaAvaplPeglsElefaGalrgepvelvkcet 231
                                       v++knkl+ ++++ ++  + ++ka ++g e+lpva++iG+dP++ +a+++++P + +E+e+a+alrg  +el+kc+ 
  gi|298675931|ref|YP_003727681.1| 142 VVGKNKLAARLVPPRHTYILHKKASENG-ERLPVAIVIGADPVIGFASTTRVP-TGKEFEYAAALRGDTIELFKCD- 215
                                       ***************************9.9***********************.779******************5. PP

                                       SSSEEETT-SEEEEEEEECCEEEECTTTC-TTSCEEC--CCEEEEEEEEEEE-TT-EEEE-SSSCCSHHHHCHHHHH CS
                              UbiD 232 vdlevpadAEivleGeidpgetapEGPfgdhtGyysevrdefpvfkVtaithRkdpiypttvvgkppeedallgkal 308
                                       ++++vp ++EivleG+i+p+e+a+EGPf+d+tG+y++vr+e pv+++t+i+hRkdpiy+ +++    e+ +++g+++
  gi|298675931|ref|YP_003727681.1| 216 NGIKVP-HSEIVLEGYIEPEERAEEGPFVDITGTYDHVRPE-PVITITKIMHRKDPIYHGILPAGA-EHLLMMGVPY 289
                                       59****.*******************************996.*****************9978877.********** PP

                                       HHHHHHHHHCCSTTEEEEEE-GGGTTTCEEEEECHHHTCCHHHHHHHHHHCCTTGGC-SEEEEEEETTS-TTSHHHH CS
                              UbiD 309 ealflpllkkqvpevkdvhlpeeggfhllavvsikkrypghakkvmealwalkqqlsltKlvivvDedvdvrdlkev 385
                                       e+ +++++ + v +vk+v l+e g+++l+avv+i+k+++g+ k++++a++a++   sl K+v+vvD+d+d++d  ++
  gi|298675931|ref|YP_003727681.1| 290 EPKIYNAVDE-VTTVKNVVLTEGGCCYLHAVVQIEKQTEGDGKNAIMAAFAAHS--SL-KHVVVVDDDIDIFDSGDI 362
                                       ********66.778**************************************99..88.****************** PP

                                       HHHHHHC--CCCCEEEECCC CS
                              UbiD 386 lwaiatrvdpdrDlviiegt 405
                                       + aiatr++ d D++ ++++
  gi|298675931|ref|YP_003727681.1| 363 EFAIATRLKGDIDILTVSNV 382
                                       ****************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2773.67
//
Query:       gi|298675932|ref|YP_003727682.1|  [L=252]
Description: metallophosphoesterase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   4.2e-116  386.8   0.6   4.6e-116  386.6   0.6    1.0  1  Metallophos_3  Metallophosphoesterase, calcineurin superfamil
    3.4e-24   85.9   0.0    5.8e-24   85.1   0.0    1.4  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    9.2e-17   62.2   0.0    1.2e-16   61.8   0.0    1.1  1  Metallophos    Calcineurin-like phosphoesterase


Domain annotation for each model (and alignments):
>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  386.6   0.6  7.8e-120  4.6e-116       7     257 .]       2     252 .]       1     252 [] 0.99

  Alignments for each domain:
  == domain 1  score: 386.6 bits;  conditional E-value: 7.8e-120
                                       EEEEEE--TT-GGGHHHHHHHHHHH--SEEEEES-----HHHHHHHHHHHHTT---..-THHHHHHHHHHHHHHHHH CS
                     Metallophos_3   7 kvlaisdlkgevellerlveviedkdpDllvlvGdlvkaeakadeyesaqeerrep..dkkeileekneiiklldkl 81 
                                       k+laisd++ge+el+++lve+iedk+pDl++++Gd+vk++a++de+ saqee+rep  dk+eil+ekne++kl+d++
  gi|298675932|ref|YP_003727682.1|   2 KILAISDFHGETELMNSLVEKIEDKSPDLIIFTGDVVKGQARGDEWLSAQEEGREPvkDKEEILNEKNEDFKLYDEF 78 
                                       9**************************************************************************** PP

                                       HHHHHTT-SEEEEE--TTS--HHHHHHHHHHTTTT-TTEEE-SSEEEEETTTEEEEEE-SEEESS--BSSSS-EEEH CS
                     Metallophos_3  82 frelgeldvpafvvPGkrDaPlevflreayeaevvfpnlkvvhesfaekeGevliaGmGGeivdgekeeefrLkYPa 158
                                       +++l++ld+p++++PG++DaP++vf++++++ +++++n+k+++e+++ekeG +li+GmGGei++g+ke++f+L+YP+
  gi|298675932|ref|YP_003727682.1|  79 YDTLDTLDIPVMCIPGNMDAPEDVFFSYLLG-KYMRSNIKIAQENIFEKEG-YLISGMGGEITNGSKEDFFTLQYPY 153
                                       *******************************.*******************.************************* PP

                                       HHHHHHGGGGGGS---EEEEEESS--S-SSTBTTBS---S-HHHHHHHHHH--SEEEE-SS--EE..EEETTEEEEE CS
                     Metallophos_3 159 weveyrLkvlkelkdrrkvlllatpPigelvadkglkekgsevvaelvktlnPevvvvghavkeh..eelgktlvvn 233
                                       +e++++L+++k++ +++k+lll++pP+g+l++dkg k+k+++vv+el+++++Pe+v++gha+k++  e+++ktlvvn
  gi|298675932|ref|YP_003727682.1| 154 KEADFALRRFKYA-PQKKILLLHSPPTGQLDLDKG-KHKSEDVVNELIRDIKPEIVFCGHAHKAQgkEQIDKTLVVN 228
                                       *************.*********************.****************************999********** PP

                                       --BGGGTEEEEEETTTTEEEEEE- CS
                     Metallophos_3 234 PGaleeGdfavvdleekkveleqv 257
                                       PGal++Gdfavv++e+k+v++++v
  gi|298675932|ref|YP_003727682.1| 229 PGALKYGDFAVVNTENKEVDFGTV 252
                                       *********************986 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.1   0.0   9.8e-28   5.8e-24       1     163 [.       1     243 [.       1     245 [. 0.78

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 9.8e-28
                     Metallophos_2   1 MklaiiSDlHsnldaleavlealkevgvdaiihaGD...........................leeeep........ 42 
                                       Mk+++iSD+H++ ++ + ++e++++ ++d+ii++GD                           +    +        
  gi|298675932|ref|YP_003727682.1|   1 MKILAISDFHGETELMNSLVEKIEDKSPDLIIFTGDvvkgqargdewlsaqeegrepvkdkeeI----Lneknedfk 73 
                                       ************************************7777777777766655555555555552....055555554 PP

                     Metallophos_2  43 ...evleellela.....pvlaVrGNnD..................................eev.veedvlreaae 76 
                                          e    + + +     pv  ++GN+D                                  + +  e + + ++ +
  gi|298675932|ref|YP_003727682.1|  74 lydE----FYDTLdtldiPVMCIPGNMDapedvffsyllgkymrsnikiaqenifekegyliSGMgGEITNGSKEDF 146
                                       4433....4444444469**************************999999999998887777333455567788888 PP

                     Metallophos_2  77 lgtdlp.eeaelelagek......vlliHgdpl..........gvkdalaellkeaeegsdvvvcGHtHvp.eveke 135
                                       ++ ++p +ea++ l+++k      +ll+H+ p           + +d + el+++   + ++v+cGH H++ ++e++
  gi|298675932|ref|YP_003727682.1| 147 FTLQYPyKEADFALRRFKyapqkkILLLHSPPTgqldldkgkhKSEDVVNELIRD--IKPEIVFCGHAHKAqGKEQI 221
                                       888889999999995555555555******988******9997777777778887..6666*********9889999 PP

                     Metallophos_2 136 ggvlvvnPGsvgeprdgdpetyaildtd 163
                                       +++lvvnPG+++ +      ++a+++t+
  gi|298675932|ref|YP_003727682.1| 222 DKTLVVNPGALKYG------DFAVVNTE 243
                                       ***********999......66666665 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.8   0.0     2e-20   1.2e-16       1     203 [.       1     214 [.       1     215 [. 0.72

  Alignments for each domain:
  == domain 1  score: 61.8 bits;  conditional E-value: 2e-20
                                       EEEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS............................HH CS
                       Metallophos   1 lrilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrg............................dl 49 
                                       ++il i+D H     g  +  + l++++ ++  pdl++++GD+v +                             + 
  gi|298675932|ref|YP_003727682.1|   1 MKILAISDFH-----GETELMNSLVEKIEDK-SPDLIIFTGDVVKGQargdewlsaqeegrepvkdkeeilneknE- 70 
                                       89********.....*************999.**************999999999999999887765555543320. PP

                                       HHHHHHHHHHHHHH..............TSEEEEEC-TTSCHHHHHHHHHHHHHHH.HHHHEHHHCEEETSEEEEEE CS
                       Metallophos  50 ekellellaalvky..............pipvylllGNHegfeeellnkygylgif.sepwrsdaevfnnlplaslg 111
                                                                   +ipv++++GN +   e+++ +y   +++ s+++          ++++  
  gi|298675932|ref|YP_003727682.1|  71 -------------DfklydefydtldtlDIPVMCIPGNMD-APEDVFFSYLLGKYMrSNIK------IAQENIFE-K 126
                                       .............12222444555777799**********.55666666665444432222......22222222.1 PP

                                       TTEEEEEEEESECEEETHHHHHHHHHHHSCHHHHCC..HHHHHHHHHHTTCSEEEEEESSESS....CSSSCSCCHH CS
                       Metallophos 112 sgslkvlllhGgspellvsldklgslnleleapepg..dewlkdlekrekadwvivlgHsply....rgsgylfgde 182
                                       +g  +++   Gg  e +++ +k + ++l+ +++e +     +k        + +i+l Hsp++      +g++++++
  gi|298675932|ref|YP_003727682.1| 127 EG--YLISGMGG--E-ITNGSKEDFFTLQYPYKEADfaLRRFKY-----APQKKILLLHSPPTgqldLDKGKHKSED 193
                                       12..22222222..2.4666777777777777777766555555.....77799*************9999999999 PP

                                       HHHHHHHHTTESEEEEESSSS CS
                       Metallophos 183 aledllkkygvdlvisGHtHv 203
                                       ++ +l ++ ++ +v++GH H+
  gi|298675932|ref|YP_003727682.1| 194 VVNELIRDIKPEIVFCGHAHK 214
                                       999**99999**********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1780.27
//
Query:       gi|298675933|ref|YP_003727683.1|  [L=347]
Description: hypothetical protein Metev_2058 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.3e-05   23.2   0.8    0.00018   21.9   0.8    1.6  1  sCache_3_3       Single cache domain 3
    0.00041   19.7   2.5    0.00041   19.7   2.5    2.0  2  Cache_3-Cache_2  Cache 3/Cache 2 fusion domain


Domain annotation for each model (and alignments):
>> sCache_3_3  Single cache domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.8     2e-08   0.00018       3     101 ..     107     207 ..     105     210 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2e-08
                        sCache_3_3   3 ingntelvDqikeltggevTiFl..ddvriaTtvkkedgeravGtklseevaeavlkkGetysgraeilgkkyltaY 77 
                                       +++n++++ ++k+++++   iF+  ++  ++  +   + +  + +++++++++avl++   y+++    +++yl +Y
  gi|298675933|ref|YP_003727683.1| 107 LKNNSDFISNLKDNNDVVTNIFKieNNRSVSVLLNSGNVSNNLFKTIPDDAYNAVLNNSTAYYKKTMSSDNNYLVMY 183
                                       578999********99******765666666666666667888899**********99999**************** PP

                        sCache_3_3  78 ePlkdadgkviGmlfvGlpeeevq 101
                                       + l +++ kv  +l +++pe+++ 
  gi|298675933|ref|YP_003727683.1| 184 TLLENNNTKVKNILSMAVPENKIL 207
                                       *****9999*99999999998775 PP

>> Cache_3-Cache_2  Cache 3/Cache 2 fusion domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   2.5   4.5e-08   0.00041      63     182 ..      92     208 ..      65     219 .. 0.74
   2 ?   -0.2   0.3     0.053   4.8e+02      56      88 ..     285     317 ..     211     325 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 4.5e-08
                   Cache_3-Cache_2  63 vgevslPklklggewlnknfelvdefteltgatatvFqrmnddllRVsTsvkkedGkraigtylpasspvykavlag 139
                                       v++ +lP+ ++  e+l++n++++ ++++  +++  +F   n++ + V   +   + + ++   +p+   +y avl++
  gi|298675933|ref|YP_003727683.1|  92 VAKDELPSENVTREILKNNSDFISNLKDNNDVVTNIFKIENNRSVSV--LLNSGNVSNNLFKTIPD--DAYNAVLNN 164
                                       55556666666666666666666666666666666666666654433..34444444455555555..599*99988 PP

                   Cache_3-Cache_2 140 et.YvGrakvfgkwYvTaYePikdadgkViGilyVgvdqsealk 182
                                        t Y+++ +  + +Y+  Y+ + +++ kV  il  +v+++++l+
  gi|298675933|ref|YP_003727683.1| 165 STaYYKKTMSSDNNYLVMYTLLENNNTKVKNILSMAVPENKILD 208
                                       6549***********************************88875 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.053
                   Cache_3-Cache_2  56 dnqetvkvgevslPklklggewlnknfelvdef 88 
                                       d+++t+++ + ++ ++k+ ++ ln++f lv+++
  gi|298675933|ref|YP_003727683.1| 285 DKNNTKNTLNKTADSIKVVDDNLNQTFRLVQNL 317
                                       444444444444445555555555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1153  (0.0643092); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2567.43
//
Query:       gi|298675934|ref|YP_003727684.1|  [L=193]
Description: rubrerythrin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.2e-33  114.6   2.3    5.6e-33  114.2   2.3    1.2  1  Rubrerythrin    Rubrerythrin
    1.6e-11   44.3   0.7      2e-11   44.0   0.7    1.1  1  Ferritin        Ferritin-like domain
    0.00077   19.3   2.3      0.094   12.5   0.1    2.1  2  COQ7            Ubiquinone biosynthesis protein COQ7
     0.0011   19.1   0.9       0.14   12.2   0.1    2.1  2  DUF892          Domain of unknown function (DUF892)
     0.0044   17.0   2.2      0.011   15.8   2.2    1.9  1  HypA            Hydrogenase/urease nickel incorporation, meta
  ------ inclusion threshold ------
      0.016   14.9   0.1        1.9    8.1   0.0    2.1  2  RE_TdeIII       Type II restriction endonuclease, TdeIII
      0.031   13.7   0.2      0.058   12.8   0.2    1.5  1  BAR_3_WASP_bdg  WASP-binding domain of Sorting nexin protein
      0.037   14.0   0.1      0.067   13.2   0.1    1.4  1  zf-C2HC5        Putative zinc finger motif, C2HC5-type
      0.067   12.7   1.0       0.44   10.1   0.9    2.0  1  Arfaptin        Arfaptin-like domain
       0.11   12.4   0.2       0.11   12.4   0.2    2.1  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
       0.14   12.0   2.1       0.24   11.2   2.1    1.3  1  MCM_OB          MCM OB domain
       0.92    9.3   3.7       0.74    9.6   0.2    2.6  3  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
        1.4    9.4   6.5         18    5.8   6.4    2.6  2  DUF4379         Probable Zinc-ribbon domain
        3.7    7.3   7.5        1.9    8.3   0.5    2.6  2  Rubredoxin_2    Rubredoxin metal binding domain
        4.1    6.9   7.2         15    5.1   0.7    2.9  3  zf-ribbon_3     zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.2   2.3   4.7e-36   5.6e-33       1     137 []       6     141 ..       6     141 .. 0.95

  Alignments for each domain:
  == domain 1  score: 114.2 bits;  conditional E-value: 4.7e-36
                                       HHHHHHHHHHHHHHHHHHHHHHCHH.TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS------- CS
                      Rubrerythrin   1 eiLekAiagEssarrlYkelaekak.egypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakp 76 
                                       e+++kA++gEs ar++Y+++a+ ak egy+qi+e+F+ +Ae+EreHak++ kl+++l+ +     + ++++     p
  gi|298675934|ref|YP_003727684.1|   6 ENMTKAFIGESLARNRYTNFAKVAKeEGYEQISEIFLNTAENEREHAKWMMKLINELKSKSG--NSPDKVNLDVDIP 80 
                                       799******************************************************99999..5566666666778 PP

                                       TTGGHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  77 kflttaknLeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlrkll 137
                                          +t +nL++ i g+++e + my+++++ a+ke  +e++++f+++ e Ek+H+er++kll
  gi|298675934|ref|YP_003727684.1|  81 VCGSTIDNLKDSISGEEYETTSMYPEFANTADKENLPEIAERFRAIGEVEKHHQERFKKLL 141
                                       999********************************************************95 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.7   1.7e-14     2e-11       7     140 ..      11     145 ..       5     147 .. 0.86

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 1.7e-14
                                       HHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHHC-SSSSCS.SHH CS
                          Ferritin   7 qladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraeleeieapkefg.sve 82 
                                       ++  e  a + y ++a ++k++g+e+++e f   ae ereha+ +++ i++l  +   ++ ++  + + + +g +++
  gi|298675934|ref|YP_003727684.1|  11 AFIGESLARNRYTNFAKVAKEEGYEQISEIFLNTAENEREHAKWMMKLINELKSKSGNSPDKVNLDVDIPVCGsTID 87 
                                       555688999********************************************855555555555434444886777 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin  83 evleaalehekkvteslrelielaeeegDpatadfledfleeqeeheweleallekle 140
                                       +    +   e+++t+++ e ++ a++e+ p  a+ +  + e + +h++ +++ll++le
  gi|298675934|ref|YP_003727684.1|  88 NLKDSISGEEYETTSMYPEFANTADKENLPEIAERFRAIGEVEKHHQERFKKLLNELE 145
                                       777777788999*******************************************997 PP

>> COQ7  Ubiquinone biosynthesis protein COQ7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.1   7.9e-05     0.094      12      62 ..      14      65 ..      10      68 .. 0.90
   2 !    6.7   0.2    0.0047       5.6      24      60 ..     108     145 ..      95     152 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.9e-05
                              COQ7 12 GElgAvaiYkgqlavl.akkdpelkpllkemleqEkeHlatfeellkerrvr 62
                                      GE  A   Y+  + v+ ++ ++++ +++ +++e+E+eH +++ +l++e + +
  gi|298675934|ref|YP_003727684.1| 14 GESLARNRYTNFAKVAkEEGYEQISEIFLNTAENEREHAKWMMKLINELKSK 65
                                      899999999999999977788899**********************998765 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0047
                              COQ7  24 lavl.akkdpelkpllkemleqEkeHlatfeellkerr 60 
                                       + ++ +++ pe+ + ++ + e Ek+H + f++ll+e +
  gi|298675934|ref|YP_003727684.1| 108 ANTAdKENLPEIAERFRAIGEVEKHHQERFKKLLNELE 145
                                       5555456778899999999***************9975 PP

>> DUF892  Domain of unknown function (DUF892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.1   0.00012      0.14     111     153 ..      20      62 ..       2      67 .. 0.89
   2 ?    5.7   0.0     0.012        14       8      67 ..      87     150 ..      85     164 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                                       HHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            DUF892 111 AsYgtLialAeqlgekeaaklLeqtleeekatdekltelaesl 153
                                        +Y+  +++A++ g++++ +++ +t e+e++ ++++ +l+++l
  gi|298675934|ref|YP_003727684.1|  20 NRYTNFAKVAKEEGYEQISEIFLNTAENEREHAKWMMKLINEL 62 
                                       5899***********************************9876 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHH.HHHHHHHHHHHH-SS...HHHHHHHHHHHHHHHHHHHHHHHHHHHTT----- CS
                            DUF892   8 deLrDlyaaEk.qllkalpkmakaaes...peLkaaleqHleeTegqierLeqvferlgesase 67 
                                       d L+D  + E+ + +++ p+ a+ a++   pe++++++   e  +++ er ++++++l+ +   
  gi|298675934|ref|YP_003727684.1|  87 DNLKDSISGEEyETTSMYPEFANTADKenlPEIAERFRAIGEVEKHHQERFKKLLNELENHSVY 150
                                       6788877776536788889888888653367778888888888888999999999988766555 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   2.2   8.8e-06     0.011      25      95 ..     118     182 ..      16     192 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.8e-06
                                       EEEEEEEEEETTCT--HHHHHHHHHHHHCC.TTTT-EEEEEEE--EEEETTTS-EEECHHHHHS-TTTSSS CS
                              HypA  25 kvtkvkvevGelsgvepeaLefafellaegtvlegaeLeieevpvkvrCreCgkefeleekalrCpkCgsa 95 
                                       ++ +    +Ge+++ ++e ++  ++ l++++v +      ++++v+  Cr+Cg+  + +e  ++Cp+C++ 
  gi|298675934|ref|YP_003727684.1| 118 EIAERFRAIGEVEKHHQERFKKLLNELENHSVYK------KDKEVQWVCRKCGYVHTGTEPPEKCPSCDHP 182
                                       5555555677777777777777777777777776......899**********99886654568****875 PP

>> RE_TdeIII  Type II restriction endonuclease, TdeIII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.014        16      86     136 ..      28      77 ..       4      85 .. 0.71
   2 ?    8.1   0.0    0.0016       1.9      60     116 ..     102     157 ..     100     180 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.014
                         RE_TdeIII  86 tiseeaqerIdeil.deltkskkkpdleeeleaireaqegeekkaksvkaDl 136
                                         +ee  e+I+ei  +  +++++++++  +++ i+e ++++ +++ +v+ D+
  gi|298675934|ref|YP_003727684.1|  28 VAKEEGYEQISEIFlNTAENEREHAKW--MMKLINELKSKSGNSPDKVNLDV 77 
                                       335667899***997778888888888..77777776666666666666665 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0016
                         RE_TdeIII  60 tifEkvAkiiAkeefkeaksqkevsgtiseeaqerIdeildeltkskkkpdleeele 116
                                       +++ + A++  ke+  e+ ++ ++ g++++++qer +++l+el++++ + ++++e++
  gi|298675934|ref|YP_003727684.1| 102 SMYPEFANTADKENLPEIAERFRAIGEVEKHHQERFKKLLNELENHSVY-KKDKEVQ 157
                                       57778999999*****************************999987654.3445544 PP

>> BAR_3_WASP_bdg  WASP-binding domain of Sorting nexin protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   4.9e-05     0.058      83     163 ..       3      92 ..       1     157 [. 0.75

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.9e-05
                    BAR_3_WASP_bdg  83 kafkalsqafevdeqvassaLnealaatgktYeeigevf...aeqpkkDleflletleeYkGllanfPDiigvhk.. 154
                                       k+++++++af  +  ++++  n a  a  + Ye+i+e+f   ae+ ++  + ++ + +e k   +n PD ++++   
  gi|298675934|ref|YP_003727684.1|   3 KTIENMTKAFIGESLARNRYTNFAKVAKEEGYEQISEIFlntAENEREHAKWMMKLINELKSKSGNSPDKVNLDVdi 79 
                                       67889999**9999999999999999999********98666889999999******************99876555 PP

                    BAR_3_WASP_bdg 155 ....galekvkes 163
                                           + ++ +k+s
  gi|298675934|ref|YP_003727684.1|  80 pvcgSTIDNLKDS 92 
                                       5555677777777 PP

>> zf-C2HC5  Putative zinc finger motif, C2HC5-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   5.6e-05     0.067      18      43 ..     158     182 ..     147     188 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.6e-05
                          zf-C2HC5  18 pnClnCGkiiCakeglskpCsfCgsp 43 
                                         C +CG +    e + ++C++C++p
  gi|298675934|ref|YP_003727684.1| 158 WVCRKCGYVHTGTEPP-EKCPSCDHP 182
                                       57**************.******987 PP

>> Arfaptin  Arfaptin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.9   0.00037      0.44      54     116 ..       3      64 ..       1     144 [. 0.68

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00037
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH..H-CCGHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Arfaptin  54 klaknlskallklsqtekelGdvfkdlskrekqealgeaftatgealrllakqgeallkalkr 116
                                       k ++n++ka++  s + +   + f++ +k+e  e+++e f  t+e  r  ak  ++l++ lk 
  gi|298675934|ref|YP_003727684.1|   3 KTIENMTKAFIGESLARNRYTN-FAKVAKEEGYEQISEIFLNTAENEREHAKWMMKLINELKS 64 
                                       6789999****99999999986.7888999****************************99986 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   9.1e-05      0.11      12      30 ..     149     166 ..     145     170 .. 0.78
   2 ?   -2.2   0.8       3.3   3.9e+03       4       7 ..     176     179 ..     175     181 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.1e-05
                                       EEEECSCCCEEEESSSS-E CS
                    RNA_POL_M_15KD  12 lpkedkegknfeCrqCgYe 30 
                                        +k+dke++   Cr+CgY+
  gi|298675934|ref|YP_003727684.1| 149 VYKKDKEVQ-WVCRKCGYV 166
                                       577888875.56******8 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.3
                                       ESTT CS
                    RNA_POL_M_15KD   4 CpkC 7  
                                       Cp+C
  gi|298675934|ref|YP_003727684.1| 176 CPSC 179
                                       8888 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   2.1    0.0002      0.24      24      62 ..     147     182 ..     144     192 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0002
                                       ---EEEEEEEEEEETTT-.-EEES----SB-..TTT-HH CS
                            MCM_OB  24 sevkpklkkavfeckkcgktveveleePrkCeekeCesk 62 
                                       ++v +k k++   c+kcg+ v++ +e P+kC  ++C++ 
  gi|298675934|ref|YP_003727684.1| 147 HSVYKKDKEVQWVCRKCGY-VHTGTEPPEKC--PSCDHP 182
                                       678899999*********8.5558899****..999943 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       3.5   4.1e+03       2      14 ..      86      98 ..      85     104 .. 0.74
   2 ?    9.6   0.2   0.00061      0.74      38      52 ..     151     165 ..     144     167 .. 0.83
   3 ?   -1.3   0.3       1.5   1.8e+03      46      52 ..     175     181 ..     175     184 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.5
                    zinc_ribbon_10  2 fDrvldvLvGdde 14
                                      +D++ d ++G++ 
  gi|298675934|ref|YP_003727684.1| 86 IDNLKDSISGEEY 98
                                      6888999999876 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00061
                    zinc_ribbon_10  38 eeleevkyrCpkCga 52 
                                       ++ +ev+++C kCg 
  gi|298675934|ref|YP_003727684.1| 151 KKDKEVQWVCRKCGY 165
                                       66789********97 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.5
                    zinc_ribbon_10  46 rCpkCga 52 
                                       +Cp+C +
  gi|298675934|ref|YP_003727684.1| 175 KCPSCDH 181
                                       5999975 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   6.4     0.015        18      22      45 ..     150     168 ..     131     179 .. 0.67
   2 ?    1.0   0.3      0.47   5.6e+02      31      40 ..     175     184 ..     175     185 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.015
                           DUF4379  22 pgskkkvwWkCakCgheWeasvsn 45 
                                       +++ k+v W C+kCg+     v++
  gi|298675934|ref|YP_003727684.1| 150 YKKDKEVQWVCRKCGY-----VHT 168
                                       45589**********5.....344 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.47
                           DUF4379  31 kCakCgheWe 40 
                                       kC+ C+h ++
  gi|298675934|ref|YP_003727684.1| 175 KCPSCDHPYN 184
                                       7999999885 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.5    0.0016       1.9       1      10 [.     158     167 ..     158     169 .. 0.89
   2 ?    1.7   1.4      0.18   2.2e+02      16      21 ..     175     180 ..     175     181 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0016
                      Rubredoxin_2   1 YvCsqCGfes 10 
                                       +vC++CG+++
  gi|298675934|ref|YP_003727684.1| 158 WVCRKCGYVH 167
                                       89******87 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.18
                      Rubredoxin_2  16 rCpsCg 21 
                                       +CpsC 
  gi|298675934|ref|YP_003727684.1| 175 KCPSCD 180
                                       7****7 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.1   1.3e+03       6      11 ..      80      86 ..      80      88 .. 0.71
   2 ?    4.2   0.2     0.024        29      18      25 ..     159     166 ..     157     166 .. 0.88
   3 ?    5.1   0.7     0.013        15       4      11 ..     175     182 ..     174     183 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.1
                       zf-ribbon_3  6 PnCGa.p 11
                                      P CG+ +
  gi|298675934|ref|YP_003727684.1| 80 PVCGStI 86
                                      7899844 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.024
                       zf-ribbon_3  18 vCpyCGtk 25 
                                       vC +CG++
  gi|298675934|ref|YP_003727684.1| 159 VCRKCGYV 166
                                       7*****96 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.013
                       zf-ribbon_3   4 rCPnCGap 11 
                                       +CP+C++p
  gi|298675934|ref|YP_003727684.1| 175 KCPSCDHP 182
                                       79999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1531  (0.0853924); expected 358.6 (0.02)
Passed bias filter:                      858  (0.0478554); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 1139.91
//
Query:       gi|298675935|ref|YP_003727685.1|  [L=93]
Description: hypothetical protein Metev_2060 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 712.25
//
Query:       gi|298675936|ref|YP_003727686.1|  [L=183]
Description: class II aldolase/adducin family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.3e-33  115.7   0.0    2.6e-33  115.5   0.0    1.0  1  Aldolase_II  Class II Aldolase and Adducin N-terminal domain


Domain annotation for each model (and alignments):
>> Aldolase_II  Class II Aldolase and Adducin N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.5   0.0   1.4e-37   2.6e-33       2     185 ..       4     175 ..       3     176 .. 0.93

  Alignments for each domain:
  == domain 1  score: 115.5 bits;  conditional E-value: 1.4e-37
                                       HHHHHHHHHHHTTSSCTTBCEEEEEETSTTEEEEEBTSS-GGGHTGGGEEEEETTSCEEEECECSSSTB-TTHHHHH CS
                       Aldolase_II   2 elaeasrllarrglvegtgGniSvrvpeedsflitpsgvdfeeltaedlvvvdldsgevvegkekggkpssetplHl 78 
                                       e+ +++++l ++glve   GniSvrv   ++++it+sg +++e+t+ ++v++d+d  ++ ++   +  +sse  +H+
  gi|298675936|ref|YP_003727686.1|   4 EISRIGKKLVEHGLVESHFGNISVRVG--NKMIITRSGCPLDEVTEGNVVEIDVD--NPCSM---DIIASSESIVHR 73 
                                       7888999******************76..9************************9..78844...5689******** PP

                                       HHHHH-TT-SEEEEE--HHHHHHHTCCSTSCHCCSSHHHHC.HSSSEEEEES-SSTTCHHHHHHHHHHHHHS-SEEE CS
                       Aldolase_II  79 aiykarpdaravvHtHspaavalsalagkeglppltqeaaklllgdevpvipyaapgteelgealaealkedakavl 155
                                       +iyk+ + a a++H+H p+av+ s+l +k+ l p++ e++ +l  de+pvi+   +gte+l+ ++a+al+ + k+ +
  gi|298675936|ref|YP_003727686.1|  74 EIYKN-TSALAIIHAHCPYAVTQSLLNDKNSLVPVDSEGKYFL--DEIPVIKGD-IGTEKLAYNTADALG-KYKGTI 145
                                       ****6.9*****************9999999********9977..99***9655.5*************8.889*** PP

                                       ETTTEEEEEESSHHHHHHHHHHHHHHHHHH CS
                       Aldolase_II 156 lrnHGlltvGetleeAvalaetleeaaeiq 185
                                       + +HG +++G+ l++A+  ++ +e++++i 
  gi|298675936|ref|YP_003727686.1| 146 VYSHGTFAAGKILDDAYITTTQIEHSCKIK 175
                                       ***************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1251.88
//
Query:       gi|298675937|ref|YP_003727687.1|  [L=202]
Description: CDP-alcohol phosphatidyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-12   48.5   2.2    1.1e-12   48.5   2.2    2.5  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase


Domain annotation for each model (and alignments):
>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   2.2     6e-17   1.1e-12       2      66 .]      27      95 ..      26      95 .. 0.86
   2 ?   -2.2   4.2      0.41   7.4e+03      10      27 ..     152     174 ..     100     193 .. 0.67

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 6e-17
                                      -HHHHHHHHHHHHHHHHHGGGS-H......HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                   CDP-OH_P_transf  2 lPnaiTllrlllsvlailllltyyp....lvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                       Pn++++l+l+++++a ++++++y     +++a ll+ + s++Da+DG +AR +++ s+ G++lD+++D
  gi|298675937|ref|YP_003727687.1| 27 SPNIVSFLSLIFAIIAGVFFYYSYTnplfVLIAGLLVALNSFLDAMDGIMARHMQTASSKGDFLDHVID 95
                                      6****************86655554999666666666699**************99899********99 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.41
                                       HHHHHHHHHHGGGS-H........ CS
                   CDP-OH_P_transf  10 rlllsvlailllltyyp......l 27 
                                       rl+l+++a  l++++yp       
  gi|298675937|ref|YP_003727687.1| 152 RLILIIAAS-LIYFLYPsliygfS 174
                                       455544455.45455555554431 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       897  (0.0500307); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1399.42
//
Query:       gi|298675938|ref|YP_003727688.1|  [L=174]
Description: hypothetical protein Metev_2064 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-46  158.1   0.2    1.7e-46  157.9   0.2    1.1  1  Archease  Archease protein family (MTH1598/TM1083)


Domain annotation for each model (and alignments):
>> Archease  Archease protein family (MTH1598/TM1083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.9   0.2   9.7e-51   1.7e-46       1     138 []      36     174 .]      36     174 .] 0.98

  Alignments for each domain:
  == domain 1  score: 157.9 bits;  conditional E-value: 9.7e-51
                                       EEE---SSEEEEEEE-SSSHHHHHHHHHHHHHHHS--TT---S-EEEEEEEESSSHHHHHHHHHHHHHHHHHT--S- CS
                          Archease   1 yeyldhtADviieawGksleeafesaalalfeymtdlskvepkeekeieveaedledlLfdfLdellylfdteyfvf 77 
                                       +e+l+htAD +++a+G++leeafe+aala+f++m+d+++v ++ +++i++e+ dl+ lL+d+L+ellyl d+++ v+
  gi|298675938|ref|YP_003727688.1|  36 FEFLEHTADAQFRAYGNTLEEAFENAALAMFNVMVDTDNVSNNISESINIESPDLDILLVDWLSELLYLSDVNQSVY 112
                                       9**************************************************************************** PP

                                       ---EEEE..E-SSSEEEEEEEE----.-TT--------B--S---EEEEETTEEEEEEEEE- CS
                          Archease  78 kevkvde.eeeeeeleleaeargekfdkekhevqtevKAvTyhelrieeeddgweayvvvDi 138
                                       + ++vd  +e+++++ l+a+++ge+++ +khe++tevKAvTy++l++++  dgw ++vvvDi
  gi|298675938|ref|YP_003727688.1| 113 STFNVDPiKEKDDGYFLSAQIYGETLNLDKHEIDTEVKAVTYNQLEVKNLPDGWMLQVVVDI 174
                                       ***9966458899************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1227.15
//
Query:       gi|298675939|ref|YP_003727689.1|  [L=487]
Description: hypothetical protein Metev_2065 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     9e-171  568.6   0.2     1e-170  568.4   0.2    1.0  1  RtcB      tRNA-splicing ligase RtcB


Domain annotation for each model (and alignments):
>> RtcB  tRNA-splicing ligase RtcB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  568.4   0.2  5.8e-175    1e-170       1     412 []      56     487 .]      56     487 .] 0.99

  Alignments for each domain:
  == domain 1  score: 568.4 bits;  conditional E-value: 5.8e-175
                                       HHHHHTTSTTB-S-EEEEEEEE--SSS-EEEEEEE-...-EE-HHHC-SST.-EEEEEEEEEEHHHHGGGHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB   1 qlknvaslpgivkhvaamPDvHlGkgapiGsViatk...gviiPaaVGvDI.CGvrllktnltaeeleeklkelvke 73 
                                       q++nvaslpgi+k+++amPD+HlG+g+piG+V+a++   gvi+P++VG+DI CGvrll+tnl+ e++++++++lv++
  gi|298675939|ref|YP_003727689.1|  56 QMANVASLPGIQKYSMAMPDAHLGYGFPIGGVAAFDkdeGVISPGGVGFDInCGVRLLRTNLKIEDIRPHMNRLVNN 132
                                       89*************************************************************************** PP

                                       HHHHS-------------HHHHHHHHHHTHHHHHHTTSS-GGGGGGBGGGG--TT--GGGS-HHHHHHHGGGTT--- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB  74 lekavpvglgskkkvklskkeleevleegakwaveeglgeeedlekieeegalkeadlekvskkakerarkqlGtlG 150
                                       l++++p+glgsk+ +k+s++el++v+++ga+wav++g+g + d+e++e +g +k+ad+++vsk+a++r+r+qlGtlG
  gi|298675939|ref|YP_003727689.1| 133 LFNKIPSGLGSKSGLKVSDAELDDVFRHGAQWAVDNGYGVKADVEHCEGNGLIKGADPSQVSKEARKRGRPQLGTLG 209
                                       ***************************************************************************** PP

                                       STT-EEEEEEEEEES-HHHHHHHT--TTEEEEEEEE--HHHHHHHHHHHHHHHHCCHHHCT---SSGGG--EETTSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB 151 sGNHFiEvqlveeildeeaakalgleegqvvvmlHsGSRglGhqiaedylkiakkalkkkgiklpdrdLaylpagse 227
                                       sGNHF+Evq+v++i+d+ +a+ +gleegqv+v +H+GSRg Ghqi++d+l+ +++a+kk+gi+lpd++La++pa+s+
  gi|298675939|ref|YP_003727689.1| 210 SGNHFLEVQYVDKIYDDVIASDFGLEEGQVTVSIHCGSRGAGHQICSDHLRELTQAVKKYGIQLPDKQLACAPANSR 286
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT.T--HHHH--EEEEEEESEEEEEEEE..T...EEEEEEEES-E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x...xxxxxxxxxxx RF
                              RtcB 228 egqaYlkamqaaanyAkaNRqvitervreilekvlkkekedlelelvvdvaHNiakkEehe.d...ekvlVhRKGAt 300
                                       e+q+Y+kam++aanyA+aNRqvi +++re++e++++k   d++++lv+dvaHN+ak Eeh+ +   ++v+VhRKGAt
  gi|298675939|ref|YP_003727689.1| 287 EAQNYFKAMACAANYAWANRQVINHWTREVFENIFGK---DIDMNLVYDVAHNVAKLEEHTiNgekKQVYVHRKGAT 360
                                       ***********************************75...6789*****************945789********** PP

                                       E-.............TT--EEEE--STTS-EEEEE--HHHH..SSSEE---S-----------------TTTTTCCC CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB 301 rA.............kvgqpviipGsmgtkSyivkGkgnae..sfgStsHGAGRlmsRakakkkfkleevkkdleeq 362
                                       rA             + gqpv+ipGsmgt+S++++G+++++  sfgS++HG+GRlmsR++akk++++ee++k+l+++
  gi|298675939|ref|YP_003727689.1| 361 RAfppehpelsddyqQSGQPVLIPGSMGTHSFVLHGTKDSMdiSFGSACHGSGRLMSRKHAKKELSGEEIQKELASK 437
                                       ***************************************************************************** PP

                                       T-EEEE------------------HHHHHHHHCTS-EEEEEEEEEEEEE- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB 363 gigvearkkegvleEapeaYKdideVveaqaeaglvevvarlkpvlvvkg 412
                                       gi+v++++ + + eEapeaYK+ +eVv+++++ g++++varl+pv+v+kg
  gi|298675939|ref|YP_003727689.1| 438 GITVKVANPRMISEEAPEAYKSSSEVVDVVHDVGIARKVARLSPVGVIKG 487
                                       *************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (487 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.45
# Mc/sec: 3286.93
//
Query:       gi|298675940|ref|YP_003727690.1|  [L=154]
Description: PUA domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-27   95.2   0.0    5.6e-27   93.7   0.0    1.7  2  TGT_C2    Patch-forming domain C2 of tRNA-guanine transglycos
    3.4e-14   52.6   0.1    6.4e-14   51.7   0.1    1.5  1  PUA       PUA domain
     0.0013   18.3   0.1       0.19   11.4   0.0    2.4  2  AbrB_C    AbrB C-terminal domain
  ------ inclusion threshold ------
      0.011   16.0   0.0      0.018   15.3   0.0    1.4  1  UPF0113   UPF0113 PUA domain
      0.018   14.8   0.0      0.099   12.5   0.0    2.0  2  PUA_3     PUA-like domain
       0.12   11.3   0.0        4.2    6.3   0.0    2.1  2  DUF4788   Domain of unknown function (DUF4788)


Domain annotation for each model (and alignments):
>> TGT_C2  Patch-forming domain C2 of tRNA-guanine transglycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.7   0.0   1.9e-30   5.6e-27       2      71 .]       7      76 ..       6      76 .. 0.97
   2 ?   -1.4   0.0       0.9   2.7e+03      40      54 ..     110     124 ..      91     128 .. 0.73

  Alignments for each domain:
  == domain 1  score: 93.7 bits;  conditional E-value: 1.9e-30
                            TGT_C2  2 rlraiadYqFGagagdaLfpedvtitrsatgrirqvlvdgerlatlraqdgrltLsleGarrlheslppP 71
                                      ++r +adYqF +g+g++Lfpedv++ +s+tgrirq+l+++er+at+ra+dg+ltLs++Ga   h+ l+ P
  gi|298675940|ref|YP_003727690.1|  7 TVRIMADYQFCKGCGEKLFPEDVSFLLSRTGRIRQILYNNERIATVRASDGVLTLSIKGADTVHKYLSKP 76
                                      79***************************************************************99877 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.9
                            TGT_C2  40 dgerlatlraqdgrl 54 
                                        ge ++ + ++d++l
  gi|298675940|ref|YP_003727690.1| 110 AGEEVLVVDESDNLL 124
                                       477777778888887 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   0.1   2.1e-17   6.4e-14       2      72 ..      79     149 ..      78     151 .. 0.96

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 2.1e-17
                                       EEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEE CS
                               PUA   2 rvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveier 72 
                                       rv+  ++Av +++ g+  + + v++++ ++++g++V +vde ++l+a G   +s ee+ +i++g +v+i+ 
  gi|298675940|ref|YP_003727690.1|  79 RVTMCEEAVPFVSAGKTAFSKHVIDIDPELRAGEEVLVVDESDNLLATGQLILSPEEIHSIERGSAVDIRT 149
                                       688889***************************************************************86 PP

>> AbrB_C  AbrB C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.7   0.0    0.0078        23      17      28 ..      56      67 ..      55      75 .. 0.85
   2 !   11.4   0.0   6.4e-05      0.19      11      28 ..     121     137 ..     116     139 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0078
                            AbrB_C 17 nGkivLSkeGAe 28
                                      +G ++LS +GA+
  gi|298675940|ref|YP_003727690.1| 56 DGVLTLSIKGAD 67
                                      899********8 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 6.4e-05
                            AbrB_C  11 eNisLanGkivLSkeGAe 28 
                                       +N  La G+++LS+e+++
  gi|298675940|ref|YP_003727690.1| 121 DN-LLATGQLILSPEEIH 137
                                       55.89**********998 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0     6e-06     0.018      15      53 ..      93     131 ..      80     145 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6e-06
                           UPF0113  15 GrdvlkesilkitesvkenqvvvVlnengeplGiGkirk 53 
                                       G+  + ++++ i+++++ ++ v+V++e +++l+ G ++ 
  gi|298675940|ref|YP_003727690.1|  93 GKTAFSKHVIDIDPELRAGEEVLVVDESDNLLATGQLIL 131
                                       8999*******************************9865 PP

>> PUA_3  PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.3e-05     0.099      19      49 ..      97     127 ..      94     130 .. 0.94
   2 ?   -0.6   0.0      0.39   1.2e+03      28      38 ..     135     147 ..     128     150 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.3e-05
                             PUA_3  19 fsneiasvegeledGdvVdvfsekgkflGtG 49 
                                       fs+ + +++ el++G+ V v++e+++ l+tG
  gi|298675940|ref|YP_003727690.1|  97 FSKHVIDIDPELRAGEEVLVVDESDNLLATG 127
                                       8899999999********************9 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.39
                             PUA_3  28 g..eledGdvVdv 38 
                                       +   +e G++Vd+
  gi|298675940|ref|YP_003727690.1| 135 EihSIERGSAVDI 147
                                       3334557777776 PP

>> DUF4788  Domain of unknown function (DUF4788)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0014       4.2     135     166 ..      11      42 ..       2     103 .. 0.75
   2 ?    3.5   0.0    0.0098        29      66      93 ..     114     141 ..      87     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0014
                           DUF4788 135 secsrscrnldksinpqDimFvlgdsqrcpia 166
                                       +++++ c+  ++ + p+D+ F+l+++ r ++ 
  gi|298675940|ref|YP_003727690.1|  11 MADYQFCKGCGEKLFPEDVSFLLSRTGRIRQI 42 
                                       678999*******************9998544 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.0098
                           DUF4788  66 pvtvryngkvlGtgtlsfpqefidkiek 93 
                                       +++v +++++l tg+l +++e i +ie+
  gi|298675940|ref|YP_003727690.1| 114 VLVVDESDNLLATGQLILSPEEIHSIER 141
                                       57899******************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 905.74
//
Query:       gi|298675941|ref|YP_003727691.1|  [L=304]
Description: hypothetical protein Metev_2067 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    9.3e-11   41.9  15.8    9.4e-07   29.1   0.9    3.8  4  Bactofilin  Polymer-forming cytoskeletal
  ------ inclusion threshold ------
      0.039   13.6   6.1      0.044   13.4   0.2    2.7  2  DUF3494     Protein of unknown function (DUF3494)
        9.4    6.1  30.2         14    5.6   1.0    7.0  8  Hexapep     Bacterial transferase hexapeptide (six repeats)


Domain annotation for each model (and alignments):
>> Bactofilin  Polymer-forming cytoskeletal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   4.8   7.1e-06     0.042      26      96 ..      22      95 ..       8      96 .. 0.77
   2 !   16.4   2.5   1.3e-06    0.0081       2      54 ..      49     104 ..      48     124 .. 0.80
   3 !    6.7   0.0    0.0014       8.6      61      97 ..     182     218 ..     177     219 .. 0.91
   4 !   29.1   0.9   1.6e-10   9.4e-07       3      81 ..     191     272 ..     189     286 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.1e-06
                        Bactofilin 26 eGdieakgklvvgeggkvegnikaeevvvaGt...vkGnveaeekvelkktakveGdikaksle.ieegavfeGk 96
                                      e++i  +g ++vg++++++  i a+++++ G+   v+G+++ +++v+++  +k+ G++k++s + i e ++++Gk
  gi|298675941|ref|YP_003727691.1| 22 EHNIVVDGGVIVGSHSNINYGIIANSAIL-GEsvqVSGDLTTTSEVRIDTLSKIGGSVKTDSNAyIGELVSINGK 95
                                      67888889999999999999999988877.555556699999999999999999999999654336667777776 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 1.3e-06
                        Bactofilin   2 ligegtkikGelevegdlridG..kveGdieakgklvvgeggkvegnika.eevvv 54 
                                       ++ge+++++G+l++++++rid   k+ G+++++++  +ge  +++g++ + ++++v
  gi|298675941|ref|YP_003727691.1|  49 ILGESVQVSGDLTTTSEVRIDTlsKIGGSVKTDSNAYIGELVSINGKLIVnGDLDV 104
                                       7899999*************988799999999999999999999998554344555 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0014
                        Bactofilin  61 nveaeekvelkktakveGdikaksleieegavfeGkl 97 
                                       ++++ ++ ++ +++++ G+i+++s+++ ++ ++ G++
  gi|298675941|ref|YP_003727691.1| 182 SIHVPAHASIGNNCRLIGNIRSSSFDMGDDTTLYGSI 218
                                       78999999**********************9999986 PP

  == domain 4  score: 29.1 bits;  conditional E-value: 1.6e-10
                        Bactofilin   3 igegtkikGeleve.gdlridGkveGdieakgklvvgeggkvegnika.eevvvaGt..vkGnveaeekvelkktak 75 
                                       ig+++++ G+++++  d+  d ++ G+i++++++++g++ +++gni + ++v+++ +  + G+v a+ ++ ++++a+
  gi|298675941|ref|YP_003727691.1| 191 IGNNCRLIGNIRSSsFDMGDDTTLYGSIRTHNDITIGKNNNIHGNIVSkKNVTIDKEthILGEVSAN-TIFIHENAR 266
                                       6777777777775535666677777777777777777777777776664667777552244777777.777777777 PP

                        Bactofilin  76 veGdik 81 
                                       v+G ++
  gi|298675941|ref|YP_003727691.1| 267 VDGLMR 272
                                       777655 PP

>> DUF3494  Protein of unknown function (DUF3494)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   1.1      0.04   2.4e+02     164     188 ..      48      72 ..      22     108 .. 0.53
   2 ?   13.4   0.2   7.4e-06     0.044     163     198 ..     223     258 ..     217     265 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.04
                                       EEE-TT-EEEEEEEESS-EEE-TT- CS
                           DUF3494 164 atlgtgstfeGtilaqtsitlstga 188
                                       a lg   +++G     +++ ++t +
  gi|298675941|ref|YP_003727691.1|  48 AILGESVQVSGDLTTTSEVRIDTLS 72 
                                       4444444444444444444444444 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 7.4e-06
                                       -EEE-TT-EEEEEEEESS-EEE-TT-EEEEEEEESS CS
                           DUF3494 163 satlgtgstfeGtilaqtsitlstgatvnGrllaqt 198
                                        +t+g +++++G+i++++++t+++++ + G++ a+t
  gi|298675941|ref|YP_003727691.1| 223 DITIGKNNNIHGNIVSKKNVTIDKETHILGEVSANT 258
                                       689*****************************9987 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   1.0    0.0023        14      13      29 ..      24      40 ..      11      42 .. 0.77
   2 ?   -1.5   0.0      0.41   2.5e+03      10      21 ..      44      55 ..      43      57 .. 0.54
   3 ?    4.9   0.1     0.004        24       8      34 ..      66      92 ..      59      94 .. 0.69
   4 ?    4.5   2.2    0.0052        31       2      29 ..      84     111 ..      83     113 .. 0.83
   5 ?    4.1   0.1     0.007        42      19      27 ..     188     196 ..     181     202 .. 0.54
   6 ?    3.8   1.4    0.0088        53      17      30 ..     221     234 ..     208     237 .. 0.71
   7 ?    0.4   0.0       0.1     6e+02       6      20 ..     240     254 ..     239     255 .. 0.84
   8 ?   -2.0   0.0       0.6   3.6e+03       2      10 ..     259     267 ..     258     269 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0023
                                      TEEEETTEEE-TTEEEE CS
                           Hexapep 13 faviggnVkIGdnvkIg 29
                                      + v+ g+V++G+++ I 
  gi|298675941|ref|YP_003727691.1| 24 NIVVDGGVIVGSHSNIN 40
                                      77888899999988885 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.41
                                      E-TTEEEETTEE CS
                           Hexapep 10 IgpfaviggnVk 21
                                      I + a++g+ V+
  gi|298675941|ref|YP_003727691.1| 44 IANSAILGESVQ 55
                                      455555555555 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.004
                                      EEE-TTEEEETTEEE-TTEEEETTEEE CS
                           Hexapep  8 vlIgpfaviggnVkIGdnvkIgagvvi 34
                                      v I+  ++igg Vk  +n++Ig+ v i
  gi|298675941|ref|YP_003727691.1| 66 VRIDTLSKIGGSVKTDSNAYIGELVSI 92
                                      677777777777777777777776655 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.0052
                                       EEEETTEEE-TTEEEETTEEE-TTEEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIg 29 
                                       + IG+ v I    ++ g+  +G+nvkI 
  gi|298675941|ref|YP_003727691.1|  84 AYIGELVSINGKLIVNGDLDVGNNVKIN 111
                                       6788888899999999999999999996 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.007
                                       TEEE-TTEE CS
                           Hexapep  19 nVkIGdnvk 27 
                                       ++ IG+n++
  gi|298675941|ref|YP_003727691.1| 188 HASIGNNCR 196
                                       444444443 PP

  == domain 6  score: 3.8 bits;  conditional E-value: 0.0088
                                       ETTEEE-TTEEEET CS
                           Hexapep  17 ggnVkIGdnvkIga 30 
                                       +++++IG+n  I+ 
  gi|298675941|ref|YP_003727691.1| 221 HNDITIGKNNNIHG 234
                                       67888888888876 PP

  == domain 7  score: 0.4 bits;  conditional E-value: 0.1
                                       TTEEE-TTEEEETTE CS
                           Hexapep   6 snvlIgpfaviggnV 20 
                                       +nv+I++ ++i+g V
  gi|298675941|ref|YP_003727691.1| 240 KNVTIDKETHILGEV 254
                                       699999999999877 PP

  == domain 8  score: -2.0 bits;  conditional E-value: 0.6
                                       EEEETTEEE CS
                           Hexapep   2 tvIGsnvlI 10 
                                       ++I++n+ +
  gi|298675941|ref|YP_003727691.1| 259 IFIHENARV 267
                                       578888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2187.96
//
Query:       gi|298675942|ref|YP_003727692.1|  [L=176]
Description: ArsR family transcriptional regulator [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-14   53.7   0.8    2.8e-14   52.7   0.3    1.7  2  HTH_5            Bacterial regulatory protein, arsR family
    9.6e-11   41.6   0.0    1.4e-10   41.1   0.0    1.2  1  HTH_20           Helix-turn-helix domain
    9.1e-09   35.1   0.1    1.5e-08   34.4   0.1    1.3  1  MarR             MarR family
    6.8e-08   32.3   0.2    1.2e-07   31.4   0.2    1.3  1  HxlR             HxlR-like helix-turn-helix
    2.2e-06   27.1   0.2    4.5e-06   26.1   0.2    1.6  1  HTH_24           Winged helix-turn-helix DNA-binding
    2.3e-06   27.4   0.0    3.7e-06   26.7   0.0    1.3  1  MarR_2           MarR family
    9.8e-06   26.0   0.1    1.6e-05   25.3   0.1    1.4  1  HTH_27           Winged helix DNA-binding domain
    3.8e-05   23.5   0.1    6.5e-05   22.7   0.1    1.3  1  TrmB             Sugar-specific transcriptional regulator Trm
    7.4e-05   22.9   0.1    0.00012   22.2   0.1    1.3  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
    0.00038   20.2   0.0    0.00073   19.3   0.0    1.5  1  HTH_IclR         IclR helix-turn-helix domain
    0.00049   20.0   0.1    0.00086   19.2   0.1    1.5  1  HTH_36           Helix-turn-helix domain
    0.00062   19.7   0.3    0.00092   19.1   0.3    1.2  1  HTH_45           Winged helix-turn-helix
      0.001   18.8   0.0      0.002   17.9   0.0    1.4  1  HTH_10           HTH DNA binding domain
     0.0011   19.1   0.0     0.0017   18.4   0.0    1.3  1  HTH_28           Helix-turn-helix domain
     0.0013   18.6   0.2     0.0022   17.9   0.2    1.3  1  PadR             Transcriptional regulator PadR-like family
     0.0016   18.2   0.3     0.0037   17.0   0.2    1.7  1  IF2_N            Translation initiation factor IF-2, N-termin
     0.0016   18.8   0.1     0.0023   18.2   0.1    1.2  1  Penicillinase_R  Penicillinase repressor
      0.002   17.7   0.1     0.0027   17.3   0.1    1.1  1  DDRGK            DDRGK domain
     0.0029   17.5   0.3     0.0049   16.8   0.3    1.3  1  HTH_11           HTH domain
      0.003   17.5   0.0     0.0047   16.9   0.0    1.3  1  HTH_Crp_2        Crp-like helix-turn-helix domain
     0.0031   17.7   0.1     0.0047   17.1   0.1    1.3  1  HTH_34           Winged helix DNA-binding domain
     0.0035   17.0   0.1     0.0061   16.2   0.1    1.3  1  HTH_41           Helix-turn-helix domain
     0.0038   17.5   0.0     0.0065   16.8   0.0    1.3  1  Rrf2             Transcriptional regulator
      0.004   17.1   0.0      0.006   16.6   0.0    1.2  1  HTH_29           Winged helix-turn helix
     0.0049   16.6   0.1     0.0076   16.0   0.1    1.2  1  HTH_DeoR         DeoR-like helix-turn-helix domain
     0.0062   16.2   0.1     0.0094   15.6   0.1    1.3  1  GntR             Bacterial regulatory proteins, gntR family
     0.0085   16.1   0.3      0.015   15.3   0.3    1.4  1  BLACT_WH         Beta-lactamase associated winged helix domai
  ------ inclusion threshold ------
      0.015   15.4   0.0       0.13   12.4   0.0    2.2  1  HTH_22           HTH domain
      0.015   15.9   0.3      0.025   15.1   0.3    1.3  1  Mga              Mga helix-turn-helix domain
      0.027   14.9   0.0      0.042   14.3   0.0    1.3  1  HTH_40           Helix-turn-helix domain
      0.036   14.4   0.0      0.065   13.6   0.0    1.3  1  FaeA             FaeA-like protein
      0.056   13.4   0.2       0.15   12.1   0.1    1.6  2  Phage_holin_2_1  Bacteriophage P21 holin S
      0.058   13.2   0.1      0.096   12.5   0.1    1.4  1  LexA_DNA_bind    LexA DNA binding domain
      0.092   12.2   0.0       0.13   11.7   0.0    1.2  1  RepL             Firmicute plasmid replication protein (RepL)
      0.093   12.7   0.2       0.17   11.9   0.2    1.6  1  HTH_12           Ribonuclease R winged-helix domain
      0.095   12.9   0.0       0.15   12.3   0.0    1.4  1  PaaX             PaaX-like protein
       0.14   12.3   1.7       0.87    9.7   0.3    2.2  2  DUF2250          Uncharacterized protein conserved in archaea
       0.14   12.0   0.2       0.27   11.1   0.0    1.5  1  HTH_30           PucR C-terminal helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7   0.3     6e-17   2.8e-14       3      46 ..      18      61 ..      16      62 .. 0.96
   2 ?   -1.6   0.0       5.4   2.6e+03       3      10 ..      88      95 ..      86      95 .. 0.80

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 6e-17
                                      HHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  3 tRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                       R++I+k+L+e+++ v++lae+++ls++t+ +HLkkL+e+GL++
  gi|298675942|ref|YP_003727692.1| 18 SRIEIIKYLNEKSMRVTDLAEKMQLSKPTLIEHLKKLEESGLID 61
                                      7*****************************************96 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5.4
                                      HHHHHHHH CS
                             HTH_5  3 tRlkILkl 10
                                       R+kIL++
  gi|298675942|ref|YP_003727692.1| 88 IRVKILFA 95
                                      7****975 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.0   2.9e-13   1.4e-10       4      60 ..      11      66 ..       8      67 .. 0.96

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 2.9e-13
                                      HHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20  4 aeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                      ++ALa+ +R +i ++L  ++ + +++lae ++lsk tl  HL++Lee gL++++  g
  gi|298675942|ref|YP_003727692.1| 11 FKALASDSRIEIIKYL-NEKSMRVTDLAEKMQLSKPTLIEHLKKLEESGLIDRENRG 66
                                      89**************.***********************************99876 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.1   3.1e-11   1.5e-08      15      50 ..      28      63 ..      20      67 .. 0.92

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 3.1e-11
                                      STTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR 15 qgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      + +++v++La+k+++sk+t+ + l++Le+ Gli+R+
  gi|298675942|ref|YP_003727692.1| 28 EKSMRVTDLAEKMQLSKPTLIEHLKKLEESGLIDRE 63
                                      5789*******************************7 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.2   2.6e-10   1.2e-07      10      74 ..      22      83 ..      18      88 .. 0.90

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 2.6e-10
                                      HHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHH CS
                              HxlR 10 ilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslep 74
                                      i+  l ++++R ++l++++ ++s+ +L+++L++Le++gli+re   e  + v Y+lt+k r+l++
  gi|298675942|ref|YP_003727692.1| 22 IIKYLNEKSMRVTDLAEKM-QLSKPTLIEHLKKLEESGLIDRENRGE--KWVYYRLTDKSRNLME 83
                                      7888999************.**********************97665..5679*******99975 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.2   9.5e-09   4.5e-06       5      47 ..      19      60 ..      16      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 9.5e-09
                            HTH_24  5 drkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      +++I+++L +  ++  ++LAe+  lS++t+ ++lk+Lee+GlI
  gi|298675942|ref|YP_003727692.1| 19 RIEIIKYLNE-KSMRVTDLAEKMQLSKPTLIEHLKKLEESGLI 60
                                      5677777777.778899*************************9 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   7.9e-09   3.7e-06      21      54 ..      30      63 ..      15      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 7.9e-09
                                      EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 21 dltvgelarrlglsksavsrilkrLvaaGLverr 54
                                       ++v++la++++lsk+++  +lk+L++ GL+ r+
  gi|298675942|ref|YP_003727692.1| 30 SMRVTDLAEKMQLSKPTLIEHLKKLEESGLIDRE 63
                                      489****************************998 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.1   3.5e-08   1.6e-05      18      67 ..      30      77 ..      20      78 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 3.5e-08
                            HTH_27 18 rkkladlcgrlnvedshisyslkkLtekGLvertgdeadrre..krvrlTdk 67
                                       ++ +dl++++++++ + ++ lkkL+e GL+    d+++r+e  + +rlTdk
  gi|298675942|ref|YP_003727692.1| 30 SMRVTDLAEKMQLSKPTLIEHLKKLEESGLI----DRENRGEkwVYYRLTDK 77
                                      45679**************************....8889999889******8 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1   1.4e-07   6.5e-05      18      62 ..      26      72 ..      23      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.4e-07
                                      HHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT..EE CS
                              TrmB 18 lklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpk..lY 62
                                      l++++++++++ae+  +++++  e L++Le+ Gl++re +  k  +Y
  gi|298675942|ref|YP_003727692.1| 26 LNEKSMRVTDLAEKMQLSKPTLIEHLKKLEESGLIDRENRGEKwvYY 72
                                      78999*********************************966333244 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.1   2.5e-07   0.00012      21      56 ..      29      64 ..      22      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.5e-07
                                      SSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                    Fe_dep_repress 21 kvvktkdlaerLnvspssVsemlkkLekdGyveyek 56
                                      k  +++dlae ++ s+++  e lkkLe+ G+++ e 
  gi|298675942|ref|YP_003727692.1| 29 KSMRVTDLAEKMQLSKPTLIEHLKKLEESGLIDREN 64
                                      56789**************************99776 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.6e-06   0.00073      17      50 ..      29      62 ..      20      64 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.6e-06
                                      SS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 17 qeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                        +++++lA++  l+k+t   +L+ L+e G++ +
  gi|298675942|ref|YP_003727692.1| 29 KSMRVTDLAEKMQLSKPTLIEHLKKLEESGLIDR 62
                                      3488***************************987 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   1.8e-06   0.00086      28      55 .]      33      60 ..      12      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.8e-06
                            HTH_36 28 qetlakrlglsknTvsraikeLeqlGyi 55
                                      + +la+++ lsk T + ++k+Le+ G+i
  gi|298675942|ref|YP_003727692.1| 33 VTDLAEKMQLSKPTLIEHLKKLEESGLI 60
                                      789***********************98 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.3     2e-06   0.00092      10      68 ..      21      84 ..      17      92 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2e-06
                            HTH_45 10 dILeaisegeakkTkimykanLsykllnkYLdmLvekgli.....kkskekYvlTekGlellek 68
                                      +I ++++e++ + T +  k  Ls  +l + L++L e gli      ++   Y+lT+k ++l+e 
  gi|298675942|ref|YP_003727692.1| 21 EIIKYLNEKSMRVTDLAEKMQLSKPTLIEHLKKLEESGLIdrenrGEKWVYYRLTDKSRNLMEP 84
                                      8999************************************986544556679******999985 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   4.2e-06     0.002      22      49 ..      29      56 ..      25      58 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4.2e-06
                            HTH_10 22 RrvtlkeLAkelGIskstlsehLrkaes 49
                                      + +++ +LA+++ +sk+tl ehL+k e+
  gi|298675942|ref|YP_003727692.1| 29 KSMRVTDLAEKMQLSKPTLIEHLKKLEE 56
                                      678899******************9886 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   3.6e-06    0.0017       2      47 ..      19      62 ..      18      67 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.6e-06
                            HTH_28  2 RleiikllaaG.hsvreaArelgisrrtvyrWikryeegGiagLvpr 47
                                      R+eiik+l +  ++v+++A+++++s  t+   +k++ee G   L +r
  gi|298675942|ref|YP_003727692.1| 19 RIEIIKYLNEKsMRVTDLAEKMQLSKPTLIEHLKKLEESG---LIDR 62
                                      99*******7626*************************66...5776 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.2   4.6e-06    0.0022      26      71 ..      39      80 ..      21      83 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4.6e-06
                                      -CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCH CS
                              PadR 26 llelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrr 71
                                       ++ls+ +l   Lk+Le++gl+++e++    g +  yYrlTd+ r+
  gi|298675942|ref|YP_003727692.1| 39 KMQLSKPTLIEHLKKLEESGLIDRENR----GEKWVYYRLTDKSRN 80
                                      3789999999*************9966....679********9886 PP

>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.2   7.9e-06    0.0037       2      28 ..      29      54 ..      28      59 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 7.9e-06
                             IF2_N  2 skirVyeLAkeLgvkskevikkLfkel 28
                                      + +rV +LA++++++   +i++L+k l
  gi|298675942|ref|YP_003727692.1| 29 KSMRVTDLAEKMQLSKPTLIEHLKK-L 54
                                      679********************44.6 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1     5e-06    0.0023      25      97 ..      34     107 ..      18     110 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 5e-06
                                       HT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE----XXX.XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                   Penicillinase_R  25 eeleeekelaysTVktllrrLvkKgllsrekegrafiYsplvseee.avasavkqlldklfegsvkelvaafve 97 
                                       + l+e+++l++ T    l++L++ gl++re+ g + +Y+ l+++++ +++ +++  ++ lf++sv ++++ f++
  gi|298675942|ref|YP_003727692.1|  34 TDLAEKMQLSKPTLIEHLKKLEESGLIDRENRGEKWVYYRLTDKSRnLMEPKSDIRVKILFATSVVAFISGFAQ 107
                                       5699999******************************9999998751666777778888899999998888875 PP

>> DDRGK  DDRGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   5.6e-06    0.0027     103     143 ..      21      60 ..       5      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.6e-06
                                       HHHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS CS
                             DDRGK 103 efinyikekKvvlleelavkfklktqevierikeLeeqgsl 143
                                       e+i+y++e K + +++la k++l+    ie +k+Lee+g +
  gi|298675942|ref|YP_003727692.1|  21 EIIKYLNE-KSMRVTDLAEKMQLSKPTLIEHLKKLEESGLI 60 
                                       78999875.7889************************9987 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.3     1e-05    0.0049       4      45 ..      21      59 ..      19      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1e-05
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvp 45
                                       i++ L ++++ +   +LAe++ +S+ t   ++k+Lee+g  
  gi|298675942|ref|YP_003727692.1| 21 EIIKYL-NEKS-MRVTDLAEKMQLSKPTLIEHLKKLEESG-L 59
                                      689999.6665.999************************9.3 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     1e-05    0.0047      22      55 ..      31      65 ..      11      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1e-05
                                      HHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE.TE CS
                         HTH_Crp_2 22 ltqeelAsmlGltretvsrilseLkreglisr.gr 55
                                      +  ++lA+ + l+  t+   l++L++ gli+r +r
  gi|298675942|ref|YP_003727692.1| 31 MRVTDLAEKMQLSKPTLIEHLKKLEESGLIDReNR 65
                                      6678***************************6233 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   9.9e-06    0.0047       2      68 ..      19      81 ..      18      88 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 9.9e-06
                            HTH_34  2 RlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGrea 68
                                      R++++ yL++ +++  ++l e++++++  L  hlkkLe+ g i ++   +   +   +r+T++ r+ 
  gi|298675942|ref|YP_003727692.1| 19 RIEIIKYLNE-KSMRVTDLAEKMQLSKPTLIEHLKKLEESGLIDRENRGE---KWVYYRLTDKSRNL 81
                                      8899999985.68999*************************998775433...45778888877765 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   1.3e-05    0.0061       7      42 ..      31      66 ..      27      68 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.3e-05
                            HTH_41  7 ktIeelakeleLSvGlvQkALklLeddkaislerrG 42
                                       ++++la+++ LS  +    Lk+Le+++ i  e rG
  gi|298675942|ref|YP_003727692.1| 31 MRVTDLAEKMQLSKPTLIEHLKKLEESGLIDRENRG 66
                                      589******************************999 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.4e-05    0.0065      21      56 ..      26      61 ..      10      69 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.4e-05
                                      STCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 21 eeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                       +e++++++++ae++++s++ l   l+kL+++gl+ 
  gi|298675942|ref|YP_003727692.1| 26 LNEKSMRVTDLAEKMQLSKPTLIEHLKKLEESGLID 61
                                      456679****************************96 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.3e-05     0.006       1      51 [.      19      66 ..      19      71 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.3e-05
                            HTH_29  1 RaqallllaeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsg 51
                                      R++++  l+e  ++v ++A+ ++ls++t   +lk  ee G   l+dr ++g
  gi|298675942|ref|YP_003727692.1| 19 RIEIIKYLNEKSMRVTDLAEKMQLSKPTLIEHLKKLEESG---LIDRENRG 66
                                      8999999999999***************************...78855444 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   1.6e-05    0.0076       4      46 ..      21      62 ..      19      67 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.6e-05
                          HTH_DeoR  4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltR 46
                                      +i+++l++  +++v++l+e  + S+ T    L++Lee+gl+ R
  gi|298675942|ref|YP_003727692.1| 21 EIIKYLNE-KSMRVTDLAEKMQLSKPTLIEHLKKLEESGLIDR 62
                                      69999986.58******************************98 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1     2e-05    0.0094      20      59 ..      27      65 ..      17      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2e-05
                                      TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                              GntR 20 pGdkLPsereLaaefgVsrttvReALrrLeaeglverrqg 59
                                       +  + ++ +La+++  s++t+ e L++Le+ gl+ r+++
  gi|298675942|ref|YP_003727692.1| 27 NEKSM-RVTDLAEKMQLSKPTLIEHLKKLEESGLIDRENR 65
                                      56778.999***************************9987 PP

>> BLACT_WH  Beta-lactamase associated winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.3   3.1e-05     0.015      25      47 .]      47      69 ..      44      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.1e-05
                          BLACT_WH 25 vlahLeKLeeeGkVkregdkgkW 47
                                      ++ hL+KLee G++ re   +kW
  gi|298675942|ref|YP_003727692.1| 47 LIEHLKKLEESGLIDRENRGEKW 69
                                      789*************9887888 PP

>> HTH_22  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00028      0.13      17      62 ..      11      51 ..       2      52 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00028
                            HTH_22 17 verltkeekieivraLdekGiFllkgavekvAekLgiSraTvYryL 62
                                       ++l ++ +iei+++L+ek +      v  +Aek++ S++T+  +L
  gi|298675942|ref|YP_003727692.1| 11 FKALASDSRIEIIKYLNEKSM-----RVTDLAEKMQLSKPTLIEHL 51
                                      578999*************65.....58899999999999986666 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.3   5.3e-05     0.025      13      56 ..      14      56 ..       4      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.3e-05
                                      HHHSHHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHHH CS
                               Mga 13 lkeslkyqllkflfeeeevsieelaqelyiSestlkrkikelnk 56
                                      l+++  ++++k+l +e+++ +++la+++ +S+ tl  ++k+l++
  gi|298675942|ref|YP_003727692.1| 14 LASDSRIEIIKYL-NEKSMRVTDLAEKMQLSKPTLIEHLKKLEE 56
                                      6677778888887.59*************************986 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   8.8e-05     0.042       8      44 ..      26      61 ..      19      89 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.8e-05
                            HTH_40  8 lleeglsieeIAkerglkesTIegHLaelieegeeid 44
                                      l e+++ + + A++ +l++ T ++HL +l e+g  id
  gi|298675942|ref|YP_003727692.1| 26 LNEKSMRVTDLAEKMQLSKPTLIEHLKKLEESGL-ID 61
                                      33899************************99985.55 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   0.00014     0.065       4      49 ..      21      64 ..      19      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00014
                                      HHHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE- CS
                              FaeA  4 eIleylnsikapckTreiAdalglsaYQaRyYLeqLekegkikrsp 49
                                      eI++yln+   + + +++A+ + ls       L++Le  g i r +
  gi|298675942|ref|YP_003727692.1| 21 EIIKYLNE--KSMRVTDLAEKMQLSKPTLIEHLKKLEESGLIDREN 64
                                      7*******..9********************************987 PP

>> Phage_holin_2_1  Bacteriophage P21 holin S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       9.2   4.3e+03       6      24 ..      91     109 ..      86     116 .. 0.63
   2 ?   12.1   0.1   0.00032      0.15      25      58 ..     141     172 ..     140     175 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 9.2
                   Phage_holin_2_1   6 gvsYgaSggsigywlkqll 24 
                                        + +++S    + +++ql+
  gi|298675942|ref|YP_003727692.1|  91 KILFATSVVAFISGFAQLY 109
                                       5556666666666777776 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00032
                   Phage_holin_2_1  25 dklspeeWsaigvlgglvigllTyltnlYFKrke 58 
                                       d +s   W a+ +lg  +  +lT +t +YFK ++
  gi|298675942|ref|YP_003727692.1| 141 DVVSAIPWDAVILLG--IAVVLTSITIWYFKTRN 172
                                       567888899998887..55699*********986 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1    0.0002     0.096      28      60 ..      33      64 ..      20      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0002
                                      HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE-GG CS
                     LexA_DNA_bind 28 ireiaralglkSpsaveehLkaLerKGyierdp 60
                                      + ++a++++l+ p +  ehLk+Le  G+i+r++
  gi|298675942|ref|YP_003727692.1| 33 VTDLAEKMQLSKP-TLIEHLKKLEESGLIDREN 64
                                      568999****855.56689***********986 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00027      0.13      77     111 ..      32      66 ..      19      77 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00027
                              RepL  77 tnRelaeetgislktvsetlkileeanilkkkanG 111
                                        +  lae+  +s  t +e lk lee++++ +++ G
  gi|298675942|ref|YP_003727692.1|  32 RVTDLAEKMQLSKPTLIEHLKKLEESGLIDRENRG 66 
                                       45689***************************988 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   0.00036      0.17      31      55 ..      43      67 ..      20      82 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00036
                            HTH_12 31 geravRyrLrkleergltrrvgyag 55
                                      ++ ++  +L+klee gl+ r  ++ 
  gi|298675942|ref|YP_003727692.1| 43 SKPTLIEHLKKLEESGLIDRENRGE 67
                                      4455567*************99983 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00032      0.15      32      69 ..      39      77 ..      29      78 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00032
                              PaaX 32 elGiseslvRaalsRlakaGwlvrekegr.rsfYrLsdk 69
                                      ++ +s  ++   l  l++ G+++re+ g   ++YrL+dk
  gi|298675942|ref|YP_003727692.1| 39 KMQLSKPTLIEHLKKLEESGLIDRENRGEkWVYYRLTDK 77
                                      55566666666788999*********999789******8 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.3    0.0019      0.87       9      57 ..      18      65 ..      12      67 .. 0.78
   2 ?    1.7   0.1      0.59   2.8e+02      77      89 ..      69      81 ..      63      83 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0019
                           DUF2250  9 lalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerveg 57
                                        ++++k+l++        +a+++++++    e lkkLee GL++r ++
  gi|298675942|ref|YP_003727692.1| 18 SRIEIIKYLNEKSMRV-TDLAEKMQLSKPTLIEHLKKLEESGLIDRENR 65
                                      5677777777765543.467888999999999*************9875 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.59
                           DUF2250 77 HtYYrltreGell 89
                                        YYrlt++   l
  gi|298675942|ref|YP_003727692.1| 69 WVYYRLTDKSRNL 81
                                      58*****998766 PP

>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00056      0.27      10      38 ..      28      56 ..      21      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00056
                                      HTTT-HHHHHHHHTS-HHHHHHHHHHHHH CS
                            HTH_30 10 enggnisatAkaLhvHrnTlryRLrriee 38
                                      e ++++++ A+++ +++ Tl   L+++ee
  gi|298675942|ref|YP_003727692.1| 28 EKSMRVTDLAEKMQLSKPTLIEHLKKLEE 56
                                      56799***********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      639  (0.0356406); expected 358.6 (0.02)
Passed Vit filter:                       126  (0.00702772); expected 17.9 (0.001)
Passed Fwd filter:                        38  (0.00211947); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              38  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1225.63
//
Query:       gi|298675943|ref|YP_003727693.1|  [L=464]
Description: hypothetical protein Metev_2069 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.017   15.2   0.2      0.058   13.6   0.2    2.0  1  Top6b_C   Type 2 DNA topoisomerase 6 subunit B C-terminal dom
      0.033   14.3   0.0      0.083   13.0   0.0    1.6  1  SM-ATX    Ataxin 2 SM domain
      0.055   13.9   0.1       0.14   12.6   0.1    1.6  1  DUF4140   N-terminal domain of unknown function (DUF4140)
      0.058   13.1   0.1        0.2   11.4   0.1    1.9  1  LSM       LSM domain
       0.93    9.2   4.6        4.4    7.0   1.3    3.2  2  DUF4139   Domain of unknown function (DUF4139)


Domain annotation for each model (and alignments):
>> Top6b_C  Type 2 DNA topoisomerase 6 subunit B C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   1.6e-05     0.058      31      97 ..     381     445 ..     345     460 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.6e-05
                                       EEEEEEE---------EEE--EES-----------EEE-SSSEEE-EEE---TT-EEEE----SS-G CS
                           Top6b_C  31 vevslkvkNfsdkkeefelheilpaeieeaspeakvvemdneydlkWelsvsageskvleYsvdsea 97 
                                        + ++++ Nf+++ +++++  + ++     s + + ve + + +++W++ v+ ++ k++e++v+++ 
  gi|298675943|ref|YP_003727693.1| 381 RTGEINITNFGNNPKTVTVRYMWEFGELLDS-SVEPVETNAD-FVEWDIRVGVNSDKTIEFEVAEDI 445
                                       456899*****************99764444.7888998888.589*****************9875 PP

>> SM-ATX  Ataxin 2 SM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.3e-05     0.083      10      35 ..     104     129 ..     100     166 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.3e-05
                                       TTTTSEEEEEETTS-EEEEEEEEE-T CS
                            SM-ATX  10 slvGkevevtvknGevyeGifstvsl 35 
                                       + +Gkeve+++++G++ +G++  +  
  gi|298675943|ref|YP_003727693.1| 104 TNIGKEVEIELTSGKTVSGVLLRIED 129
                                       569*****************977666 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   3.8e-05      0.14       9      64 ..      47     104 ..      42     128 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.8e-05
                           DUF4140   9 evtreikvelkaGtnevtiegLpp..tldedSlrVegagaatildvqvervpnreaee 64 
                                        v+++i++el++G + v++e++ +  ++d+dS++ e +++ ++  v++++++++++++
  gi|298675943|ref|YP_003727693.1|  47 IVEKSISLELEQGVQWVELEDMENldNVDPDSIKLEPENSDVLEVVDIKTDFRDNIKT 104
                                       58999******************999**********8888455555555555555444 PP

>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   5.5e-05       0.2       3      29 ..     102     128 ..     100     131 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.5e-05
                                       HHHTTTSEEEEEETTSEEEEEEEEEEE CS
                               LSM   3 lkklinkkvtvelkngrelrGtLkgfD 29 
                                       +k  i+k+v +el++g++++G+L  ++
  gi|298675943|ref|YP_003727693.1| 102 IKTNIGKEVEIELTSGKTVSGVLLRIE 128
                                       78899*****************97765 PP

>> DUF4139  Domain of unknown function (DUF4139)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1     0.086   3.1e+02     130     157 ..     105     133 ..      89     168 .. 0.78
   2 ?    7.0   1.3    0.0012       4.4       2      43 ..     180     221 ..     179     445 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.086
                                       xxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                           DUF4139 130 rveyaytitvkNtks.epvtlkvedqvPv 157
                                        + ++++i+++  k+ ++v l++ed++P 
  gi|298675943|ref|YP_003727693.1| 105 NIGKEVEIELTSGKTvSGVLLRIEDNYPY 133
                                       5567899999999999**********995 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0012
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4139   2 kvsyvvseagWsPlYdlrldtakeevqltykAkvyQktgeDW 43 
                                       ++ y v+  +W ++Ydl +++++++  ++    + + +  ++
  gi|298675943|ref|YP_003727693.1| 180 QLRYRVNGITWDASYDLYMKDSDSSSRFSGDMIIKNPSNTNY 221
                                       689*****************9999877776666666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 3095.39
//
Query:       gi|298675944|ref|YP_003727694.1|  [L=410]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-23   83.8   0.1    4.9e-23   81.6   0.0    2.2  3  OrfB_IS605      Probable transposase
    2.8e-10   40.0   0.2    9.6e-10   38.3   0.1    2.1  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0041   16.9   0.5      0.012   15.5   0.5    1.8  1  DUF919          Nucleopolyhedrovirus protein of unknown funct
  ------ inclusion threshold ------
      0.011   16.1   0.0      0.033   14.6   0.0    1.8  2  RuvX            Holliday junction resolvase


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.8   8.2e+03      71      86 ..      16      31 ..       7      44 .. 0.65
   2 ?   -1.8   0.0      0.76   3.4e+03      37      59 ..      39      61 ..      27      73 .. 0.74
   3 !   81.6   0.0   1.1e-26   4.9e-23      10     119 ..     185     292 ..     176     293 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.8
                        OrfB_IS605 71 kkasrklarlhrkrsr 86
                                       ++ ++l++l++++++
  gi|298675944|ref|YP_003727694.1| 16 YETLKRLTKLSKNLYN 31
                                      4455566666666655 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.76
                        OrfB_IS605 37 twflykgrrlksdykylakeiae 59
                                      + f+++g+ l++d  y + +  e
  gi|298675944|ref|YP_003727694.1| 39 QYFFNHGKYLDKDTAYHTVKENE 61
                                      45888999999999998877665 PP

  == domain 3  score: 81.6 bits;  conditional E-value: 1.1e-26
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsr 86 
                                        ++ + n++++iDlG+ n+at+vt++gt+f+ +gr++ks +++++ke+ +lqs ++k++       k+ r +++r  
  gi|298675944|ref|YP_003727694.1| 185 IAELDYNSHLSIDLGVDNFATCVTTSGTAFILDGRSIKSYNRWWNKEKSRLQSVYDKQN--IDNGIKMDRFSNNRFW 259
                                       56677899**************************************************9..8*************** PP

                        OrfB_IS605  87 rrkhllhklathliktlkevgvetLnvgnmkdi 119
                                       ++++++++ ++h++k++ e+ ++++++g++k+i
  gi|298675944|ref|YP_003727694.1| 260 KINDFMNQCVNHIVKHCLENKIGNVVIGELKEI 292
                                       ******************************987 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.3     6e+03       9      21 ..     167     179 ..     164     181 .. 0.88
   2 !   38.3   0.1   2.1e-13   9.6e-10       1      69 []     311     385 ..     311     385 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.3
                    OrfB_Zn_ribbon   9 eykakeyGikvee 21 
                                       +yk +++ i++++
  gi|298675944|ref|YP_003727694.1| 167 KYKGRWFEIEFVY 179
                                       79*******9987 PP

  == domain 2  score: 38.3 bits;  conditional E-value: 2.1e-13
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke......alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f+++k +l+ k++ +Gik++ev++ayTSk  +   +  k+      ++s+r    ++ g  +++D+n+a+Nil++
  gi|298675944|ref|YP_003727694.1| 311 FARFKYKLASKCEYHGIKYHEVDEAYTSKVDALALEPIKKnkkylgRRSKRGIFQSSTGRLINADINGALNILRK 385
                                       899**************************988777666666679**9*************************986 PP

>> DUF919  Nucleopolyhedrovirus protein of unknown function (DUF919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.5   2.6e-06     0.012      15      58 ..       4      45 ..       2      47 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.6e-06
                            DUF919 15 qaKrkltiksqHfErlkkitKnpkElqdlekklnklRqeFLnfg 58
                                       +K  l+ + q +E lk++tK +k l +   +l ++Rq+F+n g
  gi|298675944|ref|YP_003727694.1|  4 TQKNHLRADKQTYETLKRLTKLSKNLYNF--TLYTIRQYFFNHG 45
                                      58999******************888765..8**********98 PP

>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       2.6   1.2e+04       4      52 ..     194     244 ..     193     247 .. 0.61
   2 ?   14.6   0.0   7.4e-06     0.033      37     107 ..     266     346 ..     253     366 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.6
                                       EEEEESSSEEEEEEE-S--SS---EEEEE---H..HHHHHHHHHHHHHTT- CS
                              RuvX   4 lglDvGtkriGvAvsdplgilaspletierksk..ekdleelkelvkeeev 52 
                                       l++D+G  +    v+ + +++    + i++ ++  +k+ ++l+++ +++++
  gi|298675944|ref|YP_003727694.1| 194 LSIDLGVDNFATCVTTSGTAFILDGRSIKSYNRwwNKEKSRLQSVYDKQNI 244
                                       567777777666666666666666666665555556666667766666666 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 7.4e-06
                                       HHHHHHHHHHHHHTT--EEEEE--........----SSS---SSTTHHHHHHHHHT....T-EEEEE--S----XXX CS
                              RuvX  37 ekdleelkelvkeeeveeiVvGlP........lnldgsegesakkvrkfaeeLakrl..kklpvelvDErlttveae 103
                                       ++ ++++ + + e+++ ++V+G          +  +++++ ++  +++f  +La+++  ++++ + vDE +t++  +
  gi|298675944|ref|YP_003727694.1| 266 NQCVNHIVKHCLENKIGNVVIGELkeikqeqnIGKQNTQNFQTIPFARFKYKLASKCeyHGIKYHEVDEAYTSKVDA 342
                                       68899*****************9867777766666777788888889999999999877899***********9766 PP

                                       XXXX CS
                              RuvX 104 rilr 107
                                        +l+
  gi|298675944|ref|YP_003727694.1| 343 LALE 346
                                       5553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1069  (0.0596241); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2663.31
//
Query:       gi|298675945|ref|YP_003727695.1|  [L=386]
Description: acetylornithine and succinylornithine aminotransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.3e-126  422.6   0.1   1.5e-126  422.3   0.1    1.1  1  Aminotran_3    Aminotransferase class-III
    4.6e-05   22.6   0.1    0.00015   20.8   0.1    1.8  2  Aminotran_5    Aminotransferase class-V
    0.00017   20.9   0.0    0.00076   18.7   0.0    1.9  1  Aminotran_1_2  Aminotransferase class I and II
  ------ inclusion threshold ------
      0.026   13.8   0.1      0.051   12.8   0.1    1.4  1  StbA           StbA protein
       0.12   12.5   0.2       0.82    9.8   0.0    2.2  2  Sigma70_r1_1   Sigma-70 factor, region 1.1
       0.18   11.7   0.3        8.2    6.4   0.0    2.5  3  OAM_alpha      D-ornithine 4,5-aminomutase alpha-subunit


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  422.3   0.1  5.1e-130  1.5e-126       4     405 ..      20     386 .]      17     386 .] 0.97

  Alignments for each domain:
  == domain 1  score: 422.3 bits;  conditional E-value: 5.1e-130
                                       TTB--SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHH CS
                       Aminotran_3   4 reednlllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekll 80 
                                       ++++  +++++k+eG++++dvd+++y+D +++iav+n+Gh+hP+vv+a+k+q ++l hvs +++ ++ + +laekl+
  gi|298675945|ref|YP_003727695.1|  20 QNYTRQPIALKKGEGAVVYDVDDNQYIDCLAGIAVNNVGHCHPNVVNAIKKQSEQLIHVS-NLYYTQIQTQLAEKLV 95 
                                       55666689****************************************************.999999********** PP

                                       HHCT-..SEEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSE CS
                       Aminotran_3  81 klapkgldkvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpev 157
                                       +l+    d++f++nsG+eA+e+A+Klar+        +kt ++a +++fHGrt g+lsvt++ +k ++ f p++ +v
  gi|298675945|ref|YP_003727695.1|  96 ELTEM--DRIFFCNSGAEAIESAMKLARS------VSKKTDFVAAEQSFHGRTIGSLSVTHK-EKFRKPFAPLIEDV 163
                                       ***98..**********************......99*************************.************** PP

                                       EEE-TTBGGGTB-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-T CS
                       Aminotran_3 158 vrlkypdeevlkeneeeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEv 234
                                        +++y+d                  +a+ + +++++aAvivEpiqgegGv+++s+++l++lr++c++ + lli+DEv
  gi|298675945|ref|YP_003727695.1| 164 NFVPYND-----------------SQAVADSITNNTAAVIVEPIQGEGGVNIPSNDYLKELRKICDDTGTLLIFDEV 223
                                       ******9.................567778999******************************************** PP

                                       TTTTTTTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHHHHHHT CS
                       Aminotran_3 235 qtGfGrTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgshgsTfgGnplacavalavleiieee 311
                                       qtGfGrTGk+f+ +h gv+pD+m++aKa++gG+p+ a++ ++ +  ++ +g+h+sTfgGnplaca++l ++++ie++
  gi|298675945|ref|YP_003727695.1| 224 QTGFGRTGKWFCKQHSGVQPDIMAMAKAMGGGFPIGAIASKEGI--TFDKGEHASTFGGNPLACAASLGAIRAIEDD 298
                                       ****************************************9999..5889*************************** PP

                                       THHHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTCHHHHHHHHHCTEE-EEETTTEEEE---T CS
                       Aminotran_3 312 kllenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevkekeilkkakekGvlilsaGdnvirllppl 388
                                        l+++ +elg+++ e+L++++ ++  + evRg+Glmi++elk++ +    +il+ a+e+Gvl+  + d+v+r++ppl
  gi|298675945|ref|YP_003727695.1| 299 SLVQRSKELGDYFVERLKNISRDD--VVEVRGRGLMIGMELKSDCK----KILNYARENGVLLNCTSDSVLRIVPPL 369
                                       *********************776..99*****************9....8***********999999********* PP

                                       T--HHHHHHHHHHHHHH CS
                       Aminotran_3 389 iitdeeidelleilkka 405
                                       +it+e+id++++ +++a
  gi|298675945|ref|YP_003727695.1| 370 VITSEQIDKVVDVIEQA 386
                                       *************9986 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   5.1e-08   0.00015      44     179 ..      82     225 ..      54     230 .. 0.81
   2 ?   -1.2   0.0      0.26   7.6e+02     260     296 ..     284     320 ..     246     354 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 5.1e-08
                                       HHHHHHHHHH.HHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEE CS
                       Aminotran_5  44 aveearekva.elinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvi 119
                                        ++++++++a +l++ ++ ++i f+ +++eai+ +++ + rs+++++ +v  e   h+ ++    + ++++++  ++
  gi|298675945|ref|YP_003727695.1|  82 YYTQIQTQLAeKLVELTEMDRIFFCNSGAEAIESAMKLA-RSVSKKTDFVAAEQSFHGRTIGSLSVTHKEKFRKPFA 157
                                       345555555424677777789************988766.88*********************************** PP

                                       EBETTSCBE....GGGHHHH--TTEEEEEEESBETTTTEB--....HHHHHHHHHHTT-EEEEE-TTT CS
                       Aminotran_5 120 pldeegeld....ldelekllnektklvaithvsnvtGtiqp....veeigklakkkgalvlvDaaqa 179
                                       pl e+ +       +++++ ++++t++v++  ++ + G+  p    ++e+ k++ + g l++ D +q+
  gi|298675945|ref|YP_003727695.1| 158 PLIEDVNFVpyndSQAVADSITNNTAAVIVEPIQGEGGVNIPsndyLKELRKICDDTGTLLIFDEVQT 225
                                       *999998753334899999********************655344478999999999*********97 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.26
                                       HHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTT CS
                       Aminotran_5 260 glgaaleyleeigleaiekhekelaeyllerlkslpg 296
                                       +++a l  +++i+ ++  +++kel +y +erlk++  
  gi|298675945|ref|YP_003727695.1| 284 ACAASLGAIRAIEDDSLVQRSKELGDYFVERLKNISR 320
                                       5667777788888899999999999999999999865 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.6e-07   0.00076      18     363 .]      62     383 ..      51     383 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.6e-07
                                       HHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHH.HTTT CS
                     Aminotran_1_2  18 ptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllk.lnpg 93 
                                       p + +++k++ e  +  +  n y ++  + +l e+l ++           + ++ +++   ++ie ++ l++ + ++
  gi|298675945|ref|YP_003727695.1|  62 PNVVNAIKKQSE--QLIHVSNLYYTQI-QTQLAEKLVELTE--------MD-RIFFCNSGAEAIESAMKLARsVSKK 126
                                       444455555555..6666666666665.7999999999999........77.8888887777787777777754444 PP

                                       -EEEEEESS.-THHHHHHHHTTSEEEEEEBEET...TTT..EE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B CS
                     Aminotran_1_2  94 deilvpdpt.yasyknilrlsggevvryplyse...edf..hldlealeealkeapegnkktkvilvesphNPtGtv 164
                                       +++++ +++ ++  +  l   + e +r p+ +     +f   +d +a+ + +++       t  ++ve ++   G+ 
  gi|298675945|ref|YP_003727695.1| 127 TDFVAAEQSfHGRTIGSLSVTHKEKFRKPFAPLiedVNFvpYNDSQAVADSITN------NTAAVIVEPIQGEGGVN 197
                                       444444444133444444444444444443332432122114677888887777......788************86 PP

                                       --.HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHH CS
                     Aminotran_1_2 165 at.leeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavv 240
                                       ++  + l++l ++++  + ll++De+  gf  + + + +++++v++++       ++Ka+G  G+ +G+i++++ + 
  gi|298675945|ref|YP_003727695.1| 198 IPsNDYLKELRKICDDTGTLLIFDEVQTGFGRTGKWFCKQHSGVQPDIM-----AMAKAMG-GGFPIGAIASKEGI- 267
                                       6515668999999********************9999999******988.....9*****9.47777887776644. PP

                                       HHHHHHHHHHTS.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS...TEEEECCSCSSEEEEEET CS
                     Aminotran_1_2 241 sqlrklsrpfls.ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael...glkvlasqsgmflltdls 313
                                          +  +    s     + a+aa+l +   +  e +  +qr +++ ++++++L+++   ++  +   + m+ + + s
  gi|298675945|ref|YP_003727695.1| 268 ---TFDKGEHAStFGGNPLACAASLGAIRAI--EDDSLVQRSKELGDYFVERLKNIsrdDVVEVRGRGLMIGMELKS 339
                                       ...3333333332244455555555555544..77899999999999999999999976666666655555554444 PP

                                       HHCHHHHHHHHHHTCTEEEEEGGGGTSTTEEEEEC.TTS-HHHHHHHHHHH CS
                     Aminotran_1_2 314 aetakelskkLleevgvyvtpgtsftvpgrlRitv.Aglteeeleelveal 363
                                           k++    +e+ gv++      t  + lRi +    t+e+++++v+ +
  gi|298675945|ref|YP_003727695.1| 340 -D-CKKILNYAREN-GVLLNC----TSDSVLRIVPpLVITSEQIDKVVDVI 383
                                       .4.35555555555.666555....55888999987778899999888765 PP

>> StbA  StbA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   1.7e-05     0.051     241     306 ..      69     134 ..      58     139 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.7e-05
                              StbA 241 edkresvlevinekvkkLkerviravsefsgythvmvvGGGaeliaeaikkatevsdekvikvdnp 306
                                       +++ e++++v n    +++ ++ +++ e++++ +++    Gae i++a+k a  vs+++ +++ + 
  gi|298675945|ref|YP_003727695.1|  69 KKQSEQLIHVSNLYYTQIQTQLAEKLVELTEMDRIFFCNSGAEAIESAMKLARSVSKKTDFVAAEQ 134
                                       4678899********************************************999988876665555 PP

>> Sigma70_r1_1  Sigma-70 factor, region 1.1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1      0.42   1.3e+03      19      42 ..      80     103 ..      73     105 .. 0.89
   2 ?    9.8   0.0   0.00027      0.82       5      48 ..     339     385 ..     336     386 .] 0.89

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.42
                                       CEEHHHHHHHGCCSS--HHHHHHH CS
                      Sigma70_r1_1  19 yLtyeEindaLpddeldseqiedi 42 
                                       +L y +i++ L ++ ++  +++ i
  gi|298675945|ref|YP_003727695.1|  80 NLYYTQIQTQLAEKLVELTEMDRI 103
                                       58899*********9999999987 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00027
                                       HHHHHHHHHHHHHSCE...EHHHHHHHGCCSS--HHHHHHHHHHHHC CS
                      Sigma70_r1_1   5 aavkeLikkgKkkGyL...tyeEindaLpddeldseqiediiemLed 48 
                                       +  k++++ +++ G+L   t++ +    p+ +++seqi+++++ +e+
  gi|298675945|ref|YP_003727695.1| 339 SDCKKILNYARENGVLlncTSDSVLRIVPPLVITSEQIDKVVDVIEQ 385
                                       6779999999999997677999*********************9986 PP

>> OAM_alpha  D-ornithine 4,5-aminomutase alpha-subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.035     1e+02      65      96 ..      17      49 ..       9      68 .. 0.74
   2 ?   -3.6   0.0       3.4     1e+04      27      39 ..      85      97 ..      69     102 .. 0.54
   3 ?    6.4   0.0    0.0027       8.2      14      87 ..     293     365 ..     288     378 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.035
                                      HHHHHHHHTTG.GGG-HHHHHHHHHHHTT--HH CS
                         OAM_alpha 65 aivekvlekgl.lgkGaGhvvyrlakeknidir 96
                                       ++++   + + l kG G vvy +  ++ id  
  gi|298675945|ref|YP_003727695.1| 17 YVMQNYTRQPIaLKKGEGAVVYDVDDNQYIDCL 49
                                      555555555443799*********999998865 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3.4
                                      HHHHHHHHHHHHH CS
                         OAM_alpha 27 elaekivdPliel 39
                                      ++ +++ + l+el
  gi|298675945|ref|YP_003727695.1| 85 QIQTQLAEKLVEL 97
                                      3444444444444 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0027
                                       TTS-HHHHHHHHHHHHHHHHHHHHHHHHHEE-HHHHHHHHHHTT--HHHHHHHHHHHHHTTGGGG-HHHHHHHH CS
                         OAM_alpha  14 aelsdeeleerfWelaekivdPlielarkhtspsiersvLLrmGlssleakaivekvlekgllgkGaGhvvyrl 87 
                                       + ++d+ l +r  el +  v+ l +++r    +   r  ++ m l+s ++k+i++ + e+g+l +   + v+r+
  gi|298675945|ref|YP_003727695.1| 293 RAIEDDSLVQRSKELGDYFVERLKNISRDDVVEVRGRGLMIGMELKS-DCKKILNYARENGVLLNCTSDSVLRI 365
                                       6789*****************************************99.9*************999999988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.65u 0.36s 00:00:01.01 Elapsed: 00:00:00.55
# Mc/sec: 2098.18
//
Query:       gi|298675946|ref|YP_003727696.1|  [L=365]
Description: histidinol-phosphate aminotransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-62  212.2   0.0    1.4e-62  212.0   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    9.8e-12   44.8   0.0    1.6e-11   44.2   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    4.9e-06   25.3   0.0    1.4e-05   23.8   0.0    1.6  2  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    9.5e-06   24.7   0.0      6e-05   22.1   0.0    1.9  2  Alliinase_C      Allinase
     0.0016   17.5   0.0     0.0041   16.1   0.0    1.6  2  Aminotran_5      Aminotransferase class-V


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.0   0.0   3.9e-66   1.4e-62       3     363 .]      37     359 ..      35     359 .. 0.95

  Alignments for each domain:
  == domain 1  score: 212.0 bits;  conditional E-value: 3.9e-66
                                       EEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEE.ESHHH CS
                     Aminotran_1_2   3 vinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvv.gsGag 78 
                                       +i+Lgsne++ +    ++pe++ a  +      +l  y+  d + el eal  + g        +e+++v  g+G +
  gi|298675946|ref|YP_003727696.1|  37 IIKLGSNENPLG----PSPEAVDALDR-YKHLYQLSVYPSAD-SGELVEALSGYTG-------YPESNIVAsGPGMD 100
                                       89**********....***********.**************.*************.......56666665178*** PP

                                       HHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEE CS
                     Aminotran_1_2  79 aliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilve 155
                                        li+ l++l  +  gde+++p+pt++ y+ ++r++g+  v ++    ++f++d e++++a +       +tk+i+++
  gi|298675946|ref|YP_003727696.1| 101 GLIDNLMRLV-ISQGDEVIIPTPTFSYYEIAARANGAVPVFVK--RDNEFQIDSESVLKAETP------RTKMIFIC 168
                                       **********.********************************..55************8887......******** PP

                                       SS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEE CS
                     Aminotran_1_2 156 sphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGy 232
                                       sp+NP+G+++++++l+ +   a++ + l+fvDeaY +f+  ++       +v++++nl+i +++sKafGlaG R+Gy
  gi|298675946|ref|YP_003727696.1| 169 SPNNPSGDLIDEKKLRRI---AESTKGLVFVDEAYVEFADRNM-----ANLVDDYDNLIIGRTFSKAFGLAGMRIGY 237
                                       ******************...99999***************65.....899************************** PP

                                       EEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEE CS
                     Aminotran_1_2 233 ilgnaavvsqlrklsrpflsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmfll 309
                                        +  ++++s   ++s+pf+ s +   a  aalsd++    +l+++++   k rk+l+d++    ++v+ sq++++l+
  gi|298675946|ref|YP_003727696.1| 238 GIMPKWLKSEYMRISTPFNLSGPSITAGIAALSDTK----HLKQSVELARKGRKYLKDNI---PFNVYNSQANFVLV 307
                                       ************************************....9******************9...**********9999 PP

                                       EEETHHCHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHHH CS
                     Aminotran_1_2 310 tdlsaetakelskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelveal 363
                                        + +++ ak++++ Llee g++v+ +tsf+    + +R+tv  +t+++++++vea+
  gi|298675946|ref|YP_003727696.1| 308 DVAPQK-AKDVCERLLEE-GIIVRDCTSFRDagDSLIRVTV--GTKDQNKRVVEAF 359
                                       655555.***********.***********9999*******..**********985 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.0   4.4e-15   1.6e-11      30     144 ..      79     197 ..      64     200 .. 0.85

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 4.4e-15
                                       HHHHHHHT..-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGC CS
                   DegT_DnrJ_EryC1  30 kafaaylg..vkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaai 104
                                       +a++ y+g  + + +a   G ++l   L+ l +++gdeVI+p+ tF     a++ +ga+pvfv  d + ++id +++
  gi|298675946|ref|YP_003727696.1|  79 EALSGYTGypESNIVASGPGMDGLIDNLMRLVISQGDEVIIPTPTFSYYEIAARANGAVPVFVKRD-NEFQIDSESV 154
                                       677788885555667777789*******************************************99.99******** PP

                                       GGG--TTEEEEEEB...-GGGB---HHHHHHHHHHCT-EEEEE CS
                   DegT_DnrJ_EryC1 105 eaaitertkaIlpV...hlyGqvadmdalkaiaakhglkvieD 144
                                        +a t+rtk I++    +  G+  d ++l++ia++++  v+ D
  gi|298675946|ref|YP_003727696.1| 155 LKAETPRTKMIFICspnNPSGDLIDEKKLRRIAESTKGLVFVD 197
                                       ***********97622256788889999999999876555555 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   3.8e-09   1.4e-05      72     176 ..      94     200 ..      76     204 .. 0.78
   2 ?   -2.1   0.0      0.29     1e+03     356     369 ..     337     350 ..     332     353 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 3.8e-09
                                       EESSHHHHHHHHHHTT.S-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEEST.....TSHHHHHHHCCTTEEEEE CS
                   Cys_Met_Meta_PP  72 avssGmaAiaaailal.lkaGdeivvsddlYggtqrllkkvlkklgievkfvdt.....sdleelekaikentklvy 142
                                       a   Gm  +   +++l +++Gde+++ +     t+++ +  ++  g    fv        d e++ ka +++tk+++
  gi|298675946|ref|YP_003727696.1|  94 ASGPGMDGLIDNLMRLvISQGDEVIIPTP----TFSYYEIAARANGAVPVFVKRdnefqIDSESVLKAETPRTKMIF 166
                                       44446767666666661577*****9975....66777777777777777777622222456778899999****** PP

                                       EESS-TTTT----HHHHHHHHHHTT-EEEEEGTT CS
                   Cys_Met_Meta_PP 143 lEtptnpllkvvDiekiaklakkagvlvvvDntf 176
                                       + +p np  +++D +k+ ++a + + lv+vD ++
  gi|298675946|ref|YP_003727696.1| 167 ICSPNNPSGDLIDEKKLRRIAESTKGLVFVDEAY 200
                                       *******************************876 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.29
                                       S-TTEEEEE--SS- CS
                   Cys_Met_Meta_PP 356 vtddliRlsvGiEd 369
                                         d+liR+ vG  d
  gi|298675946|ref|YP_003727696.1| 337 AGDSLIRVTVGTKD 350
                                       6799*******877 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.7e-08     6e-05      98     208 ..     116     240 ..      92     259 .. 0.76
   2 ?    0.4   0.0     0.066   2.4e+02     298     349 ..     298     350 ..     272     361 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.7e-08
                                       EEEE-SS--THHHHHTT......TT-BTTEEEEEESTT-.--S..S-EEEEEESS-TTT---.....------TT-E CS
                       Alliinase_C  98 kvvaavPyysvykeqts......lldsklykweGdaaayvkkknpeefielvtsPnnPdgll.....reavvkgsea 163
                                       +v+  +P +s y+  ++      ++ ++  +++ d+++  k ++p+  + ++ sPnnP g l      + + +++++
  gi|298675946|ref|YP_003727696.1| 116 EVIIPTPTFSYYEIAARangavpVFVKRDNEFQIDSESVLKAETPRTKMIFICSPNNPSGDLidekkLRRIAESTKG 192
                                       56666676666654332112222688899999999999999999999999**********8833221134669999* PP

                                       EEEEE-TT-S...TTTS---S-B--SEEEEEHHHHHS-GGG-EEEEEE CS
                       Alliinase_C 164 kviyDlayYW...PhytpitskadedimLftlskltGhaGsrlGWalv 208
                                        v +D ay      + +++    d+ i+  t+sk  G aG r+G++++
  gi|298675946|ref|YP_003727696.1| 193 LVFVDEAYVEfadRNMANLVDDYDNLIIGRTFSKAFGLAGMRIGYGIM 240
                                       9******97411245677777778888999***************986 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.066
                                       EE---SEEEEEESSSS..-HHHHHHTTTEEEEEGGGG.TS-TTEEEEESSS-H CS
                       Alliinase_C 298 repsPayaWlkcekeededcaevlrekkiltrsGevf.eaesryvrlsllkrd 349
                                        +++  +  + +  ++ +d+ e l e++i+ r+ + f +a+ + +r+++  +d
  gi|298675946|ref|YP_003727696.1| 298 YNSQANFVLVDVAPQKAKDVCERLLEEGIIVRDCTSFrDAGDSLIRVTVGTKD 350
                                       56677788888888999999999999999999998884578899999864444 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.1e-06    0.0041     107     177 ..     129     199 ..      94     202 .. 0.82
   2 ?   -2.4   0.0      0.48   1.7e+03     286     336 ..     284     329 ..     268     334 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.1e-06
                                       HHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-T CS
                       Aminotran_5 107 elakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaa 177
                                        +a++ ga  ++++ d+e ++d + + k+ +++tk+++i+  +n +G + + +++ ++a   + lv+vD a
  gi|298675946|ref|YP_003727696.1| 129 IAARANGAVPVFVKRDNEFQIDSESVLKAETPRTKMIFICSPNNPSGDLIDEKKLRRIAESTKGLVFVDEA 199
                                       355566777778899999***************************************************76 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.48
                                       HHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTCSHHHHHHHHHHTTEEEE CS
                       Aminotran_5 286 yllerlkslpgvrlygpdkaerrasivsfnfkgvhaedvatlLdeegIavr 336
                                       + ++ lk+   +++y     + +a+ v + ++  +a+dv   L eegI vr
  gi|298675946|ref|YP_003727696.1| 284 KGRKYLKDNIPFNVY-----NSQANFVLVDVAPQKAKDVCERLLEEGIIVR 329
                                       445555544444443.....4577888888888889999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2267.09
//
Query:       gi|298675947|ref|YP_003727697.1|  [L=254]
Description: hypothetical protein Metev_2074 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.9e-34  117.2   0.4      1e-33  116.7   0.4    1.3  1  RNase_H_2       RNase_H superfamily
     0.0039   16.4   0.0     0.0053   16.0   0.0    1.3  1  DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
  ------ inclusion threshold ------
      0.066   12.9   0.0        3.5    7.3   0.0    2.2  2  DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the ex


Domain annotation for each model (and alignments):
>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.7   0.4   1.7e-37     1e-33       2     164 ..      89     237 ..      88     239 .. 0.92

  Alignments for each domain:
  == domain 1  score: 116.7 bits;  conditional E-value: 1.7e-37
                         RNase_H_2   2 ffDiEttGlspkknliyliGvldvdekeiekltqllaeepeeekailelflellekkkalvtfngksFDvpflkrlf 78 
                                       ++DiEttGls  +++i+++Gv+  ++++++++++    + +  + + e     l+k++ +vt+ng++FD+pf+++ f
  gi|298675947|ref|YP_003727697.1|  89 YVDIETTGLSNTHDHITVVGVY--NGNQTKTFVH----GINLDDVADE-----LNKYEFIVTYNGACFDLPFIRKEF 154
                                       99********************..7999998886....6677777777.....99********************** PP

                         RNase_H_2  79 kkykldeeefrhiDLlkelrkkklesysLksvekelgier..reedlsGsqavklyqeylrtgdeellekilaYNed 153
                                        + +++   + h+DL ++l+k ++++ +Lk+ e++lgi r  +++++sG +avkl+++y ++gd+++l+ +l+YN++
  gi|298675947|ref|YP_003727697.1| 155 PELEFN---QLHVDLIYPLKKLGYKG-GLKQAEEKLGISRsdNTTKMSGLDAVKLWNRY-QKGDNDALDLLLEYNRE 226
                                       886666...5****************.*************766788*************.69*************** PP

                         RNase_H_2 154 Dvralatlyek 164
                                       D+++l+t+ ++
  gi|298675947|ref|YP_003727697.1| 227 DIVNLETILST 237
                                       *******9876 PP

>> DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   8.8e-07    0.0053     251     278 ..     133     158 ..     124     208 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8.8e-07
                                       HH--SEEEESSTTTTHHHHHHHHHHHCC CS
                    DNA_pol_B_exo1 251 qydPdvitgYNidnFDlpYilnRakely 278
                                       +y  ++i++YN+  FDlp+i +   el+
  gi|298675947|ref|YP_003727697.1| 133 KY--EFIVTYNGACFDLPFIRKEFPELE 158
                                       55..9***************88666555 PP

>> DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the exonuclease domain of PolB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0   0.00058       3.5      47      68 ..     130     150 ..      87     153 .. 0.79
   2 ?    3.7   0.0    0.0072        43     137     165 ..     199     230 ..     158     250 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00058
                    DNA_pol_B_exo2  47 gvekkkpqlVsfngrgfDlpvl 68 
                                        ++k++  +V++ng  fDlp +
  gi|298675947|ref|YP_003727697.1| 130 ELNKYE-FIVTYNGACFDLPFI 150
                                       555555.69***********87 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0072
                    DNA_pol_B_exo2 137 gvdGskVaelyqegklkeir...eYcetDvln 165
                                       g+d+ k ++ yq+g+ ++++   eY++ D++n
  gi|298675947|ref|YP_003727697.1| 199 GLDAVKLWNRYQKGDNDALDlllEYNREDIVN 230
                                       55666666666666544432222666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1570.27
//
Query:       gi|298675948|ref|YP_003727698.1|  [L=603]
Description: excinuclease ABC subunit C [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.7e-54  183.2   0.0    8.3e-54  181.7   0.0    1.9  2  UvrC_HhH_N  UvrC Helix-hairpin-helix N-terminal
    1.4e-14   53.9   0.1    4.3e-14   52.3   0.1    1.9  1  HHH_2       Helix-hairpin-helix motif
    4.5e-12   46.1   0.4    4.6e-11   42.8   0.3    2.6  2  GIY-YIG     GIY-YIG catalytic domain
    1.2e-10   41.9   0.0    3.2e-10   40.5   0.0    1.7  1  HHH_5       Helix-hairpin-helix domain
      5e-10   38.8   2.8    1.2e-09   37.6   2.8    1.7  1  UVR         UvrB/uvrC motif
    1.3e-06   27.9   0.0     0.0028   17.4   0.0    2.8  2  HHH         Helix-hairpin-helix motif
     0.0004   20.6   0.1     0.0027   17.9   0.0    2.2  2  HHH_3       Helix-hairpin-helix motif
     0.0008   20.0   2.0     0.0027   18.3   0.0    2.9  3  5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold


Domain annotation for each model (and alignments):
>> UvrC_HhH_N  UvrC Helix-hairpin-helix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.4   5.3e+03      53      82 ..     284     313 ..     278     367 .. 0.73
   2 !  181.7   0.0   3.7e-57   8.3e-54       3     154 .]     383     530 ..     381     530 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.4
                                       S--HHHHHHHHHHHHHTTS.....---SEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        UvrC_HhH_N  53 egdDyaamrevlrRrfkrllkefsklPdLi 82 
                                       +gdD  ++ evl+  +k++ +++   P+++
  gi|298675948|ref|YP_003727698.1| 284 RGDDEVSIPEVLSGFIKQYYQDSPVPPEIL 313
                                       478888888888888888887555555544 PP

  == domain 2  score: 181.7 bits;  conditional E-value: 3.7e-57
                                       HTT-SS---EEEEEEEEEETTTEEEEEEEEEETTEE-GGG-EEEEEE.-SS--HHHHHHHHHHHHHTTS.....--- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        UvrC_HhH_N   3 llglkekpkriecyDiShiqgtntvgsmvvfedgkpkkseyRkfkiksvkegdDyaamrevlrRrfkrllkefsklP 79 
                                        l+l++ p++ie++DiS+i+gt++vgs+vvfe+g p++s+yR+f+ik+v++ dD+a+m+ev++Rrf+r+l+e+++lP
  gi|298675948|ref|YP_003727698.1| 383 DLSLETLPYHIEGFDISNISGTDAVGSLVVFENGVPANSKYRQFNIKNVEGIDDFAMMAEVVHRRFSRILDENKPLP 459
                                       699************************************************************************** PP

                                       SEEEESSSHHHHHHHHHHHHHTT-.---EEEEES............SSSEEEE--TT-HHHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        UvrC_HhH_N  80 dLiliDGGkgqlnaakevleelgl.kipvvglaKdkkrktrakaeereeevlelkkssealkllqrirdeaHrfAI 154
                                       dLiliDGG gq++aak  l++l+l +ip++glaK+ ++  + +     ++v++l+++s+ +kll+rirdeaHrfA+
  gi|298675948|ref|YP_003727698.1| 460 DLILIDGGPGQVSAAKGSLDNLNLdNIPLIGLAKQYEHIITPE-----NKVIILSQKSDSMKLLMRIRDEAHRFAV 530
                                       **********************************777754443.....468************************7 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.3   0.1   1.9e-17   4.3e-14       7      61 ..     548     602 ..     544     603 .] 0.97

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 1.9e-17
                             HHH_2   7 GIrhVGektAklLakrFksldaLkkasleeLlevddiGeeiAqsivefFeneknr 61 
                                       GI+ +Ge+  ++L ++F+++d++ +as+++L +v++i +  Aq+iv++Fen++n+
  gi|298675948|ref|YP_003727698.1| 548 GIPGIGESKKRALLEHFGTVDNIINASIKDLKQVEGISNNLAQKIVDYFENDDNK 602
                                       9****************************************************98 PP

>> GIY-YIG  GIY-YIG catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   0.3     2e-14   4.6e-11       3      78 .]      15      90 ..      13      90 .. 0.91
   2 ?   -0.4   0.0      0.62   1.4e+03      18      37 ..     583     602 ..     582     603 .] 0.90

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 2e-14
                                      EEEEEEETTT--EEEEEESSHHHHHHHH.HHHHHHT--S-HS.STEEEEEEEE----HHHHHHHHHHHHHHTTSSSS CS
                           GIY-YIG  3 gvYiirskenkliYvGstknlekRlkqH.nagkkakytrkkgkkpfeliileifptksealelEkklikkyksnkyn 78
                                      gvY+++++ + +iY+G++++l+kR +q+  ++k +  ++++ +k+ + i + + +++ eal  E++likk+k+ +yn
  gi|298675948|ref|YP_003727698.1| 15 GVYLMKDNSDTVIYIGKARSLKKRVSQYfQSQKYHSPKTRTLVKHIADIEYIVTQSEVEALITEASLIKKHKP-RYN 90
                                      9***************************55566666666669*******************************.998 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.62
                                       EEESSHHHHHHHHHHHHHHT CS
                           GIY-YIG  18 GstknlekRlkqHnagkkak 37 
                                       G+++nl + + ++++++++k
  gi|298675948|ref|YP_003727698.1| 583 GISNNLAQKIVDYFENDDNK 602
                                       99***********9998876 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.0   1.4e-13   3.2e-10       4      53 ..     546     594 ..     544     597 .. 0.96

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 1.4e-13
                                       HHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHH CS
                             HHH_5   4 LlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriil 53 
                                       L +++GiG++  +all++ +++v+ +++a++++L ++ Gi++ +A++i++
  gi|298675948|ref|YP_003727698.1| 546 LDGIPGIGESKKRALLEH-FGTVDNIINASIKDLKQVEGISNNLAQKIVD 594
                                       889***************.*****************************85 PP

>> UVR  UvrB/uvrC motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   2.8   5.3e-13   1.2e-09       1      35 [.     202     236 ..     202     237 .. 0.96

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 5.3e-13
                               UVR   1 kklikeLeeemeeAaenedFEkAAklRDqinalkk 35 
                                       ++l+keLe++m++++ n+++E A+ +RDqi+alk+
  gi|298675948|ref|YP_003727698.1| 202 DELVKELEDKMYQLSLNQEYEAASVVRDQIEALKN 236
                                       689*******************************8 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0017       3.8      13      30 .]     546     563 ..     542     563 .. 0.85
   2 !   17.4   0.0   1.2e-06    0.0028       2      30 .]     567     595 ..     566     595 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0017
                                       HHTSTT-SHHHHHHHHHH CS
                               HHH  13 LlalPGVGpktAeaIlsy 30 
                                       L  +PG+G+++ +a l++
  gi|298675948|ref|YP_003727698.1| 546 LDGIPGIGESKKRALLEH 563
                                       778***********9985 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 1.2e-06
                                       HHHHHTSSHHHHHTSTT-SHHHHHHHHHH CS
                               HHH   2 leglipasreeLlalPGVGpktAeaIlsy 30 
                                       ++++i+as+++L++++G+    A++I +y
  gi|298675948|ref|YP_003727698.1| 567 VDNIINASIKDLKQVEGISNNLAQKIVDY 595
                                       79******************999999987 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.91     2e+03      14      31 ..     544     561 ..     540     563 .. 0.75
   2 !   17.9   0.0   1.2e-06    0.0027      10      33 ..     572     595 ..     567     599 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.91
                             HHH_3  14 eeLqklpGlgpklAknIv 31 
                                       + L+ +pG+g+++ ++++
  gi|298675948|ref|YP_003727698.1| 544 SALDGIPGIGESKKRALL 561
                                       779999999998766665 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 1.2e-06
                             HHH_3  10 tAsaeeLqklpGlgpklAknIvay 33 
                                        As ++L++++G++ +lA++Iv+y
  gi|298675948|ref|YP_003727698.1| 572 NASIKDLKQVEGISNNLAQKIVDY 595
                                       79*********************9 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       5.5   1.2e+04      37      49 ..      59      71 ..      51      98 .. 0.47
   2 ?   -1.4   0.1       1.6   3.6e+03      56      83 ..     362     387 ..     343     401 .. 0.56
   3 !   18.3   0.0   1.2e-06    0.0027      20      62 ..     546     590 ..     542     600 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 5.5
                        5_3_exonuc 37 eygsleeilenld 49
                                      ++ ++e i+ + +
  gi|298675948|ref|YP_003727698.1| 59 HIADIEYIVTQSE 71
                                      4444554444332 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.6
                        5_3_exonuc  56 lkekLeenkeearlskkLatiktdvple 83 
                                        +e+L++  ++ + ++ L ++ktd+ le
  gi|298675948|ref|YP_003727698.1| 362 KQEQLKK--DHQHPNEVLENLKTDLSLE 387
                                       2333433..3444566677777776655 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 1.2e-06
                        5_3_exonuc  20 ipGvpgiGektAakLlkeygsleeilenl.delke.kklkekLee 62 
                                       + G+pgiGe +  +Ll+++g++++i+++  ++lk+ + + ++L++
  gi|298675948|ref|YP_003727698.1| 546 LDGIPGIGESKKRALLEHFGTVDNIINASiKDLKQvEGISNNLAQ 590
                                       68************************9442344444234444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (603 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       983  (0.0548274); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.49
# Mc/sec: 3700.85
//
Query:       gi|298675949|ref|YP_003727699.1|  [L=243]
Description: glucose-6-phosphate isomerase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.2e-46  158.2   3.3    1.5e-46  157.9   3.3    1.1  1  GPI        Glucose-6-phosphate isomerase (GPI)
    0.00016   21.3   0.0    0.00029   20.5   0.0    1.4  1  Cupin_2    Cupin domain
  ------ inclusion threshold ------
       0.18   11.9   0.1       0.29   11.2   0.1    1.3  1  TetR_C_27  Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> GPI  Glucose-6-phosphate isomerase (GPI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.9   3.3   2.6e-50   1.5e-46       2     172 ..      17     185 ..      16     194 .. 0.94

  Alignments for each domain:
  == domain 1  score: 157.9 bits;  conditional E-value: 2.6e-50
                               GPI   2 rkardlaavladeealkaltetldddvaYevsdslktaeegerlaadqliydvtvilPgkiGeEriktrGHyHkevd 78 
                                       r  +d+  vl d+   k++   ++ + +Y+ +d  k + + e +++ +l+yd+tvi+P  iG E++kt GH H++v 
  gi|298675949|ref|YP_003727699.1|  17 RMLNDMHDVLYDK---KQMSIKKNPELYYMYRDLYKDDYDFETIKKHNLRYDITVIPPKMIGREYVKTAGHCHPKVP 90 
                                       5667888888888...77888999***************************************************97 PP

                               GPI  79 .rrstrPEvYevlkGealmlLekPeglkvddvivvevkartvvivPPnygHvsinigeedLvmanlvpkdagqdYdv 154
                                            +PEvY+ l+G a +lL+k eg+kv+dv+v++ +a++ v++PP y H++in ++e L man+v+++++++Yd+
  gi|298675949|ref|YP_003727699.1|  91 dTDVSYPEVYQILEGYATYLLQKMEGGKVEDVVVINAQAGDYVVIPPDYCHITINTSDETLKMANWVCREFSSIYDP 167
                                       7999************************************************************************* PP

                               GPI 155 iakarGmaayiieegevl 172
                                       i+++ G a+y+ ++g  +
  gi|298675949|ref|YP_003727699.1| 168 IKQRSGGAYYLLDTGFIK 185
                                       ************988655 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   4.8e-08   0.00029      22      67 ..      99     153 ..      91     158 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 4.8e-08
                                       EEEEEESEEEEEEC....TE.....EEEEETTEEEEE-TT-EEEEEE-SSS-EEE CS
                           Cupin_2  22 ffyVleGegeltvd....ge.....eveleaGdsvyfpagtpHrfrNtgdeparl 67 
                                       ++ +leG++++ +     g+     ++  +aGd+v++p+   H  +Nt+de +++
  gi|298675949|ref|YP_003727699.1|  99 VYQILEGYATYLLQkmegGKvedvvVINAQAGDYVVIPPDYCHITINTSDETLKM 153
                                       566777776666443444336666688899**********************998 PP

>> TetR_C_27  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   4.9e-05      0.29       5      44 ..      19      60 ..      14      66 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.9e-05
                                      HHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHH-..HHHHHHH CS
                         TetR_C_27  5 LrewlaalfeakrrkarddpelFatyvvlieee..levvekh 44
                                      L ++ + l+++k+  ++++pel+ +y+ l +++  +e+++kh
  gi|298675949|ref|YP_003727699.1| 19 LNDMHDVLYDKKQMSIKKNPELYYMYRDLYKDDydFETIKKH 60
                                      66777889*********************9986224556665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1704.19
//
Query:       gi|298675950|ref|YP_003727700.1|  [L=257]
Description: hypothetical protein Metev_2077 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-98  328.1   3.0    2.8e-98  327.9   3.0    1.0  1  NRD1_2    NrpR regulatory domains NRD1 and 2


Domain annotation for each model (and alignments):
>> NRD1_2  NrpR regulatory domains NRD1 and 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  327.9   3.0  1.6e-102   2.8e-98       1     237 [.      12     250 ..      12     251 .. 0.99

  Alignments for each domain:
  == domain 1  score: 327.9 bits;  conditional E-value: 1.6e-102
                                       ---HHHHHHHHHCC---BTTTTB-EEEEEEEEEEGGGHHHHHHHHHHHHHTT-SSSSEEEEEE-SSE.......... CS
                            NRD1_2   1 vgfviskieelaykvtfdpetgkGkVivNlslidkedleealeilkeviksglsvsdrvkileegek..elevpegk 75 
                                       v+f++ski +l++ +t+dp+tgkG+Vi+N+s+i+k+dl+++lei+k+++ sgl+vs+ +kil+ege+  +l+++egk
  gi|298675950|ref|YP_003727700.1|  12 VQFTLSKIVNLMFSTTYDPKTGKGDVIANVSIINKHDLNRVLEIFKTAMMSGLTVSPFIKILHEGESigDLTIKEGK 88 
                                       79*************************************************************************** PP

                                       EEEEEE-CHHHHHHHHCTT--EEEEEEEEEEE-SS.-EEEEEEEESTT-SS-HHHHCGGG.........--SSSEEE CS
                            NRD1_2  76 vgiatvCSitidgvLlknGIpvkpkyGGlleiedkepvrFtelIsYegtsidPlevfiskklTsvlevietgegkil 152
                                       +g+at+CSitidg+Llk+GI v+pk+GGl++ie+++pvrFt++++Y +tsidPle+++s+++Tsv+++i+tg+gkil
  gi|298675950|ref|YP_003727700.1|  89 IGLATMCSITIDGILLKRGILVNPKFGGLVQIEEGSPVRFTDVLTYASTSIDPLEALMSQEITSVTQMISTGSGKIL 165
                                       ***************************************************************************** PP

                                       EEEEEEETTTHHHHHHHHHHH...T-TTEEEE--TT--BTTB---TTEEEEEEE-TTHHHHHHHHTT---EEEEEEE CS
                            NRD1_2 153 AnlReipvsarekveeileklkkagisgvleigepneevlgvpveeekvgivvvgGlnpiaalkeagikveikalsg 229
                                       AnlRe+p +ar +++++l+++ +ag+sg+le+gepn+++l+vp+e++++givv+gG+np+a+++e+gi++e++a+s+
  gi|298675950|ref|YP_003727700.1| 166 ANLREVPIAARYDIDHVLSDIMDAGLSGILEVGEPNRKILDVPIERDHLGIVVIGGTNPMAIVREHGIPIETNAMST 242
                                       ***************************************************************************** PP

                                       EEEGGGSE CS
                            NRD1_2 230 lidiselk 237
                                       ++di e++
  gi|298675950|ref|YP_003727700.1| 243 IVDITEMS 250
                                       ******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1837.53
//
Query:       gi|298675951|ref|YP_003727701.1|  [L=393]
Description: class V aminotransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     4e-127  424.2   0.0   4.5e-127  424.0   0.0    1.0  1  Aminotran_5      Aminotransferase class-V
    8.9e-12   45.0   0.5    1.5e-11   44.3   0.1    1.4  2  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    2.5e-08   32.9   0.0    4.5e-08   32.0   0.0    1.4  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    1.3e-07   31.1   0.0    8.4e-07   28.5   0.0    1.8  2  Aminotran_1_2    Aminotransferase class I and II
    5.2e-05   22.7   0.0    6.3e-05   22.4   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.052   12.1   0.0      0.079   11.5   0.0    1.3  1  SHMT             Serine hydroxymethyltransferase


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  424.0   0.0  1.5e-130  4.5e-127       1     371 []      18     381 ..      18     381 .. 0.99

  Alignments for each domain:
  == domain 1  score: 424.0 bits;  conditional E-value: 1.5e-130
                                       EEEBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHH CS
                       Aminotran_5   1 iyldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlv 77 
                                       iyldsaAttq+p +V+ a+++y+++y+++  r++h+l+ e t+ +e+ rekva ++n+es +++i t+++te+in+v
  gi|298675951|ref|YP_003727701.1|  18 IYLDSAATTQTPVQVVSAINDYFYKYSGSYGRGAHRLARESTNHYEDSREKVAGFLNVES-SKTIMTKNATESINIV 93 
                                       8**********************************************************9.**************** PP

                                       HHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTE CS
                       Aminotran_5  78 alslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGt 154
                                       al+++  ++ gd+iv+t++ehh+nl+pw +l+ ++g++v+v++ d++g +++d++ + ++e+t+lva+thvsn+ G 
  gi|298675951|ref|YP_003727701.1|  94 ALGMG--WNSGDHIVTTSLEHHSNLLPWMNLK-DCGVDVTVVSPDDTGIVNPDDIYDSITERTRLVAVTHVSNIFGS 167
                                       ****5..8***********************7.99****************************************** PP

                                       B--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTT.TTSSTT-EEEEEEHHHHHTS..SS.STTS CS
                       Aminotran_5 155 iqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghK.llgPtGiGvlyvrkellekleplllggem 230
                                       +q++++i+++ +k+ga+vl+D+aq+vgh p+dv  +g+Df+a+sghK llgP+G+G+lyv++   e+l p ++gg+m
  gi|298675951|ref|YP_003727701.1| 168 VQDIKQITRISHKNGAMVLIDGAQSVGHFPVDVGSIGCDFFAASGHKgLLGPQGTGILYVKE--PENLDPSYFGGGM 242
                                       **************************************************************..************* PP

                                       EEEEETTEEEEHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CT CS
                       Aminotran_5 231 veevsleettfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaer 307
                                       v++v+  +  ++  p+kfe+GTpn++g+iglg+ +ey+ ++g+++iekhek+l + + ++l+++p v++ygp   e 
  gi|298675951|ref|YP_003727701.1| 243 VHSVTTSGFDIEPCPTKFESGTPNIPGVIGLGKGVEYVHDLGISNIEKHEKSLVKDMASKLSEMPYVEIYGP---ED 316
                                       ***********************************************************************9...9* PP

                                       CBSEEEEEETTCSHHHHHHHHHHT.TEEEEEE-TTTHHHHHHTT.S-EEEEE--TTS-HHHHHHH CS
                       Aminotran_5 308 rasivsfnfkgvhaedvatlLdee.gIavrsGhhcaqplmkrlalegtvRaSlyiynteeevdrl 371
                                       r+++v fn++g++++dva++Lde+ gI+vrsGhhca+p+++ l+++g+vRaS ++ynt+ee+d +
  gi|298675951|ref|YP_003727701.1| 317 RSGVVPFNIAGLNSHDVAMILDETkGICVRSGHHCAMPALQALNVDGAVRASVGLYNTQEEIDTF 381
                                       **************************************************************976 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.1   4.9e-15   1.5e-11      32     151 ..      69     195 ..      56     216 .. 0.82
   2 ?   -3.1   0.0       1.3   3.8e+03      38      60 ..     339     361 ..     332     363 .. 0.57

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 4.9e-15
                                       HHHHHT..-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHH...HHHTT-EEEEE-B-TTTSSB-GGG CS
                   DegT_DnrJ_EryC1  32 faaylg..vkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatana...vlelgakpvfvDvdpdtynidpaa 103
                                       +a +l+  +   i + ++t+++ ++   +g + gd ++++sl   +   +      +g ++  v  d dt  ++p++
  gi|298675951|ref|YP_003727701.1|  69 VAGFLNveSSKTIMTKNATESINIVALGMGWNSGDHIVTTSLEHHSNLLPwmnLKDCGVDVTVVSPD-DTGIVNPDD 144
                                       555655225678999*********99999999*********98887665411155677777777777.9******** PP

                                       CGGG--TTEEEEEEB-...GGGB---HHHHHHHHHHCT-EEEEE-TT-TT- CS
                   DegT_DnrJ_EryC1 104 ieaaitertkaIlpVh...lyGqvadmdalkaiaakhglkvieDaAhAlGa 151
                                       i   itert+ + + h   ++G v d++++++i++k g +v+ D A+++G 
  gi|298675951|ref|YP_003727701.1| 145 IYDSITERTRLVAVTHvsnIFGSVQDIKQITRISHKNGAMVLIDGAQSVGH 195
                                       *********888877733469****************************95 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.3
                                       -SEEEEESSHHHHHHHHHHHTTT CS
                   DegT_DnrJ_EryC1  38 vkhaiavssGtaAlhlaLralgv 60 
                                       +   i v sG +  + aL+al+v
  gi|298675951|ref|YP_003727701.1| 339 ETKGICVRSGHHCAMPALQALNV 361
                                       44555666666666666666655 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.0   1.5e-11   4.5e-08      86     201 ..      97     217 ..      49     236 .. 0.79

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 1.5e-11
                                       TTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEEST.....TSHHHHHHHCCTTEEEEEEESS-TTTT----HH CS
                   Cys_Met_Meta_PP  86 allkaGdeivvsddlYggtqrllkkvlkklgievkfvdt.....sdleelekaikentklvylEtptnpllkvvDie 157
                                          ++Gd+iv+++     ++ l    lk  g++v++v +      +++++   i+e+t+lv +  ++n++ +v Di+
  gi|298675951|ref|YP_003727701.1|  97 MGWNSGDHIVTTSLE-HHSNLLPWMNLKDCGVDVTVVSPddtgiVNPDDIYDSITERTRLVAVTHVSNIFGSVQDIK 172
                                       446789999987654.4556666677899*******99833344467999*************************** PP

                                       HHHHHHHHTT-EEEEEGTTTHTTT.S-GGGGT-SEEEEETTTTTT CS
                   Cys_Met_Meta_PP 158 kiaklakkagvlvvvDntfaspll.qrplklgaDivvhSaTKylg 201
                                       +i+++ +k+g++v++D + + + + +   + g+D    S+ K l 
  gi|298675951|ref|YP_003727701.1| 173 QITRISHKNGAMVLIDGAQSVGHFpVDVGSIGCDFFAASGHKGLL 217
                                       ****************99888854144445667777777776555 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   2.8e-10   8.4e-07      11     193 ..      19     194 ..      13     214 .. 0.77
   2 ?    0.4   0.0     0.094   2.8e+02     281     362 ..     288     384 ..     285     385 .. 0.73

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 2.8e-10
                                       TTSTTSS.HHHHHHHHHHHH.........HHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHH CS
                     Aminotran_1_2  11 ylgdsgk.ptlpevakaeke.........galaggtlneygpidglpeleealakflgrseklklkreaavvvgsGa 77 
                                       yl+ +++  t+  v+ a ++         g +a++       + ++ + +e++a fl+      ++ ++++ + + +
  gi|298675951|ref|YP_003727701.1|  19 YLDSAATtQTPVQVVSAINDyfykysgsyGRGAHRL--ARESTNHYEDSREKVAGFLN------VESSKTIMTKNAT 87 
                                       666666767777788888888888888444444444..444455579***********......7777455555555 PP

                                       HHHHHHHHHHHHHTTT-EEEEEESS-.THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEE CS
                     Aminotran_1_2  78 galiealifllklnpgdeilvpdpty.asyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvil 153
                                        +++ ++  +   n gd i+  ++ + ++  +  +l ++ v    +++ ++  ++ +++ + ++e      +t++++
  gi|298675951|ref|YP_003727701.1|  88 ESINIVALGMG-WNSGDHIVTTSLEHhSNLLPWMNLKDCGVDVTVVSPDDTGIVNPDDIYDSITE------RTRLVA 157
                                       55555555555.9*********997625666666666666555555599****************......****** PP

                                       EESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTC CS
                     Aminotran_1_2 154 vesphNPtGtvatleeleklldlakkynlllfvDeaYagf 193
                                       v+ ++N  G+v + ++++ +    +k+++++++D a +++
  gi|298675951|ref|YP_003727701.1| 158 VTHVSNIFGSVQDIKQITRI---SHKNGAMVLIDGAQSVG 194
                                       ********************...***********886665 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.094
                                       HHHHHHHHHHHHHHS.....TEEEECCS..CSSEEEEEETHHCHHHHHHHHHHTCTEEEEEGGGGTS........TT CS
                     Aminotran_1_2 281 lqkrrkelrdeLael.....glkvlasq..sgmflltdlsaetakelskkLleevgvyvtpgtsftv........pg 342
                                       ++k+ k+l++ +a++     ++++++++  sg++++     ++ ++++  L e +g+ v+ g ++ +         g
  gi|298675951|ref|YP_003727701.1| 288 IEKHEKSLVKDMASKlsempYVEIYGPEdrSGVVPFNIAG-LNSHDVAMILDETKGICVRSGHHCAMpalqalnvDG 363
                                       6667777777776667777977777777679999995544.446777777777799999998888888888888899 PP

                                       EEEEEC.TTS-HHHHHHHHHH CS
                     Aminotran_1_2 343 rlRitv.Aglteeeleelvea 362
                                        +R +v    t+ee++ +++a
  gi|298675951|ref|YP_003727701.1| 364 AVRASVgLYNTQEEIDTFIDA 384
                                       999999666688888888876 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   2.1e-08   6.3e-05      99     234 ..     130     304 ..      64     376 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2.1e-08
                                       EEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHH CS
                   Beta_elim_lyase  99 rdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaa 175
                                       + +  +++G ++++++ + i+e      +++l+ +t   n+      s++ +++++ i +k+g  +++DgA      
  gi|298675951|ref|YP_003727701.1| 130 TVVSPDDTGIVNPDDIYDSITE------RTRLVAVTHVSNI----FGSVQDIKQITRISHKNGAMVLIDGA------ 190
                                       4455555577778888777777......699*********7....559999*******************8...... PP

                                       HHHTS-CHHHHTT.SSEEEEESSSTT--SS-.EEEEE-HH..................................... CS
                   Beta_elim_lyase 176 kslgeivkemfsy.vDsvtmslkKdllanvG.gvlafrddel................................... 215
                                       +s+g+ + ++ s  +D + +s+ K+ll + G g+l +++ e                                    
  gi|298675951|ref|YP_003727701.1| 191 QSVGHFPVDVGSIgCDFFAASGHKGLLGPQGtGILYVKEPENldpsyfgggmvhsvttsgfdiepcptkfesgtpni 267
                                       56677677777554**********************99997667777777777777777777766666666666666 PP

                                       ....................HHHHHHHHHHHHT---S CS
                   Beta_elim_lyase 216 ..................edylaerveqrkylggglr 234
                                                          +  ++   ++k ++++l+
  gi|298675951|ref|YP_003727701.1| 268 pgviglgkgveyvhdlgiSNIEKHEKSLVKDMASKLS 304
                                       6666666666666666644444444455666666665 PP

>> SHMT  Serine hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.6e-05     0.079     152     247 ..     136     229 ..      96     241 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.6e-05
                                       TTSSB-HHHHHHHHHHH--SEEEEE-S.ST-S---HHHHHHHHHHTT-EEEEE-GGGHHHHHTTSS--GCCTSSEEE CS
                              SHMT 152 etglidydelekkakefkPklivaGts.aysrlidyarlreiadevgayllvdmahiaGlvaagvipsPfeyadvvt 227
                                       +tg+++ d++  + +e    + v+  s  +  + d +++ +i+++ ga++l+d a   G    +v +     +d+ +
  gi|298675951|ref|YP_003727701.1| 136 DTGIVNPDDIYDSITERTRLVAVTHVSnIFGSVQDIKQITRISHKNGAMVLIDGAQSVGHFPVDVGSI---GCDFFA 209
                                       6888888888888777666666777763588999**********************999998888765...588999 PP

                                       EESSSTT-S-S-EEEEEC-S CS
                              SHMT 228 ttthktlrGprgglillrkg 247
                                       +  hk l Gp+g+ il+ k 
  gi|298675951|ref|YP_003727701.1| 210 ASGHKGLLGPQGTGILYVKE 229
                                       ************99998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 2393.01
//
Query:       gi|298675952|ref|YP_003727702.1|  [L=52]
Description: hypothetical protein Metev_2079 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 364.44
//
Query:       gi|298675953|ref|YP_003727703.1|  [L=426]
Description: methanogenesis marker protein 1 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.1e-83  279.3   0.0    6.6e-83  278.7   0.0    1.3  2  YcaO          YcaO cyclodehydratase, ATP-ad Mg2+-binding
  ------ inclusion threshold ------
      0.017   14.9   0.0      0.044   13.6   0.0    1.7  1  PRAI          N-(5'phosphoribosyl)anthranilate (PRA) isomeras
      0.029   14.4   0.3       0.15   12.0   0.2    2.3  2  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
      0.039   13.5   0.1      0.075   12.6   0.1    1.5  1  DUF4290       Domain of unknown function (DUF4290)


Domain annotation for each model (and alignments):
>> YcaO  YcaO cyclodehydratase, ATP-ad Mg2+-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       1.2   5.6e+03     286     318 ..      26      58 ..      15      60 .. 0.57
   2 !  278.7   0.0   1.5e-86   6.6e-83       1     323 []      71     393 ..      71     393 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.2
                              YcaO 286 letllerlkaagldvlvvdltrp.dlglpvvkvi 318
                                       le+   +lk+ g   + +d+t+   +g+pv+ +i
  gi|298675953|ref|YP_003727703.1|  26 LEKTKSQLKKIGVTRI-ADITHLdRVGIPVYSAI 58 
                                       5555555666666533.45555446777776666 PP

  == domain 2  score: 278.7 bits;  conditional E-value: 1.5e-86
                              YcaO   1 nGkGateeaArasalgEalErysae..gffr.......gdekrvrasyrel.egegaldpeelglyseeekdaadfv 67 
                                       +GkG+t ++Ar+sa++E++Er  ae                + +++s++++ e+   ++p++l +            
  gi|298675953|ref|YP_003727703.1|  71 SGKGVTSTQARISAMMEGFERCLAEkkD--MnnniqedIPGDEFVDSFDNIkETYYIVNPAKLLIS----------- 134
                                       6*********************867440..144444445556677******99**********999........... PP

                              YcaO  68 lepfdpdrpidwvpgwsltdgeevlvPanlvyl.yeppegearlfletsnGlAaGntleeAilhGllEliERdafal 143
                                        e+++ d+ i+w+ gw+l++++e++vP n vy+ y+  ++  +lf++++nGlAaGn +eeA+lhGllE+ ERda+++
  gi|298675953|ref|YP_003727703.1| 135 -EDVRTDDMIEWTSGWDLINDNEIYVPSNSVYHpYDATNQCVKLFRSNTNGLAAGNVIEEAVLHGLLEVTERDALSI 210
                                       .789*****************************766666666*********************************** PP

                              YcaO 144 awyerlplpridlasd.peirellerlreagievrlldatldlgipvvaavlvd....pklllvagaGahldpevAl 215
                                       a ++r p +r+ l++d    +el++++++agi+vrl+   +d++i++v+a ++d    ++++lv+gaGahl+pe+A 
  gi|298675953|ref|YP_003727703.1| 211 AEMNRNPGKRLMLDEDdGISYELMQKFNDAGINVRLWVPYHDTEITTVVASVDDaqlkDPAMLVMGAGAHLNPEIAT 287
                                       **********9999555*************************************765433999************** PP

                              YcaO 216 erAltElaqsrltlisgaredpdfdeeladvatleradreallwl.peaaakrldfllfaewassgdleedletlle 291
                                       +rAl E+aqsr  +i+gared+++ +++ ++ ++er++r++ +w+ +e +++++  +l  ++ s ++++e+++t+++
  gi|298675953|ref|YP_003727703.1| 288 IRALNEVAQSRVVQIHGAREDTER-DKFVRNIGYERMKRMNGFWYkDEDIDTTTLKDL--NDLSRNSPAENINTVID 361
                                       ************************.69******************9888887555555..555669*********** PP

                              YcaO 292 rlkaagldvlvvdltrpdlglpvvkvivPgle 323
                                       +lk+   +v+vv+l+r+++++pvv+vi+P +e
  gi|298675953|ref|YP_003727703.1| 362 QLKNLVDNVVVVNLSRESVNIPVVRVIIPTFE 393
                                       *****************************876 PP

>> PRAI  N-(5'phosphoribosyl)anthranilate (PRA) isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   9.7e-06     0.044      51      91 ..     276     316 ..     248     351 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.7e-06
                                       EEEEESSS-HHHHHHHHHHCTECEEEE-CGG.-HHHHHHHH CS
                              PRAI  51 lVGVfvNqpieevlriaqelgldvvQLHGdedeqeyeellk 91 
                                         G   N +i+++ ++ ++ +  vvQ+HG  +++e  ++++
  gi|298675953|ref|YP_003727703.1| 276 GAGAHLNPEIATIRALNEVAQSRVVQIHGAREDTERDKFVR 316
                                       568889************************99999888876 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       0.3   1.3e+03      35      54 ..     102     122 ..      74     126 .. 0.72
   2 ?   12.0   0.2   3.4e-05      0.15      22      68 ..     118     171 ..     100     186 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.3
                      MMR_HSR1_Xtn  35 liredvtvDdlidvieg.nrv 54 
                                        i+ed+  D+++d   + + +
  gi|298675953|ref|YP_003727703.1| 102 NIQEDIPGDEFVDSFDNiKET 122
                                       47999999****998653334 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 3.4e-05
                      MMR_HSR1_Xtn  22 kilkeykihn.aevliredvtvDdli......dviegnrvYipclyvlNKiDli 68 
                                       +i + y i+n a++li edv +Dd+i      d i++n  Y+p+  v+   D+ 
  gi|298675953|ref|YP_003727703.1| 118 NIKETYYIVNpAKLLISEDVRTDDMIewtsgwDLINDNEIYVPSNSVYHPYDAT 171
                                       566677776659*************97777778999********9999888875 PP

>> DUF4290  Domain of unknown function (DUF4290)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   1.7e-05     0.075     115     166 ..     298     350 ..     282     367 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.7e-05
                           DUF4290 115 liekaleleegeerealvklia.nqmkksylqwnkdsvddekilkdlkelseg 166
                                        + ++   +e++er+++v+ i+ ++mk+    w kd+  d++ lkdl++ls++
  gi|298675953|ref|YP_003727703.1| 298 RVVQIHGAREDTERDKFVRNIGyERMKRMNGFWYKDEDIDTTTLKDLNDLSRN 350
                                       55667778999**********8468**************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       847  (0.0472419); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.56
# Mc/sec: 2299.74
//
Query:       gi|298675954|ref|YP_003727704.1|  [L=230]
Description: TfuA domain-containing protein core [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-47  160.2   0.0    2.1e-46  156.5   0.0    2.5  3  TfuA            TfuA-like protein
  ------ inclusion threshold ------
      0.038   13.2   0.0          7    5.8   0.0    2.2  2  Regulator_TrmB  Archaeal transcriptional regulator TrmB
       0.11   13.4   5.4       0.15   13.0   0.8    2.8  4  DUF2624         Protein of unknown function (DUF2624)


Domain annotation for each model (and alignments):
>> TfuA  TfuA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.29   1.7e+03       7      27 ..      39      59 ..      37      60 .. 0.86
   2 !  156.5   0.0   3.6e-50   2.1e-46       1     120 []      62     179 ..      62     179 .. 0.99
   3 ?    0.0   0.0      0.11   6.6e+02      90     113 ..     184     207 ..     181     214 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.29
                              TfuA  7 epavahkEilaalkegvavvG 27
                                      +p+v    i +a+keg +++G
  gi|298675954|ref|YP_003727704.1| 39 KPPVYRCNIDKAMKEGYNIIG 59
                                      57788889999*****99998 PP

  == domain 2  score: 156.5 bits;  conditional E-value: 3.6e-50
                              TfuA   1 DGvfeqepavahkEilaalkegvavvGaasmGALRAaElaafGmigvGeiyeayrsgeledDdeVavlhapaelgye 77 
                                       DGvf++++av+hkEi++alk++v vvG++smGALRA+El+++Gmig G+iye+yr+g++e+DdeVav+++p+  ++e
  gi|298675954|ref|YP_003727704.1|  62 DGVFFDKAAVSHKEIIKALKNNVIVVGGCSMGALRASELDDYGMIGAGKIYEQYRDGVIEADDEVAVATNPD--TFE 136
                                       9**********************************************************************9..9** PP

                              TfuA  78 alsealvnlratlkaaveegiiseeeaaallelakelyykert 120
                                       ++s++l+n+r+tlkaa e++ii++++ ++l+e+ak++yy+ r+
  gi|298675954|ref|YP_003727704.1| 137 PVSKPLINIRQTLKAAYEDDIIDDKTYSNLIEIAKHTYYPYRS 179
                                       ****************************************996 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.11
                              TfuA  90 lkaaveegiiseeeaaallelake 113
                                       +k+av+++i+++++++++l+ ++e
  gi|298675954|ref|YP_003727704.1| 184 IKQAVKNNILTKKDSNNILRYCRE 207
                                       689999*********999998775 PP

>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0012         7     145     215 ..      18      89 ..       4      94 .. 0.85
   2 ?    5.3   0.0    0.0016       9.8      11      45 ..     111     145 ..     106     152 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0012
                                       EEES-HHHHHHHHHHHT.TTS-EEEEEEEEETTT--EEEEEEEEEEEEEETTTTEEEEEEEETTE.EEEEE- CS
                    Regulator_TrmB 145 itfssirlavedikkllraglkveaeveGrdtetgeevtieGrvveatlnstpgvaslvvetedg.evtVGG 215
                                       + f+   ++ ed+k++l+a++k+ +    +d + +e   i G + ++++++ +  +  +++  ++ ++ VGG
  gi|298675954|ref|YP_003727704.1|  18 TVFAGTSITHEDAKEILNADYKPPVYRCNIDKAMKEGYNIIGIIDGVFFDKAAVSHKEIIKALKNnVIVVGG 89 
                                       457777888999***********9999999999*********************99999998666699***9 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0016
                                       HHHHHHHHHHH-SSEEEEEE-GGGHHHHHHHHHHH CS
                    Regulator_TrmB  11 vierieelIesAenelivslpselLeelreeliaa 45 
                                       + e+ ++ + +A+ e+ v++++  +e ++++li+ 
  gi|298675954|ref|YP_003727704.1| 111 IYEQYRDGVIEADDEVAVATNPDTFEPVSKPLINI 145
                                       6788889999*********************9975 PP

>> DUF2624  Protein of unknown function (DUF2624)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.099   5.9e+02      29      41 ..      23      35 ..      21      50 .. 0.88
   2 ?   -3.9   0.1         3   1.8e+04      37      46 ..      74      83 ..      72      85 .. 0.64
   3 ?   -3.2   0.0       2.7   1.6e+04      49      61 ..     156     168 ..     146     174 .. 0.61
   4 ?   13.0   0.8   2.4e-05      0.15      20      68 ..     183     229 ..     180     230 .] 0.80

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.099
                           DUF2624 29 veltksqAekivk 41
                                       ++t+++A++i++
  gi|298675954|ref|YP_003727704.1| 23 TSITHEDAKEILN 35
                                      68*********98 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 3
                           DUF2624 37 ekivkilrek 46
                                      ++i+k l+++
  gi|298675954|ref|YP_003727704.1| 74 KEIIKALKNN 83
                                      4667777665 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 2.7
                           DUF2624  49 difnkeerkkllk 61 
                                       di++++  ++l++
  gi|298675954|ref|YP_003727704.1| 156 DIIDDKTYSNLIE 168
                                       5555555555554 PP

  == domain 4  score: 13.0 bits;  conditional E-value: 2.4e-05
                           DUF2624  20 llkyakqygveltksqAekivkilrekkidifnkeerkkllkelakits 68 
                                       ++k+a ++++ ltk++ ++i+ + re++idi +++++  +l+ + +i++
  gi|298675954|ref|YP_003727704.1| 183 IIKQAVKNNI-LTKKDSNNILRYCRENEIDI-KRQDAIAVLNTIIEIVD 229
                                       5788888888.99999999999999999999.77777777777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1479.77
//
Query:       gi|298675955|ref|YP_003727705.1|  [L=399]
Description: hypothetical protein Metev_2082 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-10   41.1  25.6    8.3e-05   22.2   3.4    5.5  5  Paired_CXXCH_1   Doubled CXXCH motif (Paired_CXXCH_1)
    1.2e-09   38.0  28.6    0.00061   19.7   7.9    4.9  5  Cytochrome_C7    Cytochrome c7 and related cytochrome c
    9.4e-09   35.6  26.7    0.00065   20.1   4.7    4.0  4  Cytochrom_c3_2   Cytochrome c3
    3.1e-08   33.3   0.1    4.5e-08   32.8   0.1    1.2  1  PGF-CTERM        PGF-CTERM motif
     0.0025   17.5  27.0        1.4    8.6   2.7    5.6  3  Cytochrom_NNT    NapC/NirT cytochrome c family, N-terminal re
     0.0039   18.1  38.8       0.18   12.7   0.7    6.3  7  Cytochrome_C554  Cytochrome c554 and c-prime
  ------ inclusion threshold ------
      0.085   13.5   2.8       0.19   12.4   1.6    2.1  2  SlyX             SlyX
       0.29   12.3   0.1       0.29   12.3   0.1    6.0  3  Cytochrom_C      Cytochrome c
        0.3   11.6  12.2          5    7.7   1.0    4.2  3  zf-C4pol         C4-type zinc-finger of DNA polymerase delta
       0.52   10.7  28.3          1    9.7   0.0    6.9  4  Cytochrome_CBB3  Cytochrome C oxidase, cbb3-type, subunit III
       0.59   10.5  29.5        4.3    7.7  12.0    4.6  5  Cytochrom_CIII   Class III cytochrome C family


Domain annotation for each model (and alignments):
>> Paired_CXXCH_1  Doubled CXXCH motif (Paired_CXXCH_1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.8     0.021        34       7      13 ..      25      31 ..      20      51 .. 0.66
   2 !   14.6   1.7   1.3e-05     0.021       5      40 ..      47      92 ..      43      94 .. 0.81
   3 ?   -0.9   0.1      0.86   1.4e+03       6      12 ..     130     136 ..     124     145 .. 0.69
   4 !   22.2   3.4   5.1e-08   8.3e-05       9      39 ..     172     198 ..     165     201 .. 0.90
   5 !   12.3   0.0   6.4e-05       0.1       3      39 ..     229     280 ..     228     283 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.021
                    Paired_CXXCH_1  7 geClsCH 13
                                      ++C++CH
  gi|298675955|ref|YP_003727705.1| 25 EDCSQCH 31
                                      4688888 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.3e-05
                    Paired_CXXCH_1  5 aege..ClsCHnphgsdnpkll........kkakgaalCysCHdek 40
                                      +e +  C+ CH+p  + +++ +          +  a+lC +CH+e 
  gi|298675955|ref|YP_003727705.1| 47 NESDvgCEVCHSPPEEGYEAHIdnpteidpGMNYSAELCGKCHNEP 92
                                      555444**********99999999999999447799*******985 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.86
                    Paired_CXXCH_1   6 egeClsC 12 
                                       +++C +C
  gi|298675955|ref|YP_003727705.1| 130 SDDCVAC 136
                                       357*999 PP

  == domain 4  score: 22.2 bits;  conditional E-value: 5.1e-08
                    Paired_CXXCH_1   9 ClsCHnphgsdnpkllkkakgaalCysCHde 39 
                                       C +CH+ph++   +l  ++++ +lC +CH++
  gi|298675955|ref|YP_003727705.1| 172 CVACHEPHST---GLH-VEDEVKLCSNCHNS 198
                                       ********99...888.9***********97 PP

  == domain 5  score: 12.3 bits;  conditional E-value: 6.4e-05
                    Paired_CXXCH_1   3 PvaegeClsCH...............nphgsdnpkll........kkakgaalCysCHde 39 
                                       Pv+ g C +CH                       + +        ++++ ++ C  CH +
  gi|298675955|ref|YP_003727705.1| 229 PVEIG-CVDCHmgakpfnettnesaeT-------GHTfdmnvslvVDSESTNNCSRCHGA 280
                                       89999.********8888755443322.......22245556667999**********75 PP

>> Cytochrome_C7  Cytochrome c7 and related cytochrome c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   5.5   1.2e-05     0.019      12      73 .]      23      90 ..      14      90 .. 0.66
   2 !   13.5   7.3   3.2e-05     0.053       4      71 ..      42     136 ..      38     177 .. 0.58
   3 !   10.0   6.5   0.00042      0.69      14      73 .]     131     197 ..     126     197 .. 0.56
   4 !   19.7   7.9   3.8e-07   0.00061       8      72 ..     184     278 ..     179     279 .. 0.71
   5 !    6.7   0.3    0.0043       7.1      12      23 ..     270     281 ..     257     310 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.2e-05
                     Cytochrome_C7 12 tgykCtdCHsklfeskakkkmaemekgkskkaeves.ltCgaCHdgknaf..............svakkaeCakCHt 73
                                      +  +C++CH +++ +++       ++++ +  + es + C  CH   ++                + +++ C+kCH+
  gi|298675955|ref|YP_003727705.1| 23 NPEDCSQCHPDVY-ETW-------NMSNHSGLN-ESdVGCEVCHSPPEEGyeahidnpteidpgMNYSAELCGKCHN 90
                                      5579*******94.222.......111221122.22367*****999985566777777888885667999*****6 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 3.2e-05
                     Cytochrome_C7   4 shkshlkatgykCtdCHsklfeskakkk.maemekgkskkaeveslt...CgaCHdgkna......f.......... 60 
                                       +h++  + +   C+ CHs++      ++ +a++++ +     ++  +   Cg+CH++ ++      +          
  gi|298675955|ref|YP_003727705.1|  42 NHSGLNE-SDVGCEVCHSPPE-----EGyEAHIDNPTEIDPGMNY-SaelCGKCHNEPHKpifdewDeyskddfdte 111
                                       4555444.58899****9992.....2222222222222223333.1347*****9998844444404444444555 PP

                     Cytochrome_C7  61 ..............svakkaeCakC 71 
                                                      v++ ++C  C
  gi|298675955|ref|YP_003727705.1| 112 nmashsepsdvtepFVQDSDDCVAC 136
                                       5555555555555534445555555 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00042
                     Cytochrome_C7  14 ykCtdCHskl.feskak....kk.maemekgkskkaeves..ltCgaCHdgknaf..svakkaeCakCHt 73 
                                        +C +C s+  +  + +    ++ ++e   +     +ve+  ltC aCH+   +    + + + C++CH+
  gi|298675955|ref|YP_003727705.1| 131 DDCVACKSTEgAVVNLEgadvHDfNEENLPNP---SDVEEwrLTCVACHEPHSTGlhVEDEVKLCSNCHN 197
                                       57888888773322222222222333322222...233333477*****999886554556899*****6 PP

  == domain 4  score: 19.7 bits;  conditional E-value: 3.8e-07
                     Cytochrome_C7   8 hlkatgykCtdCHskl.f..eskak...kk..maemekgkskkaeves.lt..CgaCHdgknaf............. 60 
                                       h++++ + C++CH++  +  +   +   ++  + ++  ++s+ ++ e+ ++  C +CH g + f             
  gi|298675955|ref|YP_003727705.1| 184 HVEDEVKLCSNCHNSRgAepD--GEttiARytQWDI-YSNSSYVNGEHpVEigCVDCHMGAKPFnettnesaetght 257
                                       77777889*******944321..1123322322222.2333345555555599**********99999999999999 PP

                     Cytochrome_C7  61 .........svakkaeCakCH 72 
                                                +++++++C++CH
  gi|298675955|ref|YP_003727705.1| 258 fdmnvslvvDSESTNNCSRCH 278
                                       999****997789******** PP

  == domain 5  score: 6.7 bits;  conditional E-value: 0.0043
                     Cytochrome_C7  12 tgykCtdCHskl 23 
                                       ++++C+ CH++ 
  gi|298675955|ref|YP_003727705.1| 270 STNNCSRCHGAE 281
                                       456788888776 PP

>> Cytochrom_c3_2  Cytochrome c3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   4.3   1.6e-05     0.026       8      67 ..      26      91 ..      20      99 .. 0.63
   2 !   20.1   4.7     4e-07   0.00065      24      80 .]     128     197 ..     104     197 .. 0.72
   3 !   10.6   1.7   0.00037      0.59      27      66 ..     232     279 ..     206     290 .. 0.60
   4 !   10.0   2.5   0.00055       0.9       7      35 ..     232     280 ..     227     315 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.6e-05
                                      TGGGTSS..SST..-SSTTHHHHHH....HHHHH--HHHCHTTSST..TSSBTTSSCTSSS-GGGTS-T CS
                    Cytochrom_c3_2  8 kCadCHt..kek..pkkdkaveeek....ClsCHgkleelakktkea.keanphkshekeleCteCHke 67
                                      +C++CH    e+  +++++  +  +    C+ CH+  ee  +++ ++ +e++p  +++    C +CH+e
  gi|298675955|ref|YP_003727705.1| 26 DCSQCHPdvYETwnMSNHSGLN--EsdvgCEVCHSPPEEGYEAHIDNpTEIDPGMNYS-AELCGKCHNE 91
                                      7*****9442331133344333..13467******98887666655425566655554.456*****97 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 4e-07
                                       HHHHHHHHHH--HHHCHTTSST........TSSBTTSSCTSSS-GGGTS-TTT......SBT-GGGGT-S CS
                    Cytochrom_c3_2  24 veeekClsCHgkleelakktkea.......keanphkshekeleCteCHkeHk......ksekvCaeCHe 80 
                                        ++++C++C ++  ++ + +          +  np++  e +l+C +CH+ H+      +++k+C++CH+
  gi|298675955|ref|YP_003727705.1| 128 QDSDDCVACKSTEGAVVNLEGADvhdfneeNLPNPSDVEEWRLTCVACHEPHStglhveDEVKLCSNCHN 197
                                       45678****9998877765544445665545556666667999**********888776666*******6 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00037
                                       HHHHHHH--HHHCHTTSST.........TSSBTTSSCTSSS-GGGTS- CS
                    Cytochrom_c3_2  27 ekClsCHgkleelakktkea........keanphkshekeleCteCHk 66 
                                         C+ CH  ++ ++++t+e+         +++     e++ +C++CH 
  gi|298675955|ref|YP_003727705.1| 232 IGCVDCHMGAKPFNETTNESaetghtfdMNVSLVVDSESTNNCSRCHG 279
                                       346667766666666666553444332211111222235555666664 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.00055
                                       .TGGGTSSSST-SSTTHHHHHH....................HHHHH-- CS
                    Cytochrom_c3_2   7 vkCadCHtkekpkkdkaveeek....................ClsCHgk 35 
                                       + C dCH  +kp ++++ e+++                    C +CHg 
  gi|298675955|ref|YP_003727705.1| 232 IGCVDCHMGAKPFNETTNESAEtghtfdmnvslvvdsestnnCSRCHGA 280
                                       5677777766655444444444566777777777777777777777764 PP

>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.1   2.8e-11   4.5e-08       2      23 .]     375     396 ..     374     396 .. 0.98

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 2.8e-11
                         PGF-CTERM   2 PGFGavlAlaGLLaaalLaRRr 23 
                                       PGF+a++ +aGLL +++L+RR+
  gi|298675955|ref|YP_003727705.1| 375 PGFEAIYSIAGLLLVFYLVRRK 396
                                       *********************8 PP

>> Cytochrom_NNT  NapC/NirT cytochrome c family, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0  11.6    0.0054       8.8      19     165 ..       7     177 ..       2     180 .. 0.54
   2 !    8.6   2.7   0.00088       1.4      31      79 ..     184     245 ..     179     260 .. 0.56
   3 ?    3.3   0.4     0.036        59     121     155 ..     267     302 ..     246     310 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0054
                     Cytochrom_NNT  19 gvvflggfntaleatsteeFCvsCHemednveeykesiHysnrsgvraeCsdCHvPkelv.kklark.......iqa 87 
                                        vv++++  t+ +++ + e C +CH   d +e ++ s H  + +   + C+ CH P e   ++ +         ++ 
  gi|298675955|ref|YP_003727705.1|   7 VVVTILILMTTTSMALNPEDCSQCH--PDVYETWNMSNHS-GLNESDVGCEVCHSPPEEGyEAHIDNpteidpgMNY 80 
                                       34445555555566667788*****..588*********8.45556789******9844323333221111111444 PP

                     Cytochrom_NNT  88 skevlaklvgk.....idt.....kekfeakrlelaerew....armkandsreCrnCHseeamdlekqkkkaakah 150
                                       s e++ k+ ++     +d+     k+ f+   +++a++      ++   +ds +C +C s+e   ++ + ++ ++  
  gi|298675955|ref|YP_003727705.1|  81 SAELCGKCHNEphkpiFDEwdeysKDDFD--TENMASHSEpsdvTEPFVQDSDDCVACKSTEGAVVNLEGADVHDFN 155
                                       55665555443111222221001123333..3444444331000233347888999999888666666666555555 PP

                     Cytochrom_NNT 151 kkaa.......eeektCidCHk 165
                                       ++         e + tC+ CH+
  gi|298675955|ref|YP_003727705.1| 156 EENLpnpsdveEWRLTCVACHE 177
                                       5555566665344459999996 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00088
                     Cytochrom_NNT  31 eatsteeFCvsCHeme............dn.veeykesiHysnrsgvraeCsdCHvPkelvk 79 
                                       ++  + + C +CH+ +            ++  + y++s  +++++ v+  C dCH+  + ++
  gi|298675955|ref|YP_003727705.1| 184 HVEDEVKLCSNCHNSRgaepdgettiarYTqWDIYSNSSYVNGEHPVEIGCVDCHMGAKPFN 245
                                       55555666666665431111111111111112335667777777778888888888776665 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.036
                     Cytochrom_NNT 121 kandsreCrnCHsee.amdlekqkkkaakahkkaae 155
                                        ++  ++C +CH  e +  +e+q+++ +++ ++ ++
  gi|298675955|ref|YP_003727705.1| 267 DSESTNNCSRCHGAElSGVIENQQSRISSRLQDLET 302
                                       455667999999999777778887777776666654 PP

>> Cytochrome_C554  Cytochrome c554 and c-prime
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.7   0.00011      0.18       2      19 ..      27      44 ..      26      49 .. 0.91
   2 ?    5.3   2.1     0.023        37      74      84 .]      48      58 ..      46      58 .. 0.86
   3 !    8.2   5.7    0.0028       4.6       2      83 ..      85     176 ..      84     177 .. 0.51
   4 ?   -0.6   3.9       1.6   2.6e+03      50      58 ..     171     179 ..     143     202 .. 0.62
   5 ?    3.2   6.1       0.1   1.7e+02       2      84 .]     192     279 ..     191     279 .. 0.52
   6 ?    3.2   2.1      0.11   1.7e+02      36      56 ..     259     279 ..     233     294 .. 0.50
   7 ?    4.5   0.3     0.041        67       2      45 ..     274     320 ..     273     343 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                                      HHHHTHHHHHHHTTSTGG CS
                   Cytochrome_C554  2 CaeCHeeqyeswkkskha 19
                                      C++CH + ye+w+ s+h+
  gi|298675955|ref|YP_003727705.1| 27 CSQCHPDVYETWNMSNHS 44
                                      ****************97 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.023
                                      GBSS-HHHHH- CS
                   Cytochrome_C554 74 lagVqCesCHg 84
                                      +++V+Ce+CH+
  gi|298675955|ref|YP_003727705.1| 48 ESDVGCEVCHS 58
                                      579*******5 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0028
                                       HHHHTHH....HHHHHTTSTGGGTTGGGSTTSSHHHHHHTT--TTS--TT-TTTGGGSBSTTTSTT--......-SS CS
                   Cytochrome_C554   2 CaeCHee....qyeswkkskhakaleslkkekkaeakkkakldpakdaeeapeClkCHatgagkdkgf......vlk 68 
                                       C +CH+e    ++++w + ++ + +++ ++ +++e    ++++ +  ++ + +C++C  t  +  +         ++
  gi|298675955|ref|YP_003727705.1|  85 CGKCHNEphkpIFDEWDEYSK-DDFDTENMASHSE---PSDVT-EPFVQDSDDCVACKSTEGAVVNLEgadvhdFNE 156
                                       9****87666699***98754.4566555544333...22222.23356789******9975432221111111112 PP

                                       S--GGGB.....SS-HHHHH CS
                   Cytochrome_C554  69 ektklla.....gVqCesCH 83 
                                       e+ +  +       +C +CH
  gi|298675955|ref|YP_003727705.1| 157 ENLPNPSdveewRLTCVACH 176
                                       22222221112344677777 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 1.6
                                       TTGGGSBST CS
                   Cytochrome_C554  50 eClkCHatg 58 
                                       +C++CH + 
  gi|298675955|ref|YP_003727705.1| 171 TCVACHEPH 179
                                       455555432 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.1
                                       HHHHTHHHHHHHTTSTGGGTTGGGSTTSSHHHHHHTT--TTS--TT-TTTGGGSBSTTTSTT---SSS--GGGB... CS
                   Cytochrome_C554   2 CaeCHeeqyeswkkskhakaleslkkekkaeakkkakldpakdaeeapeClkCHatgagkdkgfvlkektklla... 75 
                                       C++CH++  ++  +      + +++  +++   +   +  + ++  +  C++CH+ +   ++++  +++t +     
  gi|298675955|ref|YP_003727705.1| 192 CSNCHNSRGAEPDGETTIARYTQWDIYSNS---SY--V--NGEHPVEIGCVDCHMGAKPFNETTNESAETGHTFdmn 261
                                       999999999998888877778777754332...22..2..2445667899999996653222222222211111011 PP

                                       .........SS-HHHHH- CS
                   Cytochrome_C554  76 .........gVqCesCHg 84 
                                                  +C +CHg
  gi|298675955|ref|YP_003727705.1| 262 vslvvdsesTNNCSRCHG 279
                                       111112222456777776 PP

  == domain 6  score: 3.2 bits;  conditional E-value: 0.11
                                       HTT--TTS--TT-TTTGGGSB CS
                   Cytochrome_C554  36 kakldpakdaeeapeClkCHa 56 
                                        ++++   d+e++++C +CH 
  gi|298675955|ref|YP_003727705.1| 259 DMNVSLVVDSESTNNCSRCHG 279
                                       222333455666777777775 PP

  == domain 7  score: 4.5 bits;  conditional E-value: 0.041
                                       HHHHTHHHH...HHHTTSTGGGTTGGGSTTSSHHHHHHTT--TTS-- CS
                   Cytochrome_C554   2 CaeCHeeqy...eswkkskhakaleslkkekkaeakkkakldpakda 45 
                                       C++CH  ++    + ++s+ ++ l+ l++++++  ++  +l+ ++ +
  gi|298675955|ref|YP_003727705.1| 274 CSRCHGAELsgvIENQQSRISSRLQDLETKRENAEESLEELNGTQIY 320
                                       99***876622234455556666666666665554444455544444 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.6   0.00012      0.19       2      32 ..     294     324 ..     281     328 .. 0.94
   2 ?   -1.2   0.0         2   3.2e+03       7      29 ..     347     369 ..     345     372 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SlyX   2 eerleeLEiklafqedtieeLndvvaeqqqq 32 
                                        +rl++LE+k    e+ +eeLn + + q+qq
  gi|298675955|ref|YP_003727705.1| 294 SSRLQDLETKRENAEESLEELNGTQIYQEQQ 324
                                       58********************999999887 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                              SlyX   7 eLEiklafqedtieeLndvvaeq 29 
                                       ++E+ ++++ +  e+ ++v+ +q
  gi|298675955|ref|YP_003727705.1| 347 NMEMAISYLNNSEERFDEVINAQ 369
                                       68999999999999999888877 PP

>> Cytochrom_C  Cytochrome c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       2.5   4.1e+03      10      16 ..      25      31 ..      19      36 .. 0.85
   2 ?    2.4   2.6      0.22   3.6e+02      11      44 ..      52      97 ..      45     124 .. 0.66
   3 ?   12.3   0.1   0.00018      0.29       9      89 ..     271     356 ..     268     359 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.5
                                      TTGGGTB CS
                       Cytochrom_C 10 anCaaCH 16
                                      ++C +CH
  gi|298675955|ref|YP_003727705.1| 25 EDCSQCH 31
                                      58***** PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.22
                                      TGGGTB-SSSBSSS................--HHHHHHHTTT-HHH CS
                       Cytochrom_C 11 nCaaCHgvegggakqgg............gptlsgaaerasaasig 44
                                      +C  CH++ ++g +++             ++ l g    ++++ i 
  gi|298675955|ref|YP_003727705.1| 52 GCEVCHSPPEEGYEAHIdnpteidpgmnySAELCGKCHNEPHKPIF 97
                                      79*********99977665555555555544444444444444444 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00018
                                       HTTGGGTB-SSSBSSS........--HHHHHHHTTT-HHHHHHHHTTSS--SSSHHHHHHHGGGGGGG...TT--HH CS
                       Cytochrom_C   9 tanCaaCHgvegggakqgg....gptlsgaaerasaasigasvanpaavsaprddfekkkltaempark..erlteq 79 
                                       t+nC  CHg+e  g+ +++    + +l+++++++  a++     n+ +  +  ++  ++ l +++   +    l   
  gi|298675955|ref|YP_003727705.1| 271 TNNCSRCHGAELSGVIENQqsriSSRLQDLETKRENAEESLEELNGTQIYQEQQAVFNNALYYMTAV-EedGSLGVH 346
                                       78************99888999988888888888888888888887665555444433333333322.235666666 PP

                                       HHHHHHHHHH CS
                       Cytochrom_C  80 eiadlaaYLk 89 
                                       +++  ++YL+
  gi|298675955|ref|YP_003727705.1| 347 NMEMAISYLN 356
                                       7776777765 PP

>> zf-C4pol  C4-type zinc-finger of DNA polymerase delta
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   1.0    0.0031         5      10      54 ..      50      93 ..      27     144 .. 0.68
   2 ?    6.6   0.3    0.0064        10       1      21 [.     172     200 ..     172     217 .. 0.71
   3 ?    2.7   0.4      0.11   1.8e+02      10      43 ..     271     302 ..     234     323 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0031
                          zf-C4pol 10 kalCkkCrsdkqesllkllsrlkelekklneletvCqsCaqgsle 54
                                      +  C+ C+s ++e + + +++ +e+   +n   ++C +C +++++
  gi|298675955|ref|YP_003727705.1| 50 DVGCEVCHSPPEEGYEAHIDNPTEIDPGMNYSAELCGKC-HNEPH 93
                                      455777766666667777777777777777777777777.44443 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0064
                          zf-C4pol   1 ClvCk..eklk........kalCkkCrsdkq 21 
                                       C+ C+  +  +         +lC++C++++ 
  gi|298675955|ref|YP_003727705.1| 172 CVACHepH--StglhvedeVKLCSNCHNSRG 200
                                       999**551..34455666789*****86654 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.11
                          zf-C4pol  10 kalCkkCrsdkqesllkllsrlkelekklnelet 43 
                                       ++ C++C+  +      + ++++++ ++l++let
  gi|298675955|ref|YP_003727705.1| 271 TNNCSRCHGAEL--SGVIENQQSRISSRLQDLET 302
                                       667999953332..33334444444444444444 PP

>> Cytochrome_CBB3  Cytochrome C oxidase, cbb3-type, subunit III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.4      0.02        32      10      24 ..     168     182 ..     165     191 .. 0.76
   2 ?    5.7   0.2     0.011        19      13      29 ..     191     207 ..     188     226 .. 0.75
   3 ?    2.6   0.4       0.1   1.7e+02       5      22 ..     225     241 ..     221     260 .. 0.74
   4 ?    9.7   0.0   0.00064         1      12      25 ..     272     295 ..     267     355 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.02
                   Cytochrome_CBB3  10 ykknCasCHgkggag 24 
                                       ++ +C++CH ++  g
  gi|298675955|ref|YP_003727705.1| 168 WRLTCVACHEPHSTG 182
                                       7789*****977666 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.011
                   Cytochrome_CBB3  13 nCasCHgkggagpslag 29 
                                        C+ CH + ga p+ + 
  gi|298675955|ref|YP_003727705.1| 191 LCSNCHNSRGAEPDGET 207
                                       6******9999987764 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.1
                   Cytochrome_CBB3   5 aGaalykknCasCHgkgg 22 
                                       +G++  +  C+ CH  g+
  gi|298675955|ref|YP_003727705.1| 225 NGEHPVEIGCVDCHM-GA 241
                                       577777889*****8.43 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.00064
                   Cytochrome_CBB3  12 knCasCHgkggag..........p 25 
                                       +nC++CHg++  g           
  gi|298675955|ref|YP_003727705.1| 272 NNCSRCHGAELSGvienqqsrisS 295
                                       79******6555544455555441 PP

>> Cytochrom_CIII  Class III cytochrome C family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   7.1      0.16   2.7e+02      33      85 ..      26      91 ..      16      95 .. 0.55
   2 ?    3.1   4.8     0.072   1.2e+02      25      84 ..      43     138 ..      38     145 .. 0.60
   3 ?    7.7  12.0    0.0027       4.3      33     101 ..     171     277 ..     161     278 .. 0.62
   4 ?    6.2   1.7    0.0079        13      31      86 ..     232     281 ..     221     295 .. 0.61
   5 ?    3.5   0.2     0.056        92      30      40 ..     270     280 ..     243     312 .. 0.63

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.16
                                      THHHTSTT..........CTTSCSTS-CTCTS-SSSTTTSTTCHHHHHHCSSTT....TCHHHHHHH CS
                    Cytochrom_CIII 33 eCeeCHhk..........eeekeeiekcstcHaeekekkekkslekavHkkkaa....ksCvgCHkk 85
                                      +C++CH               +e+   c+ cH+  + ++ + ++++    +  +    + C +CH++
  gi|298675955|ref|YP_003727705.1| 26 DCSQCHPDvyetwnmsnhSGLNESDVGCEVCHSPPE-EGYEAHIDNPTEIDPGMnysaELCGKCHNE 91
                                      788888877777665543222344456777888874.333333322222222112233678888886 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.072
                                       HHHHTTSH.THHHTSTT................CTTSCSTS-CTCTS-SSS.......TTTSTTCH...HHHHHCSS CS
                    Cytochrom_CIII  25 HkaHaevk.eCeeCHhk................eeekeeiekcstcHaeek.......ekkekksl...ekavHkkk 74 
                                       H+  +e +  Ce CH                     + + e c +cH+e +       ++ +k+ +   + a H++ 
  gi|298675955|ref|YP_003727705.1|  43 HSGLNESDvGCEVCHSPpeegyeahidnpteidPGMNYSAELCGKCHNEPHkpifdewDEYSKDDFdteNMASHSEP 119
                                       55444444578888888888888887777764333345566788899888666666663333333333356666655 PP

                                       TT.........TCHHHHHH CS
                    Cytochrom_CIII  75 aa.........ksCvgCHk 84 
                                       ++           Cv C +
  gi|298675955|ref|YP_003727705.1| 120 SDvtepfvqdsDDCVACKS 138
                                       5555666665566777755 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0027
                                       THHHTSTT....CTTSCSTS-CTCTS-SSS.....TTTSTTCH.....HHHHHCSSTT........TCHHHHHHHHH CS
                    Cytochrom_CIII  33 eCeeCHhk....eeekeeiekcstcHaeek.....ekkekksl.....ekavHkkkaa........ksCvgCHkkkk 87 
                                       +C +CH       + ++e++ cs+cH+++      e     ++     +  + ++++           Cv+CH  +k
  gi|298675955|ref|YP_003727705.1| 171 TCVACHEPhstgLHVEDEVKLCSNCHNSRGaepdgE-----TTiarytQWDIYSNSSYvngehpveIGCVDCHMGAK 242
                                       899**987668888999***********98554421.....221222322223323326676777789*****9887 PP

                                       HTSHH.....................HCHHSHHHH CS
                    Cytochrom_CIII  88 kekke.....................keptkCaec 101
                                         +++                     ++  +C++c
  gi|298675955|ref|YP_003727705.1| 243 PFNETtnesaetghtfdmnvslvvdsESTNNCSRC 277
                                       55554444555555555555555555555555555 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.0079
                                       SHTHHHTSTTCTTSCSTS-CTCTS-SSSTTTSTTCHHHHHHCSSTTTCHHHHHHHH CS
                    Cytochrom_CIII  31 vkeCeeCHhkeeekeeiekcstcHaeekekkekkslekavHkkkaaksCvgCHkkk 86 
                                       +  C +CH   +  +e+   ++  a e++++ +++++ +v ++++ ++C  CH ++
  gi|298675955|ref|YP_003727705.1| 232 I-GCVDCHMGAKPFNET---TNESA-ETGHTFDMNVSLVVDSEST-NNCSRCHGAE 281
                                       3.788888873322222...22112.2234444777777777555.5999999765 PP

  == domain 5  score: 3.5 bits;  conditional E-value: 0.056
                                       TSHTHHHTSTT CS
                    Cytochrom_CIII  30 evkeCeeCHhk 40 
                                       ++++C++CH +
  gi|298675955|ref|YP_003727705.1| 270 STNNCSRCHGA 280
                                       12244444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1184  (0.0660383); expected 358.6 (0.02)
Passed bias filter:                      747  (0.0416643); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.72u 0.31s 00:00:01.03 Elapsed: 00:00:00.47
# Mc/sec: 2574.85
//
Query:       gi|298675956|ref|YP_003727706.1|  [L=228]
Description: hypothetical protein Metev_2083 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      8e-64  215.3   0.1      9e-64  215.2   0.1    1.0  1  DUF169    Uncharacterised ArCR, COG2043


Domain annotation for each model (and alignments):
>> DUF169  Uncharacterised ArCR, COG2043
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.2   0.1     5e-68     9e-64       2     205 ..      13     220 ..      12     221 .. 0.99

  Alignments for each domain:
  == domain 1  score: 215.2 bits;  conditional E-value: 5e-68
                            DUF169   2 LaealrlktePVavkfsdekpelpekkekieekkrlCqmvalarakgktvvftaetlgCpgGaaalGfkelpeklks 78 
                                       L++  +lkt+PVavk++ + +e+pe++e+i+e++r+Cqm+  +r+ g+++++  e+++C+gGaa++G++e++ kl +
  gi|298675956|ref|YP_003727706.1|  13 LKKVYKLKTSPVAVKLVSSTQEIPEGIERIQEPTRHCQMIDNVRQTGTSFYTLVEDQKCKGGAAVMGLREMDGKLAK 89 
                                       8999************************************************************************* PP

                            DUF169  79 g.....egylkspeaakkfveslprleagevkyvvvapLekaefePdvvvffanpeqlmrLvqlalydrgggrlnvs 150
                                       g     +g +++ +aa+++++++pr++a +vk+v+++pLekaef Pdvvv++++p+q+m+++q++ly++gg r n++
  gi|298675956|ref|YP_003727706.1|  90 GevyykLGAFETSNAARRTMQKVPRVPADSVKAVIYEPLEKAEFIPDVVVLIGTPKQMMQISQSLLYKQGG-RINAD 165
                                       *9*******************************************************************99.***** PP

                            DUF169 151 fpgngaaCadivaypykegepniglgdpgarkfaklkddelafgiPyelleemve 205
                                       f+g+++ Cad va py++g+  +++g+ g+rk++++++de+a+giP e+le++++
  gi|298675956|ref|YP_003727706.1| 166 FAGKQSLCADGVAEPYMSGQVCVTVGCGGSRKHTQINEDEMAIGIPLEQLEDLAD 220
                                       ***************************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1600.60
//
Query:       gi|298675957|ref|YP_003727707.1|  [L=94]
Description: GYD family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-28   97.3   0.1    4.2e-28   97.1   0.1    1.0  1  GYD             GYD domain
  ------ inclusion threshold ------
      0.018   15.0   0.0      0.023   14.6   0.0    1.2  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain


Domain annotation for each model (and alignments):
>> GYD  GYD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.1   0.1   4.7e-32   4.2e-28       1      90 [.       4      92 ..       4      93 .. 0.99

  Alignments for each domain:
  == domain 1  score: 97.1 bits;  conditional E-value: 4.7e-32
                               GYD  1 YivlvnytdegvkglkdsperreeakealveslGgkleslyatlGeyDvvvivEapDdetaaalslalaasGtvrtetl 79
                                      Y++++++tdeg+++lk++p+r++e++++l e++G+k+ +++++lG++D+++ivEa+D++++ +++++la++G+++t+t+
  gi|298675957|ref|YP_003727707.1|  4 YVMISQLTDEGARTLKNNPKRVKEVNDEL-EQMGVKVLEQFFVLGDFDFLNIVEAEDESSVSKAAVELASRGSIKTKTY 81
                                      9****************************.************************************************* PP

                               GYD 80 rafteeefdea 90
                                      +a+++ ef +a
  gi|298675957|ref|YP_003727707.1| 82 TAIPMHEFTSA 92
                                      ********876 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.6e-06     0.023      12      70 ..      24      81 ..      15      87 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.6e-06
                                      HHHHHHHHHHTST.TEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEE CS
                    AsnC_trans_reg 12 qleefeealaelp.eVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartets 70
                                       ++e+ ++l+++   V+e + v Gd+d+l +v ++d  + ++  +e las   + +t+t+
  gi|298675957|ref|YP_003727707.1| 24 RVKEVNDELEQMGvKVLEQFFVLGDFDFLNIVEAEDESSVSKAAVE-LASRGSI-KTKTY 81
                                      46666666666533799************************99999.7776444.55555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 647.54
//
Query:       gi|298675958|ref|YP_003727708.1|  [L=217]
Description: DNA-(apurinic or apyrimidinic site) lyase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.016   15.1   0.3      0.067   13.1   0.1    2.2  2  DUF3781   Protein of unknown function (DUF3781)
      0.047   14.1   0.0      0.081   13.4   0.0    1.4  1  HhH-GPD   HhH-GPD superfamily base excision DNA repair protei


Domain annotation for each model (and alignments):
>> DUF3781  Protein of unknown function (DUF3781)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   7.5e-06     0.067      20      64 ..      17      59 ..       8      61 .. 0.87
   2 ?   -2.8   0.0      0.66   5.9e+03      16      32 ..     129     146 ..     114     149 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.5e-06
                           DUF3781 20 nLslseddvveyckeiildknakiekkGKnyYveakniilTvNas 64
                                         l+ dd+ e + ++i + ++  +k +K +++e   + lT N+s
  gi|298675958|ref|YP_003727708.1| 17 D--LKADDISEIVDKRIREFESLYKKGNKEWFNELCFCLLTANSS 59
                                      3..6699************999999999**************986 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.66
                           DUF3781  16 RIkknLs.lseddvveyc 32 
                                        I k+++ + +++  +++
  gi|298675958|ref|YP_003727708.1| 129 WIVKKIKgIGYKESSHFL 146
                                       445555556666665555 PP

>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     9e-06     0.081      33      90 ..      76     172 ..      54     188 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9e-06
                                       HHHSHHHHHHHHHTT..STTHHHHHHHHHHHHHHHH.......................................S- CS
                                       xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx.......................................xx RF
                           HhH-GPD  33 ladadeekLrelire..lGfyrrKakyikelArilv.......................................gk 68 
                                       ++ +d+++L + +++  ++fy+++a+yi+ lAr  +                                       g+
  gi|298675958|ref|YP_003727708.1|  76 FLTYDQKELSTVLKQmgHRFYEKRAEYII-LARDNAadirdkitsmeneftarewivkkikgigykesshflrnvGY 151
                                       567888888888887779**********8.5555555999**********************************988 PP

                                       SSS--TTSHHHHHHHHHHTTSS CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                           HhH-GPD  69 pdvlivvDvhvrrilkrlrsik 90 
                                       +  l + D h+ ril+  ++i+
  gi|298675958|ref|YP_003727708.1| 152 KH-LAILDKHILRILSNSGLIE 172
                                       65.9999*******99887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.55
# Mc/sec: 1183.54
//
Query:       gi|298675959|ref|YP_003727709.1|  [L=273]
Description: ABC-3 protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.7e-81  271.6  28.4    7.6e-81  271.4  28.4    1.0  1  ABC-3         ABC 3 transport family
    3.7e-12   45.9  20.2    3.7e-12   45.9  20.2    1.8  2  FecCD         FecCD transport family


Domain annotation for each model (and alignments):
>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  271.4  28.4   8.5e-85   7.6e-81       1     256 [.       8     263 ..       8     265 .. 0.99

  Alignments for each domain:
  == domain 1  score: 271.4 bits;  conditional E-value: 8.5e-85
                             ABC-3   1 qyeflqrallasilvslacallgsfvvlrrqsllgdalsHaalpGvalayllgvnlllgailvgliaavalellkrk 77 
                                       qyef+++al a+il s+ac+++g++vv++r++++g++++Ha+++G++++y+lg+n++lg++ +g++ a+++++++++
  gi|298675959|ref|YP_003727709.1|   8 QYEFMRNALFAAILASIACGIIGAYVVVKRIVFIGGGIAHASFGGIGMGYYLGFNPILGILPFGIASALGIGWITKR 84 
                                       79*************************************************************************** PP

                             ABC-3  78 tklkedtaigivlsvflalglvlvslikkskvdldsyLfGniltisqedliliaiieavvllllllfwkelllitfd 154
                                       + l ed+aigi++++++a+g+v+++l+++++ +l+ yLfGnilt+   d+il++i+++v+++++ +f+ke+l+i+fd
  gi|298675959|ref|YP_003727709.1|  85 SSLPEDSAIGILWASGMAIGIVFLNLTPGYAPNLMTYLFGNILTVPVFDVILMLILDVVIVSVVYIFYKEFLAISFD 161
                                       ***************************************************************************** PP

                             ABC-3 155 eelAkveglsvkllkllllalialavvvalqavGviLvialliiPaatArrltrslesllivAillglvsvvaGlll 231
                                       ee+ +v g++ + l++lll++ial+v v +++vG+iLviall+iPaa+ r++t+++++++i+++l+g+++++ Gl +
  gi|298675959|ref|YP_003727709.1| 162 EEMTTVMGVPAEKLYYLLLCMIALTVMVLVRVVGIILVIALLTIPAALSRQMTSDFKRMMILSVLFGAIFSTGGLGI 238
                                       ***************************************************************************** PP

                             ABC-3 232 SyyldlatGavivlvatllfllall 256
                                       Sy +d+++Ga+i+lv+++++++ +l
  gi|298675959|ref|YP_003727709.1| 239 SYLYDIPSGATIILVMSVFYFAYSL 263
                                       *******************998766 PP

>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   1.5      0.14   1.3e+03     222     246 ..      18      42 ..       7      55 .. 0.60
   2 !   45.9  20.2   4.2e-16   3.7e-12     149     311 ..     103     264 ..      91     265 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.14
                             FecCD 222 llllllvalltavavalvGpigFvG 246
                                        ++l+ +a+ +  a+++v  i F+G
  gi|298675959|ref|YP_003727709.1|  18 AAILASIACGIIGAYVVVKRIVFIG 42 
                                       3333333334444566666666666 PP

  == domain 2  score: 45.9 bits;  conditional E-value: 4.2e-16
                             FecCD 149 sllllll.neealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrlll 224
                                         +++l  ++  + +++++l+G++ ++   +v+l+l+l ++++ +++++++++ ++++++e+ + +Gv+ e++ +ll
  gi|298675959|ref|YP_003727709.1| 103 IGIVFLNlTPGYAPNLMTYLFGNILTVPVFDVILMLILDVVIVSVVYIFYKEFLAISFDEEMTTVMGVPAEKLYYLL 179
                                       333333238899***************************************************************** PP

                             FecCD 225 lllvalltavavalvGpigFvGLi.vPhiarllvgadhrkllplsallGallllladllarlllsptelpvg.ivta 299
                                       l+++al + v v +vG+i  ++L+ +P  +++ + +d++++++ls+l+Ga++ +    ++ l+    ++p g  ++ 
  gi|298675959|ref|YP_003727709.1| 180 LCMIALTVMVLVRVVGIILVIALLtIPAALSRQMTSDFKRMMILSVLFGAIFSTGGLGISYLY----DIPSGaTIIL 252
                                       **********************86479999999999****************99998887766....6666634555 PP

                             FecCD 300 liGapffiylll 311
                                       ++ + +f+y l+
  gi|298675959|ref|YP_003727709.1| 253 VMSVFYFAYSLV 264
                                       566677877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       984  (0.0548832); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 1831.07
//
Query:       gi|298675960|ref|YP_003727710.1|  [L=253]
Description: ABC transporter-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-28  100.4   0.0    1.6e-28   99.9   0.0    1.2  1  ABC_tran  ABC transporter
    1.4e-14   54.7   1.6    1.3e-07   31.8   0.0    2.1  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    2.6e-07   30.3   0.2    1.2e-06   28.1   0.2    1.8  1  SMC_N     RecF/RecN/SMC N terminal domain
    2.4e-06   27.5   0.0     0.0017   18.1   0.0    2.1  2  AAA_15    AAA ATPase domain
    0.00015   22.2   0.2       0.53   10.7   0.0    2.1  2  AAA       ATPase family associated with various cellular acti
     0.0012   19.4   0.1     0.0022   18.5   0.1    1.4  1  AAA_23    AAA domain
     0.0029   17.3   0.1      0.013   15.2   0.1    1.9  1  AAA_30    AAA domain
     0.0054   16.7   0.1      0.096   12.6   0.0    2.0  2  ATPase_2  ATPase domain predominantly from Archaea
     0.0091   15.7   0.1      0.018   14.7   0.1    1.5  1  AAA_29    P-loop containing region of AAA domain
     0.0095   15.0   0.0       0.02   14.0   0.0    1.5  2  T2SSE     Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.015   15.6   0.1       0.22   11.8   0.0    2.1  2  AAA_22    AAA domain
      0.015   15.5   0.4       0.48   10.7   0.1    2.4  1  SbcCD_C   Putative exonuclease SbcCD, C subunit
      0.048   13.6   0.3       0.14   12.1   0.2    1.8  2  NACHT     NACHT domain
      0.053   13.1   0.0       0.09   12.4   0.0    1.3  1  AAA_27    AAA domain
      0.058   13.3   0.0       0.11   12.4   0.0    1.4  1  Rad17     Rad17 P-loop domain
      0.095   12.1   0.0       0.17   11.3   0.0    1.3  1  Pox_A32   Poxvirus A32 protein
      0.099   13.0   0.4       0.74   10.1   0.1    2.0  2  AAA_19    AAA domain
       0.14   12.2   0.1        5.6    7.0   0.0    2.2  2  AAA_14    AAA domain
       0.16   11.8   0.1       0.36   10.7   0.1    1.5  1  NTPase_1  NTPase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.9   0.0   1.7e-31   1.6e-28       1     137 []      23     170 ..      23     170 .. 0.89

  Alignments for each domain:
  == domain 1  score: 99.9 bits;  conditional E-value: 1.7e-31
                                       EEEEEEEEET.TSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSB. CS
                                       xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                          ABC_tran   1 lknvslklke.gekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpelt. 75 
                                       l++++l++++   ++ai+G+nG GK+tLlk+++gl kp +G+++l g++  +      rk +g++pq+++++++   
  gi|298675960|ref|YP_003727710.1|  23 LEDINLTIEQpRDLLAIIGPNGGGKTTLLKVILGLIKPSNGKVKLFGESPAK-----NRKYVGYVPQHSSFDYDFPi 94 
                                       678999997526799****************************999877766.....9**********888888752 PP

                                       .HHHH.................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEES CS
                                       .xxxx.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  76 .vren.................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDE 134
                                        v +                  e++ +++kal+++++++ +++ +     +LSgGq+qrv +aral+ +p++lllDE
  gi|298675960|ref|YP_003727710.1|  95 sVWDVvlmgrmghtgilkryssEDKFKANKALKTVNMEDYANHQI----GKLSGGQRQRVFIARALAAEPEVLLLDE 167
                                       25555*************987666667*****************9....**************************** PP

                                       TTT CS
                                       xxx RF
                          ABC_tran 135 pta 137
                                       p+a
  gi|298675960|ref|YP_003727710.1| 168 PSA 170
                                       *75 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   1.2   1.9e-07   0.00018       2      24 ..      37      59 ..      36      94 .. 0.75
   2 !   31.8   0.0   1.3e-10   1.3e-07     220     300 ..     125     201 ..     101     204 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.9e-07
                            AAA_21  2 nvliGpNgsGKSnLLdaldllar 24
                                       ++iGpNg GK++LL+ + +l  
  gi|298675960|ref|YP_003727710.1| 37 LAIIGPNGGGKTTLLKVILGLIK 59
                                      58****************88843 PP

  == domain 2  score: 31.8 bits;  conditional E-value: 1.3e-10
                            AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltT 296
                                        + ++ ++d+ + ++ +lS G+++  +++ al++ +    +ll+DEp +gL+ +++ +l+ell++l++ +  +i++T
  gi|298675960|ref|YP_003727710.1| 125 ALKTVNMEDYANHQIGKLSGGQRQRVFIARALAAEP---EVLLLDEPSAGLDTHMQGELYELLSKLKK-DMAIIMVT 197
                                       56778889999999***********55555555555...9***********************99988.9******* PP

                            AAA_21 297 HSpl 300
                                       H+ +
  gi|298675960|ref|YP_003727710.1| 198 HDLT 201
                                       *975 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.2   1.3e-09   1.2e-06      21     202 ..      31     203 ..      23     215 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1.3e-09
                                       ETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCC.CCC--BTTCSSTTEEEEEEEEEETTEESSSSSSC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  21 pfsksftaivGpNGSGKsnlldAilFvLGersakklrsekls.dlihkskekasvkkaeveitfdnedkklkiekee 96 
                                       +  + + ai+GpNG GK+ ll  i   LG      ++ ++ + +l  +s +k++   ++v  + +  d +++i+  +
  gi|298675960|ref|YP_003727710.1|  31 EQPRDLLAIIGPNGGGKTTLLKVI---LGL-----IKPSNGKvKLFGESPAKNRKYVGYVPQH-SSFDYDFPISVWD 98 
                                       55667889***************9...995.....4444444045555677777778888886.7777789****** PP

                                       EEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCT...T-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  97 vsisrrvkrkgeseykingkevtkkevsellesa...giskelLSgGektLvalaLlfAiqkvkpaplyllDeidaa 170
                                       v+++ r+ ++g  + +  + + + ++  + ++++   + ++  LSgG+++ v +a  +A    +p+ + llDe  a 
  gi|298675960|ref|YP_003727710.1|  99 VVLMGRMGHTGILKRYSSEDKFKANKALKTVNMEdyaNHQIGKLSGGQRQRVFIARALAA---EPE-VLLLDEPSAG 171
                                       ********99996666666666665555555554011445668*******9999988774...555.5689****** PP

                                       S-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 171 LDeknvkkvaellkeksknaQfivislreeml 202
                                       LD +   ++ ell + +k++ +i+++++ + +
  gi|298675960|ref|YP_003727710.1| 172 LDTHMQGELYELLSKLKKDMAIIMVTHDLTAV 203
                                       **************************987665 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.8e-06    0.0017      18      83 ..      27      98 ..      22     143 .. 0.57
   2 !    8.0   0.1    0.0022       2.1     322     365 ..     158     199 ..     110     203 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.8e-06
                            AAA_15 18 eidlsee..ltvliGkNnsGKSsilealdlFlnnkekkn.............kkvikiekedleifeniseskdikIdv 81
                                       + ++    l  +iG+N+ GK+++l+++  +++ +   n                    k    + ++ s+++d+ I v
  gi|298675960|ref|YP_003727710.1| 27 NLTIEQPrdLLAIIGPNGGGKTTLLKVILGLIKPS---NgkvklfgespaknR------KYVGYVPQHSSFDYDFPISV 96
                                      4444443679******************9999988...333456564333330......33333344444444444444 PP

                            AAA_15 82 ef 83
                                      + 
  gi|298675960|ref|YP_003727710.1| 97 WD 98
                                      44 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0022
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                       +++ +ll++EP a L + +q +l++ll +l +d    +i+ TH 
  gi|298675960|ref|YP_003727710.1| 158 AEPEVLLLDEPSAGLDTHMQGELYELLSKLKKDMA--IIMVTHD 199
                                       35679****************************96..******7 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0    0.0011       1.1       3      23 ..      39      59 ..      37      90 .. 0.74
   2 !   10.7   0.0   0.00056      0.53      23     112 ..     123     200 ..      99     217 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0011
                                      EESSTTSSHHHHHHHHHHHHT CS
                               AAA  3 lyGppGtGKTllakavakelg 23
                                      ++Gp G GKT+l k +   ++
  gi|298675960|ref|YP_003727710.1| 39 IIGPNGGGKTTLLKVILGLIK 59
                                      79*************988764 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00056
                                       THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTT CS
                               AAA  23 gvefleisgsellskyvgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkk 98 
                                       +  + ++++ +  ++ +g+ +   r+ +  a++ a +p +l++DE  a   +           ++ +L++ l+++kk
  gi|298675960|ref|YP_003727710.1| 123 NKALKTVNMEDYANHQIGKLSGGQRQRVFIARALAaEPEVLLLDEPSAGLDTH----------MQGELYELLSKLKK 189
                                       45678889999999999999999999999999999999********9999999..........999*********99 PP

                                       SSSTEEEEEEESSG CS
                               AAA  99 keskvivigatnrp 112
                                          ++ +i++t++ 
  gi|298675960|ref|YP_003727710.1| 190 ---DMAIIMVTHDL 200
                                       ...47788888875 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   2.3e-06    0.0022      14      39 ..      29      54 ..      16      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.3e-06
                            AAA_23 14 eidFskgltlItGpNGaGKTTildAi 39
                                      +i+  + l +I+GpNG GKTT+l  i
  gi|298675960|ref|YP_003727710.1| 29 TIEQPRDLLAIIGPNGGGKTTLLKVI 54
                                      444467899*************9876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   1.4e-05     0.013      14      57 ..      30      73 ..      24     203 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.4e-05
                            AAA_30 14 ltsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgk 57
                                      +++++ + ++ Gp G GKtt+lk++  +++ ++g+v ++  + +
  gi|298675960|ref|YP_003727710.1| 30 IEQPRDLLAIIGPNGGGKTTLLKVILGLIKPSNGKVKLFGESPA 73
                                      567788999*********************99888887766654 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0    0.0001     0.096      11      43 ..      26      57 ..      22      76 .. 0.81
   2 ?    2.1   0.0      0.16   1.5e+02      32     155 ..     106     227 ..     102     235 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0001
                          ATPase_2 11 leeilerepneiyfiYGpegsGKtaLlkeiien 43
                                      ++  +e+ p++ + i Gp g GKt+Llk i+  
  gi|298675960|ref|YP_003727710.1| 26 INLTIEQ-PRDLLAIIGPNGGGKTTLLKVILGL 57
                                      5555555.999*****************99765 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.16
                          ATPase_2  32 GKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekalgiavpkaeleeilkeksklvfkaiel 108
                                       G t +lk+  ++ + k  + +   ++++++++++ +  + ++++ ++++al+ + +   l    +e s+ ++  ++ 
  gi|298675960|ref|YP_003727710.1| 106 GHTGILKRYSSEDKFKANKALKTVNMEDYANHQIGKLSGGQRQRVFIARALAAEPEVLLL----DEPSAGLDTHMQG 178
                                       666666666666666666666677777777777666644555555555555433333333....3444444444443 PP

                          ATPase_2 109 llekikkkgkk...iiiiiDelqklidlglngaellvkeLlnliesltke 155
                                        l ++  k kk   ii++  +l  +  l +++ + l  +L++   +  ++
  gi|298675960|ref|YP_003727710.1| 179 ELYELLSKLKKdmaIIMVTHDLTAVS-LHVDKVACLNRKLFYHGSKEISH 227
                                       33333333333344788888888777.89999988888888766665555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1     2e-05     0.018      22      50 ..      34      62 ..      23      68 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2e-05
                            AAA_29 22 kgatlltGpsGsGKSTllDAiqalLvpak 50
                                      ++   ++Gp+G GK+Tll  i  l+ p++
  gi|298675960|ref|YP_003727710.1| 34 RDLLAIIGPNGGGKTTLLKVILGLIKPSN 62
                                      45789*************88888888876 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   2.1e-05      0.02     116     159 ..      24      64 ..       7      72 .. 0.88
   2 ?   -2.7   0.0       2.5   2.4e+03     146     162 ..     180     196 ..     124     227 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.1e-05
                             T2SSE 116 ekiaevlrkavrerglilvsGgTgsGKttllyallkeinksder 159
                                       e+i+ +++++   r l+ + G+ g GKttll ++l  i+ s+ +
  gi|298675960|ref|YP_003727710.1|  24 EDINLTIEQP---RDLLAIIGPNGGGKTTLLKVILGLIKPSNGK 64 
                                       6777889999...99999********************988665 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.5
                             T2SSE 146 lyallkeinksderivt 162
                                       ly ll++++k+   i++
  gi|298675960|ref|YP_003727710.1| 180 LYELLSKLKKDMAIIMV 196
                                       34444444444333333 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00023      0.22       4      25 ..      33      54 ..      30      86 .. 0.87
   2 ?    1.7   0.0      0.29   2.8e+02      88     117 ..     153     189 ..     109     205 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00023
                            AAA_22  4 tagilvvtGesGtGKTtllrrl 25
                                       + +l+++G+ G GKTtll+ +
  gi|298675960|ref|YP_003727710.1| 33 PRDLLAIIGPNGGGKTTLLKVI 54
                                      56789*************9865 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.29
                            AAA_22  88 arav...ielliiDEaqh.lr...seealeeLrslln 117
                                       ara    +e+l++DE    l+   + e++e L++l +
  gi|298675960|ref|YP_003727710.1| 153 ARALaaePEVLLLDEPSAgLDthmQGELYELLSKLKK 189
                                       3333556789999999888877555777777766654 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1    0.0005      0.48      25      89 ..     134     185 ..     112     186 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0005
                           SbcCD_C  25 elsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                         ++++g+lSGG++q ++   +a ala            +++++LDE  ++lD +++ +l ell 
  gi|298675960|ref|YP_003727710.1| 134 YANHQIGKLSGGQRQRVF---IARALA----A------EPEVLLLDEPSAGLDTHMQGELYELLS 185
                                       367889999999996554...332222....2......367899999999999999999888875 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   0.00015      0.14       2      25 ..      36      59 ..      35      68 .. 0.83
   2 ?   -1.6   0.0       2.3   2.2e+03      87     120 ..     165     189 ..     131     202 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00015
                                      CEEEEC-TTTCHHHHHHHHHHHHC CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawa 25
                                      l+++ G++G GKTtLl+ +  +++
  gi|298675960|ref|YP_003727710.1| 36 LLAIIGPNGGGKTTLLKVILGLIK 59
                                      789*************99987766 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.3
                                       EE-STT-SS-TCH.........HHHHHCTTTTT- CS
                             NACHT  87 lDglDelvtdlgqkekqpvrtlLselirkkllpe 120
                                       l   De ++ l+     +++  L el++k  l++
  gi|298675960|ref|YP_003727710.1| 165 L---DEPSAGLDT----HMQGELYELLSK--LKK 189
                                       3...344444444....455566666666..444 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   9.5e-05      0.09      14      49 ..      23      57 ..      15      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.5e-05
                            AAA_27 14 ftdrsldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                      ++d +l+++ + +dl  i+GpN  GK+t+l+ i  l
  gi|298675960|ref|YP_003727710.1| 23 LEDINLTIE-QPRDLLAIIGPNGGGKTTLLKVILGL 57
                                      478889998.7999999*************988766 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00012      0.11      42      65 ..      31      54 ..      11     103 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                             Rad17 42 srkkriLLisGPsGCgkstvvkvL 65
                                      ++++ +L i GP G gk+t +kv+
  gi|298675960|ref|YP_003727710.1| 31 EQPRDLLAIIGPNGGGKTTLLKVI 54
                                      56788*****************86 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00018      0.17      16      63 ..      37      85 ..      28      90 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00018
                           Pox_A32 16 lalvGgsGsGktvyLlsLlrtlvkkykhifLl..tpvknseYdkyvwPdh 63
                                      la++G  G Gkt+ L+ +l  +      + L+   p kn +Y +yv P+h
  gi|298675960|ref|YP_003727710.1| 37 LAIIGPNGGGKTTLLKVILGLIKPSNGKVKLFgeSPAKNRKYVGYV-PQH 85
                                      79***********99999888877777777773367*********9.776 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00079      0.74       7      35 ..      31      59 ..      26      68 .. 0.83
   2 ?    0.8   0.0      0.62   5.8e+02     102     135 ..     159     196 ..     117     201 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00079
                            AAA_19  7 alkekvllvtaGpGtGKTrvlkhivallv 35
                                      + ++++l+++++ G GKT++lk i+ l++
  gi|298675960|ref|YP_003727710.1| 31 EQPRDLLAIIGPNGGGKTTLLKVILGLIK 59
                                      5678899***************9998776 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.62
                            AAA_19 102 eeellivDEfqd.vd.elq...yrLlkallgekkklllv 135
                                       e e+l+ DE +  +d  +q   y+Ll++l+ +++ +++v
  gi|298675960|ref|YP_003727710.1| 159 EPEVLLLDEPSAgLDtHMQgelYELLSKLK-KDMAIIMV 196
                                       344888888763244333322277788887.45547666 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0059       5.6       4      23 ..      36      55 ..      33      77 .. 0.85
   2 ?    3.3   0.0     0.085        81      12      72 ..     104     167 ..      99     195 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0059
                            AAA_14  4 ilvitGaRrvGKTtllkqli 23
                                      +l+i G+   GKTtllk ++
  gi|298675960|ref|YP_003727710.1| 36 LLAIIGPNGGGKTTLLKVIL 55
                                      689************98765 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.085
                            AAA_14  12 rvGKTtllkqlikell.vkkesilyinldderdkkladpe..kllelilek.lkeekktylflDE 72 
                                       r+G T +lk++ +e     ++    +n++d  + ++ + +  +  +++ ++ l + + ++l+lDE
  gi|298675960|ref|YP_003727710.1| 104 RMGHTGILKRYSSEDKfKANKALKTVNMEDYANHQIGKLSggQRQRVFIARaLAA-EPEVLLLDE 167
                                       7888999999988888777788889999999998877665665667777773444.8999****9 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00038      0.36       3      31 ..      38      66 ..      36      77 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00038
                                      EEE--TTSSHHHHHHHHHHHH...GGGEE CS
                          NTPase_1  3 fiTGppGvGKtTlvkkvlellkssgvkvg 31
                                      +i Gp G GKtTl+k +l l+k s+ kv+
  gi|298675960|ref|YP_003727710.1| 38 AIIGPNGGGKTTLLKVILGLIKPSNGKVK 66
                                      688*******************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 1545.35
//
Query:       gi|298675961|ref|YP_003727711.1|  [L=285]
Description: periplasmic solute-binding protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-58  198.2   0.4    1.8e-58  198.0   0.4    1.0  1  ZnuA            Zinc-uptake complex component A periplasmic
  ------ inclusion threshold ------
      0.027   13.3   0.0      0.048   12.4   0.0    1.3  1  Aminotran_MocR  Alanine-glyoxylate amino-transferase
       0.15   12.1   1.9       0.95    9.5   0.1    2.3  2  SLAM            Signaling lymphocytic activation molecule (SL
       0.25   12.4   0.2       0.57   11.2   0.2    1.6  1  Conotoxin       Conotoxin


Domain annotation for each model (and alignments):
>> ZnuA  Zinc-uptake complex component A periplasmic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.0   0.4     4e-62   1.8e-58       1     255 [.      37     281 ..      37     282 .. 0.89

  Alignments for each domain:
  == domain 1  score: 198.0 bits;  conditional E-value: 4e-62
                                       EEESSHHHHHHHHHHHGGGCEEEECS-TTSTTTT----HHHHHHHHHSSEEEESSTTTS...GTHHHHHHHHTTCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxx RF
                              ZnuA   1 VvattsplgdlvrqvaGdrvevtvLvppgadpHsyeptprdvrklaeAdllvynglelE...twldkllasssqatr 74 
                                       V +++ p +++v+q++G++v+  v++ppga+p + ept  ++r+l++A ++   g +l    +w++k+ +s++  ++
  gi|298675961|ref|YP_003727711.1|  37 VAVSILPQAEFVEQIGGEKVNTIVMIPPGANPATHEPTSGQLRDLSNALMYAKLGSGLPferSWMNKI-SSVN--DE 110
                                       789************************************************99998877556778777.3443..44 PP

                                       EEEEETTTTCCSEBCSSESTGGGSHHHHHHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ZnuA  75 vevidlsegveeeeeeeDpHiWlspknaiamveniadaLveadpanadtyeanaaayiekLeeldaeireelaeipe 151
                                       + +++ s+g++    ++DpH+W+sp+na++mveni+++L+++dp+n+d+y++n ++yi+kL+eld +i+++l+e ++
  gi|298675961|ref|YP_003727711.1| 111 MLIVNSSDGIT--IRNNDPHVWTSPENAKTMVENIYEGLIQVDPENKDYYSQNKDKYIQKLDELDFYINNTLSEYEN 185
                                       46777888874..5567********************************************************8887 PP

                                       TEGEEEESSSTTHHHHHHTT-EEEEEE..SSSSS..HHHHHHHHHHHHHTT-SEEEEETTS-THHHHHHHHHHT-EE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ZnuA 152 ekrklvtthdafgylarayglevagia..giste..aaqiaalieeikeagvkaifveplaspklaetlaeeagvkv 224
                                       ++  ++++h+ +gy+a++ygl+++ +   g   e  a+++++l++ +k++++ +i+v++++s+++ae++a+e + kv
  gi|298675961|ref|YP_003727711.1| 186 QS--FMVYHPTWGYFAQEYGLDMIPVEseGK--EpsAKELQQLVDIAKKKNISVIYVQEQFSTSSAESIANEVNGKV 258
                                       76..********************7764344..256***************************************** PP

                                       EEE-STSSSTSTTSTTSHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ZnuA 225 atlysldslgdegsaetYidmmranleslke 255
                                       +tl++l +        +Y++ +r+  e+++e
  gi|298675961|ref|YP_003727711.1| 259 VTLDPLAK--------DYVSNLRNVSEVFAE 281
                                       *****443........899999998888776 PP

>> Aminotran_MocR  Alanine-glyoxylate amino-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.1e-05     0.048     140     209 ..     198     269 ..     179     282 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.1e-05
                                       HHHHHT-EEEEEEEETTEE-HHHHHHHH..HC-TTEEEEEE-SSS-TTT-----HHHHHHHHT---SSTT-E CS
                    Aminotran_MocR 140 lleelGielltvdlqddGpdvdaveklv..aedasvkGilavpkysnptGetiseevarrlaalkaaapdfr 209
                                       + +e+G++++ v+ +   p  + +++lv  a+   +  i++  ++s  + e i++ev  ++++l+  a d+ 
  gi|298675961|ref|YP_003727711.1| 198 FAQEYGLDMIPVESEGKEPSAKELQQLVdiAKKKNISVIYVQEQFSTSSAESIANEVNGKVVTLDPLAKDYV 269
                                       4699***********************7558999*******************************9999985 PP

>> SLAM  Signaling lymphocytic activation molecule (SLAM) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.2     0.047   2.1e+02      67     116 ..     136     185 ..     105     191 .. 0.84
   2 ?    9.5   0.1   0.00021      0.95      65     103 ..     245     283 ..     222     285 .] 0.85

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.047
                              SLAM  67 aespessvkkkivsldlsegsspryledgYkfhlenlsLeilesrkedeG 116
                                       a+   +++   ++ +d++++++ +  +d+Y  +l++l+  i ++  e e 
  gi|298675961|ref|YP_003727711.1| 136 AKTMVENIYEGLIQVDPENKDYYSQNKDKYIQKLDELDFYINNTLSEYEN 185
                                       556667788889999**********************9999887777665 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00021
                              SLAM  65 tvaespessvkkkivsldlsegsspryledgYkfhlenl 103
                                       + aes  ++v+ k+v ld+  +++ ++l +  +   en+
  gi|298675961|ref|YP_003727711.1| 245 SSAESIANEVNGKVVTLDPLAKDYVSNLRNVSEVFAENF 283
                                       6799*************************9999888886 PP

>> Conotoxin  Conotoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00013      0.57       3      24 ..       8      33 ..       6      44 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
                                      XXXXXXXXXXXXX....XXXXXXXXX CS
                         Conotoxin  3 LtcvlivavLllt....tlvtadldg 24
                                      L +vl++avL++t    ++ t+++dg
  gi|298675961|ref|YP_003727711.1|  8 LSVVLVIAVLFVTgcseQTQTQKDDG 33
                                      889**********7765444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       971  (0.0541581); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2073.99
//
Query:       gi|298675962|ref|YP_003727712.1|  [L=141]
Description: DtxR family iron (metal) dependent repressor [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.6e-19   67.2   0.1    1.6e-18   66.6   0.1    1.3  1  Fe_dep_repr_C   Iron dependent repressor, metal binding and d
    5.2e-13   49.0   0.0    7.5e-13   48.5   0.0    1.3  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    5.4e-09   35.8   0.0      1e-06   28.5   0.0    2.2  2  MarR_2          MarR family
    1.3e-06   27.8   0.0    0.00018   21.0   0.0    2.2  2  HTH_24          Winged helix-turn-helix DNA-binding
    3.3e-06   27.5   0.0      1e-05   25.9   0.0    1.7  2  HTH_27          Winged helix DNA-binding domain
    4.9e-06   26.4   0.0    9.6e-06   25.4   0.0    1.5  1  MarR            MarR family
    2.7e-05   24.0   0.0    9.4e-05   22.2   0.0    1.8  2  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00017   21.4   0.1    0.00062   19.7   0.0    1.8  2  HTH_11          HTH domain
    0.00036   20.8   0.0     0.0006   20.1   0.0    1.3  1  Rrf2            Transcriptional regulator
    0.00094   18.9   0.3       0.41   10.4   0.1    2.2  2  HTH_DeoR        DeoR-like helix-turn-helix domain
     0.0011   18.7   0.0     0.0023   17.7   0.0    1.6  1  HTH_IclR        IclR helix-turn-helix domain
     0.0014   17.5   0.0      0.002   17.0   0.0    1.1  1  HTH_micro       HTH-like
     0.0035   17.1   0.0        2.9    7.8   0.0    2.5  2  HTH_23          Homeodomain-like domain
     0.0073   16.3   0.1      0.021   14.8   0.1    1.8  1  HTH_45          Winged helix-turn-helix
     0.0094   15.8   0.0      0.019   14.9   0.0    1.5  1  RuvB_C          RuvB C-terminal winged helix domain
  ------ inclusion threshold ------
       0.01   15.8   0.0        1.8    8.6   0.0    2.2  2  HTH_6           Helix-turn-helix domain, rpiR family
      0.014   15.3   0.0      0.042   13.8   0.0    1.7  2  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.021   15.1   0.0      0.042   14.1   0.0    1.5  1  A_thal_3526     Plant protein 1589 of unknown function (A_tha
      0.023   14.6   0.0       0.15   12.0   0.0    2.1  2  HTH_5           Bacterial regulatory protein, arsR family
      0.024   13.7   0.0      0.031   13.3   0.0    1.1  1  Topoisom_bac    DNA topoisomerase
      0.024   14.7   0.0       0.11   12.5   0.0    2.0  2  FeoC            FeoC like transcriptional regulator
      0.047   13.7   0.1       0.21   11.6   0.0    2.1  2  HTH_36          Helix-turn-helix domain
       0.15   12.3   0.0       0.29   11.4   0.0    1.5  2  YjcQ            YjcQ protein


Domain annotation for each model (and alignments):
>> Fe_dep_repr_C  Iron dependent repressor, metal binding and dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.6   0.1     2e-21   1.6e-18       1      65 [.      67     130 ..      67     134 .. 0.94

  Alignments for each domain:
  == domain 1  score: 66.6 bits;  conditional E-value: 2e-21
                                       -HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHCT-.SB-TTS CS
                     Fe_dep_repr_C   1 TekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldellgfpeecPhg 65 
                                       Te Gre+A++l+rrhr+l  +L  ++g++ ++a+ee++r+E ++s+ +++r+++ +g+p+ + +g
  gi|298675962|ref|YP_003727712.1|  67 TEYGREYAEFLLRRHRILSLLL-SHYGLSTNDACEEVSRFEGHVSKYAVDRICKSMGHPQLSNCG 130
                                       9*********************.66**********************************987666 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.0   9.6e-16   7.5e-13       2      60 .]       9      64 ..       8      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 9.6e-16
                                      --HHHHHHHHHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTEE CS
                    Fe_dep_repress  2 LvestEdYLetIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyveyekykgl 60
                                      L++++ +YL+ +++   + + v+t+d+++ Lnv ps+ ++ +++L k Gyv++++y+g+
  gi|298675962|ref|YP_003727712.1|  9 LTPRKIQYLKFLLE---KDETVRTTDISSQLNVDPSTTTKVINELTKSGYVNHVPYRGV 64
                                      66777778887655...5589************************************97 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   1.3e-09     1e-06       3      54 ..       9      59 ..       6      63 .. 0.93
   2 ?    5.1   0.0     0.026        21       7      45 ..      80     121 ..      75     121 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.3e-09
                                      --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      ltp   + L +L   ++  ++ +++   l++++s++++++++L + G+v  +
  gi|298675962|ref|YP_003727712.1|  9 LTPRKIQYLKFLLEKDET-VRTTDISSQLNVDPSTTTKVINELTKSGYVNHV 59
                                      89**************96.9*****************************776 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.026
                                       HHHHHHHHHCTTTSEEEHHHHHH.....HHTSSHHHHHHHHHHH CS
                            MarR_2   7 qarvLaaLgrrpgrdltvgelar.....rlglsksavsrilkrL 45 
                                        +r+L  L  + g  l+ ++ ++     + ++sk av ri+k +
  gi|298675962|ref|YP_003727712.1|  80 RHRILSLLLSHYG--LSTNDACEevsrfEGHVSKYAVDRICKSM 121
                                       6777777777777..877777777777899**********9975 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   2.3e-07   0.00018      11      47 ..      20      56 ..      17      57 .. 0.94
   2 ?    4.8   0.0     0.027        21       5      27 ..      80     102 ..      78     104 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.3e-07
                            HTH_24 11 lLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      lL+k+     ++++ +l++ pst+++ +++L+++G++
  gi|298675962|ref|YP_003727712.1| 20 LLEKDETVRTTDISSQLNVDPSTTTKVINELTKSGYV 56
                                      6888999999**************************8 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.027
                            HTH_24   5 drkILelLqknprisqreLAerl 27 
                                       + +IL+lL  + ++s ++ +e++
  gi|298675962|ref|YP_003727712.1|  80 RHRILSLLLSHYGLSTNDACEEV 102
                                       579*************9999987 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   1.3e-08     1e-05       1      52 [.       9      60 ..       9      67 .. 0.91
   2 ?   -1.4   0.0       4.5   3.5e+03      32      44 ..     106     119 ..      94     120 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.3e-08
                            HTH_27  1 ltrqqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertg 52
                                      lt+  +++L  + + +++++ +d++  lnv+ s++ +++++Lt+ G+v + +
  gi|298675962|ref|YP_003727712.1|  9 LTPRKIQYLKFLLEKDETVRTTDISSQLNVDPSTTTKVINELTKSGYVNHVP 60
                                      7899999******9**********************************7665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.5
                            HTH_27  32 dshis.yslkkLte 44 
                                         h+s y++++ ++
  gi|298675962|ref|YP_003727712.1| 106 EGHVSkYAVDRICK 119
                                       67999999999875 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   1.2e-08   9.6e-06      11      48 ..      20      57 ..       9      60 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.2e-08
                                      HHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR 11 ilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                      +l+  +  + +++ ++l+v++st+t+v+ +L k G+++
  gi|298675962|ref|YP_003727712.1| 20 LLEKDETVRTTDISSQLNVDPSTTTKVINELTKSGYVN 57
                                      3444455999**************************96 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   1.2e-07   9.4e-05       4      56 ..       7      60 ..       4      73 .. 0.88
   2 ?   -1.2   0.0       2.4   1.9e+03       1      11 [.      88      98 ..      87      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.2e-07
                                      CHHHHHCCCHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB  4 lGLseyEakvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                      l L+   ++  + Ll k +  ++++i+++l+v+ s+  +v+++L + G+V+ ++
  gi|298675962|ref|YP_003727712.1|  7 LELTPRKIQYLKFLLeKDETVRTTDISSQLNVDPSTTTKVINELTKSGYVNHVP 60
                                      678888888889999888999*****************************9875 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.4
                                      HHHCHHHHHCC CS
                              TrmB  1 LqklGLseyEa 11
                                      L+++GLs ++a
  gi|298675962|ref|YP_003727712.1| 88 LSHYGLSTNDA 98
                                      779****9997 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   7.9e-07   0.00062       1      50 [.      12      60 ..      12      65 .. 0.88
   2 ?   -0.9   0.0       2.1   1.6e+03       1      12 [.      79      90 ..      79      97 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 7.9e-07
                            HTH_11  1 RllqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIesep 50
                                      R+ q l++Lle+++++   +++ +Lnv  +t  + I +L+++g  +  +p
  gi|298675962|ref|YP_003727712.1| 12 RKIQYLKFLLEKDETVRTTDISSQLNVDPSTTTKVINELTKSG-YVNHVP 60
                                      67899**************************************.555555 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.1
                            HTH_11  1 RllqilelLlea 12
                                      R+  il lLl++
  gi|298675962|ref|YP_003727712.1| 79 RRHRILSLLLSH 90
                                      78899***9765 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   7.7e-07    0.0006      21      58 ..      22      59 ..      12      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 7.7e-07
                                      STCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              Rrf2 21 eeeepvsseeiaerqnispsylekilakLrkaglvksv 58
                                      e++e+v++++i+++ n+ ps   k++++L+k+g+v+ v
  gi|298675962|ref|YP_003727712.1| 22 EKDETVRTTDISSQLNVDPSTTTKVINELTKSGYVNHV 59
                                      45667******************************865 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.1   0.00052      0.41       8      44 ..      20      56 ..      13      59 .. 0.89
   2 !    6.5   0.0    0.0088       6.8       1      23 [.      79     101 ..      79     104 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00052
                          HTH_DeoR  8 llkqqgklsveelvellgvSeaTiRRDLneLeeqgll 44
                                      ll+++ ++++++++ +l+v + T  + +neL+++g +
  gi|298675962|ref|YP_003727712.1| 20 LLEKDETVRTTDISSQLNVDPSTTTKVINELTKSGYV 56
                                      899*********************9*****9999975 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0088
                          HTH_DeoR   1 Rieqilellkqqgklsveelvel 23 
                                       R+  il ll ++  ls+++++e+
  gi|298675962|ref|YP_003727712.1|  79 RRHRILSLLLSHYGLSTNDACEE 101
                                       8899*****************97 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   2.9e-06    0.0023       9      49 ..      17      57 ..      12      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.9e-06
                                      HCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  9 LdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      L++l e ++ ++ ++++ ++ + +St+   ++ L++ Gyv 
  gi|298675962|ref|YP_003727712.1| 17 LKFLLEKDETVRTTDISSQLNVDPSTTTKVINELTKSGYVN 57
                                      88999**********************************96 PP

>> HTH_micro  HTH-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   2.6e-06     0.002      97     137 ..      17      57 ..       9      64 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.6e-06
                         HTH_micro  97 vdflvkakdyvkaaelraklnidpKklfYvikkLakkglie 137
                                       + fl+++++ v + ++ ++ln+dp ++  vi+ L k+g+++
  gi|298675962|ref|YP_003727712.1|  17 LKFLLEKDETVRTTDISSQLNVDPSTTTKVINELTKSGYVN 57 
                                       789************************************97 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0038       2.9      11      45 ..      20      54 ..      12      57 .. 0.81
   2 !    6.9   0.0     0.007       5.5       4      27 ..      77     102 ..      74     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0038
                            HTH_23 11 llllaeGlsvreIAreLgvsrrTvyrwlkryreeG 45
                                      ll  +e  ++++I+ +L+v ++T  ++++   ++G
  gi|298675962|ref|YP_003727712.1| 20 LLEKDETVRTTDISSQLNVDPSTTTKVINELTKSG 54
                                      55555577899*************99999876666 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.007
                            HTH_23   4 ereRlrillllae..GlsvreIAreL 27 
                                        ++R ril ll+   Gls+ ++++e 
  gi|298675962|ref|YP_003727712.1|  77 LLRRHRILSLLLShyGLSTNDACEEV 102
                                       579*********99*88888888875 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   2.7e-05     0.021      18      72 ..      25      80 ..      13      85 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.7e-05
                            HTH_45 18 geakkTkimykanLsykllnkYLdmLvekglikk.skekYvlTekGlelleklkel 72
                                      +  + T i  + n + +++ k ++ L++ g++++      +lTe G+e+ e l + 
  gi|298675962|ref|YP_003727712.1| 25 ETVRTTDISSQLNVDPSTTTKVINELTKSGYVNHvPYRGVCLTEYGREYAEFLLRR 80
                                      556789**************************8879999*********98876655 PP

>> RuvB_C  RuvB C-terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.4e-05     0.019       4      70 ..       9      73 ..       6      75 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.4e-05
                                      --HHHHHHHHHHHHT.TT--B-HHHHHHHTT--HHHHHHTTHHHHHHTTSEEEET.TEEEE-HHHHHH CS
                            RuvB_C  4 LdeldikyLkllkekfkggpvglktlaailgeeketiedviEPyLlkeglIerts.rGRilTkkglky 70
                                      L++  i+yLk+l e  k+++v+ + +++ l+++ +t ++vi   L k+g+++  + rG  lT+ g +y
  gi|298675962|ref|YP_003727712.1|  9 LTPRKIQYLKFLLE--KDETVRTTDISSQLNVDPSTTTKVIN-ELTKSGYVNHVPyRGVCLTEYGREY 73
                                      78889********9..8********************99996.5888888876543777777777665 PP

>> HTH_6  Helix-turn-helix domain, rpiR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.027        21      35      64 ..      27      56 ..       7      58 .. 0.77
   2 ?    8.6   0.0    0.0023       1.8      19      59 ..      81     122 ..      66     124 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.027
                                      --HHHHHHHTT--HHHHHHHH---S-SSHH CS
                             HTH_6 35 lsikalAkaaavSeativrfakkLGfkGFs 64
                                      +   +++ +++v  +t +++  +L  +G+ 
  gi|298675962|ref|YP_003727712.1| 27 VRTTDISSQLNVDPSTTTKVINELTKSGYV 56
                                      3356899*********************96 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0023
                                       HHHHHHHHH-S---TT--HHHHHH.HTT--HHHHHHHH---S CS
                             HTH_6  19 kkiaeyilaspdkaielsikalAk.aaavSeativrfakkLG 59 
                                        +i+  +l++   +++ + ++++  +  vS+ ++ r++k++G
  gi|298675962|ref|YP_003727712.1|  81 HRILSLLLSHYGLSTNDACEEVSRfEGHVSKYAVDRICKSMG 122
                                       5899999999999999999999985778*************9 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   5.4e-05     0.042      22      53 ..      27      59 ..      13      70 .. 0.83
   2 ?   -1.6   0.0       3.5   2.7e+03       2       8 ..      82      88 ..      74     110 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.4e-05
                                      HHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.E CS
                         HTH_Crp_2 22 ltqeelAsmlGltretvsrilseLkreglis.r 53
                                      +  ++++s l++ ++t++++++eL + g++   
  gi|298675962|ref|YP_003727712.1| 27 VRTTDISSQLNVDPSTTTKVINELTKSGYVNhV 59
                                      56689***********************99853 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.5
                                      HHHHHHH CS
                         HTH_Crp_2  2 RlArfLl 8 
                                      R+ ++Ll
  gi|298675962|ref|YP_003727712.1| 82 RILSLLL 88
                                      3444444 PP

>> A_thal_3526  Plant protein 1589 of unknown function (A_thal_3526)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   5.4e-05     0.042       7      42 ..      15      52 ..      14      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.4e-05
                       A_thal_3526  7 rCLqlymskeevvra..LeeqanIepeftslVWkkLek 42
                                      ++L++ + k+e+vr+  ++ q n++p++t  V ++L k
  gi|298675962|ref|YP_003727712.1| 15 QYLKFLLEKDETVRTtdISSQLNVDPSTTTKVINELTK 52
                                      6899**********94459*****************87 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00019      0.15       2      46 ..      11      57 ..      10      58 .. 0.83
   2 ?   -0.2   0.0       1.2   9.3e+02       4      13 ..      80      89 ..      79     103 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00019
                                      HHHHHHHHHHTT.SS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  2 ptRlkILklLae.ge.lcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      p +++ Lk+L e  e    ++++ +l++ +st+    + L ++G+V+
  gi|298675962|ref|YP_003727712.1| 11 PRKIQYLKFLLEkDEtVRTTDISSQLNVDPSTTTKVINELTKSGYVN 57
                                      67777789999943335568***************999999999997 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.2
                                      HHHHHHHHTT CS
                             HTH_5  4 RlkILklLae 13
                                      R +IL+lL +
  gi|298675962|ref|YP_003727712.1| 80 RHRILSLLLS 89
                                      789***9986 PP

>> Topoisom_bac  DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     4e-05     0.031     343     386 ..      40      84 ..      39      90 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4e-05
                      Topoisom_bac 343 paTraeiieklvergYverkk.kslvptelGkalvellekfkdlv 386
                                       p+T  ++i++l+++gYv+    + +  te G++ +e+l + +++ 
  gi|298675962|ref|YP_003727712.1|  40 PSTTTKVINELTKSGYVNHVPyRGVCLTEYGREYAEFLLRRHRIL 84 
                                       8*******************99***************94445655 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00015      0.11       5      53 ..      17      65 ..      14      72 .. 0.90
   2 ?   -1.0   0.2       2.5   1.9e+03      42      61 ..     107     130 ..     105     138 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                              FeoC  5 lkeyleergrvslkeLsrhfkaspealeamLeqwvrkGrvekvaatacc 53
                                      lk +le+ + v   ++s +++++p++  + ++ +++ G v++v+  + c
  gi|298675962|ref|YP_003727712.1| 17 LKFLLEKDETVRTTDISSQLNVDPSTTTKVINELTKSGYVNHVPYRGVC 65
                                      788899***********************************99986665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.5
                              FeoC  42 Grvekvaatacc....sgsCkkCg 61 
                                       G+v k a +  c    + + ++Cg
  gi|298675962|ref|YP_003727712.1| 107 GHVSKYAVDRICksmgHPQLSNCG 130
                                       677777766666433322222344 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00027      0.21      28      55 .]      29      56 ..      19      56 .. 0.93
   2 ?   -0.8   0.0         2   1.5e+03      42      42 ..      98      98 ..      82     122 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00027
                            HTH_36 28 qetlakrlglsknTvsraikeLeqlGyi 55
                                        +++++l+++ +T  + i+eL + Gy+
  gi|298675962|ref|YP_003727712.1| 29 TTDISSQLNVDPSTTTKVINELTKSGYV 56
                                      579***********************96 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2
                            HTH_36 42 v 42
                                      +
  gi|298675962|ref|YP_003727712.1| 98 A 98
                                      1 PP

>> YjcQ  YjcQ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00037      0.29       5      52 ..      15      61 ..      12      83 .. 0.88
   2 ?   -2.6   0.0       8.3   6.5e+03       3      38 ..      83     118 ..      81     124 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00037
                                      HHHHHH........-S---HHHHTS-HHHHHHHHHHHHHHTSEE--EE CS
                              YjcQ  5 keLeealdegeevdnkelsaekldisesrfndiiemlveegyikGvkv 52
                                      ++L+  l+++e+v  +++s+ +l+++ s  +++i++l ++gy++ v +
  gi|298675962|ref|YP_003727712.1| 15 QYLKFLLEKDETVRTTDISS-QLNVDPSTTTKVINELTKSGYVNHVPY 61
                                      7899999***********96.69********************87655 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 8.3
                                       HHHHHHHH........-S---HHHHTS-HHHHHHHH CS
                              YjcQ   3 iLkeLeealdegeevdnkelsaekldisesrfndii 38 
                                       iL+ L + +   +++  +e+s  + ++s+   + i 
  gi|298675962|ref|YP_003727712.1|  83 ILSLLLSHYGLSTNDACEEVSRFEGHVSKYAVDRIC 118
                                       666676666666777777777666666666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 997.56
//
Query:       gi|298675963|ref|YP_003727713.1|  [L=97]
Description: putative small heat shock protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    0.00026   21.1   0.1      0.011   15.9   0.0    2.0  2  HSP20       Hsp20/alpha crystallin family
  ------ inclusion threshold ------
       0.02   15.9   0.1      0.041   14.9   0.1    1.5  1  CS          CS domain
      0.045   13.3   0.0       0.45   10.1   0.0    2.1  2  ArsA_HSP20  HSP20-like domain found in ArsA
       0.12   12.4   0.0       0.13   12.3   0.0    1.1  1  GvpH        GvpH


Domain annotation for each model (and alignments):
>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.4e-06     0.011       4      39 ..      15      50 ..      13      60 .. 0.87
   2 ?    3.6   0.0     0.016        72      70      98 ..      67      93 ..      62      97 .] 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.4e-06
                                      SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE-- CS
                             HSP20  4 eeeeefevkldvpglkkeelkvkvednrvlvkgehe 39
                                      e+ e+ ++++d+pg++ke+++ k++dn+ +v++ ++
  gi|298675963|ref|YP_003727713.1| 15 EKGENLNIEIDLPGINKENIDFKMHDNSYTVRAVND 50
                                      5668899*********************99998665 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.016
                                      TT-EEEEETTEEEEEEEBSS--..----- CS
                             HSP20 70 dkvkaslkdGvLtvtvpkkepekkkkerk 98
                                      +k  a++ +  L +tvp +ep+   k+++
  gi|298675963|ref|YP_003727713.1| 67 EKAVAKYTNEKLIITVPFQEPHM--KSID 93
                                      6678999999********99984..4444 PP

>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   9.2e-06     0.041       7      73 ..      15      81 ..      14      83 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9.2e-06
                                      EETTEEEEEEE-TTCTTTTTCEEEEEETTEEEEEE.TSCEEEEECE..BSS-BETTTEEEEEETTEEEEE CS
                                CS  7 QtldeVvvtiyvkkvnikkkdvkvefkerslkvki.gkeklliege..LfgpIdpeesswtieskkveit 73
                                      ++ ++++++i ++++  +k+++++++  +s +v   ++  +   g    + p+ pe++  + ++ k+ it
  gi|298675963|ref|YP_003727713.1| 15 EKGENLNIEIDLPGI--NKENIDFKMHDNSYTVRAvND-DIKYAGTfpTCCPVIPEKAVAKYTNEKLIIT 81
                                      77899*********9..*************77777433.2222233334899999999999999999998 PP

>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0001      0.45       4      31 ..      20      47 ..      17      51 .. 0.82
   2 ?    1.1   0.0     0.063   2.8e+02      52      62 ..      71      81 ..      64      95 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0001
                        ArsA_HSP20  4 yvlkldLPfvdkeeidlsrsgdeLtIki 31
                                        + +dLP+++ke+id   +++  t+++
  gi|298675963|ref|YP_003727713.1| 20 LNIEIDLPGINKENIDFKMHDNSYTVRA 47
                                      5689************998888877776 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.063
                        ArsA_HSP20 52 AkfedgvLeIr 62
                                      Ak+ ++ L I+
  gi|298675963|ref|YP_003727713.1| 71 AKYTNEKLIIT 81
                                      88999999886 PP

>> GvpH  GvpH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.9e-05      0.13      96     136 ..      13      52 ..       5      78 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.9e-05
                              GvpH  96 asddsdelvvvadlpGvtdedvdvaletdeqaltlrvdddv 136
                                       a +++++l +  dlpG+  e++d  ++ d+      v+dd+
  gi|298675963|ref|YP_003727713.1|  13 ADEKGENLNIEIDLPGINKENIDFKMH-DNSYTVRAVNDDI 52 
                                       5678999******************99.6655555689987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 645.10
//
Query:       gi|298675964|ref|YP_003727714.1|  [L=100]
Description: putative small heat shock protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    0.00018   22.5   0.9     0.0011   19.9   0.2    2.0  2  CS          CS domain
     0.0002   21.4   0.3     0.0061   16.7   0.3    2.0  1  HSP20       Hsp20/alpha crystallin family
    0.00068   19.1   0.1     0.0034   16.9   0.1    2.0  1  ArsA_HSP20  HSP20-like domain found in ArsA
    0.00077   19.8   0.0    0.00092   19.6   0.0    1.1  1  PIH1_CS     PIH1 CS-like domain
  ------ inclusion threshold ------
       0.14   12.2   0.0       0.19   11.8   0.0    1.2  1  GvpH        GvpH


Domain annotation for each model (and alignments):
>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.2   3.1e-07    0.0011       7      73 ..      18      84 ..      17      86 .. 0.81
   2 ?    4.3   0.2     0.023        81       8      29 ..      77      98 ..      75     100 .] 0.72

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.1e-07
                                      EETTEEEEEEE-TTCTTTTTCEEEEEETTEEEEEE.TS.CEEEEECE..BSS-BETTTEEEEEETTEEEEE CS
                                CS  7 QtldeVvvtiyvkkvnikkkdvkvefkerslkvki.gk.eklliege..LfgpIdpeesswtieskkveit 73
                                      ++ d+++++i +++v  kk++++++++e+s+ v   +   k +  g+   + p+ p+++  +  ++k+ +t
  gi|298675964|ref|YP_003727714.1| 18 EKGDNLNIEIDLPGV--KKDNIEFKITEDSFAVRAnNTdIKYV--GSfaVCCPVMPDKAVAKYSNDKLIVT 84
                                      7889**********9..*************9999843333333..34458999999999999998888776 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.023
                                      ETTEEEEEEE-TTCTTTTTCEE CS
                                CS  8 tldeVvvtiyvkkvnikkkdvk 29
                                      ++d+++vt+++k+++ +  +vk
  gi|298675964|ref|YP_003727714.1| 77 SNDKLIVTVPFKELHETPVEVK 98
                                      589**********944444444 PP

>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.3   1.7e-06    0.0061       4      91 ..      18      91 ..      16     100 .] 0.68

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.7e-06
                                      SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--..---TT----SS---EEEEEE--STTB-TTT-EEEEETTEEE CS
                             HSP20  4 eeeeefevkldvpglkkeelkvkvednrvlvkgeheeeeedekglikerssrkFsrkftLPenvdadkvkaslkdGvLt 82
                                      e+ ++ ++++d+pg+kk++++ k+++++  v+++++    d k          ++ +f++   v +dk  a++++  L 
  gi|298675964|ref|YP_003727714.1| 18 EKGDNLNIEIDLPGVKKDNIEFKITEDSFAVRANNT----DIK----------YVGSFAVCCPVMPDKAVAKYSNDKLI 82
                                      5678899*************************9988....222..........22223333344666666666666666 PP

                                      EEEEBSS-- CS
                             HSP20 83 vtvpkkepe 91
                                      vtvp ke +
  gi|298675964|ref|YP_003727714.1| 83 VTVPFKELH 91
                                      666666655 PP

>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   9.6e-07    0.0034       2      33 ..      21      52 ..      20      85 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 9.6e-07
                        ArsA_HSP20  2 deyvlkldLPfvdkeeidlsrsgdeLtIkign 33
                                      d+  + +dLP+v+k++i+  +++d   ++++n
  gi|298675964|ref|YP_003727714.1| 21 DNLNIEIDLPGVKKDNIEFKITEDSFAVRANN 52
                                      677899**********************9996 PP

>> PIH1_CS  PIH1 CS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   2.6e-07   0.00092      23      91 ..      13      82 ..       5      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.6e-07
                           PIH1_CS 23 rskkenvpkelaieielPllksikevklrvgerrleleskk..akyfLslkLpYpvdedkveAkFvkktkl 91
                                      +++ ++  ++l iei+lP++    +++ +++e+++ + +++   ky+ s  +  pv  dk+ Ak+++++  
  gi|298675964|ref|YP_003727714.1| 13 YACADEKGDNLNIEIDLPGV-KKDNIEFKITEDSFAVRANNtdIKYVGSFAVCCPVMPDKAVAKYSNDKLI 82
                                      4777778899**********.6789************8887789*********************988744 PP

>> GvpH  GvpH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.2e-05      0.19      94     128 ..      14      48 ..       4      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.2e-05
                              GvpH  94 trasddsdelvvvadlpGvtdedvdvaletdeqal 128
                                       + a +++d+l +  dlpGv  ++++  +  d  a+
  gi|298675964|ref|YP_003727714.1|  14 ACADEKGDNLNIEIDLPGVKKDNIEFKITEDSFAV 48 
                                       668899*******************9999777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 587.05
//
Query:       gi|298675965|ref|YP_003727715.1|  [L=67]
Description: 4Fe-4S ferredoxin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-12   46.5  14.3    8.4e-07   28.6   5.7    2.2  2  Fer4      4Fe-4S binding domain
    4.8e-11   42.6   6.2    5.8e-11   42.3   6.2    1.1  1  Fer4_10   4Fe-4S dicluster domain
    1.4e-08   35.2   7.9    2.4e-08   34.4   8.0    1.3  1  Fer4_7    4Fe-4S dicluster domain
    1.7e-07   31.3   6.1    2.3e-07   30.8   6.1    1.2  1  Fer4_9    4Fe-4S dicluster domain
    1.1e-06   29.5   5.4    0.00026   21.9   1.8    2.1  2  Fer4_16   4Fe-4S double cluster binding domain
    5.2e-06   27.0  12.2    0.00034   21.3   3.6    2.2  2  Fer4_3    4Fe-4S binding domain
    6.2e-06   26.1  14.2     0.0062   16.6   6.6    2.1  2  Fer4_6    4Fe-4S binding domain
    7.8e-06   25.9  12.9    0.00031   20.8  13.0    2.0  1  Fer4_21   4Fe-4S dicluster domain
    0.00012   22.4   4.2     0.0054   17.1   0.7    2.1  2  Fer4_8    4Fe-4S dicluster domain
    0.00046   20.1  12.7      0.005   16.9   4.0    2.4  2  Fer4_2    4Fe-4S binding domain
     0.0037   17.4   4.4     0.0037   17.4   4.4    2.0  2  Fer4_18   4Fe-4S dicluster domain
     0.0068   16.9   8.9       0.53   10.9   8.9    2.1  1  Fer4_17   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.012   16.2  12.6       0.07   13.7  12.6    1.9  1  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
      0.014   15.8   4.2      0.014   15.8   4.2    2.5  2  Fer4_4    4Fe-4S binding domain
       0.14   12.3   2.2       0.14   12.3   2.2    1.1  1  ETF_QO    Electron transfer flavoprotein-ubiquinone oxidoredu
        1.2    9.9  14.2         96    3.8  14.2    2.8  1  Fer4_15   4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   1.3   2.7e-08   3.1e-05       1      21 [.       3      23 ..       3      26 .. 0.94
   2 !   28.6   5.7   7.5e-10   8.4e-07       4      23 ..      42      61 ..      39      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2.7e-08
                                      EEEETTTSSS-THHHHHSTTT CS
                              Fer4  1 vvideekCigCGaCvevCPvg 21
                                      +vid++ C g  aC+evCPv+
  gi|298675965|ref|YP_003727715.1|  3 PVIDYSVCEGDLACYEVCPVD 23
                                      69*****************98 PP

  == domain 2  score: 28.6 bits;  conditional E-value: 7.5e-10
                                      ETTTSSS-THHHHHSTTTEE CS
                              Fer4  4 deekCigCGaCvevCPvgAI 23
                                       +e+Ci C +C+evCPv+A 
  gi|298675965|ref|YP_003727715.1| 42 RPEDCIECEQCIEVCPVDAV 61
                                      59*****************7 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   6.2   5.1e-14   5.8e-11       2      56 .]       3      57 ..       2      57 .. 0.98

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 5.1e-14
                           Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      +vid + C +  +C ++CP+dl  vg+++e+++e av   +e+C++c++C+e+CP
  gi|298675965|ref|YP_003727715.1|  3 PVIDYSVCEGDLACYEVCPVDLFDVGNNEEKEIEVAVVARPEDCIECEQCIEVCP 57
                                      589***************************************************9 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   8.0   2.1e-11   2.4e-08       6      52 .]      14      60 ..       8      60 .. 0.82

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 2.1e-11
                            Fer4_7  6 gaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                       aC ++Cpv+ +++ + e+++    v+ +pe+C+ C++C++vCP++a
  gi|298675965|ref|YP_003727715.1| 14 LACYEVCPVDLFDVGNNEEKEIEVAVVARPEDCIECEQCIEVCPVDA 60
                                      49************997655554556678****************97 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   6.1   2.1e-10   2.3e-07       6      50 ..      14      60 ..       9      61 .. 0.71

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 2.1e-10
                            Fer4_9  6 gaCveaCpagvvvedaaerkarlraase..eaCigCgaCveaCpkga 50
                                       aC e+Cp +++   ++e+k    a  +  e+Ci+C++C+e+Cp +a
  gi|298675965|ref|YP_003727715.1| 14 LACYEVCPVDLFDVGNNEEKEIEVAVVArpEDCIECEQCIEVCPVDA 60
                                      57*********965555544433333234689************997 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.1    0.0015       1.7       4      24 ..      12      32 ..       9      42 .. 0.70
   2 !   21.9   1.8   2.3e-07   0.00026       2      20 ..      46      64 ..      45      67 .] 0.88

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0015
                           Fer4_16  4 tCgkCaevCPtnaikekkeke 24
                                      +  +C evCP++ ++  +++e
  gi|298675965|ref|YP_003727715.1| 12 GDLACYEVCPVDLFDVGNNEE 32
                                      5558*******9988664433 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 2.3e-07
                           Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                      C++C++C+evCP++a++  
  gi|298675965|ref|YP_003727715.1| 46 CIECEQCIEVCPVDAVRLV 64
                                      ***************9865 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   1.4   0.00068      0.76       4      14 ..      10      23 ..       9      23 .. 0.83
   2 !   21.3   3.6     3e-07   0.00034       1      15 []      46      60 ..      46      60 .. 0.98

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00068
                            Fer4_3  4 Cg...aCvevCPvg 14
                                      C+   aC evCPv+
  gi|298675965|ref|YP_003727715.1| 10 CEgdlACYEVCPVD 23
                                      766779******86 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 3e-07
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+ C++C evCPv+A
  gi|298675965|ref|YP_003727715.1| 46 CIECEQCIEVCPVDA 60
                                      *************98 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.8   2.5e-05     0.028       2      22 ..       3      23 ..       2      26 .. 0.91
   2 !   16.6   6.6   5.5e-06    0.0062       2      23 ..      39      60 ..      38      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.5e-05
                            Fer4_6  2 veidpdkCigCgdCvrvCPeg 22
                                      ++id++ C g  +C+ vCP +
  gi|298675965|ref|YP_003727715.1|  3 PVIDYSVCEGDLACYEVCPVD 23
                                      79*****************86 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 5.5e-06
                            Fer4_6  2 veidpdkCigCgdCvrvCPega 23
                                      v+  p+ Ci C+ C+ vCP +a
  gi|298675965|ref|YP_003727715.1| 39 VVARPEDCIECEQCIEVCPVDA 60
                                      6777999************987 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8  13.0   2.8e-07   0.00031       3      58 ..       5      62 ..       4      63 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.8e-07
                           Fer4_21  3 idedkCigCgkCliaCedtshqaieidakt..vlkvv..edeCvGCnlCssvCPvedcie 58
                                      id + C g   C+ +C+    +  + ++k+  v +vv   ++C+ C+ C++vCPv d+++
  gi|298675965|ref|YP_003727715.1|  5 IDYSVCEGDLACYEVCPVDLFDVGNNEEKEieV-AVVarPEDCIECEQCIEVCPV-DAVR 62
                                      78888888899******7666666555544222.3333489*************9.7775 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.1    0.0075       8.4      51      64 ..      10      23 ..       6      24 .. 0.82
   2 !   17.1   0.7   4.8e-06    0.0054      49      63 ..      44      58 ..      26      62 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0075
                            Fer4_8 51 CttcgaCtevCpvg 64
                                      C +  aC evCpv+
  gi|298675965|ref|YP_003727715.1| 10 CEGDLACYEVCPVD 23
                                      777889*****997 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 4.8e-06
                            Fer4_8 49 wsCttcgaCtevCpv 63
                                      + C +c++C evCpv
  gi|298675965|ref|YP_003727715.1| 44 EDCIECEQCIEVCPV 58
                                      567777777777776 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   1.5    0.0021       2.3       3      21 ..       3      21 ..       1      22 [. 0.78
   2 !   16.9   4.0   4.4e-06     0.005       4      21 ..      40      57 ..      36      58 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0021
                            Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                      +v+d   C g  aC+ +CP
  gi|298675965|ref|YP_003727715.1|  3 PVIDYSVCEGDLACYEVCP 21
                                      677888887756******* PP

  == domain 2  score: 16.9 bits;  conditional E-value: 4.4e-06
                            Fer4_2  4 vvdtdrCigCgaCvsaCP 21
                                      v+ ++ Ci+C+ C+ +CP
  gi|298675965|ref|YP_003727715.1| 40 VARPEDCIECEQCIEVCP 57
                                      455777************ PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.5      0.18     2e+02      65      75 ..      14      24 ..       4      30 .. 0.74
   2 !   17.4   4.4   3.3e-06    0.0037      47      74 ..      32      59 ..      26      63 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.18
                           Fer4_18 65 escvkvcPtgi 75
                                       +c +vcP+++
  gi|298675965|ref|YP_003727715.1| 14 LACYEVCPVDL 24
                                      47999999864 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 3.3e-06
                           Fer4_18 47 lkekeerkekgagdcidcescvkvcPtg 74
                                       ke e    +   dci+ce+c++vcP++
  gi|298675965|ref|YP_003727715.1| 32 EKEIEVAVVARPEDCIECEQCIEVCPVD 59
                                      5556666677789*************85 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   8.9   0.00047      0.53      25      58 ..      35      58 ..       9      60 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00047
                           Fer4_17 25 llraaklglleeaeke....ekaslCieCgeCerkCPq 58
                                      +              e     + ++CieC++C ++CP 
  gi|298675965|ref|YP_003727715.1| 35 I--------------EvavvARPEDCIECEQCIEVCPV 58
                                      2..............2333346799***********96 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7  12.6   6.2e-05      0.07       1      56 [.       5      61 ..       5      62 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.2e-05
                           Fer4_13  1 VDrdtCiacgaCvelaP.dvFeeddeggasvvaeqptseeekadaeeAadaCPvesI 56
                                      +D + C ++ aC+e++P d+F+  +++++ + ++    +e+  ++e+ ++ CPv+++
  gi|298675965|ref|YP_003727715.1|  5 IDYSVCEGDLACYEVCPvDLFDVGNNEEKEIEVAVVARPEDCIECEQCIEVCPVDAV 61
                                      68889************99****99999999999999999***************97 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   2.2     0.077        86       9      16 ..      15      22 ..      10      26 .. 0.84
   2 ?   15.8   4.2   1.3e-05     0.014       2      16 ..      44      58 ..      43      60 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.077
                            Fer4_4  9 sCvaaCPq 16
                                      +C+ +CP+
  gi|298675965|ref|YP_003727715.1| 15 ACYEVCPV 22
                                      6******7 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.3e-05
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      e Ci+C +C+ +CP+
  gi|298675965|ref|YP_003727715.1| 44 EDCIECEQCIEVCPV 58
                                      78************7 PP

>> ETF_QO  Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.2   0.00013      0.14      46      86 ..      16      57 ..       4      67 .] 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                                      HHHH-TTS-EEEEETT.TTSSEEEEE-CCC--S--HHHHH-T CS
                            ETF_QO 46 eqryCPagvyeivede.eakekklqinaqnCvhCktCdikdp 86
                                      +  +CP   +++ ++e ++ e+ ++   ++C+ C  C    p
  gi|298675965|ref|YP_003727715.1| 16 CYEVCPVDLFDVGNNEeKEIEVAVVARPEDCIECEQCIEVCP 57
                                      5679********99884567788888999********65555 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8  14.2     0.085        96       2      65 ..       4      62 ..       4      63 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.085
                           Fer4_15  2 vvDrdaCigcglCvaeapevfeldedglasvllddgeiaeg.evpddeeeaaqeAaraCPvdAIr 65
                                      v+D + C+g+ +C++++p  + l + g +    +++ei+ +    +++  + ++  ++CPvdA r
  gi|298675965|ref|YP_003727715.1|  4 VIDYSVCEGDLACYEVCP--VDLFDVGNN----EEKEIEVAvVARPEDCIECEQCIEVCPVDAVR 62
                                      69***************8..333334444....12233334223455556668999******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 445.31
//
Query:       gi|298675966|ref|YP_003727716.1|  [L=334]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-23   82.8   0.8    4.6e-23   80.9   0.1    2.4  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0031   17.7   0.5     0.0066   16.7   0.5    1.5  1  OrfB_IS605      Probable transposase
  ------ inclusion threshold ------
      0.031   13.9   0.9      0.058   13.0   0.9    1.5  1  Zn_ribbon_17    Zinc-ribbon, C4HC2 type
       0.15   11.8   0.0       0.15   11.8   0.0    2.7  3  DUF501          Protein of unknown function (DUF501)
       0.41   10.7   4.5        2.2    8.3   0.6    2.9  3  HypA            Hydrogenase/urease nickel incorporation, meta
       0.61   10.2   3.2        8.7    6.5   0.5    2.5  2  UPF0547         Uncharacterised protein family UPF0547
        1.7    8.3   5.5       0.29   10.8   0.5    2.1  3  TackOD1         Thaumarchaeal output domain 1
        7.3    6.4   9.1          2    8.2   2.3    2.9  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       1.3   2.8e+03      32      50 ..     213     232 ..     209     237 .. 0.67
   2 !   80.9   0.1     2e-26   4.6e-23       1      68 [.     244     309 ..     244     310 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.3
                    OrfB_Zn_ribbon  32 seCgsknke.alsgrtfkCp 50 
                                       ++Cg ++++ +  ++ +kC+
  gi|298675966|ref|YP_003727716.1| 213 NNCGIRMENlKGIRDSVKCK 232
                                       46777777765566666665 PP

  == domain 2  score: 80.9 bits;  conditional E-value: 2e-26
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       f++l+ +leyka+  G+k+e v+p+yTS++Cs+Cg+ + +  +g+ fkC +Cg++ ++D nAa+Ni+ 
  gi|298675966|ref|YP_003727716.1| 244 FYQLQFMLEYKARLLGVKIEFVKPEYTSQNCSRCGYLGIR--NGDSFKCLHCGHVDHADANAAFNIAM 309
                                       899*************************************..************************96 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.5   2.9e-06    0.0066       3     107 ..     118     214 ..     114     225 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.9e-06
                        OrfB_IS605   3 pvevevelpkpkgnkaagiDlGin.nLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrkla 78 
                                        v+v++  ++ +++  +g+Dl+   ++a++++ ++    + g++++    ++++ +++lq k k         +k++
  gi|298675966|ref|YP_003727716.1| 118 SVTVPE-REQIEPEDYLGVDLNTTgHIAVMSNPKTGKVWKLGKKAQHIHLKYKNDRRKLQVKGKY--------KKVK 185
                                       344443.88999**********98356666666655566668******************98443........5799 PP

                        OrfB_IS605  79 rlhrkrsrrrkhllhklathliktlkevg 107
                                        + ++ sr++++l +k+++++++t  +++
  gi|298675966|ref|YP_003727716.1| 186 QVNDRESRIVRDLNQKISSRIVETAAANN 214
                                       9**********************988775 PP

>> Zn_ribbon_17  Zinc-ribbon, C4HC2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.9   2.6e-05     0.058       5      34 ..     272     303 ..     268     317 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.6e-05
                      Zn_ribbon_17   5 ksCayCe.lav.kgrvvlcgvCeHvlHasCar 34 
                                       ++C+ C  l + +g  + c  C+Hv Ha+  +
  gi|298675966|ref|YP_003727716.1| 272 QNCSRCGyLGIrNGDSFKCLHCGHVDHADANA 303
                                       5677775344515899************9765 PP

>> DUF501  Protein of unknown function (DUF501)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       3.2   7.2e+03      59      74 ..       7      22 ..       4      50 .. 0.65
   2 ?    1.1   1.0      0.14   3.2e+02      64     101 ..     156     194 ..     136     232 .. 0.67
   3 ?   11.8   0.0   6.9e-05      0.15      89     120 ..     262     293 ..     249     308 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.2
                            DUF501 59 laedeelaqalekaha 74
                                      +++d++++++l+ka++
  gi|298675966|ref|YP_003727716.1|  7 IKHDRDFSEELAKAKQ 22
                                      6667777777666654 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.14
                            DUF501  64 elaqalekahaeyaakReellteeerseleksees.sel 101
                                       +l ++ ++ h +y + R++l  + + +++++ +++ s++
  gi|298675966|ref|YP_003727716.1| 156 KLGKKAQHIHLKYKNDRRKLQVKGKYKKVKQVNDReSRI 194
                                       555666777888888888877666666665544443333 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 6.9e-05
                            DUF501  89 rselekseesselkdlgvgGianvtrVKCLHa 120
                                        + ++ + +s++ +++g+ Gi+n +  KCLH 
  gi|298675966|ref|YP_003727716.1| 262 IEFVKPEYTSQNCSRCGYLGIRNGDSFKCLHC 293
                                       5567777888999******************7 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.046     1e+02       9      35 ..      46      73 ..      40      79 .. 0.75
   2 ?   -3.7   0.0       5.5   1.2e+04      27      42 ..     115     130 ..     105     131 .. 0.77
   3 ?    8.3   0.6     0.001       2.2      59      96 ..     259     297 ..     191     308 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.046
                                      HHHHHHHHHH.CCTT..EEEEEEEEEET CS
                              HypA  9 sivevveeea.keaaarkvtkvkvevGe 35
                                      +i +++ ++  k+++a+kv++vk+++ +
  gi|298675966|ref|YP_003727716.1| 46 AISNQILNKYaKDKSAKKVNSVKLTIPN 73
                                      5666666666377999********9865 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 5.5
                                       EEEEEEEETTCT--HH CS
                              HypA  27 tkvkvevGelsgvepe 42 
                                         v v+v e +++epe
  gi|298675966|ref|YP_003727716.1| 115 VYVSVTVPEREQIEPE 130
                                       5688899999999887 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.001
                                       T-EEE.EEEE--EEEETTTS-EEECHHHHHS-TTTSSS- CS
                              HypA  59 gaeLe.ieevpvkvrCreCgkefeleekalrCpkCgsad 96 
                                       g ++e ++ +  +  C++Cg+ +  + ++++C +Cg+ d
  gi|298675966|ref|YP_003727716.1| 259 GVKIEfVKPEYTSQNCSRCGYLGIRNGDSFKCLHCGHVD 297
                                       455552334445678*****9988776799******876 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.028        62      15      22 ..     272     279 ..     270     280 .. 0.89
   2 ?    6.5   0.5    0.0039       8.7      16      25 ..     289     298 ..     286     299 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.028
                           UPF0547  15 qfCphCGy 22 
                                       q C+ CGy
  gi|298675966|ref|YP_003727716.1| 272 QNCSRCGY 279
                                       78*****9 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0039
                           UPF0547  16 fCphCGyvFq 25 
                                       +C hCG+v+ 
  gi|298675966|ref|YP_003727716.1| 289 KCLHCGHVDH 298
                                       799****985 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       1.3     3e+03      16      54 ..      26      65 ..      11      86 .. 0.59
   2 ?   -1.7   0.0       0.9     2e+03     142     172 ..     205     235 ..     162     242 .. 0.67
   3 ?   10.8   0.5   0.00013      0.29      88     115 ..     272     299 ..     262     308 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.3
                           TackOD1 16 yllsrdeeklepvldpkskelysypllealskeke.esee 54
                                      y ++  +++ + v +   k+++s ++l+++ k+k+ + ++
  gi|298675966|ref|YP_003727716.1| 26 YGVKYRTRSSKDVKHIGLKSAISNQILNKYAKDKSaKKVN 65
                                      4444444555555555556666666666666655545444 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.9
                           TackOD1 142 rplevykCnsCkslfsepevkarClsCekes 172
                                       r+ e+   n+C+  + + +   + ++C+k++
  gi|298675966|ref|YP_003727716.1| 205 RIVETAAANNCGIRMENLKGIRDSVKCKKSF 235
                                       4445555555555555555555555555554 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00013
                           TackOD1  88 evCpkCkSidieeqelihhftCgnvgpe 115
                                       + C+ C+   i++  ++++ +Cg+v+  
  gi|298675966|ref|YP_003727716.1| 272 QNCSRCGYLGIRNGDSFKCLHCGHVDHA 299
                                       6799999999999999999999999865 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.6      0.19   4.2e+02       6      21 ..     215     232 ..     212     233 .. 0.65
   2 ?    8.2   2.3   0.00088         2       2      25 ..     273     295 ..     273     296 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.19
                                       S--B--.--S.SS----S CS
                    DNA_RNApol_7kD   6 Cgaevs.lkk.gdpiRCk 21 
                                       Cg +++ lk  +d+++Ck
  gi|298675966|ref|YP_003727716.1| 215 CGIRMEnLKGiRDSVKCK 232
                                       666666555336889998 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00088
                                       B-SSS--B----SSS----SSS-- CS
                    DNA_RNApol_7kD   2 iCgeCgaevslkkgdpiRCkeCGh 25 
                                       +C +Cg    +++gd+ +C +CGh
  gi|298675966|ref|YP_003727716.1| 273 NCSRCGY-LGIRNGDSFKCLHCGH 295
                                       5999985.78*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1400  (0.0780858); expected 358.6 (0.02)
Passed bias filter:                      638  (0.0355848); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2072.63
//
Query:       gi|298675967|ref|YP_003727717.1|  [L=218]
Description: metallo-beta-lactamase superfamily protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-11   43.8   0.0    3.9e-11   43.3   0.0    1.2  1  Lactamase_B    Metallo-beta-lactamase superfamily
    2.1e-09   37.2   0.0    2.6e-09   36.9   0.0    1.2  1  Lactamase_B_2  Beta-lactamase superfamily domain
     0.0017   17.8   0.1     0.0037   16.7   0.1    1.6  2  Lactamase_B_6  Metallo-beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   0.0   6.4e-15   3.9e-11       8     131 ..      22     149 ..      20     155 .. 0.80

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 6.4e-15
                                       EEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHC CS
                       Lactamase_B   8 syliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfm 84 
                                       s li+++ + iL+DtG+++        l+ l++ p+++  v+l+H+H+DH+Ggl  + +a +   ++v+e   ++++
  gi|298675967|ref|YP_003727717.1|  22 SCLIDTGQSKILFDTGWDGYLLIHN--LKMLDVSPLEIGKVVLSHHHWDHMGGLTSILNANPDLEVYVPESFSKYLK 96 
                                       6799****************99985..8**************************************99999988888 PP

                                       HHHHHHHHHCCHH......TTCHCGCCEEEEETTTEECCCTEEEEEHECTTST CS
                       Lactamase_B  85 eeaddaasrkgll......lagvsadkpdvdeeeldgnaggrralyvtggpgh 131
                                       +e    a   ++       + +++  k ++++ e+++ +    ++yv+ g +h
  gi|298675967|ref|YP_003727717.1|  97 DEISSRAKLIEISqpteihPSIYTTGKLGNKIKEQALLLETSAGVYVITGCAH 149
                                       88855555554446666666666666666666666666666666666666665 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.0   4.4e-13   2.6e-09       2      91 ..      31     115 ..      30     160 .. 0.78

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 4.4e-13
                                       EEEES--TT...HHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCG CS
                     Lactamase_B_2   2 riLiDagpd...lrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfv 75 
                                        iL+D+g+d   l  + l+      l  ++ +i  V+l+h H+DH+ gl ++    p +l++y+p++ +++l+++++
  gi|298675967|ref|YP_003727717.1|  31 KILFDTGWDgylLIHN-LKM-----LDVSPLEIGKVVLSHHHWDHMGGLTSILNANP-DLEVYVPESFSKYLKDEIS 100
                                       59*******6632222.333.....3445668999*******************666.6****************87 PP

                                       HHHCHTTTTEEEEEE- CS
                     Lactamase_B_2  76 ylaleeepavnvheld 91 
                                         a+  e + + +e++
  gi|298675967|ref|YP_003727717.1| 101 SRAKLIE-ISQPTEIH 115
                                       7777666.44444443 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   6.2e-07    0.0037       3      58 ..      26      79 ..      24      93 .. 0.81
   2 ?   -2.3   0.0      0.43   2.6e+03      25      52 ..      91     119 ..      86     132 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.2e-07
                     Lactamase_B_6  3 eldnvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyak 58
                                         + kiL D Gwd++ +   + lk l+    ++  ++Lsh   +h+G+++ ++++
  gi|298675967|ref|YP_003727717.1| 26 DTGQSKILFDTGWDGYLL--IHNLKMLDVSPLEIGKVVLSHHHWDHMGGLTSILNA 79
                                      455789*********955..368999999999*****************9887754 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.43
                     Lactamase_B_6  25 alkelekvi.ptvdliLLshatlehlGay 52 
                                        +k+l++ i ++  li +s++t  h + y
  gi|298675967|ref|YP_003727717.1|  91 FSKYLKDEIsSRAKLIEISQPTEIHPSIY 119
                                       56677766535778888888888776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1596.66
//
Query:       gi|298675968|ref|YP_003727718.1|  [L=188]
Description: hypothetical protein Metev_2095 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-51  173.2   3.3    3.4e-51  173.0   3.3    1.1  1  DUF1847   Protein of unknown function (DUF1847)
  ------ inclusion threshold ------
       0.12   12.0   0.1       0.42   10.3   0.0    1.8  2  DUF188    Uncharacterized BCR, YaiI/YqxD family COG1671


Domain annotation for each model (and alignments):
>> DUF1847  Protein of unknown function (DUF1847)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.0   3.3   3.8e-55   3.4e-51      18     157 .]      25     161 ..       9     161 .. 0.93

  Alignments for each domain:
  == domain 1  score: 173.0 bits;  conditional E-value: 3.8e-55
                           DUF1847  18 k.deeekkiakaaaeveaegyakltRveeiiefakrmgykkiGiafCvglleeakalakileakgfevvsviCkvgs 93 
                                       + + ++ k +k ++++e+++y+++tR+ee++ +ak+m+ykk+GiafC+gl +ea+++++il+ k+f+v+sv+Ckv++
  gi|298675968|ref|YP_003727718.1|  25 TyKGKDYKSMKISSQIESRYYMEKTRIEEVVLYAKKMNYKKLGIAFCIGLENEANIVHNILS-KEFDVYSVCCKVCG 100
                                       337889999****************************************************6.56************ PP

                           DUF1847  94 vdkeelgieeeekvkkkkkeamCnPilQAellneaktdlnvvlGLCvGhDslfikyseapvttL 157
                                       ++k+e ++++ +    k +e +CnP +QA +ln++ktdln+ lGLC+GhD+lf+++s+apvt+L
  gi|298675968|ref|YP_003727718.1| 101 TSKDEYDLDKFH---DKGFEVTCNPKAQAMVLNNNKTDLNIQLGLCIGHDILFNNNSNAPVTVL 161
                                       ********9977...699********************************************98 PP

>> DUF188  Uncharacterized BCR, YaiI/YqxD family COG1671
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   4.7e-05      0.42      73     104 ..      23      54 ..      18      73 .. 0.86
   2 ?   -1.7   0.0      0.23   2.1e+03      63      82 ..     159     178 ..     153     186 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 4.7e-05
                            DUF188  73 alsprGevyteenIdellamRdlmkklRrage 104
                                        ++ +G+ y++ +I ++++ R+ m+k R + +
  gi|298675968|ref|YP_003727718.1|  23 NITYKGKDYKSMKISSQIESRYYMEKTRIEEV 54 
                                       68899***********************8765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.23
                            DUF188  63 AarvlekgaaalsprGevyt 82 
                                         +v++ ++ a +p G +y+
  gi|298675968|ref|YP_003727718.1| 159 TVLVVKDRMLAHNPLGAIYS 178
                                       45566666777777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       817  (0.0455686); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1151.60
//
Query:       gi|298675969|ref|YP_003727719.1|  [L=285]
Description: cobyrinic acid ac-diamide synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.2e-14   51.6   0.0    1.2e-13   51.2   0.0    1.2  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
    1.4e-11   43.7  11.3    1.2e-05   24.9   0.9    2.6  2  Fer4          4Fe-4S binding domain
    2.6e-11   43.4   3.0    5.8e-06   25.9   0.1    2.9  2  ParA          NUBPL iron-transfer P-loop NTPase
    1.7e-07   31.7   3.7      0.002   18.7   0.2    2.5  2  Fer4_7        4Fe-4S dicluster domain
    5.5e-07   30.4   3.3      0.004   18.1   0.1    2.7  2  Fer4_16       4Fe-4S double cluster binding domain
    1.8e-06   28.0   0.4      0.028   14.3   0.0    2.3  2  AAA_31        AAA domain
    9.6e-06   25.7   9.9     0.0078   16.6   0.9    2.7  2  Fer4_4        4Fe-4S binding domain
    1.6e-05   24.7  13.6      0.011   15.7   1.4    2.5  2  Fer4_6        4Fe-4S binding domain
    0.00011   22.2   9.2    0.00011   22.2   9.2    2.2  1  Fer4_21       4Fe-4S dicluster domain
    0.00017   21.7   9.8     0.0018   18.4  10.7    2.1  3  Fer4_9        4Fe-4S dicluster domain
    0.00026   20.5   4.1      0.066   12.6   0.1    2.7  3  Fer4_NifH     4Fe-4S iron sulfur cluster binding proteins, Ni
    0.00037   20.4  11.9      0.051   13.7   2.0    2.6  2  Fer4_2        4Fe-4S binding domain
    0.00046   20.1   0.9        1.2    9.0   0.1    2.6  3  RsgA_GTPase   RsgA GTPase
    0.00087   19.4  10.2     0.0065   16.6  11.1    1.9  2  Fer4_10       4Fe-4S dicluster domain
     0.0027   17.2   0.8       0.52    9.7   0.5    2.2  2  PhoH          PhoH-like protein
     0.0028   17.4   0.1     0.0066   16.2   0.0    1.7  2  AAA_24        AAA domain
     0.0031   17.9   6.8       0.59   10.6   0.1    2.3  3  Fer4_8        4Fe-4S dicluster domain
     0.0039   17.6   0.0      0.024   15.0   0.0    2.1  2  AAA_16        AAA ATPase domain
     0.0046   17.5  11.3       0.27   11.8   2.6    2.5  3  Fer4_17       4Fe-4S dicluster domain
     0.0088   15.3   0.3      0.023   13.9   0.3    1.6  1  ArsA_ATPase   Anion-transporting ATPase
     0.0091   15.7   0.0       0.37   10.5   0.0    2.3  2  RuvB_N        Holliday junction DNA helicase RuvB P-loop doma
     0.0094   15.2   0.3       0.33   10.1   0.0    2.1  2  DUF2075       Uncharacterized conserved protein (DUF2075)
  ------ inclusion threshold ------
      0.013   15.2   0.1       0.14   11.9   0.1    2.2  2  AAA_30        AAA domain
      0.017   15.4   0.0        0.3   11.3   0.0    2.4  2  AAA_22        AAA domain
      0.025   15.1   0.1        0.2   12.2   0.0    2.2  2  ABC_tran      ABC transporter
      0.027   15.4  13.0       0.56   11.3   3.8    2.6  2  Fer4_3        4Fe-4S binding domain
      0.029   12.6   0.0      0.048   11.9   0.0    1.2  1  FTHFS         Formate--tetrahydrofolate ligase
      0.041   13.1   0.4        1.5    7.9   0.2    2.2  2  NB-ARC        NB-ARC domain
      0.046   13.5   0.0        5.5    6.7   0.0    2.2  2  AAA_11        AAA domain
      0.058   13.8   0.1        1.1    9.6   0.0    2.3  2  AAA           ATPase family associated with various cellular 
      0.077   12.7   0.2        0.2   11.3   0.1    1.7  2  AAA_15        AAA ATPase domain
      0.078   12.4   0.0         12    5.3   0.0    2.1  2  CBP_BcsQ      Cellulose biosynthesis protein BcsQ
      0.081   12.3   1.1       0.55    9.5   0.2    2.2  2  ATPase        KaiC
      0.099   13.2   0.8          1    9.9   0.0    2.3  2  AAA_18        AAA domain
        0.1   12.4   0.1        1.5    8.5   0.0    2.2  2  IstB_IS21     IstB-like ATP binding protein
       0.12   12.4   0.2        2.8    7.9   0.1    2.5  3  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
       0.14   12.7   0.1       0.25   11.8   0.1    1.4  1  AAA_23        AAA domain
       0.18   10.4   0.0       0.23   10.1   0.0    1.2  1  AAA_13        AAA domain
       0.21   11.5   0.0       0.58   10.1   0.0    1.7  1  NACHT         NACHT domain
       0.34   11.1   0.2       0.34   11.1   0.2    1.7  1  AAA_28        AAA domain
       0.41   10.2   2.4       0.59    9.7   1.3    1.7  2  AAA_25        AAA domain
       0.53   10.1   4.0        0.6    9.9   0.5    2.5  2  AAA_29        P-loop containing region of AAA domain
        3.2    8.4   9.1         10    6.8   0.8    2.5  2  Fer4_13       4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.0   2.9e-16   1.2e-13       1     124 [.       4     258 ..       4     262 .. 0.92

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 2.9e-16
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       ++++s+kGG+GKTtl+ ++a +  +     +  D+D++a    ++   e+   +                       
  gi|298675969|ref|YP_003727719.1|   4 LTVISGKGGTGKTTLTSAFASLAEN----AVISDCDVDAADIYLILNPEIM--Etfefigskvayvnnnlctecglc 74 
                                       589****************995555....8999*****8886644333333..35588999999999********** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|298675969|ref|YP_003727719.1|  75 ksycrfdaitedfnvntficegcgvceyicpedaislndrisgkyyksstrygpmshanlkageeasgklitavrnt 151
                                       ***************************************************************************** PP

                                       ...............................................CCHCCCHHHHHHCHCHHHH..EEEEEEEEE CS
                                       ...............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ...............................................dlkrllellealgkkkalllkiagvvlnrv 84 
                                                                                      d kr+le+ + ++++         v +n++
  gi|298675969|ref|YP_003727719.1| 152 sselaekynsdlilidgppgtgcsvissitgvnmtlvvtepsisgihDFKRILEVTNYFDIP-------TLVCINKY 221
                                       ************************************************************98.......99****** PP

                                       SS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  85 dgeneetllkealeelkqrygvpvlgviprdeavaeapar 124
                                       d + e+t+ +e+++++k   gv+v+g+ip+d+  +ea  +
  gi|298675969|ref|YP_003727719.1| 222 DINVENTRVIEDYCREK---GVEVVGKIPYDTIPVEAMIQ 258
                                       ***************99...***********977777655 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.9   2.9e-08   1.2e-05       2      24 .]      62      84 ..      61      84 .. 0.95
   2 !   22.9   3.7   1.2e-07     5e-05       3      24 .]      89     110 ..      87     110 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 2.9e-08
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                      +++ ++C+ CG+C + C ++AIt
  gi|298675969|ref|YP_003727719.1| 62 YVNNNLCTECGLCKSYCRFDAIT 84
                                      89********************7 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 1.2e-07
                                       EETTTSSS-THHHHHSTTTEEE CS
                              Fer4   3 ideekCigCGaCvevCPvgAIt 24 
                                       +++  C gCG C+ +CP +AI+
  gi|298675969|ref|YP_003727719.1|  89 VNTFICEGCGVCEYICPEDAIS 110
                                       66778***************96 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   8.4e-06    0.0035       5      34 ..       3      32 ..       1      64 [. 0.74
   2 !   25.9   0.1   1.4e-08   5.8e-06     112     245 ..     161     281 ..     146     282 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8.4e-06
                              ParA  5 viavlSgKGGVGKStvavnlAlaLakkglk 34
                                       ++v+SgKGG GK+t+++ +A   ++  ++
  gi|298675969|ref|YP_003727719.1|  3 QLTVISGKGGTGKTTLTSAFASLAENAVIS 32
                                      579**************9998755544443 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 1.4e-08
                              ParA 112 lDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvkkaiemfkkvkvkvlGvveNmsgfvcpkcgektei 188
                                        D+++iD PPGtg   ++ +  ++   +++Vt p    ++d k+ +e+++  +++ l  ++   + v          
  gi|298675969|ref|YP_003727719.1| 161 SDLILIDGPPGTGCSVISSITGVN--MTLVVTEPSISGIHDFKRILEVTNYFDIPTLVCINKYDINVE--------- 226
                                       699**********99998888875..689**************************9988776554443......... PP

                              ParA 189 fgkgggeklaeelgvpllgeipldpeireasdegkplvlkepeseaakaleeiaekv 245
                                        ++   e++++e gv+++g+ip d+  +ea+ + k+ +++ ++s+ ++++++i e+v
  gi|298675969|ref|YP_003727719.1| 227 -NTRVIEDYCREKGVEVVGKIPYDTIPVEAMIQEKT-IIEYSDSDLSRTIRDIWERV 281
                                       .45667999***************988888877775.55667999999999998876 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.4   0.00018     0.076       2      19 ..      68      85 ..      48      91 .. 0.83
   2 !   18.7   0.2   4.8e-06     0.002       2      24 ..      94     116 ..      93     140 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00018
                            Fer4_7  2 CigCgaCvaaCpvkaiel 19
                                      C++Cg C ++C  +ai+ 
  gi|298675969|ref|YP_003727719.1| 68 CTECGLCKSYCRFDAITE 85
                                      888888888888888875 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 4.8e-06
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeen 24 
                                       C gCg C+  Cp +ai+l+++ +
  gi|298675969|ref|YP_003727719.1|  94 CEGCGVCEYICPEDAISLNDRIS 116
                                       99***************998743 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.4   0.00053      0.22       2      20 ..      68      86 ..      67      92 .. 0.88
   2 !   18.1   0.1   9.5e-06     0.004       2      23 ..      94     115 ..      93     154 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00053
                           Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                      C++Cg C + C  +ai+e+
  gi|298675969|ref|YP_003727719.1| 68 CTECGLCKSYCRFDAITED 86
                                      *****************98 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 9.5e-06
                           Fer4_16   2 CgtCgkCaevCPtnaikekkek 23 
                                       C +Cg C  +CP++ai+ + + 
  gi|298675969|ref|YP_003727719.1|  94 CEGCGVCEYICPEDAISLNDRI 115
                                       *****************98444 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.2   0.00044      0.18       1      25 [.       1      25 [.       1      39 [. 0.84
   2 !   14.3   0.0   6.8e-05     0.028     108     164 ..     149     207 ..     128     215 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00044
                            AAA_31  1 gkvIaianqKGGvGKTTtsvnlaaa 25
                                      +k ++++  KGG GKTT + ++a+ 
  gi|298675969|ref|YP_003727719.1|  1 MKQLTVISGKGGTGKTTLTSAFASL 25
                                      6788999************999864 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 6.8e-05
                            AAA_31 108 kellekvkdeY..DyiiiDcpPsLglltenaLvasdsviipvqaeayaleGleqllkti 164
                                       +++ +++ ++Y  D+i+iD pP  g+ ++++++  ++ +++++++   ++ ++++l+  
  gi|298675969|ref|YP_003727719.1| 149 RNTSSELAEKYnsDLILIDGPPGTGCSVISSITGVNMTLVVTEPSISGIHDFKRILEVT 207
                                       45556666666669******************************776666666666654 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   2.5   0.00035      0.15       2      15 ..      66      79 ..      65      81 .. 0.87
   2 !   16.6   0.9   1.9e-05    0.0078       4      16 ..      94     106 ..      90     119 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00035
                            Fer4_4  2 erCigCgsCvaaCP 15
                                      + C++Cg C ++C 
  gi|298675969|ref|YP_003727719.1| 66 NLCTECGLCKSYCR 79
                                      56***********7 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.9e-05
                            Fer4_4   4 CigCgsCvaaCPq 16 
                                       C gCg+C+++CP 
  gi|298675969|ref|YP_003727719.1|  94 CEGCGVCEYICPE 106
                                       88**********4 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   1.4   2.7e-05     0.011       1      24 []      60      83 ..      60      83 .. 0.93
   2 !   13.9   4.9   0.00011     0.044       9      24 .]      94     109 ..      92     109 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.7e-05
                            Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                      v+ ++ ++C+ Cg C + C ++ai
  gi|298675969|ref|YP_003727719.1| 60 VAYVNNNLCTECGLCKSYCRFDAI 83
                                      6789***************99997 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 0.00011
                            Fer4_6   9 CigCgdCvrvCPegai 24 
                                       C gCg C+ +CPe+ai
  gi|298675969|ref|YP_003727719.1|  94 CEGCGVCEYICPEDAI 109
                                       99************98 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   9.2   2.7e-07   0.00011       1      58 [.      61     110 ..      61     111 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.7e-07
                           Fer4_21   1 AridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                       A ++++ C +Cg+C   C+    +ai+ d    ++v +  C GC +C  +CP ed+i+
  gi|298675969|ref|YP_003727719.1|  61 AYVNNNLCTECGLCKSYCR---FDAITED----FNVNTFICEGCGVCEYICP-EDAIS 110
                                       7899***************...8***976....7888999************.89997 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   1.6    0.0011      0.44      34      51 .]      66      83 ..      46      83 .. 0.74
   2 !   18.4  10.7   4.4e-06    0.0018       2      51 .]      68     109 ..      67     109 .. 0.95
   3 !   12.7   2.4   0.00025      0.11       2      19 ..      94     111 ..      93     122 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0011
                            Fer4_9 34 eaCigCgaCveaCpkgai 51
                                      + C++Cg C   C  +ai
  gi|298675969|ref|YP_003727719.1| 66 NLCTECGLCKSYCRFDAI 83
                                      579999999999988776 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 4.4e-06
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       Ct+Cg C + C +++++ed + ++          C gCg C+ +Cp++ai
  gi|298675969|ref|YP_003727719.1|  68 CTECGLCKSYCRFDAITEDFNVNTFI--------CEGCGVCEYICPEDAI 109
                                       ******************99999988........9************997 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 0.00025
                            Fer4_9   2 CtgCgaCveaCpagvvve 19 
                                       C gCg C++ Cp ++++ 
  gi|298675969|ref|YP_003727719.1|  94 CEGCGVCEYICPEDAISL 111
                                       888888888888888765 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.1    0.0031       1.3       4      54 ..       6      52 ..       3     100 .. 0.82
   2 ?   -1.3   0.1       2.9   1.2e+03      90     106 ..     169     185 ..     162     190 .. 0.87
   3 !   12.6   0.1   0.00016     0.066     182     240 ..     219     277 ..     188     284 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0031
                         Fer4_NifH  4 aiyGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggkaqet 54
                                       i GkGG Gk+t     ++a+a+  +  +i  CD  a    l+l+  ++et
  gi|298675969|ref|YP_003727719.1|  6 VISGKGGTGKTTL----TSAFASLAENAVISDCDVDAADIYLILNPEIMET 52
                                      688*******874....456666666789999**99999989998887776 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.9
                         Fer4_NifH  90 epGvGCaGrgvitaiel 106
                                       +pG+GC+  + it++++
  gi|298675969|ref|YP_003727719.1| 169 PPGTGCSVISSITGVNM 185
                                       48*****9999999998 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.00016
                         Fer4_NifH 182 nsrkv.ddereliekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqakeyrel 240
                                       n+ ++ ++++ +ie++ +e g++v+ ++P d i  +a +++kt+iey+++   + + r++
  gi|298675969|ref|YP_003727719.1| 219 NKYDInVENTRVIEDYCREKGVEVVGKIPYDTIPVEAMIQEKTIIEYSDSD-LSRTIRDI 277
                                       433331456789***********************************8754.35555555 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   2.6   0.00073       0.3       3      20 ..      61      78 ..      59      79 .. 0.89
   2 !   13.7   2.0   0.00012     0.051       6      22 .]      90     106 ..      87     106 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00073
                            Fer4_2  3 vvvdtdrCigCgaCvsaC 20
                                      ++v+ + C++Cg C s C
  gi|298675969|ref|YP_003727719.1| 61 AYVNNNLCTECGLCKSYC 78
                                      689999********9999 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00012
                            Fer4_2   6 dtdrCigCgaCvsaCPa 22 
                                       +t +C gCg C   CP+
  gi|298675969|ref|YP_003727719.1|  90 NTFICEGCGVCEYICPE 106
                                       5668************5 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.1    0.0029       1.2      99     124 ..       2      27 ..       1      36 [. 0.83
   2 ?   -1.0   0.0       3.4   1.4e+03      88     115 ..     150     177 ..     141     194 .. 0.74
   3 !    8.6   0.1    0.0037       1.6      32      80 ..     197     243 ..     175     263 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0029
                                       TSEEEEECSTTSSHHHHHHHHCTT-- CS
                       RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpele 124
                                       ++++v+ G+ G GK+tL  a+++ +e
  gi|298675969|ref|YP_003727719.1|   2 KQLTVISGKGGTGKTTLTSAFASLAE 27 
                                       5899*************999887554 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.4
                                       TTHHHHHHHCTTSEEEEECSTTSSHHHH CS
                       RsgA_GTPase  88 egleelkellkdktsvlvGqSGvGKStL 115
                                       ++ +el+e+ +++++++ G+ G G S +
  gi|298675969|ref|YP_003727719.1| 150 NTSSELAEKYNSDLILIDGPPGTGCSVI 177
                                       4567899999999999999999997643 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0037
                                       HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEE CS
                       RsgA_GTPase  32 lnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelealgyevl 80 
                                        +  +r+L + +  +i+ ++++nK D+  e++  + +++  ++ g+ev+
  gi|298675969|ref|YP_003727719.1| 197 IHDFKRILEVTNYFDIPTLVCINKYDINVENT--RVIEDYCREKGVEVV 243
                                       456799********************998888..556666666666654 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6  11.1   1.6e-05    0.0065       3      56 .]      62     105 ..      60     105 .. 0.92
   2 !   13.7   1.2   0.00012     0.051       5      40 ..      90     117 ..      86     135 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.6e-05
                           Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +++ + C++Cg C++ C           ++ + e  +++   C+gcg C  +CP
  gi|298675969|ref|YP_003727719.1|  62 YVNNNLCTECGLCKSYC----------RFDAITEDFNVNTFICEGCGVCEYICP 105
                                       578899***********..........7999999999999*************9 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00012
                           Fer4_10   5 dddtCirCgkCvkaCPadltsvgakgeaseeeavrk 40 
                                       ++  C +Cg C   CP d+        +s ++++++
  gi|298675969|ref|YP_003727719.1|  90 NTFICEGCGVCEYICPEDA--------ISLNDRISG 117
                                       6778************954........333333333 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.5    0.0013      0.52      19      40 ..       2      23 ..       1      32 [. 0.87
   2 ?    5.6   0.0     0.023       9.6      18      44 ..     160     186 ..     145     194 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0013
                                      -SEEEEE--TTSSTTHHHHHHH CS
                              PhoH 19 ndivfaiGpaGtGKtylavala 40
                                      ++++++ G+ GtGKt l+ a a
  gi|298675969|ref|YP_003727719.1|  2 KQLTVISGKGGTGKTTLTSAFA 23
                                      5799*************99987 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.023
                                       H-SEEEEE--TTSSTTHHHHHHHHHHH CS
                              PhoH  18 kndivfaiGpaGtGKtylavalaveal 44 
                                       ++d++ + Gp GtG + ++  ++v+++
  gi|298675969|ref|YP_003727719.1| 160 NSDLILIDGPPGTGCSVISSITGVNMT 186
                                       6789*******************9986 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.6e-05    0.0066       3      47 ..       3      50 ..       1     118 [. 0.83
   2 ?   -2.2   0.0         7   2.9e+03       5      36 ..     164     195 ..     163     211 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.6e-05
                            AAA_24  3 lkiliyGpsgiGKTtlakel...gpkplfidtekGlksldadkfpdie 47
                                      +  +i G+ g+GKTtl + +    +++++ d++  +++++ +  p+i 
  gi|298675969|ref|YP_003727719.1|  3 QLTVISGKGGTGKTTLTSAFaslAENAVISDCDVDAADIYLILNPEIM 50
                                      557999***************************988888888877665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 7
                            AAA_24   5 iliyGpsgiGKTtlakelgpkplfidtekGlk 36 
                                       ili Gp+g+G + + +  g +  ++ te +  
  gi|298675969|ref|YP_003727719.1| 164 ILIDGPPGTGCSVISSITGVNMTLVVTEPSIS 195
                                       67889999998877777666666666666554 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   3.2    0.0096         4       5      15 ..      68      78 ..      58      82 .. 0.71
   2 !    9.3   2.3    0.0035       1.5       5      16 ..      68      79 ..      64      93 .. 0.75
   3 !   10.6   0.1    0.0014      0.59       4      17 ..      93     119 ..      90     161 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0096
                            Fer4_8  5 CieCgaCqsaC 15
                                      C+eCg+C+s C
  gi|298675969|ref|YP_003727719.1| 68 CTECGLCKSYC 78
                                      66666666666 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0035
                            Fer4_8  5 CieCgaCqsaCp 16
                                      C+eCg+C+s C 
  gi|298675969|ref|YP_003727719.1| 68 CTECGLCKSYCR 79
                                      888888888885 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.0014
                            Fer4_8   4 kCieCgaCqsaCp.............v 17 
                                        C +Cg C+  Cp              
  gi|298675969|ref|YP_003727719.1|  93 ICEGCGVCEYICPedaislndrisgkY 119
                                       588999999999866554444443331 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   5.8e-05     0.024      26      63 ..       4      37 ..       1      61 [. 0.77
   2 ?   -0.1   0.0       2.6   1.1e+03      25      38 ..     162     175 ..     141     178 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.8e-05
                            AAA_16 26 lvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                      l+++sG  G+GK++l  +++  +e +    +  +cd  
  gi|298675969|ref|YP_003727719.1|  4 LTVISGKGGTGKTTLTSAFASLAENA----VISDCDVD 37
                                      689*****************555554....66666665 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2.6
                            AAA_16  25 elvllsGesGvGKs 38 
                                        l+l+ G++G+G s
  gi|298675969|ref|YP_003727719.1| 162 DLILIDGPPGTGCS 175
                                       6899*******966 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   2.6   0.00064      0.27      42      57 ..      64      79 ..      40      83 .. 0.83
   2 !    9.5   1.6    0.0034       1.4      43      59 ..      91     107 ..      80     109 .. 0.80
   3 !    9.4   1.9    0.0036       1.5       2      17 ..      94     109 ..      93     147 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00064
                           Fer4_17 42 kaslCieCgeCerkCP 57
                                      + +lC+eCg+C+++C 
  gi|298675969|ref|YP_003727719.1| 64 NNNLCTECGLCKSYCR 79
                                      6799***********5 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0034
                           Fer4_17  43 aslCieCgeCerkCPqg 59 
                                          C +Cg Ce+ CP++
  gi|298675969|ref|YP_003727719.1|  91 TFICEGCGVCEYICPED 107
                                       56799999999999986 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0036
                           Fer4_17   2 CiqCgyClpeCpsyea 17 
                                       C +Cg C+  Cp  ++
  gi|298675969|ref|YP_003727719.1|  94 CEGCGVCEYICPEDAI 109
                                       7777777777776555 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.3   5.6e-05     0.023       4      23 ..       5      24 ..       2      35 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.6e-05
                                      EEEEESTTSSHHHHHHHHHH CS
                       ArsA_ATPase  4 ilvgGKGGVGKttvsaatav 23
                                       +++GKGG GKtt+ +a+a 
  gi|298675969|ref|YP_003727719.1|  5 TVISGKGGTGKTTLTSAFAS 24
                                      579**************984 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.22        90      37      55 ..       6      24 ..       2      37 .. 0.83
   2 !   10.5   0.0    0.0009      0.37      30      87 ..     158     212 ..     132     242 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.22
                            RuvB_N 37 llyGpPGlGkttlakiiak 55
                                      +++G  G Gkttl++  a+
  gi|298675969|ref|YP_003727719.1|  6 VISGKGGTGKTTLTSAFAS 24
                                      789**********998775 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0009
                            RuvB_N  30 eealdhvllyGpPGlGkttlakiiakelgvklkitsgPvlekagdlaalltnleekdv 87 
                                       + + d +l+ GpPG G + +++i   ++   +   + P ++   d+  +l   +  d+
  gi|298675969|ref|YP_003727719.1| 158 KYNSDLILIDGPPGTGCSVISSITGVNMTLVV---TEPSISGIHDFKRILEVTNYFDI 212
                                       456799**********9999999988887644...46777777777777766666665 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00079      0.33       1      46 [.       2      52 ..       2      61 .. 0.81
   2 ?    3.2   0.1       0.1        42       3      18 ..     163     178 ..     161     191 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00079
                           DUF2075  1 kavvlVtGvaGtGKtvvllnllael.....eddeeertavylsvNhplvlv 46
                                      k++ +++G+ GtGKt + ++++  +     +d + +   +yl+ N + +++
  gi|298675969|ref|YP_003727719.1|  2 KQLTVISGKGGTGKTTLTSAFASLAenaviSDCDVDAADIYLILNPEIMET 52
                                      6789***********998876665566777777788888888888887766 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.1
                           DUF2075   3 vvlVtGvaGtGKtvvl 18 
                                       ++l+ G +GtG +v+ 
  gi|298675969|ref|YP_003727719.1| 163 LILIDGPPGTGCSVIS 178
                                       89************96 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00033      0.14      19      45 ..       3      29 ..       1      37 [. 0.89
   2 ?    0.9   0.0      0.75   3.1e+02      20      33 ..     163     176 ..     152     207 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00033
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaa 45
                                      +++v+ G  GtGKtt+ +a + ++e+a
  gi|298675969|ref|YP_003727719.1|  3 QLTVISGKGGTGKTTLTSAFASLAENA 29
                                      689****************99998865 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.75
                            AAA_30  20 vavltGpAGtGKtt 33 
                                       + ++ Gp+GtG + 
  gi|298675969|ref|YP_003727719.1| 163 LILIDGPPGTGCSV 176
                                       78999*****9765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00073       0.3       5      31 ..       2      28 ..       1      59 [. 0.87
   2 ?    1.4   0.0      0.84   3.5e+02       6      19 ..     162     175 ..     156     179 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00073
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqlde 31
                                      ++++v+ G  GtGKTtl   +++ +++
  gi|298675969|ref|YP_003727719.1|  2 KQLTVISGKGGTGKTTLTSAFASLAEN 28
                                      5789****************9998854 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.84
                            AAA_22   6 gilvvtGesGtGKT 19 
                                        ++++ G++GtG +
  gi|298675969|ref|YP_003727719.1| 162 DLILIDGPPGTGCS 175
                                       6899********66 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00047       0.2      12      37 ..       3      28 ..       1      74 [. 0.78
   2 ?    0.2   0.0       2.4     1e+03      12      28 ..     162     178 ..     156     194 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00047
                                      SEEEEEESTTSSHHHHHHHHTTSS-- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 12 ekvaivGenGaGKStLlkllagllkp 37
                                      ++++i G+ G+GK+tL +++a l ++
  gi|298675969|ref|YP_003727719.1|  3 QLTVISGKGGTGKTTLTSAFASLAEN 28
                                      7899****************998765 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 2.4
                                       SEEEEEESTTSSHHHHH CS
                                       xxxxxxxxxxxxxxxxx RF
                          ABC_tran  12 ekvaivGenGaGKStLl 28 
                                        ++ i G+ G+G+S + 
  gi|298675969|ref|YP_003727719.1| 162 DLILIDGPPGTGCSVIS 178
                                       567888*******9875 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.8    0.0072         3       1      15 []      68      82 ..      68      82 .. 0.94
   2 ?   11.3   3.8    0.0013      0.56       1      15 []      94     108 ..      94     108 .. 0.96

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0072
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      Ct Cg+C   C+ +A
  gi|298675969|ref|YP_003727719.1| 68 CTECGLCKSYCRFDA 82
                                      ***********9887 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0013
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C gCg C+  CP++A
  gi|298675969|ref|YP_003727719.1|  94 CEGCGVCEYICPEDA 108
                                       99**********998 PP

>> FTHFS  Formate--tetrahydrofolate ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00011     0.048     355     404 ..     195     243 ..     180     251 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHHHHCTTT--EEEEEE--TT--HHHHHHHHHHHHCTTSEEE CS
                             FTHFS 355 kGlanlekhienvkkfgvpvvvainkfktDteaelelvkelaeakaveva 404
                                       +G++++++ +e ++ f++p++v+ink++   e +++++++++++k+vev+
  gi|298675969|ref|YP_003727719.1| 195 SGIHDFKRILEVTNYFDIPTLVCINKYDINVE-NTRVIEDYCREKGVEVV 243
                                       699999*********************98775.679******99999987 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.2    0.0036       1.5      24      39 ..       6      21 ..       2      31 .. 0.83
   2 ?    2.8   0.0      0.13        55       6      38 ..     149     179 ..     145     189 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0036
                                      EEEESTTSSHHHHHHH CS
                            NB-ARC 24 alvGmgGvGKttlakq 39
                                       ++G+gG GKttl + 
  gi|298675969|ref|YP_003727719.1|  6 VISGKGGTGKTTLTSA 21
                                      699**********875 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.13
                                       HHHHHHHHCTTTSCSEEEEEEESTTSSHHHHHH CS
                            NB-ARC   6 ekviekLlekdelqslvvalvGmgGvGKttlak 38 
                                       ++   +L ek +++  ++ + G +G G +++++
  gi|298675969|ref|YP_003727719.1| 149 RNTSSELAEKYNSD--LILIDGPPGTGCSVISS 179
                                       55667888888888..9*************975 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.047        20      18      39 ..       3      24 ..       1      47 [. 0.83
   2 ?    6.7   0.0     0.013       5.5      15      38 ..     160     184 ..     144     219 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.047
                            AAA_11 18 eitliqGPPGtgKTktivells 39
                                      ++t+i+G+ GtgKT+   ++ s
  gi|298675969|ref|YP_003727719.1|  3 QLTVISGKGGTGKTTLTSAFAS 24
                                      5799**********87666554 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.013
                            AAA_11  15 seseitliqGPPGtgKT..ktivell 38 
                                       ++ ++ li GPPGtg +  + i+++ 
  gi|298675969|ref|YP_003727719.1| 160 NS-DLILIDGPPGTGCSviSSITGVN 184
                                       33.378*********88665555555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0027       1.1       3      25 ..       7      29 ..       5      65 .. 0.77
   2 ?    1.9   0.0      0.66   2.8e+02       1      15 [.     164     178 ..     164     206 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0027
                                      EESSTTSSHHHHHHHHHHHHTHE CS
                               AAA  3 lyGppGtGKTllakavakelgve 25
                                      ++G  GtGKT+l +a a+ ++  
  gi|298675969|ref|YP_003727719.1|  7 ISGKGGTGKTTLTSAFASLAENA 29
                                      7899***********99987543 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.66
                                       EEEESSTTSSHHHHH CS
                               AAA   1 vllyGppGtGKTlla 15 
                                       +l+ GppGtG + + 
  gi|298675969|ref|YP_003727719.1| 164 ILIDGPPGTGCSVIS 178
                                       5788******77765 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00049       0.2      24      55 ..       3      40 ..       1      94 [. 0.75
   2 ?   -1.8   0.0       4.7     2e+03     242     261 ..     141     160 ..     108     214 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00049
                            AAA_15 24 eltvliGkNnsGKSsilealdlFlnnkekkn......k 55
                                      +ltv+ Gk ++GK++++ a+  + +n    +      +
  gi|298675969|ref|YP_003727719.1|  3 QLTVISGKGGTGKTTLTSAFASLAENAVISDcdvdaaD 40
                                      49******************999998722223344442 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.7
                            AAA_15 242 lkeiqeklkeidkklaeelk 261
                                       + ++ +++++++++lae+++
  gi|298675969|ref|YP_003727719.1| 141 SGKLITAVRNTSSELAEKYN 160
                                       33444444444444444444 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.028        12       1      24 [.       1      24 [.       1      41 [. 0.79
   2 ?    5.3   0.0     0.028        12     102     150 ..     145     195 ..     124     277 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.028
                          CBP_BcsQ  1 mkvlalqGvRGGvGttsllaaLaw 24
                                      mk+l++   +GG+G+t+l++a a 
  gi|298675969|ref|YP_003727719.1|  1 MKQLTVISGKGGTGKTTLTSAFAS 24
                                      7777777779********998774 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.028
                          CBP_BcsQ 102 aeallaalkelkeqy..rwillDlpagasaltrellaladlvllvvepdan 150
                                         a+ ++ +el+e+y  ++il+D p g+   + + ++  +++l v+ep  +
  gi|298675969|ref|YP_003727719.1| 145 ITAVRNTSSELAEKYnsDLILIDGPPGTGCSVISSITGVNMTLVVTEPSIS 195
                                       4556677788885553389**********999999999********99865 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.2    0.0013      0.55      20      40 ..       3      23 ..       1      30 [. 0.89
   2 ?    0.9   0.0      0.58   2.4e+02      20      36 ..     162     178 ..     158     185 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0013
                            ATPase 20 rvvlitGepGtGKtifalqFl 40
                                      + + i+G+ GtGKt++   F+
  gi|298675969|ref|YP_003727719.1|  3 QLTVISGKGGTGKTTLTSAFA 23
                                      7899*************9997 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.58
                            ATPase  20 rvvlitGepGtGKtifa 36 
                                         +li G pGtG ++++
  gi|298675969|ref|YP_003727719.1| 162 DLILIDGPPGTGCSVIS 178
                                       679*********99886 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0    0.0025         1       2      24 ..       6      28 ..       6      67 .. 0.76
   2 ?    1.0   0.4       1.4     6e+02       1      15 [.     164     178 ..     164     191 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0025
                            AAA_18  2 lltGtpGvGKttlakeLskrlgf 24
                                      +++G+ G+GKttl+ + +++ ++
  gi|298675969|ref|YP_003727719.1|  6 VISGKGGTGKTTLTSAFASLAEN 28
                                      589************99988755 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 1.4
                            AAA_18   1 IlltGtpGvGKttla 15 
                                       Il+ G+pG+G + ++
  gi|298675969|ref|YP_003727719.1| 164 ILIDGPPGTGCSVIS 178
                                       8999******88776 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0037       1.5      48      71 ..       3      26 ..       1      45 [. 0.82
   2 ?    1.6   0.0      0.48     2e+02      48      66 ..     162     180 ..     135     190 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0037
                         IstB_IS21 48 enivllGpsGvGKshlaialgvea 71
                                      +  v+ G  G+GK+ l+ a++  a
  gi|298675969|ref|YP_003727719.1|  3 QLTVISGKGGTGKTTLTSAFASLA 26
                                      567999************998655 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.48
                         IstB_IS21  48 enivllGpsGvGKshlaia 66 
                                       + i++ Gp+G+G s ++  
  gi|298675969|ref|YP_003727719.1| 162 DLILIDGPPGTGCSVISSI 180
                                       557888******9987755 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1    0.0068       2.8      21      42 ..       4      25 ..       1      34 [. 0.81
   2 ?    1.8   0.0      0.56   2.3e+02       8      54 ..     149     195 ..     143     243 .. 0.71
   3 ?   -1.6   0.0         6   2.5e+03      48      65 ..     210     227 ..     195     273 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0068
                                      EEEEEESTTSSHHHHHHHHHHH CS
                              TsaE 21 vilLeGdLGaGKTtlvrglaka 42
                                      + +++G+ G+GKTtl+ ++a+ 
  gi|298675969|ref|YP_003727719.1|  4 LTVISGKGGTGKTTLTSAFASL 25
                                      56889************99875 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.56
                                       HHHHHHHHHCH.TEEEEEEESTTSSHHHHHHHHHHHTT--.----TTTT CS
                              TsaE   8 ealgkklakal.gdvilLeGdLGaGKTtlvrglakalgve.evkSPTFt 54 
                                       ++  ++la++  +d+il++G+ G+G ++++     ++  +  v+ P+ +
  gi|298675969|ref|YP_003727719.1| 149 RNTSSELAEKYnSDLILIDGPPGTGCSVISSITGVNM--TlVVTEPSIS 195
                                       5666777776667899999999999887765544433..3356666555 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 6
                                       ---TTTTSEEEEEE..SS CS
                              TsaE  48 vkSPTFtlveeYelekeg 65 
                                          PT + +++Y+ + e+
  gi|298675969|ref|YP_003727719.1| 210 FDIPTLVCINKYDINVEN 227
                                       555777777777665443 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1    0.0006      0.25      20      39 ..       3      22 ..       2      62 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0006
                            AAA_23 20 gltlItGpNGaGKTTildAi 39
                                       lt+I+G+ G+GKTT+  A+
  gi|298675969|ref|YP_003727719.1|  3 QLTVISGKGGTGKTTLTSAF 22
                                      79**************8886 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00055      0.23      19      43 ..       5      29 ..       1      66 [. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00055
                            AAA_13 19 NliYGwNGaGKTtLSrllrslelge 43
                                       +i G+ G+GKTtL ++++sl +++
  gi|298675969|ref|YP_003727719.1|  5 TVISGKGGTGKTTLTSAFASLAENA 29
                                      5789****************98765 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0014      0.58       2      26 ..       4      28 ..       3      48 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0014
                                      CEEEEC-TTTCHHHHHHHHHHHHCT CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawae 26
                                      l ++ G+ G GKTtL   +a+++  
  gi|298675969|ref|YP_003727719.1|  4 LTVISGKGGTGKTTLTSAFASLAEN 28
                                      679*************999988765 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00081      0.34       3      22 ..       6      25 ..       4      39 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00081
                            AAA_28  3 vitGgestGKTtlleaLaar 22
                                      vi+G  +tGKTtl++a+a+ 
  gi|298675969|ref|YP_003727719.1|  6 VISGKGGTGKTTLTSAFASL 25
                                      99**************9964 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.3    0.0014      0.59      33      54 ..       2      23 ..       1      26 [. 0.88
   2 ?   -1.8   0.0       4.7   1.9e+03      34      45 ..     162     173 ..     131     189 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0014
                            AAA_25 33 gelallaGapgtGKttlaldla 54
                                      + l+++ G +gtGKttl++  a
  gi|298675969|ref|YP_003727719.1|  2 KQLTVISGKGGTGKTTLTSAFA 23
                                      5789**************9876 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.7
                            AAA_25  34 elallaGapgtG 45 
                                       +l+l+ G+pgtG
  gi|298675969|ref|YP_003727719.1| 162 DLILIDGPPGTG 173
                                       455555666666 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.5    0.0014       0.6      24      45 ..       4      25 ..       1      29 [. 0.85
   2 ?    0.2   0.0       1.6   6.6e+02      23      38 ..     162     177 ..     152     181 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0014
                            AAA_29 24 atlltGpsGsGKSTllDAiqal 45
                                       t+++G+ G+GK+Tl  A++ l
  gi|298675969|ref|YP_003727719.1|  4 LTVISGKGGTGKTTLTSAFASL 25
                                      699************9888766 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.6
                            AAA_29  23 gatlltGpsGsGKSTl 38 
                                       + +l+ Gp G+G S +
  gi|298675969|ref|YP_003727719.1| 162 DLILIDGPPGTGCSVI 177
                                       4789********9875 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.8     0.024        10       1      16 [.      63      78 ..      63      80 .. 0.92
   2 ?    5.5   1.9      0.06        25       5      18 ..      93     106 ..      89     107 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.024
                           Fer4_13  1 VDrdtCiacgaCvela 16
                                      V+++ C++cg+C + +
  gi|298675969|ref|YP_003727719.1| 63 VNNNLCTECGLCKSYC 78
                                      88999*******9988 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.06
                           Fer4_13   5 tCiacgaCvelaPd 18 
                                        C +cg+C  ++P+
  gi|298675969|ref|YP_003727719.1|  93 ICEGCGVCEYICPE 106
                                       599**********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); expected 17.9 (0.001)
Passed Fwd filter:                        47  (0.00262145); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              43  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 1761.75
//
Query:       gi|298675970|ref|YP_003727720.1|  [L=280]
Description: cobyrinic acid ac-diamide synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-19   69.8   0.0    2.7e-19   69.5   0.0    1.1  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    2.3e-16   60.0   0.1    7.3e-08   32.2   0.0    2.9  2  ParA         NUBPL iron-transfer P-loop NTPase
    6.3e-09   36.0   0.2    4.4e-06   26.7   0.0    2.2  2  AAA_31       AAA domain
    1.3e-08   34.3  13.0    4.5e-06   26.2   3.0    3.2  3  Fer4         4Fe-4S binding domain
    1.8e-06   28.0   8.0    3.9e-06   26.9   8.0    1.6  1  Fer4_21      4Fe-4S dicluster domain
    3.2e-06   28.0   7.6     0.0022   18.9   0.5    2.8  3  Fer4_16      4Fe-4S double cluster binding domain
    4.5e-06   27.2   6.4      0.014   16.0   0.1    2.6  2  Fer4_7       4Fe-4S dicluster domain
    5.5e-05   23.1   0.2     0.0015   18.4   0.0    2.5  3  AAA_26       AAA domain
    8.8e-05   22.6  12.3    0.00016   21.8  10.3    2.4  2  Fer4_9       4Fe-4S dicluster domain
    0.00013   22.0  13.3      0.006   16.7   0.7    3.0  3  Fer4_10      4Fe-4S dicluster domain
     0.0014   18.1   1.3        1.2    8.5   0.0    2.8  3  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
     0.0023   17.2   0.1     0.0058   15.8   0.1    1.7  1  ArsA_ATPase  Anion-transporting ATPase
     0.0081   16.2  20.8      0.036   14.1   3.3    3.4  3  Fer4_6       4Fe-4S binding domain
  ------ inclusion threshold ------
      0.057   13.9   7.8        1.7    9.2   0.9    2.6  2  Fer4_8       4Fe-4S dicluster domain
      0.067   14.0   4.7        5.2    8.0   0.7    2.5  2  Fer4_22      4Fe-4S dicluster domain
      0.083   12.2   0.0       0.11   11.7   0.0    1.2  1  MipZ         ATPase MipZ
      0.093   12.3   0.0       0.14   11.7   0.0    1.2  1  AAA_25       AAA domain
       0.12   11.8   0.1       0.22   11.0   0.1    1.4  1  PhoH         PhoH-like protein
       0.18   12.6   5.3        3.2    8.6   1.3    2.6  2  Fer4_15      4Fe-4S single cluster domain
       0.24   11.9  13.5       0.24   11.9   2.5    2.6  3  Fer4_17      4Fe-4S dicluster domain
        1.6    9.5  17.5        1.2    9.8   3.8    3.1  2  Fer4_4       4Fe-4S binding domain
        9.5    6.6  17.0       0.39   10.9   1.9    3.3  3  Fer4_2       4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.5   0.0   3.3e-22   2.7e-19       1     127 [.       3     255 ..       3     256 .. 0.96

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 3.3e-22
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH...HTTEB-HHHH.................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxx.................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai...leglendiep.................... 54 
                                       iaias+kGG+GKTt+++nLa +l +     +l+D+D++ +n +i   +  +++d  +                    
  gi|298675970|ref|YP_003727720.1|   3 IAIASGKGGTGKTTISVNLALSLDD----AQLLDCDVEEPNCNIflgYNLVKKDDVNiltpvidknncnfcgkcadf 75 
                                       89**********************9....9*************976644444444448999**************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|298675970|ref|YP_003727720.1|  76 cqfnaiavlpgdimlfntlchgcggcgivcpmdaideekrsigtiekseteygnleffqgllnigeamaspvikdlk 152
                                       ***************************************************************************** PP

                                       ...........................................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS.. CS
                                       ...........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ...........................................dlkrllellealgkkkalllkiagvvlnrvdgen 88 
                                                                                  dl   l ++++lg++        g+++nr d   
  gi|298675970|ref|YP_003727720.1| 153 kninknkntiidappgtacpaiatledtdycilvteptpfgyhDLLLTLDVVRELGIP-------FGIIINRCDVG- 221
                                       ********************************************************99.......9*********9. PP

                                       .-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  89 eetllkealeelkqrygvpvlgviprdeavaeapargep 127
                                        + + +e++  +    ++pvl +ip+d+++a+++++g p
  gi|298675970|ref|YP_003727720.1| 222 -DSKVEEFCYSE----NIPVLMKIPYDKNIAQLYSNGIP 255
                                       .99999999998....8*******************987 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0     9e-11   7.3e-08       6      68 ..       3      60 ..       1      69 [. 0.81
   2 !   23.3   0.0   4.6e-08   3.8e-05     115     241 ..     161     274 ..     141     277 .. 0.82

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 9e-11
                              ParA  6 iavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPv 68
                                      ia++SgKGG GK+t++vnlAl+L +      llD D+  p+   +lg +  k    +  l+Pv
  gi|298675970|ref|YP_003727720.1|  3 IAIASGKGGTGKTTISVNLALSLDDA----QLLDCDVEEPNCNIFLGYNLVKKDDVN-ILTPV 60
                                      89*********************876....48**********999998875433333.45566 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 4.6e-08
                              ParA 115 LiiDlPPGtgDeqltvaqklplagaviVttpqevaladvkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgk 191
                                        iiD PPGt+  +++ ++    + +++Vt p     +d   ++++++++ ++  G++ N     c+         g+
  gi|298675970|ref|YP_003727720.1| 161 TIIDAPPGTACPAIATLEDT--DYCILVTEPTPFGYHDLLLTLDVVRELGIPF-GIIIN----RCD--------VGD 222
                                       59***********9999988..689**************************95.88877....344........367 PP

                              ParA 192 gggeklaeelgvpllgeipldpeireasdegkplvlkepe..seaakaleei 241
                                       +++e+++ + ++p+l +ip d++i++   +g p+v+k pe  ++ a+++e+i
  gi|298675970|ref|YP_003727720.1| 223 SKVEEFCYSENIPVLMKIPYDKNIAQLYSNGIPFVQKMPEwkKQFAQMFESI 274
                                       789999*****************************99976434444444444 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   5.5e-09   4.4e-06       4      92 ..       3      92 ..       1      95 [. 0.69
   2 !    7.3   0.0    0.0049         4     114     163 ..     155     203 ..     126     209 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 5.5e-09
                            AAA_31  4 IaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlD.pQanattglgiekneiektlyevlieeknikeaii...ktkv 78
                                      Iaia  KGG GKTT svnla +l   + + L +D+  p  n   g+++ k++ + ++++ +i+++n++ + +     ++
  gi|298675970|ref|YP_003727720.1|  3 IAIASGKGGTGKTTISVNLALSLD--DAQLLDCDVEePNCNIFLGYNLVKKD-DVNILTPVIDKNNCNFCGKcadFCQF 78
                                      9*******************8886..56788888743777777777776766.44555555544444433330013446 PP

                            AAA_31 79 enldlipssidLae 92
                                      + + ++p++i L +
  gi|298675970|ref|YP_003727720.1| 79 NAIAVLPGDIMLFN 92
                                      66699999998865 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0049
                            AAA_31 114 vkdeYDyiiiDcpPsLglltenaLvasdsviipvqaeayaleGleqllkt 163
                                       +++     iiD+pP   + ++  L   d++i +++++++ ++ l   l+ 
  gi|298675970|ref|YP_003727720.1| 155 INK-NKNTIIDAPPGTACPAIATLEDTDYCILVTEPTPFGYHDLLLTLDV 203
                                       333.344699***************************9998876655555 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   3.0   5.6e-09   4.5e-06       1      23 [.      59      81 ..      59      82 .. 0.96
   2 !   20.9   2.5   2.7e-07   0.00022       6      24 .]      93     111 ..      89     111 .. 0.92
   3 ?   -2.0   0.1       4.5   3.7e+03       4       9 ..     179     184 ..     178     185 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 5.6e-09
                                      EEEETTTSSS-THHHHHSTTTEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAI 23
                                      +vid++ C +CG+C++ C ++AI
  gi|298675970|ref|YP_003727720.1| 59 PVIDKNNCNFCGKCADFCQFNAI 81
                                      69********************9 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 2.7e-07
                                       TTSSS-THHHHHSTTTEEE CS
                              Fer4   6 ekCigCGaCvevCPvgAIt 24 
                                        +C gCG C  vCP +AI+
  gi|298675970|ref|YP_003727720.1|  93 TLCHGCGGCGIVCPMDAID 111
                                       58***************95 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 4.5
                                       ETTTSS CS
                              Fer4   4 deekCi 9  
                                       d++ Ci
  gi|298675970|ref|YP_003727720.1| 179 DTDYCI 184
                                       8999*9 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   8.0   4.8e-09   3.9e-06       2      57 ..      60     110 ..      59     112 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 4.8e-09
                           Fer4_21   2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57 
                                       +id+++C  CgkC+  C+    +ai + +  +  + +  C GC  C +vCP+ d+i
  gi|298675970|ref|YP_003727720.1|  60 VIDKNNCNFCGKCADFCQ---FNAIAVLPGDI-MLFNTLCHGCGGCGIVCPM-DAI 110
                                       79****************...79998887776.67899*************7.888 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   1.0   0.00034      0.28      53      67 .]      65      79 ..      34      84 .. 0.69
   2 !   18.9   0.5   2.7e-06    0.0022       2      30 ..      95     123 ..      94     172 .. 0.67
   3 ?   -2.1   0.0       9.7   7.9e+03      11      24 ..     170     183 ..     168     189 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00034
                           Fer4_16 53 aitgCdiCqdvCPan 67
                                      ++ +C++C+d C +n
  gi|298675970|ref|YP_003727720.1| 65 NCNFCGKCADFCQFN 79
                                      555555555555554 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 2.7e-06
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearec 30 
                                       C++Cg C  vCP +ai+e+k+    ++++
  gi|298675970|ref|YP_003727720.1|  95 CHGCGGCGIVCPMDAIDEEKRSIGTIEKS 123
                                       ******************95443333332 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 9.7
                           Fer4_16  11 vCPtnaikekkeke 24 
                                       +CP+ a  e+++++
  gi|298675970|ref|YP_003727720.1| 170 ACPAIATLEDTDYC 183
                                       89998888776655 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   2.1   0.00019      0.15      30      52 .]      58      80 ..      33      83 .. 0.77
   2 !   16.0   0.1   1.7e-05     0.014       2      22 ..      95     115 ..      94     136 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00019
                            Fer4_7 30 kveidpekClgCgaCvavCPtga 52
                                      +++id ++C +Cg+C++ C ++a
  gi|298675970|ref|YP_003727720.1| 58 TPVIDKNNCNFCGKCADFCQFNA 80
                                      45788889999999999998876 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.7e-05
                            Fer4_7   2 CigCgaCvaaCpvkaieldee 22 
                                       C gCg C  +Cp++ai+ +++
  gi|298675970|ref|YP_003727720.1|  95 CHGCGGCGIVCPMDAIDEEKR 115
                                       ***************997664 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.22   1.8e+02       3      25 ..       3      25 ..       1      30 [. 0.84
   2 ?   -2.5   0.0       4.7   3.8e+03     147     185 ..      44      84 ..      41      88 .. 0.71
   3 !   18.4   0.0   1.9e-06    0.0015     132     194 ..     184     246 ..     178     249 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.22
                            AAA_26  3 ifvtgtdtgvGKTvvslgLvral 25
                                      i +++   g GKT++s  L+ +l
  gi|298675970|ref|YP_003727720.1|  3 IAIASGKGGTGKTTISVNLALSL 25
                                      678888999********999877 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.7
                            AAA_26 147 ltiealrqknvrvlGvilNkvrnpe...nvetlekksgipvl 185
                                       l ++++++ +v++l  ++ k +n +   + + +++++ i vl
  gi|298675970|ref|YP_003727720.1|  44 LGYNLVKKDDVNILTPVIDK-NNCNfcgKCADFCQFNAIAVL 84 
                                       66889999999999999988.666444466666666666665 PP

  == domain 3  score: 18.4 bits;  conditional E-value: 1.9e-06
                            AAA_26 132 ilVargglgtinqllltiealrqknvrvlGvilNkv.rnpenvetlekksgipvlGvvPylpdl 194
                                       ilV+ ++     +lllt++++r+ +++ +G+i+N++   + +ve+++ + +ipvl  +Py++++
  gi|298675970|ref|YP_003727720.1| 184 ILVTEPTPFGYHDLLLTLDVVRELGIP-FGIIINRCdVGDSKVEEFCYSENIPVLMKIPYDKNI 246
                                       788888888899***********8886.8******834457*******************9976 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   2.8   8.8e-05     0.072      18      51 .]      50      81 ..      32      81 .. 0.67
   2 !   21.8  10.3     2e-07   0.00016       1      51 []      65     110 ..      65     110 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.8e-05
                            Fer4_9 18 vedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      ++d+++    +  +  ++C +Cg+C++ C+ +ai
  gi|298675970|ref|YP_003727720.1| 50 KKDDVNILTPVIDK--NNCNFCGKCADFCQFNAI 81
                                      44444444444333..57***********99876 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 2e-07
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       +C+ Cg+C + C+++++    +  +  ++      C+gCg C  +Cp +ai
  gi|298675970|ref|YP_003727720.1|  65 NCNFCGKCADFCQFNAIAVLPGDIMLFNT-----LCHGCGGCGIVCPMDAI 110
                                       5****************999999888874.....6*************997 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   3.1    0.0004      0.32       2      19 ..      59      76 ..      58      92 .. 0.86
   2 !   16.7   0.7   7.4e-06     0.006       7      29 ..      93     117 ..      87     132 .. 0.67
   3 ?   -1.0   0.0       2.4   1.9e+03      17      23 ..     169     175 ..     168     194 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0004
                           Fer4_10  2 vvidddtCirCgkCvkaC 19
                                      +vid++ C  CgkC ++C
  gi|298675970|ref|YP_003727720.1| 59 PVIDKNNCNFCGKCADFC 76
                                      589*************** PP

  == domain 2  score: 16.7 bits;  conditional E-value: 7.4e-06
                           Fer4_10   7 dtCirCgkCvkaCPadl..tsvgak 29 
                                         C +Cg C  +CP+d+  ++++ +
  gi|298675970|ref|YP_003727720.1|  93 TLCHGCGGCGIVCPMDAidEEKRSI 117
                                       57*************7744222222 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2.4
                           Fer4_10  17 kaCPadl 23 
                                       +aCPa +
  gi|298675970|ref|YP_003727720.1| 169 TACPAIA 175
                                       5899854 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0031       2.5       3      25 ..       3      26 ..       1      45 [. 0.84
   2 ?   -1.3   0.3       1.5   1.2e+03      93     110 ..      96     113 ..      93     116 .. 0.85
   3 !    8.5   0.0    0.0014       1.2     178     244 ..     212     274 ..     204     280 .] 0.81

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0031
                         Fer4_NifH  3 iai.yGkGGiGksttsqnlsaala 25
                                      iai  GkGG Gk+t s nl+ +l 
  gi|298675970|ref|YP_003727720.1|  3 IAIaSGKGGTGKTTISVNLALSLD 26
                                      56535**************98886 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.5
                         Fer4_NifH  93 vGCaGrgvitaielleel 110
                                        GC+G g++  ++ ++e+
  gi|298675970|ref|YP_003727720.1|  96 HGCGGCGIVCPMDAIDEE 113
                                       69******9999988875 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0014
                         Fer4_NifH 178 GliinsrkvddereliekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqakeyrelarki 244
                                       G+iin r  d ++  +e+f  + +++vl ++P d+++ +   +    ++  pe++  k++ ++ + i
  gi|298675970|ref|YP_003727720.1| 212 GIIIN-R-CDVGDSKVEEFCYSENIPVLMKIPYDKNIAQLYSNGIPFVQKMPEWK--KQFAQMFESI 274
                                       9****.5.899999***********************998888888888888877..5555554444 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   7.2e-06    0.0058       2      27 ..       2      27 ..       1      31 [. 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.2e-06
                                      EEEEEEESTTSSHHHHHHHHHHHHHH CS
                       ArsA_ATPase  2 kvilvgGKGGVGKttvsaatavklse 27
                                      ++ + +GKGG GKtt+s  +a+ l +
  gi|298675970|ref|YP_003727720.1|  2 NIAIASGKGGTGKTTISVNLALSLDD 27
                                      567889***************99865 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   3.3   4.4e-05     0.036       2      24 .]      59      81 ..      58      81 .. 0.94
   2 !   11.0   4.1   0.00043      0.35       8      24 .]      94     110 ..      92     110 .. 0.94
   3 ?   -0.9   0.3       2.6   2.1e+03      17      23 ..     169     175 ..     169     176 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.4e-05
                            Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                      ++id+++C+ Cg+C++ C ++ai
  gi|298675970|ref|YP_003727720.1| 59 PVIDKNNCNFCGKCADFCQFNAI 81
                                      89****************99997 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00043
                            Fer4_6   8 kCigCgdCvrvCPegai 24 
                                       +C gCg C +vCP++ai
  gi|298675970|ref|YP_003727720.1|  94 LCHGCGGCGIVCPMDAI 110
                                       8**************98 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.6
                            Fer4_6  17 rvCPega 23 
                                       ++CP+ a
  gi|298675970|ref|YP_003727720.1| 169 TACPAIA 175
                                       69**976 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.9    0.0054       4.4      49      62 ..      64      77 ..      39      81 .. 0.81
   2 ?    9.2   0.9    0.0021       1.7      50      64 ..      94     108 ..      91     114 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0054
                            Fer4_8 49 wsCttcgaCtevCp 62
                                      ++C+ cg+C++ C 
  gi|298675970|ref|YP_003727720.1| 64 NNCNFCGKCADFCQ 77
                                      56777777777775 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0021
                            Fer4_8  50 sCttcgaCtevCpvg 64 
                                        C++cg C  vCp++
  gi|298675970|ref|YP_003727720.1|  94 LCHGCGGCGIVCPMD 108
                                       699999999999975 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.2     0.011       8.8      76      93 ..      60      77 ..      46      80 .. 0.80
   2 ?    8.0   0.7    0.0064       5.2      81      94 ..      94     107 ..      90     124 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.011
                           Fer4_22 76 kfgesgCvGCgRCieacp 93
                                       ++++ C  Cg+C + c+
  gi|298675970|ref|YP_003727720.1| 60 VIDKNNCNFCGKCADFCQ 77
                                      568999***********7 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0064
                           Fer4_22  81 gCvGCgRCieacpv 94 
                                        C GCg C  +cp+
  gi|298675970|ref|YP_003727720.1|  94 LCHGCGGCGIVCPM 107
                                       56666666666654 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00014      0.11       3      27 ..       3      27 ..       1      58 [. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
                                      EEE--SSTTSSHHHHHHHHHHHHHT CS
                              MipZ  3 ivlgnekGGsGksttavhvavaLlk 27
                                      i ++  kGG+Gk+t++v +a +L +
  gi|298675970|ref|YP_003727720.1|  3 IAIASGKGGTGKTTISVNLALSLDD 27
                                      778999**************99965 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00017      0.14      35      57 ..       3      25 ..       1      38 [. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                            AAA_25 35 lallaGapgtGKttlaldlalav 57
                                      +a+  G +gtGKtt+ ++lal++
  gi|298675970|ref|YP_003727720.1|  3 IAIASGKGGTGKTTISVNLALSL 25
                                      57899***************985 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00027      0.22      20      43 ..       2      25 ..       1      32 [. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00027
                                      SEEEEE--TTSSTTHHHHHHHHHH CS
                              PhoH 20 divfaiGpaGtGKtylavalavea 43
                                      +i +a G+ GtGKt ++v la+++
  gi|298675970|ref|YP_003727720.1|  2 NIAIASGKGGTGKTTISVNLALSL 25
                                      68899***************9975 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   1.3    0.0039       3.2       2      18 ..      60      76 ..      60      83 .. 0.90
   2 ?    5.0   0.1     0.052        43       6      33 ..      93     121 ..      89     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0039
                           Fer4_15  2 vvDrdaCigcglCvaea 18
                                      v+D+++C  cg C++ +
  gi|298675970|ref|YP_003727720.1| 60 VIDKNNCNFCGKCADFC 76
                                      69************987 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.052
                           Fer4_15   6 daCigcglCvaeap.evfeldedglasvl 33 
                                       ++C gcg C  ++p + + ++++ + ++ 
  gi|298675970|ref|YP_003727720.1|  93 TLCHGCGGCGIVCPmDAIDEEKRSIGTIE 121
                                       78*******99996367777777776555 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   3.7     0.084        69      44      57 ..      64      77 ..      37      80 .. 0.77
   2 ?    4.3   3.1     0.072        59       1      15 [.      65      79 ..      65      89 .. 0.79
   3 ?   11.9   2.5    0.0003      0.24      44      59 ..      93     108 ..      87     109 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.084
                           Fer4_17 44 slCieCgeCerkCP 57
                                      ++C+ Cg+C+  C 
  gi|298675970|ref|YP_003727720.1| 64 NNCNFCGKCADFCQ 77
                                      56666666666664 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.072
                           Fer4_17  1 rCiqCgyClpeCpsy 15
                                      +C+ Cg C++ C ++
  gi|298675970|ref|YP_003727720.1| 65 NCNFCGKCADFCQFN 79
                                      588888888888776 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.0003
                           Fer4_17  44 slCieCgeCerkCPqg 59 
                                        lC++Cg+C  +CP++
  gi|298675970|ref|YP_003727720.1|  93 TLCHGCGGCGIVCPMD 108
                                       68************97 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   3.8    0.0014       1.2       1      16 [.      63      78 ..      63      79 .. 0.88
   2 ?    8.0   1.8    0.0055       4.5       4      16 ..      95     107 ..      92     111 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0014
                            Fer4_4  1 qerCigCgsCvaaCPq 16
                                      +++C+ Cg+C ++C +
  gi|298675970|ref|YP_003727720.1| 63 KNNCNFCGKCADFCQF 78
                                      689***********65 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0055
                            Fer4_4   4 CigCgsCvaaCPq 16 
                                       C gCg C ++CP+
  gi|298675970|ref|YP_003727720.1|  95 CHGCGGCGIVCPM 107
                                       ************7 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.9   0.00047      0.39       3      20 ..      59      76 ..      57      78 .. 0.93
   2 ?    5.4   1.2     0.028        22       4      21 ..      90     106 ..      87     107 .. 0.82
   3 ?   -1.4   0.6         4   3.2e+03      18      22 .]     169     173 ..     169     173 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00047
                            Fer4_2  3 vvvdtdrCigCgaCvsaC 20
                                      +v+d ++C+ Cg+C + C
  gi|298675970|ref|YP_003727720.1| 59 PVIDKNNCNFCGKCADFC 76
                                      789*************** PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.028
                            Fer4_2   4 vvdtdrCigCgaCvsaCP 21 
                                        ++t  C gCg C  +CP
  gi|298675970|ref|YP_003727720.1|  90 LFNTL-CHGCGGCGIVCP 106
                                       56666.999****999*9 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 4
                            Fer4_2  18 saCPa 22 
                                       +aCPa
  gi|298675970|ref|YP_003727720.1| 169 TACPA 173
                                       79**8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.63u 0.35s 00:00:00.98 Elapsed: 00:00:00.56
# Mc/sec: 1503.76
//
Query:       gi|298675971|ref|YP_003727721.1|  [L=119]
Description: dinitrogenase iron-molybdenum cofactor biosynthesis protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-21   76.7   0.0    1.7e-21   76.3   0.0    1.1  1  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor


Domain annotation for each model (and alignments):
>> Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.3   0.0   9.6e-26   1.7e-21       3      93 ..      15     100 ..      14     102 .. 0.96

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 9.6e-26
                                       SCB-STCCC-SEEEEEEESSSCEEEEEEEE.GCCCTSSCSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTTTSEEE CS
                     Nitro_FeMo-Co   3 srvdqhFGrapyFaiyeveegevkivenrveeaadaegggggklaqllaeegvdvvivgkiGpralakleaagievy 79 
                                         +++hFGra y++++++++++v+++ n      +++ gg +k++++l+e+gv+v+++++iGp+a++ +e+  i+vy
  gi|298675971|ref|YP_003727721.1|  15 ASICEHFGRASYYTLVDTDTNTVEVLPNI-----GEHMGGTRKPPEILSESGVEVMLCSGIGPGAINMFENYCIDVY 86 
                                       579**************************.....9999*************************************** PP

                                       ES-SSBHHHHHHHH CS
                     Nitro_FeMo-Co  80 kgaggtveealkev 93 
                                       +ga+gtv++alk +
  gi|298675971|ref|YP_003727721.1|  87 VGAKGTVKDALKLW 100
                                       ***********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 821.93
//
Query:       gi|298675972|ref|YP_003727722.1|  [L=122]
Description: dinitrogenase iron-molybdenum cofactor biosynthesis protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-22   79.4   0.0    2.3e-22   79.1   0.0    1.1  1  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor


Domain annotation for each model (and alignments):
>> Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.1   0.0   1.3e-26   2.3e-22       2      94 ..      13     102 ..      12     103 .. 0.97

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 1.3e-26
                                       TSCB-STCCC-SEEEEEEESSSCEEEEEEEE.GCCCTSSCSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTTTSEE CS
                     Nitro_FeMo-Co   2 gsrvdqhFGrapyFaiyeveegevkivenrveeaadaegggggklaqllaeegvdvvivgkiGpralakleaagiev 78 
                                       ++ +d++FGr++y+++++ e+ e+++ en+     +a+gg+g+k+aq + ++++d++i+g++Gp+a+  l++a+i v
  gi|298675972|ref|YP_003727722.1|  13 DEPLDPRFGRSQYIVLADSESMEFEVFENP---GESAPGGAGIKAAQAIVDKDIDALITGNVGPNAFSVLSKANINV 86 
                                       6789**************************...******************************************** PP

                                       EES-SSBHHHHHHHHH CS
                     Nitro_FeMo-Co  79 ykgaggtveealkevl 94 
                                       y+ga+gt+++a+++++
  gi|298675972|ref|YP_003727722.1|  87 YTGASGTIRKAIDDFK 102
                                       ************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 820.04
//
Query:       gi|298675973|ref|YP_003727723.1|  [L=78]
Description: hypothetical protein Metev_2100 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-22   80.4   0.1    1.2e-22   80.3   0.1    1.0  1  DUF134        Protein of unknown function  DUF134
    2.4e-05   23.9   0.1    3.3e-05   23.5   0.1    1.2  1  Sigma70_r4_2  Sigma-70, region 4
     0.0003   20.3   0.3    0.00045   19.7   0.3    1.3  1  Sigma70_r4    Sigma-70, region 4
     0.0026   17.5   0.3     0.0059   16.4   0.0    1.7  2  HTH_10        HTH DNA binding domain
     0.0088   15.9   0.6     0.0099   15.8   0.6    1.1  1  Sigma70_ECF   ECF sigma factor
  ------ inclusion threshold ------
      0.014   15.7   0.2      0.017   15.4   0.2    1.2  1  KORA          TrfB plasmid transcriptional repressor
      0.015   15.2   0.0       0.02   14.8   0.0    1.3  1  HTH_11        HTH domain
      0.017   15.1   0.0      0.019   14.9   0.0    1.3  1  HTH_1         Bacterial regulatory helix-turn-helix protein, 
      0.019   14.8   0.0      0.025   14.4   0.0    1.3  1  HTH_23        Homeodomain-like domain
      0.019   15.0   0.2       0.03   14.4   0.2    1.4  1  HTH_3         Helix-turn-helix
      0.075   13.1   0.0       0.11   12.6   0.0    1.2  1  HTH_29        Winged helix-turn helix


Domain annotation for each model (and alignments):
>> DUF134  Protein of unknown function  DUF134
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.3   0.1   7.2e-26   1.2e-22      29      95 ..       5      71 ..       1      74 [. 0.94

  Alignments for each domain:
  == domain 1  score: 80.3 bits;  conditional E-value: 7.2e-26
                            DUF134 29 etgkvaisldeleairlvdyedlkqeeaaklmGiskatlwrlltearkkiakalveGraiilkGGey 95
                                      e + v ++++e+ea+rlvd e+++qeeaa++mGis++++w  +++ rkkia al +G+ai +kGG +
  gi|298675973|ref|YP_003727723.1|  5 ELEVVSLTVEEVEALRLVDLEEMQQEEAAQKMGISRRAFWEDIQNVRKKIAFALTNGKAIEIKGGTH 71
                                      456799***********************************************************76 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.1     2e-08   3.3e-05      10      54 .]      10      54 ..       7      54 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2e-08
                                      TS-HHHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHHH CS
                      Sigma70_r4_2 10 eLperqreifllryleglsykEIAellgisegtVksrlsRArkkL 54
                                      +L+ ++ e++ l +le++ ++E+A+++gis ++    ++  rkk+
  gi|298675973|ref|YP_003727723.1| 10 SLTVEEVEALRLVDLEEMQQEEAAQKMGISRRAFWEDIQNVRKKI 54
                                      67778889*************************999999999985 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.3   2.8e-07   0.00045       4      35 ..      10      41 ..       8      42 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.8e-07
                                      HS-HHHHHHHHHHHTTT--HHHHHHHHTS-HH CS
                        Sigma70_r4  4 sLpererevlelrfgeglTleEIgerlgiSre 35
                                      sL+ +e e l+l+ +e++ +eE ++++giSr 
  gi|298675973|ref|YP_003727723.1| 10 SLTVEEVEALRLVDLEEMQQEEAAQKMGISRR 41
                                      6888999***********************95 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       1.8   2.9e+03       1      10 [.      11      20 ..      11      21 .. 0.84
   2 !   16.4   0.0   3.6e-06    0.0059      27      52 ..      30      55 ..      25      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.8
                            HTH_10  1 LTdkqlevlk 10
                                      LT  ++e+l+
  gi|298675973|ref|YP_003727723.1| 11 LTVEEVEALR 20
                                      7889999998 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 3.6e-06
                            HTH_10 27 keLAkelGIskstlsehLrkaeskli 52
                                      +e A+++GIs+ +++e ++++ +k++
  gi|298675973|ref|YP_003727723.1| 30 EEAAQKMGISRRAFWEDIQNVRKKIA 55
                                      788*********************96 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.6   6.1e-06    0.0099     136     182 ..      11      57 ..       3      60 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.1e-06
                       Sigma70_ECF 136 ldpeqarlvelrkleGlsveEiAeklgvskrtverrlalaRawlere 182
                                       l +e  + + l  le +  eE+A+k+g+s+r+   + + +R++++ +
  gi|298675973|ref|YP_003727723.1|  11 LTVEEVEALRLVDLEEMQQEEAAQKMGISRRAFWEDIQNVRKKIAFA 57 
                                       4455555555666666789**********************998765 PP

>> KORA  TrfB plasmid transcriptional repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.2     1e-05     0.017      15      56 ..      10      51 ..       4      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1e-05
                              KORA 15 elaeqtveiargvLVegkkqadvatelgltkqavsqavkrvw 56
                                       l+ + ve+ r v  e+ +q++ a+++g++++a ++ +++v 
  gi|298675973|ref|YP_003727723.1| 10 SLTVEEVEALRLVDLEEMQQEEAAQKMGISRRAFWEDIQNVR 51
                                      5788999***************************99999985 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.2e-05      0.02      19      43 ..      30      54 ..      17      70 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.2e-05
                            HTH_11 19 eeLAeeLnvSrrtvrrdIkaLeelg 43
                                      ee A+++++Srr+ + dI+  +++ 
  gi|298675973|ref|YP_003727723.1| 30 EEAAQKMGISRRAFWEDIQNVRKKI 54
                                      6669***************998875 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.2e-05     0.019      17      46 ..      30      59 ..      14      76 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.2e-05
                                      HHHHHHHTS-HHHHHHHHHHHHHHHTS-SE CS
                             HTH_1 17 trAAeeLglsqpavsrqikrLEeelgvpLf 46
                                       +AA+++g+s  a +  i++ ++ +   L 
  gi|298675973|ref|YP_003727723.1| 30 EEAAQKMGISRRAFWEDIQNVRKKIAFALT 59
                                      68*******************999888775 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.6e-05     0.025       9      35 ..      17      44 ..      12      53 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.6e-05
                            HTH_23  9 rilllla.eGlsvreIAreLgvsrrTvy 35
                                      ++l+l++ e + ++e+A+++g+srr  +
  gi|298675973|ref|YP_003727723.1| 17 EALRLVDlEEMQQEEAAQKMGISRRAFW 44
                                      6889999559***************876 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.2   1.9e-05      0.03       4      24 ..      19      41 ..      16      42 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.9e-05
                                      HHH..HTTHHHHHHHHHHTSSHH CS
                             HTH_3  4 lRk..qlglsqeeLAeklGvsrs 24
                                      lR+     ++qee+A+k+G+sr+
  gi|298675973|ref|YP_003727723.1| 19 LRLvdLEEMQQEEAAQKMGISRR 41
                                      566667889************97 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.6e-05      0.11       3      29 ..      17      43 ..      16      44 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.6e-05
                            HTH_29  3 qallllaeGvstvsqiAkllglsrrtv 29
                                      +al+l++ ++++  ++A+ +g+srr +
  gi|298675973|ref|YP_003727723.1| 17 EALRLVDLEEMQQEEAAQKMGISRRAF 43
                                      69999999999*************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       914  (0.0509789); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 491.07
//
Query:       gi|298675974|ref|YP_003727724.1|  [L=297]
Description: ParA/MinD-like ATPase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-97  324.6   0.0    4.3e-97  324.4   0.0    1.0  1  ParA          NUBPL iron-transfer P-loop NTPase
    2.7e-14   53.3   0.0      4e-14   52.8   0.0    1.5  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
    1.4e-10   41.4   0.1    4.6e-09   36.4   0.1    2.2  1  AAA_31        AAA domain
    1.1e-08   34.7   0.0    1.6e-08   34.2   0.0    1.3  1  MipZ          ATPase MipZ
    2.8e-08   33.3   0.0    1.3e-07   31.1   0.0    1.9  2  ArsA_ATPase   Anion-transporting ATPase
    0.00023   21.0   0.2      0.065   13.1   0.1    2.2  2  AAA_26        AAA domain
    0.00061   19.6   0.0     0.0011   18.9   0.0    1.4  1  CLP1_P        mRNA cleavage and polyadenylation factor CLP1 P
    0.00065   18.8   0.6     0.0032   16.5   0.1    2.0  2  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
    0.00076   19.4   0.0     0.0013   18.7   0.0    1.4  1  APS_kinase    Adenylylsulphate kinase
    0.00092   18.7   0.0      0.013   15.0   0.1    2.1  2  Fer4_NifH     4Fe-4S iron sulfur cluster binding proteins, Ni
     0.0011   18.6   0.0       0.03   13.9   0.0    2.1  2  AAA_25        AAA domain
     0.0038   16.6   0.0     0.0055   16.0   0.0    1.2  1  VirC1         VirC1 protein
     0.0053   16.3   0.0      0.083   12.4   0.0    2.0  2  CBP_BcsQ      Cellulose biosynthesis protein BcsQ
     0.0077   16.2   0.2      0.013   15.4   0.2    1.3  1  RsgA_GTPase   RsgA GTPase
     0.0083   15.4   0.2      0.019   14.2   0.0    1.6  2  Zeta_toxin    Zeta toxin
     0.0087   15.7   0.0      0.014   15.0   0.0    1.3  1  SRP54         SRP54-type protein, GTPase domain
  ------ inclusion threshold ------
      0.011   15.6   0.0       0.02   14.8   0.0    1.4  1  MobB          Molybdopterin guanine dinucleotide synthesis pr
      0.012   14.8   0.3      0.024   13.8   0.3    1.4  1  NB-ARC        NB-ARC domain
      0.032   14.2   0.3      0.082   12.8   0.0    1.7  2  NTPase_1      NTPase
      0.056   13.8   0.0       0.15   12.5   0.0    1.8  1  RNA_helicase  RNA helicase
      0.064   13.8   0.0       0.12   13.0   0.0    1.4  1  AAA_18        AAA domain
      0.067   13.6   0.1       0.11   12.8   0.1    1.3  1  AAA_16        AAA ATPase domain
      0.093   12.5   0.0       0.17   11.6   0.0    1.4  1  IstB_IS21     IstB-like ATP binding protein
       0.11   12.4   0.2       0.17   11.8   0.2    1.2  1  NACHT         NACHT domain
       0.13   11.7   0.0        0.2   11.1   0.0    1.3  1  KTI12         Chromatin associated protein KTI12
       0.14   11.9   0.1       0.24   11.1   0.1    1.3  1  AAA_30        AAA domain
       0.14   12.6   0.1       0.24   11.9   0.1    1.4  1  ABC_tran      ABC transporter
       0.14   12.2   0.4       0.25   11.4   0.4    1.4  1  DUF87         Helicase HerA, central domain
        0.2   10.7   0.1       0.66    9.0   0.0    1.7  2  LpxK          Tetraacyldisaccharide-1-P 4'-kinase


Domain annotation for each model (and alignments):
>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  324.4   0.0    7e-100   4.3e-97       2     245 ..      40     285 ..      39     286 .. 0.99

  Alignments for each domain:
  == domain 1  score: 324.4 bits;  conditional E-value: 7e-100
                              ParA   2 vkkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPvea.kgikvmS 77 
                                       vk++i+++SgKGGVGKSt+a+ lA +Lak+g++vgllD Di+Gpsip+++g+e++kpe++ek+++Pv + +++kvmS
  gi|298675974|ref|YP_003727724.1|  40 VKNKIMIMSGKGGVGKSTIAAYLASSLAKRGYRVGLLDSDIHGPSIPKMFGLENKKPEVDEKGIVPVPVsENLKVMS 116
                                       99******************************************************************9899***** PP

                              ParA  78 igfllesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqkl.plagaviVttpqevaladv 153
                                       i+flle ed +v+wrGp k++aikq+l++v+wg lD+LiiDlPPGtgDe l++aq + + +ga++Vttpq+val+ v
  gi|298675974|ref|YP_003727724.1| 117 IAFLLEGEDFPVIWRGPAKMGAIKQFLQEVSWGVLDFLIIDLPPGTGDEPLSIAQLIsDFDGAIVVTTPQDVALTSV 193
                                       *********************************************************999***************** PP

                              ParA 154 kkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvlkep 230
                                       +k+i++++ v+v+v+G+veNmsg++cp+cg+++e+fg gg+ek+a+++g+++l+e+p++p++++++d+g ++ ++ +
  gi|298675974|ref|YP_003727724.1| 194 RKSINFLDLVDVPVIGLVENMSGVICPSCGDEIEVFGGGGVEKAASDFGISVLAELPIEPQVSQKADTGATYSYEGN 270
                                       ***************************************************************************** PP

                              ParA 231 eseaakaleeiaekv 245
                                       ese  + ++++++++
  gi|298675974|ref|YP_003727724.1| 271 ESEWDRRFSNVVDSI 285
                                       **********99876 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   0.0   6.5e-17     4e-14       1      55 [.      44     181 ..      44     291 .. 0.76

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 6.5e-17
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       i+i+s+kGGvGK+t+aa La +la+rg+rV l+D D  +++    +glen++ +                       
  gi|298675974|ref|YP_003727724.1|  44 IMIMSGKGGVGKSTIAAYLASSLAKRGYRVGLLDSDIHGPSIPKMFGLENKKPEvdekgivpvpvsenlkvmsiafl 120
                                       89***************************************999999999988888899999999998888888888 PP

                                       ............................................................C CS
                                       ............................................................x RF
                              CbiA  55 ............................................................d 55 
                                                                                                    
  gi|298675974|ref|YP_003727724.1| 121 legedfpviwrgpakmgaikqflqevswgvldfliidlppgtgdeplsiaqlisdfdgaiV 181
                                       8888888888888888877777777777777777777777777744444444443333330 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.1   7.4e-12   4.6e-09       3     167 ..      43     203 ..      41     209 .. 0.76

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 7.4e-12
                            AAA_31   3 vIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanatt.glgiekneiektlyevlieeknikeaiiktkv 78 
                                        I i+  KGGvGK+T +  la++lak+g++v l D D  + +    +g+e+++      ev  +ek i  + +   +
  gi|298675974|ref|YP_003727724.1|  43 KIMIMSGKGGVGKSTIAAYLASSLAKRGYRVGLLDSDIHGPSIPkMFGLENKK-----PEV--DEKGIVPVPV---S 109
                                       589999*******************************9987654144543332.....233..3444444444...7 PP

                            AAA_31  79 enldlipssidLaeaeielvelekk.eeilkellekvkde.YDyiiiDcpPsLg..lltenaLva.sdsviipvqae 150
                                       enl+++     L + +  ++        ++k++l++v+    D+ iiD pP  g   l +  L++  d  i+++ ++
  gi|298675974|ref|YP_003727724.1| 110 ENLKVMSIAFLLEGEDFPVIWRGPAkMGAIKQFLQEVSWGvLDFLIIDLPPGTGdePLSIAQLISdFDGAIVVTTPQ 186
                                       899999999999999998877666525567*******97659*********9974334444443314779******* PP

                            AAA_31 151 ayaleGleqllktieev 167
                                       + al  +++ +++++ v
  gi|298675974|ref|YP_003727724.1| 187 DVALTSVRKSINFLDLV 203
                                       ********999998876 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   2.6e-11   1.6e-08       3     113 ..      44     165 ..      42     194 .. 0.72

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 2.6e-11
                                       EEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHH..HHHHHHHHHHT-.......-----EEE-S CS
                              MipZ   3 ivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlaryl..enraataerkgl.......sLplpealal 70 
                                       i++   kGG Gkst+a ++a +L+k+G rv+ +d d+   ++ + +  en++  +++kg+       +L++ ++  l
  gi|298675974|ref|YP_003727724.1|  44 IMIMSGKGGVGKSTIAAYLASSLAKRGYRVGLLDSDIHGPSIPKMFglENKKPEVDEKGIvpvpvseNLKVMSIAFL 120
                                       667788************************************9985448**99999999832222222333333334 PP

                                       SS-HHHHTTS-HHHHHHHHHHHHHHHHH.H-SEEEEE--.SS--H CS
                              MipZ  71 seaeeaeveeeeeaevaeleelvadlea.eldfividtP.Gsdsa 113
                                        e+e   v     a++ ++++ +++++   ldf++id P G+ ++
  gi|298675974|ref|YP_003727724.1| 121 LEGEDFPVIWRGPAKMGAIKQFLQEVSWgVLDFLIIDLPpGTGDE 165
                                       445555555555566778888888887525799999986355444 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   2.1e-10   1.3e-07       2      68 ..      43     118 ..      42     128 .. 0.83
   2 ?   -0.5   0.0       0.9   5.6e+02     114     145 ..     140     173 ..     127     217 .. 0.58

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 2.1e-10
                                       EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S.TTTHHHHHHTS........--BSS-EEETSSEEEEE-- CS
                       ArsA_ATPase   2 kvilvgGKGGVGKttvsaatavklsekgkkvllistD.PAhslsDsfdq........klgkeptkvkeNLsavEid 68 
                                       k+++++GKGGVGK+t++a +a  l++ g++v l+  D   +s+  +f          + g  p  v+eNL ++ i 
  gi|298675974|ref|YP_003727724.1|  43 KIMIMSGKGGVGKSTIAAYLASSLAKRGYRVGLLDSDiHGPSIPKMFGLenkkpevdEKGIVPVPVSENLKVMSIA 118
                                       7999***************************999999457899999998666666655666777788999998885 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.9
                                       HHHHHHHHCSSSSEEEEESBS.CCH.TCGGGGHH CS
                       ArsA_ATPase 114 eellkyvkeeeydvvvlDtaP.TGh.tlrllslp 145
                                       +++l++v+    d +++D +P TG+  l + +l 
  gi|298675974|ref|YP_003727724.1| 140 KQFLQEVSWGVLDFLIIDLPPgTGDePLSIAQLI 173
                                       5566666666667777777775553134444444 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.1    0.0001     0.065       2      33 ..      43      74 ..      42      78 .. 0.94
   2 ?    6.0   0.0     0.015       9.4     132     196 ..     180     257 ..     161     259 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0001
                            AAA_26  2 tifvtgtdtgvGKTvvslgLvralkrkgvkvg 33
                                      +i++ +   gvGK+++++ L+++l ++g++vg
  gi|298675974|ref|YP_003727724.1| 43 KIMIMSGKGGVGKSTIAAYLASSLAKRGYRVG 74
                                      79****************************98 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.015
                            AAA_26 132 ilVargglgtinqllltiealrqknvrvlGvilNk..vrnp....e.......nvetlekksgipvlGvvPylpdle 195
                                       i+V+++++ +++ +  +i++l   +v+v+G++ N   v  p    e        ve++ + +gi vl+++P +p+++
  gi|298675974|ref|YP_003727724.1| 180 IVVTTPQDVALTSVRKSINFLDLVDVPVIGLVENMsgVICPscgdEievfgggGVEKAASDFGISVLAELPIEPQVS 256
                                       667777778888888888888888899999998763333334454166777779******************99987 PP

                            AAA_26 196 a 196
                                       +
  gi|298675974|ref|YP_003727724.1| 257 Q 257
                                       6 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.7e-06    0.0011       1      36 [.      49      84 ..      49     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.7e-06
                            CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqse 36
                                      G+  +GKST+a++L+  ++++g+++ ++D D+  ++
  gi|298675974|ref|YP_003727724.1| 49 GKGGVGKSTIAAYLASSLAKRGYRVGLLDSDIHGPS 84
                                      66789**************************97665 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   5.2e-06    0.0032      30      66 ..      43      79 ..      22      88 .. 0.84
   2 ?    0.2   0.0       0.5   3.1e+02     137     167 ..     205     235 ..     202     258 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.2e-06
                                      EEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                              MeaB 30 qvvGltGvPGaGkstlvealglelrrrGkrvavlavD 66
                                      + + + G  G+Gkst+   l+ +l++rG+rv++l  D
  gi|298675974|ref|YP_003727724.1| 43 KIMIMSGKGGVGKSTIAAYLASSLAKRGYRVGLLDSD 79
                                      55668999************************99755 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.5
                                       HHHHTT-SEEEEEEESSTTTTTTT--CCCHH CS
                              MeaB 137 vdvaevvdtfvvlllpeaGDelqgikkGile 167
                                       v v+ +v+ +  ++ p+ GDe+ ++  G +e
  gi|298675974|ref|YP_003727724.1| 205 VPVIGLVENMSGVICPSCGDEIEVFGGGGVE 235
                                       779999999999**********999877665 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0     2e-06    0.0013       3      40 ..      43      80 ..      41     109 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2e-06
                                      EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHH CS
                        APS_kinase  3 vvvwltGlsgsGKstianalekkLvekgisvylLdGdn 40
                                       ++ ++G  g GKstia  l+++L ++g++v lLd d 
  gi|298675974|ref|YP_003727724.1| 43 KIMIMSGKGGVGKSTIAAYLASSLAKRGYRVGLLDSDI 80
                                      57889******************************985 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1     2e-05     0.013       3      37 ..      45      79 ..      43     104 .. 0.85
   2 ?    1.3   0.0       0.3   1.8e+02     192     245 ..     233     286 ..     208     294 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2e-05
                         Fer4_NifH  3 iaiyGkGGiGksttsqnlsaalaemgkkvlivGCD 37
                                      + + GkGG+Gkst ++ l+++la++g +v ++  D
  gi|298675974|ref|YP_003727724.1| 45 MIMSGKGGVGKSTIAAYLASSLAKRGYRVGLLDSD 79
                                      5578***********************99776655 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.3
                         Fer4_NifH 192 liekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqakeyrelarkil 245
                                        +ek a++ g+ vl+ +P + +v ++     t     +ese    + ++ + i 
  gi|298675974|ref|YP_003727724.1| 233 GVEKAASDFGISVLAELPIEPQVSQKADTGATYSYEGNESEWDRRFSNVVDSIE 286
                                       478899999************999887777666655566666777888777775 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   4.9e-05      0.03      32      60 ..      41      70 ..      23      79 .. 0.88
   2 ?    2.5   0.0      0.16        97      51      96 ..     239     284 ..     229     295 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.9e-05
                            AAA_25 32 agelallaGapgtGKttlaldlalava.tG 60
                                      ++++ +  G +g+GK+t+a  la ++a +G
  gi|298675974|ref|YP_003727724.1| 41 KNKIMIMSGKGGVGKSTIAAYLASSLAkRG 70
                                      678899*******************99655 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.16
                            AAA_25  51 ldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgea 96 
                                       +d +++v+   p   +v  +  +   +s E++e+e+ rR++ v   
  gi|298675974|ref|YP_003727724.1| 239 SDFGISVLAELPIEPQVSQKADTGATYSYEGNESEWDRRFSNVVDS 284
                                       566667776666655666688888899*************988765 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     9e-06    0.0055       4      41 ..      44      81 ..      41      87 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9e-06
                             VirC1  4 itfcslkGGaGkttalmglcsalasdgkrvalfeaden 41
                                      i + s kGG Gk+t    l s+la +g rv+l+++d  
  gi|298675974|ref|YP_003727724.1| 44 IMIMSGKGGVGKSTIAAYLASSLAKRGYRVGLLDSDIH 81
                                      678899****************************9965 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00013     0.083       7      38 ..      48      78 ..      42      84 .. 0.86
   2 ?    1.6   0.0      0.26   1.6e+02     101     148 ..     135     186 ..     125     195 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                          CBP_BcsQ  7 qGvRGGvGttsllaaLawalhelgesvlviDl 38
                                      +G +GGvG+++++a La +l + g++v ++D 
  gi|298675974|ref|YP_003727724.1| 48 SG-KGGVGKSTIAAYLASSLAKRGYRVGLLDS 78
                                      44.8***********************99985 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.26
                          CBP_BcsQ 101 kaeallaalkelk.eqyrwillDlpagasa...ltrellaladlvllvvepd 148
                                       k +a++++l+e++ +  +++++Dlp g+ +      +l++  d  + v++p+
  gi|298675974|ref|YP_003727724.1| 135 KMGAIKQFLQEVSwGVLDFLIIDLPPGTGDeplSIAQLISDFDGAIVVTTPQ 186
                                       56788899999999999********977651113456666677778887775 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.2   2.2e-05     0.013      97     124 ..      40      67 ..      16      78 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.2e-05
                                       CTTSEEEEECSTTSSHHHHHHHHCTT-- CS
                       RsgA_GTPase  97 lkdktsvlvGqSGvGKStLinallpele 124
                                       +k+k++++ G+ GvGKSt+   l+++l 
  gi|298675974|ref|YP_003727724.1|  40 VKNKIMIMSGKGGVGKSTIAAYLASSLA 67 
                                       789*****************99998765 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   3.1e-05     0.019      15      67 ..      41      94 ..      33     100 .. 0.76
   2 ?   -2.5   0.0       4.3   2.6e+03     158     177 ..     273     292 ..     270     295 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.1e-05
                        Zeta_toxin 15 rPklillgGqpGAGKselaellkdelerqgnvv.rldpDdlRelhPeyeeilka 67
                                      + k+++++G  G GKs++a++l+ +l+++g  v  ld D   + +P+  +++++
  gi|298675974|ref|YP_003727724.1| 41 KNKIMIMSGKGGVGKSTIAAYLASSLAKRGYRVgLLDSDIHGPSIPKMFGLENK 94
                                      56899*********************9655544156777666777776666665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.3
                        Zeta_toxin 158 ehdeafeglresvealeeek 177
                                       e d+ f+++ +s+e+le+++
  gi|298675974|ref|YP_003727724.1| 273 EWDRRFSNVVDSIEKLENNT 292
                                       56888999999999999987 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.3e-05     0.014       2      39 ..      43      80 ..      42      84 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.3e-05
                                      EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                             SRP54  2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                      +++++ G  G+GK t +a La  l k+g++v l   D+
  gi|298675974|ref|YP_003727724.1| 43 KIMIMSGKGGVGKSTIAAYLASSLAKRGYRVGLLDSDI 80
                                      578999**************************998886 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   3.3e-05      0.02       2      40 ..      45      83 ..      44      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.3e-05
                              MobB  2 lgivgksgsGKTtLleklipelkarglrvgtiKhahhgf 40
                                      + + gk g GK t+   l + l++rg+rvg++  + hg 
  gi|298675974|ref|YP_003727724.1| 45 MIMSGKGGVGKSTIAAYLASSLAKRGYRVGLLDSDIHGP 83
                                      5678999*************************9999975 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3   3.9e-05     0.024      16      43 ..      38      65 ..      32      72 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.9e-05
                                      TTSCSEEEEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC 16 delqslvvalvGmgGvGKttlakqilnk 43
                                      d+++  ++ ++G+gGvGK+t+a+   ++
  gi|298675974|ref|YP_003727724.1| 38 DGVKNKIMIMSGKGGVGKSTIAAYLASS 65
                                      567778****************977665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00013     0.082       3      31 ..      46      74 ..      44      76 .. 0.93
   2 ?   -2.3   0.0       5.9   3.7e+03      79     109 ..     183     213 ..     178     218 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                                      EEE--TTSSHHHHHHHHHHHH...GGGEE CS
                          NTPase_1  3 fiTGppGvGKtTlvkkvlellkssgvkvg 31
                                      +++G+ GvGK+T+   +++ l+++g++vg
  gi|298675974|ref|YP_003727724.1| 46 IMSGKGGVGKSTIAAYLASSLAKRGYRVG 74
                                      789***********************996 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.9
                                       HHHHHHHHHHHHHHHHHH-EEEE---STTGG CS
                          NTPase_1  79 esfeelalealrkalseadviviDEiGkmEl 109
                                       +  +++al ++rk+++  d++ +  iG  E 
  gi|298675974|ref|YP_003727724.1| 183 TTPQDVALTSVRKSINFLDLVDVPVIGLVEN 213
                                       3445666777777776666666666666555 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00024      0.15       2      25 ..      46      69 ..      45      98 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00024
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkk 25
                                      +++G+ g+GKSt+a +La++l+k+
  gi|298675974|ref|YP_003727724.1| 46 IMSGKGGVGKSTIAAYLASSLAKR 69
                                      689*****************9976 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00019      0.12       4      27 ..      48      72 ..      45     108 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00019
                            AAA_18  4 tGtpGvGKttlakeLskrl.gfgvn 27
                                      +G+ GvGK+t+a +L+++l + g++
  gi|298675974|ref|YP_003727724.1| 48 SGKGGVGKSTIAAYLASSLaKRGYR 72
                                      7999***********9987444333 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   0.00018      0.11      25      54 ..      43      72 ..      32      88 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00018
                            AAA_16 25 elvllsGesGvGKsslvrellralekdggi 54
                                       +++ sG  GvGKs+++  l+ +l k+g  
  gi|298675974|ref|YP_003727724.1| 43 KIMIMSGKGGVGKSTIAAYLASSLAKRGYR 72
                                      678899******************999644 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00028      0.17      47      78 ..      42      73 ..      22      78 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00028
                         IstB_IS21 47 kenivllGpsGvGKshlaialgveavraglsv 78
                                      ++ +++ G  GvGKs +a+ l+ + +++g++v
  gi|298675974|ref|YP_003727724.1| 42 NKIMIMSGKGGVGKSTIAAYLASSLAKRGYRV 73
                                      5567899***********************98 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   0.00028      0.17       2      29 ..      44      71 ..      43      76 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00028
                                      CEEEEC-TTTCHHHHHHHHHHHHCTS-S CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawaegkl 29
                                      ++i+ G+ G+GK+t ++ la+ +a++ +
  gi|298675974|ref|YP_003727724.1| 44 IMIMSGKGGVGKSTIAAYLASSLAKRGY 71
                                      6899********************9875 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00032       0.2       4      40 ..      45      81 ..      43     110 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00032
                                      EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHH CS
                             KTI12  4 vvltGlPssGKstrakeLakaleeekrsvvviddesl 40
                                      ++++G   +GKst+a+ La+ l++++++v ++d++  
  gi|298675974|ref|YP_003727724.1| 45 MIMSGKGGVGKSTIAAYLASSLAKRGYRVGLLDSDIH 81
                                      6899999**********************99998765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00038      0.24      18      51 ..      42      75 ..      36      79 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00038
                            AAA_30 18 drvavltGpAGtGKttalkalreaweaaggrvig 51
                                      ++++++ G  G GK+t+ + l+  ++++g+rv +
  gi|298675974|ref|YP_003727724.1| 42 NKIMIMSGKGGVGKSTIAAYLASSLAKRGYRVGL 75
                                      6799**************************9965 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00039      0.24       4      39 ..      35      70 ..      32     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00039
                                      EEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  4 vslklkegekvaivGenGaGKStLlkllagllkpte 39
                                      v+l+  +++++ + G+ G GKSt+++ la  l +  
  gi|298675974|ref|YP_003727724.1| 35 VNLDGVKNKIMIMSGKGGVGKSTIAAYLASSLAKRG 70
                                      677777899999***************998876655 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.4   0.00041      0.25      30      59 ..      49      77 ..      20      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00041
                             DUF87 30 gsTGsGKSntvavLleellekkgatililD 59
                                      g+ G+GKS+ +a+L ++l+ k+g+++ +lD
  gi|298675974|ref|YP_003727724.1| 49 GKGGVGKSTIAAYLASSLA-KRGYRVGLLD 77
                                      788****************.9999888876 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0011      0.66      46      71 ..      51      76 ..      48      78 .. 0.95
   2 ?   -1.7   0.0         2   1.2e+03      95     107 ..     162     174 ..     159     202 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0011
                                      S-HSHHHHHHHHHHHTTTS..-EEEE CS
                              LpxK 46 GGtGKTPlvialvkllqarglkvgvl 71
                                      GG GK  ++++l+  l++rg++vg l
  gi|298675974|ref|YP_003727724.1| 51 GGVGKSTIAAYLASSLAKRGYRVGLL 76
                                      9**********************976 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2
                                       H-HHHHHHHHHST CS
                              LpxK  95 vGDEplllarrtg 107
                                       +GDEpl +a+ + 
  gi|298675974|ref|YP_003727724.1| 162 TGDEPLSIAQLIS 174
                                       6999999998543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                       113  (0.00630264); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2130.53
//
Query:       gi|298675975|ref|YP_003727725.1|  [L=233]
Description: hypothetical protein Metev_2102 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.9e-56  189.2   0.0      9e-56  189.1   0.0    1.0  1  DUF169    Uncharacterised ArCR, COG2043


Domain annotation for each model (and alignments):
>> DUF169  Uncharacterised ArCR, COG2043
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.1   0.0     5e-60     9e-56       1     205 [.       9     218 ..       9     219 .. 0.98

  Alignments for each domain:
  == domain 1  score: 189.1 bits;  conditional E-value: 5e-60
                            DUF169   1 kLaealrlktePVavkfsdekpelpekkekieekkrlCqmvalarakgktvvftaetlgCpgGaaalGfkelpeklk 77 
                                       kL ++l+l+ +PVav ++++++++p + e++++++r+Cqm ++ar ++ t ++t ++++C+gGaaa+G+++ p+klk
  gi|298675975|ref|YP_003727725.1|   9 KLVDLLNLTGKPVAVSLLKQEEDIPHGLEEVSNPERYCQMLQKARLNEITSFATIDKHACKGGAAAVGLQDYPDKLK 85 
                                       6999**************************9999******************************************* PP

                            DUF169  78 sg......egylkspeaakkfveslprleagevkyvvvapLekaefePdvvvffanpeqlmrLvqlalydrgggrln 148
                                       sg      +g+  s  +ak++v+++pr e+g++ ++v++pL+++   Pdv+++++n+  ++r++q++ y++gg r++
  gi|298675975|ref|YP_003727725.1|  86 SGklyvdkLGKEVSYSVAKRVVANMPRPEPGSTIATVISPLDNTATRPDVIIVIGNTLVARRIAQAIIYKHGG-RMT 161
                                       ******9888888*************99*******************************************99.*** PP

                            DUF169 149 vsfpgngaaCadivaypykegepniglgdpgarkfaklkddelafgiPyelleemve 205
                                       ++f+g++++Cad++  py +ge ni++g+ ga k+a+lkdde+++giP e le++v+
  gi|298675975|ref|YP_003727725.1| 162 ANFAGIQSTCADATGSPYITGEVNISIGCDGAAKNAGLKDDEMVVGIPEEILEDVVN 218
                                       *****************************************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1504.35
//
Query:       gi|298675976|ref|YP_003727726.1|  [L=303]
Description: methionine aminopeptidase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-38  131.4   0.0    4.1e-38  131.2   0.0    1.1  1  Peptidase_M24  Metallopeptidase family M24


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.2   0.0   2.3e-42   4.1e-38       2     209 .]      19     295 ..      18     295 .. 0.87

  Alignments for each domain:
  == domain 1  score: 131.2 bits;  conditional E-value: 2.3e-42
                                       HHHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBC..SSSB--TTEE CS
                     Peptidase_M24   2 lirkaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytp..ndrvlkegdl 76 
                                       ++  a++i s+a+e+ ++++k+g +  e+a+ +e+t + +  ++++afp  + ++ n++++h+tp  +d+++  +d+
  gi|298675976|ref|YP_003727726.1|  19 KYMDAGDILSKAREEGKKRVKKGEKLLEVADSVEQT-IVDL-GGQPAFP--CNISRNDEAAHATPsiDDDSVFGDDM 91 
                                       56789*****************************99.5554.5789***..9999**********7767778888** PP

                                       EEEEEEEEETTEEEEEEEEE.ECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSC CS
                     Peptidase_M24  77 vlidagaeydgyasDitrTv.lvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphg 152
                                       v++d+g+++dgy++D+++Tv l G  ++   +l++a ++a++ ai+ +k Gv+++ei++++++ ++ +g+ k++ ++
  gi|298675976|ref|YP_003727726.1|  92 VKLDMGVHLDGYIADSAVTVdLSG--NN---DLVKASEDALNSAIDVIKSGVNTAEIGRVIEDAITGYGF-KPVVNL 162
                                       ********************7777..33...6**************************************.****** PP

                                       SEEEESS.SSSEEEEEESS.STTCSSB--TTBEEEEEE...............EEEEETTT................ CS
                     Peptidase_M24 153 lGHgvGl.evhdegpsvsr.esndgrkleeGmvftiEp...............giyfapge................ 196
                                       +GHg+ +   h + ps+++ + ++g +l eG++++iEp               +                       
  gi|298675976|ref|YP_003727726.1| 163 TGHGLERyIAHAS-PSIPNrHVDQGIVLNEGDIIAIEPfatdgagkigngpwaE------Iyslidkksvrlpaark 232
                                       ******9788877.**96535669**************7777665444444443......04555556777788888 PP

                                       .................................................E.EEEEBEEEEEES CS
                     Peptidase_M24 197 .................................................g.gvriedtvlvte 209
                                                                                        g + + e+tv+vte
  gi|298675976|ref|YP_003727726.1| 233 lmkevekyrtlpfakrwlqsstksldfallqlekagairsypvlkeiegGlVSQAEHTVIVTE 295
                                       88888899999999999*******************************988**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2050.12
//
Query:       gi|298675977|ref|YP_003727727.1|  [L=386]
Description: peptidase M24 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-47  162.2   0.0    1.7e-47  161.9   0.0    1.2  1  Peptidase_M24  Metallopeptidase family M24


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.9   0.0   9.2e-52   1.7e-47       3     209 .]     150     371 ..     148     371 .. 0.89

  Alignments for each domain:
  == domain 1  score: 161.9 bits;  conditional E-value: 9.2e-52
                                       HHHHHHHHHHHHHHHHHHHHT.............TCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBC CS
                     Peptidase_M24   3 irkaariasaaleavleaikp.............gvterelaaeieattlkrhgarglafppivasgenaavlhytp 66 
                                       i+ +++++++a++ +++ i                 t++ + ++ie++ l + g++     +iva+g+ ++++h+  
  gi|298675977|ref|YP_003727727.1| 150 IETVQNACEEAMDTAVNLISNssesdgvlynegvELTSEYVRNAIEHR-LLDFGCEA--ETTIVACGKQSSTPHWMG 223
                                       667788888888888887775555555555443335899999999966.77766655..589*************99 PP

                                       SSSB--TTEEEEEEEEEEET..TEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHH CS
                     Peptidase_M24  67 ndrvlkegdlvlidagaeyd..gyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevle 141
                                        + +lk +++++id+ ++ +  +y sD++rTv+ G+++ + +++y+av eaq++a+++vkpGv ++ei++a+++v+e
  gi|298675977|ref|YP_003727727.1| 224 -EGTLKVNEPIIIDIFPRSKtnRYFSDMSRTVVKGTPSRQLKDMYDAVIEAQNKALELVKPGVLCNEIHNAVCDVFE 299
                                       .799*************99888*************9999************************************** PP

                                       HTTB.........CCGBSSCSEEEESSSSSEEEEEESSSTTCSSB--TTBEEEEEEEEEEETTTEEEEEBEEEEEES CS
                     Peptidase_M24 142 sagl.........akffphglGHgvGlevhdegpsvsresndgrkleeGmvftiEpgiyfapgeggvriedtvlvte 209
                                       ++g+         ++ f h++GHgvGlevh+  ps+    +++ +le G+v+t+Epg+y  p+ ggvried v+vte
  gi|298675977|ref|YP_003727727.1| 300 EKGYdtvrnnpklKSGFLHSTGHGVGLEVHEL-PSLG---DNENQLESGNVITVEPGLY-YPDIGGVRIEDIVVVTE 371
                                       *999999*99*999999*************98.**98...5699***************.99**************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.53
# Mc/sec: 2172.45
//
Query:       gi|298675978|ref|YP_003727728.1|  [L=78]
Description: hypothetical protein Metev_2105 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.011   15.9   0.3      0.012   15.7   0.3    1.1  1  Sld3_N    Sld3 N-terminal domain


Domain annotation for each model (and alignments):
>> Sld3_N  Sld3 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   0.3   6.7e-07     0.012      35      74 ..      20      63 ..       9      76 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.7e-07
                                      STTTS-TT-EEEEE....-SS-EEEEEE-STTEEE.EEEBSS-- CS
                            Sld3_N 35 elenspislKHllk...daddkyflLErYgkeywv.lWevvsvd 74
                                       le+++i  +H+ k   + +d+y++L  Y ++ w+ +W v s++
  gi|298675978|ref|YP_003727728.1| 20 YLEQNNIEFNHISKvlnEINDEYLMLDSYRQGVWIpKWVVESEK 63
                                      57999999***988774699***************779985554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       805  (0.0448993); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 595.58
//
Query:       gi|298675979|ref|YP_003727729.1|  [L=732]
Description: signal transduction histidine kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-41  140.2   0.0    1.2e-19   70.6   0.0    4.4  4  PAS_4            PAS fold
    2.8e-34  117.5  10.3    7.7e-12   45.4   0.2    5.4  6  PAS_9            PAS domain
    1.6e-30  105.0   7.6    3.2e-30  104.0   3.2    3.3  2  HisKA_2          Histidine kinase
    5.5e-30  103.7   0.0    1.2e-07   31.7   0.0    4.7  4  PAS              PAS fold
    8.4e-26   90.1   0.0    2.5e-15   56.5   0.0    5.0  4  PAS_3            PAS fold
    2.4e-12   46.6   0.0    0.00041   20.3   0.0    4.1  4  PAS_8            PAS domain
    1.1e-09   38.8   1.2    4.9e-09   36.7   0.4    2.5  2  HATPase_c        Histidine kinase-, DNA gyrase B-, and HSP90-
    4.3e-07   30.5   0.1    1.5e-06   28.8   0.1    2.0  1  HWE_HK           HWE histidine kinase
    1.3e-05   25.7   2.5      0.053   14.1   0.0    4.4  4  PAS_10           PAS domain
    0.00038   20.4   0.0    0.00086   19.3   0.0    1.5  1  HATPase_c_2      Histidine kinase-like ATPase domain
     0.0077   15.9   0.7      0.021   14.4   0.7    1.7  1  DUF572           Family of unknown function (DUF572)
  ------ inclusion threshold ------
      0.011   15.5   0.2      0.046   13.5   0.2    2.0  1  HATPase_c_3      Histidine kinase-, DNA gyrase B-, and HSP90-
       0.02   15.3   0.0         14    6.2   0.0    3.3  3  sCache_3_3       Single cache domain 3
      0.096   12.8   0.4         13    5.9   0.0    3.2  3  sCache_3_2       Single cache domain 3
       0.11   12.1   2.4       0.49   10.0   0.1    2.6  2  Phage_GPO        Phage capsid scaffolding protein (GPO) serin
       0.46    9.8   5.5          1    8.6   5.5    1.5  1  DUF3450          Protein of unknown function (DUF3450)
        1.8    7.8   6.6        2.5    7.3   0.1    3.0  3  Cache_3-Cache_2  Cache 3/Cache 2 fusion domain
        7.7    4.7   4.4         12    4.1   4.4    1.1  1  Atrophin-1       Atrophin-1 family


Domain annotation for each model (and alignments):
>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.08        80      25     107 ..      40     124 ..      19     127 .. 0.77
   2 !   28.7   0.0   1.2e-09   1.2e-06       2     109 ..     144     249 ..     143     250 .. 0.91
   3 !   70.6   0.0   1.2e-22   1.2e-19       1     110 []     266     377 ..     266     377 .. 0.97
   4 !   32.2   0.0     1e-10     1e-07       2     109 ..     394     500 ..     393     501 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.08
                             PAS_4  25 aelfgappeel.lGktlaellpeedaarleralrrvlegeepiefleelll..pgeerhyelrl..lPlrdesGevi 96 
                                        +++g+  e++ l+++l  ++p+ d +++ ++l+ +++  +p++  +   +  +ge r++ +    +++  +s +++
  gi|298675979|ref|YP_003727729.1|  40 KKILGVKKEQMsLDESLNIVHPD-DLPAVKADLQNAIDNYKPYSIKHRIICqdNGEIRYIKVYGkiTRF--DSTKPV 113
                                       55555555555234555545555.9999*******************9999***********9974554..59**** PP

                             PAS_4  97 gvlvisrDiTe 107
                                        + ++++D+T 
  gi|298675979|ref|YP_003727729.1| 114 KIHFTMQDVTK 124
                                       *********96 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 1.2e-09
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee..daarleralrrvlegeepiefleelllpg 76 
                                       ++l+da+++ld dg +l++N++ a  +g++ +ell  + a++  ++     +   ++++ +e ++ +++  + +++g
  gi|298675979|ref|YP_003727729.1| 144 NNLNDAVFILDIDGYILDINKTTANRLGYSKQELLSLHTADI--DClyNEINTKKQIQKIIENRQKVFESVHIKRNG 218
                                       799*************************************86..552234556789********************* PP

                             PAS_4  77 eerhyelrllPlrdesGevigvlvisrDiTerr 109
                                       +  ++e++ + + + +G+  ++l ++rDiTer+
  gi|298675979|ref|YP_003727729.1| 219 KKLPVEINSTFI-KYEGK-PAILSVARDITERK 249
                                       ************.68***.9************8 PP

  == domain 3  score: 70.6 bits;  conditional E-value: 1.2e-22
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll..p 75 
                                       l+s+p++++ +d  +++l +N a+++++  + e + Gkt+++l+pe  a+ ++++++ v+e +ep++ lee  +  +
  gi|298675979|ref|YP_003727729.1| 266 LSSTPALVYLKDNKLNYLTVNDAFCKVVDSTVENIKGKTDFDLFPEKEAEKYRSYDTSVMEAGEPVYNLEESYTtpE 342
                                       5799****************************************************************99988889* PP

                             PAS_4  76 geerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                       ge r+ +++++P  d +G vig+++ s DiTer++
  gi|298675979|ref|YP_003727729.1| 343 GEKRWALTSKVPYYDFEGNVIGIVGSSLDITERKQ 377
                                       *********************************85 PP

  == domain 4  score: 32.2 bits;  conditional E-value: 1e-10
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarle..ralrrvlegeepiefleelllpg 76 
                                       +s+++ +++ d +++++++N+aa +++g++  +++G++++ l+       ++  ++++++++++e+ e +    + +
  gi|298675979|ref|YP_003727729.1| 394 NSTSEQITYQDLNYNIIWCNKAAFDHLGLDYNDIIGMRCYKLWIGANVNTICenCPVEACIKTGEHSEGTM--GT-P 467
                                       6777788899*******************************999985555541157888888886665555..44.7 PP

                             PAS_4  77 eerhyelrllPlrdesGevigvlvisrDiTerr 109
                                       + r++ +++ P+rd++G +ig++ i+ DiTer+
  gi|298675979|ref|YP_003727729.1| 468 DFRVFHVSADPVRDSNGNIIGIIKILNDITERV 500
                                       89*****************************97 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.14   1.4e+02      16     104 .]      35     124 ..      27     124 .. 0.68
   2 !   45.4   0.2   7.7e-15   7.7e-12       2     104 .]     148     247 ..     147     247 .. 0.95
   3 !   36.3   0.0   5.2e-12   5.1e-09       6     104 .]     275     374 ..     270     374 .. 0.83
   4 !   35.3   0.2   1.1e-11   1.1e-08       8     104 .]     404     498 ..     398     498 .. 0.90
   5 ?   -3.0   0.1       8.8   8.8e+03      49      75 ..     527     551 ..     507     575 .. 0.53
   6 ?   -0.7   0.0       1.7   1.6e+03      60      79 ..     709     728 ..     640     732 .] 0.63

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.14
                             PAS_9  16 aNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwvlltaspvkdddg 90 
                                        +e+++++lG ++e++      +++  ++ p  + +l++a+++ +     +  ++  +nge  ++++     + d+ 
  gi|298675979|ref|YP_003727729.1|  35 LSEGWKKILGVKKEQMSLDESLNIVhpDDLPAVKADLQNAIDNYKPYS-IKHRIICQDNGEIRYIKVYGKITRFDST 110
                                       678889999988777433333333358888888999999999999333.3333344445777777899988888877 PP

                             PAS_9  91 elvgiivilrDite 104
                                       + v i ++++D+t+
  gi|298675979|ref|YP_003727729.1| 111 KPVKIHFTMQDVTK 124
                                       77778899999995 PP

  == domain 2  score: 45.4 bits;  conditional E-value: 7.7e-15
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgks...itdlfvtdpeanerlraaleqgrkkerevevvlirknget 75 
                                       d+++i + dg il++N++ ++ lGys++e+l  +   i++l+ ++ ++++ +++++e+ +   + +e v+i++ng++
  gi|298675979|ref|YP_003727729.1| 148 DAVFILDIDGYILDINKTTANRLGYSKQELLSLHtadIDCLY-NEINTKKQIQKIIENRQ---KVFESVHIKRNGKK 220
                                       7899999**********************9999988889999.9999**********999...************** PP

                             PAS_9  76 fwvlltaspvkdddgelvgiivilrDite 104
                                       ++v+++ + +k +++  ++  ++ rDite
  gi|298675979|ref|YP_003727729.1| 221 LPVEINSTFIKYEGKPAIL--SVARDITE 247
                                       *************999999..*******8 PP

  == domain 3  score: 36.3 bits;  conditional E-value: 5.2e-12
                             PAS_9   6 idnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk...kerevevvlirkngetfwvl 79 
                                       + +++ + l +N+a++++  ++ e + gk  +dlf  +++++e+ r +  +  +   ++++ e  +++++ge+ w+l
  gi|298675979|ref|YP_003727729.1| 275 LKDNKLNYLTVNDAFCKVVDSTVENIKGKTDFDLF--PEKEAEKYRSYDTSVMEagePVYNLEESYTTPEGEKRWAL 349
                                       4456667999*************************..44444444444444433566******************** PP

                             PAS_9  80 ltaspvkdddgelvgiivilrDite 104
                                        + +p +d +g+++gi++ + Dite
  gi|298675979|ref|YP_003727729.1| 350 TSKVPYYDFEGNVIGIVGSSLDITE 374
                                       *******99***************8 PP

  == domain 4  score: 35.3 bits;  conditional E-value: 1.1e-11
                             PAS_9   8 npdgrilyaNeaalrllGyspeevlgksitdlf....vtdpeanerlraaleqgrkkerevevvlirkngetfwvll 80 
                                       + + +i+++N+aa + lG + ++++g ++  l     v+   +n+ ++a++++g+    + e ++ +++ + f+  +
  gi|298675979|ref|YP_003727729.1| 404 DLNYNIIWCNKAAFDHLGLDYNDIIGMRCYKLWiganVNTICENCPVEACIKTGE----HSEGTMGTPDFRVFH--V 474
                                       56789**************************************************....555566666666666..* PP

                             PAS_9  81 taspvkdddgelvgiivilrDite 104
                                       +a pv+d++g+++gii il+Dite
  gi|298675979|ref|YP_003727729.1| 475 SADPVRDSNGNIIGIIKILNDITE 498
                                       ***********************8 PP

  == domain 5  score: -3.0 bits;  conditional E-value: 8.8
                             PAS_9  49 rlraaleqgrkkerevevvlirknget 75 
                                       + +++ ++ r   re e++++ kn+ +
  gi|298675979|ref|YP_003727729.1| 527 KTEQIKNAER--MRELELHHRVKNNLQ 551
                                       2222223333..555666666665533 PP

  == domain 6  score: -0.7 bits;  conditional E-value: 1.7
                             PAS_9  60 kerevevvlirkngetfwvl 79 
                                        + +++ +l ++ng++f ++
  gi|298675979|ref|YP_003727729.1| 709 DQLNGNFELDTSNGTKFIIE 728
                                       46667777777777777766 PP

>> HisKA_2  Histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.45   4.5e+02      46      69 ..     378     401 ..     372     406 .. 0.85
   2 !  104.0   3.2   3.2e-33   3.2e-30       1      75 [.     541     615 ..     541     616 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.45
                           HisKA_2  46 iheeLyksedletvdfseylekLv 69 
                                       ++e+Lykse+ ++v +++  e+++
  gi|298675979|ref|YP_003727729.1| 378 MYEKLYKSEKEKEVILNSTSEQIT 401
                                       79**********999998887776 PP

  == domain 2  score: 104.0 bits;  conditional E-value: 3.2e-33
                           HisKA_2   1 EihHRvkNnLqvisslLslqarkakdeevkealresqnRvlsialiheeLyksedletvdfseylekLvenlfks 75 
                                       E+hHRvkNnLqvisslLslq++k++deev ea++++qnRv s+al+he+Ly+++ le++d+++y+++Lv++l  +
  gi|298675979|ref|YP_003727729.1| 541 ELHHRVKNNLQVISSLLSLQSEKFDDEEVYEAFKDTQNRVVSMALVHEKLYRTNHLENIDLNDYVNDLVNHLKGL 615
                                       99*********************************************************************9865 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00021      0.21      14     113 .]      23     122 ..      12     122 .. 0.87
   2 !   26.5   0.0   5.1e-09   5.1e-06       6     113 .]     142     245 ..     137     245 .. 0.77
   3 !   31.7   0.0   1.2e-10   1.2e-07       4     111 ..     263     370 ..     260     372 .. 0.92
   4 !   28.2   0.0   1.5e-09   1.5e-06       3     113 .]     389     496 ..     387     496 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00021
                                       EEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEE CS
                               PAS  14 ifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda.elaelleqlleqgeesrageisfklrdgrpihl 89 
                                          +D  +++   ++ + ++lG + e+++    l  i+++dd   +++ l++++ + ++ +++ + ++  +g+++++
  gi|298675979|ref|YP_003727729.1|  23 SAEWDIEHDVATLSEGWKKILGVKKEQMSLDESLN-IVHPDDLpAVKADLQNAIDNYKPYSIKHRIICQDNGEIRYI 98 
                                       56799999*****************7666655554.555555569*******************99999******** PP

                                       EEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  90 evraspvrdaggeilgflgvlrdi 113
                                        v  + +r+ + ++  + ++++d+
  gi|298675979|ref|YP_003727729.1|  99 KVYGKITRFDSTKPVKIHFTMQDV 122
                                       **************9**9999997 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 5.1e-09
                                       HHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGG...GBSTTHHHHHHHHHHHHHHHTT-ECCCCEEE CS
                               PAS   6 ileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslld...liheeddaelaelleqlleqgeesrageisf 79 
                                       + ++l d++f++D dg il +N++++  lG+s +e+l+ +  d   l++e     +++++++ +e++++     + +
  gi|298675979|ref|YP_003727729.1| 142 LYNNLNDAVFILDIDGYILDINKTTANRLGYSKQELLSLHTADidcLYNEI---NTKKQIQKIIENRQKVFE-SVHI 214
                                       6899*************************************9543333333...366666666666555555.7778 PP

                                       ECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  80 klrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       k+ +g++ ++e++ + +  +g+ +  +l v+rdi
  gi|298675979|ref|YP_003727729.1| 215 KR-NGKKLPVEINSTFIKYEGK-P-AILSVARDI 245
                                       88.********99766555554.4.899988887 PP

  == domain 3  score: 31.7 bits;  conditional E-value: 1.2e-10
                                       HHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEE CS
                               PAS   4 raileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfk 80 
                                       +a+l+s+p+ + + D + + l vN+a+++    + e + gk+ +dl++e++ ++ ++  + ++e+ge+  + e s +
  gi|298675979|ref|YP_003727729.1| 263 KALLSSTPALVYLKDNKLNYLTVNDAFCKVVDSTVENIKGKTDFDLFPEKEAEKYRSYDTSVMEAGEPVYNLEESYT 339
                                       6899*******************************************998655555555789*************** PP

                                       CTTSSEEEEEEEEEEEEETTEEEEEEEEEEE CS
                               PAS  81 lrdgrpihlevraspvrdaggeilgflgvlr 111
                                       ++ g+++++++  +p++d +g+++g++g   
  gi|298675979|ref|YP_003727729.1| 340 TPEGEKRWALTSKVPYYDFEGNVIGIVGSSL 370
                                       **************************99655 PP

  == domain 4  score: 28.2 bits;  conditional E-value: 1.5e-09
                                       HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEE CS
                               PAS   3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisf 79 
                                        + il+s+ + i   D + +i+++N+aa + lGl+ ++++g   + l++       +  + +++ +  + ++ge+s+
  gi|298675979|ref|YP_003727729.1| 389 KEVILNSTSEQITYQDLNYNIIWCNKAAFDHLGLDYNDIIGMRCYKLWIGA----NVNTICENCPVEACIKTGEHSE 461
                                       577899999999999***********************************9....9999999999999999999999 PP

                                       EC.TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  80 kl.rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                        +     ++ ++v a pvrd  g+i+g++ +l+di
  gi|298675979|ref|YP_003727729.1| 462 GTmGTPDFRVFHVSADPVRDSNGNIIGIIKILNDI 496
                                       99544446899*********************998 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   0.0   2.5e-18   2.5e-15       3      86 ..      34     116 ..      32     119 .. 0.96
   2 !    7.5   0.0    0.0048       4.8       2      83 ..     160     237 ..     159     242 .. 0.77
   3 !   15.0   0.0   2.3e-05     0.023       2      87 ..     283     367 ..     282     369 .. 0.92
   4 ?    4.9   0.0     0.032        31      65      88 ..     469     492 ..     409     493 .. 0.70

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 2.5e-18
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrk.dGeyrwveararvirde 78 
                                       ++se +++ilG+ +e++  +  + l++vhp+D++ v+++lq+a+++ +py++ +Ri+++ +Ge+r+++ +++++r +
  gi|298675979|ref|YP_003727729.1|  34 TLSEGWKKILGVKKEQMSLD--ESLNIVHPDDLPAVKADLQNAIDNYKPYSIKHRIICQdNGEIRYIKVYGKITRFD 108
                                       689************99999..*************************************9***************** PP

                             PAS_3  79 ngkpvrvi 86 
                                       + kpv++ 
  gi|298675979|ref|YP_003727729.1| 109 STKPVKIH 116
                                       *****997 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0048
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvird 77 
                                       + ++++  + lGys++ell+   + +d+       ++++++q+++++++ ++e     ++++G+   ve   + i  
  gi|298675979|ref|YP_003727729.1| 160 LDINKTTANRLGYSKQELLSL--HTADIDCLYNEINTKKQIQKIIENRQkVFES--VHIKRNGKKLPVEINSTFI-K 231
                                       578999999************..5555555555559999999999999945444..4488999999999999999.7 PP

                             PAS_3  78 engkpv 83 
                                        +gkp 
  gi|298675979|ref|YP_003727729.1| 232 YEGKPA 237
                                       777775 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 2.3e-05
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvird 77 
                                       ++v+++++++++ + e ++gk  +  dl    + e++r+    +++ ge +y+ e  + ++ Ge rw  ++ ++++d
  gi|298675979|ref|YP_003727729.1| 283 LTVNDAFCKVVDSTVENIKGK--TDFDLFPEKEAEKYRSYDTSVMEAGEpVYNLEESYTTPEGEKRWALTSKVPYYD 357
                                       689******************..8889888888888888888888****999************************* PP

                             PAS_3  78 engkpvrvig 87 
                                        +g+++ ++g
  gi|298675979|ref|YP_003727729.1| 358 FEGNVIGIVG 367
                                       ********99 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.032
                             PAS_3  65 yrwveararvirdengkpvrvigv 88 
                                        r ++ +a ++rd+ng+++ +i++
  gi|298675979|ref|YP_003727729.1| 469 FRVFHVSADPVRDSNGNIIGIIKI 492
                                       577999999**********99987 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       5.9   5.8e+03      53      53 ..      36      36 ..      15      73 .. 0.56
   2 !   20.3   0.0   4.1e-07   0.00041       4      42 ..     140     179 ..     138     203 .. 0.77
   3 ?    4.5   0.0     0.038        38       5      36 ..     264     295 ..     262     324 .. 0.62
   4 !   16.4   0.0     7e-06     0.007      17      49 ..     403     436 ..     389     451 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.9
                             PAS_8 53 r 53
                                       
  gi|298675979|ref|YP_003727729.1| 36 S 36
                                      2 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 4.1e-07
                             PAS_8   4 ralfesspdgiavvd.lgdrivdvNqaalellGys.adlkg 42 
                                         l+++++d+++++d +g  i+d+N++++  lGys ++l+ 
  gi|298675979|ref|YP_003727729.1| 140 YYLYNNLNDAVFILDiDGY-ILDINKTTANRLGYSkQELLS 179
                                       5789***********8888.**************9766655 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.038
                             PAS_8   5 alfesspdgiavvdlgd..rivdvNqaalellGy 36 
                                       al+ s p  + + d  +  + + vN+a+++    
  gi|298675979|ref|YP_003727729.1| 264 ALLSSTPALVYLKD--NklNYLTVNDAFCKVVDS 295
                                       56677777777544..2347999******99872 PP

  == domain 4  score: 16.4 bits;  conditional E-value: 7e-06
                             PAS_8  17 vd.lgdrivdvNqaalellGys.adlkgellgqll 49 
                                        d +++ i+++N+aa + lG++ +d++g+ + +l+
  gi|298675979|ref|YP_003727729.1| 403 QDlNYN-IIWCNKAAFDHLGLDyNDIIGMRCYKLW 436
                                       454555.**********************997544 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       5.2   5.2e+03      36      54 ..     208     226 ..     185     256 .. 0.67
   2 !   36.7   0.4   4.9e-12   4.9e-09       8     107 ..     642     728 ..     636     731 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 5.2
                                       TEEEEEEEESSSSSTTHHH CS
                         HATPase_c  36 ddlvisveDnGiGipkedl 54 
                                       +  ++ ++ nG+ +p+e+ 
  gi|298675979|ref|YP_003727729.1| 208 VFESVHIKRNGKKLPVEIN 226
                                       5556788888888888654 PP

  == domain 2  score: 36.7 bits;  conditional E-value: 4.9e-12
                                       HHHHHHHHHHHHHHS...TTTEEEEEEEEEE.TEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHH CS
                         HATPase_c   8 qiisnlvdNavkfat...kageieveikase.ddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsi 80 
                                        +i+++v+N++k+a    ++ge++++++++e +++ + + DnG+Gi+++                  ++ + lGl +
  gi|298675979|ref|YP_003727729.1| 642 MLINEIVSNSLKYAFsedESGEVTIKLSQDEeGYNILIIADNGRGISENVNI---------------KESESLGLQL 703
                                       689**********44434777777777764479**************95555...............24778***** PP

                                       HHHHHHHTTTEEEEEEETTTEEEEEEE CS
                         HATPase_c  81 vkklvelmgGeiwvesepgrGttftft 107
                                       v++lv++++G+++++++   Gt+f+++
  gi|298675979|ref|YP_003727729.1| 704 VNSLVDQLNGNFELDTSN--GTKFIIE 728
                                       **************9999..***9985 PP

>> HWE_HK  HWE histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.1   1.5e-09   1.5e-06       1      69 [.     541     612 ..     541     624 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1.5e-09
                                       HHHHHHHHHHHHHHHHHHHHSSSXS-HH..HHHHHHHHHHHHHHHHHHHHHHCT.TS-EEHHHHHHHHHHHH CS
                            HWE_HK   1 ElnHRvKNlLavvqsiarqtlrsaesle..efaeklsgRLqALsaahdllsree.wagaeLaelleeelapy 69 
                                       El+HRvKN L v++s+ +  +++ ++ e  e+ ++ ++R+ +++ +h+ l r++  + ++L++ +++ +++ 
  gi|298675979|ref|YP_003727729.1| 541 ELHHRVKNNLQVISSLLSLQSEKFDDEEvyEAFKDTQNRVVSMALVHEKLYRTNhLENIDLNDYVNDLVNHL 612
                                       9****************999876555441155667789**********998876157788888877776665 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       1.5   1.5e+03      45      79 ..     191     219 ..     141     234 .. 0.63
   2 !    7.8   0.0     0.005         5      69     106 .]     335     373 ..     262     373 .. 0.67
   3 !   14.1   0.0   5.3e-05     0.053       3     106 .]     391     497 ..     390     497 .. 0.84
   4 ?   -1.6   0.2       4.3   4.2e+03      24      55 ..     509     540 ..     500     582 .. 0.59

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.5
                            PAS_10  45 dihpkkavknveeviealrtgekdevevvvpkngk 79 
                                       +i+        +++ + + +++k+ ++v++++ngk
  gi|298675979|ref|YP_003727729.1| 191 EIN------TKKQIQKIIENRQKVFESVHIKRNGK 219
                                       333......33333334444455555666666665 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.005
                            PAS_10  69 evevvvp.kngkwvlvrylpyrdedgeiaGvvetfvDit 106
                                       e+++  p  +++w l    py+d +g++ G+v   +Dit
  gi|298675979|ref|YP_003727729.1| 335 EESYTTPeGEKRWALTSKVPYYDFEGNVIGIVGSSLDIT 373
                                       33333335889***********************99997 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 5.3e-05
                            PAS_10   3 nlLnstpieltflDdnlqirrFtpaakklfklipad.vGrpladihpkkavknv.ee.viealrtgekdevevvvpk 76 
                                        +Lnst  ++t+ D n +i++ ++aa  ++ l  +d +G +  ++    +v+ + e+  +ea++++ ++ + ++ + 
  gi|298675979|ref|YP_003727729.1| 391 VILNSTSEQITYQDLNYNIIWCNKAAFDHLGLDYNDiIGMRCYKLWIGANVNTIcENcPVEACIKTGEHSEGTMGTP 467
                                       589*********************99888888766637*99999987766666633335688887777777777789 PP

                            PAS_10  77 ngkwvlvrylpyrdedgeiaGvvetfvDit 106
                                       + +++ v   p+rd +g+i G++ ++ Dit
  gi|298675979|ref|YP_003727729.1| 468 DFRVFHVSADPVRDSNGNIIGIIKILNDIT 497
                                       ****************************97 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 4.3
                            PAS_10  24 FtpaakklfklipadvGrpladihpkkavknv 55 
                                       ++++ +k+ +  ++ v ++ ++i++ +++ ++
  gi|298675979|ref|YP_003727729.1| 509 YSEQLEKINRELEKRVQDKTEQIKNAERMREL 540
                                       44444444444444444444444444444333 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   8.7e-07   0.00086      33     113 ..     641     712 ..     628     728 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 8.7e-07
                       HATPase_c_2  33 rlaveEactNavehayleapegpvevrlesdeealtv.evaDsGpgfdpetlpdpteeepkeslkegGrGlalikgl 108
                                        + ++E+++N  ++a  e+++g+v+++l++dee   +  +aD+G+g               + ++++ +Gl l+++l
  gi|298675979|ref|YP_003727729.1| 641 GMLINEIVSNSLKYAFSEDESGEVTIKLSQDEEGYNIlIIADNGRGISENV----------NIKESESLGLQLVNSL 707
                                       57799*****************************999459******87764..........6667788********* PP

                       HATPase_c_2 109 vDeve 113
                                       vD+++
  gi|298675979|ref|YP_003727729.1| 708 VDQLN 712
                                       **983 PP

>> DUF572  Family of unknown function (DUF572)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.7   2.1e-05     0.021     109     192 ..     497     577 ..     467     661 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.1e-05
                            DUF572 109 eeeeakreekekeeeeaedamkklEkrtkdskkemealesLeeLqelnqr.qakvdfdanlelrkefreekkereee 184
                                       +e+  +r++ +k +e+ e   ++lEkr++d++++++  e++ eL+ l+ r + +  + ++l  +++ + + +e  e 
  gi|298675979|ref|YP_003727729.1| 497 TERVKNRKKLKKYSEQLEKINRELEKRVQDKTEQIKNAERMRELE-LHHRvKNNLQVISSLLSLQSEKFDDEEVYE- 571
                                       34444556666666777777789**********************.555503333333333333322222222222. PP

                            DUF572 185 eedeealk 192
                                           ++++
  gi|298675979|ref|YP_003727729.1| 572 --AFKDTQ 577
                                       ..223333 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   4.6e-05     0.046       8      52 ..     645     695 ..     641     707 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.6e-05
                       HATPase_c_3   8 aelvdNsld.Adaen....vkievnknrgktgeivieDdGkGmsee.elkn 52 
                                        e+v Nsl  A +e     v+i+++++++  + + i D+G G+se+ ++k+
  gi|298675979|ref|YP_003727729.1| 645 NEIVSNSLKyAFSEDesgeVTIKLSQDEEGYNILIIADNGRGISENvNIKE 695
                                       69999*9997444446677********9989999***********977775 PP

>> sCache_3_3  Single cache domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.033        32      69     105 ..     344     380 ..     314     382 .. 0.79
   2 ?    6.2   0.0     0.014        14      73      93 ..     472     492 ..     438     505 .. 0.69
   3 ?   -1.5   0.0       3.5   3.4e+03      76      93 ..     569     586 ..     562     595 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.033
                        sCache_3_3  69 lgkkyltaYePlkdadgkviGmlfvGlpeeevqalik 105
                                         ++ lt  +P +d +g+viG++  +l+++e +++++
  gi|298675979|ref|YP_003727729.1| 344 EKRWALTSKVPYYDFEGNVIGIVGSSLDITERKQMYE 380
                                       4578888999******************999999876 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.014
                        sCache_3_3  73 yltaYePlkdadgkviGmlfv 93 
                                       +    +P++d++g++iG++ +
  gi|298675979|ref|YP_003727729.1| 472 FHVSADPVRDSNGNIIGIIKI 492
                                       555678***********9866 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 3.5
                        sCache_3_3  76 aYePlkdadgkviGmlfv 93 
                                       +Ye  kd +++v+ m  v
  gi|298675979|ref|YP_003727729.1| 569 VYEAFKDTQNRVVSMALV 586
                                       688889999999988776 PP

>> sCache_3_2  Single cache domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.08        80      85     122 ..     329     366 ..     233     382 .. 0.83
   2 ?    5.9   0.0     0.013        13      89     124 ..     456     492 ..     449     500 .. 0.77
   3 ?   -2.0   0.3       3.7   3.6e+03       6      43 ..     516     553 ..     513     562 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.08
                        sCache_3_2  85 aalkagrayvgtvtgtlgpslrvklPvfdadgrviGiv 122
                                       + +   ++ + t  g +  +l+ k+P+ d +g viGiv
  gi|298675979|ref|YP_003727729.1| 329 EPVYNLEESYTTPEGEKRWALTSKVPYYDFEGNVIGIV 366
                                       44455555555566667778999*************98 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.013
                        sCache_3_2  89 agrayvgtvtgtlgpslrvk.lPvfdadgrviGivsv 124
                                        g++  gt+ + + ++++v   Pv+d++g +iGi+ +
  gi|298675979|ref|YP_003727729.1| 456 TGEHSEGTMGTPDFRVFHVSaDPVRDSNGNIIGIIKI 492
                                       5666666665556677777526************987 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 3.7
                        sCache_3_2   6 laealeeralalatsvagsrivrvaltdrapesglqal 43 
                                       + ++le+r+++ +++++ +++ r++    + +++lq +
  gi|298675979|ref|YP_003727729.1| 516 INRELEKRVQDKTEQIKNAERMRELELHHRVKNNLQVI 553
                                       67788888888888888888887776666666666655 PP

>> Phage_GPO  Phage capsid scaffolding protein (GPO) serine peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00049      0.49      78     107 ..     188     217 ..     176     220 .. 0.92
   2 ?    0.8   0.5      0.31   3.1e+02     196     223 ..     506     533 ..     475     595 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00049
                         Phage_GPO  78 LyaeidptddLvalnkkrqKvytSieinpk 107
                                       Ly ei+  +++ ++ ++rqKv+ S+ i+ +
  gi|298675979|ref|YP_003727729.1| 188 LYNEINTKKQIQKIIENRQKVFESVHIKRN 217
                                       9*************************9865 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.31
                         Phage_GPO 196 fadveeavelvAeevkelsekveallal 223
                                        ++ +e +e++ +e+++  ++ +++ ++
  gi|298675979|ref|YP_003727729.1| 506 LKKYSEQLEKINRELEKRVQDKTEQIKN 533
                                       2222222222222222211111111111 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   5.5     0.001         1      50      96 ..     493     539 ..     491     542 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.001
                           DUF3450  50 laeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeier 96 
                                       l+++++  +  ++l++y eqle++ +++e+++++ +eqi+++e++++
  gi|298675979|ref|YP_003727729.1| 493 LNDITERVKNRKKLKKYSEQLEKINRELEKRVQDKTEQIKNAERMRE 539
                                       667777788999********************************985 PP

>> Cache_3-Cache_2  Cache 3/Cache 2 fusion domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       4.1   4.1e+03     151     174 ..     346     367 ..     344     380 .. 0.78
   2 ?    7.3   0.1    0.0025       2.5     158     187 ..     477     505 ..     472     511 .. 0.84
   3 ?    1.9   1.5      0.11   1.1e+02       6      51 ..     514     559 ..     509     587 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4.1
                   Cache_3-Cache_2 151 kwYvTaYePikdadgkViGilyVg 174
                                       +w +T   P  d +g+ViGi+  g
  gi|298675979|ref|YP_003727729.1| 346 RWALTSKVPYYDFEGNVIGIV--G 367
                                       578888899999999***998..3 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0025
                   Cache_3-Cache_2 158 ePikdadgkViGilyVgvdqsealkslrke 187
                                       +P++d++g++iGi+ +  d++e +k+ rk+
  gi|298675979|ref|YP_003727729.1| 477 DPVRDSNGNIIGIIKILNDITERVKN-RKK 505
                                       7*******************998876.444 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.11
                   Cache_3-Cache_2   6 eevnklieeelekevedlaetletqdellrekverdlnvfakllsn 51 
                                       e++n++ e++++ ++e++++  ++++  l+ +v+++l+v+++lls 
  gi|298675979|ref|YP_003727729.1| 514 EKINRELEKRVQDKTEQIKNAERMRELELHHRVKNNLQVISSLLSL 559
                                       57899999**********************************9987 PP

>> Atrophin-1  Atrophin-1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   4.4     0.012        12     574     612 ..     504     542 ..     499     561 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.012
                        Atrophin-1 574 klakkreealekakreaeqkareekerekerekererer 612
                                       k  kk  e lek++re e++ +++ e+ k+ e+ re e 
  gi|298675979|ref|YP_003727729.1| 504 KKLKKYSEQLEKINRELEKRVQDKTEQIKNAERMRELEL 542
                                       667999******************999998888887664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (732 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2140  (0.11936); expected 358.6 (0.02)
Passed bias filter:                      656  (0.0365888); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.80u 0.32s 00:00:01.12 Elapsed: 00:00:00.49
# Mc/sec: 4467.00
//
Query:       gi|298675980|ref|YP_003727730.1|  [L=481]
Description: hypothetical protein Metev_2107 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-69  234.0   0.0    3.1e-69  232.6   0.0    1.6  2  tRNA_deacylase  D-aminoacyl-tRNA deacylase
  ------ inclusion threshold ------
       0.43    9.9   5.9       0.53    9.6   0.5    2.6  3  CPV_Polyhedrin  Cypovirus polyhedrin


Domain annotation for each model (and alignments):
>> tRNA_deacylase  D-aminoacyl-tRNA deacylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  232.6   0.0   3.4e-73   3.1e-69       7     204 ..      92     287 ..      87     288 .. 0.98
   2 ?   -2.4   0.0      0.31   2.8e+03     174     202 ..     339     370 ..     326     373 .. 0.65

  Alignments for each domain:
  == domain 1  score: 232.6 bits;  conditional E-value: 3.4e-73
                                       EEEEEEEEE-TT---EEEEE--B-SS--TTSS-TT-B--B-HHHHHHHHHHHHGGGGGSTT-EEEE--S-SS----- CS
                    tRNA_deacylase   7 liiflSrHssesgkplLTvHvtGnlgeaelGGkpeelapaaPrllkallralkkiaekleefevtlEatHHGPtelk 83 
                                       l+if+S+H+s++g +lLT+H+tGn+g+a++GG+p++la+aaP +++a+l+++kk + ++ +++v++EatHHGP+elk
  gi|298675980|ref|YP_003727730.1|  92 LLIFASKHRSKDGYKLLTAHFTGNTGTADYGGNPKQLAVAAPYAMRAILTEIKKQS-ENLDYDVSMEATHHGPSELK 167
                                       78******************************************************.999***************** PP

                                       S-EEEEEEEESHHHHT-HHHHHHHHHHHHHHHH------EEEEEE-S-TT-HHHHHHHHHBSEEEEEEE-GGGGGG- CS
                    tRNA_deacylase  84 vPslFvEiGSteeeWkdedaaeavaeavlelleseeekekvlvgiGGgHYaprftklvletevavGhilskyaleel 160
                                       +Ps++vEiGSt+++Wkd++ ++++a+a+l++  ++ ++++v++g+GGgHYa+r++kl++et  ++Ghi+++y+le++
  gi|298675980|ref|YP_003727730.1| 168 TPSVYVEIGSTQRQWKDSEPGRIIADAILSVDFDKCKHCPVALGFGGGHYAKRQSKLLFETYTTFGHIIPDYQLENV 244
                                       *******************************99999***************************************** PP

                                       -HHHHHHHHHHH.T-SEEEE-TTT--HHHHHHHHHHHHHHT-EE CS
                    tRNA_deacylase 161 keevikqaleksegadvalidkkslkseqkeaieelleelgiev 204
                                       + ++++qa++ks + d++++d+ks++++++++i ++++ l+++v
  gi|298675980|ref|YP_003727730.1| 245 DMDIVRQAINKS-SPDFVYFDRKSMSTKERNRIMDIVKPLEMDV 287
                                       ************.************************9998876 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.31
                                       T-SEEEE-TTT--HHH...HHHHHHHHHHHT- CS
                    tRNA_deacylase 174 gadvalidkkslkseq...keaieelleelgi 202
                                        +++a+id++ lk+++   +++i+++l++++i
  gi|298675980|ref|YP_003727730.1| 339 PVEAAIIDENLLKETEkisRDQIIKYLQNQEI 370
                                       67888899876666551115777777777766 PP

>> CPV_Polyhedrin  Cypovirus polyhedrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       0.2   1.8e+03     128     166 ..      36      72 ..      22      78 .. 0.58
   2 ?    9.6   0.5   5.9e-05      0.53     161     232 ..     312     382 ..     308     388 .. 0.74
   3 ?    2.0   0.2     0.012   1.1e+02     188     226 ..     390     427 ..     387     434 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.2
                                       -SSSSGGG--SS-TT-EEGGGSEE-SSSEEEEEEE--SS CS
                    CPV_Polyhedrin 128 lthkDWrearawsPeaikgnqlkkvgalsrflyvpldeq 166
                                       lt + W++ +   P+ ++++ +  + + ++f +v+ld +
  gi|298675980|ref|YP_003727730.1|  36 LTLNNWQQIK--HPKELENSGVSSIYESGNFRIVELDMH 72 
                                       4444554443..366666666666666666666666554 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 5.9e-05
                                       EE--SSSEEEEEEEB--B.TTB-TTSTTTHHHHHHH---EE--EEE-SHHHHHHHHHHHT--EE-TTS-EEE- CS
                    CPV_Polyhedrin 161 vpldeqetlkvvlpaksd.galnrynsrtiaqvitenivkknviyltgErdvidymkakklaYidsaavivsk 232
                                       ++l+ +  lk++   k+  ++ n  + +  a +i en+ k++ +      ++i y++++++aY+++a++ +++
  gi|298675980|ref|YP_003727730.1| 312 MSLCPDSNLKLTDRFKNRlKTINTSDLPVEAAIIDENLLKETEKIS--RDQIIKYLQNQEIAYVENANSTLAN 382
                                       5666666666665555432556666666778899999999887664..569****************998877 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.012
                                       THHHHHHH---EE--EEE-SHHHHHHHHHHHT--EE-TT CS
                    CPV_Polyhedrin 188 tiaqvitenivkknviyltgErdvidymkakklaYidsa 226
                                       +  ++i +n+v++ +  ++     i+y  + ++ Yi+++
  gi|298675980|ref|YP_003727730.1| 390 QEVKTIANNLVRQCINFIEKKH-EIEYSPEGNILYIVNK 427
                                       55789******99988777655.59**********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       859  (0.0479112); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 3374.80
//
Query:       gi|298675981|ref|YP_003727731.1|  [L=367]
Description: cell division protein FtsZ [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-41  141.5   0.4    5.4e-41  141.0   0.4    1.3  1  Tubulin         Tubulin/FtsZ family, GTPase domain
    1.2e-33  115.3   0.6    3.4e-33  113.8   0.6    1.9  1  FtsZ_C          FtsZ family, C-terminal domain
    0.00086   19.2   0.1     0.0025   17.7   0.1    1.7  1  NAD_binding_10  NAD(P)H-binding
  ------ inclusion threshold ------
      0.077   13.3   0.4       0.25   11.7   0.4    1.9  1  CENP-X          CENP-S associating Centromere protein X
        4.6    6.3   7.9         23    4.0   7.8    2.1  1  Tubulin_2       Tubulin like


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.0   0.4   1.5e-44   5.4e-41       1     196 [.      42     202 ..      42     203 .. 0.98

  Alignments for each domain:
  == domain 1  score: 141.0 bits;  conditional E-value: 1.5e-44
                                       EEEEEEEHHHHHHHHHHHHH...HHHCH....HHHT.....TTEEEEE....EEESBHHHHHTS-GS......EEEE CS
                           Tubulin   1 eiivigvGqcGnqignelwellakehgiqsdgdslesfFsesgkveyiprsvaidtdpqvlneikagselfnpnkll 77 
                                       +i+vig+G++G++ + ++ +    e gi             +g +e++    a++td+q+l +++a+      nk+l
  gi|298675981|ref|YP_003727731.1|  42 NIKVIGCGGGGSNSIARMLD----E-GI-------------QG-AELL----ALNTDAQHLLNTNAD------NKIL 89 
                                       699*****************....8.**.............88.8999....***************......**** PP

                                       --CCCCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEE CS
                           Tubulin  78 lgkegagnngaggypevgkeaaeeileeirkevekcdslqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvv 154
                                       +gk++++++gag+ p++g+ aa e+ ee+ ++v+++d+   +fita+lgGGTG+G +pv++e++++   +al+++vv
  gi|298675981|ref|YP_003727731.1|  90 IGKKKTKGLGAGSLPQIGEDAALESVEELNQTVQGSDM---VFITAGLGGGTGTGSAPVVAEAARDA--GALTIAVV 161
                                       **************************************...**************************..******** PP

                                       EE--GG.G-HHHHHHHHHHHHHHHHT-SEEEEEEHHHHHCCS CS
                           Tubulin 155 vlPsefsevvvepynailalkelieesdavividNdaLlkil 196
                                        lP++  e+ v+  na+ +l++l++ +d+viv++Nd+Ll+++
  gi|298675981|ref|YP_003727731.1| 162 SLPFGV-EGEVRRTNAEAGLERLRDVADTVIVVPNDKLLEVV 202
                                       ******.*******************************9986 PP

>> FtsZ_C  FtsZ family, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.8   0.6   9.6e-37   3.4e-33       1      95 []     250     344 ..     250     344 .. 0.99

  Alignments for each domain:
  == domain 1  score: 113.8 bits;  conditional E-value: 9.6e-37
                                       EEEEEEEEEEESTTHHHHHHHHHHTSGGGT--GGG-SEEEEEEEE-TT--HHHHHHHHHHHHHHS-TTSEEEEEEEE CS
                            FtsZ_C   1 GvAmmgvGeasgedraeeaaeaaisspLLdvdlsgAkgvlvnitggsdltlkEveevaetireevdeeanvivGavi 77 
                                       GvAm+g+Ge+++e+++ e++++a++spLLd+d+sgA+++lvn+ gg+d+t++E+e+v++++++++d++a++i+Ga++
  gi|298675981|ref|YP_003727731.1| 250 GVAMIGLGESDDENKGVESVQKALRSPLLDLDISGATSALVNVVGGQDMTVSEAESVVQEVYNRIDPSARLIWGAQV 326
                                       99*************************************************************************** PP

                                       -TT--SEEEEEEEEES-X CS
                            FtsZ_C  78 deeledeirvtvvatglk 95 
                                       d+ele+++r+++v+tg+k
  gi|298675981|ref|YP_003727731.1| 327 DPELEQTVRTMIVVTGVK 344
                                       ****************96 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1     7e-07    0.0025      46     108 ..     110     174 ..     102     191 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 7e-07
                                       --TT-CCHHHHHHTT-SEEEES---TCCHHHH.HHHHHHHHHHCT--EEEEEEE.TTTTSGCGCH CS
                    NAD_binding_10  46 gdvtdvedlaealkgadaVvsalggggkdeeg.aknivdaakeagvkRfvlvsa.igvgdevpge 108
                                       + +++ve+l ++++g d V++++g gg++ +g a  +++aa+ ag   + +vs  +gv+ ev ++
  gi|298675981|ref|YP_003727731.1| 110 AALESVEELNQTVQGSDMVFITAGLGGGTGTGsAPVVAEAARDAGALTIAVVSLpFGVEGEVRRT 174
                                       66899*****************98777755555999999*************9867888776654 PP

>> CENP-X  CENP-S associating Centromere protein X
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.4   6.9e-05      0.25      31      69 ..       1      37 [.       1      41 [. 0.64

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.9e-05
                                      HHHHHHHHHHHHHHHHHHTT-SE.....EEC.HHHHHHCH CS
                            CENP-X 31 lklFvrEavaRaaeeaeeegkeeseksklev.edLekiap 69
                                      ++  v+Ea+aR+a+e++++ ++ +e+   +v   Le+++ 
  gi|298675981|ref|YP_003727731.1|  1 MDSIVEEAMARSAQEERTNPNNPEEN---DVnAELEEMLN 37
                                      6778**********888765555333...33334555544 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   7.8    0.0064        23     132     181 ..     115     151 ..      27     164 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0064
                         Tubulin_2 132 leeirealrdaikrlrgsage.eeglnvfVvgSLaGGTGSGiflDvayllr 181
                                       +ee ++              + +++  vf+  +L GGTG G++  va   r
  gi|298675981|ref|YP_003727731.1| 115 VEELNQ--------------TvQGSDMVFITAGLGGGTGTGSAPVVAEAAR 151
                                       222222..............2244478**************9987766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 2809.86
//
Query:       gi|298675982|ref|YP_003727732.1|  [L=69]
Description: protein translocase SEC61 complex subunit gamma [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-05   23.4   0.1    4.2e-05   23.4   0.1    1.1  1  SecE      SecE/Sec61-gamma subunits of protein translocation 


Domain annotation for each model (and alignments):
>> SecE  SecE/Sec61-gamma subunits of protein translocation complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.1   2.3e-09   4.2e-05       5      49 ..      20      64 ..      16      69 .] 0.88

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2.3e-09
                                      HHHHHHHHCCCCCHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SecE  5 kevkaElkKVtWPtrkEllkttvvVlvfvvimglflflvDlvfsk 49
                                      +   + +k   +P+r+E+l +++v  ++++  g+++f++  +++ 
  gi|298675982|ref|YP_003727732.1| 20 RSYLRVMKLTKKPSRDEFLMIAKVAGAGILAAGFVGFVIYILMTE 64
                                      666789*********************************888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 461.98
//
Query:       gi|298675983|ref|YP_003727733.1|  [L=157]
Description: NusG antitermination factor [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.9e-24   83.1   0.2    1.5e-23   82.5   0.2    1.3  1  Spt5-NGN  Early transcription elongation factor of RNA pol II
    1.6e-06   27.8   1.1    3.5e-05   23.6   0.2    2.7  2  KOW       KOW motif


Domain annotation for each model (and alignments):
>> Spt5-NGN  Early transcription elongation factor of RNA pol II, NGN section
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.5   0.2   1.7e-27   1.5e-23       2      84 .]      11      89 ..      10      89 .. 0.97

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 1.7e-27
                          Spt5-NGN  2 iwavkctagqErevalslmkkilelakkenleIkSvfapdelkGyiyvEAdrkaaveralegipnvrgvvqglvpikEv 80
                                      i+ vk+ta+qEr+va ++++      +k +l+I++v+apdelkGy++vEA ++a ve+a++ +p+++++v+g+++i+E+
  gi|298675983|ref|YP_003727733.1| 11 IFVVKTTANQERSVANMVAQV----TRKDKLDIRAVIAPDELKGYVLVEALDSATVEQAIQRVPHAKALVKGQSSIDEI 85
                                      9*****************888....67888************************************************* PP

                          Spt5-NGN 81 edll 84
                                      +++l
  gi|298675983|ref|YP_003727733.1| 86 THFL 89
                                      **98 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.2   3.9e-09   3.5e-05       2      32 .]     101     131 ..     100     131 .. 0.89
   2 ?    2.1   0.0     0.023   2.1e+02       1       8 [.     144     151 ..     144     156 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3.9e-09
                                       TSEEEESSSTTTTCEEEEEEEETTTTEEEEE CS
                               KOW   2 GdhVkVvsGphkGktGkVvkvdqhkvrVfvd 32 
                                       G + +++sGp+kG++++V++vd+  + ++v+
  gi|298675983|ref|YP_003727733.1| 101 GTIIEITSGPFKGEKARVKRVDEGHEEITVE 131
                                       67789*****************998888876 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.023
                                       TTSEEEES CS
                               KOW   1 pGdhVkVv 8  
                                       +Gd+V+V+
  gi|298675983|ref|YP_003727733.1| 144 RGDTVRVL 151
                                       59999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 980.67
//
Query:       gi|298675984|ref|YP_003727734.1|  [L=159]
Description: 50S ribosomal protein L11 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-24   85.4   2.5    1.8e-24   85.3   1.2    1.7  2  Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain
    3.6e-18   65.8   0.5      6e-18   65.1   0.1    1.5  2  Ribosomal_L11    Ribosomal protein L11, RNA binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.3   1.2     2e-28   1.8e-24       5      64 ..       2      61 ..       1      62 [. 0.96
   2 ?   -2.0   0.0      0.38   3.4e+03      44      59 ..     119     134 ..     115     138 .. 0.69

  Alignments for each domain:
  == domain 1  score: 85.3 bits;  conditional E-value: 2e-28
                   Ribosomal_L11_N  5 vkvvklrvpaGkAtpaPplGpaLGplGlnikkfckefnkaTkdkkglripVkitvyqdrs 64
                                      ++vv+  vp+GkAtp+PplGpaLGplG+nik+++ ++n++Tk+++g+ +pVk+ v +d++
  gi|298675984|ref|YP_003727734.1|  2 TNVVEALVPGGKATPGPPLGPALGPLGINIKDVIAQINEKTKEYNGMDVPVKVIVDDDKN 61
                                      7899***************************************************99985 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.38
                   Ribosomal_L11_N  44 aTkdkkglripVkitv 59 
                                       a k+  g+ +p  +tv
  gi|298675984|ref|YP_003727734.1| 119 AMKEIVGTCVPIGVTV 134
                                       5566678888888888 PP

>> Ribosomal_L11  Ribosomal protein L11, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.93   8.3e+03      38      47 ..      35      44 ..      31      58 .. 0.53
   2 !   65.1   0.1   6.7e-22     6e-18       2      70 .]      68     134 ..      67     134 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.93
                                      HHHHHGGGHT CS
                     Ribosomal_L11 38 IAkiKksdln 47
                                      IA+i  + ++
  gi|298675984|ref|YP_003727734.1| 35 IAQINEKTKE 44
                                      6666555444 PP

  == domain 2  score: 65.1 bits;  conditional E-value: 6.7e-22
                                       --SHHHHHHHHHTXSSXXSSTTTSXXEEEEHHHHHHHHHHHGGGHTXS.SHHHHHHHHHHHHCTTTEEE CS
                     Ribosomal_L11   2 tPptsylLkkaagiekgsgkpgketvGtvslkqvyeIAkiKksdlnaalsleaavksilgtArsmGikV 70 
                                       tPpts+l++k++giekg+g +  ++vG++s++q+++I + K++d  ++ s+++a+k+i+gt+  +G++V
  gi|298675984|ref|YP_003727734.1|  68 TPPTSALIMKEVGIEKGTGDT-YNVVGNLSMDQIMKITRLKREDVLSY-SFKNAMKEIVGTCVPIGVTV 134
                                       9*******************6.688*****************999999.******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1115.97
//
Query:       gi|298675985|ref|YP_003727735.1|  [L=213]
Description: 50S ribosomal protein L1 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-49  168.6   0.0    1.8e-49  168.3   0.0    1.0  1  Ribosomal_L1  Ribosomal protein L1p/L10e family


Domain annotation for each model (and alignments):
>> Ribosomal_L1  Ribosomal protein L1p/L10e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.3   0.0   9.8e-54   1.8e-49       5     203 ..      18     207 ..      13     208 .. 0.95

  Alignments for each domain:
  == domain 1  score: 168.3 bits;  conditional E-value: 9.8e-54
                                       S-SSS--EEEEEEEESSS-TTSGGG--EEEEE-STSTSSCS-EEEEE-HHHHH...HHHHTT..-SEEETCHHHHHH CS
                      Ribosomal_L1   5 akkkfdesveialnlttkkpkkadqrkpgkipLphplgkevkiclitkdpqaeyakeakeagriakviglkklkkky 81 
                                        +++f esv++a+nl++++  k+ +r+ ++i+Lph+lgk+ ++c+++k++      +ak+ag  + v + +++ +  
  gi|298675985|ref|YP_003727735.1|  18 PNRNFPESVDLAINLKNLDLSKPHNRVDKEISLPHGLGKSRNVCVFAKGEVGL---KAKDAG-AKYVFSDEDIDDLA 90 
                                       3779*************************************************...9*****.77788999999999 PP

                                       T-HHHHHHTCCH-SEEEEEGGGHHHHHHHCHHHHGGGT-S-ECC..CT.BTS-HHHHHHHHCTTEEEEE-TTTSEEE CS
                      Ribosomal_L1  82 ksfeakrkllkefdlfladdrimpllpklLGkvfgkrkkmPipvltkgtvkedvkkevekalkstvvvrldkgtcls 158
                                       +++++ ++l+ke+dlf+a+ ++mp+++k+LG v+g+r+kmP+p   +   ++dv++ +++a + tv vr++++ +++
  gi|298675985|ref|YP_003727735.1|  91 SDKKRAKSLAKECDLFIAEAQYMPTIGKALGTVLGPRGKMPTPL--T--PNKDVSELIKSAQN-TVHVRSKDNPSFH 162
                                       999999**************************************..3..4789********99.************* PP

                                       EEEEETTSSHHHHHHHHHHHHHHHHHTSTTTSGSEEEEEEEETTS CS
                      Ribosomal_L1 159 vkvGklsftaeelaeNieavvkalvekvpkkwkniksiylkttms 203
                                       v vG+ + ++++la+Ni+av++ ++++++k+ +n++s+y++ttm+
  gi|298675985|ref|YP_003727735.1| 163 VSVGQRNEEPDKLADNIDAVISGVENSLEKGRQNLRSVYVTTTMG 207
                                       ********************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1633.66
//
Query:       gi|298675986|ref|YP_003727736.1|  [L=346]
Description: 50S ribosomal protein L10 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-25   89.8   0.2    2.1e-25   88.8   0.1    1.6  2  Ribosomal_L10  Ribosomal protein L10
    2.4e-19   69.1   0.0    6.1e-19   67.8   0.0    1.7  1  RL10P_insert   Insertion domain in 60S ribosomal protein L10P
    9.8e-08   32.5   2.4    2.3e-07   31.3   2.4    1.7  1  Ribosomal_60s  60s Acidic ribosomal protein
  ------ inclusion threshold ------
        2.6    6.8   7.3        2.3    7.0   0.0    2.2  2  HSP90          Hsp90 protein


Domain annotation for each model (and alignments):
>> Ribosomal_L10  Ribosomal protein L10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.8   0.1   4.6e-29   2.1e-25       3      98 ..      15     110 ..      13     112 .. 0.96
   2 ?   -3.8   0.0       3.2   1.4e+04      54      68 ..     300     314 ..     298     321 .. 0.78

  Alignments for each domain:
  == domain 1  score: 88.8 bits;  conditional E-value: 4.6e-29
                                       CCCHCCCCCCCCCCCTTSSEEEEEE-TTS-HHHHHHCCCHHHHHGCEEEEESCCCCCCCCHCCTSS..SSCGCCSSS CS
                     Ribosomal_L10   3 kekKeelvkelkellkkyksvvvvdyegltvaqlqelRkklrengaelkvvKntlmrrAleetgeee.klkellkgp 78 
                                       +++K+e v+++k+l+++y+ + +v+++g++++qlq +R++l++  a lkv +ntl+ rAle++g  + +l++++  +
  gi|298675986|ref|YP_003727736.1|  15 PQWKIEEVEDIKNLIQSYSLFGIVSISGIPAKQLQVMRRELKDI-AVLKVSRNTLVTRALEKAGGTAkDLEDYVDAQ 90 
                                       79*****************************************9.********************9866******** PP

                                       EEEEEESS-TCHHHHCCCCC CS
                     Ribosomal_L10  79 valvftnedpvalakvleef 98 
                                       ++l+ftne+p++++k+le+ 
  gi|298675986|ref|YP_003727736.1|  91 IGLIFTNENPFKIYKILEKS 110
                                       *****************986 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 3.2
                                       SCCCCCCCCHCCTSS CS
                     Ribosomal_L10  54 KntlmrrAleetgee 68 
                                       K tl++ A  +++ e
  gi|298675986|ref|YP_003727736.1| 300 KQTLTSAATSKQETE 314
                                       889999998887765 PP

>> RL10P_insert  Insertion domain in 60S ribosomal protein L10P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.8   0.0   1.4e-22   6.1e-19       2      71 .]     117     186 ..     117     186 .. 0.99

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 1.4e-22
                      RL10P_insert   2 raGtiAtedviipagplelaPgsiepeLrklglptklkkGkivleedylvckkGetltseqaqlLklLgi 71 
                                       ++G+iA++d+++++g ++  Pg+i+  L+++g+p+ ++ Gk+ ++e ++v+++G++++++ a++L++L+i
  gi|298675986|ref|YP_003727736.1| 117 KPGAIAPKDIVVEEGATGFPPGPIIGDLQSVGIPAAIDSGKVSISETTTVAREGDKVSQKLAAMLNRLEI 186
                                       89******************************************************************98 PP

>> Ribosomal_60s  60s Acidic ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   2.4   5.2e-11   2.3e-07       1      88 []     237     345 ..     237     345 .. 0.88

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 5.2e-11
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...................XXXXXXXXXXX CS
                     Ribosomal_60s   1 eptaenikkvlkaagveveaarvkllvkalegkdieellangaakla...................aaaaaaaaaaa 58 
                                       +ptaeni++++++     ea  + + ++ +e + ++  l++++++++                   +  ++aa + +
  gi|298675986|ref|YP_003727736.1| 237 YPTAENITTLISKGVS--EARNLGVNATIIEPQLMDTHLSKAYSQMLsvaqivydkdenavdddlkQTLTSAATSKQ 311
                                       69**********9999..9999999999******************9*******************88888888888 PP

                                       XXXXXXXXXXXXXXXXX.XX--S...S--.STTT CS
                     Ribosomal_60s  59 aaaaaaaaeekkkeeeeeEeedd...dmG.fgLF 88 
                                       + ++ +  ee+ ke eeeEe+++   ++G ++LF
  gi|298675986|ref|YP_003727736.1| 312 ETESGPTTEEETKESEEEEESEEesgMAGlGSLF 345
                                       8889999999888888887887746666666776 PP

>> HSP90  Hsp90 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0   0.00052       2.3     166     227 ..      24      86 ..      20     104 .. 0.87
   2 ?    0.4   4.4     0.052   2.3e+02      13      61 ..     275     332 ..     268     339 .. 0.43

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00052
                                       XXTTSSXGGGTTXEEEEEESSSX...SSSTHHHHHTCHHHHHHHHHHHHHHHHHHHTSXHHH..H CS
                             HSP90 166 efedllPkyLsFvkGvvdsddLP...LNvsREtlqqnkilkvikkklvrKvlemlkklaeekeey 227
                                       ++++l+ +y  F  G+v    +P   L v R  l++ ++lkv +++lv+++le     a++ e+y
  gi|298675986|ref|YP_003727736.1|  24 DIKNLIQSYSLF--GIVSISGIPakqLQVMRRELKDIAVLKVSRNTLVTRALEKAGGTAKDLEDY 86 
                                       677778888666..99999999988899*************************988888877776 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.052
                                       HHCCTTSSS-EEEEEEEEXXXXXXXXXXXXXXXXXX.........XXXXXXXXXXXXX CS
                             HSP90  13 kkySeFinfpiyllkekeeekeveeeeeeeeeeeee.........eeeeakveeeeee 61 
                                       k yS+ ++    ++ + e+ ++ + +++ +++++++         eee ++ eeeee+
  gi|298675986|ref|YP_003727736.1| 275 KAYSQMLSVAQIVYDKDENAVDDDLKQTLTSAATSKqetesgpttEEETKESEEEEES 332
                                       6677777777666666666666553322222222211222233222222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1229  (0.0685482); expected 358.6 (0.02)
Passed bias filter:                      695  (0.038764); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 2169.72
//
Query:       gi|298675987|ref|YP_003727737.1|  [L=106]
Description: 50S ribosomal protein 60S [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.8e-19   68.7  16.2    5.7e-19   68.5  16.2    1.1  1  Ribosomal_60s  60s Acidic ribosomal protein
     0.0056   17.0   0.0     0.0096   16.2   0.0    1.4  1  EF-hand_14     EF-hand domain
  ------ inclusion threshold ------
       0.01   15.5   0.6      0.018   14.8   0.6    1.4  1  DUF348         G5-linked-Ubiquitin-like domain
      0.018   15.2   0.0      0.018   15.2   0.0    1.7  2  PhetRS_B1      Phe-tRNA synthetase beta subunit B1 domain
      0.047   13.9   0.0      0.067   13.5   0.0    1.2  1  HTH_Tnp_Tc3_2  Transposase
      0.095   12.9   0.3       0.11   12.7   0.3    1.4  1  HD             HD domain
        5.3    7.2   6.4        9.2    6.4   6.4    1.4  1  DUF4632        Domain of unknown function (DUF4632)


Domain annotation for each model (and alignments):
>> Ribosomal_60s  60s Acidic ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.5  16.2   2.2e-22   5.7e-19       2      88 .]      17     105 ..      16     105 .. 0.84

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 2.2e-22
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XX CS
                     Ribosomal_60s   2 ptaenikkvlkaagveveaarvkllvkalegkdieellangaaklaaaaaaaaaaaaaaaaaaaaeekkkeeeeeEe 78 
                                       +t++++k+vl aag+ev++arvk+lv+ale++diee+++++a ++ aa++++ +++  +aa++ a+e+k+eeee Ee
  gi|298675987|ref|YP_003727737.1|  17 ITEDTVKNVLDAAGIEVDDARVKALVAALEDVDIEEAMSQAAFAAPAAGGSSPSGESGGAAEESAAEEKEEEEE-EE 92 
                                       9****************************************877667777777777777777777777777776.57 PP

                                       --S..S--.STTT CS
                     Ribosomal_60s  79 edd..dmG.fgLF 88 
                                       +++  ++G ++LF
  gi|298675987|ref|YP_003727737.1|  93 SEEsgMAGlGALF 105
                                       7777899999999 PP

>> EF-hand_14  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.7e-06    0.0096      12      53 ..      12      53 ..       2      62 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.7e-06
                        EF-hand_14 12 eetdklsvakllkaLaetGirkdDpRLkellkklkkvekeks 53
                                      +  +++   +  ++L ++Gi+ dD R+k l+ +l++v+ e++
  gi|298675987|ref|YP_003727737.1| 12 NAGKDITEDTVKNVLDAAGIEVDDARVKALVAALEDVDIEEA 53
                                      5556778889999***********************998764 PP

>> DUF348  G5-linked-Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.6   6.8e-06     0.018      15      32 ..      18      35 ..      17      50 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.8e-06
                                      --SSHHHHHHHTT----T CS
                            DUF348 15 aadTVgdlLeeagitlge 32
                                      ++dTV+ +L++agi++++
  gi|298675987|ref|YP_003727737.1| 18 TEDTVKNVLDAAGIEVDD 35
                                      89*************876 PP

>> PhetRS_B1  Phe-tRNA synthetase beta subunit B1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0     7e-06     0.018       7      41 ..       5      39 ..       3      61 .. 0.84
   2 ?   -2.5   0.8       2.4   6.2e+03      45      48 ..      87      90 ..      77      98 .. 0.45

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7e-06
                         PhetRS_B1  7 kkeaLfkalgkelteeeledllfefGlElDeivee 41
                                       ++ L+++ gk++te+ ++++l   G+E+D++  +
  gi|298675987|ref|YP_003727737.1|  5 YAALLLHNAGKDITEDTVKNVLDAAGIEVDDARVK 39
                                      56789999***********************8765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.4
                         PhetRS_B1 45 kkad 48
                                      ++++
  gi|298675987|ref|YP_003727737.1| 87 EEEE 90
                                      1111 PP

>> HTH_Tnp_Tc3_2  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.6e-05     0.067      23      55 ..      10      42 ..       6      45 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.6e-05
                     HTH_Tnp_Tc3_2 23 lkeeGksvsreTirrrLrkaglkkrkprkkplL 55
                                      l+++Gk +   T++++L +ag+    +r k l+
  gi|298675987|ref|YP_003727737.1| 10 LHNAGKDITEDTVKNVLDAAGIEVDDARVKALV 42
                                      6788*******************9999998775 PP

>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   4.5e-05      0.11      26      76 ..       2      52 ..       1      99 [. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.5e-05
                                      HHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHH CS
                                HD 26 ellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgl 76
                                      e +++a LlH+ Gk+ ++d+  +  + ++++++ + v a ++  +  + ++
  gi|298675987|ref|YP_003727737.1|  2 EYIYAALLLHNAGKDITEDTVKNVLDAAGIEVDDARVKALVAALEDVDIEE 52
                                      6799**************977776666788787777777665555555444 PP

>> DUF4632  Domain of unknown function (DUF4632)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   6.4    0.0036       9.2       2      24 ..      74      96 ..      67     104 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0036
                           DUF4632  2 Gspakesgdadgeadeeeesekg 24
                                      G  a+es+ +++e++eeeese+ 
  gi|298675987|ref|YP_003727737.1| 74 GGAAEESAAEEKEEEEEEESEES 96
                                      67899999999999999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       979  (0.0546043); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 746.66
//
Query:       gi|298675988|ref|YP_003727738.1|  [L=141]
Description: histidine triad (HIT) protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.5e-30  103.8   0.0    8.2e-30  103.4   0.0    1.1  1  HIT       HIT domain
    2.1e-15   57.2   0.0    2.6e-15   56.9   0.0    1.2  1  DcpS_C    Scavenger mRNA decapping enzyme C-term binding
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.017   15.1   0.0    1.2  1  DUF1441   Protein of unknown function (DUF1441)
       0.03   14.2   0.1      0.053   13.4   0.1    1.4  1  CwfJ_C_1  Protein similar to CwfJ C-terminus 1


Domain annotation for each model (and alignments):
>> HIT  HIT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.4   0.0   1.8e-33   8.2e-30       2      97 ..      15     110 ..      14     111 .. 0.98

  Alignments for each domain:
  == domain 1  score: 103.4 bits;  conditional E-value: 1.8e-33
                                       GCC-CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEES CS
                               HIT   2 keipstvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinng 78 
                                       +eips +vyed+ v+afldi p + gh+L++pkkh+++++++++e+ a +++ v+k+ak ++k ++++g ++  nng
  gi|298675988|ref|YP_003727738.1|  15 GEIPSSKVYEDESVYAFLDIAPSSIGHTLIMPKKHIENFNEMSPEDAASFFKSVNKIAKGVEKGVSADGSNIGLNNG 91 
                                       79*************************************************************************** PP

                                       GGGT-SSSS-EEEEEEC-T CS
                               HIT  79 ahagqsvahlHiHviprre 97 
                                         agq+v+h+HiH+ipr+e
  gi|298675988|ref|YP_003727738.1|  92 TVAGQEVPHVHIHLIPRYE 110
                                       *****************97 PP

>> DcpS_C  Scavenger mRNA decapping enzyme C-term binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   0.0   5.8e-19   2.6e-15       2     106 ..       7     111 ..       6     122 .. 0.91

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 5.8e-19
                                       -HHHHHHTTSS-B-EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T.- CS
                            DcpS_C   2 wvfnilakgkepervvyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekyne.v 77 
                                       ++f+++++g++p++ vyede++ ++ Di p +  h l++pk++i++ +++++e+     + ++k+ k +e+  ++ +
  gi|298675988|ref|YP_003727738.1|   7 CLFCKIISGEIPSSKVYEDESVYAFLDIAPSSIGHTLIMPKKHIENFNEMSPEDAASFFKSVNKIAKGVEKGVSAdG 83 
                                       99*******************************************************************99886677 PP

                                       EEEEE--SCCCT--S-S--EEEEE..... CS
                            DcpS_C  78 daeelrvgvhyqPsvyhlHlHvisldfes 106
                                           l+ g  + + v h+H+H+i  ++es
  gi|298675988|ref|YP_003727738.1|  84 SNIGLNNGTVAGQEVPHVHIHLIP-RYES 111
                                       77789999**************97.5554 PP

>> DUF1441  Protein of unknown function (DUF1441)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   3.8e-06     0.017      27      78 ..      18      70 ..      10      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.8e-06
                           DUF1441 27 paagsnkknkvYaltdviaall.elevsaekeeadpdkltPkdRrawfdsEke 78
                                      p++   +++ vYa+ d+++  + ++ ++++k+ ++ ++++P+d   +f+s ++
  gi|298675988|ref|YP_003727738.1| 18 PSSKVYEDESVYAFLDIAPSSIgHTLIMPKKHIENFNEMSPEDAASFFKSVNK 70
                                      6666778999************55556677888899*************9775 PP

>> CwfJ_C_1  Protein similar to CwfJ C-terminus 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.2e-05     0.053      33     108 ..      26     107 ..       2     114 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.2e-05
                                       SSEEEE---S-SSTT-EEEEESS--SSTTSS-H....HHHHHHHHHHHHHHHHHHHTT--EEEEEE-..SSS----- CS
                          CwfJ_C_1  33 nkvYlalpkgpLssgHvliipieHisallslde....evldeirkfrkalvkmykkqdkdavvfEis..sersvHla 103
                                       ++vY+ l   p s gH li+p +Hi++  +++        ++++k  k++ k  ++ ++++ +   +   ++ +H++
  gi|298675988|ref|YP_003727738.1|  26 ESVYAFLDIAPSSIGHTLIMPKKHIENFNEMSPedaaSFFKSVNKIAKGVEKGVSADGSNIGLNNGTvaGQEVPHVH 102
                                       67899998899999*************98887733444567788888888888777776655444335688899999 PP

                                       EEEEE CS
                          CwfJ_C_1 104 iqvip 108
                                       i++ip
  gi|298675988|ref|YP_003727738.1| 103 IHLIP 107
                                       99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 989.10
//
Query:       gi|298675989|ref|YP_003727739.1|  [L=461]
Description: hypothetical protein Metev_2116 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-95  308.5  41.2    3.2e-10   39.4   0.0   12.1 12  TPR_1          Tetratricopeptide repeat
    1.9e-75  243.0  36.7    1.3e-07   31.2   0.3   12.1 12  TPR_2          Tetratricopeptide repeat
    1.3e-62  202.8  44.7    4.3e-07   29.6   0.0   12.2 12  TPR_8          Tetratricopeptide repeat
    1.1e-60  201.0  43.2    1.9e-10   40.3   1.7   11.2 11  TPR_11         TPR repeat
    4.1e-46  152.1  31.4    3.1e-05   24.1   0.3   10.8 10  TPR_17         Tetratricopeptide repeat
    9.2e-46  150.6   1.4     0.0013   19.4   0.0   11.2 11  TPR_14         Tetratricopeptide repeat
    1.7e-40  137.4   1.3    8.7e-07   29.5   0.0    7.6  9  TPR_16         Tetratricopeptide repeat
    1.8e-38  130.7  21.7    4.8e-07   30.0   0.5    8.7  8  TPR_12         Tetratricopeptide repeat
    3.3e-33  114.0  12.6      6e-05   23.5   0.0    7.1  7  TPR_19         Tetratricopeptide repeat
    3.2e-31  107.3   0.0    0.00015   21.8   0.0    7.2  9  TPR_9          Tetratricopeptide repeat
    1.3e-18   66.3  21.2       0.84   10.4   0.2   11.2 11  TPR_6          Tetratricopeptide repeat
    1.7e-16   58.9  15.9       0.41   10.8   0.0   10.4 10  TPR_7          Tetratricopeptide repeat
    2.5e-13   50.0  24.0     0.0025   18.0   0.2    6.0  6  ANAPC3         Anaphase-promoting complex, cyclosome, subunit
    3.3e-13   49.0  14.8      0.097   12.6   0.0    9.2  9  TPR_10         Tetratricopeptide repeat
    6.8e-12   45.2   8.2    0.00076   18.8   0.1    4.7  4  TPR_15         Tetratricopeptide repeat
      5e-11   42.5  27.6       0.13   12.3   0.1   10.8 11  MIT            MIT (microtubule interacting and transport) do
    1.2e-10   41.7  11.7      0.033   14.2   0.1    7.5  9  DUF3856        Domain of Unknown Function (DUF3856)
    1.9e-10   40.3  17.6     0.0011   18.0   0.3    5.7  7  NARP1          NMDA receptor-regulated protein 1
    1.7e-09   37.7  14.8      0.017   15.1   4.2    5.3  6  SRP_TPR_like   Putative TPR-like repeat
    5.1e-08   32.9  17.4       0.77    9.9   0.1    7.9  8  Fis1_TPR_C     Fis1 C-terminal tetratricopeptide repeat
    1.2e-05   24.5   9.0     0.0031   16.6   0.9    4.5  5  ChAPs          ChAPs (Chs5p-Arf1p-binding proteins)
    1.3e-05   25.7   4.2        2.4    8.6   0.0    5.1  5  BTAD           Bacterial transcriptional activator domain
    0.00026   20.8   8.0        3.4    7.3   0.2    5.7  6  TPR_21         Tetratricopeptide repeat-like domain
     0.0004   19.8  13.7        5.4    6.5   0.1    7.2  7  SHNi-TPR       SHNi-TPR
    0.00041   20.4   6.9        4.1    7.5   0.0    5.6  5  ANAPC5         Anaphase-promoting complex subunit 5
    0.00053   19.5  12.1         13    5.4   0.0    7.8  8  HTH_Bact       Helix-turn-helix bacterial domain
    0.00074   19.3   0.0         20    4.9   0.0    5.3  6  FAD_binding_4  FAD binding domain
     0.0012   18.5   9.4        1.4    8.8   0.1    5.1  4  PPTA           Protein prenyltransferase alpha subunit repeat
     0.0031   17.8   3.2        2.6    8.5   0.1    4.2  4  TPR_20         Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.021   14.2   8.2       0.12   11.7   1.0    3.9  4  Coatomer_E     Coatomer epsilon subunit
       0.14   12.3   5.8         61    3.9   0.0    5.6  6  DUF1510        Domain of unknown function (DUF1510)
       0.18   11.8  26.6        3.2    7.8   0.1    6.8  7  Strep_SA_rep   Streptococcal surface antigen repeat
          1    9.6  12.9        7.5    6.9   0.0    4.9  4  UPF0122        Putative helix-turn-helix protein, YlxM / p13 
        4.3    7.8   7.1         10    6.6   0.1    4.7  3  NOP5NT         NOP5NT (NUC127) domain
        6.7    6.5  18.8       0.95    9.3   0.1    6.5  7  Sda            Sporulation inhibitor A


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   2.3e-06    0.0012       8      34 .]      37      63 ..      31      63 .. 0.91
   2 !   25.8   0.0   1.2e-08     6e-06       3      34 .]      66      97 ..      64      97 .. 0.96
   3 !   21.7   0.0   2.3e-07   0.00012       3      34 .]     100     131 ..      99     131 .. 0.95
   4 !   24.4   0.0   3.5e-08   1.8e-05       2      34 .]     133     165 ..     132     165 .. 0.95
   5 !   37.0   0.2   3.6e-12   1.8e-09       3      34 .]     168     199 ..     167     199 .. 0.96
   6 !   39.4   0.0   6.3e-13   3.2e-10       3      34 .]     202     233 ..     201     233 .. 0.98
   7 !   26.0   0.1   1.1e-08   5.4e-06       7      33 ..     240     266 ..     236     267 .. 0.95
   8 !   19.2   0.6   1.5e-06   0.00075       4      34 .]     271     301 ..     269     301 .. 0.94
   9 !   34.5   0.6   2.2e-11   1.1e-08       3      33 ..     304     334 ..     303     335 .. 0.97
  10 !   39.3   0.1   6.7e-13   3.4e-10       3      34 .]     338     369 ..     336     369 .. 0.95
  11 !   36.0   0.2   7.5e-12   3.8e-09       4      34 .]     373     403 ..     371     403 .. 0.94
  12 !    7.4   1.6     0.008       4.1       1      32 [.     404     435 ..     404     437 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.3e-06
                                      HHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  8 GnayfklgkydeAleyyekALelnPnn 34
                                      G +y++ +++++Al  +++AL+lnP +
  gi|298675989|ref|YP_003727739.1| 37 GELYRYANRHKDALNIFNRALKLNPRD 63
                                      899**********************75 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 1.2e-08
                                      HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  3 alynlGnayfklgkydeAleyyekALelnPnn 34
                                      a++n+G  +  l+k++eAle+++k++ + P++
  gi|298675989|ref|YP_003727739.1| 66 AWKNKGFELNTLEKHEEALEAFSKVVDIKPDD 97
                                      9*****************************96 PP

  == domain 3  score: 21.7 bits;  conditional E-value: 2.3e-07
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                        + ++G a+  l++y+eA e++++A ++ P++
  gi|298675989|ref|YP_003727739.1| 100 GWIGKGIALTALERYEEATEAFDEAAKISPED 131
                                       5999*************************986 PP

  == domain 4  score: 24.4 bits;  conditional E-value: 3.5e-08
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                        a++ +G+ + +l+ yd Ale ++kA  lnP++
  gi|298675989|ref|YP_003727739.1| 133 VAWKSKGLSLKNLNHYDLALETFKKASDLNPED 165
                                       59*****************************86 PP

  == domain 5  score: 37.0 bits;  conditional E-value: 3.6e-12
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                       ++  +G +y  l+ky++Ale y+kALe+nP+n
  gi|298675989|ref|YP_003727739.1| 168 IWIEKGILYDGLEKYEKALESYDKALEINPDN 199
                                       5999**************************98 PP

  == domain 6  score: 39.4 bits;  conditional E-value: 6.3e-13
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+ n+G+++ kl++y++Al++++kA+++nP+n
  gi|298675989|ref|YP_003727739.1| 202 AWINKGHTLNKLERYEDALKAFNKAITINPDN 233
                                       9*****************************98 PP

  == domain 7  score: 26.0 bits;  conditional E-value: 1.1e-08
                                       HHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   7 lGnayfklgkydeAleyyekALelnPn 33 
                                       +G +  kl+ y++Al+ y++A++lnP+
  gi|298675989|ref|YP_003727739.1| 240 KGIVQEKLNLYEDALQSYNRAIKLNPE 266
                                       799***********************7 PP

  == domain 8  score: 19.2 bits;  conditional E-value: 1.5e-06
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   4 lynlGnayfklgkydeAleyyekALelnPnn 34 
                                       +  +G+++  ++  ++Al+ y+  LelnP++
  gi|298675989|ref|YP_003727739.1| 271 WAKKGYILKIQEHSEKALDSYNNSLELNPEY 301
                                       8899*************************86 PP

  == domain 9  score: 34.5 bits;  conditional E-value: 2.2e-11
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPn 33 
                                       a++ +G ++ + gkydeAl++y+k LelnPn
  gi|298675989|ref|YP_003727739.1| 304 AWFYKGTILEEFGKYDEALKAYNKSLELNPN 334
                                       9*****************************9 PP

  == domain 10  score: 39.3 bits;  conditional E-value: 6.7e-13
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                       ++yn+G ++ k+++y+eAle+y+k LelnP++
  gi|298675989|ref|YP_003727739.1| 338 VWYNKGFLLTKMQMYNEALEAYNKSLELNPED 369
                                       8*****************************86 PP

  == domain 11  score: 36.0 bits;  conditional E-value: 7.5e-12
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   4 lynlGnayfklgkydeAleyyekALelnPnn 34 
                                       l  +G++y ++g+y++Al++y+kAL +nP++
  gi|298675989|ref|YP_003727739.1| 373 LTSKGLIYTYMGQYNKALKAYDKALNINPKY 403
                                       7889*************************97 PP

  == domain 12  score: 7.4 bits;  conditional E-value: 0.008
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnP 32 
                                       a+a+yn+  +y  l + d Al y + A+e + 
  gi|298675989|ref|YP_003727739.1| 404 ANAWYNMSCVYSLLDDADSALLYLKFAIEYDS 435
                                       79***************************885 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.2   4.2e-07   0.00022       4      34 .]      33      63 ..      31      63 .. 0.92
   2 !   10.9   0.0    0.0008      0.41       3      34 .]      66      97 ..      64      97 .. 0.85
   3 !   21.8   0.0   2.5e-07   0.00013       3      34 .]     100     131 ..      98     131 .. 0.94
   4 !   18.6   0.0   2.7e-06    0.0014       3      34 .]     134     165 ..     132     165 .. 0.95
   5 !   29.2   0.1   1.1e-09   5.4e-07       3      34 .]     168     199 ..     167     199 .. 0.96
   6 !   24.6   0.0   3.3e-08   1.7e-05       3      34 .]     202     233 ..     200     233 .. 0.96
   7 !   23.0   0.1   1.1e-07   5.5e-05       2      33 ..     235     266 ..     234     267 .. 0.95
   8 !   15.7   0.2   2.3e-05     0.012       3      34 .]     270     301 ..     268     301 .. 0.93
   9 !   31.2   0.3   2.5e-10   1.3e-07       3      33 ..     304     334 ..     302     335 .. 0.96
  10 !   30.1   0.0   5.5e-10   2.8e-07       2      34 .]     337     369 ..     336     369 .. 0.95
  11 !   27.5   0.1     4e-09     2e-06       7      34 .]     376     403 ..     372     403 .. 0.93
  12 ?    7.4   0.9     0.011       5.4       1      31 [.     404     434 ..     404     437 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 4.2e-07
                             TPR_2  4 lynlGlayyklgdyeeAleafekAleldPnn 34
                                      l   G++y++++++++Al+ f++Al+l+P++
  gi|298675989|ref|YP_003727739.1| 33 LVKEGELYRYANRHKDALNIFNRALKLNPRD 63
                                      5678*************************86 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0008
                             TPR_2  3 alynlGlayyklgdyeeAleafekAleldPnn 34
                                      a+ n G  +  l ++eeAleaf k++ + P++
  gi|298675989|ref|YP_003727739.1| 66 AWKNKGFELNTLEKHEEALEAFSKVVDIKPDD 97
                                      67777777777999****************96 PP

  == domain 3  score: 21.8 bits;  conditional E-value: 2.5e-07
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                       ++   G a+ +l +yeeA eaf++A ++ P++
  gi|298675989|ref|YP_003727739.1| 100 GWIGKGIALTALERYEEATEAFDEAAKISPED 131
                                       79999*************************86 PP

  == domain 4  score: 18.6 bits;  conditional E-value: 2.7e-06
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a+   Gl++ +l++y+ Ale f+kA  l+P++
  gi|298675989|ref|YP_003727739.1| 134 AWKSKGLSLKNLNHYDLALETFKKASDLNPED 165
                                       78999*************************86 PP

  == domain 5  score: 29.2 bits;  conditional E-value: 1.1e-09
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                       ++ + G +y  l +ye+Ale ++kAle++P+n
  gi|298675989|ref|YP_003727739.1| 168 IWIEKGILYDGLEKYEKALESYDKALEINPDN 199
                                       6999**************************98 PP

  == domain 6  score: 24.6 bits;  conditional E-value: 3.3e-08
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a+ n G  + kl +ye+Al+af+kA+ ++P+n
  gi|298675989|ref|YP_003727739.1| 202 AWINKGHTLNKLERYEDALKAFNKAITINPDN 233
                                       899***************************98 PP

  == domain 7  score: 23.0 bits;  conditional E-value: 1.1e-07
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                       e + + G + +kl+ ye+Al+ +++A++l+P+
  gi|298675989|ref|YP_003727739.1| 235 ETWDYKGIVQEKLNLYEDALQSYNRAIKLNPE 266
                                       6799***************************7 PP

  == domain 8  score: 15.7 bits;  conditional E-value: 2.3e-05
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                        +   G+++  + + e+Al+ ++ +lel+P++
  gi|298675989|ref|YP_003727739.1| 270 FWAKKGYILKIQEHSEKALDSYNNSLELNPEY 301
                                       68999*************************85 PP

  == domain 9  score: 31.2 bits;  conditional E-value: 2.5e-10
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                       a+++ G ++++ g+y+eAl+a++k+lel+Pn
  gi|298675989|ref|YP_003727739.1| 304 AWFYKGTILEEFGKYDEALKAYNKSLELNPN 334
                                       9*****************************8 PP

  == domain 10  score: 30.1 bits;  conditional E-value: 5.5e-10
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                        ++yn G ++ k++ y+eAlea++k+lel+P++
  gi|298675989|ref|YP_003727739.1| 337 IVWYNKGFLLTKMQMYNEALEAYNKSLELNPED 369
                                       58*****************************86 PP

  == domain 11  score: 27.5 bits;  conditional E-value: 4e-09
                             TPR_2   7 lGlayyklgdyeeAleafekAleldPnn 34 
                                        Gl+y ++g+y++Al+a++kAl ++P++
  gi|298675989|ref|YP_003727739.1| 376 KGLIYTYMGQYNKALKAYDKALNINPKY 403
                                       69************************85 PP

  == domain 12  score: 7.4 bits;  conditional E-value: 0.011
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleld 31 
                                       a a+yn+ ++y  l+d + Al +++ A+e+d
  gi|298675989|ref|YP_003727739.1| 404 ANAWYNMSCVYSLLDDADSALLYLKFAIEYD 434
                                       689******************9998777765 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   0.00023      0.12       3      33 ..      32      62 ..      30      63 .. 0.91
   2 !   14.7   0.0     5e-05     0.026       3      34 .]      66      97 ..      64      97 .. 0.90
   3 !   14.6   0.0   5.5e-05     0.028       4      34 .]     101     131 ..     100     131 .. 0.91
   4 !   16.9   0.1     1e-05    0.0052       7      34 .]     138     165 ..     134     165 .. 0.92
   5 !   26.6   0.3   8.1e-09   4.1e-06       3      34 .]     168     199 ..     168     199 .. 0.95
   6 !   29.6   0.0   8.4e-10   4.3e-07       3      34 .]     202     233 ..     200     233 .. 0.96
   7 !   13.8   0.1    0.0001     0.052       9      33 ..     242     266 ..     235     267 .. 0.89
   8 !   14.5   0.5   5.9e-05      0.03       3      33 ..     270     300 ..     269     301 .. 0.95
   9 !   22.2   0.3   2.1e-07   0.00011       3      33 ..     304     334 ..     303     335 .. 0.94
  10 !   25.2   0.2   2.2e-08   1.1e-05       3      34 .]     338     369 ..     337     369 .. 0.96
  11 !   24.1   0.4   4.8e-08   2.5e-05       5      33 ..     374     402 ..     372     403 .. 0.93
  12 !   12.1   1.6   0.00035      0.18       1      31 [.     404     434 ..     404     437 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00023
                                      HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8  3 ayynlgsiylklgdyeeAkeyyekaleldpd 33
                                      ++++ g +y+  ++++ A   +++al+l+p 
  gi|298675989|ref|YP_003727739.1| 32 SLVKEGELYRYANRHKDALNIFNRALKLNPR 62
                                      677889***********************96 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 5e-05
                                      HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8  3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34
                                      a+ n+g  + +l+++eeA e++ k+++++pd+
  gi|298675989|ref|YP_003727739.1| 66 AWKNKGFELNTLEKHEEALEAFSKVVDIKPDD 97
                                      5668999999********************96 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 5.5e-05
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       +  +g ++  l++yeeA e++ +a +++p++
  gi|298675989|ref|YP_003727739.1| 101 WIGKGIALTALERYEEATEAFDEAAKISPED 131
                                       667888999********************85 PP

  == domain 4  score: 16.9 bits;  conditional E-value: 1e-05
                                       HHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   7 lgsiylklgdyeeAkeyyekaleldpdn 34 
                                       +g+ +++l+ y+ A e+++ka +l+p++
  gi|298675989|ref|YP_003727739.1| 138 KGLSLKNLNHYDLALETFKKASDLNPED 165
                                       7999**********************86 PP

  == domain 5  score: 26.6 bits;  conditional E-value: 8.1e-09
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       ++  +g +y+ l++ye+A e+y kale++pdn
  gi|298675989|ref|YP_003727739.1| 168 IWIEKGILYDGLEKYEKALESYDKALEINPDN 199
                                       58999*************************97 PP

  == domain 6  score: 29.6 bits;  conditional E-value: 8.4e-10
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       a+ n+g+++ kl++ye A ++++ka++++pdn
  gi|298675989|ref|YP_003727739.1| 202 AWINKGHTLNKLERYEDALKAFNKAITINPDN 233
                                       8*****************************97 PP

  == domain 7  score: 13.8 bits;  conditional E-value: 0.0001
                                       HHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   9 siylklgdyeeAkeyyekaleldpd 33 
                                        + +kl+ ye A ++y++a++l+p+
  gi|298675989|ref|YP_003727739.1| 242 IVQEKLNLYEDALQSYNRAIKLNPE 266
                                       56789*******************7 PP

  == domain 8  score: 14.5 bits;  conditional E-value: 5.9e-05
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                        + ++g+i++ ++  e+A  +y+  lel+p+
  gi|298675989|ref|YP_003727739.1| 270 FWAKKGYILKIQEHSEKALDSYNNSLELNPE 300
                                       599***************************8 PP

  == domain 9  score: 22.2 bits;  conditional E-value: 2.1e-07
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a++ +g i+++ g+y+eA ++y+k lel+p+
  gi|298675989|ref|YP_003727739.1| 304 AWFYKGTILEEFGKYDEALKAYNKSLELNPN 334
                                       68889*************************8 PP

  == domain 10  score: 25.2 bits;  conditional E-value: 2.2e-08
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       ++yn+g ++ k++ y+eA e+y+k lel+p++
  gi|298675989|ref|YP_003727739.1| 338 VWYNKGFLLTKMQMYNEALEAYNKSLELNPED 369
                                       7*****************************86 PP

  == domain 11  score: 24.1 bits;  conditional E-value: 4.8e-08
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   5 ynlgsiylklgdyeeAkeyyekaleldpd 33 
                                         +g+iy  +g+y++A ++y kal ++p+
  gi|298675989|ref|YP_003727739.1| 374 TSKGLIYTYMGQYNKALKAYDKALNINPK 402
                                       569*************************8 PP

  == domain 12  score: 12.1 bits;  conditional E-value: 0.00035
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleld 31 
                                       a a+yn++++y+ l d ++A  y++ a+e+d
  gi|298675989|ref|YP_003727739.1| 404 ANAWYNMSCVYSLLDDADSALLYLKFAIEYD 434
                                       689**********************999988 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   3.4e-06    0.0017       1      35 [.      37      71 ..      37      74 .. 0.94
   2 !   10.3   0.0   0.00082      0.42       8      27 ..      78      97 ..      73     108 .. 0.84
   3 !   12.3   0.1    0.0002       0.1       3      28 ..     107     132 ..     105     146 .. 0.83
   4 !   12.2   0.0   0.00021      0.11       6      38 ..     144     176 ..     139     179 .. 0.84
   5 !   31.5   0.4     2e-10     1e-07       8      38 ..     180     210 ..     178     214 .. 0.92
   6 !   26.0   0.1   1.1e-08   5.5e-06       1      41 [.     207     247 ..     207     248 .. 0.91
   7 !   20.7   0.4   4.7e-07   0.00024       9      38 ..     249     278 ..     246     281 .. 0.87
   8 !   15.1   0.3   2.6e-05     0.013       1      37 [.     275     311 ..     275     315 .. 0.84
   9 !   29.3   0.1   9.5e-10   4.9e-07       8      41 ..     316     349 ..     309     350 .. 0.92
  10 !   15.6   0.4   1.9e-05    0.0098       6      27 ..     348     369 ..     345     370 .. 0.87
  11 !   40.3   1.7   3.6e-13   1.9e-10       1      34 [.     377     410 ..     377     417 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.4e-06
                            TPR_11  1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLG 35
                                      G +y+  ++ ++A++ +++Alkl+P +++a+ n G
  gi|298675989|ref|YP_003727739.1| 37 GELYRYANRHKDALNIFNRALKLNPRDVTAWKNKG 71
                                      789***************************98887 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00082
                            TPR_11  8 GkyeeAieaYkkAlkldPdn 27
                                       k eeA+ea++k ++++Pd+
  gi|298675989|ref|YP_003727739.1| 78 EKHEEALEAFSKVVDIKPDD 97
                                      689****************8 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.0002
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdna 28 
                                       a++++ +yeeA ea+ +A k++P++ 
  gi|298675989|ref|YP_003727739.1| 107 ALTALERYEEATEAFDEAAKISPEDS 132
                                       78999******************985 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 0.00021
                            TPR_11   6 eqGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                        ++ y+ A+e +kkA +l+P++  ++ + G +y
  gi|298675989|ref|YP_003727739.1| 144 NLNHYDLALETFKKASDLNPEDDFIWIEKGILY 176
                                       5788*****************988887777766 PP

  == domain 5  score: 31.5 bits;  conditional E-value: 2e-10
                            TPR_11   8 GkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                        kye+A+e+Y kAl+++Pdn +a+ n G+++
  gi|298675989|ref|YP_003727739.1| 180 EKYEKALESYDKALEINPDNETAWINKGHTL 210
                                       59**************************987 PP

  == domain 6  score: 26.0 bits;  conditional E-value: 1.1e-08
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                                       G+ + ++ +ye+A++a++kA+ ++Pdn e +   G ++ k+
  gi|298675989|ref|YP_003727739.1| 207 GHTLNKLERYEDALKAFNKAITINPDNEETWDYKGIVQEKL 247
                                       7889999**********************998888888776 PP

  == domain 7  score: 20.7 bits;  conditional E-value: 4.7e-07
                            TPR_11   9 kyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                        ye+A+++Y++A+kl+P++  ++ + G+++
  gi|298675989|ref|YP_003727739.1| 249 LYEDALQSYNRAIKLNPESGYFWAKKGYIL 278
                                       59****************998888888765 PP

  == domain 8  score: 15.1 bits;  conditional E-value: 2.6e-05
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGla 37 
                                       G+++  q   e+A+ +Y++ l+l+P++  a++  G +
  gi|298675989|ref|YP_003727739.1| 275 GYILKIQEHSEKALDSYNNSLELNPEYDLAWFYKGTI 311
                                       56666677779********************998865 PP

  == domain 9  score: 29.3 bits;  conditional E-value: 9.5e-10
                            TPR_11   8 GkyeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                                       Gky+eA++aY+k l+l+P+   ++yn G+++ k+
  gi|298675989|ref|YP_003727739.1| 316 GKYDEALKAYNKSLELNPNKSIVWYNKGFLLTKM 349
                                       9***************************998776 PP

  == domain 10  score: 15.6 bits;  conditional E-value: 1.9e-05
                            TPR_11   6 eqGkyeeAieaYkkAlkldPdn 27 
                                       + + y+eA+eaY+k l+l+P++
  gi|298675989|ref|YP_003727739.1| 348 KMQMYNEALEAYNKSLELNPED 369
                                       5566****************97 PP

  == domain 11  score: 40.3 bits;  conditional E-value: 3.6e-13
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynL 34 
                                       G +y+  G+y++A++aY kAl+++P++a+a+yn+
  gi|298675989|ref|YP_003727739.1| 377 GLIYTYMGQYNKALKAYDKALNINPKYANAWYNM 410
                                       89*******************************7 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00064      0.33       2      33 ..      53      84 ..      52      85 .. 0.90
   2 !   12.0   0.0   0.00042      0.21       2      34 .]     121     153 ..     120     153 .. 0.94
   3 !    8.6   0.0    0.0052       2.7       2      34 .]     155     187 ..     154     187 .. 0.94
   4 !   22.8   0.1   1.5e-07   7.6e-05       2      33 ..     189     220 ..     188     221 .. 0.96
   5 !   12.3   0.1   0.00035      0.18       2      34 .]     223     255 ..     222     255 .. 0.95
   6 !   17.3   0.0   8.8e-06    0.0045       2      33 ..     257     288 ..     256     289 .. 0.95
   7 !   22.7   0.1   1.6e-07   8.4e-05       2      33 ..     291     322 ..     290     323 .. 0.96
   8 !   24.1   0.3     6e-08   3.1e-05       1      33 [.     324     356 ..     324     357 .. 0.94
   9 !   14.0   0.1   9.6e-05     0.049       1      33 [.     358     390 ..     358     391 .. 0.95
  10 !   21.3   1.5   4.5e-07   0.00023       1      32 [.     392     423 ..     392     424 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00064
                            TPR_17  2 ylkaleldPnnadaynnLAelllknGdlmtAr 33
                                      + +al+l+P ++ a+ n++  l  + ++++A+
  gi|298675989|ref|YP_003727739.1| 53 FNRALKLNPRDVTAWKNKGFELNTLEKHEEAL 84
                                      89*****************9999999888887 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00042
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       + +a+++ P +++a+  ++  l++++ ++ A++
  gi|298675989|ref|YP_003727739.1| 121 FDEAAKISPEDSVAWKSKGLSLKNLNHYDLALE 153
                                       789**************************9975 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0052
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       ++ka +l+P +   + +++ l+  + ++++A++
  gi|298675989|ref|YP_003727739.1| 155 FKKASDLNPEDDFIWIEKGILYDGLEKYEKALE 187
                                       89***************************9975 PP

  == domain 4  score: 22.8 bits;  conditional E-value: 1.5e-07
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       y kale++P+n  a+ n++ +l k+ ++++A+
  gi|298675989|ref|YP_003727739.1| 189 YDKALEINPDNETAWINKGHTLNKLERYEDAL 220
                                       99****************************97 PP

  == domain 5  score: 12.3 bits;  conditional E-value: 0.00035
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       + ka+ ++P+n + + +++ +++k++ +++A+q
  gi|298675989|ref|YP_003727739.1| 223 FNKAITINPDNEETWDYKGIVQEKLNLYEDALQ 255
                                       89***************************9987 PP

  == domain 6  score: 17.3 bits;  conditional E-value: 8.8e-06
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       y +a++l+P + +++  ++++l+ +  +++A+
  gi|298675989|ref|YP_003727739.1| 257 YNRAIKLNPESGYFWAKKGYILKIQEHSEKAL 288
                                       99************************999996 PP

  == domain 7  score: 22.7 bits;  conditional E-value: 1.6e-07
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       y ++lel+P +  a+++++++l++ G++++A+
  gi|298675989|ref|YP_003727739.1| 291 YNNSLELNPEYDLAWFYKGTILEEFGKYDEAL 322
                                       999****************************7 PP

  == domain 8  score: 24.1 bits;  conditional E-value: 6e-08
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       +y k+lel+Pn + +++n++ ll k   + +A+
  gi|298675989|ref|YP_003727739.1| 324 AYNKSLELNPNKSIVWYNKGFLLTKMQMYNEAL 356
                                       59**********************999999997 PP

  == domain 9  score: 14.0 bits;  conditional E-value: 9.6e-05
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       +y k+lel+P + + ++ ++ ++   G++ +A+
  gi|298675989|ref|YP_003727739.1| 358 AYNKSLELNPEDEVTLTSKGLIYTYMGQYNKAL 390
                                       59****************************997 PP

  == domain 10  score: 21.3 bits;  conditional E-value: 4.5e-07
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       +y kal ++P++a+a++n+  +++ + d + A
  gi|298675989|ref|YP_003727739.1| 392 AYDKALNINPKYANAWYNMSCVYSLLDDADSA 423
                                       59***********************9999877 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   2.6e-06    0.0013       8      42 ..      37      71 ..      32      74 .. 0.91
   2 ?    5.1   0.0       0.1        51      12      38 ..      75     101 ..      70     105 .. 0.84
   3 !   15.7   0.1   3.9e-05      0.02       8      39 ..     105     136 ..      99     141 .. 0.91
   4 !   10.4   0.0    0.0019      0.97       4      42 ..     135     173 ..     134     175 .. 0.87
   5 !   17.7   0.0   8.9e-06    0.0045       8      41 ..     173     206 ..     169     209 .. 0.86
   6 !   16.3   0.0   2.4e-05     0.013       9      41 ..     208     240 ..     206     243 .. 0.89
   7 !   13.0   0.0   0.00029      0.15       3      41 ..     236     274 ..     235     277 .. 0.86
   8 !   12.5   0.0   0.00041      0.21       4      42 ..     271     309 ..     270     311 .. 0.91
   9 !   13.7   0.0   0.00016     0.084      10      42 ..     311     343 ..     308     345 .. 0.86
  10 !    9.1   0.0     0.005       2.5      10      38 ..     345     373 ..     337     379 .. 0.82
  11 !   12.3   0.0   0.00049      0.25      10      41 ..     379     410 ..     375     411 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.6e-06
                            TPR_14  8 aeallalGdpdeAiallrralalaPddaeawllla 42
                                      +e+++ + ++++A+++++ral+l+P d +aw   +
  gi|298675989|ref|YP_003727739.1| 37 GELYRYANRHKDALNIFNRALKLNPRDVTAWKNKG 71
                                      688999*************************8765 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.1
                            TPR_14  12 lalGdpdeAiallrralalaPddaeaw 38 
                                        +l++++eA++++ ++++  Pdd   w
  gi|298675989|ref|YP_003727739.1|  75 NTLEKHEEALEAFSKVVDIKPDDNIGW 101
                                       56889****************996555 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 3.9e-05
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeawl 39 
                                       + al al++++eA +++++a +  P+d +aw 
  gi|298675989|ref|YP_003727739.1| 105 GIALTALERYEEATEAFDEAAKISPEDSVAWK 136
                                       789***************************96 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.0019
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       ++  +  l +l  +d A++ +++a +l+P+d+ +w++ +
  gi|298675989|ref|YP_003727739.1| 135 WKSKGLSLKNLNHYDLALETFKKASDLNPEDDFIWIEKG 173
                                       666677789999***********************9876 PP

  == domain 5  score: 17.7 bits;  conditional E-value: 8.9e-06
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeawlll 41 
                                       + ++  l+++++A++ +++al+ +Pd+++aw+  
  gi|298675989|ref|YP_003727739.1| 173 GILYDGLEKYEKALESYDKALEINPDNETAWINK 206
                                       566777899**********************875 PP

  == domain 6  score: 16.3 bits;  conditional E-value: 2.4e-05
                            TPR_14   9 eallalGdpdeAiallrralalaPddaeawlll 41 
                                       + l  l+++++A++++++a+  +Pd++e+w + 
  gi|298675989|ref|YP_003727739.1| 208 HTLNKLERYEDALKAFNKAITINPDNEETWDYK 240
                                       6788899**********************9765 PP

  == domain 7  score: 13.0 bits;  conditional E-value: 0.00029
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawlll 41 
                                        +   + + + l  +++A++ ++ra++l+P++  +w   
  gi|298675989|ref|YP_003727739.1| 236 TWDYKGIVQEKLNLYEDALQSYNRAIKLNPESGYFWAKK 274
                                       67788999999********************98888665 PP

  == domain 8  score: 12.5 bits;  conditional E-value: 0.00041
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       +++ + +l  ++  ++A++ ++  l+l+P+ + aw++ +
  gi|298675989|ref|YP_003727739.1| 271 WAKKGYILKIQEHSEKALDSYNNSLELNPEYDLAWFYKG 309
                                       778889999999***********************9987 PP

  == domain 9  score: 13.7 bits;  conditional E-value: 0.00016
                            TPR_14  10 allalGdpdeAiallrralalaPddaeawllla 42 
                                       +l++ G++deA++++++ l+l+P+   +w+  +
  gi|298675989|ref|YP_003727739.1| 311 ILEEFGKYDEALKAYNKSLELNPNKSIVWYNKG 343
                                       78999******************9888887666 PP

  == domain 10  score: 9.1 bits;  conditional E-value: 0.005
                            TPR_14  10 allalGdpdeAiallrralalaPddaeaw 38 
                                       +l   + + eA++++++ l+l+P+d++++
  gi|298675989|ref|YP_003727739.1| 345 LLTKMQMYNEALEAYNKSLELNPEDEVTL 373
                                       566778899***************99876 PP

  == domain 11  score: 12.3 bits;  conditional E-value: 0.00049
                            TPR_14  10 allalGdpdeAiallrralalaPddaeawlll 41 
                                       ++   G++ +A++++++al  +P+ a aw+ +
  gi|298675989|ref|YP_003727739.1| 379 IYTYMGQYNKALKAYDKALNINPKYANAWYNM 410
                                       56678************************876 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   1.7e-09   8.7e-07       2      67 ..      35      97 ..      34      98 .. 0.97
   2 !   22.3   0.0     3e-07   0.00015      11      67 ..      78     131 ..      76     132 .. 0.95
   3 !   17.5   0.1   9.5e-06    0.0048       4      66 ..     105     164 ..     102     166 .. 0.87
   4 !   20.2   0.0   1.4e-06   0.00072       3      67 ..     138     199 ..     136     200 .. 0.92
   5 !   28.4   0.0   3.8e-09   1.9e-06       3      67 ..     172     233 ..     170     234 .. 0.94
   6 !   12.1   0.0   0.00045      0.23       9      48 ..     246     282 ..     240     288 .. 0.82
   7 !   27.0   0.0   9.9e-09   5.1e-06      10      66 ..     281     334 ..     272     336 .. 0.92
   8 ?    2.1   0.0      0.61   3.1e+02      13      30 ..     352     369 ..     340     373 .. 0.85
   9 !   12.4   0.0   0.00038      0.19       3      39 ..     376     409 ..     374     432 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 1.7e-09
                            TPR_16  2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67
                                      +++ ++++a++  dA++ +++alk++   P+++ A+ ++g  +  +  ++eA++++ + ++  pd+
  gi|298675989|ref|YP_003727739.1| 35 KEGELYRYANRHKDALNIFNRALKLN---PRDVTAWKNKGFELNTLEKHEEALEAFSKVVDIKPDD 97
                                      57899*********************...***********************************98 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 3e-07
                            TPR_16  11 gdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                        + ++A++a+  +++     Pd+   + ++g a+ ++ r++eA +++++a++ +p +
  gi|298675989|ref|YP_003727739.1|  78 EKHEEALEAFSKVVDIK---PDDNIGWIGKGIALTALERYEEATEAFDEAAKISPED 131
                                       5789*************...**********************************987 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 9.5e-06
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       + a+ ++ +y++A +a+++a k  p++++   A+  +g+++  ++ +++A++ +++a +  p 
  gi|298675989|ref|YP_003727739.1| 105 GIALTALERYEEATEAFDEAAKISPEDSV---AWKSKGLSLKNLNHYDLALETFKKASDLNPE 164
                                       56667889****************77777...**********************999777775 PP

  == domain 4  score: 20.2 bits;  conditional E-value: 1.4e-06
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       +++++ ++++yd A++ ++ a +++   P++   + ++g ++  +  +++A++ y++al+  pd+
  gi|298675989|ref|YP_003727739.1| 138 KGLSLKNLNHYDLALETFKKASDLN---PEDDFIWIEKGILYDGLEKYEKALESYDKALEINPDN 199
                                       57888899*****************...55555******************************98 PP

  == domain 5  score: 28.4 bits;  conditional E-value: 3.8e-09
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       ++ ++  + +y++A++ ++ al+ +   Pd+  A+ ++g  + ++ r+++A+ ++++a++  pd+
  gi|298675989|ref|YP_003727739.1| 172 KGILYDGLEKYEKALESYDKALEIN---PDNETAWINKGHTLNKLERYEDALKAFNKAITINPDN 233
                                       577888999****************...**********************************998 PP

  == domain 6  score: 12.1 bits;  conditional E-value: 0.00045
                            TPR_16   9 ragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqg 48 
                                       +++ y+dA+  +++a+k++   P+   ++  +g ++  q 
  gi|298675989|ref|YP_003727739.1| 246 KLNLYEDALQSYNRAIKLN---PESGYFWAKKGYILKIQE 282
                                       5667***************...999999999999887665 PP

  == domain 7  score: 27.0 bits;  conditional E-value: 9.9e-09
                            TPR_16  10 agdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       + + ++A+  ++  l+++   P+   A++++g ++ ++g ++eA+ +y++ l+  p+
  gi|298675989|ref|YP_003727739.1| 281 QEHSEKALDSYNNSLELN---PEYDLAWFYKGTILEEFGKYDEALKAYNKSLELNPN 334
                                       67899*************...****************************99999987 PP

  == domain 8  score: 2.1 bits;  conditional E-value: 0.61
                            TPR_16  13 yddAaaaleaalkrdpss 30 
                                       y +A++a++  l+++p++
  gi|298675989|ref|YP_003727739.1| 352 YNEALEAYNKSLELNPED 369
                                       789999999999999665 PP

  == domain 9  score: 12.4 bits;  conditional E-value: 0.00038
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAlll 39 
                                       +++++ + g+y +A++a++ al  +   P  a A+++
  gi|298675989|ref|YP_003727739.1| 376 KGLIYTYMGQYNKALKAYDKALNIN---PKYANAWYN 409
                                       57788899*****************...*******97 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   2.8e-05     0.014      47      74 ..      32      59 ..      28      62 .. 0.89
   2 !   14.4   0.1   6.9e-05     0.035       5      75 ..      66     128 ..      62     130 .. 0.79
   3 !   14.5   0.2   6.2e-05     0.032       8      74 ..     103     161 ..      96     164 .. 0.84
   4 !   16.3   0.2   1.7e-05    0.0088      24      75 ..     146     196 ..     133     198 .. 0.76
   5 !   26.8   0.1   9.2e-09   4.7e-06       4      74 ..     201     263 ..     198     266 .. 0.92
   6 !   20.8   0.0   6.7e-07   0.00034      21      74 ..     279     331 ..     273     334 .. 0.88
   7 !   30.0   0.5   9.4e-10   4.8e-07       4      74 ..     337     399 ..     335     399 .. 0.93
   8 !   27.2   0.5   6.7e-09   3.5e-06       5      69 ..     372     428 ..     368     434 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.8e-05
                            TPR_12 47 tlrnLgrlyralgryeeAlelleealai 74
                                      +l   g+lyr+++r+++Al+++++al++
  gi|298675989|ref|YP_003727739.1| 32 SLVKEGELYRYANRHKDALNIFNRALKL 59
                                      567789********************97 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 6.9e-05
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       a+ n +  l+ l++++eAle + k+++i      pd  +  ++  +++ +  al+ryeeA e++ ea +i 
  gi|298675989|ref|YP_003727739.1|  66 AWKNKGFELNTLEKHEEALEAFSKVVDIK-----PDD-NIGWIGKGIALT--ALERYEEATEAFDEAAKIS 128
                                       5667777789999***************9.....766.566655555555..8999999999999998875 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 6.2e-05
                            TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                         + +l++l+ry+eA e +++a  i      p+    + +    g  +  l++y+ Ale +++a ++
  gi|298675989|ref|YP_003727739.1| 103 GKGIALTALERYEEATEAFDEAAKIS-----PED---SVAWKSKGLSLKNLNHYDLALETFKKASDL 161
                                       678999****************9999.....664...677788888888899**********99876 PP

  == domain 4  score: 16.3 bits;  conditional E-value: 1.7e-05
                            TPR_12  24 ellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                        +++ ale ++++  + +p+   + +  g+ly+ l++ye+Ale + +al+i 
  gi|298675989|ref|YP_003727739.1| 146 NHYDLALETFKKA-SDLNPEDDFIWIEKGILYDGLEKYEKALESYDKALEIN 196
                                       4555555555444.34456667899999*********************995 PP

  == domain 5  score: 26.8 bits;  conditional E-value: 9.2e-09
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       ta+ n +++l++l+ry++Al+ ++ka+ i      pd+++   t    g+++++l+ ye+Al+ +++a+++
  gi|298675989|ref|YP_003727739.1| 201 TAWINKGHTLNKLERYEDALKAFNKAITIN-----PDNEE---TWDYKGIVQEKLNLYEDALQSYNRAIKL 263
                                       7899**********************9999.....99955...7************************987 PP

  == domain 6  score: 20.8 bits;  conditional E-value: 6.7e-07
                            TPR_12  21 eAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       + +e+ ekal+ ++++l+  +p++  + +  g++++++g+y+eAl++++++l++
  gi|298675989|ref|YP_003727739.1| 279 KIQEHSEKALDSYNNSLE-LNPEYDLAWFYKGTILEEFGKYDEALKAYNKSLEL 331
                                       568999999999987775.58999999999**********************98 PP

  == domain 7  score: 30.0 bits;  conditional E-value: 9.4e-10
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       ++++n + +l++++ y eAle ++k+le+      p+      tl   g +y ++g+y +Al+++ +al+i
  gi|298675989|ref|YP_003727739.1| 337 IVWYNKGFLLTKMQMYNEALEAYNKSLELN-----PED---EVTLTSKGLIYTYMGQYNKALKAYDKALNI 399
                                       6889**************************.....665...459*************************87 PP

  == domain 8  score: 27.2 bits;  conditional E-value: 6.7e-09
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelle 69 
                                       +l+  +++++++g+y +Al+ ++kal+i      p+   +a++ +n++ +y++l++ + Al +l+
  gi|298675989|ref|YP_003727739.1| 372 TLTSKGLIYTYMGQYNKALKAYDKALNIN-----PK---YANAWYNMSCVYSLLDDADSALLYLK 428
                                       566789***********************.....87...6***********************98 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0093       4.8       4      28 ..      43      67 ..      40      69 .. 0.87
   2 !   20.8   0.0   8.2e-07   0.00042       6      62 ..      79     135 ..      77     140 .. 0.94
   3 !   18.3   0.0   4.9e-06    0.0025       7      60 ..     148     201 ..     145     206 .. 0.94
   4 !   23.5   0.0   1.2e-07     6e-05       5      65 ..     214     274 ..     210     277 .. 0.93
   5 !   16.3   0.0   2.1e-05     0.011       7      57 ..     284     334 ..     280     340 .. 0.91
   6 !   23.1   0.1   1.5e-07   7.7e-05       5      58 ..     316     369 ..     312     373 .. 0.95
   7 !   20.8   0.4   7.9e-07    0.0004       3      47 ..     382     426 ..     380     435 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0093
                            TPR_19  4 egdyaeAlalleqalqedpknaear 28
                                      ++++ +Al+++ +al+ +p +  a+
  gi|298675989|ref|YP_003727739.1| 43 ANRHKDALNIFNRALKLNPRDVTAW 67
                                      7899***************998776 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 8.2e-07
                            TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                       +++eAl++++++ + +p++   +++  +al al +++eA ++ d++ +  p d+ ++
  gi|298675989|ref|YP_003727739.1|  79 KHEEALEAFSKVVDIKPDDNIGWIGKGIALTALERYEEATEAFDEAAKISPEDSVAW 135
                                       799************************************************998776 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 4.9e-06
                            TPR_19   7 yaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddar 60 
                                       y+ Al+ +++a + +p+++ +++   +++  l  +++A +  d+++e +pd++ 
  gi|298675989|ref|YP_003727739.1| 148 YDLALETFKKASDLNPEDDFIWIEKGILYDGLEKYEKALESYDKALEINPDNET 201
                                       899************************************************754 PP

  == domain 4  score: 23.5 bits;  conditional E-value: 1.2e-07
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasLl 65 
                                       ++y++Al+++ +a++ +p+n+e + +  +++ +l+ +++A +  +++ + +p + + ++ +
  gi|298675989|ref|YP_003727739.1| 214 ERYEDALKAFNKAITINPDNEETWDYKGIVQEKLNLYEDALQSYNRAIKLNPESGYFWAKK 274
                                       68**************************************************988887765 PP

  == domain 5  score: 16.3 bits;  conditional E-value: 2.1e-05
                            TPR_19   7 yaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                        + Al+ + + l+ +p+++ a+ +   +l + g +deA ++ ++ +e +p+
  gi|298675989|ref|YP_003727739.1| 284 SEKALDSYNNSLELNPEYDLAWFYKGTILEEFGKYDEALKAYNKSLELNPN 334
                                       578999******************************************999 PP

  == domain 6  score: 23.1 bits;  conditional E-value: 1.5e-07
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd 58 
                                       g+y+eAl+++ + l+ +p+ + ++++   +l ++  ++eA ++ ++ +e +p d
  gi|298675989|ref|YP_003727739.1| 316 GKYDEALKAYNKSLELNPNKSIVWYNKGFLLTKMQMYNEALEAYNKSLELNPED 369
                                       99***********************************************99986 PP

  == domain 7  score: 20.8 bits;  conditional E-value: 7.9e-07
                            TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAeal 47 
                                       ++g+y  Al+++ +al  +pk+a+a++++  ++  l + d A   
  gi|298675989|ref|YP_003727739.1| 382 YMGQYNKALKAYDKALNINPKYANAWYNMSCVYSLLDDADSALLY 426
                                       69***************************9999999999999755 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0     3e-07   0.00015       4      62 ..      39      97 ..      37     100 .. 0.95
   2 !   17.6   0.0     6e-06    0.0031       9      64 ..      78     133 ..      76     135 .. 0.95
   3 !   11.0   0.0   0.00071      0.36       6      62 ..     109     165 ..     104     168 .. 0.88
   4 !   17.1   0.0   8.6e-06    0.0044       9      65 ..     146     202 ..     138     204 .. 0.91
   5 !   13.8   0.0   9.6e-05     0.049       9      62 ..     214     267 ..     207     269 .. 0.94
   6 !   15.6   0.0   2.6e-05     0.013       8      60 ..     281     333 ..     274     335 .. 0.94
   7 !   21.1   0.0     5e-07   0.00026      10      64 ..     317     371 ..     310     379 .. 0.93
   8 !   18.3   0.0   3.8e-06    0.0019      11      61 ..     352     402 ..     345     426 .. 0.90
   9 !    9.4   0.0    0.0022       1.1       9      57 ..     384     432 ..     377     451 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3e-07
                             TPR_9  4 iaireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62
                                      ++  ++++  al + +r l l+P+d+  +   G+ l  l+  ++Al+++   +++ pd+
  gi|298675989|ref|YP_003727739.1| 39 LYRYANRHKDALNIFNRALKLNPRDVTAWKNKGFELNTLEKHEEALEAFSKVVDIKPDD 97
                                      5777899**************************************************98 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 6e-06
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapd 64 
                                       e++e+al++   ++ ++Pdd   +   G++l  l+++++A ++++ ++ ++p++  
  gi|298675989|ref|YP_003727739.1|  78 EKHEEALEAFSKVVDIKPDDNIGWIGKGIALTALERYEEATEAFDEAAKISPEDSV 133
                                       789*************************************************9976 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00071
                             TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                          e++e+a ++ +    + P+d   +   Gl l  l+++  Al+ +  + +l+p++
  gi|298675989|ref|YP_003727739.1| 109 TALERYEEATEAFDEAAKISPEDSVAWKSKGLSLKNLNHYDLALETFKKASDLNPED 165
                                       55689999999999999999999999999***********99999999999999987 PP

  == domain 4  score: 17.1 bits;  conditional E-value: 8.6e-06
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                       ++++ al++      l+P+d   + + G+l+  l+ +++Al+  + +l+++pd+++a
  gi|298675989|ref|YP_003727739.1| 146 NHYDLALETFKKASDLNPEDDFIWIEKGILYDGLEKYEKALESYDKALEINPDNETA 202
                                       78888889999999999***9********************************9987 PP

  == domain 5  score: 13.8 bits;  conditional E-value: 9.6e-05
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                       e++e al++ +  + ++Pd  e +   G+++++l+ ++ Al+  ++++ l+p+ 
  gi|298675989|ref|YP_003727739.1| 214 ERYEDALKAFNKAITINPDNEETWDYKGIVQEKLNLYEDALQSYNRAIKLNPES 267
                                       899***********************************************9975 PP

  == domain 6  score: 15.6 bits;  conditional E-value: 2.6e-05
                             TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                       +e++e+al  ++  l l+P+    ++  G +l++ G + +Al++ +  l+l+p
  gi|298675989|ref|YP_003727739.1| 281 QEHSEKALDSYNNSLELNPEYDLAWFYKGTILEEFGKYDEALKAYNKSLELNP 333
                                       799*******************************************9999998 PP

  == domain 7  score: 21.1 bits;  conditional E-value: 5e-07
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapd 64 
                                       ++++al++++  l l+P+    ++  G+ll ++  +++Al++ +  l+l+p+++ 
  gi|298675989|ref|YP_003727739.1| 317 KYDEALKAYNKSLELNPNKSIVWYNKGFLLTKMQMYNEALEAYNKSLELNPEDEV 371
                                       789************************************************9985 PP

  == domain 8  score: 18.3 bits;  conditional E-value: 3.8e-06
                             TPR_9  11 weralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       + +al++++  l l+P+d   +   Gl++  +G++++Al++ + +l ++p+
  gi|298675989|ref|YP_003727739.1| 352 YNEALEAYNKSLELNPEDEVTLTSKGLIYTYMGQYNKALKAYDKALNINPK 402
                                       679*******************************************99995 PP

  == domain 9  score: 9.4 bits;  conditional E-value: 0.0022
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeayla 57 
                                        ++ +al++++  l ++P+ +  ++    ++  l++   Al  L  +++
  gi|298675989|ref|YP_003727739.1| 384 GQYNKALKAYDKALNINPKYANAWYNMSCVYSLLDDADSALLYLKFAIE 432
                                       5788999999999999999999999999999999999999988887775 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0043       2.2       3      32 ..      33      62 ..      31      63 .. 0.90
   2 ?    3.6   0.0      0.25   1.3e+02      15      31 ..      79      95 ..      73      97 .. 0.83
   3 ?    0.2   0.1       2.9   1.5e+03      11      31 ..     109     129 ..     104     131 .. 0.72
   4 ?    5.6   0.0     0.054        28       7      31 ..     139     163 ..     138     165 .. 0.89
   5 ?    7.7   0.0     0.012       6.3       8      33 .]     174     199 ..     171     199 .. 0.86
   6 ?    7.5   0.0     0.014       6.9      12      33 .]     212     233 ..     202     233 .. 0.85
   7 !    9.3   0.1    0.0037       1.9       7      33 .]     241     267 ..     238     267 .. 0.91
   8 !   10.0   0.0    0.0021       1.1       2      32 ..     304     334 ..     303     335 .. 0.89
   9 ?    5.9   0.0     0.043        22       3      31 ..     339     367 ..     338     369 .. 0.85
  10 !   10.4   0.2    0.0016      0.84       7      32 ..     377     402 ..     376     403 .. 0.91
  11 ?   -0.2   0.1       3.8     2e+03       2      24 ..     406     428 ..     405     433 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0043
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6  3 lyklalsyrklgdtdkAlealerlikeYPd 32
                                      l k +++yr ++++ +Al +++r +k  P 
  gi|298675989|ref|YP_003727739.1| 33 LVKEGELYRYANRHKDALNIFNRALKLNPR 62
                                      7888******99**************9985 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.25
                                      HHHHHHHHHHHHHHH-T CS
                             TPR_6 15 dtdkAlealerlikeYP 31
                                      ++++Alea+ ++++  P
  gi|298675989|ref|YP_003727739.1| 79 KHEEALEAFSKVVDIKP 95
                                      789*********98755 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 2.9
                                       HHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6  11 rklgdtdkAlealerlikeYP 31 
                                        +l ++++A ea+++  k  P
  gi|298675989|ref|YP_003727739.1| 109 TALERYEEATEAFDEAAKISP 129
                                       455589999999998887766 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.054
                                       HHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYP 31 
                                       +ls+++l+ +d Ale++++  +  P
  gi|298675989|ref|YP_003727739.1| 139 GLSLKNLNHYDLALETFKKASDLNP 163
                                       89999999**********9988777 PP

  == domain 5  score: 7.7 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHHHHHHHHHHHHH-TT- CS
                             TPR_6   8 lsyrklgdtdkAlealerlikeYPdS 33 
                                        +y  l +++kAle +++ ++  Pd+
  gi|298675989|ref|YP_003727739.1| 174 ILYDGLEKYEKALESYDKALEINPDN 199
                                       56777679****************95 PP

  == domain 6  score: 7.5 bits;  conditional E-value: 0.014
                                       HHHHHHHHHHHHHHHHHH-TT- CS
                             TPR_6  12 klgdtdkAlealerlikeYPdS 33 
                                       kl ++++Al+a+++ i+  Pd+
  gi|298675989|ref|YP_003727739.1| 212 KLERYEDALKAFNKAITINPDN 233
                                       5569****************95 PP

  == domain 7  score: 9.3 bits;  conditional E-value: 0.0037
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPdS 33 
                                       +  ++kl+ +++Al+ ++r ik  P+S
  gi|298675989|ref|YP_003727739.1| 241 GIVQEKLNLYEDALQSYNRAIKLNPES 267
                                       67889999*****************98 PP

  == domain 8  score: 10.0 bits;  conditional E-value: 0.0021
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYPd 32 
                                       A ++ +  +++ g++d+Al+a+++ ++  P+
  gi|298675989|ref|YP_003727739.1| 304 AWFYKGTILEEFGKYDEALKAYNKSLELNPN 334
                                       7899999999966***********9998887 PP

  == domain 9  score: 5.9 bits;  conditional E-value: 0.043
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   3 lyklalsyrklgdtdkAlealerlikeYP 31 
                                        y+ + ++ k++ + +Alea+++ ++  P
  gi|298675989|ref|YP_003727739.1| 339 WYNKGFLLTKMQMYNEALEAYNKSLELNP 367
                                       588899999988**********9888777 PP

  == domain 10  score: 10.4 bits;  conditional E-value: 0.0016
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                       +l y  +g++ kAl+a+++ ++  P+
  gi|298675989|ref|YP_003727739.1| 377 GLIYTYMGQYNKALKAYDKALNINPK 402
                                       78889999**************9996 PP

  == domain 11  score: -0.2 bits;  conditional E-value: 3.8
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   2 AlyklalsyrklgdtdkAleale 24 
                                       A y++   y  l+d+d Al +l+
  gi|298675989|ref|YP_003727739.1| 406 AWYNMSCVYSLLDDADSALLYLK 428
                                       88999999999999999988776 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.027        14       6      34 ..      37      63 ..      37      65 .. 0.84
   2 ?    1.0   0.0       1.1   5.5e+02       8      28 ..     107     125 ..     104     133 .. 0.70
   3 ?    5.4   0.0     0.043        22       9      34 ..     142     165 ..     134     166 .. 0.83
   4 !   10.2   0.0    0.0013      0.64       6      31 ..     173     198 ..     170     201 .. 0.83
   5 ?    5.4   0.0     0.043        22       1      34 [.     202     233 ..     202     235 .. 0.81
   6 ?    5.9   0.0     0.029        15       2      32 ..     237     265 ..     236     267 .. 0.83
   7 !   10.8   0.0    0.0008      0.41       1      30 [.     304     333 ..     304     338 .. 0.85
   8 ?    5.0   0.1     0.056        29       8      32 ..     345     369 ..     338     371 .. 0.81
   9 !    8.9   0.0    0.0032       1.6       2      26 ..     373     397 ..     372     403 .. 0.86
  10 ?   -1.1   0.3       5.2   2.7e+03       1      23 [.     406     428 ..     406     436 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.027
                             TPR_7  6 arlysrlGdyeeAielyeqsLaltkdped 34
                                      ++ly+  +++++A+ ++ +  al   p d
  gi|298675989|ref|YP_003727739.1| 37 GELYRYANRHKDALNIFNR--ALKLNPRD 63
                                      789****************..77766665 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 1.1
                             TPR_7   8 lysrlGdyeeAielyeqsLal 28 
                                       +  +l +yeeA e + +  a 
  gi|298675989|ref|YP_003727739.1| 107 ALTALERYEEATEAFDE--AA 125
                                       66788899999988888..44 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.043
                             TPR_7   9 ysrlGdyeeAielyeqsLaltkdped 34 
                                         +l++y+ A+e +++  a +  ped
  gi|298675989|ref|YP_003727739.1| 142 LKNLNHYDLALETFKK--ASDLNPED 165
                                       5689************..88888776 PP

  == domain 4  score: 10.2 bits;  conditional E-value: 0.0013
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkd 31 
                                       + ly  l +ye+A+e y ++L++  d
  gi|298675989|ref|YP_003727739.1| 173 GILYDGLEKYEKALESYDKALEINPD 198
                                       6689999************8877655 PP

  == domain 5  score: 5.4 bits;  conditional E-value: 0.043
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdped 34 
                                       a+ n +++  +l +ye+A++ + +  a+t  p++
  gi|298675989|ref|YP_003727739.1| 202 AWINKGHTLNKLERYEDALKAFNK--AITINPDN 233
                                       5778899999************99..77755554 PP

  == domain 6  score: 5.9 bits;  conditional E-value: 0.029
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdp 32 
                                       +++ + ++++l+ ye+A++ y +  a+   p
  gi|298675989|ref|YP_003727739.1| 237 WDYKGIVQEKLNLYEDALQSYNR--AIKLNP 265
                                       66778999**************9..776655 PP

  == domain 7  score: 10.8 bits;  conditional E-value: 0.0008
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltk 30 
                                       a+++ + + ++ G+y+eA++ y +sL+l  
  gi|298675989|ref|YP_003727739.1| 304 AWFYKGTILEEFGKYDEALKAYNKSLELNP 333
                                       57788999****************998865 PP

  == domain 8  score: 5.0 bits;  conditional E-value: 0.056
                             TPR_7   8 lysrlGdyeeAielyeqsLaltkdp 32 
                                       l  +++ y eA+e y +sL+l  ++
  gi|298675989|ref|YP_003727739.1| 345 LLTKMQMYNEALEAYNKSLELNPED 369
                                       5678999**********99887665 PP

  == domain 9  score: 8.9 bits;  conditional E-value: 0.0032
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsL 26 
                                       L   + +y  +G+y +A++ y ++L
  gi|298675989|ref|YP_003727739.1| 373 LTSKGLIYTYMGQYNKALKAYDKAL 397
                                       666799*****************66 PP

  == domain 10  score: -1.1 bits;  conditional E-value: 5.2
                             TPR_7   1 aLlnLarlysrlGdyeeAielye 23 
                                       a++n+  +ys l d + A+ +++
  gi|298675989|ref|YP_003727739.1| 406 AWYNMSCVYSLLDDADSALLYLK 428
                                       68999999999999999998887 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1    0.0009      0.46      30      81 ..      37      89 ..      24      90 .. 0.91
   2 ?    2.2   0.0      0.42   2.1e+02      65      81 ..     107     123 ..     104     124 .. 0.85
   3 ?    6.0   0.2     0.027        14       4      54 ..     113     164 ..     110     176 .. 0.69
   4 !   18.0   0.2   4.9e-06    0.0025      37      81 ..     180     225 ..     173     226 .. 0.95
   5 !   14.0   3.9   8.8e-05     0.045      18      81 ..     297     361 ..     244     362 .. 0.83
   6 !   16.5   2.4   1.5e-05    0.0075       2      62 ..     349     410 ..     348     428 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0009
                                      HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3 30 AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81
                                      ++ +  ++++k A++++++a kln+++  ++  ++  l  L+k+eeA+ a++k
  gi|298675989|ref|YP_003727739.1| 37 GELYRYANRHKDALNIFNRAlKLNPRDVTAWKNKGFELNTLEKHEEALEAFSK 89
                                      67888899******************************************987 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.42
                                       HHHHTT-HHHHHHHH-S CS
                            ANAPC3  65 cllkLkkyeeAiaaLek 81 
                                       +l +L++yeeA  a+++
  gi|298675989|ref|YP_003727739.1| 107 ALTALERYEEATEAFDE 123
                                       5779*******999986 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.027
                                       -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC CS
                            ANAPC3   4 nyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnsk 54 
                                       +y++A   ++ + + ++e++ +   ++l+l +++ y+ A+e ++ka +ln++
  gi|298675989|ref|YP_003727739.1| 113 RYEEATEAFDEAAKISPEDSVAWKSKGLSLKNLNHYDLALETFKKAsDLNPE 164
                                       5666777777777555555555555688888888888888888888777766 PP

  == domain 4  score: 18.0 bits;  conditional E-value: 4.9e-06
                                       T-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  37 gqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       ++y++A+e ++ka ++n+ ++ +++ ++++l kL++ye+A++a+ k
  gi|298675989|ref|YP_003727739.1| 180 EKYEKALESYDKAlEINPDNETAWINKGHTLNKLERYEDALKAFNK 225
                                       79*****************************************987 PP

  == domain 5  score: 14.0 bits;  conditional E-value: 8.8e-05
                                       HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  18 aetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                        ++e + + ++++  l + g+y++A++ ++k+ +ln++   ++y ++  l k++ y+eA+ a+ k
  gi|298675989|ref|YP_003727739.1| 297 LNPEYDLAWFYKGTILEEFGKYDEALKAYNKSlELNPNKSIVWYNKGFLLTKMQMYNEALEAYNK 361
                                       4444444556679999999*****************************************99876 PP

  == domain 6  score: 16.5 bits;  conditional E-value: 1.5e-05
                                       TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHH CS
                            ANAPC3   2 qnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylf 62 
                                       +++y++A+  +++ l+ ++e++  +  ++l +  +gqy++A++ ++ka ++n+k  +++y +
  gi|298675989|ref|YP_003727739.1| 349 MQMYNEALEAYNKSLELNPEDEVTLTSKGLIYTYMGQYNKALKAYDKAlNINPKYANAWYNM 410
                                       579*************************************************9999999965 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.1    0.0093       4.8       9      30 ..      37      58 ..      37      60 .. 0.90
   2 ?   -1.1   0.0       3.7   1.9e+03      15      30 ..      77      92 ..      71      94 .. 0.70
   3 !    7.5   0.1    0.0073       3.8       9      31 ..     105     127 ..     104     128 .. 0.92
   4 ?    4.4   0.0     0.073        37       9      31 ..     173     195 ..     172     196 .. 0.86
   5 ?    4.7   0.0     0.055        28       7      31 ..     205     229 ..     204     230 .. 0.90
   6 ?    6.9   0.0     0.011       5.7      19      35 ..     244     260 ..     243     266 .. 0.88
   7 ?    4.9   0.0     0.051        26      10      31 ..     310     331 ..     309     332 .. 0.85
   8 ?    1.1   0.0      0.76   3.9e+02      22      37 ..     349     364 ..     340     369 .. 0.62
   9 !   12.6   0.0   0.00019     0.097       5      31 ..     373     399 ..     371     400 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0093
                            TPR_10  9 analrqrgrydeAealleeala 30
                                      + ++r  +r+++A++++ +al 
  gi|298675989|ref|YP_003727739.1| 37 GELYRYANRHKDALNIFNRALK 58
                                      568****************997 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3.7
                            TPR_10 15 rgrydeAealleeala 30
                                      + +++eA++ + ++++
  gi|298675989|ref|YP_003727739.1| 77 LEKHEEALEAFSKVVD 92
                                      5678888887766665 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0073
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       ++al+++ ry+eA + ++ea  i
  gi|298675989|ref|YP_003727739.1| 105 GIALTALERYEEATEAFDEAAKI 127
                                       89*****************9876 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.073
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       ++++  + +y++A++ +++al+i
  gi|298675989|ref|YP_003727739.1| 173 GILYDGLEKYEKALESYDKALEI 195
                                       67888889999999999999987 PP

  == domain 5  score: 4.7 bits;  conditional E-value: 0.055
                            TPR_10   7 NLanalrqrgrydeAealleealai 31 
                                       N +++l ++ ry++A++ + +a+ i
  gi|298675989|ref|YP_003727739.1| 205 NKGHTLNKLERYEDALKAFNKAITI 229
                                       56899***************99986 PP

  == domain 6  score: 6.9 bits;  conditional E-value: 0.011
                            TPR_10  19 deAealleealairrrl 35 
                                       +e ++l+e+al+ + r+
  gi|298675989|ref|YP_003727739.1| 244 QEKLNLYEDALQSYNRA 260
                                       89************997 PP

  == domain 7  score: 4.9 bits;  conditional E-value: 0.051
                            TPR_10  10 nalrqrgrydeAealleealai 31 
                                        +l + g+ydeA++ + ++l++
  gi|298675989|ref|YP_003727739.1| 310 TILEEFGKYDEALKAYNKSLEL 331
                                       567789**********999985 PP

  == domain 8  score: 1.1 bits;  conditional E-value: 0.76
                            TPR_10  22 ealleealairrrllG 37 
                                       ++++ eal+++ + l+
  gi|298675989|ref|YP_003727739.1| 349 MQMYNEALEAYNKSLE 364
                                       3556666666666655 PP

  == domain 9  score: 12.6 bits;  conditional E-value: 0.00019
                            TPR_10   5 lnNLanalrqrgrydeAealleealai 31 
                                       l+  + +++ +g+y++A++ +++al+i
  gi|298675989|ref|YP_003727739.1| 373 LTSKGLIYTYMGQYNKALKAYDKALNI 399
                                       666699*******************97 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   1.5e-06   0.00076     149     248 ..      33     132 ..      26     138 .. 0.92
   2 !   10.5   0.1   0.00049      0.25     133     245 ..     152     265 ..     139     271 .. 0.81
   3 !   12.1   0.2   0.00017     0.085     130     247 ..     251     369 ..     239     371 .. 0.80
   4 !   15.1   0.6     2e-05      0.01     123     238 ..     312     428 ..     304     437 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.5e-06
                            TPR_15 149 llaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkaraesdasLwgplaaAll 225
                                       l+  +elyr ++++++Al+++ +Al+l+p + ++ ++  + l+ l++ +e+ e+ ++  + +  d+  w   + Al 
  gi|298675989|ref|YP_003727739.1|  33 LVKEGELYRYANRHKDALNIFNRALKLNPRDVTAWKNKGFELNTLEKHEEALEAFSKVVDIKPDDNIGWIGKGIALT 109
                                       667789********************************************999999999999*************** PP

                            TPR_15 226 lLgrpkkALeylrkqakenrkdp 248
                                       +L+r+++A e +   ak  ++d 
  gi|298675989|ref|YP_003727739.1| 110 ALERYEEATEAFDEAAKISPEDS 132
                                       **************999998874 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00049
                            TPR_15 133 lksleeeeaae.qsaafllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawka 208
                                       l++ ++ ++++ ++ ++++  + ly    + ++Al+ y +Al+ +pd++++  +   +l+ l+r++    +lka+++
  gi|298675989|ref|YP_003727739.1| 152 LETFKKASDLNpEDDFIWIEKGILYDGLEKYEKALESYDKALEINPDNETAWINKGHTLNKLERYED---ALKAFNK 225
                                       55555566677688999999999**************************999999999999999985...8888888 PP

                            TPR_15 209 ra...esdasLwgplaaAlllLgrpkkALeylrkqakenr 245
                                       +      +++ w   +  + +L+ ++ AL+ +++  k n+
  gi|298675989|ref|YP_003727739.1| 226 AItinPDNEETWDYKGIVQEKLNLYEDALQSYNRAIKLNP 265
                                       8877778888888888999999999999998888877766 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.00017
                            TPR_15 130 aellksleeeeaae.qsaafllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellka 205
                                       ++ l+s  +  +++ +s +f++  + + + + ++++Al  y + l+l+p+ + +      +l + g+++e   +lka
  gi|298675989|ref|YP_003727739.1| 251 EDALQSYNRAIKLNpESGYFWAKKGYILKIQEHSEKALDSYNNSLELNPEYDLAWFYKGTILEEFGKYDE---ALKA 324
                                       566777777777887888999999999999*******************933322222224668899997...7777 PP

                            TPR_15 206 wkara...esdasLwgplaaAlllLgrpkkALeylrkqakenrkd 247
                                       +++      +++  w   ++ l +++ +++ALe ++k ++ n++d
  gi|298675989|ref|YP_003727739.1| 325 YNKSLelnPNKSIVWYNKGFLLTKMQMYNEALEAYNKSLELNPED 369
                                       7776666699999************************99999988 PP

  == domain 4  score: 15.1 bits;  conditional E-value: 2e-05
                            TPR_15 123 akdydriaellksleeeeaae.qsaafllaraelyrqegqtdaAlrdyreAlalapdss..elraallWlliDlgrr 196
                                       ++++ + +e lk   +  +++ + + +++  + l ++    ++Al++y + l+l+p+++     ++l++++   g++
  gi|298675989|ref|YP_003727739.1| 312 LEEFGKYDEALKAYNKSLELNpNKSIVWYNKGFLLTKMQMYNEALEAYNKSLELNPEDEvtLTSKGLIYTYM--GQY 386
                                       555666666666666555555578889999999999999999999999999999998752134578999999..777 PP

                            TPR_15 197 aeLrellkawkara...esdasLwgplaaAlllLgrpkkALeylr 238
                                       ++   +lka+ ++     + a+ w  +   ++lL + + AL yl+
  gi|298675989|ref|YP_003727739.1| 387 NK---ALKAYDKALninPKYANAWYNMSCVYSLLDDADSALLYLK 428
                                       74...6777776665557778888889999999999999998875 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.82   4.2e+02      27      52 ..      46      70 ..      31      74 .. 0.78
   2 ?    0.5   0.0       1.3   6.4e+02      24      39 ..      77      92 ..      68      99 .. 0.71
   3 ?    5.5   0.1     0.034        18      22      40 ..     109     128 ..     105     144 .. 0.79
   4 ?    0.9   0.0      0.97   4.9e+02      16      33 ..     144     161 ..     136     162 .. 0.78
   5 !   12.3   0.1   0.00026      0.13       8      32 ..     170     194 ..     168     195 .. 0.91
   6 ?    5.0   0.0      0.05        26      24      44 ..     213     235 ..     205     248 .. 0.78
   7 ?    6.2   0.2     0.022        11      11      33 ..     241     263 ..     239     263 .. 0.86
   8 ?    1.0   0.0      0.86   4.4e+02      19      33 ..     283     297 ..     280     297 .. 0.86
   9 !    9.2   0.1    0.0024       1.2      14      33 ..     312     331 ..     306     331 .. 0.87
  10 ?    5.4   0.1     0.038        20      18      33 ..     350     365 ..     341     365 .. 0.89
  11 ?    4.6   0.2     0.066        34      18      32 ..     384     398 ..     374     399 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.82
                               MIT 27 YkealelLlqalkekneerrellrek 52
                                       k+al++++ alk  n+++  ++++k
  gi|298675989|ref|YP_003727739.1| 46 HKDALNIFNRALK-LNPRDVTAWKNK 70
                                      5889999999998.466766666655 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.3
                               MIT 24 lelYkealelLlqalk 39
                                      le+ +eale +++++ 
  gi|298675989|ref|YP_003727739.1| 77 LEKHEEALEAFSKVVD 92
                                      5677777777777776 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.034
                               MIT  22 eAlelYkealelLlqalk.e 40 
                                       +Ale Y+ea e + +a k  
  gi|298675989|ref|YP_003727739.1| 109 TALERYEEATEAFDEAAKiS 128
                                       69**************9943 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.97
                               MIT  16 nagnyeeAlelYkealel 33 
                                       n ++y+ Ale +k+a +l
  gi|298675989|ref|YP_003727739.1| 144 NLNHYDLALETFKKASDL 161
                                       678899999999998875 PP

  == domain 5  score: 12.3 bits;  conditional E-value: 0.00026
                               MIT   8 vkkAveeDnagnyeeAlelYkeale 32 
                                       ++k + +D  ++ye+Ale Y +ale
  gi|298675989|ref|YP_003727739.1| 170 IEKGILYDGLEKYEKALESYDKALE 194
                                       5688999****************98 PP

  == domain 6  score: 5.0 bits;  conditional E-value: 0.05
                               MIT  24 lelYkealelLlqalk.e.knee 44 
                                       le Y++al+ +++a++ + +nee
  gi|298675989|ref|YP_003727739.1| 213 LERYEDALKAFNKAITiNpDNEE 235
                                       68899999999999996665554 PP

  == domain 7  score: 6.2 bits;  conditional E-value: 0.022
                               MIT  11 AveeDnagnyeeAlelYkealel 33 
                                        + +++ + ye+Al+ Y  a++l
  gi|298675989|ref|YP_003727739.1| 241 GIVQEKLNLYEDALQSYNRAIKL 263
                                       567889999***********975 PP

  == domain 8  score: 1.0 bits;  conditional E-value: 0.86
                               MIT  19 nyeeAlelYkealel 33 
                                       + e+Al+ Y ++lel
  gi|298675989|ref|YP_003727739.1| 283 HSEKALDSYNNSLEL 297
                                       5699********996 PP

  == domain 9  score: 9.2 bits;  conditional E-value: 0.0024
                               MIT  14 eDnagnyeeAlelYkealel 33 
                                       +++ g+y+eAl++Y ++lel
  gi|298675989|ref|YP_003727739.1| 312 LEEFGKYDEALKAYNKSLEL 331
                                       57779************996 PP

  == domain 10  score: 5.4 bits;  conditional E-value: 0.038
                               MIT  18 gnyeeAlelYkealel 33 
                                       + y eAle+Y ++lel
  gi|298675989|ref|YP_003727739.1| 350 QMYNEALEAYNKSLEL 365
                                       669**********996 PP

  == domain 11  score: 4.6 bits;  conditional E-value: 0.066
                               MIT  18 gnyeeAlelYkeale 32 
                                       g+y +Al++Y +al+
  gi|298675989|ref|YP_003727739.1| 384 GQYNKALKAYDKALN 398
                                       89***********97 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.023        12      78     128 ..      46      92 ..      30     100 .. 0.84
   2 !    7.5   0.1    0.0077         4      74     129 ..      76     127 ..      70     138 .. 0.88
   3 ?    3.2   0.0      0.16        82      66     127 ..     109     125 ..      91     168 .. 0.54
   4 ?    5.8   0.0     0.026        13      75     128 ..     145     194 ..     131     195 .. 0.72
   5 !   14.2   0.1   6.5e-05     0.033      73     127 ..     177     227 ..     165     238 .. 0.82
   6 ?    4.6   0.1     0.062        32      72     128 ..     244     296 ..     234     302 .. 0.79
   7 !   10.2   0.0    0.0011      0.58      78     129 ..     284     331 ..     279     342 .. 0.84
   8 ?    1.1   0.0      0.76   3.9e+02     104     131 ..     340     367 ..     335     379 .. 0.67
   9 ?    2.4   0.0       0.3   1.5e+02      65      83 ..     380     398 ..     369     405 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.023
                                       HHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  78 adkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmage 128
                                        + al+ fnr  +l+  +   W     +++  l+ l +++eal+af ++++
  gi|298675989|ref|YP_003727739.1|  46 HKDALNIFNRALKLNPRDVTAW----KNKGFELNTLEKHEEALEAFSKVVD 92 
                                       567999********99998777....689*****************99876 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0077
                                       HHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  74 alesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                       +le  ++al+ f +  +++ d+   Wi     ++ al  l r++ea +af  a+ +
  gi|298675989|ref|YP_003727739.1|  76 TLEKHEEALEAFSKVVDIKPDDNIGWIG----KGIALTALERYEEATEAFDEAAKI 127
                                       6888999*******************95....99****************998765 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.16
                                       HHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856  66 aklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmag 127
                                       + l ry+ea                                              +af  a+
  gi|298675989|ref|YP_003727739.1| 109 TALERYEEAT---------------------------------------------EAFDEAA 125
                                       3333333333.............................................3333332 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.026
                                       HHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  75 lesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmage 128
                                       l+  d al+ f +  +l+ ++  +Wi    +++  +++l ++++al+++ +a e
  gi|298675989|ref|YP_003727739.1| 145 LNHYDLALETFKKASDLNPEDDFIWI----EKGILYDGLEKYEKALESYDKALE 194
                                       55567777777777777777777777....467777777777777777777766 PP

  == domain 5  score: 14.2 bits;  conditional E-value: 6.5e-05
                                       HHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856  73 ealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmag 127
                                       ++le  +kal+ +++  e++ d+   Wi    +++++l++l r+++alkaf++a 
  gi|298675989|ref|YP_003727739.1| 177 DGLEKYEKALESYDKALEINPDNETAWI----NKGHTLNKLERYEDALKAFNKAI 227
                                       4556666666666666699********8....79******************996 PP

  == domain 6  score: 4.6 bits;  conditional E-value: 0.062
                                       HHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  72 dealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmage 128
                                       +e l+  + al+ +nr  +l+ + G  W     +++  l+   ++++al++++ + e
  gi|298675989|ref|YP_003727739.1| 244 QEKLNLYEDALQSYNRAIKLNPESGYFWA----KKGYILKIQEHSEKALDSYNNSLE 296
                                       57788889999999999999999999995....577777777777777777777666 PP

  == domain 7  score: 10.2 bits;  conditional E-value: 0.0011
                                       HHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  78 adkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                       ++kal  +n   el+ +    W    f +++ lee G++dealka++++ e+
  gi|298675989|ref|YP_003727739.1| 284 SEKALDSYNNSLELNPEYDLAW----FYKGTILEEFGKYDEALKAYNKSLEL 331
                                       5788888888888887777666....789******************99886 PP

  == domain 8  score: 1.1 bits;  conditional E-value: 0.76
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                           DUF3856 104 fsravaleelGrkdealkafrmagemia 131
                                       ++++  l ++  ++eal+a++++ e+  
  gi|298675989|ref|YP_003727739.1| 340 YNKGFLLTKMQMYNEALEAYNKSLELNP 367
                                       5666666677777777777777666655 PP

  == domain 9  score: 2.4 bits;  conditional E-value: 0.3
                                       HHHTT-HHHHHHHHHHHHH CS
                           DUF3856  65 laklgrydealesadkalr 83 
                                       ++ +g+y++al++ dkal+
  gi|298675989|ref|YP_003727739.1| 380 YTYMGQYNKALKAYDKALN 398
                                       5678999999999999985 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1     0.032        16      15      73 ..      41      99 ..      33     130 .. 0.67
   2 ?    2.9   0.1      0.08        41      18      72 ..      78     132 ..      74     165 .. 0.74
   3 ?    4.9   0.1     0.019       9.9      19      72 ..     147     200 ..     129     206 .. 0.71
   4 !   13.4   0.3   5.4e-05     0.027      17      73 ..     179     235 ..     168     244 .. 0.90
   5 ?    5.3   0.1     0.015       7.6     204     252 ..     246     294 ..     236     300 .. 0.64
   6 !   18.0   0.3   2.1e-06    0.0011       7      71 ..     305     369 ..     300     374 .. 0.95
   7 !    6.7   0.2    0.0058         3     202     246 ..     380     424 ..     372     440 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.032
                                      HHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CH CS
                             NARP1 15 eeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpensk 73
                                      + a+++++Al+ ++++ k     ++  ++k+  l  L+++eeA +++++ ++  p++  
  gi|298675989|ref|YP_003727739.1| 41 RYANRHKDALNIFNRALKLNPRDVTAWKNKGFELNTLEKHEEALEAFSKVVDIKPDDNI 99
                                      55677788888888776665555555556777777899999999999999988888654 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.08
                                       THHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-C CS
                             NARP1  18 gkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpens 72 
                                       +k+eeAle ++++ +   D       k+  l++L+r+eeA++++ +  +  pe+s
  gi|298675989|ref|YP_003727739.1|  78 EKHEEALEAFSKVVDIKPDDNIGWIGKGIALTALERYEEATEAFDEAAKISPEDS 132
                                       6788888888886655555544455688899999999999999999888888765 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.019
                                       HHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-C CS
                             NARP1  19 kleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpens 72 
                                       +++ Ale ++++++   +   +   k+ l+  L+++e+A + y + le np+n+
  gi|298675989|ref|YP_003727739.1| 147 HYDLALETFKKASDLNPEDDFIWIEKGILYDGLEKYEKALESYDKALEINPDNE 200
                                       556666666665554444444444577788888999999999999999999986 PP

  == domain 4  score: 13.4 bits;  conditional E-value: 5.4e-05
                                       HTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CH CS
                             NARP1  17 agkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpensk 73 
                                        +k+e+Ale  +++ +   D+ +   +k++ l kL+r+e+A +++++ ++ np+n++
  gi|298675989|ref|YP_003727739.1| 179 LEKYEKALESYDKALEINPDNETAWINKGHTLNKLERYEDALKAFNKAITINPDNEE 235
                                       5899**********99999*999999*****************************87 PP

  == domain 5  score: 5.3 bits;  conditional E-value: 0.015
                                       HHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                             NARP1 204 klgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeea 252
                                       kl+ +e Al+  ++ai+ +p++  ++  K+ ilk +   +kA +  +++
  gi|298675989|ref|YP_003727739.1| 246 KLNLYEDALQSYNRAIKLNPESGYFWAKKGYILKIQEHSEKALDSYNNS 294
                                       4455667777777777777777777777777777766666666655554 PP

  == domain 6  score: 18.0 bits;  conditional E-value: 2.1e-06
                                       HHHHHHHHHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT- CS
                             NARP1   7 lLyknqiieeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpen 71 
                                         yk +i+ee gk++eAl+  +++ +   +k  v  +k+ ll+k+++++eA ++y++ le npe+
  gi|298675989|ref|YP_003727739.1| 305 WFYKGTILEEFGKYDEALKAYNKSLELNPNKSIVWYNKGFLLTKMQMYNEALEAYNKSLELNPED 369
                                       579************************************************************97 PP

  == domain 7  score: 6.7 bits;  conditional E-value: 0.0058
                                       HHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHH CS
                             NARP1 202 ydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAa 246
                                       y ++g+++kAl+  dka++ +p+  + +++ + ++    d + A 
  gi|298675989|ref|YP_003727739.1| 380 YTYMGQYNKALKAYDKALNINPKYANAWYNMSCVYSLLDDADSAL 424
                                       777888888888888888888888777777776666666665555 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       1.9   9.5e+02      24      40 ..      74      90 ..      49      99 .. 0.76
   2 !   11.6   0.1   0.00043      0.22       9      93 ..      84     184 ..      76     186 .. 0.63
   3 !   11.6   0.1   0.00043      0.22      27      71 ..     179     226 ..     164     234 .. 0.76
   4 !   10.9   0.2   0.00071      0.36       3      66 ..     187     255 ..     186     260 .. 0.71
   5 ?    3.5   0.1      0.13        69      14      72 ..     234     292 ..     228     298 .. 0.80
   6 !   15.1   4.2   3.4e-05     0.017      19      98 ..     307     393 ..     279     416 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.9
                      SRP_TPR_like 24 liklekyeeaLkllkkg 40
                                      l +lek+eeaL++ +k 
  gi|298675989|ref|YP_003727739.1| 74 LNTLEKHEEALEAFSKV 90
                                      56799999999988875 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00043
                      SRP_TPR_like   9 lrlegkelkkf.........kvvaliklekyeeaLkllkkgsals..edvrfE.kaYvlYklkkykkalkilkkvea 73 
                                       l++ +k+++           k +al  le+yeea ++ +++ ++s  ++v +  k   l  l++y  al+++kk+++
  gi|298675989|ref|YP_003727739.1|  84 LEAFSKVVDIKpddnigwigKGIALTALERYEEATEAFDEAAKISpeDSVAWKsKGLSLKNLNHYDLALETFKKASD 160
                                       44444444443555666677999*************99999988732344444256677789999999999999876 PP

                      SRP_TPR_like  74 ee...kvkvlksqvlYr.lgsyek 93 
                                        +       ++  +lY  l++yek
  gi|298675989|ref|YP_003727739.1| 161 LNpedDFIWIEKGILYDgLEKYEK 184
                                       432114444555555533555555 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00043
                      SRP_TPR_like  27 lekyeeaLkllkkgsal...sedvrfEkaYvlYklkkykkalkilkkv 71 
                                       lekye aL+  +k+ ++   +e     k   l kl++y++alk ++k+
  gi|298675989|ref|YP_003727739.1| 179 LEKYEKALESYDKALEInpdNETAWINKGHTLNKLERYEDALKAFNKA 226
                                       789999998888877551114566788889999999999999988875 PP

  == domain 4  score: 10.9 bits;  conditional E-value: 0.00071
                      SRP_TPR_like   3 eeyekilrlegkelkkf..kvvaliklekyeeaLkllkkgsals...edvrfEkaYvlYklkkykkalk 66 
                                       e+y+k l+++ ++ + +  k  +l kle+ye+aLk+ +k+ +++   e++   k  v  kl+ y++al+
  gi|298675989|ref|YP_003727739.1| 187 ESYDKALEINPDNETAWinKGHTLNKLERYEDALKAFNKAITINpdnEETWDYKGIVQEKLNLYEDALQ 255
                                       56777777777776666668888999***********99987761113344446667778888888776 PP

  == domain 5  score: 3.5 bits;  conditional E-value: 0.13
                      SRP_TPR_like  14 kelkkfkvvaliklekyeeaLkllkkgsalsedvrfEkaYvlYklkkykkalkilkkve 72 
                                       +e   +k +   kl+ ye+aL+  + + +l+ +  +  a   Y lk  +++ k l++ +
  gi|298675989|ref|YP_003727739.1| 234 EETWDYKGIVQEKLNLYEDALQSYNRAIKLNPESGYFWAKKGYILKIQEHSEKALDSYN 292
                                       5666788999999**********999999999888888888888887777777777665 PP

  == domain 6  score: 15.1 bits;  conditional E-value: 3.4e-05
                      SRP_TPR_like  19 fkvvaliklekyeeaLkllkkgsals...edvrfEkaYvlYklkkykkalkilkkveaee..kvkvlksq..vlYrl 88 
                                       +k + l + +ky+eaLk+ +k  +l+   + v + k + l k++ y++al+  +k  + +     +l+s+  ++ ++
  gi|298675989|ref|YP_003727739.1| 307 YKGTILEEFGKYDEALKAYNKSLELNpnkSIVWYNKGFLLTKMQMYNEALEAYNKSLELNpeDEVTLTSKglIYTYM 383
                                       488899999***********9987762224578*****************999875433322333444433377799 PP

                      SRP_TPR_like  89 gsyekAYklL 98 
                                       g+y+kA k  
  gi|298675989|ref|YP_003727739.1| 384 GQYNKALKAY 393
                                       *****96654 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       4.3   2.2e+03      16      33 ..      45      62 ..      42      65 .. 0.87
   2 ?    1.5   0.0      0.61   3.1e+02       9      34 ..     106     131 ..     105     134 .. 0.86
   3 !    9.9   0.1    0.0015      0.77      14      36 ..     179     201 ..     176     203 .. 0.91
   4 !    8.8   0.1    0.0033       1.7      13      46 ..     212     245 ..     210     248 .. 0.84
   5 ?    0.6   0.1       1.2   6.3e+02      13      33 ..     246     266 ..     239     267 .. 0.88
   6 ?    2.4   0.1      0.32   1.7e+02      15      33 ..     316     334 ..     314     336 .. 0.91
   7 ?    4.9   0.0     0.052        27      12      34 ..     347     369 ..     343     374 .. 0.92
   8 !    9.1   0.2    0.0025       1.3      14      36 ..     383     405 ..     378     407 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 4.3
                                      -HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C 16 eYseArryvdalLeiEPe 33
                                      ++++A++  ++ L++ P+
  gi|298675989|ref|YP_003727739.1| 45 RHKDALNIFNRALKLNPR 62
                                      67899*********9997 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.61
                                       HHHHHHT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C   9 lGhyklgeYseArryvdalLeiEPen 34 
                                       ++ + l +Y+eA +  d   +i Pe 
  gi|298675989|ref|YP_003727739.1| 106 IALTALERYEEATEAFDEAAKISPED 131
                                       5667799**********999999986 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0015
                                       HT-HHHHHHHHHHHHHHTTS-HH CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPenrQ 36 
                                       l +Y++A++  d  Lei P+n+ 
  gi|298675989|ref|YP_003727739.1| 179 LEKYEKALESYDKALEINPDNET 201
                                       789******************85 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.0033
                                       HHT-HHHHHHHHHHHHHHTTS-HHHHHHHHHHHH CS
                        Fis1_TPR_C  13 klgeYseArryvdalLeiEPenrQaqsLkelied 46 
                                       kl +Y++A++  +  + i P+n+   + k ++++
  gi|298675989|ref|YP_003727739.1| 212 KLERYEDALKAFNKAITINPDNEETWDYKGIVQE 245
                                       99********************987666666655 PP

  == domain 5  score: 0.6 bits;  conditional E-value: 1.2
                                       HHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  13 klgeYseArryvdalLeiEPe 33 
                                       kl  Y++A++  ++ +++ Pe
  gi|298675989|ref|YP_003727739.1| 246 KLNLYEDALQSYNRAIKLNPE 266
                                       8899******99999999997 PP

  == domain 6  score: 2.4 bits;  conditional E-value: 0.32
                                       T-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  15 geYseArryvdalLeiEPe 33 
                                       g+Y+eA++  +  Le+ P+
  gi|298675989|ref|YP_003727739.1| 316 GKYDEALKAYNKSLELNPN 334
                                       89*************9997 PP

  == domain 7  score: 4.9 bits;  conditional E-value: 0.052
                                       HHHT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  12 yklgeYseArryvdalLeiEPen 34 
                                       +k++ Y+eA++  +  Le+ Pe 
  gi|298675989|ref|YP_003727739.1| 347 TKMQMYNEALEAYNKSLELNPED 369
                                       69******************986 PP

  == domain 8  score: 9.1 bits;  conditional E-value: 0.0025
                                       HT-HHHHHHHHHHHHHHTTS-HH CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPenrQ 36 
                                       +g+Y++A++  d  L+i P+  +
  gi|298675989|ref|YP_003727739.1| 383 MGQYNKALKAYDKALNINPKYAN 405
                                       8******************9766 PP

>> ChAPs  ChAPs (Chs5p-Arf1p-binding proteins)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0       0.3   1.5e+02     214     271 ..      44     101 ..      25     124 .. 0.59
   2 ?    4.4   0.1     0.031        16     245     289 ..     143     187 ..     116     192 .. 0.89
   3 ?    3.3   0.1     0.065        33     244     292 ..     210     258 ..     185     264 .. 0.75
   4 ?    1.8   0.1      0.18        94     244     292 ..     312     360 ..     276     374 .. 0.81
   5 !   16.6   0.9     6e-06    0.0031     184     292 ..     317     428 ..     309     443 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.3
                                       T-HHHHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHHHHH-TT-HHHH CS
                             ChAPs 214 deEvdavkllneeleeeekdaelLllqaefllskkkeelAlevakravksaPsefktW 271
                                       ++  da+++ n++l+ +++d+   + +   l   +k+e Ale+ ++ v++ P +   W
  gi|298675989|ref|YP_003727739.1|  44 NRHKDALNIFNRALKLNPRDVTAWKNKGFELNTLEKHEEALEAFSKVVDIKPDDNIGW 101
                                       4444555555555555555555554444444444445556666666666666665555 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.031
                                       HHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHH CS
                             ChAPs 245 lskkkeelAlevakravksaPsefktWalLvkvYikledienALl 289
                                        + ++++lAle+ k+a ++ P +   W++    Y  le +e+AL 
  gi|298675989|ref|YP_003727739.1| 143 KNLNHYDLALETFKKASDLNPEDDFIWIEKGILYDGLEKYEKALE 187
                                       456788************************************996 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.065
                                       HHHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHH CS
                             ChAPs 244 llskkkeelAlevakravksaPsefktWalLvkvYikledienALltLN 292
                                       l + +++e Al++ ++a+++ P + +tW +   v  kl+ +e+AL + N
  gi|298675989|ref|YP_003727739.1| 210 LNKLERYEDALKAFNKAITINPDNEETWDYKGIVQEKLNLYEDALQSYN 258
                                       4455677888888899999999999999888888888888888888776 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.18
                                       HHHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHH CS
                             ChAPs 244 llskkkeelAlevakravksaPsefktWalLvkvYikledienALltLN 292
                                       l +  k++ Al++ +++ ++ P+++  W+      +k++ +++AL + N
  gi|298675989|ref|YP_003727739.1| 312 LEEFGKYDEALKAYNKSLELNPNKSIVWYNKGFLLTKMQMYNEALEAYN 360
                                       556678899999999*************999999999999999998877 PP

  == domain 5  score: 16.6 bits;  conditional E-value: 6e-06
                                       -HHHHHHHHHHHHTT-GGGHHHH.HHHHHH..TT-HHHHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHH CS
                             ChAPs 184 rydralellekLkeeepevvill.arvlll..adeEvdavkllneeleeeekdaelLllqaefllskkkeelAleva 257
                                       +yd+al+  +k  e +p+ +i+   + +ll  ++   +a++  n++le +++d   L+ +        +++ Al++ 
  gi|298675989|ref|YP_003727739.1| 317 KYDEALKAYNKSLELNPNKSIVWyNKGFLLtkMQMYNEALEAYNKSLELNPEDEVTLTSKGLIYTYMGQYNKALKAY 393
                                       6666777666666666666655413444441133444799999**********999999999999999********* PP

                                       HHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHH CS
                             ChAPs 258 kravksaPsefktWalLvkvYikledienALltLN 292
                                       ++a ++ P   + W+ ++ vY  l+d ++ALl L 
  gi|298675989|ref|YP_003727739.1| 394 DKALNINPKYANAWYNMSCVYSLLDDADSALLYLK 428
                                       ********************************985 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0      0.14        74      73     125 ..      75     127 ..      58     134 .. 0.86
   2 ?    7.4   0.0     0.011       5.5      75     122 ..     179     226 ..     175     232 .. 0.93
   3 !    8.6   0.0    0.0047       2.4      74     124 ..     212     262 ..     205     266 .. 0.93
   4 ?   -0.8   0.0       3.8   1.9e+03      79     121 ..     285     327 ..     279     332 .. 0.69
   5 ?    7.1   0.1     0.013       6.6      75     122 ..     349     396 ..     306     399 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.14
                                       HHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                              BTAD  73 lrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrl 125
                                        +l+++eeal+  ++ v+ +P +   +     Al +++r +eA e+++++ ++
  gi|298675989|ref|YP_003727739.1|  75 NTLEKHEEALEAFSKVVDIKPDDNIGWIGKGIALTALERYEEATEAFDEAAKI 127
                                       4688999999999********99999999999999999999999999998765 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.011
                                       TT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  75 lGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                       l+++e+al+ ++++++ +P +E+++      l +++r ++AL++++++
  gi|298675989|ref|YP_003727739.1| 179 LEKYEKALESYDKALEINPDNETAWINKGHTLNKLERYEDALKAFNKA 226
                                       67899****************************************986 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0047
                                       HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  74 rlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                       +l+r+e+al+  +++++ +P +E+++        +++  ++AL+ Y+r+ +
  gi|298675989|ref|YP_003727739.1| 212 KLERYEDALKAFNKAITINPDNEETWDYKGIVQEKLNLYEDALQSYNRAIK 262
                                       689********************************************9865 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 3.8
                                       HHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHH CS
                              BTAD  79 eealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYer 121
                                       e+al+ +++ ++++P  + ++    + l   G+  eAL++Y++
  gi|298675989|ref|YP_003727739.1| 285 EKALDSYNNSLELNPEYDLAWFYKGTILEEFGKYDEALKAYNK 327
                                       5566666666666666666666666667778888899999976 PP

  == domain 5  score: 7.1 bits;  conditional E-value: 0.013
                                       TT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  75 lGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                       +  ++eal+ +++ ++++P +E +     + + ++G+ ++AL++Y+++
  gi|298675989|ref|YP_003727739.1| 349 MQMYNEALEAYNKSLELNPEDEVTLTSKGLIYTYMGQYNKALKAYDKA 396
                                       5567899999999********************************976 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1      0.36   1.9e+02     152     180 ..     104     132 ..      74     146 .. 0.72
   2 ?   -1.0   0.0       2.3   1.2e+03     152     178 ..     172     198 ..     142     206 .. 0.70
   3 ?    4.1   0.1     0.064        33     152     189 ..     206     248 ..     178     256 .. 0.79
   4 ?   -1.1   0.0       2.5   1.3e+03     151     174 ..     273     296 ..     250     303 .. 0.82
   5 ?    6.7   0.0      0.01       5.2     152     181 ..     308     342 ..     303     354 .. 0.81
   6 !    7.3   0.2    0.0066       3.4     148     176 ..     372     400 ..     344     411 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.36
                            TPR_21 152 rGDilvaqgkldeAraaYqaAlaaleeka 180
                                       +G +l+a ++ +eA +a+++A +   e++
  gi|298675989|ref|YP_003727739.1| 104 KGIALTALERYEEATEAFDEAAKISPEDS 132
                                       66778888888888888888877666654 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.3
                            TPR_21 152 rGDilvaqgkldeAraaYqaAlaalee 178
                                       +G ++   +k ++A + Y++Al+ + +
  gi|298675989|ref|YP_003727739.1| 172 KGILYDGLEKYEKALESYDKALEINPD 198
                                       566666677888888888888876555 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.064
                            TPR_21 152 rGDilvaqgkldeAraaYqaAlaaleeka.....rellqlKld 189
                                       +G  l + ++ ++A +a+++A++ + +++     + ++q Kl+
  gi|298675989|ref|YP_003727739.1| 206 KGHTLNKLERYEDALKAFNKAITINPDNEetwdyKGIVQEKLN 248
                                       899999****************999888888999999999996 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 2.5
                            TPR_21 151 lrGDilvaqgkldeAraaYqaAla 174
                                        +G il  q++ ++A + Y+++l+
  gi|298675989|ref|YP_003727739.1| 273 KKGYILKIQEHSEKALDSYNNSLE 296
                                       588899999999999999999887 PP

  == domain 5  score: 6.7 bits;  conditional E-value: 0.01
                            TPR_21 152 rGDilvaqgkldeAraaYqaAlaaleeka.....r 181
                                       +G il + gk deA +aY+++l+ + +k+     +
  gi|298675989|ref|YP_003727739.1| 308 KGTILEEFGKYDEALKAYNKSLELNPNKSivwynK 342
                                       899*******************9888876666555 PP

  == domain 6  score: 7.3 bits;  conditional E-value: 0.0066
                            TPR_21 148 vaelrGDilvaqgkldeAraaYqaAlaal 176
                                           +G i++ +g+ ++A +aY++Al+ +
  gi|298675989|ref|YP_003727739.1| 372 TLTSKGLIYTYMGQYNKALKAYDKALNIN 400
                                       45689********************9865 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       3.5   1.8e+03      15      27 ..     112     124 ..     111     127 .. 0.72
   2 ?    4.9   0.1     0.035        18      15      30 ..     180     195 ..     179     196 .. 0.96
   3 ?    3.3   0.0      0.11        58      15      30 ..     214     229 ..     213     230 .. 0.92
   4 ?    1.5   0.0       0.4   2.1e+02      17      30 ..     250     263 ..     248     266 .. 0.94
   5 ?    6.5   0.1     0.011       5.4      15      30 ..     316     331 ..     314     332 .. 0.92
   6 ?    3.0   0.0      0.14        71      17      30 ..     352     365 ..     351     366 .. 0.94
   7 ?    2.8   0.0      0.16        81      16      31 ..     385     400 ..     383     406 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.5
                          SHNi-TPR  15 enFpqAveDlrka 27 
                                       e++++A e +++a
  gi|298675989|ref|YP_003727739.1| 112 ERYEEATEAFDEA 124
                                       7888887766665 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.035
                          SHNi-TPR  15 enFpqAveDlrkaLeL 30 
                                       e+++ A+e ++kaLe+
  gi|298675989|ref|YP_003727739.1| 180 EKYEKALESYDKALEI 195
                                       89************98 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.11
                          SHNi-TPR  15 enFpqAveDlrkaLeL 30 
                                       e++++A++ ++ka+ +
  gi|298675989|ref|YP_003727739.1| 214 ERYEDALKAFNKAITI 229
                                       9***********9976 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.4
                          SHNi-TPR  17 FpqAveDlrkaLeL 30 
                                       +++A++ +++a++L
  gi|298675989|ref|YP_003727739.1| 250 YEDALQSYNRAIKL 263
                                       89*********998 PP

  == domain 5  score: 6.5 bits;  conditional E-value: 0.011
                          SHNi-TPR  15 enFpqAveDlrkaLeL 30 
                                       +++++A++ ++k+LeL
  gi|298675989|ref|YP_003727739.1| 316 GKYDEALKAYNKSLEL 331
                                       69*************8 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.14
                          SHNi-TPR  17 FpqAveDlrkaLeL 30 
                                       +++A+e ++k+LeL
  gi|298675989|ref|YP_003727739.1| 352 YNEALEAYNKSLEL 365
                                       89***********8 PP

  == domain 7  score: 2.8 bits;  conditional E-value: 0.16
                          SHNi-TPR  16 nFpqAveDlrkaLeLr 31 
                                       +++ A++ ++kaL++ 
  gi|298675989|ref|YP_003727739.1| 385 QYNKALKAYDKALNIN 400
                                       8999**********95 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       4.6   2.4e+03      54      70 ..      77      93 ..      73      96 .. 0.85
   2 ?    3.6   0.2      0.14        70      53      73 ..     110     130 ..     104     135 .. 0.86
   3 ?    6.8   0.0     0.014         7      40      76 ..     199     235 ..     141     253 .. 0.78
   4 !    7.5   0.0     0.008       4.1      36      67 ..     290     328 ..     238     335 .. 0.81
   5 ?    0.8   0.0         1   5.2e+02      50      70 ..     379     399 ..     347     433 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 4.6
                            ANAPC5 54 fghneeAvkaleeairl 70
                                      ++++eeA++a++ ++ +
  gi|298675989|ref|YP_003727739.1| 77 LEKHEEALEAFSKVVDI 93
                                      68899******999876 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.14
                            ANAPC5  53 dfghneeAvkaleeairlAre 73 
                                       +++ +eeA++a+ ea +++ e
  gi|298675989|ref|YP_003727739.1| 110 ALERYEEATEAFDEAAKISPE 130
                                       5789***********999866 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.014
                            ANAPC5  40 yqyalLnlaslhadfghneeAvkaleeairlArenkD 76 
                                        ++a +n   +  +++ +e+A+ka++ ai++  +n++
  gi|298675989|ref|YP_003727739.1| 199 NETAWINKGHTLNKLERYEDALKAFNKAITINPDNEE 235
                                       4789999999999*****************9877765 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.008
                            ANAPC5  36 q.......kksyqyalLnlaslhadfghneeAvkaleea 67 
                                       +       + +y+ a +   ++  +fg+++eA+ka + +
  gi|298675989|ref|YP_003727739.1| 290 SynnslelNPEYDLAWFYKGTILEEFGKYDEALKAYNKS 328
                                       03334444699***********************98765 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 1
                            ANAPC5  50 lhadfghneeAvkaleeairl 70 
                                       + +++g++++A+ka   a ++
  gi|298675989|ref|YP_003727739.1| 379 IYTYMGQYNKALKAYDKALNI 399
                                       455667777777776666655 PP

>> HTH_Bact  Helix-turn-helix bacterial domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       3.3   1.7e+03       1      16 [.     113     128 ..     113     132 .. 0.89
   2 ?   -2.5   0.0       7.6   3.9e+03       2      12 ..     148     158 ..     147     159 .. 0.89
   3 ?    4.3   0.0     0.059        30       1      15 [.     181     195 ..     181     200 .. 0.91
   4 ?    5.4   0.0     0.026        13       1      15 [.     215     229 ..     215     234 .. 0.91
   5 ?    3.5   0.0       0.1        52       2      15 ..     250     263 ..     249     267 .. 0.92
   6 ?    2.1   0.4      0.29   1.5e+02       1      15 [.     317     331 ..     317     359 .. 0.77
   7 ?    0.4   0.0      0.96   4.9e+02       2      15 ..     352     365 ..     351     368 .. 0.88
   8 ?    2.9   0.1      0.16        81       1      15 [.     385     399 ..     385     406 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3.3
                                       -HHHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAieiS 16 
                                       rYeea e  + A +iS
  gi|298675989|ref|YP_003727739.1| 113 RYEEATEAFDEAAKIS 128
                                       7*********999999 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7.6
                                       HHHHHHHHHHH CS
                          HTH_Bact   2 YeeaLeqvnkA 12 
                                       Y+ aLe  +kA
  gi|298675989|ref|YP_003727739.1| 148 YDLALETFKKA 158
                                       9*****99998 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.059
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       +Ye+aLe  +kA+ei
  gi|298675989|ref|YP_003727739.1| 181 KYEKALESYDKALEI 195
                                       6************98 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.026
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       rYe aL+  nkAi i
  gi|298675989|ref|YP_003727739.1| 215 RYEDALKAFNKAITI 229
                                       7************87 PP

  == domain 5  score: 3.5 bits;  conditional E-value: 0.1
                                       HHHHHHHHHHHHHH CS
                          HTH_Bact   2 YeeaLeqvnkAiei 15 
                                       Ye aL+  n+Ai++
  gi|298675989|ref|YP_003727739.1| 250 YEDALQSYNRAIKL 263
                                       9***********96 PP

  == domain 6  score: 2.1 bits;  conditional E-value: 0.29
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       +Y+eaL+  nk +e+
  gi|298675989|ref|YP_003727739.1| 317 KYDEALKAYNKSLEL 331
                                       599999999998886 PP

  == domain 7  score: 0.4 bits;  conditional E-value: 0.96
                                       HHHHHHHHHHHHHH CS
                          HTH_Bact   2 YeeaLeqvnkAiei 15 
                                       Y+eaLe  nk +e+
  gi|298675989|ref|YP_003727739.1| 352 YNEALEAYNKSLEL 365
                                       9********99875 PP

  == domain 8  score: 2.9 bits;  conditional E-value: 0.16
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       +Y++aL+  +kA++i
  gi|298675989|ref|YP_003727739.1| 385 QYNKALKAYDKALNI 399
                                       7***********987 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.26   1.3e+02      50      80 ..      84     114 ..      37     129 .. 0.69
   2 ?    2.3   0.0      0.25   1.3e+02      48      80 ..     150     182 ..     132     186 .. 0.85
   3 ?    4.9   0.0     0.038        20      52      80 ..     188     216 ..     185     236 .. 0.86
   4 ?   -0.4   0.0       1.7   8.8e+02      50      74 ..     254     278 ..     253     300 .. 0.84
   5 ?    0.9   0.0      0.66   3.4e+02      51      92 ..     289     333 ..     286     339 .. 0.74
   6 ?    0.0   0.0       1.2   6.4e+02      51     109 ..     323     384 ..     321     393 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.26
                                       ETTS--EEEEETTTTEEEEETTSBHHHHHHH CS
                     FAD_binding_4  50 lsrlnrileideeegtatveaGvtlgdlvea 80 
                                       l+++ ++++i++++++ +++ G+ l +l+++
  gi|298675989|ref|YP_003727739.1|  84 LEAFSKVVDIKPDDNIGWIGKGIALTALERY 114
                                       3346779999999999999999999999887 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.25
                                       EEETTS--EEEEETTTTEEEEETTSBHHHHHHH CS
                     FAD_binding_4  48 ldlsrlnrileideeegtatveaGvtlgdlvea 80 
                                       l l+ +++  ++++e+  +++e G+ ++ l+++
  gi|298675989|ref|YP_003727739.1| 150 LALETFKKASDLNPEDDFIWIEKGILYDGLEKY 182
                                       456559999*****************9999886 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.038
                                       TS--EEEEETTTTEEEEETTSBHHHHHHH CS
                     FAD_binding_4  52 rlnrileideeegtatveaGvtlgdlvea 80 
                                        +++ lei++++ ta++  G tl++l+++
  gi|298675989|ref|YP_003727739.1| 188 SYDKALEINPDNETAWINKGHTLNKLERY 216
                                       577889********************987 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 1.7
                                       ETTS--EEEEETTTTEEEEETTSBH CS
                     FAD_binding_4  50 lsrlnrileideeegtatveaGvtl 74 
                                       l+ +nr +++++e+g+ +++ G +l
  gi|298675989|ref|YP_003727739.1| 254 LQSYNRAIKLNPESGYFWAKKGYIL 278
                                       6669999************999876 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 0.66
                                       TTS--EEEEETTTTEEEEETTSBHHHH...HHHHHHHTTECSSGG CS
                     FAD_binding_4  51 srlnrileideeegtatveaGvtlgdl...vealaakglllglep 92 
                                       + +n+ le+++e+  a++  G++l+++   +eal+a++  l l+p
  gi|298675989|ref|YP_003727739.1| 289 DSYNNSLELNPEYDLAWFYKGTILEEFgkyDEALKAYNKSLELNP 333
                                       4578889***************99988222455666666666655 PP

  == domain 6  score: 0.0 bits;  conditional E-value: 1.2
                                       TTS--EEEEETTTTEEEEETTSBHHHH...HHHHHHHTTECSSGGGTTCGSBHHHTTTTT-E CS
                     FAD_binding_4  51 srlnrileideeegtatveaGvtlgdl...vealaakglllglepgsgipgtvGGaiatnag 109
                                       +++n+ le+++++ +++   G  l ++   +eal+a++  l l+p++  + t  G+i t  g
  gi|298675989|ref|YP_003727739.1| 323 KAYNKSLELNPNKSIVWYNKGFLLTKMqmyNEALEAYNKSLELNPEDEVTLTSKGLIYTYMG 384
                                       45889999999999999999987777622257788888888888888777777777766555 PP

>> PPTA  Protein prenyltransferase alpha subunit repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.12        61       6      19 ..      54      67 ..      49      68 .. 0.87
   2 !    8.8   0.1    0.0027       1.4       7      19 ..     191     203 ..     190     205 .. 0.91
   3 ?    5.7   0.1     0.026        13       6      21 ..     224     239 ..     220     240 .. 0.93
   4 ?    2.4   0.6      0.28   1.4e+02       7      21 ..     395     409 ..     394     415 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.12
                                      HHHHHH-TT-CHHH CS
                              PPTA  6 ekliekdpkNYsaW 19
                                      + +++++p++ +aW
  gi|298675989|ref|YP_003727739.1| 54 NRALKLNPRDVTAW 67
                                      789*********** PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0027
                                       HHHHH-TT-CHHH CS
                              PPTA   7 kliekdpkNYsaW 19 
                                       k++e +p+N++aW
  gi|298675989|ref|YP_003727739.1| 191 KALEINPDNETAW 203
                                       89*********** PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.026
                                       HHHHHH-TT-CHHHHH CS
                              PPTA   6 ekliekdpkNYsaWny 21 
                                       +k+i  +p+N+ +W y
  gi|298675989|ref|YP_003727739.1| 224 NKAITINPDNEETWDY 239
                                       689***********99 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.28
                                       HHHHH-TT-CHHHHH CS
                              PPTA   7 kliekdpkNYsaWny 21 
                                       k+++ +pk   aW+ 
  gi|298675989|ref|YP_003727739.1| 395 KALNINPKYANAWYN 409
                                       89***********97 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0      0.12        62       7      55 ..      49      97 ..      43     105 .. 0.85
   2 !    8.5   0.1     0.005       2.6       6      54 ..     184     232 ..     179     241 .. 0.88
   3 ?    1.7   0.0      0.64   3.3e+02       5      53 ..     353     401 ..     349     408 .. 0.82
   4 ?    1.6   0.1      0.67   3.4e+02       5      60 ..     387     442 ..     383     445 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.12
                            TPR_20  7 elaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkw 55
                                       l  + +al+ np d+ a  +    l+  +++eeAle++ +++  + ++
  gi|298675989|ref|YP_003727739.1| 49 ALNIFNRALKLNPRDVTAWKNKGFELNTLEKHEEALEAFSKVVDIKPDD 97
                                      55667789999****************************9999877665 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.005
                            TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrk 54 
                                       + l++ ++al+ npd+  a ++    l++ +rye+Al+++ + +  + +
  gi|298675989|ref|YP_003727739.1| 184 KALESYDKALEINPDNETAWINKGHTLNKLERYEDALKAFNKAITINPD 232
                                       56788999******************************99888877665 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.64
                            TPR_20   5 apelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdr 53 
                                       ++ l++  + l+ np+d  +     l +   g+y +Al++  + l  + 
  gi|298675989|ref|YP_003727739.1| 353 NEALEAYNKSLELNPEDEVTLTSKGLIYTYMGQYNKALKAYDKALNINP 401
                                       567889999999*****9999999*************987666665555 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.67
                            TPR_20   5 apelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkweddaa 60 
                                       ++ l++ ++al+ np+  +a ++++ ++    + + Al  L   ++ d+ +++ a 
  gi|298675989|ref|YP_003727739.1| 387 NKALKAYDKALNINPKYANAWYNMSCVYSLLDDADSALLYLKFAIEYDSYYKERAK 442
                                       567889999************************99999999888888887755444 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.22   1.1e+02     181     229 ..      78     126 ..      66     134 .. 0.84
   2 ?    1.8   0.2      0.25   1.3e+02     214     254 ..     179     219 ..     148     258 .. 0.69
   3 ?   -1.4   0.0       2.4   1.2e+03     109     132 ..     309     332 ..     296     352 .. 0.80
   4 ?   11.7   1.0   0.00024      0.12     183     285 ..     352     450 ..     344     454 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.22
                                       THHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                        Coatomer_E 181 ekiqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLd 229
                                       ek ++A+  f+ + +  +   +   gk ++  +l+ryeeA +   ea +
  gi|298675989|ref|YP_003727739.1|  78 EKHEEALEAFSKVVDIKPDDNIGWIGKGIALTALERYEEATEAFDEAAK 126
                                       7788888888888888777777889999**************9999965 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.25
                                       TT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHH CS
                        Coatomer_E 214 lgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaev 254
                                       l++ye+A ++  +aL+ ++ +e + iN   + ++l++ +++
  gi|298675989|ref|YP_003727739.1| 179 LEKYEKALESYDKALEINPDNETAWINKGHTLNKLERYEDA 219
                                       67888888888888888888888888876666666655443 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.4
                                       HHHHHHTT-HHHHHHHHTT--SHH CS
                        Coatomer_E 109 aivflkegdfddalkllkksenLe 132
                                       ++++ + g++d+alk+ +ks  L+
  gi|298675989|ref|YP_003727739.1| 309 GTILEEFGKYDEALKAYNKSLELN 332
                                       567777788888888888876554 PP

  == domain 4  score: 11.7 bits;  conditional E-value: 0.00024
                                       HHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHHHHH CS
                        Coatomer_E 183 iqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevsernl 259
                                       +++A+  ++   e  ++  ++l+ k  +   +g+y++A +   +aL+ ++k++++  N+  +  +l+      +  l
  gi|298675989|ref|YP_003727739.1| 352 YNEALEAYNKSLELNPEDEVTLTSKGLIYTYMGQYNKALKAYDKALNINPKYANAWYNMSCVYSLLDDA----DSAL 424
                                       78888888888888889999**************************************98887777665....4568 PP

                                       HHHHHH-TT-HHHHHHHHHHHHHHHH CS
                        Coatomer_E 260 sqlklshpehklvkdlnekeaeFdrl 285
                                         lk +     + k+ ++k+a+F ++
  gi|298675989|ref|YP_003727739.1| 425 LYLKFAIEYDSYYKERAKKDADFKKI 450
                                       88888888899999999999999876 PP

>> DUF1510  Domain of unknown function (DUF1510)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.61   3.1e+02      28      50 ..      80     102 ..      50     107 .. 0.87
   2 ?    3.9   0.0      0.12        61      28      52 ..     114     138 ..     109     170 .. 0.91
   3 ?   -1.1   0.0       4.2   2.2e+03      28      52 ..     182     206 ..     176     215 .. 0.77
   4 ?    1.4   0.0      0.72   3.7e+02      28      51 ..     216     239 ..     211     248 .. 0.87
   5 ?    2.2   0.0       0.4     2e+02      28      51 ..     318     341 ..     313     345 .. 0.91
   6 ?   -2.1   0.0       8.6   4.4e+03      27      47 ..     351     371 ..     346     377 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.61
                           DUF1510  28 wnEmekavskatglsednmivww 50 
                                        +E ++a+sk+++++ d+ i w 
  gi|298675989|ref|YP_003727739.1|  80 HEEALEAFSKVVDIKPDDNIGWI 102
                                       57999***********9998774 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.12
                           DUF1510  28 wnEmekavskatglsednmivwwlg 52 
                                       ++E ++a+ +a+ +s ++++ w  +
  gi|298675989|ref|YP_003727739.1| 114 YEEATEAFDEAAKISPEDSVAWKSK 138
                                       899******************9764 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 4.2
                           DUF1510  28 wnEmekavskatglsednmivwwlg 52 
                                       ++  ++   ka +++ dn + w  +
  gi|298675989|ref|YP_003727739.1| 182 YEKALESYDKALEINPDNETAWINK 206
                                       566678889999***9999998754 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.72
                           DUF1510  28 wnEmekavskatglsednmivwwl 51 
                                       +++ +ka++ka+ ++ dn  +w  
  gi|298675989|ref|YP_003727739.1| 216 YEDALKAFNKAITINPDNEETWDY 239
                                       78899*************999976 PP

  == domain 5  score: 2.2 bits;  conditional E-value: 0.4
                           DUF1510  28 wnEmekavskatglsednmivwwl 51 
                                       ++E +ka +k  +l+ +++ivw+ 
  gi|298675989|ref|YP_003727739.1| 318 YDEALKAYNKSLELNPNKSIVWYN 341
                                       7899******************85 PP

  == domain 6  score: -2.1 bits;  conditional E-value: 8.6
                           DUF1510  27 DwnEmekavskatglsednmi 47 
                                        +nE ++a +k  +l+ ++ +
  gi|298675989|ref|YP_003727739.1| 351 MYNEALEAYNKSLELNPEDEV 371
                                       58999****999999988755 PP

>> Strep_SA_rep  Streptococcal surface antigen repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       5.5   2.8e+03      14      20 ..     111     117 ..     109     121 .. 0.59
   2 ?    7.8   0.1    0.0063       3.2       6      22 ..     178     194 ..     177     197 .. 0.88
   3 ?    7.1   0.0     0.011       5.4       6      21 ..     212     227 ..     211     230 .. 0.94
   4 ?   -1.0   0.3       3.7   1.9e+03       4      17 ..     244     257 ..     243     262 .. 0.59
   5 ?    4.1   0.5     0.094        48       2      14 ..     317     329 ..     316     330 .. 0.69
   6 ?    2.7   0.5      0.26   1.3e+02       7      20 ..     349     362 ..     347     365 .. 0.58
   7 ?    5.0   0.2     0.049        25       8      22 ..     384     398 ..     383     401 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 5.5
                                       HHHHHHH CS
                      Strep_SA_rep  14 LAaVQKa 20 
                                       L+++ +a
  gi|298675989|ref|YP_003727739.1| 111 LERYEEA 117
                                       5566555 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0063
                                       HHHHHHHHHHHHHHHHH CS
                      Strep_SA_rep   6 KLakYeaeLAaVQKana 22 
                                       +L+kYe+ L+ + Ka++
  gi|298675989|ref|YP_003727739.1| 178 GLEKYEKALESYDKALE 194
                                       79999999999999986 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHHHHHH CS
                      Strep_SA_rep   6 KLakYeaeLAaVQKan 21 
                                       KL+ Ye  L+a +Ka+
  gi|298675989|ref|YP_003727739.1| 212 KLERYEDALKAFNKAI 227
                                       9*************97 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 3.7
                                       XXHHHHHHHHHHHH CS
                      Strep_SA_rep   4 eaKLakYeaeLAaV 17 
                                       ++KL  Ye  L  +
  gi|298675989|ref|YP_003727739.1| 244 QEKLNLYEDALQSY 257
                                       56666666555555 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.094
                                       XXXXHHHHHHHHH CS
                      Strep_SA_rep   2 eYeaKLakYeaeL 14 
                                       +Y+++L++Y + L
  gi|298675989|ref|YP_003727739.1| 317 KYDEALKAYNKSL 329
                                       6888888886654 PP

  == domain 6  score: 2.7 bits;  conditional E-value: 0.26
                                       HHHHHHHHHHHHHH CS
                      Strep_SA_rep   7 LakYeaeLAaVQKa 20 
                                       +  Y   L+a++K 
  gi|298675989|ref|YP_003727739.1| 349 MQMYNEALEAYNKS 362
                                       55555556666665 PP

  == domain 7  score: 5.0 bits;  conditional E-value: 0.049
                                       HHHHHHHHHHHHHHH CS
                      Strep_SA_rep   8 akYeaeLAaVQKana 22 
                                        +Y + L+a+ Ka++
  gi|298675989|ref|YP_003727739.1| 384 GQYNKALKAYDKALN 398
                                       599999999999987 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0     0.015       7.5      45      74 ..     170     199 ..     165     205 .. 0.87
   2 ?    0.5   0.1       1.4   7.1e+02      58      74 ..     210     226 ..     200     257 .. 0.73
   3 ?   -1.2   0.0       4.6   2.3e+03      56      75 ..     283     302 ..     272     321 .. 0.82
   4 ?    6.3   0.8     0.021        11      17      75 ..     345     404 ..     338     419 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.015
                           UPF0122  45 vsrqavydnikrtekllekyEekLklleky 74 
                                       +++  +yd +++ ek le+y+++L++  ++
  gi|298675989|ref|YP_003727739.1| 170 IEKGILYDGLEKYEKALESYDKALEINPDN 199
                                       677889******************998766 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.4
                           UPF0122  58 ekllekyEekLklleky 74 
                                        + le+yE++Lk ++k 
  gi|298675989|ref|YP_003727739.1| 210 LNKLERYEDALKAFNKA 226
                                       44577777777777664 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 4.6
                           UPF0122  56 rtekllekyEekLkllekyk 75 
                                       + ek l +y + L+l  +y+
  gi|298675989|ref|YP_003727739.1| 283 HSEKALDSYNNSLELNPEYD 302
                                       57899999999999988776 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.021
                           UPF0122  17 LLTekqany.lelyyadDlSlsEiAeefnvsrqavydnikrtekllekyEekLkllekyk 75 
                                       LLT+ q+     + y++ l l+   e   +s+  +y  + + +k l+ y+++L++  ky 
  gi|298675989|ref|YP_003727739.1| 345 LLTKMQMYNeALEAYNKSLELNPEDEVTLTSKGLIYTYMGQYNKALKAYDKALNINPKYA 404
                                       888888743133468889999999999999*************************99986 PP

>> NOP5NT  NOP5NT (NUC127) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1      0.02        10      37      63 ..     102     128 ..      71     129 .. 0.86
   2 ?    0.1   0.0       2.1   1.1e+03      41      60 ..     208     227 ..     180     230 .. 0.78
   3 ?   -0.2   0.1       2.7   1.4e+03      20      42 ..     440     461 .]     424     461 .] 0.75

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.02
                            NOP5NT  37 fsklvkLkaFqkFesaaeALenanais 63 
                                       ++k + L a +++e a+eA ++a++is
  gi|298675989|ref|YP_003727739.1| 102 IGKGIALTALERYEEATEAFDEAAKIS 128
                                       5677899*****************997 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 2.1
                            NOP5NT  41 vkLkaFqkFesaaeALenan 60 
                                         L + +++e+a +A ++a 
  gi|298675989|ref|YP_003727739.1| 208 HTLNKLERYEDALKAFNKAI 227
                                       56888889999999988875 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 2.7
                            NOP5NT  20 llkkddlvkdsvsdlekfsklvk 42 
                                       + kkd   k+ +++ e f++lvk
  gi|298675989|ref|YP_003727739.1| 440 RAKKDADFKK-IQNREDFKSLVK 461
                                       4445446788.999999999987 PP

>> Sda  Sporulation inhibitor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1    0.0019      0.95       8      26 ..     150     168 ..     147     172 .. 0.89
   2 ?    3.7   0.2       0.1        53      10      22 ..     186     198 ..     179     200 .. 0.85
   3 ?   -2.0   0.0       6.1   3.1e+03      11      18 ..     214     221 ..     213     232 .. 0.63
   4 ?    1.1   0.0      0.67   3.4e+02      10      20 ..     254     264 ..     248     266 .. 0.90
   5 ?   -2.2   0.0       6.9   3.6e+03      10      20 ..     322     332 ..     319     334 .. 0.86
   6 ?   -0.2   0.2       1.7   8.6e+02      10      20 ..     356     366 ..     351     370 .. 0.85
   7 ?   -1.5   0.1       4.3   2.2e+03      10      20 ..     390     400 ..     389     400 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0019
                               Sda   8 lLieaYekAlelnLdpDFI 26 
                                       l +e+++kA  ln ++DFI
  gi|298675989|ref|YP_003727739.1| 150 LALETFKKASDLNPEDDFI 168
                                       569**************** PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.1
                               Sda  10 ieaYekAlelnLd 22 
                                       +e+Y+kAle n d
  gi|298675989|ref|YP_003727739.1| 186 LESYDKALEINPD 198
                                       79******99855 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 6.1
                               Sda  11 eaYekAle 18 
                                       e Ye+Al+
  gi|298675989|ref|YP_003727739.1| 214 ERYEDALK 221
                                       55666665 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.67
                               Sda  10 ieaYekAleln 20 
                                       +++Y +A++ln
  gi|298675989|ref|YP_003727739.1| 254 LQSYNRAIKLN 264
                                       689******98 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 6.9
                               Sda  10 ieaYekAleln 20 
                                       ++aY k leln
  gi|298675989|ref|YP_003727739.1| 322 LKAYNKSLELN 332
                                       699***99998 PP

  == domain 6  score: -0.2 bits;  conditional E-value: 1.7
                               Sda  10 ieaYekAleln 20 
                                       +eaY k leln
  gi|298675989|ref|YP_003727739.1| 356 LEAYNKSLELN 366
                                       79******998 PP

  == domain 7  score: -1.5 bits;  conditional E-value: 4.3
                               Sda  10 ieaYekAleln 20 
                                       ++aY+kAl  n
  gi|298675989|ref|YP_003727739.1| 390 LKAYDKALNIN 400
                                       79*****9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       941  (0.0524848); expected 358.6 (0.02)
Passed bias filter:                      638  (0.0355848); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        37  (0.0020637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              35  [number of targets reported over threshold]
# CPU time: 1.04u 0.33s 00:00:01.37 Elapsed: 00:00:00.65
# Mc/sec: 2130.53
//
Query:       gi|298675990|ref|YP_003727740.1|  [L=320]
Description: radical SAM domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-17   64.0   0.2    5.2e-17   62.7   0.1    1.7  2  Radical_SAM  Radical SAM superfamily
    9.4e-07   28.7   0.3    1.8e-06   27.8   0.3    1.5  1  DUF3463      Domain of unknown function (DUF3463)
     0.0025   18.1   0.0     0.0075   16.5   0.0    1.8  1  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.7   0.1   8.7e-21   5.2e-17       6     166 ..      30     171 ..      27     172 .. 0.93
   2 ?   -2.3   0.0      0.85   5.1e+03     124     143 ..     203     222 ..     187     240 .. 0.57

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 8.7e-21
                                       EESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   6 gCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritv 82 
                                        Cn+rC+fC  ++     ++  ++s++e+ + ++ + ++ g++       epll++d+  +le++++l   g+ +++
  gi|298675990|ref|YP_003727740.1|  30 QCNMRCKFCEYWK-----EDKVEMSTDEVFRMLDDA-KSFGIGIYNAWTVEPLLRDDLSSILEHAHRL---GMMTSL 97 
                                       5***********5.....9*****************.6999***************************...****** PP

                                       EECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  83 etngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendee 159
                                       +tng l+ e+kl++l    +d +s++++ +d+    k + rg ++e +l +++k++e+ ++    +  ++ G n ++
  gi|298675990|ref|YP_003727740.1|  98 ITNGKLL-EKKLDELEY--LDLLSVSVDGLDSY---KEI-RGIDIETILPGIKKAKER-LP--LMINCVISGKNLDD 164
                                       *******.999999998..89***********9...899.99****************.**..66666778899999 PP

                                       HHHHHHH CS
                                       xxxxxxx RF
                       Radical_SAM 160 leellel 166
                                       +++l++l
  gi|298675990|ref|YP_003727740.1| 165 IVDLINL 171
                                       9999886 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.85
                                       TSHHHHHHHHHHHHHHTTSE CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 124 ghtfeevlealeklreagik 143
                                        + ++++++ +  +++ g +
  gi|298675990|ref|YP_003727740.1| 203 VDKYQRTVDKIIQMKKQGYP 222
                                       34445555555555555555 PP

>> DUF3463  Domain of unknown function (DUF3463)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.3     3e-10   1.8e-06       4     130 ..     182     315 ..     179     319 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 3e-10
                           DUF3463   4 spgysYekapdq..dlf..lerektkelfrkilelkkkkyklnesplyldflagkq.eykCtpWg.nptrnvlGwqk 74 
                                       +p y++e ++++  d+f   + +k ++ + ki+++kk++y +++s +yl+++ +   +ykC +    +++   G  +
  gi|298675990|ref|YP_003727740.1| 182 EPMYEFEGISEEvwDEFgiKDVDKYQRTVDKIIQMKKQGYPIINSLTYLKMVRDLDmDYKCHANDvILNIAEDGTIE 258
                                       5666666554332222211466789999**************************665****997615699999**** PP

                           DUF3463  75 PCYllee..gyakt.fkelleetdwekygkgkdpkCanCmvhsgyEasavsdtvksllk 130
                                        C +  +  gy ++ +++++++   +  +  + ++C+ C    + E+s++ +   +++k
  gi|298675990|ref|YP_003727740.1| 259 DCRVHRNklGYINEgIENVWSSSRHNVRE--TANQCRGCLFFGYVENSLLYELKPEVMK 315
                                       ****9773356544256677766666555..7899**************9988877766 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.3e-06    0.0075      13     117 ..      29     123 ..      19     130 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.3e-06
                           Fer4_12  13 sgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiw 89 
                                       s Cn++Ck+   +e w+ ++ +  t+e+  ++++d+k   i        EPll   +++l +++++  + ++  + +
  gi|298675990|ref|YP_003727740.1|  29 SQCNMRCKF---CEYWKEDKVEMSTDEVF-RMLDDAKSFGIGIYNAWTVEPLL---RDDLSSILEHAHRLGM-MTSL 97 
                                       78*******...67999999888888776.56677744444444566779***...9**************9.699* PP

                           Fer4_12  90 lytgytleelskkekeellkeidvlvdG 117
                                       +++g  le+ +  +  e l+ + v vdG
  gi|298675990|ref|YP_003727740.1|  98 ITNGKLLEKKL--DELEYLDLLSVSVDG 123
                                       *********99..5699999******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       746  (0.0416086); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 1808.92
//
Query:       gi|298675991|ref|YP_003727741.1|  [L=261]
Description: hypothetical protein Metev_2118 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-82  275.3   0.3    4.2e-82  275.1   0.3    1.0  1  SAM_adeno_trans  S-adenosyl-l-methionine hydroxide adenosyltr


Domain annotation for each model (and alignments):
>> SAM_adeno_trans  S-adenosyl-l-methionine hydroxide adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  275.1   0.3   2.4e-86   4.2e-82       1     234 [.       4     254 ..       4     255 .. 0.90

  Alignments for each domain:
  == domain 1  score: 275.1 bits;  conditional E-value: 2.4e-86
                                       EEEEESSTSSSSHHHHHHHHHHHH-TTSEEEEEES-S-TT-HHHHHHHHHHHHGGS-TTEEEEEE--TTTTSS--EE CS
                   SAM_adeno_trans   1 itLlTDFGlkdpyvgamkgvilsiapdarivDitHdippfdvreaaflLaaalpyfpkgtvhlavVDpgvgterral 77 
                                       itLlTDFG  + y++amkgvil+i+ +++ivDitH+ip+ d+ ++af L+++++yfp+gtvh+ vVDpgvgterr++
  gi|298675991|ref|YP_003727741.1|   4 ITLLTDFG--SLYPAAMKGVILKINDSVDIVDITHSIPQADIYTGAFSLYSIVEYFPEGTVHIGVVDPGVGTERRPV 78 
                                       9*******..******************************************************************* PP

                                       EEEETTSEEEEESSSTTHHHH.....SEEEEEEGSSCC.....--TS-HHHHTHHHHHHHHHCT--GGGCSEEESGG CS
                   SAM_adeno_trans  78 vveakggyfvgPDNGlltlal.....lleeaveieeee.....ssatFhgrDvFapvaarlaagvsleelgeeldpe 144
                                       +++a+g+yfvgPDNGl+ +a+     +  e+++i++++      satFhgrD+Fapv+a++++g+++e++g+++d+ 
  gi|298675991|ref|YP_003727741.1|  79 AIRAGGHYFVGPDNGLMIPAArkienNNFEVFDITNKSltgskISATFHGRDIFAPVGAHISNGLNIENVGHRIDD- 154
                                       *********************866553389*****9999999988*****************************86. PP

                                       GS-SSS......ECSCEEEEEEEE-TTS-EEEEEE...EHHHHHTTCEE.......EEEEESSGGGSTTTSEEEEE- CS
                   SAM_adeno_trans 145 elvrle......ederlegevlyvDrFGNvitniskelleelekerkva.......klkkvetyaevaegellalvn 208
                                        +++l+      +++++eg+++y+D+FGN+itni++e+  +l++    +       ++  +++y+ v+e+el+al++
  gi|298675991|ref|YP_003727741.1| 155 -YIDLDfgkaklQNDTVEGRIIYIDDFGNIITNIPAETIFKLAEFG--TylkifnkTIPLLQSYGFVNEKELIALIS 228
                                       .7777776764438899******************77665554433..1345668554555**************** PP

                                       TTSEEEEEETTC-HHHHHT--TT-EE CS
                   SAM_adeno_trans 209 ssglleiavnkgsaaellglkvgdev 234
                                       ssg++e++vnkg+aa++l+++v+d++
  gi|298675991|ref|YP_003727741.1| 229 SSGFFEVSVNKGNAANKLNVDVNDKI 254
                                       ***********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 2086.13
//
Query:       gi|298675992|ref|YP_003727742.1|  [L=426]
Description: thiamine biosynthesis protein ThiC [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   7.4e-174  578.4   0.5   8.4e-174  578.2   0.5    1.0  1  ThiC_Rad_SAM  Radical SAM ThiC family
  ------ inclusion threshold ------
      0.031   13.6   0.1      0.044   13.1   0.1    1.3  1  EAP30         EAP30/Vps36 family


Domain annotation for each model (and alignments):
>> ThiC_Rad_SAM  Radical SAM ThiC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  578.2   0.5  9.4e-178  8.4e-174       1     417 [.       2     419 ..       2     420 .. 0.99

  Alignments for each domain:
  == domain 1  score: 578.2 bits;  conditional E-value: 9.4e-178
                      ThiC_Rad_SAM   1 tqleaarkgiiteemeevaekenvepefvreevaeGrivipanknhkekpvaiGkglrtkvnaniGtsadasdieeE 77 
                                       t le+a +g+it+em+ va+ke+++pe++r+++a+Grivip+   ++ k ++iG+gl+tkvna+iG+s+d+s+i  E
  gi|298675992|ref|YP_003727742.1|   2 TLLEDAVNGKITDEMKVVAQKEGLDPEYIRRGIANGRIVIPTSPYRDVKLCGIGEGLSTKVNASIGSSSDISNIGLE 78 
                                       77999************************************************************************ PP

                      ThiC_Rad_SAM  78 veKlkvalkagadtvmdLstggdideirekileespvpvgtvpiYqalee...kekkveelteeellevieeqaedG 151
                                       veK+k+a++agadt+m+L tggd+ e+r++++++++++vg+vp+Yqa+ e   k+++++++te++l+++ eeqa+ G
  gi|298675992|ref|YP_003727742.1|  79 VEKAKAAEEAGADTLMELGTGGDFLEVRKEVVDNTSLSVGSVPLYQAFIEaaqKRGSITDMTEDDLFKATEEQAKLG 155
                                       ************************************************99888999********************* PP

                      ThiC_Rad_SAM 152 vdfltiHagvtlellellkkekRltgivSrgGsllaawmlanekenplyeefdelleilkeydvtlSlgdglRpGsi 228
                                        +f++iH+gv++ +l++lkk++R+ g++SrgG+++++wml nekenply+efd+lleilke++v+lS+g+g+R+G++
  gi|298675992|ref|YP_003727742.1| 156 TNFMAIHTGVNNITLDRLKKHGRYGGLCSRGGAFMSTWMLYNEKENPLYSEFDYLLEILKEHEVVLSMGNGMRAGAV 232
                                       ***************************************************************************** PP

                      ThiC_Rad_SAM 229 aDatdeaqlaelivlgelvkrareagvqvmveGPGHvpldeieanvklqkklckeaPfyvlGplvtDiapgYDhits 305
                                       +Datd+aq++eli+++el+++a+++gvqv+veGPGHvp+deie+nvkl+k+++ + Pfy+lGplvtD+apg Dhi++
  gi|298675992|ref|YP_003727742.1| 233 HDATDRAQIQELIINTELAEQAQNEGVQVIVEGPGHVPMDEIETNVKLMKSMSGNRPFYMLGPLVTDVAPGQDHIVT 309
                                       ***************************************************************************** PP

                      ThiC_Rad_SAM 306 aiGaalaaaaGadllCyvtpaEHlglPdeedvkeGviaakiaahaadlakglkkarerdkalskaRkeldwekqfel 382
                                       +iGa+ ++aaG+d+lCyvtpaEHl+lP+++dv+eGv a+kiaah++d++k   ++r++d ++++aR +ldwek+++l
  gi|298675992|ref|YP_003727742.1| 310 SIGASASSAAGCDFLCYVTPAEHLALPNVDDVREGVKASKIAAHVGDMVKL--GKRDNDLDMARARCNLDWEKMYSL 384
                                       **************************************************8..78899******************* PP

                      ThiC_Rad_SAM 383 aldpekareireeklpeeeeaCsmCgekCavkive 417
                                       a+d+++ar+ir++++pe+e+aC+mCg++Ca+kiv+
  gi|298675992|ref|YP_003727742.1| 385 AIDSQTARTIRNDRAPEDEDACTMCGDFCALKIVN 419
                                       ********************************997 PP

>> EAP30  EAP30/Vps36 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   4.9e-06     0.044      67     163 ..      72     166 ..      56     264 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.9e-06
                             EAP30  67 caslGvdplssk...kseslgfl....ellglgdfyyeLavqivevclatraengglisleelyalvnrarggvalv 136
                                       ++++G+++   k   +++    +    el + gdf+ e+ +++v+        + g ++l + +    ++rg +  +
  gi|298675992|ref|YP_003727742.1|  72 ISNIGLEVEKAKaaeEAG----AdtlmELGTGGDFL-EVRKEVVDNTS----LSVGSVPLYQAFIEAAQKRGSITDM 139
                                       467777543333332222....12334666678886.68888888776....4558888888888888899667*** PP

                             EAP30 137 spdDllraiekllvlgsglsvlqvggk 163
                                       ++dDl +a e   +lg +++++++g +
  gi|298675992|ref|YP_003727742.1| 140 TEDDLFKATEEQAKLGTNFMAIHTGVN 166
                                       ***********************6633 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 2628.86
//
Query:       gi|298675993|ref|YP_003727743.1|  [L=109]
Description: hypothetical protein Metev_2120 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-14   54.2   0.8      2e-14   53.7   0.8    1.3  1  Pyr_excise  Pyrimidine dimer DNA glycosylase
  ------ inclusion threshold ------
      0.079   13.1   0.0        0.1   12.7   0.0    1.1  1  MukF_C      MukF C-terminal domain


Domain annotation for each model (and alignments):
>> Pyr_excise  Pyrimidine dimer DNA glycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.7   0.8   2.2e-18     2e-14       3      82 ..       2      74 ..       1     104 [. 0.81

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 2.2e-18
                                      ----S-GGGS-HHHHHHHHHHTHHH.HHHHHH-GGGS---SS--SSTTTTGGGTTBHHHHHHHHHHHHHHHHHTT---S CS
                        Pyr_excise  3 rinleliseLpdqhLlaeyrElpri.nalakkergngkipkhftlgtGHvtfFynkleyLrkrylllieEmlkRgynvn 80
                                      ri  +++++L+++hLl+e+rEl ++ ++++ +++  ++ p+++         +++kl  L+ r+++l+eEm kRgyn +
  gi|298675993|ref|YP_003727743.1|  2 RIWDIPPDKLCRNHLLGEHRELHALwSIIINNKKAYSNHPETLR--------WKDKLRALHLRHEKLVEEMDKRGYNHQ 72
                                      455689*******************9999988888888887655........5***********************987 PP

                                      -- CS
                        Pyr_excise 81 ee 82
                                        
  gi|298675993|ref|YP_003727743.1| 73 SP 74
                                      64 PP

>> MukF_C  MukF C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.1e-05       0.1      24      91 ..      35     104 ..      28     108 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.1e-05
                                       HHGGGS-EEEEEE----EEE--XXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                            MukF_C  24 kdyfdepwlltvadaerlldlrdeela..lrdeevtGelPeeleyeeleeieeqlaerieealavykekg 91 
                                       k y ++p +l+  d+ r l lr e+l+  + +     + P ++++ + ++ +++++++ e+++++ kek+
  gi|298675993|ref|YP_003727743.1|  35 KAYSNHPETLRWKDKLRALHLRHEKLVeeMDKRGYNHQSPLDVRFATGSDTQDEFIDSYEKQVKILKEKN 104
                                       68***********************86213444566789**********************999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 702.70
//
Query:       gi|298675994|ref|YP_003727744.1|  [L=308]
Description: family 2 glycosyl transferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-17   62.8   0.0      5e-17   62.2   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    8.4e-10   38.9   0.0    1.2e-09   38.4   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.011   16.3   0.0      0.021   15.3   0.0    1.5  1  Glyco_tranf_2_4  Glycosyl transferase family 2
      0.078   12.9   0.0        0.2   11.5   0.0    1.6  2  DUF5420          Family of unknown function (DUF5420)
      0.089   13.3   0.0       0.82   10.2   0.0    2.5  2  CBS              CBS domain


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2   0.0   1.4e-20     5e-17       1     145 [.      12     144 ..      12     168 .. 0.84

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 1.4e-20
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       ++ ipt Nee+t+ e ++  ++      + i+v+D +StD+t e++e       +  ++ ++ + Gk+ a+ +++  
  gi|298675994|ref|YP_003727744.1|  12 CILIPTLNEESTIVEIIRGFKSE---GFDNIFVIDGNSTDRTCELAEGE-----GASIVVQSGK-GKGQAVQEAFNI 79 
                                       699*****************999...888888888889***********.....9999999955.************ PP

                                       --SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS.EEEECCHCCCCHC CS
                   Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrv.generlyfkerkr 145
                                         ++y++ +D D ++ p ++  ++ ++ +++a  v+g+r+++f  + + + n+   +      +k    
  gi|298675994|ref|YP_003727744.1|  80 IESEYVVMVDGDGTYLPSDIHAMLSPILNGEAEHVIGNRFANFEPDAFTRLNLIGnR----ALNKLFSY 144
                                       **************************************************9987432....22222222 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0   3.3e-13   1.2e-09       4     136 ..      11     130 ..       8     181 .. 0.83

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 3.3e-13
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksraln 80 
                                       + +l+pt+nee++++e+++ + +  ++ + ++v++ +s++ t+e ae+       ++ ++vv++     +gk +a++
  gi|298675994|ref|YP_003727744.1|  11 VCILIPTLNEESTIVEIIRGFKS--EGFDNIFVIDGNSTDRTCELAEG-------EGASIVVQSG----KGKGQAVQ 74 
                                       789*******************9..78899**************8876.......4557777755....69****** PP

                   Glyco_tranf_2_3  81 ealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrstlvsal 136
                                       ea+++++s++v++vD+D    P  + ++l  +l  ++++v +++f++ +  ++++l
  gi|298675994|ref|YP_003727744.1|  75 EAFNIIESEYVVMVDGDGTYLPSDIHAMLSPILNGEAEHVIGNRFANFEPDAFTRL 130
                                       *****************99988888887877778899********99876664444 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0     6e-06     0.021       2      50 ..      19      67 ..      18     103 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6e-06
                   Glyco_tranf_2_4  2 neadiLpeflahhlalgfdrilvydndstDgtrailkelpevkllhvdk 50
                                      ne+ ++ e ++  ++ gfd+i+v+d +stD+t ++ +   +  ++++ k
  gi|298675994|ref|YP_003727744.1| 19 NEESTIVEIIRGFKSEGFDNIFVIDGNSTDRTCELAEGEGASIVVQSGK 67
                                      899999999999999*******************998865544444443 PP

>> DUF5420  Family of unknown function (DUF5420)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0         1   3.7e+03      74      74 ..      52      52 ..      13      86 .. 0.54
   2 ?   11.5   0.0   5.5e-05       0.2     102     156 ..     148     199 ..     122     213 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1
                           DUF5420 74 k 74
                                       
  gi|298675994|ref|YP_003727744.1| 52 E 52
                                      2 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 5.5e-05
                           DUF5420 102 qaireilkklpdFstymlkkLnllllvfgvssgrsylavsgvaedalivkiPvke 156
                                       +++++il  +++F +  +k L+l    f++    s +++ ++ ++ ++v++P+  
  gi|298675994|ref|YP_003727744.1| 148 KKLNDILSGYRAFTHEAIKTLELKETGFEIE---SEMTIESIKKEFIVVEVPITY 199
                                       689**********************999999...99****************975 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00023      0.82      10      39 ..      16      45 ..       9      51 .. 0.90
   2 ?   -0.8   0.0      0.61   2.2e+03      18      40 ..      73      92 ..      70      95 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00023
                                      EEEETTSBHHHHHHHHHHHTSSEEEEEETT CS
                               CBS 10 vtvppdttleealelmrekgvsrlPVVded 39
                                      +t+++++t+ e+++ ++++g++ ++V+d++
  gi|298675994|ref|YP_003727744.1| 16 PTLNEESTIVEIIRGFKSEGFDNIFVIDGN 45
                                      79**************9999*******765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.61
                                      HHHHHHHHHHHTSSEEEE.EETTT CS
                               CBS 18 leealelmrekgvsrlPV.Vdedg 40
                                      + ea++++ e   s + V Vd+dg
  gi|298675994|ref|YP_003727744.1| 73 VQEAFNII-E---SEYVVmVDGDG 92
                                      67888999.6...44435469998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2201.38
//
Query:       gi|298675995|ref|YP_003727745.1|  [L=187]
Description: TATA-box-binding family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-55  184.2   0.1    2.7e-26   91.4   0.0    2.0  2  TBP       Transcription factor TFIID (or TATA-binding protein
    3.1e-08   33.6   0.0     0.0067   16.5   0.0    2.3  2  DUF3378   Domain of unknown function (DUF3378)
      0.005   16.5   0.0        4.4    7.1   0.0    2.5  2  NdhS      NAD(P)H dehydrogenase subunit S


Domain annotation for each model (and alignments):
>> TBP  Transcription factor TFIID (or TATA-binding protein, TBP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.1   0.2   5.2e-30   3.1e-26       2      84 ..      10      90 ..       9      91 .. 0.96
   2 !   91.4   0.0   4.5e-30   2.7e-26       2      79 ..     101     178 ..     100     183 .. 0.94

  Alignments for each domain:
  == domain 1  score: 91.1 bits;  conditional E-value: 5.2e-30
                                      EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHH CS
                               TBP  2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiap 80
                                      +ki+Nvvas++l  e+dL+k++ +   ++aeY++++fpglvyr+++pk+++l+F+sGkvv+tGak++++++ ++ ++a+
  gi|298675995|ref|YP_003727745.1| 10 IKIENVVASTKLAEEFDLTKIEAEF--EGAEYNKQKFPGLVYRVSNPKAAFLVFTSGKVVCTGAKNVDDVHVVIGNMAK 86
                                      89*******************8665..**************************************************** PP

                                      HHHH CS
                               TBP 81 ilkk 84
                                      +l++
  gi|298675995|ref|YP_003727745.1| 87 KLND 90
                                      9986 PP

  == domain 2  score: 91.4 bits;  conditional E-value: 4.5e-30
                                       EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHH CS
                               TBP   2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakki 78 
                                       +++qN+vasa+l+  l+L+++a  +  +n+eYepe+fpglvyr+++pkv++liFssGk+v+tG ks++++++ ++ +
  gi|298675995|ref|YP_003727745.1| 101 ITVQNIVASADLHAVLNLNAIAIGLGLENIEYEPEQFPGLVYRIDDPKVVVLIFSSGKLVVTGGKSPDHCERGVEVV 177
                                       68********************99779*******************************************9999876 PP

                                       H CS
                               TBP  79 a 79 
                                        
  gi|298675995|ref|YP_003727745.1| 178 R 178
                                       5 PP

>> DUF3378  Domain of unknown function (DUF3378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   3.6e-06     0.022      11      55 ..      27      72 ..      18      89 .. 0.83
   2 !   16.5   0.0   1.1e-06    0.0067      24      55 ..     134     165 ..     129     171 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.6e-06
                           DUF3378 11 ikkmkeyyksk.lrskkppyavfaakkndttItaYtSgKVlFQGkn 55
                                      ++k++ +++    +++k p+ v++  ++++   ++tSgKV+  G++
  gi|298675995|ref|YP_003727745.1| 27 LTKIEAEFEGAeYNKQKFPGLVYRVSNPKAAFLVFTSGKVVCTGAK 72
                                      667777777663456679***********************98875 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.1e-06
                           DUF3378  24 skkppyavfaakkndttItaYtSgKVlFQGkn 55 
                                        ++ p+ v++++++++++ ++ SgK+++ G +
  gi|298675995|ref|YP_003727745.1| 134 PEQFPGLVYRIDDPKVVVLIFSSGKLVVTGGK 165
                                       5789***********************99865 PP

>> NdhS  NAD(P)H dehydrogenase subunit S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0   0.00073       4.4      18      34 ..      43      59 ..      34      65 .. 0.82
   2 !    6.9   0.0   0.00084         5      18      34 ..     136     152 ..     128     158 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00073
                              NdhS 18 gfeGlvQrvsdgkaaVl 34
                                      +f Glv rvs+ kaa l
  gi|298675995|ref|YP_003727745.1| 43 KFPGLVYRVSNPKAAFL 59
                                      68899999999999976 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00084
                              NdhS  18 gfeGlvQrvsdgkaaVl 34 
                                       +f Glv r+ d k+ Vl
  gi|298675995|ref|YP_003727745.1| 136 QFPGLVYRIDDPKVVVL 152
                                       799***********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1302.25
//
Query:       gi|298675996|ref|YP_003727746.1|  [L=79]
Description: hypothetical protein Metev_2123 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-30  105.0   0.1    1.4e-30  104.8   0.1    1.0  1  MTH865    MTH865-like family


Domain annotation for each model (and alignments):
>> MTH865  MTH865-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.8   0.1     8e-35   1.4e-30       1      70 []       6      75 ..       6      75 .. 0.98

  Alignments for each domain:
  == domain 1  score: 104.8 bits;  conditional E-value: 8e-35
                                      HHHHHHHHHHTTSSSTTBHHHHHHHH-TTSS-----BTTB---TTTTGGGS-GGGSB-SHHHHHHHHHHH CS
                            MTH865  1 elkeqivealegadFPikspeeLlaalPkGaettceagdvevtagelgkklkdsdFPyksaedladdive 70
                                      +++eqi +al+++dFPi+ peeLl+a+P+Ga+ttc++gdvevtage+gk+lk++dFP++sa+++ad+iv+
  gi|298675996|ref|YP_003727746.1|  6 DIHEQIKGALQSVDFPINIPEELLNAFPEGADTTCKSGDVEVTAGEAGKLLKEDDFPFNSAKEVADTIVD 75
                                      69******************************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.19s 00:00:00.52 Elapsed: 00:00:00.33
# Mc/sec: 707.62
//
Query:       gi|298675997|ref|YP_003727747.1|  [L=250]
Description: regulatory protein ArsR [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.1e-07   29.0   0.0    1.5e-06   28.0   0.0    1.6  1  HTH_5          Bacterial regulatory protein, arsR family
    3.7e-05   23.6   0.6    0.00012   22.0   0.6    1.9  1  HTH_45         Winged helix-turn-helix
     0.0019   18.2   0.0     0.0035   17.4   0.0    1.5  1  HTH_20         Helix-turn-helix domain
     0.0091   16.2   0.0      0.027   14.6   0.0    1.9  1  HTH_34         Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.013   15.1   5.8      0.013   15.1   5.8    2.5  2  PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subun
      0.018   14.6   0.0      0.034   13.7   0.0    1.5  1  HTH_24         Winged helix-turn-helix DNA-binding
      0.045   14.2   0.1       0.28   11.6   0.0    2.3  3  GlutR_dimer    Glutamyl-tRNAGlu reductase, dimerisation domai
      0.073   13.2   4.2       0.35   11.0   2.5    2.2  2  KaiA           KaiA C-terminal domain
       0.38    9.8   4.7       0.47    9.5   4.7    1.1  1  Peptidase_C50  Peptidase family C50
        0.9    9.6   4.7        0.6   10.2   0.5    2.3  2  OSCP           ATP synthase delta (OSCP) subunit
        1.2    9.1   5.4        6.7    6.7   5.4    2.4  1  DUF1043        Protein of unknown function (DUF1043)
        5.1    7.3   9.1        0.6   10.3   2.4    2.5  2  GED            Dynamin GTPase effector domain


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   9.8e-10   1.5e-06       2      46 ..     176     220 ..     175     221 .. 0.96

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 9.8e-10
                                       HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5   2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46 
                                       ++Rl ILk+ a   +++++l++ +gl+ +++  HL kL ++G+++
  gi|298675997|ref|YP_003727747.1| 176 KQRLTILKSIATDTKSFTQLSKLTGLNGGNLLFHLDKLLNSGMIQ 220
                                       78****************************************986 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.6   7.8e-08   0.00012      10      71 ..     180     243 ..     178     249 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 7.8e-08
                            HTH_45  10 dILeaisegeakkTkimykanLsykllnkYLdmLvekglikk..skekYvlTekGlelleklke 71 
                                        IL++i  + ++ T++ +   L+  +l   Ld+L++ g+i++  + + Y +T kG  +l+ + +
  gi|298675997|ref|YP_003727747.1| 180 TILKSIATDTKSFTQLSKLTGLNGGNLLFHLDKLLNSGMIQQrsERGDYIITGKGYATLKGIFN 243
                                       69**************************************76447889*********9997755 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   2.4e-06    0.0035       7      60 ..     173     225 ..     167     226 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.4e-06
                                       HS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20   7 LahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60 
                                       +a++ R+ il+ +   +  ++++l ++ +l   +l +HL++L   g + ++ e+
  gi|298675997|ref|YP_003727747.1| 173 IANKQRLTILKSI-ATDTKSFTQLSKLTGLNGGNLLFHLDKLLNSGMIQQRSER 225
                                       68999********.**********************************998775 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.8e-05     0.027       2      46 ..     178     221 ..     177     243 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.8e-05
                            HTH_34   2 RlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYiev 46 
                                       Rl +l + a +d  +f++l++ ++++ gnL  hl+kL + g i+ 
  gi|298675997|ref|YP_003727747.1| 178 RLTILKSIA-TDTKSFTQLSKLTGLNGGNLLFHLDKLLNSGMIQQ 221
                                       566666654.67779************************999975 PP

>> PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   1.4     0.074   1.1e+02      35      60 ..       7      32 ..       4      43 .. 0.85
   2 ?   15.1   5.8   8.7e-06     0.013      32      88 ..     103     159 ..      80     188 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.074
                     PI3K_P85_iSH2 35 qlkeeynkiseeiqlkrqaleaFnea 60
                                      ++k+e  +i+eei+ +r  ++ F e 
  gi|298675997|ref|YP_003727747.1|  7 EYKNELREIKEEISSMRKEFNRFFEY 32
                                      57889999999**9999999999775 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 8.7e-06
                     PI3K_P85_iSH2  32 eydqlkeeynkiseeiqlkrqaleaFneaikmFeeqiklqekfskeaqehEieklqe 88 
                                       + +q++e++n++++e +        F+ea k+Fe qi+l  +++   +e ++e++q+
  gi|298675997|ref|YP_003727747.1| 103 TIEQYYEQFNELKKEKAKYPKCETCFSEAAKLFEKQINLMRSLKIYEKEDDKENIQN 159
                                       579************999999999*******************99999999999986 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.3e-05     0.034      19      48 .]     191     220 ..     175     220 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.3e-05
                            HTH_24  19 sqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                       s ++L++ +gl  ++++ +l++L ++G I+
  gi|298675997|ref|YP_003727747.1| 191 SFTQLSKLTGLNGGNLLFHLDKLLNSGMIQ 220
                                       889************************995 PP

>> GlutR_dimer  Glutamyl-tRNAGlu reductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00019      0.28       7      81 ..      23     101 ..      17     116 .. 0.81
   2 ?    0.6   0.0      0.54   8.1e+02      25      40 ..     103     118 ..      98     137 .. 0.88
   3 ?   -2.2   0.0         4     6e+03      49      59 ..     149     158 ..     126     177 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00019
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHS-S..-------.-TTHHHHHHHHHHHHHHHHHHSS. CS
                       GlutR_dimer   7 eeeveefeawlkslevvptIkalrekaeeir.eeeleralkklaldgedree.lekltrslvnkllheptarLkea. 80 
                                       ++e+++f++  +++ ++++++++++++++i  +  +e  ++ l+ d+  ++  ++++ +s++n +l+e+ + L+++ 
  gi|298675997|ref|YP_003727747.1|  23 RKEFNRFFEYSNQQYLEQILQDMKNNFSRILiDYVVEDSKNSLN-DNMVQDCkMKDFCESIFNDFLQETAQLLNNDs 98 
                                       57999************************972567899999999.66666666******************999985 PP

                                       ..- CS
                       GlutR_dimer  81 ..e 81 
                                          
  gi|298675997|ref|YP_003727747.1|  99 vgP 101
                                       332 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.54
                                       HHHHHHHHHHHHHHHH CS
                       GlutR_dimer  25 tIkalrekaeeireee 40 
                                       tI +++e+++e+++e 
  gi|298675997|ref|YP_003727747.1| 103 TIEQYYEQFNELKKEK 118
                                       8999999999999886 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 4
                                       ..--------T CS
                       GlutR_dimer  49 aldgedreele 59 
                                       + +++d+e+++
  gi|298675997|ref|YP_003727747.1| 149 E-KEDDKENIQ 158
                                       2.333333344 PP

>> KaiA  KaiA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.5   0.00024      0.35      12      68 ..      24      79 ..      20      97 .. 0.82
   2 ?    1.3   0.0      0.24   3.6e+02       6      52 ..     145     192 ..     140     201 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00024
                                      --GGGSCCCSTHHHHHHHHHHHHHHHHHHHHHCTSTTSSHHHHHHHHHHHHHHTT-- CS
                              KaiA 12 rdpkkflrnlskeekkelleelkseyreivleyfkddsevnqkidefvnkaffadls 68
                                      ++ ++f+   +++  +++l+++k+++ +i+++y  +ds+ n+  d++v+ + + d  
  gi|298675997|ref|YP_003727747.1| 24 KEFNRFFEYSNQQYLEQILQDMKNNFSRILIDYVVEDSK-NSLNDNMVQDCKMKDFC 79
                                      5667899999999999******************99875.77788888888777764 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.24
                                       CECEEE--GGGSCCCSTHHHH.HHHHHHHHHHHHHHHHHCTSTTSSHH CS
                              KaiA   6 lgvyykrdpkkflrnlskeek.kelleelkseyreivleyfkddsevn 52 
                                       l +y k d k+ ++nl+ ee  k++ + + ++ r  +l+  ++d++  
  gi|298675997|ref|YP_003727747.1| 145 LKIYEKEDDKENIQNLPVEEVvKDVCDPIANKQRLTILKSIATDTKSF 192
                                       679999999999999998885267889999999999998888877655 PP

>> Peptidase_C50  Peptidase family C50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   4.7   0.00032      0.47      40     165 ..      32     158 ..       7     199 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00032
                                       HHHHHHHHHHHHHHHHHHHCH.CCHHCCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTGGGGGGGS-E---HHHHHHH CS
                     Peptidase_C50  40 eevkeelkeiieesnestksa.kdvktkeakkeWWkeReeLDkrLkeLleniekvwLggfkgilsqeerekellekf 115
                                        + ++ l++i+++ +++ ++   d+   e+ k+  ++    D ++k+++e+i + +L     +l++++  + ++e+ 
  gi|298675997|ref|YP_003727747.1|  32 YSNQQYLEQILQDMKNNFSRIlIDYVV-EDSKNSLNDNMVQDCKMKDFCESIFNDFLQETAQLLNNDSVGPGTIEQY 107
                                       356788999999999999996466555.5555556777888************************************ PP

                                       HHHHHHHHHHHSCHHHHSCHCCCCHTBTHHHHHHHHTCHTT.TTTHHHHHH CS
                     Peptidase_C50 116 qkkfekilkkhlpsrkqkkkekkklelddrllelflglgda.eedldeele 165
                                        ++f+++ k++ +  k ++  ++  +l ++ ++l+ +l+ + +ed +e+++
  gi|298675997|ref|YP_003727747.1| 108 YEQFNELKKEKAKYPKCETCFSEAAKLFEKQINLMRSLKIYeKEDDKENIQ 158
                                       *********999777777777888888888888888888765333333333 PP

>> OSCP  ATP synthase delta (OSCP) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.3      0.33   4.9e+02      11      63 ..      31      85 ..       4      99 .. 0.54
   2 ?   10.2   0.5    0.0004       0.6      17      93 ..     102     190 ..      96     197 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.33
                              OSCP 11 elAkekgaleeveeelea.leavlaed..kklaellsnpavsaeekkdlleelfke 63
                                      e+++++  le++ +++++ ++++l +   ++ ++ l++  v++ + kd+ e++f++
  gi|298675997|ref|YP_003727747.1| 31 EYSNQQY-LEQILQDMKNnFSRILIDYvvEDSKNSLNDNMVQDCKMKDFCESIFND 85
                                      4443322.444444443312333322211344555555555555555555555555 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0004
                              OSCP  17 galeeveeelealeavlaedkklaellsnpavsaeekkdlleelfke............klseavknflkllaenkR 81 
                                       g++e+++e++++l++  a+ +k ++ +s+ a   e++ +l+++l                ++e+vk ++  +a+++R
  gi|298675997|ref|YP_003727747.1| 102 GTIEQYYEQFNELKKEKAKYPKCETCFSEAAKLFEKQINLMRSLKIYekeddkeniqnlPVEEVVKDVCDPIANKQR 178
                                       578999*************************999999999998544455999999999999**************** PP

                              OSCP  82 lalLpeiaeefe 93 
                                       l++L++ia+  +
  gi|298675997|ref|YP_003727747.1| 179 LTILKSIATDTK 190
                                       *******98655 PP

>> DUF1043  Protein of unknown function (DUF1043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   5.4    0.0045       6.7      28      67 ..       7      47 ..       2     161 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0045
                           DUF1043 28 klekelekakaeleeqkqeledHfaqsa.elLetlaedyqk 67
                                      + ++el + k+e++  ++e +++f++s+ + Le++ +d+++
  gi|298675997|ref|YP_003727747.1|  7 EYKNELREIKEEISSMRKEFNRFFEYSNqQYLEQILQDMKN 47
                                      6789*********************9972568888777765 PP

>> GED  Dynamin GTPase effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   2.4    0.0004       0.6      14      68 ..      35      93 ..      16      98 .. 0.88
   2 ?    0.1   0.5      0.61   9.2e+02      52      84 ..     114     150 ..     104     153 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0004
                                      HHHHHHHHHHHHHHHHHHHHHHHTHHHHCCCCCHHHCCTTSGGG....HHHHT---SCH CS
                               GED 14 ksYfnivrktiadqiPkaimhllvneakeslqkellakLykked....ldeLLkEdeei 68
                                      ++Y++ + + ++++   + +  +v+++k+sl+++++++   k+     ++++L+E +++
  gi|298675997|ref|YP_003727747.1| 35 QQYLEQILQDMKNNFSRILIDYVVEDSKNSLNDNMVQDCKMKDFcesiFNDFLQETAQL 93
                                      68***********************************9998887667788888888766 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.61
                                       TTSGGG....HHHHT---SCHCCCCHHHHHHHHHHHH CS
                               GED  52 Lykked....ldeLLkEdeeiaekRkelkkrlealkk 84 
                                       L k+++    +++ ++E +++ ek+ +l ++l++++k
  gi|298675997|ref|YP_003727747.1| 114 LKKEKAkypkCETCFSEAAKLFEKQINLMRSLKIYEK 150
                                       4454445555899999999999999999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1912  (0.106643); expected 358.6 (0.02)
Passed bias filter:                      757  (0.0422221); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 1499.37
//
Query:       gi|298675998|ref|YP_003727748.1|  [L=373]
Description: chromosome segregation and condensation protein ScpB [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.7e-39  133.1   0.3    8.2e-38  129.5   0.0    2.2  2  SMC_ScpB  Segregation and condensation complex subunit ScpB
  ------ inclusion threshold ------
       0.16   12.1   0.0       0.28   11.2   0.0    1.4  1  HTH_20    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.5   0.0   9.2e-42   8.2e-38       2     154 ..      13     157 ..      12     161 .. 0.98
   2 ?    1.1   0.1      0.03   2.7e+02      15      48 ..     260     292 ..     255     305 .. 0.79

  Alignments for each domain:
  == domain 1  score: 129.5 bits;  conditional E-value: 9.2e-42
                          SMC_ScpB   2 iiEAiLfvageplsleeLakilelskeeveealeeLkeeyeeedrglelvevaggyrlvtkpelaevvkklvkekkk 78 
                                       iiEA+Lf+ag+ +++++L +i++ sk+ + ++++ L eey+ +d+gle+  ++++y +++kpe++e+v+kl+++   
  gi|298675998|ref|YP_003727748.1|  13 IIEAALFAAGNTVDIQTLTRIISKSKKHTISVVQTLIEEYNGSDTGLEILDLGERYVMQVKPEFSELVSKLAPR--- 86 
                                       8*********************999*************************************************... PP

                          SMC_ScpB  79 trLsqaaletLaiIaykqpvtraeieeiRGvnsdsvvrtLlerglieekgrkeepgrpilYgtTekFleyfglksl 154
                                        +Ls+  l+tL++Iay+qp+t++++ ++RG +++++v++L +rg+i+ +      gr+ l++tT  F +yfgl+s 
  gi|298675998|ref|YP_003727748.1|  87 -ELSSPILRTLSMIAYHQPITQSDLVDLRGNSAYDHVKELHDRGFIRTNA----YGRTKLLETTPLFADYFGLESN 157
                                       .**********************************************999....9******************995 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.03
                          SMC_ScpB  15 sleeLakilels.keeveealeeLkeeyeeedrgl 48 
                                       s+++L++i + + ++e  + + +Lke+y+  +++l
  gi|298675998|ref|YP_003727748.1| 260 SIKKLENISDSDkSQESIDYIRDLKEKYS--SKAL 292
                                       56788888876678899999********4..4444 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.2e-05      0.28      32      57 ..     109     134 ..      90     138 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.2e-05
                                       HHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20  32 erldlskntlsyHLrvLeeagLvevv 57 
                                       +++dl+ n++++H+++L + g++++ 
  gi|298675998|ref|YP_003727748.1| 109 DLVDLRGNSAYDHVKELHDRGFIRTN 134
                                       45689******************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2386.44
//
Query:       gi|298675999|ref|YP_003727749.1|  [L=287]
Description: chromosome segregation and condensation protein ScpA [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-22   81.0   5.1    4.5e-21   75.9   5.1    2.1  1  SMC_ScpA         Segregation and condensation protein ScpA
  ------ inclusion threshold ------
       0.03   13.6   0.0      0.059   12.7   0.0    1.6  1  Rad21_Rec8       Conserved region of Rad21 / Rec8 like protei
       0.16   11.5   0.5       0.22   11.1   0.5    1.2  1  Questin_oxidase  Questin oxidase-like


Domain annotation for each model (and alignments):
>> SMC_ScpA  Segregation and condensation protein ScpA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.9   5.1   7.6e-25   4.5e-21       1     238 [.      66     278 ..      66     280 .. 0.78

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 7.6e-25
                                       HHHHHHHHHTSSSSXXXXHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHSXXXXXXXXXXXXXXXXXXXXXX CS
                          SMC_ScpA   1 LiiakeldvtdvavakvtdqflayiktllnkleleesteylviastlvelKaasLlpleqveeeedeeleleelrdk 77 
                                       L++++ +d++d++++++td+fl  i+ + + ++l +s+  l+ as l+++K+  + + e+++e e+++   +e+  +
  gi|298675999|ref|YP_003727749.1|  66 LANDGDIDPWDIDIVDITDKFLDKIEQM-KLMDLRISARTLLYASVLLRMKSTGIIQEEEEDEDEEPD--SLEMDGE 139
                                       7899************************.**************************9999988866666..4444333 PP

                                       XXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          SMC_ScpA  78 LiarLleYrkykeeakl.fkeleaerlksfskarsdleefikeveevavkieksvfklieafnkllkrakivalaek 153
                                            +   ++ e+ +    +l    ++  sk++++l+e++ e+++ + k+e  + k+ +  +k + r++ +     
  gi|298675999|ref|YP_003727749.1| 140 -----I---EFSEVEDYpVPNLP---VRRNSKRPVTLNELVTELKKAE-KVESRR-KERNHSKKEIDRKEEKEQSS- 202
                                       .....3...24444333123333...45557999**********9865.788774.55556666666664433333. PP

                                       XX...HHHHHHHHHHHH...............HHHTS-EEGGGSSTT...--HHHHHHHHHHHHHHHHTT-EEEEES CS
                          SMC_ScpA 154 qiseleisieeqleellaqleqflqarlkevLldlrswvdlseLladnkledkkelvgvFlAlLeLiknqavaleQe 230
                                       + + l+i++ee  +  +      l  +l+e++++  s++++se+       ++ e+v ++l lL L  +++++l+Qe
  gi|298675999|ref|YP_003727749.1| 203 TDEVLDIAHEEDITGRAE----GLYEKLEEMFQNK-SYTSFSEISYG----ERSEKVMTYLSLLFLAADRKIKLNQE 270
                                       3489*******9998874....4455666666665.99*****8665....99************************ PP

                                       STTS-EEE CS
                          SMC_ScpA 231 eflddLqv 238
                                       e +++L++
  gi|298675999|ref|YP_003727749.1| 271 ELFGELYI 278
                                       *******9 PP

>> Rad21_Rec8  Conserved region of Rad21 / Rec8 like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   9.9e-06     0.059      23      52 ..     252     281 ..     231     284 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.9e-06
                                       HHHHHHHHHHHTSEEEEESSTT--EEEEE- CS
                        Rad21_Rec8  23 lFyelLvLatkgvIkvkQeaPYgdIlitlg 52 
                                       +  +lL La  ++Ik++Qe+ +g++ i +g
  gi|298675999|ref|YP_003727749.1| 252 TYLSLLFLAADRKIKLNQEELFGELYIFPG 281
                                       56689********************99876 PP

>> Questin_oxidase  Questin oxidase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.5   3.6e-05      0.22     143     220 ..     139     231 ..     101     246 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.6e-05
                   Questin_oxidase 143 s..............s.raessegsslleilerilkderldaaarpgnedddkirdgvlkr..aadeileyanawkv 202
                                       +              + r++s+++++l e++ ++ k+e++++ ++++n+++++i  +  k+    de+l++a++ ++
  gi|298675999|ref|YP_003727749.1| 139 EiefsevedypvpnlPvRRNSKRPVTLNELVTELKKAEKVESRRKERNHSKKEIDRKEEKEqsSTDEVLDIAHEEDI 215
                                       1444455555555442577888899********9999***9996665676555555555556568***********9 PP

                   Questin_oxidase 203 seeedkeeleekleeliw 220
                                       + +  +e l eklee+++
  gi|298675999|ref|YP_003727749.1| 216 TGR--AEGLYEKLEEMFQ 231
                                       666..578********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1706  (0.0951531); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 1891.36
//
Query:       gi|298676000|ref|YP_003727750.1|  [L=1174]
Description: chromosome segregation protein SMC [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.3e-44  149.6 106.6    2.9e-41  141.3 106.6    3.9  1  SMC_N            RecF/RecN/SMC N terminal domain
    1.9e-33  115.2   0.0      1e-32  112.9   0.0    2.4  1  SMC_hinge        SMC proteins Flexible Hinge Domain
      5e-18   66.3   8.4      5e-18   66.3   8.4    8.6  3  AAA_23           AAA domain
    4.6e-09   35.6 158.8     0.0015   17.5  23.5    8.1  8  Spc7             Spc7 kinetochore protein
    9.6e-09   35.4  32.5    9.6e-09   35.4  32.5    4.4  2  AAA_15           AAA ATPase domain
    3.2e-08   34.2 170.8      0.011   16.2  15.7    9.8  8  APG6_N           Apg6 coiled-coil region
    2.2e-06   27.4 115.1     0.0017   17.9  19.4    6.1  6  MscS_porin       Mechanosensitive ion channel porin domain
    2.9e-06   26.9   0.0    6.5e-06   25.8   0.0    1.6  1  AAA_29           P-loop containing region of AAA domain
    5.3e-06   26.5 168.0      0.046   13.7  27.3    8.3  7  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
    5.1e-05   23.3   2.2    5.1e-05   23.3   2.2   10.5  8  TolA_bind_tri    TolA binding protein trimerisation
    0.00013   19.7 128.6     0.0016   16.1  57.8    3.0  2  DUF3584          Protein of unknown function (DUF3584)
    0.00017   21.5   0.1    0.00017   21.5   0.1    5.1  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    0.00037   18.8  26.1    0.00037   18.8  26.1    7.0  5  EzrA             Septation ring formation regulator, EzrA
    0.00043   20.5 105.7      0.059   13.6   6.5    9.6 10  FliJ             Flagellar FliJ protein
    0.00073   19.9   1.6    0.00073   19.9   1.6   10.3  9  Snapin_Pallidin  Snapin/Pallidin
    0.00093   18.3  20.7    0.00093   18.3  20.7    6.9  7  IFT57            Intra-flagellar transport protein 57
     0.0015   18.8  21.5     0.0015   18.8  21.5    8.1  4  ATG16            Autophagy protein 16 (ATG16)
     0.0018   17.9 140.2      0.084   12.4   9.7    8.1  8  Filament         Intermediate filament protein
     0.0027   16.5  31.6     0.0027   16.5  31.6    4.4  3  WEMBL            Weak chloroplast movement under blue light
     0.0044   16.5  34.7     0.0044   16.5  34.7    6.3  6  Golgin_A5        Golgin subfamily A member 5
     0.0055   15.4 139.9       0.01   14.5  19.8    5.9  6  AAA_13           AAA domain
  ------ inclusion threshold ------
      0.011   15.8  10.5      0.011   15.8  10.5    8.8  9  Laminin_II       Laminin Domain II
      0.053   14.0 137.4       0.41   11.1  15.6    7.4  7  Fez1             Fez1
      0.057   13.6 121.9       0.27   11.4  10.6    8.6  8  Fib_alpha        Fibrinogen alpha/beta chain family
        0.5    9.6 121.4      0.075   12.3  16.3    9.0  9  DUF3450          Protein of unknown function (DUF3450)
        0.5   10.4 103.5       0.04   14.0   8.0   10.5 10  DUF1664          Protein of unknown function (DUF1664)
        0.7   10.4  73.4       0.14   12.7   3.8   10.3  9  NPV_P10          Nucleopolyhedrovirus P10 protein
        3.8    7.1 145.5      0.012   15.2  16.2    7.1  5  Lebercilin       Ciliary protein causing Leber congenital ama
        7.9    6.2 130.8      0.028   14.2  16.8    7.3  7  TACC_C           Transforming acidic coiled-coil-containing p


Domain annotation for each model (and alignments):
>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.3 106.6   4.7e-44   2.9e-41       1     218 [.       2    1165 ..       2    1167 .. 1.00

  Alignments for each domain:
  == domain 1  score: 141.3 bits;  conditional E-value: 4.7e-44
                                        EEEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N    1 vlkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvk 75  
                                        ++k++e  nFks+ gk+v++pf + ft i GpNGSGKsn++d ilF LG ++++++r+ekl+dli++ +++++ +
  gi|298676000|ref|YP_003727750.1|    2 YIKEIEFLNFKSF-GKKVKIPFFDDFTTISGPNGSGKSNIIDGILFALGLSNSRTMRAEKLTDLIYNPDSSNKPQ 75  
                                        79***********.5************************************************************ PP

                                        EEEEEEEEEETTEESSSSSSCEEEEEEEETTSE...EEEEETTEEE-HHHHHHHHHCTT-STT............ CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx............ RF
                             SMC_N   76 kaeveitfdnedkklkiekeevsisrrvkrkge...seykingkevtkkevsellesagiske............ 135 
                                         a+v+i fdn+d+++++e++ev+i+r++k++g+   s +++ngk+v+ k++++ l++a++++e            
  gi|298676000|ref|YP_003727750.1|   76 YAQVKIRFDNSDNEMPVEADEVEITRKIKETGSgyySYFYFNGKSVSLKDIHNYLAKAKVTPEgynvvmqgdvtq 150 
                                        ********************************988889999********************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|298676000|ref|YP_003727750.1|  151 iitmtpverrkiideiagvsefdnkkeramneletvrehiervdiiieevnnqldklkderdqalkyqslkqeka 225 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|298676000|ref|YP_003727750.1|  226 kyegfvilsklkdakkelesvnsdiesknnsveelqksldekneqlqelektlsdltnqiqnmgekeqiqikkdi 300 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|298676000|ref|YP_003727750.1|  301 eeirgeisrcngsieiaeneiqdidtrrrktlvdiddakskveeleskindeeirkesinselserknelkllqs 375 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|298676000|ref|YP_003727750.1|  376 kindvdakfaetrdklselknereqiknekselireenrlldavrrksaekrdieneiqdskekiessdsdtrsv 450 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|298676000|ref|YP_003727750.1|  451 qheidklnekieslnkdlddlesnrsqlkeilneheeelrkhqqeyaqvearvraaeenskyskavdtvisaknn 525 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|298676000|ref|YP_003727750.1|  526 kelqgiygtiaelgqadekystalqiaaggrmqavvtendedaseaieylkrykagratflpltklekrrpykdl 600 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|298676000|ref|YP_003727750.1|  601 sdkkgvvgyaidlidfddkfepafwyvfrdtlvmdslenarklmgglrivtldgelveksgamsggskqqrsgls 675 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|298676000|ref|YP_003727750.1|  676 faaaekekltkiaekiteydskrnntikklddvesqisdvkqeinnheneiskkqmqleeissreerlsqfiesk 750 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|298676000|ref|YP_003727750.1|  751 nkeleeieesrkelkeemdkvvadkdektkkeneldekiseleeeladseipelnekadnlneeiqrlegrirdt 825 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|298676000|ref|YP_003727750.1|  826 dsninslnldleyankrisddrelieeldekksshqgriesfkekikeledslaskqerekelgdelkelqdera 900 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|298676000|ref|YP_003727750.1|  901 nkqteydnlkkdynsikskfenasnrlqalestksslkeqidelrseleqrgieeteevpnyetvrtriasieka 975 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|298676000|ref|YP_003727750.1|  976 medlepvnmraideydevlnrheemknrrdtlsnereqilerieqyenlkketfmetfnginkafssifnelsdg 1050
                                        *************************************************************************** PP

                                        ................................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHH CS
                                        ................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  136 ................................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkk 178 
                                                                        ++SgGek+L+ala++fAiq+++pap+y +Deid+ LD +n ++
  gi|298676000|ref|YP_003727750.1| 1051 tgelaldnyeepfsggltlkaqpkdkslqrleAMSGGEKSLTALAFVFAIQSYRPAPFYAFDEIDMFLDGANSER 1125
                                        *************************************************************************** PP

                                        HHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEEEEETTE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  179 vaellkeksknaQfivislreemlekadklvgvtkvengv 218 
                                        va+++k++ + aQfiv+slr+ m+e a++++gvt++en+ 
  gi|298676000|ref|YP_003727750.1| 1126 VAQRIKKSVNGAQFIVVSLRKPMIESASRTLGVTMQENNN 1165
                                        ***********************************99875 PP

>> SMC_hinge  SMC proteins Flexible Hinge Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.9   0.0   1.7e-35     1e-32       2     116 ..     529     643 ..     528     644 .. 0.96

  Alignments for each domain:
  == domain 1  score: 112.9 bits;  conditional E-value: 1.7e-35
                         SMC_hinge   2 kgvlGrladlievdegyekAveaalgnrlqalvvedeetakkiieflkkknagratflpldrikqknkadgandkns 78 
                                       +g++G++a+l + de+y +A+++a+g+r+qa+v+e++e+a ++ie+lk+ +agratflpl +++++++ ++  dk+ 
  gi|298676000|ref|YP_003727750.1| 529 QGIYGTIAELGQADEKYSTALQIAAGGRMQAVVTENDEDASEAIEYLKRYKAGRATFLPLTKLEKRRPYKDLSDKKG 605
                                       79**********************************************************99999988888877777 PP

                         SMC_hinge  79 gavplidlvevddelrkalryllgdtlvvdsldeAeel 116
                                        ++++idl+++dd++++a+ y+++dtlv dsl++A++l
  gi|298676000|ref|YP_003727750.1| 606 VVGYAIDLIDFDDKFEPAFWYVFRDTLVMDSLENARKL 643
                                       ************************************98 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   8.4   8.1e-21     5e-18       2     200 .]       6     251 ..       5     255 .. 0.68
   2 ?    0.5  17.3       1.2   7.4e+02     148     200 .]     236     286 ..     232     315 .. 0.56
   3 ?    0.7  11.5       1.1   6.5e+02     142     197 ..     671     738 ..     613     741 .. 0.68

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 8.1e-21
                            AAA_23   2 Lkienfrsf.rdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiese..gkvkayv 75 
                                       ++  nf+sf ++++i F + +t I+GpNG+GK+ i+d i +aL+   +r+ r ++    ++ +   ++  + + a+v
  gi|298676000|ref|YP_003727750.1|   6 IEFLNFKSFgKKVKIPFFDDFTTISGPNGSGKSNIIDGILFALGLSNSRTMRAEK---LTDLIYNPDSsnKPQYAQV 79 
                                       7788*****77788*******************************9999999775...4444443444113556669 PP

                            AAA_23  76 eltfenkdgry...trsiererelskkkgktt..kkaklelleideleqfise........llgskkiilnlilflg 139
                                       +++f n d++     +++e +r+ +++ + ++     ++++++ ++  +++ +        ++  + +  ++i + +
  gi|298676000|ref|YP_003727750.1|  80 KIRFDNSDNEMpveADEVEITRKIKETGSGYYsyFYFNGKSVSLKDIHNYLAKakvtpegyNVVMQGDVTQIITMTP 156
                                       99999999976877444444444444444333223335555555555555555666666777778888999999*** PP

                            AAA_23 140 qer..............feefelkdkke..................rleelekeleeledekkllekl...eqekek 181
                                        er              +       kke                   +ee++++l++l+de+++  k    +qek  
  gi|298676000|ref|YP_003727750.1| 157 VERrkiideiagvsefdN-------KKEramneletvrehiervdiIIEEVNNQLDKLKDERDQALKYqslKQEK-- 224
                                       **9666666666555331.......22234455567888999999999999999999999887544442333333.. PP

                            AAA_23 182 ek.........eleeleeeleeilkele 200
                                        +         +l++ ++ele++++++e
  gi|298676000|ref|YP_003727750.1| 225 -AkyegfvilsKLKDAKKELESVNSDIE 251
                                       .224488888877777777777777765 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.2
                            AAA_23 148 lkdkkerleelekeleeledekkllekleqekekekeleeleeeleeilkele 200
                                       lkd k++le+++ ++e +++  ++l+k ++  ek+++l+ele++l +++++++
  gi|298676000|ref|YP_003727750.1| 236 LKDAKKELESVNSDIESKNNSVEELQKSLD--EKNEQLQELEKTLSDLTNQIQ 286
                                       456666666666666666666666666532..233444444444444444432 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 1.1
                            AAA_23 142 r.......feefelkdkkerleelekeleeledekkllekl.....eqekekekeleeleeeleeilk 197
                                       r       +e+++l +  e++ e+  + +   ++ + +e +     +++++ e+e+++++ +leei +
  gi|298676000|ref|YP_003727750.1| 671 RsglsfaaAEKEKLTKIAEKITEYDSKRNNTIKKLDDVESQisdvkQEINNHENEISKKQMQLEEISS 738
                                       23333222223334444555555544444444444444444666666777888899999999999865 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5  23.5   2.4e-06    0.0015     143     252 ..     175     287 ..     159     295 .. 0.77
   2 !    9.3  12.0   0.00077      0.48     192     281 ..     290     376 ..     286     379 .. 0.91
   3 ?    2.9  21.6     0.067        42     175     274 ..     341     439 ..     339     442 .. 0.60
   4 !    9.0  27.8   0.00095      0.59     143     279 ..     393     507 ..     378     529 .. 0.47
   5 ?    1.9  29.1      0.13        81     142     242 ..     689     795 ..     668     800 .. 0.44
   6 ?    5.5  27.8     0.011       6.9     144     260 ..     764     887 ..     762     903 .. 0.73
   7 !   10.5  13.7   0.00032       0.2     194     273 ..     885     964 ..     879     976 .. 0.87
   8 !    7.4  17.3    0.0028       1.7     145     270 ..     903    1038 ..     899    1052 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.4e-06
                              Spc7 143 gleenlegleedkelLekqeeeldellpeleeekaelee..eleklqeaaeelesid.keeLeelreelaelkaeie 216
                                       + e+ +++le+ +e++e+    ++e+ ++l++ k+e  +  ++++l++++++ e      +L+ +++el++++++ie
  gi|298676000|ref|YP_003727750.1| 175 KKERAMNELETVREHIERVDIIIEEVNNQLDKLKDERDQalKYQSLKQEKAKYEGFViLSKLKDAKKELESVNSDIE 251
                                       4455555555555666665555555555555555555541134577888888888666******************* PP

                              Spc7 217 ekkkelaelqeqleeleekieelkeqkseleeeiae 252
                                       +k++ ++elq+ l+e++e+++el++  s+l ++i++
  gi|298676000|ref|YP_003727750.1| 252 SKNNSVEELQKSLDEKNEQLQELEKTLSDLTNQIQN 287
                                       **********************************96 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00077
                              Spc7 192 elesid.keeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsese 267
                                       e e+i+ k+++ee+r e+++++  ie  ++e+++  +++ +   +i+++k++ +ele++i+      e +k++ +se
  gi|298676000|ref|YP_003727750.1| 290 EKEQIQiKKDIEEIRGEISRCNGSIEIAENEIQDIDTRRRKTLVDIDDAKSKVEELESKIN----DEEIRKESINSE 362
                                       457788899****************************************************....5567788999** PP

                              Spc7 268 vsrlkeevkaleel 281
                                       +s+ k+e+k l+++
  gi|298676000|ref|YP_003727750.1| 363 LSERKNELKLLQSK 376
                                       ***********987 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.067
                              Spc7 175 ekaeleeeleklqeaaeeles...idkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkselee 248
                                       + +ele+++++++ ++e+++s     k+eL+ l++++++++a+ +e +++l+el++++e+++++ +el  + ++l +
  gi|298676000|ref|YP_003727750.1| 341 KVEELESKINDEEIRKESINSelsERKNELKLLQSKINDVDAKFAETRDKLSELKNEREQIKNEKSELIREENRLLD 417
                                       56777777777777777766655333667777777777777777777777777777777766666666666555555 PP

                              Spc7 249 eiaeaervleeckgwsesevsrlkee 274
                                       +++     + ++k+  e+e++  ke+
  gi|298676000|ref|YP_003727750.1| 418 AVR----RKSAEKRDIENEIQDSKEK 439
                                       555....3344444555666666665 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.00095
                              Spc7 143 gleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekk 219
                                       +l+++ e+++++k++L ++e+ l +++ + ++ek ++e+                  e++  +e++++ +++ ++ +
  gi|298676000|ref|YP_003727750.1| 393 ELKNEREQIKNEKSELIREENRLLDAVRRKSAEKRDIEN------------------EIQDSKEKIESSDSDTRSVQ 451
                                       233333444444444444444444444444444444444..................55555555555555555555 PP

                              Spc7 220 kelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkale 279
                                        e+++l+e++e+l++++++l++++s+l+e ++e+e+ l+++    ++e  +++++v+a e
  gi|298676000|ref|YP_003727750.1| 452 HEIDKLNEKIESLNKDLDDLESNRSQLKEILNEHEEELRKH----QQEYAQVEARVRAAE 507
                                       55555555555555555555555555555555444444332....223333333333333 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 0.13
                              Spc7 142 egleenlegleedkelLekqeeeldellpeleeekaeleeeleklqe......aaeelesidkeeLeelreelaelk 212
                                       e+++e  ++ ++  ++L++ e++++++++e++++++e++++  +l+e      +  ++ +++++eLee+ e+ +elk
  gi|298676000|ref|YP_003727750.1| 689 EKITEYDSKRNNTIKKLDDVESQISDVKQEINNHENEISKKQMQLEEissreeRLSQFIESKNKELEEIEESRKELK 765
                                       33333333334444555555555555555555555555555555555222111111222233333333333333333 PP

                              Spc7 213 aeieekkkelaelqeqleeleekieelkeq 242
                                       +e+++  ++ +e++++ +el+eki+el+e+
  gi|298676000|ref|YP_003727750.1| 766 EEMDKVVADKDEKTKKENELDEKISELEEE 795
                                       333333333333333333333344333333 PP

  == domain 6  score: 5.5 bits;  conditional E-value: 0.011
                              Spc7 144 leenlegleedkelLekqeeeldellpeleeeka.....eleeeleklqeaaeeles...idkeeLeelreelaelk 212
                                       l+e+++++ +dk++ +k+e+elde   eleee a     el+e++++l+e+ + le     +  ++++l  +l+ ++
  gi|298676000|ref|YP_003727750.1| 764 LKEEMDKVVADKDEKTKKENELDEKISELEEELAdseipELNEKADNLNEEIQRLEGrirDTDSNINSLNLDLEYAN 840
                                       66677777777777777777777777777777766666777777777777777777665334788999999999999 PP

                              Spc7 213 aeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleec 260
                                       + i+  ++ ++el e++ + + +ie+ ke+++ele+ +a++++ +e++
  gi|298676000|ref|YP_003727750.1| 841 KRISDDRELIEELDEKKSSHQGRIESFKEKIKELEDSLASKQE-REKE 887
                                       9999999999999999999999999999999999999985544.3333 PP

  == domain 7  score: 10.5 bits;  conditional E-value: 0.00032
                              Spc7 194 esidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsr 270
                                       e+   +eL+el++e a+ ++e++++kk++++ +++ e+ ++++++l++ ks+l+e+i e ++ le++   +++ev +
  gi|298676000|ref|YP_003727750.1| 885 EKELGDELKELQDERANKQTEYDNLKKDYNSIKSKFENASNRLQALESTKSSLKEQIDELRSELEQRGIEETEEVPN 961
                                       445579**********************************************************9888888888877 PP

                              Spc7 271 lke 273
                                       +++
  gi|298676000|ref|YP_003727750.1| 962 YET 964
                                       765 PP

  == domain 8  score: 7.4 bits;  conditional E-value: 0.0028
                              Spc7  145 eenlegleedkelLekqeeeldellpeleeekaeleeeleklqe........aaeelesidkeeLeelreelael 211 
                                        + ++++l++d++ ++++ e++++ l++le+ k++l+e++++l++        + ee       + e++r ++a++
  gi|298676000|ref|YP_003727750.1|  903 QTEYDNLKKDYNSIKSKFENASNRLQALESTKSSLKEQIDELRSeleqrgieETEE-----VPNYETVRTRIASI 972 
                                        6788999**********************************999664333322233.....33445556666666 PP

                              Spc7  212 kaeieekk.......kelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsr 270 
                                        ++ +e ++       +e++e+ ++ ee +++ ++l+++++++ e+i++ e++++e+ + + + +++
  gi|298676000|ref|YP_003727750.1|  973 EKAMEDLEpvnmraiDEYDEVLNRHEEMKNRRDTLSNEREQILERIEQYENLKKETFMETFNGINK 1038
                                        666555442222122677777788888888888888888889999998888888877766666665 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4  32.5   1.6e-11   9.6e-09       1     271 [.       1     303 [.       1     327 [. 0.42
   2 ?    1.3  28.4      0.37   2.3e+02      69     334 ..     824    1116 ..     819    1142 .. 0.63

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 1.6e-11
                            AAA_15   1 MkIkkikikNFRslkd.veidlseeltvliGkNnsGKSsilealdlFlnnkekkn...............kkvikie 61 
                                       M+Ik+i+  NF+s+ + v+i++ +++t++ G+N+sGKS+i++ + + l  +   n                      
  gi|298676000|ref|YP_003727750.1|   1 MYIKEIEFLNFKSFGKkVKIPFFDDFTTISGPNGSGKSNIIDGILFALGLS---NsrtmraekltdliynP------ 68 
                                       **************888***************************6666666...22445554333333330...... PP

                            AAA_15  62 kedleifeniseskdikIdvef..................................aekekakeyektlkskekkka 104
                                              ++ ++ +  ++++ f                                                       
  gi|298676000|ref|YP_003727750.1|  69 -------DSSNKPQYAQVKIRFdnsdnempveadeveitrkiketgsgyysyfyfnG-------------------- 118
                                       .......33333344444444433323222222222222222333333333333320.................... PP

                            AAA_15 105 dlllkkkesdlkktikdkklklkknelsdekisvekkks.............................kkelpkeke 152
                                                 ++  +kd + +l k +++ e ++v ++ +                             ++  +++++
  gi|298676000|ref|YP_003727750.1| 119 ----------KSVSLKDIHNYLAKAKVTPEGYNVVMQGDvtqiitmtpverrkiideiagvsefdnkkERAMNELET 185
                                       ..........2233444455555555555555555555521111111111111111111111111111222222222 PP

                            AAA_15 153 eklekekeelkid..kedlkklikkleeslkkee..elknvlksaiiklllisakRnvsd..edsekkssllgklke 223
                                         ++ e  ++ i+  ++ l+kl ++  + lk+++  + k +++ + i+++l  ak++ ++  +d e+k+++ ++l++
  gi|298676000|ref|YP_003727750.1| 186 VREHIERVDIIIEevNNQLDKLKDERDQALKYQSlkQEKAKYEGFVILSKLKDAKKELESvnSDIESKNNSVEELQK 262
                                       22222222222223333333333333333333333333344444444444444444444432222222222222222 PP

                            AAA_15 224 kileealqekleeelteklkeiqeklkeidkklaeelkkilkkkidki 271
                                       ++ e       + e+ ++l++++++l++++++++e+++  +kk+i++i
  gi|298676000|ref|YP_003727750.1| 263 SLDE-------KNEQLQELEKTLSDLTNQIQNMGEKEQIQIKKDIEEI 303
                                       2222.......3444444444444444444444444443344444333 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.37
                            AAA_15   69 eniseskdikIdvefaekekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkks 143 
                                        + +s+ +++ +d+e+            ++ +++++   +l++k+s+++ +i+++k k+k+ e+s  +++  +k  
  gi|298676000|ref|YP_003727750.1|  824 DTDSNINSLNLDLEY----------ANKRISDDRELIEELDEKKSSHQGRIESFKEKIKELEDSLASKQEREK-- 886 
                                        567777888889999..........234455666666788899999999999999999844444444332222.. PP

                            AAA_15  144 kkelpkekeeklekekeelkidkedlkklikkleeslkkee.......elknvlksaiiklllisakRnvsdeds 211 
                                          el   + ++l+ e ++ +++ ++lkk ++ ++++++  +       + k++lk++i++l+   ++R ++++++
  gi|298676000|ref|YP_003727750.1|  887 --ELG-DELKELQDERANKQTEYDNLKKDYNSIKSKFENASnrlqaleSTKSSLKEQIDELRSELEQRGIEETEE 958 
                                        ..222.2223333344444444444444444444444444445558889999********************999 PP

                            AAA_15  212 ekkssllgklkekileealqekl............................eeelteklkeiqeklkeidkklae 258 
                                          + ++  + + +i +  + e l                            +           ++ +        
  gi|298676000|ref|YP_003727750.1|  959 VPNYETVRTRIASIEKA-M-EDLepvnmraideydevlnrheemknrrdtlS-----------NERE-------- 1012
                                        99888888888888664.4.44558999987666666666544333322221...........2222........ PP

                            AAA_15  259 elk........................kilkkkidkikkfnykgkkneeieik...........ddeelplnknG 298 
                                          +                        k + ++++++ ++    + +++ e++           d+  + l+ ++
  gi|298676000|ref|YP_003727750.1| 1013 --QilerieqyenlkketfmetfnginKAFSSIFNELSDGTGELALDNYEEPFsggltlkaqpkDKSLQRLEAMS 1085
                                        ..2222222222233444445555665666666666666666666666666668999999999888888999999 PP

                            AAA_15  299 sGvqrllllillileaekkdekeeknvilliEEPEa 334 
                                         G ++l  l++  +  + +     +  +++++E++ 
  gi|298676000|ref|YP_003727750.1| 1086 GGEKSLTALAFVFAIQSYR-----PAPFYAFDEIDM 1116
                                        9999888888876666666.....777777777765 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   2.9     0.014         9      53     103 ..     166     216 ..     122     219 .. 0.81
   2 !   16.2  15.7   1.8e-05     0.011      17      97 ..     216     298 ..     212     307 .. 0.89
   3 !    9.6  24.2     0.002       1.3      11     131 ..     321     438 ..     314     440 .. 0.92
   4 !   13.1  18.5   0.00017       0.1      21     100 ..     419     498 ..     414     523 .. 0.74
   5 ?    6.8  32.8     0.014       8.9      12     122 ..     692     799 ..     655     802 .. 0.81
   6 ?    6.3  20.9     0.022        14      19     130 ..     809     924 ..     798     926 .. 0.54
   7 !   16.0  13.3   2.2e-05     0.013      32     122 ..     892     979 ..     892     981 .. 0.91
   8 ?    1.3   6.2      0.77   4.8e+02      48     101 ..     968    1021 ..     957    1042 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.014
                            APG6_N  53 eeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwr 103
                                          +++ ++++e++++eL+ + ++ e+++  +++  ++l++l++e ++ ++
  gi|298676000|ref|YP_003727750.1| 166 IAGVSEFDNKKERAMNELETVREHIERVDIIIEEVNNQLDKLKDERDQALK 216
                                       3447889999***********************************998765 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.8e-05
                            APG6_N  17 qleqaekerdaYeef..lkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeel 91 
                                       +++++++e+ +Ye f  l+klk+ kke e+ ++++e+ ++++e+l+k  +e+ e+L+elek+ ++l +++++  e++
  gi|298676000|ref|YP_003727750.1| 216 KYQSLKQEKAKYEGFviLSKLKDAKKELESVNSDIESKNNSVEELQKSLDEKNEQLQELEKTLSDLTNQIQNMGEKE 292
                                       78999*********97789999999999989*****************************************99888 PP

                            APG6_N  92 ealeee 97 
                                       +   ++
  gi|298676000|ref|YP_003727750.1| 293 QIQIKK 298
                                       765554 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.002
                            APG6_N  11 leeldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaal 87 
                                       ++ +d++ +++  ++d+ ++  ++l+++ ++ee      e+++ el++ ++e + l++++++++++ +e +++l++l
  gi|298676000|ref|YP_003727750.1| 321 IQDIDTRRRKTLVDIDDAKSKVEELESKINDEE---IRKESINSELSERKNELKLLQSKINDVDAKFAETRDKLSEL 394
                                       677888888889999999999999999988877...47789************************************ PP

                            APG6_N  88 eeelealeeeeerfwreynelqlelleleeeldsleaqyehaqn 131
                                       ++e e++++e+ + +re n l   + ++  e++ +e+++++ ++
  gi|298676000|ref|YP_003727750.1| 395 KNEREQIKNEKSELIREENRLLDAVRRKSAEKRDIENEIQDSKE 438
                                       **************************************998876 PP

  == domain 4  score: 13.1 bits;  conditional E-value: 0.00017
                            APG6_N  21 aekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeee 97 
                                       ++++  + ++ +++++++k++ e++d+++++ ++e++kl+++ e+l + L++le++r++l++ l++ eeel++ ++e
  gi|298676000|ref|YP_003727750.1| 419 VRRKSAEKRDIENEIQDSKEKIESSDSDTRSVQHEIDKLNEKIESLNKDLDDLESNRSQLKEILNEHEEELRKHQQE 495
                                       45555555566667777777766678888888888888888888888888888888888888888888888888777 PP

                            APG6_N  98 eer 100
                                        ++
  gi|298676000|ref|YP_003727750.1| 496 YAQ 498
                                       654 PP

  == domain 5  score: 6.8 bits;  conditional E-value: 0.014
                            APG6_N  12 eeldkqleqaekerdaYeeflkklkkekkeeek....qdeeleeleeeleklekeeeelleeLkelekereeleael 84 
                                       +e+d++ +++ k+ d+ e+  + +k       +    +++e+ + + +le++++ ee+l + ++   ke ee+e+ +
  gi|298676000|ref|YP_003727750.1| 692 TEYDSKRNNTIKKLDDVESQISDVK-------QeinnHENEISKKQMQLEEISSREERLSQFIESKNKELEEIEESR 761
                                       3444444445555555555555555.......05555789************************************* PP

                            APG6_N  85 aaleeelealeeeeerfwreynelqlelleleeeldsl 122
                                       ++l+ee +++ ++++++ ++ nel+ + +eleeel+  
  gi|298676000|ref|YP_003727750.1| 762 KELKEEMDKVVADKDEKTKKENELDEKISELEEELADS 799
                                       **********************************9876 PP

  == domain 6  score: 6.3 bits;  conditional E-value: 0.022
                            APG6_N  19 eqaekerdaYeeflkklkkekkeeek....qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeel 91 
                                       +++++e++ +e   +  +++ ++ +      ++ + + +e +e+l++++++ +  ++  +++ +ele+ la+ +e +
  gi|298676000|ref|YP_003727750.1| 809 DNLNEEIQRLEGRIRDTDSNINSLNLdleyANKRISDDRELIEELDEKKSSHQGRIESFKEKIKELEDSLASKQERE 885
                                       44444444444444444444444333444433333444444666666666666666666666666666666666666 PP

                            APG6_N  92 ealeeeeerfwreynelqlelleleeeldsleaqyehaq 130
                                       ++l +e ++   e+ ++q+e  +l+++ +s+++++e a+
  gi|298676000|ref|YP_003727750.1| 886 KELGDELKELQDERANKQTEYDNLKKDYNSIKSKFENAS 924
                                       666666666666666666666666666666666666665 PP

  == domain 7  score: 16.0 bits;  conditional E-value: 2.2e-05
                            APG6_N  32 lkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynel 108
                                       lk+l++e+ ++   ++e ++l++++  ++++ e++ + L++le+++++l++++ +l++ele++  ee++++  y   
  gi|298676000|ref|YP_003727750.1| 892 LKELQDERANK---QTEYDNLKKDYNSIKSKFENASNRLQALESTKSSLKEQIDELRSELEQRGIEETEEVPNYETV 965
                                       68899886664...5899********************************************************999 PP

                            APG6_N 109 qlelleleeeldsl 122
                                       ++  ++ e+ ++ l
  gi|298676000|ref|YP_003727750.1| 966 RTRIASIEKAMEDL 979
                                       99999888887766 PP

  == domain 8  score: 1.3 bits;  conditional E-value: 0.77
                            APG6_N   48 eleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerf 101 
                                         ++++e+ +e+le    +++ e +e+ + +ee+++ + +l++e e++ e  e++
  gi|298676000|ref|YP_003727750.1|  968 RIASIEKAMEDLEPVNMRAIDEYDEVLNRHEEMKNRRDTLSNEREQILERIEQY 1021
                                        455666666666666666666666666666666666666666666655544443 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9  19.4   2.8e-06    0.0017      16     200 ..     160     349 ..     154     351 .. 0.75
   2 ?    3.6  30.3     0.069        43      36     225 ..     297     495 ..     291     500 .. 0.70
   3 ?    4.0  13.4     0.052        32      34     134 ..     428     508 ..     417     568 .. 0.60
   4 !   14.0  22.3   4.3e-05     0.027      54     213 ..     682     835 ..     666     838 .. 0.84
   5 ?    6.0   7.7     0.012       7.4      65     134 ..     786     855 ..     762     863 .. 0.81
   6 !    8.9  17.3    0.0016         1      33     139 ..     851     951 ..     846     980 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.8e-06
                        MscS_porin  16 kallqdLeqalnlLdkidkskkkaeelqkaiddaPkelrelqqelealqkkkeeaskeilaklsleeLeqrllqtss 92 
                                        ++++++    ++ +k+++  +++e  ++ i++    ++e++++l++l  k+e + + ++++l++e    +    +s
  gi|298676000|ref|YP_003727750.1| 160 RKIIDEIAGVSEFDNKKERAMNELETVREHIERVDIIIEEVNNQLDKL--KDERDQALKYQSLKQEKAKYEGFVILS 234
                                       566666666677778999999***************************..777777888888888888888888999 PP

                        MscS_porin  93 qlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLnstaaage.......alsqaqrtalqaelaale 162
                                       +l +++++l + ns++ + +++ e++q+ l e +++lqe+++ L+++  + +          +      + e + ++
  gi|298676000|ref|YP_003727750.1| 235 KLKDAKKELESVNSDIESKNNSVEELQKSLDEKNEQLQELEKTLSDLTNQIQnmgekeqIQIKKDIEEIRGEISRCN 311
                                       99999999999999999999999999999999999999998888444222221111222333444455666777777 PP

                        MscS_porin 163 aqieeleqellsnnnrqeLlklqrdllklriqqleqel 200
                                         ie  e e +  ++r+  +    d +k ++++le+++
  gi|298676000|ref|YP_003727750.1| 312 GSIEIAENEIQDIDTRRRKTLVDIDDAKSKVEELESKI 349
                                       77777777777777777777777777777777777666 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.069
                        MscS_porin  36 kkkaeelqkaiddaPkelrelqqeleal.qkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqlnsqlvel 111
                                       kk++ee +  i +    ++ +++e++   +   ++ +  ++ak + eeLe+++++++ + ++ +++l++ +++l  l
  gi|298676000|ref|YP_003727750.1| 297 KKDIEEIRGEISRCNGSIEIAENEIQDIdTRRRKTLVDIDDAKSKVEELESKINDEEIRKESINSELSERKNELKLL 373
                                       56666666677777777777777777774444555555567788899999999999877777777777777777777 PP

                        MscS_porin 112 qtrperaqqqltearqrlqeirnrLnstaaage.alsqaqrta.....lqaelaaleaqieeleqellsnnnrqeLl 182
                                       q+ ++ + ++ +e r +l+e+ n+ ++ + +++  ++++ r +       ae   +e++i+  +   +s++  +   
  gi|298676000|ref|YP_003727750.1| 374 QSKINDVDAKFAETRDKLSELKNEREQIKNEKSeLIREENRLLdavrrKSAEKRDIENEIQDSKEKIESSDSDTRSV 450
                                       77777777777777777777755443333333324444444431111146888889999****************** PP

                        MscS_porin 183 klqrdllklriqqleqelqaLqellnekR..laeaekavaqteql 225
                                       + + d l+++i+ l++ l++L+++ ++ +  l+e+e+ +++ +q+
  gi|298676000|ref|YP_003727750.1| 451 QHEIDKLNEKIESLNKDLDDLESNRSQLKeiLNEHEEELRKHQQE 495
                                       **************************9983356777777655555 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.052
                        MscS_porin  34 kskkkaeelqkaiddaPkelrelqqelealqkkkeeaskeilaklsl..eeLeqrllqtssqlqelqeqlaqlnsql 108
                                       + ++++++ +++i+++   +r++q+e+++l ++k e+ +++l+ l +  ++L   l++ +++l + q++ aq ++++
  gi|298676000|ref|YP_003727750.1| 428 DIENEIQDSKEKIESSDSDTRSVQHEIDKL-NEKIESLNKDLDDLESnrSQLKEILNEHEEELRKHQQEYAQVEARV 503
                                       445555555555555555555555555555.4444444444444433114566666666666666666666666555 PP

                        MscS_porin 109 velqtrperaqqqltearqrlqeirn 134
                                       ++++                      
  gi|298676000|ref|YP_003727750.1| 504 RAAE---------------------E 508
                                       5443.....................3 PP

  == domain 4  score: 14.0 bits;  conditional E-value: 4.3e-05
                        MscS_porin  54 relqqelealqkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlq 130
                                       ++l++  e+    +e +sk + +  +l++ e+++ +++++  + ++++++ + ql e+++r er+ q + + +++l+
  gi|298676000|ref|YP_003727750.1| 682 EKLTKIAEKI---TEYDSKRNNTIKKLDDVESQISDVKQEINNHENEISKKQMQLEEISSREERLSQFIESKNKELE 755
                                       3444444444...66688888888999************************************************** PP

                        MscS_porin 131 eirnrLnstaaagealsqaqrtalqaelaaleaqieeleqellsnnnrqeLlklqrdllklriqqleqelqaLqell 207
                                       ei+   ++++++  ++ +++  +++ e + l+ +i+ele el+ +      l+ ++d l+++iq+le ++++  +++
  gi|298676000|ref|YP_003727750.1| 756 EIEESRKELKEEMDKVVADKDEKTKKENE-LDEKISELEEELADSEI--PELNEKADNLNEEIQRLEGRIRDTDSNI 829
                                       **998888876666777777777776655.799*********87654..4577799********************* PP

                        MscS_porin 208 nekRla 213
                                       n+ +l+
  gi|298676000|ref|YP_003727750.1| 830 NSLNLD 835
                                       *98875 PP

  == domain 5  score: 6.0 bits;  conditional E-value: 0.012
                        MscS_porin  65 kkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirn 134
                                       ++k ++ +e+la   + eL+ + ++ +++ q+l+ ++ + +s++++l+  +e a +++++ r+ ++e+  
  gi|298676000|ref|YP_003727750.1| 786 DEKISELEEELADSEIPELNEKADNLNEEIQRLEGRIRDTDSNINSLNLDLEYANKRISDDRELIEELDE 855
                                       44467789999999*************************************************9999876 PP

  == domain 6  score: 8.9 bits;  conditional E-value: 0.0016
                        MscS_porin  33 dkskkkaeelqkaiddaPkelrelqqelealqkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqlnsqlv 109
                                       ++ ++k    q +i+++ ++++el+ +l++     +   +e+     l+eL+ + ++ + +  +l+++ ++++s++ 
  gi|298676000|ref|YP_003727750.1| 851 EELDEKKSSHQGRIESFKEKIKELEDSLASK----Q--EREKELGDELKELQDERANKQTEYDNLKKDYNSIKSKFE 921
                                       5566666667778888888888888888887....3..344444445678888888888888888888888888888 PP

                        MscS_porin 110 elqtrperaqqqltearqrlqeirnrLnst 139
                                       ++++r++ + ++ ++ +++++e+r++L++ 
  gi|298676000|ref|YP_003727750.1| 922 NASNRLQALESTKSSLKEQIDELRSELEQR 951
                                       888888888888888888888888888554 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   1.1e-08   6.5e-06       2      46 ..       4      48 ..       3      55 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.1e-08
                            AAA_29  2 krlqlvNWgtfdg.htieidlkgatlltGpsGsGKSTllDAiqalL 46
                                      k+++ +N  +f +  +i++  +++t ++Gp+GsGKS ++D i + L
  gi|298676000|ref|YP_003727750.1|  4 KEIEFLNFKSFGKkVKIPFF-DDFTTISGPNGSGKSNIIDGILFAL 48
                                      689999******98889987.569*****************98776 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7  27.3   7.5e-05     0.046       2     125 ..     173     301 ..     172     309 .. 0.89
   2 !   10.7  14.6   0.00063      0.39      20      88 ..     336     404 ..     329     410 .. 0.94
   3 ?    6.4  20.7     0.014       8.4      49     125 ..     421     497 ..     404     514 .. 0.79
   4 !    9.4  11.4    0.0016      0.98      13     114 ..     448     553 ..     443     577 .. 0.60
   5 !    7.1  29.3    0.0081         5       3     106 ..     696     799 ..     694     802 .. 0.96
   6 !   12.2  17.7   0.00023      0.14      14     103 ..     803     892 ..     797     916 .. 0.89
   7 !    7.2  14.8    0.0078       4.8       3     103 ..     918    1025 ..     916    1034 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.5e-05
                    CENP-F_leu_zip   2 ekkklhvlekLKeserkadsLkdkvenLerelemseenqekvi....leaEtskaevetlkeeieelaeelreleld 74 
                                       ++kk+++ ++L  ++++ + +   +e+ + +l  ++ +++++     l  E++k e   + ++++  ++el+  ++d
  gi|298676000|ref|YP_003727750.1| 173 DNKKERAMNELETVREHIERVDIIIEEVNNQLDKLKDERDQALkyqsLKQEKAKYEGFVILSKLKDAKKELESVNSD 249
                                       5688899999999999999999999999999999999998874333378899999999999**************** PP

                    CENP-F_leu_zip  75 LvalrsekeeLekelqkkqervseLeslnsslenlleek.Eqekvqmkeesk 125
                                       +++  +  eeL+k+l +k+e+ +eLe++ s+l+n++++  E+e++q+k++ +
  gi|298676000|ref|YP_003727750.1| 250 IESKNNSVEELQKSLDEKNEQLQELEKTLSDLTNQIQNMgEKEQIQIKKDIE 301
                                       *************************************965999***998765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00063
                    CENP-F_leu_zip  20 dsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLeke 88 
                                       d  k kve+Le+ +++ e  +e++  e  + k+e++ l+++i+   ++  e + +L++l++e+e++++e
  gi|298676000|ref|YP_003727750.1| 336 DDAKSKVEELESKINDEEIRKESINSELSERKNELKLLQSKINDVDAKFAETRDKLSELKNEREQIKNE 404
                                       56689************************************************************9876 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.014
                    CENP-F_leu_zip  49 tskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnsslenlleekEqekvqmkeesk 125
                                        + ae   +++ei+  +e+ +   +d  +++ e ++L+++++  ++  ++Les +s+l+++l+e E+e ++ ++e+ 
  gi|298676000|ref|YP_003727750.1| 421 RKSAEKRDIENEIQDSKEKIESSDSDTRSVQHEIDKLNEKIESLNKDLDDLESNRSQLKEILNEHEEELRKHQQEYA 497
                                       34466677899999999999999999999999999999999999999999999999999999999999777766654 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.0016
                    CENP-F_leu_zip  13 KeserkadsLkdkvenLerelemseenqekvileaEtskaevet.......lkeeieelaeelreleldLvalrsek 82 
                                       + ++++ d+L++k+e+L+++l ++e+n+++++    +  +e+ +       +++ ++  aee ++ +  ++++ s k
  gi|298676000|ref|YP_003727750.1| 448 RSVQHEIDKLNEKIESLNKDLDDLESNRSQLKEILNEHEEELRKhqqeyaqVEARVRA-AEENSKYSKAVDTVISAK 523
                                       5667777888888888888888888777776654444444444411111113333333.445555566666666777 PP

                    CENP-F_leu_zip  83 eeLekelqkkqervseLeslnsslenlleekE 114
                                       ++  kelq    ++ eL ++ ++ +  l+++ 
  gi|298676000|ref|YP_003727750.1| 524 NN--KELQGIYGTIAELGQADEKYSTALQIAA 553
                                       64..6777777777777777777777777665 PP

  == domain 5  score: 7.1 bits;  conditional E-value: 0.0081
                    CENP-F_leu_zip   3 kkklhvlekLKeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalr 79 
                                        k++++ +kL  +e++ + +k+ ++n e e+   + ++e++    E   + +e+ ++e+ee++e+++el+ +++++ 
  gi|298676000|ref|YP_003727750.1| 696 SKRNNTIKKLDDVESQISDVKQEINNHENEISKKQMQLEEISSREERLSQFIESKNKELEEIEESRKELKEEMDKVV 772
                                       6889999********************************************************************** PP

                    CENP-F_leu_zip  80 sekeeLekelqkkqervseLeslnssl 106
                                        +k+e +k+ ++  e++seLe+   + 
  gi|298676000|ref|YP_003727750.1| 773 ADKDEKTKKENELDEKISELEEELADS 799
                                       *********************987765 PP

  == domain 6  score: 12.2 bits;  conditional E-value: 0.00023
                    CENP-F_leu_zip  14 eserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelq 90 
                                       e ++kad+L++ +++Le  + + ++n +++ l+ E + + ++  +e ieel e+ +  +  ++++++  +eLe +l 
  gi|298676000|ref|YP_003727750.1| 803 ELNEKADNLNEEIQRLEGRIRDTDSNINSLNLDLEYANKRISDDRELIEELDEKKSSHQGRIESFKEKIKELEDSLA 879
                                       7789************************************************************************* PP

                    CENP-F_leu_zip  91 kkqervseLesln 103
                                        kqer +eL    
  gi|298676000|ref|YP_003727750.1| 880 SKQEREKELGDEL 892
                                       *****99996544 PP

  == domain 7  score: 7.2 bits;  conditional E-value: 0.0078
                    CENP-F_leu_zip    3 kkklhvlekLKeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelae.elrel...el 73  
                                         k++++ ++L++ e+ ++sLk+++++L +ele+ + + ++ + + Et +  + ++++ +e l+  ++r +     
  gi|298676000|ref|YP_003727750.1|  918 SKFENASNRLQALESTKSSLKEQIDELRSELEQRGIEETEEVPNYETVRTRIASIEKAMEDLEPvNMRAIdeyDE 992 
                                        5889999*********************************************99999999987412222210022 PP

                    CENP-F_leu_zip   74 dL...valrsekeeLekelqkkqervseLesln 103 
                                         L   +++++ +++L +e ++  er+++ e+l+
  gi|298676000|ref|YP_003727750.1|  993 VLnrhEEMKNRRDTLSNEREQILERIEQYENLK 1025
                                        221113444566666666666666666666554 PP

>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   1.4       4.2   2.6e+03      40      53 ..     196     209 ..     173     226 .. 0.56
   2 ?    2.9   7.1      0.19   1.2e+02       5      54 ..     242     291 ..     238     293 .. 0.80
   3 !   23.3   2.2   8.2e-08   5.1e-05       2      71 ..     274     344 ..     273     348 .. 0.91
   4 ?    1.2   4.5      0.64   3.9e+02       9      72 ..     359     422 ..     353     426 .. 0.84
   5 ?    4.4   5.9     0.065        40      28      72 ..     448     495 ..     428     499 .. 0.77
   6 !    8.6   8.6    0.0031       1.9       2      69 ..     708     775 ..     707     782 .. 0.93
   7 !    8.1   2.8    0.0044       2.7       2      51 ..     785     832 ..     784     863 .. 0.83
   8 ?    1.6   9.5      0.47   2.9e+02       4      72 ..     869     951 ..     866     954 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 4.2
                     TolA_bind_tri  40 qiEelqyqleqlee 53 
                                        iEe ++ql++l+ 
  gi|298676000|ref|YP_003727750.1| 196 IIEEVNNQLDKLKD 209
                                       34555555555542 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.19
                     TolA_bind_tri   5 rvarLErilearsqlllelqqqlealqqelreLRGqiEelqyqleqleer 54 
                                        +++++  +e+++++  elq+ l++ +++l+eL   + +l++q++++ e+
  gi|298676000|ref|YP_003727750.1| 242 ELESVNSDIESKNNSVEELQKSLDEKNEQLQELEKTLSDLTNQIQNMGEK 291
                                       57777778888888999999999999999999999999999999988775 PP

  == domain 3  score: 23.3 bits;  conditional E-value: 8.2e-08
                     TolA_bind_tri   2 ledrvarLErilears.qlllelqqqlealqqelreLRGqiEelqyqleqleerQrdlYldlDerlrklea 71 
                                       le+ ++ L +++++   + ++++ + +e+ + e+++ +G+iE  +++++++ +r r+  +d+D   +k+e+
  gi|298676000|ref|YP_003727750.1| 274 LEKTLSDLTNQIQNMGeKEQIQIKKDIEEIRGEISRCNGSIEIAENEIQDIDTRRRKTLVDIDDAKSKVEE 344
                                       7888899998888876589*********************************************9999887 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.64
                     TolA_bind_tri   9 LErilearsqlllelqqqlealqqelreLRGqiEelqyqleqleerQrdlYldlDerlrkleag 72 
                                       ++  l+ r++ l  lq+++++  +  +e R ++ el+++ eq+++   +l ++ +++l +++ +
  gi|298676000|ref|YP_003727750.1| 359 INSELSERKNELKLLQSKINDVDAKFAETRDKLSELKNEREQIKNEKSELIREENRLLDAVRRK 422
                                       556677777778889**********************************999988888776655 PP

  == domain 5  score: 4.4 bits;  conditional E-value: 0.065
                     TolA_bind_tri  28 ealqqelreLRGqiEelqyqleqlee...rQrdlYldlDerlrkleag 72 
                                        + q+e+++L+ +iE l+ +l++le    + +++ ++ +e lrk+++ 
  gi|298676000|ref|YP_003727750.1| 448 RSVQHEIDKLNEKIESLNKDLDDLESnrsQLKEILNEHEEELRKHQQE 495
                                       578*****************9999752226677777777777777665 PP

  == domain 6  score: 8.6 bits;  conditional E-value: 0.0031
                     TolA_bind_tri   2 ledrvarLErilearsqlllelqqqlealqqelreLRGqiEelqyqleqleerQrdlYldlDerlrkl 69 
                                       +e++++ + + ++++++ + + q+qle+ ++   +L   iE  + +le++ee  ++l +++D++++  
  gi|298676000|ref|YP_003727750.1| 708 VESQISDVKQEINNHENEISKKQMQLEEISSREERLSQFIESKNKELEEIEESRKELKEEMDKVVADK 775
                                       7999**********************************************************998765 PP

  == domain 7  score: 8.1 bits;  conditional E-value: 0.0044
                     TolA_bind_tri   2 ledrvarLErilearsqlllelqqqlealqqelreLRGqiEelqyqleql 51 
                                       l++++++LE+ l+   + + el ++ ++l++e+++L G i +   ++++l
  gi|298676000|ref|YP_003727750.1| 785 LDEKISELEEELAD--SEIPELNEKADNLNEEIQRLEGRIRDTDSNINSL 832
                                       7899********99..99********************987666665554 PP

  == domain 8  score: 1.6 bits;  conditional E-value: 0.47
                     TolA_bind_tri   4 drvarLErilears..............qlllelqqqlealqqelreLRGqiEelqyqleqleerQrdlYldlDerl 66 
                                       +++++LE  l++++                  + q++ ++l+++ ++++ + E  +++l+ le     l +++De+ 
  gi|298676000|ref|YP_003727750.1| 869 EKIKELEDSLASKQerekelgdelkelqDERANKQTEYDNLKKDYNSIKSKFENASNRLQALESTKSSLKEQIDELR 945
                                       566666666666666666666666655555566789999************************************** PP

                     TolA_bind_tri  67 rkleag 72 
                                       ++le++
  gi|298676000|ref|YP_003727750.1| 946 SELEQR 951
                                       ***987 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8  62.1   0.00042      0.26     202     504 ..     195     509 ..     174     541 .. 0.72
   2 !   16.1  57.8   2.6e-06    0.0016     203     531 ..     687    1026 ..     679    1033 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00042
                           DUF3584 202 mivaileealadgvvpeksr.lkkqdveeWiediqalaaiekvrpeieklqeefeqleslelrLsllkgelkadeer 277
                                       +i++ +++   d++++e  + lk q  ++  +  +  + + k ++  ++l+   +++es  +++  l++ l ++ e+
  gi|298676000|ref|YP_003727750.1| 195 IIIEEVNN-QLDKLKDERDQaLKYQSLKQEKAKYEGFVILSKLKDAKKELESVNSDIESKNNSVEELQKSLDEKNEQ 270
                                       45555555.4566666665556666666666666666667888888999999999999999999************* PP

                           DUF3584 278 laekqeevqeakaelkqqlrtledelkeaidelnqelsaakaklaakeselealeeqkkkye......dadieklka 348
                                       l+e  +      +++++  ++++ ++k+ i+e ++e+s  ++ ++ +e+e+  ++ +++k +      ++++e+l+ 
  gi|298676000|ref|YP_003727750.1| 271 LQELEKTLSDLTNQIQNMGEKEQIQIKKDIEEIRGEISRCNGSIEIAENEIQDIDTRRRKTLvdiddaKSKVEELES 347
                                       ***999999******99999***********************************9988753222111345666655 PP

                           DUF3584 349 dld....qlpsirseleeleeeldaltekhqdvqekydrrkqkikeeleeeleklkerleaireekdrlkaaieeal 421
                                       + +    + +si+sel+e ++el++l +k++dv++k+ + + k++e ++e  +  +e+ e iree+  l a+ ++  
  gi|298676000|ref|YP_003727750.1| 348 KINdeeiRKESINSELSERKNELKLLQSKINDVDAKFAETRDKLSELKNEREQIKNEKSELIREENRLLDAVRRKSA 424
                                       544122345799*******************************9987766666666668*******99955555544 PP

                           DUF3584 422 ea..lesqlrkqleaqkeelneeekelesrlselklrldsatateEele.qieeadealekaqeelekaeaevealq 495
                                       e+  +e++ ++ +e ++e+   +   +++++++l+ +++s     + le +  + +e l++ +eel+k ++e  + +
  gi|298676000|ref|YP_003727750.1| 425 EKrdIENEIQDSKE-KIESSDSDTRSVQHEIDKLNEKIESLNKDLDDLEsNRSQLKEILNEHEEELRKHQQEYAQVE 500
                                       43115555553333.34444555566666666666666666665444331444455555566666666655555555 PP

                           DUF3584 496 aeeeqlrkk 504
                                       a  ++++++
  gi|298676000|ref|YP_003727750.1| 501 ARVRAAEEN 509
                                       555554443 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 2.6e-06
                           DUF3584  203 ivaileealadgvvpeksrlkkqdveeWiediqalaaiekvrpeieklqeefeqleslelrLsllkgelkadeer 277 
                                        i++ ++e    +++ +++ +k +dve  i d++  ++i++ ++ei+k q + e++ s e+rLs       ++ e+
  gi|298676000|ref|YP_003727750.1|  687 IAEKITE---YDSKRNNTIKKLDDVESQISDVK--QEINNHENEISKKQMQLEEISSREERLSQFIESKNKELEE 756 
                                        6677777...444666777999********998..69**************************998777777777 PP

                           DUF3584  278 laekqeevqeakael...kqqlrtledelkeaideln.....qelsaakaklaakeselealeeqkkkyedadie 344 
                                        ++e+++e +e+  ++   k +  ++e+el e+i+el+     +e+ ++++k ++ ++e+ +le + ++  d++i+
  gi|298676000|ref|YP_003727750.1|  757 IEESRKELKEEMDKVvadKDEKTKKENELDEKISELEeeladSEIPELNEKADNLNEEIQRLEGRIRD-TDSNIN 830 
                                        7777777776655541113333444555556665555111125677899**************99998.89**** PP

                           DUF3584  345 klkadldqlpsirseleeleeeldaltekhqdvqekydrrkqkikeeleeeleklkerleaireekdrl...... 413 
                                        +l+ dl+ + +  s+ +el eeld   ++hq   e +++++++++++l+ ++e+ ke  ++++e +d++      
  gi|298676000|ref|YP_003727750.1|  831 SLNLDLEYANKRISDDRELIEELDEKKSSHQGRIESFKEKIKELEDSLASKQEREKELGDELKELQDERankqte 905 
                                        *******************************99999999999999999999999988766666555554332344 PP

                           DUF3584  414 kaaieealealesqlrkqleaqkeelneeekelesrlselklrldsatate.Eeleqieeadealekaqeeleka 487 
                                          + +++++ ++s+++ +  +  ++l+  +  l+++++el   l++ +++e Ee+ + e    ++   ++++e  
  gi|298676000|ref|YP_003727750.1|  906 YDNLKKDYNSIKSKFE-NASNRLQALESTKSSLKEQIDELRSELEQRGIEEtEEVPNYETVRTRIASIEKAMEDL 979 
                                        4556778888999998.6667788999999999999999999999998865478888888777776666666665 PP

                           DUF3584  488 eaevealqaeeeqlrkkrd...eadealqkaerrleqlrqaleelee 531 
                                        e  + ++ +e  ++ ++ +   +  ++l+++++++ ++ +++e+l++
  gi|298676000|ref|YP_003727750.1|  980 EPVNMRAIDEYDEVLNRHEemkNRRDTLSNEREQILERIEQYENLKK 1026
                                        55555554444444444330004445555666666666666666655 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   2.8e-07   0.00017       1      26 [.      26      54 ..      26     118 .. 0.74
   2 ?    1.0  21.8       0.5   3.1e+02      80     296 ..     963    1143 ..     675    1143 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.8e-07
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarl...d 26
                                      ++ + GpNgsGKSn++d + ++ +l   +
  gi|298676000|ref|YP_003727750.1| 26 FTTISGPNGSGKSNIIDGILFALGLsnsR 54
                                      68899**************9998763330 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.5
                            AAA_21   80 rsqveeklssvetllesgllldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsl 154 
                                        +   ++++ s e+  e+ + ++ r+ +e+d++ +++++ +  ++  s+    + e ++++ +     + ++++ +
  gi|298676000|ref|YP_003727750.1|  963 ETV-RTRIASIEKAMEDLEPVNMRAIDEYDEVLNRHEEMKNRRDTLSNEREQILERIEQYENLKKETFMETFNGI 1036
                                        222.35555555555555555555555555555555555555555555555555555555555555555555555 PP

                            AAA_21  155 lllldglrkerigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdg 229 
                                        ++ + ++      l +  ++++  + e ++ ++l+ + ++ +  l+ l+                          
  gi|298676000|ref|YP_003727750.1| 1037 NKAFSSI---FNELSDGTGELALDNYEEPFSGGLTLKAQPKDKSLQRLE-------------------------- 1082
                                        5555555...556666666666666666666666666666666666665.......................... PP

                            AAA_21  230 qelparelSdGtkrl..lalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltT 296 
                                               +S G k+l  la++ a+ + ++  +++++DE++ +L+ +  +r+++ +k+  + gaQ+i+++
  gi|298676000|ref|YP_003727750.1| 1083 ------AMSGGEKSLtaLAFVFAIQSYRPA-PFYAFDEIDMFLDGANSERVAQRIKKSVN-GAQFIVVS 1143
                                        ......56*******744778888887777.************************99999.9****986 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1  37.0    0.0043       2.7     303     490 ..     185     379 ..     174     380 .. 0.87
   2 ?    1.3  17.3      0.12        75     340     433 ..     351     443 ..     348     444 .. 0.93
   3 !    5.3  16.4    0.0076       4.7      78     165 ..     427     518 ..     422     529 .. 0.83
   4 !    5.1  35.7    0.0088       5.4     340     487 ..     699     856 ..     681     860 .. 0.78
   5 !   18.8  26.1     6e-07   0.00037      93     271 ..     861    1050 ..     856    1061 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0043
                                       HHTTTSSSSSHHHHT--HHHHTTGGG-TTTS-GGGSSTTTSTTHH..HHHHHHHHHHHHHHHHHHHHS-SS---STT CS
                              EzrA 303 eveknlkelkeklehlekqnkelkeeldrlkqsYeLseeeleklr..elekelkelekdyeeleekleekkvaYSel 377
                                       +v ++++++   +e++++q+++lk+e d+  +   L++e   k++   + ++lk+ +k++e+++ ++e+k+ +  el
  gi|298676000|ref|YP_003727750.1| 185 TVREHIERVDIIIEEVNNQLDKLKDERDQALKYQSLKQE-KAKYEgfVILSKLKDAKKELESVNSDIESKNNSVEEL 260
                                       688999999999**************9998777777555.55555125689************************** PP

                                       GGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHSS..S...-SS-S-TTTHHHHSTT CS
                              EzrA 378 qeeleeleekleeieekqeeileslkslrkdEk.rAreqldeikkelkeikrkie..k...snLPgiPesyleelke 448
                                       q+ l+e +e+l+e+e+ + ++ ++++++ ++E+ + ++ ++ei+ e++ ++ +ie  +   + +     + l+++++
  gi|298676000|ref|YP_003727750.1| 261 QKSLDEKNEQLQELEKTLSDLTNQIQNMGEKEQiQIKKDIEEIRGEISRCNGSIEiaEneiQDIDTRRRKTLVDIDD 337
                                       ****************************99887589**************98875334112455666678999**** PP

                                       TSTTTHHHHHHHT-TT--HHHHHHHHHTTTTTSGGGTHHHHH CS
                              EzrA 449 asdeieelakeLekkpinikevnkrldeardlveklyektne 490
                                       a+ ++eel+ +++ + i  + +n++l+e ++ ++ l++k+n+
  gi|298676000|ref|YP_003727750.1| 338 AKSKVEELESKINDEEIRKESINSELSERKNELKLLQSKIND 379
                                       **************************************9998 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.12
                                       TTTSTTHHHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              EzrA 340 eeeleklrelekelkelekdyeeleekleekkvaYSelqeeleeleekleeieekqeeileslkslrkdEkrAreql 416
                                       + e  + +++++el+e +++++ l+ k+++ ++ + e +++l el+++ e+i+++  e+ ++ + l +  +r   + 
  gi|298676000|ref|YP_003727750.1| 351 D-EEIRKESINSELSERKNELKLLQSKINDVDAKFAETRDKLSELKNEREQIKNEKSELIREENRLLDAVRRKSAEK 426
                                       4.4446789******************************************************************** PP

                                       HHHHHHHHHHHHHSSS- CS
                              EzrA 417 deikkelkeikrkieks 433
                                        +i++e++++k kie+s
  gi|298676000|ref|YP_003727750.1| 427 RDIENEIQDSKEKIESS 443
                                       **************986 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.0076
                                       HHHHHT-GGGT--S-SH..HHHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT- CS
                              EzrA  78 peieellfeaeelldky..kfkkakkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkkl 152
                                        +ie+++ + +e +++   +++++++++++l+e+++++ ++++++ +  ++l+e  ++++ee  k +++Y +++ ++
  gi|298676000|ref|YP_003727750.1| 427 RDIENEIQDSKEKIESSdsDTRSVQHEIDKLNEKIESLNKDLDDLESNRSQLKEILNEHEEELRKHQQEYAQVEARV 503
                                       68999999999998865226889999999999999999999999999999999999999999999999999999888 PP

                                       -..TTTTHHHHHHHH CS
                              EzrA 153 l..anrfsygealee 165
                                       +  +++ +y++a+++
  gi|298676000|ref|YP_003727750.1| 504 RaaEENSKYSKAVDT 518
                                       733567788888876 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.0088
                                       TTTSTTHHHHHHHHHHHHHHHHHHHHHHS-SS---ST.......TGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              EzrA 340 eeeleklrelekelkelekdyeeleekleekkvaYSe.......lqeeleeleekleeieekqeeileslkslrkdE 409
                                       ++ ++kl+++e++++++++++++ e+++++k++   e       l++ +e+ +++leeiee+ +e++e++++   d 
  gi|298676000|ref|YP_003727750.1| 699 NNTIKKLDDVESQISDVKQEINNHENEISKKQMQLEEissreerLSQFIESKNKELEEIEESRKELKEEMDKVVADK 775
                                       45667777777777777777777777777777766550001111556677788899999999999999999999999 PP

                                       HHHHHHHHHHHHHHHHHHHHSSS-SS-S-TT...THHHHSTTTSTTTHHHHHHHT-TT--HHHHHHHHHTTTTTSGG CS
                              EzrA 410 krAreqldeikkelkeikrkieksnLPgiPe...syleelkeasdeieelakeLekkpinikevnkrldeardlvek 483
                                        +  ++ +e++++++e++ ++ +s++P ++e   +  ee++  + +i++++ +++   ++++  nkr+++ r+l+e+
  gi|298676000|ref|YP_003727750.1| 776 DEKTKKENELDEKISELEEELADSEIPELNEkadNLNEEIQRLEGRIRDTDSNINSLNLDLEYANKRISDDRELIEE 852
                                       9999999*********************98722256788999999******************************** PP

                                       GTHH CS
                              EzrA 484 lyek 487
                                       l+ek
  gi|298676000|ref|YP_003727750.1| 853 LDEK 856
                                       9987 PP

  == domain 5  score: 18.8 bits;  conditional E-value: 6e-07
                                        SHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTTTH...HHHHHH CS
                              EzrA   93 kykfkkakkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkkllanrfs...ygeale 164 
                                        + ++ + k+k++ele+ l++ +e+ k++ +elkel++   ++++e++ lk++Y +++ k+++ ++    ++++++
  gi|298676000|ref|YP_003727750.1|  861 QGRIESFKEKIKELEDSLASKQEREKELGDELKELQDERANKQTEYDNLKKDYNSIKSKFENASNRlqaLESTKS 935 
                                        6688999******************************************************98875111678899 PP

                                        HHHHHHHHH------..----------HHHHHHHHHHHHHHHHHHHH.HHHHHHHHTTT..TTTSHHHHHHHHHH CS
                              EzrA  165 elekqleniekefse..feeltengdyveakeilkkleeeideleev.ieeiPelleel..kkelpkqleelkeg 234 
                                        +l++q++++ +e+++  +ee+ e  +y++++  + ++e+ +++le v ++ i e+ e l  ++e++++ + l++ 
  gi|298676000|ref|YP_003727750.1|  936 SLKEQIDELRSELEQrgIEETEEVPNYETVRTRIASIEKAMEDLEPVnMRAIDEYDEVLnrHEEMKNRRDTLSNE 1010
                                        *************98778**************************9653777777755441157899999999999 PP

                                        HHHSTT..S--.SGGGSSSSSHHHHHHHHHHHHHHHHTT- CS
                              EzrA  235 ykemke..egY.aleelniekeieelekkieeilerlkel 271 
                                         ++  e  e+Y +l++  + ++++ ++k+ ++i+++l++ 
  gi|298676000|ref|YP_003727750.1| 1011 REQILEriEQYeNLKKETFMETFNGINKAFSSIFNELSDG 1050
                                        9998874457756999999999999999999999998765 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   2.1    0.0021       1.3      35     102 ..     176     240 ..     166     249 .. 0.76
   2 !    7.8   8.5    0.0059       3.7       5     104 ..     255     354 ..     251     357 .. 0.77
   3 ?    4.0   7.9     0.091        56      16     108 ..     337     431 ..     329     433 .. 0.80
   4 ?    7.0  12.8      0.01       6.3      17      94 ..     422     494 ..     408     520 .. 0.76
   5 ?    6.7  11.1     0.013       7.9      17     106 ..     680     766 ..     677     770 .. 0.77
   6 ?    1.5   2.7      0.52   3.2e+02      14      71 ..     747     799 ..     738     802 .. 0.77
   7 ?    4.6   1.9     0.059        37      11      80 ..     779     841 ..     762     848 .. 0.67
   8 !    7.9   3.3    0.0054       3.3       9      91 ..     803     887 ..     797     890 .. 0.88
   9 !   13.6   6.5   9.6e-05     0.059       5      70 ..     890     950 ..     886     958 .. 0.95
  10 ?    3.3   2.6      0.14        89      56     113 ..     964    1021 ..     961    1023 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0021
                              FliJ  35 lsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekar..eewqearqerkklekLkerekke 102
                                       ++ ++     +el ++++ i+++d  i++  ++l++++ ++++a   + +++++ +++ + +L + + ++
  gi|298676000|ref|YP_003727750.1| 176 KERAM-----NELETVREHIERVDIIIEEVNNQLDKLKDERDQALkyQSLKQEKAKYEGFVILSKLKDAK 240
                                       44444.....99*******************************972245666666666666666655554 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0059
                              FliJ   5 reLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqve....k 77 
                                       + ++e q+ l++++e+l+ele++++++ +q+++ +      e+ ++++ i+ ++ +i++   +++ ae++++    +
  gi|298676000|ref|YP_003727750.1| 255 NSVEELQKSLDEKNEQLQELEKTLSDLTNQIQNMG----EKEQIQIKKDIEEIRGEISRCNGSIEIAENEIQdidtR 327
                                       678899*********************99999999....88899999999999999999999999999998733334 PP

                              FliJ  78 areewqearqerkklekLkerekkeeq 104
                                       +r+ +      + k+e L+ +  +ee+
  gi|298676000|ref|YP_003727750.1| 328 RRKTLVDIDDAKSKVEELESKINDEEI 354
                                       556666666666666666666666665 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.091
                              FliJ  16 qaeekleeleqyrqeyqkqlsgea.q.glsaaelrnyqafisaldeaiaqqkqelaqaekqvekareewqearqerk 90 
                                       +a++k+eele+ +++ + ++++   +     +el+ +q+ i+ +d + a+++ +l+ +++++e+ ++e  e  +e++
  gi|298676000|ref|YP_003727750.1| 337 DAKSKVEELESKINDEEIRKESINsElSERKNELKLLQSKINDVDAKFAETRDKLSELKNEREQIKNEKSELIREEN 413
                                       56666666776666666666655544455569**********************************99999999999 PP

                              FliJ  91 klekLkerekkeeqkeen 108
                                        l     r+ +e +  en
  gi|298676000|ref|YP_003727750.1| 414 RLLDAVRRKSAEKRDIEN 431
                                       998888888888887776 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.01
                              FliJ  17 aeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekareewqearqerkkle 93 
                                       + ++   +e+++q+ +++++++      ++ r +q+ i++l+e+i+++ ++l+++e ++++ +e + e + e++k +
  gi|298676000|ref|YP_003727750.1| 422 KSAEKRDIENEIQDSKEKIESSD-----SDTRSVQHEIDKLNEKIESLNKDLDDLESNRSQLKEILNEHEEELRKHQ 493
                                       44444566777777777777777.....******************************************9999876 PP

                              FliJ  94 k 94 
                                        
  gi|298676000|ref|YP_003727750.1| 494 Q 494
                                       5 PP

  == domain 5  score: 6.7 bits;  conditional E-value: 0.013
                              FliJ  17 aeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvek..areewqearqerkk 91 
                                       ++ekl+++ + + ey ++ +++       +l  ++++is ++++i+ +++e+++++ q+e+  +ree +++ +e k 
  gi|298676000|ref|YP_003727750.1| 680 EKEKLTKIAEKITEYDSKRNNTI-----KKLDDVESQISDVKQEINNHENEISKKQMQLEEisSREERLSQFIESKN 751
                                       68999999999999988888888.....9999999999999999999999999999999973346777777777776 PP

                              FliJ  92 lekLkerekkeeqke 106
                                        e+ + +e ++e+ke
  gi|298676000|ref|YP_003727750.1| 752 KELEEIEESRKELKE 766
                                       666555555555555 PP

  == domain 6  score: 1.5 bits;  conditional E-value: 0.52
                              FliJ  14 lqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqa 71 
                                       +++++++lee+e+ r+e+++++ +       a+     +  + lde+i+++++ela++
  gi|298676000|ref|YP_003727750.1| 747 IESKNKELEEIEESRKELKEEMDKVV-----ADKDEKTKKENELDEKISELEEELADS 799
                                       67788888888888888877777776.....777778888888888888888888876 PP

  == domain 7  score: 4.6 bits;  conditional E-value: 0.059
                              FliJ  11 qrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekare 80 
                                        ++ ++  ek+ ele+++++ + +  +e          n+++ i++l+ +i  + ++++ ++ ++e a +
  gi|298676000|ref|YP_003727750.1| 779 TKKENELDEKISELEEELADSEIPELNEK-------ADNLNEEIQRLEGRIRDTDSNINSLNLDLEYANK 841
                                       45566777777777777777766666665.......6677777777777777777777777777766655 PP

  == domain 8  score: 7.9 bits;  conditional E-value: 0.0054
                              FliJ   9 eaqrelqqaeekleeleqyrqeyqkqlsgea.q.glsaaelrnyqafisaldeaiaqqkqelaqaekqvekareewq 83 
                                       e + + ++ +e++++le  +++  +++++       +  ++   ++ i+ lde+ ++++  ++  ++++++ ++ + 
  gi|298676000|ref|YP_003727750.1| 803 ELNEKADNLNEEIQRLEGRIRDTDSNINSLNlDlEYANKRISDDRELIEELDEKKSSHQGRIESFKEKIKELEDSLA 879
                                       566777888899999999999998888888777788999************************************** PP

                              FliJ  84 earqerkk 91 
                                       +++ ++k 
  gi|298676000|ref|YP_003727750.1| 880 SKQEREKE 887
                                       ***99986 PP

  == domain 9  score: 13.6 bits;  conditional E-value: 9.6e-05
                              FliJ   5 reLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaq 70 
                                        eL+e q e+++++ + ++l++ +++ ++++++++     ++l+++++ +s+l+e+i+++++el+q
  gi|298676000|ref|YP_003727750.1| 890 DELKELQDERANKQTEYDNLKKDYNSIKSKFENAS-----NRLQALESTKSSLKEQIDELRSELEQ 950
                                       689********************************.....************************98 PP

  == domain 10  score: 3.3 bits;  conditional E-value: 0.14
                              FliJ   56 aldeaiaqqkqelaqaekqvekareewqearqerkklekLkerekkeeqkeenrrEqk 113 
                                        +++++ia+++++ +++e +  +a +e+ e   +++ ++  +++  +e+ + ++r Eq 
  gi|298676000|ref|YP_003727750.1|  964 TVRTRIASIEKAMEDLEPVNMRAIDEYDEVLNRHEEMKNRRDTLSNEREQILERIEQY 1021
                                        68999***************************************************96 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   4.9       0.2   1.3e+02      14      79 ..     182     250 ..     179     255 .. 0.87
   2 ?    4.0   9.8      0.11        66      12      77 ..     240     305 ..     236     331 .. 0.77
   3 ?    3.2   7.3       0.2   1.2e+02      12      78 ..     339     404 ..     335     416 .. 0.80
   4 ?    4.8   7.5      0.06        37      12      81 ..     437     505 ..     431     511 .. 0.83
   5 ?    2.0   1.6      0.47   2.9e+02      40      81 ..     681     721 ..     668     728 .. 0.52
   6 ?    6.4   5.9     0.019        12      11      65 ..     722     771 ..     719     777 .. 0.84
   7 ?    3.3   5.6      0.18   1.1e+02      12      86 ..     765     843 ..     762     845 .. 0.65
   8 ?    4.3   1.9     0.088        54       5      42 ..     861     898 ..     859     912 .. 0.84
   9 !   19.9   1.6   1.2e-06   0.00073      10      76 ..     915     980 ..     911     992 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.2
                   Snapin_Pallidin  14 kldeldeklkelrqsQeeLleqldrlnekLkeleeaqe.aevlpdlkeya..kKLvnikkrmsslnerl 79 
                                       +l++++e+++ +    ee+++qld+l+++ +++ ++q+ ++  ++ +  +   KL+ +kk+++s+n+ +
  gi|298676000|ref|YP_003727750.1| 182 ELETVREHIERVDIIIEEVNNQLDKLKDERDQALKYQSlKQEKAKYEGFVilSKLKDAKKELESVNSDI 250
                                       57888899999999999999*******99999999999988888888877679************9876 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.11
                   Snapin_Pallidin  12 epkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakK.Lvnikkrmsslne 77 
                                       + +l+ +++ +++  +s eeL+++ld+ ne+L+ele++ + ++ +++++  +K  ++ikk+++++  
  gi|298676000|ref|YP_003727750.1| 240 KKELESVNSDIESKNNSVEELQKSLDEKNEQLQELEKTLS-DLTNQIQNMGEKeQIQIKKDIEEIRG 305
                                       5678888888888899999999999999999999998887.77777777765524567777776655 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.2
                   Snapin_Pallidin  12 epkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslner 78 
                                       ++k++el++k+++ +   e  +++l++ +++Lk l+    ++v +++ e ++KL+++k++ +++++ 
  gi|298676000|ref|YP_003727750.1| 339 KSKVEELESKINDEEIRKESINSELSERKNELKLLQSKI-NDVDAKFAETRDKLSELKNEREQIKNE 404
                                       678999999999999999999999999999998555544.588899999999999999988777765 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.06
                   Snapin_Pallidin  12 epkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqk 81 
                                       + k++  d+  ++++ + ++L+e++++ln++L++le + + ++ + l+e+ + L++ +++  +++ r++ 
  gi|298676000|ref|YP_003727750.1| 437 KEKIESSDSDTRSVQHEIDKLNEKIESLNKDLDDLESNRS-QLKEILNEHEEELRKHQQEYAQVEARVRA 505
                                       5688899999999999999****************99999.55566677778999999988888888765 PP

  == domain 5  score: 2.0 bits;  conditional E-value: 0.47
                   Snapin_Pallidin  40 nekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqk 81 
                                       +ekL++++e    e+ ++ ++ +kKL  ++ ++s +++ +++
  gi|298676000|ref|YP_003727750.1| 681 KEKLTKIAEKIT-EYDSKRNNTIKKLDDVESQISDVKQEINN 721
                                       344444433333.34444444455555555555555544444 PP

  == domain 6  score: 6.4 bits;  conditional E-value: 0.019
                   Snapin_Pallidin  11 lepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKL 65 
                                        e ++ + +++l+e+    e L++ +++ n++L+e+ee  +     +lke  +K+
  gi|298676000|ref|YP_003727750.1| 722 HENEISKKQMQLEEISSREERLSQFIESKNKELEEIEESRK-----ELKEEMDKV 771
                                       567888999*****************************998.....555555555 PP

  == domain 7  score: 3.3 bits;  conditional E-value: 0.18
                   Snapin_Pallidin  12 epkldeldeklkelrqsQeeLleqldrlnekLkele..eaqe..aevlpdlkeyakKLvnikkrmsslnerlqklkk 84 
                                       + ++d++ +   e +++ +eL e++++l e+L++ e  e++e  +++ +++++   +++    +++sln  l+ ++k
  gi|298676000|ref|YP_003727750.1| 765 KEEMDKVVADKDEKTKKENELDEKISELEEELADSEipELNEkaDNLNEEIQRLEGRIRDTDSNINSLNLDLEYANK 841
                                       556666666667889999**************853311333322244455555555666777778888877777777 PP

                   Snapin_Pallidin  85 Ra 86 
                                       R+
  gi|298676000|ref|YP_003727750.1| 842 RI 843
                                       76 PP

  == domain 8  score: 4.3 bits;  conditional E-value: 0.088
                   Snapin_Pallidin   5 egllellepkldeldeklkelrqsQeeLleqldrlnek 42 
                                       +g +e ++ k++el+++l++ ++  +eL ++l++l+++
  gi|298676000|ref|YP_003727750.1| 861 QGRIESFKEKIKELEDSLASKQEREKELGDELKELQDE 898
                                       567788999***********************999987 PP

  == domain 9  score: 19.9 bits;  conditional E-value: 1.2e-06
                   Snapin_Pallidin  10 llepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmssln 76 
                                        +++k ++  ++l++l+ + + L+eq+d+l+++L++ + ++e+e +p+ ++ + ++++i+k m+ l+
  gi|298676000|ref|YP_003727750.1| 915 SIKSKFENASNRLQALESTKSSLKEQIDELRSELEQ-RGIEETEEVPNYETVRTRIASIEKAMEDLE 980
                                       6789999***************************85.444444559*****************9986 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3  20.7   1.5e-06   0.00093     224     361 ..     181     320 ..     157     321 .. 0.88
   2 ?    4.0  12.5     0.032        20     238     321 ..     319     405 ..     315     413 .. 0.81
   3 ?    2.1  16.5      0.12        74     205     305 ..     413     515 ..     404     532 .. 0.68
   4 !    9.2  26.6   0.00087      0.54     216     325 ..     688     800 ..     677     830 .. 0.80
   5 ?    0.0   9.7      0.53   3.3e+02     233     323 ..     815     901 ..     797     905 .. 0.55
   6 !    7.9  18.1    0.0021       1.3     218     351 ..     842     979 ..     829     985 .. 0.77
   7 ?   -0.1   1.2      0.56   3.5e+02     235     267 ..     992    1024 ..     981    1053 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.5e-06
                             IFT57 224 ahleqmkkhkksieeslpetksqlkklhedisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegv 300
                                       ++le++++h + ++  ++e+++ql+kl+++ +++l+  + +++    +    l+++++a++el++v+ +++  +++v
  gi|298676000|ref|YP_003727750.1| 181 NELETVREHIERVDIIIEEVNNQLDKLKDERDQALKYQSLKQEKAKYEGFVILSKLKDAKKELESVNSDIESKNNSV 257
                                       68999*******************************99988888888888899************************ PP

                             IFT57 301 seltrelaeiseelekvkqemeergssmtDg..splvkikkaltklkkEikqmdvrigVlqht 361
                                       +el++ l+e +e+l+++++ + + ++++ +   +  ++ikk +++++ Ei+  +  i +++++
  gi|298676000|ref|YP_003727750.1| 258 EELQKSLDEKNEQLQELEKTLSDLTNQIQNMgeKEQIQIKKDIEEIRGEISRCNGSIEIAENE 320
                                       ************9999998888777665543224459***************99999999876 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.032
                             IFT57 238 eslpetksqlkklhedisktlekiesrEkylnsq...leellqeyreaqeelsevkekykqlsegvseltrelaeis 311
                                       ++++++ +  +k   di+ + +k+e+ E+ +n +    e+  +e++e ++el+ ++ k++++ ++  e +++l+e++
  gi|298676000|ref|YP_003727750.1| 319 NEIQDIDTRRRKTLVDIDDAKSKVEELESKINDEeirKESINSELSERKNELKLLQSKINDVDAKFAETRDKLSELK 395
                                       56677777777888899999999999999998752224677788999999999999999999999999999999999 PP

                             IFT57 312 eelekvkqem 321
                                       +e e++k+e 
  gi|298676000|ref|YP_003727750.1| 396 NEREQIKNEK 405
                                       9999999885 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.12
                             IFT57 205 eRvlpqLkvtikadakdWrahleqmkkhkksieeslpetksqlkklhedi...sktlekiesrEkylnsqleellqe 278
                                       +R l + + +  a+++d +++++  k+  +s ++++ +++++++kl e+i   +k l+ +es  ++l + l+e  +e
  gi|298676000|ref|YP_003727750.1| 413 NRLLDAVRRK-SAEKRDIENEIQDSKEKIESSDSDTRSVQHEIDKLNEKIeslNKDLDDLESNRSQLKEILNEHEEE 488
                                       3333333332.356668888888888888888888888888888888776222567788888888888888888888 PP

                             IFT57 279 yreaqeelsevkekykqlsegvseltr 305
                                       +r+ q+e+++v+ +++ ++e+ +  + 
  gi|298676000|ref|YP_003727750.1| 489 LRKHQQEYAQVEARVRAAEENSKYSKA 515
                                       888888888888888887776655544 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.00087
                             IFT57 216 kadakdWrahleqmkkhkksieeslpetksqlkklhedisk...tlekiesrEkylnsqleellqeyreaqeelsev 289
                                       +++  ++ ++ +++ k  + +e++++++k+++++ +++isk   +le+i+srE++l + +e+  +e++e +e+ +e+
  gi|298676000|ref|YP_003727750.1| 688 AEKITEYDSKRNNTIKKLDDVESQISDVKQEINNHENEISKkqmQLEEISSREERLSQFIESKNKELEEIEESRKEL 764
                                       555567888888888888899*****************987444799****************************** PP

                             IFT57 290 kekykqlsegvseltrelaeiseelekvkqemeerg 325
                                       ke+++++ +   e+t++ +e++e+++++++e+ + +
  gi|298676000|ref|YP_003727750.1| 765 KEEMDKVVADKDEKTKKENELDEKISELEEELADSE 800
                                       *************************99999987643 PP

  == domain 5  score: 0.0 bits;  conditional E-value: 0.53
                             IFT57 233 kksieeslpetksqlkklhedisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelae 309
                                        + +e  + +t s+++ l  d++++ ++i+   + +++  e+     ++ q +++++kek+k+l++++ ++++  +e
  gi|298676000|ref|YP_003727750.1| 815 IQRLEGRIRDTDSNINSLNLDLEYANKRISDDRELIEELDEK----KSSHQGRIESFKEKIKELEDSLASKQEREKE 887
                                       234444555566666666666666666666555544432222....2344556677777777777777777777777 PP

                             IFT57 310 iseelekvkqemee 323
                                       + +el++++ e  +
  gi|298676000|ref|YP_003727750.1| 888 LGDELKELQDERAN 901
                                       77777776665544 PP

  == domain 6  score: 7.9 bits;  conditional E-value: 0.0021
                             IFT57 218 dakdWrahleqmkkhkksieeslpetksqlkklhedisktlek...iesrEkylnsqleellqeyreaqeelsevke 291
                                       +  d r+ +e++ + k+s +  +++ k+++k+l++ ++   e+   +    k l+ +  +  +ey ++++ ++++k 
  gi|298676000|ref|YP_003727750.1| 842 RISDDRELIEELDEKKSSHQGRIESFKEKIKELEDSLASKQERekeLGDELKELQDERANKQTEYDNLKKDYNSIKS 918
                                       44477888999999999999999999999999999988776651124444456666677777788888888888888 PP

                             IFT57 292 kykqlsegvseltrelaeiseelekvkqemeergssmtDgsplv.kikkaltklkkEikqm 351
                                       k++++s+++++l+ + ++++e+++++ +e+e+rg + t+  p   ++++ +++++k ++++
  gi|298676000|ref|YP_003727750.1| 919 KFENASNRLQALESTKSSLKEQIDELRSELEQRGIEETEEVPNYeTVRTRIASIEKAMEDL 979
                                       8889999999999999999999999999999999999998875416888888888877766 PP

  == domain 7  score: -0.1 bits;  conditional E-value: 0.56
                             IFT57  235 sieeslpetksqlkklhedisktlekiesrEky 267 
                                        ++ + ++e+k+  + l+++ ++ le+ie+ E+ 
  gi|298676000|ref|YP_003727750.1|  992 EVLNRHEEMKNRRDTLSNEREQILERIEQYENL 1024
                                        455566667777777777777777777666644 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4  12.3       3.6   2.2e+03     103     167 ..     334     398 ..     318     405 .. 0.58
   2 !   18.8  21.5   2.4e-06    0.0015       8     132 ..     397     510 ..     392     519 .. 0.86
   3 !    7.5  15.1    0.0068       4.2      68     162 ..     676     770 ..     652     774 .. 0.85
   4 !   11.1   8.7   0.00056      0.35      71     150 ..     777     854 ..     770     856 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.6
                             ATG16 103 rllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlql 167
                                        + ++++++++le+k++ +e r +++++e ++ + +lk ++ ++++ ++   + +D ls L+ + 
  gi|298676000|ref|YP_003727750.1| 334 DIDDAKSKVEELESKINDEEIRKESINSELSERKNELKLLQSKINDVDAKFAETRDKLSELKNER 398
                                       45566666666666666666666666666666666666666666666666666666666655444 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 2.4e-06
                             ATG16   8 eRdarqekafaeliqaynrLldrtsaleaenaklekaaasakssksskksakekeasasqsnskqsakiqsleqkla 84 
                                       eR++  ++  +eli+  nrLld ++  +ae++ +e++++++k+     k ++++     +++ + +++i +l++k+ 
  gi|298676000|ref|YP_003727750.1| 397 EREQI-KNEKSELIREENRLLDAVRRKSAEKRDIENEIQDSKE-----KIESSD-----SDTRSVQHEIDKLNEKIE 462
                                       78887.99999***********************999877665.....222222.....2334457999******** PP

                             ATG16  85 qlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaer 132
                                       +l+++l +l   r++l++ l+e +eel+k +++  + e+r++++e++ 
  gi|298676000|ref|YP_003727750.1| 463 SLNKDLDDLESNRSQLKEILNEHEEELRKHQQEYAQVEARVRAAEENS 510
                                       ******************************************998765 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0068
                             ATG16  68 snskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdree 144
                                        ++++++k+++ ++k+++  +   ++ k+  + ++++ ++++e+   e+++++++ +l+e++++ ++l++ ++++++
  gi|298676000|ref|YP_003727750.1| 676 FAAAEKEKLTKIAEKITEYDSKRNNTIKKLDDVESQISDVKQEINNHENEISKKQMQLEEISSREERLSQFIESKNK 752
                                       355678899999999999999999999999*********************************************** PP

                             ATG16 145 elrekeklvqdlqDElsa 162
                                       el+e e+  ++l++E++ 
  gi|298676000|ref|YP_003727750.1| 753 ELEEIEESRKELKEEMDK 770
                                       **************9975 PP

  == domain 4  score: 11.1 bits;  conditional E-value: 0.00056
                             ATG16  71 kqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelr 147
                                       ++++k ++l++k+++l eela++  +  el+++  +lnee+q+le +++  ++++++l+ + +  +++++d +e ++
  gi|298676000|ref|YP_003727750.1| 777 EKTKKENELDEKISELEEELADS--EIPELNEKADNLNEEIQRLEGRIRDTDSNINSLNLDLEYANKRISDDRELIE 851
                                       56678899**************9..789************************************************* PP

                             ATG16 148 eke 150
                                       e++
  gi|298676000|ref|YP_003727750.1| 852 ELD 854
                                       987 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0  19.3    0.0015      0.93     158     273 ..     182     298 ..     159     312 .. 0.78
   2 !    7.6   6.8    0.0039       2.4      52     113 ..     310     371 ..     297     384 .. 0.82
   3 ?    3.8   9.8     0.058        36      55     113 ..     383     441 ..     374     444 .. 0.92
   4 !   11.8  10.9   0.00021      0.13     198     273 ..     434     505 ..     433     517 .. 0.77
   5 ?    2.5  23.9      0.15        92      29     133 ..     686     796 ..     678     801 .. 0.71
   6 ?    5.9  13.1     0.013       8.3     184     276 ..     787     883 ..     778     890 .. 0.77
   7 !   12.4   9.7   0.00014     0.084      57     125 ..     886     951 ..     881     959 .. 0.90
   8 ?    5.6  11.4     0.017        10      19     110 ..     926    1023 ..     925    1047 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0015
                                       XXXXXXX.XX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHH CS
                          Filament 158 evdaark.ld.Lteilkeiraqyeelaeknreeaeewykskleelqeaaeknsealrsakeeitelrrqiqsleiel 232
                                       e++++r+ ++ ++ i++e+ +q ++l +++r++a ++ + k e+++ +     ++l+ ak+e++ ++  i+s++  +
  gi|298676000|ref|YP_003727750.1| 182 ELETVREhIErVDIIIEEVNNQLDKL-KDERDQALKYQSLKQEKAKYEGFVILSKLKDAKKELESVNSDIESKNNSV 257
                                       44443331346889**********98.5667788888889************************************* PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 233 eslkkqkasleaqlaeleerleaeleklqeklseleeelae 273
                                       e+l+k+ +  ++ql+ele++l+   +++q++ ++ + ++++
  gi|298676000|ref|YP_003727750.1| 258 EELQKSLDEKNEQLQELEKTLSDLTNQIQNMGEKEQIQIKK 298
                                       **********************9999999886654443332 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0039
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament  52 yekeleelrkqldeltkerarlqleldnlreeledlrkkyekelnkreevEaelkalrkdld 113
                                       ++  +e + ++++++ + r ++ +++d+++ ++e+l +k+++e  ++e++++el + + +l+
  gi|298676000|ref|YP_003727750.1| 310 CNGSIEIAENEIQDIDTRRRKTLVDIDDAKSKVEELESKINDEEIRKESINSELSERKNELK 371
                                       566788899999999***********************************999999887765 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.058
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament  55 eleelrkqldeltkerarlqleldnlreeledlrkkyekelnkreevEaelkalrkdld 113
                                       + +e r++l el++er++++ e ++l  e ++l   + ++ ++++++E+e+++ + +++
  gi|298676000|ref|YP_003727750.1| 383 KFAETRDKLSELKNEREQIKNEKSELIREENRLLDAVRRKSAEKRDIENEIQDSKEKIE 441
                                       67899************************************************998876 PP

  == domain 4  score: 11.8 bits;  conditional E-value: 0.00021
                                       XXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 198 eelqeaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerleaeleklqeklseleeelae 273
                                       ++ +e++e+++++ rs+++ei +l+ +i+sl+ +l++l++++++l++ l+e ee+l +  ++     +++e+ ++ 
  gi|298676000|ref|YP_003727750.1| 434 QDSKEKIESSDSDTRSVQHEIDKLNEKIESLNKDLDDLESNRSQLKEILNEHEEELRKHQQE----YAQVEARVRA 505
                                       567899999*****************************999999988888888765554444....4444444433 PP

  == domain 5  score: 2.5 bits;  conditional E-value: 0.15
                                       XXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament  29 eLeakieeleekksaevsklkelyekeleelrkqldeltkerarlqleldnlreeledlrkkyekelnkreevEael 105
                                       ++  ki+e   k++++++kl +  e++++++++++++ ++e ++ q++l+++    e+l + +e++ ++ ee+E+  
  gi|298676000|ref|YP_003727750.1| 686 KIAEKITEYDSKRNNTIKKL-DDVESQISDVKQEINNHENEISKKQMQLEEISSREERLSQFIESKNKELEEIEESR 761
                                       45667777777755555544.44699999999999999999999999999999999999888888877777777777 PP

                                       XXXX.......XXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament 106 kalr.......kdldeatlarvdLekkvesLkeel 133
                                       k+l+        d de+t +  +L++k+ +L+eel
  gi|298676000|ref|YP_003727750.1| 762 KELKeemdkvvADKDEKTKKENELDEKISELEEEL 796
                                       77774444333555566666667777777777776 PP

  == domain 6  score: 5.9 bits;  conditional E-value: 0.013
                                       XXXXXXX.XXXXXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHH CS
                          Filament 184 knreeae.ewykskleelqeaaeknsealrsakeeitelrrqiqsleieleslkkq...kasleaqlaeleerleae 256
                                       ++ +e+e e   s + el+e+a++ +e++++ +  i ++  +i+sl+ +le   k     + l ++l e +  ++  
  gi|298676000|ref|YP_003727750.1| 787 EKISELEeELADSEIPELNEKADNLNEEIQRLEGRIRDTDSNINSLNLDLEYANKRisdDRELIEELDEKKSSHQGR 863
                                       4455554145578999**********************************998876111455667777777889999 PP

                                       HHHHHHHHHHHHHHHHHHHH CS
                          Filament 257 leklqeklseleeelaeire 276
                                       +e+++ek++ele+ la+ +e
  gi|298676000|ref|YP_003727750.1| 864 IESFKEKIKELEDSLASKQE 883
                                       *************9986443 PP

  == domain 7  score: 12.4 bits;  conditional E-value: 0.00014
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament  57 eelrkqldeltkerarlqleldnlreeledlrkkyekelnkreevEaelkalrkdldeatlarvdLekk 125
                                       +el ++l+el+ era+ q e+dnl+++++ +++k+e+  n+ +++E++  +l+ ++de+   r++Le++
  gi|298676000|ref|YP_003727750.1| 886 KELGDELKELQDERANKQTEYDNLKKDYNSIKSKFENASNRLQALESTKSSLKEQIDEL---RSELEQR 951
                                       578899***************************************************96...6677665 PP

  == domain 8  score: 5.6 bits;  conditional E-value: 0.017
                                        XXXXXXXXXXXXXXXXXXXXXXX......XXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament   19 kVraLEqenkeLeakieeleekk......saevsklkelyekeleelrkqldeltkerarlqleldnlreeledl 87  
                                        + +aLE  +++L+ +i el+ +       ++e+  ++e+  + ++++ k++++l+  + r+  e+d++ + +e++
  gi|298676000|ref|YP_003727750.1|  926 RLQALESTKSSLKEQIDELRSELeqrgieETEEVPNYETVRTRIASIEKAMEDLEPVNMRAIDEYDEVLNRHEEM 1000
                                        6799************998876322333345555567777789******************************** PP

                                        XXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament   88 rkkyekelnkreevEaelkalrk 110 
                                        +++ ++  n+re++ + ++++  
  gi|298676000|ref|YP_003727750.1| 1001 KNRRDTLSNEREQILERIEQYEN 1023
                                        ************99888887654 PP

>> WEMBL  Weak chloroplast movement under blue light
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   5.1     0.094        58      33     102 ..     156     220 ..     151     228 .. 0.81
   2 !   16.5  31.6   4.4e-06    0.0027     227     399 ..     235     404 ..     219     415 .. 0.84
   3 ?    1.0  16.3      0.21   1.3e+02      45     145 ..     427     524 ..     410     568 .. 0.59

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.094
                             WEMBL  33 tverrklveeeLdkvqeeipeykkqaeaaeaaksqvleeLestkrlieeLklnLekaqteeaqAkqdsel 102
                                        verrk ++ e+      ++e+ ++ e a ++ ++v e +e+   +iee+  +L+k + e +qA +   l
  gi|298676000|ref|YP_003727750.1| 156 PVERRKIID-EIA----GVSEFDNKKERAMNELETVREHIERVDIIIEEVNNQLDKLKDERDQALKYQSL 220
                                       567777766.443....4688999999999999999999***********************99776555 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 4.4e-06
                             WEMBL 227 eLkqaeeelqrLneellsak....dlkskletasallldLkaeLaayvesklkeeaeeeeeekksetsikealasar 299
                                        Lk+a++el+ +n+++ s++    +l++ l+++++ l++L++ L++ +++     + + +  +k++ +ik+ +++ r
  gi|298676000|ref|YP_003727750.1| 235 KLKDAKKELESVNSDIESKNnsveELQKSLDEKNEQLQELEKTLSDLTNQI----Q-NMG--EKEQIQIKKDIEEIR 304
                                       799*************98761111566666666666666666666655443....2.222..5788999******** PP

                             WEMBL 300 kELeevkaniekakdevklLkvaaasLrseLekekaeLaslrqregmasiavssLeaelsrtkselelvqakekear 376
                                        E+   + +ie a++e++ +         +++  k+++ +l  + +   i  +s++ els+ k+el+l+q+k ++  
  gi|298676000|ref|YP_003727750.1| 305 GEISRCNGSIEIAENEIQDIDTRRRKTLVDIDDAKSKVEELESKINDEEIRKESINSELSERKNELKLLQSKINDVD 381
                                       **********************999999************************************************* PP

                             WEMBL 377 ekmvelpkeLqeAaqeaeeAksl 399
                                        k +e+  +L+e ++e e+ k++
  gi|298676000|ref|YP_003727750.1| 382 AKFAETRDKLSELKNEREQIKNE 404
                                       *******************9864 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.21
                             WEMBL  45 dkvqeeipeykkqaeaaeaaksqvleeLestkrlieeLklnLekaqteeaqAkqdselaklrveemeqgiaseesva 121
                                         +++ei + k+++e+ + +  +v +e+++ +  ie L  +L+  + +  q k+ ++  +  +++ +q+    ++v 
  gi|298676000|ref|YP_003727750.1| 427 RDIENEIQDSKEKIESSDSDTRSVQHEIDKLNEKIESLNKDLDDLESNRSQLKEILNEHEEELRKHQQEY---AQVE 500
                                       4466666777777777777777777777777777777777766666666666544433333333333333...4444 PP

                             WEMBL 122 akaqlevakerhaaavaeLksvke 145
                                       a+ + +  + ++++av  + s k+
  gi|298676000|ref|YP_003727750.1| 501 ARVRAAEENSKYSKAVDTVISAKN 524
                                       444444445555555555555443 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9  20.8     0.049        30      47     159 ..     174     289 ..     159     295 .. 0.74
   2 !   14.2  18.8   3.7e-05     0.023      50     159 ..     292     405 ..     286     412 .. 0.85
   3 ?    4.3  25.9     0.037        23       3     125 ..     392     512 ..     390     531 .. 0.57
   4 ?    0.6  14.3      0.49     3e+02     112     178 ..     683     749 ..     662     760 .. 0.57
   5 !   16.5  34.7   7.2e-06    0.0044      31     213 ..     750     933 ..     746     936 .. 0.89
   6 ?   -1.5  14.1       2.2   1.3e+03      50     145 ..     921    1022 ..     917    1034 .. 0.64

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.049
                         Golgin_A5  47 aeldelkqerdllreelqklnqqieqlrtelqdleaq..qqaeaeslreqlqeleeqleeerkakeeveaelerlke 121
                                        + + +++e +++re ++++ + ie++ ++l++l+++  q    +sl+++ +++e  +  +  + +++++ele+++ 
  gi|298676000|ref|YP_003727750.1| 174 NKKERAMNELETVREHIERVDIIIEEVNNQLDKLKDErdQALKYQSLKQEKAKYEGFVILS--KLKDAKKELESVNS 248
                                       4557788999999999999999999999999998665114456778888888888776644..44556777777776 PP

                         Golgin_A5 122 elry...leeelvrskatlqsrikdrekeieklrnqlttks 159
                                       ++++     eel++s  + ++++++ ek +++l+nq+++  
  gi|298676000|ref|YP_003727750.1| 249 DIESknnSVEELQKSLDEKNEQLQELEKTLSDLTNQIQNMG 289
                                       665511155899999999999****************9864 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 3.7e-05
                         Golgin_A5  50 delkqerdl..lreelqklnqqieqlrtelqdleaqqqa...eaeslreqlqeleeqleeerkakeeveaelerlke 121
                                       ++++ ++d+  +r e+ + n++ie   +e+qd+++++ +   +++ ++ +++ele++++ e+ +ke++++el++ k+
  gi|298676000|ref|YP_003727750.1| 292 EQIQIKKDIeeIRGEISRCNGSIEIAENEIQDIDTRRRKtlvDIDDAKSKVEELESKINDEEIRKESINSELSERKN 368
                                       55555555422789*******************998754333899******************************** PP

                         Golgin_A5 122 elryleeelvrskatlqsrikdrekeieklrnqlttks 159
                                       el+ l++    + a++ +  +d+ +e+++ r+q+++++
  gi|298676000|ref|YP_003727750.1| 369 ELKLLQSKINDVDAKFAE-TRDKLSELKNEREQIKNEK 405
                                       **********99999865.689************9875 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.037
                         Golgin_A5   3 esakqeledYKqkAarILQsKekliasLkegs.geeglessta.lsaeldelkqerdllreelqklnqqieqlrtel 77 
                                       +++k+e e+ K+  + ++   ++l++ ++ +s  ++++e + + ++ ++++  ++   +++e+ kln++ie+l ++l
  gi|298676000|ref|YP_003727750.1| 392 SELKNEREQIKNEKSELIREENRLLDAVRRKSaEKRDIENEIQdSKEKIESSDSDTRSVQHEIDKLNEKIESLNKDL 468
                                       56677777777777777777777777777655234445554442455577777777777777777777777777777 PP

                         Golgin_A5  78 qdleaqqqaeaeslreqlqeleeqleeerkakeeveaelerlkeelry 125
                                       +dle+++++    l+e l+e ee+l++ +++  +vea ++  +e+ +y
  gi|298676000|ref|YP_003727750.1| 469 DDLESNRSQ----LKEILNEHEEELRKHQQEYAQVEARVRAAEENSKY 512
                                       777777643....33334444444444444444444444443333333 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.49
                         Golgin_A5 112 veaelerlkeelryleeelvrskatlqsrikdrekeieklrnqlttkslsssseselesRlkqLtes 178
                                         ++++++  e ++ +++ +++  +++s+i d  +ei++ +n++++k+++  + s  e+Rl q  es
  gi|298676000|ref|YP_003727750.1| 683 KLTKIAEKITEYDSKRNNTIKKLDDVESQISDVKQEINNHENEISKKQMQLEEISSREERLSQFIES 749
                                       3344445555555555555555566666666666666666666666666555555555555555554 PP

  == domain 5  score: 16.5 bits;  conditional E-value: 7.2e-06
                         Golgin_A5  31 kegsgeeglesstalsaeldelkqerdllreelqklnqqieqlrtelqdleaqqqae.aeslreqlqeleeqleeer 106
                                       k+++ ee  es+++l+ e+d++ +++d  +++ ++l ++i++l  el+d e  + +e a++l+e++q+le +++   
  gi|298676000|ref|YP_003727750.1| 750 KNKELEEIEESRKELKEEMDKVVADKDEKTKKENELDEKISELEEELADSEIPELNEkADNLNEEIQRLEGRIRDTD 826
                                       555666777788899************************************9877663799**************99 PP

                         Golgin_A5 107 kakeeveaelerlkeel...ryleeelvrskatlqsrikdrekeieklrnqlttkslsssseselesRlkqLtesLi 180
                                       ++ ++++ +le  ++ +   r l eel ++k++ q+ri+   ++i++l+  l++k+     e+el + lk+L +   
  gi|298676000|ref|YP_003727750.1| 827 SNINSLNLDLEYANKRIsddRELIEELDEKKSSHQGRIESFKEKIKELEDSLASKQER---EKELGDELKELQDERA 900
                                       9999999999999988833245678****************************99887...69************** PP

                         Golgin_A5 181 qKQtvlEalsteknslvlQLeRleqqikevqse 213
                                       +KQt  ++l+ ++ns+   +e + + ++ ++s+
  gi|298676000|ref|YP_003727750.1| 901 NKQTEYDNLKKDYNSIKSKFENASNRLQALEST 933
                                       *****************9999888888777765 PP

  == domain 6  score: -1.5 bits;  conditional E-value: 2.2
                         Golgin_A5   50 delkqerdllreelqklnqqieqlrtelqd..l.eaqqqaeaeslreqlqeleeqlee.e..rkakeeveaeler 118 
                                        ++++++ ++l++   +l++qi++lr+el++  + e+++  + e++r +++++e+++e  e  +++  +  +e+ +
  gi|298676000|ref|YP_003727750.1|  921 ENASNRLQALESTKSSLKEQIDELRSELEQrgIeETEEVPNYETVRTRIASIEKAMEDlEpvNMRAIDEYDEVLN 995 
                                        445555555555556666666666666644122133444566777888888777665313114444555578899 PP

                         Golgin_A5  119 lkeelryleeelvrskatlqsrikdre 145 
                                         +ee++  ++ l+++++++ +ri++ e
  gi|298676000|ref|YP_003727750.1|  996 RHEEMKNRRDTLSNEREQILERIEQYE 1022
                                        999999999999999999999997765 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.2       2.2   1.4e+03      10      31 ..      18      39 ..      10      43 .. 0.78
   2 !    9.2  32.0   0.00067      0.41     277     477 ..     172     372 ..     152     381 .. 0.55
   3 !    9.0  28.0   0.00078      0.48     291     443 ..     373     521 ..     365     544 .. 0.64
   4 !   11.2  28.9   0.00017      0.11     306     467 ..     674     836 ..     660     839 .. 0.81
   5 !   14.5  19.8   1.7e-05      0.01     326     473 ..     804     954 ..     800     958 .. 0.57
   6 ?    2.7   2.1     0.064        40     396     512 ..     973    1096 ..     961    1104 .. 0.55

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.2
                            AAA_13 10 aeledfkriNliYGwNGaGKTt 31
                                       +++ f  +  i G NG+GK+ 
  gi|298676000|ref|YP_003727750.1| 18 VKIPFFDDFTTISGPNGSGKSN 39
                                      5667788888999*******85 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00067
                            AAA_13 277 FddefeekqerLekliekves...kkselleklkavsde.asensafeedkeelkaeaealeeqLkglqraleaKrk 349
                                       Fd++ e+ +++Le   e +e+    ++e+ ++l+++ de +++ ++   ++e++k e  ++             K k
  gi|298676000|ref|YP_003727750.1| 172 FDNKKERAMNELETVREHIERvdiIIEEVNNQLDKLKDErDQALKYQSLKQEKAKYEGFVIL-----------SKLK 237
                                       34433433333333333332200022223333333332212222223333333333333333...........3333 PP

                            AAA_13 350 epfksvelesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlv..........eeleseldeykk 416
                                       +  k  elesv+++ies +++v+e++++  + Ne+ ++le+  ++++++++              ee++ e+++ + 
  gi|298676000|ref|YP_003727750.1| 238 DAKK--ELESVNSDIESKNNSVEELQKSLDEKNEQLQELEKTLSDLTNQIQNMGEkeqiqikkdiEEIRGEISRCNG 312
                                       3333..33333333334444444444444444444444444444444444432223333444444678888888889 PP

                            AAA_13 417 kykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLkafGlgeleL 477
                                        ++ +e++i++ +++ ++   ++  ++ +++eLe +++de+   e in+eL++  ++el+L
  gi|298676000|ref|YP_003727750.1| 313 SIEIAENEIQDIDTRRRKTLVDIDDAKSKVEELESKINDEEIRKESINSELSER-KNELKL 372
                                       99999999999999999999999999999********************99988.676666 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00078
                            AAA_13 291 liekveskkselleklkavsdeasensafeedkeelkaeaealeeq....LkglqraleaKrk...epfksve.les 359
                                       l++k++   ++++e         ++ s+ ++++e++k+e+++l  +    L++++r+  +Kr+   e+  s e +es
  gi|298676000|ref|YP_003727750.1| 373 LQSKINDVDAKFAET-------RDKLSELKNEREQIKNEKSELIREenrlLDAVRRKSAEKRDienEIQDSKEkIES 442
                                       333333333333333.......3444555555555555554443332444888888888888422233333223777 PP

                            AAA_13 360 vkakiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaieklekelkeee 436
                                       +++++ s++++++++ne i++ N+  ++le++++++k+ l  h     e+el + +++y+++e+ +  +e++ k ++
  gi|298676000|ref|YP_003727750.1| 443 SDSDTRSVQHEIDKLNEKIESLNKDLDDLESNRSQLKEILNEH-----EEELRKHQQEYAQVEARVRAAEENSKYSK 514
                                       7777789999999999999999999999999999999877775.....56778888899999999999888777666 PP

                            AAA_13 437 aelkkle 443
                                       a    + 
  gi|298676000|ref|YP_003727750.1| 515 AVDTVIS 521
                                       5444443 PP

  == domain 4  score: 11.2 bits;  conditional E-value: 0.00017
                            AAA_13 306 lkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfk.svelesvkakiesikklvaeineliakh 381
                                       l  +++e+++  + +e++ e++++ +++ ++L+ +++++++ ++e+ + + e+++ + ++e+i++  +++ + i++ 
  gi|298676000|ref|YP_003727750.1| 674 LSFAAAEKEKLTKIAEKITEYDSKRNNTIKKLDDVESQISDVKQEINNhENEISKKQMQLEEISSREERLSQFIESK 750
                                       55566666777788888888888888888899998888888888887646778889999999*************** PP

                            AAA_13 382 Nekvanleeekeeakkklelhlv...eeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrd 455
                                       N+  +++ee+++e+k+++ + ++   e+ ++e +e+++k+++le+++  ++ e+ e ++++ +l+eei+ Le ++rd
  gi|298676000|ref|YP_003727750.1| 751 NKELEEIEESRKELKEEMDKVVAdkdEKTKKE-NELDEKISELEEEL--ADSEIPELNEKADNLNEEIQRLEGRIRD 824
                                       *****************999777444444444.47788888888655..556699999******************* PP

                            AAA_13 456 ekpaaeeinkeL 467
                                           ++ +n  L
  gi|298676000|ref|YP_003727750.1| 825 TDSNINSLNLDL 836
                                       ******999776 PP

  == domain 5  score: 14.5 bits;  conditional E-value: 1.7e-05
                            AAA_13 326 lkaeaealeeqLkglqraleaKrkepfk.svelesvkakiesikklvaeineliakhNekvanleeekeeakkklel 401
                                       l+++a++l+e+++ l+ ++ +   ++ + +++le ++++i+   +l++e+ e  ++h  ++++++e+ +e++++l  
  gi|298676000|ref|YP_003727750.1| 804 LNEKADNLNEEIQRLEGRIRDTDSNINSlNLDLEYANKRISDDRELIEELDEKKSSHQGRIESFKEKIKELEDSLAS 880
                                       55556666666666666666666666555555666666666666666666666666666666666666666666654 PP

                            AAA_13 402 hl..veeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLkafGlg 473
                                            +el +el+e++++ ++ +++  +l+k+ + ++++ +++ ++ ++Le + ++ k+ ++e+ +eL++ G++
  gi|298676000|ref|YP_003727750.1| 881 KQerEKELGDELKELQDERANKQTEYDNLKKDYNSIKSKFENASNRLQALESTKSSLKEQIDELRSELEQRGIE 954
                                       33113556666666666666666666666666666666666666666666666666666666666666666655 PP

  == domain 6  score: 2.7 bits;  conditional E-value: 0.064
                            AAA_13  396 kkklelhlveeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekql.....rdekpaaeeink 465 
                                        +k++e  +  ++  ++dey++ +++  +++++  + l++e +++ ++ e+ ++L+k++     + +++a + i +
  gi|298676000|ref|YP_003727750.1|  973 EKAMEDLEPVNM-RAIDEYDEVLNRH-EEMKNRRDTLSNEREQILERIEQYENLKKETfmetfNGINKAFSSIFN 1045
                                        333333333323.3455555444442.244444444444444444444444445444411111334555555666 PP

                            AAA_13  466 eLkafGlgeleLkfeee....kkgYrivrkggsqaa.etLSeGEktaIaflY 512 
                                        eL++ G gel L+ +ee    + + + + k++s +  e +S GEk++ a+ +
  gi|298676000|ref|YP_003727750.1| 1046 ELSD-GTGELALDNYEEpfsgGLTLKAQPKDKSLQRlEAMSGGEKSLTALAF 1096
                                        6655.68899999999999777777777788776666999999998766653 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.7      0.46   2.9e+02      43      84 ..     172     213 ..     146     228 .. 0.58
   2 ?   15.8  10.5   1.7e-05     0.011      25     100 ..     235     308 ..     231     311 .. 0.93
   3 ?    6.6  10.9     0.012       7.6      15     105 ..     296     390 ..     291     395 .. 0.85
   4 ?    0.4  13.2      0.96   5.9e+02       3      87 ..     319     403 ..     317     426 .. 0.79
   5 ?    5.9  10.8      0.02        12      17      77 ..     431     491 ..     413     525 .. 0.57
   6 ?    5.8   0.8      0.02        13      29      69 ..     680     720 ..     677     722 .. 0.91
   7 ?    5.5  15.9     0.026        16       4      97 ..     704     794 ..     700     799 .. 0.87
   8 ?    8.7   7.1    0.0027       1.7       5      95 ..     801     895 ..     797     903 .. 0.90
   9 ?    3.6   6.8       0.1        62       2     101 ..     917    1020 ..     916    1024 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.46
                                       XXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH CS
                        Laminin_II  43 tnekvkdankairdArrsvkkLeklapqLldklkelkqleea 84 
                                        ++k + a++ ++ +r+ +  ++  ++++ ++l +lk  +++
  gi|298676000|ref|YP_003727750.1| 172 FDNKKERAMNELETVREHIERVDIIIEEVNNQLDKLKDERDQ 213
                                       344444444444444444444444444444444444444433 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.7e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHHHHHHHHHH CS
                        Laminin_II  25 nlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdniseikelIa 100
                                       +l+  k++l+++n+++e  n+ v++++k +++ +++ ++Lek++ +L ++++++ ++e+    ++++i+ei+  I+
  gi|298676000|ref|YP_003727750.1| 235 KLKDAKKELESVNSDIESKNNSVEELQKSLDEKNEQLQELEKTLSDLTNQIQNMGEKEQI--QIKKDIEEIRGEIS 308
                                       6788999********************************************999999998..4*********8887 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.012
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH....... CS
                        Laminin_II  15 vleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeasss.... 87 
                                       ++++++++  ++++ + +++ ++++++ ++   ++    i+dA+++v +Le ++++ + + ++++   +++++    
  gi|298676000|ref|YP_003727750.1| 296 IKKDIEEIRGEISRCNGSIEIAENEIQDIDTRRRKTLVDIDDAKSKVEELESKINDEEIRKESINSELSERKNelkl 372
                                       567778888888888888888888888888888888889*********************9****999999999999 PP

                                       HHHHHHHHHHHHHHHHHH CS
                        Laminin_II  88 lsdniseikelIaqARka 105
                                       l  +i+ + +  a +R+ 
  gi|298676000|ref|YP_003727750.1| 373 LQSKINDVDAKFAETRDK 390
                                       999999999999999986 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.96
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHH CS
                        Laminin_II   3 elaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelk 79 
                                       + +++++    ++l ++ + + ++e++++k++  +   e +n ++++ ++ +++ ++++ +++ +  +  dkl+elk
  gi|298676000|ref|YP_003727750.1| 319 NEIQDIDTRRRKTLVDIDDAKSKVEELESKINDEEIRKESINSELSERKNELKLLQSKINDVDAKFAETRDKLSELK 395
                                       56788888889999999999999999999998777666799999999999999999999999999999999999999 PP

                                       HHHHH... CS
                        Laminin_II  80 qleeasss 87 
                                       + +e+ ++
  gi|298676000|ref|YP_003727750.1| 396 NEREQIKN 403
                                       99998544 PP

  == domain 5  score: 5.9 bits;  conditional E-value: 0.02
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHH CS
                        Laminin_II  17 eqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklke 77 
                                       + +++ ++++e   ++  +++ ++++ nek++++nk ++d +++ ++L++ +++ ++ l++
  gi|298676000|ref|YP_003727750.1| 431 NEIQDSKEKIESSDSDTRSVQHEIDKLNEKIESLNKDLDDLESNRSQLKEILNEHEEELRK 491
                                       3334444444455555555555555555555555555555555555555555554444433 PP

  == domain 6  score: 5.8 bits;  conditional E-value: 0.02
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTT CS
                        Laminin_II  29 tkeklseinrsveetnekvkdankairdArrsvkkLeklap 69 
                                       +kekl +i++++ e + k ++  k ++d+++++++++++++
  gi|298676000|ref|YP_003727750.1| 680 EKEKLTKIAEKITEYDSKRNNTIKKLDDVESQISDVKQEIN 720
                                       68999*****************************9999887 PP

  == domain 7  score: 5.5 bits;  conditional E-value: 0.026
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHH CS
                        Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkq 80 
                                       ++++++++++ v++ +++ ++++++ + +l+ei +  e+  + ++++nk +++ ++s k+L+++++++++  k  k+
  gi|298676000|ref|YP_003727750.1| 704 KLDDVESQISDVKQEINNHENEISKKQMQLEEISSREERLSQFIESKNKELEEIEESRKELKEEMDKVVAD-KDEKT 779
                                       578889999999999999999999*********99999999**************************9988.55555 PP

                                       HHHH...HHHHHHHHHH CS
                        Laminin_II  81 leeassslsdniseike 97 
                                       ++e+   l ++ise+ e
  gi|298676000|ref|YP_003727750.1| 780 KKEN--ELDEKISELEE 794
                                       5555..59999999876 PP

  == domain 8  score: 8.7 bits;  conditional E-value: 0.0027
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHH CS
                        Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkql 81 
                                       + e ne+a +  e ++ l+ ++  t ++++++n ++e  n+ ++d  + i++  ++ +  +  ++   +k+kel+  
  gi|298676000|ref|YP_003727750.1| 801 IPELNEKADNLNEEIQRLEGRIRDTDSNINSLNLDLEYANKRISDDRELIEELDEKKSSHQGRIESFKEKIKELEDS 877
                                       6789*********************************************************************9987 PP

                                       HHH.......HHHHHHHH CS
                        Laminin_II  82 eeasss....lsdnisei 95 
                                          ++     l+d+++e+
  gi|298676000|ref|YP_003727750.1| 878 LASKQErekeLGDELKEL 895
                                       777666666788887776 PP

  == domain 9  score: 3.6 bits;  conditional E-value: 0.1
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXX--TTTTTGGG CS
                        Laminin_II    2 kelaaeanetakevleqlaplsqnlentkeklseinrsveetnekvk..dankairdArrsvkkLeklapqLldk 74  
                                        k++ ++a++ +++ ++ +  l++++++++++l++  r +eet+e+ +     + i++ ++++ +Le +  + +d 
  gi|298676000|ref|YP_003727750.1|  917 KSKFENASNRLQALESTKSSLKEQIDELRSELEQ--RGIEETEEVPNyeTVRTRIASIEKAMEDLEPVNMRAIDE 989 
                                        778899**************************96..556688888775577888999999999999877666666 PP

                                        HHHHHHHHHH.......HHHHHHHHHHHHHH CS
                        Laminin_II   75 lkelkqleeasss....lsdniseikelIaq 101 
                                          e+ +++e+ ++    ls++ ++i e I+q
  gi|298676000|ref|YP_003727750.1|  990 YDEVLNRHEEMKNrrdtLSNEREQILERIEQ 1020
                                        6665555544444455699999999888887 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   5.9      0.84   5.2e+02      69     126 ..     170     226 ..     157     245 .. 0.57
   2 ?   10.7  17.1   0.00085      0.53      37     152 ..     240     357 ..     228     358 .. 0.82
   3 ?   11.1  15.6   0.00066      0.41      31     132 ..     319     418 ..     316     428 .. 0.77
   4 ?    7.6  16.2    0.0074       4.6      29     124 ..     422     517 ..     414     560 .. 0.65
   5 ?    2.5  27.0      0.27   1.7e+02      40     144 ..     705     822 ..     654     828 .. 0.55
   6 ?   -0.8  34.3       2.8   1.7e+03      12     136 ..     712     870 ..     707     891 .. 0.51
   7 ?   11.0  18.5   0.00068      0.42      17     158 ..     890    1033 ..     886    1039 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.84
                              Fez1  69 evcenelqrkkseaellrekvekleeelkelreelselsleeeeaalesdeakaqrqe 126
                                        + +n+ +r+ +e e++re++e+++  ++e+ ++l +l+ e+++ al+ ++ k+++++
  gi|298676000|ref|YP_003727750.1| 170 SEFDNKKERAMNELETVREHIERVDIIIEEVNNQLDKLKDERDQ-ALKYQSLKQEKAK 226
                                       45566667777777777777777777777777777775544333.3333333333333 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00085
                              Fez1  37 kaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekve.kleeelkelreelselsleeee 112
                                       k +l  +++++e+k+++++el++sl+ek+++l+++e+ l+  +++ +++ ek + +++++++e+r e+s+ + + e 
  gi|298676000|ref|YP_003727750.1| 240 KKELESVNSDIESKNNSVEELQKSLDEKNEQLQELEKTLSDLTNQIQNMGEKEQiQIKKDIEEIRGEISRCNGSIEI 316
                                       6677788899999999999999999999999999999999999999988887654899********99998777666 PP

                              Fez1 113 aalesdeakaq.rqeaeeleelkreverlraeLkeerqkke 152
                                       a++e ++  ++ r++  ++++ k++ve+l+++++ e+ +ke
  gi|298676000|ref|YP_003727750.1| 317 AENEIQDIDTRrRKTLVDIDDAKSKVEELESKINDEEIRKE 357
                                       6666655555415667899**************99987776 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00066
                              Fez1  31 seivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelsels 107
                                       +ei  + ++ r +  ++++  ++++ele+++++ +   e +++el+++k+e +ll+ k++ ++++++e+r++lsel+
  gi|298676000|ref|YP_003727750.1| 319 NEIQDIDTRRRKTLVDIDDAKSKVEELESKINDEEIRKESINSELSERKNELKLLQSKINDVDAKFAETRDKLSELK 395
                                       5666777788888899999999999**********************************************999987 PP

                              Fez1 108 leeeeaalesdeakaqrqeaeelee 132
                                       +e+e+ ++e++  +  r+e++ l++
  gi|298676000|ref|YP_003727750.1| 396 NEREQIKNEKS--ELIREENRLLDA 418
                                       66655543333..333444333443 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0074
                              Fez1  29 klseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelse 105
                                       k  e   + +++++ ++k+e++++ ++++++++++ ++++e ++++l+  +s+ + l+e +++ eeel++ ++e+++
  gi|298676000|ref|YP_003727750.1| 422 KSAEKRDIENEIQDSKEKIESSDSDTRSVQHEIDKLNEKIESLNKDLDDLESNRSQLKEILNEHEEELRKHQQEYAQ 498
                                       45555556677777778888888888888888877777788888888888888888888888888888888777777 PP

                              Fez1 106 lsleeeeaalesdeakaqr 124
                                       ++++ + a+++s+ +ka  
  gi|298676000|ref|YP_003727750.1| 499 VEARVRAAEENSKYSKAVD 517
                                       6665555544444433322 PP

  == domain 5  score: 2.5 bits;  conditional E-value: 0.27
                              Fez1  40 lrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeeaale 116
                                       l ++++++++  +ei+++e+++++k+++le++ ++ +r ++  e +++++e++ee  kel+ee+ ++ ++++e++++
  gi|298676000|ref|YP_003727750.1| 705 LDDVESQISDVKQEINNHENEISKKQMQLEEISSREERLSQFIESKNKELEEIEESRKELKEEMDKVVADKDEKTKK 781
                                       33444444455555555555555555555555555555555555555555555555555555555555444444433 PP

                              Fez1 117 sdeakaqrqe.............aeeleelkreverlraeL 144
                                        +e  ++ +e             +e++++l++e++rl++++
  gi|298676000|ref|YP_003727750.1| 782 ENELDEKISEleeeladseipelNEKADNLNEEIQRLEGRI 822
                                       33332222225556665555555555666666666665555 PP

  == domain 6  score: -0.8 bits;  conditional E-value: 2.8
                              Fez1  12 islLKqQLkdsqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrek 88 
                                       is +Kq + +  +e+++k   + ++ ++   l++ +e+k++e++e+ees++e ++e++++ ++ ++k+++++ l+ek
  gi|298676000|ref|YP_003727750.1| 712 ISDVKQEINNHENEISKKQMQLEEISSREERLSQFIESKNKELEEIEESRKELKEEMDKVVADKDEKTKKENELDEK 788
                                       66667777777777777777666666666667777777777777777777777777777666666666666666666 PP

                              Fez1  89 vekleeelkelre.elselsleeeeaa....................................lesdeakaqrqeae 128
                                       +++leeel++    el+e++ + +e +                                    +e de+k  +  + 
  gi|298676000|ref|YP_003727750.1| 789 ISELEEELADSEIpELNEKADNLNE-EiqrlegrirdtdsninslnldleyankrisddreliEELDEKKSSH--QG 862
                                       7766666665543233332222222.12333344444444444444443333333333333222222211111..23 PP

                              Fez1 129 eleelkre 136
                                       ++e+ k++
  gi|298676000|ref|YP_003727750.1| 863 RIESFKEK 870
                                       34444444 PP

  == domain 7  score: 11.0 bits;  conditional E-value: 0.00068
                              Fez1   17 qQLkdsqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvek 91  
                                          Lk+ q e ++k  e+ +lk +   +++k e+  ++++ le++ ++ +++++++ +el+++  e++    + e+
  gi|298676000|ref|YP_003727750.1|  890 DELKELQDERANKQTEYDNLKKDYNSIKSKFENASNRLQALESTKSSLKEQIDELRSELEQRGIEETEEVPNYET 964 
                                        579********************************************************9998877777777999 PP

                              Fez1   92 leeelkelreelselsleeeeaalesdeakaqrqe.aeeleelkreverlraeLk.eerqkkeeqassF 158 
                                        + + ++++ +++++l++ + +a+ e de+ ++++e +++ ++l++e e++ ++++ +e+ kke+ +++F
  gi|298676000|ref|YP_003727750.1|  965 VRTRIASIEKAMEDLEPVNMRAIDEYDEVLNRHEEmKNRRDTLSNEREQILERIEqYENLKKETFMETF 1033
                                        999999999999998888888887766655554442333444555555555555413444455555555 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3  15.1      0.14        87      31     130 ..     184     283 ..     170     287 .. 0.72
   2 ?    7.2  10.9    0.0087       5.4      21     118 ..     284     384 ..     282     390 .. 0.85
   3 ?    3.7   5.4       0.1        63      31      88 ..     385     442 ..     380     447 .. 0.92
   4 ?    9.9   8.6    0.0013      0.82      30     112 ..     447     533 ..     444     540 .. 0.83
   5 ?    4.1   9.7     0.079        49      66     130 ..     689     752 ..     675     753 .. 0.77
   6 ?   11.2  11.5   0.00052      0.32      27     124 ..     737     835 ..     734     842 .. 0.90
   7 ?   11.4  10.6   0.00043      0.27      25     127 ..     852     950 ..     848     954 .. 0.71
   8 ?    4.5   1.3     0.058        36      31      97 ..     963    1025 ..     959    1048 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.14
                                       CCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHH CS
                         Fib_alpha  31 kdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvL 107
                                       ++v++++e++   +ee++n+  + ++   +  ++   kq+++k +  vi +  k+ ++e + ++  i ++ +++++L
  gi|298676000|ref|YP_003727750.1| 184 ETVREHIERVDIIIEEVNNQLDKLKDERDQALKYQSLKQEKAKYEGFVILSKLKDAKKELESVNSDIESKNNSVEEL 260
                                       4566667777777777777766666666555555555555555455555555566666999**************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 108 qnvlesneqkiqkLeqdidqker 130
                                       q+ l+++++++q+Le+  + +++
  gi|298676000|ref|YP_003727750.1| 261 QKSLDEKNEQLQELEKTLSDLTN 283
                                       ***************99887765 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0087
                                       HHHHCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC...CHHH CS
                         Fib_alpha  21 glqdlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeei...lrlk 94 
                                       ++q++ +k + ++kkd+e+++ e+++ + s + ae+ +++i++  r++    +d ++ ++++++++++e    + ++
  gi|298676000|ref|YP_003727750.1| 284 QIQNMGEKEQIQIKKDIEEIRGEISRCNGSIEIAENEIQDIDTRRRKTLVDIDDAKSKVEELESKINDEEirkESIN 360
                                       57777789999******************************************************985430114466 PP

                                       HHHHCCHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  95 etidaqesnirvLqnvlesneqki 118
                                        ++++  ++++ Lq+ +++ + k 
  gi|298676000|ref|YP_003727750.1| 361 SELSERKNELKLLQSKINDVDAKF 384
                                       677777789999999999988776 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.1
                                       CCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  31 kdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskelee 88 
                                        +++++l++l+ne e+i+n+++e  +  +++ d +r+k ++k+d +n i++s++++e+
  gi|298676000|ref|YP_003727750.1| 385 AETRDKLSELKNEREQIKNEKSELIREENRLLDAVRRKSAEKRDIENEIQDSKEKIES 442
                                       678999*************************************9***********995 PP

  == domain 4  score: 9.9 bits;  conditional E-value: 0.0013
                                       CCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..HCCCHHHHHHHCCH..H CS
                         Fib_alpha  30 ekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskele..eeilrlketidaqe..s 102
                                        ++v+++++kl++++e++++   + e+  +++k++l+e++++ +++++ + +++ +++  ee +++ + +d+ +  +
  gi|298676000|ref|YP_003727750.1| 447 TRSVQHEIDKLNEKIESLNKDLDDLESNRSQLKEILNEHEEELRKHQQEYAQVEARVRaaEENSKYSKAVDTVIsaK 523
                                       57889999999999999999999999999999999999999999899999999988874357889999999988767 PP

                                       HHHHHHHHHH CS
                         Fib_alpha 103 nirvLqnvle 112
                                       n ++Lq+++ 
  gi|298676000|ref|YP_003727750.1| 524 NNKELQGIYG 533
                                       8899999875 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.079
                                       HHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  66 rekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesneqkiqkLeqdidqker 130
                                       ++  + +++ +n+ikk+ +++e++i+++k++i+++e++i + q  le+ +++ ++L q i++k++
  gi|298676000|ref|YP_003727750.1| 689 EKITEYDSKRNNTIKKL-DDVESQISDVKQEINNHENEISKKQMQLEEISSREERLSQFIESKNK 752
                                       33333333345666665.68999*********************************999998865 PP

  == domain 6  score: 11.2 bits;  conditional E-value: 0.00052
                                       CCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHCCCHHHHHHHCCHH CS
                         Fib_alpha  27 lkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskel.eeeilrlketidaqes 102
                                       ++ e+ +++ +e+ ++eleei++s ke +e + ++     ek k++++ d+ i+++++el ++ei +l+e+ d+  +
  gi|298676000|ref|YP_003727750.1| 737 SSREERLSQFIESKNKELEEIEESRKELKEEMDKVVADKDEKTKKENELDEKISELEEELaDSEIPELNEKADNLNE 813
                                       5667778888999999******************999999999999999**********9567999*********** PP

                                       HHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 103 nirvLqnvlesneqkiqkLeqd 124
                                       +i+ L + +++ +++i+ L+ d
  gi|298676000|ref|YP_003727750.1| 814 EIQRLEGRIRDTDSNINSLNLD 835
                                       *****************99866 PP

  == domain 7  score: 11.4 bits;  conditional E-value: 0.00043
                                       CCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCH CS
                         Fib_alpha  25 lllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqe 101
                                        l++++++ + ++e+ +++++e+++s  + +e  ke+ d l+e q + +++++ + +++    ++++ +k +  +  
  gi|298676000|ref|YP_003727750.1| 852 ELDEKKSSHQGRIESFKEKIKELEDSLASKQEREKELGDELKELQDERANKQTEYDNLK----KDYNSIKSKFENAS 924
                                       56777777777777777777777777777777777777777777777775555555444....45558888888888 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 102 snirvLqnvlesneqkiqkLeqdidq 127
                                       +++++L ++ +s++++i +L+++ +q
  gi|298676000|ref|YP_003727750.1| 925 NRLQALESTKSSLKEQIDELRSELEQ 950
                                       88888888888888888888877665 PP

  == domain 8  score: 4.5 bits;  conditional E-value: 0.058
                                        CCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHH CS
                         Fib_alpha   31 kdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketi 97  
                                        ++v+++++++e+ +e+++  +  a   + e +++l+++++ k+  d++ ++ ++ le +i+++++  
  gi|298676000|ref|YP_003727750.1|  963 ETVRTRIASIEKAMEDLEPVNMRA---IDEYDEVLNRHEEMKNRRDTLSNEREQILE-RIEQYENLK 1025
                                        579999999999999999988765...667778888888888888899999999999.999998764 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.2   7.4e+02     122     149 ..      52      79 ..      50      80 .. 0.91
   2 ?    1.7   2.6      0.21   1.3e+02      40      84 ..     170     214 ..     167     228 .. 0.79
   3 ?    6.1  10.5    0.0094       5.8      49     116 ..     232     299 ..     216     302 .. 0.88
   4 ?   -0.6   9.7       1.1   6.7e+02      31      95 ..     341     405 ..     296     410 .. 0.64
   5 ?   10.7  17.9   0.00038      0.24      16     127 ..     396     507 ..     391     561 .. 0.82
   6 ?   12.3  16.3   0.00012     0.075      13     112 ..     678     778 ..     672     803 .. 0.83
   7 ?    6.8   3.5    0.0058       3.6      34      90 ..     803     859 ..     783     866 .. 0.86
   8 ?    9.6  11.4   0.00081       0.5      15      92 ..     868     945 ..     863     957 .. 0.89
   9 ?   -1.4   3.2       1.8   1.1e+03      55      93 ..     985    1023 ..     947    1030 .. 0.48

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.2
                           DUF3450 122 eeRqarlakLkelmdradvslaekyrrv 149
                                       + R+ r +kL +l+ ++d s + +y +v
  gi|298676000|ref|YP_003727750.1|  52 NSRTMRAEKLTDLIYNPDSSNKPQYAQV 79 
                                       689******************9999886 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.21
                           DUF3450  40 dklddekqellaeyralkeeleslevyneqlerlvasqeqeiasl 84 
                                       ++ d++k+   +e+++++e +e+ ++  e++++++++++ e+++ 
  gi|298676000|ref|YP_003727750.1| 170 SEFDNKKERAMNELETVREHIERVDIIIEEVNNQLDKLKDERDQA 214
                                       677888899999999999999999999888888888888887654 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0094
                           DUF3450  49 llaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvpllekmidrLeqfveld 116
                                       +l++++++k+eles +   e  +++v+++++++++ +eq++e+e++ ++l+  +++m ++ +  +++d
  gi|298676000|ref|YP_003727750.1| 232 ILSKLKDAKKELESVNSDIESKNNSVEELQKSLDEKNEQLQELEKTLSDLTNQIQNMGEKEQIQIKKD 299
                                       57899****************************************************98877777776 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 1.1
                           DUF3450  31 aaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeie 95 
                                       + ++ ++ki++ +  k+++ +e+ + k+el+ l+ + + +++  a+ + ++++l+++ e+i++ +
  gi|298676000|ref|YP_003727750.1| 341 KVEELESKINDEEIRKESINSELSERKNELKLLQSKINDVDAKFAETRDKLSELKNEREQIKNEK 405
                                       22333444444444556666666666666666666666666666666666666666666666555 PP

  == domain 5  score: 10.7 bits;  conditional E-value: 0.00038
                           DUF3450  16 atldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeie 92 
                                       ++ +q+++e+++ ++++ +    + + + ek+++++e+++ ke++es +   + +++ +++++++i+sl+++++++e
  gi|298676000|ref|YP_003727750.1| 396 NEREQIKNEKSELIREENRLLDAVRRKSAEKRDIENEIQDSKEKIESSDSDTRSVQHEIDKLNEKIESLNKDLDDLE 472
                                       6678999********************************************************************** PP

                           DUF3450  93 eierelvpllekmidrLeqfveldlPflleeRqar 127
                                         +++l+ +l +  ++L+++ ++     +  R+a+
  gi|298676000|ref|YP_003727750.1| 473 SNRSQLKEILNEHEEELRKHQQEYAQVEARVRAAE 507
                                       *****************999887666666666655 PP

  == domain 6  score: 12.3 bits;  conditional E-value: 0.00012
                           DUF3450  13 al.aatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqi 88 
                                       a+ +++l+++ ++ ++  +++  + kk d+++ + +++++e+++ ++e+++ +++ e+ ++  + + q i+s ++++
  gi|298676000|ref|YP_003727750.1| 678 AAeKEKLTKIAEKITEYDSKRNNTIKKLDDVESQISDVKQEINNHENEISKKQMQLEEISSREERLSQFIESKNKEL 754
                                       33478888999999999999999999999999999****************************************** PP

                           DUF3450  89 eeieeierelvpllekmidrLeqf 112
                                       eeiee ++el+  ++k++++ ++ 
  gi|298676000|ref|YP_003727750.1| 755 EEIEESRKELKEEMDKVVADKDEK 778
                                       *****************9986654 PP

  == domain 7  score: 6.8 bits;  conditional E-value: 0.0058
                           DUF3450  34 qsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqiee 90 
                                       + ++k d+l++e q l+ ++r+  + ++sl++  e+ ++ +++ ++ i++l+e++++
  gi|298676000|ref|YP_003727750.1| 803 ELNEKADNLNEEIQRLEGRIRDTDSNINSLNLDLEYANKRISDDRELIEELDEKKSS 859
                                       6789999***************************************99999998875 PP

  == domain 8  score: 9.6 bits;  conditional E-value: 0.00081
                           DUF3450  15 aatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieei 91 
                                       +++++++++  ++ ++ +++   + ++l+de+++ + ey +lk+  +s++ + e+ ++ ++++e++ +sl+eqi+e+
  gi|298676000|ref|YP_003727750.1| 868 KEKIKELEDSLASKQEREKELGDELKELQDERANKQTEYDNLKKDYNSIKSKFENASNRLQALESTKSSLKEQIDEL 944
                                       66788899999999999999999999999999999999999999999999999999999999999999999999997 PP

                           DUF3450  92 e 92 
                                       +
  gi|298676000|ref|YP_003727750.1| 945 R 945
                                       5 PP

  == domain 9  score: -1.4 bits;  conditional E-value: 1.8
                           DUF3450   55 alkeeleslevyneqlerlvasqeqeiasleeqieeiee 93  
                                        ++ +e ++     e++++  +++ +e++++ e+ie+ e+
  gi|298676000|ref|YP_003727750.1|  985 RAIDEYDEVLNRHEEMKNRRDTLSNEREQILERIEQYEN 1023
                                        333333333333334444444444444444444444444 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   7.8      0.12        77      42     118 ..     189     265 ..     172     269 .. 0.65
   2 ?    2.4  13.6      0.24   1.5e+02      45     120 ..     245     324 ..     235     353 .. 0.52
   3 ?    4.6   3.2     0.049        30      65     122 ..     339     396 ..     329     398 .. 0.91
   4 ?   14.0   8.0   6.4e-05      0.04      49     122 ..     393     466 ..     384     468 .. 0.94
   5 ?    7.6   2.0     0.006       3.7      63     114 ..     456     507 ..     455     522 .. 0.92
   6 ?    5.9   8.5      0.02        13      49     122 ..     683     759 ..     671     761 .. 0.82
   7 ?   10.2   8.2   0.00091      0.56      50     122 ..     754     820 ..     742     835 .. 0.67
   8 ?    7.0   4.0    0.0093       5.8      48     119 ..     851     922 ..     831     926 .. 0.84
   9 ?    9.5   1.5    0.0015      0.92      38     107 ..     908     980 ..     904     993 .. 0.79
  10 ?   -0.1   0.1       1.5     9e+02      49      90 ..     999    1041 ..     989    1054 .. 0.59

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.12
                           DUF1664  42 avesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskle 118
                                        +e+v   +e+v ++l + k++  + ++    k+++ k     i +++++++++l+++++d+es ++ ve+l+++l+
  gi|298676000|ref|YP_003727750.1| 189 HIERVDIIIEEVNNQLDKLKDERDQALKYQSLKQEKAKYEGFVILSKLKDAKKELESVNSDIESKNNSVEELQKSLD 265
                                       34444455666666666666666666666666666666666667777777777777777777777777777776665 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.24
                           DUF1664  45 svskqleqvseslaatkrhL...ssridrvdkkldeqkeiskei.keevtevredlseigedvesvkeavegleskl 117
                                       sv +++e+  +s+++ ++ L   ++++++++k+l + ++ ++++ ++e  ++++d++ei+ +++  +  +e  e+++
  gi|298676000|ref|YP_003727750.1| 245 SVNSDIESKNNSVEELQKSLdekNEQLQELEKTLSDLTNQIQNMgEKEQIQIKKDIEEIRGEISRCNGSIEIAENEI 321
                                       34444444443333333333111233444444444444333333123344455555555555555555555555555 PP

                           DUF1664 118 eri 120
                                       ++i
  gi|298676000|ref|YP_003727750.1| 322 QDI 324
                                       544 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.049
                           DUF1664  65 ssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleriee 122
                                       +s+++++++k+++ +  +++i++e++e +++l+ ++++++ v++ + +   kl+++++
  gi|298676000|ref|YP_003727750.1| 339 KSKVEELESKINDEEIRKESINSELSERKNELKLLQSKINDVDAKFAETRDKLSELKN 396
                                       579999*******99999**************************99999999999875 PP

  == domain 4  score: 14.0 bits;  conditional E-value: 6.4e-05
                           DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleriee 122
                                       +l++  e++++ k +L ++ +r+ + +   ++ +++i++e+++ +e++++ ++d +sv++ + +l++k+e++++
  gi|298676000|ref|YP_003727750.1| 393 ELKNEREQIKNEKSELIREENRLLDAVRRKSAEKRDIENEIQDSKEKIESSDSDTRSVQHEIDKLNEKIESLNK 466
                                       5788899***************************************************************9975 PP

  == domain 5  score: 7.6 bits;  conditional E-value: 0.006
                           DUF1664  63 hLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                       +L+++i++++k ld+ +   +++ke ++e +e+l++ +++  +v++ v+  e
  gi|298676000|ref|YP_003727750.1| 456 KLNEKIESLNKDLDDLESNRSQLKEILNEHEEELRKHQQEYAQVEARVRAAE 507
                                       79999***************************************99998766 PP

  == domain 6  score: 5.9 bits;  conditional E-value: 0.02
                           DUF1664  49 qleqvsesla...atkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleriee 122
                                       +l+++ e+++   + +++  +++d v++++ ++k+ +++ ++e+++ + +l+ei++  e +++ +e+ +++le+iee
  gi|298676000|ref|YP_003727750.1| 683 KLTKIAEKITeydSKRNNTIKKLDDVESQISDVKQEINNHENEISKKQMQLEEISSREERLSQFIESKNKELEEIEE 759
                                       566666666511145667788999999999999999999999*********************************97 PP

  == domain 7  score: 10.2 bits;  conditional E-value: 0.00091
                           DUF1664  50 leqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleriee 122
                                       l    e++++ +++L++++d+v +  de ++  +e++e+++e++e+l++  +++ +++e   +l+++++r+e+
  gi|298676000|ref|YP_003727750.1| 754 L----EEIEESRKELKEEMDKVVADKDEKTKKENELDEKISELEEELAD--SEIPELNEKADNLNEEIQRLEG 820
                                       3....56777888888888888888888888888888888888887764..4455555555555555555543 PP

  == domain 8  score: 7.0 bits;  conditional E-value: 0.0093
                           DUF1664  48 kqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskler 119
                                       ++l++ ++s +   + ++++i++++++l + +e  ke+ +e++e++++ ++ +++ +++k+  ++++sk e+
  gi|298676000|ref|YP_003727750.1| 851 EELDEKKSSHQGRIESFKEKIKELEDSLASKQEREKELGDELKELQDERANKQTEYDNLKKDYNSIKSKFEN 922
                                       56777777777777889999****************************999999999999998888888765 PP

  == domain 9  score: 9.5 bits;  conditional E-value: 0.0015
                           DUF1664  38 slsdavesvskqleqvs...eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvk 107
                                       +l++  +s+ ++ e+ s   ++l++tk  L+++id++ ++l++     +e   + ++vr  +++i++ +e ++
  gi|298676000|ref|YP_003727750.1| 908 NLKKDYNSIKSKFENASnrlQALESTKSSLKEQIDELRSELEQRGIEETEEVPNYETVRTRIASIEKAMEDLE 980
                                       78888899999999998555677899***********999998765555555667788888888888777665 PP

  == domain 10  score: -0.1 bits;  conditional E-value: 1.5
                           DUF1664   49 qleqvseslaatkrhLssridrvdk.kldeqkeiskeikeevt 90  
                                        ++++  ++l++ ++++ +ri++ ++ k +  +e+ + i++  +
  gi|298676000|ref|YP_003727750.1|  999 EMKNRRDTLSNEREQILERIEQYENlKKETFMETFNGINKAFS 1041
                                        4555566666666666666666544244445555555555544 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.3      0.41   2.5e+02       6      33 ..     183     210 ..     167     222 .. 0.74
   2 ?   10.4   5.6    0.0012      0.72      20      63 ..     243     283 ..     230     294 .. 0.73
   3 ?    1.8   1.0      0.54   3.3e+02       8      59 ..     295     350 ..     288     351 .. 0.73
   4 ?    4.9   3.9     0.057        35      11      62 ..     333     381 ..     329     404 .. 0.85
   5 ?   12.7   3.8   0.00022      0.14       9      67 ..     429     484 ..     427     492 .. 0.86
   6 ?    2.5   5.4      0.32     2e+02       6      60 ..     684     735 ..     680     769 .. 0.69
   7 ?    6.8   1.8     0.015       9.3      21      64 ..     783     828 ..     769     837 .. 0.77
   8 ?    1.6   3.8      0.62   3.8e+02      18      56 ..     897     932 ..     820     963 .. 0.71
   9 ?    0.9   0.1         1   6.3e+02      31      66 ..     956     995 ..     934    1016 .. 0.66

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.41
                           NPV_P10   6 LlvIradikavddkVdalqqqvddvqen 33 
                                       L  +r+ i+ vd  ++ +++q+d+++++
  gi|298676000|ref|YP_003727750.1| 183 LETVREHIERVDIIIEEVNNQLDKLKDE 210
                                       5667777777777777777777777765 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0012
                           NPV_P10  20 VdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqd 63 
                                       ++++     d++++ + v+el++ Ld+ ++qL+ele+++++ ++
  gi|298676000|ref|YP_003727750.1| 243 LESV---NSDIESKNNSVEELQKSLDEKNEQLQELEKTLSDLTN 283
                                       3333...3578888899999999999999999999999888765 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.54
                           NPV_P10   8 vIradikavddkVdalqqqvddvqenlpdvtelnek....LdaqsaqLaeletkve 59 
                                       +I++di+++   ++  + +++  +++++d++    k    +d+   +++ele+k++
  gi|298676000|ref|YP_003727750.1| 295 QIKKDIEEIRGEISRCNGSIEIAENEIQDIDTRRRKtlvdIDDAKSKVEELESKIN 350
                                       78889999999888888888888888888876554433336777777777777765 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.057
                           NPV_P10  11 adikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIq 62 
                                        di + ++kV+ l+++++d +  +++ + +n++L +  ++L+ l++k+++++
  gi|298676000|ref|YP_003727750.1| 333 VDIDDAKSKVEELESKINDEE--IRK-ESINSELSERKNELKLLQSKINDVD 381
                                       699999***********9844..444.5699999999999999999999886 PP

  == domain 5  score: 12.7 bits;  conditional E-value: 0.00022
                           NPV_P10   9 IradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLnp 67 
                                       I ++i++ ++k+++ ++   +vq+++ +   lnek++++++ L++le++ ++ ++iLn+
  gi|298676000|ref|YP_003727750.1| 429 IENEIQDSKEKIESSDSDTRSVQHEIDK---LNEKIESLNKDLDDLESNRSQLKEILNE 484
                                       7788999999999999999999886555...***************************4 PP

  == domain 6  score: 2.5 bits;  conditional E-value: 0.32
                           NPV_P10   6 LlvIradikavddkVdalqqqvddvqenlpdvt.elnekLdaqsaqLaeletkven 60 
                                       L+ I + i++ d+k +   +++ddv++++ dv+ e+n++ +++s+     + ++e+
  gi|298676000|ref|YP_003727750.1| 684 LTKIAEKITEYDSKRNNTIKKLDDVESQISDVKqEINNHENEISK----KQMQLEE 735
                                       778888888888888888888888888888864245544444333....3333333 PP

  == domain 7  score: 6.8 bits;  conditional E-value: 0.015
                           NPV_P10  21 dalqqqvddvqenlpd..vtelnekLdaqsaqLaeletkvenIqdi 64 
                                       + l++++ +++e+l d  + elnek d+++++++ le  + + ++ 
  gi|298676000|ref|YP_003727750.1| 783 NELDEKISELEEELADseIPELNEKADNLNEEIQRLEGRIRDTDSN 828
                                       5677888888888776336689**************9988776654 PP

  == domain 8  score: 1.6 bits;  conditional E-value: 0.62
                           NPV_P10  18 dkVdalqqqvddvqenlpdvtelnekLdaqsaqLaelet 56 
                                       d     q++ d+++++ +    +++k+++ s+ L++le+
  gi|298676000|ref|YP_003727750.1| 897 DERANKQTEYDNLKKDYNS---IKSKFENASNRLQALES 932
                                       3333445555666666555...66777777777777776 PP

  == domain 9  score: 0.9 bits;  conditional E-value: 1
                           NPV_P10  31 qenlpdvtelnekLdaqsaqLaelet....kvenIqdiLn 66 
                                       +e++p+ + + +++ ++ +++++le     ++++ +++Ln
  gi|298676000|ref|YP_003727750.1| 956 TEEVPNYETVRTRIASIEKAMEDLEPvnmrAIDEYDEVLN 995
                                       4567777777777777777777777666666777777777 PP

>> Lebercilin  Ciliary protein causing Leber congenital amaurosis disease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3  30.9       1.2   7.3e+02      13     193 .]     190     370 ..     181     370 .. 0.84
   2 ?    7.6  34.6    0.0045       2.8       6     184 ..     363     540 ..     362     544 .. 0.88
   3 ?    5.3  23.6     0.022        14      46     140 ..     700     796 ..     668     800 .. 0.73
   4 ?   15.2  16.2     2e-05     0.012      67     185 ..     799     912 ..     797     919 .. 0.81
   5 ?   -1.0  18.3       1.9   1.2e+03      63     146 ..     900     982 ..     890    1029 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.2
                        Lebercilin  13 ikeLqnelaelqskleelrkEn.klLkrlqkrqekaLskyedteaeLpqllarhneEvrvlrerlRksqekerelek 88 
                                       i+++   ++e++++l++l+ E  ++Lk +  +qeka  kye+    + + l+  ++E++ ++ ++  + ++++el+k
  gi|298676000|ref|YP_003727750.1| 190 IERVDIIIEEVNNQLDKLKDERdQALKYQSLKQEKA--KYEGF--VILSKLKDAKKELESVNSDIESKNNSVEELQK 262
                                       6666777999***********659***********8..8*996..456668999*********************** PP

                        Lebercilin  89 klkekeaellrlkdklkklkkLsedknLaereeLqkk..LeeleakleekeekikeLerkleleeksfrrqla...a 160
                                       +l ek+++l++l+++l++l +    +n+ e+e++q k  +ee++ ++ + +  i+  e++++  +  +r+ l     
  gi|298676000|ref|YP_003727750.1| 263 SLDEKNEQLQELEKTLSDLTNQI--QNMGEKEQIQIKkdIEEIRGEISRCNGSIEIAENEIQDIDTRRRKTLVdidD 337
                                       *******************9877..67777777665555********************999888888877641116 PP

                        Lebercilin 161 ekkktkeaqeevkalqeeierlkqklkeKereL 193
                                        k+k+ e+++++++ + + e+++++l e+  eL
  gi|298676000|ref|YP_003727750.1| 338 AKSKVEELESKINDEEIRKESINSELSERKNEL 370
                                       788888888888888888888888888887765 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0045
                        Lebercilin   6 lsarllkikeLqnelaelqskleelrkEnklLkrlqkrqekaLskyedteaeLpqllarhneEvrvlrerlRksqek 82 
                                       ls+r++++k Lq+++++++ k +e+r  +  Lk+     +++ s + ++e+ L + ++r ++E r + +++ +s+ek
  gi|298676000|ref|YP_003727750.1| 363 LSERKNELKLLQSKINDVDAKFAETRDKLSELKNEREQIKNEKSELIREENRLLDAVRRKSAEKRDIENEIQDSKEK 439
                                       7999999999999999999999999988888886555555555667899**************************** PP

                        Lebercilin  83 erelekklkekeaellrlkdklkklkkLsedknLaereeLqkkLeeleakleekeekikeLerkleleeksfrrqla 159
                                        ++ ++++++ + e+ +l++k++ l+k  +d +   r++L++ L+e+e++l + +++  + e +++ +e++ +   a
  gi|298676000|ref|YP_003727750.1| 440 IESSDSDTRSVQHEIDKLNEKIESLNKDLDDLES-NRSQLKEILNEHEEELRKHQQEYAQVEARVRAAEENSKYSKA 515
                                       ***************************6656664.8***********************************999999 PP

                        Lebercilin 160 aekkktkeaqeevkalqeeierlkq 184
                                       + +    + ++e++    +i +l q
  gi|298676000|ref|YP_003727750.1| 516 VDTVISAKNNKELQGIYGTIAELGQ 540
                                       8888888888888877777777765 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.022
                        Lebercilin  46 kaLskyedteaeLpql...larhneEvrvlrerlRksqekerelekklkekeaellrlkdklkklkkLsedknLaer 119
                                       + ++k++d e++++++   +++h++E+   + +l +   +e++l++ + +k++el++++++ k+lk+   dk  a++
  gi|298676000|ref|YP_003727750.1| 700 NTIKKLDDVESQISDVkqeINNHENEISKKQMQLEEISSREERLSQFIESKNKELEEIEESRKELKEEM-DKVVADK 775
                                       555666665555554333399***************************************999998733.5555555 PP

                        Lebercilin 120 eeLqkkLeeleakleekeeki 140
                                       +e +kk +el +k+ e ee++
  gi|298676000|ref|YP_003727750.1| 776 DEKTKKENELDEKISELEEEL 796
                                       555555555555554444443 PP

  == domain 4  score: 15.2 bits;  conditional E-value: 2e-05
                        Lebercilin  67 eEvrvlrerlRksqekerelekklkekeaellrlkdklkklkk.LsedknLaereeLqkkLeeleakleekeekike 142
                                       +E+  l+e+  ++ e+ ++le +++++++++++l+ +l+  +k +s+d++L   eeL +k ++++ ++e+ +ekike
  gi|298676000|ref|YP_003727750.1| 799 SEIPELNEKADNLNEEIQRLEGRIRDTDSNINSLNLDLEYANKrISDDREL--IEELDEKKSSHQGRIESFKEKIKE 873
                                       69999**********************************99999*******..99********************** PP

                        Lebercilin 143 Lerkleleeksfrrqlaaekkktkeaqeevkalqeeierlkqk 185
                                       Le +l  + ++++++l  e    ke+q+e ++ q+e+++lk++
  gi|298676000|ref|YP_003727750.1| 874 LEDSLASK-QEREKELGDEL---KELQDERANKQTEYDNLKKD 912
                                       **999754.34455555544...45556666666666665543 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 1.9
                        Lebercilin  63 arhneEvrvlrerlRksqekerelekklkekeaellrlkdklkklkkLsedknLaereeLqkkLeeleakleekeek 139
                                       a+ + E  +l++++   + k ++++++l+  e+   +lk+++++l++  e++  +e ee+ +  e++++++ + e+ 
  gi|298676000|ref|YP_003727750.1| 900 ANKQTEYDNLKKDYNSIKSKFENASNRLQALESTKSSLKEQIDELRSELEQRGIEETEEVPN-YETVRTRIASIEKA 975
                                       56788999***************************************999****99999865.58888888888888 PP

                        Lebercilin 140 ikeLerk 146
                                       +++Le  
  gi|298676000|ref|YP_003727750.1| 976 MEDLEPV 982
                                       8888732 PP

>> TACC_C  Transforming acidic coiled-coil-containing protein (TACC), C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   1.2       1.3   7.7e+02      72     104 ..     178     210 ..     148     230 .. 0.48
   2 ?   11.9  16.8   0.00022      0.14       4     121 ..     237     351 ..     234     358 .. 0.91
   3 ?    1.6   8.9      0.32     2e+02      56     121 ..     349     414 ..     343     423 .. 0.54
   4 ?    8.4  25.7    0.0026       1.6       6     140 ..     373     503 ..     368     531 .. 0.83
   5 ?    3.2  25.7       0.1        64       4     137 ..     706     833 ..     703     848 .. 0.84
   6 ?   14.2  16.8   4.6e-05     0.028       4     128 ..     823     950 ..     820     954 .. 0.90
   7 ?    1.6   3.2      0.33   2.1e+02      89     125 ..     988    1023 ..     952    1045 .. 0.53

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.3
                            TACC_C  72 kvleekeqlladlnsveksfsdlfkryekqkev 104
                                       ++++e e + ++++ v+  ++++ ++++k+k+ 
  gi|298676000|ref|YP_003727750.1| 178 RAMNELETVREHIERVDIIIEEVNNQLDKLKDE 210
                                       222333333333333333333333333333222 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00022
                            TACC_C   4 kdldaalekvkeeveekeeeiqelkkkveelkkenqemkkivaefektiaqlieekqkqkelakkeiqkvleekeql 80 
                                       kd  + le v+ ++e k++ ++el+k+ +e++++ qe++k++++  + i+++ e++q q    kk+i+++  e +  
  gi|298676000|ref|YP_003727750.1| 237 KDAKKELESVNSDIESKNNSVEELQKSLDEKNEQLQELEKTLSDLTNQIQNMGEKEQIQI---KKDIEEIRGEISRC 310
                                       8999999******************************************99998886665...899999999***** PP

                            TACC_C  81 ladlnsveksfsdlfkryekqkevlegykkneeslkkcaee 121
                                       +  ++  e +++d+  r +k    +++ k++ e l +++++
  gi|298676000|ref|YP_003727750.1| 311 NGSIEIAENEIQDIDTRRRKTLVDIDDAKSKVEELESKIND 351
                                       ******************************99999998886 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.32
                            TACC_C  56 ieekqkqkelakkeiqkvleekeqlladlnsveksfsdlfkryekqkevlegykkneeslkkcaee 121
                                       i++++ +ke+ + e+++ ++e + l++++n+v+ +f++   ++  +k+  e+ k+ +  l ++ + 
  gi|298676000|ref|YP_003727750.1| 349 INDEEIRKESINSELSERKNELKLLQSKINDVDAKFAETRDKLSELKNEREQIKNEKSELIREENR 414
                                       445555555555666666666666666666666666665555555555555555555555444444 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.0026
                            TACC_C   6 ldaalekvkeeveekeeeiqelkkkveelkkenqemkkivaefektiaqlieekqkqkelakkeiqkvleekeqlla 82 
                                       l++++++v++++ e   +++elk++ e+ k+e+ e+       e+ + + +  k ++k+  ++eiq  +e  e   +
  gi|298676000|ref|YP_003727750.1| 373 LQSKINDVDAKFAETRDKLSELKNEREQIKNEKSELI---R-EENRLLDAVRRKSAEKRDIENEIQDSKEKIESSDS 445
                                       5677788888888888888899998888888888875...4.47778888888999999**********99****** PP

                            TACC_C  83 dlnsveksfsdlfkryekqkevlegykkneeslkkcaeeylarvkkeeqRYqaLkaha 140
                                       d +sv+ ++++l +++e + + l+++ +n  +lk+  +e  + ++k++q Y +  a  
  gi|298676000|ref|YP_003727750.1| 446 DTRSVQHEIDKLNEKIESLNKDLDDLESNRSQLKEILNEHEEELRKHQQEYAQVEARV 503
                                       ***************************************************9987752 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.1
                            TACC_C   4 kdldaalekvkeeveekeeeiqelkkkveelkkenqemkkivaefektiaqlieekqkqkelakkeiqkvleekeql 80 
                                        d+++++ +vk+e++++e+ei++ + + ee   +++++++ +++  k     +ee ++ +++ k+e++kv+++k++ 
  gi|298676000|ref|YP_003727750.1| 706 DDVESQISDVKQEINNHENEISKKQMQLEEISSREERLSQFIESKNKE----LEEIEESRKELKEEMDKVVADKDEK 778
                                       5889999******************************99777766664....4444555567889************ PP

                            TACC_C  81 ladlnsveksfsdlfkryekqkevlegykkneeslkkcaeeylarvkkeeqRYqaLk 137
                                       +++ n+++ ++s+l + +    + + ++ ++ + l+++++ +  r++  +   ++L 
  gi|298676000|ref|YP_003727750.1| 779 TKKENELDEKISELEEELA--DSEIPELNEKADNLNEEIQRLEGRIRDTDSNINSLN 833
                                       **************99998..678999*******************99887777765 PP

  == domain 6  score: 14.2 bits;  conditional E-value: 4.6e-05
                            TACC_C   4 kdldaalekvkeeveekeeeiqelkkkveelkkenqemkkivaefektiaqlie...ekqkqkelakkeiqkvleek 77 
                                       +d d+ ++ ++ + e ++++i++ ++ +eel++++   +  +++f + i++l +   +kq+++++   e+++++ e+
  gi|298676000|ref|YP_003727750.1| 823 RDTDSNINSLNLDLEYANKRISDDRELIEELDEKKSSHQGRIESFKEKIKELEDslaSKQEREKELGDELKELQDER 899
                                       79999999999999999********************************99865111566666677789******** PP

                            TACC_C  78 eqlladlnsveksfsdlfkryekqkevlegykkneeslkkcaeeylarvkk 128
                                        + +++  +++k ++ + +++e+  + l+ + + + slk++++e+ + +++
  gi|298676000|ref|YP_003727750.1| 900 ANKQTEYDNLKKDYNSIKSKFENASNRLQALESTKSSLKEQIDELRSELEQ 950
                                       ********************************************9988876 PP

  == domain 7  score: 1.6 bits;  conditional E-value: 0.33
                            TACC_C   89 ksfsdlfkryekqkevlegykkneeslkkcaeeylar 125 
                                         +++++++r+e +k+  + + +  e+  + +e+y  +
  gi|298676000|ref|YP_003727750.1|  988 DEYDEVLNRHEEMKNRRDTLSNEREQILERIEQYE-N 1023
                                        23455555555555555555555555555555443.2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3694  (0.206035); expected 358.6 (0.02)
Passed bias filter:                      818  (0.0456244); expected 358.6 (0.02)
Passed Vit filter:                       404  (0.0225333); expected 17.9 (0.001)
Passed Fwd filter:                       272  (0.015171); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 6.57u 0.38s 00:00:06.95 Elapsed: 00:00:01.14
# Mc/sec: 3102.32
//
Query:       gi|298676001|ref|YP_003727751.1|  [L=268]
Description: hypothetical protein Metev_2128 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.077   12.9   0.4      0.077   12.9   0.4    2.2  2  ApoC-I          Apolipoprotein C-I (ApoC-1)
       0.16   12.6   8.4       0.72   10.5   0.1    3.1  3  SlyX            SlyX
       0.16   12.5   1.8       0.43   11.2   1.8    1.7  1  UPF0113_N       UPF0113 Pre-PUA domain
       0.26   11.0   4.4       0.46   10.2   4.4    1.4  1  DUF745          Protein of unknown function (DUF745)
       0.29   11.1   0.1       0.29   11.1   0.1    3.9  4  Tnp_22_trimer   L1 transposable element trimerization domain
       0.34    8.8   3.9       0.37    8.7   3.9    1.2  1  Prominin        Prominin
       0.46   10.3  13.8      0.026   14.4   7.4    1.9  2  PIN_8           PIN like domain
        0.6    8.9  15.5      0.063   12.1  11.1    1.5  2  Spc7            Spc7 kinetochore protein
       0.64   10.5   8.1       0.84   10.2   6.5    2.0  2  Spectrin        Spectrin repeat
       0.72    9.9  10.2       0.14   12.2   6.6    1.6  1  DUF1664         Protein of unknown function (DUF1664)
       0.85   10.0   3.8        8.7    6.8   0.8    2.4  2  HHH_8           Helix-hairpin-helix domain
        1.3    9.0  18.6       0.68    9.9   3.9    2.8  3  Prefoldin_2     Prefoldin subunit
          2    8.4  10.3        9.3    6.3  10.3    2.1  1  Laminin_II      Laminin Domain II
        3.5    8.2  14.7       0.29   11.7   9.4    1.9  2  APG6_N          Apg6 coiled-coil region
        3.6    7.7   8.1        9.4    6.3   8.1    1.7  1  COG2            COG (conserved oligomeric Golgi) complex comp
        3.9    7.7  16.8       0.35   11.1   9.1    2.2  2  Fib_alpha       Fibrinogen alpha/beta chain family
        4.5    8.0   8.3       0.74   10.5   3.7    2.0  2  DUF2203         Uncharacterized conserved protein (DUF2203)
        5.5    7.5  10.5       0.68   10.4   0.5    2.6  2  NPV_P10         Nucleopolyhedrovirus P10 protein
        5.6    7.3  11.0         69    3.8   3.1    3.0  2  ABC_tran_CTD    ABC transporter C-terminal domain
        6.8    6.2   8.8         14    5.2   1.2    2.6  2  DUF4635         Domain of unknown function (DUF4635)
        9.3    6.5   7.7        1.6    8.9   0.1    3.1  3  DUF2802         Protein of unknown function (DUF2802)
        9.6    5.5  10.0        6.9    5.9   7.8    1.8  2  DUF4407         Domain of unknown function (DUF4407)


Domain annotation for each model (and alignments):
>> ApoC-I  Apolipoprotein C-I (ApoC-1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.3       2.4   1.9e+03      30      56 ..      24      30 ..      11      41 .. 0.61
   2 ?   12.9   0.4   9.5e-05     0.077       3      23 ..      59      79 ..      57      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.4
                                      CCCHCTTSSSSCCHHHHHHHHHHHHHH CS
                            ApoC-I 30 ieeIkqSelpaktrnWfsetfekvkek 56
                                      i++Ik                    + 
  gi|298676001|ref|YP_003727751.1| 24 IKKIK--------------------DS 30
                                      33333....................33 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 9.5e-05
                                      -TTSSC....HHHCHHHHHHH CS
                            ApoC-I  3 dlesafeslpdklkEfgktle 23
                                      +le++  +++dk+kE+gktle
  gi|298676001|ref|YP_003727751.1| 59 ELEKRVSKIEDKVKELGKTLE 79
                                      79999***************9 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.5     0.022        18      18      41 ..       9      32 ..       5      50 .. 0.79
   2 ?   10.5   0.1   0.00089      0.72       3      50 ..      55     102 ..      53     116 .. 0.74
   3 ?   -0.8   0.2         3   2.4e+03      27      45 ..     162     180 ..     150     198 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.022
                                      HHHHHHHHHHHHHHHHHHHHHHHH CS
                              SlyX 18 tieeLndvvaeqqqqidrlqrqlr 41
                                      +ie+L ++va+ +q+i++++  l+
  gi|298676001|ref|YP_003727751.1|  9 VIERLEKQVADKEQEIKKIKDSLK 32
                                      688888888888888888877665 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00089
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXX CS
                              SlyX   3 erleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkel 50 
                                       e +eeLE +++  ed ++eL +++    +++  ++  l+ l+++ ++ 
  gi|298676001|ref|YP_003727751.1|  55 ENVEELEKRVSKIEDKVKELGKTLEGMMEELLDQKSILKNLENQSQTP 102
                                       567888888888888888888888888888888888888888777654 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 3
                                       HHHHHHHHHHHHHHHHHHH CS
                              SlyX  27 aeqqqqidrlqrqlrllae 45 
                                       + q q+id +q q ++ +e
  gi|298676001|ref|YP_003727751.1| 162 YTQIQEIDTIQPQEQQENE 180
                                       5666777777766555444 PP

>> UPF0113_N  UPF0113 Pre-PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.8   0.00053      0.43       4      56 ..      20      77 ..      19      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00053
                         UPF0113_N  4 seeetrivfekLtkyigdnvkelld.....rkdgtycfrlkkkrVyyvseellklaet 56
                                      +e+e+++++++L+  i++++++ ld     ++ +t+++ + +krV  +++++ +l +t
  gi|298676001|ref|YP_003727751.1| 20 KEQEIKKIKDSLKDSIIEEIHQELDinnleNNGSTENVEELEKRVSKIEDKVKELGKT 77
                                      699**************************86677999********9999888877655 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   4.4   0.00056      0.46      62     147 ..       8      98 ..       4     105 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00056
                            DUF745  62 qlveqleqelreaeavvqeekkslqss.....eanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqe 133
                                        ++e+le+++++ e+ ++++k+sl+ s     ++ +++ +  ++  ++++e l++ + +++++++++ ++ +g+ +e
  gi|298676001|ref|YP_003727751.1|   8 FVIERLEKQVADKEQEIKKIKDSLKDSiieeiHQELDINNLENNGSTENVEELEKRVSKIEDKVKELGKTLEGMMEE 84 
                                       589*********************998554445677777788888999***************************** PP

                            DUF745 134 laektqlleaAkkR 147
                                       l +++++l++ +++
  gi|298676001|ref|YP_003727751.1|  85 LLDQKSILKNLENQ 98 
                                       ********987765 PP

>> Tnp_22_trimer  L1 transposable element trimerization domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.5      0.57   4.7e+02       2      23 ..      10      31 ..       9      35 .. 0.74
   2 ?   11.1   0.1   0.00036      0.29       2      22 ..      57      77 ..      56      79 .. 0.88
   3 ?   -1.0   0.1       2.2   1.8e+03       3      21 ..     152     170 ..     147     177 .. 0.77
   4 ?   -2.5   1.5       6.5   5.3e+03       6      21 ..     250     265 ..     248     268 .] 0.80

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.57
                                      HHHHHHHHHHHHHHHHHHHHHH CS
                     Tnp_22_trimer  2 idelEERvSaaEDeieeidrev 23
                                      i+ lE  v   E ei  i+   
  gi|298676001|ref|YP_003727751.1| 10 IERLEKQVADKEQEIKKIKDSL 31
                                      5677888888888888887655 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00036
                                      HHHHHHHHHHHHHHHHHHHHH CS
                     Tnp_22_trimer  2 idelEERvSaaEDeieeidre 22
                                      ++elE RvS  ED + e+ ++
  gi|298676001|ref|YP_003727751.1| 57 VEELEKRVSKIEDKVKELGKT 77
                                      689************998765 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2.2
                                       HHHHHHHHHHHHHHHHHHH CS
                     Tnp_22_trimer   3 delEERvSaaEDeieeidr 21 
                                       +++ E  S+   +i+eid+
  gi|298676001|ref|YP_003727751.1| 152 QNIDESASGSYTQIQEIDT 170
                                       4566777777778888887 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 6.5
                                       HHHHHHHHHHHHHHHH CS
                     Tnp_22_trimer   6 EERvSaaEDeieeidr 21 
                                       EE+v   EDe  ei +
  gi|298676001|ref|YP_003727751.1| 250 EEKVEHREDEDAEIIT 265
                                       9999999**9888766 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   3.9   0.00046      0.37     628     713 ..      12      97 ..       3     178 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00046
                          Prominin 628 tlaekleelanelsngkknlkqslkneaqdlraiqqelvlplessvkklkksvkkldeensdlqesikkllaavera 704
                                        l++++ ++ +e+++ k++lk s+ +e  +  +i++  +   +++v++l+k+v k++++ ++l+++++ +++++ + 
  gi|298676001|ref|YP_003727751.1|  12 RLEKQVADKEQEIKKIKDSLKDSIIEEIHQELDINNLENNGSTENVEELEKRVSKIEDKVKELGKTLEGMMEELLDQ 88 
                                       55666666667776666777777777777777787777778888888888888888888888888888888887777 PP

                          Prominin 705 enflkkngs 713
                                       + +lk+  +
  gi|298676001|ref|YP_003727751.1|  89 KSILKNLEN 97 
                                       777766544 PP

>> PIN_8  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   7.4   3.2e-05     0.026      46     140 ..       4     101 ..       3     118 .. 0.90
   2 ?   -0.4   0.4       1.1   8.9e+02     111     142 ..     152     183 ..     129     236 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.2e-05
                             PIN_8  46 rnresviskekkayedlekeleklkkaaekkleealkkwakkkald...teelrkelkkqleelkeelkaeleelkk 119
                                       +nr+ vi++ +k++ d e+e++k+k+++++++ e ++++   ++l+    +e  +el+k ++++++++k+  ++l++
  gi|298676001|ref|YP_003727751.1|   4 ENRDFVIERLEKQVADKEQEIKKIKDSLKDSIIEEIHQELDINNLEnngSTENVEELEKRVSKIEDKVKELGKTLEG 80 
                                       69****************************9999999999999999888889999*************9999***** PP

                             PIN_8 120 sskadkeedpilkkleelleg 140
                                         ++  ++++ilk+le+  + 
  gi|298676001|ref|YP_003727751.1|  81 MMEELLDQKSILKNLENQSQT 101
                                       ***************997665 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.1
                             PIN_8 111 kaeleelkksskadkeedpilkkleellegki 142
                                       ++  e++++s+++++e d+i  + ++  e+++
  gi|298676001|ref|YP_003727751.1| 152 QNIDESASGSYTQIQEIDTIQPQEQQENENNV 183
                                       22222233333333333333333222222222 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1  11.1   7.7e-05     0.063     177     265 ..      11     100 ..       6     105 .. 0.86
   2 ?   -3.7   0.1       5.1   4.2e+03      26      41 ..     166     180 ..     150     192 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.7e-05
                              Spc7 177 aeleeeleklqeaaeelesid.keeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiae 252
                                       ++le+++++ +++ ++++++     +ee+++el+ ++ e +   ++++el++++ ++e+k++el +  + ++ee+  
  gi|298676001|ref|YP_003727751.1|  11 ERLEKQVADKEQEIKKIKDSLkDSIIEEIHQELDINNLENNGSTENVEELEKRVSKIEDKVKELGKTLEGMMEELLD 87 
                                       568888877777777777755166789*************************************************9 PP

                              Spc7 253 aervleeckgwse 265
                                       ++++l++ ++ s+
  gi|298676001|ref|YP_003727751.1|  88 QKSILKNLENQSQ 100
                                       9999998776665 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 5.1
                              Spc7  26 krrstiaptaeekeee 41 
                                       ++  ti p+++++ +e
  gi|298676001|ref|YP_003727751.1| 166 QEIDTIQPQEQQE-NE 180
                                       3333333333333.23 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   6.5     0.001      0.84      36     104 ..      10      86 ..       9      87 .. 0.82
   2 ?    8.0   0.6    0.0049         4      24      71 ..      60     106 ..      53     117 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.001
                                       HHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHH.HHTT.....HTTH..HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  36 vqallkkhkaleaelaaqqervka..lnelaekl.ldeg.....hsas..eeieerleelnerWeeLkelaaerkqk 102
                                       +++l+k+  + e+e++  ++ +k+  ++e+ ++l +++         +  ee+e+r+++++++ +eL ++++ + ++
  gi|298676001|ref|YP_003727751.1|  10 IERLEKQVADKEQEIKKIKDSLKDsiIEEIHQELdINNLenngsT--EnvEELEKRVSKIEDKVKELGKTLEGMMEE 84 
                                       68899999***********99997446699999988887555433..256999999999999999999999999998 PP

                                       HH CS
                          Spectrin 103 Le 104
                                       L 
  gi|298676001|ref|YP_003727751.1|  85 LL 86 
                                       86 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0049
                                       HCCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                          Spectrin  24 lssedlgkdleevqallkkhkaleaelaaqqervkalnelaeklldeg 71 
                                       l +++++k  ++v++l k+++++++el +q+  +k+l+ +++  +++g
  gi|298676001|ref|YP_003727751.1|  60 L-EKRVSKIEDKVKELGKTLEGMMEELLDQKSILKNLENQSQTPTSNG 106
                                       3.4444566677777777888888888888888888887777665555 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   6.6   0.00017      0.14      43     117 ..      10      85 ..       4      93 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                           DUF1664  43 vesvskqleqvseslaatkrhLssr.idrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskl 117
                                       +e++ kq+ +  +++++ k+ L++  i+++ ++ld ++   +  +e+v+e+++ +s+i+++v+++ ++ eg+ ++l
  gi|298676001|ref|YP_003727751.1|  10 IERLEKQVADKEQEIKKIKDSLKDSiIEEIHQELDINNLENNGSTENVEELEKRVSKIEDKVKELGKTLEGMMEEL 85 
                                       57889999999***********976369*********9999999*********************99999986654 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.8     0.011       8.7      34      66 ..       9      39 ..       8      41 .. 0.86
   2 ?    3.7   0.1       0.1        81      34      67 ..      56      86 ..      53      87 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.011
                                      CCCC-SS-HHHHTTHCTTSTT--HHHHHHH.HHH CS
                             HHH_8 34 aiealpeeitsleeeltklpgiGkkiaaki.eei 66
                                      +ie+l++++++ +e  ++++ i +++ + i eei
  gi|298676001|ref|YP_003727751.1|  9 VIERLEKQVAD-KE--QEIKKIKDSLKDSIiEEI 39
                                      69*********.77..89*****99999996776 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.1
                                      CCCC-SS-HHHHTTHCTTSTT--HHHHHHHHHHH CS
                             HHH_8 34 aiealpeeitsleeeltklpgiGkkiaakieeil 67
                                      ++e+l++++  +e+   k++ +Gk +   +ee+l
  gi|298676001|ref|YP_003727751.1| 56 NVEELEKRVSKIED---KVKELGKTLEGMMEELL 86
                                      68999999999766...99999**9999999998 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   1.6    0.0015       1.2      77     101 ..       9      33 ..       3      38 .. 0.87
   2 ?    9.9   3.9   0.00083      0.68      64     101 ..      57      94 ..      50      99 .. 0.84
   3 ?   -2.4   0.3       5.5   4.4e+03      13      29 ..     164     180 ..     152     189 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0015
                                       HHHHHHHHHHHHHHHHHHHHHHHHC CS
                       Prefoldin_2  77 eiktlekqleklekeleelkeelqk 101
                                       +i++lekq  ++e+e++++k++l+ 
  gi|298676001|ref|YP_003727751.1|   9 VIERLEKQVADKEQEIKKIKDSLKD 33 
                                       6999****************99985 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00083
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                       Prefoldin_2  64 keeLeerketlekeiktlekqleklekeleelkeelqk 101
                                        eeLe+r  ++e ++k+l k le + +el ++k+ l++
  gi|298676001|ref|YP_003727751.1|  57 VEELEKRVSKIEDKVKELGKTLEGMMEELLDQKSILKN 94 
                                       68999999999999999999999999999999998876 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 5.5
                                       HHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  13 qlqqlaqqikqletqlk 29 
                                       q+q++++   q +++ +
  gi|298676001|ref|YP_003727751.1| 164 QIQEIDTIQPQEQQENE 180
                                       44444444444444444 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3  10.3     0.011       9.3      15      84 ..      13      80 ..       7     105 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.011
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH CS
                        Laminin_II 15 vleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleea 84
                                       ++q+a+ +q+++++k++l+     +ee++++++  n   +   ++v +Lek + +++dk+kel +  e+
  gi|298676001|ref|YP_003727751.1| 13 LEKQVADKEQEIKKIKDSLKDS--IIEEIHQELDINNLENNGSTENVEELEKRVSKIEDKVKELGKTLEG 80
                                      4667777777777777777643..3458888888888888888899999999999999999998776655 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   9.4   0.00036      0.29       8      92 ..       7     100 ..       6     121 .. 0.76
   2 ?   -2.3   0.2       7.2   5.9e+03      58      64 ..     170     176 ..     139     201 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00036
                            APG6_N   8 dlLleeldkqleqaekerdaYeeflkklkkekkeeek.........qdeeleeleeeleklekeeeelleeLkelek 75 
                                       d ++e+l+kq+++ e+e+++ ++ lk    e+ ++e          + e++eele++++k+e++ +el + L+ + +
  gi|298676001|ref|YP_003727751.1|   7 DFVIERLEKQVADKEQEIKKIKDSLKDSIIEEIHQELdinnlenngSTENVEELEKRVSKIEDKVKELGKTLEGMME 83 
                                       56899*****************9999877665555446877777777777777777777777777777777777777 PP

                            APG6_N  76 ereeleaelaaleeele 92 
                                       e  + ++ l++le++++
  gi|298676001|ref|YP_003727751.1|  84 ELLDQKSILKNLENQSQ 100
                                       77777777777777766 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7.2
                            APG6_N  58 klekeee 64 
                                       +++ +e+
  gi|298676001|ref|YP_003727751.1| 170 TIQPQEQ 176
                                       2222222 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   8.1     0.012       9.4      23     112 ..      12      98 ..       4     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.012
                              COG2  23 rhgvpLeslrrdLeaylkllekellelvnedyadFvslSghLvglqeeleevesplaaarkkvesvreklsereeev 99 
                                       r  +++++  ++++++  +l+++++e + +++ d  +l ++  g  e++ee+e+ ++++ +kv+++ + l+ ++ee+
  gi|298676001|ref|YP_003727751.1|  12 RLEKQVADKEQEIKKIKDSLKDSIIEEIHQEL-DINNLENN--GSTENVEELEKRVSKIEDKVKELGKTLEGMMEEL 85 
                                       45567788899999999999999999999997.55666664..99*******************************9 PP

                              COG2 100 eskleeakeleek 112
                                        ++ +  k+le++
  gi|298676001|ref|YP_003727751.1|  86 LDQKSILKNLENQ 98 
                                       9888877777776 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   9.1   0.00043      0.35      36     127 ..       9     101 ..       3     113 .. 0.84
   2 ?    1.2   0.9      0.47   3.9e+02      46      75 ..     153     182 ..     139     212 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00043
                                       HHCCCCCCCCCCCCHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHH CS
                         Fib_alpha  36 dlekleneleeisnstkeaeelvk.eikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvl 111
                                        +e+le+++++ +++ k++++  k +i + ++++   ++ ++n  ++  +ele++++++++++++  ++++ + + l
  gi|298676001|ref|YP_003727751.1|   9 VIERLEKQVADKEQEIKKIKDSLKdSIIEEIHQELDINNLENNGSTENVEELEKRVSKIEDKVKELGKTLEGMMEEL 85 
                                       58999999999999998888766525777777777777767889999999*************************** PP

                                       HHHHHHHHHHHHHHHH CS
                         Fib_alpha 112 esneqkiqkLeqdidq 127
                                        ++++ +++Le+++++
  gi|298676001|ref|YP_003727751.1|  86 LDQKSILKNLENQSQT 101
                                       ***********99876 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.47
                                       CCCCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  46 eisnstkeaeelvkeikdslrekqkskkdn 75 
                                       +i +s + +++ ++ei+++  ++q+++++n
  gi|298676001|ref|YP_003727751.1| 153 NIDESASGSYTQIQEIDTIQPQEQQENENN 182
                                       677778888888888888877777777755 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   3.7   0.00091      0.74      16      91 ..      11      93 ..       7      97 .. 0.77
   2 ?   -1.5   0.1       4.9     4e+03      36      36 ..     171     171 ..     138     219 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00091
                           DUF2203 16 kelleelralrkeleeleeeleeakaeaekse.......aaeleaeleeleaeieelveeieelGvevkdleaglvDFp 87
                                      ++l ++++++++e+++++++l+++  e+ ++e        +   +++eele++++++ ++++elG  + ++ + l+D  
  gi|298676001|ref|YP_003727751.1| 11 ERLEKQVADKEQEIKKIKDSLKDSIIEEIHQEldinnleNNGSTENVEELEKRVSKIEDKVKELGKTLEGMMEELLDQK 89
                                      455566666777777777766665555544446777788999999**************************99999987 PP

                           DUF2203 88 akld 91
                                      + l+
  gi|298676001|ref|YP_003727751.1| 90 SILK 93
                                      7665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.9
                           DUF2203  36 l 36 
                                       +
  gi|298676001|ref|YP_003727751.1| 171 I 171
                                       2 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   3.5     0.059        48      13      63 ..      10      69 ..       8      69 .. 0.79
   2 ?   10.4   0.5   0.00084      0.68      13      57 ..      57      98 ..      53     104 .. 0.58

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.059
                           NPV_P10 13 ikavddkVdalqqqvddvqenlpd..vtelnekLd.......aqsaqLaeletkvenIqd 63
                                      i+ ++++V   +q+++++++ l+d  ++e++++Ld       + +++++ele+ v++I+d
  gi|298676001|ref|YP_003727751.1| 10 IERLEKQVADKEQEIKKIKDSLKDsiIEEIHQELDinnlennGSTENVEELEKRVSKIED 69
                                      678889999999999999999999778999999974444444568899999999999986 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00084
                           NPV_P10 13 ikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletk 57
                                      +++++++V+ ++++v+++ + l+    + e+L +q   L++le++
  gi|298676001|ref|YP_003727751.1| 57 VEELEKRVSKIEDKVKELGKTLEG---MMEELLDQKSILKNLENQ 98
                                      666666666666666666665555...445555555566666554 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   6.3      0.14   1.1e+02      10      53 ..      10      46 ..       3      61 .. 0.69
   2 ?    3.8   3.1     0.085        69      10      31 ..      57      78 ..      36     101 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.14
                      ABC_tran_CTD 10 leeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleel 53
                                      +e+le++ +  E+ei+++ + l d         + e+++el+  
  gi|298676001|ref|YP_003727751.1| 10 IERLEKQVADKEQEIKKIKDSLKDSI-------IEEIHQELDIN 46
                                      68999999999999999999998875.......55555555555 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.085
                      ABC_tran_CTD 10 leeleaeIeaLEeeiaeleael 31
                                       eele++  ++E + +el + l
  gi|298676001|ref|YP_003727751.1| 57 VEELEKRVSKIEDKVKELGKTL 78
                                      4666666666666666665554 PP

>> DUF4635  Domain of unknown function (DUF4635)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   1.2     0.018        14      93     130 ..       4      42 ..       3      46 .. 0.80
   2 ?    4.7   1.2     0.025        20      99     127 ..      57      85 ..      45      91 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.018
                           DUF4635  93 enlhvflekleeevreleqlvrdleeWl.dallgdlkle 130
                                       en + ++e+le++v + eq ++ +   l d ++++ ++e
  gi|298676001|ref|YP_003727751.1|   4 ENRDFVIERLEKQVADKEQEIKKIKDSLkDSIIEEIHQE 42 
                                       6778899**************999876646666666665 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.025
                           DUF4635  99 lekleeevreleqlvrdleeWldallgdl 127
                                       +e+le+ v ++e  v++l + l+ ++++l
  gi|298676001|ref|YP_003727751.1|  57 VEELEKRVSKIEDKVKELGKTLEGMMEEL 85 
                                       699***************99999888775 PP

>> DUF2802  Protein of unknown function (DUF2802)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.5         1   8.2e+02       3      23 ..      14      34 ..      11      46 .. 0.75
   2 ?    8.9   0.1    0.0019       1.6       3      34 ..      54     108 ..      52     114 .. 0.79
   3 ?   -1.0   0.1       2.5     2e+03      25      37 ..     154     166 ..     137     182 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1
                           DUF2802  3 gqrlaelekrlkqleerleel 23
                                      ++++a+ e+++k++++ l++ 
  gi|298676001|ref|YP_003727751.1| 14 EKQVADKEQEIKKIKDSLKDS 34
                                      678888899999998888765 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0019
                           DUF2802   3 gqrlaelekrlkqleerleel.......................eqqdpqsklYs 34 
                                        + ++elekr++++e++++el                       ++q p+s  Y+
  gi|298676001|ref|YP_003727751.1|  54 TENVEELEKRVSKIEDKVKELgktlegmmeelldqksilknlenQSQTPTSNGYE 108
                                       5778999999999999999998888888888888888888887444447777775 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2.5
                           DUF2802  25 qqdpqsklYsqAi 37 
                                       +++++s++Y+q +
  gi|298676001|ref|YP_003727751.1| 154 IDESASGSYTQIQ 166
                                       4556666666644 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1         2   1.6e+03     137     155 ..      12      30 ..       9      36 .. 0.50
   2 ?    5.9   7.8    0.0085       6.9     106     239 ..      37     181 ..      21     194 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2
                           DUF4407 137 eleaqiaalqaeidaaear 155
                                       +le+q+a+ ++ei++ ++ 
  gi|298676001|ref|YP_003727751.1|  12 RLEKQVADKEQEIKKIKDS 30 
                                       4455555555555544444 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0085
                           DUF4407 106 keIdaelaeeqqeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk...gtgttgva 179
                                       +eI++el+ ++ e++ + ++  +  l+++++++e+++++l ++++   ++l +++  +++  ++ +   ++g     
  gi|298676001|ref|YP_003727751.1|  37 EEIHQELDINNLENNGSTENVEE--LEKRVSKIEDKVKELGKTLEGMMEELLDQKSILKNLENQSQtptSNG--YES 109
                                       59999999999999999988877..99999999999999999999999999888777775544444333333..234 PP

                           DUF4407 180 Gkgpaake..............kkaqldaaqaelaelkakld..............atarlaalraelaeleaerak 228
                                       G+  ++k+                               + +              +++++++  +   +  +e+++
  gi|298676001|ref|YP_003727751.1| 110 GNSSNTKSldsngidsgyagfsG----------------ETSgskiseytkkftgrKDQNIDESASGSYTQIQEIDT 170
                                       56566655555555555555542................32233333333333333555565555555555555666 PP

                           DUF4407 229 eraasqaaaaa 239
                                       ++ + q+++++
  gi|298676001|ref|YP_003727751.1| 171 IQPQEQQENEN 181
                                       65555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2653  (0.147973); expected 358.6 (0.02)
Passed bias filter:                      792  (0.0441742); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); expected 17.9 (0.001)
Passed Fwd filter:                        38  (0.00211947); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.78u 0.39s 00:00:01.17 Elapsed: 00:00:00.57
# Mc/sec: 1423.10
//
Query:       gi|298676002|ref|YP_003727752.1|  [L=888]
Description: SMC domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-21   77.3  12.9    2.2e-21   77.3  12.9    6.4  2  AAA_23          AAA domain
    8.1e-10   38.5   0.6    8.1e-10   38.5   0.6    3.4  1  SMC_N           RecF/RecN/SMC N terminal domain
    4.6e-07   29.9  43.1    4.6e-07   29.9  43.1    4.5  1  AAA_15          AAA ATPase domain
    1.6e-05   24.6  21.8    1.6e-05   24.6  21.8    5.4  5  MscS_porin      Mechanosensitive ion channel porin domain
    0.00013   21.6   0.0    0.00026   20.7   0.0    1.4  1  AAA_29          P-loop containing region of AAA domain
    0.00062   19.8  13.0    0.00062   19.8  13.0    8.1  9  TPR_MLP1_2      TPR/MLP1/MLP2-like protein
    0.00085   18.3 118.5      0.087   11.7  17.0    6.3  6  Spc7            Spc7 kinetochore protein
    0.00089   18.0 116.1     0.0079   14.9  34.2    5.9  6  AAA_13          AAA domain
     0.0021   17.7   0.1     0.0021   17.7   0.1    6.0  7  AAA_27          AAA domain
  ------ inclusion threshold ------
      0.016   15.4   0.0      0.043   14.0   0.0    1.7  1  SbcCD_C         Putative exonuclease SbcCD, C subunit
      0.018   15.4   0.0       0.12   12.8   0.0    2.4  1  AAA_16          AAA ATPase domain
      0.083   12.9  81.7       0.37   10.8   6.3    7.8 10  DUF1664         Protein of unknown function (DUF1664)
       0.15   11.6  98.6       0.18   11.4   8.4    6.6  6  Filament        Intermediate filament protein
       0.18   11.6   0.0       0.18   11.6   0.0    5.2  5  MukB            MukB N-terminal
       0.48    9.7   0.0       0.48    9.7   0.0    3.1  4  FtsK_SpoIIIE    FtsK/SpoIIIE family
       0.94    9.9  98.8       0.14   12.6  21.8    5.5  4  Fez1            Fez1
        6.2    7.1  30.1        4.7    7.5   0.1    7.6  8  WXG100          Proteins of 100 residues with WXG
        8.4    6.6  94.3        4.3    7.5  29.2    5.6  6  ATG16           Autophagy protein 16 (ATG16)


Domain annotation for each model (and alignments):
>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.3  12.9   2.2e-24   2.2e-21       1     198 [.       5     233 ..       5     235 .. 0.79
   2 ?   -1.1  16.4       2.3   2.3e+03      92     195 ..     631     751 ..     617     753 .. 0.57

  Alignments for each domain:
  == domain 1  score: 77.3 bits;  conditional E-value: 2.2e-24
                            AAA_23   1 kLkienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayvel 77 
                                       +L +en+rs++  ++ F++g+ +++G NG+GK+++l+A+  +L+g   r+ +  ++    + ++   +g  ka++ l
  gi|298676002|ref|YP_003727752.1|   5 RLYVENIRSYEYLDLSFNNGVSVVSGANGSGKSSLLEAFFTGLFGS--RTLS--KEYVLADMIR---KGASKASIYL 74 
                                       799******************************************4..3333..3445555555...5688999999 PP

                            AAA_23  78 tfenkdgrytrsiererelskkkgkttkka.....klelleideleqfise...llgskkiilnlilflgqerfeef 146
                                       ++e ++++y   i ++ +++++k+++ +++        ++ +d+ +q+ +    ll+ +++  ++++++ q++ + +
  gi|298676002|ref|YP_003727752.1|  75 ELEQNGNEY---IIEQGFRYDTKNDRAYNSksvfkSNGNIVVDQATQTYDAvckLLNMDEEAYRNCVYIRQGEIDIL 148
                                       999999976...667777777766666444233323334444455555555565*******************7666 PP

                            AAA_23 147 elkdkke..............................rleelekeleeledekkllekl...eqekekekeleelee 190
                                        ++++ke                               l+++ + ++  e e+++++++   e++++ +++ +++++
  gi|298676002|ref|YP_003727752.1| 149 INATPKErqnmiddllqigklehyrerasnakkgvkrHLRDVDNRIKNTESEIEKIKNEnpyENLNKLREKSKNIQS 225
                                       77666666677777777888888888888888888889999*99999999999999999999999************ PP

                            AAA_23 191 eleeilke 198
                                       ++ e++++
  gi|298676002|ref|YP_003727752.1| 226 KIDELNQK 233
                                       ****9998 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.3
                            AAA_23  92 rerelskkkgkttkkaklelleideleqfisellgskkiil.nlilflgqer...feefelkdkkerleelekelee 164
                                       +++ + + +  +  k+k   ++id l+++++++ +  ++i  ++  ++++++   +e  +l+++ +rl++l k+l+ 
  gi|298676002|ref|YP_003727752.1| 631 DSQITERRERLKEIKDKMGDVDIDGLRKTLKQYESAHQNITnEIDKLYQDKDsvlKEAGRLENEINRLNNLHKDLQY 707
                                       22333333333445555666677777777776433333333133333444445555555557777788888888888 PP

                            AAA_23 165 ledekkllekl.............eqekekekeleeleeeleei 195
                                       le++k+ l+ +             ++++ +ek++++l + ++ei
  gi|298676002|ref|YP_003727752.1| 708 LENKKNYLNSVyedseslenmymrIRANLREKNIKALDSLINEI 751
                                       88888888888777777777777766667777888888888876 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.6   8.1e-13   8.1e-10       2     128 ..       3     128 ..       2     132 .. 0.71

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 8.1e-13
                                       EEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTT.TCHCCCCCC--BTTCSSTTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N   2 lkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakkl.rseklsdlihkskekasvkka 77 
                                       lkrl +en +sy  +  +l f+++++++ G+NGSGKs+ll+A  F  G   +++l ++  l d+i k      ++ka
  gi|298676002|ref|YP_003727752.1|   3 LKRLYVENIRSY--EYLDLSFNNGVSVVSGANGSGKSSLLEAF-F-TGLFGSRTLsKEYVLADMIRK-----GASKA 70 
                                       89**********..7***************************8.5.344455566145567899987.....67778 PP

                                       EEEEEEEETTEE........SSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHH CS
                                       xxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  78 eveitfdnedkk........lkiekeevsisrrvkrkgeseykingkevtkkevselle 128
                                       ++ + +++++++          +++++ + s++v++++  ++ +++ + t+  v +ll+
  gi|298676002|ref|YP_003727752.1|  71 SIYLELEQNGNEyiieqgfrYDTKNDRAYNSKSVFKSNG-NIVVDQATQTYDAVCKLLN 128
                                       888887777777555555444445555555555555555.5666666667777766666 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9  43.1   4.6e-10   4.6e-07       1     259 [.       1     321 [.       1     327 [. 0.52

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 4.6e-10
                            AAA_15   1 MkIkkikikNFRslkdveidlseeltvliGkNnsGKSsilealdlFlnnkekkn....................... 54 
                                       Mk+k++ ++N Rs+++ ++++++ ++v+ G+N+sGKSs+lea+   ++     +                       
  gi|298676002|ref|YP_003727752.1|   1 MKLKRLYVENIRSYEYLDLSFNNGVSVVSGANGSGKSSLLEAF---FTGL---Fgsrtlskeyvladmirkgaskas 71 
                                       ******************************************9...3322...122334456999877776666666 PP

                            AAA_15  55 ....................................................kkvikiekedleifeni.seskdik 78 
                                                                                           +k ++ ++e ++++ +i + ++di 
  gi|298676002|ref|YP_003727752.1|  72 iyleleqngneyiieqgfrydtkndraynsksvfksngnivvdqatqtydavCKLLNMDEEAYRNCVYIrQGEIDIL 148
                                       66666666666666666666666666665555555555555555555555554455555555554444312334444 PP

                            AAA_15  79 Idvef.......aekekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkkskkelp 148
                                       I+ +        +  +  ++   +++++++  a++ +k+  +d +++ik+ + +++       ki++e+  ++ +  
  gi|298676002|ref|YP_003727752.1| 149 INATPkerqnmiD--DLLQIGKLEHYRERASNAKKGVKRHLRDVDNRIKNTESEIE-------KIKNENPYENLNKL 216
                                       4444432222110..11111122222222222233333333333333333333333.......22222222333333 PP

                            AAA_15 149 kekeeklekekeelkidkedlkklikkleeslkkeeelknvlksaiiklllisakRnvsd..edsekkssllgklke 223
                                        ek+++ +++++el  +k+++k+ i++l++s++ ++             +l ++k+++++  +d + k++ + k +e
  gi|298676002|ref|YP_003727752.1| 217 REKSKNIQSKIDELNQKKDSAKSKIDELNNSITTYS-------------ELEEKKKSINEeiQDFNTKKTQMYKDIE 280
                                       333333344444444445555555554544554444.............7777777777766666677777777777 PP

                            AAA_15 224 kileealqekl.....eeelteklkeiqeklkeidkklaee 259
                                       +i+ +++++++      +++ e  ++i+ ++++i+++++++
  gi|298676002|ref|YP_003727752.1| 281 DIKADISKKRQylkqlQDKNSELENQIDFNIDDIENTVNKK 321
                                       77777555555444444444444444444444444444444 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.76   7.6e+02      65     120 ..     151     206 ..     142     208 .. 0.67
   2 ?    3.1  18.0     0.061        60      22     115 ..     210     307 ..     187     309 .. 0.85
   3 ?    3.1  13.0     0.057        57      23     137 ..     350     455 ..     310     470 .. 0.51
   4 !    8.0  18.0    0.0018       1.8       5      88 ..     471     559 ..     469     562 .. 0.79
   5 !   24.6  21.8   1.6e-08   1.6e-05      28     205 ..     540     710 ..     536     719 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.76
                        MscS_porin  65 kkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqq 120
                                       ++ +e  + i++ l +  Le   + +s++   +++ l + ++++ ++++ +e++ +
  gi|298676002|ref|YP_003727752.1| 151 ATPKERQNMIDDLLQIGKLEHYRERASNAKKGVKRHLRDVDNRIKNTESEIEKIKN 206
                                       55555566666667777777777777777777777777777777777777777765 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.061
                        MscS_porin  22 LeqalnlLdkidkskkkaeelqkaiddaPkelrelqqeleal....qkkkeeaskeilaklsleeLeqrllqtssql 94 
                                       +e+  +l +k ++ ++k++el+++ d+a  +++el++++ ++    +kkk+ + + ++ +++ ++  + +++ +++ 
  gi|298676002|ref|YP_003727752.1| 210 YENLNKLREKSKNIQSKIDELNQKKDSAKSKIDELNNSITTYseleEKKKSINEEIQDFNTKKTQMYKDIEDIKADI 286
                                       666667889999*****************************988877777777777888999*************** PP

                        MscS_porin  95 qelqeqlaqlnsqlvelqtrp 115
                                       ++ ++ l+ql+++  el++++
  gi|298676002|ref|YP_003727752.1| 287 SKKRQYLKQLQDKNSELENQI 307
                                       *************99999986 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.057
                        MscS_porin  23 eqalnlLdk.idkskkkaeelqkaiddaPkelrelqqelealqkkkeeaskeilaklsleeLeqrllqtssqlqelq 98 
                                       +++l+ +dk i +s+k +++ ++++++ +ke+++ + + ++    ++++  +  +++sl   e +l++  + ++ l+
  gi|298676002|ref|YP_003727752.1| 350 NDTLKDIDKqITESNKNIQKKKESVESVQKEIENFEISMKEW---ENKKKTALENAISLGFTEDKLDNIDDTMELLN 423
                                       333333332134444444444444444444444444444444...33333333334455555555555555555555 PP

                        MscS_porin  99 eqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLn 137
                                        q+++l  + +elqt+++++ ++l e ++        L+
  gi|298676002|ref|YP_003727752.1| 424 DQQKDLHGRERELQTSISEVEKRLNEHKK-------LLE 455
                                       55555555555555555555555555554.......443 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.0018
                        MscS_porin   5 lekak.ldeaeqkallqdLeqalnlLdkidkskkk...aeelqkaiddaPkelrelqqelealqkkkeeaskei.la 76 
                                       +e+++ +de+++k l ++L ++ + L+  ++  kk   a+++ k+i+d+++e++ +q+++e+l+k+ e+ +++i  +
  gi|298676002|ref|YP_003727752.1| 471 IEESTsEDEKQKKSLEEQLSKTREDLKSVQERLKKvktARKYSKTINDSQNEIQIIQNKIESLKKQIEDYNNNIeEE 547
                                       566666789999999999*9999999888877765222789**********************77776666665146 PP

                        MscS_porin  77 klsleeLeqrll 88 
                                       k+ ++eLe+r +
  gi|298676002|ref|YP_003727752.1| 548 KTNINELENRKK 559
                                       788999999865 PP

  == domain 5  score: 24.6 bits;  conditional E-value: 1.6e-08
                        MscS_porin  28 lLdkidkskkkaeelqkaiddaPkelrelqqelealqkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaql 104
                                       + ++i++ k  ++el+ + ++   +++el++e+ +l++k+e+a ke+ + l + ++ + + + +++ ++ q++++ql
  gi|298676002|ref|YP_003727752.1| 540 YNNNIEEEKTNINELENRKKEVNGLIDELNKEILTLKQKEETAGKEHQKVLNSLDIVKNIRNNLNEYEKIQSDINQL 616
                                       5689************************************************************************* PP

                        MscS_porin 105 nsqlvelqtrperaqqqltearqrlqeirnrLnstaaagealsqaqrtalqaelaaleaqieeleqellsnnnrqeL 181
                                       + ++ + q+  + + +q+te r+rl+ei ++  +      ++   ++t+ q e+a  +  +e  ++ +   +++ e 
  gi|298676002|ref|YP_003727752.1| 617 EYKIKSNQDNASLLDSQITERRERLKEIKDKMGDV-----DIDGLRKTLKQYESAHQNITNEIDKLYQDKDSVLKEA 688
                                       ******************************77666.....************************************* PP

                        MscS_porin 182 lklqrdllklriqqleqelqaLqe 205
                                       ++l+ +    r+++l + lq L++
  gi|298676002|ref|YP_003727752.1| 689 GRLENEIN--RLNNLHKDLQYLEN 710
                                       *9998874..66777777777776 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   2.6e-07   0.00026       1      50 [.       3      51 ..       3      55 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.6e-07
                            AAA_29  1 LkrlqlvNWgtfdghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      Lkrl + N  +++  +++++ +g+ +++G++GsGKS+ll A+ + L +++
  gi|298676002|ref|YP_003727752.1|  3 LKRLYVENIRSYEYLDLSFN-NGVSVVSGANGSGKSSLLEAFFTGLFGSR 51
                                      56777777788888888898.779*****************998887765 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8  13.0   6.2e-07   0.00062      14     128 ..     170     281 ..     158     282 .. 0.80
   2 ?    5.6   6.0     0.015        15       2      44 ..     257     299 ..     253     305 .. 0.94
   3 ?   -0.1   7.2      0.91     9e+02      55     110 ..     275     330 ..     270     340 .. 0.54
   4 ?   -1.4  17.2       2.2   2.2e+03      10     105 ..     311     403 ..     301     425 .. 0.75
   5 ?    4.6   1.5     0.032        32      80     116 ..     415     451 ..     408     454 .. 0.83
   6 ?    4.9  22.7     0.027        26       5     110 ..     470     570 ..     466     580 .. 0.48
   7 !    7.7  11.2    0.0035       3.5      12      94 ..     511     593 ..     507     604 .. 0.77
   8 ?    4.1  10.4     0.045        45      20     106 ..     557     646 ..     552     650 .. 0.70
   9 ?    3.0   4.3       0.1     1e+02       5      90 ..     655     739 ..     652     744 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 6.2e-07
                        TPR_MLP1_2  14 keekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaelees 90 
                                       +   e+a ++ + +++ l+   ++ k+ +   e e +k+++  ++l++lre++++++++i el+++ +sak++++e 
  gi|298676002|ref|YP_003727752.1| 170 EHYRERASNAKKGVKRHLRDVDNRIKNTES--EIEKIKNENPYENLNKLREKSKNIQSKIDELNQKKDSAKSKIDEL 244
                                       333445555555555555555566666666..6677999999*********************************** PP

                        TPR_MLP1_2  91 eesweeqkeelekelselekriedlneqNklLhdQlEs 128
                                        +s+++  +ele++++++++ i+d n++ + +++ +E 
  gi|298676002|ref|YP_003727752.1| 245 NNSITT-YSELEEKKKSINEEIQDFNTKKTQMYKDIED 281
                                       ***976.5789*************99998888877775 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.015
                        TPR_MLP1_2   2 elksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqk 44 
                                       ++ks +eei++ +++k++  ++++ ++ d+ k+++++k+ q+k
  gi|298676002|ref|YP_003727752.1| 257 KKKSINEEIQDFNTKKTQMYKDIEDIKADISKKRQYLKQLQDK 299
                                       7999************************************997 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.91
                        TPR_MLP1_2  55 dvkelqalreelnelkaeiaelkaeaesakaeleeseesweeqkeelekelselek 110
                                         k+++++++++++ ++ +++l++++ +++++++ +   +e++ ++ e+e + +++
  gi|298676002|ref|YP_003727752.1| 275 MYKDIEDIKADISKKRQYLKQLQDKNSELENQIDFNIDDIENTVNKKEEEERVARE 330
                                       44556666666666666666666666666666555555555555555554444444 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 2.2
                        TPR_MLP1_2  10 ikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakae 86 
                                       i+++++  ++ e++++ ++e+l++ ++  ++a +  e+el ++++++k++ +  +e+n+  ++ +e  +++++  ++
  gi|298676002|ref|YP_003727752.1| 311 IDDIENTVNKKEEEERVARENLNTVSS--NRAIK--ENELKLKNDTLKDIDKQITESNKNIQKKKESVESVQKEIEN 383
                                       556666677777777777777776654..44444..77*************************************** PP

                        TPR_MLP1_2  87 leeseesweeqkee.lekel 105
                                       +e s ++we++k++ le+ +
  gi|298676002|ref|YP_003727752.1| 384 FEISMKEWENKKKTaLENAI 403
                                       *********98875155544 PP

  == domain 5  score: 4.6 bits;  conditional E-value: 0.032
                        TPR_MLP1_2  80 aesakaeleeseesweeqkeelekelselekriedln 116
                                        +++ + l+ +++ ++ ++ el++ +se+ekr+++ +
  gi|298676002|ref|YP_003727752.1| 415 IDDTMELLNDQQKDLHGRERELQTSISEVEKRLNEHK 451
                                       5667788899999999999999999999999998865 PP

  == domain 6  score: 4.9 bits;  conditional E-value: 0.027
                        TPR_MLP1_2   5 sleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeae 81 
                                       s ee  ++ +++k+++e++l+k +edl++ +e++k+ +           + +k++++  +e++ ++++i++lk++ e
  gi|298676002|ref|YP_003727752.1| 470 SIEESTSEDEKQKKSLEEQLSKTREDLKSVQERLKKVKT--------ARKYSKTINDSQNEIQIIQNKIESLKKQIE 538
                                       455555666666666666666666666666666666554........333344444444455555555555555555 PP

                        TPR_MLP1_2  82 sakaeleeseesw...eeqkeelekelselek 110
                                       + ++++ee++ ++   e++k+e    ++el+k
  gi|298676002|ref|YP_003727752.1| 539 DYNNNIEEEKTNInelENRKKEVNGLIDELNK 570
                                       55555544443330003334444444444444 PP

  == domain 7  score: 7.7 bits;  conditional E-value: 0.0035
                        TPR_MLP1_2  12 slkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaele 88 
                                       ++++ ++++++++q +q+++e+ +++ ++ +++ e+e ++ +e  +  ++++  ++el++ei +lk++ e+a +e++
  gi|298676002|ref|YP_003727752.1| 511 KYSKTINDSQNEIQIIQNKIESLKKQIEDYNNNIEEEKTNINELENRKKEVNGLIDELNKEILTLKQKEETAGKEHQ 587
                                       56677788888888888888888888888888888887777777777777777778999999999999999988888 PP

                        TPR_MLP1_2  89 eseesw 94 
                                       +  +s+
  gi|298676002|ref|YP_003727752.1| 588 KVLNSL 593
                                       776665 PP

  == domain 8  score: 4.1 bits;  conditional E-value: 0.045
                        TPR_MLP1_2  20 aeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalr...eelnelkaeiaelkaeaesakaeleesees 93 
                                        +++++ l ++l+k+   +k+ ++   +e +k  + ++ ++++r   +e+++++++i++l+ + +s + + +   ++
  gi|298676002|ref|YP_003727752.1| 557 RKKEVNGLIDELNKEILTLKQKEETAGKEHQKVLNSLDIVKNIRnnlNEYEKIQSDINQLEYKIKSNQDNASLLDSQ 633
                                       44555555566666666666666666666666555555555555111566999************************ PP

                        TPR_MLP1_2  94 weeqkeelekels 106
                                       ++e++e+l++ ++
  gi|298676002|ref|YP_003727752.1| 634 ITERRERLKEIKD 646
                                       ********98665 PP

  == domain 9  score: 3.0 bits;  conditional E-value: 0.1
                        TPR_MLP1_2   5 sleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeae 81 
                                        l++++k++++  ++ ++++ kl +d  +  ++a + ++   r  ++h +d++ l++ ++ ln++ ++ ++l++   
  gi|298676002|ref|YP_003727752.1| 655 GLRKTLKQYESAHQNITNEIDKLYQDKDSVLKEAGRLENEINRLNNLH-KDLQYLENKKNYLNSVYEDSESLENMYM 730
                                       577788888888888888888888888888888888888877766666.4678888888888888888888888888 PP

                        TPR_MLP1_2  82 sakaelees 90 
                                       + +a+l e+
  gi|298676002|ref|YP_003727752.1| 731 RIRANLREK 739
                                       888887776 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7  17.0   8.7e-05     0.087     157     253 ..     168     268 ..     148     277 .. 0.86
   2 ?    3.0  10.2     0.038        37     205     261 ..     276     332 ..     271     349 .. 0.86
   3 !    6.9  18.5    0.0024       2.4     153     261 ..     348     458 ..     338     464 .. 0.79
   4 !   10.0  27.6   0.00028      0.28     152     272 ..     472     593 ..     461     602 .. 0.66
   5 ?    0.5  12.6      0.23   2.3e+02     179     282 ..     568     667 ..     567     668 .. 0.55
   6 !    9.0   7.0   0.00059      0.59     150     235 ..     655     742 ..     650     755 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.7e-05
                              Spc7 157 lLekqeeeldellpeleeekaeleeeleklqeaaeelesid.keeLeelreelaelkaeieekkkelaelqeqleel 232
                                       +Le+ +e ++++++ ++++  ++ +++++ +++ e++++ +  e+L++lre+ ++++++i+e++++ ++ +++++el
  gi|298676002|ref|YP_003727752.1| 168 KLEHYRERASNAKKGVKRHLRDVDNRIKNTESEIEKIKNENpYENLNKLREKSKNIQSKIDELNQKKDSAKSKIDEL 244
                                       588899999999***************************997899****************************9999 PP

                              Spc7 233 eeki...eelkeqkseleeeiaea 253
                                       +++i   +el+e+k++++eei+  
  gi|298676002|ref|YP_003727752.1| 245 NNSIttySELEEKKKSINEEIQDF 268
                                       998822246788899999998864 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.038
                              Spc7 205 reelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeck 261
                                        ++++++ka+i++k++ l++lq++  ele++i+   + ++++ ++ +e+erv +e+ 
  gi|298676002|ref|YP_003727752.1| 276 YKDIEDIKADISKKRQYLKQLQDKNSELENQIDFNIDDIENTVNKKEEEERVARENL 332
                                       5789999**************************999999999999999999998864 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0024
                              Spc7 153 edkelLekqeeeldellpeleeeka...eleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelq 226
                                         +++L++  ++++e  ++++++k+   ++++e+e+ +   +e e+ +k+ Le++  +l   + ++++  + ++ l+
  gi|298676002|ref|YP_003727752.1| 348 LKNDTLKDIDKQITESNKNIQKKKEsveSVQKEIENFEISMKEWENKKKTALENA-ISLGFTEDKLDNIDDTMELLN 423
                                       4445555566666665555555555333788888888889999999999999998.679999999999999999999 PP

                              Spc7 227 eqleeleekieelkeqkseleeeiaeaervleeck 261
                                       +q ++l  +  el++++se+e++++e++++le+ k
  gi|298676002|ref|YP_003727752.1| 424 DQQKDLHGRERELQTSISEVEKRLNEHKKLLEKGK 458
                                       99999999999******************999877 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.00028
                              Spc7 152 eedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesid..keeLeelreelaelkaeieekkkelaelq 226
                                       ee  ++ ekq++ l+e l +++e  ++++e+l+k ++a++  ++i+  ++e++ +++++++lk++ie  +++++e +
  gi|298676002|ref|YP_003727752.1| 472 EESTSEDEKQKKSLEEQLSKTREDLKSVQERLKKVKTARKYSKTINdsQNEIQIIQNKIESLKKQIEDYNNNIEEEK 548
                                       44444446677777777777777777777777777776665555444577788888888888888888888888888 PP

                              Spc7 227 eqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlk 272
                                       ++++ele++ +e++  ++el++ei   ++ +ee+ g +++ v +  
  gi|298676002|ref|YP_003727752.1| 549 TNINELENRKKEVNGLIDELNKEILTLKQ-KEETAGKEHQKVLNSL 593
                                       88888888888888888888888775544.4555555555555555 PP

  == domain 5  score: 0.5 bits;  conditional E-value: 0.23
                              Spc7 179 leeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiae.ae 254
                                       l++e+ +l++++e   +  ++ L++l   ++    +i++  +e+++ q+++++le ki++ +++ s l ++i e  e
  gi|298676002|ref|YP_003727752.1| 568 LNKEILTLKQKEETAGKEHQKVLNSLD-IVK----NIRNNLNEYEKIQSDINQLEYKIKSNQDNASLLDSQITErRE 639
                                       666777777766655555566666553.222....233333355666666666666666666666666666654134 PP

                              Spc7 255 rvleeckgwsesevsrlkeevkaleelt 282
                                       r++e + ++ + +++ l++++k+ e+ +
  gi|298676002|ref|YP_003727752.1| 640 RLKEIKDKMGDVDIDGLRKTLKQYESAH 667
                                       5556666677777777777777777665 PP

  == domain 6  score: 9.0 bits;  conditional E-value: 0.00059
                              Spc7 150 gleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles..idkeeLeelreelaelkaeieekkkelae 224
                                       gl++  ++ e+  +++++  ++l + k+++ +e+ +l+++ + l++   d ++Le+ ++ l+++ ++ e++++++ +
  gi|298676002|ref|YP_003727752.1| 655 GLRKTLKQYESAHQNITNEIDKLYQDKDSVLKEAGRLENEINRLNNlhKDLQYLENKKNYLNSVYEDSESLENMYMR 731
                                       44555555555555555556666666667777777777777777773346889**********************99 PP

                              Spc7 225 lqeqleeleek 235
                                        +++l e++ k
  gi|298676002|ref|YP_003727752.1| 732 IRANLREKNIK 742
                                       99999998866 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.2       0.2     2e+02      20      35 ..      27      42 ..      17      52 .. 0.85
   2 !    9.8  28.5   0.00027      0.27     287     454 ..     144     308 ..     132     323 .. 0.77
   3 !    8.4  20.8   0.00072      0.72     341     459 ..     325     453 ..     308     458 .. 0.67
   4 !   14.9  34.2   7.9e-06    0.0079     255     457 ..     456     645 ..     450     652 .. 0.62
   5 ?    3.0   5.4     0.032        32      97     193 ..     652     744 ..     647     760 .. 0.77
   6 ?   -0.2   0.0      0.29   2.9e+02     487     579 ..     773     870 ..     760     886 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.2
                            AAA_13 20 liYGwNGaGKTtLSrl 35
                                      ++ G+NG+GK++L ++
  gi|298676002|ref|YP_003727752.1| 27 VVSGANGSGKSSLLEA 42
                                      567*********9665 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00027
                            AAA_13 287 rLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqralea.Krkepfksvelesvka 362
                                       +++ li+   ++++++++ l ++ + ++ ++++ ++k+ +k++++ +++++k+ ++++e+ K ++p +  +l+++ +
  gi|298676002|ref|YP_003727752.1| 144 EIDILINATPKERQNMIDDLLQIGKLEHYRERASNAKKGVKRHLRDVDNRIKNTESEIEKiKNENPYE--NLNKLRE 218
                                       56667777888888999999999999999999999999999999999999999999997545566666..7778888 PP

                            AAA_13 363 kiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaieklekelkeeeael 439
                                       k+++i+++++e+n+   +   k+++l+++ ++  +  e+   +++++e++ +++k+ ++ k+ie+ +++++++ + l
  gi|298676002|ref|YP_003727752.1| 219 KSKNIQSKIDELNQKKDSAKSKIDELNNSITTYSELEEK--KKSINEEIQDFNTKKTQMYKDIEDIKADISKKRQYL 293
                                       888777777777776666666666665555554433333..578999****************************** PP

                            AAA_13 440 kkleeeikeLekqlr 454
                                       k+l+++ +eLe+q+ 
  gi|298676002|ref|YP_003727752.1| 294 KQLQDKNSELENQID 308
                                       ************985 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.00072
                            AAA_13 341 qraleaKrkepfksvelesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlv..........eel 407
                                       +r+  +  + ++++  +++ + k++  ++ +++i ++i++ N+ +++ +e++e+++k++e +++            l
  gi|298676002|ref|YP_003727752.1| 325 ERVARENLNTVSSNRAIKENELKLK--NDTLKDIDKQITESNKNIQKKKESVESVQKEIENFEIsmkewenkkkTAL 399
                                       4444555555666666666666666..77888888888888888888888888888888888885555554444222 PP

                            AAA_13 408 eseld..eykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpa 459
                                       e++++    ++k++++++++e l++++k+   + ++l+  i+e ek+l+++k+ 
  gi|298676002|ref|YP_003727752.1| 400 ENAISlgFTEDKLDNIDDTMELLNDQQKDLHGRERELQTSISEVEKRLNEHKKL 453
                                       222222134588888888888888888888888888888888888888888875 PP

  == domain 4  score: 14.9 bits;  conditional E-value: 7.9e-06
                            AAA_13 255 sdtCpFCgqplpaerkaaLeahFddefeekqerLekliekveskkselleklkavsdeasensafeedkeelkaeae 331
                                       +++Cp Cgq l+++ +++ ++    e e+++++Le+ ++k  ++ ++++e+lk+v ++     ++ + +++ ++e++
  gi|298676002|ref|YP_003727752.1| 456 KGKCPTCGQDLKNSSIEESTS----EDEKQKKSLEEQLSKTREDLKSVQERLKKVKTAR----KYSKTINDSQNEIQ 524
                                       478999999999987775433....2356678999999999999999999998887743....34577888888888 PP

                            AAA_13 332 aleeqLkglqraleaKrkepfksvelesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlv.... 404
                                        +++++++l++++e+  +++      e+ k +i+++++  +e+n li + N+ +  l++++e+a k+ ++ l     
  gi|298676002|ref|YP_003727752.1| 525 IIQNKIESLKKQIEDYNNNI------EEEKTNINELENRKKEVNGLIDELNKEILTLKQKEETAGKEHQKVLNsldi 595
                                       88888888888877766544......445666666666677777777777777777777777766665543322111 PP

                            AAA_13 405 .eeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdek 457
                                        ++++++l+ey+    k++ +i++le ++k +++++  l+ +i e +++l+++k
  gi|298676002|ref|YP_003727752.1| 596 vKNIRNNLNEYE----KIQSDINQLEYKIKSNQDNASLLDSQITERRERLKEIK 645
                                       166666655544....55555555555555555555555555555555555444 PP

  == domain 5  score: 3.0 bits;  conditional E-value: 0.032
                            AAA_13  97 kieklkkeikkleekleaaeaqlqkaekekkklekeledeawkkivkkknsalsealkglkyeekfkerllkelkkk 173
                                        i+ l+k +k+ e+  ++ +++++k++++k+   ke+ +   ++i  +  ++l+++l++l++++++ + + ++ ++ 
  gi|298676002|ref|YP_003727752.1| 652 DIDGLRKTLKQYESAHQNITNEIDKLYQDKDSVLKEAGRLE-NEI--NRLNNLHKDLQYLENKKNYLNSVYEDSESL 725
                                       58888999999999899999999999998887777655444.335..357889999999999999999999988887 PP

                            AAA_13 174 nrkaaellsdeelkakletv 193
                                        ++   + + + ++++++++
  gi|298676002|ref|YP_003727752.1| 726 -ENMYMRIRANLREKNIKAL 744
                                       .5777777777777776665 PP

  == domain 6  score: -0.2 bits;  conditional E-value: 0.29
                            AAA_13 487 rivrkggsqaa.etLSeGEktaIaf...lYFlkslk...eddseigkdkivviDDPvSSLDsnslfivfsliksrll 556
                                       +i  k+g   + + LS GE+ +  +   +  + +l+   +++s  ++    ++D P   LD +++   + li+    
  gi|298676002|ref|YP_003727752.1| 773 TIYEKDGTPLDpKLLSGGERAIFNLvlrCAIYRLLSygvSNSSSSSELPPLILDEPTVFLDRGHIHQLIKLIDMMR- 848
                                       55555555555455666666554442122334444444544444456667899*******************9874. PP

                            AAA_13 557 kkkkakQlfiLTHnleffkevkk 579
                                        ++ + Q++i  H  ++   +++
  gi|298676002|ref|YP_003727752.1| 849 -DSGVGQILIVSHDESLIDSADY 870
                                       .9***********9887766665 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   2.2e-06    0.0021       1      57 [.       1      54 [.       1      63 [. 0.86
   2 ?   -0.6   0.6      0.81   8.1e+02     155     193 ..     213     251 ..     186     268 .. 0.74
   3 ?   -1.6   0.1       1.7   1.7e+03     157     194 ..     260     297 ..     241     306 .. 0.50
   4 ?   -0.3   1.3      0.69   6.9e+02     159     207 .]     342     391 ..     321     391 .. 0.69
   5 ?    0.4   0.1       0.4     4e+02     157     199 ..     414     456 ..     408     461 .. 0.87
   6 ?   -1.2   0.7       1.2   1.2e+03     159     197 ..     490     530 ..     471     546 .. 0.51
   7 ?    0.0   0.1      0.54   5.4e+02     148     193 ..     660     705 ..     628     716 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.2e-06
                            AAA_27  1 MrlerLdLeryGkftdrsldfsaeeadlhliyGpNEAGKstalrAisdllfGipert 57
                                      M+l+rL +e   +++   l+f+   +++ ++ G+N +GKs++l+A+   lfG  + +
  gi|298676002|ref|YP_003727752.1|  1 MKLKRLYVENIRSYEYLDLSFN---NGVSVVSGANGSGKSSLLEAFFTGLFGSRTLS 54
                                      8888888888888888888887...8*************************987655 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.81
                            AAA_27 155 laslrevleaLeaeadelfkprkskkrainealeeleea 193
                                       l++lre  ++++++ del +++ s+k +i e ++++++ 
  gi|298676002|ref|YP_003727752.1| 213 LNKLREKSKNIQSKIDELNQKKDSAKSKIDELNNSITTY 251
                                       567888888999999999988888886655555444333 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.7
                            AAA_27 157 slrevleaLeaeadelfkprkskkrainealeeleeak 194
                                       s++e ++++++++++++k+ +  k+ i ++++ l++++
  gi|298676002|ref|YP_003727752.1| 260 SINEEIQDFNTKKTQMYKDIEDIKADISKKRQYLKQLQ 297
                                       33344444444444444444444444444444444433 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.69
                            AAA_27 159 revleaLeaea.delfkprkskkrainealeeleeakkelreaqvraeew 207
                                       +e   +L+++  +++ k+ ++++++i++++e++e+++ke+++ +++ +ew
  gi|298676002|ref|YP_003727752.1| 342 KENELKLKNDTlKDIDKQITESNKNIQKKKESVESVQKEIENFEISMKEW 391
                                       5555555554413344444555589999999**********999999998 PP

  == domain 5  score: 0.4 bits;  conditional E-value: 0.4
                            AAA_27 157 slrevleaLeaeadelfkprkskkrainealeeleeakkelre 199
                                       ++ +++e L++++++l+ ++++ +++i e +++l+e kk l++
  gi|298676002|ref|YP_003727752.1| 414 NIDDTMELLNDQQKDLHGRERELQTSISEVEKRLNEHKKLLEK 456
                                       677889999*************999**********99987765 PP

  == domain 6  score: -1.2 bits;  conditional E-value: 1.2
                            AAA_27 159 revleaLeaeadelfkprkskk..rainealeeleeakkel 197
                                       ++++e+L++ +++l k ++++k  ++in++++e++  ++++
  gi|298676002|ref|YP_003727752.1| 490 SKTREDLKSVQERLKKVKTARKysKTINDSQNEIQIIQNKI 530
                                       33333333333333222222211234555544444444444 PP

  == domain 7  score: 0.0 bits;  conditional E-value: 0.54
                            AAA_27 148 LfeasaGlaslrevleaLeaeadelfkprkskkrainealeeleea 193
                                       L + +++ +++++ +++L +++d++ k+ ++ +++in+ ++ ++++
  gi|298676002|ref|YP_003727752.1| 660 LKQYESAHQNITNEIDKLYQDKDSVLKEAGRLENEINRLNNLHKDL 705
                                       4445556666666666666666666666666666665555544444 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.3e-05     0.043      32      89 ..     786     845 ..     765     846 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.3e-05
                           SbcCD_C  32 tlSGGekqflaylalaaalaalyssae..g.repalrlvfLDEAFsklDeesiatllelle 89 
                                        lSGGe+  ++ l+l  a+  l+s     + +++ l +++LDE    lD   i++l++l++
  gi|298676002|ref|YP_003727752.1| 786 LLSGGER-AIFNLVLRCAIYRLLSYGVsnSsSSSELPPLILDEPTVFLDRGHIHQLIKLID 845
                                       58*****.************998764321346777**********************9975 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00012      0.12      28      51 ..      27      50 ..      16     104 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00012
                            AAA_16 28 llsGesGvGKsslvrellralekd 51
                                      ++sG+ G+GKssl++++++ l ++
  gi|298676002|ref|YP_003727752.1| 27 VVSGANGSGKSSLLEAFFTGLFGS 50
                                      79****************865554 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   6.3   0.00037      0.37      36     121 ..     156     245 ..     148     248 .. 0.85
   2 ?    6.9   6.4     0.006         6      54     110 ..     251     307 ..     242     324 .. 0.60
   3 ?    7.5   4.9    0.0041       4.1      74     123 ..     345     394 ..     339     395 .. 0.90
   4 ?    3.2   0.8     0.087        86      49      82 ..     421     454 ..     408     459 .. 0.66
   5 ?    1.3   5.5      0.32   3.2e+02      38     108 ..     435     508 ..     434     511 .. 0.65
   6 ?    3.3  14.7     0.079        79      36     117 ..     482     572 ..     468     579 .. 0.54
   7 ?    5.2   4.4      0.02        20      49     119 ..     553     622 ..     550     627 .. 0.62
   8 ?    6.1   3.7     0.011        11      61     107 ..     606     652 ..     579     664 .. 0.81
   9 ?    9.3   3.9    0.0011       1.1      40     116 ..     624     701 ..     621     712 .. 0.86
  10 ?    5.5   0.8     0.017        17      36     103 ..     660     729 ..     654     751 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00037
                           DUF1664  36 krslsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikee.....vtevredlseigedvesvk 107
                                       ++++ d + +++k le+  e  +++k+  ++++  vd+++++++  +++ik+e     ++++re+ ++i++++++++
  gi|298676002|ref|YP_003727752.1| 156 RQNMIDDLLQIGK-LEHYRERASNAKKGVKRHLRDVDNRIKNTESEIEKIKNEnpyenLNKLREKSKNIQSKIDELN 231
                                       6788888888886.9*************************9999999999865344449999999999999999999 PP

                           DUF1664 108 eaveglesklerie 121
                                       +   + +sk+++++
  gi|298676002|ref|YP_003727752.1| 232 QKKDSAKSKIDELN 245
                                       99999999999886 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.006
                           DUF1664  54 seslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeav 110
                                       +++l++ k+ ++++i+  ++k  ++ + +++ik+++++ r+ l++++++ +++++ +
  gi|298676002|ref|YP_003727752.1| 251 YSELEEKKKSINEEIQDFNTKKTQMYKDIEDIKADISKKRQYLKQLQDKNSELENQI 307
                                       455666666666666666666666666666666666666666666666655555433 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0041
                           DUF1664  74 kldeqkeiskeikeevtevredlseigedvesvkeaveglesklerieek 123
                                       +l+  +++ k+i++++te ++++++ +e vesv++ +e++e ++++ e+k
  gi|298676002|ref|YP_003727752.1| 345 ELKLKNDTLKDIDKQITESNKNIQKKKESVESVQKEIENFEISMKEWENK 394
                                       5666788999**********************************999887 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.087
                           DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkeis 82 
                                        l++ +++l+   r+L+  i +v+k+l+e k++ 
  gi|298676002|ref|YP_003727752.1| 421 LLNDQQKDLHGRERELQTSISEVEKRLNEHKKLL 454
                                       3455567777788888888888888888877765 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.32
                           DUF1664  38 slsdavesvskqleqvseslaatkr.hLssridr..vdkkldeqkeiskeikeevtevredlseigedvesvke 108
                                        l+  +++v k+l++ ++ l++ k     +++++  ++++  e ++ +k+++e++++ redl++++e +++vk+
  gi|298676002|ref|YP_003727752.1| 435 ELQTSISEVEKRLNEHKKLLEKGKCpTCGQDLKNssIEESTSEDEKQKKSLEEQLSKTREDLKSVQERLKKVKT 508
                                       56666677777777777777666642344555432266777777777888888888888888888888888775 PP

  == domain 6  score: 3.3 bits;  conditional E-value: 0.079
                           DUF1664  36 krslsdavesvskqleqvseslaatk..rhLss.......ridrvdkkldeqkeiskeikeevtevredlseigedv 103
                                       k+sl++ +++  ++l++v+e l+++k  r+ s+       +i+ +++k+++ k+ +++ +++++e + +++e+++  
  gi|298676002|ref|YP_003727752.1| 482 KKSLEEQLSKTREDLKSVQERLKKVKtaRKYSKtindsqnEIQIIQNKIESLKKQIEDYNNNIEEEKTNINELENRK 558
                                       56666666666666666666666555333444400000004455555555555555555555555555555555555 PP

                           DUF1664 104 esvkeavegleskl 117
                                       ++v+ ++ +l++++
  gi|298676002|ref|YP_003727752.1| 559 KEVNGLIDELNKEI 572
                                       55555555555555 PP

  == domain 7  score: 5.2 bits;  conditional E-value: 0.02
                           DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskler 119
                                       +le+ +++++   ++L+++i ++ +k +   +  +++ + ++ v +++++  ++ e++++ +++le k+++
  gi|298676002|ref|YP_003727752.1| 553 ELENRKKEVNGLIDELNKEILTLKQKEETAGKEHQKVLNSLDIV-KNIRNNLNEYEKIQSDINQLEYKIKS 622
                                       45555555555556666666666666555555555555555444.3455555678899999*****99987 PP

  == domain 8  score: 6.1 bits;  conditional E-value: 0.011
                           DUF1664  61 krhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvk 107
                                        ++++s+i++++ k++++++ ++ +++++te re l+ei++++  v+
  gi|298676002|ref|YP_003727752.1| 606 YEKIQSDINQLEYKIKSNQDNASLLDSQITERRERLKEIKDKMGDVD 652
                                       467899***********************************999875 PP

  == domain 9  score: 9.3 bits;  conditional E-value: 0.0011
                           DUF1664  40 sdavesvskqleqvseslaatkrhLss.ridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegles 115
                                       +d  + + +q+++  e l++ k+++ + +id + k+l++ + + ++i++e++++ +d +++ ++   +++ ++ l++
  gi|298676002|ref|YP_003727752.1| 624 QDNASLLDSQITERRERLKEIKDKMGDvDIDGLRKTLKQYESAHQNITNEIDKLYQDKDSVLKEAGRLENEINRLNN 700
                                       5667778899***************8648***************************************999988775 PP

                           DUF1664 116 k 116
                                        
  gi|298676002|ref|YP_003727752.1| 701 L 701
                                       4 PP

  == domain 10  score: 5.5 bits;  conditional E-value: 0.017
                           DUF1664  36 krslsdavesvskqleqvs...eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedv 103
                                        +  ++a +++++++++++   +s+ +   +L+++i+r+++ l +  +  ++ k+ +++v ed +++++  
  gi|298676002|ref|YP_003727752.1| 660 LKQYESAHQNITNEIDKLYqdkDSVLKEAGRLENEINRLNN-LHKDLQYLENKKNYLNSVYEDSESLENMY 729
                                       45556777777777777775555666666777777777754.44444444444555555555544444443 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   7.0     0.059        59     199     275 ..     168     245 ..     163     252 .. 0.60
   2 ?    8.5  11.3    0.0014       1.4     197     279 ..     251     333 ..     248     340 .. 0.90
   3 ?   11.4   8.4   0.00018      0.18     203     280 ..     345     421 ..     336     425 .. 0.86
   4 ?    3.7   1.8     0.039        39     243     290 ..     409     455 ..     405     457 .. 0.85
   5 ?    9.2  19.8   0.00084      0.84     175     290 ..     482     591 ..     473     595 .. 0.63
   6 ?    8.0  10.0    0.0019       1.9     202     301 ..     597     697 ..     592     703 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.059
                                       XXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 199 elqeaaeknsealrsakeeitelrrqiqsleieleslkkqka.sleaqlaeleerleaeleklqeklseleeelaei 274
                                       +l++  e+ s+a + +k+ + ++  +i++ e+e+e++k+++     ++l+e  +++++++++l++k ++  +++ e+
  gi|298676002|ref|YP_003727752.1| 168 KLEHYRERASNAKKGVKRHLRDVDNRIKNTESEIEKIKNENPyENLNKLREKSKNIQSKIDELNQKKDSAKSKIDEL 244
                                       55555566666666667777777777777777777777766413346666666666666666666666655555554 PP

                                       H CS
                          Filament 275 r 275
                                        
  gi|298676002|ref|YP_003727752.1| 245 N 245
                                       4 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0014
                                       XXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 197 leelqeaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerleaeleklqeklseleeelae 273
                                       ++el+e+ ++ +e+++  ++  t++ + i+  ++++++ ++  ++l+++ +ele++++ ++++++++++++eee + 
  gi|298676002|ref|YP_003727752.1| 251 YSELEEKKKSINEEIQDFNTKKTQMYKDIEDIKADISKKRQYLKQLQDKNSELENQIDFNIDDIENTVNKKEEEERV 327
                                       678899999999999999999999999*********************************************99999 PP

                                       HHHHHH CS
                          Filament 274 ireema 279
                                       +re+++
  gi|298676002|ref|YP_003727752.1| 328 ARENLN 333
                                       999876 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00018
                                       XXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 203 aaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerleaeleklqeklseleeelaeireema 279
                                       + + ++++l+   ++ite++++iq+++  +es++k+ ++ e +++e e++ +++le++ + l   e++l +i ++m+
  gi|298676002|ref|YP_003727752.1| 345 ELKLKNDTLKDIDKQITESNKNIQKKKESVESVQKEIENFEISMKEWENKKKTALENAIS-LGFTEDKLDNIDDTME 420
                                       56678999***********************************************99854.6677777777777777 PP

                                       H CS
                          Filament 280 r 280
                                        
  gi|298676002|ref|YP_003727752.1| 421 L 421
                                       5 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.039
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 243 eaqlaeleerleaeleklqeklseleeelaeireemarqlreYqeLLd 290
                                       e++l ++++++e  l++ q+ l+  e+el++  +e++++l+e ++LL+
  gi|298676002|ref|YP_003727752.1| 409 EDKLDNIDDTMEL-LNDQQKDLHGRERELQTSISEVEKRLNEHKKLLE 455
                                       6777777777765.6788999999*********************996 PP

  == domain 5  score: 9.2 bits;  conditional E-value: 0.00084
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 175 raqyeelaeknreeaeewykskleelqeaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaelee 251
                                       ++  ee+ +k re+++++ +++l++++ +a+k s++++ +++ei+ ++ +i+sl+ ++e++ ++ +  +++++ele+
  gi|298676002|ref|YP_003727752.1| 482 KKSLEEQLSKTREDLKSV-QERLKKVK-TARKYSKTINDSQNEIQIIQNKIESLKKQIEDYNNNIEEEKTNINELEN 556
                                       334455555555555443.44454443.2344555555555555555555555555555555555555555555555 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 252 rleaeleklqeklseleeelaeireemarqlreYqeLLd 290
                                       r     ++++  ++el++e+ +++++ +   +e q+ L+
  gi|298676002|ref|YP_003727752.1| 557 R----KKEVNGLIDELNKEILTLKQKEETAGKEHQKVLN 591
                                       4....578999*************************998 PP

  == domain 6  score: 8.0 bits;  conditional E-value: 0.0019
                                       XXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 202 eaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerl.eaeleklqeklseleeelaeiree 277
                                       +++++n ++ ++ +++i++l  +i+s + + + l +q    +++l+e+++++ + +++ l+++l++ e++ ++i +e
  gi|298676002|ref|YP_003727752.1| 597 KNIRNNLNEYEKIQSDINQLEYKIKSNQDNASLLDSQITERRERLKEIKDKMgDVDIDGLRKTLKQYESAHQNITNE 673
                                       56677888888999999999999999999999999999999999999987652789********************* PP

                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 278 marqlreYqeLLdvKlaLdiEIat 301
                                       +++  ++ ++ L    +L+ EI+ 
  gi|298676002|ref|YP_003727752.1| 674 IDKLYQDKDSVLKEAGRLENEINR 697
                                       **********************85 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00018      0.18      23      65 ..      20      62 ..       2      90 .. 0.72
   2 ?   -0.3   1.9       0.8   7.9e+02     135     158 ..     216     239 ..     167     284 .. 0.52
   3 ?    0.0   2.5      0.61   6.1e+02     104     160 ..     495     552 ..     479     571 .. 0.72
   4 ?   -1.2   0.1       1.4   1.4e+03     125     170 ..     620     666 ..     578     674 .. 0.61
   5 ?   -1.6   0.1       1.9   1.9e+03     124     173 ..     673     721 ..     665     757 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                                      -HHHHHHHHHS--SHHHHHHHHHHHHHHS--TTT--------- CS
                              MukB 23 dldelvttlsGgnGaGksttmaafvtaliPdlsllhfrnttea 65
                                       +++ v  +sG+nG+Gks  + af+t l    +l +   +++ 
  gi|298676002|ref|YP_003727752.1| 20 SFNNGVSVVSGANGSGKSSLLEAFFTGLFGSRTLSKEYVLADM 62
                                      5678899*********************999888765544444 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.8
                                       HEE--SSS--EE--HHHHHHHHHT CS
                              MukB 135 lleklddkkarvrelnelkeklee 158
                                       l ek ++ ++++ eln+ k+ +++
  gi|298676002|ref|YP_003727752.1| 216 LREKSKNIQSKIDELNQKKDSAKS 239
                                       334444444444444444444333 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.61
                                       EEEE-SSTTT-EEEEEEEEES--TT--HHHHHEE--SSS--EE--HHH.HHHHHHTST CS
                              MukB 104 rleqvagrdkkvdikpfalqgleedvkltdvlleklddkkarvrelne.lkekleele 160
                                        l+ v +r kkv+      + ++++++ ++++ +k++  k+++ + n+ + e+ ++++
  gi|298676002|ref|YP_003727752.1| 495 DLKSVQERLKKVKTARKYSKTINDSQNEIQIIQNKIESLKKQIEDYNNnIEEEKTNIN 552
                                       5788999999999998888999999999999999999988888776531333333333 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 1.4
                                       --TT--HHHHHEE--SSS--EE--HHHHHHHHHTSTT-E..EEE-S-H CS
                              MukB 125 leedvkltdvlleklddkkarvrelnelkekleelegvr..lkkfnsv 170
                                       +++++   ++l +++ ++++r++e+++    ++  +g+r  lk+++s+
  gi|298676002|ref|YP_003727752.1| 620 IKSNQDNASLLDSQITERRERLKEIKDKMGDVDI-DGLRktLKQYESA 666
                                       3444555566666777766666555554444332.4433226666665 PP

  == domain 5  score: -1.6 bits;  conditional E-value: 1.9
                                       S--TT--HHHHHEE--SSS--EE--HHHHHHHHHTSTT-EEEE-S-HHHH CS
                              MukB 124 gleedvkltdvlleklddkkarvrelnelkekleelegvrlkkfnsvtdy 173
                                       ++++  + +d +l++ +  ++++++ln+l++ l+ le+ + +  nsv + 
  gi|298676002|ref|YP_003727752.1| 673 EIDKLYQDKDSVLKEAGRLENEINRLNNLHKDLQYLEN-KKNYLNSVYED 721
                                       56677777888888899999999999999999998887.55666666655 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00048      0.48      26      63 ..      10      47 ..       4      52 .. 0.85
   2 ?   -1.6   0.6       1.4   1.4e+03     133     156 ..     289     314 ..     213     360 .. 0.60
   3 ?   -1.6   0.6       1.4   1.4e+03     129     175 ..     514     560 ..     484     568 .. 0.64
   4 ?   -3.1   0.3       4.1   4.1e+03     104     141 ..     625     666 ..     604     704 .. 0.47

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00048
                                      TTS-EEEEEGGGS-.SEEEE--TTSSHHHHHHHHHHHH CS
                      FtsK_SpoIIIE 26 isgnplvldlkkmashllvaGatgsGKStalntLilSl 63
                                       +++ ++ldl+ + +  +v Ga gsGKS  l ++ ++l
  gi|298676002|ref|YP_003727752.1| 10 NIRSYEYLDLSFNNGVSVVSGANGSGKSSLLEAFFTGL 47
                                      577888999999998899**************998776 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.4
                                       H..HHHHHHHHHHTT---B-TT-... CS
                      FtsK_SpoIIIE 133 a..ydgeiaedpldifgdvflvlDny 156
                                       +  y ++ ++++ ++++ +++ +D+ 
  gi|298676002|ref|YP_003727752.1| 289 KrqYLKQLQDKNSELENQIDFNIDDI 314
                                       12233334444444444444444444 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.4
                                       SSHHHHHHHHHHHHHTT---B-TT-...................... CS
                      FtsK_SpoIIIE 129 rsiaaydgeiaedpldifgdvflvlDnyddlaaeneritsLsnqgps 175
                                       ++i++ ++ei+  +++i+ +   + D  +++++e++ i++L n+  +
  gi|298676002|ref|YP_003727752.1| 514 KTINDSQNEIQIIQNKIESLKKQIEDYNNNIEEEKTNINELENRKKE 560
                                       33444566666666666666666667777777777789988888765 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 4.1
                                       HHHHHHHHHHHHHHHHH....HHHHHTT-SSHHHHHHHHHHH CS
                      FtsK_SpoIIIE 104 ralraleeLvkemeery....alfreagvrsiaaydgeiaed 141
                                       + +++l+  + e++er      ++ +  ++ +++  ++ +++
  gi|298676002|ref|YP_003727752.1| 625 DNASLLDSQITERRERLkeikDKMGDVDIDGLRKTLKQYESA 666
                                       445566666666666653222333333333333322222222 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5  23.3      0.01        10      15     149 ..     183     319 ..     181     326 .. 0.74
   2 ?    4.4  21.2     0.046        45      21     153 ..     267     397 ..     265     402 .. 0.75
   3 ?   12.6  21.8   0.00014      0.14      12     174 ..     530     686 ..     514     686 .. 0.83
   4 ?    5.6   8.8     0.019        19      31     146 ..     632     738 ..     621     753 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.01
                              Fez1  15 LKqQLkdsqaevtqklseivalkaql.relrakleekeeeikeleesleektlelevcenelqrkkseaellrekve 90 
                                       +K  L+d+ + + +  sei ++k++   e  +kl+ek ++i++  ++l++k+++ +   +el+++ ++ + l+ek +
  gi|298676002|ref|YP_003727752.1| 183 VKRHLRDVDNRIKNTESEIEKIKNENpYENLNKLREKSKNIQSKIDELNQKKDSAKSKIDELNNSITTYSELEEKKK 259
                                       6999*******************98736999********************************************** PP

                              Fez1  91 kleeelkelreelselsleeeeaalesdeakaq..rqeaeeleelkreverlraeLkeerq 149
                                       +++ee++++ ++ +++ ++ e+ +++ ++ k q  +q +++ +el+++++     +++  +
  gi|298676002|ref|YP_003727752.1| 260 SINEEIQDFNTKKTQMYKDIEDIKADISK-KRQylKQLQDKNSELENQIDFNIDDIENTVN 319
                                       *********99777766554444333333.2221122234444444444444444433333 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.046
                              Fez1  21 dsqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelk 97 
                                       d  +  tq  ++i  +ka++   r+ l++ +++++ele+++   + +++ +en +++k++e+ + re++++++++ +
  gi|298676002|ref|YP_003727752.1| 267 DFNTKKTQMYKDIEDIKADISKKRQYLKQLQDKNSELENQI---DFNIDDIENTVNKKEEEERVARENLNTVSSNRA 340
                                       777788999999999**********************9998...567888999***************999988755 PP

                              Fez1  98 elreelselsleeeeaalesde.akaqrqeaeeleelkreverlraeLkeerqkkee 153
                                          +el+ ++ + ++  ++ +e +k+ ++++e++e+ ++e+e+ + ++ke ++kk++
  gi|298676002|ref|YP_003727752.1| 341 IKENELKLKNDTLKDIDKQITEsNKNIQKKKESVESVQKEIENFEISMKEWENKKKT 397
                                       555555544433333333333303444555689999999999999999887776654 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.00014
                              Fez1  12 islLKqQLkdsqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrek 88 
                                       i  LK+Q+ d+ +++ +   +i +l ++ +e++  ++e ++ei +l+++ e+  +e +++ n l+  k+  ++l+e 
  gi|298676002|ref|YP_003727752.1| 530 IESLKKQIEDYNNNIEEEKTNINELENRKKEVNGLIDELNKEILTLKQKEETAGKEHQKVLNSLDIVKNIRNNLNE- 605
                                       6779*********************************************************************999. PP

                              Fez1  89 vekleeelkelreelselsleeeeaalesdeakaqrqeaeeleelkreverlraeLkeerqkkeeqassFeqERrtW 165
                                        ek+++++++l  ++++++ +++   ++ +e + +r ++ + +  + +++ lr+ Lk+ + ++    ++  +E  + 
  gi|298676002|ref|YP_003727752.1| 606 YEKIQSDINQLEYKIKSNQDNASLLDSQITE-RRERLKEIKDKMGDVDIDGLRKTLKQYESAH----QNITNEIDKL 677
                                       999********99999976665555566666.4445555677777788888888888766664....4557777778 PP

                              Fez1 166 qeeKekVir 174
                                        ++K+ V++
  gi|298676002|ref|YP_003727752.1| 678 YQDKDSVLK 686
                                       888888875 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.019
                              Fez1  31 seivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelsels 107
                                       s i + + +l+e++ k+ +    i+ l+++l++ +   +++ ne+++  ++++ + +++++le+e+++l +  ++l+
  gi|298676002|ref|YP_003727752.1| 632 SQITERRERLKEIKDKMGD--VDIDGLRKTLKQYESAHQNITNEIDKLYQDKDSVLKEAGRLENEINRLNNLHKDLQ 706
                                       5566667777777777764..45888888888888888999999999877777666668999999988887555544 PP

                              Fez1 108 leeeeaalesdeakaqrqeaeeleelkreverlraeLke 146
                                         e+++++        ++  e++e+l++   r+ra+L+e
  gi|298676002|ref|YP_003727752.1| 707 YLENKKNYL-------NSVYEDSESLENMYMRIRANLRE 738
                                       333332211.......11234444555555555555544 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.2     0.012        12       7      39 ..     214     246 ..     212     248 .. 0.90
   2 ?    2.0   0.3      0.25   2.5e+02       5      39 ..     250     284 ..     247     308 .. 0.79
   3 ?    1.8   0.2      0.29   2.9e+02      52      81 ..     359     388 ..     351     400 .. 0.61
   4 ?   -1.4   0.1       2.9   2.9e+03       9      36 ..     415     442 ..     409     451 .. 0.58
   5 ?    4.9   1.5      0.03        30      17      82 ..     479     545 ..     470     547 .. 0.88
   6 ?   -1.5   0.1       3.1   3.1e+03      18      38 ..     556     576 ..     548     617 .. 0.57
   7 ?    7.5   0.1    0.0047       4.7       4      37 ..     651     684 ..     649     689 .. 0.92
   8 ?   -0.6   0.0       1.6   1.6e+03      22      37 ..     690     705 ..     682     750 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGC CS
                            WXG100   7 eelrqaaarfqkqaeeledelqrlkaevdalqs 39 
                                       ++lr++++++q++ +el +  ++ k+++d+l++
  gi|298676002|ref|YP_003727752.1| 214 NKLREKSKNIQSKIDELNQKKDSAKSKIDELNN 246
                                       5799**************************965 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.25
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGC CS
                            WXG100   5 dpeelrqaaarfqkqaeeledelqrlkaevdalqs 39 
                                       +++el+++ ++++++ ++  +  ++++++++++++
  gi|298676002|ref|YP_003727752.1| 250 TYSELEEKKKSINEEIQDFNTKKTQMYKDIEDIKA 284
                                       77888888888888888888888888888887754 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.29
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  52 efeewkqaaqklvdaLeeisealkqaanaf 81 
                                       +++e ++++qk ++  e++++++++   ++
  gi|298676002|ref|YP_003727752.1| 359 QITESNKNIQKKKESVESVQKEIENFEISM 388
                                       445555555555555555555555555555 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 2.9
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100   9 lrqaaarfqkqaeeledelqrlkaevda 36 
                                       ++++   +++q+++l+++ ++l+ ++++
  gi|298676002|ref|YP_003727752.1| 415 IDDTMELLNDQQKDLHGRERELQTSISE 442
                                       4444444555555555555555555554 PP

  == domain 5  score: 4.9 bits;  conditional E-value: 0.03
                                       HHHHHHHHHHHHHHHHHHHHCGCGCT.HHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  17 qkqaeeledelqrlkaevdalqsgWs.GaaadafqaefeewkqaaqklvdaLeeisealkqaanafe 82 
                                        kq+++le++l++ + +++++q+  +  ++a ++ ++++  ++++q ++++ e++ ++++  +n+ e
  gi|298676002|ref|YP_003727752.1| 479 EKQKKSLEEQLSKTREDLKSVQERLKkVKTARKYSKTINDSQNEIQIIQNKIESLKKQIEDYNNNIE 545
                                       5789999999999999999999999977999999999999999999999999999999999888876 PP

  == domain 6  score: -1.5 bits;  conditional E-value: 3.1
                                       HHHHHHHHHHHHHHHHHHHCG CS
                            WXG100  18 kqaeeledelqrlkaevdalq 38 
                                       + ++e+ +++++l++e+  l+
  gi|298676002|ref|YP_003727752.1| 556 NRKKEVNGLIDELNKEILTLK 576
                                       444444444555544444442 PP

  == domain 7  score: 7.5 bits;  conditional E-value: 0.0047
                                       SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                            WXG100   4 vdpeelrqaaarfqkqaeeledelqrlkaevdal 37 
                                       vd + lr++ +++ ++++++++e+++l+++ d++
  gi|298676002|ref|YP_003727752.1| 651 VDIDGLRKTLKQYESAHQNITNEIDKLYQDKDSV 684
                                       89999************************99987 PP

  == domain 8  score: -0.6 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHHHHHHC CS
                            WXG100  22 eledelqrlkaevdal 37 
                                       +le+e++rl++  ++l
  gi|298676002|ref|YP_003727752.1| 690 RLENEINRLNNLHKDL 705
                                       5555555554444333 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1  21.0    0.0057       5.7      34     167 ..     169     307 ..     160     326 .. 0.74
   2 ?    4.4  10.3      0.04        40      77     151 ..     319     393 ..     312     408 .. 0.84
   3 ?    2.3   4.0      0.17   1.7e+02      72     119 ..     408     455 ..     392     458 .. 0.52
   4 ?    7.5  29.2    0.0043       4.3      27     166 ..     422     578 ..     417     592 .. 0.73
   5 ?   -0.5   8.2       1.2   1.2e+03      70     160 ..     583     674 ..     574     677 .. 0.67
   6 ?    4.5   4.0     0.036        36      74     150 ..     665     740 ..     655     753 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0057
                             ATG16  34 leaenaklekaaasaks..sksskksakekeasasq....snskqsakiqsleqklaqlreelaelyksrgelaqrl 104
                                       le+ ++++++a + +k   + + ++ +++++    +    +n++  +++++l +k + +++   el +++   ++++
  gi|298676002|ref|YP_003727752.1| 169 LEHYRERASNAKKGVKRhlRDVDNRIKNTES----EiekiKNENPYENLNKLREKSKNIQSKIDELNQKKDSAKSKI 241
                                       5555555544444444444333333333333....233457889999****************************** PP

                             ATG16 105 lelneel...qkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlql 167
                                        eln+++   ++leek k+ +e++++ +++++++ + ++d ++ +  k++ +++lqD  s L+ q 
  gi|298676002|ref|YP_003727752.1| 242 DELNNSIttySELEEKKKSINEEIQDFNTKKTQMYKDIEDIKADISKKRQYLKQLQDKNSELENQI 307
                                       ****9762226899*******************************************999997664 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.04
                             ATG16  77 qsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekek 151
                                       ++ e++    re l ++   r+  ++ l+ +n++l++ +++++e ++++++ +++++++++++++ e  ++e+e+
  gi|298676002|ref|YP_003727752.1| 319 NKKEEEERVARENLNTVSSNRAIKENELKLKNDTLKDIDKQITESNKNIQKKKESVESVQKEIENFEISMKEWEN 393
                                       555566666799999999999999999999999999999999999999999999999999999999999999876 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.17
                             ATG16  72 qsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklk 119
                                       +++k+ + ++++  l++++++l+ +  el++++ e+++ l + ++ l+
  gi|298676002|ref|YP_003727752.1| 408 TEDKLDNIDDTMELLNDQQKDLHGRERELQTSISEVEKRLNEHKKLLE 455
                                       444555555555555555555555555666666665555555555443 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.0043
                             ATG16  27 Lldrtsaleaenaklekaaasaks...........sksskksakekeasasq.........snskqsakiqsleqkl 83 
                                       L d+++ l+ + ++l+++++++++              +  +         q         s+s+++++ +sle++l
  gi|298676002|ref|YP_003727752.1| 422 LNDQQKDLHGRERELQTSISEVEKrlnehkkllekG--KCPTCG-------QdlknssieeSTSEDEKQKKSLEEQL 489
                                       567777888888888777777777665443355331..112222.......13444444668889999********* PP

                             ATG16  84 aqlreelaely......ksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvq 154
                                       +++re+l+ ++      k+  + ++ +++ ++e+q  ++k+++ ++++++ ++++++ +t+++++e++ +e + l++
  gi|298676002|ref|YP_003727752.1| 490 SKTREDLKSVQerlkkvKTARKYSKTINDSQNEIQIIQNKIESLKKQIEDYNNNIEEEKTNINELENRKKEVNGLID 566
                                       *******9998555544566777888999999999999999999999999999999999999999999999999999 PP

                             ATG16 155 dlqDElsaLqlq 166
                                       +l  E+ +L+ +
  gi|298676002|ref|YP_003727752.1| 567 ELNKEILTLKQK 578
                                       999999888755 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 1.2
                             ATG16  70 skqsakiqsleqklaqlreelaelyksrg...elaqrllelneelqkleeklkedeerlaeleaeraaletklkdre 143
                                        k+++k+ ++ + ++ +r+ l e  k ++   +l++++++ ++  + l+++++e++erl+e++++  ++   ++ ++
  gi|298676002|ref|YP_003727752.1| 583 GKEHQKVLNSLDIVKNIRNNLNEYEKIQSdinQLEYKIKSNQDNASLLDSQITERRERLKEIKDKMGDVD--IDGLR 657
                                       3566777777778888888888887777533367889999999999999999999999999888776654..33555 PP

                             ATG16 144 eelrekeklvqdlqDEl 160
                                       ++l++ e ++q++  E+
  gi|298676002|ref|YP_003727752.1| 658 KTLKQYESAHQNITNEI 674
                                       56666666666666655 PP

  == domain 6  score: 4.5 bits;  conditional E-value: 0.036
                             ATG16  74 akiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelreke 150
                                       +  q+ ++++ +l ++   ++k+ g l++ +++ln+ +++l+  l+++++ l+++ ++ ++le  + + +++lrek+
  gi|298676002|ref|YP_003727752.1| 665 SAHQNITNEIDKLYQDKDSVLKEAGRLENEINRLNNLHKDLQ-YLENKKNYLNSVYEDSESLENMYMRIRANLREKN 740
                                       456788899999999*****************9998777766.5778888999999999999999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (888 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3912  (0.218194); expected 358.6 (0.02)
Passed bias filter:                      758  (0.0422779); expected 358.6 (0.02)
Passed Vit filter:                       333  (0.0185733); expected 17.9 (0.001)
Passed Fwd filter:                       185  (0.0103185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 4.40u 0.38s 00:00:04.78 Elapsed: 00:00:00.92
# Mc/sec: 2926.06
//
Query:       gi|298676003|ref|YP_003727753.1|  [L=497]
Description: metallophosphoesterase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-12   48.2   0.3    1.7e-12   48.2   0.3    2.5  3  Metallophos    Calcineurin-like phosphoesterase
    2.4e-10   40.9   0.0    8.4e-10   39.1   0.0    1.9  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
  ------ inclusion threshold ------
        1.8    8.9   9.4        4.7    7.5   9.4    1.8  1  Grg1           Glucose-repressible protein Grg1


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.2   0.3   2.9e-16   1.7e-12       2     122 ..       6     157 ..       5     205 .. 0.69
   2 ?   -2.2   0.0      0.84     5e+03       4      50 ..     223     291 ..     220     308 .. 0.62
   3 ?    0.1   0.3      0.16   9.4e+02     128     158 ..     429     475 ..     357     493 .. 0.60

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 2.9e-16
                                       EEEEEESBTB........TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS....HHHHHHHHHHHHHHHHTSE CS
                       Metallophos   2 rilvigDlHl........algggqlddllkllddllreekpdlvllaGDlvdrg....dlekellellaalvkypip 66 
                                       ++l+++D+H+        +++   ld++ ++++d+++  ++d+v++aGDl+d      +   e+++ +++l +++ip
  gi|298676003|ref|YP_003727753.1|   6 KLLHTADTHIgyrqyqseSRRQDFLDAFSTVINDAIEM-QVDAVVHAGDLFDSRnptlEDILETMRIISRLKSSNIP 81 
                                       89*********999888888888888888888888666.**************999886666688888999999*** PP

                                       EEEEC-TTS.......................CHHH.HHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTE.EEEE CS
                       Metallophos  67 vylllGNHe.......................gfee.ellnkygylgifsepwrsdaevfnnlplaslgsgs.lkvl 118
                                       + ++ GNHe                        +++ e++ +  ++   s++ + d +vfnn+  +     s +++l
  gi|298676003|ref|YP_003727753.1|  82 FLAIVGNHEskqhtqwldlfekmgiavrlgyePYKIdEVSIFGIDSVPKSKIPYFDYSVFNNYSNN-----SqYNLL 153
                                       *********999988888555555555554432222222222222222233333333444444433.....234555 PP

                                       EEES CS
                       Metallophos 119 llhG 122
                                       ++h 
  gi|298676003|ref|YP_003727753.1| 154 VMHQ 157
                                       5554 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.84
                                       EEEESBTB...................TTCCTHHHHHHHHHHHHHHHTTESEEEEEST...SSSSSHHH CS
                       Metallophos   4 lvigDlHl...................algggqlddllkllddllreekpdlvllaGD...lvdrgdle 50 
                                       + i+D ++                   ++ +  +dd+ +++++ + e+ + +v + GD    +  +++e
  gi|298676003|ref|YP_003727753.1| 223 VTINDSGIdisrrnlptrdfefipvtiKDKDNAYDDIFNTVKEYNIENSVTIVEISGDpniTISYSEIE 291
                                       556666666666666666666666666666677777777777777776777777777765544444444 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.16
                                       THHHHHHHHHHHSCHHHHCC...............HHHHHH.HHHHT CS
                       Metallophos 128 lvsldklgslnleleapepg...............dewlkd.lekre 158
                                       +v++++ +++n+e++++  +               ++w +d +++++
  gi|298676003|ref|YP_003727753.1| 429 SVTTESSENYNKEQPSDVIKddtknkpnnvlensgYNWVEDrTDNKK 475
                                       33333333444443333333333444444555667888888633333 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.0   1.4e-13   8.4e-10       2     164 ..       6     227 ..       5     228 .. 0.67

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 1.4e-13
                     Metallophos_2   2 klaiiSDlH.............snldaleavlealkevgvdaiihaGDl.eeeep......evleellela...... 52 
                                       kl++ +D+H             + lda  +v++++ e +vda++haGDl   ++p      e   +           
  gi|298676003|ref|YP_003727753.1|   6 KLLHTADTHigyrqyqsesrrqDFLDAFSTVINDAIEMQVDAVVHAGDLfDSRNPtledilE---T----Mriisrl 75 
                                       7999**************9999999999999*****************99888883432222...2....2233355 PP

                     Metallophos_2  53 .....pvlaVrGNnD...........eevveedvlreaaelgtdl..........................peeael 87 
                                            p+la+ GN++           e            ++g ++                                
  gi|298676003|ref|YP_003727753.1|  76 kssniPFLAIVGNHEskqhtqwldlfE------------KMGIAVrlgyepykidevsifgidsvpkskipY----- 135
                                       7999***********654444444441............333333333343333333333333333332220..... PP

                     Metallophos_2  88 el...........agekvlliHgdpl...gvkdalaellkeaeegsdvvvcGHtHvpevekeggvlvvnPGsvgepr 150
                                        +            + ++l++H+  +    ++ + +e+++++  ++  +++G  H++e+ + ++++v + Gs ++ +
  gi|298676003|ref|YP_003727753.1| 136 -FdysvfnnysnnSQYNLLVMHQLMKpfaFGEWDCEEVIEYTPFDVHAILLGDYHKHEKIDVNNTWVTYCGSTERTS 211
                                       .02222222222234449999998668884455555555553333559***************************98 PP

                     Metallophos_2 151 dgdpe..tyaildtde 164
                                        +++e  +y i+++++
  gi|298676003|ref|YP_003727753.1| 212 SSEREtrSYNIVTIND 227
                                       8887778999998875 PP

>> Grg1  Glucose-repressible protein Grg1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   9.4   0.00078       4.7       3      67 .]     415     485 ..     413     485 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00078
                              Grg1   3 tiknaanyVsekvqgataeaskeanKe....vaK.ds.nasigdRasAakdavsDKidekkhdakAeanKe 67 
                                       ti ++ n   ++  ++t e+s+  nKe    v+K d+ n++     +++ + v D++d kkh++k+ ++K+
  gi|298676003|ref|YP_003727753.1| 415 TITDKKNESENEQTSVTTESSENYNKEqpsdVIKdDTkNKPNNVLENSGYNWVEDRTDNKKHQKKKATHKK 485
                                       667777777777788999999999998333357744455555555689*********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (497 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1759  (0.0981092); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.48
# Mc/sec: 3141.35
//
Query:       gi|298676004|ref|YP_003727754.1|  [L=166]
Description: IS605 family transposase OrfB [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0014   18.5   0.5     0.0027   17.5   0.5    1.5  1  DUF919    Nucleopolyhedrovirus protein of unknown function (D


Domain annotation for each model (and alignments):
>> DUF919  Nucleopolyhedrovirus protein of unknown function (DUF919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.5   1.5e-07    0.0027      15      58 ..       4      45 ..       2      48 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.5e-07
                            DUF919 15 qaKrkltiksqHfErlkkitKnpkElqdlekklnklRqeFLnfg 58
                                       +K  l+ + q +E lk++tK +k l +   +l ++Rq+F+n g
  gi|298676004|ref|YP_003727754.1|  4 TQKNHLRADKQTYETLKRLTKLSKNLYNF--TLYTIRQYFFNHG 45
                                      58999******************888765..8**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1017  (0.0567237); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.34
# Mc/sec: 1468.97
//
Query:       gi|298676005|ref|YP_003727755.1|  [L=165]
Description: rubredoxin-type Fe(Cys)4 protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0037   15.9   0.0     0.0047   15.5   0.0    1.0  1  PAF-AH_p_II    Platelet-activating factor acetylhydrolase, is
  ------ inclusion threshold ------
      0.027   14.3   0.6       0.06   13.2   0.6    1.6  1  zf-C3HC4_3     Zinc finger, C3HC4 type (RING finger)
       0.77    9.6   5.5         19    5.1   5.5    2.6  1  A2L_zn_ribbon  A2L zinc ribbon domain


Domain annotation for each model (and alignments):
>> PAF-AH_p_II  Platelet-activating factor acetylhydrolase, isoform II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   7.8e-07    0.0047     253     346 ..      41     157 ..      31     162 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.8e-07
                                       -EEEEES---TTS-GGGGGG--S-EEEEEETTT--HHHHHHHHT.......................T--TTS-EEE CS
                       PAF-AH_p_II 253 rcaialDaWmlPveeevyskvrqPllfinsekfqtaedikkmkk.......................vvslkkeskv 306
                                       +c+  +D    Pv + v      P l i  +++q ++d+k  +                        + + + ++k 
  gi|298676005|ref|YP_003727755.1|  41 KCSRGYDVQETPVTDSVTRLSSVPKLGIEHASYQINKDNKIHQIdcpssfdtsikpmdeiifthfhfLGASNLYRKY 117
                                       89999********************************987665589********************989999***** PP

                                       EEETT--GGGGSGGGGSS-HHHHHHTTSS-SS-HHHHHHH CS
                       PAF-AH_p_II 307 itvkGsvHqnfsDftfvlgkligkvlklkgeidpeealdi 346
                                       +  k s+Hq+ sDf +  g    +++++ +  +  ea++i
  gi|298676005|ref|YP_003727755.1| 118 FSSKVSIHQSDSDFKLCRGFSFDNTFQTSFIKNGIEAVHI 157
                                       ******************9999999999887777777665 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.6     1e-05      0.06      23      49 ..       8      35 ..       5      36 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1e-05
                                      EEE-HHHHHHHHH.TT-B-TTT--B--E CS
                        zf-C3HC4_3 23 lvlCeeCaekllk.rkkkCpiCrrpiek 49
                                      +++C  C+ ++     ++Cp+C++p +k
  gi|298676005|ref|YP_003727755.1|  8 QYVCTVCSYNMVGyLPERCPFCNAPKDK 35
                                      579********889*********99876 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   5.5    0.0032        19       2      28 ..       7      30 ..       6      32 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0032
                     A2L_zn_ribbon  2 nlkvCsvCggngilnseqgylvCieCg 28
                                       ++vC+vC  n++ +     + C++C+
  gi|298676005|ref|YP_003727755.1|  7 EQYVCTVCSYNMVGYL---PERCPFCN 30
                                      589*********9642...24455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1168.00
//
Query:       gi|298676006|ref|YP_003727756.1|  [L=68]
Description: hypothetical protein Metev_2133 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.13   10.1   1.2       0.13   10.1   1.2    1.0  1  PolC_DP2      DNA polymerase II large subunit DP2
       0.33   10.5   5.5        0.6    9.7   5.5    1.4  1  zn-ribbon_14  Zinc-ribbon


Domain annotation for each model (and alignments):
>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.2   1.4e-05      0.13     620     680 ..       2      62 ..       1      67 [. 0.75

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 1.4e-05
                          PolC_DP2 620 kCkkCgketlearCeeCgekteeklvCkkcee.eve.eekcekcekeakavkkkkidlkelle 680
                                       +C+ Cg e+ ++ C+eC++  +e  v ++++e + +  e+c+      k+v+k ++ ++++++
  gi|298676006|ref|YP_003727756.1|   2 NCQICGVESNSKYCQECEKILNE--VVRRVGEaRWNaMEDCSFIYPMIKRVAKGELTVNDIIQ 62 
                                       7*****************99998..44555542333367788888888888888888877766 PP

>> zn-ribbon_14  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   5.5   6.7e-05       0.6       2      18 ..       2      18 ..       1      20 [. 0.94

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 6.7e-05
                      zn-ribbon_14  2 kCerCGylSSqkiCkAC 18
                                      +C+ CG  S+ k+C+ C
  gi|298676006|ref|YP_003727756.1|  2 NCQICGVESNSKYCQEC 18
                                      8**************88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       966  (0.0538792); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 457.70
//
Query:       gi|298676007|ref|YP_003727757.1|  [L=198]
Description: NADPH-dependent FMN reductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.8e-24   84.9   0.0    6.2e-24   84.5   0.0    1.1  1  FMN_red       NADPH-dependent FMN reductase
    3.1e-10   40.1   0.0    4.2e-10   39.7   0.0    1.2  1  Flavodoxin_2  Flavodoxin-like fold


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.5   0.0   6.9e-28   6.2e-24       2     100 ..       3     106 ..       2     126 .. 0.93

  Alignments for each domain:
  == domain 1  score: 84.5 bits;  conditional E-value: 6.9e-28
                                       EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS..--.....---HCHGHT.CGGSHHHHHHHHHHHH- CS
                           FMN_red   2 kilvisGSlrkgsntrklaewaaealkeagaevelidladl.ilpc...alcdkdlese.gqtsddvaellekiaaa 73 
                                       k+l++sGS+rk++nt+ l++ +++ +ke+g+++e i+l+d+ i+pc     c kd+++   +++d ++ l+ k +++
  gi|298676007|ref|YP_003727757.1|   3 KVLGLSGSPRKKGNTDILLDNFLKGVKEEGVDTETIHLRDYvIQPCigcERCRKDKTCTrLYDGDGMKLLYPKFEES 79 
                                       9***********************************************989999999989***************** PP

                                       SCEEEEEEECTTCE-HHHHHHHHCHT- CS
                           FMN_red  74 daliivtPeYngsysgllKnalDrlsr 100
                                        +l++++P +n+++++ +K+++Drl +
  gi|298676007|ref|YP_003727757.1|  80 KGLVMGSPSHNYNVTSWIKAFIDRLYP 106
                                       ************************954 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.0   4.7e-14   4.2e-10       2     175 ..       3     171 ..       2     193 .. 0.75

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 4.7e-14
                                       EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCC.T-----CCCCHCC.HHHHTT.C.HHHHHHH..H CS
                      Flavodoxin_2   2 kiLiinahprpeksfssalaqafvealekagphevtvrdLyad.flpvlttrdlaak.layeek.p.adveseq..i 72 
                                       k+L + ++pr+ k ++  l++ f+++++++g  + ++++L +    p +  +   ++        + +d +  +   
  gi|298676007|ref|YP_003727757.1|   3 KVLGLSGSPRK-KGNTDILLDNFLKGVKEEG-VDTETIHLRDYvIQPCIGCERCRKDkT----CtRlYDGDGMKllY 73 
                                       8999******9.7******************.99********86677666554443322....13335544333356 PP

                                       HHHHCSSEEEEEEE-BTTB--HHHHHHHHHHS-TTTSC.EETTCSSCCCCTTT..TSEEEEEEEESS-GGGSSTTSS CS
                      Flavodoxin_2  73 ekllaadaivlqfPlwwfgvPailKgwiDrvltagfaf.yteeggegrgggLk..gkkalvivttGgpeesyqergl 146
                                        k++++  +v+++P ++++v +  K++iDr + +     + +++  + + +L+  g+ka+v   +  p +  +   +
  gi|298676007|ref|YP_003727757.1|  74 PKFEESKGLVMGSPSHNYNVTSWIKAFIDRLYPYYNFTeDRPRN--Y-SSRLEgqGRKAIVFGICEQP-DM-D---G 142
                                       9*****************************98887755444444..6.5667669**********999.33.3...5 PP

                                       S-S-HHHHHHHHHHHHHHTT-EEEEEEEE CS
                      Flavodoxin_2 147 egaamdellpplrgilgfiGikdvepvlv 175
                                       +g+++d + +pl++    i  k   + ++
  gi|298676007|ref|YP_003727757.1| 143 MGYTLDAMSKPLETLGYKIETKFPVTSYF 171
                                       799******99998766665555444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1428.18
//
Query:       gi|298676008|ref|YP_003727758.1|  [L=239]
Description: uroporphyrinogen III synthase HEM4 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-34  119.7   0.0    1.6e-31  109.5   0.0    1.8  2  HEM4           Uroporphyrinogen-III synthase HemD
     0.0084   16.4   0.0        1.1    9.7   0.0    2.9  2  IMS_HHH        IMS family HHH motif
  ------ inclusion threshold ------
      0.052   13.9   0.0       0.19   12.1   0.0    2.0  2  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
      0.064   13.2   0.1        5.9    7.0   0.0    2.6  2  HHH            Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> HEM4  Uroporphyrinogen-III synthase HemD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.5   0.0   3.6e-35   1.6e-31       6     220 ..      23     222 ..      18     225 .. 0.92
   2 !   15.3   0.0   2.2e-06    0.0096      71     107 ..     197     233 ..     187     237 .. 0.83

  Alignments for each domain:
  == domain 1  score: 109.5 bits;  conditional E-value: 3.6e-35
                                       HHHHTTEEEEE---EECCECCHHHHHHHHHT.....--SEEEE--HHHHHHHHHHHHHTT---HHHHHCSEEESSHH CS
                              HEM4   6 alearGaeplelPlieiepaedraelraalddleagkydwliftSanavealfealkreeedvkalaslkvaavGpa 82 
                                       +++++G++++++P+i+ + ++d+++++ +l++le++ +d+liftS+ +v  +f+         + + ++k+++vGp+
  gi|298676008|ref|YP_003727758.1|  23 LFKKYGLDAILIPTIQSREPSDKSSMQTLLKKLESRCIDFLIFTSTLGVIKFFKWTT------EIPDRTKIISVGPK 93 
                                       789************************************************887765......9999********** PP

                                       HHHHHHHTT---SEE-..SSSHHHHGGGS-.---EEEEEE-SS.S--HHHHHHHHHTTEEEEEE-SEEEEE-HHHHH CS
                              HEM4  83 TaraLeelglrvdlvpseegtaegLaeelaeslagkrvlllrgeiarddlaegLeergaevdevevYetvpaeeepe 159
                                       Ta+ + ++g++ +++ s  + +e++a  l e+++gk+v + r++  +  l++ L+++ga+v e  +Ye    +e+p 
  gi|298676008|ref|YP_003727758.1|  94 TAEKINQYGYHTEVLDS--YYSEHFATHLGEKVSGKTVGITRANTPDSGLKQSLQSMGATVIEGFCYEL---VETPN 165
                                       ************98887..888***********************************************...89*** PP

                                       HHHHHHHTT--SEEEESSHHHHHHHHHH-S-HHHHHCTSEEEEESHHHHHHHHHTT---SE CS
                              HEM4 160 elkealkagevdavvftSpstvrnllellkdegdelkevkvaaiGptTaealkklglkvdv 220
                                       elk+ + ++++d+vvftS+ +   l + l++  +e k++  +aiGp Tae ++++ +++ +
  gi|298676008|ref|YP_003727758.1| 166 ELKDYIVDKKIDGVVFTSTKSF--LASKLTN--SEVKDIITVAIGPKTAESMENHDITPTL 222
                                       ******************8764..3444444..3899******************998765 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.2e-06
                                       HHHCSEEESSHHHHHHHHHTT---SEE-..SSSHHHH CS
                              HEM4  71 laslkvaavGpaTaraLeelglrvdlvpseegtaegL 107
                                        +++  +a+Gp+Ta+++e++ ++++lv+s + ++ +L
  gi|298676008|ref|YP_003727758.1| 197 VKDIITVAIGPKTAESMENHDITPTLVGSGTLDSCAL 233
                                       4688999*********************977666555 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   0.00025       1.1      14      31 ..      85     102 ..      85     103 .. 0.92
   2 ?    3.7   0.0      0.02        88      19      32 .]     205     218 ..     188     218 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00025
                           IMS_HHH  14 tkipGiGgklgekLeklG 31 
                                       tki  +G+k++ek++++G
  gi|298676008|ref|YP_003727758.1|  85 TKIISVGPKTAEKINQYG 102
                                       79999***********99 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.02
                           IMS_HHH  19 iGgklgekLeklGi 32 
                                       iG+k++e +e+++i
  gi|298676008|ref|YP_003727758.1| 205 IGPKTAESMENHDI 218
                                       8*******999987 PP

>> Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.2   9.7e+03      63      75 ..      90     102 ..      88     105 .. 0.82
   2 ?   12.1   0.0   4.2e-05      0.19      45      88 ..     187     230 ..     158     236 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.2
                                       SCHHHHHHHCTTT CS
                     Nitro_FeMo-Co  63 iGpralakleaag 75 
                                       +Gp+ ++k+++ g
  gi|298676008|ref|YP_003727758.1|  90 VGPKTAEKINQYG 102
                                       7999999999988 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 4.2e-05
                                       HHHHHHHHTT-SEEEESSSCHHHHHHHCTTTSEEEES-SSBHHH CS
                     Nitro_FeMo-Co  45 klaqllaeegvdvvivgkiGpralakleaagievykgaggtvee 88 
                                        la+ l ++ v+ +i+++iGp+ ++ +e++ i++  + +gt++ 
  gi|298676008|ref|YP_003727758.1| 187 FLASKLTNSEVKDIITVAIGPKTAESMENHDITPTLVGSGTLDS 230
                                       578899999*************************9999999875 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0013       5.9      19      27 ..      90      98 ..      90     101 .. 0.92
   2 ?    3.6   0.0     0.015        68      19      26 ..     205     212 ..     205     212 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0013
                                      -SHHHHHHH CS
                               HHH 19 VGpktAeaI 27
                                      VGpktAe+I
  gi|298676008|ref|YP_003727758.1| 90 VGPKTAEKI 98
                                      9******99 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.015
                                       -SHHHHHH CS
                               HHH  19 VGpktAea 26 
                                       +GpktAe+
  gi|298676008|ref|YP_003727758.1| 205 IGPKTAES 212
                                       9*****95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1631.12
//
Query:       gi|298676009|ref|YP_003727759.1|  [L=68]
Description: hypothetical protein Metev_2136 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 499.33
//
Query:       gi|298676010|ref|YP_003727760.1|  [L=172]
Description: nicotinamide-nucleotide adenylyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-16   60.2   0.0    1.5e-15   57.7   0.0    1.9  1  CTP_transf_like  Cytidylyltransferase-like
  ------ inclusion threshold ------
      0.013   15.4   0.0      0.021   14.8   0.0    1.4  1  SAM_4            SAM domain (Sterile alpha motif)
      0.061   13.2   0.0      0.084   12.8   0.0    1.3  1  FAD_syn          FAD synthetase
      0.068   12.8   0.0        1.8    8.2   0.0    2.2  2  Citrate_ly_lig   Citrate lyase ligase C-terminal domain
       0.19   10.9   0.0          7    5.7   0.0    2.1  2  HIGH_NTase1      HIGH Nucleotidyl Transferase


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.7   0.0   4.1e-19   1.5e-15       1     142 [.       7     134 ..       7     135 .. 0.85

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 4.1e-19
                                       EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHH CS
                   CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlelakevdevisvdpweltrevl 77 
                                       ++ G+F+p HlGH  ++++++++++e +++g+ s++++++   ++++a eR+ m++ a e+++   v  + l    +
  gi|298676010|ref|YP_003727760.1|   7 FYIGRFQPYHLGHNSIINRIADEVDE-VVIGIGSAQKSHSP-SDPFTAGERVMMIRNALEKEK---VPNYALP---I 75 
                                       589***********************.************99.****************88888...4444444...4 PP

                                       HHTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHHH CS
                   CTP_transf_like  78 kklkpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkire 142
                                       ++++++   l +++ + ++      ++ +++n++lv++ ++e    v+  ++++++ +S+t+ir+
  gi|298676010|ref|YP_003727760.1|  76 EDIQQN--SLWVSHVLSRTP----LFDVVYSNNPLVIQLFEEAGIPVKQSPMYQREQYSGTRIRK 134
                                       445554..455555444444....699**************9999999****************8 PP

>> SAM_4  SAM domain (Sterile alpha motif)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   5.9e-06     0.021      11      75 ..     105     170 ..      97     172 .] 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.9e-06
                             SAM_4  11 wiqffkeagipaglavnyav.sfvdnriqknmlldlskeimnelgitvvgdiiailkhakvvyrqd 75 
                                        iq+f eagip   +  y    +   ri+k+m+ d +   +    ++ + d i  +   k v r d
  gi|298676010|ref|YP_003727760.1| 105 VIQLFEEAGIPVKQSPMYQReQYSGTRIRKKMIEDNDWRHLVPDAVADIIDEIDGITRLKNVSRTD 170
                                       59************99997527999*********99866665555655555555556677777766 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.3e-05     0.084       6      35 ..       3      32 ..       1      68 [. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.3e-05
                           FAD_syn  6 egavvtlGnFDGvHlGHqallkkaveaake 35
                                      ++ +  +G F   HlGH+++++++ ++ +e
  gi|298676010|ref|YP_003727760.1|  3 RKRAFYIGRFQPYHLGHNSIINRIADEVDE 32
                                      677889****************99887665 PP

>> Citrate_ly_lig  Citrate lyase ligase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0   0.00051       1.8       9      53 ..      13      62 ..       9      72 .. 0.80
   2 ?    2.5   0.0     0.029     1e+02     120     175 ..      96     147 ..      81     154 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00051
                    Citrate_ly_lig  9 nPftlGhryLvekaakendvvhlfvvkedksl.....fsyeerlklvkkG 53
                                       P+ lGh+ ++++ a+e d v + + + +ks+     f++ er+ ++++ 
  gi|298676010|ref|YP_003727760.1| 13 QPYHLGHNSIINRIADEVDEVVIGIGSAQKSHspsdpFTAGERVMMIRNA 62
                                      69***********************9999987333335566788887765 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.029
                    Citrate_ly_lig 120 evtaaYnqalkevlekaeievveierkekeeelisaskvrkllke.knleklaelvP 175
                                        v    n  + + +e+a+i v++ +   ++ e  s +++rk + e +++    +lvP
  gi|298676010|ref|YP_003727760.1|  96 DVVYSNNPLVIQLFEEAGIPVKQSP--MYQREQYSGTRIRKKMIEdNDWR---HLVP 147
                                       5556666677778888888877665..456677899***98765505554...4555 PP

>> HIGH_NTase1  HIGH Nucleotidyl Transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.013        47      10      33 ..      12      34 ..       8      41 .. 0.78
   2 ?    5.7   0.0    0.0019         7     201     237 ..     124     157 ..     113     169 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.013
                       HIGH_NTase1 10 YNPfHnGHlyhlekakeltgadvv 33
                                      + P+H GH   ++ +  +++ +vv
  gi|298676010|ref|YP_003727760.1| 12 FQPYHLGHNSIINRIADEVD-EVV 34
                                      78************998854.444 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0019
                       HIGH_NTase1 201 eeiaSAtaiRkalkeekkleelkklvPestleilkee 237
                                       +e  S t iRk + e+   ++ ++lvP+++++i++e 
  gi|298676010|ref|YP_003727760.1| 124 REQYSGTRIRKKMIED---NDWRHLVPDAVADIIDEI 157
                                       4678*********655...78***********99764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1326.64
//
Query:       gi|298676011|ref|YP_003727761.1|  [L=341]
Description: coenzyme F420 hydrogenase/dehydrogenase beta subunit domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.3e-35  121.7   1.1    2.5e-35  121.6   0.0    1.6  2  FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta su
    7.7e-16   58.0   0.0    1.3e-15   57.2   0.0    1.3  1  FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta su
    2.7e-08   34.3  10.3    2.7e-08   34.3  10.3    2.1  2  Fer4_7       4Fe-4S dicluster domain
    1.5e-07   30.9  21.4    7.4e-07   28.7   7.0    2.6  2  Fer4         4Fe-4S binding domain
    4.8e-06   26.6   8.9    4.8e-06   26.6   8.9    2.2  2  Fer4_9       4Fe-4S dicluster domain
      1e-05   25.6  13.0      1e-05   25.6  13.0    2.5  2  Fer4_10      4Fe-4S dicluster domain
    0.00013   22.4   7.2       0.16   12.6   2.5    2.7  2  Fer4_13      4Fe-4S single cluster domain of Ferredoxin I
    0.00014   22.2   9.3    0.00058   20.2   9.4    2.1  1  Fer4_8       4Fe-4S dicluster domain
    0.00031   21.2   6.4    0.00031   21.2   6.4    1.9  1  Fer4_17      4Fe-4S dicluster domain
    0.00034   21.5  16.9     0.0019   19.1  13.2    3.0  2  Fer4_16      4Fe-4S double cluster binding domain
     0.0015   18.5   6.1     0.0015   18.5   6.1    3.2  3  Fer4_6       4Fe-4S binding domain
     0.0028   17.6  17.7      0.004   17.2   4.4    2.8  2  Fer4_2       4Fe-4S binding domain
  ------ inclusion threshold ------
      0.018   15.8   2.6       0.14   12.9   0.4    2.8  2  Fer4_15      4Fe-4S single cluster domain
      0.034   14.7   3.7      0.034   14.7   3.7    3.0  2  Fer4_4       4Fe-4S binding domain
      0.059   13.5  23.4      0.084   13.0  16.8    3.1  2  Fer4_21      4Fe-4S dicluster domain
      0.066   14.1   4.5       0.97   10.3   0.4    2.6  2  Fer4_22      4Fe-4S dicluster domain
       0.59   10.0   1.6       0.72    9.7   0.2    1.9  2  SHOCT        Short C-terminal domain


Domain annotation for each model (and alignments):
>> FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.3       9.5     1e+04      88      96 ..      53      61 ..      30      65 .. 0.58
   2 !  121.6   0.0   2.3e-38   2.5e-35       2     150 ..     160     303 ..     159     306 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 9.5
                       FrhB_FdhB_C 88 firpsCkvC 96
                                       + + C+ C
  gi|298676011|ref|YP_003727761.1| 53 SVCEDCYAC 61
                                      445556666 PP

  == domain 2  score: 121.6 bits;  conditional E-value: 2.3e-38
                       FrhB_FdhB_C   2 kkvavvGtPCqiaalrklqkkklkekilltiglfCggnfspealrk..lleelgvdpedvkklefrgkgkfrvelkd 76 
                                       +++avvG+PCq+++ r + + + ++ki+++iglfC+++f +e + +  + + lg+d e+v+k++f  kgkf++++kd
  gi|298676011|ref|YP_003727761.1| 160 DRIAVVGVPCQAHGARLIFE-NINDKIAVIIGLFCMESFHHETMLNdiIPKVLGLDIEQVVKMDF-AKGKFWAYTKD 234
                                       69******************.9*****************988887779999**************.9********** PP

                       FrhB_FdhB_C  77 ..ekeislkeleefirpsCkvCkdktaelADisvGdvwgpekkgdddegvstvlvrtekgeellekaveagelele 150
                                          +++++  + e+ r+ C++C d+ta  ADis+G+v      g  ++g++ vl+rt+ ge+ ++ka ++ e+ ++
  gi|298676011|ref|YP_003727761.1| 235 geGHSVKIPTVAEYARNPCHNCCDYTAVHADISIGSV------G-APDGWNSVLIRTDIGEKYFKKASKDLEIMEN 303
                                       886677788****************************......8.**********************999888765 PP

>> FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   0.0   1.3e-18   1.3e-15      15      77 ..      91     152 ..      83     153 .. 0.94

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 1.3e-18
                       FrhB_FdhB_N  15 aqsGGivtallkylLeegiidgvivvapskdpwrpkpviattkeellaaaGskYtlspnlklL 77 
                                       +q+GG+++a+lk+lL++g+id+v+ ++++ ++w+++ v++t+++++ ++aG+kYt+ +++++L
  gi|298676011|ref|YP_003727761.1|  91 GQDGGVTSAILKSLLDKGEIDCVVGITRN-ENWETELVLMTEPSQVDQTAGTKYTYDSVISAL 152
                                       8****************************.79*************************999998 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3  10.3   2.5e-11   2.7e-08       2      50 ..      14      67 ..      13      68 .. 0.80
   2 ?   -1.1   0.1       2.9     3e+03       8      18 ..     253     263 ..     249     285 .. 0.77

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 2.5e-11
                            Fer4_7  2 CigCgaCvaaCpvkaieldeeenek.....gtekveidpekClgCgaCvavCPt 50
                                      C+ CgaC+a+Cpv+ai++d++++ +     +  +    p+ C +C+aC +vCP+
  gi|298676011|ref|YP_003727761.1| 14 CTACGACAAVCPVGAITIDKKAQIRdpnnlELYEKGAAPSVCEDCYACGNVCPV 67
                                      *******************9988874332211222456899************7 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.9
                            Fer4_7   8 CvaaCpvkaie 18 
                                       C + C + a+ 
  gi|298676011|ref|YP_003727761.1| 253 CHNCCDYTAVH 263
                                       77777776665 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   7.0     7e-10   7.4e-07       2      24 .]       8      30 ..       7      30 .. 0.94
   2 !    7.6   6.4    0.0033       3.5       5      20 ..      52      67 ..      51      67 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 7e-10
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                      vi  + C++CGaC+ vCPvgAIt
  gi|298676011|ref|YP_003727761.1|  8 VIENDVCTACGACAAVCPVGAIT 30
                                      68899*****************7 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0033
                                      TTTSSS-THHHHHSTT CS
                              Fer4  5 eekCigCGaCvevCPv 20
                                      ++ C  C aC +vCPv
  gi|298676011|ref|YP_003727761.1| 52 PSVCEDCYACGNVCPV 67
                                      678************7 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   8.9   4.6e-09   4.8e-06       2      47 ..      14      66 ..      13      69 .. 0.94
   2 ?   -0.9   0.1       1.9     2e+03      36      39 ..     253     256 ..     227     265 .. 0.71

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 4.6e-09
                            Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraase.......eaCigCgaCveaCp 47
                                      Ct CgaC ++Cp g+++ d++++++  ++ +        + C +C aC ++Cp
  gi|298676011|ref|YP_003727761.1| 14 CTACGACAAVCPVGAITIDKKAQIRDPNNLELyekgaapSVCEDCYACGNVCP 66
                                      ************************9988877799*****99***********9 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.9
                            Fer4_9  36 CigC 39 
                                       C+ C
  gi|298676011|ref|YP_003727761.1| 253 CHNC 256
                                       3333 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6  13.0   9.5e-09     1e-05       2      56 .]       7      66 ..       6      66 .. 0.79
   2 !   12.2   1.9   0.00014      0.15       6      23 ..      52      69 ..      47      95 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 9.5e-09
                           Fer4_10  2 vvidddtCirCgkCvkaCPadl.....tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                       vi+ d C+ Cg+C ++CP+ +     +++   + + e  ++  +++ C++c aC  +CP
  gi|298676011|ref|YP_003727761.1|  7 DVIENDVCTACGACAAVCPVGAitidkKAQIRDPNNLELYEKGAAPSVCEDCYACGNVCP 66
                                      5899****************9998885444444444444555559999***********9 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00014
                           Fer4_10  6 ddtCirCgkCvkaCPadl 23
                                      ++ C  C +C ++CP+ +
  gi|298676011|ref|YP_003727761.1| 52 PSVCEDCYACGNVCPVIH 69
                                      678999********9943 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   2.5   0.00015      0.16       1      17 [.       9      25 ..       9      42 .. 0.94
   2 !   11.6   0.2    0.0003      0.31       6      31 ..      55      79 ..      52     102 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00015
                           Fer4_13  1 VDrdtCiacgaCvelaP 17
                                      +++d C+acgaC++++P
  gi|298676011|ref|YP_003727761.1|  9 IENDVCTACGACAAVCP 25
                                      68899***********9 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.0003
                           Fer4_13  6 CiacgaCvelaPdvFeeddeggasvv 31
                                      C +c aC++++P +  + +++ +  v
  gi|298676011|ref|YP_003727761.1| 55 CEDCYACGNVCPVIHGYVEDELY-NV 79
                                      99**************9998554.44 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   9.4   5.5e-07   0.00058       4      63 ..      13      67 ..      10      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 5.5e-07
                            Fer4_8  4 kCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63
                                       C+ CgaC + Cpv   t + + + r+ ++  +  e++     a   C  c aC +vCpv
  gi|298676011|ref|YP_003727761.1| 13 VCTACGACAAVCPVGAITIDKKAQIRDPNNL-ELYEKG----AAPSVCEDCYACGNVCPV 67
                                      6*****************9888999998888.444444....589**************7 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   6.4   2.9e-07   0.00031       2      57 ..      14      66 ..      13      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.9e-07
                           Fer4_17  2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCP 57
                                      C+ Cg+C+++Cp ++++ +++++++   +l+l e+     + s C  C  C  +CP
  gi|298676011|ref|YP_003727761.1| 14 CTACGACAAVCPVGAITIDKKAQIRDPNNLELYEK---GAAPSVCEDCYACGNVCP 66
                                      *******************9999999966655555...677788888888888888 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1  13.2   1.8e-06    0.0019       2      66 ..      14      67 ..      13      67 .. 0.73
   2 ?   -2.1   0.1       7.5   7.9e+03      56      60 ..     252     256 ..     219     262 .. 0.64

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.8e-06
                           Fer4_16  2 CgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCPa 66
                                      C+ Cg+Ca vCP++ai+ +  k++++r+        + +l+e+ ++      +  C +C +vCP+
  gi|298676011|ref|YP_003727761.1| 14 CTACGACAAVCPVGAITID--KKAQIRDPN------NLELYEKGAAPS---VCEDCYACGNVCPV 67
                                      *******************..444444442......234444444444...688999******96 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 7.5
                           Fer4_16  56 gCdiC 60 
                                        C +C
  gi|298676011|ref|YP_003727761.1| 252 PCHNC 256
                                       34444 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   6.1   1.4e-06    0.0015       4      24 .]       9      29 ..       8      29 .. 0.91
   2 ?    5.1   4.2     0.025        27       7      21 ..      53      67 ..      51      71 .. 0.86
   3 ?   -0.9   1.1       1.9     2e+03       2      12 ..     246     256 ..     245     258 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.4e-06
                            Fer4_6  4 idpdkCigCgdCvrvCPegai 24
                                      i  d C+ Cg+C++vCP gai
  gi|298676011|ref|YP_003727761.1|  9 IENDVCTACGACAAVCPVGAI 29
                                      66788***************8 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.025
                            Fer4_6  7 dkCigCgdCvrvCPe 21
                                      + C +C++C +vCP 
  gi|298676011|ref|YP_003727761.1| 53 SVCEDCYACGNVCPV 67
                                      5699**********5 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.9
                            Fer4_6   2 veidpdkCigC 12 
                                       +e+ +++C  C
  gi|298676011|ref|YP_003727761.1| 246 AEYARNPCHNC 256
                                       77889999998 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   4.4   3.8e-06     0.004       5      21 ..       9      25 ..       6      26 .. 0.88
   2 ?    5.4   5.4     0.021        22       8      21 ..      53      66 ..      50      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.8e-06
                            Fer4_2  5 vdtdrCigCgaCvsaCP 21
                                      ++ d C++CgaC  +CP
  gi|298676011|ref|YP_003727761.1|  9 IENDVCTACGACAAVCP 25
                                      6779************* PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.021
                            Fer4_2  8 drCigCgaCvsaCP 21
                                        C  C aC ++CP
  gi|298676011|ref|YP_003727761.1| 53 SVCEDCYACGNVCP 66
                                      68************ PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.4   0.00014      0.14       2      33 ..       8      38 ..       8      48 .. 0.82
   2 ?    1.7   0.1      0.42   4.5e+02       8      21 ..      55      68 ..      52     110 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00014
                           Fer4_15  2 vvDrdaCigcglCvaeapevfeldedglasvl 33
                                      v++ d C+ cg+C+a++p v  +  d +a+++
  gi|298676011|ref|YP_003727761.1|  8 VIENDVCTACGACAAVCP-VGAITIDKKAQIR 38
                                      6899*************9.7677777777776 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.42
                           Fer4_15  8 CigcglCvaeapev 21
                                      C+ c +C  ++p +
  gi|298676011|ref|YP_003727761.1| 55 CEDCYACGNVCPVI 68
                                      99******999843 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   3.7   3.2e-05     0.034       2      17 .]      12      27 ..      11      27 .. 0.91
   2 ?    6.1   1.2     0.017        18       3      15 ..      54      66 ..      52      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.2e-05
                            Fer4_4  2 erCigCgsCvaaCPqg 17
                                      + C+ Cg+C a+CP+g
  gi|298676011|ref|YP_003727761.1| 12 DVCTACGACAAVCPVG 27
                                      67************86 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.017
                            Fer4_4  3 rCigCgsCvaaCP 15
                                       C +C +C ++CP
  gi|298676011|ref|YP_003727761.1| 54 VCEDCYACGNVCP 66
                                      699********** PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0  16.8   7.9e-05     0.084       2      54 ..       8      68 ..       8      73 .. 0.80
   2 ?   -0.5   0.5       1.3   1.4e+03      13      25 ..     252     264 ..     249     271 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.9e-05
                           Fer4_21  2 ridedkCigCgkCliaCedtshqaieidaktvl...........kvvedeCvGCnlCssvCPve 54
                                      +i++d C  Cg C+ +C+   + ai+id+k+++               + C  C  C +vCPv 
  gi|298676011|ref|YP_003727761.1|  8 VIENDVCTACGACAAVCP---VGAITIDKKAQIrdpnnlelyekGAAPSVCEDCYACGNVCPVI 68
                                      5999**************...78998888876666666666653445789************94 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.3
                           Fer4_21  13 kCliaCedtshqa 25 
                                        C+  C+ t++ a
  gi|298676011|ref|YP_003727761.1| 252 PCHNCCDYTAVHA 264
                                       6999999887765 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.4   0.00092      0.97       2      94 ..      14      26 ..       4      43 .. 0.70
   2 ?    4.6   0.3     0.057        60       2      19 ..      55      72 ..      54      88 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00092
                           Fer4_22  2 ClsCgaCtlvCptCsCfdvedetkeeskegervrvwdsClleeftkvaggenvrkekkerlrqrllhklsefkekfges 80
                                      C +CgaC++vCp                                                                   
  gi|298676011|ref|YP_003727761.1| 14 CTACGACAAVCP------------------------------------------------------------------- 25
                                      555555555555................................................................... PP

                           Fer4_22 81 gCvGCgRCieacpv 94
                                                   v
  gi|298676011|ref|YP_003727761.1| 26 -------------V 26
                                      .............4 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.057
                           Fer4_22  2 ClsCgaCtlvCptCsCfd 19
                                      C +C aC  vCp  + + 
  gi|298676011|ref|YP_003727761.1| 55 CEDCYACGNVCPVIHGYV 72
                                      999*********988764 PP

>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       3.7   3.9e+03       8      14 ..      44      50 ..      44      50 .. 0.89
   2 ?    9.7   0.2   0.00069      0.72       5      16 ..     100     111 ..      99     111 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.7
                             SHOCT  8 eLyarGe 14
                                      eLy++G+
  gi|298676011|ref|YP_003727761.1| 44 ELYEKGA 50
                                      8****96 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00069
                             SHOCT   5 kLkeLyarGeIt 16 
                                       +Lk+L+++GeI+
  gi|298676011|ref|YP_003727761.1| 100 ILKSLLDKGEID 111
                                       8**********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2185.65
//
Query:       gi|298676012|ref|YP_003727762.1|  [L=328]
Description: 5,10-methylenetetrahydromethanopterin reductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-66  225.3   0.0    1.4e-66  225.1   0.0    1.0  1  Bac_luciferase  Luciferase-like monooxygenase
  ------ inclusion threshold ------
      0.044   14.1   0.0      0.056   13.7   0.0    1.4  1  PHP             PHP domain


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.1   0.0   1.6e-70   1.4e-66      25     314 .]      16     302 ..       8     302 .. 0.94

  Alignments for each domain:
  == domain 1  score: 225.1 bits;  conditional E-value: 1.6e-70
                    Bac_luciferase  25 lvelaraaEelGfdavwvaehhggpggaldaftllaalaaaTerirlgtavtplytrhPavlAqqaatLdhlsgGRf 101
                                       ++++a++aE+ Gfd vwv++h ++    +d +t+la+la+ T+ i+lgt+vt++ytr+  ++A ++  ++++sgGR+
  gi|298676012|ref|YP_003727762.1|  16 IAHYAKLAEQSGFDNVWVTDHFNN----RDVYTTLAVLANNTNSIKLGTGVTNPYTRNIGITASSIGAINEISGGRA 88 
                                       6889*******************9....************************************************* PP

                    Bac_luciferase 102 glglgtggpaveerrfGvdhderyarlrEfvevlrrlwrgeevdfeGeffsvkgalllprpgqgpiPvyvaaaspag 178
                                       +lg+g g  a+  + +G+++++++  ++E v++lr+ ++ge v+ +Ge ++v ga    ++g+  iP+y++a +p++
  gi|298676012|ref|YP_003727762.1|  89 ILGIGPGDKATF-DSMGISWEKPLTTTKESVTALRGYFAGENVSLDGEMVKVGGAKMAFKTGD--IPIYLGAQGPKM 162
                                       *******99887.999************************************99999999943..7*********** PP

                    Bac_luciferase 179 lelaarhadglllageppeeaaelierlragaaeagrdpadirvgisltvivadteeeAraea...raliagldfya 252
                                       l+la+++adg+l++g++p +   +++++++ga++agrd +di++++ + +++++++e+A++ea    a+i  +    
  gi|298676012|ref|YP_003727762.1| 163 LQLAGEVADGILINGSHPRDFDVALDKIKEGAENAGRDMNDIDIAAYTCFSIDKDAEKAKQEAkvvVAFIVAGSPDV 239
                                       ***************************************************************88877776655666 PP

                    Bac_luciferase 253 ldsegagreaeaaeiqeeedanlwagaadav.pdelvaatalvGtpeqvaerlaayaeagvde 314
                                         +++  + ++ ++i+++ +++++++ +  + +d++v+a+ ++Gtpe++ +r++++ ++gv++
  gi|298676012|ref|YP_003727762.1| 240 VLERHGIDPEAKKNISDAISKGDFKSLMGDMvTDDMVNAFSVCGTPEDCKQRVDELFNTGVTQ 302
                                       666666666677799***********998888****************************985 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.2e-06     0.056      12      65 ..      11      63 ..       6     263 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.2e-06
                                      .S-H..HHHHHHHHHCT-SEEEEEEEEBTTHHHHHHHHHHHHTTTTSEEEEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP 12 dgalsieelvkkakelglkaiaiTDhgnlfgyvefykaakkkykagikpiiGle 65
                                      d +l+i  ++k a++ g++ + +TDh n  +++     + +++ + ik+  G+ 
  gi|298676012|ref|YP_003727762.1| 11 DPVLKIAHYAKLAEQSGFDNVWVTDHFNNRDVYTTLAVL-ANNTNSIKLGTGVT 63
                                      678999***********************9999999998.55558899888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2244.86
//
Query:       gi|298676013|ref|YP_003727763.1|  [L=76]
Description: hypothetical protein Metev_2140 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 530.80
//
Query:       gi|298676014|ref|YP_003727764.1|  [L=40]
Description: desulfoferrodoxin dfx domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-14   51.8  10.8    4.6e-14   51.8  10.8    1.0  1  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
  ------ inclusion threshold ------
      0.012   15.8   1.7      0.013   15.6   1.7    1.1  1  zf-UDP           Zinc-binding RING-finger
      0.094   12.5   0.1      0.097   12.5   0.1    1.1  1  DUF3449          Domain of unknown function (DUF3449)
        0.2   11.3   1.6       0.22   11.2   0.1    1.7  2  zf_UBZ           Ubiquitin-Binding Zinc Finger


Domain annotation for each model (and alignments):
>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8  10.8     1e-17   4.6e-14       3      35 ..       6      38 ..       4      39 .. 0.94

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 1e-17
                                      TT-EEE-TTT--EEEECC--SS-EEETTEE-EE CS
                   Desulfoferrod_N  3 klevYkCevCGniVeVleaGgGeLVCCgepMkl 35
                                       +e+Y Ce+CGn+VeV+ +GgG LVCCge M+l
  gi|298676014|ref|YP_003727764.1|  6 VGEKYVCEICGNEVEVTVVGGGVLVCCGEEMEL 38
                                      789****************************98 PP

>> zf-UDP  Zinc-binding RING-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   1.7   2.8e-06     0.013       8      31 ..       9      33 ..       3      39 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.8e-06
                            zf-UDP  8 gqiCqiCgddvglted.gelFvacn 31
                                      + +C+iCg++v++t+  g + v c 
  gi|298676014|ref|YP_003727764.1|  9 KYVCEICGNEVEVTVVgGGVLVCCG 33
                                      679*********9976156777775 PP

>> DUF3449  Domain of unknown function (DUF3449)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   2.2e-05     0.097      85      99 ..       5      19 ..       1      22 [. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.2e-05
                                      XXXXXXXXXXXXXXX CS
                           DUF3449 85 gLgkeykCeiCgnav 99
                                       +g +y CeiCgn v
  gi|298676014|ref|YP_003727764.1|  5 SVGEKYVCEICGNEV 19
                                      56899********75 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   4.9e-05      0.22       1      14 [.       8      21 ..       8      24 .. 0.87
   2 ?   -0.7   0.2      0.25   1.1e+03       8      13 ..      32      37 ..      31      40 .] 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.9e-05
                            zf_UBZ  1 dtylCerCgkeipe 14
                                      + y+Ce Cg e+++
  gi|298676014|ref|YP_003727764.1|  8 EKYVCEICGNEVEV 21
                                      57********9987 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.25
                            zf_UBZ  8 Cgkeip 13
                                      Cg+e++
  gi|298676014|ref|YP_003727764.1| 32 CGEEME 37
                                      999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 262.03
//
Query:       gi|298676015|ref|YP_003727765.1|  [L=79]
Description: hypothetical protein Metev_2142 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-25   88.2  11.1      3e-25   88.0  11.1    1.1  1  DUF2180          Uncharacterized protein conserved in archaea
     0.0022   18.1   5.9       0.13   12.4   0.3    2.4  2  zf-AN1           AN1-like Zinc finger
  ------ inclusion threshold ------
      0.023   15.5   1.3      0.023   15.5   1.3    2.2  2  Tnp_zf-ribbon_2  DDE_Tnp_1-like zinc-ribbon
       0.26   11.2   9.8        1.2    9.1   2.2    2.3  2  zf-C3HC4_3       Zinc finger, C3HC4 type (RING finger)
       0.28   11.3   6.6        0.7   10.1   6.6    1.7  1  FYVE             FYVE zinc finger
        4.2    7.5   9.7    1.2e+02    2.8   9.7    2.2  1  DZR              Double zinc ribbon
        6.5    6.8  10.5          6    6.9   2.5    3.2  3  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
        7.6    6.8  10.8        1.6    9.0   5.9    2.2  2  zf-AD            Zinc-finger associated domain (zf-AD)


Domain annotation for each model (and alignments):
>> DUF2180  Uncharacterized protein conserved in archaea (DUF2180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.0  11.1   1.3e-28     3e-25       1      67 [.       1      76 [.       1      77 [. 0.98

  Alignments for each domain:
  == domain 1  score: 88.0 bits;  conditional E-value: 1.3e-28
                           DUF2180  1 mkCYeCakegkdtdavaiCivCGkGvCkdHlvreeievweGgypfpak.........klkktlprilCkeClealk 67
                                      m CY+Ca++gkd d ++iCi+CG+G+Ck+H+vre+++v +G+y+++++         k++++lp++lC++C++++k
  gi|298676015|ref|YP_003727765.1|  1 MLCYDCAQQGKDVDTIGICILCGRGICKEHSVREDLPVMKGEYDVELEcgmgvecstKDMQHLPQMLCPTCHKVVK 76
                                      78**********************************************************************9987 PP

>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.3   5.9e-05      0.13       6      32 ..       6      35 ..       3      35 .. 0.73
   2 !    8.2   1.1    0.0012       2.7       5      22 ..      54      74 ..      49      75 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.9e-05
                            zf-AN1  6 Ckkkd...flpfkCryCgkvFClkHrlped 32
                                      C ++     +++ C  Cg+  C++H   ed
  gi|298676015|ref|YP_003727765.1|  6 CAQQGkdvDTIGICILCGRGICKEHSVRED 35
                                      544432235679*************99886 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0012
                            zf-AN1  5 sCkkkd..flp.fkCryCgkv 22
                                      +C++kd  +lp + C++C+kv
  gi|298676015|ref|YP_003727765.1| 54 ECSTKDmqHLPqMLCPTCHKV 74
                                      699999766889******996 PP

>> Tnp_zf-ribbon_2  DDE_Tnp_1-like zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   1.3     1e-05     0.023       3      30 ..       3      30 ..       2      49 .. 0.89
   2 ?    0.1   0.9      0.69   1.5e+03      17      23 ..      66      72 ..      53      76 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1e-05
                   Tnp_zf-ribbon_2  3 CkvClkkkikkeTriiCqeCdvplCrnh 30
                                      C++C +++    T  iC  C+ ++C +h
  gi|298676015|ref|YP_003727765.1|  3 CYDCAQQGKDVDTIGICILCGRGICKEH 30
                                      ******666666**************98 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.69
                   Tnp_zf-ribbon_2 17 iiCqeCd 23
                                        C  C 
  gi|298676015|ref|YP_003727765.1| 66 MLCPTCH 72
                                      5555553 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   2.2   0.00052       1.2      25      47 ..       2      26 ..       1      29 [. 0.89
   2 ?    6.8   1.0    0.0028       6.2      28      48 ..      54      76 ..      44      78 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00052
                                      E-HHHHHHHHH..TT-B-TTT--B- CS
                        zf-C3HC4_3 25 lCeeCaekllk..rkkkCpiCrrpi 47
                                      lC++Ca++ ++      C +C r i
  gi|298676015|ref|YP_003727765.1|  2 LCYDCAQQGKDvdTIGICILCGRGI 26
                                      8********9899999*****9987 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0028
                                      HHHHHHHH..TT-B-TTT--B-- CS
                        zf-C3HC4_3 28 eCaekllk..rkkkCpiCrrpie 48
                                      eC++k ++   +  Cp C++ ++
  gi|298676015|ref|YP_003727765.1| 54 ECSTKDMQhlPQMLCPTCHKVVK 76
                                      56666655668999****99887 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   6.6   0.00031       0.7      12      67 ..       3      76 ..       1      77 [. 0.69

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00031
                                      -TTT--B--SSS--EE-TTT--EE-STTS......-EEE.EE.................GGGTEEEEEEE-HHHHHHHH CS
                              FYVE 12 CeiCakkFsllrrrhhCrlCGkvvCekCs......sklvall.................ekeaeeksvrvCkeClaels 67
                                      C  Ca++ + +     C lCG+ +C+++s            +                 +k  ++ ++ +C +C++ ++
  gi|298676015|ref|YP_003727765.1|  3 CYDCAQQGKDVDTIGICILCGRGICKEHSvredlpV-----MkgeydvelecgmgvecsTKDMQHLPQMLCPTCHKVVK 76
                                      5566666655566667*********99985444440.....1455555566677777767888889999******9886 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   9.7     0.052   1.2e+02       1      40 [.       3      77 ..       1      79 [] 0.77

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.052
                               DZR  1 CpqCgeelppdar..fCseCgtklkavaa.................................edrCpsCgekvdp 40
                                      C  C ++ ++ +    C  Cg  + ++ +                                 +  Cp C++ v++
  gi|298676015|ref|YP_003727765.1|  3 CYDCAQQGKDVDTigICILCGRGICKEHSvredlpvmkgeydvelecgmgvecstkdmqhlpQMLCPTCHKVVKE 77
                                      666777655444445788888888866668899999999999999999999999999999988999999999876 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.3     0.049   1.1e+02      20      28 ..       1       9 [.       1       9 [. 0.92
   2 ?    0.6   0.0      0.24   5.5e+02       3       9 ..      17      23 ..      15      23 .. 0.76
   3 ?    6.9   2.5    0.0027         6      19      26 ..      65      72 ..      48      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.049
                    PhnA_Zn_Ribbon 20 lvCpeCahE 28
                                      ++C +Ca +
  gi|298676015|ref|YP_003727765.1|  1 MLCYDCAQQ 9 
                                      89*****88 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.24
                    PhnA_Zn_Ribbon  3 pkCplCa 9 
                                      + C lC+
  gi|298676015|ref|YP_003727765.1| 17 GICILCG 23
                                      67****5 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0027
                    PhnA_Zn_Ribbon 19 llvCpeCa 26
                                       ++Cp+C+
  gi|298676015|ref|YP_003727765.1| 65 QMLCPTCH 72
                                      69*****8 PP

>> zf-AD  Zinc-finger associated domain (zf-AD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.2      0.46     1e+03      48      56 ..       2      10 ..       1      17 [. 0.77
   2 ?    9.0   5.9   0.00074       1.6       1      58 [.      18      77 ..      18      79 .] 0.68

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.46
                             zf-AD 48 iCesClekl 56
                                      +C +C ++ 
  gi|298676015|ref|YP_003727765.1|  2 LCYDCAQQG 10
                                      799999875 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00074
                             zf-AD  1 vCRlCl.....seeseellsifdtsnssislaeileeltglele..pddslpekiCesCleklqe 58
                                      +C lC+     +++ +e l++ +      ++   le+ +g+e++  + ++lp+++C +C++ ++e
  gi|298676015|ref|YP_003727765.1| 18 ICILCGrgickEHSVREDLPVMKG-----EYDVELECGMGVECStkDMQHLPQMLCPTCHKVVKE 77
                                      588888554333333333333333.....36668888899999988899***********98886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.49
# Mc/sec: 483.53
//
Query:       gi|298676016|ref|YP_003727766.1|  [L=72]
Description: hypothetical protein Metev_2143 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-21   76.1   2.5    1.7e-21   76.0   2.5    1.0  1  DUF2180          Uncharacterized protein conserved in archaea
    7.1e-05   23.5   5.2     0.0027   18.5   2.7    2.1  2  Tnp_zf-ribbon_2  DDE_Tnp_1-like zinc-ribbon
  ------ inclusion threshold ------
       0.03   14.5   3.5        0.1   12.8   3.5    1.9  1  FYVE             FYVE zinc finger
        0.2   11.9   9.1       0.76   10.0   5.3    2.5  3  zf-AN1           AN1-like Zinc finger
       0.29   11.3   4.5       0.13   12.4   1.2    1.9  2  C5HCH            NSD Cys-His rich domain


Domain annotation for each model (and alignments):
>> DUF2180  Uncharacterized protein conserved in archaea (DUF2180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.0   2.5   4.7e-25   1.7e-21       1      67 [.       2      67 ..       2      68 .. 0.96

  Alignments for each domain:
  == domain 1  score: 76.0 bits;  conditional E-value: 4.7e-25
                           DUF2180  1 mkCYeCakegkdtdavaiCivCGkGvCkdHlvreeievweGgypfpakklkktlprilCkeClealk 67
                                      mkCY+C++eg d++ ++ C  CGkG+C  H+++ e++v+ G yp  + +l ++lp+ +C+eC ++++
  gi|298676016|ref|YP_003727766.1|  2 MKCYDCMNEGVDKESTGTCTFCGKGICSTHTKKLELPVSVGTYPNFK-RLPEPLPKFVCNECADNII 67
                                      9*******************************************765.9**************9986 PP

>> Tnp_zf-ribbon_2  DDE_Tnp_1-like zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   2.7   7.6e-07    0.0027       2      30 ..       3      31 ..       2      31 .. 0.95
   2 !    5.7   0.0    0.0073        26      16      23 ..      56      63 ..      48      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 7.6e-07
                   Tnp_zf-ribbon_2  2 RCkvClkkkikkeTriiCqeCdvplCrnh 30
                                       C++C   ++ ke++ +C  C++++C  h
  gi|298676016|ref|YP_003727766.1|  3 KCYDCMNEGVDKESTGTCTFCGKGICSTH 31
                                      5*************************877 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0073
                   Tnp_zf-ribbon_2 16 riiCqeCd 23
                                      ++ C+eC+
  gi|298676016|ref|YP_003727766.1| 56 KFVCNECA 63
                                      799****6 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   3.5   2.8e-05       0.1      12      66 ..       4      66 ..       1      69 [. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.8e-05
                                      -TTT--B--SSS--EE-TTT--EE-STTS-EEE.EE........GGGTEEEEEEE-HHHHHHH CS
                              FYVE 12 CeiCakkFsllrrrhhCrlCGkvvCekCssklvall........ekeaeeksvrvCkeClael 66
                                      C  C ++    +    C  CGk +C+++++kl   +        ++  e  +  vC+eC +++
  gi|298676016|ref|YP_003727766.1|  4 CYDCMNEGVDKESTGTCTFCGKGICSTHTKKLELPVsvgtypnfKRLPEPLPKFVCNECADNI 66
                                      6666666555566678***********998887444666666655556666669*****9875 PP

>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2      0.52   1.8e+03      14      20 ..       2       8 ..       1      10 [. 0.73
   2 ?   10.0   5.3   0.00021      0.76      12      28 ..      16      32 ..       4      36 .. 0.73
   3 ?    3.0   0.1     0.032   1.1e+02      12      20 ..      54      63 ..      48      65 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.52
                            zf-AN1 14 fkCryCg 20
                                      +kC +C 
  gi|298676016|ref|YP_003727766.1|  2 MKCYDCM 8 
                                      6898886 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00021
                            zf-AN1 12 lpfkCryCgkvFClkHr 28
                                        ++C +Cgk  C++H 
  gi|298676016|ref|YP_003727766.1| 16 STGTCTFCGKGICSTHT 32
                                      349*************6 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.032
                            zf-AN1 12 lp.fkCryCg 20
                                      lp f C++C 
  gi|298676016|ref|YP_003727766.1| 54 LPkFVCNECA 63
                                      5679*****7 PP

>> C5HCH  NSD Cys-His rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.2   3.7e-05      0.13       8      28 ..      13      33 ..       3      41 .. 0.81
   2 ?   -0.4   0.1      0.36   1.3e+03       4       9 ..      59      64 ..      56      69 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.7e-05
                             C5HCH  8 gkaatsfCefCPssFCkeHek 28
                                      +k++t  C fC +  C  H k
  gi|298676016|ref|YP_003727766.1| 13 DKESTGTCTFCGKGICSTHTK 33
                                      578999*************87 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.36
                             C5HCH  4 CsvCgk 9 
                                      C++C  
  gi|298676016|ref|YP_003727766.1| 59 CNECAD 64
                                      888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 434.95
//
Query:       gi|298676017|ref|YP_003727767.1|  [L=126]
Description: carboxymuconolactone decarboxylase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-14   52.4   0.1    5.6e-14   52.0   0.1    1.1  1  CMD       Carboxymuconolactone decarboxylase family


Domain annotation for each model (and alignments):
>> CMD  Carboxymuconolactone decarboxylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.0   0.1   3.1e-18   5.6e-14       1      84 [.      37     119 ..      37     120 .. 0.96

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 3.1e-18
                                       HHHHHHHHHHHHHHCCGSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHSHHHHH CS
                               CMD   1 pellraltalreallareggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaqaaayagwpaar 77 
                                       p+ l +++a ++ +l+ +g+++ k++ L+alav a+ +ce C++  +  A++ G+t+eei+e++++  +++g pa+ 
  gi|298676017|ref|YP_003727767.1|  37 PDHLTRYNACNKRILS-DGEIPSKYKVLMALAVVASKQCERCAQTQMINAINHGATKEEIMETMDVIGITSGAPAVA 112
                                       7889999********9.9**********************************************************9 PP

                                       HHHHHHH CS
                               CMD  78 aAlaaae 84 
                                       a ++a++
  gi|298676017|ref|YP_003727767.1| 113 ACRDALK 119
                                       9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       774  (0.0431703); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 709.90
//
Query:       gi|298676018|ref|YP_003727768.1|  [L=467]
Description: hypothetical protein Metev_2145 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.6e-12   46.0  11.5    4.2e-10   40.4   3.1    2.6  2  Cytochrome_C554  Cytochrome c554 and c-prime
    2.4e-06   27.4  14.7     0.0032   17.5   5.1    2.8  2  Cytochrome_C7    Cytochrome c7 and related cytochrome c
    0.00057   19.6  10.2       0.37   10.6   1.3    4.7  4  Paired_CXXCH_1   Doubled CXXCH motif (Paired_CXXCH_1)
  ------ inclusion threshold ------
      0.035   14.6  17.6        2.4    8.7   2.9    3.5  3  Cytochrom_c3_2   Cytochrome c3
       0.16   11.6  15.8       0.13   11.9   1.5    3.3  3  Cytochrom_NNT    NapC/NirT cytochrome c family, N-terminal re
       0.28   10.1   7.7       0.42    9.5   0.1    2.6  2  Cytochrom_C552   Cytochrome c552
       0.35   10.8   9.9        6.4    6.7   0.1    3.5  3  C1_1             Phorbol esters/diacylglycerol binding domain
          3    8.3   6.1         26    5.3   0.4    3.8  4  FeoB_associated  FeoB-associated Cys-rich membrane protein
        3.9    7.9  16.5         47    4.4   6.0    3.0  2  Cytochrom_CIII   Class III cytochrome C family
        6.3    7.2  20.4         17    5.9   0.2    5.1  5  Cytochrome_CBB3  Cytochrome C oxidase, cbb3-type, subunit III


Domain annotation for each model (and alignments):
>> Cytochrome_C554  Cytochrome c554 and c-prime
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   3.1   2.4e-13   4.2e-10       2      84 .]      44     122 ..      43     122 .. 0.71
   2 !   10.1   1.3   0.00068       1.2      37      83 ..     156     207 ..     144     208 .. 0.64

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 2.4e-13
                                       HHHHTHHHHHHHTTSTGGGTTGGGSTTSSHHHHHHTT--TTS--TT-TTTGGGSBSTTTSTT---SSS--GG.GBSS CS
                   Cytochrome_C554   2 CaeCHeeqyeswkkskhakaleslkkekkaeakkkakldpakdaeeapeClkCHatgagkdkgfvlkektkl.lagV 77 
                                       C++CH    ++w +s+h++a+     +k  e++ ++  d   + ++++ Cl+CH++   + + +  +e +++  +gV
  gi|298676018|ref|YP_003727768.1|  44 CSTCHGITHSQWDGSMHSNAYIDPFYQK--EYQVAS-ED--TNGKTDKYCLRCHTPIGVASGEAPGEELSDVsREGV 115
                                       *********************7555444..444332.23..345689********97555555544444444277** PP

                                       -HHHHH- CS
                   Cytochrome_C554  78 qCesCHg 84 
                                       qC+ CH+
  gi|298676018|ref|YP_003727768.1| 116 QCDFCHS 122
                                       ******5 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00068
                                       TT--TTS--TT-TTTGGGSBSTTT....STT---SS.S--GGGBSS-HHHHH CS
                   Cytochrome_C554  37 akldpakdaeeapeClkCHatgag....kdkgfvlk.ektkllagVqCesCH 83 
                                       ++++ +  +++++ C  CH+   +     d ++++  +++   +g qC+ CH
  gi|298676018|ref|YP_003727768.1| 156 HDTKYSILHTKSEFCGMCHYVKNSngvlVDDTYKVWkNSSYSSEGTQCQDCH 207
                                       34445566889999*****9765434444444544404455588******** PP

>> Cytochrome_C7  Cytochrome c7 and related cytochrome c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   6.4   8.1e-06     0.015       9      73 .]      38     122 ..      28     122 .. 0.66
   2 !   17.5   5.1   1.8e-06    0.0032      10      72 ..     111     207 ..     104     208 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8.1e-06
                     Cytochrome_C7   9 lkatgykCtdCHsklfeska.k....kk.maemekgkskkaeves.lt....CgaCHdgknaf...........sva 63 
                                       +k ++ +C++CH+ ++ s++      ++    +++++++ a+ ++  +    C  CH+   +             ++
  gi|298676018|ref|YP_003727768.1|  38 FK-ESSRCSTCHGITH-SQWdGsmhsNAyIDPFYQKEYQVASEDTnGKtdkyCLRCHTPIGVAsgeapgeelsdVSR 112
                                       33.5789******994.44422344322544445555544444443225788******9999777888888887556 PP

                     Cytochrome_C7  64 kkaeCakCHt 73 
                                       +  +C+ CH+
  gi|298676018|ref|YP_003727768.1| 113 EGVQCDFCHS 122
                                       899******5 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 1.8e-06
                     Cytochrome_C7  10 katgykCtdCHskl.f.eska.k.............kk.maemekgkskkaeveslt......CgaCHdgknaf... 60 
                                       +++g +C+ CHs   +      +             ++  +e ++++++ ++ ++        Cg CH  kn +   
  gi|298676018|ref|YP_003727768.1| 111 SREGVQCDFCHSVSgNaG--IgTssapfilspgeiqRGpLKE-SESTYHDTKYSI-LhtksefCGMCHYVKNSNgvl 183
                                       446899*****9994342..3224467788877764223222.223333333333.0346788**********8888 PP

                     Cytochrome_C7  61 ............svakkaeCakCH 72 
                                                    + + ++C++CH
  gi|298676018|ref|YP_003727768.1| 184 vddtykvwknssYSSEGTQCQDCH 207
                                       88888899998844679******* PP

>> Paired_CXXCH_1  Doubled CXXCH motif (Paired_CXXCH_1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   1.3    0.0002      0.37       8      38 ..      43      93 ..      30      97 .. 0.80
   2 ?    2.8   0.0     0.056     1e+02       6      18 ..     113     126 ..     110     142 .. 0.83
   3 ?    2.8   0.1     0.056     1e+02      28      38 ..     165     175 ..     149     189 .. 0.77
   4 !    5.2   0.0    0.0098        18       7      17 ..     200     211 ..     195     224 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0002
                    Paired_CXXCH_1  8 eClsCHnphgsdnpkll....................kkakgaalCysCHd 38
                                       C++CH    s+ ++ +                    ++ k+ + C+ CH+
  gi|298676018|ref|YP_003727768.1| 43 RCSTCHGITHSQWDGSMhsnayidpfyqkeyqvasedTNGKTDKYCLRCHT 93
                                      4*****7777777777777777888999999999999889999*******7 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.056
                    Paired_CXXCH_1   6 eg.eClsCHnphgs 18 
                                       eg +C  CH+  g 
  gi|298676018|ref|YP_003727768.1| 113 EGvQCDFCHSVSGN 126
                                       5658*****98765 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.056
                    Paired_CXXCH_1  28 kgaalCysCHd 38 
                                       ++++ C  CH 
  gi|298676018|ref|YP_003727768.1| 165 TKSEFCGMCHY 175
                                       66777888884 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.0098
                    Paired_CXXCH_1   7 g.eClsCHnphg 17 
                                       g +C +CH   g
  gi|298676018|ref|YP_003727768.1| 200 GtQCQDCHMSPG 211
                                       436999996655 PP

>> Cytochrom_c3_2  Cytochrome c3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   3.9     0.003       5.4      19      65 ..      34      92 ..      28      94 .. 0.52
   2 ?    3.1   0.1     0.075   1.4e+02       4      15 ..     112     123 ..     108     135 .. 0.79
   3 ?    8.7   2.9    0.0013       2.4      23      66 ..     164     208 ..     149     214 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.003
                                      SSTTHHHHHHHHHHH--HHHCHT.TSST............TSSBTTSSCTSSS-GGGTS CS
                    Cytochrom_c3_2 19 kkdkaveeekClsCHgkleelak.ktkea...........keanphkshekeleCteCH 65
                                      ++d+  e+++C +CHg +++  + + +++           + a+++++ +++  C +CH
  gi|298676018|ref|YP_003727768.1| 34 SSDQFKESSRCSTCHGITHSQWDgSMHSNayidpfyqkeyQVASEDTNGKTDKYCLRCH 92
                                      45666788899999996655444133333556666653322222222224555566666 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.075
                                       CCT.TGGGTSSS CS
                    Cytochrom_c3_2   4 kegvkCadCHtk 15 
                                       +egv+C+ CH+ 
  gi|298676018|ref|YP_003727768.1| 112 REGVQCDFCHSV 123
                                       578899999975 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0013
                                       HHHHHHHHHHH--HHHCHTTSST.TSSBTTSSC.TSSS-GGGTS- CS
                    Cytochrom_c3_2  23 aveeekClsCHgkleelakktkeakeanphksh.ekeleCteCHk 66 
                                       ++++e C  CH  +++     +++ ++ +++s+ ++ ++C++CH+
  gi|298676018|ref|YP_003727768.1| 164 HTKSEFCGMCHYVKNSNGVLVDDTYKVWKNSSYsSEGTQCQDCHM 208
                                       456777*****9998888877777777777777358899*****7 PP

>> Cytochrom_NNT  NapC/NirT cytochrome c family, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   2.7     0.003       5.3     119     168 ..      35      96 ..      28     103 .. 0.62
   2 ?   -2.2   0.1       1.6     3e+03     126     134 ..     115     123 ..      98     127 .. 0.75
   3 ?   11.9   1.5   7.3e-05      0.13      34      75 ..     165     210 ..     154     219 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.003
                     Cytochrom_NNT 119 rmkandsreCrnCHseeamdlek.qkkka......akahkkaa..........eeektCidCHkgia 168
                                       + + ++s+ C +CH  ++ + +  ++++a      +k     +          +++k C+ CH+ i+
  gi|298676018|ref|YP_003727768.1|  35 SDQFKESSRCSTCHGITHSQWDGsMHSNAyidpfyQK-----EyqvasedtngKTDKYCLRCHTPIG 96 
                                       5667889999999987755544303333311111122.....1234557766788999*****9875 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.6
                     Cytochrom_NNT 126 reCrnCHse 134
                                        +C  CHs 
  gi|298676018|ref|YP_003727768.1| 115 VQCDFCHSV 123
                                       577777775 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 7.3e-05
                     Cytochrom_NNT  34 steeFCvsCHemedn.veeykesiH.ysnrsg..vraeCsdCHvPk 75 
                                        ++eFC  CH +++     + ++   ++n s      +C+dCH+  
  gi|298676018|ref|YP_003727768.1| 165 TKSEFCGMCHYVKNSnGVLVDDTYKvWKNSSYssEGTQCQDCHMSP 210
                                       4679******9888733333333332444433225689*****965 PP

>> Cytochrom_C552  Cytochrome c552
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   3.5     0.046        83      62     106 ..      60     104 ..      28     177 .. 0.69
   2 ?    9.5   0.1   0.00023      0.42     233     254 ..     188     209 ..     185     214 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.046
                                       GGGHHHHHHHSGGG---SSTT-SSSBGGGGTTT-THHHHHHHHHH CS
                    Cytochrom_C552  62 HayaveDvletlrtgapkeaeegkqpaaCltCkspdvprlieekg 106
                                       H  a  D +  +  ++++e+++gk+   Cl C++p  +   e+ g
  gi|298676018|ref|YP_003727768.1|  60 HSNAYIDPFYQKEYQVASEDTNGKTDKYCLRCHTPIGVASGEAPG 104
                                       555666666666677777777788888888888876665555544 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00023
                                       HHHHHTSHHHHTT--HHHHHS- CS
                    Cytochrom_C552 233 fElysegvHakngvsCaDCHmP 254
                                       + +++++   ++g  C DCHm 
  gi|298676018|ref|YP_003727768.1| 188 YKVWKNSSYSSEGTQCQDCHMS 209
                                       889******************5 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.2     0.026        46      25      40 ..      38      53 ..      31      60 .. 0.72
   2 ?    6.7   0.1    0.0036       6.4       9      36 ..      83     122 ..      78     124 .. 0.86
   3 ?    4.1   0.9     0.024        43      24      36 ..     196     208 ..     163     210 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.026
                                      SS-EEEETTT--EE-C CS
                              C1_1 25 ekqglkCswCkllvHk 40
                                      +k   +Cs+C+ + H 
  gi|298676018|ref|YP_003727768.1| 38 FKESSRCSTCHGITHS 53
                                      4555677777777775 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0036
                                       SS--B-TTT-SB-............-SSSS-EEEETTT-- CS
                              C1_1   9 kqptfCkhCgefl............wgkekqglkCswCkl 36 
                                       k  ++C  C  ++            +  ++ g++C+ C+ 
  gi|298676018|ref|YP_003727768.1|  83 KTDKYCLRCHTPIgvasgeapgeelSDVSREGVQCDFCHS 122
                                       67789999*99999999999999966699*********95 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.024
                                       SSS-EEEETTT-- CS
                              C1_1  24 kekqglkCswCkl 36 
                                        ++ g +C++C++
  gi|298676018|ref|YP_003727768.1| 196 YSSEGTQCQDCHM 208
                                       568899*****98 PP

>> FeoB_associated  FeoB-associated Cys-rich membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.52   9.3e+02      31      38 ..      42      49 ..       9      52 .. 0.76
   2 ?   -3.1   0.1       6.4   1.1e+04      26      37 ..     113     121 ..     111     124 .. 0.59
   3 ?    2.7   0.0     0.098   1.8e+02      18      37 ..     188     207 ..     182     210 .. 0.73
   4 ?    5.3   0.4     0.014        26       5      24 ..     446     466 ..     446     467 .] 0.72

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.52
                   FeoB_associated 31 ggCsgCss 38
                                      + Cs C++
  gi|298676018|ref|YP_003727768.1| 42 SRCSTCHG 49
                                      46888875 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.4
                   FeoB_associated  26 kGsCgggCsgCs 37 
                                       +G     C+ C+
  gi|298676018|ref|YP_003727768.1| 113 EG---VQCDFCH 121
                                       66...4566665 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.098
                   FeoB_associated  18 rrlikk...kkkGsCgggCsgCs 37 
                                       ++++k+   + +G     C +C+
  gi|298676018|ref|YP_003727768.1| 188 YKVWKNssySSEG---TQCQDCH 207
                                       8888887778888...6666665 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.014
                   FeoB_associated   5 Vgliiaaavafv.irrlikkk 24 
                                       V+++i+++++++  +r++kk+
  gi|298676018|ref|YP_003727768.1| 446 VLILIFSILVVIlYYRNHKKR 466
                                       789999777766477888875 PP

>> Cytochrom_CIII  Class III cytochrome C family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   7.2     0.053        95      30     102 .]      40     121 ..      27     121 .. 0.54
   2 ?    4.4   6.0     0.026        47      46      84 ..     166     208 ..     106     219 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.053
                                       TSHTHHHTSTTCTTSCSTS-CTCTS-SSSTTTSTTCHHHHHHCSSTT..TCHHHHHHHHHHTSHH..........HC CS
                    Cytochrom_CIII  30 evkeCeeCHhkeeekeeiekcstcHaeekekkekkslekavHkkkaa..ksCvgCHkkkkkekke..........ke 94 
                                       e ++C++CH  ++++ + +  s++  +      +k+++ a  +++ +  k C+ CH+    ++ e          +e
  gi|298676018|ref|YP_003727768.1|  40 ESSRCSTCHGITHSQWDGSMHSNAYIDP---FYQKEYQVASEDTNGKtdKYCLRCHTPIGVASGEapgeelsdvsRE 113
                                       3336777777744444444434444433...22333333333333324589*****976655554556666666666 PP

                                       HHSHHHHC CS
                    Cytochrom_CIII  95 ptkCaech 102
                                        ++C  ch
  gi|298676018|ref|YP_003727768.1| 114 GVQCDFCH 121
                                       67777666 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.026
                                       STS-CTCTS-SSS.TTTSTTCHHHHHHCSSTT...TCHHHHHH CS
                    Cytochrom_CIII  46 eiekcstcHaeek.ekkekkslekavHkkkaa...ksCvgCHk 84 
                                       + e c  cH  ++ +    + ++k++ +++ +   ++C++CH 
  gi|298676018|ref|YP_003727768.1| 166 KSEFCGMCHYVKNsNGVLVDDTYKVWKNSSYSsegTQCQDCHM 208
                                       4566888888886422334455666666544455678888886 PP

>> Cytochrome_CBB3  Cytochrome C oxidase, cbb3-type, subunit III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   1.1     0.033        59      12      20 ..      42      51 ..      36      77 .. 0.76
   2 ?    5.9   0.2    0.0092        17      11      24 ..      85      98 ..      76     115 .. 0.67
   3 ?    2.6   2.2     0.099   1.8e+02      13      25 ..     116     146 ..     111     178 .. 0.64
   4 ?    0.7   0.1      0.38   6.8e+02      12      25 ..     168     181 ..     162     200 .. 0.72
   5 ?    3.6   0.4     0.046        82      13      24 ..     202     213 ..     194     254 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.033
                   Cytochrome_CBB3 12 knCasCHg.k 20
                                      + C++CHg +
  gi|298676018|ref|YP_003727768.1| 42 SRCSTCHGiT 51
                                      48******63 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0092
                   Cytochrome_CBB3 11 kknCasCHg.kggag 24
                                      +k+C +CH+   g++
  gi|298676018|ref|YP_003727768.1| 85 DKYCLRCHTpI-GVA 98
                                      68******952.332 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.099
                   Cytochrome_CBB3  13 nCasCHg.kggag.................p 25 
                                       +C  CH  +g+ag                  
  gi|298676018|ref|YP_003727768.1| 116 QCDFCHSvSGNAGigtssapfilspgeiqrG 146
                                       7*****9888888766665555554444443 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.38
                   Cytochrome_CBB3  12 knCasCHgkggagp 25 
                                       + C  CH  ++ + 
  gi|298676018|ref|YP_003727768.1| 168 EFCGMCHYVKNSNG 181
                                       58*****8444444 PP

  == domain 5  score: 3.6 bits;  conditional E-value: 0.046
                   Cytochrome_CBB3  13 nCasCHgkggag 24 
                                       +C+ CH + g  
  gi|298676018|ref|YP_003727768.1| 202 QCQDCHMSPGIT 213
                                       8*****855443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.76u 0.34s 00:00:01.10 Elapsed: 00:00:00.55
# Mc/sec: 2579.42
//
Query:       gi|298676019|ref|YP_003727769.1|  [L=210]
Description: NADPH-dependent FMN reductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.1e-32  110.5   0.0    7.7e-32  110.2   0.0    1.1  1  FMN_red       NADPH-dependent FMN reductase
    7.7e-05   22.5   0.0    0.00012   21.9   0.0    1.4  1  Flavodoxin_2  Flavodoxin-like fold
  ------ inclusion threshold ------
       0.14   12.4   0.1       0.43   10.9   0.0    1.7  2  Ycf54         Protein of unknown function (DUF2488)


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.2   0.0   1.3e-35   7.7e-32       2     149 ..       9     162 ..       8     167 .. 0.92

  Alignments for each domain:
  == domain 1  score: 110.2 bits;  conditional E-value: 1.3e-35
                                       EEEEEES--STT-HHHHHHHHHHCCT-T..T-CEEEEETTTS..--.....---HCHGHTCGGSHHHHHHHHHHHH- CS
                           FMN_red   2 kilvisGSlrkgsntrklaewaaealkea.gaevelidladl.ilpc...alcdkdlesegqtsddvaellekiaaa 73 
                                       k+l+isGS+r ++ t+ ++++a+++++e+  ae++++  +++  + c   ++c   +++ + + dd+ +l+ek+++a
  gi|298676019|ref|YP_003727769.1|   9 KLLGISGSPR-KKATDYIIREALKHAEEKySAETDYFSASGKeLKFCihcDYCI-RTQKGCIHEDDIVDLYEKMKWA 83 
                                       99*******8.778************99988*******9999889988866666.44466***************** PP

                                       SCEEEEEEECTTCE-HHHHHHHHCHT-...SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHH.HTT-EEEECSE CS
                           FMN_red  74 daliivtPeYngsysgllKnalDrlsr..trgkkelrgKpvalvavgggrrgglraeeqlrqvla.elgaivvpraa 147
                                       da+ii+tP Y+g+ s++ K+++Dr+++   +++k + +K++a++avgg+r gg++ + q+ + +  ++++ +v+++ 
  gi|298676019|ref|YP_003727769.1|  84 DAWIIGTPAYQGTLSAQTKTIMDRCRAvvAQDPKVFLNKVGAAAAVGGDRVGGQEPAIQAIHNFYvINEMLPVSGGS 160
                                       *************************99**************************************89*****99987 PP

                                       EE CS
                           FMN_red 148 va 149
                                       + 
  gi|298676019|ref|YP_003727769.1| 161 FG 162
                                       75 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0     2e-08   0.00012      60     103 ..      63     108 ..       9     144 .. 0.65

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2e-08
                                       HHTT..C.HHHHHHHHHHHHCSSEEEEEEE-BTTB--HHHHHHHHHH CS
                      Flavodoxin_2  60 yeek..p.adveseqiekllaadaivlqfPlwwfgvPailKgwiDrv 103
                                       ++++     d+     ek+++ada ++++P +  +++a+ K  +Dr 
  gi|298676019|ref|YP_003727769.1|  63 TQKGciHeDDIVDLY-EKMKWADAWIIGTPAYQGTLSAQTKTIMDRC 108
                                       333344335555566.*****************************94 PP

>> Ycf54  Protein of unknown function (DUF2488)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.78   4.7e+03      20      32 ..      27      39 ..      20      53 .. 0.52
   2 ?   10.9   0.0   7.2e-05      0.43      30      73 ..      76     117 ..      67     122 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.78
                                      HHHHHHHHHHHHH CS
                             Ycf54 20 eevLkerarnyke 32
                                       e Lk+ +++y++
  gi|298676019|ref|YP_003727769.1| 27 REALKHAEEKYSA 39
                                      3444444444433 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 7.2e-05
                                       HHHTT----EEEEESBGGGGSGGGHHHHHHS-SSEEEEEES-HH CS
                             Ycf54  30 ykeknkeidfwlvkePaFleapelkeikkklpkpaaAivstdkk 73 
                                         ek k  d w++ +Pa+  +  l++++k +   + A+v+ d k
  gi|298676019|ref|YP_003727769.1|  76 LYEKMKWADAWIIGTPAYQGT--LSAQTKTIMDRCRAVVAQDPK 117
                                       5688999***********877..*****************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1294.24
//
Query:       gi|298676020|ref|YP_003727770.1|  [L=232]
Description: oxidoreductase FAD-binding domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-18   67.1   0.0    2.7e-18   66.6   0.0    1.2  1  NAD_binding_1  Oxidoreductase NAD-binding domain
    1.2e-14   54.4   0.0    1.9e-14   53.8   0.0    1.3  1  FAD_binding_6  Oxidoreductase FAD-binding domain
    2.6e-07   30.9   0.9      2e-06   28.0   0.1    2.1  2  NAD_binding_6  Ferric reductase NAD binding domain
    8.6e-07   29.0   0.1    3.2e-06   27.2   0.1    1.9  1  FAD_binding_8  FAD-binding domain


Domain annotation for each model (and alignments):
>> NAD_binding_1  Oxidoreductase NAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.6   0.0   5.9e-22   2.7e-18       1     107 [.     107     210 ..     107     212 .. 0.95

  Alignments for each domain:
  == domain 1  score: 66.6 bits;  conditional E-value: 5.9e-22
                                       EEEEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGSTTHHHHHHHHHHCTTEEEEEEEESSCTTTSSSEESSH CS
                     NAD_binding_1   1 miagGtGiaPvrsvlraileeakdktkvvlvyGnrteedllyreeleelakklpgrlkvvavvsreeagweggkgrv 77 
                                       +++gG Gi+P+ s+ + +++  + +t ++lv  ++te+d+++  ele+l+k +++ lkvv +++r +++w+g + ++
  gi|298676020|ref|YP_003727770.1| 107 LLSGGIGITPMISICKYCTDL-NLDTSITLVSSYKTEDDIVFYSELENLQKLNEN-LKVVITLTRASSEWOGCREHI 181
                                       789*****************8.889************************888888.9999999************** PP

                                       HHHHHHHHHHHSSTTEEEEEECSHHHHHHH CS
                     NAD_binding_1  78 qdalleellslkkeethvyvCGppgMikav 107
                                        ++l+   ++ + +++++y+CGppgM++ v
  gi|298676020|ref|YP_003727770.1| 182 CENLITREIP-DFKDHMYYLCGPPGMVNSV 210
                                       ******9999.79999***********987 PP

>> FAD_binding_6  Oxidoreductase FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.8   0.0   4.2e-18   1.9e-14       4      98 ..       7      97 ..       4      98 .. 0.93

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 4.2e-18
                                      EEEEEECCTTEEEEEEEESTTTS-----TT-EEEEEECETTCCEEEEEE.BSSTTECCEEEEEEE--TT-HHHHHHHCS CS
                     FAD_binding_6  4 ltekeevsedtrifrfklpsekqklglpvGqhvflrlkikgeaviRsYtpissenekGelellvkvypgGkmsqaLdel 82
                                      +t++ + ++d++ frf+ p   + +++ +Gq+vf++++++ge v +++t+ ss++ek++le+  k++ g + s++Ld++
  gi|298676020|ref|YP_003727770.1|  7 VTKVIQRTHDVKSFRFNRP---EGFDYKAGQYVFITIPVNGEMVRKPFTLSSSPTEKNHLEFT-KKLTGHEYSNVLDSM 81
                                      77888899*********99...4567***********************************97.888999********* PP

                                      -TT-EEEEEEEE-SEE CS
                     FAD_binding_6 83 kigdtleikGPlGkfe 98
                                        gd l+i+GP+Gk++
  gi|298676020|ref|YP_003727770.1| 82 GSGDLLKIDGPYGKMT 97
                                      *************986 PP

>> NAD_binding_6  Ferric reductase NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.1   4.5e-10     2e-06       1      80 [.     102     173 ..     102     199 .. 0.79
   2 ?    1.4   0.0     0.068     3e+02     140     152 ..     199     211 ..     194     215 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 4.5e-10
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                     NAD_binding_6   1 yenvllvagGiGitpfisilkdllkkskkealktkkikliwvvressslewfkdvLneleeekse.gnieihiYlTs 76 
                                       ye + l++gGiGitp+isi+k +           ++i+l+ + + ++++  ++    ele++++   n+++ i lT+
  gi|298676020|ref|YP_003727770.1| 102 YEKIALLSGGIGITPMISICKYCTDLNL-----DTSITLVSSYKTEDDIVFYS----ELENLQKLnENLKVVITLTR 169
                                       799*****************99987665.....799*************9999....55555555445777777776 PP

                                       xxxx RF
                     NAD_binding_6  77 eyea 80 
                                        +++
  gi|298676020|ref|YP_003727770.1| 170 ASSE 173
                                       6655 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.068
                                       xxxxxxxxxxxxx RF
                     NAD_binding_6 140 fvCGppklvkevk 152
                                       + CGpp++v+ v 
  gi|298676020|ref|YP_003727770.1| 199 YLCGPPGMVNSVV 211
                                       58*******9886 PP

>> FAD_binding_8  FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.1   7.2e-10   3.2e-06       7     107 ..       8      95 ..       3      97 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 7.2e-10
                     FAD_binding_8   7 akvalleedliklkvskpkkslkykaGqyvyinipslsklfwqsHPFtiasapeddklslvikvksgltkklakkll 83 
                                        kv    +d+ + ++++p+  + ykaGqyv+i ip   ++     PFt+ s+p ++       ++ ++tkkl  + +
  gi|298676020|ref|YP_003727770.1|   8 TKVIQRTHDVKSFRFNRPEG-FDYKAGQYVFITIPVNGEM--VRKPFTLSSSPTEK-------NHLEFTKKLTGHEY 74 
                                       5677777899999******9.*************988866..899******99864.......45566666666666 PP

                     FAD_binding_8  84 ssskkelenkkaklkvlidGPYGa 107
                                       s+    l+++ +   + idGPYG+
  gi|298676020|ref|YP_003727770.1|  75 SN---VLDSMGSGDLLKIDGPYGK 95 
                                       65...3333444445778999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1493.11
//
Query:       gi|298676021|ref|YP_003727771.1|  [L=191]
Description: rubrerythrin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.4e-35  120.3   3.8    9.5e-35  120.0   3.8    1.1  1  Rubrerythrin    Rubrerythrin
    7.7e-11   42.1   0.7      1e-10   41.7   0.7    1.1  1  Ferritin        Ferritin-like domain
     0.0048   16.9   0.1     0.0089   16.0   0.1    1.4  1  HypA            Hydrogenase/urease nickel incorporation, meta
     0.0071   16.2   0.1      0.017   15.0   0.1    1.6  1  zf-like         Cysteine-rich small domain
  ------ inclusion threshold ------
      0.015   15.4   1.4      0.031   14.4   1.4    1.5  1  Zn-ribbon_8     Zinc ribbon domain
      0.017   14.8   0.1       0.11   12.0   0.1    1.9  2  DUF4125         Protein of unknown function (DUF4125)
      0.026   14.9   0.2      0.052   13.9   0.2    1.6  1  DUF4379         Probable Zinc-ribbon domain
       0.03   14.3   0.3      0.078   13.0   0.4    1.7  1  RNHCP           RNHCP domain
      0.038   13.8   0.4        1.8    8.3   0.2    2.1  2  COQ7            Ubiquinone biosynthesis protein COQ7
      0.057   13.3   1.0         10    6.1   0.1    2.5  2  TFIIS_C         Transcription factor S-II (TFIIS)
       0.08   12.8   0.2       0.12   12.2   0.2    1.2  1  MCM_OB          MCM OB domain
      0.094   12.7   1.7       0.65   10.0   0.5    2.1  2  DUF892          Domain of unknown function (DUF892)
       0.11   12.1   0.4       0.24   11.0   0.4    1.5  1  RecR            RecR protein
       0.19   11.5   0.3       0.19   11.5   0.3    2.5  3  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
       0.35   10.6   2.2        0.8    9.5   2.2    1.7  1  zinc_ribbon_2   zinc-ribbon domain
       0.63   10.2   4.3          4    7.6   0.2    2.6  2  DUF2387         Probable metal-binding protein (DUF2387)
          1    9.1   3.6        1.3    8.8   0.1    2.1  2  Rubredoxin_2    Rubredoxin metal binding domain
        3.5    7.6   5.8        1.2    9.1   0.5    2.5  3  HalOD2          Halobacterial output domain 2


Domain annotation for each model (and alignments):
>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.0   3.8   9.5e-38   9.5e-35       1     137 []      11     139 ..      11     139 .. 0.97

  Alignments for each domain:
  == domain 1  score: 120.0 bits;  conditional E-value: 9.5e-38
                                       HHHHHHHHHHHHHHHHHHHHHHCHH.TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS------- CS
                      Rubrerythrin   1 eiLekAiagEssarrlYkelaekak.egypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakp 76 
                                       ++L +A+agEs+ar++Y ++a++ak egy+qia+lF e+Ae+E+eH k+l+k+le  + e           ++++  
  gi|298676021|ref|YP_003727771.1|  11 KNLLAAFAGESQARNRYAYFASQAKkEGYEQIAALFTETAENEKEHGKRLFKFLEGGDTEIT---------ATYPSG 78 
                                       699*****************************************************666665.........9***** PP

                                       TTGGHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  77 kflttaknLeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlrkll 137
                                        +  t +nLe+a++g+ +e+++my++++++ae e+++e++ +++++a aEk+He+r+r+l+
  gi|298676021|ref|YP_003727771.1|  79 VIGNTLQNLESAANGENYENTQMYPEFADIAETERFPEIASVMRNIAVAEKGHEDRFRALM 139
                                       **********************************************************996 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.7     1e-13     1e-10       2     140 ..      11     143 ..      10     144 .. 0.90

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 1e-13
                                       HHHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHHC-SSSSC CS
                          Ferritin   2 kaLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraeleeieapkef 78 
                                       k L +++a e +a + y ++a+ +k +g+e++a++f e ae e eh+++l++++   Gg     + e+ + ++    
  gi|298676021|ref|YP_003727771.1|  11 KNLLAAFAGESQARNRYAYFASQAKKEGYEQIAALFTETAENEKEHGKRLFKFLE--GG-----DTEITATYPSGVI 80 
                                       6788999*********************************************986..66.....7788887777778 PP

                                       SSHHHHHHHHHHHH.HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin  79 gsveevleaalehe.kkvteslrelielaeeegDpatadfledfleeqeeheweleallekle 140
                                       g++++ le a + e ++ t+++ e +++ae+e+ p  a+ + ++   +  he+ ++al+++++
  gi|298676021|ref|YP_003727771.1|  81 GNTLQNLESAANGEnYENTQMYPEFADIAETERFPEIASVMRNIAVAEKGHEDRFRALMDNIN 143
                                       977777777777762689*****************************************9985 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   8.9e-06    0.0089      20      96 ..     111     181 ..      99     185 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8.9e-06
                                       CTT..EEEEEEEEEETTCT--HHHHHHHHHHHHCC.TTTT-EEEEEEE--EEEETTTS-EEECHHHHHS-TTTSSS- CS
                              HypA  20 eaaarkvtkvkvevGelsgvepeaLefafellaegtvlegaeLeieevpvkvrCreCgkefeleekalrCpkCgsad 96 
                                       ++++ ++ +v  ++   ++ +++ ++  ++ +++g+v++      +++ v  +Cr+Cg+  e+ ++ + Cp+C + +
  gi|298676021|ref|YP_003727771.1| 111 TERFPEIASVMRNIAVAEKGHEDRFRALMDNINNGQVFK------KDETVIWKCRNCGYLHEEMAAPEVCPACAHPQ 181
                                       456667777777777777777788888888888888877......788999*******99996655457****9876 PP

>> zf-like  Cysteine-rich small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   1.7e-05     0.017      36      68 ..     142     174 ..     135     185 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.7e-05
                           zf-like  36 eelGefvetengkvkdCskCllvHkkevadell 68 
                                        + G++ ++++  +++C +C ++H++ +a e+ 
  gi|298676021|ref|YP_003727771.1| 142 INNGQVFKKDETVIWKCRNCGYLHEEMAAPEVC 174
                                       3459999999999************99888775 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.4   3.1e-05     0.031       7      34 ..     157     179 ..     155     182 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.1e-05
                       Zn-ribbon_8   7 rCeeCghefevlqsisdapltaCPeCgs 34 
                                       +C++Cg  +e++++     +++CP+C +
  gi|298676021|ref|YP_003727771.1| 157 KCRNCGYLHEEMAA-----PEVCPACAH 179
                                       8*********9983.....567****76 PP

>> DUF4125  Protein of unknown function (DUF4125)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00011      0.11      70     143 ..      25     100 ..      11     105 .. 0.81
   2 ?    0.5   0.0       0.4     4e+02     118     137 ..     112     131 ..     104     137 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                           DUF4125  70 eKYarmmestapeeyekiedllpelseekeeliekIvkiqvewqeelakkYPk..lakkarkleseedteektsfe 143
                                       ++Ya+   ++++e ye+i+ l+ e+ e+++e  ++  k+      e+++ YP   + ++ ++les+ + e+ ++ +
  gi|298676021|ref|YP_003727771.1|  25 NRYAYFASQAKKEGYEQIAALFTETAENEKEHGKRLFKFLEGGDTEITATYPSgvIGNTLQNLESAANGENYENTQ 100
                                       68****99999*****************************************832445555555555555555555 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.4
                           DUF4125 118 kkYPklakkarkleseedte 137
                                       +++P++a+ +r+++ +e+ +
  gi|298676021|ref|YP_003727771.1| 112 ERFPEIASVMRNIAVAEKGH 131
                                       79**********99888654 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   5.2e-05     0.052      24      56 .]     150     177 ..     132     177 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.2e-05
                           DUF4379  24 skkkvwWkCakCgheWeasvsnrtkgsskCpkC 56 
                                       + + v WkC++Cg+ +e++ +  +     Cp C
  gi|298676021|ref|YP_003727771.1| 150 KDETVIWKCRNCGYLHEEMAAPEV-----CPAC 177
                                       36789********99999888888.....8888 PP

>> RNHCP  RNHCP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.4   7.9e-05     0.078      42      82 ..     131     171 ..     119     178 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.9e-05
                             RNHCP  42 raseCkglmepiavevkkkkewvivhrCekCgelkknrvak 82 
                                        + + ++lm+ i+  +  kk+ +++++C++Cg l+++ +a+
  gi|298676021|ref|YP_003727771.1| 131 HEDRFRALMDNINNGQVFKKDETVIWKCRNCGYLHEEMAAP 171
                                       556678999****99999****************9998876 PP

>> COQ7  Ubiquinone biosynthesis protein COQ7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.2    0.0018       1.8      11      68 ..      18      76 ..      10     102 .. 0.83
   2 ?    3.8   0.0     0.046        45      27      58 ..     109     141 ..      96     146 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0018
                              COQ7 11 aGElgAvaiYkgqlavl.akkdpelkpllkemleqEkeHlatfeellkerrvrpslllp 68
                                      aGE  A   Y+  +  + ++ ++++ +l++e++e+EkeH + + + l+  +++ ++ +p
  gi|298676021|ref|YP_003727771.1| 18 AGESQARNRYAYFASQAkKEGYEQIAALFTETAENEKEHGKRLFKFLEGGDTEITATYP 76
                                      99****9999999988867788889**************99988888877777777666 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.046
                              COQ7  27 l.akkdpelkpllkemleqEkeHlatfeellke 58 
                                       + +++ pe+ +++++++  Ek H + f++l+++
  gi|298676021|ref|YP_003727771.1| 109 AeTERFPEIASVMRNIAVAEKGHEDRFRALMDN 141
                                       44567789999*****************99986 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.018        18      25      36 ..     152     163 ..     150     164 .. 0.88
   2 ?    6.1   0.1      0.01        10       3      13 ..     174     184 ..     172     188 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.018
                           TFIIS_C  25 mtvfykCtkCgh 36 
                                       +tv+ kC +Cg+
  gi|298676021|ref|YP_003727771.1| 152 ETVIWKCRNCGY 163
                                       69999*****96 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.01
                           TFIIS_C   3 CpkCgsreayf 13 
                                       Cp C + +ayf
  gi|298676021|ref|YP_003727771.1| 174 CPACAHPQAYF 184
                                       **********8 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   0.00012      0.12      25      63 ..     146     181 ..     142     190 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                                       --EEEEEEEEEEETTT-.-EEES----SB-..TTT-HHH CS
                            MCM_OB  25 evkpklkkavfeckkcgktveveleePrkCeekeCeskd 63 
                                       +v++k +++  +c++cg+ +e e+  P+ C  ++C + +
  gi|298676021|ref|YP_003727771.1| 146 QVFKKDETVIWKCRNCGYLHE-EMAAPEVC--PACAHPQ 181
                                       7888889999*******9666.9*******..99*9544 PP

>> DUF892  Domain of unknown function (DUF892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.5   0.00065      0.65     106     152 ..      20      66 ..       2      75 .. 0.83
   2 ?    2.0   0.0      0.19   1.9e+02     101     155 ..      89     144 ..      70     147 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00065
                                       HHHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            DUF892 106 ehyEiAsYgtLialAeqlgekeaaklLeqtleeekatdekltelaes 152
                                       e     +Y   ++ A++ g++++a+l+++t e+ek+  ++l +++e 
  gi|298676021|ref|YP_003727771.1|  20 ESQARNRYAYFASQAKKEGYEQIAALFTETAENEKEHGKRLFKFLEG 66 
                                       5555568999999**************************99998874 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.19
                                       HHHHHHHHHHH.HHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            DUF892 101 aaqavehyEiA.sYgtLialAeqlgekeaaklLeqtleeekatdekltelaeslvn 155
                                       +a   e+yE +  Y   + +Ae+   +e+a++++++   ek  +++ ++l++++ n
  gi|298676021|ref|YP_003727771.1|  89 SAANGENYENTqMYPEFADIAETERFPEIASVMRNIAVAEKGHEDRFRALMDNINN 144
                                       55666777755269999999999999999999999999999999999999987655 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.4   0.00024      0.24      18      37 ..     157     180 ..     153     181 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00024
                                       E-TTT--EESSS....S-CCCCST CS
                              RecR  18 hCsrCgnlteed....lCaICsdp 37 
                                        C++Cg l ee     +C+ C+ p
  gi|298676021|ref|YP_003727771.1| 157 KCRNCGYLHEEMaapeVCPACAHP 180
                                       7*******888666669*****98 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       5.8   5.8e+03       8      22 ..      16      28 ..      12      28 .. 0.66
   2 ?   11.5   0.3   0.00019      0.19      31      53 ..     143     164 ..     141     165 .. 0.88
   3 ?   -1.3   0.2       1.9   1.9e+03      46      51 ..     173     178 ..     172     181 .. 0.59

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 5.8
                    zinc_ribbon_10  8 vLvGddetsaknrya 22
                                       ++G+ +  a nrya
  gi|298676021|ref|YP_003727771.1| 16 AFAGESQ--ARNRYA 28
                                      5666666..888886 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00019
                    zinc_ribbon_10  31 hnGlapkeeleevkyrCpkCgal 53 
                                       +nG++  ++ e+v ++C +Cg l
  gi|298676021|ref|YP_003727771.1| 143 NNGQV-FKKDETVIWKCRNCGYL 164
                                       79999.889999*********86 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.9
                    zinc_ribbon_10  46 rCpkCg 51 
                                       +Cp C 
  gi|298676021|ref|YP_003727771.1| 173 VCPACA 178
                                       455554 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   2.2    0.0008       0.8       1      22 [.     157     180 ..     157     181 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0008
                     zinc_ribbon_2   1 fCpnCGaelqdnakF..CpyCGtp 22 
                                       +C nCG+ +++ a    Cp C +p
  gi|298676021|ref|YP_003727771.1| 157 KCRNCGYLHEEMAAPevCPACAHP 180
                                       8*********977777*****887 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.2     0.004         4      21      42 ..     146     167 ..     137     172 .. 0.77
   2 ?    3.8   0.6     0.066        66       9      18 ..     172     181 ..     167     191 .] 0.70

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.004
                           DUF2387  21 rmweedeveyrECvsCgftdel 42 
                                       +++++de+ +  C +Cg++ e 
  gi|298676021|ref|YP_003727771.1| 146 QVFKKDETVIWKCRNCGYLHEE 167
                                       69****************8764 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.066
                           DUF2387   9 avCPrCsemD 18 
                                        vCP+C++  
  gi|298676021|ref|YP_003727771.1| 172 EVCPACAHPQ 181
                                       69****9865 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1    0.0013       1.3       1      10 [.     156     165 ..     153     169 .. 0.73
   2 ?    0.7   0.7      0.45   4.5e+02      17      21 ..     174     178 ..     173     179 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0013
                      Rubredoxin_2   1 YvCsqCGfes 10 
                                       + C++CG+ +
  gi|298676021|ref|YP_003727771.1| 156 WKCRNCGYLH 165
                                       5677777765 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.45
                      Rubredoxin_2  17 CpsCg 21 
                                       Cp+C 
  gi|298676021|ref|YP_003727771.1| 174 CPACA 178
                                       ****6 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0         6     6e+03      19      29 ..      34      44 ..      27      45 .. 0.76
   2 ?    9.1   0.5    0.0012       1.2      28      40 ..     152     164 ..     140     172 .. 0.74
   3 ?    0.4   0.5      0.61     6e+02       2       9 ..     171     178 ..     170     182 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 6
                            HalOD2 19 glGeGyrqLGa 29
                                      +  eGy+q+ a
  gi|298676021|ref|YP_003727771.1| 34 AKKEGYEQIAA 44
                                      55679999865 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0012
                            HalOD2  28 GayvWkCtrCGev 40 
                                        + +WkC +CG  
  gi|298676021|ref|YP_003727771.1| 152 ETVIWKCRNCGYL 164
                                       5679*******65 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.61
                            HalOD2   2 PekCseCs 9  
                                       Pe C++C 
  gi|298676021|ref|YP_003727771.1| 171 PEVCPACA 178
                                       999****6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       857  (0.0477997); expected 358.6 (0.02)
Passed bias filter:                      642  (0.0358079); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1252.11
//
Query:       gi|298676022|ref|YP_003727772.1|  [L=183]
Description: archaeoflavoprotein AfpA [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-19   70.1   0.0    3.9e-19   69.0   0.0    1.5  2  Flavoprotein  Flavoprotein


Domain annotation for each model (and alignments):
>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.0   0.0   2.2e-23   3.9e-19       2     106 ..       6     127 ..       5     132 .. 0.88
   2 ?   -2.2   0.0      0.17   3.1e+03     116     136 ..     151     173 ..     146     180 .. 0.70

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 2.2e-23
                                       EEEEEE-SSCGGGCH.HHHHHHHHH.TTEEEEEEESCHHHHCCHHGGS....TCSSHHHHHHCT............. CS
                      Flavoprotein   2 killgiTGsvaaika.lellekLkk.egievqvvltkaAkkfiskeklklaaredpilhielrr............. 63 
                                       +i++giTGs + ik+  + +  +k+ ++ie+ v+l+k+++ +++  +  +++++++  + + ++             
  gi|298676022|ref|YP_003727772.1|   6 RIAWGITGSGDLIKEtYNTMVDIKSkSDIETMVFLSKEGETVMK-WYQMWDSIQKDFPNYKTENgpnspfivgplqv 81 
                                       8**************988888888868*****************.54566666777777777779999999999999 PP

                                       .TESEEEEEEEEHHHHHHHHTT--SSHHHHHH..HTHCCTTEEEEE CS
                      Flavoprotein  64 .wadllviaPasantlakianGiadnlltlil..ratakkpiliaP 106
                                        ++d+lviaPa+ nt+aki++Giad+l+t+++   a+ ++pi+++P
  gi|298676022|ref|YP_003727772.1|  82 gHYDALVIAPATSNTVAKIVYGIADTLVTNTVaqTAKGQTPIYMLP 127
                                       9*******************************44448899****99 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.17
                                       STCHHHHHHH.H.T......... CS
                      Flavoprotein 116 pqtlknlekl.e.egvtvikPse 136
                                       ++++ n ekl + e+++++k se
  gi|298676022|ref|YP_003727772.1| 151 EIDVSNTEKLaQmENIHILKSSE 173
                                       56677777777668888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1095.40
//
Query:       gi|298676023|ref|YP_003727773.1|  [L=287]
Description: hypothetical protein Metev_2150 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00044   20.1   0.0     0.0021   17.9   0.0    1.9  1  DUF429         Protein of unknown function (DUF429)
  ------ inclusion threshold ------
       0.14   12.4   0.6       0.28   11.4   0.6    1.4  1  Baculo_LEF-10  Baculovirus late expression factor 10 (LEF-10)


Domain annotation for each model (and alignments):
>> DUF429  Protein of unknown function (DUF429)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.4e-07    0.0021      41     195 ..      81     261 ..      24     272 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.4e-07
                            DUF429  41 aaeeaavvaiDaPiglpe..............retggRaaDraarkllarrgasvfpvparaalaag.....kglse 98 
                                       a++  +v+++D+P+g+pe               +     ++ + ++ l+++g   +  ++++  +a+      +l +
  gi|298676023|ref|YP_003727773.1|  81 AENINVVFGLDVPFGVPEtimdgydwkyytknFAYMFNSPEGFRNSCLRKTGFKELKRNTDIDKKAPfcvynLRLYK 157
                                       34667899999999999999999999999888455556666666777777777778888887777777888866777 PP

                            DUF429  99 rafg.....llpklrevdelldar...pelrgrvvEvhPeaafvalnggaplakkkktaegraeRrellaraiaell 167
                                       ++f      ++p +re +  + +    ++ + +++E+ P+  + +  ++  + +k kt++ ++ R+++++ +    +
  gi|298676023|ref|YP_003727773.1| 158 QTFYgirdiIYPLIRENQVSIPPMeslNNEKSWLIEICPACTLKQ--KQLYIPYKGKTEKEQKSRMKIVEYF-NSRF 231
                                       777533333777778777555444677999*********988777..577888888899***********55.5556 PP

                            DUF429 168 lesea..kkeklvaadDvlDAvacaltArr 195
                                       + s++  + + + ++ D+lD+v++  + ++
  gi|298676023|ref|YP_003727773.1| 232 NLSPKvkESAIKDKEGDALDSVIATIATYN 261
                                       6666664666677788******99876555 PP

>> Baculo_LEF-10  Baculovirus late expression factor 10 (LEF-10)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.6   3.1e-05      0.28      11      43 ..      41      73 ..      36      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.1e-05
                     Baculo_LEF-10 11 ngiLkDnlfLvdnkYlilnvldqetdelRrlCl 43
                                       g+++Dn  L++n + i + ld+++ + R  C 
  gi|298676023|ref|YP_003727773.1| 41 EGVIQDNNLLINNCWQISDFLDNNQKKDRYSCH 73
                                      699******************999999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2079.28
//
Query:       gi|298676024|ref|YP_003727774.1|  [L=367]
Description: Myo-inositol-1-phosphate synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.6e-32  110.5   0.5    1.5e-31  108.8   0.0    2.1  3  Inos-1-P_synth  Myo-inositol-1-phosphate synthase
  ------ inclusion threshold ------
      0.012   15.0   0.0      0.032   13.6   0.0    1.8  2  NAD_binding_5   Myo-inositol-1-phosphate synthase
      0.052   13.8   0.0       0.11   12.7   0.0    1.5  1  DUF1611_N       Domain of unknown function (DUF1611_N) Rossma


Domain annotation for each model (and alignments):
>> Inos-1-P_synth  Myo-inositol-1-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.75   4.5e+03      73     101 ..      23      50 ..      18      53 .. 0.74
   2 ?   -2.5   0.0         1   6.3e+03      44      76 ..     117     143 ..     103     154 .. 0.66
   3 !  108.8   0.0   2.6e-35   1.5e-31       1     109 []     199     307 ..     199     307 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.75
                                       EE-GGGTTEEEEEEEEEEEEGGGEEEEEE CS
                    Inos-1-P_synth  73 kYvpylgDsKvaldeieseiflggkntie 101
                                       +Y++  +D+K+a+  ++ ei +  +  ie
  gi|298676024|ref|YP_003727774.1|  23 EYYK-NNDDKEAIGLMHWEIGGYKPSDIE 50 
                                       5555.478999999999998777666665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1
                                       HHHHHHHHHHHHHHHSS--EEE....EEEEE-G CS
                    Inos-1-P_synth  44 ksKkisKssvvddivkanellyvdhevvikYvp 76 
                                       ++K+  K  vv+++ ++        e+ ++Y+p
  gi|298676024|ref|YP_003727774.1| 117 NEKELDKDGVVKALKDSGA------EMLVNYLP 143
                                       4677777777777654422......34555555 PP

  == domain 3  score: 108.8 bits;  conditional E-value: 2.6e-35
                                       SHHHHHHHHHHHHHHTT-EEEEEEEEEEE-HHHHHHTTSHHHHHHHHHHHHHHHHHHHSS--EEE....EEE...EE CS
                    Inos-1-P_synth   1 GqTklksvLaellverglkvksivslNilGnnDgknlseeerfksKkisKssvvddivkanellyvdhevvi...kY 74 
                                       G+T+++++L +l+++rg+k++++++lN +Gn+D++n+ +++r++sKk+sK+++v++++++ +l+  d ++++   +Y
  gi|298676024|ref|YP_003727774.1| 199 GATIVHRTLSHLFQNRGVKIDRTYQLNTGGNTDFLNMLNRDRLNSKKKSKTEAVQSVLDE-PLD--DDNIHVgpsDY 272
                                       9*********************************************************98.664..67899999*** PP

                                       -GGGTTEEEEEEEEEEEEGGGEEEEEEEEEEEEH. CS
                    Inos-1-P_synth  75 vpylgDsKvaldeieseiflggkntielkleceDS 109
                                       v + +D+Kv++ ++e+++f+++++++e++l++eDS
  gi|298676024|ref|YP_003727774.1| 273 VAWQKDNKVCFLRMEGRLFGDVPMNLEMRLSVEDS 307
                                       **********************************9 PP

>> NAD_binding_5  Myo-inositol-1-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.24   1.4e+03      14      60 ..      16      31 ..       5      70 .. 0.51
   2 ?   13.6   0.0   5.3e-06     0.032     207     258 ..     151     203 ..     129     336 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.24
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     NAD_binding_5 14 tTlvagvlankkglswetkeglkkanylGsvtqsstirlGkdeeege 60
                                      + l+ g+   k++                                 +
  gi|298676024|ref|YP_003727774.1| 16 SSLIQGIEYYKNNDD-------------------------------K 31
                                      555555544444332...............................2 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 5.3e-06
                                       xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     NAD_binding_5 207 tiyavAailegvpyingsPqntl.vpglvelAekkgvfiaGdDfKtlLAaPli 258
                                         ya  a+++gv++in+ P      p   e  ++k+++i+GdD+K  + a ++
  gi|298676024|ref|YP_003727774.1| 151 RFYAECALEAGVAFINSMPVFIAsNPEWSERFNEKNIPIIGDDIKAQIGATIV 203
                                       57999**************9998899999999*************95554444 PP

>> DUF1611_N  Domain of unknown function (DUF1611_N) Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.9e-05      0.11      47      89 ..     148     190 ..     115     192 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.9e-05
                         DUF1611_N  47 eswreavkeAleaGldvvsGlHerLsddpelaalakkkgvkii 89 
                                       e+ r +++ AleaG+  ++++  +++++pe+++  ++k++ ii
  gi|298676024|ref|YP_003727774.1| 148 EATRFYAECALEAGVAFINSMPVFIASNPEWSERFNEKNIPII 190
                                       567789999****************************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2643.08
//
Query:       gi|298676025|ref|YP_003727775.1|  [L=163]
Description: rubrerythrin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-19   70.6   2.5    2.1e-19   70.3   2.5    1.1  1  Rubrerythrin  Rubrerythrin
    1.6e-08   34.8   0.1    4.7e-08   33.3   0.1    1.7  1  Ferritin_2    Ferritin-like domain
      2e-05   24.9   0.8      0.082   13.3   0.2    2.3  2  DUF2383       Domain of unknown function (DUF2383)
  ------ inclusion threshold ------
       0.26   11.2   2.9        8.2    6.4   0.5    2.5  2  DUF1657       Protein of unknown function (DUF1657)
       0.31   11.5   2.5        1.1    9.8   0.1    2.5  3  DUF2533       Protein of unknown function (DUF2533)
       0.34   11.4   4.6       0.15   12.5   1.8    1.8  2  TBCC_N        Tubulin-specific chaperone C N-terminal domain
          3    8.4   4.8         14    6.3   2.1    2.8  3  YtxH          YtxH-like protein


Domain annotation for each model (and alignments):
>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.3   2.5   8.1e-23   2.1e-19       1     133 [.      20     149 ..      20     153 .. 0.93

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 8.1e-23
                                       HHHHHHHHHHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------T CS
                      Rubrerythrin   1 eiLekAiagEssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpk 77 
                                       e +++Ai+ E ++r++Y e a+++k  +p ++ ++e+lA+eE++H++ l ++ ++ + +  +e ++    ++ +  +
  gi|298676025|ref|YP_003727775.1|  20 EAIDMAISLEQQGREFYLEKASQIK--NPGVKDMYEYLADEEKKHEQYLQQFKKDKQVSPVVEEEKAPDFKVSFSSE 94 
                                       67899********************..****************************9999998888888888889999 PP

                                       TGGHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  78 flttaknLeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerl 133
                                       f  + + +  ++ ga   e++++ fy++lae++g+ e k++fk++a  E++H+e+ 
  gi|298676025|ref|YP_003727775.1|  95 FDDRLDEIG-VLLGALRLERKSEDFYKQLAEMTGDMEQKQFFKNIASVERGHYELI 149
                                       987777777.*******************************************986 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.1   1.8e-11   4.7e-08       6     133 ..      22     152 ..      18     155 .. 0.84

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.8e-11
                        Ferritin_2   6 LnfAlnlEyleaafYtaalegaslddkalldaevrevaeeiakheeaHveflkaaleGaaav.......akptfdf. 74 
                                       + +A+ lE++  +fY + ++       +  ++ v++++e +a++e++H ++l++  + ++ v       ++p   f 
  gi|298676025|ref|YP_003727775.1|  22 IDMAISLEQQGREFYLEKAS-------QIKNPGVKDMYEYLADEEKKHEQYLQQFKK-DKQVspvveeeKAPD--Fk 88 
                                       678**************998.......67899***********************86.444422256443333..34 PP

                        Ferritin_2  75 .....afdpfadeksflalaavlEdvgvsAYlgaapllsnkelltaaasIlsvEArHaavirtl 133
                                            +fd+  de  +l +a  lE+   + Y++ a++  + e ++   +I+svE  H  +i+ +
  gi|298676025|ref|YP_003727775.1|  89 vsfssEFDDRLDEIGVLLGALRLERKSEDFYKQLAEMTGDMEQKQFFKNIASVERGHYELIDGI 152
                                       466778888888999******************************************8877665 PP

>> DUF2383  Domain of unknown function (DUF2383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.2   3.2e-05     0.082       6      55 ..      22      71 ..      17      94 .. 0.87
   2 !   10.3   0.0   0.00026      0.66      10      48 ..     109     147 ..     100     158 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.2e-05
                                      HHHHHHHHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           DUF2383  6 LndLietlkdgeegykeaaekvkdpqlktlleriaeereeaaeeLqseir 55
                                      +   i  +  g+e+y e a ++k+p +k+++e  a+e +++ + Lq++ +
  gi|298676025|ref|YP_003727775.1| 22 IDMAISLEQQGREFYLEKASQIKNPGVKDMYEYLADEEKKHEQYLQQFKK 71
                                      5556788899*********************************9999755 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00026
                                       HHHHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHH CS
                           DUF2383  10 ietlkdgeegykeaaekvkdpqlktlleriaeereeaae 48 
                                       ++ ++ +e++yk+ ae   d + k+++++ia   + + e
  gi|298676025|ref|YP_003727775.1| 109 LRLERKSEDFYKQLAEMTGDMEQKQFFKNIASVERGHYE 147
                                       677899************************998776655 PP

>> DUF1657  Protein of unknown function (DUF1657)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.5    0.0032       8.2      23      47 ..      44      68 ..      40      68 .. 0.88
   2 ?    4.3   0.1     0.015        38      15      36 ..     119     140 ..     118     145 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0032
                           DUF1657 23 edeeAKqmYeqaaeqleeviqdLep 47
                                      +++  K mYe +a++ +++ q L++
  gi|298676025|ref|YP_003727775.1| 44 KNPGVKDMYEYLADEEKKHEQYLQQ 68
                                      79999**************999985 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.015
                           DUF1657  15 LetFaLqTedeeAKqmYeqaae 36 
                                       ++++a  T d e Kq ++++a+
  gi|298676025|ref|YP_003727775.1| 119 YKQLAEMTGDMEQKQFFKNIAS 140
                                       6889999***********9986 PP

>> DUF2533  Protein of unknown function (DUF2533)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00042       1.1      28      53 ..      18      43 ..       4      46 .. 0.86
   2 ?    0.9   0.1      0.25   6.4e+02       5      23 ..      53      71 ..      49      82 .. 0.80
   3 ?   -2.0   0.0         2   5.1e+03      13      34 ..     130     151 ..     113     157 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00042
                           DUF2533 28 REaaIeeavelckkgkpfsvekiNev 53
                                       E+aI++a++l ++g++f +ek  ++
  gi|298676025|ref|YP_003727775.1| 18 IEEAIDMAISLEQQGREFYLEKASQI 43
                                      599****************9998776 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.25
                           DUF2533  5 kaitahvkkqnaalkqfle 23
                                      + ++++ kk+++ l+qf +
  gi|298676025|ref|YP_003727775.1| 53 EYLADEEKKHEQYLQQFKK 71
                                      5678889999999999965 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2
                           DUF2533  13 kqnaalkqfleLeqkREaaIee 34 
                                       +q++  k+++++e    ++I+ 
  gi|298676025|ref|YP_003727775.1| 130 EQKQFFKNIASVERGHYELIDG 151
                                       4566666666666666666665 PP

>> TBCC_N  Tubulin-specific chaperone C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       1.1   2.9e+03      65      77 ..       5      17 ..       2      35 .. 0.63
   2 ?   12.5   1.8   5.9e-05      0.15       3      74 ..      55     131 ..      53     142 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.1
                            TBCC_N 65 ldeitaeiqeLqk 77
                                      ldei+++++++++
  gi|298676025|ref|YP_003727775.1|  5 LDEINEDLNNIES 17
                                      5555555555544 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 5.9e-05
                            TBCC_N   3 LekReqerqeqlekrkeereseaveeekvds.....FlkaFteekaaieellesveesadksklkqkldeitaeiqe 74 
                                       L+  e++ +++l++ k++++ + v ee+ +      F+++F+++ ++i  ll +++ + ++++  ++l+e+t ++++
  gi|298676025|ref|YP_003727775.1|  55 LADEEKKHEQYLQQFKKDKQVSPVVEEEKAPdfkvsFSSEFDDRLDEIGVLLGALRLERKSEDFYKQLAEMTGDMEQ 131
                                       5666677777777777777777766554443477779*******************888888888999998887775 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.57   1.5e+03      34      60 ..      18      44 ..       6      46 .. 0.60
   2 ?    6.3   2.1    0.0055        14      28      73 ..      49     101 ..      48     132 .. 0.92
   3 ?    1.0   0.1      0.26   6.5e+02      30      51 ..     111     132 ..     102     157 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.57
                              YtxH 34 addlkekakelleeakekakekaedlk 60
                                       +++ + a +l ++ +e   eka+++k
  gi|298676025|ref|YP_003727775.1| 18 IEEAIDMAISLEQQGREFYLEKASQIK 44
                                      455555555555555555577777776 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0055
                              YtxH  28 kdlkekaddlkekakelleeakeka.......kekaedlkekvkekadelkek 73 
                                       kd+ e++ d  +k +++l+++k+         +eka d+k ++++++d+  ++
  gi|298676025|ref|YP_003727775.1|  49 KDMYEYLADEEKKHEQYLQQFKKDKqvspvveEEKAPDFKVSFSSEFDDRLDE 101
                                       57778888889999999999999999********************9997765 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.26
                              YtxH  30 lkekaddlkekakelleeakek 51 
                                       l +k +d+ +++ e++ ++++k
  gi|298676025|ref|YP_003727775.1| 111 LERKSEDFYKQLAEMTGDMEQK 132
                                       4556666666666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1585  (0.0884043); expected 358.6 (0.02)
Passed bias filter:                      749  (0.0417759); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 977.71
//
Query:       gi|298676026|ref|YP_003727776.1|  [L=401]
Description: flavodoxin/nitric oxide synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.7e-10   39.6   0.0    1.2e-09   38.5   0.0    1.6  1  Flavodoxin_1   Flavodoxin
    3.6e-06   27.1   0.0    7.1e-06   26.2   0.0    1.6  1  Lactamase_B    Metallo-beta-lactamase superfamily
     0.0059   16.2   0.0     0.0094   15.5   0.0    1.3  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.072   12.8   0.2       0.86    9.3   0.2    2.3  1  FMN_red        NADPH-dependent FMN reductase


Domain annotation for each model (and alignments):
>> Flavodoxin_1  Flavodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.0   2.7e-13   1.2e-09       1     137 [.     259     385 ..     259     391 .. 0.72

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 2.7e-13
                                       EEEETSSSHHHHHHHHHHHHHHHTTTEEEEEEEEGTTSC..GGGGGTHSEEEEEEEEETTTBEEGGGHHHHHHHHHH CS
                      Flavodoxin_1   1 ilYgSetGnteklAkqlaeelgehgfnadvvslsdydes..lseieeealllvvtsTfgnGdppengesffqdllel 75 
                                       ++Y+++ G+te +Ak++ e+++++g+++++++l++ + s  ++ei +  +++++  T +nG +       +++ +  
  gi|298676026|ref|YP_003727776.1| 259 VIYDTMWGSTEIMAKEVLEGIRSAGVETELLHLRKNNLStiIKEILDAPVIALGSTTINNGMFH------SVAGFLT 329
                                       89***********************************555555555555555555555555444......2333333 PP

                                       HCHHGCCSTTTTEEEEEEEEECTTSSSTTHHHHHHHHHHHHTTCEEESSSEEEETTST.HGHH CS
                      Flavodoxin_1  76 kgdeledgdlsgvrfavfglGdsayenFcaagkkldekleelGaerllkllegdednq.egqe 137
                                           l+  + +g++  vf  G++++ +    +++ ++ l + G e l k+l+++  ++ e+++
  gi|298676026|ref|YP_003727776.1| 330 H---LKGLKPKGKKAVVF--GSYGWGG--GGVQRAEDELDKGGIELLEKGLKVKFRPDsEDLK 385
                                       3...45544566666555..5556666..66***********************999766655 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   1.6e-09   7.1e-06       4     163 ..      36     203 ..      33     244 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 1.6e-09
                                       CSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHH CS
                       Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeap 80 
                                       +  nsyli  d++  LiDt  s+ +++++ +  ++ ++p ++d+v+  H   DH + l  ++e ++ ++++ ++ ++
  gi|298676026|ref|YP_003727776.1|  36 GTYNSYLI-VDDKIALIDTVKSQFTEDFV-NSIRQIVDPSEIDYVVANHVEMDHSSSLSRIMELAPDAKIYTSKRGK 110
                                       5679****.5*******************.599999**********************************9999999 PP

                                       CCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHC CS
                       Lactamase_B  81 alfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallaget 157
                                        ++  + +          +g    + +v+  ++++ +g   +  +    +h +++++ ++++ k+lf+ Da+ ++  
  gi|298676026|ref|YP_003727776.1| 111 TGLCAYYKE---------EGCENWDFEVVGTGDELSLGNKTLMFIEAVMLHWPDSMHTYLKENKILFSNDAFGQHIA 178
                                       998777754.........34566677799999999999999999999************************997776 PP

                                       CCCCC.................... CS
                       Lactamase_B 158 gridl...................t 163
                                        + ++                    
  gi|298676026|ref|YP_003727776.1| 179 TSQRFdyevddviddaaeyyanilM 203
                                       6666655555555555553333330 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.1e-06    0.0094       4     116 ..      50     154 ..      49     182 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.1e-06
                                       EES--TT.HHHH..HTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHH CS
                     Lactamase_B_2   4 LiDagpd.lrqq..alralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvyl 77 
                                       LiD++ + +      ++ +    +  ++++id V+  h ++DH   l  + el+p+ +++y +k+    l+a   y 
  gi|298676026|ref|YP_003727776.1|  50 LIDTVKSqF-TEdfVNSIR----QIVDPSEIDYVVANHVEMDHSSSLSRIMELAPD-AKIYTSKRGKTGLCAY--YK 118
                                       677777732.222222222....4557899**********************9995.89****9999999999..45 PP

                                       HCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--C CS
                     Lactamase_B_2  78 aleeepavnvheldwgesfelgdggleitatparhksgr 116
                                         + e + +++ + +g++++lg+   ++ +++a   + +
  gi|298676026|ref|YP_003727776.1| 119 EEGCE-NWDFEVVGTGDELSLGNK--TLMFIEAVMLHWP 154
                                       55555.678888888999888843..5777777666655 PP

>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.2   0.00019      0.86      14      44 ..     266     296 ..     255     366 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00019
                                       -HHHHHHHHHHCCT-T.T-CEEEEETTTS.- CS
                           FMN_red  14 sntrklaewaaealkeagaevelidladlil 44 
                                       ++t+ +a++++e ++ ag+e+el++l++ +l
  gi|298676026|ref|YP_003727776.1| 266 GSTEIMAKEVLEGIRSAGVETELLHLRKNNL 296
                                       6899*********************998654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 2709.78
//
Query:       gi|298676027|ref|YP_003727777.1|  [L=113]
Description: hypothetical protein Metev_2154 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.2e-34  116.0   3.8    9.3e-34  115.8   3.8    1.0  1  CGGC      CGGC domain
  ------ inclusion threshold ------
          1   10.0   7.1        5.8    7.6   0.1    3.3  3  zf-C2H2   Zinc finger, C2H2 type


Domain annotation for each model (and alignments):
>> CGGC  CGGC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.8   3.8     1e-37   9.3e-34       1     106 []       8     112 ..       8     112 .. 0.98

  Alignments for each domain:
  == domain 1  score: 115.8 bits;  conditional E-value: 1e-37
                              CGGC   1 kiaiirCekvedvCpgvkClkalkerkgaFeeyeeevelvgfvtCggCpgkkvveklkelkkegvdvihlssCiktk 77 
                                       kia++rCe+v++vC+g++C+ka+++r+  F++y++++e+++f+tCggC+g++v + +k+lkk+gvd++hlssC+ + 
  gi|298676027|ref|YP_003727777.1|   8 KIAVVRCETVSEVCSGIGCFKAFNNRDVYFRDYDSSAEMIAFFTCGGCSGRRVYRLVKSLKKHGVDIVHLSSCMMNM 84 
                                       8************************************************************************8566 PP

                              CGGC  78 kakkeCpeieeikeaieeklgievvegth 106
                                       ++ +eCp++e+ik++i+++ gi+++egth
  gi|298676027|ref|YP_003727777.1|  85 DNCPECPHVESIKKTIKDN-GIDILEGTH 112
                                       899****************.********9 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.2      0.01        92       2      14 ..      20      34 ..      20      38 .. 0.85
   2 ?    7.6   0.1   0.00065       5.8       1      19 [.      50      70 ..      50      72 .. 0.95
   3 ?    1.2   0.2     0.068   6.1e+02       3       8 ..      87      92 ..      85      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.01
                                      EET..TTTEEESSHH CS
                           zf-C2H2  2 kCp..dCgksFkrks 14
                                      +C+  +C k F++++
  gi|298676027|ref|YP_003727777.1| 20 VCSgiGCFKAFNNRD 34
                                      599999*****9976 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00065
                                      EEETTTT..EEESSHHHHHHH CS
                           zf-C2H2  1 ykCpdCg..ksFkrksnLkrH 19
                                      ++C++C+  ++++   +Lk+H
  gi|298676027|ref|YP_003727777.1| 50 FTCGGCSgrRVYRLVKSLKKH 70
                                      89***********99999999 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.068
                                      ETTTTE CS
                           zf-C2H2  3 CpdCgk 8 
                                      Cp+C+ 
  gi|298676027|ref|YP_003727777.1| 87 CPECPH 92
                                      ****84 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 687.55
//
Query:       gi|298676028|ref|YP_003727778.1|  [L=122]
Description: 4Fe-4S ferredoxin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-09   37.9   5.7    1.4e-09   37.9   5.7    2.3  3  Fer4_21   4Fe-4S dicluster domain
    1.5e-09   37.2  17.1    1.7e-05   24.4   4.8    3.1  3  Fer4      4Fe-4S binding domain
    3.2e-09   36.5  15.7    2.1e-06   27.6   3.8    3.3  4  Fer4_6    4Fe-4S binding domain
    1.1e-07   32.4  11.9     0.0014   19.1   0.9    2.7  2  Fer4_7    4Fe-4S dicluster domain
    1.2e-06   29.4  10.1      0.001   20.0   0.3    2.7  3  Fer4_16   4Fe-4S double cluster binding domain
    4.2e-06   26.8  18.3    4.7e-05   23.5   7.1    3.0  3  Fer4_9    4Fe-4S dicluster domain
    2.5e-05   24.1  17.7    5.4e-05   23.0   2.7    3.5  3  Fer4_2    4Fe-4S binding domain
     0.0001   22.3  16.2    0.00014   21.9   8.6    2.9  2  Fer4_10   4Fe-4S dicluster domain
    0.00043   21.0  11.1     0.0063   17.2   1.3    2.7  2  Fer4_15   4Fe-4S single cluster domain
     0.0063   17.0  10.5       0.26   11.8   0.8    2.7  3  Fer4_17   4Fe-4S dicluster domain
     0.0096   16.0   2.2         11    6.1   0.1    3.3  3  Fer4_19   Divergent 4Fe-4S mono-cluster
  ------ inclusion threshold ------
       0.16   12.9   1.9       0.16   12.9   1.9    2.7  2  Fer4_22   4Fe-4S dicluster domain
        1.3    9.6  18.5    1.1e+03    0.2  18.5    3.2  1  Fer4_8    4Fe-4S dicluster domain
        1.6    9.4  18.8       0.38   11.4   4.3    3.6  4  Fer4_4    4Fe-4S binding domain
        8.7    7.5  21.6        2.2    9.4   1.5    3.2  3  Fer4_3    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   5.7   1.2e-12   1.4e-09       2      58 ..       8      60 ..       7      61 .. 0.84
   2 ?    0.3   0.1      0.65   7.7e+02      33      47 ..      76      90 ..      63      93 .. 0.64
   3 ?   -2.4   0.1       4.7   5.6e+03      11      14 ..     112     115 ..     107     117 .. 0.72

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 1.2e-12
                           Fer4_21  2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58
                                      +ide+kC gCgkC++ C ++++q   + + +   v e+ C G   C+ vCP+ ++++
  gi|298676028|ref|YP_003727778.1|  8 KIDEEKCNGCGKCVTPCAEGAIQ---FVNGRAKVVSEELCDGMGFCVGVCPT-GALT 60
                                      69****************86555...5555666788***************6.7765 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.65
                           Fer4_21 33 vlkvvedeCvGCnlC 47
                                        +  +d+ + C +C
  gi|298676028|ref|YP_003727778.1| 76 SQEKNTDSTISCFIC 90
                                      445567777777777 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 4.7
                           Fer4_21  11 CgkC 14 
                                       C++C
  gi|298676028|ref|YP_003727778.1| 112 CTRC 115
                                       6666 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   4.8   1.5e-08   1.7e-05       1      23 [.       7      29 ..       7      30 .. 0.90
   2 !   21.4   0.3   1.3e-07   0.00016       2      24 .]      38      60 ..      37      60 .. 0.93
   3 ?   -1.7   0.4       2.5     3e+03       8      11 ..     112     115 ..     111     116 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.5e-08
                                      EEEETTTSSS-THHHHHSTTTEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAI 23
                                      v+ideekC gCG+Cv  C  gAI
  gi|298676028|ref|YP_003727778.1|  7 VKIDEEKCNGCGKCVTPCAEGAI 29
                                      68****************88888 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 1.3e-07
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                      v+ ee+C g G Cv vCP+gA+t
  gi|298676028|ref|YP_003727778.1| 38 VVSEELCDGMGFCVGVCPTGALT 60
                                      789******************96 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.5
                                       SSS- CS
                              Fer4   8 CigC 11 
                                       C++C
  gi|298676028|ref|YP_003727778.1| 112 CTRC 115
                                       8988 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   3.8   1.7e-09   2.1e-06       1      24 []       6      29 ..       6      29 .. 0.96
   2 !   16.7   0.1   4.8e-06    0.0057       3      24 .]      38      59 ..      37      59 .. 0.93
   3 ?   -2.5   0.0       5.6   6.7e+03       2       8 ..      67      73 ..      66      73 .. 0.82
   4 ?   -1.9   0.4       3.5   4.1e+03      12      15 ..     112     115 ..     111     116 .. 0.71

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.7e-09
                            Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                      +v id++kC+gCg+Cv+ C egai
  gi|298676028|ref|YP_003727778.1|  6 IVKIDEEKCNGCGKCVTPCAEGAI 29
                                      699********************8 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 4.8e-06
                            Fer4_6  3 eidpdkCigCgdCvrvCPegai 24
                                      ++ +++C+g g Cv vCP+ga+
  gi|298676028|ref|YP_003727778.1| 38 VVSEELCDGMGFCVGVCPTGAL 59
                                      5789****************97 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 5.6
                            Fer4_6  2 veidpdk 8 
                                      ve++++k
  gi|298676028|ref|YP_003727778.1| 67 VEFNQEK 73
                                      89**986 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 3.5
                            Fer4_6  12 CgdC 15 
                                       C +C
  gi|298676028|ref|YP_003727778.1| 112 CTRC 115
                                       7777 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.9   1.2e-06    0.0014      31      52 .]       7      28 ..       2      39 .. 0.78
   2 !   17.4   4.2   4.3e-06    0.0052       2      42 ..      44      91 ..      43     118 .. 0.51

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.2e-06
                            Fer4_7 31 veidpekClgCgaCvavCPtga 52
                                      v+id+ekC gCg+Cv+ C  ga
  gi|298676028|ref|YP_003727778.1|  7 VKIDEEKCNGCGKCVTPCAEGA 28
                                      6778888888888888887665 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 4.3e-06
                            Fer4_7  2 CigCgaCvaaCpvkaieldeeenek................gtekveidpekClgCg 42
                                      C g g+Cv +Cp++a++++++e  +                          +C  Cg
  gi|298676028|ref|YP_003727778.1| 44 CDGMGFCVGVCPTGALTIEQRETVEfnqekaesqekntdstI---------SCFICG 91
                                      9999*************9975333332222322222222220.........333333 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   1.7   4.3e-05     0.051       1      20 [.      13      32 ..      13      42 .. 0.84
   2 !   20.0   0.3   8.4e-07     0.001       2      43 ..      44      85 ..      43      99 .. 0.81
   3 ?   -1.5   0.0       4.3   5.2e+03       5       8 ..     112     115 ..     102     117 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.3e-05
                           Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                      +C +CgkC+  C ++ai+  
  gi|298676028|ref|YP_003727778.1| 13 KCNGCGKCVTPCAEGAIQFV 32
                                      5****************976 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 8.4e-07
                           Fer4_16  2 CgtCgkCaevCPtnaikekkekeiearecisyntaekkdlae 43
                                      C + g C+ vCPt+a++ ++++++e +++++++++++ d ++
  gi|298676028|ref|YP_003727778.1| 44 CDGMGFCVGVCPTGALTIEQRETVEFNQEKAESQEKNTDSTI 85
                                      888889***********9999999999999987777666555 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 4.3
                           Fer4_16   5 CgkC 8  
                                       C++C
  gi|298676028|ref|YP_003727778.1| 112 CTRC 115
                                       5555 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   3.4   1.4e-05     0.017      31      51 .]       9      29 ..       3      29 .. 0.77
   2 !   23.5   7.1     4e-08   4.7e-05       1      50 [.      13      58 ..      13      59 .. 0.94
   3 !    6.6   6.9    0.0075       8.9       2      41 ..      44      92 ..      42     117 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.4e-05
                            Fer4_9 31 aseeaCigCgaCveaCpkgai 51
                                       +ee+C gCg+Cv  C +gai
  gi|298676028|ref|YP_003727778.1|  9 IDEEKCNGCGKCVTPCAEGAI 29
                                      34469***********99987 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 4e-08
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50
                                      kC+gCg+Cv+ C  g+++  +++ k+  ++     C g g Cv +Cp+ga
  gi|298676028|ref|YP_003727778.1| 13 KCNGCGKCVTPCAEGAIQFVNGRAKVVSEE----LCDGMGFCVGVCPTGA 58
                                      7************************99876....6*************97 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0075
                            Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraase.........eaCigCga 41
                                      C g g Cv +Cp+g+ + ++ e+   ++++ e          +C+ Cg+
  gi|298676028|ref|YP_003727778.1| 44 CDGMGFCVGVCPTGALTIEQRETVEFNQEKAEsqekntdstISCFICGQ 92
                                      555566*********9888888777776666678999999966766665 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   2.7   4.5e-08   5.4e-05       3      20 ..       7      24 ..       5      26 .. 0.92
   2 !    9.7   0.3   0.00077      0.92       5      22 .]      39      56 ..      35      56 .. 0.82
   3 ?    1.6   0.1       0.3   3.6e+02       9      14 ..     111     116 ..     104     117 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 4.5e-08
                            Fer4_2  3 vvvdtdrCigCgaCvsaC 20
                                      v++d+++C+gCg+Cv+ C
  gi|298676028|ref|YP_003727778.1|  7 VKIDEEKCNGCGKCVTPC 24
                                      789*************99 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00077
                            Fer4_2  5 vdtdrCigCgaCvsaCPa 22
                                      v ++ C g g Cv +CP+
  gi|298676028|ref|YP_003727778.1| 39 VSEELCDGMGFCVGVCPT 56
                                      5678898889*******7 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.3
                            Fer4_2   9 rCigCg 14 
                                        C++C 
  gi|298676028|ref|YP_003727778.1| 111 VCTRCL 116
                                       699995 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   8.6   1.1e-07   0.00014       2      56 .]       7      55 ..       6      55 .. 0.77
   2 !    9.7   5.0   0.00075       0.9       3      51 ..      38      90 ..      36     117 .. 0.65

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.1e-07
                           Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      v+id+++C +CgkCv+ C a     ga+++ ++ ++v    e C+g g Cv +CP
  gi|298676028|ref|YP_003727778.1|  7 VKIDEEKCNGCGKCVTPC-A----EGAIQFVNGRAKVV-SEELCDGMGFCVGVCP 55
                                      78****************.5....45555444444433.3677***********9 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00075
                           Fer4_10  3 vidddtCirCgkCvkaCPadl.......tsvgakgeaseeeavrkkvekCtgcgaC 51
                                      v+ ++ C + g Cv +CP+ +       t   ++  +++ e ++k+ ++ + c+ C
  gi|298676028|ref|YP_003727778.1| 38 VVSEELCDGMGFCVGVCPTGAltieqreT---VEFNQEKAESQEKNTDSTISCFIC 90
                                      566789*************9999996641...333333333333333333333333 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   1.3   5.3e-06    0.0063       1      20 [.       7      26 ..       7      42 .. 0.73
   2 !   10.6   0.9    0.0006      0.72       3      20 ..      39      56 ..      38      85 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.3e-06
                           Fer4_15  1 VvvDrdaCigcglCvaeape 20
                                      V++D+++C gcg Cv+ + e
  gi|298676028|ref|YP_003727778.1|  7 VKIDEEKCNGCGKCVTPCAE 26
                                      89**************9954 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0006
                           Fer4_15  3 vDrdaCigcglCvaeape 20
                                      v +++C+g+g Cv ++p+
  gi|298676028|ref|YP_003727778.1| 39 VSEELCDGMGFCVGVCPT 56
                                      55799***********85 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.8   0.00022      0.26      44      58 ..      12      26 ..       3      37 .. 0.82
   2 !   11.3   0.7   0.00032      0.38       2      51 ..      44      92 ..      43      96 .. 0.70
   3 ?   -1.9   0.1       4.3   5.1e+03       2      52 ..     112     115 ..     105     118 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00022
                           Fer4_17 44 slCieCgeCerkCPq 58
                                      ++C++Cg+C++ C +
  gi|298676028|ref|YP_003727778.1| 12 EKCNGCGKCVTPCAE 26
                                      578888888888865 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00032
                           Fer4_17  2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaeke.ekaslCieCge 51
                                      C + g+C+ +Cp+++ + ++++++  +   ++ e +ek+ +   +C  Cg+
  gi|298676028|ref|YP_003727778.1| 44 CDGMGFCVGVCPTGALTIEQRETVEFN--QEKAESQEKNtDSTISCFICGQ 92
                                      99999*********9988766654333..3444444444257788888887 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 4.3
                           Fer4_17   2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeC 52 
                                       C+                                               +C
  gi|298676028|ref|YP_003727778.1| 112 CT-----------------------------------------------RC 115
                                       22...............................................22 PP

>> Fer4_19  Divergent 4Fe-4S mono-cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.1    0.0096        11      33      62 ..       3      32 ..       1      34 [. 0.80
   2 ?    3.6   0.1     0.057        68      11      22 ..      40      51 ..      37      53 .. 0.87
   3 ?    5.6   0.2     0.014        17      51      61 ..      51      61 ..      50      64 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0096
                           Fer4_19 33 rkpwikpdeasteeiievverCPSGALsyv 62
                                      ++ ++k de++ +   + v  C  GA+++v
  gi|298676028|ref|YP_003727778.1|  3 KRNIVKIDEEKCNGCGKCVTPCAEGAIQFV 32
                                      567888899999999999999999998887 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.057
                           Fer4_19 11 nrelCihsgnCv 22
                                      ++elC++ g+Cv
  gi|298676028|ref|YP_003727778.1| 40 SEELCDGMGFCV 51
                                      679********9 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.014
                           Fer4_19 51 verCPSGALsy 61
                                      v  CP GAL++
  gi|298676028|ref|YP_003727778.1| 51 VGVCPTGALTI 61
                                      678******98 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.9   0.00013      0.16      75      94 ..       7      26 ..       1      28 [. 0.83
   2 ?    6.2   1.9     0.015        18       2      42 ..      44      89 ..      43     104 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00013
                           Fer4_22 75 ekfgesgCvGCgRCieacpv 94
                                       k++e++C GCg+C++ c +
  gi|298676028|ref|YP_003727778.1|  7 VKIDEEKCNGCGKCVTPCAE 26
                                      567999************86 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.015
                           Fer4_22  2 ClsCgaCtlvCptCsCfdvedet.....keeskegervrvwdsCll 42
                                      C + g C  vCpt   +  + et     ++++++ + +  + sC++
  gi|298676028|ref|YP_003727778.1| 44 CDGMGFCVGVCPTGALTIEQRETvefnqEKAESQEKNTDSTISCFI 89
                                      667789*******876655555567643222233333444556665 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2  18.5      0.91   1.1e+03       3      54 ..      12     115 ..      10     116 .. 0.47

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.91
                            Fer4_8   3 ekCieCgaCqsaCp..............vlrr....................tkkhlldargeaaedvqeeqvlee. 44 
                                       ekC++Cg C + C               +  +                    ++++  + ++e+ae    +q   e 
  gi|298676028|ref|YP_003727778.1|  12 EKCNGCGKCVTPCAegaiqfvngrakvvS--EelcdgmgfcvgvcptgaltiEQRETVEFNQEKAE----SQ---Ek 79 
                                       69********9995555554444444330..13333333333333322222211111111111111....11...11 PP

                            Fer4_8  45 ..........................eealwsCttc 54 
                                                                  e+lw Ct c
  gi|298676028|ref|YP_003727778.1|  80 ntdstiscficgqgetsgylmplrhdMESLWVCTRC 115
                                       222344566666666666666777777788888887 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   4.3   0.00032      0.38       2      12 ..      12      22 ..      11      27 .. 0.86
   2 ?    6.7   0.2      0.01        12       5      17 .]      45      57 ..      41      63 .. 0.80
   3 ?   -0.6   0.1       2.2   2.6e+03       3       9 ..      86      92 ..      78      92 .. 0.82
   4 ?   -0.3   0.2       1.7   2.1e+03       4       7 ..     112     115 ..     106     115 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00032
                            Fer4_4  2 erCigCgsCva 12
                                      e+C+gCg+Cv 
  gi|298676028|ref|YP_003727778.1| 12 EKCNGCGKCVT 22
                                      89*******96 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.01
                            Fer4_4  5 igCgsCvaaCPqg 17
                                       g g Cv +CP+g
  gi|298676028|ref|YP_003727778.1| 45 DGMGFCVGVCPTG 57
                                      44468******86 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 2.2
                            Fer4_4  3 rCigCgs 9 
                                      +C+ Cg+
  gi|298676028|ref|YP_003727778.1| 86 SCFICGQ 92
                                      4888886 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 1.7
                            Fer4_4   4 CigC 7  
                                       C++C
  gi|298676028|ref|YP_003727778.1| 112 CTRC 115
                                       8888 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   6.9    0.0077       9.2       1      15 []      14      28 ..      14      28 .. 0.95
   2 ?    9.4   1.5    0.0018       2.2       6      15 .]      49      58 ..      43      58 .. 0.77
   3 ?   -1.3   0.3         5   5.9e+03       1       4 [.     112     115 ..     111     117 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0077
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+gCg Cv  C +gA
  gi|298676028|ref|YP_003727778.1| 14 CNGCGKCVTPCAEGA 28
                                      ***********9998 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0018
                            Fer4_3  6 aCvevCPvgA 15
                                       Cv vCP+gA
  gi|298676028|ref|YP_003727778.1| 49 FCVGVCPTGA 58
                                      5********9 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 5
                            Fer4_3   1 CtgC 4  
                                       Ct C
  gi|298676028|ref|YP_003727778.1| 112 CTRC 115
                                       5544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 808.44
//
Query:       gi|298676029|ref|YP_003727779.1|  [L=149]
Description: hypothetical protein Metev_2156 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-24   85.4   2.5    3.9e-12   46.4   0.2    2.5  3  CBS       CBS domain
     0.0016   17.8   1.1     0.0022   17.3   1.1    1.2  1  DUF1786   Putative pyruvate format-lyase activating enzyme (D


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.1     1e-13   9.2e-10       1      55 [.      12      66 ..      12      68 .. 0.87
   2 ?   -1.4   0.0      0.36   3.3e+03      22      34 ..      68      81 ..      59      88 .. 0.70
   3 !   46.4   0.2   4.3e-16   3.9e-12       3      54 ..      91     141 ..      82     144 .. 0.93

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 1e-13
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE.ETTTBEEEEEEHHHHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVV.dedgklvGivtlrDllral 55
                                      V +im + +vtv++++t+ ++lel+++++++ +PVV d++ +lvG v +  +l+ l
  gi|298676029|ref|YP_003727779.1| 12 VYEIMVKSLVTVNENDTINDILELFKNYNFHTYPVVnDKY-ELVGEVNQDIILEIL 66
                                      5699*********************9999*******4444.6***99998888876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.36
                                      HHHHH.HHTSSEEE CS
                               CBS 22 lelmr.ekgvsrlP 34
                                      l++++ +k+++r+ 
  gi|298676029|ref|YP_003727779.1| 68 LDRIKsSKNIHRIA 81
                                      35555457788885 PP

  == domain 3  score: 46.4 bits;  conditional E-value: 4.3e-16
                                       HHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS   3 dimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                        im +  +t++pdt+l+ a++lm++++v+++++V e+ kl+Gi+++rD+++ 
  gi|298676029|ref|YP_003727779.1|  91 GIMEHHTLTLSPDTNLHHAADLMVKHKVNHVYIV-EYRKLIGILSKRDIINH 141
                                       5899999***************************.8*************986 PP

>> DUF1786  Putative pyruvate format-lyase activating enzyme (DUF1786)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   1.1   2.5e-07    0.0022     174     221 ..      76     124 ..      56     127 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.5e-07
                           DUF1786 174 ngHtlaalvkegrivgvfEhHTsaltke.kleelieklaegeltneevf 221
                                       n H +a+    ++i+g++EhHT +l+++ +l++  + ++++++++  ++
  gi|298676029|ref|YP_003727779.1|  76 NIHRIAIKSISENIKGIMEHHTLTLSPDtNLHHAADLMVKHKVNHVYIV 124
                                       89******99****************97689999999999999887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1081.27
//
Query:       gi|298676030|ref|YP_003727780.1|  [L=393]
Description: sodium/hydrogen exchanger [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-58  197.9  52.5    2.6e-58  197.7  52.5    1.0  1  Na_H_Exchanger   Sodium/hydrogen exchanger family
  ------ inclusion threshold ------
        1.2    9.0   4.5         17    5.4   0.4    2.4  2  Rick_17kDa_Anti  Glycine zipper 2TM domain
        2.2    8.5   0.0        2.2    8.5   0.0    3.1  4  COX6C            Cytochrome c oxidase subunit VIc


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.7  52.5   4.3e-62   2.6e-58       2     377 ..       5     377 ..       4     381 .. 0.91

  Alignments for each domain:
  == domain 1  score: 197.7 bits;  conditional E-value: 4.3e-62
                                       HHHHHHHHHHHH...HHHHTTSXHHHHHHHHHHHHTTTTTS.....HHHCHCCHHHHCHHCCHHHHC.TCGCCTGCC CS
                    Na_H_Exchanger   2 vllillallvgl...larrlklpeivgliiaGlllGpsglgliepseedlevlselglilllFlaGl.eldlrelrk 74 
                                       ++++++++l+++   +++r + ++i+g+i+aG++l  ++l   +++ e +++l+elg i+llF aG+ e++l+elr+
  gi|298676030|ref|YP_003727780.1|   5 LIIFVILFLAKVlgeFFERTGFSSILGEIFAGIILSMFLLS--HDP-ETFSFLAELGAIFLLFTAGYkEVHLQELRS 78 
                                       5667777888887767*************************..999.*******************978******** PP

                                       THHHHHHHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHH CS
                    Na_H_Exchanger  75 nlksilllallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvln 151
                                         k++++  ++++++++   G++l+l  i+++ +le+l++++++sat+++v+++il +++ ++++ g+l+l  ++++
  gi|298676030|ref|YP_003727780.1|  79 ASKKAIIPTITQIVLAFSS-GFILGL--IFNFQILESLFMAVAFSATSIGVLVKILIDYNYLSSKPGSLMLTSAIFD 152
                                       *******************.*****7..89*********************************************** PP

                                       HHHCCCCCHHHHHHTX.XXXXTSSSTSXHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHSCTHHHHHHHHHHHHHHHH CS
                    Na_H_Exchanger 152 Davavvllavllalak.eeaggetslllllliflvvavgglllgl.vigwllrlitrftdddrelevllvlllalla 226
                                       D++++++l++++++a+ ++    +++l+++  ++++ +  ++lgl + + l+ +i ++  +++e+ + +v+++al++
  gi|298676030|ref|YP_003727780.1| 153 DIAGIFMLSIVVTVAElQHLPSFSQILTIFAKLAFFMLSMVVLGLkIYPKLFDYIHKM--HIKESIFSFVIIIALFS 227
                                       ***************9988888888888887777777777777764889999999999..***************** PP

                                       HHHHHTSXXXHHHHHHHHHHHHHHHHHHTT..HHHHHHHHHHHHHHHHHHHHHHHHSXHHHHHXXHHHHHHHHHHHH CS
                    Na_H_Exchanger 227 allaellgvsgilgaflaGlvlseyefsnk..lseklesfreglfnplfFvlvGlsldlkvlnnhlsvlilvllilv 301
                                       a++ae++ +++++gaf+ G++ls+ + ++   ++ k++ + +g+f p+fF+++G ++dl+vl   +   ++ +l++v
  gi|298676030|ref|YP_003727780.1| 228 AYFAEAFELHAVIGAFVGGIILSRIPIAKIedVQSKVSGLSYGIFTPIFFAYIGFTVDLSVL---ETTSLFTILVVV 301
                                       ***********************7666663337777**************************...555666666666 PP

                                       HHHTHHHHHHHHHTTTXSSXHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTTSSTTTCSTSXHHHHHHHHHHH CS
                    Na_H_Exchanger 302 aillgrilavflllrllglslrealiigfgglqrgavalalaalgpalgllarelyallivvvlftvlvqGlslkp 377
                                       + llg+++++f+ ++++gl+++++li+g+g  +r  + l+++ +g++ g++  e y++++++v+++++v ++ lk+
  gi|298676030|ref|YP_003727780.1| 302 MALLGKLVGGFIGSKIVGLDSSDSLIFGIGVMPRAGIELVVITVGRNRGIIGDEIYSAIVLMVIVSIIVSPMLLKF 377
                                       6669****************************************************************77777765 PP

>> Rick_17kDa_Anti  Glycine zipper 2TM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.3    0.0032        19       3      13 ..     238     248 ..     236     252 .. 0.79
   2 ?    5.4   0.4    0.0029        17       3      18 ..     303     319 ..     301     331 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0032
                   Rick_17kDa_Anti   3 aliGAaaGgva 13 
                                       a+iGA +Gg++
  gi|298676030|ref|YP_003727780.1| 238 AVIGAFVGGII 248
                                       78888888876 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0029
                   Rick_17kDa_Anti   3 aliGAaaGgvaGaai.g 18 
                                       al+G ++Gg +G++i g
  gi|298676030|ref|YP_003727780.1| 303 ALLGKLVGGFIGSKIvG 319
                                       67777899999999966 PP

>> COX6C  Cytochrome c oxidase subunit VIc
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.3       0.7   4.2e+03      14      28 ..     108     122 ..      88     132 .. 0.60
   2 ?   -1.0   0.1      0.33     2e+03      11      32 ..     146     167 ..     144     168 .. 0.84
   3 ?   -3.0   0.1       1.4   8.5e+03      13      28 ..     210     226 ..     206     234 .. 0.41
   4 ?    8.5   0.0   0.00037       2.2       8      45 ..     349     387 ..     347     389 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.7
                             COX6C  14 rlkrhlvvafvlslg 28 
                                       ++   l++a++ s++
  gi|298676030|ref|YP_003727780.1| 108 QILESLFMAVAFSAT 122
                                       455556666666554 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.33
                             COX6C  11 lakrlkrhlvvafvlslgvaaa 32 
                                       l++ +   +++ f+ls++v++a
  gi|298676030|ref|YP_003727780.1| 146 LTSAIFDDIAGIFMLSIVVTVA 167
                                       67778888999******99986 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.4
                             COX6C  13 krlkrhlvvaf.vlslg 28 
                                        ++k  ++  + +++l+
  gi|298676030|ref|YP_003727780.1| 210 MHIKESIFSFViIIALF 226
                                       34444444332022333 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.00037
                             COX6C   8 rgllakrlkrhlvvafvlslgv.aaaykfavaepRKkay 45 
                                       rg+  +++   +v+++++s++v ++++kfa++ + K a 
  gi|298676030|ref|YP_003727780.1| 349 RGIIGDEIYSAIVLMVIVSIIVsPMLLKFAINAKEKSAL 387
                                       77888889999********87648**********99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       986  (0.0549947); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2783.74
//
Query:       gi|298676031|ref|YP_003727781.1|  [L=170]
Description: putative signal transduction protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-23   81.6   2.9    1.8e-11   44.3   0.1    2.1  2  CBS             CBS domain
  ------ inclusion threshold ------
       0.26   10.2   0.0       0.35    9.8   0.0    1.2  1  Glyco_hydro_56  Hyaluronidase


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.3   2.1e-13   1.9e-09       3      55 ..      38      90 ..      36      92 .. 0.91
   2 !   44.3   0.1     2e-15   1.8e-11       2      56 ..     113     166 ..     111     167 .. 0.94

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 2.1e-13
                                      HHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS  3 dimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55
                                      di  +d+vt+++ + +e++++++++++++ +PV+++ g+l G++t+  +l+ +
  gi|298676031|ref|YP_003727781.1| 38 DIIKKDIVTLSEGDLIEDIINIFTKHRFHTYPVINDKGNLTGVITQNLILKII 90
                                      88999****************************************98777765 PP

  == domain 2  score: 44.3 bits;  conditional E-value: 2e-15
                                       HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       + im + +vtv+ d++l ++++lm++++v++++ V ++g+lvGiv++ D+++ ++
  gi|298676031|ref|YP_003727781.1| 113 KGIMDPHPVTVNLDSNLCDVAKLMVKHNVNQVFAV-DNGRLVGIVSKLDVINEIS 166
                                       569******************************9*.6**************9886 PP

>> Glyco_hydro_56  Hyaluronidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   3.9e-05      0.35      17      80 ..      29      88 ..      26     112 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 3.9e-05
                                      HHHHHHH------TTSSEE--TT--S--SSEEEE-TTSSS---EE-TTS-.EETTSSGGGS-HH CS
                    Glyco_hydro_56 17 ekCkeklkveldlsafgivanenesftgqnitifykdrlGlYPyideekekavngGlPqnasLk 80
                                      ++C+ +++++ d+ + +iv+ ++ ++ ++ i+if k+r+ +YP+i+++++  + g + qn  Lk
  gi|298676031|ref|YP_003727781.1| 29 NRCQ-RIGIN-DIIKKDIVTLSEGDLIEDIINIFTKHRFHTYPVINDKGN--LTGVITQNLILK 88
                                      6788.88888.88889999999999**********************988..899999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1165.56
//
Query:       gi|298676032|ref|YP_003727782.1|  [L=392]
Description: sodium/hydrogen exchanger [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-53  180.6  50.4    4.8e-53  180.3  50.4    1.0  1  Na_H_Exchanger  Sodium/hydrogen exchanger family
  ------ inclusion threshold ------
      0.055   13.7   0.2       0.13   12.5   0.2    1.5  1  AAA_lid_1       AAA+ lid domain
        2.1    7.9   9.0        2.5    7.6   0.8    2.9  3  TRAP-gamma      Translocon-associated protein, gamma subunit 


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.3  50.4     8e-57   4.8e-53       1     376 [.       7     376 ..       4     380 .. 0.91

  Alignments for each domain:
  == domain 1  score: 180.3 bits;  conditional E-value: 8e-57
                                       XHHHHHHHHHHHHHHHHTTSXHHHHHHHHHHHHTTTTTS.....HHHCHCCHHHHCHHCCHHHHC.TCGCCTGCCTH CS
                    Na_H_Exchanger   1 ivllillallvgllarrlklpeivgliiaGlllGpsglgliepseedlevlselglilllFlaGl.eldlrelrknl 76 
                                       i+l++lla ++g l+ rl+lp+i+g i+aG++lGp++     ++ e++ +l+elg ill F a++ e+++r++++  
  gi|298676032|ref|YP_003727782.1|   7 IFLVVLLAKIFGELSIRLGLPSILGGILAGIVLGPFFAD--PNG-EIFLFLAELGAILLFFTAAYnEVSIRYIQALS 80 
                                       45666666666669***********************99..666.********************67******9999 PP

                                       HHHHHHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHH CS
                    Na_H_Exchanger  77 ksilllallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDa 153
                                       k +l+  ++ +l+++v+ G++l++  i+++ +le +++g+++s t+++ v+ +l   + ++++ g l+l+ ++ln  
  gi|298676032|ref|YP_003727782.1|  81 KYTLIPTFTHILVAFVC-GYTLGY--IFNLGFLENIFIGIAFSSTSIGSVVNMLISCNYLSKNPGPLVLSSAILNNF 154
                                       99999999999999999.*****8..89************************************************* PP

                                       HCCCCCHHHHHHTX..XXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTHHHHHHHHHHHHHHHHHH CS
                    Na_H_Exchanger 154 vavvllavllalak..eeaggetslllllliflvvavgglllglvigwllrlitrftdddrelevllvlllallaal 228
                                       v+v++l +++++a+     gg   l  +++++ +++++++l+  v ++l+++i r+  +++e+ +++v+++al++a+
  gi|298676032|ref|YP_003727782.1| 155 VGVIMLGLIVSVATyqRLPGGKEILTIISGVVGFLVIMIVLGYKVYPVLFKYIHRM--QIKESIFAFVIIIALVSAY 229
                                       **************966666666666777788888888888899***********9..******************* PP

                                       HHHTSXXXHHHHHHHHHHHHHHHHHHTT..HHHHHHHHHHHHHHHHHHHHHHHHSXHHHHHXXHHHHHHHHHHHHHH CS
                    Na_H_Exchanger 229 laellgvsgilgaflaGlvlseyefsnk..lseklesfreglfnplfFvlvGlsldlkvlnnhlsvlilvllilvai 303
                                       lae+lg+++++gaf+ G+ lse +++    ++ k++ + +g+f+p+f++++G+s+d+++l     + ++ ++++v+ 
  gi|298676032|ref|YP_003727782.1| 230 LAEILGLHSVIGAFIGGIFLSEIPLARIedIQSKVSGISYGVFIPMFYAFIGMSIDFSIL---QTNGLFTIAVIVLA 303
                                       *********************6666653338889**************************...67777777777777 PP

                                       HTHHHHHHHHHTTTXSSXHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTTSSTTTCSTSXHHHHHHHHHH CS
                    Na_H_Exchanger 304 llgrilavflllrllglslrealiigfgglqrgavalalaalgpalgllarelyallivvvlftvlvqGlslk 376
                                       llg++ ++++ +r+l++++ ++li+g+g  ++  v l+++++g + g++ ++ y++++++v ++v+v +l lk
  gi|298676032|ref|YP_003727782.1| 304 LLGKLFGGYIGSRILKVNSYDSLIFGIGSMPKADVELVVISIGLSMGVIGNASYSAIVLMVAISVVVSPLLLK 376
                                       79****************************************************************6666554 PP

>> AAA_lid_1  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   2.1e-05      0.13      22      46 ..     100     124 ..      86     137 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.1e-05
                         AAA_lid_1  22 kfhyvfnlrdlsnifqgllfssaev 46 
                                        + y+fnl  l nif g+ fss+ +
  gi|298676032|ref|YP_003727782.1| 100 TLGYIFNLGFLENIFIGIAFSSTSI 124
                                       578******************9875 PP

>> TRAP-gamma  Translocon-associated protein, gamma subunit (TRAP-gamma)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.8   0.00041       2.5      35      61 ..     203     230 ..     183     236 .. 0.80
   2 ?    4.9   0.1    0.0029        17     120     141 ..     283     304 ..     281     313 .. 0.89
   3 ?   -3.5   0.2       1.1   6.7e+03      21      31 ..     361     371 ..     348     381 .. 0.49

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00041
                        TRAP-gamma  35 lfwrihqmelleslilfviv.tllstyl 61 
                                       lf  ih+m++ es++ fvi+ +l+s+yl
  gi|298676032|ref|YP_003727782.1| 203 LFKYIHRMQIKESIFAFVIIiALVSAYL 230
                                       89***************97615667776 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0029
                        TRAP-gamma 120 sttfsifynNalflalllvlsf 141
                                       s+ fsi+ +N lf + ++vl++
  gi|298676032|ref|YP_003727782.1| 283 SIDFSILQTNGLFTIAVIVLAL 304
                                       789**************99984 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 1.1
                        TRAP-gamma  21 fyvnalivsai 31 
                                       + + a+ v++ 
  gi|298676032|ref|YP_003727782.1| 361 VLMVAISVVVS 371
                                       22233333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       986  (0.0549947); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 2339.08
//
Query:       gi|298676033|ref|YP_003727783.1|  [L=72]
Description: hypothetical protein Metev_2160 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 527.29
//
Query:       gi|298676034|ref|YP_003727784.1|  [L=498]
Description: radical SAM domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.1e-20   72.3   0.1    6.1e-20   72.3   0.1    1.8  2  Radical_SAM  Radical SAM superfamily
    4.9e-05   23.6   0.2    0.00016   22.0   0.0    1.9  1  Fer4_12      4Fe-4S single cluster domain
    5.9e-05   23.2   1.4      8e-05   22.8   0.0    2.0  2  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.8       1.9   1.2e+04       7      19 ..      73      85 ..      71      88 .. 0.87
   2 !   72.3   0.1     1e-23   6.1e-20       3     166 ..      94     256 ..      92     257 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.9
                                      ESS--TTTSCCTT CS
                                      xxxxxxxxxxxxx RF
                       Radical_SAM  7 CnlrCsfCarpet 19
                                      C+++C  C++++t
  gi|298676034|ref|YP_003727784.1| 73 CPQDCGLCSTHKT 85
                                      *********9975 PP

  == domain 2  score: 72.3 bits;  conditional E-value: 1e-23
                                       EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHH.HHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelk.aekg.vkevilgggepllypdfvellerlaklavpg 77 
                                        t+ Cnl+C+ C  + +   +g+ ++ s e+i + ++ l+ +e+  +  v ++ggep++++d+ +++++++      
  gi|298676034|ref|YP_003727784.1|  94 LTNRCNLNCPICFANAK--ERGYIYEPSFEQIRDMLQMLRnEEPTpCYAVQFSGGEPTVRDDLPDIIAMARDM--GF 166
                                       589************96..*********************988889***************************..9* PP

                                       EEEEEEECSSCHG..HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEB CS
                                       xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  78 iritvetngtlpd..eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivgl 152
                                       i i + tng+++    e+ ++l+e+g+ +++l  + +++e+++   + +  + ++ +++e++re+gik+++ + ++ 
  gi|298676034|ref|YP_003727784.1| 167 IQIQIATNGIRLAkdVEFTRKLKEAGLHTLYLQFDGVTEEPYKMVRGFNALPMKQ-QVVENCREVGIKSITLVPTLA 242
                                       ****************************************666666565555555.9******************** PP

                                       TTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxx RF
                       Radical_SAM 153 pGendeeleellel 166
                                       +G+nd+++ +++++
  gi|298676034|ref|YP_003727784.1| 243 KGVNDHQIGDMIRF 256
                                       **********9998 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   2.6e-08   0.00016      12      98 ..      95     180 ..      88     205 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.6e-08
                           Fer4_12  12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesi...egltllGGEPllpenaeallelvkevkeekpe 85 
                                       +++Cnl+C+ Cf  ++++  +  e ++e ++ +++ l +e+      + ++GGEP +   +++l +++   +  ++ 
  gi|298676034|ref|YP_003727784.1|  95 TNRCNLNCPICF-ANAKERGYIYEPSFEQIRDMLQMLRNEEPtpcYAVQFSGGEPTV---RDDLPDIIAMARDMGFI 167
                                       578*********.556666666666788888888888886655669***********...55555666655655554 PP

                           Fer4_12  86 kdiwlytgytlee 98 
                                       +  ++++g  l +
  gi|298676034|ref|YP_003727784.1| 168 QIQIATNGIRLAK 180
                                       4567777776665 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -5.0   1.5         3   1.8e+04       7      19 ..      72      84 ..      72      87 .. 0.80
   2 !   22.8   0.0   1.3e-08     8e-05       5      96 ..      95     183 ..      93     202 .. 0.66

  Alignments for each domain:
  == domain 1  score: -5.0 bits;  conditional E-value: 3
                           Fer4_14  7 gCnlsCkgCdnke 19
                                      +C+  C  C +++
  gi|298676034|ref|YP_003727784.1| 72 QCPQDCGLCSTHK 84
                                      59999****9776 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 1.3e-08
                           Fer4_14   5 lsgCnlsCkgCdnketwkselgkpqtee..lleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeyp 79 
                                       +++Cnl+C+ C+ +++ +    +p+ e+  ++ q+l++ + + +    + ++GGeP      ++l +++ + ++ + 
  gi|298676034|ref|YP_003727784.1|  95 TNRCNLNCPICFANAKERGYIYEPSFEQirDMLQMLRNEEPTPC--YAVQFSGGEPTVR---DDLPDIIAMARDMG- 165
                                       69**********77755554444443330134455544444444..6699******955...78888888888888. PP

                           Fer4_14  80 ekkiwletngt.leiele 96 
                                        ++i++ tng  l++++e
  gi|298676034|ref|YP_003727784.1| 166 FIQIQIATNGIrLAKDVE 183
                                       799999999852344444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (498 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 3438.08
//
Query:       gi|298676035|ref|YP_003727785.1|  [L=118]
Description: ArsR family transcriptional regulator [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-14   53.2   0.7    2.8e-14   52.7   0.7    1.2  1  HTH_5     Bacterial regulatory protein, arsR family
    5.8e-10   39.1   0.1    7.8e-10   38.7   0.1    1.2  1  HTH_20    Helix-turn-helix domain
     0.0018   18.2   0.3     0.0024   17.8   0.3    1.2  1  HTH_45    Winged helix-turn-helix
     0.0036   17.6   0.2     0.0073   16.6   0.1    1.5  1  DUF2513   Hypothetical protein (DUF2513)
  ------ inclusion threshold ------
      0.011   15.9   1.4       0.03   14.5   1.4    1.7  1  Rio2_N    Rio2, N-terminal
      0.029   12.8   0.1      0.029   12.8   0.1    1.2  1  DUF505    Protein of unknown function (DUF505)
      0.029   14.0   0.1       0.04   13.5   0.1    1.2  1  ArsR      ArsR transcriptional regulator
      0.065   13.2   0.2       0.12   12.3   0.2    1.6  1  HTH_12    Ribonuclease R winged-helix domain


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7   0.7   1.2e-17   2.8e-14       1      47 []      43      89 ..      43      89 .. 0.98

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 1.2e-17
                                      SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                      dp RlkIL++L+ +elcvc l+e ++   s++S+HLk L++++LVe+
  gi|298676035|ref|YP_003727785.1| 43 DPIRLKILRALETQELCVCVLVELTDYKYSALSYHLKLLKDENLVES 89
                                      8********************************************96 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.1   3.5e-13   7.8e-10       3      59 ..      37      92 ..      36      94 .. 0.97

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 3.5e-13
                                      HHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20  3 iaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                      ++++L++P R++ilraL + ++l++  l e+ d + + lsyHL+ L +  Lve++r 
  gi|298676035|ref|YP_003727785.1| 37 LFKVLSDPIRLKILRAL-ETQELCVCVLVELTDYKYSALSYHLKLLKDENLVESRRD 92
                                      599**************.*************************************96 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.3   1.1e-06    0.0024       7      71 ..      45     113 ..      42     118 .] 0.88

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.1e-06
                            HTH_45   7 IiadILeaisegeakkTkimykanLsykllnkYLdmLvekgli....kkskekYvlTekGlelleklke 71 
                                       I + IL+a++ +e     ++   + +y+ l+  L+ L +++l+    +ks + Y+lT  G  ll+++++
  gi|298676035|ref|YP_003727785.1|  45 IRLKILRALETQELCVCVLVELTDYKYSALSYHLKLLKDENLVesrrDKSYQIYYLTGFGYSLLKSIDK 113
                                       6678999999999999999999999******************88776778889***********9976 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   3.2e-06    0.0073      32      85 ..      58     111 ..      42     115 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.2e-06
                           DUF2513  32 s......aidgyskeeiiyhlkllaeagLieaekkkakssiislvvkrLtweGhdFLdsi 85 
                                              ++++y+   ++yhlkll +++L+e+  +k+++       + Lt  G+ +L si
  gi|298676035|ref|YP_003727785.1|  58 LcvcvlvELTDYKYSALSYHLKLLKDENLVESRRDKSYQI------YYLTGFGYSLLKSI 111
                                       13344458999********************988877655......66777777766665 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.4   1.3e-05      0.03      10      74 ..      48     108 ..      40     111 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.3e-05
                            Rio2_N  10 rvLtavEmgmrnhevVptelieeisrlkeeevkkrlsrllkaklisr.ktakydGYkLtyeGyDyL 74 
                                       ++L+a+E+         + ++ e++ +k + ++++l+ l +++l++  ++++y+ Y Lt  Gy  L
  gi|298676035|ref|YP_003727785.1|  48 KILRALETQE-----LCVCVLVELTDYKYSALSYHLKLLKDENLVESrRDKSYQIYYLTGFGYSLL 108
                                       5666666542.....345578899*********************9889**************876 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   1.3e-05     0.029     365     411 ..      73     118 .]      15     118 .] 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.3e-05
                            DUF505 365 dlreaLysLesfeLieseveekgkevyvlTeyGekvledqekklrev 411
                                        l   L+ L+  +L+es+  +k  ++y+lT +G ++l+  +k++++v
  gi|298676035|ref|YP_003727785.1|  73 ALSYHLKLLKDENLVESR-RDKSYQIYYLTGFGYSLLKSIDKEFKSV 118
                                       568899************.569****************999888876 PP

>> ArsR  ArsR transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   1.8e-05      0.04       3      60 ..      30      90 ..      28      97 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.8e-05
                              ArsR  3 dpveLvpllqvfdsetkkkvyeelskeWlteeeleeklgee...veealklLkkikliEsq 60
                                      d+ ++v l++v++++   k++++l+++ l    l e ++ +    +  lklLk  +l+Es+
  gi|298676035|ref|YP_003727785.1| 30 DVDDMVYLFKVLSDPIRLKILRALETQELCVCVLVELTDYKysaLSYHLKLLKDENLVESR 90
                                      999***********************9988877777666553337889***********98 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   5.4e-05      0.12      23      52 ..      64      91 ..      47     108 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.4e-05
                            HTH_12 23 LkkrgydigeravRyrLrkleergltrrvg 52
                                      +++++y++   a+ y+L+ l +++l++  +
  gi|298676035|ref|YP_003727785.1| 64 VELTDYKY--SALSYHLKLLKDENLVESRR 91
                                      57789999..9*************997544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.52
# Mc/sec: 687.55
//
Query:       gi|298676036|ref|YP_003727786.1|  [L=140]
Description: transcriptional regulator NikR [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-32  111.1   0.8    3.1e-32  110.6   0.8    1.2  1  NikR_C           NikR C terminal nickel binding domain
    4.5e-12   45.4   0.5      8e-12   44.6   0.1    1.6  2  RHH_1            Ribbon-helix-helix protein, copG family
      0.001   19.2   0.0     0.0047   17.0   0.0    1.9  2  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit
  ------ inclusion threshold ------
       0.04   14.1   0.1      0.058   13.6   0.1    1.4  1  RHH_8            Ribbon-Helix-Helix transcriptional regulator
       0.13   12.6   0.1       0.36   11.1   0.0    1.7  2  DUF4090          Protein of unknown function (DUF4090)
        0.2   11.6   0.0       0.33   10.9   0.0    1.4  1  RHH_5            CopG-like RHH_1 or ribbon-helix-helix domain


Domain annotation for each model (and alignments):
>> NikR_C  NikR C terminal nickel binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.6   0.8     1e-35   3.1e-32       1      76 [.      58     133 ..      58     134 .. 0.99

  Alignments for each domain:
  == domain 1  score: 110.6 bits;  conditional E-value: 1e-35
                                       EEEEEEEEETTSTTHHHHHHHHHHHHSSEEEEEEEEEESSSEEEEEEEEEE-HHHHHHHHHHHHTSTTEEEEEEEE CS
                            NikR_C   1 vGvitivydhhqrelserltdiqheyhdliisslhvhldhdncLevivlkGeaeeikelaeklralkgVkhvkltl 76 
                                       vG++t++ydh++r+ls++lt+iqhe+ ++i+ss+h+hld+dncLevi+l+G++++ k++ ek++alkgVk++kl++
  gi|298676036|ref|YP_003727786.1|  58 VGTLTLMYDHTKRGLSNTLTEIQHEHAEIIQSSVHIHLDQDNCLEVIILDGDGANFKDFGEKVMALKGVKYSKLNT 133
                                       7*************************************************************************97 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   0.1   2.7e-15     8e-12       1      38 [.       7      45 ..       7      46 .. 0.96
   2 ?   -2.4   0.0       1.8   5.3e+03       2       9 ..      91      98 ..      90      98 .. 0.78

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 2.7e-15
                                      EEEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHHHH CS
                             RHH_1  1 rvsirldeellerLdelarrrg.rSrSelIReAlreyle 38
                                      r+ ++l+e+lle++de++++rg +SrSe IR+A+r+y+ 
  gi|298676036|ref|YP_003727786.1|  7 RIGVSLPENLLEKFDEIIEKRGySSRSEGIRDAIRNYIV 45
                                      899**********************************96 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.8
                                      EEEEEEHH CS
                             RHH_1  2 vsirldee 9 
                                      v i+ld++
  gi|298676036|ref|YP_003727786.1| 91 VHIHLDQD 98
                                      56999987 PP

>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.6e-06    0.0047      86     117 ..       2      34 ..       1      39 [. 0.86
   2 ?   -0.1   0.0      0.33   9.8e+02       3      19 ..      91     107 ..      72     135 .. 0.58

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.6e-06
                   HicB_lk_antitox  86 dgkaeriNitlpervlkriDaavkaag.esRSg 117
                                       d+   ri ++lpe++l++ D++++++g +sRS 
  gi|298676036|ref|YP_003727786.1|   2 DQDLMRIGVSLPENLLEKFDEIIEKRGySSRSE 34 
                                       56678**********************669997 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.33
                   HicB_lk_antitox   3 iaiekdedsaygvvvPd 19 
                                       + i+ d+d++  v++ d
  gi|298676036|ref|YP_003727786.1|  91 VHIHLDQDNCLEVIILD 107
                                       33444444444444444 PP

>> RHH_8  Ribbon-Helix-Helix transcriptional regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.9e-05     0.058      15      56 ..      17      57 ..       4     104 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.9e-05
                             RHH_8 15 LgqiDlLveeGfYsnRtDlirtairaqLakhddalkqavkrk 56
                                      L + D ++e+  Ys+R++ ir air+ + +h+  ++++  r+
  gi|298676036|ref|YP_003727786.1| 17 LEKFDEIIEKRGYSSRSEGIRDAIRNYIVRHE-WMSDIKGRR 57
                                      778899999999**************999885.444554444 PP

>> DUF4090  Protein of unknown function (DUF4090)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00012      0.36      17      53 ..       9      46 ..       2      51 .. 0.92
   2 ?   -1.6   0.0       1.1   3.3e+03      58      63 ..      94      99 ..      68     123 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                           DUF4090 17 Gspipaeklelykevmaleakrqrs.Gvkksmrsrivr 53
                                      G  +p++ le ++e++++ +   rs G+++++r+ ivr
  gi|298676036|ref|YP_003727786.1|  9 GVSLPENLLEKFDEIIEKRGYSSRSeGIRDAIRNYIVR 46
                                      7889*****************999989**********9 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.1
                           DUF4090 58 hldqee 63
                                      hldq++
  gi|298676036|ref|YP_003727786.1| 94 HLDQDN 99
                                      555554 PP

>> RHH_5  CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00011      0.33       3      18 ..       7      22 ..       5      30 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                             RHH_5  3 RvnvtLPeelleeLee 18
                                      R+ v+LPe+lle+++e
  gi|298676036|ref|YP_003727786.1|  7 RIGVSLPENLLEKFDE 22
                                      9************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.37s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 760.95
//
Query:       gi|298676037|ref|YP_003727787.1|  [L=238]
Description: phosphoribosylaminoimidazole-succinocarboxamide synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-62  210.6   1.8    3.4e-62  210.3   1.8    1.1  1  SAICAR_synt  SAICAR synthetase


Domain annotation for each model (and alignments):
>> SAICAR_synt  SAICAR synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.3   1.8   1.9e-66   3.4e-62       2     251 ..       7     231 ..       6     232 .. 0.96

  Alignments for each domain:
  == domain 1  score: 210.3 bits;  conditional E-value: 1.9e-66
                                       EEE-SSEEEEE-SSTTEEEEEEESEEEECCCTEEEEETTHHHHHHHHHHHHHHHHHH..--BSEEEE.....-SSSE CS
                       SAICAR_synt   2 lyeGKvrdvYeledddklllvakDrisAfdvvlkeeipgKGkvltqlsafwfeklek..ipnhliksldpeqlegrs 76 
                                       ly+GK++++Y+++d++kl+++++D ++Afd+ +k+e ++KG ++ q+s+ +fe+le+  i++h+i+      +++++
  gi|298676037|ref|YP_003727787.1|   7 LYSGKAKSIYKTDDENKLVVEFRDSLTAFDGSKKSEAKNKGYYNAQISRKVFEMLESndIKTHYIDM-----ISDTE 78 
                                       89**********999*****************************************557******66.....99*** PP

                                       EEEE-EEEESEEEEEEEE--HHH.......HH....HH..T--TT-EEEEEEEEEEE--CCCT.S-EE-HHHHH.HT CS
                       SAICAR_synt  77 mlvkklkmlpvEvvvRgyltGslwkeykksgkvcgirlpeglkegeklpepiftpstKaeegehDeniseeevveal 153
                                       mlv+ ++++p+Ev+vR++++Gs+       +k    ++   +++g+++++pi+ + +K++e + D++i+e+ +v al
  gi|298676037|ref|YP_003727787.1|  79 MLVESVEIVPIEVIVRNIAAGSI-------TK----KY--PMEKGTRFKNPILVLDYKSDEYS-DPMINEDIAV-AL 140
                                       ***********************.......66....56..89*******************98.********99.88 PP

                                       T..-HHHHHHHHHHHHHHHHHHHHHHHHTTEEEEEEEEEEEEETTTTEEEEES--.STTTEEEEETTT.....GGGB CS
                       SAICAR_synt 154 g..teeeaeeieelalavyekaaelaaergiilvDtKlEFGldeedgelvLaDevltpDssRfwdaetyeegkeqes 228
                                       g  + ee+e++++lal+++e + +++++++++l D+KlEFG++  dgel+LaDe+ + D++R+wd+et      +es
  gi|298676037|ref|YP_003727787.1| 141 GitDYEEIEKLRSLALKINELLVDYLDKSNLLLPDFKLEFGRK--DGELLLADEI-SCDTCRLWDKET------EES 208
                                       99999************************************98..8*********.************......9** PP

                                       -STHHHHTT-STHHHHHHHHHHH CS
                       SAICAR_synt 229 lDKqfvRdwleeveekwkekler 251
                                       +DK+++R + ++ ++ ++e+++r
  gi|298676037|ref|YP_003727787.1| 209 MDKDVFRYDKGDLSKVYEEVARR 231
                                       *****************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1830.15
//
Query:       gi|298676038|ref|YP_003727788.1|  [L=408]
Description: hypothetical protein Metev_2166 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   2.1e-105  352.4   0.0   2.7e-105  352.1   0.0    1.1  1  Nre_N          Archaeal Nre, N-terminal
    2.4e-41  140.1   0.0    4.4e-41  139.2   0.0    1.4  1  Nre_C          Archaeal Nre, C-terminal
  ------ inclusion threshold ------
      0.024   15.0   0.1       0.12   12.7   0.0    2.1  2  Peptidase_C21  Tymovirus endopeptidase


Domain annotation for each model (and alignments):
>> Nre_N  Archaeal Nre, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  352.1   0.0  4.5e-109  2.7e-105       1     270 []      15     286 ..      15     286 .. 0.99

  Alignments for each domain:
  == domain 1  score: 352.1 bits;  conditional E-value: 4.5e-109
                             Nre_N   1 Lcglkkcpileklravekakkki.sskeleGsspPsvfVGrygYPkVsvgplvppveg..dasvldspekwlglsle 74 
                                       Lcg+++cpile++ ++e++++ki ++++++G+spP+vfVGr+gYP+Vs+gp++pp+++  + +v+d p++wlg++++
  gi|298676038|ref|YP_003727788.1|  15 LCGRPRCPILERFASIESLSSKIpKNDSVFGASPPAVFVGRHGYPDVSAGPMIPPETTgdESAVMDLPDEWLGMDIQ 91 
                                       8*******************************************************9998999************** PP

                             Nre_N  75 diiklrlslvrgekkvkvkkak.edklleeiqelalsekpvdvevelekkpkaklkfdevlaPvGpsaeleklkvae 150
                                       dii++r++lvr+++++++k+a   ++l+ + qelals++pvd+e++++k+++++l+fd+vl+P+Gpsa+l++++++e
  gi|298676038|ref|YP_003727788.1|  92 DIISMRSRLVRSNTNINIKDALsDNNLILKSQELALSTNPVDTEAWYSKTIENNLRFDSVLTPTGPSATLKNFEITE 168
                                       ********************99788899************************************************* PP

                             Nre_N 151 npkvprkveklveDtdlkAeeavveLyrsgvdvykiqrlLSvGlLGekkkrrlVPTrWsITAvddivgkelkkeikd 227
                                       np+vp+kv++lv+Dtd+ A+++v eL ++++++++i+rlLS+GlLG+  +r lVPTrWsITAvdd+ gk+++++i d
  gi|298676038|ref|YP_003727788.1| 169 NPNVPKKVDYLVYDTDALAKDSVSELINKNISTEHITRLLSIGLLGK--DRCLVPTRWSITAVDDMAGKDIINNIID 243
                                       **********************************************8..**************************** PP

                             Nre_N 228 lpeidevevfsgeylgNrflviLaPgkwsfelvEawapgslwn 270
                                       +p+ide+++fsg ++gN+f ++ +P+++sfelvE+w p+s+w+
  gi|298676038|ref|YP_003727788.1| 244 YPQIDEITLFSGGIFGNHFEILYVPKNYSFELVEIWLPKSVWS 286
                                       ******************************************6 PP

>> Nre_C  Archaeal Nre, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.2   0.0   7.3e-45   4.4e-41       1     110 []     297     406 ..     297     406 .. 0.99

  Alignments for each domain:
  == domain 1  score: 139.2 bits;  conditional E-value: 7.3e-45
                             Nre_C   1 egyegrkeyseiaGaYyaarlavleaLekikrqakvivlreitpeYwaPvGvWqvReavrkalekkpkefesleeal 77 
                                       eg++g+++ys+++G+Yyaarl++le+L +ikrqa+++++rei+p+YwaP+GvW+vRe+vr+al+++pk+fes+e+al
  gi|298676038|ref|YP_003727788.1| 297 EGFNGKSKYSPLSGGYYAARLGALEYLLNIKRQASIFIIREIRPDYWAPLGVWVVREGVRQALQNTPKTFESIETAL 373
                                       6899************************************************************************* PP

                             Nre_C  78 eevseklklplkkllkkskllkelkkqktLddF 110
                                       + +s+++k+p ++++++ kll+++ +qktLddF
  gi|298676038|ref|YP_003727788.1| 374 SDISTRIKTPYSDWRNQMKLLSDVCTQKTLDDF 406
                                       ********************************9 PP

>> Peptidase_C21  Tymovirus endopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     2e-05      0.12      28      92 ..     112     175 ..      93     191 .. 0.80
   2 ?   -0.9   0.0      0.34     2e+03      39      52 ..     191     207 ..     180     210 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2e-05
                                       HS-GGGTSSHHHHHH---HHHHHHHHHH.HTEEEEEEETTEEEEES-SS-SEEEEEEEE-SSS... CS
                     Peptidase_C21  28 ilPdsdlsneevsdlGlstehltalafl.yqflvtlrsdelvilfGlldaikaieithttgvPpat 92 
                                        l d +l   + ++l lst+ + + a+        lr d      G++ + k++eit  + vP   
  gi|298676038|ref|YP_003727788.1| 112 ALSDNNL-ILKSQELALSTNPVDTEAWYsKTIENNLRFDSVLTPTGPSATLKNFEITENPNVP-KK 175
                                       5556666.556789*******98888651557789***************************9.44 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.34
                                       HHHH...---HHHHHHH CS
                     Peptidase_C21  39 vsdl...Glstehltal 52 
                                       vs+l    +steh+t l
  gi|298676038|ref|YP_003727788.1| 191 VSELinkNISTEHITRL 207
                                       4444222699****987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2873.44
//
Query:       gi|298676039|ref|YP_003727789.1|  [L=122]
Description: hypothetical protein Metev_2167 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.3e-05   22.7   0.0    0.00014   21.3   0.0    1.6  2  HTH_24          Winged helix-turn-helix DNA-binding
    6.4e-05   22.4   0.0    0.00013   21.4   0.0    1.4  1  Sigma70_r4      Sigma-70, region 4
    0.00072   19.2   0.0     0.0015   18.1   0.0    1.5  1  Sigma70_r4_2    Sigma-70, region 4
     0.0011   19.0   0.0     0.0016   18.4   0.0    1.4  1  HTH_3           Helix-turn-helix
     0.0024   17.7   0.0     0.0056   16.5   0.0    1.6  1  MarR_2          MarR family
     0.0055   16.7   0.0      0.011   15.7   0.0    1.5  1  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0083   16.1   0.0      0.011   15.8   0.0    1.4  1  KorB            KorB domain
     0.0085   16.0   0.0       0.05   13.5   0.0    1.8  2  Sigma70_ECF     ECF sigma factor
  ------ inclusion threshold ------
      0.021   15.1   0.0        0.1   12.9   0.0    2.0  2  KORA            TrfB plasmid transcriptional repressor
      0.027   14.3   0.0      0.064   13.1   0.0    1.7  1  HTH_5           Bacterial regulatory protein, arsR family
      0.028   14.0   0.0       0.08   12.5   0.0    1.8  2  GerE            Bacterial regulatory proteins, luxR family
       0.04   13.7   0.0       0.09   12.6   0.0    1.7  1  HTH_23          Homeodomain-like domain
      0.046   13.7   0.0      0.072   13.0   0.0    1.4  1  HTH_11          HTH domain
        0.1   12.8   0.0       0.22   11.8   0.0    1.6  1  HTH_17          Helix-turn-helix domain
       0.14   12.0   0.0       0.41   10.5   0.0    1.8  2  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
       0.15   11.9   0.0       0.39   10.5   0.0    1.6  1  HTH_10          HTH DNA binding domain
       0.15   12.1   0.0       0.16   12.1   0.0    1.2  1  Phage_CI_repr   Bacteriophage CI repressor helix-turn-helix d
       0.17   12.4   0.0       0.22   12.0   0.0    1.2  1  HTH_40          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   1.5e-07   0.00014      17      38 ..      29      50 ..      27      51 .. 0.94
   2 ?   -2.8   0.0       4.8   4.8e+03      18      25 ..      63      70 ..      61      71 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.5e-07
                            HTH_24 17 risqreLAerlglSpstvnrrl 38
                                      +++q+e+A+ lglS+++v++++
  gi|298676039|ref|YP_003727789.1| 29 GCTQNEIADILGLSRAAVSQYV 50
                                      79******************98 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.8
                            HTH_24 18 isqreLAe 25
                                       ++ e+++
  gi|298676039|ref|YP_003727789.1| 63 ATNDEISK 70
                                      69999987 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.3e-07   0.00013      14      39 ..      23      48 ..      16      51 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.3e-07
                                      HHHHTTT--HHHHHHHHTS-HHHHHH CS
                        Sigma70_r4 14 elrfgeglTleEIgerlgiSrerVrq 39
                                      ++ f+ g T+ EI+++lg+Sr +V+q
  gi|298676039|ref|YP_003727789.1| 23 VMMFEYGCTQNEIADILGLSRAAVSQ 48
                                      578999*******************9 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.5e-06    0.0015      20      48 ..      23      51 ..      12      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.5e-06
                                      HHHHTS---HHHHHHHHT--HHHHHHHHH CS
                      Sigma70_r4_2 20 llryleglsykEIAellgisegtVksrls 48
                                      ++ ++ g+++ EIA +lg+s ++V +++s
  gi|298676039|ref|YP_003727789.1| 23 VMMFEYGCTQNEIADILGLSRAAVSQYVS 51
                                      46799*******************99986 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.6e-06    0.0016       7      31 ..      27      51 ..      21      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.6e-06
                                      HTTHHHHHHHHHHTSSHHHHHHHHT CS
                             HTH_3  7 qlglsqeeLAeklGvsrstisriEn 31
                                      + g +q e+A+ lG+sr+++s++ +
  gi|298676039|ref|YP_003727789.1| 27 EYGCTQNEIADILGLSRAAVSQYVS 51
                                      5799*******************87 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   5.6e-06    0.0056      22      42 ..      30      50 ..      16      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.6e-06
                                      EEHHHHHHHHTSSHHHHHHHH CS
                            MarR_2 22 ltvgelarrlglsksavsril 42
                                      +t++e+a+ lgls++avs+ +
  gi|298676039|ref|YP_003727789.1| 30 CTQNEIADILGLSRAAVSQYV 50
                                      79****************977 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.1e-05     0.011      19      41 ..      27      49 ..      12      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-05
                                      EEEHHHHHHHHHTTSSHHHHHHH CS
                         HTH_Crp_2 19 elpltqeelAsmlGltretvsri 41
                                      e   tq e+A++lGl+r  vs+ 
  gi|298676039|ref|YP_003727789.1| 27 EYGCTQNEIADILGLSRAAVSQY 49
                                      5568*****************85 PP

>> KorB  KorB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.1e-05     0.011       3      27 ..      29      53 ..      27      98 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.1e-05
                              KorB  3 gvkqadIAkaLGksksfvslylkll 27
                                      g +q++IA++LG s++ vs+y +l 
  gi|298676039|ref|YP_003727789.1| 29 GCTQNEIADILGLSRAAVSQYVSLK 53
                                      889******************9986 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   5.1e-05      0.05     137     176 ..      14      54 ..       4      60 .. 0.85
   2 ?    1.2   0.0       0.3     3e+02     133     161 ..      60      88 ..      47     101 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.1e-05
                       Sigma70_ECF 137 dpeqarlvelrkle.GlsveEiAeklgvskrtverrlalaR 176
                                       +   a+lv ++++e G + +EiA+ lg+s+++v +   l R
  gi|298676039|ref|YP_003727789.1|  14 PSIRAELVRVMMFEyGCTQNEIADILGLSRAAVSQYVSLKR 54 
                                       555789999*99987******************99888877 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.3
                       Sigma70_ECF 133 llsldpeqarlvelrkleGlsveEiAekl 161
                                       + +  ++   + + + ++Gl+v+E ++ +
  gi|298676039|ref|YP_003727789.1|  60 FSKATNDEISKFASQLIDGLTVKEKSKGM 88 
                                       445566666778889999****9988766 PP

>> KORA  TrfB plasmid transcriptional repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0    0.0001       0.1      31      52 ..      29      50 ..      10      56 .. 0.82
   2 ?   -0.8   0.0         2     2e+03      44      71 ..      64      91 ..      56      97 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0001
                              KORA 31 gkkqadvatelgltkqavsqav 52
                                      g +q+++a+ lgl++ avsq v
  gi|298676039|ref|YP_003727789.1| 29 GCTQNEIADILGLSRAAVSQYV 50
                                      679*****************98 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2
                              KORA 44 tkqavsqavkrvwaahaereepaglerV 71
                                      t+  +s+   + ++  + +e+ +g  rV
  gi|298676039|ref|YP_003727789.1| 64 TNDEISKFASQLIDGLTVKEKSKGMCRV 91
                                      5566666666666666666666666666 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.5e-05     0.064      16      35 ..      30      49 ..      15      52 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.5e-05
                                      EEHHHHHHHHTS-HHHHHHH CS
                             HTH_5 16 lcvcelaeelglsqstvShH 35
                                      ++  e+a++lgls+++vS++
  gi|298676039|ref|YP_003727789.1| 30 CTQNEIADILGLSRAAVSQY 49
                                      6678**************96 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   8.1e-05      0.08      14      39 ..      26      51 ..      19      52 .. 0.88
   2 ?   -2.5   0.0       3.8   3.8e+03      14      22 ..      75      83 ..      73      86 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.1e-05
                                      HCTTS-HHHHHHHHTS-HHHHHHHHH CS
                              GerE 14 laeGksnkeIAeelniSekTVkvhks 39
                                      +  G + +eIA++l++S   V+ ++s
  gi|298676039|ref|YP_003727789.1| 26 FEYGCTQNEIADILGLSRAAVSQYVS 51
                                      566999***************99875 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.8
                                      HCTTS-HHH CS
                              GerE 14 laeGksnke 22
                                      l++G+++ke
  gi|298676039|ref|YP_003727789.1| 75 LIDGLTVKE 83
                                      567787776 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     9e-05      0.09      19      40 ..      31      52 ..      18      59 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9e-05
                            HTH_23 19 svreIAreLgvsrrTvyrwlkr 40
                                      ++ eIA++Lg sr  v+++++ 
  gi|298676039|ref|YP_003727789.1| 31 TQNEIADILGLSRAAVSQYVSL 52
                                      6779**************9875 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.2e-05     0.072      17      37 ..      31      51 ..      17      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.2e-05
                            HTH_11 17 sgeeLAeeLnvSrrtvrrdIk 37
                                      + +e+A+ L++Sr++v +++ 
  gi|298676039|ref|YP_003727789.1| 31 TQNEIADILGLSRAAVSQYVS 51
                                      889**************9985 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00022      0.22       3      23 ..      31      51 ..      30      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00022
                            HTH_17  3 tveEaAelLgvsrstvyrlir 23
                                      t +E+A++Lg+sr+ v ++++
  gi|298676039|ref|YP_003727789.1| 31 TQNEIADILGLSRAAVSQYVS 51
                                      668**************9995 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00042      0.41      10      35 ..      31      56 ..      27      70 .. 0.87
   2 ?   -2.4   0.0       4.4   4.4e+03      28      41 ..     100     112 ..      98     117 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00042
                    YdaS_antitoxin 10 gqkaLAealgvsqqaVsqWlkgkkqv 35
                                      +q + A+ lg s++aVsq ++ k+++
  gi|298676039|ref|YP_003727789.1| 31 TQNEIADILGLSRAAVSQYVSLKRGA 56
                                      6899****************988874 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.4
                    YdaS_antitoxin  28 Wlkgkkqvpaervp 41 
                                       Wl+ k    a +++
  gi|298676039|ref|YP_003727789.1| 100 WLY-KNAPEAGYCI 112
                                       887.3445788887 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0004      0.39      24      44 ..      30      50 ..      27      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0004
                            HTH_10 24 vtlkeLAkelGIskstlsehL 44
                                      +t +e+A++lG+s++++s+++
  gi|298676039|ref|YP_003727789.1| 30 CTQNEIADILGLSRAAVSQYV 50
                                      7889**************997 PP

>> Phage_CI_repr  Bacteriophage CI repressor helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00016      0.16       4      33 ..      22      50 ..      19     116 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
                                      HHHHHHHT-SSCHHHHCCTT--HHHHHHHH CS
                     Phage_CI_repr  4 eRlmsaygvkmqkeLAdlLgiakssvstwv 33
                                      + +m  yg+ ++ e Ad Lg +++ vs  v
  gi|298676039|ref|YP_003727789.1| 22 RVMMFEYGCTQN-EIADILGLSRAAVSQYV 50
                                      557889***988.**************544 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00023      0.22       7      55 ..      24      70 ..      19      96 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00023
                            HTH_40  7 elleeglsieeIAkerglkesTIegHLaelieegeeidlerlvseeeek 55
                                       ++e g++  eIA++ gl+++ + +++    + g e+ +++ +++e+ k
  gi|298676039|ref|YP_003727789.1| 24 MMFEYGCTQNEIADILGLSRAAVSQYVSL--KRGAEVGFSKATNDEISK 70
                                      699***********************987..777778887776655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 703.71
//
Query:       gi|298676040|ref|YP_003727790.1|  [L=102]
Description: translation initiation factor SUI1 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.6e-22   77.3   0.1    1.2e-21   76.9   0.1    1.2  1  SUI1      Translation initiation factor SUI1
  ------ inclusion threshold ------
      0.019   14.7   1.0      0.024   14.4   1.0    1.2  1  DTW       DTW domain
      0.029   14.7   0.1      0.063   13.6   0.1    1.7  1  Img2      Mitochondrial large subunit ribosomal protein (Img2
       0.11   13.3   0.1       0.15   12.8   0.1    1.2  1  CsgA      Minor curli fiber component A


Domain annotation for each model (and alignments):
>> SUI1  Translation initiation factor SUI1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.9   0.1   2.8e-25   1.2e-21       1      76 [.      24      95 ..      24      96 .. 0.94

  Alignments for each domain:
  == domain 1  score: 76.9 bits;  conditional E-value: 2.8e-25
                              SUI1  1 akpkihirleqrggrKkvTtvsgleafgidlkklakelkkkfacsgsvvkdggeeiqvQGdqrkkvaelLtekygv 76
                                      ++++i++++ +r+ +K vT+v+gl+a++idl++la  lk+kfac+g+v   g + i++QG++r + +++L+ k g+
  gi|298676040|ref|YP_003727790.1| 24 EQQRITVKVNRRRYGKEVTIVEGLDANEIDLNELATYLKSKFACGGTV--RG-NAIELQGNHRSRMKDVLVAK-GF 95
                                      5899*******************************************9..44.47*****************9.87 PP

>> DTW  DTW domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.0   5.3e-06     0.024       2      29 ..       4      30 ..       3      43 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.3e-06
                               DTW  2 elCerCllpaevclcsslppleklpikv 29
                                      e+C  C lp+e+c+c+++ + e+++i v
  gi|298676040|ref|YP_003727790.1|  4 EMCSVCGLPKELCICEEVAK-EQQRITV 30
                                      68*****************9.7675665 PP

>> Img2  Mitochondrial large subunit ribosomal protein (Img2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.4e-05     0.063      36      80 .]      53      95 ..      11      95 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.4e-05
                              Img2 36 DiaalredLrkalee..lvkvnevtgkieikGdrveevkkfLeskgF 80
                                      D++    +L+++l++  ++  + + + ie++G+++++ k++L +kgF
  gi|298676040|ref|YP_003727790.1| 53 DLN----ELATYLKSkfACGGTVRGNAIELQGNHRSRMKDVLVAKGF 95
                                      333....444444443236777799*********************9 PP

>> CsgA  Minor curli fiber component A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   3.4e-05      0.15      18      50 ..      21      53 ..      13      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.4e-05
                              CsgA 18 esevgkeiykkleekeykseeefvkdLseeEie 50
                                        ++ ++i  k+++++y +e + v+ L+ +Ei+
  gi|298676040|ref|YP_003727790.1| 21 VAKEQQRITVKVNRRRYGKEVTIVEGLDANEID 53
                                      567889*************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.50
# Mc/sec: 612.43
//
Query:       gi|298676041|ref|YP_003727791.1|  [L=117]
Description: hypothetical protein Metev_2169 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-25   88.0   0.0    3.8e-25   87.9   0.0    1.0  1  DUF192    Uncharacterized ACR, COG1430


Domain annotation for each model (and alignments):
>> DUF192  Uncharacterized ACR, COG1430
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.9   0.0   2.1e-29   3.8e-25       2      94 ..      13     112 ..      12     114 .. 0.94

  Alignments for each domain:
  == domain 1  score: 87.9 bits;  conditional E-value: 2.1e-29
                                       EEEEE-SHHHHHHTTTT-----TTEEEEEEECCEEEEEE--TT--S-EEEEEE-TTSBEEEEEEEE-TT....-... CS
                            DUF192   2 tvevAdteeerarGLmgreslpedegmlfvfdkerehsfwMkntripLdiifldadgriveieealkpq....s... 71 
                                       +ve+A t+ ++++GLm+++++p+d++++fvfdk+ + s++M ++r+p+d++fld+++ri++ + +lkp+    s   
  gi|298676041|ref|YP_003727791.1|  13 DVEFATTFFSQSKGLMFKKNVPNDYALVFVFDKPIKTSVHMLFVRFPIDVLFLDDSKRIIKAT-TLKPWlgtsSsek 88 
                                       69***********************************************************99.578**87651677 PP

                                       .ECEEEEEETTHHHHHT--TT-EE CS
                            DUF192  72 .vryvLElpaGaakklgikpGdrl 94 
                                        v+y++E+++  ++++g+ +G++l
  gi|298676041|ref|YP_003727791.1|  89 iVKYIIEMKQHKISEHGLVEGEQL 112
                                       8********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.31s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 857.33
//
Query:       gi|298676042|ref|YP_003727792.1|  [L=715]
Description: phosphoribosylformylglycinamidine synthase II [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-45  152.9   0.4    7.7e-23   81.0   0.0    3.1  3  AIRS            AIR synthase related protein, N-terminal doma
    3.5e-43  147.4   1.9      2e-29  102.8   0.2    2.2  2  AIRS_C          AIR synthase related protein, C-terminal doma
    1.9e-07   31.5   0.1    8.5e-07   29.4   0.0    2.1  2  FGAR-AT_linker  Formylglycinamide ribonucleotide amidotransfe


Domain annotation for each model (and alignments):
>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.0   0.0   1.3e-26   7.7e-23       1      93 [.      59     172 ..      59     173 .. 0.94
   2 ?   -1.0   0.0      0.47   2.8e+03      53      81 ..     237     266 ..     225     284 .. 0.71
   3 !   68.4   0.0   1.1e-22   6.6e-19       5      93 ..     433     538 ..     420     539 .. 0.92

  Alignments for each domain:
  == domain 1  score: 81.0 bits;  conditional E-value: 1.3e-26
                                       SSSE.........EEEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.........HHHHHH CS
                              AIRS   1 dDaa.........vvvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp.........wleevv 59 
                                       dDaa         +++ ++shn+p++v+p+++ +a++v+++++D+++mGArP+al++ l ++          +e ++
  gi|298676042|ref|YP_003727792.1|  59 DDAAiiqfddewvLALGMESHNHPSYVDPYNG-AATGVGGIVRDILSMGARPIALMDPLYFGplnnsknlyLFEHII 134
                                       8999665555555599****************.******************************************** PP

                                       HHHHHHHHHTT-EEEEEEEEEESS....EEEEEEEEEE CS
                              AIRS  60 rglaeaaeelgvplvgGdtsfsne....ptisvtavGl 93 
                                       +g+a +++++gvp+v G+  f+++    p+++v+++Gl
  gi|298676042|ref|YP_003727792.1| 135 EGIAGYGNCIGVPVVRGEAFFDDSysgnPLVNVVCIGL 172
                                       *********************999999**********8 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.47
                                       C.HHHHHHHHHHHHHHHTT-EEEEEEEEEE CS
                              AIRS  53 p.wleevvrglaeaaeelgvplvgGdtsfs 81 
                                       + +le++ +g  + ++ lg++ + G +s++
  gi|298676042|ref|YP_003727792.1| 237 EaTLEGIDKGYVKSCRDLGAAGIVGASSEM 266
                                       456777778888888888887777776654 PP

  == domain 3  score: 68.4 bits;  conditional E-value: 1.1e-22
                                       EEEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.........HHHHHHHHHHHHHHHTT-E CS
                              AIRS   5 vvvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp.........wleevvrglaeaaeelgvp 72 
                                       +vv++ +++r++l++p+++ G+ +v +n+ +la+ G++ +a++++l+++         ++++++ gl+++a+el +p
  gi|298676042|ref|YP_003727792.1| 433 LVVSCGCNPRHTLLDPYKG-GRGTVFENAMNLAVKGGKAIAMVDCLNFGnpeksdiywQFKQAILGLGDCARELSIP 508
                                       59*****************.********************************************************* PP

                                       EEEEEEEEESS.........EEEEEEEEEE CS
                              AIRS  73 lvgGdtsfsne.........ptisvtavGl 93 
                                       +vgG++s +ne         pt+s++ +G+
  gi|298676042|ref|YP_003727792.1| 509 VVGGNVSLYNEseergtaiaPTPSIGLIGI 538
                                       *********999*****************8 PP

>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.8   0.2   3.3e-33     2e-29       1     152 [.     185     338 ..     185     341 .. 0.94
   2 !   44.1   0.1   3.9e-15   2.3e-11       2     124 ..     553     665 ..     552     686 .. 0.83

  Alignments for each domain:
  == domain 1  score: 102.8 bits;  conditional E-value: 3.3e-33
                                       STTEEEEEEET....SSCTCCHHHHHHHCHHHCTSHTT.TSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHH CS
                            AIRS_C   1 kpGdvliltgs....lGlggagtslkrkileeegldds.avqlgdvlleptliyvkralaalkglvkaahDvTgGGL 72 
                                       k+G++l+l+g     +Glgga+ +++r + ee++ +++ + q+gd++ e+ li++ ++ + + g vk+++D+++ G+
  gi|298676042|ref|YP_003727792.1| 185 KAGNKLVLMGAttgrDGLGGAS-FASRDLSEEAESEERpSIQIGDPFTEKLLIEATLEGIDK-GYVKSCRDLGAAGI 259
                                       69********************.6667777777777667**********************7.************** PP

                                       HHHHHHHHHTTTEEEEEECGTHHHHHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESS CS
                            AIRS_C  73 lgalaemapasgvgaeidldkvpifdelesplemllsensGrllvavppeeadavlaileeeglpeaavIGevtake 149
                                       +ga +ema ++++ga ++ld+v +++  ++p+e+l++e+++r l+ v+pe+ d  l+++e+++l  a+vIGe+ +++
  gi|298676042|ref|YP_003727792.1| 260 VGASSEMASKGNLGAYMYLDNVVLRESGMKPFEILIAESQERILLEVEPENVDYMLDVAEKYEL-SASVIGELKNDQ 335
                                       ****************************************************************.7*********99 PP

                                       SEE CS
                            AIRS_C 150 els 152
                                       + +
  gi|298676042|ref|YP_003727792.1| 336 KYT 338
                                       876 PP

  == domain 2  score: 44.1 bits;  conditional E-value: 3.9e-15
                                       TTEEEEEEET..SSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHH CS
                            AIRS_C   2 pGdvliltgs..lGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgal 76 
                                       +G ++il+g+  + lgg+ ++  r + +++g       ++ +   +  ++ +r++  +  +v++ahDv+ GGL++al
  gi|298676042|ref|YP_003727792.1| 553 EGETIILVGEthDELGGSEYYN-RIGYRTHGNT-----PDVPDNAESILDGVRKAVIS-SKVSSAHDVSQGGLVVAL 622
                                       799****************777.6566666654.....899999999**********8.****************** PP

                                       HHHHHTTTEEEEEECGTHHHHHHHHHHHHHHHCSTTTEEEEEEEHGGH CS
                            AIRS_C  77 aemapasgvgaeidldkvpifdelesplemllsensGrllvavppeea 124
                                        em++   +ga ++l+   + + l    e+l+se+  r +++ +++  
  gi|298676042|ref|YP_003727792.1| 623 CEMCDR--IGADVNLN--SVGAGL-RTDEILFSESHARAIISTSEPVY 665
                                       *****8..9*******..555555.459*************9998766 PP

>> FGAR-AT_linker  Formylglycinamide ribonucleotide amidotransferase linker domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   1.4e-10   8.5e-07      15      49 ..       5      36 ..       1      37 [. 0.85
   2 ?   -1.4   0.0      0.61   3.6e+03       7      30 ..     692     712 ..     688     715 .] 0.75

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.4e-10
                    FGAR-AT_linker 15 eEidylqeafeklgrnPtdvElemfaqvwSEHCrH 49
                                      ++ + ++e    +gr+P+ vE ++f   wSEHC++
  gi|298676042|ref|YP_003727792.1|  5 NDLKIITEK---MGRKPNLVEQGCFLNLWSEHCSY 36
                                      555666666...9*********************9 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.61
                    FGAR-AT_linker   7 elglaLsdeEidylqeafeklgrn 30 
                                       +++  L+++Ei+  ++    l+r 
  gi|298676042|ref|YP_003727792.1| 692 DQEIVLTLDEISNSRSS---LKRL 712
                                       6778899***9988887...6665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (715 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.47
# Mc/sec: 4568.79
//
Query:       gi|298676043|ref|YP_003727793.1|  [L=217]
Description: DtxR family iron (metal) dependent repressor [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-23   82.0   0.3    4.7e-23   81.0   0.3    1.5  1  Fe_dep_repr_C  Iron dependent repressor, metal binding and di
    6.2e-14   52.0   0.0    9.1e-13   48.3   0.0    2.2  2  FeoA           FeoA domain


Domain annotation for each model (and alignments):
>> Fe_dep_repr_C  Iron dependent repressor, metal binding and dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.0   0.3   5.3e-27   4.7e-23       3      69 ..      62     127 ..      61     128 .. 0.96

  Alignments for each domain:
  == domain 1  score: 81.0 bits;  conditional E-value: 5.3e-27
                                       HHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHCT-.SB-TTS-B-- CS
                     Fe_dep_repr_C   3 kGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldellgfpeecPhgdpip 69 
                                       +G   Ak++vrrhrl+er+Lvdvl+ ++e +h+ A+++Eh+l++ + ++++ llg+p++cPhg+pip
  gi|298676043|ref|YP_003727793.1|  62 EGYFNAKNVVRRHRLAERLLVDVLD-KKEGVHKSACEFEHILHDGVDDKVCVLLGHPRTCPHGNPIP 127
                                       67788********************.8***************************************9 PP

>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.041   3.7e+02      29      55 ..      47      73 ..      32      89 .. 0.80
   2 !   48.3   0.0     1e-16   9.1e-13       2      73 ..     145     213 ..     144     214 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.041
                                      HHHT--TT-EEEEEEE-TTS-SEEEEE CS
                              FeoA 29 remGlvpGarievvarapfggplvvrv 55
                                      + + l+ +++i++ +++ f+   vvr 
  gi|298676043|ref|YP_003727793.1| 47 DNIDLNSDSKITLKHEGYFNAKNVVRR 73
                                      567889999999999999988777775 PP

  == domain 2  score: 48.3 bits;  conditional E-value: 1e-16
                                       EGGG--TT-EEEEEEE-TT.SSHHHHHHHHT--TT-EEEEEEE-TTS-SEEEEETTEEEEE-HHHHTTEEEE CS
                              FeoA   2 pLsdlkeGergeiarisdedpellrrLremGlvpGarievvarapfggplvvrvgdtrvaLgreeAqaIlVe 73 
                                       pLs+lk +++g+ia +  +d e l++L++mG+ pG  +++v+ +     +v  +++tr a+++e+A+ I+V+
  gi|298676043|ref|YP_003727793.1| 145 PLSELKLNQKGKIAYFEIQDNEKLQKLMSMGILPGMPVTLVQ-SY--PSYVFDLDQTRYAVDKEMADYIFVR 213
                                       9****************************************5.43..47**********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1416.41
//
Query:       gi|298676044|ref|YP_003727794.1|  [L=56]
Description: hypothetical protein Metev_2172 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-05   24.3  12.2      0.014   15.5   0.2    2.8  2  UPF0547         Uncharacterised protein family UPF0547
    9.3e-05   22.0  14.2     0.0067   16.1   0.4    2.4  3  zinc_ribbon_2   zinc-ribbon domain
    0.00024   21.1   8.2    0.00044   20.2   8.2    1.4  1  DZR             Double zinc ribbon
     0.0064   15.9  14.3      0.041   13.3   0.6    2.5  3  zf-ribbon_3     zinc-ribbon domain
  ------ inclusion threshold ------
       0.01   15.8   9.0       0.53   10.3   0.6    2.3  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
      0.012   15.5   5.9      0.043   13.6   0.2    2.3  2  Rad50_zn_hook   Rad50 zinc hook motif
      0.024   14.5   5.9        1.6    8.6   0.0    2.2  2  Cys_rich_CPCC   Cysteine-rich CPCC
      0.031   13.9   6.9       0.85    9.3   0.2    3.2  3  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
      0.051   13.5   8.3        3.2    7.8   8.3    2.6  1  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
      0.069   13.1   7.8      0.081   12.9   7.8    1.1  1  zinc-ribbons_6  zinc-ribbons
        0.1   12.5   7.5       0.56   10.2   3.1    2.2  3  Prok-RING_1     Prokaryotic RING finger family 1
       0.14   12.1   7.1       0.39   10.6   0.0    2.8  2  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
       0.18   12.3   9.8        1.6    9.4   0.2    3.3  3  zf-C2H2         Zinc finger, C2H2 type
       0.18   12.3   3.0       0.36   11.4   0.3    2.3  2  Zn-C2H2_12      Autophagy receptor zinc finger-C2H2 domain
       0.21   11.3   9.3       0.58    9.9   5.6    2.4  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
       0.23   11.2   9.7        4.8    7.0   0.2    3.2  3  A2L_zn_ribbon   A2L zinc ribbon domain
       0.24   11.6   9.2       0.52   10.5   9.2    1.7  1  zf-piccolo      Piccolo Zn-finger
       0.34   10.9   8.7        2.6    8.1   0.5    2.4  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.69   10.5   0.5       0.69   10.5   0.5    3.1  2  zf-H2C2_2       Zinc-finger double domain
       0.71    9.9   8.8        0.8    9.8   0.5    2.9  3  CpXC            CpXC protein
       0.87    9.6   8.6        7.4    6.6   8.6    2.0  1  HypA            Hydrogenase/urease nickel incorporation, meta
          1    9.3  10.0        9.2    6.3   0.4    3.5  3  zinc_ribbon_4   zinc-ribbon domain
        1.3    8.6  11.6        2.6    7.6   0.3    2.6  2  TF_Zn_Ribbon    TFIIB zinc-binding
        1.4    9.1  12.8    1.2e+02    3.0  12.8    2.5  1  Zn-ribbon_8     Zinc ribbon domain
        1.8    9.4  11.3        4.3    8.1  11.3    1.6  1  zinc_ribbon_15  zinc-ribbon family
        2.3    6.9   5.1        2.4    6.8   5.1    1.2  1  NRDD            Anaerobic ribonucleoside-triphosphate reducta
        2.7    9.1   0.1        2.7    9.1   0.1    3.1  3  zf-C2H2_4       C2H2-type zinc finger
        2.8    7.9  10.9        6.8    6.7   0.2    3.2  3  Zn_ribbon_SprT  SprT-like zinc ribbon domain
        4.8    7.2  12.1         13    5.8   0.6    3.1  3  YhfH            YhfH-like protein
        5.9    6.9  14.4        3.9    7.5   0.5    3.2  3  zf-C2HC_2       zinc-finger of a C2HC-type
        5.9    7.2   7.7        7.8    6.9   3.6    2.5  2  Ribosomal_L32p  Ribosomal L32p protein family


Domain annotation for each model (and alignments):
>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   2.3e-05     0.014      16      25 ..       2      11 ..       1      12 [. 0.89
   2 !   10.8   7.3   0.00072      0.42       3      23 ..      18      38 ..      16      41 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.3e-05
                           UPF0547 16 fCphCGyvFq 25
                                      +Cp+CGy+F 
  gi|298676044|ref|YP_003727794.1|  2 KCPLCGYEFT 11
                                      7********6 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00072
                           UPF0547  3 CPeCeakvPvaaqfCphCGyv 23
                                      C +C    + ++q+Cp CGy+
  gi|298676044|ref|YP_003727794.1| 18 CSGCGKLHSCNMQRCPNCGYE 38
                                      6667777788**********7 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   6.1    0.0031       1.8       1      20 [.       2      22 ..       2      24 .. 0.92
   2 !   14.8   7.9   2.9e-05     0.017       2      23 .]      18      39 ..      17      39 .. 0.95
   3 !   16.1   0.4   1.2e-05    0.0067       1      14 [.      31      44 ..      31      45 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0031
                     zinc_ribbon_2  1 fCpnCGael.qdnakFCpyCG 20
                                      +Cp CG+e  +++ + C+ CG
  gi|298676044|ref|YP_003727794.1|  2 KCPLCGYEFtEPDKNQCSGCG 22
                                      8********668********* PP

  == domain 2  score: 14.8 bits;  conditional E-value: 2.9e-05
                     zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGtpl 23
                                      C+ CG+ ++ n + Cp+CG+++
  gi|298676044|ref|YP_003727794.1| 18 CSGCGKLHSCNMQRCPNCGYEI 39
                                      999****************985 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 1.2e-05
                     zinc_ribbon_2  1 fCpnCGaelqdnak 14
                                      +CpnCG+e+ ++ k
  gi|298676044|ref|YP_003727794.1| 31 RCPNCGYEIVPETK 44
                                      6********88765 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   8.2   7.7e-07   0.00044       1      42 [.       3      43 ..       3      47 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 7.7e-07
                               DZR  1 CpqCgee.lppdarfCseCgtklkavaaedrCpsCgekvdpea 42
                                      Cp Cg e ++pd++ Cs Cg+  +   +++rCp+Cg+++ pe+
  gi|298676044|ref|YP_003727794.1|  3 CPLCGYEfTEPDKNQCSGCGKLHS--CNMQRCPNCGYEIVPET 43
                                      999999967788889999998765..56999999999976665 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   5.4    0.0034         2       4      24 ..       2      23 ..       1      24 [. 0.94
   2 !   11.6   8.6   0.00023      0.14       3      26 .]      16      39 ..      14      39 .. 0.91
   3 !   13.3   0.6   7.1e-05     0.041       2      10 ..      29      37 ..      28      43 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0034
                       zf-ribbon_3  4 rCPnCGa.plssddnvCpyCGt 24
                                      +CP CG    ++d n C  CG+
  gi|298676044|ref|YP_003727794.1|  2 KCPLCGYeFTEPDKNQCSGCGK 23
                                      6********************7 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00023
                       zf-ribbon_3  3 vrCPnCGa.plssddnvCpyCGtkl 26
                                      ++C+ CG+ + s  ++ Cp+CG+++
  gi|298676044|ref|YP_003727794.1| 16 NQCSGCGKlH-SCNMQRCPNCGYEI 39
                                      68******88.***********986 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 7.1e-05
                       zf-ribbon_3  2 tvrCPnCGa 10
                                      ++rCPnCG 
  gi|298676044|ref|YP_003727794.1| 29 MQRCPNCGY 37
                                      789999985 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   2.2    0.0012      0.67      20      45 ..       2      23 ..       1      24 [. 0.93
   2 ?   10.3   0.6   0.00092      0.53      19      28 ..      30      42 ..      25      56 .] 0.68

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0012
                     Zn_Tnp_IS1595 20 vCPhCgsrkayriktrglfqCkeCrk 45
                                       CP Cg    y+++ + + qC+ C+k
  gi|298676044|ref|YP_003727794.1|  2 KCPLCG----YEFTEPDKNQCSGCGK 23
                                      6*****....9*************96 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00092
                     Zn_Tnp_IS1595 19 fvCPhCgsr...k 28
                                      ++CP+Cg++   +
  gi|298676044|ref|YP_003727794.1| 30 QRCPNCGYEivpE 42
                                      78*****986554 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   7.5e-05     0.043      21      35 ..       2      16 ..       1      17 [. 0.89
   2 ?    4.4   1.2     0.059        34      20      40 ..      30      48 ..      23      54 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.5e-05
                                      E-TTT--EE-HHHHH CS
                     Rad50_zn_hook 21 cCPlCgReldeehrs 35
                                      +CPlCg e++e +++
  gi|298676044|ref|YP_003727794.1|  2 KCPLCGYEFTEPDKN 16
                                      7**********9875 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.059
                                      EE-TTT--EE-HHHHHHHHHH CS
                     Rad50_zn_hook 20 gcCPlCgReldeehrseLike 40
                                      ++CP Cg e+ +e   +Lik+
  gi|298676044|ref|YP_003727794.1| 30 QRCPNCGYEIVPET--KLIKK 48
                                      49*****9998887..34444 PP

>> Cys_rich_CPCC  Cysteine-rich CPCC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   2.5    0.0065       3.8       2      24 ..       2      21 ..       1      25 [. 0.73
   2 ?    8.6   0.0    0.0028       1.6       2      15 ..      31      44 ..      30      52 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0065
                     Cys_rich_CPCC  2 qCpcCgyltleeeegsydiCpvC 24
                                      +Cp Cgy   e ++   + C+ C
  gi|298676044|ref|YP_003727794.1|  2 KCPLCGYEFTEPDK---NQCSGC 21
                                      8******9887773...345544 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0028
                     Cys_rich_CPCC  2 qCpcCgyltleeee 15
                                      +Cp Cgy  ++e++
  gi|298676044|ref|YP_003727794.1| 31 RCPNCGYEIVPETK 44
                                      7********99875 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.051        29      22      30 ..       1       9 [.       1      10 [. 0.75
   2 ?    3.0   0.5      0.14        79      23      29 ..      17      23 ..      15      25 .. 0.64
   3 ?    9.3   0.2    0.0015      0.85      22      30 ..      30      38 ..      29      40 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.051
                     zf-NADH-PPase 22 rvCpaCgle 30
                                      + Cp Cg+e
  gi|298676044|ref|YP_003727794.1|  1 MKCPLCGYE 9 
                                      678888887 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.14
                     zf-NADH-PPase 23 vCpaCgl 29
                                      +C+ Cg 
  gi|298676044|ref|YP_003727794.1| 17 QCSGCGK 23
                                      5666665 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0015
                     zf-NADH-PPase 22 rvCpaCgle 30
                                       +Cp+Cg+e
  gi|298676044|ref|YP_003727794.1| 30 QRCPNCGYE 38
                                      59*****98 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   8.3    0.0055       3.2       4      29 ..       2      39 ..       1      40 [. 0.91

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0055
                    PhnA_Zn_Ribbon  4 kCplCaSeytY............edgallvCpeCahEw 29
                                      kCplC+ e+t             +   +  Cp+C++E+
  gi|298676044|ref|YP_003727794.1|  2 KCPLCGYEFTEpdknqcsgcgklHSCNMQRCPNCGYEI 39
                                      8****9999999999999999988888889*******9 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   7.8   0.00014     0.081       2      39 ..       2      39 ..       1      44 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00014
                                      --SSS-S--EE-SSEEE-TTT--.EEEEEEE-SSS-S-- CS
                    zinc-ribbons_6  2 kCpeCqqelekrgeqyhCeaCqe.dlkkealCpeCeqel 39
                                      kCp C  e ++ + + +C+ C + +  + + Cp+C+ e+
  gi|298676044|ref|YP_003727794.1|  2 KCPLCGYEFTEPD-KNQCSGCGKlHSCNMQRCPNCGYEI 39
                                      7********9776.89******98888999*****9775 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   3.1   0.00096      0.56       6      28 ..       2      23 ..       1      28 [. 0.89
   2 ?    2.9   4.4      0.19   1.1e+02       4      27 ..      15      36 ..      12      38 .. 0.79
   3 ?    4.6   0.4     0.054        31       5      16 ..      30      41 ..      26      46 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00096
                       Prok-RING_1  6 kCpvCgkelkeedDiVvCpeCgt 28
                                      kCp+Cg e++e  D  +C  Cg 
  gi|298676044|ref|YP_003727794.1|  2 KCPLCGYEFTEP-DKNQCSGCGK 23
                                      8********998.999*****96 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.19
                       Prok-RING_1  4 gkkCpvCgkelkeedDiVvCpeCg 27
                                      +++C+ Cgk  + +  +  Cp+Cg
  gi|298676044|ref|YP_003727794.1| 15 KNQCSGCGKLHSCN--MQRCPNCG 36
                                      68899999876666..77899998 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.054
                       Prok-RING_1  5 kkCpvCgkelke 16
                                      ++Cp Cg e+ +
  gi|298676044|ref|YP_003727794.1| 30 QRCPNCGYEIVP 41
                                      678888888765 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.5     0.061        35      13      21 ..      17      25 ..      16      25 .. 0.86
   2 ?   10.6   0.0   0.00068      0.39      12      23 ..      30      41 ..      29      45 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.061
                           DUF35_N 13 rCpdCGtvq 21
                                      +C+ CG+++
  gi|298676044|ref|YP_003727794.1| 17 QCSGCGKLH 25
                                      7*****975 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00068
                           DUF35_N 12 qrCpdCGtvqfP 23
                                      qrCp+CG  ++P
  gi|298676044|ref|YP_003727794.1| 30 QRCPNCGYEIVP 41
                                      9******76666 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.2    0.0027       1.6       2      13 ..       2      13 ..       1      15 [. 0.86
   2 ?    3.9   0.3      0.14        83       2       8 ..      17      23 ..      16      24 .. 0.92
   3 ?    4.8   0.1     0.079        46       2       8 ..      31      37 ..      30      46 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0027
                                      EETTTTEEESSH CS
                           zf-C2H2  2 kCpdCgksFkrk 13
                                      kCp Cg+ F+ +
  gi|298676044|ref|YP_003727794.1|  2 KCPLCGYEFTEP 13
                                      8********976 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.14
                                      EETTTTE CS
                           zf-C2H2  2 kCpdCgk 8 
                                      +C++Cgk
  gi|298676044|ref|YP_003727794.1| 17 QCSGCGK 23
                                      7*****8 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.079
                                      EETTTTE CS
                           zf-C2H2  2 kCpdCgk 8 
                                      +Cp Cg+
  gi|298676044|ref|YP_003727794.1| 31 RCPNCGY 37
                                      7****96 PP

>> Zn-C2H2_12  Autophagy receptor zinc finger-C2H2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   0.00062      0.36       2      11 ..       2      11 ..       2      17 .. 0.86
   2 ?    0.9   0.2       1.1   6.4e+02       3       8 ..      32      37 ..      30      38 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00062
                        Zn-C2H2_12  2 eCPlCseqFp 11
                                      +CPlC++ F 
  gi|298676044|ref|YP_003727794.1|  2 KCPLCGYEFT 11
                                      7******995 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.1
                        Zn-C2H2_12  3 CPlCse 8 
                                      CP C++
  gi|298676044|ref|YP_003727794.1| 32 CPNCGY 37
                                      **9*96 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1       0.2   1.2e+02      19      25 ..       2       8 ..       1      10 [. 0.86
   2 ?    9.9   5.6     0.001      0.58       3      28 ..      18      40 ..      16      40 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.2
                                      --SSS-- CS
                    DNA_RNApol_7kD 19 RCkeCGh 25
                                      +C  CG+
  gi|298676044|ref|YP_003727794.1|  2 KCPLCGY 8 
                                      7999*98 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.001
                                      -SSS--B----SSS----SSS----- CS
                    DNA_RNApol_7kD  3 CgeCgaevslkkgdpiRCkeCGhRil 28
                                      C +Cg+ +s + +   RC +CG+ i+
  gi|298676044|ref|YP_003727794.1| 18 CSGCGKLHSCNMQ---RCPNCGYEIV 40
                                      9999999999999...*******886 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.2    0.0083       4.8      24      32 ..       3      11 ..       1      11 [. 0.85
   2 ?    3.7   1.2     0.093        54       4      11 ..      16      23 ..      14      23 .. 0.80
   3 ?    5.3   0.1     0.028        16      24      30 ..      32      38 ..      29      40 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0083
                     A2L_zn_ribbon 24 CieCgasfp 32
                                      C+ Cg++f+
  gi|298676044|ref|YP_003727794.1|  3 CPLCGYEFT 11
                                      ******985 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.093
                     A2L_zn_ribbon  4 kvCsvCgg 11
                                      + Cs+Cg+
  gi|298676044|ref|YP_003727794.1| 16 NQCSGCGK 23
                                      78****96 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.028
                     A2L_zn_ribbon 24 CieCgas 30
                                      C++Cg++
  gi|298676044|ref|YP_003727794.1| 32 CPNCGYE 38
                                      *****95 PP

>> zf-piccolo  Piccolo Zn-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   9.2   0.00091      0.52       2      43 ..       2      44 ..       1      49 [. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00091
                        zf-piccolo  2 lCplCktelnvgskep.pnyntCteCkkqvCnlCGFnptphlt 43
                                       CplC  e +   k++     +  +C+ q C  CG++  p+++
  gi|298676044|ref|YP_003727794.1|  2 KCPLCGYEFTEPDKNQcSGCGKLHSCNMQRCPNCGYEIVPETK 44
                                      5*****99986654441334455789************99876 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   8.8     0.095        55      30      55 ..      17      38 ..       1      40 [. 0.65
   2 ?    8.1   0.5    0.0044       2.6      29      40 ..      30      41 ..      25      55 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.095
                    OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfe 55
                                      +Cs Cg+ ++     +  +CpnCg+e
  gi|298676044|ref|YP_003727794.1| 17 QCSGCGKLHSC----NMQRCPNCGYE 38
                                      56666666666....77788888886 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0044
                    OrfB_Zn_ribbon 29 ktCseCgsknke 40
                                      ++C++Cg++  +
  gi|298676044|ref|YP_003727794.1| 30 QRCPNCGYEIVP 41
                                      789999988766 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.5    0.0012      0.69      16      25 ..       2      11 ..       2      12 .. 0.92
   2 ?   -0.1   6.0       2.6   1.5e+03      16      22 ..      31      37 ..      13      39 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0012
                         zf-H2C2_2 16 eCplCdkaFk 25
                                      +CplC++ F+
  gi|298676044|ref|YP_003727794.1|  2 KCPLCGYEFT 11
                                      7*******97 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2.6
                         zf-H2C2_2 16 eCplCdk 22
                                       Cp C++
  gi|298676044|ref|YP_003727794.1| 31 RCPNCGY 37
                                      6999998 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1       0.1        60      39      48 ..       2      11 ..       1      15 [. 0.63
   2 ?    2.1   1.0      0.33   1.9e+02      39      51 ..      17      29 ..      13      30 .. 0.77
   3 ?    9.8   0.5    0.0014       0.8      35      54 ..      27      46 ..      25      51 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.1
                              CpXC 39 tCpkCgatak 48
                                      +Cp Cg++++
  gi|298676044|ref|YP_003727794.1|  2 KCPLCGYEFT 11
                                      5666666654 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.33
                              CpXC 39 tCpkCgataklea 51
                                      +C  Cg+ ++ ++
  gi|298676044|ref|YP_003727794.1| 17 QCSGCGKLHSCNM 29
                                      8999999887765 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0014
                              CpXC 35 lfeatCpkCgatakleapll 54
                                       ++ +Cp+Cg+++ +e +l+
  gi|298676044|ref|YP_003727794.1| 27 CNMQRCPNCGYEIVPETKLI 46
                                      57889*******99998875 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   8.6     0.013       7.4      73      94 ..       3      37 ..       1      49 [. 0.57

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.013
                                      ETTTS-EEECHHHHH.............S-TTTSS CS
                              HypA 73 CreCgkefeleekal.............rCpkCgs 94
                                      C  Cg+ef++ +k+              rCp+Cg 
  gi|298676044|ref|YP_003727794.1|  3 CPLCGYEFTEPDKNQcsgcgklhscnmqRCPNCGY 37
                                      66666666644321123344444444447888875 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.035        20      26      36 .]       1      11 [.       1      11 [. 0.79
   2 ?    3.1   0.5      0.16        93      27      33 ..      17      23 ..      12      26 .. 0.82
   3 ?    6.3   0.4     0.016       9.2      27      32 ..      31      36 ..      28      40 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.035
                     zinc_ribbon_4 26 vrCskCghvFr 36
                                      ++C+ Cg  F+
  gi|298676044|ref|YP_003727794.1|  1 MKCPLCGYEFT 11
                                      58999998875 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.16
                     zinc_ribbon_4 27 rCskCgh 33
                                      +Cs Cg+
  gi|298676044|ref|YP_003727794.1| 17 QCSGCGK 23
                                      8999986 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.016
                     zinc_ribbon_4 27 rCskCg 32
                                      rC++Cg
  gi|298676044|ref|YP_003727794.1| 31 RCPNCG 36
                                      677777 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   5.9      0.07        40       1      26 [.       1      22 [.       1      24 [. 0.74
   2 ?    7.6   0.3    0.0046       2.6       2       7 ..      31      36 ..      30      44 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.07
                                      EEETTTTCEECHEETSTTCEEESSSS CS
                      TF_Zn_Ribbon  1 ykCPnCgstnlveDpergelvCtdCG 26
                                      +kCP Cg ++++ D       C+ CG
  gi|298676044|ref|YP_003727794.1|  1 MKCPLCGYEFTEPD----KNQCSGCG 22
                                      79*****8875555....34788888 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0046
                                      EETTTT CS
                      TF_Zn_Ribbon  2 kCPnCg 7 
                                      +CPnCg
  gi|298676044|ref|YP_003727794.1| 31 RCPNCG 36
                                      688887 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0  12.8       0.2   1.2e+02       7      33 ..       2      36 ..       1      41 [. 0.74

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.2
                       Zn-ribbon_8  7 rCeeCghefe...........vlqsisdapltaCPeCg 33
                                      +C  Cg ef+           +l+s +   ++ CP+Cg
  gi|298676044|ref|YP_003727794.1|  2 KCPLCGYEFTepdknqcsgcgKLHSCN---MQRCPNCG 36
                                      799999999977777777666666655...67788888 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1  11.3    0.0075       4.3      43      86 .]       6      36 ..       1      36 [. 0.79

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0075
                    zinc_ribbon_15 43 CkslleaskelgkeiekkessekkeCknCgkeveeefkyCpkCg 86
                                      C++ +++ +             k++C+ Cgk  + +++ Cp+Cg
  gi|298676044|ref|YP_003727794.1|  6 CGYEFTEPD-------------KNQCSGCGKLHSCNMQRCPNCG 36
                                      555555544.............99*******************9 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   5.1    0.0042       2.4     498     527 ..       6      37 ..       1      51 [. 0.77

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0042
                                       --EEEEE--EEEETT.--..EESSSB-TTT-- CS
                              NRDD 498 igYfsinpkidvCnecgy..kgeiekCpkCgs 527
                                       +gY  + p+ + C  cg+  +  +++Cp+Cg 
  gi|298676044|ref|YP_003727794.1|   6 CGYEFTEPDKNQCSGCGKlhSCNMQRCPNCGY 37 
                                       56777778889999999986666689999993 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1    0.0046       2.7       2      13 ..       2      13 ..       1      15 [. 0.85
   2 ?    3.0   1.2      0.42   2.4e+02       2      12 ..      17      27 ..      16      31 .. 0.78
   3 ?    1.7   0.5       1.1   6.1e+02       2       7 ..      31      36 ..      30      41 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0046
                         zf-C2H2_4  2 kCpiCgksFssk 13
                                      kCp+Cg  F+ +
  gi|298676044|ref|YP_003727794.1|  2 KCPLCGYEFTEP 13
                                      7********876 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.42
                         zf-C2H2_4  2 kCpiCgksFss 12
                                      +C+ Cgk  s+
  gi|298676044|ref|YP_003727794.1| 17 QCSGCGKLHSC 27
                                      7****997765 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 1.1
                         zf-C2H2_4  2 kCpiCg 7 
                                      +Cp Cg
  gi|298676044|ref|YP_003727794.1| 31 RCPNCG 36
                                      6****6 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1     0.031        18       6      14 ..       2      10 ..       2      12 .. 0.80
   2 ?    1.3   1.7      0.56   3.2e+02       6      15 ..      17      23 ..      15      27 .. 0.82
   3 ?    6.7   0.2     0.012       6.8       6      13 ..      31      38 ..      31      44 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.031
                    Zn_ribbon_SprT  6 rCtgCgrey 14
                                      +C+ Cg e+
  gi|298676044|ref|YP_003727794.1|  2 KCPLCGYEF 10
                                      6*****765 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.56
                    Zn_ribbon_SprT  6 rCtgCgreyt 15
                                      +C gCg   +
  gi|298676044|ref|YP_003727794.1| 17 QCSGCG---K 23
                                      7****9...4 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.012
                    Zn_ribbon_SprT  6 rCtgCgre 13
                                      rC++Cg e
  gi|298676044|ref|YP_003727794.1| 31 RCPNCGYE 38
                                      8*****65 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   3.8      0.19   1.1e+02      15      37 .]       2      21 ..       2      21 .. 0.74
   2 ?   -1.4   9.1       4.1   2.4e+03      15      37 .]      17      35 ..      11      35 .. 0.78
   3 ?    5.8   0.6     0.023        13      15      23 ..      31      39 ..      26      42 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.19
                              YhfH 15 kCteCGkeieEqaecYgneCekC 37
                                      kC+ CG e+ E     +n+C  C
  gi|298676044|ref|YP_003727794.1|  2 KCPLCGYEFTEPD---KNQCSGC 21
                                      7*****9998865...4666655 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.1
                              YhfH 15 kCteCGkeieEqaecYgneCekC 37
                                      +C+ CGk     + c ++ C +C
  gi|298676044|ref|YP_003727794.1| 17 QCSGCGK----LHSCNMQRCPNC 35
                                      8*****8....588888888888 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.023
                              YhfH 15 kCteCGkei 23
                                       C++CG ei
  gi|298676044|ref|YP_003727794.1| 31 RCPNCGYEI 39
                                      7*****988 PP

>> zf-C2HC_2  zinc-finger of a C2HC-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.7     0.049        29       4       9 ..       2       7 ..       1      15 [. 0.77
   2 ?    3.8   1.1     0.094        55       4       9 ..      17      22 ..      14      24 .. 0.87
   3 ?    7.5   0.5    0.0068       3.9       2       9 ..      29      36 ..      28      36 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.049
                         zf-C2HC_2 4 pCpkCg 9
                                     +Cp Cg
  gi|298676044|ref|YP_003727794.1| 2 KCPLCG 7
                                     7****9 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.094
                         zf-C2HC_2  4 pCpkCg 9 
                                      +C +Cg
  gi|298676044|ref|YP_003727794.1| 17 QCSGCG 22
                                      9****9 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0068
                         zf-C2HC_2  2 lvpCpkCg 9 
                                      ++ Cp+Cg
  gi|298676044|ref|YP_003727794.1| 29 MQRCPNCG 36
                                      899****9 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   1.6      0.46   2.7e+02      23      34 ..      12      23 ..       1      25 [. 0.47
   2 ?    6.9   3.6     0.013       7.8      20      33 ..      23      36 ..      14      44 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.46
                                      ---EEEETTTCC CS
                    Ribosomal_L32p 23 apnlvecpncge 34
                                       p+ ++c+ cg+
  gi|298676044|ref|YP_003727794.1| 12 EPDKNQCSGCGK 23
                                      333445555555 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.013
                                      ------EEEETTTC CS
                    Ribosomal_L32p 20 klkapnlvecpncg 33
                                      kl   n+++cpncg
  gi|298676044|ref|YP_003727794.1| 23 KLHSCNMQRCPNCG 36
                                      67788999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       771  (0.043003); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        36  (0.00200792); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 337.69
//
Query:       gi|298676045|ref|YP_003727795.1|  [L=681]
Description: ferrous iron transport protein B [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-50  171.1   0.0    2.3e-50  170.2   0.0    1.5  1  FeoB_N       Ferrous iron transport protein B
    1.1e-20   73.9  21.4    3.4e-14   53.1   4.0    2.9  2  Gate         Nucleoside recognition
      2e-20   73.0   0.0    4.8e-20   71.7   0.0    1.7  1  MMR_HSR1     50S ribosome-binding GTPase
    2.8e-10   40.6   1.3      6e-10   39.5   1.3    1.6  1  FeoB_Cyto    FeoB cytosolic helical domain
    5.6e-10   38.8   2.4    5.6e-10   38.8   2.4    3.1  2  FeoB_C       Ferrous iron transport protein B C terminus
     0.0011   18.4   0.2     0.0029   17.0   0.0    1.8  2  AIG1         AIG1 family
     0.0042   17.3   0.0     0.0098   16.1   0.0    1.7  1  Roc          Ras of Complex, Roc, domain of DAPkinase
     0.0065   16.4   0.5        5.3    6.9   0.1    2.8  2  RsgA_GTPase  RsgA GTPase
  ------ inclusion threshold ------
      0.012   15.2   0.0      0.041   13.4   0.0    1.8  1  GTP_EFTU     Elongation factor Tu GTP binding domain
      0.012   15.3   0.1       0.03   14.1   0.0    1.7  2  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
      0.016   14.6   0.0      0.031   13.7   0.0    1.4  1  SRPRB        Signal recognition particle receptor beta subuni
      0.047   12.7   0.0        2.1    7.3   0.0    2.5  2  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
       0.05   13.4   0.1       0.14   11.9   0.0    1.8  1  ATP_bind_1   Conserved hypothetical ATP binding protein
       0.15   12.1   5.3        1.4    9.0   0.0    3.1  3  Dynamin_N    Dynamin family


Domain annotation for each model (and alignments):
>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.2   0.0   1.8e-53   2.3e-50       2     156 .]      25     178 ..      24     178 .. 0.97

  Alignments for each domain:
  == domain 1  score: 170.2 bits;  conditional E-value: 1.8e-53
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHHCTS CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardflleee 78 
                                       +++lvG pnvGk+++fnal++++   +N+pG+tve ++g   + +k++ei+D PG Ysl +++eee+va++++  e+
  gi|298676045|ref|YP_003727795.1|  25 RIVLVGSPNVGKSVIFNALSDSYAIASNYPGTTVEISKGDGVIGNKKYEIIDTPGSYSLLPITEEERVAQRLFF-EK 100
                                       589******************************************************************98766.88 PP

                                       SSEEEEEEEGGGHHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHHHHH CS
                            FeoB_N  79 pdvvvnvvdatnlernLyLtlqllelgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieellka 155
                                       + + ++v+da+nl+r L  tlql+e g+p++l+lnm+dea ++gi+id++kL+++L++pv++++++k+egieel+k+
  gi|298676045|ref|YP_003727795.1| 101 ASIYLHVIDAKNLRRMLPHTLQLIEAGKPLILVLNMMDEAAERGIRIDIQKLEQMLKIPVIPAVSNKGEGIEELKKT 177
                                       9**************************************************************************98 PP

                                       H CS
                            FeoB_N 156 i 156
                                       i
  gi|298676045|ref|YP_003727795.1| 178 I 178
                                       6 PP

>> Gate  Nucleoside recognition
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.1   4.0   2.7e-17   3.4e-14       4     111 ..     394     487 ..     391     488 .. 0.95
   2 !   32.4   2.9   6.8e-11   8.8e-08       2     111 ..     549     649 ..     548     650 .. 0.95

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 2.7e-17
                              Gate   4 agpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqgfd 80 
                                       ++pi+ +++++ +++++s++l r++ l++ vf+++g  l+++a+++l++gf+   ++  + ++++         + +
  gi|298676045|ref|YP_003727795.1| 394 ILPIVGAFFFVFSIIEDSGYLPRLAMLIDRVFKKIG--LSGRAVIPLVLGFG---CGTMATMVTR---------TLE 456
                                       6899********************************..**************...8888888888.........*** PP

                              Gate  81 tpksalafllfvllytpcvatlavivrelgs 111
                                        p++++ + l+++l++pc a+l+vi +++++
  gi|298676045|ref|YP_003727795.1| 457 KPREKILTTLLLSLAIPCSAQLGVILGIMSA 487
                                       *************************999876 PP

  == domain 2  score: 32.4 bits;  conditional E-value: 6.8e-11
                              Gate   2 lkagpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqg 78 
                                       l ++p++++asiliw+ + ++++g +  ll+   +++g  l+ +a+  +l+gf+ +  +++ l +l        + g
  gi|298676045|ref|YP_003727795.1| 549 LEVMPLFIIASILIWLGKITGIFGLLIELLKYPTQWIG--LPSEAADVFLLGFFRRDFGAAGLYELN-------KTG 616
                                       6799**********************************..***********************8885.......889 PP

                              Gate  79 fdtpksalafllfvllytpcvatlavivrelgs 111
                                         + ++ l++ ++++l +pc+a++ +  +e g 
  gi|298676045|ref|YP_003727795.1| 617 VMNGVDMLVAAVTLTLFMPCIAQFMMTLKERGL 649
                                       ******99999999999*********9999986 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.7   0.0   3.8e-23   4.8e-20       1     113 [.      25     135 ..      25     136 .. 0.81

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 3.8e-23
                                       EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS..HHHHHHHHHHHHHHHHC CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGlie..gaseekglgkaflalee 75 
                                       ++++vG pNvGKS ++nal+++ ai+s++pgtT +i +g   +++k++e++DtpG ++     ee+++++++   e+
  gi|298676045|ref|YP_003727795.1|  25 RIVLVGSPNVGKSVIFNALSDSYAIASNYPGTTVEISKGDGVIGNKKYEIIDTPGSYSllPITEEERVAQRLF-FEK 100
                                       699*************************************99999**********653321223444444444.578 PP

                                       TSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEE CS
                          MMR_HSR1  76 adlillvvdaseeklkpldeeleelleeakkplilvln 113
                                       a++ l+v+da+ + l+++  +  +l+ ea+kplilvln
  gi|298676045|ref|YP_003727795.1| 101 ASIYLHVIDAK-N-LRRMLPHTLQLI-EAGKPLILVLN 135
                                       9********76.4.666666666664.589******99 PP

>> FeoB_Cyto  FeoB cytosolic helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   1.3   4.7e-13     6e-10       1      90 [.     192     278 ..     192     279 .. 0.97

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 4.7e-13
                         FeoB_Cyto   1 YgeeiEkaiekleellkesnlkaklppRwlAlklLegDeelleelkedpelraeveearkeleaelgedledvIvda 77 
                                       Y ++iE+ai+ +e+ lke+    ++++R ++  lL++D+ + e+++e+ e+ ++++ ++++ e++++  +  v++ +
  gi|298676045|ref|YP_003727795.1| 192 YNDDIENAIKDIESNLKEN---YEVSKRSISQLLLQRDQVAFERIQEKGEDVDAIKDIVSNTENKFNTPTNYVMTVE 265
                                       99****************6...******************************************************* PP

                         FeoB_Cyto  78 rykfiegilrevv 90 
                                       r+++ ++i+++v 
  gi|298676045|ref|YP_003727795.1| 266 RQQLTNRIVNSVT 278
                                       *********9986 PP

>> FeoB_C  Ferrous iron transport protein B C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   2.4   4.4e-13   5.6e-10       2      53 .]     493     543 ..     492     543 .. 0.96
   2 ?   -1.1   1.4       1.2   1.6e+03       2      21 ..     653     672 ..     652     676 .. 0.85

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 4.4e-13
                            FeoB_C   2 fslYllgilvallvalllkkttlkgepspfvmELPpYrlPslknvliktweR 53 
                                       +++ +++il +l++++++ k+ l+ge+++f++E+P +++P+l nvlikt+ R
  gi|298676045|ref|YP_003727795.1| 493 LLWVVVMILEFLFIGYIAAKV-LPGEKPSFFLEIPSLKVPKLSNVLIKTYSR 543
                                       7899****************9.***************************987 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.2
                            FeoB_C   2 fslYllgilvallvalllkk 21 
                                       +s+ ++ + +a++v+++++ 
  gi|298676045|ref|YP_003727795.1| 653 LSMAAFIFPFAFFVGFVVNY 672
                                       7899999999*****99876 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   2.2e-06    0.0029       2      67 ..      25      88 ..      24     124 .. 0.85
   2 ?   -2.4   0.2       1.9   2.4e+03     183     194 ..     245     256 ..     200     299 .. 0.57

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.2e-06
                                      EEEEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEEEEEE--SCCCTTCCHH CS
                              AIG1  2 tivlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkkinViDTPglfdlsvsad 67
                                      +ivlvG   +GkS   N++ ++ a  s++   + t + +k  ++  +kk ++iDTPg  +l   ++
  gi|298676045|ref|YP_003727795.1| 25 RIVLVGSPNVGKSVIFNALSDSYAIASNY--PGTTVEISKGDGVIGNKKYEIIDTPGSYSLLPITE 88
                                      8*************************995..8889999*******************877766554 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.9
                                       HHHHHTTTT--B CS
                              AIG1 183 aivkenggkpyt 194
                                       +iv+++++k  t
  gi|298676045|ref|YP_003727795.1| 245 DIVSNTENKFNT 256
                                       222222222222 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   7.6e-06    0.0098       1     119 [.      25     138 ..      25     139 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7.6e-06
                                       EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SG.......GCTT CS
                               Roc   1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGq.......erfr 70 
                                       ++vlvG  +vGK+ +++ + ++    ++ + + v++++ +     gv     + + k++i Dt G        e+ r
  gi|298676045|ref|YP_003727795.1|  25 RIVLVGSPNVGKSVIFNALSDSYAIASNYPGTTVEISKGD-----GV-----IGNKKYEIIDTPGSysllpitEEER 91 
                                       69******************98887777776666665543.....22.....2234689999999644444447788 PP

                                       TT-HHHHCTSCEEEEEEEGHHHHCH.HHHHHHHHHHCSSS-EEEEEE-TT CS
                               Roc  71 slhplylreaalailvydsrssenl.keWlkelkkvagkspvilvgnkiD 119
                                         ++l++++a++++ v+d+++ +++  + l+        +p+ilv n +D
  gi|298676045|ref|YP_003727795.1|  92 VAQRLFFEKASIYLHVIDAKNLRRMlPHTLQ---LIEAGKPLILVLNMMD 138
                                       8999**************9876554133333...3444678888888887 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.1    0.0041       5.3      98     124 ..      22      48 ..      17      83 .. 0.81
   2 !    6.7   0.0    0.0047         6      33      99 ..     111     180 ..     101     184 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0041
                                       TTSEEEEECSTTSSHHHHHHHHCTT-- CS
                       RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpele 124
                                       +++ +vlvG+  vGKS + nal  +  
  gi|298676045|ref|YP_003727795.1|  22 SSDRIVLVGSPNVGKSVIFNALSDSYA 48 
                                       556789****************98754 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0047
                                       HHHHHHH...HHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT CS
                       RsgA_GTPase  33 nlldrfL...vlaeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkellkd 99 
                                       + l r+L   +++ e+g ++++vln +D + e+    ++++  + l ++v+   ++++eg+eelk+ +++
  gi|298676045|ref|YP_003727795.1| 111 KNLRRMLphtLQLIEAGKPLILVLNMMDEAAERGIRIDIQKLEQMLKIPVIPAVSNKGEGIEELKKTISE 180
                                       555555522234456778999*************44455555556789999999999********99876 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.2e-05     0.041      67     191 ..      67     181 ..      50     184 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.2e-05
                                       CSSEEEEEEEESSSGGGHHHHHHH.......HHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST. CS
                          GTP_EFTU  67 tkkylinliDtPGHvdFskevirg.......lrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl. 135
                                         ++++ +iDtPG  +    +++         +++ +++ v+da+     +   +  ++++ g p+i+++N mD++ 
  gi|298676045|ref|YP_003727795.1|  67 IGNKKYEIIDTPGSYSLLPITEEErvaqrlfFEKASIYLHVIDAK--NLRRMLPHTLQLIEAGKPLILVLNMMDEAa 141
                                       567899********99654333322245667778999*******9..5677889999*******************5 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHH CS
                          GTP_EFTU 136 kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvel 191
                                       +  ++  +++++q l                ++pv+++ + kgeg+++l +++ e+
  gi|298676045|ref|YP_003727795.1| 142 ERGIRIDIQKLEQML----------------KIPVIPAVSNKGEGIEELKKTISEY 181
                                       555666667777666................5899999999999999888888766 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.3e-05      0.03       3     142 ..      25     179 ..      23     180 .. 0.78
   2 ?   -3.7   0.0       6.9   8.8e+03      75      89 ..     251     265 ..     234     290 .. 0.52

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.3e-05
                         PduV-EutP   3 killiGkvgsGKttLtqalkg..........eelkYkktqai..efsdeviDtPGeylenr...klysalivtsaea 64 
                                       +i+l+G+ ++GK  + +al++           +++ +k   +  + + e+iDtPG y       +   a + +  +a
  gi|298676045|ref|YP_003727795.1|  25 RIVLVGSPNVGKSVIFNALSDsyaiasnypgTTVEISKGDGVigNKKYEIIDTPGSYSLLPiteEERVAQRLFFEKA 101
                                       89999999999999999999988888777776666666665523556678*******65430002334555666789 PP

                         PduV-EutP  65 dvialvqdateeesvfppgfasv.fnkeviGiitkidlaedeenieaveelLksaGaekifevsavekegieellky 140
                                       ++   v da++ + ++p +++ +   k++i ++  +d a  e  i++  ++L+++    ++   + + egieel+k 
  gi|298676045|ref|YP_003727795.1| 102 SIYLHVIDAKNLRRMLPHTLQLIeAGKPLILVLNMMDEA-AERGIRIDIQKLEQMLKIPVIPAVSNKGEGIEELKKT 177
                                       99999************999877356************9.899999999999998777777777778899****998 PP

                         PduV-EutP 141 le 142
                                       ++
  gi|298676045|ref|YP_003727795.1| 178 IS 179
                                       86 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 6.9
                         PduV-EutP  75 eeesvfppgfasvfn 89 
                                       e++   p +++ +++
  gi|298676045|ref|YP_003727795.1| 251 ENKFNTPTNYVMTVE 265
                                       333333333333332 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.4e-05     0.031       3      62 ..      23      83 ..      21     117 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.4e-05
                                      --EEEEE-STTSSHHHHHHHHHHSS---B---S.S-EEETTG...GGTT-SEEEETT-GCC CS
                             SRPRB  3 kpavllvGlsdsGKTslftrLttdsvkktvtSq.essaalkvksekgskltliDfPGhekl 62
                                      + +++lvG  + GK  +f+ L+   +  +       ++++      ++k ++iD PG  +l
  gi|298676045|ref|YP_003727795.1| 23 SDRIVLVGSPNVGKSVIFNALSDSYAIASNYPGtTVEISKGDGVIGNKKYEIIDTPGSYSL 83
                                      6789*****************98844333322213333332233577899*******9887 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.046        59      28      51 ..      22      45 ..       7      52 .. 0.85
   2 ?    7.3   0.0    0.0016       2.1     197     230 ..     149     183 ..     109     216 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.046
                                      -SEEEEEEE-TTSSHHHHHHHHHH CS
                              MeaB 28 raqvvGltGvPGaGkstlvealgl 51
                                       + ++ l G+P +Gks + +al  
  gi|298676045|ref|YP_003727795.1| 22 SSDRIVLVGSPNVGKSVIFNALSD 45
                                      678999************999975 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0016
                                       STT.BTTB--EEEEEBCCCTBSHHHHHHHHHHHHH CS
                              MeaB 197 eek.ekeWrpkvlktsavegeGidelvdaieehre 230
                                        +k e+  + +v+ +++ +geGi+el ++i+e+ +
  gi|298676045|ref|YP_003727795.1| 149 IQKlEQMLKIPVIPAVSNKGEGIEELKKTISEYSS 183
                                       33447788899*********************976 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00011      0.14      90     231 ..      69     203 ..      47     213 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                        ATP_bind_1  90 eddyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsalsamlrlelPhvvvlnkf 166
                                       +++y ++DtPG   l  + e+ + + ++L  e a + ++++D++ l+        +l     +++++ P + vln +
  gi|298676045|ref|YP_003727795.1|  69 NKKYEIIDTPGSYSLLPITEEER-VAQRLFFEKASIYLHVIDAKNLRR-------MLPHTLQLIEAGKPLILVLNMM 137
                                       679*****************999.999999999*********999988.......44445568999*********** PP

                        ATP_bind_1 167 Dllkek....lekeleffedvealslllekeeekykklaeaiaelleefalvlrflplssekeesiedl 231
                                       D ++e+    + ++le +  +  + ++ +k  e  ++l+++i+e+ ++++    ++ ++ + e++i+d+
  gi|298676045|ref|YP_003727795.1| 138 DEAAERgiriDIQKLEQMLKIPVIPAVSNKG-EGIEELKKTISEYSSNPQDF--TIKYNDDIENAIKDI 203
                                       **99777555555555555555555555544.33455666666655555555..555555555555555 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2     0.039        50       1      22 [.      26      47 ..      26      62 .. 0.81
   2 ?    9.0   0.0    0.0011       1.4     100     140 ..      69     112 ..      58     130 .. 0.88
   3 ?   -1.5   1.0       1.8   2.3e+03      58      85 ..     233     260 ..     177     303 .. 0.65

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.039
                                      EEEEEBTTTTHHHHHHHHHTS- CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLlged 22
                                      i++vGs + GKS + naL  + 
  gi|298676045|ref|YP_003727795.1| 26 IVLVGSPNVGKSVIFNALSDSY 47
                                      89****************8765 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0011
                                       S-SEEEEE---B-S..SSGTTSHHHHHHH.STTEEEEEEEETTS CS
                         Dynamin_N 100 vkgltlvDlPGlds..vnkrdqelvkeyi.kkadiilavtsanh 140
                                       +k+++++D+PG  s    ++++++++++  +ka+i l+v +a++
  gi|298676045|ref|YP_003727795.1|  69 NKKYEIIDTPGSYSllPITEEERVAQRLFfEKASIYLHVIDAKN 112
                                       6899*********9877778889****99***********9986 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.8
                                       ET-EB--CHHHHHHHHHHHHHHHTSSSS CS
                         Dynamin_N  58 kekkledfsevreeieketekiagankg 85 
                                        ++k ed++++++ +++ ++k ++  + 
  gi|298676045|ref|YP_003727795.1| 233 IQEKGEDVDAIKDIVSNTENKFNTPTNY 260
                                       2445555555555555555544433333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (681 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1480  (0.0825478); expected 358.6 (0.02)
Passed bias filter:                      780  (0.0435049); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.85u 0.39s 00:00:01.24 Elapsed: 00:00:00.56
# Mc/sec: 3672.40
//
Query:       gi|298676046|ref|YP_003727796.1|  [L=216]
Description: hypothetical protein Metev_2174 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.6e-22   78.1   0.0    7.2e-22   77.8   0.0    1.1  1  FMN_red       NADPH-dependent FMN reductase
    2.1e-07   30.9   0.0    2.9e-07   30.4   0.0    1.2  1  Flavodoxin_2  Flavodoxin-like fold


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.8   0.0     8e-26   7.2e-22       2     150 ..       4     156 ..       3     159 .. 0.90

  Alignments for each domain:
  == domain 1  score: 77.8 bits;  conditional E-value: 8e-26
                                       EEEEEES--STT...-HHHHHHHHHHCCT-T.T-CEEEEETTTS.--..---HCHGHTCGGSHHHHHHHHHHHH-SC CS
                           FMN_red   2 kilvisGSlrkg...sntrklaewaaealkeagaevelidladlilpcalcdkdlesegqtsddvaellekiaaada 75 
                                       k l ++ +l+k    sntr+l++ a + ++e+++e+e+i++ad++ p  + +      ++++d+  ++l+ki+++d+
  gi|298676046|ref|YP_003727796.1|   4 KALFLNCTLKKSpevSNTRALIDKAVKLFEEQEVETEVIRIADYNIP--VGVTSY---EGEGDEWPDILKKIKESDI 75 
                                       556677777755555*****************************999..555455...369**************** PP

                                       EEEEEEECTTCE-HHHHHHHHCHT-........SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHHHTT-EEEEC CS
                           FMN_red  76 liivtPeYngsysgllKnalDrlsr.......trgkkelrgKpvalvavgggrrgglraeeqlrqvlaelgaivvpr 145
                                       li+++P+++g+ s+ll  +++rl+        + g+ +l gK+++++ +g +++g++++++     l++lg++v+p+
  gi|298676046|ref|YP_003727796.1|  76 LIMGSPIWFGTRSSLLQKVIERLDGtymetdpETGQFPLYGKVAGVIITG-NEDGAHNVAANTLFNLTHLGCTVPPN 151
                                       ***********************98**********************776.89***********************9 PP

                                       SEEEE CS
                           FMN_red 146 aavav 150
                                       ++ ++
  gi|298676046|ref|YP_003727796.1| 152 VDSYW 156
                                       77665 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   3.3e-11   2.9e-07       7     138 ..      13     129 ..       4     144 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 3.3e-11
                                       E--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCCT-----CCCCHCCHHHHTTCHHHHHHHHHHHHCSSEEEE CS
                      Flavodoxin_2   7 nahprpeksfssalaqafvealekagphevtvrdLyadflpvlttrdlaaklayeekpadveseqiekllaadaivl 83 
                                       + +p+   s+++al +++v+ +e+++  e +v+ +++  +pv  t       +ye +  d+  + ++k++++d++++
  gi|298676046|ref|YP_003727796.1|  13 KKSPEV--SNTRALIDKAVKLFEEQE-VETEVIRIADYNIPVGVT-------SYEGE-GDEWPDILKKIKESDILIM 78 
                                       344544..******************.9*********99999988.......77664.3333333679********* PP

                                       EEE-BTTB--HHHHHHHHHHS-TTTSC.EETTCSSCCCCTTTTSEEEEEEEESS-G CS
                      Flavodoxin_2  84 qfPlwwfgvPailKgwiDrvltagfaf.yteeggegrgggLkgkkalvivttGgpe 138
                                       ++P+w+ + +++l++ i+r    g +   ++e+   ++  L gk a vi+t + ++
  gi|298676046|ref|YP_003727796.1|  79 GSPIWFGTRSSLLQKVIERL--DGTYMeTDPET---GQFPLYGKVAGVIITGNEDG 129
                                       *******************8..66655333333...345566********998874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1241.14
//
Query:       gi|298676047|ref|YP_003727797.1|  [L=70]
Description: deoxyribonuclease/rho motif-like TRAM protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-16   58.3   1.1    6.2e-16   58.2   1.1    1.1  1  TRAM      TRAM domain


Domain annotation for each model (and alignments):
>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.2   1.1   3.4e-20   6.2e-16       3      62 .]      13      68 ..      11      68 .. 0.95

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 3.4e-20
                                      XXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEEE CS
                              TRAM  3 yvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGell 62
                                      + G+++eV++e+ + +eg+gi+r++ g+v+fvp+++   Gd+ ++kItkv r+++++e +
  gi|298676047|ref|YP_003727797.1| 13 EAGEEYEVTIEDIA-REGDGIARVE-GFVIFVPDTQV--GDTENIKITKVLRKFAFAEKV 68
                                      67***********9.**********.*********99..******************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 461.64
//
Query:       gi|298676048|ref|YP_003727798.1|  [L=399]
Description: hypothetical protein Metev_2176 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   3.4e-126  421.3   0.6   3.9e-126  421.1   0.6    1.0  1  DUF111    Protein of unknown function DUF111
  ------ inclusion threshold ------
       0.62   10.4   5.7        3.4    8.0   0.8    2.4  2  DUF1031   Protein of unknown function (DUF1031)


Domain annotation for each model (and alignments):
>> DUF111  Protein of unknown function DUF111
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  421.1   0.6  4.3e-130  3.9e-126       1     372 [.       4     384 ..       4     385 .. 0.97

  Alignments for each domain:
  == domain 1  score: 421.1 bits;  conditional E-value: 4.3e-130
                            DUF111   1 lyldcssGisGDmllgALldlgadkeeleealeklgleeveleiekvkksgisatkvdveeeehehehrslaeieei 77 
                                       l+++++sG+sGDm++++L+ lgad++ ++e++e+++  +v+++++++kk+gis+++vdv +++++++ +++ ei +i
  gi|298676048|ref|YP_003727798.1|   4 LVFEPFSGASGDMIIASLIGLGADQSIIKETMESVA--DVSVSVNHTKKHGISSINVDVVTRKEHEHSKTYYEIIDI 78 
                                       789*******************************87..79*******************999999999********* PP

                            DUF111  78 ieaaslsekvkekalaiferlaeAeakvhgvpleevhfhEvGavDaivdivgaalaldeLgvekvvasplalGsGtv 154
                                       i++++l+e++k++al+if+++a+Ae+++h++ le++hfhE+G++Dai+d+vga++a++e +++k++++p+++G+G+v
  gi|298676048|ref|YP_003727798.1|  79 IKSSHLPENIKNDALDIFSIMADAESSIHNQYLEDLHFHEIGQMDAIADVVGACTAIHEFNFDKIYCTPITTGGGFV 155
                                       ***************************************************************************** PP

                            DUF111 155 rcahGilPvPaPAvlellkelklkl..gevegElvTPTGaAilaalaeefgslpamkvekiGyGaGkrdleeipnvl 229
                                       + +hGilPvP+PA+le+lk+ ++    g++++El+TPTGaAil+++++ ++s+p+ k+++iGyG G+ d+++ pnvl
  gi|298676048|ref|YP_003727798.1| 156 KSEHGILPVPVPATLEILKTGSMVFqqGNISNELLTPTGAAILSHFSQPVDSYPQSKIKQIGYGSGDMDIDKQPNVL 232
                                       ******************98887778999************************************************ PP

                            DUF111 230 RvlleeeeeelekeevvvletniDDlspevlgyvlerLleaGAlDvfltpilmKKgRpavllsvlckeedaeeleel 306
                                       R+ ++e +++l +++v vletn+DD++++vlg+++++Ll++GA Dv++tp++mKKgRp+ +++v++++ d+++l++ 
  gi|298676048|ref|YP_003727798.1| 233 RTSISEIDDALIQDSVEVLETNVDDVTGQVLGNLVDELLSSGAKDVTITPATMKKGRPGNMIHVVSEPIDTSKLARK 309
                                       ***************************************************************************** PP

                            DUF111 307 lfretttlGvRese.verlvlereietvetelg....evrvKva....eevvkvkpEyedvkkiAeetglplkev 372
                                       +++et++lGvR  +  +rl+++r i++++++++    +v++K+a    ++ +++++Ey+d+kkiA+ tg+++k+v
  gi|298676048|ref|YP_003727798.1| 310 IITETGSLGVRVVPvRHRLTAKRYIKNLKIKINneyhNVSIKIArdtnGSLLNISAEYDDCKKIADYTGIAVKDV 384
                                       **************889**********9998877777*******986444**********************998 PP

>> DUF1031  Protein of unknown function (DUF1031)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.8   0.00038       3.4      20      52 ..      46      78 ..      32      91 .. 0.82
   2 ?    4.4   0.3    0.0049        44       5      48 ..     327     369 ..     323     377 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00038
                           DUF1031 20 rfdvnykelsvkisvrtkgsheLvelYlDiksk 52
                                      +    ++  s+ + v t+++he ++ Y +i + 
  gi|298676048|ref|YP_003727798.1| 46 NHTKKHGISSINVDVVTRKEHEHSKTYYEIIDI 78
                                      455579999******************999765 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0049
                           DUF1031   5 riitlkkLfnLakkarfdvnykelsvkisvrtkgsh.eLvelYlD 48 
                                       r+ + + + nL +k + +  y + s+ki+  t gs  +++  Y D
  gi|298676048|ref|YP_003727798.1| 327 RLTAKRYIKNLKIKINNE--YHNVSIKIARDTNGSLlNISAEYDD 369
                                       555556677888877665..**********999984245555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2502.78
//
Query:       gi|298676049|ref|YP_003727799.1|  [L=741]
Description: AAA ATPase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-96  319.9   0.2    1.4e-47  161.4   0.0    2.9  2  AAA              ATPase family associated with various cellul
      6e-30  103.3   0.0    2.2e-29  101.5   0.0    2.0  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    7.3e-29   99.3   0.5    1.8e-13   50.0   0.2    2.7  2  AAA_lid_3        AAA+ lid domain
    1.4e-14   54.6   0.0    8.4e-07   29.3   0.0    2.8  2  AAA_2            AAA domain (Cdc48 subfamily)
    8.2e-14   51.1   0.2    4.6e-13   48.8   0.2    2.2  2  CDC48_2          Cell division protein 48 (CDC48), domain 2
    5.4e-13   49.0   0.0    4.3e-05   23.3   0.0    3.0  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    8.6e-12   45.2   0.7    5.9e-05   23.1   0.1    3.8  2  AAA_5            AAA domain (dynein-related subfamily)
      2e-11   44.5   0.0    0.00026   21.4   0.0    3.7  3  AAA_16           AAA ATPase domain
    5.4e-11   42.7   0.0    7.9e-06   25.9   0.0    3.2  3  AAA_14           AAA domain
    9.7e-11   42.1   0.6       0.01   16.1   0.0    4.5  4  AAA_22           AAA domain
    6.9e-09   36.0   0.0    0.00055   20.1   0.0    2.5  2  AAA_33           AAA domain
    6.4e-08   32.2   0.0     0.0029   16.9   0.0    2.7  2  TIP49            TIP49 P-loop domain
    6.1e-07   29.3   0.1      0.051   13.3   0.0    2.7  2  IstB_IS21        IstB-like ATP binding protein
    6.4e-07   29.2   0.0      0.069   12.9   0.0    3.6  3  Sigma54_activat  Sigma-54 interaction domain
      1e-06   29.3   0.0      0.085   13.4   0.0    4.2  4  AAA_18           AAA domain
    1.2e-06   28.4   2.6     0.0038   17.2   0.1    3.1  2  Vps4_C           Vps4 C terminal oligomerisation domain
    5.7e-06   26.0   0.0       0.16   11.5   0.0    2.7  2  AAA_7            P-loop containing dynein motor region
    1.7e-05   24.3   0.6      0.083   12.3   0.0    2.6  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    2.5e-05   24.8   0.8       0.19   12.2   0.0    3.0  2  ABC_tran         ABC transporter
      3e-05   23.6   0.0       0.11   11.9   0.0    2.7  2  PhoH             PhoH-like protein
      5e-05   23.6   0.0       0.45   10.9   0.0    2.6  2  RNA_helicase     RNA helicase
    8.8e-05   21.9   0.0       0.36   10.1   0.0    2.5  2  Zeta_toxin       Zeta toxin
    0.00016   21.6   0.0      0.017   15.0   0.0    2.4  2  Bac_DnaA         Bacterial dnaA  protein
    0.00023   21.5   0.0       0.71   10.1   0.0    2.7  2  AAA_28           AAA domain
    0.00026   21.0   0.1        1.3    9.0   0.0    2.9  3  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    0.00033   20.3   0.0        2.6    7.6   0.0    3.5  3  AAA_25           AAA domain
    0.00033   20.0   0.0       0.75    9.0   0.0    2.3  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    0.00066   19.7   0.0        1.8    8.5   0.0    2.9  2  ResIII           Type III restriction enzyme, res subunit
    0.00078   18.7   0.0        1.1    8.3   0.0    2.4  2  DUF815           Protein of unknown function (DUF815)
     0.0008   18.7   0.0       0.52    9.5   0.0    3.0  2  NB-ARC           NB-ARC domain
    0.00097   18.9   0.0        1.5    8.5   0.0    2.6  2  AAA_24           AAA domain
     0.0013   18.1   1.6        1.4    8.2   0.0    3.7  3  ATPase           KaiC
     0.0016   18.4   0.1      0.089   12.7   0.0    2.7  2  Rad17            Rad17 P-loop domain
     0.0018   18.1   0.1       0.86    9.3   0.0    2.5  2  Cytidylate_kin   Cytidylate kinase
     0.0019   18.2   1.6       0.84    9.5   0.1    3.9  3  ATPase_2         ATPase domain predominantly from Archaea
     0.0021   17.0   0.0        0.6    8.9   0.0    2.3  2  AFG1_ATPase      AFG1-like ATPase
     0.0022   17.8   0.0       0.61    9.8   0.0    2.4  2  AAA_11           AAA domain
     0.0023   17.7   0.4        1.9    8.1   0.0    2.9  2  AAA_30           AAA domain
     0.0023   17.6   0.0        1.1    8.8   0.0    2.3  2  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
      0.004   17.6   0.0        0.2   12.1   0.0    3.0  2  AAA_17           AAA domain
      0.004   17.3   0.0       0.99    9.5   0.0    2.6  2  Sigma54_activ_2  Sigma-54 interaction domain
     0.0054   16.4   0.7          8    6.1   0.0    3.8  3  Guanylate_kin    Guanylate kinase
     0.0067   16.5   0.1        4.5    7.4   0.0    2.8  2  Torsin           Torsin
     0.0075   15.7   0.1        6.6    6.1   0.0    3.6  3  TniB             Bacterial TniB protein
     0.0076   16.2   0.2        5.8    6.8   0.0    3.6  3  NACHT            NACHT domain
  ------ inclusion threshold ------
      0.011   16.1   1.4          2    8.8   0.0    3.5  3  AAA_19           AAA domain
      0.013   15.4   0.0        2.4    8.0   0.0    2.6  2  AAA_3            ATPase family associated with various cellul
      0.013   15.2   0.2         12    5.6   0.0    3.9  4  DEAD             DEAD/DEAH box helicase
       0.02   14.0   0.0        3.9    6.5   0.0    2.2  2  Parvo_NS1        Parvovirus non-structural protein NS1
      0.026   14.2   0.2        2.7    7.6   0.0    3.4  3  Zot              Zonular occludens toxin (Zot)
      0.027   14.0   0.0       0.11   12.0   0.0    1.8  2  UFD1             Ubiquitin fusion degradation protein UFD1
      0.027   14.6   0.0        7.1    6.7   0.0    2.9  2  SKI              Shikimate kinase
      0.029   14.1   0.0        3.9    7.1   0.0    2.5  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.057   13.2   0.0         12    5.7   0.0    2.4  2  AAA_29           P-loop containing region of AAA domain
      0.064   12.6   0.1        1.6    8.1   0.0    2.5  2  IPT              Isopentenyl transferase
       0.13   12.7   0.8        4.7    7.6   0.0    3.0  2  AAA_23           AAA domain
       0.19   11.4   0.1       0.19   11.4   0.1    1.9  1  LID              LIM interaction domain (LID)
        1.2    9.0   9.7         16    5.3   0.0    4.8  5  NTPase_1         NTPase


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.4   0.0   4.6e-50   1.4e-47       1     131 [.     229     358 ..     229     359 .. 0.97
   2 !  155.4   0.0   3.4e-48   1.1e-45       1     130 [.     501     631 ..     501     633 .. 0.95

  Alignments for each domain:
  == domain 1  score: 161.4 bits;  conditional E-value: 4.6e-50
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       v+++Gp GtGKTl+akava+e+ ++fl i g+e++ ky gese++ir++f+ea+e+a psi+fiDEid++a++r++ 
  gi|298676049|ref|YP_003727799.1| 229 VIMHGPSGTGKTLIAKAVANESRANFLYIAGPEIMGKYYGESEERIRKIFEEASENA-PSIIFIDEIDSIAPKRENV 304
                                       689*****************************************************9.******************* PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       + e+e+rvv+qLlt++dg++++ ++v+vigatnr+d+ldpal+r gRfdr++ei+
  gi|298676049|ref|YP_003727799.1| 305 TGEVERRVVSQLLTMMDGLEER-GQVVVIGATNRVDSLDPALRRpGRFDREVEIG 358
                                       *********************7.56**************************9986 PP

  == domain 2  score: 155.4 bits;  conditional E-value: 3.4e-48
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH..T CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr..s 75 
                                       +ll+GppGtGKTl+a+ava+e++v+f++++g+++l k+vgesek ir++fk+ak+ a p+++f+DE+d++ ++r   
  gi|298676049|ref|YP_003727799.1| 501 LLLFGPPGTGKTLVAQAVANESNVNFISVKGPQILHKWVGESEKAIRDTFKKAKQVA-PCVIFFDELDSISSTRsgM 576
                                       69******************************************************9.****************776 PP

                                       TCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEET CS
                               AAA  76 gseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkiei 130
                                       +++ + +e+v+nqLlte+dg++   ++vivi+atnrp+ +dpallr gRfdr + +
  gi|298676049|ref|YP_003727799.1| 577 TEDGRTSEKVLNQLLTEMDGLEPL-NDVIVIAATNRPEIIDPALLRsGRFDRLVLV 631
                                       7788899****************7.66************************98766 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.5   0.0     7e-32   2.2e-29       2      84 ..       6      88 ..       5      89 .. 0.97

  Alignments for each domain:
  == domain 1  score: 101.5 bits;  conditional E-value: 7e-32
                                      EEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEE CS
                           CDC48_N  2 LrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtV 80
                                       +V++a ++d grgi+r+dp+++ el+l+pgd+vei+g+++T+a+vw+a+++d+++g Ir+dg++R+nagvsiG++V+ 
  gi|298676049|ref|YP_003727799.1|  6 RKVEKAHPNDFGRGIIRLDPNTLLELQLSPGDIVEITGQKRTAAKVWRADRQDWEQGFIRIDGFIRQNAGVSIGERVSL 84
                                      58*****99*****************************999************************************** PP

                                      EEE- CS
                           CDC48_N 81 rkae 84
                                      +k+e
  gi|298676049|ref|YP_003727799.1| 85 KKIE 88
                                      9986 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.0     6e-15   1.9e-12       2      44 ..     382     440 ..     381     441 .. 0.81
   2 !   50.0   0.2   5.9e-16   1.8e-13       1      44 [.     655     700 ..     655     701 .. 0.91

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 6e-15
                         AAA_lid_3   2 vdlkeLAerTeGySGADlaalcreAallAlrr..............gike..itmedfe 44 
                                       v+l+ LA+ T+G++GADl+al++eAa++ l+r              +++e  +t+edfe
  gi|298676049|ref|YP_003727799.1| 382 VQLDYLAKNTQGFVGADLKALVQEAAMCSLQRflphlnldeeipqeTLEEivVTTEDFE 440
                                       99****************************99777776666666653332258888887 PP

  == domain 2  score: 50.0 bits;  conditional E-value: 5.9e-16
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgik..eitmedfe 44 
                                       dv+++eLAe+T+Gy GAD++++creA++l lr++++  +++ + f+
  gi|298676049|ref|YP_003727799.1| 655 DVSISELAEMTDGYIGADIESVCREAVMLSLRDNFEadKVELKYFK 700
                                       9*********************************995458888776 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   2.7e-09   8.4e-07       6     105 ..     229     322 ..     225     326 .. 0.89
   2 !   22.1   0.0   4.3e-07   0.00013       6     105 ..     501     596 ..     496     598 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 2.7e-09
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +++ gp+g+Gkt++aka+a+  ++    ++  +   e++     + + ++++  ++   +a e+   i+++DEid i
  gi|298676049|ref|YP_003727799.1| 229 VIMHGPSGTGKTLIAKAVANESRA----NFLYIAGPEIMG----KYYGESEERIRKIFEEASENApsIIFIDEIDSI 297
                                       5678****************9996....************....99999999999999999999999********** PP

                                       ---.---------HHHHHHHHHHHH- CS
                             AAA_2  81 hpk.essgadvSregVqrdLLqileg 105
                                       +pk e+ + +v r  V+  LL +++g
  gi|298676049|ref|YP_003727799.1| 298 APKrENVTGEVERR-VVSQLLTMMDG 322
                                       **977888888775.77778899987 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 4.3e-07
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll gp g+Gkt++a+a+a+  +v    ++i +   ++l     + + ++++  ++  ++a++    ++++DE+d i
  gi|298676049|ref|YP_003727799.1| 501 LLLFGPPGTGKTLVAQAVANESNV----NFISVKGPQILH----KWVGESEKAIRDTFKKAKQVApcVIFFDELDSI 569
                                       5788*******************8....************....77777777778888888888899********** PP

                                       ---.------.---HHHHHHHHHHHH- CS
                             AAA_2  81 hpk.essgad.vSregVqrdLLqileg 105
                                       +++ + +++d   +e V++ LL  ++g
  gi|298676049|ref|YP_003727799.1| 570 SSTrSGMTEDgRTSEKVLNQLLTEMDG 596
                                       **9955555526899******987776 PP

>> CDC48_2  Cell division protein 48 (CDC48), domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       7.7   2.4e+03      19      29 ..      33      43 ..      26      58 .. 0.76
   2 !   48.8   0.2   1.5e-15   4.6e-13       7      63 ..     111     180 ..     107     181 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 7.7
                                      E-TTEEEEECC CS
                           CDC48_2 19 vtkGdlvvfef 29
                                      +++Gd+v ++ 
  gi|298676049|ref|YP_003727799.1| 33 LSPGDIVEITG 43
                                      78888887654 PP

  == domain 2  score: 48.8 bits;  conditional E-value: 1.5e-15
                                       CH.HHHCCCTTEEE-TTEEEEECCT...........CCCEEEEEEEECCCC.SCEEECTSCCEEESTTCC CS
                           CDC48_2   7 ma.ylkrqFlgrpvtkGdlvvfefk...........gqeiklvVvstePkg.pvgitetTeielgtkpve 63 
                                        +  +kr++l+rp+++ d++++  +           gq+i+l Vv+teP + + +i+etTeiel++kp++
  gi|298676049|ref|YP_003727799.1| 111 TSdIIKRNILKRPIVQDDVIPIISSmnqpmsgpvagGQAIPLIVVETEPEDsILIIDETTEIELSQKPAR 180
                                       4559****************9977558899999******************777**************86 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   1.4e-07   4.3e-05      31     103 ..     224     304 ..     202     353 .. 0.79
   2 !   22.2   0.0     3e-07   9.4e-05      35      71 ..     500     536 ..     463     574 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.4e-07
                            RuvB_N  31 ealdhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsra 99 
                                       e+   v+++Gp G Gkt +ak +a+e  +++   +gP +      e +  +  ++ + +e+   ++fidei  ++++
  gi|298676049|ref|YP_003727799.1| 224 EPPKGVIMHGPSGTGKTLIAKAVANESRANFLYIAGPEImgkyygESEERIRKIFEEASENapSIIFIDEIDSIAPK 300
                                       556679*******************************995544444567788999888765337*********9999 PP

                            RuvB_N 100 veev 103
                                        e+v
  gi|298676049|ref|YP_003727799.1| 301 RENV 304
                                       8876 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 3e-07
                            RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvlek 71 
                                        +ll+GpPG Gkt +a+ +a+e +v++ +  gP + +
  gi|298676049|ref|YP_003727799.1| 500 GLLLFGPPGTGKTLVAQAVANESNVNFISVKGPQILH 536
                                       579******************************9865 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1   1.9e-07   5.9e-05       1     136 [.     228     347 ..     228     348 .. 0.76
   2 !   17.0   0.1   1.5e-05    0.0046       2     131 ..     501     616 ..     500     622 .. 0.66

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.9e-07
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEver 76 
                                       +v++ Gp+GtgK+ +a+ +a   +++++y+++++      + g++   ++ +++  +++ +a +  ++i+++DE++ 
  gi|298676049|ref|YP_003727799.1| 228 GVIMHGPSGTGKTLIAKAVANESRANFLYIAGPE------IMGKYY--GESEERIRKIFEEASEnAPSIIFIDEIDS 296
                                       599*****************************98......777777..6777777888887777789*********8 PP

                                       --H...HHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHT CS
                             AAA_5  77 aes...evlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrs 136
                                       + +   +v++++ +    + l +++g e+ +         + vi+++n++d    +l+palr+
  gi|298676049|ref|YP_003727799.1| 297 IAPkreNVTGEVERRVVSQLLTMMDGLEERGQ--------VVVIGATNRVD----SLDPALRR 347
                                       87511144444444444444444444444432........9**********....99999987 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1.5e-05
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGGG- CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEvera 77 
                                       +lL GppGtgK+ +a+ +a   n ++  v +++      ++ ++   ++ ++     +++a +  ++++++DE++  
  gi|298676049|ref|YP_003727799.1| 501 LLLFGPPGTGKTLVAQAVANESNVNFISVKGPQ------ILHKWV--GESEKAIRDTFKKAKQvAPCVIFFDELD-- 567
                                       89******************9999999999887......777777..3333333444444444688888888888.. PP

                                       -HHHHHHHHHHHHSSEEE..-SSSEEE---.......-EEEEEESS--.-TT-TT CS
                             AAA_5  78 esevlnsLlslleerrllleeggelvkakndd.llerfrviatanpldrslnels 131
                                         ++ ++   + e+ r +   +++l  +      l+++ via++n+++     ++
  gi|298676049|ref|YP_003727799.1| 568 --SISSTRSGMTEDGRTSEKVLNQLLTEMDGLePLNDVIVIAATNRPE----IID 616
                                       ..5555555555666666555555555544444455577777777776....455 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   8.6e-07   0.00026      14     139 ..     216     331 ..     212     345 .. 0.72
   2 !   14.8   0.0   9.3e-05     0.029      24      61 ..     498     532 ..     488     540 .. 0.78
   3 ?    3.5   0.0      0.27        84     124     163 ..     547     595 ..     539     606 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 8.6e-07
                            AAA_16  14 salervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde.a 89 
                                       ++++r++   p  v+ +G+sG+GK+ ++++++++ +++   fl+    +  ++  y         ee +r++ +e +
  gi|298676049|ref|YP_003727799.1| 216 ELFKRLNIEPPKGVIMHGPSGTGKTLIAKAVANESRAN---FLYIAGPEI-MGKYY----GE--SEERIRKIFEEaS 282
                                       578888888889********************988877...888888888.33333....22..2355555555524 PP

                            AAA_16  90 esaeleawrekleealaavpelagaeasrllellkrllallsrderplvl 139
                                       e+a    + +++++ +    +++g+ ++r+  +l  +++ l+++++ +v+
  gi|298676049|ref|YP_003727799.1| 283 ENAPSIIFIDEIDSIAPKRENVTGEVERRVVSQLLTMMDGLEERGQ-VVV 331
                                       4445555556666666677778888889999999999999998777.444 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 9.3e-05
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcd 61 
                                       p  +ll G++G+GK+ ++++++++ +   + f++ k  
  gi|298676049|ref|YP_003727799.1| 498 PKGLLLFGPPGTGKTLVAQAVANESN---VNFISVKGP 532
                                       5889*****************97544...446666655 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.27
                            AAA_16 124 krllallsrderplvlvlDdlqwade..........aslqllaaLlrlle 163
                                       ++ ++++++   p v+++D+l+ + +          +s ++l +Ll++++
  gi|298676049|ref|YP_003727799.1| 547 RDTFKKAKQ-VAPCVIFFDELDSISStrsgmtedgrTSEKVLNQLLTEMD 595
                                       555566777.668*********7776555555555577777777776655 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       2.2   6.7e+02      61      88 ..     158     184 ..     125     209 .. 0.78
   2 !   25.9   0.0   2.6e-08   7.9e-06       5     108 ..     229     342 ..     226     357 .. 0.78
   3 !   11.8   0.0   0.00059      0.18       5      78 ..     501     571 ..     498     607 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 2.2
                            AAA_14  61 keekktylflDEiqevpewekalkslvd 88 
                                       + +++++l++DE  e++  +k  +++ +
  gi|298676049|ref|YP_003727799.1| 158 E-PEDSILIIDETTEIELSQKPARGYAN 184
                                       3.48899*****9999766666665555 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 2.6e-08
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev..... 76 
                                       +++ G+  +GKT ++k +++e+     ++lyi+  +   k + ++e+ ++ i+e+++e+  +++f+DEi  +     
  gi|298676049|ref|YP_003727799.1| 229 VIMHGPSGTGKTLIAKAVANESR---ANFLYIAGPEIMGKYYGESEERIRKIFEEASENAPSIIFIDEIDSIapkre 302
                                       7999***************9999...**********9998888777666666666666799***********88888 PP

                            AAA_14  77 .......pewekalkslvd.egknldvivtGSnskllske 108
                                              +++ + l  ++d  +++++v+v G  + + s +
  gi|298676049|ref|YP_003727799.1| 303 nvtgeveRRVVSQLLTMMDgLEERGQVVVIGATNRVDSLD 342
                                       8888877777777777777422577888888877766655 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00059
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderd..kkladpekllelileklkeekktylflDEiqevpe 78 
                                       l++ G+  +GKT +++ +++e+      + +i+++ ++   k   ++ek ++  ++k+k+    ++f+DE   +++
  gi|298676049|ref|YP_003727799.1| 501 LLLFGPPGTGKTLVAQAVANESN-----VNFISVKGPQIlhKWVGESEKAIRDTFKKAKQVAPCVIFFDELDSISS 571
                                       7899**********999987766.....5555555555521555555555555555545557899*****998843 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   0.00037      0.12       9      41 ..     230     253 ..     224     265 .. 0.81
   2 ?    6.5   0.0     0.032       9.8      72     131 ..     268     335 ..     259     341 .. 0.74
   3 !   16.1   0.0   3.4e-05      0.01       8      42 ..     501     526 ..     495     536 .. 0.82
   4 ?    0.9   0.0       1.6   4.9e+02      82     112 ..     546     590 ..     539     606 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00037
                            AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaeeerpe 41 
                                       + +G+sGtGKT+ ++ ++++          r+ 
  gi|298676049|ref|YP_003727799.1| 230 IMHGPSGTGKTLIAKAVANES---------RAN 253
                                       679**************9986.........444 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.032
                            AAA_22  72 rlsseellealeqalraravielliiDEaqhlr..s........eealeeLrsllnlsrkgvqliLvGtp 131
                                       + s+e++++ +e+a++++    ++ iDE++ +   +         +++++L ++++  +   q++++G +
  gi|298676049|ref|YP_003727799.1| 268 GESEERIRKIFEEASENAPS--IIFIDEIDSIApkRenvtgeveRRVVSQLLTMMDGLEERGQVVVIGAT 335
                                       46778888888888888877..**********88624555667788888888888877777777777766 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 3.4e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpev 42 
                                       l+++G++GtGKT++++ ++++          ++ +
  gi|298676049|ref|YP_003727799.1| 501 LLLFGPPGTGKTLVAQAVANES---------NVNF 526
                                       79*****************997.........4444 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 1.6
                            AAA_22  82 leqalrarav..ielliiDEaqhlr...s.........eealeeL 112
                                       +++ +++++   + ++  DE + ++   s         e++l++L
  gi|298676049|ref|YP_003727799.1| 546 IRDTFKKAKQvaPCVIFFDELDSISstrSgmtedgrtsEKVLNQL 590
                                       55666666667889*********9765414445555556666666 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   1.8e-06   0.00055       2      79 ..     229     336 ..     229     375 .. 0.69
   2 !   13.5   0.0   0.00019      0.06       3      47 ..     502     548 ..     501     634 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.8e-06
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt............................dy 48 
                                       v+++G++G+GK+  a+ ++++    +  ++ ++++ +++g+ +++++                              
  gi|298676049|ref|YP_003727799.1| 229 VIMHGPSGTGKTLIAKAVANESRanFLYIAGPEIMGKYYGESEERIRkifeeasenapsiifideidsiapkrenVT 305
                                       89*****************999988899***********98888877666666666666666666666666444322 PP

                            AAA_33  49 trvldrlyqilnelarkalsagrnvildatn 79 
                                        +v+ r+  +l  + +   ++g+ v++ atn
  gi|298676049|ref|YP_003727799.1| 306 GEVERRVVSQLLTMMDGLEERGQVVVIGATN 336
                                       2344444455555555555555556666664 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00019
                            AAA_33   3 llvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqsktd 47 
                                       ll G+pG+GK+ +a+ ++++    ++ +  ++++ + +g+ ++ ++d
  gi|298676049|ref|YP_003727799.1| 502 LLFGPPGTGKTLVAQAVANESNvnFISVKGPQILHKWVGESEKAIRD 548
                                       789***************99997777788888777666655554443 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00023     0.072      51      90 ..     227     264 ..     214     296 .. 0.84
   2 !   16.9   0.0   9.3e-06    0.0029      51     106 ..     499     553 ..     492     557 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00023
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevys 90 
                                       ++v++ GpsgtGkt +a a+++e      f  ++g e+  
  gi|298676049|ref|YP_003727799.1| 227 KGVIMHGPSGTGKTLIAKAVANES--RANFLYIAGPEIMG 264
                                       89*******************995..57899999988865 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 9.3e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte.vltqalrks 106
                                       +++Ll Gp+gtGkt +a a+++e   +v f++++g ++    v  +e ++ ++++k+
  gi|298676049|ref|YP_003727799.1| 499 KGLLLFGPPGTGKTLVAQAVANES--NVNFISVKGPQILHKWVGESEkAIRDTFKKA 553
                                       899*******************95..5***********9999988874677888887 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   0.00017     0.051      44      71 ..     223     250 ..     206     334 .. 0.86
   2 !   13.2   0.0   0.00018     0.055      48      71 ..     499     522 ..     493     557 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00017
                         IstB_IS21  44 iekkenivllGpsGvGKshlaialgvea 71 
                                       ie  +++++ GpsG+GK+ +a a++ e 
  gi|298676049|ref|YP_003727799.1| 223 IEPPKGVIMHGPSGTGKTLIAKAVANES 250
                                       6667899****************99875 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00018
                         IstB_IS21  48 enivllGpsGvGKshlaialgvea 71 
                                       ++++l+Gp+G+GK+ +a a++ e 
  gi|298676049|ref|YP_003727799.1| 499 KGLLLFGPPGTGKTLVAQAVANES 522
                                       6799*************9998765 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   0.00022     0.069      23      48 ..     227     252 ..     212     265 .. 0.84
   2 ?    1.1   0.0      0.92   2.8e+02      76     108 ..     264     300 ..     259     340 .. 0.69
   3 !   10.5   0.0    0.0012      0.37      23      47 ..     499     523 ..     483     539 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00022
                                       S-EEEECSTTSSHHHHHHHHHHHSTT CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheaskr 48 
                                         v+++G sGtGK+l+a+a+ ++s+ 
  gi|298676049|ref|YP_003727799.1| 227 KGVIMHGPSGTGKTLIAKAVANESRA 252
                                       6799****************998864 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.92
                                       SSSTTTSS-BE.HHHHHTTT...SEEEEETGGGS-HH CS
                   Sigma54_activat  76 GaFtGAekekk.Glfekadg...GtlfLDeigelple 108
                                       G + G ++e+    fe+a++   +++f+Dei ++ ++
  gi|298676049|ref|YP_003727799.1| 264 GKYYGESEERIrKIFEEASEnapSIIFIDEIDSIAPK 300
                                       5566666666656788887633369******999876 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.0012
                                       S-EEEECSTTSSHHHHHHHHHHHST CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheask 47 
                                         +l+ G  GtGK+l+a+a+ ++s+
  gi|298676049|ref|YP_003727799.1| 499 KGLLLFGPPGTGKTLVAQAVANESN 523
                                       6689****************99876 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       5.7   1.8e+03      78     111 ..     165     222 ..     102     225 .. 0.64
   2 !    9.0   0.0    0.0061       1.9       2      35 ..     230     284 ..     229     338 .. 0.60
   3 !   13.4   0.0   0.00028     0.085       2      25 ..     502     543 ..     501     646 .. 0.70
   4 ?    0.6   0.0       2.5   7.9e+02      16      64 ..     659     706 ..     657     721 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 5.7
                            AAA_18  78 vidghlaeleseaakdikk........................vvLtaspeelleRle 111
                                       +id   +  +s +  +++                         + L ++++el++Rl+
  gi|298676049|ref|YP_003727799.1| 165 IIDETTEIELSQKPARGYAnaakgikyedigglgseiqrvremIELPLKNNELFKRLN 222
                                       5555555555554444443445555555555555566666666888899999999985 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0061
                            AAA_18   2 lltGtpGvGKttlakeLskrl.gf....................gvnlrdvaken 35 
                                       +  G++G+GKt +ak+++++  ++                     +++ + a+en
  gi|298676049|ref|YP_003727799.1| 230 IMHGPSGTGKTLIAKAVANESrANflyiagpeimgkyygeseerIRKIFEEASEN 284
                                       667**************77643334666766666666666655544444444444 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 0.00028
                            AAA_18   2 lltGtpGvGKttlakeLskrlgf..................g 25 
                                       ll G+pG+GKt +a++++++ ++                   
  gi|298676049|ref|YP_003727799.1| 502 LLFGPPGTGKTLVAQAVANESNVnfisvkgpqilhkwvgesE 543
                                       689**************8885444576666666666655553 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 2.5
                            AAA_18  16 keLskrl.gf.gvnlrdvakenglllevdpealdeskrldedkldklldal 64 
                                        eL++++ g+ g  + +v++e  +l  +d++   e ++++ ++ +++++++
  gi|298676049|ref|YP_003727799.1| 659 SELAEMTdGYiGADIESVCREAVMLSLRDNF---EADKVELKYFKEAIKKV 706
                                       5899999999*******************99...66666666666666555 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0    0.0023      0.73      18      44 ..     423     449 ..     418     458 .. 0.90
   2 !   17.2   0.1   1.2e-05    0.0038      26      60 ..     691     725 ..     677     725 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0023
                            Vps4_C  18 dipsdkllePpvtlkDflkalkkarpt 44 
                                       +ip++ l e  vt +Df++al +  p+
  gi|298676049|ref|YP_003727799.1| 423 EIPQETLEEIVVTTEDFENALVEIEPS 449
                                       79*******************999998 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 1.2e-05
                            Vps4_C  26 ePpvtlkDflkalkkarptVskeDLekheeFTkef 60 
                                       + +v+lk f++a+kk+rptV+ke ++ +e+  ++f
  gi|298676049|ref|YP_003727799.1| 691 ADKVELKYFKEAIKKVRPTVTKEMVDYYEKIKEQF 725
                                       55899*********************999866665 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00057      0.17      28      58 ..     221     251 ..     213     260 .. 0.80
   2 !   11.5   0.0   0.00051      0.16      30      58 ..     495     523 ..     485     571 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00057
                             AAA_7  28 lllknkkpvllvGptGtGKtviikdllkkld 58 
                                       l ++  k v++ Gp+GtGKt+i+k + ++  
  gi|298676049|ref|YP_003727799.1| 221 LNIEPPKGVIMHGPSGTGKTLIAKAVANESR 251
                                       556777899***************9888765 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00051
                             AAA_7  30 lknkkpvllvGptGtGKtviikdllkkld 58 
                                       +k  k +ll Gp GtGKt++++ + ++ +
  gi|298676049|ref|YP_003727799.1| 495 IKPPKGLLLFGPPGTGKTLVAQAVANESN 523
                                       5666889***************9998877 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.1    0.0018      0.56      25      42 ..     229     246 ..     226     249 .. 0.90
   2 !   12.3   0.0   0.00027     0.083      25      42 ..     501     518 ..     495     521 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0018
                      Mg_chelatase  25 lllvGppGsGKtmlakrl 42 
                                       +++ Gp+G+GKt++ak++
  gi|298676049|ref|YP_003727799.1| 229 VIMHGPSGTGKTLIAKAV 246
                                       79*************987 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00027
                      Mg_chelatase  25 lllvGppGsGKtmlakrl 42 
                                       lll+GppG+GKt++a+++
  gi|298676049|ref|YP_003727799.1| 501 LLLFGPPGTGKTLVAQAV 518
                                       89*************987 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00061      0.19       6      67 ..     221     280 ..     219     337 .. 0.76
   2 !    9.7   0.0    0.0036       1.1       7      80 ..     494     578 ..     491     609 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00061
                                       EEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe 67 
                                       l++++ + v + G++G+GK+ ++k++a++++     + + g ++  +   +++++i+ +++e
  gi|298676049|ref|YP_003727799.1| 221 LNIEPPKGVIMHGPSGTGKTLIAKAVANESRA--NFLYIAGPEIMGKYYGESEERIRKIFEE 280
                                       6788888999******************9975..4444566666666677777777777776 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0036
                                       EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx... RF
                          ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren... 79 
                                        +k+ + + ++G+ G+GK+ +++++a++++     i ++g ++ ++   +++k i+  +++ +q+ p +   ++   
  gi|298676049|ref|YP_003727799.1| 494 GIKPPKGLLLFGPPGTGKTLVAQAVANESNV--NFISVKGPQILHKWVGESEKAIRDTFKKaKQVAPCVIFFDElds 568
                                       677788899*******************975..77888999999988888888888888776666666655444555 PP

                                       .........H CS
                                       .........x RF
                          ABC_tran  80 .........e 80 
                                                e
  gi|298676049|ref|YP_003727799.1| 569 isstrsgmtE 578
                                       5555665553 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00036      0.11      20      41 ..     227     248 ..     212     255 .. 0.83
   2 !    8.5   0.0     0.004       1.2      23      41 ..     502     520 ..     492     530 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00036
                                       SEEEEE--TTSSTTHHHHHHHH CS
                              PhoH  20 divfaiGpaGtGKtylavalav 41 
                                       + v++ Gp+GtGKt++a a+a 
  gi|298676049|ref|YP_003727799.1| 227 KGVIMHGPSGTGKTLIAKAVAN 248
                                       56899************99985 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.004
                                       EEE--TTSSTTHHHHHHHH CS
                              PhoH  23 faiGpaGtGKtylavalav 41 
                                         +Gp GtGKt++a a+a 
  gi|298676049|ref|YP_003727799.1| 502 LLFGPPGTGKTLVAQAVAN 520
                                       579***********99986 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0    0.0025      0.76       1      26 [.     229     254 ..     229     299 .. 0.86
   2 !   10.9   0.0    0.0014      0.45       2      34 ..     502     539 ..     501     611 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0025
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                       ++++Gpsg+GK+++ak +a++   ++
  gi|298676049|ref|YP_003727799.1| 229 VIMHGPSGTGKTLIAKAVANESRANF 254
                                       689**************988766555 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0014
                      RNA_helicase   2 wlyGpsgeGKStlakeLakallkkl.....klkkkdsv 34 
                                       +l+Gp+g+GK+++a+ +a++   ++      ++ +++v
  gi|298676049|ref|YP_003727799.1| 502 LLFGPPGTGKTLVAQAVANESNVNFisvkgPQILHKWV 539
                                       79**************8888765444554433333444 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0    0.0011      0.36      13      49 ..     223     257 ..     214     284 .. 0.85
   2 !    9.0   0.0    0.0025      0.77      14      50 ..     496     530 ..     486     535 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0011
                        Zeta_toxin  13 qerPklillgGqpGAGKselaellkdelerqgnvvrl 49 
                                        e Pk +++ G +G GK+ +a+++++e   + n++ +
  gi|298676049|ref|YP_003727799.1| 223 IEPPKGVIMHGPSGTGKTLIAKAVANES--RANFLYI 257
                                       578************************8..6777665 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0025
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrld 50 
                                       + Pk +ll G pG GK+ +a+++++e   + n++ ++
  gi|298676049|ref|YP_003727799.1| 496 KPPKGLLLFGPPGTGKTLVAQAVANES--NVNFISVK 530
                                       569999********************8..88888776 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   5.4e-05     0.017      37     199 ..     229     392 ..     223     411 .. 0.76
   2 ?    3.9   0.0      0.13        41      37      62 ..     501     526 ..     493     563 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.4e-05
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHTT-.SEEEEE-GGGGTT- CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklrkv.DvLliDDiqflagk 112
                                       ++++g++G Gkt + ka++ne +     +  +Y+ + e + +     +++  + f e   ++  ++ iD+i  +a k
  gi|298676049|ref|YP_003727799.1| 229 VIMHGPSGTGKTLIAKAVANESR-----ANFLYIAGPEIMGKYYGESEERIRKIFEEASENApSIIFIDEIDSIAPK 300
                                       689*********99999998765.....5579*************9999999999998886527899*******988 PP

                                       HH.........HHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHHHHH CS
                          Bac_DnaA 113 ek.........tqeelfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkkkie 180
                                        +         +  +l+++++ l e g+ vv+ +    +++++l+  lr   +    v+i  pd++ r +il+  i+
  gi|298676049|ref|YP_003727799.1| 301 REnvtgeverrVVSQLLTMMDGLEERGQVVVIGAT---NRVDSLDPALRRPGRFDREVEIGVPDTDARHEILQ--IH 372
                                       64221111111334566777777777777777765...57888888888654445567778899*******96..88 PP

                                       HTT----TTH.HHHHHHH-- CS
                          Bac_DnaA 181 aeklevpeev.lefiaervt 199
                                       + ++ ++eev l ++a++ +
  gi|298676049|ref|YP_003727799.1| 373 TRGMPITEEVqLDYLAKNTQ 392
                                       89999999986788888865 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.13
                                       EEEE-SSSSSHHHHHHHHHHHHHHHS CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlena 62 
                                       l+++g+ G Gkt + +a++ne   n+
  gi|298676049|ref|YP_003727799.1| 501 LLLFGPPGTGKTLVAQAVANESNVNF 526
                                       89*****************9977665 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0    0.0023      0.71       2      43 ..     229     275 ..     228     306 .. 0.80
   2 !    8.5   0.0    0.0073       2.2       4      26 ..     503     526 ..     501     558 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0023
                            AAA_28   2 ivitGgestGKTtlleaLaar...gypvv..pEaareileeklakge 43 
                                       +++ G+++tGKT +++a a++   ++ ++  pE++ +++ e  ++ +
  gi|298676049|ref|YP_003727799.1| 229 VIMHGPSGTGKTLIAKAVANEsraNFLYIagPEIMGKYYGESEERIR 275
                                       6789***************6655777777789999888877665555 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0073
                            AAA_28   4 itGgestGKTtlleaLaar.gypv 26 
                                       ++G+++tGKT +++a a++ +++ 
  gi|298676049|ref|YP_003727799.1| 503 LFGPPGTGKTLVAQAVANEsNVNF 526
                                       89***************7655544 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0075       2.3      19      46 ..     226     253 ..     199     272 .. 0.75
   2 ?   -1.0   0.0       5.4   1.7e+03      80     103 ..     463     486 ..     460     497 .. 0.73
   3 !    9.0   0.0    0.0043       1.3      20      51 ..     499     532 ..     484     544 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0075
                                       TEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve 46 
                                        + ++++G+ G+GKT +++++a++   +
  gi|298676049|ref|YP_003727799.1| 226 PKGVIMHGPSGTGKTLIAKAVANESRAN 253
                                       44599****************9987655 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 5.4
                                       HHHCTTCCCCSTSCEEEEETGGGG CS
                              TsaE  80 leelgleeyleeeavvlvEWpekl 103
                                       + ++g  e +++e + +vEWp k 
  gi|298676049|ref|YP_003727799.1| 463 WSDIGGLENVKQEIIEAVEWPLKR 486
                                       5667777777777899****9874 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0043
                                       EEEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                              TsaE  20 dvilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                       + +lL G+ G+GKT  ++++a++ +v+  +vk P
  gi|298676049|ref|YP_003727799.1| 499 KGLLLFGPPGTGKTLVAQAVANESNVNfiSVKGP 532
                                       3589*******************99988888877 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.26        81      36      51 ..     229     244 ..     222     250 .. 0.85
   2 ?    5.5   0.0     0.037        12     128     175 ..     272     319 ..     254     336 .. 0.84
   3 !    7.6   0.0    0.0084       2.6      36      54 ..     501     519 ..     473     522 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.26
                            AAA_25  36 allaGapgtGKttlal 51 
                                       ++  G++gtGKt +a 
  gi|298676049|ref|YP_003727799.1| 229 VIMHGPSGTGKTLIAK 244
                                       5789********9985 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.037
                            AAA_25 128 advdaleaaieevegvrlvviDplsralggdensnsdv.galvealeri 175
                                       + ++++ +++ e + +  + iD ++++ +  en   +v +++v++l  +
  gi|298676049|ref|YP_003727799.1| 272 ERIRKIFEEASE-NAPSIIFIDEIDSIAPKRENVTGEVeRRVVSQLLTM 319
                                       567788888888.67**********************888888887655 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0084
                            AAA_25  36 allaGapgtGKttlaldla 54 
                                        ll+G+pgtGKt +a  +a
  gi|298676049|ref|YP_003727799.1| 501 LLLFGPPGTGKTLVAQAVA 519
                                       589**********998765 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0028      0.86       4      49 ..     229     268 ..     226     308 .. 0.69
   2 !    9.0   0.0    0.0024      0.75       7      44 ..     504     534 ..     499     577 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0028
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvl.vlre 49 
                                       v+ +G +GtGKt+++ ++++e        +a++l+  +p+++ +++ 
  gi|298676049|ref|YP_003727799.1| 229 VIMHGPSGTGKTLIAKAVANES-------RANFLYIAGPEIMgKYYG 268
                                       6889************999998.......566666665555424444 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0024
                           DUF2075   7 tGvaGtGKtvvllnllaeleddeeertavylsvNhplv 44 
                                        G +GtGKt+v+ ++++e        +++++sv +p++
  gi|298676049|ref|YP_003727799.1| 504 FGPPGTGKTLVAQAVANES-------NVNFISVKGPQI 534
                                       599***********99998.......566666666654 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0086       2.7      17      57 ..     219     254 ..     199     303 .. 0.78
   2 !    8.5   0.0     0.006       1.8       7      50 ..     472     524 ..     467     587 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0086
                                       ......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-E CS
                            ResIII  17 eklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekf 57 
                                       + l+++  k ++++ + GtGKTl+a +++ + +      +f
  gi|298676049|ref|YP_003727799.1| 219 KRLNIEPPKGVIMHGPSGTGKTLIAKAVANESRA-----NF 254
                                       44444778899999**********9877766555.....45 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.006
                                       HHHHHHHHHT...............TTSEEEEEESTTSTHHHHHHHHHHHH-S CS
                            ResIII   7 yQeeaienlleklks.........krdkrglikmaTGtGKTlvaaklierllk 50 
                                         +e+ie+++  lk          k  k +l+  + GtGKTlva +++ +   
  gi|298676049|ref|YP_003727799.1| 472 VKQEIIEAVEWPLKRpekfeqmgiKPPKGLLLFGPPGTGKTLVAQAVANESNV 524
                                       5567777777555445555557778889999************9887766544 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0036       1.1      48      92 ..     221     267 ..     184     337 .. 0.72
   2 !    7.8   0.0    0.0052       1.6      22     116 ..     458     566 ..     443     619 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0036
                            DUF815  48 leglpannvLLwGarGtGKSslvkallneyaeegLrli..evekedl 92 
                                       l+ +p + v++ G  GtGK  + ka+ ne +++ L +   e+  +  
  gi|298676049|ref|YP_003727799.1| 221 LNIEPPKGVIMHGPSGTGKTLIAKAVANESRANFLYIAgpEIMGKYY 267
                                       55678899*********************999988765335555544 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0052
                            DUF815  22 vdevklddLvgidkqkealvente.......qfle..glpannvLLwGarGtGKSslvkallneyaeeg..Lrliev 87 
                                       + +vk++d+ g+++ k++++e +e       +f +   +p + +LL+G  GtGK  + +a+ ne + +   ++  ++
  gi|298676049|ref|YP_003727799.1| 458 IPSVKWSDIGGLENVKQEIIEAVEwplkrpeKFEQmgIKPPKGLLLFGPPGTGKTLVAQAVANESNVNFisVKGPQI 534
                                       56677788888888888887776522222224433214788999************99**99987766522222344 PP

                            DUF815  88 ekedlkelp.klvellrerp..erfilfvDDL 116
                                        ++ + e + ++ ++ ++++    +++f D L
  gi|298676049|ref|YP_003727799.1| 535 LHKWVGESEkAIRDTFKKAKqvAPCVIFFDEL 566
                                       44444333303444444333113466666666 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0017      0.52      10      44 ..     219     250 ..     213     256 .. 0.75
   2 ?    5.5   0.0     0.027       8.4      24      46 ..     502     523 ..     494     552 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0017
                                       HHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCSH CS
                            NB-ARC  10 ekLlekdelqslvvalvGmgGvGKttlakqilnks 44 
                                       ++L   + ++   v ++G  G GKt +ak + n+s
  gi|298676049|ref|YP_003727799.1| 219 KRLN-IEPPK--GVIMHGPSGTGKTLIAKAVANES 250
                                       5555.33333..4889***************9984 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.027
                                       EEEESTTSSHHHHHHHHCCSHCC CS
                            NB-ARC  24 alvGmgGvGKttlakqilnksde 46 
                                        l G +G GKt +a+ + n+ ++
  gi|298676049|ref|YP_003727799.1| 502 LLFGPPGTGKTLVAQAVANE-SN 523
                                       689**************999.43 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0091       2.8       5      29 ..     229     257 ..     226     305 .. 0.66
   2 !    8.5   0.0    0.0049       1.5       5      29 ..     501     527 ..     498     583 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0091
                            AAA_24   5 iliyGpsgiGKTtlakel....gpkplfi 29 
                                       +++ Gpsg+GKT +ak        ++l+i
  gi|298676049|ref|YP_003727799.1| 229 VIMHGPSGTGKTLIAKAVanesRANFLYI 257
                                       6788************9987666666666 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0049
                            AAA_24   5 iliyGpsgiGKTtlakel..gpkplfi 29 
                                       +l++Gp+g+GKT +a     + ++ fi
  gi|298676049|ref|YP_003727799.1| 501 LLLFGPPGTGKTLVAQAVanESNVNFI 527
                                       789**********99988665555555 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1      0.12        39      22      38 ..     229     245 ..     223     261 .. 0.80
   2 ?    3.0   0.1      0.18        55     116     154 ..     282     323 ..     257     337 .. 0.67
   3 !    8.2   0.0    0.0045       1.4      14      39 ..     493     518 ..     469     553 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.12
                            ATPase  22 vlitGepGtGKtifalq 38 
                                       v + G +GtGKt++a+ 
  gi|298676049|ref|YP_003727799.1| 229 VIMHGPSGTGKTLIAKA 245
                                       5678**********986 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.18
                            ATPase 116 keikakrvviDsitgl...ayeekeavaReilrqlvrvlkkl 154
                                       +e   + + iD i+++    ++ + +v R+ + ql++++ +l
  gi|298676049|ref|YP_003727799.1| 282 SENAPSIIFIDEIDSIapkRENVTGEVERRVVSQLLTMMDGL 323
                                       334446677777777742144455677899999999999655 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0045
                            ATPase  14 gGipegrvvlitGepGtGKtifalqF 39 
                                        Gi   +  l+ G pGtGKt++a+  
  gi|298676049|ref|YP_003727799.1| 493 MGIKPPKGLLLFGPPGTGKTLVAQAV 518
                                       5788888899***********99864 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.51   1.6e+02      48      68 ..     229     249 ..     212     258 .. 0.82
   2 !   12.7   0.0   0.00029     0.089      45     131 ..     498     582 ..     472     636 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.51
                             Rad17  48 LLisGPsGCgkstvvkvLske 68 
                                       +++ GPsG gk+ + k ++ e
  gi|298676049|ref|YP_003727799.1| 229 VIMHGPSGTGKTLIAKAVANE 249
                                       6789********999998877 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00029
                             Rad17  45 kriLLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdn.qksdfkgltekesrflsqiesfkeleLkdakyl 120
                                        + LL+ GP+G gk+ v + ++ e  ++++    p  l++     ++ ++  ++k ++  + +  f el   ++   
  gi|298676049|ref|YP_003727799.1| 498 PKGLLLFGPPGTGKTLVAQAVANESNVNFISVKGPQILHKWVGeSEKAIRDTFKKAKQVAPCVIFFDELDSISSTRS 574
                                       456999**************************999888665443888999999999999999999999976666665 PP

                             Rad17 121 klqklGddlrt 131
                                        +    +d rt
  gi|298676049|ref|YP_003727799.1| 575 GMT---EDGRT 582
                                       665...33344 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0028      0.86       3      27 ..     231     255 ..     229     259 .. 0.88
   2 ?    6.1   0.0     0.026       7.9       5      28 ..     505     528 ..     502     531 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0028
                                       EE-STTSSHHHHHHHHHHHHT-EEE CS
                    Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyl 27 
                                       + GP+g+GK  +a+a+a++  +++l
  gi|298676049|ref|YP_003727799.1| 231 MHGPSGTGKTLIAKAVANESRANFL 255
                                       67***************99888876 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.026
                                       -STTSSHHHHHHHHHHHHT-EEEE CS
                    Cytidylate_kin   5 GPagsGKssvaralaeklglkyld 28 
                                       GP g+GK  va+a+a++ ++++++
  gi|298676049|ref|YP_003727799.1| 505 GPPGTGKTLVAQAVANESNVNFIS 528
                                       9******************99986 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.1    0.0027      0.84       9     113 ..     215     323 ..     213     334 .. 0.59
   2 ?    2.6   0.0      0.35   1.1e+02      23      44 ..     501     522 ..     491     530 .. 0.75
   3 ?    1.9   0.0      0.56   1.7e+02     104     151 ..     544     596 ..     523     627 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0027
                          ATPase_2   9 keleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal... 82 
                                       +el + l+ ep + +   Gp g GKt + k ++++++      + yia  e+  +++ e+  ee+ +k +e+a    
  gi|298676049|ref|YP_003727799.1| 215 NELFKRLNIEPPKGVIMHGPSGTGKTLIAKAVANESRA----NFLYIAGPEIMGKYYGES--EERIRKIFEEASena 285
                                       56778888999999999*********888888888844....567788888888888888..444444444444333 PP

                          ATPase_2  83 .........giavpkaeleeilkeksklvfkaiellleki 113
                                                       + e++  e  + v +++  +++ +
  gi|298676049|ref|YP_003727799.1| 286 psiifideiD--SIAPKRENVTGEVERRVVSQLLTMMDGL 323
                                       3333333221..2222222233344444555555555555 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.35
                          ATPase_2  23 yfiYGpegsGKtaLlkeiienl 44 
                                       ++++Gp g GKt + + +++++
  gi|298676049|ref|YP_003727799.1| 501 LLLFGPPGTGKTLVAQAVANES 522
                                       689********97766666654 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.56
                          ATPase_2 104 kaielllekikkkgkk...iiiiiDelqklidlgln......gaellvkeLlnlies 151
                                       kai + +    kk+k+    +i++Del  + +  +        +e+++++Ll+ ++ 
  gi|298676049|ref|YP_003727799.1| 544 KAIRDTF----KKAKQvapCVIFFDELDSISSTRSGmtedgrTSEKVLNQLLTEMDG 596
                                       3333333....3444456689******999955544666666666666666666655 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0019       0.6      53      78 ..     218     242 ..     181     249 .. 0.83
   2 ?    5.6   0.0     0.021       6.4      59      79 ..     495     515 ..     466     525 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0019
                       AFG1_ATPase  53 grkrksvepvrglYlwGgvGrGKtyl 78 
                                       + kr + ep++g+ ++G+ G GKt +
  gi|298676049|ref|YP_003727799.1| 218 F-KRLNIEPPKGVIMHGPSGTGKTLI 242
                                       3.345899****************76 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.021
                       AFG1_ATPase  59 vepvrglYlwGgvGrGKtylm 79 
                                        +p++gl l G+ G GKt + 
  gi|298676049|ref|YP_003727799.1| 495 IKPPKGLLLFGPPGTGKTLVA 515
                                       579***************875 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.038        12      19      41 ..     228     250 ..     209     287 .. 0.77
   2 !    9.8   0.0     0.002      0.61      20      58 ..     501     535 ..     484     713 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.038
                            AAA_11  19 itliqGPPGtgKTktivellsql 41 
                                        ++++GP GtgKT    ++ ++ 
  gi|298676049|ref|YP_003727799.1| 228 GVIMHGPSGTGKTLIAKAVANES 250
                                       4789*********7766666655 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.002
                            AAA_11  20 tliqGPPGtgKTktivellsqllsrrkseeeksakpriL 58 
                                        l+ GPPGtgKT +  ++ ++ +     +    ++p+iL
  gi|298676049|ref|YP_003727799.1| 501 LLLFGPPGTGKTLVAQAVANESNV----NFISVKGPQIL 535
                                       5788********999999999852....22333333333 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0063       1.9      20      40 ..     228     248 ..     215     260 .. 0.82
   2 ?    6.4   0.0     0.021       6.5      22      39 ..     502     519 ..     491     527 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0063
                            AAA_30  20 vavltGpAGtGKttalkalre 40 
                                        ++++Gp GtGKt + ka+++
  gi|298676049|ref|YP_003727799.1| 228 GVIMHGPSGTGKTLIAKAVAN 248
                                       5799************99976 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.021
                            AAA_30  22 vltGpAGtGKttalkalr 39 
                                       +l Gp+GtGKt + +a++
  gi|298676049|ref|YP_003727799.1| 502 LLFGPPGTGKTLVAQAVA 519
                                       678*********999986 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.021       6.5      19      66 ..     231     284 ..     227     336 .. 0.72
   2 !    8.8   0.0    0.0036       1.1      18      65 ..     502     592 ..     498     621 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.021
                                       EEESTTSSHHHHHHHHHHHSSTSSEEEEEE........ESEEHHHHHHHHHHCHHS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  19 ipgafgvGktvisqslskqsnsddaiiyvg........iGergnevaevleefpeg 66 
                                       + g +g+Gkt i+++++++s+++    y++         Ge ++ +++++ee  e+
  gi|298676049|ref|YP_003727799.1| 231 MHGPSGTGKTLIAKAVANESRAN--FLYIAgpeimgkyYGESEERIRKIFEEASEN 284
                                       6799***************8666..4444435554444777777777777776663 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0036
                                       EEEESTTSSHHHHHHHHHHHSSTSSEEEEEE.............................................E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............................................x RF
                       ATP-synt_ab  18 lipgafgvGktvisqslskqsnsddaiiyvg.............................................i 49 
                                       l++g  g+Gkt ++q+++++sn +   i v                                              +
  gi|298676049|ref|YP_003727799.1| 502 LLFGPPGTGKTLVAQAVANESNVN--FISVKgpqilhkwvgesekairdtfkkakqvapcviffdeldsisstrsgM 576
                                       789*****************9988..444444666666766666666666666666666666666666666666666 PP

                                       SEEHHHHHHHHHHCHH CS
                                       xxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  50 Gergnevaevleefpe 65 
                                        e g++ ++vl+++ +
  gi|298676049|ref|YP_003727799.1| 577 TEDGRTSEKVLNQLLT 592
                                       6666666666666555 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.86   2.7e+02       2      24 ..     233     257 ..     232     304 .. 0.76
   2 !   12.1   0.0   0.00064       0.2       1      81 [.     504     583 ..     504     627 .. 0.62

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.86
                                       E-TTSSHHHHHHHHHHHH..TEEEE CS
                            AAA_17   2 GgPGsGKgtqceklveky..gfthl 24 
                                       G+ G GK+ +++ ++ +   +f ++
  gi|298676049|ref|YP_003727799.1| 233 GPSGTGKTLIAKAVANESraNFLYI 257
                                       999********99998763345444 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00064
                                       EE-TTSSHHHHHHHHHHHHTEEEEEH.HHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEE CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsa.Gdllreeakrgglakardemrklpleekkelqkeaaekiaeeakkkgvlv 76 
                                       +G+PG GK+ +++ ++ + ++ ++s  G  +      ++ +  rd ++k++++  + +     ++i  +  ++g+  
  gi|298676049|ref|YP_003727799.1| 504 FGPPGTGKTLVAQAVANESNVNFISVkGPQILHKWVGESEKAIRDTFKKAKQVAPCVIFFDELDSISST--RSGMTE 578
                                       6*****************999998877766665555555567888888888887776655555566553..556666 PP

                                       EE-SE CS
                            AAA_17  77 dghpr 81 
                                       dg  +
  gi|298676049|ref|YP_003727799.1| 579 DGRTS 583
                                       66654 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.087        27      24      48 ..     229     253 ..     216     303 .. 0.73
   2 !    9.5   0.0    0.0032      0.99      24      47 ..     501     524 ..     490     574 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.087
                                       EEEEEETT--HHHHHHCC--TTS-E CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpw 48 
                                       v + G+ G+gk+l+A++ +++s  +
  gi|298676049|ref|YP_003727799.1| 229 VIMHGPSGTGKTLIAKAVANESRAN 253
                                       7789**************9987664 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0032
                                       EEEEEETT--HHHHHHCC--TTS- CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgp 47 
                                       ++l G++G+gk+lvA++ +++s  
  gi|298676049|ref|YP_003727799.1| 501 LLLFGPPGTGKTLVAQAVANESNV 524
                                       89***************9998764 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.026         8       3      32 ..     227     256 ..     226     262 .. 0.88
   2 ?    5.3   0.0     0.045        14      73      95 ..     261     283 ..     250     304 .. 0.80
   3 ?    0.7   0.0       1.2   3.7e+02       4      30 ..     500     526 ..     498     534 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.026
                                       SEEEEESTTTSSHHHHHHHHHHHSTTTEEE CS
                     Guanylate_kin   3 rpvvlvgpsgaGksslkkaLlselpekfgv 32 
                                       + v++ gpsg+Gk  + ka+ +e   +f +
  gi|298676049|ref|YP_003727799.1| 227 KGVIMHGPSGTGKTLIAKAVANESRANFLY 256
                                       569*****************9999888864 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.045
                                       EETTEEEEEEHHHHHHHHHTTSE CS
                     Guanylate_kin  73 efsgnlygtsveaieevlekgki 95 
                                       e  g++yg+s e i++++e++ +
  gi|298676049|ref|YP_003727799.1| 261 EIMGKYYGESEERIRKIFEEASE 283
                                       47899*************99865 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 1.2
                                       EEEEESTTTSSHHHHHHHHHHHSTTTE CS
                     Guanylate_kin   4 pvvlvgpsgaGksslkkaLlselpekf 30 
                                        + l gp g+Gk  + +a+ +e + +f
  gi|298676049|ref|YP_003727799.1| 500 GLLLFGPPGTGKTLVAQAVANESNVNF 526
                                       5789***********999988877666 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0     0.015       4.5      56      76 ..     229     249 ..     216     256 .. 0.85
   2 ?    5.8   0.0     0.044        14      53      76 ..     498     521 ..     464     539 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.015
                                       EEEEE-TTSSHHHHHHHHHHH CS
                            Torsin  56 lsfhGwtGtGknfvaeiiaen 76 
                                       + +hG +GtGk  +a+ +a++
  gi|298676049|ref|YP_003727799.1| 229 VIMHGPSGTGKTLIAKAVANE 249
                                       568**************9986 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.044
                                       -EEEEEEE-TTSSHHHHHHHHHHH CS
                            Torsin  53 pLvlsfhGwtGtGknfvaeiiaen 76 
                                       p  l + G +GtGk  va+ +a++
  gi|298676049|ref|YP_003727799.1| 498 PKGLLLFGPPGTGKTLVAQAVANE 521
                                       4556789*************9986 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       5.8   1.8e+03     122     133 ..     163     174 ..     157     189 .. 0.78
   2 ?    6.1   0.0     0.022       6.6      24      59 ..     215     250 ..     203     260 .. 0.85
   3 ?    4.8   0.0     0.052        16      35      59 ..     498     522 ..     471     533 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5.8
                              TniB 122 vLiiDEihnlla 133
                                       +LiiDE  +++ 
  gi|298676049|ref|YP_003727799.1| 163 ILIIDETTEIEL 174
                                       8*****999875 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.022
                              TniB  24 eeLleypkrkrmpnlllvGdsnnGKtmivekFarlh 59 
                                       +eL+++ + + ++ ++++G+s +GKt i++  a++ 
  gi|298676049|ref|YP_003727799.1| 215 NELFKRLNIEPPKGVIMHGPSGTGKTLIAKAVANES 250
                                       57888888888899**************99887765 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.052
                              TniB  35 mpnlllvGdsnnGKtmivekFarlh 59 
                                       ++ lll+G++ +GKt +++  a++ 
  gi|298676049|ref|YP_003727799.1| 498 PKGLLLFGPPGTGKTLVAQAVANES 522
                                       4789************999877665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.019       5.8       3      23 ..     229     249 ..     227     256 .. 0.88
   2 ?    4.4   0.0       0.1        32       4      22 ..     502     520 ..     500     525 .. 0.87
   3 ?   -0.7   0.0       3.7   1.1e+03      81     133 ..     557     613 ..     533     647 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.019
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       vi++G++G GKT  ++ +a +
  gi|298676049|ref|YP_003727799.1| 229 VIMHGPSGTGKTLIAKAVANE 249
                                       899************999876 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.1
                                       EEEC-TTTCHHHHHHHHHH CS
                             NACHT   4 ilqGeaGsGKTtLlqklal 22 
                                       +l G++G GKT  +q +a 
  gi|298676049|ref|YP_003727799.1| 502 LLFGPPGTGKTLVAQAVAN 520
                                       688************9986 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 3.7
                                       CCEEEEEE-STT-SS-TCH...........HHHHHCTT..TTT--EEEEEEECCCHH CS
                             NACHT  81 erlLlilDglDelvtdlgq..kekqpvrtlLselirkk..llpeasllltvrpralr 133
                                          ++ +D lD +++  +   ++ + ++++L++l+++   l p + +++++ +++ +
  gi|298676049|ref|YP_003727799.1| 557 APCVIFFDELDSISSTRSGmtEDGRTSEKVLNQLLTEMdgLEPLNDVIVIAATNRPE 613
                                       445577889998888666677777888888999988732245555555555555555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1       5.9   1.8e+03     103     118 ..     161     176 ..     152     178 .. 0.76
   2 ?    3.6   0.0      0.24        75      12      32 ..     228     248 ..     221     257 .. 0.80
   3 ?    8.8   0.0    0.0064         2      11      32 ..     499     520 ..     493     573 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 5.9
                            AAA_19 103 eellivDEfqdvdelq 118
                                         +li+DE+ +++  q
  gi|298676049|ref|YP_003727799.1| 161 DSILIIDETTEIELSQ 176
                                       349*******998655 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.24
                            AAA_19  12 vllvtaGpGtGKTrvlkhiva 32 
                                        +++ ++ GtGKT + k++ +
  gi|298676049|ref|YP_003727799.1| 228 GVIMHGPSGTGKTLIAKAVAN 248
                                       57788999*****99887655 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0064
                            AAA_19  11 kvllvtaGpGtGKTrvlkhiva 32 
                                       k ll+ ++pGtGKT v +++ +
  gi|298676049|ref|YP_003727799.1| 499 KGLLLFGPPGTGKTLVAQAVAN 520
                                       56899*********99887665 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.076        24       2      30 ..     229     257 ..     228     339 .. 0.80
   2 ?    8.0   0.0    0.0078       2.4       2      30 ..     501     529 ..     500     619 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.076
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       v+++g  G++ktl++ka+a+   ++f  i
  gi|298676049|ref|YP_003727799.1| 229 VIMHGPSGTGKTLIAKAVANESRANFLYI 257
                                       7899999************9999888766 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0078
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       +ll g PG++ktl+++a+a+  +++f  +
  gi|298676049|ref|YP_003727799.1| 501 LLLFGPPGTGKTLVAQAVANESNVNFISV 529
                                       58899***************999999766 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.039        12      15      32 ..     227     244 ..     206     258 .. 0.85
   2 ?    0.9   0.0       1.1   3.4e+02     120     169 ..     284     336 ..     266     342 .. 0.73
   3 ?    1.2   0.0      0.87   2.7e+02      18      37 ..     502     521 ..     494     536 .. 0.77
   4 ?    1.9   0.0      0.54   1.7e+02      97     169 ..     531     610 ..     512     616 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.039
                                       CEEEEEESTTSSHHHHHH CS
                                       xxxxxxxxxxxxxxxxxx RF
                              DEAD  15 gdvlvaaeTGsGKTlafl 32 
                                       + v+++++ G+GKTl++ 
  gi|298676049|ref|YP_003727799.1| 227 KGVIMHGPSGTGKTLIAK 244
                                       679***********9975 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.1
                                       TTEEEEEEETHHHHHHT...TTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSB CS
                                       xxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 120 sqvrflVlDEadrlldq...gfsdfinrilnqlpqitcdgklqrqvivlSATl 169
                                       +  +++ +DE+d +  +     ++  +r+++ql ++ +  ++  qv+v+ AT 
  gi|298676049|ref|YP_003727799.1| 284 NAPSIIFIDEIDSIAPKrenVTGEVERRVVSQLLTMMDGLEERGQVVVIGATN 336
                                       55577889****99988665677777889999976666666777899999996 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.87
                                       EEEESTTSSHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                              DEAD  18 lvaaeTGsGKTlaflipvlq 37 
                                       l+ ++ G+GKTl+++  + +
  gi|298676049|ref|YP_003727799.1| 502 LLFGPPGTGKTLVAQAVANE 521
                                       667899*******9887665 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.54
                                       TCSEEEEEHHHHHHHHHCTSSHCTTE..EEEEEETHHHHHHT.....TTHHHHHHHHHHSHHHCTTSTTTSEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  97 gvdivvgtpgrlddllstgklnlsqv..rflVlDEadrlldq.....gfsdfinrilnqlpqitcdgklqrqvivlS 166
                                       g++i+    g   + +++   + +qv   ++ +DE d +++      + +++ +++lnql +  +  +  + viv+ 
  gi|298676049|ref|YP_003727799.1| 531 GPQILHKWVGESEKAIRDTFKKAKQVapCVIFFDELDSISSTrsgmtEDGRTSEKVLNQLLTEMDGLEPLNDVIVIA 607
                                       455554444444444422222467773234558******99988555566778889999855544444444699999 PP

                                       SSB CS
                                       xxx RF
                              DEAD 167 ATl 169
                                       AT 
  gi|298676049|ref|YP_003727799.1| 608 ATN 610
                                       996 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.036        11     117     137 ..     229     249 ..     209     252 .. 0.87
   2 ?    6.5   0.0     0.013       3.9     117     137 ..     501     521 ..     491     527 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.036
                         Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                                       v ++Gp  tGkt +a+a a+ 
  gi|298676049|ref|YP_003727799.1| 229 VIMHGPSGTGKTLIAKAVANE 249
                                       6788*************9985 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.013
                         Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                                       ++++Gp+ tGkt +a+a a+ 
  gi|298676049|ref|YP_003727799.1| 501 LLLFGPPGTGKTLVAQAVANE 521
                                       5789*************9986 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       1.8   5.4e+02      78      92 ..     158     172 ..     151     179 .. 0.84
   2 ?    7.6   0.0    0.0088       2.7       4      64 ..     230     295 ..     228     313 .. 0.79
   3 ?    1.3   0.0      0.74   2.3e+02       6      61 ..     504     564 ..     501     583 .. 0.60

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.8
                               Zot  78 idkgallviDEcqei 92 
                                        +++++l+iDE+ ei
  gi|298676049|ref|YP_003727799.1| 158 EPEDSILIIDETTEI 172
                                       359********9876 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0088
                               Zot   4 lvtGapGsgKts..gavkkdllpalk..egRkiitnidGlrlerieqvlgekvs.tarliridnpe 64 
                                       + +G+ G+gKt+  +av ++ +      +g +i+ +  G   eri+++++e+ + ++ +i+id+ +
  gi|298676049|ref|YP_003727799.1| 230 IMHGPSGTGKTLiaKAVANESRANFLyiAGPEIMGKYYGESEERIRKIFEEASEnAPSIIFIDEID 295
                                       89*********822456666555333357**********************9999999***99333 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.74
                               Zot   6 tGapGsgKtsga..vkkdllp..alkegRkiitnidGlrlerieqvlgekvs.tarlirid 61 
                                        G+pG+gKt++a  v ++ +    +++g +i  +  G   ++i+  ++++++ ++ +i+ d
  gi|298676049|ref|YP_003727799.1| 504 FGPPGTGKTLVAqaVANESNVnfISVKGPQILHKWVGESEKAIRDTFKKAKQvAPCVIFFD 564
                                       5899999998751144432223233366666666666666666666666666666666655 PP

>> UFD1  Ubiquitin fusion degradation protein UFD1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       6.4     2e+03      77     101 ..      27      51 ..      18      61 .. 0.72
   2 ?   12.0   0.0   0.00035      0.11      67     171 ..      60     175 ..      58     177 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 6.4
                              UFD1  77 mmenlgleegdlveiesvslpkgkf 101
                                        + +l+l+ gd+vei+  +   +k+
  gi|298676049|ref|YP_003727799.1|  27 TLLELQLSPGDIVEITGQKRTAAKV 51 
                                       5567899999999999877776665 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00035
                              UFD1  67 eegtvylPewmmenlgleegdlveiesvslpkgkfvklqpqsedfldisd.pkavLekaLrnfatLtkgdvieikyn 142
                                       e+g++ +  ++ +n g++ g+ v++++++ + ++ v l p +  +++  d    ++++++ +   + ++dvi+i  +
  gi|298676049|ref|YP_003727799.1|  60 EQGFIRIDGFIRQNAGVSIGERVSLKKIEAKPAEKVVLAPPEGMMMEFGDnTSDIIKRNILKR-PIVQDDVIPIISS 135
                                       679999999*************************************99651567888777775.567999*999887 PP

                              UFD1 143 dkv...........yelkvlevkpesavsiietdlevdfa 171
                                        ++             l v+e++pe+++ ii+   e+++ 
  gi|298676049|ref|YP_003727799.1| 136 MNQpmsgpvaggqaIPLIVVETEPEDSILIIDETTEIELS 175
                                       77678999999999******************99999875 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.093        29       1      21 [.     235     255 ..     235     285 .. 0.80
   2 ?    6.7   0.0     0.023       7.1       1      22 [.     507     528 ..     507     553 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.093
                                       TTSSHHHHHHHHHHHHTSEEE CS
                               SKI   1 mGaGKstvGkllAkklglefi 21 
                                       +G+GK+ ++k++A++ + +f+
  gi|298676049|ref|YP_003727799.1| 235 SGTGKTLIAKAVANESRANFL 255
                                       59*************999885 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.023
                                       TTSSHHHHHHHHHHHHTSEEEE CS
                               SKI   1 mGaGKstvGkllAkklglefiD 22 
                                       +G+GK+ v++++A++ +++fi 
  gi|298676049|ref|YP_003727799.1| 507 PGTGKTLVAQAVANESNVNFIS 528
                                       69******************95 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.091        28       2      71 ..     230     294 ..     229     299 .. 0.74
   2 ?    7.1   0.0     0.013       3.9       4      70 ..     504     565 ..     501     570 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.091
                   Viral_helicase1   2 vvhGvpGcGKStlirkllrtsliltvnrptaelltegk....pklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                       ++hG  G GK+ + + ++++       ++++ l+ +g     ++ + +s ++++++ + +++     i+++DE+
  gi|298676049|ref|YP_003727799.1| 230 IMHGPSGTGKTLIAKAVANE-------SRANFLYIAGPeimgKYYG-ESEERIRKIFEEASEN-APSIIFIDEI 294
                                       78*********999999999.......6669999999999954444.4445555555555554.4789999997 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.013
                   Viral_helicase1   4 hGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDE 70 
                                        G pG GK+ + + ++++s +++ +++    +l +++ ++++    t++++ + +   +   ++++DE
  gi|298676049|ref|YP_003727799.1| 504 FGPPGTGKTLVAQAVANESnVNFISVKG-PQILHKWVGESEKAIRDTFKKAKQVAP--C---VIFFDE 565
                                       588****************977777777.89******9999999999998776444..3...788888 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.039        12      11      38 ..     217     242 ..     209     248 .. 0.71
   2 ?    4.7   0.0     0.082        25      18      37 ..     494     513 ..     479     520 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.039
                            AAA_29  11 tfdghtieidlkgatlltGpsGsGKSTl 38 
                                        f++  ie   kg +++ GpsG+GK+ +
  gi|298676049|ref|YP_003727799.1| 217 LFKRLNIEPP-KG-VIMHGPSGTGKTLI 242
                                       5555555553.67.99*********866 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.082
                            AAA_29  18 eidlkgatlltGpsGsGKST 37 
                                        i++    ll Gp G+GK+ 
  gi|298676049|ref|YP_003727799.1| 494 GIKPPKGLLLFGPPGTGKTL 513
                                       44444449**********75 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.54   1.7e+02       5      25 ..     230     250 ..     227     257 .. 0.86
   2 ?    8.1   0.0    0.0051       1.6       5      55 ..     502     552 ..     499     557 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.54
                               IPT   5 lifGatttGKtaeaiklaket 25 
                                       +++G+ +tGKt  a ++a+e 
  gi|298676049|ref|YP_003727799.1| 230 IMHGPSGTGKTLIAKAVANES 250
                                       578**************9986 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0051
                               IPT   5 lifGatttGKtaeaiklaketgapvivlDRvqcyselavgsGrpleeeleg 55 
                                       l+fG+ +tGKt +a ++a+e  +  i++   q  ++    s +++ + +++
  gi|298676049|ref|YP_003727799.1| 502 LLFGPPGTGKTLVAQAVANESNVNFISVKGPQILHKWVGESEKAIRDTFKK 552
                                       89*********************9999988887777776666666666665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0     0.015       4.7       4      39 ..     212     246 ..     209     247 .. 0.86
   2 ?    1.7   0.5         1   3.1e+02      24      39 ..     503     518 ..     489     733 .. 0.52

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.015
                            AAA_23   4 ienfrsfrdqeidFskgltlItGpNGaGKTTildAi 39 
                                       ++n   f++ +i+  kg+ + +Gp G+GKT i  A+
  gi|298676049|ref|YP_003727799.1| 212 LKNNELFKRLNIEPPKGV-IMHGPSGTGKTLIAKAV 246
                                       677778999999999999.99*********999885 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 1
                            AAA_23  24 ItGpNGaGKTTildAi 39 
                                       ++Gp G+GKT + +A+
  gi|298676049|ref|YP_003727799.1| 503 LFGPPGTGKTLVAQAV 518
                                       5555555555554443 PP

>> LID  LIM interaction domain (LID)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00062      0.19       8      22 ..     260     274 ..     256     276 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00062
                               LID   8 PSmMGgdFGeeDERv 22 
                                       P +MG+ +Ge+ ER+
  gi|298676049|ref|YP_003727799.1| 260 PEIMGKYYGESEERI 274
                                       899***********6 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1       2.4   7.5e+02      94     112 ..     159     177 ..     146     181 .. 0.72
   2 ?    2.7   0.0      0.35   1.1e+02       2      24 ..     229     251 ..     228     262 .. 0.80
   3 ?    2.1   0.1      0.52   1.6e+02      72     119 ..     264     309 ..     259     320 .. 0.68
   4 ?   -0.4   0.1       3.1   9.5e+02      72     123 ..     430     485 ..     418     491 .. 0.64
   5 ?    5.3   0.0     0.053        16       3      32 ..     502     531 ..     500     541 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 2.4
                                       HHH-EEEE---STTGGG-H CS
                          NTPase_1  94 seadviviDEiGkmElksk 112
                                        e  +++iDE  ++El+ k
  gi|298676049|ref|YP_003727799.1| 159 PEDSILIIDETTEIELSQK 177
                                       3445*********999865 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.35
                                       EEEE--TTSSHHHHHHHHHHHH. CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellk 24 
                                       v++ Gp+G+GKt + k v+++ +
  gi|298676049|ref|YP_003727799.1| 229 VIMHGPSGTGKTLIAKAVANESR 251
                                       6788********99999988765 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.52
                                       TTEEE-HHHHHHHHHHHHHHHH.HHH-EEEE---STTGGG-HHHHHHHH CS
                          NTPase_1  72 gkyvvdvesfeelalealrkal.seadviviDEiGkmElkskkfkeave 119
                                       gky+ +    ee + +++++a  + + +i iDEi ++  k +++  +ve
  gi|298676049|ref|YP_003727799.1| 264 GKYYGE---SEERIRKIFEEASeNAPSIIFIDEIDSIAPKRENVTGEVE 309
                                       555554...455666677777645667*******877666666666655 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 3.1
                                       TTEEE-HHHHHHHHHHHHHHHH....HHH-EEEE---STTGGG-HHHHHHHHHHHT CS
                          NTPase_1  72 gkyvvdvesfeelalealrkal....seadviviDEiGkmElkskkfkeaveevLk 123
                                       +++vv++e+fe+  +e+   al     e   +    iG +E   ++++eave  Lk
  gi|298676049|ref|YP_003727799.1| 430 EEIVVTTEDFENALVEIEPSALrevlVEIPSVKWSDIGGLENVKQEIIEAVEWPLK 485
                                       56677777777766654333331111222233345699999999999999987776 PP

  == domain 5  score: 5.3 bits;  conditional E-value: 0.053
                                       EEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   3 fiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       ++ GppG+GKt + + v+++ + + ++v+G
  gi|298676049|ref|YP_003727799.1| 502 LLFGPPGTGKTLVAQAVANESNVNFISVKG 531
                                       677**************9998777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (741 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); expected 17.9 (0.001)
Passed Fwd filter:                        58  (0.00323498); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              58  [number of targets reported over threshold]
# CPU time: 0.87u 0.32s 00:00:01.19 Elapsed: 00:00:00.47
# Mc/sec: 4753.65
//
Query:       gi|298676050|ref|YP_003727800.1|  [L=88]
Description: PRC-barrel domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-12   46.0   0.1      5e-12   45.7   0.1    1.1  1  PRC       PRC-barrel domain


Domain annotation for each model (and alignments):
>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.1   2.8e-16     5e-12       3      73 ..       3      77 ..       1      81 [. 0.94

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 2.8e-16
                                      ECCS---TT-EEEETTSSEEEEEEEEEEETTTTEEEEEEEEETTT..........-EEEEEGG.CEECCCTEEEET CS
                               PRC  3 efrasdliGkeVytedGeklGkVkDvvidekegrvralvvsvggflgi.....gekevliPfdlavkigkdriivd 73
                                       ++a +l  k+V+t+dG++lG+++++ +d ++ +++ l ++  +  +      ++ ++l+Pf+  v+++kd+i+vd
  gi|298676050|ref|YP_003727800.1|  3 KVFAKNLSSKQVMTTDGTELGTLYNITMDLDTSELVDLMIKPDMNVDTsdfqkDDQYILLPFE-SVRAIKDYIVVD 77
                                      67899*************************************887666***************.***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 557.82
//
Query:       gi|298676051|ref|YP_003727801.1|  [L=234]
Description: SPP-like hydrolase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-32  113.0   3.7    5.6e-21   75.4   1.5    2.2  2  Hydrolase_3  haloacid dehalogenase-like hydrolase
    1.4e-10   41.8   0.1    0.00075   19.8   0.0    3.2  3  Hydrolase    haloacid dehalogenase-like hydrolase
    2.3e-08   33.9   0.1    7.5e-06   25.6   0.0    2.1  2  S6PP         Sucrose-6F-phosphate phosphohydrolase
    5.8e-05   23.6   0.1        1.8    8.9   0.0    3.2  3  HAD          haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
       0.01   15.9   0.0      0.026   14.7   0.0    1.7  1  Hydrolase_6  Haloacid dehalogenase-like hydrolase
      0.062   13.3   0.1       0.14   12.2   0.1    1.6  1  B1           Protein L b1 domain
      0.068   13.2   0.1       0.18   11.8   0.0    1.9  2  HAD_2        Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.0   5.6e-13   1.4e-09       2      69 ..       7      74 ..       6      99 .. 0.91
   2 !   75.4   1.5   2.2e-24   5.6e-21     176     255 .]     142     221 ..      85     221 .. 0.86

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 5.6e-13
                                      EEEIIIIIS-TTS---HHHHHHHHHHHH.TTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEEECT CS
                       Hydrolase_3  2 alDlDGTLlnsdkkisektkeaikklke.kgikvviATGRslravlpvleelgldlpvialNGalidde 69
                                      + D+DGT+ +++ +++ k++e + +l +  gi vv+ATG+ l + +   + +gl+ +via NG+++  e
  gi|298676051|ref|YP_003727801.1|  7 VADIDGTITHQNRRLNLKAAEMLYRLNDeSGIPVVLATGNILCFSHAASKLIGLSGYVIAENGGVV-SE 74
                                      78************************9769***********************************9.33 PP

  == domain 2  score: 75.4 bits;  conditional E-value: 2.2e-24
                                       TTEEEEEETT-SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGGTHHH CS
                       Hydrolase_3 176 kgyleimpkgvsKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnnedGVa 252
                                       ++ + i ++ ++Kgt+l k+a+ ++++++e +a+GD+eND+eM+e ag+g+A++n++++  ++Ad vt+    +GV+
  gi|298676051|ref|YP_003727801.1| 142 GYAVHIKSNTMNKGTGLVKIAELMGLNPKEFVAIGDSENDLEMIEFAGIGIAVANSDQKTRSIADIVTDASYGEGVV 218
                                       4556688999******************************************************************* PP

                                       HHH CS
                       Hydrolase_3 253 kal 255
                                       +a+
  gi|298676051|ref|YP_003727801.1| 219 EAI 221
                                       997 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0   0.00069       1.8       1      19 [.       3      21 ..       3      23 .. 0.88
   2 !   10.1   0.0   0.00029      0.73     122     160 ..      24      64 ..      19      79 .. 0.78
   3 !   19.8   0.0   2.9e-07   0.00075     173     210 .]     152     189 ..     114     189 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00069
                                      SSEEEEESBTTTBCHHHHH CS
                                      xxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  1 iktvvfDkdGTLttgepsv 19
                                      +k++v D+dGT+t+ ++++
  gi|298676051|ref|YP_003727801.1|  3 YKALVADIDGTITHQNRRL 21
                                      69***********998765 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00029
                                       THHHHHHHHHHT.TEEEEEEESSEHHHHHHHHHHTT.GGGE CS
                                       xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                         Hydrolase 122 eaaeavasLkaa.gievvlltgdnpetaeraanqlG.ddyf 160
                                       +aae++++L++  gi+vvl+tg+   + ++a + +G   y+
  gi|298676051|ref|YP_003727801.1|  24 KAAEMLYRLNDEsGIPVVLATGNILCFSHAASKLIGlSGYV 64 
                                       799*******999****************999999943333 PP

  == domain 3  score: 19.8 bits;  conditional E-value: 2.9e-07
                                       TTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 173 kpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                         +  g+v++++ ++ +p+e +++GD+ nD+++++ Ag
  gi|298676051|ref|YP_003727801.1| 152 MNKGTGLVKIAELMGLNPKEFVAIGDSENDLEMIEFAG 189
                                       458899***************************99886 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0    0.0022       5.7       3      44 ..       4      46 ..       2      60 .. 0.78
   2 !   25.6   0.0   2.9e-09   7.5e-06     154     243 ..     142     222 ..     123     225 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0022
                                      EEEEE-TBTTTB..S-HHHHHHHHHHHH.GGGGGEEEEEE-SS CS
                              S6PP  3 lllvsdLDntlv.dgdnealarlnelleaeerkdvllvfaTGR 44
                                      ++lv+d+D+t++ ++ + +l++ + l + ++++ + +v+aTG 
  gi|298676051|ref|YP_003727801.1|  4 KALVADIDGTIThQNRRLNLKAAEMLYRLNDESGIPVVLATGN 46
                                      679*********5445556666666666889999*******96 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 2.9e-09
                                       TTEEEEEETT-SHHHHHHHHHHHHT--GGGEEEEE-SGGGHHHHTSSSEEEE-TT--HHHHHHHHHH--TTE..EE- CS
                              S6PP 154 gkdlDvlPkraskgeAlryLakkleleleqilvcGdsgnDeellignvlgVvVgnaqeellqwllenakeneriyla 230
                                       g ++ +  +  +kg  l  +a+ ++l++++++  Gds+nD e+++    g+ V+n++++        +++    ++ 
  gi|298676051|ref|YP_003727801.1| 142 GYAVHIKSNTMNKGTGLVKIAELMGLNPKEFVAIGDSENDLEMIEFAGIGIAVANSDQK--------TRSIAD-IVT 209
                                       566667777889********************************************999........333332.346 PP

                                       SS-THHHHHHHHH CS
                              S6PP 231 eercaaGilegla 243
                                        +++ +G++e+++
  gi|298676051|ref|YP_003727801.1| 210 DASYGEGVVEAIE 222
                                       7778888888876 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.04     1e+02       2      13 ..       7      18 ..       6      24 .. 0.86
   2 !    8.2   0.0    0.0012         3      90     130 ..      25      67 ..      17      92 .. 0.74
   3 !    8.9   0.0    0.0007       1.8     166     187 ..     164     185 ..     118     186 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.04
                               HAD  2 lfDfDgTLldgd 13
                                      + D+DgT+++++
  gi|298676051|ref|YP_003727801.1|  7 VADIDGTITHQN 18
                                      78*******996 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0012
                               HAD  90 alella.ahraaGdrvvvvSgglrplvepllaelg.adevlat 130
                                       a e+l     + G++vv+ +g++  + ++  ++ g + +v+a+
  gi|298676051|ref|YP_003727801.1|  25 AAEMLYrLNDESGIPVVLATGNILCFSHAASKLIGlSGYVIAE 67 
                                       44444424469************************66666666 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0007
                               HAD 166 gegidleevvayGDspsDlpll 187
                                         g+ ++e va+GDs++Dl++ 
  gi|298676051|ref|YP_003727801.1| 164 LMGLNPKEFVAIGDSENDLEMI 185
                                       456666778***********96 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0     1e-05     0.026       2      39 ..       7      46 ..       6      81 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1e-05
                                      EEESTTTSEETTE.E-TTHHHHHHHHHHT.T-EEEEEE-- CS
                       Hydrolase_6  2 lfDidGvLwrgdk.aipgaaealnalraa.gkpvvllTNn 39
                                      + DidG++ ++++ +  +aae+l +l+++ g+pvvl T n
  gi|298676051|ref|YP_003727801.1|  7 VADIDGTITHQNRrLNLKAAEMLYRLNDEsGIPVVLATGN 46
                                      78******9977615569********98769*****9977 PP

>> B1  Protein L b1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   5.5e-05      0.14      40      65 ..     124     148 ..     117     151 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.5e-05
                                B1  40 yadllkkenGeytadledgGytinik 65 
                                       ya  + k  G+y +dl d Gy++ ik
  gi|298676051|ref|YP_003727801.1| 124 YAKNVIK-SGKYNVDLIDTGYAVHIK 148
                                       5555554.6***************98 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.3   3.3e+03       4      13 ..       9      18 ..       7      40 .. 0.69
   2 ?   11.8   0.0   7.2e-05      0.18     140     175 ..     157     192 ..     108     195 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.3
                             HAD_2  4 DlDgTlldte 13
                                      D+DgT+  ++
  gi|298676051|ref|YP_003727801.1|  9 DIDGTITHQN 18
                                      7888886554 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 7.2e-05
                             HAD_2 140 viekaleklklkkeeviyvGDsptDieaakkagikv 175
                                        + k+ e ++l+++e + +GDs +D+e    agi +
  gi|298676051|ref|YP_003727801.1| 157 GLVKIAELMGLNPKEFVAIGDSENDLEMIEFAGIGI 192
                                       667889999******************999999866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1696.67
//
Query:       gi|298676052|ref|YP_003727802.1|  [L=325]
Description: DNA repair and recombination protein RadA [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-87  291.1   0.0    8.1e-87  290.7   0.0    1.1  1  Rad51            Rad51
    1.3e-10   41.2   0.0    1.3e-08   34.6   0.0    2.1  1  RecA             recA bacterial DNA recombination protein
    1.5e-09   38.3   0.0    3.2e-09   37.3   0.0    1.6  1  HHH_5            Helix-hairpin-helix domain
      2e-08   34.0   0.0      3e-08   33.5   0.0    1.2  1  AAA_25           AAA domain
    8.7e-08   31.8   0.2    1.4e-07   31.1   0.2    1.4  1  ATPase           KaiC
    3.5e-05   23.8   0.0    7.3e-05   22.8   0.0    1.5  1  HHH_2            Helix-hairpin-helix motif
    0.00072   20.0   0.1      0.011   16.2   0.1    2.3  1  AAA              ATPase family associated with various cellul
    0.00074   19.3   0.0     0.0017   18.1   0.0    1.6  1  AAA_24           AAA domain
     0.0013   19.0   0.0     0.0031   17.8   0.0    1.7  1  AAA_22           AAA domain
     0.0031   17.7   0.0      0.007   16.6   0.0    1.6  1  Cdd1             Pathogenicity locus
      0.005   17.4   0.1      0.081   13.5   0.1    2.6  2  AAA_18           AAA domain
  ------ inclusion threshold ------
      0.012   15.4   0.0      0.031   14.1   0.0    1.7  1  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
      0.018   14.3   0.1        5.6    6.2   0.0    2.5  2  Zeta_toxin       Zeta toxin
      0.028   14.0   0.1       0.45   10.1   0.1    2.2  1  CobU             Cobinamide kinase / cobinamide phosphate gua
      0.031   13.9   0.0      0.051   13.2   0.0    1.3  1  SRP54            SRP54-type protein, GTPase domain
      0.043   13.7   0.0      0.061   13.2   0.0    1.3  1  ATPase_2         ATPase domain predominantly from Archaea
      0.077   12.9   0.0       0.17   11.8   0.0    1.6  1  NACHT            NACHT domain


Domain annotation for each model (and alignments):
>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  290.7   0.0   7.7e-90   8.1e-87       2     253 ..      65     323 ..      64     325 .] 0.94

  Alignments for each domain:
  == domain 1  score: 290.7 bits;  conditional E-value: 7.7e-90
                                       S-EBHHHHHHHHHSS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEE CS
                             Rad51   2 gfvsavellekrsellqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyid 78 
                                       gf ++  ++e+r+++ +l+tG++++De+++GGi+t+site++Gef+sGktq++h+l+v vqlp e+gG +g +++id
  gi|298676052|ref|YP_003727802.1|  65 GFETGDLVMERRKQVGKLSTGCSEFDEMMEGGIDTQSITELYGEFGSGKTQIAHQLAVNVQLPNEQGGLNGSVIFID 141
                                       788999999******************************************************************** PP

                                       SSS---GGGGHHHH....HHT..T--HHHHGGGEEEEE--STTHHHHHHHHTHHHHHHS-.....EEEEEEETTTGG CS
                             Rad51  79 tegtfrperlveia....ery..kldkeevlenvayaRaytiehqeellqqaaallaedk.....fallivDsvtal 144
                                       te tfrper+ ++     e++  + d+ee l+n+ +aRay+++hq  l+++a +l  e+k     ++llivDs+ta+
  gi|298676052|ref|YP_003727802.1| 142 TENTFRPERIKQMVqgasEHHniDYDPEEFLKNIHVARAYNSNHQILLMDSAMELAEESKnweqpVRLLIVDSLTAH 218
                                       ************988888555347789*******************999988777666543333389********** PP

                                       GCH-------THHHHHHHHHHHHHHHHHHHHH--EEEEEEE-------.------------HHHHHHHH-SEEEEEE CS
                             Rad51 145 yRtdfsgrgelakRqqklgkllrtLrkladefevavvitnqvvaqvdgqaalfsadpkkPigGlvlahasttRlalr 221
                                       +R+++ grg la+Rqqkl+k+l++L++++d +++ +++tnqv++++d+    f +dp+kPigG++++h++t R++lr
  gi|298676052|ref|YP_003727802.1| 219 FRAEYIGRGTLADRQQKLNKHLHALQRFSDLYNAVIIVTNQVMSKPDA----FFGDPTKPIGGHIIGHTATFRMYLR 291
                                       ************************************************....99*********************** PP

                                       E-STTEEEEEEES-SSS-S-EEEEEEETTEEE CS
                             Rad51 222 kgkgeeRivkvvdsPnlpeleavfaigeeGie 253
                                       k kg++Riv++vdsPnlp+ e +++++  G++
  gi|298676052|ref|YP_003727802.1| 292 KSKGDKRIVRLVDSPNLPDGESIISVTPLGLT 323
                                       **************************999876 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   1.3e-11   1.3e-08      27     223 ..      75     294 ..      64     304 .. 0.73

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 1.3e-11
                                       .-----EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHH...HTT...--EEEEESS----HHH CS
                              RecA  27 eklkvetissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaq...kkg...gvaafidaehaldpky 97 
                                       ++++v  +s+G   +d  +  GG+    i+e+yG   sGkt +a ++ +++q   ++g   g + fid+e ++ p+ 
  gi|298676052|ref|YP_003727802.1|  75 RRKQVGKLSTGCSEFDEMME-GGIDTQSITELYGEFGSGKTQIAHQLAVNVQlpnEQGglnGSVIFIDTENTFRPER 150
                                       468999**********9997.***********************999999884443442226789*********998 PP

                                       HHHT........T--GG......G-EEE--SSHHH.......HHHHHHHHHT.TT--SEEEEE-TTT---STT-.-- CS
                              RecA  98 akkl........Gvdid......ellvsqpdtGeq.......aleiadalvr.sgaidlivvdsvaalvpkaei.eG 151
                                        k++         +d d      ++ v++  + ++       a+e+a+   +    + l++vds++a      i  G
  gi|298676052|ref|YP_003727802.1| 151 IKQMvqgasehhNIDYDpeeflkNIHVARAYNSNHqillmdsAMELAEESKNwEQPVRLLIVDSLTAHFRAEYIgRG 227
                                       8765332222223443232222267788776665411111115555555444245799*******998755555346 PP

                                       --------HHHHHHHHHHHHHHHHHTTT--EEEEEEE-----------------HHHHHHH-SEEEEEEEES CS
                              RecA 152 emgdskvglqarlmsqalrkltgaisksntvvifinqirekiGvmfgnpetttGGralkfyasvrldvrrie 223
                                        ++d +  l+  l  +al+++    +  n+v+i  nq+  k    fg+p    GG+ +   a+ r+ +r+++
  gi|298676052|ref|YP_003727802.1| 228 TLADRQQKLNKHL--HALQRF---SDLYNAVIIVTNQVMSKPDAFFGDPTKPIGGHIIGHTATFRMYLRKSK 294
                                       7777776665554..455555...5667899**************************************986 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0     3e-12   3.2e-09       4      56 ..       6      58 ..       3      59 .. 0.95

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 3e-12
                                      HHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHH CS
                             HHH_5  4 LlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelk 56
                                      L +++ +Gp+tA +l + G++sve++a a++ +L+   +iG+  A +ii +++
  gi|298676052|ref|YP_003727802.1|  6 LEDLDHVGPATAQKLRESGYNSVEAIAVASPTDLSLSADIGESAASKIINSAR 58
                                      789999*******************************************9998 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.0   2.9e-11     3e-08      22     186 ..      89     257 ..      71     263 .. 0.72

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 2.9e-11
                            AAA_25  22 rrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal. 97 
                                        +  ++g +  ++++ l+G  g+GKt +a +la+ v +  +  g     +g V+++++E++    ++R++++ + + 
  gi|298676052|ref|YP_003727802.1|  89 FDEMMEGGIDTQSITELYGEFGSGKTQIAHQLAVNVQLPNEQGG----LNGSVIFIDTENTF--RPERIKQMVQGAs 159
                                       566788889999*************************6554434....69***********8..7999999999984 PP

                            AAA_25  98 .......rddarllvldlagv.eslpLfak.drggtl.ltadvdaleaaieeveg.vrlvviDplsralgg.....d 158
                                              ++         +++ ++++++ +  +++++ l     +l+++ +  e+ vrl+++D+l++ +++     +
  gi|298676052|ref|YP_003727802.1| 160 ehhnidyDP---------EEFlKNIHVARAyNSNHQIlLMDSAMELAEESKNWEQpVRLLIVDSLTAHFRAeyigrG 227
                                       444443333.........444555665544234444455555669*******9999**********98887555543 PP

                            AAA_25 159 ensnsd..vgalvealeriarrtgaavllv 186
                                         ++++   ++ + al+r+++ ++a ++++
  gi|298676052|ref|YP_003727802.1| 228 TLADRQqkLNKHLHALQRFSDLYNAVIIVT 257
                                       333333324777778888888888777776 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.2   1.4e-10   1.4e-07       2     131 ..      83     218 ..      82     304 .. 0.55

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 1.4e-10
                            ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaek...yge..pgvfvtveepa.....edlrenak 68 
                                       +tg  ++De+++gGi  ++++ ++Ge G+GKt +a q +++        g    ++f+ +e +      +++ + a+
  gi|298676052|ref|YP_003727802.1|  83 STGCSEFDEMMEGGIDTQSITELYGEFGSGKTQIAHQLAVNVQLPneqGGLngSVIFIDTENTFrperiKQMVQGAS 159
                                       79**************************************9654300023211458888887767755534433332 PP

                            ATPase  69 ...slGwdlekleeegklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitgl 131
                                          +++ d e++ ++  + +  a++s++++      ++++el+ee ++   e  ++ +++Ds+t++
  gi|298676052|ref|YP_003727802.1| 160 ehhNIDYDPEEFLKN--IHVARAYNSNHQIL---LMDSAMELAEESKNW--EQPVRLLIVDSLTAH 218
                                       211333334444444..44444444433322...233444444433332..334477777887776 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   6.9e-08   7.3e-05      10      54 ..      11      56 ..       9      64 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 6.9e-08
                             HHH_2 10 hVGektAklLakr.FksldaLkkasleeLlevddiGeeiAqsivef 54
                                      hVG +tA++L ++ ++s++a++ as  +L+   diGe  A++i++ 
  gi|298676052|ref|YP_003727802.1| 11 HVGPATAQKLRESgYNSVEAIAVASPTDLSLSADIGESAASKIINS 56
                                      9*********9866*****************************975 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1     1e-05     0.011       3     114 ..     105     263 ..     104     270 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1e-05
                                       EESSTTSSHHHHHHHHHHHHTHE.........EEEEETTTCSSS................................. CS
                               AAA   3 lyGppGtGKTllakavakelgve.........fleisgsellsk................................. 37 
                                       lyG  G GKT +a+++a +++ +         ++ i+  + +                                   
  gi|298676052|ref|YP_003727802.1| 105 LYGEFGSGKTQIAHQLAVNVQLPneqgglngsVIFIDTENTFRPerikqmvqgasehhnidydpeeflknihvaray 181
                                       8******************7544444444455555555555522355555556666666666666666666654432 PP

                                       ......STTHHHHHHHHHHHHHHHTS...TS.EEEEEETGGGHHHHH..TTCCCHHHHHHHHHHHHHHHHTTTSSST CS
                               AAA  38 ......yvgesekkirelfkeakeka...kp.silfiDEidalaksr..sgseseeeervvnqLlteldgvkkkesk 102
                                             ++ +s+      ++ a+e++   +p   l++D + a ++++   +++  ++++ +n+ l++l+++++  + 
  gi|298676052|ref|YP_003727802.1| 182 nsnhqiLLMDSA------MELAEESKnweQPvRLLIVDSLTAHFRAEyiGRGTLADRQQKLNKHLHALQRFSDLYN- 251
                                       222222222222......2222333256566688888888888888888777778888888888888888888766. PP

                                       EEEEEEESS.GGG CS
                               AAA 103 vivigatnr.pdk 114
                                         vi++tn+ ++k
  gi|298676052|ref|YP_003727802.1| 252 -AVIIVTNQvMSK 263
                                       .777888874444 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.7e-06    0.0017       7      79 ..     105     220 ..     102     263 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.7e-06
                            AAA_24   7 iyGpsgiGKTtlakel.............gpkplfidtekGlksldadkfpdie.....................sw 49 
                                       +yG+ g+GKT +a +l               +++fidte+ +    + +++++                        
  gi|298676052|ref|YP_003727802.1| 105 LYGEFGSGKTQIAHQLavnvqlpneqgglNGSVIFIDTENTF---RPERIKQMVqgasehhnidydpeeflknihV- 177
                                       8***************************99**********55...6666665555667888888855544444440. PP

                            AAA_24  50 edfldevvel......................aaeladyktlviDtidelee 79 
                                                                       + ++++ + l++D+++   +
  gi|298676052|ref|YP_003727802.1| 178 ---------AraynsnhqillmdsamelaeesKNWEQPVRLLIVDSLTAHFR 220
                                       .........3444444455555555555555588999999999999987654 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.9e-06    0.0031       4     108 ..      99     202 ..      94     259 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.9e-06
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka.......... 70 
                                       t++i+ ++Ge G+GKT  + +l+ + +  +++   + +v+f++  +   ++ + +++  a ++ + +          
  gi|298676052|ref|YP_003727802.1|  99 TQSITELYGEFGSGKTQIAHQLAVNVQLPNEQGGLNGSVIFIDTENTFRPERIKQMVQGASEHHNIDydpeeflkni 175
                                       8999********************9977777777*******************999999999888774444444444 PP

                            AAA_22  71 .....erlsseellealeqalraravielliiDEaqhlr.seea 108
                                            ++ +                  ++l+ D a  l  + ++
  gi|298676052|ref|YP_003727802.1| 176 hvaraYNSNH-----------------QILLMDSAMELAeESKN 202
                                       4444433333.................35555544444322222 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   6.6e-06     0.007       7      41 ..       5      39 ..       2      53 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.6e-06
                              Cdd1  7 elqdiPniGkalaedlvelGirsveelkgedpeel 41
                                      +l+d+  +G+a+a++l+e G++sve ++  +p++l
  gi|298676052|ref|YP_003727802.1|  5 TLEDLDHVGPATAQKLRESGYNSVEAIAVASPTDL 39
                                      6999****************************998 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.93   9.8e+02      15      66 ..      17      68 ..      15      83 .. 0.80
   2 !   13.5   0.1   7.6e-05     0.081       3      89 ..     105     222 ..     104     242 .. 0.52

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.93
                            AAA_18 15 akeLskrlgf.gvnlrdvakenglllevdpealdeskrldedkldklldalee 66
                                      a+ L+++ g+ +v+ + va+  +l+l+ d  +   sk+++  ++ +++ ++e 
  gi|298676052|ref|YP_003727802.1| 17 AQKLRES-GYnSVEAIAVASPTDLSLSADIGESAASKIINSARRSANIGGFET 68
                                      7888888.566888888999999999999989999999999999999999887 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 7.6e-05
                            AAA_18   3 ltGtpGvGKttlakeLskrlgf.....................gvnlrdvakenglllevdpe...aldeskrlded 55 
                                       l G  G+GKt++a+ L+   ++                                    e+ ++     +e++ +d d
  gi|298676052|ref|YP_003727802.1| 105 LYGEFGSGKTQIAHQLAVNVQLpneqgglngsvifidtentfrP--------------ERIKQmvqGASEHHNIDYD 167
                                       67889***********5553335566656555554444444441..............4444444433444444444 PP

                            AAA_18  56 kldklldaleenss....................aleegknl.vidghlaelese 89 
                                         + l +++ + +                     ++e++  l ++d++ a+++ e
  gi|298676052|ref|YP_003727802.1| 168 PEEFLKNIHVARAYnsnhqillmdsamelaeeskNWEQPVRLlIVDSLTAHFRAE 222
                                       4333333333332211122222222222222222233333333777777777666 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.9e-05     0.031       9      42 ..      12      46 ..      10      52 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.9e-05
                   DNA_pol_lambd_f  9 VGpktAkkwyakGirtledlra.krakLtreqqiG 42
                                      VGp+tA+k+ + G+ ++e +    + +L+ + +iG
  gi|298676052|ref|YP_003727802.1| 12 VGPATAQKLRESGYNSVEAIAVaSPTDLSLSADIG 46
                                      9*****************99876556776666666 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0053       5.6     101     137 ..       3      41 ..       1      46 [. 0.87
   2 ?    5.6   0.1    0.0079       8.3      23      42 ..     107     129 ..     101     208 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0053
                        Zeta_toxin 101 egtlrspdvvkk.laealkkaGYe.vevvvvavkkelSr 137
                                       e tl++ d v   +a++l++ GY+ ve+++va +  lS 
  gi|298676052|ref|YP_003727802.1|   3 EVTLEDLDHVGPaTAQKLRESGYNsVEAIAVASPTDLSL 41 
                                       7899999999988**********6489*****9999986 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0079
                        Zeta_toxin  23 GqpGAGKselaellkdele...r 42 
                                       G  G+GK+++a+ l+ +++   +
  gi|298676052|ref|YP_003727802.1| 107 GEFGSGKTQIAHQLAVNVQlpnE 129
                                       888**********9999876552 PP

>> CobU  Cobinamide kinase / cobinamide phosphate guanyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00043      0.45      56     127 ..     189     261 ..     103     264 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00043
                              CobU  56 tveepldlaealkeeek.kevvLvDcltlwltnllleeeaek.veekleeeveellealkelkatvvlVsnEvg 127
                                       ++++  +lae  k+ e+  + ++vD+lt         + + +  ++kl++++++ l+ +++l + v++V+n v 
  gi|298676052|ref|YP_003727802.1| 189 LMDSAMELAEESKNWEQpVRLLIVDSLTAHFRAEYIGRGTLAdRQQKLNKHLHA-LQRFSDLYNAVIIVTNQVM 261
                                       345556677777775555777888888877666555544332255555555554.4556667789******985 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.8e-05     0.051       5     100 ..     104     201 ..     100     212 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.8e-05
                                       EEEESTTSSHHHHHHHHHHHHHHT.......TS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHH CS
                             SRP54   5 llvGlqGaGKTttlaKLaallkke.......gkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavake 74 
                                        l G  G+GKT+ + +La  ++         g  + + +  tfR+  ++Q+ + a++ +      + + dp +++k+
  gi|298676052|ref|YP_003727802.1| 104 ELYGEFGSGKTQIAHQLAVNVQLPneqgglnGSVIFIDTENTFRPERIKQMVQGASEHH------NIDYDPEEFLKN 174
                                       578999************988754224644234445557779*********99998877......456677777766 PP

                                       .HHHHHHHTTSSEEEEEE--SSTTHHH CS
                             SRP54  75 .avekakeekidvvlvDTaGrlqndke 100
                                         v +a +++++++l+D+a  l+++++
  gi|298676052|ref|YP_003727802.1| 175 iHVARAYNSNHQILLMDSAMELAEESK 201
                                       368899999999*****9987777665 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.8e-05     0.061      19     125 ..      99     213 ..      87     249 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.8e-05
                          ATPase_2  19 pneiyfiYGpegsGKtaLlkeiienledkdk......yviyyialreesiskldefieeeeekkklekalgiavpka 89 
                                       +++i  +YG  gsGKt++  +++ n +  ++       vi+++  ++ + ++++++++  +e  +++    + +++ 
  gi|298676052|ref|YP_003727802.1|  99 TQSITELYGEFGSGKTQIAHQLAVNVQLPNEqgglngSVIFIDTENTFRPERIKQMVQGASEHHNIDYDPEEFLKNI 175
                                       6889999***************9999766666888889****99999999999999884444444444443333333 PP

                          ATPase_2  90 eleeilk..eksklvfkaielllekikkkgkkiiiiiD 125
                                        + + ++  +++ l+++a+el+ e+ + ++    +i+D
  gi|298676052|ref|YP_003727802.1| 176 HVARAYNsnHQILLMDSAMELAEESKNWEQPVRLLIVD 213
                                       33333332344444555555544444433333455555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00016      0.17       5     115 ..     105     217 ..     101     247 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00016
                                       EEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHH..CCCCTS--SSS-C....CHHH CS
                             NACHT   5 lqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladll..fsqlpepaapvse....vwav 75 
                                       l Ge GsGKT  +++la+  + ++ ++g    v+f+    + r++++   ++++  +s+ + +  +++e    + + 
  gi|298676052|ref|YP_003727802.1| 105 LYGEFGSGKTQIAHQLAVNVQLPNEQGGLNGSVIFIDTENTFRPERI---KQMVqgASEHHNIDYDPEEflknIHVA 178
                                       78*******************99999888667777777766666644...444411334444444444455444445 PP

                                       HCCSCCCEEEEEE-STT-SS-TCH.........HHHHHCT CS
                             NACHT  76 llelperlLlilDglDelvtdlgqkekqpvrtlLselirk 115
                                       ++ + +   l++D++ el+++ ++  +qpvr l+ + +++
  gi|298676052|ref|YP_003727802.1| 179 RAYNSNHQILLMDSAMELAEESKN-WEQPVRLLIVDSLTA 217
                                       555556666788888888886666.778888888777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      630  (0.0351386); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.71u 0.37s 00:00:01.08 Elapsed: 00:00:00.55
# Mc/sec: 1790.85
//
Query:       gi|298676053|ref|YP_003727803.1|  [L=153]
Description: cytidyltransferase-like domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-12   46.1   0.0    6.7e-12   45.8   0.0    1.1  1  CTP_transf_like  Cytidylyltransferase-like
  ------ inclusion threshold ------
      0.028   14.3   0.0       0.05   13.5   0.0    1.5  1  FAD_syn          FAD synthetase
      0.051   14.0   1.5      0.093   13.1   1.5    1.3  1  Ribosomal_L22e   Ribosomal L22e protein family


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.0   1.1e-15   6.7e-12       2     141 ..       6     141 ..       5     143 .. 0.87

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 1.1e-15
                                       EEE--TT--HHHHHHHHHHHHHSSES.EEEEEESSTHCSST-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHH CS
                   CTP_transf_like   2 agGtFDpiHlGHlrlleqakklleed.livgvpsdeppkkkkkplasaeeRlemlelakevdevisvdpweltrevl 77 
                                       +gGtF+ iH GH +l+++ ++l +   + +g++sde ++k+  +++++++R ++l  ++++    + + +++ + ++
  gi|298676053|ref|YP_003727803.1|   6 VGGTFQYIHDGHKKLINKSFELANDGqVDIGITSDEMARKQRLKVTDYNTRKKNLVDYIKTLT-NKNSSYQIFK-LT 80 
                                       69********************9988999************9*************99955444.3566666665.66 PP

                                       HHTTT......TEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHH CS
                   CTP_transf_like  78 kklkp......dklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkir 141
                                       + ++p      d  y+v++ +++e++ e ++l++  g +++ +v+++          ++++ +iSst+i 
  gi|298676053|ref|YP_003727803.1|  81 DPYGPtltdgyD--YIVVSSETYESALELNKLRQKRGLKPIEIVKIE-------CVMAEDSLPISSTRIM 141
                                       666665555558..******************************998.......88888999******96 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   8.4e-06      0.05      11      42 ..       6      37 ..       2      75 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.4e-06
                           FAD_syn 11 tlGnFDGvHlGHqallkkaveaakekglpsvv 42
                                      + G F  +H GH++l++k  e+a++ ++ + +
  gi|298676053|ref|YP_003727803.1|  6 VGGTFQYIHDGHKKLINKSFELANDGQVDIGI 37
                                      4589999****************998887765 PP

>> Ribosomal_L22e  Ribosomal L22e protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.5   1.6e-05     0.093      35      97 ..      15      76 ..      11      80 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.6e-05
                    Ribosomal_L22e 35 ngktgnlgdkveieregkskvtvtsevkfskrylkyltkkyLkkkqlrdwlrvvasskesYeL 97
                                      +g+++ ++++ e++++g+  + +ts+   +k+ lk  t    +kk+l d+++ + ++++sY++
  gi|298676053|ref|YP_003727803.1| 15 DGHKKLINKSFELANDGQVDIGITSDEMARKQRLKV-TDYNTRKKNLVDYIKTLTNKNSSYQI 76
                                      5667777788999***999****************6.55568999****************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1090.39
//
Query:       gi|298676054|ref|YP_003727804.1|  [L=111]
Description: hypothetical protein Metev_2182 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00054   20.0   0.1     0.0032   17.5   0.1    2.2  1  DUF4351   Domain of unknown function (DUF4351)


Domain annotation for each model (and alignments):
>> DUF4351  Domain of unknown function (DUF4351)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   1.8e-07    0.0032      11      48 ..      35      72 ..      28     107 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.8e-07
                           DUF4351 11 LilrlLtrrfGelspeleeqIksLsleqLEdLgealLD 48
                                      +ilr +  +f e s++++++I++L+ ++L+ L e  LD
  gi|298676054|ref|YP_003727804.1| 35 FILRPISHKFVESSEDFKQRIDRLTPDELDYLVELALD 72
                                      79********************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.33s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 655.67
//
Query:       gi|298676055|ref|YP_003727805.1|  [L=278]
Description: xylose isomerase domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.2e-15   55.8   0.0    4.9e-15   55.5   0.0    1.1  1  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.0   2.8e-19   4.9e-15       2     209 ..      26     237 ..      25     238 .. 0.88

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 2.8e-19
                                       HHHHHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHH CS
                      AP_endonuc_2   2 aaaaeaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederearreesvdalkraiel 78 
                                       + ++e+G d++El +  +v ++e   ++++ +   ++   + ++++ +++ + ++ e   +++ ++sv+++ + + +
  gi|298676055|ref|YP_003727805.1|  26 EYVSEIGLDCMELEFVRGVRMKE---DKAQSVNVTARNSSVALSVHAPYYINLNSAE---QKKIDDSVERIYQSASI 96 
                                       6799*****************95...8***************************888...555899*********** PP

                                       HHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHT..SEEEEE--TTTTSSSTCHHHHHHHHHHTT CS
                      AP_endonuc_2  79 aaaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekeg..vklalEtlagsgvelgdeelarlldavds 153
                                        + +Ga+ +v+hp    +++k++ +  + r+ + ln+l   +e+ +  v l  Et+ + +++   +e++ l ++ + 
  gi|298676055|ref|YP_003727805.1|  97 GSLCGAESIVFHPA---YYHKDTSDRVYSRVHNLLNDLSSRLEEDDipVVLRPETTGKGTQFGNLDEILSLSSEMEK 170
                                       **************...9*************************9998899999999999987777**********95 PP

                                       TTEEEEEEHHHHHHH.......TTTHHHHHHHHHGG.......EEEEEE.EESSTTTTSSTTEESTTSSS CS
                      AP_endonuc_2 154 pnvgvclDtgHllia.......eedvddalraladr.......ikhvHikDakgdlgagrdrhvpigeGe 209
                                         v  c+D++Hl+++        + + ++l +++d          h H++ ++  +++g+ +hv++ e +
  gi|298676055|ref|YP_003727805.1| 171 --VQPCIDFSHLHARtnggmnsFDEFKSVLSKIEDIlgkeglnNMHAHVSGIEY-NSKGERNHVNLEESD 237
                                       ..*************888665544444444444444888898888888888888.999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1839.46
//
Query:       gi|298676056|ref|YP_003727806.1|  [L=135]
Description: hypothetical protein Metev_2184 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.6e-07   28.8   0.2    1.6e-06   27.6   0.2    1.7  1  HTH_24          Winged helix-turn-helix DNA-binding
    0.00012   22.1   0.0     0.0002   21.3   0.0    1.4  1  HTH_20          Helix-turn-helix domain
    0.00012   21.8   0.1    0.00026   20.8   0.1    1.6  1  HTH_5           Bacterial regulatory protein, arsR family
    0.00048   20.0   0.0     0.0012   18.7   0.0    1.6  2  MarR_2          MarR family
     0.0015   18.4   0.1     0.0027   17.6   0.1    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0023   18.6   0.0     0.0041   17.8   0.0    1.5  2  RPA_C           Replication protein A C terminal
      0.004   17.1   0.1     0.0064   16.4   0.1    1.3  1  MarR            MarR family
  ------ inclusion threshold ------
      0.011   15.3   0.1       0.16   11.5   0.0    2.3  2  GerE            Bacterial regulatory proteins, luxR family
      0.018   15.2   0.1      0.029   14.5   0.1    1.4  1  DUF2250         Uncharacterized protein conserved in archaea 
      0.051   13.9   0.1      0.086   13.2   0.1    1.4  1  Rrf2            Transcriptional regulator
      0.081   13.1   0.1       0.14   12.3   0.0    1.5  1  B-block_TFIIIC  B-block binding subunit of TFIIIC


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.2   9.6e-10   1.6e-06       6      47 ..      46      87 ..      41      88 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 9.6e-10
                            HTH_24  6 rkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      + +L+ L  ++ +s   +A+ l++ +s vn+++++L+++Gl+
  gi|298676056|ref|YP_003727806.1| 46 ISLLKNLSNDGVTSSEAIAQDLDIKVSRVNYHIRNLINSGLV 87
                                      567888999999****************************98 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   1.2e-07    0.0002      15      57 ..      48      90 ..      38      92 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.2e-07
                                      HHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20 15 ilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                      +l+ L+ ++  + +++a+ ld++ + ++yH+r L   gLv ++
  gi|298676056|ref|YP_003727806.1| 48 LLKNLSNDGVTSSEAIAQDLDIKVSRVNYHIRNLINSGLVYRE 90
                                      567778888888999************************9665 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   1.6e-07   0.00026       7      46 ..      48      88 ..      43      89 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.6e-07
                                      HHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  7 ILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      +Lk L++ g +++  +a +l++  s v +H + L ++GLV+
  gi|298676056|ref|YP_003727806.1| 48 LLKNLSNdGVTSSEAIAQDLDIKVSRVNYHIRNLINSGLVY 88
                                      466667789999999*************************6 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.2   3.6e+03      24      35 ..      22      33 ..       7      35 .. 0.77
   2 !   18.7   0.0   7.1e-07    0.0012      10      62 .]      48      98 ..      42      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.2
                                      HHHHHHHHTSSH CS
                            MarR_2 24 vgelarrlglsk 35
                                      ++ +++ lg s 
  gi|298676056|ref|YP_003727806.1| 22 AKWICESLGFSS 33
                                      678999998875 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 7.1e-07
                                      HHHHHHCTTTSEE.EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSSS CS
                            MarR_2 10 vLaaLgrrpgrdl.tvgelarrlglsksavsrilkrLvaaGLverrpgpeDkRa 62
                                      +L +L + +   + +  ++a+ l+++ s+v+++++ L   GLv r++ + ++R+
  gi|298676056|ref|YP_003727806.1| 48 LLKNLSNDG---VtSSEAIAQDLDIKVSRVNYHIRNLINSGLVYREKKLLHLRG 98
                                      566665555...4377889***************************99999996 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   1.7e-06    0.0027      19      57 ..      54      92 ..      36      96 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.7e-06
                                      HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                              TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57
                                      + g  + + ia++l++  s+v+  +r+L++ GlV+rek+
  gi|298676056|ref|YP_003727806.1| 54 NDGVTSSEAIAQDLDIKVSRVNYHIRNLINSGLVYREKK 92
                                      556777889***************************985 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.5e-06    0.0041      48      98 ..      39      88 ..       7      90 .. 0.87
   2 ?   -2.9   0.0       6.9   1.1e+04      15      29 ..     110     124 ..      95     131 .. 0.49

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.5e-06
                                      XHHHHHHHHHHHH.SXSTTTEEH.HHHHHHSTSXHHHHHHHHHHHHHTTSEE CS
                             RPA_C 48 talaqqvlnlikqspeseeGvhv.deiaqklrlsvndvkqavdeLsneGiiY 98
                                      +  ++++++l+k+   s++Gv   + iaq l + v+ v+  +++L+n G++Y
  gi|298676056|ref|YP_003727806.1| 39 HTSTKVIISLLKN--LSNDGVTSsEAIAQDLDIKVSRVNYHIRNLINSGLVY 88
                                      56688999*****..8999*976156************************** PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.9
                                       ......XXXXXXXXX CS
                             RPA_C  15 aagaavavsaggsam 29 
                                       ++++ ++++  + a 
  gi|298676056|ref|YP_003727806.1| 110 KDTDRIFEELEYVAE 124
                                       345555555555444 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   3.9e-06    0.0064       6      52 ..      46      92 ..      42      93 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.9e-06
                                      HHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                              MarR  6 fviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsks 52
                                      +++L +l++ g  s   +a  l ++ s v   ++ L+  Gl++R+k+
  gi|298676056|ref|YP_003727806.1| 46 ISLLKNLSNDGVTSSEAIAQDLDIKVSRVNYHIRNLINSGLVYREKK 92
                                      579999999999********************************986 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0    0.0001      0.16      19      42 ..      59      82 ..      55      83 .. 0.91
   2 ?    1.3   0.0      0.15   2.4e+02      11      21 ..     119     129 ..     112     135 .] 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0001
                                      -HHHHHHHHTS-HHHHHHHHHHHH CS
                              GerE 19 snkeIAeelniSekTVkvhksnim 42
                                      s++ IA++l+i+   V++h++n+ 
  gi|298676056|ref|YP_003727806.1| 59 SSEAIAQDLDIKVSRVNYHIRNLI 82
                                      6789******************85 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.15
                                       HHHHCTTS-HH CS
                              GerE  11 LrllaeGksnk 21 
                                       L+++aeG  nk
  gi|298676056|ref|YP_003727806.1| 119 LEYVAEGIDNK 129
                                       88889988887 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   1.8e-05     0.029       6      56 ..      41      91 ..      37     113 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.8e-05
                           DUF2250  6 edelalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerve 56
                                       +++ + +lk l + +v  +  ia+ l+i++++v+  +++L + GL+ r +
  gi|298676056|ref|YP_003727806.1| 41 STKVIISLLKNLSNDGVTSSEAIAQDLDIKVSRVNYHIRNLINSGLVYREK 91
                                      56788999***************************************9875 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   5.3e-05     0.086      14      56 ..      46      88 ..      39      91 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.3e-05
                                      HHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 14 llyLakeeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      +  L++ ++++  sse+ia+  +i+ s +   +++L ++glv 
  gi|298676056|ref|YP_003727806.1| 46 ISLLKNLSNDGVTSSEAIAQDLDIKVSRVNYHIRNLINSGLVY 88
                                      4556778888999****************************96 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   8.7e-05      0.14      17      52 ..      55      91 ..      44     110 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.7e-05
                    B-block_TFIIIC 17 sGitqsdLa.keskqdprslfyrlksLekkgLIvkqs 52
                                      +G+t+s+ + + ++++++ + y+++ L ++gL+++ +
  gi|298676056|ref|YP_003727806.1| 55 DGVTSSEAIaQDLDIKVSRVNYHIRNLINSGLVYREK 91
                                      79999998779999********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.46u 0.33s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 834.14
//
Query:       gi|298676057|ref|YP_003727807.1|  [L=90]
Description: chaperonin Cpn10 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-24   84.5   1.7    4.4e-24   84.3   1.7    1.0  1  Cpn10     Chaperonin 10 Kd subunit


Domain annotation for each model (and alignments):
>> Cpn10  Chaperonin 10 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.3   1.7   2.5e-28   4.4e-24       2      93 .]       3      88 ..       2      88 .. 0.95

  Alignments for each domain:
  == domain 1  score: 84.3 bits;  conditional E-value: 2.5e-28
                                      -EE-TTEEEEEESGG-TTS-TT----HHHHHSEEEEEEEEE-T........TS-TTS--T-EEEEEGGGTSS-GG---. CS
                             Cpn10  2 ikplgdrVlvkraeeeekteggiilpdsakekpeqGvVvaVGegarnekgedvplevkvgdkVlfpkyagtkvkvdgke 80
                                      ikp+g+rVl+k+ ++eekt+gg+++p+sa+ + ++G VvaVG+    e+g+  +l v++gdk+++  y+  ++++dg++
  gi|298676057|ref|YP_003727807.1|  3 IKPIGERVLIKV-KKEEKTSGGVYIPESAQSENKEGYVVAVGT---YEDGS--ELPVNEGDKIIYGGYQTDEIDIDGEK 75
                                      9**********9.6899**************************...77788..788*********************** PP

                                      EEEEEGGG--EE- CS
                             Cpn10 81 ylilkekdIlavi 93
                                      +++++ kdIla++
  gi|298676057|ref|YP_003727807.1| 76 HIFVDLKDILAKV 88
                                      ***********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 600.76
//
Query:       gi|298676058|ref|YP_003727808.1|  [L=536]
Description: chaperonin GroEL [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-99  334.2  15.7    2.4e-99  333.2  15.7    1.4  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  333.2  15.7  1.3e-103   2.4e-99       1     488 [.      23     521 ..      23     524 .. 0.93

  Alignments for each domain:
  == domain 1  score: 333.2 bits;  conditional E-value: 1.3e-103
                                       HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHH....HHHHHHHHHHCCCCCTTCHHHHHHHHHHH CS
                        Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPa....akllveaaesqdeevGDGTttvviLageL 73 
                                       ++d+vk tlGPkG++++l n+  ++++TnDG+ti+ke+e+++      akl+ e+a+++++ +GDGTtt+++La ++
  gi|298676058|ref|YP_003727808.1|  23 VSDTVKITLGPKGRYVVLDNSE-SPTITNDGVTIAKEIELKDKFenmgAKLVKEVASKTQDTTGDGTTTATLLANSM 98 
                                       689***************7655.9***************************************************** PP

                                       HHHHHHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHH CS
                        Cpn60_TCP1  74 leeaekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAv 150
                                       l+e+ k + ag++p ++++g++k  ++++++Lk +++++s +    e++++va++s++++      ee+++l+ dA+
  gi|298676058|ref|YP_003727808.1|  99 LREGIKNVTAGANPMDLKRGIDKSSKEVVQYLKDKSKDVSER----EKIYQVATVSANND------EEIGSLISDAM 165
                                       ********************************9997777765....**************......9********** PP

                                       HCHCCCSEECSCCCEECCCCEECEC..TTSEEESEEEESS--SST.......TSSCEEECEEEEEESS-BS--HHCC CS
                        Cpn60_TCP1 151 klieenekeldlgrikvvkieggsl..edselveGlvldkgvlsp.......dmpkklenakvllldvsLeiektet 218
                                                 ++g  +v+++e+++   ++ e+veG+++d+g+lsp        m  +++++++l++d ++++ ++  
  gi|298676058|ref|YP_003727808.1| 166 ---------DKAGYDGVITVEESNTleNELEFVEGMQFDRGYLSPymvtdqeHMVCEFDDPYILITDEKINTVNQ-- 231
                                       .........899***********9988889999************8888666667777****************9.. PP

                                       HHHCCCCSCCHHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S-...........-HH CS
                        Cpn60_TCP1 219 kttvvlsdaeeleklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrv...........kkk 284
                                                             + + lek++++g+++++++++i+  a++ l+ n +++  rv           +k+
  gi|298676058|ref|YP_003727808.1| 232 ----------------------IVPALEKVANEGRPLLIIAQEIEGDAQAALVLNILRGSLRVcavrapgfgdeQKE 286
                                       ......................******************************************************* PP

                                       HHHHHHHHHT--EBSCG.....GGGGCGC-EEEEEEEECCETTCCEEEEE........................... CS
                        Cpn60_TCP1 285 dlerlakatGatavssl.....edltpeelGtakkveeekigsekttiie........................... 329
                                       +l+++a +tG+t++s+      e++t++ lG a+k+   ++ ++ktt+ie                           
  gi|298676058|ref|YP_003727808.1| 287 MLDDIAVLTGGTVISEDkdmkvENFTEDMLGRARKC---TVDDKKTTVIEgkgekvdiddrtsmiksqidsaesdrk 360
                                       ****************9777778888888*******...9**********988888888888777777777766666 PP

                                       ........CESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHHHHHHCCCCTSXCCH CS
                        Cpn60_TCP1 330 ........evksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelelakklkeyaksvsgee 398
                                                 + g+i ++++++at+t+l+e++++ +dAln++k+a+e e++v GGG+t+  +ak+l  + ++++g++
  gi|298676058|ref|YP_003727808.1| 361 keklqerlAKLTGGITIVKVGAATETELKEKKMRADDALNATKAAVE-EGIVTGGGVTLYNAAKQL--EDMKLEGDQ 434
                                       665555553399***********************************.******************..666799*** PP

                                       HHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTXEEEHHHHHHHHHHHHH CS
                        Cpn60_TCP1 399 qlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveagvvDplkvkrqalksAte 475
                                       q+++ +++++Le++++++a N+G ++ ev+a++++  ++++ ++g++++s+e++dl+eag+++p+kv r+al++A++
  gi|298676058|ref|YP_003727808.1| 435 QIGVSIVKRSLEEPLRQIALNSGREGAEVVARVKS--ESND-QFGYNAKSDEYEDLFEAGIIEPTKVIRSALQNASS 508
                                       ***********************************..6677.89********************************* PP

                                       HHHHHHCEEEEEX CS
                        Cpn60_TCP1 476 aastiLrideiik 488
                                       +a t+L++++ + 
  gi|298676058|ref|YP_003727808.1| 509 IAGTVLTTEALVT 521
                                       *********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (536 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1122  (0.0625802); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.72u 0.31s 00:00:01.03 Elapsed: 00:00:00.51
# Mc/sec: 3158.55
//
Query:       gi|298676059|ref|YP_003727809.1|  [L=436]
Description: cobalt ABC transporter ATPase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-32  113.5   0.0    1.6e-32  112.9   0.0    1.3  1  ABC_tran        ABC transporter
    2.5e-12   47.2   0.2    8.9e-07   29.0   0.0    2.2  2  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
    2.2e-06   27.3   0.0    5.4e-06   26.0   0.0    1.5  1  SMC_N           RecF/RecN/SMC N terminal domain
    0.00083   19.1   0.1     0.0022   17.7   0.1    1.6  1  AAA_29          P-loop containing region of AAA domain
     0.0015   18.4   0.2     0.0069   16.1   0.2    1.9  2  AAA_15          AAA ATPase domain
     0.0075   15.0   0.2        1.2    7.7   0.0    2.1  2  AAA_13          AAA domain
  ------ inclusion threshold ------
      0.034   13.6   0.0      0.073   12.5   0.0    1.6  1  Pr_beta_C       Proteasome beta subunits C terminal
      0.035   14.6   0.5      0.069   13.6   0.5    1.4  1  AAA_23          AAA domain
      0.087   12.7   0.0       0.18   11.7   0.0    1.4  1  RsgA_GTPase     RsgA GTPase
       0.19   11.6   0.0         17    5.3   0.0    2.2  2  Ploopntkinase3  P-loop Nucleotide Kinase3


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.9   0.0   8.7e-36   1.6e-32       2     136 ..      21     167 ..      20     168 .. 0.92

  Alignments for each domain:
  == domain 1  score: 112.9 bits;  conditional E-value: 8.7e-36
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS..--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx..xxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke..qeleslrkeigvlpqe..pqlfpel 74 
                                       +nv++++++g+k+a+vG+nG+GKStL+ ll g l+p+eGeil+ ++++k+  ++l++ rk++g+++q+  +q+f  +
  gi|298676059|ref|YP_003727809.1|  21 NNVDIEINKGKKIAFVGRNGSGKSTLFLLLNGTLEPDEGEILYHNEPIKYdsKSLREIRKNVGIVFQNpdDQIFAPT 97 
                                       89************************************************9999**************877777777 PP

                                       BHHHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  75 tvren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                        +++              e de +++ l+ +glk+lkd++     ++LSgGqk+rva+a +++ +p++++lDEp 
  gi|298676059|ref|YP_003727809.1|  98 -IYQDvgfgptnlgyskdEVDEVVNNTLEYMGLKHLKDKPP----HHLSGGQKKRVAIAGVVAMDPEVVILDEPL 167
                                       .55556********776666666999999999999999998....*****************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2     5e-06     0.009       3      47 ..      34      72 ..      33      93 .. 0.74
   2 !   29.0   0.0     5e-10   8.9e-07     195     299 ..     102     199 ..      96     202 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5e-06
                            AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkips 47
                                      +++G+NgsGKS+L+ +l      ++ +e++  e   +++++k++s
  gi|298676059|ref|YP_003727809.1| 34 AFVGRNGSGKSTLFLLL------NGTLEPDEGEILYHNEPIKYDS 72
                                      68**************9......4445666666655555555554 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 5e-10
                            AAA_21 195 veielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLH 271
                                       v++ +++lg+ +++ ++v +     ++ ++  ++ ++ p+++lS G+k+  a++  ++ ++    ++++DEp ++L+
  gi|298676059|ref|YP_003727809.1| 102 VGFGPTNLGYSKDEVDEVVNN----TLEYMGLKHLKDKPPHHLSGGQKKRVAIAGVVAMDP---EVVILDEPLSNLD 171
                                       555555555444444444444....7778888888999*********************99...9************ PP

                            AAA_21 272 PkllrrllellkelsrngaQviltTHSp 299
                                       P    +ll+ll+e +  g  +i++TH+ 
  gi|298676059|ref|YP_003727809.1| 172 PVGADELLDLLNEYNHFGKTIIISTHNV 199
                                       ***********888888*********96 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0     3e-09   5.4e-06      26     200 ..      32     199 ..      18     217 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 3e-09
                                       EEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  26 ftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrr 102
                                         a vG+NGSGKs l+  +  +L  ++ + l     ++ i++ +++ +  + +v i+f+n+d+++   +    +   
  gi|298676059|ref|YP_003727809.1|  32 KIAFVGRNGSGKSTLFLLLNGTLEPDEGEILY---HNEPIKYDSKSLREIRKNVGIVFQNPDDQIFAPTIYQDVGFG 105
                                       35789*********988887777766664443...344566666777777889***********8877777888888 PP

                                       EETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 103 vkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkv 179
                                         + g s+ ++++   +  e++ l + ++  ++ LSgG+k+ va+a ++A+    p+ +++lDe  ++LD     ++
  gi|298676059|ref|YP_003727809.1| 106 PTNLGYSKDEVDEVVNNTLEYMGLKHLKDKPPHHLSGGQKKRVAIAGVVAMD---PE-VVILDEPLSNLDPVGADEL 178
                                       88899999999999999999999999999999**************998875...54.689**************** PP

                                       HHHHHHHCTTSEEEEE-SSHH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 180 aellkeksknaQfivislree 200
                                        +ll+e ++    i+is ++ 
  gi|298676059|ref|YP_003727809.1| 179 LDLLNEYNHFGKTIIISTHNV 199
                                       ********9999888887664 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   1.2e-06    0.0022      13      39 ..      21      47 ..      18      54 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.2e-06
                            AAA_29 13 dghtieidlkg.atlltGpsGsGKSTll 39
                                      ++ +iei+  g  + ++G++GsGKSTl+
  gi|298676059|ref|YP_003727809.1| 21 NNVDIEINK-GkKIAFVGRNGSGKSTLF 47
                                      567889985.559*************96 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.2   3.8e-06    0.0069      14      44 ..      20      51 ..      19     123 .. 0.81
   2 ?   -0.2   0.0      0.36   6.5e+02     346     365 ..     176     198 ..     157     202 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.8e-06
                            AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsileald 44
                                      + +v+i++++     ++G+N+sGKS++  +l+
  gi|298676059|ref|YP_003727809.1| 20 INNVDIEINKGkKIAFVGRNGSGKSTLFLLLN 51
                                      56788999888899************988775 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.36
                            AAA_15 346 kllkelandnkt...QviitTHS 365
                                       + l++l+n+ ++    +ii+TH+
  gi|298676059|ref|YP_003727809.1| 176 DELLDLLNEYNHfgkTIIISTHN 198
                                       56667777777677799*****8 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.1    0.0033         6      16      38 ..      31      52 ..      17      86 .. 0.75
   2 !    7.7   0.0   0.00066       1.2     526     578 ..     157     206 ..     109     226 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0033
                            AAA_13 16 kriNliYGwNGaGKTtLSrllrs 38
                                      k+i ++ G+NG+GK+tL  ll+ 
  gi|298676059|ref|YP_003727809.1| 31 KKIAFV-GRNGSGKSTLFLLLNG 52
                                      555554.**********888765 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00066
                            AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevk 578
                                         ++v++D P S LD         l++++    +  k ++i+THn+++  ++ 
  gi|298676059|ref|YP_003727809.1| 157 DPEVVILDEPLSNLDPVGADELLDLLNEYN---HFGKTIIISTHNVDLAYQWA 206
                                       5689***********999999999999985...77799********9988876 PP

>> Pr_beta_C  Proteasome beta subunits C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.1e-05     0.073       6      25 ..       6      25 ..       5      29 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.1e-05
                                      --SS-----TTSS-EEEEEE CS
                         Pr_beta_C  6 eRqgsYkfkrGTTaVLkekV 25
                                      +++++Y ++ GTTa+ + ++
  gi|298676059|ref|YP_003727809.1|  6 TKNLKYTYPDGTTAINNVDI 25
                                      699***********977666 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.5   3.9e-05     0.069      12      36 ..      22      47 ..      15      57 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.9e-05
                            AAA_23 12 dqeidFsk.gltlItGpNGaGKTTil 36
                                      +++i+ +k +  +++G NG+GK+T++
  gi|298676059|ref|YP_003727809.1| 22 NVDIEINKgKKIAFVGRNGSGKSTLF 47
                                      6677776635789************8 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   9.8e-05      0.18      90     130 ..      20      61 ..       5      74 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.8e-05
                                       HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                       RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinallpelelktgev 130
                                       ++++  ++++ k +++vG  G GKStL   l+++le   ge+
  gi|298676059|ref|YP_003727809.1|  20 INNVDIEINKgKKIAFVGRNGSGKSTLFLLLNGTLEPDEGEI 61 
                                       55555566655999**************99999887777666 PP

>> Ploopntkinase3  P-loop Nucleotide Kinase3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.022        39       6      24 ..      33      51 ..      28      67 .. 0.83
   2 ?    5.3   0.0    0.0095        17      43     119 ..     352     433 ..     338     435 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.022
                    Ploopntkinase3  6 iylvGqPGaGkstlmaelt 24
                                      i +vG  G+Gkstl   l 
  gi|298676059|ref|YP_003727809.1| 33 IAFVGRNGSGKSTLFLLLN 51
                                      778**********987665 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0095
                    Ploopntkinase3  43 vlvdrttGevvgaelGkrreafsGtdalassi....idkavPwvetkPydlllaeGarl..ankrfldaaleaGyev 113
                                       +l++ ++ ev+ga +Gk+ ++ +  + ++ si    id+++    +    l+l++G  +  a kr  d a ++G e+
  gi|298676059|ref|YP_003727809.1| 352 ELIKDADIEVIGA-MGKKSKSIAEDEGIPLSIttnvIDRSILTALCGKRCLILTNGGMVdhALKRINDYAENSGIEL 427
                                       6889999999998.99999999998877765433338999888888888999*99987544889************* PP

                    Ploopntkinase3 114 tlalld 119
                                       ++++l+
  gi|298676059|ref|YP_003727809.1| 428 HVGILN 433
                                       ****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2810.81
//
Query:       gi|298676060|ref|YP_003727810.1|  [L=260]
Description: cobalt ABC transporter inner membrane subunit CbiQ [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-42  146.1  11.5    1.1e-42  146.1  11.5    2.0  2  CbiQ      Cobalt transport protein


Domain annotation for each model (and alignments):
>> CbiQ  Cobalt transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.1  11.5   6.2e-47   1.1e-42      12     211 ..      21     221 ..      12     226 .. 0.95
   2 !    2.5   0.4    0.0051        92     133     155 ..     228     250 ..     223     254 .. 0.88

  Alignments for each domain:
  == domain 1  score: 146.1 bits;  conditional E-value: 6.2e-47
                                       HHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHTTS---..HHHHHHHCCCHCHHHHHHHHHHE.......EECTTE CS
                              CbiQ  12 vkliwlfllllalvlapnlvtlliiiallllllllvilp..rvlaqalilpllflllgllillfqlittegefvfag 86 
                                       +kli++ + ll+ v ++++vt+l+i+  + ++ ++ +++  ++++++l  pl+f ++g+++++f++ + ++ + f++
  gi|298676060|ref|YP_003727810.1|  21 LKLIIVAFGLLVGVSSTSPVTPLFIALSMSIATVFLGKTplKLYLKILTAPLGFAFAGAVVIFFFFGSGSEILSFNI 97 
                                       79***********************9999999999998899***********************7777778888999 PP

                                       EE....E-TTHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHCCCSS--HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              CbiQ  87 gg.qisitseGllrglllalRiltllslllllalTTppeeltsslerlgvPlelalillLayRfiflLleevqrikq 162
                                       +g  +  +seG+  ++l++ R+++ +++l++la+TTp+ el++ l++ + P+ ++++ +L+yR+if++l+ + +ik+
  gi|298676060|ref|YP_003727810.1|  98 FGyPFIANSEGVNMAALVVSRTFSGMCCLFFLAFTTPMVELFAVLKKTRLPESFIELSMLIYRYIFVFLDVAMSIKY 174
                                       9999************************************************************************* PP

                                       HHHHTTTTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS-SS CS
                              CbiQ 163 AqklRlgdsklgirrslrslgkliaalflralkraervalAmeaRGYtg 211
                                       Aq++Rlg++   +++s+ s  +l+ +lflr+++++e+++lAm++R+Y+g
  gi|298676060|ref|YP_003727810.1| 175 AQTIRLGYK--DVKSSIYSFSMLVSTLFLRSWEQGEKLYLAMDSRCYNG 221
                                       *********..************************************** PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.0051
                                       SS--HHHHHHHHHHHHHHHHHHH CS
                              CbiQ 133 lgvPlelalillLayRfiflLle 155
                                       +++P el++i++  + fif+L  
  gi|298676060|ref|YP_003727810.1| 228 AKRPVELSEIITASLYFIFILTV 250
                                       67999***************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1855.67
//
Query:       gi|298676061|ref|YP_003727811.1|  [L=95]
Description: cobalt transport protein cbiN [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-27   94.1   0.9    4.9e-27   93.7   0.9    1.1  1  CbiN      Cobalt transport protein component CbiN
  ------ inclusion threshold ------
      0.089   12.2   0.3        1.1    8.7   0.1    1.9  2  DUF3552   Domain of unknown function (DUF3552)


Domain annotation for each model (and alignments):
>> CbiN  Cobalt transport protein component CbiN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.7   0.9   5.5e-31   4.9e-27       3      67 .]       5      72 ..       3      72 .. 0.93

  Alignments for each domain:
  == domain 1  score: 93.7 bits;  conditional E-value: 5.5e-31
                              CbiN  3 lllllvvllavvplflv...kgaeFgGaDdqaeevIeeiapdyepwfeplweppsGEiESlLFalQAA 67
                                      ++++++v+l+ +++++v   ++a FgGaD++ae +I+eiapdy+p+++p+weppsGEiESlLF+lQAA
  gi|298676061|ref|YP_003727811.1|  5 IIVAVLVVLFTAQFLYVssaTDAAFGGADGEAEGIIQEIAPDYDPIANPVWEPPSGEIESLLFGLQAA 72
                                      68899999********96666666*******************************************8 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1   0.00012       1.1       5      42 ..       5      42 ..       1      46 [. 0.88
   2 ?    1.9   0.0     0.015   1.3e+02       5      22 ..      71      88 ..      68      94 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00012
                           DUF3552  5 laivalvvglvvgylvrkkiaekkiaeAeeeAkkiiee 42
                                      +++++lvv +++ +l+  + +++  + A  eA+ ii+e
  gi|298676061|ref|YP_003727811.1|  5 IIVAVLVVLFTAQFLYVSSATDAAFGGADGEAEGIIQE 42
                                      5677788999999999********************98 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.015
                           DUF3552  5 laivalvvglvvgylvrk 22
                                      +ai al++g+++gy+  k
  gi|298676061|ref|YP_003727811.1| 71 AAIGALIIGFFMGYYKGK 88
                                      5677999*******9766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 637.93
//
Query:       gi|298676062|ref|YP_003727812.1|  [L=231]
Description: cobalamin biosynthesis protein CbiM [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.7e-54  182.3  20.5    1.1e-53  182.2  20.5    1.0  1  CbiM      Cobalt uptake substrate-specific transmembrane regi


Domain annotation for each model (and alignments):
>> CbiM  Cobalt uptake substrate-specific transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.2  20.5   6.1e-58   1.1e-53       1     206 [.       2     210 ..       2     211 .. 0.95

  Alignments for each domain:
  == domain 1  score: 182.2 bits;  conditional E-value: 6.1e-58
                              CbiM   1 HipdgiLspavllaayavalallalalrrlrkeldear..vpllallaafifaaqminipipggtslHllgavlaai 75 
                                       Hi++g+L+++++ +++a++++++++++++l+k ++ +r  +plla+++afif+++++++p  +g+++H++g++l ai
  gi|298676062|ref|YP_003727812.1|   2 HIMEGFLPSPWWQLWFAISIPVIMFGIYKLNKMVEHKReiLPLLAVAGAFIFVLSSLKLPSVTGSCSHPTGTGLGAI 78 
                                       *********************************9966679************************************* PP

                              CbiM  76 LlGpwaaflavavvlllqallfgdGGitaLGaNilnmavigvllaylvyrllsrlasskkrvalaaflaallsvvla 152
                                       L+Gp+++++  ++vll qa+++++GG+t+LGaN++ m++ig+l++y++y++  +    + +  + +flaa ++ +++
  gi|298676062|ref|YP_003727812.1|  79 LFGPAVTAVLSTIVLLYQAIFLAHGGLTTLGANVFAMGIIGPLVGYAIYKAGMKF---NFNAYAVVFLAATFADWAT 152
                                       **************************************************87665...56899999*********** PP

                              CbiM 153 allvalelalsgleas....lsltaalaamllvhlpvgilEgviTaaivkalkkvrpe 206
                                       ++++a +l+l+  ++      s++a++ +++++++p++i+Eg++T +i+k++ ++++e
  gi|298676062|ref|YP_003727812.1| 153 YVATASQLSLAFPAEAggilGSFKAFAGIFAVTQVPLAIMEGAVTTLIFKYIVQLKSE 210
                                       ***********5544479*99********************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1693.85
//
Query:       gi|298676063|ref|YP_003727813.1|  [L=194]
Description: precorrin-6y C5,15-methyltransferase subunit CbiE [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-24   87.3   0.0      1e-23   84.4   0.0    1.9  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
  ------ inclusion threshold ------
      0.075   12.7   0.0        3.7    7.2   0.1    2.1  2  DUF460        Protein of unknown function (DUF460)
       0.14   12.3   0.0        0.4   10.9   0.0    1.6  2  DUF1912       Domain of unknown function (DUF1912)


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.4   0.0   1.7e-27     1e-23       2     206 ..       3     173 ..       2     178 .. 0.84

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 1.7e-27
                      TP_methylase   2 lylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealra 78 
                                       +++VGvGpG    lT +A++a+k+a+vv+g++ ra e +++++                   + ++  + ++ +   
  gi|298676063|ref|YP_003727813.1|   3 IVGVGVGPGM---LTEEAIEAIKNAPVVYGSK-RAIETAEKYIT------------------GKANKIRDYKNLHLL 57 
                                       5778888877...*******************.******87762..................223334445555555 PP

                      TP_methylase  79 gkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllpglakeeerele 155
                                         d+v+l++GDPl++g g +      +++     ++iPG+ssl +a+arlg+ +te   ++++  +g ++ ++ +l 
  gi|298676063|ref|YP_003727813.1|  58 PDDAVVLSTGDPLFSGLGKYAS----KND-----RIIPGISSLHLACARLGVNMTELAAITAHG-RG-GNHSKHLLV 123
                                       557*****************65....422.....8*****************************.66.456677777 PP

                      TP_methylase 156 allangdtlvllkapr.klaelaelLkealyddttpvavveragtedervvr 206
                                       + l+ g +++ll + +  ++e+a++L e+  d + +++ +e++g+++er++ 
  gi|298676063|ref|YP_003727813.1| 124 QELKLGKNVLLLPDASfGPNEVAKVLHEF--DINADIYTCEELGYPNERITG 173
                                       77888*******999999***********..7888**************985 PP

>> DUF460  Protein of unknown function (DUF460)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1   0.00063       3.7      34      66 ..       6      38 ..       1      43 [. 0.88
   2 ?    3.6   0.0    0.0084        50      68     104 ..     122     160 ..      76     172 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00063
                            DUF460 34 vGiDPGittgiavldldgevlalkssreldree 66
                                      vG+ PG+ t  a+  ++  ++   s+r ++++e
  gi|298676063|ref|YP_003727813.1|  6 VGVGPGMLTEEAIEAIKNAPVVYGSKRAIETAE 38
                                      7899************************99876 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0084
                            DUF460  68 ieliselGkpvivAtDvspppetvkklarsl..kavlyv 104
                                       +    +lGk v++  D s  p+ v k+  ++  +a +y+
  gi|298676063|ref|YP_003727813.1| 122 LVQELKLGKNVLLLPDASFGPNEVAKVLHEFdiNADIYT 160
                                       4444689*******************9887622566776 PP

>> DUF1912  Domain of unknown function (DUF1912)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   6.7e-05       0.4      33      77 ..      13      60 ..       9      64 .. 0.86
   2 ?   -2.4   0.0      0.96   5.7e+03      65      81 ..     126     142 ..     123     144 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.7e-05
                                      ------HHHHHHHHHHHHHH...HHHHHHHHHHHHHHHT--TTS---- CS
                           DUF1912 33 leedkderakdaliryeskl...daykfllgkfenykagkgfhdlPde 77
                                      l+e+  e  k+a + y sk     a k++ gk +  ++ k++h lPd+
  gi|298676063|ref|YP_003727813.1| 13 LTEEAIEAIKNAPVVYGSKRaieTAEKYITGKANKIRDYKNLHLLPDD 60
                                      5778888999999***9996333589*********************8 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.96
                                       HHHT--TTS----XXXX CS
                           DUF1912  65 ykagkgfhdlPdelfGe 81 
                                        k gk+   lPd  fG 
  gi|298676063|ref|YP_003727813.1| 126 LKLGKNVLLLPDASFGP 142
                                       5778999999*999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1377.29
//
Query:       gi|298676064|ref|YP_003727814.1|  [L=338]
Description: cobalamin (vitamin B12) biosynthesis protein CbiD [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-49  167.5   0.5    3.3e-49  167.5   0.5    1.6  2  CbiD      CbiD


Domain annotation for each model (and alignments):
>> CbiD  CbiD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.5   0.5   1.8e-53   3.3e-49       1     248 [.      43     277 ..      43     280 .. 0.87
   2 ?   -2.0   0.1     0.095   1.7e+03     114     140 ..     305     330 ..     300     333 .. 0.79

  Alignments for each domain:
  == domain 1  score: 167.5 bits;  conditional E-value: 1.8e-53
                              CbiD   1 lrsGyTtGscAaAAakaAllallkgekleeveielpkgekleipiekvalleeeaavikdaGd.dpDvTngaeivae 76 
                                       l++GyTtG++Aa AakaA+l l  ++ +++v++ +p g +++++++  +    + +v k   d + D+T+g+e  a 
  gi|298676064|ref|YP_003727814.1|  43 LKRGYTTGTTAAIAAKAAVLSL--RKDIDSVTVPTPVGLRARMEVDAHHG---HSVVSKLNNDhESDITRGIEFEAY 114
                                       589*******************..7889****************776665...4566666666267*********99 PP

                              CbiD  77 ve..eeieiegGeGvGrvtkpgLevevgeaAInpvprkmieenveevleea.kegvevtisvpeGeelAkkTlNprl 150
                                           +e  i +GeG+G+v ++gL+++ g++AInp p ++i+++v e++ee   +gv+v+is+p+G+++A++TlN r+
  gi|298676064|ref|YP_003727814.1| 115 AMesDETSIFAGEGIGTVIQDGLQIKKGNPAINPRPMQQIQDSVCEAVEELgINGVRVKISLPRGADVARNTLNDRI 191
                                       9889779*****************************************999967*********************** PP

                              CbiD 151 GivgGiSiLGTtGivepmSeeallesireelkvaaaeglkelvlvtGnkgeklakkklglpeealvkvsnfvgeale 227
                                       Gi+gGiSiLG tG vep+S++  l +++e+l     +  +++v++tG++g ++ +    +p++++v ++  + e le
  gi|298676064|ref|YP_003727814.1| 192 GITGGISILGSTGFVEPWSDH--LGEMKEDLL----KTASKVVITTGRIGVRYSTM--LFPDHTVVLFGSRISEGLE 260
                                       ******************975..555555554....44567***********9987..69*********99999999 PP

                              CbiD 228 eaaekgvkkvllvghiGKlvK 248
                                        a+     +v+++g  G ++K
  gi|298676064|ref|YP_003727814.1| 261 VAT----GDVIICGLPGLILK 277
                                       876....46666666666666 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.095
                              CbiD 114 ieenveevleeakegvevtisvpeGee 140
                                       ++e++e+++++  eg++v i+  eGe 
  gi|298676064|ref|YP_003727814.1| 305 LQEAFEKTIKK-AEGARVVIVNREGEI 330
                                       67788888887.779999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2193.64
//
Query:       gi|298676065|ref|YP_003727815.1|  [L=626]
Description: DNA mismatch repair protein MutL [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-40  136.3   0.0    7.2e-40  135.4   0.0    1.5  1  DNA_mis_repair  DNA mismatch repair protein, C-terminal domai
    4.3e-35  120.7   0.0      9e-35  119.6   0.0    1.5  1  MutL_C          MutL C terminal dimerisation domain
    5.6e-15   55.4   0.6    5.6e-15   55.4   0.6    2.1  3  HATPase_c_3     Histidine kinase-, DNA gyrase B-, and HSP90-l
    6.6e-09   36.3   0.1    2.7e-08   34.3   0.1    2.1  1  HATPase_c       Histidine kinase-, DNA gyrase B-, and HSP90-l


Domain annotation for each model (and alignments):
>> DNA_mis_repair  DNA mismatch repair protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.4   0.0   1.6e-43   7.2e-40       2     118 ..     212     328 ..     211     329 .. 0.98

  Alignments for each domain:
  == domain 1  score: 135.4 bits;  conditional E-value: 1.6e-43
                                       HHHHHHHHHCCEEEEEEEETTEEEEEEEE-CCG-BTTGGEEEEEETTEEE--HHHHHHHHHHHHCCSSSSSB-EEEE CS
                    DNA_mis_repair   2 aavlgkevaenlleiekeeeqlkieGfiskpelsrskrdkqflfvNgRlvkskelkkaireaYkellpkgrypvvvL 78 
                                        +v+g++va++++++++e+e ++++G+iskpe++rs +d q++f+N+R v+s+ +++a+r++Y +llpkgryp++vL
  gi|298676065|ref|YP_003727815.1| 212 VHVYGRDVARSMIPVDHESELIRVSGYISKPEFTRSGTDFQSFFINNRSVSSRAISNALRTGYYTLLPKGRYPAAVL 288
                                       689************************************************************************** PP

                                       EEEESSGGEE-TSSTT----EETTHHCHHHHHHHHHHHHH CS
                    DNA_mis_repair  79 nleidpeevDvNvhPtKreVrfqdeeevieaieealkeal 118
                                       n++i+peevD+NvhP+K+ Vr+++e+ +++ai+e++k+al
  gi|298676065|ref|YP_003727815.1| 289 NIQINPEEVDINVHPRKSHVRLSHEQDIMDAISESVKTAL 328
                                       ************************************9987 PP

>> MutL_C  MutL C terminal dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.6   0.0     2e-38     9e-35       4     145 ..     438     577 ..     436     579 .. 0.96

  Alignments for each domain:
  == domain 1  score: 119.6 bits;  conditional E-value: 2e-38
                                       EEEEEETTTEEEEEETTEEEEEEHHHHHHHHHHHHHHHHCCHSSB-EEEEEEEEEEE--HHHHHHHHHCHHHHHHCT CS
                            MutL_C   4 kalgqvhgtyilaenedglvlvDqhaAherilyeklkeqlkeeelksQpLliPlvlelspeeaalleehkeeLaklG 80 
                                       k+lgqv++ yi+ae ++ lvl+DqhaAheri+ye+++++ +      Q+L+ P++lels +e  l+ee+   L+++G
  gi|298676065|ref|YP_003727815.1| 438 KVLGQVDELYIVAEMDSRLVLIDQHAAHERIMYEHIRNSKNP---DWQELISPITLELSIKEKVLMEEYIPYLEEFG 511
                                       79***********************************99999...89****************************** PP

                                       -EEEE-STTEEEEEEEECCCTTTSHHHHHHHHHHHHCCCSS.-H-HCCHHHHHHHHCTTSSSSSS- CS
                            MutL_C  81 feleefgpnslivravPallrqqnleelirelleelaekgk.esleekleellatmachssvkagr 145
                                       f ++efgp ++i+++vP+++++ + + +++++++e+ ++g+ ++     + +++t+ac+s++kag+
  gi|298676065|ref|YP_003727815.1| 512 FAISEFGPSTYIITSVPVIFGNIEKPDTLHDMISEILSAGRiKNDVGIYDYMCKTIACRSAIKAGH 577
                                       ****************************************985567899***************97 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.4   0.6   1.2e-18   5.6e-15       4     104 ..      27     127 ..      23     150 .. 0.80
   2 ?   -2.5   0.1      0.93   4.2e+03      98     113 ..     344     362 ..     327     392 .. 0.55
   3 ?   -2.6   0.2         1   4.6e+03      90     120 ..     393     410 ..     372     432 .. 0.44

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 1.2e-18
                       HATPase_c_3   4 ekAlaelvdNsldAdaenvkievnknrgktgeivieDdGkGmseeelknalrlatsskeak.r...kstslGkkGiG 76 
                                        +++ el++Ns+dA a+++ki v++  g +++i++ D+G+Gms+++++ a++ + +sk  k +   + t+lG +G  
  gi|298676065|ref|YP_003727815.1|  27 ASVVKELIENSIDAGATEIKIDVKE--GGAKKITVSDNGTGMSYDDVRLAFTKHATSKIWKlEdlySTTTLGFRGEA 101
                                       689*********************9..568*******************9965555555442434467888888755 PP

                       HATPase_c_3  77 lklAslslgkkltvitkkegesstltld 104
                                         l+s+ + +k+++it+++++   + + 
  gi|298676065|ref|YP_003727815.1| 102 --LSSIASVSKVEMITRQKDDLAGTMIV 127
                                       ..9***************9998755444 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.93
                       HATPase_c_3  98 ss...tltldvdkidkene 113
                                       +s    ++l+++ + ++++
  gi|298676065|ref|YP_003727815.1| 344 KSqetSVQLNIKEVGNKSQ 362
                                       2222245555555444332 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1
                       HATPase_c_3  90 vitkkegesstltldvdkidkenekvleelt 120
                                       v + k++e+   +              e+lt
  gi|298676065|ref|YP_003727815.1| 393 VSSIKDTEKRLKRS-------------ERLT 410
                                       22222222222222.............2222 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.1     6e-12   2.7e-08       5      85 ..      25     109 ..      21     144 .. 0.75

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 6e-12
                                       HHHHHHHHHHHHHHHHHSTTTEEEEEEEEEE.TEEEEEEEESSSSSTTHHHTGTCSTTCH......HCSTCHTS.TS CS
                         HATPase_c   5 rLrqiisnlvdNavkfatkageieveikase.ddlvisveDnGiGipkedlkklfekfsq......ddstkrgg.gg 73 
                                       r   ++++l++N++++   a+ei++ +k  e + ++i+v+DnG G++ +d+ + f+k+ +      +d +++++ g 
  gi|298676065|ref|YP_003727815.1|  25 RPASVVKELIENSIDA--GATEIKIDVK--EgGAKKITVSDNGTGMSYDDVRLAFTKHATskiwklEDLYSTTTlGF 97 
                                       56689**********6..7999999999..558***********************888878888865665555244 PP

                                       SSHHHHHHHHHH CS
                         HATPase_c  74 tGlGlsivkklv 85 
                                       +G  ls   +++
  gi|298676065|ref|YP_003727815.1|  98 RGEALSSIASVS 109
                                       444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (626 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1290  (0.0719505); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.73u 0.34s 00:00:01.07 Elapsed: 00:00:00.53
# Mc/sec: 3535.93
//
Query:       gi|298676066|ref|YP_003727816.1|  [L=887]
Description: DNA mismatch repair protein MutS [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.1e-84  280.3   0.1    1.5e-83  279.5   0.1    1.4  1  MutS_V    MutS domain V
    2.4e-44  150.2   0.0    7.2e-44  148.6   0.0    1.9  2  MutS_I    MutS domain I
    8.9e-40  136.9   2.3    1.5e-38  133.0   0.1    2.4  2  MutS_III  MutS domain III
    2.7e-30  104.6   0.9    8.1e-30  103.0   0.9    1.9  1  MutS_IV   MutS family domain IV
    8.2e-27   94.2   0.0    2.7e-26   92.5   0.0    2.0  1  MutS_II   MutS domain II
  ------ inclusion threshold ------
      0.038   13.6   0.0      0.078   12.6   0.0    1.5  1  AAA_27    AAA domain
       0.13   12.0   0.0       0.33   10.7   0.0    1.6  1  AAA_29    P-loop containing region of AAA domain
       0.23   11.9  10.2        1.8    9.0   0.0    3.5  4  AAA_23    AAA domain


Domain annotation for each model (and alignments):
>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  279.5   0.1   6.5e-87   1.5e-83       1     188 []     622     811 ..     622     811 .. 0.97

  Alignments for each domain:
  == domain 1  score: 279.5 bits;  conditional E-value: 6.5e-87
                                       EEEE-STTSSHHHHHHHHHHHHHHHHHT--BSSSEEEEE--SEEEEEE--------SS-HHHHHHHHHHHHHTT--T CS
                            MutS_V   1 llitGpnmaGkstylrqvalivllaqiGsfvpaekaeisivdkiftRvgasDdlakgkstFmvEmlEtasilknate 77 
                                       llitGpnmaGksty+rq++li+++aq Gsfvpa++a+i+ivd++ftRvga Ddla+g+stFmvEm+E+a+il+nat 
  gi|298676066|ref|YP_003727816.1| 622 LLITGPNMAGKSTYMRQNSLITIMAQAGSFVPASYASIGIVDRVFTRVGAFDDLASGQSTFMVEMVELANILNNATP 698
                                       58*************************************************************************** PP

                                       TSEEEEESTS-SS-HHHHHHHHHHHHHHHHHT..T--EEEEEES-GGGGGHHHHSTTEEEEEEEEEEETTEEEEEEE CS
                            MutS_V  78 kslvilDElGRGtstydGlaialavaeyllek..ikaktlfatHyheltklaekleevknlhlavkeeeedivflyk 152
                                       kslv+lDE+GRGtst+dG++ia+av+ey+++k  +  ++lfatHyh+lt+l++kl++v+n+h+avkee +++vfl+k
  gi|298676066|ref|YP_003727816.1| 699 KSLVLLDEIGRGTSTFDGYSIAKAVVEYIHKKdgVGVRSLFATHYHQLTDLENKLKRVSNYHIAVKEEGDNLVFLRK 775
                                       ******************************87336789*************************************** PP

                                       EEES--SS--HHHHHHHTT--HHHHHHHHHHHHHTT CS
                            MutS_V 153 vkegaaeksyGikvaklaglPesvverArevlkele 188
                                       + +ga++ksyGi+va+ ag+P++v +rAre+lk++e
  gi|298676066|ref|YP_003727816.1| 776 IVPGATDKSYGIQVARYAGVPKKVTSRAREILKDIE 811
                                       *******************************99875 PP

>> MutS_I  MutS domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.6   0.0   3.2e-47   7.2e-44       1     112 [.       5     117 ..       5     118 .. 0.96
   2 ?   -2.8   0.0       3.2   7.2e+03      55      76 ..     788     809 ..     775     832 .. 0.58

  Alignments for each domain:
  == domain 1  score: 148.6 bits;  conditional E-value: 3.2e-47
                                       HHHHHHHHCCCHH-TTCEEEEEETTEEEEECHHHHHHHHHCSSSSTT.E.SSSSC.EEEEEEEHHHHHHHHHHHHHT CS
                            MutS_I   1 tplmkqylelkkkykdavlffrvGdfYelfgeDAviaareleitltkrk.kssekeipmagvPehalekylrkLvek 76 
                                       tp m+qy e+kkky da+lffr+GdfYe+f eDA+++++eleitlt+r+ ++++++ p ag+P+ha+++yl +L++k
  gi|298676066|ref|YP_003727816.1|   5 TPAMQQYYEMKKKYSDALLFFRMGDFYECFDEDAKTVSEELEITLTNRNgNKKGEKRPLAGIPYHAVDNYLPRLIKK 81 
                                       89**********************************************95555555********************* PP

                                       T-EEEEEEE-S-HHHHS.S--EEEEEEEBTTC-TTS CS
                            MutS_I  77 gykVavveqtetpaekkgvvkrevvrviTpGtltde 112
                                       gykVa++eq e+p e+kgvvkr vvrv+TpGt +d+
  gi|298676066|ref|YP_003727816.1|  82 GYKVAICEQLEDPREAKGVVKRGVVRVVTPGTAIDS 117
                                       ********************************9986 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.2
                                       ..EEEEEEEHHHHHHHHHHHHHT CS
                            MutS_I  55 e.ipmagvPehalekylrkLvek 76 
                                       +  ++agvP++  ++ +r++++ 
  gi|298676066|ref|YP_003727816.1| 788 QvARYAGVPKKVTSR-AREILKD 809
                                       447889999876655.4444443 PP

>> MutS_III  MutS domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.0   0.1   6.5e-42   1.5e-38       2     191 .]     276     570 ..     275     570 .. 0.92
   2 ?    3.4   0.3     0.035        77      74     152 ..     743     868 ..     721     887 .] 0.53

  Alignments for each domain:
  == domain 1  score: 133.0 bits;  conditional E-value: 6.5e-42
                                       HHHHTTSSS-TTS.SSSS-HHHHH---SSHHHHHHHHHHHH--BS-HHHHHHHHHHHHH.T..TT.HHHHHHHHTT- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                          MutS_III   2 TlrnLeilenlrggskegsLlgvldrTvTamGaRlLrewllqPltdleeInaRldaVee.leneelreelrellrrl 77 
                                       TlrnLe++++ rg++++ ++l+vld T+T+mG RlL++wl +Pl+++++In+RldaV+   e++ +r +lr+ l  +
  gi|298676066|ref|YP_003727816.1| 276 TLRNLEVIKSVRGEGNDATILKVLDDTKTPMGGRLLQKWLVKPLISIDKINRRLDAVQNlKEETLVRFDLRSYLSYV 352
                                       9********999998899****************************************9445566677777888889 PP

                                       --HHHHHHHHHTT---HHHHHHHHHHHHHHHTTTTT---SSTHHHHH..............HHHHHHHHHHB-SS-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..............xxxxxxxxxxxxxxxx RF
                          MutS_III  78 pDleRllsrislgkakardlkallealkaleelvallekeklaesee..............eslaelleeaideepl 140
                                       +D+eRl+ ri +g+++ardl al ++l+ +++++  l++ +++  +                ++ el+e+ i +ep+
  gi|298676066|ref|YP_003727816.1| 353 KDVERLIGRIVYGNSNARDLVALKKSLEVVPDIIGCLKECDQS--DIlkeihnelssftelGDITELIEKGITDEPP 427
                                       9***************************999999998665543..335588877766644434559*********** PP

                                       SSGGGS--B-T.................................................................. CS
                                       xxxxxxxxxxx.................................................................. RF
                          MutS_III 141 alekegedlra.................................................................. 151
                                       a  +eg+ ++                                                                   
  gi|298676066|ref|YP_003727816.1| 428 ATVREGGLIKPgyseeldelkdmsrhskewiasfqkqerertginslkvgynkvfgyyievtkpnikyvpddyirkq 504
                                       ***************************************************************************** PP

                                       ..........................HHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHH CS
                                       ..........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          MutS_III 152 ..........................iealeqelfqelleeveealerlrrlaealaeLDvllSlA 191
                                                                 i +le++lf ++ ++v+++++ l+r+a+++  LDvl+ lA
  gi|298676066|ref|YP_003727816.1| 505 tmanaerfytpelkerenmiisadekIVSLEYNLFTDINSKVASHSKNLQRTATLIGKLDVLANLA 570
                                       **************************9************************************998 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.035
                                       HTT---HHHHHHHHHTT---HHH.......HHHH...........................HHHHHHHHTTTTT--- CS
                                       xxxxxxxxxxxxxxxxxxxxxxx.......xxxx...........................xxxxxxxxxxxxxxxx RF
                          MutS_III  74 lrrlpDleRllsrislgkakard.......lkal...........................lealkaleelvallek 116
                                        ++l Dle  l+r+s+ +  +++       l+++                           +e lk++e+ + +  +
  gi|298676066|ref|YP_003727816.1| 743 YHQLTDLENKLKRVSNYHIAVKEegdnlvfLRKIvpgatdksygiqvaryagvpkkvtsraREILKDIEKNASIG-D 818
                                       556669999999998874443333334333122133333333333334444444444444477777766554444.4 PP

                                       SSTHHHHHHHHHHHHHHHB-SS--SSGGGS--B-T................H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................x RF
                          MutS_III 117 eklaeseeeslaelleeaideeplalekegedlra................i 152
                                       e++++++++++ +l+    d +++++++++ed+r+                i
  gi|298676066|ref|YP_003727816.1| 819 EDNKKDKKKKYTQLVF--FDPDQSQKQNDKEDERHpvvnelkdlntneltpI 868
                                       4444444445667777..7777777777777777788887777766666542 PP

>> MutS_IV  MutS family domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.0   0.9   3.6e-33   8.1e-30       1      91 [.     439     529 ..     439     530 .. 0.97

  Alignments for each domain:
  == domain 1  score: 103.0 bits;  conditional E-value: 3.6e-33
                                       TTSHHHHHHHHHHHHHHHHHHHHHCCCCCCCT-TTBEECCCSSSEEEEEE-TCCCTTT--SEEEEEECTCEEEEECC CS
                           MutS_IV   1 gfdeeLdelrdrleelekeleeleekereklgikslkveynkvlGyylevtrseakkvpkefirlqtlknserytta 77 
                                       g++eeLdel+d+ ++ ++++++ +++ere++gi+slkv+ynkv+Gyy+evt+ + k vp+++ir+qt+ n+er++t+
  gi|298676066|ref|YP_003727816.1| 439 GYSEELDELKDMSRHSKEWIASFQKQERERTGINSLKVGYNKVFGYYIEVTKPNIKYVPDDYIRKQTMANAERFYTP 515
                                       799************************************************************************** PP

                                       CHHHHHHHHHHHHH CS
                           MutS_IV  78 elkkleaelleaee 91 
                                       elk+ e+ + +a e
  gi|298676066|ref|YP_003727816.1| 516 ELKERENMIISADE 529
                                       ******99988866 PP

>> MutS_II  MutS domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.5   0.0   1.2e-29   2.7e-26       1     136 [.     126     258 ..     126     259 .. 0.98

  Alignments for each domain:
  == domain 1  score: 92.5 bits;  conditional E-value: 1.2e-29
                                       -EEEEEEEETTTSEEEEEEEETTTTEEEEEEEEE...-HHHHHHHHHH-ESEEEEESS-SCCCHHHHHHCHCTTT-E CS
                           MutS_II   1 nylaAisekregrrvGlafiDlstgefvvsefed...feeleaeLsrlsPkElllpedlsestaeeessklrelrsr 74 
                                       nyl+Aise  +++ +Gl+f+D+stgef +++ +d   ++++++e++r  P+E++lp+ l+++  +e  + l++    
  gi|298676066|ref|YP_003727816.1| 126 NYLMAISE--KNNEFGLSFLDVSTGEFLTTQLSDeppYDRIASEIARMRPAECILPPYLYNN--SEIAQLLKDMKIT 198
                                       9*******..9999*********************************************998..78*********** PP

                                       EEEESCCCCSHCCHHHHCHHHB--STTTTTTTGGG-HHHHHHHHHHHHHCCCCCSCCCCT-C CS
                           MutS_II  75 vgvretvefesekaserleedfsvedldgfglekekklalaAlgalisYleetqkekelshl 136
                                       +  +++  fe  +a+ +l ++f+v +l+g+g+   + la++A ga ++Y  etq++ el+h+
  gi|298676066|ref|YP_003727816.1| 199 LHEYDSSAFETNTARLQLLQHFNVSTLKGMGC-DDLTLAISASGATLQYTLETQMR-ELGHV 258
                                       ********************************.9**********************.*9996 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.5e-05     0.078      20      44 ..     613     637 ..     606     642 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.5e-05
                            AAA_27  20 dfsaeeadlhliyGpNEAGKstalr 44 
                                       +++ +++++ li GpN AGKst +r
  gi|298676066|ref|YP_003727816.1| 613 EMNCTDNQFLLITGPNMAGKSTYMR 637
                                       44556899**************997 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00015      0.33      20      39 ..     617     636 ..     606     651 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00015
                            AAA_29  20 dlkgatlltGpsGsGKSTll 39 
                                       + +++ l+tGp+ +GKST +
  gi|298676066|ref|YP_003727816.1| 617 TDNQFLLITGPNMAGKSTYM 636
                                       434489************76 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   1.0       1.7   3.7e+03     153     171 ..     424     453 ..     320     531 .. 0.59
   2 ?   -1.9   0.2       1.7   3.9e+03      70      70 ..     480     480 ..     421     571 .. 0.54
   3 ?    9.0   0.0   0.00079       1.8      18      36 ..     618     636 ..     607     640 .. 0.85
   4 ?    6.2   2.0    0.0059        13     101     185 ..     796     881 ..     711     886 .. 0.56

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.7
                            AAA_23 153 e...........rleelekeleeledekkl 171
                                       +               +++el+el+d+ + 
  gi|298676066|ref|YP_003727816.1| 424 DeppatvregglIKPGYSEELDELKDMSRH 453
                                       134444444444222344444444444433 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.7
                            AAA_23  70 k 70 
                                       k
  gi|298676066|ref|YP_003727816.1| 480 K 480
                                       1 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00079
                            AAA_23  18 skgltlItGpNGaGKTTil 36 
                                       ++ + lItGpN aGK+T +
  gi|298676066|ref|YP_003727816.1| 618 DNQFLLITGPNMAGKSTYM 636
                                       56778************76 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.0059
                            AAA_23 101 gkttkkaklellei.deleqfise.llgskkiilnlilflgqerfeefelkdkke.....rleelekeleeledekk 170
                                        k++   ++e+l++ +++  + +e + + kk+  ++++f++ ++ +++++k+++      +       ++ +++e  
  gi|298676066|ref|YP_003727816.1| 796 PKKVTSRAREILKDiEKNASIGDEdNKKDKKKKYTQLVFFDPDQSQKQNDKEDERhpvvnE------LKDLNTNELT 866
                                       4444555556555546666667773333444466777776666664444333222343331......2222222333 PP

                            AAA_23 171 llekleqekekekel 185
                                        +++l++++e ++++
  gi|298676066|ref|YP_003727816.1| 867 PIDALNKLNELQNKI 881
                                       333333322222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (887 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.63u 0.26s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 5912.96
//
Query:       gi|298676067|ref|YP_003727817.1|  [L=203]
Description: flavoprotein WrbA [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.4e-14   52.0   0.0    9.1e-14   51.5   0.0    1.2  1  FMN_red       NADPH-dependent FMN reductase
    0.00014   21.6   0.0    0.00018   21.3   0.0    1.2  1  Flavodoxin_2  Flavodoxin-like fold
     0.0003   21.0   0.1     0.0022   18.2   0.1    2.0  1  Flavodoxin_1  Flavodoxin


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   0.0   1.5e-17   9.1e-14       1     144 [.       1     145 [.       1     152 [. 0.83

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 1.5e-17
                                       -EEEEEES--STT-HHHHHHHHHHCCT-T..T-CEEEEETTTS.--...---HCHGHT.CGGSHHHHHHHHHHHH-S CS
                           FMN_red   1 mkilvisGSlrkgsntrklaewaaealkea.gaevelidladlilpc.alcdkdlese.gqtsddvaellekiaaad 74 
                                       mki +i+ Sl   +  ++lae++ae ++e  g +v + ++ +  l + +l +k+  ++ +  s    + l+++++ad
  gi|298676067|ref|YP_003727817.1|   1 MKINIIFHSLF--GHIYQLAEAVAEGAREVeGSDVNIYQVEET-LSDeVLEKKGALESkETFSHIPTATLDTLTEAD 74 
                                       66777777774..77899*********7777899999998887.3333332333322246677788*********** PP

                                       CEEEEEEECTTCE-HHHHHHHHCHT-.SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHH.HTT-EEEE CS
                           FMN_red  75 aliivtPeYngsysgllKnalDrlsrtrgkkelrgKpvalvavgggrrgglraeeqlrqvla.elgaivvp 144
                                       +li++tP+ +g++++++ +++D ++  + +  l gK++ +++ +++++gg++ +   ++    ++g+i+v+
  gi|298676067|ref|YP_003727817.1|  75 GLIFGTPTRFGMMTAQMRTLFDATGKLWANGDLIGKVGSVFTSSATQHGGQESTILNFHTTLlHHGMIIVG 145
                                       ****************************************************9999888888788888876 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0     3e-08   0.00018       1     103 [.       1      98 [.       1     150 [. 0.76

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3e-08
                                       -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCC.T-----CCCCHCC..HHHHTT.CHHHHHHHHH CS
                      Flavodoxin_2   1 mkiLiinahprpeksfssalaqafvealekagphevtvrdLyad.flpvlttrdlaak..layeek.padveseqie 73 
                                       mki ii+ +  +  +  ++la+a++e++++ +  +v +  + ++  + vl++     k  l+++e  ++  ++   +
  gi|298676067|ref|YP_003727817.1|   1 MKINIIFHSLFG--HI-YQLAEAVAEGAREVEGSDVNIYQVEETlSDEVLEK-----KgaLESKETfSHIPTATL-D 68 
                                       677777766655..44.99***********9986699999999866666666.....333344443245555555.9 PP

                                       HHHCSSEEEEEEE-BTTB--HHHHHHHHHH CS
                      Flavodoxin_2  74 kllaadaivlqfPlwwfgvPailKgwiDrv 103
                                        l +ad +++++P  + ++ a++   +D  
  gi|298676067|ref|YP_003727817.1|  69 TLTEADGLIFGTPTRFGMMTAQMRTLFDAT 98 
                                       ***************************974 PP

>> Flavodoxin_1  Flavodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   3.6e-07    0.0022       1     123 [.       5     120 ..       5     128 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.6e-07
                                       EEEETSSSHHHHHHHHHHHHHHHTTTEEEEEEEEGTTSC.GGGGGTHSEEEEEEEEETTTBEEGGGHHHHHHHHHHH CS
                      Flavodoxin_1   1 ilYgSetGnteklAkqlaeelgehgfnadvvslsdydes.lseieeealllvvtsTfgnGdppengesffqdllelk 76 
                                       i+++S  G+  +lA+++ae+++e  ++   v++++++e+  +e+ e++ +l    Tf    p+ +  + ++++  ++
  gi|298676067|ref|YP_003727817.1|   5 IIFHSLFGHIYQLAEAVAEGARE--VEGSDVNIYQVEETlSDEVLEKKGALESKETFSHI-PTATLDTLTEADGLIF 78 
                                       89*******************97..56788999999988788999989888888888855.8888887777777777 PP

                                       CHHGCCSTTTTEEEEEEEEECTTSSSTTHHHHHHHHHHHHTTCEEES CS
                      Flavodoxin_1  77 gdeledgdlsgvrfavfglGdsayenFcaagkkldekleelGaerll 123
                                       g+    + +  ++ ++  l+d +++   +a + l  k++ ++ +  +
  gi|298676067|ref|YP_003727817.1|  79 GT---PTRFGMMTAQMRTLFDATGKL--WANGDLIGKVGSVFTSSAT 120
                                       64...445788999999999999988..8888888887777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1306.36
//
Query:       gi|298676068|ref|YP_003727818.1|  [L=263]
Description: ABC-2 type transporter [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-21   76.0  26.3    2.7e-21   76.0  26.3    1.5  2  ABC2_membrane    ABC-2 type transporter
    1.8e-06   27.3  36.4    2.4e-06   26.9  36.4    1.2  1  ABC2_membrane_3  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.0  26.3     3e-25   2.7e-21       8     208 ..      14     226 ..       9     228 .. 0.89
   2 ?   -4.3   1.6       1.1   9.7e+03     103     117 ..     237     251 ..     233     257 .. 0.47

  Alignments for each domain:
  == domain 1  score: 76.0 bits;  conditional E-value: 3e-25
                     ABC2_membrane   8 kreflqrwrdpslgll.......wrliqplllalvfgtvfgnlgnsedglnr.....pgllffsvlflafsaltsva 72 
                                        r f+ ++r++  ++         +l++pll+++ +g+  g   n+ +g+++     p +++ s+++ +f+ +t  +
  gi|298676068|ref|YP_003727818.1|  14 YRVFKVWLRNKDVFMTtlkvnllPPLLSPLLYLFAIGLGLGTYINNIEGVSYiefiaPAMIAVSMMYASFFECTFGS 90 
                                       56666666666666335555555999**************953355666655899********************** PP

                     ABC2_membrane  73 pvferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldls.rfflflllllltalaasslg 148
                                        v+++ +++++   ++pl +  +++++ +l+ +++s++ a+++++iv ++ gl    + +l++++ +++++++ +lg
  gi|298676068|ref|YP_003727818.1|  91 YVRMYYQKTFDAIIATPL-TIEEVITGEMLWGATRSTINATLVVIIVSIM-GLAEYpHSLLIIPFSFISGFLFACLG 165
                                       ******************.******************************9.88886556****************** PP

                     ABC2_membrane 149 llisalapsfedasqlaslvllpllllsGffipidsmpkwlqw.iaylnPltyavealrsn 208
                                       +++ a++p++ + +  + l+++p++l+sG f+p++ +p+ lq+  + ++Plt++v ++rs 
  gi|298676068|ref|YP_003727818.1| 166 MCFTAISPNINTLTYPSILFITPMFLFSGTFFPLSLLPQILQYlAYAILPLTHIVMIIRSL 226
                                       *************************************99***9566799*******99985 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 1.1
                     ABC2_membrane 103 velpvsllqalifll 117
                                       ++++++++++li+++
  gi|298676068|ref|YP_003727818.1| 237 GNFIWIAAASLILFV 251
                                       344444444444444 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9  36.4   2.7e-10   2.4e-06     157     343 ..      63     253 ..      30     254 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 2.7e-10
                   ABC2_membrane_3 157 snvasflvgliliilifitasf..iavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll..af 229
                                        ++  f++++++++++++ ++f  +  s+v+   +++   ++ ++++  + +++ +l+ ++ + + + l++++  + 
  gi|298676068|ref|YP_003727818.1|  63 VSYIEFIAPAMIAVSMMYASFFecTFGSYVRMYYQKTFDAIIATPLTIEEVITGEMLWGATRSTINATLVVIIvsIM 139
                                       56778899977777777775553345589*************************************99988877899 PP

                   ABC2_membrane_3 230 glgipfg.nlglllllfllfglayialgyllsslfknset.aqilifivilllsgffgglfpledlpsalkwifs.i 303
                                       g  +  + +++l++ ++++ g+++++lg+ +++++ n  t ++   +++i ++++f+g +fpl+ lp +l+++++ i
  gi|298676068|ref|YP_003727818.1| 140 G--LAEYpHSLLIIPFSFISGFLFACLGMCFTAISPNINTlTYP-SILFITPMFLFSGTFFPLSLLPQILQYLAYaI 213
                                       9..88888*****************************9662555.44555557777777788**********87759 PP

                   ABC2_membrane_3 304 iPffapglgllrlitgdplweillsliilalfavvyllla 343
                                       +P++++ + + +l tg   + +l ++i+ a+ ++++++l+
  gi|298676068|ref|YP_003727818.1| 214 LPLTHIVMIIRSLTTGSLDIIMLGNFIWIAAASLILFVLS 253
                                       9*********9999999333455***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:01.80
# Mc/sec: 441.62
//
Query:       gi|298676069|ref|YP_003727819.1|  [L=306]
Description: ABC transporter-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.7e-33  115.0   0.0    7.4e-33  114.0   0.0    1.5  2  ABC_tran    ABC transporter
    3.8e-15   56.5   0.0    8.1e-08   32.4   0.0    2.2  2  AAA_21      AAA domain, putative AbiEii toxin, Type IV TA sys
    7.4e-07   29.2   0.9     0.0011   18.7   0.1    2.5  3  AAA_15      AAA ATPase domain
    5.2e-05   22.8   0.1    0.00056   19.4   0.1    2.1  1  SMC_N       RecF/RecN/SMC N terminal domain
    0.00023   21.8   0.2    0.00093   19.9   0.1    2.0  2  DUF4162     Domain of unknown function (DUF4162)
    0.00046   20.8   1.1    0.00074   20.1   0.4    1.7  2  AAA_23      AAA domain
  ------ inclusion threshold ------
      0.044   14.2   0.9        1.4    9.4   0.4    3.1  2  AAA         ATPase family associated with various cellular ac
      0.044   13.5   0.0        0.1   12.3   0.0    1.5  2  AAA_30      AAA domain
      0.056   13.2   0.1        2.3    7.9   0.0    2.4  2  ATP_bind_1  Conserved hypothetical ATP binding protein
      0.065   11.9   0.0      0.096   11.3   0.0    1.2  1  AAA_13      AAA domain
       0.11   12.2   0.1        9.8    5.9   0.0    2.3  2  IstB_IS21   IstB-like ATP binding protein


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.0   0.0   4.5e-36   7.4e-33       2     136 ..      25     167 ..      24     168 .. 0.96
   2 ?   -2.7   0.0       4.7   7.7e+03      68      76 ..     256     264 ..     209     293 .. 0.55

  Alignments for each domain:
  == domain 1  score: 114.0 bits;  conditional E-value: 4.5e-36
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       + ++++++++e+ +++G+nGaGK+t ++++   + ++ G++++ g d+++   ++ +k+igv+pqe++l+p+ tv+e
  gi|298676069|ref|YP_003727819.1|  25 DGINFTVEKSEVFGFLGPNGAGKTTAMRMIQCVSPKDDGKLEVFGMDVNT-HQKEIKKNIGVVPQENNLDPDFTVYE 100
                                       789**********************************************9.9999********************** PP

                                       H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n             es+e+++ +l+ ++l+e+kd      ++ LSgG+k+r+ laral+++p+ll+lDEpt
  gi|298676069|ref|YP_003727819.1| 101 NlfvysryfdipkkESKERVNSLLEFVQLEEKKDVM----TYMLSGGMKRRLILARALVNNPSLLILDEPT 167
                                       *************999999************55555....59****************************9 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.7
                                       --S-TTSBH CS
                                       xxxxxxxxx RF
                          ABC_tran  68 pqlfpeltv 76 
                                       ++l++++++
  gi|298676069|ref|YP_003727819.1| 256 ETLDSTVQI 264
                                       233333333 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   5.1e-08   8.3e-05       2      95 ..      37     116 ..      36     134 .. 0.85
   2 !   32.4   0.0     5e-11   8.1e-08     231     298 ..     134     198 ..     111     201 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 5.1e-08
                            AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrl 78 
                                        ++ GpNg+GK++ ++ ++++              s++ + +   +  d +   ++++  i  ++ q+++ +  +++
  gi|298676069|ref|YP_003727819.1|  37 FGFLGPNGAGKTTAMRMIQCV--------------SPKDDGKLEVFGMDVNTHQKEIKKNIG-VVPQENNLDPDFTV 98 
                                       5789****************9..............7899***********************.************** PP

                            AAA_21  79 ersqv.eeklssvetlle 95 
                                       +++ + + + ++ +++++
  gi|298676069|ref|YP_003727819.1|  99 YENLFvYSRYFDIPKKES 116
                                       *****6444444444333 PP

  == domain 2  score: 32.4 bits;  conditional E-value: 5e-11
                            AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                       ++  + lS G+kr l l+ al   +   sll++DEp  gL+P++ + l+e ++ l++ ++ ++ltTH 
  gi|298676069|ref|YP_003727819.1| 134 DVMTYMLSGGMKRRLILARALVNNP---SLLILDEPTVGLDPQARHLLWEKIRGLKKQNVTIVLTTHY 198
                                       5555779*******55555555555...9***********************8888889********6 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   0.00038      0.62      23      50 ..      35      61 ..      27      96 .. 0.68
   2 !   18.7   0.1   6.9e-07    0.0011     245     364 ..      75     197 ..      60     198 .. 0.81
   3 ?   -2.4   0.1       1.8   2.9e+03     191     217 ..     250     276 ..     224     292 .. 0.49

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00038
                            AAA_15 23 eeltvliGkNnsGKSsilealdlFlnnk 50
                                      e +  + G+N++GK++++++++    ++
  gi|298676069|ref|YP_003727819.1| 35 E-VFGFLGPNGAGKTTAMRMIQCVSPKD 61
                                      4.77799**************9877644 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 6.9e-07
                            AAA_15 245 iqeklkeidkklaeelk.....kilkkkidkikkfnykgkkneeieik........ddeelplnknGsGvqrlllli 308
                                        q+++k+ ++ + +e +      ++++ +  + +f +++k++ e+ ++        ++ ++  ++ + G++r l l+
  gi|298676069|ref|YP_003727819.1|  75 HQKEIKKNIGVVPQENNldpdfTVYENLFVYSRYFDIPKKESKERVNSllefvqleEKKDVMTYMLSGGMKRRLILA 151
                                       34444444444444444888888888888888899999999999998899999999****************98776 PP

                            AAA_15 309 llileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                         +++  +         +l+++EP + L pqa   l+++++ l ++n   +++tTH
  gi|298676069|ref|YP_003727819.1| 152 RALVN--NP-------SLLILDEPTVGLDPQARHLLWEKIRGLKKQNV-TIVLTTH 197
                                       55544..33.......77*****************************7.9****** PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.8
                            AAA_15 191 ksaiiklllisakRnvsdedsekkssl 217
                                       k  i +  l+s ++ +++e ++ ++ l
  gi|298676069|ref|YP_003727819.1| 250 KTDINYETLDSTVQIYTNEPKDISDRL 276
                                       222333333333333333333333333 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   3.5e-07   0.00056      29     205 ..      39     202 ..      27     214 .. 0.67

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 3.5e-07
                                       EEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEET CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  29 ivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvkr 105
                                        +GpNG+GK+  +  i+ v   ++  kl    ++   h+  ++ +    ++ ++ + e++     ++++++  +++ 
  gi|298676069|ref|YP_003727819.1|  39 FLGPNGAGKTTAMRMIQCVSP-KDDGKLEVFGMDVNTHQ--KEIKK---NIGVVPQ-ENNL----DPDFTVYENLFV 104
                                       579999999999999965555.44447777666644443..33333...3444322.2332....455666666666 PP

                                       TSEEEEEETTEEE-HHHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 106 kgeseykingkevtkkevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknv 176
                                         +  + i  k+ +k+ v++lle ++++++      +LSgG k      L++A   v+  +l +lDe    LD + +
  gi|298676069|ref|YP_003727819.1| 105 YSR-YFDIP-KKESKERVNSLLEFVQLEEKkdvmtyMLSGGMKR----RLILARALVNNPSLLILDEPTVGLDPQAR 175
                                       555.33443.33445566666666666665566666*****997....89999999********************* PP

                                       HHHHHHHHHHCTTSEEEEE-SSHHHCCC- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 177 kkvaellkeksknaQfivislreemleka 205
                                       + + e ++  +k+   i   l+++ le+a
  gi|298676069|ref|YP_003727819.1| 176 HLLWEKIRGLKKQNVTI--VLTTHYLEEA 202
                                       ********999555444..4555555554 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       2.7   4.5e+03      25      56 ..     121     152 ..     106     157 .. 0.63
   2 !   19.9   0.1   5.7e-07   0.00093       1      81 []     221     300 ..     221     300 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.7
                                       -..---EEEE-TTS-EEEEE------------ CS
                           DUF4162  25 leepgveeveeeggelelkledeeaanellka 56 
                                       +++ ++ ++ee+++ ++  l+++ +++ +l++
  gi|298676069|ref|YP_003727819.1| 121 NSLLEFVQLEEKKDVMTYMLSGGMKRRLILAR 152
                                       33344555666667777777777777777766 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 5.7e-07
                                       E-HHHHHTTS.-SSEEEEE-------..---EEEE-TTS-EEEEE-----------------EEEEEEEE---HHHH CS
                           DUF4162   1 GtleeiKrsy.gknrieveadaeelleepgveeveeeggelelkledeeaanellkaltsgveirsFeeeePsLndI 76 
                                       G++++i ++y g++ +ev +  + + +  + ++++ e+ + ++++ + + ++++ ++l++ +e ++++++ ++L+d+
  gi|298676069|ref|YP_003727819.1| 221 GDPDDIVKKYiGSDVVEVDNT-KPVISCLNKTDINYETLDSTVQIYT-NEPKDISDRLMKECEFEKITVRSATLEDV 295
                                       667777777768888888833.2233333445554444334444443.579************************** PP

                                       HHHHH CS
                           DUF4162  77 Fiekv 81 
                                       F++++
  gi|298676069|ref|YP_003727819.1| 296 FLKLT 300
                                       **975 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.4   4.6e-07   0.00074      15      40 ..      27      55 ..      16     136 .. 0.82
   2 ?   -3.2   0.0         6   9.7e+03     146     148 ..     256     258 ..     214     293 .. 0.53

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.6e-07
                            AAA_23 15 idF...skgltlItGpNGaGKTTildAik 40
                                      i+F   ++ ++ + GpNGaGKTT ++ i+
  gi|298676069|ref|YP_003727819.1| 27 INFtveKSEVFGFLGPNGAGKTTAMRMIQ 55
                                      888888889****************9987 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6
                            AAA_23 146 fel 148
                                       + l
  gi|298676069|ref|YP_003727819.1| 256 ETL 258
                                       222 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.4   0.00083       1.4       3     111 ..      39     198 ..      37     211 .. 0.57
   2 ?   -0.9   0.0       1.3   2.1e+03     104     125 ..     261     281 ..     224     288 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00083
                                       EESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSS..................................... CS
                               AAA   3 lyGppGtGKTllakavakel.....gvefleisgsellsk..................................... 37 
                                       + Gp G GKT++++ +   +     + e++ +++ +  ++                                     
  gi|298676069|ref|YP_003727819.1|  39 FLGPNGAGKTTAMRMIQCVSpkddgKLEVFGMDVNTHQKEikknigvvpqennldpdftvyenlfvysryfdipkke 115
                                       68**********99997765444332333333333332223334444444444444444444444444444444444 PP

                                       ......................STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHH CS
                               AAA  38 ......................yvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlte 92 
                                                             y+  + +k r ++++a  ++ ps l++DE       +          +   L ++
  gi|298676069|ref|YP_003727819.1| 116 skervnsllefvqleekkdvmtYMLSGGMKRRLILARALVNN-PSLLILDEPTVGLDPQ----------ARHLLWEK 181
                                       444455555555555555555577788888888887777776.8888888865555444..........45566666 PP

                                       HHHTTTSSSTEEEEEEESS CS
                               AAA  93 ldgvkkkeskvivigatnr 111
                                       + g+kk  ++v+++++t++
  gi|298676069|ref|YP_003727819.1| 182 IRGLKK--QNVTIVLTTHY 198
                                       666666..35666666665 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.3
                                       EEEEEESSGGGSTHHHHSTTSS CS
                               AAA 104 ivigatnrpdkldpallrgRfd 125
                                       +v + tn+p+++++ l+ + ++
  gi|298676069|ref|YP_003727819.1| 261 TVQIYTNEPKDISDRLM-KECE 281
                                       66778999999999999.4443 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.2e-05       0.1      17      51 ..      33      67 ..      27     100 .. 0.77
   2 ?   -2.7   0.0       2.5     4e+03      82      99 ..     151     168 ..     113     186 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.2e-05
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaweaaggrvig 51
                                      +  v    Gp G+GKtta++ ++ +  ++ g++ +
  gi|298676069|ref|YP_003727819.1| 33 KSEVFGFLGPNGAGKTTAMRMIQCVSPKDDGKLEV 67
                                      44577889*************99888777544444 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.5
                            AAA_30  82 grarlepgtllivDEagm 99 
                                       +ra +++ +lli DE  +
  gi|298676069|ref|YP_003727819.1| 151 ARALVNNPSLLILDEPTV 168
                                       445556668888888655 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0014       2.3       2      33 ..      40      71 ..      39      94 .. 0.86
   2 ?    3.0   0.0     0.045        73     151     191 ..     236     277 ..     194     299 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0014
                        ATP_bind_1  2 vGpaGsGKttfvgalseilelrgrsvavvNLD 33
                                      +Gp G+GKtt ++ ++ + ++   +++v  +D
  gi|298676069|ref|YP_003727819.1| 40 LGPNGAGKTTAMRMIQCVSPKDDGKLEVFGMD 71
                                      7*************999999888888777777 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.045
                        ATP_bind_1 151 amlrlelPhvvvlnkfDllkeklekeleffe.dvealsllle 191
                                       + +    P + +lnk+D+  e l+  ++ ++ +++++s  l 
  gi|298676069|ref|YP_003727819.1| 236 VEVDNTKPVISCLNKTDINYETLDSTVQIYTnEPKDISDRLM 277
                                       56677789**********877777777666515666655544 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   5.9e-05     0.096      23      73 ..      41     106 ..      35     127 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.9e-05
                            AAA_13  23 GwNGaGKTtLSrllrslelgetepkfangsi....eitnge..............eldirVfNrdFvee 73 
                                       G NGaGKTt  r++++++ +    k++   +    +++++e               +d  V+ + Fv +
  gi|298676069|ref|YP_003727819.1|  41 GPNGAGKTTAMRMIQCVSPKDD-GKLEV--FgmdvNTHQKEikknigvvpqennlDPDFTVYENLFVYS 106
                                       99**************965442.23322..244553333334455566777777755555555555433 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0      0.02        33      44      61 ..      31      48 ..      10      57 .. 0.79
   2 ?    5.9   0.0     0.006       9.8     105     147 ..     154     195 ..     119     205 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.02
                         IstB_IS21 44 iekkenivllGpsGvGKs 61
                                      +ek+e + +lGp G+GK+
  gi|298676069|ref|YP_003727819.1| 31 VEKSEVFGFLGPNGAGKT 48
                                      67889999*********9 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.006
                         IstB_IS21 105 rllkvdllilDdlgllpldqaeaellfeviekryerrsiiits 147
                                        + +++llilD+  ++ ld ++++ll+e i    +++ +i+ +
  gi|298676069|ref|YP_003727819.1| 154 LVNNPSLLILDEP-TVGLDPQARHLLWEKIRGLKKQNVTIVLT 195
                                       455679******7.5689**********999887776655433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 1908.62
//
Query:       gi|298676070|ref|YP_003727820.1|  [L=121]
Description: hypothetical protein Metev_2198 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.4e-32  111.8   0.8    1.7e-32  111.6   0.8    1.1  1  FeThRed_B  Ferredoxin thioredoxin reductase catalytic beta ch


Domain annotation for each model (and alignments):
>> FeThRed_B  Ferredoxin thioredoxin reductase catalytic beta chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.6   0.8   9.7e-37   1.7e-32       3     105 ..      12     113 ..      10     114 .. 0.97

  Alignments for each domain:
  == domain 1  score: 111.6 bits;  conditional E-value: 9.7e-37
                                       HHHHHHHHHHHHHTT-B-BSSHHHHHHHHHHHHHHHHHHSS-B-SSC--S-HHHHHHH-TTBSS-HH.HHHH....- CS
                         FeThRed_B   3 ektrkflekvakklgtkfnpdeevtevvieglarnkeeyGkrlCPCrlvedkeeeekkavwnCPCvp.lreeldeek 78 
                                       +k+r+++++v++ lg+kf+pdee++++++e+++++++e+G+++CPC+++ +++ee++k v  CPC+p +r+++d +k
  gi|298676070|ref|YP_003727820.1|  12 NKLRELFTRVVDPLGYKFSPDEELVDFLLEQEVMTEREKGAPYCPCQALPGNREEDMKLV--CPCIPfNRKHFDIMK 86 
                                       6899********************************************************..*************** PP

                                       --TTSSSB-TTSTTB-S-S---HHHHH CS
                         FeThRed_B  79 eChCglfvtkdnaeekeeqeisleeik 105
                                       +C+Cglfv+kd+++ ++ ++is +e++
  gi|298676070|ref|YP_003727820.1|  87 RCWCGLFVHKDVTDPDKLEQISPKELE 113
                                       **********************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 872.64
//
Query:       gi|298676071|ref|YP_003727821.1|  [L=85]
Description: glutaredoxin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-14   53.9   0.2    2.2e-14   53.4   0.2    1.2  1  Glutaredoxin   Glutaredoxin
    3.2e-05   24.1   0.1    3.9e-05   23.9   0.1    1.1  1  DUF1462        Protein of unknown function (DUF1462)
     0.0013   18.9   0.6        0.6   10.3   0.0    2.0  2  Thioredoxin_4  Thioredoxin
     0.0055   17.1   0.0     0.0068   16.8   0.0    1.1  1  GST_N_3        Glutathione S-transferase, N-terminal domain
      0.006   16.7   0.1     0.0065   16.6   0.1    1.1  1  SH3BGR         SH3-binding, glutamic acid-rich protein
     0.0066   16.5   0.2      0.011   15.7   0.2    1.4  1  Thioredoxin_3  Thioredoxin domain
  ------ inclusion threshold ------
      0.032   14.7   1.1      0.094   13.2   1.1    1.6  1  Thioredoxin_2  Thioredoxin-like domain


Domain annotation for each model (and alignments):
>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.2   8.5e-18   2.2e-14       1      60 []       4      69 ..       4      69 .. 0.92

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 8.5e-18
                                      EEEEESTSSHHHHHHHHHHHHTTGGEEEEEGCCSH......HHHHHHHHHHTSSSSSEEEETTEEE CS
                      Glutaredoxin  1 vvlftkptCpyCkkakrlLkelgvkfeeidvdkde......eireelkelsgvrtvPqvfidgkhv 60
                                      v+++t +tCp+Ckk+k+++++++++++++d+dk +       i ee+k+ +g  + P v i+++++
  gi|298676071|ref|YP_003727821.1|  4 VFMYTLSTCPWCKKTKKFFEKRKIPYDYVDIDKLKdenekeRIIEEMKREAGSTATPFVIIGDEVI 69
                                      799*****************************9977777777888888888************987 PP

>> DUF1462  Protein of unknown function (DUF1462)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.1   1.5e-08   3.9e-05      30      80 ..      19      71 ..       8      80 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.5e-08
                           DUF1462 30 krkypeqkleleyvDieeekeeeekkefaekiled..elfyPlvviedevvae 80
                                      k+ ++++k+ ++yvDi++ k+e+ek++++e+++ +      P v+i dev+  
  gi|298676071|ref|YP_003727821.1| 19 KKFFEKRKIPYDYVDIDKLKDENEKERIIEEMKREagSTATPFVIIGDEVIIG 71
                                      5568899*************************988335789********9865 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.3     0.001       2.6      17      49 ..       4      38 ..       2      40 .. 0.85
   2 !   10.3   0.0   0.00023       0.6     124     155 ..      41      73 ..      34      83 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.001
                                      EEEEE-TT-HHHHHHHHHHH..HHHHHHHHTTSEE CS
                     Thioredoxin_4 17 vieyedlrCphCakfeeeve..klleeyidtGkvk 49
                                      v  y+  +Cp C+k ++  e  k+  +y+d +k+k
  gi|298676071|ref|YP_003727821.1|  4 VFMYTLSTCPWCKKTKKFFEkrKIPYDYVDIDKLK 38
                                      6789999*******999987678999999988876 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00023
                                       HHHHHHHHHH.HHHT--SS-EEEETTEEE-TT- CS
                     Thioredoxin_4 124 alveaeskea.kkagiestPtfiingekveepq 155
                                       ++ e+  +e+ ++ag ++tP +ii++e++ +++
  gi|298676071|ref|YP_003727821.1|  41 NEKERIIEEMkREAGSTATPFVIIGDEVIIGYK 73 
                                       55566778888999**************85332 PP

>> GST_N_3  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.7e-06    0.0068       2      57 ..       7      69 ..       6      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.7e-06
                                      ES-TTSHHHHHHHHHHHHHT--EEEE---......TTTT.HHHHHHH-TT--SSEEETTS-EE CS
                           GST_N_3  2 ygfpaSpyarrvrlaLnekglpvevvevt......pgeh.deellaknplgkvPvLeddgeal 57
                                      y   ++p++++ + + + +++p+ +v+++      ++e+  ee++++ +    P+  +++e++
  gi|298676071|ref|YP_003727821.1|  7 YTLSTCPWCKKTKKFFEKRKIPYDYVDIDklkdenEKERiIEEMKREAGSTATPFVIIGDEVI 69
                                      78899***********************97766554444689999999999999999888876 PP

>> SH3BGR  SH3-binding, glutamic acid-rich protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   2.6e-06    0.0065      22      68 ..      17      61 ..       2      77 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.6e-06
                                      HHHHHHHHTT--EEEEETTT..-HHHHHHHHHCST-CCCS-SSSS--S- CS
                            SH3BGR 22 evlriLdakkiefdevDitk..deeerelmrenaapeekkpengkplPP 68
                                      ++ ++ + +ki++d vDi k  de+e+e + e+     k+ + ++++P 
  gi|298676071|ref|YP_003727821.1| 17 KTKKFFEKRKIPYDYVDIDKlkDENEKERIIEEM----KREAGSTATPF 61
                                      45689*************9986666666655554....33333334443 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   4.4e-06     0.011       8      61 ..      10      70 ..       3      81 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.4e-06
                                      SSSTTCHHHHHHHHHHCHCCT.CEC.....EEECCTTHHHH.HHCT-SSSSEEECTTCEEE CS
                     Thioredoxin_3  8 pgCakCpklekavkeaaaekg.ika.....evekvtdfeei.ekygVmsvPalvidgkvvv 61
                                      ++C+ C+k++k++++     + +++     e ek   +ee+  + g +++P ++i ++v +
  gi|298676071|ref|YP_003727821.1| 10 STCPWCKKTKKFFEKRKIPYDyVDIdklkdENEKERIIEEMkREAGSTATPFVIIGDEVII 70
                                      67***********985433332666667779999999****9*************998864 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.1   3.7e-05     0.094       9     104 ..       4      76 ..       2      81 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.7e-05
                     Thioredoxin_2   9 lvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelark.ygvrgtPti 84 
                                       ++++t ++Cp Ckk kk +++               ++   +v+i++ k+++    ++e+  e +++  g ++tP +
  gi|298676071|ref|YP_003727821.1|   4 VFMYTLSTCPWCKKTKKFFEKR--------------KIPYDYVDIDKLKDEN----EKERIIEEMKReAGSTATPFV 62 
                                       7889999*******99977777..............3455678888888887....446666666664799999999 PP

                     Thioredoxin_2  85 vfldgkeivarlpGyvpaee 104
                                       ++ d+      + Gy p+ +
  gi|298676071|ref|YP_003727821.1|  63 IIGDEV-----IIGYKPK-K 76 
                                       999998.....7788654.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       904  (0.0504211); expected 358.6 (0.02)
Passed bias filter:                      638  (0.0355848); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 558.44
//
Query:       gi|298676072|ref|YP_003727822.1|  [L=106]
Description: rieske (2Fe-2S) iron-sulfur domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-17   63.9   0.0    1.2e-17   63.6   0.0    1.1  1  Rieske    Rieske [2Fe-2S] domain
    6.6e-13   48.5   0.0    7.8e-13   48.3   0.0    1.1  1  Rieske_2  Rieske-like [2Fe-2S] domain


Domain annotation for each model (and alignments):
>> Rieske  Rieske [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.6   0.0   1.3e-21   1.2e-17       1      81 [.       4      83 ..       4      90 .. 0.92

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 1.3e-21
                                      CEEEEEEGGGC-TTCEEEEEETTEEEEEEE-TTS-EEEEESC-TTTT-BCGGSEEETT.EEE-TTT--EEE.TTSBEEE CS
                            Rieske  1 swvavakesdvpegdpltvkvggeplvvlrdedgevyAlsdvCtHrgaplsegkidekgvleCpcHgwayd.adGkvik 78
                                      swv +  es +++++ +++k+ g+ +++++  d e+yAls+ C H+++ ls+g++ e+ +++CpcH w++d ++G+ ++
  gi|298676072|ref|YP_003727822.1|  4 SWVFAIDESSLQDNSLKGIKLEGNLILLVK-IDREIYALSNKCAHMECLLSKGSL-EGYTVKCPCHDWKFDvRTGEFVT 80
                                      5999999***********************.6***********************.899*****************998 PP

                                      -TT CS
                            Rieske 79 gPa 81
                                      +  
  gi|298676072|ref|YP_003727822.1| 81 ANE 83
                                      755 PP

>> Rieske_2  Rieske-like [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.0   8.7e-17   7.8e-13       2     103 ..       5     100 ..       4     101 .. 0.93

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 8.7e-17
                                       EEEEEECCCS-TTB-EEEEETTEEEEEEE-TTS-EEEEESS-TTTSSSTCCCSEEEECTTCEEEE-TTT--EEETTT CS
                          Rieske_2   2 wvpvckledlvketgvaalvdgkqvalfrlekeevyAidnldpaseanvlsrGlvgdkkgelvvasPlykqkfdLkt 78 
                                       wv  +  + l  ++ +   ++g+ ++l+ + + e+yA++n++    +  ls+G ++     ++v++P ++ kfd +t
  gi|298676072|ref|YP_003727822.1|   5 WVFAIDESSLQDNSLKGIKLEGNLILLVKI-DREIYALSNKCAH-MECLLSKGSLEG----YTVKCPCHDWKFDVRT 75 
                                       88889999999999999999***9999999.99*********99.6999****9865....6*************** PP

                                       -BBSS-TTSB-BEE-EEESTSEEEE CS
                          Rieske_2  79 Gecledeevslkvypvrvedgkvev 103
                                       Ge + ++e+++++y++++++g+++v
  gi|298676072|ref|YP_003727822.1|  76 GEFVTANEIKIPTYQTKISEGSIYV 100
                                       ***********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 810.86
//
Query:       gi|298676073|ref|YP_003727823.1|  [L=327]
Description: hypothetical protein Metev_2201 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-98  329.3   3.6    3.6e-97  325.2   3.6    2.0  1  DUF3179   Protein of unknown function (DUF3179)


Domain annotation for each model (and alignments):
>> DUF3179  Protein of unknown function (DUF3179)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  325.2   3.6    2e-101   3.6e-97       1     285 []      65     322 ..      65     322 .. 0.95

  Alignments for each domain:
  == domain 1  score: 325.2 bits;  conditional E-value: 2e-101
                           DUF3179   1 kDgIPaidnPefasaeeasksldddepVigvelngearaYPlrilvwheiVNdtlggepvavTYCpLcgtalaferr 77 
                                       kDgIP+id+P++++++ea+++l+dde V+++++ng+ ++YPl+i+vwheiVNd+++++pv +TYCpLcg++lafer+
  gi|298676073|ref|YP_003727823.1|  65 KDGIPSIDSPTYNTVDEADRYLSDDELVMALNYNGKKQVYPLQIMVWHEIVNDNINNQPVLITYCPLCGSTLAFERK 141
                                       7**************************************************************************** PP

                           DUF3179  78 idggelefgvsGkLvnsnlvmyDreteslwqQllgeaiaGklegteLeelpvvtttwekwkeahpdtkVlseetgss 154
                                       ++g+e+efg+sGkL+nsnlvmyDr+t+++w Ql+g+ai+G+l+g+eL+ +++ t+ w++wk++hpd++Vls++tg +
  gi|298676073|ref|YP_003727823.1| 142 VQGDEVEFGTSGKLYNSNLVMYDRKTDTYWAQLTGQAIVGELTGEELTPISIDTVYWGDWKRSHPDSQVLSRDTGAR 218
                                       ***************************************************************************** PP

                           DUF3179 155 rdYgrdPygsyepasdrplfpvekrddrlppkerVvgvevgddavaypkaelkeegvvedtvgdkevvvvldadaes 231
                                       r+Yg+dPy++y+ +++++lfpve+rd+r++pk++V+g++v+d  +ay++++lk++g+++d+v ++++ +        
  gi|298676073|ref|YP_003727823.1| 219 RPYGEDPYTGYY-NDSSLLFPVENRDNRIHPKTVVFGIKVNDSFKAYQEDDLKNQGTISDNVSGTDIEIE------- 287
                                       ************.8889****************************************************1....... PP

                           DUF3179 232 aldakrvvldeesgtlwdlangealdgklkgarlervaaaeafWFawaaFhpet 285
                                                d+   ++++l+            + e++ ++++fWFaw+aFhpet
  gi|298676073|ref|YP_003727823.1| 288 -------RNDTGIVSVTNLD------------TGEKIIKVRTFWFAWYAFHPET 322
                                       .......2233343333433............5699****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2123.77
//
Query:       gi|298676074|ref|YP_003727824.1|  [L=238]
Description: 3,4-dihydroxy-2-butanone 4-phosphate synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.1e-58  195.5   0.0    7.5e-58  195.2   0.0    1.1  1  DHBP_synthase  3,4-dihydroxy-2-butanone 4-phosphate synthase


Domain annotation for each model (and alignments):
>> DHBP_synthase  3,4-dihydroxy-2-butanone 4-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.2   0.0   4.2e-62   7.5e-58       2     191 ..      13     231 ..      12     232 .. 0.92

  Alignments for each domain:
  == domain 1  score: 195.2 bits;  conditional E-value: 4.2e-62
                                       HHHHHHHTT--EEEESSTTTT-BEEEEEEGGG--HHHHHHHHHHB-S--EEEEEHHHHHHTT--BSSSS-S...... CS
                     DHBP_synthase   2 eaiealkaGkfvivvDdedrenegdLiiaAekvtpekvafmirhasGlicvalteeradeLeLplmveene...... 72 
                                       ++i+a k+G++ +++D+e re+e+dL ++A+++tp++v++m+++++Glic+a++ +  ++++Lp+m++         
  gi|298676074|ref|YP_003727824.1|  13 KVIDAAKNGQMFLLYDSEGREGETDLTVPATSITPADVKWMRKDGGGLICTAIDFRASNNFGLPFMAD--Vlkeasr 87 
                                       6899***************************************************************7..2335567 PP

                                       ................STT---BB--EEESST-SSS-SHHHHHHHHHHHH-T............T--GGGEEEEEEE CS
                     DHBP_synthase  73 ................dkhktaftvsvdaaegttTGIsaaDRalTirkladp............kakpedfrrPGhv 121
                                                          +++f+++v+++ +t+TGI ++DR+lTi+kl ++            +   ++fr+PGhv
  gi|298676074|ref|YP_003727824.1|  88 tnnslksiveqsgdleYDTRSSFSLWVNHR-DTRTGIPDNDRSLTINKLGEAvqktingedfdfG---AEFRSPGHV 160
                                       7788*********9994568**********.9*******************76677777665332...89******* PP

                                       EEEEE-TTGGGTS-SHHHHHHHHHHHTTS-SBEEEEEBB-TT.SCB-BHHHHHHHHHHHT-EEEEHHHHHH CS
                     DHBP_synthase 122 fplrareggvleRrghTEaavdLarlaglkpaavicellndd.gtmarrdeleefakkhglkiitiedlie 191
                                        +l+a+eg v++R g+TE+++++a+++g++pa v+ce+l+d+ g+++++d+++e+a+kh+l +++++d++e
  gi|298676074|ref|YP_003727824.1| 161 AILKAAEGEVNKRMGQTELSIAIANMSGITPAMVVCEMLDDNnGKALSKDDAMEYARKHNLVFVEGKDILE 231
                                       *******************************99******999899***********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1586.39
//
Query:       gi|298676075|ref|YP_003727825.1|  [L=224]
Description: CTP-dependent riboflavin kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.5e-47  158.4   0.0    1.2e-46  157.7   0.0    1.4  1  CTP-dep_RFKase  Domain of unknown function DUF120
     0.0034   17.3   0.1     0.0064   16.4   0.1    1.5  1  MarR            MarR family
  ------ inclusion threshold ------
      0.021   14.8   0.1       0.05   13.6   0.1    1.7  1  HTH_Crp_2       Crp-like helix-turn-helix domain
       0.14   11.8   0.7       0.23   11.1   0.1    1.5  2  YscJ_FliF       Secretory protein of YscJ/FliF family


Domain annotation for each model (and alignments):
>> CTP-dep_RFKase  Domain of unknown function DUF120
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.7   0.0   2.8e-50   1.2e-46       1     119 [.      96     214 ..      96     216 .. 0.99

  Alignments for each domain:
  == domain 1  score: 157.7 bits;  conditional E-value: 2.8e-50
                                       EE--SSHHHHHHCSHHHHHHHHHHHSS---SS-EEEEESCCGHHHHCHHHHS--EEE--EEETTEEE--EEEEEEEE CS
                    CTP-dep_RFKase   1 VvsGlgeGkyyvslegykeqfeeklgfepypGTLNvkldeeslelrkaleklkgieiegfedeertfgavkvypaki 77 
                                       Vv+GlgeGkyy++l+gyk+qfe+kl+f+pypGTLNv l + s ++r++le+l +++i+gf+d+ertfg+ k+y+a i
  gi|298676075|ref|YP_003727825.1|  96 VVNGLGEGKYYINLDGYKKQFENKLNFTPYPGTLNVCLANYSKHTREKLEELPATQINGFTDGERTFGSGKCYKAII 172
                                       89*************************************************************************** PP

                                       CCEEEEEEEESS-SS.TTEEEEE-SS-HHHHTT--TT-EEEE CS
                    CTP-dep_RFKase  78 ekikaavvvperthyeedvlEiiapekLReklelkdgdevev 119
                                       e+i++a+++p+r+hy++d+lEiia+++LR+kl+l+dgd v++
  gi|298676075|ref|YP_003727825.1| 173 EDIECAIILPSRSHYPSDLLEIIASVNLRKKLNLNDGDDVKI 214
                                       ****************************************99 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   1.4e-06    0.0064      14      50 ..      19      55 ..       7      59 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.4e-06
                                      HSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR 14 eqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      e   +s se  ++++ s+ t+ r+l++L +++li+R+
  gi|298676075|ref|YP_003727825.1| 19 ECIKISSSEFTEHISSSSKTAARILKKLDDENLINRE 55
                                      55668889****************************7 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.1e-05      0.05      20      54 ..      21      55 ..       8      74 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.1e-05
                                      EEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEET CS
                         HTH_Crp_2 20 lpltqeelAsmlGltretvsrilseLkreglisrg 54
                                      ++++  e  +++ ++  t  ril++L +e+li r+
  gi|298676075|ref|YP_003727825.1| 21 IKISSSEFTEHISSSSKTAARILKKLDDENLINRE 55
                                      7889999999**********************953 PP

>> YscJ_FliF  Secretory protein of YscJ/FliF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   5.2e-05      0.23      29      71 ..      35      78 ..      23      81 .. 0.90
   2 ?   -2.7   0.0      0.87   3.9e+03      23      47 ..     199     223 ..     195     223 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.2e-05
                         YscJ_FliF 29 sekdaaeivekLdeeg.ipyklsddggtilVpedqvsearlkla 71
                                      s+k aa+i++kLd+e+ i+ ++ +dg+ i+V e+ ++++r + a
  gi|298676075|ref|YP_003727825.1| 35 SSKTAARILKKLDDENlINREIVQDGQLITVTEQGLKKLRDEYA 78
                                      7899********999979*****************999997765 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.87
                         YscJ_FliF  23 vLysnlsekdaaeivekLdeegipy 47 
                                        L ++l+ +d  +++  L++++ +y
  gi|298676075|ref|YP_003727825.1| 199 NLRKKLNLNDGDDVKILLKQNNHKY 223
                                       6778888899999999999998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1571.02
//
Query:       gi|298676076|ref|YP_003727826.1|  [L=226]
Description: fibrillarin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.9e-86  287.0   0.1    7.6e-86  286.9   0.1    1.0  1  Fibrillarin  Fibrillarin


Domain annotation for each model (and alignments):
>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  286.9   0.1   4.2e-90   7.6e-86       3     224 ..       3     225 ..       1     226 [] 0.96

  Alignments for each domain:
  == domain 1  score: 286.9 bits;  conditional E-value: 4.2e-90
                                       EECSSTTEEEEETTSSEEEEEE-SSTT--SSSSEEEEETTEEEEEE-TTTSHHHHHHHTT-S--S--TTSEEEEEST CS
                       Fibrillarin   3 eheklegvyivkekgdarlatknlvpgekvYgEklikveeeEyRvWnpfrsKlaaailkglkelpikkgskvLYlGa 79 
                                        +e  +g++++++ ++++lat+nl+pg++vY+E l+ v++ EyR W+ +rsK++a++lk+ + +p++++skvLYlGa
  gi|298676076|ref|YP_003727826.1|   3 IKEISQGIFELSKGKKKQLATRNLNPGNSVYSEPLVVVDDVEYRRWDVHRSKFGAMVLKKFD-VPLSPESKVLYLGA 78 
                                       577899******778888******************************************98.9************* PP

                                       TTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHTTSTTEEEEES-TTSGGGGTTTS--EEEEEEESSSTTHHHH CS
                       Fibrillarin  80 asGttvsHvsDivgeegvvyavefsprvlrelievakkRknivPileDArkPekYralvekvDvifaDvaqpdqari 156
                                       asGttvsH+sDi + +g++yavefs+r++r+l+ +++kR+ni+P+l+DA +P++Y+++vekvDvif+Dv+qp+qa+i
  gi|298676076|ref|YP_003727826.1|  79 ASGTTVSHISDIAT-NGLIYAVEFSSRTMRDLVMLCEKRPNIIPVLADAGHPSHYSHIVEKVDVIFQDVSQPNQAEI 154
                                       ************99.************************************************************** PP

                                       HHHHHHHHEEEEEEEEEEEEHHHHHSSSSHHHHHHHHHHHHHH...TTEEEEEEEE-TTTSTTEEEEEEEE CS
                       Fibrillarin 157 laknaklflkeggyllisikarsidvtkepeevfkeeveklke...eglkvleqvklepyekdhalvvgky 224
                                       +akna++flk++g ll++ikarsid++++p+++fkeev+kl +    ++++l+  +lep ++dh+ ++++ 
  gi|298676076|ref|YP_003727826.1| 155 AAKNAEAFLKKDGFLLLAIKARSIDTVANPKKIFKEEVKKLTKdfaVEFEILKRSELEPNHEDHLGILARL 225
                                       *****************************************9955559*****************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1397.39
//
Query:       gi|298676077|ref|YP_003727827.1|  [L=327]
Description: pre-mRNA processing ribonucleoprotein,-binding domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-54  183.8   0.0    4.8e-54  183.3   0.0    1.2  1  Nop       snoRNA binding domain, fibrillarin


Domain annotation for each model (and alignments):
>> Nop  snoRNA binding domain, fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.3   0.0   2.7e-58   4.8e-54       2     229 ..     101     310 ..     100     313 .. 0.90

  Alignments for each domain:
  == domain 1  score: 183.3 bits;  conditional E-value: 2.7e-58
                                       HHHHHHHHHHHHHHHHHHHTTTSTCHHHHS-SHHHHHHHHHHCCCCHCCT.HHTT.HHHHHHHHHHHHCHHHH-SSS CS
                               Nop   2 ldeidkeintlhkrvrewYswhFpELeslvkdnleYakvvkligneredlekkeedeelakevimaakvtastsmga 78 
                                       ld+id+++n l++r+ ewY++ FpEL+ +   + + a+ v++ g ++++++        ++e + +a+     smga
  gi|298676077|ref|YP_003727827.1| 101 LDDIDETTNLLSERLSEWYGMFFPELNLT---SEDLAQFVAKHG-SKSNIT-------QDNEWYSIAND----SMGA 162
                                       79************************976...566788899999.789993.......35789999999....**** PP

                                       -S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHCHHHHHHHHHHHHSSHHHHHCS-HHHHTTTT- CS
                               Nop  79 elseedlknikelcdrvleleelrkelleYlesrmsaiAPNlsaLvGeevaarLishaGgLtnLakmPastiqilGa 155
                                       els ++ k ik+++ ++ +++++rke+++Y+ +++++ APNl+++ G+ +++rLis +G+L++La++P+stiq++Ga
  gi|298676077|ref|YP_003727827.1| 163 ELSGSEEKIIKDFAINLCSFYKNRKEIEDYIVENVEHAAPNLTNIAGALLGSRLISMTGSLERLASLPSSTIQVIGA 239
                                       ***************************************************************************** PP

                                       HHHHCCCHH.T---SSSCHHHCSHHHHHTS-CCCHHHHHHHHHHHHHHHHHHHHTT----SHHHHHHHHHHHHHH CS
                               Nop 156 ekalfralk.kkntpkyGliyhselvqkatppklkkkiaRllaaKvalaaRiDafsekdgslGkklreeiekklk 229
                                       + alf++l+ + ++pk+G+i++++l+++a p+++++kiaR+ a+K++laaRiD +s   g++ +kl  ++++k++
  gi|298676077|ref|YP_003727827.1| 240 NNALFKHLRsRATSPKHGVIFNHPLIKNA-PWWQRGKIARAFASKISLAARIDYYS---GEVNDKLSINLDEKIN 310
                                       *********7779**************66.***********************663...5555555555555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2086.88
//
Query:       gi|298676078|ref|YP_003727828.1|  [L=319]
Description: beta-ribofuranosylaminobenzene 5'-phosphate synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-08   33.6   0.0    9.4e-08   32.3   0.0    1.7  1  GHMP_kinases_C  GHMP kinases C terminal
    4.2e-07   30.1   1.9    5.5e-07   29.7   0.7    1.9  2  GHMP_kinases_N  GHMP kinases N terminal domain


Domain annotation for each model (and alignments):
>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0     1e-11   9.4e-08       2      83 ..     216     296 ..     215     298 .. 0.90

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 1e-11
                    GHMP_kinases_C   2 lealergdlellgellnlsqrs.elkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvar 77 
                                       ++a++++d++++g+++n +q    +k +++  ++ +++l++++ + Ga g ++s  ++Gp vf++ ++k + +++++
  gi|298676078|ref|YP_003727828.1| 216 IPAILENDIDTFGRGINHLQSTgFKKREIALQSEDIKNLIRFMNDTGAKGCGMS--SFGPDVFGFSDSKLQSKKIRE 290
                                       899**************99999*9999********************6666665..55******************* PP

                    GHMP_kinases_C  78 alreef 83 
                                        +++ +
  gi|298676078|ref|YP_003727828.1| 291 DVQSML 296
                                       998865 PP

>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0      0.98   8.8e+03       4      13 ..      63      72 ..      62      73 .. 0.86
   2 !   29.7   0.7   6.1e-11   5.5e-07       2      66 .]      75     135 ..      74     135 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.98
                                      EEESSHTTSS CS
                    GHMP_kinases_N  4 ikseiPvgaG 13
                                      +ks +P+g+G
  gi|298676078|ref|YP_003727828.1| 63 VKSVLPDGKG 72
                                      7999****99 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 6.1e-11
                                       EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                    GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglsleeaklaleaerlaqggngsggDvaasvyGg 66 
                                       ++i+ +iP++ GLGS++  a++++ A+++ ++l l   +   e  +++++g +sg+ va +  Gg
  gi|298676078|ref|YP_003727828.1|  75 LNIEDDIPPHVGLGSGTQSALSAASAVNEVYNLGL---D-VRELAEKVGRGGTSGIGVASFESGG 135
                                       78999**************************6333...1.333335568899******9998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2167.29
//
Query:       gi|298676079|ref|YP_003727829.1|  [L=201]
Description: hypothetical protein Metev_2207 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-10   39.1   0.0    1.5e-09   37.8   0.0    1.8  1  DUF2953   Protein of unknown function (DUF2953)


Domain annotation for each model (and alignments):
>> DUF2953  Protein of unknown function (DUF2953)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.0   8.2e-14   1.5e-09       1      52 [.     111     159 ..     111     160 .. 0.91

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 8.2e-14
                           DUF2953   1 leiGleDaadTgilyGliwaikgllygllsnlfni.kkpeievtPvFneevfe 52 
                                       l++G++D++ Tgi+yG++++++g++    +++ n   ++++ ++PvFn++ ++
  gi|298676079|ref|YP_003727829.1| 111 LTYGFSDPSETGIYYGFLCSVMGFI----DEKCNNnCDYRCTINPVFNDNLLK 159
                                       69**********************9....66666669*************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       984  (0.0548832); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1452.63
//
Query:       gi|298676080|ref|YP_003727830.1|  [L=81]
Description: Sporulation protein YtfJ, partial [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      3e-19   69.0   5.5    3.9e-19   68.6   5.5    1.2  1  Spore_YtfJ  Sporulation protein YtfJ (Spore_YtfJ)


Domain annotation for each model (and alignments):
>> Spore_YtfJ  Sporulation protein YtfJ (Spore_YtfJ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.6   5.5   2.2e-23   3.9e-19       6      54 ..      32      80 ..      28      81 .] 0.94

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 2.2e-23
                        Spore_YtfJ  6 gtviiPvskvsfGfgaGgsefkskkekepfgggsgaGvsitPvAfLvik 54
                                      g++iiPv++vsfGfg+Gg+e k+++++++fggg+gaG++i+PvAf+vi+
  gi|298676080|ref|YP_003727830.1| 32 GKTIIPVTRVSFGFGSGGGEEKKNESESGFGGGGGAGAKIEPVAFIVIS 80
                                      69*******************9999***********************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 513.43
//
Query:       gi|298676081|ref|YP_003727831.1|  [L=726]
Description: DEAD/DEAH box helicase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.7e-28   98.0   0.0    2.8e-27   95.9   0.0    2.0  2  Helicase_C_2  Helicase C-terminal domain
    3.3e-19   69.2   4.6    2.7e-18   66.2   4.6    2.1  1  DEAD_2        DEAD_2
    4.8e-06   26.5   1.0    0.00077   19.3   0.2    3.1  3  DEAD          DEAD/DEAH box helicase
    2.4e-05   24.4   8.0     0.0059   16.6   8.0    2.5  1  ResIII        Type III restriction enzyme, res subunit
    3.2e-05   23.5   0.3    0.00055   19.5   0.1    2.5  2  PhoH          PhoH-like protein
    0.00038   19.8   0.4      0.074   12.3   0.1    2.4  2  DUF2075       Uncharacterized conserved protein (DUF2075)
    0.00049   19.8   0.2       0.11   12.2   0.0    2.7  2  Zot           Zonular occludens toxin (Zot)
     0.0099   14.8   0.0      0.024   13.5   0.0    1.6  2  AAA_34        P-loop containing NTP hydrolase pore-1
  ------ inclusion threshold ------
      0.023   14.4   0.0      0.072   12.8   0.0    1.9  1  AAA_30        AAA domain
      0.023   14.0   0.0      0.054   12.8   0.0    1.7  1  ATPase        KaiC
      0.028   13.8   0.0      0.052   12.9   0.0    1.4  1  HK            Hydroxyethylthiazole kinase family
       0.12   12.6   0.1       0.98    9.7   0.0    2.4  2  DUF3110       Protein of unknown function (DUF3110)
       0.17   12.6   0.5         11    6.8   0.0    3.6  4  WGG           Pre-rRNA-processing protein TSR2
        0.2   12.1   5.1         11    6.5   1.1    3.7  3  AAA           ATPase family associated with various cellular 


Domain annotation for each model (and alignments):
>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       3.4   4.4e+03      39      74 ..      66     101 ..      45     116 .. 0.62
   2 !   95.9   0.0   2.2e-30   2.8e-27       2     160 ..     528     685 ..     527     691 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.4
                      Helicase_C_2  39 eifveekeesrekvleeykekkkkgaillavcrGkl 74 
                                        i+  + +++  ++++e ++ kk++ i  av++Gk 
  gi|298676081|ref|YP_003727831.1|  66 VIIATNVHQQMVQFIQEARDIKKTNDIKAAVIKGKT 101
                                       333333444455555555555888888888888875 PP

  == domain 2  score: 95.9 bits;  conditional E-value: 2.2e-30
                      Helicase_C_2   2 lellevvpggvlvffpSyklleevverlkeeleskkieifveekeesrekvleeyke..kkkkgaillavcrGklsE 76 
                                       l+ +e+  g+v++ff++ +  ++ + +l+++l   +i++f  e   s ++v +e+ +  + + +a++l+ + G+lsE
  gi|298676081|ref|YP_003727831.1| 528 LDSIEQSTGNVIIFFQNSHEAKRYHGKLDSQL---NIPVFLDEVGVSAQQVRQEFFDigEDGGKAVMLSYIWGTLSE 601
                                       66788999**********************99...69999988999**********975599*************** PP

                      Helicase_C_2  77 GidfsddllraviivglPfpnpkdpeveakreyldekgkknsgke.wylpealravnQaiGRliRhkdDygaivllD 152
                                       G+d+++ ++r viivg+++p ++d   +a  + +d+ ++  +g++ + + +++r+++Qa+GR++R+ +Dyga +l+D
  gi|298676081|ref|YP_003727831.1| 602 GLDYREGRGRTVIIVGVGYPALNDRM-NAVESAYDSVFGYGAGWDyAVQIPTIRKIRQAMGRVVRSPTDYGARILID 677
                                       **********************8765.777788899998666665167889************************** PP

                      Helicase_C_2 153 eRfakeei 160
                                        Rf +e+ 
  gi|298676081|ref|YP_003727831.1| 678 GRFLTESP 685
                                       ****9883 PP

>> DEAD_2  DEAD_2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.2   4.6   2.1e-21   2.7e-18       3     175 ..      70     284 ..      68     285 .. 0.83

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 2.1e-21
                                       ESSHHHHHHHHHHHHHHHHHCHHHS---EEEE--CCCC-SC.....HHCCCHHCCCCHHHHHHHHHCCHHCCH.... CS
                            DEAD_2   3 sRThsqleqvvkelkklesykkkkekvkvviLgSRknlCin.....eevkkekkekavneaCkelkkkkaeek.... 70 
                                       +  h+q+ q+++e + ++++    +++k+ +++++ n+C +     e  +k +++ ++ e+ k+ + k++e k    
  gi|298676081|ref|YP_003727831.1|  70 TNVHQQMVQFIQEARDIKKT----NDIKAAVIKGKTNMCPHgidydECTVKRENTFDLIELEKDIQLKRQELKsank 142
                                       56799***********9644....46*************76222222233333444444555555555544446778 PP

                                       ................................TTTTTT-SCC..CCHHHHHHHHHHC---CHHHHHHHHHCT--HHH CS
                            DEAD_2  71 ................................eekCsffenl..eelkklkkllleevvdiedlvelgeklklCPYy 113
                                                                         +Cs   ++  ++++k ++ l++ v + e++ ++  ++++C Y 
  gi|298676081|ref|YP_003727831.1| 143 nykqskdpelirlrdelskelenseekarnlrGRTCSELYEVlnYDSEKFRDWLFKDVRTPEEVNDFAYQNSMCGYE 219
                                       999**************************999888987766656778888*************************** PP

                                       HHHHHHCCTSEEEEEHHHHTSCCCHHHHH...T..GCGCEEEECTCCCHHHHHHHCC-EEEECHH CS
                            DEAD_2 114 lsrelledadiiilpYqyLldekireslk...gislknsivilDEAhNiedvceeaasveisees 175
                                       l ++ ++ ad++i+ ++ +l++ i ++l      + ++ ivi+DEAhNie+ +++  s+ i+e++
  gi|298676081|ref|YP_003727831.1| 220 LLKREIKYADLVIANFHHVLNQDIFSTLLswiDREPQDVIVIFDEAHNIESAARSHSSITITEHT 284
                                       ************************9998766555789*************************987 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.2     6e-07   0.00077       4      84 ..      20     100 ..      17     116 .. 0.81
   2 ?    3.7   0.1     0.037        48     124     149 ..     259     284 ..     222     296 .. 0.83
   3 ?   -0.4   0.0      0.68   8.7e+02     160     173 ..     460     474 ..     428     476 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6e-07
                                       HHHHHHHHH....TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTS CS
                                       xxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   4 Qaeaiplil....gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidl 76 
                                       Q+ a+++i     +++ vl +++ G+GKTl +l p+lq      ++  + ++i +  ++ + q +++++ +kk+ d+
  gi|298676081|ref|YP_003727831.1|  20 QEDAMENIHsallKKQIVLFEGACGTGKTLSALAPALQVG----KQLDKTVIIATNVHQQMVQFIQEARDIKKTNDI 92 
                                       66666666544458899********************776....34455788888899***************9999 PP

                                       EEEEEETT CS
                                       xxxxxxxx RF
                              DEAD  77 rvlliigg 84 
                                       ++ +i g+
  gi|298676081|ref|YP_003727831.1|  93 KAAVIKGK 100
                                       98866554 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.037
                                       EEEEETHHHHHHTTTHHHHHHHHHHS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 124 flVlDEadrlldqgfsdfinrilnql 149
                                       ++++DEa+++ +  +s    +i +++
  gi|298676081|ref|YP_003727831.1| 259 IVIFDEAHNIESAARSHSSITITEHT 284
                                       69**********98888777777665 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.68
                                       SEEEEEESSBS.HHH CS
                                       xxxxxxxxxxx.xxx RF
                              DEAD 160 rqvivlSATlp.kdv 173
                                          i++SATl  +d+
  gi|298676081|ref|YP_003727831.1| 460 YSSILMSATLRpFDM 474
                                       4589******98875 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   8.0   4.6e-06    0.0059       4     147 ..      16     271 ..      13     299 .. 0.48

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.6e-06
                                       E-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSH.HHHHHHHHHG..... CS
                            ResIII   4 lreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprk.slleqtleef..... 74 
                                        ++ Qe+a+en+ ++l   +++ +l++ a+GtGKTl a++ + ++ k+ +  k+++++ +  + + q ++e      
  gi|298676081|ref|YP_003727831.1|  16 CYPNQEDAMENIHSAL--LKKQIVLFEGACGTGKTLSALAPALQVGKQLD--KTVIIATNVhQQMVQFIQEArdikk 88 
                                       5789*********999..5899999*********************9876..8888875531334444455444444 PP

                                       ....................................................GGGTGG....GEEEESSS-B--... CS
                            ResIII  75 ....................................................kkflseaykeigkkvsgdkkkakek 99 
                                                                                           +                     k++
  gi|298676081|ref|YP_003727831.1|  89 tndikaavikgktnmcphgidydectvkrentfdlielekdiqlkrqelksaN---------------------KNY 144
                                       44444444444444444444444443333333333333333333322222220.....................222 PP

                                       ....-SEEEEEHHHHHHTH.......................................................... CS
                            ResIII 100 dstnkkilvttiqsldadseee....................................................... 121
                                       ++++   l+   ++l++++e+                                                        
  gi|298676081|ref|YP_003727831.1| 145 KQSKDPELIRLRDELSKELENSeekarnlrgrtcselyevlnydsekfrdwlfkdvrtpeevndfayqnsmcgyell 221
                                       22222222222222222222223333333333333333333333444444444444444444444444444444444 PP

                                       ................HHHTTT-S......................EEEEETGGGTTS. CS
                            ResIII 122 ...........eeeseellrdrfd......................viiiDEaHrlgak 147
                                                   +                                 ++i+DEaH++ ++
  gi|298676081|ref|YP_003727831.1| 222 kreikyadlviANF---------HhvlnqdifstllswidrepqdvIVIFDEAHNIESA 271
                                       44333333333111.........022222222244444444445566777777777665 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   4.3e-07   0.00055       8      55 ..      19      70 ..      15      83 .. 0.81
   2 ?    1.2   0.0      0.17   2.2e+02     119     134 ..     256     271 ..     253     281 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.3e-07
                                      HHHHHHHHHH....H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEE CS
                              PhoH  8 eQkeylealk....kndivfaiGpaGtGKtylavalavealkkkkvkriilt 55
                                      +Q++++e+++    k++iv   G  GtGKt+ a+a a+++ k+ + + ii t
  gi|298676081|ref|YP_003727831.1| 19 NQEDAMENIHsallKKQIVLFEGACGTGKTLSALAPALQVGKQLDKTVIIAT 70
                                      66666666666666*************************9888776666654 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.17
                                       -SEEEEE-SGGG--HH CS
                              PhoH 119 ndafvilDEAQnttke 134
                                       +d +vi+DEA n++++
  gi|298676081|ref|YP_003727831.1| 256 QDVIVIFDEAHNIESA 271
                                       5789********9876 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.1   5.8e-05     0.074       1      68 [.      34     100 ..      34     124 .. 0.72
   2 !    5.3   0.0    0.0075       9.6      64     110 ..     225     278 ..     206     296 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.8e-05
                           DUF2075   1 kavvlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplv.lvlrealakkeekkkkkeafekls 68 
                                       k++vl +G+ GtGKt+ +l+ + ++  +++++t+++++  h+++ + ++ea + k+  +++k+a+ k +
  gi|298676081|ref|YP_003727831.1|  34 KQIVLFEGACGTGKTLSALAPALQV-GKQLDKTVIIATNVHQQMvQFIQEARDIKK-TNDIKAAVIKGK 100
                                       68999*******************9.888888888877666665155565555555.566666555544 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0075
                           DUF2075  64 feklssfinnlsef.......kkaeekkeepkedvvivDEAhrlltksdqaekq 110
                                       +++ + +i n+++              ++ep+  +vi+DEAh + + ++++ + 
  gi|298676081|ref|YP_003727831.1| 225 IKYADLVIANFHHVlnqdifsTLLSWIDREPQDVIVIFDEAHNIESAARSHSSI 278
                                       5555566666666565545433333445677777899*****999954444333 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   8.3e-05      0.11       2      55 ..      36      90 ..      35     121 .. 0.73
   2 ?    4.9   0.0     0.014        18      62      97 ..     237     273 ..     217     339 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.3e-05
                               Zot  2 islvtGapGsgKtsgavkkdllp..alkegRkiitnidGlrlerieqvlgekvsta 55
                                      i+l++Ga G+gKt+ a+   l+   +l +  +i+tn++  ++ ++ q  ++ ++t+
  gi|298676081|ref|YP_003727831.1| 36 IVLFEGACGTGKTLSALAPALQVgkQLDKTVIIATNVH-QQMVQFIQEARDIKKTN 90
                                      899***************98877535557888899***.44444444455444443 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.014
                               Zot  62 npegaetlkefakwatid.kgallviDEcqeifpvra 97 
                                       + + + + + +  w   + ++ ++++DE+++i ++ +
  gi|298676081|ref|YP_003727831.1| 237 HVLNQDIFSTLLSWIDREpQDVIVIFDEAHNIESAAR 273
                                       5556666666677766445***********9966655 PP

>> AAA_34  P-loop containing NTP hydrolase pore-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   1.9e-05     0.024     158     213 ..     241     303 ..     214     330 .. 0.69
   2 ?   -3.3   0.0       2.6   3.3e+03     173     188 ..     537     552 ..     517     558 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.9e-05
                            AAA_34 158 ksrleqlveWlg.edfdGvivfDEchkaknlakse......ekkatktgkavlelqkklpkAr 213
                                       +  ++ l++W++ e  d +++fDE+h+++++a s+      e++ +k+ + v e   ++p+ r
  gi|298676081|ref|YP_003727831.1| 241 QDIFSTLLSWIDrEPQDVIVIFDEAHNIESAARSHssititEHTIEKAMSEVNEYIGQVPDER 303
                                       4567899*****888888999*********999774444333333444455555555666655 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.6
                            AAA_34 173 dGvivfDEchkaknla 188
                                       + +i+f ++h+ak  +
  gi|298676081|ref|YP_003727831.1| 537 NVIIFFQNSHEAKRYH 552
                                       3378899999999876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.6e-05     0.072       4      68 ..      18      86 ..      15     120 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.6e-05
                            AAA_30  4 aeQaaaveallts..gdrvavltGpAGtGKtt.alkalreaweaaggrviglAptgkaAkv.Laeelgi 68
                                      ++Q++a+e++++   ++++++ +G+ GtGKt  al+ + ++ ++  ++vi+++  +++  + ++e+ +i
  gi|298676081|ref|YP_003727831.1| 18 PNQEDAMENIHSAllKKQIVLFEGACGTGKTLsALAPALQVGKQLDKTVIIATNVHQQMVQfIQEARDI 86
                                      6899999988775446789************62678888888888999998887665544436665555 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.3e-05     0.054      13      84 ..      28     102 ..      22     161 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.3e-05
                            ATPase  13 kgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepa..edlrenakslG..wdlekleeegkla 84 
                                       +  + ++++vl  G  GtGKt+ al  +++  ++  +++v+++++ ++  ++++++a+ +    d+++   +gk +
  gi|298676081|ref|YP_003727831.1|  28 HSALLKKQIVLFEGACGTGKTLSALAPALQVGKQ-LDKTVIIATNVHQqmVQFIQEARDIKktNDIKAAVIKGKTN 102
                                       5678899*******************99998666.78899999998886678888887553114555555555554 PP

>> HK  Hydroxyethylthiazole kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.1e-05     0.052      27      98 ..     501     579 ..     492     595 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.1e-05
                                       HHHHT-EEEE--STTTHHHHHHTSSEEE..E.....E-TT--HHHHHHHHHHHHHHHHTT--EEEE-TTBTTBHHHH CS
                                HK  27 llAlgaSPimseaeeEvselakianaLl..l.....NiGtleekaiealkaAvksakevnrPvvlDPVgvgAtelRr 96 
                                       ++A+   P+ +++ ++ +++  i + Ll  +     N+ +  +++ ea +  +k   ++n+Pv lD Vgv+A ++R+
  gi|298676081|ref|YP_003727831.1| 501 TIAASVPPLFAKNRDDPQNIETIEQILLdsIeqstgNVIIFFQNSHEAKRYHGKLDSQLNIPVFLDEVGVSAQQVRQ 577
                                       45555557777777777777777777663322222244455678889999999999********************9 PP

                                       HH CS
                                HK  97 el 98 
                                       e+
  gi|298676081|ref|YP_003727831.1| 578 EF 579
                                       87 PP

>> DUF3110  Protein of unknown function (DUF3110)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.6   2.1e+03      20      54 ..     253     287 ..     237     297 .. 0.70
   2 ?    9.7   0.0   0.00077      0.98      17      46 ..     530     559 ..     514     576 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.6
                           DUF3110  20 lkdrnvvlaFeseddAtryallLeaqdfpeptvea 54 
                                       ++ ++v+++F ++ + +  a+  +     e t+e+
  gi|298676081|ref|YP_003727831.1| 253 REPQDVIVIFDEAHNIESAARSHSSITITEHTIEK 287
                                       444999****9999988888776666666666665 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00077
                           DUF3110  17 tlelkdrnvvlaFeseddAtryallLeaqd 46 
                                       ++e++  nv++ F+++ +A+ry + L+ q 
  gi|298676081|ref|YP_003727831.1| 530 SIEQSTGNVIIFFQNSHEAKRYHGKLDSQL 559
                                       7889999******************99984 PP

>> WGG  Pre-rRNA-processing protein TSR2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       3.4   4.3e+03      27      59 ..     165     197 ..     161     201 .. 0.72
   2 ?    0.8   0.0      0.61   7.9e+02      17      65 ..     209     254 ..     206     259 .. 0.89
   3 ?   -3.0   0.0       9.8   1.3e+04      48      62 ..     401     415 ..     355     417 .. 0.54
   4 ?    6.8   0.0    0.0083        11      24      64 ..     491     533 ..     485     536 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3.4
                               WGG  27 dsadkrdwlagaivdlfkakeeldqedvedvLl 59 
                                       +s++k+++l g  ++ +++  + d+e+  d+L 
  gi|298676081|ref|YP_003727831.1| 165 NSEEKARNLRGRTCSELYEVLNYDSEKFRDWLF 197
                                       678888888886666666667777777777775 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.61
                               WGG  17 lavengwggpdsadkrdwlagaivdlfkakeeldqedvedvLlqvmede 65 
                                       +a++n++ g +  ++  + a+ ++  f   + + ++d+ ++Ll +++ e
  gi|298676081|ref|YP_003727831.1| 209 FAYQNSMCGYELLKREIKYADLVIANF---HHVLNQDIFSTLLSWIDRE 254
                                       799********99999999**999999...4799999999999999876 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 9.8
                               WGG  48 eldqedvedvLlqvm 62 
                                         d ++ +d+Ll +m
  gi|298676081|ref|YP_003727831.1| 401 HSDIKYAADFLLSYM 415
                                       245555667777777 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.0083
                               WGG  24 ggpdsadkrdwlagaivdlfkakee..ldqedvedvLlqvmed 64 
                                       g + s+dkr  +a  +  lf+++++   + e +e++Ll+ +e+
  gi|298676081|ref|YP_003727831.1| 491 GSSFSEDKRLTIAASVPPLFAKNRDdpQNIETIEQILLDSIEQ 533
                                       66679***************75444446778999999998876 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   1.1    0.0085        11       1      35 [.      37      76 ..      37     193 .. 0.80
   2 ?    4.4   0.1     0.036        47      56      77 ..     254     276 ..     222     304 .. 0.68
   3 ?   -0.7   0.0       1.3   1.7e+03      40      67 ..     532     568 ..     509     619 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0085
                                      EEEESSTTSSHHHHHHHHHHHHT.....HEEEEEETTTCS CS
                               AAA  1 vllyGppGtGKTllakavakelg.....vefleisgsell 35
                                      vl+ G  GtGKTl a a a ++g     + ++ +++++ +
  gi|298676081|ref|YP_003727831.1| 37 VLFEGACGTGKTLSALAPALQVGkqldkTVIIATNVHQQM 76
                                      7999**********99988777522222334555555444 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.036
                                       TSTSEEEEEETGGGHHHHH.TTC CS
                               AAA  56 kakpsilfiDEidalaksr.sgs 77 
                                       + + +i+++DE++++ ++  s+s
  gi|298676081|ref|YP_003727831.1| 254 EPQDVIVIFDEAHNIESAArSHS 276
                                       22359999999999987773322 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.3
                                       THHHHHHHHHHHHHHHTS........TS.EEEEEETG CS
                               AAA  40 gesekkirelfkeakeka........kp.silfiDEi 67 
                                       ++s  ++  +f++  e +        +    +f+DE+
  gi|298676081|ref|YP_003727831.1| 532 EQSTGNVIIFFQNSHEAKryhgkldsQLnIPVFLDEV 568
                                       3444444444444333333334444322233555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (726 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1019  (0.0568353); expected 358.6 (0.02)
Passed bias filter:                      607  (0.0338558); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.80u 0.26s 00:00:01.06 Elapsed: 00:00:00.45
# Mc/sec: 4829.32
//
Query:       gi|298676082|ref|YP_003727832.1|  [L=58]
Description: 4Fe-4S ferredoxin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-16   57.9  20.4    1.8e-08   33.9   6.3    2.1  2  Fer4      4Fe-4S binding domain
    1.8e-11   43.6  19.7    3.6e-06   26.8   5.3    2.1  2  Fer4_6    4Fe-4S binding domain
      1e-10   41.5  24.4    9.1e-08   32.1  13.4    1.8  2  Fer4_10   4Fe-4S dicluster domain
    2.6e-10   40.3  10.9    3.6e-10   39.9  10.9    1.2  1  Fer4_9    4Fe-4S dicluster domain
      4e-10   40.1  12.8    7.5e-10   39.3  12.8    1.4  1  Fer4_7    4Fe-4S dicluster domain
    5.9e-10   39.1  15.7    1.6e-09   37.8  15.7    1.6  1  Fer4_21   4Fe-4S dicluster domain
    1.2e-09   39.0  11.4    0.00016   22.5   2.8    2.0  2  Fer4_16   4Fe-4S double cluster binding domain
    1.2e-08   34.6  15.5    0.00027   20.8   3.9    2.1  2  Fer4_2    4Fe-4S binding domain
    1.8e-08   34.3  13.4    0.00018   21.8   1.9    2.1  2  Fer4_4    4Fe-4S binding domain
     0.0002   21.8  13.8       0.04   14.5   3.1    2.1  2  Fer4_17   4Fe-4S dicluster domain
    0.00024   21.2   5.2    0.00025   21.1   5.2    1.0  1  Fer4_11   4Fe-4S dicluster domain
    0.00026   21.4  14.8      0.045   14.2  14.8    2.0  1  Fer4_8    4Fe-4S dicluster domain
     0.0003   20.9  15.6     0.0012   19.1   3.8    2.0  2  Fer4_18   4Fe-4S dicluster domain
    0.00031   21.5  18.8      0.034   15.1   4.5    2.2  2  Fer4_3    4Fe-4S binding domain
     0.0011   19.8   9.6      0.099   13.5   1.7    2.1  2  Fer4_22   4Fe-4S dicluster domain
     0.0021   18.6  18.7      0.022   15.3   4.3    2.9  3  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
  ------ inclusion threshold ------
      0.066   14.0  18.3        3.8    8.3  18.3    2.9  1  Fer4_15   4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   6.1   1.9e-10     2e-07       2      24 .]       4      26 ..       3      26 .. 0.94
   2 !   33.9   6.3   1.7e-11   1.8e-08       2      24 .]      34      56 ..      33      56 .. 0.95

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 1.9e-10
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                      vi+ e C+gC +Cv+ CPv+AI+
  gi|298676082|ref|YP_003727832.1|  4 VIISENCVGCATCVDECPVEAIS 26
                                      899******************96 PP

  == domain 2  score: 33.9 bits;  conditional E-value: 1.7e-11
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                      v+de  C  CG+Cv+vCP++AI+
  gi|298676082|ref|YP_003727832.1| 34 VVDEGECSDCGECVDVCPTEAIE 56
                                      8*********************6 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   6.4   4.7e-08     5e-05       1      24 []       2      25 ..       2      25 .. 0.95
   2 !   26.8   5.3   3.5e-09   3.6e-06       1      24 []      32      55 ..      32      55 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 4.7e-08
                            Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                      v++i  ++C+gC  Cv+ CP  ai
  gi|298676082|ref|YP_003727832.1|  2 VAVIISENCVGCATCVDECPVEAI 25
                                      689******************998 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 3.5e-09
                            Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                      ++++d+  C +Cg+Cv+vCP+ ai
  gi|298676082|ref|YP_003727832.1| 32 IAVVDEGECSDCGECVDVCPTEAI 55
                                      6899******************98 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1  13.4   8.6e-11   9.1e-08       3      56 .]       4      51 ..       2      51 .. 0.78
   2 !   20.3   3.1     4e-07   0.00043       2      21 ..      33      52 ..      32      58 .] 0.85

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 8.6e-11
                           Fer4_10  3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      vi ++ C++C++Cv+ CP+           ++e+   ++ ++C +cg+Cv++CP
  gi|298676082|ref|YP_003727832.1|  4 VIISENCVGCATCVDECPV------EAISLDGENIAVVDEGECSDCGECVDVCP 51
                                      78889**************......3333333444444689************9 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 4e-07
                           Fer4_10  2 vvidddtCirCgkCvkaCPa 21
                                      +v+d+  C  Cg+Cv++CP+
  gi|298676082|ref|YP_003727832.1| 33 AVVDEGECSDCGECVDVCPT 52
                                      6789999************9 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9  10.9   3.4e-13   3.6e-10       1      51 []       9      55 ..       8      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 3.4e-13
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      +C+gC +Cv+ Cp ++++ d  +  +  +     +C +Cg+Cv++Cp++ai
  gi|298676082|ref|YP_003727832.1|  9 NCVGCATCVDECPVEAISLDGENIAVVDEG----ECSDCGECVDVCPTEAI 55
                                      6*******************9999988765....5*************987 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3  12.8   7.1e-13   7.5e-10       2      52 .]      10      54 ..       9      54 .. 0.93

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 7.1e-13
                            Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      C+gC  Cv+ Cpv+ai+ld e        +++d+ +C++Cg+Cv+vCPt+a
  gi|298676082|ref|YP_003727832.1| 10 CVGCATCVDECPVEAISLDGE------NIAVVDEGECSDCGECVDVCPTEA 54
                                      ******************886......568899****************87 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8  15.7   1.5e-12   1.6e-09       1      58 [.       3      56 ..       3      57 .. 0.95

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 1.5e-12
                           Fer4_21  1 AridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58
                                      A+i +++C+gC  C+  C+   ++ai++d+++++ v e eC  C  C++vCP+ ++ie
  gi|298676082|ref|YP_003727832.1|  3 AVIISENCVGCATCVDECP---VEAISLDGENIAVVDEGECSDCGECVDVCPT-EAIE 56
                                      78999**************...8*****************************7.8887 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   3.4   3.7e-07   0.00039       1      29 [.       9      39 ..       9      41 .. 0.78
   2 !   22.5   2.8   1.5e-07   0.00016       2      18 ..      40      56 ..      39      58 .] 0.92

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3.7e-07
                           Fer4_16  1 rCgtCgkCaevCPtnaikek..kekeieare 29
                                      +C++C  C++ CP++ai+ +  + ++++  e
  gi|298676082|ref|YP_003727832.1|  9 NCVGCATCVDECPVEAISLDgeNIAVVDEGE 39
                                      6*****************8844555556555 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 1.5e-07
                           Fer4_16  2 CgtCgkCaevCPtnaik 18
                                      C +Cg+C++vCPt+ai+
  gi|298676082|ref|YP_003727832.1| 40 CSDCGECVDVCPTEAIE 56
                                      ****************7 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   3.8     5e-07   0.00052       3      21 ..       3      21 ..       1      22 [. 0.90
   2 !   20.8   3.9   2.6e-07   0.00027       3      22 .]      33      52 ..      31      52 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 5e-07
                            Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                      +v+ +++C+gC +Cv+ CP
  gi|298676082|ref|YP_003727832.1|  3 AVIISENCVGCATCVDECP 21
                                      57889************** PP

  == domain 2  score: 20.8 bits;  conditional E-value: 2.6e-07
                            Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                                      +vvd+  C  Cg Cv++CP+
  gi|298676082|ref|YP_003727832.1| 33 AVVDEGECSDCGECVDVCPT 52
                                      5899999************7 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   1.9   1.7e-07   0.00018       1      16 [.       7      22 ..       7      29 .. 0.92
   2 !   18.3   4.1   2.1e-06    0.0022       3      16 ..      39      52 ..      36      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.7e-07
                            Fer4_4  1 qerCigCgsCvaaCPq 16
                                      +e+C+gC  Cv+ CP+
  gi|298676082|ref|YP_003727832.1|  7 SENCVGCATCVDECPV 22
                                      699************7 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 2.1e-06
                            Fer4_4  3 rCigCgsCvaaCPq 16
                                       C +Cg Cv++CP+
  gi|298676082|ref|YP_003727832.1| 39 ECSDCGECVDVCPT 52
                                      5************8 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   2.4   4.8e-05     0.051       1      17 [.       9      25 ..       9      36 .. 0.77
   2 !   14.5   3.1   3.8e-05      0.04      45      58 ..      39      52 ..      26      55 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.8e-05
                           Fer4_17  1 rCiqCgyClpeCpsyea 17
                                      +C +C+ C++eCp  ++
  gi|298676082|ref|YP_003727832.1|  9 NCVGCATCVDECPVEAI 25
                                      58888888888887655 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3.8e-05
                           Fer4_17 45 lCieCgeCerkCPq 58
                                      +C+ CgeC+ +CP 
  gi|298676082|ref|YP_003727832.1| 39 ECSDCGECVDVCPT 52
                                      78888888888886 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   5.2   2.4e-07   0.00025       4      59 ..       4      55 ..       1      58 [] 0.85

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.4e-07
                           Fer4_11  4 lflpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykiv 59
                                      ++++e+C  C    Cv+ +p+eai  d e  + ++de +++ ++ e+v++cP +++
  gi|298676082|ref|YP_003727832.1|  4 VIISENCVGCA--TCVDECPVEAISLDGE-NIAVVDEGECS-DCGECVDVCPTEAI 55
                                      67899999995..7**************5.56678999997.**********8765 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2  14.8   4.2e-05     0.045       3      64 ..       8      53 ..       6      54 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.2e-05
                            Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                      e+C++C  C ++Cpv         +  ge+++ v++e         ++C+ cg+C++vCp++
  gi|298676082|ref|YP_003727832.1|  8 ENCVGCATCVDECPVEA------ISLDGENIA-VVDE---------GECSDCGECVDVCPTE 53
                                      79************644......445566666.5554.........46************85 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   4.8     0.002       2.1      59      75 ..       8      24 ..       3      36 .. 0.73
   2 !   19.1   3.8   1.1e-06    0.0012      51      74 ..      30      53 ..      22      58 .] 0.81

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.002
                           Fer4_18 59 gdcidcescvkvcPtgi 75
                                       +c+ c +cv+ cP++ 
  gi|298676082|ref|YP_003727832.1|  8 ENCVGCATCVDECPVEA 24
                                      57999999999999865 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 1.1e-06
                           Fer4_18 51 eerkekgagdcidcescvkvcPtg 74
                                      e+ +  ++g+c dc+ cv+vcPt+
  gi|298676082|ref|YP_003727832.1| 30 ENIAVVDEGECSDCGECVDVCPTE 53
                                      55667789**************96 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   6.3   0.00022      0.23       1      15 []      10      24 ..      10      24 .. 0.94
   2 !   15.1   4.5   3.2e-05     0.034       1      15 []      40      54 ..      40      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00022
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+gC +Cv+ CPv A
  gi|298676082|ref|YP_003727832.1| 10 CVGCATCVDECPVEA 24
                                      ************976 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 3.2e-05
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C  Cg Cv+vCP+ A
  gi|298676082|ref|YP_003727832.1| 40 CSDCGECVDVCPTEA 54
                                      888*********976 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   1.7   9.4e-05     0.099      80      95 ..       8      23 ..       2      24 .. 0.87
   2 !   11.4   1.3   0.00043      0.45       1      14 [.      39      52 ..      31      55 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.4e-05
                           Fer4_22 80 sgCvGCgRCieacpvk 95
                                      + CvGC  C++ cpv+
  gi|298676082|ref|YP_003727832.1|  8 ENCVGCATCVDECPVE 23
                                      78***********986 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00043
                           Fer4_22  1 rClsCgaCtlvCpt 14
                                      +C +Cg+C  vCpt
  gi|298676082|ref|YP_003727832.1| 39 ECSDCGECVDVCPT 52
                                      46667777777776 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   5.7    0.0024       2.5       4      17 ..       8      21 ..       6      23 .. 0.93
   2 ?    6.3   0.1     0.014        14      49      57 ..      18      26 ..      17      27 .. 0.87
   3 !   15.3   4.3     2e-05     0.022       1      17 [.      35      51 ..      35      57 .. 0.96

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0024
                           Fer4_13  4 dtCiacgaCvelaP 17
                                      ++C++c++Cv+ +P
  gi|298676082|ref|YP_003727832.1|  8 ENCVGCATCVDECP 21
                                      79***********9 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.014
                           Fer4_13 49 daCPvesIg 57
                                      d+CPve+I 
  gi|298676082|ref|YP_003727832.1| 18 DECPVEAIS 26
                                      89******6 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 2e-05
                           Fer4_13  1 VDrdtCiacgaCvelaP 17
                                      VD+ +C++cg Cv+++P
  gi|298676082|ref|YP_003727832.1| 35 VDEGECSDCGECVDVCP 51
                                      89*************** PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3  18.3    0.0036       3.8       6      66 .]       8      57 ..       4      57 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0036
                           Fer4_15  6 daCigcglCvaeapevfeldedglasvllddgeiaegevpddeeeaaqeAaraCPvdAIrv 66
                                      ++C gc+ Cv+e+p v  +  dg +           + v++ e  +  e +++CP++AI++
  gi|298676082|ref|YP_003727832.1|  8 ENCVGCATCVDECP-VEAISLDGEN----------IAVVDEGECSDCGECVDVCPTEAIEI 57
                                      79***********8.4444444444..........23477899999*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 427.88
//
Query:       gi|298676083|ref|YP_003727833.1|  [L=343]
Description: aspartate-semialdehyde dehydrogenase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-33  116.2   0.0    1.7e-33  115.7   0.0    1.3  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
    1.3e-33  116.7   0.0    2.1e-33  116.0   0.0    1.4  1  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
      0.009   16.7   0.0      0.017   15.8   0.0    1.5  1  DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomer
  ------ inclusion threshold ------
      0.025   14.5   0.0      0.042   13.7   0.0    1.4  1  NAD_binding_10   NAD(P)H-binding
      0.034   14.3   0.0      0.052   13.7   0.0    1.4  1  DapB_N           Dihydrodipicolinate reductase, N-terminus


Domain annotation for each model (and alignments):
>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.7   0.0   4.6e-37   1.7e-33       1     118 [.       6     128 ..       6     131 .. 0.95

  Alignments for each domain:
  == domain 1  score: 115.7 bits;  conditional E-value: 4.6e-37
                                       EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSG......GGTTTECEBEEEGGGGGCTT-SEEE CS
                    Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavk......aleegkdlkvedvdeeelkevdivf 71 
                                       k++++GatG+vGq++++ L +hp++e++ l++s+rsaGk++++a++       ++e+k   v +vd+ ++ ++d+vf
  gi|298676083|ref|YP_003727833.1|   6 KAGVLGATGAVGQRFIEALTDHPWFEITSLAASERSAGKTYENAANwrldsqLPDEVKGKDVVPVDPSKV-DADVVF 81 
                                       689**********************************************998777778888888889999.9***** PP

                                       E-SCHHHHHHHHHHHHHTTSEEEESSSTTTTSTTSEBE-HHHHGGGG CS
                    Semialdhyde_dh  72 lalpagvskelapklaeagvkviDlssdfRlkddavyvlpevnreai 118
                                       +alp++ +k ++p++aeag+ v +++s +R++dd+++v+pevn++++
  gi|298676083|ref|YP_003727833.1|  82 SALPSSSAKTVEPEFAEAGFAVASNASSYRMEDDVPLVVPEVNPDHL 128
                                       *********************************************98 PP

>> Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.0   0.0   5.7e-37   2.1e-33       1     182 [.     159     322 ..     159     324 .. 0.91

  Alignments for each domain:
  == domain 1  score: 116.0 bits;  conditional E-value: 5.7e-37
                                       HHHHHHCTT.EEEEEEEEEEEGGGCHHHHHHHHHHHHHHHHHSTTS.CTTTSSHHTTSEESTCSTBTTTTCHCBHHH CS
                   Semialdhyde_dhC   1 LkPLldalgelervivatyqavSGaGkkgvreLlkqvaelqrsdeakpgvfgvpiagNlipyidkeedkgepetree 77 
                                       LkPLl+  ++l++v+vat+qavSGaG                      gv+++ i +N++pyi++ee+k+e+et + 
  gi|298676083|ref|YP_003727833.1| 159 LKPLLQ--FGLNNVNVATMQAVSGAGF--------------------DGVSSMSIIDNILPYIKTEEEKMENETLKL 213
                                       8*****..569****************....................7***************************** PP

                                       HHHHHHHHHHCTESC.SEEEEEEEESBSSEEEEEEEEEES..SSHHHHHHHHHHHHCS.......TTEEEEESSHCH CS
                   Semialdhyde_dhC  78 lkavaetkkilefte.kvsatcvrVPvlrGhseavtiklk..lkdveveeveellaaa.......pevkvvvneeed 144
                                       l++ + +  il+ ++ +vs +c+rVPvl+Gh+ea+++ ++  +++++v++++  +          pe  +vv +e+d
  gi|298676083|ref|YP_003727833.1| 214 LGEFNGS-EILN-PDiHVSSSCHRVPVLDGHTEAIWAGMDdnPTPEDVRQAFLDFDPGledlpskPENSLVVWDEPD 288
                                       *****94.4555.6668**********************9999999999999999999*******999999999*** PP

                                       HSSHHHHTTC..SSSEEEEEEEEETTCTTEEEEEEEEETT CS
                   Semialdhyde_dhC 145 rPtpaavagg..tnsvsVGRirkdemgdeglklvvvgDNl 182
                                       rP+p+++ +   +++v+VGRir+         ++++g+N+
  gi|298676083|ref|YP_003727833.1| 289 RPQPRLDKNIgnGMAVNVGRIREGI------RYIALGHNT 322
                                       ******9988889*********865......566666666 PP

>> DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   4.8e-06     0.017       3      47 ..       9      53 ..       7      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.8e-06
                                      EESTTSHHHHHHHHHHHHCTTTEEEEEEEE.SSTHHHHHHHHHHHT CS
                   DXP_reductoisom  3 iLGsTGSIGtqtLdvieenpdkfevvalaa.gsnvellaeqakefk 47
                                      +LG+TG +G+  ++ ++++p  fe+++laa +++  + +e a++++
  gi|298676083|ref|YP_003727833.1|  9 VLGATGAVGQRFIEALTDHP-WFEITSLAAsERSAGKTYENAANWR 53
                                      9*******************.9********7788888888888776 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.2e-05     0.042       1      69 [.      11      87 ..      11     130 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.2e-05
                                      TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHT........T-SEEEES-..- CS
                    NAD_binding_10  1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealk........gadaVvsal..g 69
                                      GAtG vG++ ++ l ++  +e+t l+ ++ ++ +    e++    +d + +++++            +ad+V+sal  +
  gi|298676083|ref|YP_003727833.1| 11 GATGAVGQRFIEALTDHPWFEITSLAASERSAGKTY--ENAANWRLDSQLPDEVKGKDVvpvdpskvDADVVFSALpsS 87
                                      9***********999999********9999998654..45555555555555554333233666666888899998531 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.5e-05     0.052       1      39 [.       5      43 ..       5     116 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.5e-05
                                      EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTT CS
                            DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkesel 39
                                      ik +v+Ga+G +G++ ++a+++++ +e+++   +++s+ 
  gi|298676083|ref|YP_003727833.1|  5 IKAGVLGATGAVGQRFIEALTDHPWFEITSLAASERSAG 43
                                      6889************************99888877432 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2229.09
//
Query:       gi|298676084|ref|YP_003727834.1|  [L=235]
Description: uridylate kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.2e-27   95.0   0.6    2.2e-26   93.0   0.6    1.8  1  AA_kinase  Amino acid kinase family


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.0   0.6   1.2e-30   2.2e-26       1     240 [.       1     201 [.       1     202 [. 0.88

  Alignments for each domain:
  == domain 1  score: 93.0 bits;  conditional E-value: 1.2e-30
                                       TEEEEEE-TTCCC.CTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HHHHHH CS
                         AA_kinase   1 krvVvKlGGsslt.dkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstleeagev 76 
                                       ++vV+ +GGs+++ d + +++  + + +++l   +++lv+V+Ggg+ ++ +++ ++ + s+e               
  gi|298676084|ref|YP_003727834.1|   1 MLVVLSIGGSIIAnDLDPERFVFYKNALSKL-LPDHQLVIVTGGGKAARDYINVARSVGSNEVVC------------ 64 
                                       789**********555557777777778888.7779******************88888888873............ PP

                                       HHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTT CS
                         AA_kinase  77 atrdalaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigldeeg 153
                                          d++++  +rl+a+ll +++ +  ++  + +                   ++ +  l++++v+v++g +    +g
  gi|298676084|ref|YP_003727834.1|  65 ---DFIGIEITRLNAQLLISAFGEDAYPEPPRT------------------YKEAKLALASDKVVVMGGVV----PG 116
                                       ...***************999955555544333..................56788899999*******88....88 PP

                                       EEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH..CSSS.TTTHHHHCHHHHHH CS
                         AA_kinase 154 elgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee..saselatgGmkvkhpaala 228
                                       +    ++D ++a+lAe+l+Ad l+i+t+VdGVy++dp+++p+a++++++s++e+ +  ++ e   g+  +++p a++
  gi|298676084|ref|YP_003727834.1| 117 Q----TTDAVSAILAEYLNADFLVIATSVDGVYSKDPRQDPNAKRYEKLSAKELVDvvISTEIKAGSKSPVDPLAAK 189
                                       8....9***************************************************8888888899999******* PP

                                       HHHCTT-EEEEE CS
                         AA_kinase 229 aarrggipvvIt 240
                                       +++r ++p+ I+
  gi|298676084|ref|YP_003727834.1| 190 IIERCKMPTTIM 201
                                       ********9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1470.59
//
Query:       gi|298676085|ref|YP_003727835.1|  [L=203]
Description: adenosylcobinamide hydrolase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-41  143.1   0.0    1.2e-41  142.9   0.0    1.0  1  CbiZ      Adenosylcobinamide amidohydrolase


Domain annotation for each model (and alignments):
>> CbiZ  Adenosylcobinamide amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.9   0.0   6.8e-46   1.2e-41       8     192 .]      18     189 ..      12     189 .. 0.93

  Alignments for each domain:
  == domain 1  score: 142.9 bits;  conditional E-value: 6.8e-46
                              CbiZ   8 vlssavlngGlrelravlnhqvpegyeredpeeyleeyleelglppektvgllTaadmenaaiaeeefedlevtavv 84 
                                        ls+  +ngG + ++ ++nh+v++g+e +dp +yl++++e  ++  +   gllTa++men++i++++    + t++v
  gi|298676085|ref|YP_003727835.1|  18 GLSTG-INGGRGYVKSIFNHEVNNGFEFKDPVQYLDNVAEYNEV-YKPYFGLLTAVEMENLCIKTDD----NLTTFV 88 
                                       56777.99********************************9999.8*********************....****** PP

                              CbiZ  85 TaGvesnavragdedeeaekpGTINiivlinaaLtdaalvralitatEAKtaalqdlgvrsrysegatGTgTDaiav 161
                                       TaG+ +++        +   pGTINii++++a+L+++a++ a+itatEAK  al+++g++      + GT+TDa++v
  gi|298676085|ref|YP_003727835.1|  89 TAGI-THPSVYRL---DGYYPGTINIILVVDAELSEGAMAGAIITATEAKGLALMKMGYD------FLGTTTDAVVV 155
                                       ****.88888777...4899***************************************9......*********** PP

                              CbiZ 162 aadkegee...eltyaGkhtklGeliaraVyeAv 192
                                       a +k++++    ++yaG+ t++G+ i ++V ++v
  gi|298676085|ref|YP_003727835.1| 156 AYQKQNKNsspYIEYAGSYTDFGKKITDTVVKGV 189
                                       *99766666889******************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1425.78
//
Query:       gi|298676086|ref|YP_003727836.1|  [L=240]
Description: xylose isomerase domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-16   60.5   0.1    4.4e-16   59.0   0.0    1.7  2  AP_endonuc_2  Xylose isomerase-like TIM barrel
  ------ inclusion threshold ------
       0.15   10.2   0.6        0.2    9.8   0.6    1.1  1  HOOK          HOOK protein


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.0   0.0   4.9e-20   4.4e-16      40     210 .]      48     201 ..      44     201 .. 0.86
   2 ?   -3.0   0.0      0.46   4.1e+03      66      84 ..     221     239 ..     211     240 .] 0.61

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 4.9e-20
                                       TTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHHHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHH CS
                      AP_endonuc_2  40 lglriaslslftrfgypdederearreesvdalkraielaaaLGapllvlhpGtagagpkgseeeawerlaeslnel 116
                                       ++l+ +++ ++t+ +      re+ r++  + ++ +++++++++a++lv+hpG   + ++ ++++a+  l +sl el
  gi|298676086|ref|YP_003727836.1|  48 YNLEYTVHAPNTDLNIGSI--REPMRKAGMELIQGMVDICSQIDARVLVVHPG--YFTYSCDIPDARVSLKKSLLEL 120
                                       5666555555555555443..33448888************************..9********************* PP

                                       HHHHHHHTSEEEEE--TTTTSSSTCHHHHHHHHHHTTTTEEEEEEHHHHHHHTTTHHHHHHHHHGG.EEEEEE.EES CS
                      AP_endonuc_2 117 adyaekegvklalEtlagsgvelgdeelarlldavdspnvgvclDtgHlliaeedvddalraladr.ikhvHikDak 192
                                        ++++  ++k+++E+++++ + ++  ++ +l       n g++lD+gH++       ++l+++ ++ i+h+Hi+D+ 
  gi|298676086|ref|YP_003727836.1| 121 EKITDGTDIKICVENMPSDWNCFL-FQYPDLDLG----NNGFALDVGHANTT-----QTLDKFLEYnISHFHIHDNT 187
                                       ********************8777.666555433....45*********987.....99******99********** PP

                                       STTTTSSTTEESTTSSSS CS
                      AP_endonuc_2 193 gdlgagrdrhvpigeGei 210
                                       g    + d+h+ +g G+i
  gi|298676086|ref|YP_003727836.1| 188 G----KSDEHLWVGAGNI 201
                                       *....**********987 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.46
                                       HHHHHHHHHHHHHHHHHTB CS
                      AP_endonuc_2  66 eesvdalkraielaaaLGa 84 
                                        +s+d++++ +++ ++L++
  gi|298676086|ref|YP_003727836.1| 221 HRSRDYVEKSLKAIKDLDI 239
                                       3456666666666666655 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.6   2.2e-05       0.2     582     612 ..     210     240 .]     203     240 .] 0.90

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 2.2e-05
                              HOOK 582 kkkdedlkameerYkkyveKAksViktLdpk 612
                                        kk++ +k++e+r + yveK  + ik Ld k
  gi|298676086|ref|YP_003727836.1| 210 LKKNSGMKVLEHRSRDYVEKSLKAIKDLDIK 240
                                       5899************************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1642.84
//
Query:       gi|298676087|ref|YP_003727837.1|  [L=172]
Description: ArsR family transcriptional regulator [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-08   33.7   0.4    5.7e-08   32.5   0.2    1.8  2  HTH_5     Bacterial regulatory protein, arsR family
    4.1e-07   30.0   0.0      1e-06   28.7   0.0    1.7  2  HTH_20    Helix-turn-helix domain
    0.00015   21.7   0.2    0.00053   19.9   0.1    1.9  2  MarR      MarR family
    0.00057   19.4   0.0     0.0014   18.1   0.0    1.8  1  HTH_24    Winged helix-turn-helix DNA-binding
     0.0037   17.8   1.4      0.028   15.0   1.4    2.2  1  DUF4430   Domain of unknown function (DUF4430)
     0.0065   16.4   0.1      0.015   15.2   0.1    1.6  1  HTH_11    HTH domain
     0.0089   16.0   0.2      0.071   13.1   0.1    2.2  2  HTH_45    Winged helix-turn-helix
  ------ inclusion threshold ------
      0.052   13.2   0.1      0.084   12.6   0.1    1.4  1  DUF4423   Domain of unknown function (DUF4423)
      0.054   13.5   0.0      0.092   12.7   0.0    1.3  1  HTH_1     Bacterial regulatory helix-turn-helix protein, lysR
        0.1   12.9   0.1       0.29   11.5   0.0    1.7  2  Rrf2      Transcriptional regulator
       0.14   12.1   0.0       0.25   11.3   0.0    1.4  1  MarR_2    MarR family
       0.62   10.4   2.9        5.6    7.4   0.0    3.2  3  NUMOD1    NUMOD1 domain


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.2   3.8e-11   5.7e-08       2      46 ..      15      59 ..      14      60 .. 0.97
   2 ?   -2.3   0.0       2.9   4.4e+03      23      32 ..      67      76 ..      66      78 .. 0.82

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 3.8e-11
                                      HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      +tRl++L +L+++e+ ++  a++lg+s +    H k+L+ea LV+
  gi|298676087|ref|YP_003727837.1| 15 STRLQMLEILSDSETHITGMAKKLGISVPVAAKHVKILEEAELVN 59
                                      8*******************************************8 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.9
                                      HHHTS-HHHH CS
                             HTH_5 23 eelglsqstv 32
                                      ++l+++ s++
  gi|298676087|ref|YP_003727837.1| 67 DILKINTSNI 76
                                      6899999998 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0     7e-10     1e-06       2      60 ..       7      64 ..       6      65 .. 0.96
   2 ?   -2.3   0.0       3.2   4.8e+03      45      56 ..      98     109 ..      96     115 .. 0.63

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 7e-10
                                      HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                      ++++AL+  +R+ +l  L ++ +   +  a+ l++s   + +H+++Leea+Lv + r g
  gi|298676087|ref|YP_003727837.1|  7 KVFKALGCSTRLQMLEIL-SDSETHITGMAKKLGISVPVAAKHVKILEEAELVNRKRFG 64
                                      689***************.***********************************99987 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.2
                                       HHHHHHCTTEEE CS
                            HTH_20  45 LrvLeeagLvev 56 
                                       L++L ++ +vev
  gi|298676087|ref|YP_003727837.1|  98 LDALKKVSAVEV 109
                                       456666666665 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   3.5e-07   0.00053       6      51 ..      18      62 ..      15      63 .. 0.85
   2 ?   -1.9   0.0       2.2   3.3e+03      27      41 ..      69      83 ..      67      84 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.5e-07
                                      HHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR  6 fviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                      +  L+il++++ + ++ +akklg+s + + + ++ Le+++l++R++
  gi|298676087|ref|YP_003727837.1| 18 LQMLEILSDSETH-ITGMAKKLGISVPVAAKHVKILEEAELVNRKR 62
                                      5567777777766.789***************************86 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.2
                                      HTS-HHHHHHHHHHH CS
                              MarR 27 lgvskstvtrvldrL 41
                                      l++++s++ ++ldr 
  gi|298676087|ref|YP_003727837.1| 69 LKINTSNIYTILDRF 83
                                      789999999999985 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   9.5e-07    0.0014      11      47 ..      22      58 ..      15      59 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 9.5e-07
                            HTH_24 11 lLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      ++  ++ + ++  A++lg+S++   +++k Lee++l+
  gi|298676087|ref|YP_003727837.1| 22 EILSDSETHITGMAKKLGISVPVAAKHVKILEEAELV 58
                                      4455588888999*********************997 PP

>> DUF4430  Domain of unknown function (DUF4430)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   1.4   1.9e-05     0.028       1      71 [.      94     155 ..      94     156 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.9e-05
                           DUF4430   1 GttvfdvleaaakkkedkteaqsgehyitsIngleqdtakksyWmyevNGepsdvGagsyklkdgdkivfr 71 
                                       Gtt++d+l+++  ++ ++   + +   + +        ++k + +yev+G++sd+ +++++ +++ ++ ++
  gi|298676087|ref|YP_003727837.1|  94 GTTLLDALKKVSAVEVKQIGDRDA---VVAT------DGDKGFYVYEVDGTFSDKTVNECTFDKDATVKWK 155
                                       789999999998888888866653...4444......45799********************999999996 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   9.9e-06     0.015       2      42 ..      17      55 ..      16      62 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.9e-06
                            HTH_11  2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeel 42
                                      +lq+le+L +++ +i+g  +A++L++S  +  +++k+Lee+
  gi|298676087|ref|YP_003727837.1| 17 RLQMLEILSDSETHITG--MAKKLGISVPVAAKHVKILEEA 55
                                      789*****999999999..8******************986 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.1   4.8e-05     0.071       9      52 ..      18      61 ..      15      80 .. 0.92
   2 ?    0.1   0.0      0.53     8e+02      60      74 ..      92     106 ..      87     108 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.8e-05
                            HTH_45  9 adILeaisegeakkTkimykanLsykllnkYLdmLvekglikks 52
                                      +++Le++s++e++ T + +k  +s  ++ k +++L e +l++ +
  gi|298676087|ref|YP_003727837.1| 18 LQMLEILSDSETHITGMAKKLGISVPVAAKHVKILEEAELVNRK 61
                                      589**************************************654 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.53
                            HTH_45  60 ekGlelleklkelee 74 
                                       +kG  ll+ lk++  
  gi|298676087|ref|YP_003727837.1|  92 DKGTTLLDALKKVSA 106
                                       79********99876 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   5.6e-05     0.084      32      76 ..      24      66 ..       4      84 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.6e-05
                           DUF4423 32 lkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgky 76
                                      l d +  +  +ak+l+  is+  ++k +++L++++l+ +++ gk 
  gi|298676087|ref|YP_003727837.1| 24 LSDSETHITGMAKKLG--ISVPVAAKHVKILEEAELVNRKRFGKT 66
                                      5566778999******..*********************998776 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.1e-05     0.092       4      40 ..      18      55 ..      16      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.1e-05
                                      HHHHHHHHHHS.SHHHHHHHHTS-HHHHHHHHHHHHHH CS
                             HTH_1  4 lrlfvavaeeg.sftrAAeeLglsqpavsrqikrLEee 40
                                      l+ ++ + +++ ++t+ A++Lg+s p + +++k LEe+
  gi|298676087|ref|YP_003727837.1| 18 LQMLEILSDSEtHITGMAKKLGISVPVAAKHVKILEEA 55
                                      6667777777779***********************84 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00019      0.29      16      59 ..      20      62 ..       4      66 .. 0.85
   2 ?   -1.7   0.0       2.6   3.8e+03      64      79 ..      94     109 ..      69     113 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
                                      HHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                              Rrf2 16 yLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvr 59
                                      +L+  +++e   ++ +a++ +is ++++k ++ L++a+lv+ +r
  gi|298676087|ref|YP_003727837.1| 20 MLEILSDSE-THITGMAKKLGISVPVAAKHVKILEEAELVNRKR 62
                                      445555655.8999**************************9776 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.6
                                       CEEESSHCCCSBHHHH CS
                              Rrf2  64 GyrLakppeeItlldv 79 
                                       G +L  ++++++  +v
  gi|298676087|ref|YP_003727837.1|  94 GTTLLDALKKVSAVEV 109
                                       4466666666666655 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00017      0.25       8      54 ..      18      61 ..      12      67 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                                      HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      ++ L  L +++     ++  a++lg+s + + +++k L++a Lv r+
  gi|298676087|ref|YP_003727837.1| 18 LQMLEILSDSET---HITGMAKKLGISVPVAAKHVKILEEAELVNRK 61
                                      566777777774...88889************************887 PP

>> NUMOD1  NUMOD1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0037       5.6      20      36 ..      32      48 ..      31      49 .. 0.86
   2 ?   -2.1   0.3       3.5   5.3e+03      25      34 ..      68      77 ..      67      80 .. 0.72
   3 ?    1.9   0.1      0.19   2.8e+02       1      12 [.     125     136 ..     125     144 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0037
                            NUMOD1 20 reAakyLgishntInky 36
                                      + +ak+Lgis +   k+
  gi|298676087|ref|YP_003727837.1| 32 TGMAKKLGISVPVAAKH 48
                                      569*********99998 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.5
                            NUMOD1 25 yLgishntIn 34
                                      +L+i+ ++I+
  gi|298676087|ref|YP_003727837.1| 68 ILKINTSNIY 77
                                      6888888876 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.19
                            NUMOD1   1 kpVyvYDlntkt 12 
                                       k  yvY +++++
  gi|298676087|ref|YP_003727837.1| 125 KGFYVYEVDGTF 136
                                       578*****9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1235.52
//
Query:       gi|298676088|ref|YP_003727838.1|  [L=696]
Description: DNA mismatch repair protein MutS domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.8e-11   43.0   0.1    8.6e-11   42.2   0.1    1.4  1  MutS_V       MutS domain V
    3.8e-06   27.4   0.3    1.5e-05   25.5   0.0    2.2  2  HHH_5        Helix-hairpin-helix domain
    0.00025   21.6   1.7       0.57   10.8   0.0    4.2  4  5_3_exonuc   5'-3' exonuclease, C-terminal SAM fold
     0.0031   17.6   0.1     0.0094   16.0   0.1    1.8  1  HHH_2        Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.017   15.6   0.0       0.04   14.3   0.0    1.6  1  AAA          ATPase family associated with various cellular a
       0.81    9.7   4.9       0.23   11.5   0.2    2.4  3  Baculo_LEF5  Baculoviridae late expression factor 5
        9.1    6.7  12.0         48    4.4   0.0    2.9  2  AAA_23       AAA domain


Domain annotation for each model (and alignments):
>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.1   3.3e-14   8.6e-11       2     130 ..     511     635 ..     510     667 .. 0.86

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 3.3e-14
                                       EEE-STTSSHHHHHHHHHHHHHHHHHT--BSSSEEEEE--SEEEEEE--------SS-HHHHHHHHHHHHHTT--TT CS
                            MutS_V   2 litGpnmaGkstylrqvalivllaqiGsfvpaekaeisivdkiftRvgasDdlakgkstFmvEmlEtasilknatek 78 
                                       l+ G n +Gk + l   a +v+la++G  vpa+++ei+i+d ++    ++ +l  g  +F   +++ + + +n+++ 
  gi|298676088|ref|YP_003727838.1| 511 LLSGVNSGGKTSMLELLAQCVILAHMGFPVPANASEIGITDGLYYFAKSKGTLDAG--AFESSLTDFSVVADNSSK- 584
                                       799*****************************************988777777655..79999***9999888765. PP

                                       SEEEEESTS-SS-HHHHHHHHHHHHHHHHHTT--EEEEEES-GGGGGHHHHS CS
                            MutS_V  79 slvilDElGRGtstydGlaialavaeyllekikaktlfatHyheltklaekl 130
                                        +v++DEl   t       i   ++e l+e+ k++++f  H  el   ++++
  gi|298676088|ref|YP_003727838.1| 585 -VVLVDELESITEPGASAKIIAGILETLSENEKSMSVFVSHLSELIMENTQC 635
                                       .8999****9999999999**************************8776654 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   5.8e-09   1.5e-05       2      52 ..       2      55 ..       1      59 [. 0.85
   2 ?   -3.8   0.0         7   1.8e+04      35      53 ..     589     609 ..     585     612 .. 0.64

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 5.8e-09
                                      HHHHTSTT--HHHHHHHHTTT--S....HHHHHHS-HHHHHTSTTS-HHHHHHHH CS
                             HHH_5  2 eeLlsvsGiGpktAlallsaGies....vedlaaadveeLakipGiGkktAerii 52
                                      e+L++v+ iG ktA + + + ++s    + ++++ d++ +++i GiG+k A +++
  gi|298676088|ref|YP_003727838.1|  2 ESLQDVPRIGDKTAQRFIGH-FGSeeaaLNAILNGDIASISEIEGIGQKFAISLV 55
                                      689*****************.7764455679******************876665 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 7
                                       HHHHTS..TTS-HHHHHHHHH CS
                             HHH_5  35 eeLaki..pGiGkktAeriil 53 
                                       +eL +i  pG ++k    i++
  gi|298676088|ref|YP_003727838.1| 589 DELESItePGASAKIIAGILE 609
                                       666666667777776666655 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00022      0.57      20      48 ..       4      32 ..       1      39 [. 0.87
   2 !    7.2   0.1     0.003       7.8      19      41 ..      39      61 ..      31      94 .. 0.75
   3 ?   -1.0   0.2       1.1   2.7e+03      38      64 ..     357     379 ..     296     410 .. 0.61
   4 ?   -2.6   0.0       3.4   8.6e+03      45      82 ..     412     449 ..     399     459 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00022
                        5_3_exonuc 20 ipGvpgiGektAakLlkeygsleeilenl 48
                                      ++ vp iG+ktA++ + ++gs e+ l+++
  gi|298676088|ref|YP_003727838.1|  4 LQDVPRIGDKTAQRFIGHFGSEEAALNAI 32
                                      678******************99998865 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.003
                        5_3_exonuc 19 nipGvpgiGektAakLlkeygsl 41
                                       i  ++giG+k A++L++e   +
  gi|298676088|ref|YP_003727838.1| 39 SISEIEGIGQKFAISLVHETRGI 61
                                      6899*************998765 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.1
                        5_3_exonuc  38 ygsleeilenldelkekklkekLeenk 64 
                                       y+s ++ile+++    +++ ++L+ +k
  gi|298676088|ref|YP_003727838.1| 357 YQSYQSILEEAK----DSITNELKLEK 379
                                       333333333222....24444444444 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 3.4
                        5_3_exonuc  45 lenldelke...kklkekLeenkeearlskkLatiktdvpl 82 
                                       ++++++ k     ++ ++L+   e+ ++ ++L+  + d+++
  gi|298676088|ref|YP_003727838.1| 412 VRRIQKKKVdhkRQISKTLH---EYHDIIRELVYSVLDFDV 449
                                       44444322111112333333...344556666655555555 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   3.7e-06    0.0094       8      52 ..       7      55 ..       2      57 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.7e-06
                             HHH_2  8 IrhVGektAklLakrFks....ldaLkkasleeLlevddiGeeiAqsiv 52
                                      ++ +G ktA+    +F+s    l a+ + ++  ++e+++iG++ A s v
  gi|298676088|ref|YP_003727838.1|  7 VPRIGDKTAQRFIGHFGSeeaaLNAILNGDIASISEIEGIGQKFAISLV 55
                                      589**************7555588899999***************8865 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.6e-05      0.04       1     103 [.     510     620 ..     510     640 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.6e-05
                                       EEEESSTTSSHHHHHHHHHHHH....................THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS CS
                               AAA   1 vllyGppGtGKTllakavakel....................gvefleisgsellskyvgesekkirelfkeakeka 57 
                                       vll+G    GKT++ + +a+ +                    g +++  s  +l     g+ e+++ ++   a +++
  gi|298676088|ref|YP_003727838.1| 510 VLLSGVNSGGKTSMLELLAQCVilahmgfpvpanaseigitdGLYYFAKSKGTLD---AGAFESSLTDFSVVADNSS 583
                                       799******************5444443333333333322222335555555555...7888888888888777776 PP

                                       TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTE CS
                               AAA  58 kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskv 103
                                         +++++DE++++++         + ++++ +l+ l++ +k+ s v
  gi|298676088|ref|YP_003727838.1| 584 --KVVLVDELESITEPG------ASAKIIAGILETLSENEKSMS-V 620
                                       ..***********8877......888899999999888888654.3 PP

>> Baculo_LEF5  Baculoviridae late expression factor 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   9.1e-05      0.23      18      82 ..      66     136 ..      53     169 .. 0.82
   2 ?   -2.8   0.0       2.3   5.9e+03      77      99 ..     269     291 ..     256     332 .. 0.56
   3 ?   -1.4   0.5      0.83   2.1e+03      58     115 ..     351     409 ..     303     437 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.1e-05
                       Baculo_LEF5  18 klidylkenfPknvknktfn....lsntGhlfhalyayvPsssdker..kqirldeekleklaentkndfk 82 
                                        l d+lk+n   n+ ++ ++    ++ntG+    l+ y+P +s k    kqi+   ++  k a++   d k
  gi|298676088|ref|YP_003727838.1|  66 TLTDFLKTNEAVNIYQRLLDvikqFANTGYARDKLHIYIPYPSSKINliKQIQDTVNYYRKTADVFGKDDK 136
                                       6899*****99999998764333399***************999653339999888888887777665555 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.3
                       Baculo_LEF5  77 tkndfklytelleliekseiddy 99 
                                        + d+ + +e leli++ + +  
  gi|298676088|ref|YP_003727838.1| 269 DNKDLEILKETLELIDEKGDVAT 291
                                       45567777777777775544443 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.83
                       Baculo_LEF5  58 kerkqirldee.kleklaentkndfklytelleliekseiddyicPceliskslleiks 115
                                         rk i    +  le+  +  +n++kl ++   +++    d+   P e+ +++++  k+
  gi|298676088|ref|YP_003727838.1| 351 LMRKEIYQSYQsILEEAKDSITNELKLEKQEKLFVDSLFPDEISYPIEIDDSQVNALKQ 409
                                       44666644433156777778888888888878888877788888888887777766554 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   9.4      0.12   3.1e+02     117     197 ..     228     416 ..     150     437 .. 0.80
   2 ?    4.4   0.0     0.019        48      19      42 ..     507     530 ..     486     602 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.12
                            AAA_23 117 leqfise........llgskkiilnlilflgqerfeefelkdkke................................ 153
                                        +q+i+e        +l   +++l++i++l + +f+ fe++d k+                                
  gi|298676088|ref|YP_003727838.1| 228 DWQIIPEkeiafyakNLPAIDNSLDVIQCLRSNDFNFFEQMDNKDleilketlelidekgdvatgtdpeidrlskih 304
                                       33344433333332255556668999999999999999998888888999999999999999999999999999999 PP

                            AAA_23 154 ................................................rleelekeleeledekkllekleqekeke 182
                                                                                       r e ++  +  le+ k+ + ++++++++e
  gi|298676088|ref|YP_003727838.1| 305 eriyetvsktveyanakldkcleeskmtlsgqdmlrvmngsmeiqdlmRKEIYQSYQSILEEAKDSITNELKLEKQE 381
                                       99999999999999999999999999999999999999999999999988888888888888999999998888888 PP

                            AAA_23 183 k....................eleeleeeleeilk 197
                                       k                    + ++l++++   ++
  gi|298676088|ref|YP_003727838.1| 382 KlfvdslfpdeisypieiddsQVNALKQDIVRRIQ 416
                                       88888888888888887777777777777765555 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.019
                            AAA_23  19 kgltlItGpNGaGKTTildAikla 42 
                                       +  +l++G N  GKT+ l+ +  +
  gi|298676088|ref|YP_003727838.1| 507 NRHVLLSGVNSGGKTSMLELLAQC 530
                                       556899*************99877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (696 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       854  (0.0476323); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.76u 0.32s 00:00:01.08 Elapsed: 00:00:00.50
# Mc/sec: 4164.11
//
Query:       gi|298676089|ref|YP_003727839.1|  [L=191]
Description: imidazoleglycerol-phosphate dehydratase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-63  211.2   1.2    8.7e-63  210.9   1.2    1.1  1  IGPD      Imidazoleglycerol-phosphate dehydratase


Domain annotation for each model (and alignments):
>> IGPD  Imidazoleglycerol-phosphate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.9   1.2   4.8e-67   8.7e-63       1     144 []      31     173 ..      31     173 .. 0.99

  Alignments for each domain:
  == domain 1  score: 210.9 bits;  conditional E-value: 4.8e-67
                                       ....HHHHHHHHHHHHHT--EEEEEEESSH...HHHHHHHHHHHHHHHHHHS..-SSB--EEEEEEEETTEEEEEEE CS
                              IGPD   1 TgigfldhmLdqlakhggfdlkvkvkgdlevddHhtvedvgialGqalkealgdkrgikRfgsallpmDealaeval 77 
                                       Tgigf+dhmL+++akh++fdl+++++gdlevd+Hh++ed+gi++Gqa+++algdk+gi+R+g+a +pmDe+la v+l
  gi|298676089|ref|YP_003727839.1|  31 TGIGFFDHMLSSFAKHSSFDLSISANGDLEVDEHHLIEDTGIVMGQAIDNALGDKKGIARYGEARIPMDESLADVVL 107
                                       9**************************************************************************** PP

                                       E--SS-EEE--..-SB--TT.--HHHHHHHHHHHHHHHT-EEEEEEEE--BHHHHHHHHHHHHHHHH CS
                              IGPD  78 dlsgrpylvleaelkrekigeldtelveeffeslaeaagitlhvkvlrgenahhivealfKafaraL 144
                                       dl gr+ylv++ae+++ ++g ++t+lv++ffes++++a+++lh +v  g+n+hh++ealfKafa+a+
  gi|298676089|ref|YP_003727839.1| 108 DLGGRSYLVMNAEFESLYVGYFSTQLVRHFFESIVQNANMNLHASVY-GDNDHHKIEALFKAFAHAM 173
                                       *********************************************98.*****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1343.88
//
Query:       gi|298676090|ref|YP_003727840.1|  [L=248]
Description: phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-75  252.0   2.7    5.3e-75  251.8   2.7    1.0  1  His_biosynth   Histidine biosynthesis protein
      7e-11   41.8   0.2    5.4e-05   22.4   0.0    2.1  2  Dus            Dihydrouridine synthase (Dus)
    8.7e-09   35.0   1.0      1e-06   28.2   0.1    2.1  2  DHO_dh         Dihydroorotate dehydrogenase
    4.8e-07   29.3   1.6      0.016   14.5   0.2    2.1  2  ThiG           Thiazole biosynthesis protein ThiG
      2e-06   27.4   0.7    8.6e-06   25.4   0.1    1.9  2  NMO            Nitronate monooxygenase
    2.8e-06   26.6   4.1      2e-05   23.8   3.9    1.9  1  IMPDH          IMP dehydrogenase / GMP reductase domain
    5.1e-06   25.9   1.0    0.00023   20.5   0.1    2.1  2  TMP-TENI       Thiamine monophosphate synthase
    8.2e-06   25.1   0.3      0.049   12.8   0.1    2.1  2  NanE           Putative N-acetylmannosamine-6-phosphate epime
    3.6e-05   23.3   2.6     0.0021   17.6   0.1    2.1  2  PcrB           PcrB family
    0.00013   21.4   1.5       0.12   11.8   0.2    2.3  2  G3P_antiterm   Glycerol-3-phosphate responsive antiterminator
    0.00026   20.2   0.1    0.00042   19.6   0.1    1.3  1  DUF561         Protein of unknown function (DUF561)
    0.00089   18.4   0.6       0.63    9.0   0.0    2.1  2  FMN_dh         FMN-dependent dehydrogenase
     0.0011   17.9   1.1       0.06   12.2   0.2    2.1  2  Trp_syntA      Tryptophan synthase alpha chain
     0.0025   17.1   0.2      0.025   13.8   0.0    2.0  2  IGPS           Indole-3-glycerol phosphate synthase
  ------ inclusion threshold ------
      0.013   15.3   0.1        2.1    8.1   0.1    2.3  2  GRDA           Glycine reductase complex selenoprotein A
      0.051   12.7   0.4       0.18   10.9   0.0    1.8  2  Glu_synthase   Conserved region in glutamate synthase
      0.079   13.6   0.0        0.4   11.4   0.0    1.9  2  NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
       0.11   12.5   0.4        7.1    6.7   0.0    2.4  2  ETF_alpha      Electron transfer flavoprotein FAD-binding dom


Domain annotation for each model (and alignments):
>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  251.8   2.7   5.3e-78   5.3e-75       1     228 [.       4     233 ..       4     234 .. 0.99

  Alignments for each domain:
  == domain 1  score: 251.8 bits;  conditional E-value: 5.3e-78
                                       EEEEEEEEETTEEEEECTTCSTCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-S...S CS
                      His_biosynth   1 riipalDlkdGkvVrlvkGdrfqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevf...i 74 
                                       +iipa+D+++Gk+V+lv+G+  +e +  +dpve+a +++++ga+ +h++Dld+a eg+++n  ++++i+++++   +
  gi|298676090|ref|YP_003727840.1|   4 EIIPAIDIREGKCVQLVQGVPGSEIVCLDDPVEAAVDWYNKGARIFHLIDLDGAIEGERKNAPIIQNIVDKFKtedV 80 
                                       69********************************************************************9987779 PP

                                       EEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEECEEEEETTTTEEEEEEHHH CS
                      His_biosynth  75 pvqvGGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarrgykvaikgwreetgldave 151
                                        +qvGGGIrs ed+++ll++g+d+vi++taa++np lik la++fgs++++va+D+++g k+ ++gw++e++++av+
  gi|298676090|ref|YP_003727840.1|  81 VIQVGGGIRSEEDAAQLLNIGVDRVILSTAALENPGLIKGLAKRFGSKSVMVALDSKKG-KISVEGWTKESEFTAVD 156
                                       9**********************************************************.***************** PP

                                       HHHHHHHTT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTCSEEEESHHHHTTSS CS
                      His_biosynth 152 lakkleelgageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelksegvdavivgsalyegel 228
                                       +  k+e+lgag+il+t+id++G ++G + + ++el e+v+ipviasGGv+s++dl ++k+ g+++v+vgsaly++++
  gi|298676090|ref|YP_003727840.1| 157 MGIKFENLGAGSILFTNIDTEGLMQGTETKPIEELVESVTIPVIASGGVTSIDDLLTIKNVGASGVVVGSALYKNKF 233
                                       **************************************************************************998 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.4e-06    0.0014     170     225 ..      63     120 ..      57     143 .. 0.85
   2 !   22.4   0.0   5.4e-08   5.4e-05     171     224 ..     184     236 ..     140     247 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.4e-06
                                       --CHHHHHHHHH-S...S-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHH CS
                               Dus 170 adweaIkevkqavs...ipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfae 225
                                        +   I+++ ++++   +++ + G+I++ eda + l+  G+d v+ + +al+nP l++ 
  gi|298676090|ref|YP_003727840.1|  63 KNAPIIQNIVDKFKtedVVIQVGGGIRSEEDAAQLLNI-GVDRVILSTAALENPGLIKG 120
                                       566678899999988899******************99.*****************985 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 5.4e-08
                                       -CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHH CS
                               Dus 171 dweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfa 224
                                       + + I+e+ ++v+ipvia G++++++d+  i +  Ga gv++g + ++n + +a
  gi|298676090|ref|YP_003727840.1| 184 ETKPIEELVESVTIPVIASGGVTSIDDLLTIKNV-GASGVVVGSALYKNKFKLA 236
                                       55779************************99888.**********999866555 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.1    0.0084       8.3     235     276 ..      69     111 ..      57     126 .. 0.74
   2 !   28.2   0.1     1e-09     1e-06     231     287 ..     185     239 ..     179     243 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0084
                                       HHHHHHTTT.S-EEEE.SS--SHHHHHHHHHHTECEEEESHHH CS
                            DHO_dh 235 relykrlkkeipiIgv.GGiesgeDalekieaGAslvqvytal 276
                                       +++ +++k e  +I v GGi s eDa   ++ G   v + ta 
  gi|298676090|ref|YP_003727840.1|  69 QNIVDKFKTEDVVIQVgGGIRSEEDAAQLLNIGVDRVILSTAA 111
                                       5555555555455555278***********9999988888886 PP

  == domain 2  score: 28.2 bits;  conditional E-value: 1e-09
                                       HHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHH CS
                            DHO_dh 231 lkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakki 287
                                       +k i el + +   ip+I++GG++s +D l   + GAs v v++al+++  k+a+ i
  gi|298676090|ref|YP_003727840.1| 185 TKPIEELVESVT--IPVIASGGVTSIDDLLTIKNVGASGVVVGSALYKNKFKLADAI 239
                                       778899999999..********************************99988888777 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   2.1e-05     0.021     163     207 ..      64     111 ..      45     132 .. 0.83
   2 !   14.5   0.2   1.6e-05     0.016     159     219 ..     181     238 ..     155     244 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.1e-05
                                       -HHHHHHHHHH-...SS-BEEES---SHHHHHHHHHTT-SEEEESHHH CS
                              ThiG 163 nkealkiiieea...kvPvivDAGigspsdaaqamelGadavllntav 207
                                       n+  ++ i++++   +v + v  Gi+s +daaq +++G+d v+l ta 
  gi|298676090|ref|YP_003727840.1|  64 NAPIIQNIVDKFkteDVVIQVGGGIRSEEDAAQLLNIGVDRVILSTAA 111
                                       566788888887544677888999**********************96 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.6e-05
                                       ---S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHH CS
                              ThiG 159 lGllnkealkiiieeakvPvivDAGigspsdaaqamelGadavllntavaeakdpvamAra 219
                                       +G ++ + ++ ++e++++Pvi   G+ s  d  +  ++Ga++v++ +a+ +     ++A a
  gi|298676090|ref|YP_003727840.1| 181 QGTET-KPIEELVESVTIPVIASGGVTSIDDLLTIKNVGASGVVVGSALYKN--KFKLADA 238
                                       55444.56999************************************98754..4555555 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.35   3.5e+02     193     225 ..      76     111 ..      55     114 .. 0.69
   2 !   25.4   0.1   8.6e-09   8.6e-06     181     225 ..     184     228 ..     143     245 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.35
                               NMO 193 d...iPviAaGGiidrrgvaaaLalGAsgvqigtrf 225
                                       +   + +   GGi  +++ a  L +G   v + t+ 
  gi|298676090|ref|YP_003727840.1|  76 KtedVVIQVGGGIRSEEDAAQLLNIGVDRVILSTAA 111
                                       244465666788888888888888888888888875 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 8.6e-09
                               NMO 181 lfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrf 225
                                       +++ +++ ++ v iPviA GG+    ++ ++  +GAsgv +g+++
  gi|298676090|ref|YP_003727840.1| 184 ETKPIEELVESVTIPVIASGGVTSIDDLLTIKNVGASGVVVGSAL 228
                                       3455677888999******************************97 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   3.9     2e-08     2e-05      98     239 ..      83     228 ..      70     248 .] 0.78

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 2e-08
                                       EE-SSTTHHHHHHHHHHTT-SEEEEE-STSSSHHHHHHHHH...HHHHTTTSEEEEEEE-SHHHHHHHHHTT-S.EE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                             IMPDH  98 avgvkedalervkalveagvdvlvvdsahghsekvleavke...ikkkveeveviaGnvataegakaLieagad.av 170
                                        vg    ++e +++l++ gvd +++ +a  ++ + ++ +++    k+ +  ++   G +  +  +k+   + +d ++
  gi|298676090|ref|YP_003727840.1|  83 QVGGGIRSEEDAAQLLNIGVDRVILSTAALENPGLIKGLAKrfgSKSVMVALDSKKGKISVEGWTKESEFTAVDmGI 159
                                       44555556789999****************99999998866222244444577778999866655554444444235 PP

                                       EE.-SS-STTBHHHHHCSB---HHHHHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCC CS
                                       xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 171 kv.GiGpGsiCttrvvagvGvpqltAvaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGsll 239
                                       k   +G+Gsi  t +    G  q t    + e +++  +pvia GG+++  d+     +Ga+ v++Gs l
  gi|298676090|ref|YP_003727840.1| 160 KFeNLGAGSILFTNI-DTEGLMQGTETKPIEELVESVTIPVIASGGVTSIDDLLTIKNVGASGVVVGSAL 228
                                       6534799******86.678*************************************************98 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.022        22     141     179 ..      67     109 ..      59     111 .. 0.78
   2 !   20.5   0.1   2.3e-07   0.00023     118     181 .]     162     228 ..     142     228 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.022
                          TMP-TENI 141 glkelaeale...iPvvaiGGit.lenvaevleagadgvavvs 179
                                        +++++++++   + + + GGi+ +e++a++l+ g+d+v + +
  gi|298676090|ref|YP_003727840.1|  67 IIQNIVDKFKtedVVIQVGGGIRsEEDAAQLLNIGVDRVILST 109
                                       5777888888777788889***72578***********98766 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 2.3e-07
                          TMP-TENI 118 dYigvGpifpTdtKkdaeplgleg..lkelaealeiPvvaiGGitl.envaevleagadgvavvsai 181
                                         +g+G+i  T+  ++  ++g e+  ++el+e+++iPv+a GG+t  +++ ++ + ga+gv v sa+
  gi|298676090|ref|YP_003727840.1| 162 ENLGAGSILFTNIDTEGLMQGTETkpIEELVESVTIPVIASGGVTSiDDLLTIKNVGASGVVVGSAL 228
                                       56899**********997777665338*****************8548999999*********9985 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00022      0.22     120     175 ..      54     110 ..      34     128 .. 0.83
   2 !   12.8   0.1   4.9e-05     0.049     130     179 ..     181     231 ..     134     243 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00022
                                       TTTSSTTS-.SS--H.HHHHHHHHTT--EEEES---SHHHHHHHHTT--SEEEE-HH CS
                              NanE 120 lsGytkeeekaepDf.alvkalseaglkviaeGrintPekakkaieiGvdavvvGsa 175
                                       l G ++ e+k+ p + ++v +++ +++ + + G i + e a++ ++iGvd v++ +a
  gi|298676090|ref|YP_003727840.1|  54 LDGAIEGERKNAPIIqNIVDKFKTEDVVIQVGGGIRSEEDAAQLLNIGVDRVILSTA 110
                                       56777777777776525899********************************99876 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 4.9e-05
                                       SS--HHHHHHHHHT.T--EEEES---SHHHHHHHHTT--SEEEE-HHHH-H CS
                              NanE 130 aepDfalvkalsea.glkviaeGrintPekakkaieiGvdavvvGsaitrl 179
                                       +  + + +++l+e+  + via G + + +   ++ ++G+  vvvGsa+ + 
  gi|298676090|ref|YP_003727840.1| 181 QGTETKPIEELVESvTIPVIASGGVTSIDDLLTIKNVGASGVVVGSALYKN 231
                                       556667788888762678*****************************9775 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   2.1e-06    0.0021     175     215 ..      74     115 ..      35     124 .. 0.79
   2 !    6.0   0.3    0.0071       7.1     180     222 ..     196     242 ..     174     245 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.1e-06
                                       HHHHSSSEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHH CS
                              PcrB 175 kkklekarlivGGGirsaEkAkevvea.ADvivvGnvveekd 215
                                       k k e+  + vGGGirs+E+A++ ++   D ++  ++  e++
  gi|298676090|ref|YP_003727840.1|  74 KFKTEDVVIQVGGGIRSEEDAAQLLNIgVDRVILSTAALENP 115
                                       3356778889*****************99*999988877765 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0071
                                       SSEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHH...HCHHHHH CS
                              PcrB 180 karlivGGGirsaEkAkevvea.ADvivvGnvveekd...erkidai 222
                                       ++ +i  GG+ s ++   + +  A  +vvG ++++++    ++ida+
  gi|298676090|ref|YP_003727840.1| 196 TIPVIASGGVTSIDDLLTIKNVgASGVVVGSALYKNKfklADAIDAV 242
                                       4567899********99999999***********9995555566655 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.1    0.0012       1.2     127     171 ..      68     111 ..      65     112 .. 0.87
   2 !   11.8   0.2   0.00012      0.12     123     168 ..     180     225 ..     168     228 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0012
                                       GHHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE--HH CS
                      G3P_antiterm 127 vpkvikeikkelkipiiaGGLietkedveealkaGaiavstsnke 171
                                       ++++++++k+e ++ i  GG i+++ed  ++l+ G++ v  s+ +
  gi|298676090|ref|YP_003727840.1|  68 IQNIVDKFKTE-DVVIQVGGGIRSEEDAAQLLNIGVDRVILSTAA 111
                                       57788888888.899999*********************999876 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00012
                                       ESGGGHHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE- CS
                      G3P_antiterm 123 lPglvpkvikeikkelkipiiaGGLietkedveealkaGaiavsts 168
                                       + g+  k i+e+ ++++ip+ia+G +++ +d+ ++ + Ga++v ++
  gi|298676090|ref|YP_003727840.1| 180 MQGTETKPIEELVESVTIPVIASGGVTSIDDLLTIKNVGASGVVVG 225
                                       556668889********************************99765 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   4.2e-07   0.00042     180     231 ..     190     240 ..     176     246 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 4.2e-07
                            DUF561 180 eiskkvslPvicasGlsdvtvplals.lgasGiGigsavsklndeeemvalls 231
                                       e++++v++Pvi++ G++++   l+++ +gasG+ +gsa+ k  ++ ++  +++
  gi|298676090|ref|YP_003727840.1| 190 ELVESVTIPVIASGGVTSIDDLLTIKnVGASGVVVGSALYK--NKFKLADAID 240
                                       68899*******************9747*********9854..5555555555 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.1    0.0015       1.5     264     300 ..      71     108 ..      57     113 .. 0.59
   2 !    9.0   0.0   0.00064      0.63     263     303 ..     190     228 ..     181     239 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0015
                                       HHHHH...SS-EEEESS--SHHHHHHHHHTT-SEEEES CS
                            FMN_dh 264 iveavgg.rievlvDgGirrGsDvlkAlalGAdavllG 300
                                       iv++ +  ++ + v gGir+ +D+++ l +G d v+l 
  gi|298676090|ref|YP_003727840.1|  71 IVDKFKTeDVVIQVGGGIRSEEDAAQLLNIGVDRVILS 108
                                       55555532455555666666666666665555555543 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00064
                                       HHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHH CS
                            FMN_dh 263 eiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpf 303
                                       e+ve v   i+v+++gG+++  D l    +GA++v++G ++
  gi|298676090|ref|YP_003727840.1| 190 ELVESV--TIPVIASGGVTSIDDLLTIKNVGASGVVVGSAL 228
                                       445555..49***************************9765 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.012        12     184     227 ..      66     109 ..      51     123 .. 0.78
   2 !   12.2   0.2     6e-05      0.06     190     232 ..     188     231 ..     177     246 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.012
                                       TTHHHHHHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-H CS
                         Trp_syntA 184 aevdelverlkkltavPvavGFGistkeqvkqva.kvadGvivGS 227
                                         ++++v + k+  +v + vG Gi+++e+++q+   + d vi   
  gi|298676090|ref|YP_003727840.1|  66 PIIQNIVDKFKTE-DVVIQVGGGIRSEEDAAQLLnIGVDRVILST 109
                                       4566777777655.5999*************99956678887655 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 6e-05
                                       HHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHHH CS
                         Trp_syntA 190 verlkkltavPvavGFGistkeqvkqva.kvadGvivGSalvkk 232
                                       +e+l +  + Pv    G+ + ++  ++   +a+Gv+vGSal k+
  gi|298676090|ref|YP_003727840.1| 188 IEELVESVTIPVIASGGVTSIDDLLTIKnVGASGVVVGSALYKN 231
                                       6677777789*99999***********9899*********9775 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.19   1.9e+02     201     242 ..      70     112 ..      66     121 .. 0.76
   2 !   13.8   0.0   2.5e-05     0.025     202     245 ..     188     232 ..     180     241 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.19
                                       HHCHCC-TT.SEEEEESSS-SHHHHHHHCCTT-SEEEESHHHH CS
                              IGPS 201 eLaklvpkd.vllvaeSGiktredveklkeegvnafLvGeslm 242
                                       +++++++++ v++    Gi+++ed+ +l + gv+ ++  ++ +
  gi|298676090|ref|YP_003727840.1|  70 NIVDKFKTEdVVIQVGGGIRSEEDAAQLLNIGVDRVILSTAAL 112
                                       566677755266666789************9999988776655 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 2.5e-05
                                       HCHCC-TT.SEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-T CS
                              IGPS 202 Laklvpkd.vllvaeSGiktredveklkeegvnafLvGeslmrqe 245
                                       + +lv++  + ++a  G+++ +d+ ++k++g++++ vG++l +++
  gi|298676090|ref|YP_003727840.1| 188 IEELVESVtIPVIASGGVTSIDDLLTIKNVGASGVVVGSALYKNK 232
                                       444444333889*****************************9875 PP

>> GRDA  Glycine reductase complex selenoprotein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1    0.0021       2.1      50      82 ..      63      98 ..      16     105 .. 0.74
   2 ?    5.0   0.0     0.019        19      48      76 ..     111     139 ..     105     150 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0021
                              GRDA 50 enqkrvkelaekfgaenvvvllGa...aeaeaagla 82
                                      +n   ++++ +kf +e+vv+ +G+   +e +aa+l 
  gi|298676090|ref|YP_003727840.1| 63 KNAPIIQNIVDKFKTEDVVIQVGGgirSEEDAAQLL 98
                                      466679****************97444677777765 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.019
                              GRDA  48 dlenqkrvkelaekfgaenvvvllGaaea 76 
                                        len   +k la++fg++ v+v l + ++
  gi|298676090|ref|YP_003727840.1| 111 ALENPGLIKGLAKRFGSKSVMVALDSKKG 139
                                       589999****************9987655 PP

>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00018      0.18     266     307 ..      71     112 ..      65     120 .. 0.87
   2 ?   -0.6   0.1      0.58   5.8e+02     275     305 ..     197     227 ..     176     229 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00018
                                       HHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-SHHHH CS
                      Glu_synthase 266 lkeeglrdrvsliadGglktgadvvkalalGAdavgigtaal 307
                                       ++++   + v++++ Gg+++ +d +  l +G d v ++taal
  gi|298676090|ref|YP_003727840.1|  71 IVDKFKTEDVVIQVGGGIRSEEDAAQLLNIGVDRVILSTAAL 112
                                       555556788*******************************98 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.58
                                       -EEEEESS--SHHHHHHHHHHT-SEEE-SHH CS
                      Glu_synthase 275 vsliadGglktgadvvkalalGAdavgigta 305
                                       + +ia+Gg+ + +d++    +GA  v +g+a
  gi|298676090|ref|YP_003727840.1| 197 IPVIASGGVTSIDDLLTIKNVGASGVVVGSA 227
                                       5578999999999999999999999998875 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0004       0.4      41     106 ..      61     124 ..      41     135 .. 0.84
   2 ?   -0.4   0.0       1.7   1.7e+03      41      71 ..     178     207 ..     165     215 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0004
                                       HHT--CB---HHHHHHHHS-EEEEE-S--HHHHTTHHHHHHTTEEEE-S--CGGG-HHHHHHHTSS CS
                     NAD_binding_3  41 llasealtldlddliahldpdvvVEcasseavaelvlkaLkagkdvvtankgaladealyeeLrea 106
                                       +++++++ +++ d ++    dvv+ +++    +e +++ L+ g+d v+ + +al +++l + L++ 
  gi|298676090|ref|YP_003727840.1|  61 ERKNAPIIQNIVDKFK--TEDVVIQVGGGIRSEEDAAQLLNIGVDRVILSTAALENPGLIKGLAKR 124
                                       5667777778777777..8*******999999**********************999888888765 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.7
                                       HHT--CB---HHHHHHHHS-EEEEE-S--HH CS
                     NAD_binding_3  41 llasealtldlddliahldpdvvVEcassea 71 
                                        l + ++t+++++l++ + ++v+   +++++
  gi|298676090|ref|YP_003727840.1| 178 GLMQGTETKPIEELVESVTIPVI-ASGGVTS 207
                                       56678899999999995555443.3355555 PP

>> ETF_alpha  Electron transfer flavoprotein FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0072       7.1       3      26 ..      75      98 ..      73     129 .. 0.89
   2 ?    3.6   0.1     0.066        65      15      66 ..     178     229 ..     176     231 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0072
                                      TTT-S-EEEE-GGGSSGGGHHHHH CS
                         ETF_alpha  3 LeeakvvvsgGrGlkskenlelle 26
                                      +++++vv+ +G G++s+e+ ++l 
  gi|298676090|ref|YP_003727840.1| 75 FKTEDVVIQVGGGIRSEEDAAQLL 98
                                      57899***********99987665 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.066
                                       GGSSGGGHHHHHHHHHHHT-EEEE-HHHHTTTSS-CCCB-SSSS-----S-E CS
                         ETF_alpha  15 GlkskenlelleelaealgaavgasRavvdagwipeerqvGqtGktvaPkly 66 
                                       Gl +  + + +eel e +   v as  v+  + +   + vG +G +v   ly
  gi|298676090|ref|YP_003727840.1| 178 GLMQGTETKPIEELVESVTIPVIASGGVTSIDDLLTIKNVGASGVVVGSALY 229
                                       667777888899999999999999999999888888899********99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 1580.99
//
Query:       gi|298676091|ref|YP_003727841.1|  [L=284]
Description: ATP phosphoribosyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.1e-49  167.6   0.2      3e-49  167.1   0.2    1.2  1  HisG       ATP phosphoribosyltransferase
      8e-28   96.4   0.3    3.7e-27   94.3   0.2    2.2  3  HisG_C     HisG, C-terminal domain
      0.002   17.6   0.0     0.0028   17.1   0.0    1.3  1  SBP_bac_3  Bacterial extracellular solute-binding proteins, f
     0.0027   17.7   0.0      0.071   13.0   0.0    2.2  2  NMT1       NMT1/THI5 like


Domain annotation for each model (and alignments):
>> HisG  ATP phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.1   0.2   6.7e-53     3e-49       1     158 [.      50     202 ..      50     204 .. 0.96

  Alignments for each domain:
  == domain 1  score: 167.1 bits;  conditional E-value: 6.7e-53
                                       -GGGHHHHHHTTSSSEEEEEHHHHHHCT...TEEEEEEESESEEEEEEEEETTSS--SGCGG.TT-.EEEEES-HHH CS
                              HisG   1 raadiptyVeegavdlGitGkDvveEskeeeeveelldLgfgkcklvvavpeesevkslkdlvedkgkriaTsypnl 77 
                                       raadip+yV++ga+d+GitG D+v E++  ++v+ +ldL++gk++l++avpe+s+++s+++l   +g++i+T++pn+
  gi|298676091|ref|YP_003727841.1|  50 RAADIPEYVQDGAADIGITGIDLVSETD--ADVDLMLDLNYGKSNLMLAVPEDSSIESVEEL---EGMKIGTEFPNI 121
                                       89************************75..57*************************99988...567********* PP

                                       HHHHHHHTT-EEEEEE-SS-CTHHHHTTS-SEEEEEESSSHHHHHTTEEEEEEEEEEEEEEEEEHHHHHSHHHHHHH CS
                              HisG  78 akkyfeekglkveiiklsGsvEaapalglaDaIvDlvetGeTLrangLkaietilessavLiankkslkkkekieel 154
                                       +kk+f++k++++e+ik+sG++E++p +g+aDaIvD+ ++G+T   n+Lk +e++++ss  +ian++s k+k+ki+++
  gi|298676091|ref|YP_003727841.1| 122 TKKFFDSKNINIEVIKVSGACEMTPYIGVADAIVDISSSGTTFVLNNLKPVEKVFSSSVYMIANHQSAKRKDKIHHI 198
                                       ********************************************************************988899999 PP

                                       HHHH CS
                              HisG 155 lerl 158
                                        + +
  gi|298676091|ref|YP_003727841.1| 199 KTAF 202
                                       8876 PP

>> HisG_C  HisG, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.2   9.8e+03      27      36 ..      13      22 ..      12      25 .. 0.69
   2 ?   -1.7   0.0      0.77   3.5e+03       7      25 ..      93     111 ..      84     116 .. 0.59
   3 !   94.3   0.2   8.2e-31   3.7e-27       1      73 []     208     281 ..     208     281 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.2
                                      SS-EEEE-.S CS
                            HisG_C 27 rsPTvsplad 36
                                      ++PTv  l++
  gi|298676091|ref|YP_003727841.1| 13 NEPTVKLLKE 22
                                      7899987765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.77
                                       EEEEEEGGGHHHHHHH--- CS
                            HisG_C   7 lmynvpkesleevlkilPG 25 
                                       lm+ vp++s  e ++ l G
  gi|298676091|ref|YP_003727841.1|  93 LMLAVPEDSSIESVEELEG 111
                                       4555555555444444444 PP

  == domain 3  score: 94.3 bits;  conditional E-value: 8.2e-31
                                       TTTEEEEEEEEEGGGHHHHHHH---SSS-EEEE-..SS-EEEEEEEEECCCHHHHHHHHHCTT-EEEEEEE-S- CS
                            HisG_C   1 ArkyvllmynvpkesleevlkilPGlrsPTvspla.degwvaVsavveekevaevideLkaaGAsdIlvlpiek 73 
                                       A+++++lm+nvpk+sl+ev+++lPGl++PTv++++ ++ ++aV+avv+ +++++++++Lk++GA+dIlv+pie+
  gi|298676091|ref|YP_003727841.1| 208 AEGKRYLMMNVPKDSLDEVKEVLPGLSGPTVMKVEsESSTLAVHAVVDSDMIFTTVNNLKEVGARDILVVPIER 281
                                       899*******************************98999*********************************96 PP

>> SBP_bac_3  Bacterial extracellular solute-binding proteins, family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   6.3e-07    0.0028      47     161 ..      51     159 ..      36     201 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.3e-07
                                       GGGHHHHHHTTSSSEEESSEB--HHHHTTEEEES..ESEEEEEEEEEEETTSHGTCCHSSCGCGTTSEEEEETTSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3  47 wdelipalksgkvDiaiaaititpeReekvdFsq..pyfsagqvllvrkkdaskissiksladLkgkkvgvqagsta 121
                                        +++ + +++g +Di i++i    e  + vd+     y ++++ l+v+++     ssi+s+++L+g+k+g+     +
  gi|298676091|ref|YP_003727841.1|  51 AADIPEYVQDGAADIGITGIDLVSETDADVDLMLdlNYGKSNLMLAVPED-----SSIESVEELEGMKIGTEFPNIT 122
                                       55666789***********************9875689999999999954.....4799999**********99999 PP

                                       HHHHHHHHHCTSEEEEESSHHHHHHHHHTTSSSEEEEEHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3 122 eellkeelkkgaeivefdtleealqaLkngrvdavvadsp 161
                                       ++++ +++  ++e++ +    e++     g +da+v  s+
  gi|298676091|ref|YP_003727841.1| 123 KKFFDSKNI-NIEVIKVSGACEMTP--YIGVADAIVDISS 159
                                       999998544.444444333333333..4444444444444 PP

>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   1.6e-05     0.071      31      98 ..      51     116 ..      43     123 .. 0.80
   2 ?    2.6   0.0     0.025   1.1e+02      12      54 ..     122     164 ..     118     222 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.6e-05
                                       TTHHHHHHHCTS-SEEEE-HHHHHHHHHTT--EEEEEEEE-S--EEEEEECCC--SSGGGGTTSEEEE CS
                              NMT1  31 psdatelvasgkadfgvsyqesllaarakglpvvsvaallqeplsglivlkdsgikspkDLkGkrigy 98 
                                        +d +e+v  g+ad+g++   +l+ + ++++++    ++  +++  l+v +ds i+s+++L+G +ig+
  gi|298676091|ref|YP_003727841.1|  51 AADIPEYVQDGAADIGITGI-DLVSETDADVDLMLDLNYG-KSNLMLAVPEDSSIESVEELEGMKIGT 116
                                       47899************975.5665777777776666655.5566789999999************97 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.025
                                       HTTHHHHTTEEEEEE--SSTTHHHHHHHCTS-SEEEE-HHHHH CS
                              NMT1  12 ekGYFkeeGldVeivepadpsdatelvasgkadfgvsyqesll 54 
                                       +k +F  +++++e+++ ++ ++ t++++  +a + +s++ +++
  gi|298676091|ref|YP_003727841.1| 122 TKKFFDSKNINIEVIKVSGACEMTPYIGVADAIVDISSSGTTF 164
                                       5789***************999999999888888777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1861.77
//
Query:       gi|298676092|ref|YP_003727842.1|  [L=127]
Description: response regulator receiver protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.7e-30  103.8   0.5    6.5e-30  103.6   0.5    1.0  1  Response_reg  Response regulator receiver domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.6   0.5   3.6e-34   6.5e-30       1     111 [.       8     119 ..       8     120 .. 0.96

  Alignments for each domain:
  == domain 1  score: 103.6 bits;  conditional E-value: 3.6e-34
                                       EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCT..TTSEEE CS
                      Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireed..pelpvi 75 
                                       vl+v+D+  ++el+ +ll++ gy +v++aedg  ale+lk+ k+dlillD+++p+mdGlell+++++++   ++pv+
  gi|298676092|ref|YP_003727842.1|   8 VLVVEDNVFNMELTVDLLKSYGY-NVTKAEDGYIALEKLKNIKIDLILLDMQLPKMDGLELLSKLKNDPetMNIPVV 83 
                                       8**********************.*******************************************9977789*** PP

                                       EEESSTSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                      Response_reg  76 iltahseeedavealkagaddflsKpfdpeeLlkal 111
                                       +ltah+   d+++ ++ag d+++sKp+d+ + ++ +
  gi|298676092|ref|YP_003727842.1|  84 ALTAHAMLGDKKRFIDAGCDGYISKPMDIYKFKSQI 119
                                       ***************************998877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 904.64
//
Query:       gi|298676093|ref|YP_003727843.1|  [L=185]
Description: cobalt transport protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-35  123.2   9.0    1.3e-35  123.0   9.0    1.0  1  CbiQ             Cobalt transport protein
  ------ inclusion threshold ------
      0.056   13.0   0.2       0.39   10.3   0.1    1.9  2  Cyto_heme_lyase  Cytochrome c/c1 heme lyase


Domain annotation for each model (and alignments):
>> CbiQ  Cobalt transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.0   9.0   1.5e-39   1.3e-35      40     214 ..       2     173 ..       1     176 [. 0.89

  Alignments for each domain:
  == domain 1  score: 123.0 bits;  conditional E-value: 1.5e-39
                                       HHHHHTTS---HHHHHHHCCCHCHHHHHHHHHHE.......EECTTEEE...E-TTHHHHHHHHHHHHHHHHHHHHH CS
                              CbiQ  40 lllllllvilprvlaqalilpllflllgllillfqlittegefvfagggqisitseGllrglllalRiltllsllll 116
                                       ++++ll+  +  +++++  +++ +l++   ++++  +t++g +++++ + i++t eG+++g l+++R +t+++l++ 
  gi|298676093|ref|YP_003727843.1|   2 ITFTLLIISKLPFKFIFNHVKWVSLFILPFLIIM-PFTVNGDVLVNISN-ITVTHEGITYGFLITVRAFTAILLVFT 76 
                                       5777777777767777777777666655555554.46899999999999.*************************** PP

                                       HHHHS-HHHHHHHCCCSS--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTS..SHHHHHHHHHHHHHHHHHHH CS
                              CbiQ 117 lalTTppeeltsslerlgvPlelalillLayRfiflLleevqrikqAqklRlgdsklgirrslrslgkliaalflra 193
                                       ++ T  + + +++l+ l++P +l+ +l+ +yR+if++l+e+qr+++A+++ +++  l+i + ++++gk +++l++++
  gi|298676093|ref|YP_003727843.1|  77 MLGTMRFDTTIKALHMLKIPNPLIQMLMFTYRYIFVFLDEFQRMWTAMTSKGFKPGLNISS-MSKIGKSVGMLVVKS 152
                                       *******************************************************888888.9************** PP

                                       HHHHHHHHHHHHTTS-SS... CS
                              CbiQ 194 lkraervalAmeaRGYtgsee 214
                                       ++ra+rv++Am ++GYtg+++
  gi|298676093|ref|YP_003727843.1| 153 YERAQRVYQAMLSKGYTGNPN 173
                                       ******************654 PP

>> Cyto_heme_lyase  Cytochrome c/c1 heme lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.025   2.2e+02     125     137 ..     118     130 ..     116     147 .. 0.80
   2 ?   10.3   0.1   4.4e-05      0.39     118     145 ..     150     177 ..     132     183 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.025
                   Cyto_heme_lyase 125 qqmynAmlrKGye 137
                                       q+m+ Am  KG++
  gi|298676093|ref|YP_003727843.1| 118 QRMWTAMTSKGFK 130
                                       99*********84 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 4.4e-05
                   Cyto_heme_lyase 118 lWeYPspqqmynAmlrKGyedipedave 145
                                       +  Y   q++y+Aml KGy+  p++ v+
  gi|298676093|ref|YP_003727843.1| 150 VKSYERAQRVYQAMLSKGYTGNPNTIVK 177
                                       5578999************999988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1360.77
//
Query:       gi|298676094|ref|YP_003727844.1|  [L=266]
Description: hypothetical protein Metev_2223 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.9e-51  173.1   0.2    7.1e-51  172.8   0.2    1.1  1  Met_10           Met-10+ like-protein
    2.8e-05   23.9   0.0    0.00073   19.3   0.0    2.1  1  UPF0020          Putative RNA methylase family UPF0020
    3.4e-05   23.5   0.1    8.3e-05   22.2   0.0    1.6  2  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    3.8e-05   23.4   0.0    6.8e-05   22.6   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
     0.0006   19.7   0.1     0.0012   18.7   0.0    1.5  2  PRMT5            PRMT5 arginine-N-methyltransferase
  ------ inclusion threshold ------
      0.022   15.4   0.0       0.05   14.3   0.0    1.6  2  Methyltransf_25  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.8   0.2   2.4e-54   7.1e-51       2     199 .]      22     220 ..      21     220 .. 0.97

  Alignments for each domain:
  == domain 1  score: 172.8 bits;  conditional E-value: 2.4e-54
                                       EEEEETTEEEEEB-TTSSHHHHHHHHHHHHHS.S-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEE CS
                            Met_10   2 kfeiiGdvvilnlreelkeykkvigevildkt.kvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklD 77 
                                       +f+iiGd++++ ++ el+ yk +i+++i  ++ +vkt+l+k+++v+g  Rt ++++l G++ t+t h+E+g ++k+D
  gi|298676094|ref|YP_003727844.1|  22 RFDIIGDIAVVSIPYELDTYKFDIARAITAVHrNVKTILNKTNKVDGYKRTSDFKILFGNE-TITTHREHGFSYKFD 97 
                                       79***********************************************************.*************** PP

                                       TTTS---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEE CS
                            Met_10  78 vskvyfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvk 154
                                       v kv+f+++l+ Er+rl++++++ e ++  f G+Gpfaip+a y+ +   +ai++nPe++k+l+en+ lNkv++ ++
  gi|298676094|ref|YP_003727844.1|  98 VGKVFFNNRLSYERQRLIAKINPYEKILIPFCGVGPFAIPAAFYGFKA--VAIEKNPEAFKWLQENVCLNKVKDSIT 172
                                       ******************************************977555..9************************** PP

                                       EEES-GGG---...TT-EEEEEE--TTTGGGGHHHHHHHEEEEEEEEE CS
                            Met_10 155 pileDgrevir...eqladrvvmnlpksaieFldkvlaalkdggvihy 199
                                        i++D+ ++ +   +  +drv+ + p+   + l  + +++k +g+ih+
  gi|298676094|ref|YP_003727844.1| 173 LIQKDVTDISTflnSYDFDRVIVPTPYGMDNILLYIAEFVKSKGFIHF 220
                                       ****9998776666999******************************9 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   2.5e-07   0.00073      24     132 ..     116     200 ..     113     203 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.5e-07
                                       TT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHHHHHHHTT CS
                           UPF0020  24 agwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvvqgareNaekag 100
                                       a+++p e++l P+CG G ++I aa  g +++                          ++++++++ +  +eN    +
  gi|298676094|ref|YP_003727844.1| 116 AKINPYEKILIPFCGVGPFAIPAAFYGFKAV--------------------------AIEKNPEAFKWLQENVCLNK 166
                                       67788899999******************99..........................89999999999999999999 PP

                                       -GGGEEEEE--GGG--..STTS---EEEE----- CS
                           UPF0020 101 vgdliefsqadaakLr..lkegevdvivtnpPYG 132
                                       v+d+i++ q+d++++   l++ ++d ++   PYG
  gi|298676094|ref|YP_003727844.1| 167 VKDSITLIQKDVTDIStfLNSYDFDRVIVPTPYG 200
                                       9999999999999999876666999999999999 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.1   3.4e+03      45      65 ..      43      63 ..      38      71 .. 0.72
   2 !   22.2   0.0   2.8e-08   8.3e-05       3      82 ..     123     200 ..     121     203 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.1
                   Methyltransf_15 45 Ygvsdkitlvlgdvfellakl 65
                                      ++++  it v+ +v+++l+k+
  gi|298676094|ref|YP_003727844.1| 43 FDIARAITAVHRNVKTILNKT 63
                                      567777888888888777765 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 2.8e-08
                   Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflSp 79 
                                        il +f+G G  +i  a ++ k +aie+n+e  +  q+N  +  v+d itl++ dv+++  +l++     d v++  
  gi|298676094|ref|YP_003727844.1| 123 KILIPFCGVGPFAIPAAFYGFKAVAIEKNPEAFKWLQENVCLNKVKDSITLIQKDVTDISTFLNSYDF--DRVIVPT 197
                                       57889**************889************************************9999766665..9999888 PP

                   Methyltransf_15  80 PwG 82 
                                       P G
  gi|298676094|ref|YP_003727844.1| 198 PYG 200
                                       887 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   2.3e-08   6.8e-05      44     141 ..     123     217 ..     112     233 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2.3e-08
                                       EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEEE- CS
                     Cons_hypoth95  44 rvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivflD 120
                                       ++L  f+G G  ++ A+  g  kav++ek++ea+k l+en+   k++++++ +++d ++    l  ++  fd v + 
  gi|298676094|ref|YP_003727844.1| 123 KILIPFCGVGPFAIPAAFYG-FKAVAIEKNPEAFKWLQENVCLNKVKDSITLIQKDVTDISTFL--NSYDFDRVIVP 196
                                       56677999999999999999.57899*******************9997777777776666555..7889******* PP

                                       -SSSTTCH.HHHHHHHHHTT- CS
                     Cons_hypoth95 121 PPyakellieevlelleekkl 141
                                        Py  ++++  + e +++k+ 
  gi|298676094|ref|YP_003727844.1| 197 TPYGMDNILLYIAEFVKSKGF 217
                                       ****99986666666666555 PP

>> PRMT5  PRMT5 arginine-N-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.2   6.6e+03      95     109 ..      48      62 ..      36      73 .. 0.53
   2 !   18.7   0.0     4e-07    0.0012      94     134 ..     143     183 ..     135     210 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.2
                                       EEEEEES-HHHHHHH CS
                             PRMT5  95 kivavEKnpnavvtL 109
                                        i+av +n ++++  
  gi|298676094|ref|YP_003727844.1|  48 AITAVHRNVKTILNK 62 
                                       344444444444433 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 4e-07
                                       EEEEEEES-HHHHHHHHHHHHHHTTCCGCEEEES-CCCCCH CS
                             PRMT5  94 vkivavEKnpnavvtLqkkvneekWeekveviksdmrelka 134
                                       +k va+EKnp+a+  Lq++v  +k ++++++i++d+ ++++
  gi|298676094|ref|YP_003727844.1| 143 FKAVAIEKNPEAFKWLQENVCLNKVKDSITLIQKDVTDIST 183
                                       6889*******************************988765 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0         6   1.8e+04      65      90 ..      43      53 ..      31      63 .. 0.54
   2 ?   14.3   0.0   1.7e-05      0.05       6      69 ..     129     194 ..     124     214 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 6
                                      EEEEEEESTGGGSSHHHHHHHHHHHH CS
                   Methyltransf_25 65 fDlvvssgalhhlsdedlekalkeia 90
                                      fD+  +               +  ++
  gi|298676094|ref|YP_003727844.1| 43 FDIARA---------------ITAVH 53
                                      333333...............33333 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.7e-05
                                       -TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSS..STTTEEEEE CS
                   Methyltransf_25   6 cGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpf..edgsfDlvv 69 
                                       cG G +++ +a   g  k ++++ ++e+ +  +e++  +++  +++++q+d++d++   ++  fD v+
  gi|298676094|ref|YP_003727844.1| 129 CGVGPFAIPAAFY-G-FKAVAIEKNPEAFKWLQENVCLNKVkdSITLIQKDVTDISTflNSYDFDRVI 194
                                       **********987.5.********************9999999***********99512444666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1975.89
//
Query:       gi|298676095|ref|YP_003727845.1|  [L=96]
Description: hypothetical protein Metev_2224 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.037   14.3   0.5        8.3    6.8   0.0    2.1  2  Stap_Strp_tox_C  Staphylococcal/Streptococcal toxin, beta-gra
        1.7    8.5   6.1       0.19   11.6   1.2    1.8  2  Myosin_N         Myosin N-terminal SH3-like domain


Domain annotation for each model (and alignments):
>> Stap_Strp_tox_C  Staphylococcal/Streptococcal toxin, beta-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1    0.0014        12      45      82 ..      10      49 ..       5      54 .. 0.83
   2 ?    6.8   0.0   0.00092       8.3      15      45 ..      64      94 ..      58      95 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0014
                   Stap_Strp_tox_C 45 yniY..ekeskyekGklklalndekkisydlfdlgeedre 82
                                      y ++  + es y  G+++  ++ ++k+ + + d+++ +++
  gi|298676095|ref|YP_003727845.1| 10 YSLFsiDDESGYVVGNVTAVNEKGDKFAVTIEDAEGYYED 49
                                      677777899*****************99988887776555 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.00092
                   Stap_Strp_tox_C 15 kveisavkidKkevTiqEldvkvRkyLikky 45
                                       ve++ v  +K +vT  E+d kv    i+ky
  gi|298676095|ref|YP_003727845.1| 64 IVETEIVMGKKLKVTYTEIDGKVSAIRIEKY 94
                                      566788889999***********99988888 PP

>> Myosin_N  Myosin N-terminal SH3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.2   2.1e-05      0.19       8      32 ..      16      42 ..      15      44 .. 0.93
   2 ?   -1.3   0.3      0.23   2.1e+03      22      28 ..      71      77 ..      63      86 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.1e-05
                                      TSTTS-EEEEEE..EEESSEEEEEETT CS
                          Myosin_N  8 DpkegyvkGeIk..eeeGdkvtVeted 32
                                      D++ gyv G ++   e+Gdk+ V  ed
  gi|298676095|ref|YP_003727845.1| 16 DDESGYVVGNVTavNEKGDKFAVTIED 42
                                      999******************999987 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.23
                                      ESSEEEE CS
                          Myosin_N 22 eGdkvtV 28
                                      +G k+ V
  gi|298676095|ref|YP_003727845.1| 71 MGKKLKV 77
                                      3344444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 714.69
//
Query:       gi|298676096|ref|YP_003727846.1|  [L=222]
Description: type 11 methyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-19   71.0   0.0    1.7e-19   70.3   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    8.1e-19   68.0   0.0      1e-18   67.8   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    1.1e-18   67.7   0.0    1.6e-18   67.1   0.0    1.2  1  Methyltransf_11  Methyltransferase domain
      3e-17   62.8   0.0    3.7e-17   62.5   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
      7e-14   52.4   0.0    1.3e-13   51.5   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    5.1e-13   48.9   0.1    3.1e-12   46.3   0.1    1.9  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    1.8e-05   24.5   0.0    2.5e-05   24.0   0.0    1.2  1  NodS             Nodulation protein S (NodS)
    2.4e-05   23.8   0.0    3.8e-05   23.1   0.0    1.3  1  CMAS             Mycolic acid cyclopropane synthetase
     0.0001   21.5   0.0    0.00018   20.7   0.0    1.4  1  DREV             DREV methyltransferase
    0.00025   20.6   0.0    0.00047   19.7   0.0    1.4  1  Methyltransf_4   Putative methyltransferase
    0.00043   20.2   0.0     0.0013   18.7   0.0    1.7  2  Methyltransf_18  Methyltransferase domain
    0.00045   20.0   0.0    0.00064   19.5   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    0.00066   19.5   0.0      0.001   18.9   0.0    1.3  1  DUF938           Protein of unknown function (DUF938)
     0.0011   18.5   0.0     0.0017   17.8   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0019   17.3   0.0     0.0027   16.8   0.0    1.3  1  RrnaAD           Ribosomal RNA adenine dimethylase
     0.0071   15.9   0.0       0.01   15.4   0.0    1.2  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
      0.022   14.4   0.0      0.038   13.6   0.0    1.3  1  MetW             Methionine biosynthesis protein MetW
      0.057   12.8   0.0      0.086   12.2   0.0    1.3  1  TehB             Tellurite resistance protein TehB
       0.15   11.7   0.0       0.21   11.2   0.0    1.2  1  UPF0020          Putative RNA methylase family UPF0020


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.3   0.0   1.8e-22   1.7e-19       1      96 [.      57     149 ..      57     149 .. 0.94

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 1.8e-22
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalhh 76 
                                       vL++G+GtG++++++a ++  ++vtg+Dis++m+++ar+++ e+g+ n++f++ da +lpf++++f  +vs+++l+ 
  gi|298676096|ref|YP_003727846.1|  57 VLEIGTGTGEIAFYIAPKC--KNVTGIDISPGMIDIARKKNTESGYnNLSFQVEDAYNLPFDKNEFTKIVSCNVLQT 131
                                       9*****************9..9*************************************************988999 PP

                                       SSHHHHHHHHHHHHHHEEEE CS
                   Methyltransf_25  77 lsdedlekalkeiarvLkpg 96 
                                       ++++   + ++e+ ++L +g
  gi|298676096|ref|YP_003727846.1| 132 MKNPY--RSIQECGKILDKG 149
                                       88665..7799999998765 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.8   0.0   1.1e-21     1e-18       7     164 ..      38     204 ..      28     205 .. 0.82

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 1.1e-21
                   Methyltransf_23   7 eelsdklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae......kakkaqkdqfdeqeaa 77 
                                       e+++++  +++ + ++g +vL+iG+GtG+ + +++++ ++vtg+D+sp +++ia+      +  +  ++ +d+ + +
  gi|298676096|ref|YP_003727846.1|  38 EQYKAFKSKIASYTQSGDSVLEIGTGTGEIAFYIAPKCKNVTGIDISPGMIDIARkkntesGYNNLSFQVEDAYNLP 114
                                       67788888899999***********************99******************98875555666666666888 PP

                   Methyltransf_23  78 epqgkfdlIvlrevlehvpdppellrqiatllkpg.Gylllse.p.laslkedrllldw..lylvpagrhisffsar 149
                                       ++++ f  Iv+ +vl ++++p + ++  +++l  g  yl +++ + ++sl e  +l +w  +y  p+  + + f ++
  gi|298676096|ref|YP_003727846.1| 115 FDKNEFTKIVSCNVLQTMKNPYRSIQECGKILDKGnEYLSITYcFgDSSLFEQVKLIKWviHYGKPK-YW-HNFKSD 189
                                       8********************************9967777777532444456666555545677766.44.55566* PP

                   Methyltransf_23 150 slkelleeaGlevve 164
                                       +l +l++eaG+e++e
  gi|298676096|ref|YP_003727846.1| 190 ELVNLFQEAGFEIIE 204
                                       *************98 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.1   0.0   1.7e-21   1.6e-18       1      91 [.      58     149 ..      58     153 .. 0.97

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 1.7e-21
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC-CC CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhhved 76 
                                       L++G+GtG +a ++a ++++v+g+D+s+ m+++a++k+ e+g  +++f+v+da +lpf +n f  +vs +vl+++++
  gi|298676096|ref|YP_003727846.1|  58 LEIGTGTGEIAFYIAPKCKNVTGIDISPGMIDIARKKNTESGYnNLSFQVEDAYNLPFDKNEFTKIVSCNVLQTMKN 134
                                       89**************************************9999********************************* PP

                                       HHHHHHHHHHHEEEE CS
                   Methyltransf_11  77 pekalkeiaRvLkpg 91 
                                       p + ++e+ ++L +g
  gi|298676096|ref|YP_003727846.1| 135 PYRSIQECGKILDKG 149
                                       ***********9987 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.0   3.9e-20   3.7e-17       2     122 ..      52     168 ..      51     199 .. 0.84

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 3.9e-20
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkae.vvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDl 77 
                                       ++g +vl++G+GtGe++f +a    pk++ v+GiDis+ +i  Ar++  + g++n++F+++d+ +l+  + ++ f  
  gi|298676096|ref|YP_003727846.1|  52 QSGDSVLEIGTGTGEIAFYIA----PKCKnVTGIDISPGMIDIARKKNTESGYNNLSFQVEDAYNLP--FDKNEFTK 122
                                       57899****************....55555*************************************..99****** PP

                   Methyltransf_31  78 ilsnevlnaladpdkileeiervlkpggilliedpr.llaelpakv 122
                                       i+s +vl+++++p   ++e  + l +g ++l+ +++ + + l ++v
  gi|298676096|ref|YP_003727846.1| 123 IVSCNVLQTMKNPYRSIQECGKILDKGNEYLSITYCfGDSSLFEQV 168
                                       ************************9998888776664444444443 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   0.0   1.4e-16   1.3e-13       1      96 [.      58     149 ..      58     152 .. 0.84

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 1.4e-16
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       LeiG+GtG++++++++k   +++tg+Disp +i+ a++k  + + nn ++   +a +l  ++  + f  +v++nvl+
  gi|298676096|ref|YP_003727846.1|  58 LEIGTGTGEIAFYIAPK--CKNVTGIDISPGMIDIARKKNTESGYNNLSFQVEDAYNLPFDK--NEFTKIVSCNVLQ 130
                                       8****************..**************77777777777666555555556655333..69*********** PP

                   Methyltransf_12  78 hlkdirevldnirklLkpg 96 
                                        +k++ ++++++ k L +g
  gi|298676096|ref|YP_003727846.1| 131 TMKNPYRSIQECGKILDKG 149
                                       ***************9887 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.1   3.3e-15   3.1e-12      12     149 ..      20     152 ..       7     169 .. 0.83
   2 ?    0.3   0.0      0.38   3.6e+02     201     217 ..     188     204 ..     182     207 .. 0.86

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 3.3e-15
                                       XXX-HHHHHHHHHHHHHTTTHHHHHHHHHHH--.S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHH CS
                   Ubie_methyltran  12 vfesvaskyDlmndvlslgihrlWkkfveklva.vkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkv 87 
                                        +++v+++yD   d +  g  + +k+f  k+ + +++g +vl++ +Gtg++af ++ + +   +v+++Di++ m+++
  gi|298676096|ref|YP_003727846.1|  20 FWSKVSNSYD---DWIEHGFKEQYKAFKSKIASyTQSGDSVLEIGTGTGEIAFYIAPKCK---NVTGIDISPGMIDI 90 
                                       5789999999...67888999999998887765267899***************988765...699*********** PP

                                       HHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEE CS
                   Ubie_methyltran  88 gekklkeegkinieflqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrl 149
                                       ++kk  e+g+ n+ f + +a +Lpf+++ f  +     l+ + +  ++++e  ++l  G + 
  gi|298676096|ref|YP_003727846.1|  91 ARKKNTESGYNNLSFQVEDAYNLPFDKNEFTKIVSCNVLQTMKNPYRSIQECGKILDKGNEY 152
                                       ******************************99887777888888888888888888777665 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.38
                                       HHHHHHHHHHTTEEEEE CS
                   Ubie_methyltran 201 qetlkeliedaGfksve 217
                                        ++l +l+++aGf+ +e
  gi|298676096|ref|YP_003727846.1| 188 SDELVNLFQEAGFEIIE 204
                                       57899********9875 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   2.7e-08   2.5e-05      41     120 ..      51     133 ..      25     142 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.7e-08
                              NodS  41 qgsiadalevGcaaGalterlapyckrltvvdvveeaiararervkes..shiswivsdvqqfstd.ekfdlivvae 114
                                        +s  ++le+G  +G ++  +ap ck++t +d+ +  i+ ar++  es  +++s+ v d  ++  d ++f  iv ++
  gi|298676096|ref|YP_003727846.1|  51 TQSGDSVLEIGTGTGEIAFYIAPKCKNVTGIDISPGMIDIARKKNTESgyNNLSFQVEDAYNLPFDkNEFTKIVSCN 127
                                       4555689*****************************99999888777522789*******9998762579******* PP

                              NodS 115 vlyyie 120
                                       vl  ++
  gi|298676096|ref|YP_003727846.1| 128 VLQTMK 133
                                       998766 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0     4e-08   3.8e-05      60     214 ..      51     204 ..      29     210 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 4e-08
                                       --TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS.-EEEEES-GGG---.--SEEEEE CS
                              CMAS  60 lkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldler.kvevklldyedlde.kvdrvvsv 134
                                        + G+ +L+iG+G G+++ + + +   +v g+ +S      a+k+  e + ++ + +v+ +    +d+ ++ ++vs 
  gi|298676096|ref|YP_003727846.1|  51 TQSGDSVLEIGTGTGEIAFYIAPK-CKNVTGIDISPGMIDIARKKNTESGYNNlSFQVEDAYNLPFDKnEFTKIVSC 126
                                       489*********************.88********************99977624566666556777789******* PP

                                       S-GGGTSGGGHHHHHHHHHHHS-TT-EEEEEEEEE--HHHHHCTTCCC.HHHHHHTSTTS--.-BHHHHHHHHHHTT CS
                              CMAS 135 gafehvgkenydtffkklkkllkedGllllhtitslhkkelaerglkl.kfidkeiFPgGel.psieeieeeiseag 209
                                       ++++ +++  y + ++++ k+l ++   l  t   +  ++   +++kl k++ ++  P+     +++e+++ ++eag
  gi|298676096|ref|YP_003727846.1| 127 NVLQTMKN-PY-RSIQECGKILDKGNEYLSIT--YCFGDSSLFEQVKLiKWVIHYGKPKYWHnFKSDELVNLFQEAG 199
                                       **998753.34.45677888887777766444..4443333333333337877777776543145566777777777 PP

                                       -EEEE CS
                              CMAS 210 ftvvd 214
                                       f++++
  gi|298676096|ref|YP_003727846.1| 200 FEIIE 204
                                       77765 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   1.9e-07   0.00018      83     235 ..      41     202 ..      31     209 .. 0.66

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.9e-07
                              DREV  83 aiekespas.dqedkklldlGaGdGeitkrvaptfeevyatelsetmrdrlkkkk....ynvlsal.e.lqe...td 149
                                       ++ k + as  q    +l++G+G Gei+  +ap  ++v   ++s  m+d  +kk+    yn ls   e   +    +
  gi|298676096|ref|YP_003727846.1|  41 KAFKSKIASyTQSGDSVLEIGTGTGEIAFYIAPKCKNVTGIDISPGMIDIARKKNtesgYNNLSFQvEdAYNlpfDK 117
                                       4444555552456789*******************************998888754445888774312233311134 PP

                              DREV 150 vkldlilclnlldrcfdplklledirsalepngrvivalvlPvshyvetntgksekpsellevkG..rsyee.evar 223
                                        ++  i++ n+l  + +p++ +++  ++l+ +g+  +++   +     +      k+ + +   G  + + + + ++
  gi|298676096|ref|YP_003727846.1| 118 NEFTKIVSCNVLQTMKNPYRSIQECGKILD-KGNEYLSITYCFGDSSLFEQ---VKLIKWVIHYGkpKYWHNfKSDE 190
                                       4677788899**999999999999988876.56666666666655444444...33333333333334444425667 PP

                              DREV 224 lievlkkagfev 235
                                       l++++++agfe+
  gi|298676096|ref|YP_003727846.1| 191 LVNLFQEAGFEI 202
                                       888888888877 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0     5e-07   0.00047       4      76 ..      56     123 ..      53     130 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 5e-07
                                       EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHHHHCS-TTSEEEE CS
                    Methyltransf_4   4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkvllelledgsleki 76 
                                        vleiG+G Ge+   +A+k   kn+ Gi+i+  +++ + kk  +++++Nl     da + l   + +++++ki
  gi|298676096|ref|YP_003727846.1|  56 SVLEIGTGTGEIAFYIAPKC--KNVTGIDISPGMIDIARKKNTESGYNNLSFQVEDA-YNL--PFDKNEFTKI 123
                                       689**************995..8999******************************9.555..4777777777 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.4e-06    0.0013       7      74 ..      46     110 ..      45     128 .. 0.84
   2 ?   -1.9   0.0         3   2.8e+03     122     144 ..     189     211 ..     185     214 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.4e-06
                   Methyltransf_18   7 aiaslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdG 74 
                                       +ias+ ++g++v+ iGt  g +++y++   k+k+v+ +Di++g ++ a+++ +++g++ ++++ + d 
  gi|298676096|ref|YP_003727846.1|  46 KIASYTQSGDSVLEIGTGTGEIAFYIA--PKCKNVTGIDISPGMIDIARKKNTESGYN-NLSFQVEDA 110
                                       79************************9..799*******************9999885.466666555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3
                   Methyltransf_18 122 eelRkylvengfkiedEelvkee 144
                                       +el +  +e gf+i++ + v e+
  gi|298676096|ref|YP_003727846.1| 189 DELVNLFQEAGFEIIEKDWVWEK 211
                                       66777889999999999888776 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   6.8e-07   0.00064      72     134 ..      52     111 ..      41     140 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 6.8e-07
                                       -TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GG CS
                              PCMT  72 kkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGr 134
                                       + g++vLe+G+G+G  +  +a   ++++   +i+ ++ +++ a+++  +++++n++++v D +
  gi|298676096|ref|YP_003727846.1|  52 QSGDSVLEIGTGTGEIAFYIAPKCKNVT---GIDISPGMIDIARKKNTESGYNNLSFQVEDAY 111
                                       6799**********98877776666555...***************************99975 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.1e-06     0.001      25      81 ..      50     107 ..      38     151 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.1e-06
                            DUF938  25 tte...rvLEiasGtGqHAvffApalpnlkwqpsdqdeelresiaawadelalsnlkpPl 81 
                                        t+    vLEi++GtG+ A ++Ap+ +n++    d  + + +  ++  +e + +nl++ +
  gi|298676096|ref|YP_003727846.1|  50 YTQsgdSVLEIGTGTGEIAFYIAPKCKNVTG--IDISPGMIDIARKKNTESGYNNLSFQV 107
                                       3332337******************999864..466666665556666666777766555 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.8e-06    0.0017     156     236 ..      48     130 ..      44     139 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.8e-06
                              PrmA 156 eklvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkvea.klevalseell..keekadv 229
                                        ++ ++g++vl +GtG+G +a   a    k+v+++Di +  +++a++  +  + ++ +++v  + +l+  k+e   +
  gi|298676096|ref|YP_003727846.1|  48 ASYTQSGDSVLEIGTGTGEIAFYIAP-KCKNVTGIDISPGMIDIARKKNTESGYNNlSFQVEDAYNLPfdKNEFTKI 123
                                       578999************99876554.689***************87666666666689887777777544666788 PP

                              PrmA 230 ivaNILa 236
                                       + +N+L 
  gi|298676096|ref|YP_003727846.1| 124 VSCNVLQ 130
                                       8899996 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.8e-06    0.0027      29      95 ..      52     120 ..      37     150 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.8e-06
                                       GTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S-CCGHHHHHHHC CS
                            RrnaAD  29 eekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls..kdeklkvvhqDflkfetpeevt 95 
                                       +  + vleig+G+G     +a  +k+v+ + + + ++ + +kk +   +++l    +D+++  + ++  
  gi|298676096|ref|YP_003727846.1|  52 QSGDSVLEIGTGTGEIAFYIAPKCKNVTGIDISPGMIDIARKKNTesGYNNLSFQVEDAYNLPFDKNEF 120
                                       57799*************************************998888999999999999998887544 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.1e-05      0.01      31     102 ..      53     124 ..      42     139 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.1e-05
                                       TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTST.TS-EEEEE CS
                               MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeve.ekkfdliv 102
                                         ++vl +G+G+G ++  +a ++++  vt +d++   +++a++  ++++ + +++  +d+++    +++f  iv
  gi|298676096|ref|YP_003727846.1|  53 SGDSVLEIGTGTGEIAFYIAPKCKN--VTGIDISPGMIDIARKKNTESGYNnLSFQVEDAYNLPFdKNEFTKIV 124
                                       45679****************9999..9*************999999988889999999998544255666666 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     4e-05     0.038       6     101 ..      46     145 ..      41     153 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4e-05
                              MetW   6 liaelikpgsrvldlGcGdGellellk.eekqvdgrGleldeegva....ecvakGlsviqgdldkdlen.fedksf 76 
                                        ia + ++g  vl++G+G Ge+  +++ + k+v+  G++++   +     + ++ G + +  ++++  +  f+ ++f
  gi|298676096|ref|YP_003727846.1|  46 KIASYTQSGDSVLEIGTGTGEIAFYIApKCKNVT--GIDISPGMIDiarkKNTESGYNNLSFQVEDAYNLpFDKNEF 120
                                       68889999*************9877751446665..5555555554001134566777777777766654489999* PP

                              MetW  77 dyvvlsqtlqatrnpkevldellri 101
                                         +v    lq+++np + ++e  +i
  gi|298676096|ref|YP_003727846.1| 121 TKIVSCNVLQTMKNPYRSIQECGKI 145
                                       ***************9999987766 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   9.1e-05     0.086      31     109 ..      54     133 ..      29     150 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.1e-05
                                       S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----S-.EEEEEEESSGG CS
                              TehB  31 pgkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydineaklder.ydfilstvvlm 106
                                          vl++g g g  ++y++ +  +vt +d     i   ++ +     +n+s ++ d  ++ +d++ +  i+s  vl 
  gi|298676096|ref|YP_003727846.1|  54 GDSVLEIGTGTGEIAFYIAPKCKNVTGIDISPGMIDIARKKNTESGYNNLSFQVEDAYNLPFDKNeFTKIVSCNVLQ 130
                                       4579****************************999999998888999***************986478899999987 PP

                                       GS- CS
                              TehB 107 fle 109
                                        ++
  gi|298676096|ref|YP_003727846.1| 131 TMK 133
                                       665 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00022      0.21      78     127 ..      76     125 ..      38     128 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                                       -.EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE CS
                           UPF0020  78 k.lygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivt 127
                                       k + g+D+ + +++ ar++  + g ++l +f++ da +L+ +++e+  iv+
  gi|298676096|ref|YP_003727846.1|  76 KnVTGIDISPGMIDIARKKNTESGYNNL-SFQVEDAYNLPFDKNEFTKIVS 125
                                       4599********************9875.67777******88889999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 1315.98
//
Query:       gi|298676097|ref|YP_003727847.1|  [L=204]
Description: binding-protein-dependent transporter inner membrane component [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.4e-22   78.7  14.7    4.4e-22   78.7  14.7    1.3  1  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.7  14.7   2.5e-26   4.4e-22       3     184 ..      27     198 ..      25     199 .. 0.94

  Alignments for each domain:
  == domain 1  score: 78.7 bits;  conditional E-value: 2.5e-26
                      BPD_transp_1   3 llGilaa..lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalr 77 
                                       +++i +a     + kl ++++ ++++l+++Psf+++ ++v        +g +++p++i++l+ a+ +++ +++ +l 
  gi|298676097|ref|YP_003727847.1|  27 VISIPLAfiSVESEKLANWIMKVSNLLQAVPSFAVVAIVV------PLIGIGFTPALIAILVRALLPIIKNTYIGLL 97 
                                       56666666666999**************************......99***************************** PP

                      BPD_transp_1  78 slpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis 154
                                       +++ +l+ +a+  G++rwqi r+++lPn+ p i++g+++++ ++   avl+ ++g ++Glg l++e + +++++   
  gi|298676097|ref|YP_003727847.1|  98 NIDPSLIDYAHGVGLTRWQINRYIRLPNSYPAIFAGIRFSALLANSIAVLTALIG-GGGLGELVFEGLVSFNID--- 170
                                       ********************************************99999999999.557***************... PP

                      BPD_transp_1 155 nggvlalviavlllnlvadilqrlldprvr 184
                                          +la++i  +ll l++d l ++++++++
  gi|298676097|ref|YP_003727847.1| 171 --RILAGAIPAILLALASDSLLAMIEKKLT 198
                                       ..677**********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1336.27
//
Query:       gi|298676098|ref|YP_003727848.1|  [L=214]
Description: binding-protein-dependent transporter inner membrane component [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.1e-26   91.3  14.6    8.2e-26   90.9  14.6    1.2  1  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.9  14.6   4.6e-30   8.2e-26       3     183 ..      37     207 ..      35     209 .. 0.96

  Alignments for each domain:
  == domain 1  score: 90.9 bits;  conditional E-value: 4.6e-30
                      BPD_transp_1   3 llGilaa..lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalr 77 
                                       ++G++++   ++n+kl++ ++++ +++ ++P ++l+++l+       i+g + lp ii+++l+++ +++++++ +l+
  gi|298676098|ref|YP_003727848.1|  37 VIGVVLGitIYYNSKLSNPVLNILNIFETTPDIALLVILL------PIAGMGTLPTIIASILYSLLPITRNTYTGLK 107
                                       68888888888*****************************......9****************************** PP

                      BPD_transp_1  78 slpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis 154
                                        +++ +++ aralG+s ++i++k+++P++lp i+ g+++a+++ +g  +l  +++++ Glgt+l + i+ y ++   
  gi|298676098|ref|YP_003727848.1| 108 GVDRKYINIARALGLSSREILFKIRIPMSLPLIAGGIRIALVFTMGLVTLGGLIAAG-GLGTTLQTGIQLYEVN--- 180
                                       *******************************************************66.7***************... PP

                      BPD_transp_1 155 nggvlalviavlllnlvadilqrlldprv 183
                                         ++l ++i + ll +++d ++ ++++r+
  gi|298676098|ref|YP_003727848.1| 181 --TILLAGIWTGLLAVILDGFAGMVEKRL 207
                                       ..6779999999999999***99999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1554.80
//
Query:       gi|298676099|ref|YP_003727849.1|  [L=374]
Description: glycine betaine/L-proline ABC transporter ATPase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-34  119.1   0.0    3.2e-34  118.4   0.0    1.4  1  ABC_tran         ABC transporter
    8.1e-10   39.0   0.1    8.3e-05   22.5   0.0    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    5.1e-05   23.7   0.0    0.00011   22.7   0.0    1.7  1  AAA_16           AAA ATPase domain
     0.0001   22.2   0.3    0.00037   20.3   0.3    2.0  1  AAA_15           AAA ATPase domain
    0.00081   19.2   0.0     0.0015   18.3   0.0    1.4  1  AAA_30           AAA domain
    0.00089   19.5   0.0     0.0022   18.3   0.0    1.6  1  AAA_22           AAA domain
     0.0012   18.5   0.0     0.0025   17.5   0.0    1.5  1  AAA_29           P-loop containing region of AAA domain
     0.0018   18.3   0.0     0.0039   17.2   0.0    1.6  1  AAA_5            AAA domain (dynein-related subfamily)
      0.003   16.7   0.0     0.0049   16.0   0.0    1.3  1  T2SSE            Type II/IV secretion system protein
     0.0059   16.5   0.1      0.017   15.0   0.0    1.7  2  RsgA_GTPase      RsgA GTPase
     0.0065   15.9   0.0      0.012   15.0   0.0    1.5  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0092   16.5   0.3      0.022   15.3   0.3    1.6  1  AAA_23           AAA domain
  ------ inclusion threshold ------
       0.01   15.0   0.0      0.021   14.0   0.0    1.4  1  G-alpha          G-protein alpha subunit
      0.013   15.6   0.0        0.1   12.7   0.0    2.0  2  AAA_33           AAA domain
      0.014   15.1   0.0       0.33   10.6   0.0    2.2  2  AAA_24           AAA domain
      0.016   14.9   0.0      0.028   14.2   0.0    1.3  1  DEAD             DEAD/DEAH box helicase
      0.021   14.7   0.0      0.052   13.5   0.0    1.6  1  Rad17            Rad17 P-loop domain
      0.023   15.0   0.0      0.051   13.9   0.0    1.5  1  AAA_19           AAA domain
      0.041   13.5   0.0        0.2   11.2   0.0    2.0  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.058   13.8   0.0       0.15   12.5   0.0    1.9  1  AAA              ATPase family associated with various cellul
      0.084   12.0   0.4       0.14   11.3   0.4    1.3  1  ABC2_membrane_3  ABC-2 family transporter protein
       0.12   12.3   0.0       0.23   11.4   0.0    1.4  1  NACHT            NACHT domain
       0.13   11.9   0.0       0.35   10.5   0.0    1.7  1  SRP54            SRP54-type protein, GTPase domain
       0.15   12.6   0.0        0.9   10.1   0.0    2.1  2  AAA_18           AAA domain
       0.18   11.0   0.0       0.33   10.2   0.0    1.3  1  Zeta_toxin       Zeta toxin


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.4   0.0   4.5e-37   3.2e-34       2     136 ..      29     174 ..      28     175 .. 0.90

  Alignments for each domain:
  == domain 1  score: 118.4 bits;  conditional E-value: 4.5e-37
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       ++++l+++ ge++ ++G++G+GK+t l+++ +l +p+eG+i ++++d+ + +  +lr++ig++ q+  lfp++t+r+
  gi|298676099|ref|YP_003727849.1|  29 QDLNLEIHGGELLILIGPSGSGKTTTLRMINQLIEPDEGRIFINNQDIMQFDSVKLRRNIGYVIQDIGLFPHMTIRN 105
                                       799************************************************************************** PP

                                       H.........HHHTC.HHHHHHHSTTGGTT.CBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x.........xxxxx.xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.........esdee.iekalsklglkelk.dtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n         +s++e i+k+ + l+ + l+ ++ +++ p++LSgGq+qrv laral+ +p+lll+DEp+
  gi|298676099|ref|YP_003727849.1| 106 NiglipklegWSNNEiIDKVKTLLDFVSLPpEQFLYRYPNQLSGGQQQRVGLARALAMDPPLLLMDEPF 174
                                       *********966666444555555555543177778888*****************************6 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   3.1e-05     0.022       2      24 ..      41      63 ..      40      99 .. 0.73
   2 !   22.5   0.0   1.2e-07   8.3e-05     204     298 ..     117     206 ..      79     209 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.1e-05
                            AAA_21  2 nvliGpNgsGKSnLLdaldllar 24
                                       +liGp gsGK++ L+ +  l  
  gi|298676099|ref|YP_003727849.1| 41 LILIGPSGSGKTTTLRMINQLIE 63
                                      58****************99852 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 1.2e-07
                            AAA_21 204 egeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrlle 280
                                         +e i++v+ +l   ++v l +++   + +++lS G+++  +l+ al+ ++   +lll DEp   L+P l r l +
  gi|298676099|ref|YP_003727849.1| 117 SNNEIIDKVKTLL---DFVSLPPEQFLYRYPNQLSGGQQQRVGLARALAMDP---PLLLMDEPFGALDPILRRQLQD 187
                                       4444444444444...889999999999*************9********99...**************88888888 PP

                            AAA_21 281 ll.kelsrngaQviltTHS 298
                                        + +++++ g  ++++TH+
  gi|298676099|ref|YP_003727849.1| 188 EFcRIKQELGRTIVFVTHD 206
                                       887888889*********8 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   1.5e-07   0.00011      22      57 ..      36      72 ..      27     216 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.5e-07
                            AAA_16 22 grpelvllsGesGvGKsslvrellralekdg.giflr 57
                                      +++el++l+G+sG+GK++ +r++ + +e d+  if++
  gi|298676099|ref|YP_003727849.1| 36 HGGELLILIGPSGSGKTTTLRMINQLIEPDEgRIFIN 72
                                      55699********************999995466643 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.3   5.1e-07   0.00037      18      71 ..      34      82 ..      10     367 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 5.1e-07
                            AAA_15 18 eidlseeltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeni 71
                                      ei+  e l +liG+ +sGK++ l++++ +++ +    +  i+i+++d+ +f++ 
  gi|298676099|ref|YP_003727849.1| 34 EIHGGE-LLILIGPSGSGKTTTLRMINQLIEPD----EGRIFINNQDIMQFDSV 82
                                      444445.9***********************99....89999999999999654 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   2.1e-06    0.0015      18      50 ..      38      70 ..      30      86 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.1e-06
                            AAA_30 18 drvavltGpAGtGKttalkalreaweaaggrvi 50
                                        + +l Gp G+GKtt+l+ +++++e ++gr++
  gi|298676099|ref|YP_003727849.1| 38 GELLILIGPSGSGKTTTLRMINQLIEPDEGRIF 70
                                      4589*********************99866665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   3.1e-06    0.0022       4      29 ..      37      62 ..      34      89 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.1e-06
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleql 29
                                      +  +l+++G+sG+GKTt+lr++ +  
  gi|298676099|ref|YP_003727849.1| 37 GGELLILIGPSGSGKTTTLRMINQLI 62
                                      56789***************998765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   3.5e-06    0.0025      16      55 ..      30      72 ..      21      74 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.5e-06
                            AAA_29 16 tieidlkg..atlltGpsGsGKSTllDAiqalLvpak.kvrfN 55
                                      +++++ +g    +l+GpsGsGK+T l  i+ l+ p++ ++  N
  gi|298676099|ref|YP_003727849.1| 30 DLNLEIHGgeLLILIGPSGSGKTTTLRMINQLIEPDEgRIFIN 72
                                      44444445468899***********999999998888565555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   5.5e-06    0.0039       2      90 ..      41     130 ..      40     147 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.5e-06
                                       EEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT.--HHHHH--B--.........--------.G-SEEEEESGG CS
                             AAA_5   2 vlLvGppGtgKselaerlaaal.nreveyvqltrd.tteedlkgrreikngttslvdsplvraar.egeilvlDEve 75 
                                       ++L+Gp+G+gK++  + + +++  +e  +  +++d ++ + +k rr+i   +++ +d  l   ++ +  i ++  +e
  gi|298676099|ref|YP_003727849.1|  41 LILIGPSGSGKTTTLRMINQLIePDEGRIFINNQDiMQFDSVKLRRNI---GYVIQDIGLFPHMTiRNNIGLIPKLE 114
                                       79*********************6666655555552677888888888...77777777777777744444444444 PP

                                       G--.HHHHHHHHHHHH CS
                             AAA_5  76 rae.sevlnsLlslle 90 
                                         +  e+++++ +ll+
  gi|298676099|ref|YP_003727849.1| 115 GWSnNEIIDKVKTLLD 130
                                       4333677777777766 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   6.9e-06    0.0049     123     161 ..      32      70 ..       9      75 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.9e-06
                             T2SSE 123 rkavrerglilvsGgTgsGKttllyallkeinksderiv 161
                                       +  ++   l+++ G+ gsGKtt+l ++ + i+ ++ ri 
  gi|298676099|ref|YP_003727849.1|  32 NLEIHGGELLILIGPSGSGKTTTLRMINQLIEPDEGRIF 70 
                                       5555666789999*******************9999986 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.4e-05     0.017      70     121 ..       8      60 ..       3      77 .. 0.80
   2 ?   -2.3   0.0         5   3.6e+03      46     130 ..     291     324 ..     279     359 .. 0.46

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.4e-05
                                       HHHHHTTSEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  70 eelealgyevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                       +++ ++++e ++ + +++ ++++l+ ++++ ++ +l+G+SG GK+t + ++++
  gi|298676099|ref|YP_003727849.1|   8 DRIDSIQLENITKKYNNSFAVQDLNLEIHGgELLILIGPSGSGKTTTLRMINQ 60 
                                       566777888888888889999*******999**************96655543 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5
                                       T-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  46 giepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkellkdktsvlvGqSGvGKStLinallpe 122
                                       +ie+ +v n  D + + e                                                   ++n l+ e
  gi|298676099|ref|YP_003727849.1| 291 NIELGLVYNGSDFMGTVE---------------------------------------------------MVNLLKYE 316
                                       555555555555555444...................................................22222222 PP

                                       -----S-- CS
                       RsgA_GTPase 123 lelktgev 130
                                        + k ++v
  gi|298676099|ref|YP_003727849.1| 317 GDEKLQDV 324
                                       22222222 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.7e-05     0.012      11      59 ..      27      75 ..      15     104 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.7e-05
                      Mg_chelatase 11 akraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeealevak 59
                                      a + l++ + Gg  l+l+Gp+GsGKt   + +++l+ p + +  ++ + 
  gi|298676099|ref|YP_003727849.1| 27 AVQDLNLEIHGGELLILIGPSGSGKTTTLRMINQLIEPDEGRIFINNQD 75
                                      5566888899**********************99998876665555554 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.3     3e-05     0.022       8      40 ..      24      59 ..      12      73 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3e-05
                            AAA_23  8 rsf..rdqeidF.skgltlItGpNGaGKTTildAik 40
                                      +sf  +d +++  +  l +++Gp G+GKTT l+ i 
  gi|298676099|ref|YP_003727849.1| 24 NSFavQDLNLEIhGGELLILIGPSGSGKTTTLRMIN 59
                                      344666666777777899**************9886 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.9e-05     0.021      25      61 ..      40      81 ..       8     133 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.9e-05
                                      EEEEEESTTSSHHHHHHHHHHHCS--.....--HHHHHCCHH CS
                           G-alpha 25 kllllGqseSGKsTilkqlkllykkg.....fseeelatwra 61
                                       l+l+G s+SGK+T+l+ +  l ++      ++++++ ++ +
  gi|298676099|ref|YP_003727849.1| 40 LLILIGPSGSGKTTTLRMINQLIEPDegrifINNQDIMQFDS 81
                                      5899***************97776665778666665566544 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00014       0.1       1      17 [.      40      56 ..      40      98 .. 0.88
   2 ?    0.5   0.0      0.84   6.1e+02      78     110 ..     179     209 ..     135     212 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00014
                            AAA_33  1 lvllvGlpGsGKstlae 17
                                      l++l+G++GsGK+t ++
  gi|298676099|ref|YP_003727849.1| 40 LLILIGPSGSGKTTTLR 56
                                      789***********987 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.84
                            AAA_33  78 tnlsrrerarflklarrlgvpvrivvvetdeet 110
                                       + l+r+ +++f+++ ++lg  ++iv+v+ d e+
  gi|298676099|ref|YP_003727849.1| 179 PILRRQLQDEFCRIKQELG--RTIVFVTHDIEE 209
                                       4788899999999999999..678887777665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00046      0.33       6      22 ..      42      58 ..      39      80 .. 0.85
   2 ?    1.9   0.0      0.21   1.5e+02     116     146 ..     191     221 ..     183     266 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00046
                            AAA_24  6 liyGpsgiGKTtlakel 22
                                      +++Gpsg+GKTt+++++
  gi|298676099|ref|YP_003727849.1| 42 ILIGPSGSGKTTTLRMI 58
                                      79***********9988 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.21
                            AAA_24 116 kklqelrknvifiahektrkdedpegeakyt 146
                                       +  qel+ +++f+ h  ++ ++ +++ a  +
  gi|298676099|ref|YP_003727849.1| 191 RIKQELGRTIVFVTHDIEEAFKLGDRIAIMD 221
                                       55689999***********999987764444 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.9e-05     0.028      11      78 ..      35     261 ..      27     287 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.9e-05
                                       HHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS........................................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................................ RF
                              DEAD  11 ilgggdvlvaaeTGsGKTlaflipvlqivyetkgktg........................................ 47 
                                       i gg+ +++ ++ GsGKT+   + ++++++e   ++g                                        
  gi|298676099|ref|YP_003727849.1|  35 IHGGELLILIGPSGSGKTTT--LRMINQLIE--PDEGrifinnqdimqfdsvklrrnigyviqdiglfphmtirnni 107
                                       668889999*********98..788888887..444457888889999999************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              DEAD  48 ............................................................................. 47 
                                                                                                                    
  gi|298676099|ref|YP_003727849.1| 108 glipklegwsnneiidkvktlldfvslppeqflyrypnqlsggqqqrvglaralamdpplllmdepfgaldpilrrq 184
                                       ***************************************************************************** PP

                                       ..............................................-EEEEEESSHHHHHHHHHHHHHHTTTSTSEE CS
                                       ..............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  48 ..............................................pkalivePtreLaeqtlnnlkkfkkyidlrv 78 
                                                                                     p  li  P  eL+ ++++   kfk+  +l+v
  gi|298676099|ref|YP_003727849.1| 185 lqdefcrikqelgrtivfvthdieeafklgdriaimdganliqigkPEDLIFNPVNELVSDIVDSNHKFKHMDTLNV 261
                                       ********************************************************************999533554 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   7.3e-05     0.052      40      67 ..      33      60 ..      18      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.3e-05
                             Rad17 40 LesrkkriLLisGPsGCgkstvvkvLsk 67
                                      Le +  ++L++ GPsG gk+t+++++ +
  gi|298676099|ref|YP_003727849.1| 33 LEIHGGELLILIGPSGSGKTTTLRMINQ 60
                                      55555679***************99876 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   7.1e-05     0.051       9      34 ..      37      62 ..      29      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.1e-05
                            AAA_19  9 kekvllvtaGpGtGKTrvlkhivall 34
                                        ++l+++++ G+GKT++l++i +l+
  gi|298676099|ref|YP_003727849.1| 37 GGELLILIGPSGSGKTTTLRMINQLI 62
                                      567899**************998766 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00028       0.2       3      49 ..      41      87 ..      39     113 .. 0.81
   2 ?   -0.7   0.0       1.2   8.9e+02     100     131 ..     201     232 ..     196     264 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00028
                                      EEEEESTTCCHHHHHHHHHCT--SS-EEEEESS-SSCHCCCCCCHCC CS
                              cobW  3 tvltGflGsGKTtLlnhllenraglklavivNefgevsiDaellret 49
                                      ++l G+ GsGKTt l+ + +  +  +  + +N++  ++ D+  lr++
  gi|298676099|ref|YP_003727849.1| 41 LILIGPSGSGKTTTLRMINQLIEPDEGRIFINNQDIMQFDSVKLRRN 87
                                      6899***********99998888888888888888788887777666 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.2
                                       HTTSHHHHHCCCECEEEEEEETTTH.CCHCCH CS
                              cobW 100 afteeelksdltldavvavvDaknleaeeeki 131
                                       +f +++++++++l   +a++D++nl + ++++
  gi|298676099|ref|YP_003727849.1| 201 VFVTHDIEEAFKLGDRIAIMDGANLIQIGKPE 232
                                       5678999999999999*****99985544444 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00021      0.15       1      22 [.      41      62 ..      41     196 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00021
                                      EEEESSTTSSHHHHHHHHHHHH CS
                               AAA  1 vllyGppGtGKTllakavakel 22
                                      ++l+Gp G GKT++ + + + +
  gi|298676099|ref|YP_003727849.1| 41 LILIGPSGSGKTTTLRMINQLI 62
                                      589*************998876 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.4   0.00019      0.14      44     163 ..     239     355 ..     209     364 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00019
                   ABC2_membrane_3  44 lsqqlvealeaspsvelvyevdseeeakkalkng.didgilvipkgfskdllkgesatvtvlinssnlnsskailna 119
                                         + + ++++++++++ +    + ++++  ++n+  +dg + i++  ++  ++ +++++ +++n+s++  + ++ n 
  gi|298676099|ref|YP_003727849.1| 239 VNELVSDIVDSNHKFK-HMDTLNVKDLMSPMDNKyIFDGNIKINDAVTR--MTDNNIELGLVYNGSDFMGTVEMVNL 312
                                       4455668888999999.999999*********99456788889988888..579**************999877777 PP

                   ABC2_membrane_3 120 lnsllqqlnasalv...lqseatstsaninvestqleeelsnvasfl 163
                                       l+     ++ ++l+   ++s++ s++ ++++ + +l+++++++a  +
  gi|298676099|ref|YP_003727849.1| 313 LKY----EGDEKLQdvaQSSTTFSPMHSVSSALSELKNKNESFAVVF 355
                                       664....3333333444556677777888888888899998887665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00032      0.23       2      24 ..      40      62 ..      39      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00032
                                      CEEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalaw 24
                                      l+il G++GsGKTt l+ + +++
  gi|298676099|ref|YP_003727849.1| 40 LLILIGPSGSGKTTTLRMINQLI 62
                                      689*************9998766 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00048      0.35       4      39 ..      41      76 ..      39      83 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00048
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                             SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                      ++l+G+ G+GKTttl  + +l++ ++ ++ +   D+
  gi|298676099|ref|YP_003727849.1| 41 LILIGPSGSGKTTTLRMINQLIEPDEGRIFINNQDI 76
                                      789************998888887777777766665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0013       0.9       2      21 ..      42      61 ..      41     129 .. 0.76
   2 ?   -0.3   0.0       2.1   1.5e+03      24      69 ..     219     264 ..     196     291 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0013
                            AAA_18  2 lltGtpGvGKttlakeLskr 21
                                      +l G++G+GKtt  + ++++
  gi|298676099|ref|YP_003727849.1| 42 ILIGPSGSGKTTTLRMINQL 61
                                      799**********9988665 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.1
                            AAA_18  24 f..gvnlrdvakenglllevdpealdeskrldedkldklldaleenss 69 
                                       +  g nl+++ k ++l +   +e    s+++d +   k++d+l+  + 
  gi|298676099|ref|YP_003727849.1| 219 ImdGANLIQIGKPEDLIFNPVNE--LVSDIVDSNHKFKHMDTLNVKDL 264
                                       26688888888888888888888..77777777777777777766555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00045      0.33      18      54 ..      40      76 ..      36      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00045
                        Zeta_toxin 18 lillgGqpGAGKselaellkdelerqgnvvrldpDdl 54
                                      l++l G +G+GK+++++++++ +e++++ + ++  d+
  gi|298676099|ref|YP_003727849.1| 40 LLILIGPSGSGKTTTLRMINQLIEPDEGRIFINNQDI 76
                                      5788899**************9999988888887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.47
# Mc/sec: 2391.72
//
Query:       gi|298676100|ref|YP_003727850.1|  [L=311]
Description: glycine betaine ABC transporter substrate-binding protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.2e-62  209.7   1.3    7.4e-62  209.2   1.3    1.2  1  OpuAC        Substrate binding domain of ABC-type glycine bet
  ------ inclusion threshold ------
      0.089   12.5   0.1       0.13   12.0   0.1    1.2  1  Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase cha


Domain annotation for each model (and alignments):
>> OpuAC  Substrate binding domain of ABC-type glycine betaine transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.2   1.3   8.2e-66   7.4e-62       2     257 .]      39     303 ..      38     303 .. 0.98

  Alignments for each domain:
  == domain 1  score: 209.2 bits;  conditional E-value: 8.2e-66
                                       EEEEEEESSHHHHHHHHHHHHHHHHTTE.EEEEEEEESHHHHHHHHHTTSSSEEEEEEHHHH............... CS
                             OpuAC   2 tivigsknwteqevlaeilkqllekkGy.kveltnlgstavlfaalasGdiDvypeewtgta............... 62 
                                       tivigsk ++e+++la++l+ lle++Gy ++ +++lg+t v ++al++G+iD+y+ e++gta               
  gi|298676100|ref|YP_003727850.1|  39 TIVIGSKLFQESYILAHMLSILLEDNGYnTEVEQGLGGTFVNYEALKQGQIDAYV-EYSGTAysqilkkpspdtwdp 114
                                       9***************************98889999999****************.********************* PP

                                       ...HHHHHHHHHHHHEEEEEEEESEEECEEEEEEHHHHHHHTTTBHHHHCTHHGGTEEEEEHHCCHSTTSHHCCHHH CS
                             OpuAC  63 ...yeaykkaveekkglevlgplgagnteglavpkyvaekygiksisDLkkpaedlelgakgeflgrpdgwgcekvt 136
                                          ye+ kk++ ++++++++++lg++n++++av+++ ae+++i+++s+L  +a+++  g + ef +r+dg++     
  gi|298676100|ref|YP_003727850.1| 115 qmiYEETKKGLMQEDNVKIANRLGFENAYAIAVDENWAEEHNITKLSQLEGYASNMVIGTDPEFATREDGLP----- 186
                                       ************************************************************************..... PP

                                       HHHHHHHT-TTCEEEGSCEEEEHHHHHHHHHTTCSSEEEEETTSTHHHHTTEEE-B-TTSTS-SSEEEEEEEEHHHH CS
                             OpuAC 137 egllkaYgldkvelvegseaamdaelyaaykrgepvvvyawtPdwaikkydlvvLedpkglfppaynvvpvvrkefa 213
                                          +++Yg+    +++   ++  + +y+++k++e++++ a+t+d  + k++l+vLed+kg++pp y++ ++++++fa
  gi|298676100|ref|YP_003727850.1| 187 -RIKEVYGF----EFKDYKQGAPSIMYQSIKNDEVDAISAYTTDTKNEKFGLRVLEDDKGALPP-YDAITLMTSDFA 257
                                       .********....67666888888****************************************.************ PP

                                       HHSCTHHHHHHHHC..--HHHHHHHHHHHHTTTT-HHHHHHHHHHH CS
                             OpuAC 214 ekaPevaafLekls..ldtetlnelnaqvdvegkdpeevAkawlae 257
                                       + +P+v++ L +l+  +d+et++ ln+q dve+k+++++A+++l++
  gi|298676100|ref|YP_003727850.1| 258 SSHPDVMDTLGQLNntIDQETMRNLNYQYDVENKEAKDIARQFLEN 303
                                       ********************************************85 PP

>> Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase chain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   1.4e-05      0.13      78     134 ..       6      61 ..       1      62 [. 0.69

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.4e-05
                                       HHHHHHHHHHHHHTT--......--------TT-HHHHHHHHTTTTHHHHHHHHHHH CS
                       Oxidored_q3  78 aalligllllalllllllessssavdaqvadvsnieaigsllftkyllpfelasllL 134
                                       + +++ +l+ a+++    +++++++++++++ +++  igs lf++ +++  ++s+lL
  gi|298676100|ref|YP_003727850.1|   6 I-AMVLMLITAIMVSGCAQNPQTNESNSNPNSDETIVIGSKLFQESYILAHMLSILL 61 
                                       2.3344444444444445557777788999999***********9888888889887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2091.11
//
Query:       gi|298676101|ref|YP_003727851.1|  [L=545]
Description: thiamine pyrophosphate domain-containing TPP-binding protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-51  173.4   0.0    1.4e-50  171.3   0.0    2.0  2  TPP_enzyme_N    Thiamine pyrophosphate enzyme, N-terminal TPP
    2.1e-39  134.7   0.1    3.9e-39  133.9   0.1    1.4  1  TPP_enzyme_C    Thiamine pyrophosphate enzyme, C-terminal TPP
    7.6e-33  113.2   0.0    2.6e-32  111.4   0.0    1.9  2  TPP_enzyme_M    Thiamine pyrophosphate enzyme, central domain
     0.0025   17.1   0.0      0.007   15.6   0.0    1.7  1  DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.021   14.6   0.0    1.5  1  CO_dh           CO dehydrogenase beta subunit/acetyl-CoA synt


Domain annotation for each model (and alignments):
>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.3   0.0   3.9e-54   1.4e-50       1     168 [.       1     165 [.       1     169 [. 0.97
   2 ?   -0.9   0.0       0.3   1.1e+03      66     143 ..     425     513 ..     396     516 .. 0.64

  Alignments for each domain:
  == domain 1  score: 171.3 bits;  conditional E-value: 3.9e-54
                                       EEHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHH CS
                      TPP_enzyme_N   1 mtvaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGat 77 
                                       m++++++v++L+++gve+vfg+pG++ l+l+d+ls + +i+++++rhEqgaaf+Ad y r+t+kpgv+l t gpGat
  gi|298676101|ref|YP_003727851.1|   1 MKASDLFVKCLENEGVEYVFGIPGEETLDLMDSLSHS-SIKFIVTRHEQGAAFMADVYGRLTHKPGVCLSTLGPGAT 76 
                                       789**********************************.6************************************** PP

                                       HCHHHHHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--E CS
                      TPP_enzyme_N  78 naltalaeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtkyaervtspeelpealrrAirtalsgrpgP 154
                                       n++t++a+A++dr Pl++++g+++ +++++++ q  ++ ++ ++++t++++++t+p+ +pe++r+ +++a  + pg+
  gi|298676101|ref|YP_003727851.1|  77 NLMTGIADAYLDRAPLVAVTGQASLEKTHKEAHQ-YINVVDTLKNITNWNRKITRPDFIPEIVRKTFDIA-CDAPGA 151
                                       *****************************99999.***********************************.99**** PP

                                       EEEEEEHHHCC-EE CS
                      TPP_enzyme_N 155 vylelpkdvlleev 168
                                       v++elp+d+  e++
  gi|298676101|ref|YP_003727851.1| 152 VHVELPEDIAIEDT 165
                                       ********987665 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.3
                                       EEEEE-CHHHHHHCHHHHHHHHHHT--EEEEEEE--CCCHH............S..TC--T...-CCHHHCCCSSEE CS
                      TPP_enzyme_N  66 gvvlvtsgpGatnaltalaeAkvdriPllvlsgdrptslrg............qgvlqqel...dqlalfrpvtkya 127
                                        vv+v    G++  +  l +Ak+ ++ l+v+  + + + +                +   +   d +++++++    
  gi|298676101|ref|YP_003727851.1| 425 NVVAVVGDGGFMMNVQELETAKRIGTDLIVIIFNDSKYGVIewnelekfktsyG--ID--FsnpDFVQMAQSFGVNG 497
                                       456666656777777888888888888888877766665554555555444221..11..12236677777777777 PP

                                       EE-SSGGGHHHHHHHH CS
                      TPP_enzyme_N 128 ervtspeelpealrrA 143
                                       ++++s++el + l+ A
  gi|298676101|ref|YP_003727851.1| 498 VKIESADELTSKLQYA 513
                                       7777777777766666 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.9   0.1   1.1e-42   3.9e-39       1     153 []     378     524 ..     378     524 .. 0.96

  Alignments for each domain:
  == domain 1  score: 133.9 bits;  conditional E-value: 1.1e-42
                                       ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEE CS
                      TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitv 77 
                                       d+G ++lw+ rl+++++p++++ s+gl++mG++lp+Ai+akl +p+++vva+vGDGgf+m++qel+ta r + +++v
  gi|298676101|ref|YP_003727851.1| 378 DVGAHKLWVGRLFPAYKPNTVQISNGLASMGFALPGAIAAKLVHPEKNVVAVVGDGGFMMNVQELETAKRIGTDLIV 454
                                       89*************************************************************************** PP

                                       EEEE-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                      TPP_enzyme_C  78 vvlnNegygmtggqqepfggkrksgpagkdlkpvdfaklaealGakgarvekadveeleealkealekkgpaliev 153
                                       +++n++ yg +++++  +++ +++g +   + ++df+++a+++G++g+++e+a  +el  +l+ ale++g  + +v
  gi|298676101|ref|YP_003727851.1| 455 IIFNDSKYGVIEWNELEKFK-TSYGID---FSNPDFVQMAQSFGVNGVKIESA--DELTSKLQYALENGGIWVFDV 524
                                       *************9888885.666666...9999*******************..*************99988876 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.4   0.0   7.2e-36   2.6e-32       1     137 []     186     320 ..     186     320 .. 0.94
   2 ?   -2.7   0.0       1.2   4.4e+03       4      22 ..     416     434 ..     415     441 .. 0.84

  Alignments for each domain:
  == domain 1  score: 111.4 bits;  conditional E-value: 7.2e-36
                                       HHHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHHHH CS
                      TPP_enzyme_M   1 iekaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylgmlglhgskaanealee 77 
                                       +eka+el++++ +p+il+G+gv r++ +e+l++++++l+iP +tt+mgkg ip d++ly+g++gl ++++    ++ 
  gi|298676101|ref|YP_003727851.1| 186 LEKAVELIEQSNKPLILAGNGVTREQSAEQLEKFVNRLKIPATTTFMGKGNIPTDNDLYIGSVGLQRKDYLMCGFDV 262
                                       589************************************************************************** PP

                                       -SEEEEES-SSSTCCCTTTTT.TTTTT-..EEEEEESSCCCCTTCC--SEEEECTHHHHHHHH CS
                      TPP_enzyme_M  78 aDlvlalGarfddirttgsep.efapea..kiihididpaeigknyqvdlaivgdvketleaL 137
                                       aDlv+++G++  +     ++p  ++p++  kiihi+ ++ ei+ +y ++ +++g++k +l +L
  gi|298676101|ref|YP_003727851.1| 263 ADLVICVGVDPVE-----YSPrLWNPDGskKIIHIHNSHPEIDSSYLPECSLIGNLKHSLYRL 320
                                       ********66444.....5666999997779**************************999776 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.2
                                       HHHHHHH-SSEEEEE-CHH CS
                      TPP_enzyme_M   4 aaellkaakrpvilvGggv 22 
                                       aa+l++  k++v +vG g 
  gi|298676101|ref|YP_003727851.1| 416 AAKLVHPEKNVVAVVGDGG 434
                                       7888999999999999986 PP

>> DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.9e-06     0.007     115     173 ..     405     462 ..     395     476 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.9e-06
                    DXP_synthase_N 115 tsisaalGlavardlkgekkkvvaviGDgaltgGmafealnnigelkkkllv.ilNdNem 173
                                       +s+  al  a+a++l + +k+vvav+GDg++   m  + l++++++ ++l+v i+Nd + 
  gi|298676101|ref|YP_003727851.1| 405 ASMGFALPGAIAAKLVHPEKNVVAVVGDGGFM--MNVQELETAKRIGTDLIViIFNDSKY 462
                                       566777777899999999************97..88899999999999987615688765 PP

>> CO_dh  CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   5.8e-06     0.021       5      70 ..     167     231 ..     163     273 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.8e-06
                                       XXXXXXXXXXXXX--EEE--SHHHHHHHHHSSSEEEEE-S--.-HH.HHHHHHHHHTSSSEEEEET CS
                             CO_dh   5 kiPfdeaaianskkatleealkvvakmikkakrPllivGpqvlkaeneeakekkilekklkvvata 70 
                                       + P +++  + + + ++ e  + ++++i + ++Pl++ G+ v ++   e+ ek     k++   t 
  gi|298676101|ref|YP_003727851.1| 167 ETPLQKKMYSHKSEHDENEL-EKAVELIEQSNKPLILAGNGVTREQSAEQLEKFVNRLKIPATTTF 231
                                       67766666666666666655.9********************999988888888777777766664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (545 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.70u 0.36s 00:00:01.06 Elapsed: 00:00:00.55
# Mc/sec: 2994.60
//
Query:       gi|298676102|ref|YP_003727852.1|  [L=455]
Description: aldehyde Dehydrogenase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     9e-149  495.9   0.1     1e-148  495.7   0.1    1.0  1  Aldedh    Aldehyde dehydrogenase family
     0.0047   16.0   0.0      0.016   14.3   0.0    1.8  1  LuxC      Acyl-CoA reductase (LuxC)
  ------ inclusion threshold ------
      0.037   13.2   1.5      0.053   12.7   1.5    1.2  1  Taxilin   Myosin-like coiled-coil protein


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  495.7   0.1  1.7e-152    1e-148       8     461 ..       3     451 ..       1     452 [. 0.98

  Alignments for each domain:
  == domain 1  score: 495.7 bits;  conditional E-value: 1.7e-152
                                       EEEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HH CS
                            Aldedh   8 tievinPatgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletGkpla 84 
                                       +i +inPat++v  +++  ++e+vd ++++++eaf++w++l+++eRae+L++aa+ l+erkeela ++t+e+Gkp++
  gi|298676102|ref|YP_003727852.1|   3 KIVSINPATEKVNKEYNYYSQEKVDGILKKSNEAFEQWKNLDVSERAEYLNNAAAKLRERKEELAPTITKEMGKPIR 79 
                                       5789************************************************************************* PP

                                       HHHHHHHHHHHHHHHHHHHHHH.HSEEEEEECTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEE CS
                            Aldedh  85 earaeveeaidvlryyaelaek.legevlpssegklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlK 160
                                       +++ e+e+++ vl+ +ae  ++ +e e + ++  +++ ++ ePlG+++ I+PWNfP+  a++  a+ala GN+++lK
  gi|298676102|ref|YP_003727852.1|  80 QSESEIEKCAWVLEHFAEKSKQyIEPEFVDTD-AETSGIVFEPLGTILTIMPWNFPFWQALRVGAAALAGGNVILLK 155
                                       **********************8888*99995.89999999************************************ PP

                                       E-TTSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE- CS
                            Aldedh 161 PaeetplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElG 237
                                        ++ +p++al +  +f+e g+P+gv + +  +g+++++ l+  +e++ vsftGst+ gr++a++a+kn+k+++lElG
  gi|298676102|ref|YP_003727852.1| 156 HSSHVPMCALEIEGVFRESGFPEGVYQTLLLDGKSTSS-LIGRDEIAGVSFTGSTSAGRNVAEEAGKNIKKCVLELG 231
                                       *******************************9987665.66668********************************* PP

                                       --EEEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SSH CS
                            Aldedh 238 GknplivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPlise 314
                                       G +p+ivl+daDldka+ea+++g f n+GQ C++a+r++v esi+def++k+v+a+++l++gdp+de+td+GPl+s 
  gi|298676102|ref|YP_003727852.1| 232 GSDPFIVLDDADLDKAAEAAAAGRFTNTGQSCVSAKRFIVMESIADEFISKFVNATRNLTIGDPMDENTDIGPLVSD 308
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHTTSEEEE-TTE.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHHHHH CS
                            Aldedh 315 aqlekvekyveeakeegaklllGgereeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaieiaN 391
                                       +q + +e++v++a+++ga++ll+g    + + kg++++P++l+nv++d+r+++eE+FGPV+++i++++e+eai+ aN
  gi|298676102|ref|YP_003727852.1| 309 KQIKLIEEQVNDAVSKGAEVLLEG---GKTEGKGFYYSPVILTNVSKDSRVITEETFGPVAPIITVSSEKEAIKEAN 382
                                       **********************88...67899********************************************* PP

                                       SSSEESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEEEEE CS
                            Aldedh 392 dteyGLaagvftkdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeytevkt 461
                                       dt++GL+a ++t+d e+a r+++++eaGnv +N+ t++++   pfgG+k+Sg+Gre ++ g+ e++++k+
  gi|298676102|ref|YP_003727852.1| 383 DTQFGLGANIWTEDREKAVRLTRDIEAGNVSVNSVTKSDPRL-PFGGIKKSGVGRELSRFGFYEFMNIKS 451
                                       *****************************************9.*************************97 PP

>> LuxC  Acyl-CoA reductase (LuxC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   2.6e-06     0.016      75     259 ..     106     282 ..      22     292 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.6e-06
                              LuxC  75 eflktke.ksyekaqprglvlhvlsgNvpllpvmsilqglLv.knvnllkvSssdpflaaallksladvdenhtlad 149
                                       ef+ t++  s +   p g +l +++ N p      +  ++L+ +nv+llk Ss  p+ a ++   + +      + +
  gi|298676102|ref|YP_003727852.1| 106 EFVDTDAeTSGIVFEPLGTILTIMPWNFPFWQALRVGAAALAgGNVILLKHSSHVPMCALEIEGVFRESGFPEGVYQ 182
                                       566555535667889******************999998887369**********************9999988998 PP

                              LuxC 150 slsvvyfksgdtkleeeiv.qnaDvvvawGgeeaikaiseklkpg..kqlikfGakvSfavvdkealeeealdkaae 223
                                       +l  +  ++++t+    i  ++  +v+  G+ +a ++++e++  +  k +++ G    f v+d ++     ldkaae
  gi|298676102|ref|YP_003727852.1| 183 TL-LL--DGKSTS--SLIGrDEIAGVSFTGSTSAGRNVAEEAGKNikKCVLELGGSDPFIVLDDAD-----LDKAAE 249
                                       87.44..444443..2222467899***************5544311446789*********9877.....****** PP

                              LuxC 224 raAkDiivfdQqAClspqvvfvekddkieidefaea 259
                                       +aA    +   q+C+s++   v+++    +def ++
  gi|298676102|ref|YP_003727852.1| 250 AAAAGRFTNTGQSCVSAKRFIVMES---IADEFISK 282
                                       *****************99888844...56666555 PP

>> Taxilin  Myosin-like coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.5   8.8e-06     0.053     216     280 ..      16      76 ..       2      92 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.8e-06
                           Taxilin 216 eqlnlYaeKfeefqdtLakSnelFatFkkEmekmtkktkklEketnlwkskfektnkallemaee 280
                                       +  n+Y++  e++ ++L+kSne+F+++k+   ++++  + l  +  +++++ e+   ++++ + +
  gi|298676102|ref|YP_003727852.1|  16 KEYNYYSQ--EKVDGILKKSNEAFEQWKN--LDVSERAEYLNNAAAKLRERKEELAPTITKEMGK 76 
                                       55566665..789***************8..799********************99999976654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.69u 0.37s 00:00:01.06 Elapsed: 00:00:00.55
# Mc/sec: 2496.61
//
Query:       gi|298676103|ref|YP_003727853.1|  [L=55]
Description: hypothetical protein Metev_2232 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 370.89
//
Query:       gi|298676104|ref|YP_003727854.1|  [L=455]
Description: aldehyde Dehydrogenase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   3.9e-143  477.3   0.0   4.4e-143  477.2   0.0    1.0  1  Aldedh    Aldehyde dehydrogenase family
  ------ inclusion threshold ------
      0.015   14.4   1.5      0.032   13.3   0.3    2.0  2  LuxC      Acyl-CoA reductase (LuxC)
      0.095   13.1   0.0        0.2   12.1   0.0    1.4  1  nsp9      nsp9 replicase
        0.1   12.1   0.0        0.2   11.1   0.0    1.4  1  DUF2117   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  477.2   0.0  9.7e-147  4.4e-143       8     461 ..       3     451 ..       1     452 [. 0.97

  Alignments for each domain:
  == domain 1  score: 477.2 bits;  conditional E-value: 9.7e-147
                                       EEEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HH CS
                            Aldedh   8 tievinPatgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletGkpla 84 
                                       ti +inPat+e+ ++++  ++++vd+++++++eaf +w++l+++eRa +L ++a++l++rk +l +++t+e+Gkp++
  gi|298676104|ref|YP_003727854.1|   3 TITSINPATEEINGTYELYSQNKVDKVLKKSEEAFLEWSNLKVSERAIYLSRVANVLRKRKSQLGTVITKEMGKPIK 79 
                                       6899************************************************************************* PP

                                       HHHHHHHHHHHHHHHHHHHHHH.HSEEEEEECTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEE CS
                            Aldedh  85 earaeveeaidvlryyaelaek.legevlpssegklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlK 160
                                       ++++e+e+++ +++y+a+ ae+ ++ e ++s + k++ ++ ePlG++++I PWNfP+  a+  +a+ala GN+++lK
  gi|298676104|ref|YP_003727854.1|  80 QSMGEIEKCAVTFDYFAKNAENlMQPEPVES-DAKNCGIYFEPLGIILSIKPWNFPFWQAISFAAHALAGGNVILLK 155
                                       **********************555587777.589999999************************************ PP

                                       E-TTSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE- CS
                            Aldedh 161 PaeetplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElG 237
                                        ++ +p++al +  +f+e g+P+gv + +  +g+++++ l+  +e++ vsftGst+ g  ia++a+kn+k+++lElG
  gi|298676104|ref|YP_003727854.1| 156 HSSHVPMCALEIEGVFRESGFPEGVYQTLLLDGKSTSS-LIGRDEIAGVSFTGSTSAGGSIAEEAGKNIKKCVLELG 231
                                       *******************************9987665.66668********************************* PP

                                       --EEEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SSH CS
                            Aldedh 238 GknplivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPlise 314
                                       G +p+i+l+daDldka+ea++ + ++naGQ+Ci+a+r++v+e+i+++f++++vea+k+ + gdp+de+t++GPl++ 
  gi|298676104|ref|YP_003727854.1| 232 GSDPFIILDDADLDKAAEAAAVSRCMNAGQTCISAKRFIVEEGIAEQFTSRFVEAMKSYTHGDPMDENTKLGPLVRD 308
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHTTSEEEE-TTE.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHHHHH CS
                            Aldedh 315 aqlekvekyveeakeegaklllGgereeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaieiaN 391
                                       +q++ +e++v++a+++ga++ll+g    + + kg++++P+vl+nv++d+r+++eE+FGPV+++i +k++eea+e+aN
  gi|298676104|ref|YP_003727854.1| 309 EQRSLLEEQVNDAVSKGAEVLLEG---GKTEGKGFYYSPVVLTNVSKDSRVITEETFGPVAPIIIVKNDEEAVEVAN 382
                                       **********************88...67899********************************************* PP

                                       SSSEESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEEEEE CS
                            Aldedh 392 dteyGLaagvftkdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeytevkt 461
                                       +t+yGL+a+++++d+e+a+ + ++l++G+v +N+  + +++  pfgGvk+Sg+Gre +k g+ e+++ kt
  gi|298676104|ref|YP_003727854.1| 383 NTRYGLGATIYSQDEEKAHSIGRQLNTGTVFVNSVLKPEPQL-PFGGVKDSGTGRELSKFGFYEFMNKKT 451
                                       ***********************************9999999.************************997 PP

>> LuxC  Acyl-CoA reductase (LuxC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0      0.94   4.2e+03      42      69 ..      46      76 ..      21      82 .. 0.58
   2 ?   13.3   0.3   7.1e-06     0.032      88     269 ..     120     292 ..     101     302 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 0.94
                              LuxC 42 allei.lkalaallkre..eLkkvleseLgq 69
                                         +i l ++a++l+++  +L +v+ +e+g+
  gi|298676104|ref|YP_003727854.1| 46 SERAIyLSRVANVLRKRksQLGTVITKEMGK 76
                                      3333445666666655422566777777766 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 7.1e-06
                              LuxC  88 qprglvlhvlsgNvpllpvmsilqglLv.knvnllkvSssdpflaaallksladvdenhtladslsvvyfksgdtkl 163
                                        p g++l + + N p    +s +  +L+ +nv+llk Ss  p+ a ++   + +      + ++l  +  ++++t+ 
  gi|298676104|ref|YP_003727854.1| 120 EPLGIILSIKPWNFPFWQAISFAAHALAgGNVILLKHSSHVPMCALEIEGVFRESGFPEGVYQTL-LL--DGKSTS- 192
                                       69999999999999999888877665552799999***999999999999999999988888887.34..444443. PP

                              LuxC 164 eeeiv.qnaDvvvawGgeeaikaiseklkpg..kqlikfGakvSfavvdkealeeealdkaaeraAkDiivfdQqAC 237
                                          i  ++  +v+  G+ +a  +i+e++  +  k +++ G    f ++d ++     ldkaae+aA   ++   q C
  gi|298676104|ref|YP_003727854.1| 193 -SLIGrDEIAGVSFTGSTSAGGSIAEEAGKNikKCVLELGGSDPFIILDDAD-----LDKAAEAAAVSRCMNAGQTC 263
                                       .2222367789**************954443114467899999****99877.....******************** PP

                              LuxC 238 lspqvvfvekddkieidefaeaLaaaLekrar 269
                                       +s++   ve++    +++f ++  +a++ +++
  gi|298676104|ref|YP_003727854.1| 264 ISAKRFIVEEG---IAEQFTSRFVEAMKSYTH 292
                                       *********54...678899999899988876 PP

>> nsp9  nsp9 replicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.4e-05       0.2      56      96 ..      63     103 ..      41     106 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.4e-05
                                       E-TTSSEEEEEB---EEEEEEETTSEEEEEEEEBTT--HHH CS
                              nsp9  56 ekedgnvivveLepPcrfvvdtvkgvkvkYLYfvknlntlr 96 
                                       +++ g+vi+ e+  P++ ++ + ++  v + Yf kn ++l 
  gi|298676104|ref|YP_003727854.1|  63 KSQLGTVITKEMGKPIKQSMGEIEKCAVTFDYFAKNAENLM 103
                                       567799*******************************9996 PP

>> DUF2117  Uncharacterized protein conserved in archaea (DUF2117)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   4.4e-05       0.2       4      83 ..     328     411 ..     326     423 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.4e-05
                           DUF2117   4 fLlnygksketGhvFgkiVverskekkpliqierpgekdgeiilwn.ekaeklakklseelglkivkpeevekeiv. 78 
                                       +Ll+ gk++  G  +  +V+ + +++  +i  e+ g     ii+ n e+a+++a++ +  lg  i ++ e + + + 
  gi|298676104|ref|YP_003727854.1| 328 VLLEGGKTEGKGFYYSPVVLTNVSKDSRVITEETFGPVAPIIIVKNdEEAVEVANNTRYGLGATIYSQDEEKAHSIg 404
                                       79***********************************999999998455666***9999999999877766665554 PP

                           DUF2117  79 .e.skgk 83 
                                        + ++g+
  gi|298676104|ref|YP_003727854.1| 405 rQlNTGT 411
                                       3244454 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 3046.25
//
Query:       gi|298676105|ref|YP_003727855.1|  [L=283]
Description: hypothetical protein Metev_2234 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.11   13.3  12.4       0.11   13.3   1.3    3.3  4  Tmemb_14       Transmembrane proteins 14C
       0.38   10.7   1.3          9    6.3   0.0    2.5  2  UPF0542        Uncharacterised protein family UPF0542


Domain annotation for each model (and alignments):
>> Tmemb_14  Transmembrane proteins 14C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   1.1     0.043   3.9e+02      49      73 ..      19      43 ..       7      65 .. 0.66
   2 ?    6.1   1.1    0.0021        19       8      71 ..      28      93 ..      21     110 .. 0.77
   3 ?   13.3   1.3   1.2e-05      0.11      33      90 ..     146     206 ..     118     208 .. 0.78
   4 ?   -2.5   0.1      0.98   8.8e+03      51      51 ..     257     257 ..     232     276 .. 0.52

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.043
                          Tmemb_14 49 ka.kelslvislvlllvmgkrllktr 73
                                      ++   l lvi++++++v ++ l +  
  gi|298676105|ref|YP_003727855.1| 19 QNfAMLILVIAAIITGVVIYAL-NNY 43
                                      4467788999999999988844.333 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0021
                          Tmemb_14  8 allavGGilgYlkag.Sv.pSLiaGlllGallllagyllsknkkakelslvislvlllvmgkrllk 71
                                      +  ++ G++ Y+  + S+  S+  ++ +G+ ++l++ l+++ + ++els + s+ ++++ ++ l+ 
  gi|298676105|ref|YP_003727855.1| 28 IAAIITGVVIYALNNySLyDSILQAIKSGISVFLSWALARELDPDNELSALFSAGIIFILISSLIT 93
                                      566778888888766233259999999999999999999888888999999999888888877665 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 1.2e-05
                          Tmemb_14  33 lGallllagyl..lsknkka.kelslvislvlllvmgkrllktrkfmpaglvavlsalmll 90 
                                        +++++l g +   +kn+++ + +sl+is+v+++++g  +lkt + + + +++++s+l ll
  gi|298676105|ref|YP_003727855.1| 146 TSLVFFLDGSMdfPNKNNRYfTIISLIISAVIIIFNGNVVLKTPATLNVLVILIVSLLFLL 206
                                       33333333333655677777899*********************************99875 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 0.98
                          Tmemb_14  51 k 51 
                                        
  gi|298676105|ref|YP_003727855.1| 257 L 257
                                       2 PP

>> UPF0542  Uncharacterised protein family UPF0542
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.001         9      37      50 ..      57      70 ..      55      76 .. 0.88
   2 ?    1.2   1.7      0.04   3.6e+02      18      40 ..     187     209 ..     166     215 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.001
                           UPF0542 37 lsaflsyKLakelk 50
                                      +s+fls+ La+el+
  gi|298676105|ref|YP_003727855.1| 57 ISVFLSWALARELD 70
                                      79**********97 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.04
                           UPF0542  18 kdPweFlttvlliltPllllsaf 40 
                                       k P      v+li++ l+ll +f
  gi|298676105|ref|YP_003727855.1| 187 KTPATLNVLVILIVSLLFLLHIF 209
                                       6677777889**********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1076  (0.0600145); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 1836.05
//
Query:       gi|298676106|ref|YP_003727856.1|  [L=114]
Description: hypothetical protein Metev_2235 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-11   44.0  30.7    2.4e-11   43.8  30.7    1.0  1  DUF5518          Family of unknown function (DUF5518)


Domain annotation for each model (and alignments):
>> DUF5518  Family of unknown function (DUF5518)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8  30.7   1.3e-15   2.4e-11       2     118 .]       6     112 ..       5     112 .. 0.92

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 1.3e-15
                           DUF5518   2 raaliGavvaivlslllglllpsvgsllgllvgGlvaGylaggdskdgavaGalaGligaipvlvlllvlllglvaa 78 
                                       + a+iG v +i+l+ll++      +++l++l+gG++ Gy   +d+  g+ +G+l+++++ ip+++l+++l++  +  
  gi|298676106|ref|YP_003727856.1|   6 KGAVIGLVSTIILYLLPF------IDILAPLIGGIIGGYAGAKDAWGGFKVGILMTVLMIIPGVILATLLGS--ILS 74 
                                       789***************......****************************************99999996..777 PP

                           DUF5518  79 igglagfvallvalllvvllllvvllvilgaiGGaiGgll 118
                                       +++l+g+++++ ++ll+  +llv+ ++ilg+ G+++Ggll
  gi|298676106|ref|YP_003727856.1|  75 FVPLLGAFFAGSTILLT--ILLVAHTAILGIFGAIVGGLL 112
                                       88888888877777777..9******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 784.82
//
Query:       gi|298676107|ref|YP_003727857.1|  [L=308]
Description: aIF-2BI family translation initiation factor [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.4e-85  284.4   3.6    9.5e-85  284.2   3.6    1.0  1  IF-2B     Initiation factor 2 subunit family


Domain annotation for each model (and alignments):
>> IF-2B  Initiation factor 2 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  284.2   3.6   5.3e-89   9.5e-85       1     282 []      15     289 ..      15     289 .. 0.99

  Alignments for each domain:
  == domain 1  score: 284.2 bits;  conditional E-value: 5.3e-89
                                       SS-SHHHHHHHHHHHHHHHHHHCCCSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHH CS
                             IF-2B   1 kvrGspaiaiaalevllevikdaktskvaeLkeelrkaidlLkkarPtavslgnairrllkeiselksssdvkeakk 77 
                                       ++rG+ +ia aa+ ++ +++k+ ++++ +e+  +++ka++ L ++rPtavsl na+ +  k     +s+++v++a++
  gi|298676107|ref|YP_003727857.1|  15 EIRGAGRIASAAATAIHDYVKNLDAETIQEFDDKVQKAAKILVNTRPTAVSLPNAVWMSVK-----HSKTNVDDARE 86 
                                       589*****************************************************99888.....9********** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SHHHHHHHHHHHTTEEEEEEEEEXTTTTHHHTHHHHH CS
                             IF-2B  78 sliekikelikeieeadekigdiaaelikdgdtilTicnsktvlevlraaakekkkfkVivvEsrPrlqGrltakeL 154
                                       ++i++++++ik++  a e+ig+i++++i+dgd+i+T+cns ++l+ + +a +++k+++Vi +EsrPr qG l +k L
  gi|298676107|ref|YP_003727857.1|  87 EIINNANRFIKQADYALENIGKIGSKRIQDGDVIMTHCNSHAALSAITTAFEQGKNISVITTESRPRKQGLLNIKHL 163
                                       ***************************************************************************** PP

                                       HHTTXEEEEEEGGGHHHHHHCTESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGGBESTSSSGGG CS
                             IF-2B 155 vqagipvtlitdsavayvmseevdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslkfservqlded 231
                                       ++ +ip+t+i+dsav+ +m++ vdkvivGAd+i  nGa++nkiGTs+lA++A+e+++++lv+ae++kfs+ +  +e 
  gi|298676107|ref|YP_003727857.1| 164 NDYNIPTTYIVDSAVRSCMKN-VDKVIVGADAISVNGALINKIGTSQLALAAHESRVNLLVAAETYKFSPSTIQGEM 239
                                       *********************.******************************************************* PP

                                       SSXXBEXTHHHHEETTEESSTTTEEEEEBSEEEEEGGGXSEEEETTEEEXC CS
                             IF-2B 232 ifieerdpeellnitgeriaeeelkvvnpafDvtPpelItliITevGvlpp 282
                                       i ie r+ +e++n ++ r  +  ++v npafDvtP+e+I+liIT+ Gv+pp
  gi|298676107|ref|YP_003727857.1| 240 IEIEDRPTDEVINPDELRDLP-YVEVKNPAFDVTPAEYIDLIITDAGVIPP 289
                                       ******************999.***************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       832  (0.0464053); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2067.50
//
Query:       gi|298676108|ref|YP_003727858.1|  [L=45]
Description: hypothetical protein Metev_2239 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1014  (0.0565564); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 330.75
//
Query:       gi|298676109|ref|YP_003727859.1|  [L=432]
Description: hypothetical protein Metev_2240 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0026   16.9  12.2     0.0026   16.9  12.2    3.1  3  Atg14            Vacuolar sorting 38 and autophagy-related su
     0.0065   15.2  42.3       0.17   10.5  21.4    2.1  2  AAA_13           AAA domain
     0.0065   16.3   3.0     0.0065   16.3   3.0    4.3  2  TACC_C           Transforming acidic coiled-coil-containing p
  ------ inclusion threshold ------
      0.021   14.9   7.0      0.021   14.9   7.0    5.4  5  TssO             Type VI secretion system, TssO
      0.056   13.5  24.5       0.13   12.4   4.6    4.8  4  DUF2730          Protein of unknown function (DUF2730)
       0.16   11.5  26.5       0.38   10.2   0.4    3.6  4  Allexi_40kDa     Allexivirus 40kDa protein
       0.16   10.7  33.7      0.065   12.0  10.8    4.1  3  Tektin           Tektin family
       0.17   12.4  19.9        2.5    8.6   8.8    3.8  3  T3SSipB          Type III cell invasion protein SipB
       0.43   10.7   7.6        3.1    7.9   0.5    3.1  2  Aurora-A_bind    Aurora-A binding
       0.46   10.7  29.1        5.5    7.2   4.0    4.3  4  FliJ             Flagellar FliJ protein
       0.65    9.8   8.5       0.59   10.0   0.9    3.3  3  sCache_2         Single Cache domain 2
       0.75    9.8  26.1          4    7.5   2.7    4.9  7  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
       0.86    9.9  13.8          4    7.8   0.5    4.6  4  DUF948           Bacterial protein of unknown function (DUF94
        1.3    8.6  13.2       0.13   11.8   1.1    3.0  2  DUF2968          Protein of unknown function (DUF2968)
        1.4    9.2  11.4         34    4.8   0.1    5.2  4  WXG100           Proteins of 100 residues with WXG
        1.4    8.2  23.3       0.46    9.8   5.6    2.8  3  DUF4407          Domain of unknown function (DUF4407)
        1.5    8.7  23.4        4.6    7.1   3.8    3.8  2  Wtap             WTAP/Mum2p family
        1.7    8.7  31.4      0.051   13.6   3.3    5.1  6  DUF1664          Protein of unknown function (DUF1664)
        3.5    6.8  30.2       0.98    8.7   7.7    3.4  3  DUF3450          Protein of unknown function (DUF3450)
        4.3    7.3  54.9       0.56   10.2  10.3    4.4  4  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
        6.3    6.7  42.8       0.31   10.9   0.3    4.3  4  DASH_Spc19       Spc19
        6.8    6.6  26.8        2.7    7.9  10.8    4.1  4  Sec8_exocyst     Sec8 exocyst complex component specific doma
          7    5.4  51.1       0.14   11.1  15.1    3.9  4  Spc7             Spc7 kinetochore protein
        7.1    6.4  26.0       0.12   12.1   6.3    3.3  3  She9_MDM33       She9 / Mdm33 family
        7.9    6.0  32.8         37    3.8   0.4    3.3  1  Exonuc_VII_L     Exonuclease VII, large subunit
        7.9    7.0  22.6        3.9    8.0   0.2    5.8  4  LPP              Lipoprotein leucine-zipper


Domain annotation for each model (and alignments):
>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   2.1         1   7.1e+02      36      78 ..      37      73 ..       5      96 .. 0.42
   2 !   16.9  12.2   3.8e-06    0.0026      15     133 ..     127     250 ..     122     294 .. 0.81
   3 ?    3.5  10.1     0.046        32      33      99 ..     336     418 ..     316     431 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1
                             Atg14 36 sekeslkkkiekalegkeeaeqledkiknkkakleelksliad 78
                                      se++   + ++ ++++k+      ++ik++ ++le+ k++ + 
  gi|298676109|ref|YP_003727859.1| 37 SESNDAFSDMKPYITQKY------EEIKTHLDSLEKDKKELEN 73
                                      222222222222222222......3333333333333333333 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 3.8e-06
                             Atg14  15 sClrng...........perlyelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlr 80 
                                       +C+ n+           pe +  l  +l  ++s    l+ ki+ +  + +      +++  k + ++++k++i+d++
  gi|298676109|ref|YP_003727859.1| 127 TCVENSiksqhyikpifPEIFKNLSNDLSEINSSLSDLGDKINNIKDRLD----IYENLPEKIDEVNQIKKQIEDKK 199
                                       79888888889999999999999999****************97766666....7899******************* PP

                             Atg14  81 erlqelkdklsqlkkeieekkkklaklsdklkkRrsdleslqneleerrkkqi 133
                                       +++qel++k ++ k ++ +++ +l++l+++  + +++   l+ne+++ + +++
  gi|298676109|ref|YP_003727859.1| 200 SNIQELEKKYESSKHSLSDAQSRLETLKASENYQKAE--ELENEIQKLKDEKL 250
                                       *****************************97644444..78888777665543 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.046
                             Atg14  33 klksekeslkkkiekalegke................eaeqledkiknkkakleelksliadlrerlqelkdklsql 93 
                                       + ++e++++ + +ek l+ ++                e+ +le++i n+k+ +++ +s+i + r++l el++k +ql
  gi|298676109|ref|YP_003727859.1| 336 NHLLESDEFSNLVEKRLSYTSrieeleieldrltvykEKANLEKQISNNKNTMDTVQSEIDSERKHLDELNQKKDQL 412
                                       56678888888888888888866666666667777777777777777777777777777777777777777777777 PP

                             Atg14  94 kkeiee 99 
                                        +e++ 
  gi|298676109|ref|YP_003727859.1| 413 LEELQS 418
                                       776654 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9  18.6    0.0015         1     285     453 ..      25     242 ..      13     244 .. 0.80
   2 !   10.5  21.4   0.00024      0.17     279     454 ..     236     410 ..     219     423 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0015
                            AAA_13 285 qerLekliekveskkselleklkavsdeasensafeed.keelkaeaealeeqLkglqraleaKrkepfksvelesv 360
                                       + +Le+++++++s+++ ++  +k  ++++ e+++++ d  e+ k+e+e++e + +g+ ra++  +++ +k++++  +
  gi|298676109|ref|YP_003727859.1|  25 TLSLEEIQDWMKSESNDAFSDMKPYITQKYEEIKTHLDsLEKDKKELENVEIKNQGIPRAVQSNKENFVKNLNI--I 99 
                                       45789999999999999999999999988888887777578888899999999999******9999*9996664..3 PP

                            AAA_13 361 kakie............................................sikklvaeineliakhNekvanleeeke 393
                                        +ki+                                            +++++++ein + ++   k++n++++  
  gi|298676109|ref|YP_003727859.1| 100 LDKISipydidpstahrfyteatstlntcvensiksqhyikpifpeifkNLSNDLSEINSSLSDLGDKINNIKDRLD 176
                                       44443344577888999999999999999999999999999999999998999999999999999999999988887 PP

                            AAA_13 394 eakkklel.hlveeleseldeykkkykklekaieklekelkeeeaelkkleee.....ikeLekql 453
                                         ++  e+ ++v++++++++  k+++++lek+ e+ +++l++++++l++l++      ++eLe+++
  gi|298676109|ref|YP_003727859.1| 177 IYENLPEKiDEVNQIKKQIEDKKSNIQELEKKYESSKHSLSDAQSRLETLKASenyqkAEELENEI 242
                                       777766553568999999999999999999999999999999999999888766666678888877 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00024
                            AAA_13 279 defeekqerLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksv 355
                                       +e e+++++L++ + +++s+ + l++ l +++   + +++ ++d+++l+ e++++ e++++++  l +K k  +   
  gi|298676109|ref|YP_003727859.1| 236 EELENEIQKLKDEKLNIDSELKDLFAPLSKAIS--RMEKQDKSDRHTLSPEFREVIEKINNNEVHLLDKDKLASF-- 308
                                       344444555555555555555555444444444..556678999*************************976665.. PP

                            AAA_13 356 elesvkakie..sikklvaeineliakhNekvanleeekeeakkklelhl.veeleseldeyk..kkykklekaiek 427
                                        l+++k+++e  s+  ++ + n++i++ N   ++ +e  + ++k l +   +eele eld+++  k++++lek+i++
  gi|298676109|ref|YP_003727859.1| 309 -LNDMKNRVEdgSLGLKQRKGNNIIEQVNHLLES-DEFSNLVEKRLSYTSrIEELEIELDRLTvyKEKANLEKQISN 383
                                       .778888885225667788899999999987654.55566666777664439999999998777799********** PP

                            AAA_13 428 lekelkeeeaelkkleeeikeLekqlr 454
                                       +++ ++  ++e+   ++   eL ++  
  gi|298676109|ref|YP_003727859.1| 384 NKNTMDTVQSEIDSERKHLDELNQKKD 410
                                       **************9999999987654 PP

>> TACC_C  Transforming acidic coiled-coil-containing protein (TACC), C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   5.1      0.25   1.7e+02       3      72 ..      10      78 ..       8     105 .. 0.66
   2 !   16.3   3.0   9.4e-06    0.0065      78     137 ..     148     213 ..     115     220 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.25
                            TACC_C  3 qkdldaalekvkeeveekeeeiqelkkkveelkkenqemk.kivaefektiaqlieekqkqkelakkeiqk 72
                                      +k+ d+ +++  e+++   eeiq++ k+  e++     mk  i +++e++ ++l + ++ +kel++ ei++
  gi|298676109|ref|YP_003727859.1| 10 KKEKDEEVQEEPEKITLSLEEIQDWMKS--ESNDAFSDMKpYITQKYEEIKTHLDSLEKDKKELENVEIKN 78
                                      5677777777777777777888888775..44455556662477888887777777777777777777764 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 9.4e-06
                            TACC_C  78 eqlladlnsveksfsdlfkryekqkevlegykknee......slkkcaeeylarvkkeeqRYqaLk 137
                                       ++l++dl++++ s+sdl  ++++ k+ l+ y +  e      + kk++e+ ++++++ e++Y++ k
  gi|298676109|ref|YP_003727859.1| 148 KNLSNDLSEINSSLSDLGDKINNIKDRLDIYENLPEkidevnQIKKQIEDKKSNIQELEKKYESSK 213
                                       57889**************************98766222222479*****************9887 PP

>> TssO  Type VI secretion system, TssO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   5.3     0.098        68      81     138 ..      17      72 ..       1      96 [. 0.62
   2 ?   14.9   7.0   3.1e-05     0.021      85     146 ..     155     214 ..     146     216 .. 0.87
   3 ?   -0.4   1.3       1.6   1.1e+03      46      69 ..     231     254 ..     215     279 .. 0.51
   4 ?    0.1   0.5       1.1   7.7e+02      69     122 ..     287     340 ..     263     369 .. 0.66
   5 ?    1.0   4.2      0.58     4e+02      44      80 ..     372     411 ..     354     428 .. 0.53

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.098
                              TssO  81 vfle.neIkkdlndikntygknssdeRykmyaqiakfykmlledKkelksvseniklfk 138
                                       v++e ++I+ +l++i++ ++ +s+d   +m + i + y+++   K  l s+++++k+++
  gi|298676109|ref|YP_003727859.1|  17 VQEEpEKITLSLEEIQDWMKSESNDAFSDMKPYITQKYEEI---KTHLDSLEKDKKELE 72 
                                       44442679999999999999999998777766666666543...333333333333322 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 3.1e-05
                              TssO  85 neIkkdlndikntygknssdeRykmyaqiakfykmlledKkelksvseniklfkkqLeecei 146
                                       +eI+ +l+d+ ++++  + + R ++y+++ + +++  + Kk++ ++++ni++++k++e  ++
  gi|298676109|ref|YP_003727859.1| 155 SEINSSLSDLGDKIN--NIKDRLDIYENLPEKIDEVNQIKKQIEDKKSNIQELEKKYESSKH 214
                                       678888888888874..56778**********************************997765 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.6
                              TssO  46 elerkkkfeekqkelkkkvdsiyk 69 
                                       + ++ +++e++ ++lk++  +i++
  gi|298676109|ref|YP_003727859.1| 231 NYQKAEELENEIQKLKDEKLNIDS 254
                                       333333333333333333333333 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 1.1
                              TssO  69 kkIdsLkpevnavfleneIkkdlndikntygknssdeRykmyaqiakfykmlle 122
                                       + I++++ ++     ++++   lnd+kn  ++ s   + +   +i+++ + lle
  gi|298676109|ref|YP_003727859.1| 287 EVIEKINNNEVHLLDKDKLASFLNDMKNRVEDGSLGLKQRKGNNIIEQVNHLLE 340
                                       456777777777778888888888888887776665555555555555555555 PP

  == domain 5  score: 1.0 bits;  conditional E-value: 0.58
                              TssO  44 lkelerkkkfeekqk...elkkkvdsiykkIdsLkpevna 80 
                                       +++++ +k++ + ++   ++++++ds  k++d L++++ +
  gi|298676109|ref|YP_003727859.1| 372 KEKANLEKQISNNKNtmdTVQSEIDSERKHLDELNQKKDQ 411
                                       3333333333333330003345555555555555544444 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.3      0.11        74      31      64 ..      53      86 ..      46     103 .. 0.85
   2 ?    8.1   0.7     0.004       2.8      35      91 ..     161     214 ..     151     218 .. 0.77
   3 ?    5.5   2.3     0.025        18      31      89 ..     198     259 ..     197     276 .. 0.86
   4 ?   12.4   4.6   0.00019      0.13      33      94 ..     342     403 ..     335     417 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.11
                           DUF2730 31 kredleklaekveendkrlteletkvenLPtakd 64
                                      k e++++  +++e+ +k l+++e+k + +P a++
  gi|298676109|ref|YP_003727859.1| 53 KYEEIKTHLDSLEKDKKELENVEIKNQGIPRAVQ 86
                                      557888888999*****************98876 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.004
                           DUF2730  35 leklaekveendkrlteletkvenLPta.kdlekLkllladlrgelkaleaevrqlsh 91 
                                       l+ l +k+++++ rl+      enLP + ++++++k++++d + ++++le++ ++ +h
  gi|298676109|ref|YP_003727859.1| 161 LSDLGDKINNIKDRLDIY----ENLPEKiDEVNQIKKQIEDKKSNIQELEKKYESSKH 214
                                       455666667777777665....489987468*******************99888777 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.025
                           DUF2730  31 kredleklaekveendkrlteletkvenLPta...kdlekLkllladlrgelkaleaevrql 89 
                                       k++++++l++k e+ ++ l+++++++e+L      +  e+L+ ++++l+ e  +++ e++ l
  gi|298676109|ref|YP_003727859.1| 198 KKSNIQELEKKYESSKHSLSDAQSRLETLKASenyQKAEELENEIQKLKDEKLNIDSELKDL 259
                                       899**************************866111556789999999999998888888765 PP

  == domain 4  score: 12.4 bits;  conditional E-value: 0.00019
                           DUF2730  33 edleklaekveendkrlteletkvenLPtakdlekLkllladlrgelkaleaevrqlshqvd 94 
                                       ++ ++l+ek  ++ +r++ele++++ L   k+ ++L++++++ +  +++++ e+++ ++ +d
  gi|298676109|ref|YP_003727859.1| 342 DEFSNLVEKRLSYTSRIEELEIELDRLTVYKEKANLEKQISNNKNTMDTVQSEIDSERKHLD 403
                                       6889999999**********************999999988877777777766665444443 PP

>> Allexi_40kDa  Allexivirus 40kDa protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.4   0.00055      0.38      79     157 ..      13      91 ..       2     122 .. 0.86
   2 ?    8.9   6.3    0.0014      0.95      66     147 ..     155     236 ..     144     263 .. 0.66
   3 ?    3.4   4.0     0.068        47      63     162 ..     287     393 ..     277     404 .. 0.63
   4 ?    3.0   3.5     0.091        63      85     142 ..     356     410 ..     323     425 .. 0.43

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00055
                      Allexi_40kDa  79 lLselrdalrtltklldklksvekklelsaetasdskllkklesietsleelhakldelsssetsesegPsssptka 155
                                       +  e++++ +++t  l+++++ +k+ +++a ++++  +++k e i+t+l++l +  +el + e +++  P++ ++++
  gi|298676109|ref|YP_003727859.1|  13 KDEEVQEEPEKITLSLEEIQDWMKSESNDAFSDMKPYITQKYEEIKTHLDSLEKDKKELENVEIKNQGIPRAVQSNK 89 
                                       557899999*******************************************************9999999888776 PP

                      Allexi_40kDa 156 ss 157
                                       ++
  gi|298676109|ref|YP_003727859.1|  90 EN 91 
                                       65 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0014
                      Allexi_40kDa  66 nklnpvsllsqttlLselrdalrtltklldklksvekklelsa.etasdskllkklesietsleelhakldelssse 141
                                       +++n++ l   + ++++++d+l   ++l +k+ +v++ +++ + ++ + ++l kk es ++sl + + +l++l +se
  gi|298676109|ref|YP_003727859.1| 155 SEINSS-LSDLGDKINNIKDRLDIYENLPEKIDEVNQIKKQIEdKKSNIQELEKKYESSKHSLSDAQSRLETLKASE 230
                                       333333.444788999999999887777777777666444433033444566799***************9999888 PP

                      Allexi_40kDa 142 tseseg 147
                                       + ++++
  gi|298676109|ref|YP_003727859.1| 231 NYQKAE 236
                                       766554 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.068
                      Allexi_40kDa  63 siinklnpvslls.....qttlLselrdalr..tltklldklksvekklelsaetasdskllkklesietsleelha 132
                                       ++i+k+n++++        ++ L++++++++   l  +  k +++ +++++  e+++ s+l++k  s   ++eel +
  gi|298676109|ref|YP_003727859.1| 287 EVIEKINNNEVHLldkdkLASFLNDMKNRVEdgSLGLKQRKGNNIIEQVNHLLESDEFSNLVEKRLSYTSRIEELEI 363
                                       55666655443322222222233333333331123333344455566666666666667777777788899****** PP

                      Allexi_40kDa 133 kldelsssetsesegPsssptkassaeaaa 162
                                       +ld+l+  +++++ + + s++k+++   ++
  gi|298676109|ref|YP_003727859.1| 364 ELDRLTVYKEKANLEKQISNNKNTMDTVQS 393
                                       ********9999999999999988876665 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.091
                      Allexi_40kDa  85 dalrtltklldklksvekklelsaetasdskllkklesietsleelhakldelssset 142
                                       +++++l+ +ld+l+  ++k +l+++  +++   +++++++ ++++  ++ldel ++++
  gi|298676109|ref|YP_003727859.1| 356 SRIEELEIELDRLTVYKEKANLEKQISNNK---NTMDTVQSEIDSERKHLDELNQKKD 410
                                       233444444444444444333333222222...2344444444444444444444443 PP

>> Tektin  Tektin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   3.1    0.0091       6.3      15      81 ..      10      76 ..       1      99 [. 0.87
   2 ?   12.0  10.8   9.4e-05     0.065     204     342 ..     116     258 ..      84     276 .. 0.68
   3 ?    2.6   4.7     0.068        47      46     362 ..     375     417 ..     326     429 .. 0.59

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0091
                            Tektin 15 erneaerlrnesrrlideteektkktqadsnkrLeeRiediefwkeeLekeleelkeeieaLeeekr 81
                                      ++++ e++++e +++  ++ee  ++++++sn+ +++    i++  ee++++l+ l++  ++Le+ + 
  gi|298676109|ref|YP_003727859.1| 10 KKEKDEEVQEEPEKITLSLEEIQDWMKSESNDAFSDMKPYITQKYEEIKTHLDSLEKDKKELENVEI 76
                                      667789999999999*****************************************99999998765 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 9.4e-05
                            Tektin 204 kftkdnieraekerqasakLreaidsilkqtandlraqaeavnealrkrieetedaknkle.........eqlkkvl 271
                                       +f  +  +  ++++++s k ++ i+ i  ++ ++l +  + +n +l++   +++++k+ l          ++ ++++
  gi|298676109|ref|YP_003727859.1| 116 RFYTEATSTLNTCVENSIKSQHYIKPIFPEIFKNLSNDLSEINSSLSDLGDKINNIKDRLDiyenlpekiDEVNQIK 192
                                       55555556666677777777777777777777777777777777766544444444444432112222224567888 PP

                            Tektin 272 eeiaeleknieeLekairdkeaplklaqtRlenRtqRpnvElcrDeaqyrLveEvkeleetieaLkeklae 342
                                       ++i++ + ni+eLek+ ++ +++l  aq+Rle+ +   n    ++     L +E+++l+++  + +++l++
  gi|298676109|ref|YP_003727859.1| 193 KQIEDKKSNIQELEKKYESSKHSLSDAQSRLETLKASENYQKAEE-----LENEIQKLKDEKLNIDSELKD 258
                                       9*********************************99999887765.....667777766666655555554 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.068
                            Tektin  46 krLeeRiediefwkeeLekeleelkeeieaLeeekrrlekalealeeplhiaqeclelRekRqgidlvhDevekeLl 122
                                                                                                                    
  gi|298676109|ref|YP_003727859.1| 375 A---------------------------------------------------------------------------- 375
                                       2............................................................................ PP

                            Tektin 123 kEveliegvqellkrtleqaeeqlrllraakhkLekdlsdKkeAleiDeeclslkntsanisykpgaerlpetsstp 199
                                                                                                                    
  gi|298676109|ref|YP_003727859.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                            Tektin 200 eeWekftkdnieraekerqasakLreaidsilkqtandlraqaeavnealrkrieetedaknkleeqlkkvleeiae 276
                                                                                                                    
  gi|298676109|ref|YP_003727859.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                            Tektin 277 leknieeLekairdkeaplklaqtRlenRtqRpnvElcrDeaqyrLveEvkeleetieaLkeklaeaeaslkaLert 353
                                                                                   +L + + + ++t+++ +++++  ++ l++L+++
  gi|298676109|ref|YP_003727859.1| 376 --------------------------------------------NLEKQISNNKNTMDTVQSEIDSERKHLDELNQK 408
                                       ............................................344444444444444444444444444444444 PP

                            Tektin 354 rleleedia 362
                                       + +l e+++
  gi|298676109|ref|YP_003727859.1| 409 KDQLLEELQ 417
                                       444444443 PP

>> T3SSipB  Type III cell invasion protein SipB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.2     0.041        29      56     111 ..      29      79 ..       7     100 .. 0.61
   2 ?    8.6   8.8    0.0036       2.5      46     115 ..     179     247 ..     154     278 .. 0.80
   3 ?    4.5   0.3     0.066        46      53      93 ..     372     412 ..     353     425 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.041
                                       HHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHTT---------CHHHHHHHHH CS
                           T3SSipB  56 kgatddleaaiekadqaksaad.aatkkvdeaqkrlkeLaPdePekakleaaeqQag 111
                                       ++++d ++   +   +a s+++   t+k +e++++l++L   e +k++le+ e+  +
  gi|298676109|ref|YP_003727859.1|  29 EEIQDWMKSESN---DAFSDMKpYITQKYEEIKTHLDSL---EKDKKELENVEIKNQ 79 
                                       555554443332...33344442579999**********...777777777666555 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0036
                                       STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---------CHHHHHHHHH..HH CS
                           T3SSipB  46 delqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPdePekakleaaeqQagaaad 115
                                       ++l + ++e +++++++e++  ++++++++++  ++ +++aq rl+ L  ++ +++k+e+ e+  ++ +d
  gi|298676109|ref|YP_003727859.1| 179 ENLPEKIDEVNQIKKQIEDKKSNIQELEKKYESSKHSLSDAQSRLETL-KASENYQKAEELENEIQKLKD 247
                                       667788999***************************************.777788888777666664444 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.066
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT- CS
                           T3SSipB  53 seakgatddleaaiekadqaksaadaatkkvdeaqkrlkeL 93 
                                       +e +++ +++ +  + +d+++s++d   k +de  ++ ++L
  gi|298676109|ref|YP_003727859.1| 372 KEKANLEKQISNNKNTMDTVQSEIDSERKHLDELNQKKDQL 412
                                       56666666777777777777777777777777765544333 PP

>> Aurora-A_bind  Aurora-A binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.5    0.0045       3.1       9      58 ..      39      88 ..      34      96 .. 0.83
   2 ?    5.9   0.1      0.02        13      35      58 ..     371     394 ..     364     403 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0045
                     Aurora-A_bind  9 sfDaPtdfinFtsLddeedvenvDsWFeekANLENkfpgkngvgelfqsk 58
                                      s Da +d+  + + + ee  ++ Ds   +k  LEN+  +++g++  +qs+
  gi|298676109|ref|YP_003727859.1| 39 SNDAFSDMKPYITQKYEEIKTHLDSLEKDKKELENVEIKNQGIPRAVQSN 88
                                      667777777788888999999***********************999864 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.02
                     Aurora-A_bind  35 FeekANLENkfpgkngvgelfqsk 58 
                                       + ekANLE ++++++++ + +qs+
  gi|298676109|ref|YP_003727859.1| 371 YKEKANLEKQISNNKNTMDTVQSE 394
                                       689*******99999898888865 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.3    0.0097       6.7      10      68 ..      13      71 ..      10      79 .. 0.84
   2 ?    5.8   0.1     0.022        15      12      58 ..      52      97 ..      45     103 .. 0.89
   3 ?    4.5  10.6     0.057        39      54     107 ..     188     241 ..     148     253 .. 0.57
   4 ?    7.2   4.0     0.008       5.5      13      83 ..     350     417 ..     340     423 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0097
                              FliJ 10 aqrelqqaeekleeleqyrqeyqkqlsgea.qglsaaelrnyqafisaldeaiaqqkqel 68
                                         e+q++ ek++   +++q+ +k+ s++a + ++++  ++y++ + +ld+ +++ k+el
  gi|298676109|ref|YP_003727859.1| 13 KDEEVQEEPEKITLSLEEIQDWMKSESNDAfSDMKPYITQKYEEIKTHLDS-LEKDKKEL 71
                                      5678999***********************99************9999986.44445555 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.022
                              FliJ 12 relqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisald 58
                                      +++++ + +l++le+  +e+++   +++ g++ a + n ++f ++l+
  gi|298676109|ref|YP_003727859.1| 52 QKYEEIKTHLDSLEKDKKELENVEIKNQ-GIPRAVQSNKENFVKNLN 97
                                      789999**************88888886.**************9997 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.057
                              FliJ  54 isaldeaiaqqkqelaqaekqvekareewqearqerkklekLkerekkeeqkee 107
                                        ++++++i+  k++++ +ek+ e +++ +  a+ ++++l+  +  +k+ee+++e
  gi|298676109|ref|YP_003727859.1| 188 VNQIKKQIEDKKSNIQELEKKYESSKHSLSDAQSRLETLKASENYQKAEELENE 241
                                       456666666666666666666666666666666666555544444444433322 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.008
                              FliJ  13 elqqaeekleeleqyrqey..qkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekareewq 83 
                                       ++ ++ +++eele +++++   k++++        ++ n ++ +++++++i++ ++ l+ ++++ ++  ee+q
  gi|298676109|ref|YP_003727859.1| 350 KRLSYTSRIEELEIELDRLtvYKEKANLE-----KQISNNKNTMDTVQSEIDSERKHLDELNQKKDQLLEELQ 417
                                       44444555555555544442123333333.....677777777777777777777777777777777777777 PP

>> sCache_2  Single Cache domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.9   0.00085      0.59       7      52 ..     189     234 ..     185     301 .. 0.80
   2 ?   -0.4   0.0       1.3   8.9e+02      52      52 ..     296     296 ..     245     349 .. 0.58
   3 ?    2.2   1.1       0.2   1.4e+02       5      49 ..     373     417 ..     370     424 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00085
                          sCache_2   7 aelknqvetaislieavykqvesgkiteeeaqeevkelvnglkfgd 52 
                                       +++k+q+e+  s i++++k++es+k ++ +aq + ++l  + ++++
  gi|298676109|ref|YP_003727859.1| 189 NQIKKQIEDKKSNIQELEKKYESSKHSLSDAQSRLETLKASENYQK 234
                                       699******************************9999877777766 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.3
                          sCache_2  52 d 52 
                                       +
  gi|298676109|ref|YP_003727859.1| 296 E 296
                                       2 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.2
                          sCache_2   5 keaelknqvetaislieavykqvesgkiteeeaqeevkelvnglk 49 
                                       ++a+l++q+++  ++++ v+++  s  ++++e  ++  +l+++l+
  gi|298676109|ref|YP_003727859.1| 373 EKANLEKQISNNKNTMDTVQSEIDSERKHLDELNQKKDQLLEELQ 417
                                       6899***************************99998888877765 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0         1   7.1e+02      36      53 ..      50      67 ..      15      82 .. 0.45
   2 ?    0.6   0.3      0.76   5.3e+02      36      77 ..      50      97 ..      42     131 .. 0.62
   3 ?    7.5   2.7    0.0058         4      81     108 ..     148     175 ..      68     191 .. 0.50
   4 ?    7.0   5.9    0.0081       5.6      31     126 ..     145     234 ..     120     245 .. 0.67
   5 ?    6.6   1.0     0.011       7.3      19      94 ..     189     256 ..     176     270 .. 0.45
   6 ?    6.5   3.2     0.011       7.8      22     139 ..     223     340 ..     200     352 .. 0.83
   7 ?    4.1   2.6     0.064        44      34      74 ..     375     418 ..     353     429 .. 0.61

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1
                      Baculo_PEP_C 36 latlldaietqLnalsed 53
                                      +++  ++i+t L++l++d
  gi|298676109|ref|YP_003727859.1| 50 ITQKYEEIKTHLDSLEKD 67
                                      222223333333332222 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.76
                      Baculo_PEP_C 36 latlldaietqLnalsedlksllaeldt.......rldtlltnLtdaln 77
                                      +++  ++i+t L++l++d k+l  +++        +++++ +n  + ln
  gi|298676109|ref|YP_003727859.1| 50 ITQKYEEIKTHLDSLEKDKKELE-NVEIknqgiprAVQSNKENFVKNLN 97
                                      56667777777777776665532.2222224444433333333333333 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0058
                      Baculo_PEP_C  81 dtlrneLtnlnsiltnLlssvtNinstL 108
                                       ++l+n+L  +ns l++L  ++ Ni+  L
  gi|298676109|ref|YP_003727859.1| 148 KNLSNDLSEINSSLSDLGDKINNIKDRL 175
                                       4455555555555555555555554433 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.0081
                      Baculo_PEP_C  31 qilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnLlssvtNinst 107
                                       +i  +l+++l +i+++L++l +++++    +++rld   +nL +++ +++ +++++++  +s++ +L  +    + +
  gi|298676109|ref|YP_003727859.1| 145 EIFKNLSNDLSEINSSLSDLGDKINN----IKDRLD-IYENLPEKIDEVN-QIKKQIEDKKSNIQELEKKYESSKHS 215
                                       46667777777777777777777777....555664.5677777777777.67777777777777777666666666 PP

                      Baculo_PEP_C 108 Lnnllqalnnldlgalsqe 126
                                       L+   + l+ l+  +  q+
  gi|298676109|ref|YP_003727859.1| 216 LSDAQSRLETLKASENYQK 234
                                       6655555555555555555 PP

  == domain 5  score: 6.6 bits;  conditional E-value: 0.011
                      Baculo_PEP_C  19 tnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsil 94 
                                       +++ ++i  ++++i  +l++  ++ + +L++ +++l+ l a+   +  + +++L++ +++l+     e  n++s+l
  gi|298676109|ref|YP_003727859.1| 189 NQIKKQIEDKKSNI-QELEKKYESSKHSLSDAQSRLETLKAS---ENYQKAEELENEIQKLK----DEKLNIDSEL 256
                                       33333344444444.444444444444444444444444332...12223333444444333....2222333333 PP

  == domain 6  score: 6.5 bits;  conditional E-value: 0.011
                      Baculo_PEP_C  22 Lnairl.qnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnL 97 
                                       L+++++  n q + +l++ +++++ +  +++++lk+l a l+++++ + ++ ++   +l+ ++r+ ++ +n++   L
  gi|298676109|ref|YP_003727859.1| 223 LETLKAsENYQKAEELENEIQKLKDEKLNIDSELKDLFAPLSKAISRMEKQDKSDRHTLSPEFREVIEKINNNEVHL 299
                                       55555315778888999999999999999999999999999999999999999999999999999999999998888 PP

                      Baculo_PEP_C  98 lssvtNinstLnnllqalnnldlgalsqeledaldtveeile 139
                                       l +   + s Ln + + ++   lg  + ++++++++v+++le
  gi|298676109|ref|YP_003727859.1| 300 L-DKDKLASFLNDMKNRVEDGSLGLKQRKGNNIIEQVNHLLE 340
                                       8.4477888888888888888888888888888888888886 PP

  == domain 7  score: 4.1 bits;  conditional E-value: 0.064
                      Baculo_PEP_C  34 aqlatlldaietqLnalsedlksllaeldt...rldtlltnLtd 74 
                                       a+l++++ + +++++++++++ s  ++ld+   + d+ll++L++
  gi|298676109|ref|YP_003727859.1| 375 ANLEKQISNNKNTMDTVQSEIDSERKHLDElnqKKDQLLEELQS 418
                                       67777777777777777777776433332211133333333333 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.5    0.0058         4      22      73 ..     148     205 ..     142     221 .. 0.53
   2 ?    4.8   0.8     0.048        33      27      87 ..     184     245 ..     177     247 .. 0.66
   3 ?    0.6   0.2         1   7.1e+02      33      39 ..     265     271 ..     228     349 .. 0.62
   4 ?    6.1   1.6     0.019        13      23      68 ..     376     421 ..     368     426 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0058
                            DUF948  22 lklkktldeaaatieelekqvdpil......kevedllakvnelledvneklekvdpl 73 
                                       ++l++ l+e+++++ +l++++++i       +++ + +++vn++ +++++k  ++++l
  gi|298676109|ref|YP_003727859.1| 148 KNLSNDLSEINSSLSDLGDKINNIKdrldiyENLPEKIDEVNQIKKQIEDKKSNIQEL 205
                                       4555555555555555554444433000000444555555555555555555555544 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.048
                            DUF948  27 tldeaaatieelekqvdpilkevedllakvnelledvneklekvdp..lteavadlgesvsel 87 
                                        +de+++  +++e++ ++ ++e+e+  + ++  l+d +++le++++    +++++l + +++l
  gi|298676109|ref|YP_003727859.1| 184 KIDEVNQIKKQIEDK-KSNIQELEKKYESSKHSLSDAQSRLETLKAseNYQKAEELENEIQKL 245
                                       466666666666655.44557888888888889999999998886511466666666666665 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 1
                            DUF948  33 atieele 39 
                                       ++i  +e
  gi|298676109|ref|YP_003727859.1| 265 KAISRME 271
                                       3333333 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.019
                            DUF948  23 klkktldeaaatieelekqvdpilkevedllakvnelledvnekle 68 
                                       +l+k ++++++t++++++++d+  k +++l +k  +lle++++ l+
  gi|298676109|ref|YP_003727859.1| 376 NLEKQISNNKNTMDTVQSEIDSERKHLDELNQKKDQLLEELQSDLK 421
                                       7889999999999999999999999999999999999999988776 PP

>> DUF2968  Protein of unknown function (DUF2968)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   1.4     0.087        60     137     178 ..     189     230 ..     166     232 .. 0.83
   2 ?   11.8   1.1   0.00019      0.13      96     151 ..     362     417 ..     351     424 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.087
                           DUF2968 137 qavaerQkqarkeaaaLeaqreaaqaqlralqrqirqLqaqq 178
                                       ++++++ ++ +++ + Le++ e+ ++ l+++q ++++L+a +
  gi|298676109|ref|YP_003727859.1| 189 NQIKKQIEDKKSNIQELEKKYESSKHSLSDAQSRLETLKASE 230
                                       456666677889999999999999999999999999999876 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00019
                           DUF2968  96 eveirrikleaqkaqlerqiaasearaerLqadlavarqQeqavaerQkqarkeaa 151
                                       e+e+ r+ +  +ka le+qi ++++ + ++q++++ +r+   +++++ +q+ +e +
  gi|298676109|ref|YP_003727859.1| 362 EIELDRLTVYKEKANLEKQISNNKNTMDTVQSEIDSERKHLDELNQKKDQLLEELQ 417
                                       6788999999**************************************99998876 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.049        34      20      73 ..      14      67 ..      11      74 .. 0.85
   2 ?    0.7   0.0       0.9   6.2e+02      53      80 ..     147     174 ..     143     180 .. 0.67
   3 ?    1.5   0.1      0.52   3.6e+02      17      37 ..     232     252 ..     224     259 .. 0.69
   4 ?    2.0   0.4      0.35   2.4e+02       6      39 ..     385     418 ..     374     423 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.049
                                      HHHHHHHHHHHHHHHHHCGCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100 20 aeeledelqrlkaevdalqsgWsGaaadafqaefeewkqaaqklvdaLeeisea 73
                                       ee+++e +++  +++++q+  + ++ daf ++   ++q+ +++++ L+++++ 
  gi|298676109|ref|YP_003727859.1| 14 DEEVQEEPEKITLSLEEIQDWMKSESNDAFSDMKPYITQKYEEIKTHLDSLEKD 67
                                      5778888888888899999999999***********************999875 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.9
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  53 feewkqaaqklvdaLeeisealkqaana 80 
                                       f+++ + + +++  L+++++++++++++
  gi|298676109|ref|YP_003727859.1| 147 FKNLSNDLSEINSSLSDLGDKINNIKDR 174
                                       4555666677777777777777777665 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.52
                                       HHHHHHHHHHHHHHHHHHHHC CS
                            WXG100  17 qkqaeeledelqrlkaevdal 37 
                                        ++aeele+e+q+lk e  ++
  gi|298676109|ref|YP_003727859.1| 232 YQKAEELENEIQKLKDEKLNI 252
                                       567888888888888776555 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.35
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGC CS
                            WXG100   6 peelrqaaarfqkqaeeledelqrlkaevdalqs 39 
                                        + ++++ +++++++++l ++ q+ ++ +++lqs
  gi|298676109|ref|YP_003727859.1| 385 KNTMDTVQSEIDSERKHLDELNQKKDQLLEELQS 418
                                       4567777777777777777777777777777766 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.3       1.2     8e+02     132     160 ..      51      72 ..       9     104 .. 0.45
   2 ?    9.8   5.6   0.00067      0.46     130     234 ..     132     257 ..     112     282 .. 0.69
   3 ?    7.7   5.1    0.0029         2     187     253 ..     356     423 ..     263     430 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.2
                           DUF4407 132 taelaeleaqiaalqaeidaaearldalr 160
                                       t++++       ++++ +d++e++ ++l+
  gi|298676109|ref|YP_003727859.1|  51 TQKYE-------EIKTHLDSLEKDKKELE 72 
                                       22222.......22222222222222222 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00067
                           DUF4407 130 a.................ltaelaeleaqiaalqaeidaaearldalra..eaqkeldgtk...gtgttgvaGkgpa 184
                                       +                 l+++l+e+++ +++l  +i++ ++rld  ++  e  +e+++ k    ++ ++++  ++ 
  gi|298676109|ref|YP_003727859.1| 132 SiksqhyikpifpeifknLSNDLSEINSSLSDLGDKINNIKDRLDIYENlpEKIDEVNQIKkqiEDKKSNIQELEKK 208
                                       35555666666666666666777777777777777777777777655552223334433334555556667888888 PP

                           DUF4407 185 akekkaqldaaqaelaelkakldatarlaalraelaeleaerakeraasq 234
                                       +++ k  l +aq +l++lka+ ++ ++ ++l++e+++l++e+ ++ ++ +
  gi|298676109|ref|YP_003727859.1| 209 YESSKHSLSDAQSRLETLKAS-ENYQKAEELENEIQKLKDEKLNIDSELK 257
                                       888999999999999999999.8999999999999999999988777655 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0029
                           DUF4407 187 ekkaqldaaqaelaelkakldatarlaalraelaeleaerakeraasqaaaaaddGllarlea.ldrl 253
                                       ++ ++l+    +l+ +k+k + ++++++++++++++++e+++er+  ++ ++++d ll++l+  l+++
  gi|298676109|ref|YP_003727859.1| 356 SRIEELEIELDRLTVYKEKANLEKQISNNKNTMDTVQSEIDSERKHLDELNQKKDQLLEELQSdLKYV 423
                                       34445555555555666665599999999999999999999999999999999999999988666555 PP

>> Wtap  WTAP/Mum2p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5  11.3     0.042        29      55     105 ..     202     252 ..      49     299 .. 0.85
   2 ?    7.1   3.8    0.0067       4.6      99     149 ..     371     420 ..     344     426 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.042
                              Wtap  55 fsrlrkeleeaenkleeaqeeLqalkftpdsqtGkrLmakcrvLeqENeEL 105
                                       +++l k+ e+++ +l+ aq+ L++lk +++ q++ +L + +++L++E  ++
  gi|298676109|ref|YP_003727859.1| 202 IQELEKKYESSKHSLSDAQSRLETLKASENYQKAEELENEIQKLKDEKLNI 252
                                       89*******************************************997666 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0067
                              Wtap  99 eqENeELgkvleegr..vakLeselalqkkfveelkkaleeleelleeleeev 149
                                       ++E ++L+k++++++  +  ++se+  ++k+++el+++     +lleel++++
  gi|298676109|ref|YP_003727859.1| 371 YKEKANLEKQISNNKntMDTVQSEIDSERKHLDELNQKKD---QLLEELQSDL 420
                                       6788889988776543389999999999999999987664...5566666665 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.5      0.68   4.7e+02      85     102 ..      50      67 ..      10     104 .. 0.54
   2 ?   13.6   3.3   7.3e-05     0.051      37     112 ..     148     225 ..     145     231 .. 0.70
   3 ?    4.0   3.1     0.071        49      50     120 ..     202     270 ..     199     275 .. 0.66
   4 ?    0.6   0.3       0.8   5.5e+02      97      97 ..     324     324 ..     254     368 .. 0.53
   5 ?    5.2   5.7      0.03        20      55     119 ..     345     411 ..     321     417 .. 0.66
   6 ?    6.9   2.9    0.0086       5.9      35      80 ..     373     418 ..     368     431 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.68
                           DUF1664  85 ikeevtevredlseiged 102
                                       i+++ +e++ +l+++++d
  gi|298676109|ref|YP_003727859.1|  50 ITQKYEEIKTHLDSLEKD 67 
                                       222222222222222222 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 7.3e-05
                           DUF1664  37 rslsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikee...vtevredlseigedvesvkeav 110
                                       ++ls+ ++++ ++l ++ +++++ k++L    +++ +k+de+++i+k+i+++   ++e++++ ++ ++ ++  ++  
  gi|298676109|ref|YP_003727859.1| 148 KNLSNDLSEINSSLSDLGDKINNIKDRLDI-YENLPEKIDEVNQIKKQIEDKksnIQELEKKYESSKHSLSDAQSRL 223
                                       799999999999999999999999999964.5899999999999988887761114444444444444444444444 PP

                           DUF1664 111 eg 112
                                       e+
  gi|298676109|ref|YP_003727859.1| 224 ET 225
                                       44 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.071
                           DUF1664  50 leqvseslaatkrhLssridrvdk.kldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                       ++++ ++ ++ k+ Ls+   r+++ k  e+ + ++e+++e+++++++  +i+++++ + +    l + ++r+
  gi|298676109|ref|YP_003727859.1| 202 IQELEKKYESSKHSLSDAQSRLETlKASENYQKAEELENEIQKLKDEKLNIDSELKDLFAP---LSKAISRM 270
                                       5666666677777776555555432556667778999**********99999998877653...34444444 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.8
                           DUF1664  97 s 97 
                                       +
  gi|298676109|ref|YP_003727859.1| 324 K 324
                                       1 PP

  == domain 5  score: 5.2 bits;  conditional E-value: 0.03
                           DUF1664  55 eslaatkrhLssridrvdkkldeqkeisk..eikeevtevredlseigedvesvkeavegleskler 119
                                       ++l + +   +sri++++ +ld  +  ++  ++++++++ ++ +++++++++s ++   +l++k ++
  gi|298676109|ref|YP_003727859.1| 345 SNLVEKRLSYTSRIEELEIELDRLTVYKEkaNLEKQISNNKNTMDTVQSEIDSERKHLDELNQKKDQ 411
                                       5666777777888888888888776654411567778888888888888887777777777776554 PP

  == domain 6  score: 6.9 bits;  conditional E-value: 0.0086
                           DUF1664  35 TkrslsdavesvskqleqvseslaatkrhLssridrvdkkldeqke 80 
                                        k +l++ +++  + +++v++++ + ++hL +  ++ d+ l+e + 
  gi|298676109|ref|YP_003727859.1| 373 EKANLEKQISNNKNTMDTVQSEIDSERKHLDELNQKKDQLLEELQS 418
                                       5788999999999999999999999999998877777777777654 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.9     0.064        44      39      73 ..      40      74 ..      14     101 .. 0.65
   2 ?    8.7   7.7    0.0014      0.98      23     132 ..     186     293 ..     150     310 .. 0.65
   3 ?    5.8   6.7     0.011       7.6      40     110 ..     345     421 ..     340     431 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.064
                           DUF3450 39 idklddekqellaeyralkeeleslevyneqlerl 73
                                       d+ +d k  + ++y+++k+ l+sle+ +++le++
  gi|298676109|ref|YP_003727859.1| 40 NDAFSDMKPYITQKYEEIKTHLDSLEKDKKELENV 74
                                      45555566666666666666666666666666554 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0014
                           DUF3450  23 keaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelv 99 
                                       +e +++ ++ ++  ++i++l+++ ++ +  + +++++le l++ +++++   +++e+ei++l+ ++ +i+   ++l 
  gi|298676109|ref|YP_003727859.1| 186 DEVNQIKKQIEDKKSNIQELEKKYESSKHSLSDAQSRLETLKASENYQK--AEELENEIQKLKDEKLNIDSELKDLF 260
                                       2222333333333333333333333344444555555666666555555..46788888888888888888888888 PP

                           DUF3450 100 pllekmidrLeqfveldlPflleeRqarlakLk 132
                                         l k i+r+e+  ++d   l  e ++ ++k++
  gi|298676109|ref|YP_003727859.1| 261 APLSKAISRMEKQDKSDRHTLSPEFREVIEKIN 293
                                       888888888888777777777777777777665 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.011
                           DUF3450  40 dklddekqellaeyralkeeleslevyneq..lerlvasqeqeiasleeqiee....ieeierelvpllekmidrLe 110
                                       ++l +++ ++ +++++l+ el++l+vy+e+  le+++++ +++++ ++ +i++    ++e++++  +lle++ ++L+
  gi|298676109|ref|YP_003727859.1| 345 SNLVEKRLSYTSRIEELEIELDRLTVYKEKanLEKQISNNKNTMDTVQSEIDSerkhLDELNQKKDQLLEELQSDLK 421
                                       66778888888899999999999999876433788888888888888877764222266677777777777777776 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   4.3      0.29     2e+02      34      87 ..      15      73 ..       6      98 .. 0.67
   2 ?   10.2  10.3   0.00081      0.56       7     100 ..     149     239 ..     145     242 .. 0.73
   3 ?    1.7   9.9      0.36   2.5e+02      11      98 ..     234     318 ..     222     335 .. 0.68
   4 ?    7.2  13.5     0.007       4.8      53     129 ..     343     421 ..     323     431 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.29
                    CENP-F_leu_zip 34 emseenqekvileaEtskaevet.....lkeeieelaeelreleldLvalrsekeeLek 87
                                      e+++e+ ek++l  E+ +  +++     + +++  ++++ +e+++ L++l ++k+eLe+
  gi|298676109|ref|YP_003727859.1| 15 EEVQEEPEKITLSLEEIQDWMKSesndaFSDMKPYITQKYEEIKTHLDSLEKDKKELEN 73
                                      44556666666666665544444444456777777778888888888888888887754 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00081
                    CENP-F_leu_zip   7 hvlekLKeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrseke 83 
                                       ++ + L e++++ + L dk++n++  l +  en+ + i e+ + k+++e  k++i+el+++ +  ++ L++ +s  e
  gi|298676109|ref|YP_003727859.1| 149 NLSNDLSEINSSLSDLGDKINNIKDRLDIY-ENLPEKIDEVNQIKKQIEDKKSNIQELEKKYESSKHSLSDAQSRLE 224
                                       566778888888888888888887777655.4566667788888888888888888888888888888888888888 PP

                    CENP-F_leu_zip  84 eLekelqkkqervseLe 100
                                       +L  +  ++ ++ +eLe
  gi|298676109|ref|YP_003727859.1| 225 TL--KASENYQKAEELE 239
                                       88..4445555566666 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.36
                    CENP-F_leu_zip  11 kLKeserkadsLkdkvenLerelemseenqekvileaEts.kaevetlkeeieelaeelreleldLvalrsekeeLe 86 
                                       k  e e +  +Lkd  +n+++el+++ + ++k+i  +E++ k    tl  e +e  e+ ++ e+ L     +k++L+
  gi|298676109|ref|YP_003727859.1| 234 KAEELENEIQKLKDEKLNIDSELKDLFAPLSKAISRMEKQdKSDRHTLSPEFREVIEKINNNEVHLL----DKDKLA 306
                                       3344555556666666666677777777777777777765366667777777777777777776664....688888 PP

                    CENP-F_leu_zip  87 kelqkkqervse 98 
                                         l+++++rv++
  gi|298676109|ref|YP_003727859.1| 307 SFLNDMKNRVED 318
                                       888888888875 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.007
                    CENP-F_leu_zip  53 evetlkeeieelaeelreleldLvalr..sekeeLekelqkkqervseLeslnsslenlleekEqekvqmkeeskaa 127
                                       e ++l e+    +++ +ele++L+ l+  +ek +Lek++ ++++++++ +s   s ++ l e+ q+k q+ ee ++ 
  gi|298676109|ref|YP_003727859.1| 343 EFSNLVEKRLSYTSRIEELEIELDRLTvyKEKANLEKQISNNKNTMDTVQSEIDSERKHLDELNQKKDQLLEELQSD 419
                                       5666777777778999999**9999888899***************************************9999987 PP

                    CENP-F_leu_zip 128 ve 129
                                       ++
  gi|298676109|ref|YP_003727859.1| 420 LK 421
                                       65 PP

>> DASH_Spc19  Spc19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.3   0.00045      0.31      58      95 ..      43      80 ..      35      96 .. 0.83
   2 ?    1.9  14.9      0.27   1.9e+02      68     147 ..     187     249 ..     134     275 .. 0.60
   3 ?    2.5   2.8      0.18   1.2e+02      70     128 ..     236     294 ..     232     318 .. 0.64
   4 ?    3.5  11.8     0.088        61      58     155 ..     328     417 ..     323     418 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00045
                                      HHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        DASH_Spc19 58 aeeiePqieellekaekeleklerreetLkaklelqeg 95
                                       ++++P i++++e+++++l++le+ +++L++   +++g
  gi|298676109|ref|YP_003727859.1| 43 FSDMKPYITQKYEEIKTHLDSLEKDKKELENVEIKNQG 80
                                      5789**************************98777776 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.27
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHT-XXXXXXXXXXXX....XXXXXXXXXXXXXXXXX CS
                        DASH_Spc19  68 llekaekeleklerreetLkaklelqegrlsnaesskkeeeeseeskeeeeeeenkeeekskkkltkeelerlkkLk 144
                                        +++++k++e  ++  ++L++k+e  ++ ls+a+s+ ++ ++se+ +++ee e                 ++++kLk
  gi|298676109|ref|YP_003727859.1| 187 EVNQIKKQIEDKKSNIQELEKKYESSKHSLSDAQSRLETLKASENYQKAEELE-----------------NEIQKLK 246
                                       34567777777777777777777777777777544444444444333333332.................2233333 PP

                                       XXX CS
                        DASH_Spc19 145 qkK 147
                                       ++K
  gi|298676109|ref|YP_003727859.1| 247 DEK 249
                                       333 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHT-XXXXXXXXXXXX....X CS
                        DASH_Spc19  70 ekaekeleklerreetLkaklelqegrlsnaesskkeeeeseeskeeeeeeenkeeeks 128
                                       e++e+e++kl+ ++ ++ ++l+ +   ls+a s+ +++++s++ + + e +e  e+ ++
  gi|298676109|ref|YP_003727859.1| 236 EELENEIQKLKDEKLNIDSELKDLFAPLSKAISRMEKQDKSDRHTLSPEFREVIEKINN 294
                                       78999999999999999999999998898877776666666666555444444443333 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.088
                                       HHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHT-XXXXXXXXXXXX....XXXXXXX CS
                        DASH_Spc19  58 aeeiePqieellekaekeleklerreetLkaklelqegrlsnaesskkeeeeseeskeeeeeeenkeeekskkkltk 134
                                        ++i  q+++lle  ++e + l +++ +  +++e +e  l++  +  ke+++ e++ ++++++ ++      ++   
  gi|298676109|ref|YP_003727859.1| 328 GNNIIEQVNHLLE--SDEFSNLVEKRLSYTSRIEELEIELDRL-TVYKEKANLEKQISNNKNTMDT-----VQSEID 396
                                       5778888888887..5888888888888888999999888884.3333444444444333332322.....222346 PP

                                       XXXXXXXXXXXXXXXXXXXXX CS
                        DASH_Spc19 135 eelerlkkLkqkKerLkytle 155
                                       +e + l +L qkK++L ++l+
  gi|298676109|ref|YP_003727859.1| 397 SERKHLDELNQKKDQLLEELQ 417
                                       7899************99987 PP

>> Sec8_exocyst  Sec8 exocyst complex component specific domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.2       1.6   1.1e+03      86     104 ..      55      66 ..       9     110 .. 0.60
   2 ?    4.3   0.6     0.051        35      72     141 ..     123     197 ..     113     198 .. 0.59
   3 ?    7.9  10.8    0.0039       2.7      64     135 ..     178     248 ..     150     255 .. 0.82
   4 ?    6.5   2.0      0.01         7      85     119 ..     378     412 ..     367     426 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.6
                      Sec8_exocyst  86 ekvselKesleeakkklst 104
                                       e+++           +l++
  gi|298676109|ref|YP_003727859.1|  55 EEIKTH-------LDSLEK 66 
                                       111111.......122222 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.051
                      Sec8_exocyst  72 asYskilssiqesqekvselK.esleeakkklstkkkeLkelnarsakykevieiL....daieelkkvpdkieq 141
                                       ++ +  +++  +sq+ ++ +  e  ++  ++ls+ +++L++l ++  + k+ ++i     ++i+e++++ ++ie+
  gi|298676109|ref|YP_003727859.1| 123 STLNTCVENSIKSQHYIKPIFpEIFKNLSNDLSEINSSLSDLGDKINNIKDRLDIYenlpEKIDEVNQIKKQIED 197
                                       455555555555666665554133455566777777777777777777777776651112467888888888875 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0039
                      Sec8_exocyst  64 hqaFnssiasYskilssiqesqekvselKesleeakkklstkkkeLkelnarsakykevieiLdaieelkkv 135
                                       ++   + i   ++i ++i++ +++++el ++ e++k++ls+ ++ L+ l+  s +y++  e+ ++i++lk  
  gi|298676109|ref|YP_003727859.1| 178 YENLPEKIDEVNQIKKQIEDKKSNIQELEKKYESSKHSLSDAQSRLETLK-ASENYQKAEELENEIQKLKDE 248
                                       667778899999**********************************9886.578999999999999998865 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.01
                      Sec8_exocyst  85 qekvselKesleeakkklstkkkeLkelnarsaky 119
                                       ++++s+ K+ +   ++++  ++k+L+eln++  ++
  gi|298676109|ref|YP_003727859.1| 378 EKQISNNKNTMDTVQSEIDSERKHLDELNQKKDQL 412
                                       68999************************987654 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   3.3    0.0048       3.3     145     197 ..      22      75 ..      11      95 .. 0.76
   2 ?   11.1  15.1    0.0002      0.14     156     255 ..     148     247 ..     140     265 .. 0.79
   3 ?   -2.5   8.7       2.7   1.9e+03     157     220 ..     234     297 ..     227     351 .. 0.58
   4 ?    2.4  12.2     0.084        58     168     237 ..     350     417 ..     322     430 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0048
                              Spc7 145 eenlegleedkelLekq.eeeldellpeleeekaeleeeleklqeaaeelesid 197
                                       e++  +lee ++ ++++ ++ +++++p ++++++e++  l++l++ ++ele+++
  gi|298676109|ref|YP_003727859.1|  22 EKITLSLEEIQDWMKSEsNDAFSDMKPYITQKYEEIKTHLDSLEKDKKELENVE 75 
                                       55555555555555544045569999*******************999999976 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0002
                              Spc7 156 elLekqeeeldellpeleeekaeleeeleklqeaaeelesid..keeLeelreelaelkaeieekkkelaelqeqle 230
                                       ++L+++ +e+++ l +l  + ++++++l+  ++  e++++++  k+++e  +++++el++++e+ k  l++ q++le
  gi|298676109|ref|YP_003727859.1| 148 KNLSNDLSEINSSLSDLGDKINNIKDRLDIYENLPEKIDEVNqiKKQIEDKKSNIQELEKKYESSKHSLSDAQSRLE 224
                                       67888888899999999999999999988888888888887766788999999999999999999999999999888 PP

                              Spc7 231 eleekieelkeqkseleeeiaeaer 255
                                       +l++  +e  ++ +ele+ei++ ++
  gi|298676109|ref|YP_003727859.1| 225 TLKA--SENYQKAEELENEIQKLKD 247
                                       8865..4555677777777776554 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 2.7
                              Spc7 157 lLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkk 220
                                       + e+ e+e+++l++e  +  +el++ ++ l +a   +e+ dk + ++l  e++e+ ++i++ + 
  gi|298676109|ref|YP_003727859.1| 234 KAEELENEIQKLKDEKLNIDSELKDLFAPLSKAISRMEKQDKSDRHTLSPEFREVIEKINNNEV 297
                                       3344455555555555555555555555555566666666666666666666666666654443 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.084
                              Spc7 168 llpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekie 237
                                          +++++ +ele el++l   +e+ +++ ++++ + +++++++++ei++ +k l+el++++++l e+++
  gi|298676109|ref|YP_003727859.1| 350 KRLSYTSRIEELEIELDRLTVYKEK-ANL-EKQISNNKNTMDTVQSEIDSERKHLDELNQKKDQLLEELQ 417
                                       3344556666777777777664433.332.5567777777777777777777777777777777766664 PP

>> She9_MDM33  She9 / Mdm33 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.9       2.6   1.8e+03      93     119 ..      51      77 ..      11      97 .. 0.55
   2 ?   12.1   6.3   0.00018      0.12       3     106 ..     148     255 ..     146     286 .. 0.74
   3 ?    6.1   3.5     0.013       8.7      13      75 ..     355     417 ..     343     422 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.6
                        She9_MDM33  93 telyrkdhanekeeeeakeklkeaeak 119
                                       t+ y + +++  + e+ k++l+++e k
  gi|298676109|ref|YP_003727859.1|  51 TQKYEEIKTHLDSLEKDKKELENVEIK 77 
                                       333333333334444444444444443 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00018
                        She9_MDM33   3 kkleelldslqetlltaskalndvtG....Yseieklkksieeleeeleeakeevreakeayeeaiekrsksqrevn 75 
                                       k+l++ l++++++l+ ++ ++n++      Y+++ +  ++++++++++e++k++++e+ ++ye++ ++ s++q  ++
  gi|298676109|ref|YP_003727859.1| 148 KNLSNDLSEINSSLSDLGDKINNIKDrldiYENLPEKIDEVNQIKKQIEDKKSNIQELEKKYESSKHSLSDAQSRLE 224
                                       5677788899999999999999887622224444444455677799******************************* PP

                        She9_MDM33  76 eLLqRkssWspedlerftelyrkdhanekee 106
                                       +L +  +    e+le+  + +++++ n  +e
  gi|298676109|ref|YP_003727859.1| 225 TLKASENYQKAEELENEIQKLKDEKLNIDSE 255
                                       **99999999999999888888777665544 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.013
                        She9_MDM33  13 qetlltaskalndvtGYseieklkksieeleeeleeakeevreakeayeeaiekrsksqrevn 75 
                                        +++ ++  +l+++t Y+e  +l k+i++++++++++++e+ + +++ +e ++k+ +   e++
  gi|298676109|ref|YP_003727859.1| 355 TSRIEELEIELDRLTVYKEKANLEKQISNNKNTMDTVQSEIDSERKHLDELNQKKDQLLEELQ 417
                                       5678888899*************************************9999999988766665 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.4     0.053        37     139     216 ..      18      94 ..      12     165 .. 0.62

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.053
                      Exonuc_VII_L 139 vpdkaeleeqleelerrlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkqlkkkrerle 215
                                        ++ ++++ +lee+++ ++++ + ++++ k  +++  +++k+  + le+++++l+++e + +  + +++++++e++ 
  gi|298676109|ref|YP_003727859.1|  18 QEEPEKITLSLEEIQDWMKSESNDAFSDMKPYITQKYEEIKTHLDSLEKDKKELENVEIKNQG-IPRAVQSNKENFV 93 
                                       555566777778888888888888887777777777777777777777777777777666665.5555554444433 PP

                      Exonuc_VII_L 216 e 216
                                       +
  gi|298676109|ref|YP_003727859.1|  94 K 94 
                                       3 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.2    0.0056       3.9       3      29 ..     148     174 ..     147     179 .. 0.85
   2 ?    3.3   2.3      0.16   1.1e+02       2      34 ..     188     220 ..     186     224 .. 0.83
   3 ?    5.7   0.2     0.029        20       1      28 [.     234     261 ..     234     271 .. 0.84
   4 ?   -1.2   3.0         4   2.8e+03       7      30 ..     379     402 ..     375     422 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0056
                               LPP   3 deLssqVsqLkskvdqlssdvnsakaa 29 
                                       ++Ls+++s+ +s  + l +++n++k+ 
  gi|298676109|ref|YP_003727859.1| 148 KNLSNDLSEINSSLSDLGDKINNIKDR 174
                                       589999999999999999999999875 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.16
                               LPP   2 ldeLssqVsqLkskvdqlssdvnsakaaaqaak 34 
                                       ++++ +q+++ ks++++l+++ +s+k  + +a+
  gi|298676109|ref|YP_003727859.1| 188 VNQIKKQIEDKKSNIQELEKKYESSKHSLSDAQ 220
                                       788999999999999999999988888888887 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.029
                               LPP   1 kldeLssqVsqLkskvdqlssdvnsaka 28 
                                       k +eL +++++Lk++  ++ s+++++ a
  gi|298676109|ref|YP_003727859.1| 234 KAEELENEIQKLKDEKLNIDSELKDLFA 261
                                       6689************999999887655 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 4
                               LPP   7 sqVsqLkskvdqlssdvnsakaaa 30 
                                       +q+s+ k+ +d ++s+++s ++ +
  gi|298676109|ref|YP_003727859.1| 379 KQISNNKNTMDTVQSEIDSERKHL 402
                                       566666666666666655544433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3010  (0.167884); expected 358.6 (0.02)
Passed bias filter:                      613  (0.0341904); expected 358.6 (0.02)
Passed Vit filter:                       143  (0.0079759); expected 17.9 (0.001)
Passed Fwd filter:                        96  (0.00535445); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 1.53u 0.39s 00:00:01.92 Elapsed: 00:00:00.59
# Mc/sec: 2191.69
//
Query:       gi|298676110|ref|YP_003727860.1|  [L=70]
Description: hypothetical protein Metev_2242 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       842  (0.046963); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.34s 00:00:00.87 Elapsed: 00:00:00.55
# Mc/sec: 386.37
//
Query:       gi|298676111|ref|YP_003727861.1|  [L=366]
Description: signal peptide peptidase SppA [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.9e-44  149.5   0.0    9.9e-44  149.0   0.0    1.2  1  Peptidase_S49   Peptidase family S49
     0.0013   18.7   1.0     0.0088   15.9   0.3    2.1  2  CLP_protease    Clp protease
      0.006   16.8   0.1     0.0098   16.1   0.1    1.4  1  Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
  ------ inclusion threshold ------
      0.027   14.0   0.3      0.047   13.3   0.3    1.4  1  Peripla_BP_4    Periplasmic binding protein domain
        0.1   12.9   0.2       0.21   11.9   0.2    1.5  1  Sigma_reg_N     Sigma factor regulator N-terminal


Domain annotation for each model (and alignments):
>> Peptidase_S49  Peptidase family S49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.0   0.0   2.8e-47   9.9e-44       2     152 ..     165     315 ..     164     317 .. 0.98

  Alignments for each domain:
  == domain 1  score: 149.0 bits;  conditional E-value: 2.8e-47
                                       HHHTT--EEEEEEEEEETHHHHHHTTSSEEEE-TT-EEE---EEEEEEE-HHHHHHTT-EEEEEESSTTCCCCCTTS CS
                     Peptidase_S49   2 akkakkPvvasaenvaaSggYylasaadkivanpstivgsiGvitqllnlenlldklgvevqvvkaGeyksavslrr 78 
                                       ak++++Pvv+s+++vaaS++Yy+++ ad i+anpst++gsiGvi    n ++++d  g+e +v+k+Ge+k+++ + r
  gi|298676111|ref|YP_003727861.1| 165 AKDKGIPVVVSMGDVAASAAYYVSAPADVIMANPSTMTGSIGVIWTFQNRSEFYDEEGIEHEVIKSGELKDMGAPWR 241
                                       799************************************************************************** PP

                                       S--HHHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHCHHCCHEEEHHHHHHTTSSSEETSHHHHHHHHHHHCH CS
                     Peptidase_S49  79 elteeereilqrlldetyqqFvqtVaknRnlsveqvdkiAegrvltgqqAlklgLvdelgtvddavaeleelak 152
                                        lteeer++ ++ + e+y++Fv+ Va+nR l+ + v++i +gr++tg  A++lgLvd+ g++ + ++ ++el +
  gi|298676111|ref|YP_003727861.1| 242 GLTEEERNYANKIVQEIYKNFVDHVAENRDLNRSFVNEISDGRIYTGMRAKELGLVDKFGNLYESINLAAELGD 315
                                       *****************************************************************999998765 PP

>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.3   2.5e-06    0.0088      25      95 ..     117     190 ..     102     204 .. 0.75
   2 ?    1.0   0.0     0.098   3.5e+02     153     177 ..     275     299 ..     242     302 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.5e-06
                                       BSHHHHHHHHHHHHHHHHH-SSS-EEEEEEE--B-HHHHHHHHHHHHHSSS-..EEEEEEE.EEETHHHHHHHT CS
                      CLP_protease  25 iddevankiiaqLllLeaedpdkdillyinspGGsvtaglaIydtmqyikpd..vsticlG.laaSmgslllaa 95 
                                       i  ++++++ + +  ++  ++ k i++ +nspGGs +a+ +I   ++  k +   +++ +G +aaS++  + a 
  gi|298676111|ref|YP_003727861.1| 117 IGYSTSEDVASSIRKASDRSDVKAIVMRVNSPGGSPSAAEEISREIERAKDKgiPVVVSMGdVAASAAYYVSAP 190
                                       5667788888888888899999*************************996652255677773455555544443 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.098
                                       HHHHHHCSTEEEEHHHHHHHTSSSE CS
                      CLP_protease 153 kiekdldrdtflsaeeAveyGLide 177
                                        + ++++  ++ + + A+e GL+d+
  gi|298676111|ref|YP_003727861.1| 275 SFVNEISDGRIYTGMRAKELGLVDK 299
                                       3444666678889999*******98 PP

>> Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   2.7e-06    0.0098      21      59 ..     135     176 ..      81     203 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.7e-06
                                       HTT--EEEEEEBTTTB--H...HHHHHHHHHHTTT-EEEEEE CS
                    Asparaginase_C  21 kkgakGvvlegtGvGnlps...allealkeakargivvvats 59 
                                       ++ +k++v+     G+ ps   ++ +++++ak++gi+vv++ 
  gi|298676111|ref|YP_003727861.1| 135 RSDVKAIVMRVNSPGGSPSaaeEISREIERAKDKGIPVVVSM 176
                                       4589**************9999*****************985 PP

>> Peripla_BP_4  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   1.3e-05     0.047      56     102 ..     138     189 ..     117     192 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.3e-05
                                       -SEEEE--SSH.......HHHHHHHHHHHHTT-EEEEESTTGCTTT-CEEEEEC CS
                      Peripla_BP_4  56 vdgiivapvds.......talapalkkakaaGIpVvafdsddapsgerlayvgf 102
                                       v++i++ ++++       ++++  +++ak++GIpVv+   d  ++++ ++yv++
  gi|298676111|ref|YP_003727861.1| 138 VKAIVMRVNSPggspsaaEEISREIERAKDKGIPVVVSMGD--VAASAAYYVSA 189
                                       555555555544444444788899*************9999..89999999975 PP

>> Sigma_reg_N  Sigma factor regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   5.9e-05      0.21       5      44 ..      59      98 ..      55     117 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.9e-05
                       Sigma_reg_N  5 kkakrksilrivlislivlllifvilvvtllylaekegnk 44
                                      +k++++++l+i+++ ++++ + f+ +v t++ ++ + ++k
  gi|298676111|ref|YP_003727861.1| 59 RKGRKRQYLTIFFLLITIIAASFAAIVYTFDGDLYSTNDK 98
                                      9*************************99988776555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1021  (0.0569468); expected 358.6 (0.02)
Passed bias filter:                      691  (0.0385409); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 2251.80
//
Query:       gi|298676112|ref|YP_003727862.1|  [L=679]
Description: methionyl-tRNA synthetase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   4.3e-152  506.4   2.5   6.2e-152  505.9   2.5    1.2  1  tRNA-synt_1g  tRNA synthetases class I (M)
    5.1e-26   90.6   1.2    1.1e-25   89.6   1.2    1.6  1  tRNA_bind     Putative tRNA binding domain
    5.5e-17   61.2   1.8    2.9e-08   32.5   0.7    3.9  3  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
    3.5e-15   56.3   0.7    7.7e-15   55.2   0.7    1.6  1  Anticodon_1   Anticodon-binding domain of tRNA
    4.5e-14   52.5   5.4      2e-10   40.5   0.1    2.6  3  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
    0.00026   20.0   0.0      0.062   12.2   0.0    2.6  2  tRNA-synt_1f  tRNA synthetases class I (K)
  ------ inclusion threshold ------
       0.23   11.1   2.8       0.65    9.6   2.8    1.7  1  BBIP10        Cilia BBSome complex subunit 10


Domain annotation for each model (and alignments):
>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  505.9   2.5  2.4e-155  6.2e-152       1     390 [.      10     395 ..      10     396 .. 0.98

  Alignments for each domain:
  == domain 1  score: 505.9 bits;  conditional E-value: 2.4e-155
                                       EEEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHH CS
                      tRNA-synt_1g   1 vlvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikel 77 
                                       vlvt++lpYangk H+Ghl+++i+aDi++R  +++g++v+fvcg+D+hGtpi  +Ae+ ++tpeel++++h++++++
  gi|298676112|ref|YP_003727862.1|  10 VLVTCGLPYANGKAHIGHLRTYIPADIYVRALKKHGQDVTFVCGSDTHGTPIVFNAEEYNTTPEELIKTYHKHFDDI 86 
                                       69*************************************************************************** PP

                                       HHHTT---SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-EE........-TTS-EE.- CS
                      tRNA-synt_1g  78 fkklnisfdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryvegtCPkckseeargdqc.e 153
                                       fk++n+ fd++g+t++ ++++ +++i++kl ++g++y+k+ie +ycp ++r+lpdryv+g+CP+c  e argd+c +
  gi|298676112|ref|YP_003727862.1|  87 FKSMNVYFDAFGTTEDATNHNRTHAIVNKLIDNGYVYSKTIEIAYCPVCDRYLPDRYVKGKCPHCA-EAARGDECdQ 162
                                       *****************************************************************9.89******88 PP

                                       TTSSB-E................EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS CS
                      tRNA-synt_1g 154 ecgkkleptelinpksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrd 230
                                        cgk+lep el+ p+++++g+++e+ke+eh+ffkls+f+++l++++  e+ e ++n+++++  w+k+gL d++i+r+
  gi|298676112|ref|YP_003727862.1| 163 GCGKHLEPGELESPVCTLCGDAAEYKEQEHYFFKLSQFQDFLQNYL--ENLEGTSNARNYAMGWVKKGLDDWCITRN 237
                                       9*********************************************..55569************************ PP

                                       -SSS-EETTECCEEE-HHHHHHHHHHHTTTTT-...TTSGGGG.G--S......EEEEEGGGHHHHHTHHHHHHHHT CS
                      tRNA-synt_1g 231 ldwGipvPgaekkvlYVWldAligYisatkelakkkgeeekwkeyWakdkevelvhfigkdiikFHtifwPaillga 307
                                       l+wG+++Pg+++ v+YVW+dA+igYis+t+e+a  + ++e+w++ W  ++++++vhfig dii++H+ifwPa+l+ga
  gi|298676112|ref|YP_003727862.1| 238 LEWGVKFPGRDDLVVYVWVDAPIGYISFTEEWA--NANNESWEKIW--KDDSRIVHFIGGDIIYHHCIFWPAMLKGA 310
                                       ********************************9..55799******..579************************** PP

                                       T----S-EEEE--EEE--------------H.HHHHHH.H-HHHHHHHHHHHS-TTS-EEE-HHHHHHHHHHHCCCH CS
                      tRNA-synt_1g 308 elklpkkvvaheyltvegkKlSkSrgvvvka.kealer.ldadllRYylaaeapekkDldfswedfvervNseLadk 382
                                       e+++p +vva+++l++e+k +SkSrg+vv++ +++l++ +++dllRYyla+ ++++k+l+fsw  f+e++NseL++ 
  gi|298676112|ref|YP_003727862.1| 311 EYTQPWSVVASGMLKIENKTFSKSRGYVVWVeEDYLNHgFHPDLLRYYLATYTSHTKELNFSWPFFQEKINSELVGV 387
                                       ******************************956899999************************************** PP

                                       HHHHHHHH CS
                      tRNA-synt_1g 383 lgnlvnRv 390
                                       +gn+ +R+
  gi|298676112|ref|YP_003727862.1| 388 FGNFFYRS 395
                                       *****997 PP

>> tRNA_bind  Putative tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.6   1.2   4.3e-29   1.1e-25       1      96 []     585     677 ..     585     677 .. 0.98

  Alignments for each domain:
  == domain 1  score: 89.6 bits;  conditional E-value: 4.3e-29
                                       EEEEEEEEEEEETTSSTEEEEEEEESSSSEEEEEESCTTTSTHHHHTTEEEEEETTSESEEETTEEESSEE-EEECC CS
                         tRNA_bind   1 lrvGkvleaeehpnadkLlvlkvdvGeeeprqivsgaknvyepeelvakkvvvvanlkpkklrGveSeGMilsaeel 77 
                                       +rvGk+++ae++++++kLl+l+vd+Ge++prq+v+g+++  +pee+++ +vvv+an++p+kl Gv S+GM+l+ e  
  gi|298676112|ref|YP_003727862.1| 585 IRVGKIVNAEKVEKSNKLLRLEVDIGENSPRQVVAGIAKTHNPEEIIGHQVVVLANMEPAKLCGVDSKGMVLAGE-- 659
                                       79*************************************************************************.. PP

                                       ESSCEEEEEESST--TTCE CS
                         tRNA_bind  78 dekevgilelpadveaGek 96 
                                        ++   +l+++++v++G+k
  gi|298676112|ref|YP_003727862.1| 660 -DNGAVLLKPEREVTLGTK 677
                                       .78899**********986 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.7   1.1e-11   2.9e-08      26     113 ..      11      81 ..       3     147 .. 0.69
   2 !   22.4   0.0   1.2e-08   3.1e-05     353     432 ..     166     245 ..     158     294 .. 0.77
   3 ?    0.8   0.0     0.042   1.1e+02     552     602 .]     320     372 ..     247     372 .. 0.75

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 1.1e-11
                       tRNA-synt_1  26 ilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakvekklgakekkerkklgreefre 102
                                        ++ g Py++G+ HiGh  + +  di +r  + +G++v++v G D++G +i  + e+                  + 
  gi|298676112|ref|YP_003727862.1|  11 LVTCGLPYANGKAHIGHLRTYIPADIYVRALKKHGQDVTFVCGSDTHGTPIVFNAEEY-----------------NT 70 
                                       567789********************************************97665554.................33 PP

                       tRNA-synt_1 103 kvrewkaeyae 113
                                          e  ++y++
  gi|298676112|ref|YP_003727862.1|  71 TPEELIKTYHK 81 
                                       33333333333 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 1.2e-08
                       tRNA-synt_1 353 lkaekiehsvpfcerskkpiiyrateqWfvrvkeladaalkavekvqfvpkskekryaswleniqdWciSRqrwWGh 429
                                        + e+ e++ p+c   ++  +y+ +e +f ++++++d + + +e+ + + + ++  +    +   dWci R++ WG+
  gi|298676112|ref|YP_003727862.1| 166 KHLEPGELESPVCTLCGDAAEYKEQEHYFFKLSQFQDFLQNYLENLEGTSNARNYAMGWVKKGLDDWCITRNLEWGV 242
                                       6778889999***************************9999999999998887776665556799************ PP

                       tRNA-synt_1 430 rip 432
                                       + p
  gi|298676112|ref|YP_003727862.1| 243 KFP 245
                                       988 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.042
                       tRNA-synt_1 552 vhglvrdeeGrKmSKslgNvidpld..vikkygadalRltli.lsdvgrdinls 602
                                        +g++   e +  SKs g v+  ++  + +    d lR++l+ +++ ++++n+s
  gi|298676112|ref|YP_003727862.1| 320 ASGML-KIENKTFSKSRGYVVWVEEdyLNHGFHPDLLRYYLAtYTSHTKELNFS 372
                                       44443.3455788999999875544004444557********9******99986 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   0.7     3e-18   7.7e-15       4     139 ..     415     561 ..     412     574 .. 0.77

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 3e-18
                       Anticodon_1   4 ilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedk.raaqevllevletllrllaP 79 
                                       +l  +++++  +tea+e+y+f+ka++ + ++   ++ ++y+++++p+   ++++ +  ++ +++  ++++l+ l++P
  gi|298676112|ref|YP_003727862.1| 415 VLDNIQSTIDGYTEAMENYEFKKAIDTALSL--ASYGNTYFQSNEPWRLIKEDKTEcGRVIANCIQIAKALVVLFEP 489
                                       78899*************************8..889***********999887666555669999999********* PP

                       Anticodon_1  80 fmPfitEelwqreeeelgkkesimlaewpekaeel.ekel...e.........eeevellkei....vkairklrse 139
                                       ++P  +E++w    +++g +++++ + +  +a+el e +    +         +e++e +++i    vk ++++  e
  gi|298676112|ref|YP_003727862.1| 490 VVPEKMEDAW----KQIGMSSDVHASRYS-DATELvESNTpipKprilfkkieDEKIEEMEKIssdrVKKAQEKEHE 561
                                       **********....**************9.66666433333342667777788555555555533335555555444 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.1   7.9e-14     2e-10      14     125 ..      13     126 ..       5     139 .. 0.87
   2 !   14.1   0.0   8.9e-06     0.023     234     292 ..     309     372 ..     284     381 .. 0.75
   3 ?   -2.6   0.3       1.1   2.8e+03     140     178 ..     534     574 ..     494     580 .. 0.69

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 7.9e-14
                                       EEE.EBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1e  14 vCG.ptvydashlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeksvkelaekfieefkkdlea 89 
                                       +CG p +  ++h+Gh R+++  Di  r l++ g dv+fv         i+ +a+e +++ +el +++ ++f + +++
  gi|298676112|ref|YP_003727862.1|  13 TCGlPYANGKAHIGHLRTYIPADIYVRALKKHGQDVTFVCGSDTHGTPIVFNAEEYNTTPEELIKTYHKHFDDIFKS 89 
                                       67734567799****************************998888899***************************** PP

                                       TT----SB.--BGGGGHHHHHHHHHHHHHTTSEEE-T CS
                      tRNA-synt_1e  90 Lnvlkptl.eprvsekvdeiielvekliekgyaYavs 125
                                       +nv    + ++  + + +    +v+kli++gy Y+ +
  gi|298676112|ref|YP_003727862.1|  90 MNVYFDAFgTTEDATNHNRTHAIVNKLIDNGYVYSKT 126
                                       ***9766525555666788999************876 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 8.9e-06
                                       SS--EEEE..EEE--EEETTBE--TTTT---BHHH.HHTT.S-HHHHHHHHHS.S-TTS-EEE- CS
                      tRNA-synt_1e 234 dkqlvkyf..lhnghlkiegekmsksLknfitikd.vlkk.fdprqlRlllls.ahyrsqldfk 292
                                       + ++++ +  + +g+lkie++  sks + ++ +++  l++ f+p  lR++l++ + + ++l+f+
  gi|298676112|ref|YP_003727862.1| 309 GAEYTQPWsvVASGMLKIENKTFSKSRGYVVWVEEdYLNHgFHPDLLRYYLATyTSHTKELNFS 372
                                       4556665544689******************99753676559*********8724577889987 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.1
                                       TTTTT--HHHHHHT----S-..-S-SSTT-EEEEEE--TTS CS
                      tRNA-synt_1e 140 gklskqnleelelgaegevs..eekkdkkDfaLWkaskege 178
                                        k++ +++ee+e++ +++v+  +ek+++k     k++ e++
  gi|298676112|ref|YP_003727862.1| 534 KKIEDEKIEEMEKISSDRVKkaQEKEHEKGMREDKMESEEN 574
                                       45566666666666666555334455555554455555555 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   2.4e-05     0.062      24      70 ..       9      56 ..       2      60 .. 0.86
   2 !    4.8   0.0    0.0042        11     264     321 ..     313     371 ..     307     378 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.4e-05
                      tRNA-synt_1f 24 evvvesGis.pSGliHiGnlrevltadlvaralrkrgeevrlilisDd 70
                                       v+v  G+  + G+ HiG lr  + ad+ +ral+k g++v +++ sD+
  gi|298676112|ref|YP_003727862.1|  9 PVLVTCGLPyANGKAHIGHLRTYIPADIYVRALKKHGQDVTFVCGSDT 56
                                      566777765257********************************9997 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0042
                      tRNA-synt_1f 264 eaPekvvYelillkggekmssSkGnvltled.wl.evaepevlrflilrrkPkkakkldl 321
                                       ++P +vv   +l  +++  s+S+G v+ +e+  l +  +p++lr++++     + k+l++
  gi|298676112|ref|YP_003727862.1| 313 TQPWSVVASGMLKIENKTFSKSRGYVVWVEEdYLnHGFHPDLLRYYLAT-YTSHTKELNF 371
                                       566666666555566679*********99763551457********998.6666666666 PP

>> BBIP10  Cilia BBSome complex subunit 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.8   0.00025      0.65      29      63 ..     527     560 ..     518     561 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00025
                            BBIP10  29 cKPKllPlKSvtLEklEkMqkeaqekvkqqeeaek 63 
                                        KP++l  K +  Ek+E+M+k   ++vk+++e+e+
  gi|298676112|ref|YP_003727862.1| 527 PKPRIL-FKKIEDEKIEEMEKISSDRVKKAQEKEH 560
                                       699999.899*******************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (679 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1395  (0.0778069); expected 358.6 (0.02)
Passed bias filter:                      782  (0.0436165); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.82u 0.33s 00:00:01.14 Elapsed: 00:00:00.52
# Mc/sec: 3907.12
//
Query:       gi|298676113|ref|YP_003727863.1|  [L=177]
Description: adenylyl cyclase CyaB [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.8e-38  130.6   3.2    6.6e-38  130.4   3.2    1.0  1  CYTH       CYTH domain
    0.00065   19.1   0.3     0.0015   18.0   0.1    1.6  2  Med20      TATA-binding related factor (TRF) of subunit 20 of
  ------ inclusion threshold ------
       0.06   13.4   0.1      0.099   12.7   0.1    1.4  1  Rootletin  Ciliary rootlet component, centrosome cohesion


Domain annotation for each model (and alignments):
>> CYTH  CYTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.4   3.2   1.1e-41   6.6e-38       1     179 []       1     167 [.       1     167 [. 0.91

  Alignments for each domain:
  == domain 1  score: 130.4 bits;  conditional E-value: 1.1e-41
                                       EEEEEEEEEE-HHHHHHHHHH.HHHCTCEEEEEEEEEEEEEE-TTTHHHHTTEEEEEEEETTTEEE.EEEEEECSSS CS
                              CYTH   1 miEvEvKflvsaaeyedlelr.laelrakeettveqrdtYydtpdrdlartdeaLRiRraegdgee.ltlKgpgvdg 75 
                                       miEvEvK++ +    e+   + l++ +a   +t++  d Yy++p+rd+a+tdeaLRiR  + d+++ lt+Kg ++d+
  gi|298676113|ref|YP_003727863.1|   1 MIEVEVKARTD---LETA-RKmLEDEGARFIETEHHFDSYYNAPHRDFASTDEALRIR--SRDNKTfLTYKGKKMDS 71 
                                       89*******94...4432.3359999********************************..6777777********99 PP

                                       T...EEEEEEEECCCEEECCCCHHHHHHHHHHHTT-EEEEEEEEEEEEEEETTEEEEEEEETTTTEEEEEEEEEESS CS
                              CYTH  76 e...reevegevsreEyeeplsdaaeaaelldglglepvasvkklRrkyklegvevalDaveflegeevEiEleved 149
                                           ree+e++v+           + + ++l +lg++++++v+k+R++ykl+++ +alD ve+l ge++E+Ele+e 
  gi|298676113|ref|YP_003727863.1|  72 VsktREEFETPVD----------SENMRNILLSLGFREYGIVEKEREVYKLDDFVIALDSVEQL-GEFIEVELESEP 137
                                       6666666666654..........788999***********************************.************ PP

                                       HHHHHHHHHHHHHHHHHTTEEGGGBSCSHH CS
                              CYTH 150 eeevkeaaekllallrelglssaskirrsy 179
                                        ++ ++   k++++l++lg+++++ ir+sy
  gi|298676113|ref|YP_003727863.1| 138 GSDIEHNSSKIFEFLNKLGIEEKDSIRKSY 167
                                       ****************************99 PP

>> Med20  TATA-binding related factor (TRF) of subunit 20 of Mediator complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       0.2   1.2e+03     160     183 ..       2      22 ..       1      50 [. 0.75
   2 !   18.0   0.1   2.5e-07    0.0015     134     197 ..     107     164 ..      49     177 .] 0.78

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.2
                                       EEEEE-S...SS-CCCCHHHHHHC CS
                             Med20 160 vEieyrgadpdaeyeaaaaliref 183
                                       +E+e+   ++ +++e+a++++++ 
  gi|298676113|ref|YP_003727863.1|   2 IEVEV---KARTDLETARKMLEDE 22 
                                       88999...7788888888888765 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 2.5e-07
                                       EE.BEESSEEEEEEEEECSSS---EEEEEEE-S...SS-CCCCHHHHHHCSCTTT-TSCTT--- CS
                             Med20 134 ggvYelgdfrvRvgdvfqtqrvrGllvEieyrgadpdaeyeaaaalireflsklgiegareail 197
                                       ++vY+l df + + +v q +++    +E+e ++  p +++e +++ i efl+klgie ++ +i+
  gi|298676113|ref|YP_003727863.1| 107 REVYKLDDFVIALDSVEQLGEF----IEVELES-EPGSDIEHNSSKIFEFLNKLGIE-EKDSIR 164
                                       456*************998776....7777765.***********************.666663 PP

>> Rootletin  Ciliary rootlet component, centrosome cohesion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   1.7e-05     0.099     113     149 ..       7      43 ..       3      81 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.7e-05
                         Rootletin 113 kltkdwerlreeleqkekewreeeeafneylssehsr 149
                                       k ++d+e +r+ le++ +++ e e++f +y+++ h+ 
  gi|298676113|ref|YP_003727863.1|   7 KARTDLETARKMLEDEGARFIETEHHFDSYYNAPHRD 43 
                                       6689*****************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1368.22
//
Query:       gi|298676114|ref|YP_003727864.1|  [L=132]
Description: hypothetical protein Metev_2247 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-18   65.9   0.0    3.3e-18   65.4   0.0    1.2  1  OB_aCoA_assoc   DUF35 OB-fold domain, acyl-CoA-associated
    3.1e-10   39.7   0.9    4.3e-10   39.3   0.9    1.2  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
    0.00027   20.9   0.4    0.00033   20.7   0.4    1.1  1  FdhE            Protein involved in formate dehydrogenase for
  ------ inclusion threshold ------
      0.064   13.2   0.3      0.093   12.7   0.3    1.2  1  zinc-ribbons_6  zinc-ribbons
      0.069   13.3   1.8       0.13   12.5   1.8    1.4  1  Laminin_EGF     Laminin EGF domain


Domain annotation for each model (and alignments):
>> OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.4   0.0   9.3e-22   3.3e-18       4      65 .]      49     109 ..      46     109 .. 0.94

  Alignments for each domain:
  == domain 1  score: 65.4 bits;  conditional E-value: 9.3e-22
                                       E-GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT...-EE-EEEEEEES..TT-B-EEE-S CS
                     OB_aCoA_assoc   4 lsgrGtvysftvvhrappgfaeeaPyvvgvVeLdegvrimarlvgvdpdevriGmrVravfr 65 
                                       + g+G+v+++t++h a++gf+++ Py++++V+Ldeg  +++ +v +dp+e+ iGmrV+ vfr
  gi|298676114|ref|YP_003727864.1|  49 FEGKGEVVTYTIIHSAAEGFENQSPYPLAIVKLDEGASLTSPIV-ADPEEMYIGMRVKPVFR 109
                                       689*****************************************.5677788********97 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.9   1.2e-13   4.3e-10       4      34 ..      11      41 ..       8      45 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 1.2e-13
                           DUF35_N  4 aaegrLvgqrCpdCGtvqfPPravCphCgsd 34
                                        ++ L g++C +C+ +++PPr  Cp C++ 
  gi|298676114|ref|YP_003727864.1| 11 VNRYNLEGTHCNSCDEYFYPPRSMCPTCRRE 41
                                      6799************************543 PP

>> FdhE  Protein involved in formate dehydrogenase formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.4   9.1e-08   0.00033     181     232 ..       2      56 ..       1      63 [. 0.90

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 9.1e-08
                                       EEEE-------EEE....EEETTT--EEE--TTS-TTT---SS-EEE------C-E CS
                              FdhE 181 svvriggeaeglRy....lhCslCeteWhvvRvkCsnCeetkelaylsledekaav 232
                                       svvr++  ++  Ry     hC+ C   +   R  C +C  + +l+ +++e++ + v
  gi|298676114|ref|YP_003727864.1|   2 SVVRFWR-NQVNRYnlegTHCNSCDEYFYPPRSMCPTCRREGKLESHRFEGKGEVV 56 
                                       9999999.99999966666*******************************998765 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   2.6e-05     0.093      15      38 ..      17      41 ..       5      51 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.6e-05
                                      SEEE-TTT--.EEEEEEE-SSS-S- CS
                    zinc-ribbons_6 15 eqyhCeaCqe.dlkkealCpeCeqe 38
                                      e +hC++C+e  +    +Cp+C+ e
  gi|298676114|ref|YP_003727864.1| 17 EGTHCNSCDEyFYPPRSMCPTCRRE 41
                                      789*******4456799*****875 PP

>> Laminin_EGF  Laminin EGF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.8   3.5e-05      0.13      24      49 .]      14      38 ..      13      40 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.5e-05
                                      TTEESTTS-EE-TTEEEGTTSCCSSE CS
                       Laminin_EGF 24 enveGrkCdrCkpgyyglpsdsgegC 49
                                       n eG++C+ C + +y  +s+ + +C
  gi|298676114|ref|YP_003727864.1| 14 YNLEGTHCNSCDEYFYPPRSMCP-TC 38
                                      699*************7666555.66 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 914.49
//
Query:       gi|298676115|ref|YP_003727865.1|  [L=390]
Description: acetyl-CoA acetyltransferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.2e-25   87.5   1.0    5.7e-24   84.9   1.0    2.1  1  Thiolase_N       Thiolase, N-terminal domain
    3.8e-12   45.9   2.2    2.4e-11   43.4   1.1    2.7  2  Thiolase_C       Thiolase, C-terminal domain
    1.6e-08   34.4   5.9    8.3e-07   28.8   4.2    2.7  2  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
  ------ inclusion threshold ------
      0.015   15.3   0.4       0.98    9.5   0.1    2.9  2  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.9   1.0   1.3e-27   5.7e-24       1     259 [.       4     226 ..       4     227 .. 0.89

  Alignments for each domain:
  == domain 1  score: 84.9 bits;  conditional E-value: 1.3e-27
                                       EEEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCT.TSTSC.HHHHHHHHTTS-T. CS
                        Thiolase_N   1 vvivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqa.gegqn.iarqaalkagipe. 74 
                                       v+i++ + t++g+    l d s +++  ea+ +++++ag++ +e+d ++vGn+  + + +q  i   +a  +g+++ 
  gi|298676115|ref|YP_003727865.1|   4 VAIIGIKSTKFGE----LWDYSFRDIFVEAGVGAIKDAGISGDEIDGLYVGNMSGGqFVDQEhIGALIADYSGLARn 76 
                                       7899999999999....9***********************************988888887677777878888762 PP

                                       .TSEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETT CS
                        Thiolase_N  75 .evpavtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdgladaf 150
                                        ++p+++v+ +c+Sg  a+ +++ ++a+g  d vva GvE+m++++ a++++  + +   d++ ++++  +      
  gi|298676115|ref|YP_003727865.1|  77 lHIPSTRVEAACASGGLALRQGVMAVASGYQDFVVAAGVEKMTDVNSAAASS--ALAAASDREWEGIMGAT------ 145
                                       3799******************************************999844..44555566666666544...... PP

                                       TTSEHHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHH CS
                        Thiolase_N 151 neehmGltaenlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLa 227
                                            ++ a++  +ky+ + e+++ +Avk+h +++ ++ ++ +k++i              +++  ++s ++a++L+
  gi|298676115|ref|YP_003727865.1| 146 FPGLYAMIARKHIHKYGTTSEQLADVAVKNHLNGSMNPISQ-YKKKI--------------TRESVLNSIMVADPLH 207
                                       33467899*********************************.99999..............8899************ PP

                                       TS-BSSSTTSS-BTTSB--BEEEEEEEEEEEH CS
                        Thiolase_N 228 klkpaFkkeGtvtAgnasqisDGaaavllmse 259
                                                      ++s+i+DGaaa++l+++
  gi|298676115|ref|YP_003727865.1| 208 IF-------------DCSPITDGAAALVLAPA 226
                                       *9.............**************875 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.0       2.8   1.2e+04      31      43 ..      33      45 ..      29      49 .. 0.81
   2 !   43.4   1.1   5.3e-15   2.4e-11      24     114 ..     263     371 ..     240     384 .. 0.87

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 2.8
                                      HHHHHT--GGGES CS
                        Thiolase_C 31 vlkkagltvedid 43
                                      ++k+ag++ ++id
  gi|298676115|ref|YP_003727865.1| 33 AIKDAGISGDEID 45
                                      7899999999998 PP

  == domain 2  score: 43.4 bits;  conditional E-value: 5.3e-15
                                       HHHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT--HHHH-B-T CS
                        Thiolase_C  24 PayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldl..................ekvNvnGGaialGHPl 82 
                                        + a k++ + a l+ edid+ E+++ F+   + ++++l++ +                    vN  GG  + GHP+
  gi|298676115|ref|YP_003727865.1| 263 TVAAGKRAYDMANLRPEDIDVAEVHDCFTIAEICAIEDLGFVKkgeggkytedgytavngqIPVNTSGGLKSCGHPV 339
                                       467889999********************************999***************9888************** PP

                                       TTHHHHHHHHHHHHHHHCTTSEEEEEEEETTT CS
                        Thiolase_C  83 GasGaRivvtllselkkeggklgvaalCiggg 114
                                       Ga+G++++v ++++l+ e gk  v  + ig  
  gi|298676115|ref|YP_003727865.1| 340 GATGVKQAVEIVHQLRGEAGKRQVENAEIGMT 371
                                       ****************9999988877666643 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.7   0.0    0.0044        20      91     130 ..      25      64 ..      21      73 .. 0.83
   2 !   28.8   4.2   1.8e-10   8.3e-07     160     222 ..      73     135 ..      56     143 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0044
                                       HHHHHHHHHHHHHTS-HHTCTTGGEEEEEEESSTHHHHHH CS
                     ketoacyl-synt  91 llleaawealedagltpeeldgsrvgvfiGvgagdyaala 130
                                       +++ea   a++dag++ +e+dg  vg++ G    d++++ 
  gi|298676115|ref|YP_003727865.1|  25 IFVEAGVGAIKDAGISGDEIDGLYVGNMSGGQFVDQEHIG 64 
                                       67899999*************9999999998877776655 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 1.8e-10
                                       HHHT--SSEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTTBB-T CS
                     ketoacyl-synt 160 yalglrGpsvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaagllsp 222
                                       +a +l+ ps  v++AC+S+  a+ + v+++ sg +d ++a Gve ++  ++ a+ sa+++ s+
  gi|298676115|ref|YP_003727865.1|  73 LARNLHIPSTRVEAACASGGLALRQGVMAVASGYQDFVVAAGVEKMTDVNSAAASSALAAASD 135
                                       5578999********************************************999999997665 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   0.00022      0.98      23      52 ..     260     289 ..     238     294 .. 0.80
   2 ?    2.6   0.0     0.029   1.3e+02      86     108 ..     334     356 ..     325     364 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00022
                                       HHHHHHHHHHHHHHHT--GGGEEEEE-SS- CS
                   Ketoacyl-synt_C  23 geaqaraiekalaeagvdpedvdyveahgt 52 
                                        +a  +a ++a+++a+++ped+d+ e h+ 
  gi|298676115|ref|YP_003727865.1| 260 LDATVAAGKRAYDMANLRPEDIDVAEVHDC 289
                                       567778899*******************86 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.029
                                       HH-B-GGGHHHHHHHHHHHHHHH CS
                   Ketoacyl-synt_C  86 niGHleaAaGvaelikvvlalkh 108
                                       + GH  +A Gv +++ +v +l+ 
  gi|298676115|ref|YP_003727865.1| 334 SCGHPVGATGVKQAVEIVHQLRG 356
                                       57****************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2596.18
//
Query:       gi|298676116|ref|YP_003727866.1|  [L=349]
Description: hydroxymethylglutaryl-CoA synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-10   40.4   0.0    6.5e-10   39.0   0.0    1.7  1  ACP_syn_III_C   3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha
    1.6e-06   28.0   0.1    6.5e-05   22.7   0.0    2.3  2  HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C t
  ------ inclusion threshold ------
      0.045   13.6   0.3      0.062   13.2   0.3    1.2  1  HMG_CoA_synt_N  Hydroxymethylglutaryl-coenzyme A synthase N t
      0.074   12.9   0.0       0.13   12.1   0.0    1.4  1  Activator-TraM  Transcriptional activator TraM


Domain annotation for each model (and alignments):
>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.0   1.5e-13   6.5e-10       1      86 [.     221     306 ..     221     310 .. 0.90

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 1.5e-13
                                       HHHTT--GGG-SEEEE-SSSHHHHHHHHHHHT--GGGB-..-THHHH-B-GGGHHHHHHHHHHHTTSS-TT-EEEEE CS
                     ACP_syn_III_C   1 Lekagltpedidalvphqanlriidavakklglpeekvv..vnldeyGntsaasiplaLdeaveegklkpgdlvllv 75 
                                       +ek g  ped d+ v+hq n ++   v k lg++++k+   + + ++Gn+ + s ++ ++  ++  + kpgd++  +
  gi|298676116|ref|YP_003727866.1| 221 MEKMGTGPEDYDYAVFHQPNGKFPTRVSKDLGFSRDKIEpgMVITKLGNIYSGSCMMGIAATLD--QAKPGDRIFAT 295
                                       5788999*****************************88522566********************..89********* PP

                                       EEETTTEEEEE CS
                     ACP_syn_III_C  76 gfGaGltwgaa 86 
                                       +fG G    a 
  gi|298676116|ref|YP_003727866.1| 296 AFGSGAGADAF 306
                                       *****877765 PP

>> HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.014        62      63      82 ..     224     243 ..     180     254 .. 0.77
   2 !   22.7   0.0   1.4e-08   6.5e-05     141     209 ..     255     318 ..     245     330 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.014
                                       ----GGG-SEEEE--SSHHH CS
                    HMG_CoA_synt_C  63 keftlddfdyvifhsPfckl 82 
                                         ++ +d+dy +fh P  k+
  gi|298676116|ref|YP_003727866.1| 224 MGTGPEDYDYAVFHQPNGKF 243
                                       4556789*********9996 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 1.4e-08
                                       HHHTGGGGHHHHHH---GGGHHHHHHHHHHHHS-HHHHTT-EEEEEEEETTTEEEEEEEEE-S--STTS CS
                    HMG_CoA_synt_C 141 kkkvkpsllvptevGnmYtaslyaalasllskvsadelagkriglfsYGsGlaaslfslrvkqdvseds 209
                                        +k++p +++ t+ Gn+Y  s    +a+ l    ++   g ri + ++GsG  a  fs++v++++++++
  gi|298676116|ref|YP_003727866.1| 255 RDKIEPGMVI-TKLGNIYSGSCMMGIAATL----DQAKPGDRIFATAFGSGAGADAFSIKVTDKMEQFQ 318
                                       5677777665.789****************....566679**********************9998755 PP

>> HMG_CoA_synt_N  Hydroxymethylglutaryl-coenzyme A synthase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   1.4e-05     0.062       4     172 ..       2     167 ..       1     169 [. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                    HMG_CoA_synt_N   4 dvgilaleiylpaqyvdqaelekfdgveagkytiglgqtrmgfvsdredinslsltvvqkllertkldydaigrlev 80 
                                        vgi++   y+p   ++  ++ +  g +a     gl  ++ +  +  ed  ++++   +  +++ ++d   ig +  
  gi|298676116|ref|YP_003727866.1|   2 SVGIVSYGSYIPRYRIKVEDIARVWGEDAETLKAGLMVSEKSVPDLDEDTATIAVESARAAIKNGNIDPVRIGAVYT 78 
                                       59*************************************************************************** PP

                    HMG_CoA_synt_N  81 gtetiidksksvksvlmqlfeesgntdiegidtlnacyggtaalfnavnwiessawdgryalvvagdiaiydsgna. 156
                                       g+e+     k   +++ + +       +   d   ac  g+a++  ++    s + d    + +  d++  + g+a 
  gi|298676116|ref|YP_003727866.1|  79 GSESHPYAVKPTSTIVAEAISA--TPVMTAADFEFACKAGSATVQSCMGLTSSGMIDL--GMGIGADVSQGAPGDAl 151
                                       ***9887777777777776655..4456788999**********99999999999985..46678899999999873 PP

                    HMG_CoA_synt_N 157 rptggagavalligpd 172
                                         t  ag va+++g +
  gi|298676116|ref|YP_003727866.1| 152 EYTAAAGGVAFIMGNK 167
                                       5689999999999875 PP

>> Activator-TraM  Transcriptional activator TraM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.9e-05      0.13      48     107 ..      13      67 ..       7     100 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.9e-05
                    Activator-TraM  48 dqfkeeleaiasrWgddakekaervlnaalaaskealvkllqegakeaaevvrkeveaal 107
                                        +++  +e+ia+ Wg+da      +l a l  s +++  l +++a  a+e++r  +++  
  gi|298676116|ref|YP_003727866.1|  13 PRYRIKVEDIARVWGEDAE-----TLKAGLMVSEKSVPDLDEDTATIAVESARAAIKNGN 67 
                                       68999************95.....8***********99999999999*******999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2456.10
//
Query:       gi|298676117|ref|YP_003727867.1|  [L=246]
Description: transcriptional regulator, XRE family [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-08   33.2   0.0    9.9e-08   31.9   0.0    1.7  1  HTH_3           Helix-turn-helix
    5.8e-05   23.0   0.0    0.00014   21.8   0.0    1.7  1  HTH_19          Helix-turn-helix domain
     0.0095   16.3   0.0       0.02   15.2   0.0    1.6  1  HTH_31          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.038   14.1   0.0       0.38   10.8   0.0    2.1  2  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito
       0.13   12.0   0.0        0.2   11.4   0.0    1.2  1  DUF2436         Domain of unknown function (DUF2436)


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   2.8e-11   9.9e-08       1      48 [.      32      80 ..      32      81 .. 0.96

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 2.8e-11
                                      HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTT.SSCSBHHHHHHHHHHH CS
                             HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnG.ernPsletlkklakaL 48
                                      lk++R+     q++L+ +lGvs+s is++E+G + +P + ++ k+ +aL
  gi|298676117|ref|YP_003727867.1| 32 LKKWRLNFEVAQTDLSNYLGVSPSVISDYESGrRKSPGILIVSKIVEAL 80
                                      7999999999***********************999**********998 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   3.8e-08   0.00014       1      52 [.      29      80 ..      29      99 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.8e-08
                            HTH_19  1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaeal 52
                                      Ge Lk+ R ++   q +l++ lg+s+s is +E+g+++ p++  + ki+eal
  gi|298676117|ref|YP_003727867.1| 29 GEALKKWRLNFEVAQTDLSNYLGVSPSVISDYESGRRKSPGILIVSKIVEAL 80
                                      89*********************************999*******9999975 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   5.7e-06      0.02       3      48 ..      29      74 ..      29      87 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.7e-06
                            HTH_31  3 GalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavle 48
                                      G+ L+ +R    + q+++   lgvs+s +s++E+Grr  p    + 
  gi|298676117|ref|YP_003727867.1| 29 GEALKKWRLNFEVAQTDLSNYLGVSPSVISDYESGRRKSPGILIVS 74
                                      667888888888889999999****************977555555 PP

>> MqsA_antitoxin  Antitoxin component of bacterial toxin-antitoxin system, MqsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00011      0.38      49     114 ..       7      72 ..       1      82 [. 0.81
   2 ?    1.1   0.0      0.11   3.9e+02      60     107 ..     132     182 ..      97     193 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
                    MqsA_antitoxin  49 eedrlseellefrkkvnaelvdpafiarvrkkleldqreaaeifGgGvnafsryekGkvrpplalv 114
                                       +e+  ++   ++  ++  +   ++ +++ r ++e++q ++++ +G+     s ye+G+ ++p  l+
  gi|298676117|ref|YP_003727867.1|   7 HENVRQRLSEKMAGEITLSEKPGEALKKWRLNFEVAQTDLSNYLGVSPSVISDYESGRRKSPGILI 72 
                                       44444555566777788888889999********************************99986655 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.11
                    MqsA_antitoxin  60 frkkvnaelvdpafiarvrkkleldqreaaeifGgGv...nafsryekGkv 107
                                       ++k v+  l   + i + +  lel+ +e ++++G  +   + f++  +Gk+
  gi|298676117|ref|YP_003727867.1| 132 INKGVEKPLYGFTVIDSKKAILELSSHEFQKLYGWSTeraMVFTKVSTGKS 182
                                       445555555555667777778999999999999965422255777666665 PP

>> DUF2436  Domain of unknown function (DUF2436)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   5.6e-05       0.2      45      86 ..      79     119 ..      76     138 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.6e-05
                           DUF2436  45 llldadhntygqviPadtgtletgtaspadyeanfeytlPan 86 
                                        ll+ d ++ gq i a+ g+l+t+t+s a y   +eyt P++
  gi|298676117|ref|YP_003727867.1|  79 ALLNIDAERGGQKIHAYEGMLYTETSSRAVYAT-YEYTYPMQ 119
                                       5899999**********************9988.******86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 1930.26
//
Query:       gi|298676118|ref|YP_003727868.1|  [L=141]
Description: hypothetical protein Metev_2251 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 1125.47
//
Query:       gi|298676119|ref|YP_003727869.1|  [L=369]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.5e-25   86.6   1.6    2.5e-24   85.0   1.1    2.1  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    5.8e-10   39.4   1.1    1.4e-09   38.2   1.1    1.6  1  OrfB_IS605      Probable transposase
  ------ inclusion threshold ------
      0.068   13.2   0.1       0.12   12.4   0.1    1.4  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.073   13.2   1.1       0.89    9.7   0.1    2.2  2  UPF0547         Uncharacterised protein family UPF0547
       0.44   10.3   5.5        1.7    8.4   5.5    1.9  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
        1.2    9.3   4.2         13    6.1   1.9    3.0  2  DUF2387         Probable metal-binding protein (DUF2387)
        8.5    6.4   7.3    1.2e+02    2.7   7.6    2.3  2  zinc_ribbon_4   zinc-ribbon domain


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.95   2.4e+03      15      29 ..     195     209 ..     192     214 .. 0.85
   2 !   85.0   1.1   9.7e-28   2.5e-24       1      69 []     285     354 ..     285     354 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.95
                    OrfB_Zn_ribbon  15 yGikveevnpayTSk 29 
                                       +G k  e+ ++yTS 
  gi|298676119|ref|YP_003727869.1| 195 KGTKADEIRKRYTSL 209
                                       58899999*****96 PP

  == domain 2  score: 85.0 bits;  conditional E-value: 9.7e-28
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f++l+ ++ ykak +G++v+++np yTS++CseCg+++k+ ++++ ++kC++Cg++ ++D+nA+ Ni++r
  gi|298676119|ref|YP_003727869.1| 285 FSELTDFILYKAKLEGVPVVVINPMYTSQQCSECGYIDKNnRQKQANLKCKRCGHKENADYNASKNIAHR 354
                                       899*************************************99*************************997 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   1.1   5.5e-13   1.4e-09       4     106 ..     162     254 ..     159     264 .. 0.86

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 5.5e-13
                        OrfB_IS605   4 vevevelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarl 80 
                                       +ev++  +++ +  + g+DlG+ n+at+++++    +ykg ++++  k+++  + +lqs    s     a++ l++l
  gi|298676119|ref|YP_003727869.1| 162 MEVGE-NEVEYNDDVMGVDLGVVNIATTYDNE----IYKGTKADEIRKRYTSLKSRLQSAGTWS-----AKKHLKKL 228
                                       56665.6677778899****************....***********************95555.....79999999 PP

                        OrfB_IS605  81 hrkrsrrrkhllhklathliktlkev 106
                                       ++k +r+ ++l h +a++l++  k++
  gi|298676119|ref|YP_003727869.1| 229 SKKERRFKRDLNHRVAKQLVRSAKDT 254
                                       99***************999987766 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   4.6e-05      0.12      60      96 ..     296     341 ..     252     351 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.6e-05
                                       -EEE......EEEE--EEEETTTS-EEECHH..H.HHS-TTTSSS- CS
                              HypA  60 aeLe......ieevpvkvrCreCgkefelee..k.alrCpkCgsad 96 
                                       a+Le      i+ +  + +C+eCg+  + ++  + +l+C++Cg+++
  gi|298676119|ref|YP_003727869.1| 296 AKLEgvpvvvINPMYTSQQCSECGYIDKNNRqkQaNLKCKRCGHKE 341
                                       455555554577788899******9888555333688******874 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00035      0.89      15      25 ..     313     323 ..     311     324 .. 0.87
   2 ?    2.0   0.1      0.09   2.3e+02      16      22 ..     333     339 ..     330     340 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00035
                           UPF0547  15 qfCphCGyvFq 25 
                                       q C++CGy+++
  gi|298676119|ref|YP_003727869.1| 313 QQCSECGYIDK 323
                                       89******986 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.09
                           UPF0547  16 fCphCGy 22 
                                       +C  CG+
  gi|298676119|ref|YP_003727869.1| 333 KCKRCGH 339
                                       5666776 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   5.5   0.00065       1.7       3      26 ..     315     340 ..     314     340 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00065
                                       -SSS-..-B----SSS----SSS--- CS
                    DNA_RNApol_7kD   3 CgeCg..aevslkkgdpiRCkeCGhR 26 
                                       C eCg  +++  +k++ ++Ck CGh+
  gi|298676119|ref|YP_003727869.1| 315 CSECGyiDKNNRQKQANLKCKRCGHK 340
                                       999996678889999**********7 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.12   3.1e+02      38      68 ..     224     254 ..     221     260 .. 0.81
   2 ?    6.1   1.9    0.0049        13      31      49 ..     313     331 ..     307     352 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.12
                           DUF2387  38 ftdelsekgqsvakelktrvnkdeekeasak 68 
                                       ++ +ls+k++ ++++l+ rv+k+  ++a+++
  gi|298676119|ref|YP_003727869.1| 224 HLKKLSKKERRFKRDLNHRVAKQLVRSAKDT 254
                                       788999999************9987655554 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0049
                           DUF2387  31 rECvsCgftdelsekgqsv 49 
                                         C +Cg++d+ + ++q+ 
  gi|298676119|ref|YP_003727869.1| 313 QQCSECGYIDKNNRQKQAN 331
                                       57999*****999994432 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.2      0.18   4.7e+02      27      33 ..     314     320 ..     306     322 .. 0.81
   2 ?    2.7   7.6     0.046   1.2e+02      20      34 ..     326     340 ..     313     340 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.18
                     zinc_ribbon_4  27 rCskCgh 33 
                                       +Cs Cg 
  gi|298676119|ref|YP_003727869.1| 314 QCSECGY 320
                                       8999996 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.046
                     zinc_ribbon_4  20 pakgvkvrCskCghv 34 
                                       ++k ++++C++Cgh+
  gi|298676119|ref|YP_003727869.1| 326 RQKQANLKCKRCGHK 340
                                       78899********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1010  (0.0563333); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2249.14
//
Query:       gi|298676120|ref|YP_003727870.1|  [L=645]
Description: phosphoadenosine phosphosulfate reductase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.1e-46  157.6   0.0    5.6e-46  156.7   0.0    1.4  1  PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
    4.4e-16   58.6   0.2    9.5e-16   57.5   0.2    1.6  1  PUA          PUA domain
    6.4e-07   29.4   9.4    6.4e-07   29.4   9.4    2.5  1  Fer4_9       4Fe-4S dicluster domain
    1.5e-06   28.7  13.6    1.5e-06   28.7  13.6    2.4  1  Fer4_7       4Fe-4S dicluster domain
    3.8e-06   26.5  23.8    9.8e-06   25.2   3.4    3.0  3  Fer4         4Fe-4S binding domain
    2.7e-05   24.0  15.5     0.0076   16.3   3.4    2.7  2  Fer4_6       4Fe-4S binding domain
    9.4e-05   22.5  14.8    9.4e-05   22.5  14.8    2.5  3  Fer4_21      4Fe-4S dicluster domain
    0.00034   21.1  11.0      0.012   16.1   0.4    3.1  2  Fer4_17      4Fe-4S dicluster domain
    0.00042   20.4  14.3    0.00042   20.4  14.3    2.7  3  Fer4_10      4Fe-4S dicluster domain
    0.00097   19.3   8.8    0.00097   19.3   8.8    2.3  2  Fer4_18      4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.015   16.2  12.5      0.025   15.5   2.5    3.5  4  Fer4_16      4Fe-4S double cluster binding domain
      0.015   15.7   1.8      0.015   15.7   1.8    3.5  2  Fer4_4       4Fe-4S binding domain
      0.049   14.6  21.8       0.13   13.3   5.7    3.1  2  Fer4_3       4Fe-4S binding domain
      0.075   12.6   0.0       0.15   11.7   0.0    1.4  1  Herpes_IE68  Herpesvirus immediate early protein
       0.94   10.0  22.2        1.6    9.2   3.4    4.2  6  Fer4_8       4Fe-4S dicluster domain
        1.2    9.4  24.9       0.25   11.5   4.3    3.2  2  Fer4_2       4Fe-4S binding domain
        1.6    9.3  11.7        3.6    8.2   2.4    2.8  2  Fer4_13      4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.7   0.0   5.3e-49   5.6e-46       2     174 .]     256     429 ..     255     429 .. 0.97

  Alignments for each domain:
  == domain 1  score: 156.7 bits;  conditional E-value: 5.3e-49
                                       EEEE--SSCTCHHHHHHHHHHCTTHEEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-THH CS
                       PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpvpvvfvdtghefpetiefvdeleeryglrlkvyepeeevaekinaekhgssly 78 
                                       + vs+sgGkdsl++l+L+++++++++++f+dtg efpet+e     +++y+ +lk+ +  + ++e++  ++ +s  +
  gi|298676120|ref|YP_003727870.1| 256 VSVSYSGGKDSLAVLQLVSECLNDFTIIFADTGLEFPETVENTYMAADKYNQDLKTESAGNAFWESVDNFGPPSIEV 332
                                       579************************************************************************** PP

                                       HCHHHHHHTHHHHHHHHHCT..TECEEE----CCCTTTTTTSSSEEECTTT-SCEEE-CCCT--HHHHHHHHHHCT- CS
                       PAPS_reduct  79 eeaaeriaKveplkkaLekl..dedalltGaRrdesksraklpiveidedfekslrvfPllnWteedvwqyilreni 153
                                       ++ +++++K+ p+++ +e++  +  ++++G+R++es+sra+ + v+++ + ++++   P+ nWt  +vw y+ ++n 
  gi|298676120|ref|YP_003727870.1| 333 RW-CCKVCKLGPITRLIENNfeNGCLTFIGQRKYESSSRARSKNVWKNPWVNNQIAASPIQNWTALHVWLYLFKTNA 408
                                       **.************99998777789*************************************************** PP

                                       -B-CCCCTT-SS--BCTTB-S CS
                       PAPS_reduct 154 pynpLydqgfrsiGcvpctga 174
                                       pynpLy++gf++iGc+ c++a
  gi|298676120|ref|YP_003727870.1| 409 PYNPLYEKGFDRIGCWLCPSA 429
                                       ******************975 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.5   0.2     9e-19   9.5e-16       2      71 ..     133     202 ..     132     203 .. 0.97

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 9e-19
                                       EEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEE CS
                               PUA   2 rvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveie 71 
                                        v++dd+Avk +++ga+ l pG+++++  + + d+V+++++++++va G+a+++++ + +  +g +v+++
  gi|298676120|ref|YP_003727870.1| 133 WVIIDDSAVKPIANGANALSPGIIDADYGIVKEDEVVVLTPENKVVATGRAKMTGNKMVESSRGEAVKTR 202
                                       59****************************************************************9975 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   9.4   6.1e-10   6.4e-07       1      48 [.     596     637 ..     580     639 .. 0.95

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 6.1e-10
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpk 48 
                                       kC gCg Cv+ Cp+++++ ++++  +        +C++C +C+ +Cp 
  gi|298676120|ref|YP_003727870.1| 596 KCSGCGVCVAHCPNNAIQIKSGTAVVGD------DCTHCSECIRVCPV 637
                                       7********************9999886......6***********95 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7  13.6   1.4e-09   1.5e-06       1      50 [.     596     637 ..     596     638 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.4e-09
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPt 50 
                                       +C gCg Cva Cp++ai+++          ++++ ++C++C +C++vCP+
  gi|298676120|ref|YP_003727870.1| 596 KCSGCGVCVAHCPNNAIQIKSG--------TAVVGDDCTHCSECIRVCPV 637
                                       7******************774........67889**************7 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.9       7.8   8.2e+03       9      14 ..     421     426 ..     421     426 .. 0.89
   2 !   25.2   3.4   9.3e-09   9.8e-06       7      24 .]     596     613 ..     593     613 .. 0.94
   3 !   13.4   4.8   4.7e-05      0.05       6      20 ..     623     637 ..     619     638 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 7.8
                                       SS-THH CS
                              Fer4   9 igCGaC 14 
                                       igC +C
  gi|298676120|ref|YP_003727870.1| 421 IGCWLC 426
                                       899999 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 9.3e-09
                                       TSSS-THHHHHSTTTEEE CS
                              Fer4   7 kCigCGaCvevCPvgAIt 24 
                                       kC gCG Cv  CP++AI+
  gi|298676120|ref|YP_003727870.1| 596 KCSGCGVCVAHCPNNAIQ 613
                                       9***************95 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 4.7e-05
                                       TTSSS-THHHHHSTT CS
                              Fer4   6 ekCigCGaCvevCPv 20 
                                       ++C++C +C+ vCPv
  gi|298676120|ref|YP_003727870.1| 623 DDCTHCSECIRVCPV 637
                                       89************8 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   3.4   7.2e-06    0.0076       8      24 .]     596     612 ..     591     612 .. 0.95
   2 !   12.6   4.3   0.00011      0.11       8      20 ..     624     636 ..     622     640 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.2e-06
                            Fer4_6   8 kCigCgdCvrvCPegai 24 
                                       kC gCg Cv++CP +ai
  gi|298676120|ref|YP_003727870.1| 596 KCSGCGVCVAHCPNNAI 612
                                       8************9998 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00011
                            Fer4_6   8 kCigCgdCvrvCP 20 
                                        C++C +C+rvCP
  gi|298676120|ref|YP_003727870.1| 624 DCTHCSECIRVCP 636
                                       5************ PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1         8   8.5e+03      42      48 ..     421     427 ..     419     429 .. 0.73
   2 !   12.2   3.3   0.00014      0.15      33      58 ..     588     613 ..     581     614 .. 0.75
   3 !   22.5  14.8   8.9e-08   9.4e-05       7      54 ..     596     638 ..     590     642 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 8
                           Fer4_21  42 vGCnlCs 48 
                                       +GC lC 
  gi|298676120|ref|YP_003727870.1| 421 IGCWLCP 427
                                       6888885 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00014
                           Fer4_21  33 vlkvv.edeCvGCnlCssvCPvedcie 58 
                                        + v+ + +C GC +C++ CP +++i+
  gi|298676120|ref|YP_003727870.1| 588 EFSVRrALKCSGCGVCVAHCP-NNAIQ 613
                                       455542569************.69987 PP

  == domain 3  score: 22.5 bits;  conditional E-value: 8.9e-08
                           Fer4_21   7 kCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPve 54 
                                       kC gCg C+  C++   +ai+i++ t  +vv d+C+ C  C+ vCPv 
  gi|298676120|ref|YP_003727870.1| 596 KCSGCGVCVAHCPN---NAIQIKSGT--AVVGDDCTHCSECIRVCPVV 638
                                       8************6...889987555..59****************96 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.4   1.1e-05     0.012      40      59 ..     586     610 ..     563     611 .. 0.71
   2 !   11.0   0.8   0.00047       0.5      45      57 ..     624     636 ..     614     642 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.1e-05
                           Fer4_17  40 e.....ekaslCieCgeCerkCPqg 59 
                                       +     ++a +C++Cg C++ CP++
  gi|298676120|ref|YP_003727870.1| 586 KaefsvRRALKCSGCGVCVAHCPNN 610
                                       1233357899*************97 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00047
                           Fer4_17  45 lCieCgeCerkCP 57 
                                       +C++C eC r+CP
  gi|298676120|ref|YP_003727870.1| 624 DCTHCSECIRVCP 636
                                       5666666666666 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.2       8.3   8.7e+03      15      24 ..     335     358 ..     333     378 .. 0.48
   2 !   20.4  14.3   3.9e-07   0.00042       6      56 .]     594     636 ..     589     636 .. 0.80
   3 !   13.6   3.6   5.2e-05     0.055       7      21 ..     623     637 ..     619     643 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 8.3
                           Fer4_10  15 CvkaCPadl................t 24 
                                       C k+C  +l                t
  gi|298676120|ref|YP_003727870.1| 335 CCKVC--KLgpitrliennfengclT 358
                                       66666..4444444444444444443 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 3.9e-07
                           Fer4_10   6 ddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       + +C +Cg Cv+ CP         +++ +++   ++ ++Ct+c +C+++CP
  gi|298676120|ref|YP_003727870.1| 594 ALKCSGCGVCVAHCPN--------NAIQIKSGTAVVGDDCTHCSECIRVCP 636
                                       568*************........555555555555569***********9 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 5.2e-05
                           Fer4_10   7 dtCirCgkCvkaCPa 21 
                                       d C++C +C ++CP+
  gi|298676120|ref|YP_003727870.1| 623 DDCTHCSECIRVCPV 637
                                       78************9 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       7.7   8.1e+03       2      40 ..     164     202 ..     163     223 .. 0.75
   2 !   19.3   8.8   9.2e-07   0.00097      35      98 ..     572     638 ..     552     642 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 7.7
                           Fer4_18   2 redvcvyvcPyarvqsvlydeetllvvydakrGekiagr 40 
                                       +ed  v++ P  +v +    + t   + +  rGe ++ r
  gi|298676120|ref|YP_003727870.1| 164 KEDEVVVLTPENKVVATGRAKMTGNKMVESSRGEAVKTR 202
                                       677777888888888888888888888888888887765 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 9.2e-07
                           Fer4_18  35 ekiagrkkekkalkekeerkekgagdcidcescvkvcPt.gidirkGlql...eciscllcidacdkv 98 
                                         + g++k++k+l++k e + + a +c  c++cv+ cP   i i+ G  +   +c  c++ci  c  v
  gi|298676120|ref|YP_003727870.1| 572 S-RGGTQKKTKKLMKKAEFSVRRALKCSGCGVCVAHCPNnAIQIKSGTAVvgdDCTHCSECIRVCPVV 638
                                       2.23445555556666666788899*************7369*****9875668***********876 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       8.6   9.1e+03       8      25 ..     335     352 ..     331     381 .. 0.63
   2 ?   14.6   2.5   4.5e-05     0.047      34      67 .]     577     610 ..     559     610 .. 0.76
   3 ?   15.5   2.5   2.4e-05     0.025       1      20 [.     596     615 ..     596     623 .. 0.87
   4 ?    7.1   4.7    0.0098        10       2      14 ..     625     637 ..     624     641 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 8.6
                           Fer4_16   8 CaevCPtnaikekkekei 25 
                                       C +vC  + i+   e+++
  gi|298676120|ref|YP_003727870.1| 335 CCKVCKLGPITRLIENNF 352
                                       777776666665544444 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 4.5e-05
                           Fer4_16  34 ntaekkdlaedeekckkqeaitgCdiCqdvCPan 67 
                                       +++ kk +++ e++  ++ ++ gC++C++ CP+n
  gi|298676120|ref|YP_003727870.1| 577 QKKTKKLMKKAEFSVRRALKCSGCGVCVAHCPNN 610
                                       4566677778888888999*************98 PP

  == domain 3  score: 15.5 bits;  conditional E-value: 2.4e-05
                           Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                       +C +Cg C+  CP nai+ k
  gi|298676120|ref|YP_003727870.1| 596 KCSGCGVCVAHCPNNAIQIK 615
                                       5****************976 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.0098
                           Fer4_16   2 CgtCgkCaevCPt 14 
                                       C+ C +C+ vCP+
  gi|298676120|ref|YP_003727870.1| 625 CTHCSECIRVCPV 637
                                       9999999999997 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   1.8   1.4e-05     0.015       3      16 ..     596     609 ..     594     617 .. 0.92
   2 ?   10.5   3.5   0.00067       0.7       3      16 ..     624     637 ..     622     640 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.4e-05
                            Fer4_4   3 rCigCgsCvaaCPq 16 
                                       +C gCg+Cva CP 
  gi|298676120|ref|YP_003727870.1| 596 KCSGCGVCVAHCPN 609
                                       7************5 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00067
                            Fer4_4   3 rCigCgsCvaaCPq 16 
                                        C++C  C+++CP+
  gi|298676120|ref|YP_003727870.1| 624 DCTHCSECIRVCPV 637
                                       6************5 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   8.1      0.03        31       1      15 []     597     611 ..     597     611 .. 0.97
   2 ?   13.3   5.7   0.00012      0.13       1      13 [.     625     637 ..     625     639 .. 0.94

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.03
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C gCg Cv  CP++A
  gi|298676120|ref|YP_003727870.1| 597 CSGCGVCVAHCPNNA 611
                                       99***********98 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00012
                            Fer4_3   1 CtgCgaCvevCPv 13 
                                       Ct+C+ C +vCPv
  gi|298676120|ref|YP_003727870.1| 625 CTHCSECIRVCPV 637
                                       ************6 PP

>> Herpes_IE68  Herpesvirus immediate early protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00014      0.15      52      93 ..      77     118 ..      49     133 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
                       Herpes_IE68  52 nstgsanrLRrlvlDiylmGrtraRlkqatWerllqlsptqs 93 
                                       n  +s++r+  +++D  ++G +r+ ++  +W+ ll+ls+ ++
  gi|298676120|ref|YP_003727870.1|  77 NKIPSEDRMEEIIVDGEIIGSIRYEIEDLKWKLLLRLSGARK 118
                                       677899********************************8765 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1       1.5   1.6e+03       7      31 ..      14      43 ..      13      54 .. 0.81
   2 ?   -1.2   0.0       2.8     3e+03       8      12 ..     336     340 ..     295     400 .. 0.66
   3 ?   -2.5   0.0       6.8   7.2e+03      15      36 ..     426     446 ..     421     471 .. 0.58
   4 ?    8.6   4.0    0.0024       2.5      48      63 ..     594     609 ..     562     611 .. 0.65
   5 ?    8.8   3.2    0.0021       2.2       3      16 ..     595     608 ..     593     623 .. 0.78
   6 ?    9.2   3.4    0.0015       1.6       4      19 ..     624     639 ..     621     644 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.5
                            Fer4_8  7 eCgaCq.....saCpvlrrtkkhlldarge 31
                                       C  C+     ++C   ++t++   +++g+
  gi|298676120|ref|YP_003727870.1| 14 WCRSCNlpvlgENCNCGSDTDNLEVTPPGD 43
                                      588999999999999999999877777776 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.8
                            Fer4_8   8 CgaCq 12 
                                       C  C+
  gi|298676120|ref|YP_003727870.1| 336 CKVCK 340
                                       34444 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 6.8
                            Fer4_8  15 Cpvlrrtkkhlldargeaaedv 36 
                                       Cp+++  +  +l++ +  +e +
  gi|298676120|ref|YP_003727870.1| 426 CPSASLADFKRLKNTHPEME-K 446
                                       77777777433433333344.3 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.0024
                            Fer4_8  48 lwsCttcgaCtevCpv 63 
                                       + +C++cg C+  Cp+
  gi|298676120|ref|YP_003727870.1| 594 ALKCSGCGVCVAHCPN 609
                                       5566666666666665 PP

  == domain 5  score: 8.8 bits;  conditional E-value: 0.0021
                            Fer4_8   3 ekCieCgaCqsaCp 16 
                                        kC +Cg C ++Cp
  gi|298676120|ref|YP_003727870.1| 595 LKCSGCGVCVAHCP 608
                                       67888888888888 PP

  == domain 6  score: 9.2 bits;  conditional E-value: 0.0015
                            Fer4_8   4 kCieCgaCqsaCpvlr 19 
                                       +C++C+ C   Cpv++
  gi|298676120|ref|YP_003727870.1| 624 DCTHCSECIRVCPVVK 639
                                       5777777777777766 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   4.3   0.00023      0.25       9      22 .]     596     609 ..     591     609 .. 0.90
   2 ?   10.3   4.5   0.00059      0.63       8      21 ..     623     636 ..     619     637 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00023
                            Fer4_2   9 rCigCgaCvsaCPa 22 
                                       +C gCg Cv  CP+
  gi|298676120|ref|YP_003727870.1| 596 KCSGCGVCVAHCPN 609
                                       8********99**5 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00059
                            Fer4_2   8 drCigCgaCvsaCP 21 
                                       d C++C+ C+ +CP
  gi|298676120|ref|YP_003727870.1| 623 DDCTHCSECIRVCP 636
                                       56************ PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   2.4    0.0034       3.6       5      18 ..     596     609 ..     595     610 .. 0.93
   2 ?    5.3   2.0     0.027        28       4      19 ..     623     638 ..     620     642 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0034
                           Fer4_13   5 tCiacgaCvelaPd 18 
                                       +C++cg+Cv+ +P+
  gi|298676120|ref|YP_003727870.1| 596 KCSGCGVCVAHCPN 609
                                       7************7 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.027
                           Fer4_13   4 dtCiacgaCvelaPdv 19 
                                       d C+ c  C  ++P v
  gi|298676120|ref|YP_003727870.1| 623 DDCTHCSECIRVCPVV 638
                                       78************65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (645 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.73u 0.27s 00:00:01.00 Elapsed: 00:00:00.48
# Mc/sec: 4018.75
//
Query:       gi|298676121|ref|YP_003727871.1|  [L=144]
Description: hypothetical protein Metev_2255 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-09   36.9   7.8    4.3e-05   23.4   0.6    2.7  2  TPR_8            Tetratricopeptide repeat
    4.7e-09   35.7   7.1    0.00015   21.6   0.7    2.6  2  TPR_2            Tetratricopeptide repeat
    9.2e-09   35.5  10.0      8e-07   29.3   3.8    2.4  2  TPR_12           Tetratricopeptide repeat
    3.2e-08   33.1   8.4    0.00074   19.2   0.9    2.6  2  TPR_1            Tetratricopeptide repeat
    3.8e-05   24.1   0.5      0.078   13.8   0.1    2.8  2  TPR_14           Tetratricopeptide repeat
      4e-05   24.0   1.0    6.2e-05   23.4   0.2    1.7  2  TPR_19           Tetratricopeptide repeat
    4.2e-05   23.1   3.7     0.0017   18.0   0.3    2.7  2  TPR_11           TPR repeat
    4.3e-05   23.6   1.7     0.0011   19.2   0.1    2.8  3  TPR_17           Tetratricopeptide repeat
    7.9e-05   23.2   1.0    0.00013   22.5   1.0    1.4  1  TPR_16           Tetratricopeptide repeat
    0.00027   21.2   0.3       0.57   10.4   0.0    2.7  3  TPR_5            Tetratrico peptide repeat
     0.0014   18.4   2.0       0.57   10.1   0.1    2.4  2  TPR_10           Tetratricopeptide repeat
     0.0051   16.7   1.2       0.34   11.0   0.2    2.5  2  TPR_7            Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.016   15.1   0.1      0.023   14.6   0.1    1.3  1  Wzy_C_2          Virulence factor membrane-bound polymerase, 
      0.042   14.1   3.1        0.2   11.9   3.1    2.0  2  ANAPC3           Anaphase-promoting complex, cyclosome, subun
       0.13   13.0   0.0       0.45   11.3   0.0    1.9  2  TPR_4            Tetratricopeptide repeat
       0.15   12.8   0.6         12    6.8   0.1    2.6  2  TPR_6            Tetratricopeptide repeat
       0.21   12.1   0.4         16    6.0   0.0    2.2  2  SeleniumBinding  Selenium binding protein


Domain annotation for each model (and alignments):
>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.2   2.2e-06    0.0023       1      33 [.      77     109 ..      77     110 .. 0.96
   2 !   23.4   0.6   4.1e-08   4.3e-05       2      33 ..     112     143 ..     111     144 .] 0.94

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.2e-06
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a+ay+n ++i  ++gd ++A+  y+ alel+p+
  gi|298676121|ref|YP_003727871.1|  77 AQAYHNAALIETSTGDENKAEDHYRIALELSPE 109
                                       79******************************7 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 4.1e-08
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +a+yn + +++klg+ +eA++ y+ka +l+ +
  gi|298676121|ref|YP_003727871.1| 112 RAHYNYAGLLDKLGRTDEAEKHYKKAKSLEAN 143
                                       89************************999875 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.3   2.6e-06    0.0027       1      34 []      77     110 ..      77     110 .. 0.95
   2 !   21.6   0.7   1.4e-07   0.00015       2      31 ..     112     141 ..     111     144 .] 0.92

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.6e-06
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a+a++n +l+    gd ++A+++++ Alel P++
  gi|298676121|ref|YP_003727871.1|  77 AQAYHNAALIETSTGDENKAEDHYRIALELSPEY 110
                                       689*****************************85 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 1.4e-07
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleld 31 
                                       +a+yn + ++ klg+ +eA+++++kA +l+
  gi|298676121|ref|YP_003727871.1| 112 RAHYNYAGLLDKLGRTDEAEKHYKKAKSLE 141
                                       69************************8886 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.4   8.3e-06    0.0088      40      75 ..      72     107 ..      62     109 .. 0.83
   2 !   29.3   3.8   7.6e-10     8e-07       3      71 ..      77     137 ..      75     140 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.3e-06
                            TPR_12  40 dhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       d+ + a++++n + +   +g+  +A+++++ al++ 
  gi|298676121|ref|YP_003727871.1|  72 DNGEKAQAYHNAALIETSTGDENKAEDHYRIALELS 107
                                       555899***********************9999986 PP

  == domain 2  score: 29.3 bits;  conditional E-value: 7.6e-10
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleea 71 
                                       a+a++n a++++  g+  +A+++++ ale+      p+   ++++ +n++ l+++lgr++eA++++++a
  gi|298676121|ref|YP_003727871.1|  77 AQAYHNAALIETSTGDENKAEDHYRIALELS-----PE---YIRAHYNYAGLLDKLGRTDEAEKHYKKA 137
                                       899****************************.....87...5*************************98 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.2   1.1e-06    0.0012       1      34 []      77     110 ..      77     110 .. 0.96
   2 !   19.2   0.9     7e-07   0.00074       2      30 ..     112     140 ..     111     143 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.1e-06
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+a+ n +++  + g+ ++A+++y+ ALel P++
  gi|298676121|ref|YP_003727871.1|  77 AQAYHNAALIETSTGDENKAEDHYRIALELSPEY 110
                                       79******************************86 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 7e-07
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALel 30 
                                       +a+yn + ++ klg+ deA+++y+kA +l
  gi|298676121|ref|YP_003727871.1| 112 RAHYNYAGLLDKLGRTDEAEKHYKKAKSL 140
                                       789999999*****************877 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   7.4e-05     0.078       4      42 ..      80     118 ..      77     120 .. 0.87
   2 !   12.4   0.1   0.00021      0.22       2      27 ..     112     137 ..     111     143 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.4e-05
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       +  +a ++   Gd  +A++++r al+l P+  +a++ +a
  gi|298676121|ref|YP_003727871.1|  80 YHNAALIETSTGDENKAEDHYRIALELSPEYIRAHYNYA 118
                                       555677788899999********************9998 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00021
                            TPR_14   2 eallalaeallalGdpdeAiallrra 27 
                                       +a++ +a +l  lG++deA++++++a
  gi|298676121|ref|YP_003727871.1| 112 RAHYNYAGLLDKLGRTDEAEKHYKKA 137
                                       68999*******************98 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0         5   5.2e+03      35      35 ..      69      69 ..      47      85 .. 0.56
   2 !   23.4   0.2   5.9e-08   6.2e-05       5      51 ..      91     137 ..      89     143 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 5
                            TPR_19 35 l 35
                                      +
  gi|298676121|ref|YP_003727871.1| 69 Q 69
                                      3 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 5.9e-08
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdal 51 
                                       gd   A ++++ al+ +p++ +a +++A +l +lg++deAe+  +++
  gi|298676121|ref|YP_003727871.1|  91 GDENKAEDHYRIALELSPEYIRAHYNYAGLLDKLGRTDEAEKHYKKA 137
                                       5667899999*******************************977665 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.3   1.6e-06    0.0017       3      35 ..      86     118 ..      84     125 .. 0.84
   2 !    6.4   0.1    0.0066         7       6      22 ..     123     139 ..     120     143 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.6e-06
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLG 35 
                                       + ++ G+ ++A  +Y+ Al+l+P++ +a+yn +
  gi|298676121|ref|YP_003727871.1|  86 IETSTGDENKAEDHYRIALELSPEYIRAHYNYA 118
                                       5677888899999*****************966 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0066
                            TPR_11   6 eqGkyeeAieaYkkAlk 22 
                                       ++G+ +eA ++YkkA  
  gi|298676121|ref|YP_003727871.1| 123 KLGRTDEAEKHYKKAKS 139
                                       58************955 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.96     1e+03      16      32 ..      63      79 ..      53      81 .. 0.61
   2 ?    2.6   0.1       0.2   2.2e+02      13      33 ..      77      97 ..      71      98 .. 0.84
   3 !   19.2   0.1     1e-06    0.0011       2      34 .]     100     132 ..      99     132 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.96
                            TPR_17 16 ynnLAelllknGdlmtA 32
                                      y++  + +l nG++++A
  gi|298676121|ref|YP_003727871.1| 63 YTLASVQFLDNGEKAQA 79
                                      33333345689988887 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.2
                            TPR_17 13 adaynnLAelllknGdlmtAr 33
                                      a ay+n A +  + Gd  +A+
  gi|298676121|ref|YP_003727871.1| 77 AQAYHNAALIETSTGDENKAE 97
                                      889*****9999999988886 PP

  == domain 3  score: 19.2 bits;  conditional E-value: 1e-06
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       y+ alel P +  a++n+A ll k+G++++A++
  gi|298676121|ref|YP_003727871.1| 100 YRIALELSPEYIRAHYNYAGLLDKLGRTDEAEK 132
                                       5569***************************86 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   1.0   1.3e-07   0.00013      11      60 ..      91     137 ..      74     142 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.3e-07
                            TPR_16  11 gdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraa 60 
                                       gd  +A+  +++al++    P+  +A+++++ ++ ++gr +eA+  y++a
  gi|298676121|ref|YP_003727871.1|  91 GDENKAEDHYRIALELS---PEYIRAHYNYAGLLDKLGRTDEAEKHYKKA 137
                                       77789************...*************************99997 PP

>> TPR_5  Tetratrico peptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.6   1.7e+03      56      81 ..      40      66 ..      19      80 .. 0.66
   2 !   10.4   0.0   0.00054      0.57       3      29 ..      79     105 ..      76     113 .. 0.86
   3 !    8.1   0.0    0.0028         3       3      27 ..     113     137 ..     111     142 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.6
                             TPR_5 56 ealaLLraelea.psdelddalaafla 81
                                      +++ LL+  +++  ++++d a   +la
  gi|298676121|ref|YP_003727871.1| 40 DGIDLLELSIQErVNNNYDIAYVYTLA 66
                                      678888877666256677777555555 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00054
                             TPR_5   3 aaFeragarDstGhedkavplYrraLa 29 
                                       a  ++a ++ stG+e+ka+  Yr aL+
  gi|298676121|ref|YP_003727871.1|  79 AYHNAALIETSTGDENKAEDHYRIALE 105
                                       5667888999***************97 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0028
                             TPR_5   3 aaFeragarDstGhedkavplYrra 27 
                                       a ++ ag  D  G+ d+a++ Y++a
  gi|298676121|ref|YP_003727871.1| 113 AHYNYAGLLDKLGRTDEAEKHYKKA 137
                                       67899******************98 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.4    0.0039       4.1       2      30 ..      77     105 ..      77     107 .. 0.90
   2 !   10.1   0.1   0.00054      0.57       7      28 ..     116     137 ..     115     140 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0039
                            TPR_10   2 AsslnNLanalrqrgrydeAealleeala 30 
                                       A +++N a + +++g+ ++Ae++++ al+
  gi|298676121|ref|YP_003727871.1|  77 AQAYHNAALIETSTGDENKAEDHYRIALE 105
                                       789********************996666 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00054
                            TPR_10   7 NLanalrqrgrydeAealleea 28 
                                       N a +l ++gr deAe+++++a
  gi|298676121|ref|YP_003727871.1| 116 NYAGLLDKLGRTDEAEKHYKKA 137
                                       77889999***********998 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1      0.05        53       1      31 [.      79     107 ..      72     109 .. 0.80
   2 !   11.0   0.2   0.00032      0.34       3      25 ..     115     137 ..     113     143 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.05
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkd 31 
                                       a++n a +  + Gd  +A+++y+   al+ +
  gi|298676121|ref|YP_003727871.1|  79 AYHNAALIETSTGDENKAEDHYRI--ALELS 107
                                       5777777778899999********..55544 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00032
                             TPR_7   3 lnLarlysrlGdyeeAielyeqs 25 
                                       +n a l  +lG+++eA+++y+++
  gi|298676121|ref|YP_003727871.1| 115 YNYAGLLDKLGRTDEAEKHYKKA 137
                                       566778999************93 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   2.1e-05     0.023     110     170 ..      77     138 ..      45     140 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.1e-05
                           Wzy_C_2 110 yadllelgllplspenlaaklalarklihlsPe.pavierlilslallGdedeAeqilarar 170
                                        +++ +++l++ s  +  +  + +r +++lsPe  +  ++++ +l  lG++deAe+++++a+
  gi|298676121|ref|YP_003727871.1|  77 AQAYHNAALIETSTGDENKAEDHYRIALELSPEyIRAHYNYAGLLDKLGRTDEAEKHYKKAK 138
                                       56789999999999999999************746999*********************997 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.3       0.2   2.1e+02      20      44 ..      56      81 ..      43      85 .. 0.62
   2 ?   11.9   3.1   0.00019       0.2       2      81 ..      54     136 ..      53     137 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.2
                                      H--HHHHHHHHHHHHH.TT-HHHHHH CS
                            ANAPC3 20 tespedayllAlclyl.ngqykrAye 44
                                      +++   +y lA + +l ng+  +Ay+
  gi|298676121|ref|YP_003727871.1| 56 NYDIAYVYTLASVQFLdNGEKAQAYH 81
                                      33444466667766542677888876 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00019
                                       TT-HHHHHHHHHHHH.HHH--HHHHHHH..HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHH CS
                            ANAPC3   2 qnnyknAiflaerllaaetespedayll..AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeA 75 
                                       +nny+ A+ +    ++   + +++  ++  Al   ++g+ ++A + +r a +l ++ ++++y +A  l kL++ +eA
  gi|298676121|ref|YP_003727871.1|  54 NNNYDIAYVYTLASVQFLDNGEKAQAYHnaALIETSTGDENKAEDHYRIAlELSPEYIRAHYNYAGLLDKLGRTDEA 130
                                       5677777776666666444444444443559999999**************************************** PP

                                       HHHH-S CS
                            ANAPC3  76 iaaLek 81 
                                       +++++k
  gi|298676121|ref|YP_003727871.1| 131 EKHYKK 136
                                       ***987 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       6.3   6.6e+03       3       8 ..      79      84 ..      74     101 .. 0.57
   2 ?   11.3   0.0   0.00043      0.45       2      21 ..     112     131 ..     111     134 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 6.3
                             TPR_4  3 allaLA 8 
                                      a+++ A
  gi|298676121|ref|YP_003727871.1| 79 AYHNAA 84
                                      444444 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00043
                             TPR_4   2 rallaLArallalGdldeAr 21 
                                       ra++++A +l  lG+ deA+
  gi|298676121|ref|YP_003727871.1| 112 RAHYNYAGLLDKLGRTDEAE 131
                                       8******************8 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.085        89       1      31 [.      78     108 ..      59     110 .. 0.86
   2 ?    6.8   0.1     0.012        12       2      26 ..     113     137 ..     112     141 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.085
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeYP 31 
                                       +A+ ++al   ++gd  kA + ++  ++  P
  gi|298676121|ref|YP_003727871.1|  78 QAYHNAALIETSTGDENKAEDHYRIALELSP 108
                                       5777888888887999999999998888777 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerl 26 
                                       A y+ a ++ klg+td+A + +++ 
  gi|298676121|ref|YP_003727871.1| 113 AHYNYAGLLDKLGRTDEAEKHYKKA 137
                                       8899999999*99*****9999986 PP

>> SeleniumBinding  Selenium binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.015        16      30      61 ..       2      33 ..       1      37 [. 0.87
   2 ?    5.4   0.1     0.024        26      11      38 ..      35      62 ..      28      92 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.015
                   SeleniumBinding 30 vesdnvdkilkaleekvkekkglaligfklta 61
                                      +e++n+d++ k ++  +++k+ ++ i  ++  
  gi|298676121|ref|YP_003727871.1|  2 SENKNLDELQKKVKSCIQSKEPVTCINQTIRF 33
                                      79********************9999877765 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.024
                   SeleniumBinding 11 taneiPGvelyylgivsavvesdnvdki 38
                                        n+i G++l  l i   v ++ ++  +
  gi|298676121|ref|YP_003727871.1| 35 NENDIDGIDLLELSIQERVNNNYDIAYV 62
                                      5699***********9999999888655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 863.61
//
Query:       gi|298676122|ref|YP_003727872.1|  [L=544]
Description: phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   4.1e-101  338.3   0.0   6.3e-101  337.7   0.0    1.3  1  AICARFT_IMPCHas  AICARFT/IMPCHase bienzyme
    4.9e-28   97.2   0.1    1.2e-27   95.9   0.1    1.7  1  MGS              MGS-like domain
  ------ inclusion threshold ------
      0.047   13.6   0.0       0.14   12.1   0.0    1.8  1  MgsA_C           MgsA AAA+ ATPase C terminal
       0.18   12.1   0.0       0.32   11.3   0.0    1.3  1  NSP2_assoc       Non-essential region of nsp2 of arterivirus 


Domain annotation for each model (and alignments):
>> AICARFT_IMPCHas  AICARFT/IMPCHase bienzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  337.7   0.0  1.4e-104  6.3e-101       1     294 [.     140     455 ..     140     457 .. 0.92

  Alignments for each domain:
  == domain 1  score: 337.7 bits;  conditional E-value: 1.4e-104
                                       HHHTTTT-EEE-SGGGHHHHHHHHHC.T.B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCS..E...EEEEEEEEE CS
                   AICARFT_IMPCHas   1 AAKNhksVtvvvdpadYeevleelkk.gevsletrkklaakaFahtaaYDaaiaeylskqlp..etlklslekkqkL 74 
                                       AAKN++sV+v++dp+dY +vl+e+++ g vs +t+k+la+kaF+hta+YD+ai +ylsk+l   e+++l++++ ++L
  gi|298676122|ref|YP_003727872.1| 140 AAKNYQSVAVISDPNDYGTVLKEMRSsGIVSDKTKKHLAVKAFRHTANYDSAIDTYLSKELLdeEVIRLNFTQGRQL 216
                                       9*************************99*****************************99944346999********* PP

                                       SSSSSTTS-EEEEE-TT..STTHHH-EEEESS---HHHHHHHHHHHHHHCTS....EEEEEEETTEEEEEEEESSHH CS
                   AICARFT_IMPCHas  75 rYGeNphQkaalyeeee..eeglakaeqlqGkelsynNllDadaalelvkef....aavaivKHanpcGvAvgetla 145
                                       rYGeN+hQ+a++y+e +    +la+++ql+Gk+lsynN++Dad+al++vk++     +vaivKH+npcG+A+g++l+
  gi|298676122|ref|YP_003727872.1| 217 RYGENWHQNATFYKEPDvtGPSLANTKQLHGKALSYNNYVDADNALQTVKQLgnekPSVAIVKHNNPCGLATGDSLN 293
                                       *************988888889****************************9876543899***************** PP

                                       HHHHHHHCCSHHHHTTEEEEECCEE-HHHHHHHTTS-ECEEEECEE-CCHHHCCTTS.SS-EEEE-SS..-...... CS
                   AICARFT_IMPCHas 146 eAyekAlaaDpvSaFGgiialnrevdaetaeeikkefleviiApsfeeealeilkkk.knlrvlelke..e...... 213
                                       +A+++A+++Dp+SaFG+ii++n+++d eta+ +k +f+e ++Ap++e+eale+lk+k +n+r+lel+e  +      
  gi|298676122|ref|YP_003727872.1| 294 DALRAAWDGDPISAFGSIICTNTTFDLETAQFLKGKFVELVLAPDYEPEALEFLKNKsDNIRILELPElnDksnidy 370
                                       *******************************************************9999*******99651567788 PP

                                       EEEEETTEEEEEE--G..TTCCCSEEECSC---HHHHHHHHHHHHHCCCS-SS-EEEEETTE.....EEEEE-SSSS CS
                   AICARFT_IMPCHas 214 elrsvsgglLvqerdeakieeeelkvvtkkkpteeeledllfawkvvkhvkSNaivlakdgq.....tvgiGaGqms 285
                                       +++ ++gglL q++d    +++++++vt++   e++    +f+++++k +kSNa++la + +     ++++GaGq++
  gi|298676122|ref|YP_003727872.1| 371 TYKYITGGLLKQSKDV--GTHKKWECVTETPFPENKKPLGEFCINACKSTKSNAVTLAYEYKegcymMLAMGAGQPN 445
                                       9**************6..44568*****987667777777******************976555666********** PP

                                       HHHHHH.HHH CS
                   AICARFT_IMPCHas 286 Rvdsar.lAv 294
                                       Rvds+r lA+
  gi|298676122|ref|YP_003727872.1| 446 RVDSIRkLAA 455
                                       ****984565 PP

>> MGS  MGS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.9   0.1   2.7e-31   1.2e-27       1      95 []      20     135 ..      20     135 .. 0.91

  Alignments for each domain:
  == domain 1  score: 95.9 bits;  conditional E-value: 2.7e-31
                                       THHHHHHHHHHTTCEEEEEHHHHHHHHHTT--EEECCCCHSTGSGGTHCH..................HHHHHHHTT CS
                               MGS   1 glvelakklkelgfellATgGTakllkeagipvtevvektgegerlggrv..................eildaikng 59 
                                       g+ve+a++l++ g+e+++TgGT+++l+e+gi+vt+v+e+t+++e+++gr+                  ++ ++ k  
  gi|298676122|ref|YP_003727872.1|  20 GIVEFAHELSKFGVEIISTGGTGRILQENGIEVTDVSEITNFPEMMEGRIktlhpmihggvlclrensNHIEEAKMA 96 
                                       69***************************************************************999444444444 PP

                                       SCC...EEEEE--THHHHHHCHHHHHHHHHHHTTSHEES CS
                               MGS  60 eid...lvintlypfkatvakdgykirraaenidIplpt 95 
                                       +i+   +v+++lypf+ tv+kdg+++++a+e idI++pt
  gi|298676122|ref|YP_003727872.1|  97 NIKlidMVVVNLYPFEVTVSKDGVNLDEAIEYIDIGGPT 135
                                       444555*******************************98 PP

>> MgsA_C  MgsA AAA+ ATPase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     3e-05      0.14      49      87 ..     390     428 ..     382     494 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3e-05
                                       HHHHHHHHH-TTTTHHHHHHHHHHHHCS----GG.GHHH CS
                            MgsA_C  49 aaaeaveriGlpEariaLaqavvylalapKSnaaykAik 87 
                                       + +e+v++  +pE + +L + +++ + + KSna++ A++
  gi|298676122|ref|YP_003727872.1| 390 KKWECVTETPFPENKKPLGEFCINACKSTKSNAVTLAYE 428
                                       5688899999**************************997 PP

>> NSP2_assoc  Non-essential region of nsp2 of arterivirus polyprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   7.2e-05      0.32      85     144 ..     230     291 ..     211     296 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.2e-05
                        NSP2_assoc  85 dePLDLsrpapaatttlvreqtpdnpgsdagalpvtvrefvptglilrhveh...cGtesgds 144
                                       +eP D+  p++a t+ l ++ ++ n   da+    tv+++   ++ +  v+h   cG  +gds
  gi|298676122|ref|YP_003727872.1| 230 KEP-DVTGPSLANTKQLHGKALSYNNYVDADNALQTVKQLGNEKPSVAIVKHnnpCGLATGDS 291
                                       566.9999******************************998877766666665559*999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (544 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 3153.93
//
Query:       gi|298676123|ref|YP_003727873.1|  [L=261]
Description: ArsR family transcriptional regulator [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-22   79.3   1.6    3.2e-22   78.4   1.6    1.5  1  DUF1724   Domain of unknown function (DUF1724)
    1.4e-05   24.9   1.1    2.2e-05   24.2   0.1    1.9  2  HTH_5     Bacterial regulatory protein, arsR family
     0.0005   20.1   0.0     0.0043   17.1   0.0    2.3  2  HemN_C    HemN C-terminal domain
     0.0023   17.8   0.0     0.0048   16.8   0.0    1.5  1  MarR_2    MarR family
      0.004   17.1   0.0     0.0098   15.8   0.0    1.6  1  MarR      MarR family
     0.0072   16.4   0.0      0.015   15.4   0.0    1.4  1  HTH_20    Helix-turn-helix domain
  ------ inclusion threshold ------
      0.023   14.7   0.0      0.058   13.4   0.0    1.9  1  DUF1803   Domain of unknown function (DUF1803)
      0.072   13.6   0.0       0.23   12.0   0.0    1.8  2  HTH_27    Winged helix DNA-binding domain
      0.087   12.8   0.3       0.37   10.8   0.0    2.1  2  HTH_11    HTH domain
       0.12   12.2   0.0       0.27   11.1   0.0    1.6  1  TrmB      Sugar-specific transcriptional regulator TrmB


Domain annotation for each model (and alignments):
>> DUF1724  Domain of unknown function (DUF1724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.4   1.6   1.8e-25   3.2e-22       1      62 []     197     257 ..     197     257 .. 0.95

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 1.8e-25
                           DUF1724   1 tklyvydeeikplsltvtDkflslslfdkdgkydhk.dlisfdesAlkWGeeLFeyYlkrSep 62 
                                       t+lyv+d+   +l+++vtD+f+slsl++++g++d + dl+ fd+sAl+WG +LF+yY+++S++
  gi|298676123|ref|YP_003727873.1| 197 TSLYVLDDA--KLAFVVTDYFFSLSLYFENGRFDPHkDLLGFDDSALNWGDDLFNYYKNKSRE 257
                                       579***984..9************************9************************85 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.1   1.2e-08   2.2e-05       2      45 ..      14      57 ..      13      59 .. 0.96
   2 ?   -2.5   0.1       2.8   4.9e+03      36      45 ..     110     119 ..     106     121 .. 0.58

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.2e-08
                                      HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      ++R ++L+lL e++++ +e+ +++g+s + +S   k ++ea+L+
  gi|298676123|ref|YP_003727873.1| 14 EKRKELLFLLLEEPKSLSEIKNYFGVSSPEISPRIKEMEEANLI 57
                                      89****************************************98 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.8
                                       HHHHHHTTSE CS
                             HTH_5  36 LkkLreaGLV 45 
                                       L+ L ++ L+
  gi|298676123|ref|YP_003727873.1| 110 LSDLNNCELL 119
                                       5566666665 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.4e-06    0.0043      16      62 ..      23      68 ..      16      70 .. 0.89
   2 ?   -0.4   0.1      0.67   1.2e+03      26      58 ..      94     126 ..      91     131 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.4e-06
                            HemN_C 16 RlreGldlaafeqrfgldleellaaaleklqeqGLLeldggrlrltp 62
                                       l e  +l++++ +fg++ +++  + +++++e++L++ +++r++ t 
  gi|298676123|ref|YP_003727873.1| 23 LLEEPKSLSEIKNYFGVS-SPEISPRIKEMEEANLICKSDKRYHITS 68
                                      556666899********9.9999*********************996 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.67
                            HemN_C  26 feqrfgldleellaaaleklqeqGLLeldggrl 58 
                                       +++ + +d+ e+l   l +l +  LLe++ +++
  gi|298676123|ref|YP_003727873.1|  94 WKEHTLQDIPEELLERLSDLNNCELLEDSTEHI 126
                                       566666665555666688888888888888876 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.7e-06    0.0048      10      61 ..      19      63 ..      15      64 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.7e-06
                                      HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                            MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                      +L+ L  +p    + +e+  ++g+s + +s ++k++++a L+ ++    DkR
  gi|298676123|ref|YP_003727873.1| 19 LLFLLLEEPK---SLSEIKNYFGVSSPEISPRIKEMEEANLICKS----DKR 63
                                      7888888887...*****************************988....666 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   5.5e-06    0.0098      16      50 ..      26      60 ..      18      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.5e-06
                                      TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR 16 gplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      +p s+se+ + +gvs++ ++  ++++e+++li +s
  gi|298676123|ref|YP_003727873.1| 26 EPKSLSEIKNYFGVSSPEISPRIKEMEEANLICKS 60
                                      6789***************************9766 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   8.2e-06     0.015      12      54 ..      16      57 ..       7      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.2e-06
                                      HHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTE CS
                            HTH_20 12 RrrilraLaraegltaselaerldlskntlsyHLrvLeeagLv 54
                                      R ++l +L  +e+ ++se++  +++s  ++s +++++eea L+
  gi|298676123|ref|YP_003727873.1| 16 RKELLFLL-LEEPKSLSEIKNYFGVSSPEISPRIKEMEEANLI 57
                                      66666667.8*******************************98 PP

>> DUF1803  Domain of unknown function (DUF1803)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.2e-05     0.058      21      65 ..      22      67 ..      16     128 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.2e-05
                           DUF1803 21 LaehddviLRelkkeFa.dqkkldrlldelidaglikRenkrYkln 65
                                      L  ++   L e+k+ F  + ++++  + e+ +a+li +++krY+++
  gi|298676123|ref|YP_003727873.1| 22 LLLEEPKSLSEIKNYFGvSSPEISPRIKEMEEANLICKSDKRYHIT 67
                                      55556667999*****636789*********************985 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00013      0.23       9      59 ..      20      64 ..      16      69 .. 0.84
   2 ?   -3.2   0.0       6.9   1.2e+04      20      34 ..     184     198 ..     178     200 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                            HTH_27  9 LhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrre 59
                                      L+l+   +++k+l+++  +  v++  is  +k+++e+ L+    ++ d+r+
  gi|298676123|ref|YP_003727873.1| 20 LFLLL--EEPKSLSEIKNYFGVSSPEISPRIKEMEEANLI----CKSDKRY 64
                                      56666..89*******************************....6555554 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6.9
                            HTH_27  20 kladlcgrlnvedsh 34 
                                       + +++  +l+ e+++
  gi|298676123|ref|YP_003727873.1| 184 HTEQIQTYLDAESTS 198
                                       568888999999886 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00021      0.37       2      45 ..      16      57 ..      15      71 .. 0.77
   2 ?   -1.0   0.1      0.94   1.7e+03      26      37 ..     136     147 ..     136     149 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00021
                            HTH_11  2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvp 45
                                      ++ +l lLle+ +  s +e++ +++vS   +  +Ik++ee+ + 
  gi|298676123|ref|YP_003727873.1| 16 RKELLFLLLEEPK--SLSEIKNYFGVSSPEISPRIKEMEEANLI 57
                                      4566777766665..***********************999843 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.94
                            HTH_11  26 nvSrrtvrrdIk 37 
                                       n+S++tv++ + 
  gi|298676123|ref|YP_003727873.1| 136 NISKSTVVKGLS 147
                                       89*****99765 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00015      0.27      13      61 ..      19      66 ..       7      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
                                      HCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTE CS
                              TrmB 13 vYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpkl 61
                                        + Ll ++p++ +ei +  gv+ + +   ++++e++ l+ ++++r+++
  gi|298676123|ref|YP_003727873.1| 19 LLF-LLLEEPKSLSEIKNYFGVSSPEISPRIKEMEEANLICKSDKRYHI 66
                                      444.55699********************************99998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1869.89
//
Query:       gi|298676124|ref|YP_003727874.1|  [L=317]
Description: prenyltransferase UbiA [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-17   61.6   9.9    9.9e-17   61.1   9.9    1.2  1  UbiA      UbiA prenyltransferase family
  ------ inclusion threshold ------
        0.6   10.4   0.0        0.6   10.4   0.0    3.0  4  YwiC      YwiC-like protein


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.1   9.9   1.1e-20   9.9e-17      18     248 ..      66     296 ..      46     298 .. 0.74

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 1.1e-20
                              UbiA  18 dlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilgllll....alllnp 90 
                                       ++ + ll+++++ l++  +++l++ +D ++Da   ++ +     G   +k a++++++ +i+g ++l    ++l+ +
  gi|298676124|ref|YP_003727874.1|  66 NAHISLLTCFAGGLIIYTVYTLDRTLDSDEDAV--NRSEL---GGSY-KKVAFLVSLAAFIVGTSILimkgLYLIPF 136
                                       4456678888888********************..75555...5555.59*************99997787777777 PP

                              UbiA  91 ltallgllallly..vvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavflltwaialandl 165
                                       l +++g l+   +    Y+ l lK    ++++v+g+++g+++++ + +  +sl +l++++  +   l++   ++ d+
  gi|298676124|ref|YP_003727874.1| 137 LPFITGYLYSKGLkvGGYS-LKLKGGLGVKNLVVGLTWGVFITGIAGISINSLIPLFFIFIYFSSKLFINSTMF-DF 211
                                       7777777655443358888.999999999************997777765665444444444444555555555.** PP

                              UbiA 166 rdregDrkagiktlpvvlGrkaarillalllavllla.llllllalllllylllalllaalallraarlvrrrdakk 241
                                       +d +gD+ agiktlp+ lG+k+a++ll+ +l +++ + l++++++++  + ++++++++++++l+   + +  +++ 
  gi|298676124|ref|YP_003727874.1| 212 KDAKGDAMAGIKTLPLALGEKKAKNLLL-VLQLMSHMgLFVAVMFGYIAFEPVILIYSFIIGILYIREFSTPAENEP 287
                                       *************************433.233333336788888888888888888888888888777777777777 PP

                              UbiA 242 aakff..lf 248
                                       ++k+f  lf
  gi|298676124|ref|YP_003727874.1| 288 KRKRFkrLF 296
                                       777774444 PP

>> YwiC  YwiC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.3      0.15   1.4e+03      66      98 ..      53      85 ..      33      95 .. 0.61
   2 ?   -2.1   3.5       0.5   4.5e+03      55      87 ..     105     137 ..      58     147 .. 0.65
   3 ?   -3.2   0.1       1.1   9.8e+03      90      94 ..     189     193 ..     166     206 .. 0.48
   4 ?   10.4   0.0   6.7e-05       0.6      24      48 ..     242     266 ..     220     298 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.15
                              YwiC 66 avallllllalllqpallwwallflplvavavy 98
                                        al + l++lll++++ ++   +  l++  vy
  gi|298676124|ref|YP_003727874.1| 53 SGALRIYLALLLLNAHISLLTCFAGGLIIYTVY 85
                                      445555555566666555555544444444444 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.5
                              YwiC  55 arylkplliYgavallllllalllqpallwwal 87 
                                       + y+k +++  ++a ++++ +l+++   l++ l
  gi|298676124|ref|YP_003727874.1| 105 GSYKKVAFLVSLAAFIVGTSILIMKGLYLIPFL 137
                                       456666666666666666666666665444444 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 1.1
                              YwiC  90 lplva 94 
                                       +pl+ 
  gi|298676124|ref|YP_003727874.1| 189 IPLFF 193
                                       22222 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 6.7e-05
                              YwiC  24 pvwahllllvawlvgYlaffpllll 48 
                                       + + h+ l+va+++gY+af+p+ l+
  gi|298676124|ref|YP_003727874.1| 242 QLMSHMGLFVAVMFGYIAFEPVILI 266
                                       6788999**************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2013.03
//
Query:       gi|298676125|ref|YP_003727875.1|  [L=148]
Description: hypothetical protein Metev_2259 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 924.34
//
Query:       gi|298676126|ref|YP_003727876.1|  [L=377]
Description: pyridoxal-dependent decarboxylase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-29  103.2   0.0    5.5e-29  101.0   0.0    1.8  1  Pyridoxal_deC    Pyridoxal-dependent decarboxylase conserved 
    1.2e-10   41.1   0.0    2.2e-09   37.0   0.0    2.1  1  Aminotran_1_2    Aminotransferase class I and II
    4.1e-09   35.9   0.1    4.4e-08   32.5   0.0    1.9  2  Aminotran_5      Aminotransferase class-V
     0.0006   19.2   0.0     0.0008   18.8   0.0    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
     0.0039   16.5   0.0     0.0056   16.0   0.0    1.4  1  Beta_elim_lyase  Beta-eliminating lyase


Domain annotation for each model (and alignments):
>> Pyridoxal_deC  Pyridoxal-dependent decarboxylase conserved domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.0   0.0   1.5e-32   5.5e-29      62     355 ..      46     305 ..      27     320 .. 0.86

  Alignments for each domain:
  == domain 1  score: 101.0 bits;  conditional E-value: 1.5e-32
                                       HHHT-BTSSTTTSHHHHHHHHHHHHHHHHHTT--GGGTCCT-EEEEESSHHHHHHHHHHHHHHHHHHHHHHHTTTS. CS
                     Pyridoxal_deC  62 dainkngftweesPaltelevvvldwlaellglpeeflekegggvlqvgssestllallAartkvikemkekgkelk 138
                                       + i  n+ +    P +  le  v++++++ll+ +    +    g +++g++es++ al   r      m ++++   
  gi|298676126|ref|YP_003727876.1|  46 KFIEANMGDPGLFPGTYSLEKEVINMMGQLLHCS----S--VHGYITTGGTESNIQAL---R-----TMVNSSN--- 105
                                       55677777777789999*****************....3..4799*********9876...3.....3333332... PP

                                       HHHHHCCEEEEEETTS-HHHHHHHHHHT-EEEEE--BTTTBB-HHHHHHHHHHHHCTT.EEEEEEEEBS-TTT-BB- CS
                     Pyridoxal_deC 139 eaeildklvlytsdqahssvekaalvlgvklrvipldengklrgaalekaieedkekGlipffvvatlGttvlgaFd 215
                                           ++ +++   + ah s +k+a++lg++++  +ld ++k+   + + +i ++     ++   v ++G+t  g+ d
  gi|298676126|ref|YP_003727876.1| 106 ----VANPNVIVPESAHFSFDKIANILGIEVKKAELDSKFKVDIGSVKSLIDSN-----TI-GLVGIAGSTEFGQID 172
                                       ....45788888999******************************999999653.....34.56679********** PP

                                       -HHHHHHHHHHCT-EEEEE-TTGGGGGGSGGGGG...GGTTGGGESEEEEECCCCTS--SS-EEEEESSCCGCHHHH CS
                     Pyridoxal_deC 216 dlkelgdicekydlwlHvDAAyaGsaficpeirh...llkgieradSitvnphKlllvlldcsalivkdkealqqal 289
                                        ++ l di  + +l lHvDAA++G  f+ p+  +   +++ ++ + Si++ phK++  ++  + ++++++e+l++ l
  gi|298676126|ref|YP_003727876.1| 173 PINSLSDIALENNLYLHVDAAFGG--FVIPFLETsyhFDFVLDGVTSIALDPHKMGFSTIPSGGILFRNREDLNH-L 246
                                       ************************..****9876666************************************87.5 PP

                                       -EEECCCT.TTTTTSEECCCGSSSSSG.HHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                     Pyridoxal_deC 290 qleaeYLehedsdvaadlgtkaiplsr.rvrilklwfvlralGveglqnqirksvelakyleklirk 355
                                       q +  YL      ++++         r    ++  + v+  lG eg+++ ++++++l + l +  +k
  gi|298676126|ref|YP_003727876.1| 247 QTHTPYLT-----ISTQSSLT---GTRsGASVAATYAVMSYLGKEGYRQIVKQCMDLTNDLVEGAKK 305
                                       6999****.....66666544...44445667779**********************9998877665 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.0   6.2e-13   2.2e-09      44     361 ..      59     368 ..      33     370 .. 0.77

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 6.2e-13
                                       THHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHH..HTTT-EEEEEESS-THHHHHHHHTTSEEE CS
                     Aminotran_1_2  44 dglpeleealakflgrseklklkreaavvvgsGagaliealifllk..lnpgdeilvpdptyasyknilrlsggevv 118
                                        g ++le++++  +g  + l        ++++G+ ++i+al ++ +  + +  +++vp+  + s+++i+++ g+ev 
  gi|298676126|ref|YP_003727876.1|  59 PGTYSLEKEVINMMG--QLLHCSSVHGYITTGGTESNIQALRTMVNssNVANPNVIVPESAHFSFDKIANILGIEVK 133
                                       466788888888888..7777999999*****************9755445556*********************** PP

                                       EEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBS CS
                     Aminotran_1_2 119 ryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvf 195
                                       + +l+   +f++d+ +++ ++++       t +++    +   G++ + + l ++   a ++nl+l vD a++gfv 
  gi|298676126|ref|YP_003727876.1| 134 KAELD--SKFKVDIGSVKSLIDS------NTIGLVGIAGSTEFGQIDPINSLSDI---ALENNLYLHVDAAFGGFVI 199
                                       ***99..****************......56677777778899************...******************9 PP

                                       SSSHTHHHHGGSTTSTT.EEEEEESSSTTSSGGG-EEEEEEEH...............HHHHHHHHHHHHHTS.... CS
                     Aminotran_1_2 196 gsldavatranveeepn.llivgslsKafGlaGeRvGyilgna...............avvsqlrklsrpfls.... 252
                                                 ++e+  + ++++ ++ ++ +l    +G+ ++ +                        ++p+l     
  gi|298676126|ref|YP_003727876.1| 200 P---------FLETSYHfDFVLDGV-TSIALDPHKMGFSTIPSggilfrnredlnhlqT--------HTPYLTistq 258
                                       8.........333333335777777.477777777777777777777766544444431........2233323344 PP

                                       .....SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCS.CSSEEEEEETHHCHHHHHHH CS
                     Aminotran_1_2 253 .....ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasq.sgmflltdlsaetakelskk 323
                                            + +++ ++a+ +  + l ++   + +++  +++  l+++ +++g++ l+++  ++++l + ++     l   
  gi|298676126|ref|YP_003727876.1| 259 ssltgTRSGASVAATYAVMSYLGKEGYRQIVKQCMDLTNDLVEGAKKIGINPLIEPvMNVVTLDVQDPD---TLRAR 332
                                       212244444444444444444444489999999999999999999999****99999999999999999...89999 PP

                                       HHHTCTEEEEEGGGGTSTTEEEEEC.TTS-HHHHHHHHH CS
                     Aminotran_1_2 324 LleevgvyvtpgtsftvpgrlRitv.Aglteeeleelve 361
                                       L++e+g yv+  + +     lR+ + ++lt+++l+ +++
  gi|298676126|ref|YP_003727876.1| 333 LRDEFGWYVSITRNP---RALRLVLmPHLTHKNLDLFLQ 368
                                       *********995555...59*****9*******998776 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.0   1.2e-11   4.4e-08      55     178 ..      75     194 ..      59     225 .. 0.85
   2 ?    1.3   0.0     0.037   1.3e+02     250     294 ..     262     306 ..     230     323 .. 0.82

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 1.2e-11
                                       HHT-STGGGEEEESSHHHHHHHHHHHCCCC.-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGG CS
                       Aminotran_5  55 linaeseeeiiftsGtteainlvalslars.lkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldld 130
                                       l++ +s    + t G+te++  +++++ +s   +  +++v e+ h +      ++a+  g++vk+++ld++ ++d+ 
  gi|298676126|ref|YP_003727876.1|  75 LLHCSS-VHGYITTGGTESNIQALRTMVNSsNVANPNVIVPESAHFSFD----KIANILGIEVKKAELDSKFKVDIG 146
                                       555665.444568899995555555555555999999****99999877....99999******************* PP

                                       GHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TT CS
                       Aminotran_5 131 elekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaq 178
                                        +++l++ +t  +   + s++ G i+p++++ ++a +++ +++vDaa 
  gi|298676126|ref|YP_003727876.1| 147 SVKSLIDSNTIGLVGIAGSTEFGQIDPINSLSDIALENNLYLHVDAAF 194
                                       *******9999999999*****************************95 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.037
                                       .SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTS CS
                       Aminotran_5 250 aGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlksl 294
                                        GT   a++ +  a++ yl + g+++i k+   l++ l+e+ k++
  gi|298676126|ref|YP_003727876.1| 262 TGTRSGASVAATYAVMSYLGKEGYRQIVKQCMDLTNDLVEGAKKI 306
                                       488889999999999999999999999999999998888876665 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   2.2e-07    0.0008      37     146 ..      79     193 ..      25     196 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.2e-07
                                       T-SEEEEESSHHHHHHHHHHH...TTTT..TT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG- CS
                   DegT_DnrJ_EryC1  37 gvkhaiavssGtaAlhlaLra...lgvg..pgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaai 108
                                        + h   ++ Gt+++  aLr       +  ++  VIvp    ++  + +  lg ++  ++ d   + +d  +++++i
  gi|298676126|ref|YP_003727876.1|  79 SSVHGYITTGGTESNIQALRTmvnS--SnvANPNVIVPESAHFSFDKIANILGIEVKKAELD-SKFKVDIGSVKSLI 152
                                       4556667889999999999996431..245699*****************************.89************ PP

                                       -TTE...EEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-T CS
                   DegT_DnrJ_EryC1 109 tert...kaIlpVhlyGqvadmdalkaiaakhglkvieDaA 146
                                        ++t    +I     +Gq+  +++l +ia + +l++  DaA
  gi|298676126|ref|YP_003727876.1| 153 DSNTiglVGIAGSTEFGQIDPINSLSDIALENNLYLHVDAA 193
                                       ****88888888899*************************9 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.6e-06    0.0056      32     169 ..      59     193 ..      38     323 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.6e-06
                                       HHHHHHHHHHHHHTT-SEEEE......ES-HHHHHHHHHHHH--T....TEEEEEETT-HHHHSSTTHHHHCC--EE CS
                   Beta_elim_lyase  32 ktvnrLedavaelfgkeaalf......vpqGtaAnsillkillqr....geevivtepahihfdetgaiaelagvkl 98 
                                       ++++ Le++v +++g            ++ Gt +n  +l++++++    +++viv e ah+ fd   +i    g+++
  gi|298676126|ref|YP_003727876.1|  59 PGTYSLEKEVINMMGQLLHCSsvhgyiTTGGTESNIQALRTMVNSsnvaNPNVIVPESAHFSFDKIANI---LGIEV 132
                                       56677777777766644333234444488999999999977774412226799999********88777...67777 PP

                                       EEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEET CS
                   Beta_elim_lyase  99 rdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgA 169
                                       ++++ +++ k+d+ +++++i+      + i+l+ ++  ++   Gq+     ++ +++ia ++++ lh+D+A
  gi|298676126|ref|YP_003727876.1| 133 KKAELDSKFKVDIGSVKSLIDS-----NTIGLVGIAGSTEF--GQID---PINSLSDIALENNLYLHVDAA 193
                                       777777777*************.....589**********9..9875...566678999***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2507.93
//
Query:       gi|298676128|ref|YP_003727877.1|  [L=400]
Description: orc1/cdc6 family replication initiation protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-18   65.7   0.1    5.9e-18   64.6   0.1    1.6  1  Cdc6_C           CDC6, C terminal winged helix domain
    3.5e-11   43.8   0.0    2.6e-10   41.0   0.0    2.3  2  AAA_16           AAA ATPase domain
    4.4e-10   40.0   0.0    8.7e-10   39.0   0.0    1.4  1  AAA_22           AAA domain
    6.2e-07   29.9   0.0    1.7e-06   28.5   0.0    1.8  1  AAA              ATPase family associated with various cellul
      1e-06   28.9   0.2    2.2e-06   27.8   0.2    1.6  1  ATPase_2         ATPase domain predominantly from Archaea
    8.2e-06   25.4   0.0    1.5e-05   24.5   0.0    1.4  1  TniB             Bacterial TniB protein
    1.2e-05   24.6   0.0    2.4e-05   23.6   0.0    1.4  1  DUF815           Protein of unknown function (DUF815)
    0.00026   21.0   0.0    0.00041   20.3   0.0    1.3  1  NACHT            NACHT domain
     0.0022   16.9   0.3       0.41    9.4   0.0    2.3  2  AAA_32           AAA domain
      0.003   17.1   0.0     0.0088   15.6   0.0    1.8  2  AAA_7            P-loop containing dynein motor region
     0.0043   17.4   0.2      0.019   15.3   0.2    2.2  1  RNA_helicase     RNA helicase
      0.006   15.6   0.0      0.036   13.0   0.0    2.1  2  Kinesin          Kinesin motor domain
     0.0061   16.9   0.0      0.017   15.5   0.0    1.7  1  AAA_assoc_2      AAA C-terminal domain
     0.0069   16.4   0.2      0.048   13.7   0.0    2.3  3  ResIII           Type III restriction enzyme, res subunit
     0.0077   15.9   0.0       0.02   14.6   0.0    1.7  1  Sigma54_activat  Sigma-54 interaction domain
     0.0088   15.3   0.0       0.02   14.1   0.0    1.7  2  PIF1             PIF1-like helicase
  ------ inclusion threshold ------
      0.013   15.5   0.1       0.67   10.0   0.0    2.7  2  AAA_5            AAA domain (dynein-related subfamily)
      0.019   14.2   0.0      0.023   13.9   0.0    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.019   14.2   0.0      0.036   13.4   0.0    1.4  1  Zeta_toxin       Zeta toxin
      0.061   13.4   0.0       0.17   12.0   0.0    1.7  1  AAA_2            AAA domain (Cdc48 subfamily)
      0.063   13.3   0.0       0.12   12.4   0.0    1.6  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.083   13.2   0.0       0.19   12.1   0.0    1.7  1  AAA_19           AAA domain
       0.09   12.5   0.0       0.17   11.6   0.0    1.5  1  AAA_24           AAA domain
      0.097   12.4   0.0       0.17   11.6   0.0    1.4  1  AAA_11           AAA domain


Domain annotation for each model (and alignments):
>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.6   0.1   7.9e-21   5.9e-18       1      83 [.     304     384 ..     304     385 .. 0.95

  Alignments for each domain:
  == domain 1  score: 64.6 bits;  conditional E-value: 7.9e-21
                                       HHHHHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSS CS
                            Cdc6_C   1 LcalvlllrksgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLnvd 77 
                                       L+ +++l++ ++k+ +ttgev ++Y+++C+   vd+l++++vs+++ eL+mlg++++  + kG r grtr i++n +
  gi|298676128|ref|YP_003727877.1| 304 LLGIIELHK-DQKKNCTTGEVVQKYQQICNINSVDALSRTRVSKMIGELDMLGLINAPLKTKGIR-GRTRTITINKH 378
                                       667899999.******************************************************7.**********9 PP

                                       CHHHHH CS
                            Cdc6_C  78 pddvle 83 
                                        d +++
  gi|298676128|ref|YP_003727877.1| 379 IDVMEN 384
                                       998875 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.0   3.5e-13   2.6e-10       1      60 [.      27      94 ..      27     173 .. 0.84
   2 ?   -2.0   0.0       5.5   4.1e+03      90     107 ..     203     238 ..     181     273 .. 0.49

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 3.5e-13
                            AAA_16  1 rlvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekd.......ggif..lrgkc 60
                                      rl+ R+ ++eq+++++e+v sg+   + +++G  G+GK+++vr +l++l+k+       +  +  +  +c
  gi|298676128|ref|YP_003727877.1| 27 RLIARDSQIEQIAELVEPVLSGEKpDNAFIYGKTGTGKTAVVRYVLKELQKElstdnssH--VmpIFINC 94
                                      6899********************9*************************9966665431..22244444 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.5
                            AAA_16  90 esaeleawrekleeala..................a 107
                                       + + +++++e+l++ l+                   
  gi|298676128|ref|YP_003727877.1| 203 NFSFPPYDAEQLTQILNdraeiafnedvldnmvipL 238
                                       444555555555555553333333333333333332 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.0   1.2e-12   8.7e-10       8     115 ..      54     164 ..      49     185 .. 0.81

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 1.2e-12
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv..fvtlpsstsskdllrellralglelka..erlsseelle 80 
                                        +++G +GtGKT ++r +l++l++e   ++++++v+  f+++++ ++ + +l+e+ + ++ + k   ++ s +e+++
  gi|298676128|ref|YP_003727877.1|  54 AFIYGKTGTGKTAVVRYVLKELQKE-LSTDNSSHVMpiFINCNEIGNTSHVLHEIIKTVDFNYKIpsSGISISEYYR 129
                                       689******************9654.444456666677********99999999999999655548889******** PP

                            AAA_22  81 aleqalraravielliiDEaqhlrs.eealeeLrsl 115
                                       +l+  l++     +++ DE++hl + +++l +L++ 
  gi|298676128|ref|YP_003727877.1| 130 HLWWVLNKNNYSIIVVFDEIEHL-KdDNVLYNLSRA 164
                                       ******99999899999******.659999988654 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   2.3e-09   1.7e-06       3     125 ..      56     201 ..      54     208 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 2.3e-09
                                       EESSTTSSHHHHHHHHHHHH..........THEEEEEETTTCSSS......................STTHHHHHHH CS
                               AAA   3 lyGppGtGKTllakavakel..........gvefleisgsellsk......................yvgesekkir 47 
                                       +yG  GtGKT++++ v kel          +v  + i++ e+ +                        ++e  +++ 
  gi|298676128|ref|YP_003727877.1|  56 IYGKTGTGKTAVVRYVLKELqkelstdnssHVMPIFINCNEIGNTshvlheiiktvdfnykipssgiSISEYYRHLW 132
                                       8******************94444443322355789999999977899999*******9988877666666666666 PP

                                       HHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS.SSTEEEEEEESS...GGGSTHHHH CS
                               AAA  48 elfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk.eskvivigatnr...pdkldpall 120
                                        ++++   ++   i+++DEi+ l  ++          v+  L ++ + +k + + ++ +ig+tn+    d++dp ++
  gi|298676128|ref|YP_003727877.1| 133 WVLNK---NNYSIIVVFDEIEHLKDDN----------VLYNLSRAGEYMKVNpNVNIGIIGTTNDlmlKDQIDPRVM 196
                                       66654...33249**********5555..........7888888777777766667999******999999999999 PP

                                       STTSS CS
                               AAA 121 rgRfd 125
                                       ++ ++
  gi|298676128|ref|YP_003727877.1| 197 SSLAQ 201
                                       54444 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.2   2.9e-09   2.2e-06       6     172 ..      33     188 ..      28     228 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 2.9e-09
                          ATPase_2   6 kelkelee....ilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkkl 78 
                                         ++++ e    +l+ e+ +  fiYG  g GKta+++ ++++l++         +l+++++s++   + + +e  + 
  gi|298676128|ref|YP_003727877.1|  33 SQIEQIAElvepVLSGEKPDNAFIYGKTGTGKTAVVRYVLKELQK---------ELSTDNSSHVMPIFINCNEIGNT 100
                                       555555551111567899999*********************944.........57777777777666655666666 PP

                          ATPase_2  79 ekalgiavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnliesltke 155
                                       + +l + ++++ ++  + +    + ++   l   ++k+   ii+++De+  l+    +   +++++L ++ e+   +
  gi|298676128|ref|YP_003727877.1| 101 SHVLHEIIKTVDFNYKIPSSGISISEYYRHLWWVLNKNNYSIIVVFDEIEHLK----D--DNVLYNLSRAGEYMKVN 171
                                       6777777777777655557777899****************************....4..77888998888888777 PP

                          ATPase_2 156 khlcvviclsSeglfie 172
                                        ++ + i+++ + l+++
  gi|298676128|ref|YP_003727877.1| 172 PNVNIGIIGTTNDLMLK 188
                                       77766666666655554 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0     2e-08   1.5e-05      21     132 ..      36     153 ..      26     195 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2e-08
                              TniB  21 erLeeLley.pkrkrmpnlllvGdsnnGKtmivekFarlhppekded.aekvpvlvvqappkpdekrlyaaiLealg 95 
                                       e+++eL+e   + +++ n+ ++G++ +GKt++v+   ++ ++e ++d +++v  + +++ +  ++++  ++i++++ 
  gi|298676128|ref|YP_003727877.1|  36 EQIAELVEPvLSGEKPDNAFIYGKTGTGKTAVVRYVLKELQKELSTDnSSHVMPIFINCNEIGNTSHVLHEIIKTVD 112
                                       455555554255778899****************99988887755541456666789******************99 PP

                              TniB  96 aplkara...rvskleqqvlrllrelkvrvL.iiDEihnll 132
                                        ++k      ++s+ +++   +l++ +  ++ ++DEi++l 
  gi|298676128|ref|YP_003727877.1| 113 FNYKIPSsgiSISEYYRHLWWVLNKNNYSIIvVFDEIEHLK 153
                                       99887664567899999999*****999987257****986 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   3.2e-08   2.4e-05      28      80 ..      26      78 ..      14     114 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3.2e-08
                            DUF815 28 ddLvgidkqkealventeqfleglpannvLLwGarGtGKSslvkallneyaee 80
                                      ++L+  d+q e++ e +e  l+g++  n++++G+ GtGK ++v+ +l+e+++e
  gi|298676128|ref|YP_003727877.1| 26 ERLIARDSQIEQIAELVEPVLSGEKPDNAFIYGKTGTGKTAVVRYVLKELQKE 78
                                      679999*******************************************9987 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   5.4e-07   0.00041       4      97 ..      55     156 ..      52     169 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 5.4e-07
                                       EEEC-TTTCHHHHHHHHHHHHCTS-SCCCC.-SEEEEEETTTTTTS-..........-HCHHHCCCCTS--SSS-CC CS
                             NACHT   4 ilqGeaGsGKTtLlqklalawaegklpqga.fklvFflslrelsrsgna.......rsladllfsqlpepaapvsev 72 
                                       ++ G+ G GKT+ ++ +  +++++    +  + +++f+++ e+   + +         + + + s +  +++  ++ 
  gi|298676128|ref|YP_003727877.1|  55 FIYGKTGTGKTAVVRYVLKELQKELSTDNSsHVMPIFINCNEIGNTSHVlheiiktVDFNYKIPSSGISISEYYRHL 131
                                       799******************99876665558999********999888766655555566666666666666666* PP

                                       HHHHCCSCCCEEEEEE-STT-SS-T CS
                             NACHT  73 wavllelperlLlilDglDelvtdl 97 
                                       w vl ++  ++  ++D ++ l++d+
  gi|298676128|ref|YP_003727877.1| 132 WWVLNKNNYSIIVVFDEIEHLKDDN 156
                                       *********************9976 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   0.00055      0.41      32      60 ..      53      81 ..      48      87 .. 0.90
   2 ?    5.2   0.1      0.01       7.8     481     507 ..     254     280 ..     245     285 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00055
                            AAA_32 32 NifvlGesgtGrttlvkrlleeiakkept 60
                                      N f+ G++gtG+t +v+ +l+e +k+ +t
  gi|298676128|ref|YP_003727877.1| 53 NAFIYGKTGTGKTAVVRYVLKELQKELST 81
                                      89********************9998766 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.01
                            AAA_32 481 adllrEAdywakkegaevveaehVekA 507
                                        +ll+ A ++ak+e++ vv++ehV kA
  gi|298676128|ref|YP_003727877.1| 254 LKLLENAGTIAKHENSPVVTEEHVYKA 280
                                       589*********************999 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.2e-05    0.0088      35      61 ..      53      79 ..      33     112 .. 0.76
   2 ?   -2.7   0.0       4.7   3.5e+03     159     180 ..     186     206 ..     149     207 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-05
                             AAA_7 35 pvllvGptGtGKtviikdllkkldkek 61
                                      + +++G+tGtGKt++++ +lk+l+ke 
  gi|298676128|ref|YP_003727877.1| 53 NAFIYGKTGTGKTAVVRYVLKELQKEL 79
                                      67899**************99999653 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.7
                             AAA_7 159 gggrneitpRllrhfnvlaite 180
                                          + +i+pR+++  +  ++++
  gi|298676128|ref|YP_003727877.1| 186 ML-KDQIDPRVMSSLAQHNFSF 206
                                       33.4789999998888777766 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   2.6e-05     0.019       2      34 ..      55      87 ..      54     176 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.6e-05
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsv 34
                                      ++yG++g+GK+ +++++ k+l+k+l ++++++v
  gi|298676128|ref|YP_003727877.1| 55 FIYGKTGTGKTAVVRYVLKELQKELSTDNSSHV 87
                                      79**********************987776665 PP

>> Kinesin  Kinesin motor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   4.9e-05     0.036      55      89 ..      30      65 ..       5     116 .. 0.79
   2 ?   -0.6   0.0      0.64   4.8e+02     269     296 ..     194     220 ..     193     223 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.9e-05
                                      HHHHHHHHHHHHHHHHHTTSE.EEEEEEESTTSSHH CS
                           Kinesin 55 qeevyeetakplvesvleGyn.atifaYGqtgsGKT 89
                                       ++ + e +++lve vl+G +    f YG+tg+GKT
  gi|298676128|ref|YP_003727877.1| 30 ARDSQIEQIAELVEPVLSGEKpDNAFIYGKTGTGKT 65
                                      4455556679*********983579**********9 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.64
                                       HHHHHHHHTCCTSTSCGGGSHHHHHTGG CS
                           Kinesin 269 rvisaLaekkkskhipYRdSkLTrlLqd 296
                                       rv+s+La++ + ++ pY   +LT++L+d
  gi|298676128|ref|YP_003727877.1| 194 RVMSSLAQH-NFSFPPYDAEQLTQILND 220
                                       689999999.89999***********87 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.2e-05     0.017      13      54 ..     240     280 ..     233     294 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.2e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXX CS
                       AAA_assoc_2  13 ealaeladGDaRkaLnlLElaaeaaeakegkieitledleea 54 
                                       +ala+  +GDaR aL+lLE a + a++ e++ ++t+e++ +a
  gi|298676128|ref|YP_003727877.1| 240 SALAAKEHGDARIALKLLENAGTIAKH-ENSPVVTEEHVYKA 280
                                       67888889***********99999986.88899999988765 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   6.5e-05     0.048       4      53 ..      30      80 ..      27      92 .. 0.83
   2 ?   -0.9   0.0         2   1.5e+03     130     148 ..     138     156 ..     124     182 .. 0.71
   3 ?   -2.3   0.0       5.1   3.8e+03     132     146 ..     301     315 ..     239     339 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.5e-05
                                      E-HHHHHHHHHHT.......TTSEEEEEESTTSTHHHHHHHHHHHH-S... CS
                            ResIII  4 lreyQeeaienlleklks.krdkrglikmaTGtGKTlvaaklierllkkgk 53
                                       r+ Q+e i +l+e + s ++  +++i   TGtGKT v   + ++l+k+ +
  gi|298676128|ref|YP_003727877.1| 30 ARDSQIEQIAELVEPVLSgEKPDNAFIYGKTGTGKTAVVRYVLKELQKELS 80
                                      58999999999998776558888***************9999999888765 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2
                                       TTT-SEEEEETGGGTTS.T CS
                            ResIII 130 rdrfdviiiDEaHrlgakk 148
                                       ++++ ++++DE  +l++++
  gi|298676128|ref|YP_003727877.1| 138 NNYSIIVVFDEIEHLKDDN 156
                                       5666799999999998864 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 5.1
                                       T-SEEEEETGGGTTS CS
                            ResIII 132 rfdviiiDEaHrlga 146
                                       ++ ++ i E H+ ++
  gi|298676128|ref|YP_003727877.1| 301 KIVLLGIIELHKDQK 315
                                       222222334444444 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.7e-05      0.02       2      61 ..      29      97 ..      28     108 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.7e-05
                                      ---SHHHHHHHHHHHHHCTSS..S-EEEECSTTSSHHHHHHHHHH.....HSTTTTS..-EEEEETTTS CS
                   Sigma54_activat  2 igesealkelleqikkvaktd..lsvlitGesGtGKellaraihe.....askrkek..pfvavncaai 61
                                      i+++++++++ e ++ v + +   + +i G++GtGK+ + r + +      s+ +++    + +nc +i
  gi|298676128|ref|YP_003727877.1| 29 IARDSQIEQIAELVEPVLSGEkpDNAFIYGKTGTGKTAVVRYVLKelqkeLSTDNSShvMPIFINCNEI 97
                                      6788899999999999986554489****************9988555542222222113356777766 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   2.6e-05      0.02       6      49 ..      34      78 ..      30     161 .. 0.78
   2 ?   -2.4   0.0       2.7     2e+03     226     280 ..     177     234 ..     147     247 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.6e-05
                                      HHHHHHHH.......HCTS-EEEEESTTSSCHHHHHHHHHHCHCT CS
                              PIF1  6 Qkkvfdaiieavln.ekgklfFvtGsgGtgKtflwkallkklrse 49
                                      Q + + + +e vl+ ek+ + F++G  GtgKt + + +lk l++e
  gi|298676128|ref|YP_003727877.1| 34 QIEQIAELVEPVLSgEKPDNAFIYGKTGTGKTAVVRYVLKELQKE 78
                                      4444555557666659****************9999888888764 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.7
                                       ...................HHCHCCS---S.S--...........EEEESSCCHHHHH CS
                              PIF1 226 alieiPedlllkksedk..ieeivsevygd.llqeltdkeyleerailcptnedvdei 280
                                        +i   +dl+lk++ d+  +++++++ +     +  + ++ l++ra+++ +++  d++
  gi|298676128|ref|YP_003727877.1| 177 GIIGTTNDLMLKDQIDPrvMSSLAQHNFSFpPYDAEQLTQILNDRAEIAFNEDVLDNM 234
                                       4566667777777765522455555555544445555666677777776666655554 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00089      0.67       3      28 ..      55      80 ..      53      89 .. 0.87
   2 ?    2.5   0.1      0.18   1.4e+02      68     124 ..     143     186 ..     125     199 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00089
                                      EEE--SSSSHHHHHHHGGGGBS--EE CS
                             AAA_5  3 lLvGppGtgKselaerlaaalnreve 28
                                      ++ G++GtgK+ +++++++ l++e+ 
  gi|298676128|ref|YP_003727877.1| 55 FIYGKTGTGKTAVVRYVLKELQKELS 80
                                      799***************99988765 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.18
                                       EEEEESGGG--.HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS-- CS
                             AAA_5  68 ilvlDEverae.sevlnsLlslleerrllleeggelvkaknddllerfrviatanpld 124
                                       i+v+DE+e+++ ++vl  L +            ge++k++++    ++ +i+t+n+l+
  gi|298676128|ref|YP_003727877.1| 143 IVVFDEIEHLKdDNVLYNLSR-----------AGEYMKVNPN---VNIGIIGTTNDLM 186
                                       455555555554444444433...........3344444443...2255666666655 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.1e-05     0.023       4     136 ..      54     185 ..      51     260 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.1e-05
                           DUF2075   4 vlVtGvaGtGKtvvllnllael.....eddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnls 75 
                                        ++ G++GtGKt v   +l el     +d++++   +    N +++    + l +  +  +++ ++  +   i ++ 
  gi|298676128|ref|YP_003727877.1|  54 AFIYGKTGTGKTAVVRYVLKELqkelsTDNSSHVMPI--FINCNEIGNTSHVLHEIIKTVDFNYKIPSSGISISEYY 128
                                       79********************776433333444444..44555554444444443333334444444433333333 PP

                           DUF2075  76 efkka.eekkeepkedvvivDEAhrlltksdqaekqseenqlkelmkr.akvvvalvDegQel 136
                                         ++     ++++   +v++DE   l + +      ++     e mk   +v + +++    l
  gi|298676128|ref|YP_003727877.1| 129 --RHLwWVLNKNNYSIIVVFDEIEHLKDDNVL----YNLSRAGEYMKVnPNVNIGIIGTTNDL 185
                                       ..222044455555566778887777773333....333344444554334666666555555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.8e-05     0.036      10      42 ..      45      77 ..      36      89 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.8e-05
                        Zeta_toxin 10 ypsqerPklillgGqpGAGKselaellkdeler 42
                                      + s+e+P+  ++ G +G GK+++ +++ +el++
  gi|298676128|ref|YP_003727877.1| 45 VLSGEKPDNAFIYGKTGTGKTAVVRYVLKELQK 77
                                      56789*************************983 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00022      0.17       7      82 ..      55     154 ..      50     165 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00022
                                       EEE--TTSSHHHHHHHHHHHTT-..........-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS....... CS
                             AAA_2   7 lllgptgvGktelakalaellfv......kkekkliradaselleeeevehlvsrligappgyvgaeegG....... 70 
                                        + g+tg+Gkt + + + + l+       +++   i ++++e+      +h++ + i + +++ +   +G       
  gi|298676128|ref|YP_003727877.1|  55 FIYGKTGTGKTAVVRYVLKELQKelstdnSSHVMPIFINCNEIGN---TSHVLHEIIKTVDFNYKIPSSGisiseyy 128
                                       5789********666555555544444433444446678888877...99*************************** PP

                                       ..............EEEEETGGG--- CS
                             AAA_2  71 ..............ivllDEidKihp 82 
                                                     iv +DEi+  + 
  gi|298676128|ref|YP_003727877.1| 129 rhlwwvlnknnysiIVVFDEIEHLKD 154
                                       **********************8776 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00016      0.12       6      46 ..      34      78 ..      29     129 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00016
                                      HHHHHHHHHHHCH....TEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                              TsaE  6 etealgkklakal....gdvilLeGdLGaGKTtlvrglakalgve 46
                                      ++e++++ +  +l     d  +++G+ G+GKT+ vr ++k+l+ e
  gi|298676128|ref|YP_003727877.1| 34 QIEQIAELVEPVLsgekPDNAFIYGKTGTGKTAVVRYVLKELQKE 78
                                      55566666655556544456999*****************99765 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00025      0.19      11      42 ..      52      83 ..      45     164 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00025
                            AAA_19 11 kvllvtaGpGtGKTrvlkhivallvelggvkp 42
                                      ++ ++ +  GtGKT v++ ++++l+++ + + 
  gi|298676128|ref|YP_003727877.1| 52 DNAFIYGKTGTGKTAVVRYVLKELQKELSTDN 83
                                      5778999******************9987754 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00023      0.17       4      79 ..      53     154 ..      50     168 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                            AAA_24   4 kiliyGpsgiGKTtlakel.gpkplfidtekGlksldadkfpdie.......swedfldevvel............. 59 
                                       + +iyG+ g+GKT +++   ++    + t+++++ +    f +++        + +++++v+++             
  gi|298676128|ref|YP_003727877.1|  53 NAFIYGKTGTGKTAVVRYVlKELQKELSTDNSSHVMPI--FINCNeigntshVLHEIIKTVDFNykipssgisisey 127
                                       568**************998777778888888866532..2233334444443333333333337778888888888 PP

                            AAA_24  60 ......aaeladyktl.viDtidelee 79 
                                               ++++y+++ v+D i++l +
  gi|298676128|ref|YP_003727877.1| 128 yrhlwwVLNKNNYSIIvVFDEIEHLKD 154
                                       888888666666766515688888765 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00023      0.17      18      44 ..      50      78 ..      31     107 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                            AAA_11 18 e..itliqGPPGtgKTktivellsqllsr 44
                                      +   + i G+ GtgKT ++ ++l++l ++
  gi|298676128|ref|YP_003727877.1| 50 KpdNAFIYGKTGTGKTAVVRYVLKELQKE 78
                                      244789********************433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.70u 0.33s 00:00:01.03 Elapsed: 00:00:00.53
# Mc/sec: 2271.23
//
Query:       gi|298676129|ref|YP_003727878.1|  [L=323]
Description: transposase IS4 family protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.8e-21   74.9   0.1    8.1e-21   73.8   0.1    1.6  1  DUF772       Transposase domain (DUF772)
    2.1e-12   47.1   1.8    5.4e-12   45.8   1.8    1.7  1  DDE_Tnp_1    Transposase DDE domain
    0.00017   21.3   0.1    0.00047   19.9   0.1    1.7  1  DDE_Tnp_4    DDE superfamily endonuclease
     0.0011   19.0   0.2     0.0033   17.4   0.1    1.8  2  DDE_Tnp_1_3  Transposase DDE domain


Domain annotation for each model (and alignments):
>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.8   0.1   1.8e-24   8.1e-21       1      70 [.      60     129 ..      60     135 .. 0.92

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 1.8e-24
                            DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlf 70 
                                       Grp +++ +mlk+l+lq+++glSd e+e+++ +++sfr fl +    + +pd +t + fRkr+++    ++++
  gi|298676129|ref|YP_003727878.1|  60 GRPEADVIVMLKMLILQQWHGLSDQEIEKQCIDRISFRHFLKFP---EYIPDSTTVWLFRKRIIDtnkEKEVW 129
                                       9*****************************************96...88**************9988766555 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   1.8   1.2e-15   5.4e-12       6     214 .]     146     311 ..     142     311 .. 0.88

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 1.2e-15
                         DDE_Tnp_1   6 vlivDattvrvpgtk................edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglk 66 
                                       + i Dat++     +                +d+ w +k gk+++gyklh+++dt   li ++++t++ vhd+k+  
  gi|298676129|ref|YP_003727878.1| 146 GMIQDATFIHSDPGHagadkprgseaktrrnKDGTWAKKSGKSHFGYKLHTIIDTDYQLIRRFETTTATVHDNKVDL 222
                                       566688888765555788888888888888899*****************************************733 PP

                         DDE_Tnp_1  67 qlldelrprkgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnk 143
                                             r  ++ +v++D+GY++ ++  + +                           ++ ++ r+++l  ++++rn 
  gi|298676129|ref|YP_003727878.1| 223 S-----R--ENEVVYRDKGYFGSKCCGYDA---------------------------TMQRAVRGRPLGIREILRNS 265
                                       3.....4..9***********777766666...........................79****************** PP

                         DDE_Tnp_1 144 skkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                                                +++ +R + Erv +  k +f+ + + + +  rv +++l++++ +nl
  gi|298676129|ref|YP_003727878.1| 266 -------------------------RISAIRVTGERVYAVTKGVFKSGTTLVTTVKRVNLKMLFTAFGFNL 311
                                       .........................********************************99999998877765 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   1.1e-07   0.00047      25     132 ..     187     286 ..     165     304 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.1e-07
                         DDE_Tnp_4  25 kkkntlkvlivvdpngkiifvskgypGsvsDkeilensgllkalkeavkpgdvilaDkgFklsekllvpykk..... 96 
                                       k++ ++k+  ++d +++ i   +  ++ v+D+++    +l++       +++v+  Dkg+ +s+  ++ y+      
  gi|298676129|ref|YP_003727878.1| 187 KSHFGYKLHTIIDTDYQLIRRFETTTATVHDNKV----DLSR-------ENEVVYRDKGYFGSK--CCGYDAtmqra 250
                                       7777999999999999999999999999999887....4443.......4589999********..55554455556 PP

                         DDE_Tnp_4  97 kkkkqlseeevefnraiasarihvErvigrlkgrfr 132
                                        ++ +l  +e  +n++i+ +r++ Erv +  kg f+
  gi|298676129|ref|YP_003727878.1| 251 VRGRPLGIREILRNSRISAIRVTGERVYAVTKGVFK 286
                                       9********************************998 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   7.4e-07    0.0033      35      95 ..     181     239 ..     145     249 .. 0.78
   2 ?   -1.7   0.0      0.59   2.7e+03      96     116 ..     280     301 ..     271     308 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 7.4e-07
                       DDE_Tnp_1_3  35 rGkssmGWfyGfkLhliindkGeila.vkltpgnvdDrepveelakellgklfaDkgyiskk 95 
                                       + k s    +G+kLh ii+   ++++ ++ t++ v+D++    l++e  + ++ Dkgy + k
  gi|298676129|ref|YP_003727878.1| 181 WAKKSGKSHFGYKLHTIIDTDYQLIRrFETTTATVHDNKVD--LSRE-NEVVYRDKGYFGSK 239
                                       4455555679*********9999985389999999998763..5655.789*******9876 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.59
                       DDE_Tnp_1_3  96 laeelleegielitklrk.nmk 116
                                       +++ ++++g +l+t++++ n+k
  gi|298676129|ref|YP_003727878.1| 280 VTKGVFKSGTTLVTTVKRvNLK 301
                                       5667888999999998752444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1981.85
//
Query:       gi|298676130|ref|YP_003727879.1|  [L=1084]
Description: CnaB domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.5e-257  836.8 109.3    2.2e-37  127.7   4.0    8.2  8  SdrD_B           SdrD B-like domain
    1.4e-72  239.9  44.7    1.8e-09   37.8   1.2    8.7  8  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
      1e-27   96.2   0.0     0.0034   17.4   0.0    8.3  8  bMG3             Bacterial alpha-2-macroglobulin MG3 domain
    1.7e-25   88.8  40.0     0.0048   16.9   0.2    8.5  8  CarbopepD_reg_2  CarboxypepD_reg-like domain
      2e-16   60.1  69.5    1.6e-05   25.1   0.6   10.2  8  SpaA             Prealbumin-like fold domain
    1.4e-12   47.6   4.4      0.088   12.9   0.0    6.7  7  UDP-g_GGTase     UDP-glucose:Glycoprotein Glucosyltransferase
    1.4e-12   48.1  10.4        3.6    8.4   0.0    8.7  8  TTR-52           Transthyretin-like family
    2.7e-11   43.9   7.7        0.7   10.4   0.1    5.9  5  AdenylateSensor  Adenylate sensor of SNF1-like protein kinase
    3.5e-11   43.3  14.0        3.6    7.7   0.0    8.3  8  DUF2012          Protein of unknown function (DUF2012)
    3.6e-06   27.0  35.3       0.18   11.8   0.3    8.1  8  phage_tail_N     Prophage tail fibre N-terminal
    0.00028   20.8   3.4         14    5.8   0.0    5.5  5  DUF2025          Protein of unknown function (DUF2025)
    0.00062   19.3  17.5          1    8.7   0.0    7.1  8  Dioxygenase_C    Dioxygenase
     0.0025   18.0  40.8      0.098   12.9   0.1    9.3  9  MetallophosN     N terminal of Calcineurin-like phosphoestera
     0.0026   17.9   0.6    1.6e+02    2.6   0.0    5.8  6  HupF_HypC        HupF/HypC family
     0.0031   17.5  42.6       0.56   10.3   0.1   10.3 11  Big_1            Bacterial Ig-like domain (group 1)
  ------ inclusion threshold ------
       0.03   14.4  18.9        6.9    6.8   0.0    8.0  8  DUF3244          Domain of unknown function (DUF3244)
      0.033   14.1  10.6         50    3.9   0.0    6.4  6  PEGA             PEGA domain
      0.035   12.9  38.2       0.57    8.9   1.2    5.9  6  PLRV_ORF5        Potato leaf roll virus readthrough protein
       0.05   13.6   7.5         25    5.0   0.0    5.7  5  CooC_C           CS1-pili formation C-terminal
      0.084   12.6   0.4        5.6    6.8   0.1    3.1  2  Glyco_hydro_42C  Beta-galactosidase C-terminal domain
       0.66    9.9  28.2          7    6.6   0.1    7.2  8  EMP24_GP25L      emp24/gp25L/p24 family/GOLD


Domain annotation for each model (and alignments):
>> SdrD_B  SdrD B-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.7   4.0   2.6e-40   2.2e-37       1     112 []     162     273 ..     162     273 .. 0.98
   2 !  109.2   9.7   1.5e-34   1.3e-31       1     112 []     283     392 ..     283     392 .. 0.94
   3 !  101.7   7.8   3.1e-32   2.6e-29       2     112 .]     397     506 ..     396     506 .. 0.94
   4 !  104.8   6.4   3.4e-33   2.9e-30       1     112 []     510     618 ..     510     618 .. 0.94
   5 !  111.3   6.4   3.3e-35   2.8e-32       2     112 .]     623     731 ..     622     731 .. 0.93
   6 !  107.7   6.0   4.2e-34   3.6e-31       1     112 []     735     844 ..     735     844 .. 0.96
   7 !  113.4   8.6   7.3e-36   6.2e-33       1     112 []     848     957 ..     848     957 .. 0.93
   8 !  106.1   4.6   1.3e-33   1.1e-30       1     103 [.     961    1061 ..     961    1067 .. 0.91

  Alignments for each domain:
  == domain 1  score: 127.7 bits;  conditional E-value: 2.6e-40
                            SdrD_B   1 asiGdfVweDanknGiqdagekgisgvtVtLkdakgevv.atttTdasGkYkFtnltpGeYkVeftapagytvtakk 76 
                                       as+Gd+Vw+D+nkn iqd++e g +gvtV+L++ +g+++ atttTd++G+Y+Ftnl+pG+Y+V+ft p ++++t ++
  gi|298676130|ref|YP_003727879.1| 162 ASLGDYVWNDMNKNDIQDDEEVGLTGVTVNLYNCSGDSLrATTTTDENGYYNFTNLEPGNYYVNFTIPPEFEFTLQD 238
                                       58*************************************99************************************ PP

                            SdrD_B  77 aGsddaldSdadpatgltktvtlasgesnetidaGl 112
                                       aG d+ +dSd++++tg+t+++ lasge+n tidaGl
  gi|298676130|ref|YP_003727879.1| 239 AGPDN-IDSDVNSTTGNTSCIILASGENNDTIDAGL 273
                                       **887.7****************************7 PP

  == domain 2  score: 109.2 bits;  conditional E-value: 1.5e-34
                            SdrD_B   1 asiGdfVweDanknGiqdagekgisgvtVtLkdakgevv.atttTdasGkYkFtnltpGeYkVeftapagytvtakk 76 
                                       a+iGd+VweD+n+nGiqd+ge gis++ VtL + +++++ ++ttTda+G+Y+Ft +tpG+Y+V+f+ ++gy++t+++
  gi|298676130|ref|YP_003727879.1| 283 ATIGDRVWEDSNGNGIQDDGELGISDIIVTLHNCSDDTIvSSTTTDADGYYNFT-VTPGSYYVNFS-SDGYVFTSAN 357
                                       58*****************************8877777769************9.9*********5.68******** PP

                            SdrD_B  77 aGsddaldSdadpatgltktvtlasgesnetidaGl 112
                                       +G+dd +dSda++ +g+t++v+l+++e+n t+daGl
  gi|298676130|ref|YP_003727879.1| 358 QGTDDGVDSDANS-SGITDCVNLDNNETNYTVDAGL 392
                                       **********976.77******************97 PP

  == domain 3  score: 101.7 bits;  conditional E-value: 3.1e-32
                            SdrD_B   2 siGdfVweDanknGiqdagekgisgvtVtLkd.akgevvatttTdasGkYkFtnltpGeYkVeftapagytvtakka 77 
                                       siGd+VweD n++Giq++g++gi +vt++L+d ++g+++a+ tTd +G Y+Ft+l+pG+Y+V+f+ap+gy++t   +
  gi|298676130|ref|YP_003727879.1| 397 SIGDYVWEDVNADGIQNDGNTGIGNVTINLYDcDTGNKIANNTTDVDGDYNFTGLSPGNYYVNFEAPHGYEFTILGQ 473
                                       8*****************************872567788************************************** PP

                            SdrD_B  78 GsddaldSdadpatgltktvtlasgesnetidaGl 112
                                       G++ + d +a+   g+t+++tl sge+n tid+Gl
  gi|298676130|ref|YP_003727879.1| 474 GANYE-DNNANI-LGNTTCITLVSGENNDTIDVGL 506
                                       ***99.999875.66999***************96 PP

  == domain 4  score: 104.8 bits;  conditional E-value: 3.4e-33
                            SdrD_B   1 asiGdfVweDanknGiqdagekgisgvtVtLkdakgevv.atttTdasGkYkFtnltpGeYkVeftapagytvtakk 76 
                                       a+iGdfVweD++k+G+qd ge+gisg tV+L++ +++++ ++t+T+asG+Y+F+ +tpG+Y+V+f+ ++gy++t+++
  gi|298676130|ref|YP_003727879.1| 510 ATIGDFVWEDSDKDGVQDPGETGISGLTVELYNCSTDELeSSTITNASGYYNFS-VTPGNYYVQFS-SDGYNFTQAN 584
                                       58*******************************99999989************8.9*********5.68*******9 PP

                            SdrD_B  77 aGsddaldSdadpatgltktvtlasgesnetidaGl 112
                                       + s+d +dSdad+ +g+t+++t+ sge+netidaGl
  gi|298676130|ref|YP_003727879.1| 585 KESED-VDSDADS-SGNTTCITVVSGETNETIDAGL 618
                                       99887.6****86.67999****************7 PP

  == domain 5  score: 111.3 bits;  conditional E-value: 3.3e-35
                            SdrD_B   2 siGdfVweDanknGiqdagekgisgvtVtLkdakgevv.atttTdasGkYkFtnltpGeYkVeftapagytvtakka 77 
                                        iGdfVweD++ +Giqd+ge+gi ++ V+L++ +++ + ++ttT++sG+Y+Ft ++pGeY+V+f+ ++gy++t +++
  gi|298676130|ref|YP_003727879.1| 623 MIGDFVWEDSDMDGIQDDGETGIPDIRVELYNCSTDNLvSNTTTNNSGYYNFT-VEPGEYYVNFS-SDGYEFTLQNQ 697
                                       69****************************8866555549************9.9*********5.68********* PP

                            SdrD_B  78 GsddaldSdadpatgltktvtlasgesnetidaGl 112
                                       G +d++dSda++ +g+t+++tl+s+e+n tidaGl
  gi|298676130|ref|YP_003727879.1| 698 GGEDTVDSDANS-SGVTECITLESNETNDTIDAGL 731
                                       *********976.77*******************7 PP

  == domain 6  score: 107.7 bits;  conditional E-value: 4.2e-34
                            SdrD_B   1 asiGdfVweDanknGiqdagekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapagytvtakka 77 
                                       asiGd+VweD n++G+q++g++gi++vtV+L++ +g+ ++tt T++sG+Y+Ft+l+pG+Y+++f+ + gy++t   +
  gi|298676130|ref|YP_003727879.1| 735 ASIGDYVWEDVNGDGVQNDGDTGIDNVTVNLYNCNGDFLETTKTNESGYYNFTGLAPGDYYINFIDSPGYEFTILGQ 811
                                       68*************************************************************************** PP

                            SdrD_B  78 GsddaldSdadpatgltktvtlasgesnetidaGl 112
                                       G+  + d +ad   g+t+++tl sge+n tidaGl
  gi|298676130|ref|YP_003727879.1| 812 GASYE-DNNADL-LGNTTCITLVSGENNDTIDAGL 844
                                       *9998.989875.56999****************7 PP

  == domain 7  score: 113.4 bits;  conditional E-value: 7.3e-36
                            SdrD_B   1 asiGdfVweDanknGiqdagekgisgvtVtLkdakgevv.atttTdasGkYkFtnltpGeYkVeftapagytvtakk 76 
                                       a+iGdfVweD+nknG+qd ge+gisg tV+L++ +++ + ++ttT+asG+Y+F+ ++pGeY+V+f+ ++gy++t ++
  gi|298676130|ref|YP_003727879.1| 848 ATIGDFVWEDTNKNGKQDIGESGISGLTVELYNCSTDDLvSNTTTNASGYYNFS-VEPGEYYVNFS-SDGYEFTLAN 922
                                       58*****************************8877666659************8.9*********5.68******** PP

                            SdrD_B  77 aGsddaldSdadpatgltktvtlasgesnetidaGl 112
                                       +G+d+++dSdad+ +g+t+++t++sge+n t+daGl
  gi|298676130|ref|YP_003727879.1| 923 QGVDNTVDSDADS-SGNTTCITVESGETNDTVDAGL 957
                                       ***********86.6799****************97 PP

  == domain 8  score: 106.1 bits;  conditional E-value: 1.3e-33
                            SdrD_B    1 asiGdfVweDanknGiqdagekgisgvtVtLkdakgevv.atttTdasGkYkFtnltpGeYkVeftapagytvta 74  
                                        a+iGdfVweD+nknG+qd ge+gisg tV+L++ +++++ ++ttT+asG+Y+F+ +tpG+Y+V+f+ ++gy++t+
  gi|298676130|ref|YP_003727879.1|  961 ATIGDFVWEDTNKNGKQDIGESGISGLTVELYNCSTDELeSSTTTNASGYYNFS-VTPGSYYVQFS-SDGYEFTS 1033
                                        58*******************************99999989************8.9*********5.68****** PP

                            SdrD_B   75 kkaGsddaldSdadpatgltktvtlasge 103 
                                        +++G+dd++dSdad+ +g+t+++t++ ++
  gi|298676130|ref|YP_003727879.1| 1034 SNQGTDDSMDSDADS-SGNTTCITVEIRR 1061
                                        *************87.5688888887764 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.1   1.7e-11   1.5e-08       8      56 ..     179     228 ..     176     249 .. 0.87
   2 !   33.0   0.8   6.2e-11   5.3e-08      10      60 ..     302     352 ..     292     391 .. 0.85
   3 !   29.3   0.2   8.7e-10   7.4e-07      10      64 ..     415     470 ..     411     506 .. 0.79
   4 !   37.8   1.2   2.1e-12   1.8e-09       6      61 ..     525     580 ..     524     617 .. 0.84
   5 !   33.3   0.4   5.3e-11   4.5e-08       8      62 ..     639     693 ..     637     726 .. 0.88
   6 !   29.3   0.2   8.8e-10   7.5e-07       8      59 ..     752     804 ..     749     821 .. 0.90
   7 !   33.8   0.9   3.5e-11     3e-08      12      63 ..     869     920 ..     864     963 .. 0.79
   8 !   35.9   0.8   7.7e-12   6.6e-09      12      63 ..     982    1033 ..     977    1053 .. 0.87

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 1.7e-11
                   CarboxypepD_reg   8 dasgapiagatVtvtn.adtgtvastttdadGafrlrglppgtysvtvsa 56 
                                       d    +++g+tV ++n ++++ +a+tttd++G++++++l+pg+y v ++ 
  gi|298676130|ref|YP_003727879.1| 179 DDEEVGLTGVTVNLYNcSGDSLRATTTTDENGYYNFTNLEPGNYYVNFTI 228
                                       6677899*********778899************************9875 PP

  == domain 2  score: 33.0 bits;  conditional E-value: 6.2e-11
                   CarboxypepD_reg  10 sgapiagatVtvtn.adtgtvastttdadGafrlrglppgtysvtvsapGya 60 
                                          +i+   Vt+ n +d++ v+stttdadG+++++ ++pg+y v +s++Gy 
  gi|298676130|ref|YP_003727879.1| 302 GELGISDIIVTLHNcSDDTIVSSTTTDADGYYNFT-VTPGSYYVNFSSDGYV 352
                                       445789999****97788889*************9.**************96 PP

  == domain 3  score: 29.3 bits;  conditional E-value: 8.7e-10
                   CarboxypepD_reg  10 sgapiagatVtvtnadtg.tvastttdadGafrlrglppgtysvtvsapGyatatr 64 
                                        +++i ++t+ +++ dtg + a+ ttd dG+++++gl pg+y v ++ap   ++t+
  gi|298676130|ref|YP_003727879.1| 415 GNTGIGNVTINLYDCDTGnKIANNTTDVDGDYNFTGLSPGNYYVNFEAPHGYEFTI 470
                                       56799*********6665278***************************98887776 PP

  == domain 4  score: 37.8 bits;  conditional E-value: 2.1e-12
                   CarboxypepD_reg   6 VtdasgapiagatVtvtn.adtgtvastttdadGafrlrglppgtysvtvsapGyat 61 
                                       V d+  ++i+g tV+++n + ++ ++st t+a+G+++++ ++pg+y v++s++Gy  
  gi|298676130|ref|YP_003727879.1| 525 VQDPGETGISGLTVELYNcSTDELESSTITNASGYYNFS-VTPGNYYVQFSSDGYNF 580
                                       88999*************5566789*************7.***************73 PP

  == domain 5  score: 33.3 bits;  conditional E-value: 5.3e-11
                   CarboxypepD_reg   8 dasgapiagatVtvtn.adtgtvastttdadGafrlrglppgtysvtvsapGyata 62 
                                       d   ++i+  +V+++n + ++ v++ttt+++G+++++ ++pg+y v +s++Gy+ +
  gi|298676130|ref|YP_003727879.1| 639 DDGETGIPDIRVELYNcSTDNLVSNTTTNNSGYYNFT-VEPGEYYVNFSSDGYEFT 693
                                       667789**********777899**************9.***************754 PP

  == domain 6  score: 29.3 bits;  conditional E-value: 8.8e-10
                   CarboxypepD_reg   8 dasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtv.sapGy 59 
                                       +  +++i ++tV ++n ++++  +t+t+++G+++++gl+pg+y + +  +pGy
  gi|298676130|ref|YP_003727879.1| 752 NDGDTGIDNVTVNLYNCNGDFLETTKTNESGYYNFTGLAPGDYYINFiDSPGY 804
                                       556789**************************************998677777 PP

  == domain 7  score: 33.8 bits;  conditional E-value: 3.5e-11
                   CarboxypepD_reg  12 apiagatVtvtn.adtgtvastttdadGafrlrglppgtysvtvsapGyatat 63 
                                        +i+g tV+++n + ++ v++ttt+a+G+++++ ++pg+y v +s++Gy+ + 
  gi|298676130|ref|YP_003727879.1| 869 SGISGLTVELYNcSTDDLVSNTTTNASGYYNFS-VEPGEYYVNFSSDGYEFTL 920
                                       579*********667789**************7.***************8433 PP

  == domain 8  score: 35.9 bits;  conditional E-value: 7.7e-12
                   CarboxypepD_reg   12 apiagatVtvtn.adtgtvastttdadGafrlrglppgtysvtvsapGyatat 63  
                                         +i+g tV+++n + ++ ++sttt+a+G+++++ ++pg+y v++s++Gy+ ++
  gi|298676130|ref|YP_003727879.1|  982 SGISGLTVELYNcSTDELESSTTTNASGYYNFS-VTPGSYYVQFSSDGYEFTS 1033
                                        579*********5566789*************7.***************8554 PP

>> bMG3  Bacterial alpha-2-macroglobulin MG3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.4e-05     0.012      28      60 ..     185     218 ..     180     264 .. 0.86
   2 !    7.9   0.0    0.0036       3.1      28      61 ..     306     340 ..     301     370 .. 0.74
   3 !   10.2   0.0    0.0007       0.6      28      60 ..     419     452 ..     413     482 .. 0.84
   4 ?    6.3   0.0     0.012       9.8      28      59 ..     533     565 ..     530     590 .. 0.85
   5 !    9.5   0.0    0.0012         1      28      59 ..     645     677 ..     639     703 .. 0.81
   6 !   17.4   0.0     4e-06    0.0034      28      60 ..     758     790 ..     753     808 .. 0.91
   7 !    8.6   0.0    0.0021       1.8      28      59 ..     871     903 ..     868     935 .. 0.79
   8 !    8.2   0.0    0.0029       2.5      28      59 ..     984    1016 ..     981    1042 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.4e-05
                              bMG3  28 vagaeVrlldkkgevl.aegtTDaqGvarfaall 60 
                                       ++g++V+l++++g+ l a++tTD++G+++f++l+
  gi|298676130|ref|YP_003727879.1| 185 LTGVTVNLYNCSGDSLrATTTTDENGYYNFTNLE 218
                                       689*************668899********9884 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0036
                              bMG3  28 vagaeVrlldkkgevla.egtTDaqGvarfaalla 61 
                                       ++++ V+l +++++++  ++tTDa+G+++f+ +  
  gi|298676130|ref|YP_003727879.1| 306 ISDIIVTLHNCSDDTIVsSTTTDADGYYNFTVTPG 340
                                       578889****999887516789********98744 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.0007
                              bMG3  28 vagaeVrlld.kkgevlaegtTDaqGvarfaall 60 
                                       + +++++l+d ++g+ +a+ tTD +G ++f++l+
  gi|298676130|ref|YP_003727879.1| 419 IGNVTINLYDcDTGNKIANNTTDVDGDYNFTGLS 452
                                       679*******5579****************9984 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.012
                              bMG3  28 vagaeVrlldkkgevlaegt.TDaqGvarfaal 59 
                                       ++g +V+l++++ ++l + t T+a+G+++f+ +
  gi|298676130|ref|YP_003727879.1| 533 ISGLTVELYNCSTDELESSTiTNASGYYNFSVT 565
                                       6899************97655********9876 PP

  == domain 5  score: 9.5 bits;  conditional E-value: 0.0012
                              bMG3  28 vagaeVrlldkkge.vlaegtTDaqGvarfaal 59 
                                       +++++V+l++++ + ++ ++tT+++G+++f+ +
  gi|298676130|ref|YP_003727879.1| 645 IPDIRVELYNCSTDnLVSNTTTNNSGYYNFTVE 677
                                       799*******876515667899********976 PP

  == domain 6  score: 17.4 bits;  conditional E-value: 4e-06
                              bMG3  28 vagaeVrlldkkgevlaegtTDaqGvarfaall 60 
                                       + +++V+l++++g+ l +++T+++G+++f++l+
  gi|298676130|ref|YP_003727879.1| 758 IDNVTVNLYNCNGDFLETTKTNESGYYNFTGLA 790
                                       679**************************9874 PP

  == domain 7  score: 8.6 bits;  conditional E-value: 0.0021
                              bMG3  28 vagaeVrlldkkg.evlaegtTDaqGvarfaal 59 
                                       ++g +V+l++++  +++ ++tT+a+G+++f+ +
  gi|298676130|ref|YP_003727879.1| 871 ISGLTVELYNCSTdDLVSNTTTNASGYYNFSVE 903
                                       68999*****875156678899********977 PP

  == domain 8  score: 8.2 bits;  conditional E-value: 0.0029
                              bMG3   28 vagaeVrlldkkgevlae.gtTDaqGvarfaal 59  
                                        ++g +V+l++++ ++l + +tT+a+G+++f+ +
  gi|298676130|ref|YP_003727879.1|  984 ISGLTVELYNCSTDELESsTTTNASGYYNFSVT 1016
                                        6899************862678*******9876 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.2   6.6e-06    0.0056      13      50 ..     184     226 ..     177     229 .. 0.72
   2 !   14.7   0.6   2.6e-05     0.022      27      56 ..     324     352 ..     317     375 .. 0.87
   3 !    7.1   0.3    0.0062       5.3      25      52 ..     435     462 ..     412     471 .. 0.83
   4 !   16.9   0.2   5.6e-06    0.0048      20      58 ..     544     581 ..     527     602 .. 0.82
   5 !   15.9   0.4   1.1e-05    0.0095      22      57 ..     658     692 ..     647     711 .. 0.85
   6 !    8.7   0.3     0.002       1.7      13      50 ..     757     798 ..     745     806 .. 0.72
   7 !   16.3   0.4   8.4e-06    0.0072      23      57 ..     885     918 ..     871     940 .. 0.83
   8 !   16.8   0.3   5.8e-06    0.0049      20      58 ..     995    1032 ..     984    1050 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.6e-06
                   CarbopepD_reg_2  13 plpgatVyvkg.....tkkgtvTdenGnFelknlpagkytLvv 50 
                                        l g+tV + +      ++ t+TdenG+++++nl++g+y +++
  gi|298676130|ref|YP_003727879.1| 184 GLTGVTVNLYNcsgdsLRATTTTDENGYYNFTNLEPGNYYVNF 226
                                       566666655432222256899******************8877 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.6e-05
                   CarbopepD_reg_2  27 gtvTdenGnFelknlpagkytLvvsyvGyk 56 
                                        t+Td++G+++++ +++g y +++s+ Gy 
  gi|298676130|ref|YP_003727879.1| 324 STTTDADGYYNFT-VTPGSYYVNFSSDGYV 352
                                       69**********7.999***********96 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0062
                   CarbopepD_reg_2  25 kkgtvTdenGnFelknlpagkytLvvsy 52 
                                        ++ +Td +G ++++ l +g+y +++++
  gi|298676130|ref|YP_003727879.1| 435 IANNTTDVDGDYNFTGLSPGNYYVNFEA 462
                                       46789*****************999876 PP

  == domain 4  score: 16.9 bits;  conditional E-value: 5.6e-06
                   CarbopepD_reg_2  20 yvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktq 58 
                                       +  + +  t+T+++G+++++ +++g+y +++s+ Gy+  
  gi|298676130|ref|YP_003727879.1| 544 STDELESSTITNASGYYNFS-VTPGNYYVQFSSDGYNFT 581
                                       56677889***********6.999************864 PP

  == domain 5  score: 15.9 bits;  conditional E-value: 1.1e-05
                   CarbopepD_reg_2  22 kgtkkgtvTdenGnFelknlpagkytLvvsyvGykt 57 
                                        +   +t+T+ +G+++++ +++g+y +++s+ Gy+ 
  gi|298676130|ref|YP_003727879.1| 658 DNLVSNTTTNNSGYYNFT-VEPGEYYVNFSSDGYEF 692
                                       556679***********7.***************85 PP

  == domain 6  score: 8.7 bits;  conditional E-value: 0.002
                   CarbopepD_reg_2  13 plpgatVyvkgtk....kgtvTdenGnFelknlpagkytLvv 50 
                                        +  +tV + + +      t T+e+G+++++ l +g+y +++
  gi|298676130|ref|YP_003727879.1| 757 GIDNVTVNLYNCNgdflETTKTNESGYYNFTGLAPGDYYINF 798
                                       555555555443333336788*****************8875 PP

  == domain 7  score: 16.3 bits;  conditional E-value: 8.4e-06
                   CarbopepD_reg_2  23 gtkkgtvTdenGnFelknlpagkytLvvsyvGykt 57 
                                       +   +t+T+++G+++++ +++g+y +++s+ Gy+ 
  gi|298676130|ref|YP_003727879.1| 885 DLVSNTTTNASGYYNFS-VEPGEYYVNFSSDGYEF 918
                                       55678***********6.***************85 PP

  == domain 8  score: 16.8 bits;  conditional E-value: 5.8e-06
                   CarbopepD_reg_2   20 yvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktq 58  
                                        +  + +  t+T+++G+++++ +++g y +++s+ Gy+  
  gi|298676130|ref|YP_003727879.1|  995 STDELESSTTTNASGYYNFS-VTPGSYYVQFSSDGYEFT 1032
                                        56677889***********6.999************864 PP

>> SpaA  Prealbumin-like fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   1.2   1.1e-07   9.4e-05       3      59 ..     182     225 ..     180     232 .. 0.84
   2 !    7.8   2.9    0.0046         4      28      58 ..     303     344 ..     230     356 .. 0.63
   3 !   25.1   0.6   1.9e-08   1.6e-05       2      68 ..     415     467 ..     402     471 .. 0.88
   4 ?    5.3   0.9     0.029        25       3      59 ..     530     572 ..     527     613 .. 0.88
   5 !    7.8   0.2    0.0049       4.2       2      58 ..     641     683 ..     630     684 .. 0.87
   6 !   14.2   5.8   4.8e-05     0.041       8      58 ..     689     796 ..     687     802 .. 0.55
   7 !    7.7   2.2    0.0051       4.3      20      58 ..     860     909 ..     800     910 .. 0.67
   8 ?    3.1   6.9      0.14   1.2e+02      18      59 ..     971    1023 ..     913    1033 .. 0.53

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.1e-07
                                       CCB-TS-EEEEEETTTSCCCHCHHTT.TTCCEESEEE-BTTSEEEEEEEESEEEEEE CS
                              SpaA   3 gkpLaGaeFtlykvdtttdgkdaleakktgtevttlttdenGkatfegLplGtYllv 59 
                                       +  L G++  ly+++              ++  +t ttdenG+ +f++L++G+Y++ 
  gi|298676130|ref|YP_003727879.1| 182 EVGLTGVTVNLYNCS-------------GDSLRATTTTDENGYYNFTNLEPGNYYVN 225
                                       567899999999999.............35678999*******************96 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0046
                                       T.............TTCCEESEEE-BTTSEEEEEEEESEEEEE CS
                              SpaA  28 a............kktgtevttlttdenGkatfegLplGtYll 58 
                                       +              ++t v + ttd++G+ +f+ + +G+Y++
  gi|298676130|ref|YP_003727879.1| 303 ElgisdiivtlhnCSDDTIVSSTTTDADGYYNFT-VTPGSYYV 344
                                       03333344444443455666999***********.99****98 PP

  == domain 3  score: 25.1 bits;  conditional E-value: 1.9e-08
                                       CCCB-TS-EEEEEETTTSCCCHCHHTT.TTCCEESEEE-BTTSEEEEEEEESEEEEEEEEE-STTEE CS
                              SpaA   2 tgkpLaGaeFtlykvdtttdgkdaleakktgtevttlttdenGkatfegLplGtYllvEtkaPegYv 68 
                                       +++ + +++  ly++d             tg+++++ ttd +G  +f+gL +G+Y++   +aP gY+
  gi|298676130|ref|YP_003727879.1| 415 GNTGIGNVTINLYDCD-------------TGNKIANNTTDVDGDYNFTGLSPGNYYVN-FEAPHGYE 467
                                       5677777888888888.............89*************************97.88999997 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.029
                                       CCB-TS-EEEEEETTTSCCCHCHHTT.TTCCEESEEE-BTTSEEEEEEEESEEEEEE CS
                              SpaA   3 gkpLaGaeFtlykvdtttdgkdaleakktgtevttlttdenGkatfegLplGtYllv 59 
                                       ++ ++G + +ly+++             t++   +  t++ G+ +f+ + +G+Y+++
  gi|298676130|ref|YP_003727879.1| 530 ETGISGLTVELYNCS-------------TDELESSTITNASGYYNFS-VTPGNYYVQ 572
                                       577889999999999.............456667777**********.99*****96 PP

  == domain 5  score: 7.8 bits;  conditional E-value: 0.0049
                                       CCCB-TS-EEEEEETTTSCCCHCHHTT.TTCCEESEEE-BTTSEEEEEEEESEEEEE CS
                              SpaA   2 tgkpLaGaeFtlykvdtttdgkdaleakktgtevttlttdenGkatfegLplGtYll 58 
                                       +++ +++++ +ly+++             t++ v + tt++ G+ +f+ +++G+Y++
  gi|298676130|ref|YP_003727879.1| 641 GETGIPDIRVELYNCS-------------TDNLVSNTTTNNSGYYNFT-VEPGEYYV 683
                                       5667777777888888.............7899***************.******98 PP

  == domain 6  score: 14.2 bits;  conditional E-value: 4.8e-05
                                       S-EEEEEET............................TTSCCCHCHHTT.TTCCEE..................... CS
                              SpaA   8 GaeFtlykv............................dtttdgkdaleakktgtev..................... 35 
                                       G eFtl+++                            +                 +                     
  gi|298676130|ref|YP_003727879.1| 689 GYEFTLQNQggedtvdsdanssgvtecitlesnetndT-----------------Idaglyqpasigdyvwedvngd 748
                                       66788887733333333333333333333322222220.................2333334444444444444444 PP

                                       .........................SEEE-BTTSEEEEEEEESEEEEE CS
                              SpaA  36 .........................ttlttdenGkatfegLplGtYll 58 
                                                                +t +t+e G+ +f+gL++G+Y++
  gi|298676130|ref|YP_003727879.1| 749 gvqndgdtgidnvtvnlyncngdflETTKTNESGYYNFTGLAPGDYYI 796
                                       4444444445555555555555555*********************98 PP

  == domain 7  score: 7.7 bits;  conditional E-value: 0.0051
                                       CCCHCHHTT.............TTCCEESEEE-BTTSEEEEEEEESEEEEE CS
                              SpaA  20 tdgkdalea............kktgtevttlttdenGkatfegLplGtYll 58 
                                       ++gk+++++              t++ v + tt++ G+ +f+ +++G+Y++
  gi|298676130|ref|YP_003727879.1| 860 KNGKQDIGEsgisgltvelynCSTDDLVSNTTTNASGYYNFS-VEPGEYYV 909
                                       4444444445555566666554478999**************.******98 PP

  == domain 8  score: 3.1 bits;  conditional E-value: 0.14
                                        TSCCCHCHHTT.............TTCCEESEEE-BTTSEEEEEEEESEEEEEE CS
                              SpaA   18 tttdgkdalea............kktgtevttlttdenGkatfegLplGtYllv 59  
                                        t+++gk+++++              t++   + tt++ G+ +f+ + +G+Y+++
  gi|298676130|ref|YP_003727879.1|  971 TNKNGKQDIGEsgisgltvelynCSTDELESSTTTNASGYYNFS-VTPGSYYVQ 1023
                                        2333333333344444444444433455559999**********.9******96 PP

>> UDP-g_GGTase  UDP-glucose:Glycoprotein Glucosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.79   6.8e+02      14      52 ..     186     225 ..     176     259 .. 0.84
   2 ?    4.1   0.0     0.057        48      24      54 ..     317     347 ..     304     381 .. 0.69
   3 !   12.9   0.0    0.0001     0.088      13      89 ..     533     608 ..     525     613 .. 0.75
   4 !    7.8   0.0    0.0041       3.5      18      72 ..     650     702 ..     636     725 .. 0.66
   5 ?   -1.9   0.0       4.1   3.5e+03      29      59 ..     773     804 ..     755     833 .. 0.73
   6 !    6.8   0.0    0.0085       7.2      13      54 ..     871     912 ..     863     950 .. 0.68
   7 !    9.1   0.0    0.0016       1.3      13      69 ..     984    1036 ..     976    1064 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.79
                                       TT-EEEEE-SS-S-SEEEE--SGGGEEEEEE.-SEEEEEE CS
                      UDP-g_GGTase  14 rGlqleLgtekkksvaDTivmanlGYfQlka.nPGvwkle 52 
                                        G++++L + + +s+  T+     GY+ +   +PG + ++
  gi|298676130|ref|YP_003727879.1| 186 TGVTVNLYNCSGDSLRATTTTDENGYYNFTNlEPGNYYVN 225
                                       699999999999999999999999****975489999776 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.057
                                       S-S-SEEEE--SGGGEEEEEE-SEEEEEEE- CS
                      UDP-g_GGTase  24 kkksvaDTivmanlGYfQlkanPGvwklelr 54 
                                       ++++++ ++     GY+ +  +PG + ++ +
  gi|298676130|ref|YP_003727879.1| 317 SDDTIVSSTTTDADGYYNFTVTPGSYYVNFS 347
                                       33444444444556************98875 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 0.0001
                                       -TT-EEEEE-SS-S-SEEEE--SGGGEEEEEE-SEEEEEEE-TTHHHHHEEEEE--SS-S..--TT--.--EEEE-S CS
                      UDP-g_GGTase  13 prGlqleLgtekkksvaDTivmanlGYfQlkanPGvwklelregrssdiyeiesvgaegl..sspkde.gkevvlts 86 
                                        +Gl++eL + ++++++ +++ +  GY+ +  +PG + ++ +    sd y+++++++e+   +s  d+ g++  +t 
  gi|298676130|ref|YP_003727879.1| 533 ISGLTVELYNCSTDELESSTITNASGYYNFSVTPGNYYVQFS----SDGYNFTQANKESEdvDSDADSsGNTTCITV 605
                                       5799****9999999999999999**************9985....7888888886665421333333466666665 PP

                                       TT- CS
                      UDP-g_GGTase  87 feg 89 
                                       ++g
  gi|298676130|ref|YP_003727879.1| 606 VSG 608
                                       555 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.0041
                                       EEEE-SS-S-SEEEE--SGGGEEEEEE-SEEEEEEE-TTHHHHHEEEEE--SS-S CS
                      UDP-g_GGTase  18 leLgtekkksvaDTivmanlGYfQlkanPGvwklelregrssdiyeiesvgaegl 72 
                                       +eL + ++++++  +  +n GY+ +  +PG + ++ ++      ++++++g e++
  gi|298676130|ref|YP_003727879.1| 650 VELYNCSTDNLVSNTTTNNSGYYNFTVEPGEYYVNFSSD--GYEFTLQNQGGEDT 702
                                       566554444545555679**************9998732..23355666655553 PP

  == domain 5  score: -1.9 bits;  conditional E-value: 4.1
                                       EEEE--SGGGEEEEEE.-SEEEEEEE-TTHHH CS
                      UDP-g_GGTase  29 aDTivmanlGYfQlka.nPGvwklelregrss 59 
                                        +T+  +  GY+ +    PG + ++  ++ + 
  gi|298676130|ref|YP_003727879.1| 773 LETTKTNESGYYNFTGlAPGDYYINFIDSPGY 804
                                       56777778899999875899999988776655 PP

  == domain 6  score: 6.8 bits;  conditional E-value: 0.0085
                                       -TT-EEEEE-.SS-S-SEEEE--SGGGEEEEEE-SEEEEEEE- CS
                      UDP-g_GGTase  13 prGlqleLgt.ekkksvaDTivmanlGYfQlkanPGvwklelr 54 
                                        +Gl++eL + ++++ v++T+  +  GY+ +  +PG + ++ +
  gi|298676130|ref|YP_003727879.1| 871 ISGLTVELYNcSTDDLVSNTT-TNASGYYNFSVEPGEYYVNFS 912
                                       579999998834455556665.5667************99876 PP

  == domain 7  score: 9.1 bits;  conditional E-value: 0.0016
                                        -TT-EEEEE-SS-S-SEEEE--SGGGEEEEEE-SEEEEEEE-TTHHHHHEEEEE--S CS
                      UDP-g_GGTase   13 prGlqleLgtekkksvaDTivmanlGYfQlkanPGvwklelregrssdiyeiesvga 69  
                                         +Gl++eL + ++++++ ++  +  GY+ +  +PG + ++ +    sd ye++s ++
  gi|298676130|ref|YP_003727879.1|  984 ISGLTVELYNCSTDELESSTTTNASGYYNFSVTPGSYYVQFS----SDGYEFTSSNQ 1036
                                        579999**99888888888899999************99985....67777766633 PP

>> TTR-52  Transthyretin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.035        30      12      44 ..     186     215 ..     181     235 .. 0.81
   2 ?    4.2   0.1     0.082        70      19      46 ..     314     338 ..     302     361 .. 0.77
   3 ?    5.0   0.0     0.047        40      12      45 ..     420     450 ..     415     461 .. 0.86
   4 ?    3.8   0.0      0.11        95      11      46 ..     533     565 ..     529     584 .. 0.82
   5 ?    6.9   0.0     0.012        10      12      49 ..     646     680 ..     641     693 .. 0.82
   6 ?    6.6   0.0     0.015        13      11      45 ..     758     788 ..     754     798 .. 0.86
   7 !    8.4   0.0    0.0042       3.6      11      49 ..     871     906 ..     867     919 .. 0.83
   8 ?    4.6   0.0     0.062        53      11      46 ..     984    1016 ..     980    1033 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.035
                                       SS-EEEEEEHHHHTS--EEEEEE--TTSEEEEE CS
                            TTR-52  12 knvkVkLwekdtldpddlldetkTdedGnFels 44 
                                        +v+V+L++   +  d+l ++t+Tde+G+++ +
  gi|298676130|ref|YP_003727879.1| 186 TGVTVNLYN---CSGDSLRATTTTDENGYYNFT 215
                                       678999999...578**************9987 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.082
                                       EEHHHHTS--EEEEEE--TTSEEEEEEE CS
                            TTR-52  19 wekdtldpddlldetkTdedGnFelsgs 46 
                                       ++   +  d+++++t+Td+dG+++ + +
  gi|298676130|ref|YP_003727879.1| 314 HN---CSDDTIVSSTTTDADGYYNFTVT 338
                                       33...477999**********9998865 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.047
                                       SS-EEEEEEHHHHTS--EEEEEE--TTSEEEEEE CS
                            TTR-52  12 knvkVkLwekdtldpddlldetkTdedGnFelsg 45 
                                        nv+++L++ dt    +++++++Td dG ++ +g
  gi|298676130|ref|YP_003727879.1| 420 GNVTINLYDCDT---GNKIANNTTDVDGDYNFTG 450
                                       6899*****877...899************9987 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.11
                                       GSS-EEEEEEHHHHTS--EEEEEE--TTSEEEEEEE CS
                            TTR-52  11 aknvkVkLwekdtldpddlldetkTdedGnFelsgs 46 
                                       +++ +V+L++     +d+l ++t T+++G+++ s +
  gi|298676130|ref|YP_003727879.1| 533 ISGLTVELYNCS---TDELESSTITNASGYYNFSVT 565
                                       577899999965...59999**********999865 PP

  == domain 5  score: 6.9 bits;  conditional E-value: 0.012
                                       SS-EEEEEEHHHHTS--EEEEEE--TTSEEEEEEEE-- CS
                            TTR-52  12 knvkVkLwekdtldpddlldetkTdedGnFelsgsene 49 
                                        +++V+L++     +d+l+++t+T+++G+++ + +  e
  gi|298676130|ref|YP_003727879.1| 646 PDIRVELYNCS---TDNLVSNTTTNNSGYYNFTVEPGE 680
                                       678999*9965...5**************998876555 PP

  == domain 6  score: 6.6 bits;  conditional E-value: 0.015
                                       GSS-EEEEEEHHHHTS--EEEEEE--TTSEEEEEE CS
                            TTR-52  11 aknvkVkLwekdtldpddlldetkTdedGnFelsg 45 
                                       + nv+V+L++ +     d l++tkT+e+G+++ +g
  gi|298676130|ref|YP_003727879.1| 758 IDNVTVNLYNCN----GDFLETTKTNESGYYNFTG 788
                                       67999****975....59*************9987 PP

  == domain 7  score: 8.4 bits;  conditional E-value: 0.0042
                                       GSS-EEEEEEHHHHTS--EEEEEE--TTSEEEEEEEE-- CS
                            TTR-52  11 aknvkVkLwekdtldpddlldetkTdedGnFelsgsene 49 
                                       +++ +V+L++     +ddl+++t+T+++G+++ s +  e
  gi|298676130|ref|YP_003727879.1| 871 ISGLTVELYNCS---TDDLVSNTTTNASGYYNFSVEPGE 906
                                       677899999965...5**************999976555 PP

  == domain 8  score: 4.6 bits;  conditional E-value: 0.062
                                        GSS-EEEEEEHHHHTS--EEEEEE--TTSEEEEEEE CS
                            TTR-52   11 aknvkVkLwekdtldpddlldetkTdedGnFelsgs 46  
                                        +++ +V+L++     +d+l ++t+T+++G+++ s +
  gi|298676130|ref|YP_003727879.1|  984 ISGLTVELYNCS---TDELESSTTTNASGYYNFSVT 1016
                                        577899999965...599************999865 PP

>> AdenylateSensor  Adenylate sensor of SNF1-like protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.069        59      66      92 ..     335     361 ..     325     376 .. 0.76
   2 !   10.4   0.1   0.00082       0.7      65      98 ..     561     595 ..     537     605 .. 0.74
   3 !    9.8   0.0    0.0013       1.1      64      96 ..     672     706 ..     642     716 .. 0.71
   4 !    8.8   0.0    0.0026       2.2      66      98 ..     900     934 ..     878     942 .. 0.76
   5 !    9.7   0.0    0.0013       1.1      62      97 ..    1009    1044 ..     988    1055 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.069
                                       EEEETTEEEEEEEEEEEEESSSSSTTT CS
                   AdenylateSensor  66 fqlepnnylvdfkfdGwessssekeet 92 
                                       f + p +y v+f +dG+  +s ++ + 
  gi|298676130|ref|YP_003727879.1| 335 FTVTPGSYYVNFSSDGYVFTSANQGTD 361
                                       8899*************9776554332 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00082
                                       EEEEETTEEEEEEEEEEEEESSSSS.TTTTTSSTT CS
                   AdenylateSensor  65 lfqlepnnylvdfkfdGwessssek.eetaeeded 98 
                                        f + p ny v f +dG++ ++ +k +e +++d d
  gi|298676130|ref|YP_003727879.1| 561 NFSVTPGNYYVQFSSDGYNFTQANKeSEDVDSDAD 595
                                       5899***************8776652344444433 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0013
                                       EEEEEETTEEEEEEEEEEEEESSSSS..TTTTTSS CS
                   AdenylateSensor  64 qlfqlepnnylvdfkfdGwessssek..eetaeed 96 
                                         f +ep  y v+f +dG+e + +++  e+t+++d
  gi|298676130|ref|YP_003727879.1| 672 YNFTVEPGEYYVNFSSDGYEFTLQNQggEDTVDSD 706
                                       5699****************988877334444443 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.0026
                                       EEEETTEEEEEEEEEEEEESSSSS..TTTTTSSTT CS
                   AdenylateSensor  66 fqlepnnylvdfkfdGwessssek..eetaeeded 98 
                                       f +ep  y v+f +dG+e +  ++  ++t+++d d
  gi|298676130|ref|YP_003727879.1| 900 FSVEPGEYYVNFSSDGYEFTLANQgvDNTVDSDAD 934
                                       99****************87665533555555554 PP

  == domain 5  score: 9.7 bits;  conditional E-value: 0.0013
                                        EEEEEEEETTEEEEEEEEEEEEESSSSSTTTTTSST CS
                   AdenylateSensor   62 eiqlfqlepnnylvdfkfdGwessssekeetaeede 97  
                                            f + p +y v f +dG+e +ss++ +  + d+
  gi|298676130|ref|YP_003727879.1| 1009 GYYNFSVTPGSYYVQFSSDGYEFTSSNQGTDDSMDS 1044
                                        555699****************88777643333332 PP

>> DUF2012  Protein of unknown function (DUF2012)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0042       3.6      12      48 ..     190     228 ..     173     236 .. 0.71
   2 ?    5.8   0.0     0.017        15      22      54 ..     323     354 ..     303     385 .. 0.82
   3 !    6.8   0.0    0.0082         7      10      53 ..     422     468 ..     413     471 .. 0.75
   4 ?    5.2   0.0     0.026        22      21      55 ..     549     582 ..     480     615 .. 0.81
   5 ?    3.6   0.1     0.079        67       8      54 ..     646     693 ..     641     695 .. 0.74
   6 !    7.1   0.0    0.0066       5.6      22      54 ..     774     807 ..     753     810 .. 0.75
   7 ?    3.5   0.0     0.084        71      23      54 ..     889     919 ..     868     961 .. 0.80
   8 ?    4.7   0.1     0.037        31      21      54 ..    1000    1032 ..     981    1036 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0042
                           DUF2012  12 vlL...dsgqqrkfkalvrrDGsFifrdlpegsYlLeves 48 
                                       v L   + g +   ++ + ++G ++f++l++g Y+++   
  gi|298676130|ref|YP_003727879.1| 190 VNLyncS-GDSLRATTTTDENGYYNFTNLEPGNYYVNFTI 228
                                       3335533.333367889999**************998765 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.017
                           DUF2012  22 fkalvrrDGsFifrdlpegsYlLevespeyvFe 54 
                                        ++ + +DG ++f+ + +gsY+++  s +yvF 
  gi|298676130|ref|YP_003727879.1| 323 SSTTTDADGYYNFT-VTPGSYYVNFSSDGYVFT 354
                                       4788999******6.999**************7 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0082
                           DUF2012  10 trvlL...dsgqqrkfkalvrrDGsFifrdlpegsYlLevesp.eyvF 53 
                                       +++ L   d+g +   +  + +DG ++f+ l++g Y+++ e+p +y+F
  gi|298676130|ref|YP_003727879.1| 422 VTINLydcDTGNK-IANNTTDVDGDYNFTGLSPGNYYVNFEAPhGYEF 468
                                       4555565555555.6678899*****************9998724555 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.026
                           DUF2012  21 kfkalvrrDGsFifrdlpegsYlLevespeyvFep 55 
                                       + ++ ++++G ++f+ + +g Y+++  s +y+F +
  gi|298676130|ref|YP_003727879.1| 549 ESSTITNASGYYNFS-VTPGNYYVQFSSDGYNFTQ 582
                                       568999********6.999**************98 PP

  == domain 5  score: 3.6 bits;  conditional E-value: 0.079
                           DUF2012   8 antrvlL.....dsgqqrkfkalvrrDGsFifrdlpegsYlLevespeyvFe 54 
                                       +++rv L     d       ++ ++++G ++f+ +++g+Y+++  s +y+F 
  gi|298676130|ref|YP_003727879.1| 646 PDIRVELyncstD--NL-VSNTTTNNSGYYNFT-VEPGEYYVNFSSDGYEFT 693
                                       5666777433211..11.346889999****96.****************95 PP

  == domain 6  score: 7.1 bits;  conditional E-value: 0.0066
                           DUF2012  22 fkalvrrDGsFifrdlpegsYlLe.vespeyvFe 54 
                                        +++++++G ++f+ l +g Y+++ ++sp+y+F 
  gi|298676130|ref|YP_003727879.1| 774 ETTKTNESGYYNFTGLAPGDYYINfIDSPGYEFT 807
                                       47899**************88885489*****96 PP

  == domain 7  score: 3.5 bits;  conditional E-value: 0.084
                           DUF2012  23 kalvrrDGsFifrdlpegsYlLevespeyvFe 54 
                                       ++ ++++G ++f+ +++g+Y+++  s +y+F 
  gi|298676130|ref|YP_003727879.1| 889 NTTTNASGYYNFS-VEPGEYYVNFSSDGYEFT 919
                                       5778899999995.*****************7 PP

  == domain 8  score: 4.7 bits;  conditional E-value: 0.037
                           DUF2012   21 kfkalvrrDGsFifrdlpegsYlLevespeyvFe 54  
                                        + ++ ++++G ++f+ + +gsY+++  s +y+F 
  gi|298676130|ref|YP_003727879.1| 1000 ESSTTTNASGYYNFS-VTPGSYYVQFSSDGYEFT 1032
                                        46789999******6.999*************96 PP

>> phage_tail_N  Prophage tail fibre N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       5.5   4.7e+03      40      61 ..     203     225 ..     200     231 .. 0.81
   2 !    9.9   0.3   0.00084      0.71      37      69 ..     321     353 ..     296     378 .. 0.81
   3 ?    4.6   0.9     0.035        29       7      86 ..     410     485 ..     405     501 .. 0.78
   4 !    7.4   0.1    0.0048       4.1      39      72 ..     550     583 ..     508     603 .. 0.84
   5 !   11.8   0.3   0.00021      0.18      36      80 ..     659     706 ..     633     722 .. 0.76
   6 !    8.2   0.2    0.0027       2.3      37      68 ..     886     917 ..     864     925 .. 0.80
   7 ?    0.9   0.1       0.5   4.2e+02      34      81 ..     925     971 ..     917     979 .. 0.80
   8 ?    5.2   0.1     0.022        19      40      69 ..    1002    1031 ..     984    1048 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.5
                      phage_tail_N  40 senpdeaGrysl.dvetGkysvi 61 
                                         ++de+G y + + e G+y v 
  gi|298676130|ref|YP_003727879.1| 203 TTTTDENGYYNFtNLEPGNYYVN 225
                                       6789******9845799999886 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00084
                      phage_tail_N  37 tvasenpdeaGrysldvetGkysvilkvdgfpe 69 
                                        v+s ++d +G y + v  G y v +  dg+  
  gi|298676130|ref|YP_003727879.1| 321 IVSSTTTDADGYYNFTVTPGSYYVNFSSDGYVF 353
                                       4788999**********************9864 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.035
                      phage_tail_N   7 GvlkdGtGkPvqnctiqlkarrtsttvvvntvasenpdeaGrysld.vetGkysvilkv.dgfpeshaGditvyeds 81 
                                       G+ +dG  + + n+ti l  + t        +a++++d +G+y +     G+y v ++   g++    G+ + yed 
  gi|298676130|ref|YP_003727879.1| 410 GIQNDGN-TGIGNVTINLYDCDTGN-----KIANNTTDVDGDYNFTgLSPGNYYVNFEApHGYEFTILGQGANYEDN 480
                                       6666764.56788899998888875.....5678889*******973678*****9986368888889999***998 PP

                      phage_tail_N  82 kPGtl 86 
                                       +   l
  gi|298676130|ref|YP_003727879.1| 481 NANIL 485
                                       87666 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0048
                      phage_tail_N  39 asenpdeaGrysldvetGkysvilkvdgfpesha 72 
                                       +s  ++ +G y + v  G+y v +  dg++  +a
  gi|298676130|ref|YP_003727879.1| 550 SSTITNASGYYNFSVTPGNYYVQFSSDGYNFTQA 583
                                       46678899*********************98776 PP

  == domain 5  score: 11.8 bits;  conditional E-value: 0.00021
                      phage_tail_N  36 ntvasenpdeaGrysldvetGkysvilkvdgfp...eshaGditvyed 80 
                                       n v++ +++++G y + ve G+y v +  dg++   + + G+ tv  d
  gi|298676130|ref|YP_003727879.1| 659 NLVSNTTTNNSGYYNFTVEPGEYYVNFSSDGYEftlQNQGGEDTVDSD 706
                                       56788899***********************97322344555566555 PP

  == domain 6  score: 8.2 bits;  conditional E-value: 0.0027
                      phage_tail_N  37 tvasenpdeaGrysldvetGkysvilkvdgfp 68 
                                        v++ +++ +G y + ve G+y v +  dg++
  gi|298676130|ref|YP_003727879.1| 886 LVSNTTTNASGYYNFSVEPGEYYVNFSSDGYE 917
                                       3667778999********************96 PP

  == domain 7  score: 0.9 bits;  conditional E-value: 0.5
                      phage_tail_N  34 vvntvasenpdeaGrysldvetGkysvilkvdgfpeshaGditvyeds 81 
                                       v ntv s+        ++ ve G+   ++    +++  +Gd  v+ed+
  gi|298676130|ref|YP_003727879.1| 925 VDNTVDSDADSSGNTTCITVESGETNDTVDAGLYQPATIGDF-VWEDT 971
                                       6689988877777789************************97.56665 PP

  == domain 8  score: 5.2 bits;  conditional E-value: 0.022
                      phage_tail_N   40 senpdeaGrysldvetGkysvilkvdgfpe 69  
                                        s +++ +G y + v  G y v +  dg++ 
  gi|298676130|ref|YP_003727879.1| 1002 STTTNASGYYNFSVTPGSYYVQFSSDGYEF 1031
                                        5678889********************863 PP

>> DUF2025  Protein of unknown function (DUF2025)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.28   2.4e+02      13      42 ..     327     356 ..     316     365 .. 0.80
   2 ?    2.6   0.0      0.16   1.4e+02      15      40 ..     556     581 ..     545     590 .. 0.83
   3 ?    3.2   0.0       0.1        87       8      41 ..     661     694 ..     655     705 .. 0.81
   4 ?    5.8   0.0     0.016        14       8      48 ..     887     927 ..     881     941 .. 0.84
   5 ?    2.1   0.0      0.23     2e+02      14      40 ..    1006    1032 ..     995    1044 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.28
                                       GS---EEEEETTTTEEEEES-GGG-SSSS- CS
                           DUF2025  13 dqlkGfvGfnrktGkyivrfsedsfGldva 42 
                                        +  G+  f    G y v fs d + +  a
  gi|298676130|ref|YP_003727879.1| 327 TDADGYYNFTVTPGSYYVNFSSDGYVFTSA 356
                                       45679999***************9876655 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.16
                                       ---EEEEETTTTEEEEES-GGG-SSS CS
                           DUF2025  15 lkGfvGfnrktGkyivrfsedsfGld 40 
                                         G+  f    G+y v+fs d + + 
  gi|298676130|ref|YP_003727879.1| 556 ASGYYNFSVTPGNYYVQFSSDGYNFT 581
                                       479999***************98765 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.1
                                       GGGGGGS---EEEEETTTTEEEEES-GGG-SSSS CS
                           DUF2025   8 ickaadqlkGfvGfnrktGkyivrfsedsfGldv 41 
                                       + +++ +  G+  f    G+y v fs d + + +
  gi|298676130|ref|YP_003727879.1| 661 VSNTTTNNSGYYNFTVEPGEYYVNFSSDGYEFTL 694
                                       5666777899******************987655 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.016
                                       GGGGGGS---EEEEETTTTEEEEES-GGG-SSSS-GGG-EE CS
                           DUF2025   8 ickaadqlkGfvGfnrktGkyivrfsedsfGldvaddsitp 48 
                                       + +++ +  G+  f    G+y v fs d + + +a++ +  
  gi|298676130|ref|YP_003727879.1| 887 VSNTTTNASGYYNFSVEPGEYYVNFSSDGYEFTLANQGVDN 927
                                       566777889*********************99999887765 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.23
                                        S---EEEEETTTTEEEEES-GGG-SSS CS
                           DUF2025   14 qlkGfvGfnrktGkyivrfsedsfGld 40  
                                        +  G+  f    G y v+fs d + + 
  gi|298676130|ref|YP_003727879.1| 1006 NASGYYNFSVTPGSYYVQFSSDGYEFT 1032
                                        5679999***************98765 PP

>> Dioxygenase_C  Dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0012         1      73      98 ..     199     224 ..     182     233 .. 0.88
   2 ?    4.9   0.0     0.019        16      70      99 ..     317     345 ..     304     359 .. 0.81
   3 ?    5.6   0.1     0.011       9.8      78     106 ..     438     466 ..     422     477 .. 0.82
   4 ?    1.5   0.0       0.2   1.7e+02      73      99 ..     547     572 ..     532     587 .. 0.81
   5 ?    1.4   0.1      0.22   1.9e+02      69      99 ..     655     684 ..     641     701 .. 0.78
   6 ?    2.5   0.1       0.1        86      76      99 ..     774     797 ..     752     806 .. 0.84
   7 ?   -2.9   0.1       4.4   3.8e+03      77      98 ..     889     909 ..     879     919 .. 0.77
   8 ?   -1.3   0.0       1.4   1.2e+03      74      99 ..     999    1023 ..     988    1031 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0012
                                       TTEEEEE--TTSEEEEEEE----EE- CS
                     Dioxygenase_C  73 nlrgriltdeeGryrirtikPapYpi 98 
                                        lr ++ tde+G+y+++ ++P+ Y +
  gi|298676130|ref|YP_003727879.1| 199 SLRATTTTDENGYYNFTNLEPGNYYV 224
                                       5788999*****************76 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.019
                                       STTTTEEEEE--TTSEEEEEEE----EE-- CS
                     Dioxygenase_C  70 pelnlrgriltdeeGryrirtikPapYpip 99 
                                       ++  +  ++ td++G+y++ t+ P++Y ++
  gi|298676130|ref|YP_003727879.1| 317 SDDTIVSSTTTDADGYYNF-TVTPGSYYVN 345
                                       5666778899*******98.89*****765 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.011
                                       EE--TTSEEEEEEE----EE--TTSHHHH CS
                     Dioxygenase_C  78 iltdeeGryrirtikPapYpipndGptgk 106
                                         td +G y+++ + P+ Y ++ + p g 
  gi|298676130|ref|YP_003727879.1| 438 NTTDVDGDYNFTGLSPGNYYVNFEAPHGY 466
                                       569****************9998888765 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.2
                                       TTEEEEE--TTSEEEEEEE----EE-- CS
                     Dioxygenase_C  73 nlrgriltdeeGryrirtikPapYpip 99 
                                        l+ +++t++ G+y++ ++ P+ Y ++
  gi|298676130|ref|YP_003727879.1| 547 ELESSTITNASGYYNF-SVTPGNYYVQ 572
                                       567899********98.699***9765 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.22
                                       SSTTTTEEEEE--TTSEEEEEEE----EE-- CS
                     Dioxygenase_C  69 apelnlrgriltdeeGryrirtikPapYpip 99 
                                        +  nl  ++ t++ G+y++ t++P+ Y ++
  gi|298676130|ref|YP_003727879.1| 655 CSTDNLVSNTTTNNSGYYNF-TVEPGEYYVN 684
                                       556688889999****9998.89****9765 PP

  == domain 6  score: 2.5 bits;  conditional E-value: 0.1
                                       EEEE--TTSEEEEEEE----EE-- CS
                     Dioxygenase_C  76 griltdeeGryrirtikPapYpip 99 
                                        ++ t+e G+y+++ + P+ Y i+
  gi|298676130|ref|YP_003727879.1| 774 ETTKTNESGYYNFTGLAPGDYYIN 797
                                       566799***************875 PP

  == domain 7  score: -2.9 bits;  conditional E-value: 4.4
                                       EEE--TTSEEEEEEE----EE- CS
                     Dioxygenase_C  77 riltdeeGryrirtikPapYpi 98 
                                       ++ t++ G+y++ +++P+ Y +
  gi|298676130|ref|YP_003727879.1| 889 NTTTNASGYYNF-SVEPGEYYV 909
                                       566888898887.689998865 PP

  == domain 8  score: -1.3 bits;  conditional E-value: 1.4
                                        TEEEEE--TTSEEEEEEE----EE-- CS
                     Dioxygenase_C   74 lrgriltdeeGryrirtikPapYpip 99  
                                        l+ ++ t++ G+y++ ++ P++Y ++
  gi|298676130|ref|YP_003727879.1|  999 LESSTTTNASGYYNF-SVTPGSYYVQ 1023
                                        5678889999*9998.699*999764 PP

>> MetallophosN  N terminal of Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.1   0.00011     0.098      20      56 ..     202     239 ..     177     251 .. 0.82
   2 ?    6.4   0.3     0.013        11      20      49 ..     323     351 ..     305     362 .. 0.83
   3 ?    6.7   0.1      0.01       8.9      22      52 ..     438     469 ..     415     479 .. 0.89
   4 ?    1.5   0.4      0.43   3.7e+02      22      53 ..     552     582 ..     545     590 .. 0.72
   5 ?    1.7   1.1      0.38   3.2e+02      20      54 ..     662     695 ..     657     702 .. 0.79
   6 ?    0.1   0.1       1.2     1e+03      16      39 ..     687     710 ..     685     715 .. 0.85
   7 ?    3.9   0.2     0.073        63       6      35 ..     754     790 ..     749     813 .. 0.73
   8 ?    2.9   0.3      0.15   1.3e+02      19      52 ..     887     919 ..     877     930 .. 0.79
   9 ?    4.7   0.5     0.042        36      21      56 ..    1002    1036 ..     996    1048 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                      MetallophosN  20 nvtkTdakGrYeLk.sdkkakfVyistPagyevptedg 56 
                                        +t+Td++G Y+++  +  + +V +++P ++e+  +d+
  gi|298676130|ref|YP_003727879.1| 202 ATTTTDENGYYNFTnLEPGNYYVNFTIPPEFEFTLQDA 239
                                       4789**********889999************988875 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.013
                      MetallophosN  20 nvtkTdakGrYeLksdkkakfVyistPagy 49 
                                       + t+Tda+G Y+++ +  + +V +s  +gy
  gi|298676130|ref|YP_003727879.1| 323 SSTTTDADGYYNFTVTPGSYYVNFSS-DGY 351
                                       679***********999999998875.455 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.01
                      MetallophosN  22 tkTdakGrYeLk.sdkkakfVyistPagyevp 52 
                                        +Td +G Y+++  +  + +V +  P gye+ 
  gi|298676130|ref|YP_003727879.1| 438 NTTDVDGDYNFTgLSPGNYYVNFEAPHGYEFT 469
                                       58**********9999*************986 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.43
                      MetallophosN  22 tkTdakGrYeLksdkkakfVyistPagyevpt 53 
                                       t T+a+G Y+++ +  + +V +s  +gy++ +
  gi|298676130|ref|YP_003727879.1| 552 TITNASGYYNFSVTPGNYYVQFSS-DGYNFTQ 582
                                       678888888888888888887775.5555554 PP

  == domain 5  score: 1.7 bits;  conditional E-value: 0.38
                      MetallophosN  20 nvtkTdakGrYeLksdkkakfVyistPagyevpte 54 
                                       + t+T+++G Y+++ +    +V +s  +gye+  +
  gi|298676130|ref|YP_003727879.1| 662 SNTTTNNSGYYNFTVEPGEYYVNFSS-DGYEFTLQ 695
                                       5689*********9999988888875.66666555 PP

  == domain 6  score: 0.1 bits;  conditional E-value: 1.2
                      MetallophosN  16 sDGvnvtkTdakGrYeLksdkkak 39 
                                       sDG+++t  ++ G+ + +sd +++
  gi|298676130|ref|YP_003727879.1| 687 SDGYEFTLQNQGGEDTVDSDANSS 710
                                       8**********9998888777765 PP

  == domain 7  score: 3.9 bits;  conditional E-value: 0.073
                      MetallophosN   6 kgkgvagVvVs......DGvnvtkTdakGrYeLk.sd 35 
                                        ++g+ +V+V+      D  ++tkT+++G Y+++  +
  gi|298676130|ref|YP_003727879.1| 754 GDTGIDNVTVNlyncngDFLETTKTNESGYYNFTgLA 790
                                       567888888876666556689**********998544 PP

  == domain 8  score: 2.9 bits;  conditional E-value: 0.15
                      MetallophosN  19 vnvtkTdakGrYeLksdkkakfVyistPagyevp 52 
                                       v+ t+T+a+G Y+++ +    +V +s  +gye+ 
  gi|298676130|ref|YP_003727879.1| 887 VSNTTTNASGYYNFSVEPGEYYVNFSS-DGYEFT 919
                                       6789***********999998988875.666665 PP

  == domain 9  score: 4.7 bits;  conditional E-value: 0.042
                      MetallophosN   21 vtkTdakGrYeLksdkkakfVyistPagyevptedg 56  
                                         t+T+a+G Y+++ +  + +V +s  +gye+ ++++
  gi|298676130|ref|YP_003727879.1| 1002 STTTNASGYYNFSVTPGSYYVQFSS-DGYEFTSSNQ 1036
                                        699******************9997.8898888776 PP

>> HupF_HypC  HupF/HypC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.41   3.5e+02      22      42 ..     382     402 ..     371     406 .. 0.84
   2 ?    0.5   0.0      0.81   6.9e+02      22      42 ..     496     516 ..     483     517 .. 0.81
   3 ?    1.4   0.0      0.43   3.6e+02      18      42 ..     604     628 ..     593     629 .. 0.82
   4 ?    1.9   0.0      0.28   2.4e+02      20      42 ..     719     741 ..     709     745 .. 0.87
   5 ?   -0.6   0.0       1.7   1.5e+03      22      42 ..     834     854 ..     823     855 .. 0.82
   6 ?    2.6   0.0      0.18   1.6e+02      18      42 ..     943     967 ..     931     968 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.41
                                       TTEEEEEEGTTCTTB-TT-EE CS
                         HupF_HypC  22 gGvrrevslalveevkvGdyV 42 
                                       +++  +v+ +l  +v++GdyV
  gi|298676130|ref|YP_003727879.1| 382 NETNYTVDAGLYRPVSIGDYV 402
                                       566778999***99******9 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.81
                                       TTEEEEEEGTTCTTB-TT-EE CS
                         HupF_HypC  22 gGvrrevslalveevkvGdyV 42 
                                       g++  +++++l +++ +Gd+V
  gi|298676130|ref|YP_003727879.1| 496 GENNDTIDVGLYQPATIGDFV 516
                                       345789*************99 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.43
                                       EEECTTEEEEEEGTTCTTB-TT-EE CS
                         HupF_HypC  18 lvdvgGvrrevslalveevkvGdyV 42 
                                       +v  g++ ++++ +l +++ +Gd+V
  gi|298676130|ref|YP_003727879.1| 604 TVVSGETNETIDAGLYQQAMIGDFV 628
                                       4555567899*************99 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.28
                                       ECTTEEEEEEGTTCTTB-TT-EE CS
                         HupF_HypC  20 dvgGvrrevslalveevkvGdyV 42 
                                       + +++  +++ +l +++++GdyV
  gi|298676130|ref|YP_003727879.1| 719 ESNETNDTIDAGLYQPASIGDYV 741
                                       55677899**************9 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 1.7
                                       TTEEEEEEGTTCTTB-TT-EE CS
                         HupF_HypC  22 gGvrrevslalveevkvGdyV 42 
                                       g++  +++ +l +++ +Gd+V
  gi|298676130|ref|YP_003727879.1| 834 GENNDTIDAGLYQPATIGDFV 854
                                       3457899************99 PP

  == domain 6  score: 2.6 bits;  conditional E-value: 0.18
                                       EEECTTEEEEEEGTTCTTB-TT-EE CS
                         HupF_HypC  18 lvdvgGvrrevslalveevkvGdyV 42 
                                       +v+ g++  +v+ +l +++ +Gd+V
  gi|298676130|ref|YP_003727879.1| 943 TVESGETNDTVDAGLYQPATIGDFV 967
                                       7899999****************99 PP

>> Big_1  Bacterial Ig-like domain (group 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.1   0.00066      0.56      14      51 ..     178     215 ..     176     224 .. 0.91
   2 !    9.5   0.5    0.0011      0.96      20      53 ..     305     338 ..     291     346 .. 0.79
   3 ?   -2.1   0.0       4.8   4.1e+03      26      43 ..     344     362 ..     340     363 .. 0.72
   4 ?   -0.8   0.9       1.8   1.6e+03      18      51 ..     416     449 ..     411     452 .. 0.71
   5 !    7.7   0.0    0.0041       3.5      13      53 ..     525     565 ..     525     575 .. 0.90
   6 ?    3.4   0.1     0.092        78      15      52 ..     639     676 ..     637     679 .. 0.81
   7 ?    1.9   0.2      0.26   2.3e+02      15      51 ..     752     787 ..     750     789 .. 0.82
   8 ?    1.6   0.1      0.33   2.8e+02      20      52 ..     870     902 ..     864     904 .. 0.73
   9 ?   -1.1   1.3       2.3     2e+03      21      48 ..     920     949 ..     911     953 .. 0.80
  10 !    7.0   0.1     0.007         6      20      53 ..     983    1016 ..     977    1024 .. 0.82
  11 ?   -2.1   0.0       4.7     4e+03      26      44 ..    1022    1041 ..    1019    1042 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00066
                             Big_1  14 kDangnpvagatVtfsvsggalsassgtTdanGkatvt 51 
                                       +D +   + g+tV++   +g+ + +++tTd+nG + +t
  gi|298676130|ref|YP_003727879.1| 178 QDDEEVGLTGVTVNLYNCSGDSLRATTTTDENGYYNFT 215
                                       68888899********9999999**********99886 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0011
                             Big_1  20 pvagatVtfsvsggalsassgtTdanGkatvtlt 53 
                                        ++++ Vt+   +++++ ss+tTda+G + +t+t
  gi|298676130|ref|YP_003727879.1| 305 GISDIIVTLHNCSDDTIVSSTTTDADGYYNFTVT 338
                                       5666666666666888899**************9 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 4.8
                             Big_1  26 Vtfsvsggals.assgtTd 43 
                                       V+fs++g + + a++gt d
  gi|298676130|ref|YP_003727879.1| 344 VNFSSDGYVFTsANQGTDD 362
                                       99****9666636666554 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 1.8
                             Big_1  18 gnpvagatVtfsvsggalsassgtTdanGkatvt 51 
                                       ++ + ++t+++   ++ +  ++ tTd +G + +t
  gi|298676130|ref|YP_003727879.1| 416 NTGIGNVTINLYDCDTGNKIANNTTDVDGDYNFT 449
                                       56677777777655544447899******98876 PP

  == domain 5  score: 7.7 bits;  conditional E-value: 0.0041
                             Big_1  13 vkDangnpvagatVtfsvsggalsassgtTdanGkatvtlt 53 
                                       v+D   + ++g tV +   +++ ++ss++T+a+G + +++t
  gi|298676130|ref|YP_003727879.1| 525 VQDPGETGISGLTVELYNCSTDELESSTITNASGYYNFSVT 565
                                       6788889999****9998888888**************998 PP

  == domain 6  score: 3.4 bits;  conditional E-value: 0.092
                             Big_1  15 DangnpvagatVtfsvsggalsassgtTdanGkatvtl 52 
                                       D   + ++++ V +   +++++ s++tT+++G + +t+
  gi|298676130|ref|YP_003727879.1| 639 DDGETGIPDIRVELYNCSTDNLVSNTTTNNSGYYNFTV 676
                                       666778888888888777666789**********9997 PP

  == domain 7  score: 1.9 bits;  conditional E-value: 0.26
                             Big_1  15 DangnpvagatVtfsvsggalsassgtTdanGkatvt 51 
                                       +   + + ++tV++   +g+    +++T+++G + +t
  gi|298676130|ref|YP_003727879.1| 752 NDGDTGIDNVTVNLYNCNGDF-LETTKTNESGYYNFT 787
                                       556788999999999999998.5699******99887 PP

  == domain 8  score: 1.6 bits;  conditional E-value: 0.33
                             Big_1  20 pvagatVtfsvsggalsassgtTdanGkatvtl 52 
                                        ++g tV +   +++ + s++tT+a+G + +++
  gi|298676130|ref|YP_003727879.1| 870 GISGLTVELYNCSTDDLVSNTTTNASGYYNFSV 902
                                       56777777766664444789*******999876 PP

  == domain 9  score: -1.1 bits;  conditional E-value: 2.3
                             Big_1  21 vagatVtfsvsg.gals.assgtTdanGka 48 
                                       +a++ V  +v++ ++ s +++ +T ++G++
  gi|298676130|ref|YP_003727879.1| 920 LANQGVDNTVDSdADSSgNTTCITVESGET 949
                                       789999999999766668999999999985 PP

  == domain 10  score: 7.0 bits;  conditional E-value: 0.007
                             Big_1   20 pvagatVtfsvsggalsassgtTdanGkatvtlt 53  
                                         ++g tV +   +++ ++ss+tT+a+G + +++t
  gi|298676130|ref|YP_003727879.1|  983 GISGLTVELYNCSTDELESSTTTNASGYYNFSVT 1016
                                        678888888877777779*************998 PP

  == domain 11  score: -2.1 bits;  conditional E-value: 4.7
                             Big_1   26 Vtfsvsg.galsassgtTda 44  
                                        V fs++g + +s+++gt d+
  gi|298676130|ref|YP_003727879.1| 1022 VQFSSDGyEFTSSNQGTDDS 1041
                                        89999996666677777765 PP

>> DUF3244  Domain of unknown function (DUF3244)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.49   4.2e+02      39      89 ..     182     228 ..     171     233 .. 0.76
   2 ?   -0.7   0.1       1.8   1.5e+03      43      93 ..     307     352 ..     301     354 .. 0.70
   3 ?    6.8   0.0    0.0081       6.9      41      93 ..     418     466 ..     406     470 .. 0.84
   4 ?    2.9   0.1      0.14   1.2e+02      42      92 ..     533     578 ..     530     581 .. 0.80
   5 ?    1.5   0.1      0.36   3.1e+02      43      92 ..     646     690 ..     640     693 .. 0.79
   6 ?    1.1   0.0       0.5   4.3e+02      42      91 ..     758     803 ..     745     807 .. 0.71
   7 ?    3.4   0.0     0.092        79      42      92 ..     871     916 ..     867     919 .. 0.78
   8 ?    2.1   0.1      0.24   2.1e+02      42      92 ..     984    1029 ..     980    1033 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.49
                                       SS--SEEEEEEEETTT--EEEEEEE-GGGTTEEEEE-TTS-SEEEEEEEEE CS
                           DUF3244  39 esplsdvtitikdeetgevvyestivnasgstisidlsgeesgeYklelts 89 
                                       e+ l+ vt+ +++   g  +   t++++ + +++   +++e+g+Y + +t 
  gi|298676130|ref|YP_003727879.1| 182 EVGLTGVTVNLYNC-SGDSLRATTTTDE-NGYYN--FTNLEPGNYYVNFTI 228
                                       55677888888888.6888888888877.45555..58**********994 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.8
                                       SEEEEEEEETTT--EEEEEEE-GGGTTEEEEE-TTS-SEEEEEEEEESS-E CS
                           DUF3244  43 sdvtitikdeetgevvyestivnasgstisidlsgeesgeYkleltskggy 93 
                                       sd+ +t+ +   + ++ +st+++a + ++++ ++   +g Y + ++s+g++
  gi|298676130|ref|YP_003727879.1| 307 SDIIVTLHNC-SDDTIVSSTTTDA-DGYYNFTVT---PGSYYVNFSSDGYV 352
                                       5667777777.4566666666666.588888764...78899988888765 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0081
                                       --SEEEEEEEETTT--EEEEEEE-GGGTTEEEEE-TTS-SEEEEEEEEESS-E CS
                           DUF3244  41 plsdvtitikdeetgevvyestivnasgstisidlsgeesgeYkleltskggy 93 
                                        +++vti ++d +tg+ + ++t+  +    +  + +g+++g+Y + ++ + gy
  gi|298676130|ref|YP_003727879.1| 418 GIGNVTINLYDCDTGNKIANNTTDVD--GDY--NFTGLSPGNYYVNFEAPHGY 466
                                       579****************9998866..444..568**********9977665 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.14
                                       -SEEEEEEEETTT--EEEEEEE-GGGTTEEEEE-TTS-SEEEEEEEEESS- CS
                           DUF3244  42 lsdvtitikdeetgevvyestivnasgstisidlsgeesgeYkleltskgg 92 
                                       +s +t+ +++ +t   +++sti+na + +++++++   +g+Y ++++s+g+
  gi|298676130|ref|YP_003727879.1| 533 ISGLTVELYNCST-DELESSTITNA-SGYYNFSVT---PGNYYVQFSSDGY 578
                                       5678999999955.55789999988.79****986...899***9999886 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.36
                                       SEEEEEEEETTT--EEEEEEE-GGGTTEEEEE-TTS-SEEEEEEEEESS- CS
                           DUF3244  43 sdvtitikdeetgevvyestivnasgstisidlsgeesgeYkleltskgg 92 
                                        d+ + +++ +t++ v + t+ n+   ++++ +   e+geY + ++s+g+
  gi|298676130|ref|YP_003727879.1| 646 PDIRVELYNCSTDNLVSNTTTNNS--GYYNFTV---EPGEYYVNFSSDGY 690
                                       678888899988888887777776..9999986...68999999998876 PP

  == domain 6  score: 1.1 bits;  conditional E-value: 0.5
                                       -SEEEEEEEETTT--EEEEEEE-GGGTTEEEEE-TTS-SEEEEEEEE.ESS CS
                           DUF3244  42 lsdvtitikdeetgevvyestivnasgstisidlsgeesgeYklelt.skg 91 
                                       +++vt+ +++  +g  +++ t +n+ + ++  + +g+++g+Y + +  s+g
  gi|298676130|ref|YP_003727879.1| 758 IDNVTVNLYNC-NGDFLET-TKTNE-SGYY--NFTGLAPGDYYINFIdSPG 803
                                       67888888888.5666554.55555.2555..558*********9985655 PP

  == domain 7  score: 3.4 bits;  conditional E-value: 0.092
                                       -SEEEEEEEETTT--EEEEEEE-GGGTTEEEEE-TTS-SEEEEEEEEESS- CS
                           DUF3244  42 lsdvtitikdeetgevvyestivnasgstisidlsgeesgeYkleltskgg 92 
                                       +s +t+ +++ +t+  v +  ++na + ++++++   e+geY + ++s+g+
  gi|298676130|ref|YP_003727879.1| 871 ISGLTVELYNCSTDDLVSNT-TTNA-SGYYNFSV---EPGEYYVNFSSDGY 916
                                       67899999999888887655.5555.59****98...58*******99886 PP

  == domain 8  score: 2.1 bits;  conditional E-value: 0.24
                                        -SEEEEEEEETTT--EEEEEEE-GGGTTEEEEE-TTS-SEEEEEEEEESS- CS
                           DUF3244   42 lsdvtitikdeetgevvyestivnasgstisidlsgeesgeYkleltskgg 92  
                                        +s +t+ +++ +t+  +++st++na + +++++++   +g Y ++++s+g+
  gi|298676130|ref|YP_003727879.1|  984 ISGLTVELYNCSTD-ELESSTTTNA-SGYYNFSVT---PGSYYVQFSSDGY 1029
                                        67889999999655.5677888877.69****986...8999999998876 PP

>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.76   6.5e+02      29      46 ..     335     352 ..     333     357 .. 0.86
   2 ?   -3.1   0.0       8.6   7.3e+03      31      43 ..     451     463 ..     447     467 .. 0.76
   3 ?    3.8   0.0     0.064        55      29      46 ..     562     579 ..     560     586 .. 0.86
   4 ?    3.1   0.1       0.1        86      29      46 ..     674     691 ..     672     696 .. 0.88
   5 ?    3.9   0.0     0.059        50      29      46 ..     900     917 ..     898     928 .. 0.88
   6 ?    3.0   0.0      0.11        97      29      46 ..    1013    1030 ..    1011    1035 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.76
                              PEGA  29 lsleaGnyslrvekeGYe 46 
                                        ++ +G+y +  + +GY 
  gi|298676130|ref|YP_003727879.1| 335 FTVTPGSYYVNFSSDGYV 352
                                       56899************5 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 8.6
                              PEGA  31 leaGnyslrveke 43 
                                       l +Gny +  e++
  gi|298676130|ref|YP_003727879.1| 451 LSPGNYYVNFEAP 463
                                       789*****99987 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.064
                              PEGA  29 lsleaGnyslrvekeGYe 46 
                                        s+ +Gny ++ + +GY 
  gi|298676130|ref|YP_003727879.1| 562 FSVTPGNYYVQFSSDGYN 579
                                       6799*************4 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.1
                              PEGA  29 lsleaGnyslrvekeGYe 46 
                                        ++e+G+y +  + +GYe
  gi|298676130|ref|YP_003727879.1| 674 FTVEPGEYYVNFSSDGYE 691
                                       579**************8 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.059
                              PEGA  29 lsleaGnyslrvekeGYe 46 
                                        s+e+G+y +  + +GYe
  gi|298676130|ref|YP_003727879.1| 900 FSVEPGEYYVNFSSDGYE 917
                                       689**************8 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.11
                              PEGA   29 lsleaGnyslrvekeGYe 46  
                                         s+ +G+y ++ + +GYe
  gi|298676130|ref|YP_003727879.1| 1013 FSVTPGSYYVQFSSDGYE 1030
                                        6799*************7 PP

>> PLRV_ORF5  Potato leaf roll virus readthrough protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.64   5.5e+02     209     285 ..     180     255 ..     158     297 .. 0.81
   2 ?    8.9   1.2   0.00066      0.57      70     111 ..     323     364 ..     314     396 .. 0.80
   3 ?    4.7   1.0     0.012        10      66     111 ..     550     591 ..     534     600 .. 0.78
   4 ?    4.9   1.2     0.011       9.2      65     109 ..     661     701 ..     646     751 .. 0.63
   5 ?    8.5   2.5   0.00085      0.73      69     152 ..     887     979 ..     876     984 .. 0.84
   6 ?    7.6   1.7    0.0016       1.3      68     110 ..     999    1041 ..     988    1056 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.64
                         PLRV_ORF5 209 dmelGlisvvldehlesdveaervrrpirekhilvaeryepegkivgnklrdktpiqeqerqtdstesddvsdagsv 285
                                       d e+Gl  v+++   + ++++ r +    e+  +   + ep    v+  +  +     q+  +d+ +sd+ s +g+ 
  gi|298676130|ref|YP_003727879.1| 180 DEEVGLTGVTVN-LYNCSGDSLRATTTTDENGYYNFTNLEPGNYYVNFTIPPEFEFTLQDAGPDNIDSDVNSTTGNT 255
                                       568999999998.77889999999999999999999999**999999999999999999*********999776653 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00066
                         PLRV_ORF5  70 sqssvsavaayvfnvpkGsysvdisceGyqsvdsisdnedGr 111
                                       s ++ +a   y f v  Gsy v+ s +Gy  ++   + +dG 
  gi|298676130|ref|YP_003727879.1| 323 SSTTTDADGYYNFTVTPGSYYVNFSSDGYVFTSANQGTDDGV 364
                                       5667789999*******************9999887777774 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.012
                         PLRV_ORF5  66 seyssqssvsavaayvfnvpkGsysvdisceGyqsvdsisdnedGr 111
                                       s     +  +a   y f+v  G+y v+ s +Gy+ ++   ++ed  
  gi|298676130|ref|YP_003727879.1| 550 S----STITNASGYYNFSVTPGNYYVQFSSDGYNFTQANKESEDVD 591
                                       3....34446788999******************999888877755 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.011
                         PLRV_ORF5  65 dseyssqssvsavaayvfnvpkGsysvdisceGyqsvdsisdned 109
                                            s+++ +    y f v  G+y v+ s +Gy  + +  + ed
  gi|298676130|ref|YP_003727879.1| 661 V----SNTTTNNSGYYNFTVEPGEYYVNFSSDGYEFTLQNQGGED 701
                                       3....444555567899*****************87644433332 PP

  == domain 5  score: 8.5 bits;  conditional E-value: 0.00085
                         PLRV_ORF5  69 ssqssvsavaayvfnvpkGsysvdisceGy......qsvdsisdne...dGrsdGliaysnadsdywnvGeadGvki 136
                                        s+++ +a   y f+v  G+y v+ s +Gy      q vd++ d++    G    +   s    d  + G ++   i
  gi|298676130|ref|YP_003727879.1| 887 VSNTTTNASGYYNFSVEPGEYYVNFSSDGYeftlanQGVDNTVDSDadsSGNTTCITVESGETNDTVDAGLYQPATI 963
                                       6788899999*******************966666677888877542225777888888999999************ PP

                         PLRV_ORF5 137 kklradntyrqGhkel 152
                                        ++  ++t ++G++++
  gi|298676130|ref|YP_003727879.1| 964 GDFVWEDTNKNGKQDI 979
                                       ********99999986 PP

  == domain 6  score: 7.6 bits;  conditional E-value: 0.0016
                         PLRV_ORF5   68 yssqssvsavaayvfnvpkGsysvdisceGyqsvdsisdnedG 110 
                                          s ++ +a   y f+v  Gsy v+ s +Gy  ++s  + +d 
  gi|298676130|ref|YP_003727879.1|  999 LESSTTTNASGYYNFSVTPGSYYVQFSSDGYEFTSSNQGTDDS 1041
                                        445556678899*********************9998877764 PP

>> CooC_C  CS1-pili formation C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.28   2.4e+02      42      70 ..     324     352 ..     312     364 .. 0.79
   2 ?    5.0   0.0      0.03        25      42      92 ..     551     602 ..     539     603 .. 0.83
   3 ?    3.0   0.1      0.12   1.1e+02      33      83 ..     654     702 ..     651     709 .. 0.79
   4 ?    1.0   0.0      0.51   4.3e+02      42      80 ..     889     925 ..     876     941 .. 0.75
   5 ?    0.7   0.0      0.64   5.5e+02      42      72 ..    1002    1030 ..     991    1054 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.28
                            CooC_C  42 vavteedGvFtlevdakapsltvengdtl 70 
                                        + t++dG++ ++v+ ++ +  +++++ +
  gi|298676130|ref|YP_003727879.1| 324 STTTDADGYYNFTVTPGSYYVNFSSDGYV 352
                                       577899*********99999999988754 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.03
                            CooC_C  42 vavteedGvFtlevdakapsltvengdt.lyeveldlertrdevvlvGevtC 92 
                                        ++t++ G++ ++v+ ++ + ++++++  + +++ ++e++  ++   G++tC
  gi|298676130|ref|YP_003727879.1| 551 STITNASGYYNFSVTPGNYYVQFSSDGYnFTQANKESEDVDSDADSSGNTTC 602
                                       6899********************9998566666666777778888888888 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.12
                            CooC_C  33 nakilnhagvavteedGvFtlevdakapsltvengdtlyeveldlertrde 83 
                                       n +  n ++ + t++ G++ ++v+ ++ +  +++++  ye +l+ ++ +d+
  gi|298676130|ref|YP_003727879.1| 654 NCSTDNLVSNTTTNNSGYYNFTVEPGEYYVNFSSDG--YEFTLQNQGGEDT 702
                                       556677788888999999999999999999999998..7777777766655 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.51
                            CooC_C  42 vavteedGvFtlevdakapsltvengdtlyeveldlert 80 
                                        + t++ G++ ++v+ ++ +  +++++  ye +l  +++
  gi|298676130|ref|YP_003727879.1| 889 NTTTNASGYYNFSVEPGEYYVNFSSDG--YEFTLANQGV 925
                                       5778999********999999999998..5555544444 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 0.64
                            CooC_C   42 vavteedGvFtlevdakapsltvengdtlye 72  
                                         + t++ G++ ++v+ ++ + ++++++   e
  gi|298676130|ref|YP_003727879.1| 1002 STTTNASGYYNFSVTPGSYYVQFSSDGY--E 1030
                                        577889***************9999984..3 PP

>> Glyco_hydro_42C  Beta-galactosidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0065       5.6      17      46 ..     682     712 ..     680     723 .. 0.85
   2 ?    2.5   0.0      0.14   1.2e+02      17      42 ..     908     934 ..     906     946 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0065
                                       EEE-SSS-EE---.-TT-EEEES-......S CS
                   Glyco_hydro_42C  17 vlNfsneevtvtl.pasagdlltgelaeggv 46 
                                       ++Nfs++ +++tl +++++d+++ ++ + gv
  gi|298676130|ref|YP_003727879.1| 682 YVNFSSDGYEFTLqNQGGEDTVDSDANSSGV 712
                                       69********************998777764 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.14
                                       EEE-SSS-EE---.-TT-EEEES-... CS
                   Glyco_hydro_42C  17 vlNfsneevtvtl.pasagdlltgela 42 
                                       ++Nfs++ +++tl +++  ++++ ++ 
  gi|298676130|ref|YP_003727879.1| 908 YVNFSSDGYEFTLaNQGVDNTVDSDAD 934
                                       69***********99988888887655 PP

>> EMP24_GP25L  emp24/gp25L/p24 family/GOLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.013        11      39      82 ..     188     229 ..     171     260 .. 0.79
   2 ?    2.7   0.1      0.12   1.1e+02      38      83 ..     308     350 ..     291     372 .. 0.83
   3 ?    6.6   0.1    0.0082         7      39      83 ..     422     464 ..     411     471 .. 0.80
   4 ?   -1.4   0.1       2.2   1.9e+03      54      88 ..     549     582 ..     493     613 .. 0.77
   5 ?    5.3   1.1      0.02        17      37     118 ..     646     718 ..     596     729 .. 0.70
   6 ?    2.7   0.3      0.13   1.1e+02      10      79 ..     712     798 ..     708     808 .. 0.65
   7 ?    2.0   0.4      0.21   1.8e+02      52      88 ..     885     920 ..     854     987 .. 0.72
   8 ?   -1.4   0.2       2.2   1.9e+03      56      86 ..    1002    1031 ..     935    1061 .. 0.54

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.013
                       EMP24_GP25L  39 vdlsvkdpdgngerlvkkkdresegdfsftakesgeykvCfdns 82 
                                       v ++++  + +g  l  +  +++ g + ft++e+g+y+v f+ +
  gi|298676130|ref|YP_003727879.1| 188 VTVNLY--NCSGDSLRATTTTDENGYYNFTNLEPGNYYVNFTIP 229
                                       666677..44446666666677778**************99864 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.12
                       EMP24_GP25L  38 dvdlsvkdpdgngerlvkkkdresegdfsftakesgeykvCfdnsf 83 
                                       d+ +++++   ++ ++v++  ++++g + ft+ ++g y+v f++  
  gi|298676130|ref|YP_003727879.1| 308 DIIVTLHN--CSDDTIVSSTTTDADGYYNFTV-TPGSYYVNFSSDG 350
                                       55566674..4448999999************.8******999865 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0082
                       EMP24_GP25L  39 vdlsvkdpdgngerlvkkkdresegdfsftakesgeykvCfdnsf 83 
                                       v ++++d d  g+ + ++  ++ +gd+ ft +++g+y+v f+ ++
  gi|298676130|ref|YP_003727879.1| 422 VTINLYDCDT-GNKIANN-TTDVDGDYNFTGLSPGNYYVNFEAPH 464
                                       6677777666.7788888.666678**************999875 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 2.2
                       EMP24_GP25L  54 vkkkdresegdfsftakesgeykvCfdnsfstkss 88 
                                        ++ ++ ++g + f++ ++g+y+v f++  +++++
  gi|298676130|ref|YP_003727879.1| 549 ESSTITNASGYYNFSV-TPGNYYVQFSSDGYNFTQ 582
                                       4444555566788888.789999999888777655 PP

  == domain 5  score: 5.3 bits;  conditional E-value: 0.02
                       EMP24_GP25L  37 ldvdlsvkdpdgngerlvkkkdresegdfsftakesgeykvCfdnsfstksskkvsfdievgseasdykdsakkekl 113
                                        d+++++++ +    +lv++  + ++g + ft+ e+gey+v f++  +      ++++ + g++  d +d++ +   
  gi|298676130|ref|YP_003727879.1| 646 PDIRVELYNCST--DNLVSNTTTNNSGYYNFTV-EPGEYYVNFSSDGYE-----FTLQNQGGEDTVD-SDANSSGVT 713
                                       578888884444..5555555666677******.*********997654.....4555555554433.334444444 PP

                       EMP24_GP25L 114 etles 118
                                       e+++ 
  gi|298676130|ref|YP_003727879.1| 714 ECITL 718
                                       44555 PP

  == domain 6  score: 2.7 bits;  conditional E-value: 0.13
                       EMP24_GP25L  10 eekCfyeelkk.gtllt.gsyqvtdgg..................aaldvdlsvkdpdgngerlvkkkdresegdfs 66 
                                        ++C++ e ++ ++++  g yq  + g                     +v ++++  + ng  l ++k +es+  + 
  gi|298676130|ref|YP_003727879.1| 712 VTECITLESNEtNDTIDaGLYQPASIGdyvwedvngdgvqndgdtGIDNVTVNLY--NCNGDFLETTKTNESG-YYN 785
                                       5666666655555555424455554444555555555666665553356777788..6666777888778777.*** PP

                       EMP24_GP25L  67 ftakesgeykvCf 79 
                                       ft + +g+y++ f
  gi|298676130|ref|YP_003727879.1| 786 FTGLAPGDYYINF 798
                                       **********977 PP

  == domain 7  score: 2.0 bits;  conditional E-value: 0.21
                       EMP24_GP25L  52 rlvkkkdresegdfsftakesgeykvCfdnsfstkss 88 
                                        lv++  + ++g + f++ e+gey+v f++  + ++ 
  gi|298676130|ref|YP_003727879.1| 885 DLVSNTTTNASGYYNFSV-EPGEYYVNFSSDGYEFTL 920
                                       444444555566999999.9********998776654 PP

  == domain 8  score: -1.4 bits;  conditional E-value: 2.2
                       EMP24_GP25L   56 kkdresegdfsftakesgeykvCfdnsfstk 86  
                                        +  + ++g + f++ ++g y+v f++  + +
  gi|298676130|ref|YP_003727879.1| 1002 STTTNASGYYNFSV-TPGSYYVQFSSDGYEF 1031
                                        22222333444444.4555555555444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1084 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.86u 0.30s 00:00:01.15 Elapsed: 00:00:00.51
# Mc/sec: 6400.88
//
Query:       gi|298676131|ref|YP_003727880.1|  [L=602]
Description: hypothetical protein Metev_2265 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   7.2e-131  428.8  48.6    5.9e-34  116.7   8.7    4.8  5  SdrD_B           SdrD B-like domain
    1.4e-33  115.0  20.7    1.5e-09   38.0   0.9    5.8  6  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    4.1e-13   49.3   0.0      0.062   13.3   0.0    4.5  4  bMG3             Bacterial alpha-2-macroglobulin MG3 domain
    2.4e-12   46.7   9.2     0.0015   18.5   0.4    4.7  4  CarbopepD_reg_2  CarboxypepD_reg-like domain
    2.6e-06   28.0   0.5         24    5.7   0.0    5.1  5  TTR-52           Transthyretin-like family
    4.7e-06   26.7   0.3       0.55   10.4   0.0    4.1  4  UDP-g_GGTase     UDP-glucose:Glycoprotein Glucosyltransferase
      2e-05   24.4   0.3       0.15   11.9   0.0    3.8  4  DUF1416          Protein of unknown function (DUF1416)
    4.3e-05   24.0   0.1       0.18   12.3   0.0    2.7  2  AdenylateSensor  Adenylate sensor of SNF1-like protein kinase
    0.00084   19.6   5.7        3.7    7.9   2.0    4.4  3  CARDB            CARDB
     0.0025   17.8  18.2        1.8    8.7   0.1    6.8  7  Big_1            Bacterial Ig-like domain (group 1)
  ------ inclusion threshold ------
      0.012   15.6   7.5        7.1    6.6   0.3    4.4  5  phage_tail_N     Prophage tail fibre N-terminal
      0.026   14.8   8.9       0.59   10.5   8.9    3.1  1  DUF11            Domain of unknown function DUF11
       0.03   13.1  13.8       0.41    9.3   0.8    3.3  3  PLRV_ORF5        Potato leaf roll virus readthrough protein
      0.079   13.3  38.8       0.54   10.6   6.6    6.7  4  SpaA             Prealbumin-like fold domain
      0.094   13.0   3.0         46    4.3   0.1    4.2  3  Tgi2PP           Effector immunity protein Tgi2PP
       0.16   11.4   0.9        3.5    7.0   0.0    3.1  3  Dioxygenase_C    Dioxygenase


Domain annotation for each model (and alignments):
>> SdrD_B  SdrD B-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.7   8.7   5.3e-37   5.9e-34       1     112 []       5     114 ..       5     114 .. 0.95
   2 !  114.6   8.4   2.2e-36   2.5e-33       1     112 []     118     227 ..     118     227 .. 0.95
   3 !  113.9   2.9   3.8e-36   4.2e-33       1     112 []     235     347 ..     235     347 .. 0.92
   4 !  105.2   0.4   1.8e-33   2.1e-30       2     112 .]     352     460 ..     351     460 .. 0.97
   5 ?   -0.9   0.4       1.6   1.8e+03      21      61 ..     516     556 ..     499     571 .. 0.63

  Alignments for each domain:
  == domain 1  score: 116.7 bits;  conditional E-value: 5.3e-37
                            SdrD_B   1 asiGdfVweDanknGiqdagekgisgvtVtLkdakgevv.atttTdasGkYkFtnltpGeYkVeftapagytvtakk 76 
                                       a+iGdfVweD+nknG+qd ge+gisg tV+L++ +++++ ++ttT+asG+Y+F+ +tpG+Y+V+f+ ++gy++t+++
  gi|298676131|ref|YP_003727880.1|   5 ATIGDFVWEDTNKNGKQDIGESGISGLTVELYNCSTDELeSSTTTNASGYYNFS-VTPGNYYVQFS-SDGYEFTSAN 79 
                                       58*******************************99999989************8.9*********5.68******** PP

                            SdrD_B  77 aGsddaldSdadpatgltktvtlasgesnetidaGl 112
                                       +G+dd++dSdad+ +g+t+++t++sge+n t+daGl
  gi|298676131|ref|YP_003727880.1|  80 QGTDDSMDSDADS-SGNTTCITVESGETNDTVDAGL 114
                                       ***********86.6799*****************7 PP

  == domain 2  score: 114.6 bits;  conditional E-value: 2.2e-36
                            SdrD_B   1 asiGdfVweDanknGiqdagekgisgvtVtLkdakgevv.atttTdasGkYkFtnltpGeYkVeftapagytvtakk 76 
                                       a+iGdfVweD+nknG+qd ge+gisg tV+L++ +++++ ++ttT+asG+Y+F+ +tpG+Y+V+f+ ++gy++t ++
  gi|298676131|ref|YP_003727880.1| 118 ATIGDFVWEDTNKNGKQDIGETGISGLTVELYNCSTDELeSSTTTNASGYYNFS-VTPGSYYVNFS-SDGYEFTLAN 192
                                       58*******************************99999989************8.9*********5.68******** PP

                            SdrD_B  77 aGsddaldSdadpatgltktvtlasgesnetidaGl 112
                                       +G+dd +dSdad+ +g+t+++t++sg++n tidaGl
  gi|298676131|ref|YP_003727880.1| 193 QGTDDGVDSDADS-SGNTTCITVESGKTNDTIDAGL 227
                                       ***********86.6799*****************7 PP

  == domain 3  score: 113.9 bits;  conditional E-value: 3.8e-36
                            SdrD_B   1 asiGdfVweDanknGiqdagekgisgvtVtLkda.kgevvatttTdasGkYkFtnltpGeYkVefta..pagytvta 74 
                                       as+GdfVweD +++G+qd ge+gi +vtV L+d  +g+++att Td++G+Y Ft+ltpG Y+V+f+a   +gy++t+
  gi|298676131|ref|YP_003727880.1| 235 ASMGDFVWEDLDGDGTQDIGEPGIFNVTVYLYDCvTGNLIATTNTDEDGEYLFTGLTPGVYNVSFAAppESGYVFTP 311
                                       589****************************886266777*************************99644799**** PP

                            SdrD_B  75 kkaGsddaldSdadpatgltktvtlasgesnetidaGl 112
                                       k++Gsd++ dSda++ tg+t++++l sge+n tidaG+
  gi|298676131|ref|YP_003727880.1| 312 KDQGSDEK-DSDANS-TGNTTCINLVSGETNDTIDAGM 347
                                       ******98.***975.889*****************96 PP

  == domain 4  score: 105.2 bits;  conditional E-value: 1.8e-33
                            SdrD_B   2 siGdfVweDanknGiqdagekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapagytvtakkaG 78 
                                       s+ dfVw+D+n nGiqd gekg+++v+V+L++ +g+ +++ +T+asG YkF  + pG+Y+++f+ p+g +++++  G
  gi|298676131|ref|YP_003727880.1| 352 SVSDFVWNDTNCNGIQDPGEKGVANVEVRLYNIDGDYITSEITNASGFYKFL-VPPGHYYLNFVLPEGHEFSPQFMG 427
                                       799************************************************7.9*********************** PP

                            SdrD_B  79 sddaldSdadpatgltktvtlasgesnetidaGl 112
                                        d ++dSd+d+ tg+t+++ l+sge+n tidaG+
  gi|298676131|ref|YP_003727880.1| 428 GDINKDSDVDN-TGNTSIIMLTSGENNVTIDAGI 460
                                       *********87.779******************7 PP

  == domain 5  score: -0.9 bits;  conditional E-value: 1.6
                            SdrD_B  21 ekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYk 61 
                                          ++  + tL  ++  v +   T + G+Y+  +    eY+
  gi|298676131|ref|YP_003727880.1| 516 GVEVNCLNTTLEPDESMVCNAIGTAKLGQYSNYGNVTAEYN 556
                                       33344444555444555557888888899976666666664 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.9   1.4e-12   1.5e-09      12      74 ..      26     106 ..      21     115 .. 0.75
   2 !   35.6   0.8   7.5e-12   8.4e-09      12      61 ..     139     188 ..     134     227 .. 0.81
   3 !   26.3   0.2     6e-09   6.7e-06      14      57 ..     258     302 ..     250     310 .. 0.89
   4 ?   -0.9   0.0       1.8   2.1e+03      29      68 ..     318     357 ..     305     362 .. 0.80
   5 !   25.6   0.0   9.8e-09   1.1e-05       7      63 ..     367     422 ..     365     459 .. 0.86
   6 ?   -2.9   0.2       7.7   8.6e+03      65      67 ..     507     509 ..     485     526 .. 0.51

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 1.4e-12
                   CarboxypepD_reg  12 apiagatVtvtn.adtgtvastttdadGafrlrglppgtysvtvsapGyatatr..................eevtl 69 
                                        +i+g tV+++n + ++ ++sttt+a+G+++++ ++pg+y v++s++Gy+ ++                   + +t+
  gi|298676131|ref|YP_003727880.1|  26 SGISGLTVELYNcSTDELESSTTTNASGYYNFS-VTPGNYYVQFSSDGYEFTSAnqgtddsmdsdadssgntTCITV 101
                                       579*********5566789*************7.***************8555544666655555555555555555 PP

                   CarboxypepD_reg  70 tagqt 74 
                                       + g+t
  gi|298676131|ref|YP_003727880.1| 102 ESGET 106
                                       55555 PP

  == domain 2  score: 35.6 bits;  conditional E-value: 7.5e-12
                   CarboxypepD_reg  12 apiagatVtvtn.adtgtvastttdadGafrlrglppgtysvtvsapGyat 61 
                                       ++i+g tV+++n + ++ ++sttt+a+G+++++ ++pg+y v +s++Gy+ 
  gi|298676131|ref|YP_003727880.1| 139 TGISGLTVELYNcSTDELESSTTTNASGYYNFS-VTPGSYYVNFSSDGYEF 188
                                       689*********5566789*************7.***************74 PP

  == domain 3  score: 26.3 bits;  conditional E-value: 6e-09
                   CarboxypepD_reg  14 iagatVtvtn.adtgtvastttdadGafrlrglppgtysvtvsap 57 
                                       i ++tV +++   ++  a+t td+dG++ ++gl+pg y+v + ap
  gi|298676131|ref|YP_003727880.1| 258 IFNVTVYLYDcVTGNLIATTNTDEDGEYLFTGLTPGVYNVSFAAP 302
                                       5689999999667889*************************9886 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 1.8
                   CarboxypepD_reg  29 vastttdadGafrlrglppgtysvtvsapGyatatreevt 68 
                                       ++    +++G+ ++ +l  g+ + t+ a  y++a++++++
  gi|298676131|ref|YP_003727880.1| 318 EKDSDANSTGNTTCINLVSGETNDTIDAGMYQPASVSDFV 357
                                       5556678999999999999999999999999999988775 PP

  == domain 5  score: 25.6 bits;  conditional E-value: 9.8e-09
                   CarboxypepD_reg   7 tdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatat 63 
                                        d+  +++a+++V+++n d++  +s  t+a+G +++  +ppg y + +  p  ++++
  gi|298676131|ref|YP_003727880.1| 367 QDPGEKGVANVEVRLYNIDGDYITSEITNASGFYKFL-VPPGHYYLNFVLPEGHEFS 422
                                       689999******************************7.********99777666554 PP

  == domain 6  score: -2.9 bits;  conditional E-value: 7.7
                   CarboxypepD_reg  65 eev 67 
                                       +++
  gi|298676131|ref|YP_003727880.1| 507 TNI 509
                                       223 PP

>> bMG3  Bacterial alpha-2-macroglobulin MG3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0   0.00068      0.76      28      60 ..      28      61 ..      25      94 .. 0.76
   2 !    9.3   0.0   0.00097       1.1      28      59 ..     141     173 ..     138     203 .. 0.82
   3 !   10.6   0.0   0.00039      0.44      30      60 ..     260     291 ..     254     322 .. 0.84
   4 !   13.3   0.0   5.6e-05     0.062      26      59 ..     372     405 ..     370     426 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00068
                              bMG3 28 vagaeVrlldkkgevlae.gtTDaqGvarfaall 60
                                      ++g +V+l++++ ++l + +tT+a+G+++f+ + 
  gi|298676131|ref|YP_003727880.1| 28 ISGLTVELYNCSTDELESsTTTNASGYYNFSVTP 61
                                      6899************862678********9874 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00097
                              bMG3  28 vagaeVrlldkkgevlae.gtTDaqGvarfaal 59 
                                       ++g +V+l++++ ++l + +tT+a+G+++f+ +
  gi|298676131|ref|YP_003727880.1| 141 ISGLTVELYNCSTDELESsTTTNASGYYNFSVT 173
                                       6899************862678*******9876 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00039
                              bMG3  30 gaeVrlld.kkgevlaegtTDaqGvarfaall 60 
                                       +++V l+d  +g+++a+++TD++G + f++l 
  gi|298676131|ref|YP_003727880.1| 260 NVTVYLYDcVTGNLIATTNTDEDGEYLFTGLT 291
                                       899*****559*****************9874 PP

  == domain 4  score: 13.3 bits;  conditional E-value: 5.6e-05
                              bMG3  26 kPvagaeVrlldkkgevlaegtTDaqGvarfaal 59 
                                       k va++eVrl++ +g+ + +  T+a+G ++f  +
  gi|298676131|ref|YP_003727880.1| 372 KGVANVEVRLYNIDGDYITSEITNASGFYKFLVP 405
                                       679**************************99765 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.4   1.3e-06    0.0015      20      58 ..      39      76 ..      27      96 .. 0.84
   2 !   16.4   0.4     6e-06    0.0068      20      56 ..     152     187 ..     140     202 .. 0.87
   3 !    9.2   0.0    0.0011       1.2      25      50 ..     274     299 ..     251     306 .. 0.80
   4 ?    4.4   0.0     0.032        36      26      50 ..     390     413 ..     366     416 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.3e-06
                   CarbopepD_reg_2 20 yvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktq 58
                                      +  + +  t+T+++G+++++ +++g+y +++s+ Gy+  
  gi|298676131|ref|YP_003727880.1| 39 STDELESSTTTNASGYYNFS-VTPGNYYVQFSSDGYEFT 76
                                      56677889***********6.999************965 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 6e-06
                   CarbopepD_reg_2  20 yvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyk 56 
                                       +  + +  t+T+++G+++++ +++g y +++s+ Gy+
  gi|298676131|ref|YP_003727880.1| 152 STDELESSTTTNASGYYNFS-VTPGSYYVNFSSDGYE 187
                                       56677889***********6.999************8 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0011
                   CarbopepD_reg_2  25 kkgtvTdenGnFelknlpagkytLvv 50 
                                        + t Tde+G++ ++ l++g y + +
  gi|298676131|ref|YP_003727880.1| 274 IATTNTDEDGEYLFTGLTPGVYNVSF 299
                                       46688****************98766 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.032
                   CarbopepD_reg_2  26 kgtvTdenGnFelknlpagkytLvv 50 
                                       +  +T+++G +++  +p+g y L++
  gi|298676131|ref|YP_003727880.1| 390 TSEITNASGFYKF-LVPPGHYYLNF 413
                                       5568*********.5******9986 PP

>> TTR-52  Transthyretin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.022        24      11      46 ..      28      60 ..      24      79 .. 0.82
   2 ?    5.5   0.0     0.025        28      11      46 ..     141     173 ..     137     188 .. 0.82
   3 ?    5.5   0.0     0.026        29      13      47 ..     260     291 ..     254     301 .. 0.82
   4 ?    4.4   0.0     0.054        61       8      42 ..     371     401 ..     369     408 .. 0.88
   5 ?   -1.5   0.0       3.9   4.4e+03      14      64 ..     517     574 ..     510     582 .. 0.56

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.022
                                      GSS-EEEEEEHHHHTS--EEEEEE--TTSEEEEEEE CS
                            TTR-52 11 aknvkVkLwekdtldpddlldetkTdedGnFelsgs 46
                                      +++ +V+L++     +d+l ++t+T+++G+++ s +
  gi|298676131|ref|YP_003727880.1| 28 ISGLTVELYNCS---TDELESSTTTNASGYYNFSVT 60
                                      677899999965...599************999865 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.025
                                       GSS-EEEEEEHHHHTS--EEEEEE--TTSEEEEEEE CS
                            TTR-52  11 aknvkVkLwekdtldpddlldetkTdedGnFelsgs 46 
                                       +++ +V+L++     +d+l ++t+T+++G+++ s +
  gi|298676131|ref|YP_003727880.1| 141 ISGLTVELYNCS---TDELESSTTTNASGYYNFSVT 173
                                       577899999965...599************999865 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.026
                                       S-EEEEEEHHHHTS--EEEEEE--TTSEEEEEEEE CS
                            TTR-52  13 nvkVkLwekdtldpddlldetkTdedGnFelsgse 47 
                                       nv+V L++     + +l+++t+TdedG++  +g +
  gi|298676131|ref|YP_003727880.1| 260 NVTVYLYDC---VTGNLIATTNTDEDGEYLFTGLT 291
                                       788888884...5689************9988865 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.054
                                       T-GGSS-EEEEEEHHHHTS--EEEEEE--TTSEEE CS
                            TTR-52   8 gkpaknvkVkLwekdtldpddlldetkTdedGnFe 42 
                                       +k ++nv+V+L++ d     d ++++ T+++G ++
  gi|298676131|ref|YP_003727880.1| 371 EKGVANVEVRLYNIDG----DYITSEITNASGFYK 401
                                       67899********775....99**********987 PP

  == domain 5  score: -1.5 bits;  conditional E-value: 3.9
                                       -EEEEEEHHHHTS--EEEEEE..--TTSEEEEEEEE-.--......S--EEEEEE---- CS
                            TTR-52  14 vkVkLwekdtldpddlldetk..TdedGnFelsgsen.el.....tsidPylkiyhkCn 64 
                                       v+V+  +  tl+pd+ +  +   T + G+++  g+ + e+     ++ dP  ++ h+ +
  gi|298676131|ref|YP_003727880.1| 517 VEVNCLNT-TLEPDESMVCNAigTAKLGQYSNYGNVTaEYngvqvNDSDPSHYFGHDHW 574
                                       55555554.33555555544445888888877766543442222246666666666655 PP

>> UDP-g_GGTase  UDP-glucose:Glycoprotein Glucosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00049      0.55      13      71 ..      28      82 ..      20     108 .. 0.74
   2 !    9.0   0.0    0.0013       1.5      13      55 ..     141     183 ..     133     221 .. 0.72
   3 ?   -0.1   0.0      0.89     1e+03      45      88 ..     291     336 ..     284     341 .. 0.70
   4 ?    1.0   0.0      0.41   4.6e+02      33      54 ..     393     414 ..     368     454 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00049
                                      -TT-EEEEE-SS-S-SEEEE--SGGGEEEEEE-SEEEEEEE-TTHHHHHEEEEE--SS- CS
                      UDP-g_GGTase 13 prGlqleLgtekkksvaDTivmanlGYfQlkanPGvwklelregrssdiyeiesvgaeg 71
                                       +Gl++eL + ++++++ ++  +  GY+ +  +PG + ++ +    sd ye++s+++ +
  gi|298676131|ref|YP_003727880.1| 28 ISGLTVELYNCSTDELESSTTTNASGYYNFSVTPGNYYVQFS----SDGYEFTSANQGT 82
                                      579999**99888888888999999*************9985....7778887774333 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0013
                                       -TT-EEEEE-SS-S-SEEEE--SGGGEEEEEE-SEEEEEEE-T CS
                      UDP-g_GGTase  13 prGlqleLgtekkksvaDTivmanlGYfQlkanPGvwklelre 55 
                                        +Gl++eL + ++++++ ++  +  GY+ +  +PG + ++ ++
  gi|298676131|ref|YP_003727880.1| 141 ISGLTVELYNCSTDELESSTTTNASGYYNFSVTPGSYYVNFSS 183
                                       5799999*99888888888899999************999863 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.89
                                       -SEEEEEEE-.TTHHHHHEEEEE--SS-S--TT--.--EEEE-STT CS
                      UDP-g_GGTase  45 nPGvwklelr.egrssdiyeiesvgaeglsspkde.gkevvltsfe 88 
                                       +PGv++++   + +s  +++ +++g+++ +s  ++ g++  ++ ++
  gi|298676131|ref|YP_003727880.1| 291 TPGVYNVSFAaPPESGYVFTPKDQGSDEKDSDANStGNTTCINLVS 336
                                       7******998456799999999998888544443335665555555 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.41
                                       --SGGGEEEEEE-SEEEEEEE- CS
                      UDP-g_GGTase  33 vmanlGYfQlkanPGvwklelr 54 
                                       + +  G++ +   PG + l+  
  gi|298676131|ref|YP_003727880.1| 393 ITNASGFYKFLVPPGHYYLNFV 414
                                       566789***********99864 PP

>> DUF1416  Protein of unknown function (DUF1416)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.044        49      31      71 ..      26      67 ..      12      85 .. 0.81
   2 ?    3.6   0.0     0.054        60      30      71 ..     138     180 ..     124     199 .. 0.82
   3 ?   -2.8   0.0       5.3   5.9e+03      44      68 ..     270     295 ..     258     302 .. 0.74
   4 !   11.9   0.0   0.00014      0.15      27      77 ..     368     418 ..     349     426 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.044
                           DUF1416 31 epvggayvRLLd.ssgeFtaevvtsaeGefrFfaapGeWtvR 71
                                      + ++g  v L + s++e  +  +t+a+G + F  +pG++ v 
  gi|298676131|ref|YP_003727880.1| 26 SGISGLTVELYNcSTDELESSTTTNASGYYNFSVTPGNYYVQ 67
                                      55666677777746899999******************9986 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.054
                           DUF1416  30 gepvggayvRLLd.ssgeFtaevvtsaeGefrFfaapGeWtvR 71 
                                       ++ ++g  v L + s++e  +  +t+a+G + F  +pG++ v 
  gi|298676131|ref|YP_003727880.1| 138 ETGISGLTVELYNcSTDELESSTTTNASGYYNFSVTPGSYYVN 180
                                       556677777777746899999******************9885 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 5.3
                           DUF1416  44 sgeFtaevvtsaeGefrFfa.apGeW 68 
                                       +g+  a   t ++Ge+ F   +pG +
  gi|298676131|ref|YP_003727880.1| 270 TGNLIATTNTDEDGEYLFTGlTPGVY 295
                                       78888999999999998864245655 PP

  == domain 4  score: 11.9 bits;  conditional E-value: 0.00014
                           DUF1416  27 trdgepvggayvRLLdssgeFtaevvtsaeGefrFfaapGeWtvRalarkg 77 
                                         +++ v++  vRL + +g++ +   t+a+G ++F   pG++ +  + ++g
  gi|298676131|ref|YP_003727880.1| 368 DPGEKGVANVEVRLYNIDGDYITSEITNASGFYKFLVPPGHYYLNFVLPEG 418
                                       44678899999**********99999***************9998877766 PP

>> AdenylateSensor  Adenylate sensor of SNF1-like protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00016      0.18      61      96 ..      52      89 ..      32      99 .. 0.67
   2 !    8.7   0.0    0.0021       2.4      61      91 ..     165     195 ..     145     211 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                                      EEEEEEEEETTEEEEEEEEEEEEESSSSS..TTTTTSS CS
                   AdenylateSensor 61 leiqlfqlepnnylvdfkfdGwessssek..eetaeed 96
                                           f + p ny v f +dG+e +s ++  ++++++d
  gi|298676131|ref|YP_003727880.1| 52 SGYYNFSVTPGNYYVQFSSDGYEFTSANQgtDDSMDSD 89
                                      5556699****************877665223333333 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0021
                                       EEEEEEEEETTEEEEEEEEEEEEESSSSSTT CS
                   AdenylateSensor  61 leiqlfqlepnnylvdfkfdGwessssekee 91 
                                            f + p +y v+f +dG+e +  ++ +
  gi|298676131|ref|YP_003727880.1| 165 SGYYNFSVTPGSYYVNFSSDGYEFTLANQGT 195
                                       5556699****************87665532 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.023        25      54      87 ..      35      73 ..       3      84 .. 0.79
   2 ?    4.4   0.0     0.039        44      54      87 ..     146     186 ..     115     197 .. 0.78
   3 !    7.9   2.0    0.0033       3.7      15      41 ..     486     512 ..     480     562 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.023
                                      E.....SEE-CTEEEEEEEEEE-S-S-CEEEEEEEESTT CS
                             CARDB 54 v.....psLaagesttvsftwtteategevtltvvvDpd 87
                                      +      +L+++++t+ s  +  + t+g+++++++ D +
  gi|298676131|ref|YP_003727880.1| 35 LyncstDELESSTTTNASGYYNFSVTPGNYYVQFSSDGY 73
                                      155555899**********99999**********99986 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.039
                                       E.......SEE-CTEEEEEEEEEE-S-S-CEEEEEEEESTT CS
                             CARDB  54 v.......psLaagesttvsftwtteategevtltvvvDpd 87 
                                       v        +L+++++t+ s  +  + t+g+++++++ D +
  gi|298676131|ref|YP_003727880.1| 146 VelyncstDELESSTTTNASGYYNFSVTPGSYYVNFSSDGY 186
                                       14455555899*********999999**********99976 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0033
                                       EETTSEEEEEEEEEE-SSS-EEEEEEE CS
                             CARDB  15 afvgeentitvtvkNqGtaasgatkva 41 
                                       + vg+++t t++v+N+G+ + ++++v+
  gi|298676131|ref|YP_003727880.1| 486 VQVGTQVTWTYNVTNTGNVNLTNINVT 512
                                       6789*****************999986 PP

>> Big_1  Bacterial Ig-like domain (group 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.1    0.0036       4.1      20      53 ..      27      60 ..      21      63 .. 0.83
   2 ?   -0.6   0.1       1.2   1.3e+03      26      44 ..      66      85 ..      62      98 .. 0.79
   3 !    8.7   0.1    0.0016       1.8      17      53 ..     137     173 ..     134     181 .. 0.84
   4 ?   -1.8   0.0       2.8   3.2e+03      26      43 ..     179     197 ..     175     198 .. 0.79
   5 ?    2.2   0.0      0.17   1.9e+02      37      51 ..     274     288 ..     258     299 .. 0.74
   6 ?    0.5   0.0      0.54     6e+02      16      50 ..     369     402 ..     366     404 .. 0.73
   7 ?    3.6   2.4     0.061        69      23      47 ..     489     517 ..     486     527 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0036
                             Big_1 20 pvagatVtfsvsggalsassgtTdanGkatvtlt 53
                                       ++g tV +   +++ ++ss+tT+a+G + +++t
  gi|298676131|ref|YP_003727880.1| 27 GISGLTVELYNCSTDELESSTTTNASGYYNFSVT 60
                                      688888888877777779*************998 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.2
                             Big_1 26 Vtfsvsg.galsassgtTda 44
                                      V fs++g + +sa++gt d+
  gi|298676131|ref|YP_003727880.1| 66 VQFSSDGyEFTSANQGTDDS 85
                                      88999996666677777775 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0016
                             Big_1  17 ngnpvagatVtfsvsggalsassgtTdanGkatvtlt 53 
                                         + ++g tV +   +++ ++ss+tT+a+G + +++t
  gi|298676131|ref|YP_003727880.1| 137 GETGISGLTVELYNCSTDELESSTTTNASGYYNFSVT 173
                                       56789999999998887777**************998 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 2.8
                             Big_1  26 Vtfsvsg.galsassgtTd 43 
                                       V+fs++g + ++a++gt d
  gi|298676131|ref|YP_003727880.1| 179 VNFSSDGyEFTLANQGTDD 197
                                       99****9666668888876 PP

  == domain 5  score: 2.2 bits;  conditional E-value: 0.17
                             Big_1  37 assgtTdanGkatvt 51 
                                        +++ Td++G++ +t
  gi|298676131|ref|YP_003727880.1| 274 IATTNTDEDGEYLFT 288
                                       5799*******9875 PP

  == domain 6  score: 0.5 bits;  conditional E-value: 0.54
                             Big_1  16 angnpvagatVtfsvsggalsassgtTdanGkatv 50 
                                          + va+++V +   +g+   +s +T+a+G + +
  gi|298676131|ref|YP_003727880.1| 369 PGEKGVANVEVRLYNIDGDY-ITSEITNASGFYKF 402
                                       55677888888887666666.57999***998876 PP

  == domain 7  score: 3.6 bits;  conditional E-value: 0.061
                             Big_1  23 gatVtfsvsg...gals.assgtTdanGk 47 
                                       g++Vt++ +    g+++ ++  +Td++G+
  gi|298676131|ref|YP_003727880.1| 489 GTQVTWTYNVtntGNVNlTNINVTDSKGV 517
                                       789999866643555559**********8 PP

>> phage_tail_N  Prophage tail fibre N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.3    0.0063       7.1      40      71 ..      46      77 ..      28      88 .. 0.85
   2 ?   -1.3   0.0       1.8     2e+03      45      81 ..      92     128 ..      82     137 .. 0.67
   3 ?    5.5   0.2     0.014        16      39      68 ..     158     187 ..     134     203 .. 0.85
   4 ?    4.2   0.0     0.034        39      34      61 ..     270     298 ..     247     306 .. 0.77
   5 ?   -3.4   0.0       7.8   8.8e+03      38      60 ..     389     411 ..     387     431 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0063
                      phage_tail_N 40 senpdeaGrysldvetGkysvilkvdgfpesh 71
                                      s +++ +G y + v  G+y v +  dg++   
  gi|298676131|ref|YP_003727880.1| 46 STTTNASGYYNFSVTPGNYYVQFSSDGYEFTS 77
                                      5678889********************97654 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.8
                      phage_tail_N  45 eaGr.ysldvetGkysvilkvdgfpeshaGditvyeds 81 
                                        +G+  ++ ve G+   ++    +++  +Gd  v+ed+
  gi|298676131|ref|YP_003727880.1|  92 SSGNtTCITVESGETNDTVDAGLYQPATIGDF-VWEDT 128
                                       44432578888888888888888888888886.45554 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.014
                      phage_tail_N  39 asenpdeaGrysldvetGkysvilkvdgfp 68 
                                       +s +++ +G y + v  G y v +  dg++
  gi|298676131|ref|YP_003727880.1| 158 SSTTTNASGYYNFSVTPGSYYVNFSSDGYE 187
                                       46678889********************97 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.034
                      phage_tail_N  34 vvntvasenpdeaGrysld.vetGkysvi 61 
                                         n +a  n+de+G+y +     G y v 
  gi|298676131|ref|YP_003727880.1| 270 TGNLIATTNTDEDGEYLFTgLTPGVYNVS 298
                                       4478999*********9972455777775 PP

  == domain 5  score: -3.4 bits;  conditional E-value: 7.8
                      phage_tail_N  38 vasenpdeaGrysldvetGkysv 60 
                                       ++se ++ +G y + v  G+y +
  gi|298676131|ref|YP_003727880.1| 389 ITSEITNASGFYKFLVPPGHYYL 411
                                       67899999999*99999999965 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   8.9   0.00053      0.59       9      46 ..     485     520 ..     473     583 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00053
                             DUF11   9 evrpGdtvtytltvtNtgpasangvvvtDtlPaglayv 46 
                                        v+ G +vt t  vtNtg+++++++ vtD    g++  
  gi|298676131|ref|YP_003727880.1| 485 VVQVGTQVTWTYNVTNTGNVNLTNINVTD--SKGVEVN 520
                                       799**************************..5555544 PP

>> PLRV_ORF5  Potato leaf roll virus readthrough protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   2.4   0.00048      0.54      68     152 ..      43     136 ..      27     143 .. 0.70
   2 ?    9.3   0.8   0.00037      0.41      68     111 ..     156     199 ..     144     221 .. 0.80
   3 ?    1.0   0.0      0.12   1.3e+02      61      93 ..     381     413 ..     371     435 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00048
                         PLRV_ORF5  68 yssqssvsavaayvfnvpkGsysvdisceGyqsvdsisdned.........GrsdGliaysnadsdywnvGeadGvk 135
                                         s ++ +a   y f+v  G+y v+ s +Gy  ++   + +d         G    +   s    d  + G ++   
  gi|298676131|ref|YP_003727880.1|  43 LESSTTTNASGYYNFSVTPGNYYVQFSSDGYEFTSANQGTDDsmdsdadssGNTTCITVESGETNDTVDAGLYQPAT 119
                                       345556678899*******************8777654443311111111255555666777778888888888888 PP

                         PLRV_ORF5 136 ikklradntyrqGhkel 152
                                       i ++  ++t ++G++++
  gi|298676131|ref|YP_003727880.1| 120 IGDFVWEDTNKNGKQDI 136
                                       88888888888888775 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00037
                         PLRV_ORF5  68 yssqssvsavaayvfnvpkGsysvdisceGyqsvdsisdnedGr 111
                                         s ++ +a   y f+v  Gsy v+ s +Gy  +    + +dG 
  gi|298676131|ref|YP_003727880.1| 156 LESSTTTNASGYYNFSVTPGSYYVNFSSDGYEFTLANQGTDDGV 199
                                       345556678899*******************9998888877775 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.12
                         PLRV_ORF5  61 tkkidseyssqssvsavaayvfnvpkGsysvdi 93 
                                          id  y + +  +a   y f vp G+y ++ 
  gi|298676131|ref|YP_003727880.1| 381 LYNIDGDYITSEITNASGFYKFLVPPGHYYLNF 413
                                       5679999**********************9985 PP

>> SpaA  Prealbumin-like fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5  13.3         6   6.7e+03      36      59 ..      45      67 ..       9     180 .. 0.52
   2 ?   10.6   6.6   0.00048      0.54      35      59 ..     223     298 ..     183     314 .. 0.50
   3 ?    5.1   0.0     0.026        29       3      58 ..     371     411 ..     368     423 .. 0.89
   4 ?   -1.4   1.1       2.7   3.1e+03      34      52 ..     492     510 ..     429     545 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 6
                                      SEEE-BTTSEEEEEEEESEEEEEE CS
                              SpaA 36 ttlttdenGkatfegLplGtYllv 59
                                       + tt++ G+ +f+ + +G+Y+++
  gi|298676131|ref|YP_003727880.1| 45 SSTTTNASGYYNFS-VTPGNYYVQ 67
                                      44455555555555.555555543 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00048
                                       E...................................................SEEE-BTTSEEEEEEEESEEEEEE CS
                              SpaA  35 v...................................................ttlttdenGkatfegLplGtYllv 59 
                                       +                                                   +t  tde+G+  f+gL +G Y + 
  gi|298676131|ref|YP_003727880.1| 223 IdaglyqpenpkasmgdfvwedldgdgtqdigepgifnvtvylydcvtgnliATTNTDEDGEYLFTGLTPGVYNVS 298
                                       13333333333333333334444444444444444444444444444444449999*****************886 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.026
                                       CCB-TS-EEEEEETTTSCCCHCHHTT.TTCCEESEEE-BTTSEEEEEEEESEEEEE CS
                              SpaA   3 gkpLaGaeFtlykvdtttdgkdaleakktgtevttlttdenGkatfegLplGtYll 58 
                                       +k +a++e  ly++d              g+ +t+  t++ G  +f  +p+G Y+l
  gi|298676131|ref|YP_003727880.1| 371 EKGVANVEVRLYNID--------------GDYITSEITNASGFYKFL-VPPGHYYL 411
                                       678999999999999..............88899999*********9.9*****98 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 2.7
                                       EESEEE-BTTSEEEEEEEE CS
                              SpaA  34 evttlttdenGkatfegLp 52 
                                       +++t+   ++G+++ ++++
  gi|298676131|ref|YP_003727880.1| 492 VTWTYNVTNTGNVNLTNIN 510
                                       3333333334554444443 PP

>> Tgi2PP  Effector immunity protein Tgi2PP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.051        57      25      32 ..      53      60 ..      50      62 .. 0.90
   2 ?    4.3   0.1     0.041        46      25      32 ..     166     173 ..     163     176 .. 0.88
   3 ?    1.4   0.0      0.33   3.7e+02      10      31 ..     383     404 ..     379     405 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.051
                                      TEEEEEEE CS
                            Tgi2PP 25 GYadFlvl 32
                                      GY++F+v+
  gi|298676131|ref|YP_003727880.1| 53 GYYNFSVT 60
                                      *******8 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.041
                                       TEEEEEEE CS
                            Tgi2PP  25 GYadFlvl 32 
                                       GY++F+v+
  gi|298676131|ref|YP_003727880.1| 166 GYYNFSVT 173
                                       *******8 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.33
                                       EEE--B--TSS-SSTTEEEEEE CS
                            Tgi2PP  10 fIevDlqDaGkpylpGYadFlv 31 
                                       +I++D     +    G++ Flv
  gi|298676131|ref|YP_003727880.1| 383 NIDGDYITSEITNASGFYKFLV 404
                                       899999888899999*****98 PP

>> Dioxygenase_C  Dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.64   7.2e+02      74      99 ..      43      67 ..      30      80 .. 0.80
   2 ?   -0.1   0.0      0.48   5.4e+02      74      99 ..     156     180 ..     143     196 .. 0.79
   3 ?    7.0   0.0    0.0031       3.5      73      99 ..     272     298 ..     255     305 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.64
                                      TEEEEE--TTSEEEEEEE----EE-- CS
                     Dioxygenase_C 74 lrgriltdeeGryrirtikPapYpip 99
                                      l+ ++ t++ G+y++ ++ P+ Y ++
  gi|298676131|ref|YP_003727880.1| 43 LESSTTTNASGYYNF-SVTPGNYYVQ 67
                                      567888999999998.6999999765 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.48
                                       TEEEEE--TTSEEEEEEE----EE-- CS
                     Dioxygenase_C  74 lrgriltdeeGryrirtikPapYpip 99 
                                       l+ ++ t++ G+y++ ++ P++Y ++
  gi|298676131|ref|YP_003727880.1| 156 LESSTTTNASGYYNF-SVTPGSYYVN 180
                                       5678889999*9998.699*999765 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0031
                                       TTEEEEE--TTSEEEEEEE----EE-- CS
                     Dioxygenase_C  73 nlrgriltdeeGryrirtikPapYpip 99 
                                       nl  ++ tde+G+y ++ + P+ Y++ 
  gi|298676131|ref|YP_003727880.1| 272 NLIATTNTDEDGEYLFTGLTPGVYNVS 298
                                       7777888*****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (602 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.49
# Mc/sec: 3715.99
//
Query:       gi|298676132|ref|YP_003727881.1|  [L=995]
Description: multi-sensor signal transduction histidine kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.2e-37  125.7   0.0      2e-12   47.1   0.0    5.0  4  PAS            PAS fold
    1.6e-36  124.7   0.2    5.6e-10   39.4   0.0    5.1  4  PAS_9          PAS domain
    1.3e-34  119.1   0.2    4.3e-34  117.4   0.1    2.0  1  HATPase_c      Histidine kinase-, DNA gyrase B-, and HSP90-li
    2.7e-33  114.5   0.0    2.5e-11   43.8   0.0    4.9  5  PAS_4          PAS fold
    2.3e-28   97.7   0.6    2.6e-06   27.3   0.0    4.7  4  PAS_8          PAS domain
    3.2e-24   84.7   0.7    2.2e-22   78.9   0.2    2.9  2  HisKA          His Kinase A (phospho-acceptor) domain
    3.3e-17   62.5   0.1    4.5e-05   23.7   0.0    5.3  4  PAS_3          PAS fold
    0.00029   20.5   0.0        1.1    8.8   0.0    4.0  4  PAS_12         UPF0242 C-terminal PAS-like domain
    0.00044   20.4   0.1      0.071   13.3   0.0    4.0  5  PAS_7          PAS fold
    0.00056   20.2   0.0     0.0018   18.6   0.0    1.9  1  GAF_2          GAF domain
     0.0017   18.2   0.0     0.0049   16.7   0.0    1.8  1  HATPase_c_5    GHKL domain
      0.006   16.4   0.0      0.013   15.3   0.0    1.6  1  HATPase_c_3    Histidine kinase-, DNA gyrase B-, and HSP90-li
     0.0087   16.6   0.1       0.92   10.1   0.0    3.7  3  PAS_10         PAS domain
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.033   14.2   0.0    1.8  2  HATPase_c_2    Histidine kinase-like ATPase domain
        3.4    7.5   5.6        3.3    7.5   0.1    2.8  2  Synaptobrevin  Synaptobrevin


Domain annotation for each model (and alignments):
>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   1.7e-07    0.0002       6      53 ..     251     298 ..     246     348 .. 0.82
   2 !   14.1   0.0     3e-05     0.035       6      46 ..     384     424 ..     379     495 .. 0.86
   3 !   36.9   0.0   2.5e-12     3e-09       2      99 ..     513     608 ..     512     617 .. 0.80
   4 !   47.1   0.0   1.6e-15     2e-12       2     113 .]     633     741 ..     632     741 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.7e-07
                                       HHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTT CS
                               PAS   6 ileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldlihee 53 
                                       +l+s+ ++if++D    ++++N+ +e+ +G++re+++gk    l+  +
  gi|298676132|ref|YP_003727881.1| 251 VLDSSKVGIFILDSCFHVVWINEPMEDYFGIDREDIIGKDKRQLVEDK 298
                                       799************************************988777443 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 3e-05
                                       HHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBG CS
                               PAS   6 ileslpdpifvvDedgrilyvNaaaeellGlsreevlgksl 46 
                                       + +++p  i  vD++g i+y+N+aae  lGls + +  +++
  gi|298676132|ref|YP_003727881.1| 384 VADTSPICITKVDRNGYIVYANHAAEMVLGLSKSKIQERTY 424
                                       5566777777799*******************988777765 PP

  == domain 3  score: 36.9 bits;  conditional E-value: 2.5e-12
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHH..HTT-ECCCC CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlle..qgeesrage 76 
                                       ++r+ ++++p +ifv ++dg  + vN+aa +++G++r+e+l+ +l+dl + +    + e++ q+++  + + ++++e
  gi|298676132|ref|YP_003727881.1| 513 KFRNYIDHSPIGIFVANKDGYYVDVNPAASSITGYTRDELLSMNLIDLHPQD----VLEQIYQAYNylVENGKTSVE 585
                                       578899****************************************998887....999998876511555555555 PP

                                       EEEECTTSSEEEEEEEEEEEEET CS
                               PAS  77 isfklrdgrpihlevraspvrda 99 
                                         f +++ + +++ + a+++ d 
  gi|298676132|ref|YP_003727881.1| 586 LPFITKKSELRYFILDAVKLSDD 608
                                       55555888888888888777776 PP

  == domain 4  score: 47.1 bits;  conditional E-value: 1.6e-15
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       ++r+++e+++d+i++ D dg+ilyvN+ +++ lG++ +e+l+ +l d  ++ d +e +++++  l+  ++  ++ ++
  gi|298676132|ref|YP_003727881.1| 633 RFRTVIEQAADAIIAHDFDGNILYVNDLTCDNLGYTKDELLSMNLADIDPNIDTYEPRKRYWDKLSYHSSYLIETVN 709
                                       799*******************************************999999999********************** PP

                                       EECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  79 fklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       +++ dg+++++ev ++ +   g+    +lg++rdi
  gi|298676132|ref|YP_003727881.1| 710 RRK-DGSEFPVEVKMTLMNLSGKP--VILGFVRDI 741
                                       ***.**********9988777666..9*******8 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   9.8e-10   1.2e-06       2      77 ..     257     324 ..     256     360 .. 0.75
   2 !   23.1   0.0   5.6e-08   6.7e-05       4     104 .]     390     499 ..     387     499 .. 0.86
   3 !   27.2   0.0     3e-09   3.6e-06       2     104 .]     523     619 ..     522     619 .. 0.77
   4 !   39.4   0.0   4.7e-13   5.6e-10       4     103 ..     645     742 ..     642     743 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 9.8e-10
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfw 77 
                                       +gi+i ++ ++++++Ne +++ +G ++e+++gk+ ++l+      +++l++++e+ +  e++  +  ++++++++ 
  gi|298676132|ref|YP_003727881.1| 257 VGIFILDSCFHVVWINEPMEDYFGIDREDIIGKDKRQLV------EDKLKHIFEDSD--EFANRLLATYDDNSYIE 324
                                       699*998888*****************************......666777777666..66666655555554444 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 5.6e-08
                             PAS_9   4 ili..dnpdgrilyaNeaalrllGyspeevlgksitdlf....vtdpeanerlraaleqgrk...kerevevvlirk 71 
                                       i+i  ++ +g i+yaN aa+ +lG s+  +  + ++d+     ++d +    ++  +e  +k   ++++v   ++ +
  gi|298676132|ref|YP_003727881.1| 390 ICItkVDRNGYIVYANHAAEMVLGLSKSKIQERTYDDVKwkitDFDGNYYPQEELPFELVQKylePVYDVRHAIQWP 466
                                       5555689***************************9999966665555555555555566666999************ PP

                             PAS_9  72 ngetfwvlltaspvkdddgelvgiivilrDite 104
                                       +g++ +  ++a+p++dd +++ g+++ +++i+e
  gi|298676132|ref|YP_003727881.1| 467 DGQRKLLSINAAPIFDDYNRFDGLVAAIENISE 499
                                       *******************************98 PP

  == domain 3  score: 27.2 bits;  conditional E-value: 3e-09
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetf 76 
                                        gi++ n+dg  +++N+aa  ++Gy+++e+l  ++ dl   +  ++  +  + ++e+      +ve+ +i+k+ e  
  gi|298676132|ref|YP_003727881.1| 523 IGIFVANKDGYYVDVNPAASSITGYTRDELLSMNLIDLHpqDVLEQIYQAYNYLVEN---GKTSVELPFITKKSELR 596
                                       699**99*************************9999999333333333333444444...56999999999999999 PP

                             PAS_9  77 wvlltaspvkdddgelvgiivilrDite 104
                                       ++ l a+ + dd+     ++++ +Dite
  gi|298676132|ref|YP_003727881.1| 597 YFILDAVKLSDDK-----YLGFTTDITE 619
                                       9888888885554.....4479999997 PP

  == domain 4  score: 39.4 bits;  conditional E-value: 4.7e-13
                             PAS_9   4 ilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfwvl 79 
                                       i+  + dg+ily+N+  ++ lGy+++e+l  ++ d+  ++ ++ e  +++++ ++  + +  e+v++rk+g++f+v+
  gi|298676132|ref|YP_003727881.1| 645 IIAHDFDGNILYVNDLTCDNLGYTKDELLSMNLADID-PNIDTYEPRKRYWDKLSYhSSYLIETVNRRKDGSEFPVE 720
                                       55555799****************************9.77777777777777777788******************* PP

                             PAS_9  80 ltaspvkdddgelvgiivilrDit 103
                                       ++++ +  +++ +++  +++rDit
  gi|298676132|ref|YP_003727881.1| 721 VKMTLMNLSGKPVIL--GFVRDIT 742
                                       ******877888888..******9 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.4   0.1   3.6e-37   4.3e-34       2     111 ..     879     988 ..     878     989 .. 0.97

  Alignments for each domain:
  == domain 1  score: 117.4 bits;  conditional E-value: 3.6e-37
                                       HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTSSSHH CS
                         HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsq.ddstkrggggtGlG 77 
                                       de++Lrqi+ nl+ Na+kf t++g+++v++++++d +++sv D+GiGip+++++++fe+f q d +++r++ gtGlG
  gi|298676132|ref|YP_003727881.1| 879 DEIKLRQILYNLIYNAIKF-TNKGSVTVTVRQKNDAYQFSVIDTGIGIPEDKQDEIFESFRQlDTGASRRYAGTGLG 954
                                       899****************.***********7779****************************************** PP

                                       HHHHHHHHHHTTTEEEEEEETTTEEEEEEEEESS CS
                         HATPase_c  78 lsivkklvelmgGeiwvesepgrGttftftlple 111
                                       l++vk+lve +gG+iwvese+ +Gttftft+p +
  gi|298676132|ref|YP_003727881.1| 955 LALVKRLVEIHGGQIWVESEESKGTTFTFTIPST 988
                                       *******************************976 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0         6   7.2e+03       7      23 ..     113     129 ..     111     141 .. 0.78
   2 !   27.9   0.0   1.9e-09   2.2e-06       1     109 [.     252     368 ..     252     369 .. 0.93
   3 !   15.2   0.0   1.5e-05     0.018       2     108 ..     386     500 ..     385     502 .. 0.88
   4 !   43.8   0.0   2.1e-14   2.5e-11       2     109 ..     519     621 ..     518     622 .. 0.98
   5 !   21.5   0.0   1.8e-07   0.00021       2     110 .]     639     746 ..     638     746 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 6
                             PAS_4   7 alavldpdgrvlyaNaa 23 
                                       +++ +d+dg++++ +++
  gi|298676132|ref|YP_003727881.1| 113 WIILFDEDGNITASSES 129
                                       67888****99986655 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 1.9e-09
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee......daarleralrrvlegeepieflee 71 
                                       lds+ +++++ld+ ++v+++N+ ++++fg+++e+++Gk  ++l+ +       d +++++ l +  + +  ie  e+
  gi|298676132|ref|YP_003727881.1| 252 LDSSKVGIFILDSCFHVVWINEPMEDYFGIDREDIIGKDKRQLVEDKlkhifeDSDEFANRLLATYDDNSYIENFEC 328
                                       79***************************************999999999999999999999999999********* PP

                             PAS_4  72 lll...pgeerhyelrllPlrdesGe.vigvlvisrDiTerr 109
                                       ++l   ++eer++e    P+   sG  + g +++ +DiT r+
  gi|298676132|ref|YP_003727881.1| 329 HVLpdsNREERWLEHWSQPI--KSGLyAGGRIEHYYDITYRK 368
                                       *999***********99999..56777999999999999775 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 1.5e-05
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee......daarleralrrvlegeepiefleel 72 
                                       d +p +++ +d++g ++yaN aa+ ++g++   +  +t+ ++  +         ++ e + + v +  ep++++ + 
  gi|298676132|ref|YP_003727881.1| 386 DTSPICITKVDRNGYIVYANHAAEMVLGLSKSKIQERTYDDVKWKItdfdgnYYPQEELPFELVQKYLEPVYDVRHA 462
                                       6799999***************999***************9644447778889999999999999999999999988 PP

                             PAS_4  73 ll..pgeerhyelrllPlrdesGevigvlvisrDiTer 108
                                           +g+++ +++++ P++d+  + +g+++ +  i+e 
  gi|298676132|ref|YP_003727881.1| 463 IQwpDGQRKLLSINAAPIFDDYNRFDGLVAAIENISEK 500
                                       88999999999999999999999999999999888875 PP

  == domain 4  score: 43.8 bits;  conditional E-value: 2.1e-14
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgee 78 
                                       d++p +++v ++dg ++++N+aa ++ g++++ell + l +l+p+++ +++ +a++ ++e +++  +l + +   e 
  gi|298676132|ref|YP_003727881.1| 519 DHSPIGIFVANKDGYYVDVNPAASSITGYTRDELLSMNLIDLHPQDVLEQIYQAYNYLVENGKTSVELPFITKKSEL 595
                                       89*************************************************************************** PP

                             PAS_4  79 rhyelrllPlrdesGevigvlvisrDiTerr 109
                                       r++ l ++ l d     + +l++++DiTer+
  gi|298676132|ref|YP_003727881.1| 596 RYFILDAVKLSD-----DKYLGFTTDITERK 621
                                       ***********9.....9************8 PP

  == domain 5  score: 21.5 bits;  conditional E-value: 1.8e-07
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee.daarleralrrvlegeepiefleelllpge 77 
                                       ++  da+++ d dg++ly+N   ++ +g++ +ell + la++ p     ++  r+++++      ++++  ++ +g+
  gi|298676132|ref|YP_003727881.1| 639 EQAADAIIAHDFDGNILYVNDLTCDNLGYTKDELLSMNLADIDPNIdTYEPRKRYWDKLSYHSSYLIETVNRRKDGS 715
                                       678899***********************************9999999***********999877777777777*** PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerrr 110
                                       e ++e+ ++ + + sG+   +l+++rDiT r++
  gi|298676132|ref|YP_003727881.1| 716 EFPVEVKMTLM-NLSGK-PVILGFVRDITVRKQ 746
                                       *********99.89***.889********9985 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   1.2e-08   1.5e-05       1      53 [.     242     299 ..     242     315 .. 0.77
   2 !   14.3   0.0   2.7e-05     0.032       9      54 ..     387     436 ..     379     450 .. 0.65
   3 !   27.3   0.0   2.2e-09   2.6e-06       2      46 ..     513     558 ..     512     572 .. 0.84
   4 !   25.6   0.0   7.4e-09   8.9e-06       2      54 ..     633     686 ..     632     697 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.2e-08
                             PAS_8   1 erlral....fesspdgiavvdlgd..rivdvNqaalellGys.adlkgellgqllpvlr 53 
                                       er+r++    ++ss +gi+++d     ++v++N+ +++ +G + +d++g++ +ql+++  
  gi|298676132|ref|YP_003727881.1| 242 ERHRTIvddvLDSSKVGIFILD--ScfHVVWINEPMEDYFGIDrEDIIGKDKRQLVEDKL 299
                                       688885444488*********9..666**************9999999999987766544 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 2.7e-05
                             PAS_8   9 sspdgiavvd.lgdrivdvNqaalellGys....adlkgellgqllpvlrp 54 
                                       +sp  i  vd +g  iv++N aa++ lG+s    ++   +++ + ++++++
  gi|298676132|ref|YP_003727881.1| 387 TSPICITKVDrNGY-IVYANHAAEMVLGLSkskiQERTYDDVKWKITDFDG 436
                                       55555554786888.*************77744444444444455555555 PP

  == domain 3  score: 27.3 bits;  conditional E-value: 2.2e-09
                             PAS_8   2 rlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellg 46 
                                       ++r+ +++sp gi+v++ +g   vdvN+aa  ++Gy+ ++l+ + l 
  gi|298676132|ref|YP_003727881.1| 513 KFRNYIDHSPIGIFVANkDGY-YVDVNPAASSITGYTrDELLSMNLI 558
                                       79999***********97777.***************8888877664 PP

  == domain 4  score: 25.6 bits;  conditional E-value: 7.4e-09
                             PAS_8   2 rlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellgqllpvlrp 54 
                                       r+r+++e+++d+i+  d +g+ i++vN+ +++ lGy+ ++l+ + l ++ p ++ 
  gi|298676132|ref|YP_003727881.1| 633 RFRTVIEQAADAIIAHDfDGN-ILYVNDLTCDNLGYTkDELLSMNLADIDPNIDT 686
                                       9*************9999999.***************888888777655554444 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.076        91      43      64 ..     236     257 ..     210     258 .. 0.86
   2 !   78.9   0.2   1.8e-25   2.2e-22       1      67 []     764     832 ..     764     832 .. 0.96

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.076
                                       HHHHHHHHHHHHHHHHHHHCCH CS
                             HisKA  43 tiesearrldhlvedlLdlsri 64 
                                       ++++ ++r + +v+d+Ld s+ 
  gi|298676132|ref|YP_003727881.1| 236 KLIEKEERHRTIVDDVLDSSKV 257
                                       5677888***********9985 PP

  == domain 2  score: 78.9 bits;  conditional E-value: 1.8e-25
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH.HHC...T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                             HisKA   1 slgrflagvaHELrtPLsailgnaea.Lkre.gklteelkeyletiesearrldhlvedlLdlsrieag 67 
                                       +++++la+v+HELrtPL++i+g++++ Lkr+ g+l++++ +yl++i++++++l++l++d+Ldl++ie+g
  gi|298676132|ref|YP_003727881.1| 764 AKSELLANVSHELRTPLTSIIGFSDViLKRKvGDLNDNQTRYLDKIHKSGQHLLDLINDILDLAKIESG 832
                                       589***********************55888************************************97 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.032        38       2      30 ..     269     295 ..     268     350 .. 0.80
   2 ?    5.2   0.0     0.022        26       2      86 ..     402     491 ..     401     494 .. 0.77
   3 !   23.7   0.0   3.7e-08   4.5e-05       2      71 ..     535     601 ..     534     609 .. 0.86
   4 !   22.1   0.0   1.1e-07   0.00013       2      87 ..     655     736 ..     654     738 .. 0.95

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.032
                             PAS_3   2 iyvserveeilGyspeellgkveswldlv 30 
                                       + ++e +e+++G+++e+++gk  + ++lv
  gi|298676132|ref|YP_003727881.1| 269 VWINEPMEDYFGIDREDIIGK--DKRQLV 295
                                       67899****************..544444 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.022
                             PAS_3   2 iyvserveeilGyspeellgk.veswldlvhpeDrervrea...lqealkkge.pyegeyRirrkdGeyrwvearar 73 
                                       +y++ + e +lG+s++ ++++ +++++  +   D +++ ++   ++ + k  e +y++ + i+++dG+   ++  a 
  gi|298676132|ref|YP_003727881.1| 402 VYANHAAEMVLGLSKSKIQERtYDDVKWKITDFDGNYYPQEelpFELVQKYLEpVYDVRHAIQWPDGQRKLLSINAA 478
                                       79999999999999999999988888888888885555444111445557777788999999999999999999999 PP

                             PAS_3  74 virdengkpvrvi 86 
                                       +i+d+ ++ + ++
  gi|298676132|ref|YP_003727881.1| 479 PIFDDYNRFDGLV 491
                                       9999888877665 PP

  == domain 3  score: 23.7 bits;  conditional E-value: 3.7e-08
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeD.rervrealqealkkgepyegeyRirrkdGeyrwvear 71 
                                       + v+++ + i+Gy+++ell+   +++dl hp+D +e++++a++ ++++g+  ++e  +++k  e r++   
  gi|298676132|ref|YP_003727881.1| 535 VDVNPAASSITGYTRDELLSM--NLIDL-HPQDvLEQIYQAYNYLVENGK-TSVELPFITKKSELRYFILD 601
                                       689******************..99996.77777*********9999999.7999999*999999988655 PP

  == domain 4  score: 22.1 bits;  conditional E-value: 1.1e-07
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       +yv++  ++ lGy+++ell+   +++d+    D  + r+ +++ l+  ++y +e   rrkdG+ + ve +++ + + 
  gi|298676132|ref|YP_003727881.1| 655 LYVNDLTCDNLGYTKDELLSM--NLADIDPNIDTYEPRKRYWDKLSYHSSYLIETVNRRKDGSEFPVEVKMTLM-NL 728
                                       89*******************..***************************************************.99 PP

                             PAS_3  79 ngkpvrvig 87 
                                       +gkpv ++g
  gi|298676132|ref|YP_003727881.1| 729 SGKPV-ILG 736
                                       99999.555 PP

>> PAS_12  UPF0242 C-terminal PAS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.22   2.6e+02      67      99 ..     266     299 ..     233     308 .. 0.71
   2 ?    4.6   0.0     0.019        22      68      93 ..     400     425 ..     374     434 .. 0.86
   3 ?   -2.0   0.0       2.1   2.5e+03      63      89 ..     528     554 ..     520     592 .. 0.80
   4 !    8.8   0.0   0.00096       1.1      54     137 ..     639     725 ..     635     730 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.22
                            PAS_12  67 nkllfaNaqirallGwssdkfl.qdfseivqegl 99 
                                        +++++N+ +++  G   ++++ +d  ++v++ l
  gi|298676132|ref|YP_003727881.1| 266 FHVVWINEPMEDYFGIDREDIIgKDKRQLVEDKL 299
                                       3699**************9998345667777655 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.019
                            PAS_12  68 kllfaNaqirallGwssdkflqdfse 93 
                                        +++aN+  +++lG+s+ k+ ++  +
  gi|298676132|ref|YP_003727881.1| 400 YIVYANHAAEMVLGLSKSKIQERTYD 425
                                       599****************9887655 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2.1
                            PAS_12  63 sqkenkllfaNaqirallGwssdkflq 89 
                                       ++k+   + +N    +++G+  d++l+
  gi|298676132|ref|YP_003727881.1| 528 ANKDGYYVDVNPAASSITGYTRDELLS 554
                                       666666677899999******999986 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.00096
                            PAS_12  54 EnlgailvysqkenkllfaNaqirallGwssdkflqdfseivqegleeW...kralaklsskteskirlvlKtKagq 127
                                       E+++  ++   ++  +l++N+ + + lG+ +d++l+     +++ ++++   kr  +kls +    i+ v + K g 
  gi|298676132|ref|YP_003727881.1| 639 EQAADAIIAHDFDGNILYVNDLTCDNLGYTKDELLSMNLADIDPNIDTYeprKRYWDKLSYHSSYLIETVNRRKDGS 715
                                       55666677778999********************9987777777666552225667788888888888888888888 PP

                            PAS_12 128 evllncllgi 137
                                       e ++++++ +
  gi|298676132|ref|YP_003727881.1| 716 EFPVEVKMTL 725
                                       7777776655 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0     6e-05     0.071       2     114 ..     253     371 ..     252     372 .. 0.79
   2 ?    1.5   0.0      0.27   3.3e+02       8     114 ..     392     504 ..     388     505 .. 0.73
   3 ?   -0.7   0.1       1.3   1.6e+03     103     114 ..     613     624 ..     518     625 .. 0.65
   4 ?   -3.1   0.0       6.9   8.3e+03       2      33 ..     639     670 ..     638     680 .. 0.79
   5 ?   -3.1   0.0         7   8.4e+03     105     115 .]     739     749 ..     726     749 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6e-05
                             PAS_7   2 enmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaeverrl......aaara 72 
                                       ++ + Gi ++D+   +v +N+ + + +++ +e + +g+  ++l++   ++  f+  d++++++r l      + +++
  gi|298676132|ref|YP_003727881.1| 253 DSSKVGIFILDSCFHVVWINEPMEDYFGIDREDI-IGKDKRQLVEDKLKH-IFE--DSDEFANRLLatyddnSYIEN 325
                                       66678***************************99.999999998877543.333..555555555522233235667 PP

                             PAS_7  73 gkphsfererpdgrvievrgnpl....pdgGfVttytDiTerrrae 114
                                       ++ h +  + +++r++e  ++p+      gG +  y DiT r+  e
  gi|298676132|ref|YP_003727881.1| 326 FECHVLPDSNREERWLEHWSQPIksglYAGGRIEHYYDITYRKIIE 371
                                       9999******************94444569***********98766 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.27
                             PAS_7   8 isvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagd..veaeverrlaaaragkphsferer 82 
                                       i+ +D+++ +v  N+    +l+l+++ +q  +  +   +++   g++ +++  + + v++ l+ +  + +h+++   
  gi|298676132|ref|YP_003727881.1| 392 ITKVDRNGYIVYANHAAEMVLGLSKSKIQERTYDDVKWKITDFDGNYYPQEelPFELVQKYLEPVY-DVRHAIQWPD 467
                                       556899999999999999999999999977766555566666677777444236667888886554.4778888888 PP

                             PAS_7  83 pdgrvievrgnpl.....pdgGfVttytDiTerrrae 114
                                        + + +++++ p+        G+V+  + i+e++++e
  gi|298676132|ref|YP_003727881.1| 468 GQRKLLSINAAPIfddynRFDGLVAAIENISEKIEKE 504
                                       8888999999998544433478888888888888876 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.3
                             PAS_7 103 tytDiTerrrae 114
                                         tDiTer++ e
  gi|298676132|ref|YP_003727881.1| 613 FTTDITERKKVE 624
                                       457777777765 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 6.9
                             PAS_7   2 enmsqGisvfDadlrLvawNrrylelldlpee 33 
                                       e+  ++i+  D d++++ +N+  ++ l+++++
  gi|298676132|ref|YP_003727881.1| 639 EQAADAIIAHDFDGNILYVNDLTCDNLGYTKD 670
                                       67778899999999999999999888888776 PP

  == domain 5  score: -3.1 bits;  conditional E-value: 7
                             PAS_7 105 tDiTerrraee 115
                                        DiT r++aee
  gi|298676132|ref|YP_003727881.1| 739 RDITVRKQAEE 749
                                       7*******996 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.5e-06    0.0018       2     137 ..      90     228 ..      89     228 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.5e-06
                                       HHHHHHHHHHHHHHHHS.S..EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B--....-TTHHHHHHHHTS-EEES- CS
                             GAF_2   2 adleelldlvldelvel.gaalgyillvdddgglrlaawgeaeeefgaaldrpl....geglvgealrtgrpvilnd 73 
                                       +++e+ll++++d l++  +++  +i l d+dg+++ ++ ++ +++f++ l r      +++l    +++   +++++
  gi|298676132|ref|YP_003727881.1|  90 KNVEQLLQRTCDILTNSrTFESTWIILFDEDGNITASSESGVGPSFNDFLKRYErgemSRCLQDLFYQSDNLLVIEN 166
                                       689*************856**************99999999999*99999663332224444333444456777999 PP

                                       GGG-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  74 leedpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                        +++ + ++l + + g++  l+  l ++++++G+l++ +  ++  +e+  +l+ e+ ++i+ a+
  gi|298676132|ref|YP_003727881.1| 167 KKSNCSDCPLILKETGYN-ALVSRLEHGNKLYGILAV-SGSDDIISERGKQLFHEVTSDISYAL 228
                                       999999999996666654.5666777789*******8.7777789**************99987 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   4.1e-06    0.0049       3      92 ..     880     976 ..     878     985 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.1e-06
                       HATPase_c_5   3 dldlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg.......ek....kkless.kskkeeh 67 
                                       ++ l  il nl+ NAi   +k +     +++tvr+k++++ +s+  +  g       e+    ++l +  +++    
  gi|298676132|ref|YP_003727881.1| 880 EIKLRQILYNLIYNAIKFTNKGS-----VTVTVRQKNDAYQFSVIDTGIGipedkqdEIfesfRQLDTGaSRRYAGT 951
                                       5678899*********8877766.....9****************99666666655422433455554435667788 PP

                       HATPase_c_5  68 GiGlksireivkkykgnlsieaedg 92 
                                       G+Gl  ++++v+ ++g++++e e+ 
  gi|298676132|ref|YP_003727881.1| 952 GLGLALVKRLVEIHGGQIWVESEES 976
                                       999****************998875 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.1e-05     0.013       4      76 ..     884     954 ..     881     989 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.1e-05
                       HATPase_c_3   4 ekAlaelvdNsld.AdaenvkievnknrgktgeivieDdGkGmseeelknalr.latsskeakrkstslGkkGiG 76 
                                       ++ l  l+ N++   +  +v+++v ++ +++ ++++ D G G++e++ ++ ++ + + ++     s+ +   G+G
  gi|298676132|ref|YP_003727881.1| 884 RQILYNLIYNAIKfTNKGSVTVTVRQK-NDAYQFSVIDTGIGIPEDKQDEIFEsFRQLDTG---ASRRYAGTGLG 954
                                       566889******9889999******97.589***************999988624444444...34444444555 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.37   4.5e+02       4      39 ..     251     286 ..     248     348 .. 0.86
   2 !   10.1   0.0   0.00077      0.92       6     105 ..     386     497 ..     381     498 .. 0.74
   3 ?   -1.0   0.0       2.2   2.6e+03      42      83 ..     556     598 ..     515     619 .. 0.60

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.37
                            PAS_10   4 lLnstpieltflDdnlqirrFtpaakklfklipadv 39 
                                       +L+s ++++  lD+  ++ + ++  + +f + ++d+
  gi|298676132|ref|YP_003727881.1| 251 VLDSSKVGIFILDSCFHVVWINEPMEDYFGIDREDI 286
                                       79999************************9999885 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00077
                            PAS_10   6 nstpieltflDdnlqirrFtpaa........kklfklipadvGrpladihpk...kavknveeviealrtgekdeve 71 
                                       ++ pi +t +D+n  i + ++aa        +k+ +++ +dv  +++d+  +   +++  +e v + l    ++++ 
  gi|298676132|ref|YP_003727881.1| 386 DTSPICITKVDRNGYIVYANHAAemvlglskSKIQERTYDDVKWKITDFDGNyypQEELPFELVQKYLEPVYDVRHA 462
                                       67899999*************87111211114555555566666666664333336666678899999999999999 PP

                            PAS_10  72 vvvp.kngkwvlvrylpyrdedgeiaGvvetfvDi 105
                                       ++ p  + k+  ++  p+ d+ ++++G+v  + +i
  gi|298676132|ref|YP_003727881.1| 463 IQWPdGQRKLLSINAAPIFDDYNRFDGLVAAIENI 497
                                       9998789999********************99998 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2.2
                            PAS_10  42 pladihpkkavknveeviealrtgekdevevvv.pkngkwvlv 83 
                                       +l d+hp++ ++++ +  + l ++ k  ve +  +k+ ++ + 
  gi|298676132|ref|YP_003727881.1| 556 NLIDLHPQDVLEQIYQAYNYLVENGKTSVELPFiTKKSELRYF 598
                                       5667777777777777777777777766666553344333333 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       9.3   1.1e+04      86     112 ..     615     645 ..     571     655 .. 0.55
   2 ?   14.2   0.0   2.7e-05     0.033      41     113 ..     888     968 ..     877     985 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 9.3
                       HATPase_c_2  86 pteeep....keslkegGrGlalikglvDev 112
                                        + +e     +e ++++Gr   +i++ +D +
  gi|298676132|ref|YP_003727881.1| 615 TDITERkkveDELKESEGRFRTVIEQAADAI 645
                                       3333333343456666666666666666665 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 2.7e-05
                       HATPase_c_2  41 tNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeep........keslkegGrGlalikglv 109
                                       +N +  a +  ++g+v+v+++++++a +++v D G g +  ++++  e  +        +      G+Glal+k+lv
  gi|298676132|ref|YP_003727881.1| 888 YNLIYNAIKFTNKGSVTVTVRQKNDAYQFSVIDTGIGIPEDKQDEIFE--SfrqldtgaSRRYAGTGLGLALVKRLV 962
                                       555555555556699*********************976665444333..2357788778888999**********9 PP

                       HATPase_c_2 110 Dev..e 113
                                       +    +
  gi|298676132|ref|YP_003727881.1| 963 EIHggQ 968
                                       866554 PP

>> Synaptobrevin  Synaptobrevin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   1.5      0.47   5.6e+02      62      85 ..       6      29 ..       2      31 .. 0.83
   2 ?    7.5   0.1    0.0028       3.3      21      52 ..      80     111 ..      68     113 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.47
                                      HHHTXXXXXXXXXXXXXXXXXXXX CS
                     Synaptobrevin 62 wwknmkliiililvvlililiiii 85
                                      ++kn k +ii++l++ ++i++i i
  gi|298676132|ref|YP_003727881.1|  6 YFKNKKSVIIVTLMLGFFIILIDI 29
                                      579999999999999999998855 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0028
                                       CHHHHCHCCCCCHHHHCCCCHHHHHHHHHHHH CS
                     Synaptobrevin  21 eNidkvlergekldeLvdktenLqssaqqFkk 52 
                                       +++++++ r++++++L ++t ++ +++++F++
  gi|298676132|ref|YP_003727881.1|  80 SDVNQLIIREKNVEQLLQRTCDILTNSRTFES 111
                                       679999************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (995 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1029  (0.0573931); expected 358.6 (0.02)
Passed bias filter:                      701  (0.0390987); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.84u 0.32s 00:00:01.15 Elapsed: 00:00:00.49
# Mc/sec: 6053.29
//
Query:       gi|298676133|ref|YP_003727882.1|  [L=569]
Description: von Willebrand factor type A [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-17   64.2   1.6    3.6e-17   63.2   1.6    1.5  1  VWA              von Willebrand factor type A domain
    5.8e-17   61.6   0.0      1e-16   60.8   0.0    1.4  1  DUF1194          Protein of unknown function (DUF1194)
    4.4e-09   37.0   0.5    7.6e-09   36.2   0.5    1.4  1  VWA_2            von Willebrand factor type A domain
    1.2e-05   25.5  27.4      0.033   14.4   1.4    4.3  4  CARDB            CARDB
    0.00022   21.5  14.8       0.23   11.8   1.0    4.2  3  DUF11            Domain of unknown function DUF11
     0.0012   18.8   2.9       0.38   10.7   0.1    3.3  3  DUF2393          Protein of unknown function (DUF2393)
      0.003   17.5   8.9       0.22   11.6   0.8    3.8  3  DUF1573          Protein of unknown function (DUF1573)
     0.0054   16.3   0.5      0.085   12.4   0.1    2.3  2  Glucodextran_N   Glucodextranase, domain N
     0.0074   15.7  10.6       0.12   11.8   0.1    3.8  3  TRAP_beta        Translocon-associated protein beta (TRAPB)
  ------ inclusion threshold ------
      0.053   12.4   0.5        1.6    7.5   0.1    2.4  2  Integrin_alpha2  Integrin alpha
       0.19   12.0   5.7         26    5.1   0.1    4.6  5  NPCBM_assoc      NPCBM-associated, NEW3 domain of alpha-galac
       0.82    9.9   3.4       0.55   10.4   1.1    1.9  2  Ecm33            GPI-anchored cell wall organization protein


Domain annotation for each model (and alignments):
>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.2   1.6   2.4e-20   3.6e-17       1     173 [.      22     201 ..      22     203 .. 0.85

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 2.4e-20
                                       EEEEEEE-STTSCHHHHHHHHHHHHHHHHHHTB..TTTTEEEEEEEESSSEEEEEETTSHC...HHHHHHHHHHTGS CS
                               VWA   1 DivfvlDgSgsmgeenfekvkefikklveklev..gpegtrvglvqfssevktefslndys...skeellsalnnlk 72 
                                       D+++++DgSgs++ ++fe  +e + + +++ ++  +  +++++++qfs+ +++e++l++ +   + + + s++ +++
  gi|298676133|ref|YP_003727882.1|  22 DLYLLVDGSGSISSSDFELQLEGMANTINNSSIvpQDGSVSISVIQFSNIAQVEIPLTTINsqsDADNISSDIIAIN 98 
                                       9*******************************768999999******************887877799999999999 PP

                                       GGGGSSC-HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CS.S.....HTHHHHHHHHGCTEEEEEEEESSSH CS
                               VWA  73 ysgggttntgkalkyaleklfkssagaRenakkviilltdGksnd.g.....dpkeaaneakeqgikvfavGvgnad 143
                                       + gg+t+ +  a++  ++kl +  +g     k++i l tdG +n  g     d +++an+   +  ++ ++Gvg  +
  gi|298676133|ref|YP_003727882.1|  99 QVGGSTN-ISGAINLSVQKLPDDLSG-----KQIIDLSTDGVPNVnGiqasyDARDNANNSGFE--ELNTLGVGIGV 167
                                       9999999.******************.....************994587655555555555544..57777777788 PP

                                       HHHHHHHHSSSSC....HHCEEEESSHHHHHHHH CS
                               VWA 144 ekelLnkiasepg....eghvftvtdfeeleelf 173
                                       ++++L+++         +g++ ++ df+++++ f
  gi|298676133|ref|YP_003727882.1| 168 NETFLKELVFPQPsdeyPGFYTFAGDFDTFQKEF 201
                                       8999****44333356689999999999888655 PP

>> DUF1194  Protein of unknown function (DUF1194)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.8   0.0   6.8e-20     1e-16       4     203 ..      21     210 ..      18     213 .. 0.82

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 6.8e-20
                           DUF1194   4 leLvLavDvSgSvdeeElrlQreGyaaAlrdpevleallagalgriavtyveWsgeseqevvvdWtviesaedaeaf 80 
                                       ++L L+vD SgS+++++++lQ eG a+ +++ +++ +      g++++++++ s+    +v ++ t+i+s++da+++
  gi|298676133|ref|YP_003727882.1|  21 VDLYLLVDGSGSISSSDFELQLEGMANTINNSSIVPQ-----DGSVSISVIQFSNI--AQVEIPLTTINSQSDADNI 90 
                                       78*****************************998753.....489*********95..5688999************ PP

                           DUF1194  81 aaklaaapraaarrtaigeAlefaaallaenpveglrrviDvSGDGpnn.eglepvtaardaaeakgv.tingLaie 155
                                       ++ + a + +  ++t i++A++ +++ l +      +++iD+S DG  n +g++   +ard+a+++g    n L ++
  gi|298676133|ref|YP_003727882.1|  91 SSDIIAIN-QVGGSTNISGAINLSVQKLPDDLS--GKQIIDLSTDGVPNvNGIQASYDARDNANNSGFeELNTLGVG 164
                                       ****9876.56778**************98665..9**********88868999999**********9889999998 PP

                           DUF1194 156 tkeaeasaeldayyeeevigGpgaFvltanefedfaeairrKLvrEia 203
                                          +e++   +  + +   + pg F   a +f++f++  ++K   E+ 
  gi|298676133|ref|YP_003727882.1| 165 IGVNETFL-KELVFPQPSDEYPG-FYTFAGDFDTFQKEFEKKAGKEVG 210
                                       87764322.12245555555555.777777777777777777777765 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.5   5.1e-12   7.6e-09       2     106 ..      24     133 ..      23     134 .. 0.81

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 5.1e-12
                             VWA_2   2 vfvlDtSgSmrngdygptrleaakdaveallksl.....pgd.rvglvtfsdgpevliplt.....kdkakilnalr 67 
                                        +++D+SgS++++d     +e + + + + +++      +g+  +++++fs+ ++v+iplt     +d + i + + 
  gi|298676133|ref|YP_003727882.1|  24 YLLVDGSGSISSSD-----FELQLEGMANTINNSsivpqDGSvSISVIQFSNIAQVEIPLTtinsqSDADNISSDII 95 
                                       69***********7.....777777777777744456434446*****************87867788999999999 PP

                             VWA_2  68 nleakgggtnlaaaLqlarkalkkrrkgekrvivlitDg 106
                                       ++++ gg tn+  a++l  + l+++  + k++i l tDg
  gi|298676133|ref|YP_003727882.1|  96 AINQVGGSTNISGAINLSVQKLPDDL-SGKQIIDLSTDG 133
                                       99999*************99999885.666666666677 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.5      0.14   2.1e+02      11      72 ..      11      81 ..       5      98 .. 0.64
   2 !   14.4   1.4   2.2e-05     0.033      10      79 ..     228     292 ..     225     310 .. 0.81
   3 !    9.0   0.6    0.0011       1.6      14      78 ..     339     398 ..     331     411 .. 0.78
   4 !   13.7   5.1   3.8e-05     0.057      14      92 ..     446     522 ..     440     529 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.14
                                      C-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE.........EEEEESEE-CTEEEEEEEEEE-S CS
                             CARDB 11 npseafvgeentitvtvkNqGtaasgatkvalyldgelv.........gtvtvpsLaagesttvsftwtte 72
                                      + s+  ++e++ +++ v  +G+++s +++++l    ++          g+v+++ ++ ++ ++v++  tt+
  gi|298676133|ref|YP_003727882.1| 11 TGSASAANEKVDLYLLVDGSGSISSSDFELQLEGMANTInnssivpqdGSVSISVIQFSNIAQVEIPLTTI 81
                                      55677889999999999999999999999998655555521222333333333555555555555555554 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2.2e-05
                                       EC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CEEE CS
                             CARDB  10 lnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtteategevt 79 
                                        + ++  vge++t +++v+NqG+++ ++++++  + g    t +  +L +ge  +v+++ t+e  +g+++
  gi|298676133|ref|YP_003727882.1| 228 KPGQQILVGETVTWSYNVTNQGDKNLTNVTIKDDVTG---FTHDCGKLVPGEWCNVTYSSTAE--KGQYE 292
                                       56788999******************99998755555...45789999999999999999997..66665 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0011
                                       EEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CEE CS
                             CARDB  14 eafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtteategev 78 
                                       e  +++++t +++v+N+G+ + +++ ++   d+e+  t +  +L++ge  +v+ + ++e  +g++
  gi|298676133|ref|YP_003727882.1| 339 EILENDTVTWSYNVTNNGNVNLTDVIIK---DDETGFTHYCGKLEPGEWCNVTNSSKAE--KGQY 398
                                       5678999************998776544...6666678899999999999998888876..5554 PP

  == domain 4  score: 13.7 bits;  conditional E-value: 3.8e-05
                                       EEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CEEEEEEEESTT-SS CS
                             CARDB  14 eafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtteategevtltvvvDpdnev 90 
                                       ++ vg+e+t t++++N+G+ + +++  +++ +g+  +t +  +L++ges t s+t + ++ ++++  +v++  +ne 
  gi|298676133|ref|YP_003727882.1| 446 AVQVGNEVTWTYEITNTGNVNLTEI--NITKNGSIEKTYPNINLEPGESFTYSTTGVSKLGQQNYNGNVTAVYENEM 520
                                       67899*************9998665..567899998899999*****************999999999999999987 PP

                                       -- CS
                             CARDB  91 aE 92 
                                        +
  gi|298676133|ref|YP_003727882.1| 521 YD 522
                                       65 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   1.0   0.00016      0.23       9      40 ..     232     274 ..     220     312 .. 0.73
   2 !    7.9   0.2    0.0025       3.8      10      37 ..     340     367 ..     329     395 .. 0.91
   3 !    7.5   2.3    0.0034       5.1       9      36 ..     446     473 ..     437     512 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00016
                             DUF11   9 evrpGdtvtytltvtNtgpasangvvvtDtl...........P 40 
                                       ++  G+tvt    vtN+g +++++v+++D +           P
  gi|298676133|ref|YP_003727882.1| 232 QILVGETVTWSYNVTNQGDKNLTNVTIKDDVtgfthdcgklvP 274
                                       7889*************************76444444444443 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0025
                             DUF11  10 vrpGdtvtytltvtNtgpasangvvvtD 37 
                                       +   dtvt    vtN+g++++++v ++D
  gi|298676133|ref|YP_003727882.1| 340 ILENDTVTWSYNVTNNGNVNLTDVIIKD 367
                                       5567999*****************9998 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0034
                             DUF11   9 evrpGdtvtytltvtNtgpasangvvvt 36 
                                       +v+ G +vt t   tNtg+++++++ +t
  gi|298676133|ref|YP_003727882.1| 446 AVQVGNEVTWTYEITNTGNVNLTEINIT 473
                                       799*******************998776 PP

>> DUF2393  Protein of unknown function (DUF2393)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1   0.00025      0.38      42      90 ..     218     266 ..     213     298 .. 0.81
   2 ?    2.8   0.1     0.073   1.1e+02      56      82 ..     339     365 ..     320     374 .. 0.80
   3 ?    3.8   0.1     0.035        52      56      83 ..     446     473 ..     430     526 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00025
                           DUF2393  42 kylkkaeltilsqkrllyteafvvdgtitNeGkftikeCkleiklvnks 90 
                                       ky+   +      +++l+ e++  + ++tN+G++++++++++ ++  + 
  gi|298676133|ref|YP_003727882.1| 218 KYTNGKDSDTKPGQQILVGETVTWSYNVTNQGDKNLTNVTIKDDVTGFT 266
                                       55555555555667899***********************987666555 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.073
                           DUF2393  56 rllyteafvvdgtitNeGkftikeCkl 82 
                                        +l ++++  + ++tN+G+ +++ +++
  gi|298676133|ref|YP_003727882.1| 339 EILENDTVTWSYNVTNNGNVNLTDVII 365
                                       5667899999*************9987 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.035
                           DUF2393  56 rllyteafvvdgtitNeGkftikeCkle 83 
                                       ++++ + +  + +itN+G+ +++e  ++
  gi|298676133|ref|YP_003727882.1| 446 AVQVGNEVTWTYEITNTGNVNLTEINIT 473
                                       57899999999************99886 PP

>> DUF1573  Protein of unknown function (DUF1573)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.3    0.0062       9.3      12      70 ..     232     286 ..     223     297 .. 0.70
   2 ?    2.8   0.1     0.082   1.2e+02      13      33 ..     340     360 ..     336     405 .. 0.84
   3 !   11.6   0.8   0.00015      0.22      14      70 ..     448     503 ..     442     530 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0062
                           DUF1573  12 kieegekvtatFeftNtgkaplvitnvktsCgCttpeypkepiapGesgkikvtfnakg 70 
                                       +i  ge+vt ++++tN+g+++l  tnv+ + + t  + +  ++ pGe ++  vt+++++
  gi|298676133|ref|YP_003727882.1| 232 QILVGETVTWSYNVTNQGDKNL--TNVTIKDDVTGFTHDCGKLVPGEWCN--VTYSSTA 286
                                       457799**************87..56666666666666666666776654..4455554 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.082
                           DUF1573  13 ieegekvtatFeftNtgkapl 33 
                                       i e+++vt ++++tN+g+ +l
  gi|298676133|ref|YP_003727882.1| 340 ILENDTVTWSYNVTNNGNVNL 360
                                       668999***********9876 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00015
                           DUF1573  14 eegekvtatFeftNtgkaplvitnvktsCgCttpeypkepiapGesgkikvtfnakg 70 
                                       + g++vt t+e+tNtg+ +l+  n++++ g ++ +yp+  ++pGes++ + t  +k 
  gi|298676133|ref|YP_003727882.1| 448 QVGNEVTWTYEITNTGNVNLTEINITKN-GSIEKTYPNINLEPGESFTYSTTGVSKL 503
                                       66899*************9998888765.9999*************98776655554 PP

>> Glucodextran_N  Glucodextranase, domain N
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.1   5.7e-05     0.085     139     223 ..     289     373 ..     278     377 .. 0.81
   2 ?    1.7   0.0       0.1   1.5e+02     190     212 ..     447     469 ..     388     481 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.7e-05
                    Glucodextran_N 139 sgagdsasvveakggkalvAsdgsvalAlaasvpferasvGyvGasDgltdLkadgtltweyesasdGnvaltgeld 215
                                          ++ + ++ + +++    +d+s +   + s ++e++++G+  +s    ++ ++ t+tw+y+ +++Gnv lt  + 
  gi|298676133|ref|YP_003727882.1| 289 GQYENIGNATGQYNDTNYSDQDSSYYFGANPSIDMEKYTNGMNASSPTGPEILENDTVTWSYNVTNNGNVNLTDVII 365
                                       55667777766666666666667899999999*****************************************9887 PP

                    Glucodextran_N 216 lgtskeft 223
                                        ++++ ft
  gi|298676133|ref|YP_003727882.1| 366 KDDETGFT 373
                                       76666665 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.1
                    Glucodextran_N 190 LkadgtltweyesasdGnvaltg 212
                                        +  +++tw+ye +++Gnv lt+
  gi|298676133|ref|YP_003727882.1| 447 VQVGNEVTWTYEITNTGNVNLTE 469
                                       5667899************9985 PP

>> TRAP_beta  Translocon-associated protein beta (TRAPB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.1     8e-05      0.12      32      70 ..     235     274 ..     230     289 .. 0.80
   2 ?    3.3   0.4     0.032        48      33      60 ..     342     369 ..     340     374 .. 0.88
   3 ?    3.8   1.7     0.022        33      33      63 ..     449     479 ..     445     540 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8e-05
                         TRAP_beta  32 vegedltveytiyNvGssaAldVslvD..dsfpeeaFevvs 70 
                                       v ge +t +y+++N+G+   ++V+++D  ++f  +  ++v 
  gi|298676133|ref|YP_003727882.1| 235 V-GETVTWSYNVTNQGDKNLTNVTIKDdvTGFTHDCGKLVP 274
                                       4.899**********************55577776666555 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.032
                         TRAP_beta  33 egedltveytiyNvGssaAldVslvDds 60 
                                       e+  +t +y+++N G+   +dV ++Dd 
  gi|298676133|ref|YP_003727882.1| 342 ENDTVTWSYNVTNNGNVNLTDVIIKDDE 369
                                       5677999*******************74 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.022
                         TRAP_beta  33 egedltveytiyNvGssaAldVslvDdsfpe 63 
                                        g+++t +y+i+N G+   ++++++ ++  e
  gi|298676133|ref|YP_003727882.1| 449 VGNEVTWTYEITNTGNVNLTEINITKNGSIE 479
                                       588999999****999998888888776444 PP

>> Integrin_alpha2  Integrin alpha
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.037        55     345     370 ..     233     258 ..     211     259 .. 0.80
   2 ?    7.5   0.1    0.0011       1.6     337     368 ..     436     470 ..     426     473 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.037
                                       XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                   Integrin_alpha2 345 deiGseVehtyeiqNkGpstvpeael 370
                                         +G+ V+  y+++N+G++++ ++++
  gi|298676133|ref|YP_003727882.1| 233 ILVGETVTWSYNVTNQGDKNLTNVTI 258
                                       558****************9999875 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0011
                                       XXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                   Integrin_alpha2 337 gesame...sedeiGseVehtyeiqNkGpstvpea 368
                                       ge+a+e      ++G+eV+ tyei+N+G+ ++ e 
  gi|298676133|ref|YP_003727882.1| 436 GEDADEpqgPAVQVGNEVTWTYEITNTGNVNLTEI 470
                                       5555555557789***************9888765 PP

>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.018        26       4      27 ..     236     259 ..     233     262 .. 0.92
   2 ?   -1.6   0.0       2.2   3.3e+03      58      71 ..     279     292 ..     276     298 .. 0.84
   3 ?    0.1   0.1      0.68     1e+03       5      25 ..     344     364 ..     342     366 .. 0.86
   4 ?   -1.5   0.0         2     3e+03      58      71 ..     386     399 ..     381     405 .. 0.86
   5 ?    4.8   0.2     0.022        33       2      27 ..     448     473 ..     447     476 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.018
                       NPCBM_assoc   4 Getvtltltvtndgtaaatnvsls 27 
                                       Getvt    vtn+g++ +tnv ++
  gi|298676133|ref|YP_003727882.1| 236 GETVTWSYNVTNQGDKNLTNVTIK 259
                                       99*******************985 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.2
                       NPCBM_assoc  58 kVtppagaaaGdye 71 
                                       +Vt +++a+ G+ye
  gi|298676133|ref|YP_003727882.1| 279 NVTYSSTAEKGQYE 292
                                       7999********97 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.68
                       NPCBM_assoc   5 etvtltltvtndgtaaatnvs 25 
                                       +tvt    vtn+g+  +t+v 
  gi|298676133|ref|YP_003727882.1| 344 DTVTWSYNVTNNGNVNLTDVI 364
                                       68899999*******999985 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 2
                       NPCBM_assoc  58 kVtppagaaaGdye 71 
                                       +Vt +++a+ G+ye
  gi|298676133|ref|YP_003727882.1| 386 NVTNSSKAEKGQYE 399
                                       69999*******97 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.022
                       NPCBM_assoc   2 epGetvtltltvtndgtaaatnvsls 27 
                                       + G +vt t ++tn+g+  +t+++++
  gi|298676133|ref|YP_003727882.1| 448 QVGNEVTWTYEITNTGNVNLTEINIT 473
                                       6699******************9986 PP

>> Ecm33  GPI-anchored cell wall organization protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.1   0.00037      0.55      28      40 .]      79      91 ..      78      91 .. 0.94
   2 ?   -3.1   0.0       6.3   9.5e+03      30      35 ..     245     250 ..     243     250 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00037
                             Ecm33 28 ttIenQgDAdgLa 40
                                      ttI++Q+DAd+++
  gi|298676133|ref|YP_003727882.1| 79 TTINSQSDADNIS 91
                                      8*********998 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.3
                             Ecm33  30 IenQgD 35 
                                       ++nQgD
  gi|298676133|ref|YP_003727882.1| 245 VTNQGD 250
                                       79***9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (569 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 3633.35
//
Query:       gi|298676134|ref|YP_003727883.1|  [L=410]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.1e-22   78.7   0.2    1.6e-21   76.7   0.0    2.1  2  OrfB_IS605      Probable transposase
    4.9e-10   39.2   0.3    1.8e-09   37.4   0.1    2.1  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0046   17.3   0.0      0.011   16.1   0.0    1.6  1  RuvX            Holliday junction resolvase
     0.0055   16.5   0.4      0.015   15.1   0.4    1.7  1  DUF919          Nucleopolyhedrovirus protein of unknown funct


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.2      0.86   3.9e+03      37      52 ..      39      54 ..      18      70 .. 0.51
   2 !   76.7   0.0   3.7e-25   1.6e-21      10     119 ..     185     292 ..     176     293 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.86
                        OrfB_IS605 37 twflykgrrlksdyky 52
                                      + f+++g+ l ++  y
  gi|298676134|ref|YP_003727883.1| 39 QYFFNNGKYLNKNTAY 54
                                      2234444444444444 PP

  == domain 2  score: 76.7 bits;  conditional E-value: 3.7e-25
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsr 86 
                                        ++ + n++++iDlG+ n+at+vt++gt+f+ +gr +ks +++++ke+ +lqs ++k++       k+   + kr  
  gi|298676134|ref|YP_003727883.1| 185 IAELDYNNHLSIDLGVDNFATCVTTSGTAFILDGRGIKSYNRWWNKEKSRLQSVYDKQN--VDDGLKMNQFSWKRFW 259
                                       6667789***************************************************9..9*************** PP

                        OrfB_IS605  87 rrkhllhklathliktlkevgvetLnvgnmkdi 119
                                       ++++++++ ++h++k++ e+ ++++++g++k+i
  gi|298676134|ref|YP_003727883.1| 260 KINDYMNQCVNHIVKHCLENRIGNVVIGELKEI 292
                                       ******************************987 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.3     6e+03       9      21 ..     167     179 ..     164     181 .. 0.88
   2 !   37.4   0.1   4.1e-13   1.8e-09       1      69 []     311     385 ..     311     385 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.3
                    OrfB_Zn_ribbon   9 eykakeyGikvee 21 
                                       +yk +++ i++++
  gi|298676134|ref|YP_003727883.1| 167 KYKGRWFEIEFVY 179
                                       79*******9987 PP

  == domain 2  score: 37.4 bits;  conditional E-value: 4.1e-13
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke......alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f+++k++l+ k+k +Gik++ev++a+TSk  +   +  ++      ++s+r    ++ g  +++D+n+a+Nil++
  gi|298676134|ref|YP_003727883.1| 311 FARFKQKLASKCKYHGIKYHEVDEAFTSKVDALALEPIRKhkkylgKRSKRGIFQSSTGRLINADINGALNILRK 385
                                       899**************************8766655544445588*99************************986 PP

>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.4e-06     0.011      37     106 ..     266     345 ..     253     367 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.4e-06
                                       HHHHHHHHHHHHHTT--EEEEE--........----SSS---SSTTHHHHHHHHHT....T-EEEEE--S----XXX CS
                              RuvX  37 ekdleelkelvkeeeveeiVvGlP........lnldgsegesakkvrkfaeeLakrl..kklpvelvDErlttveae 103
                                       ++ ++++ + + e+++ ++V+G          +  +++++ ++  +++f ++La+++  ++++ + vDE +t++  +
  gi|298676134|ref|YP_003727883.1| 266 NQCVNHIVKHCLENRIGNVVIGELkeinqeqnIGKENTQNFQTIPFARFKQKLASKCkyHGIKYHEVDEAFTSKVDA 342
                                       78999*****************98666666555566777778888899******99977889***********9766 PP

                                       XXX CS
                              RuvX 104 ril 106
                                        +l
  gi|298676134|ref|YP_003727883.1| 343 LAL 345
                                       555 PP

>> DUF919  Nucleopolyhedrovirus protein of unknown function (DUF919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.4   3.5e-06     0.015      15      58 ..       4      45 ..       2      47 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.5e-06
                            DUF919 15 qaKrkltiksqHfErlkkitKnpkElqdlekklnklRqeFLnfg 58
                                       +K  l+ + q +E lk++tK +k l +   +l ++Rq+F+n g
  gi|298676134|ref|YP_003727883.1|  4 TQKNHLRADKQTYETLKRLTKLSKNLYNF--TLYNIRQYFFNNG 45
                                      58999******************888765..8**********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       985  (0.0549389); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2498.67
//
Query:       gi|298676135|ref|YP_003727884.1|  [L=284]
Description: undecaprenyl diphosphate synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-69  234.3   0.1    1.5e-69  234.0   0.1    1.1  1  Prenyltransf  Putative undecaprenyl diphosphate synthase


Domain annotation for each model (and alignments):
>> Prenyltransf  Putative undecaprenyl diphosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.0   0.1   8.4e-74   1.5e-69       1     219 [.      33     255 ..      33     260 .. 0.93

  Alignments for each domain:
  == domain 1  score: 234.0 bits;  conditional E-value: 8.4e-74
                                       EE--HHHHHHHTT.S-HHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEEGGGGGS-HHHHHHHHHHHH...HHHHHH CS
                      Prenyltransf   1 imDGNrRwAkkrgleereeGhkaGaealkeilelclelgvkvvtvYafSteNfkRskeevdalmellk...eellke 74 
                                       imDGNrR+Ak+ g +   +Ghk G ++ ++++e++ e+g++ +tvYafSteNf+R++ee ++l+el++   +e++++
  gi|298676135|ref|YP_003727884.1|  33 IMDGNRRYAKNMG-KAGYYGHKLGSDTTEKVIEWACEIGIEEMTVYAFSTENFSRPPEETEKLFELIDtrlNEMVED 108
                                       9************.99999************************************************8777778877 PP

                                       HHHHHHHTTEEEEEESSGGGS-HHHHHHHHHHHHHHT.TTTSEEEEEEEEE-HHHHHHHHHHHHHHTT..SSSG.GG CS
                      Prenyltransf  75 elkellkegvrvrviGdlellpedvlealekaeeatkknnkklvlniavnYgsrdeiveavrelvkekseekkk.ee 150
                                       e  +++++++++r++Gd+++lp+ +++++e+ae+at + ++ ++ln+a++Yg+r++i++av+e+++++++ + + e+
  gi|298676135|ref|YP_003727884.1| 109 E--RTHNRQMKIRAVGDRKRLPQYLQDSIERAEKATCHYEN-FKLNVALAYGGRQDIIQAVQEIARKVKRGDLTvEK 182
                                       7..99999*****************************7766.**********************9999776666566 PP

                                       HSHHHHHCTSTT..T..SSS-SEEEEESS--S-TTSSTTTTTT-E..EEEESSSGGG--HHHHHHHHHHHHHC CS
                      Prenyltransf 151 ideetlekhlytaka..lpdpDlliRtsGeeRlSnFllwqlayse..lyfldvlWPdfskedllealleyqkr 219
                                       ++e+t+++hly   +  + d+D+++Rt+G+eR+SnFl wq+  +e   yf+  +WP f+k d+l+a++ yq+r
  gi|298676135|ref|YP_003727884.1| 183 VNESTISNHLYPDCEqpVSDVDMIVRTGGNERVSNFLPWQANGNEctAYFCAPYWPMFRKIDFLRAIRVYQAR 255
                                       79*********64336799*********************99998999***********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1919.41
//
Query:       gi|298676136|ref|YP_003727885.1|  [L=1914]
Description: APHP domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-39  133.3  20.6    7.8e-10   38.4   0.3    8.7  9  PD40             WD40-like Beta Propeller Repeat
      6e-18   65.0  12.6    7.7e-17   61.4   1.6    3.5  3  CARDB            CARDB
    5.6e-11   42.6   0.6    2.1e-08   34.3   0.0    3.5  3  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    5.9e-08   32.6   6.7    6.1e-07   29.3   0.3    3.4  3  CarbopepD_reg_2  CarboxypepD_reg-like domain
    7.4e-08   31.5  23.0      0.017   13.9   0.3    6.8  6  DPPIV_N          Dipeptidyl peptidase IV (DPP IV) N-terminal 
    1.5e-06   27.2   4.4       0.03   13.0   0.0    3.9  4  Pectate_lyase22  Oligogalacturonate lyase
    5.1e-06   26.7   0.2    5.1e-06   26.7   0.2    4.5  5  SdrD_B           SdrD B-like domain
      2e-05   24.7   0.0      8e-05   22.7   0.0    2.1  1  DUF2012          Protein of unknown function (DUF2012)
  ------ inclusion threshold ------
       0.42   11.0   4.2       0.77   10.1   0.5    3.2  2  SpaA             Prealbumin-like fold domain
        9.2    6.6  14.0        1.5    9.1   0.5    5.1  5  Glyco_hydro_30C  Glycosyl hydrolase family 30 beta sandwich d


Domain annotation for each model (and alignments):
>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.1   0.00047      0.85       3      37 ..     491     526 ..     489     527 .. 0.86
   2 !   18.3   0.1   8.8e-07    0.0016       4      25 ..     538     559 ..     536     571 .. 0.93
   3 !    5.8   0.0    0.0077        14       5      25 ..     584     603 ..     580     603 .. 0.79
   4 !   11.2   0.0   0.00015      0.28       4      24 ..     628     648 ..     626     651 .. 0.83
   5 !   19.9   0.1   2.9e-07   0.00052      16      38 .]     688     709 ..     687     709 .. 0.96
   6 !   38.4   0.3   4.4e-13   7.8e-10       2      38 .]     718     753 ..     717     753 .. 0.96
   7 !   37.6   0.2   8.2e-13   1.5e-09       3      37 ..     763     796 ..     761     797 .. 0.93
   8 ?   -2.3   0.0       2.6   4.7e+03      20      34 ..     855     870 ..     855     872 .. 0.80
   9 ?   -3.0   0.1       4.5     8e+03      23      32 ..    1832    1840 ..    1831    1843 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00047
                                       E--SSSS.EEEEEE-TTSSEEEEEEECT..TCEEEE CS
                              PD40   3 rltntpgnegaPsfSPDGkrlaFsSdRg.sGkpdIy 37 
                                       + t++p+ + +P +SP G+ ++F  + + + k+dIy
  gi|298676136|ref|YP_003727885.1| 491 QFTFNPEKDSNPVWSPTGNEIVFGKSIPtEEKYDIY 526
                                       6799999************99998887788888887 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 8.8e-07
                                       --SSSS.EEEEEE-TTSSEEEE CS
                              PD40   4 ltntpgnegaPsfSPDGkrlaF 25 
                                       ltn p +eg P++SPDG+++ +
  gi|298676136|ref|YP_003727885.1| 538 LTNLPNIEGHPRWSPDGNKILY 559
                                       7999****************87 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0077
                                       -SSSS.EEEEEE-TTSSEEEE CS
                              PD40   5 tntpgnegaPsfSPDGkrlaF 25 
                                       tn  +  ++  +SP G+++++
  gi|298676136|ref|YP_003727885.1| 584 TNDAQ-SECAVWSPSGSKIVY 603
                                       44444.899**********98 PP

  == domain 4  score: 11.2 bits;  conditional E-value: 0.00015
                                       --SSSS.EEEEEE-TTSSEEE CS
                              PD40   4 ltntpgnegaPsfSPDGkrla 24 
                                       +++++++   +s+SPDG+++a
  gi|298676136|ref|YP_003727885.1| 628 ILTGQKYANRFSWSPDGSKIA 648
                                       56777788899*********8 PP

  == domain 5  score: 19.9 bits;  conditional E-value: 2.9e-07
                                       E-TTSSEEEEEEECT.TCEEEEE CS
                              PD40  16 fSPDGkrlaFsSdRgsGkpdIyv 38 
                                       +SPDG+++++ Sd + G+ dIy+
  gi|298676136|ref|YP_003727885.1| 688 WSPDGSKIVYHSDEN-GNRDIYT 709
                                       ***************.******5 PP

  == domain 6  score: 38.4 bits;  conditional E-value: 4.4e-13
                                       EE--SSSS.EEEEEE-TTSSEEEEEEECT.TCEEEEE CS
                              PD40   2 krltntpgnegaPsfSPDGkrlaFsSdRgsGkpdIyv 38 
                                       ++lt++++ +++ +fSPDG++++F+S+R+ G+ dI++
  gi|298676136|ref|YP_003727885.1| 718 TQLTTNSAKDTDSFFSPDGSKIVFVSNRE-GNNDIWM 753
                                       79***************************.******7 PP

  == domain 7  score: 37.6 bits;  conditional E-value: 8.2e-13
                                       E--SSSS.EEEEEE-TTSSEEEEEEECT.TCEEEE CS
                              PD40   3 rltntpgnegaPsfSPDGkrlaFsSdRgsGkpdIy 37 
                                       +lt ++++++ P++ PDG+++aFsS+R  G++dI+
  gi|298676136|ref|YP_003727885.1| 763 QLTVNSADDMYPTWNPDGTKIAFSSNRA-GNYDIW 796
                                       6777899*********************.****** PP

  == domain 8  score: -2.3 bits;  conditional E-value: 2.6
                                       SSEEEEEEECT..TCE CS
                              PD40  20 GkrlaFsSdRg.sGkp 34 
                                       G + +++Sd+   G p
  gi|298676136|ref|YP_003727885.1| 855 GDKVTWTSDKAsPGEP 870
                                       77899****9887776 PP

  == domain 9  score: -3.0 bits;  conditional E-value: 4.5
                                        EEEEEECT.T CS
                              PD40   23 laFsSdRgsG 32  
                                        ++F Sd + G
  gi|298676136|ref|YP_003727885.1| 1832 MYFESDTP-G 1840
                                        67777766.5 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.4   1.6   4.3e-20   7.7e-17       1     102 []     906    1008 ..     906    1008 .. 0.93
   2 !   10.0   0.3   0.00044      0.78      16      73 ..    1116    1180 ..    1102    1192 .. 0.68
   3 ?   -3.4   0.3       6.4   1.2e+04      49      70 ..    1614    1636 ..    1598    1659 .. 0.50

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 4.3e-20
                                        S--EEE..EEEC-SEEETTSEEEEEEEEEE-SSS-.EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S- CS
                             CARDB    1 tpDLtv.tntlnpseafvgeentitvtvkNqGtaa.sgatkvalyldgelvgtvtvpsLaagesttvsftwttea 73  
                                        +pDLt+ + ++  +++  g+e+t++++vkN G+a+   +++ +ly+++el +t++   La+ges++  ft t++a
  gi|298676136|ref|YP_003727885.1|  906 KPDLTItNISWDKENPKIGDELTFSYEVKNLGKADtKSKFTNKLYINDELWDTSQC-TLASGESKKNIFTRTWKA 979 
                                        69****777888999********************8999***********999998.9****************6 PP

                                        S-CEEEEEEEESTT-SS--SSCCCSEEEE CS
                             CARDB   74 tegevtltvvvDpdnevaEsnEtNNeltk 102 
                                        t +e+ +++v+D+++e+++++ +NN+ltk
  gi|298676136|ref|YP_003727885.1|  980 TGSEYIIKIVADESGEIDDTDNSNNTLTK 1008
                                        667777********************986 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00044
                                        ETTSEEEEEEEEEE-SSS-...EEEEEEEEEETTEEE.EEEEESEE-CTEEEEEEEEEE-S...- CS
                             CARDB   16 fvgeentitvtvkNqGtaa...sgatkvalyldgelv.gtvtvpsLaagesttvsftwtte...a 73  
                                          g+e+ +t+t+kN+G+ +       ++++  + e   +  +   L+++e+++v++tw+++   a
  gi|298676136|ref|YP_003727885.1| 1116 IIGDEIPVTYTIKNTGNVKhkfYAGYSTRCAFSNEIWdAPYKAITLEPSETEDVTLTWKVQnnvA 1180
                                        568999*********986622233455555555555545555589*************9984322 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 6.4
                                        E.EEEEESEE-CTEEEEEEEEEE CS
                             CARDB   49 v.gtvtvpsLaagesttvsftwt 70  
                                        + +t+t ++++ +e+tt ++++ 
  gi|298676136|ref|YP_003727885.1| 1614 AiKTATYKNISINENTTAKVNVN 1636
                                        33444444555555555444443 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.6   4.6e+03      18      56 ..     105     142 ..      95     149 .. 0.71
   2 !   34.3   0.0   1.2e-11   2.1e-08       2      75 ..    1015    1084 ..    1014    1088 .. 0.87
   3 ?    4.3   0.1     0.028        50      40      79 ..    1593    1635 ..    1592    1637 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.6
                   CarboxypepD_reg  18 tVtvtnadtgtvastttdadGafrlrglppgtysvtvsa 56 
                                       +++++++ +  + +ttt  +G+     l pg+y+  +++
  gi|298676136|ref|YP_003727885.1| 105 QISFYDN-SANKPYTTTVVKGSTERLELVPGDYNWIAEK 142
                                       6666632.2334557777888888888999999988875 PP

  == domain 2  score: 34.3 bits;  conditional E-value: 1.2e-11
                   CarboxypepD_reg    2 isGrVt.dasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagqtt 75  
                                        ++G+V  d+s+++i+ +tV +t        + tt ++G++++++lp g+y++ ++++Gy+  +  +v ++   tt
  gi|298676136|ref|YP_003727885.1| 1015 LEGKVLlDSSKNGISDVTVKLT----PGDITKTTYPNGYYSFKNLPSGKYNILAEKNGYKFNSL-DVKISSSSTT 1084
                                        689996489*************....88899999*************************98886.5888777666 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.028
                   CarboxypepD_reg   40 frlrglppgtysvtv...sapGyatatreevtltagqtttldi 79  
                                        f +++l  g++++t    +++  +tat++++++++++t+ +++
  gi|298676136|ref|YP_003727885.1| 1593 FEIDALDKGNFTLTLtqkTKSAIKTATYKNISINENTTAKVNV 1635
                                        9999***********877788889**************99998 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.3   3.4e-10   6.1e-07       2      71 ..    1016    1085 ..    1015    1093 .. 0.95
   2 ?    5.0   0.5     0.014        24      33      84 ..    1600    1645 ..    1589    1646 .. 0.65
   3 ?   -3.5   0.0       6.1   1.1e+04      30      68 ..    1826    1864 ..    1820    1877 .. 0.74

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 3.4e-10
                   CarbopepD_reg_2    2 sGtVvdketkeplpgatVyvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvskektld 71  
                                        +G+V+ +++k+ +  +tV ++      +T  nG++++knlp+gky + ++  Gyk  +  v++s+ +t++
  gi|298676136|ref|YP_003727885.1| 1016 EGKVLLDSSKNGISDVTVKLTPGDITKTTYPNGYYSFKNLPSGKYNILAEKNGYKFNSLDVKISSSSTTK 1085
                                        7**************************************************************9988765 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.014
                   CarbopepD_reg_2   33 nGnFelknlpagkytLvvsyvGyktqekkvtvskektldvnillkeealele 84  
                                        +GnF+l+  ++ k     s++   t  k++++++++t +vn+++++e+  ++
  gi|298676136|ref|YP_003727885.1| 1600 KGNFTLTLTQKTK-----SAIKTAT-YKNISINENTTAKVNVNQSDESYLMD 1645
                                        5566665322222.....3444444.467999999*******9999998776 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 6.1
                   CarbopepD_reg_2   30 TdenGnFelknlpagkytLvvsyvGyktqekkvtvskek 68  
                                        ++++G+  +++ ++g   + ++++G ++++k  t s+e+
  gi|298676136|ref|YP_003727885.1| 1826 SEDEGYMYFESDTPGFSPFAITAMGIEEESKATTGSNES 1864
                                        566777777777777777889999999999888877765 PP

>> DPPIV_N  Dipeptidyl peptidase IV (DPP IV) N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.019        34      33      60 ..     487     514 ..     469     517 .. 0.79
   2 !   12.1   5.0   3.5e-05     0.062      21     136 ..     519     622 ..     516     650 .. 0.83
   3 !    8.4   0.3   0.00045      0.82      35      82 ..     676     724 ..     641     731 .. 0.74
   4 !   13.9   0.3   9.7e-06     0.017      35      85 ..     717     771 ..     706     773 .. 0.80
   5 !   13.2   0.2   1.6e-05     0.028       2      74 ..     734     805 ..     733     825 .. 0.75
   6 ?   -3.3   0.1       1.6   2.8e+03     232     267 ..    1391    1426 ..    1379    1437 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.019
                                       EECEEEETTTT.BSEEEEESSTTEEEEE CS
                           DPPIV_N  33 neveelspgeeklqlakwSPagdklafv 60 
                                       +++e+ + + ek + + wSP+g+ ++f 
  gi|298676136|ref|YP_003727885.1| 487 KKIEQFTFNPEKDSNPVWSPTGNEIVFG 514
                                       56777777789***************96 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3.5e-05
                                       ETTEEEEEETTT.EECEEEETT.TT.BSEEEEESSTTEEEEEETT.....EEEEESTTTSEEEECES-STTTEEESB CS
                           DPPIV_N  21 ytaeyyiydlet.neveelspg.eeklqlakwSPagdklafvrnn.....nLyvrelatgkeiqlTsdgsagifnGv 90 
                                       ++++y+iy+++  n+ e++  +  +    ++wSP+g+k+ + ++n     n+++ ++  +++++lT+d         
  gi|298676136|ref|YP_003727885.1| 519 TEEKYDIYKVSVdNKYESVLTNlPNIEGHPRWSPDGNKILYKKDNtngwyNVWIMNSDGSSQTALTNDA-------- 587
                                       57899999999768888888887888999**************9888888*******999********9........ PP

                                       --HHHHHHTSSSSBEEEE-TTSSEEEEEEEECTTS-EEEEEESSSS CS
                           DPPIV_N  91 adWvyeEEvlgsnsavwWspdgsrlaylrfdeseVpeitlpsytde 136
                                            + E         Wsp+gs+++y   d s  pe  + +  d 
  gi|298676136|ref|YP_003727885.1| 588 -----QSE------CAVWSPSGSKIVYKHSDNSDLPEDVIIMNPDG 622
                                       .....667......77888888888888888888877666655555 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.00045
                                       CEEEETTTT.BSEEEEESSTTEEEEEE....TTEEEEESTTTSEEEECES-S CS
                           DPPIV_N  35 veelspgeeklqlakwSPagdklafvr....nnnLyvrelatgkeiqlTsdg 82 
                                       ++++++   + q   wSP+g k+++      n+++y  ++    ++qlT++ 
  gi|298676136|ref|YP_003727885.1| 676 FRPQTQ---PWQSQIWSPDGSKIVYHSdengNRDIYTINIDGTDRTQLTTNS 724
                                       444444...4888899999999999872222457999999999999999987 PP

  == domain 4  score: 13.9 bits;  conditional E-value: 9.7e-06
                                       CEEEETTTT.BSEEEEESSTTEEEEEE....TTEEEEESTTTSEEEECES-STTT CS
                           DPPIV_N  35 veelspgeeklqlakwSPagdklafvr....nnnLyvrelatgkeiqlTsdgsag 85 
                                        ++l+ +++k ++  +SP+g k++fv     nn++++ ++  ++++qlT +  ++
  gi|298676136|ref|YP_003727885.1| 717 RTQLTTNSAKDTDSFFSPDGSKIVFVSnregNNDIWMMNVDGSNKTQLTVNSADD 771
                                       4667777899****************8444459****************988555 PP

  == domain 5  score: 13.2 bits;  conditional E-value: 1.6e-05
                                       TTSSEEEEEECEEEESSSEETTEEEEEETTTEECEEEETTTT.BSEEEEESSTTEEEEEE....TTEEEEESTTTS. CS
                           DPPIV_N   2 pdgkflllatnaeknwRhsytaeyyiydletneveelspgeeklqlakwSPagdklafvr....nnnLyvrelatg. 73 
                                       pdg+++++ +n       ++ ++ ++ ++   + ++l+ ++++ ++++w+P+g+k+af      n ++++ el+++ 
  gi|298676136|ref|YP_003727885.1| 734 PDGSKIVFVSN------REGNNDIWMMNVDGSNKTQLTVNSADDMYPTWNPDGTKIAFSSnragNYDIWLIELKEDi 804
                                       56666666444......467899999999999999999999*****************8622225799999988774 PP

                                       E CS
                           DPPIV_N  74 k 74 
                                       +
  gi|298676136|ref|YP_003727885.1| 805 N 805
                                       4 PP

  == domain 6  score: -3.3 bits;  conditional E-value: 1.6
                                        S-SSS-S-EEE-TTTSSEEEEEEETTSSEEEEEEES CS
                           DPPIV_N  232 gWvelhdevhflkrdesgflwisekdGfkHLylfdl 267 
                                         W +  ++ h+ +++ ++ ++++e+++ +++y ++ 
  gi|298676136|ref|YP_003727885.1| 1391 LWADSVHKLHLASNNLDNAIKVIENHDKNKVYTYQE 1426
                                        699999999999999999*************99986 PP

>> Pectate_lyase22  Oligogalacturonate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.1    0.0014       2.5     169     256 ..     524     605 ..     500     629 .. 0.72
   2 ?   -0.9   0.0      0.27   4.9e+02     218     267 ..     615     662 ..     603     673 .. 0.70
   3 !   13.0   0.0   1.7e-05      0.03      41     101 ..     686     745 ..     671     749 .. 0.90
   4 !    5.8   0.1    0.0026       4.6     217     313 ..     750     837 ..     745     843 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0014
                   Pectate_lyase22 169 rlirvdlktgeaevilkenqwlghpiyrpfddstvafchegphdlvdarmwlinedgsnlrkvkehaegescthevw 245
                                        + +v ++    +v+ +  +  ghp + p d + + + ++         +w++n dgs    + + a+ e     vw
  gi|298676136|ref|YP_003727885.1| 524 DIYKVSVDNKYESVLTNLPNIEGHPRWSP-DGNKILYKKDNTNGW--YNVWIMNSDGSSQTALTNDAQSEC---AVW 594
                                       55666666666666666667777777777.555666666655554..468*****************9985...48* PP

                   Pectate_lyase22 246 vpdgsalayvs 256
                                        p gs ++y  
  gi|298676136|ref|YP_003727885.1| 595 SPSGSKIVYKH 605
                                       ********964 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.27
                   Pectate_lyase22 218 mwlinedgsnlrkvkehaegesc.thevwvpdgsalayvsylkgsterviy 267
                                       + ++n dgsn   + +   g+       w pdgs +a   ++  +  r+i 
  gi|298676136|ref|YP_003727885.1| 615 VIIMNPDGSNKETILT---GQKYaNRFSWSPDGSKIAVSGHIGNQGIRIIN 662
                                       4578999999888865...444404556*******9987777777666653 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 1.7e-05
                   Pectate_lyase22  41 kcftrdgskllfggafdgprnyylldlntqqavqltegkgdntfggflssdddalfyvkne 101
                                       + ++ dgsk+++  + +g+r+ y ++++    +qlt     +t   f+s+d   + +v n 
  gi|298676136|ref|YP_003727885.1| 686 QIWSPDGSKIVYHSDENGNRDIYTINIDGTDRTQLTTNSAKDT-DSFFSPDGSKIVFVSNR 745
                                       56899*******************************9999888.6799***9999999875 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.0026
                   Pectate_lyase22 217 rmwlinedgsnlrkvkehaegescthevwvpdgsalayvsylkgsterviysadpvtlenreltempacshlmsnyd 293
                                        +w++n dgsn  ++   +      +  w pdg+ +a+ s   g+ +  +++ +      +++ + p    +  n  
  gi|298676136|ref|YP_003727885.1| 750 DIWMMNVDGSNKTQLTVNSAD--DMYPTWNPDGTKIAFSSNRAGNYDIWLIELK------EDINHRPVINDIQVN-P 817
                                       58*********8887765554..46789************99999887776654......345555656665555.4 PP

                   Pectate_lyase22 294 gtlmvgdgsdapvdvkddsg 313
                                        t++ g+ +d  vd  d  g
  gi|298676136|ref|YP_003727885.1| 818 STIFEGNSCDIIVDASDPDG 837
                                       56777777777777777666 PP

>> SdrD_B  SdrD B-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       2.4   4.4e+03      72      98 ..      25      51 ..      16      59 .. 0.73
   2 !   26.7   0.2   2.9e-09   5.1e-06      17      82 ..    1021    1081 ..    1013    1110 .. 0.73
   3 ?   -2.8   0.0       4.1   7.3e+03      52      88 ..    1595    1634 ..    1589    1646 .. 0.62
   4 ?    0.7   0.4      0.34   6.2e+02      10      38 ..    1647    1673 ..    1643    1685 .. 0.72
   5 ?   -2.7   0.0       3.7   6.7e+03      23      84 ..    1801    1866 ..    1798    1884 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.4
                            SdrD_B 72 vtakkaGsddaldSdadpatgltktvt 98
                                       +++k +++++ +Sd ++at++ + ++
  gi|298676136|ref|YP_003727885.1| 25 ESSSKFSVNENFESDTKKATDKYNNIN 51
                                      56677889999*****99998776664 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 2.9e-09
                            SdrD_B   17 qdagekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapagytvtakkaGsdda 82  
                                         d+ ++gis+vtV+L  + g++  t tT  +G+Y+F+nl +G+Y++   + +gy++ + +    ++
  gi|298676136|ref|YP_003727885.1| 1021 LDSSKNGISDVTVKL--TPGDI--TKTTYPNGYYSFKNLPSGKYNILA-EKNGYKFNSLDVKISSS 1081
                                        49999**********..44444..688999***************977.55677776655544444 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 4.1
                            SdrD_B   52 FtnltpGeYkVefta.pagy..tvtakkaGsddaldSdad 88  
                                         + l++G++++++t+ ++    t+t+k+ + ++++ + ++
  gi|298676136|ref|YP_003727885.1| 1595 IDALDKGNFTLTLTQkTKSAikTATYKNISINENTTAKVN 1634
                                        5677888888888664333334666666666666555544 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.34
                            SdrD_B   10 DanknGiqdagekgisgvtVtLkdakgev 38  
                                        D n++Gi+d +e+    ++ tL+++++++
  gi|298676136|ref|YP_003727885.1| 1647 DDNGDGIKDRTENP--HIKTTLIEKDDKQ 1673
                                        99*********964..4555555555554 PP

  == domain 5  score: -2.7 bits;  conditional E-value: 3.7
                            SdrD_B   23 gisgvtVtLkdakgevvatttTd....asGkYkFtnltpGeYkVeftapagytvtakkaGsddald 84  
                                         i+  t++L + ++ + +  tT      +G+  F++ tpG    ++ta    + +++++Gs++++ 
  gi|298676136|ref|YP_003727885.1| 1801 NIDESTIRLCRCNDGTWDPLTTRklseDEGYMYFESDTPGFSPFAITAMGIEEESKATTGSNESMY 1866
                                        566677888777776665444443333789999999999975555544433366677777777655 PP

>> DUF2012  Protein of unknown function (DUF2012)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   4.5e-08     8e-05      19      76 ..    1037    1095 ..    1009    1140 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 4.5e-08
                           DUF2012   19 qrkfkalvrrDGsFifrdlpegsYlLevespeyvFepyrVdvkdkgkaka.sklrivet 76  
                                          +++  +  +G ++f++lp+g+Y++ +e+ +y F+ + V+++++ + ka ++++ + +
  gi|298676136|ref|YP_003727885.1| 1037 PGDITKTTYPNGYYSFKNLPSGKYNILAEKNGYKFNSLDVKISSSSTTKAdPIIGNIDE 1095
                                        44567888899********************************5555544044444444 PP

>> SpaA  Prealbumin-like fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.5   0.00043      0.77      35      58 ..    1013    1062 ..     939    1080 .. 0.72
   2 ?   -0.6   0.2      0.99   1.8e+03      45      81 ..    1592    1628 ..    1566    1651 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00043
                                        E..........................SEEE-BTTSEEEEEEEESEEEEE CS
                              SpaA   35 v..........................ttlttdenGkatfegLplGtYll 58  
                                        +                           t+tt  nG+ +f++Lp G+Y +
  gi|298676136|ref|YP_003727885.1| 1013 InlegkvlldsskngisdvtvkltpgdITKTTYPNGYYSFKNLPSGKYNI 1062
                                        13333333444444445555556666699*******************76 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.99
                                        EEEEEEEESEEEEEEEEE-STTEEE-SSEEEEEECEE CS
                              SpaA   45 katfegLplGtYllvEtkaPegYvldkepfevtvtat 81  
                                        ++++++L+ G+++l+ t+  +   ++++   ++++++
  gi|298676136|ref|YP_003727885.1| 1592 NFEIDALDKGNFTLTLTQKTKSAIKTATYKNISINEN 1628
                                        5666666666666666666666666666666665554 PP

>> Glyco_hydro_30C  Glycosyl hydrolase family 30 beta sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.6   2.9e+03      25      49 ..     564     588 ..     562     602 .. 0.61
   2 ?    9.1   0.5   0.00085       1.5      16      41 ..     725     751 ..     714     770 .. 0.66
   3 ?   -2.1   0.0       2.5   4.5e+03      24      37 ..     777     790 ..     776     795 .. 0.81
   4 ?    1.9   0.1      0.15   2.6e+02      31      64 ..    1582    1617 ..    1579    1618 .. 0.77
   5 ?    0.7   1.7      0.35   6.3e+02      11      50 ..    1609    1651 ..    1603    1666 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.6
                   Glyco_hydro_30C  25 pDGsivvvilNrsessvtitvsdss 49 
                                       ++G + v i+N+ +ss+t+  +d +
  gi|298676136|ref|YP_003727885.1| 564 TNGWYNVWIMNSDGSSQTALTNDAQ 588
                                       5566667788887777776555543 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00085
                   Glyco_hydro_30C  16 nvetvAFlnpDGsivvvilNr.sessv 41 
                                         +t +F +pDGs++v + Nr +++++
  gi|298676136|ref|YP_003727885.1| 725 AKDTDSFFSPDGSKIVFVSNReGNNDI 751
                                       447779***************655544 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.5
                   Glyco_hydro_30C  24 npDGsivvvilNrs 37 
                                       npDG++++   Nr+
  gi|298676136|ref|YP_003727885.1| 777 NPDGTKIAFSSNRA 790
                                       9******9998885 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.15
                   Glyco_hydro_30C   31 vvilNrsessvtitvsdsskskgslsv...parSivT 64  
                                        ++i+N+s ++++++++   k++++l++    + +i T
  gi|298676136|ref|YP_003727885.1| 1582 IIIFNQS-EDINFEIDALDKGNFTLTLtqkTKSAIKT 1617
                                        699**88.99999998666677999987755555655 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 0.35
                   Glyco_hydro_30C   11 psvssnvetvAFln...pDGsivvvilNrsessvtitvsdssk 50  
                                        ++++s ++t  ++n    +++++ v +N+s++s   +v+d+++
  gi|298676136|ref|YP_003727885.1| 1609 QKTKSAIKTATYKNisiNENTTAKVNVNQSDESYLMDVDDNGD 1651
                                        3445789999999999999*******************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1914 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 1.13u 0.35s 00:00:01.48 Elapsed: 00:00:00.54
# Mc/sec: 10767.41
//
Query:       gi|298676137|ref|YP_003727886.1|  [L=303]
Description: hypothetical protein Metev_2272 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.9e-09   36.0   0.1     0.0051   16.7   0.0    3.1  3  TrmB           Sugar-specific transcriptional regulator TrmB
    1.1e-05   25.2   1.3      0.015   15.2   0.0    3.4  4  MarR           MarR family
    0.00048   20.0   0.1        0.7    9.9   0.0    2.8  2  HTH_11         HTH domain
    0.00064   19.2   0.0     0.0012   18.3   0.0    1.5  1  Aph-1          Aph-1 protein
    0.00069   19.5   0.1        0.4   10.7   0.0    2.9  2  HTH_36         Helix-turn-helix domain
    0.00075   19.3   0.0      0.082   12.8   0.0    2.5  2  MarR_2         MarR family
     0.0072   16.2   0.8        1.3    9.0   0.0    2.7  2  HTH_5          Bacterial regulatory protein, arsR family
     0.0076   16.2   0.2      0.017   15.0   0.1    1.6  1  DUF1441        Protein of unknown function (DUF1441)
  ------ inclusion threshold ------
      0.018   15.7   0.2        5.5    7.7   0.1    2.5  2  RPA_C          Replication protein A C terminal
      0.022   14.7   0.0      0.045   13.7   0.0    1.5  1  BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
      0.035   14.0   0.0       0.14   12.2   0.0    1.8  2  HTH_43         Winged helix-turn helix
      0.045   14.2   0.0        4.9    7.7   0.0    2.6  2  HTH_27         Winged helix DNA-binding domain
      0.053   13.3   0.0        1.6    8.6   0.0    2.4  2  HTH_IclR       IclR helix-turn-helix domain
      0.065   13.7   0.1         13    6.3   0.0    2.6  2  HTH_40         Helix-turn-helix domain
       0.11   12.9   0.9        1.7    9.0   0.1    2.7  3  Rrf2           Transcriptional regulator
       0.13   12.2   0.1        1.1    9.3   0.0    2.3  2  HTH_Crp_2      Crp-like helix-turn-helix domain
       0.18   11.4   3.1         16    5.1   0.0    3.8  3  HTH_24         Winged helix-turn-helix DNA-binding


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.3e-05     0.013      17      56 ..      12      50 ..       2      59 .. 0.81
   2 !   16.7   0.0   4.9e-06    0.0051      17      58 ..      94     135 ..      92     141 .. 0.91
   3 ?   -0.9   0.0       1.5   1.5e+03      41      63 ..     158     180 ..     157     181 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.3e-05
                                      HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB 17 LlklgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                      L+ ++p++++++ +el++++s+v  +++sL++ G+  +  
  gi|298676137|ref|YP_003727886.1| 12 LV-SEPKNISQLKNELKLDHSTVSLAVKSLISNGFAIKYS 50
                                      44.89******************************87755 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 4.9e-06
                                       HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB  17 LlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58 
                                       +lk+++++++ei+  +g+ r+++ +v++sL+  G++ ++ g 
  gi|298676137|ref|YP_003727886.1|  94 VLKNDSLNIKEISYVTGLHRNTISSVINSLSMYGVILKSNGC 135
                                       799*******************************99887765 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.5
                                       HHHHHHHHCTSEEEESSTTTEEE CS
                              TrmB  41 evLrsLedkGlVerekgrpklYr 63 
                                       + L++L + G +  ++g+  l++
  gi|298676137|ref|YP_003727886.1| 158 KKLKKLAKEGTIIWQRGSEFLFK 180
                                       5699*******999998877765 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.4e-05     0.015      15      46 ..      14      45 ..       2      51 .. 0.90
   2 ?    0.2   0.0      0.68   7.2e+02      11      34 ..      71      94 ..      70      96 .. 0.89
   3 !    6.9   0.1    0.0055       5.8       4      48 ..      87     130 ..      84     133 .. 0.81
   4 ?   -2.0   0.0       3.4   3.6e+03      37      47 ..     159     169 ..     156     172 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.4e-05
                                      STTEEHHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                              MarR 15 qgplsvseLakklgvskstvtrvldrLekkGl 46
                                      ++p ++s+L + l+++ stv+ +++ L+ +G+
  gi|298676137|ref|YP_003727886.1| 14 SEPKNISQLKNELKLDHSTVSLAVKSLISNGF 45
                                      47899**************************9 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.68
                                      HHHHSTTEEHHHHHHHHTS-HHHH CS
                              MarR 11 ilyeqgplsvseLakklgvskstv 34
                                      +l+e + l  s+L +k++++ ++v
  gi|298676137|ref|YP_003727886.1| 71 LLKEYPRLPWSKLLNKSSLHVMSV 94
                                      6899999***********999887 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0055
                                       HHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR   4 tqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48 
                                       + ++++  l+ +++l+++e+    g+++ t++ v+  L   G i 
  gi|298676137|ref|YP_003727886.1|  87 SSLHVMSVLK-NDSLNIKEISYVTGLHRNTISSVINSLSMYGVIL 130
                                       5566666655.589**********************998888775 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 3.4
                                       HHHHHHHTTSE CS
                              MarR  37 vldrLekkGli 47 
                                        l++L k+G i
  gi|298676137|ref|YP_003727886.1| 159 KLKKLAKEGTI 169
                                       57888888865 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0057         6      17      52 ..      18      53 ..       5      53 .. 0.87
   2 !    9.9   0.0   0.00066       0.7       7      48 ..      93     132 ..      88     137 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0057
                            HTH_11 17 sgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepgr 52
                                      ++++L+ eL++  +tv   +k+L + g+ I  ++g+
  gi|298676137|ref|YP_003727886.1| 18 NISQLKNELKLDHSTVSLAVKSLISNGFAIKYSQGK 53
                                      5789**************************988875 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00066
                            HTH_11   7 elLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIes 48 
                                         L ++++ ++++e++  +++ r t+   I +L++ gv + s
  gi|298676137|ref|YP_003727886.1|  93 SVL-KNDS-LNIKEISYVTGLHRNTISSVINSLSMYGVILKS 132
                                       556.6776.9***************************88776 PP

>> Aph-1  Aph-1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.2e-06    0.0012      59     127 ..      59     125 ..      53     204 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.2e-06
                             Aph-1  59 reqlafgvvfsvlfqelfRylfykllkkaeegLkkisessklkeskhqlayvsGlGfGvmsgvfslvni 127
                                       +++la ++v+svl+ e+ R+   kll+k +  + ++ +  + + + ++++yv+Gl   ++s+v+  +++
  gi|298676137|ref|YP_003727886.1|  59 QSELAHSIVLSVLLKEYPRLPWSKLLNKSSLHVMSVLK--NDSLNIKEISYVTGLHRNTISSVINSLSM 125
                                       678999********************998766655555..66678999***************998876 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.014        15      29      54 ..      20      45 ..      16      46 .. 0.88
   2 !   10.7   0.0   0.00038       0.4      31      54 ..     105     128 ..      90     129 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.014
                            HTH_36 29 etlakrlglsknTvsraikeLeqlGy 54
                                      + l + l+l+ +Tvs a+k+L+  G+
  gi|298676137|ref|YP_003727886.1| 20 SQLKNELKLDHSTVSLAVKSLISNGF 45
                                      6788899***************9985 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00038
                            HTH_36  31 lakrlglsknTvsraikeLeqlGy 54 
                                       ++  +gl++nT+s+ i++L  +G 
  gi|298676137|ref|YP_003727886.1| 105 ISYVTGLHRNTISSVINSLSMYGV 128
                                       55568**************98886 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   7.8e-05     0.082      12      51 ..      10      46 ..       2      53 .. 0.87
   2 ?    4.0   0.0     0.042        45      16      46 ..      96     124 ..      61     134 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.8e-05
                                      HHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSE CS
                            MarR_2 12 aaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLv 51
                                      ++L  +p    ++++l  +l+l++s+vs ++k L + G+ 
  gi|298676137|ref|YP_003727886.1| 10 FNLVSEPK---NISQLKNELKLDHSTVSLAVKSLISNGFA 46
                                      67777776...99***********************9986 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.042
                                       CTTTSEEEHHHHHHHHTSSHHHHHHHHHHHH CS
                            MarR_2  16 rrpgrdltvgelarrlglsksavsrilkrLv 46 
                                        ++   l+++e+   +gl + ++s +++ L+
  gi|298676137|ref|YP_003727886.1|  96 KNDS--LNIKEISYVTGLHRNTISSVINSLS 124
                                       3343..99********************998 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0012       1.3      11      33 ..      12      34 ..       7      48 .. 0.85
   2 ?    5.0   0.1     0.022        23       6      33 ..      90     117 ..      85     124 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0012
                                      HTTSSEEHHHHHHHHTS-HHHHH CS
                             HTH_5 11 LaegelcvcelaeelglsqstvS 33
                                      L ++++ +++l +el+l  stvS
  gi|298676137|ref|YP_003727886.1| 12 LVSEPKNISQLKNELKLDHSTVS 34
                                      66789*****************9 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.022
                                       HHHHHHTTSSEEHHHHHHHHTS-HHHHH CS
                             HTH_5   6 kILklLaegelcvcelaeelglsqstvS 33 
                                        +++ L + +l + e++  +gl + t+S
  gi|298676137|ref|YP_003727886.1|  90 HVMSVLKNDSLNIKEISYVTGLHRNTIS 117
                                       67899999**************999998 PP

>> DUF1441  Protein of unknown function (DUF1441)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   1.6e-05     0.017       2      42 ..     100     140 ..      99     145 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.6e-05
                           DUF1441   2 lnitqlaeitglhRqtvkkRlkgvepaagsnkknkvYaltd 42 
                                       lni++++ +tglhR+t+++ ++ +++ +   k n  Y+l +
  gi|298676137|ref|YP_003727886.1| 100 LNIKEISYVTGLHRNTISSVINSLSMYGVILKSNGCYYLNQ 140
                                       79**********************99999999999999875 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.025        26      69      96 ..      18      45 ..      14      66 .. 0.95
   2 ?    7.7   0.1    0.0052       5.5      64      97 ..      96     129 ..      82     132 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.025
                                      EHHHHHHHSTSXHHHHHHHHHHHHHTTS CS
                             RPA_C 69 hvdeiaqklrlsvndvkqavdeLsneGi 96
                                      ++++++++l+l+ ++v  av++L+++G 
  gi|298676137|ref|YP_003727886.1| 18 NISQLKNELKLDHSTVSLAVKSLISNGF 45
                                      6889*********************995 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0052
                                       STTTEEHHHHHHHSTSXHHHHHHHHHHHHHTTSE CS
                             RPA_C  64 seeGvhvdeiaqklrlsvndvkqavdeLsneGii 97 
                                       +++ ++++ei+  ++l  n++ +++++Ls  G+i
  gi|298676137|ref|YP_003727886.1|  96 KNDSLNIKEISYVTGLHRNTISSVINSLSMYGVI 129
                                       45889***************************99 PP

>> BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.2e-05     0.045      33      81 ..      50     103 ..      42     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.2e-05
                                       SS-B-B--B-TTSEEEEEEEEESS...-CCGTHHHHHHHHHHHHHHH........ CS
                     BPL_LplA_LipB  33 tgGrnvwhspkgeltyslllspeqktfqnrvlelyvsllvlavlealg......y 81 
                                       + G+n++++ ++el+ s++ls+  k++++ + + + + ++l v+ +l+      +
  gi|298676137|ref|YP_003727886.1|  50 SQGKNTFVH-QSELAHSIVLSVLLKEYPRLPWSKLLNKSSLHVMSVLKndslniK 103
                                       689******.77***********************************86543221 PP

>> HTH_43  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       2.3   2.4e+03      18      55 ..      14      51 ..       8      60 .. 0.80
   2 ?   12.2   0.0   0.00013      0.14      10      77 ..      89     152 ..      84     165 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.3
                                      HS-B-HHHHHHHH---HHHHHHHHHGGGGGT-EEEEE- CS
                            HTH_43 18 eeeanvpklieltgmPRRtlqDtlkalaeldielefvq 55
                                      +e +n+ +l +  ++   t+  ++k+l   +  +++ q
  gi|298676137|ref|YP_003727886.1| 14 SEPKNISQLKNELKLDHSTVSLAVKSLISNGFAIKYSQ 51
                                      56679999999999999999999999998888888877 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHS-B-HHHHHHHH---HHHHHHHHHGGGGGT-EEEEE--TTS-S--EEEEEE-TTB-HHH CS
                            HTH_43  10 lylaylideeeanvpklieltgmPRRtlqDtlkalaeldielefvqegernnaGyyrisdWGpidkeW 77 
                                       l+++ ++++++ n+ ++  +tg+ R t+  ++++l+  ++ l+   +g    + ++risd+   d  W
  gi|298676137|ref|YP_003727886.1|  89 LHVMSVLKNDSLNIKEISYVTGLHRNTISSVINSLSMYGVILK--SNGCYYLNQKHRISDFI--DYYW 152
                                       778889999999************************9999887..67777777778888763..3333 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0046       4.9      16      47 ..      14      45 ..       2      57 .. 0.86
   2 ?    3.8   0.0      0.08        85      16      48 ..      97     129 ..      88     135 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0046
                            HTH_27 16 rrrkkladlcgrlnvedshisyslkkLtekGL 47
                                       ++k +++l   l+++ s++s ++k L+ +G+
  gi|298676137|ref|YP_003727886.1| 14 SEPKNISQLKNELKLDHSTVSLAVKSLISNGF 45
                                      489*************************9997 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.08
                            HTH_27  16 rrrkkladlcgrlnvedshisyslkkLtekGLv 48 
                                       ++   +++++ ++ +   +is++++ L  +G++
  gi|298676137|ref|YP_003727886.1|  97 NDSLNIKEISYVTGLHRNTISSVINSLSMYGVI 129
                                       6777899********************999998 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.16   1.7e+02      20      47 ..      18      45 ..       8      47 .. 0.88
   2 ?    8.6   0.0    0.0015       1.6      18      46 ..      99     127 ..      85     131 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.16
                                      BHHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                          HTH_IclR 20 tlselArrtglpkStvhRlLqtLvelGy 47
                                      ++s+l +++ l  Stv+  +++L+  G+
  gi|298676137|ref|YP_003727886.1| 18 NISQLKNELKLDHSTVSLAVKSLISNGF 45
                                      58999999***************99998 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0015
                                       S-BHHHHHHHHTS-HHHHHHHHHHHHHTT CS
                          HTH_IclR  18 eltlselArrtglpkStvhRlLqtLvelG 46 
                                        l+++e++  tgl++ t +  +++L   G
  gi|298676137|ref|YP_003727886.1|  99 SLNIKEISYVTGLHRNTISSVINSLSMYG 127
                                       5899****************999998766 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.036        38       6      47 ..      10      51 ..       5      76 .. 0.83
   2 ?    6.3   0.0     0.012        13      10      71 ..      97     162 ..      88     168 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.036
                            HTH_40  6 lelleeglsieeIAkerglkesTIegHLaelieegeeidler 47
                                      ++l+ e ++i +  +e +l  sT+   + +li +g  i++++
  gi|298676137|ref|YP_003727886.1| 10 FNLVSEPKNISQLKNELKLDHSTVSLAVKSLISNGFAIKYSQ 51
                                      6889999****************************9999854 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.012
                            HTH_40  10 eeglsieeIAkerglkesTIegHLaelieegeeidlerlvseeeekeIeeaiek....vgseklkp 71 
                                       +++l+i+eI+   gl ++TI + + +l   g  ++ +  +  +++ +I + i+     ++++klk+
  gi|298676137|ref|YP_003727886.1|  97 NDSLNIKEISYVTGLHRNTISSVINSLSMYGVILKSNGCYYLNQKHRISDFIDYywnyINNKKLKK 162
                                       789******************999998888865555555444444444444443333455555555 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       5.2   5.5e+03      27      54 ..      18      45 ..      13      57 .. 0.71
   2 ?    9.0   0.1    0.0017       1.7      16      60 ..      91     134 ..      86     143 .. 0.80
   3 ?    1.1   0.0       0.5   5.3e+02      44      61 ..     158     175 ..     143     176 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.2
                                      -HHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                              Rrf2 27 sseeiaerqnispsylekilakLrkagl 54
                                      +++++ ++ ++ +s ++  ++ L  +g+
  gi|298676137|ref|YP_003727886.1| 18 NISQLKNELKLDHSTVSLAVKSLISNGF 45
                                      6777888888888888888888888876 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0017
                                       HHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                              Rrf2  16 yLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrG 60 
                                       +++  ++++ ++++ei+  ++++++ ++ +++ L+  g++    G
  gi|298676137|ref|YP_003727886.1|  91 VMSVLKNDS-LNIKEISYVTGLHRNTISSVINSLSMYGVILKSNG 134
                                       444445555.99************************999977666 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.5
                                       HHHHHHHHTTSEEEETTT CS
                              Rrf2  44 kilakLrkaglvksvrGk 61 
                                       k l+kL+k+g +  +rG 
  gi|298676137|ref|YP_003727886.1| 158 KKLKKLAKEGTIIWQRGS 175
                                       7799***********996 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0011       1.1      23      53 ..     101     131 ..      83     145 .. 0.85
   2 ?   -0.5   0.0       1.2   1.2e+03      39      53 ..     157     172 ..     157     179 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0011
                                       HHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE CS
                         HTH_Crp_2  23 tqeelAsmlGltretvsrilseLkreglisr 53 
                                       + +e++   Gl+r t+s +++ L+  g+i +
  gi|298676137|ref|YP_003727886.1| 101 NIKEISYVTGLHRNTISSVINSLSMYGVILK 131
                                       5689999********************9975 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.2
                                       HHHHHHHHHTTSEE.E CS
                         HTH_Crp_2  39 srilseLkreglis.r 53 
                                       ++ l++L +eg i  +
  gi|298676137|ref|YP_003727886.1| 157 NKKLKKLAKEGTIIwQ 172
                                       5789*******99754 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.028        29      20      46 ..      19      45 ..       2      46 .. 0.72
   2 ?    5.1   0.0     0.016        16      13      47 ..      95     129 ..      71     129 .. 0.92
   3 ?   -0.9   0.1       1.1   1.2e+03      36      47 ..     158     169 ..     157     170 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.028
                            HTH_24 20 qreLAerlglSpstvnrrlkrLeeeGl 46
                                      +++L  +l l  stv+  +k L+++G+
  gi|298676137|ref|YP_003727886.1| 19 ISQLKNELKLDHSTVSLAVKSLISNGF 45
                                      455667899999***********9996 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.016
                            HTH_24  13 qknprisqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                        kn +++++e++  +gl ++t++  ++ L   G+I
  gi|298676137|ref|YP_003727886.1|  95 LKNDSLNIKEISYVTGLHRNTISSVINSLSMYGVI 129
                                       689*********************99999877776 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.1
                            HTH_24  36 rrlkrLeeeGlI 47 
                                       + lk+L +eG I
  gi|298676137|ref|YP_003727886.1| 158 KKLKKLAKEGTI 169
                                       569*******88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.56
# Mc/sec: 1629.08
//
Query:       gi|298676138|ref|YP_003727887.1|  [L=268]
Description: hypothetical protein Metev_2273 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00011   22.1   0.1     0.0002   21.1   0.1    1.4  1  TrmB           Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
       0.01   15.7   0.2       0.11   12.4   0.1    2.4  3  AhpC-TSA       AhpC/TSA family
      0.018   15.5   0.4      0.073   13.6   0.1    2.0  2  PCI            PCI domain
      0.062   13.6   0.0       0.14   12.5   0.0    1.6  1  PG_binding_2   Putative peptidoglycan binding domain
       0.11   12.5   0.0       0.29   11.2   0.0    1.7  1  Dimerisation2  Dimerisation domain


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   5.7e-08    0.0002      15      58 ..     219     262 ..     216     267 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 5.7e-08
                                       HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB  15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58 
                                       + Llk++p++ ++++ +l+v +    ++L++L+ k+++e+  ++
  gi|298676138|ref|YP_003727887.1| 219 IDLLKEKPSDLETVSTRLNVNKKETDKILKNLLAKDIIEKTASS 262
                                       57*************************************99776 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   3.1e-05      0.11      48      98 ..      36      84 ..      32     120 .. 0.86
   2 ?   -1.5   0.0      0.62   2.2e+03      56      89 ..     120     165 ..     111     168 .. 0.74
   3 ?   -0.3   0.0      0.26   9.3e+02      74      91 ..     189     206 ..     186     213 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.1e-05
                                      HHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH-H.SSEEEE-TTSHHHHHT CS
                          AhpC-TSA 48 laklyeefkergvevigvsvdspeshkkfiekeslnfpllsDeegkvakay 98
                                      ++kl ++ k  +++v+ +svd+++s+kk     +++ p lsDe +k++ ++
  gi|298676138|ref|YP_003727887.1| 36 FQKLKDATK--DIDVVVLSVDELKSLKKSLSSLGYKKPHLSDEYNKLSANL 84
                                      555555555..899*****************************99998876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.62
                                       CCTTEEEEEEESSSCHHHHHHHHH-H.............SSEEEE- CS
                          AhpC-TSA  56 kergvevigvsvdspeshkkfiekes............lnfpllsD 89 
                                       +  ++ v+ +++++ +  k+   +e             l f+++ D
  gi|298676138|ref|YP_003727887.1| 120 DLTNISVYSITPEDIFIFKSITSREHdlldmytlfssgLDFEIIKD 165
                                       5568889999999999877777766667777777777777777777 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.26
                                       HHHHHH-H.SSEEEE-TT CS
                          AhpC-TSA  74 kkfiekeslnfpllsDee 91 
                                       ++f ++++l  pl+sD  
  gi|298676138|ref|YP_003727887.1| 189 EEFLDEYNLSHPLFSDLR 206
                                       6899************65 PP

>> PCI  PCI domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.91   3.3e+03      30      51 ..      68      89 ..      43      90 .. 0.67
   2 ?   13.6   0.1     2e-05     0.073      15      90 ..     185     256 ..     180     260 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.91
                                      HHHTTHHHHHHHHHHHHHHHHH CS
                               PCI 30 laddglaqllesLekkvrerll 51
                                       ++++l++ +++L  +++++++
  gi|298676138|ref|YP_003727887.1| 68 YKKPHLSDEYNKLSANLILENI 89
                                      4567777777777777777776 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2e-05
                                       HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHCESEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSS CS
                               PCI  15 lsgfseelkdleeelladdglaqllesLekkvrerllrqvskiyssislerlaklldlsvdevEkilvklIrdgei 90 
                                       ++gf+e+l ++    l ++  ++l ++ ++++ e+ ++ + k  +  +le++++ l+++++e++kil +l +++ i
  gi|298676138|ref|YP_003727887.1| 185 YTGFEEFLDEY---NLSHPLFSDLRDMAYENMMEQMIIDLLK-EKPSDLETVSTRLNVNKKETDKILKNLLAKDII 256
                                       57888888888...5677777888888888888888888888.7778***********************999887 PP

>> PG_binding_2  Putative peptidoglycan binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     4e-05      0.14       6      35 ..      44      71 ..      39      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4e-05
                      PG_binding_2  6 kpeeervlaedvaeevqaaLsrLGyydgea 35
                                      k+ + +vl  d+ ++++++Ls+LGy++  +
  gi|298676138|ref|YP_003727887.1| 44 KDIDVVVLSVDELKSLKKSLSSLGYKK--P 71
                                      6778999******************54..3 PP

>> Dimerisation2  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0     8e-05      0.29      22      76 ..     217     266 ..     208     268 .] 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8e-05
                     Dimerisation2  22 gvFdlLkeeeplsaeevaeelgasvkGterLldacvaLgLLerekkeekkalYsn 76 
                                        + dlLke +p ++e+v+++l+++ k t+ +l+ + a ++ e  k+ +  + Y+n
  gi|298676138|ref|YP_003727887.1| 217 MIIDLLKE-KPSDLETVSTRLNVNKKETDKILKNLLAKDIIE--KTAS--SCYKN 266
                                       688*****.**************************9999999..4444..47777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1137  (0.0634168); expected 358.6 (0.02)
Passed bias filter:                      677  (0.0377601); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 1577.47
//
Query:       gi|298676139|ref|YP_003727888.1|  [L=395]
Description: nucleotidyl transferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-47  162.0   0.0    2.8e-47  161.4   0.0    1.2  1  NTP_transferase  Nucleotidyl transferase
    2.8e-15   55.4  28.7    1.3e-08   34.2   3.0    5.1  6  Hexapep          Bacterial transferase hexapeptide (six repea
    2.1e-12   47.7   0.0    2.9e-12   47.2   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
    1.6e-06   27.7  16.8    0.00013   21.6   2.7    4.5  5  Hexapep_2        Hexapeptide repeat of succinyl-transferase
    0.00012   21.9   0.0    0.00031   20.6   0.0    1.7  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
     0.0039   15.4   4.4     0.0081   14.3   4.4    1.5  1  DUF4954          Domain of unknown function (DUF4954)
  ------ inclusion threshold ------
       0.16   10.9   0.0       0.36    9.7   0.0    1.7  2  Fucokinase       L-fucokinase


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.4   0.0   1.1e-50   2.8e-47       1     247 [.       2     231 ..       2     232 .. 0.92

  Alignments for each domain:
  == domain 1  score: 161.4 bits;  conditional E-value: 1.1e-50
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEE CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevli 77 
                                       kavILa G+GtR++PLt + +k +++v++k +++++ + + + +gi+e  v +t +h+  v+e++++gs +gv++++
  gi|298676139|ref|YP_003727888.1|   2 KAVILAAGEGTRMRPLTYSCPKVMLTVANK-PILEHIMDATIGAGIDE-FVFITGFHENAVKEYFGDGSSWGVDIQY 76 
                                       79****************************.*****************.555566********************** PP

                                       EEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEEC CS
                   NTP_transferase  78 alepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGviead 154
                                       +++ e+kgtAdA++ a  +++ ++     +vL+gD+l+++   +++kk ++k++  ++++ +++v++++e+Gvi ++
  gi|298676139|ref|YP_003727888.1|  77 VTQLEQKGTADAIKHADGYVDGHF-----IVLNGDVLVTK---DYLKKLVSKKS--DAVITAKEVDNPSEFGVIDVS 143
                                       ****************99999766.....9*********5...55778888888..7999****************9 PP

                                       TTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEE CS
                   NTP_transferase 155 eegrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsD 231
                                       + ++v+++vEK ++++ ++la++GiY+f  ++++++ +    ++rge eitd ++ ++++gk+  +    d+e W D
  gi|298676139|ref|YP_003727888.1| 144 G-DNVTQIVEKSSNPP-TNLANTGIYLFHDSIFEYI-DRTPLSERGELEITDSMQMMIDDGKQVTY-KLLDNE-WID 215
                                       7.69************.*******************.66788899***************988766.666665.*** PP

                                       XSSHHHHHHHHHHHHH CS
                   NTP_transferase 232 vGtldslleaneklae 247
                                       +G + ++l+an+ l++
  gi|298676139|ref|YP_003727888.1| 216 IGRPWDMLDANKLLLQ 231
                                       ***********98765 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       2.3   5.8e+03       9      21 ..      96     108 ..      91     111 .. 0.79
   2 !   18.1   0.5   6.2e-07    0.0016      10      36 .]     241     267 ..     240     267 .. 0.93
   3 !   34.2   3.0   5.1e-12   1.3e-08       2      35 ..     251     284 ..     250     285 .. 0.96
   4 !   26.7   3.7   1.2e-09   3.1e-06       2      35 ..     269     302 ..     268     303 .. 0.91
   5 !   14.4   0.9   9.3e-06     0.024       1      35 [.     303     336 ..     303     337 .. 0.87
   6 ?    1.3   0.6      0.12   3.2e+02       7      26 ..     368     387 ..     362     388 .. 0.55

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.3
                                       EE-TTEEEETTEE CS
                           Hexapep   9 lIgpfaviggnVk 21 
                                       + g+f v+ g+V 
  gi|298676139|ref|YP_003727888.1|  96 VDGHFIVLNGDVL 108
                                       6789999999995 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 6.2e-07
                                       E-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep  10 IgpfaviggnVkIGdnvkIgagvvigg 36 
                                       + p+a+i g V+IG+n+++ +g++i g
  gi|298676139|ref|YP_003727888.1| 241 VEPYATIKGEVVIGKNTVVKNGSYIEG 267
                                       679*********************976 PP

  == domain 3  score: 34.2 bits;  conditional E-value: 5.1e-12
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       +vIG+n+++ ++++i g+V+IG+++ Ig++++i+
  gi|298676139|ref|YP_003727888.1| 251 VVIGKNTVVKNGSYIEGPVVIGEDCDIGPNCYIR 284
                                       79******************************97 PP

  == domain 4  score: 26.7 bits;  conditional E-value: 1.2e-09
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       +vIG+++ Igp+++i++ + IG++vkIg+ v ++
  gi|298676139|ref|YP_003727888.1| 269 VVIGEDCDIGPNCYIRPSTCIGNHVKIGNAVEVK 302
                                       89**************************977775 PP

  == domain 5  score: 14.4 bits;  conditional E-value: 9.3e-06
                                       TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       +t++ + + Ig+ a++ g+ ++G+++  gag+ ++
  gi|298676139|ref|YP_003727888.1| 303 NTIVMDATNIGHLAYV-GDSVVGKRCNFGAGTKVA 336
                                       57889999********.5555***********987 PP

  == domain 6  score: 1.3 bits;  conditional E-value: 0.12
                                       TEEE-TTEEEETTEEE-TTE CS
                           Hexapep   7 nvlIgpfaviggnVkIGdnv 26 
                                       +v+ g ++ i  +V++ +n+
  gi|298676139|ref|YP_003727888.1| 368 DVHTGINTSINVGVVLERNT 387
                                       55555555555555555554 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.2   0.0   1.1e-15   2.9e-12       1     122 [.       3     129 ..       3     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 1.1e-15
                                       EEEEEESS-TTTT..T...THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSHCH..HHHHHTTC......TS-EEE CS
                      NTP_transf_3   1 aviLAGGrSsRmg..g...dKallplggkpllervldalraagvdevvvvggdee..vlaalarl......gvrvve 64 
                                       aviLA+G+++Rm   +   +K +l +++kp+le+++da   ag+de v ++g +e  v++++         ++++v+
  gi|298676139|ref|YP_003727888.1|   3 AVILAAGEGTRMRplTyscPKVMLTVANKPILEHIMDATIGAGIDEFVFITGFHEnaVKEYFG-DgsswgvDIQYVT 78 
                                       79**********8551559********************************997511444333.2355533455666 PP

                                       -TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEE CS
                      NTP_transf_3  65 dedpgkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvpt 122
                                       +  ++kg++ ++++a   +  + +++vl +D+ l+t++ +++l+ +    +++v+ ++
  gi|298676139|ref|YP_003727888.1|  79 QL-EQKGTADAIKHADGYV--DGHFIVLNGDV-LVTKDYLKKLVSKK---SDAVITAK 129
                                       65.5899999999999987..89*********.88*********984...34444444 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.5   6.4e+03      23      30 ..      39      46 ..      39      46 .. 0.70
   2 !    9.3   0.1   0.00036      0.93      14      32 ..     245     265 ..     243     266 .. 0.87
   3 !   21.6   2.7   5.1e-08   0.00013       1      28 [.     268     297 ..     268     302 .. 0.93
   4 ?    4.7   0.1      0.01        26       4      13 ..     323     332 ..     322     335 .. 0.88
   5 ?   -1.4   0.1      0.79     2e+03      11      23 ..     372     386 ..     367     387 .. 0.64

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.5
                                      T-EE-TT- CS
                         Hexapep_2 23 ncvvgaGv 30
                                      ++++gaG+
  gi|298676139|ref|YP_003727888.1| 39 DATIGAGI 46
                                      57788885 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00036
                                       -EE.S.EEE-TT-EE-TT-EE CS
                         Hexapep_2  14 agi.G.vslGdncvvgaGvvi 32 
                                       a+i G v +G+n vv +G++i
  gi|298676139|ref|YP_003727888.1| 245 ATIkGeVVIGKNTVVKNGSYI 265
                                       5677779*************9 PP

  == domain 3  score: 21.6 bits;  conditional E-value: 5.1e-08
                                       .EEE-TT-EE-TT-EE..SEEE-TT-EE-T CS
                         Hexapep_2   1 pviIGdnCliGanagi..GvslGdncvvga 28 
                                       pv IG++C iG+n++i   + +G+ +++g+
  gi|298676139|ref|YP_003727888.1| 268 PVVIGEDCDIGPNCYIrpSTCIGNHVKIGN 297
                                       8****************99*****999998 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.01
                                       E-TT-EE-TT CS
                         Hexapep_2   4 IGdnCliGan 13 
                                       +G++C++Ga 
  gi|298676139|ref|YP_003727888.1| 323 VGKRCNFGAG 332
                                       8*******96 PP

  == domain 5  score: -1.4 bits;  conditional E-value: 0.79
                                       -TT.-E.ESEEE-TT CS
                         Hexapep_2  11 Gan.ag.iGvslGdn 23 
                                       G n ++ +Gv l++n
  gi|298676139|ref|YP_003727888.1| 372 GINtSInVGVVLERN 386
                                       556344458888776 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.2e-07   0.00031       2      42 ..       2      45 ..       1      66 [. 0.81

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.2e-07
                                      EEEEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTT CS
                              IspD  2 vvvipAAGsGkRmk...aglpKqflelkgqtllehtvdallask 42
                                       +vi AAG+G+Rm+     +pK  l+++++++leh +da  + +
  gi|298676139|ref|YP_003727888.1|  2 KAVILAAGEGTRMRpltYSCPKVMLTVANKPILEHIMDATIGAG 45
                                      69**********9633369*******************998744 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   4.4   3.2e-06    0.0081     175     259 ..     252     334 ..     220     339 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.2e-06
                           DUF4954 175 eigekvkilnaglikN.vkigdyatiegasklengtinSskeapveiGegViledfiissGskikdgavisrcfvGq 250
                                       +ig++++++n ++i+  v ig+ + i     ++  t + +    v+iG+ V+++++i++  ++i + a + +++vG+
  gi|298676139|ref|YP_003727888.1| 252 VIGKNTVVKNGSYIEGpVVIGEDCDIGPNCYIRPSTCIGN---HVKIGNAVEVKNTIVMDATNIGHLAYVGDSVVGK 325
                                       5899999999999985489999999999999999998876...599******************************* PP

                           DUF4954 251 avklkkqfs 259
                                        ++++ + +
  gi|298676139|ref|YP_003727888.1| 326 RCNFGAGTK 334
                                       **9987765 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       0.7   1.8e+03     105     153 ..      72     119 ..      66     138 .. 0.70
   2 ?    9.7   0.0   0.00014      0.36     271     334 ..     237     311 ..     159     345 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.7
                        Fucokinase 105 leirsvkkflhKpseeelqasgavlkdekvlldsGvvffdhktaekLlk 153
                                       + i++v ++ +K++++ +++    ++  + +l    v++ ++  +kL++
  gi|298676139|ref|YP_003727888.1|  72 VDIQYVTQLEQKGTADAIKHADGYVDGHFIVLNG-DVLVTKDYLKKLVS 119
                                       5678888888888888888776666665555554.66666666666665 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00014
                        Fucokinase 271 kesavvinSvlessvsvgegsvieh.sslkgnvsigsnsiv.sglelessee.........slelpddtilqtls 334
                                       ++++v   + ++++v +g+++v+++ s ++g+v ig+ + +  +++++ s++          +e+++ +++  ++
  gi|298676139|ref|YP_003727888.1| 237 NKGSVEPYATIKGEVVIGKNTVVKNgSYIEGPVVIGEDCDIgPNCYIRPSTCignhvkignAVEVKNTIVMDATN 311
                                       555556677888899999999998536777888888888662578888887777766666667777777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2740.10
//
Query:       gi|298676140|ref|YP_003727889.1|  [L=434]
Description: phosphoglucomutase/phosphomannomutase alpha/beta/alpha domain I [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.2e-35  119.7   0.0    1.3e-34  118.9   0.0    1.3  1  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
    1.8e-28   99.1   0.1    4.2e-28   98.0   0.1    1.6  1  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
    4.1e-20   72.1   0.0    7.6e-20   71.2   0.0    1.4  1  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet
    5.2e-12   45.8   0.0    1.2e-11   44.6   0.0    1.6  1  PGM_PMM_IV   Phosphoglucomutase/phosphomannomutase, C-termina
  ------ inclusion threshold ------
      0.045   13.9   0.1        7.8    6.7   0.0    3.0  2  CinA_KH      Damage-inducible protein CinA KH domain
        0.1   11.4   0.0       0.17   10.7   0.0    1.3  1  DUF2957      Protein of unknown function (DUF2957)


Domain annotation for each model (and alignments):
>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.9   0.0   4.2e-38   1.3e-34       2     134 ..       2     125 ..       1     128 [. 0.95

  Alignments for each domain:
  == domain 1  score: 118.9 bits;  conditional E-value: 4.2e-38
                                       GGBBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB- CS
                         PGM_PMM_I   2 qkfgtsGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllp 78 
                                       ++fg sG+Rg ++++ +t el++klg+ +++  k+      +v+G+D Rvs ++++ a+++gl+++G +v+++gl++
  gi|298676140|ref|YP_003727889.1|   2 KLFGSSGIRGMANKD-VTVELALKLGHVLGKKYKN------IVIGKDPRVSAEMIEYAMISGLTSSGGSVMRTGLVT 71 
                                       68***********55.9******999999998887......************************************ PP

                                       HHHHHHHHHHCCECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHHHHCCT CS
                         PGM_PMM_I  79 tPavsfairklkadagimitaSHnppeyngiKvylsnGgpispeveekIeaiieke 134
                                       tP +++a++   +d+g+mitaSHnp+ey giK+ +++G+ ++++++e+Ie++ie +
  gi|298676140|ref|YP_003727889.1|  72 TPTLAYAAKD--YDCGVMITASHNPAEYIGIKLWNPDGMAFDSSQQEEIEQEIEDY 125
                                       *********9..799*************************************9976 PP

>> PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.0   0.1   1.4e-31   4.2e-28      10     103 .]     152     244 ..     145     244 .. 0.92

  Alignments for each domain:
  == domain 1  score: 98.0 bits;  conditional E-value: 1.4e-31
                                       TS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHHGGGGG-SEE CS
                        PGM_PMM_II  10 kvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealkllielvkkegadlg 86 
                                       ++d++    +++kvv+d++ Gag++i++ ll+elg++v++lna+ d++fp + p+p+e ++l+ll e+vk+ +adlg
  gi|298676140|ref|YP_003727889.1| 152 IMDKTNPVTKPVKVVVDCGSGAGSTITPYLLRELGCEVITLNAQLDGHFPARKPEPNE-KNLQLLKETVKSADADLG 227
                                       445555667899**********************************************.****************** PP

                                       EEE-TTS-BEEEEETTE CS
                        PGM_PMM_II  87 lafDgDaDRlgvvderG 103
                                       +a+DgDaDR+++vd++G
  gi|298676140|ref|YP_003727889.1| 228 IAHDGDADRMMAVDKNG 244
                                       ***************98 PP

>> PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.2   0.0   2.5e-23   7.6e-20       2     112 ..     249     350 ..     248     352 .. 0.92

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 2.5e-23
                                       HHHHHHHHHHHHHCHCSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETTCEEEETT CS
                       PGM_PMM_III   2 gdqllallakylleeklkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeSghiifld 78 
                                       gd++la++a +++ +   ++ +v+++v ts++l+++   l++++ +t+vGd yv+ee+k++ga +GgE Sg +if++
  gi|298676140|ref|YP_003727889.1| 249 GDEMLAIFAMNVCGS---DS-TVIAPVDTSMILDDA---LDCEIKRTRVGDVYVAEEIKRTGADFGGEASGSWIFPK 318
                                       9***********873...44.5*************9...89************************************ PP

                                       TBSS--HHHHHHHHHHHHHHHTS-HHHHHHHHHH CS
                       PGM_PMM_III  79 eattkDGilaallvleilaetgkslselleellk 112
                                        +++ DGi+aa++++ei+++  ++l el e+l++
  gi|298676140|ref|YP_003727889.1| 319 ISYCPDGIYAAAKLVEIVQD--RPLGELREQLPE 350
                                       ******************77..699999977654 PP

>> PGM_PMM_IV  Phosphoglucomutase/phosphomannomutase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   0.0   4.1e-15   1.2e-11      23      71 ..     375     430 ..     357     432 .. 0.79

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 4.1e-15
                                       H.......HCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEES.SHHHHHHHHHHHHH CS
                        PGM_PMM_IV  23 a.......sikeglkilledGrrlavRpSGTepllrvyvEak.sdeelarlaeevae 71 
                                       +       + ++g++i+   G++l vRpSGTep++r+ vE++ + eel +lae+ ++
  gi|298676140|ref|YP_003727889.1| 375 QlsqygeiNSIDGVRIDMDGGWVL-VRPSGTEPKIRITVESRdDVEELYQLAEDTIK 430
                                       23334455789*************.*****************999999999998765 PP

>> CinA_KH  Damage-inducible protein CinA KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0026       7.8      25      47 ..      71      93 ..      62      97 .. 0.86
   2 ?    3.8   0.0     0.022        65      34      64 ..     402     433 ..     397     434 .] 0.74

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0026
                                      SSSEEEEEEETTEEEEEEE...E CS
                           CinA_KH 25 enptlAiyakegevtvRltakaa 47
                                      + ptlA+ ak+ ++ v +ta+ +
  gi|298676140|ref|YP_003727889.1| 71 TTPTLAYAAKDYDCGVMITASHN 93
                                      789****************9876 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.022
                                       ETTEEEEEEE....EEHHHHHHHHH....HHH CS
                           CinA_KH  34 kegevtvRlta.kaaneeeaealiapveeeir 64 
                                       +  e ++R+t+ + ++ ee  +l++++++e++
  gi|298676140|ref|YP_003727889.1| 402 SGTEPKIRITVeSRDDVEELYQLAEDTIKEVM 433
                                       56678999998556777888888888888775 PP

>> DUF2957  Protein of unknown function (DUF2957)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   5.8e-05      0.17     245     332 ..     216     303 ..     208     316 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.8e-05
                           DUF2957 245 nllalvaDdeigisilapataiaagslkGeyiGvdssfnYrstalqgataalldPleasaslasalklDytqavpGv 321
                                       +++   aD++ gi+    a  + a   +Ge++  d  +   +  + g++ +++ P+++s+ l  al+ +  ++  G 
  gi|298676140|ref|YP_003727889.1| 216 KETVKSADADLGIAHDGDADRMMAVDKNGEFVSGDEMLAIFAMNVCGSDSTVIAPVDTSMILDDALDCEIKRTRVGD 292
                                       556778***************************************************99999999999998888888 PP

                           DUF2957 322 vttveksaptG 332
                                       v  +e+   tG
  gi|298676140|ref|YP_003727889.1| 293 VYVAEEIKRTG 303
                                       88777766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.74
# Mc/sec: 1766.42
//
Query:       gi|298676141|ref|YP_003727890.1|  [L=609]
Description: glucosamine/fructose-6-phosphate aminotransferase, isomerizing [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-60  202.0   3.7    2.8e-30  104.8   0.1    3.6  4  SIS       SIS domain
    6.4e-22   78.2   0.0    1.2e-21   77.3   0.0    1.4  1  GATase_6  Glutamine amidotransferase domain
    1.2e-15   57.6   0.0    3.2e-15   56.1   0.0    1.8  1  GATase_7  Glutamine amidotransferase domain
    0.00079   19.4   0.1      0.072   13.1   0.0    2.6  2  SIS_2     SIS domain
     0.0057   15.6   0.0     0.0095   14.9   0.0    1.2  1  GATase_4  Glutamine amidotransferases class-II
  ------ inclusion threshold ------
        0.1   13.4   0.0       0.26   12.1   0.0    1.7  1  DUF5124   Domain of unknown function (DUF5124)


Domain annotation for each model (and alignments):
>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.58   1.7e+03      65      91 ..      13      39 ..       8      44 .. 0.83
   2 ?   -0.1   0.0      0.26   7.7e+02      84      95 ..     166     177 ..     156     202 .. 0.86
   3 !   95.3   0.2   8.4e-31   2.5e-27       3     130 ..     289     417 ..     287     418 .. 0.96
   4 !  104.8   0.1   9.4e-34   2.8e-30       7     129 ..     467     590 ..     461     592 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.58
                                      HHHHHHHHHHHHHHTTSEEEEEESSTT CS
                               SIS 65 etkdlvaaaelakergakiiaITdskg 91
                                       + +l+++++++  rg   ++IT  ++
  gi|298676141|ref|YP_003727890.1| 13 AKQELIDSLKKLEYRGYDSVGITILNS 39
                                      578999*************99997654 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.26
                                       EEEESSTTSHHH CS
                               SIS  84 iaITdskgspla 95 
                                       i+IT++k+spl+
  gi|298676141|ref|YP_003727890.1| 166 IIITGKKNSPLV 177
                                       99*******996 PP

  == domain 3  score: 95.3 bits;  conditional E-value: 8.4e-31
                                       CTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEE.EEEESSSHHHHHHHHHHHHHH CS
                               SIS   3 akakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlv.ilisfsgetkdlvaaaelake 78 
                                       ++  ri ++++Gtsy++++ +++ +e+++gi+  ++  se+++++   +d+dd++ i+is+sget+d++aa++ +k+
  gi|298676141|ref|YP_003727890.1| 289 RNLTRIELIACGTSYNAGLIAKYLFEQLAGIHTNIDTGSEYRYRYPVFCDSDDVLsIAISQSGETADTIAALQSLKS 365
                                       5667999*************************************999999999877********************* PP

                                       TTSEEEEEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHHHHH CS
                               SIS  79 rgakiiaITdskgsplareadlalyinaepetlvastksltaqlaaldalav 130
                                        g +++aIT+  gs++ r+ad ++yi a+pe +va+tk++t+ql+ l++lav
  gi|298676141|ref|YP_003727890.1| 366 SGCRTLAITNVMGSSITRDADDVMYIKAGPELGVAATKTFTSQLTILYLLAV 417
                                       ************************************************9986 PP

  == domain 4  score: 104.8 bits;  conditional E-value: 9.4e-34
                                       EEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHH.HHHHTTSE CS
                               SIS   7 riyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaae.lakergak 82 
                                         +++G+  +y++a+e+alkl+ei++i++e+++a+elkhg+lali+ed++v++i++sg+t d++ ++  ++k+r+a+
  gi|298676141|ref|YP_003727890.1| 467 DYFFIGRYMNYPVALEGALKLKEISYIHAEGYAAGELKHGPLALITEDTPVVAIATSGHTYDKIISNImEVKARNAT 543
                                       5699************************************************************99999******** PP

                                       EEEEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHHHH CS
                               SIS  83 iiaITdskgsplareadlalyinaepetlvastksltaqlaaldala 129
                                       +ia++ ++++ + ++ dl+l+i++ +e l ++++++++ql+a+++++
  gi|298676141|ref|YP_003727890.1| 544 VIAVAEEDDNEIEKYVDLVLRIPKTDELLSPILSNIVLQLLAYYTAL 590
                                       *******************************************9987 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.3   0.0     4e-25   1.2e-21      11     123 ..      62     179 ..      51     189 .. 0.84

  Alignments for each domain:
  == domain 1  score: 77.3 bits;  conditional E-value: 4e-25
                          GATase_6  11 edevalaHvRlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall....ee 83 
                                       ++ ++++H+R+a++g ++++ a+P    +g++++vhNG i+ny++l+eel + +g++frs++Dtev+++ll    ++
  gi|298676141|ref|YP_003727890.1|  62 DGYTGIGHTRWATHGQPTKQNAHPH--LSGNISIVHNGIIENYQQLKEELIE-AGYEFRSETDTEVIAHLLnsyyQQ 135
                                       55689************88888***..*************************.****************99888833 PP

                          GATase_6  84 lG......eevlerlrGmfafaiwdkrentlilardrlgvkplyya 123
                                        +      + +l+rl+G +a+a++  +   +i++  +  ++pl+++
  gi|298676141|ref|YP_003727890.1| 136 NDdfhtafQNTLKRLDGSYAVAAVCDDMPDIIITGKK--NSPLVVG 179
                                       335767889999*********9988877777776333..6777776 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1   0.0   1.1e-18   3.2e-15      10     122 ..      80     195 ..      69     196 .. 0.81

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 1.1e-18
                          GATase_7  10 eagaQPmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea.........ewgeealerlnGm 77 
                                       +++a P +   +g++ iv+nG i Ny++l+eeL ++g++fr+++Dtev+++ll++            +++l+rl+G+
  gi|298676141|ref|YP_003727890.1|  80 KQNAHPHL---SGNISIVHNGIIENYQQLKEELIEAGYEFRSETDTEVIAHLLNSyyqqnddfhTAFQNTLKRLDGS 153
                                       44445555...699***************************************999*******999*********** PP

                          GATase_7  78 fAfaiwdeeekrlllaRDrlGikPLyygedkgdallfaSelkall 122
                                       +A+a + ++  ++++   +    PL +g  +g   + aS + a+l
  gi|298676141|ref|YP_003727890.1| 154 YAVAAVCDDMPDIIITGKK--NSPLVVGLGNG-CNFAASDITAFL 195
                                       ***9887777766665554..67888888864.777777777765 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   2.4e-05     0.072     102     137 ..     338     374 ..     303     375 .. 0.87
   2 ?    3.8   0.1     0.019        56     107     136 ..     517     547 ..     475     549 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.4e-05
                                       -TT-EE.EEE-SS--SHHHHHHHHHHHHHT-EEEEEE CS
                             SIS_2 102 kpgDvL.lviSnsGnnavvveaaeaakergmkviAlt 137
                                       ++ DvL + iS+sG+ a  ++a++  k+ g+++ A+t
  gi|298676141|ref|YP_003727890.1| 338 DSDDVLsIAISQSGETADTIAALQSLKSSGCRTLAIT 374
                                       7889995669**************************9 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.019
                                       EEEE-SS--S.HHHHHHHHHHHHHT-EEEEE CS
                             SIS_2 107 LlviSnsGnn.avvveaaeaakergmkviAl 136
                                        + i +sG+    ++  ++++k+r ++viA+
  gi|298676141|ref|YP_003727890.1| 517 VVAIATSGHTyDKIISNIMEVKARNATVIAV 547
                                       46688899987899****************8 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   3.2e-06    0.0095      68     146 ..      60     137 ..      41     157 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.2e-06
                          GATase_4  68 piksknvvaHiRkatqGevklenthpFvRelwgrewifAHnGdlkeykpkl....egrfePvGsTDsElafCellee 140
                                       +i     + H R at+G+ +++n+hp    l g ++ + HnG +++y++      e  +e   +TD+E++  +ll++
  gi|298676141|ref|YP_003727890.1|  60 DIDGYTGIGHTRWATHGQPTKQNAHPH---LSG-NISIVHNGIIENYQQLKeeliEAGYEFRSETDTEVI-AHLLNS 131
                                       577777899*****************6...455.56678*****99877655557788999999***976.577777 PP

                          GATase_4 141 lasrfe 146
                                         ++++
  gi|298676141|ref|YP_003727890.1| 132 YYQQND 137
                                       666664 PP

>> DUF5124  Domain of unknown function (DUF5124)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   8.7e-05      0.26      21      67 ..     455     504 ..     439     534 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.7e-05
                           DUF5124  21 iydclekyskaevyylvGdfmql...essdaklscialvdtkGsvagkwn 67 
                                       + + + ++s+   y+ +G +m+     ++  kl+ i+++  +G  ag+ +
  gi|298676141|ref|YP_003727890.1| 455 VRKYAKQFSEVSDYFFIGRYMNYpvaLEGALKLKEISYIHAEGYAAGELK 504
                                       55667899*************976667999****************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (609 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       825  (0.0460148); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.70u 0.30s 00:00:01.00 Elapsed: 00:00:00.49
# Mc/sec: 3754.69
//
Query:       gi|298676142|ref|YP_003727891.1|  [L=404]
Description: nucleotidyl transferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.3e-45  153.9   0.2    8.2e-45  153.3   0.2    1.3  1  NTP_transferase  Nucleotidyl transferase
    1.6e-22   78.3  20.6    2.3e-08   33.4   0.3    4.7  4  Hexapep          Bacterial transferase hexapeptide (six repea
    2.6e-15   57.1   0.0    3.7e-15   56.7   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
    5.4e-09   35.6  21.0    4.7e-07   29.4   0.7    4.8  4  Hexapep_2        Hexapeptide repeat of succinyl-transferase
    8.2e-06   25.7   0.1      2e-05   24.5   0.1    1.7  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
    1.6e-05   24.8   0.1    2.7e-05   24.0   0.1    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    0.00015   21.8   0.9    0.00026   21.0   0.9    1.3  1  CTP_transf_3     Cytidylyltransferase
     0.0011   19.0   0.1     0.0021   18.0   0.1    1.4  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.075   13.3   1.0        0.5   10.6   0.1    2.9  3  DapH_N           Tetrahydrodipicolinate succinyltransferase N


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.3   0.2   4.1e-48   8.2e-45       1     231 [.       2     218 ..       2     232 .. 0.92

  Alignments for each domain:
  == domain 1  score: 153.3 bits;  conditional E-value: 4.1e-48
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEE CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevli 77 
                                       kavILa G+G+R +PLt t +k ++pv++k +++++ ++ l + +i++ii+++ +++++++ +++++g++fgv++++
  gi|298676142|ref|YP_003727891.1|   2 KAVILAAGEGSRCRPLTLTKSKVMLPVANK-PVLEHIIESLEKCSITDIILIV-DYEKERIMDHFEDGKDFGVNITY 76 
                                       79****************************.*****************66665.578889999************** PP

                                       EEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEEC CS
                   NTP_transferase  78 alepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGviead 154
                                       ++++ + gtA+A+++ +e ++de++   +lvL+gD +++    e++ + ie+a+ g++++++++ ++ ++yGv+ +d
  gi|298676142|ref|YP_003727891.1|  77 IHQSAQLGTAHALLQTQEHVKDENQ---FLVLNGDNVVE---PETISDLIEDAE-GDASVLTQKMKNTSNYGVVITD 146
                                       ************************7...***********...667777777777.7888***************999 PP

                                       TTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEE CS
                   NTP_transferase 155 eegrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsD 231
                                       + +++e++vEKP+e+  s+l+++GiY+f++++++++ k+   +++ge  itd+l+ +++ g++  ++  k    W D
  gi|298676142|ref|YP_003727891.1| 147 N-KKIEKIVEKPEEKI-SNLVNTGIYLFTPNIFQII-KQTPISEKGEYAITDTLQLMIDYGYQVTNVNTKS--RWID 218
                                       8.6**********988.*******************.87999999*******************9987777..5988 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   1.2   3.2e-08   6.4e-05      10      36 .]     245     271 ..     245     271 .. 0.93
   2 !   33.4   0.3   1.2e-11   2.3e-08       2      33 ..     273     304 ..     272     307 .. 0.92
   3 !   10.2   0.4   0.00024      0.49       2      30 ..     308     335 ..     307     336 .. 0.87
   4 !   24.2   0.9   9.2e-09   1.8e-05       1      34 [.     360     393 ..     360     394 .. 0.96

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 3.2e-08
                                       E-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep  10 IgpfaviggnVkIGdnvkIgagvvigg 36 
                                       I  +avi g+V+IG+n++I +g++i g
  gi|298676142|ref|YP_003727891.1| 245 IEDGAVIKGDVEIGENTTIRSGCYIIG 271
                                       7889********************975 PP

  == domain 2  score: 33.4 bits;  conditional E-value: 1.2e-11
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvv 33 
                                       ++IG+n+ Igp+avi++ ++IG n+ +++++ 
  gi|298676142|ref|YP_003727891.1| 273 VIIGDNCEIGPNAVILPSTTIGHNSSVESFTH 304
                                       79**************************9876 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00024
                                       EEEETTEEE-TTEEEETTEEE-TTEEEET CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIga 30 
                                       +++ +++ I   +++ +n +IG+n +Ig 
  gi|298676142|ref|YP_003727891.1| 308 AIVMNDTRISTHSYL-SNSVIGNNNTIGT 335
                                       78899999999****.7788*******96 PP

  == domain 4  score: 24.2 bits;  conditional E-value: 9.2e-09
                                       TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                           Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                       +t+IG+++lI+ ++ + +++ IG ++++++g v+
  gi|298676142|ref|YP_003727891.1| 360 GTIIGDDNLIRDNVLVKAGTLIGTDCRVESGNVV 393
                                       699****************************997 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.7   0.0   1.8e-18   3.7e-15       1     115 [.       3     127 ..       3     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 1.8e-18
                                       EEEEEESS-TTTT.....TTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHH...TTCTS-EEE-TT CS
                      NTP_transf_3   1 aviLAGGrSsRmg.....gdKallplggkpllervldalraagvdevvvvggd..eevlaal...arlgvrvveded 67 
                                       aviLA+G++sR       + K +lp+++kp+le+++++l+++++ ++++++++  e + +++   +++gv +++  +
  gi|298676142|ref|YP_003727891.1|   3 AVILAAGEGSRCRpltltKSKVMLPVANKPVLEHIIESLEKCSITDIILIVDYekERIMDHFedgKDFGVNITYIHQ 79 
                                       79**********7554435********************************99444566655222555766655444 PP

                                       S.S-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHT CS
                      NTP_transf_3  68 p.gkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasg 115
                                       + + g++++l+   ++++d+ ++lvl +D + ++pe++  l++ a+ + 
  gi|298676142|ref|YP_003727891.1|  80 SaQLGTAHALLQTQEHVKDENQFLVLNGDNV-VEPETISDLIEDAEGDA 127
                                       4289**************************6.6***********87332 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.8    0.0028       5.6      14      32 ..     249     269 ..     247     270 .. 0.88
   2 !   29.4   0.7   2.4e-10   4.7e-07       1      27 [.     272     300 ..     272     301 .. 0.95
   3 ?   -0.1   0.2      0.41   8.2e+02       7      16 ..     324     333 ..     323     336 .. 0.47
   4 !   10.6   1.5   0.00018      0.36       2      32 ..     361     393 ..     360     395 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0028
                                       -EE.S.EEE-TT-EE-TT-EE CS
                         Hexapep_2  14 agi.G.vslGdncvvgaGvvi 32 
                                       a+i G v++G+n ++ +G++i
  gi|298676142|ref|YP_003727891.1| 249 AVIkGdVEIGENTTIRSGCYI 269
                                       788855*************98 PP

  == domain 2  score: 29.4 bits;  conditional E-value: 2.4e-10
                                       .EEE-TT-EE-TT-EE..SEEE-TT-EE- CS
                         Hexapep_2   1 pviIGdnCliGanagi..GvslGdncvvg 27 
                                       pviIGdnC iG+na+i   +++G n+ v+
  gi|298676142|ref|YP_003727891.1| 272 PVIIGDNCEIGPNAVIlpSTTIGHNSSVE 300
                                       8***************999******9997 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.41
                                       T-EE-TT-EE CS
                         Hexapep_2   7 nCliGanagi 16 
                                       n++iG n +i
  gi|298676142|ref|YP_003727891.1| 324 NSVIGNNNTI 333
                                       4444444444 PP

  == domain 4  score: 10.6 bits;  conditional E-value: 0.00018
                                       EEE-TT-EE-TT-EE..SEEE-TT-EE-TT-EE CS
                         Hexapep_2   2 viIGdnCliGanagi..GvslGdncvvgaGvvi 32 
                                       +iIGd+ li  n  +  G+ +G +c v++G v+
  gi|298676142|ref|YP_003727891.1| 361 TIIGDDNLIRDNVLVkaGTLIGTDCRVESGNVV 393
                                       79************888*************888 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.1   9.9e-09     2e-05       2     219 ..       2     232 ..       1     234 [. 0.70

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 9.9e-09
                                       EEEEECTTSSCT...T-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGG.....CCEEE CS
                              IspD   2 vvvipAAGsGkR...mkaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllld.....ksiql 70 
                                        +vi AAG+G+R   +   + K  l ++++++leh +++l +  ++  i+++v+ ++ e++++   d      +i+ 
  gi|298676142|ref|YP_003727891.1|   2 KAVILAAGEGSRcrpLTLTKSKVMLPVANKPVLEHIIESLEK-CSITDIILIVDYEK-ERIMDHFEDgkdfgVNITY 76 
                                       69**********44445799*******************998.67777777777666.5565555555666766777 PP

                                       EE--SS..HHHHHHHHHHTTSSTTSEEEE--TT-TT--HHHHHHHHHHHHTTCSEEEEEEE-SSE....EEEEETTT CS
                              IspD  71 vaGGde..RaesVlnglkalegeakfVLvHDaARpllkaadiaellaaaeqstqgailalpvkDt....ikrveadg 141
                                       ++   +   a++ l++ + +++e++f Lv ++   ++++++i +l++ ae    + +l   +k+t    + ++++++
  gi|298676142|ref|YP_003727891.1|  77 IHQSAQlgTAHALLQTQEHVKDENQF-LVLNGDN-VVEPETISDLIEDAEG--DASVLTQKMKNTsnygVVITDNKK 149
                                       77655422578888888888888765.6667776.99*********99996..788888888887444444566554 PP

                                       ..BEEEEETG..TTEEEE....EEEEEEEHHHHHHHHHHHHHCT---SSHHHHHHHTT--EEEEE--TTG----SHH CS
                              IspD 142 ..lvaetedR..egLwaa....qtPqgFrvdlllaahakgeqegaeitDdaslvekiGlsvkvVeGeednlKittpe 210
                                          ++e ++   ++L +      tP  F++  ++++     +  + itD  +l+   G +v  V+ ++  +    + 
  gi|298676142|ref|YP_003727891.1| 150 ieKIVEKPEEkiSNLVNTgiylFTPNIFQI--IKQTPISE-KGEYAITDTLQLMIDYGYQVTNVNTKSRWIDAIFAW 223
                                       444555554412334332111145666543..33333333.334789999999999999999999999999999999 PP

                                       HHHHHHHHH CS
                              IspD 211 DlalAeail 219
                                       Dl++A+ i+
  gi|298676142|ref|YP_003727891.1| 224 DLLTANSIV 232
                                       999999886 PP

>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.1   1.4e-08   2.7e-05      11     132 ..      32     150 ..      24     184 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.4e-08
                                       TTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SS.EEEEE CS
                   Glycos_transf_2  11 ktlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgd.yilfl 86 
                                       + l+  +esl +    +  +ii++ D ++++  +  e+  + + ++++i+++   G a al +  ++++ +  +l+l
  gi|298676142|ref|YP_003727891.1|  32 PVLEHIIESLEKC---SITDIILIVDYEKERIMDHFEDGKDFGVNITYIHQSAQLGTAHALLQTQEHVKDEnQFLVL 105
                                       6666677766665...7889999999999999999999989************************************ PP

                                       ESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS CS
                   Glycos_transf_2  87 DaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrv 132
                                       + D +++p+++++l+e +e  +a+v  ++   ++     i+ nk++
  gi|298676142|ref|YP_003727891.1| 106 NGDNVVEPETISDLIEDAEG-DASVLTQKMKNTSNYGVVITDNKKI 150
                                       *******************9.8878777777777766666666654 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.9   1.3e-07   0.00026      14     149 ..      21     157 ..      20     220 .. 0.67

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.3e-07
                                       TTGGGSEETTEEHHHHHHHHHHHTTTTSE.EEEEES-HHHHHHHHHTT...SEEEE--TTCSSHHHHHHHHHHHHTT CS
                      CTP_transf_3  14 pgKnlldlggkpliayvleaalkskafek.vivaTDseeiknvakefg...asvlvtrsslesdterflevvkaflm 86 
                                       + K++l+ ++kp +++++e + k+   +  +iv+  +e+i+++ ++     + +  + +s++ +t+  l   +++  
  gi|298676142|ref|YP_003727891.1|  21 KSKVMLPVANKPVLEHIIESLEKCSITDIiLIVDYEKERIMDHFEDGKdfgVNITYIHQSAQLGTAHALLQTQEHVK 97 
                                       67**********************9988878999********99754441177777777777777777777777666 PP

                                       T.TTSEEEEE-TT-TT--HHHHHHHHHHHHHSTTSSEEEEEEETTSHH.HHTSTTSTEEEETTT CS
                      CTP_transf_3  87 seneeiivnlqGdnPllqeevikkaietlkenqedylstlvkkvgkee.evlnandlkvlldda 149
                                       +  e+  + l Gdn+ +++e+i+ +ie+ +   +  l+++ k++ +    +++ ++++++++++
  gi|298676142|ref|YP_003727891.1|  98 D--ENQFLVLNGDNV-VEPETISDLIEDAEGDAS-VLTQKMKNTSNYGvVITDNKKIEKIVEKP 157
                                       6..556666779996.8999*******9988855.44444444444330334444455555544 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1     1e-06    0.0021       6     107 ..      24     118 ..      22     145 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1e-06
                   Glyco_tranf_2_3   6 vlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnea 82 
                                       v+ p++n  +vl+ ++esl ++  + ++++++vd +++   + +e   ++++   +++++++ +lg   +++al ++
  gi|298676142|ref|YP_003727891.1|  24 VMLPVANK-PVLEHIIESLEKC--SITDIILIVDYEKERIMDHFED-GKDFGV-NITYIHQSAQLG---TAHALLQT 92 
                                       56677666.7788888888776..6699999999999999999987.899988.7******99888...5899**** PP

                   Glyco_tranf_2_3  83 lravksd.lvllvDdDtvvePdtlkr 107
                                        ++vk++   l++++D+vveP+t+  
  gi|298676142|ref|YP_003727891.1|  93 QEHVKDEnQFLVLNGDNVVEPETISD 118
                                       *****5559999***********975 PP

>> DapH_N  Tetrahydrodipicolinate succinyltransferase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00025       0.5      39      70 ..     133     164 ..     112     166 .. 0.85
   2 ?   -2.1   0.0       2.4   4.7e+03      47      58 ..     230     241 ..     226     256 .. 0.81
   3 ?   -1.8   0.0         2   3.9e+03      22      56 ..     337     369 ..     320     388 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00025
                                       EEEE-SSEEEEEEEHHHHHHHHHHTTTTEEEE CS
                            DapH_N  39 kvfgsedsgvvfGdwkeieevleenkdkiedy 70 
                                       k+  +++ gvv++d k+ie+++e+ ++ki+++
  gi|298676142|ref|YP_003727891.1| 133 KMKNTSNYGVVITDNKKIEKIVEKPEEKISNL 164
                                       55678899*********************875 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.4
                                       EEEEEEHHHHHH CS
                            DapH_N  47 gvvfGdwkeiee 58 
                                        +v+G+++++++
  gi|298676142|ref|YP_003727891.1| 230 SIVLGEYEDFKR 241
                                       689999999875 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 2
                                       EEEE-.C.TC----TTSEEEE-SSEEEEEEEHHHH CS
                            DapH_N  22 YvkgelkeeelefpeevkvfgsedsgvvfGdwkei 56 
                                       ++ +e+++ ++e+  +      ++ g+++Gd + i
  gi|298676142|ref|YP_003727891.1| 337 FITEEKDSLKIEI--KGMLHKADRLGTIIGDDNLI 369
                                       4555544444443..23444556677777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2416.29
//
Query:       gi|298676143|ref|YP_003727892.1|  [L=363]
Description: transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.1e-25   86.7   3.4    1.4e-24   85.7   1.0    2.5  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    6.4e-10   39.3   1.6    6.4e-10   39.3   1.6    1.7  2  OrfB_IS605      Probable transposase
  ------ inclusion threshold ------
      0.058   13.4   0.1       0.14   12.2   0.1    1.6  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.13   12.4   1.6       0.88    9.7   0.1    2.3  2  UPF0547         Uncharacterised protein family UPF0547
       0.88    9.3   6.7        3.4    7.4   6.7    2.0  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
          1    9.4   4.8        2.7    8.1   4.8    1.7  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
        1.8    8.8   5.8         13    6.0   1.9    3.0  2  DUF2387         Probable metal-binding protein (DUF2387)
        2.2    8.1   4.5         21    4.9   0.4    2.4  2  Rubredoxin_2    Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.38   8.5e+02      15      30 ..     187     202 ..     183     230 .. 0.83
   2 !   85.7   1.0   6.4e-28   1.4e-24       1      69 []     277     346 ..     277     346 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.38
                    OrfB_Zn_ribbon  15 yGikveevnpayTSkt 30 
                                       +G k  e+ ++yTS +
  gi|298676143|ref|YP_003727892.1| 187 KGTKADEIRERYTSLK 202
                                       5788889999999965 PP

  == domain 2  score: 85.7 bits;  conditional E-value: 6.4e-28
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f++l+ ++ ykak +G++v+ +np yTS++CseCg+++k+ ++++ +fkC++Cg++ ++D+nA+ Ni++r
  gi|298676143|ref|YP_003727892.1| 277 FSELTDFILYKAKLEGVPVVIINPMYTSQQCSECGYIDKNnRQKQANFKCKRCGHRENADYNASKNIAHR 346
                                       899*************************************9**************************997 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   1.6   2.9e-13   6.4e-10      15     106 ..     164     246 ..     151     256 .. 0.87
   2 ?   -3.2   0.1       4.1   9.3e+03      40      68 ..     313     341 ..     304     347 .. 0.64

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 2.9e-13
                        OrfB_IS605  15 gnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsrrrkhl 91 
                                        + + g+DlG+ n+at+++++    +ykg ++++  ++++  + +lqsk   s     a++ l++l++k +r+ ++l
  gi|298676143|ref|YP_003727892.1| 164 YEDVMGVDLGVVNIATTSDNE----VYKGTKADEIRERYTSLKSRLQSKGTWS-----AKKHLKKLSKKERRFKRDL 231
                                       56789****************....************************6665.....7999*************** PP

                        OrfB_IS605  92 lhklathliktlkev 106
                                        h +a++l+++ k++
  gi|298676143|ref|YP_003727892.1| 232 NHRVAKQLVERAKDT 246
                                       *********998765 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.1
                        OrfB_IS605  40 lykgrrlksdykylakeiaelqsklkksk 68 
                                       + k +r k+++++ +++  +    ++ sk
  gi|298676143|ref|YP_003727892.1| 313 IDKNNRQKQANFKCKRCGHRENADYNASK 341
                                       55556666666666666666555555555 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   6.2e-05      0.14      60      96 ..     288     333 ..     259     343 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.2e-05
                                       -EEE......EEEE--EEEETTTS-EEECHH..H.HHS-TTTSSS- CS
                              HypA  60 aeLe......ieevpvkvrCreCgkefelee..k.alrCpkCgsad 96 
                                       a+Le      i+ +  + +C+eCg+  + ++  + +++C++Cg+++
  gi|298676143|ref|YP_003727892.1| 288 AKLEgvpvviINPMYTSQQCSECGYIDKNNRqkQaNFKCKRCGHRE 333
                                       5555555555777788999*****9888555333788*****9874 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00039      0.88      15      25 ..     305     315 ..     303     316 .. 0.87
   2 ?    1.5   0.2      0.15   3.3e+02      16      22 ..     325     331 ..     322     332 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00039
                           UPF0547  15 qfCphCGyvFq 25 
                                       q C++CGy+++
  gi|298676143|ref|YP_003727892.1| 305 QQCSECGYIDK 315
                                       89******986 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.15
                           UPF0547  16 fCphCGy 22 
                                       +C  CG+
  gi|298676143|ref|YP_003727892.1| 325 KCKRCGH 331
                                       5777887 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   6.7    0.0015       3.4       3      26 ..     307     332 ..     306     333 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0015
                                       -SSS-..-B----SSS----SSS--- CS
                    DNA_RNApol_7kD   3 CgeCg..aevslkkgdpiRCkeCGhR 26 
                                       C eCg  +++  +k++  +Ck CGhR
  gi|298676143|ref|YP_003727892.1| 307 CSECGyiDKNNRQKQANFKCKRCGHR 332
                                       9999966788899999*********9 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   4.8    0.0012       2.7      19      45 ..     305     331 ..     301     332 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0012
                     Zn_Tnp_IS1595  19 fvCPhCgsr.kayriktrglfqCkeCrk 45 
                                       + C  Cg+  k  r k+   f+Ck+C++
  gi|298676143|ref|YP_003727892.1| 305 QQCSECGYIdKNNRQKQ-ANFKCKRCGH 331
                                       57*******77777777.********98 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.046     1e+02      38      72 ..     216     250 ..     213     253 .. 0.86
   2 ?    6.0   1.9    0.0059        13      31      49 ..     305     323 ..     299     350 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.046
                           DUF2387  38 ftdelsekgqsvakelktrvnkdeekeasakvqtv 72 
                                       ++ +ls+k++ ++++l+ rv+k+  ++a+++ +++
  gi|298676143|ref|YP_003727892.1| 216 HLKKLSKKERRFKRDLNHRVAKQLVERAKDTSRSI 250
                                       7889999****************998888887766 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0059
                           DUF2387  31 rECvsCgftdelsekgqsv 49 
                                         C +Cg++d+ + ++q+ 
  gi|298676143|ref|YP_003727892.1| 305 QQCSECGYIDKNNRQKQAN 323
                                       57999*****999995543 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.3     0.014        31       2       8 ..     306     312 ..     306     315 .. 0.89
   2 ?    4.9   0.4    0.0096        21       1      10 [.     324     333 ..     324     335 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.014
                      Rubredoxin_2   2 vCsqCGf 8  
                                       +Cs+CG+
  gi|298676143|ref|YP_003727892.1| 306 QCSECGY 312
                                       7*****9 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0096
                      Rubredoxin_2   1 YvCsqCGfes 10 
                                       + C++CG++ 
  gi|298676143|ref|YP_003727892.1| 324 FKCKRCGHRE 333
                                       78*****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1052  (0.0586759); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 2063.68
//
Query:       gi|298676144|ref|YP_003727893.1|  [L=108]
Description: hypothetical protein Metev_2279 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0099   14.7   0.4      0.013   14.3   0.4    1.1  1  DUF2207   Predicted membrane protein (DUF2207)
  ------ inclusion threshold ------
      0.013   15.5   0.3      0.014   15.3   0.3    1.0  1  DsbD_2    Cytochrome C biogenesis protein transmembrane regio
       0.11   12.4   0.4       0.15   12.0   0.4    1.2  1  TraQ      Type-F conjugative transfer system pilin chaperone 
        7.4    6.4   6.8         61    3.4   6.5    2.2  2  DUF3188   Protein of unknown function (DUF3188)


Domain annotation for each model (and alignments):
>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.4   2.8e-06     0.013     391     450 ..      18      83 ..       8      85 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.8e-06
                           DUF2207 391 iilglilillallllvll......lvfllilllillliaiivlllfsrllgrrteeGaellakwkg 450
                                       ++lg++++l++ ++++l         +++i++++l+ i+i++++++ +++  +++  +++++k++g
  gi|298676144|ref|YP_003727893.1|  18 LVLGILFVLVGGVFYQLYrmdaysDPIFSIPMFVLGGILIVYYFFSGAFVVNLSAGNKDYRYKIDG 83 
                                       333333333333333333566778**********************99999999998888888887 PP

>> DsbD_2  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.3   3.1e-06     0.014      42      95 ..      13      67 ..       5      95 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.1e-06
                            DsbD_2 42 RilsYallGalvgllgsvlqlagel.eglrallgvllgllllllglklllkkkll 95
                                      R  +Y +lG+l++l+g v+ +  ++ ++   ++++ + +l+ +l++++++++ ++
  gi|298676144|ref|YP_003727893.1| 13 RNGAYLVLGILFVLVGGVFYQLYRMdAYSDPIFSIPMFVLGGILIVYYFFSGAFV 67
                                      7789***************998777556677777777777777777777655443 PP

>> TraQ  Type-F conjugative transfer system pilin chaperone (TraQ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.4   3.3e-05      0.15      19      59 ..      18      58 ..      12      78 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.3e-05
                              TraQ 19 lslGvwfhlvarlvyrkPelavllaeilavglvliGgyril 59
                                      l lG+ f lv+++ y+   +      i+++ + ++Gg  i+
  gi|298676144|ref|YP_003727893.1| 18 LVLGILFVLVGGVFYQLYRMDAYSDPIFSIPMFVLGGILIV 58
                                      579*********************************98776 PP

>> DUF3188  Protein of unknown function (DUF3188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   1.0      0.03   1.4e+02      27      45 ..      18      33 ..      10      38 .. 0.79
   2 ?    3.4   6.5     0.014        61       4      38 ..      23      58 ..      18      66 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.03
                           DUF3188 27 lPallvGlgLivsgavgrg 45
                                      l   + G++ +++g+v++ 
  gi|298676144|ref|YP_003727893.1| 18 L---VLGILFVLVGGVFYQ 33
                                      4...889999999999886 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.014
                           DUF3188  4 lLillgllill.ysqrqgsdrlqslPallvGlgLiv 38
                                      l +l+g +  + y +   sd ++s+P ++ G  Liv
  gi|298676144|ref|YP_003727893.1| 23 LFVLVGGVFYQlYRMDAYSDPIFSIPMFVLGGILIV 58
                                      556666665555777777888**********99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 756.50
//
Query:       gi|298676145|ref|YP_003727894.1|  [L=294]
Description: NAD-dependent epimerase/dehydratase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-56  191.9   0.0    1.5e-56  191.6   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    3.1e-49  168.2   0.1    7.8e-49  166.8   0.1    1.6  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    1.7e-22   79.9   0.6    4.7e-21   75.2   0.6    2.6  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    1.2e-21   77.0   0.0    1.7e-21   76.5   0.0    1.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    1.7e-11   43.8   0.0    2.2e-11   43.4   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    6.9e-09   35.3   0.0      2e-05   23.9   0.0    2.4  2  NAD_binding_4    Male sterility protein
      4e-06   26.8   0.0    4.6e-05   23.4   0.0    2.4  2  NAD_binding_10   NAD(P)H-binding
     0.0003   20.3   0.0     0.0028   17.2   0.0    2.3  2  adh_short        short chain dehydrogenase
    0.00031   20.4   0.2    0.00084   19.0   0.0    1.8  2  NmrA             NmrA-like family
     0.0042   17.0   0.0     0.0085   16.0   0.0    1.6  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
  ------ inclusion threshold ------
       0.08   13.5   0.0       0.27   11.8   0.0    1.9  1  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
      0.098   12.6   0.0          1    9.2   0.0    2.3  2  KR               KR domain


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.6   0.0     1e-59   1.5e-56       1     241 []       3     231 ..       3     231 .. 0.94

  Alignments for each domain:
  == domain 1  score: 191.6 bits;  conditional E-value: 1e-59
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---H CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggv 77 
                                       ilVtG++GfiGs++++++l++g++v  +d+lss+ +++  e +e+v+ d+   s   ++f+  ++d+v+h Aa  +v
  gi|298676145|ref|YP_003727894.1|   3 ILVTGGAGFIGSHIAEYFLSEGHNVRIVDNLSSGYQENIPESAEFVNEDIYSVS--PDVFE--GVDYVFHEAALVSV 75 
                                       8**************************************9999*******9755..89999..9************* PP

                                       HHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHH CS
                         Epimerase  78 aassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklve 154
                                       ++s ++p++ +++n+ gt+n+l+ + +agv++++ +sS++vYG+++  pk e++     +p spYa++K+  e l+ 
  gi|298676145|ref|YP_003727894.1|  76 PVSCQQPEEAFRINTLGTMNVLQNSLDAGVEKVVLASSAAVYGNNPILPKMEDM---LPEPASPYAISKMDCEYLAG 149
                                       *******************************************99988*99998...5699***************9 PP

                                       HHHHHHT-EEEEEEESEEESTT.S-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHT CS
                         Epimerase 155 ayaaqyglnaiilrlfnlyGpr.ngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvd 230
                                        +++++ l++++lr+fn+yGpr ++++  + vip ++++++egk +++++gdgt+ Rdf+ ++Dv++a+++++++  
  gi|298676145|ref|YP_003727894.1| 150 MFHDKG-LRTTCLRYFNVYGPRqDPNSPYAAVIPIFMKRAKEGK-DLVIYGDGTQTRDFVNIQDVVRANVAAMDN-- 222
                                       997776.***************555555****************.******************************.. PP

                                       T-STTEEEEES CS
                         Epimerase 231 agdkgeiyniG 241
                                          +g+++n++
  gi|298676145|ref|YP_003727894.1| 223 --GDGDVFNVA 231
                                       ..567899986 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.8   0.1   5.2e-52   7.8e-49       1     328 [.       4     288 ..       4     292 .. 0.84

  Alignments for each domain:
  == domain 1  score: 166.8 bits;  conditional E-value: 5.2e-52
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L+TG+aGfiGs++ae++l++g++v +++++ss  + ++i +           + ++++ D+   s   ++++ v  d
  gi|298676145|ref|YP_003727894.1|   4 LVTGGAGFIGSHIAEYFLSEGHNVRIVDNLSSG-YQENIPE-----------SAEFVNEDIYSVS--PDVFEGV--D 64 
                                       9***********************988887776.5455543...........3479*****8755..8999998..9 PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYa 154
                                        v++ AA   V+vs ++Pe+ +++n lGt+++L+   ++g+e   +++ aS++ vYG+    p  E+   +P sPYa
  gi|298676145|ref|YP_003727894.1|  65 YVFHEAALVSVPVSCQQPEEAFRINTLGTMNVLQNSLDAGVE---KVVLASSAAVYGNNPILPKMEDMLPEPASPYA 138
                                       ****************************************97...8999**************************** PP

                                       HHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCC.HHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHH CS
                     GDP_Man_Dehyd 155 aaKlyadwivvnyreayglfavngilfnhesprrgetfvtr.kitravarialgkqevlylGnldakRdwghvkDyv 230
                                       ++K+ +++++  +++  gl ++  ++fn ++pr+ ++ +    i+ ++ r+++gk + +++G++ ++Rd+  ++D+v
  gi|298676145|ref|YP_003727894.1| 139 ISKMDCEYLAGMFHD-KGLRTTCLRYFNVYGPRQDPNSPYAaVIPIFMKRAKEGK-DLVIYGDGTQTRDFVNIQDVV 213
                                       **********99887.8999999*************9887715555556666665.8999***************** PP

                                       HHHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB-- CS
                     GDP_Man_Dehyd 231 eamwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlll 307
                                       +a ++++ ++  + +++atg+++sv+e++e  ++ +g + +                     + ++  r+g+ +  +
  gi|298676145|ref|YP_003727894.1| 214 RANVAAMDNGDGDVFNVATGTSVSVQEIAETIIEITGSSSD---------------------IVYEEEREGDIKDSV 269
                                       ***************************99965555554322.....................333445555555556 PP

                                       B-THHHHHHH----SS-HHHH CS
                     GDP_Man_Dehyd 308 gdaskakeeLgWkpkvsfeel 328
                                       +d sk+     W+ kv++ee+
  gi|298676145|ref|YP_003727894.1| 270 ADVSKISG--WWESKVDLEEG 288
                                       66666552..24555555555 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.2   0.6   3.1e-24   4.7e-21       1     252 [.       3     254 ..       3     268 .. 0.77

  Alignments for each domain:
  == domain 1  score: 75.2 bits;  conditional E-value: 3.1e-24
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES.-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT.. CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiiller.dElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleel 76 
                                       +lvtG++G iGs++ + +l++   +++++++ +   + +i ++   e+ +          i +v       +++e  
  gi|298676145|ref|YP_003727894.1|   3 ILVTGGAGFIGSHIAEYFLSEGH-NVRIVDNlSSGYQENIPESA--EFVN--------EDIYSVS-----PDVFE-- 61 
                                       89**************9999865.56666651444555555544..2222........2244554.....57899.. PP

                                       T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE..............GGGSS--SHHH CS
                   Polysacc_synt_2  77 kvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliSt..............DKAvnPtnvmG 139
                                       +vd+vfh AAl  VP+  ++p ea++ N lgt+nv++ +++agv+kvvl S+              D   +P + + 
  gi|298676145|ref|YP_003727894.1|  62 GVDYVFHEAALVSVPVSCQQPEEAFRINTLGTMNVLQNSLDAGVEKVVLASSaavygnnpilpkmeDMLPEPASPYA 138
                                       *************************************************9983333332333222233345666666 PP

                                       HHHHHHHHHHHHGGG--SSS--EEEEEEE-EETTGT.......TSSHHHHHHHHHTTSSEEE.S-TT-EEEEE-HHH CS
                   Polysacc_synt_2 140 atKrlaekllqalakeseekktkfvvvRfGNVlgSr.......GSviplFkkqikeggpvtv.TdpemtRyfmtiee 208
                                       ++K+ +e l+  ++++      + ++ R+ NV g r         vip+F k+ keg+++ +  d + tR f+ i++
  gi|298676145|ref|YP_003727894.1| 139 ISKMDCEYLAGMFHDKG----LRTTCLRYFNVYGPRqdpnspyAAVIPIFMKRAKEGKDLVIyGDGTQTRDFVNIQD 211
                                       66666666666665555....999**********87444444458************99888468999********* PP

                                       HHHHHHHHHHH--SS-EEEE--.-EEEHHHHHHHH......... CS
                   Polysacc_synt_2 209 avqLvlqalalakggeifvldmGepvkivdlakalielsgleek 252
                                        v+  + a+ ++ +g++f +  G +v+++++a+++ie++g +++
  gi|298676145|ref|YP_003727894.1| 212 VVRANVAAMDNG-DGDVFNVATGTSVSVQEIAETIIEITGSSSD 254
                                       ***998888776.589***********************97665 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.5   0.0   1.1e-24   1.7e-21       1     229 [.       4     220 ..       4     232 .. 0.84

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 1.1e-24
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslv 77 
                                       +vtGgaGF+G+++ + +++++  ++vr++D   s    e++ ++  +++++ D+ + +   ++ egvd v+h a+lv
  gi|298676145|ref|YP_003727894.1|   4 LVTGGAGFIGSHIAEYFLSEG--HNVRIVDNLSSGYQ-ENIPES--AEFVNEDIYSVS--PDVFEGVDYVFHEAALV 73 
                                       69*******************..5******7766655.444333..347899**9876..589************** PP

                         3Beta_HSD  78 dvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKala 153
                                        v    ++ +e  ++n  GT nvl+  ++agv+++v  Ssa v g+    ++il   E   + + + ++y+ sK   
  gi|298676145|ref|YP_003727894.1|  74 SVPVsCQQPEEAFRINTLGTMNVLQNSLDAGVEKVVLASSAAVYGN----NPILPKME--DMLPEPASPYAISKMDC 144
                                       99754889999***********************************....67774444..45567899********* PP

                         3Beta_HSD 154 EklvlkaNgrtlknggrlyTcaLRpagiyGegdk......llvpllkqlaklglalfkigdeevlsdrvYvgNvawa 224
                                       E l        +++   l T +LR   +yG++++       + p + + ak g+ l+ +gd  ++ d+v    v+ a
  gi|298676145|ref|YP_003727894.1| 145 EYLAGM-----FHDK-GLRTTCLRYFNVYGPRQDpnspyaAVIPIFMKRAKEGKDLVIYGDGTQTRDFVNIQDVVRA 215
                                       *99644.....4444.599************9972222224566778999*************************** PP

                         3Beta_HSD 225 hilAa 229
                                        + A+
  gi|298676145|ref|YP_003727894.1| 216 NVAAM 220
                                       *9987 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.0   1.5e-14   2.2e-11       1     236 [.       1     254 [.       1     270 [. 0.78

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 1.5e-14
                                       EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT....T--T.TSHHHHHHHHHHH--S......EEEE------HHH CS
                     RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre....eldl.tdaeavaellkeakpd......vvvnaAAytavDk 66 
                                       m+ilvtG+ G +Gs++a+ + +eg++v  +++     + ++ + ae v+e + +++pd       v + AA   v  
  gi|298676145|ref|YP_003727894.1|   1 MNILVTGGAGFIGSHIAEYFLSEGHNVRIVDNLssgyQENIpESAEFVNEDIYSVSPDvfegvdYVFHEAALVSVPV 77 
                                       89**********************99988866567886776234566788887777774444447************ PP

                                       HHHSHHHHHHHHTHHHHHHHHHHHHCT-.EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHH...HHHH CS
                     RmlD_sub_bind  67 aEseeeaayavnaeavealAeaaaavga.lLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqa...vlaa 139
                                         +++e+a+++n  +++++ +    +g+ +++  S+  V+  +   p  ed  ++P + Y+ +K++ E       ++
  gi|298676145|ref|YP_003727894.1|  78 SCQQPEEAFRINTLGTMNVLQNSLDAGVeKVVLASSAAVYGNNPILPKMEDMLPEPASPYAISKMDCEYLagmFHDK 154
                                       ***************************9458899*********999**********************861115669 PP

                                       -SSEEEEEE-SEESS.SSS-.....HHHHHHHHHHH-SEEEEESS-EE--EEHHHHHHHHHHHHHHCHH..GGG-EE CS
                     RmlD_sub_bind 140 gkkalivRtswvyge.kgkn.....fvktmlrlakereelkvvaDqlgsPTsardlAevllqllekaae.ekelagv 209
                                       g +++ +R   vyg  ++ n      +  ++++ake + l +  D     T++rd  ++   + ++ a+ ++ +  v
  gi|298676145|ref|YP_003727894.1| 155 GLRTTCLRYFNVYGPrQDPNspyaaVIPIFMKRAKEGKDLVIYGD----GTQTRDFVNIQDVVRANVAAmDNGDGDV 227
                                       99***********98533332211134456888999999988665....566666555433332222220224489* PP

                                       EE---BS-EEHHHHHHHHHHHHCHTTS CS
                     RmlD_sub_bind 210 yHlanegetswlefArailkeagadse 236
                                       + +a   ++s  e+A+ i++ +g++s 
  gi|298676145|ref|YP_003727894.1| 228 FNVATGTSVSVQEIAETIIEITGSSSD 254
                                       *******************99988764 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0   0.00046      0.68       1      26 [.       5      30 ..       5      40 .. 0.92
   2 !   23.9   0.0   1.3e-08     2e-05      85     209 ..      60     172 ..      55     216 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00046
                                      EE-TTSHHHHHHHHHHHHHS-.TEEE CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpevkiy 26
                                      +TG+ GF+G+++ e  L++  +v+i+
  gi|298676145|ref|YP_003727894.1|  5 VTGGAGFIGSHIAEYFLSEGHNVRIV 30
                                      7****************999998875 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 1.3e-08
                                       HHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H..... CS
                     NAD_binding_4  85 aeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegeke 158
                                        e vd ++h aA v++  + ++   ++r+N++Gt +vl+ +        ++  S+a+v+g++               
  gi|298676145|ref|YP_003727894.1|  60 FEGVDYVFHEAALVSVPVSCQQpeeAFRINTLGTMNVLQNSLDAGVE-KVVLASSAAVYGNNP-------------- 121
                                       6789***********9876554444***************9987777.799999999999999.............. PP

                                       .HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-...- CS
                     NAD_binding_4 159 ekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg...e 209
                                            ++++ l + +  Y  sK+  E+l    +++ gl+++ +R  +++g   +
  gi|298676145|ref|YP_003727894.1| 122 --ILPKMEDMLPEPASPYAISKMDCEYLAGMFHDK-GLRTTCLRYFNVYGprqD 172
                                       ..345667777888889999999999999999977.999999998888885542 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   3.1e-08   4.6e-05       1     142 [.       7     162 ..       7     223 .. 0.72
   2 ?   -0.0   0.1      0.48   7.1e+02     162     180 ..     230     248 ..     218     251 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3.1e-08
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETT.HHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES-........ CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRn.peklaeleaeeglevvegdvtdvedlaealkgadaVvsal........ 68 
                                       G+ G +G+++++  l++ gh+v+++  n ++  +e    e +e v  d+ +v+   ++++g+d V+  +        
  gi|298676145|ref|YP_003727894.1|   7 GGAGFIGSHIAEYFLSE-GHNVRIV-DNlSSGYQENI-PESAEFVNEDIYSVS--PDVFEGVDYVFHEAalvsvpvs 78 
                                       99***************.5**9865.66144444433.478888888888765..4899******999966666654 PP

                                       ..--TCCHHHH.......HHHHHHHHHHCT--EEEEEEETTTTSGCG..CHHHHHHHHCCHHHHHHHHHHHHH...H CS
                    NAD_binding_10  69 ..ggggkdeeg.......aknivdaakeagvkRfvlvsaigvgdevp..gefgewnkellkaylaakraaeel...l 131
                                               ee+       + n+++    agv+++vl s++ v+ + p   + +++  e  ++y++ k   e l    
  gi|298676145|ref|YP_003727894.1|  79 cqQ----PEEAfrintlgTMNVLQNSLDAGVEKVVLASSAAVYGNNPilPKMEDMLPEPASPYAISKMDCEYLagmF 151
                                       431....11113445556************************97533113344444555567776666655552223 PP

                                       HHSSSEEEEEE CS
                    NAD_binding_10 132 rasgldwTivr 142
                                        ++gl  T +r
  gi|298676145|ref|YP_003727894.1| 152 HDKGLRTTCLR 162
                                       44666666655 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.48
                                       S----EEEHHHHHHHHHHH CS
                    NAD_binding_10 162 pfkggsisradVAdvlvav 180
                                         +g+s+s + +A++++++
  gi|298676145|ref|YP_003727894.1| 230 VATGTSVSVQEIAETIIEI 248
                                       457899*********9997 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.8e-06    0.0028       3      58 ..       3      59 ..       1      71 [. 0.86
   2 ?    0.8   0.0      0.19   2.8e+02      96     122 ..      77     103 ..      50     120 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.8e-06
                                      EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT.TSEEEEEE-TT CS
                         adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee.gakalaiqvDv 58
                                      +lvtG+++ IG  ia+ +++eG +v +vd+ ++  +e + e  e  +++++ ++ Dv
  gi|298676145|ref|YP_003727894.1|  3 ILVTGGAGFIGSHIAEYFLSEGHNVRIVDNLSSGYQENIPESAEFvNEDIYSVSPDV 59
                                      8*****************************999998888887766666777666666 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.19
                                       CSHHHHHHHHHHHTHHHHHHHHHHHHH CS
                         adh_short  96 lseeewervievNltgvflltravlpa 122
                                       +s ++ e+ + +N  g++++ +  l+a
  gi|298676145|ref|YP_003727894.1|  77 VSCQQPEEAFRINTLGTMNVLQNSLDA 103
                                       4566778999*********99988776 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   5.6e-07   0.00084       1      73 [.       3      71 ..       3     114 .. 0.80
   2 ?   -1.3   0.0      0.87   1.3e+03     160     196 ..     187     222 ..     177     256 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 5.6e-07
                                      EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE--- CS
                              NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtg 73
                                      Ilv+G++G +G+++++++l++gh+vr++  ++ s   ++   + +e+v++d+++ +    +++gvd vf   +
  gi|298676145|ref|YP_003727894.1|  3 ILVTGGAGFIGSHIAEYFLSEGHNVRIV-DNL-SSGYQENIPESAEFVNEDIYSVS--PDVFEGVDYVFHEAA 71
                                      9*************************85.444.45555555567899999988654..578888888887655 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.87
                                       E-TTS.-EEEEESS-TTS-EE-HHHHHHHHHHHHHHH CS
                              NmrA 160 tappedkvtllgpgnpkavlldaeeDiGafvikilkd 196
                                        a++++ +++ g+g     ++ + +D+ ++ ++++++
  gi|298676145|ref|YP_003727894.1| 187 RAKEGKDLVIYGDGTQTRDFV-NIQDVVRANVAAMDN 222
                                       444455788888888777777.888888887777776 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   5.7e-06    0.0085       6      33 ..       8      35 ..       3      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.7e-06
                                      --SCCHHHHHHHHHHTT-EEEEE-S-HH CS
                           3HCDH_N  6 GaGtmGagiaavfasagleVvlvdisee 33
                                      GaG +G+ ia+ f+s+g++V++vd  ++
  gi|298676145|ref|YP_003727894.1|  8 GAGFIGSHIAEYFLSEGHNVRIVDNLSS 35
                                      99*********************98444 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00018      0.27       3      32 ..       5      34 ..       3      46 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                                      EEECSSHHHHHHHHHHHHTTSEEEEEESSS CS
                         Pyr_redox  3 vvvGgGyiglElAgalaelgkkVtvversd 32
                                      v  G+G+ig   A+++   g++V +v++ +
  gi|298676145|ref|YP_003727894.1|  5 VTGGAGFIGSHIAEYFLSEGHNVRIVDNLS 34
                                      5569**********************9875 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00069         1       4      26 ..       4      27 ..       2      50 .. 0.84
   2 ?    0.5   0.0      0.32   4.8e+02     107     139 ..      84     116 ..      60     122 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00069
                                      EEETTTSHHHHHHHHHHHHHH.S- CS
                                KR  4 litGGlGgLGlelarwlaekg.ar 26
                                      l+tGG+G +G ++a+  +++g + 
  gi|298676145|ref|YP_003727894.1|  4 LVTGGAGFIGSHIAEYFLSEGhNV 27
                                      9***************99999444 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.32
                                       HHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHH CS
                                KR 107 qvlapKvkGawnLhelledesldffvlfSSiag 139
                                       ++++    G+ n+ + + d  ++ +vl SS+a 
  gi|298676145|ref|YP_003727894.1|  84 EAFRINTLGTMNVLQNSLDAGVEKVVLASSAAV 116
                                       556666678999999999999999999999874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.65u 0.40s 00:00:01.05 Elapsed: 00:00:00.62
# Mc/sec: 1428.12
//
Query:       gi|298676146|ref|YP_003727895.1|  [L=296]
Description: glycosyl transferase family 2 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-24   85.1   0.2    7.8e-24   84.4   0.2    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    8.1e-05   22.6   0.1    0.00012   22.1   0.1    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
     0.0041   17.6   0.0      0.011   16.2   0.0    1.8  2  Glyco_tranf_2_4  Glycosyl transferase family 2
  ------ inclusion threshold ------
        3.6    7.0   6.1          1    8.7   0.8    2.1  2  DUF373           Domain of unknown function (DUF373)


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.4   0.2   1.7e-27   7.8e-24       4     168 ..       8     162 ..       6     164 .. 0.94

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 1.7e-27
                                       EEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--S CS
                   Glycos_transf_2   4 iptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatg 80 
                                       +p+yNe++t+ e+++ + +      ++++vvDDgS D+t +i+e+l     +  v+r+++n+G++++l+  ++ a  
  gi|298676146|ref|YP_003727895.1|   8 MPAYNEANTIGEVIHGCQKY----VDKVVVVDDGSVDDTIKIAESL-----GAYVVRHPQNEGYGASLRDCFKTALK 75 
                                       9******************9....**********************.....9*********************9855 PP

                                       S...EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTC CS
                   Glycos_transf_2  81 d...yilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfe 154
                                            ++++D+D ++dpd +  ++e+l++ g  v++g+r+ ++ ++d    +k      ++    +++  ++n+s+ 
  gi|298676146|ref|YP_003727895.1|  76 LdadMMVIIDSDGQHDPDEITHVLEPLDR-GINVAIGSRFINGNGDDVPAYRK---VGMKVLDVATNFVGGINVSDT 148
                                       4455*************************.999*********99999999997...59******************* PP

                                       STCCCEEEEHHHHH CS
                   Glycos_transf_2 155 igsaallrrealee 168
                                        ++++++ +ea+++
  gi|298676146|ref|YP_003727895.1| 149 QCGFRAYDKEAIKN 162
                                       **********9975 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   2.6e-08   0.00012       7     129 ..       7     119 ..       3     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.6e-08
                   Glyco_tranf_2_3   7 lVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralneal 83 
                                       + p++ne+ ++gev++   ++    ++vvvv+d+s ++t++ ae     l++    vv+ ++n g ++  r  + + 
  gi|298676146|ref|YP_003727895.1|   7 AMPAYNEANTIGEVIHGCQKY---VDKVVVVDDGSVDDTIKIAES----LGA---YVVRHPQNEGYGASLRDCFKTA 73 
                                       679**************9996...99***************9976....555...4677777788766666666666 PP

                   Glyco_tranf_2_3  84 ravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfll.nr 129
                                          + d+ +++D+D   +Pd +  +l  + ++++ ++ +++f + n+
  gi|298676146|ref|YP_003727895.1|  74 LKLDADMMVIIDSDGQHDPDEITHVLEPL-DRGINVAIGSRFINgNG 119
                                       6677*********************9998.88888887777776554 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   2.5e-06     0.011       1      81 [.      11      87 ..      11      94 .. 0.73
   2 ?   -0.1   0.0      0.32   1.4e+03       8      33 ..      67      92 ..      58     104 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.5e-06
                   Glyco_tranf_2_4  1 rneadiLpeflahhlalgfdrilvydndstDgtrailkelpevkllhvdksyederrqvellkallaryaeadwvlvvD 79
                                      +nea++++e++    ++ +d+++v+d++s D+t +i ++l ++ + h +++    +  ++  k++l+   +ad ++ +D
  gi|298676146|ref|YP_003727895.1| 11 YNEANTIGEVIHGCQKY-VDKVVVVDDGSVDDTIKIAESLGAYVVRHPQNEG-YGASLRDCFKTALKL--DADMMVIID 85
                                      69*********999999.*********************8665544444322.223334444444433..577777777 PP

                   Glyco_tranf_2_4 80 aD 81
                                      +D
  gi|298676146|ref|YP_003727895.1| 86 SD 87
                                      76 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.32
                   Glyco_tranf_2_4  8 peflahhlalgfdrilvydndstDgt 33
                                        + + +l+l++d ++++d d + + 
  gi|298676146|ref|YP_003727895.1| 67 RDCFKTALKLDADMMVIIDSDGQHDP 92
                                      55667788899999998887655444 PP

>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.4     0.063   2.8e+02      98     113 ..      28      43 ..      14      48 .. 0.76
   2 ?    8.7   0.8   0.00023         1     143     211 ..     213     294 ..     205     296 .] 0.86

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.063
                            DUF373  98 adsaivVsDGaeDesv 113
                                       +d+++vV DG+ D+++
  gi|298676146|ref|YP_003727895.1|  28 VDKVVVVDDGSVDDTI 43 
                                       489********99986 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00023
                            DUF373 143 llkkalkdpelrk..tiLvplGlllliyallll............lglpelalaiillllGlylllrGfgldellee 205
                                        l ++lkd e+r+  + ++ +Gll+ +++++l             l++    l+i+l+l+G ++ + G+ l+  +++
  gi|298676146|ref|YP_003727895.1| 213 ALVQILKDMEFRRplYYFTAPGLLMGLVGVFLGlsflqdfyhgdsLSFGPTLLMILLTLVGTFMAFTGIILHA-MSK 288
                                       5689999999999667899*******99999988999*****999777779999**************99997.777 PP

                            DUF373 206 lleklk 211
                                       l++++k
  gi|298676146|ref|YP_003727895.1| 289 LIRETK 294
                                       766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.37s 00:00:00.97 Elapsed: 00:00:00.55
# Mc/sec: 1618.92
//
Query:       gi|298676147|ref|YP_003727896.1|  [L=323]
Description: glycosyl transferase family 2 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-27   94.5   0.1    9.3e-27   93.9   0.1    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
    4.6e-16   59.4   0.0    6.8e-16   58.8   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    8.5e-12   45.1   2.6    7.3e-11   42.0   2.6    2.0  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
    2.5e-09   37.3   0.1    3.8e-09   36.8   0.1    1.3  1  Glyco_trans_2_3  Glycosyl transferase family group 2
    4.2e-05   24.0   0.3    0.00097   19.6   0.0    2.4  2  Glyco_tranf_2_4  Glycosyl transferase family 2
  ------ inclusion threshold ------
      0.029   13.8   0.1      0.054   12.9   0.0    1.4  2  Anp1             Anp1
       0.32    9.7   3.2       0.43    9.3   3.2    1.2  1  DUF2207          Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.9   0.1   3.6e-30   9.3e-27       1     124 [.       7     125 ..       7     176 .. 0.88

  Alignments for each domain:
  == domain 1  score: 93.9 bits;  conditional E-value: 3.6e-30
                                       EEEEEESS-TTTHHHHHHHHHHH.GGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaq.dpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglr 76 
                                       s+v+ t Neek+++e+++sll+  +p++ fei++vD  StD+t++i++++     +v ++ +e+    a+a+n g++
  gi|298676147|ref|YP_003727896.1|   7 SIVVGTRNEEKYIAECINSLLNLnYPKDSFEILIVDGMSTDNTQNIVKNY-----PVNLLINEKI-NVASARNLGIK 77 
                                       89************************************************.....9999999977.9********** PP

                                       H--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCC CS
                   Glycos_transf_2  77 aatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetd 124
                                       +++gd+i+f D D+ ++  wl+ lv ++++ ++dv++++ p    ++d
  gi|298676147|ref|YP_003727896.1|  78 HSQGDLIAFTDGDCKVNNLWLKTLVYEIQNAPEDVACVGGPNLVIDND 125
                                       *************************************98766555555 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   0.0   2.7e-19   6.8e-16       1     226 [.       4     226 ..       4     228 .. 0.84

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 2.7e-19
                   Glyco_tranf_2_3   1 prdlavlVptfneedvlgevlesllaqeypr..vevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgk 75 
                                       p+ ++++V t nee+++ e+++sll+  yp   +e+ +v+ +s++ t + ++     +    v++++n++   ++++
  gi|298676147|ref|YP_003727896.1|   4 PF-VSIVVGTRNEEKYIAECINSLLNLNYPKdsFEILIVDGMSTDNTQNIVKN----Y---PVNLLINEK---INVA 69 
                                       67.9*********************99995556****************8875....6...556999999...4666 PP

                   Glyco_tranf_2_3  76 sralnealravksdlvllvDdDtvvePdtlkrllqff.ltp.kvgavgtpvfl.lnrstlvsalgalefaerhlrfl 149
                                       s   n ++++ ++dl+++ D+D+ v    lk l+  + ++p +v++vg+p ++ +n+  + +++g+++  e++l+  
  gi|298676147|ref|YP_003727896.1|  70 SA-RNLGIKHSQGDLIAFTDGDCKVNNLWLKTLVYEIqNAPeDVACVGGPNLViDNDPIFARVVGYVQ--ETFLSSG 143
                                       55.78***************************9999974446*********88679887777776643..5555333 PP

                   Glyco_tranf_2_3 150 aar....ralgv.ltlnGsg.slirrevlkelegldplflltdDyelglrlrragfrtayvpgaavrevfpsslkay 220
                                         +    +++++ + + +++  l+  ++ ++ + +d+ f ++ D +l +r+ + g+r  y p+a v++ ++ +lk +
  gi|298676147|ref|YP_003727896.1| 144 GSAqchsYSKKQyVQSIPNCnALYKKSIIRNVGFFDEYFKVGQDGDLNFRISKIGYRFLYIPEAKVWHHRRGNLKSF 220
                                       3333333555543778887769**********99******************************************* PP

                   Glyco_tranf_2_3 221 ikqrnR 226
                                        kq++ 
  gi|298676147|ref|YP_003727896.1| 221 SKQMFK 226
                                       ***985 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   2.6   2.9e-14   7.3e-11       4     237 ..       8     236 ..       5     245 .. 0.69

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 2.9e-14
                   Glyco_tranf_2_2   4 iplraseerhyieerv..lqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGas 78 
                                       i +++ +e++yi e +  l++ +y  + +e+++vd+ S++++ + v++    nll+  ++        a arN+G++
  gi|298676147|ref|YP_003727896.1|   8 IVVGTRNEEKYIAECInsLLNLNYPKDSFEILIVDGMSTDNTQNIVKNY-PVNLLIN-EK-----INVASARNLGIK 77 
                                       77788888889*****97777777799**************99999986.5788887.33.....479********* PP

                   Glyco_tranf_2_2  79 kaesdlvlFlDaDcfissDkfekilklitikklrenidaavvlpvvdl.nkedsevlkdvedltassrvledllaak 154
                                       ++++dl+ F D+Dc +    ++ ++      ++++ ++        +l +++d  + + v+++    +      a  
  gi|298676147|ref|YP_003727896.1|  78 HSQGDLIAFTDGDCKVNNLWLKTLVY-----EIQNAPEDVACVGGPNLvIDNDPIFARVVGYVQETFLSS-GGSAQC 148
                                       **************998777766666.....788887655555544441555555555555543322222.222222 PP

                   Glyco_tranf_2_2 155 stlvk.ffapss..ssilinrraflevGGyDErfrGhgaEDfdlllRlaka.ikslekmpvellykarakslsnykG 227
                                        ++ k  +++s    ++l ++  + +vG +DE f  +   D dl  R+ k  +++l   p    ++ r ++l++++ 
  gi|298676147|ref|YP_003727896.1| 149 HSYSKkQYVQSIpnCNALYKKSIIRNVGFFDEYF--KVGQDGDLNFRISKIgYRFL-YIPEAKVWHHRRGNLKSFSK 222
                                       23332233333223578999999999********..88899999999998725555.66666666899999987753 PP

                   Glyco_tranf_2_2 228 ....frrflealak 237
                                           + +++ +l k
  gi|298676147|ref|YP_003727896.1| 223 qmfkYGSWMAELFK 236
                                       22114466666655 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.1   1.5e-12   3.8e-09       2     193 ..      84     282 ..      83     309 .. 0.74

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 1.5e-12
                   Glyco_trans_2_3   2 illlDaDtvlppdclreiaaela.sp.evaivqgpvlvmnvanwleelaalf...faedhgkdilvrealgr..vvp 71 
                                       i++ D D  ++   l+ +++e++  p +va v gp lv  + ++++++  +    f ++ g +    +++++  v +
  gi|298676147|ref|YP_003727896.1|  84 IAFTDGDCKVNNLWLKTLVYEIQnAPeDVACVGGPNLVIDNDPIFARVVGYVqetF-LSSGGSAQCHSYSKKqyVQS 159
                                       77889999999999********955669*******999777899999999887754.33333444444555544889 PP

                   Glyco_trans_2_3  72 svGsgaflrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGc.ele 147
                                       ++  +a+   s ++ vg++d   + v+ D d+ +r+ + Gyr+ ++pe+ v+ + + +l+ + +Q+ ++     el+
  gi|298676147|ref|YP_003727896.1| 160 IPNCNALYKKSIIRNVGFFD-EYFKVGQDGDLNFRISKIGYRFLYIPEAKVWHHRRGNLKSFSKQMFKYGSWMaELF 235
                                       9*******************.679********************************************865543556 PP

                   Glyco_trans_2_3 148 klillvrllgylgsllwsalplhlallllfsllalalvl.lllllla 193
                                       k+++ ++++  l  +++  ++l  +++ + +l+ l+ ++ ll+++ +
  gi|298676147|ref|YP_003727896.1| 236 KKHRDLVRWYALIPPIAILFSLVSIISSIVNLNLLYIFIcLLFTYII 282
                                       66665555544444444444443344444443332222212222222 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   3.8e-07   0.00097       1      41 [.      13      57 ..      13      91 .. 0.81
   2 ?    1.7   0.1      0.14   3.6e+02      41      76 ..     205     246 ..     198     248 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.8e-07
                   Glyco_tranf_2_4  1 rneadiLpeflahhlalgf..dr..ilvydndstDgtrailkelp 41
                                      rne++++ e++  +l+l +  d   il++d +stD+t +i+k++p
  gi|298676147|ref|YP_003727896.1| 13 RNEEKYIAECINSLLNLNYpkDSfeILIVDGMSTDNTQNIVKNYP 57
                                      8*****************7553244*****************975 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.14
                   Glyco_tranf_2_4  41 pevkllhvd....ksyederrq.vellkallaryaea.dwvl 76 
                                       pe+k++h++    ks++++ ++  +++ +l++++++  +w +
  gi|298676147|ref|YP_003727896.1| 205 PEAKVWHHRrgnlKSFSKQMFKyGSWMAELFKKHRDLvRWYA 246
                                       678999999888888888999944699999999988548875 PP

>> Anp1  Anp1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.1e-05     0.054      25      79 ..       8      60 ..       4      90 .. 0.83
   2 ?   -4.0   0.0         3   7.6e+03     170     191 ..     208     231 ..     207     234 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.1e-05
                              Anp1 25 iltplrdaekflpeyfenllkltyphelidLaflvsdtsegdktlealeeelkkl 79
                                      i++  r++ek++ e ++ ll+l+yp++ +++ ++ + ++  d+t++ ++++  +l
  gi|298676147|ref|YP_003727896.1|  8 IVVGTRNEEKYIAECINSLLNLNYPKDSFEILIVDGMST--DNTQNIVKNYPVNL 60
                                      88899************************9955555555..99999988876555 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 3
                              Anp1 170 nvlrklpdelek..eqpYDlnsWv 191
                                       +v+ ++  +l++  +q + + sW+
  gi|298676147|ref|YP_003727896.1| 208 KVWHHRRGNLKSfsKQMFKYGSWM 231
                                       678877766664558999999997 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   3.2   0.00017      0.43     358     441 ..     218     300 ..     177     304 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00017
                           DUF2207 358 kkwksavkk..kergyfdkkgkkklkklsalglgliilglilillallllvlllvfllilllillliaiivlllfsr 432
                                       k++ +   +  k+  ++ +  kk++  ++ ++l+  i++l+ ++ ++ ++v l+ ++ +++l++  i++i+l  +++
  gi|298676147|ref|YP_003727896.1| 218 KSFSK---QmfKYGSWMAELFKKHRDLVRWYALIPPIAILFSLVSIISSIVNLNLLYIFICLLFTYIILILLTALKI 291
                                       33333...244477788888888887777777777777777777777777766777777777777777777777777 PP

                           DUF2207 433 llgrrteeG 441
                                        ++  + +G
  gi|298676147|ref|YP_003727896.1| 292 SFKMKSVYG 300
                                       777666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1077  (0.0600703); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.65u 0.35s 00:00:01.00 Elapsed: 00:00:00.54
# Mc/sec: 1815.32
//
Query:       gi|298676148|ref|YP_003727897.1|  [L=453]
Description: capsular polysaccharide biosynthesis protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0015   17.2   0.0     0.0021   16.8   0.0    1.2  1  AMP-binding  AMP-binding enzyme
  ------ inclusion threshold ------
      0.025   14.5   0.1      0.051   13.5   0.1    1.5  1  RNaseH_like  Ribonuclease H-like


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.3e-07    0.0021     219     369 ..     173     310 ..      41     316 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.3e-07
                                       HHHHHHHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS CS
                       AMP-binding 219 lelllallsGatvvllpkdaa.ldpklllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllgge 293
                                       + l+l ll+  +++ +  +++ +  ++ ++ i+k+k+ vi+g  + l al +     +  ++ +dl+ l+ +++  e
  gi|298676148|ref|YP_003727897.1| 173 AKLYLKLLRQKRLGTFGANDKiF--QRYVNIIKKFKPKVIYGYSSSLYALSKyL---Y-RYNINDLN-LKSIISDSE 242
                                       55666666666666666555533..47889********************8833...2.24455766.9999***** PP

                                       -EBHHHHHHHHHHHTCEEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEE CS
                       AMP-binding 294 plspellrffralfgeevlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellv 369
                                        l p+  + +++ f ++v++ YG  E+t +     +ee+    g +  +  +v ++ +D + g++v +g+ G+++v
  gi|298676148|ref|YP_003727897.1| 243 TLYPHYRKMIEKQFNCKVYDHYGSKEATYAQE---CEEH---DG-YHIAAENVFLEFLDSN-GKRVNEGNFGKIFV 310
                                       ****************************8752...3333...22.4456668888888988.88888898898887 PP

>> RNaseH_like  Ribonuclease H-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   5.7e-06     0.051      55     118 ..     384     450 ..     353     452 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.7e-06
                       RNaseH_like  55 kke.rkikslrekiflEtslslevaskleelllea..kkkkaelkleihiDiGengktkelikevvg 118
                                       + + + i++l  ki+ E ++  e+ +++++ l+e+  ++  +++++  +iD+ e+gk + +i++v++
  gi|298676148|ref|YP_003727897.1| 384 QIVqNSINELDIKIVPEENYNDEITKQIKNSLKEYfdEDCVIKFNFVEDIDVPESGKHRFIISNVID 450
                                       333489************************999994344557788888***************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       875  (0.0488036); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.35s 00:00:01.02 Elapsed: 00:00:00.54
# Mc/sec: 2537.82
//
Query:       gi|298676149|ref|YP_003727898.1|  [L=359]
Description: glycosyl transferase group 1 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-33  115.9   0.6    2.5e-33  115.0   0.6    1.4  1  Glycos_transf_1  Glycosyl transferases group 1
    6.4e-29  101.1   0.0    1.9e-28   99.6   0.0    1.7  2  Glyco_trans_1_4  Glycosyl transferases group 1
    8.1e-10   39.0   0.1    1.7e-09   37.9   0.1    1.6  1  Glyco_transf_4   Glycosyltransferase Family 4
    9.9e-08   32.3   0.0    2.2e-07   31.2   0.0    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1
     0.0022   18.5   0.0     0.0032   17.9   0.0    1.2  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.0   0.6     7e-37   2.5e-33      17     170 ..     181     335 ..     169     337 .. 0.96

  Alignments for each domain:
  == domain 1  score: 115.0 bits;  conditional E-value: 7e-37
                                       EEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES...STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHH CS
                   Glycos_transf_1  17 iilsvgrlekeKgvdllikafallkkqlnpnvklviaG..ngeeekelkklaeelelsdnviflgevsredleellk 91 
                                        + +vgrlek Kg+  l+ a++++  +  + v++v++G  +++++ ++ +  +++++ +nv+++g +s+ ++ + l+
  gi|298676149|ref|YP_003727898.1| 181 NVTFVGRLEKSKGIYELLNAIPHVLNK-YKYVNFVLVGpyEKKDFIRINSFLKQHNICNNVFLTGPISKLKVYQELS 256
                                       578*********************988.************999********************************** PP

                                       CESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHHHH CS
                   Glycos_transf_1  92 nadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerlgen 168
                                       +++ifvlps+ E+f+i++lEAm +glp+ia+ +g ++e+v+++ +G+l+k+n+  ++a++i  l+e+eelr ++ +n
  gi|298676149|ref|YP_003727898.1| 257 KSKIFVLPSHVEAFPISILEAMGIGLPIIATPIGDVPEIVENNINGFLIKENDFLDMANKIMYLIENEELRLKMVNN 333
                                       **************************************************************************999 PP

                                       HH CS
                   Glycos_transf_1 169 ar 170
                                         
  gi|298676149|ref|YP_003727898.1| 334 NL 335
                                       75 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.94   3.4e+03       4      50 ..       7      55 ..       5      64 .. 0.62
   2 !   99.6   0.0   5.2e-32   1.9e-28       3     134 .]     181     323 ..     179     323 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.94
                                      EEEES---GG.GTHHHHHHHH.HHHH.HHEEEEEES---...HHHHHHH CS
                   Glyco_trans_1_4  4 ilfvGrleenvkgvdllleav.pllrkkdvrlvivGdgp.rpeeleela 50
                                      il +G   +++ g+  ++e+v +  +k++++l+ +  +  ++++l+e +
  gi|298676149|ref|YP_003727898.1|  7 ILILGPTPPPYGGIATFVEEVlKSNLKNEYNLLHINTNRnNSKSLKENI 55
                                      7778877558889999999997665545576665554433445565544 PP

  == domain 2  score: 99.6 bits;  conditional E-value: 5.2e-32
                                       EEEEES---GG.GTHHHHHHHHHHHH.H.H.EEEEEES---.......HHHHHHHT..T-T.TEEEE---TH..HHH CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkk.d.vrlvivGdgprp.....eeleelaa..gleerveftGfved..lae 68 
                                       ++ fvGrl e+ kg+  ll+a+p++++k + v++v+vG  +++     +   + ++  ++ ++v +tG +++  + +
  gi|298676149|ref|YP_003727898.1| 181 NVTFVGRL-EKSKGIYELLNAIPHVLNKyKyVNFVLVGPYEKKdfiriN---SFLKqhNICNNVFLTGPISKlkVYQ 253
                                       689*****.667**************99658*******66533353332...3332457889********5445999 PP

                                       HHHH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
                   Glyco_trans_1_4  69 llaaadvfvaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLled 134
                                        l+++++fv+Ps  e f++++lEam  glp++at++g ++e+v  + ng+l++++d  ++a++i  L+e+
  gi|298676149|ref|YP_003727898.1| 254 ELSKSKIFVLPShvEAFPISILEAMGIGLPIIATPIGDVPEIVenNINGFLIKENDFLDMANKIMYLIEN 323
                                       9***********************************99*****9889********************986 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.1   4.6e-13   1.7e-09      53     169 ..      54     168 ..      17     169 .. 0.78

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 4.6e-13
                    Glyco_transf_4  53 rllrslaflrrlrrllkrekpDvvHah..spaalg...aallalrr.rlgiplVltvHglyekrllkarlkplsrll 123
                                       +    l+  ++l  ll   +p +vH+h  s+ +++   + ++      +  ++V+++Hg +      +++  ++ l+
  gi|298676149|ref|YP_003727898.1|  54 NINVFLRVTFQLLYLLSYKRPKLVHIHasSYLSFWektFFAFI--SkLYLRKVVYHIHGGA------FKQFYEQSLF 122
                                       4555677788999999999*****8883234444332222222..245999**********......5666677889 PP

                    Glyco_transf_4 124 ralerrllrradrviavSeatadelrerygvppekitVipnGvDle 169
                                       +++ r+ +   d +i+ S+  +++l+e     +eki V+ n vDl+
  gi|298676149|ref|YP_003727898.1| 123 KKIIRFCFYFFDGIIVLSDNWKNYLHEQNLTYKEKIFVVNNFVDLN 168
                                       9999999999*****************666777***********96 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   6.2e-11   2.2e-07       2      83 ..     261     344 ..     260     351 .. 0.93

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 6.2e-11
                   Glyco_trans_1_2   2 vLnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarer 76 
                                       ++ ps+ e +   ++Ea++ G +++++++ +++e+++++  ++l++  d  ++a ki yl++n+e+r ++ +++ ++
  gi|298676149|ref|YP_003727898.1| 261 FVLPSHVEAFPISILEAMGIGLPIIATPIGDVPEIVENNINGFLIKenDFLDMANKIMYLIENEELRLKMVNNNLKK 337
                                       6778999999999*********************************9****************************99 PP

                   Glyco_trans_1_2  77 vlaehty 83 
                                       + ++++ 
  gi|298676149|ref|YP_003727898.1| 338 FNEKYNI 344
                                       9988875 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0     9e-07    0.0032      57     159 ..      59     163 ..      36     163 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 9e-07
                   Glyco_trans_4_4  57 laalralrrllrqrrerpdvvhahs.ptag.....laarlarrrrgiplvvtlhglllrrgsgavrrlyralerrll 127
                                       l+ +++l  ll     rp +vh+h  ++++     ++a + +     ++v+++hg ++ +    +++l++ + r+++
  gi|298676149|ref|YP_003727898.1|  59 LRVTFQLLYLL--SYKRPKLVHIHAsSYLSfwektFFAFISK-LYLRKVVYHIHGGAFKQ--FYEQSLFKKIIRFCF 130
                                       56677777777..889********955544123335555556.778899******99974..67899********** PP

                   Glyco_trans_4_4 128 rradavlvvseaeaeelralg.vpadrvvvvpn 159
                                         +d+++v+s+ +  +l++++    +++ vv n
  gi|298676149|ref|YP_003727898.1| 131 YFFDGIIVLSDNWKNYLHEQNlTYKEKIFVVNN 163
                                       *******************66367778877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.35s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 2048.11
//
Query:       gi|298676150|ref|YP_003727899.1|  [L=397]
Description: glycosyl transferase group 1 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-36  125.7   0.2    2.8e-35  121.4   0.2    2.4  1  Glycos_transf_1  Glycosyl transferases group 1
    3.6e-24   85.7   0.0    6.4e-24   84.9   0.0    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1
    2.2e-12   47.3   0.0    3.2e-12   46.8   0.0    1.3  1  Glyco_transf_4   Glycosyltransferase Family 4
     0.0013   19.1   0.0     0.0051   17.2   0.0    2.0  1  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
       0.02   14.9   0.1      0.052   13.5   0.1    1.8  1  DUF4649          Domain of unknown function (DUF4649)
      0.038   14.2   0.6       0.14   12.4   0.6    2.0  1  DUF1359          Protein of unknown function (DUF1359)
       0.12   12.8   0.0       0.17   12.3   0.0    1.2  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.4   0.2   1.1e-38   2.8e-35      14     167 ..     200     374 ..     190     379 .. 0.92

  Alignments for each domain:
  == domain 1  score: 121.4 bits;  conditional E-value: 1.1e-38
                                       T-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHH CS
                   Glycos_transf_1  14 kkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleell 90 
                                       + ++i+ vgrl+ +Kg+++likaf ++k++  +n+klv+ G ge e+elk+lae++ l+++++f g+++  +  +++
  gi|298676150|ref|YP_003727899.1| 200 ESPVIINVGRLVDVKGQNHLIKAFSKVKDE-VDNAKLVFLGRGELENELKELAEKYRLENDIFFMGFQK--NPFKFI 273
                                       5799***********************997.**************************************..9***** PP

                                       HCESEEEEEESSBSS-HHHHHHHHTT--EEEET.TTTHCHHCHTTT........................SEEEE-T CS
                   Glycos_transf_1  91 knadifvlpsisEgfGivllEAmaaglpviasn.aggpaevvkdge........................tGllvkp 142
                                       kn+++fvl+s++Egf+ +++E+ma+g+p+i+++  +gp+e++++                          + l  k+
  gi|298676150|ref|YP_003727899.1| 274 KNSSVFVLSSTNEGFPNAIVESMACGIPIISTDcFSGPREILAPDTdinyqtnvveyapygiltpvcndgDRLSLKN 350
                                       *******************************************9999999999999999999988888766666665 PP

                                       T-HHHHHHHHHHHHHSHHHHHHHHH CS
                   Glycos_transf_1 143 nnaealaeairklledeelrerlge 167
                                       +   +l++ai+++l+++el e++g 
  gi|298676150|ref|YP_003727899.1| 351 E-ENMLSDAINQILKNDELKEKYGL 374
                                       5.89999999999999999988775 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.9   0.0   2.5e-27   6.4e-24       2     110 ..     202     317 ..     201     365 .. 0.89

  Alignments for each domain:
  == domain 1  score: 84.9 bits;  conditional E-value: 2.5e-27
                                       EEEEEES---GG.GTHHHHHHHHHHHH.H.H.EEEEEES---...HHHHHHHT..T-T.TEEEE---THHHHHHHH- CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk.d.vrlvivGdgp.rpeeleelaa..gleerveftGfvedlaellaaa 73 
                                       pvi+ vGrl+  vkg+  l++a+ +++++ d ++lv+ G+g+ + +el+ela+  +le+++ f+Gf ++  ++++++
  gi|298676150|ref|YP_003727899.1| 202 PVIINVGRLV-DVKGQNHLIKAFSKVKDEvDnAKLVFLGRGElE-NELKELAEkyRLENDIFFMGFQKNPFKFIKNS 276
                                       89*******5.67**************99856*********955.699999976999999***************** PP

                                       SEEEE--..---SHHHHHHHHTT-EEEE-TGG.GTTT--.T CS
                   Glyco_trans_1_4  74 dvfvaPs..egfglkllEamaaglpvVatdvg.giaevv.g 110
                                       +vfv+ s  egf+++++E+ma+g+p+++td+  g++e++  
  gi|298676150|ref|YP_003727899.1| 277 SVFVLSStnEGFPNAIVESMACGIPIISTDCFsGPREILaP 317
                                       ********99*********************6598997652 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.0   1.3e-15   3.2e-12       2     169 ..      15     181 ..      14     182 .. 0.83

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 1.3e-15
                    Glyco_transf_4   2 GGverhvleLaraLarrGheVtvvtpgddgpleeev....elvvrvprvplpllkrllrslaflr...rlrrllkre 71 
                                       GG+e +v +L+ +L+++ +++ + + ++d+  ++      +l +++p +   l++ + r ++f++   + +++ k++
  gi|298676150|ref|YP_003727899.1|  15 GGAEKVVSNLSINLPDK-YKIKLMVYHTDQIDYQYNgeiiDLNISIPEPDKSLKNMFIRVFTFFSliqKSKNIKKQY 90 
                                       9***************9.99998877777766666656787777777777778888888777755111556677777 PP

                    Glyco_transf_4  72 kpDvvHahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadel 148
                                       +p    +   a+ ++ l+     l   ++++vH+       ++ ++++ ++ + l + ++++a  +iavS+ ++++l
  gi|298676150|ref|YP_003727899.1|  91 EPQATISFLTAPNILNLFSK---LSDNVIISVHSQI----SQGLKGLEGKIHKQLIKLFYNHAYLIIAVSKGVKKDL 160
                                       99999888888887776654...578**********....68999999***************************** PP

                    Glyco_transf_4 149 rerygvppekitVipnGvDle 169
                                       + +++++peki Vi+n+  ++
  gi|298676150|ref|YP_003727899.1| 161 VNNFRIKPEKIKVIHNPYETD 181
                                       *****************9998 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0     2e-06    0.0051       5      79 ..     282     381 ..     277     394 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2e-06
                   Glyco_trans_1_2   5 psrsespnlrlfEaaacGafaltdda.egleelftpgk.........................evilfedleelaek 55 
                                        s +e++   ++E +acG++++++d  +g++e++ p++                          + l  +++ l ++
  gi|298676150|ref|YP_003727899.1| 282 SSTNEGFPNAIVESMACGIPIISTDCfSGPREILAPDTdinyqtnvveyapygiltpvcndgdRLSLKNEENMLSDA 358
                                       556677888899************99************999999999999999999999988555555588888899 PP

                   Glyco_trans_1_2  56 iryllanpeerraiaeaarervla 79 
                                       i++ l+n+e+ ++ +  a++r  +
  gi|298676150|ref|YP_003727899.1| 359 INQILKNDELKEKYGLLAQKR-AE 381
                                       999999999988888888887.44 PP

>> DUF4649  Domain of unknown function (DUF4649)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1     2e-05     0.052      31      58 ..      26      55 ..      14      65 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2e-05
                           DUF4649 31 vtvpDsypvtkltykgkkldYq..Gtygdl 58
                                      +++pD y+++ ++y   ++dYq  G++ dl
  gi|298676150|ref|YP_003727899.1| 26 INLPDKYKIKLMVYHTDQIDYQynGEIIDL 55
                                      99*****************98633666555 PP

>> DUF1359  Protein of unknown function (DUF1359)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.6   5.4e-05      0.14      22      82 ..     158     217 ..     148     234 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.4e-05
                           DUF1359  22 kdvihdvkdqtelvklleddlksneikkddkleleltdrfsvlkssvkinvGtlisllkdn 82 
                                       kd++ + + + e +k++ +  ++++i+k   +e+e      +++s v invG l+ +  +n
  gi|298676150|ref|YP_003727899.1| 158 KDLVNNFRIKPEKIKVIHNPYETDKIQKLADYEIEQE-YQDIFESPVIINVGRLVDVKGQN 217
                                       89999**************************999987.789**************988777 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.7e-05      0.17      98     159 ..     114     176 ..      97     177 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.7e-05
                   Glyco_trans_4_4  98 plvvtlhglllrrgsgavrrlyralerrllrradavlvvseaeaeelra.lgvpadrvvvvpn 159
                                        +++++h+   ++ +g ++ + + l ++ +++a ++++vs ++ ++l+  + + ++++ v++n
  gi|298676150|ref|YP_003727899.1| 114 NVIISVHSQISQGLKGLEGKIHKQLIKLFYNHAYLIIAVSKGVKKDLVNnFRIKPEKIKVIHN 176
                                       57888998877777999999999999***********************888**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.65u 0.35s 00:00:01.00 Elapsed: 00:00:00.54
# Mc/sec: 2195.63
//
Query:       gi|298676151|ref|YP_003727900.1|  [L=618]
Description: hypothetical protein Metev_2288 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        9.9    6.1   5.8        0.9    9.4   0.3    2.1  2  Tmemb_9   TMEM9


Domain annotation for each model (and alignments):
>> Tmemb_9  TMEM9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -5.1   1.0         1   1.8e+04      54      68 ..     296     310 ..     292     316 .. 0.58
   2 ?    9.4   0.3     5e-05       0.9      43      86 ..     448     492 ..     444     513 .. 0.77

  Alignments for each domain:
  == domain 1  score: -5.1 bits;  conditional E-value: 1
                           Tmemb_9  54 viivivvislLviYm 68 
                                       v+i+ +v s+ + Y+
  gi|298676151|ref|YP_003727900.1| 296 VLIIFIVFSMWSSYL 310
                                       455555555555555 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 5e-05
                           Tmemb_9  43 esRntttikvvviivivvi.slLviYmlflllldpllnkrkkkas 86 
                                       ++ nt+ i ++++ +i ++ s+L+iY l+l  l   +n++ ++a+
  gi|298676151|ref|YP_003727900.1| 448 KKINTKQISCILLCIILILfSILSIYSLYLSPLTKTVNSQVTEAQ 492
                                       5679999*99998877765379********999999999855554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (618 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1245  (0.0694406); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.77u 0.33s 00:00:01.10 Elapsed: 00:00:00.53
# Mc/sec: 3520.99
//
Query:       gi|298676152|ref|YP_003727901.1|  [L=301]
Description: glycosyl transferase family 2 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-41  142.0   0.1    2.4e-41  141.4   0.1    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
    1.2e-19   71.1   0.0    1.9e-19   70.5   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    2.6e-19   69.8   2.8    3.4e-19   69.4   2.8    1.2  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.014   15.8   0.1      0.035   14.6   0.1    1.7  1  Glyco_tranf_2_4  Glycosyl transferase family 2
      0.039   14.1   0.0      0.082   13.1   0.0    1.6  1  TPR_2            Tetratricopeptide repeat
       0.04   13.5   0.0      0.063   12.8   0.0    1.2  1  NTP_transferase  Nucleotidyl transferase
      0.041   13.7   0.0      0.094   12.6   0.0    1.6  1  TPR_1            Tetratricopeptide repeat
      0.088   12.8   0.1       0.23   11.4   0.1    1.8  1  Peptidase_S24    Peptidase S24-like


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.4   0.1   1.1e-44   2.4e-41       1     164 [.       5     163 ..       5     169 .. 0.80

  Alignments for each domain:
  == domain 1  score: 141.4 bits;  conditional E-value: 1.1e-44
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       sv+iptyN+++t+ +t++s+l+q +y+dfeii+vDD+S+D+t+ i++++++ d rv++i++++n+G   a+n+g+++
  gi|298676152|ref|YP_003727901.1|   5 SVIIPTYNRSQTVSKTIKSVLNQ-TYQDFEIIIVDDNSSDNTEFIIKSFSHFDSRVKYIKHNKNKGAPEARNTGIKN 80 
                                       8**********************.***************************************************** PP

                                       --SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTC CS
                   Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfe 154
                                       ++gdyi++lD+Dde+ p++lek v+ + k+ +d+ l +  + + +++ +        + +l+++ +++ +  ++ ++
  gi|298676152|ref|YP_003727901.1|  81 SKGDYIALLDDDDEWFPQKLEKQVKLFAKESDDIGLIHCGYEKIDENGNILI----PKKKLKETGNMFYELLESNII 153
                                       *****************************87765444443333333333333....234555555555555555555 PP

                                       STCCCEEEEH CS
                   Glycos_transf_2 155 igsaallrre 164
                                        ++  l+r e
  gi|298676152|ref|YP_003727901.1| 154 GSPTNLIRSE 163
                                       5555555555 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.5   0.0   8.4e-23   1.9e-19       4     208 ..       4     200 ..       2     212 .. 0.89

  Alignments for each domain:
  == domain 1  score: 70.5 bits;  conditional E-value: 8.4e-23
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksraln 80 
                                       ++v++pt+n+++++ +++ s+l+q+y ++e+++v+d+s++ t   ++ +   + d rv+++   +n   +g+ +a n
  gi|298676152|ref|YP_003727901.1|   4 VSVIIPTYNRSQTVSKTIKSVLNQTYQDFEIIIVDDNSSDNTEFIIKSF-SHF-DSRVKYIKHNKN---KGAPEARN 75 
                                       89***************************************99888874.445.55***9966554...689***** PP

                   Glyco_tranf_2_3  81 ealravksdlvllvDdDtvvePdtlkrllqff..ltpkvgavg.tpvfllnrstlvsalgalefaerhlrflaarra 154
                                        ++++ k+d+++l+DdD+ + P  l++++ +f  +++++g +  + +  +   + + +  +l+ + + +++l+ ++ 
  gi|298676152|ref|YP_003727901.1|  76 TGIKNSKGDYIALLDDDDEWFPQKLEKQVKLFakESDDIGLIHcGYEKIDENGNILIPKKKLKETGNMFYELLESNI 152
                                       ********************************99999******66678898888888899999999999999999*9 PP

                   Glyco_tranf_2_3 155 lgvltlnGsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaa 208
                                       +g +t      lir e++k ++  d +     D++l+ r+ ++ +++ y p+ +
  gi|298676152|ref|YP_003727901.1| 153 IGSPT-----NLIRSECFKKIGYCDVQLKSCQDWDLWIRISKH-YKINYIPEIL 200
                                       99997.....9***********9***77777********9987.6777777665 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.4   2.8   1.5e-22   3.4e-19       1     250 [.       5     236 ..       5     267 .. 0.79

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 1.5e-22
                   Glyco_tranf_2_2   1 svviplraseerhyieerv...lqkakyydeeielivvddgSsekfleevssiidlnllv.ylkdeddkayslaaar 73 
                                       sv+ip ++  ++  +  ++   l+++ +   ++e+i+vdd Ss+++   ++s+ +   +v y+k++  k  +   ar
  gi|298676152|ref|YP_003727901.1|   5 SVIIPTYNRSQT--VSKTIksvLNQTYQ---DFEIIIVDDNSSDNTEFIIKSFSHFDSRVkYIKHN--KNKGAPEAR 74 
                                       89*********9..99999554555555...9****************************888888..6668999** PP

                   Glyco_tranf_2_2  74 NrGaskaesdlvlFlDaDcfissDkfekilklitikklrenidaavvlpvvdlnkedsevlkdvedltassrvledl 150
                                       N G++++++d++  lD D+ + + k+ek++k    +  +e  d  ++   ++ ++e+ ++l   + l   +++  +l
  gi|298676152|ref|YP_003727901.1|  75 NTGIKNSKGDYIALLDDDDEWFPQKLEKQVK----LFAKESDDIGLIHCGYEKIDENGNILIPKKKLKETGNMFYEL 147
                                       *******************************....5568889999******************99999999999888 PP

                   Glyco_tranf_2_2 151 laakstlvkffapssssilinrraflevGGyDErfrGhgaEDfdlllRlakaikslekmpvellykarakslsnykG 227
                                       l         ++  s + li+ + f ++G  D ++  ++  D+dl +R+ k++k    +     y+ +  s+s  k 
  gi|298676152|ref|YP_003727901.1| 148 LE------SNIIG-SPTNLIRSECFKKIGYCDVQL--KSCQDWDLWIRISKHYKINYIPEILARYNVSDVSIS--KN 213
                                       87......55554.56679****************..9***************97744444445666666666..44 PP

                   Glyco_tranf_2_2 228 frrflealakeaaalglvvfhlY 250
                                         + l+   +    + l++ +  
  gi|298676152|ref|YP_003727901.1| 214 IDSVLSGHKQILDKYFLYICKNN 236
                                       44444444444444444444444 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   1.6e-05     0.035      14      81 ..      24      92 ..      11     105 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.6e-05
                   Glyco_tranf_2_4 14 hlalgfd..rilvydndstDgtrailkelpevkllhvdksy...ederrqvellkallaryaeadwvlvvDaD 81
                                       l+  ++  +i+++d++s+D+t  i+k+    ++++++ +y   ++ + + e++++ +++ +++d+++ +D D
  gi|298676152|ref|YP_003727901.1| 24 VLNQTYQdfEIIIVDDNSSDNTEFIIKSF---SHFDSRVKYikhNKNKGAPEARNTGIKN-SKGDYIALLDDD 92
                                      4444443125*****************94...4555554443211223346788887766.589999999977 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.7e-05     0.082       7      33 ..     246     272 ..     243     273 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.7e-05
                             TPR_2   7 lGlayyklgdyeeAleafekAleldPn 33 
                                       +Gl+y+++gdy + l+++  ++ ++P 
  gi|298676152|ref|YP_003727901.1| 246 IGLLYLHKGDYSKSLKYLTLSIHYNPL 272
                                       79*****************99999996 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.8e-05     0.063      25     143 ..       8     125 ..       5     129 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.8e-05
                                       SEETTETETTHHHHHHHHHTT-SEE.EEEEETTTHHHHHHHHTTSGGGTSEEEEEEESS--BGGHHHHHTHHHHTTS CS
                   NTP_transferase  25 vpvlgkerliqatlsrlansgieei.ivvltqehsflveeqlkegskfgvevlialepegkgtAdAvalaaellede 100
                                       +p ++ +  + +t++ ++n+ +++  i+++ ++ s   e  +k+ s+f+ +v+++  +++kg+ +A   +++  + +
  gi|298676152|ref|YP_003727901.1|   8 IPTYNRSQTVSKTIKSVLNQTYQDFeIIIVDDNSSDNTEFIIKSFSHFDSRVKYIKHNKNKGAPEARNTGIKNSKGD 84 
                                       678888899999*******99999735666666778889999************************99998888887 PP

                                       SE..EEEEETTEEEESTTHHHHHHHHHTHSSTT.SEEEEEEESS CS
                   NTP_transferase 101 ksdelvlvLggDhlikdayeeavkkaiekaakg.tvtfgivpve 143
                                       +   ++l   +D ++ +++e+ vk +++++ ++ ++ +g ++ +
  gi|298676152|ref|YP_003727901.1|  85 Y---IALLDDDDEWFPQKLEKQVKLFAKESDDIgLIHCGYEKID 125
                                       7...566667889*******************999999987655 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.2e-05     0.094       7      32 ..     246     271 ..     243     273 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.2e-05
                                       HHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   7 lGnayfklgkydeAleyyekALelnP 32 
                                       +G++y+++g+y + l+y    +  nP
  gi|298676152|ref|YP_003727901.1| 246 IGLLYLHKGDYSKSLKYLTLSIHYNP 271
                                       8****************999988888 PP

>> Peptidase_S24  Peptidase S24-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1    0.0001      0.23       9      57 ..      27     118 ..      22     135 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0001
                                       CTXXTTXEEEEECTS.....................................---TTSEEEEEETTCE......-EE CS
                     Peptidase_S24   9 ptlldGdlilVdkfs.....................................epkrGdivvfrlpgee......eay 42 
                                        t++d ++i+Vd +s                                     +  +Gd+++  ++++e      e  
  gi|298676152|ref|YP_003727901.1|  27 QTYQDFEIIIVDDNSsdntefiiksfshfdsrvkyikhnknkgapearntgiKNSKGDYIALLDDDDEwfpqklEKQ 103
                                       69**********999999**********************************************99999**999999 PP

                                       EEEEEEETTEEEEE. CS
                     Peptidase_S24  43 iKrviglpgdrvlla 57 
                                       +K + ++ +d+ l++
  gi|298676152|ref|YP_003727901.1| 104 VKLFAKESDDIGLIH 118
                                       99999****998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       834  (0.0465168); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.62u 0.35s 00:00:00.97 Elapsed: 00:00:00.54
# Mc/sec: 1667.25
//
Query:       gi|298676153|ref|YP_003727902.1|  [L=417]
Description: glycosyl transferase group 1 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-40  138.4   0.0    3.6e-40  137.3   0.0    1.5  1  Glycos_transf_1  Glycosyl transferases group 1
    2.7e-30  105.5   0.0    4.4e-30  104.9   0.0    1.3  1  Glyco_trans_1_4  Glycosyl transferases group 1
    2.2e-15   57.0   0.0    1.8e-13   50.8   0.0    2.8  2  Glyco_transf_4   Glycosyltransferase Family 4
    4.9e-10   39.6   1.0    2.2e-07   31.0   1.0    2.5  1  Glyco_trans_4_2  Glycosyl transferase 4-like
    1.2e-06   28.8   0.0    3.1e-06   27.5   0.0    1.7  1  Glyco_trans_1_2  Glycosyl transferases group 1
     0.0026   18.2   0.0       0.04   14.4   0.0    2.5  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
  ------ inclusion threshold ------
      0.051   13.2   0.1        0.1   12.3   0.1    1.5  1  Glyco_transf_5   Starch synthase catalytic domain
      0.085   11.7   0.0       0.18   10.6   0.0    1.5  2  Trp_syntA        Tryptophan synthase alpha chain


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.3   0.0   1.6e-43   3.6e-40      14     171 ..     229     391 ..     219     392 .. 0.97

  Alignments for each domain:
  == domain 1  score: 137.3 bits;  conditional E-value: 1.6e-43
                                       T-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHH CS
                   Glycos_transf_1  14 kkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleell 90 
                                       k+  +lsvgrl+++Kg++++i+a+ ++ k+  +nv ++i+G+g+  ++l+kl+ +l+++++v++lg ++++ l +++
  gi|298676153|ref|YP_003727902.1| 229 KPIKLLSVGRLVEKKGHEYAIEAMYEVLKR-YQNVEYLIVGDGPLYNYLQKLISKLNIENHVKLLGSIDDKSLFQVY 304
                                       78899***********************98.********************************************** PP

                                       HCESEEEEEESS......BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHH CS
                   Glycos_transf_1  91 knadifvlpsis......EgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeel 161
                                       ++++ifv+ps +      Eg G+vl EA a+glpvi++ + g++e v dg +G+lv++++++ala++++ l+e++ l
  gi|298676153|ref|YP_003727902.1| 305 QKSHIFVFPSVTskegdkEGQGLVLQEAQAVGLPVISTFHNGIPEGVIDGISGFLVPEKDVDALADKMEYLIENPFL 381
                                       ***************************************************************************** PP

                                       HHHHHHHHHH CS
                   Glycos_transf_1 162 rerlgenark 171
                                         ++g+n+rk
  gi|298676153|ref|YP_003727902.1| 382 WSHMGYNGRK 391
                                       ********98 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.9   0.0   1.9e-33   4.4e-30       3     134 .]     232     378 ..     230     378 .. 0.90

  Alignments for each domain:
  == domain 1  score: 104.9 bits;  conditional E-value: 1.9e-33
                                       EEEEES---GG.GTHHHHHHHHHHHH.H.H.EEEEEES---...HHHHHHHT..T-T.TEEEE---TH..HHHHHHH CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkk.d.vrlvivGdgp.rpeeleelaa..gleerveftGfved..laellaa 72 
                                       ++l vGrl+e+ kg+++ +ea+ +++k+ + v+ +ivGdgp  +  l++l++  ++e++v+++G ++d  l +++++
  gi|298676153|ref|YP_003727902.1| 232 KLLSVGRLVEK-KGHEYAIEAMYEVLKRyQnVEYLIVGDGPlYN-YLQKLISklNIENHVKLLGSIDDksLFQVYQK 306
                                       6899****665.**********888888636**********775.99998865899999*******5567******* PP

                                       -SEEEE--........---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
                   Glyco_trans_1_4  73 advfvaPs........egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLled 134
                                       +++fv+Ps        eg gl+l Ea a+glpv++t   gi+e v  g +g+lvp++d++ala++++ L+e+
  gi|298676153|ref|YP_003727902.1| 307 SHIFVFPSvtskegdkEGQGLVLQEAQAVGLPVISTFHNGIPEGVidGISGFLVPEKDVDALADKMEYLIEN 378
                                       **********9987777*******************999**9977799*********************986 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.0   8.1e-17   1.8e-13       5     168 ..      23     215 ..      22     217 .. 0.89
   2 ?    2.3   0.0     0.067   1.5e+02      94     108 ..     334     348 ..     325     383 .. 0.76

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 8.1e-17
                    Glyco_transf_4   5 erhvleLaraLarrGheVtvvtpgddgpleeev.....................................elvvrvp 44 
                                       e+++l+ + +L ++Gh+V +++++++ +   ++                                       v  ++
  gi|298676153|ref|YP_003727902.1|  23 ETFILNQITGLLDNGHDVKIFASSHPNENIVHEdikkynlmsrvhylnlpknfifrflkgitlivfnlykNPVLIIR 99 
                                       899******************98888887777789*******************************99998889999 PP

                    Glyco_transf_4  45 rvplpllkrllrslaflrrlrrllkrekpDvvHahspaalgaallalrr.rlgiplVltvHglyekrllkarlkpls 120
                                       + ++++++++ +sl +l    + l ++++D++H+h+ + ++++ ++l+    ++++++++Hg +       ++ p++
  gi|298676153|ref|YP_003727902.1| 100 SLNIFKFGKFALSLKMLYITINFLNKNEFDIIHCHFGPNGILG-VYLKEiGVNAKYITSFHGYD------VNKYPKK 169
                                       999999999******9999****************96666555.5666679*************......4444554 PP

                    Glyco_transf_4 121 rllralerrllrradrviavSeatadelrerygvppekitVipnGvDl 168
                                        +  +++++l+   d +++++e+t++++++ +g++++k++++p G ++
  gi|298676153|ref|YP_003727902.1| 170 -YGCNVYNKLFEEGDLFTVNTEYTKNQVKK-LGCNENKLVTLPVGLNI 215
                                       .4445688899*******************.************99875 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.067
                    Glyco_transf_4  94 rlgiplVltvHglye 108
                                       + g+p++ t+H+  +
  gi|298676153|ref|YP_003727902.1| 334 AVGLPVISTFHNGIP 348
                                       3699********997 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   1.0   9.8e-11   2.2e-07       1     118 [.      10     170 ..      10     189 .. 0.74

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 9.8e-11
                   Glyco_trans_4_2   1 killlanls....svhtlrlakeLakrgyeVhvitpkkgakdeleaegihvhrl.......kvd............. 53 
                                       ki++++n+     +++ l+ + +L ++g++V+++ +  +  ++ + e+i+ ++l       +++             
  gi|298676153|ref|YP_003727902.1|  10 KIAFIVNAFpklsETFILNQITGLLDNGHDVKIFASSHP-NENIVHEDIKKYNLmsrvhylNLPknfifrflkgitl 85 
                                       567777665555599********************9777.5556667777777755455553335577777777777 PP

                   Glyco_trans_4_2  54 ..................rkg.pley.lkafkl.kklikkikPDvvhahyakpygllgslaarlsgvipvvlsvwGl 109
                                                          k+ ++ + lk++ + ++ ++k+++D++h+h   p g+lg  ++ ++   ++++s++G 
  gi|298676153|ref|YP_003727902.1|  86 ivfnlyknpvliirslniFKFgKFALsLKMLYItINFLNKNEFDIIHCHF-GPNGILGVYLKEIGVNAKYITSFHGY 161
                                       777777777999766555444544442467888899*************9.6679********************** PP

                   Glyco_trans_4_2 110 dvlkfpkks 118
                                       dv k pkk 
  gi|298676153|ref|YP_003727902.1| 162 DVNKYPKKY 170
                                       **8888876 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   1.4e-09   3.1e-06       9      85 ..     323     401 ..     308     407 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.4e-09
                   Glyco_trans_1_2   9 espnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervlaehty 83 
                                       e+  l+l Ea a G +++++   g++e + +g +++l+   d++ la+k++yl++np +++ ++ ++r++v+++++ 
  gi|298676153|ref|YP_003727902.1| 323 EGQGLVLQEAQAVGLPVISTFHNGIPEGVIDGISGFLVPekDVDALADKMEYLIENPFLWSHMGYNGRKFVEKNYDI 399
                                       67788999************88****************************************************987 PP

                   Glyco_trans_1_2  84 dh 85 
                                       ++
  gi|298676153|ref|YP_003727902.1| 400 NK 401
                                       75 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   1.8e-05      0.04       8     160 .]      27     212 ..      22     212 .. 0.59
   2 ?    0.5   0.0      0.34   7.6e+02      88     107 ..     329     347 ..     323     376 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.8e-05
                   Glyco_trans_4_4   8 aelaraLaarGheVtvltpapapg...........apeleedgvrvhrlpvprr.....pspladlaal........ 60 
                                        + + +L + Gh+V +++++ +++                    rvh l +p +      ++ +    +        
  gi|298676153|ref|YP_003727902.1|  27 LNQITGLLDNGHDVKIFASSHPNEnivhedikkynL------MSRVHYLNLPKNfifrfLKGITL---Ivfnlyknp 94 
                                       556667778888888888655555454433322220......22333333332211000211111...111122222 PP

                   Glyco_trans_4_4  61 .........ralrrl.............lrqrrerpdvvhahsptaglaarlar.rrrgiplvvtlhglllrrgsga 114
                                                + +  +             l   +  +d++h+h  + g++++ ++  + +++++ ++hg +++++   
  gi|298676153|ref|YP_003727902.1|  95 vliirslniFKFGKFalslkmlyitinfL--NKNEFDIIHCHFGPNGILGVYLKeIGVNAKYITSFHGYDVNKY--- 166
                                       22222223322211122222222222225..7999********99*****99997788**********999888... PP

                   Glyco_trans_4_4 115 vrrlyralerrllrradavlvvseaeaeelralgvpadrvvvvpng 160
                                        + +   +   l+   d+++v++e+   ++  lg   +++v++p g
  gi|298676153|ref|YP_003727902.1| 167 PKKYGCNVYNKLFEEGDLFTVNTEYTKNQVKKLGCNENKLVTLPVG 212
                                       334455577899999*******************999999999987 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.34
                   Glyco_trans_4_4  88 arlarrrrgiplvvtlhgll 107
                                          a+ + g+p++ t+h+  
  gi|298676153|ref|YP_003727902.1| 329 LQEAQ-AVGLPVISTFHNGI 347
                                       44455.89*********743 PP

>> Glyco_transf_5  Starch synthase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   4.5e-05       0.1     100     171 ..     103     160 ..      31     201 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.5e-05
                    Glyco_transf_5 100 lYgdkgedyednaerfalfsraalellek.l.gwkpdvihahDWhtalvpallkelykerglfkkiktvftiHN 171
                                       ++         +  +fa +s  +l +  + l ++++d+ih+h    ++++++lke+        ++k++ + H 
  gi|298676153|ref|YP_003727902.1| 103 IF---------KFGKFA-LSLKMLYITINfLnKNEFDIIHCHFGPNGILGVYLKEIGV------NAKYITSFHG 160
                                       33.........223333.33333333333243347********************974......4888888875 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       1.8   4.1e+03      13      40 ..      11      40 ..       7      40 .. 0.74
   2 ?   10.6   0.0   8.1e-05      0.18      84     168 ..     225     312 ..     209     325 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.8
                                      EEEEETTSS-HHHH..HHHHHHHHHCT-SS CS
                         Trp_syntA 13 vpyvtagdpdleqs..leilkalekagadv 40
                                      +++++  +p+l ++  l+ +++l ++g dv
  gi|298676153|ref|YP_003727902.1| 11 IAFIVNAFPKLSETfiLNQITGLLDNGHDV 40
                                      889999999987762357788888888775 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 8.1e-05
                                       HCSSS-EEEEE-CHHHCCC-HHHHCHHHHHC.....TEEEEEETTSBCCCHHHHHHHHHHTT-E.EEEEE-TTS-HH CS
                         Trp_syntA  84 kevevPivlltylnlvlsygeerflaelkea.....gvdglivpDlPleeaeelveaakkkgle.lvflvapttsde 154
                                        +++ Pi ll+   lv ++g+e+ ++++ e+     +v+ liv D Pl   ++l+++++k ++e  v l+   ++d+
  gi|298676153|ref|YP_003727902.1| 225 YDSRKPIKLLSVGRLVEKKGHEYAIEAMYEVlkryqNVEYLIVGDGPLY--NYLQKLISKLNIEnHVKLLGS-IDDK 298
                                       56789***********999999866666554333348**********96..6899********835888776.9*** PP

                                       HHHHHHHH--S-EE CS
                         Trp_syntA 155 rlkevveqaegfvY 168
                                        l +v ++++ fv+
  gi|298676153|ref|YP_003727902.1| 299 SLFQVYQKSHIFVF 312
                                       **********9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.53
# Mc/sec: 2371.90
//
Query:       gi|298676154|ref|YP_003727903.1|  [L=483]
Description: multi antimicrobial extrusion protein MatE [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-19   70.3  17.4    1.5e-19   70.3  17.4    2.3  2  Polysacc_synt_3  Polysaccharide biosynthesis protein
    2.1e-18   66.7  26.8    2.1e-18   66.7  26.8    3.6  3  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
    2.5e-15   56.6  28.8    2.5e-15   56.6  28.8    2.5  3  Polysacc_synt    Polysaccharide biosynthesis protein
    7.3e-09   34.7  43.2    7.3e-09   34.7  43.2    2.9  2  MurJ             Lipid II flippase MurJ
    1.8e-08   34.2   2.1    1.8e-08   34.2   2.1    4.5  4  MatE             MatE


Domain annotation for each model (and alignments):
>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.3  17.4   4.2e-23   1.5e-19       7     283 ..      37     320 ..      31     324 .. 0.89
   2 ?   -1.6  11.2      0.33   1.2e+03      50     126 ..     365     433 ..     326     474 .. 0.50

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 4.2e-23
                   Polysacc_synt_3   7 spedFGvvaialvvislanlfvdmGlssal......iqkedlteedlstvftfnlvlgllialvlfllapliasfyn 77 
                                         +d+G+ a +++ ++l+  fv +Gl++a+      i+++++ +e + +   f l+++l i++++++++ +ias++ 
  gi|298676154|ref|YP_003727903.1|  37 PVQDYGIWAQIVITLGLVPEFVMLGLQRAMhrfvpsIKTKENLQELVYSFLIFVLFTSLTISILIYIFSGIIASALF 113
                                       579**************************8555555666666666677777888999*****************665 PP

                   Polysacc_synt_3  78 qpelvtvlrvlalvlilsglssvqeallrrelkFkklfkitlvssvvgvivaivlAllglgvwALvigtllssllsl 154
                                       ++++  ++++l++ +++++l++  ++++r   + k  ++ +++ + + +++ ++ +l   g+   + g l+ss l +
  gi|298676154|ref|YP_003727903.1| 114 DNQI-LIVKILSIIVLIESLNAFLKNYFRATQQVKIHSILQFTKTSLKIFFVVLFVLNNGGIIGAISGLLISSSLVF 189
                                       5443.489*****************************************************************9999 PP

                   Polysacc_synt_3 155 vllwlaskwrprlkf.slkslkelfsfglklllsnllnylarnldnlliGkvlssaaLGlYsvakrlaslpvaeits 230
                                        + +l++ +++++k+ s+ ++k+++++gl l+  +l ++++  +d  liG +l+++ +G+Y+ ++ l +++ +++  
  gi|298676154|ref|YP_003727903.1| 190 FITILTVIYQINIKIpSFINIKKYLKYGLPLIPGSLSKWIIDASDRYLIGFFLGTTFVGYYNPGYALGDIL-KIFFI 265
                                       9999999999999875899************************************************9986.55666 PP

                   Polysacc_synt_3 231 viakVlfPalSrlqddkk..klrelylkvlrlialivlPiavglavvaellvkvl 283
                                       +++ +l  +lS+  d+++  ++++l+  + +    +++P ++gl +++++++++l
  gi|298676154|ref|YP_003727903.1| 266 PLNFMLPMVLSKHYDEHEidEVKNLLSYTSKYFFAVTIPSVFGLSLLSKPILRIL 320
                                       8888888899999988744489999999999999*****************9987 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.33
                   Polysacc_synt_3  50 vftfnlvlgllialvlfllapliasfynqpelvtvlrvlalvlilsglssvqeallrrelkFkklfkitlvssvvgv 126
                                       ++++  +l l++ ++l+ l  +ia +        ++++l++++ l  +s  +  +l+ +++Fk + k  l+s+++++
  gi|298676154|ref|YP_003727903.1| 365 IWVIAAILNLVLNIILIPLIGIIAAA--------LTTLLSFTISLVIVSYYSLKILKFNMNFKFILKSILASIIMSL 433
                                       34444444444444444444444432........3333333333333333344444445555555555444444443 PP

>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   5.7       2.3   8.4e+03      93     136 ..      85     104 ..       6     118 .. 0.56
   2 !   14.2  11.6   9.7e-06     0.035       2      97 ..     120     216 ..     119     250 .. 0.81
   3 !   66.7  26.8     6e-22   2.1e-18       4     142 ..     335     465 ..     332     466 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.3
                   Polysacc_synt_C  93 kpllaalvmgivvylllllllgllllaalalllavlvgalvYll 136
                                         l++                        +l+ ++ + +l+Y++
  gi|298676154|ref|YP_003727903.1|  85 SFLIF------------------------VLFTSLTISILIYIF 104
                                       11111........................222222233333322 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 9.7e-06
                   Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllli.plfgivGaaiatvlallvvavlnlyal 77 
                                       + il++++++ sl+ +l +++ ++ ++ki  +  +    +k+ + +l++    gi+Ga+ + +++  +v+++ +  +
  gi|298676154|ref|YP_003727903.1| 120 VKILSIIVLIESLNAFLKNYFRATQQVKIHSILQFTKTSLKIFFVVLFVlNNGGIIGAISGLLISSSLVFFITILTV 196
                                       689**********************************************55668**********************9 PP

                   Polysacc_synt_C  78 rrllgikl.ellrrllkplla 97 
                                         +++ik+ + + ++ k+l  
  gi|298676154|ref|YP_003727903.1| 197 IYQINIKIpS-FINIKKYLKY 216
                                       999*999953.4444344433 PP

  == domain 3  score: 66.7 bits;  conditional E-value: 6e-22
                   Polysacc_synt_C   4 ilalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyalrrl 80 
                                       ++alsi++++ + ++  ++   +++ki +k+ vi+a+++l+ln++lipl+gi+ aa+ t+l++++++v+  y+  ++
  gi|298676154|ref|YP_003727903.1| 335 FVALSILLYGTFEIFKKVILLEKKTKIDAKIWVIAAILNLVLNIILIPLIGIIAAALTTLLSFTISLVIVSYYSLKI 411
                                       679************************************************************************** PP

                   Polysacc_synt_C  81 lgiklellrrllkpllaalvmgivvylllllllgllllaalalllavlvgalvYlllllllr 142
                                       l++++  ++ +lk +la+++m+++   ++ l+++ +l    +l++ ++v+a+ Y+++l+ll+
  gi|298676154|ref|YP_003727903.1| 412 LKFNM-NFKFILKSILASIIMSLL---IFILNPSGIL----NLIFTICVCAISYFVILILLN 465
                                       *****.6*****************...8888887665....99****************986 PP

>> Polysacc_synt  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6  28.8   6.9e-19   2.5e-15       5     261 ..      11     267 ..       7     274 .. 0.85
   2 ?   -1.0  23.6      0.26   9.5e+02      53     218 ..     268     439 ..     258     460 .. 0.76
   3 ?   -1.0   0.1      0.26   9.2e+02      77     107 ..     442     472 ..     438     475 .. 0.79

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 6.9e-19
                     Polysacc_synt   5 vivlllsqlitkllafvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrek...kelvslil 78 
                                       +    l +l++   +++ l++l+  ++  ++G+ a+++ +++l   ++ lGl  a  r++   ++k   +elv ++l
  gi|298676154|ref|YP_003727903.1|  11 IGLVGLTNLLVSFSGIILLPILTKNIPVQDYGIWAQIVITLGLVPEFVMLGLQRAMHRFVPSIKTKenlQELVYSFL 87 
                                       566678888889999**********************************************9999966777777776 PP

                     Polysacc_synt  79 lnvllv.llvlvllfllllliaa.flglpelavlylilalmllllvgvasfrrglfqglermkyaavsqvveqlsrv 153
                                       + vl++ l++++l+++++  ia  ++++++  +++ il++++l + + ++f  ++f++ +  k  ++ q+ +    +
  gi|298676154|ref|YP_003727903.1|  88 IFVLFTsLTISILIYIFSGIIASaLFDNQI--LIVKILSIIVL-IESLNAFLKNYFRATQQVKIHSILQFTKTSLKI 161
                                       666554145777777777777544444444..34555555555.99*************************999999 PP

                     Polysacc_synt 154 ilvliavflfldivaavlgavlaalvggivslavlrkkfrprfvilslklvrellsfsapltisslaillytyidsi 230
                                        +v+++v+  + i +a+ g+++++ +   +++++l++++  + +i+s  ++++ l++++pl+ +sl+  ++  +d++
  gi|298676154|ref|YP_003727903.1| 162 FFVVLFVLNNGGIIGAISGLLISSSLV--FFITILTVIYQINIKIPSFINIKKYLKYGLPLIPGSLSKWIIDASDRY 236
                                       999999999999**********99776..66666666699999999999**************************** PP

                     Polysacc_synt 231 llglllgaeavGiYnaayqllvaisgllapi 261
                                       l+g++lg++ vG+Yn +y l  ++ ++++p 
  gi|298676154|ref|YP_003727903.1| 237 LIGFFLGTTFVGYYNPGYALGDILKIFFIPL 267
                                       ***********************99999886 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.26
                     Polysacc_synt  53 dlGlnaalvreiakyrek..kelvslillnvllvllv.lvllfllllliaaflglpelavlylil....almllllv 122
                                       ++ l+  l+++ ++++ +  k+l s++ +  + v++  ++ l ll+ +i ++l+ p+ a+   i+    al++ll  
  gi|298676154|ref|YP_003727903.1| 268 NFMLPMVLSKHYDEHEIDevKNLLSYTSKYFFAVTIPsVFGLSLLSKPILRILSTPDIASQAYIItpfvALSILLYG 344
                                       666788899999999987654444444444444444434568899999999***99998765554222278888999 PP

                     Polysacc_synt 123 gvasfrrglfqglermkyaavsqvveqlsrvilvliavflfldivaavlgavlaalvggivslavlrkkfr..prfv 197
                                       ++ +f   ++ +++    a +++++  l  v l +i++ l++ i aa+l+++l+  +++++  +++ k+++   +f+
  gi|298676154|ref|YP_003727903.1| 345 TFEIFKKVILLEKKTKIDAKIWVIAAILNLV-LNIILIPLIG-IIAAALTTLLSFTISLVIVSYYSLKILKfnMNFK 419
                                       9999999999999999999999999999988.999*******.9999999999999999999999998996236666 PP

                     Polysacc_synt 198 ilslklvrellsfsapltiss 218
                                       ++ lk +  ++ +s+ ++i  
  gi|298676154|ref|YP_003727903.1| 420 FI-LKSILASIIMSLLIFILN 439
                                       66.99**99999999998854 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.26
                     Polysacc_synt  77 illnvllvllvlvllfllllliaaflglpel 107
                                       ++ln++++++v+++ ++++l +   ++++el
  gi|298676154|ref|YP_003727903.1| 442 GILNLIFTICVCAISYFVILILLNGFDKKEL 472
                                       6789999999999999999888777777666 PP

>> MurJ  Lipid II flippase MurJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.8  16.3       2.1   7.4e+03     125     301 ..       9     178 ..       6     183 .. 0.74
   2 !   34.7  43.2     2e-12   7.3e-09      50     431 ..      77     436 ..      68     465 .. 0.80

  Alignments for each domain:
  == domain 1  score: -4.8 bits;  conditional E-value: 2.1
                              MurJ 125 kkFfapafsPvllNvsvIltllllanklgeeail..aLaiGvliGgvlqllvqlpalkkaglllkprfafrdeglkk 199
                                       k+ ++++++ +l+++s I+ l +l +++   +++  +  i++++G+v ++++     +++ +  +  ++ ++e+l++
  gi|298676154|ref|YP_003727903.1|   9 KRIGLVGLTNLLVSFSGIILLPILTKNIP-VQDYgiWAQIVITLGLVPEFVMLGLQRAMHRFVPS--IK-TKENLQE 81 
                                       56678999*******************99.777755689**********9987777677766644..45.4566777 PP

                              MurJ 200 flklllptllgvs..vsqlnllvdtalAsflaegsvsilayadrilqlPlglfgvsistvlLPrlSrsakekdedev 274
                                       ++  +l  +l+ s  +s+l  + + ++As       ++  +  +i+++   +  +  ++++L +  r+ ++    ++
  gi|298676154|ref|YP_003727903.1|  82 LVYSFLIFVLFTSltISILIYIFSGIIAS-------ALFDNQILIVKILSIIVLIESLNAFLKNYFRATQQVKIHSI 151
                                       77777766665541245555666667777.......66777777777888888888888888888888888888888 PP

                              MurJ 275 rdllsqairltllllipvsfgllvlsk 301
                                        + +++++++ +++l+++  g ++ ++
  gi|298676154|ref|YP_003727903.1| 152 LQFTKTSLKIFFVVLFVLNNGGIIGAI 178
                                       888888888888888888777777765 PP

  == domain 2  score: 34.7 bits;  conditional E-value: 2e-12
                              MurJ  50 ekaaefvrkvltllilvlllvtligilaapllirllatgfdeetlelavsllrillpylllvslsavfgavLnarkk 126
                                       e+ +e+v ++l+++  + l + ++  +++ ++++ l   +        + +++il   +l+ sl a++     a ++
  gi|298676154|ref|YP_003727903.1|  77 ENLQELVYSFLIFVLFTSLTISILIYIFSGIIASALFDNQ--------ILIVKILSIIVLIESLNAFLKNYFRATQQ 145
                                       4667788888888888888888887888888877776666........78899999999999999999999999999 PP

                              MurJ 127 FfapafsPvllNvsvIltllllanklgeeailaLaiGvliGgvlqllvq.lpalkkaglllkprfafrdeglkkflk 202
                                         + ++ +       I++++l+  + g   i++   G+li   l + ++ l  ++++ ++  p       ++kk lk
  gi|298676154|ref|YP_003727903.1| 146 VKIHSILQFTKTSLKIFFVVLFVLNNG--GIIGAISGLLISSSLVFFITiLTVIYQINIKI-P----SFINIKKYLK 215
                                       888888887777677777777766666..46665556666654444444034445555553.3....3345999*** PP

                              MurJ 203 lllptllgvsvsqlnllvdtalAsflaegsvsilayadrilqlPlglfgvsistvlLPrlSrsakekdedevrdlls 279
                                         lp + g++++ + ++ d  l  f+  +++  +++    l   l +f + +  +l   lS++++e + dev++lls
  gi|298676154|ref|YP_003727903.1| 216 YGLPLIPGSLSKWIIDASDRYLIGFFLGTTFVGYYNPGYALGDILKIFFIPLNFMLPMVLSKHYDEHEIDEVKNLLS 292
                                       **************************************************988877779****************** PP

                              MurJ 280 qairltllllipvsfgllvlskpivsllferGnFseedveataevLaay.algLipyalvklllrvfYAredtktPv 355
                                        + +  ++++ip++fgl +lskpi+++l       + d++  a+++  + al+++ y  ++++++v   ++ tk  +
  gi|298676154|ref|YP_003727903.1| 293 YTSKYFFAVTIPSVFGLSLLSKPILRILS------TPDIASQAYIITPFvALSILLYGTFEIFKKVILLEKKTKIDA 363
                                       ***************************96......999********998789************************* PP

                              MurJ 356 kislislvlnillsllllpplgvvglalatslsaliglvllyvllrkrlklteargiktflaklvvllalaavvil 431
                                       ki +i+++ln++l+++l+p +g ++ al t ls++i+lv++ ++  k lk+     +k+ l++ +++ ++++  i 
  gi|298676154|ref|YP_003727903.1| 364 KIWVIAAILNLVLNIILIPLIGIIAAALTTLLSFTISLVIVSYYSLKILKF--NMNFKFILKS-ILASIIMSLLIF 436
                                       ****************************************99999998663..3333344444.222333333322 PP

>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1  10.0   6.3e-05      0.23      63     158 ..      74     163 ..      14     166 .. 0.79
   2 ?   -1.3   1.6      0.42   1.5e+03      77     124 ..     174     223 ..     167     270 .. 0.62
   3 !   34.2   2.1   5.1e-12   1.8e-08       1     161 []     219     379 ..     219     379 .. 0.94
   4 ?   -8.2  10.3         5   1.8e+04     117     133 ..     420     436 ..     380     465 .. 0.47

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.3e-05
                              MatE  63 knfkrakealrqglilllllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgag 139
                                       k +++++e ++  li++l+ sl i++l+++fs +i+s + +++    l+ ++l+i++l +   +l+  l++++r+++
  gi|298676154|ref|YP_003727903.1|  74 KTKENLQELVYSFLIFVLFTSLTISILIYIFSGIIASALFDNQI---LIVKILSIIVLIE---SLNAFLKNYFRATQ 144
                                       56789999*******************************99995...6667777777665...55588999999999 PP

                              MatE 140 ktkvplyislislllnipl 158
                                        +k+  ++ +  + l i +
  gi|298676154|ref|YP_003727903.1| 145 QVKIHSILQFTKTSLKIFF 163
                                       9999999988888888776 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.42
                              MatE  77 illlllsliiallvllfseqilslftqdee..vlelakrylrililgipa 124
                                       i++++ +l+i+  +++f+ ++  +++ + +      +k+yl++ ++ ip+
  gi|298676154|ref|YP_003727903.1| 174 IIGAISGLLISSSLVFFITILTVIYQINIKipSFINIKKYLKYGLPLIPG 223
                                       56666666666666666666555555554422222334444444444444 PP

  == domain 3  score: 34.2 bits;  conditional E-value: 5.1e-12
                              MatE   1 Pialenllesllslidtllvgrl.gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgl 76 
                                       P++  +l  +++ + d +l+g + g++ ++ ++ +  +  +l +f++ l+  l  + ++ + ++  +++k+ l ++ 
  gi|298676154|ref|YP_003727903.1| 219 PLIPGSLSKWIIDASDRYLIGFFlGTTFVGYYNPGYALGDILKIFFIPLNFMLPMVLSKHYDEHEIDEVKNLLSYTS 295
                                       6666777888899999999999999999999999999999999999999999************************* PP

                              MatE  77 illlllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislisll 153
                                       +  +++ ++ ++ + l+s++il+++ ++++++++a  + ++++l+i++++ +++++++    +ktk+ + i +i+++
  gi|298676154|ref|YP_003727903.1| 296 KYFFAVTIPSVFGLSLLSKPILRIL-STPDIASQAYIITPFVALSILLYGTFEIFKKVILLEKKTKIDAKIWVIAAI 371
                                       *************************.5666*********************************************** PP

                              MatE 154 lniplnyl 161
                                       ln++ln +
  gi|298676154|ref|YP_003727903.1| 372 LNLVLNII 379
                                       *****976 PP

  == domain 4  score: -8.2 bits;  conditional E-value: 5
                              MatE 117 ililgipalalqlvlsg 133
                                       +++ +i+a ++  +l  
  gi|298676154|ref|YP_003727903.1| 420 FILKSILASIIMSLLIF 436
                                       22222222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (483 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1318  (0.0735122); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.77u 0.36s 00:00:01.12 Elapsed: 00:00:00.52
# Mc/sec: 2793.48
//
Query:       gi|298676155|ref|YP_003727904.1|  [L=302]
Description: sulfotransferase domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-10   39.8   0.0    3.6e-08   34.1   0.0    2.8  1  Sulfotransfer_3  Sulfotransferase family
  ------ inclusion threshold ------
       0.02   13.4   0.0      0.029   12.9   0.0    1.1  1  Proteasom_PSMB   Proteasome non-ATPase 26S subunit


Domain annotation for each model (and alignments):
>> Sulfotransfer_3  Sulfotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0     4e-12   3.6e-08       2     215 ..      14     231 ..      14     233 .. 0.58

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 4e-12
                                       EEEE--TTSSHHHHHHHHHTSTTEE--S--.--TT.-SBH..................HHHHHHHTT.-S...TTTH CS
                   Sulfotransfer_3   2 ifivGlpRSGTTlLhrlLaahpdvripeetlfvaprllal..................leawskdgr.elrrlldag 59 
                                       i i+G  RSG+Tl+  +L++hp++++++e++++++++  +                   ++w+++ + + ++  ++ 
  gi|298676155|ref|YP_003727904.1|  14 IYILGSGRSGSTLIDIVLGNHPEIESKGELYDIIKKYENNelcscdtpsqicpfwidvINRWKEQTKiDDLAFYEN- 89 
                                       78******************************99988877666666666665554444222222211012221122. PP

                                       HHHHHHHHH.....T--HHHHHHHHHHHHHTT-B.HHHHHHHHHHHTTTSEEEE..EESSGGG-HHHHHHHBSSEEE CS
                   Sulfotransfer_3  60 ltqeeaelp.....hledaeepeedlqllraala.svilealarvpsyarwlvd..KsPshlfrldlllelfPdAkf 128
                                       l+++  +l+           ++++  ++ ++ +  ++++++   + s+++ +vd  K Ps + ++  +  +  d ++
  gi|298676155|ref|YP_003727904.1|  90 LQKKVESLKglsllL-----KNKNNSNINDYIFYtQALYHS-ISTVSGKNIIVDssKKPSRALAISMMPNV--DLCL 158
                                       333333333443321.....222222222222220222333.23336666677677887766655444444..6789 PP

                                       EEEE--H.HHHHHHHHHTT----------..-.HHHHHHHHHHHHHHHHHHHHHHS-TTSEEEEEHHHHHH-HHHHH CS
                   Sulfotransfer_3 129 ihlvRdpvdtvlssyvslfgkkresysedsld.eledaleewarayerllaararlppdrfldvrYedLvadpegtl 204
                                       ihlvRd++  ++s +++     ++s     l+ +l+++++    ++        +++ ++  ++rYed+v+ p++tl
  gi|298676155|ref|YP_003727904.1| 159 IHLVRDGRGVTYSGMKEG----KKS-----LRfPLGWMYNNLLSEIV-----FYTIG-SNKAQIRYEDFVNYPVKTL 220
                                       *******77777766655....233.....33345533333333332.....23354.56789************** PP

                                       HHHHHHHT--- CS
                   Sulfotransfer_3 205 rriyeflglpw 215
                                       + i e  g+ +
  gi|298676155|ref|YP_003727904.1| 221 KLIGEVAGINL 231
                                       ***99999876 PP

>> Proteasom_PSMB  Proteasome non-ATPase 26S subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.2e-06     0.029     350     402 ..      93     145 ..      81     152 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.2e-06
                    Proteasom_PSMB 350 kkrlLdalsslfelkteqateelleiaeswYellaekalenvildivkkPFpe 402
                                       k+ +L+ ls+l+++k +++ ++ +  ++ +Y++++    +n+i+d +kkP   
  gi|298676155|ref|YP_003727904.1|  93 KVESLKGLSLLLKNKNNSNINDYIFYTQALYHSISTVSGKNIIVDSSKKPSRA 145
                                       7789**********************************************665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1980.92
//
Query:       gi|298676156|ref|YP_003727905.1|  [L=246]
Description: nucleotidyl transferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.7e-43  146.7   0.0    9.8e-43  146.5   0.0    1.0  1  NTP_transferase  Nucleotidyl transferase
    4.3e-15   56.4   0.0    5.6e-15   56.1   0.0    1.1  1  NTP_transf_3     MobA-like NTP transferase domain
    9.9e-08   32.0   0.1    5.8e-07   29.5   0.1    2.1  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
     0.0037   17.1   0.2     0.0062   16.4   0.2    1.4  1  Glycos_transf_2  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.5   0.0   2.2e-46   9.8e-43       1     247 [.       2     239 ..       2     240 .. 0.92

  Alignments for each domain:
  == domain 1  score: 146.5 bits;  conditional E-value: 2.2e-46
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEE CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevli 77 
                                       k++I a GsGtRL P t++++k l+pv++k  +i+++++  +++gi++ i+++ + +++ + +++++g++fgv++++
  gi|298676156|ref|YP_003727905.1|   2 KGLIPAAGSGTRLGPFTHAMPKELLPVGDK-AVIEHVVESFVKAGIDD-IIIVVSPNKHGLSDYFGSGERFGVDITY 76 
                                       57899*************************.*****************.777777999******************* PP

                                       EEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEEC CS
                   NTP_transferase  78 alepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGviead 154
                                       ++++ + g+A+Ava ++ +++ +     ++vLg++ +  d++ + +k++ e+++  ++t+g+++v + t+ G+i++d
  gi|298676156|ref|YP_003727905.1|  77 VVQDDRLGLANAVAAGEHVVNGSPV---AVVLGDNFFSPDTILQDLKQFHEDNN-ADATVGVMEVLDVTRHGIIQTD 149
                                       *********************9995...***********966666666555555.49******************** PP

                                       TTSBEEEEECS-SSHSH.CSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EE CS
                   NTP_transferase 155 eegrverfvEKPkeaka.selassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWs 230
                                       ++ ++ +++EKP+  +a s+l  +G Yvf++e+++ + +d ++  + e ++td ++ ++e+gk+ ++    +     
  gi|298676156|ref|YP_003727905.1| 150 GN-NIVDLIEKPEVGEApSKLGIAGMYVFEPEIFDAI-SDTKPGYKDEYQLTDSIKVMVEQGKNVVYREIGGI--HI 222
                                       95.899*******99986888899*************.67**************************9888885..5* PP

                                       EXSSHHHHHHHHHHHHH CS
                   NTP_transferase 231 DvGtldslleaneklae 247
                                       DvGt+++l++ane +++
  gi|298676156|ref|YP_003727905.1| 223 DVGTPEDLMKANEYYLK 239
                                       ************98765 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1   0.0   1.2e-18   5.6e-15       2     121 ..       4     133 ..       3     146 .. 0.80

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 1.2e-18
                                       EEEEESS-TTTT..T...THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHH...TTCTS-E..EE-T CS
                      NTP_transf_3   2 viLAGGrSsRmg..g...dKallplggkpllervldalraagvdevvvvggd..eevlaal...arlgvrv..vede 66 
                                       +i A+G ++R+g  +   +K llp+g+k ++e+v++++ +ag+d++++v+ +  + + +++   +r+gv++  v+++
  gi|298676156|ref|YP_003727905.1|   4 LIPAAGSGTRLGpfThamPKELLPVGDKAVIEHVVESFVKAGIDDIIIVVSPnkHGLSDYFgsgERFGVDItyVVQD 80 
                                       677*********651578*****************************998773344444334446667665115554 PP

                                       TSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEE CS
                      NTP_transf_3  67 dpgkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvp 121
                                           g + ++aa+ + + + ++v+v+++D  + +  +++ l + +++++ad++v 
  gi|298676156|ref|YP_003727905.1|  81 -DRLGLANAVAAGEHVV-NGSPVAVVLGDNFFSPDTILQDLKQFHEDNNADATVG 133
                                       .479**********998.8***********9888888888888888888888775 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.1   1.3e-10   5.8e-07       4     100 ..       4     108 ..       1     240 [. 0.56

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 1.3e-10
                                       EEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGG....CCEEEEE- CS
                              IspD   4 vipAAGsGkRmk...aglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllld....ksiqlvaG 73 
                                       +ipAAGsG+R++     +pK +l + +++++eh v+++ +   +d i++vvs+++ +    + +      +i+ v+ 
  gi|298676156|ref|YP_003727905.1|   4 LIPAAGSGTRLGpftHAMPKELLPVGDKAVIEHVVESFVK-AGIDDIIIVVSPNKHGLSDYFGSGerfgVDITYVVQ 79 
                                       8*********96443789********************99.88**********997666555554566545665555 PP

                                       -SSH..HHHHHHHHHTTSSTTSEEEE--T CS
                              IspD  74 GdeR..aesVlnglkalegeakfVLvHDa 100
                                        d    a++V +g ++++g+   V++ D 
  gi|298676156|ref|YP_003727905.1|  80 DDRLglANAVAAGEHVVNGSPVAVVLGDN 108
                                       44323367777777777777655555443 PP

>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.2   1.4e-06    0.0062      27     133 ..      45     163 ..      30     216 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.4e-06
                                       CEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SSEEEEEESSEEE-TT.HHHHHHH CS
                   Glycos_transf_2  27 pdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgdyilflDaDdepdpd.wleklve 102
                                         ++ii+v    + ++ +   +  + + +++++ ++ + G+a+a+ ag   ++g  ++++  D  ++pd  l++l +
  gi|298676156|ref|YP_003727905.1|  45 GIDDIIIVVSPNKHGLSDYFGSGERFGVDITYVVQDDRLGLANAVAAGEHVVNGSPVAVVLGDNFFSPDtILQDLKQ 121
                                       55556666666666666666666667889**************************999999********88899999 PP

                                       HHHH.TTCEEEEEEEEEECCCCCCCHC-SS...........E CS
                   Glycos_transf_2 103 alekdgadvvlgqrprifgetdeiernkrv...........g 133
                                       + e+++ad+ +g   + ++ ++ i ++ ++           g
  gi|298676156|ref|YP_003727905.1| 122 FHEDNNADATVGVMEVLDVTRHGIIQTDGNnivdliekpevG 163
                                       999999999999988888877777777665555555555550 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1638.37
//
Query:       gi|298676157|ref|YP_003727906.1|  [L=186]
Description: hypothetical protein Metev_2294 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.018   15.6   0.0      0.069   13.7   0.0    1.8  1  DUF2408   Protein of unknown function (DUF2408)


Domain annotation for each model (and alignments):
>> DUF2408  Protein of unknown function (DUF2408)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.8e-06     0.069      39     120 ..      71     180 ..       6     185 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.8e-06
                           DUF2408  39 e......................vkeelkelkeeLkkieskrde....egkFkseegke......vvekgqavlngL 83 
                                                               + e +++k++L++i++  d+     + F  e++++       v +++  ++  
  gi|298676157|ref|YP_003727906.1|  71 MeiglteenkeiitsdvgeirifYDPETDSWKKDLHDIQKALDSikplGNDFWDEKTDDngditePVIENKGSVEFV 147
                                       05555555555666666677777444555556666666665555555533354444433445555777889999*** PP

                           DUF2408  84 lddcfdlvedlkaqdgeekkvasslqpiYdrLleikt 120
                                       +ddc + + d++++    ++ ++ ++ i++ L ++k 
  gi|298676157|ref|YP_003727906.1| 148 YDDCDECCLDVEQR----RRAEEFFNAIFRYLWDLKD 180
                                       ************99....4789999*******99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1177.56
//
Query:       gi|298676158|ref|YP_003727907.1|  [L=396]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.4e-22   77.6   0.0    1.7e-21   76.6   0.0    1.5  1  OrfB_IS605      Probable transposase
      8e-12   44.9   0.0    1.7e-11   43.9   0.0    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0001   21.7   0.1    0.00018   20.9   0.1    1.4  1  Glyco_hydro_97  Glycoside hydrolase 97
  ------ inclusion threshold ------
      0.067   12.5   0.0       0.11   11.7   0.0    1.4  1  EAP30           EAP30/Vps36 family
       0.15   12.4   0.0        0.3   11.5   0.0    1.5  1  RuvX            Holliday junction resolvase
       0.16   12.4   1.7       0.23   11.8   0.7    1.8  2  HEPN_Swt1       Swt1-like HEPN


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.6   0.0   5.8e-25   1.7e-21       2     117 ..     164     278 ..     163     281 .. 0.97

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 5.8e-25
                        OrfB_IS605   2 ipvevevelpkpkgnkaagiDlGinnLatvvtedgtw.flykgrrlksdykylakeiaelqsklkksknykkasrkl 77 
                                       i++e + e+p  ++++ a+iDlGinn++t+v++ g+  +++kg  +ks ++ ++k+  +l s+++k +   k s+kl
  gi|298676158|ref|YP_003727907.1| 164 IVYEKDLETPDLNEENIASIDLGINNIVTMVNNIGEKpIVIKGGVAKSINQFYNKKSGKLKSIYDKLG--IKNSKKL 238
                                       78999999****************************99*****************************9..9****** PP

                        OrfB_IS605  78 arlhrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       ++l++k + ++++++hk+++++++ + + +++tL++g+  
  gi|298676158|ref|YP_003727907.1| 239 KKLYHKYKMKINDFFHKASKRIVDFCVKHNIGTLVIGYNE 278
                                       *************************************986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   5.6e-15   1.7e-11       1      69 []     299     373 ..     299     373 .. 0.93

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 5.6e-15
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke......alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f++l eql+yka++ G kv+e +++yTSk +   g+ +++      ++ +r +  ++ g+ +++Dvn+a+Ni+k+
  gi|298676158|ref|YP_003727907.1| 299 FHRLLEQLKYKAEDVGLKVIEQEESYTSKCSFLDGEPVERrtsylgKRIKRGLFQSSNGTIINADVNGAYNIMKK 373
                                       899**************************999******999****9777777777779***************96 PP

>> Glyco_hydro_97  Glycoside hydrolase 97
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1     6e-08   0.00018      34     106 ..     254     325 ..     215     348 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 6e-08
                    Glyco_hydro_97  34 tetvkryiDfAaengleyvlvegwdegWee..kkkkekefdftkpypdfdleelvaYakekgvgvelwlhsetsg 106
                                        +  kr +Df+ ++++ ++++ g++egW++  ++ k ++++ ++++p  +l e ++Y k+ +vg++++ ++e ++
  gi|298676158|ref|YP_003727907.1| 254 HKASKRIVDFCVKHNIGTLVI-GYNEGWKQevDMGK-RNNQKFTQIPFHRLLEQLKY-KAEDVGLKVIEQEESYT 325
                                       56789****************.*******9865554.45555667788888888888.44566788887777655 PP

>> EAP30  EAP30/Vps36 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.8e-05      0.11      63     124 ..     223     281 ..     207     351 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.8e-05
                             EAP30  63 ftkmcaslGvdplsskkseslgfl...ellglgdfyyeLavqivevclatraengglisleelya 124
                                        +++ ++lG+     k+s++l++l     ++++df+ + +++iv++c + +     +i   e ++
  gi|298676158|ref|YP_003727907.1| 223 LKSIYDKLGI-----KNSKKLKKLyhkYKMKINDFFHKASKRIVDFCVKHN-IGTLVIGYNEGWK 281
                                       4458899999.....3344555666666777****************9543.2225555555555 PP

>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0    0.0001       0.3      14     100 ..     231     327 ..     227     340 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0001
                                       EEEEE-S--SS---EEEEE---HHHHHHHHHHHHHHTT--EEEEE--......----SSS---SSTT..HHHHHHHH CS
                              RuvX  14 GvAvsdplgilaspletierkskekdleelkelvkeeeveeiVvGlP......lnldgsegesakkv..rkfaeeLa 82 
                                       G+  s++l++l +++++  ++  +k+ +++ +++ ++++ ++V+G+       +++ ++++++  ++  +++ e+L+
  gi|298676158|ref|YP_003727907.1| 231 GIKNSKKLKKLYHKYKMKINDFFHKASKRIVDFCVKHNIGTLVIGYNegwkqeVDMGKRNNQKFTQIpfHRLLEQLK 307
                                       555666666666666666666568999********************999888555444444444433488888888 PP

                                       HT....T-EEEEE--S---- CS
                              RuvX  83 krl..kklpvelvDErlttv 100
                                        +    +l+v+  +E++t++
  gi|298676158|ref|YP_003727907.1| 308 YKAedVGLKVIEQEESYTSK 327
                                       887444569*********98 PP

>> HEPN_Swt1  Swt1-like HEPN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.7   7.8e-05      0.23      10      70 ..      26      85 ..      18      97 .. 0.67
   2 ?   -2.8   0.0       2.6   7.6e+03      41      64 ..     287     310 ..     269     327 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.8e-05
                         HEPN_Swt1 10 Lrpfverelskayged.wweeveaslekdeeekkesekeiskldvqdllrvitenWkevFkk 70
                                      L++  + +++++++++  w ++e+ l +++ ++ e+ + +  +++q+ l+++++nWk++F++
  gi|298676158|ref|YP_003727907.1| 26 LYNQANFIVKQSLNDEgGWVRYEE-L-NKQLKGTENYSVLPTQTAQQTLKLMDKNWKSFFQS 85
                                      555555566666666664444444.2.444444455666677889999**********7775 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.6
                         HEPN_Swt1  41 kkesekeiskldvqdllrvitenW 64 
                                       +k+++++  ++ +++ll+ ++ + 
  gi|298676158|ref|YP_003727907.1| 287 GKRNNQKFTQIPFHRLLEQLKYKA 310
                                       334455566666666666555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1103  (0.0615204); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.60u 0.25s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 2687.01
//
Query:       gi|298676159|ref|YP_003727908.1|  [L=373]
Description: restriction endonuclease [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.9e-27   93.4   0.1    6.4e-25   87.4   0.2    2.4  2  Mrr_cat        Restriction endonuclease
    1.1e-06   28.6   0.3    1.1e-06   28.6   0.3    2.0  3  Mrr_cat_2      Restriction endonuclease
    0.00015   21.7   0.8        0.5   10.4   0.1    3.5  3  CARD           Caspase recruitment domain
     0.0049   16.5   0.8     0.0093   15.6   0.4    1.7  2  FAD_binding_1  FAD binding domain
  ------ inclusion threshold ------
       0.17   11.8   3.5       0.47   10.4   1.0    2.6  2  Ferritin       Ferritin-like domain
        0.2   12.4   0.1         63    4.7   0.0    3.2  3  HEAT_PBS       PBS lyase HEAT-like repeat


Domain annotation for each model (and alignments):
>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.023        69      48      77 ..      51      82 ..      35      95 .. 0.79
   2 !   87.4   0.2   2.1e-28   6.4e-25       2     115 .]     251     362 ..     250     362 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.023
                                      EEEEEEEE--..TS-B-HHHHHHHHHHCTTS. CS
                           Mrr_cat 48 erilvqaKry..knkvgvkeVqeligalkkrg 77
                                      e  ++q+K    +++ +++ ++e+++ l+++ 
  gi|298676159|ref|YP_003727908.1| 51 EPAVIQVKEEirNDENSEELIREFLSILENND 82
                                      689*******8447899999*****9999874 PP

  == domain 2  score: 87.4 bits;  conditional E-value: 2.1e-28
                                       TTT-TTCHHHHHHHHHHHHSSSEEE---B-T..TSSB--EEEETTEEEEEEEEEEE--TS-B-HHHHHHHHHHCTTS CS
                           Mrr_cat   2 dkmspkeFeklvaellealGykeveltgrsg..DggiDliakkdplgserilvqaKryknkvgvkeVqeligalkkr 76 
                                       dk++pke+e+ v ++++ +Gy    +t++++  D+g+D+i++k  lgs+ri+vq+K++++kvg  +Vqe+++++ ++
  gi|298676159|ref|YP_003727908.1| 251 DKLTPKELEQAVCKIYRDKGYY-ASRTKKTNdkDQGADVILTK--LGSKRIAVQVKQSSSKVGNSAVQEVVASMRYY 324
                                       689******************9.7777776633789*****98..999***************************** PP

                                       ..SEEEEEESS-B-HHHHHHHHTT--EEEE-HHHHHHHH CS
                           Mrr_cat  77 gadkgifvttsdftkaAreeaeelnkieLldgdeLaell 115
                                        ++ +++vt++++t++A + a++ n ++L++++eL +l+
  gi|298676159|ref|YP_003727908.1| 325 LCNSAMVVTNNYYTSEAVDLAKA-NDVKLINREELRNLI 362
                                       ***********************.***********9985 PP

>> Mrr_cat_2  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.89   2.6e+03      46      84 ..      54     111 ..      46     127 .. 0.62
   2 ?   -3.4   0.1       2.8   8.4e+03       3      23 ..     182     202 ..     180     210 .. 0.75
   3 !   28.6   0.3   3.6e-10   1.1e-06      22     124 ..     274     372 ..     253     373 .] 0.81

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.89
                         Mrr_cat_2  46 AIQcKfYaedekiqkedidsFlsasgkk...................kftkrliisTt 84 
                                        IQ+K    + + ++e i++Fls+ +++                   ++ +r+ i T 
  gi|298676159|ref|YP_003727908.1|  54 VIQVKEEIRNDENSEELIREFLSILENNdsavpfvlhelrnklprpeTIHHRIKIFTY 111
                                       5777766666666677788888877776555555555555555555555555555555 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.8
                         Mrr_cat_2   3 dpayaeefkeVwlwkewpeek 23 
                                       dp+ +e +++  + ++++++ 
  gi|298676159|ref|YP_003727908.1| 182 DPETRELLEDMLKDEDFEDRL 202
                                       899999999999999998873 PP

  == domain 3  score: 28.6 bits;  conditional E-value: 3.6e-10
                         Mrr_cat_2  22 e..krlgkkDtGIDlVakerkegeywAIQcKfYaedekiqkedidsFlsasgkkkftkrliisTtdkwsknaeealk 96 
                                       +  k+++ kD+G D++ ++   ++ +A+Q+K  ++++k+ ++ +++ +++  +    ++ +++T +  +++a +  k
  gi|298676159|ref|YP_003727908.1| 274 SrtKKTNDKDQGADVILTK-LGSKRIAVQVK--QSSSKVGNSAVQEVVAS-MRYYLCNSAMVVTNNYYTSEAVDLAK 346
                                       3347889**********99.889999*****..899**********7765.566677777777***********955 PP

                         Mrr_cat_2  97 nqkipvkridledLeeseidwsklslgk 124
                                       +   +vk+i+ e+L+++ i  +kl++++
  gi|298676159|ref|YP_003727908.1| 347 A--NDVKLINREELRNLIISHHKLFKKE 372
                                       5..56**************999998876 PP

>> CARD  Caspase recruitment domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.011        32      57      78 ..      19      40 ..      16      43 .. 0.89
   2 ?    3.1   0.1     0.033        99      36      67 ..      58      88 ..      39      99 .. 0.75
   3 !   10.4   0.1   0.00017       0.5      30      83 ..     129     190 ..     113     192 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.011
                                      HTSCHHHHHHHHHHHHHHSHHH CS
                              CARD 57 qkkgekacqaflealkegqpdl 78
                                       ++geka + ++++lke++p +
  gi|298676159|ref|YP_003727908.1| 19 VNHGEKAVEPLINCLKETYPNS 40
                                      579***************9975 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.033
                                      HHHHHTSSSHHHHHHHHHHHHHTSCHHHHHHH CS
                              CARD 36 eekikakttrlskareLldlvqkkgekacqaf 67
                                       e+i+++ ++++  re+l++++  ++ a    
  gi|298676159|ref|YP_003727908.1| 58 KEEIRNDENSEELIREFLSILE-NNDSAVPFV 88
                                      478******************9.555555555 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00017
                                       SS-HHHHHHHHTSSS.......HHHHHHHHHHHHHTSCHHHHHHHHHHHHH.HSHHHHHHHH CS
                              CARD  30 VLteeeeekikaktt.......rlskareLldlvqkkgekacqaflealke.gqpdlaslle 83 
                                        L  ee e+ik+++t       +++  + L+++ q+  ++a + +++al e ++p+  +lle
  gi|298676159|ref|YP_003727908.1| 129 YLRHEEREMIKELSTlvyfresVEDEREILIEIFQELEPEAIDPIINALNEnWDPETRELLE 190
                                       57778888888877777777779999999**********************9***9999887 PP

>> FAD_binding_1  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.4   3.1e-06    0.0093      53     161 ..      65     164 ..      63     180 .. 0.84
   2 ?   -1.9   0.0       0.7   2.1e+03     125     146 ..     182     204 ..     156     214 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.1e-06
                                       ---HHHHHHHHHHHT--T..T-EEEEEESSTT..S--SSSSSEEHHHHHHHTB--SS---HHHHHHHGGG-SSHHHH CS
                     FAD_binding_1  53 sNneelVeellellgldpkadevvelkaldeesaekeprleptTlrqalkyylditgppskqlleaLaefaseeeek 129
                                       +N+eel+ e+l++l+ ++    ++ l++l     +k pr+e++  r  +  y  i++  sk   + ++ +    ee+
  gi|298676159|ref|YP_003727908.1|  65 ENSEELIREFLSILENND-SAVPFVLHELR----NKLPRPETIHHRIKIFTYKSILNRHSKYTANLIIDYLRH-EER 135
                                       69***************9.88899999999....489999999999999999******************876.578 PP

                                       HHHHHHHH-HHHHHTTTTT--HHHHHHHHHTT CS
                     FAD_binding_1 130 qkLekLssdegakeykelklneartllevlee 161
                                       + ++ Ls+      + e + +e++ l+e+++e
  gi|298676159|ref|YP_003727908.1| 136 EMIKELSTL---VYFRESVEDEREILIEIFQE 164
                                       999999995...55555555556777777665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.7
                                       SHHHHHHHHHHHH-.HHHHHTTT CS
                     FAD_binding_1 125 eeeekqkLekLssd.egakeyke 146
                                       ++e+++ Le++ +d  ++++++e
  gi|298676159|ref|YP_003727908.1| 182 DPETRELLEDMLKDeDFEDRLQE 204
                                       78899999999998666666655 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.31   9.1e+02     113     134 ..     121     143 ..     112     149 .. 0.68
   2 ?   10.4   1.0   0.00016      0.47      97     139 ..     168     209 ..     154     212 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.31
                                       HHHHHHHHHHHH.HHHHHHHHHH CS
                          Ferritin 113 atadfledflee.qeehewelea 134
                                        ta+++ d+l+  + e ++el++
  gi|298676159|ref|YP_003727908.1| 121 YTANLIIDYLRHeEREMIKELST 143
                                       58888888887624444555554 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00016
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin  97 eslrelielaeeegDpatadfledfleeqeeheweleallekl 139
                                       e++  +i+  +e+ Dp t+++led+l++ e+ e+ l+++l+++
  gi|298676159|ref|YP_003727908.1| 168 EAIDPIINALNENWDPETRELLEDMLKD-EDFEDRLQEYLKET 209
                                       568889999*******************.8999******9876 PP

>> HEAT_PBS  PBS lyase HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.033        99      15      26 ..      23      34 ..      13      35 .. 0.79
   2 ?   -3.1   0.0         6   1.8e+04       9      19 ..      46      56 ..      45      57 .. 0.83
   3 ?    4.7   0.0     0.021        63      15      26 ..     167     178 ..     147     179 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.033
                                      GGGHHHHHHHCT CS
                          HEAT_PBS 15 eeaipaLleaLq 26
                                      e a+++L+++L+
  gi|298676159|ref|YP_003727908.1| 23 EKAVEPLINCLK 34
                                      59*********8 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6
                                      HHHCTSGGGHH CS
                          HEAT_PBS  9 Lgqlgdeeaip 19
                                      L+ ++ +++i+
  gi|298676159|ref|YP_003727908.1| 46 LADIREPAVIQ 56
                                      89999999987 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.021
                                       GGGHHHHHHHCT CS
                          HEAT_PBS  15 eeaipaLleaLq 26 
                                       +eai+++++aL+
  gi|298676159|ref|YP_003727908.1| 167 PEAIDPIINALN 178
                                       8*********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1052  (0.0586759); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 2198.94
//
Query:       gi|298676160|ref|YP_003727909.1|  [L=243]
Description: restriction endonuclease [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.9e-23   82.7   0.2    3.7e-23   81.7   0.2    1.5  1  Mrr_cat    Restriction endonuclease
    5.6e-06   26.3   0.4    1.2e-05   25.2   0.2    1.7  1  Mrr_cat_2  Restriction endonuclease
  ------ inclusion threshold ------
      0.019   15.2   1.3       0.48   10.7   0.1    2.9  2  BTB        BTB/POZ domain
      0.081   12.4   1.1       0.11   11.9   1.1    1.3  1  HECT       HECT-domain (ubiquitin-transferase)


Domain annotation for each model (and alignments):
>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.7   0.2   8.3e-27   3.7e-23       1     114 [.     130     240 ..     130     241 .. 0.93

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 8.3e-27
                                       HTTT-TTCHHHHHHHHHHHHSSSEEE---B-TTSSB--EEEETTEEEEEEEEEEE--T..S-B-HHHHHHHHHHCTT CS
                           Mrr_cat   1 ldkmspkeFeklvaellealGykeveltgrsgDggiDliakkdplgserilvqaKryk..nkvgvkeVqeligalkk 75 
                                       ld+ms+keFe++++++++ +Gy  ve+tg  +D g+D+++++ +   er++v +K+ +  +kv +++Vqe+++a  +
  gi|298676160|ref|YP_003727909.1| 130 LDEMSWKEFEDFIESMYRDKGYL-VERTG-IKDMGADFVITEYG--VERTAVLIKHLNpgQKVTRNAVQEIVAAKSY 202
                                       689*******************9.****8.9**********965..678888888885549**************** PP

                                       S..SEEEEEESS-B-HHHHHHHHTT--EEEE-HHHHHHH CS
                           Mrr_cat  76 rgadkgifvttsdftkaAreeaeelnkieLldgdeLael 114
                                       ++++ +i+v+++dft++A + ae+ n++ L+++++L e+
  gi|298676160|ref|YP_003727909.1| 203 YHCNSAIVVSNQDFTQKAVKLAES-NNVSLINREQLEEM 240
                                       ************************.***********998 PP

>> Mrr_cat_2  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.2   2.8e-09   1.2e-05      23     113 ..     154     240 ..     131     242 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.8e-09
                         Mrr_cat_2  23 krlgkkDtGIDlVakerkegeywAIQcKfYaedekiqkedidsFlsasgkkkftkrliisTtdkwsknaeealknqk 99 
                                       +r+g kD+G D V++e    e +A+  K  ++ +k++++ +++ ++a++  +   ++++s  d ++++a +   +++
  gi|298676160|ref|YP_003727909.1| 154 ERTGIKDMGADFVITE-YGVERTAVLIKHLNPGQKVTRNAVQEIVAAKSYYHCNSAIVVSNQD-FTQKAVKL--AES 226
                                       567889**********.888999**************************99999999997776.99999999..677 PP

                         Mrr_cat_2 100 ipvkridledLees 113
                                        +v++i+ e+Lee 
  gi|298676160|ref|YP_003727909.1| 227 NNVSLINREQLEEM 240
                                       79*******99985 PP

>> BTB  BTB/POZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1     0.065   2.9e+02      63     102 ..      13      51 ..       5      65 .. 0.59
   2 ?   10.7   0.1   0.00011      0.48      47      78 ..     121     152 ..     108     220 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.065
                                       HHHHHHHHHHHSEEEC-CGGGHHHHHHHHHHHT-HHHHHH CS
                               BTB  63 afealLefiYtgeleitseenleelLaaadllqiprlkka 102
                                       a+e++Le++ +     t ++++e+ L   ++l  + ++++
  gi|298676160|ref|YP_003727909.1|  13 AVESMLEVMLSTDSHCT-KKEIEDCLIRMEHLAADTIIEH 51 
                                       55566666655555554.5556655555555555555444 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00011
                                       TTCCCEEEEETTSGHHHHHHHHHHHHHSEEEC CS
                               BTB  47 eessvseielddvepeafealLefiYtgelei 78 
                                       + +s+++ +ld+++ ++fe ++e +Y+++  +
  gi|298676160|ref|YP_003727909.1| 121 TGNSQQNNNLDEMSWKEFEDFIESMYRDKGYL 152
                                       3445556789*****************98765 PP

>> HECT  HECT-domain (ubiquitin-transferase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.1   2.5e-05      0.11      73     187 ..     131     241 ..      88     242 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.5e-05
                                       .---TCHHHHH-HHHHHHHHHHH..HS-GGG...GT-BSEEEEETTEEEEEESSTT.GGGSB--TTTHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                              HECT  73 ekitledleeidpelakslkellslesnteevedlaLtFtipenagasatieLipn.GanipVtnenkkeYiklyvn 148
                                       ++++++++e++ +++++   +l     + + ++d++ +F+i+e +g ++t  Li+      +Vt + ++e + +   
  gi|298676160|ref|YP_003727909.1| 131 DEMSWKEFEDFIESMYRDKGYLV----ERTGIKDMGADFVITE-YGVERTAVLIKHlNPGQKVTRNAVQEIVAAKSY 202
                                       34556667777777777777776....333499*******997.588887888888555578*************** PP

                                       HHHTGGGHHHHHHHHHHHHTTS-HHHHTTS-HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              HECT 149 yllkksvekqleaflkGfsevipskalklfdaeelelli 187
                                       y+ +  +    + f++   ++ +s+ ++l++ e+le+++
  gi|298676160|ref|YP_003727909.1| 203 YHCNSAIVVSNQDFTQKAVKLAESNNVSLINREQLEEMV 241
                                       ************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1628  (0.0908026); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 1626.36
//
Query:       gi|298676161|ref|YP_003727910.1|  [L=110]
Description: hypothetical protein Metev_2299 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.8e-11   43.3   0.0    4.2e-11   43.2   0.0    1.0  1  PemK_toxin  PemK-like, MazF-like toxin of type II toxin-antit
  ------ inclusion threshold ------
      0.046   13.6   0.0      0.053   13.4   0.0    1.2  1  FliW        FliW protein


Domain annotation for each model (and alignments):
>> PemK_toxin  PemK-like, MazF-like toxin of type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.0   4.7e-15   4.2e-11       2     110 ..       6     107 ..       5     108 .. 0.85

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 4.7e-15
                                       TTEEEEEEE-S--TTS--SEEEEEE-S-HHHHCHSEEEEEEEESSSTSSGCSTTEEEE-HHHCSS.SSSSSSEEEEC CS
                        PemK_toxin   2 rGeIvlvdldpsrgseqgkrRpvvVvsndafnekntvivvpltskdkdkkklpfhveleseildl.ngldkdswvkl 77 
                                       +G++v  ++ p +     k+Rp++V+ n +++    +i +++ts    k++  + ++l+ + + +   l+k+s ++ 
  gi|298676161|ref|YP_003727910.1|   6 KGDVVVLPF-PFSDMSNSKKRPALVLANLQGE---DIILCMITSAV--KID-NYSITLNDN-DFEyGTLRKNSNIRP 74 
                                       69*******.95555558**********9877...7*********9..666.999999877.44434455******* PP

                                       CCEEEEEGGGEEEEEEE--HHHHHHHHHHHHHH CS
                        PemK_toxin  78 dqirtvdkarlrkkigklsredlaevqralakl 110
                                         i+t dk+ +  k+g l++++ +ev+++l  +
  gi|298676161|ref|YP_003727910.1|  75 NRIFTADKSLILYKVGYLKNDKTDEVEKKLVNI 107
                                       *********9999***************99765 PP

>> FliW  FliW protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     6e-06     0.053      21      80 ..      21      80 ..      14     100 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6e-06
                                      .STTS-EEEEEESS-TT-EEEEE-GGGT-TT------HHHHHHTT--SGGGEEEEEEEE- CS
                              FliW 21 eeeespflwLqsleeeelafvvidPflffpdYelelsdeelelleleseedvlvlvivtv 80
                                      ++++ p l+L  l+ e++ + +i  ++  ++Y+++l+d++ e   l++++++    i t+
  gi|298676161|ref|YP_003727910.1| 21 NSKKRPALVLANLQGEDIILCMITSAVKIDNYSITLNDNDFEYGTLRKNSNIRPNRIFTA 80
                                      4556999***********************************999999998876666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 701.58
//
Query:       gi|298676162|ref|YP_003727911.1|  [L=82]
Description: AbrB family transcriptional regulator [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-09   36.0   0.1      6e-09   35.6   0.1    1.3  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
     0.0038   17.6   0.1     0.0055   17.1   0.1    1.5  1  PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin
  ------ inclusion threshold ------
      0.091   12.8   0.0       0.12   12.4   0.0    1.3  1  MraZ            MraZ protein, putative antitoxin-like
        0.2   11.6   0.0       0.21   11.5   0.0    1.1  1  Phage_T4_gp36   Phage T4 tail fibre


Domain annotation for each model (and alignments):
>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.1   1.3e-12     6e-09       2      40 ..      10      48 ..       9      54 .. 0.91

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 1.3e-12
                                      EETTEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCCCC CS
                    MazE_antitoxin  2 kvGnsgavriPkevrfelgireGdevelevdgdkiilrp 40
                                      k++++g+++iPke+r+  +++eG+++++   +d+i lr 
  gi|298676162|ref|YP_003727911.1| 10 KITKKGQISIPKEIRELENFKEGSKIVILAYDDRIELRS 48
                                      899******************************998875 PP

>> PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   1.2e-06    0.0055       2      36 ..       9      42 ..       8      80 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.2e-06
                    PrlF_antitoxin  2 stltergqttiPasvRkaLklkkgrdkiaytildd 36
                                      +++t++gq  iP+ +R+  + k+g+ ki+    dd
  gi|298676162|ref|YP_003727911.1|  9 AKITKKGQISIPKEIRELENFKEGS-KIVILAYDD 42
                                      69********************987.666544443 PP

>> MraZ  MraZ protein, putative antitoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.6e-05      0.12      12      54 ..      13      57 ..       7      75 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.6e-05
                                      TTSEEE--CHHHH..HTTSCSEEEEEECCSEEEEEEHHHHHHHHH CS
                              MraZ 12 akGRlllPaklre..eaklekevvviGvsncLeiwpraeWekyee 54
                                      +kG +++P++ re   +k+   +v+ ++++++e++++++ ++ ++
  gi|298676162|ref|YP_003727911.1| 13 KKGQISIPKEIREleNFKEGSKIVILAYDDRIELRSMDQLDEKIS 57
                                      89********99643899999***************998754444 PP

>> Phage_T4_gp36  Phage T4 tail fibre
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.8e-05      0.21      66     109 ..       3      61 ..       1      79 [. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.8e-05
                     Phage_T4_gp36  66 vfdtRsgnintkGkvgigtrvpa...............dkkltvkGkvd.llnvkltvsa 109
                                        +d Rs+ i+ kG+++i ++++                d  +  + ++d l++ + t  a
  gi|298676162|ref|YP_003727911.1|   3 LIDFRSAKITKKGQISIPKEIRElenfkegskivilayDDRIELR-SMDqLDEKISTALA 61 
                                       589*******************98888888888877777777777.55545555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 621.50
//
Query:       gi|298676163|ref|YP_003727912.1|  [L=2251]
Description: S-layer-related duplication domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.5e-154  511.8  32.1    5.1e-78  261.7  13.5    3.1  2  S-layer          S-layer protein
    6.8e-48  163.4   8.4    6.8e-48  163.4   8.4    3.7  2  Peptidase_S8     Subtilase family
    7.8e-08   32.1   2.6    7.8e-08   32.1   2.6    5.7  5  Big_2            Bacterial Ig-like domain (group 2)
    0.00021   21.1   0.1    0.00021   21.1   0.1    6.4  7  FlgD_ig          FlgD Ig-like domain
    0.00052   19.7   0.6      0.024   14.3   0.1    3.3  3  DUF2271          Predicted periplasmic protein (DUF2271)
     0.0074   16.5  20.4       0.35   11.1   0.6    6.7  6  DUF4625          Domain of unknown function (DUF4625)
  ------ inclusion threshold ------
      0.058   13.9   3.1       0.55   10.7   0.1    3.6  2  DUF4179          Domain of unknown function (DUF4179)
       0.31   11.1   2.2       0.66   10.0   2.2    1.4  1  Peptidase_S49_N  Peptidase family S49 N-terminal
        2.4    8.5   6.9        8.3    6.8   0.0    5.0  4  RGI_lyase        Rhamnogalacturonan I lyases beta-sheet domai


Domain annotation for each model (and alignments):
>> S-layer  S-layer protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.7  13.5   2.5e-81   5.1e-78       2     258 .]     837    1092 ..     836    1092 .. 0.97
   2 !  254.7  10.6   3.6e-79   7.2e-76       4     258 .]    1116    1364 ..    1113    1364 .. 0.95

  Alignments for each domain:
  == domain 1  score: 261.7 bits;  conditional E-value: 2.5e-81
                           S-layer    2 eneeeseeltwtasnFsgfyydiddglssEsltlelesksdrtieegelvYsttpvekefefeewgsYevigfla 76  
                                        +n++ s ++ wt++++sg+y ++ ++ ssEs+ ++l++ksdr+i+e++++Ys++pve++f++ee+g+Y+ igfla
  gi|298676163|ref|YP_003727912.1|  837 ANKDLSLNYLWTSDSYSGLYRNLGSENSSESIKIHLDDKSDRNINEDDFEYSAKPVETAFKYEEFGTYKEIGFLA 911 
                                        5677889999***************************************************************** PP

                           S-layer   77 ekYfagydnsa.etsddvsllsdekLskvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgee 150 
                                        + Yfagy+ns+ +ts++ ++l+ ++L+kv+++++e++ +++gs+++L++gY++++kqiD+dg+kvw+eL+kdg++
  gi|298676163|ref|YP_003727912.1|  912 KPYFAGYSNSTnFTSNSSNMLAGDQLTKVVLNDNESRYVSVGSKISLKNGYTITPKQIDTDGNKVWFELSKDGNF 986 
                                        *******666559************************************************************** PP

                           S-layer  151 vdskvissskadstyvyekdlgdeddvviiavhvdevfrgtedslvviegifqisddvleieegdefgkmevksv 225 
                                        vd+k+++ +++++ +vy+kdlg++ +v +ia  v ++++++e+  v ++gifqis+d + ++ g+++ k++ +sv
  gi|298676163|ref|YP_003727912.1|  987 VDDKIVDINDDSDYFVYSKDLGSVSNVSVIALDVGDIYKSNET--VLVKGIFQISEDLIGLDIGNTYSKLQLESV 1059
                                        ********999*****************************998..899*************************** PP

                           S-layer  226 seneiemenddsitLsrdktieimddlkfkvaD 258 
                                        s+n++ m+n+dsi+L+r++t++++dd+ ++ aD
  gi|298676163|ref|YP_003727912.1| 1060 SSNKLLMKNSDSISLDRGTTTDVADDIIIRAAD 1092
                                        ******************************998 PP

  == domain 2  score: 254.7 bits;  conditional E-value: 3.6e-79
                           S-layer    4 eeeseeltwtasnFsgfyydiddglssEsltlelesksdrtieegelvYsttpvekefefeewgsYevigflaek 78  
                                        ++e e++ w + nF g+yy++d+gl sEs+ + ++  +dr+i+eg+l+Y++ ++e++fe+ +wg+Ye +gf++ek
  gi|298676163|ref|YP_003727912.1| 1116 VAEGENCGWFPINFDGLYYNLDNGLMSESFNVVYD--NDRSIDEGNLEYNSCAIETDFEYPDWGKYESMGFMGEK 1188
                                        66788999***********************9965..7************************************* PP

                           S-layer   79 Yfagydnsa.etsddvsllsdekLskvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevd 152 
                                        Y+ gy +s+ + +++++l+s++ L+kvlid+++ kt+k +s l L++gY l ++qiD+dg+kvw++L+kdg++vd
  gi|298676163|ref|YP_003727912.1| 1189 YVSGYTSSTkFAENNTNLVSNNRLTKVLIDNNNVKTIKLDSALFLKNGYVLVPEQIDTDGNKVWFSLYKDGSFVD 1263
                                        *****5555499*************************************************************** PP

                           S-layer  153 skvissskadstyvyekdlgdeddvviiavhvdevfrgtedslvviegifqisddvleieegdefgkmevksvse 227 
                                        +kv+++   ++++vy  d+g    v+iiavh++++ ++++   +  +g+fq+s+++ +i++gd fg+m+ ++vs 
  gi|298676163|ref|YP_003727912.1| 1264 DKVVTV---NDNFVYRIDMGTISHVPIIAVHISDIDKQSQ--EIEADGTFQVSENYESIHTGDMFGNMQLDTVSA 1333
                                        ******...**************************55544..4788***************************** PP

                           S-layer  228 neiemenddsitLsrdktieimddlkfkvaD 258 
                                        ++i+me+++sitL +++t+++mdd+kfkvaD
  gi|298676163|ref|YP_003727912.1| 1334 SQITMESNSSITLGKGETVYFMDDFKFKVAD 1364
                                        ******************************9 PP

>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.4   8.4   3.4e-51   6.8e-48       1     298 []     257     530 ..     257     530 .. 0.90
   2 ?  -30.2  35.4         9   1.8e+04      23     130 ..    1405    1526 ..    1394    1945 .. 0.59

  Alignments for each domain:
  == domain 1  score: 163.4 bits;  conditional E-value: 3.4e-51
                                       -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG.GGEETT-SS-TT-SC-SSS....HHHHHHHHHH-B.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                      Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegagfngadsettstnwarddngnsieHGthvAGiaaan.a 76 
                                       g+g ++a++DtG+d++  d s +                  + +ds t++++ ++ ++ +   HGthvAG +++  +
  gi|298676163|ref|YP_003727912.1| 257 GSGQTIAIADTGIDTGVDDSSMH-----------------PDLQDSLTGIREYEDAEDYSG--HGTHVAGSVVGDgK 314
                                       789***********999997722.................667788888877777777644..************99 PP

                                       .SSSSSB-SSTTSEEEEEE-SSTTSB-HH...HHHHHHHHHHHHCT-SEEEE-EESCETTCHHCHHHHHHHHHHHH. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8  77 peegekngvapgakilsvkvldtsggsmetg.teliraieeaaedkvdvinmslgestslpktgrsiealainravn 152
                                       +++g+  g ap+ +++ ++ l++++++       l++ +++a ++++ ++++s+g   + +++g++++   ++++++
  gi|298676163|ref|YP_003727912.1| 315 KSSGKYRGTAPNTDLY-FQSLSPKDSKYLYPpNPLTELFKDAYNNGASIHSNSWG---HSGNYGSQSS--SVDEFMW 385
                                       999*************.7777777777776679**********************...99****9999..9****** PP

                                       CC.T-EEEEE--SS-T-HHEEE-TTCEECTTTSTTCEEEEEES..TTSSB-TT--B-TT.......-EEEE-S-CCC CS
                                       xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 153 kk.gvlvviSaGNngktgsslqagspvgtpstsknvitvgayt..tegkiapfSsrGpssdgklkpdivapGgnivs 226
                                       ++ ++l+ ++aGN+g       + +++ +p+++kn +tvga +  +++++a+fSsrGp+ dg++kpd+vapG+ i s
  gi|298676163|ref|YP_003727912.1| 386 NHkDMLILFAAGNSG------ANQETIISPGNAKNCLTVGASEssDPKDVASFSSRGPTEDGRVKPDVVAPGTYINS 456
                                       ***************......8999*****************988999**************************888 PP

                                       CCCCCCHHHTTTHHEEEE-SHHHCHHHHHHHHHHHHHHHTT....--HHHHHHHHHCCS-EE......SSSSSSTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 227 twsrqsnnsaglssyqsmsGTSmAsPnaagaaAlllsalpk....ltpetvraallntAqdlgkadniesfaqGaG 298
                                       t s  ++++ g+  y+ + GTSmA+P+ agaaA +++++ +     t+  ++++l+n A d++ +dn  ++aqG+G
  gi|298676163|ref|YP_003727912.1| 457 TRSSYDSDGSGY--YTEKHGTSMATPLTAGAAASIRQYYVEnsiqPTASLIKTTLINGAHDISSNDNRPNYAQGWG 530
                                       777777666666..9**********************6655585555555*************************9 PP

  == domain 2  score: -30.2 bits;  conditional E-value: 9
                                        GEEE..EEEE---TTSG.GGEETT-SS-TT-SC-SSS....HHHHHHHHHH-B..........SSSSSB-SSTTS CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxx RF
                      Peptidase_S8   23 ttdgerklvdvideegagfngadsettstnwarddngnsieHGthvAGiaaan........apeegekngvapga 89  
                                        +++++ ++++ id + +++++++s +t   +++++ +       +v  ia ++        +++ +++  +ap++
  gi|298676163|ref|YP_003727912.1| 1405 NIHNTGNITWNIDGNTQKTDTQTSSSTYKVSYDTNGM------FNVTAIASYSnfteqyewSWNVSYNDTIAPNV 1473
                                        5555556666666555555555544444444444322......35555555555556666666666666666666 PP

                                        EEE...............EEE-SSTTSB-HH..HHHHHHHHHHHHCT-SEEEE-EE CS
                                        xxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8   90 kil...............svkvldtsggsmetgteliraieeaaedkvdvinmslg 130 
                                        +++               sv + d+  ++    + li+ i++++  +  + +   g
  gi|298676163|ref|YP_003727912.1| 1474 SLTadtvellsvnnpasiSVSITDKYPNNT---EFLIKDISDEIMLEKNITSHVNG 1526
                                        666666666666666644444444444332...56666666666655555444444 PP

>> Big_2  Bacterial Ig-like domain (group 2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   2.6   3.9e-11   7.8e-08       2      65 ..     659     724 ..     658     738 .. 0.92
   2 ?   -1.5   0.7       1.2   2.4e+03      18      67 ..    1398    1447 ..    1390    1456 .. 0.56
   3 ?   -0.9   1.1      0.79   1.6e+03      20      61 ..    1565    1608 ..    1561    1608 .. 0.78
   4 ?    0.7   1.2      0.25     5e+02      26      49 ..    1777    1801 ..    1763    1807 .. 0.81
   5 ?   -2.6   5.3       2.6   5.3e+03       8      78 ..    1911    1995 ..    1909    1996 .. 0.67

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 3.9e-11
                                       -SEEEEEEC-CEEETT-EEEEEEEEESTT-S-..--EEEEECC-SSEEEETCCEECCCSSEEEEEE CS
                             Big_2   2 vtsvtvsptevtvkkgatqqltvevtpssasd..kkvtwtssngsvAtVsatGlVtavaaGkatit 65 
                                       v ++++ p++vt  +++t+ + + v+ ++ +     v wt++n++v++V+ tGl ta+  G++ti+
  gi|298676163|ref|YP_003727912.1| 659 VSNIEINPENVTAYEDETLSFNADVYDQDGNEveLPVNWTITNTTVGVVNETGLFTAKNIGSTTIE 724
                                       889**************************9998889*****************************8 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.2
                                        -EEEEEEEEESTT-S---EEEEECC-SSEEEE.....TCCEECCCSSEEEEEEEE CS
                             Big_2   18 atqqltvevtpssasdkkvtwtssngsvAtVs.....atGlVtavaaGkatitat 67  
                                         tq ++  +  +    + +tw++++++   ++     +t +V+  + G  ++ta+
  gi|298676163|ref|YP_003727912.1| 1398 HTQEFSINIHNT----GNITWNIDGNTQ-KTDtqtssSTYKVSYDTNGMFNVTAI 1447
                                        555555444433....458999955432.22223445666666666666666665 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.79
                                        EEEEEEEESTT-S-..--EEEEECC-SSEEEETCCEECCCSSEE CS
                             Big_2   20 qqltvevtpssasd..kkvtwtssngsvAtVsatGlVtavaaGk 61  
                                        +  +v+v+ ++ +   k++t t s+g+++ +++t++++a+a G+
  gi|298676163|ref|YP_003727912.1| 1565 KNISVTVDNEKPTIdiKDITGTHSAGDKVYTNSTLTINASASGT 1608
                                        555666666665556699999999****************9995 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.25
                                        EESTT-S-.--EEEEECC-SSEEEE CS
                             Big_2   26 vtpssasd.kkvtwtssngsvAtVs 49  
                                        + +s+ ++  ++t+++s+++++tV+
  gi|298676163|ref|YP_003727912.1| 1777 GKMSNEKTgTSITFNTSDNTKGTVT 1801
                                        566777777899**********998 PP

  == domain 5  score: -2.6 bits;  conditional E-value: 2.6
                                        EEC-CEEETT-EEEEEEEEESTT-S-......--EEEEECC-SSEEEE......TCCEECCCSSEEE..EEEEEE CS
                             Big_2    8 sptevtvkkgatqqltvevtpssasd......kkvtwtssngsvAtVs......atGlVtavaaGka..titats 68  
                                         p+e +++ + t +++v + +s+ ++       +++++s+++++   +      at + t +++Gk   t+t+ +
  gi|298676163|ref|YP_003727912.1| 1911 YPAEGSILDSSTSKVKVKFSYSDGQSgintskTTIKFESDDKTTSDNTtitseyATYNSTELSVGKYnsTVTVYD 1985
                                        566677777777778888777777777777555666777666554222334788888889999998533788888 PP

                                        TTTSSEEEEE CS
                             Big_2   69 kdgndkatlt 78  
                                        + gn+k++ t
  gi|298676163|ref|YP_003727912.1| 1986 NAGNSKTYTT 1995
                                        8888888766 PP

>> FlgD_ig  FlgD Ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.3   4.6e+03      67      77 ..     628     638 ..     625     640 .. 0.86
   2 ?   -0.7   0.1      0.69   1.4e+03      23      64 ..     650     691 ..     641     693 .. 0.79
   3 ?   -2.2   0.1         2   3.9e+03      61      76 ..     794     809 ..     791     811 .. 0.84
   4 ?    0.4   0.1       0.3   5.9e+02      25      47 ..     990    1012 ..     967    1019 .. 0.77
   5 !   21.1   0.1     1e-07   0.00021      23      77 ..    1501    1557 ..    1478    1559 .. 0.76
   6 ?   -3.6   0.0       5.4   1.1e+04      66      77 ..    1656    1667 ..    1655    1668 .. 0.86
   7 ?   -0.2   0.2      0.47   9.4e+02      12      39 ..    1966    1992 ..    1955    1996 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.3
                                       EEEEEEEEEET CS
                           FlgD_ig  67 GaYtvkvtats 77 
                                       G+Ytvkv+ ++
  gi|298676163|ref|YP_003727912.1| 628 GRYTVKVKGSN 638
                                       9******9875 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.69
                                       EEEEEEEE-SS--EEEEEEEEESSSEEEEEEE-SB-TTS-B- CS
                           FlgD_ig  23 devtvtikDasGevVrtidlgaqsaGvvsftWdGtdndGnkl 64 
                                       ++++++  D s+ +++  +++a +  + sf+ d +d+dGn +
  gi|298676163|ref|YP_003727912.1| 650 TSGSIKTVDVSNIEINPENVTAYEDETLSFNADVYDQDGNEV 691
                                       567777788888888888888888888888888888888876 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2
                                       S-B--SEEEEEEEEEE CS
                           FlgD_ig  61 GnkladGaYtvkvtat 76 
                                        n +  G Y++++ta+
  gi|298676163|ref|YP_003727912.1| 794 NNTADVGVYNITATAE 809
                                       678899********96 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.3
                                        EEEEEE-SS--EEEEEEEEESSS CS
                           FlgD_ig   25 vtvtikDasGevVrtidlgaqsa 47  
                                          v i+D+s   V++ dlg++s 
  gi|298676163|ref|YP_003727912.1|  990 KIVDINDDSDYFVYSKDLGSVSN 1012
                                        4699***************9875 PP

  == domain 5  score: 21.1 bits;  conditional E-value: 1e-07
                                        EEEEEEEE-SS--EEEEEEEEESSSE..EEEEEE-SB-TTS-B--SEEEEEEEEEET CS
                           FlgD_ig   23 devtvtikDasGevVrtidlgaqsaG..vvsftWdGtdndGnkladGaYtvkvtats 77  
                                         ++++ ikD s e+    + +++  G  +++ftW+ t+++ +++a+G+Y + v++t+
  gi|298676163|ref|YP_003727912.1| 1501 NNTEFLIKDISDEIMLEKNITSHVNGenQYNFTWNATNSSNEPVANGKYYLVVNSTD 1557
                                        45588899999999966666666666115789*********************9996 PP

  == domain 6  score: -3.6 bits;  conditional E-value: 5.4
                                        SEEEEEEEEEET CS
                           FlgD_ig   66 dGaYtvkvtats 77  
                                        dG+Y+v v+a++
  gi|298676163|ref|YP_003727912.1| 1656 DGRYNVIVEAAD 1667
                                        8*******9975 PP

  == domain 7  score: -0.2 bits;  conditional E-value: 0.47
                                        EEEEEE.ESSSEEEEEEEE-SS--EEEE CS
                           FlgD_ig   12 aplgvelpeaadevtvtikDasGevVrt 39  
                                        ++ + el+ +  + tvt++D +G+  +t
  gi|298676163|ref|YP_003727912.1| 1966 TYNSTELSVGKYNSTVTVYDNAGNS-KT 1992
                                        455555777777889******9997.55 PP

>> DUF2271  Predicted periplasmic protein (DUF2271)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   1.2e-05     0.024      72     123 ..    1525    1575 ..    1511    1588 .. 0.86
   2 ?    1.3   0.0      0.13   2.5e+02      92     118 ..    1655    1681 ..    1634    1690 .. 0.80
   3 ?   -2.7   0.1       2.2   4.3e+03      89     126 ..    1970    2008 ..    1957    2022 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.2e-05
                           DUF2271   72 rapGkyklkvdekddklkklkaGkYklvvEaaredggrelvrveielttkaa 123 
                                         ++ +y+++++ ++++ +++++GkY lvv ++   g++  +++ ++++++ +
  gi|298676163|ref|YP_003727912.1| 1525 NGENQYNFTWNATNSSNEPVANGKYYLVVNSTDDAGNTASKNISVTVDNE-K 1575
                                        55558999***************************************999.3 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.13
                           DUF2271   92 kaGkYklvvEaaredggrelvrveiel 118 
                                        ++G Y++ vEaa   ++ + ++  i+l
  gi|298676163|ref|YP_003727912.1| 1655 DDGRYNVIVEAADSANNSNSSKSGIDL 1681
                                        68**********999998888776665 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 2.2
                           DUF2271   89 kklkaGkYklvvEaaredggrelvrveielttk.aakka 126 
                                         +l  GkY+  v +    g+ ++++  +e+ ++ + +++
  gi|298676163|ref|YP_003727912.1| 1970 TELSVGKYNSTVTVYDNAGNSKTYTTSFEIAEQkTDENV 2008
                                        466667777777777777777777777777666333333 PP

>> DUF4625  Domain of unknown function (DUF4625)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.54   1.1e+03      17      48 ..     657     687 ..     651     693 .. 0.76
   2 ?   -0.7   0.4      0.78   1.6e+03      49      88 ..    1398    1441 ..    1374    1458 .. 0.68
   3 !    9.0   0.8   0.00078       1.6      51     130 ..    1489    1570 ..    1477    1572 .. 0.74
   4 ?    4.8   0.1     0.016        31      10      43 ..    1571    1604 ..    1565    1609 .. 0.90
   5 ?   -1.5   0.0       1.4   2.7e+03     105     130 ..    1655    1680 ..    1626    1682 .. 0.85
   6 !   11.1   0.6   0.00017      0.35      74     131 ..    1942    1999 ..    1893    2000 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.54
                           DUF4625  17 idllevsaepeeeevlkiGetlhfeaklsdne 48 
                                       +d+++++ +p e+ +++ +etl+f+a++ d++
  gi|298676163|ref|YP_003727912.1| 657 VDVSNIEINP-ENVTAYEDETLSFNADVYDQD 687
                                       4555555544.556788999********9986 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.78
                           DUF4625   49 alasykvdihn......nfDhhshsseakegekewsfeksydlsgs 88  
                                        + ++++++ihn      n D+++++++++  +++ +++ syd++g 
  gi|298676163|ref|YP_003727912.1| 1398 HTQEFSINIHNtgnitwNIDGNTQKTDTQ--TSSSTYKVSYDTNGM 1441
                                        44566677766444444568887777776..777788888877664 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00078
                           DUF4625   51 asykvdihnnfDhhshsseakegekewsfeksy.dlsgskkeyelheeieiPad..aeaGdYhlvirvtDasGne 122 
                                        as++v+i   + +++     k+   e   ek++ +  +++++y+++ + +  ++  +++G+Y lv+  tD +Gn+
  gi|298676163|ref|YP_003727912.1| 1489 ASISVSITDKYPNNTEFLI-KDISDEIMLEKNItSHVNGENQYNFTWNATNSSNepVANGKYYLVVNSTDDAGNT 1562
                                        5666677444444444443.34577888888886677788888888888777777799***************** PP

                           DUF4625  123 teesreik 130 
                                          ++++++
  gi|298676163|ref|YP_003727912.1| 1563 ASKNISVT 1570
                                        99998876 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.016
                           DUF4625   10 edtekPvidllevsaepeeeevlkiGetlhfeak 43  
                                         d+ekP+id+  ++ +++ ++++++ +tl+++a 
  gi|298676163|ref|YP_003727912.1| 1571 VDNEKPTIDIKDITGTHSAGDKVYTNSTLTINAS 1604
                                        599***************************9986 PP

  == domain 5  score: -1.5 bits;  conditional E-value: 1.4
                           DUF4625  105 eaGdYhlvirvtDasGneteesreik 130 
                                        ++G Y++++ + D + n++  +  i+
  gi|298676163|ref|YP_003727912.1| 1655 DDGRYNVIVEAADSANNSNSSKSGID 1680
                                        57*************99999887776 PP

  == domain 6  score: 11.1 bits;  conditional E-value: 0.00017
                           DUF4625   74 ekewsfeksydlsgskkeyelheeieiPadaeaGdYhlvirvtDasGneteesreiki 131 
                                        ++  +fe + +++  +++ + +      ++   G+Y+ +++v D++Gn++ + ++++i
  gi|298676163|ref|YP_003727912.1| 1942 KTTIKFESDDKTTSDNTTITSEYATYNSTELSVGKYNSTVTVYDNAGNSKTYTTSFEI 1999
                                        45666777666666655555555555567799*********************99998 PP

>> DUF4179  Domain of unknown function (DUF4179)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00028      0.55      24      82 ..     909     977 ..     907     981 .. 0.73
   2 ?    0.7   0.4      0.37   7.4e+02      25      84 ..    1194    1254 ..    1186    1256 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00028
                                       XXXXXXXXXXX..--SS-HHHHT--SS-.........HHHHSEEEEEEEEETTEEEEEEEEEE-SSEEE CS
                           DUF4179  24 rllspalAsaln.pvigslfeklsdskg.........eqeyvkpvnksaednGitvtvnevvaDgnkli 82 
                                        l+ p +A + n + + s  +++  +++         e+ yv++  k   +nG+t+t +++ +Dgnk++
  gi|298676163|ref|YP_003727912.1| 909 FLAKPYFAGYSNsTNFTSNSSNMLAGDQltkvvlndnESRYVSVGSKISLKNGYTITPKQIDTDGNKVW 977
                                       5677888877754444444444444333667777777888888889999******************97 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.37
                                        XXXXXXXXXX.--SS-HHHHT--SS-..HHHHSEEEEEEE...EETTEEEEEEEEEE-SSEEEEE CS
                           DUF4179   25 llspalAsalnpvigslfeklsdskg..eqeyvkpvnksa...ednGitvtvnevvaDgnklivs 84  
                                        ++s+ +A++      +l+++ + +k    ++ vk +        +nG+ +  +++ +Dgnk+++s
  gi|298676163|ref|YP_003727912.1| 1194 TSSTKFAENN----TNLVSNNRLTKVliDNNNVKTIKLDSalfLKNGYVLVPEQIDTDGNKVWFS 1254
                                        5566677666....3444444444446677777777555456799****************9986 PP

>> Peptidase_S49_N  Peptidase family S49 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   2.2   0.00033      0.66      52     117 ..      25     115 ..       5     134 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00033
                   Peptidase_S49_N  52 elkeeleealldeeelkaaekkekkeekeekkaekkkake...........................eeekkrvfvl 101
                                       ++++++++   +  ++ +++k e+ke k++++++kk+ ++                            ++k++++++
  gi|298676163|ref|YP_003727912.1|  25 KVSTNVSDDNSS--NQLEFKKYEEKELKTNNNEKKKSINKnkiylkqgaietnksnlttqskpkqfyPDSKEKIYLI 99 
                                       333333322221..1222233333333333333333333234455566666788888888889999999******** PP

                   Peptidase_S49_N 102 dFkGdikAsevesLre 117
                                       +Fk  ik + ++sL+ 
  gi|298676163|ref|YP_003727912.1| 100 QFKDVIKDEWIQSLKS 115
                                       ****999999999975 PP

>> RGI_lyase  Rhamnogalacturonan I lyases beta-sheet domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       8.5   1.7e+04      38      59 ..     356     377 ..     354     381 .. 0.84
   2 ?   -0.5   0.1       0.8   1.6e+03      15      48 ..     958     991 ..     954    1014 .. 0.78
   3 ?    6.8   0.0    0.0041       8.3      26      56 ..    1244    1274 ..    1230    1300 .. 0.87
   4 ?   -0.2   0.5      0.62   1.2e+03      47      74 ..    1414    1440 ..    1396    1448 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 8.5
                                       EETTEE-CSSSB-SSSEEEETT CS
                         RGI_lyase  38 YrdgkkinsapitdstnylDak 59 
                                       Y +g+ i+s++  +s ny  ++
  gi|298676163|ref|YP_003727912.1| 356 YNNGASIHSNSWGHSGNYGSQS 377
                                       99********999999997665 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.8
                                       ETTEEEEE--B-TTS-TT-EEEEEETTEE-CSSS CS
                         RGI_lyase  15 teegvfvsWRllgteeeevaFnvYrdgkkinsap 48 
                                        ++g  ++ + + t+ ++v F++ +dg+ + ++ 
  gi|298676163|ref|YP_003727912.1| 958 LKNGYTITPKQIDTDGNKVWFELSKDGNFVDDKI 991
                                       5677777778888999999999999999886654 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0041
                                        -TTS-TT-EEEEEETTEE-CSSSB-SSSEEE CS
                         RGI_lyase   26 lgteeeevaFnvYrdgkkinsapitdstnyl 56  
                                        + t+ ++v F +Y+dg+ + ++ +t + n++
  gi|298676163|ref|YP_003727912.1| 1244 IDTDGNKVWFSLYKDGSFVDDKVVTVNDNFV 1274
                                        5689999*****************9999997 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.62
                                        SSB-SSSEEEETT--TT-EEEEEEEETT CS
                         RGI_lyase   47 apitdstnylDakgtasskYtvkavvng 74  
                                         +i  +t+ +D++ t+ss+Y+v+  +ng
  gi|298676163|ref|YP_003727912.1| 1414 WNIDGNTQKTDTQ-TSSSTYKVSYDTNG 1440
                                        5788899999999.5599****988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (2251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1178  (0.0657036); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 1.14u 0.29s 00:00:01.43 Elapsed: 00:00:00.47
# Mc/sec: 14252.85
//
Query:       gi|298676164|ref|YP_003727913.1|  [L=609]
Description: hypothetical protein Metev_2305 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (609 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 3993.64
//
Query:       gi|298676165|ref|YP_003727914.1|  [L=568]
Description: hypothetical protein Metev_2306 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.086   13.1   0.8       0.21   11.9   0.8    1.7  1  KxDL      Uncharacterized conserved protein


Domain annotation for each model (and alignments):
>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.8   1.2e-05      0.21      20      84 ..     227     293 ..     220     295 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.2e-05
                              KxDL  20 qtsgrlnkknreLlelnalsqerl..aklrarfkqgtkllkevkkdLesifkkirslkaklakkyPe 84 
                                        + ++ln++++ L+++n+l+++    +  ++ fk+  +++    ++L+++  +i++++a+l k+ P+
  gi|298676165|ref|YP_003727914.1| 227 TIEAHLNSTKENLKNVNHLVNKSNdaEVKNEYFKEMLNVITLSVNQLQTSGYNIEQIRANLDKRLPN 293
                                       56789***************87642145566789999**************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (568 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1035  (0.0577277); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 3456.04
//
Query:       gi|298676166|ref|YP_003727915.1|  [L=486]
Description: hypothetical protein Metev_2307 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.053   13.6   0.2       0.15   12.1   0.2    1.7  1  TaqI_C    TaqI-like C-terminal specificity domain


Domain annotation for each model (and alignments):
>> TaqI_C  TaqI-like C-terminal specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   8.3e-06      0.15       8      71 ..     315     380 ..     310     397 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.3e-06
                            TaqI_C   8 dikrysieikgnYldlikkklkneka....kelfeekpKilv.rdiskkldaaydekayyvlntlylli 71 
                                       +i+   i+++g+Yl+ i++ +k+ ++    +++f+   Ki++  d +++l + +d + y+ + +l++  
  gi|298676166|ref|YP_003727915.1| 315 NISLQTIDYPGEYLKQIPDAIKGTSElitkDRYFQ---KIFFnVDSANTLIFLIDIERYFNKDKLNISD 380
                                       788899*******************8888577777...***9567888*************99999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (486 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       781  (0.0435607); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2999.97
//
Query:       gi|298676167|ref|YP_003727916.1|  [L=1066]
Description: hypothetical protein Metev_2308 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.1e-09   36.5   0.0    3.1e-09   36.5   0.0    2.4  2  Tubulin_2  Tubulin like
    4.4e-07   30.3   0.0    4.4e-07   30.3   0.0    4.1  4  Tubulin    Tubulin/FtsZ family, GTPase domain
  ------ inclusion threshold ------
      0.024   14.7   0.9       0.23   11.6   0.2    3.1  2  DUF1563    Protein of unknown function (DUF1563)


Domain annotation for each model (and alignments):
>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.0   5.2e-13   3.1e-09     100     227 ..     124     237 ..      10     343 .. 0.67
   2 ?   -3.9   1.1      0.98   5.8e+03      49      79 ..     534     564 ..     493     606 .. 0.54

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 5.2e-13
                         Tubulin_2 100 WlppeleelrkapeseGAGqiRtvGRlalfanleeirealrdaikrlrgsageeeglnvfVvgSLaGGTGSGiflDv 176
                                       W  +++ ++ ++   +G   +R +G+++ ++ + e  + ++++++  +++       +v +v++L GGTGSG+++D+
  gi|298676167|ref|YP_003727916.1| 124 WWIKSEYINENLDFATGVIRKRGLGKALYYKAYAE-DDDISNVVDLPENG-------KVALVVGLGGGTGSGLMIDM 192
                                       44455555555544455555666666544444443.66777777777774.......9******************* PP

                         Tubulin_2 177 ayllrkilkeekqkvkiiglvllPdvfplnkeggervkaNayaaLkELna...l 227
                                       a  l+   + +    +i+++ +lP+       +g + ++Naya+L EL++   +
  gi|298676167|ref|YP_003727916.1| 193 ARHLKRQQPTT----EITLFGVLPNQ-----VEGVKENTNAYATLSELEYlnlI 237
                                       98777655554....59********7.....33567789***********5441 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 0.98
                         Tubulin_2  49 kdatdetaekageslksrekealsissaevd 79 
                                       +++ +e ++k ++ +++ +k + s  +++v+
  gi|298676167|ref|YP_003727916.1| 534 QQKVREFVQKIQTPVQQYQKIQDSNLETDVT 564
                                       2223333333333333333333333333333 PP

>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   7.3e-11   4.4e-07     106     178 ..     162     232 ..     146     239 .. 0.88
   2 ?    2.0   0.4     0.034   2.1e+02      25     115 ..     332     412 ..     320     424 .. 0.62
   3 ?   -3.6   1.5       1.8   1.1e+04      58     114 ..     494     545 ..     459     553 .. 0.65
   4 ?   -1.7   0.1      0.47   2.8e+03     172     192 ..     621     641 ..     608     678 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 7.3e-11
                                       HHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEEEE--GG.G-HHHHHHHHHHHHHHH CS
                           Tubulin 106 irkevekcdslqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvvvlPsefsevvvepynailalkeli 178
                                       i + v+  ++  ++ ++ +lgGGTGSGl   +++ lk++ p + ++ + vlP++  e+v e+ na  +l+el 
  gi|298676167|ref|YP_003727916.1| 162 ISNVVDLPEN-GKVALVVGLGGGTGSGLMIDMARHLKRQQPTTEITLFGVLPNQV-EGVKENTNAYATLSELE 232
                                       5555555555.568999**************************************.**************996 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.034
                                       HHCH....HHHT......TTEEEEE....EEESBHHHHHTS-GS......EEEE--CCCCTTC--TT-HHHHHHHHH CS
                           Tubulin  25 ehgiqsdgdslesfFse.sgkveyiprsvaidtdpqvlneikagselfnpnklllgkegagnngaggypevgkeaae 100
                                       +++++ ++d  +s+F+  ++ ++y p  + + + +q++ne+++    f++ + ll      n++ + ++    +   
  gi|298676167|ref|YP_003727916.1| 332 QQSLEAENDLYSSIFRYlENIEKYHPDKLQVQLKEQDINELQER---FSNINSLLNL----NLFKKLNY----QSLS 397
                                       3444444466666665556667888****************999...5555555532....23322222....2444 PP

                                       HTHHHHHHHHTT-SE CS
                           Tubulin 101 eileeirkevekcds 115
                                          ++i++++e+cds
  gi|298676167|ref|YP_003727916.1| 398 VYTDIIKNAAEQCDS 412
                                       445555555555555 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 1.8
                                       HHHHHTS-GS......EEEE--CCC.CTTC--TT-HHHHHHHHHHTHHHHHHHHTT-S CS
                           Tubulin  58 pqvlneikagselfnpnklllgkeg.agnngaggypevgkeaaeeileeirkevekcd 114
                                        q l+++ ++   f+++k  l+ke   ++ ++++ +e   +  +e+++++r+ v+k +
  gi|298676167|ref|YP_003727916.1| 494 LQRLQSSYNN---FKERKERLKKEFkEKEDYIQSLQE---KENDENQQKVREFVQKIQ 545
                                       3344444444...777777776665566666666666...556777777777777655 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 0.47
                                       HHHHHHHHT-SEEEEEEHHHH CS
                           Tubulin 172 lalkelieesdavividNdaL 192
                                       ++lk+l++   a ++i+N++ 
  gi|298676167|ref|YP_003727916.1| 621 ESLKKLKQAKKAFLLIHNENV 641
                                       677777777777777777765 PP

>> DUF1563  Protein of unknown function (DUF1563)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.2   7.4e+03      11      22 ..     789     800 ..     787     815 .. 0.72
   2 ?   11.6   0.2   3.9e-05      0.23      24      40 ..     960     976 ..     938     978 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.2
                           DUF1563  11 LETLENLYaTYV 22 
                                          L NL +T+ 
  gi|298676167|ref|YP_003727916.1| 789 FKNLQNLRTTFT 800
                                       567899999975 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 3.9e-05
                           DUF1563  24 ysLKQiFLDkiQKisKa 40 
                                        ++  iFLD+iQKi Ka
  gi|298676167|ref|YP_003727916.1| 960 VFITGIFLDNIQKIVKA 976
                                       46788***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1066 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3161  (0.176307); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 1.03u 0.36s 00:00:01.39 Elapsed: 00:00:00.51
# Mc/sec: 6248.63
//
Query:       gi|298676168|ref|YP_003727917.1|  [L=313]
Description: flagellin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-31  109.6   7.0    1.7e-31  109.6   7.0    2.1  2  Arch_flagellin  Archaebacterial flagellin
  ------ inclusion threshold ------
      0.034   13.8   0.1       0.11   12.2   0.1    1.7  1  VanW            VanW like protein


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.6   7.0   1.9e-35   1.7e-31       1     137 [.      21     176 ..      21     197 .. 0.89
   2 ?    3.0   2.9     0.012     1e+02     103     164 .]     213     297 ..     192     297 .. 0.62

  Alignments for each domain:
  == domain 1  score: 109.6 bits;  conditional E-value: 1.9e-35
                                       X--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEE.EEE-SSSSSE....EEEE CS
                    Arch_flagellin   1 GfvgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvg.dsatngtine....itiy 72 
                                       ++vgigtlI+fIAm+lVAAvaa vli+t+g lqqkaq+tgee+t+qv+s+l++  + g  ++t+gt++       i 
  gi|298676168|ref|YP_003727917.1|  21 AQVGIGTLIIFIAMILVAAVAAAVLIQTSGNLQQKAQTTGEEATSQVASNLNVRTIEGlRGSTSGTLEPtvdqFLIR 97 
                                       79********************************************************8455555544466567777 PP

                                       EE--TTS--EEGGG-EEEEEESS--EE--E................................T-EE-TT-EEEEEEE CS
                    Arch_flagellin  73 vklnaGsspidlnkttisvtddgqetlltad..............efgivvisdtdgsltngdevlekgekvelevn 135
                                          +aG++++dl++ +++v+d ++ ++l ++               f+  +i d+d+s++++++v++kg++++l + 
  gi|298676168|ref|YP_003727917.1|  98 TSISAGGNRMDLSQLIVTVSDLNKTNTLEYNysekeaflfnksksYFTAKAIRDEDQSFSSDSPVMNKGDLIALSIS 174
                                       7777*******************999999999********************************************9 PP

                                       -- CS
                    Arch_flagellin 136 vn 137
                                       + 
  gi|298676168|ref|YP_003727917.1| 175 TL 176
                                       74 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.012
                                       ..........................T-EE-TT-EEEEEEE--..................TTT---TT-EEEEEEE CS
                    Arch_flagellin 103 d.......efgivvisdtdgsltng.devlekgekvelevnvn..................eddgitagdevsvevv 153
                                       d       ++++++ sd  +++++g + v e ++++el    n                   d +++++++ +++++
  gi|298676168|ref|YP_003727917.1| 213 DhygvdnsSTTLYNASD--DTVDSGnYTVFESNNTIELDGH-NlsdneytltygysenwnsSDLKLKPRTDLKITLT 286
                                       23334422222222222..2222223466666666666644.257888888888999999978889*********** PP

                                       -SSS--EEEEE CS
                    Arch_flagellin 154 penGasttief 164
                                       pe+G s ++ef
  gi|298676168|ref|YP_003727917.1| 287 PETGTSKILEF 297
                                       *****999887 PP

>> VanW  VanW like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   1.2e-05      0.11      41     122 ..     200     291 ..     187     297 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.2e-05
                              VanW  41 eakvivngklvkgvGGGvcqvsttlynaall....agleiverh......pHslpvsyvplglDAtvaygslDlkfk 107
                                       +++ i+++++ k    Gv + sttlyna        ++++ e +       H+l ++ ++l  +   +++s Dlk+k
  gi|298676168|ref|YP_003727917.1| 200 DGTYISSNQTYKLDHYGVDNSSTTLYNASDDtvdsGNYTVFESNntieldGHNLSDNEYTLTYGYSENWNSSDLKLK 276
                                       678889999999999************976533322455555543333337888888888888888899999***99 PP

                              VanW 108 Nntdypilieasvsd 122
                                         td +i +  ++ +
  gi|298676168|ref|YP_003727917.1| 277 PRTDLKITLTPETGT 291
                                       999999988776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1042  (0.0581181); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2036.18
//
Query:       gi|298676169|ref|YP_003727918.1|  [L=68]
Description: hypothetical protein Metev_2310 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.045   14.0   0.2      0.062   13.5   0.2    1.2  1  Clr5      Clr5 domain
       0.14   12.5   0.0       0.16   12.3   0.0    1.1  1  SF1-HH    Splicing factor 1 helix-hairpin domain


Domain annotation for each model (and alignments):
>> Clr5  Clr5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   6.9e-06     0.062       3      33 ..      28      57 ..      27      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.9e-06
                              Clr5  3 edWeahkatIrrLYleenrsLkdvmeiMeee 33
                                       dW+++ + I +LY +e+  ++++++ ++ e
  gi|298676169|ref|YP_003727918.1| 28 IDWDDLTEKILDLY-TEGFDIDEIIQKLKSE 57
                                      79************.9**********99875 PP

>> SF1-HH  Splicing factor 1 helix-hairpin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.8e-05      0.16      27      53 ..      29      58 ..      12      66 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.8e-05
                            SF1-HH 27 n...ltqeqleayllqlrieeitrkLrtgd 53
                                      +   lt++ l+ y   + i+ei +kL++++
  gi|298676169|ref|YP_003727918.1| 29 DwddLTEKILDLYTEGFDIDEIIQKLKSEE 58
                                      33359**********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 406.06
//
Query:       gi|298676170|ref|YP_003727919.1|  [L=59]
Description: hypothetical protein Metev_2311 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.016   14.9   0.1      0.018   14.8   0.1    1.0  1  TraT       Enterobacterial TraT complement resistance protein
      0.049   13.2   0.1      0.056   13.0   0.1    1.2  1  AHJR-like  REase_AHJR-like


Domain annotation for each model (and alignments):
>> TraT  Enterobacterial TraT complement resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1     2e-06     0.018      18      56 ..       9      47 ..       5      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2e-06
                              TraT 18 akekrtiyvqirntSdkqeldleqkiiskLeakGYkvvn 56
                                      +++++t  + ++n+ + +e +l++kii+k +++GY++ +
  gi|298676170|ref|YP_003727919.1|  9 GPNQKTSNLTLKNADKLSESELKKKIIEKYKENGYTIKQ 47
                                      57899999****************************965 PP

>> AHJR-like  REase_AHJR-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   6.2e-06     0.056       5      33 ..      22      51 ..      11      58 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.2e-06
                         AHJR-like  5 tsel.ererleslaeqyrekGyevllhPnr 33
                                      + +l e e  ++++e+y+e+Gy++ + P +
  gi|298676170|ref|YP_003727919.1| 22 ADKLsESELKKKIIEKYKENGYTIKQLPIS 51
                                      4444055555789***********999943 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1091  (0.0608511); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 384.64
//
Query:       gi|298676171|ref|YP_003727920.1|  [L=414]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.4e-26   90.6   0.8    2.2e-25   89.2   0.0    2.0  2  OrfB_IS605      Probable transposase
    8.9e-12   44.8   0.3    2.4e-11   43.4   0.1    1.9  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.018   15.5   0.0      0.037   14.4   0.0    1.5  1  RuvX            Holliday junction resolvase


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.2      0.45   2.7e+03      71      86 ..      16      31 ..       4      64 .. 0.66
   2 !   89.2   0.0   3.7e-29   2.2e-25      15     119 ..     190     292 ..     176     293 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.45
                        OrfB_IS605 71 kkasrklarlhrkrsr 86
                                       ++ +++++l++++++
  gi|298676171|ref|YP_003727920.1| 16 YEVLKRITKLSKNLYN 31
                                      3444444444444444 PP

  == domain 2  score: 89.2 bits;  conditional E-value: 3.7e-29
                        OrfB_IS605  15 gnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsrrrkhl 91 
                                        nk+++iDlG+nn+at+v+++gt+f+++gr lks +++++k +  lqs ++k++   k  +kl  l++kr+++++++
  gi|298676171|ref|YP_003727920.1| 190 YNKHLSIDLGVNNFATCVDTNGTAFIIEGRGLKSYNRWWNKVKSGLQSVYDKQG--IKSGQKLNWLFEKRKNKLNDF 264
                                       699**************************************************9..9******************** PP

                        OrfB_IS605  92 lhklathliktlkevgvetLnvgnmkdi 119
                                       +++ +++++k++ +++++++++g++kdi
  gi|298676171|ref|YP_003727920.1| 265 MNQSVNYIVKHCIDNNIGNIIIGELKDI 292
                                       *************************998 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       2.4   1.4e+04       9      22 ..     167     180 ..     167     181 .. 0.81
   2 !   43.4   0.1     4e-15   2.4e-11       1      69 []     311     385 ..     311     385 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 2.4
                    OrfB_Zn_ribbon   9 eykakeyGikveev 22 
                                       +y  +++ i++++ 
  gi|298676171|ref|YP_003727920.1| 167 KYNGQWFEIEYVYR 180
                                       68899999999885 PP

  == domain 2  score: 43.4 bits;  conditional E-value: 4e-15
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke......alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f+k+k++l+ k++ yGi+ +ev++ayTSkt +   +  ++      ++ +r +  ++ g  +++Dvn+a+Nil++
  gi|298676171|ref|YP_003727920.1| 311 FGKFKQKLRSKCEYYGINCIEVDEAYTSKTDALALEPIEKhqkymgKRVKRGLFQSSTGKLLNADVNGALNILRK 385
                                       89****************************887776666666688977788888888***************986 PP

>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   6.1e-06     0.037      36     107 ..     263     346 ..     241     362 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.1e-06
                                       H..HHHHHHHHHHHHHTT--EEEEE--......---..-SSS---SSTTHHHHHHHHHT....T-EEEEE--S---- CS
                              RuvX  36 k..ekdleelkelvkeeeveeiVvGlP......lnl..dgsegesakkvrkfaeeLakrl..kklpvelvDErlttv 100
                                       +  +++++ + + + ++++ +i++G         n+  +++++ ++  + kf ++L++++  ++++ + vDE +t++
  gi|298676171|ref|YP_003727920.1| 263 DfmNQSVNYIVKHCIDNNIGNIIIGELkdikqnSNMgkKNNQTFQTIPFGKFKQKLRSKCeyYGINCIEVDEAYTSK 339
                                       14479999*****************88677777444114455555556699*******9977899***********9 PP

                                       XXXXXXX CS
                              RuvX 101 eaerilr 107
                                       + + +l+
  gi|298676171|ref|YP_003727920.1| 340 TDALALE 346
                                       8776664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1095  (0.0610742); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2516.45
//
Query:       gi|298676172|ref|YP_003727921.1|  [L=835]
Description: hypothetical protein Metev_2313 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-36  123.5   0.2    1.1e-35  121.6   0.1    2.1  2  MTES_1575        REase_MTES_1575
    1.8e-14   53.8   3.5      3e-13   49.9   1.7    2.8  2  AAA_12           AAA domain
    1.5e-09   38.1   0.1    3.1e-09   37.0   0.1    1.6  1  AAA_11           AAA domain
    0.00027   20.7   0.0    0.00079   19.3   0.0    1.8  1  DUF559           Protein of unknown function (DUF559)
     0.0014   18.6   0.5     0.0053   16.8   0.1    2.3  3  RAP              RAP domain
     0.0021   18.4   0.0     0.0043   17.4   0.0    1.7  1  AAA_19           AAA domain
      0.004   16.9   0.0      0.009   15.7   0.0    1.5  1  AAA_30           AAA domain
     0.0091   15.6   1.5      0.021   14.4   1.5    1.7  1  UvrD-helicase    UvrD/REP helicase N-terminal domain
  ------ inclusion threshold ------
      0.016   15.0   0.0      0.035   13.9   0.0    1.5  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase


Domain annotation for each model (and alignments):
>> MTES_1575  REase_MTES_1575
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       4.1   8.3e+03      11      42 ..     542     572 ..     536     585 .. 0.79
   2 !  121.6   0.1   5.8e-39   1.1e-35       1      95 []     722     819 ..     722     819 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.1
                         MTES_1575  11 ergykvkpqvgvggfriDlvvedpgkyllaIe 42 
                                       + g ++k+  +v++  ++++ ++p ++ l++ 
  gi|298676172|ref|YP_003727921.1| 542 KGGTNIKEAQRVAEAAVEFMQTNP-EQSLGVV 572
                                       568889999999999999999999.7777775 PP

  == domain 2  score: 121.6 bits;  conditional E-value: 5.8e-39
                         MTES_1575   1 FeeeVaeaLrergykvkpqvgvggfriDlvvedp...gkyllaIecdgdkyhsskeardrdierqevLerlGWkilR 74 
                                       Fe++V e+L++rg++v  qvgv+g+ iDl+v +p   ++yl++Iecdg++yhs+k+ardrd++rqe+Le+lGW+i+R
  gi|298676172|ref|YP_003727921.1| 722 FERHVKEHLEKRGFDVDCQVGVSGYFIDLAVSHPafsDGYLAGIECDGATYHSAKSARDRDRLRQEILENLGWDIYR 798
                                       9**************************************************************************** PP

                         MTES_1575  75 iwssdwyrnpeeeleklveal 95 
                                       +ws+dw+ np++e++kl++++
  gi|298676172|ref|YP_003727921.1| 799 VWSTDWFANPKKETDKLEQYI 819
                                       *****************9987 PP

>> AAA_12  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.6   3.2e+03     119     134 ..     185     200 ..     165     256 .. 0.63
   2 !   49.9   1.7   1.5e-16     3e-13       3     195 ..     476     674 ..     474     678 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.6
                            AAA_12 119 pYraqvellkkklkek 134
                                        Y++q+++l+k+ ++ 
  gi|298676172|ref|YP_003727921.1| 185 DYKSQKDYLSKMAANI 200
                                       6889999998888752 PP

  == domain 2  score: 49.9 bits;  conditional E-value: 1.5e-16
                            AAA_12   3 rSlferllkkekekvvlLdtqYRm.hpeIsrfpsklfYkgkLkdaesvkkreleaqealeepleplvfidvekseee 78 
                                       +S++e  +++  +++  L   YR+ h+++ +f++k+fY+++L   +s  +++ +            + +++e    +
  gi|298676172|ref|YP_003727921.1| 476 ESILEMAMRCW-QPYRRLLWHYRSrHESLIDFSNKKFYNDQLIVFPSPVTNHPS------------YGVHMEYVGGT 539
                                       69999999999.9999999****86899*************9987754444333............33333333333 PP

                            AAA_12  79 kekkeksyiNeeEaelvvklvekllkkgseeerkkigvitpYraqvellkkklkekeeekseke............. 142
                                        +   k  +N +Ea+ v++   +++++ +e+   ++gv+++ + q +l+++++++  +e+++               
  gi|298676172|ref|YP_003727921.1| 540 CR---KGGTNIKEAQRVAEAAVEFMQTNPEQ---SLGVVAMNKVQTDLIEDEVSRLLTENTAAYnyiehwdkinggl 610
                                       33...4578*****************99999...9*******************98877766558999999999**9 PP

                            AAA_12 143 ..ievntvdgfQGrekdviilslVRsn......ekkeig...flkderrlNValTRAkskliiv 195
                                         + v+  +++QG e+dvi++s+           ++++g       +rrlNV +TRAk+++ ++
  gi|298676172|ref|YP_003727921.1| 611 esFFVKNLENVQGDERDVIFISTTYGPdsesgkVHQRFGpinSNVGYRRLNVLFTRAKEQVQLF 674
                                       99**********************99533333333355530033458************98776 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.1   1.6e-12   3.1e-09     209     258 ..     407     455 ..     312     458 .. 0.88

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 1.6e-12
                            AAA_11 209 klleklakkfdvviIDEAaqavEpstliPlrlgakkvvLvGDpkQLpatv 258
                                       + l+  + +fd+v+IDEA+q     +l +l +  k++v vGDpkQLp+t 
  gi|298676172|ref|YP_003727921.1| 407 QYLKPGTSEFDLVVIDEASQMKPEDSLGALARS-KQIVVVGDPKQLPPTS 455
                                       556666679************999999999999.**************96 PP

>> DUF559  Protein of unknown function (DUF559)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0     4e-07   0.00079      31     105 ..     733     816 ..     713     820 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4e-07
                                       TT--EEEEEEETTEEEEEEETTTTEE......EEEE---.----..----HHHHHHHHHTT-EEEEEEHHHHHH-HH CS
                            DUF559  31 sglkfrRqkpigsYivDfvclkakli......velDGaq.hdee..eeyDaeRtelLeslGftvlRfkndevlknie 98 
                                        g+    q+ +  Y++D +  +          +e DGa  h+ +  +++D  R+e+Le+lG+ + R +  +  +n++
  gi|298676172|ref|YP_003727921.1| 733 RGFDVDCQVGVSGYFIDLAVSHPAFSdgylagIECDGATyHSAKsaRDRDRLRQEILENLGWDIYRVWSTDWFANPK 809
                                       467788899999999999877655422222359****862655566889999****************999999988 PP

                                       HHHHHHH CS
                            DUF559  99 evleeil 105
                                       + ++++ 
  gi|298676172|ref|YP_003727921.1| 810 KETDKLE 816
                                       8777665 PP

>> RAP  RAP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1       6.6   1.3e+04      46      58 .]     184     196 ..     173     196 .. 0.72
   2 ?   -2.9   0.0       3.9   7.8e+03      24      34 ..     727     737 ..     727     737 .. 0.87
   3 !   16.8   0.1   2.6e-06    0.0053       1      56 [.     765     820 ..     765     822 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 6.6
                               RAP  46 knkedkveylkkk 58 
                                       k+ + +++yl k+
  gi|298676172|ref|YP_003727921.1| 184 KDYKSQKDYLSKM 196
                                       6777788888775 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.9
                               RAP  24 kriLsklGykv 34 
                                       k++L+k G+ v
  gi|298676172|ref|YP_003727921.1| 727 KEHLEKRGFDV 737
                                       579******87 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 2.6e-06
                               RAP   1 IevdGpshyykns.knltgktklKkriLsklGykvinIpyfeWnql.knkedkve.ylk 56 
                                       Ie+dG + +  +s +      +l+++iL++lG+ + ++   +W    k++ dk+e y+ 
  gi|298676172|ref|YP_003727921.1| 765 IECDGATYHSAKSaR---DRDRLRQEILENLGWDIYRVWSTDWFANpKKETDKLEqYIH 820
                                       899999998888833...4689*********************9988888888887876 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   2.2e-06    0.0043      99     143 ..     411     453 ..     156     456 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.2e-06
                            AAA_19  99 klqeee.llivDEfqdvdelqyrLlkallgekkklllvGDpdQliy 143
                                       + ++e+ l+++DE++++++     l al+ ++k++++vGDp+Ql++
  gi|298676172|ref|YP_003727921.1| 411 PGTSEFdLVVIDEASQMKPEDS--LGALA-RSKQIVVVGDPKQLPP 453
                                       33455669**********7654..89999.6677**********97 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   4.5e-06     0.009      89     130 ..     415     453 ..     385     456 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.5e-06
                            AAA_30  89 g.tllivDEagmvdtkqlaallkaaekagakvilvGDerQlas 130
                                       + +l+++DEa+ +  ++    l++      ++++vGD++Ql++
  gi|298676172|ref|YP_003727921.1| 415 EfDLVVIDEASQMKPEDSLGALARS----KQIVVVGDPKQLPP 453
                                       449********99777654444333....67**********97 PP

>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   1.5     1e-05     0.021     168     294 ..     215     450 ..      52     451 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1e-05
                                       H.........................................HHHCCCHHHHHCHHHHHHHHHHHTTCCTTHHCHSS CS
                     UvrD-helicase 168 k.........................................keelslskskaeelrelvskakekqlspkelkkaf 203
                                       k                                         k+  + +k +   ++ +++++ +++l  ++l+   
  gi|298676172|ref|YP_003727921.1| 215 KdiahidfedffkgdsekleiqylidtivraennpeelqnwsKFIDTVEKASEAGISPVIDTYLSGDLYFENLDT-T 290
                                       133333333333333333333333333333333333333333555555555555555555555555555555555.3 PP

                                       TSCSHHHHHHHHHHHHHHHHHHHHTC................................................... CS
                     UvrD-helicase 204 ekasdlqkkiaeflkeyqeqkkeena................................................... 229
                                       +++  +++ +  ++++y e  +++ +                                                   
  gi|298676172|ref|YP_003727921.1| 291 YEQVLYRNLAHIAYEKYPELNRFSGLkqeearerfrktdrelidlerkylraklakapitrrnseglprdktelgli 367
                                       45555555555666666666666666777777777777777777777777777777777888888888888888888 PP

                                       ..........EEHHHHHHHHHHHHHH...........CHHHHHHHHHHSSEEEESSGGG-BHHHHHHHHHHHTTTTT CS
                     UvrD-helicase 230 ..........lDfsdllhallellee...........neelaealrerykeiliDEyQDTnkiQyrilkllasghee 285
                                                 + f dl++++ ++ +e            ++ ++   ++++ + iDE+ +  +  ++ l  la+++ +
  gi|298676172|ref|YP_003727921.1| 368 nherskkrkhISFRDLMNRAGKAIQElkpcfmmsplsVSQYLKPGTSEFDLVVIDEASQMKP--EDSLGALARSK-Q 441
                                       8888888888************9999999***99999899999999**********987776..78899***998.7 PP

                                       EEEEE-GGG CS
                     UvrD-helicase 286 lfmvGDpkQ 294
                                       +++vGDpkQ
  gi|298676172|ref|YP_003727921.1| 442 IVVVGDPKQ 450
                                       ********* PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.7e-05     0.035      50     103 ..     405     454 ..     400     459 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.7e-05
                   Viral_helicase1  50 vdsflmalvkstkgkililDEylllhaGyill.laalskaklvilfGDplQipfh 103
                                       v ++l++ + +  ++++++DE+ ++++   +  l al+++k+++++GDp+Q p  
  gi|298676172|ref|YP_003727921.1| 405 VSQYLKPGTSE--FDLVVIDEASQMKP---EDsLGALARSKQIVVVGDPKQLPPT 454
                                       56777777765..9***********96...5559*****************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (835 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.93u 0.36s 00:00:01.29 Elapsed: 00:00:00.61
# Mc/sec: 4128.81
//
Query:       gi|298676173|ref|YP_003727922.1|  [L=449]
Description: putative PAS/PAC sensor protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-45  153.7   0.9      1e-20   73.8   0.3    3.7  4  PAS_3     PAS fold
    3.9e-32  110.6   6.2      4e-13   49.5   0.0    4.1  4  PAS_9     PAS domain
    2.7e-25   88.6   0.1      4e-15   55.8   0.0    4.1  4  PAS       PAS fold
      4e-25   88.2   0.0    2.1e-10   40.8   0.0    4.2  4  PAS_4     PAS fold
    7.1e-09   35.8   0.0    5.3e-06   26.5   0.0    2.7  2  PAS_11    PAS domain
    4.4e-06   26.6   0.0       0.73    9.9   0.0    4.3  4  PAS_8     PAS domain
  ------ inclusion threshold ------
      0.018   15.2   0.5          2    8.6   0.0    3.9  4  PAS_7     PAS fold


Domain annotation for each model (and alignments):
>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   0.00048       1.2       4      87 ..      31     112 ..      29     114 .. 0.91
   2 !   66.7   0.0   6.5e-22   1.7e-18       2      86 ..     155     237 ..     154     239 .. 0.96
   3 !   73.8   0.3     4e-24     1e-20       3      89 .]     282     371 ..     280     371 .. 0.95
   4 ?   -2.5   0.0       2.6   6.6e+03      45      64 ..     397     417 ..     385     434 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00048
                             PAS_3   4 vserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirdeng 80 
                                       ++++  + lG++++e+++   +++++   +  ++++++ ++++k++e++++   +++ +G  r ++ + ++  d+ +
  gi|298676173|ref|YP_003727922.1|  31 ANKAHADFLGLDKNEFENV--NIYNVFTRDVADYCFKENEKIFKENEKIHTRRWFKNSNGVSRLLSITKTPKLDSFN 105
                                       6888999************..****************************999999999**99999999999888888 PP

                             PAS_3  81 kpvrvig 87 
                                       ++ ++i+
  gi|298676173|ref|YP_003727922.1| 106 NVEYIIC 112
                                       8888876 PP

  == domain 2  score: 66.7 bits;  conditional E-value: 6.5e-22
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       +y+ ++++  lGy+pe l+gk  s+ ++vhp+D++r++++++ +l++  p + eyR++++dG+y w+e++++ i+d+
  gi|298676173|ref|YP_003727922.1| 155 VYAGPSYKSNLGYDPENLIGK--SVFNFVHPDDLDRIKSEFNSLLETLIPRKSEYRCLHADGHYLWLETYGNFIYDD 229
                                       799999***************..****************************************************** PP

                             PAS_3  79 ngkpvrvi 86 
                                        g++ +++
  gi|298676173|ref|YP_003727922.1| 230 VGNIKKIV 237
                                       **999887 PP

  == domain 3  score: 73.8 bits;  conditional E-value: 4e-24
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyege...yRirrkdGeyrwveararvir 76 
                                       yvs++v +i+Gy+ + + g + s++d++hp+D+ervr++++++ ++  +++++   yRi++k G++rwv++r+++ir
  gi|298676173|ref|YP_003727922.1| 282 YVSNNVVDIFGYTVDYFSGGKLSYADIIHPDDLERVRSEVETYSDDPDRFKFQhkpYRIITKTGDIRWVDDRTTIIR 358
                                       9*******************************************999977666678********************* PP

                             PAS_3  77 dengkpvrvigva 89 
                                       ++ g++++++gv+
  gi|298676173|ref|YP_003727922.1| 359 NDFGEITHYQGVI 371
                                       ***********96 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 2.6
                             PAS_3  45 alkkge.pyegeyRirrkdGe 64 
                                       ++++g   +++e+ ++r++ +
  gi|298676173|ref|YP_003727922.1| 397 SIQDGIsIIDTEFNVLRANSK 417
                                       455555355888777777643 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.7   4.7e-10   1.2e-06       5     104 .]      21     119 ..      17     119 .. 0.92
   2 !   49.5   0.0   1.6e-16     4e-13       2     104 .]     143     245 ..     142     245 .. 0.88
   3 !   24.1   0.1   1.2e-08   3.2e-05       7     104 .]     273     376 ..     265     376 .. 0.86
   4 !    8.7   0.0   0.00076         2       2      41 ..     400     440 ..     399     448 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 4.7e-10
                             PAS_9   5 lidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwvl 79 
                                       +++ ++ +   aN+a +++lG +++e+ + +i ++f  + +++  ++ ++++++ +    +    + ++ng   +  
  gi|298676173|ref|YP_003727922.1|  21 IFI-DEQTYYLANKAHADFLGLDKNEFENVNIYNVFtrDVADYCFKENEKIFKENE--KIHTRRWFKNSNGVSRLLS 94 
                                       334.4555789*************************99999999999999999999..******************* PP

                             PAS_9  80 ltaspvkdddgelvgiivilrDite 104
                                       +t +p  d+ +++  ii+  +Dite
  gi|298676173|ref|YP_003727922.1|  95 ITKTPKLDSFNNVEYIICSAEDITE 119
                                       ************************8 PP

  == domain 2  score: 49.5 bits;  conditional E-value: 1.6e-16
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk..kerevevvlirkngetf 76 
                                       ++i++++++g+ +ya ++ +  lGy+pe ++gks+++++  +p++ +r++  ++++ +  ++r  e+ + + +g ++
  gi|298676173|ref|YP_003727922.1| 143 EMICLTDKNGNFVYAGPSYKSNLGYDPENLIGKSVFNFV--HPDDLDRIKSEFNSLLEtlIPRKSEYRCLHADGHYL 217
                                       6789999********************************..44444444444444444488**************** PP

                             PAS_9  77 wvlltaspvkdddgelvgiivilrDite 104
                                       w +     ++dd g+++ i+++ rDit+
  gi|298676173|ref|YP_003727922.1| 218 WLETYGNFIYDDVGNIKKIVFTGRDITK 245
                                       **************************95 PP

  == domain 3  score: 24.1 bits;  conditional E-value: 1.2e-08
                             PAS_9   7 dnpdgril.yaNeaalrllGyspeevlgks..itdlfvtdpeanerlraaleqgrk.....kerevevvlirknget 75 
                                       d ++g  + y+++ + +++Gy+ + + g +  + d++  +p++ er+r  +e+ ++     k++++++ +i+k+g  
  gi|298676173|ref|YP_003727922.1| 273 DKENGWPVeYVSNNVVDIFGYTVDYFSGGKlsYADII--HPDDLERVRSEVETYSDdpdrfKFQHKPYRIITKTGDI 347
                                       567885555*******************998899999..777777777777777768889***************** PP

                             PAS_9  76 fwvlltaspvkdddgelvgiivilrDite 104
                                        wv+ + + +++d ge++++ +++ Dit+
  gi|298676173|ref|YP_003727922.1| 348 RWVDDRTTIIRNDFGEITHYQGVILDITD 376
                                       ***************************96 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.00076
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGys.peevlgksitdlf..v 41 
                                       dgi i+++++++l+aN ++ +++  +    + gk++ +++  +
  gi|298676173|ref|YP_003727922.1| 400 DGISIIDTEFNVLRANSKMGEWY--KvNTPLEGKKCYQVYhnS 440
                                       8999999***************5..5234499******99433 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.0    0.0054        14      25     113 .]      30     117 ..       9     117 .. 0.73
   2 !   55.8   0.0   1.6e-18     4e-15       2     113 .]     133     243 ..     132     243 .. 0.96
   3 !   18.2   0.0   7.1e-07    0.0018       6     113 .]     259     374 ..     257     374 .. 0.88
   4 ?    3.7   0.0     0.024        61       3      32 ..     391     420 ..     389     422 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0054
                                       EECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEEC......TTSSEEEEEEEEEE CS
                               PAS  25 yvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfkl......rdgrpihlevrasp 95 
                                       ++N+a +++lGl+ +e  + +++ ++  +           + +++e+   ++ ++ +       +g  + l ++ +p
  gi|298676173|ref|YP_003727922.1|  30 LANKAHADFLGLDKNEFENVNIYNVFTRD-------VADYCFKENEKIFKENEKIHTrrwfknSNGVSRLLSITKTP 99 
                                       78999999999999999999999988544.......3333333333333333333333344679************* PP

                                       EEETTEEEEEEEEEEEES CS
                               PAS  96 vrdaggeilgflgvlrdi 113
                                        +d   ++ ++++ + di
  gi|298676173|ref|YP_003727922.1| 100 KLDSFNNVEYIICSAEDI 117
                                       *************99997 PP

  == domain 2  score: 55.8 bits;  conditional E-value: 1.6e-18
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                        +r+i e++ ++i+++D++g+++y+ +++ + lG+++e ++gks++ ++h++d +  ++++  lle+  +++++ ++
  gi|298676173|ref|YP_003727922.1| 133 LFREITENMVEMICLTDKNGNFVYAGPSYKSNLGYDPENLIGKSVFNFVHPDDLDRIKSEFNSLLETLIPRKSEYRC 209
                                       6899*************************************************999999999999999999999999 PP

                                       EECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  79 fklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       +   dg + +le+  + ++d  g+i+ +++++rdi
  gi|298676173|ref|YP_003727922.1| 210 LHA-DGHYLWLETYGNFIYDDVGNIKKIVFTGRDI 243
                                       999.******************************8 PP

  == domain 3  score: 18.2 bits;  conditional E-value: 7.1e-07
                                       HHHHSSSEEEEEE...TTSB.EEEECHHHHHHHSSTHHHCT.TSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCE CS
                               PAS   6 ileslpdpifvvD...edgr.ilyvNaaaeellGlsreevl.gkslldliheeddaelaelleqlleqgeesragei 77 
                                       i++++++  f++    e+g+ + yv+ +  +++G++ +  + gk  + +i+++dd e+++   + +++  ++  +++
  gi|298676173|ref|YP_003727922.1| 259 IINNSRVVAFLWKndkENGWpVEYVSNNVVDIFGYTVDYFSgGKLSYADIIHPDDLERVRSEVETYSDDPDRFKFQH 335
                                       7777777777776567777745599************66652688899***************************** PP

                                       EEEC...TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  78 sfkl...rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       +  +   + g +++++ r++ +r+  gei+++ gv+ di
  gi|298676173|ref|YP_003727922.1| 336 KPYRiitKTGDIRWVDDRTTIIRNDFGEITHYQGVILDI 374
                                       8888999*****************************998 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.024
                                       HHHHHHHSSSEEEEEETTSBEEEECHHHHH CS
                               PAS   3 lraileslpdpifvvDedgrilyvNaaaee 32 
                                       l+  +es+ d+i ++D   ++l +N+++ e
  gi|298676173|ref|YP_003727922.1| 391 LDDTFESIQDGISIIDTEFNVLRANSKMGE 420
                                       556689********************9975 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.1e-05     0.028       2     108 ..      13     120 ..      12     122 .. 0.84
   2 !   40.8   0.0   8.1e-14   2.1e-10       2     110 .]     139     248 ..     138     248 .. 0.91
   3 !   15.2   0.0   7.4e-06     0.019      17     109 ..     280     378 ..     275     379 .. 0.97
   4 !   12.3   0.0   5.9e-05      0.15       1      43 [.     395     436 ..     395     444 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.1e-05
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pge 77 
                                       d+++  ++++ +++++  aN+a a+ +g++  e+ +   + +++ ++a+      ++  +++e i++    +  +g 
  gi|298676173|ref|YP_003727922.1|  13 DQTNTQIFIFIDEQTYYLANKAHADFLGLDKNEFENVNIYNVFTRDVADYCFKENEKIFKENEKIHTRRWFKNsNGV 89 
                                       566666777777889999**************************987777666677776666666666655556*** PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTer 108
                                        r ++++++P +d+   v  +++ + DiTe 
  gi|298676173|ref|YP_003727922.1|  90 SRLLSITKTPKLDSFNNVEYIICSAEDITEK 120
                                       *****************************97 PP

  == domain 2  score: 40.8 bits;  conditional E-value: 8.1e-14
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pge 77 
                                       +++ ++++  d++g+++ya +++ + +g++pe l+Gk+++ ++ ++d +r+ +  + +le+  p +++   l+ +g 
  gi|298676173|ref|YP_003727922.1| 139 ENMVEMICLTDKNGNFVYAGPSYKSNLGYDPENLIGKSVFNFVHPDDLDRIKSEFNSLLETLIPRKSEYRCLHaDGH 215
                                       688899***********************************99999***********************99995555 PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerrr 110
                                         ++e+  + + d+ G +  +++++rDiT r++
  gi|298676173|ref|YP_003727922.1| 216 YLWLETYGNFIYDDVGNIKKIVFTGRDITKRKE 248
                                       55555555999*******************985 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 7.4e-06
                             PAS_4  17 vlyaNaaaaelfgappeellGktla..ellpeedaarleralrrvlegeepiefleelll....pgeerhyelrllP 87 
                                       v+y++++  ++fg++ + + G +l   ++  ++d +r+++ ++   +  ++ +f++ + +     g+ r+++ r + 
  gi|298676173|ref|YP_003727922.1| 280 VEYVSNNVVDIFGYTVDYFSGGKLSyaDIIHPDDLERVRSEVETYSDDPDRFKFQHKPYRiitkTGDIRWVDDRTTI 356
                                       789999***************999999999999***********************9999***************** PP

                             PAS_4  88 lrdesGevigvlvisrDiTerr 109
                                       +r++ Ge+ ++ +++ DiT+r+
  gi|298676173|ref|YP_003727922.1| 357 IRNDFGEITHYQGVILDITDRK 378
                                       ********************97 PP

  == domain 4  score: 12.3 bits;  conditional E-value: 5.9e-05
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlael 43 
                                       ++s++d++ ++d++++vl+aN  + e++++    l Gk+++++
  gi|298676173|ref|YP_003727922.1| 395 FESIQDGISIIDTEFNVLRANSKMGEWYKVN-TPLEGKKCYQV 436
                                       79************************99875.56777777665 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   2.1e-09   5.3e-06       8      92 ..     148     228 ..     141     239 .. 0.90
   2 !    6.1   0.0    0.0046        12      38      84 ..     303     351 ..     298     367 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 2.1e-09
                            PAS_11   8 ldidgkIisvDtsaLrasfslglekeelvgrsiydLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvkvk 84 
                                        d +g+++   +   + +  lg+  e+l+g+s+++++hp+dl ++ks +   + ++   ++s yR   ++++++++ 
  gi|298676173|ref|YP_003727922.1| 148 TDKNGNFVYAGP---SYKSNLGYDPENLIGKSVFNFVHPDDLDRIKSEFNSLL-ETLIPRKSEYRCLHADGHYLWLE 220
                                       678899999999...99999*********************************.999999***************** PP

                            PAS_11  85 tksklfkn 92 
                                       t + + ++
  gi|298676173|ref|YP_003727922.1| 221 TYGNFIYD 228
                                       *9888765 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0046
                            PAS_11  38 rsiydLchpqdlstlkshlrevissngeatssl..yRLrlsqdkfvkvk 84 
                                       +s+ d++hp+dl++++s  +   + +++++ +   yR++++++++ +v 
  gi|298676173|ref|YP_003727922.1| 303 LSYADIIHPDDLERVRSEVETYSDDPDRFKFQHkpYRIITKTGDIRWVD 351
                                       6889**************99888888877655555*****999987665 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.012        31       7      42 ..      12      48 ..       9      73 .. 0.68
   2 ?    4.5   0.0     0.015        37       1      45 [.     132     177 ..     132     201 .. 0.73
   3 ?    1.5   0.0      0.12   3.1e+02       6      52 ..     259     309 ..     251     325 .. 0.69
   4 !    9.9   0.0   0.00028      0.73       7      37 ..     395     425 ..     389     446 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.012
                             PAS_8  7 fesspdgiav.vdlgdrivdvNqaalellGys.adlkg 42
                                      +++ +  i++ +d+++    +N+a +++lG++ +++  
  gi|298676173|ref|YP_003727922.1| 12 LDQTNTQIFIfIDEQT-YYLANKAHADFLGLDkNEFEN 48
                                      5555555665456555.778**********77766655 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.015
                             PAS_8   1 erlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgell 45 
                                       e +r + e++ + i+++d +g+ +v++ +++   lGy+ + l+g+ +
  gi|298676173|ref|YP_003727922.1| 132 ELFREITENMVEMICLTDkNGN-FVYAGPSYKSNLGYDpENLIGKSV 177
                                       67999*************8888.*99977777777776555555444 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.12
                             PAS_8   6 lfesspdgiavvdlgdr....ivdvNqaalellGys.adlkgellgqllpvl 52 
                                       ++++s++  +++++++     + +v +   +++Gy+ + ++g +l  + + +
  gi|298676173|ref|YP_003727922.1| 259 IINNSRVVAFLWKNDKEngwpVEYVSNNVVDIFGYTvDYFSGGKLS-YADII 309
                                       567777766667655534677999999999*****98877777774.33333 PP

  == domain 4  score: 9.9 bits;  conditional E-value: 0.00028
                             PAS_8   7 fesspdgiavvd.lgdrivdvNqaalellGys 37 
                                       fes++dgi ++d +  +++ +N ++ e + ++
  gi|298676173|ref|YP_003727922.1| 395 FESIQDGISIIDtEF-NVLRANSKMGEWYKVN 425
                                       9***********454.5******998777665 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.5   3.9e+03     101     114 ..     111     124 ..     109     125 .. 0.81
   2 ?    1.7   0.0      0.11   2.8e+02       3      41 ..     140     177 ..     138     251 .. 0.53
   3 ?   -2.3   0.0       1.8   4.7e+03      88     114 ..     372     381 ..     337     382 .. 0.70
   4 ?    8.6   0.0   0.00077         2       1      30 [.     395     424 ..     395     434 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.5
                             PAS_7 101 VttytDiTerrrae 114
                                       + + +DiTe+ ++e
  gi|298676173|ref|YP_003727922.1| 111 ICSAEDITEKNQSE 124
                                       56779****99987 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.11
                             PAS_7   3 nmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpl 41 
                                       nm + i++ D++++ v     y + l++ +e + +g+++
  gi|298676173|ref|YP_003727922.1| 140 NMVEMICLTDKNGNFVYAGPSYKSNLGYDPENL-IGKSV 177
                                       666666666666666666666666665555544.34433 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.8
                             PAS_7  88 ievrgnplpdgGfVttytDiTerrrae 114
                                       +                 DiT+r+ ae
  gi|298676173|ref|YP_003727922.1| 372 L-----------------DITDRKLAE 381
                                       3.................666666555 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.00077
                             PAS_7   1 lenmsqGisvfDadlrLvawNrrylelldl 30 
                                       +e++++Gis++D + +++  N+++ e +++
  gi|298676173|ref|YP_003727922.1| 395 FESIQDGISIIDTEFNVLRANSKMGEWYKV 424
                                       589********************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1075  (0.0599587); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.75u 0.38s 00:00:01.12 Elapsed: 00:00:00.60
# Mc/sec: 2265.74
//
Query:       gi|298676174|ref|YP_003727923.1|  [L=254]
Description: signal transduction histidine kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.2e-30  102.6   5.1    9.2e-30  102.6   5.1    2.4  2  HisKA_2          Histidine kinase
    1.7e-07   31.7   0.0    1.7e-06   28.5   0.0    2.4  1  HATPase_c        Histidine kinase-, DNA gyrase B-, and HSP90-
    4.6e-07   30.4   1.6    1.5e-06   28.8   0.2    2.3  2  HWE_HK           HWE histidine kinase
    0.00049   20.0   0.0     0.0011   18.9   0.0    1.6  1  HATPase_c_2      Histidine kinase-like ATPase domain
  ------ inclusion threshold ------
      0.011   15.6   2.9      0.013   15.4   2.9    1.1  1  Apolipoprotein   Apolipoprotein A1/A4/E domain
      0.011   15.9   1.3      0.018   15.3   1.3    1.4  1  Gluconate_2-dh3  Gluconate 2-dehydrogenase subunit 3
      0.031   14.1   5.7      0.043   13.7   5.7    1.2  1  PIN_8            PIN like domain
       0.08   12.7   8.1       0.12   12.1   1.6    3.4  4  SPOB_a           Sensor_kinase_SpoOB-type, alpha-helical doma
      0.091   12.8   1.9       0.16   12.0   1.9    1.3  1  Succ_DH_flav_C   Fumarate reductase flavoprotein C-term
       0.23   11.6   6.5       0.36   11.0   6.5    1.4  1  Fib_alpha        Fibrinogen alpha/beta chain family
       0.37   10.4   4.3       0.45   10.1   4.3    1.1  1  DUF572           Family of unknown function (DUF572)
        2.7    7.8   9.9        4.6    7.0   0.3    2.1  2  Spc29            Spindle Pole Component 29


Domain annotation for each model (and alignments):
>> HisKA_2  Histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.3       1.1   1.6e+03       1       6 [.      42      47 ..       8      58 .. 0.63
   2 !  102.6   5.1   6.1e-33   9.2e-30       1      76 []      64     139 ..      64     139 .. 0.99

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.1
                           HisKA_2  1 EihHRv 6 
                                      E++HRv
  gi|298676174|ref|YP_003727923.1| 42 ELEHRV 47
                                      344444 PP

  == domain 2  score: 102.6 bits;  conditional E-value: 6.1e-33
                           HisKA_2   1 EihHRvkNnLqvisslLslqarkakdeevkealresqnRvlsialiheeLyksedletvdfseylekLvenlfksy 76 
                                       E+hHR+kNnLqvisslL+lq++k++d++v+ea+r++qnRv+s++l+h+++y++++le++++++y+e+L+e+l+++y
  gi|298676174|ref|YP_003727923.1|  64 ELHHRIKNNLQVISSLLNLQSEKFNDDTVNEAFRDTQNRVISMSLVHQKIYHTKGLESINVRDYIEDLIEHLISLY 139
                                       99**********************************************************************9976 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   1.2e-09   1.7e-06       5     107 ..     162     251 ..     158     253 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.2e-09
                                       HHHHHHHHHHHHHHHHHS...TTTEEEEEEEEEE.TEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHH CS
                         HATPase_c   5 rLrqiisnlvdNavkfat...kageieveikase.ddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlG 77 
                                        L  +i++lv+N++k+a    k ge+ v    s+ + +++ v+DnG+Gip+ d++     +++          + lG
  gi|298676174|ref|YP_003727923.1| 162 PLGMLINELVSNSLKYAYpedKYGELNVIFYESNpGLYTLIVSDNGKGIPE-DID-----LDN---------PSSLG 223
                                       67789***********5442244444555443336899************8.555.....344.........6679* PP

                                       HHHHHHHHHHTTTEEEEEEETTTEEEEEEE CS
                         HATPase_c  78 lsivkklvelmgGeiwvesepgrGttftft 107
                                       + i k+lv +++G++ v+ +   Gttf+++
  gi|298676174|ref|YP_003727923.1| 224 MQIIKSLVGQIDGDLDVDGNN--GTTFIIN 251
                                       ******9999*******7777..***9986 PP

>> HWE_HK  HWE histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1      0.97   1.4e+03      24      39 ..      33      48 ..      23      52 .. 0.67
   2 !   28.8   0.2   9.8e-10   1.5e-06       1      69 [.      64     139 ..      64     151 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.97
                                      XS-HHHHHHHHHHHHH CS
                            HWE_HK 24 aesleefaeklsgRLq 39
                                      a++l++++e+l+ R+q
  gi|298676174|ref|YP_003727923.1| 33 ATKLKQMNEELEHRVQ 48
                                      5566666666666654 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 9.8e-10
                                       HHHHHHHHHHHHHHHHHHHHSS..SXS-HHHHHHHHHHHHHHHHHHHHHHHHCTT.S-E....EHHHHHHHHHHHH CS
                            HWE_HK   1 ElnHRvKNlLavvqsiarqtlr..saesleefaeklsgRLqALsaahdllsreew.aga....eLaelleeelapy 69 
                                       El+HR+KN L v++s+ +  ++  + ++++e+ ++ ++R+ ++s +h+ + +++  +++     +++l+e+ ++ y
  gi|298676174|ref|YP_003727923.1|  64 ELHHRIKNNLQVISSLLNLQSEkfNDDTVNEAFRDTQNRVISMSLVHQKIYHTKGlESInvrdYIEDLIEHLISLY 139
                                       9****************9877623467889999999***********98665543133311113455555555555 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   7.6e-07    0.0011      32     113 ..     163     235 ..     151     251 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 7.6e-07
                       HATPase_c_2  32 irlaveEactNavehayleapegpvevr.lesdeealtvevaDsGpgfdpetlpdpteeepkeslkegGrGlalikg 107
                                       + + ++E+++N  ++ay+e++ g+++v  +es+++  t+ v+D+G+g +             + + ++ +G+ +ik+
  gi|298676174|ref|YP_003727923.1| 163 LGMLINELVSNSLKYAYPEDKYGELNVIfYESNPGLYTLIVSDNGKGIPEDI----------DLDNPSSLGMQIIKS 229
                                       66789****************655555549999999***********66643..........667788899999999 PP

                       HATPase_c_2 108 lvDeve 113
                                       lv +++
  gi|298676174|ref|YP_003727923.1| 230 LVGQID 235
                                       987774 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   2.9   8.8e-06     0.013       5      97 ..       8     103 ..       4     133 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.8e-06
                                       CCCCHHHHHCCHHHCHHCHHH..HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHCCCHHHHHHHHHCCHHH CS
                    Apolipoprotein   5 sldelkayaeeleeqlaplaq..elrdrlskeleelrarlraeleevrarlepyrdevqeqlgqnleelrqrlapyt 79 
                                       +++ +++++ ++ e+++   q  + +++l +  eel  r+++++ee +++   ++ e++++++ nl+ + + l+  +
  gi|298676174|ref|YP_003727923.1|   8 KISAVVEFVRDITEKVKTEKQlkKYATKLKQMNEELEHRVQKQTEEIKNAERLRVLELHHRIKNNLQVISSLLNLQS 84 
                                       677888888889999998888866999***************************************99999999999 PP

                                       HHHHH.HHHHCHHCCHHCH CS
                    Apolipoprotein  80 eelre.rlaadaeelqeql 97 
                                       e+ ++  ++++ ++ q+++
  gi|298676174|ref|YP_003727923.1|  85 EKFNDdTVNEAFRDTQNRV 103
                                       9998877888888888876 PP

>> Gluconate_2-dh3  Gluconate 2-dehydrogenase subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   1.3   1.2e-05     0.018      28      87 ..      11      70 ..       3     120 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-05
                   Gluconate_2-dh3 28 gvaafidrqladaplppeqeayrkglaaldayaraeygksFveldgaqqdalLealekea 87
                                       v++f+  + +++ ++++ + y  +l++++++++++ +k+  e+++a++ ++Le   + +
  gi|298676174|ref|YP_003727923.1| 11 AVVEFVRDITEKVKTEKQLKKYATKLKQMNEELEHRVQKQTEEIKNAERLRVLELHHRIK 70
                                      599**************************************************9877664 PP

>> PIN_8  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   5.7   2.9e-05     0.043      41     130 ..      12     100 ..       9     136 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.9e-05
                             PIN_8  41 alEfqrnresviskekkayedlekeleklkkaaekkleealkkwakkkaldteelrkelkkqleelkeelkaeleel 117
                                       + Ef+r  ++ ++  +k++++++++l+++++++e+ +++ +++ ++ ++l++ el++++k++l+ +++ l+ ++e++
  gi|298676174|ref|YP_003727923.1|  12 VVEFVRDITEKVK-TEKQLKKYATKLKQMNEELEHRVQKQTEEIKNAERLRVLELHHRIKNNLQVISSLLNLQSEKF 87 
                                       6799988888777.6677888999*******************************************9994444444 PP

                             PIN_8 118 kksskadkeedpi 130
                                       ++++ +++ +d+ 
  gi|298676174|ref|YP_003727923.1|  88 NDDTVNEAFRDTQ 100
                                       4444444333333 PP

>> SPOB_a  Sensor_kinase_SpoOB-type, alpha-helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1     0.098   1.5e+02      36      59 ..       6      29 ..       4      32 .. 0.89
   2 ?   -1.8   0.1       1.7   2.5e+03      40      57 ..      41      58 ..      34      65 .. 0.63
   3 ?   12.1   1.6   7.8e-05      0.12      16      54 ..      63     100 ..      46     108 .. 0.75
   4 ?   -0.6   0.0      0.74   1.1e+03      42      54 ..     124     136 ..     122     140 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.098
                            SPOB_a 36 Lgkydkaeeyieevvkelkeeski 59
                                      +gk+  ++e++ ++++ +k+e+++
  gi|298676174|ref|YP_003727923.1|  6 TGKISAVVEFVRDITEKVKTEKQL 29
                                      588999***************987 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.7
                            SPOB_a 40 dkaeeyieevvkelkees 57
                                      ++ e+ +++ ++e+k+ +
  gi|298676174|ref|YP_003727923.1| 41 EELEHRVQKQTEEIKNAE 58
                                      455555666666666655 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 7.8e-05
                            SPOB_a  16 LrsqRHDflNhLQvIsGylqLgkydkaeeyieevvkelk 54 
                                       L  ++H   N+LQvIs++l L+     ++ ++e+ ++++
  gi|298676174|ref|YP_003727923.1|  63 L-ELHHRIKNNLQVISSLLNLQSEKFNDDTVNEAFRDTQ 100
                                       4.568999*************987777776666666665 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 0.74
                            SPOB_a  42 aeeyieevvkelk 54 
                                       +++yie+++++l 
  gi|298676174|ref|YP_003727923.1| 124 VRDYIEDLIEHLI 136
                                       7899999999875 PP

>> Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.9   0.00011      0.16      15      70 ..      23      78 ..      14      83 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                                      SB-HHHHHHHHHHHHHHHHHHTTB--S---SSS-HHHHHHHHHHHHHHHHHHHHHH CS
                    Succ_DH_flav_C 15 fRteegLkealkelkelrerlknvkvtdkskvaNqelvealelanllelAeaiaks 70
                                      ++te++Lk+  ++lk+++e+l++   ++++++ N e +++lel++ +++  +++ s
  gi|298676174|ref|YP_003727923.1| 23 VKTEKQLKKYATKLKQMNEELEHRVQKQTEEIKNAERLRVLELHHRIKNNLQVISS 78
                                      689*****************9998889999**************999988887766 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   6.5   0.00024      0.36      49     123 ..       7      81 ..       1     115 [. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00024
                                       CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCH.HHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  49 nstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqe.snirvLqnvlesneqkiqkLeq 123
                                        + + + e v++i+++++ +++ kk   + +k++++ele+++++  e+i++ e  ++ +L   +++n q i+ L +
  gi|298676174|ref|YP_003727923.1|   7 GKISAVVEFVRDITEKVKTEKQLKK-YATKLKQMNEELEHRVQKQTEEIKNAErLRVLELHHRIKNNLQVISSLLN 81 
                                       4556666778888888777777666.7999*******************99998899999********99998855 PP

>> DUF572  Family of unknown function (DUF572)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   4.3    0.0003      0.45     111     185 ..      21      94 ..       8     149 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0003
                            DUF572 111 eeakreekeke.eeeaedamkklEkrtkdskkemealesLeeLqelnqrqakvdfdanlelrkefreekkereeee 185
                                       e++k e++ k+ +++ +   ++lE+r++++++e++  e+L  L+  ++ + +  +   ++l++   e+ +  + +e
  gi|298676174|ref|YP_003727923.1|  21 EKVKTEKQLKKyATKLKQMNEELEHRVQKQTEEIKNAERLRVLELHHRIKNNLQV--ISSLLNLQSEKFNDDTVNE 94 
                                       4445555554404455666679*********************944444444444..4444433333333333332 PP

>> Spc29  Spindle Pole Component 29
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   4.0     0.018        27     114     168 ..       7      61 ..       1      74 [. 0.82
   2 ?    7.0   0.3    0.0031       4.6       3      21 ..      76      94 ..      74     107 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.018
                             Spc29 114 ssvkkivelekklddqkleIkeLkreleqqrtvnseLqekvaeleeevkrlaale 168
                                        +++ +ve  + + ++  + k+Lk+   + + +n+eL ++v++  ee+k+ + l+
  gi|298676174|ref|YP_003727923.1|   7 GKISAVVEFVRDITEKVKTEKQLKKYATKLKQMNEELEHRVQKQTEEIKNAERLR 61 
                                       56788889999999999999999*999999************9999997655554 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0031
                             Spc29  3 vsqflNsadkklkDDTLnn 21
                                      +s++lN +++k++DDT n+
  gi|298676174|ref|YP_003727923.1| 76 ISSLLNLQSEKFNDDTVNE 94
                                      79**************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2968  (0.165542); expected 358.6 (0.02)
Passed bias filter:                     1151  (0.0641977); expected 358.6 (0.02)
Passed Vit filter:                       155  (0.00864521); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.74u 0.42s 00:00:01.15 Elapsed: 00:00:00.57
# Mc/sec: 1347.93
//
Query:       gi|298676175|ref|YP_003727924.1|  [L=398]
Description: hypothetical protein Metev_2316 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 2312.54
//
Query:       gi|298676176|ref|YP_003727925.1|  [L=174]
Description: membrane-bound metal-dependent hydrolase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-15   55.2   3.8    6.5e-15   54.9   3.8    1.1  1  YdjM      LexA-binding, inner membrane-associated putative hy


Domain annotation for each model (and alignments):
>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   3.8   3.7e-19   6.5e-15       1     157 [.       1     153 [.       1     171 [. 0.77

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 3.7e-19
                              YdjM   1 MdgltHallGaalglalaallgaakeavllavavlgAllPD.iD..hpsstlgrklgllskklaklvgHRgftHSll 74 
                                       M  ++H+ ++++++ ++ + l  +k  + + ++++ A+lPD +D  ++ + + +++          +  R   H+l+
  gi|298676176|ref|YP_003727925.1|   1 MFIFAHIGFTIIIFYLVTKILRLDKP-IDYRLVAFVAILPDlVDkgFGILLFPEQV----------GNGRIYAHTLI 66 
                                       7889******************9876.9999999999****999333333333333..........459******** PP

                              YdjM  75 flallalvlllllrlfgrsalrlglllllgvlsHlllDlltkyGvpllwPfskkkvrlsllfiiidplltll..... 146
                                       f++l+ +++ +++r++g +   +  ++ +g++ HlllD +++ +  l+wP+ + +++ +  ++ +d  ++       
  gi|298676176|ref|YP_003727925.1|  67 FAVLFIVAGDYFVRRRGSY---FVSIIGWGFMCHLLLDKMWTIPQTLYWPLLGLNFKADYEVVQTDFSVYIMqvidn 140
                                       *****************99...56669999***********************999999999977765555466666 PP

                              YdjM 147 ...srrglvalelv 157
                                          s+ ++v l + 
  gi|298676176|ref|YP_003727925.1| 141 vftSGLSQV-LIFE 153
                                       655333333.2222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 1167.93
//
Query:       gi|298676177|ref|YP_003727926.1|  [L=47]
Description: hypothetical protein Metev_2318 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0012   19.2   0.5     0.0014   19.0   0.5    1.1  1  Lar_restr_allev  Restriction alleviation protein Lar
     0.0019   17.7   0.8     0.0027   17.2   0.8    1.3  1  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0048   16.6   0.3     0.0054   16.5   0.3    1.0  1  FlhC             Flagellar transcriptional activator (FlhC)
  ------ inclusion threshold ------
      0.029   14.4   0.9       0.12   12.4   0.9    2.0  1  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
      0.038   14.1   0.5      0.043   13.9   0.5    1.1  1  Opiods_neuropep  Vertebrate endogenous opioids neuropeptide
      0.049   13.6   1.3      0.074   13.0   1.3    1.4  1  DUF4428          Domain of unknown function (DUF4428)
      0.072   13.2   2.9       0.88    9.7   0.1    2.1  2  DUF1272          Protein of unknown function (DUF1272)
       0.16   12.3   0.6       0.16   12.3   0.6    1.5  1  zinc_ribbon_9    zinc-ribbon
       0.21   11.5   2.6        2.8    7.8   2.6    2.0  1  VATC             Vms1-associating treble clef domain


Domain annotation for each model (and alignments):
>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.5   6.8e-07    0.0014       4      36 ..       6      34 ..       4      46 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 6.8e-07
                   Lar_restr_allev  4 kpCPfCggravlersqrvvaeigqcvyCad.Cga 36
                                      k CP Cgg+ v+ ++  +       vyC+  C  
  gi|298676177|ref|YP_003727926.1|  6 KSCPICGGKFVVMEDAANE-----AVYCTLeCLS 34
                                      89************98888.....6999555977 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.8   1.4e-06    0.0027       3      23 ..       8      29 ..       7      35 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.4e-06
                                      ETTTTCEE.CHEETSTTCEEES CS
                      TF_Zn_Ribbon  3 CPnCgstn.lveDpergelvCt 23
                                      CP+Cg+++ + eD+++  ++Ct
  gi|298676177|ref|YP_003727926.1|  8 CPICGGKFvVMEDAANEAVYCT 29
                                      ********889999999999*8 PP

>> FlhC  Flagellar transcriptional activator (FlhC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.3   2.7e-06    0.0054     134     169 ..       5      39 ..       2      43 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.7e-06
                              FlhC 134 lasCkrCkgefvthaedlesefvCglCqlpsRagkt 169
                                       ++sC  C+g+fv+++++ ++++ C+l + +s+a k+
  gi|298676177|ref|YP_003727926.1|   5 MKSCPICGGKFVVMEDAANEAVYCTL-ECLSKAEKS 39 
                                       689*********************99.455666665 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.9   6.3e-05      0.12       2      20 ..       8      28 ..       7      45 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.3e-05
                    DNA_ligase_ZBD  2 CPvCGsavvRee...geaiyRC 20
                                      CP+CG + v  e   +ea+ +C
  gi|298676177|ref|YP_003727926.1|  8 CPICGGKFVVMEdaaNEAV-YC 28
                                      *******996661434555.55 PP

>> Opiods_neuropep  Vertebrate endogenous opioids neuropeptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.5   2.2e-05     0.043       4      35 ..       6      38 ..       5      42 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.2e-05
                   Opiods_neuropep  4 kdCllCayklqdqqksfntlv.ClleCegklss 35
                                      k C  C+ k    +++ n  v C+leC  k+  
  gi|298676177|ref|YP_003727926.1|  6 KSCPICGGKFVVMEDAANEAVyCTLECLSKAEK 38
                                      6899******999999998888*****888766 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.3   3.7e-05     0.074       2      37 ..       8      43 ..       7      47 .] 0.68

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.7e-05
                           DUF4428  2 CaiCgkKigllkrlkleDg.yvCk.dClkKlseflsdv 37
                                      C+iCg+K  +++  + +++ + C+ +Cl+K+  ++ +v
  gi|298676177|ref|YP_003727926.1|  8 CPICGGKFVVME--DAANEaVYCTlECLSKAEKSMNKV 43
                                      ***********9..444443455549****94443444 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00044      0.88      40      52 ..       4      16 ..       1      19 [. 0.83
   2 ?    4.8   0.3     0.015        30      17      29 ..      20      32 ..      17      43 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00044
                           DUF1272 40 lenvCPncgGelv 52
                                      + + CP cgG++v
  gi|298676177|ref|YP_003727926.1|  4 IMKSCPICGGKFV 16
                                      4689*******98 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.015
                           DUF1272 17 pdseearicsyEc 29
                                       +++ea+ c+ Ec
  gi|298676177|ref|YP_003727926.1| 20 DAANEAVYCTLEC 32
                                      567899******9 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.6     8e-05      0.16      23      32 ..       7      16 ..       2      18 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8e-05
                     zinc_ribbon_9 23 lCPhCgggFV 32
                                      +CP Cgg FV
  gi|298676177|ref|YP_003727926.1|  7 SCPICGGKFV 16
                                      6********9 PP

>> VATC  Vms1-associating treble clef domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   2.6    0.0014       2.8       5      33 ..       7      34 ..       4      42 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0014
                              VATC  5 rCsiCgeslegkvyFekfdfrYCstkClr 33
                                      +C iCg +++  +     + +YC+ +Cl 
  gi|298676177|ref|YP_003727926.1|  7 SCPICGGKFVVME-DAANEAVYCTLECLS 34
                                      6777777777533.2445789******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 312.53
//
Query:       gi|298676178|ref|YP_003727927.1|  [L=298]
Description: hypothetical protein Metev_2319 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   3.3e-113  377.9   0.2   3.8e-113  377.7   0.2    1.0  1  DUF1616   Protein of unknown function (DUF1616)
    2.3e-06   26.8   1.8    3.5e-06   26.2   1.8    1.2  1  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
      0.044   14.1   0.1      0.044   14.1   0.1    2.7  2  DUF4064   Protein of unknown function (DUF4064)
       0.22   11.7   0.9         26    5.0   0.0    2.4  2  DUF872    Eukaryotic protein of unknown function (DUF872)


Domain annotation for each model (and alignments):
>> DUF1616  Protein of unknown function (DUF1616)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  377.7   0.2  8.5e-117  3.8e-113       2     293 .]      15     294 ..      14     294 .. 0.96

  Alignments for each domain:
  == domain 1  score: 377.7 bits;  conditional E-value: 8.5e-117
                           DUF1616   2 lvlalllllailvpvlnetplRivlglplvLflPGYaliaaLFPekrdidgieRlaLSfglSiaivpliglvlnvtp 78 
                                       ++l++l+++++lvp+lnetp+Ri+lglp+vLf+PGY liaaLFP+k+d+dgieR+aLSfglSia+vpligl+ln+tp
  gi|298676178|ref|YP_003727927.1|  15 IILVILTIVFVLVPPLNETPIRIILGLPMVLFIPGYSLIAALFPKKDDLDGIERIALSFGLSIAVVPLIGLGLNYTP 91 
                                       789************************************************************************** PP

                           DUF1616  79 wgirlepilvslslftlllalvAivrRsrlpeeerfsvplralieslkeeleek.sesr...ldkalnvlLvvsivl 151
                                       wgirl pi+vsls ft+l++++ i+rRs+l e+e f+vp+++ +es+k+el +  ++s    ldkal+++Lv+si++
  gi|298676178|ref|YP_003727927.1|  92 WGIRLIPIIVSLSTFTILMCVATIIRRSSLDENEVFTVPFKSSLESIKTELLTPpEDSTrpkLDKALSIILVISIIA 168
                                       **************************************************998744433566*************** PP

                           DUF1616 152 avaalgyavvaPkegekfTelyllgedgdelvaenypteltagesqevivgieNhEheevnYtvvvllqevtdeeev 228
                                       ++a+l+y+v++Pk+gekfTe+y+lg++g   +a++yptel+ ge+ +vi+gi+NhE+e+++Yt++++l+++  +   
  gi|298676178|ref|YP_003727927.1| 169 SIATLAYVVTTPKQGEKFTEFYVLGPNG---MADDYPTELEKGEKGTVIIGITNHEYEKTEYTLKMQLENN--T--- 237
                                       ****************************...*************************************983..2... PP

                           DUF1616 229 evlerteldrrevtladnetweqelevepeatgenlrleflLYkdevpeeptteeayrslhlwVn 293
                                             + + +++ l++n+twe++l+++p++tg+n++leflLYkd     ++ +e+yr+lhlwVn
  gi|298676178|ref|YP_003727927.1| 238 ---LPIDNNAKTIALKHNQTWEDTLKFTPHNTGTNMKLEFLLYKD-----NNFTEPYRNLHLWVN 294
                                       ...23567899**********************************.....**************7 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   1.8   7.8e-10   3.5e-06      65     231 ..      14     180 ..       9     195 .. 0.68

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 7.8e-10
                             MFS_1  65 lllglllfalglllllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllg 141
                                       +++ ++l+++++l    +++l      r++ Gl + +lf  g++lia++fpk++   +i  ++++f+l++++ pl+g
  gi|298676178|ref|YP_003727927.1|  14 IIILVILTIVFVL----VPPLN-ETPIRIILGLPM-VLFIPGYSLIAALFPKKDDLDGIERIALSFGLSIAVVPLIG 84 
                                       3333333333322....23333.5569*******7.***************************************** PP

                             MFS_1 142 glla.sslgWravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdp.......... 207
                                         l  + +g r++ +i+ + ++  +++++  + ++ +  +++  +      ++++l ++ ++ll++p          
  gi|298676178|ref|YP_003727927.1|  85 LGLNyTPWGIRLIPIIVSLSTFTILMCVATII-RRSSLDENEVFTVP----FKSSLESIKTELLTPPedstrpkldk 156
                                       *****************999999988766666.33333333333333....45555554555555554444432222 PP

                             MFS_1 208 vlw.illialllfffgfsglltllp 231
                                         + i+l++++++++++ ++++++p
  gi|298676178|ref|YP_003727927.1| 157 A-LsIILVISIIASIATLAYVVTTP 180
                                       1.24566666666666666666665 PP

>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   4.6       1.5   6.6e+03      66      80 ..      12      26 ..       4      32 .. 0.62
   2 ?   14.1   0.1   9.8e-06     0.044       9      84 ..      95     181 ..      91     192 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.5
                           DUF4064 66 vialiaivlgivgal 80
                                      +  +i+ +l+iv++l
  gi|298676178|ref|YP_003727927.1| 12 ITIIILVILTIVFVL 26
                                      445555555555554 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 9.8e-06
                           DUF4064   9 glIGgilgillglllllflfllssgefsqeltee...........qalsgedasavleflstllivlgvialiaivl 74 
                                       +lI +i+++  + +l+ ++ ++ +++ +++  ++           ++l +   +++   l + l +++vi++ia+++
  gi|298676178|ref|YP_003727927.1|  95 RLIPIIVSLSTFTILMCVATIIRRSSLDENEVFTvpfksslesikTELLTPPEDSTRPKLDKALSIILVISIIASIA 171
                                       78999**************************999*******9999999999999999******************** PP

                           DUF4064  75 givgalllkk 84 
                                       +++ ++   k
  gi|298676178|ref|YP_003727927.1| 172 TLAYVVTTPK 181
                                       **99987665 PP

>> DUF872  Eukaryotic protein of unknown function (DUF872)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   1.1     0.013        60      56      91 ..      15      50 ..       3      59 .. 0.77
   2 ?    5.0   0.0    0.0058        26      47      83 ..     157     193 ..     132     194 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.013
                            DUF872 56 GlvLlllgvvilvepseGvssavflvlGlllfiPGv 91
                                       ++++l+ v++lv p + +   + l l ++lfiPG 
  gi|298676178|ref|YP_003727927.1| 15 IILVILTIVFVLVPPLNETPIRIILGLPMVLFIPGY 50
                                      345566678899999999999999***********5 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0058
                            DUF872  47 laallLlllGlvLlllgvvilvepseGvssavflvlG 83 
                                       +++++L++  ++ +++ ++++++p++G++ + f+vlG
  gi|298676178|ref|YP_003727927.1| 157 ALSIILVISIIASIATLAYVVTTPKQGEKFTEFYVLG 193
                                       578999999999999999***************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       931  (0.051927); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2125.72
//
Query:       gi|298676179|ref|YP_003727928.1|  [L=282]
Description: abortive infection protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-17   63.2   5.4    2.3e-17   63.2   5.4    2.4  2  CPBP      CPBP intramembrane metalloprotease
  ------ inclusion threshold ------
       0.15   12.2   0.4        2.2    8.4   0.1    2.4  2  DUF1419   Protein of unknown function (DUF1419)


Domain annotation for each model (and alignments):
>> CPBP  CPBP intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   1.0     0.093   8.4e+02      60      77 ..      59      76 ..      23     159 .. 0.81
   2 !   63.2   5.4   2.5e-21   2.3e-17       4      91 ..     177     266 ..     172     267 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.093
                                      HHHHHHHHHHHHHHHHTT CS
                              CPBP 60 llaalaGlvlgylylktg 77
                                       l++l+Glvl+ ++++++
  gi|298676179|ref|YP_003727928.1| 59 HLIILIGLVLSTVWIQEK 76
                                      566777888887777665 PP

  == domain 2  score: 63.2 bits;  conditional E-value: 2.5e-21
                                       THHHHHHHHHHHHHHHHHHHTTCHHHHHHHH.S-HHHHHHHHHHHHHCSGGG.HHH.HHHHHHHHHHHHHHHHHTT- CS
                              CPBP   4 lllvfllalllapllEEllfRglllqllqergsstlailissilFglaHlpn.gps.vllaalaGlvlgylylktgs 78 
                                       +l + ++++++++l+EEl+fR++l+++l++ ++ +  +li+s+lFg++H ++ +++ +++++laGlv+gy++ kt+s
  gi|298676179|ref|YP_003727928.1| 177 ILELSIVMIFFVGLVEELIFRSILQTRLENSFGLLPGLLITSLLFGMMHSIYgNVYeIFFTSLAGLVIGYMFQKTRS 253
                                       566778999**********************888***************99977778******************** PP

                                       HHHHHHHHHHHHH CS
                              CPBP  79 llaaillHallnl 91 
                                       l +++++H+ +n+
  gi|298676179|ref|YP_003727928.1| 254 LPVVAITHGTVNI 266
                                       ***********97 PP

>> DUF1419  Protein of unknown function (DUF1419)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.042   3.8e+02      63      93 ..      46      76 ..       5      84 .. 0.81
   2 ?    8.4   0.1   0.00024       2.2      50      87 ..     200     237 ..     195     244 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.042
                           DUF1419 63 Plflrgdmfalrefltgsvtsvffalkidgr 93
                                       l+++++ fa+   l   ++ v+ +++i+++
  gi|298676179|ref|YP_003727928.1| 46 MLYMQKQSFAIGLHLIILIGLVLSTVWIQEK 76
                                      489*********9999999999999999886 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00024
                           DUF1419  50 seaehdymleilPPlflrgdmfalrefltgsvtsvffa 87 
                                        +++ +  + +lP l + + +f++ + + g+v  +ff+
  gi|298676179|ref|YP_003727928.1| 200 LQTRLENSFGLLPGLLITSLLFGMMHSIYGNVYEIFFT 237
                                       5667778899**************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1817.65
//
Query:       gi|298676180|ref|YP_003727929.1|  [L=86]
Description: hypothetical protein Metev_2321 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 563.57
//
Query:       gi|298676181|ref|YP_003727930.1|  [L=405]
Description: hypothetical protein Metev_2322 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.7e-06   26.5   1.0    0.00031   20.7   0.0    3.0  3  Y_Y_Y       Y_Y_Y domain
  ------ inclusion threshold ------
      0.028   14.6   0.2         12    6.0   0.0    3.2  4  DUF669      Protein of unknown function (DUF669)
      0.043   13.8   1.1        1.7    8.7   0.7    3.3  4  BsuPI       Intracellular proteinase inhibitor
      0.067   13.4   2.0          9    6.6   0.6    3.6  3  Big_3_5     Bacterial Ig-like domain (group 3)
      0.076   12.0   0.8       0.11   11.4   0.8    1.2  1  Tox-ODYAM1  Toxin in Odyssella and Amoebophilus


Domain annotation for each model (and alignments):
>> Y_Y_Y  Y_Y_Y domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.1       3.8   1.4e+04       3      33 ..     121     128 ..     111     131 .. 0.53
   2 ?    3.2   0.0     0.024        88      25      45 ..     186     207 ..     178     212 .. 0.77
   3 !   20.7   0.0   8.5e-08   0.00031      17      55 ..     324     364 ..     322     375 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 3.8
                                       TCCTTEEEEEEEETTESSEEEESSTS.EEEE CS
                             Y_Y_Y   3 dnperllYrYrlegidkeWveasdysqeasy 33 
                                       ++ +                       +++y
  gi|298676181|ref|YP_003727930.1| 121 SGKN-----------------------NVTY 128
                                       2333.......................3333 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.024
                                       SSTS..EEEEES--SEEEEEEE CS
                             Y_Y_Y  25 sdysq.easytnlppGdYtlkV 45 
                                       +d++  + ++ nl +G+Y +++
  gi|298676181|ref|YP_003727930.1| 186 DDNGDtNGEFENLDAGEYSVLI 207
                                       444445789*********9865 PP

  == domain 3  score: 20.7 bits;  conditional E-value: 8.5e-08
                                       TESSEEEESSTS...EEEEES--SEEEEEEEEEEETTS-B- CS
                             Y_Y_Y  17 idkeWveasdysq..easytnlppGdYtlkVkakdndgqwn 55 
                                       ++++ ++ +++++  ++s   lppG+Y+l+V+a++ +    
  gi|298676181|ref|YP_003727930.1| 324 LSGKTMTVDSNQTslNISTEGLPPGNYKLLVQASNQNDPIV 364
                                       567888888888899*******************9876555 PP

>> DUF669  Protein of unknown function (DUF669)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0    0.0034        12       5      25 ..     188     209 ..     184     231 .. 0.80
   2 ?   -2.5   0.0       1.5   5.2e+03     106     128 ..     238     259 ..     223     268 .. 0.71
   3 ?   -2.6   0.0       1.5   5.5e+03      44      69 ..     271     295 ..     267     308 .. 0.71
   4 ?    4.7   0.0    0.0082        29       2      27 ..     330     358 ..     329     362 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0034
                            DUF669   5 ssnve.gfealpsGeYevtivs 25 
                                       + +++ +fe+l++GeY v i+ 
  gi|298676181|ref|YP_003727930.1| 188 NGDTNgEFENLDAGEYSVLIIL 209
                                       5566746***********9984 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.5
                            DUF669 106 lnkplkvkVkleedkngkkYpeV 128
                                       ++++lkv+++le+   + +Y  +
  gi|298676181|ref|YP_003727930.1| 238 VGNNLKVDIELEDAP-DTEYTYI 259
                                       467778888877766.5666555 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.5
                            DUF669  44 evRsDldgklkgrkikydnlvvikdn 69 
                                       +vR + +g  +g+ ++ +n ++i+ +
  gi|298676181|ref|YP_003727930.1| 271 DVRLETNGHKTGTDLLVNNEYIID-D 295
                                       566677788888888888888884.3 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.0082
                            DUF669   2 tfdssnve.g..fealpsGeYevtivsae 27 
                                       t+ds++++ +  +e lp+G+Y+  +++++
  gi|298676181|ref|YP_003727930.1| 330 TVDSNQTSlNisTEGLPPGNYKLLVQASN 358
                                       7999999874669**********998775 PP

>> BsuPI  Intracellular proteinase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.7   0.00047       1.7       8      66 ..      87     143 ..      81     164 .. 0.80
   2 ?   -0.3   0.0      0.31   1.1e+03      79      98 ..     194     212 ..     172     214 .. 0.74
   3 ?   -2.5   0.0       1.5   5.5e+03      68      95 ..     236     262 ..     229     267 .. 0.63
   4 ?    0.1   0.0      0.23   8.1e+02      81      98 ..     341     359 ..     324     361 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00047
                                       EE-SS-EEEEEEEEE-SSS-EEEEESSS--EEEEEE-TT--EEEETTTT-------EEE CS
                             BsuPI   8 easgeavelaltvtNesdeavtlqFssgqkydlvvkdeegeevwrysegrmFtqalsse 66 
                                       ++ +++v+++l v+N +d  ++  F++ q y       ++++ +++   + F+   s++
  gi|298676181|ref|YP_003727930.1|  87 STDSKNVDIKLNVKNYTDYVIEYPFETHQMYTNTS--GKNNVTYQFNGSKYFANKESKV 143
                                       455668***********************997655..7888888888888888765555 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.31
                                       EE.S---SEEEEEEEEE--E CS
                             BsuPI  79 twdedlepGeYtleaelvae 98 
                                       ++ e+l +GeY++ ++l++e
  gi|298676181|ref|YP_003727930.1| 194 EF-ENLDAGEYSVLIILNNE 212
                                       34.78999****99998876 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.5
                                       E-TT-EEEEEEEE.S---SEEEEEEEEE CS
                             BsuPI  68 lepgesatyeetwdedlepGeYtleael 95 
                                       +  g+++ ++ ++ ed +  eYt+ a +
  gi|298676181|ref|YP_003727930.1| 236 ITVGNNLKVDIEL-EDAPDTEYTYIAGI 262
                                       4556666666666.67777777776655 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.23
                                       ..S---SEEEEEEEEE--E CS
                             BsuPI  81 d.edlepGeYtleaelvae 98 
                                       + e l+pG+Y+l ++  ++
  gi|298676181|ref|YP_003727930.1| 341 StEGLPPGNYKLLVQASNQ 359
                                       137899****999877665 PP

>> Big_3_5  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.6    0.0025         9      55      81 ..     118     144 ..      85     148 .. 0.86
   2 ?   -0.0   0.0      0.28     1e+03      38      63 ..     181     205 ..     172     219 .. 0.81
   3 ?    2.7   0.0      0.04   1.4e+02      38      64 ..     326     353 ..     315     361 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0025
                                       -SS-EEEEEEEEEE-TTS---S--EEE CS
                           Big_3_5  55 alaaGthsitAtYsGdanyaastssav 81 
                                       + + G++++t +++G++ +a   s  v
  gi|298676181|ref|YP_003727930.1| 118 TNTSGKNNVTYQFNGSKYFANKESKVV 144
                                       3579*****************999866 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.28
                                       SS-EE--TTSEEEEEEE-SS-EEEEE CS
                           Big_3_5  38 gtavllsanGtAtltvsalaaGthsi 63 
                                        t+  l++nG  +  +++l aG++s+
  gi|298676181|ref|YP_003727930.1| 181 ETKD-LDDNGDTNGEFENLDAGEYSV 205
                                       4444.4559***************98 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.04
                                       SS-EE--.TTSEEEEEEE-SS-EEEEEE CS
                           Big_3_5  38 gtavlls.anGtAtltvsalaaGthsit 64 
                                       g +++++ ++ + ++++++l++G++++ 
  gi|298676181|ref|YP_003727930.1| 326 GKTMTVDsNQTSLNISTEGLPPGNYKLL 353
                                       6677777234567777788******975 PP

>> Tox-ODYAM1  Toxin in Odyssella and Amoebophilus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.8   3.2e-05      0.11      41     112 ..     103     177 ..      87     189 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.2e-05
                        Tox-ODYAM1  41 dkivldynakycqevtklsrfskakqkf..skafaklakvikdvvlGpeinslkklqqkveaaygs...evlkldrg 112
                                          v++y     q +t+ s  +++  +f  sk fa+  k +k v++  +insl+++ +k +++  +   ++l ld++
  gi|298676181|ref|YP_003727930.1| 103 TDYVIEYPFETHQMYTNTSGKNNVTYQFngSKYFAN--KESKVVLIESDINSLIDILDKFKQGQIDsinDILSLDKV 177
                                       557999**99***********999988743677876..67898899*************999976511145556554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       847  (0.0472419); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2697.96
//
Query:       gi|298676182|ref|YP_003727931.1|  [L=262]
Description: hypothetical protein Metev_2323 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1836.35
//
Query:       gi|298676183|ref|YP_003727932.1|  [L=181]
Description: hypothetical protein Metev_2324 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-26   93.2   9.9    1.2e-26   92.9   9.4    1.4  1  UPF0228   Uncharacterised protein family (UPF0228)
  ------ inclusion threshold ------
       0.26   11.7   2.9       0.52   10.7   0.4    2.2  2  DUF3221   Protein of unknown function (DUF3221)


Domain annotation for each model (and alignments):
>> UPF0228  Uncharacterised protein family (UPF0228)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.9   9.4   1.4e-30   1.2e-26       6     120 ..      63     176 ..      58     179 .. 0.96

  Alignments for each domain:
  == domain 1  score: 92.9 bits;  conditional E-value: 1.4e-30
                           UPF0228   6 tieydsniveekyYivvdkdnitdvrkelekeknwtssipaikkgdeyiievseqaiedeevlaiLekydlqvkkfv 82 
                                       +++y+ n+ +++yY+vv++d+ + +++el k + w+   ++ikkgd+y+i vs+ + +++++l iL+k dlq+kkfv
  gi|298676183|ref|YP_003727932.1|  63 KLDYNINHLHNQYYLVVNQDKKSVLYNELMKANIWIRDEEVIKKGDNYLIVVSKSIANNKDFLDILSKQDLQLKKFV 139
                                       79*************************************************************************** PP

                           UPF0228  83 wCyiefgdgsekywineedairikneLeknekilsvsl 120
                                        Cyi f++ ++++ +  +   +ik+eL +++ki+ v l
  gi|298676183|ref|YP_003727932.1| 140 NCYIYFSKQPKDW-VGYDKGQKIKKELLEKDKIIRVAL 176
                                       ***********65.99999***************9976 PP

>> DUF3221  Protein of unknown function (DUF3221)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1     0.059   5.3e+02      21      61 ..      59      98 ..      46     101 .. 0.62
   2 ?   10.7   0.4   5.8e-05      0.52       4      58 ..     103     162 ..     102     165 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.059
                           DUF3221 21 eeaenlseeeiekykgeaiwvlidsdkvsnlevGqkVrVwf 61
                                       e+++l+++ i   +++ ++v+++++k   + + +k ++w+
  gi|298676183|ref|YP_003727932.1| 59 REDIKLDYN-INHLHNQYYLVVNQDKKSVLYNELMKANIWI 98
                                      455554444.4666677777766666666666666666666 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 5.8e-05
                           DUF3221   4 vieksdnriLvvse...iekeeaenlseee..iekykgeaiwvlidsdkvsnlevGqkVr 58 
                                       vi+k dn ++vvs+   ++k+  + ls+++  ++k+ +  i+++ + ++  ++ +Gqk++
  gi|298676183|ref|YP_003727932.1| 103 VIKKGDNYLIVVSKsiaNNKDFLDILSKQDlqLKKFVNCYIYFSKQPKDWVGYDKGQKIK 162
                                       899*********9854469999999999999999999999999***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       904  (0.0504211); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1198.94
//
Query:       gi|298676184|ref|YP_003727933.1|  [L=115]
Description: hypothetical protein Metev_2325 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 760.23
//
Query:       gi|298676185|ref|YP_003727934.1|  [L=494]
Description: hypothetical protein Metev_2326 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.041   13.9   4.3      0.069   13.1   4.3    1.3  1  PGF-CTERM  PGF-CTERM motif
      0.042   14.2   0.1          2    8.8   0.0    2.5  2  TraA       TraA


Domain annotation for each model (and alignments):
>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   4.3   7.7e-06     0.069       6      23 .]     477     494 .]     477     494 .] 0.95

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.7e-06
                         PGF-CTERM   6 avlAlaGLLaaalLaRRr 23 
                                       +++A++G+L+a+lL++Rr
  gi|298676185|ref|YP_003727934.1| 477 ILIAVIGILGAVLLVKRR 494
                                       689**************9 PP

>> TraA  TraA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00022         2      23      55 ..      11      43 ..       2      80 .. 0.83
   2 ?    2.7   0.0     0.017   1.6e+02      61      84 ..     257     279 ..     244     288 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00022
                              TraA 23 rvftkkkllklakvvlpvavliaffpdlamaat 55
                                        ++k k+++lak+ + ++ +i+f+p +    t
  gi|298676185|ref|YP_003727934.1| 11 NEYNKNKAIHLAKALIFITLIILFIPSVNAEVT 43
                                      469***********************9875554 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.017
                              TraA  61 mksgdatvkatfgkdssvvkwvvl 84 
                                       m+s +  vk+ f k+s  vk++ +
  gi|298676185|ref|YP_003727934.1| 257 MRS-NQLVKSEFNKESNPVKYINI 279
                                       554.778*************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (494 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1374  (0.0766356); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.55
# Mc/sec: 2701.52
//
Query:       gi|298676186|ref|YP_003727935.1|  [L=228]
Description: hypothetical protein Metev_2327 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00014   22.7   0.1    0.00041   21.2   0.0    1.9  2  Pilin_N   Archaeal Type IV pilin, N-terminal


Domain annotation for each model (and alignments):
>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   2.3e-08   0.00041      12      72 ..       1      78 [.       1      88 [. 0.70
   2 ?   -2.8   0.0      0.73   1.3e+04      60      76 ..     138     154 ..     125     158 .. 0.63

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.3e-08
                           Pilin_N 12 mvaitvIlaAviaafvlgl.asneekapqasi.............evkidssastgkna.....vslehkgGdsidtkd 71
                                      mvaitvIlaAv++ + +gl    + ++p+ ++                 d s++t++ +     v++ ++ G +id ++
  gi|298676186|ref|YP_003727935.1|  1 MVAITVILAAVLGESLFGLgITSKLTEPKDQLvfdntqvllgveyRS-WDGSGGTEN-NgdidhVYMDYQHGPVIDGQE 77
                                      9******************7567778888777667776666553211.222222322.246778999999999998876 PP

                           Pilin_N 72 l 72
                                      +
  gi|298676186|ref|YP_003727935.1| 78 I 78
                                      6 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.73
                           Pilin_N  60 ehkgGdsidtkdlkivl 76 
                                       + ++G  ++ +d+ +++
  gi|298676186|ref|YP_003727935.1| 138 KGQSGGKTNPEDIGVQY 154
                                       44556666667776664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1403.47
//
Query:       gi|298676187|ref|YP_003727936.1|  [L=243]
Description: hypothetical protein Metev_2328 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1605.66
//
Query:       gi|298676188|ref|YP_003727937.1|  [L=180]
Description: hypothetical protein Metev_2329 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-41  139.1   4.1    6.3e-41  139.1   4.1    2.0  2  UPF0228   Uncharacterised protein family (UPF0228)


Domain annotation for each model (and alignments):
>> UPF0228  Uncharacterised protein family (UPF0228)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.4   0.2    0.0074   1.3e+02      53      77 ..      40      63 ..      27      65 .. 0.84
   2 !  139.1   4.1   3.5e-45   6.3e-41       3     124 .]      64     179 ..      62     179 .. 0.97

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.0074
                           UPF0228 53 yiievseqaiedeevlaiLekydlq 77
                                      y+i+  e  + ++e+ +iL +ydl 
  gi|298676188|ref|YP_003727937.1| 40 YYIAF-EDNVTEQEIESILTNYDLI 63
                                      78887.78888899********996 PP

  == domain 2  score: 139.1 bits;  conditional E-value: 3.5e-45
                           UPF0228   3 vnYtieydsniveekyYivvdkdnitdvrkelekeknwtssipaikkgdeyiievseqaiedeevlaiLekydlqvk 79 
                                       +nYtieyd++++++ yY++vdk+n+t+v++ +  +++w+s++++ k++d+yii++ ++ i+d evl++Le+y+lq+k
  gi|298676188|ref|YP_003727937.1|  64 INYTIEYDEGRRPS-YYTSVDKNNFTSVYYGDLLSRTWASRGMVSKNNDDYIISI-RKPIND-EVLETLESYNLQLK 137
                                       7*********8887.****************************************.9*****.9************* PP

                           UPF0228  80 kfvwCyiefgdgsekywineedairikneLeknekilsvsldyiv 124
                                       kfvwCyi++g+gs+   +n++d+i+ik++Leknekil+v++dyiv
  gi|298676188|ref|YP_003727937.1| 138 KFVWCYIDYGTGSH---VNRKDSIKIKDKLEKNEKILFVRFDYIV 179
                                       **************...9*************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1122.14
//
Query:       gi|298676189|ref|YP_003727938.1|  [L=75]
Description: hypothetical protein Metev_2330 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.012   15.2   2.3      0.012   15.2   2.3    2.2  3  DUF3149       Protein of unknown function (DUF3149)
        0.6    9.6   1.7       0.67    9.5   1.7    1.1  1  E1-E2_ATPase  E1-E2 ATPase
        1.3    7.7   6.1        1.5    7.5   6.1    1.0  1  DUF2207       Predicted membrane protein (DUF2207)
        3.1    7.9   5.6        3.8    7.6   5.6    1.0  1  DHHC          DHHC palmitoyltransferase


Domain annotation for each model (and alignments):
>> DUF3149  Protein of unknown function (DUF3149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.2      0.31   1.4e+03      14      20 ..      14      20 ..      10      26 .. 0.71
   2 ?   -3.5   0.3       1.8   8.2e+03      27      32 ..      36      41 ..      34      42 .. 0.64
   3 ?   15.2   2.3   2.7e-06     0.012      15      33 ..      54      72 ..      53      75 .] 0.89

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.31
                           DUF3149 14 liVIvft 20
                                      l+VI++ 
  gi|298676189|ref|YP_003727938.1| 14 LLVILLL 20
                                      6777765 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.8
                           DUF3149 27 firyFi 32
                                       +++F 
  gi|298676189|ref|YP_003727938.1| 36 LYSFFR 41
                                      577875 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 2.7e-06
                           DUF3149 15 iVIvftigmgaffiryFir 33
                                      ++I+++ig+++ff+ry ++
  gi|298676189|ref|YP_003727938.1| 54 LGIFVIIGIVGFFLRYLVK 72
                                      68**************876 PP

>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   1.7   0.00015      0.67     115     170 ..       2      61 ..       1      68 [. 0.72

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00015
                                       HHHHHHHHHHHHHHHHHHHHHS-STTTSSTT....HHHHHHHHHHHHHS-TTHHHHHHHH CS
                      E1-E2_ATPase 115 ldklgkvlvpvvlliallvflialllgksla....eallralallvaaiPcaLplavpla 170
                                       l+kl + l+ +vll++ll++ ++++l++++     ++++r ++ +++ +  aL+++v + 
  gi|298676189|ref|YP_003727938.1|   2 LQKLNSNLISTVLLVILLLLTLLYYLEEFIHpgalYSFFRYISQFIGGVCYALGIFVIIG 61 
                                       45555666666666666666666666666556666******************9998775 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   6.1   0.00034       1.5     387     437 ..       9      74 ..       2      75 .] 0.70

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00034
                           DUF2207 387 glgliilglilillallllvll..................lvfllilllillliaiivlllfsrllgrr 437
                                       ++  ++l+++l+l +l+    l                  +++ + ++l++++i+ iv +++++l++r+
  gi|298676189|ref|YP_003727938.1|   9 LISTVLLVILLLLTLLYY---LeefihpgalysffryisqFIGGVCYALGIFVIIGIVGFFLRYLVKRF 74 
                                       333333333333333333...13458899********************************99999985 PP

>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   5.6   0.00085       3.8      55     118 ..       9      70 ..       7      74 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00085
                              DHHC  55 llylllllilalvlllialvklveeekkseflavtllkkllsilllvlsllfllllgllllfhl 118
                                       l++++ll+il l++ll++l + ++     +f ++    +++  ++++l +++++ ++ ++l++l
  gi|298676189|ref|YP_003727938.1|   9 LISTVLLVILLLLTLLYYLEEFIHPGALYSFFRYIS--QFIGGVCYALGIFVIIGIVGFFLRYL 70 
                                       789999999999999999999999999998887754..45777777777777777777776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1053  (0.0587317); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 542.58
//
Query:       gi|298676190|ref|YP_003727939.1|  [L=273]
Description: hypothetical protein Metev_2331 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.083   12.6   0.0       0.65    9.7   0.0    1.9  2  MMADHC    Methylmalonic aciduria and homocystinuria type D pr


Domain annotation for each model (and alignments):
>> MMADHC  Methylmalonic aciduria and homocystinuria type D protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   3.6e-05      0.65     191     220 ..     116     145 ..     112     151 .. 0.89
   2 ?    0.5   0.0     0.024   4.2e+02      16      53 ..     211     251 ..     201     268 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 3.6e-05
                            MMADHC 191 saLqseGyWaDFidPssGraffgsytnatl 220
                                       ++L s GyW DFi    G+  +g +t+++ 
  gi|298676190|ref|YP_003727939.1| 116 DKLSSGGYWDDFIAKKDGKIMMGFKTDNSQ 145
                                       68999*****************99999875 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.024
                            MMADHC  16 sdepaiaispanlskrtvwpdeamgpf...gpqdqrfqLpg 53 
                                       +++  i+is + +  rt  pde +g++    ++ +r +L +
  gi|298676190|ref|YP_003727939.1| 211 KTTVDIEISITCYNDRTNRPDEYQGYYecyVENKHRTNLIN 251
                                       5566689999999***********99855545555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1984.21
//
Query:       gi|298676191|ref|YP_003727940.1|  [L=56]
Description: hypothetical protein Metev_2332 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.084   13.6   0.4      0.092   13.4   0.4    1.0  1  GRP       Glycine rich protein family


Domain annotation for each model (and alignments):
>> GRP  Glycine rich protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.4   5.1e-06     0.092       1      46 [.       1      48 [.       1      52 [. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.1e-06
                               GRP  1 Maska.lilLglllaavlLissevaaael.skeeksekeeevkdekyg 46
                                      M++k   +l+ ++l+++ ++s  + +++  +k++ s+k++++  ek g
  gi|298676191|ref|YP_003727940.1|  1 MKAKSsTLLMVMVLISMAFVSAVIGQNNIsNKTQYSDKTDNISLEKAG 48
                                      55554378888999999****999999886677889999999888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 447.93
//
Query:       gi|298676192|ref|YP_003727941.1|  [L=400]
Description: carbohydrate-binding and sugar hydrolysis protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-44  151.4 123.7      2e-19   69.8  35.8    3.1  3  NosD             Periplasmic copper-binding protein (NosD)
    4.7e-36  124.0 133.2    1.2e-17   64.2  39.8    3.4  4  Beta_helix       Right handed beta helix region


Domain annotation for each model (and alignments):
>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.8  35.8   2.3e-23     2e-19       5     173 ..      47     228 ..      43     229 .. 0.81
   2 !   62.9  29.0   2.9e-21   2.6e-17      59     172 ..     205     315 ..     203     316 .. 0.97
   3 !   46.3  42.9   3.4e-16   3.1e-12      39     178 ..     229     366 ..     228     379 .. 0.76

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 2.3e-23
                              NosD   5 isgdevlvsa..rgngiqlens............egseisnneisnsrdgilldnssnntitgntienl....ryGi 63 
                                        sgd+++v+   +     +en+            ++ e +  + +++++++   ns++++i+g +i       ++G+
  gi|298676192|ref|YP_003727941.1|  47 NSGDNIVVYPgkY-----VENIvidkevsiesksKNPENTVIQSKTPEKNVIQVNSNKVNISGFKIMGAkntnQSGV 118
                                       5667776664441.....33333222244443332222344555566677788899999999996666556679*** PP

                              NosD  64 hlensesntiedntlssnesGialmsssnntlenNtisnnenyGillsdssnntisnNtis.nnnkGiflensssnt 139
                                       +l+  e+++i+++++s+n +G+++ +s+ ntl nNt+++n+n+Gi+l++s+nn + nN +  n+ +Gifl++s +n 
  gi|298676192|ref|YP_003727941.1| 119 YLDRVEKCNISNSIFSKNFNGVSFIKSEWNTLVNNTVKSNKNHGIYLKKSKNNRVINNIVGsNSRYGIFLQRSINNN 195
                                       ************************************************************76*************** PP

                              NosD 140 itgNriesnqkiGilllsssegntiynNyFinns 173
                                       i  N+i+++ + Gil +++s++n + +N F++n+
  gi|298676192|ref|YP_003727941.1| 196 IITNHIQNHSNNGIL-VDHSNNNFLGDNKFFGNE 228
                                       ***************.***************996 PP

  == domain 2  score: 62.9 bits;  conditional E-value: 2.9e-21
                              NosD  59 lryGihlensesntiedntlssnesGialmsssnntlenNtisnnenyGillsdssnntisnNtisnnnkGiflens 135
                                       +++Gi ++ s++n + dn++++ne+Gi+++ss+ n l+ N+isnn++ Gi    s++n++ nN i++n+ Gifl++ 
  gi|298676192|ref|YP_003727941.1| 205 SNNGILVDHSNNNFLGDNKFFGNEYGIYIHSSQSNKLKVNNISNNKI-GIQGGLSNKNELINNSILKNKVGIFLYKC 280
                                       578********************************************.***************************** PP

                              NosD 136 ssntitgNriesnqkiGilllsssegntiynNyFinn 172
                                       ++n i  N i++n   Gil l++s +n+i nN++ n+
  gi|298676192|ref|YP_003727941.1| 281 NGNDIIANIINENIHKGIL-LQYSVDNKISNNTL-NS 315
                                       *******************.**************.53 PP

  == domain 3  score: 46.3 bits;  conditional E-value: 3.4e-16
                              NosD  39 dgilldnssnntitgntienlryGihlensesntiedntlssnesGialmsssnntlenNtisnnenyGillsdssn 115
                                       +gi++ +s++n+++ n i+n++ Gi    s++n + +n + +n+ Gi+l++ ++n +  N+i++n  +Gill++s +
  gi|298676192|ref|YP_003727941.1| 229 YGIYIHSSQSNKLKVNNISNNKIGIQGGLSNKNELINNSILKNKVGIFLYKCNGNDIIANIINENIHKGILLQYSVD 305
                                       57888888888888888888888888888888888888888888888888888886668888888888888888888 PP

                              NosD 116 ntisnNtisnnnkGiflens.ssntitgNriesnqkiGilllsssegntiynNyFinnsenvky 178
                                       n+isnNt  +n+ Gi +e+  ++nt+  N++++n    i   ++++ n+i nNy+ nns +  +
  gi|298676192|ref|YP_003727941.1| 306 NKISNNTLNSNGLGIIMEDFsNNNTVHYNSLSKN-RDNIR--ANYSINQIKNNYMNNNSSQNLN 366
                                       8888888888888888888657888888888888.77777..6666888888888665555444 PP

>> Beta_helix  Right handed beta helix region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   1.3      0.17   1.6e+03     100     129 ..      34      65 ..      20      86 .. 0.62
   2 !   64.2  39.8   1.3e-21   1.2e-17       3     157 ..      93     245 ..      91     246 .. 0.94
   3 !   51.1  33.4   1.4e-17   1.3e-13      16     144 ..     199     321 ..     199     324 .. 0.96
   4 !   36.2  44.0   5.5e-13   4.9e-09       1     158 []     229     379 ..     229     379 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.17
                                       -S--EEES-EEESTT--SEE---TT..---EE CS
                        Beta_helix 100 ssnntienNiidnnagsGividdss..snvtv 129
                                       ++ ++i++ + d+n+g+ iv+++++   n+++
  gi|298676192|ref|YP_003727941.1|  34 NNYTSIKKAVNDANSGDNIVVYPGKyvENIVI 65 
                                       44466777777778888888888884333333 PP

  == domain 2  score: 64.2 bits;  conditional E-value: 1.3e-21
                                       EEE-SS-E.EEESEEEES-...SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT- CS
                        Beta_helix   3 isingssnvtiknntisns...ggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfg 76 
                                       i +n++++ +i++++i+++   +++G+yl+  +++ i+n+ +++ +++G++  +s+ nt+ nnt+  n++ gi+l++
  gi|298676192|ref|YP_003727941.1|  93 IQVNSNKV-NISGFKIMGAkntNQSGVYLDRVEKCNISNSIFSK-NFNGVSFIKSEWNTLVNNTVKSNKNHGIYLKK 167
                                       45555555.*****************************999999.******************************** PP

                                       -S--EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EE CS
                        Beta_helix  77 asnnlienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtv 153
                                       ++nn + nn +  n+++Gi+l+ s nn i  N+i n +++Gi +d s+ n+   +N++++n  +Gi++ +s+s +++
  gi|298676192|ref|YP_003727941.1| 168 SKNNRVINNIVGSNSRYGIFLQRSINNNIITNHIQNHSNNGILVDHSN-NNFLGDNKFFGNE-YGIYIHSSQS-NKL 241
                                       ************************************************.8889********8.*******999.777 PP

                                       ES-E CS
                        Beta_helix 154 rnNt 157
                                       + N+
  gi|298676192|ref|YP_003727941.1| 242 KVNN 245
                                       7666 PP

  == domain 3  score: 51.1 bits;  conditional E-value: 1.4e-17
                                       EEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS CS
                        Beta_helix  16 ntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnlienneitdngg 92 
                                       n+i+n +++Gi +++s+n+ + +n++ + +++Giyi++s+ n+++ n+is+n+  gi    +++n + nn i +n+ 
  gi|298676192|ref|YP_003727941.1| 199 NHIQNHSNNGILVDHSNNNFLGDNKFFG-NEYGIYIHSSQSNKLKVNNISNNK-IGIQGGLSNKNELINNSILKNKV 273
                                       789*************************.************************.*********************87 PP

                                       -SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE- CS
                        Beta_helix  93 sGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiav 144
                                        Gi+l+ ++ n+i  Nii++n + Gi +++s  +++++nNt+++n+  Gi +
  gi|298676192|ref|YP_003727941.1| 274 -GIFLYKCNGNDIIANIINENIHKGILLQYSV-DNKISNNTLNSNG-LGI-I 321
                                       .*******************************.************7.777.4 PP

  == domain 4  score: 36.2 bits;  conditional E-value: 5.5e-13
                                       -SEEE-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT-- CS
                        Beta_helix   1 sgisingssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfga 77 
                                       +gi+i +s++ ++k n+isn ++ Gi+ + s+++ + nn i + +  Gi ++++++n i  n i++n + gi l+++
  gi|298676192|ref|YP_003727941.1| 229 YGIYIHSSQSNKLKVNNISN-NKIGIQGGLSNKNELINNSILK-NKVGIFLYKCNGNDIIANIINENIHKGILLQYS 303
                                       68999999999999999999.5999999999999999999999.999999999999999999999999999999999 PP

                                       S--EEES-EEES-SS-SEE-TT.-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EE CS
                        Beta_helix  78 snnlienneitdnggsGiylny.ssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtv 153
                                         n i+nn+ + ng  Gi +++ s+nnt+++N ++ n+ + i  ++s   + ++nN ++nn+  + +++++s+++ +
  gi|298676192|ref|YP_003727941.1| 304 VDNKISNNTLNSNGL-GIIMEDfSNNNTVHYNSLSKNR-DNIRANYSI--NQIKNNYMNNNS--SQNLNSDSHEIPF 374
                                       999999999999988.9999987889999999999999.999999999..666999999998..5556777777888 PP

                                       ES-E. CS
                        Beta_helix 154 rnNti 158
                                        n t+
  gi|298676192|ref|YP_003727941.1| 375 INSTF 379
                                       88776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1239  (0.0691059); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 2757.73
//
Query:       gi|298676193|ref|YP_003727942.1|  [L=46]
Description: hypothetical protein Metev_2334 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.43
# Mc/sec: 323.49
//
Query:       gi|298676194|ref|YP_003727943.1|  [L=1594]
Description: hypothetical protein Metev_2335 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-10   40.0  49.9     0.0035   17.5   1.9    7.7  7  FixG_C          IG-like fold at C-terminal of FixG, putative 
    0.00011   22.0   0.4    0.00017   21.4   0.4    1.3  1  PGF-CTERM       PGF-CTERM motif
     0.0015   18.7  57.0      0.011   16.0   1.6    6.9  7  DUF11           Domain of unknown function DUF11
     0.0021   17.8   2.5       0.92    9.2   0.4    3.1  2  Ail_Lom         Enterobacterial Ail/Lom protein
  ------ inclusion threshold ------
      0.057   13.5   0.0         19    5.4   0.0    4.3  3  Fn3-like        Fibronectin type III-like domain
      0.088   13.0   0.1       0.38   10.9   0.1    2.1  1  Pentapeptide_4  Pentapeptide repeats (9 copies)
        1.2    9.2  26.1        3.2    7.8   0.8    8.2 10  BsuPI           Intracellular proteinase inhibitor
        2.4    8.4  33.7       0.76   10.0   0.8    6.8  7  ASH             Abnormal spindle-like microcephaly-assoc'd, A


Domain annotation for each model (and alignments):
>> FixG_C  IG-like fold at C-terminal of FixG, putative oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   1.3    0.0046        10      34     102 ..     388     452 ..     370     470 .. 0.74
   2 !   17.5   1.9   1.6e-06    0.0035      34      89 ..     490     543 ..     478     575 .. 0.83
   3 !   16.0   0.5   4.8e-06     0.011      34      88 ..     598     652 ..     595     670 .. 0.86
   4 ?    4.4   0.6     0.019        42      34      89 ..     701     754 ..     683     793 .. 0.84
   5 !   10.4   1.3   0.00026      0.58      34     101 ..     806     868 ..     779     883 .. 0.79
   6 !   13.5   1.3   2.8e-05     0.064      34     111 ..     905     982 ..     890     990 .. 0.70
   7 ?    1.7   1.9      0.13   2.9e+02      34     109 ..    1016    1090 ..    1003    1104 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0046
                                       EEEEEEEE-SSS-EEEEEEEES-SS-EE.E.S--EEEE-TT-EEEEEEEEEE-GGG-SSSEEEEEEEEE CS
                            FixG_C  34 sYtlkilNktekprrytlsveglpglelagraekeitvapgekrkvpvfvrvpaealkkkstpitfkvt 102
                                        Y lki N   k+ +++l+ +   g+   + +e++i+v p+e++ +++ v+  +     k+ p+ +k++
  gi|298676194|ref|YP_003727943.1| 388 IYDLKIKNIGLKKETINLTKTKVRGVNA-EFNESQISVMPDETKIIKLKVSSSQIG---KNYPVIVKAS 452
                                       49*****************998876666.43679*********9999999886644...3346666665 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 1.6e-06
                                       EEEEEEEE-SSS-EEEEEEEES-SS-EE.E.S--EEEE-TT-EEEEEEEEEE-GGG CS
                            FixG_C  34 sYtlkilNktekprrytlsveglpglelagraekeitvapgekrkvpvfvrvpaea 89 
                                       +Yt++++N+ ++++++++s ++  ++ +   ++++it++ g++ +v  +v   ++ 
  gi|298676194|ref|YP_003727943.1| 490 TYTFTVTNTGNQEHTFNISSTNPSDIGI-L-KNDSITLKGGQSDTVEYVVNSSSKG 543
                                       7********************9999*99.5.47*************9999887665 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 4.8e-06
                                       EEEEEEEE-SSS-EEEEEEEES-S..S-EE.E.S--EEEE-TT-EEEEEEEEEE-GG CS
                            FixG_C  34 sYtlkilNktekprrytlsveglp..glelagraekeitvapgekrkvpvfvrvpae 88 
                                       +Y+++i+N+ +++ +y+l+v +    +++l  +++k++++ pgek+  ++ v++p +
  gi|298676194|ref|YP_003727943.1| 598 TYNITITNTGNQKDTYDLTVISPRtnNTSL--NNSKPVNLNPGEKTFRKLNVSAPVS 652
                                       7********************843347777..467***********99999999865 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.019
                                       EEEEEEEE-SSS-EEEEEEEES.-SS-EE.E.S--EEEE-TT-EEEEEEEEEE-GGG CS
                            FixG_C  34 sYtlkilNktekprrytlsveg.lpglelagraekeitvapgekrkvpvfvrvpaea 89 
                                        Yt+ + N+ + +  ++l+ +   +++e+   ++   +v+pg+++++ v ++ p + 
  gi|298676194|ref|YP_003727943.1| 701 NYTVNVKNTGNVEDDFKLTNKTnIDSIEM---PSVIKNVKPGKTESFDVAISNPDSG 754
                                       4******************9975789999...4578899**********99988766 PP

  == domain 5  score: 10.4 bits;  conditional E-value: 0.00026
                                       EEEEEEEE-SSS-EEEEEEEES-SS-EE.E.S--EEEE-TT-EEEEEEEEEE-GGG-SSSEEEEEEEE CS
                            FixG_C  34 sYtlkilNktekprrytlsveglpglelagraekeitvapgekrkvpvfvrvpaealkkkstpitfkv 101
                                       +Y l i N+ + + +y++s e l ++ +  +  +++t+ pge+++++v v+   ++ +  s+p+++k 
  gi|298676194|ref|YP_003727943.1| 806 TYILNIKNTGNIKDTYEISSE-LTDANI-VD--NKTTLYPGESTSITVNVSGFNDS-NIYSIPVKVKS 868
                                       6********************.89****.55..8999*************986665.33344555554 PP

  == domain 6  score: 13.5 bits;  conditional E-value: 2.8e-05
                                       EEEEEEEE-SSS-EEEEEEEES-S...S-EE.E.S--EEEE-TT-EEEEEEEEEE-GGG-SSSEEEEEEEEE.EGGG CS
                            FixG_C  34 sYtlkilNktekprrytlsveglp...glelagraekeitvapgekrkvpvfvrvpaealkkkstpitfkvt.ddde 106
                                       sYt+k++N+  ++++y+l+v ++    ++ la   ++  ++ pge+++v ++   +++  +  +++  +k++ ++++
  gi|298676194|ref|YP_003727943.1| 905 SYTIKVTNTGVHTHTYDLKVADNSsntTANLAI--NSIPDLNPGESTTVDFTFNNTQDTDR--RIEAVIKAEvQNNP 977
                                       7********************854444444433..467789********999888777734..44555555543433 PP

                                       TEEEE CS
                            FixG_C 107 ketve 111
                                       +++++
  gi|298676194|ref|YP_003727943.1| 978 EKSAT 982
                                       33332 PP

  == domain 7  score: 1.7 bits;  conditional E-value: 0.13
                                        EEEEEEEE-SSS-EEEEEEEES.-SS-EE.E.S--EEEE-TT-EEEEEEEEEE-GGG-SSSEEEEEEEEE..EGG CS
                            FixG_C   34 sYtlkilNktekprrytlsveg.lpglelagraekeitvapgekrkvpvfvrvpaealkkkstpitfkvt..ddd 105 
                                        +Y l++ N  +++ +++l++ + +++ +  +  +k++++ + ++ + + ++++++  +  +++++++ ++  +  
  gi|298676194|ref|YP_003727943.1| 1016 TYFLELKNLGNTNNSFNLEIVEgKEKYTTFK--KKSVDLNASGTNNDTEIIKLTHYPEGVGEHTVKINANssN-- 1086
                                        6999999999999999999874366666634..4888888888888777777777776678888888886321.. PP

                                        GTEE CS
                            FixG_C  106 eket 109 
                                        ++ t
  gi|298676194|ref|YP_003727943.1| 1087 SNDT 1090
                                        2222 PP

>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.4   7.7e-08   0.00017       1      22 [.    1571    1592 ..    1571    1593 .. 0.97

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 7.7e-08
                         PGF-CTERM    1 tPGFGavlAlaGLLaaalLaRR 22  
                                        +PGF a ++l+G+  +a+L+RR
  gi|298676194|ref|YP_003727943.1| 1571 IPGFKATFTLVGMVTIAYLIRR 1592
                                        6********************9 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   6.3    0.0018       4.1      10      79 ..     483     570 ..     475     577 .. 0.69
   2 !    9.6   4.9   0.00047       1.1       6      83 ..     587     654 ..     582     661 .. 0.76
   3 !   16.0   1.6   5.1e-06     0.011       7      40 ..     691     751 ..     676     804 .. 0.62
   4 ?    0.6   1.4      0.32   7.1e+02      11      28 ..     800     817 ..     787     858 .. 0.74
   5 !   14.1   3.5   1.9e-05     0.042      15      83 ..     903     962 ..     866     969 .. 0.76
   6 ?   -2.8   0.2       3.5   7.9e+03      15      29 ..    1014    1028 ..    1002    1033 .. 0.78
   7 ?   -2.8   0.4       3.6   8.1e+03      61      90 ..    1108    1139 ..    1077    1140 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0018
                             DUF11  10 vrpGdtvtytltvtNtgpasangvvvtDtl..................Paglayvsvsasqgtasaltsv.gsLeag 67 
                                        +   + tyt tvtNtg++   +  ++ t                      ++yv +s+s+g++  + +v +s +  
  gi|298676194|ref|YP_003727943.1| 483 TATNTNATYTFTVTNTGNQEH-TFNISSTNpsdigilkndsitlkggqSDTVEYVVNSSSKGVYVSDITVnESTNHN 558
                                       4445579************99.6666666633666666666666666668999999999988888887776666666 PP

                             DUF11  68 esatlsftvrvt 79 
                                        + tl +  +v+
  gi|298676194|ref|YP_003727943.1| 559 ITETLFVITNVK 570
                                       666666655555 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00047
                             DUF11   6 dksevrpGdtvtytltvtNtgpasangvvvtDtlP..aglayvsvsasqgtasaltsvgsLeagesatlsftvrvtr 80 
                                       +k++v+   + ty++t tNtg+++  ++ +t + P   ++++  ++             +L++ge++  ++ v++++
  gi|298676194|ref|YP_003727943.1| 587 TKPPVDVNKNATYNITITNTGNQKD-TYDLTVISPrtNNTSLNNSKPV-----------NLNPGEKTFRKLNVSAPV 651
                                       466899999*************999.5555555553255555555555...........999999999999998888 PP

                             DUF11  81 taa 83 
                                       +++
  gi|298676194|ref|YP_003727943.1| 652 SGD 654
                                       887 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 5.1e-06
                             DUF11   7 ksevrpGdtvtytltvtNtgpasangvvvtDtl............................P 40 
                                       +++++pG tv+yt+ v+Ntg++   + ++t                               P
  gi|298676194|ref|YP_003727943.1| 691 SATANPGNTVNYTVNVKNTGNVED-DFKLTNKTnidsiempsviknvkpgktesfdvaisnP 751
                                       458******************998.8888876666777776666666644444444444443 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.32
                             DUF11  11 rpGdtvtytltvtNtgpa 28 
                                          ++vty+l  +Ntg+ 
  gi|298676194|ref|YP_003727943.1| 800 ENNENVTYILNIKNTGNI 817
                                       566899999999999975 PP

  == domain 5  score: 14.1 bits;  conditional E-value: 1.9e-05
                             DUF11  15 tvtytltvtNtgpasa.ngvvvtDtlPaglayvsvsasqgtasaltsv.gsLeagesatlsftvrvtrtaa 83 
                                       + +yt+ vtNtg  +  ++++v D     +           a+ + ++ ++L++ges+t+ ft + t+ ++
  gi|298676194|ref|YP_003727943.1| 903 ASSYTIKVTNTGVHTHtYDLKVADNSSNTT-----------ANLAINSiPDLNPGESTTVDFTFNNTQDTD 962
                                       557**********99989******322222...........344444559*************99988776 PP

  == domain 6  score: -2.8 bits;  conditional E-value: 3.5
                             DUF11   15 tvtytltvtNtgpas 29  
                                        + ty l ++N g+++
  gi|298676194|ref|YP_003727943.1| 1014 NATYFLELKNLGNTN 1028
                                        789*******99976 PP

  == domain 7  score: -2.8 bits;  conditional E-value: 3.6
                             DUF11   61 v...gsLeagesatlsftvrvtrtaasgaltnv 90  
                                        +   +s+  g+sa  + t+ +++ ++s+ ++n+
  gi|298676194|ref|YP_003727943.1| 1108 SeiiKSVVDGQSAVKNSTIDPSTVKNSL-INNT 1139
                                        1235777888888888888888888876.6665 PP

>> Ail_Lom  Enterobacterial Ail/Lom protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0021       4.7     132     189 ..     601     658 ..     591     666 .. 0.79
   2 !    9.2   0.4   0.00041      0.92     129     192 ..     905     969 ..     881     973 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0021
                           Ail_Lom 132 vrltddkrkkqevltrsddarrsntalaysagvqinptesvvvdlayeasgrgdwrte 189
                                       +++t+  ++k+ +     + r  nt+l  s  v++np e+    l   a  +gd+  +
  gi|298676194|ref|YP_003727943.1| 601 ITITNTGNQKDTYDLTVISPRTNNTSLNNSKPVNLNPGEKTFRKLNVSAPVSGDYNVK 658
                                       56666655555555556789**********************************9865 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00041
                           Ail_Lom 129 gdyvrltddkrkkqev.ltrsddarrsntalaysagvqinptesvvvdlayeasgrgdwrteafi 192
                                          +++t+   +++ + l  +d++  + + la ++  ++np es +vd +++ +   d r ea i
  gi|298676194|ref|YP_003727943.1| 905 SYTIKVTNTGVHTHTYdLKVADNSSNTTANLAINSIPDLNPGESTTVDFTFNNTQDTDRRIEAVI 969
                                       445678887777776437888999999999********************************998 PP

>> Fn3-like  Fibronectin type III-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.3   2.9e+03      27      49 ..     523     545 ..     521     552 .. 0.81
   2 ?    2.0   0.0       0.1   2.3e+02      26      42 ..     836     852 ..     835     861 .. 0.88
   3 ?    5.4   0.0    0.0086        19      28      43 ..     942     957 ..     940     962 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.3
                                       EEE-TT-EEEEEEEEECGGG-EE CS
                          Fn3-like  27 veLapGesktvtftldrkdlsvw 49 
                                       ++L+ G+s tv+  +++++  v+
  gi|298676194|ref|YP_003727943.1| 523 ITLKGGQSDTVEYVVNSSSKGVY 545
                                       67999*******99998776665 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.1
                                       EEEE-TT-EEEEEEEEE CS
                          Fn3-like  26 kveLapGesktvtftld 42 
                                       k++L pGes+ +t++++
  gi|298676194|ref|YP_003727943.1| 836 KTTLYPGESTSITVNVS 852
                                       99************986 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.0086
                                       EE-TT-EEEEEEEEEC CS
                          Fn3-like  28 eLapGesktvtftldr 43 
                                       +L+pGes+tv ft++ 
  gi|298676194|ref|YP_003727943.1| 942 DLNPGESTTVDFTFNN 957
                                       59***********986 PP

>> Pentapeptide_4  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00017      0.38       4      49 ..    1132    1177 ..    1118    1184 .. 0.46

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00017
                    Pentapeptide_4    4 trcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfa 49  
                                        +++  nn++ ++ + ++++l ++++ +++l+n +F++ ++++ +++
  gi|298676194|ref|YP_003727943.1| 1132 KNSLINNTNITDSTVKNSKLVGSTIIDSNLNNIEFRNGHIENNKIY 1177
                                        3333344444444444444444444444444444444444443333 PP

>> BsuPI  Intracellular proteinase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.7     0.004       8.9       8      67 ..      83     140 ..      77     160 .. 0.79
   2 ?   -3.0   0.0       3.3   7.4e+03      80      98 ..     191     208 ..     176     209 .. 0.78
   3 ?    7.8   0.8    0.0014       3.2       4      45 ..     479     520 ..     475     527 .. 0.84
   4 ?   -3.2   0.1       3.9   8.6e+03      13      28 ..     596     611 ..     585     615 .. 0.75
   5 ?    2.4   0.0      0.07   1.6e+02      66      99 ..     633     665 ..     629     666 .. 0.89
   6 ?   -3.0   0.3       3.4   7.6e+03       8      27 ..     694     713 ..     690     724 .. 0.69
   7 ?    3.7   0.0     0.028        62      67      98 ..     735     765 ..     732     767 .. 0.88
   8 ?   -2.3   0.2       2.1   4.7e+03       6      33 ..     797     824 ..     795     842 .. 0.79
   9 ?   -2.8   0.1         3   6.7e+03       7      29 ..     897     919 ..     894     930 .. 0.73
  10 ?   -0.3   0.0      0.48   1.1e+03      68      92 ..     943     966 ..     936     974 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.004
                                       EE-SS-EEEEEEEEE-SSS-EEEEESSS--EEEEEE-TT--EEEETTTT-------EEEE CS
                             BsuPI   8 easgeavelaltvtNesdeavtlqFssgqkydlvvkdeegeevwrysegrmFtqalsset 67 
                                       ++ +++v+++l v+N +d  ++  F++ q y       ++++ +++   + F+   +++ 
  gi|298676194|ref|YP_003727943.1|  83 STDSKNVDIKLNVKNYTDYVIEYPFETHQMYTNTS--GKNNVTYQFNGSKYFANKETQVV 140
                                       455668***********************997655..78888888888888887666555 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.3
                                       E.S---SEEEEEEEEE--E CS
                             BsuPI  80 wdedlepGeYtleaelvae 98 
                                       + ++l +GeY++ ++l++e
  gi|298676194|ref|YP_003727943.1| 191 F-GNLDAGEYSVLIILRNE 208
                                       4.78999*****9999865 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0014
                                       EEEEEE-SS-EEEEEEEEE-SSS-EEEEESSS--EEEEEE-T CS
                             BsuPI   4 aleaeasgeavelaltvtNesdeavtlqFssgqkydlvvkde 45 
                                       + +++a++ +   ++tvtN+++++ t++ ss+   d+ + ++
  gi|298676194|ref|YP_003727943.1| 479 TTKTTATNTNATYTFTVTNTGNQEHTFNISSTNPSDIGILKN 520
                                       56778888899********************99999888544 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 3.9
                                       -EEEEEEEEE-SSS-E CS
                             BsuPI  13 avelaltvtNesdeav 28 
                                       +   ++t+tN+++++ 
  gi|298676194|ref|YP_003727943.1| 596 NATYNITITNTGNQKD 611
                                       5667899999998765 PP

  == domain 5  score: 2.4 bits;  conditional E-value: 0.07
                                       EEE-TT-EEEEEEEE.S---SEEEEEEEEE--EE CS
                             BsuPI  66 etlepgesatyeetwdedlepGeYtleaelvaee 99 
                                       ++l+pge++  + ++ + + +G+Y+++++ v+++
  gi|298676194|ref|YP_003727943.1| 633 VNLNPGEKTFRKLNV-SAPVSGDYNVKVVGVSQN 665
                                       5799****9999999.8**********9988876 PP

  == domain 6  score: -3.0 bits;  conditional E-value: 3.4
                                       EE-SS-EEEEEEEEE-SSS- CS
                             BsuPI   8 easgeavelaltvtNesdea 27 
                                       ++ g++v+ ++ v+N+++ +
  gi|298676194|ref|YP_003727943.1| 694 ANPGNTVNYTVNVKNTGNVE 713
                                       55667888888888887644 PP

  == domain 7  score: 3.7 bits;  conditional E-value: 0.028
                                       EE-TT-EEEEEEEE.S---SEEEEEEEEE--E CS
                             BsuPI  67 tlepgesatyeetwdedlepGeYtleaelvae 98 
                                       +++pg++ +++  + +++ +G+Y+++++ +++
  gi|298676194|ref|YP_003727943.1| 735 NVKPGKTESFDVAI-SNPDSGNYNANITAISK 765
                                       679***********.8*********9987765 PP

  == domain 8  score: -2.3 bits;  conditional E-value: 2.1
                                       EEEE-SS-EEEEEEEEE-SSS-EEEEES CS
                             BsuPI   6 eaeasgeavelaltvtNesdeavtlqFs 33 
                                       e+++++e+v   l ++N+++ + t + s
  gi|298676194|ref|YP_003727943.1| 797 EVTENNENVTYILNIKNTGNIKDTYEIS 824
                                       5778899999999999999877776655 PP

  == domain 9  score: -2.8 bits;  conditional E-value: 3
                                       EEE-SS-EEEEEEEEE-SSS-EE CS
                             BsuPI   7 aeasgeavelaltvtNesdeavt 29 
                                       +++  +a + +++vtN++ ++ t
  gi|298676194|ref|YP_003727943.1| 897 TTKGHNASSYTIKVTNTGVHTHT 919
                                       55566677788889998877665 PP

  == domain 10  score: -0.3 bits;  conditional E-value: 0.48
                                       E-TT-EEEEEEEE.S---SEEEEEE CS
                             BsuPI  68 lepgesatyeetwdedlepGeYtle 92 
                                       l+pges+t++ t+ ++ +  + ++e
  gi|298676194|ref|YP_003727943.1| 943 LNPGESTTVDFTF-NNTQDTDRRIE 966
                                       6777777777777.44444444444 PP

>> ASH  Abnormal spindle-like microcephaly-assoc'd, ASPM-SPD-2-Hydin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.71   1.6e+03      29      73 ..     391     435 ..     380     444 .. 0.86
   2 ?    2.6   1.9     0.067   1.5e+02      19      82 ..     483     545 ..     467     559 .. 0.81
   3 ?   10.0   0.8   0.00034      0.76      19      68 ..     591     641 ..     589     648 .. 0.95
   4 ?    6.7   0.5    0.0036         8      18      86 ..     735     805 ..     732     821 .. 0.83
   5 ?   -0.5   0.1      0.63   1.4e+03      28      73 ..     808     850 ..     798     854 .. 0.70
   6 ?    8.3   0.7    0.0012       2.7      27      81 ..     906     962 ..     897     980 .. 0.69
   7 ?   -2.2   0.2       2.3   5.1e+03      23      65 ..    1013    1055 ..    1007    1085 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.71
                                       -EEESS-SS--EEEEEEEE--XXXXXXXXXXXXXXXXXXXXXXXX CS
                               ASH  29 LtveNpseepaevkvskvpaaekgfsveetelevqpgesvtltvt 73 
                                       L+++N + ++ +++++k+  +  +   +e+++ v p+e+  ++++
  gi|298676194|ref|YP_003727943.1| 391 LKIKNIGLKKETINLTKTKVRGVNAEFNESQISVMPDETKIIKLK 435
                                       8999999999999999999999999999999*****999888765 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.067
                                       ---EEEEEEE-EEESS-SS--EEEEEEEE--XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                               ASH  19 vkvGssaerlLtveNpseepaevkvskvpaaekgfsveetelevqpgesvtltvtwtPteegav 82 
                                       ++ +++a+ + tv+N+++++++ ++s ++ ++    ++++++++++g+s t++ + + +++g  
  gi|298676194|ref|YP_003727943.1| 483 TATNTNATYTFTVTNTGNQEHTFNISSTN-PSDIGILKNDSITLKGGQSDTVEYVVNSSSKGVY 545
                                       66788999999*********999999999.7777778999999999999999877776666655 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00034
                                       ---EEEEEEE-EEESS-SS--EEEEEEEE--XXXXXXXXXX.XXXXXXXXX CS
                               ASH  19 vkvGssaerlLtveNpseepaevkvskvpaaekgfsveete.levqpgesv 68 
                                       v v+++a+ ++t++N+++++ + +++ +++++++ s+++++ +++ pge++
  gi|298676194|ref|YP_003727943.1| 591 VDVNKNATYNITITNTGNQKDTYDLTVISPRTNNTSLNNSKpVNLNPGEKT 641
                                       89**********************************************985 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.0036
                                       ----EEEEEEE-EEESS-SS--EEEEEEEE--XXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXX.XXXXX CS
                               ASH  18 dvkvGssaerlLtveNpseepaevkvskvpaaekgfsveete.levqpgesvtltvtwtPteega.vrevL 86 
                                       +vk G++++  + ++Np+  + + +++ ++++   +s + +  l+v+ + +++++vt +P +e++  +e +
  gi|298676194|ref|YP_003727943.1| 735 NVKPGKTESFDVAISNPDSGNYNANITAISKSYVDISNSVNLsLNVSDKPDHSVSVTANPISEVTeNNENV 805
                                       7999**************************9999999888878*****************99964333333 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 0.63
                                       E-EEESS-SS--EEEEEEEE--XXXXXXXXXXXXXXXXXXXXXXXX CS
                               ASH  28 lLtveNpseepaevkvskvpaaekgfsveetelevqpgesvtltvt 73 
                                        L ++N+++ +   ++  ++ + +  ++  +++++ pges+++tv+
  gi|298676194|ref|YP_003727943.1| 808 ILNIKNTGNIK---DTYEISSELTDANIVDNKTTLYPGESTSITVN 850
                                       45666666632...3333444667888888899**********997 PP

  == domain 6  score: 8.3 bits;  conditional E-value: 0.0012
                                       EE-EEESS-SS--EEEEEEEE--XXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXX CS
                               ASH  27 rlLtveNpseepaevkvskvpaaekgfsveete...levqpgesvtltvtwtPteega 81 
                                        +++v+N++ ++++ +++ +   + + + + +     ++ pges+t+++t+++t+ + 
  gi|298676194|ref|YP_003727943.1| 906 YTIKVTNTGVHTHTYDLKVAD-NSSNTTANLAInsiPDLNPGESTTVDFTFNNTQDTD 962
                                       457888888877444443333.4444444443334789****************9864 PP

  == domain 7  score: -2.2 bits;  conditional E-value: 2.3
                                        EEEEEE-EEESS-SS--EEEEEEEE--XXXXXXXXXXXXXXXX CS
                               ASH   23 ssaerlLtveNpseepaevkvskvpaaekgfsveetelevqpg 65  
                                        ++a+ +L+++N ++++ + +++ v ++ek  + +++++++ + 
  gi|298676194|ref|YP_003727943.1| 1013 KNATYFLELKNLGNTNNSFNLEIVEGKEKYTTFKKKSVDLNAS 1055
                                        4667779999999999999999998888888888888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1594 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1301  (0.072564); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 1.06u 0.33s 00:00:01.39 Elapsed: 00:00:00.59
# Mc/sec: 8133.16
//
Query:       gi|298676195|ref|YP_003727944.1|  [L=181]
Description: hypothetical protein Metev_2336 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-24   85.7   1.5      3e-24   85.7   1.5    1.9  2  Pilin_N   Archaeal Type IV pilin, N-terminal


Domain annotation for each model (and alignments):
>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.7   1.5   1.7e-28     3e-24       1      79 [.      31     106 ..      31     110 .. 0.86
   2 ?   -0.5   0.0      0.14   2.5e+03      26      42 ..     147     163 ..     128     179 .. 0.61

  Alignments for each domain:
  == domain 1  score: 85.7 bits;  conditional E-value: 1.7e-28
                           Pilin_N   1 eAVSpViGviLmvaitvIlaAviaafvlglasneekapqasievkidssastgknavslehkgGdsidtkdlkivln 77 
                                       +AVSpViGviLmvaitvIlaAvi+++++gl + +e+apqasi+ + d+++st  + ++leh+gG+s+  +d++  l+
  gi|298676195|ref|YP_003727944.1|  31 DAVSPVIGVILMVAITVILAAVIGSYAFGL-GSPEQAPQASISGSADTENST--QIIKLEHQGGESVLFEDTATKLT 104
                                       69****************************.9**********7777777765..56***********9977665544 PP

                           Pilin_N  78 se 79 
                                        +
  gi|298676195|ref|YP_003727944.1| 105 VN 106
                                       43 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.14
                           Pilin_N  26 fvlglasneekapqasi 42 
                                       +v  l+s+ e++++++i
  gi|298676195|ref|YP_003727944.1| 147 SVSHLNSTGETTTSVKI 163
                                       34444555555565555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       966  (0.0538792); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1063.49
//
Query:       gi|298676196|ref|YP_003727945.1|  [L=123]
Description: response regulator receiver protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.4e-28   97.7   0.1    4.9e-28   97.5   0.1    1.0  1  Response_reg  Response regulator receiver domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.5   0.1   2.7e-32   4.9e-28       1     111 [.       6     117 ..       6     118 .. 0.97

  Alignments for each domain:
  == domain 1  score: 97.5 bits;  conditional E-value: 2.7e-32
                                       EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCT..TTSEEE CS
                      Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireed..pelpvi 75 
                                       +liv+Dd+ +r+l++++l+ egy  +++a dg+eal+++k++k+ li+lDi++p+++G +ll+e r+ +  +++p+i
  gi|298676196|ref|YP_003727945.1|   6 ILIVEDDKCNRDLISDILDLEGY-YIDTAIDGEEALRKTKNKKYELIILDIKLPKLNGCDLLSEFRKCPetKNTPII 81 
                                       8**********************.*******************************************998899**** PP

                                       EEESSTSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                      Response_reg  76 iltahseeedavealkagaddflsKpfdpeeLlkal 111
                                       +ltah+   d+++  ++g d++lsKp+d ++ +k +
  gi|298676196|ref|YP_003727945.1|  82 VLTAHAMRGDKEKFESLGCDEYLSKPIDVTKFTKVV 117
                                       *****************************9999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.35s 00:00:00.88 Elapsed: 00:00:00.55
# Mc/sec: 675.43
//
Query:       gi|298676197|ref|YP_003727946.1|  [L=211]
Description: hypothetical protein Metev_2338 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.071   12.7   0.1       0.12   11.9   0.1    1.4  1  Ras       Ras family
        0.2   11.6   6.8       0.26   11.2   1.1    2.8  3  Imm6      Immunity protein Imm6


Domain annotation for each model (and alignments):
>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   1.4e-05      0.12      78     148 ..     120     201 ..     107     208 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.4e-05
                                       EEETTBHHHHHTHH..HHHHHHHHHST........TTSEEEEEEE.TTTGGGG-SS-HHHHHHHHHHHTSEEEEEBT CS
                               Ras  78 vyditsresfenvk..kwveeikrvae........envpivLvGn.KvDleekravsteegeelakelglkfletSA 143
                                       ++d  + + f+nv+  +w+ e  + a         ++v+ +L    K+D ++++++++e   ++  ++++k++etSA
  gi|298676197|ref|YP_003727946.1| 120 LFDFMKDSGFKNVNnlRWFPEYDEAALdllnknnkNTVETALSKLwKIDWTKNKKITEEMILKYGINIDTKYIETSA 196
                                       57888888899988677888877766556666665667777765459****************************** PP

                                       TTTCT CS
                               Ras 144 ktnen 148
                                         + +
  gi|298676197|ref|YP_003727946.1| 197 CPAAE 201
                                       87665 PP

>> Imm6  Immunity protein Imm6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1     0.023     2e+02      92     108 ..      50      66 ..      44      75 .. 0.82
   2 ?   -0.0   0.0     0.088   7.9e+02      25      54 ..      99     126 ..      75     136 .. 0.65
   3 ?   11.2   1.1   2.9e-05      0.26      11      69 ..     143     201 ..     141     208 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.023
                              Imm6  92 kkekekylPetlesidd 108
                                       kke+ +y+P +l+ i +
  gi|298676197|ref|YP_003727946.1|  50 KKEYTYYYPGILDLILN 66 
                                       79***********9865 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.088
                              Imm6  25 evveeaLdvckkwlegenvtadeLydlldn 54 
                                       e + + Ld  k++le  +++ d+L+d++  
  gi|298676197|ref|YP_003727946.1|  99 EYIPKGLDLNKNYLE--QLKEDALFDFMKD 126
                                       555666666666665..4556666666654 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 2.9e-05
                              Imm6  11 ekllslikkkddevevveeaLdvckk..wlegenvtadeLydlldnedeedilefaeqeed 69 
                                       e++l l++k+++  + ve aL++ +k  w++++++t + + ++  n d + i + a+ +++
  gi|298676197|ref|YP_003727946.1| 143 EAALDLLNKNNK--NTVETALSKLWKidWTKNKKITEEMILKYGINIDTKYIETSACPAAE 201
                                       667888888887..9**********777***************999999999887776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       852  (0.0475208); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1312.72
//
Query:       gi|298676198|ref|YP_003727947.1|  [L=171]
Description: hypothetical protein Metev_2339 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.016   15.3   0.3      0.034   14.2   0.3    1.5  1  RAMP4      Ribosome associated membrane protein RAMP4
      0.018   15.0   1.1      0.025   14.5   0.5    1.6  2  GatB_Yqey  GatB domain


Domain annotation for each model (and alignments):
>> RAMP4  Ribosome associated membrane protein RAMP4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.3   3.8e-06     0.034       3      43 ..      63     106 ..      62     107 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.8e-06
                             RAMP4   3 kremrrknekfakni.tkrGkvpkslk..kkekkspvgpwlLgl 43 
                                       k +++++n  + +   t+rG+v+   k  k+++k+++g+++L++
  gi|298676198|ref|YP_003727947.1|  63 KERQTVQNGEYVNYMdTNRGHVKVIHKriKEKTKKSIGTIMLAI 106
                                       7899999****************99999**************86 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.58   5.2e+03     107     126 ..      10      29 ..       7      31 .. 0.77
   2 ?   14.5   0.5   2.8e-06     0.025      34     105 ..      90     157 ..      52     166 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.58
                                       HHHHHHTTXXTTSTHHHHHH CS
                         GatB_Yqey 107 kavedyksgkekalkflvGq 126
                                       k v d  ++  k + f+ Gq
  gi|298676198|ref|YP_003727947.1|  10 KNVTDATRKLSKEFTFFTGQ 29 
                                       66778888888889999998 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.8e-06
                                       XTTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHHTXXHHHHHHHCTXXXXXXSSXHHHHHHHHHHTX CS
                         GatB_Yqey  34 eieelkltpeqlaellkliaegkIskkiakevleelleegkspeeiieekgLkqisdeeeleklveeviaen 105
                                        i+e   t++++  ++  i+ g Is+k  +e+++ ++++     ++ ee      +deee+e++v +v++++
  gi|298676198|ref|YP_003727947.1|  90 RIKE--KTKKSIGTIMLAIKMGLISEKDMEEIVANIMDNFDYYYQMTEEAI--FYTDEEEIENFVLNVLKNE 157
                                       4444..577899999999********************9999999999984..57899***********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1015  (0.0566122); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1046.81
//
Query:       gi|298676199|ref|YP_003727948.1|  [L=117]
Description: hypothetical protein Metev_2340 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    0.00075   18.6   0.9    0.00086   18.4   0.9    1.1  1  SNF2_assoc  Bacterial SNF2 helicase associated
  ------ inclusion threshold ------
       0.02   14.7   0.7      0.024   14.5   0.7    1.1  1  GatB_Yqey   GatB domain
      0.057   14.0   0.3       0.11   13.2   0.1    1.6  2  FRP         Photoprotection regulator fluorescence recovery p


Domain annotation for each model (and alignments):
>> SNF2_assoc  Bacterial SNF2 helicase associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.9   1.4e-07   0.00086     252     306 ..      44      99 ..      23     109 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.4e-07
                        SNF2_assoc 252 sieeegnlLelsfdidgideeElaeilka.yrekkkYyrLkdGsfldLeeeelkel 306
                                       +++++ + L l ++++ i+ee+l++i++  +re   Yy+L  +++ +L+e+e+++l
  gi|298676199|ref|YP_003727948.1|  44 KTKKSIGTLALVIKMGLINEEDLKDIISDtLREFDYYYKLTENAVFKLDEDEVEAL 99 
                                       567778999******************864899999***************99987 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.7   4.1e-06     0.024      38     111 ..      42     113 ..       4     116 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.1e-06
                                       SSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHHTXXHHHHHHHCTXXXXXXSSXHHHHHHHHHHTXHHHHHH CS
                         GatB_Yqey  38 lkltpeqlaellkliaegkIskkiakevleelleegkspeeiieekgLkqisdeeeleklveeviaenpkaved 111
                                       ++ t++++  l   i+ g I+++  k+++   l e     ++ e    +++ de+e+e+lv  +i+ n+++++ 
  gi|298676199|ref|YP_003727948.1|  42 NSKTKKSIGTLALVIKMGLINEEDLKDIISDTLREFDYYYKLTENA-VFKL-DEDEVEALVMSIISGNEEKIDS 113
                                       3567889999999********************8877777776655.5666.568*************999875 PP

>> FRP  Photoprotection regulator fluorescence recovery protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.8e-05      0.11      50      93 ..      32      75 ..       5      79 .. 0.81
   2 ?   -2.2   0.0       1.1   6.4e+03      15      28 ..      90     103 ..      82     114 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.8e-05
                               FRP 50 akRydidgkydfreskllfvlarlvkeklleleeLeGLeaekla 93
                                       + ++i+ + +++++k + +la ++k +l+++e+L+ + +++l+
  gi|298676199|ref|YP_003727948.1| 32 GHIWTIEKRINSKTKKSIGTLALVIKMGLINEEDLKDIISDTLR 75
                                      4457899*****************************99888876 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.1
                               FRP  15 kayereiealiaev 28 
                                       k  e e+eal+ ++
  gi|298676199|ref|YP_003727948.1|  90 KLDEDEVEALVMSI 103
                                       44556677776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       781  (0.0435607); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 673.41
//
Query:       gi|298676200|ref|YP_003727949.1|  [L=68]
Description: hypothetical protein Metev_2341 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 478.95
//
Query:       gi|298676201|ref|YP_003727950.1|  [L=94]
Description: hypothetical protein Metev_2343 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 599.22
//
Query:       gi|298676202|ref|YP_003727951.1|  [L=361]
Description: hypothetical protein Metev_2344 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.6e-13   49.5  51.1    8.1e-06   26.0  19.6    3.1  2  EamA          EamA-like transporter family


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8  23.5   5.4e-10   9.7e-06       2     135 ..      18     177 ..      17     179 .. 0.73
   2 !   26.0  19.6   4.5e-10   8.1e-06       2     137 .]     195     338 ..     194     338 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 5.4e-10
                              EamA   2 lgillallaalfwaiyfvlskil.....lrkv..................spltltfvrfliagilllii..allke 53 
                                       +g+++al+ a+fw+++++   i+     +                        +++++  l+a + l+i+  +ll+ 
  gi|298676202|ref|YP_003727951.1|  18 SGYMWALICAVFWGLWYIPGEIIwninpF--NemlsevshmmsssgsmvvVAAEVSALNALFAVLSLIIWngCLLRL 92 
                                       79******************998554442..0334444544444432221111333355555555555556644444 PP

                              EamA  54 gkl....aklslkd..wllllllgllgtvlafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllg 124
                                       + l    +++   +   ++ll  ++lg+ +a +  f+a+  +++++a+++++l Pv+  + ++l++gek+t +  +g
  gi|298676202|ref|YP_003727951.1|  93 NELgrtiKNF---NlcSKWLLAGSVLGGPVAIFGSFMAMAFIGSAFAAVASLLYPVVGSVAAFLWYGEKITRRASIG 166
                                       4445333333...3556999********************************************************* PP

                              EamA 125 ivlillGvlli 135
                                       i++i++G + i
  gi|298676202|ref|YP_003727951.1| 167 IFIIIVGSISI 177
                                       *******9876 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 4.5e-10
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagill.liiallkegkl........aklslkdwlllll 69 
                                       lg+l  l aa  w++ + ++ i+l++ ++ t ++ rf++  ++  lii++++++          a++ + ++  l++
  gi|298676202|ref|YP_003727951.1| 195 LGYLGGLMAASGWGLEGAIAGIGLEFSESDTGLTARFIFELLFWwLIIIPIFAIAGfpmyeyatAVFQPVPLMVLAF 271
                                       79999**********************99999999999777777655555555555556888889999999999999 PP

                              EamA  70 lgllgtvlafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllill 137
                                       +g l++ ++++ +++++  +++++   + +l  ++++il  l+ g +++++ ++g +l+++G++++++
  gi|298676202|ref|YP_003727951.1| 272 TG-LASGFCYVTWYKSFPLIGVGRGQGVANLYGLISIILLLLFVGSTPGWTVFIGGLLCVAGAVVMFT 338
                                       99.5777777******************************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 2614.01
//
Query:       gi|298676203|ref|YP_003727952.1|  [L=59]
Description: hypothetical protein Metev_2345 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 416.07
//
Query:       gi|298676204|ref|YP_003727953.1|  [L=49]
Description: hypothetical protein Metev_2346 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.084   12.6   2.4        0.1   12.4   2.4    1.0  1  Rer1      Rer1 family


Domain annotation for each model (and alignments):
>> Rer1  Rer1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   2.4   5.6e-06       0.1     121     152 ..      13      44 ..       9      47 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.6e-06
                              Rer1 121 ltffevfdvpVfwpiLlvyfivlfvltmrrqi 152
                                       + f+++f + ++ p Ll +f+v+ +  mr+++
  gi|298676204|ref|YP_003727953.1|  13 TLFISIFLIAIYAPSLLGFFVVMSIYIMRHRF 44 
                                       56899***********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.27s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 357.74
//
Query:       gi|298676205|ref|YP_003727954.1|  [L=168]
Description: integrase catalytic subunit [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-21   76.7   0.1      2e-21   76.3   0.1    1.2  1  DDE_3     DDE superfamily endonuclease
    9.7e-05   22.1   0.1    0.00012   21.8   0.1    1.3  1  DDE_1     DDE superfamily endonuclease
    0.00031   20.9   0.0    0.00046   20.4   0.0    1.2  1  rve       Integrase core domain


Domain annotation for each model (and alignments):
>> DDE_3  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.3   0.1   3.4e-25     2e-21       5     144 ..       1     133 [.       1     135 [. 0.87

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 3.4e-25
                             DDE_3   5 iDEsgfqlgtvrrrawakkGkrerleeygrrgrvnligaldekgglafvtfeetlnaedfaeflerlletalqakki 81 
                                       +DEs  q++++ +r w+       +++++   + n++++++ +g   ++ f+++ +++d+ efle++ +      +i
  gi|298676205|ref|YP_003727954.1|   1 MDESSPQTRANTQRLWSFDKPV--IYKNTDYIKANAFAFYSING-NNLIEFKDSSKSDDVCEFLEEISRINHGR-PI 73 
                                       6****************97555..66666667888999999988.4567789999*****************98.** PP

                             DDE_3  82 vlilDnasiHkseslrelveeeadrlellylPpySPelNpiEivwsklkrellkrrsfkslde 144
                                       vli+Dna+ H++ + + ++++   ++ l++lPpySP+lNp+E +w+++kre+   r+++s++ 
  gi|298676205|ref|YP_003727954.1|  74 VLIMDNARAHHALKTTMKAKQ--LGIILVFLPPYSPDLNPVEFIWKSIKREISV-RFVQSKQH 133
                                       **********98666666555..*****************************99.88888765 PP

>> DDE_1  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   1.9e-08   0.00012      72     163 ..      68     155 ..      24     167 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.9e-08
                             DDE_1  72 aekrkilLlldssrshetvel.leselqniklvflPassasllqPldqgvvselKarYrrqllqalleeqnrlskeq 147
                                       + +r i+L++d++r+h++++  ++ ++  i lvflP+ s + l P++  +++ +K++    ++q  ++ ++ ++   
  gi|298676205|ref|YP_003727954.1|  68 NHGRPIVLIMDNARAHHALKTtMKAKQLGIILVFLPPYSPD-LNPVEF-IWKSIKREISVRFVQSKQHMRSIIKT-- 140
                                       57899************888879999999*******88876.689985.9*********9999999998888887.. PP

                             DDE_1 148 kkltlldalkfikkAw 163
                                         + + + l f +kAw
  gi|298676205|ref|YP_003727954.1| 141 VFMKIGNSLSF-AKAW 155
                                       44444555444.3344 PP

>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   7.7e-08   0.00046      44     118 ..      50     122 ..      43     123 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 7.7e-08
                               rve  44 demdastvlalleravarfggvepervlsDngseytskafrefladlgirvsftrpgrpqdnGkvErfhrtlkde 118
                                       d++++++v+++le+  +  +g+ p ++++Dn+++  + +++  +++lgi + f +p++p+ n  vE +++ +k+e
  gi|298676205|ref|YP_003727954.1|  50 DSSKSDDVCEFLEEISRINHGR-PIVLIMDNARAHHALKTTMKAKQLGIILVFLPPYSPDLNP-VEFIWKSIKRE 122
                                       455899*******999999999.**********99999**********************997.67777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1241.89
//
Query:       gi|298676206|ref|YP_003727955.1|  [L=170]
Description: ISA1083-3 transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.6e-11   42.9   0.1    1.1e-10   42.0   0.1    1.5  1  HTH_32         Homeodomain-like domain
    3.8e-08   32.9   0.2    1.2e-07   31.3   0.0    1.9  2  HTH_23         Homeodomain-like domain
    1.7e-07   30.7   0.3    1.4e-06   27.8   0.1    2.4  2  HTH_33         Winged helix-turn helix
    7.7e-07   29.1   0.0    1.7e-06   28.0   0.0    1.6  1  HTH_28         Helix-turn-helix domain
    7.4e-06   25.9   0.0    1.6e-05   24.9   0.0    1.4  1  HTH_29         Winged helix-turn helix
     0.0021   17.9   0.3      0.006   16.4   0.1    1.8  2  DUF559         Protein of unknown function (DUF559)
     0.0025   17.8   0.4     0.0043   17.1   0.2    1.5  1  HTH_Tnp_IS630  Transposase
  ------ inclusion threshold ------
       0.03   15.1   0.3      0.057   14.2   0.2    1.5  1  Tau95          RNA polymerase III transcription factor (TF)II
       0.15   12.7   0.0       0.23   12.0   0.0    1.4  1  LZ_Tnp_IS481   leucine-zipper of insertion element IS481
       0.42   10.7   4.4       0.43   10.7   0.3    2.7  3  U3_assoc_6     U3 small nucleolar RNA-associated protein 6


Domain annotation for each model (and alignments):
>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.1   5.9e-14   1.1e-10       1      72 [.      61     132 ..      61     133 .. 0.95

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 5.9e-14
                            HTH_32   1 TvsrwlkRyneeGlegLkdrprrgrprklsdevrariiallreeprWsprqlaarlaeregvkvShstvyri 72 
                                       T + w  R+n++G+e+L +  ++gr +kl++++ ++++++l+e++ W++ ++++ + +++gv++S  +++ i
  gi|298676206|ref|YP_003727955.1|  61 TGYYWQDRWNKGGYEALVPMVSKGREHKLTQQQFDELKDILKERSLWTTNEVRQLVIQKYGVEYSLKQIRII 132
                                       889*****************9********************8889*********999999********9966 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.0   6.9e-11   1.2e-07       9      49 ..      31      77 ..      24      78 .. 0.79
   2 ?   -1.5   0.0       1.4   2.5e+03       5      23 ..     111     129 ..     107     132 .. 0.77

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 6.9e-11
                            HTH_23  9 rilllla..e....GlsvreIAreLgvsrrTvyrwlkryreeGlegl 49
                                      r+l+ l   +    G+sv+e+A++ g++++T y w  r++++G e+l
  gi|298676206|ref|YP_003727955.1| 31 RMLRRLYfcKfrylGDSVSEAADKVGITKMTGYYWQDRWNKGGYEAL 77
                                      44444444423355*****************************9998 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.4
                            HTH_23   5 reRlrillllaeGlsvreI 23 
                                       + R+++++ + + +s ++I
  gi|298676206|ref|YP_003727955.1| 111 EVRQLVIQKYGVEYSLKQI 129
                                       6789999988777777776 PP

>> HTH_33  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.43   7.7e+02       6      21 ..      16      31 ..      14      35 .. 0.85
   2 !   27.8   0.1   7.8e-10   1.4e-06       2      41 ..     104     143 ..     103     152 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.43
                            HTH_33  6 tlarlaqlieerfgvs 21
                                      tl++l +li+++++ +
  gi|298676206|ref|YP_003727955.1| 16 TLDQLNTLIKTETNAR 31
                                      9999******998865 PP

  == domain 2  score: 27.8 bits;  conditional E-value: 7.8e-10
                            HTH_33   2 fgrWtlarlaqlieerfgvsysvsgvyrlLkrlGfsyqkP 41 
                                         +Wt+ +++ql+ +++gv+ys ++++ ++   G+   kP
  gi|298676206|ref|YP_003727955.1| 104 RSLWTTNEVRQLVIQKYGVEYSLKQIRIIMIQFGMKHSKP 143
                                       579************************9999999988887 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   9.5e-10   1.7e-06      12      49 ..      45      84 ..      34      87 .. 0.91

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 9.5e-10
                            HTH_28 12 GhsvreaArelgisrrtvyrWikryeegGiagLvp..rrr 49
                                      G+sv+eaA ++gi+  t y W  r+++gG ++Lvp   ++
  gi|298676206|ref|YP_003727955.1| 45 GDSVSEAADKVGITKMTGYYWQDRWNKGGYEALVPmvSKG 84
                                      78********************************964444 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   8.7e-09   1.6e-05      11      61 ..      45      93 ..      43      94 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 8.7e-09
                            HTH_29 11 GvstvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsgrprnrlseeq 61
                                      G s vs++A  +g+++ t y w++r+++gG +al +  ++gr  ++l+++q
  gi|298676206|ref|YP_003727955.1| 45 GDS-VSEAADKVGITKMTGYYWQDRWNKGGYEALVPMVSKGRE-HKLTQQQ 93
                                      666.********************************8888987.4799887 PP

>> DUF559  Protein of unknown function (DUF559)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.2   2.2e+03      75      94 ..      30      49 ..      10      57 .. 0.64
   2 !   16.4   0.1   3.4e-06     0.006      20      75 ..      96     151 ..      81     158 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.2
                                      HHHHHHTT-EEEEEEHHHHH CS
                            DUF559 75 telLeslGftvlRfkndevl 94
                                      +++L +l f  +R+  d v 
  gi|298676206|ref|YP_003727955.1| 30 ARMLRRLYFCKFRYLGDSVS 49
                                      34455555555555555555 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 3.4e-06
                                       HHHHHHGGGTTTT--EEEEEEETTEEEEEEETTTTEEEEEE-----------HHHH CS
                            DUF559  20 kLWqllrnrrlsglkfrRqkpigsYivDfvclkaklivelDGaqhdeeeeyDaeRt 75 
                                       +L   l++r l      Rq +i++Y v++  ++ ++i+   G +h++  +yD ++ 
  gi|298676206|ref|YP_003727955.1|  96 ELKDILKERSLWTTNEVRQLVIQKYGVEYSLKQIRIIMIQFGMKHSKPYTYDYRKP 151
                                       57778999999999999***********************************8875 PP

>> HTH_Tnp_IS630  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.2   2.4e-06    0.0043      13      97 ..      40     132 ..      29     146 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.4e-06
                     HTH_Tnp_IS630  13 dyiesGggitkaskvfkvgratvyrWlkreela......atkvetrkrkidrkelke..dvkknpdallkerakkfg 81 
                                       ++   G+++ +a    ++++ t y W +r + +      ++  + r++k+ +++++e  d+ k+      + ++++ 
  gi|298676206|ref|YP_003727955.1|  40 KFRYLGDSVSEAADKVGITKMTGYYWQDRWNKGgyealvPMVSKGREHKLTQQQFDElkDILKERSLWTTNEVRQLV 116
                                       556679*********************997766111111556799*****999887444999999999999****** PP

                     HTH_Tnp_IS630  82 vtpasllyalkklkit 97 
                                       ++   + y lk+++i 
  gi|298676206|ref|YP_003727955.1| 117 IQKYGVEYSLKQIRII 132
                                       ************9985 PP

>> Tau95  RNA polymerase III transcription factor (TF)IIIC subunit HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   3.2e-05     0.057      55     100 ..      81     128 ..      46     139 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.2e-05
                                       ----...HHHHHHHHHHHHHHHH-SEEEHHHHHTTS-GGGT..TTHHH CS
                             Tau95  55 vkelkekkelqkaveelkklfeerPiwtrraLknklekker..kklkl 100
                                       v++  e+k  q++++elk++++er +wt++++++ + +k    ++lk+
  gi|298676206|ref|YP_003727955.1|  81 VSKGREHKLTQQQFDELKDILKERSLWTTNEVRQLVIQKYGveYSLKQ 128
                                       4555667999*********************99988866655655554 PP

>> LZ_Tnp_IS481  leucine-zipper of insertion element IS481
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00013      0.23      27      65 ..      47      85 ..      29     105 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                      LZ_Tnp_IS481 27 tvaqvarelGvslrtaykwlarfraeGldGlldrssrPr 65
                                      +v ++a ++G+++ t+y w +r+   G + l+   s+ r
  gi|298676206|ref|YP_003727955.1| 47 SVSEAADKVGITKMTGYYWQDRWNKGGYEALVPMVSKGR 85
                                      57899************************9998887665 PP

>> U3_assoc_6  U3 small nucleolar RNA-associated protein 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.33     6e+02      40      69 ..      14      43 ..       1      59 [. 0.68
   2 ?   10.7   0.3   0.00024      0.43       6      38 ..      95     128 ..      91     136 .. 0.86
   3 ?   -1.0   0.0       1.1   1.9e+03      22      37 ..     154     169 ..     150     170 .] 0.81

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.33
                        U3_assoc_6 40 gkkkedflkYieyElnLeklrkkRrkrlkl 69
                                      + ++++  + i+ E+n   lr+ +  + ++
  gi|298676206|ref|YP_003727955.1| 14 HVTLDQLNTLIKTETNARMLRRLYFCKFRY 43
                                      455666777899999999999988877776 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00024
                        U3_assoc_6   6 peled.leekglFtkeEikeIvkkrrkfEyklqr 38 
                                       +el+d l+e+ l t +E++++v +    Ey+l++
  gi|298676206|ref|YP_003727955.1|  95 DELKDiLKERSLWTTNEVRQLVIQKYGVEYSLKQ 128
                                       566664799**********************985 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.1
                        U3_assoc_6  22 ikeIvkkrrkfEyklq 37 
                                         eI+kk r + y+l+
  gi|298676206|ref|YP_003727955.1| 154 ADEILKKPRRHTYSLK 169
                                       5789999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1149.48
//
Query:       gi|298676207|ref|YP_003727956.1|  [L=410]
Description: putative PAS/PAC sensor protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-40  138.5   1.6    2.9e-40  137.8   1.6    1.4  1  MetOD1         Metanogen output domain 1
    3.9e-23   81.7   1.4    4.2e-11   43.0   0.1    2.8  3  PAS_9          PAS domain
    9.5e-17   60.6   0.2    9.4e-09   35.1   0.0    2.5  2  PAS_8          PAS domain
    5.9e-16   58.7   0.0    1.7e-07   31.5   0.0    2.2  2  PAS_4          PAS fold
    3.9e-13   49.4   0.1    1.2e-05   25.3   0.0    2.7  2  PAS            PAS fold
    4.8e-07   30.0   0.0     0.0082   16.4   0.0    2.5  2  PAS_3          PAS fold
     0.0034   17.3   0.1      0.011   15.6   0.1    2.0  2  DUF3877        Domain of unknown function, E. rectale Gene de
  ------ inclusion threshold ------
       0.21   12.4   1.3       0.73   10.6   1.3    1.9  1  ATC_hydrolase  L-2-amino-thiazoline-4-carboxylic acid hydrola


Domain annotation for each model (and alignments):
>> MetOD1  Metanogen output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.8   1.6   1.3e-43   2.9e-40       1     153 [.     257     409 ..     257     410 .] 0.95

  Alignments for each domain:
  == domain 1  score: 137.8 bits;  conditional E-value: 1.3e-43
                            MetOD1   1 elkkkkvkaelrsfllsaiPtlaskippeekkilikqfadrveknlkpkfkeelkeaekeeedaekvlkayiewlnq 77 
                                       e ++++ ++++rs+l+ ++Ptl+++ p+e++ +++kq+ d++ek + +    ++ ++e ++ ++++v+ + +e++nq
  gi|298676207|ref|YP_003727956.1| 257 EHDQLEKQNQIRSILTGILPTLLKESPKEKRRVILKQMLDMIEKCMFHGECLNMTQFEYNNINTSNVGYMSCEVINQ 333
                                       678999**************************************77666555999********************** PP

                            MetOD1  78 lfanfgiktekkedeknvlleftnCpWge.earknPifCllcraivsrsftwtglkgsveqkktlgngdekCvFeik 153
                                       l+++f ++t  ++++ ++++++t CpWg  +a++nPi+C+l+ +i+ r+++ ++ + +v+++kt+gngde+C+F i+
  gi|298676207|ref|YP_003727956.1| 334 LGGDFSVDTS-NQNDVQFAIKGTGCPWGIeQAKMNPILCNLTNGIIARTVSNVYKNPNVKTMKTMGNGDECCYFLIH 409
                                       **********.58888999********988********************************************998 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.0   1.5e-12   3.4e-09       4     104 .]      26     123 ..      23     123 .. 0.93
   2 !   43.0   0.1   1.9e-14   4.2e-11       2     103 ..     143     245 ..     142     245 .. 0.82
   3 ?   -2.7   0.0       3.3   7.4e+03      42      60 ..     283     309 ..     256     331 .. 0.61

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 1.5e-12
                             PAS_9   4 ilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfwvl 79 
                                        ++ +  g+ l++N++a++ lGy ++e+l    + +   +pe +e+++++++q+++ k+ ++e v+i+k+ge+++v+
  gi|298676207|ref|YP_003727956.1|  26 AFVHDLAGNFLDINNTAIQRLGYPKDELLSMGPHSID--APEYAEKVNNIIKQISEeKQLTFESVHITKSGERIPVE 100
                                       556558899*********************9999999..************************************** PP

                             PAS_9  80 ltaspvkdddgelvgiivilrDite 104
                                       ++   ++ +++  ++  +i rDite
  gi|298676207|ref|YP_003727956.1| 101 ISSNIIQYKEQPAIL--SIARDITE 123
                                       ******999988888..*******8 PP

  == domain 2  score: 43.0 bits;  conditional E-value: 1.9e-14
                             PAS_9   2 dgili....dnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirknge 74 
                                       d+i+i     +  g+i++aN++a+++ Gys +e+l+ +itdl  t + a+e+  ++ +  + +   +e+ + +kng+
  gi|298676207|ref|YP_003727956.1| 143 DAIFIlegeGDGTGNIVDANQKAADIHGYSLDEILNMHITDLG-TQSVADEFPLRLKRVFEGEWIKDELNHLDKNGN 218
                                       56666343323445*****************************.55555555555555555578************* PP

                             PAS_9  75 tfwvlltaspvkdddgelvgiivilrDit 103
                                        +w +++a  v  d+ ++++  +i rDit
  gi|298676207|ref|YP_003727956.1| 219 VIWMEVNAGQVELDGHKYIF--AIERDIT 245
                                       ************99999999..******9 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 3.3
                             PAS_9  42 tdpeanerlraaleqgrk........k 60 
                                       ++++++  l+++l++++k        +
  gi|298676207|ref|YP_003727956.1| 283 PKEKRRVILKQMLDMIEKcmfhgeclN 309
                                       445555556666666665555544442 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   2.3e-08   5.3e-05       4      42 ..      16      55 ..      13      74 .. 0.86
   2 !   35.1   0.0   4.2e-12   9.4e-09       2      52 ..     133     188 ..     132     206 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2.3e-08
                             PAS_8  4 ralfesspdgiavvd.lgdrivdvNqaalellGys.adlkg 42
                                        lf++++d+ +v d +g+ ++d+N++a++ lGy+ ++l+ 
  gi|298676207|ref|YP_003727956.1| 16 FYLFNNMNDAAFVHDlAGN-FLDINNTAIQRLGYPkDELLS 55
                                      679**********9*7777.***************777765 PP

  == domain 2  score: 35.1 bits;  conditional E-value: 4.2e-12
                             PAS_8   2 rlralfesspdgiavvd.lgd...rivdvNqaalellGys.adlkgellgqllpvl 52 
                                       r+r lfe ++d+i+++  +gd   +ivd+Nq+a+++ Gys ++++ + + +l++++
  gi|298676207|ref|YP_003727956.1| 133 RYRLLFEKADDAIFILEgEGDgtgNIVDANQKAADIHGYSlDEILNMHITDLGTQS 188
                                       9**************9874445788***************9999987775544444 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   5.9e-09   1.3e-05       1     110 []      19     126 ..      19     126 .. 0.88
   2 !   31.5   0.0   7.6e-11   1.7e-07       1     108 [.     138     247 ..     138     249 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 5.9e-09
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pg 76 
                                       +++++da +v d  g++l++N++a + +g+p +ell + ++++  +e a+ + +++++  e+ + ++f+ ++ + +g
  gi|298676207|ref|YP_003727956.1|  19 FNNMNDAAFVHDLAGNFLDINNTAIQRLGYPKDELLSMGPHSIDAPEYAEKVNNIIKQISEE-KQLTFESVHITkSG 94 
                                       7899*******************9999**************988888999999999998887.566666666667** PP

                             PAS_4  77 eerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                       e+ ++e++ + +     e  ++l i+rDiTer+r
  gi|298676207|ref|YP_003727956.1|  95 ERIPVEISSNIIQY--KEQPAILSIARDITERKR 126
                                       *********88844..4567************97 PP

  == domain 2  score: 31.5 bits;  conditional E-value: 7.6e-11
                             PAS_4   1 ldslpdalavl....dpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleell 73 
                                       +++  da+++l    d  g++++aN+ aa++ g++ +e+l+++  +l ++++a+++   l+rv ege  i+++  +l
  gi|298676207|ref|YP_003727956.1| 138 FEKADDAIFILegegDGTGNIVDANQKAADIHGYSLDEILNMHITDLGTQSVADEFPLRLKRVFEGE-WIKDELNHL 213
                                       6788999****9999***************************************************7.555555555 PP

                             PAS_4  74 l.pgeerhyelrllPlrdesGevigvlvisrDiTer 108
                                       + +g   ++e+++  + + +G    +++i rDiT r
  gi|298676207|ref|YP_003727956.1| 214 DkNGNVIWMEVNAGQV-ELDGH-KYIFAIERDITWR 247
                                       56***********999.68999.9999999999966 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   8.6e-08   0.00019       6     113 .]      18     121 ..      13     121 .. 0.90
   2 !   25.3   0.0   5.3e-09   1.2e-05       2     113 .]     133     244 ..     132     244 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 8.6e-08
                                       HHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECT CS
                               PAS   6 ileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfklr 82 
                                       +++++ d+ fv D  g++l +N +a + lG++ +e+l+     +i  ++ ae +  + +++++ ++ + + + +++ 
  gi|298676207|ref|YP_003727956.1|  18 LFNNMNDAAFVHDLAGNFLDINNTAIQRLGYPKDELLSMGPH-SIDAPEYAEKVNNIIKQISEEKQLTFESVHITK- 92 
                                       689*********************************998777.999998899999999999999999999999999. PP

                                       TSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  83 dgrpihlevraspvrdaggeilgflgvlrdi 113
                                        g+ i++e+  + +  +++    +l ++rdi
  gi|298676207|ref|YP_003727956.1|  93 SGERIPVEISSNIIQYKEQP--AILSIARDI 121
                                       **********9999999887..888888887 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 5.3e-09
                                       HHHHHHHHSSSEEEEE....ETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECC CS
                               PAS   2 dlraileslpdpifvv....DedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesra 74 
                                       ++r ++e ++d+if++    D  g+i+ +N++a+++ G+s +e+l+ ++ dl        +a+++   l+ ++ +++
  gi|298676207|ref|YP_003727956.1| 133 RYRLLFEKADDAIFILegegDGTGNIVDANQKAADIHGYSLDEILNMHITDLGTQS----VADEFP--LRLKRVFEG 203
                                       899*************55555999****************************9876....777775..555678888 PP

                                       CCEEEEC....TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  75 geisfkl....rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       ++i+ +l    ++g +i++ev+a  v   g++  +++ + rdi
  gi|298676207|ref|YP_003727956.1| 204 EWIKDELnhldKNGNVIWMEVNAGQVELDGHK--YIFAIERDI 244
                                       888888888999***********999888876..777776665 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   3.7e-06    0.0082       3      79 ..      37     110 ..      35     118 .. 0.88
   2 !   11.1   0.0   0.00016      0.37       2      72 ..     159     226 ..     158     238 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.7e-06
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirden 79 
                                        ++++  + lGy ++ell+      ++  pe  e+v++ ++++ ++++ +++e   ++k+Ge + ve + ++i++++
  gi|298676207|ref|YP_003727956.1|  37 DINNTAIQRLGYPKDELLSM--GPHSIDAPEYAEKVNNIIKQISEEKQ-LTFESVHITKSGERIPVEISSNIIQYKE 110
                                       6778888899**********..9*******************998888.8999999*****************5544 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00016
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveara 72 
                                       + ++++  +i Gys +e+l+   ++ dl      +++   l++++ +ge ++ e   + k+G ++w+e  a
  gi|298676207|ref|YP_003727956.1| 159 VDANQKAADIHGYSLDEILNM--HITDLGTQSVADEFPLRLKRVF-EGEWIKDELNHLDKNGNVIWMEVNA 226
                                       7899*****************..8888888888888888888888.56658****************9876 PP

>> DUF3877  Domain of unknown function, E. rectale Gene description (DUF3877)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   4.8e-06     0.011      27     152 ..      45     172 ..      14     182 .. 0.73
   2 ?   -2.3   0.0       1.5   3.4e+03      66     103 ..     338     376 ..     319     387 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.8e-06
                           DUF3877  27 rlyyPlssLn....hlleaeedaeelkealeefaeeakeklGevevtekkdrfcveipeegaeyvheeikeneFlke 99 
                                       rl yP + L     h ++a e ae++++ +++++ee++ ++ +v++t++++r+ vei+ +  +y ++  ++   +++
  gi|298676207|ref|YP_003727956.1|  45 RLGYPKDELLsmgpHSIDAPEYAEKVNNIIKQISEEKQLTFESVHITKSGERIPVEISSNIIQYKEQ--PAILSIAR 119
                                       677887777611124456666899***********************************99999433..22233333 PP

                           DUF3877 100 liellkkhectledilelFkkyskkvvvekieedefdyliyFedeeedeyyYc 152
                                        i+  k+ e + ++ + lF+k ++ + + + e d  + ++  ++++ d + Y 
  gi|298676207|ref|YP_003727956.1| 120 DITERKRAELNEKRYRLLFEKADDAIFILEGEGDGTGNIVDANQKAADIHGYS 172
                                       34444444555555666777777777777777777666666666666666665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.5
                           DUF3877  66 vevt.ekkdrfcveipeegaeyvheeikeneFlkeliel 103
                                        +v  ++++ +++ i  +g+ +  e++k n+ l +l + 
  gi|298676207|ref|YP_003727956.1| 338 FSVDtSNQNDVQFAIKGTGCPWGIEQAKMNPILCNLTNG 376
                                       454315667799999999999999999999999888765 PP

>> ATC_hydrolase  L-2-amino-thiazoline-4-carboxylic acid hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.3   0.00033      0.73      26     143 ..     288     406 ..     268     408 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00033
                     ATC_hydrolase  26 keiirkal...erlg....kergkklaekakakkdkadvekflalyseifek.enalkfevleedkdeleidvtrCp 94 
                                       + i++++l   e++     + +++++  +++    +++  ++++   e+ ++ ++++ +++  +++ ++ i+ t Cp
  gi|298676207|ref|YP_003727956.1| 288 RVILKQMLdmiEKCMfhgeCLNMTQFEYNNI----NTSNVGYMS--CEVINQlGGDFSVDTSNQNDVQFAIKGTGCP 358
                                       4444443322222222002333333333333....333334444..3555557999********************* PP

                     ATC_hydrolase  95 yceawkkeGlpelgkllCeiDkavaeginpk....vklertktlaeGgdcCdf 143
                                       +          +  ++lC++ + ++    ++     + +  kt++ G++cC f
  gi|298676207|ref|YP_003727956.1| 359 WGIEQA-----KMNPILCNLTNGIIARTVSNvyknPNVKTMKTMGNGDECCYF 406
                                       *64333.....344777766555555544443444456779**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       997  (0.0556082); expected 358.6 (0.02)
Passed bias filter:                      640  (0.0356964); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2697.19
//
Query:       gi|298676208|ref|YP_003727957.1|  [L=78]
Description: hypothetical protein Metev_2350 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 609.24
//
Query:       gi|298676209|ref|YP_003727958.1|  [L=1962]
Description: periplasmic copper-binding protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.3e-48  158.3 187.2    0.00053   20.2   2.5   25.7 26  Glug         The GLUG motif
    1.5e-31  109.6  94.6      2e-24   86.2  34.8    6.2  6  NosD         Periplasmic copper-binding protein (NosD)
  ------ inclusion threshold ------
      0.014   15.4   2.6       0.04   13.9   2.6    1.8  1  Trypan_PARP  Procyclic acidic repetitive protein (PARP)


Domain annotation for each model (and alignments):
>> Glug  The GLUG motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.2      0.22   1.3e+03      18      28 .]     103     114 ..     101     114 .. 0.89
   2 ?    0.7   2.7      0.15     9e+02      13      28 .]     148     167 ..     145     176 .. 0.75
   3 ?   -3.0   0.5       2.2   1.3e+04      17      25 ..     336     344 ..     332     346 .. 0.78
   4 ?    2.3   0.5     0.045   2.7e+02       7      28 .]     544     565 ..     543     565 .. 0.90
   5 !    9.0   2.1   0.00032       1.9       2      28 .]     567     592 ..     566     592 .. 0.90
   6 !    9.6   0.7   0.00022       1.3       5      28 .]     597     619 ..     593     619 .. 0.87
   7 !    9.9   1.0   0.00018       1.1       7      27 ..     626     644 ..     626     645 .. 0.93
   8 ?    3.8   0.1     0.016        94       7      22 ..     785     799 ..     785     799 .. 0.91
   9 ?   -2.9   0.2         2   1.2e+04      14      28 .]     968     983 ..     963     983 .. 0.79
  10 !   14.9   2.6   4.4e-06     0.026       2      28 .]     988    1012 ..     987    1012 .. 0.91
  11 !   13.8   3.8   9.6e-06     0.057       1      28 []    1014    1040 ..    1014    1040 .. 0.94
  12 !   20.2   2.5   8.9e-08   0.00053       1      28 []    1043    1068 ..    1043    1068 .. 0.93
  13 !    7.4   0.7    0.0011       6.5       4      22 ..    1073    1090 ..    1070    1090 .. 0.85
  14 !   18.1   0.8   4.1e-07    0.0025       1      28 []    1273    1299 ..    1273    1299 .. 0.93
  15 !   19.3   1.6   1.7e-07     0.001       4      28 .]    1303    1326 ..    1300    1326 .. 0.91
  16 !    5.1   3.8    0.0057        34       4      28 .]    1330    1359 ..    1327    1359 .. 0.85
  17 !   14.8   2.1   4.7e-06     0.028       2      28 .]    1361    1386 ..    1360    1386 .. 0.92
  18 !   10.5   0.1   0.00011      0.69       4      28 .]    1396    1418 ..    1393    1418 .. 0.89
  19 !   17.7   0.3   5.8e-07    0.0035       1      28 []    1421    1450 ..    1421    1450 .. 0.94
  20 !   20.0   0.4     1e-07   0.00062       1      28 []    1451    1477 ..    1451    1477 .. 0.94
  21 !   13.4   0.0   1.3e-05      0.08       3      27 ..    1480    1503 ..    1478    1504 .. 0.87
  22 !   16.8   1.6   1.1e-06    0.0065       5      28 .]    1523    1545 ..    1520    1545 .. 0.92
  23 !   16.4   0.2   1.4e-06    0.0085       3      27 ..    1550    1575 ..    1548    1576 .. 0.93
  24 !   15.9   0.4     2e-06     0.012       1      27 [.    1577    1602 ..    1577    1603 .. 0.95
  25 !    5.9   1.1    0.0032        19       4      28 .]    1607    1630 ..    1604    1630 .. 0.82
  26 !   11.4   0.2   5.8e-05      0.35       2      21 ..    1633    1652 ..    1632    1653 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.22
                              Glug  18 ienctatg.tvt 28 
                                       ++n+ta++ t++
  gi|298676209|ref|YP_003727958.1| 103 VDNSTAENgTII 114
                                       89******9995 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.15
                              Glug  13 ggg...gsienctatg.tvt 28 
                                       +g     s++n++++g ++t
  gi|298676209|ref|YP_003727958.1| 148 TGStisISVDNVNVSGfNIT 167
                                       54456678888888888887 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 2.2
                              Glug  17 sienctatg 25 
                                        i n+++tg
  gi|298676209|ref|YP_003727958.1| 336 KINNSSVTG 344
                                       6899***98 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.045
                              Glug   7 GLvGgaggggsienctatg.tvt 28 
                                       GL G+++g+ si+n++ ++ ++t
  gi|298676209|ref|YP_003727958.1| 544 GLFGYTDGN-SISNVSLKDvNIT 565
                                       6779****9.*******999987 PP

  == domain 5  score: 9.0 bits;  conditional E-value: 0.00032
                              Glug   2 atavGGLvGgaggggsienctatgtvt 28 
                                        +avG LvG++  +g +  +++tg+vt
  gi|298676209|ref|YP_003727958.1| 567 DSAVGALVGYNN-DGFVYQSYSTGNVT 592
                                       689********6.59**********98 PP

  == domain 6  score: 9.6 bits;  conditional E-value: 0.00022
                              Glug   5 vGGLvGgaggggsienctatgtvt 28 
                                       vGGLvG+    ++++ +++ ++vt
  gi|298676209|ref|YP_003727958.1| 597 VGGLVGYIN-ESNVTKSYSIANVT 619
                                       9*****995.5********99998 PP

  == domain 7  score: 9.9 bits;  conditional E-value: 0.00018
                              Glug   7 GLvGgaggggsienctatgtv 27 
                                       G+vG++   g+i+n+++ gtv
  gi|298676209|ref|YP_003727958.1| 626 GFVGYSS--GNISNSYSIGTV 644
                                       9*****8..5**********9 PP

  == domain 8  score: 3.8 bits;  conditional E-value: 0.016
                              Glug   7 GLvGgaggggsienct 22 
                                       GL+G+++  g+++n++
  gi|298676209|ref|YP_003727958.1| 785 GLIGYNDE-GTVDNSY 799
                                       9*****97.8****96 PP

  == domain 9  score: -2.9 bits;  conditional E-value: 2
                              Glug  14 gggsienctatg.tvt 28 
                                       g++ ++n+  ++ +vt
  gi|298676209|ref|YP_003727958.1| 968 GNSKVSNVGLENiNVT 983
                                       3489999999998887 PP

  == domain 10  score: 14.9 bits;  conditional E-value: 4.4e-06
                              Glug    2 atavGGLvGgaggggsienctatgtvt 28  
                                        + +vGGLvG+++  g++  +++tg+vt
  gi|298676209|ref|YP_003727958.1|  988 YAYVGGLVGHSY--GTVNQSYSTGNVT 1012
                                        569********7..6***********8 PP

  == domain 11  score: 13.8 bits;  conditional E-value: 9.6e-06
                              Glug    1 gatavGGLvGgaggggsienctatgtvt 28  
                                        ++++vGGLvG ++g g++  +++t +vt
  gi|298676209|ref|YP_003727958.1| 1014 SGYSVGGLVGWNDG-GTVNQSYSTSNVT 1040
                                        589**********8.8*********998 PP

  == domain 12  score: 20.2 bits;  conditional E-value: 8.9e-08
                              Glug    1 gatavGGLvGgaggggsienctatgtvt 28  
                                        g+++vGGLvG ++  gsi+ +++tg+vt
  gi|298676209|ref|YP_003727958.1| 1043 GSSSVGGLVGWNY--GSIDQSYSTGNVT 1068
                                        6899********7..6***********8 PP

  == domain 13  score: 7.4 bits;  conditional E-value: 0.0011
                              Glug    4 avGGLvGgaggggsienct 22  
                                        +vGGLvG +   gs +n++
  gi|298676209|ref|YP_003727958.1| 1073 YVGGLVGLNNS-GSTDNSY 1090
                                        8********65.8999986 PP

  == domain 14  score: 18.1 bits;  conditional E-value: 4.1e-07
                              Glug    1 gatavGGLvGgaggggsienctatgtvt 28  
                                        ga  vGGLvG +++ g++ ++++tg+v+
  gi|298676209|ref|YP_003727958.1| 1273 GAKLVGGLVGWNDQ-GTVNHSYSTGDVN 1299
                                        5778*********9.8**********97 PP

  == domain 15  score: 19.3 bits;  conditional E-value: 1.7e-07
                              Glug    4 avGGLvGgaggggsienctatgtvt 28  
                                         vGGLvG++++ g++ ++++tg+v+
  gi|298676209|ref|YP_003727958.1| 1303 DVGGLVGYNYQ-GTVNHSYSTGDVN 1326
                                        69********9.8**********97 PP

  == domain 16  score: 5.1 bits;  conditional E-value: 0.0057
                              Glug    4 avGGLvGgaggg.......gsienctatgtvt 28  
                                        +vGGLvG    +       g++  +++tg+v+
  gi|298676209|ref|YP_003727958.1| 1330 NVGGLVGEY--NvgtvdhvGTVYQSYSTGNVS 1359
                                        8******66..4558**************995 PP

  == domain 17  score: 14.8 bits;  conditional E-value: 4.7e-06
                              Glug    2 atavGGLvGgaggggsienctatgtvt 28  
                                        +  vGGL+G++ g ++i  ++a+gtvt
  gi|298676209|ref|YP_003727958.1| 1361 SEDVGGLAGINKG-ATILQSSASGTVT 1386
                                        677********98.9***********8 PP

  == domain 18  score: 10.5 bits;  conditional E-value: 0.00011
                              Glug    4 avGGLvGgaggggsienctatgtvt 28  
                                        + GGL+G +   g+ie ++atg+v+
  gi|298676209|ref|YP_003727958.1| 1396 NFGGLIGFNI--GHIELSNATGDVN 1418
                                        67*******8..5**********97 PP

  == domain 19  score: 17.7 bits;  conditional E-value: 5.8e-07
                              Glug    1 gatavGGLvGgaggg..gsienctatgtvt 28  
                                        gat+vGGLvG++++    +++ ++atg+++
  gi|298676209|ref|YP_003727958.1| 1421 GATYVGGLVGYNLASepKTVSESYATGDIS 1450
                                        79***********87**9*********995 PP

  == domain 20  score: 20.0 bits;  conditional E-value: 1e-07
                              Glug    1 gatavGGLvGgaggggsienctatgtvt 28  
                                        g+ +vGGLvG+++++  +++++atg+v+
  gi|298676209|ref|YP_003727958.1| 1451 GYEYVGGLVGQNEND-FVTDSYATGDVS 1477
                                        689***********8.**********95 PP

  == domain 21  score: 13.4 bits;  conditional E-value: 1.3e-05
                              Glug    3 tavGGLvGgaggggsienctatgtv 27  
                                         ++GGLvG++   g+i+n++a g+v
  gi|298676209|ref|YP_003727958.1| 1480 RNLGGLVGRNKR-GTIDNSSAMGKV 1503
                                        689*******88.8******97776 PP

  == domain 22  score: 16.8 bits;  conditional E-value: 1.1e-06
                              Glug    5 vGGLvGgaggggsienctatgtvt 28  
                                         GGLvG ++g g+++ ++atg++t
  gi|298676209|ref|YP_003727958.1| 1523 FGGLVGFNLG-GTVKTSNATGDIT 1545
                                        6********8.8***********8 PP

  == domain 23  score: 16.4 bits;  conditional E-value: 1.4e-06
                              Glug    3 tavGGLvGgaggg.gsienctatgtv 27  
                                        ++vGGL+G++  g ++++ ++atg+v
  gi|298676209|ref|YP_003727958.1| 1550 NNVGGLIGYNSKGlTTVKQSYATGSV 1575
                                        79*********88***********98 PP

  == domain 24  score: 15.9 bits;  conditional E-value: 2e-06
                              Glug    1 gatavGGLvGgaggggsienctatgtv 27  
                                        g+ +vGGL+G ++++  ++n +a g+v
  gi|298676209|ref|YP_003727958.1| 1577 GNENVGGLIGWNEYD-LVTNTYALGDV 1602
                                        799**********97.********998 PP

  == domain 25  score: 5.9 bits;  conditional E-value: 0.0032
                              Glug    4 avGGLvGgaggggsienctatgtvt 28  
                                        +vGGLvG +   g++  +++tg vt
  gi|298676209|ref|YP_003727958.1| 1607 NVGGLVGLNSP-GTVNLSYSTGEVT 1630
                                        8******9975.7888888888886 PP

  == domain 26  score: 11.4 bits;  conditional E-value: 5.8e-05
                              Glug    2 atavGGLvGgaggggsienc 21  
                                        ++ +GGL+G++++++++e++
  gi|298676209|ref|YP_003727958.1| 1633 GSTIGGLIGTNENDATVEDA 1652
                                        6789**************97 PP

>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -6.1  14.3         3   1.8e+04      38     133 ..      52     155 ..      23     161 .. 0.69
   2 !   39.4  51.7   6.3e-14   3.8e-10      23     173 ..     155     309 ..     142     316 .. 0.91
   3 !   86.2  34.8   3.4e-28     2e-24     119     238 ..     310     444 ..     306     447 .. 0.92
   4 ?  -14.3  18.3         3   1.8e+04      46     154 ..     525     644 ..     454     699 .. 0.53
   5 ?   -7.7   6.0         3   1.8e+04      99     102 ..    1094    1097 ..    1002    1146 .. 0.48
   6 ?   -3.1   0.8      0.63   3.8e+03      26      78 ..    1633    1685 ..    1619    1710 .. 0.55

  Alignments for each domain:
  == domain 1  score: -6.1 bits;  conditional E-value: 3
                              NosD  38 rdgilldnssnntitgntienlryGihlensesntiedntlssnesGialmsssnn.tlenNtisnnen..yGills 111
                                       ++++ll n+s+n i g   e +++G+++ n++s+ + +     n++ ia+++  +n t en ti+  ++  +  +l+
  gi|298676209|ref|YP_003727958.1|  52 KQQVLLINNSDNVIAG-LWEGNNSGVYYYNNSSTSWVNESG-VNNKTIAIQRAVDNsTAENGTIIVGDGlyN-GSLK 125
                                       4455788888888888.5888899****9999966665555.555689999999888***999999888643.3333 PP

                              NosD 112 dssn..ntisnNti......snnnkGifle 133
                                         +   +++++N+       +n+++ i+++
  gi|298676209|ref|YP_003727958.1| 126 IDNPnvTELTYNNSkpvidgLNTGSTISIS 155
                                       333312445555555665555555555555 PP

  == domain 2  score: 39.4 bits;  conditional E-value: 6.3e-14
                              NosD  23 nsegseisnneisnsrdgi.lldnssnntitgntienlryGihlensesntiedntlssne.....sGialmsssnn 93 
                                       ++++  +s+ +i+ns++++  ++n++ +++t+n i+++++G+ l++s++++++dn + +n+     ++i+l+ss+++
  gi|298676209|ref|YP_003727958.1| 155 SVDNVNVSGFNITNSSNTLvNVSNANYINLTNNNITDNSKGVILQKSNNSNVKDNYFINNGgdgfdYAICLESSNKT 231
                                       458888999999999999978899999999******************************99888889*******99 PP

                              NosD  94 tlenNtisnnenyGillsdssnntisnNtisnnnkGiflensssntitgNriesnqkiGilllsssegntiynNyFi 170
                                        ++ N++++n +  i   +s++n++ nNt++nn + i+ +ns+sn it+N+i++n + Gi ll +s++n++++N  i
  gi|298676209|ref|YP_003727958.1| 232 NVSSNIFKENYI-CICSFNSNYNNLVNNTFLNNLATIYNRNSESNNITNNYIANN-SLGIGLLGTSSKNNVTGNKII 306
                                       **********99.******************************************.********************7 PP

                              NosD 171 nns 173
                                       n +
  gi|298676209|ref|YP_003727958.1| 307 NTT 309
                                       754 PP

  == domain 3  score: 86.2 bits;  conditional E-value: 3.4e-28
                              NosD 119 snNtisnnnkGiflens.ssntitgNriesnqkiGilllssseg......ntiynNyFinnsenvkydgsn.nneWn 187
                                        ++t+  ++ Gi ++++ ++n++ gN+i+++  +Gi  l+++++      n+iynNy+ nn++n++ ++s  +n+Wn
  gi|298676209|ref|YP_003727958.1| 310 YDDTVDTSGVGILISGNsENNKVNGNKINNSSVTGIS-LDQNSNgnapsnNLIYNNYL-NNTNNAYVNDSCtGNNWN 384
                                       567888999*****98769******************.887766688888********.********99989***** PP

                              NosD 188 ttktsgtniiggpylgGNyWsdydg.......eDadgDGigDtpYeindgv..iDylplv 238
                                        +k+sgtni+ggpylgGNyW++ +g        D++gDGi+D++Y+in++   +D+lpl 
  gi|298676209|ref|YP_003727958.1| 385 ISKKSGTNIMGGPYLGGNYWANRSGdgfsqtnIDENGDGICDSSYTINSNTdsVDNLPLN 444
                                       ************************************************777779****96 PP

  == domain 4  score: -14.3 bits;  conditional E-value: 3
                              NosD  46 ssnntitgntienl...ryGihlenses.....ntiedntlssne.sGialmsssnntlenNtisnnen....yGil 109
                                        ++ +i++ +i+ l   + G++  ++++     + ++d  +++++  G ++ ++++ ++ ++ +++n +     G l
  gi|298676209|ref|YP_003727958.1| 525 GNGYNISNLVINRLgenNVGLF-GYTDGnsisnVSLKDVNITGDSaVGALVGYNNDGFVYQSYSTGNVTgsekVGGL 600
                                       2333333333333342233333.333332344444444444444457777777777766655444444334336777 PP

                              NosD 110 lsdssnntisnNtisnnnkGiflensssntitgNriesnqkiGil 154
                                       + +++++++++     n +G++ ++     +++ +i+++ +iG +
  gi|298676209|ref|YP_003727958.1| 601 VGYINESNVTKSYSIANVTGFSETS-GFVGYSSGNISNSYSIGTV 644
                                       7777777777766655555544333.3344444444444444444 PP

  == domain 5  score: -7.7 bits;  conditional E-value: 3
                              NosD   99 tisn 102 
                                        + s+
  gi|298676209|ref|YP_003727958.1| 1094 ETSG 1097
                                        1111 PP

  == domain 6  score: -3.1 bits;  conditional E-value: 0.63
                              NosD   26 gseisnneisnsrdgilldnssnntitgntienlryGihlenses..ntiedntl 78  
                                        gs+i +   +n++d+   d+ ++ + tg t +++  G  l++se+  n + dn +
  gi|298676209|ref|YP_003727958.1| 1633 GSTIGGLIGTNENDATVEDAYWDTDTTGQTSSDG--GTALTTSEMvgNAAMDNMA 1685
                                        5555555555555555555555555555555554..4444444444455555555 PP

>> Trypan_PARP  Procyclic acidic repetitive protein (PARP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   2.6   6.7e-06      0.04      78     116 ..    1907    1945 ..    1899    1957 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.7e-06
                       Trypan_PARP   78 epetepeeepepepepepepepepepepepepepgaatl 116 
                                        e et  ee++epepe ep+p++e +   e e  pg ++l
  gi|298676209|ref|YP_003727958.1| 1907 EIETVEEEKTEPEPETEPKPDTEQNESEESESTPGFSSL 1945
                                        345555556666666666666666655666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1962 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.88u 0.25s 00:00:01.12 Elapsed: 00:00:00.43
# Mc/sec: 13777.98
//
Query:       gi|298676210|ref|YP_003727959.1|  [L=128]
Description: hypothetical protein Metev_2353 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   12.4   9.0       0.15   12.1   9.0    1.2  1  DUF5094   Domain of unknown function (DUF5094)


Domain annotation for each model (and alignments):
>> DUF5094  Domain of unknown function (DUF5094)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   9.0   8.4e-06      0.15      19      96 ..      22     101 ..       2     118 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.4e-06
                           DUF5094  19 kknklssknlkeke.nvkvkeaeekkeekvtstkenkenekqdkdsllkeikdienelieaykeeNeyLrsl.knev 93 
                                       +k++ +   ++  + ++  +++e++++ k+++ ++n++n++ d ++++ +i++i  + +  +++e  +L++  k+++
  gi|298676210|ref|YP_003727959.1|  22 SKKPNPVVVTETLNlYFYGSKKEDENNYKSADDNNNNANNQTDDNKMILDINSIMYQWVYDLRAERDTLKEQlKEKD 98 
                                       333333333333335555555555555555555666666666666*************************8534444 PP

                           DUF5094  94 llt 96 
                                       +l 
  gi|298676210|ref|YP_003727959.1|  99 SLD 101
                                       444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1821  (0.101567); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 821.19
//
Query:       gi|298676211|ref|YP_003727960.1|  [L=120]
Description: hypothetical protein Metev_2354 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 843.30
//
Query:       gi|298676212|ref|YP_003727961.1|  [L=192]
Description: hypothetical protein Metev_2355 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   13.0   0.0       0.21   12.2   0.0    1.5  1  ThiS      ThiS family
       0.15   13.0   0.4       0.42   11.6   0.4    1.9  1  Pilin_N   Archaeal Type IV pilin, N-terminal


Domain annotation for each model (and alignments):
>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.4e-05      0.21      40      66 ..     109     136 ..      71     137 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.4e-05
                                       TTTTEEEEETTEEEGC.CTTTSB--TTC CS
                              ThiS  40 lerrvavavNgeivpr.lwldtelkdgD 66 
                                        ++   v +Nge +++ l++dt lk+gD
  gi|298676212|ref|YP_003727961.1| 109 TKEETTVKINGEKINYyLGEDTNLKKGD 136
                                       568889*********************9 PP

>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4   4.7e-05      0.42      32      78 ..      73     119 ..      40     122 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.7e-05
                           Pilin_N  32 sneekapqasievkidssastgkna..vslehkgGdsidt..kdlkivlns 78 
                                         +ekapq si  + d+ ++    +  ++l+h+ G+si+   +++++ +n+
  gi|298676212|ref|YP_003727961.1|  73 VSTEKAPQLSIGASFDTIKG----NkvIKLKHQWGESITFtkEETTVKING 119
                                       34566777777555555554....235***********9855666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1058  (0.0590105); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1334.02
//
Query:       gi|298676213|ref|YP_003727962.1|  [L=82]
Description: hypothetical protein Metev_2356 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 534.89
//
Query:       gi|298676214|ref|YP_003727963.1|  [L=90]
Description: plasmid stabilization system [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-06   27.9   0.5    4.1e-06   27.3   0.5    1.3  1  ParE_toxin       ParE toxin of type II toxin-antitoxin system
    0.00015   21.8   0.0    0.00018   21.6   0.0    1.1  1  Gp49             Phage derived protein Gp49-like (DUF891)
    0.00017   21.5   0.5    0.00026   20.9   0.5    1.3  1  ParE-like_toxin  ParE-like toxin of type II bacterial toxin-a
     0.0034   17.2   0.4     0.0041   16.9   0.4    1.0  1  DUF4364          Domain of unknown function (DUF4364)


Domain annotation for each model (and alignments):
>> ParE_toxin  ParE toxin of type II toxin-antitoxin system, parDE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.5   9.1e-10   4.1e-06       1      90 []       5      85 ..       5      85 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 9.1e-10
                                      EEEEHHHHHHHHHHHHHHHCC-HHHHHHHHHHHHHHHHHHHHTTTSEECTSTC.....CTTEEEEEECTEEEEEEEETS CS
                        ParE_toxin  1 vrltprAlkdlkkiadyiardgpaakrfldaleealellaenpalgrprrelg.....lkglrririgdyriiYridde 74
                                      v +t +A+k lkk+ + i      a+ ++  +    ++l  np    +    +        +++ r+g yr+i +i+++
  gi|298676214|ref|YP_003727963.1|  5 VTYTTKARKNLKKLPEEI------ARNIIYSI----DELRHNPYYSVK----KisgtgKHSIYSHRVGQYRVILTIENN 69
                                      679***********8877......65555555....666666655544....222355889****************** PP

                                      TTEEEEEEEEEHHHHC CS
                        ParE_toxin 75 elvvvilrvlhrsedy 90
                                      e v+ +l ++ r+ +y
  gi|298676214|ref|YP_003727963.1| 70 EMVIMVLELGDRKHIY 85
                                      **********999765 PP

>> Gp49  Phage derived protein Gp49-like (DUF891)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   3.9e-08   0.00018       2      67 ..      14      75 ..      13      88 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 3.9e-08
                              Gp49  2 eldalpkkarakilaaldlleeggpdlgkplvkkledglwElrpksaggiiRvlyafdpgrkvilL 67
                                       l++lp+++ ++i++ +d l+++     k++ +++++ ++  r+    g++Rv+ +   ++ vi++
  gi|298676214|ref|YP_003727963.1| 14 NLKKLPEEIARNIIYSIDELRHNPYYSVKKISGTGKHSIYSHRV----GQYRVILTIENNEMVIMV 75
                                      699*****************999888******************....9*********99988775 PP

>> ParE-like_toxin  ParE-like toxin of type II bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.5   5.9e-08   0.00026       2      85 ..       6      87 ..       5      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 5.9e-08
                   ParE-like_toxin  2 lqtrrfkkalkklkeklkadldkavkeiiedPelGeeKkGDLsgvfvykfklnkqltllaYeldekkrvlvlllvGthe 80
                                      + t++++k lkkl e+ ++++   ++e+ ++P+   +K        +y  ++   ++++  +++++++v+++l +G ++
  gi|298676214|ref|YP_003727963.1|  6 TYTTKARKNLKKLPEEIARNIIYSIDELRHNPYYSVKKISGTGKHSIYSHRV--GQYRVILTIENNEMVIMVLELGDRK 82
                                      67899******************************99976666555555554..57888889***************** PP

                   ParE-like_toxin 81 NfYre 85
                                        Yr+
  gi|298676214|ref|YP_003727963.1| 83 HIYRK 87
                                      ***96 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.4   9.2e-07    0.0041      61     132 ..       6      78 ..       2      82 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 9.2e-07
                           DUF4364  61 kiTekGketlelfenripksirekideylkenkeelkkesev.kadyykkengeytVklkikekdstllelkl 132
                                       + T k +++l+ + ++i+ +i   ide  ++  +++kk s + k  +y ++ g+y+V l+i ++++ ++ l+l
  gi|298676214|ref|YP_003727963.1|   6 TYTTKARKNLKKLPEEIARNIIYSIDELRHNPYYSVKKISGTgKHSIYSHRVGQYRVILTIENNEMVIMVLEL 78 
                                       6799************************999998888876553899***********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 652.29
//
Query:       gi|298676215|ref|YP_003727964.1|  [L=76]
Description: hypothetical protein Metev_2358 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00061   19.7   0.0    0.00073   19.5   0.0    1.1  1  Gag_p24   gag gene protein p24 (core nucleocapsid protein)


Domain annotation for each model (and alignments):
>> Gag_p24  gag gene protein p24 (core nucleocapsid protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   4.1e-08   0.00073     115     154 ..       7      47 ..       3      56 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.1e-08
                                       HHHH--S.-CCC----TT--HHHHHHHHHHHH..HH----HH CS
                           Gag_p24 115 prsgsktesladirQGpkEpyqdfvaRlekal..rkeladek 154
                                       +++ +k   l+++rQ pkEpy++ ++Rl   +  ++el+de+
  gi|298676215|ref|YP_003727964.1|   7 VNPQTKE-MLNELRQYPKEPYNSVIERLARMAidDNELSDEA 47 
                                       5555555.9*******************87543345666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       877  (0.0489152); expected 358.6 (0.02)
Passed bias filter:                      678  (0.0378158); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 521.64
//
Query:       gi|298676216|ref|YP_003727965.1|  [L=73]
Description: hypothetical protein Metev_2359 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 534.25
//
Query:       gi|298676217|ref|YP_003727966.1|  [L=203]
Description: zinc finger C2H2-type domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.1e-08   32.3  34.4     0.0031   18.2   1.6    5.9  6  zf-C2H2_4       C2H2-type zinc finger
    3.9e-07   30.2  19.8       0.08   13.3   0.1    4.0  3  zf-Di19         Drought induced 19 protein (Di19), zinc-bindi
    8.3e-07   29.1  12.4    0.00033   20.9   2.5    4.6  3  zf-C2H2_jaz     Zinc-finger double-stranded RNA-binding
    0.00054   19.9  13.0      0.015   15.3   1.7    3.2  3  DZR             Double zinc ribbon
     0.0014   19.0  38.9      0.016   15.6   3.3    5.7  6  zf-C2H2         Zinc finger, C2H2 type
     0.0061   16.4   4.8      0.084   12.8   0.4    4.4  4  zf-C2HC_2       zinc-finger of a C2HC-type
      0.008   16.5  27.1        0.1   12.9   6.0    3.6  3  zf-C2H2_2       C2H2 type zinc-finger (2 copies)
  ------ inclusion threshold ------
      0.013   15.9  18.9       0.22   12.0   1.8    4.1  3  zf-met          Zinc-finger of C2H2 type
      0.018   14.9  12.9      0.098   12.6   0.4    3.3  3  PyrI_C          Aspartate carbamoyltransferase regulatory cha
      0.019   14.1   0.3        1.8    7.6   0.0    2.0  2  NAD_binding_4   Male sterility protein
      0.029   13.8   1.8        3.8    6.8   0.1    2.3  2  HSP33           Hsp33 protein
       0.03   14.4   0.4        4.8    7.3   0.0    2.9  3  NinD            Family of unknown function
      0.056   13.4  14.1        1.4    8.9   0.9    3.8  4  zinc-ribbons_6  zinc-ribbons
      0.085   12.7   0.4       0.12   12.2   0.4    1.2  1  DUF4370         Domain of unknown function (DUF4370)
      0.096   12.8  13.4        1.5    9.0   0.1    4.3  5  zf-CHCC         Zinc-finger domain
        0.1   12.8   7.3        6.6    7.0   0.0    4.1  4  zf-RING_7       C4-type zinc ribbon domain
       0.12   12.0  11.7        3.4    7.3   0.2    3.7  3  Sgf11           Sgf11 (transcriptional regulation protein)
        0.4   10.5   3.7       0.88    9.4   0.2    2.2  2  T6PP_N          Trehalose-6-phosphate phosphatase N-terminal 
       0.58    8.6  17.9        2.5    6.5   2.6    3.2  3  DUF629          Protein of unknown function (DUF629)
          1    9.7  14.4        4.7    7.6   2.4    3.5  3  GFA             Glutathione-dependent formaldehyde-activating
        1.3    9.1  13.6       0.85    9.7   0.4    3.7  3  CpXC            CpXC protein
        1.7    8.7  11.7        5.1    7.1   0.3    3.4  2  zf-TFIIIC       Putative zinc-finger of transcription factor 
        3.1    8.1  10.0         27    5.1   1.9    3.1  2  BolA            BolA-like protein
        3.2    8.0  29.9       0.26   11.5   1.5    3.8  4  zf-AN1          AN1-like Zinc finger
        9.4    6.5  24.4        1.5    9.0   0.4    4.8  5  HNH             HNH endonuclease


Domain annotation for each model (and alignments):
>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.6       7.9   5.6e+03       3       8 ..       4       9 ..       3      10 .. 0.82
   2 ?    1.2   0.2       1.2   8.9e+02       3       9 ..      17      24 ..      16      33 .. 0.73
   3 !   17.3   0.4   8.2e-06    0.0059       1      24 []      77     100 ..      77     100 .. 0.96
   4 !   18.2   1.6   4.4e-06    0.0031       1      24 []     104     127 ..     104     127 .. 0.96
   5 ?    2.2   0.3      0.61   4.4e+02       9      24 .]     137     151 ..     136     151 .. 0.85
   6 !   15.1   1.8   4.4e-05     0.032       1      24 []     155     178 ..     155     178 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 7.9
                         zf-C2H2_4 3 CpiCgk 8
                                     C+ Cgk
  gi|298676217|ref|YP_003727966.1| 4 CKNCGK 9
                                     9***97 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 1.2
                         zf-C2H2_4  3 CpiC.gks 9 
                                      C +C ++s
  gi|298676217|ref|YP_003727966.1| 17 CQQCgTRS 24
                                      ****5555 PP

  == domain 3  score: 17.3 bits;  conditional E-value: 8.2e-06
                         zf-C2H2_4   1 fkCpiCgksFsskkaLlrHlkthH 24 
                                       ++C iC+  F  k++L +H+++ H
  gi|298676217|ref|YP_003727966.1|  77 HICGICSSEFDGKNKLINHMEKKH 100
                                       68********************99 PP

  == domain 4  score: 18.2 bits;  conditional E-value: 4.4e-06
                         zf-C2H2_4   1 fkCpiCgksFsskkaLlrHlkthH 24 
                                       f+C++C++ F s +aL++H + +H
  gi|298676217|ref|YP_003727966.1| 104 FTCEYCSRKFISEHALNQHKNDVH 127
                                       89*****************99988 PP

  == domain 5  score: 2.2 bits;  conditional E-value: 0.61
                         zf-C2H2_4   9 sFsskkaLlrHlkthH 24 
                                       +F sk++ l H+++ H
  gi|298676217|ref|YP_003727966.1| 137 TFDSKNK-LIHMEKKH 151
                                       6888888.89**9999 PP

  == domain 6  score: 15.1 bits;  conditional E-value: 4.4e-05
                         zf-C2H2_4   1 fkCpiCgksFsskkaLlrHlkthH 24 
                                       f+C++C++ F s + L++H + +H
  gi|298676217|ref|YP_003727966.1| 155 FTCEYCSRKFISEHVLNQHKNDVH 178
                                       89*****************99988 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.1   0.00011      0.08      28      54 .]      73     101 ..      68     101 .. 0.82
   2 !   12.3   5.1   0.00022      0.16       2      32 ..     103     134 ..     102     152 .. 0.90
   3 !   12.1   2.4   0.00025      0.18       2      30 ..     154     183 ..     153     187 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                           zf-Di19  28 eskevvCPvCaekvt..kdlvaHltleha 54 
                                       ++++++C +C+++ +  + l++H++ +h+
  gi|298676217|ref|YP_003727966.1|  73 KKHNHICGICSSEFDgkNKLINHMEKKHG 101
                                       6789*******88653269******9996 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00022
                           zf-Di19   2 sftCPyCgke.ltvkeLveHvedeHrveskev 32 
                                       +ftC yC+++ +++++L +H +d H+ ++++ 
  gi|298676217|ref|YP_003727966.1| 103 EFTCEYCSRKfISEHALNQHKNDVHHTSKESL 134
                                       7*******9659**************999876 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.00025
                           zf-Di19   2 sftCPyCgke.ltvkeLveHvedeHrvesk 30 
                                       +ftC yC+++ ++++ L +H +d H+  ++
  gi|298676217|ref|YP_003727966.1| 154 EFTCEYCSRKfISEHVLNQHKNDVHHAFKE 183
                                       7*******9659***********9987555 PP

>> zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.4     0.016        11       2      21 ..      77      96 ..      76     100 .. 0.90
   2 !   20.9   2.5   4.6e-07   0.00033       2      22 ..     104     124 ..     103     124 .. 0.95
   3 !   20.5   2.4   5.8e-07   0.00042       2      22 ..     155     175 ..     154     175 .. 0.95

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.016
                                      CBBTTTTBBBSSHHHHHCCT CS
                       zf-C2H2_jaz  2 fYCvlCdKyFksenaldnHl 21
                                      + C +C+  F   n l nH+
  gi|298676217|ref|YP_003727966.1| 77 HICGICSSEFDGKNKLINHM 96
                                      78*****************8 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 4.6e-07
                                       CBBTTTTBBBSSHHHHHCCTT CS
                       zf-C2H2_jaz   2 fYCvlCdKyFksenaldnHlk 22 
                                       f C++C++ F+se+al +H++
  gi|298676217|ref|YP_003727966.1| 104 FTCEYCSRKFISEHALNQHKN 124
                                       99*****************87 PP

  == domain 3  score: 20.5 bits;  conditional E-value: 5.8e-07
                                       CBBTTTTBBBSSHHHHHCCTT CS
                       zf-C2H2_jaz   2 fYCvlCdKyFksenaldnHlk 22 
                                       f C++C++ F+se++l +H++
  gi|298676217|ref|YP_003727966.1| 155 FTCEYCSRKFISEHVLNQHKN 175
                                       99*****************87 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   1.7   2.1e-05     0.015       1      21 [.       4      23 ..       4      42 .. 0.88
   2 !    9.3   0.5    0.0016       1.2       7      42 ..      71     117 ..      67     121 .. 0.87
   3 ?    4.2   1.6     0.061        44      14      41 ..     105     167 ..     103     172 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.1e-05
                               DZR  1 CpqCgeelppdarfCseCgtk 21
                                      C++Cg++ p++  fC++Cgt+
  gi|298676217|ref|YP_003727966.1|  4 CKNCGKK-PNHFGFCQQCGTR 23
                                      9****99.9**********98 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0016
                               DZR   7 elppdarfCseCgtklkavaa...........edrCpsCgekvdpea 42 
                                       +++++++ C+ C ++ +  ++           e +C  C++k  +e+
  gi|298676217|ref|YP_003727966.1|  71 KNKKHNHICGICSSEFDGKNKlinhmekkhglEFTCEYCSRKFISEH 117
                                       68999**********9877779999999************9977766 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.061
                               DZR  14 fCseCgtklkavaa...................................edrCpsCgekvdpe 41 
                                       +C++C  k  ++ a                                   e +C  C++k  +e
  gi|298676217|ref|YP_003727966.1| 105 TCEYCSRKFISEHAlnqhkndvhhtskeslistfdsknklihmekkhslEFTCEYCSRKFISE 167
                                       689999887766667888888888888888888888888888888988888999999886655 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.9       0.5   3.6e+02       2       8 ..       3       9 ..       2      10 .. 0.87
   2 ?    0.3   0.2       1.6   1.1e+03       3       9 ..      17      24 ..      16      30 .. 0.74
   3 !   10.8   0.6   0.00075      0.54       1      23 []      77     100 ..      77     100 .. 0.95
   4 !   15.6   3.3   2.3e-05     0.016       1      23 []     104     127 ..     104     128 .. 0.94
   5 ?   -1.6   0.1       6.8   4.9e+03      15      23 .]     142     151 ..     137     151 .. 0.69
   6 !   12.5   3.5   0.00023      0.16       1      23 []     155     178 ..     155     179 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.5
                                     EETTTTE CS
                           zf-C2H2 2 kCpdCgk 8
                                     +C+ Cgk
  gi|298676217|ref|YP_003727966.1| 3 VCKNCGK 9
                                     7*****9 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.6
                                      ETTTT.EE CS
                           zf-C2H2  3 CpdCg.ks 9 
                                      C  Cg +s
  gi|298676217|ref|YP_003727966.1| 17 CQQCGtRS 24
                                      99999555 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00075
                                       EEETTTTEEESSHHHHHHHHHC.C CS
                           zf-C2H2   1 ykCpdCgksFkrksnLkrHirt.H 23 
                                       + C++C+  F  k  L +H+ + H
  gi|298676217|ref|YP_003727966.1|  77 HICGICSSEFDGKNKLINHMEKkH 100
                                       67******************9999 PP

  == domain 4  score: 15.6 bits;  conditional E-value: 2.3e-05
                                       EEETTTTEEESSHHHHHHHHHC.C CS
                           zf-C2H2   1 ykCpdCgksFkrksnLkrHirt.H 23 
                                       ++C++C+++F + + L++H +  H
  gi|298676217|ref|YP_003727966.1| 104 FTCEYCSRKFISEHALNQHKNDvH 127
                                       89*****************98776 PP

  == domain 5  score: -1.6 bits;  conditional E-value: 6.8
                                       HHHHHHHC.C CS
                           zf-C2H2  15 nLkrHirt.H 23 
                                       n   H+ + H
  gi|298676217|ref|YP_003727966.1| 142 NKLIHMEKkH 151
                                       5567998888 PP

  == domain 6  score: 12.5 bits;  conditional E-value: 0.00023
                                       EEETTTTEEESSHHHHHHHHHC.C CS
                           zf-C2H2   1 ykCpdCgksFkrksnLkrHirt.H 23 
                                       ++C++C+++F + + L++H +  H
  gi|298676217|ref|YP_003727966.1| 155 FTCEYCSRKFISEHVLNQHKNDvH 178
                                       89*****************98776 PP

>> zf-C2HC_2  zinc-finger of a C2HC-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.4      0.33   2.4e+02       5      11 ..       4      10 ..       1      10 [. 0.82
   2 ?   -0.2   0.2       1.4   9.9e+02       4      20 ..      78      95 ..      77      99 .. 0.72
   3 !   12.8   0.4   0.00012     0.084       4      21 ..     105     123 ..     103     124 .. 0.81
   4 !   12.5   0.4   0.00015      0.11       4      20 ..     156     173 ..     154     175 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.33
                         zf-C2HC_2  5 CpkCgRs 11
                                      C++Cg +
  gi|298676217|ref|YP_003727966.1|  4 CKNCGKK 10
                                      *****76 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.4
                         zf-C2HC_2  4 pCpkCgRsF.npdrlekH 20
                                       C +C+  F +   l +H
  gi|298676217|ref|YP_003727966.1| 78 ICGICSSEFdGKNKLINH 95
                                      588898777777788888 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 0.00012
                         zf-C2HC_2   4 pCpkCgRsF.npdrlekHe 21 
                                        C++C+R+F  + +l  H+
  gi|298676217|ref|YP_003727966.1| 105 TCEYCSRKFiSEHALNQHK 123
                                       7********7777777775 PP

  == domain 4  score: 12.5 bits;  conditional E-value: 0.00015
                         zf-C2HC_2   4 pCpkCgRsF.npdrlekH 20 
                                        C++C+R+F  +  l  H
  gi|298676217|ref|YP_003727966.1| 156 TCEYCSRKFiSEHVLNQH 173
                                       7********666666666 PP

>> zf-C2H2_2  C2H2 type zinc-finger (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   3.5    0.0007       0.5      51      74 ..      77     100 ..       3     104 .. 0.79
   2 !   12.9   6.0   0.00014       0.1      37      77 ..      90     130 ..      90     136 .. 0.93
   3 !    7.6  15.7    0.0065       4.6       2      77 ..     106     181 ..     105     194 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0007
                         zf-C2H2_2  51 leClyCekefkslealreHmkkkg 74 
                                       ++C +C++ef+ +++l +Hm+kk+
  gi|298676217|ref|YP_003727966.1|  77 HICGICSSEFDGKNKLINHMEKKH 100
                                       556666666666666666665543 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00014
                         zf-C2H2_2  37 eglleylrekieekleClyCekefkslealreHmkkkgHck 77 
                                       ++l++++++k   +++C yC+++f s +al++H ++ +H+ 
  gi|298676217|ref|YP_003727966.1|  90 NKLINHMEKKHGLEFTCEYCSRKFISEHALNQHKNDVHHTS 130
                                       589**********************************9986 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0065
                         zf-C2H2_2   2 ClfcekkskeveellehmskkhgffipereylvdleglleylrekieekleClyCekefkslealreHmkkkgHck 77 
                                       C +c++k+ + ++l +h ++ h+   ++  +  d+++ l ++++k + +++C yC+++f s + l++H ++ +H  
  gi|298676217|ref|YP_003727966.1| 106 CEYCSRKFISEHALNQHKNDVHHTSKESLISTFDSKNKLIHMEKKHSLEFTCEYCSRKFISEHVLNQHKNDVHHAF 181
                                       999*999999999999999999887775544446666666777777888*******************99999975 PP

>> zf-met  Zinc-finger of C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.6      0.35   2.5e+02       2      21 ..      78      97 ..      77     100 .. 0.85
   2 ?   12.0   1.8   0.00031      0.22       1      21 [.     104     124 ..     104     124 .. 0.94
   3 ?   11.4   1.9   0.00047      0.33       1      21 [.     155     175 ..     155     175 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.35
                            zf-met  2 yCelCnvtfnsesqlksHlq 21
                                       C +C   f +++ l++H+ 
  gi|298676217|ref|YP_003727966.1| 78 ICGICSSEFDGKNKLINHME 97
                                      5****999999999999986 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00031
                            zf-met   1 fyCelCnvtfnsesqlksHlq 21 
                                       f+Ce C ++f se +l++H +
  gi|298676217|ref|YP_003727966.1| 104 FTCEYCSRKFISEHALNQHKN 124
                                       89*****************75 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00047
                            zf-met   1 fyCelCnvtfnsesqlksHlq 21 
                                       f+Ce C ++f se +l++H +
  gi|298676217|ref|YP_003727966.1| 155 FTCEYCSRKFISEHVLNQHKN 175
                                       89*****************75 PP

>> PyrI_C  Aspartate carbamoyltransferase regulatory chain, metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.2       4.8   3.5e+03      36      42 ..       4      10 ..       2      13 .. 0.77
   2 ?    9.0   2.0    0.0018       1.3      26      44 ..      96     114 ..      75     117 .. 0.79
   3 ?   12.6   0.4   0.00014     0.098      24      47 ..     145     168 ..     129     169 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 4.8
                                      ETTT--E CS
                            PyrI_C 36 CkYCeke 42
                                      Ck C+k+
  gi|298676217|ref|YP_003727966.1|  4 CKNCGKK 10
                                      9999987 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0018
                                       EEETTTTEEEETTT--EEE CS
                            PyrI_C  26 vedkekvklkCkYCekeis 44 
                                       +e+k+ +++ C+YC +++ 
  gi|298676217|ref|YP_003727966.1|  96 MEKKHGLEFTCEYCSRKFI 114
                                       488999********99985 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.00014
                                       EEEEETTTTEEEETTT--EEEHHH CS
                            PyrI_C  24 FkvedkekvklkCkYCekeiseee 47 
                                        ++e+k+ +++ C+YC +++  e+
  gi|298676217|ref|YP_003727966.1| 145 IHMEKKHSLEFTCEYCSRKFISEH 168
                                       35588************9987665 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.014        10     156     191 ..      60     123 ..       4     128 .. 0.75
   2 ?    7.6   0.0    0.0025       1.8     147     208 ..     130     188 ..     124     202 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.014
                                       ................................HHH--EEEETTTCCCHHHHHHHHHHHHHHHHH CS
                     NAD_binding_4 156 e............................keekldederaklkglpntYeqsKalaEklvrear 191
                                                                    k++  + +e++++ +++ +Y   K+++E+ +++++
  gi|298676217|ref|YP_003727966.1|  60 VgkrkkttsggknkkhnhicgicssefdgKNKLINHMEKKHGLEFTCEYCSRKFISEHALNQHK 123
                                       0444444455566777778888888888899999***************************998 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0025
                                       --SSS-H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE- CS
                     NAD_binding_4 147 veekvyeegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg 208
                                        +e ++++ ++++kl  +e++++ +++ +Y   K+++E+++++++  +++    ++ s it+
  gi|298676217|ref|YP_003727966.1| 130 SKESLISTFDSKNKLIHMEKKHSLEFTCEYCSRKFISEHVLNQHK--NDVH-HAFKESLITS 188
                                       4566666667899999***************************99..4554.5566666665 PP

>> HSP33  Hsp33 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1    0.0087       6.2     243     264 ..      93     113 ..      88     115 .. 0.80
   2 ?    6.8   0.1    0.0053       3.8     238     264 ..     138     164 ..     127     167 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0087
                                       HHHHHHCCTEEEEE-TTT--EE CS
                             HSP33 243 leeileedgkievtCefCgkkY 264
                                       ++++ e+++++e tCe+C++k+
  gi|298676217|ref|YP_003727966.1|  93 INHM-EKKHGLEFTCEYCSRKF 113
                                       4566.66999*********986 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0053
                                       T-CHH.HHHHHHCCTEEEEE-TTT--EE CS
                             HSP33 238 lgkee.leeileedgkievtCefCgkkY 264
                                       ++ +  l ++ e+++++e tCe+C++k+
  gi|298676217|ref|YP_003727966.1| 138 FDSKNkLIHM-EKKHSLEFTCEYCSRKF 164
                                       5444424455.669***********986 PP

>> NinD  Family of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.6         5   3.6e+03       1      13 [.       1      13 [.       1      25 [. 0.64
   2 ?    7.3   0.0    0.0067       4.8      27      53 ..     106     132 ..     102     136 .. 0.91
   3 ?    3.9   0.0     0.081        58      27      51 ..     157     181 ..     149     187 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5
                              NinD  1 mkrcyrcGesked 13
                                      m  c  cG+  + 
  gi|298676217|ref|YP_003727966.1|  1 MSVCKNCGKKPNH 13
                                      5667777765444 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0067
                              NinD  27 clrcersPvGvlPlPeekedvwrdsde 53 
                                       c  c r  +    l ++k+dv + s e
  gi|298676217|ref|YP_003727966.1| 106 CEYCSRKFISEHALNQHKNDVHHTSKE 132
                                       7789********************988 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.081
                              NinD  27 clrcersPvGvlPlPeekedvwrds 51 
                                       c  c r  +    l ++k+dv +  
  gi|298676217|ref|YP_003727966.1| 157 CEYCSRKFISEHVLNQHKNDVHHAF 181
                                       78899****************9965 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.9     0.002       1.4      18      38 ..       3      23 ..       1      29 [. 0.85
   2 ?    0.6   0.1      0.79   5.7e+02      14      27 ..      74      87 ..      62      92 .. 0.65
   3 ?    6.2   1.3     0.014       9.9       3      30 ..      79     117 ..      77     132 .. 0.72
   4 ?    5.0   0.2     0.033        23      10      30 ..     147     168 ..     140     179 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.002
                                      E-TTT--EEEEEEE-SSS-S- CS
                    zinc-ribbons_6 18 hCeaCqedlkkealCpeCeqe 38
                                       C++C ++ +   +C++C+ +
  gi|298676217|ref|YP_003727966.1|  3 VCKNCGKKPNHFGFCQQCGTR 23
                                      599999999999999999875 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.79
                                      SSEEE-TTT--EEE CS
                    zinc-ribbons_6 14 geqyhCeaCqedlk 27
                                      +++  C  C+++++
  gi|298676217|ref|YP_003727966.1| 74 KHNHICGICSSEFD 87
                                      34556777766665 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.014
                                       -SSS-S--E.E-S..........SEEE-TTT--EEEEEE CS
                    zinc-ribbons_6   3 CpeCqqele.krg..........eqyhCeaCqedlkkea 30 
                                       C  C +e + k++           +++Ce C++++  e 
  gi|298676217|ref|YP_003727966.1|  79 CGICSSEFDgKNKlinhmekkhgLEFTCEYCSRKFISEH 117
                                       6666666664333666666666699*******9987665 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.033
                                       -E.E-SSEEE-TTT--EEEEEE CS
                    zinc-ribbons_6  10 le.krgeqyhCeaCqedlkkea 30 
                                       +e k++ +++Ce C++++  e 
  gi|298676217|ref|YP_003727966.1| 147 MEkKHSLEFTCEYCSRKFISEH 168
                                       554566899******9987665 PP

>> DUF4370  Domain of unknown function (DUF4370)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.4   0.00017      0.12      15     102 ..     109     195 ..      96     202 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                           DUF4370  15 aaassrlsaaaaasaalekhlssrslfavlsasskavlsdlrsp..lalslGsvrsfsedvshlPeikdsevkkafk 89 
                                       + ++    +a++++++  +h+s+ sl++ + +++k + ++ ++   ++++  s+++ se v    + + ++v++afk
  gi|298676217|ref|YP_003727966.1| 109 CSRKFISEHALNQHKNDVHHTSKESLISTFDSKNKLIHMEKKHSleFTCEYCSRKFISEHV---LNQHKNDVHHAFK 182
                                       566666777888888999999******9988888887777776522677778888888755...567889******* PP

                           DUF4370  90 dllaaswdelPda 102
                                       + l +s + l + 
  gi|298676217|ref|YP_003727966.1| 183 ESLITSKESLISN 195
                                       *999998888665 PP

>> zf-CHCC  Zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.2       4.7   3.4e+03      29      35 ..       3       9 ..       2      10 .. 0.81
   2 ?   -1.4   0.1       3.6   2.6e+03      30      36 ..      17      23 ..      12      23 .. 0.84
   3 ?    2.2   0.0      0.26   1.9e+02      24      37 .]      73      86 ..      71      86 .. 0.87
   4 ?    8.6   0.2    0.0026       1.9      29      37 .]     105     113 ..      96     113 .. 0.86
   5 ?    9.0   0.1     0.002       1.5      28      37 .]     155     164 ..     145     164 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.7
                                      EETTTTE CS
                           zf-CHCC 29 dCgYCgl 35
                                      +C+ Cg+
  gi|298676217|ref|YP_003727966.1|  3 VCKNCGK 9 
                                      6999*97 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.6
                                      ETTTTEE CS
                           zf-CHCC 30 CgYCglr 36
                                      C+ Cg+r
  gi|298676217|ref|YP_003727966.1| 17 CQQCGTR 23
                                      999**98 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.26
                                      TTSEEEETTTTEEE CS
                           zf-CHCC 24 kkgpvdCgYCglrF 37
                                      kk+ + Cg C+  F
  gi|298676217|ref|YP_003727966.1| 73 KKHNHICGICSSEF 86
                                      8899******9887 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.0026
                                       EETTTTEEE CS
                           zf-CHCC  29 dCgYCglrF 37 
                                       +C YC+++F
  gi|298676217|ref|YP_003727966.1| 105 TCEYCSRKF 113
                                       8******99 PP

  == domain 5  score: 9.0 bits;  conditional E-value: 0.002
                                       EEETTTTEEE CS
                           zf-CHCC  28 vdCgYCglrF 37 
                                        +C YC+++F
  gi|298676217|ref|YP_003727966.1| 155 FTCEYCSRKF 164
                                       58******99 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       2.2   1.6e+03      26      30 ..       4       8 ..       1       9 [. 0.82
   2 ?    0.3   0.5       1.2   8.3e+02      25      30 ..      16      21 ..      12      22 .. 0.91
   3 ?    7.0   0.0    0.0091       6.6      21      31 ..     101     111 ..      90     111 .. 0.74
   4 ?    6.2   0.0     0.016        12      24      31 ..     155     162 ..     140     162 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.2
                                      -TTT- CS
                         zf-RING_7 26 CpeCG 30
                                      C +CG
  gi|298676217|ref|YP_003727966.1|  4 CKNCG 8 
                                      99**9 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.2
                                      E-TTT- CS
                         zf-RING_7 25 tCpeCG 30
                                      +C +CG
  gi|298676217|ref|YP_003727966.1| 16 FCQQCG 21
                                      7****9 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0091
                                       TB-EE-TTT-- CS
                         zf-RING_7  21 devvtCpeCGR 31 
                                       +  +tC++C+R
  gi|298676217|ref|YP_003727966.1| 101 GLEFTCEYCSR 111
                                       5569*****99 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.016
                                       EE-TTT-- CS
                         zf-RING_7  24 vtCpeCGR 31 
                                       +tC++C+R
  gi|298676217|ref|YP_003727966.1| 155 FTCEYCSR 162
                                       8*****99 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   1.9     0.099        71       6      16 ..       3      13 ..       1      21 [. 0.78
   2 ?    6.6   0.2    0.0079       5.7       5      13 ..     104     112 ..     102     113 .. 0.90
   3 ?    7.3   0.2    0.0048       3.4       4      13 ..     154     163 ..     151     164 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.099
                                      E-TTTSSEEEG CS
                             Sgf11  6 tCpnCgRqiaa 16
                                      +C+nCg++ ++
  gi|298676217|ref|YP_003727966.1|  3 VCKNCGKKPNH 13
                                      7*****98555 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0079
                                       EE-TTTSSE CS
                             Sgf11   5 vtCpnCgRq 13 
                                       +tC++C+R+
  gi|298676217|ref|YP_003727966.1| 104 FTCEYCSRK 112
                                       9*******6 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0048
                                       EEE-TTTSSE CS
                             Sgf11   4 yvtCpnCgRq 13 
                                        +tC++C+R+
  gi|298676217|ref|YP_003727966.1| 154 EFTCEYCSRK 163
                                       79*******6 PP

>> T6PP_N  Trehalose-6-phosphate phosphatase N-terminal helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.5      0.24   1.7e+02      23      62 ..     113     152 ..     108     159 .. 0.76
   2 ?    9.4   0.2    0.0012      0.88      15      53 ..     161     200 ..     153     203 .] 0.80

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.24
                            T6PP_N  23 vLkgieirehfvesLknakesLeadcetgtevlelrttee 62 
                                        +++ ++++h +++ + +kesL    +++++ ++++++++
  gi|298676217|ref|YP_003727966.1| 113 FISEHALNQHKNDVHHTSKESLISTFDSKNKLIHMEKKHS 152
                                       5677888899999999999999977778888888888743 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0012
                            T6PP_N  15 vRrqIvervLkgie..irehfvesLknakesLeadcetgte 53 
                                        R+ I e+vL++ +  ++++f esL  +kesL  ++ ++++
  gi|298676217|ref|YP_003727966.1| 161 SRKFISEHVLNQHKndVHHAFKESLITSKESLI-SNIDENQ 200
                                       6999******985433****************9.5554444 PP

>> DUF629  Protein of unknown function (DUF629)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   2.2    0.0042         3      57      86 ..      77     106 ..      69     111 .. 0.87
   2 ?    4.1   3.3     0.019        14      57      97 ..     104     139 ..     102     152 .. 0.71
   3 ?    6.5   2.6    0.0035       2.5      57      98 ..     155     198 ..     141     202 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0042
                            DUF629  57 WvCrtCsekfsdaeeckqHlvqeHvaklkp 86 
                                        +C +Cs +f   ++  +H++++H  ++  
  gi|298676217|ref|YP_003727966.1|  77 HICGICSSEFDGKNKLINHMEKKHGLEFTC 106
                                       57**********************988865 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.019
                            DUF629  57 WvCrtCsekfsdaeeckqHlvqeHvaklkpklqkvlpqevd 97 
                                       ++C  Cs+kf++     +H +++H +++++ ++++l  + d
  gi|298676217|ref|YP_003727966.1| 104 FTCEYCSRKFIS-----EHALNQHKNDVHHTSKESLISTFD 139
                                       58*********9.....555666666666656655555555 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0035
                            DUF629  57 WvCrtCsekfsdaeeckqHlvqeHvak..lkpklqkvlpqevdk 98 
                                       ++C  Cs+kf++ +  +qH  + H a       ++++l  ++d+
  gi|298676217|ref|YP_003727966.1| 155 FTCEYCSRKFISEHVLNQHKNDVHHAFkeSLITSKESLISNIDE 198
                                       68**********87777777777765211333445555666655 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   2.4    0.0066       4.7      45      67 ..       9      32 ..       1      38 [. 0.71
   2 ?    5.4   0.1     0.032        23      38      59 ..      64      86 ..      41     101 .. 0.71
   3 ?    3.5   1.2      0.12        88       5      63 ..     106     168 ..     102     184 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0066
                               GFA 45 nkvtr.sfCpeCgsplyseesaap 67
                                      +k ++  fC++Cg++ y+ ++++ 
  gi|298676217|ref|YP_003727966.1|  9 KKPNHfGFCQQCGTRSYVVSDEKY 32
                                      4444559*********98766554 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.032
                               GFA 38 kkt.adsgnkvtrsfCpeCgspl 59
                                      kkt +  +nk+++++C  C s++
  gi|298676217|ref|YP_003727966.1| 64 KKTtSGGKNKKHNHICGICSSEF 86
                                      4442556677777******9986 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.12
                               GFA   5 CsdCrkasgsaftanavvkaealellegelkeykkt...adsgnkvtr.sfCpeCgsplysee 63 
                                       C+ C +   s +++n   ++ + +  e+ +++++++    + ++k++    C+ C  +++se 
  gi|298676217|ref|YP_003727966.1| 106 CEYCSRKFISEHALNQHKNDVHHTSKESLISTFDSKnklIHMEKKHSLeFTCEYCSRKFISEH 168
                                       999999999999999877766666555588888877555445555554367999999888764 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   2.5       2.6   1.9e+03      40      49 ..      17      26 ..       2      42 .. 0.74
   2 ?    9.7   0.4    0.0012      0.85      24      68 ..      90     139 ..      71     152 .. 0.76
   3 ?    6.6   0.2     0.011       7.6      35      58 ..     152     175 ..     141     200 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.6
                              CpXC 40 CpkCgatakl 49
                                      C++Cg++ ++
  gi|298676217|ref|YP_003727966.1| 17 CQQCGTRSYV 26
                                      7777776655 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0012
                              CpXC  24 pelkeklldgslfeatCpkCgatakleapll.....yhdpekellillvp 68 
                                       ++l + + ++  +e+tC++C +++  e+ l      +h  +ke li  + 
  gi|298676217|ref|YP_003727966.1|  90 NKLINHMEKKHGLEFTCEYCSRKFISEHALNqhkndVHHTSKESLISTFD 139
                                       56666666777789***************996666666666666665555 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.011
                              CpXC  35 lfeatCpkCgatakleapllyhdp 58 
                                        +e+tC++C +++  e+ l  h+ 
  gi|298676217|ref|YP_003727966.1| 152 SLEFTCEYCSRKFISEHVLNQHKN 175
                                       579***********9998886664 PP

>> zf-TFIIIC  Putative zinc-finger of transcription factor IIIC complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   6.1      0.16   1.2e+02      53      82 ..     103     133 ..       3     147 .. 0.85
   2 ?    7.1   0.3    0.0071       5.1      53      77 ..     154     178 ..     135     200 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.16
                         zf-TFIIIC  53 skvCilcstevldeelveaqelik.eeseks 82 
                                       + +C  cs+++++e+ +++++ +  ++s++s
  gi|298676217|ref|YP_003727966.1| 103 EFTCEYCSRKFISEHALNQHKNDVhHTSKES 133
                                       448***********99998884441333333 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0071
                         zf-TFIIIC  53 skvCilcstevldeelveaqelike 77 
                                       + +C  cs+++++e+++++++ + +
  gi|298676217|ref|YP_003727966.1| 154 EFTCEYCSRKFISEHVLNQHKNDVH 178
                                       448**********999988874442 PP

>> BolA  BolA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   1.9     0.037        27      12      49 ..      51      95 ..      44     136 .. 0.69
   2 ?    3.6   2.1      0.11        79      15      59 ..     139     184 ..     126     189 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.037
                              BolA 12 vedeShkhagha......eaggetHFk.vvivseaFegkslvarh 49
                                      +++ S   ++ +      ++++++H + + i+s++F+gk+++  h
  gi|298676217|ref|YP_003727966.1| 51 IVNSSVPSEVGKrkkttsGGKNKKHNHiCGICSSEFDGKNKLINH 95
                                      555555544444444544223444443167888888888887666 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.11
                              BolA  15 eShkhaghaeaggetHFkvvivseaFegkslvarhRl.vyalLkee 59 
                                       +S+++  h e++    F+++ +s +F  +  +++h+  v+++ ke 
  gi|298676217|ref|YP_003727966.1| 139 DSKNKLIHMEKKHSLEFTCEYCSRKFISEHVLNQHKNdVHHAFKES 184
                                       5666667767788889*******************95477777776 PP

>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   5.2      0.41   2.9e+02       1      21 [.       4      22 ..       4      23 .. 0.87
   2 ?   -2.4   0.4         8   5.7e+03      15      21 ..      78      84 ..      72      86 .. 0.55
   3 ?   11.5   1.5   0.00036      0.26       8      30 ..      98     120 ..      94     123 .. 0.85
   4 ?   11.1   1.9   0.00049      0.35       8      30 ..     149     171 ..     146     174 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.41
                            zf-AN1  1 CsfksCkkkdflpfkCryCgk 21
                                      C+  +C+kk +  + C++Cg 
  gi|298676217|ref|YP_003727966.1|  4 CK--NCGKKPNHFGFCQQCGT 22
                                      55..8*****999******96 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 8
                            zf-AN1 15 kCryCgk 21
                                       C  C+ 
  gi|298676217|ref|YP_003727966.1| 78 ICGICSS 84
                                      4556655 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00036
                            zf-AN1   8 kkdflpfkCryCgkvFClkHrlp 30 
                                       kk  l f+C+yC+++F ++H l 
  gi|298676217|ref|YP_003727966.1|  98 KKHGLEFTCEYCSRKFISEHALN 120
                                       566788**********9999875 PP

  == domain 4  score: 11.1 bits;  conditional E-value: 0.00049
                            zf-AN1   8 kkdflpfkCryCgkvFClkHrlp 30 
                                       kk +l f+C+yC+++F ++H l 
  gi|298676217|ref|YP_003727966.1| 149 KKHSLEFTCEYCSRKFISEHVLN 171
                                       566778**********9999775 PP

>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.2      0.96   6.9e+02       1       7 [.       4      10 ..       1      14 [. 0.64
   2 ?   -2.3   0.6       7.5   5.4e+03       1       5 [.      17      21 ..      17      25 .. 0.81
   3 ?    4.1   0.3     0.076        54       1      23 [.      79     100 ..      79     103 .. 0.85
   4 ?    9.0   0.4    0.0021       1.5       1      22 [.     106     132 ..     106     144 .. 0.85
   5 ?    8.9   0.8    0.0024       1.7       1      33 [.     157     196 ..     157     197 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.96
                               HNH  1 CeyCgrk 7 
                                      C +Cg+k
  gi|298676217|ref|YP_003727966.1|  4 CKNCGKK 10
                                      5555554 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7.5
                               HNH  1 CeyCg 5 
                                      C+ Cg
  gi|298676217|ref|YP_003727966.1| 17 CQQCG 21
                                      89998 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.076
                               HNH   1 CeyCgrkfhksealevdHiipis 23 
                                       C +C ++f+++  + ++H++ ++
  gi|298676217|ref|YP_003727966.1|  79 CGICSSEFDGK-NKLINHMEKKH 100
                                       9*********9.88888887665 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.0021
                               HNH   1 CeyCgrkfhks.....ealevdHiipi 22 
                                       CeyC rkf  +       + v+H    
  gi|298676217|ref|YP_003727966.1| 106 CEYCSRKFISEhalnqHKNDVHHTSKE 132
                                       ********9999999889999998665 PP

  == domain 5  score: 8.9 bits;  conditional E-value: 0.0024
                               HNH   1 CeyCgrkfhks.....ealevdHiipisq..ggaddieNl 33 
                                       CeyC rkf  +       + v+H    s   +++  i+N+
  gi|298676217|ref|YP_003727966.1| 157 CEYCSRKFISEhvlnqHKNDVHHAFKESLitSKESLISNI 196
                                       ********99899999999999987777555666667775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1360  (0.0758548); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        45  (0.0025099); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1397.75
//
Query:       gi|298676218|ref|YP_003727967.1|  [L=197]
Description: transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-32  111.3   0.1      4e-32  111.0   0.1    1.1  1  DDE_3     DDE superfamily endonuclease
  ------ inclusion threshold ------
      0.057   12.9   0.2       0.11   12.0   0.1    1.5  2  AviRa     RRNA methyltransferase AviRa
        0.1   12.2   0.0       0.17   11.5   0.0    1.5  1  SMC_ScpB  Segregation and condensation complex subunit ScpB


Domain annotation for each model (and alignments):
>> DDE_3  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.0   0.1   6.7e-36     4e-32       2     142 ..      18     164 ..      17     167 .. 0.97

  Alignments for each domain:
  == domain 1  score: 111.0 bits;  conditional E-value: 6.7e-36
                             DDE_3   2 vvfiDEsgfqlgt.vrrrawakkGkrer.leeygrrgrvnligaldekgglafvtfeetlnaedfaeflerlletal 76 
                                       vv++DEs+ ql + +r +  a  Gk e+ ++ey+r+ ++n+++a ++ +g+++v+++++ +++d+++f+e+++ ++ 
  gi|298676218|ref|YP_003727967.1|  18 VVCMDESPKQLISeTRNKIQASAGKPEKyDYEYRRKCSCNIFMACEPLTGERIVQITKRKTKKDWVQFIEKIATKYN 94 
                                       9************9************999************************************************ PP

                             DDE_3  77 qakkivlilDnasiHkseslrelveee.....adrlellylPpySPelNpiEivwsklkrellkrrsfksl 142
                                       +ak+i li+Dn ++H+  s++e+++ e     +dr+el+++P++ ++lN+ Ei  ++l++++l+ r++ ++
  gi|298676218|ref|YP_003727967.1|  95 SAKRITLIMDNYNTHTPGSFYEAFHPEkakqlLDRFELVFTPKHGSWLNMAEIELNVLNKQCLN-RRIGDI 164
                                       ****************************************************************.887765 PP

>> AviRa  RRNA methyltransferase AviRa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0      0.67     4e+03     224     224 ..      87      87 ..      64     119 .. 0.53
   2 ?   12.0   0.1   1.8e-05      0.11      89     141 ..     139     191 ..     121     197 .] 0.89

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.67
                             AviRa 224 r 224
                                       +
  gi|298676218|ref|YP_003727967.1|  87 E 87 
                                       1 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 1.8e-05
                             AviRa  89 eevlelakkNLsLLtkeglakreeelrelaeeyekeshaealesaerleella 141
                                        + l++a+  L++L k+ l++r+ +++ + ++ e+  h+e  ++ae + +ll+
  gi|298676218|ref|YP_003727967.1| 139 GSWLNMAEIELNVLNKQCLNRRIGDIQVSLTKSEHGNHIEMRNTAESIGNLLH 191
                                       67899************************************999999999884 PP

>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.9e-05      0.17       7      46 ..      58      98 ..      52     131 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.9e-05
                          SMC_ScpB  7 LfvageplsleeLakilels.keeveealeeLkeeyeeedr 46
                                      +f+a epl+ e++ +i++ + k++  + +e+++++y++++r
  gi|298676218|ref|YP_003727967.1| 58 IFMACEPLTGERIVQITKRKtKKDWVQFIEKIATKYNSAKR 98
                                      899**************86679**************77666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1370.39
//
Query:       gi|298676219|ref|YP_003727968.1|  [L=152]
Description: transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-10   41.8   0.0    4.3e-10   40.1   0.0    1.8  2  HTH_32    Homeodomain-like domain
    6.4e-10   38.9   0.0      1e-09   38.3   0.0    1.3  1  HTH_29    Winged helix-turn helix
    4.7e-05   23.0   0.1    0.00016   21.3   0.0    1.9  2  HTH_23    Homeodomain-like domain
  ------ inclusion threshold ------
       0.03   14.2   0.3      0.051   13.4   0.3    1.4  1  Clathrin  Region in Clathrin and VPS
       0.17   11.7   1.4        3.4    7.5   0.1    2.0  2  ATG27     Autophagy-related protein 27


Domain annotation for each model (and alignments):
>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.68   2.4e+03      28      41 ..      11      24 ..       5      40 .. 0.72
   2 !   40.1   0.0   1.2e-13   4.3e-10       2      73 .]      69     148 ..      68     148 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.68
                            HTH_32 28 klsdevrariiall 41
                                      +l++e+r+++  ++
  gi|298676219|ref|YP_003727968.1| 11 TLTKEERKELESIV 24
                                      47788888887776 PP

  == domain 2  score: 40.1 bits;  conditional E-value: 1.2e-13
                            HTH_32   2 vsrwlkRyneeGle.gLkdrprrg.rprklsdevrariiallreep.....rWsprqlaarlaere.gvkvShstvy 70 
                                       + r+ kR+ e+Gl+ +L  ++  +   +k++ + +a+iial +++p     + s+r+la++++e e  +++S++++ 
  gi|298676219|ref|YP_003727968.1|  69 IDRVKKRFVEDGLDmALNGKEYERtYEKKIDGDMEAHIIALSCSDPsqghsQCSLRLLADKVVELEyIDSISYESIK 145
                                       67999*************88554223358***************999**99***********88885777******* PP

                            HTH_32  71 riL 73 
                                       r+L
  gi|298676219|ref|YP_003727968.1| 146 RVL 148
                                       *98 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.0   2.8e-13     1e-09       1      63 []      36     104 ..      36     104 .. 0.92

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 2.8e-13
                            HTH_29   1 RaqallllaeGvs.....tvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsgrprn.rlseeqea 63 
                                       +a++ll+++eG++     t   +  +l++ +r+++r++krf+e+Gl+ +l++++  r ++ ++++++ea
  gi|298676219|ref|YP_003727968.1|  36 NALILLNCDEGEYqkqkhTNEVVSSVLNIGMRKIDRVKKRFVEDGLDMALNGKEYERTYEkKIDGDMEA 104
                                       589************************************************87755555559****997 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   4.6e-08   0.00016       6      48 ..      35      83 ..      31      85 .. 0.89
   2 ?   -2.2   0.1       1.1     4e+03      29      40 ..     139     150 ..     138     151 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 4.6e-08
                            HTH_23  6 eRlrillllae......GlsvreIAreLgvsrrTvyrwlkryreeGleg 48
                                      + ++ill ++e      +++ + ++  L++  r ++r++kr++e+Gl+ 
  gi|298676219|ref|YP_003727968.1| 35 QNALILLNCDEgeyqkqKHTNEVVSSVLNIGMRKIDRVKKRFVEDGLDM 83
                                      67899999997777788*****************************986 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.1
                            HTH_23  29 vsrrTvyrwlkr 40 
                                       +s+  + r+lk+
  gi|298676219|ref|YP_003727968.1| 139 ISYESIKRVLKK 150
                                       788999999886 PP

>> Clathrin  Region in Clathrin and VPS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   1.4e-05     0.051      30      60 ..      20      50 ..      11      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.4e-05
                                      HCCHHHCHTS--HHHHHHHHHHHHHTT-HHH CS
                          Clathrin 30 Lekvlkedskenpalqtallelyakyddpqe 60
                                      Le+++++++++++++q+al+ l+++++++q+
  gi|298676219|ref|YP_003727968.1| 20 LESIVSKGKHKSQKYQNALILLNCDEGEYQK 50
                                      9*************************99987 PP

>> ATG27  Autophagy-related protein 27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.3     0.001       3.7     114     169 ..      12      65 ..       5      68 .. 0.74
   2 ?    7.5   0.1   0.00094       3.4      90     146 ..      52     112 ..      46     146 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.001
                             ATG27 114 lkesdekeglrlelkggkygkkkqkaiieflCdekslkfksydeeeeeekdvlrle 169
                                       l+++++ke  ++  kg++ ++k q+a i + Cde + + +++++e    + vl++ 
  gi|298676219|ref|YP_003727968.1|  12 LTKEERKELESIVSKGKHKSQKYQNALILLNCDEGEYQKQKHTNEV--VSSVLNIG 65 
                                       444456677788889999999***********99888888877743..45556665 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00094
                             ATG27  90 kdekdeitqvipiggksldpkvtrlkesdekeglrlelkggky........gkkkqkaiieflCd 146
                                       k+ ++ +++v++ig +++d   +r+     ++gl + l+g++y         + +   ii + C 
  gi|298676219|ref|YP_003727968.1|  52 KHTNEVVSSVLNIGMRKIDRVKKRF----VEDGLDMALNGKEYertyekkiDGDMEAHIIALSCS 112
                                       3345559999999888888888888....889**********99999988877888889999994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1049  (0.0585086); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1026.48
//
Query:       gi|298676220|ref|YP_003727969.1|  [L=941]
Description: fibronectin type III domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.2e-05   23.5   1.6    5.2e-05   23.5   1.6    3.3  3  fn3              Fibronectin type III domain
  ------ inclusion threshold ------
        2.2    8.9   7.2        1.2    9.8   0.2    4.1  4  YtkA             YtkA-like


Domain annotation for each model (and alignments):
>> fn3  Fibronectin type III domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1      0.89     8e+03      12      44 ..      55      87 ..      49     119 .. 0.61
   2 !   23.5   1.6   5.8e-09   5.2e-05       1      85 []     154     236 ..     154     236 .. 0.93
   3 ?   -3.4   0.1       1.5   1.3e+04      32      57 ..     646     675 ..     641     678 .. 0.50

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.89
                                      SSSEEEEEEE-CSSSSSTEEEEEEEEEETTSTS CS
                               fn3 12 tstsltvsWeppkdgggpitgYeveyrekgsee 44
                                      ++ ++ ++ +p  d + ++++ +v+ +++++ +
  gi|298676220|ref|YP_003727969.1| 55 NNETAEINITPLADNSVDLSSISVTSQNTSNDG 87
                                      556666777777767777777777766654444 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 5.8e-09
                                       TCECEEEEEEESSSEEEEEEE-CSSSSSTEEEEEEEEEETTSTSTEEEEEECSTSSEEEEESSSTTEEEEEEEEEEE CS
                               fn3   1 saPsnlsvsevtstsltvsWeppkdgggpitgYeveyrekgseeewneftvprtttsvtltgLkpgteYevrVqavn 77 
                                       ++P+++++s+ +   ++++W+  +dgg+ +  Y+v  +e+++++  +e+t +++t + t +gL++g+ Y  +V av 
  gi|298676220|ref|YP_003727969.1| 154 PQPTGITASP-SQGDINLNWNGVSDGGSGLKEYNVYRAETETGS-YTEITDSSDT-QETDSGLTEGKYYYYKVSAVD 227
                                       6899******.888*********************999999998.9999999999.9999***************** PP

                                       TSE.EEEEE CS
                               fn3  78 ggg.egpes 85 
                                        +g egp s
  gi|298676220|ref|YP_003727969.1| 228 YAGnEGPNS 236
                                       999888766 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 1.5
                                       EEEEEEEETTSTS......TEEEEEECSTSSE CS
                               fn3  32 gYeveyrekgsee......ewneftvprttts 57 
                                       +  v++r +++++      ++ +f v++t++s
  gi|298676220|ref|YP_003727969.1| 646 N--VTVRAQDNTDskneniKEWSFEVDSTEPS 675
                                       3..44444444432255555555666666655 PP

>> YtkA  YtkA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.2   0.00013       1.2      33      85 ..     482     531 ..     447     532 .. 0.70
   2 ?   -2.0   0.0      0.64   5.8e+03      66      80 ..     610     625 ..     547     629 .. 0.66
   3 ?   -0.1   0.3      0.17   1.5e+03      19      42 ..     658     683 ..     642     713 .. 0.67
   4 ?   -3.4   0.0       1.8   1.6e+04      19      52 ..     753     787 ..     741     791 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00013
                              YtkA  33 kpVedadvkvefwmpameGmeemttkvelke.sedGvYeaevnfsmeGtWqvql 85 
                                        + +d +v++++ + a   m+  + + ++++ s + vY a++  s +G+++v+l
  gi|298676220|ref|YP_003727969.1| 482 GETNDINVTITGAENA--EMD--NNNFSTEDsSAPYVYTATYESSTDGDYTVTL 531
                                       4445556666666664..344..6777777788*******************98 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.64
                              YtkA  66 dGvYeae.vnfsmeGt 80 
                                       +  Y +  +nf+++Gt
  gi|298676220|ref|YP_003727969.1| 610 NKTYAGDhINFTESGT 625
                                       4467777778888876 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.17
                              YtkA  19 agen..tivvtvtqggkpVedadvkv 42 
                                       ++en  +++++v+ ++  Ve a+++ 
  gi|298676220|ref|YP_003727969.1| 658 KNENikEWSFEVDSTEPSVEHATIES 683
                                       33443368888888888888888764 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 1.8
                              YtkA  19 agenti.vvt..vtqggkpVe.dadvkvefwmpameGm 52 
                                        ++ +i +++   ++ g+ +e +++v+++ ++     m
  gi|298676220|ref|YP_003727969.1| 753 SNDYEIvEFNgiSDEAGNNIElNENVEINTFRRG---M 787
                                       3333431444557788888884556888888773...3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (941 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       848  (0.0472977); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 6481.44
//
Query:       gi|298676221|ref|YP_003727970.1|  [L=369]
Description: Gram-positive anchor protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00058   19.7   0.1     0.0012   18.7   0.1    1.5  1  Gram_pos_anchor  LPXTG cell wall anchor motif
     0.0018   18.4   1.3        1.6    8.9   0.2    2.8  2  MG4              Macroglobulin domain MG4
     0.0064   16.7   1.7      0.013   15.8   0.2    2.3  2  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
  ------ inclusion threshold ------
      0.022   14.8   0.1      0.022   14.8   0.1    3.1  4  Big_1            Bacterial Ig-like domain (group 1)
      0.023   15.0   0.6      0.088   13.2   0.0    2.2  2  Pollen_Ole_e_I   Pollen proteins Ole e I like
      0.026   15.1   2.2       0.12   12.9   0.7    2.5  2  SEP              SEP domain
       0.21   12.3   3.4       0.65   10.7   0.1    2.9  3  TTR-52           Transthyretin-like family
        0.7   10.4   3.6          2    8.9   1.9    2.5  2  Glyco_hydro_108  Glycosyl hydrolase 108
        1.2    9.3   4.4        3.2    7.9   3.2    2.3  2  Cupredoxin_1     Cupredoxin-like domain
        7.8    7.5   5.9        6.4    7.8   0.1    3.1  2  Pilin_N          Archaeal Type IV pilin, N-terminal


Domain annotation for each model (and alignments):
>> Gram_pos_anchor  LPXTG cell wall anchor motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   6.7e-07    0.0012      13      38 ..     340     366 ..     340     369 .] 0.82

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 6.7e-07
                                       XX.XXXXXXXXXXXXXXXXXXXXXXXX CS
                   Gram_pos_anchor  13 Ge.ngnifltaaGllallggllLlvkr 38 
                                       Ge +g++++ta Glla+ +++++l+++
  gi|298676221|ref|YP_003727970.1| 340 GEsQGMPGFTAIGLLAAGASAAFLKRK 366
                                       6449*********99999999997766 PP

>> MG4  Macroglobulin domain MG4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.1    0.0027       4.9      25      79 ..      41      99 ..      37     118 .. 0.84
   2 !    8.9   0.2    0.0009       1.6      42      89 ..     143     190 ..     126     195 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0027
                               MG4 25 pdgspaknvpVkiealk.....seteekeslttdedGtakfsintpedaksltitvktkd 79
                                       dg+ ++++ Vkie+ +     ++++   s++td++G  k+  n  +d+k+l++ v  kd
  gi|298676221|ref|YP_003727970.1| 41 DDGNGVNGIKVKIET-DdgtklTNDKTYVSTKTDSEGYYKLKPNGLQDGKTLSLYVDGKD 99
                                      68999**********.4455677788888899**********999999999999887665 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0009
                               MG4  42 seteekeslttdedGtakfsintpedaksltitvktkdpslpeenqat 89 
                                       s++e k+ + + ++G a+++i   +++ +++i+ + +d++ +e+++ +
  gi|298676221|ref|YP_003727970.1| 143 SDQETKQIKAELKNGKANTNIKQINKGDEVSIELESEDKDQKEQQSIK 190
                                       4455566666889***************************99888754 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2   7.1e-06     0.013       2      43 ..      35      81 ..      35     117 .. 0.79
   2 ?   -2.2   0.1         3   5.4e+03      16      36 ..     202     221 ..     195     222 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.1e-06
                   CarboxypepD_reg  2 isGrVtdasgapiagatVtvtnadtg......tvastttdadGafrlr 43
                                      ++G+++d +g+++ g +V ++++d++      t  st+td++G+++l+
  gi|298676221|ref|YP_003727970.1| 35 VHGYIKD-DGNGVNGIKVKIETDDGTkltndkTYVSTKTDSEGYYKLK 81
                                      6889998.899**********76654555555789**********996 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3
                   CarboxypepD_reg  16 gatVtvtnadtgtvastttda 36 
                                        +++++t+  ++t+ +t+td+
  gi|298676221|ref|YP_003727970.1| 202 DVNIEITD-HGETKPETVTDS 221
                                       57777773.455666777775 PP

>> Big_1  Bacterial Ig-like domain (group 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   1.2e-05     0.022      17      50 ..      42      80 ..      35      90 .. 0.85
   2 ?   -3.1   0.0       4.5   8.1e+03      45      55 ..     156     166 ..     150     170 .. 0.74
   3 ?   -1.2   0.1       1.2   2.1e+03      24      44 ..     201     221 ..     196     222 .. 0.75
   4 ?   -2.1   0.1       2.2     4e+03      21      43 ..     245     268 ..     241     269 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.2e-05
                             Big_1 17 ngnpvagatVtfsvsggals.....assgtTdanGkatv 50
                                      +gn v+g++V++++++g+ +       s++Td++G +  
  gi|298676221|ref|YP_003727970.1| 42 DGNGVNGIKVKIETDDGTKLtndktYVSTKTDSEGYYKL 80
                                      8***************66666999999********9875 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.5
                             Big_1  45 nGkatvtltst 55 
                                       nGka ++++  
  gi|298676221|ref|YP_003727970.1| 156 NGKANTNIKQI 166
                                       88888888765 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.2
                             Big_1  24 atVtfsvsg.galsassgtTda 44 
                                       + V++++++ g +  ++++Td+
  gi|298676221|ref|YP_003727970.1| 201 QDVNIEITDhGET-KPETVTDS 221
                                       6789999996666.66777775 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 2.2
                             Big_1  21 vagatVtfsvsggals.assgtTd 43 
                                       +  a++tf+v+++ +  ++ g Td
  gi|298676221|ref|YP_003727970.1| 245 IDSASITFEVDKDWVKeNNAGPTD 268
                                       567889999998544446666666 PP

>> Pollen_Ole_e_I  Pollen proteins Ole e I like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.9e-05     0.088      24      62 ..      46      83 ..      39      93 .. 0.79
   2 ?   -1.7   0.1       2.1   3.8e+03      25      55 ..     168     198 ..     153     222 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.9e-05
                    Pollen_Ole_e_I 24 lkgakvkveCknkkkeeeevklsasaktdknGyFkvelp 62
                                      ++g+kvk+e ++ +k +++ k+++s+ktd++Gy+k++ +
  gi|298676221|ref|YP_003727970.1| 46 VNGIKVKIETDDGTKLTND-KTYVSTKTDSEGYYKLKPN 83
                                      6899******995455444.789************9855 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.1
                    Pollen_Ole_e_I  25 kgakvkveCknkkkeeeevklsasaktdknG 55 
                                       kg +v++e ++++k+++e ++++s + ++nG
  gi|298676221|ref|YP_003727970.1| 168 KGDEVSIELESEDKDQKEQQSIKSISFKSNG 198
                                       5666777766655666666666666666666 PP

>> SEP  SEP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.7   6.9e-05      0.12      19      75 ..     143     198 ..     140     199 .. 0.87
   2 ?    0.5   0.0      0.53   9.5e+02      45      65 ..     279     299 ..     246     306 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.9e-05
                               SEP  19 ddpenaeflesikkGevPeelekvekgeevevnledrrneeykppkkpkfkaFsGsG 75 
                                       +d+e++++ +++k+G++  ++++++kg+ev+++le  ++++ k++++ k  +F+ +G
  gi|298676221|ref|YP_003727970.1| 143 SDQETKQIKAELKNGKANTNIKQINKGDEVSIELE-SEDKDQKEQQSIKSISFKSNG 198
                                       68999*****************************9.667777777666788898877 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.53
                               SEP  45 geevevnledrrneeykppkk 65 
                                        +evev++ d+++ +y  + k
  gi|298676221|ref|YP_003727970.1| 279 WDEVEVSMFDETEDKYIYKAK 299
                                       47899******9999987654 PP

>> TTR-52  Transthyretin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00036      0.65       8      45 ..      43      82 ..      37      99 .. 0.83
   2 ?    0.9   0.1      0.41   7.4e+02      11      38 ..     200     227 ..     196     252 .. 0.77
   3 ?   -1.9   0.0       3.2   5.8e+03       9      35 ..     277     300 ..     275     324 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00036
                                      T-GGSS-EEEEEEHHHH..TS--EEEEEE--TTSEEEEEE CS
                            TTR-52  8 gkpaknvkVkLwekdtl..dpddlldetkTdedGnFelsg 45
                                      g+ ++++kVk+  +d +  ++d+++ +tkTd++G+++l+ 
  gi|298676221|ref|YP_003727970.1| 43 GNGVNGIKVKIETDDGTklTNDKTYVSTKTDSEGYYKLKP 82
                                      566788999998876556799****************984 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.41
                                       GSS-EEEEEEHHHHTS--EEEEEE--TT CS
                            TTR-52  11 aknvkVkLwekdtldpddlldetkTded 38 
                                       a++v+++++++  ++p+++ d+  +d +
  gi|298676221|ref|YP_003727970.1| 200 AQDVNIEITDHGETKPETVTDSGDSDTE 227
                                       7889999999877788888888888764 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3.2
                                       -GGSS-EEEEEEHHHHTS--EEEEEE- CS
                            TTR-52   9 kpaknvkVkLwekdtldpddlldetkT 35 
                                       +   +v+V+++++    +d+ + ++kT
  gi|298676221|ref|YP_003727970.1| 277 DDWDEVEVSMFDET---EDKYIYKAKT 300
                                       56678899999973...5666666666 PP

>> Glyco_hydro_108  Glycosyl hydrolase 108
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.9    0.0011         2       5      40 ..     114     149 ..     112     242 .. 0.83
   2 ?   -0.3   0.0      0.83   1.5e+03      18      45 ..     263     285 ..     258     300 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0011
                                       CHCCH-EEE-TCGGCG-EECTEEHHHCCCTT-BS.. CS
                   Glyco_hydro_108   5 lahEGgyvndpkDkGGeTnkGItkktlralrkekai 40 
                                       ++hEG y  d +D  G +  GI++    + ++e+++
  gi|298676221|ref|YP_003727970.1| 114 VNHEGNYLSDSSDDDGGSSGGISAPGTGKSDQETKQ 149
                                       68*****99999999999****99877666544432 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.83
                                       GCG-EECTEEHHHCCCTT-BS....-CC CS
                   Glyco_hydro_108  18 kGGeTnkGItkktlralrkekaidadvk 45 
                                       + G+T  G+ + + +++++ +     v 
  gi|298676221|ref|YP_003727970.1| 263 NAGPTDVGVKRFHGDDWDEVE-----VS 285
                                       569999999999999995544.....33 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       2.5   4.4e+03      34      42 ..      46      54 ..       9      81 .. 0.51
   2 ?    7.9   3.2    0.0018       3.2      15      65 ..     142     193 ..     135     214 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.5
                      Cupredoxin_1 34 Pskievkag 42
                                       + i+vk +
  gi|298676221|ref|YP_003727970.1| 46 VNGIKVKIE 54
                                      444444433 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0018
                      Cupredoxin_1  15 aaaaaektveitvkdggfePskievkagekvklkiknkdktp.eefesedlg 65 
                                       ++++++k+++ ++k+g+ + +  ++++g +v+++++ +dk   e+ ++++++
  gi|298676221|ref|YP_003727970.1| 142 KSDQETKQIKAELKNGKANTNIKQINKGDEVSIELESEDKDQkEQQSIKSIS 193
                                       45788999*******************************9974444444444 PP

>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1    0.0036       6.4      15      79 ..       7      73 ..       5      75 .. 0.71
   2 ?    0.2   1.5      0.84   1.5e+03      57      57 ..     192     192 ..     135     257 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0036
                           Pilin_N 15 itvIlaAviaafvlgl.asneekapqasievkidssastgkna..vslehkgGdsidtkdlkivlnse 79
                                      +t+++  ++ ++++g  + +++ +p   ++  i+++++   n   v++e ++G  ++++++ + ++ +
  gi|298676221|ref|YP_003727970.1|  7 LTILITIFLFVSMVGAaSADTNPTPPHLVHGYIKDDGNG-VNGikVKIETDDGTKLTNDKTYVSTKTD 73
                                      677777778888888855555566666665555555554.44469**************999988765 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.84
                           Pilin_N  57 v 57 
                                       +
  gi|298676221|ref|YP_003727970.1| 192 I 192
                                       2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1253  (0.0698868); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2290.54
//
Query:       gi|298676222|ref|YP_003727971.1|  [L=43]
Description: hypothetical protein Metev_2365 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       201  (0.0112109); expected 358.6 (0.02)
Passed bias filter:                      149  (0.00831056); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.51
# Mc/sec: 254.73
//
Query:       gi|298676223|ref|YP_003727972.1|  [L=2559]
Description: hypothetical protein Metev_2366 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0023   18.2   1.2     0.0023   18.2   1.2   11.5 12  DUF4625   Domain of unknown function (DUF4625)
     0.0033   18.1  18.8     0.0046   17.7   9.0   18.0 19  Big_7     Bacterial Ig domain
     0.0049   16.3   1.0     0.0049   16.3   1.0    2.0  2  DUF1616   Protein of unknown function (DUF1616)
  ------ inclusion threshold ------
        3.3    7.7   8.2        6.7    6.7   0.0    5.3  4  Y_Y_Y     Y_Y_Y domain
        4.9    6.5   7.4        4.7    6.6   0.1    3.9  3  DUF5462   Family of unknown function (DUF5462)
        5.3    6.8   8.9        4.5    7.1   0.0    5.2  6  Big_3_4   Domain of unknown function


Domain annotation for each model (and alignments):
>> DUF4625  Domain of unknown function (DUF4625)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.18   5.3e+02      88     130 ..     193     239 ..     151     242 .. 0.75
   2 !   18.2   1.2   7.6e-07    0.0023      10      82 ..     242     310 ..     226     335 .. 0.79
   3 !   11.9   1.2   6.8e-05       0.2      10      64 ..     347     400 ..     330     440 .. 0.79
   4 ?   -2.1   0.1       1.4   4.1e+03      10      61 ..     562     605 ..     555     644 .. 0.61
   5 ?   -1.4   0.1      0.84   2.5e+03      35      62 ..     820     849 ..     803     879 .. 0.79
   6 ?   -1.5   0.0      0.92   2.8e+03      38      84 ..    1301    1351 ..    1273    1365 .. 0.63
   7 ?    1.2   0.0      0.13   3.9e+02      38      85 ..    1403    1448 ..    1374    1467 .. 0.70
   8 ?    2.1   0.7     0.069   2.1e+02       6      55 ..    1627    1678 ..    1609    1709 .. 0.69
   9 ?   -1.6   0.0      0.99     3e+03      11      47 ..    1796    1832 ..    1788    1879 .. 0.67
  10 ?    2.7   1.0     0.046   1.4e+02      87     125 ..    1941    1979 ..    1828    1985 .. 0.80
  11 ?    1.3   0.6      0.13   3.9e+02      10      87 ..    1985    2058 ..    1979    2090 .. 0.61
  12 ?    2.8   0.5     0.045   1.3e+02      56      95 ..    2152    2207 ..    2078    2215 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.18
                           DUF4625  88 skkeyelheeieiPad....aeaGdYhlvirvtDasGneteesreik 130
                                        +k  + + +i+iP++     e G   +++  +D++G    +  +++
  gi|298676223|ref|YP_003727972.1| 193 VAKGGSTKLSITIPESetenLESGTHTITVETLDNDGEGDTTTSQVE 239
                                       4455677899999976555599*************998877776665 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 7.6e-07
                           DUF4625  10 edtekPvidllevsaepeeeevlkiGetlhfeaklsdnealasykvdihnnfDhhshsseakegekewsfeks 82 
                                        d+e P i+ ++++ + + ++v+++G+t+++ a++sd  a++s++ d  ++fD  + + + +    + ++  +
  gi|298676223|ref|YP_003727972.1| 242 VDQEPPDISNVTIDDDDDGNDVVATGDTVTLSADVSDASAISSVTFDA-SDFDAGTVQLSGS---GNGTYTTD 310
                                       499********************************************9.99*9988777653...34444444 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 6.8e-05
                           DUF4625  10 edtekPvidllevsaepeeeevlkiGetlhfeaklsdnealasykvdihnnfDhh 64 
                                        d++kP i+ ++++ e + +  ++  +++++ a++sd + ++s++ d  n f   
  gi|298676223|ref|YP_003727972.1| 347 VDNTKPDISNVNITDETDGNGNVTANDSVNITANVSDANGIKSVTADA-NSFGLS 400
                                       69******************************************9997.666544 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 1.4
                           DUF4625  10 edtekPvidllevsaepeeeevlkiGetlhfeaklsdnealasykvdihnnf 61 
                                       +d  +Pvi++++        ++   G++++++++ s++  ++++++   +n 
  gi|298676223|ref|YP_003727972.1| 562 TDGANPVISDFT--------ATNPSGQSINIKFNSSEELSIKNVSITGPENV 605
                                       577888888883........33456777777777777777777777655555 PP

  == domain 5  score: -1.4 bits;  conditional E-value: 0.84
                           DUF4625  35 Get.lhfeaklsdnealasykvdihnnf.D 62 
                                       G++  ++ ++l+d +++ +++v+++++  D
  gi|298676223|ref|YP_003727972.1| 820 GDEsGTVTINLNDTVNVDNITVSLQSDGiD 849
                                       4444788999************99776544 PP

  == domain 6  score: -1.5 bits;  conditional E-value: 0.92
                           DUF4625   38 lhfeaklsdnealasykvdihnnfDhhshsseakeg......ekewsfeksyd 84  
                                         ++ ++++  e+la + +d+  + D+  ++ + ++       + ++ +  +y+
  gi|298676223|ref|YP_003727972.1| 1301 QNVSIEINSSEKLATIGIDL--DIDELGDKLTLDKSnftksgDGPYIYTATYE 1351
                                        45667777778888877776..4444444444443333445566777766664 PP

  == domain 7  score: 1.2 bits;  conditional E-value: 0.13
                           DUF4625   38 lhfeaklsdnealasykvdih.nnfDhhshsseakegekewsfeksydl 85  
                                         +++++++  e+l+ ++v ++ + fD+++ s ++   + ++ + ++y++
  gi|298676223|ref|YP_003727972.1| 1403 REINVTINTSEELSTINVGLDgKTFDENDFSLDS---NAPYIYTHTYSA 1448
                                        457888999999******9973457888888776...689999999854 PP

  == domain 8  score: 2.1 bits;  conditional E-value: 0.069
                           DUF4625    6 ddeeedtekPvidllevsaepeeeevl.kiGet.lhfeaklsdnealasykv 55  
                                        d++  d++kP+++++ +++e ++ +++ + ++t l+  ++++dn++    ++
  gi|298676223|ref|YP_003727972.1| 1627 DEKMDDSTKPTVEITGLTQETTDLSSVnYADSTtLTGTVEITDNDEDTTGSI 1678
                                        3444688999999998888755544440444444677777888876555444 PP

  == domain 9  score: -1.6 bits;  conditional E-value: 0.99
                           DUF4625   11 dtekPvidllevsaepeeeevlkiGetlhfeaklsdn 47  
                                        d+ kP i+ ++++++p + + +   +t++++++ s n
  gi|298676223|ref|YP_003727972.1| 1796 DNLKPGISSASITNAPINVSDVGDTQTVTLNFNESMN 1832
                                        6678888888777766665555444445555444444 PP

  == domain 10  score: 2.7 bits;  conditional E-value: 0.046
                           DUF4625   87 gskkeyelheeieiPadaeaGdYhlvirvtDasGnetee 125 
                                        gs+k  e++e+    + a +Gd +++++++D +Gn+  +
  gi|298676223|ref|YP_003727972.1| 1941 GSNKIDEANESSWDSTKASDGDIDFTLTAEDDAGNTGTV 1979
                                        4445555566655667899****************8765 PP

  == domain 11  score: 1.3 bits;  conditional E-value: 0.13
                           DUF4625   10 edtekPvidllevsaepeeeevlkiGetlhfeaklsdnealasykv..dihnnfDhhshsseakeg..ekewsfe 80  
                                         d+++Pvi+ ++v+ +          e+ ++ ++++  e+la + +  di+++ D+ + + ++     + ++ + 
  gi|298676223|ref|YP_003727972.1| 1985 VDNTEPVINEFKVTDPDV--------ENQNISIEVNSSEQLATIGIdlDIDEEGDEAALDLNNFTKsgDGPYIYT 2051
                                        578888888884444211........2235556666666666665511566666666655543222447777777 PP

                           DUF4625   81 ksydlsg 87  
                                         +y+ s+
  gi|298676223|ref|YP_003727972.1| 2052 ATYEGSK 2058
                                        7775444 PP

  == domain 12  score: 2.8 bits;  conditional E-value: 0.045
                           DUF4625   56 dihnnfDhhshsseakeg................ekewsfeksydlsgskkeyelh 95  
                                        +++  fD  +h+ + ++g                +kewsfe + +++  kk+y ++
  gi|298676223|ref|YP_003727972.1| 2152 EVEFTFDPAAHDVTLNDGevivnvsatdtksntqTKEWSFEVDTKAPDLKKTYPIN 2207
                                        45556788888888888888888888888888889999999999999999887665 PP

>> Big_7  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   3.8     0.012        35      12      70 .]     150     222 ..     142     222 .. 0.71
   2 !    6.5   0.4    0.0047        14       4      43 ..     202     248 ..     200     258 .. 0.82
   3 !   16.4  10.3   3.9e-06     0.012      11      70 .]     261     326 ..     251     326 .. 0.80
   4 !   17.7   9.0   1.5e-06    0.0046       3      70 .]     357     433 ..     356     433 .. 0.83
   5 ?   -5.1   3.6         6   1.8e+04      16      42 ..     515     541 ..     500     562 .. 0.51
   6 !   16.5   2.1   3.6e-06     0.011      13      67 ..     575     636 ..     572     638 .. 0.87
   7 ?   -2.7   0.2       3.5   1.1e+04      12      31 ..     772     792 ..     767     798 .. 0.73
   8 ?   -5.0   5.8         6   1.8e+04      20      42 ..     825     847 ..     813     945 .. 0.73
   9 ?   -0.9   1.9      0.97   2.9e+03      22      68 ..    1100    1152 ..    1082    1155 .. 0.76
  10 ?   -2.7   0.2       3.5   1.1e+04      44      67 ..    1233    1255 ..    1203    1263 .. 0.59
  11 ?    0.7   0.4       0.3   8.9e+02      43      69 ..    1330    1361 ..    1290    1371 .. 0.66
  12 !    9.6   1.8    0.0005       1.5      13      69 ..    1396    1457 ..    1382    1458 .. 0.80
  13 ?   -2.7   0.8       3.6   1.1e+04      23      65 ..    1537    1578 ..    1526    1580 .. 0.75
  14 ?  -13.9  20.0         6   1.8e+04      17      60 ..    1717    1766 ..    1635    1776 .. 0.75
  15 ?   -5.6   5.7         6   1.8e+04       7      60 ..    1810    1868 ..    1804    1879 .. 0.53
  16 ?   -1.8   1.0       1.9   5.7e+03      44      60 ..    1955    1971 ..    1899    1985 .. 0.48
  17 ?    0.2   4.5      0.44   1.3e+03      15      69 ..    2003    2065 ..    1954    2066 .. 0.78
  18 ?   -0.3   0.2      0.64   1.9e+03      16      42 ..    2168    2181 ..    2153    2217 .. 0.62
  19 ?   -0.6   0.4      0.81   2.4e+03      13      32 ..    2271    2293 ..    2261    2335 .. 0.56

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.012
                                       --EB.TSEEEEEEEEE-SS-E...EEEEEEETTEE........EEEE-SSSEEEEEE-.....-...SEEEEEEE CS
                             Big_7  12 atvs.ggtvtisasAsddggv...skVefyvdgtl.g......lgtdtsapysltwtt.....taltagthtltV 70 
                                       +++s g++ t++++ ++ gg+    + ++++d ++ +      +++   +   l++t+     ++l++gtht+tV
  gi|298676223|ref|YP_003727972.1| 150 EKISaGDSATVQVDIENTGGIqykYNTVLSLDSSSiKskttesVAKG--GSTKLSITIpesetENLESGTHTITV 222
                                       5789999**************77667788999888444443334444..4444444445576455*********9 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0047
                                       EEEE--TT--EB.TSEEEEEEEEE-S.....S-EEEEEEEETTEE.. CS
                             Big_7   4 titsPangatvs.ggtvtisasAsdd.....ggvskVefyvdgtl.g 43 
                                       +it P++ ++   +gt ti++++ d+     ++ s+Ve+ vd ++  
  gi|298676223|ref|YP_003727972.1| 202 SITIPESETENLeSGTHTITVETLDNdgegdTTTSQVEVIVDQEPpD 248
                                       89999999988889*********999877777779999999987644 PP

  == domain 3  score: 16.4 bits;  conditional E-value: 3.9e-06
                                       T--EB.TSEEEEEEEEE-SS-EEEEEEEETTEE.....EEEE-SSSEEEEEE--....SEEEEEEE CS
                             Big_7  11 gatvs.ggtvtisasAsddggvskVefyvdgtl.g...lgtdtsapysltwttta.ltagthtltV 70 
                                       +++v  g+tvt+sa++sd++++s+V+f + +   g   l+ + +++y++ ++  +  t+g++++tV
  gi|298676223|ref|YP_003727972.1| 261 NDVVAtGDTVTLSADVSDASAISSVTFDASDFDaGtvqLSGSGNGTYTTDIDVGSsPTEGNQSVTV 326
                                       44677899*******************76644333333999999*********8878999999998 PP

  == domain 4  score: 17.7 bits;  conditional E-value: 1.5e-06
                                       EEEEE--TT-.-EB.TSEEEEEEEEE-SS-EEEEEEEET.....TEE...EEEE-SSSEEEEEE--.....SEEEEE CS
                             Big_7   3 vtitsPanga.tvs.ggtvtisasAsddggvskVefyvd.....gtlg..lgtdtsapysltwttta..ltagthtl 68 
                                       v+it  ++g+ +v+ +++v+i+a++sd++g+++V+  ++        +  l+++ +++y+ t+t ++  ++ g+++l
  gi|298676223|ref|YP_003727972.1| 357 VNITDETDGNgNVTaNDSVNITANVSDANGIKSVTADANsfglsS--QvsLTNNGDGTYTKTITVNSklAKLGSQSL 431
                                       5666666666688999*******************9999664421..256999999*********88889999**99 PP

                                       EE CS
                             Big_7  69 tV 70 
                                       tV
  gi|298676223|ref|YP_003727972.1| 432 TV 433
                                       98 PP

  == domain 5  score: -5.1 bits;  conditional E-value: 6
                                       TSEEEEEEEEE-SS-EEEEEEEETTEE CS
                             Big_7  16 ggtvtisasAsddggvskVefyvdgtl 42 
                                       g++vt++ s + d++ s+  +  d t 
  gi|298676223|ref|YP_003727972.1| 515 GDQVTVELSSEVDNTASTTNVTYDSTA 541
                                       444555555544444444444444444 PP

  == domain 6  score: 16.5 bits;  conditional E-value: 3.6e-06
                                       -EB.TSEEEEEEEEE-SS-EEEEEE......EETTEE.EEEE-SSSEEEEEE--....SEEEE CS
                             Big_7  13 tvs.ggtvtisasAsddggvskVef......yvdgtlglgtdtsapysltwttta.ltagtht 67 
                                       t + g++++i+ + s   ++++V +      y++    ++t +sapy++t t ++  ++g +t
  gi|298676223|ref|YP_003727972.1| 575 TNPsGQSINIKFNSSEELSIKNVSItgpenvYLNSGF-STTENSAPYEYTATCDTiTSDGDYT 636
                                       556699*****************88555555788888.*****************999**999 PP

  == domain 7  score: -2.7 bits;  conditional E-value: 3.5
                                       --EBTSEEEEEEEEE-S.S-E CS
                             Big_7  12 atvsggtvtisasAsdd.ggv 31 
                                       ++v  +++ti ++ sd+ +g 
  gi|298676223|ref|YP_003727972.1| 772 EVVGVDKTTIDVTFSDSgSGL 792
                                       555567899******996665 PP

  == domain 8  score: -5.0 bits;  conditional E-value: 6
                                       EEEEEEE-SS-EEEEEEEETTEE CS
                             Big_7  20 tisasAsddggvskVefyvdgtl 42 
                                       t++ + +d ++v++++++++   
  gi|298676223|ref|YP_003727972.1| 825 TVTINLNDTVNVDNITVSLQSDG 847
                                       67777777777777777765433 PP

  == domain 9  score: -0.9 bits;  conditional E-value: 0.97
                                        EEEEE-SS-EEEEEEEETTEE........EEEE-SSSEEEEEE--...SEEEEE CS
                             Big_7   22 sasAsddggvskVefyvdgtl.g......lgtdtsapysltwtttaltagthtl 68  
                                        s++  d+g+++k +f++ + +        ++ dts++ ++++  + ++a + t+
  gi|298676223|ref|YP_003727972.1| 1100 SGTGLDNGTIDKNDFSLSTGViSsiepsiTSGDTSGTVTINLENK-VDAENVTV 1152
                                        46667889********99999768999988888888888888775.44444444 PP

  == domain 10  score: -2.7 bits;  conditional E-value: 3.5
                                        EEEE-SSSEEEEEE--...SEEEE CS
                             Big_7   44 lgtdtsapysltwtttaltagtht 67  
                                        ++ dts++ ++++  + ++a t t
  gi|298676223|ref|YP_003727972.1| 1233 INGDTSGTVTINLKNK-VNADTVT 1255
                                        5556666666655554.3333333 PP

  == domain 11  score: 0.7 bits;  conditional E-value: 0.3
                                        ......EEEE-SSSEEEEEE--...SEEEEEE CS
                             Big_7   43 g.....lgtdtsapysltwtttaltagthtlt 69  
                                        +     ++++ ++py +t t +   +g +t t
  gi|298676223|ref|YP_003727972.1| 1330 TldksnFTKSGDGPYIYTATYEGSVDGKYTAT 1361
                                        24444477888899999999988888888876 PP

  == domain 12  score: 9.6 bits;  conditional E-value: 0.0005
                                        -EB.TSEEEEEEEEE-SS-EEEEEEEETTEE.....EEEE-SSSEEEEEE--...SEEEEEE CS
                             Big_7   13 tvs.ggtvtisasAsddggvskVefyvdgtl.g...lgtdtsapysltwtttaltagthtlt 69  
                                        +v+  +  +i+++ + + + s++ + +dg++     ++ d++apy +t t +a+++g +t t
  gi|298676223|ref|YP_003727972.1| 1396 KVNnPTGREINVTINTSEELSTINVGLDGKTfDendFSLDSNAPYIYTHTYSAGSDGDYTAT 1457
                                        5554444456666666677***********987899999*********************87 PP

  == domain 13  score: -2.7 bits;  conditional E-value: 3.6
                                        EEEE-SS-EEEEEEEETTEE.EEEE-SSSEEEEEE--...SEE CS
                             Big_7   23 asAsddggvskVefyvdgtlglgtdtsapysltwtttaltagt 65  
                                        a+ s +++v +++++ ++   + ++ +++  +t++ ++ ++g+
  gi|298676223|ref|YP_003727972.1| 1537 AEFSYSTQVLNITLSENNDA-YLKNGNDGLAVTLNNDNISDGS 1578
                                        55666677888888888888.7888888888888888888887 PP

  == domain 14  score: -13.9 bits;  conditional E-value: 6
                                        SEEEEEEEEE-S..S-EEEEEE..EETTEE.....EEEE-SSSEEEEEE--. CS
                             Big_7   17 gtvtisasAsdd..ggvskVef..yvdgtlg....lgtdtsapysltwttta 60  
                                        g+  ++ s +d+  ++vs++++  + d+++g    +gt  s+p+ +t + t+
  gi|298676223|ref|YP_003727972.1| 1717 GN--VTLSSTDNtgDSVSSITWkfSTDTSSGtyseIGTGDSYPWDTTEQVTD 1766
                                        44..444555555599999966214555553577788888888888776665 PP

  == domain 15  score: -5.6 bits;  conditional E-value: 6
                                        E--TT--EB.TSEEEEEEEEE-SS-EE.EEEEEETTEE......EEEE-SSSEEEEEE--. CS
                             Big_7    7 sPangatvs.ggtvtisasAsddggvs.kVefyvdgtl.g....lgtdtsapysltwttta 60  
                                        +P n + v  ++tvt++ + s +++vs +V++   +++      +++d  + ++ t+t+++
  gi|298676223|ref|YP_003727972.1| 1810 APINVSDVGdTQTVTLNFNESMNTSVSpSVQITGTNKTySveesSYSD--SVWEGTVTIDD 1868
                                        688888888677777777777777774244443333332233222222..55666666655 PP

  == domain 16  score: -1.8 bits;  conditional E-value: 1.9
                                        EEEE-SSSEEEEEE--. CS
                             Big_7   44 lgtdtsapysltwttta 60  
                                        +++ +++   +t+t+++
  gi|298676223|ref|YP_003727972.1| 1955 STKASDGDIDFTLTAED 1971
                                        33333333333333322 PP

  == domain 17  score: 0.2 bits;  conditional E-value: 0.44
                                        BTSEEEEEEEEE-SS-EEEEEEEETTEE.........EEEE-SSSEEEEEE--...SEEEEEE CS
                             Big_7   15 sggtvtisasAsddggvskVefyvdgtl.g.......lgtdtsapysltwtttaltagthtlt 69  
                                        ++++++i+++ s + +   +++ +d +  +       ++++ ++py +t t +  ++gt++ t
  gi|298676223|ref|YP_003727972.1| 2003 ENQNISIEVNSSEQLATIGIDLDIDEEGdEaaldlnnFTKSGDGPYIYTATYEGSKDGTYNAT 2065
                                        3456666666666655555555555443335688777888889**********9******976 PP

  == domain 18  score: -0.3 bits;  conditional E-value: 0.64
                                        TSEEEEEEEEE-SS-EEEEEEEETTEE CS
                             Big_7   16 ggtvtisasAsddggvskVefyvdgtl 42  
                                         g v +++sA+d              +
  gi|298676223|ref|YP_003727972.1| 2168 DGEVIVNVSATDT-------------K 2181
                                        5555555555554.............3 PP

  == domain 19  score: -0.6 bits;  conditional E-value: 0.81
                                        -EBTSEEEEEEEEE-S..S-E.E CS
                             Big_7   13 tvsggtvtisasAsdd..ggv.s 32  
                                        t+++g+v +++sA+d   + + +
  gi|298676223|ref|YP_003727972.1| 2271 TFEEGQVVVNVSANDTnsNKMnK 2293
                                        55567777777777764333342 PP

>> DUF1616  Protein of unknown function (DUF1616)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1      0.89   2.7e+03     140     177 ..       7      44 ..       5      62 .. 0.75
   2 !   16.3   1.0   1.6e-06    0.0049     181     258 ..     142     223 ..     108     230 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.89
                           DUF1616 140 alnvlLvvsivlavaalgyavvaPkegekfTelyllge 177
                                       +l+vl+v+s+ + + al    ++++ g +   +++ g+
  gi|298676223|ref|YP_003727972.1|   7 ILSVLMVLSVFITGIALTATTASAAGGPTVDYVEISGN 44 
                                       68999999999999999888887776666555555555 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1.6e-06
                           DUF1616 181 elvaenypteltagesqevivgieNhEheevnYtvvvllqev.tdeeevevlerteldrrevtladnet...weqel 253
                                            n p++++ag+s +v+v ieN ++ + +Y++v+ l+ +  +++++e +++   ++ ++t+ + et   ++ ++
  gi|298676223|ref|YP_003727972.1| 142 SILNLNAPEKISAGDSATVQVDIENTGGIQYKYNTVLSLDSSsIKSKTTESVAKGGSTKLSITIPESETenlESGTH 218
                                       5566799*********************************99877778888899999999****9999954445556 PP

                           DUF1616 254 evepe 258
                                       ++++e
  gi|298676223|ref|YP_003727972.1| 219 TITVE 223
                                       66665 PP

>> Y_Y_Y  Y_Y_Y domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0022       6.7      34      65 ..     211     242 ..     180     243 .. 0.87
   2 ?    1.5   0.1     0.095   2.8e+02      24      50 ..     394     422 ..     385     434 .. 0.72
   3 ?   -3.5   0.2       3.5   1.1e+04      29      43 ..    1343    1360 ..    1332    1367 .. 0.72
   4 ?   -1.9   0.2       1.2   3.5e+03      45      65 ..    2281    2299 ..    2275    2310 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0022
                                       ES--SEEEEEEEEEEETTS-B-SS-EEEEEEE CS
                             Y_Y_Y  34 tnlppGdYtlkVkakdndgqwnyditslsfti 65 
                                        nl++G+ t++V++ dndg+ +  + ++++++
  gi|298676223|ref|YP_003727972.1| 211 ENLESGTHTITVETLDNDGEGDTTTSQVEVIV 242
                                       79******************998888888876 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.095
                                       ESSTS...EEEEES--SEEEEEEEEEEET CS
                             Y_Y_Y  24 asdysq..easytnlppGdYtlkVkakdn 50 
                                       a++++   ++s tn+  G+Yt ++ + ++
  gi|298676223|ref|YP_003727972.1| 394 ANSFGLssQVSLTNNGDGTYTKTITVNSK 422
                                       44444466************976666555 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 3.5
                                        ....EEEEES--SEEEEE CS
                             Y_Y_Y   29 q...easytnlppGdYtl 43  
                                        +   +a+y     G+Yt 
  gi|298676223|ref|YP_003727972.1| 1343 PyiyTATYEGSVDGKYTA 1360
                                        255689999999****95 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 1.2
                                        EEEEETTS-B-SS-EEEEEEE CS
                             Y_Y_Y   45 Vkakdndgqwnyditslsfti 65  
                                        V+a d ++++ +  ++++fti
  gi|298676223|ref|YP_003727972.1| 2281 VSANDTNSNKMN--KKWNFTI 2299
                                        444444444433..6777776 PP

>> DUF5462  Family of unknown function (DUF5462)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1    0.0016       4.7      62     110 ..     202     250 ..     192     276 .. 0.79
   2 ?    0.9   0.7     0.088   2.6e+02      30      63 ..     366     399 ..     365     447 .. 0.65
   3 ?   -1.5   0.1      0.48   1.4e+03      73     115 ..     908     950 ..     895     954 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0016
                           DUF5462  62 sLvirnAelrkasggevlvtvketlpdgsearvtlkveLvvdgkkvsis 110
                                       s++i + e  + ++g++ +tv+ +  dg+   +t +ve++vd     is
  gi|298676223|ref|YP_003727972.1| 202 SITIPESETENLESGTHTITVETLDNDGEGDTTTSQVEVIVDQEPPDIS 250
                                       6899999999*************9999999999*********9754333 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.088
                           DUF5462  30 NGqvqgnsvvkvtrtlsdpvLfraqekdellksL 63 
                                       NG+v++n+ v++t   sd   +++  +d     L
  gi|298676223|ref|YP_003727972.1| 366 NGNVTANDSVNITANVSDANGIKSVTADANSFGL 399
                                       9************999998777666555544444 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.48
                           DUF5462  73 asggevlvtvketlpdgsearvtlkveLvvdgkkvsisvkqrg 115
                                       + +  +++ v  +   ++ ++vt++++  vd   v++s ++ g
  gi|298676223|ref|YP_003727972.1| 908 NTKTDFSIDVSDINNGENRGNVTINLNNPVDTNTVNVSLQNDG 950
                                       566778889999887789999***************9999887 PP

>> Big_3_4  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.2      0.26   7.8e+02      11      39 ..     237     265 ..     233     270 .. 0.91
   2 ?   -4.0   0.0       4.2   1.2e+04      32      49 ..    1450    1468 ..    1440    1469 .. 0.81
   3 ?   -2.0   0.1         1     3e+03      20      48 ..    1856    1888 ..    1840    1903 .. 0.59
   4 ?    7.1   0.0    0.0015       4.5      32      87 ..    1959    2014 ..    1943    2030 .. 0.79
   5 ?   -1.1   0.0       0.5   1.5e+03      32      48 ..    2167    2183 ..    2163    2196 .. 0.85
   6 ?   -3.4   0.0       2.7     8e+03      33      49 ..    2274    2290 ..    2272    2328 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.26
                           Big_3_4  11 gievefdrseGdiWnvpvPldedGeyvve 39 
                                        +ev+ d+   di nv++  d dG+ vv+
  gi|298676223|ref|YP_003727972.1| 237 QVEVIVDQEPPDISNVTIDDDDDGNDVVA 265
                                       57999********************9997 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 4.2
                           Big_3_4   32 edGeyvvel.laedeaGnq 49  
                                         dG+y   l  a+d aGn 
  gi|298676223|ref|YP_003727972.1| 1450 SDGDYTATLnTAKDAAGND 1468
                                        6899999884689999996 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1
                           Big_3_4   20 eGdiWnvpvPldedGeyvvell....aedeaGn 48  
                                           +W+ +v +d d e + + +    aed aGn
  gi|298676223|ref|YP_003727972.1| 1856 SDSVWEGTVTIDDDNEDLTAEInvsgAEDLAGN 1888
                                        345677777777777655432212235666666 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.0015
                           Big_3_4   32 edGeyvvellaedeaGnqayiakllyvvdienicvevrpldylsekleteftieav 87  
                                         dG+    l aed+aGn   ++    v ++e +  e ++ d   e+++  ++++  
  gi|298676223|ref|YP_003727972.1| 1959 SDGDIDFTLTAEDDAGNTGTVTGTATVDNTEPVINEFKVTDPDVENQNISIEVNSS 2014
                                        5677777899***************************9999888888888877753 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 0.5
                           Big_3_4   32 edGeyvvellaedeaGn 48  
                                        +dGe +v++ a d   n
  gi|298676223|ref|YP_003727972.1| 2167 NDGEVIVNVSATDTKSN 2183
                                        799*******9998777 PP

  == domain 6  score: -3.4 bits;  conditional E-value: 2.7
                           Big_3_4   33 dGeyvvellaedeaGnq 49  
                                        +G+ vv++ a+d   n+
  gi|298676223|ref|YP_003727972.1| 2274 EGQVVVNVSANDTNSNK 2290
                                        78888888888887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (2559 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       867  (0.0483574); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 1.23u 0.36s 00:00:01.59 Elapsed: 00:00:00.57
# Mc/sec: 13612.69
//
Query:       gi|298676224|ref|YP_003727973.1|  [L=633]
Description: chromosome segregation ATPase-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-06   26.0  74.7      0.013   14.4  24.1    3.9  4  Spc7             Spc7 kinetochore protein
    1.2e-05   24.2  73.8    8.7e-05   21.4  34.1    2.3  2  AAA_13           AAA domain
    0.00049   20.7 100.6     0.0027   18.2  45.6    4.7  2  AAA_23           AAA domain
  ------ inclusion threshold ------
      0.015   15.6  76.1       0.23   11.8  12.9    4.4  4  OmpH             Outer membrane protein (OmpH-like)
       0.02   15.0   0.9       0.02   15.0   0.9    4.7  4  Spore_III_AB     Stage III sporulation protein AB (spore_III_
       0.28   11.0  51.7       0.19   11.5  15.5    2.4  2  ERM              Ezrin/radixin/moesin family
        0.4   10.8  84.2        1.1    9.3  13.5    4.5  4  UPF0242          Uncharacterised protein family (UPF0242) N-t
       0.43   11.0  41.9       0.14   12.7   8.9    4.9  5  T3SSipB          Type III cell invasion protein SipB
        1.6    9.0  65.7        0.5   10.6  14.9    5.0  5  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
        1.6    9.1  64.9       0.35   11.3  24.0    3.9  4  Fez1             Fez1
        2.6    7.8  70.5      0.027   14.3  31.3    3.5  2  TACC_C           Transforming acidic coiled-coil-containing p
        2.9    5.9  76.1       0.68    8.0  36.0    2.1  2  HOOK             HOOK protein
        3.8    7.8  50.7      0.049   13.9   4.9    5.1  4  FliJ             Flagellar FliJ protein
        4.1    6.1  68.3       0.16   10.8  11.9    4.2  4  Fmp27_WPPW       RNA pol II promoter Fmp27 protein domain
        4.3    6.6  84.1       0.69    9.2  23.2    3.9  3  GAS              Growth-arrest specific micro-tubule binding
        4.5    7.6   7.0        1.6    9.0   0.5    3.3  3  MHB              Haemophore, haem-binding
        9.3    6.3  62.3        2.5    8.1  11.3    5.1  5  Laminin_II       Laminin Domain II
        9.7    7.0  10.2        1.2    9.9   1.2    3.2  3  LTXXQ            LTXXQ motif family protein


Domain annotation for each model (and alignments):
>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   8.3    0.0018       1.8     220     283 ..     140     202 ..     118     207 .. 0.78
   2 !   13.3  29.5   2.8e-05     0.028     156     290 ..     147     289 ..     139     307 .. 0.78
   3 !   14.4  24.1   1.4e-05     0.013     137     277 ..     317     456 ..     314     459 .. 0.86
   4 !    5.8  14.2    0.0053       5.3     162     266 ..     419     508 ..     416     523 .. 0.48

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0018
                              Spc7 220 kelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleeltg 283
                                       +++ +l++ql + +++i++ ++q ++le++++++ ++++ + +++++e+++l ee ++le+++ 
  gi|298676224|ref|YP_003727973.1| 140 TNIPDLKNQLSKYDSQIKDNENQLNTLENKLKNETELYK-NLSITRNEIEKLDEEKSKLEKEYT 202
                                       477888899999999999999999999999886666555.778899999999999999888764 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 2.8e-05
                              Spc7 156 elLekqeeeldellpeleeekaeleeeleklqe...aaeelesid..keeLee...lreelaelkaeieekkkelae 224
                                       ++L+k  +++++  ++l++ +++l++e e  ++    ++e+e++d  k +Le+   +++  +e ++e++e  ++l++
  gi|298676224|ref|YP_003727973.1| 147 NQLSKYDSQIKDNENQLNTLENKLKNETELYKNlsiTRNEIEKLDeeKSKLEKeytAKKIDDETNKEYKEAVNKLNK 223
                                       4555555555555555555555555555555555555566666554455666533366666789999999999**** PP

                              Spc7 225 lqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleeltgwkivsls 290
                                        q+ ++ele+ki+  k++++elee  ++ e+ le+ ++ ++ +v++l++e k++ e+ + +i +++
  gi|298676224|ref|YP_003727973.1| 224 IQQSIKELENKINYNKKRYKELEETKQKYENDLEQVQHNENIDVNTLENEIKNINEKIDSNISKMK 289
                                       *********************************************************999999986 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 1.4e-05
                              Spc7 137 legLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelka 213
                                       +++L e+l+  + g + dk++Le+q++ l+++ ++l+ee ++l+++  + qe  ++ ++ +++e++++ +++ + ++
  gi|298676224|ref|YP_003727973.1| 317 IDSLAESLNCPFCGTNCDKSKLEEQKSHLTSIRDSLKEENKSLKQKSSEKQELIDSYKK-KENEINKINSKIIDTEN 392
                                       77899999999999*************************************98877544.78899999999999999 PP

                              Spc7 214 eieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevka 277
                                        i+e ++++++ q++l +++++  e ++  s+++ee++ +   + ++ +  + +++++k++ ++
  gi|298676224|ref|YP_003727973.1| 393 LISETNEQIKKAQNKLRDIKQQKIEQEDIVSKFKEEVETETADITNRLSKVNAQLESYKNKEDQ 456
                                       9999999999999999999999999999999999999988888877777777777777776655 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.0053
                              Spc7 162 eeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekiee 238
                                       e+ ++++++e+e+e a+++++l k +++ e+ ++ +++++++  e+ + +k++++e+k+++++l++++ +l++ki++
  gi|298676224|ref|YP_003727973.1| 419 EDIVSKFKEEVETETADITNRLSKVNAQLESYKN-KEDQINKSIENNRLNKEKYDELKTKIDDLNDKRSNLQKKINN 494
                                       4444555555555555555555444443333222.344444444444455555555555555555555555555555 PP

                              Spc7 239 lkeqkseleeeiaeaervleeckgwses 266
                                       +++               ++e+ +   +
  gi|298676224|ref|YP_003727973.1| 495 IEQ--------------NVRENFNNHIK 508
                                       444..............43333333333 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5  31.7   0.00068      0.68     285     444 ..     142     300 ..     130     311 .. 0.90
   2 !   21.4  34.1   8.7e-08   8.7e-05     255     450 ..     323     511 ..     311     520 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00068
                            AAA_13 285 qerLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksvelesvk 361
                                       + +L++ ++k++s+++   ++l+++ ++ + + +  ++ +  ++e+e+l+e+  +l+++ +aK+ +  ++ e++++ 
  gi|298676224|ref|YP_003727973.1| 142 IPDLKNQLSKYDSQIKDNENQLNTLENKLKNETELYKNLSITRNEIEKLDEEKSKLEKEYTAKKIDDETNKEYKEAV 218
                                       7789******************99999988889999999999*********************************** PP

                            AAA_13 362 akiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaieklekelkeeeae 438
                                       +k+++i+++++e+++ i+ + ++ ++lee k++ +++le+  ++e   +++++++++k+++++i ++  ++k  ++ 
  gi|298676224|ref|YP_003727973.1| 219 NKLNKIQQSIKELENKINYNKKRYKELEETKQKYENDLEQVQHNEN-IDVNTLENEIKNINEKIDSNISKMKTLNTY 294
                                       ****************************************888876.788899999999999998888887777777 PP

                            AAA_13 439 lkklee 444
                                       +  ++e
  gi|298676224|ref|YP_003727973.1| 295 IDGIDE 300
                                       766665 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 8.7e-08
                            AAA_13 255 sdtCpFCgqplpaerkaaLeahFddefeekqerLekliekveskkselleklkavsdeasensafeedkeelkaeae 331
                                       s +CpFCg + +++  ++ ++h ++      ++L++  +++++k+se +e +++  ++++e ++ ++++ + ++ ++
  gi|298676224|ref|YP_003727973.1| 323 SLNCPFCGTNCDKSKLEEQKSHLTS----IRDSLKEENKSLKQKSSEKQELIDSYKKKENEINKINSKIIDTENLIS 395
                                       469********************99....44579999999999999999999999999999999999********** PP

                            AAA_13 332 aleeqLkglqraleaKrkepfksvelesvkaki.esikklvaeineliakhNekvanleeekeeakkklelhlveel 407
                                       +++eq+k++q++l + +    +++e+e++ +k  e+++ + a+i +  +k N++ +++++++ +++k++e  +++  
  gi|298676224|ref|YP_003727973.1| 396 ETNEQIKKAQNKLRDIK---QQKIEQEDIVSKFkEEVETETADITNRLSKVNAQLESYKNKEDQINKSIENNRLN-- 467
                                       *********99998877...567888888888878899***********************************99.. PP

                            AAA_13 408 eseldeykkkykklekaieklekelkeeeaelk.kleeeikeLe 450
                                       ++++de+k+k+++l+++ ++l+k+++++e++++ + ++ ike  
  gi|298676224|ref|YP_003727973.1| 468 KEKYDELKTKIDDLNDKRSNLQKKINNIEQNVReNFNNHIKEVY 511
                                       88999*********************999887515677788765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2  45.6   2.7e-06    0.0027       2     199 ..      10     235 ..       9     282 .. 0.53
   2 ?    0.1  25.9         1     1e+03      88     196 ..     268     412 ..     258     417 .. 0.52

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.7e-06
                            AAA_23   2 LkienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiese....gkvkay 74 
                                       ++++n++ ++++++  ++gl++I  pN +GKT++l+ + l       + + ++++ + +s+ +++s     +++++y
  gi|298676224|ref|YP_003727973.1|  10 ISLKNVGGLKEKNLTVKSGLNIIEAPNASGKTSLLRGFLLSVLP---NGKANHYSYLLHSKSNFGSVkitdANGQEY 83 
                                       89**********************************99986543...334444444444444433333333344455 PP

                            AAA_23  75 veltfenkdgry..trsiererelskkkgkttkkaklellei....deleqfisellgskkiilnlilflgqerfee 145
                                        +  +++k+  +   ++i +  +++  +  t+ +++ ++l+     ++l++++ e+ ++ +  ++l+ +  q + +e
  gi|298676224|ref|YP_003727973.1|  84 TKEIVKDKNSVSikGDNIVDPEKENLVSRFTIAGNTNKILDAvrtgQNLKDILLEYTNIPDLKNQLSKYDSQIKDNE 160
                                       33333333333344222333333333333333333333333322234444444444444444555555555555444 PP

                            AAA_23 146 felkdkke..........rleelekeleeledekkllekl...........eqekekek......eleeleeeleei 195
                                       ++l++ ++           l   ++e+e+l +ek++lek+           +      +      +l+++++ ++e+
  gi|298676224|ref|YP_003727973.1| 161 NQLNTLENklknetelykNLSITRNEIEKLDEEKSKLEKEytakkiddetnK------EykeavnKLNKIQQSIKEL 231
                                       4443333311122223333333344444444444444444444444442222......0223444666666666666 PP

                            AAA_23 196 lkel 199
                                       ++++
  gi|298676224|ref|YP_003727973.1| 232 ENKI 235
                                       6665 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1
                            AAA_23  88 rsiererelskkkg.kttkkaklelleideleqfisellgskkiil.nlilflgqer.................... 142
                                        ++e+e++++ +k  ++++k k+ +++id  ++fi+++l++ + +  n i+ l+++                     
  gi|298676224|ref|YP_003727973.1| 268 NTLENEIKNINEKIdSNISKMKTLNTYIDGIDEFINSSLDIADVQGnNSIDSLAESLncpfcgtncdkskleeqksh 344
                                       55666666555544256677789999999999999998887766542555666666578888888666555544444 PP

                            AAA_23 143 .........feefelkdkkerleelekeleeledekkllekl.....eqekekekeleeleeeleeil 196
                                                +e+++lk+k+++ +el+++++++e+e+++++ +     + + e ++++++ +++l +i+
  gi|298676224|ref|YP_003727973.1| 345 ltsirdslkEENKSLKQKSSEKQELIDSYKKKENEINKINSKiidteNLISETNEQIKKAQNKLRDIK 412
                                       44444433222222233333333333333333333333333344443333334446666666665554 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   8.1    0.0061       6.1      12      86 ..     140     200 ..     118     205 .. 0.49
   2 ?   11.2  17.3   0.00036      0.36      17     105 ..     203     288 ..     200     295 .. 0.74
   3 ?   -0.6  19.9       1.6   1.6e+03      29     106 ..     339     416 ..     334     438 .. 0.45
   4 ?   11.8  12.9   0.00023      0.23      26     111 ..     434     516 ..     417     535 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0061
                                       HHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  12 eespegkaaqeqlekkfkklqaeleakekelqklqeelqkkakklekeekeqelqkkeqelqqkqqqkaqelqkk 86 
                                       ++ p+ k+  +++++++k+ +++l+++e++l+++ e ++              l   ++e+++ +++++ +l+k+
  gi|298676224|ref|YP_003727973.1| 140 TNIPDLKNQLSKYDSQIKDNENQLNTLENKLKNETELYK-------------NLSITRNEIEK-LDEEKSKLEKE 200
                                       344445555555555555555555555555555555553.............33333333333.33333333322 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00036
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS..-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  17 gkaaqeqlekkfkklqaeleakekelqklqeelqkkakkl.ekeekeqelqkkeqelqqkqqqkaqelqkkqqellk 92 
                                       +k+++++ +k++k+  ++l++ ++++++l+++++    ++   +e e+  qk e++l+q q +++ +++  ++e+ k
  gi|298676224|ref|YP_003727973.1| 203 AKKIDDETNKEYKEAVNKLNKIQQSIKELENKIN---YNKkRYKELEETKQKYENDLEQVQHNENIDVNTLENEI-K 275
                                       79999****************************8...33211555555566666666665555557788888774.5 PP

                                       HHHHHHHHHHHHH CS
                              OmpH  93 pildkinkaikev 105
                                       +i +ki+  i++ 
  gi|298676224|ref|YP_003727973.1| 276 NINEKIDSNISKM 288
                                       5999999888775 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  29 kklqaeleakekelqklqeelqkkakklekeekeqelqkkeqelqqkqqqka...qelqkkqqellkpildkinkai 102
                                       ++ +  l++ +++l+++ + l++k+++  k+e    ++kke+e+++  + k    ++l ++ +e +k+ ++k++++ 
  gi|298676224|ref|YP_003727973.1| 339 EEQKSHLTSIRDSLKEENKSLKQKSSE--KQELIDSYKKKENEINK-INSKIidtENLISETNEQIKKAQNKLRDIK 412
                                       444555555555555555555543333..22222224444444444.333333433344444444444444433333 PP

                                       HHHH CS
                              OmpH 103 keva 106
                                       ++  
  gi|298676224|ref|YP_003727973.1| 413 QQKI 416
                                       3322 PP

  == domain 4  score: 11.8 bits;  conditional E-value: 0.00023
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS..-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  26 kkfkklqaeleakekelqklqeelqkkakkl.ekeekeqelqkkeqelqqkqqqkaqelqkkqqellkpildkinka 101
                                       ++++++  +++a+ +++++++++++k+ +++  ++ek+ el++k ++l++k+++ ++++++ +q ++++     n+ 
  gi|298676224|ref|YP_003727973.1| 434 ADITNRLSKVNAQLESYKNKEDQINKSIENNrLNKEKYDELKTKIDDLNDKRSNLQKKINNIEQNVREN----FNNH 506
                                       223444455555666666677777666666544999999999999999997777777777777665555....5555 PP

                                       HHHHHHHTT- CS
                              OmpH 102 ikevakekgy 111
                                       ikev  e g+
  gi|298676224|ref|YP_003727973.1| 507 IKEVYDELGF 516
                                       5555555554 PP

>> Spore_III_AB  Stage III sporulation protein AB (spore_III_AB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.4      0.29   2.9e+02     120     159 ..     143     182 ..     130     184 .. 0.82
   2 ?   15.0   0.9     2e-05      0.02      21      95 ..     212     287 ..     209     318 .. 0.76
   3 ?    4.0   2.3     0.049        49     114     154 ..     330     370 ..     328     373 .. 0.91
   4 ?    0.4   9.5       0.6     6e+02      36     143 ..     393     510 ..     371     515 .. 0.57

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.29
                                       -SHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXX CS
                      Spore_III_AB 120 sdregqlkalelaleeleeeieeareeakkkeklyrtlGv 159
                                        d+++ql+  +  +++ e+++  ++++ k+ + ly+ l++
  gi|298676224|ref|YP_003727973.1| 143 PDLKNQLSKYDSQIKDNENQLNTLENKLKNETELYKNLSI 182
                                       5788888888888888999999999999999999999987 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2e-05
                                       XXXXHHHHHHHHHHHHHHHHHHHHHH-SS-HHHHHHHHHHCS-TTHHHHHHHHHHHHH.S....TSS-HHHHHHHHH CS
                      Spore_III_AB  21 krlkrrlkeleelkralellegeirygatpLpealeklaeksesplseffeevaerleek....egesfeeaweeav 93 
                                       k++k+ +++l+++++ ++ le++i+y+++  +e le++++k+e++l+++ ++  e+++ +    e ++++e + +++
  gi|298676224|ref|YP_003727973.1| 212 KEYKEAVNKLNKIQQSIKELENKINYNKKRYKE-LEETKQKYENDLEQVQHN--ENIDVNtlenEIKNINEKIDSNI 285
                                       89****************************999.999999***999998332..22222211114444444444444 PP

                                       HH CS
                      Spore_III_AB  94 ek 95 
                                       +k
  gi|298676224|ref|YP_003727973.1| 286 SK 287
                                       44 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.049
                                       HHHHT--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXX CS
                      Spore_III_AB 114 geslgysdregqlkalelaleeleeeieeareeakkkekly 154
                                       g +  +s +e+q+++l  ++  l+ee + +++++ +k+ l+
  gi|298676224|ref|YP_003727973.1| 330 GTNCDKSKLEEQKSHLTSIRDSLKEENKSLKQKSSEKQELI 370
                                       66778999****************************99886 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.6
                                       HHHHHHHHHHH-SS-H..........HHHHHHHHHCS-TTHHHHHHHHHHHHH..STSS-HHHHHHHHHHHHGGGS- CS
                      Spore_III_AB  36 alellegeirygatpL..........pealeklaeksesplseffeevaerlee.kegesfeeaweeavekllkkla 101
                                       +++  + +i+ +++ L          +++++k++e++e       +++ +rl++ + + + ++  e++++k++++  
  gi|298676224|ref|YP_003727973.1| 393 LISETNEQIKKAQNKLrdikqqkieqEDIVSKFKEEVE----TETADITNRLSKvNAQLESYKNKEDQINKSIENNR 465
                                       34444444444444442222111111334444444444....4455555555554666677777788888888889* PP

                                       --HHHHHHHHHHHHHHT..--SHHHHHHHHH.HHHHHHHHHHHHH CS
                      Spore_III_AB 102 Lkkedkeilkelgeslg..ysdregqlkale.laleeleeeieea 143
                                       L+ke  + lk+  + l   +s++++ ++++e +++e++++ i+e 
  gi|298676224|ref|YP_003727973.1| 466 LNKEKYDELKTKIDDLNdkRSNLQKKINNIEqNVRENFNNHIKEV 510
                                       ***********9999972255666666666425666777766665 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5  15.5   0.00019      0.19      10     131 ..     145     269 ..     142     318 .. 0.68
   2 ?    4.9  28.2      0.02        20       8     179 ..     339     508 ..     333     518 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
                               ERM  10 leerLkqlqeeaekaqeaLreseet...aelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerk 83 
                                       l+++L ++ ++++ ++++L+  e++     +L +++ + ++e e+L+++++++e+e ++ k++ e ++e ke+++ k
  gi|298676224|ref|YP_003727973.1| 145 LKNQLSKYDSQIKDNENQLNTLENKlknETELYKNLSITRNEIEKLDEEKSKLEKEYTAKKIDDETNKEYKEAVN-K 220
                                       7889999999999999987766655111568999*************************9999999999998764.5 PP

                               ERM  84 lreaeleaarleeeserkeeeaerLkeeleeareaeeeak.eklleals 131
                                       l++ ++ +++le++ +  ++  ++L+e  ++ ++++e+ + ++  ++ +
  gi|298676224|ref|YP_003727973.1| 221 LNKIQQSIKELENKINYNKKRYKELEETKQKYENDLEQVQhNENIDVNT 269
                                       6666666666666655555555555555555555554444122222222 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.02
                               ERM   8 releerLkqlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerkl 84 
                                       +e +  L+++++  ++ ++ L+++  + ++L  + ++ e+e ++ + k  + e+ i++ +e+ +k +++ ++++++ 
  gi|298676224|ref|YP_003727973.1| 339 EEQKSHLTSIRDSLKEENKSLKQKSSEKQELIDSYKKKENEINKINSKIIDTENLISETNEQIKKAQNKLRDIKQQK 415
                                       56677899********************************************************************* PP

                               ERM  85 reaeleaarleeeserkeeeaerLkeeleeareaeeeakekllealstpskses.eenveeseteeeeenseeesae 160
                                        e e  +++++ee+e    e+    ++l ++++++e  k+k  ++ ++ +++   +e+ +e +t+ ++ n++ ++ +
  gi|298676224|ref|YP_003727973.1| 416 IEQEDIVSKFKEEVET---ETADITNRLSKVNAQLESYKNKEDQINKSIENNRLnKEKYDELKTKIDDLNDKRSNLQ 489
                                       *************998...8888999999999999999999888888886553336667777777777777777777 PP

                               ERM 161 letdeveklsleieeeRvt 179
                                        + +++e++++e+ +++++
  gi|298676224|ref|YP_003727973.1| 490 KKINNIEQNVRENFNNHIK 508
                                       7777787877777666655 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4  34.6         1     1e+03      63     177 ..     158     258 ..     112     308 .. 0.49
   2 ?    5.9  21.9     0.012        12      65     148 ..     333     419 ..     318     430 .. 0.60
   3 ?    0.4  21.2      0.61     6e+02      69     179 ..     386     492 ..     383     493 .. 0.78
   4 ?    9.3  13.5    0.0011       1.1      57     142 ..     425     512 ..     421     524 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1
                           UPF0242  63 ekl.ekskleekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkl 138
                                        +  + ++le+k ++ tel ++l++ ++++e+l ee+ +L++e+ ak+   e  ke ++ ++ kl++i++    + +
  gi|298676224|ref|YP_003727973.1| 158 DNEnQLNTLENKLKNETELYKNLSITRNEIEKLDEEKSKLEKEYTAKKIDDETNKEYKEAVN-KLNKIQQ----SIK 229
                                       11124444455555555555555555555555555555555555554444444333333333.3333222....222 PP

                           UPF0242 139 eleeqLaekqellqeyqetieeqrsvlekrqdqieqLes 177
                                       ele+++++ +++ +e++et          +q++ ++Le 
  gi|298676224|ref|YP_003727973.1| 230 ELENKINYNKKRYKELEET----------KQKYENDLEQ 258
                                       2233333333333333332..........3333333332 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.012
                           UPF0242  65 lekskleekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkee...nqqLqekleaiaedfeelkl 138
                                        +ksklee+++ lt+ +++lk+++++l++  +e++eL + +++ke+e+++ + +    ++L +++++  +  ++ ++
  gi|298676224|ref|YP_003727973.1| 333 CDKSKLEEQKSHLTSIRDSLKEENKSLKQKSSEKQELIDSYKKKENEINKINSKiidTENLISETNEQIKKAQNKLR 409
                                       47888899999999988888888888888888888888888888888888765411122333333222222222333 PP

                           UPF0242 139 eleeqLaekq 148
                                       ++++q  e++
  gi|298676224|ref|YP_003727973.1| 410 DIKQQKIEQE 419
                                       3333222222 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.61
                           UPF0242  69 kleekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLa 145
                                       k+   e++++e++e++k+ +++l++ ++++ e ++ +++ +ee+e    e + +  +l+++ ++ e +k   e+q++
  gi|298676224|ref|YP_003727973.1| 386 KIIDTENLISETNEQIKKAQNKLRDIKQQKIEQEDIVSKFKEEVE---TETADITNRLSKVNAQLESYKN-KEDQIN 458
                                       556678899999999999999999998888887777777777665...5667788888888888888765.588888 PP

                           UPF0242 146 ekqellqeyqetieeqrsvlekrqdqieqLeskV 179
                                       +  e     +e+  e++  ++  +d+ ++L+ k+
  gi|298676224|ref|YP_003727973.1| 459 KSIENNRLNKEKYDELKTKIDDLNDKRSNLQKKI 492
                                       8888888888889999999999999999999887 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.0011
                           UPF0242  57 wekalkeklekskleekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiae.. 131
                                       ++++++  +e+  + ++ +k+ ++ e++k+ke++++++ e+++  ke++d+ ++++  l+ +  +Lq+k ++i +  
  gi|298676224|ref|YP_003727973.1| 425 FKEEVE--TETADITNRLSKVNAQLESYKNKEDQINKSIENNRLNKEKYDELKTKIDDLNDKRSNLQKKINNIEQnv 499
                                       433333..489999999******************************************************999955 PP

                           UPF0242 132 ..dfeelklelee 142
                                         +f+++ +e+ +
  gi|298676224|ref|YP_003727973.1| 500 reNFNNHIKEVYD 512
                                       5555555555555 PP

>> T3SSipB  Type III cell invasion protein SipB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   2.8      0.15   1.5e+02      21      78 ..     143     199 ..     135     212 .. 0.80
   2 ?   12.7   8.9   0.00014      0.14      22     113 ..     175     262 ..     173     290 .. 0.81
   3 ?    5.1   2.8     0.029        29      49     151 ..     268     387 ..     263     390 .. 0.78
   4 ?    0.8  14.0      0.63   6.2e+02      36     141 ..     347     448 ..     334     464 .. 0.75
   5 ?    5.2   2.3     0.026        26      59      93 ..     461     495 ..     437     505 .. 0.63

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHHHHHHHTTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           T3SSipB  21 sqLenrlaawkamskaqqeaasklSdelqtalseakgatddleaaiekadqaksaada 78 
                                        +L+n+l  + +++k +++++  l ++l++ ++  k++     + iek+d+ ks+ ++
  gi|298676224|ref|YP_003727973.1| 143 PDLKNQLSKYDSQIKDNENQLNTLENKLKNETELYKNLS-ITRNEIEKLDEEKSKLEK 199
                                       5799************************99998888875.567788888888888654 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00014
                                       HHHHHHHHHHHHHHHTTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT------ CS
                           T3SSipB  22 qLenrlaawkamskaqqeaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPdeP 98 
                                       +L ++l + +  ++   e++skl +e  ta +  ++  +++++a++k++++++ ++++++k++  +kr keL   e 
  gi|298676224|ref|YP_003727973.1| 175 ELYKNLSITRNEIEKLDEEKSKLEKEY-TAKKIDDETNKEYKEAVNKLNKIQQSIKELENKINYNKKRYKEL---EE 247
                                       566677777777777777777777665.67777889999*********************************...88 PP

                                       ---CHHHHHHHHH.. CS
                           T3SSipB  99 ekakleaaeqQagaa 113
                                        k+k e++ +Q++  
  gi|298676224|ref|YP_003727973.1| 248 TKQKYENDLEQVQHN 262
                                       889999999998854 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.029
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...............HHTT.---------CHHHHHHH CS
                           T3SSipB  49 qtalseakgatddleaaiekadqaksaadaatkkvdeaqk...............rlke.LaPdePekakleaaeqQ 109
                                       +t+ +e k++ ++++  i k+++++  +d  ++ ++  +                +l+  +   + +k kle+++  
  gi|298676224|ref|YP_003727973.1| 268 NTLENEIKNINEKIDSNISKMKTLNTYIDGIDEFINSSLDiadvqgnnsidslaeSLNCpFCGTNCDKSKLEEQKSH 344
                                       67778889999999999999999999999999999999989999999955533222221122467899999999999 PP

                                       HH..HHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHTXXXXX CS
                           T3SSipB 110 agaaadalqadeal.qKkldaasklsekakakekevDdisakv 151
                                       ++   d+l+ +++  + k +  + l +  k+ke+e+ +i +k+
  gi|298676224|ref|YP_003727973.1| 345 LTSIRDSLKEENKSlKQKSSEKQELIDSYKKKENEINKINSKI 387
                                       9999***988776526777778889999999999999999887 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.63
                                       HTTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---------CHHHHHHHHH. CS
                           T3SSipB  36 aqqeaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPdePekakleaaeqQaga 112
                                       + ++ +++  + l++  se +++ d ++++ +++++++s++ + ++ ++e  +++k+       + kl+  +qQ  +
  gi|298676224|ref|YP_003727973.1| 347 SIRDSLKEENKSLKQKSSEKQELIDSYKKKENEINKINSKIIDTENLISETNEQIKKA------QNKLRDIKQQKIE 417
                                       5566666777899***********************************9999999999......8888888888887 PP

                                       .HHHHHH.HHHH.HHHHHHHHHHHHHHHHHH CS
                           T3SSipB 113 aadalqa.deal.qKkldaasklsekakake 141
                                       + d  ++ +e + + + d++++ls+   ++e
  gi|298676224|ref|YP_003727973.1| 418 QEDIVSKfKEEVeTETADITNRLSKVNAQLE 448
                                       7776554233335888899988887764433 PP

  == domain 5  score: 5.2 bits;  conditional E-value: 0.026
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT- CS
                           T3SSipB  59 tddleaaiekadqaksaadaatkkvdeaqkrlkeL 93 
                                        ++     ek+d++k ++d+++ k ++ qk+++++
  gi|298676224|ref|YP_003727973.1| 461 IENNRLNKEKYDELKTKIDDLNDKRSNLQKKINNI 495
                                       33344455677777777777777777777777766 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   9.2      0.67   6.6e+02      17      75 ..     145     203 ..     137     213 .. 0.60
   2 ?    2.8  18.3      0.13   1.3e+02      27     102 ..     179     257 ..     163     259 .. 0.80
   3 ?    7.4  12.1    0.0048       4.8       5      83 ..     212     291 ..     208     313 .. 0.84
   4 ?   10.6  14.9    0.0005       0.5      27     106 ..     334     413 ..     310     421 .. 0.93
   5 ?    5.6   7.6     0.018        18      24      85 ..     429     490 ..     419     510 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.67
                       TMF_TATA_bd  17 lsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekelee 75 
                                       l+ ++ + +++++  +++l++le++ ++ +e   +l+ + +e ++l++e ++leke+++
  gi|298676224|ref|YP_003727973.1| 145 LKNQLSKYDSQIKDNENQLNTLENKLKNETELYKNLSITRNEIEKLDEEKSKLEKEYTA 203
                                       55566666666666666666666666665555556666666666666666666666655 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.13
                       TMF_TATA_bd  27 Elaslkeelerleaerdeareeivklm...keneelkelkkeleelekeleelqeryetlLellGeksEeveELraD 100
                                        l+ +++e+e+l +e++++++e  +     ++n e ke+ ++l++++++++el+++ +   + ++e +E  +  ++D
  gi|298676224|ref|YP_003727973.1| 179 NLSITRNEIEKLDEEKSKLEKEYTAKKiddETNKEYKEAVNKLNKIQQSIKELENKINYNKKRYKELEETKQKYEND 255
                                       57889******************99983334444555555666667779*********9999999999999999999 PP

                       TMF_TATA_bd 101 va 102
                                       ++
  gi|298676224|ref|YP_003727973.1| 256 LE 257
                                       87 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0048
                       TMF_TATA_bd   5 ssagpsvqlverlsseirrlEgElaslkeelerleaerdeareeivklm.keneelkelkkeleelekeleelqery 80 
                                       ++ +  v+ +++++++i++lE+ ++  k+++++le+ +++ ++++ ++  +en ++++l++e++++++++++  ++ 
  gi|298676224|ref|YP_003727973.1| 212 KEYKEAVNKLNKIQQSIKELENKINYNKKRYKELEETKQKYENDLEQVQhNENIDVNTLENEIKNINEKIDSNISKM 288
                                       5566778899**********************************988764677789999999999999998877777 PP

                       TMF_TATA_bd  81 etl 83 
                                       +tl
  gi|298676224|ref|YP_003727973.1| 289 KTL 291
                                       665 PP

  == domain 4  score: 10.6 bits;  conditional E-value: 0.0005
                       TMF_TATA_bd  27 ElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetlLellGeksEeveELraDvaD 103
                                       ++++l+e+ + l++ rd+++ee  +l +++ e++el +++++ e+e+++++++   +  l+ e +E+++  ++ + D
  gi|298676224|ref|YP_003727973.1| 334 DKSKLEEQKSHLTSIRDSLKEENKSLKQKSSEKQELIDSYKKKENEINKINSKIIDTENLISETNEQIKKAQNKLRD 410
                                       678999*********************************************************************** PP

                       TMF_TATA_bd 104 lKe 106
                                       +K+
  gi|298676224|ref|YP_003727973.1| 411 IKQ 413
                                       **8 PP

  == domain 5  score: 5.6 bits;  conditional E-value: 0.018
                       TMF_TATA_bd  24 lEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetlLe 85 
                                        E+E a + ++l++++a+ ++ ++   ++ k+ e+++ +k++++el++++++l+++ ++l +
  gi|298676224|ref|YP_003727973.1| 429 VETETADITNRLSKVNAQLESYKNKEDQINKSIENNRLNKEKYDELKTKIDDLNDKRSNLQK 490
                                       58899999999999999999999999999999999999999999999999999998877654 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4  26.4     0.094        94      13     147 ..     150     284 ..     126     293 .. 0.75
   2 ?    4.7  11.0     0.037        37      25     101 ..     213     290 ..     208     325 .. 0.52
   3 ?   11.3  24.0   0.00035      0.35      28     163 ..     340     466 ..     334     471 .. 0.82
   4 ?    1.7  11.1       0.3     3e+02      35     106 ..     435     502 ..     417     529 .. 0.46

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.094
                              Fez1  13 slLKqQLkdsqaevt...qklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellr 86 
                                       s   +Q+kd  ++++   +kl++  +l  +l  +r+++e+ +ee ++le++++ k+ + ++ ++e +++ ++ + ++
  gi|298676224|ref|YP_003727973.1| 150 SKYDSQIKDNENQLNtleNKLKNETELYKNLSITRNEIEKLDEEKSKLEKEYTAKKID-DETNKEYKEAVNKLNKIQ 225
                                       4455677777766542225777777788888888888888888888888888888887.566778888888888888 PP

                              Fez1  87 ekvekleeelkelreelselsleeeeaalesdeakaqrqeaeeleelkreverlraeLkee 147
                                       + +++le++++  +++++el+  e+++++e d  ++q++e+ ++++l++e++++++++  +
  gi|298676224|ref|YP_003727973.1| 226 QSIKELENKINYNKKRYKELE--ETKQKYENDLEQVQHNENIDVNTLENEIKNINEKIDSN 284
                                       888888888888888888754..45555788888888888899999999998888887665 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.037
                              Fez1  25 evtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrk.kseaellrekvekleeelkelr 100
                                       e  + ++ + +++ +++el++k++ + ++ kelee+ ++ +++le+++++ +   ++ ++ +++  ek+++++++++
  gi|298676224|ref|YP_003727973.1| 213 EYKEAVNKLNKIQQSIKELENKINYNKKRYKELEETKQKYENDLEQVQHNENIDvNTLENEIKNINEKIDSNISKMK 289
                                       33344444444555555555555555555555555555555555555433332212222223333334444444444 PP

                              Fez1 101 e 101
                                       +
  gi|298676224|ref|YP_003727973.1| 290 T 290
                                       3 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00035
                              Fez1  28 qklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreels 104
                                       ++ s + +++ +l+e +++l++k +e +el +s+++k++e++++++++  +++  + ++e+++k++++l++++++  
  gi|298676224|ref|YP_003727973.1| 340 EQKSHLTSIRDSLKEENKSLKQKSSEKQELIDSYKKKENEINKINSKIIDTENLISETNEQIKKAQNKLRDIKQQKI 416
                                       566778899***********************************************9***99999999999999444 PP

                              Fez1 105 elsleeeeaalesdeakaqrqeaeeleelkreverlraeLkeerqkkeeqassFeqERr 163
                                       e    +e+       +k +++ ++e+++ ++++ +++a+L+  ++k+++ ++s e+ R 
  gi|298676224|ref|YP_003727973.1| 417 E----QEDI-----VSKFKEEVETETADITNRLSKVNAQLESYKNKEDQINKSIENNRL 466
                                       4....2222.....233444455678888889999999999999999999999998886 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.3
                              Fez1  35 alkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelsel 106
                                        + ++l  ++a+le+  ++ +++++s+e+  l+ e++    ++ k++ + l++k ++l+++++++ ++++e+
  gi|298676224|ref|YP_003727973.1| 435 DITNRLSKVNAQLESYKNKEDQINKSIENNRLNKEKY----DELKTKIDDLNDKRSNLQKKINNIEQNVREN 502
                                       2223333444444444444444444444333333322....2224444444444444444444444444332 PP

>> TACC_C  Transforming acidic coiled-coil-containing protein (TACC), C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7  31.1       8.3   8.3e+03       4     130 ..     143     263 ..     138     290 .. 0.74
   2 ?   14.3  31.3   2.7e-05     0.027      11     141 ..     353     479 ..     339     506 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 8.3
                            TACC_C   4 kdldaalekvkeeveekeeeiqelkkkveelkkenqemkkivaefektiaqlieekqkqkelakkeiqkvl.eekeq 79 
                                        dl ++l k + +++++e++++ l++k +++++ +++++ + +e ek   +  e+++ +ke + k+i+  + +e ++
  gi|298676224|ref|YP_003727973.1| 143 PDLKNQLSKYDSQIKDNENQLNTLENKLKNETELYKNLSITRNEIEKL-DE--EKSKLEKEYTAKKIDDETnKEYKE 216
                                       58899999************************9999999887777773.22..233345555666665544489999 PP

                            TACC_C  80 lladlnsveksfsdlfkryekqkevlegykkneeslkkcaeeylarvkkee 130
                                       + ++ln++++s+++l ++++  k+    yk+ ee+ +k  +  l++v+++e
  gi|298676224|ref|YP_003727973.1| 217 AVNKLNKIQQSIKELENKINYNKK---RYKELEETKQKYEN-DLEQVQHNE 263
                                       9******************98887...79999998666555.455555544 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 2.7e-05
                            TACC_C  11 ekvkeeveekeeeiqelkkkveelkkenqemkkivaefektiaqlieekqkqkelakkeiqkvleekeqlladlnsv 87 
                                       ++ ++  ++k +e qel ++++++++e ++++  + + e+ i+++ e+ +k +++ +   q+ +e+++ +++  ++v
  gi|298676224|ref|YP_003727973.1| 353 KEENKSLKQKSSEKQELIDSYKKKENEINKINSKIIDTENLISETNEQIKKAQNKLRDIKQQKIEQEDIVSKFKEEV 429
                                       3334445568889999****************9999********99988666665555555556666677777789* PP

                            TACC_C  88 eksfsdlfkryekqkevlegykkneeslkkcaeeylarvkkeeqRYqaLkahae 141
                                       e++ +d+ +r+ k    le yk++e++ +k++e   +r++k  ++Y++Lk++ +
  gi|298676224|ref|YP_003727973.1| 430 ETETADITNRLSKVNAQLESYKNKEDQINKSIE--NNRLNK--EKYDELKTKID 479
                                       *********************************..567765..58*****7654 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6  32.1     0.014        14     477     628 ..     146     295 ..     135     307 .. 0.85
   2 ?    8.0  36.0   0.00068      0.68     396     600 ..     337     533 ..     320     537 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.014
                              HOOK 477 eekltelqelledanrrkneLetenrlanqrileLeaqveelqkalqeqgskaedssllkkkleehleklkevqeel 553
                                       +++l++  +++ d+++++n+Le++ + +++  ++L+   +e++k l+e++sk e   + kk  +e  ++ ke+ ++l
  gi|298676224|ref|YP_003727973.1| 146 KNQLSKYDSQIKDNENQLNTLENKLKNETELYKNLSITRNEIEK-LDEEKSKLEKEYTAKKIDDETNKEYKEAVNKL 221
                                       567889999999************************99777765.6777899998666666667888999******* PP

                              HOOK 554 qkkkeqleelepklssnkqkieeleeaLkkkdedlkameerYkkyveKAksViktLdpkqnpaspaevqalknql 628
                                       +k ++ + ele+k++ nk++ +elee+ +k ++dl+++++     v+   + ik ++ k +++  + +++l++ +
  gi|298676224|ref|YP_003727973.1| 222 NKIQQSIKELENKINYNKKRYKELEETKQKYENDLEQVQHNENIDVNTLENEIKNINEKIDSNI-SKMKTLNTYI 295
                                       **************************************99999999999999999999996555.7777776655 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00068
                              HOOK 396 alqkekerllaerdaLketneELkcaqlqqkelsqadalaskss..ssgenlaaellpaevreklirLqhENKmLkl 470
                                        l+ +k  l++ rd+Lke n  Lk    +++el  + + ++++    +++ + +e l +e+ e++ + q  NK   +
  gi|298676224|ref|YP_003727973.1| 337 KLEEQKSHLTSIRDSLKEENKSLKQKSSEKQELIDSYKKKENEInkINSKIIDTENLISETNEQIKKAQ--NKLRDI 411
                                       5788999*****************988888886655433333331122333444444455555554433..444444 PP

                              HOOK 471 kqegseeekltelqelledanrrkneLetenrlanqrileLeaqveelqkalqeqgskaedssllkkkleehleklk 547
                                       kq++          e+ +   + k+e+ete    ++r+++++aq+e  +++ ++ +   e+  l k+k +e+  k+ 
  gi|298676224|ref|YP_003727973.1| 412 KQQKI---------EQEDIVSKFKEEVETETADITNRLSKVNAQLESYKNKEDQINKSIENNRLNKEKYDELKTKID 479
                                       44444.........33444567778999*****************99988888878888889999************ PP

                              HOOK 548 evqeelqkkkeqleelepklssnk.qkieeleeaLkkkdedlkameerYkkyve 600
                                       ++++++++ ++ ++++e+++++n  + i+e+ + L   + d+  + + Y  y+ 
  gi|298676224|ref|YP_003727973.1| 480 DLNDKRSNLQKKINNIEQNVRENFnNHIKEVYDELGFENIDNIELSSDYNLYIT 533
                                       ***********************999********99999999888888888875 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   4.9   4.9e-05     0.049      50     107 ..     145     202 ..     130     210 .. 0.89
   2 ?    4.1   7.2     0.052        52       2      49 ..     223     272 ..     208     296 .. 0.63
   3 ?    3.0  11.5      0.11   1.1e+02      13      89 ..     337     415 ..     334     434 .. 0.72
   4 ?    2.6   4.6      0.15   1.5e+02       2      77 ..     428     501 ..     427     514 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.9e-05
                              FliJ  50 yqafisaldeaiaqqkqelaqaekqvekareewqearqerkklekLkerekkeeqkee 107
                                       +++++s+ d++i+  +++l+ +e+++++  e ++   + r+ +ekL+e++ k e +  
  gi|298676224|ref|YP_003727973.1| 145 LKNQLSKYDSQIKDNENQLNTLENKLKNETELYKNLSITRNEIEKLDEEKSKLEKEYT 202
                                       67899*******************************************9988776555 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.052
                              FliJ   2 eaareLaeaqrelqqaeekleeleqyrqeyqkqlsgea.q.glsaaelrn 49 
                                       ++++  +e +++++ ++++  ele++ q+y++ l++ + + +++++ l n
  gi|298676224|ref|YP_003727973.1| 223 KIQQSIKELENKINYNKKRYKELEETKQKYENDLEQVQhNeNIDVNTLEN 272
                                       44566666677777777777777777777777777776544555544443 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.11
                              FliJ  13 elqqaeekleeleqyrqeyqkqlsgea.q.glsaaelrnyqafisaldeaiaqqkqelaqaekqvekareewqearq 87 
                                       +l++++++l+++++ ++e  k+l++++ +    +  +++ ++ i++++++i  +++ ++  ++q++ka++++   +q
  gi|298676224|ref|YP_003727973.1| 337 KLEEQKSHLTSIRDSLKEENKSLKQKSsEkQELIDSYKKKENEINKINSKIIDTENLISETNEQIKKAQNKLRDIKQ 413
                                       56777777777777777777777777766666678999999999999999999999999999999999998876555 PP

                              FliJ  88 er 89 
                                       ++
  gi|298676224|ref|YP_003727973.1| 414 QK 415
                                       54 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.15
                              FliJ   2 eaareLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvek 77 
                                       e ++e a + ++l + +++le+ ++  ++  k+++++   l+ +++  ++  i+ l+++ + +++++++ e++v +
  gi|298676224|ref|YP_003727973.1| 428 EVETETADITNRLSKVNAQLESYKNKEDQINKSIENNR--LNKEKYDELKTKIDDLNDKRSNLQKKINNIEQNVRE 501
                                       56677777777788888888888888888888888887..889999999999999999999999999999988865 PP

>> Fmp27_WPPW  RNA pol II promoter Fmp27 protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4  13.9      0.23   2.3e+02     180     255 ..     149     223 ..     138     237 .. 0.66
   2 ?    9.8   9.3   0.00031      0.31     173     244 ..     235     306 ..     224     344 .. 0.82
   3 ?   -0.5  16.2      0.41   4.1e+02     172     251 ..     348     426 ..     309     436 .. 0.71
   4 ?   10.8  11.9   0.00016      0.16     167     285 ..     427     549 ..     418     553 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.23
                        Fmp27_WPPW 180 leeleeqiekleekleelelksekedeelkeeieelekeikelkeklefletlledlkeseesseeeeskskelsa 255
                                       l++ ++qi+++e++l++le+k ++ ++el ++++ +++ei++l+e+++ le+ ++  k+++e+++e ++  ++l++
  gi|298676224|ref|YP_003727973.1| 149 LSKYDSQIKDNENQLNTLENKLKN-ETELYKNLSITRNEIEKLDEEKSKLEKEYTAKKIDDETNKEYKEAVNKLNK 223
                                       555567888888888888888888.688888888888888888888888888887777777755533332222222 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00031
                        Fmp27_WPPW 173 kelleeRleeleeqiekleekleelelksekedeelkeeieelekeikelkeklefletlledlkeseesse 244
                                        ++ ++R +elee  +k e++le+++++++ + ++l++ei++++++i++  +k+++l+t+++ ++e  +ss 
  gi|298676224|ref|YP_003727973.1| 235 INYNKKRYKELEETKQKYENDLEQVQHNENIDVNTLENEIKNINEKIDSNISKMKTLNTYIDGIDEFINSSL 306
                                       56779********************************************************99998877555 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.41
                        Fmp27_WPPW 172 qkelleeRleeleeqiekleekleelelksekedeelkeeieelekeikelkeklefletlledlkeseesseeees 248
                                        ++ l+e  ++l+++ ++++e ++++++k+++  ++++++i ++e+ i+e++e+++  ++ l+d+k+++ ++e+  s
  gi|298676224|ref|YP_003727973.1| 348 IRDSLKEENKSLKQKSSEKQELIDSYKKKENE-INKINSKIIDTENLISETNEQIKKAQNKLRDIKQQKIEQEDIVS 423
                                       45567777888999999999999999999888.78999999999999999999999999999999998876663333 PP

                        Fmp27_WPPW 249 ksk 251
                                       k k
  gi|298676224|ref|YP_003727973.1| 424 KFK 426
                                       333 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 0.00016
                        Fmp27_WPPW 167 dpervqkelleeRleeleeqiekleekleelelksekedeelkeeieelekeikelkeklefletlledlkeseess 243
                                       +  ++ +  + +Rl+++++q+e+ ++k ++++++ e+ ++  ke+++el+++i++l++k++ l++ +++++++ +++
  gi|298676224|ref|YP_003727973.1| 427 EEVETETADITNRLSKVNAQLESYKNKEDQINKSIEN-NRLNKEKYDELKTKIDDLNDKRSNLQKKINNIEQNVREN 502
                                       45567777899********************999999.789999****************************99854 PP

                        Fmp27_WPPW 244 eeeeskskelsaastsesfselde..........lasseesaseFknRFiih 285
                                             +++ ++  ++  f+++d+          ++++++  + + +R+ i+
  gi|298676224|ref|YP_003727973.1| 503 F-----NNHIKEVYDELGFENIDNielssdynlyITRTSDEGKGYFDRYSIM 549
                                       3.....3333333333333333333334456666666666666666677665 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1  35.9     0.026        25      50     195 ..     143     286 ..     137     291 .. 0.76
   2 ?   -2.0  18.4       1.9   1.9e+03      37     114 ..     337     414 ..     332     419 .. 0.76
   3 ?    9.2  23.2   0.00069      0.69      28     145 ..     405     519 ..     397     520 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.026
                               GAS  50 seisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdely 126
                                        +++++ +++  ++k  e++++ L+++lkn  +  + l  +++++++l++e ++l+ e+  ++   ++  ke++e  
  gi|298676224|ref|YP_003727973.1| 143 PDLKNQLSKYDSQIKDNENQLNTLENKLKNETELYKNLSITRNEIEKLDEEKSKLEKEYTAKKID-DETNKEYKEAV 218
                                       56777888888888999999999999999999999999999999999999999999988876654.66777888888 PP

                               GAS 127 kkfeaaiqevqqktglknllLekklkalqeelEkkeaqleevlaaanldpaalsavsekleevlesKnq 195
                                       +k ++ iq+  ++ ++k    +k+ k+l+e+ +k e  le+v  + n+d ++l++  ++++e ++s  +
  gi|298676224|ref|YP_003727973.1| 219 NKLNK-IQQSIKELENKINYNKKRYKELEETKQKYENDLEQVQHNENIDVNTLENEIKNINEKIDSNIS 286
                                       88877.555555677888888899999999999999999999999999977776666666665555444 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.9
                               GAS  37 elkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleq 113
                                       +l++++ + +   + +++enk+lk++  + +e ++  +k+ ++ +k  +++  +++ ++e+++++k+ + + +  +q
  gi|298676224|ref|YP_003727973.1| 337 KLEEQKSHLTSIRDSLKEENKSLKQKSSEKQELIDSYKKKENEINKINSKIIDTENLISETNEQIKKAQNKLRDIKQ 413
                                       56677777777778888888888888888888888888888888888888888888888888888888877666555 PP

                               GAS 114 r 114
                                       +
  gi|298676224|ref|YP_003727973.1| 414 Q 414
                                       4 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00069
                               GAS  28 IkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdl 104
                                       +++l++  +++ ++e+  +k  +e+++e  +++  L k+++++e  +++  + +k  +  +  k+++ el+ ++ dl
  gi|298676224|ref|YP_003727973.1| 405 QNKLRDIKQQKIEQEDIVSKFKEEVETETADITNRLSKVNAQLESYKNKEDQINKSIENNRLNKEKYDELKTKIDDL 481
                                       33444444444556666778888899999999999999999999999999999999999999999999999999999 PP

                               GAS 105 kwehevleqrfekvekerdelykkfeaaiqevqqktglknl 145
                                         +  +l+++++++e+    ++++f++ i+ev  + g++n+
  gi|298676224|ref|YP_003727973.1| 482 NDKRSNLQKKINNIEQN---VRENFNNHIKEVYDELGFENI 519
                                       99999999999999875...567888889999888888885 PP

>> MHB  Haemophore, haem-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1       1.4   1.4e+03      60      75 ..     219     234 ..     202     261 .. 0.67
   2 ?   -1.0   0.1       2.2   2.2e+03      42      73 ..     360     391 ..     343     392 .. 0.71
   3 ?    9.0   0.5    0.0017       1.6       5      71 ..     433     501 ..     431     505 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.4
                               MHB  60 adLrgIrqPltdlknr 75 
                                       + L++I+q +++l+n+
  gi|298676224|ref|YP_003727973.1| 219 NKLNKIQQSIKELENK 234
                                       4566666666666553 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.2
                               MHB  42 dqaraavkaYfdanPqvaadLrgIrqPltdlk 73 
                                       +q++++ ++ +d+  + ++++++I+  + d++
  gi|298676224|ref|YP_003727973.1| 360 KQKSSEKQELIDSYKKKENEINKINSKIIDTE 391
                                       67777777777777888888888888877776 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0017
                               MHB   5 aadlarvvsgVaastsaYLdthPdvnqalt..slkgqprdqaraavkaYfdanPqvaadLrgIrqPltd 71 
                                        ad+++  s+V+a+ ++Y ++  ++n+ +    l++++ d+ ++++++  d++ + ++ +++I+q +++
  gi|298676224|ref|YP_003727973.1| 433 TADITNRLSKVNAQLESYKNKEDQINKSIEnnRLNKEKYDELKTKIDDLNDKRSNLQKKINNIEQNVRE 501
                                       57889999*********************8334566666*************************98765 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   4.2      0.35   3.5e+02      30      97 ..     146     185 ..     115     206 .. 0.47
   2 ?    7.2  11.8    0.0047       4.7       5      80 ..     214     293 ..     203     308 .. 0.81
   3 ?    2.0   0.4       0.2     2e+02      25      52 ..     337     364 ..     335     373 .. 0.81
   4 ?    8.1  10.8    0.0025       2.5       4      77 ..     351     427 ..     348     428 .. 0.88
   5 ?    8.1  11.3    0.0025       2.5      12      83 ..     426     500 ..     420     514 .. 0.62

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.35
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHHHHHHH CS
                        Laminin_II  30 keklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdniseike 97 
                                       k++ls+ +++                            + + +++l++l+++ +++  l +n+s  ++
  gi|298676224|ref|YP_003727973.1| 146 KNQLSKYDSQ----------------------------IKDNENQLNTLENKLKNETELYKNLSITRN 185
                                       2222222222............................222222222222222222222222222222 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0047
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXX--TTTTTGGGHHH CS
                        Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvk....dankairdArrsvkkLeklapqLldklke 77 
                                        +ea ++++++++ +++l+++++  k+ ++e++++ ++ +++++    + n  ++  ++++k+++++++  ++k+k+
  gi|298676224|ref|YP_003727973.1| 214 YKEAVNKLNKIQQSIKELENKINYNKKRYKELEETKQKYENDLEqvqhNENIDVNTLENEIKNINEKIDSNISKMKT 290
                                       57899999999999999999999999999999999998888877552344444567789999999999999999999 PP

                                       HHH CS
                        Laminin_II  78 lkq 80 
                                       l++
  gi|298676224|ref|YP_003727973.1| 291 LNT 293
                                       986 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.2
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II  25 nlentkeklseinrsveetnekvkdank 52 
                                       +le+ k+ l +i++s++e n+ +k+++ 
  gi|298676224|ref|YP_003727973.1| 337 KLEEQKSHLTSIRDSLKEENKSLKQKSS 364
                                       6899999999999999999999997664 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.0025
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--T...TTTTGGGHHH CS
                        Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLekl...apqLldklke 77 
                                        ++e n+++k+  + +++l    ++ ++++++in+++  t++++++ n++i+ A+++ ++++++    +++++k+ke
  gi|298676224|ref|YP_003727973.1| 351 SLKEENKSLKQKSSEKQELIDSYKKKENEINKINSKIIDTENLISETNEQIKKAQNKLRDIKQQkieQEDIVSKFKE 427
                                       56788999999999********************************************9998763225889999875 PP

  == domain 5  score: 8.1 bits;  conditional E-value: 0.0025
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHH CS
                        Laminin_II  12 akevleqlaplsqnlentkeklseinrsveetnekvk...dankairdArrsvkkLeklapqLldklkelkqlee 83 
                                        +ev+  +a++ ++l++++++l++ +++ +++n+ ++     ++  ++ ++++ +L+ +  +L +k+++++q   
  gi|298676224|ref|YP_003727973.1| 426 KEEVETETADITNRLSKVNAQLESYKNKEDQINKSIEnnrLNKEKYDELKTKIDDLNDKRSNLQKKINNIEQNVR 500
                                       468999999999999999999999999966666666533112234445555555555555555555555555433 PP

>> LTXXQ  LTXXQ motif family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.7      0.62   6.1e+02      36      80 ..     186     230 ..     146     260 .. 0.70
   2 ?    9.9   1.2    0.0012       1.2      17      85 ..     339     408 ..     338     414 .. 0.69
   3 ?   -0.4   0.2       1.9   1.9e+03      28      89 ..     399     458 ..     389     464 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.62
                                       --..-HHHHHHHHHHHTSSS--HHHHHHHH..HHHHHHHHHHHHH CS
                             LTXXQ  36 plkakkeemramrkkvlaanfdetaperlarmeamlearleavkk 80 
                                       + ++  ee+ ++ k+++a+++d+++ ++     + l++ +++ k+
  gi|298676224|ref|YP_003727973.1| 186 EIEKLDEEKSKLEKEYTAKKIDDETNKEYKEAVNKLNKIQQSIKE 230
                                       224556777777777788888877777776555555555555554 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHHHHHHHHS---..-HHHHHHHHHHHTSSS--HHHHH.HHH..HHHHHHHHHHHHHHHHHH CS
                             LTXXQ  17 daQkaalkalaeaaraeakplkakkeemramrkkvlaanfdetape.rlarmeamlearleavkkraeal 85 
                                       ++Qk +l++++++ ++e+k+lk+k  e++++ + + +++   ++++ ++   e+ +++ +e+ kk +++l
  gi|298676224|ref|YP_003727973.1| 339 EEQKSHLTSIRDSLKEENKSLKQKSSEKQELIDSYKKKENEINKINsKIIDTENLISETNEQIKKAQNKL 408
                                       79*******************9999999988876633333333332133346666667666666666665 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.9
                                       HHHHHHS---..-HHHHHHHHHHHTSSS--HHHHHHHH..HHHHHHHHHHHHHHHHHHHHHH CS
                             LTXXQ  28 eaaraeakplkakkeemramrkkvlaanfdetaperlarmeamlearleavkkraealkqfy 89 
                                       e+ ++++++l++ k+++ ++ +  + ++f+e+  ++ a   ++l++ ++++++ +++ +q+ 
  gi|298676224|ref|YP_003727973.1| 399 EQIKKAQNKLRDIKQQKIEQED--IVSKFKEEVETETADITNRLSKVNAQLESYKNKEDQIN 458
                                       5666667777777777776666..55666666666666667777777777777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (633 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      4702  (0.262257); expected 358.6 (0.02)
Passed bias filter:                      776  (0.0432818); expected 358.6 (0.02)
Passed Vit filter:                       312  (0.017402); expected 17.9 (0.001)
Passed Fwd filter:                       180  (0.0100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 2.90u 0.41s 00:00:03.31 Elapsed: 00:00:00.71
# Mc/sec: 2679.53
//
Query:       gi|298676225|ref|YP_003727974.1|  [L=238]
Description: hypothetical protein Metev_2368 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.024   15.4   0.6       0.22   12.3   0.0    2.5  2  DUF4373   Domain of unknown function (DUF4373)


Domain annotation for each model (and alignments):
>> DUF4373  Domain of unknown function (DUF4373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.2e-05      0.22      37      90 ..       8      59 ..       5      59 .. 0.92
   2 ?    0.9   0.1     0.045   8.1e+02      57      81 ..     178     204 ..      88     217 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.2e-05
                           DUF4373 37 ykekgyyiewdeeqlllladkaklevdeeevkeiveacveyglFdkelfeedgi 90
                                       +e++y+ e +++ +l +++  +++++ ++ + i+++c  ++l++ +lf+e++i
  gi|298676225|ref|YP_003727974.1|  8 PHENDYVTESEDNLALGISN--NVNIQTDKQEPIISSCRVCNLLKTDLFNEKQI 59
                                      57899*99999999999999..899**************************987 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.045
                           DUF4373  57 ka..klevdeeevkeiveacveyglFd 81 
                                       ++    +++++  ++ +e++++++l +
  gi|298676225|ref|YP_003727974.1| 178 DLkkGFDFSQNVANKALERALNRKLVS 204
                                       222244555555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       947  (0.0528195); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.56
# Mc/sec: 1281.88
//
Query:       gi|298676226|ref|YP_003727975.1|  [L=161]
Description: hypothetical protein Metev_2369 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-06   27.3   2.0     0.0012   18.8   0.1    2.3  2  HTH_45    Winged helix-turn-helix
     0.0033   17.5   0.1        2.5    8.3   0.0    2.3  2  DUF2250   Uncharacterized protein conserved in archaea (DUF22
  ------ inclusion threshold ------
       0.01   15.9   0.1       0.73    9.9   0.1    2.2  2  HTH_54    ParA helix turn helix domain
      0.027   13.6   0.2      0.036   13.2   0.2    1.2  1  DUF4835   Domain of unknown function (DUF4835)


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   2.6e-07    0.0012       9      73 ..       8      76 ..       6      79 .. 0.91
   2 !    7.9   0.3   0.00068       3.1       2      65 ..      92     157 ..      91     160 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.6e-07
                            HTH_45  9 adILeaisegeakkTkimykanLsykllnkYLdmLvekgli......kkskekYvlTekGlelleklkele 73
                                      +d+L++   +  ++T+i   + L+  + ++ ++ L + gli      + ++++++lT+ Gl+++ +++e++
  gi|298676226|ref|YP_003727975.1|  8 LDVLKIF--KILSPTRIKEFSGLTNTRSKQEINDLENLGLIelspqsTPHDKEFKLTDFGLKIYTNFREFN 76
                                      6778877..78899****************************999866699*****************997 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00068
                            HTH_45   2 RskleIiadILeaisegeakkTkimykanLsykllnkYLdmLvekgli.....kkskekYvlTekGlel 65 
                                       R k + i+d Le   +++a+   + +   L +  l+ YL +L+ ++++       +   Y++Tek  ++
  gi|298676226|ref|YP_003727975.1|  92 RKKAKTIIDTLE---DQGASFDYLRKITGLPFLDLKLYLIFLIYREYVdrkliGGDLVYYTTTEKSNKF 157
                                       666666666666...6677777777788899999999*****988876544447788999999997776 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0   0.00056       2.5      11      58 ..       5      52 ..       1      63 [. 0.70
   2 !    7.8   0.0   0.00077       3.5       3      50 ..      58     106 ..      55     115 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00056
                           DUF2250 11 lkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlervegk 58
                                      l+vl  lk  +   +  i +   +  ++ ++ +++Le+lGL+e   ++
  gi|298676226|ref|YP_003727975.1|  5 LRVLDVLKIFKILSPTRIKEFSGLTNTRSKQEINDLENLGLIELSPQS 52
                                      45555555555555566666677777889999**********976555 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00077
                           DUF2250   3 eleedelalkvlkhlkkanvdYaksiakelei.pleevrellkkLeelG 50 
                                       e + ++  lk+   +++ n +Y k  ++ l++ ++++++ +++ Le+ G
  gi|298676226|ref|YP_003727975.1|  58 EFKLTDFGLKIYTNFREFNYEYFKVSVNTLKKnERKKAKTIIDTLEDQG 106
                                       566778899***************9999988725788999******998 PP

>> HTH_54  ParA helix turn helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0      0.01        46      23      71 ..      12      61 ..       5      63 .. 0.79
   2 ?    9.9   0.1   0.00016      0.73      21      59 ..      72     110 ..      45     117 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.01
                            HTH_54 23 eyyqtyskaalaklpklsrrkvdkavsemeaeG.yefekkeagstekYal 71
                                      + ++  s + ++++++l+    ++ ++++e+ G +e++ +++   ++++l
  gi|298676226|ref|YP_003727975.1| 12 KIFKILSPTRIKEFSGLTNTRSKQEINDLENLGlIELSPQSTPHDKEFKL 61
                                      5688899999*********************9944666666665555555 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00016
                            HTH_54  21 edeyyqtyskaalaklpklsrrkvdkavsemeaeGyefe 59 
                                         e+  +y k ++++l k  r+k+++ ++ +e++G +f+
  gi|298676226|ref|YP_003727975.1|  72 FREFNYEYFKVSVNTLKKNERKKAKTIIDTLEDQGASFD 110
                                       567888999**************************9997 PP

>> DUF4835  Domain of unknown function (DUF4835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   7.9e-06     0.036     182     249 ..      67     133 ..      52     141 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.9e-06
                           DUF4835 182 ekleelrellYeYhrkGLDemaenkekgrkailealeklkevkkkkpnslllqlFfdaKsdElvnifs 249
                                       + ++++re+ YeY++  + ++++n++k  k+i+++le+  + + ++ ++++   F+d K   +  i++
  gi|298676226|ref|YP_003727975.1|  67 KIYTNFREFNYEYFKVSVNTLKKNERKKAKTIIDTLEDQGA-SFDYLRKITGLPFLDLKLYLIFLIYR 133
                                       56899******************************997443.33444445555566666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1089.18
//
Query:       gi|298676227|ref|YP_003727976.1|  [L=33]
Description: hypothetical protein Metev_2370 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (33 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       125  (0.00697194); expected 358.6 (0.02)
Passed bias filter:                      117  (0.00652574); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.25s 00:00:00.56 Elapsed: 00:00:00.41
# Mc/sec: 244.36
//
Query:       gi|298676228|ref|YP_003727977.1|  [L=375]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-27   95.6   2.1    5.1e-27   94.5   2.1    1.5  1  OrfB_IS605      Probable transposase
    5.4e-24   83.9   0.4    1.1e-23   82.9   0.4    1.5  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    1.9e-19   68.9   1.4      4e-19   67.8   1.4    1.6  1  HTH_OrfB_IS605  Helix-turn-helix domain
     0.0071   16.5   0.3      0.019   15.1   0.3    1.7  1  zf-piccolo      Piccolo Zn-finger
  ------ inclusion threshold ------
      0.031   14.1   0.9        0.4   10.5   0.2    2.2  2  LemA            LemA family
      0.036   13.9   6.7       0.21   11.4   1.3    2.7  3  Phage_GP20      Phage minor structural protein GP20
       0.37   10.8   1.8        1.3    9.1   0.8    2.2  2  HypA            Hydrogenase/urease nickel incorporation, meta
       0.59   10.4   8.1       0.22   11.8   2.0    2.4  2  MapZ_EC1        MapZ extracellular domain 1


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.5   2.1   2.3e-30   5.1e-27       9     117 ..     168     276 ..     158     278 .. 0.93

  Alignments for each domain:
  == domain 1  score: 94.5 bits;  conditional E-value: 2.3e-30
                        OrfB_IS605   9 e...lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhr 82 
                                       +   ++k ++ +++g+D+Gi+++a++++++   ++ ++r lk+  ++l+  +++l++k+k+s+ny+k + ++a++h+
  gi|298676228|ref|YP_003727977.1| 168 QlpqKQKFDEVNTVGVDVGIKDFAVTSDGE---KIDNPRYLKNSIERLKVLQKRLSRKKKGSNNYRKLKHQIAKYHE 241
                                       34447788899*******************...******************************************** PP

                        OrfB_IS605  83 krsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       k++++r +++hkl+++li ++++v++e Lnv+++ 
  gi|298676228|ref|YP_003727977.1| 242 KIANQREDFQHKLSSRLISENQAVALECLNVKGLL 276
                                       ********************************986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.9   0.4   4.8e-27   1.1e-23       1      68 [.     290     359 ..     290     360 .. 0.98

  Alignments for each domain:
  == domain 1  score: 82.9 bits;  conditional E-value: 4.8e-27
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpay.TSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       ++++ ++leyka++yG++++++ ++  +Sk C++Cg+ +++ +l++r+++Cp+C++e+drD+nA++Ni k
  gi|298676228|ref|YP_003727977.1| 290 WSSFVQKLEYKAEWYGKNIIKIGRFDpSSKICHVCGYYHQDlELKDREWECPDCKTEHDRDINASVNIKK 359
                                       99******************************************************************87 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.8   1.4   1.8e-22     4e-19       1      47 []       1      46 [.       1      46 [. 0.98

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 1.8e-22
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeegk 47
                                      M lkaykyr yP++ Q+e++a+++G++Rf+YN+aL+ + + ye+ gk
  gi|298676228|ref|YP_003727977.1|  1 M-LKAYKYRMYPNQIQQELIAKHIGACRFIYNWALENKLKSYEQDGK 46
                                      8.******************************************997 PP

>> zf-piccolo  Piccolo Zn-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.3   8.6e-06     0.019      28      56 ..     318     346 ..     314     348 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.6e-06
                        zf-piccolo  28 kqvCnlCGFnptphltekkeWlclnCQtq 56 
                                       +++C +CG+  ++   + +eW c  C t+
  gi|298676228|ref|YP_003727977.1| 318 SKICHVCGYYHQDLELKDREWECPDCKTE 346
                                       79***********999**********985 PP

>> LemA  LemA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.11   2.4e+02      37      82 ..      59     104 ..      44     108 .. 0.80
   2 ?   10.5   0.2   0.00018       0.4      58     107 ..     203     253 ..     190     260 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.11
                              LemA  37 vteaRakaaeaesveekaeaenqlssalsrllavaEnYPdLkanen 82 
                                       v +  ++  ++ + ++ + a  +l++a+ +++     +P++k+++n
  gi|298676228|ref|YP_003727977.1|  59 VLKEDHEWLNEINSQSLQGATLNLENAFTKFFREKSGFPKFKSKKN 104
                                       55555566778889999999***********************987 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00018
                              LemA  58 nqlssalsrllavaEnY.PdLkanenfleLqeelegtEnriavaRrrYnea 107
                                       + l+++++rl +++ +   + k ++n+++L++++++  ++ia++R++++++
  gi|298676228|ref|YP_003727977.1| 203 RYLKNSIERLKVLQKRLsRKKKGSNNYRKLKHQIAKYHEKIANQREDFQHK 253
                                       5667777777777666414557899**********************9876 PP

>> Phage_GP20  Phage minor structural protein GP20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.012        26     112     138 ..      42      71 ..      14      79 .. 0.77
   2 ?   -2.4   0.0       1.7   3.8e+03       9      25 ..     163     180 ..     160     181 .. 0.75
   3 ?   11.4   1.3   9.2e-05      0.21      32      90 ..     210     268 ..     196     278 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.012
                        Phage_GP20 112 kedgelkg...LdeqikkLkesdkyLFeee 138
                                       ++dg+ +    L++qi  Lke++++L e +
  gi|298676228|ref|YP_003727977.1|  42 EQDGKAISrfeLNKQIRVLKEDHEWLNEIN 71 
                                       456666644459************998733 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.7
                        Phage_GP20   9 aengkdit.kakldevee 25 
                                       ++++k ++ k+k+dev++
  gi|298676228|ref|YP_003727977.1| 163 VDDDKQLPqKQKFDEVNT 180
                                       556677888999999986 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 9.2e-05
                        Phage_GP20  32 eqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeyeakiadlkldnaielaLk 90 
                                       e+lk  +k L+  kk +++  +L+ qi+++ +k++++ ++ + k++ + +++    aL+
  gi|298676228|ref|YP_003727977.1| 210 ERLKVLQKRLSRKKKGSNNYRKLKHQIAKYHEKIANQREDFQHKLSSRLISENQAVALE 268
                                       6788889999999********************************99888776666666 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.4   3.1e+03      18      34 ..     169     186 ..     160     191 .. 0.80
   2 ?    9.1   0.8   0.00057       1.3      68      96 ..     316     347 ..     306     361 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.4
                                       H.CCTT..EEEEEEEEEE CS
                              HypA  18 a.keaaarkvtkvkvevG 34 
                                       + +++++++v++v v+vG
  gi|298676228|ref|YP_003727977.1| 169 LpQKQKFDEVNTVGVDVG 186
                                       43668899*******999 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00057
                                       --EEEETTTS-EEE.CHH.H.HHS-TTTSSS- CS
                              HypA  68 pvkvrCreCgkefe.lee.k.alrCpkCgsad 96 
                                       p +  C++Cg+  + le  + + +Cp+C++++
  gi|298676228|ref|YP_003727977.1| 316 PSSKICHVCGYYHQdLELkDrEWECPDCKTEH 347
                                       55678*****8887444333588*****9874 PP

>> MapZ_EC1  MapZ extracellular domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.5      0.12   2.8e+02      48      84 ..      34      73 ..      30      85 .. 0.78
   2 ?   11.8   2.0   9.7e-05      0.22      22      78 ..     184     246 ..     163     269 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.12
                          MapZ_EC1 48 LekkLeklk.gskeYk..klkkkldslkkqisaieavNsq 84
                                      Le+kL+ ++ + k  +  +l+k++  lk+  + ++++Nsq
  gi|298676228|ref|YP_003727977.1| 34 LENKLKSYEqDGKAISrfELNKQIRVLKEDHEWLNEINSQ 73
                                      777788777544443323799*****************97 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 9.7e-05
                          MapZ_EC1  22 ekeyaafftddketflkn.....sefaklseLekkLeklk.gskeYkklkkkldslkkqisai 78 
                                       +  +++f ++++ +++ n     + ++ l+ L+k L   k gs++Y+klk+++++  ++i+ +
  gi|298676228|ref|YP_003727977.1| 184 DVGIKDFAVTSDGEKIDNprylkNSIERLKVLQKRLSRKKkGSNNYRKLKHQIAKYHEKIANQ 246
                                       5566666666666666652222223578999*****98777*****************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1446  (0.0806515); expected 358.6 (0.02)
Passed bias filter:                      647  (0.0360868); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2345.12
//
Query:       gi|298676229|ref|YP_003727978.1|  [L=1028]
Description: hypothetical protein Metev_2372 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-05   22.3  37.7    0.00013   21.7   1.7    6.6  7  Big_3_3   Bacterial Ig-like domain (group 3)
    0.00058   20.1  31.0      0.093   13.0   0.8    7.0  8  DUF4625   Domain of unknown function (DUF4625)
  ------ inclusion threshold ------
       0.22   11.5   9.1       0.41   10.6   0.3    4.6  3  Y_Y_Y     Y_Y_Y domain


Domain annotation for each model (and alignments):
>> Big_3_3  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.5      0.12   7.4e+02      14      99 ..      99     181 ..      87     191 .. 0.58
   2 !   21.7   1.7   2.1e-08   0.00013       6      71 ..     189     257 ..     184     274 .. 0.76
   3 !   10.4   0.8   6.2e-05      0.37       3      60 ..     293     348 ..     291     357 .. 0.78
   4 ?   -0.9   0.3      0.19   1.1e+03      53      81 ..     426     456 ..     381     481 .. 0.61
   5 ?   -0.8   0.3      0.17     1e+03      57      81 ..     430     456 ..     414     532 .. 0.55
   6 !    6.1   0.8    0.0014       8.1       2      62 ..     604     669 ..     603     678 .. 0.76
   7 !    7.0   0.8   0.00072       4.3      21      95 ..     733     804 ..     724     813 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.12
                           Big_3_3  14 eGkynlvlaakdtfnn....qvtksllstilvdntpPtvsisegkkisdgavvkglenlritladaldkskltsial 86 
                                       +G+y + ++ + t+n+      + ++++t+++d   P+vs      i+     k+ e++ ++ + + d++  +s+ +
  gi|298676229|ref|YP_003727978.1|  99 DGEYDVYAYDSATVNDgddlSNNANISTTLTIDDDNPSVSS-----ITTPIYTKSSEDVPVEFTYTEDNP--SSVDI 168
                                       56666666555554444444555666667777777787764.....455555555566666665555554..34444 PP

                           Big_3_3  87 sGGpasDkVelsw 99 
                                         G+  ++  ls+
  gi|298676229|ref|YP_003727978.1| 169 IIGSNTESFTLST 181
                                       4455555555555 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 2.1e-08
                           Big_3_3   6 tfdlkelp..eGkynlvlaakdtfnnqvtksllstilvdntpPtvsisegkki.sdgavvkglenlrit 71 
                                       tf+  +lp  eGkyn++++++d+ +n+ +k++ ++++vd t P+v+ ++ + +  d+  vk+ + ++i+
  gi|298676229|ref|YP_003727978.1| 189 TFSSTNLPssEGKYNITVKITDQAGNTGNKKCENEVTVDDTKPSVTNVQITDVtDDNGFVKSGDTVKIE 257
                                       67777776338*********************************9975544440556677777777664 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 6.2e-05
                           Big_3_3   3 ytvtfdlke.lpeGkynlvlaakdtfnnqvtksllstilvdntpPtvsisegkkisdga 60 
                                       y+ tf +++   +G+ +l+++a+d+ +n   ++++ t+++d+t Pt++    ++  d++
  gi|298676229|ref|YP_003727978.1| 293 YNATFTVDSgANDGEESLTINATDKAGNSNDTETSGTLTIDTTEPTLED---AESVDKT 348
                                       6667777652568******************99999**********975...4444444 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 0.19
                           Big_3_3  53 gkkisdgavvkglenlritl..adaldkskl 81 
                                       ++++s++++v g++++  tl  a++++++k+
  gi|298676229|ref|YP_003727978.1| 426 NSNNSGSVTVTGMDSVAPTLdhASKINATKI 456
                                       3345566666777776666622233333344 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 0.17
                           Big_3_3  57 sdgavvkglenlritl..adaldkskl 81 
                                       s++++v g++++  tl  a++++++k+
  gi|298676229|ref|YP_003727978.1| 430 SGSVTVTGMDSVAPTLdhASKINATKI 456
                                       334444444444444411122222222 PP

  == domain 6  score: 6.1 bits;  conditional E-value: 0.0014
                           Big_3_3   2 nytvtfdlkelpeGkynlvl.aakdtfnn..qvtksllstilvdntpPtvsi..segkkisdgavv 62 
                                       nyt++  ++  ++G y+++l +a+d ++n      ++ s  +vd+t P+++   ++++ ++d+  v
  gi|298676229|ref|YP_003727978.1| 604 NYTYNATYEFSSDGWYKVELvTANDSNDNngSSGDEYISGAVVDTTKPVIDSvtPNNTMVTDDQKV 669
                                       788888889999*****999888888888334456778899*********8546666677776655 PP

  == domain 7  score: 7.0 bits;  conditional E-value: 0.00072
                           Big_3_3  21 laakdtfnnqvtksllstilvdntpPtvsisegkkisdgavvkglenlritladaldks..kltsialsGGpasDkV 95 
                                       +  +d ++n  tk+ +  ++vd t+P+v+    + i +g   +++ +++++  + +++s  +  s+++s G ++ ++
  gi|298676229|ref|YP_003727978.1| 733 VEVTDMYDNIQTKQWN--FTVDATSPSVEY---AVIDNGFSTNDMTGVNVKFSEGINTSvpEDISMVISNGETQKQI 804
                                       4678999998877766..99********99...8999999*************999998776668888888887665 PP

>> DUF4625  Domain of unknown function (DUF4625)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.1   8.5e-05      0.51     105     127 ..     198     220 ..     173     224 .. 0.77
   2 !   13.0   0.8   1.6e-05     0.093       3      48 ..     220     264 ..     218     272 .. 0.90
   3 !   10.6   0.1   8.6e-05      0.51      92     128 ..     291     327 ..     269     333 .. 0.86
   4 ?   -2.3   0.0       0.8   4.8e+03      35      62 ..     345     372 ..     329     378 .. 0.67
   5 ?   -2.2   0.1      0.74   4.4e+03      32      70 ..     386     426 ..     355     439 .. 0.69
   6 ?    1.8   0.2     0.043   2.6e+02      11      84 ..     542     612 ..     532     621 .. 0.60
   7 !    4.2   0.6    0.0078        47      10      58 ..     642     687 ..     625     752 .. 0.75
   8 ?   -2.2   0.1      0.75   4.5e+03     114     131 ..     842     859 ..     834     860 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 8.5e-05
                           DUF4625 105 eaGdYhlvirvtDasGneteesr 127
                                        +G+Y++++++tD++Gn+ +++ 
  gi|298676229|ref|YP_003727978.1| 198 SEGKYNITVKITDQAGNTGNKKC 220
                                       59***************988776 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 1.6e-05
                           DUF4625   3 cssddeeedtekPvidllevsaepeeeevlkiGetlhfeaklsdne 48 
                                       c+++ +  d +kP+++ ++++   +++  +k G+t+++ea+++dn 
  gi|298676229|ref|YP_003727978.1| 220 CENEVT-VDDTKPSVTNVQITDVTDDNGFVKSGDTVKIEANIIDNF 264
                                       766655.9************999*********************95 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 8.6e-05
                           DUF4625  92 yelheeieiPadaeaGdYhlvirvtDasGneteesre 128
                                        + + ++++++ a++G+  l+i +tD++Gn++ ++++
  gi|298676229|ref|YP_003727978.1| 291 DTYNATFTVDSGANDGEESLTINATDKAGNSNDTETS 327
                                       5678899************************998876 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 0.8
                           DUF4625  35 Getlhfeaklsdn.ealasykvdihnnfD 62 
                                        ++ +++++lsd+   +++ ++d  n+fD
  gi|298676229|ref|YP_003727978.1| 345 VDKTTINVTLSDDgSGINKSSIDT-NDFD 372
                                       355677888887635688888887.7777 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 0.74
                           DUF4625  32 lkiGet..lhfeaklsdnealasykvdihnnfDhhshssea 70 
                                       ++ G t    ++++l d ++ +s+ v +++  D+ +++  +
  gi|298676229|ref|YP_003727978.1| 386 VTDGATsqQIIQIELRDPVDSESVDVVLNSSNDGIKDKAGN 426
                                       44444433557788888888888888887777777666554 PP

  == domain 6  score: 1.8 bits;  conditional E-value: 0.043
                           DUF4625  11 dtekPvidllevsaepeeeevlkiGetlhfeaklsdnealasykvdihnnfDhhshsseakeg......ekewsfek 81 
                                       d  +P+i++++v +           ++ ++ ++++  e+l +++ di +  D+   ++ ++        e++++++ 
  gi|298676229|ref|YP_003727978.1| 542 DGVAPTISDYKVVN--------PNKDNRNLTIEFNSTEKLTNITADI-KTDDGSPITTINESNfneftsESNYTYNA 609
                                       55666666663333........2223356777888899999999999.44455555555444455666666666666 PP

                           DUF4625  82 syd 84 
                                       +y+
  gi|298676229|ref|YP_003727978.1| 610 TYE 612
                                       665 PP

  == domain 7  score: 4.2 bits;  conditional E-value: 0.0078
                           DUF4625  10 e....dtekPvidllevsaepeeeevlkiGetlhfeaklsdnealasykvdih 58 
                                       +    dt+kPvid +      + ++++ ++++  + +++sd   l+ ++v+i 
  gi|298676229|ref|YP_003727978.1| 642 SgavvDTTKPVIDSV------TPNNTMVTDDQKVISFNVSDTYPLK-LSVKIG 687
                                       045559*******99......4456777788888888899988886.444443 PP

  == domain 8  score: -2.2 bits;  conditional E-value: 0.75
                           DUF4625 114 rvtDasGneteesreiki 131
                                        v D++Gn   ++ +i+i
  gi|298676229|ref|YP_003727978.1| 842 NVSDKNGNDVSVNEDIEI 859
                                       5889****9999999988 PP

>> Y_Y_Y  Y_Y_Y domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.3   6.9e-05      0.41      26      65 ..     184     226 ..     169     227 .. 0.79
   2 ?    0.7   0.0     0.084     5e+02      43      65 ..     310     332 ..     305     333 .. 0.90
   3 ?    0.4   1.7      0.11   6.4e+02      22      55 ..     600     633 ..     593     637 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 6.9e-05
                                       STS...EEEEES--S..EEEEEEEEEEETTS-B-SS-EEEEEEE CS
                             Y_Y_Y  26 dysq..easytnlpp..GdYtlkVkakdndgqwnyditslsfti 65 
                                       ++    ++s tnlp+  G+Y ++Vk++d  g+  ++  + ++t+
  gi|298676229|ref|YP_003727978.1| 184 SS-EtkTFSSTNLPSseGKYNITVKITDQAGNTGNKKCENEVTV 226
                                       33.24799999999555***************999988888877 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.084
                                       EEEEEEETTS-B-SS-EEEEEEE CS
                             Y_Y_Y  43 lkVkakdndgqwnyditslsfti 65 
                                       l++ a+d+ g++n+ +ts ++ti
  gi|298676229|ref|YP_003727978.1| 310 LTINATDKAGNSNDTETSGTLTI 332
                                       7899***********9*999998 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.11
                                       EEESSTS.EEEEES--SEEEEEEEEEEETTS-B- CS
                             Y_Y_Y  22 veasdysqeasytnlppGdYtlkVkakdndgqwn 55 
                                       +++s+y+++a+y   + G Y++++ + ++++++n
  gi|298676229|ref|YP_003727978.1| 600 TSESNYTYNATYEFSSDGWYKVELVTANDSNDNN 633
                                       56677777**************988877666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1028 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       856  (0.0477439); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.72u 0.29s 00:00:01.01 Elapsed: 00:00:00.46
# Mc/sec: 6694.69
//
Query:       gi|298676230|ref|YP_003727979.1|  [L=369]
Description: Gram-positive anchor protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0003   20.6   0.2    0.00065   19.6   0.2    1.6  1  Gram_pos_anchor  LPXTG cell wall anchor motif
    0.00086   19.5   0.8    0.00086   19.5   0.8    2.3  2  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
     0.0056   16.7   0.2     0.0056   16.7   0.2    3.2  4  Big_1            Bacterial Ig-like domain (group 1)
     0.0091   16.1   1.6        1.9    8.7   0.2    2.8  2  MG4              Macroglobulin domain MG4
  ------ inclusion threshold ------
      0.047   14.3   2.0       0.25   11.9   0.6    2.5  2  SEP              SEP domain
       0.13   12.3   0.2        1.2    9.2   0.0    2.2  2  DUF617           Protein of unknown function, DUF617
       0.14   11.3   2.7       0.33   10.0   2.7    1.6  1  ABC2_membrane_3  ABC-2 family transporter protein
       0.74   10.6   3.7        1.6    9.4   0.2    2.8  3  TTR-52           Transthyretin-like family
        2.5    8.0   5.8         13    5.7   0.0    3.2  4  Glyco_hydro2_C5  Glycoside hydrolase family 2 C-terminal doma
        4.5    8.3   6.3        2.2    9.3   0.3    3.0  3  Pilin_N          Archaeal Type IV pilin, N-terminal


Domain annotation for each model (and alignments):
>> Gram_pos_anchor  LPXTG cell wall anchor motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.2   3.6e-07   0.00065      13      38 ..     340     366 ..     340     369 .] 0.82

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.6e-07
                                       XX.XXXXXXXXXXXXXXXXXXXXXXXX CS
                   Gram_pos_anchor  13 Ge.ngnifltaaGllallggllLlvkr 38 
                                       Ge +g++++ta Glla+ +g+++l+++
  gi|298676230|ref|YP_003727979.1| 340 GEsQGMPGFTAIGLLAAGAGAAFLKRK 366
                                       6449*********99999999996666 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.8   4.8e-07   0.00086       2      46 ..      35      86 ..      34     117 .. 0.71
   2 ?   -2.2   0.1         3   5.4e+03      16      36 ..     202     221 ..     195     222 .. 0.64

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.8e-07
                   CarboxypepD_reg  2 isGrVtdasgapiagatVtvtnadtg......tvastttdadGafrlr..glp 46
                                      + G+++d +g++++g +V+++++d++      t+ +t td++G++ l+  gl+
  gi|298676230|ref|YP_003727979.1| 35 VYGYIKD-DGNGVSGIQVEIRTDDGTklsndkTSVTTSTDSEGYYELKpnGLQ 86
                                      5688887.899**********7665456666689************9733444 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3
                   CarboxypepD_reg  16 gatVtvtnadtgtvastttda 36 
                                        +++++t+  ++t+ +t+td+
  gi|298676230|ref|YP_003727979.1| 202 DVNIEITD-HGETKPETVTDS 221
                                       57777773.455666777775 PP

>> Big_1  Bacterial Ig-like domain (group 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   3.1e-06    0.0056      17      50 ..      42      80 ..      38      90 .. 0.85
   2 ?   -3.4   0.0       5.6     1e+04      45      56 ..     156     167 ..     155     170 .. 0.73
   3 ?   -1.2   0.1       1.2   2.1e+03      24      44 ..     201     221 ..     196     222 .. 0.75
   4 ?   -2.1   0.1       2.2     4e+03      21      43 ..     245     268 ..     241     269 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.1e-06
                             Big_1 17 ngnpvagatVtfsvsggals.....assgtTdanGkatv 50
                                      +gn v+g++V +++++g+ +     + ++ Td++G ++ 
  gi|298676230|ref|YP_003727979.1| 42 DGNGVSGIQVEIRTDDGTKLsndktSVTTSTDSEGYYEL 80
                                      8***************66666*99999999*****9876 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 5.6
                             Big_1  45 nGkatvtltstk 56 
                                       nGka ++++  +
  gi|298676230|ref|YP_003727979.1| 156 NGKANTNIKQIN 167
                                       899999887655 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.2
                             Big_1  24 atVtfsvsg.galsassgtTda 44 
                                       + V++++++ g +  ++++Td+
  gi|298676230|ref|YP_003727979.1| 201 QDVNIEITDhGET-KPETVTDS 221
                                       6789999996666.66777775 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 2.2
                             Big_1  21 vagatVtfsvsggals.assgtTd 43 
                                       +  a++tf+v+++ +  ++ g Td
  gi|298676230|ref|YP_003727979.1| 245 IDSASITFEVDKDWVKeNNAGPTD 268
                                       567889999998544446666666 PP

>> MG4  Macroglobulin domain MG4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.1    0.0087        16      25      78 ..      41      98 ..      38     117 .. 0.82
   2 !    8.7   0.2    0.0011       1.9      42      88 ..     143     189 ..     126     196 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0087
                               MG4 25 pdgspaknvpVkiealk.....seteekeslttdedGtakfsintpedaksltitvktk 78
                                       dg+ +++++V i++ +     s+++   ++ td++G  ++  n  +d+k+l++ v  +
  gi|298676230|ref|YP_003727979.1| 41 DDGNGVSGIQVEIRT-DdgtklSNDKTSVTTSTDSEGYYELKPNGLQDGKTLSLYVDGD 98
                                      689999*********.445657778888888899***9999999999999998887655 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0011
                               MG4  42 seteekeslttdedGtakfsintpedaksltitvktkdpslpeenqa 88 
                                       s++e k+ + + ++G a+++i   +++ +++i+ + +d++ +e+++ 
  gi|298676230|ref|YP_003727979.1| 143 SDKETKQLKAELKNGKANTNIKQINKGDEVSIELESEDKDQEEQQSI 189
                                       4455666667889*************************999877765 PP

>> SEP  SEP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.6   0.00014      0.25      19      75 ..     143     198 ..     140     199 .. 0.85
   2 ?    0.5   0.0      0.53   9.5e+02      45      65 ..     279     299 ..     246     306 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                               SEP  19 ddpenaeflesikkGevPeelekvekgeevevnledrrneeykppkkpkfkaFsGsG 75 
                                       +d+e++++ +++k+G++  ++++++kg+ev+++le  ++++ +++++ k  +F+ +G
  gi|298676230|ref|YP_003727979.1| 143 SDKETKQLKAELKNGKANTNIKQINKGDEVSIELE-SEDKDQEEQQSIKSISFKSNG 198
                                       689999****************************9.667777776666777898877 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.53
                               SEP  45 geevevnledrrneeykppkk 65 
                                        +evev++ d+++ +y  + k
  gi|298676230|ref|YP_003727979.1| 279 WDEVEVSMFDETEDKYIYKAK 299
                                       47899******9999987654 PP

>> DUF617  Protein of unknown function, DUF617
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00066       1.2     134     161 ..      67      95 ..      47      96 .. 0.91
   2 ?    0.3   0.1      0.36   6.5e+02      36      64 ..     160     189 ..     143     201 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00066
                            DUF617 134 rvvgskdsesfylinpdg.sggqeLsifl 161
                                        v+ s+dse +y ++p+g ++g+ Ls+++
  gi|298676230|ref|YP_003727979.1|  67 SVTTSTDSEGYYELKPNGlQDGKTLSLYV 95 
                                       6899*************9999*****995 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.36
                            DUF617  36 salvkem.asglvriaLecekkkekkkkke 64 
                                       ++ +k++ + + v i Le+e k+++++++ 
  gi|298676230|ref|YP_003727979.1| 160 NTNIKQInKGDEVSIELESEDKDQEEQQSI 189
                                       556677745567999999999998887654 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   2.7   0.00019      0.33       2      95 ..       5     186 ..       4     257 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00019
                   ABC2_membrane_3   2 sfliitlllPiilvlllglifsnsveddentpiavvdedn...............sslsqqlv.............. 49 
                                        +l ++l+  +++v ++g +   ++++++++ ++++ +d+               +                     
  gi|298676230|ref|YP_003727979.1|   5 QTL-TILITIFLFVSMVGAASAETSKTPPHMVYGYIKDDGngvsgiqveirtddgT------Klsndktsvttstds 74 
                                       566.77777777777777775555559************97765555555544441......044455566777777 PP

                   ABC2_membrane_3  50 ............................................ealeaspsve...........lvyevdseeeak 71 
                                                                                   ++l+ s++ +           + ++ + ++++k
  gi|298676230|ref|YP_003727979.1|  75 egyyelkpnglqdgktlslyvdgddtgndityttgkveqvnhegNYLSDSSDDDggssggisapgTGKSDKETKQLK 151
                                       78888888888888888888888888888888888888888888555555554455556666887777888888888 PP

                   ABC2_membrane_3  72 kalkngdidg.ilvipkgfskdll..........k 95 
                                         lkng++++ i +i+kg++ +++          +
  gi|298676230|ref|YP_003727979.1| 152 AELKNGKANTnIKQINKGDEVSIElesedkdqeeQ 186
                                       88888888875666777777776666666664442 PP

>> TTR-52  Transthyretin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.2   0.00091       1.6       8      45 ..      43      82 ..      37     119 .. 0.84
   2 ?    0.9   0.1      0.41   7.4e+02      11      38 ..     200     227 ..     196     252 .. 0.77
   3 ?   -1.9   0.0       3.2   5.8e+03       9      35 ..     277     300 ..     275     324 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00091
                                      T-GGSS-EEEEEEHHHH..TS--EEEEEE--TTSEEEEEE CS
                            TTR-52  8 gkpaknvkVkLwekdtl..dpddlldetkTdedGnFelsg 45
                                      g+ +++++V++  +d +   +d++  +t+Td++G++el+ 
  gi|298676230|ref|YP_003727979.1| 43 GNGVSGIQVEIRTDDGTklSNDKTSVTTSTDSEGYYELKP 82
                                      6778999999999876566899999999**********94 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.41
                                       GSS-EEEEEEHHHHTS--EEEEEE--TT CS
                            TTR-52  11 aknvkVkLwekdtldpddlldetkTded 38 
                                       a++v+++++++  ++p+++ d+  +d +
  gi|298676230|ref|YP_003727979.1| 200 AQDVNIEITDHGETKPETVTDSGDSDTE 227
                                       7889999999877788888888888764 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3.2
                                       -GGSS-EEEEEEHHHHTS--EEEEEE- CS
                            TTR-52   9 kpaknvkVkLwekdtldpddlldetkT 35 
                                       +   +v+V+++++    +d+ + ++kT
  gi|298676230|ref|YP_003727979.1| 277 DDWDEVEVSMFDET---EDKYIYKAKT 300
                                       56678899999973...5666666666 PP

>> Glyco_hydro2_C5  Glycoside hydrolase family 2 C-terminal domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0    0.0074        13      10      47 ..      39      76 ..      37      85 .. 0.92
   2 ?    3.8   0.3     0.029        52      48      97 ..     134     181 ..     129     187 .. 0.78
   3 ?   -3.1   0.0       3.8   6.8e+03      37      47 ..     201     211 ..     194     226 .. 0.60
   4 ?   -3.2   0.0       4.4   7.8e+03      14      28 ..     276     290 ..     273     294 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0074
                   Glyco_hydro2_C5 10 lkadgkDlafvtvevvDknGnlvpnadnevtfeveGpG 47
                                      +k dg+ ++ ++ve+  ++G+ ++n++  vt + + +G
  gi|298676230|ref|YP_003727979.1| 39 IKDDGNGVSGIQVEIRTDDGTKLSNDKTSVTTSTDSEG 76
                                      789****************************9987766 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.029
                   Glyco_hydro2_C5  48 elvgvdngdptslesfksnerkafnGkalaivrstkeaGkitltasaegl 97 
                                        + + + g++   ++ k+ + ++ nGka   +++ ++  +++++ ++e+ 
  gi|298676230|ref|YP_003727979.1| 134 GISAPGTGKS--DKETKQLKAELKNGKANTNIKQINKGDEVSIELESEDK 181
                                       5566665554..455678888999********************999875 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 3.8
                   Glyco_hydro2_C5  37 nevtfeveGpG 47 
                                       ++v++e+++ G
  gi|298676230|ref|YP_003727979.1| 201 QDVNIEITDHG 211
                                       33444444444 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 4.4
                   Glyco_hydro2_C5  14 gkDlafvtvevvDkn 28 
                                       g+D   v+v+++D+ 
  gi|298676230|ref|YP_003727979.1| 276 GDDWDEVEVSMFDET 290
                                       788899999999986 PP

>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.3    0.0012       2.2      15      79 ..       7      73 ..       5      75 .. 0.74
   2 ?    0.3   0.3      0.79   1.4e+03      45      59 ..     177     194 ..     136     214 .. 0.54
   3 ?   -0.3   0.3       1.2   2.2e+03      63      63 ..     211     211 ..     176     257 .. 0.50

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0012
                           Pilin_N 15 itvIlaAviaafvlgl.asneekapqasievkidssastgkna..vslehkgGdsidtkdlkivlnse 79
                                      +t+++  ++ ++++g  + +++k+p  ++   i+++++  +    v+++ ++G  +++++++++++ +
  gi|298676230|ref|YP_003727979.1|  7 LTILITIFLFVSMVGAaSAETSKTPPHMVYGYIKDDGNGVS-GiqVEIRTDDGTKLSNDKTSVTTSTD 73
                                      67777778888888886667777777778555555555433.258******************98876 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.79
                           Pilin_N  45 kidssastgkna...vsl 59 
                                       ++++++++++++   +s+
  gi|298676230|ref|YP_003727979.1| 177 ESEDKDQEEQQSiksISF 194
                                       222222222222222333 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.2
                           Pilin_N  63 g 63 
                                       g
  gi|298676230|ref|YP_003727979.1| 211 G 211
                                       1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1236  (0.0689386); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2490.69
//
Query:       gi|298676231|ref|YP_003727980.1|  [L=129]
Description: transcriptional regulator TrmB [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.2e-06   25.5   0.0    1.5e-05   24.8   0.0    1.3  1  TrmB         Sugar-specific transcriptional regulator TrmB
      3e-05   23.8   0.0    4.5e-05   23.2   0.0    1.3  1  MarR_2       MarR family
    4.2e-05   23.4   0.1    7.8e-05   22.5   0.0    1.5  1  MarR         MarR family
    0.00082   19.0   0.1     0.0012   18.5   0.1    1.2  1  SMC_ScpB     Segregation and condensation complex subunit Scp
     0.0072   16.3   0.1      0.011   15.7   0.1    1.3  1  HTH_36       Helix-turn-helix domain
  ------ inclusion threshold ------
      0.016   15.2   0.1       0.02   14.9   0.1    1.2  1  DUF327       Protein of unknown function (DUF327)
      0.022   15.3   0.1      0.036   14.7   0.1    1.3  1  Phage_rep_O  Bacteriophage replication protein O
      0.046   13.7   0.1       0.11   12.5   0.0    1.7  2  HTH_37       Helix-turn-helix domain
        0.1   12.8   0.2       0.41   10.8   0.1    2.0  2  DUF2582      Winged helix-turn-helix domain (DUF2582)


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   7.5e-09   1.5e-05       1      67 [.      19      93 ..      19      94 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 7.5e-09
                                      HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST........TTEEEE--H CS
                              TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr........pklYravdp 67
                                      L+ lGL+ + + + + L   ++++ +ei  ++g+ ++ v ++ + L++kG++e+++++        +klY  v p
  gi|298676231|ref|YP_003727980.1| 19 LKNLGLTRTVSMTLACLSDGQELSSKEIETISGLRQPEVSSATKYLIEKGWIEIREEKittnkgrpTKLYTLVAP 93
                                      778999999999999999999************************************999999996668887765 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   2.3e-08   4.5e-05       1      54 [.      22      73 ..      22      81 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2.3e-08
                                      TT--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  1 lgltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      lglt++  + La L ++ +  l+ +e++   gl ++ vs + k L ++G++e r
  gi|298676231|ref|YP_003727980.1| 22 LGLTRTVSMTLACLSDGQE--LSSKEIETISGLRQPEVSSATKYLIEKGWIEIR 73
                                      69***************99..******************************987 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   3.9e-08   7.8e-05       1      48 [.      24      71 ..      24      76 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 3.9e-08
                                      --HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR  1 ltltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                      lt+t  ++L++l++ ++ls +e+   +g+ ++ v+ +++ L++kG+ie
  gi|298676231|ref|YP_003727980.1| 24 LTRTVSMTLACLSDGQELSSKEIETISGLRQPEVSSATKYLIEKGWIE 71
                                      67888899***************************************8 PP

>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1     6e-07    0.0012      79     140 ..      22      88 ..       6      91 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 6e-07
                          SMC_ScpB  79 trLsqaaletLaiIaykqpvtraeieeiRGvn...sdsvvrtLlerglieekgrkee..pgrpilYg 140
                                         L++    tLa+    q ++++eie i G +   ++s+ + L+e+g+ie +++k +  +grp+ + 
  gi|298676231|ref|YP_003727980.1|  22 LGLTRTVSMTLACLSDGQELSSKEIETISGLRqpeVSSATKYLIEKGWIEIREEKITtnKGRPTKLY 88 
                                       568999999*****************99776444499***********9988877554489997654 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   5.5e-06     0.011       3      55 .]      22      70 ..      20      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.5e-06
                            HTH_36  3 LspsaklllgslasfanknggcfpsqetlakrlglsknTvsraikeLeqlGyi 55
                                      L+   +++ ++la ++++ +    s + + + +gl    vs+a k L+++G+i
  gi|298676231|ref|YP_003727980.1| 22 LGL-TRTVSMTLACLSDGQEL---SSKEIETISGLRQPEVSSATKYLIEKGWI 70
                                      566.77888899999977777...99999999********************9 PP

>> DUF327  Protein of unknown function (DUF327)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1     1e-05      0.02      72     128 ..      57     115 ..      28     122 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1e-05
                                       HHHHHHHHHHHH.HHHHT..-----H.HHHHHHHHHHHHHHHHHHHHHHHTTSTTCHHH CS
                            DUF327  72 vkeflkevvkns.lklkkersldrkg.rsrvykivkeiDekldeLteellkeekealdi 128
                                       v++  k++++++ +++ +e+ ++ kg  ++ y++v  iD+  +++  ++l+++++ ld 
  gi|298676231|ref|YP_003727980.1|  57 VSSATKYLIEKGwIEIREEKITTNKGrPTKLYTLVAPIDKITKDIEADILSQNRNILDN 115
                                       6666666665542789999999999999************************9987664 PP

>> Phage_rep_O  Bacteriophage replication protein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   1.8e-05     0.036      34      90 ..      25      81 ..      12      83 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.8e-05
                       Phage_rep_O 34 lavirktYgfkkksdwisnsqlveltgisrtkvskalkeLirekviikegrkvgvnk 90
                                        ++++t+ +    + +s +++ ++ g+ + +vs+a k+Li+++ i ++++k+  nk
  gi|298676231|ref|YP_003727980.1| 25 TRTVSMTLACLSDGQELSSKEIETISGLRQPEVSSATKYLIEKGWIEIREEKITTNK 81
                                      56789999999999**************************************99997 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.5e-05      0.11      21      54 ..      30      63 ..      11      67 .. 0.86
   2 ?   -2.6   0.0       2.8   5.6e+03      22      34 ..      96     108 ..      87     110 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.5e-05
                                      HHHHHHHHHCT--HHHHHHHHT--HHHHHHHHTT CS
                            HTH_37 21 laiaeliekrelsqseaaqllgiaqPkvsrllrg 54
                                      +++a l +++els +e+ ++ g  qP+vs+  ++
  gi|298676231|ref|YP_003727980.1| 30 MTLACLSDGQELSSKEIETISGLRQPEVSSATKY 63
                                      56888999*********************98876 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.8
                                       HHHHHHHHCT--H CS
                            HTH_37  22 aiaeliekrelsq 34 
                                       +i++ ie+  lsq
  gi|298676231|ref|YP_003727980.1|  96 KITKDIEADILSQ 108
                                       5778888887877 PP

>> DUF2582  Winged helix-turn-helix domain (DUF2582)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.93   1.9e+03      21      36 ..      11      26 ..       8      34 .. 0.73
   2 ?   10.8   0.1    0.0002      0.41      16      56 ..      34      81 ..      30      89 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.93
                                      SSEEHHHHHHHCT-SC CS
                           DUF2582 21 geislkelkrktglsd 36
                                      ++i ++e+ ++ gl++
  gi|298676231|ref|YP_003727980.1| 11 KKIEMSEILKNLGLTR 26
                                      7889999999999865 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0002
                                      HHCCSSSEEHHHHHHHCT-SCHHHHHHH......HHH.HCTTSEEEEE CS
                           DUF2582 16 lLnengeislkelkrktglsdkelalAi......GWL.aREdKivier 56
                                       L++ +e+s ke++  +gl + e+ +A       GW   RE+Ki +++
  gi|298676231|ref|YP_003727980.1| 34 CLSDGQELSSKEIETISGLRQPEVSSATkyliekGWIeIREEKITTNK 81
                                      69999*****************99999655566699856999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 915.66
//
Query:       gi|298676232|ref|YP_003727981.1|  [L=328]
Description: hypothetical protein Metev_2378 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-13   51.3   0.1    5.2e-13   49.4   0.0    1.9  2  AAA_22    AAA domain
    7.2e-06   26.5   0.3    0.00015   22.2   0.0    2.5  2  AAA_16    AAA ATPase domain
     0.0011   18.9   0.8      0.015   15.2   0.5    2.7  2  ATPase_2  ATPase domain predominantly from Archaea
      0.007   16.7   0.1      0.036   14.4   0.0    2.1  2  AAA_19    AAA domain
  ------ inclusion threshold ------
       0.01   16.3   0.6      0.025   15.0   0.1    1.9  2  AAA       ATPase family associated with various cellular acti
      0.011   14.5   0.1      0.017   13.9   0.1    1.2  1  SNF2_N    SNF2 family N-terminal domain
      0.012   14.8   1.2        2.7    7.1   0.1    2.5  2  NB-ARC    NB-ARC domain


Domain annotation for each model (and alignments):
>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.4   0.0     2e-16   5.2e-13       5     135 ..      71     200 ..      66     202 .. 0.85
   2 ?   -1.6   0.0       1.2   3.1e+03      52      70 ..     300     318 ..     250     326 .. 0.63

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 2e-16
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelkaerlsseell. 79 
                                        +i v+++++G+GK+      l++l+e       +++++   ++++  ++ ++l+++lr+++ e k+   ++ +l+ 
  gi|298676232|ref|YP_003727981.1|  71 SSIFVIHAPVGMGKSSIRDFTLKTLNE-------SDDYYITVINNPRlTPLQILKQILRDITAEEKT--PRTMDLVw 138
                                       6799*************9999999975.......555543333344458*************99999..88888886 PP

                            AAA_22  80 ealeqalrarav...ielliiDEaqhlrseealeeLrsllnl....srkgvqliLvGtpelrk 135
                                       ++  + l++ +      ++ iDEa++l  ++ l+ Lr l+++    ++k ++++L Gtp l k
  gi|298676232|ref|YP_003727981.1| 139 NKAKNILSELKEtgiSTIIWIDEAEKL-DNKKLSLLRALADVktfdGEKVCKIVLTGTPTLKK 200
                                       888888888888999999*********.999999999999999999*************9977 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.2
                            AAA_22  52 sskdllrellralglelka 70 
                                       s++d+l++l  ++++e+++
  gi|298676232|ref|YP_003727981.1| 300 SQDDVLNALSTQIQEENSE 318
                                       4455555555555555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0     6e-08   0.00015      21     161 ..      68     179 ..      53     186 .. 0.73
   2 ?   -1.9   0.1       1.4   3.7e+03      89     106 ..     300     317 ..     257     327 .. 0.52

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 6e-08
                            AAA_16  21 sgrpelvllsGesGvGKsslvrellralekdg.giflrgkcdqlesaipysalaqalareellrqlldeaesaelea 96 
                                        +++++ +++ + G+GKss+ +  l+ l++++  + +  ++ +l   +p           ++l+q+l++ ++ e   
  gi|298676232|ref|YP_003727981.1|  68 LSESSIFVIHAPVGMGKSSIRDFTLKTLNESDdYYITVINNPRL---TP----------LQILKQILRDITA-E--- 127
                                       3455999***********************97466677777777...33..........3666666666222.1... PP

                            AAA_16  97 wrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqwadeaslqllaaLlrl 161
                                         ek ++++             ++++ k++l+ l++++  +++++D+++++d   l+ll+aL++ 
  gi|298676232|ref|YP_003727981.1| 128 --EKTPRTMD-----------LVWNKAKNILSELKETGISTIIWIDEAEKLDNKKLSLLRALADV 179
                                       ..22222233...........5688888999666666666**********************986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.4
                            AAA_16  89 aesaeleawrekleeala 106
                                       ++++ l+a +++++e+ +
  gi|298676232|ref|YP_003727981.1| 300 SQDDVLNALSTQIQEENS 317
                                       333444444444444443 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.5     6e-06     0.015      13     148 ..      64     179 ..      58     204 .. 0.69
   2 ?   -1.1   0.0      0.57   1.5e+03     212     232 ..     257     277 ..     224     278 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6e-06
                          ATPase_2  13 eilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekalgiavpka 89 
                                       + l+ ++++i +i  p g GK+++    ++ l+++d+y  y++ +++ +++ l+        k+ l++ ++      
  gi|298676232|ref|YP_003727981.1|  64 RFLSLSESSIFVIHAPVGMGKSSIRDFTLKTLNESDDY--YITVINNPRLTPLQIL------KQILRDITA------ 126
                                       56666777888888888888888777777777666653..4444444444444443......223333332...... PP

                          ATPase_2  90 eleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnl 148
                                         ee   ++  lv+++ +++l ++k++g   ii iDe+ kl     n++ +l+ +L+++
  gi|298676232|ref|YP_003727981.1| 127 --EEKTPRTMDLVWNKAKNILSELKETGISTIIWIDEAEKLD----NKKLSLLRALADV 179
                                       ..2222345699******************************....7777788888765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.57
                          ATPase_2 212 skedfeeiyryvGGkPkalve 232
                                       +k   +e+ ++ +GkP+ + +
  gi|298676232|ref|YP_003727981.1| 257 TKGAADEVIEFSDGKPRTITQ 277
                                       67778999999*****99987 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   1.4e-05     0.036       9     127 ..      70     178 ..      64     188 .. 0.76
   2 ?   -1.6   0.0       1.2     3e+03      50      77 ..     256     280 ..     240     325 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.4e-05
                            AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrlalldfddllt 85 
                                       +++++++ a+ G+GK+ +    ++ l+e  +      ++  +     + l++ l+ ++ae +T   + l+ +++ + 
  gi|298676232|ref|YP_003727981.1|  70 ESSIFVIHAPVGMGKSSIRDFTLKTLNESDDY--YITVINNPRLTPLQILKQILRDITAEEKTPRTMDLV-WNKAK- 142
                                       67788999999999999999999999999965..455555666667888899999999999999888333.33333. PP

                            AAA_19  86 ealelleeaeeekklqeeellivDEfqdvdelqyrLlkallg 127
                                       + l+ l+e    + +   +++++DE+  +d    +Ll+al++
  gi|298676232|ref|YP_003727981.1| 143 NILSELKE----TGI--STIIWIDEAEKLDNKKLSLLRALAD 178
                                       34444443....444..5699******************984 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.2
                            AAA_19  50 ftgrAakelrerlaalgaeatTiHrlal 77 
                                       ft+ Aa+e+ e     +++ +Ti +++ 
  gi|298676232|ref|YP_003727981.1| 256 FTKGAADEVIEFS---DGKPRTITQITQ 280
                                       5666666666655...444455544433 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   9.7e-06     0.025       3      88 ..      76     172 ..      74     206 .. 0.66
   2 ?   -1.6   0.1       1.4   3.5e+03      81      99 ..     300     318 ..     272     323 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9.7e-06
                                       EESSTTSSHHHHHHHHHHHHT....HEEEEEETTTCSSS..................STTHHHHHHHHHHHHHHHTS CS
                               AAA   3 lyGppGtGKTllakavakelg....vefleisgsellsk..................yvgesekkirelfkeakeka 57 
                                       ++ p G+GK+++     k+l+     ++  i+ ++l+                    ++    +k +++++e+ke  
  gi|298676232|ref|YP_003727981.1|  76 IHAPVGMGKSSIRDFTLKTLNesddYYITVINNPRLTPLqilkqilrditaeektprTMDLVWNKAKNILSELKETG 152
                                       7899***************9654556677777777773357777777777555555566666666666666666666 PP

                                       TS.EEEEEETGGGHHHHHTTCCCHHHHHHHHH CS
                               AAA  58 kp.silfiDEidalaksrsgseseeeervvnq 88 
                                          +i++iDE+++l +++           ++ 
  gi|298676232|ref|YP_003727981.1| 153 -IsTIIWIDEAEKLDNKK-----------LSL 172
                                       .559**********8887...........333 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHHHHHTTTS CS
                               AAA  81 eeervvnqLlteldgvkkk 99 
                                       ++++v+n+L t++++++++
  gi|298676232|ref|YP_003727981.1| 300 SQDDVLNALSTQIQEENSE 318
                                       5678999999999988775 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   6.6e-06     0.017     168     220 ..     143     202 ..     111     207 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.6e-06
                                       ...TTS-S-S-SEEE.ES-GGGT--TTSHHHHHHHH--.....-S-EEEE-S--SSS.-H CS
                                       xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxx.xx RF
                            SNF2_N 168 kkrsvlkqvewkrvv.lDEghtlknstskaaeavskLs.....tsnrwiltGTPiqn.sl 220
                                       ++ s+lk+  +  ++ +DE+ +l n++ ++  a+ + +        +++ltGTP+   ++
  gi|298676232|ref|YP_003727981.1| 143 NILSELKETGISTIIwIDEAEKLDNKKLSLLRALADVKtfdgeKVCKIVLTGTPTLKkKV 202
                                       67788899887776659*********988888877765333445679*******987344 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1     0.002       5.1       8     111 ..      62     161 ..      55     208 .. 0.78
   2 ?    7.1   0.1     0.001       2.7     163     208 ..     237     282 ..     224     324 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.002
                                       HHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEEEEESXXHHHHHHHXXHHHHHCCCTTSS CS
                            NB-ARC   8 viekLlekdelqslvvalvGmgGvGKttlakqilnksdevegrFdsvawvvvsktdkseeiletilkeLslseddle 84 
                                       +   L+   e+   +  ++   G+GK+ +    l+    +++  d ++ v      +  +il++il+++  +e+   
  gi|298676232|ref|YP_003727981.1|  62 LTRFLS-LSESS--IFVIHAPVGMGKSSIRDFTLKT---LNESDDYYITVINNPRLTPLQILKQILRDITAEEKTPR 132
                                       444555.44555..899************9988888...66666888999999999999**********99999999 PP

                                       SS-STTSHHHHHHHHCCCT..TEEEEEEE CS
                            NB-ARC  85 ekeeveslkrklvrlLltk..rfllvlDD 111
                                        ++ v ++++++   L++    +++ +D 
  gi|298676232|ref|YP_003727981.1| 133 TMDLVWNKAKNILSELKETgiSTIIWIDE 161
                                       99999888999988888776777777775 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.001
                                       HHHHHHHHCCTS-GGCHH..CHHHHHHHHHHCTT-HHHHHHHHHHH CS
                            NB-ARC 163 eawellenkvfekkleekesleevakeivekckGlPlalkvlggll 208
                                       e well+++    +   ++  +  a e++e + G P ++  + +++
  gi|298676232|ref|YP_003727981.1| 237 EWWELLCEYCSTDDNAINPFTKGAADEVIEFSDGKPRTITQITQMV 282
                                       67*********999999999********************998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1315  (0.0733449); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2344.53
//
Query:       gi|298676233|ref|YP_003727982.1|  [L=177]
Description: hypothetical protein Metev_2379 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1344  (0.0749624); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1279.20
//
[ok]
